Mercurial > repos > galaxy-australia > cactus_cactus
diff test-data/evolverMammals.maf @ 15:098506c54016 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/cactus commit 8fc43fe1e8c12438a14dbd174a8af3e7cb8b55dc
| author | iuc |
|---|---|
| date | Thu, 08 Feb 2024 08:52:28 +0000 |
| parents | 94b8c6013083 |
| children |
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--- a/test-data/evolverMammals.maf Mon Aug 28 23:10:21 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,238809 +0,0 @@ -##maf version=1 scoring=N/A -# hal ((simHuman_chr6:0.144018,(simMouse_chr6:0.084509,simRat_chr6:0.091589)mr:0.271974)Anc1:0.020593,(simCow_chr6:0.18908,simDog_chr6:0.16303)Anc2:0.032898)Anc0; - -a -s simMouse_chr6.simMouse.chr6 0 4 + 636262 TTTT -s Anc0.Anc0refChr9 0 4 - 35212 TCTT -s Anc1.Anc1refChr0 0 4 + 16026 TCTT -s Anc2.Anc2refChr0 0 4 + 56053 TCTT -s mr.mrrefChr0 0 4 + 130230 TTTT -s simCow_chr6.simCow.chr6 0 4 + 602619 TCTT -s simDog_chr6.simDog.chr6 0 4 + 593897 TCTT -s simHuman_chr6.simHuman.chr6 0 4 + 601863 TCTT -s simRat_chr6.simRat.chr6 0 4 + 647215 TTTT - -a -s simMouse_chr6.simMouse.chr6 4 33 + 636262 TCAGTTGCAATACCCAACCGGGAGAAACTTTCA -s Anc0.Anc0refChr9 4 33 - 35212 TCTGGTGCAATACCCAATCTGTAGACAGTTTCA -s Anc1.Anc1refChr0 4 33 + 16026 TCTGGTGCAATACCCAATCTGTAGACAGTTTCA -s Anc2.Anc2refChr0 4 33 + 56053 TCTGGTGCACTACCCAATCTGTAGACAGTCTCA -s mr.mrrefChr0 5 33 + 130230 TCAGTTGCAATACCCAACCTGGAGACACTTTCA -s simCow_chr6.simCow.chr6 4 33 + 602619 TCTGGTGCGCGACCCAATCTGTAGACGGACTTA -s simDog_chr6.simDog.chr6 5 33 + 593897 TCTGGTGCACTACCCAATCTGTAGACAGTCTCA -s simHuman_chr6.simHuman.chr6 4 33 + 601863 TCTGGTGCAATAGCCAATCTGCAAACAGTTTCA -s simRat_chr6.simRat.chr6 5 31 + 647215 --GGCTGCAATACCCAACCTGAAGACATTTTCA - -a -s simMouse_chr6.simMouse.chr6 37 60 + 636262 GTGAGCACACCTCAGGTTCCTATATCAAGCAGGCAGTCTTGCATAGCAAATGGTCTCTGG -s Anc0.Anc0refChr9 39 43 - 35212 ATGAGCACACCTTATGTGACTATATCAAGCA-----------------CATAGTCTTGCA -s Anc1.Anc1refChr0 39 60 + 16026 ATGAGCACACCTTATGTGACTATATCAAGCATACAGTCTTGCCTAGCACATAGTCTTGCA -s Anc2.Anc2refChr0 39 43 + 56053 ATGAGCACACCTTATGTGACTATATCAAGCA-----------------CATAGTCTTGCA -s mr.mrrefChr0 38 60 + 130230 GTGAGCACACCTCAGGTTCCTATATCAAGCAGACAGTCTTGCATAGCAAATGGTCTCTGA -s simCow_chr6.simCow.chr6 39 43 + 602619 CTGAGCACACCTTATGTGATTATATCAAGCA-----------------GATAGTCTTGCA -s simDog_chr6.simDog.chr6 40 41 + 593897 AT--ACAAACCTTATGTGACTATATCAAGCA-----------------CATGGTCTTGCA -s simHuman_chr6.simHuman.chr6 39 58 + 601863 ATGAGCACACCTTATATGAC--TATCAAGCATACAGTCTTGCCTAGCACACAATCTTGCA -s simRat_chr6.simRat.chr6 36 60 + 647215 GTGGGCCCACCTCAGGTTCTTATATCAAGCAGACAGTCTTGCGCAACAGATGGTCTCTGA - -a -s simMouse_chr6.simMouse.chr6 97 41 + 636262 TAGACGGTGCACTCAATCTATGTGAGGTATAGAAAATAAAG -s Anc0.Anc0refChr9 82 41 - 35212 TAGATTGTGCAATCACTCTATCTGAGAGTCAGAGACCAAAG -s Anc1.Anc1refChr0 99 41 + 16026 TAGATTGTGCAATCACTCTATCTGAGAGTCAGAGACCAAAG -s Anc2.Anc2refChr0 82 41 + 56053 TAGATTGTGCAATGACTCTATCCAAGAGTCAGAGACCAGAG -s mr.mrrefChr0 98 41 + 130230 TAGACGGTGCACTCAATCTATGTGAGGGATAGAAAACAAAG -s simCow_chr6.simCow.chr6 82 41 + 602619 TTGATTGTGCAATGACTCTATCCAAGAGTCAAAGACCAGAG -s simDog_chr6.simDog.chr6 81 41 + 593897 TAGATTGTGCAATGACTCTATCCAAGAGTCAGAGGCTGGAG -s simHuman_chr6.simHuman.chr6 98 41 + 601863 TAGATTGTACAATCTCTCGTTCTGGGAGTCAGAGACCAAAG -s simRat_chr6.simRat.chr6 96 41 + 647215 TAGACAGTGCACTCAATCTATGTGAAGGATAGAAAACAAAG - -a -s simMouse_chr6.simMouse.chr6 138 39 + 636262 GACTACACACATCTCATCAAGTATCCCGTCATATTTGTG -s Anc0.Anc0refChr9 127 37 - 35212 TACT--GCATAGTTCATCGAGTATCCTGGAGTCTTGGTC -s Anc1.Anc1refChr0 144 37 + 16026 TACT--GCATAGTTCATCGAGTATCCTGGAGTCTTGGTC -s Anc2.Anc2refChr0 127 37 + 56053 TACT--GCATAGTTCATTGAGAATCCTGGAGTCTTGGTC -s mr.mrrefChr0 139 37 + 130230 GACT--ACACATCTCATCAAGTATCCTGTCGTATTTGTG -s simCow_chr6.simCow.chr6 126 36 + 602619 TACG--GCATAGTTTATTG-GAATCCTGGAGTATGGGTC -s simDog_chr6.simDog.chr6 126 37 + 593897 TATT--ACATAGTTCTCTGAGAATCCTGGAGTCTTTATC -s simHuman_chr6.simHuman.chr6 143 37 + 601863 TACT--GTGTGGTTGATCGGGTATCCTGGAGTGTTGGTA -s simRat_chr6.simRat.chr6 137 37 + 647215 GACT--ACTCATCTCATCAAGTATCCTGTCGTATTTGTG - -a -s simMouse_chr6.simMouse.chr6 177 9 + 636262 GCAAAACAC -s Anc0.Anc0refChr9 175 9 - 35212 GCAAAGCGC -s Anc1.Anc1refChr0 192 9 + 16026 GCAAAGCGC -s Anc2.Anc2refChr0 175 9 + 56053 GCAAAGCGC -s mr.mrrefChr0 187 9 + 130230 GCAAAACAC -s simCow_chr6.simCow.chr6 173 9 + 602619 GCAAAGCAC -s simDog_chr6.simDog.chr6 174 9 + 593897 GCAAAGCGC -s simHuman_chr6.simHuman.chr6 191 4 + 601863 ATAA----- -s simRat_chr6.simRat.chr6 185 9 + 647215 GCAAAACAA - -a -s simMouse_chr6.simMouse.chr6 186 27 + 636262 ACGTACAAATGCACACTTGATGGTACT -s Anc0.Anc0refChr9 184 27 - 35212 GCTCCCAAATGCACACCAGATGGTGCT -s Anc1.Anc1refChr0 201 27 + 16026 GCTCCCAAATGCACACCAGATGGTGCT -s Anc2.Anc2refChr0 185 27 + 56053 GCTCCCGAATGCACACCAGATGGTGCT -s mr.mrrefChr0 196 27 + 130230 GCGTACAAATGCACACCTGATGGTACT -s simCow_chr6.simCow.chr6 183 27 + 602619 GGTTCCAAATGCATAGCAGATAGTACT -s simDog_chr6.simDog.chr6 184 27 + 593897 GCTCCCGAATGTACACCAGATGGTGCT -s simHuman_chr6.simHuman.chr6 195 21 + 601863 ------AAATGCACACCAGATGTTCCT -s simRat_chr6.simRat.chr6 194 27 + 647215 GTGTGCAAGTGCACACCTGATTGTACT - -a -s simMouse_chr6.simMouse.chr6 213 86 + 636262 TGCCTGGAATATGACTCTAGGTTGATCCCTGGCACACAGGCACATTAATTCCCGAATGATGGTCTGCCTGTCCAGTTCTAGATAAT -s Anc0.Anc0refChr9 213 62 - 35212 AGCCAGGTATA-----CCTGATTGA------GAAC-------------TTCCTGAATGATGGTGTGCTCCTTAAGCTCTATACAGT -s Anc1.Anc1refChr0 230 62 + 16026 AGCCAGGTATA-----CCTGATTGA------GAAC-------------TTCCTGAATGATGGTGTGCTCCTTAAGCTCTATACAGT -s Anc2.Anc2refChr0 214 62 + 56053 AGCCAGGTGTA-----CCTGATTGA------GAAA-------------TTCCTGAATGATGGTGTGCTCCTTAAGCTCTATACAGT -s mr.mrrefChr0 223 86 + 130230 TGCCTGGAATATGACTCTAGGTTGATCCCTGGCACACAGGCAGGTCAATTCCCGAATGATGGTCTGCTTGTCCAGTTCTAGATAAT -s simCow_chr6.simCow.chr6 212 62 + 602619 AGCCTGGTGCT-----CCTGACTGC------GAAA-------------TTCCTGAATGACGATGTGCTCTTCAGGCTCTATACAGT -s simDog_chr6.simDog.chr6 213 62 + 593897 ATCCAGGAGTA-----CCTGATTTA------GCAA-------------TTCCTGAATGATGGCTTCTTCCTTAAGCTATTTACAAT -s simHuman_chr6.simHuman.chr6 218 62 + 601863 AGCCAGGTATA-----CCTGATTGA------GAAC-------------TTCCTGAATAATGGTGTGCTCAGGGAGCTCTATACAGT -s simRat_chr6.simRat.chr6 221 84 + 647215 TGTCTGGAATATGACTCTAGGTTGAGCCCTGGCACACACTCAGGTCAACTCC--AATGATGGTCTGCTTGTCCAATTCTAGATAAA - -a -s simMouse_chr6.simMouse.chr6 299 16 + 636262 GTTACATTGGTGAACT -s Anc0.Anc0refChr9 276 16 - 35212 ATTACATTGGGGAACT -s Anc1.Anc1refChr0 293 16 + 16026 ATTACATTGGGGAACT -s Anc2.Anc2refChr0 277 16 + 56053 ATTACATTGGGGAACT -s mr.mrrefChr0 310 16 + 130230 ATTACATTGGTGAACT -s simCow_chr6.simCow.chr6 275 16 + 602619 ATTCCATTGGGGAACT -s simDog_chr6.simDog.chr6 276 16 + 593897 ATGACAGTGGGGAACT -s simHuman_chr6.simHuman.chr6 281 16 + 601863 TCTACATTGGGGAACT -s simRat_chr6.simRat.chr6 306 16 + 647215 ATTACATTGGTGAACT - -a -s simMouse_chr6.simMouse.chr6 315 10 + 636262 TAAAACACAG -s Anc0.Anc0refChr9 295 8 - 35212 GAAA--ACTG -s Anc1.Anc1refChr0 312 8 + 16026 GAAA--ACTG -s Anc2.Anc2refChr0 296 8 + 56053 GGAA--ACTG -s mr.mrrefChr0 329 10 + 130230 TAAAACACAG -s simCow_chr6.simCow.chr6 294 8 + 602619 GGTA--ACTG -s simDog_chr6.simDog.chr6 295 8 + 593897 GGAA--GCTG -s simHuman_chr6.simHuman.chr6 300 8 + 601863 GAAA--ACTG -s simRat_chr6.simRat.chr6 325 10 + 647215 TAAAACACAG - -a -s simMouse_chr6.simMouse.chr6 325 24 + 636262 AAATGACACATCCTTTTTAACCAA -s Anc0.Anc0refChr9 306 24 - 35212 AACTTACAAATCCCTTTTAACCAA -s Anc1.Anc1refChr0 323 24 + 16026 AACTTACAAATCCCTTTTAACCAA -s Anc2.Anc2refChr0 307 24 + 56053 AACTTACAAATTCCTTTTAACCAA -s mr.mrrefChr0 342 24 + 130230 AAATTACAAATCCTTTTTAACCAA -s simCow_chr6.simCow.chr6 305 24 + 602619 AACCTACACATTGTTTTTAACTAT -s simDog_chr6.simDog.chr6 306 24 + 593897 AAGTAAGAAATTCCTTTTAACCAA -s simHuman_chr6.simHuman.chr6 311 24 + 601863 AACTTACAAATCACTTTTAACCAA -s simRat_chr6.simRat.chr6 338 24 + 647215 AAATTACTAATCCTTTTTAGCACA - -a -s simMouse_chr6.simMouse.chr6 349 33 + 636262 GCCTAAAGTACAGAAAGTGAATGTCACCCTTGT -s Anc0.Anc0refChr9 330 32 - 35212 GCATAAAGTACAGATAGTGCACGTTACCCTTG- -s Anc1.Anc1refChr0 347 32 + 16026 GCATAAAGTACAGATAGTGCACGTTACCCTTG- -s Anc2.Anc2refChr0 331 32 + 56053 GCATAAAGTTCAGATAGTGCACATTACCCTGG- -s mr.mrrefChr0 366 33 + 130230 GCCTAAAGTACAGAAAGTGAATGTTACCCTTGT -s simCow_chr6.simCow.chr6 329 32 + 602619 GTATAAAGTTCAGATAGTGCACATTCCCCTGT- -s simDog_chr6.simDog.chr6 334 32 + 593897 GCATGAAGTTCAGACAGTGCACACTACCATGG- -s simHuman_chr6.simHuman.chr6 335 32 + 601863 GCATAAAGTACAGATAGTGCACGTTTCCCTTG- -s simRat_chr6.simRat.chr6 362 33 + 647215 GCCTAAAGTACAGAGAGTGAATGTTACCCTTTT - -a -s simMouse_chr6.simMouse.chr6 382 23 + 636262 TATATAAACCAGTATATAGGGTA -s Anc0.Anc0refChr9 362 22 - 35212 GATATGAACTAGCATATAATG-T -s Anc1.Anc1refChr0 379 22 + 16026 GATATGAACTAGCATATAATG-T -s Anc2.Anc2refChr0 363 22 + 56053 GATATGAACTAGCATATAATG-T -s mr.mrrefChr0 399 22 + 130230 GATATGAACCAGTATATAGGG-A -s simCow_chr6.simCow.chr6 361 22 + 602619 AATATGAATCAGTATATAATG-T -s simDog_chr6.simDog.chr6 367 22 + 593897 GATATGAACTAGCATATAATG-T -s simHuman_chr6.simHuman.chr6 367 14 + 601863 GACATGAACA--------ATG-C -s simRat_chr6.simRat.chr6 395 22 + 647215 GATATGCATCAGTATATAGGG-A - -a -s simMouse_chr6.simMouse.chr6 405 22 + 636262 GCCACTGCTCTCTTAGCATTTA -s Anc0.Anc0refChr9 385 22 - 35212 GCCACTGCCCCAGTAACATTTA -s Anc1.Anc1refChr0 402 22 + 16026 GCCACTGCCCCAGTAACATTTA -s Anc2.Anc2refChr0 386 22 + 56053 GCCACTGCCCCAGTAACATTTA -s mr.mrrefChr0 421 22 + 130230 GCCACTGCCCTCTTAGCATTTA -s simCow_chr6.simCow.chr6 384 22 + 602619 GCCACTGCCCTAGTAACATGTA -s simDog_chr6.simDog.chr6 390 22 + 593897 GCCAGAGCCCCTGTAACATTTA -s simHuman_chr6.simHuman.chr6 382 22 + 601863 ACCACTGCCCCACTAATATTTA -s simRat_chr6.simRat.chr6 417 22 + 647215 GCCACTGGCCTCTTAGCATTCA - -a -s simMouse_chr6.simMouse.chr6 427 4 + 636262 TTTG -s Anc0.Anc0refChr9 407 4 - 35212 TTTG -s Anc1.Anc1refChr0 424 4 + 16026 TTTG -s Anc2.Anc2refChr0 408 4 + 56053 TTTG -s mr.mrrefChr0 443 4 + 130230 TTTG -s simCow_chr6.simCow.chr6 407 4 + 602619 TTTG -s simDog_chr6.simDog.chr6 412 4 + 593897 TTTG -s simHuman_chr6.simHuman.chr6 404 4 + 601863 TGTG -s simRat_chr6.simRat.chr6 439 4 + 647215 TTTG - -a -s simMouse_chr6.simMouse.chr6 431 73 + 636262 CTGTAAAGGAACTGATGAGCTAAAGTCGTCCAGAATGTATAAGCAGAAATTTGTAACCAGCCTTAAAGGCAGC -s Anc0.Anc0refChr9 411 69 - 35212 --ATAAGGTAATTGATGAGCTGAAGTTG-CTAGAACATGTAAGTAAGAGACCTTAAGCATCC-TTAAGGCAGT -s Anc1.Anc1refChr0 428 71 + 16026 CTATAAGGTAATTGATGAGCTGAAGTTG-CTAGAACATGTAAGTAAGAGACCTTAAGCATCC-TTAAGGCAGT -s Anc2.Anc2refChr0 412 69 + 56053 --ATAAGGTAATTGATAAGCTGAAGTTG-CTAGAACATGTAAGTATGAGACCTTACGCAGCC-TTAAGGCAGT -s mr.mrrefChr0 447 72 + 130230 CTGTAAGGTAACTGATGAGCTAAAGTCGTCTAGAATGTATAAGTAAAAGTCTGTAAGCATCC-TAAAGGCAGC -s simCow_chr6.simCow.chr6 411 56 + 602619 --ATAAGGTAACTGATCAGCTGAAGTTG-CCAGAACACATAAG-------------GCAGCC-CTAAGACAGA -s simDog_chr6.simDog.chr6 416 69 + 593897 --ATAAGGTAATTGGTAAACTAAAGTTG-CTAGAACATGTAAGTATGAGACCTTACGCAGCC-TTAAGGCAGT -s simHuman_chr6.simHuman.chr6 409 70 + 601863 CTATAAGATAATTGATGAGCCGAAGTTG-CTAGAACAATTAAGTAAGAGCCCCTAAGCATCC-TTAAAGCAG- -s simRat_chr6.simRat.chr6 443 71 + 647215 CTGTAAGGTAA-TGATGCGCTAAAGTCATCTAGAATGTATAGGTAAAAGTCTGTAAGCATTG-TAAAGGCACC - -a -s simMouse_chr6.simMouse.chr6 504 28 + 636262 AGCTTTGGTTATAACGCACAATTCAAGA -s Anc0.Anc0refChr9 480 28 - 35212 AGCTTCGGATATGACCCACAATTCAAGA -s Anc1.Anc1refChr0 499 28 + 16026 AGCTTCGGATATGACCCACAATTCAAGA -s Anc2.Anc2refChr0 484 28 + 56053 AGCTTCGTATATGGCCCACAATTCAAGG -s mr.mrrefChr0 519 28 + 130230 AGCTTTGGTTATGACGCACAATTCAAGA -s simCow_chr6.simCow.chr6 470 24 + 602619 AGCTTCAGATATGGCCCACA----AAGG -s simDog_chr6.simDog.chr6 488 28 + 593897 AGCTTCGTATACAGCCCACAATTCAATG -s simHuman_chr6.simHuman.chr6 479 24 + 601863 ----TGAGATATGACCTGCAATTCAAGA -s simRat_chr6.simRat.chr6 514 28 + 647215 GGCTTTGGTTATGATGCACAATTCAAGA - -a -s simMouse_chr6.simMouse.chr6 532 14 + 636262 CCACCTGCTGGATC -s Anc0.Anc0refChr9 511 14 - 35212 CCACCTGCCTGATC -s Anc1.Anc1refChr0 530 14 + 16026 CCACCTGCCTGATC -s Anc2.Anc2refChr0 515 14 + 56053 CCGCCTGCCTGATC -s mr.mrrefChr0 547 14 + 130230 CCACCTGCTGGATC -s simCow_chr6.simCow.chr6 497 14 + 602619 TCCCCTGCCTGATC -s simDog_chr6.simDog.chr6 519 14 + 593897 CAGCCTATCTGATC -s simHuman_chr6.simHuman.chr6 507 14 + 601863 CCACTTGCCTGATC -s simRat_chr6.simRat.chr6 542 8 + 647215 CCATCTGC------ - -a -s simMouse_chr6.simMouse.chr6 546 3 + 636262 CAG -s Anc0.Anc0refChr9 525 3 - 35212 TGG -s Anc1.Anc1refChr0 544 3 + 16026 TGG -s Anc2.Anc2refChr0 529 3 + 56053 TGG -s mr.mrrefChr0 561 3 + 130230 CAG -s simCow_chr6.simCow.chr6 511 3 + 602619 TGG -s simDog_chr6.simDog.chr6 544 3 + 593897 TGG -s simHuman_chr6.simHuman.chr6 521 3 + 601863 TGG - -a -s simMouse_chr6.simMouse.chr6 549 28 + 636262 CTACATTTAGCAATATTACTGATCTGTT -s Anc0.Anc0refChr9 528 28 - 35212 GTATATTTTGCAATTCTACTGATCTGCT -s Anc1.Anc1refChr0 547 28 + 16026 GTATATTTTGCAATTCTACTGATCTGCT -s Anc2.Anc2refChr0 532 28 + 56053 GTATATTTTGCAATTCTACTAGTCTGCT -s mr.mrrefChr0 564 28 + 130230 CTACATTTAGCAATATTACTGATCTGTT -s simCow_chr6.simCow.chr6 523 28 + 602619 GCATATTTTGCAATTACACTAGTCTGCT -s simDog_chr6.simDog.chr6 547 28 + 593897 GTACACCCTGCAACTCTACTAGTCTGCT -s simHuman_chr6.simHuman.chr6 524 28 + 601863 GTATATTTTGCAATGCTACAGATCTGCT - -a -s simMouse_chr6.simMouse.chr6 577 17 + 636262 GCACAGCAATCCATCAG -s Anc0.Anc0refChr9 576 15 - 35212 CCACAG--ATGCATCAA -s Anc1.Anc1refChr0 595 15 + 16026 CCACAG--ATGCATCAA -s Anc2.Anc2refChr0 580 15 + 56053 CTACAG--ATGCATCAA -s mr.mrrefChr0 592 15 + 130230 GCACAG--ATCCATCAG -s simCow_chr6.simCow.chr6 571 15 + 602619 TGATGA--ATGCATCAA -s simDog_chr6.simDog.chr6 595 15 + 593897 CTACAG--CGGCATTAA -s simHuman_chr6.simHuman.chr6 572 15 + 601863 CCACAG--ATGCATCAA - -a -s simMouse_chr6.simMouse.chr6 594 58 + 636262 GGTGATAGAAATGCAACACACATAACTTGTTGTCCAAGAGGTTAATTATTGTAAGCGC -s Anc0.Anc0refChr9 599 51 - 35212 AGTCTCATAAACACTACCCACATTGCTTATTGTACAGGAGGTTAATTA-------CAG -s Anc1.Anc1refChr0 618 56 + 16026 AGTCTCATAAACACTACCCACATTGCTTATTGTACAGGAGGTTAATTA--GTGACCAG -s Anc2.Anc2refChr0 603 51 + 56053 AGGCTCATAAACACTTCCCACATTGCTTATTGTACAGAAGTTTAATTA-------TAG -s mr.mrrefChr0 607 58 + 130230 GGTGATAGAAATGCAACACACATAACTTGTTGTCCAAGAGGTTAATTAGTGTGACCGG -s simCow_chr6.simCow.chr6 594 51 + 602619 AGCCTCATAAACACTTCCCACATTGCTCATTGTACAGAAGTTTACTTA-------TAT -s simDog_chr6.simDog.chr6 618 38 + 593897 AGGCTCATAAACA-------------GTATTGTGCAGAAGGTTAATTA-------TTG -s simHuman_chr6.simHuman.chr6 595 56 + 601863 AGTCTCATGAACACTACCCACATTGCTTATTGTACAGGTAGAAAATTG--GTGACCAG -s simRat_chr6.simRat.chr6 550 21 + 647215 ---------------------------------CCA----GTTAATTAGTGTGACTGG - -a -s simMouse_chr6.simMouse.chr6 652 93 + 636262 ATCTACATCCATCTATCAGTGGTCCTCTCTATTCAAGGCTCAAAAACTCGTAGACTATTAGGGTCTCCAATAAACTATAAGGGCGATAGGGAA -s Anc0.Anc0refChr9 650 37 - 35212 AACTACATCCACCCATCAGTGGTCCTCTA--TCCAAGGC------------------------------------------------------ -s Anc1.Anc1refChr0 674 83 + 16026 AACTACATCCACCCATCAGTGGTCCTCTA--TCCAAGGCCTTAAaactagaagagtta--------ccactgaattagaagagtgatatgaaa -s Anc2.Anc2refChr0 654 37 + 56053 AATTATGTCCACCCATCAGTGGTCCTCTA--TCCAAAGC------------------------------------------------------ -s mr.mrrefChr0 665 93 + 130230 ATCTACATCCACCTATCAGTGGTCCTCTCTATTCAAGGCTCAAAAACTAGTAGAGTAATAGGGTCTCCAATAAACTATAAGGGCGATAGGGAA -s simCow_chr6.simCow.chr6 645 37 + 602619 TAATATGTACACCCATCAGTGGTCATCTA--TCCAAAGC------------------------------------------------------ -s simDog_chr6.simDog.chr6 663 37 + 593897 AATTATGTCCACCCATCAGTGGTCCTCTA--TCAAAAGC------------------------------------------------------ -s simHuman_chr6.simHuman.chr6 651 83 + 601863 AACTACACCCACCCATCATTGGTACTCTT--TCCAAGGCCTTAAaactagaagagtta--------ccactgaattagaagagtgatatgaaa -s simRat_chr6.simRat.chr6 571 93 + 647215 ATCCACATCCACCTATCAGTGGTCCTCTCTATTCAAAGCTCAAAAACTAGTAGAGTAATAGGGGATCCAATAAACTTTAAGGGCGATAGGGAA - -a -s simMouse_chr6.simMouse.chr6 745 8 + 636262 CTCTAGCT -s Anc1.Anc1refChr0 757 8 + 16026 ctccagct -s mr.mrrefChr0 758 8 + 130230 CTCTAGCT -s simHuman_chr6.simHuman.chr6 735 8 + 601863 ctccagct -s simRat_chr6.simRat.chr6 664 8 + 647215 CTCTAGTT - -a -s simMouse_chr6.simMouse.chr6 753 17 + 636262 TTTACTTAGCACAACAG -s Anc0.Anc0refChr9 687 11 - 35212 ------TAGCACAACAG -s Anc1.Anc1refChr0 765 17 + 16026 TCAAATTAGCACAACAG -s Anc2.Anc2refChr0 691 11 + 56053 ------TGGCACAACAG -s mr.mrrefChr0 766 17 + 130230 TTTACTTAGCACAACAG -s simCow_chr6.simCow.chr6 682 11 + 602619 ------TCGTACAACAG -s simDog_chr6.simDog.chr6 700 11 + 593897 ------TGGCACAACAG -s simHuman_chr6.simHuman.chr6 747 17 + 601863 TCAAATCATCACAATAG -s simRat_chr6.simRat.chr6 672 17 + 647215 TTTACTTAGCAAAACAG - -a -s simMouse_chr6.simMouse.chr6 770 7 + 636262 TCTATAG -s Anc0.Anc0refChr9 698 7 - 35212 CCCACAG -s Anc1.Anc1refChr0 782 7 + 16026 CCCACAG -s Anc2.Anc2refChr0 706 7 + 56053 CACACAA -s mr.mrrefChr0 783 7 + 130230 CCTACAG -s simCow_chr6.simCow.chr6 697 7 + 602619 CACACAA -s simHuman_chr6.simHuman.chr6 764 7 + 601863 CCCACTG -s simRat_chr6.simRat.chr6 689 7 + 647215 CCTACAG - -a -s simMouse_chr6.simMouse.chr6 777 75 + 636262 CCTACAACTGGTCACCAGTCACTTTTCTTCTAGCAACAAGGTACAGAGGAGGGCTGTGTGGTGGTGAGTGATGTA -s Anc0.Anc0refChr9 705 58 - 35212 -CTGCTTCT-GTCTCTGAGCACCATTCTGCTGGTAACAAAGTACAGAGTAGGGCC---------------ATGTG -s Anc1.Anc1refChr0 789 58 + 16026 -CTGCTTCT-GTCTCTGAGCACCATTCTGCTGGTAACAAAGTACAGAGTAGGGCC---------------ATGTG -s Anc2.Anc2refChr0 713 58 + 56053 -AGCCTCCT-GCCTCTGAGCACCATTATGCAGGTAATTAAGTGCAGAGTAGGGCC---------------ATGCG -s mr.mrrefChr0 790 75 + 130230 CCTGCATCTGGTCACCAGTCACCTTTCTTCTAGCAACAAGGTACAGAGTAGGGCTGTGTGGTGGTGAGTGATGTG -s simCow_chr6.simCow.chr6 704 58 + 602619 -AGCCTCCT-GCCTCTGAGCACCATTATGCAGGTAATTAAGTGCAGAGTAGGGCC---------------ATGCG -s simHuman_chr6.simHuman.chr6 771 58 + 601863 -CTGCTTCT-GTCTCTGAGCACCATTCTACTGGTAACAAAGCACAAAGTAGGGCC---------------ATGTG -s simRat_chr6.simRat.chr6 703 75 + 647215 CCTGGATCTGGTCATCTGTCACCTTTCTTCCAGCAACAAGATACAGAGTAGAGCTGTGGGGTGGTTAGTCATGCG - -a -s simMouse_chr6.simMouse.chr6 852 6 + 636262 CACCTT -s Anc0.Anc0refChr9 763 6 - 35212 TACTTT -s Anc1.Anc1refChr0 847 6 + 16026 TACTTT -s Anc2.Anc2refChr0 771 6 + 56053 TGCTTT -s mr.mrrefChr0 865 6 + 130230 TACCTT -s simCow_chr6.simCow.chr6 781 6 + 602619 TGCTTT -s simHuman_chr6.simHuman.chr6 829 6 + 601863 TATTTT -s simRat_chr6.simRat.chr6 778 6 + 647215 TACCTT - -a -s simMouse_chr6.simMouse.chr6 858 16 + 636262 GGCATGAACCCACTGT -s Anc0.Anc0refChr9 771 9 - 35212 AGC-TGGA------GT -s Anc1.Anc1refChr0 855 10 + 16026 AGCATGGA------GT -s Anc2.Anc2refChr0 779 9 + 56053 AGC-TTGA------GT -s mr.mrrefChr0 871 16 + 130230 GGCATGAACCCACTGT -s simCow_chr6.simCow.chr6 789 9 + 602619 AGC-TTGA------GT -s simHuman_chr6.simHuman.chr6 837 9 + 601863 A-CATGGA------GT -s simRat_chr6.simRat.chr6 784 16 + 647215 AGCATGAGCCCACTGT - -a -s simMouse_chr6.simMouse.chr6 874 4 + 636262 AGGT -s Anc0.Anc0refChr9 780 4 - 35212 AGGT -s Anc1.Anc1refChr0 865 4 + 16026 AGGT -s Anc2.Anc2refChr0 788 4 + 56053 GTGT -s mr.mrrefChr0 887 4 + 130230 AGGT -s simCow_chr6.simCow.chr6 801 4 + 602619 GTGT -s simHuman_chr6.simHuman.chr6 846 4 + 601863 AGGT -s simRat_chr6.simRat.chr6 800 4 + 647215 AGGT - -a -s simMouse_chr6.simMouse.chr6 878 23 + 636262 AGCAATACTCCAACTGAAGTATT -s Anc0.Anc0refChr9 791 22 - 35212 AGTAATGCCCTAATGGCAG-GTT -s Anc1.Anc1refChr0 876 22 + 16026 AGTAATGCCCTAATGGCAG-GTT -s Anc2.Anc2refChr0 799 22 + 56053 GGTAATGTCCTAGCGACAA-ATT -s mr.mrrefChr0 891 22 + 130230 AGCAATACTCCAATTGAAG-GTT -s simCow_chr6.simCow.chr6 812 22 + 602619 GGTAATGTCCTAGCGACAA-ATT -s simHuman_chr6.simHuman.chr6 857 22 + 601863 AGTAATGCCCTGATCGTAG-GGT -s simRat_chr6.simRat.chr6 804 22 + 647215 AGCAATCCTCCAATTGAAG-GTT - -a -s simMouse_chr6.simMouse.chr6 901 34 + 636262 AGCCCGAGGAGAAATGCAAGTGCGAGTCCGTGCT -s Anc0.Anc0refChr9 813 34 - 35212 AACACAAGGACAATTACTCATGGGGATTCTCAAT -s Anc1.Anc1refChr0 898 34 + 16026 AACACAAGGACAATTACTCATGGGGATTCTCAAT -s Anc2.Anc2refChr0 821 34 + 56053 AACACAAGGACAATTACTCATGGGGATTGTCAAC -s mr.mrrefChr0 913 34 + 130230 AACCCAAGGAGAAATGCAAATGGGAGTCCGTGCT -s simCow_chr6.simCow.chr6 838 34 + 602619 AACACAAGGACAAGTACAGATGGGGATTTTTATC -s simDog_chr6.simDog.chr6 713 26 + 593897 --------TACAGTCAATCATTTGCGCTGGCAAC -s simHuman_chr6.simHuman.chr6 879 34 + 601863 AACACAAGGACAATTACTCATGGGGATTCTCAAT -s simRat_chr6.simRat.chr6 826 34 + 647215 AACCCAAGGAGAAATGCAAATGGGAGTCCATGCT - -a -s simMouse_chr6.simMouse.chr6 935 8 + 636262 ATTGCAAA -s Anc0.Anc0refChr9 847 8 - 35212 ATAGCCAA -s Anc1.Anc1refChr0 932 8 + 16026 ATAGCCAA -s Anc2.Anc2refChr0 855 8 + 56053 ATAGCCAG -s mr.mrrefChr0 947 8 + 130230 ATTGCAAA -s simCow_chr6.simCow.chr6 872 8 + 602619 ATTTTCAT -s simDog_chr6.simDog.chr6 743 8 + 593897 ATAGCCAG -s simHuman_chr6.simHuman.chr6 913 8 + 601863 ATAACCAA -s simRat_chr6.simRat.chr6 860 7 + 647215 ATTGT-AT - -a -s simMouse_chr6.simMouse.chr6 943 10 + 636262 ATTGGTATAT -s Anc0.Anc0refChr9 855 10 - 35212 ATTGTTATAT -s Anc1.Anc1refChr0 940 10 + 16026 ATTGTTATAT -s Anc2.Anc2refChr0 863 10 + 56053 ATTGTTACAT -s mr.mrrefChr0 955 10 + 130230 ATTGTTATAT -s simCow_chr6.simCow.chr6 880 10 + 602619 ATTGTTACAT -s simDog_chr6.simDog.chr6 757 10 + 593897 ATTTTAGCAT -s simHuman_chr6.simHuman.chr6 921 10 + 601863 ATTGTTATGT -s simRat_chr6.simRat.chr6 867 10 + 647215 ATTGTTATAT - -a -s simMouse_chr6.simMouse.chr6 953 3 + 636262 ATT -s Anc0.Anc0refChr9 865 3 - 35212 ATT -s Anc1.Anc1refChr0 950 3 + 16026 ATT -s Anc2.Anc2refChr0 873 3 + 56053 GTT -s mr.mrrefChr0 965 3 + 130230 ATT -s simCow_chr6.simCow.chr6 890 3 + 602619 GTT -s simDog_chr6.simDog.chr6 768 3 + 593897 GTT -s simHuman_chr6.simHuman.chr6 931 3 + 601863 ATT -s simRat_chr6.simRat.chr6 877 3 + 647215 ATT - -a -s simMouse_chr6.simMouse.chr6 956 84 + 636262 CAATTTACTGGCCTTAGCTGCATTCCCCACAGTATTACATACCAATAACCCACATGGTCTCTAAAGACTCTGTTTCGCTTTGGA -s Anc0.Anc0refChr9 873 51 - 35212 CAATTTACTGGCCTTAAG--------------------------------CAGATAG-AACTAAAGACTTTGTTTCACTTTGGA -s Anc1.Anc1refChr0 958 51 + 16026 CAATTTACTGGCCTTAAG--------------------------------CAGATAG-AACTAAAGACTTTGTTTCACTTTGGA -s Anc2.Anc2refChr0 881 51 + 56053 CTATTTACTGGCCTTAAG--------------------------------CAGATAT-AACTAAAGACTTTGCTTCACTTTGGA -s mr.mrrefChr0 968 84 + 130230 CAATTTACTGGCCTTAACTGCATTCCCCGCAGTATTACATACCAATAACCCACATGGTCTCTAAAGACTCTGTTTCGCTTTGGA -s simCow_chr6.simCow.chr6 898 51 + 602619 GTATTTACTGCCCTTAAT--------------------------------CAGATAT-AACCAATGACTTTCCTTCACTTTGGA -s simDog_chr6.simDog.chr6 776 51 + 593897 CTATTTACTGGCCTTAAG--------------------------------CAGATAT-ACCTAAAGACTTTGCTTCACTGTGGA -s simHuman_chr6.simHuman.chr6 939 51 + 601863 CAATCTACTGGCCTTAAG--------------------------------CAGATAG-AACTAGAGGCTGTGTTTCACTTTGGG -s simRat_chr6.simRat.chr6 880 84 + 647215 CAATTTGCTGGCCTTAACTGTATCCCCTGCAGTGTTACATACCAACAACCCACATGGTCTCTAAAGACTTTGTTTTGTTTTGGA - -a -s simMouse_chr6.simMouse.chr6 1040 5 + 636262 TGTTG -s Anc0.Anc0refChr9 924 5 - 35212 TATTG -s Anc1.Anc1refChr0 1009 5 + 16026 TATTG -s Anc2.Anc2refChr0 932 5 + 56053 TATTG -s mr.mrrefChr0 1052 5 + 130230 TATTG -s simCow_chr6.simCow.chr6 950 5 + 602619 TATTG -s simDog_chr6.simDog.chr6 827 5 + 593897 TATCA -s simHuman_chr6.simHuman.chr6 990 5 + 601863 TATTG -s simRat_chr6.simRat.chr6 964 5 + 647215 TATTG - -a -s simMouse_chr6.simMouse.chr6 1045 13 + 636262 ACTCTCATCTATG -s Anc0.Anc0refChr9 929 13 - 35212 ATTCTATACTATC -s Anc1.Anc1refChr0 1014 13 + 16026 ATTCTATACTATC -s Anc2.Anc2refChr0 937 13 + 56053 ATTCTATACTATC -s mr.mrrefChr0 1057 13 + 130230 ACTCTAATCTATG -s simCow_chr6.simCow.chr6 968 13 + 602619 ATTCTATTCTATC -s simDog_chr6.simDog.chr6 832 13 + 593897 AGTCTATACTATC -s simHuman_chr6.simHuman.chr6 995 13 + 601863 ATTCCATACTATC -s simRat_chr6.simRat.chr6 969 13 + 647215 GCTTTACCCTATG - -a -s simMouse_chr6.simMouse.chr6 1058 13 + 636262 GGCCAAACACACC -s Anc0.Anc0refChr9 943 13 - 35212 AGCGGAGCACATC -s Anc1.Anc1refChr0 1028 13 + 16026 AGCGGAGCACATC -s Anc2.Anc2refChr0 951 13 + 56053 AGCAGAGCACATC -s mr.mrrefChr0 1071 13 + 130230 GGCGAAGCACACC -s simCow_chr6.simCow.chr6 982 13 + 602619 AGCAGGGCACATC -s simDog_chr6.simDog.chr6 846 13 + 593897 AGCATAGCACATC -s simHuman_chr6.simHuman.chr6 1009 13 + 601863 AGGGGAGCACATC -s simRat_chr6.simRat.chr6 983 13 + 647215 GGTGAAGCAAACC - -a -s simMouse_chr6.simMouse.chr6 1071 16 + 636262 TTTAAACTAATCTTCA -s Anc0.Anc0refChr9 956 1 - 35212 ---------------A -s Anc1.Anc1refChr0 1041 16 + 16026 CTTCAAGAAGTCCTCA -s Anc2.Anc2refChr0 964 1 + 56053 ---------------A -s mr.mrrefChr0 1084 16 + 130230 CTTAAACTAATCTTCA -s simCow_chr6.simCow.chr6 995 1 + 602619 ---------------A -s simDog_chr6.simDog.chr6 859 1 + 593897 ---------------A -s simHuman_chr6.simHuman.chr6 1023 16 + 601863 CTTCAAGAAGTCCTTG -s simRat_chr6.simRat.chr6 996 16 + 647215 CTTAAACTGATGTTCA - -a -s simMouse_chr6.simMouse.chr6 1087 7 + 636262 CCTTTCA -s Anc0.Anc0refChr9 957 7 - 35212 CCTTTCA -s Anc1.Anc1refChr0 1057 7 + 16026 CCTTTCA -s Anc2.Anc2refChr0 965 7 + 56053 CCTTTCA -s mr.mrrefChr0 1100 7 + 130230 CCTTTCA -s simCow_chr6.simCow.chr6 996 7 + 602619 CCTTTCA -s simDog_chr6.simDog.chr6 860 7 + 593897 CCTTTCA -s simHuman_chr6.simHuman.chr6 1106 7 + 601863 CCTGTCA -s simRat_chr6.simRat.chr6 1012 7 + 647215 CCTTTCA - -a -s simMouse_chr6.simMouse.chr6 1094 20 + 636262 AGTGATCTTGTGTCTCTATT -s Anc0.Anc0refChr9 964 19 - 35212 AGAAATCTTTCGTCTCTG-T -s Anc1.Anc1refChr0 1064 19 + 16026 AGAAATCTTTCGTCTCTG-T -s Anc2.Anc2refChr0 972 19 + 56053 AGAAATCTTTCGTCTCTG-T -s mr.mrrefChr0 1107 20 + 130230 AGTAATCTTGTGTCTCTATT -s simCow_chr6.simCow.chr6 1053 13 + 602619 AGGAACATGTCTT------- -s simDog_chr6.simDog.chr6 867 19 + 593897 AGAAATCTTCTGTCTCTG-T -s simHuman_chr6.simHuman.chr6 1113 19 + 601863 AGAAATCTTTCGTTTCTG-T -s simRat_chr6.simRat.chr6 1019 20 + 647215 AATAGTCTGGTGTCTCCATT - -a -s simMouse_chr6.simMouse.chr6 1114 11 + 636262 TGCACAGAGTA -s Anc0.Anc0refChr9 983 11 - 35212 AGCACAGAGTG -s Anc1.Anc1refChr0 1083 11 + 16026 AGCACAGAGTG -s Anc2.Anc2refChr0 991 11 + 56053 AGCACCAAGTG -s mr.mrrefChr0 1127 11 + 130230 TGCACAGAGTA -s simCow_chr6.simCow.chr6 1066 4 + 602619 -------GGTG -s simDog_chr6.simDog.chr6 887 11 + 593897 AGCACCAAGTA -s simHuman_chr6.simHuman.chr6 1132 11 + 601863 GGCACAGAATG -s simRat_chr6.simRat.chr6 1039 11 + 647215 TATACAGAGTA - -a -s simMouse_chr6.simMouse.chr6 1125 15 + 636262 AGATTATTGTGCGAT -s Anc0.Anc0refChr9 994 15 - 35212 TGATACTTGTGGTAT -s Anc1.Anc1refChr0 1094 15 + 16026 TGATACTTGTGGTAT -s Anc2.Anc2refChr0 1002 15 + 56053 TGATACTTGTGGTAT -s mr.mrrefChr0 1138 15 + 130230 TGATTATTGTGGGAT -s simCow_chr6.simCow.chr6 1070 15 + 602619 AGATATTTGTGCTAT -s simCow_chr6.simCow.chr6 1196 15 + 602619 AGATATTTGTGCTAT -s simDog_chr6.simDog.chr6 898 15 + 593897 TGATACTCATGGTAT -s simHuman_chr6.simHuman.chr6 1143 15 + 601863 TGATACTTCTGGTAT -s simRat_chr6.simRat.chr6 1050 15 + 647215 TGGTTATTGTGGGAT - -a -s simMouse_chr6.simMouse.chr6 1140 17 + 636262 TGATAGGAGCACTTGTT -s Anc0.Anc0refChr9 1009 17 - 35212 TGTCAGGAATACTTGTT -s Anc1.Anc1refChr0 1109 17 + 16026 TGTCAGGAATACTTGTT -s Anc2.Anc2refChr0 1017 17 + 56053 GGTCAGGAATACTTGTT -s mr.mrrefChr0 1153 17 + 130230 TGACAGGAGCACTTGTT -s simCow_chr6.simCow.chr6 1085 17 + 602619 GGTCAGGAACACTTGTT -s simCow_chr6.simCow.chr6 1211 17 + 602619 GGTCAGGAACACTTGTT -s simDog_chr6.simDog.chr6 913 15 + 593897 GGTCAGGAATATT--GT -s simHuman_chr6.simHuman.chr6 1159 17 + 601863 TTCCAGGGATACTTGAT -s simRat_chr6.simRat.chr6 1065 17 + 647215 TGTCAGGAGCACTTGTT - -a -s simMouse_chr6.simMouse.chr6 1157 84 + 636262 GGTAATTACTATCagactggattccatattgctcactcagttatcaggatgcaatatgactcaagtagtcccaggttttaaacc -s Anc0.Anc0refChr9 1026 84 - 35212 GGTAATTACAATCaggttggattccatattgcttgttcagttatcaggatgcaatatagctcaaggagtcccaggttttatgac -s Anc1.Anc1refChr0 1126 84 + 16026 GGTAATTACAATCaggttggattccatattgcttgttcagttatcaggatgcaatatagctcaaggagtcccaggttttatgac -s Anc2.Anc2refChr0 1034 84 + 56053 GGTGATTACAATCaggttggattccatattgcttgttcagttatcaggatgcaatatagctcaaGgagtcccaggttttatgac -s mr.mrrefChr0 1170 84 + 130230 GGTAATTACAATCagattggattccatattgctcattcagttatcaggatgcaatatgactcaagtagtcccaggttttaagcc -s simCow_chr6.simCow.chr6 1102 79 + 602619 GGTGATTACAATCAGATTGGATCCCATATTGCTTGTTTAG-TCTCAAGATGCGACATA----AAGGACTGCCAGGTTGTATGAC -s simCow_chr6.simCow.chr6 1228 79 + 602619 GGTGATTACAATCAGATTGGATCCCATATTGCTTGTTTAG-TCTCAAGATGCAACATA----AAGGACTGCCAGGTTGTATGAC -s simDog_chr6.simDog.chr6 928 83 + 593897 GGTGATTGCGATTaggttggattccttattgctcattcagtaatcaggatgcaatatagctcaa-gagtcccaggttttttgac -s simHuman_chr6.simHuman.chr6 1184 84 + 601863 GGTAATTACAATCaagttggattccatatcacttgttcagctattaggtcacaatatagctcaaggagtcccaggctttatgac -s simRat_chr6.simRat.chr6 1082 84 + 647215 GGTAATTGCAACCAGATCGGATTCCATATTGCTCATTCAATGATCAGGATGCAATATGACACAAGTAGTCCCAGGTTTTAAGCC - -a -s simMouse_chr6.simMouse.chr6 1241 5 + 636262 atcag -s Anc0.Anc0refChr9 1110 5 - 35212 tctcc -s Anc1.Anc1refChr0 1210 5 + 16026 tctcc -s Anc2.Anc2refChr0 1118 5 + 56053 tctcc -s mr.mrrefChr0 1254 5 + 130230 atcaG -s simCow_chr6.simCow.chr6 1327 5 + 602619 TCTGG -s simDog_chr6.simDog.chr6 1011 5 + 593897 tctcc -s simHuman_chr6.simHuman.chr6 1268 5 + 601863 tctca -s simRat_chr6.simRat.chr6 1166 5 + 647215 ATTAG - -a -s simMouse_chr6.simMouse.chr6 1246 19 + 636262 AGCTCACTGATAGGGGTTT -s Anc0.Anc0refChr9 1115 15 - 35212 TGTTGAGTGCTGGGG---- -s Anc1.Anc1refChr0 1215 15 + 16026 TGTTGAGTGCTGGGG---- -s Anc2.Anc2refChr0 1123 15 + 56053 TGTCGAGTGCTGGGG---- -s mr.mrrefChr0 1259 19 + 130230 AGCTCACTGATGGGGGTTT -s simCow_chr6.simCow.chr6 1181 15 + 602619 TGTTAAGTCTTGGTG---- -s simCow_chr6.simCow.chr6 1332 15 + 602619 TTGCGAGTGCTGGGG---- -s simDog_chr6.simDog.chr6 1016 15 + 593897 ggtcgAGTGCCGGAA---- -s simHuman_chr6.simHuman.chr6 1273 15 + 601863 TGGTGTGTGTTGGGG---- -s simRat_chr6.simRat.chr6 1171 19 + 647215 AGCTCACTGATGGAGGTTT - -a -s simMouse_chr6.simMouse.chr6 1265 15 + 636262 GCTGGGAACCTATAT -s Anc0.Anc0refChr9 1130 12 - 35212 G---GTAAGTTGAAT -s Anc1.Anc1refChr0 1230 15 + 16026 GCTGGTAAGTTGAAT -s Anc2.Anc2refChr0 1138 12 + 56053 G---GTTAGTTGAAT -s mr.mrrefChr0 1278 15 + 130230 GCTGGTAACCTATAT -s simCow_chr6.simCow.chr6 1347 10 + 602619 G---GTTAACTG--T -s simDog_chr6.simDog.chr6 1031 12 + 593897 G---GTTAGTTGAAT -s simHuman_chr6.simHuman.chr6 1288 15 + 601863 GCTAGTAATATGGAT -s simRat_chr6.simRat.chr6 1190 14 + 647215 GCTGGTAACCTA-AT - -a -s simMouse_chr6.simMouse.chr6 1280 48 + 636262 TGATCCAGGGAAGAGGCCACCTGCAACATGTGCGCCTTGTCTACTACA -s Anc0.Anc0refChr9 1146 47 - 35212 AGATCCAGTAAAGAGGCCACCCCTACCCCATGCGTCTTGTCTACCTT- -s Anc1.Anc1refChr0 1249 47 + 16026 AGATCCAGTAAAGAGGCCACCCCTACCCCATGCGTCTTGTCTACCTT- -s Anc2.Anc2refChr0 1154 47 + 56053 AGATGCAGTAAAGAGGCCACCCCTACCCCATGCATCTTGTCTCCCTT- -s mr.mrrefChr0 1293 48 + 130230 AGATCCAGGGAAGAGGCCACCCGCAACATGTGCGCCTTGTCTACCTTA -s simCow_chr6.simCow.chr6 1361 41 + 602619 ATATGCAGTGAGAAGGCC------ATTCTATCTATCCTGACTCCTTA- -s simDog_chr6.simDog.chr6 1046 47 + 593897 AGATGCAGTAAAGAGGCCACCCCTACCTCATGCACCTTATCTCCCTT- -s simHuman_chr6.simHuman.chr6 1307 47 + 601863 AAATCCAGTAAAGAGACCTCCCCTACCCCATGAGTCTTGTCTACCTT- -s simRat_chr6.simRat.chr6 1204 48 + 647215 AGACCCTAGGAAGAAGCCACCCACAACATGTGCACCTTGTCTACCTTA - -a -s simMouse_chr6.simMouse.chr6 1328 124 + 636262 TGTAGGATTGAAGTTGTCAAGATCGAATCTTGCAGAGAATCGGATACTTTGTATAGTTATCTCATTCTCTCCTCCACCACATTCTCTCCTCCACCACTACCTCTCAAATAGCACCTTCTGAATG -s Anc0.Anc0refChr9 1193 107 - 35212 TGTGAGCTTAAAGTTGTCAGGATGAAATCTCACAGGTAATCTCAAGCTTTGTTTGGTTATTTTTCCCTCTCTTCC-----------------AAGTCCTCCTCTTGAATAATACCTTCTTAATA -s Anc1.Anc1refChr0 1296 107 + 16026 TGTGAGCTTAAAGTTGTCAGGATGAAATCTCACAGGTAATCTCAAGCTTTGTTTGGTTATTTTTCCCTCTCTTCC-----------------AAGTCCTCCTCTTGAATAATACCTTCTTAATA -s Anc2.Anc2refChr0 1201 107 + 56053 TGTGAGCTTAAAGTTGTCAGGATAAAATCCCACAGGTAATCTCAAGCTTTGTTCGGTTATTTTTCCCCCTCTTCC-----------------AAGTCCTCCTCTTGAATAATACCTTCTTAATA -s mr.mrrefChr0 1341 107 + 130230 TGTAAGATTAAAGTTGTCAAGATGGAATCTTGCAGAGAATCGGATACTTTGTATAGTTATCTCATTCTCTCCTCC-----------------AACACTACCTCTCAAATAGCACCTTCTGAATG -s simCow_chr6.simCow.chr6 1402 107 + 602619 TGTGAGCTTAAAGTTGTCAGGATAAAATCACCTCAGTGATCTCAAGGTTTGTTCGGTTATTTCACCCCCTCTCCC-----------------AAGTCCTCCCCATGGCTACTACCTTCTTAGTC -s simDog_chr6.simDog.chr6 1094 107 + 593897 TGGGAGCCTAAAGTTGTCAGGATAAAATCCGACAGGTAATCTCAAGCTCTGTTCTGTTATCTTTCCCCCTCTTCC-----------------AAGTCCTCTTCTCAAATAATACCTTCTTGATA -s simHuman_chr6.simHuman.chr6 1354 107 + 601863 TGTGAGCTTAAAGTTGTCAGGATGAAATCTCACAGGCCATCTCAAGCTTTGTTTGGTTATTTTTCCCTCTTTTCC-----------------AATTTCTCCTCCTGAATATTATGTACTTAATA -s simRat_chr6.simRat.chr6 1252 106 + 647215 TGAAAGATTAAAGTTGTCAAGATGCAATCTTGCAGATAATTAGATACTTTGTACAGTTATCTCATTCTCTCCTCC-----------------AACACTACCTCTCAAATAGCACCTTCTCAAT- - -a -s simMouse_chr6.simMouse.chr6 1452 11 + 636262 CCAACTAGTAC -s Anc0.Anc0refChr9 1300 11 - 35212 CCAACTGATAT -s Anc1.Anc1refChr0 1403 11 + 16026 CCAACTGATAT -s Anc2.Anc2refChr0 1308 11 + 56053 CCAACTGATAT -s mr.mrrefChr0 1448 11 + 130230 CCAACTAGTAC -s simCow_chr6.simCow.chr6 1509 11 + 602619 CTAACTGATAC -s simDog_chr6.simDog.chr6 1201 11 + 593897 CCAATTGGTAT -s simHuman_chr6.simHuman.chr6 1469 11 + 601863 CCATCTGATGT -s simRat_chr6.simRat.chr6 1358 11 + 647215 CCAACTAGTAT - -a -s simMouse_chr6.simMouse.chr6 1463 30 + 636262 TCTTATTTTGCTTTTTCAGATCTACAATTA -s Anc0.Anc0refChr9 1312 30 - 35212 TCATATTTTGATTTGTCAAGTGTACATTTG -s Anc1.Anc1refChr0 1415 30 + 16026 TCATATTTTGATTTGTCAAGTGTACATTTG -s Anc2.Anc2refChr0 1320 30 + 56053 TCATATTTAGATTTGTCAAGTGTACATTTG -s mr.mrrefChr0 1459 30 + 130230 TCATATTTTGCTTTTTCAGGTCTACAATTA -s simCow_chr6.simCow.chr6 1521 30 + 602619 TCGTAGTTAGATTTGTCAAGCGTACATTTC -s simDog_chr6.simDog.chr6 1213 30 + 593897 TCATATTTAGATTTGTTGGGTGTGCATTTG -s simHuman_chr6.simHuman.chr6 1481 30 + 601863 TCATATTTTGTTTTGTCAAGTGTACCCTTG -s simRat_chr6.simRat.chr6 1369 30 + 647215 TCATATTTTCCTTTTTCCGGTCTACAATTA - -a -s simMouse_chr6.simMouse.chr6 1493 43 + 636262 GATGTGTTAGGTGCTCCCATATAGGGACTGCTCCACCATGAAA -s Anc0.Anc0refChr9 1367 43 - 35212 CATCTCTTGGCTGCTCCCATATAGAGACTCCTCCTCTATGAAA -s Anc1.Anc1refChr0 1470 43 + 16026 CATCTCTTGGCTGCTCCCATATAGAGACTCCTCCTCTATGAAA -s Anc2.Anc2refChr0 1375 43 + 56053 CATCTTATGGCTGCTCCCATATAGAGACTCCTCCTCTATGAAG -s mr.mrrefChr0 1489 43 + 130230 CATGTCTTAGGTGCTCCCATATAGGGACTGCTCCACCATGAAA -s simCow_chr6.simCow.chr6 1554 29 + 602619 --------------TCCCATATAGAGACTGCTCCTCTAGGAAG -s simDog_chr6.simDog.chr6 1268 43 + 593897 CATCTTATGGCTGCTGCCAGTTAGGGACTCCTCCTCCATGAAG -s simHuman_chr6.simHuman.chr6 1536 43 + 601863 CATTTCTTGGCTGCTCGCATATAGAGACTTGCCCTCTACAAAA -s simRat_chr6.simRat.chr6 1399 43 + 647215 CACCTCTTAGATGCTCCCATATAGGGACTGCTCCCCCATGAAA - -a -s simMouse_chr6.simMouse.chr6 1536 29 + 636262 AAGACTGAACACCATGGTGTATAGCATCC -s Anc0.Anc0refChr9 1412 28 - 35212 GAGTCTAATCACCAT-GTGCATATCATCC -s Anc1.Anc1refChr0 1515 28 + 16026 GAGTCTAATCACCAT-GTGCATATCATCC -s Anc2.Anc2refChr0 1420 28 + 56053 GACTCTAATCACCAT-ATGCATATCCCGT -s mr.mrrefChr0 1532 28 + 130230 GAGACTAAACACCAT-GTGTATAGCATCC -s simCow_chr6.simCow.chr6 1585 28 + 602619 GACTCTAATCACCTT-ATGTATATCCGTC -s simDog_chr6.simDog.chr6 1313 23 + 593897 G-----ACTCACCAT-ATGCATATTCCGT -s simHuman_chr6.simHuman.chr6 1581 24 + 601863 GAGTCTAATCACCAG-GTGCA----ATCC -s simRat_chr6.simRat.chr6 1442 28 + 647215 GAGACCAAAAACCAT-GTGTATAGCATCC - -a -s simMouse_chr6.simMouse.chr6 1565 17 + 636262 TTTGACTGATGTTCTAC -s Anc0.Anc0refChr9 1440 17 - 35212 TTTGACTCTTGTTGTGC -s Anc1.Anc1refChr0 1543 17 + 16026 TTTGACTCTTGTTGTGC -s Anc2.Anc2refChr0 1448 17 + 56053 TTTGACTCTTGTTATGC -s mr.mrrefChr0 1560 17 + 130230 TTTGACTGATGTTGTAC -s simCow_chr6.simCow.chr6 1613 8 + 602619 TTTGACTT--------- -s simDog_chr6.simDog.chr6 1336 17 + 593897 TTTGGCTCTTGTTATGC -s simHuman_chr6.simHuman.chr6 1613 17 + 601863 TTTGACTCTTGTTGTGC -s simRat_chr6.simRat.chr6 1470 17 + 647215 TTTGACTGATGTTGTAC - -a -s simMouse_chr6.simMouse.chr6 1582 15 + 636262 AGTATTGTTTAAACA -s Anc0.Anc0refChr9 1465 15 - 35212 AGTATTGTTTCCACA -s Anc1.Anc1refChr0 1568 15 + 16026 AGTATTGTTTCCACA -s Anc2.Anc2refChr0 1473 15 + 56053 AGTGTTGTTTCCACA -s mr.mrrefChr0 1577 15 + 130230 AGTATTGTTTAAACA -s simCow_chr6.simCow.chr6 1627 15 + 602619 CGTGTTATTTACACA -s simDog_chr6.simDog.chr6 1362 15 + 593897 AGTGGAGTTTCTACG -s simHuman_chr6.simHuman.chr6 1638 15 + 601863 AGCATTGTTTGCCCA -s simRat_chr6.simRat.chr6 1487 15 + 647215 AGTATTGTTTAAACT - -a -s simMouse_chr6.simMouse.chr6 1597 37 + 636262 TTACCTGTTCTAGTACACTCCATGGTACCTTGACTAC -s Anc0.Anc0refChr9 1481 37 - 35212 TTAGCTGTCCTTGCACCCCTTATACTAACTTGACTAC -s Anc1.Anc1refChr0 1584 37 + 16026 TTAGCTGTCCTTGCACCCCTTATACTAACTTGACTAC -s Anc2.Anc2refChr0 1489 37 + 56053 TTAGCTGTCCTTGCACCCCTTATACTAACTTGACTAC -s mr.mrrefChr0 1592 37 + 130230 TTAGCTGTTCTAGTACACTCCATGGTACCTTGACTAC -s simCow_chr6.simCow.chr6 1643 37 + 602619 TTAGCTGCCCCTGCATCCTCTATATTAACCTGATTAC -s simDog_chr6.simDog.chr6 1378 37 + 593897 TTAGCTGTCCTTGCACCCCTTATACCAACTTGACTAC -s simHuman_chr6.simHuman.chr6 1654 20 + 601863 TTAGCTAC-----------------TAGCTTGACAAC -s simRat_chr6.simRat.chr6 1502 37 + 647215 TTAGCTGTTCTAGTTCGCTCCATGAAACCTTGACTAC - -a -s simMouse_chr6.simMouse.chr6 1634 1 + 636262 A -s Anc0.Anc0refChr9 1518 1 - 35212 A -s Anc1.Anc1refChr0 1621 1 + 16026 A -s Anc2.Anc2refChr0 1526 1 + 56053 A -s mr.mrrefChr0 1629 1 + 130230 A -s simCow_chr6.simCow.chr6 1680 1 + 602619 A -s simDog_chr6.simDog.chr6 1417 1 + 593897 G -s simHuman_chr6.simHuman.chr6 1674 1 + 601863 A -s simRat_chr6.simRat.chr6 1539 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 1635 50 + 636262 TTCTGAGGGATTCCTTCTGTAATGTTAACACTGTTCCTAATGACTTATAA -s Anc0.Anc0refChr9 1519 35 - 35212 TT---------------CGAGATGTTAACACTGTTCCTAATAACGAAGCA -s Anc1.Anc1refChr0 1622 35 + 16026 TT---------------CGAGATGTTAACACTGTTCCTAATAACGAAGCA -s Anc2.Anc2refChr0 1527 35 + 56053 TT---------------CGAGATTTTAACACTGTTCCTAACAACGAAGCA -s mr.mrrefChr0 1630 50 + 130230 TTCTGAGGGATTCCTTCTGAGATGTTAACACTGTTCCTAATAACTTATAA -s simCow_chr6.simCow.chr6 1682 30 + 602619 TT---------------TGAGATATTAAT-TTGTTTCTAA----GAAACA -s simDog_chr6.simDog.chr6 1418 35 + 593897 TT---------------CGAGATTTTAACACTGCTCCTAACAACTAAGCC -s simHuman_chr6.simHuman.chr6 1675 35 + 601863 TT---------------GGAGGTGTTCAGACTGTTCCTAATATCGAAGCA -s simRat_chr6.simRat.chr6 1540 50 + 647215 TTCTGAGATATTACTTCTGAGCTGTTAACACTGTTCCTAATAGCCTATAA - -a -s simMouse_chr6.simMouse.chr6 1685 22 + 636262 TATAGTTTACTAGATAGTATAA -s Anc0.Anc0refChr9 1554 18 - 35212 AACA----ACTAGGCAAGATTG -s Anc1.Anc1refChr0 1657 18 + 16026 AACA----ACTAGGCAAGATTG -s Anc2.Anc2refChr0 1562 18 + 56053 AACA----ACTAAGCAAGATTG -s mr.mrrefChr0 1680 22 + 130230 TATAGTTTACTAGATAGTATAG -s simCow_chr6.simCow.chr6 1712 10 + 602619 A------------GCAAGATTG -s simDog_chr6.simDog.chr6 1579 17 + 593897 AACA----ACTAAGCAA-ATTG -s simHuman_chr6.simHuman.chr6 1710 18 + 601863 AACA----ACTAGGCAAGATTG -s simRat_chr6.simRat.chr6 1590 21 + 647215 TATTGTTTACTAGATA-TATAG - -a -s simMouse_chr6.simMouse.chr6 1707 16 + 636262 TTTACTAGGTGAGGAG -s Anc0.Anc0refChr9 1575 14 - 35212 T--ACTAGCTGAGTAG -s Anc1.Anc1refChr0 1678 16 + 16026 TTTACTAGCTGAGTAG -s Anc2.Anc2refChr0 1583 14 + 56053 T--ACTAGCTGAGTAG -s mr.mrrefChr0 1702 16 + 130230 TTTACTAGGTGAGGAG -s simCow_chr6.simCow.chr6 1725 12 + 602619 T--ACTATCT--GTTA -s simDog_chr6.simDog.chr6 1599 14 + 593897 T--ACTAGGTGAGGAG -s simHuman_chr6.simHuman.chr6 1735 16 + 601863 TTTACGAGCTGAGTAG -s simRat_chr6.simRat.chr6 1611 16 + 647215 TTTACTAGGTTAGGAG - -a -s simMouse_chr6.simMouse.chr6 1723 123 + 636262 TCATGTTGCTCCCACAGACAAAATTAATTCAACAGGAAGTCTGTAACCCAATACAATGCTGGCAGTGAAGTATGATTAGTGCTGTCAATTAATCATGATTAAATGGCCTCCTTGAACGGGCTA -s Anc0.Anc0refChr9 1589 97 - 35212 GCATTATTCTTCCACACTC--TATTAATTTAACAGTAAGTCTTTAACCGAAT---------------TACTCTAATTAG---------TGAATTATGATCAAATGACTATTTTGAAAGGGCTA -s Anc1.Anc1refChr0 1694 97 + 16026 GCATTATTCTTCCACACTC--TATTAATTTAACAGTAAGTCTTTAACCGAAT---------------TACTCTAATTAG---------TGAATTATGATCAAATGACTATTTTGAAAGGGCTA -s Anc2.Anc2refChr0 1597 97 + 56053 GCATTACTCCGACAGACTG--TATTAATTTAACAGTAGTTCATAACCCGACA---------------TACTCTCATCAA---------TGAATTATGATCAAATGACTATTTTGAAAGGGCTA -s mr.mrrefChr0 1718 123 + 130230 TCATGTTGCTTCCACAGACAAAATTAATTCAACAGGAAGTCTGTAACCCAATACAATGCTGGCAGTGAAGTATAATTAGTGCTGTCAATTAATCATGATTAAATGGCCTCCTTGAAAGGGCTA -s simCow_chr6.simCow.chr6 1737 97 + 602619 GCGGTACACCCACAGACTG--TACTAAATTCATAGTAGCTCATGACCAAGTG---------------TAGTCTTGTCAA---------TGAATTATGATCAAATGACTACTTTGAAAGGGTTA -s simDog_chr6.simDog.chr6 1615 97 + 593897 GCATTACTCCGACAGACTG--TATTAATTTAACAGTAGTTCATAACCCGACA---------------TACTCCCATCAA---------TGAATTATGATTGAATCGCTTTCTCGAAAAGGCTA -s simHuman_chr6.simHuman.chr6 1751 97 + 601863 GCATTATTCTTCCACATTC--TGTAAATGGAACAGTAAGTCTTTAACCTAAT---------------GAATCTAATTAG---------AGAACTACGATCAAATGACTATTTTGAAAGGGCTA -s simRat_chr6.simRat.chr6 1627 121 + 647215 TCATGTTGCTTTCACAGACAAACTTAATTCAACAGGAAGTCTGTAACCCAATACTATGAAGGGAGTCAATTATAATTAGTGCTGTCAATTACTCAGGATTAAATTGCCT--TTGAAAGGGCTA - -a -s simMouse_chr6.simMouse.chr6 1846 40 + 636262 GACGTTTTGGAGCTGTAGTATACCTTCTAGTTCTTTAATG -s Anc0.Anc0refChr9 1686 40 - 35212 GATTTGTTGGAACTCAGATATTCCCCCTAGTACTTTGATA -s Anc1.Anc1refChr0 1791 40 + 16026 GATTTGTTGGAACTCAGATATTCCCCCTAGTACTTTGATA -s Anc2.Anc2refChr0 1694 40 + 56053 GATTTGTTGGAAGTCAGATATTCACCCTGGTACTTAGGTA -s mr.mrrefChr0 1841 40 + 130230 GATGTTTTGGAGCTGTAGTATACCTCCTAGTTCTTTAATA -s simCow_chr6.simCow.chr6 1834 25 + 602619 GATCTGGTGGAATTGAG---------------CTTAGGTA -s simDog_chr6.simDog.chr6 1712 40 + 593897 GATTTGTGAGAAGTCAGATATTCACCCTGGTAGCTGGATA -s simHuman_chr6.simHuman.chr6 1854 37 + 601863 GATTTGTTGATACTAAGATATGCC-CCTATTCC--TGATA -s simRat_chr6.simRat.chr6 1748 40 + 647215 GATCTTTTGGAGCTGTAGTCTACCTCCTAGTACTTTAATA - -a -s simMouse_chr6.simMouse.chr6 1886 2 + 636262 TT -s Anc0.Anc0refChr9 1726 2 - 35212 TG -s Anc1.Anc1refChr0 1831 2 + 16026 TG -s Anc2.Anc2refChr0 1748 2 + 56053 TG -s mr.mrrefChr0 1881 2 + 130230 TG -s simCow_chr6.simCow.chr6 1873 2 + 602619 TG -s simDog_chr6.simDog.chr6 1769 2 + 593897 TG -s simHuman_chr6.simHuman.chr6 1891 2 + 601863 TG -s simRat_chr6.simRat.chr6 1788 2 + 647215 TG - -a -s simMouse_chr6.simMouse.chr6 1888 9 + 636262 TTAGCTTAA -s Anc0.Anc0refChr9 1728 9 - 35212 CAATCTTTA -s Anc1.Anc1refChr0 1833 9 + 16026 CAATCTTTA -s Anc2.Anc2refChr0 1750 9 + 56053 CACTCTTTC -s mr.mrrefChr0 1883 9 + 130230 TTAGCTTAA -s simCow_chr6.simCow.chr6 1886 9 + 602619 CATCCCTCC -s simDog_chr6.simDog.chr6 1771 9 + 593897 CACTCTTTC -s simHuman_chr6.simHuman.chr6 1893 9 + 601863 CGATCTGTA -s simRat_chr6.simRat.chr6 1790 9 + 647215 TTAACTTAA - -a -s simMouse_chr6.simMouse.chr6 1897 104 + 636262 TTAAACATATGCTATTGTGATTCACACTTTTCTTTGGCCTATCTGCATTATACATTGAGGTTGAGAGTACAATAACACTTCTGTTGTGTGAATTGTACTGATAG -s Anc0.Anc0refChr9 1737 71 - 35212 ---------------------------------TTGCCCGAGCCGTATTATACATTGAGGTTGAGAGTACAACATTACCCCTGCTGTGTGAACTGTAAcattcg -s Anc1.Anc1refChr0 1842 71 + 16026 ---------------------------------TTGCCCGAGCCGTATTATACATTGAGGTTGAGAGTACAACATTACCCCTGCTGTGTGAACTGTAAcattcg -s Anc2.Anc2refChr0 1759 71 + 56053 ---------------------------------TCCCCCGAGCCCTGGCCCATGTTCGGGTTGAGAGTTAAACATTACCCCTGCTGTGTGAACTGTAAcattcg -s mr.mrrefChr0 1892 104 + 130230 TTAAACATATGCTATTGTGATTCACACTTTTCTTTGGCCTATCTGCATTATACATTGAGGTTGAGAGTACAATAACACTTCTGTTGTGTGAACTGTACTGATAG -s simCow_chr6.simCow.chr6 1895 71 + 602619 ---------------------------------TTACCCTAGACCCATCCCATGTTGAAGTTCAAGGTTAAACATTATTCCTGTTGTGTGAACTTTACcattag -s simDog_chr6.simDog.chr6 1780 71 + 593897 ---------------------------------TCCCCCGAGCCCTGGCCCATGTTCGGGTTGAGAGTTAAACATTACCCCTGCTGTGTGAACTGTAACATTCG -s simHuman_chr6.simHuman.chr6 1902 45 + 601863 ---------------------------------CTGACAGAACCGTATTATTCATCGAGCT----AGTAC---------------TTATGGACCATA------- -s simRat_chr6.simRat.chr6 1825 104 + 647215 TTAAACATATGCTACTGTCAGTCACACTTTTCTTTGGGCTAGCTGCATTATATGTTGAGGTTAAGAGTAGAATAAAACTTCTGTTGTGTGAACTGAACTGACAG - -a -s simMouse_chr6.simMouse.chr6 2001 3 + 636262 TAA -s Anc0.Anc0refChr9 1808 3 - 35212 tag -s Anc1.Anc1refChr0 1913 3 + 16026 TAG -s Anc2.Anc2refChr0 1830 3 + 56053 tgg -s mr.mrrefChr0 1996 3 + 130230 TAA -s simCow_chr6.simCow.chr6 1967 3 + 602619 tgg -s simDog_chr6.simDog.chr6 1851 3 + 593897 TGg -s simHuman_chr6.simHuman.chr6 1947 3 + 601863 TAG -s simRat_chr6.simRat.chr6 1929 3 + 647215 AAA - -a -s simMouse_chr6.simMouse.chr6 2004 15 + 636262 TATATCACCCTAATG -s Anc0.Anc0refChr9 1811 14 - 35212 TATAGCATCCTGA-G -s Anc1.Anc1refChr0 1916 15 + 16026 TATAGCATCCTGATG -s Anc2.Anc2refChr0 1987 14 + 56053 TATAGCTTCCTGA-G -s mr.mrrefChr0 1999 15 + 130230 TATATCACCCTAATG -s simCow_chr6.simCow.chr6 2199 14 + 602619 TATAACTTTTTGA-G -s simDog_chr6.simDog.chr6 2035 14 + 593897 TGCTGCTTCCCGA-A -s simHuman_chr6.simHuman.chr6 1950 15 + 601863 TTTGAAAACCTGATG -s simRat_chr6.simRat.chr6 1932 15 + 647215 TGTATCACCCCAATG - -a -s simMouse_chr6.simMouse.chr6 2019 8 + 636262 CATGCATG -s Anc0.Anc0refChr9 1829 8 - 35212 CATGTAAA -s Anc1.Anc1refChr0 1935 8 + 16026 CATGTAAA -s Anc2.Anc2refChr0 2005 8 + 56053 CATATAAA -s mr.mrrefChr0 2014 8 + 130230 CATGCATG -s simCow_chr6.simCow.chr6 2217 5 + 602619 ---ACAAA -s simDog_chr6.simDog.chr6 2053 8 + 593897 CATATAAA -s simHuman_chr6.simHuman.chr6 1969 8 + 601863 CTTGTAAA -s simRat_chr6.simRat.chr6 1947 8 + 647215 CAAGCTTG - -a -s simMouse_chr6.simMouse.chr6 2027 20 + 636262 TGATTGAGCACTGTGAAATT -s Anc0.Anc0refChr9 1837 20 - 35212 TGAGTGAATATGGTAAAACC -s Anc1.Anc1refChr0 1943 20 + 16026 TGAGTGAATATGGTAAAACC -s Anc2.Anc2refChr0 2017 20 + 56053 TATGTGAATATGGTAAAACC -s mr.mrrefChr0 2022 20 + 130230 TGATTGAGCACGGTGAAATT -s simCow_chr6.simCow.chr6 2226 20 + 602619 TAAATGGATACGGTAAAACC -s simDog_chr6.simDog.chr6 2065 20 + 593897 TATGTGAATATGGTAAAACC -s simHuman_chr6.simHuman.chr6 1977 20 + 601863 TGAATAAATATGGTAGAACC -s simRat_chr6.simRat.chr6 1955 20 + 647215 TGATTGAGCAAGGTGAGATT - -a -s simMouse_chr6.simMouse.chr6 2047 58 + 636262 GAGAGTCTAGAAAGGGGTAGTTCCTCAGCTCATCATAACTCGATCTGATACACATTTG -s Anc0.Anc0refChr9 1857 7 - 35212 GACATTT--------------------------------------------------- -s Anc1.Anc1refChr0 1963 58 + 16026 GACATTTCAGAAAGGGGTAGGTCTTATCCTCATCACCATTCTTTCTAAGTCACCTCCA -s Anc2.Anc2refChr0 2038 7 + 56053 GACTTTT--------------------------------------------------- -s mr.mrrefChr0 2042 58 + 130230 GAGAGTCCAGAAAGGGGTAGTTCCTCAGCTCATCATAACTCGATCTGATACACCTTTA -s simCow_chr6.simCow.chr6 2247 7 + 602619 GACTTTT--------------------------------------------------- -s simDog_chr6.simDog.chr6 2086 7 + 593897 CACTTCT--------------------------------------------------- -s simHuman_chr6.simHuman.chr6 1997 58 + 601863 GACATTTCAGAAAGGGGTAGGTCTTATCCTCATCACCATTCTTTCTAAGTCACCTCCA -s simRat_chr6.simRat.chr6 1975 56 + 647215 -AGACTCCAG-AAGAGGTCATATGGCAGCCCATCATAGCTCAACCGGATACACCCTCA - -a -s simMouse_chr6.simMouse.chr6 2105 8 + 636262 ATACTGAG -s Anc1.Anc1refChr0 2021 8 + 16026 AAACTGAG -s mr.mrrefChr0 2100 8 + 130230 ATACTGAG -s simHuman_chr6.simHuman.chr6 2061 8 + 601863 AAACTGAG -s simRat_chr6.simRat.chr6 2031 8 + 647215 GGAATGAT - -a -s simMouse_chr6.simMouse.chr6 2113 21 + 636262 TACGGTGAAATTGGCACTCTA -s Anc1.Anc1refChr0 2029 16 + 16026 AACGG---AGGTG--ACTCTA -s mr.mrrefChr0 2108 19 + 130230 TACGGTGAAATTG--ACTCTA -s simHuman_chr6.simHuman.chr6 2126 16 + 601863 AACGG---AGGTG--ACTCTA -s simRat_chr6.simRat.chr6 2039 15 + 647215 TAGGGTGAAATTG------TA - -a -s simMouse_chr6.simMouse.chr6 2134 86 + 636262 GAAATGGGTAATTCTTCAGTGCATCATCATCCTTTGTGAACCACCTATTTGGTCCCAACTGAGATGTTCACAATTAGCATAAAGGC -s Anc0.Anc0refChr9 1864 79 - 35212 -----GGGTAGTTCTTAGGCTCATCACCATTCTTTCTAAGTCACCTCTTTAGACCCAACTGAGGTGTTCA--ATTAGCCTAAAGTT -s Anc1.Anc1refChr0 2045 86 + 16026 GGAAGGGGTAGTTCTTAGGCTCATCACCATTCTTTCTAAGTCACCTCTTTAGACCCAACTGAGGTGTTCACAATTAGCCTAAAGTT -s Anc2.Anc2refChr0 2045 79 + 56053 -----GGGCAGTACTTAGGGGTATCACCATTCTTTCTAAGTTACCTTTTTAGACCCAACTGAGGTGTTCA--ATTAGCCTAAGGTT -s mr.mrrefChr0 2127 86 + 130230 GAAAGGGGTAATTCTTCAGCTCATCATCATCCTTTGTGAACCACCTCTTTGGTCCCAACTGAGATGTTCACAATTAGCCTAAAGGC -s simCow_chr6.simCow.chr6 2254 79 + 602619 -----GGGCGGTATTTAGGGGTATCACCACTCTTTCTAAGTTACCTTTTTAGGCCCAACTGAGAGGTTCA--ATTGCCCCATGGTT -s simDog_chr6.simDog.chr6 2093 78 + 593897 -----GGG-AGTACTTATGCTCATCACCATTCTTGCTAAGTTACCCTTTTTGACCCAACTGAGGTGTTCA--GTTAGCCTAAGGTT -s simHuman_chr6.simHuman.chr6 2143 81 + 601863 GGAAGGGGTAGGTCTTATCCTCATCACCATTCTTTCTAAGTCACCTCCATACACCAAACTGAGCTGTTCA-----ATTCTAAAGTT -s simRat_chr6.simRat.chr6 2054 86 + 647215 GAAAGGGGTAACTCTTCAGCTCATCATCATCCTTCATGAACCACGTCTTTGGTCCCAACCGAGATGTTCACAATTTGCCTAAAGGC - -a -s simMouse_chr6.simMouse.chr6 2220 27 + 636262 GTACACACTAGCTGGATTATAGATGTA -s Anc0.Anc0refChr9 1943 27 - 35212 GTCTACAATAGCTGGACTATGCCTGTG -s Anc1.Anc1refChr0 2131 27 + 16026 GTCTACAATAGCTGGACTATGCCTGTG -s Anc2.Anc2refChr0 2124 27 + 56053 GTCTAAAATAGCTGGTCTATGCCTGTA -s mr.mrrefChr0 2213 27 + 130230 GTATACACTAGCTGGATTATGGATGTG -s simCow_chr6.simCow.chr6 2333 25 + 602619 GTCTAAATTAGCT--GCTATGCCTGTA -s simDog_chr6.simDog.chr6 2171 27 + 593897 GACTAAGATAGCAGGTCTATGCCTGTA -s simHuman_chr6.simHuman.chr6 2224 27 + 601863 GTCTGCAGTAGCTAAACTATGCGTGTG -s simRat_chr6.simRat.chr6 2144 27 + 647215 GGTTACACTGACTGGCTTAAGGATGTG - -a -s simMouse_chr6.simMouse.chr6 2247 17 + 636262 TAATATAAATTGCAGTG -s Anc0.Anc0refChr9 1975 17 - 35212 TAAAGTAAGTTGCAGTG -s Anc1.Anc1refChr0 2163 17 + 16026 TAAAGTAAGTTGCAGTG -s Anc2.Anc2refChr0 2156 17 + 56053 TAAAGTAGGTTGCAGTG -s mr.mrrefChr0 2240 17 + 130230 TAATATAAATTGCAGTG -s simCow_chr6.simCow.chr6 2363 17 + 602619 CAGACTAGATTGCAGTT -s simDog_chr6.simDog.chr6 2203 17 + 593897 TAATGTAGGCTGCAATG -s simHuman_chr6.simHuman.chr6 2256 17 + 601863 TGAAGTGACTTGTGGTG -s simRat_chr6.simRat.chr6 2171 17 + 647215 CAATATAAATTGCTGTG - -a -s simMouse_chr6.simMouse.chr6 2264 16 + 636262 CTTCCATAGGACAGAG -s Anc0.Anc0refChr9 1992 16 - 35212 CTTTTATGGGACACGG -s Anc1.Anc1refChr0 2180 16 + 16026 CTTTTATGGGACACGG -s Anc2.Anc2refChr0 2177 16 + 56053 CTTTTATGGGTCACGG -s mr.mrrefChr0 2257 16 + 130230 CTTCCATAGGACAGAG -s simCow_chr6.simCow.chr6 2384 16 + 602619 TGCTTATGGGTCACAG -s simDog_chr6.simDog.chr6 2224 16 + 593897 CTTCCATGGGTCACGG -s simHuman_chr6.simHuman.chr6 2273 16 + 601863 ACTTTATGGAACATGG -s simRat_chr6.simRat.chr6 2188 16 + 647215 CTTCCATAGGACAGAG - -a -s simMouse_chr6.simMouse.chr6 2280 18 + 636262 ACAGAAGTTGGTGACCCT -s Anc0.Anc0refChr9 2009 18 - 35212 CCAGAAGTTGGTGACCCT -s Anc1.Anc1refChr0 2197 18 + 16026 CCAGAAGTTGGTGACCCT -s Anc2.Anc2refChr0 2194 18 + 56053 CCATAAATTAGTGACCCT -s mr.mrrefChr0 2274 18 + 130230 ACAGAAGTTGGTGACCCT -s simCow_chr6.simCow.chr6 2401 18 + 602619 CCATAAATTAGTGATCCT -s simDog_chr6.simDog.chr6 2241 18 + 593897 CCATAAATTAGTGACCCA -s simHuman_chr6.simHuman.chr6 2290 18 + 601863 CCAGAAGTTGCTGACCCT -s simRat_chr6.simRat.chr6 2205 18 + 647215 ACAAAAGTTGGTGACTCT - -a -s simMouse_chr6.simMouse.chr6 2298 7 + 636262 TTTATTT -s Anc0.Anc0refChr9 2027 7 - 35212 CTTGTTT -s Anc1.Anc1refChr0 2215 7 + 16026 CTTGTTT -s Anc2.Anc2refChr0 2212 7 + 56053 CTTGTTT -s mr.mrrefChr0 2292 7 + 130230 TTTATTT -s simCow_chr6.simCow.chr6 2422 7 + 602619 CTTGTTT -s simDog_chr6.simDog.chr6 2259 7 + 593897 CTTACTT -s simHuman_chr6.simHuman.chr6 2308 7 + 601863 CTTGTTT -s simRat_chr6.simRat.chr6 2223 7 + 647215 TTTTTTT - -a -s simMouse_chr6.simMouse.chr6 2305 18 + 636262 GTTTGTTCTCATCCCCTG -s Anc0.Anc0refChr9 2034 18 - 35212 TTTTGCTCTTGCACCCTG -s Anc1.Anc1refChr0 2222 18 + 16026 TTTTGCTCTTGCACCCTG -s Anc2.Anc2refChr0 2219 18 + 56053 TTTTGCTGTTGCACCCTG -s mr.mrrefChr0 2299 18 + 130230 GTTTGTTCTTATCCCCTG -s simCow_chr6.simCow.chr6 2574 18 + 602619 TTTTGCTGATGTAGCCTG -s simDog_chr6.simDog.chr6 2266 18 + 593897 ATTTGCTGTTGCACCCTG -s simHuman_chr6.simHuman.chr6 2315 18 + 601863 TTTTGCTCTTTCACCCTG -s simRat_chr6.simRat.chr6 2230 18 + 647215 GTTCATTCTTGTTCCCTG - -a -s simMouse_chr6.simMouse.chr6 2323 17 + 636262 AGCAAGGAGGTCAGCTT -s Anc0.Anc0refChr9 2060 17 - 35212 AGCAAGGTGATCTGTGA -s Anc1.Anc1refChr0 2248 17 + 16026 AGCAAGGTGATCTGTGA -s Anc2.Anc2refChr0 2245 17 + 56053 AGCAAAGTGATCTGTGA -s mr.mrrefChr0 2325 17 + 130230 AGCAAGGAGGTCAGCTT -s simCow_chr6.simCow.chr6 2600 17 + 602619 GGCAATGTGATCTGTGA -s simDog_chr6.simDog.chr6 2292 14 + 593897 AG---AGCAATCTGTAA -s simHuman_chr6.simHuman.chr6 2341 17 + 601863 AGCGAGGTGATCTGTGA -s simRat_chr6.simRat.chr6 2256 12 + 647215 AGCAAGGAGGTC----- - -a -s simMouse_chr6.simMouse.chr6 2340 49 + 636262 AATTCATGGAACAGGCAGGCCCGTGAAATTTTTCTTGAAAAAGTGCACC -s Anc0.Anc0refChr9 2077 19 - 35212 AATTCATGGGA----CGGG--------------------------TACT -s Anc1.Anc1refChr0 2265 45 + 16026 AATTCATGGGA----CGGGCCCTTGAAGTCTTTCTTGGAAAGGTATACT -s Anc2.Anc2refChr0 2262 19 + 56053 AATCCATGGGA----CGCG--------------------------TACT -s mr.mrrefChr0 2342 49 + 130230 AATTCATGGGACAGGCAGGCCCGTGAAATTTTTCTTGAAAAAGTGCACT -s simCow_chr6.simCow.chr6 2617 19 + 602619 AATCCATGGGG----CCTG--------------------------TACT -s simDog_chr6.simDog.chr6 2310 19 + 593897 AATCTTTGAAA----TGCA--------------------------TACT -s simHuman_chr6.simHuman.chr6 2358 45 + 601863 AATTCAGGGGA----CGGGCCCTTGAAGTCTTTCTTGGAAAGGTATACT -s simRat_chr6.simRat.chr6 2268 49 + 647215 GATTCATGGGACAGGCAGGCCTGTGAAATTTTTCTTGATAAAGTGCCTT - -a -s simMouse_chr6.simMouse.chr6 2389 63 + 636262 GGTCATTAGTTGCATAGGAGCCACACTATAGGACTGTTAATGAACGAAATGGGGGGTAGAGTC -s Anc0.Anc0refChr9 2096 59 - 35212 TGCCTTCAGGTGTGTAGAAGCCATACTAAAGGAGTGTTTGTGAGGTAGATGTGG----AAGAA -s Anc1.Anc1refChr0 2310 59 + 16026 TGCCTTCAGGTGTGTAGAAGCCATACTAAAGGAGTGTTTGTGAGGTAGATGTGG----AAGAA -s Anc2.Anc2refChr0 2281 59 + 56053 TACCTATAGGTGTGTAGAAGCCATACTAAAGGAGTGTTTGTGAGGTAGATGTGG----AAGAA -s mr.mrrefChr0 2391 63 + 130230 TGTCATCAGTTGTGTAGGAGCCACACTATAGGACTGTTAATGAACGAAATGGGGGGTAGAGTC -s simCow_chr6.simCow.chr6 2643 56 + 602619 TATCAACAGATGCTTAGGA---ATACTGGTGGGGTGTTTATGAGGCAGATGGGG----AGGAA -s simDog_chr6.simDog.chr6 2329 59 + 593897 TACCTATAGGTGTGTAGAAGCCACACTAAAGGAGTGTATGTGAGCTAGATGTGG----AAGAA -s simHuman_chr6.simHuman.chr6 2403 13 + 601863 TG---TCAGGTATGCA----------------------------------------------- -s simRat_chr6.simRat.chr6 2317 63 + 647215 TGTCATCAATTGTGTAGAAGCCACACTAAAAGAGTGTTAATGGACTAAATGGGGGGTAGAGTC - -a -s simMouse_chr6.simMouse.chr6 2452 26 + 636262 TCACATACACGAGATCAGTGTGATCC -s Anc0.Anc0refChr9 2155 19 - 35212 TAACATTTATAAGA-------GATTG -s Anc1.Anc1refChr0 2369 19 + 16026 TAACATTTATAAGA-------GATTG -s Anc2.Anc2refChr0 2340 19 + 56053 TAACATTTATAAGA-------GATTG -s mr.mrrefChr0 2454 26 + 130230 TCACATACACGAGATCAGTGTGATCC -s simCow_chr6.simCow.chr6 2700 19 + 602619 TACCATATACAACA-------ATGTG -s simDog_chr6.simDog.chr6 2388 19 + 593897 TAACATTTATAAGA-------GATTG -s simHuman_chr6.simHuman.chr6 2416 5 + 601863 ---------------------GATTG -s simRat_chr6.simRat.chr6 2380 26 + 647215 TCACATACATAAGATCAGTGTGAACC - -a -s simMouse_chr6.simMouse.chr6 2478 9 + 636262 TTCTTAGCC -s Anc0.Anc0refChr9 2174 9 - 35212 TGGTTAGCC -s Anc1.Anc1refChr0 2388 9 + 16026 TGGTTAGCC -s Anc2.Anc2refChr0 2359 9 + 56053 TGGTCCACT -s mr.mrrefChr0 2480 9 + 130230 TTCTTAGCC -s simCow_chr6.simCow.chr6 2719 9 + 602619 TGGTCCCCG -s simDog_chr6.simDog.chr6 2410 9 + 593897 TGGTCCACT -s simHuman_chr6.simHuman.chr6 2421 9 + 601863 TGGTTAGCC -s simRat_chr6.simRat.chr6 2406 9 + 647215 TTCTTAGCC - -a -s simMouse_chr6.simMouse.chr6 2487 85 + 636262 TAGCTAAACCTAATGGGGAGTAGGCCTATTACAGGCTGCTTGTTGAGTTGCATGCTGGAAACCATAGGTTAAGTGTGACTTGCTT -s Anc0.Anc0refChr9 2191 71 - 35212 CAGTTGGTCCTAATTGGGAGTAG--CTATTATAGCTTGCT------------TGCTGAAGATCTTAGGTAAAGTGTAACTTGCTT -s Anc1.Anc1refChr0 2405 71 + 16026 CAGTTGGTCCTAATTGGGAGTAG--CTATTATAGCTTGCT------------TGCTGAAGATCTTAGGTAAAGTGTAACTTGCTT -s Anc2.Anc2refChr0 2376 71 + 56053 CATTTGGTCCTAATTGGAGGTTG--CTATTATAGCTTGCT------------TGCTGAAGATGTTAGGTAAAGTGTAATTTGTTT -s mr.mrrefChr0 2489 83 + 130230 CAGCTAATCCTAATGGGGAGTAG--CTATTACAGGTTGCTTGTTGAGTTGCATGCTGGAAACCATAGGTTAAGTGTAACTTGCTT -s simCow_chr6.simCow.chr6 2737 69 + 602619 CAATTCATGCTAATTGGAGGTTG--GAATTATAGCTTGGT------------TGCTACAAATAT--GGTAAGGTGGAAGTTATTT -s simDog_chr6.simDog.chr6 2425 71 + 593897 CATTTGGTCCAAATTGGAGGTTG--CTATTATAACTTGCT------------TGCTGAAGGTGTTAGGTAAAGTGTAATTTGTTT -s simHuman_chr6.simHuman.chr6 2439 68 + 601863 CAGTTGGTCCTAATT-GGAGTA----TATTATAGCTTGCT------------TGCTGAACATCCTAGGTAAAGTGTAACTTGCTT -s simRat_chr6.simRat.chr6 2415 83 + 647215 CAGCTAATCCTAATGGGGAGTTG--CCATTACAGTTTGCTTGTTGAGCTGTGTGCTGGAAACCTTAGGTTAAGTGAAACTTGCTT - -a -s simMouse_chr6.simMouse.chr6 2572 2 + 636262 TG -s Anc0.Anc0refChr9 2263 2 - 35212 TG -s Anc1.Anc1refChr0 2477 2 + 16026 TG -s Anc2.Anc2refChr0 2448 2 + 56053 TG -s mr.mrrefChr0 2572 2 + 130230 TG -s simCow_chr6.simCow.chr6 2807 2 + 602619 TG -s simDog_chr6.simDog.chr6 2497 2 + 593897 TG -s simHuman_chr6.simHuman.chr6 2508 2 + 601863 TG -s simRat_chr6.simRat.chr6 2498 2 + 647215 TA - -a -s simMouse_chr6.simMouse.chr6 2574 52 + 636262 GCAATTTGAGAAATACCACCCTCGGTTAAGTGTTTGGTTATAAGTGTCATTT -s Anc0.Anc0refChr9 2265 36 - 35212 GCAATTTGGGGAATGCCACCTTTGATTAAGTGT----------------CTT -s Anc1.Anc1refChr0 2479 36 + 16026 GCAATTTGGGGAATGCCACCTTTGATTAAGTGT----------------CTT -s Anc2.Anc2refChr0 2450 36 + 56053 TCAATTTGCAGAATGCCACCTTTGATTAAGTGT----------------CTT -s mr.mrrefChr0 2574 36 + 130230 GCAATTTGGGAAATACCACCCTTGGTTAAGTGT----------------TTT -s simCow_chr6.simCow.chr6 2815 36 + 602619 TCAGTTTGCAGACTGCCACCTTTGATTGAGTCT----------------CAT -s simDog_chr6.simDog.chr6 2499 36 + 593897 TCAATTTGCAGAATGCCACCTTTGATTAAGTGT----------------CTT -s simHuman_chr6.simHuman.chr6 2510 36 + 601863 GCAATTTGGGGAATGCCGCCTTTGTTTAAGTGT----------------CTT -s simRat_chr6.simRat.chr6 2500 31 + 647215 GCTATTTGGGAAATACCACCCTTGGTTAAGT--------------------- - -a -s simMouse_chr6.simMouse.chr6 2626 45 + 636262 TGAGGGATGCCAGTTTTGACAAGTTCAGGTTGATCAGGTTGATAG -s Anc0.Anc0refChr9 2301 33 - 35212 TGAGGAATGCCACCTTTGACTAAG---------TCC---CTGTGG -s Anc1.Anc1refChr0 2515 36 + 16026 TGAGGAATGCCACCTTTGACTAAG---------TCCAGTCTGTGG -s Anc2.Anc2refChr0 2488 33 + 56053 TGAGGAATACCACCTTTGATTAAG---------TCC---CTGTGA -s mr.mrrefChr0 2610 36 + 130230 TGAGGGATGCCAGTTTTGACAAGT---------TCAGGTTGATAG -s simCow_chr6.simCow.chr6 2853 33 + 602619 TGAGGAATTTCACCTTTGATTAAG---------TCC---CGGTAA -s simDog_chr6.simDog.chr6 2537 33 + 593897 TCAGGAATACCACCTTTGATTAAG---------TCC---CTCTGA -s simHuman_chr6.simHuman.chr6 2546 36 + 601863 TGGGGAATGCCACCCTTAACTAAG---------TTCAGTCAGTGG -s simRat_chr6.simRat.chr6 2531 27 + 647215 ---------CTCATTTTGCAAAGT---------TCAGGTTGATAG - -a -s simMouse_chr6.simMouse.chr6 2671 13 + 636262 AGTGACCTTTCTT -s Anc0.Anc0refChr9 2341 13 - 35212 AATAAGCTTTGCT -s Anc1.Anc1refChr0 2558 13 + 16026 AATAAGCTTTGCT -s Anc2.Anc2refChr0 2528 13 + 56053 AATAAGCTTTGCT -s mr.mrrefChr0 2646 13 + 130230 AATGACCTTTCTT -s simCow_chr6.simCow.chr6 2893 13 + 602619 AATTAACTTTTTT -s simDog_chr6.simDog.chr6 2577 13 + 593897 AATAAGCTTTGCC -s simHuman_chr6.simHuman.chr6 2589 13 + 601863 AATAAGCTTTACT -s simRat_chr6.simRat.chr6 2558 13 + 647215 AATGACCTTTCTT - -a -s simMouse_chr6.simMouse.chr6 2684 13 + 636262 TGCATAGTGGACT -s Anc0.Anc0refChr9 2356 13 - 35212 TGCATAGCTGATT -s Anc1.Anc1refChr0 2573 13 + 16026 TGCATAGCTGATT -s Anc2.Anc2refChr0 2543 13 + 56053 TGCATAGCTGATT -s mr.mrrefChr0 2661 13 + 130230 TGCATAGTGGACT -s simCow_chr6.simCow.chr6 2908 13 + 602619 TGCATACCTAATT -s simDog_chr6.simDog.chr6 2592 13 + 593897 TGCAGAGCTGATT -s simHuman_chr6.simHuman.chr6 2604 13 + 601863 GCCATAGCTGGAT -s simRat_chr6.simRat.chr6 2573 13 + 647215 TGCATAGTAGACT - -a -s simMouse_chr6.simMouse.chr6 2697 10 + 636262 TCCAGACCTT -s Anc0.Anc0refChr9 2369 10 - 35212 TTCCACCCTC -s Anc1.Anc1refChr0 2586 10 + 16026 TTCCACCCTC -s Anc2.Anc2refChr0 2556 10 + 56053 GTCCACCCTC -s mr.mrrefChr0 2674 10 + 130230 TCCAGACCTT -s simCow_chr6.simCow.chr6 2921 10 + 602619 GTCCACCCTC -s simDog_chr6.simDog.chr6 2605 10 + 593897 GTCCATCCTC -s simHuman_chr6.simHuman.chr6 2617 10 + 601863 TTTCACCTTC -s simRat_chr6.simRat.chr6 2607 10 + 647215 TCCAGACCTT - -a -s simMouse_chr6.simMouse.chr6 2707 12 + 636262 ATCAGCCTGAGT -s Anc0.Anc0refChr9 2379 9 - 35212 ATCAG---GAGA -s Anc1.Anc1refChr0 2596 9 + 16026 ATCAG---GAGA -s Anc2.Anc2refChr0 2566 9 + 56053 ATCAG---GAGA -s mr.mrrefChr0 2684 12 + 130230 ATCAGCCTGAGT -s simCow_chr6.simCow.chr6 2931 2 + 602619 A----------A -s simDog_chr6.simDog.chr6 2616 9 + 593897 ATCAG---GAGA -s simHuman_chr6.simHuman.chr6 2627 9 + 601863 ACCAG---GAGA -s simRat_chr6.simRat.chr6 2617 12 + 647215 ATCGACCCAAAT - -a -s simMouse_chr6.simMouse.chr6 2719 144 + 636262 TGACCCTGCCCCATGTGGCCATGTACACATGGCCAGTGCATGGCTACATTTGCTCCATGTGGCCATGTACACACGGTCAGTGCTTGGCTATGAGCCTGCCCCACTTGATGAAATGTCAAATGATCTCCCCGCATACATTCTGCA -s Anc0.Anc0refChr9 2388 2 - 35212 TA---------------------------------------------------------------------------------------------------------------------------------------------- -s Anc1.Anc1refChr0 2605 7 + 16026 TAGCGAT----------------------------------------------------------------------------------------------------------------------------------------- -s Anc2.Anc2refChr0 2575 2 + 56053 TA---------------------------------------------------------------------------------------------------------------------------------------------- -s mr.mrrefChr0 2696 144 + 130230 TGACCCTGCCCCATGTGGCCATGTACACATGGCCAGTGCATGGCTACATTTGCTCCATGTGGCCATGTACACACGGTCAGTGCTTGGCTATGAGCCTGCCCTACATGATGAAATGTTGGGTGATCTCCCCGCATACATTGTGCA -s simCow_chr6.simCow.chr6 2933 2 + 602619 TG---------------------------------------------------------------------------------------------------------------------------------------------- -s simDog_chr6.simDog.chr6 2625 2 + 593897 TA---------------------------------------------------------------------------------------------------------------------------------------------- -s simHuman_chr6.simHuman.chr6 2636 7 + 601863 TAGCGAT----------------------------------------------------------------------------------------------------------------------------------------- -s simRat_chr6.simRat.chr6 2703 144 + 647215 TGACCCTGCCCTGCATGGCCATGTACACATGGTCAGTGCTTGGCTATGCCTGCCCTGCGTGGCCATGCACACACAGTCAGTGCTTGGCTATGAGCCTGCCCTGCATGACAAAATGTTGGGTGATCTCCCCGTGAACATTGTAGA - -a -s simMouse_chr6.simMouse.chr6 2863 66 + 636262 TCCCTTGTCCGATTCAGGCACTGTGAAGCGATGACAGACCCCCGCGTACATTGTCGCCAGGATTAA -s Anc0.Anc0refChr9 2390 16 - 35212 --------------------------------------------------TGGCTGCCAGGGGTAC -s Anc1.Anc1refChr0 2612 16 + 16026 --------------------------------------------------TGGCTGCCAGGGGTAC -s Anc2.Anc2refChr0 2577 16 + 56053 --------------------------------------------------TGGCTGCCAGGGGTAC -s mr.mrrefChr0 2841 66 + 130230 TCCCCTGTCCGATTCAGGCACTGTGAAGCGATGACAGACCCCCGCGTACATTGTCGCCAGGATTAA -s simCow_chr6.simCow.chr6 2935 16 + 602619 --------------------------------------------------TGGCAGTCAAGAATAC -s simDog_chr6.simDog.chr6 2627 16 + 593897 --------------------------------------------------TGGCTGCCAGGGGTAC -s simHuman_chr6.simHuman.chr6 2643 14 + 601863 --------------------------------------------------TGGGTGCCAG--CTAC -s simRat_chr6.simRat.chr6 2848 66 + 647215 TCCCCTGTCCTTTTCACGCACTGTCAAACAATGACAGTCCCCTGCGTACATTGTTGCCATGATTAA - -a -s simMouse_chr6.simMouse.chr6 2929 20 + 636262 AAGTTCACCTCATGATTTTA -s Anc0.Anc0refChr9 2406 16 - 35212 CAGGACACCTCATAA----A -s Anc1.Anc1refChr0 2628 20 + 16026 CAGGACACCTCATAACTTTA -s Anc2.Anc2refChr0 2596 16 + 56053 CAAGACACCTCATAA----A -s mr.mrrefChr0 2907 20 + 130230 AAGTTCACCTCATGATTTTA -s simCow_chr6.simCow.chr6 2951 15 + 602619 CAGGACACTTGAAA-----A -s simDog_chr6.simDog.chr6 2647 15 + 593897 CAAGACGCCTCATAA----- -s simHuman_chr6.simHuman.chr6 2657 20 + 601863 CAGCACACCTCATAACTTTA -s simRat_chr6.simRat.chr6 2914 20 + 647215 AAGTTCACCTCATGATTGTA - -a -s simMouse_chr6.simMouse.chr6 2949 24 + 636262 CAACTCCATTCCCCTAACTGAGAG -s Anc0.Anc0refChr9 2429 24 - 35212 CAGCTTCCTTCCTCTAACTGGGAA -s Anc1.Anc1refChr0 2655 24 + 16026 CAGCTTCCTTCCTCTAACTGGGAA -s Anc2.Anc2refChr0 2619 24 + 56053 CAGCTTCCTTTCTCTAACTGGGGA -s mr.mrrefChr0 2927 24 + 130230 CAACTCCATTCCCCTAACTGAGAG -s simCow_chr6.simCow.chr6 2973 24 + 602619 CAGCTTCCTTTCTCACACTGAGGA -s simDog_chr6.simDog.chr6 2665 15 + 593897 CAAC---------CTAACTGGGGA -s simHuman_chr6.simHuman.chr6 2684 24 + 601863 CAGCTTCCTGCCACCAACTGGGAA -s simRat_chr6.simRat.chr6 2934 24 + 647215 CAACTCCGTTCCCCTAACTGAGGA - -a -s simMouse_chr6.simMouse.chr6 2973 14 + 636262 GATATTACTTATAT -s Anc0.Anc0refChr9 2501 9 - 35212 -----TCCTTATAA -s Anc1.Anc1refChr0 2727 14 + 16026 AGCACTCCTTATAA -s Anc2.Anc2refChr0 2691 9 + 56053 -----TCTTTATAA -s mr.mrrefChr0 2951 14 + 130230 GATATTACTTATAT -s simCow_chr6.simCow.chr6 3038 9 + 602619 -----TCTTAATAA -s simDog_chr6.simDog.chr6 2719 9 + 593897 -----TTTTTATAA -s simHuman_chr6.simHuman.chr6 2765 14 + 601863 AGCACTCCTGTTAG -s simRat_chr6.simRat.chr6 2958 13 + 647215 GATGCCACTTA-AT - -a -s simMouse_chr6.simMouse.chr6 2987 72 + 636262 AATAATACTTGTGACTGATACAGAGAATCACATCTATCTTGCCTTGTACCGACTAGAAACTTAAATAGGATT -s Anc0.Anc0refChr9 2510 72 - 35212 ACTAACACCTGTTACTAATACAGAGAATGATATCTATCTAATCTTGTACAGACTAAAAATTAAAATGAGATA -s Anc1.Anc1refChr0 2741 72 + 16026 ACTAACACCTGTTACTAATACAGAGAATGATATCTATCTAATCTTGTACAGACTAAAAATTAAAATGAGATA -s Anc2.Anc2refChr0 2700 72 + 56053 ACTAACACCTATTCATAATTTAGAGAATGATATCTATCTAATCCTGTACAGACTAAAAATTAAAATGATATA -s mr.mrrefChr0 2965 72 + 130230 AATAATACTTGTGACTGATACAGAGAATCACATCTATCTTGCCTTGTACAGACTAGAAACTTAAATAGGATT -s simCow_chr6.simCow.chr6 3048 66 + 602619 ACTAACAGCTATTGTTAATTAAGAGAGCGATATCCATCTAATCCTGTACAGACTAACAACTAAAAT------ -s simDog_chr6.simDog.chr6 2728 72 + 593897 GCTAACACATATCCATAACTTCAAGAATGATATGTATCTACTCCTGTACAGACTAAAAATCTAAATGATATA -s simHuman_chr6.simHuman.chr6 2779 72 + 601863 ACTAACATCTGTTACTAATACAGAGAATGATATCTATCTAATCTTGTACAGGCTAAAAAGTAAAATGAGATA -s simRat_chr6.simRat.chr6 2971 71 + 647215 AATAATACTGGTGACTGATACAGAGAATTGCAT-TATCTCTCCTTGTACAGATTAGAAACTTAAATAGGACT - -a -s simMouse_chr6.simMouse.chr6 3059 16 + 636262 ACAGGATAATTAGTGG -s Anc0.Anc0refChr9 2582 16 - 35212 ACTAGATAATTAGTGG -s Anc1.Anc1refChr0 2813 16 + 16026 ACTAGATAATTAGTGG -s Anc2.Anc2refChr0 2772 16 + 56053 ACTAAATAATTAGTGG -s mr.mrrefChr0 3037 16 + 130230 ACAGGATAATTAGTGG -s simCow_chr6.simCow.chr6 3114 15 + 602619 ACTCAATAATTAGT-G -s simDog_chr6.simDog.chr6 2800 16 + 593897 ACTAAATAATTAGTGG -s simHuman_chr6.simHuman.chr6 2851 16 + 601863 ACTAGATAATTAGTGG -s simRat_chr6.simRat.chr6 3047 16 + 647215 ACAGGATATTTAGCCG - -a -s simMouse_chr6.simMouse.chr6 3075 10 + 636262 ATTTCCCCTA -s Anc0.Anc0refChr9 2607 8 - 35212 TTTTCCA--T -s Anc1.Anc1refChr0 2838 8 + 16026 TTTTCCA--T -s Anc2.Anc2refChr0 2797 8 + 56053 TTTTTCA--T -s mr.mrrefChr0 3053 8 + 130230 ATTTCCA--A -s simCow_chr6.simCow.chr6 3138 5 + 602619 TCTTT----- -s simDog_chr6.simDog.chr6 2825 8 + 593897 TTCTTCA--T -s simHuman_chr6.simHuman.chr6 2876 8 + 601863 TTTTCCA--T -s simRat_chr6.simRat.chr6 3063 8 + 647215 ATTTCCA--C - -a -s simMouse_chr6.simMouse.chr6 3085 3 + 636262 CTG -s Anc0.Anc0refChr9 2616 2 - 35212 C-A -s Anc1.Anc1refChr0 2847 2 + 16026 C-A -s Anc2.Anc2refChr0 2806 2 + 56053 C-A -s mr.mrrefChr0 3062 3 + 130230 CTG -s simDog_chr6.simDog.chr6 2834 2 + 593897 C-A -s simHuman_chr6.simHuman.chr6 2885 2 + 601863 C-A -s simRat_chr6.simRat.chr6 3072 3 + 647215 CTG - -a -s simMouse_chr6.simMouse.chr6 3088 5 + 636262 GTACT -s Anc0.Anc0refChr9 2618 5 - 35212 GAACA -s Anc1.Anc1refChr0 2849 5 + 16026 GAACA -s Anc2.Anc2refChr0 2808 5 + 56053 ACACA -s mr.mrrefChr0 3065 5 + 130230 GAACT -s simCow_chr6.simCow.chr6 3143 5 + 602619 ACACT -s simDog_chr6.simDog.chr6 2839 5 + 593897 ACACA -s simHuman_chr6.simHuman.chr6 2887 5 + 601863 GAACA -s simRat_chr6.simRat.chr6 3075 5 + 647215 TAACT - -a -s simMouse_chr6.simMouse.chr6 3093 10 + 636262 AATCAATGTA -s Anc0.Anc0refChr9 2623 10 - 35212 CACGAAGATC -s Anc1.Anc1refChr0 2854 10 + 16026 CACGAAGATC -s Anc2.Anc2refChr0 2820 10 + 56053 CATGAAGATC -s mr.mrrefChr0 3070 10 + 130230 AACCAATGTA -s simCow_chr6.simCow.chr6 3155 10 + 602619 CATGAAGATC -s simHuman_chr6.simHuman.chr6 2892 10 + 601863 CACGAAGATC -s simRat_chr6.simRat.chr6 3080 10 + 647215 ATCCAATGTG - -a -s simMouse_chr6.simMouse.chr6 3103 33 + 636262 ATGAAGGTTATCTCCACAATACGAATTATAGCT -s Anc0.Anc0refChr9 2641 33 - 35212 ATGAAGATCATCTCTATCATACTGATGGTATAT -s Anc1.Anc1refChr0 2872 33 + 16026 ATGAAGATCATCTCTATCATACTGATGGTATAT -s Anc2.Anc2refChr0 2838 33 + 56053 ATGAAGACCATCTCTATCATACTGATGGTATAT -s mr.mrrefChr0 3080 33 + 130230 ATGAAGGTTATCTCCACAATACTAATTATAGCT -s simCow_chr6.simCow.chr6 3176 20 + 602619 ACAAAGA-------------ACTGGTGGTACCT -s simDog_chr6.simDog.chr6 2852 33 + 593897 ATGAAGACCATCTCTATCATACTGATGGTATAT -s simHuman_chr6.simHuman.chr6 2910 33 + 601863 ATGAAGATCATTTCTATCATACTGATGGTATGT -s simRat_chr6.simRat.chr6 3090 33 + 647215 ATGAAGGTTATGTCCACGATACTAATTATAGCT - -a -s simMouse_chr6.simMouse.chr6 3136 13 + 636262 TTTCAAGACAAAG -s Anc0.Anc0refChr9 2674 4 - 35212 TTTT--------- -s Anc1.Anc1refChr0 2905 13 + 16026 TTTTAAGACTAAG -s Anc2.Anc2refChr0 2871 4 + 56053 CTTT--------- -s mr.mrrefChr0 3113 13 + 130230 TTTTAAGACTAAG -s simCow_chr6.simCow.chr6 3220 4 + 602619 CTTT--------- -s simDog_chr6.simDog.chr6 2885 4 + 593897 CTTT--------- -s simHuman_chr6.simHuman.chr6 2943 13 + 601863 TTCTAAGACTAAG -s simRat_chr6.simRat.chr6 3123 13 + 647215 TTTTAAGACTAAG - -a -s simMouse_chr6.simMouse.chr6 3149 11 + 636262 TATTACACCTG -s Anc0.Anc0refChr9 2678 4 - 35212 -------CCTG -s Anc1.Anc1refChr0 2921 11 + 16026 TATTATGCCTG -s Anc2.Anc2refChr0 2875 4 + 56053 -------CTTG -s mr.mrrefChr0 3129 11 + 130230 TATTACACCTG -s simCow_chr6.simCow.chr6 3224 4 + 602619 -------CTGG -s simDog_chr6.simDog.chr6 2889 4 + 593897 -------CTTG -s simHuman_chr6.simHuman.chr6 2959 11 + 601863 TATTATGCCTG -s simRat_chr6.simRat.chr6 3139 11 + 647215 TATTACACCTG - -a -s simMouse_chr6.simMouse.chr6 3160 64 + 636262 GAGCATGAAATGTGCTTGACCTTGAAGAGATAAAACCCTATTAGCATACAGCTAGTGCTGGTCA -s Anc0.Anc0refChr9 2683 33 - 35212 GAG--------------ACCCTTGAACAG-----------------GACAACTAGTGCTGGTGA -s Anc1.Anc1refChr0 2933 47 + 16026 GAGTATGATATCTGTCTACCCTTGAACAG-----------------GACAACTAGTGCTGGTGA -s Anc2.Anc2refChr0 2880 33 + 56053 GAA--------------ACCCTAAAACAA-----------------GACAACAAGTGGTGAAGA -s mr.mrrefChr0 3141 64 + 130230 GAGCATGAAATGTGCTTGACCTTGAAGAGATAAAACCCTATTAGCATACAACTAGTGCTGGTGA -s simCow_chr6.simCow.chr6 3229 31 + 602619 G----------------ACCCTGAGAGAA-----------------GACAACAAGTGTTTTAGA -s simDog_chr6.simDog.chr6 2894 33 + 593897 GAA--------------ACCCTAAAGCGA-----------------GACAACAAGTGGTGAAGA -s simHuman_chr6.simHuman.chr6 2972 47 + 601863 GAGTATGATATCTGTCTAGCCTTGTACAG-----------------AACAACTAGTGCTGGTGA -s simRat_chr6.simRat.chr6 3151 64 + 647215 GAGCAGGCAATGTGCTTGCCCTTGGAGAGATAAAACCCTAATAGGATACAACTAGTACTGTTGA - -a -s simMouse_chr6.simMouse.chr6 3224 32 + 636262 GGTCAGCACATGTCTCAACAAACTATTAGTAG -s Anc0.Anc0refChr9 2716 25 - 35212 AGTTTACACATATGAAAGCGCACTA------- -s Anc1.Anc1refChr0 2980 25 + 16026 AGTTTACACATATGAAAGCGCACTA------- -s Anc2.Anc2refChr0 2913 25 + 56053 AGTTTGGACATACAAAAGCGCACTA------- -s mr.mrrefChr0 3205 32 + 130230 AGTTAACACATGTGTCAACAAACTATTAGTAG -s simCow_chr6.simCow.chr6 3260 25 + 602619 CGTTTGGACACAGTCAAACAGACTA------- -s simDog_chr6.simDog.chr6 2928 23 + 593897 AGCTT--GCATACAAAAGTGCACGA------- -s simHuman_chr6.simHuman.chr6 3019 25 + 601863 AGTTTACACATATGAAAGCTTACTA------- -s simRat_chr6.simRat.chr6 3215 32 + 647215 AGTTAACACATGTGACAACACACGATTAGTAG - -a -s simMouse_chr6.simMouse.chr6 3256 28 + 636262 AATTATCACTATCAGTGGAAATTATATA -s Anc0.Anc0refChr9 2741 19 - 35212 ---------GGTTAGTGGAGATCATTTC -s Anc1.Anc1refChr0 3005 19 + 16026 ---------GGTTAGTGGAGATCATTTC -s Anc2.Anc2refChr0 2938 19 + 56053 ---------GGTTAGTGGAGATCATTTC -s mr.mrrefChr0 3237 28 + 130230 AATTATCACTATTAGTGGAAATTATATA -s simCow_chr6.simCow.chr6 3285 19 + 602619 ---------GGTTAGTGGAGATCATTTC -s simDog_chr6.simDog.chr6 2951 19 + 593897 ---------GGTTAGTGGAGATCATTTC -s simHuman_chr6.simHuman.chr6 3044 19 + 601863 ---------GGTTAGTGGGGATCATTTC -s simRat_chr6.simRat.chr6 3248 28 + 647215 AATTATCACTATTAGTAGAAATTATGTA - -a -s simMouse_chr6.simMouse.chr6 3284 31 + 636262 TCCTAGGGAGGTTCCTCAATTCCAGACCGTT -s Anc0.Anc0refChr9 2761 27 - 35212 TCCTATGATGGCTAATCAATTCCAGAC---- -s Anc1.Anc1refChr0 3025 27 + 16026 TCCTATGATGGCTAATCAATTCCAGAC---- -s Anc2.Anc2refChr0 2958 27 + 56053 TCCAATGATGGCTAATCAATTCCAAAC---- -s mr.mrrefChr0 3266 27 + 130230 TCCTAGGAAGGCTCCTCAATTCCAGAC---- -s simCow_chr6.simCow.chr6 3305 27 + 602619 TCCCATGACTGCTACACAATTCCAAAT---- -s simDog_chr6.simDog.chr6 2971 27 + 593897 TCCAAGAATGGGAAATCAATTCCAAAC---- -s simHuman_chr6.simHuman.chr6 3064 26 + 601863 TCCTATGATGGCTGATCAATTCCAGG----- -s simRat_chr6.simRat.chr6 3277 27 + 647215 TCCTGGGAAGGCTCCTCAATTCCAACC---- - -a -s simMouse_chr6.simMouse.chr6 3315 57 + 636262 GGTTGAATCTTTGGCATAAAAGCATTGAGGATCTGTTCTTCATCGTGAGTCCAATGG -s Anc0.Anc0refChr9 2788 56 - 35212 GGCTCATTCTGAAGCAGAAGACTACCTAAGCTCTGCACTTTATTGTGGGCACAG-AG -s Anc1.Anc1refChr0 3052 56 + 16026 GGCTCATTCTGAAGCAGAAGACTACCTAAGCTCTGCACTTTATTGTGGGCACAG-AG -s Anc2.Anc2refChr0 2989 56 + 56053 AGCCCATTCTGAAGCAGAAGACTACCTAAACTCTGCACTTTATTGTGGGCACAG-AG -s mr.mrrefChr0 3293 57 + 130230 GGTTGAATCTTTGGCATAAAAGCATTGAGGATCTGTTCTTCATCGTGAGCCCAGTGG -s simCow_chr6.simCow.chr6 3342 56 + 602619 AGCCCATTCTGAAGCAGAAGACTACCTAAACTCTGCACTTTATTGTGGGCATGG-AG -s simDog_chr6.simDog.chr6 3002 56 + 593897 AGCCCATCCTGAGGCAGAAAACAACCCAGACTCTGCACTTTGTTGTGGGCACAG-AG -s simHuman_chr6.simHuman.chr6 3090 56 + 601863 GGCTCACTCTGAAGCAGAAGACTACCTAAGCTCTGCACATTATTGTGTGCACAG-AG -s simRat_chr6.simRat.chr6 3304 49 + 647215 --------CTTTGGCATAAAAGCATTGAGGATCTGTTCTTCATGGTGAGCCCAGTGG - -a -s simMouse_chr6.simMouse.chr6 3372 19 + 636262 GACATATAGATCTAATCAG -s Anc0.Anc0refChr9 2850 18 - 35212 GATATATAGAT-TAACCAG -s Anc1.Anc1refChr0 3114 18 + 16026 GATATATAGAT-TAACCAG -s Anc2.Anc2refChr0 3051 18 + 56053 TATATATAGTC-TAAGCAG -s mr.mrrefChr0 3356 19 + 130230 GACATATAGATCTAACCAG -s simCow_chr6.simCow.chr6 3404 17 + 602619 TATATATATG--TAAGCAG -s simDog_chr6.simDog.chr6 3064 18 + 593897 TATATATTGTC-TAAGCAG -s simHuman_chr6.simHuman.chr6 3152 18 + 601863 GATGTATACAT-TAACCAG -s simRat_chr6.simRat.chr6 3359 19 + 647215 GACATATAGATCTAACCAG - -a -s simMouse_chr6.simMouse.chr6 3391 3 + 636262 ATC -s Anc0.Anc0refChr9 2868 3 - 35212 ACC -s Anc1.Anc1refChr0 3132 3 + 16026 ACC -s Anc2.Anc2refChr0 3069 3 + 56053 ACC -s mr.mrrefChr0 3375 3 + 130230 ATC -s simCow_chr6.simCow.chr6 3421 3 + 602619 ACC -s simDog_chr6.simDog.chr6 3082 3 + 593897 ACC -s simHuman_chr6.simHuman.chr6 3170 3 + 601863 ACC -s simRat_chr6.simRat.chr6 3390 3 + 647215 ATC - -a -s simMouse_chr6.simMouse.chr6 3394 41 + 636262 TGCAATACCTAGCATGATAAAGGTTGACCATGGAACTTGGC -s Anc0.Anc0refChr9 2871 25 - 35212 TTAAATGCCTAGCATCATTAGAGTT---------------- -s Anc1.Anc1refChr0 3135 25 + 16026 TTAAATGCCTAGCATCATTAGAGTT---------------- -s Anc2.Anc2refChr0 3072 25 + 56053 TTAAATGCCTAGCATCATTGGAGTC---------------- -s mr.mrrefChr0 3378 41 + 130230 TGCAATACCTAGCATGATAAAAGTTAACCATGGAACTTGGC -s simCow_chr6.simCow.chr6 3424 25 + 602619 TTAAATGCCTGGCGTCATAGTAGTC---------------- -s simDog_chr6.simDog.chr6 3085 25 + 593897 TTAAATGCCTAGCATCATTGGAGTC---------------- -s simHuman_chr6.simHuman.chr6 3174 21 + 601863 TAAAATGCCTAGCAC----ATAGTT---------------- -s simRat_chr6.simRat.chr6 3393 41 + 647215 TGCAATACCTAGCATGATAAAAGTCAACCATGGAACTTGGC - -a -s simMouse_chr6.simMouse.chr6 3435 25 + 636262 CATAAAAAGAAACCATCCGATCTCC -s Anc0.Anc0refChr9 2896 15 - 35212 ----------AACCATCTAATCTTC -s Anc1.Anc1refChr0 3160 15 + 16026 ----------AACCATCTAATCTTC -s Anc2.Anc2refChr0 3097 15 + 56053 ----------AACCATCTAATCTTC -s mr.mrrefChr0 3419 25 + 130230 CATAAAAAGAAACCATCCGATCTCC -s simCow_chr6.simCow.chr6 3449 15 + 602619 ----------AACCTCCTGATCTTT -s simDog_chr6.simDog.chr6 3110 15 + 593897 ----------AACTATCCAATCTTC -s simHuman_chr6.simHuman.chr6 3195 15 + 601863 ----------AACCATCTAATCTTC -s simRat_chr6.simRat.chr6 3436 22 + 647215 TATAAGAGGAAATCATCCGATC--- - -a -s simMouse_chr6.simMouse.chr6 3460 11 + 636262 CAAATCCCTGA -s Anc0.Anc0refChr9 2911 11 - 35212 CAAATCTCCAA -s Anc1.Anc1refChr0 3175 11 + 16026 CAAATCTCCAA -s Anc2.Anc2refChr0 3112 11 + 56053 TGAATCTCCAA -s mr.mrrefChr0 3444 11 + 130230 CAAATCCCTGA -s simCow_chr6.simCow.chr6 3468 11 + 602619 TGAATGCCCAA -s simDog_chr6.simDog.chr6 3125 11 + 593897 TGAACCTCAGA -s simHuman_chr6.simHuman.chr6 3210 11 + 601863 CAAATCTCCAA -s simRat_chr6.simRat.chr6 3458 7 + 647215 ----TCCCTGA - -a -s simMouse_chr6.simMouse.chr6 3471 26 + 636262 GTTCAGTAGATATTAGTGGGCACAGG -s Anc0.Anc0refChr9 2922 17 - 35212 GATCTG--------AGTGGG-GCAGG -s Anc1.Anc1refChr0 3186 17 + 16026 GATCTG--------AGTGGG-GCAGG -s Anc2.Anc2refChr0 3131 17 + 56053 GATTTG--------AGTGGG-GCATG -s mr.mrrefChr0 3455 22 + 130230 GATCTGTAGAT---AGTGGG-ACAGG -s simCow_chr6.simCow.chr6 3487 12 + 602619 GACTT-------------GG-GCATG -s simDog_chr6.simDog.chr6 3144 17 + 593897 GATTCG--------AGTGAA-CTATG -s simHuman_chr6.simHuman.chr6 3221 17 + 601863 GATCTG--------AGTGGG-GCAGG -s simRat_chr6.simRat.chr6 3465 14 + 647215 GATCTGTAGAT------------AGA - -a -s simMouse_chr6.simMouse.chr6 3497 2 + 636262 CA -s Anc0.Anc0refChr9 2945 2 - 35212 CA -s Anc1.Anc1refChr0 3209 2 + 16026 CA -s Anc2.Anc2refChr0 3154 2 + 56053 CA -s mr.mrrefChr0 3477 2 + 130230 CA -s simCow_chr6.simCow.chr6 3505 2 + 602619 TA -s simDog_chr6.simDog.chr6 3167 2 + 593897 CA -s simHuman_chr6.simHuman.chr6 3244 2 + 601863 CA -s simRat_chr6.simRat.chr6 3479 2 + 647215 CA - -a -s simMouse_chr6.simMouse.chr6 3499 18 + 636262 TTATGTATTCACTAGCAA -s Anc0.Anc0refChr9 2947 18 - 35212 TGACCTCTTCACTAGCCA -s Anc1.Anc1refChr0 3211 18 + 16026 TGACCTCTTCACTAGCCA -s Anc2.Anc2refChr0 3156 18 + 56053 TGACCTCTTCACTAGACA -s mr.mrrefChr0 3479 18 + 130230 TTATGTCTTCACTAGCAA -s simCow_chr6.simCow.chr6 3511 15 + 602619 TGTACTCTTCACTAG--- -s simDog_chr6.simDog.chr6 3169 18 + 593897 TAACCTCTTCAGTGGACA -s simHuman_chr6.simHuman.chr6 3246 18 + 601863 TGACTTCTTCACTAGCCA -s simRat_chr6.simRat.chr6 3481 18 + 647215 TTATGTCTTCATTAGCAA - -a -s simMouse_chr6.simMouse.chr6 3517 6 + 636262 TAGATA -s Anc0.Anc0refChr9 2965 5 - 35212 TA-ATA -s Anc1.Anc1refChr0 3229 5 + 16026 TA-ATA -s Anc2.Anc2refChr0 3174 5 + 56053 TA-ATA -s mr.mrrefChr0 3497 6 + 130230 TAGATA -s simCow_chr6.simCow.chr6 3526 4 + 602619 -A-ATA -s simDog_chr6.simDog.chr6 3188 5 + 593897 TG-GTA -s simHuman_chr6.simHuman.chr6 3264 5 + 601863 TA-ATA -s simRat_chr6.simRat.chr6 3499 6 + 647215 TAGATA - -a -s simMouse_chr6.simMouse.chr6 3523 25 + 636262 CAGCAGCTACGATAGTTGTGCTGTC -s Anc0.Anc0refChr9 2970 25 - 35212 CAACATGTATAGCAGTTGTGTTGTC -s Anc1.Anc1refChr0 3234 25 + 16026 CAACATGTATAGCAGTTGTGTTGTC -s Anc2.Anc2refChr0 3179 25 + 56053 CAACATGTATAGCAGTTGTGTTGTC -s mr.mrrefChr0 3503 25 + 130230 CAGCAGCTACGATAGTTGTGCTGTC -s simCow_chr6.simCow.chr6 3531 25 + 602619 TGACAGGTATAACAGTTGTGTTGTC -s simDog_chr6.simDog.chr6 3193 25 + 593897 CAGCATGTATGGTAGTTGTGACGTC -s simHuman_chr6.simHuman.chr6 3269 25 + 601863 CAATGCATATAGCAGTTGTGTTATC -s simRat_chr6.simRat.chr6 3505 25 + 647215 CAGCAGCTACTATAGTTGTGCTGTC - -a -s simMouse_chr6.simMouse.chr6 3548 8 + 636262 TGCATTGC -s Anc1.Anc1refChr0 3259 8 + 16026 TGTGTTGT -s mr.mrrefChr0 3528 8 + 130230 TGCATTGC -s simHuman_chr6.simHuman.chr6 3320 8 + 601863 TGTGTTGT -s simRat_chr6.simRat.chr6 3530 8 + 647215 TGCATTGC - -a -s simMouse_chr6.simMouse.chr6 3556 41 + 636262 CCATTTTACATTTGCATACCTGACCATCAATCCCCTACCAA -s Anc0.Anc0refChr9 2995 37 - 35212 --CTTTTATCTTTGC-CCCCTCACTTCCAATTCCCTTTTA- -s Anc1.Anc1refChr0 3267 41 + 16026 TCCTTTTATCTTTGCACCCCTCACTTCCAATTCCCTTTTAG -s Anc2.Anc2refChr0 3204 37 + 56053 --CTTTTATCTTTGC-CCCCTCACTTCCAATTCCCTTTTA- -s mr.mrrefChr0 3536 41 + 130230 CCATTTTACATTTGCATCCCTGACCACCAATCCCCTACCAA -s simCow_chr6.simCow.chr6 3556 37 + 602619 --CTTTTATCTTTGC-CCCCTCACTTCTAATTCCCTATCA- -s simDog_chr6.simDog.chr6 3218 37 + 593897 --CTTTTATCTTTGC-TCACTCACTTCCCATTCACTTTTA- -s simHuman_chr6.simHuman.chr6 3330 41 + 601863 TCCTATTATCTAAGCACCCCTCACTTCCAATTCCCTGTTAG -s simRat_chr6.simRat.chr6 3538 41 + 647215 CCATTTTACATTTGCCTCCCTGACCACCAATCCCCTACCAA - -a -s simMouse_chr6.simMouse.chr6 3597 13 + 636262 ATCAACGATTGAT -s Anc0.Anc0refChr9 3045 13 - 35212 ATTACTGGACAAC -s Anc1.Anc1refChr0 3321 13 + 16026 ATTACTGGACAAC -s Anc2.Anc2refChr0 3254 13 + 56053 ATTACTAGACAAC -s mr.mrrefChr0 3577 13 + 130230 ATCAATGATTGAT -s simCow_chr6.simCow.chr6 3606 13 + 602619 ACTACTAAACAAC -s simDog_chr6.simDog.chr6 3268 13 + 593897 ATTACTAGAGACC -s simHuman_chr6.simHuman.chr6 3385 13 + 601863 ATTATTGGACAAC -s simRat_chr6.simRat.chr6 3579 13 + 647215 GTCTATGATTGAT - -a -s simMouse_chr6.simMouse.chr6 3610 1 + 636262 A -s Anc0.Anc0refChr9 3058 1 - 35212 A -s Anc1.Anc1refChr0 3334 1 + 16026 A -s Anc2.Anc2refChr0 3267 1 + 56053 A -s mr.mrrefChr0 3590 1 + 130230 A -s simCow_chr6.simCow.chr6 3619 1 + 602619 A -s simDog_chr6.simDog.chr6 3282 1 + 593897 T -s simHuman_chr6.simHuman.chr6 3398 1 + 601863 A -s simRat_chr6.simRat.chr6 3592 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 3611 30 + 636262 TATGCTCCCAATGCTGTTCAATACAAAGGT -s Anc0.Anc0refChr9 3059 25 - 35212 TTTTGTGTGAATGTTATTC----CAAAAG- -s Anc1.Anc1refChr0 3335 25 + 16026 TTTTGTGTGAATGTTATTC----CAAAAG- -s Anc2.Anc2refChr0 3268 25 + 56053 TTTTGTGTGAAGGTTATTC----CAAAAT- -s mr.mrrefChr0 3591 30 + 130230 TATGGTGTCAATGCTGTTCAATACAAAGGT -s simCow_chr6.simCow.chr6 3623 25 + 602619 TTTAGTGTTAAAGTTATCC----CAAAAC- -s simDog_chr6.simDog.chr6 3283 25 + 593897 TTTTGTGTGAAGACTATTG----CAAGAT- -s simHuman_chr6.simHuman.chr6 3399 25 + 601863 TTTTGTGTAAGTGTTATTC----CAAAAG- -s simRat_chr6.simRat.chr6 3593 27 + 647215 A---GTGTGAACACTGTTCGATGCAAAGGT - -a -s simMouse_chr6.simMouse.chr6 3641 2 + 636262 CC -s Anc0.Anc0refChr9 3086 2 - 35212 CT -s Anc1.Anc1refChr0 3362 2 + 16026 CT -s Anc2.Anc2refChr0 3295 2 + 56053 CT -s mr.mrrefChr0 3623 2 + 130230 CC -s simCow_chr6.simCow.chr6 3650 2 + 602619 CC -s simDog_chr6.simDog.chr6 3311 2 + 593897 CT -s simHuman_chr6.simHuman.chr6 3426 2 + 601863 CT -s simRat_chr6.simRat.chr6 3623 2 + 647215 CC - -a -s simMouse_chr6.simMouse.chr6 3643 56 + 636262 AAAGTACATTCCCTAGAGAATCTAAATAGAAGGTGTGCTGTGTATTTAGGTTTGCT -s Anc0.Anc0refChr9 3088 46 - 35212 AA----------CTGGAGAACCCAAATATAATGTGCCCTGTGTAATTAAGTGTGCT -s Anc1.Anc1refChr0 3364 46 + 16026 AA----------CTGGAGAACCCAAATATAATGTGCCCTGTGTAATTAAGTGTGCT -s Anc2.Anc2refChr0 3297 46 + 56053 AA----------CTGGTGAACCCAAATATTGTGTGCCCTGTGTAATTAAGTGTGCT -s mr.mrrefChr0 3625 56 + 130230 AAAGTACATTCCCTAGAGAATCCAAATAGAAGGTGTGCTGTGTATTTAGGTTTGCT -s simCow_chr6.simCow.chr6 3660 46 + 602619 AA----------CTGGTAAACCCAGATAGTGTGTGCCCTGAGTTATTAGGTGTGTT -s simDog_chr6.simDog.chr6 3313 44 + 593897 AA----------CCG--GAACCAAAATCTTGCGTGCCCTGTGTAATTAAGTGTGCT -s simHuman_chr6.simHuman.chr6 3428 46 + 601863 AA----------CTGGAGAACCCAAATATAATGTGCCCTGTGCAATTAAGTGTGCC -s simRat_chr6.simRat.chr6 3625 56 + 647215 AAAATACATGCTCTAGAGAATCCAAATAGAACGTGTGCTGTGTGGATAGGTTTGCT - -a -s simMouse_chr6.simMouse.chr6 3699 233 + 636262 TGAGAAGCACGCTGCTATCACCTCACTCCTCTGTAAGTTCAATAGCCTGAGGCTCATTTCCTCACAAAACATCACAAATCAAAACCACACTCCTCCGTAAGGTCAATAGACTGAGGTTCATTTCCTCACAAAACATTACAAATCAAGGTCTAGATCCTATTACTGGTGGGAGATCTTGTATGCAAAGCTTGCGGAAACTTGTTTTACTGTTGTTAGAGACCTTTTCAATTCCA -s Anc0.Anc0refChr9 3136 131 - 35212 TGATAAGCTTGCTGCCATGGCCCCACTGCTAT----------------------------------------------------------------GCAAGGTGAATAGACTGAGGTTCATTTCCTCATGAAGCATC---------------------------TGTGGAACATCTTGTGTATAAACC-----------TGTTTTCCTGCAGTGAGATCCCTCTAAAATTCCA -s Anc1.Anc1refChr0 3412 131 + 16026 TGATAAGCTTGCTGCCATGGCCCCACTGCTAT----------------------------------------------------------------GCAAGGTGAATAGACTGAGGTTCATTTCCTCATGAAGCATC---------------------------TGTGGAACATCTTGTGTATAAACC-----------TGTTTTCCTGCAGTGAGATCCCTCTAAAATTCCA -s Anc2.Anc2refChr0 3359 131 + 56053 AGGGGTTCTTGCTGCCATGGCCCCACTGCTAT----------------------------------------------------------------GCAAGGTGAATAGACTAAGGTCCATTTCCTCATGAAGCATC---------------------------TGTGGAATATCTTATGTATAAACT-----------TGTTCTCCTGCAGTGAGATCCCTCTAAAATTCCA -s mr.mrrefChr0 3683 169 + 130230 TGATAAGCATGCTGCCATCACCTCACTCCTCT----------------------------------------------------------------GTAAGGTCAATAGACTGAGGTTCATTTCCTCACAAAACATCACAAATCAAGGTCTAGATCCTATTACTGGTGGAACATCTTGTGTGCAAAGCTTGCGGAAACTTGTTTTACTGTTGTTAGAGCCCTCTTCAATTCCA -s simCow_chr6.simCow.chr6 3720 131 + 602619 ACTGGTGCCTGCTGCTATGGCCTCACTCCTAT----------------------------------------------------------------GTAAGGCAAAGAGACTAAGCTCCATTTCCTCATGAAGTATC---------------------------TGTGGAAGTCCCTATGCCTAAACT-----------TGTTCTCTTCCAGTGAGATCCCTTTTAGATTCCA -s simDog_chr6.simDog.chr6 3373 131 + 593897 AGGGGTTCTTGCTGCCATGGCCCCACTGCTCT----------------------------------------------------------------GCATGGTGACTAGACTAAGGTCCATTTCGTCATGAAGCATC---------------------------TGTCGAATATCTTATGTATAAGCT-----------TGTCCTTCTGTAGTGAGATTCCTCCACAACACCA -s simHuman_chr6.simHuman.chr6 3476 131 + 601863 TCATAAGCTTGCCGCCATGTCTCCACTGCTAT----------------------------------------------------------------GCAAAGTGAATAGATTGAGTTTCATTTCCTCATGAAGAATC---------------------------TGTGGAACATCTTGTGTATAAATC-----------GGTTTTCCTGCAGTGAGGTCCCTCTCACATTCCA -s simRat_chr6.simRat.chr6 3683 161 + 647215 TGGTAAGCATGCTGCCATAACCTCATGCCTCT----------------------------------------------------------------ATAAGGTCAATAGACTGAGGATTATTTCCTAACAAAACATCGCAGCTCAAGGTCTCAATTCTATCACTGGTGGAACACCTTGTGTGAAAAGTTTGTGAAAACTAGTTTTTCT--------CGCCCCCTGCAATTCCA - -a -s simMouse_chr6.simMouse.chr6 3932 39 + 636262 CTGCACATGAATATCAAGAGATAGAGAGCATCTCACTCA -s Anc0.Anc0refChr9 3267 1 - 35212 C-------------------------------------- -s Anc1.Anc1refChr0 3543 1 + 16026 C-------------------------------------- -s Anc2.Anc2refChr0 3493 1 + 56053 C-------------------------------------- -s mr.mrrefChr0 3852 39 + 130230 CTGCACATGAATATCAAGAGATAGAGAGCATCTCACTCA -s simCow_chr6.simCow.chr6 3854 1 + 602619 G-------------------------------------- -s simDog_chr6.simDog.chr6 3507 1 + 593897 C-------------------------------------- -s simHuman_chr6.simHuman.chr6 3607 1 + 601863 C-------------------------------------- -s simRat_chr6.simRat.chr6 3844 39 + 647215 GTGCACATGAATATCAAGTGATAGAGAACATCTCACCAG - -a -s simMouse_chr6.simMouse.chr6 3971 122 + 636262 CTTTGTGAGGTGAAGAGTCTTGGGTCCTATGTGTGCATATAGTGCTAACGATGTGCATATGGTCATGTTTGCCTTTTATTGGAGCTTTGAAAAGGTGCTATGCAAAATCTCAACAACATTAA -s Anc0.Anc0refChr9 3268 2 - 35212 ------------------------------------------------------------------------------------------------------------------------AC -s Anc1.Anc1refChr0 3544 2 + 16026 ------------------------------------------------------------------------------------------------------------------------AC -s Anc2.Anc2refChr0 3494 2 + 56053 ------------------------------------------------------------------------------------------------------------------------AC -s mr.mrrefChr0 3891 41 + 130230 CTTTGTGAGGTGAAGAGTCTTGGGTCCTTTGTGTGCATA---------------------------------------------------------------------------------AA -s simCow_chr6.simCow.chr6 3855 2 + 602619 ------------------------------------------------------------------------------------------------------------------------AC -s simDog_chr6.simDog.chr6 3508 2 + 593897 ------------------------------------------------------------------------------------------------------------------------AC -s simHuman_chr6.simHuman.chr6 3608 2 + 601863 ------------------------------------------------------------------------------------------------------------------------AC -s simRat_chr6.simRat.chr6 3884 41 + 647215 TTTTGTGGGGTAAAGAGTCTTGGGTCCTTTGTGTGTGTG---------------------------------------------------------------------------------AA - -a -s simMouse_chr6.simMouse.chr6 4093 2 + 636262 GC -s Anc0.Anc0refChr9 3270 2 - 35212 TC -s Anc1.Anc1refChr0 3546 2 + 16026 TC -s Anc2.Anc2refChr0 3496 2 + 56053 TA -s mr.mrrefChr0 3932 2 + 130230 GC -s simCow_chr6.simCow.chr6 3864 2 + 602619 TA -s simDog_chr6.simDog.chr6 3510 2 + 593897 CA -s simHuman_chr6.simHuman.chr6 3610 2 + 601863 TC -s simRat_chr6.simRat.chr6 3925 2 + 647215 GG - -a -s simMouse_chr6.simMouse.chr6 4095 6 + 636262 CTAGTT -s Anc0.Anc0refChr9 3272 6 - 35212 CTTGTT -s Anc1.Anc1refChr0 3548 6 + 16026 CTTGTT -s Anc2.Anc2refChr0 3498 6 + 56053 AATATG -s mr.mrrefChr0 3934 6 + 130230 CTAGTT -s simCow_chr6.simCow.chr6 3872 6 + 602619 AATATG -s simHuman_chr6.simHuman.chr6 3612 6 + 601863 CTTGTT -s simRat_chr6.simRat.chr6 3927 6 + 647215 CTAGTT - -a -s simMouse_chr6.simMouse.chr6 4101 33 + 636262 TCCCACTCAATATGTGGGTGTAATGTTCAATTA -s Anc0.Anc0refChr9 3279 33 - 35212 TCACATTCAATATCCTGGTGTAATGTTCAATCT -s Anc1.Anc1refChr0 3555 33 + 16026 TCACATTCAATATCCTGGTGTAATGTTCAATCT -s Anc2.Anc2refChr0 3505 33 + 56053 TCATGTTCAATATCCTGGTGTAATGTTTAATCT -s mr.mrrefChr0 3941 33 + 130230 TCCCACTCAATATGCGGGTGTAATGTTCAATTT -s simCow_chr6.simCow.chr6 3879 33 + 602619 TCATTTCAGGCATCCTGGTGTAATGTTTAATCT -s simDog_chr6.simDog.chr6 3896 26 + 593897 --ATGTTCAATATCCTAATG-----ATTAATCA -s simHuman_chr6.simHuman.chr6 3619 33 + 601863 TCACATTTAATATCCTGGTGTAGTCTTCAATCT -s simRat_chr6.simRat.chr6 3934 31 + 647215 TGCCACTCA--ATGCGGGTGGAATGTTGAATTT - -a -s simMouse_chr6.simMouse.chr6 4134 71 + 636262 TGCTAGGTGCTTAGCATATCTCAATCTCAGTATTCCCTAGCTCCTGAATTCATCAGGTCTATTTTTATCAA -s Anc0.Anc0refChr9 3318 70 - 35212 TACTATGTATTAAACA-ATCCTAATCTCAAAATTTTCTGCCTCCTGGATGTATCAGCTCTATTTTTACCAA -s Anc1.Anc1refChr0 3594 70 + 16026 TACTATGTATTAAACA-ATCCTAATCTCAAAATTTTCTGCCTCCTGGATGTATCAGCTCTATTTTTACCAA -s Anc2.Anc2refChr0 3544 70 + 56053 TACATTGCATTAAATA-ATTCTAATCTCAAAACCTTCTGCATCTTGGATGTATTAGCTCTGTTTTTACCAA -s mr.mrrefChr0 3974 71 + 130230 TGCTATGTGCTTAGCATATCCTAATCTCAGTATTTTCTAGCTCCTGAATTCATCAGGTCTATTTTTATCAA -s simCow_chr6.simCow.chr6 3920 70 + 602619 CCCATCACATTAAATA-ATTCTAATCTCAGAGCCTTCTGCGCTTTGGATGTAGTAGCCCCGTTTTTGCCAA -s simDog_chr6.simDog.chr6 3928 62 + 593897 TAGATTGCATTACATA-ATTCTAATCTCAAAA--------ATCTTGGAGTTGTTAGCTCTGTTATTACCAA -s simHuman_chr6.simHuman.chr6 3658 70 + 601863 TACTATGTATTAAACA-ATCCTAATCTCAAAATTTTCTGTCTCCTTGATGTATCAGCTCTATTTTTAAAAA -s simRat_chr6.simRat.chr6 3965 71 + 647215 TGTTATGTTCTTAGCATATCCTAATATCAGTATTTTCTAATTCTTGAATACATCAGGTCTATTTTTATCAA - -a -s simMouse_chr6.simMouse.chr6 4205 121 + 636262 GGTGTACCCTATCAATCAATACATCTTAGAATGCATTCTCACTAGAGGGTTAGTTAGTCACAACTTGTACATCCTACAACATGCATTCTCGCTAGAGGGTTAGTTAGTCACAATTTTTACA -s Anc0.Anc0refChr9 3388 70 - 35212 TATGACTGCTACTAATCAATACATCTTGCAATGCATCCTTTCCAAAGGGTCTTCTAGTC-CAATTTG--------------------------------------------------TTCA -s Anc1.Anc1refChr0 3664 70 + 16026 TATGACTGCTACTAATCAATACATCTTGCAATGCATCCTTTCCAAAGGGTCTTCTAGTC-CAATTTG--------------------------------------------------TTCA -s Anc2.Anc2refChr0 3614 70 + 56053 TATAACTGCTACTAATCAATACATCTTGCAATGCATCATTTCCAGCGGGTCTTCTAATC-CAATTTG--------------------------------------------------TTCA -s mr.mrrefChr0 4045 71 + 130230 GGTGTACGCTATCAATCAATACATCTTACAATGCATTCTCTCTAAAGGGTCATTTAGTCACAATTTG--------------------------------------------------TACA -s simCow_chr6.simCow.chr6 3990 68 + 602619 TAATACTGCTAGTAATCAATAC--CCTGCTATGCATCATTTCCAGCAGGTCTTCTAATC-CAATTTG--------------------------------------------------TTTT -s simDog_chr6.simDog.chr6 4004 70 + 593897 TATAACTGCTACTAAACACTACATGTTGCAATGCATCATTTACAGCGGGTCTTCTAATC-CAGTTTG--------------------------------------------------TTCA -s simHuman_chr6.simHuman.chr6 3728 70 + 601863 TATGACTGCTACTGATCTATGCATCTTGCAATGCATCCTGTCCAAAGGGTCTTCTGGTC-CAATTTG--------------------------------------------------TTCA -s simRat_chr6.simRat.chr6 4036 71 + 647215 GGTGTAAGCTATCAATCAATACATTGAACAATGCAATCTCTCTAAAGGGACATTTAGTCACAATTTG--------------------------------------------------TAAA - -a -s simMouse_chr6.simMouse.chr6 4326 10 + 636262 TCCTGCAACA -s Anc0.Anc0refChr9 3458 7 - 35212 TGGTG---CA -s Anc1.Anc1refChr0 3734 7 + 16026 TGGTG---CA -s Anc2.Anc2refChr0 3684 7 + 56053 TGGTG---CA -s mr.mrrefChr0 4116 10 + 130230 TCCTGCAACA -s simCow_chr6.simCow.chr6 598218 7 - 602619 TTGTG---GA -s simDog_chr6.simDog.chr6 4074 7 + 593897 TGATG---CA -s simHuman_chr6.simHuman.chr6 3798 7 + 601863 TGGTG---CA -s simRat_chr6.simRat.chr6 4107 10 + 647215 TCTAGCAACA - -a -s simMouse_chr6.simMouse.chr6 4336 7 + 636262 TAAAACT -s Anc0.Anc0refChr9 3465 7 - 35212 TAAAATT -s Anc1.Anc1refChr0 3741 7 + 16026 TAAAATT -s Anc2.Anc2refChr0 3691 7 + 56053 TAAAATT -s mr.mrrefChr0 4126 7 + 130230 TAAAACT -s simCow_chr6.simCow.chr6 598225 7 - 602619 GAAAATC -s simDog_chr6.simDog.chr6 4084 7 + 593897 TAAAGTT -s simHuman_chr6.simHuman.chr6 3805 7 + 601863 TAAAATT -s simRat_chr6.simRat.chr6 4117 7 + 647215 TAAAACC - -a -s simMouse_chr6.simMouse.chr6 4343 18 + 636262 TTTAATAGTGTCAAAAGA -s Anc0.Anc0refChr9 3472 16 - 35212 TTTAATAGTGTC--CATA -s Anc1.Anc1refChr0 3748 16 + 16026 TTTAATAGTGTC--CATA -s Anc2.Anc2refChr0 3698 16 + 56053 TTTAATAGTGCC--CATA -s mr.mrrefChr0 4133 18 + 130230 TTTAATAGTGTCAAAAGA -s simCow_chr6.simCow.chr6 598243 16 - 602619 TTTAACAGTGGC--CATA -s simDog_chr6.simDog.chr6 4091 16 + 593897 TTTAATAGTGCC--CATA -s simHuman_chr6.simHuman.chr6 3812 13 + 601863 T---ATAGAGTC--CATA -s simRat_chr6.simRat.chr6 4124 18 + 647215 TTTAATAGTGTCAAAAGA - -a -s simMouse_chr6.simMouse.chr6 4361 9 + 636262 TGGTATGTA -s Anc0.Anc0refChr9 3488 6 - 35212 TG---TGTA -s Anc1.Anc1refChr0 3764 9 + 16026 TGATATGTA -s Anc2.Anc2refChr0 3714 6 + 56053 TT---TGTA -s mr.mrrefChr0 4151 9 + 130230 TGGTATGTA -s simCow_chr6.simCow.chr6 598264 6 - 602619 CT---TGTA -s simDog_chr6.simDog.chr6 4107 6 + 593897 TT---TGTA -s simHuman_chr6.simHuman.chr6 3825 9 + 601863 TGATATGTA -s simRat_chr6.simRat.chr6 4142 9 + 647215 TGGTTTGTA - -a -s simMouse_chr6.simMouse.chr6 4370 8 + 636262 GTGGCATA -s Anc0.Anc0refChr9 3496 8 - 35212 TTGGCTTT -s Anc1.Anc1refChr0 3775 8 + 16026 TTGGCTTT -s Anc2.Anc2refChr0 3722 8 + 56053 TTAGCTTT -s mr.mrrefChr0 4160 8 + 130230 GTGGCATA -s simCow_chr6.simCow.chr6 598272 8 - 602619 TTAGCTTT -s simDog_chr6.simDog.chr6 4115 6 + 593897 TCAGTT-- -s simHuman_chr6.simHuman.chr6 3836 8 + 601863 TTGGCTTT -s simRat_chr6.simRat.chr6 4151 8 + 647215 GTGGCATA - -a -s simMouse_chr6.simMouse.chr6 4378 4 + 636262 GCAT -s Anc0.Anc0refChr9 3507 4 - 35212 GTTA -s Anc1.Anc1refChr0 3786 4 + 16026 GTTA -s Anc2.Anc2refChr0 3733 4 + 56053 GTTA -s mr.mrrefChr0 4171 4 + 130230 GTAT -s simCow_chr6.simCow.chr6 598283 4 - 602619 GTTA -s simHuman_chr6.simHuman.chr6 3847 4 + 601863 GTTA -s simRat_chr6.simRat.chr6 4162 4 + 647215 GTGG - -a -s simMouse_chr6.simMouse.chr6 4382 20 + 636262 CACACCCTATTCTACAAGTT -s Anc0.Anc0refChr9 3511 11 - 35212 TGCATCCT-------GA--T -s Anc1.Anc1refChr0 3790 11 + 16026 TGCATCCT-------GA--T -s Anc2.Anc2refChr0 3737 11 + 56053 TGCATGCT-------GT--T -s mr.mrrefChr0 4175 18 + 130230 CACACCCTATTCTACAA--T -s simCow_chr6.simCow.chr6 598287 11 - 602619 TGCATGCT-------GT--T -s simHuman_chr6.simHuman.chr6 3851 11 + 601863 TGCATCCT-------CA--T -s simRat_chr6.simRat.chr6 4174 18 + 647215 CACACCCTATTCTACAA--T - -a -s simMouse_chr6.simMouse.chr6 4402 21 + 636262 ACTCTTATCCTCAAGGGGTGT -s Anc0.Anc0refChr9 3522 20 - 35212 ACTTTAATCCCCAAGTGG-GT -s Anc1.Anc1refChr0 3801 20 + 16026 ACTTTAATCCCCAAGTGG-GT -s Anc2.Anc2refChr0 3748 20 + 56053 ACTTTAATCCCCAAGTGG-AG -s mr.mrrefChr0 4193 20 + 130230 ACTCTTATCCTCAAGGGG-GT -s simCow_chr6.simCow.chr6 598306 20 - 602619 ACTTTAATACCAAATTGG-AG -s simDog_chr6.simDog.chr6 4121 18 + 593897 --TTTAATCCCCAAGTGG-AG -s simHuman_chr6.simHuman.chr6 3862 20 + 601863 ACTTTAATCCCCAAGTGG-GT -s simRat_chr6.simRat.chr6 4192 20 + 647215 ACTCTTTCCCTCCAGGGA-GT - -a -s simMouse_chr6.simMouse.chr6 4423 19 + 636262 GTTTGGTGGGCTCGGAGGC -s Anc0.Anc0refChr9 3543 19 - 35212 ATATGGTAGGCTCAGAGGC -s Anc1.Anc1refChr0 3822 19 + 16026 ATATGGTAGGCTCAGAGGC -s Anc2.Anc2refChr0 3769 19 + 56053 ATATGGTAGGCTCAGAGGC -s mr.mrrefChr0 4213 19 + 130230 GTTTGGTAGGCTCAGAGGC -s simCow_chr6.simCow.chr6 598327 19 - 602619 ATGTGGTAGGCACAGAGGC -s simDog_chr6.simDog.chr6 4140 19 + 593897 GTATGGTAAGCTCTGAAGC -s simHuman_chr6.simHuman.chr6 3883 19 + 601863 ATATGGCAGGCTCAGAGGC -s simRat_chr6.simRat.chr6 4212 19 + 647215 GTTTGGTAGACCCAGATGC - -a -s simMouse_chr6.simMouse.chr6 4442 37 + 636262 ACAGTTAGCAATAGTTGCTACTCCATTGCAAGGATCC -s Anc0.Anc0refChr9 3562 35 - 35212 A--GGTATAAAGATTGGTTATTGCACCACAAAGATCT -s Anc1.Anc1refChr0 3841 37 + 16026 ATAGGTATAAAGATTGGTTATTGCACCACAAAGATCT -s Anc2.Anc2refChr0 3788 35 + 56053 A--GGTATAAAGATTGGTCATTGCACCACAAAGGTCT -s mr.mrrefChr0 4232 37 + 130230 ATAGTTAGCAATAGTTGCTACTGCACTGCAAGGATCC -s simCow_chr6.simCow.chr6 598348 35 - 602619 A--GGTATGAAGATTGGTTAATGCACCACAAAGTTTT -s simDog_chr6.simDog.chr6 4159 35 + 593897 A--GGTATAAAGATTGGTCATTGCACCACAAAGGTCT -s simHuman_chr6.simHuman.chr6 3902 22 + 601863 ATA---------------TATTGTACCACAAAGATCT -s simRat_chr6.simRat.chr6 4231 37 + 647215 ATAGGTAGCAGTAGTTGCTACTGCACTGCGAGGATCC - -a -s simMouse_chr6.simMouse.chr6 4479 17 + 636262 CAAAGGCTTGCACCGTG -s Anc0.Anc0refChr9 3601 15 - 35212 CAAAGGGATGGA--ATG -s Anc1.Anc1refChr0 3882 17 + 16026 CAAAGGGATGGACTATG -s Anc2.Anc2refChr0 3827 15 + 56053 CAAAGGGACGGA--GTG -s mr.mrrefChr0 4269 17 + 130230 CAAAGGCATGCACCATG -s simCow_chr6.simCow.chr6 598387 4 - 602619 CAAA------------- -s simDog_chr6.simDog.chr6 4198 15 + 593897 CATAGGGACGGA--GTG -s simHuman_chr6.simHuman.chr6 3928 16 + 601863 CAAAAGGATGTACTAT- -s simRat_chr6.simRat.chr6 4268 17 + 647215 CAAAGGCATGCACCATG - -a -s simMouse_chr6.simMouse.chr6 4496 30 + 636262 ATTTGCTCATCCCAATGAATAAGAATCATG -s Anc0.Anc0refChr9 3616 30 - 35212 ATTTGCTAGTGCTGGTCAATGGGACTCACT -s Anc1.Anc1refChr0 3899 30 + 16026 ATTTGCTAGTGCTGGTCAATGGGACTCACT -s Anc2.Anc2refChr0 3842 30 + 56053 ATTTGCTAGTGCTGGTCAATGGGACTCACT -s mr.mrrefChr0 4286 30 + 130230 ATTTGCTCATCCCAATGAATAAGAATCATG -s simCow_chr6.simCow.chr6 598391 30 - 602619 ATTTAATAGCCCTGGTCAGTGGGACTCACT -s simDog_chr6.simDog.chr6 4215 30 + 593897 ATTTGCTAGTGCTGGTCAATGGGACTCACT -s simRat_chr6.simRat.chr6 4285 30 + 647215 ATTTGCTCATGCTGATGCCTAAGAAGCACA - -a -s simMouse_chr6.simMouse.chr6 4526 10 + 636262 AACCCACCTT -s Anc0.Anc0refChr9 3646 10 - 35212 AACTCACACT -s Anc1.Anc1refChr0 3929 10 + 16026 AACTCACACT -s Anc2.Anc2refChr0 3872 10 + 56053 AACTCACACT -s mr.mrrefChr0 4316 10 + 130230 AACCCACCCT -s simCow_chr6.simCow.chr6 598424 10 - 602619 AGCTCACACT -s simDog_chr6.simDog.chr6 4245 10 + 593897 AACCTACGTT -s simHuman_chr6.simHuman.chr6 3944 10 + 601863 AACTCACACT -s simRat_chr6.simRat.chr6 4315 10 + 647215 AACCCACCCT - -a -s simMouse_chr6.simMouse.chr6 4536 42 + 636262 ACTTTGTAGGCCCAGATGCTTGAGAACCTGACAACGGGAATT -s Anc0.Anc0refChr9 3657 34 - 35212 ACTTTGTGGACCCACATGCT--------AGACAATGGGATTT -s Anc1.Anc1refChr0 3940 34 + 16026 ACTTTGTGGACCCACATGCT--------AGACAATGGGATTT -s Anc2.Anc2refChr0 3883 34 + 56053 ACTTTATGGACCCACATGCT--------AGACAATGGAATTT -s mr.mrrefChr0 4327 34 + 130230 ACTTTGTGGGCCCAGATGCT--------TGACAACGGGAATT -s simCow_chr6.simCow.chr6 598435 34 - 602619 ACTTTATGGACCTACATGCT--------AGACAATGGAATTT -s simDog_chr6.simDog.chr6 4256 34 + 593897 ACATTATGGACCCACATGCT--------GGACCACAGAATTT -s simHuman_chr6.simHuman.chr6 3955 33 + 601863 ACTTTGTGGACCCACATG-T--------AGACAATGGGATTT -s simRat_chr6.simRat.chr6 4326 34 + 647215 ACTTTGTGGGTCCAAATGCT--------TGACAAAGGGAATT - -a -s simMouse_chr6.simMouse.chr6 4578 52 + 636262 TCATTAATAGGCTAGGGATGTTGTTCACAGTACCTGATCATCGTACACCAAG -s Anc0.Anc0refChr9 3691 51 - 35212 TTATTAATAGGCTAGAGGTGTTGTCCCCAGTACCAGA-CATGCCATTCTCAG -s Anc1.Anc1refChr0 3974 51 + 16026 TTATTAATAGGCTAGAGGTGTTGTCCCCAGTACCAGA-CATGCCATTCTCAG -s Anc2.Anc2refChr0 3917 51 + 56053 TTATTACTAGGTTAGATGTGTTGTCCCCAGTAGTAGA-CTTGCCATTCTCAG -s mr.mrrefChr0 4361 51 + 130230 TTATTAATAGGCTAGGGGTGTTGTTCACAGTACCTGA-CATCGTACACCAAG -s simCow_chr6.simCow.chr6 598469 36 - 602619 CTGTTATTAGGTTAAGTATGTTTGCCC----------------CATTCTCAG -s simDog_chr6.simDog.chr6 4290 51 + 593897 TTATTACTAAGTTAGATGTGTCGTCTCCAGTAGTAGA-CTTGCCATCCTTGG -s simHuman_chr6.simHuman.chr6 3988 51 + 601863 TTATTAATAGGCTAGAGGCATTGTCCCCAATTCCAGA-CATGTCATTCTCAG -s simRat_chr6.simRat.chr6 642057 18 - 647215 TTGCTATTCGTCCAGGGG---------------------------------- - -a -s simMouse_chr6.simMouse.chr6 4630 27 + 636262 GTATAACCACTGATGCGTGCACCTCAG -s Anc0.Anc0refChr9 3742 6 - 35212 GTCT---------------------AG -s Anc1.Anc1refChr0 4025 6 + 16026 GTCT---------------------AG -s Anc2.Anc2refChr0 3970 6 + 56053 GCCT---------------------AG -s mr.mrrefChr0 4412 16 + 130230 GTATAACCA-----------ACCTCAG -s simCow_chr6.simCow.chr6 598507 6 - 602619 GCAT---------------------TG -s simDog_chr6.simDog.chr6 4343 6 + 593897 GCCT---------------------AG -s simHuman_chr6.simHuman.chr6 4039 4 + 601863 ATGT----------------------- -s simRat_chr6.simRat.chr6 642075 7 - 647215 --------------------ACCTTAG - -a -s simMouse_chr6.simMouse.chr6 4657 2 + 636262 CT -s Anc0.Anc0refChr9 3748 2 - 35212 CT -s Anc1.Anc1refChr0 4031 2 + 16026 CT -s Anc2.Anc2refChr0 3976 2 + 56053 CT -s mr.mrrefChr0 4428 2 + 130230 CT -s simCow_chr6.simCow.chr6 598513 2 - 602619 CT -s simDog_chr6.simDog.chr6 4352 2 + 593897 CT -s simRat_chr6.simRat.chr6 642082 2 - 647215 CT - -a -s simMouse_chr6.simMouse.chr6 4659 12 + 636262 TTCATCTATGTT -s Anc0.Anc0refChr9 3750 11 - 35212 CTC-TCCATGTC -s Anc1.Anc1refChr0 4033 11 + 16026 CTC-TCCATGTC -s Anc2.Anc2refChr0 3978 11 + 56053 CTC-TCCATGTC -s mr.mrrefChr0 4430 12 + 130230 TTCATCTATGTT -s simCow_chr6.simCow.chr6 598515 11 - 602619 CTC-TCAATGTC -s simDog_chr6.simDog.chr6 4358 11 + 593897 CTC-TCCATGTC -s simRat_chr6.simRat.chr6 642084 12 - 647215 TGCACCCATGTA - -a -s simMouse_chr6.simMouse.chr6 4671 9 + 636262 TATTGAGCC -s Anc0.Anc0refChr9 3761 9 - 35212 TCATGTGTT -s Anc1.Anc1refChr0 4044 9 + 16026 TCATGTGTT -s Anc2.Anc2refChr0 3993 9 + 56053 TCATGTGTT -s mr.mrrefChr0 4442 9 + 130230 TATTGAGCC -s simCow_chr6.simCow.chr6 598530 9 - 602619 CTATGCTTT -s simDog_chr6.simDog.chr6 4373 9 + 593897 TCATGTGTT -s simRat_chr6.simRat.chr6 642096 9 - 647215 TATCAAGCC - -a -s simMouse_chr6.simMouse.chr6 4680 1 + 636262 C -s Anc0.Anc0refChr9 3770 1 - 35212 C -s Anc1.Anc1refChr0 4053 1 + 16026 C -s Anc2.Anc2refChr0 4002 1 + 56053 C -s mr.mrrefChr0 4451 1 + 130230 C -s simCow_chr6.simCow.chr6 4401 1 + 602619 C -s simDog_chr6.simDog.chr6 4405 1 + 593897 C -s simRat_chr6.simRat.chr6 642105 1 - 647215 C - -a -s simMouse_chr6.simMouse.chr6 4681 11 + 636262 CCCTGTTTGTC -s Anc0.Anc0refChr9 3771 11 - 35212 CCCAGTCTATC -s Anc1.Anc1refChr0 4054 11 + 16026 CCCAGTCTATC -s Anc2.Anc2refChr0 4003 11 + 56053 CCCAGTCTATT -s mr.mrrefChr0 4452 11 + 130230 CCCTGTTTGTC -s simCow_chr6.simCow.chr6 4405 11 + 602619 CCCTGTGAATT -s simDog_chr6.simDog.chr6 4406 11 + 593897 CCCAGTCTATT -s simHuman_chr6.simHuman.chr6 4043 3 + 601863 --------ATC -s simRat_chr6.simRat.chr6 642106 11 - 647215 CCCTGTTAGTC - -a -s simMouse_chr6.simMouse.chr6 4692 29 + 636262 ATACTGAAGATTGCAAAACAAAGAATGTA -s Anc0.Anc0refChr9 3791 22 - 35212 ATAAGAAGGATTG-------ACTAATGTG -s Anc1.Anc1refChr0 4074 22 + 16026 ATAAGAAGGATTG-------ACTAATGTG -s Anc2.Anc2refChr0 4023 22 + 56053 ATAAGAAGTATTG-------ACTAACTTG -s mr.mrrefChr0 4463 29 + 130230 ATAGTGAAGATTGCAAGACAAAGAATGTG -s simCow_chr6.simCow.chr6 4425 22 + 602619 ATAAGAAGTATTG-------ACTAACTTG -s simDog_chr6.simDog.chr6 4426 22 + 593897 ATAAAAAGTATTC-------ACTAACTCG -s simHuman_chr6.simHuman.chr6 4055 22 + 601863 ATTAGAAGGCTTG-------AGTAATGTG -s simRat_chr6.simRat.chr6 642117 29 - 647215 ACAGTGAAGATTGCAAGACAAAGAAAGTG - -a -s simMouse_chr6.simMouse.chr6 4721 3 + 636262 CTG -s Anc0.Anc0refChr9 3813 3 - 35212 ATA -s Anc1.Anc1refChr0 4096 3 + 16026 ATA -s Anc2.Anc2refChr0 4049 3 + 56053 AAA -s mr.mrrefChr0 4492 3 + 130230 CTG -s simCow_chr6.simCow.chr6 4451 3 + 602619 AGA -s simDog_chr6.simDog.chr6 4452 3 + 593897 AAA -s simHuman_chr6.simHuman.chr6 4077 3 + 601863 ATA -s simRat_chr6.simRat.chr6 642146 3 - 647215 CTG - -a -s simMouse_chr6.simMouse.chr6 4724 30 + 636262 ATCTAAATTCTTTAATTAGTGGATGTGGCT -s Anc0.Anc0refChr9 3822 30 - 35212 ATCTTAATTTTTTGGTTATTGGGTTCAGCT -s Anc1.Anc1refChr0 4105 30 + 16026 ATCTTAATTTTTTGGTTATTGGGTTCAGCT -s Anc2.Anc2refChr0 4058 30 + 56053 ACCTTAATTTTTTTGTTATTGGGTTCAGCT -s mr.mrrefChr0 4495 30 + 130230 ATCTAAATTTTTTGATTAGTGGATGCAGCT -s simCow_chr6.simCow.chr6 4454 21 + 602619 ---------TATTTGTCATTGGGTTCACCT -s simDog_chr6.simDog.chr6 4461 30 + 593897 ACCTTAATTTTTTTGTTATTGAGTTCAGCT -s simHuman_chr6.simHuman.chr6 4086 30 + 601863 GTCTTAATTTTTTGGTTGCTGGGTTCAATT -s simRat_chr6.simRat.chr6 642149 30 - 647215 ATCTAAATTTTTTGATTAGTGGATACAGCT - -a -s simMouse_chr6.simMouse.chr6 4754 10 + 636262 GGTTGCACCA -s Anc0.Anc0refChr9 3852 10 - 35212 GATTGTGGCA -s Anc1.Anc1refChr0 4135 10 + 16026 GATTGTGGCA -s Anc2.Anc2refChr0 4092 10 + 56053 GATTGTGGCA -s mr.mrrefChr0 4525 10 + 130230 GGTTGCACCA -s simCow_chr6.simCow.chr6 4479 10 + 602619 GACTGTGGCA -s simDog_chr6.simDog.chr6 4495 10 + 593897 GATTGCGGCA -s simHuman_chr6.simHuman.chr6 4116 10 + 601863 GATTGTGGCA -s simRat_chr6.simRat.chr6 642179 10 - 647215 GGTTGCTCCA - -a -s simMouse_chr6.simMouse.chr6 4764 15 + 636262 TCAACACAGACAGCA -s Anc0.Anc0refChr9 3862 15 - 35212 TCAACATGGAAGATA -s Anc1.Anc1refChr0 4145 15 + 16026 TCAACATGGAAGATA -s Anc2.Anc2refChr0 4102 15 + 56053 TCAACATGGAAGATA -s mr.mrrefChr0 4535 15 + 130230 TCAACACAGACGGCA -s simCow_chr6.simCow.chr6 4489 15 + 602619 CCAGCATGGAATAAA -s simDog_chr6.simDog.chr6 4511 15 + 593897 TCAAGATGTAAGATA -s simHuman_chr6.simHuman.chr6 4126 15 + 601863 TCAACATGGAAGATA -s simRat_chr6.simRat.chr6 642189 15 - 647215 TCAGCACAGATGGCA - -a -s simMouse_chr6.simMouse.chr6 4779 3 + 636262 GCA -s Anc0.Anc0refChr9 3877 3 - 35212 GCA -s Anc1.Anc1refChr0 4160 3 + 16026 GCA -s Anc2.Anc2refChr0 4117 3 + 56053 GCA -s mr.mrrefChr0 4550 3 + 130230 GCA -s simCow_chr6.simCow.chr6 4504 3 + 602619 GCA -s simDog_chr6.simDog.chr6 4531 3 + 593897 ACA -s simHuman_chr6.simHuman.chr6 4141 3 + 601863 GCA -s simRat_chr6.simRat.chr6 642204 3 - 647215 GCA - -a -s simMouse_chr6.simMouse.chr6 4782 16 + 636262 TCACTACTTGTGATTG -s Anc0.Anc0refChr9 3883 16 - 35212 GCTTTACTTGTGATTG -s Anc1.Anc1refChr0 4166 16 + 16026 GCTTTACTTGTGATTG -s Anc2.Anc2refChr0 4123 16 + 56053 GCTTTACTTGTGATTG -s mr.mrrefChr0 4553 16 + 130230 GCATTACTTGTGATTG -s simCow_chr6.simCow.chr6 4510 16 + 602619 GCTTTACCTGTGATTG -s simDog_chr6.simDog.chr6 4537 16 + 593897 GCTCTACTTGTGATTG -s simHuman_chr6.simHuman.chr6 4147 16 + 601863 GCTTCACTTGTGATTG -s simRat_chr6.simRat.chr6 642207 16 - 647215 GCATTACTTGTGATTG - -a -s simMouse_chr6.simMouse.chr6 4798 61 + 636262 CATCAATATTGGGCAATCCCGCTGCAGACCTTGTTGCAGCCTTTTGTGGAAAGTGCTGTGG -s Anc0.Anc0refChr9 3900 61 - 35212 CACCAATACTGGGCAACCCCACTGCAGACCTTGTTGTGGTCTTTTCTGGAAACTGAAGTTG -s Anc1.Anc1refChr0 4183 61 + 16026 CACCAATACTGGGCAACCCCACTGCAGACCTTGTTGTGGTCTTTTCTGGAAACTGAAGTTG -s Anc2.Anc2refChr0 4140 61 + 56053 CACCAATACTGTGCAACTGCACAGCAAACCTTGTTGTGGTCTTTTCAGGAAACTGAAGTTG -s mr.mrrefChr0 4569 61 + 130230 CATCAATATTGGGCAATCCCACTGCAGACCTTGTTGCAGCCTTTTGTGGAAAGTGCTGTGG -s simCow_chr6.simCow.chr6 4527 61 + 602619 CACCAATGCTGTGCAACTGTACCGCGAACCTTGTTGTTGTCTTTTCAGGAAACCGAATGTG -s simDog_chr6.simDog.chr6 4554 61 + 593897 GACCAATACTATGCAAGTGCACAGAAAAACTTGTTGTGGTCTTTTCAGGAAACTGGAGTTG -s simHuman_chr6.simHuman.chr6 4164 61 + 601863 CGCCAATACTGGGGAACCCCACTGCAGACTTTGTTGTGGTCTTTCCTGTAAACTGAAGTAG -s simRat_chr6.simRat.chr6 642223 60 - 647215 CATCAATATTGGGCAATGCCACTGCAGACCTTATTGCAGCTTATTA-GGAAAGTGCTGTGG - -a -s simMouse_chr6.simMouse.chr6 4859 20 + 636262 ATGGCAGCAGCCTCCATGGG -s Anc0.Anc0refChr9 3961 20 - 35212 ATGGTGGCAAGCTCCATAGG -s Anc1.Anc1refChr0 4244 20 + 16026 ATGGTGGCAAGCTCCATAGG -s Anc2.Anc2refChr0 4201 20 + 56053 ATGGTGGCAAGTTCCATAGG -s mr.mrrefChr0 4630 20 + 130230 ATGGTGGCAGCCTCCATGGG -s simCow_chr6.simCow.chr6 4614 20 + 602619 ACGGTGATAGGTTCCATCGG -s simDog_chr6.simDog.chr6 4615 20 + 593897 ATGGTGGCAAATTCCATAGG -s simHuman_chr6.simHuman.chr6 4225 18 + 601863 ATGGTGGCAAGCTCCATA-- -s simRat_chr6.simRat.chr6 642283 20 - 647215 ACAGTGGCAGCTTCCATGGG - -a -s simMouse_chr6.simMouse.chr6 4879 26 + 636262 GTGATACCCAATGCCAGCGGCAACCA -s Anc0.Anc0refChr9 3981 26 - 35212 ATGAGACCTGATGCCACAGGCATCCT -s Anc1.Anc1refChr0 4264 26 + 16026 ATGAGACCTGATGCCACAGGCATCCT -s Anc2.Anc2refChr0 4224 26 + 56053 ATGAGACCTGATGCCACAGGCATCCT -s mr.mrrefChr0 4650 26 + 130230 GTGATACCCAATGCCAGCGGCAACCA -s simCow_chr6.simCow.chr6 4637 26 + 602619 GTGAATCTTGACACCACTGGCCTCCA -s simDog_chr6.simDog.chr6 4638 26 + 593897 ATGAGACCTGATGCCACAGGCATCCT -s simRat_chr6.simRat.chr6 642303 26 - 647215 GTGATACCCGATGCCAGTGGCAACTG - -a -s simMouse_chr6.simMouse.chr6 4905 31 + 636262 CTGTGCTGCAACTCTCGAAAGTATGAGAGAT -s Anc0.Anc0refChr9 4007 30 - 35212 TTGCGCCA-AACTCTTGTAAATGTGAGAAAT -s Anc1.Anc1refChr0 4290 30 + 16026 TTGCGCCA-AACTCTTGTAAATGTGAGAAAT -s Anc2.Anc2refChr0 4250 30 + 56053 TTGCGCCA-AACTCTTGTAAATGTGTGAAAT -s mr.mrrefChr0 4676 31 + 130230 CTGTGCTGCAACTCTTGAAAGTATGAGAGAT -s simCow_chr6.simCow.chr6 4663 30 + 602619 CTGTGCCA-AACTCTTGTAAATGTGTGTAAT -s simDog_chr6.simDog.chr6 4664 30 + 593897 TTGCGCCA-AACTCTTGTAAAGGCGTAAAAT -s simHuman_chr6.simHuman.chr6 4243 17 + 601863 --------------TTGTAAATGTGAGAAAT -s simRat_chr6.simRat.chr6 642397 31 - 647215 CTATGGTGCAGCTCTTGAAAGTATAAGAGAT - -a -s simMouse_chr6.simMouse.chr6 4936 25 + 636262 GAGCTACAGACAGTACACAGCAACC -s Anc0.Anc0refChr9 4040 25 - 35212 GACCCAAAGGGTCTACACAGTAGTC -s Anc1.Anc1refChr0 4323 25 + 16026 GACCCAAAGGGTCTACACAGTAGTC -s Anc2.Anc2refChr0 4288 25 + 56053 GGCACAAAGGGTCTACGCAGTGGTC -s mr.mrrefChr0 4707 25 + 130230 GAGCTACAGAGAGTACACAGTAGCC -s simCow_chr6.simCow.chr6 4701 25 + 602619 GCCACAAAGGGTCTGTGCAGAGGTC -s simDog_chr6.simDog.chr6 4702 25 + 593897 GGCACAAAGGGTCTACGCAGTGGTC -s simHuman_chr6.simHuman.chr6 4263 25 + 601863 GATCCAAAGGGTCTACACAGTAGTC -s simRat_chr6.simRat.chr6 642428 25 - 647215 GGGCTGCACAGGGTACGCAGTAGCC - -a -s simMouse_chr6.simMouse.chr6 4961 9 + 636262 AGCGGGGTA -s Anc0.Anc0refChr9 4073 9 - 35212 AGGAAGGTA -s Anc1.Anc1refChr0 4356 9 + 16026 AGGAAGGTA -s Anc2.Anc2refChr0 4321 9 + 56053 AGGAAGATA -s mr.mrrefChr0 4732 9 + 130230 AGGGAGGTA -s simCow_chr6.simCow.chr6 4734 9 + 602619 AGGAAGCTA -s simDog_chr6.simDog.chr6 4735 9 + 593897 AGGAACATA -s simHuman_chr6.simHuman.chr6 4296 9 + 601863 AGGAAGGTA -s simRat_chr6.simRat.chr6 642453 9 - 647215 AGGTAGGTA - -a -s simMouse_chr6.simMouse.chr6 4970 2 + 636262 TT -s Anc0.Anc0refChr9 4082 2 - 35212 TT -s Anc1.Anc1refChr0 4365 2 + 16026 TT -s Anc2.Anc2refChr0 4330 2 + 56053 TT -s mr.mrrefChr0 4741 2 + 130230 TT -s simCow_chr6.simCow.chr6 4743 2 + 602619 TT -s simDog_chr6.simDog.chr6 4754 2 + 593897 TT -s simHuman_chr6.simHuman.chr6 4305 2 + 601863 TT -s simRat_chr6.simRat.chr6 642462 2 - 647215 TT - -a -s simMouse_chr6.simMouse.chr6 4972 2 + 636262 TT -s Anc0.Anc0refChr9 4084 2 - 35212 TA -s Anc1.Anc1refChr0 4367 2 + 16026 TA -s Anc2.Anc2refChr0 4332 2 + 56053 TA -s mr.mrrefChr0 4743 2 + 130230 TT -s simCow_chr6.simCow.chr6 4746 2 + 602619 CA -s simDog_chr6.simDog.chr6 4756 2 + 593897 TA -s simHuman_chr6.simHuman.chr6 4307 2 + 601863 TG -s simRat_chr6.simRat.chr6 642464 2 - 647215 TT - -a -s simMouse_chr6.simMouse.chr6 4974 23 + 636262 ACCAGTATAGTAGGATCCTGCTA -s Anc0.Anc0refChr9 4090 23 - 35212 ACCAATGTATGAGTATCTTCCTA -s Anc1.Anc1refChr0 4373 23 + 16026 ACCAATGTATGAGTATCTTCCTA -s Anc2.Anc2refChr0 4338 23 + 56053 ACCAATATATGAGTATCTTCCTA -s mr.mrrefChr0 4745 23 + 130230 ACCAATGTAGTAGGATCTTGCTA -s simCow_chr6.simCow.chr6 4752 23 + 602619 ACCAACATCTAAGTATCTTCTTA -s simDog_chr6.simDog.chr6 4762 23 + 593897 ACCAATACATGAGTATATTCCTA -s simHuman_chr6.simHuman.chr6 4313 23 + 601863 ACCAATGTATGAGTATCTCACTA -s simRat_chr6.simRat.chr6 642466 23 - 647215 ACCAATGTAGTAGGATCTTCCTA - -a -s simMouse_chr6.simMouse.chr6 4997 5 + 636262 ACATG -s Anc0.Anc0refChr9 4113 5 - 35212 TCATG -s Anc1.Anc1refChr0 4396 5 + 16026 TCATG -s Anc2.Anc2refChr0 4361 5 + 56053 TCATG -s mr.mrrefChr0 4768 5 + 130230 ACATG -s simCow_chr6.simCow.chr6 4775 5 + 602619 TCAGG -s simDog_chr6.simDog.chr6 4785 5 + 593897 TCATG -s simHuman_chr6.simHuman.chr6 4338 5 + 601863 CCGTG -s simRat_chr6.simRat.chr6 642489 5 - 647215 AGATG - -a -s simMouse_chr6.simMouse.chr6 5002 6 + 636262 GGATTG -s Anc0.Anc0refChr9 4118 6 - 35212 GGATTG -s Anc1.Anc1refChr0 4401 6 + 16026 GGATTG -s Anc2.Anc2refChr0 4370 6 + 56053 GGGTTG -s mr.mrrefChr0 4773 6 + 130230 GGATTG -s simCow_chr6.simCow.chr6 4784 6 + 602619 GGGTTG -s simDog_chr6.simDog.chr6 4794 6 + 593897 GGGTTG -s simHuman_chr6.simHuman.chr6 4343 6 + 601863 GGATGG -s simRat_chr6.simRat.chr6 642494 6 - 647215 GGATTG - -a -s simMouse_chr6.simMouse.chr6 5008 5 + 636262 CTAAG -s Anc0.Anc0refChr9 4124 2 - 35212 CC--- -s Anc1.Anc1refChr0 4407 2 + 16026 CC--- -s Anc2.Anc2refChr0 4376 2 + 56053 TC--- -s mr.mrrefChr0 4779 5 + 130230 CTAAG -s simCow_chr6.simCow.chr6 4791 2 + 602619 TC--- -s simDog_chr6.simDog.chr6 4800 2 + 593897 TT--- -s simHuman_chr6.simHuman.chr6 4349 2 + 601863 CC--- -s simRat_chr6.simRat.chr6 642500 5 - 647215 TTAAG - -a -s simMouse_chr6.simMouse.chr6 5013 18 + 636262 GATATGCTGTACTGAGAA -s Anc0.Anc0refChr9 4126 12 - 35212 ------GTGTATTGAGAA -s Anc1.Anc1refChr0 4409 12 + 16026 ------GTGTATTGAGAA -s Anc2.Anc2refChr0 4378 12 + 56053 ------GTGTATTGAGAA -s mr.mrrefChr0 4784 18 + 130230 GATATGCTGTACTGAGAA -s simCow_chr6.simCow.chr6 4793 12 + 602619 ------GTGTATGGAGAA -s simDog_chr6.simDog.chr6 4802 12 + 593897 ------GTGTATTGAGGA -s simHuman_chr6.simHuman.chr6 4351 12 + 601863 ------GTGTATCAAGAA -s simRat_chr6.simRat.chr6 642515 18 - 647215 GTTATACTGTACTGAGAA - -a -s simMouse_chr6.simMouse.chr6 5031 5 + 636262 GAGGA -s Anc0.Anc0refChr9 4143 5 - 35212 AAGGG -s Anc1.Anc1refChr0 4426 5 + 16026 AAGGG -s Anc2.Anc2refChr0 4395 5 + 56053 AAGGG -s mr.mrrefChr0 4807 5 + 130230 GAGGA -s simCow_chr6.simCow.chr6 4810 5 + 602619 AAGAG -s simDog_chr6.simDog.chr6 4825 5 + 593897 GAGGG -s simHuman_chr6.simHuman.chr6 4368 5 + 601863 AAGGG -s simRat_chr6.simRat.chr6 642538 5 - 647215 GAGGA - -a -s simMouse_chr6.simMouse.chr6 5036 28 + 636262 ACATATAGATTCAACCAGTGACCACAAA -s Anc0.Anc0refChr9 4148 28 - 35212 ACATATAAATTCAACTAGCAATCACAAG -s Anc1.Anc1refChr0 4431 28 + 16026 ACATATAAATTCAACTAGCAATCACAAG -s Anc2.Anc2refChr0 4400 28 + 56053 ACATATAAATTCAACTAGCAATCACAAG -s mr.mrrefChr0 4812 28 + 130230 ACATATAGATTCAACTAGTGATCACAAG -s simCow_chr6.simCow.chr6 4815 28 + 602619 ACATATAGATTAAACTAATAATCACAAG -s simDog_chr6.simDog.chr6 4830 27 + 593897 ACATACGAGTTCAACTAGCAAACTCAA- -s simHuman_chr6.simHuman.chr6 4374 28 + 601863 ATGCATAAATTCAACTAGCAATAACAAG -s simRat_chr6.simRat.chr6 642543 28 - 647215 ACATATAGATTCAACTAGGGATCACAAG - -a -s simMouse_chr6.simMouse.chr6 5064 3 + 636262 AAA -s Anc0.Anc0refChr9 4176 3 - 35212 TAA -s Anc1.Anc1refChr0 4459 3 + 16026 TAA -s Anc2.Anc2refChr0 4428 3 + 56053 TAA -s mr.mrrefChr0 4840 3 + 130230 AAA -s simCow_chr6.simCow.chr6 4858 3 + 602619 GAA -s simDog_chr6.simDog.chr6 4857 3 + 593897 TAA -s simHuman_chr6.simHuman.chr6 4402 3 + 601863 CAA -s simRat_chr6.simRat.chr6 642571 3 - 647215 AAA - -a -s simMouse_chr6.simMouse.chr6 5067 35 + 636262 AAAGAATTTATGGTGAATAGCTATAGGGCTATATT -s Anc0.Anc0refChr9 4224 35 - 35212 AAAGCATTAATGGTGAATTGTGATAGGACTATACT -s Anc1.Anc1refChr0 4507 35 + 16026 AAAGCATTAATGGTGAATTGTGATAGGACTATACT -s Anc2.Anc2refChr0 4476 35 + 56053 AAAGCATTAATGGTGAATTGTGATAGTACTATACT -s mr.mrrefChr0 4843 35 + 130230 AAAGCATTTATGGTGAATTGTTATAGGGCTATATT -s simCow_chr6.simCow.chr6 4907 35 + 602619 AAAGCATTAGTGTTGAAGTGTGATGGTACTATGCT -s simDog_chr6.simDog.chr6 4894 31 + 593897 AAAGG----ATGGGGAATTGTGATAATCTTACACT -s simHuman_chr6.simHuman.chr6 4450 35 + 601863 AAAGCATTAATGGTTAACTGTGATAGGACTATACT -s simRat_chr6.simRat.chr6 642574 35 - 647215 AAAACATTTATGGTGAATTGTTATAGGGCTATATT - -a -s simMouse_chr6.simMouse.chr6 5102 7 + 636262 TGATGAC -s Anc0.Anc0refChr9 4267 7 - 35212 TCATGAC -s Anc1.Anc1refChr0 4550 7 + 16026 TCATGAC -s Anc2.Anc2refChr0 4519 7 + 56053 TCCATAC -s mr.mrrefChr0 4878 7 + 130230 TGATGAC -s simCow_chr6.simCow.chr6 4969 7 + 602619 ACTATAC -s simDog_chr6.simDog.chr6 4933 6 + 593897 T-CATGA -s simHuman_chr6.simHuman.chr6 4493 7 + 601863 TCATGAC -s simRat_chr6.simRat.chr6 642609 7 - 647215 TGAGGAC - -a -s simMouse_chr6.simMouse.chr6 5109 10 + 636262 AATATAGTAT -s Anc0.Anc0refChr9 4275 10 - 35212 AATATAGTAT -s Anc1.Anc1refChr0 4558 10 + 16026 AATATAGTAT -s Anc2.Anc2refChr0 4527 10 + 56053 AATATAGTAT -s mr.mrrefChr0 4885 10 + 130230 AATATAGTAT -s simCow_chr6.simCow.chr6 4977 10 + 602619 CAAATAGTAG -s simDog_chr6.simDog.chr6 4940 10 + 593897 AATATAGTGT -s simHuman_chr6.simHuman.chr6 4501 10 + 601863 TATATAGTAT -s simRat_chr6.simRat.chr6 642616 10 - 647215 AATATAGTAT - -a -s simMouse_chr6.simMouse.chr6 5119 16 + 636262 AAGCTGTTAAAATGGA -s Anc0.Anc0refChr9 4287 16 - 35212 AAGCTGCTAAAATGGA -s Anc1.Anc1refChr0 4570 16 + 16026 AAGCTGCTAAAATGGA -s Anc2.Anc2refChr0 4539 16 + 56053 AAGCTACTAAAATGGA -s mr.mrrefChr0 4895 16 + 130230 AAGCTGTTAAAATGGA -s simCow_chr6.simCow.chr6 4989 16 + 602619 AAGCTACTAAAAAGGA -s simDog_chr6.simDog.chr6 4952 13 + 593897 AAGCC---AAAATGGA -s simHuman_chr6.simHuman.chr6 4513 16 + 601863 AAGCTGCGAAAATGGA -s simRat_chr6.simRat.chr6 642626 16 - 647215 AAGCTGTTGAAATGGA - -a -s simMouse_chr6.simMouse.chr6 5135 47 + 636262 CATCATAATATGCAAGGCTTCTTTAATGTATATAACAACAGAGTACA -s Anc0.Anc0refChr9 4314 45 - 35212 CAGCATATTATGG-AGGCTACTTTATTTCATATAACAGCAGTATAC- -s Anc1.Anc1refChr0 4597 45 + 16026 CAGCATATTATGG-AGGCTACTTTATTTCATATAACAGCAGTATAC- -s Anc2.Anc2refChr0 4566 45 + 56053 CAGCATTTTATGG-AGGCTACTTTATTTCATATAACAGCAGTATAC- -s mr.mrrefChr0 4922 45 + 130230 CAGCATAATATGC-AGGCTTCTTTAATGTATATAACAACAGAGTAC- -s simCow_chr6.simCow.chr6 5016 41 + 602619 C----TAATATAG-AGGCTACTTTATTTTATATAGCAGCAGTGTAC- -s simDog_chr6.simDog.chr6 4976 45 + 593897 CAGCATTTTATGG-AGGCTACTGTATTTCATATAACAGCAGTATAC- -s simHuman_chr6.simHuman.chr6 4540 20 + 601863 CACTGCATAATCA-AACTT-------------------------AC- -s simRat_chr6.simRat.chr6 642653 45 - 647215 CAGCGTAATATGC-AGGCTTCTTAAATGTATTTAACAACAGAGTAC- - -a -s simMouse_chr6.simMouse.chr6 5182 7 + 636262 CATGGTT -s Anc0.Anc0refChr9 4359 7 - 35212 CATGGTT -s Anc1.Anc1refChr0 4642 7 + 16026 CATGGTT -s Anc2.Anc2refChr0 4612 7 + 56053 CATAGTT -s mr.mrrefChr0 4967 7 + 130230 CATGGTT -s simCow_chr6.simCow.chr6 5058 7 + 602619 AATATTT -s simDog_chr6.simDog.chr6 5022 7 + 593897 CATAGTT -s simHuman_chr6.simHuman.chr6 4560 7 + 601863 CTTGGTT -s simRat_chr6.simRat.chr6 642698 7 - 647215 CATGGTT - -a -s simMouse_chr6.simMouse.chr6 5189 7 + 636262 AGACTTG -s Anc0.Anc0refChr9 4366 7 - 35212 AGACTTA -s Anc1.Anc1refChr0 4649 7 + 16026 AGACTTA -s Anc2.Anc2refChr0 4619 7 + 56053 AGGTCTA -s mr.mrrefChr0 4974 7 + 130230 AGACTTA -s simCow_chr6.simCow.chr6 5065 7 + 602619 AGGTCTA -s simDog_chr6.simDog.chr6 5029 7 + 593897 AGGTCTA -s simHuman_chr6.simHuman.chr6 4570 7 + 601863 AGACTTA -s simRat_chr6.simRat.chr6 642705 7 - 647215 AGATTTA - -a -s simMouse_chr6.simMouse.chr6 5196 6 + 636262 GCACAG -s Anc0.Anc0refChr9 4373 6 - 35212 GCACAG -s Anc1.Anc1refChr0 4656 6 + 16026 GCACAG -s Anc2.Anc2refChr0 4626 6 + 56053 GCACAG -s mr.mrrefChr0 4981 6 + 130230 GCACAG -s simCow_chr6.simCow.chr6 5072 6 + 602619 GCACGG -s simDog_chr6.simDog.chr6 5036 6 + 593897 GCAGAG -s simHuman_chr6.simHuman.chr6 4588 6 + 601863 GCACTA -s simRat_chr6.simRat.chr6 642712 6 - 647215 GCACGG - -a -s simMouse_chr6.simMouse.chr6 5202 72 + 636262 AATGGATAATTCAGACAGTATGGATAATTCAGAGAGCTACCTTGAACCTTGAAATATGAGTAGTGGGAAGGA -s Anc0.Anc0refChr9 4379 27 - 35212 ATAGGATAATCCAGAC---------------------------------------------AGTGAGTTGGG -s Anc1.Anc1refChr0 4662 27 + 16026 ATAGGATAATCCAGAC---------------------------------------------AGTGAGTTGGG -s Anc2.Anc2refChr0 4638 27 + 56053 AGATAGTAGTCCATCC---------------------------------------------AGTTAGTTGGG -s mr.mrrefChr0 4987 72 + 130230 AATGGATAATTCAGACAGTATGGATAATTCAGAGAGCTACCTTGAACCTTGAAATATGAGTAGTGGGAAGGA -s simCow_chr6.simCow.chr6 5084 26 + 602619 GGACAGTGGGCAATGT---------------------------------------------A-TTAGGTGGG -s simDog_chr6.simDog.chr6 5048 27 + 593897 AGATAGCAGTCCATCC---------------------------------------------AGTTAGTTGGG -s simHuman_chr6.simHuman.chr6 4594 27 + 601863 ATAGGATAATATAGAC---------------------------------------------AGTGAGTTGGG -s simRat_chr6.simRat.chr6 642718 72 - 647215 TATAGATAATTCAGACAGTATTGATAATTCAGAGAACTACCTTGTATCTTGAAATAGGATTAGTAGGAGAGA - -a -s simMouse_chr6.simMouse.chr6 5274 21 + 636262 AAGGTTCAAGAAAAGTACCTA -s Anc0.Anc0refChr9 4406 21 - 35212 ACTGTCTAAGAAAACTTTATA -s Anc1.Anc1refChr0 4689 21 + 16026 ACTGTCTAAGAAAACTTTATA -s Anc2.Anc2refChr0 4676 21 + 56053 ACTGGCTAAGGAAACTTTATA -s mr.mrrefChr0 5059 21 + 130230 AAGGTTCAAGAAAAGTACCTA -s simCow_chr6.simCow.chr6 5121 21 + 602619 ACTGGTTACAGAAACTGTATA -s simDog_chr6.simDog.chr6 5086 21 + 593897 ACTTGCTAAGGAGACTTCATA -s simHuman_chr6.simHuman.chr6 4621 21 + 601863 ACTGTCTAAGAAACCTTTGTA -s simRat_chr6.simRat.chr6 642790 17 - 647215 AAAT----AAAAAAGTACCTA - -a -s simMouse_chr6.simMouse.chr6 5295 5 + 636262 GCTCA -s Anc0.Anc0refChr9 4430 5 - 35212 TTGTA -s Anc1.Anc1refChr0 4713 5 + 16026 TTGTA -s Anc2.Anc2refChr0 4700 5 + 56053 TTGTA -s mr.mrrefChr0 5080 5 + 130230 TTTCA -s simCow_chr6.simCow.chr6 5145 5 + 602619 TTGTA -s simDog_chr6.simDog.chr6 5110 5 + 593897 TTATG -s simHuman_chr6.simHuman.chr6 4645 5 + 601863 TTGTA -s simRat_chr6.simRat.chr6 642807 5 - 647215 TTTCA - -a -s simMouse_chr6.simMouse.chr6 5300 28 + 636262 TGAATCTGTCTCATGATATGCTATGTTT -s Anc0.Anc0refChr9 4435 26 - 35212 TGTTTTTGTGTTATAATA--CTGTCCTT -s Anc1.Anc1refChr0 4718 26 + 16026 TGTTTTTGTGTTATAATA--CTGTCCTT -s Anc2.Anc2refChr0 4775 26 + 56053 TTTTTTTGTGTTATAATG--CTGTCCTT -s mr.mrrefChr0 5085 28 + 130230 TGAATCTGTCTTATGATATGCTATGTTT -s simCow_chr6.simCow.chr6 5222 21 + 602619 ----TATGT-TTATTATC--CTATCCTT -s simDog_chr6.simDog.chr6 5206 26 + 593897 TTTTTTTGAGTTATAATG--CTGTCCTT -s simHuman_chr6.simHuman.chr6 4650 26 + 601863 TGCTTTTGTGTTATAATA--CTGTCCTC -s simRat_chr6.simRat.chr6 642812 28 - 647215 TGGATCTGTCTTGTGGTATGCTATGTTT - -a -s simMouse_chr6.simMouse.chr6 5328 22 + 636262 TGCTTAACATCACCTTGAGGGG -s Anc0.Anc0refChr9 4461 22 - 35212 TGATTAACATCCCTTTGGGGGG -s Anc1.Anc1refChr0 4744 22 + 16026 TGATTAACATCCCTTTGGGGGG -s Anc2.Anc2refChr0 4805 22 + 56053 TGATTAACATCCCTTTGGTGGG -s mr.mrrefChr0 5113 22 + 130230 TGCTTAACATCACCTTGAGGGG -s simCow_chr6.simCow.chr6 5247 20 + 602619 TGATTAAC--TCCTTTGGCGGG -s simDog_chr6.simDog.chr6 5236 22 + 593897 TGATTAACATCCCCTTGGTGGG -s simHuman_chr6.simHuman.chr6 4676 22 + 601863 TGAATAACATCCCTTTGGGGGG -s simRat_chr6.simRat.chr6 642840 10 - 647215 TGCTTAACAT------------ - -a -s simMouse_chr6.simMouse.chr6 5350 128 + 636262 TGGGGCCCTGGCAGCTGTTAAAATCTGATAATTCTAGCAAGACAAATGATAAACAAAAGCAGTGCCTAACATATTCATTTAGTTGGAGTTACGTTTTAATGAGATGTTGAGACCATTTCTAGTGTAGA -s Anc0.Anc0refChr9 4485 70 - 35212 TGGGCCTTTAGCAGCTAGTAGACTCTGATCAGTCAAGCAAG----------------------------------------------------------AGAGATGATGATGTCTTTTCCAGAGTTGG -s Anc1.Anc1refChr0 4768 70 + 16026 TGGGCCTTTAGCAGCTAGTAGACTCTGATCAGTCAAGCAAG----------------------------------------------------------AGAGATGATGATGTCTTTTCCAGAGTTGG -s Anc2.Anc2refChr0 4829 70 + 56053 TGGACCTTGAGCATTTAGTAGACTCTGACCAGGCAAGCAAG----------------------------------------------------------AGAGATCATGATGTCTTTTCCAGAGTTGG -s mr.mrrefChr0 5135 70 + 130230 TGGGGCCCTGGCAGCTGTTAAAATCTGATAATTCTAGCAAG----------------------------------------------------------TGAGATGTTGAGACCATTTCTAGTGTAGA -s simCow_chr6.simCow.chr6 5269 67 + 602619 TG---CCTCAGCGTTCAGTGGACTCTGACCAGCCAGGCAAT----------------------------------------------------------AGAGATCATGATGTCGTTTCCAGGGTTGG -s simDog_chr6.simDog.chr6 5274 70 + 593897 TAGACTTTGAGCATTTAGTAGACTTTGACCAAGCAAGCTAG----------------------------------------------------------AGAGGTCATGATGTTTTTTCTGTAGTAGG -s simHuman_chr6.simHuman.chr6 4700 70 + 601863 TGGGTCTTTAGCAGCTAGTTGATTCTGATCAGTCAAGAAAG----------------------------------------------------------CAAGAAGATGATGTCTTTTCCAGAGTTGG - -a -s simMouse_chr6.simMouse.chr6 5478 6 + 636262 TTTAAC -s Anc0.Anc0refChr9 4560 6 - 35212 TCTAAC -s Anc1.Anc1refChr0 4843 6 + 16026 TCTAAC -s Anc2.Anc2refChr0 4904 6 + 56053 TCTAAC -s mr.mrrefChr0 5205 6 + 130230 TTTAAC -s simCow_chr6.simCow.chr6 5341 6 + 602619 TCTACT -s simDog_chr6.simDog.chr6 5349 6 + 593897 TCTAAC -s simHuman_chr6.simHuman.chr6 4775 6 + 601863 CCTAAC - -a -s simMouse_chr6.simMouse.chr6 5484 37 + 636262 AGGAAATTTCAGTATTTTTTAAGAGTTGAGCAGGACT -s Anc0.Anc0refChr9 4566 37 - 35212 ATGGAATTCCAGTATCCTTTGAGGATTGACCAGCCCT -s Anc1.Anc1refChr0 4849 37 + 16026 ATGGAATTCCAGTATCCTTTGAGGATTGACCAGCCCT -s Anc2.Anc2refChr0 4910 37 + 56053 ATGGAATTCCAGTCGCCTTTGAGGAATGACCAGCCCT -s mr.mrrefChr0 5211 37 + 130230 AGGAAATTTCAGTATTTTTTAAGAGTTGAGCAGGACT -s simCow_chr6.simCow.chr6 5349 36 + 602619 TTCAAATTCCAGTTCCCTTTGATGACTGACCAGCTC- -s simDog_chr6.simDog.chr6 5355 37 + 593897 ATGGGATTCCAGCCGCATTTTAGGAATGACCAGCCCT -s simHuman_chr6.simHuman.chr6 4781 37 + 601863 ATGGAACTCCAGTATCCTTTGAGGATTGACGAGCCCT - -a -s simMouse_chr6.simMouse.chr6 5521 26 + 636262 TCACACCACTGAACACTTATCATGAG -s Anc0.Anc0refChr9 4640 26 - 35212 TCTTACCATTCAACAGTTATTAGGGG -s Anc1.Anc1refChr0 4923 26 + 16026 TCTTACCATTCAACAGTTATTAGGGG -s Anc2.Anc2refChr0 4984 26 + 56053 TCTTACCGTTCAACAGTCAATAGAGG -s mr.mrrefChr0 5248 26 + 130230 TCACACCACTGAACACTTATCATGAG -s simCow_chr6.simCow.chr6 5420 26 + 602619 TGTTACCCTTTAACAGTAAGTAGAGG -s simDog_chr6.simDog.chr6 5425 26 + 593897 TCTTACTGTTCAACAGTCAACAGAAG -s simHuman_chr6.simHuman.chr6 4859 26 + 601863 TCTTGTCATTCAAGAGTTATTAGGGG - -a -s simMouse_chr6.simMouse.chr6 5547 69 + 636262 ATACTCATAAGAGCATGTAGAGTAAAATTCAGCACAGGACTAGATAAGTTGGCTGCAGGCTATGCCTTT -s Anc0.Anc0refChr9 4666 48 - 35212 CT--TAATGCCAGTATGTAGACTAAGAGT-AGCACAGGA------------------GGCTACACTTTT -s Anc1.Anc1refChr0 4949 56 + 16026 CT--TAATGCCAGTATGTAGACTAAGAGTTAGCACAGGACTAGAT-----------AGGCTACACTTTT -s Anc2.Anc2refChr0 5015 48 + 56053 CT--TAATGCCAGTATGTAGGCTAAGAGT-AATACTGAA------------------GGCTACACTTGT -s mr.mrrefChr0 5274 56 + 130230 AT--TCATAAGAGCATGTAGAGTAAAATTCAGCACAGGACTAGAT-----------AGGCTATGCCTTT -s simCow_chr6.simCow.chr6 5451 38 + 602619 CT--TGATGCCACC----------AGAGT-AATATTAAA------------------GGCTACACTTGT -s simDog_chr6.simDog.chr6 5456 48 + 593897 CT--TAATTCCAGTATGTAGGCTAAGAGT-AATACTGAA------------------GGCTGCACTTGT -s simHuman_chr6.simHuman.chr6 4885 56 + 601863 CT--TTATGCCATTATGTAGACTAAGAGTTAGCACAGGATGAGAT-----------AGGCTACACTTTG - -a -s simMouse_chr6.simMouse.chr6 5616 11 + 636262 GTCACTAGAAA -s Anc0.Anc0refChr9 4714 11 - 35212 GTCATAAAAAA -s Anc1.Anc1refChr0 5005 11 + 16026 GTCATAAAAAA -s Anc2.Anc2refChr0 5063 11 + 56053 GCCATAAAAAA -s mr.mrrefChr0 5330 11 + 130230 GTCACTAGAAA -s simCow_chr6.simCow.chr6 5489 11 + 602619 ACCATTAAAAA -s simDog_chr6.simDog.chr6 5504 11 + 593897 GCCATAAAGAA -s simHuman_chr6.simHuman.chr6 4942 11 + 601863 GTCTGCAAAAA - -a -s simMouse_chr6.simMouse.chr6 5627 11 + 636262 TGCACACCACG -s Anc0.Anc0refChr9 4725 11 - 35212 TGCACACCACA -s Anc1.Anc1refChr0 5016 11 + 16026 TGCACACCACA -s Anc2.Anc2refChr0 5074 11 + 56053 TGCACACCACA -s mr.mrrefChr0 5341 11 + 130230 TGCACACCACG -s simCow_chr6.simCow.chr6 5533 11 + 602619 TGCTCACCAGA -s simDog_chr6.simDog.chr6 5515 11 + 593897 TGCACACCACA -s simHuman_chr6.simHuman.chr6 4953 11 + 601863 TGCACACCACA - -a -s simMouse_chr6.simMouse.chr6 5638 18 + 636262 TTTCTAATTTGAATCAAC -s Anc0.Anc0refChr9 4736 17 - 35212 TATCTAGTTTGAA-GAAC -s Anc1.Anc1refChr0 5027 18 + 16026 TATCTAGTTTGAACGAAC -s Anc2.Anc2refChr0 5085 17 + 56053 TATCTAGTTTGAG-GAAC -s mr.mrrefChr0 5352 18 + 130230 TTTCTAATTTGAATCAAC -s simCow_chr6.simCow.chr6 5544 17 + 602619 TATCTCGTTTAGT-GAAC -s simDog_chr6.simDog.chr6 5529 17 + 593897 TATCTAGGTTGAG-GAAC -s simHuman_chr6.simHuman.chr6 4964 18 + 601863 CATCTAGTTTGAACGAAC - -a -s simMouse_chr6.simMouse.chr6 5656 18 + 636262 GTTACAATGAGTGTTGAA -s Anc0.Anc0refChr9 4753 13 - 35212 G-----ATGAGCCTTGAA -s Anc1.Anc1refChr0 5045 18 + 16026 GCTTCAATGAGCCTTGAA -s Anc2.Anc2refChr0 5102 13 + 56053 G-----AAAAGCCTTGAA -s mr.mrrefChr0 5370 18 + 130230 GTTACAATGAGTGTTGAA -s simCow_chr6.simCow.chr6 5568 13 + 602619 T-----AAAAGTCTTGAC -s simDog_chr6.simDog.chr6 5546 13 + 593897 G-----AAAAACCTTGAA -s simHuman_chr6.simHuman.chr6 4982 18 + 601863 TCTTCAATGAGCCTCGAG - -a -s simMouse_chr6.simMouse.chr6 5674 123 + 636262 AGTTAGCTATAATAAGTTGCAGCCCATGCTTTTATCACTAGAAACGCACACCACGTATCTAATCTGAATCAATGTTACAATGAGTGTTGAAAGTTAGCTAGATCATGTCTCTACACTTAAATG -s Anc0.Anc0refChr9 4766 23 - 35212 AGTT----------------------------------------------------------------------------------------------------ATGCTTCTACACTTAAATG -s Anc1.Anc1refChr0 5063 23 + 16026 AGTT----------------------------------------------------------------------------------------------------ATGCTTCTACACTTAAATG -s Anc2.Anc2refChr0 5119 23 + 56053 AGTT----------------------------------------------------------------------------------------------------ATGCTTTTACACTTAAATG -s mr.mrrefChr0 5388 123 + 130230 AGTTAGCTATAATAAGTTGCAGCCTATGCTTTTATCACTAGAAACGCACACCACATATCTAATCTGAATCAATATTACAATGAGTGTTGAAAGTTAGATAGGTCATGTCTCTACACTTAAATG -s simCow_chr6.simCow.chr6 5585 23 + 602619 AGTT----------------------------------------------------------------------------------------------------ATGATTTTACACTTAAATG -s simDog_chr6.simDog.chr6 5563 23 + 593897 AGTT----------------------------------------------------------------------------------------------------ATGCGTTTACACGTAAACG -s simHuman_chr6.simHuman.chr6 5000 23 + 601863 AGTT----------------------------------------------------------------------------------------------------GTGCTTCTACACTTAAATG -s simRat_chr6.simRat.chr6 5192 106 + 647215 -----------------TGAAGGCTACGCTTTTGTCACTAGAAACTCACACCACATATCTAATTTAACTCAACATTACAATAAGTGTTGAAAGTTAGATATGTCATGTCCCTACACTTAAGTG - -a -s simMouse_chr6.simMouse.chr6 5797 10 + 636262 TTCTGATTTC -s Anc0.Anc0refChr9 4844 10 - 35212 CTCCTGTTCC -s Anc1.Anc1refChr0 5141 10 + 16026 CTCCTGTTCC -s Anc2.Anc2refChr0 5199 10 + 56053 CTCCTGTTCC -s mr.mrrefChr0 5511 10 + 130230 TTCTGGTTTC -s simCow_chr6.simCow.chr6 5666 10 + 602619 CCCATGTTCC -s simDog_chr6.simDog.chr6 5629 10 + 593897 CTCCTGTCCA -s simHuman_chr6.simHuman.chr6 5084 10 + 601863 CTCCTGTTCC -s simRat_chr6.simRat.chr6 5298 10 + 647215 TTCTGGTTTC - -a -s simMouse_chr6.simMouse.chr6 5807 46 + 636262 AACTCCAAAGAACCTGGCAACACTCTACCGTTGGTGACCTCTGTAG -s Anc0.Anc0refChr9 4854 31 - 35212 -TCT--------TATGGCAAACCTCTGC------TCATCTCTGTGG -s Anc1.Anc1refChr0 5151 32 + 16026 ATCT--------TATGGCAAACCTCTGC------TCATCTCTGTGG -s Anc2.Anc2refChr0 5209 31 + 56053 -TTT--------TATTGCAAACTTCTGC------TCATCTCTGTGG -s mr.mrrefChr0 5521 46 + 130230 AACTCCAAAGAACCTGGCAACCCTCTACCTTTGGTGACCTCTGTAG -s simCow_chr6.simCow.chr6 5676 31 + 602619 -TTT--------TATTGCAAACTTTGGC------TGATCTCTGTGG -s simDog_chr6.simDog.chr6 5639 31 + 593897 -TAT--------TATTGCAAATTTCTTC------CCATCTCTGTGG -s simHuman_chr6.simHuman.chr6 5094 32 + 601863 ATCT--------TTTGCCAAACCTCTGC------TTATCTCTGTGG -s simRat_chr6.simRat.chr6 5309 46 + 647215 AACTCAAAAGAAACTGGTGACCCTCTACCTTTGGTGACCTCTGTAG - -a -s simMouse_chr6.simMouse.chr6 5853 12 + 636262 GTATTCATAGAG -s Anc0.Anc0refChr9 4891 12 - 35212 GTAATTATATAG -s Anc1.Anc1refChr0 5189 12 + 16026 GTAATTATATAG -s Anc2.Anc2refChr0 5246 12 + 56053 GTGATTATATAG -s mr.mrrefChr0 5567 12 + 130230 GTATTCATAGAG -s simCow_chr6.simCow.chr6 5713 12 + 602619 GTGATTACATAG -s simDog_chr6.simDog.chr6 5677 12 + 593897 GTGATTATATAG -s simHuman_chr6.simHuman.chr6 5132 12 + 601863 GCAATTATACAG -s simRat_chr6.simRat.chr6 5355 12 + 647215 GTATTCATAGAG - -a -s simMouse_chr6.simMouse.chr6 5865 34 + 636262 AGTTGCACTATATACTTAAGGGATAAACAATTGA -s Anc0.Anc0refChr9 4914 34 - 35212 AGGTGCATTATATACTGATTGCATAGACAATGGA -s Anc1.Anc1refChr0 5212 34 + 16026 AGGTGCATTATATACTGATTGCATAGACAATGGA -s Anc2.Anc2refChr0 5269 34 + 56053 AAGTGCATCATATACTGATTGCATAGACAATGGA -s mr.mrrefChr0 5579 34 + 130230 AGTTGCATTATATACTTAATGCATAAACAATTGA -s simCow_chr6.simCow.chr6 5736 34 + 602619 ATGTGCATCATATACTGACTGCATAGACAATGTA -s simDog_chr6.simDog.chr6 5700 34 + 593897 AAGTACATCATAGACTGGTTACATAGACAATGGA -s simHuman_chr6.simHuman.chr6 5155 34 + 601863 AGGTGCATTATATACTGATTGCATCGACAATGGA -s simRat_chr6.simRat.chr6 5367 34 + 647215 AGTTGAATTATATACTTAATGCATAAACAATTGA - -a -s simMouse_chr6.simMouse.chr6 5899 43 + 636262 AGGGGAAGCAAGTACCACCACTAGAACATGTATAAGTACAACG -s Anc0.Anc0refChr9 4981 43 - 35212 AGGGGATGAATGTGCCACCACTAGAACTTGCAATGGTATAAAA -s Anc1.Anc1refChr0 5279 43 + 16026 AGGGGATGAATGTGCCACCACTAGAACTTGCAATGGTATAAAA -s Anc2.Anc2refChr0 5336 43 + 56053 AGGGGACAAATGTGCCACCACTAGAACTTGCAATGGTGTTAAA -s mr.mrrefChr0 5613 43 + 130230 AGGGGATGCAAGTGCCACCACTAGAACATGCAAAGGTATAAAG -s simCow_chr6.simCow.chr6 5802 41 + 602619 AGGGGACACATGTGCC-CCACTAGAAGTTGAAATAGTC-CAAA -s simDog_chr6.simDog.chr6 5767 43 + 593897 AGGGGGCAAGTGTGCCACCACTAGAACTTGCAAAGGTGTTAAA -s simHuman_chr6.simHuman.chr6 5222 43 + 601863 AGGGGATGTATGTGCCACCACTAGAGCTAGCCATGGTATAAAA -s simRat_chr6.simRat.chr6 5401 43 + 647215 AGGGGCTGCAAGTGCCACCACTAGAACATGCAAAGATATAAAG - -a -s simMouse_chr6.simMouse.chr6 5942 16 + 636262 GGAACTCACATAAAAG -s Anc0.Anc0refChr9 5025 16 - 35212 GAAACTTATATAAGGG -s Anc1.Anc1refChr0 5323 16 + 16026 GAAACTTATATAAGGG -s Anc2.Anc2refChr0 5380 16 + 56053 GAAACTTATAGAAGGG -s mr.mrrefChr0 5656 16 + 130230 GGAACTCACATAAGAG -s simCow_chr6.simCow.chr6 5844 16 + 602619 GGAACTTATAGAAGGG -s simDog_chr6.simDog.chr6 5811 13 + 593897 GAAACTTG---AAGGG -s simHuman_chr6.simHuman.chr6 5266 16 + 601863 GAAACTTATATAAGGG -s simRat_chr6.simRat.chr6 5444 16 + 647215 GGAGCTCACACAAGAG - -a -s simMouse_chr6.simMouse.chr6 5958 18 + 636262 AACAGTTGAGTTTATCTA -s Anc0.Anc0refChr9 5046 18 - 35212 AGTAATTTAATTTATCTT -s Anc1.Anc1refChr0 5344 18 + 16026 AGTAATTTAATTTATCTT -s Anc2.Anc2refChr0 5401 18 + 56053 GTTAATATAATTTGTCTT -s mr.mrrefChr0 5672 18 + 130230 AGCAGTTGAGTTTATCTA -s simCow_chr6.simCow.chr6 5865 18 + 602619 GTTAATATGATTTCCCTT -s simDog_chr6.simDog.chr6 5829 18 + 593897 GTTAGTATAAATTGTCTT -s simHuman_chr6.simHuman.chr6 5287 18 + 601863 AGTAATTCAATTTATCTC -s simRat_chr6.simRat.chr6 5460 18 + 647215 AGCAGTTGAGCTTATCTA - -a -s simMouse_chr6.simMouse.chr6 5976 35 + 636262 CTTGAATGTTATTAGAGAGTCCATGAGCTTTTTAG -s Anc0.Anc0refChr9 5064 32 - 35212 C---CATGTTACTGGAGAGTCTGTGAGGGCTTTGG -s Anc1.Anc1refChr0 5362 32 + 16026 C---CATGTTACTGGAGAGTCTGTGAGGGCTTTGG -s Anc2.Anc2refChr0 5419 32 + 56053 T---TATGATACTGGGGAGTCTGTAAGGGTTTTGG -s mr.mrrefChr0 5690 35 + 130230 CTTGCATGTTACTAGAGAGTCCATGAGCTCTTTAG -s simCow_chr6.simCow.chr6 5883 32 + 602619 T---TGTGATACTGATGAGTCTGTATGGGATTTGG -s simDog_chr6.simDog.chr6 5847 32 + 593897 T---TATGATCCTGGGGAGTCTGTAAGGATCTTGG -s simHuman_chr6.simHuman.chr6 5305 31 + 601863 C---CATGTGACTGGAGAGTCTGTGAGGGCTCT-G -s simRat_chr6.simRat.chr6 5479 35 + 647215 CTTGCATGTTACTAGAGAGTCCATAAGCTCTTTAG - -a -s simMouse_chr6.simMouse.chr6 6011 42 + 636262 TTAGATGACTTGTGGGTGCCATAAGATTAATGTAGACAAGTA -s Anc0.Anc0refChr9 5096 41 - 35212 CTGGGTAACATGTGGGTGTCAT-TGGATGGTCTGTAGAGGTA -s Anc1.Anc1refChr0 5394 41 + 16026 CTGGGTAACATGTGGGTGTCAT-TGGATGGTCTGTAGAGGTA -s Anc2.Anc2refChr0 5451 41 + 56053 CTGGGTAACATGTGGGTGTCAT-TGGATGGTCTGTAGAGGTA -s mr.mrrefChr0 5725 42 + 130230 TTAGATGACTTGTGGGTGTCATAAGGTTAATGTGGACAAGTA -s simCow_chr6.simCow.chr6 5915 41 + 602619 CCAGATAACCTGTGGGTGTCAT-TGGGTTAACTGTAAAGGTA -s simDog_chr6.simDog.chr6 5881 40 + 593897 CTGGGTAACATGT-GGTGTCAT-TGGATGGTCTGTAGAGGTA -s simHuman_chr6.simHuman.chr6 5336 41 + 601863 CTGGCTAACGTGTGGGTGTCAT-TGGCTGGTCTGAAGAGGTA -s simRat_chr6.simRat.chr6 5514 42 + 647215 GTAGATGACTTGTGGGTGTCATAAGGTTAATGTGGACAAGTA - -a -s simMouse_chr6.simMouse.chr6 6053 17 + 636262 AGCTAGGGGCTTTCATA -s Anc0.Anc0refChr9 5138 17 - 35212 AGGTAGGGGCATTCCTA -s Anc1.Anc1refChr0 5436 17 + 16026 AGGTAGGGGCATTCCTA -s Anc2.Anc2refChr0 5493 17 + 56053 AGGTAGAGGCATTCCTA -s mr.mrrefChr0 5767 17 + 130230 AGCTAGGGGCTTTCATA -s simCow_chr6.simCow.chr6 5957 17 + 602619 AGGTCGAGGCTTTCTTA -s simDog_chr6.simDog.chr6 5922 17 + 593897 AGGTAGAGGCATTCCTA -s simHuman_chr6.simHuman.chr6 5378 17 + 601863 AGGTAGGGGCATTCCTA -s simRat_chr6.simRat.chr6 5556 1 + 647215 ----------------G - -a -s simMouse_chr6.simMouse.chr6 6070 78 + 636262 AGGTAGGGGCTTTCAAACTGCTGGAAGTTCAGGATACTTTTGAAATATCCTTGTTATAGAGCCTTCTCATACATTCCA -s Anc0.Anc0refChr9 5156 66 - 35212 GGGTTGGAATGTAGCATCTTCTGGAAATTAAGGA------TGATATTTCTCTGTTTTAGAGTC------TATATCCCA -s Anc1.Anc1refChr0 5454 66 + 16026 GGGTTGGAATGTAGCATCTTCTGGAAATTAAGGA------TGATATTTCTCTGTTTTAGAGTC------TATATCCCA -s Anc2.Anc2refChr0 5556 66 + 56053 GAGTTGGAATGTAGCATCTTATGGAAATTAAGGA------TGATATTTCTCTGTTTTAAAGTC------TGTATCACA -s mr.mrrefChr0 5784 72 + 130230 AGGTAGGGGCTTTCAAACTGCTGGAAGTTCAGGA------TGAAATATCCTTGTTATAGAGCCTTCTCATACATTCCA -s simCow_chr6.simCow.chr6 6020 66 + 602619 GTGTTGGAATGTAGCATGTTATGGAAACTGAGGG------TGATATTTCTCGGTTTTAAAGTC------TGCGCTACA -s simDog_chr6.simDog.chr6 5985 66 + 593897 GAGTTGGAGTGTAACATCTTATGGAAATTAAGGA------TGAGATTTCTCTGTTTTAAACCC------TGTATCACA -s simHuman_chr6.simHuman.chr6 5396 66 + 601863 GGGTTGGAATGTAGCAGCTTCTGGAAATTTATGA------TGATTTGTCTCTGTTTTAGAGTC------TATATCCCA -s simRat_chr6.simRat.chr6 5557 71 + 647215 AGGTAGGGGCTTTCACCCTG-TGGAATTTCAGGA------CGAAATATCCTTGTTATAGAGCCTTATCATACCGTACT - -a -s simMouse_chr6.simMouse.chr6 6148 30 + 636262 GGCACTGGCATAGACATCCGAACTTCAGAC -s Anc0.Anc0refChr9 5222 30 - 35212 AGCATTGGCTTCGATGTCCAAATTCCAGGT -s Anc1.Anc1refChr0 5520 30 + 16026 AGCATTGGCTTCGATGTCCAAATTCCAGGT -s Anc2.Anc2refChr0 5627 30 + 56053 AGTAATGGCTTCGATGTCCAAATTCCAGGT -s mr.mrrefChr0 5856 30 + 130230 GGCATTGGCATAGACATCCGAACTTCAGAC -s simCow_chr6.simCow.chr6 6099 30 + 602619 AGTACTAGCATGGATCTCCAAATTCCAGCA -s simDog_chr6.simDog.chr6 6056 30 + 593897 AGTAATGGCTTCGATGTCCAGATTCCAGGT -s simHuman_chr6.simHuman.chr6 5462 11 + 601863 AACTTTGGTTT------------------- -s simRat_chr6.simRat.chr6 5628 30 + 647215 GGCATCGGCATGGACCTCCGAACTGCAGCC - -a -s simMouse_chr6.simMouse.chr6 6178 8 + 636262 AGCTCTTC -s Anc0.Anc0refChr9 5252 8 - 35212 AGCTCATC -s Anc1.Anc1refChr0 5550 8 + 16026 AGCTCATC -s Anc2.Anc2refChr0 5658 8 + 56053 AGCTCATC -s mr.mrrefChr0 5886 8 + 130230 AGCTCTTC -s simCow_chr6.simCow.chr6 6130 8 + 602619 AGCCTATC -s simDog_chr6.simDog.chr6 6087 8 + 593897 CACTCACC -s simHuman_chr6.simHuman.chr6 5473 8 + 601863 AGCTCATC -s simRat_chr6.simRat.chr6 5658 8 + 647215 AGTTCTTC - -a -s simMouse_chr6.simMouse.chr6 6186 21 + 636262 AATTAAAATCCTCTCCTCCCA -s Anc0.Anc0refChr9 5261 20 - 35212 TGT-AAAATCCTCTCCACCTA -s Anc1.Anc1refChr0 5559 21 + 16026 TGTTAAAATCCTCTCCACCTA -s Anc2.Anc2refChr0 5667 20 + 56053 TGT-AAAATCCTCTCCACCTA -s mr.mrrefChr0 5894 21 + 130230 AATTAAAATCCTCTCCTCCTA -s simCow_chr6.simCow.chr6 6139 20 + 602619 ACT-AAAATCCTCTCCTCCTA -s simDog_chr6.simDog.chr6 6096 20 + 593897 TGT-AAGATCCTCTCCACCTA -s simHuman_chr6.simHuman.chr6 5482 21 + 601863 TGTTAAAGGCCTCCCCACCTA -s simRat_chr6.simRat.chr6 5666 21 + 647215 AAGTAAAATCAACTTCTCCTA - -a -s simMouse_chr6.simMouse.chr6 6207 75 + 636262 ATTGTTGAGAGAGTGCTGGATAAGCAACATGGGCTTCATTTAGTCCAGTCCACTGCTCCCGGCATCCTGTAGATG -s Anc0.Anc0refChr9 5281 36 - 35212 TCTGGTGAAATATTGATGGCTAAGC---------------------------------------TCTTGCTGTTG -s Anc1.Anc1refChr0 5580 36 + 16026 TCTGGTGAAATATTGATGGCTAAGC---------------------------------------TCTTGCTGTTG -s Anc2.Anc2refChr0 5687 36 + 56053 TCGTGTGGAATGTTGATGGCTAAGT---------------------------------------ACTTGCTGTTA -s mr.mrrefChr0 5915 75 + 130230 ATTGTTGAGAGAGTGATGGCTAAGCAACATGGGCTTCATTTAGTCCAGTCCACTGCTCCCGGCATCCTGTAGATG -s simCow_chr6.simCow.chr6 6159 36 + 602619 TCATGTGGGAGTTTGATGGCTAAGT---------------------------------------ACTAGGTGTTA -s simDog_chr6.simDog.chr6 6117 33 + 593897 TTGTG---AGTGATGATGGCTGAGT---------------------------------------ATTTGCTGCTA -s simHuman_chr6.simHuman.chr6 5503 36 + 601863 TCTGCTGAAACATTGATGGCTAAGC---------------------------------------TCTTGCTGTTG -s simRat_chr6.simRat.chr6 5687 75 + 647215 ATTGTTGAGAGAATGATGACTAAGCAACATGGGCTTCAATTTGTCCAGTCCAATGCTCCCAGCATCCTGTAGATG - -a -s simMouse_chr6.simMouse.chr6 6282 5 + 636262 CAGCA -s Anc0.Anc0refChr9 5317 5 - 35212 CAGCA -s Anc1.Anc1refChr0 5616 5 + 16026 CAGCA -s Anc2.Anc2refChr0 5723 5 + 56053 CAGCA -s mr.mrrefChr0 5990 5 + 130230 CAGCA -s simCow_chr6.simCow.chr6 6198 5 + 602619 CAGAA -s simDog_chr6.simDog.chr6 6150 5 + 593897 CAGCA -s simHuman_chr6.simHuman.chr6 5539 5 + 601863 CAGCA -s simRat_chr6.simRat.chr6 5762 5 + 647215 CAGCA - -a -s simMouse_chr6.simMouse.chr6 6287 2 + 636262 GT -s Anc0.Anc0refChr9 5322 2 - 35212 GT -s Anc1.Anc1refChr0 5621 2 + 16026 GT -s Anc2.Anc2refChr0 5728 2 + 56053 GT -s mr.mrrefChr0 5995 2 + 130230 GT -s simCow_chr6.simCow.chr6 6203 2 + 602619 GT -s simDog_chr6.simDog.chr6 6161 2 + 593897 GT -s simHuman_chr6.simHuman.chr6 5544 2 + 601863 GT -s simRat_chr6.simRat.chr6 5767 2 + 647215 AT - -a -s simMouse_chr6.simMouse.chr6 6289 7 + 636262 ACAGGCT -s Anc0.Anc0refChr9 5333 7 - 35212 ACAGGCT -s Anc1.Anc1refChr0 5632 7 + 16026 ACAGGCT -s Anc2.Anc2refChr0 5739 7 + 56053 TGAGGCT -s mr.mrrefChr0 5997 7 + 130230 ACAGGCT -s simCow_chr6.simCow.chr6 6214 7 + 602619 TTGGGCT -s simDog_chr6.simDog.chr6 6172 6 + 593897 TGAGGT- -s simHuman_chr6.simHuman.chr6 5555 7 + 601863 ACAGGCT -s simRat_chr6.simRat.chr6 5769 7 + 647215 ACAGGCT - -a -s simMouse_chr6.simMouse.chr6 6296 3 + 636262 TTA -s Anc0.Anc0refChr9 5340 3 - 35212 TTA -s Anc1.Anc1refChr0 5639 3 + 16026 TTA -s Anc2.Anc2refChr0 5756 3 + 56053 TTA -s mr.mrrefChr0 6004 3 + 130230 TTA -s simCow_chr6.simCow.chr6 6228 3 + 602619 TCA -s simDog_chr6.simDog.chr6 6188 3 + 593897 TTA -s simHuman_chr6.simHuman.chr6 5562 3 + 601863 TTA -s simRat_chr6.simRat.chr6 5776 3 + 647215 TTA - -a -s simMouse_chr6.simMouse.chr6 6299 10 + 636262 GTGCAGGCAG -s Anc0.Anc0refChr9 5343 10 - 35212 GTACAGGCAG -s Anc1.Anc1refChr0 5642 10 + 16026 GTACAGGCAG -s Anc2.Anc2refChr0 5775 10 + 56053 GTACAGGCAG -s mr.mrrefChr0 6007 10 + 130230 GTGCAGGCAG -s simCow_chr6.simCow.chr6 6246 10 + 602619 GAAGAGGCAG -s simDog_chr6.simDog.chr6 6207 10 + 593897 GTTCAGACAT -s simHuman_chr6.simHuman.chr6 5565 10 + 601863 GTACAGGAAG -s simRat_chr6.simRat.chr6 5779 10 + 647215 GTGCAGACAG - -a -s simMouse_chr6.simMouse.chr6 6309 38 + 636262 CAATTGCCTTACAATCTTCGAGAGAGTGATGGCTAAGC -s Anc0.Anc0refChr9 5354 22 - 35212 TAATTGCCTTACAATCTTTGGA---------------- -s Anc1.Anc1refChr0 5653 38 + 16026 TAATTGCCTTACAATCTTTGGAAGGAACACTCACAATC -s Anc2.Anc2refChr0 5786 22 + 56053 TGATTGCCCTACAATCTCTGGA---------------- -s mr.mrrefChr0 6017 38 + 130230 CAATTGCCTTACAATCTTCGAGAGGGTGACGGCTAAGC -s simCow_chr6.simCow.chr6 6257 22 + 602619 TGATTGACCTACTGTCTTTGGA---------------- -s simDog_chr6.simDog.chr6 6218 22 + 593897 TGACCGCCCTACAAACTCTGGA---------------- -s simHuman_chr6.simHuman.chr6 5576 38 + 601863 TAATTGTCTCACAATTTTAGCAAGGAACACTCACAATC -s simRat_chr6.simRat.chr6 5789 38 + 647215 CAAATGCCTTACAATCCTTGAGAGGGTGACGGCTAAGC - -a -s simMouse_chr6.simMouse.chr6 6347 37 + 636262 ACCTGTAGATGCAGCAGTACAGGCTTTAATGCAGGCA -s Anc1.Anc1refChr0 5691 37 + 16026 GCTTGCTGTTGCAGCAACACAGGCTTTAGTACAGGAA -s mr.mrrefChr0 6055 37 + 130230 ACCTGTAGATGCAGCAGTACAGGCTTTAATGCAGGCA -s simHuman_chr6.simHuman.chr6 5617 37 + 601863 GCTTGCTGTTGCAGCAACACAGGCTTTAGTACAGGAA -s simRat_chr6.simRat.chr6 5827 37 + 647215 ACCTGTGGATGCAGCAGTACAGCCTGTAATGCAGGCA - -a -s simMouse_chr6.simMouse.chr6 6384 23 + 636262 CAAATTGCCTTGCTATCTCTTAG -s Anc0.Anc0refChr9 5376 1 - 35212 ----------------------G -s Anc1.Anc1refChr0 5728 22 + 16026 TTAATTGCCTTACAAT-TCCTAG -s Anc2.Anc2refChr0 5808 1 + 56053 ----------------------G -s mr.mrrefChr0 6092 23 + 130230 TAAATTGCCTTGCTATCTCTTAG -s simCow_chr6.simCow.chr6 6279 1 + 602619 ----------------------G -s simDog_chr6.simDog.chr6 6240 1 + 593897 ----------------------G -s simHuman_chr6.simHuman.chr6 5655 22 + 601863 TTAATTGCCTTACAAT-TCCTAG -s simRat_chr6.simRat.chr6 5864 23 + 647215 TAAATTGCCTTGCTATCTCTTAG - -a -s simMouse_chr6.simMouse.chr6 6407 24 + 636262 AGGAATACTCACAATCTGATGTAC -s Anc0.Anc0refChr9 5377 24 - 35212 AGGAACACTCACAATCTTATCCAC -s Anc1.Anc1refChr0 5750 24 + 16026 AGGAACACTCACAATCTTATCCAC -s Anc2.Anc2refChr0 5809 24 + 56053 AGGAACACTCACAATTTTATCCAC -s mr.mrrefChr0 6115 24 + 130230 AGGAACACTCACAATCTGATGTAC -s simCow_chr6.simCow.chr6 6280 21 + 602619 AGGGACA---AACATGTTATCCAC -s simDog_chr6.simDog.chr6 6241 24 + 593897 AGGAATACTCACAATTTTGTCCAC -s simHuman_chr6.simHuman.chr6 5679 24 + 601863 AGGAACACTCACTATCTTATCCAG -s simRat_chr6.simRat.chr6 5887 24 + 647215 AGGAACACTCACAATCTGATGTAC - -a -s simMouse_chr6.simMouse.chr6 6431 6 + 636262 TTATCA -s Anc0.Anc0refChr9 5402 6 - 35212 TTATCA -s Anc1.Anc1refChr0 5775 6 + 16026 TTATCA -s Anc2.Anc2refChr0 5834 6 + 56053 TTATCA -s mr.mrrefChr0 6139 6 + 130230 TTATCA -s simCow_chr6.simCow.chr6 6302 6 + 602619 TTATCA -s simDog_chr6.simDog.chr6 6266 6 + 593897 TTATAA -s simHuman_chr6.simHuman.chr6 5704 6 + 601863 CTATCA -s simRat_chr6.simRat.chr6 5911 6 + 647215 TTATCA - -a -s simMouse_chr6.simMouse.chr6 6437 10 + 636262 CAATTTATTA -s Anc0.Anc0refChr9 5408 10 - 35212 GTATTTATTA -s Anc1.Anc1refChr0 5781 10 + 16026 GTATTTATTA -s Anc2.Anc2refChr0 5840 10 + 56053 GTATTTATTA -s mr.mrrefChr0 6145 10 + 130230 CAATTTATTA -s simCow_chr6.simCow.chr6 6308 10 + 602619 GTTTTTGTTA -s simDog_chr6.simDog.chr6 6272 10 + 593897 ATATTTATTA -s simHuman_chr6.simHuman.chr6 5710 10 + 601863 GTATTTATTG -s simRat_chr6.simRat.chr6 5918 10 + 647215 AAATTTATTA - -a -s simMouse_chr6.simMouse.chr6 6447 2 + 636262 AT -s Anc0.Anc0refChr9 5418 2 - 35212 AT -s Anc1.Anc1refChr0 5791 2 + 16026 AT -s Anc2.Anc2refChr0 5850 2 + 56053 AT -s mr.mrrefChr0 6155 2 + 130230 AT -s simCow_chr6.simCow.chr6 6329 2 + 602619 AT -s simDog_chr6.simDog.chr6 6282 2 + 593897 AT -s simHuman_chr6.simHuman.chr6 5720 2 + 601863 AT -s simRat_chr6.simRat.chr6 5928 2 + 647215 AT - -a -s simMouse_chr6.simMouse.chr6 6449 40 + 636262 GTATATAAGGGCTAACATCCAGCGGTCAGTAGATTCAAAG -s Anc0.Anc0refChr9 5425 40 - 35212 GCACATGAGGGGTACCAACTGATGGACAGAAAATCTAGAG -s Anc1.Anc1refChr0 5798 40 + 16026 GCACATGAGGGGTACCAACTGATGGACAGAAAATCTAGAG -s Anc2.Anc2refChr0 5857 40 + 56053 GCACATGAGGGGTACCAACTGATGAATAGAAAATCTAGAG -s mr.mrrefChr0 6157 40 + 130230 GTATATGAGGGCTAACAACCGGTGGTCAGTAGATTCAAAG -s simCow_chr6.simCow.chr6 6336 40 + 602619 TCACATGATGGGTAACCTCTGATGATTAGAAGGTCTGGAG -s simDog_chr6.simDog.chr6 6289 40 + 593897 GCATATGAGGGGTACCAACTATTGAATAGAAAATCTAGAG -s simHuman_chr6.simHuman.chr6 5727 34 + 601863 GAACATGGGGGGTAGCAACTGATAGCCAGGAAAT------ -s simRat_chr6.simRat.chr6 5930 40 + 647215 GTATATGAGGGCTATCAATGGGTGGTCAGCAGATTCAAAG - -a -s simMouse_chr6.simMouse.chr6 6489 9 + 636262 TGCATTTGT -s Anc0.Anc0refChr9 5465 9 - 35212 CCCACTTGT -s Anc1.Anc1refChr0 5838 9 + 16026 CCCACTTGT -s Anc2.Anc2refChr0 5897 9 + 56053 CCCACTTGT -s mr.mrrefChr0 6197 9 + 130230 TGCATTTGT -s simCow_chr6.simCow.chr6 6376 9 + 602619 CACACCGGC -s simDog_chr6.simDog.chr6 6329 9 + 593897 CCCATTTGT -s simHuman_chr6.simHuman.chr6 5761 7 + 601863 --CACTTAT -s simRat_chr6.simRat.chr6 5975 9 + 647215 TGCATTTGT - -a -s simMouse_chr6.simMouse.chr6 6498 8 + 636262 ATCTGTAA -s Anc0.Anc0refChr9 5474 8 - 35212 CTTTGCAG -s Anc1.Anc1refChr0 5847 8 + 16026 CTTTGCAG -s Anc2.Anc2refChr0 5906 8 + 56053 CTTTGCAG -s mr.mrrefChr0 6206 8 + 130230 ATTTGTAG -s simCow_chr6.simCow.chr6 6385 8 + 602619 CTTTGCAG -s simDog_chr6.simDog.chr6 6338 8 + 593897 CTTTGCAT -s simHuman_chr6.simHuman.chr6 5768 8 + 601863 CTTTGCAG -s simRat_chr6.simRat.chr6 5985 8 + 647215 ATTTGTAG - -a -s simMouse_chr6.simMouse.chr6 6506 8 + 636262 AACTAAAA -s Anc0.Anc0refChr9 5483 8 - 35212 AATTAAAA -s Anc1.Anc1refChr0 5856 8 + 16026 AATTAAAA -s Anc2.Anc2refChr0 5915 8 + 56053 AATTAAAA -s mr.mrrefChr0 6215 8 + 130230 AACTAAAA -s simCow_chr6.simCow.chr6 6394 8 + 602619 AATTAAAA -s simDog_chr6.simDog.chr6 6347 8 + 593897 AGTTACAA -s simHuman_chr6.simHuman.chr6 5777 8 + 601863 AATTGAAA -s simRat_chr6.simRat.chr6 5994 8 + 647215 AACTAAAA - -a -s simMouse_chr6.simMouse.chr6 6514 18 + 636262 TAACCAACAGACAATTAG -s Anc0.Anc0refChr9 5492 18 - 35212 TAGCCAATAGACTATAAG -s Anc1.Anc1refChr0 5865 18 + 16026 TAGCCAATAGACTATAAG -s Anc2.Anc2refChr0 5924 18 + 56053 TAGCCAATTGACTATAAG -s mr.mrrefChr0 6223 18 + 130230 TAACCAATAGACAATTAG -s simCow_chr6.simCow.chr6 6403 18 + 602619 TAGGCAATTGACTATTAG -s simDog_chr6.simDog.chr6 6356 18 + 593897 TAGCCAATTGACTATAAG -s simHuman_chr6.simHuman.chr6 5786 18 + 601863 TAGCCAATAAACTATAGG -s simRat_chr6.simRat.chr6 6002 18 + 647215 TAACTGATAGACAGTTAG - -a -s simMouse_chr6.simMouse.chr6 6532 8 + 636262 TACACAAA -s Anc0.Anc0refChr9 5510 8 - 35212 CACGCAGG -s Anc1.Anc1refChr0 5883 8 + 16026 CACGCAGG -s Anc2.Anc2refChr0 5947 8 + 56053 CAGGCAGG -s mr.mrrefChr0 6241 8 + 130230 TACACAGA -s simCow_chr6.simCow.chr6 6426 8 + 602619 CAGGCAAG -s simDog_chr6.simDog.chr6 6379 8 + 593897 CAGGCAGG -s simHuman_chr6.simHuman.chr6 5804 8 + 601863 CACGCAGG -s simRat_chr6.simRat.chr6 6020 8 + 647215 TGCTCAGA - -a -s simMouse_chr6.simMouse.chr6 6540 17 + 636262 AGGTGTTACTGAGCTAT -s Anc0.Anc0refChr9 5518 16 - 35212 A-GTGTTATTGAGCTAT -s Anc1.Anc1refChr0 5891 16 + 16026 A-GTGTTATTGAGCTAT -s Anc2.Anc2refChr0 5955 16 + 56053 A-GTGTTATTGCGCTAT -s mr.mrrefChr0 6249 17 + 130230 AGGTGTTATTGAGCTAT -s simCow_chr6.simCow.chr6 6434 13 + 602619 ----GTTAATGTGCTAT -s simDog_chr6.simDog.chr6 6388 16 + 593897 A-GTGTTATTGCAATAT -s simHuman_chr6.simHuman.chr6 5812 16 + 601863 A-GTATTGTTGAGCTCC -s simRat_chr6.simRat.chr6 6028 17 + 647215 AGGTGTTATTGGGCTAT - -a -s simMouse_chr6.simMouse.chr6 6557 15 + 636262 CAGTCCCACAAGCTT -s Anc0.Anc0refChr9 5534 15 - 35212 CAGCCTCACAAGCTT -s Anc1.Anc1refChr0 5907 15 + 16026 CAGCCTCACAAGCTT -s Anc2.Anc2refChr0 5971 15 + 56053 CAGCCTCACAAGCTT -s mr.mrrefChr0 6266 15 + 130230 CAGCCCCACAAGCTT -s simCow_chr6.simCow.chr6 6447 15 + 602619 CAGCTTCACCGGCTT -s simDog_chr6.simDog.chr6 6404 15 + 593897 CAGGCTCCCAAGGTT -s simHuman_chr6.simHuman.chr6 5837 15 + 601863 CAGCCTCACAAGCTT -s simRat_chr6.simRat.chr6 6045 15 + 647215 CAGCCCCATGAGCTT - -a -s simMouse_chr6.simMouse.chr6 6572 6 + 636262 CACCTT -s Anc0.Anc0refChr9 5568 6 - 35212 TACCTT -s Anc1.Anc1refChr0 5941 6 + 16026 TACCTT -s Anc2.Anc2refChr0 6005 6 + 56053 TACCTT -s mr.mrrefChr0 6281 6 + 130230 CACCTT -s simCow_chr6.simCow.chr6 6535 6 + 602619 TACCTT -s simDog_chr6.simDog.chr6 6438 6 + 593897 TACCTT -s simHuman_chr6.simHuman.chr6 5871 6 + 601863 TACCTT -s simRat_chr6.simRat.chr6 6060 6 + 647215 CACCTT - -a -s simMouse_chr6.simMouse.chr6 6578 15 + 636262 AGTTGGGAACTACGT -s Anc0.Anc0refChr9 5574 10 - 35212 AGTTAGGGA-----T -s Anc1.Anc1refChr0 5947 10 + 16026 AGTTAGGGA-----T -s Anc2.Anc2refChr0 6011 10 + 56053 AGCTAGGGA-----T -s mr.mrrefChr0 6287 10 + 130230 AGTTAGGAA-----T -s simCow_chr6.simCow.chr6 6554 10 + 602619 AGCCAGGAT-----T -s simDog_chr6.simDog.chr6 6444 10 + 593897 TGCTAGGGA-----T -s simHuman_chr6.simHuman.chr6 5877 10 + 601863 AGTTAGGGA-----T -s simRat_chr6.simRat.chr6 6066 10 + 647215 AGTTAGGAA-----T - -a -s simMouse_chr6.simMouse.chr6 6593 8 + 636262 AACGTGAA -s Anc0.Anc0refChr9 5624 8 - 35212 AATGTGAG -s Anc1.Anc1refChr0 5997 8 + 16026 AATGTGAG -s Anc2.Anc2refChr0 6061 8 + 56053 AATGTGAG -s mr.mrrefChr0 6297 8 + 130230 AACGTGAA -s simCow_chr6.simCow.chr6 6612 8 + 602619 AATGTGAG -s simHuman_chr6.simHuman.chr6 5929 8 + 601863 AATATGAG -s simRat_chr6.simRat.chr6 6076 8 + 647215 AACGCTAA - -a -s simMouse_chr6.simMouse.chr6 6601 3 + 636262 CCA -s Anc0.Anc0refChr9 5671 2 - 35212 C-A -s Anc1.Anc1refChr0 6044 3 + 16026 CCA -s Anc2.Anc2refChr0 6108 2 + 56053 A-A -s mr.mrrefChr0 6305 3 + 130230 CCA -s simCow_chr6.simCow.chr6 6660 2 + 602619 A-A -s simHuman_chr6.simHuman.chr6 5980 3 + 601863 CCA -s simRat_chr6.simRat.chr6 6084 3 + 647215 CCA - -a -s simMouse_chr6.simMouse.chr6 6604 40 + 636262 CAGGTTCAGATAGGTTCCTGTGCCCATGTCTGCATGACTC -s Anc0.Anc0refChr9 5673 29 - 35212 CCAGGCTATAAAA-----TGTTACCAT------ATGACTC -s Anc1.Anc1refChr0 6047 34 + 16026 CCAGGCTATAAAACTTCCTGTTACCAT------ATGACTC -s Anc2.Anc2refChr0 6110 29 + 56053 CCAGGCTCTGAAA-----TGCTACTAT------ATGCCTT -s mr.mrrefChr0 6308 40 + 130230 CAGGTTCAGATAGCTTCCTGTGCCCATGTCTGCATGACTC -s simCow_chr6.simCow.chr6 6662 29 + 602619 CCAGGCTCTGAAA-----TGCTACTGT------ATGCCTT -s simDog_chr6.simDog.chr6 6474 13 + 593897 ---------------------TATTAT------GGGCCTT -s simHuman_chr6.simHuman.chr6 5983 34 + 601863 CCAGCCTATAAAACTTCCTGTTACCAT------ATGACTC -s simRat_chr6.simRat.chr6 6088 40 + 647215 CAGGTTCAGATAGCTTCCCGTGCCCATAAATGCATGACTC - -a -s simMouse_chr6.simMouse.chr6 6644 3 + 636262 CCA -s Anc0.Anc0refChr9 5702 3 - 35212 CCA -s Anc1.Anc1refChr0 6081 3 + 16026 CCA -s Anc2.Anc2refChr0 6139 3 + 56053 CCA -s mr.mrrefChr0 6348 3 + 130230 CCA -s simCow_chr6.simCow.chr6 6691 3 + 602619 CCA -s simDog_chr6.simDog.chr6 6492 3 + 593897 CCA -s simHuman_chr6.simHuman.chr6 6017 3 + 601863 CCA -s simRat_chr6.simRat.chr6 6128 3 + 647215 CCA - -a -s simMouse_chr6.simMouse.chr6 6647 4 + 636262 GCGC -s Anc0.Anc0refChr9 5705 4 - 35212 AAGC -s Anc1.Anc1refChr0 6084 4 + 16026 AAGC -s Anc2.Anc2refChr0 6142 4 + 56053 AATC -s mr.mrrefChr0 6351 4 + 130230 GAGC -s simCow_chr6.simCow.chr6 6695 4 + 602619 AATC -s simDog_chr6.simDog.chr6 6495 4 + 593897 GATC -s simHuman_chr6.simHuman.chr6 6020 4 + 601863 AAGC -s simRat_chr6.simRat.chr6 6131 4 + 647215 GAGC - -a -s simMouse_chr6.simMouse.chr6 6651 37 + 636262 ATGTGTCCACCGCTTATTAATGCTATTAATGCACCAA -s Anc0.Anc0refChr9 5713 25 - 35212 CTTTG--CACCACT---------TATTTATGCACT-A -s Anc1.Anc1refChr0 6092 25 + 16026 CTTTG--CACCACT---------TATTTATGCACT-A -s Anc2.Anc2refChr0 6150 25 + 56053 CTTTG--CACCACT---------TATTTATGAACT-A -s mr.mrrefChr0 6355 26 + 130230 CTGTG--CACCACT---------TATTAATGCACCAA -s simCow_chr6.simCow.chr6 6703 25 + 602619 CTTTG--CATCACT---------TATTTATGAACT-A -s simDog_chr6.simDog.chr6 6503 25 + 593897 CTTTG--CACCACT---------TATTTATGAACT-A -s simHuman_chr6.simHuman.chr6 6028 25 + 601863 CTTTG--CACCACC---------TATTTGTGCACT-A -s simRat_chr6.simRat.chr6 6135 26 + 647215 CTGTG--CACCACT---------TATTAATGCATCAG - -a -s simMouse_chr6.simMouse.chr6 6688 9 + 636262 AGCATTAGG -s Anc0.Anc0refChr9 5738 9 - 35212 AGCATTATG -s Anc1.Anc1refChr0 6117 9 + 16026 AGCATTATG -s Anc2.Anc2refChr0 6175 9 + 56053 AGCATTATG -s mr.mrrefChr0 6381 9 + 130230 AGCATTATG -s simCow_chr6.simCow.chr6 6729 9 + 602619 AGCACTATG -s simDog_chr6.simDog.chr6 6528 8 + 593897 AA-GTGATG -s simHuman_chr6.simHuman.chr6 6053 9 + 601863 AGCATTATG -s simRat_chr6.simRat.chr6 6161 9 + 647215 TGCATTATG - -a -s simMouse_chr6.simMouse.chr6 6697 67 + 636262 ATCTTAAGTAGCACTAGCACTGAATTTCAATCTAGACCGTTTGGCCCAAAAGCAATCTGATATGGAA -s Anc0.Anc0refChr9 5747 67 - 35212 AGCTTAAGTAGAAAGAGCACTGATTTTCAATGTAAAACATCCGGTCCAGAAGCAATCAAAGATGGAA -s Anc1.Anc1refChr0 6126 67 + 16026 AGCTTAAGTAGAAAGAGCACTGATTTTCAATGTAAAACATCCGGTCCAGAAGCAATCAAAGATGGAA -s Anc2.Anc2refChr0 6184 67 + 56053 AGGTTAAGTAGAAAGAGCACTCATCTACACTGTAAAACATCCGTTCCAGAAGCAATCAATGGTGGAA -s mr.mrrefChr0 6390 67 + 130230 ATCTTAAGTAGCACTAGCACTGAATTTCAATCTAGACCGTCTGGCCCAAAAGCAATCTGAGATGGAA -s simCow_chr6.simCow.chr6 6738 67 + 602619 ATGTTAAGTAGCAAGGTCACTCATCACCACTGTAAACTATCCGACCCAGAAGCAATCAATGGTGGAA -s simDog_chr6.simDog.chr6 6542 56 + 593897 AGGTCAAATAGAAAGAGCACTCATCTACA--ATGAGACATCTGTTCCAGAAGCTACTA--------- -s simHuman_chr6.simHuman.chr6 6062 67 + 601863 AACTTAAGTAGAAAACGCATTGATTTTCAATGTAAATAATCCAGTCAAGAATCAATCAAAGATGGAG -s simRat_chr6.simRat.chr6 6170 63 + 647215 ATATTAAGTAGCATTAGCACTGAATGTCAATCTA----GTCTGGCCCAAAAGCAATCTGAGATGGAA - -a -s simMouse_chr6.simMouse.chr6 6764 15 + 636262 GAATCACACAGAGAG -s Anc0.Anc0refChr9 5816 15 - 35212 GAATCACAGAGAGAG -s Anc1.Anc1refChr0 6195 15 + 16026 GAATCACAGAGAGAG -s Anc2.Anc2refChr0 6253 15 + 56053 GAATCACAGAGAGAG -s mr.mrrefChr0 6459 15 + 130230 GAATCACACAGAGAG -s simCow_chr6.simCow.chr6 6807 15 + 602619 GAATCACAGAGAGAG -s simHuman_chr6.simHuman.chr6 6131 15 + 601863 GAATCACAGAGAGAA -s simRat_chr6.simRat.chr6 6235 15 + 647215 GAATCACAAAGAGGG - -a -s simMouse_chr6.simMouse.chr6 6779 43 + 636262 AAGGGTAGTATTGATGAAGCCAGGCTACAGCTTGAAATCAACT -s Anc0.Anc0refChr9 5831 25 - 35212 AAGC------------------GGCTCCAGCTTGAAACCAACT -s Anc1.Anc1refChr0 6210 25 + 16026 AAGC------------------GGCTCCAGCTTGAAACCAACT -s Anc2.Anc2refChr0 6270 25 + 56053 AATC------------------AGCTCCAGCTTGAGATCAGCT -s mr.mrrefChr0 6474 43 + 130230 AAGGGTAGTATTGATGAAGCCAGGCTACAGCTTGAAACCAACT -s simCow_chr6.simCow.chr6 6835 25 + 602619 AATC------------------TGCTCCAGCTTGAGATCAGCT -s simDog_chr6.simDog.chr6 6600 25 + 593897 AGTC------------------AGCTCCAGCTTGAGATTAGCT -s simHuman_chr6.simHuman.chr6 6146 25 + 601863 AAGT------------------GGCTCCAGCTTTTAACCAACT -s simRat_chr6.simRat.chr6 6250 43 + 647215 AAGGGTAGTATTGGTGGGGCCAGGCTATGGCTCGGAACCAACC - -a -s simMouse_chr6.simMouse.chr6 6822 34 + 636262 AGCAAGTTTTAATTCAATACCCATAAAGAACTAA -s Anc0.Anc0refChr9 5864 34 - 35212 AGGTAGTTTTATTTCAGTAGACATGCAAAGCCAA -s Anc1.Anc1refChr0 6243 34 + 16026 AGGTAGTTTTATTTCAGTAGACATGCAAAGCCAA -s Anc2.Anc2refChr0 6303 34 + 56053 AAGTGGTATTATTTCAGTAGATGTGCAAAGTCAA -s mr.mrrefChr0 6517 34 + 130230 AGCAAGTTTTAATTCAATAGCCATAAAGAACTAA -s simCow_chr6.simCow.chr6 6868 33 + 602619 AA-TGGCATTATTTCAGTAGATGTGCAAAATCAA -s simDog_chr6.simDog.chr6 6633 34 + 593897 AAGTGGTATTATTTCACTAGATGTGCACAGTCAA -s simHuman_chr6.simHuman.chr6 6179 34 + 601863 AGGCAGTTTTACATCAGTAGACATGCAAAGCCAA -s simRat_chr6.simRat.chr6 6293 34 + 647215 AGCAAGTTTTAATCCAATAGCCATATAGAACTAA - -a -s simMouse_chr6.simMouse.chr6 6856 5 + 636262 AACCA -s Anc0.Anc0refChr9 5898 5 - 35212 AACCA -s Anc1.Anc1refChr0 6277 5 + 16026 AACCA -s Anc2.Anc2refChr0 6337 5 + 56053 AACCA -s mr.mrrefChr0 6551 5 + 130230 AACCA -s simCow_chr6.simCow.chr6 6901 5 + 602619 AACCA -s simDog_chr6.simDog.chr6 6667 5 + 593897 AACCA -s simHuman_chr6.simHuman.chr6 6213 5 + 601863 AACAG -s simRat_chr6.simRat.chr6 6375 5 + 647215 AACCA - -a -s simMouse_chr6.simMouse.chr6 6861 50 + 636262 AGCACAGTAATGTAACAGGCAGCATGGAGTGGCAAGTGACCAAAGCAGTG -s Anc0.Anc0refChr9 5904 49 - 35212 AGGGCAGTGAGGCACCAGGCAGCATAGGGTGGCAAGTGACCAG-GCAGGG -s Anc1.Anc1refChr0 6283 49 + 16026 AGGGCAGTGAGGCACCAGGCAGCATAGGGTGGCAAGTGACCAG-GCAGGG -s Anc2.Anc2refChr0 6343 49 + 56053 AGGGCAATGAGGCACCAGGCAACATAGGGTGGCAAGTGGCCAT-GCAGGG -s mr.mrrefChr0 6556 50 + 130230 AGCGCAGTAATGTAACAGGCAGCATGGAGTGGCAAGTGACCAGAGCAGTG -s simCow_chr6.simCow.chr6 6907 49 + 602619 AATGCAATGTAGCACTAGGCAACATAGGCTGGCAACTGTCCAC-GCAATG -s simDog_chr6.simDog.chr6 6673 49 + 593897 AGGGCAATGAGGCACCAGACAACATAGGGTGGCAAGTGGCAAT-GCAGGG -s simHuman_chr6.simHuman.chr6 6219 49 + 601863 AGGGCAGTGACACACCAGGCAGCATAGGGTGGCAAGTGACCAG-GCAGGG -s simRat_chr6.simRat.chr6 6380 46 + 647215 AGCGCAGTCATGTAATAGGCA----GGAGTGGCAAGTGACTAGCGCAGTT - -a -s simMouse_chr6.simMouse.chr6 6911 32 + 636262 CAGTATTGGTCATTTATGTGTTAGCAATTCTA -s Anc0.Anc0refChr9 5953 32 - 35212 TAGCGCCAGTCATTTACATATTACCTATTCTA -s Anc1.Anc1refChr0 6332 32 + 16026 TAGCGCCAGTCATTTACATATTACCTATTCTA -s Anc2.Anc2refChr0 6401 32 + 56053 TAGCGCCATTCATTTACATATTACCTATTCTA -s mr.mrrefChr0 6606 32 + 130230 CAGTATTGGTCATTTATGTATTAGCAATTCTA -s simCow_chr6.simCow.chr6 6965 29 + 602619 CACCACCATTCACTTACATATTCCCTATT--- -s simDog_chr6.simDog.chr6 6731 32 + 593897 TAGTGCCATTCATTCACATGTTACCTATTCTA -s simHuman_chr6.simHuman.chr6 6268 29 + 601863 ---CGCCAGTCATTTACATATTATCCACACTA -s simRat_chr6.simRat.chr6 6426 32 + 647215 CAGTATTGGTCATTTATGCAGTAGCAATTCTA - -a -s simMouse_chr6.simMouse.chr6 6943 56 + 636262 GATGCAATTGGTGTCAAACTATGTAGAACAGTTTTGGTTAAACCATCACAGATCAG -s Anc0.Anc0refChr9 6000 55 - 35212 AGCATAGATCGTGTCATATTATGT-AAACAGTTTTGGTGAAACCAACACAGATCAG -s Anc1.Anc1refChr0 6379 55 + 16026 AGCATAGATCGTGTCATATTATGT-AAACAGTTTTGGTGAAACCAACACAGATCAG -s Anc2.Anc2refChr0 6455 55 + 56053 AGCATAGATCGTGTCATATTATGT-AAACAGTTTTTGTGAGACCAACACAGATCAA -s mr.mrrefChr0 6638 56 + 130230 AGCACAATTGGTGTCATACTATGTAAAACAGTTTTGGTGAAACCATCACAGATCAG -s simCow_chr6.simCow.chr6 7007 55 + 602619 AGCATAGCTCGTGTCATACTATGT-AAACAGTTTTAGTGTTACCAACACATATCAA -s simDog_chr6.simDog.chr6 6785 54 + 593897 AGCATAGATGGTGGCATATT-TGT-CAACAGTTTTTGTGAGACCAACACAGATCAA -s simHuman_chr6.simHuman.chr6 6312 55 + 601863 AGCATAGATCGTGTCATATTATGT-AAACAGTTTTGGTGAAACCAACACGAATCTG -s simRat_chr6.simRat.chr6 6458 56 + 647215 AGCACAACCAGTGTCATACTATGTAAAACAGTTTTGGTGAAACCATCACAGATCAG - -a -s simMouse_chr6.simMouse.chr6 6999 14 + 636262 CAATGGGTTTTTGA -s Anc0.Anc0refChr9 6058 13 - 35212 CAATGTCTC-TTGA -s Anc1.Anc1refChr0 6437 13 + 16026 CAATGTCTC-TTGA -s Anc2.Anc2refChr0 6513 13 + 56053 TAATGTCTC-TCGA -s mr.mrrefChr0 6694 14 + 130230 CAATGTGTCTTTGA -s simCow_chr6.simCow.chr6 7065 13 + 602619 TAATGTCTC-TGGA -s simDog_chr6.simDog.chr6 6842 13 + 593897 TGATGTCTA-TCAA -s simHuman_chr6.simHuman.chr6 6370 13 + 601863 CAATGTCTC-TTGA -s simRat_chr6.simRat.chr6 6514 14 + 647215 CAATGTGTCTTTGA - -a -s simMouse_chr6.simMouse.chr6 7013 21 + 636262 ATGGAGCCCAATGATAAGATT -s Anc0.Anc0refChr9 6073 21 - 35212 ATGGACCCCCATGTTAAGATT -s Anc1.Anc1refChr0 6452 21 + 16026 ATGGACCCCCATGTTAAGATT -s Anc2.Anc2refChr0 6528 21 + 56053 ATGGACCCACATGTTGAGATT -s mr.mrrefChr0 6708 21 + 130230 ATGGAGCCCAATGATAAGATT -s simCow_chr6.simCow.chr6 7080 18 + 602619 GTGGACCCACATGT---GATT -s simDog_chr6.simDog.chr6 6857 21 + 593897 AGGGACCCACATATTGAGATT -s simHuman_chr6.simHuman.chr6 6385 21 + 601863 ATGGATCCCCCTGCTAAGGTT -s simRat_chr6.simRat.chr6 6528 21 + 647215 ATGGAACCCAATGAAAAGATT - -a -s simMouse_chr6.simMouse.chr6 7034 4 + 636262 CAAT -s Anc0.Anc0refChr9 6094 4 - 35212 CAAT -s Anc1.Anc1refChr0 6473 4 + 16026 CAAT -s Anc2.Anc2refChr0 6549 4 + 56053 CAAT -s mr.mrrefChr0 6729 4 + 130230 CAAT -s simCow_chr6.simCow.chr6 7098 4 + 602619 CAAT -s simDog_chr6.simDog.chr6 6878 4 + 593897 CAAT -s simHuman_chr6.simHuman.chr6 6406 4 + 601863 CAAT -s simRat_chr6.simRat.chr6 6550 4 + 647215 CAAT - -a -s simMouse_chr6.simMouse.chr6 7038 17 + 636262 GCCCTATTGCTAGAGGG -s Anc0.Anc0refChr9 6098 14 - 35212 CCCCCATTGCCAGA--- -s Anc1.Anc1refChr0 6477 14 + 16026 CCCCCATTGCCAGA--- -s Anc2.Anc2refChr0 6553 14 + 56053 CCCCCATTGCCAGA--- -s mr.mrrefChr0 6733 17 + 130230 GCCCTATTGCTAGAGGG -s simCow_chr6.simCow.chr6 7102 14 + 602619 TCCCCATTGCCAGA--- -s simDog_chr6.simDog.chr6 6883 14 + 593897 CCCCCATGGCCGGA--- -s simHuman_chr6.simHuman.chr6 6410 14 + 601863 ATCCCATTGCCAGA--- -s simRat_chr6.simRat.chr6 6554 17 + 647215 TCCCTATTGTTAGAGGG - -a -s simMouse_chr6.simMouse.chr6 7055 2 + 636262 AA -s Anc1.Anc1refChr6 162888 2 - 197743 AG -s mr.mrrefChr0 6750 2 + 130230 AA -s mr.mrrefChr0 119322 2 - 130230 TG -s simMouse_chr6.simMouse.chr6 624411 2 - 636262 TG -s simRat_chr6.simRat.chr6 413017 2 + 647215 TG -s simRat_chr6.simRat.chr6 6571 2 + 647215 AG - -a -s simMouse_chr6.simMouse.chr6 7057 2 + 636262 AT -s Anc1.Anc1refChr6 162890 2 - 197743 CC -s mr.mrrefChr0 6752 2 + 130230 AT -s mr.mrrefChr0 119324 2 - 130230 CC -s simMouse_chr6.simMouse.chr6 624414 2 - 636262 CC -s simRat_chr6.simRat.chr6 413019 2 + 647215 TC -s simRat_chr6.simRat.chr6 6573 2 + 647215 AT - -a -s simMouse_chr6.simMouse.chr6 7059 53 + 636262 TGACCACCCAGCTACTACACATGATGATGGAGTACCAATTCCTGAGGATATGA -s mr.mrrefChr0 6754 52 + 130230 TGACCACCCAGCTACTACACATGATGATGGAGTACCAA-TCCTGAGGATATGA -s simRat_chr6.simRat.chr6 6575 52 + 647215 TGACTACCCAGTGACTACTCATAATGACAGTGCATCAA-CCCTGAGGATATGA - -a -s simMouse_chr6.simMouse.chr6 7112 73 + 636262 AATTTCCATTGGAGCTGAATCAGGGGATAGACTGCTGACATCCAACAAAGGTGATGAAGTTACACAAAATTAC -s mr.mrrefChr0 6806 73 + 130230 AATTTCCATTGGAGCTGAATCAGGGGATAGACTGCTGACATCCAACAAAGGTGATGAAGTTACACAAAATTAC -s simRat_chr6.simRat.chr6 6630 73 + 647215 AATTTCCATTTTAGGTGAATCAGGGGATACACTGCTGATATCAAACAAAAGTCGTGAAGTTGCACAAAATTAC - -a -s simMouse_chr6.simMouse.chr6 7185 58 + 636262 ACTAAATCATAGTCATGGCTAAAAGGTATGGACAACTACATACAGTTTATTTAGGTTG -s mr.mrrefChr0 6879 58 + 130230 ACTAAATCATAGTCATGGCTAAAAGGTATGGACAACTACATACAGTTTATTTAGGTTG -s simRat_chr6.simRat.chr6 6704 58 + 647215 ACTAAATCACTGTCATGGCTAGGAGGTGTAGACAAATACATACAGTTCAATTATATTG - -a -s simMouse_chr6.simMouse.chr6 7243 104 + 636262 TACTCTGCTTTGCTATTTGCTGAGTGGCTTTCTCTTTGTAATGATTTATCAATCCATTTTTGGGATGTCATGACCCTTGTAGAAGGTGACGTGCCTTAGCTGCT -s mr.mrrefChr0 6937 97 + 130230 TACTCTGCTTTGCTATTTGCTGAGTGACTTT-------TAATGATTTATCAATCCATTTTTGGGATGTCATGACCCTTGTAGAAGGTGACCTGCCTTAGCTGCT -s simRat_chr6.simRat.chr6 6764 92 + 647215 TATTCTACTTTGCTATTTGCAGGGTGACTTC-------TAAT-----CTTGATCCATTTTTGGGATGTCATCACCTTTGGAGGAGGTGACCCACCTTAGCTGCT - -a -s simMouse_chr6.simMouse.chr6 7347 637 + 636262 GTATTTACCGACCAGCATTGCTGTCACCAAGTGCCGAGAAATTGTCTTCTTTGATGCCCTGCATGACTCAAGTGTCCACATGCATGTATCTCGCATCATGTCCTTAGATAAGCAACATTAATACCACAAGCCTTTGGGAGCTGGTACTGACTCAAATGGTCAACCCAAAAAGGTATGGGGCAATTCTGTTGAACTTCATCTTAGAAGCTGAAAACTTTCATTGAGGCAAGTATCACTAGTTCTATGAAGGGCTGCCCACAAAGAGTGCAGTCCAAACGCACAGCACGGCGTTAATAGAGCTGGGGCAGTATTATTTTTGGATCCACATTTCTGGGTGGTACACAGGTACTGACTGCTCGTCTAAATTGTAGGACAGCACTAGAGACCAAATATAATCTCTTTAGTTACTGGGTACACAAGGTCGATCACCTTAAATATACAAAAATATAATGGCACTCATTTCAACCAAACCACTCTTGTCGAATCAAGATATTGTAAAAACTATGCACCTGAATTAGTCATTGTTGCTGTAGGCCCAATGCCTATGAGAAATTACATTCTCCAATGCCATGACTGGCCAGTGATCATCAACAGAACGAGACAGCTGAGCAGTCATGAGCCTACTTTCTCTTGGATG -s mr.mrrefChr0 7034 176 + 130230 GTATTTACCGATCAGCATTGCTGTCACCAAGTGCCGGGAAGTTGTCTTCTTTG---------ATGACTCTAG-GTCCACATGCATG----------------------------------ATACCACAAGCCTTTGGGAGCTGGTACTGACTCAAATGGTCA---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AGTGATCATCAACAGAACGAGACAGCTGAGCAGTCATGAGCCTACTTTCTCTTGGATG -s simRat_chr6.simRat.chr6 6857 176 + 647215 GTATTTACCAATCGACATTGCTGTTGCCAAGCACCGGGAAGTTGTCTTCTTGG---------ATGACTCTAA-GTCCATATGCATG----------------------------------ATACCACAGGTCTTGGGAAGCTTGTACTGTCTCAGATGATCA---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AGTGCTCATCAATAGAACAAGCCAGCTGAGCAGTCATGAGTCTATCTTCTCTTGGATG - -a -s simMouse_chr6.simMouse.chr6 7984 73 + 636262 CTGGGATGGGACTAGCAATCATTCATACCTGAGAGAAGTAATAGAGTAAGCCTCTTATACATGGCCTATGTTG -s mr.mrrefChr0 7210 70 + 130230 CTGGGATGGGACTAGCAATCATTCATACCTGAGAGAAGTAATAGAGTAAGCCTCTTATACA---CCTATGTTG -s simRat_chr6.simRat.chr6 7041 70 + 647215 CTGGGATGGGACTAGCAACCACTGGCACCTGAGAGAAGCACTAGAGTAAGCCTCGTACATA---CCTATGTTG - -a -s simMouse_chr6.simMouse.chr6 8057 673 + 636262 GCTACAGACTTGATAGCGAGGTACAAAAGGAAGCTATATTTTGGTTCATATCTATGAAGTGTGCATCTATGAAGTGTGTGGGGCAGTATTGATCCAGGACAGAAAGATCAGATATTACTGACTTCTTAAAAATTTTTTTCACTTTTTGAGGTATATTGGGACAACCACACCATCAATGGATAGGAAAAACAATACATGGAAATGACAAGCCTTTCAATCCTGATATGCTGCAAAATTGATTCGCACCAGAGGTGATACACAAAGTCTCTACACCTGGACCACCTGGTCACAGGTTTCAGGAGTGCTTAATTTTTTGTGCAGAGTATTAAAAAGAAGGTGCACTTCAGTTTGCTTCTGACAGGGGTTAGGTTGTCAGGCATACTAACCTCGTTATCTAGTCCATCAGGGATAGAATGCAGGAAAAAATGCATTATTATGAGATTCAGGGCACCGCTGGCATACTGCTCGGACCCAACATCCCTCACCATCACCATTGGCTGAGAGTGGTCAAGTATCGAGTGATGCTGCACAACTTAAGGGGGGAAGGTTGTAGTCTTTGGAGCTATTGAGAGCTTTGGTTAGACTGTGGCTGACAGTCTAACGTTAGTTATTGAACAACGGCTATTAATTTAGTTCCAATTGTGGGTGCAGATTGCCccaaccctaaacaaag -s mr.mrrefChr0 7280 662 + 130230 GCTACAGACTTGATAGCGAGGTACAAAAGGAAGCTATA-TTTGGTTCATATCTATGAAGTGTG---------AGTGTGTGGGGCAGTATT-ATCCAGGACAGAAAGATCAGATATTACTGACTTCTTAAAAATTTTTTTCACTTTTTGAGGTATATTGGGACAACCACACCATCAATGGATAGGAAAAACAATACATGGAAATGACAAGCCTTTCAATCCTGATATGCTGCAAAATTGATTCGCACCAGAGGTGATACACAAAGTCTCTACACCTGGACCACCTGGTCACAGGTTTCAGGAGTGCTTAATTTTTTGTGCAGAGTATTAAAAAGAAGGTGCACTTCAGTTTGCTTCTGACAGGGGTTAGGTTGTCAGGCATACTAACCTCGTTATCTAGTCCATCAGGGATAGAATGCAGGAAAAAATGCATTATTATGAGATTCAGGGCACCGCTGGCATACTGCTCGGACCCAACATCCCTCACCATCACCATTGGCTGAGAGTGGTCAAGTATCGAGTGATGCTGCACAACTTAAGGGGGGAAGGTTGTAGTCTTTGGAGCTATTGAGAGCTTTGGTTAGACTGTGACTGATAGCCTAACGTTAGCGATAGAACAATGGCTACTAATTTGGTTCCAATTGTGGGTGCTGATAGCCCCAAGCCTAAACAAAG -s simRat_chr6.simRat.chr6 7112 662 + 647215 GCTTCAGACTTCACAGCAAGTTCCGAAAGGAAGCTATA-TTTGGTTCATGTCTACAAAGTGTG---------GGGGGCAAGGGCAGCATT-ATCCAGGACAGAAAGATCAGATTTTACTGGGTTCTTAATAATTTTTTTCACTTTTTGAGATATTTTGGGACAATCACTCCATCAATGCGTGGAAACGACAATACATGGAAATGACAAGCCTCTTAACCCTGATGTGCCCCGGAACAGAGTCACACCAGAGGTGATACACAAAGTTTCTAAACCAAGATCACCTGGTTGCAGGTTGCAGGATTGCTTACTTTTTTATGCAGAGTATTAAAAAGAAGGTGTCCCTCCAGTTGCTTCTGATGCAGGTCAGCTTGACAGGCATACCAACCTCTTTATCTAGTCCATCAGGGATGGCATGCAGGAAAAAATGCATTGTTATGAGGTTTAGGTCACCGCTAGCACACTGCTAGGACCCAGTGTCCCGCACTATCCCTATTGGCTGGGAGTGGTCAAGTATCAAGTGGTGCTGGACTACTTAAGGGGGGAAGGTTGCAGTCTTTGGAGCTATTGAGAGCTTTGGTTAGACTGTGACTGATAGCCTAACGTTAGCGATAGAACAATGGCTACTAATTTGGTTCCAATTGTGGGTGCTGATAGCCCCAAGCCTAAACTTAG -s simRat_chr6.simRat.chr6 337508 102 + 647215 -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GCTTTGGTTAGACTGTGACTGATAGCCTAACGTTAGCGATAGAACAATGGCTACTAATTTGGTTCCAATTGTGGGTGCTGATAGCCCCAAGCCTAAACCGAT - -a -s simMouse_chr6.simMouse.chr6 8730 45 + 636262 ttttgacaaatagttcgagactggattgtaatgctgaaagatggc -s mr.mrrefChr0 7942 45 + 130230 ttttgacaaatagttcgagactggattgtaatgctgaaagatggc -s simRat_chr6.simRat.chr6 7780 45 + 647215 CTTTAACAAATAGTTCAAGAGTGAATTATAATCTTGAAAGATTGC - -a -s simMouse_chr6.simMouse.chr6 8775 138 + 636262 acctcctagagtcaacagatcccaagctgaatccacttcaagcacattatgaagtcagtggccgttGTAGATCACTCAACCTGTACTATATACAGAAGACTAGAACGTCAACTCTTAAGTTACTATGTCAGCTAACCA -s mr.mrrefChr0 7987 138 + 130230 acctcctagagtcaacagatcccaagctgaatccacttcaagcacattatgaagtcagtggccgttGTAGATCACTCAACCTGTACTATATACAGAAGACTAGAACGTCAACTCTTAAGTTACTATGTCAGCTAACCA -s simRat_chr6.simRat.chr6 7830 138 + 647215 ACCTCCTAGAGTCAACAGATCCTAAGCTGAATTCAATGCAATTACATTATGAAGTCAGTGGTTGTTGTAGGTCACTCAACCTGTGCTATATACAGAAGACTAGAACGATAACTGTTAAGGCACCATGTCAGCTAAACA - -a -s simMouse_chr6.simMouse.chr6 8913 123 + 636262 TATTGTCAGTGAGGAGTACCTCAAATGGTGCCAGACAGACTTTGGCAAATAGGTTATGAACACTCCTCCTACCAATCACAGTAGTGATACATGACTTCCCCCAGGATAGATCATGTGGGTTAC -s mr.mrrefChr0 8125 122 + 130230 TATTGTCAGTGAGGAGTACCTCAAATGGTGCCAGACAGACTTTGGC-AATAGGTTATGAACACTCCTCCTACCAATCACAGTAGTGATACATGACTTCCCCCAGGATAGATCATGTGGGTTAC -s simRat_chr6.simRat.chr6 7971 122 + 647215 TTCTGTCAGTGAGGAGTAGCCCAAATGGTGCCAGACAGAATTTGGC-GGTAGGTTATAAACCCTCCTCCTACCAATCATAGTAGTGCTACATAGCATCCCCCAGGATAGGTCATGTGGGTTAC - -a -s simMouse_chr6.simMouse.chr6 9036 102 + 636262 TACATGGGGCCTGTTCACCCCACCCGCCAAACTAACAAGGCCAAGAAAGGAAGGAGCTTTAGCCTGAGTTTCTCTAACTCCAGGTGTAATTCCCTTAGGGCT -s mr.mrrefChr0 8247 102 + 130230 TACATGGGGCCTGTTCACCCCACCCGCCAAACTAACAAGGCCAAGAAAGGAAGGAGCTTTAGCCTGAGTTTCTCTAACTCCAGGTGTAATTCCCTTAGGGCT -s simRat_chr6.simRat.chr6 8132 102 + 647215 TGTATGGGGCCTGTTCACCCCACCTGCCAAACTAACAAGGCCAAGAAAGGAAGGAGTTTGAGCCTGAATGTCTCTAACTCCACTTGTAAGTCCCTTAGGGCT - -a -s simMouse_chr6.simMouse.chr6 9138 14 + 636262 TTTCCGGCCCTATG -s mr.mrrefChr0 8349 14 + 130230 TTTCCGGCCCTATG -s simRat_chr6.simRat.chr6 8235 14 + 647215 TTTCTAGCCCTATG - -a -s simMouse_chr6.simMouse.chr6 9152 37 + 636262 GCAACAATAAATTTGGTTCTGAATATGAGGTGCCTAT -s mr.mrrefChr0 8363 37 + 130230 GCAACAATAAATTTGGTTCTGAATATGAGGTGCCTAT -s simRat_chr6.simRat.chr6 8282 37 + 647215 GCAAAAATGAATTTAGTTCCAACTCGGAGGTGCCCAT - -a -s simMouse_chr6.simMouse.chr6 9189 551 + 636262 ACAAACCACTCTAATTGGATTCTACTATTCAACTTTCAAACATTTCTAAGAGAGTTACTAAATATGGCGTAAGGAGAAACTTTTTAAAAACTCTTATCATGCTACAAGGGGAATAACAGgcatccataaaatccacctctcatgcttgcctggtacattggtgcacttgagattaaggggtgacaataggaccatcagcctgatcagaagtggacaaagaaaaagggtgggaatttagttccaaccaacaagtcagacttaacttcaaatctgtaaatgtaaagaaggataaaagggggataataaagggcattcaagtgaagtccaaaggcactaacccatctcaaaggtcaaaccattctaagtgtttgcccgctttatatatgggcattatagcttaaaatacacatcatgtgtgaatctcagatagGGCCTGAAATATGCTTGTACTGGAAATTCAAGCTGGTTGTCAACTTCTTCACGTACAGAATCTAGTGAATGTCAATTCAACAGTATCAACCAATCTAAGATTCAATTGAAACTGCCTAGGC -s mr.mrrefChr0 8400 507 + 130230 ACAAACCACTCTAATTGGATTCTACTATTCAA----CAAACATTTCTAAGAGAGTTACTAAATATGGCGTAAGGAGAAACTTTTTAAAAACTCTTATCATGCTA-AAGGGGAATAACAGgcatccataaaatccacctctcatgcttgcctggtacattggtgcacttgagattaaggggtgacaataggaccatc------atcagaagtggacaaagaaaaagggtgggaatttagttccaaccaacaagtcagac--------------------------aaggataaaagggggataataaagggcattcaagtgaagtccaaaggcactaacccatctcaaaggtcaaaccattctaagtgtttgcccgctttatatatgggcattat-------aatacacatcatgtgtgaatctcagatagGGCCTGAAATATGCTTGTACTGGAAATTCAAGCTGGTTGTCAACTTCTTCACGTACAGAATCTAGTGAATGTCAATTCAACAGTATCAACCAATCTAAGATTCAATTGAAACTGCCTAGGC -s simRat_chr6.simRat.chr6 8320 507 + 647215 ACAAACCATTCTGATTGGACTCTACTATTCAA----CAAACACAGGTAAGCGAGTTACTAAATATGGTGTAAGGAGAAATTTTTTAAAAACTCTTATCAACCCA-AAAGGAAATAACTGGCATCCATACAATCCACCTCCCTTGCTTGCCTGGCATGTTGGTGCGCTCAAGATTAAGGGCTGACAATGAGACCATC------ACCAGAAGGGTATATAGAAAAGGGTTGGGAATTTAGTTCCAACGCACAAGTCAGAC--------------------------Aaggataaaagcgggataaaaaaggtcatccaagtgaagtccaaaggcacaaaccctcctcaaacgttaacccattctaagtgtttgccagcttaatatatggggattat-------aatatgcagcatgtgtgaatctcagaCGTGGTCTGAAATATGCTTGTTCTGGAAAACCTGCCTGGTTGCCAGCATCTTCACACACAGAGTCTAGTGAATGTCAATCCAACAGTGTTAACCAATCTAAGATTCAATTGACACTGCCTGGAC - -a -s simMouse_chr6.simMouse.chr6 9740 85 + 636262 AGGTAGCTGCTTATTTTTCTCTGCTCTACCTATGCCCACTCAAACCAGGCACTCAAGTGAGGACCAAAGACTTTGTTGGTATTGT -s mr.mrrefChr0 8907 84 + 130230 AGGTAGctgctta-ttttctctgctctacctatgcccactcaaaccaggcactcaagtgaggaccaaagactttgttggtattgt -s simRat_chr6.simRat.chr6 8854 84 + 647215 AGGTACctgctta-ttttctctgctctacttatgcccactcaaaccaagcattcaagtgaggaccaaagattgcgttggtattgt - -a -s simMouse_chr6.simMouse.chr6 9825 4 + 636262 GCCC -s mr.mrrefChr0 8991 4 + 130230 gccc -s simRat_chr6.simRat.chr6 8946 4 + 647215 gccc - -a -s simMouse_chr6.simMouse.chr6 9829 17 + 636262 TGTGCAAGGCTATGTTT -s mr.mrrefChr0 8995 17 + 130230 tgtgcaaggctatgttt -s simRat_chr6.simRat.chr6 8964 17 + 647215 tctgcaaggccgtgtct - -a -s simMouse_chr6.simMouse.chr6 9846 41 + 636262 acaatacaagtaacagcaaaaaacggctgctgacaacatgt -s mr.mrrefChr0 9012 41 + 130230 acaatacaagtaacagcaaaaaacggctgctgacaacatgt -s simRat_chr6.simRat.chr6 9203 41 + 647215 acaatataACTACCAGTAAAAATGGGCTGCTGACACCAGGT - -a -s simMouse_chr6.simMouse.chr6 9887 21 + 636262 caacagtgatccaaagattat -s mr.mrrefChr0 9053 21 + 130230 caacagtgatccaaagattat -s simRat_chr6.simRat.chr6 9245 21 + 647215 CAGTAGTGCTCCAAAGATCAT - -a -s simMouse_chr6.simMouse.chr6 9908 35 + 636262 gaatggaaaagctgcatgagtgagagctcacacct -s mr.mrrefChr0 9074 28 + 130230 gaatggaaaagc-------gtgagagctcacacct -s simRat_chr6.simRat.chr6 9284 28 + 647215 GAATCGAAAACC-------GTGGGCCTCTACTCGT - -a -s simMouse_chr6.simMouse.chr6 9943 18 + 636262 ccaaggatgattagactg -s mr.mrrefChr0 9102 18 + 130230 ccaaggatgattagactg -s simRat_chr6.simRat.chr6 9313 18 + 647215 CCGAACATGGTTAAACTG - -a -s simMouse_chr6.simMouse.chr6 9961 15 + 636262 ggtcatcaaggtaaa -s mr.mrrefChr0 9120 15 + 130230 ggtcatcaaggtaaa -s simRat_chr6.simRat.chr6 9334 15 + 647215 GGTCATCAGAGTTAA - -a -s simMouse_chr6.simMouse.chr6 9976 41 + 636262 tttgagctaagagagatcaagaggcaaaggataatgtctaa -s mr.mrrefChr0 9135 41 + 130230 tttgagctaagagagatcaagaggcaaaggataatgtctaa -s simRat_chr6.simRat.chr6 9352 41 + 647215 TCTGAACTAAAAGAAATCAAGAGGTTAAGGATAATGTCTAA - -a -s simMouse_chr6.simMouse.chr6 10017 20 + 636262 tcggccagtgagagagtcgg -s mr.mrrefChr0 9176 20 + 130230 tcggccagtgagagagtcgg -s simRat_chr6.simRat.chr6 9395 20 + 647215 TCAACTGGTGTGATAGTAGG - -a -s simMouse_chr6.simMouse.chr6 10037 53 + 636262 ttttgctggtcttgaggttagattaatgaaattcacaggcctcaactggacat -s mr.mrrefChr0 9196 53 + 130230 ttttgctggtcttgaggttagattaatgaaattcacaggcctcaactggacat -s simRat_chr6.simRat.chr6 9418 53 + 647215 TTCTGCTGGTCTATAGACTAGATTAATGAAATTTGCAGGCCTCTGCTGGACAT - -a -s simMouse_chr6.simMouse.chr6 10090 22 + 636262 gcatgtagagtaacaaAGGTTG -s mr.mrrefChr0 9249 22 + 130230 gcatgtagagtaacaaAGGTTG -s simRat_chr6.simRat.chr6 9473 22 + 647215 TCATGTTGAGTAACAAAGGATG - -a -s simMouse_chr6.simMouse.chr6 10112 169 + 636262 ATATCTTCAAATATACACCAATCAGTTGCACTAACTTCTTTCTGCTAAGAAGAAAGACAGCTTGGTGGTAATTGGCACAATGAGACCCCTGGGGAAAACTTAGTTGTGATTGAGGATTTTTGAGACCCCTGGGGAGGGGGGGAAGGGGAGCACCTGAGAGTCGGAGACC -s mr.mrrefChr0 9271 162 + 130230 ATATCTTCAAATATACACCAATCAGTTGCACTAACTTCTTTCTGCTAAG----AAGACAGCTTGGTGGTAATT--CACAATGAGACCCCTGGGGAAAACTTAGTTGTGATTGAGGATTTTTG-GACCCCTGGGGAGGGGGGGAAGGGGAGCACCTGAGAGTCGGAGACC -s simRat_chr6.simRat.chr6 9498 162 + 647215 ACATCTTCAAATACACTTCAATCTGTTGAACTAATTTCTTTGTGCTAAT----AAGACAACTTGGGGGTATTT--CACAATGAGTCACCTAGGCAAAACTTAGTTGTGGTTGAGGATAATCG-GACCCCTGGGGAGAGGGGTAGGGAGGGCAGCTGAGAGCTGGAGACC - -a -s simMouse_chr6.simMouse.chr6 10281 16 + 636262 ATTTCTATAAAATGAA -s mr.mrrefChr0 9433 16 + 130230 ATTTCTATAAAATGAA -s simRat_chr6.simRat.chr6 9692 16 + 647215 GTTTCTATGGCTTGAA - -a -s simMouse_chr6.simMouse.chr6 10297 553 + 636262 TTGACTATCATGACTCAGTGCATGTTGCAAGGATAGTGTTCAGGTGGTCAATCATTGGCTCTAGAATGAACTCATTTATGAGGCTACTCGACTTTATTACTAGTGAAGTTCTACAGGCAGTATAGAGTCAGTATAGATATGTCAGTTTCACTTGCAATCCAATGGACAGAAACTACTTCTTCAATGTCTGAATCTAGCAAAGGTATGATAAAAGGAACACAGAGCTACCAGGTGAAAAGAAATAGGGAAGCatagggaagcccacgcattgacaatcacttgagattcagtctggagaagctgggatggcttgggatgtataaacttataaatttcacaagactcatggtatgtaatggaatatattaacagaatcacatgattagatcattggataatggtggtgcacagattgaattaaacaaacaggatcacatcacaggttagccataatgaatgagttagaaagtgaccgataacagtgcctgaatgttgcctgcacaagcataaagctgctttccagtggttatggttggacacttgtgtaatccct -s mr.mrrefChr0 9449 472 + 130230 TTGACTATCATGACTCAGTGCATGTTGCAA-------------GTGGTCAA-----------------------------------------TTTATTACTAGTGAAGTTCTACAGGCAGTATAGAGTC-------ATATGTCAGTTTCACTTGCAAT---ATG-------ACTACTTCTTCAATGTCTGAATCTAGCAAAGGTATGATAAAAGGAACACAGAGCTACCAGGTGAAAAGA----------Catagggaagcccacgcattgacaatcacttgagattcagtctggagaagctgggatggcttgggatgtataaacttataaatttcacaagactcatggtatgtaatggaatatattaacagaatcacatgattagatcattggataatggtggtgcacagattgaattaaacaaacaggatcacatcacaggttagccataatgaatgagttagaaagtgaccgataacagtgcctgaatgttgcctgcacaagcataaagctgctttccagtggttatggttggacacttgtgtaatccct -s simRat_chr6.simRat.chr6 9710 472 + 647215 TTGACTATCATGAATCAGTGTGTGTTGTAA-------------GTGGTCAA-----------------------------------------CTTGCTACCACTGAAGTTCTACAAGCAGCATAGAGGC-------ATATGTCAGTTTCACATCTAAT---ATG-------AGTACTTCTTGAATGTCTGAGTCTGTCAAAGATATGATGAAAGGAGCACAGAGCTACTATGTCAAAAGC----------CACAgggaagcttgtacatttacaattacttgagactcattctggagaagctgggatggcttgggatatatagacttgtaaatgtcacaagactcatgctatataatggagtatattaatggaattagatcaggagatcaatggataatggtgatggacaaattgaattaaacaaacaggatcacatcacagggtaaccacaatgaacaagttaagaattgacgcatgaccgcacctgaatgttggcagCATAAGCACAAAGCTGCTTTCCAGTGATTATGGTTGGACACTTGTGTAATCACT - -a -s simMouse_chr6.simMouse.chr6 10850 47 + 636262 ttgagtgtcactagagggcaccaaggacgttccataatcatcGAGTA -s mr.mrrefChr0 9921 47 + 130230 ttgagtgtcactagagggcaccaaggacgttccataatcatcGAGTA -s simRat_chr6.simRat.chr6 10226 47 + 647215 TTGACTGGCACTAGAGGACAACGAGGATGTTGCATAACCATTACGTA - -a -s simMouse_chr6.simMouse.chr6 10897 84 + 636262 CCCAATTGTTAAAGGATCTCAAATATTCCCAGATCAGATTACAGGATCACAATCTGTCAATGCTAGAAGAATAGTGGTCTAGCA -s mr.mrrefChr0 9968 84 + 130230 CCCAATTGTTAAAGGATCTCAAATATTCCCAGATCAGATTACAGGATCACAATCTGTCAATGCTAGAAGAATAGTGGTCTAGCA -s simRat_chr6.simRat.chr6 10298 84 + 647215 CCCAATTGTTACAGGATTTCGAATACTCCCGAATCAAATTACAAGATCACAACCTGCTAGTGATAGAAGCCTAGTGTTCTAGCA - -a -s simMouse_chr6.simMouse.chr6 10981 246 + 636262 GTAATTACCGATTGCTTTCTTAAGTCATTAGGGTAGGTTGTCAAAGAGGTGTGAATAAACATGCCCGCACACTTGAGCTTTGACCTACTCTAGGGGATTGACCATCTCTGAAGCTACTGTAGCCTAAGTAGGATGCTGCTGAAGTCAGATTCTTGCATTACACACTTAAACAAGTCATCGGTTACCTGTTTGGGGCATGTCTTTATATTTGAAGCCAGCAAGCAAACCATCTTGATATTAGCCTCA -s mr.mrrefChr0 10052 243 + 130230 GTAATTACCGATTGCTTTCTTAAGTCATTAGGGTAGGTTGTCAAAGAGGTGTGAATAAACATGCCCGCACACTTGAGCTTTGACCTACTCTAGGGGATTGACCATCTCTGAAGCTACTGTAGCCTAAGTAGGATGCTGCTGAAGTCAGATTCTTGCATTA-ACACTTAAACAAGTCATCGGTTACCTGTTTGGGGCATGTCTTTATATTTGAAGCCAGCAAGCAA--CATCTTGATATTAGCCTCA -s simRat_chr6.simRat.chr6 10384 243 + 647215 GTAATAACCTATTGCTTTCTTGAGTCTCTAAGAAAGGTTGCCAAAGAGGCATGAACAAACAAGCCCACACAATTGAACTTTGACTTACTCCTGGGGCTGAACCATCTCTGAAGCTACTGTAGCCTGAATGGGACCCTGCTGAAGTCAGGTTCTGGCATTA-ACACTTAAACAGGTCATCGGTGACCTGTTTGGGGCATGTCTTTATATTTGAAGACAGCAAACTA--CATCTTGATATTAGCCTCA - -a -s simMouse_chr6.simMouse.chr6 11227 47 + 636262 TGTTAATTCCCATATGTATCAGGGGTGTTGGCTTCTTCTGTCACTGT -s mr.mrrefChr0 10295 46 + 130230 TGTTAATTCCCATATGTATCAGGGGTGTT-GCTTCTTCTGTCACTGT -s simRat_chr6.simRat.chr6 10630 46 + 647215 TGTTACCTCCCATATGTATCTGGGGAGTT-GCTTCTTGTGTCGCTGT - -a -s simMouse_chr6.simMouse.chr6 11274 10 + 636262 CTGTAACACC -s Anc1.Anc1refChr6 162892 10 - 197743 CTGCAATATC -s mr.mrrefChr0 10341 10 + 130230 CTGTAACACC -s mr.mrrefChr0 119326 10 - 130230 CTGCAATATC -s simMouse_chr6.simMouse.chr6 624416 10 - 636262 CTGCAATATC -s simRat_chr6.simRat.chr6 413021 10 + 647215 TTGCAATATC -s simRat_chr6.simRat.chr6 10677 10 + 647215 CTGCAATATC - -a -s simMouse_chr6.simMouse.chr6 11284 5 + 636262 CAATA -s Anc1.Anc1refChr6 162902 5 - 197743 CAATA -s mr.mrrefChr0 10351 5 + 130230 CAATA -s mr.mrrefChr0 119336 5 - 130230 CAATA -s mr.mrrefChr5 74040 5 - 294540 CAAAA -s simMouse_chr6.simMouse.chr6 624426 5 - 636262 CAATA -s simMouse_chr6.simMouse.chr6 262375 5 - 636262 CAAAA -s simRat_chr6.simRat.chr6 413031 5 + 647215 TAATA -s simRat_chr6.simRat.chr6 281231 5 - 647215 CAAAA -s simRat_chr6.simRat.chr6 10687 5 + 647215 CAATA - -a -s simMouse_chr6.simMouse.chr6 11289 6 + 636262 CAGACA -s Anc0.Anc0refChr2 11216 6 - 17989 CACATT -s Anc1.Anc1refChr2 30472 6 + 144309 CACATT -s Anc1.Anc1refChr6 162907 6 - 197743 CAGACA -s Anc2.Anc2refChr0 4225 6 - 56053 CACATT -s mr.mrrefChr0 10356 6 + 130230 CAGACA -s mr.mrrefChr0 119341 6 - 130230 CAGACA -s mr.mrrefChr5 74045 6 - 294540 CAGGTG -s simCow_chr6.simCow.chr6 547355 6 - 602619 CACATT -s simHuman_chr6.simHuman.chr6 50002 6 + 601863 TACACT -s simMouse_chr6.simMouse.chr6 624431 6 - 636262 CAGACA -s simMouse_chr6.simMouse.chr6 262380 6 - 636262 CAGGTG -s simRat_chr6.simRat.chr6 413036 6 + 647215 CAGACA -s simRat_chr6.simRat.chr6 281236 6 - 647215 CAGGCG -s simRat_chr6.simRat.chr6 10692 6 + 647215 CAGACA - -a -s simMouse_chr6.simMouse.chr6 11295 30 + 636262 CTACAAAGAACATTCAACCACAGGAGTACT -s Anc0.Anc0refChr2 11222 27 - 17989 CCGCACGGAATGT---GCCACAGGAGTGCT -s Anc1.Anc1refChr2 30478 27 + 144309 CCGCACGGAATGT---GCCACAGGAGTGCT -s Anc1.Anc1refChr6 162913 30 - 197743 CTACAAAGAATGTTCAACCACAGGAGTACT -s Anc2.Anc2refChr0 4231 27 - 56053 CCGCACGGAATGT---GCCACAGGAGTGCT -s mr.mrrefChr0 10362 30 + 130230 CTACAAAGAACATTCAACCACAGGAGTACT -s mr.mrrefChr0 119347 30 - 130230 CTACAAAGTATGTGCCACTACAGGAGTACT -s mr.mrrefChr5 74051 30 - 294540 CTGCAAAGAATGCTCAACCACAGGAGTACT -s simCow_chr6.simCow.chr6 547362 27 - 602619 CCGCACGGAATGT---GCCACAGGAGTGCT -s simDog_chr6.simDog.chr6 545021 3 - 593897 ---------------------------GCT -s simHuman_chr6.simHuman.chr6 50008 27 + 601863 CTACAAGTAATGT---GCCACACGAGGGCT -s simMouse_chr6.simMouse.chr6 624437 30 - 636262 CTACAAAGTATGTGCCACTACAGGAGTACT -s simMouse_chr6.simMouse.chr6 262388 30 - 636262 CTGCAAAGAATGCTCAACCACAGGAGTACT -s simRat_chr6.simRat.chr6 413042 30 + 647215 ATACAAAGAATGTTCCACTACAGGAGTACT -s simRat_chr6.simRat.chr6 281242 30 - 647215 CCGTAAAGAATGTTCAACCACAGGAGTCCT -s simRat_chr6.simRat.chr6 10698 30 + 647215 CTATAAAGAATGTTCAACCACAGGAGTACT - -a -s simMouse_chr6.simMouse.chr6 11325 12 + 636262 GTATTCAGGCAG -s Anc0.Anc0refChr2 11253 12 - 17989 GTGCTCAGGGAG -s Anc1.Anc1refChr2 30509 12 + 144309 GTGCTCAGGGAG -s Anc1.Anc1refChr6 162943 12 - 197743 ATATTCAGGTAG -s Anc2.Anc2refChr0 4262 12 - 56053 GTGCTCAGGGAG -s mr.mrrefChr0 10392 12 + 130230 GTATTCAGGCAG -s mr.mrrefChr0 119377 12 - 130230 ATATTCAGGTAG -s mr.mrrefChr5 74081 12 - 294540 ATATTCAGGTAG -s simCow_chr6.simCow.chr6 547393 12 - 602619 GTGCTCAGGTAG -s simDog_chr6.simDog.chr6 545028 12 - 593897 GTGCTCAGTGAG -s simHuman_chr6.simHuman.chr6 50039 12 + 601863 GTGCTCATGGAG -s simMouse_chr6.simMouse.chr6 624467 12 - 636262 ATATTCAGGTAG -s simMouse_chr6.simMouse.chr6 262418 12 - 636262 ATATTCAGGTAG -s simRat_chr6.simRat.chr6 413072 12 + 647215 GTATTCGGGTAG -s simRat_chr6.simRat.chr6 281272 12 - 647215 ATATTCAGGTAT -s simRat_chr6.simRat.chr6 10728 12 + 647215 GTATTCAGGTAG - -a -s simMouse_chr6.simMouse.chr6 11337 2 + 636262 TG -s Anc0.Anc0refChr2 11265 2 - 17989 TG -s Anc1.Anc1refChr2 30521 2 + 144309 TG -s Anc1.Anc1refChr6 162955 2 - 197743 TG -s Anc2.Anc2refChr0 4274 2 - 56053 TG -s mr.mrrefChr0 10404 2 + 130230 TG -s mr.mrrefChr0 119389 2 - 130230 CT -s mr.mrrefChr5 74093 2 - 294540 TG -s simCow_chr6.simCow.chr6 547405 2 - 602619 TG -s simDog_chr6.simDog.chr6 545040 2 - 593897 TG -s simHuman_chr6.simHuman.chr6 50051 2 + 601863 TG -s simMouse_chr6.simMouse.chr6 624481 2 - 636262 CT -s simMouse_chr6.simMouse.chr6 262430 2 - 636262 TG -s simRat_chr6.simRat.chr6 413084 2 + 647215 CA -s simRat_chr6.simRat.chr6 281284 2 - 647215 TG -s simRat_chr6.simRat.chr6 10740 2 + 647215 TG - -a -s simMouse_chr6.simMouse.chr6 11339 3 + 636262 CTC -s Anc0.Anc0refChr2 11285 3 - 17989 CCA -s Anc1.Anc1refChr2 30541 3 + 144309 CCA -s Anc1.Anc1refChr6 162975 3 - 197743 CCA -s Anc2.Anc2refChr0 4294 3 - 56053 CCA -s mr.mrrefChr0 10406 3 + 130230 CTC -s mr.mrrefChr0 119409 3 - 130230 CCA -s mr.mrrefChr5 74113 3 - 294540 CCA -s simCow_chr6.simCow.chr6 547425 3 - 602619 CCA -s simDog_chr6.simDog.chr6 545060 3 - 593897 CCA -s simHuman_chr6.simHuman.chr6 50071 3 + 601863 CCA -s simMouse_chr6.simMouse.chr6 624501 3 - 636262 CCA -s simMouse_chr6.simMouse.chr6 262450 3 - 636262 CCA -s simRat_chr6.simRat.chr6 413104 3 + 647215 CCA -s simRat_chr6.simRat.chr6 281304 3 - 647215 CTG -s simRat_chr6.simRat.chr6 10742 3 + 647215 CCT - -a -s simMouse_chr6.simMouse.chr6 11342 16 + 636262 ACGAAGGTTTTTACCA -s Anc0.Anc0refChr2 11288 16 - 17989 ACTCGGGTGTTCACTA -s Anc1.Anc1refChr2 30544 16 + 144309 ACTCGGGTGTTCACTA -s Anc1.Anc1refChr6 162978 16 - 197743 ACAAAGGTCTTCACCA -s Anc2.Anc2refChr0 4297 16 - 56053 ACTCGGGTGTTCACTA -s mr.mrrefChr0 10409 16 + 130230 ACGAAGGTTTTTACCA -s mr.mrrefChr0 119412 16 - 130230 ACAAACGTCTTCACCA -s mr.mrrefChr5 74116 16 - 294540 ACATAAATCTTCACCA -s simCow_chr6.simCow.chr6 547428 16 - 602619 ACGCGGGTGCTCACCA -s simDog_chr6.simDog.chr6 545063 16 - 593897 CCTCAAGCCTTCACTA -s simHuman_chr6.simHuman.chr6 50074 16 + 601863 ACAAGGGTGTTCACTA -s simMouse_chr6.simMouse.chr6 624504 16 - 636262 ACAAACGTCTTCACCA -s simMouse_chr6.simMouse.chr6 262453 16 - 636262 ACATAAATCTTCACCA -s simRat_chr6.simRat.chr6 413107 16 + 647215 ACAAAAGTCTTCACCA -s simRat_chr6.simRat.chr6 281307 16 - 647215 GCGAAGGTCTTCAACA -s simRat_chr6.simRat.chr6 10763 16 + 647215 ACAAAGGCCCTCACCA - -a -s simMouse_chr6.simMouse.chr6 11358 3 + 636262 TGA -s Anc0.Anc0refChr2 11306 3 - 17989 TGA -s Anc1.Anc1refChr2 30562 3 + 144309 TGA -s Anc1.Anc1refChr6 162994 3 - 197743 TGA -s Anc2.Anc2refChr0 4315 3 - 56053 TGA -s mr.mrrefChr0 10425 3 + 130230 TGA -s mr.mrrefChr0 119428 3 - 130230 TGA -s mr.mrrefChr5 74132 3 - 294540 TGA -s simCow_chr6.simCow.chr6 547446 3 - 602619 TCA -s simDog_chr6.simDog.chr6 545081 3 - 593897 TGA -s simHuman_chr6.simHuman.chr6 50092 3 + 601863 TGA -s simMouse_chr6.simMouse.chr6 624520 3 - 636262 TGA -s simMouse_chr6.simMouse.chr6 262469 3 - 636262 TGA -s simRat_chr6.simRat.chr6 413123 3 + 647215 TGA -s simRat_chr6.simRat.chr6 281323 3 - 647215 TGA -s simRat_chr6.simRat.chr6 10779 3 + 647215 TGA - -a -s simMouse_chr6.simMouse.chr6 11361 16 + 636262 AAATGGTATTGAGCAA -s Anc0.Anc0refChr2 11319 16 - 17989 AACTAGACTTAAATGA -s Anc1.Anc1refChr2 30575 16 + 144309 AACTAGACTTAAATGA -s Anc1.Anc1refChr6 162997 16 - 197743 AAATGGTATTGAGCAA -s Anc2.Anc2refChr0 4328 16 - 56053 AACTAGACTTAAATGA -s mr.mrrefChr0 10428 16 + 130230 AAATGGTATTGAGCAA -s mr.mrrefChr0 119431 16 - 130230 AAATGAATATGAGCGA -s mr.mrrefChr5 74135 16 - 294540 AAATGGTATTGAGCAA -s simCow_chr6.simCow.chr6 547459 8 - 602619 AACTCAAC-------- -s simDog_chr6.simDog.chr6 545094 16 - 593897 AACTAGACTTAAATGA -s simHuman_chr6.simHuman.chr6 50108 16 + 601863 CACTGGTTTTGAGCAA -s simMouse_chr6.simMouse.chr6 624523 16 - 636262 AAATGAATATGAGCGA -s simMouse_chr6.simMouse.chr6 262472 16 - 636262 AAATGGTATTGAGCAA -s simRat_chr6.simRat.chr6 413126 16 + 647215 AAATGAATATGAGCAA -s simRat_chr6.simRat.chr6 281326 16 - 647215 AAATGGAACTGAGCAA -s simRat_chr6.simRat.chr6 10782 16 + 647215 AAATGGTATTGAGCAA - -a -s simMouse_chr6.simMouse.chr6 11377 18 + 636262 ATGACCCTGTCTGACAGG -s Anc0.Anc0refChr2 11342 12 - 17989 ATAGGCCTGCCT------ -s Anc1.Anc1refChr2 30598 12 + 144309 ATAGGCCTGCCT------ -s Anc1.Anc1refChr6 163013 12 - 197743 ATGGCCCTGTCT------ -s Anc2.Anc2refChr0 4351 12 - 56053 ATAGGCCTGCCT------ -s mr.mrrefChr0 10444 12 + 130230 ATGACCCTGTCT------ -s mr.mrrefChr0 119447 12 - 130230 ATGGCCCTGTCC------ -s mr.mrrefChr5 74151 12 - 294540 AGGGCCCTGCCT------ -s simCow_chr6.simCow.chr6 547467 4 - 602619 --------AACT------ -s simDog_chr6.simDog.chr6 545117 12 - 593897 ATAGGCCTGCCT------ -s simHuman_chr6.simHuman.chr6 50131 12 + 601863 AGAGCCCTGCCC------ -s simMouse_chr6.simMouse.chr6 624539 12 - 636262 ATGGCCCTGTCC------ -s simMouse_chr6.simMouse.chr6 262488 12 - 636262 AGGGCCCTGCCT------ -s simRat_chr6.simRat.chr6 413142 12 + 647215 ATGGCCCTGTCC------ -s simRat_chr6.simRat.chr6 281342 12 - 647215 ATGGCACTGCCT------ -s simRat_chr6.simRat.chr6 10798 12 + 647215 ATGGCTCTGCCT------ - -a -s simMouse_chr6.simMouse.chr6 11395 6 + 636262 TCACTA -s Anc0.Anc0refChr2 11360 6 - 17989 TTACAA -s Anc1.Anc1refChr2 30616 6 + 144309 TTACAA -s Anc1.Anc1refChr6 163031 6 - 197743 TCACTA -s Anc2.Anc2refChr0 4369 6 - 56053 TTACAA -s mr.mrrefChr0 10456 6 + 130230 TCACTA -s mr.mrrefChr0 119465 6 - 130230 TCACCA -s mr.mrrefChr5 74169 6 - 294540 TCACTA -s simCow_chr6.simCow.chr6 547477 6 - 602619 TTACCA -s simDog_chr6.simDog.chr6 545135 6 - 593897 TCAGAC -s simHuman_chr6.simHuman.chr6 50149 6 + 601863 TTACAA -s simMouse_chr6.simMouse.chr6 624557 6 - 636262 TCACCA -s simMouse_chr6.simMouse.chr6 262506 6 - 636262 TCACTA -s simRat_chr6.simRat.chr6 413160 6 + 647215 TCACCA -s simRat_chr6.simRat.chr6 281360 6 - 647215 TCACTA -s simRat_chr6.simRat.chr6 10810 6 + 647215 TCACTA - -a -s simMouse_chr6.simMouse.chr6 11401 11 + 636262 GAAGGAACATT -s Anc0.Anc0refChr2 11366 11 - 17989 GAAAGAACATT -s Anc1.Anc1refChr2 30622 11 + 144309 GAAAGAACATT -s Anc1.Anc1refChr6 163037 11 - 197743 GAAGGAACATT -s Anc2.Anc2refChr0 4375 11 - 56053 GAAAGAACATT -s mr.mrrefChr0 10462 11 + 130230 GAAGGAACATT -s mr.mrrefChr0 119471 11 - 130230 AAAGGAAAATT -s mr.mrrefChr5 74175 11 - 294540 GAAAGAACATT -s simCow_chr6.simCow.chr6 547483 11 - 602619 AAAAGAACATT -s simDog_chr6.simDog.chr6 545169 11 - 593897 GAAGGAACACT -s simHuman_chr6.simHuman.chr6 50155 11 + 601863 GAAACGTCTTT -s simMouse_chr6.simMouse.chr6 624563 11 - 636262 AAAGGAAAATT -s simMouse_chr6.simMouse.chr6 262512 11 - 636262 GAAAGAACATT -s simRat_chr6.simRat.chr6 413166 11 + 647215 AAAGGCATATT -s simRat_chr6.simRat.chr6 281366 11 - 647215 GAGAGAACATT -s simRat_chr6.simRat.chr6 10816 11 + 647215 GAAAGAACATT - -a -s simMouse_chr6.simMouse.chr6 11412 31 + 636262 CCCAGATAATAAAGGTCTGTTCAAGACTGAG -s Anc0.Anc0refChr2 11378 31 - 17989 CCCAGATAATCAAAATCTTTCTAAGACTGAA -s Anc1.Anc1refChr2 30634 31 + 144309 CCCAGATAATCAAAATCTTTCTAAGACTGAA -s Anc1.Anc1refChr6 163048 31 - 197743 CCCAGATAATAAAGATCTGTTCAAGACTGAG -s Anc2.Anc2refChr0 4387 31 - 56053 CCCAGATAATCAAAATCTTTCTAAGACTGAA -s mr.mrrefChr0 10473 31 + 130230 CCCAGATAATAAAGGTCTGTTCAAGACTGAG -s mr.mrrefChr0 119482 31 - 130230 CCTAGACAATCAGAATTGGTCCAAGACTGAG -s mr.mrrefChr5 74186 31 - 294540 CCCAGATAATAAAGATCTGTTCAAGACTCGG -s simCow_chr6.simCow.chr6 547495 15 - 602619 CA-----AATGAAAATCTTT----------- -s simDog_chr6.simDog.chr6 545181 31 - 593897 CCCAGATAATCAAAATATATCTAAGACTGAA -s simHuman_chr6.simHuman.chr6 50167 31 + 601863 CCTGGACAATCAAAAGCTTTCCAAGGCTGAG -s simMouse_chr6.simMouse.chr6 624574 31 - 636262 CCTAGACAATCAGAATTGGTCCAAGACTGAG -s simMouse_chr6.simMouse.chr6 262523 31 - 636262 CCCAGATAATAAAGATCTGTTCAAGACTCGG -s simRat_chr6.simRat.chr6 413177 31 + 647215 CCTAGACAATCAAAATCTGTCCAAGACTGAG -s simRat_chr6.simRat.chr6 281377 31 - 647215 CCCAGATAATAAAGATCTGTTCAAGATACAG -s simRat_chr6.simRat.chr6 10827 31 + 647215 CCCAGATAATAAAGGTCTGTTCAAGACTTAA - -a -s simMouse_chr6.simMouse.chr6 11443 9 + 636262 ACAACTTTC -s Anc0.Anc0refChr2 11409 9 - 17989 TTAACATTT -s Anc1.Anc1refChr2 30665 9 + 144309 TTAACATTT -s Anc1.Anc1refChr6 163079 9 - 197743 TCAACATTC -s Anc2.Anc2refChr0 4418 9 - 56053 TTAACATTT -s mr.mrrefChr0 10504 9 + 130230 ACAACTTTC -s mr.mrrefChr0 119513 9 - 130230 TTTAGCATT -s mr.mrrefChr5 74217 9 - 294540 TCAACATTC -s simCow_chr6.simCow.chr6 547510 8 - 602619 -TAACATTT -s simDog_chr6.simDog.chr6 545212 9 - 593897 TTATCATCT -s simHuman_chr6.simHuman.chr6 50198 9 + 601863 TTAACATTT -s simMouse_chr6.simMouse.chr6 624605 9 - 636262 TTTAGCATT -s simMouse_chr6.simMouse.chr6 262554 9 - 636262 TCAACATTC -s simRat_chr6.simRat.chr6 636049 9 - 647215 TGTATAATT -s simRat_chr6.simRat.chr6 281408 9 - 647215 TCAGCACTC -s simRat_chr6.simRat.chr6 10858 9 + 647215 TCAACATTC - -a -s simMouse_chr6.simMouse.chr6 11452 2 + 636262 CA -s Anc0.Anc0refChr2 11418 2 - 17989 CA -s Anc1.Anc1refChr2 30674 2 + 144309 CA -s Anc1.Anc1refChr6 163088 2 - 197743 CA -s Anc2.Anc2refChr0 4427 2 - 56053 CA -s mr.mrrefChr0 10513 2 + 130230 CA -s mr.mrrefChr0 119522 2 - 130230 CA -s mr.mrrefChr5 74226 2 - 294540 CA -s simCow_chr6.simCow.chr6 547518 2 - 602619 CA -s simDog_chr6.simDog.chr6 545221 2 - 593897 CA -s simHuman_chr6.simHuman.chr6 50207 2 + 601863 CA -s simMouse_chr6.simMouse.chr6 624614 2 - 636262 CA -s simMouse_chr6.simMouse.chr6 262563 2 - 636262 CA -s simRat_chr6.simRat.chr6 636113 2 - 647215 CA -s simRat_chr6.simRat.chr6 281417 2 - 647215 CA -s simRat_chr6.simRat.chr6 10867 2 + 647215 CA - -a -s simMouse_chr6.simMouse.chr6 11454 9 + 636262 TGTTAATAC -s Anc0.Anc0refChr2 11420 9 - 17989 TCTTAACAC -s Anc1.Anc1refChr2 30676 9 + 144309 TCTTAACAC -s Anc1.Anc1refChr6 163090 9 - 197743 TGATAATAC -s Anc2.Anc2refChr0 4429 9 - 56053 TCTTAACAC -s mr.mrrefChr0 10515 9 + 130230 TGTTAATAC -s mr.mrrefChr0 119524 9 - 130230 TGCTAATAC -s mr.mrrefChr5 74228 9 - 294540 TGATAATAC -s simCow_chr6.simCow.chr6 547520 9 - 602619 TCTTAACAC -s simDog_chr6.simDog.chr6 545223 9 - 593897 TCTTAACAC -s simHuman_chr6.simHuman.chr6 50209 9 + 601863 TCTTTACAT -s simMouse_chr6.simMouse.chr6 624616 9 - 636262 TGCTAATAC -s simMouse_chr6.simMouse.chr6 262565 9 - 636262 TGATAATAC -s simRat_chr6.simRat.chr6 636115 9 - 647215 TACTAATAC -s simRat_chr6.simRat.chr6 281419 9 - 647215 TGTTCATAT -s simRat_chr6.simRat.chr6 10871 9 + 647215 TGTTAATAC - -a -s simMouse_chr6.simMouse.chr6 11463 2 + 636262 GC -s Anc0.Anc0refChr2 11432 2 - 17989 CC -s Anc1.Anc1refChr2 30688 2 + 144309 CC -s Anc1.Anc1refChr6 163102 2 - 197743 AC -s Anc2.Anc2refChr0 4441 2 - 56053 CC -s mr.mrrefChr0 10524 2 + 130230 GC -s mr.mrrefChr0 119536 2 - 130230 AA -s mr.mrrefChr5 74240 2 - 294540 AC -s simCow_chr6.simCow.chr6 547532 2 - 602619 CC -s simDog_chr6.simDog.chr6 545235 2 - 593897 CC -s simHuman_chr6.simHuman.chr6 50221 2 + 601863 CT -s simMouse_chr6.simMouse.chr6 624628 2 - 636262 AA -s simMouse_chr6.simMouse.chr6 262577 2 - 636262 AC -s simRat_chr6.simRat.chr6 636127 2 - 647215 AA -s simRat_chr6.simRat.chr6 281431 2 - 647215 AT -s simRat_chr6.simRat.chr6 10910 2 + 647215 GC - -a -s simMouse_chr6.simMouse.chr6 11465 4 + 636262 GTAT -s Anc0.Anc0refChr2 11434 4 - 17989 CTGT -s Anc1.Anc1refChr2 30690 4 + 144309 CTGT -s Anc1.Anc1refChr6 163104 4 - 197743 GTAT -s Anc2.Anc2refChr0 4443 4 - 56053 CTGT -s mr.mrrefChr0 10526 4 + 130230 GTAT -s mr.mrrefChr0 119538 4 - 130230 GTAT -s mr.mrrefChr5 74242 4 - 294540 CCCT -s simCow_chr6.simCow.chr6 547534 4 - 602619 CTGT -s simDog_chr6.simDog.chr6 545237 4 - 593897 CTGT -s simHuman_chr6.simHuman.chr6 50223 4 + 601863 CTGT -s simMouse_chr6.simMouse.chr6 624631 4 - 636262 GTAT -s simMouse_chr6.simMouse.chr6 262579 4 - 636262 CCCT -s simRat_chr6.simRat.chr6 636129 4 - 647215 GTAT -s simRat_chr6.simRat.chr6 281433 4 - 647215 CTCT -s simRat_chr6.simRat.chr6 10912 4 + 647215 GTGT - -a -s simMouse_chr6.simMouse.chr6 11469 3 + 636262 TGA -s Anc0.Anc0refChr2 11449 3 - 17989 TGA -s Anc1.Anc1refChr6 163119 3 - 197743 TGA -s Anc2.Anc2refChr17 28 3 - 28526 TGA -s mr.mrrefChr0 10530 3 + 130230 TGA -s mr.mrrefChr0 119554 3 - 130230 TGA -s mr.mrrefChr5 74263 3 - 294540 TGG -s simCow_chr6.simCow.chr6 256595 3 - 602619 TTA -s simDog_chr6.simDog.chr6 257006 3 - 593897 TGA -s simMouse_chr6.simMouse.chr6 624647 3 - 636262 TGA -s simMouse_chr6.simMouse.chr6 262600 3 - 636262 TGG -s simRat_chr6.simRat.chr6 636145 3 - 647215 TGA -s simRat_chr6.simRat.chr6 281454 3 - 647215 TAG -s simRat_chr6.simRat.chr6 10916 3 + 647215 TGA - -a -s simMouse_chr6.simMouse.chr6 11472 3 + 636262 ACC -s Anc0.Anc0refChr2 11452 3 - 17989 GCT -s Anc1.Anc1refChr6 163122 3 - 197743 GCT -s Anc2.Anc2refChr17 31 3 - 28526 TCT -s mr.mrrefChr0 10533 3 + 130230 ACC -s mr.mrrefChr0 119557 3 - 130230 GGT -s mr.mrrefChr5 74266 3 - 294540 GCT -s simCow_chr6.simCow.chr6 256598 3 - 602619 TCT -s simDog_chr6.simDog.chr6 257009 3 - 593897 TCT -s simMouse_chr6.simMouse.chr6 624650 3 - 636262 GGT -s simMouse_chr6.simMouse.chr6 262603 3 - 636262 GCT -s simRat_chr6.simRat.chr6 636154 3 - 647215 GAT -s simRat_chr6.simRat.chr6 281457 3 - 647215 TCT -s simRat_chr6.simRat.chr6 10919 3 + 647215 GCC - -a -s simMouse_chr6.simMouse.chr6 11475 1 + 636262 T -s Anc0.Anc0refChr2 11455 1 - 17989 T -s Anc1.Anc1refChr6 163125 1 - 197743 T -s Anc2.Anc2refChr17 34 1 - 28526 T -s mr.mrrefChr0 10536 1 + 130230 T -s mr.mrrefChr0 119560 1 - 130230 T -s mr.mrrefChr5 74269 1 - 294540 T -s simCow_chr6.simCow.chr6 256601 1 - 602619 T -s simDog_chr6.simDog.chr6 257012 1 - 593897 T -s simMouse_chr6.simMouse.chr6 624653 1 - 636262 T -s simMouse_chr6.simMouse.chr6 262606 1 - 636262 T -s simRat_chr6.simRat.chr6 636159 1 - 647215 T -s simRat_chr6.simRat.chr6 281460 1 - 647215 T -s simRat_chr6.simRat.chr6 10922 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 11476 5 + 636262 GGGAT -s Anc0.Anc0refChr2 11456 5 - 17989 GGGAT -s Anc1.Anc1refChr6 163126 5 - 197743 GGGAT -s Anc2.Anc2refChr17 39 5 - 28526 TGTAT -s mr.mrrefChr0 10537 5 + 130230 GGGAT -s mr.mrrefChr0 119561 5 - 130230 GGGAT -s mr.mrrefChr5 74270 5 - 294540 GAGAT -s simCow_chr6.simCow.chr6 256606 5 - 602619 AGTGC -s simDog_chr6.simDog.chr6 257017 5 - 593897 TGTAT -s simMouse_chr6.simMouse.chr6 624654 5 - 636262 GGGAT -s simMouse_chr6.simMouse.chr6 262607 5 - 636262 GAGAT -s simRat_chr6.simRat.chr6 636160 5 - 647215 GGGGT -s simRat_chr6.simRat.chr6 281461 5 - 647215 GAGAT -s simRat_chr6.simRat.chr6 10923 5 + 647215 GGGAG - -a -s simMouse_chr6.simMouse.chr6 11481 109 + 636262 TGAAAGACTGTGGTCATCTGGTGTGGCTCTATTAACTACCACACTGATATAACATTGATGTTCGTCAATGTTACACTAGTGTGGCAATTAATGAAGCCACAGCATATAA -s mr.mrrefChr0 10542 109 + 130230 TGAAAGACTGTGGTCATCTGGTGTGGCTCTATTAACTACCACACTGATATAACATTGATGTTCGTCAATGTTACACTAGTGTGGCAATTAATGAAGCCACAGCATATAA -s simRat_chr6.simRat.chr6 10928 109 + 647215 TAAGAGACTATGGTTATCTGGTGTGTCTCTGCTAATTACCACACTAATGTAACATTGATGTGTATCAGTGTTACACCAGTGTGGCAATTAATGAAGCCACACCAGATGG - -a -s simMouse_chr6.simMouse.chr6 11590 2 + 636262 CC -s Anc0.Anc0refChr2 11461 2 - 17989 CC -s Anc1.Anc1refChr6 163131 2 - 197743 CC -s Anc2.Anc2refChr17 44 2 - 28526 GA -s mr.mrrefChr0 10651 2 + 130230 CC -s mr.mrrefChr5 74275 2 - 294540 CC -s simCow_chr6.simCow.chr6 256611 2 - 602619 TC -s simDog_chr6.simDog.chr6 257022 2 - 593897 GA -s simMouse_chr6.simMouse.chr6 262612 2 - 636262 CC -s simRat_chr6.simRat.chr6 281466 2 - 647215 CC -s simRat_chr6.simRat.chr6 11037 2 + 647215 CC - -a -s simMouse_chr6.simMouse.chr6 11592 11 + 636262 ACAGTCTCTTA -s mr.mrrefChr0 10653 11 + 130230 ACAGTCTCTTA -s simRat_chr6.simRat.chr6 11039 11 + 647215 ACAATCTCTTA - -a -s simMouse_chr6.simMouse.chr6 11615 1 + 636262 G -s mr.mrrefChr0 10676 1 + 130230 G -s simRat_chr6.simRat.chr6 11070 1 + 647215 G - -a -s simMouse_chr6.simMouse.chr6 11616 3 + 636262 TCA -s Anc0.Anc0refChr2 6540 3 + 17989 TCA -s Anc1.Anc1refChr6 34624 3 + 197743 TCA -s Anc2.Anc2refChr17 28498 3 + 28526 ACA -s mr.mrrefChr0 10677 3 + 130230 TCA -s mr.mrrefChr5 220277 3 + 294540 TCA -s simCow_chr6.simCow.chr6 346024 3 + 602619 ACA -s simDog_chr6.simDog.chr6 336891 3 + 593897 ACA -s simMouse_chr6.simMouse.chr6 373662 3 + 636262 TCA -s simRat_chr6.simRat.chr6 365761 3 + 647215 TCA -s simRat_chr6.simRat.chr6 11071 3 + 647215 TTA - -a -s simMouse_chr6.simMouse.chr6 11619 2 + 636262 GA -s Anc0.Anc0refChr2 6543 2 + 17989 GA -s Anc1.Anc1refChr6 34627 2 + 197743 GA -s Anc2.Anc2refChr17 28520 2 + 28526 TA -s mr.mrrefChr0 10680 2 + 130230 GA -s mr.mrrefChr5 220280 2 + 294540 GA -s simCow_chr6.simCow.chr6 346060 2 + 602619 TG -s simDog_chr6.simDog.chr6 336913 2 + 593897 TA -s simMouse_chr6.simMouse.chr6 373665 2 + 636262 GA -s simRat_chr6.simRat.chr6 365764 2 + 647215 GA -s simRat_chr6.simRat.chr6 11074 2 + 647215 GA - -a -s simMouse_chr6.simMouse.chr6 11621 2 + 636262 AG -s Anc0.Anc0refChr2 6545 2 + 17989 AT -s Anc1.Anc1refChr2 113609 2 - 144309 AT -s Anc1.Anc1refChr6 34629 2 + 197743 AA -s Anc2.Anc2refChr0 51600 2 + 56053 AT -s mr.mrrefChr0 10682 2 + 130230 AG -s mr.mrrefChr5 220282 2 + 294540 AA -s simCow_chr6.simCow.chr6 55075 2 + 602619 AT -s simDog_chr6.simDog.chr6 48650 2 + 593897 AT -s simHuman_chr6.simHuman.chr6 551630 2 - 601863 GT -s simMouse_chr6.simMouse.chr6 373667 2 + 636262 AA -s simRat_chr6.simRat.chr6 365766 2 + 647215 AA -s simRat_chr6.simRat.chr6 11076 2 + 647215 GT - -a -s simMouse_chr6.simMouse.chr6 11623 4 + 636262 AAAA -s Anc0.Anc0refChr2 6547 4 + 17989 AAAA -s Anc1.Anc1refChr2 113611 4 - 144309 AAAA -s Anc1.Anc1refChr6 34631 4 + 197743 AAAA -s Anc2.Anc2refChr0 51602 4 + 56053 AAAA -s mr.mrrefChr0 10684 4 + 130230 AAAA -s mr.mrrefChr5 220290 4 + 294540 AAAG -s simCow_chr6.simCow.chr6 55077 4 + 602619 AAAA -s simDog_chr6.simDog.chr6 48652 4 + 593897 AAAA -s simHuman_chr6.simHuman.chr6 551632 4 - 601863 ATAA -s simMouse_chr6.simMouse.chr6 373675 4 + 636262 AAAG -s simRat_chr6.simRat.chr6 365774 4 + 647215 AAAG -s simRat_chr6.simRat.chr6 11078 4 + 647215 AAGG - -a -s simMouse_chr6.simMouse.chr6 11631 1 + 636262 T - -a -s simMouse_chr6.simMouse.chr6 11634 3 + 636262 TCA -s Anc0.Anc0refChr2 6557 3 + 17989 CCA -s Anc1.Anc1refChr2 113621 3 - 144309 CCA -s Anc1.Anc1refChr6 34641 3 + 197743 TCA -s Anc2.Anc2refChr0 51612 3 + 56053 CCA -s mr.mrrefChr0 10694 3 + 130230 TCA -s mr.mrrefChr5 220300 3 + 294540 CCA -s simCow_chr6.simCow.chr6 55087 3 + 602619 CCA -s simDog_chr6.simDog.chr6 48662 3 + 593897 CCA -s simHuman_chr6.simHuman.chr6 551642 3 - 601863 CCA -s simMouse_chr6.simMouse.chr6 373685 3 + 636262 CCA -s simRat_chr6.simRat.chr6 365784 3 + 647215 CCA -s simRat_chr6.simRat.chr6 11088 3 + 647215 TCA - -a -s simMouse_chr6.simMouse.chr6 11705 6 + 636262 CCTGTT -s Anc0.Anc0refChr2 6629 6 + 17989 CCTGTT -s Anc1.Anc1refChr2 113693 6 - 144309 CCTGTT -s Anc1.Anc1refChr6 34712 6 + 197743 CCTGTT -s Anc2.Anc2refChr0 51684 6 + 56053 CCTGTT -s mr.mrrefChr0 10765 6 + 130230 CCTGTT -s mr.mrrefChr5 220371 6 + 294540 CCTGTT -s simCow_chr6.simCow.chr6 55142 6 + 602619 CCTGTT -s simDog_chr6.simDog.chr6 48762 6 + 593897 CCTGTT -s simHuman_chr6.simHuman.chr6 551714 6 - 601863 CCTGTT -s simMouse_chr6.simMouse.chr6 373756 6 + 636262 CCTGTT -s simRat_chr6.simRat.chr6 365855 6 + 647215 CCTGTT -s simRat_chr6.simRat.chr6 234055 6 - 647215 CCTGTT - -a -s simMouse_chr6.simMouse.chr6 11761 18 + 636262 TCTATTCACTGGTTAGAA -s Anc0.Anc0refChr2 6704 18 + 17989 CATGTTTGCTAATAGGGG -s Anc1.Anc1refChr2 113768 18 - 144309 CATGTTTGCTAATAGGGG -s Anc1.Anc1refChr6 34768 18 + 197743 TCTGTTCGCTGGTAAGGA -s Anc2.Anc2refChr0 51759 18 + 56053 CATGTTTGCTAATAGGGG -s mr.mrrefChr0 10821 18 + 130230 TCTATTCACTGGTTAGAA -s mr.mrrefChr5 220427 18 + 294540 TGTGTTAGCTAGTAGTGG -s simCow_chr6.simCow.chr6 55194 18 + 602619 CATGATAGTTAATAGGGG -s simDog_chr6.simDog.chr6 48837 18 + 593897 GATGTTTGCAAACAGGAG -s simHuman_chr6.simHuman.chr6 551792 18 - 601863 CATGTCTGCTAATTAAGG -s simMouse_chr6.simMouse.chr6 373812 18 + 636262 TGTGTTAGCTAGTAGTGG -s simRat_chr6.simRat.chr6 365911 18 + 647215 TGCGTTAGCTAGTAGGAG -s simRat_chr6.simRat.chr6 234111 18 - 647215 TTTATTCACTGATTGGAC - -a -s simMouse_chr6.simMouse.chr6 11781 2 + 636262 AG - -a -s simMouse_chr6.simMouse.chr6 11848 1 + 636262 T - -a -s simMouse_chr6.simMouse.chr6 11851 49 + 636262 GGTTAAGTACACATTTAAGGTATAGTACTTCTTGCAATTTATGATGATC -s mr.mrrefChr0 10908 49 + 130230 GGTTAAGTACACATTTAAGGTATAGTACTTCTTGCAATTTATGATGATC -s simRat_chr6.simRat.chr6 234198 49 - 647215 GATCAAGTTCACATTTAGGGTATAGTACTTCTTGCAACTTATGATGATA - -a -s simMouse_chr6.simMouse.chr6 11900 45 + 636262 ACTGTAATTATTGATTTGGTCTTTAGCAACCTCAGGTAAAATGCT -s mr.mrrefChr0 10957 45 + 130230 ACTGTAATTATTGATTTGGTCTTTAGCAACCTCAGGTAAAATGCT -s simRat_chr6.simRat.chr6 234250 45 - 647215 ACTGTAATTATTAATTTGGTGTCTAGAAACCTCAGATAAAATGTT - -a -s simMouse_chr6.simMouse.chr6 11945 100 + 636262 AGTGATCCAGGCACAGCTTACTCCCAGCCTAACAAAGTCAAATTGGCATCCTATTAGGGGTTGGTACGAGGGGGCGTTTAAGCACAAACCTGTACTCATG -s mr.mrrefChr0 11002 67 + 130230 AGTGATCCAGGCACAGCTTACTCCCAGCCTAACAAAGTCAAATT---------------------------------TTAAGCACAAACCTGTACTCATG -s simRat_chr6.simRat.chr6 234296 67 - 647215 AATGATCCAGGCACAGTTTGCTCCCAACCTCACAAAGTCAAATT---------------------------------TTAAGCACGAACCTGTACTCATG - -a -s simMouse_chr6.simMouse.chr6 12045 69 + 636262 CCTATTCCGACACCCCCATTTTAATACCCTTATGCATATTCCATTATTGAGTGACCCCGTGTTTGTCAT -s mr.mrrefChr0 11069 69 + 130230 CCTATTCCGACACCCCCATTTTAATACCCTTATGCATATTCCATTATTGAGTGACCCCGTGTTTGTCAT -s simRat_chr6.simRat.chr6 234364 69 - 647215 CCTATTTCCACACCCCCATTTTAATACCCTTAGGCATAATCTATTATGGGGGGACCCTATGATTGTCAT - -a -s simMouse_chr6.simMouse.chr6 12114 57 + 636262 TGAACCCTTGGTAGGGGGACCCACAGTTCTTGAAAGTCTGGTCCGGGAATGGTGGCA -s Anc0.Anc0refChr2 7032 2 + 17989 -------------------------------------------------------CA -s Anc1.Anc1refChr2 114096 2 - 144309 -------------------------------------------------------CA -s Anc2.Anc2refChr0 4689 2 - 56053 -------------------------------------------------------TT -s mr.mrrefChr0 11138 57 + 130230 TGAACCCTTGGTAGGGGGACCCACAGTTCTTGAAAGTCTGGTCCGGGAATGGTGGCA -s simCow_chr6.simCow.chr6 547791 2 - 602619 -------------------------------------------------------CT -s simDog_chr6.simDog.chr6 545508 2 - 593897 -------------------------------------------------------TT -s simHuman_chr6.simHuman.chr6 552133 2 - 601863 -------------------------------------------------------CA -s simRat_chr6.simRat.chr6 234436 57 - 647215 TGACCCCATGGTGGGGGGACCCAGAGTTGCTGAAGGTTTGGTCCGGGAATGGTGGCA - -a -s simMouse_chr6.simMouse.chr6 12171 9 + 636262 ATTCTGGGA -s Anc0.Anc0refChr2 7034 9 + 17989 ATTCTGGGA -s Anc1.Anc1refChr2 114098 9 - 144309 ATTCTGGGA -s Anc2.Anc2refChr0 4691 9 - 56053 ATTCTGAGA -s mr.mrrefChr0 11195 9 + 130230 ATTCTGGGA -s simCow_chr6.simCow.chr6 547810 9 - 602619 ATTTGAAAA -s simDog_chr6.simDog.chr6 545510 9 - 593897 ATTCTGAGA -s simHuman_chr6.simHuman.chr6 552135 9 - 601863 ACCCTGGAT -s simRat_chr6.simRat.chr6 234493 9 - 647215 ATTCTGGGA - -a -s simMouse_chr6.simMouse.chr6 12180 213 + 636262 TATGCCTGGGTCAGGCCTACTTGTGTGCCTGGTTCATGACTATTCACCATTTGGGCGCTCATGCATTCTGTTGTACATCTTCATGCGACCCCCTTTGGTGAAACCGGTAACAGGTTTCAGGTTGGCTTCTCGCTAGAATCTTAACAACCCTGTGAATGTGGCACACACTAACCATCCAGAGAGTTGTAGGCTACTTTCTTTTCATCACGCATG -s Anc0.Anc0refChr2 7043 6 + 17989 TCTGT---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------G -s Anc1.Anc1refChr2 114107 6 - 144309 TCTGT---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------G -s Anc2.Anc2refChr0 4700 6 - 56053 ACTGT---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------G -s mr.mrrefChr0 11204 6 + 130230 TATGC---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------G -s simCow_chr6.simCow.chr6 547819 6 - 602619 ACTGT---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------G -s simDog_chr6.simDog.chr6 545519 6 - 593897 ACTGT---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------G -s simHuman_chr6.simHuman.chr6 552144 3 - 601863 TGT------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ -s simRat_chr6.simRat.chr6 234506 6 - 647215 TATGC---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------G - -a -s simMouse_chr6.simMouse.chr6 12393 15 + 636262 AGGTGCTTCCTTGTT -s Anc0.Anc0refChr2 7049 15 + 17989 AGCTGTTTCCTTCTC -s Anc1.Anc1refChr2 114113 15 - 144309 AGCTGTTTCCTTCTC -s Anc2.Anc2refChr0 4706 15 - 56053 AGCTGTTTCCTTCTC -s mr.mrrefChr0 11210 15 + 130230 AGGTGCTTCCTTGTT -s simCow_chr6.simCow.chr6 547825 15 - 602619 AACTGTTTCCCTCTC -s simDog_chr6.simDog.chr6 545527 15 - 593897 AGCTGTTTCCTTTTC -s simHuman_chr6.simHuman.chr6 552147 15 - 601863 AGCTCTTTCCTCCTC -s simRat_chr6.simRat.chr6 234512 15 - 647215 AGATTCTTCCTTGTC - -a -s simMouse_chr6.simMouse.chr6 12408 18 + 636262 TGGATTGAATTGTTATCT -s Anc0.Anc0refChr2 7065 18 + 17989 TCAAGTGAGTTGTTTCCT -s Anc1.Anc1refChr2 114129 18 - 144309 TCAAGTGAGTTGTTTCCT -s Anc2.Anc2refChr0 4722 18 - 56053 TCATGTGAGCTGTTTCCT -s mr.mrrefChr0 11225 18 + 130230 TGGATTGAATTGTTATCT -s simCow_chr6.simCow.chr6 547841 18 - 602619 TCCTGTCAGGTGTTTCCT -s simDog_chr6.simDog.chr6 545543 18 - 593897 TCATGCGAGCTGTTTTCT -s simHuman_chr6.simHuman.chr6 552163 18 - 601863 TCAAGTGAGTTGTTCCCT -s simRat_chr6.simRat.chr6 234527 18 - 647215 AGGATCGATTTGTTACCT - -a -s simMouse_chr6.simMouse.chr6 12426 17 + 636262 ATTTTCCTTTTCTGACA -s Anc0.Anc0refChr2 7087 12 + 17989 ATTATTAATGA-----A -s Anc1.Anc1refChr2 114151 17 - 144309 ATTATTAATGACTGTCA -s Anc2.Anc2refChr0 4747 12 - 56053 ATTATTAATGA-----A -s mr.mrrefChr0 11243 17 + 130230 ATTTTCCTTTTCTGACA -s simCow_chr6.simCow.chr6 547866 12 - 602619 ATTACTATTGA-----A -s simDog_chr6.simDog.chr6 545568 12 - 593897 ATCATTAATGA-----A -s simHuman_chr6.simHuman.chr6 552185 17 - 601863 ATTAGTGATGACTGTCA -s simRat_chr6.simRat.chr6 234545 17 - 647215 ATTTTCCTCTCATCACC - -a -s simMouse_chr6.simMouse.chr6 12443 26 + 636262 TGATCTCCTTTCTTGTGCCTATCTTC -s Anc0.Anc0refChr2 7099 26 + 17989 TGGCATCTATTCATATGTCCATCTTT -s Anc1.Anc1refChr2 114168 26 - 144309 TGGCATCTATTCATATGTCCATCTTT -s Anc2.Anc2refChr0 4759 26 - 56053 TGGCATCTATTCATATGGCCATCTTG -s mr.mrrefChr0 11260 26 + 130230 TGATCTCCTTTCTTGTGTCTATCTTT -s simCow_chr6.simCow.chr6 547878 26 - 602619 GGGCTTATATTCATATGCCCATGTTG -s simDog_chr6.simDog.chr6 545580 26 - 593897 TTGCATCTATTCACAAGGCCATCTTG -s simHuman_chr6.simHuman.chr6 552203 26 - 601863 TGGCATCTATTCATATGTCCATCCTT -s simRat_chr6.simRat.chr6 234562 26 - 647215 TGAGCTCCTTTTTTGTGTCTATCTTT - -a -s simMouse_chr6.simMouse.chr6 12469 13 + 636262 TAGGACACTTATC -s Anc0.Anc0refChr2 7125 13 + 17989 TAGGGAACTTGGC -s Anc1.Anc1refChr2 114194 13 - 144309 TAGGGAACTTGGC -s Anc2.Anc2refChr0 4785 13 - 56053 TAGTGAACTTGGC -s mr.mrrefChr0 11286 13 + 130230 TAGGACACTTATC -s simCow_chr6.simCow.chr6 547904 13 - 602619 TTGTGAACACGGC -s simDog_chr6.simDog.chr6 545606 13 - 593897 TAGTGAACTTGCT -s simHuman_chr6.simHuman.chr6 552230 13 - 601863 TAGGGAACTTGGC -s simRat_chr6.simRat.chr6 234588 13 - 647215 TAGGACACTTATA - -a -s simMouse_chr6.simMouse.chr6 12482 32 + 636262 TCAGTTGAGTCCTAGGTAAATCCCTTTAGCAC -s Anc0.Anc0refChr2 7142 31 + 17989 TCACTTTACTCCTAACTAAATCCC-TTTAAAC -s Anc1.Anc1refChr2 114211 31 - 144309 TCACTTTACTCCTAACTAAATCCC-TTTAAAC -s Anc2.Anc2refChr0 4802 31 - 56053 TCACTTTACTCCTAACTAAATCCC-TTTAACA -s mr.mrrefChr0 11299 31 + 130230 TCAGTTGACTCCTAGGTAAATCCC-TTAGCAC -s simCow_chr6.simCow.chr6 547921 21 - 602619 TCATTTTACTCC----------CC-TTTAACA -s simDog_chr6.simDog.chr6 545623 31 - 593897 TCACTCTATTCCTAACTAAATCCC-TTCAACA -s simHuman_chr6.simHuman.chr6 552247 31 - 601863 TCACTTCACCCCTAACTAAATACC-TTTAAAC -s simRat_chr6.simRat.chr6 234601 31 - 647215 TCAGTTGACTCCTAGGTACCTCCC-TTAGGAC - -a -s simMouse_chr6.simMouse.chr6 12514 15 + 636262 TTAGGGAAAGAGTTA -s Anc0.Anc0refChr2 7174 15 + 17989 TTAATGAAAAAATTT -s Anc1.Anc1refChr2 114243 15 - 144309 TTAATGAAAAAATTT -s Anc2.Anc2refChr0 4834 15 - 56053 TTAATGAAAAAATTT -s mr.mrrefChr0 11330 15 + 130230 TTAGTGAAAAAATTA -s simCow_chr6.simCow.chr6 547943 15 - 602619 TTAATGAAAAAATTT -s simDog_chr6.simDog.chr6 545655 15 - 593897 TTAATGAAAAAATTT -s simHuman_chr6.simHuman.chr6 552279 11 - 601863 TTGAAGAAA----TG -s simRat_chr6.simRat.chr6 234632 15 - 647215 TTAGTGAAAAAATTA - -a -s simMouse_chr6.simMouse.chr6 12529 54 + 636262 CTCCTACATTTTGGCACTGGGCTCCTACAACCTTAGTCCTTGCTGATCCAATAT -s Anc0.Anc0refChr2 7190 47 + 17989 CTCATTTA--TTAGCACTGCACACCTAGAACCTTATT-----CTGACATGATAT -s Anc1.Anc1refChr2 114259 54 - 144309 CTCATTTATTTTAGCACTGCACACCTAGAACCTTATTCCTTGCTGACATGATAT -s Anc2.Anc2refChr0 4850 47 - 56053 CTAATTTA--TTAGTGCTGCACACCCAGTACCTTATT-----CTGACATGATAT -s mr.mrrefChr0 11345 54 + 130230 CTCCTATATTTTGGCACTGGGCACCTACAACCTTAGTCCTTGCTGATCCAATAT -s simCow_chr6.simCow.chr6 547959 47 - 602619 GTCATGTA--TTAGTGCTGCACAACCGGTACCTTTTT-----CTAACATGAAAT -s simDog_chr6.simDog.chr6 545671 47 - 593897 CTAATTTA--TTAGTGCTGTGCACTCAGTACCTTATT-----CGGGTGGGATAT -s simHuman_chr6.simHuman.chr6 552291 54 - 601863 CTCATTTGTTTTAACACTGCACACCTATAACCTTATTCCTTGCTGACATGATAT -s simRat_chr6.simRat.chr6 234647 54 - 647215 CTCCTCTTTTTTGGCACTGGGCACCCACAACCTTAGTCCTTGCTGATCCAATAC - -a -s simMouse_chr6.simMouse.chr6 12583 37 + 636262 GTGAACAGGAGAAGTTTCAGAAATGTATAGTTATCTG -s Anc0.Anc0refChr2 7237 10 + 17989 GTGAGGAG---------------------------TG -s Anc1.Anc1refChr2 114313 10 - 144309 GTGAGGAG---------------------------TG -s Anc2.Anc2refChr0 4897 10 - 56053 GTGAGGAG---------------------------TG -s mr.mrrefChr0 11399 20 + 130230 GTGAGCAGGAGAAGTT-----------------TCTG -s simCow_chr6.simCow.chr6 548006 10 - 602619 GTGGGGAG---------------------------TG -s simDog_chr6.simDog.chr6 545822 10 - 593897 GTGAGGGG---------------------------CA -s simDog_chr6.simDog.chr6 545718 10 - 593897 GTGAGAAG---------------------------TG -s simHuman_chr6.simHuman.chr6 552345 10 - 601863 GTGAGGGG---------------------------TG -s simRat_chr6.simRat.chr6 234701 20 - 647215 GTGAGCAGGAGAGGTC-----------------TCTG - -a -s simMouse_chr6.simMouse.chr6 12620 131 + 636262 ACTACTGATCCCACTCCTACTTCTATCTCTCACCAAAACTCATTGCCGCACTCCTCCAAGTGATGTTATACAAATATGTTGTCTATTAATATATCCACACAAAGTTGTTGTCCTAGCACTAATGCATGGGC -s Anc0.Anc0refChr2 7247 115 + 17989 GGTATTAAAGCCGAAA-------------TAACCAAAATTCATTGC--CATTCCTCCAAGAGACGTT-TAAAAATACCTTGACTATCAGTACAGCCACACAAAGTTGTTACCCCAGCACTAAGTCACGAGC -s Anc1.Anc1refChr2 114323 115 - 144309 GGTATTAAAGCCGAAA-------------TAACCAAAATTCATTGC--CATTCCTCCAAGAGACGTT-TAAAAATACCTTGACTATCAGTACAGCCACACAAAGTTGTTACCCCAGCACTAAGTCACGAGC -s Anc2.Anc2refChr0 4909 115 - 56053 GGTATTAAAGCTGAAA-------------TAACCAAAATTCATTGC--CATTCCTCCAAAAGACTTG-TAAAAATACCTTGACTATCAGTACAGCCACACAAAGTTGTTACCCCAGCACTAAGTCACAAGC -s mr.mrrefChr0 11419 129 + 130230 GCTACTGATCCCGCTCCTACTTCTATCTCTCACCAAAACTCATTGC--CACTCCTCCAAGTGATGTTATACAAATACGTTGTCTATTAATATATCCACACAAAGTTGTTATCCTAGCACTAATGCATGAGC -s simCow_chr6.simCow.chr6 548020 114 - 602619 GGTACTAAAGCAGAAA-------------CAACCAAAATTCATTGC--CATTTCAGCAAGATATTTG-TAAAAATGCCTTGATTATT-GTACAGTCACACAAAGTTGTCATTACAGCTCTAGGTCACAAGC -s simDog_chr6.simDog.chr6 545834 115 - 593897 GGTATTCAAGCTGAAA-------------TAACCAAAATTCATTGC--CATTCCTCCAAAAGACTTG-TAAAAATACCTTGACTATCAGTACAGCCACGCAAAGTTGTTACCCCAGTACTAAGCCACAAGC -s simDog_chr6.simDog.chr6 545730 92 - 593897 GGTATTAATCCTGGAA-------------TATGCAGAAGTCAATAC--CCTTCCTCCATAAGACTTG-TAAAACTACCTTGGCAATCAGTACAGCCACACAAAGTTGT----------------------- -s simHuman_chr6.simHuman.chr6 552355 115 - 601863 GGTTTTAAAGCCGAAA-------------TAACCAAAATTCATTGC--CATTCCTCCAAGACAAGTT-TAGGAATACCTTGACTATCAGTACAGCCACACAAAGTTGTTACCCCAGCATTAAGTCAAGAGC -s simRat_chr6.simRat.chr6 234721 129 - 647215 GTTACTGATCCTGCTCTTTCTTGTGTCTCTGACCAAAACTCATTGC--AACTCCTCCAAATGATGTTGTAAAAATACGTGGTCTATTAATATATACACACGAAGTTGTTATCTTAGCACTAATGCATGAAC - -a -s simMouse_chr6.simMouse.chr6 12751 49 + 636262 TACACATGGGTGAGTACCATACTCTGAAGGGTCACTGAACCATTGATAA -s Anc0.Anc0refChr2 7362 49 + 17989 TACAAATGGGTGAGTACCATACAGTGAAATGTCATTAAACCCTAGATAG -s Anc1.Anc1refChr2 114438 49 - 144309 TACAAATGGGTGAGTACCATACAGTGAAATGTCATTAAACCCTAGATAG -s Anc2.Anc2refChr0 5025 49 - 56053 CACAAATGGGTGAGTACCATACAGTGAAATAGCATTAAACCCTAGTCAG -s mr.mrrefChr0 11548 49 + 130230 TACACATGGGTGAGTACCATACACTGAAGGGTCATTAAACCATTGATAG -s simCow_chr6.simCow.chr6 548135 49 - 602619 TAGACTTGGGTAAGTACCAGACAGTGAAATTGCAATAAACCTTAGTCAG -s simDog_chr6.simDog.chr6 545950 48 - 593897 CACAAATAGATGAGTACCATACAG-GAAATAGCATTAAACCCTTGTCAG -s simHuman_chr6.simHuman.chr6 552482 49 - 601863 TACAAATGGGTGAGTACCATACAATGAAATGTCATTAAAGCGTAGATAG -s simRat_chr6.simRat.chr6 234850 49 - 647215 TACACATGGGTGAGTACCATACACTGAAGGGTCATTAAACCATTGATAG - -a -s simMouse_chr6.simMouse.chr6 12800 4 + 636262 CTTC -s Anc0.Anc0refChr2 7414 4 + 17989 TTTT -s Anc1.Anc1refChr2 114490 4 - 144309 TTTT -s Anc2.Anc2refChr0 5077 4 - 56053 TTTT -s mr.mrrefChr0 11597 4 + 130230 CTTT -s simCow_chr6.simCow.chr6 548187 4 - 602619 TTTT -s simDog_chr6.simDog.chr6 546001 4 - 593897 TTTT -s simHuman_chr6.simHuman.chr6 552534 4 - 601863 TTTT -s simRat_chr6.simRat.chr6 234899 4 - 647215 CTTT - -a -s simMouse_chr6.simMouse.chr6 12804 22 + 636262 TGGGAAAGTCCTCAATGTGTTA -s Anc0.Anc0refChr2 7418 22 + 17989 TCGTTAAGTCCTTAATGTATTG -s Anc1.Anc1refChr2 114494 22 - 144309 TCGTTAAGTCCTTAATGTATTG -s Anc2.Anc2refChr0 5081 22 - 56053 TCGTTAAGTCCCTAATGTATTG -s mr.mrrefChr0 11601 22 + 130230 TGGGAAAGTCCTCAATGTGTTA -s simCow_chr6.simCow.chr6 548191 18 - 602619 T---TAAGTGCCTAACGTATT- -s simDog_chr6.simDog.chr6 546005 22 - 593897 TCGTTAAGTCCCTGATGTATTG -s simHuman_chr6.simHuman.chr6 552538 22 - 601863 CAGTCATGTCCTTAATGTATTG -s simRat_chr6.simRat.chr6 234910 22 - 647215 TGGAAAAGTCCTCAATGTGTTA - -a -s simMouse_chr6.simMouse.chr6 12826 17 + 636262 AAATTCAGAATTGGGCA -s Anc0.Anc0refChr2 7461 17 + 17989 ACATTTAAGCATGAGTA -s Anc1.Anc1refChr2 114537 17 - 144309 ACATTTAAGCATGAGTA -s Anc2.Anc2refChr0 5124 17 - 56053 GCATTTAAGCATGAGTA -s mr.mrrefChr0 11643 17 + 130230 AAATTCAGAATTGGGTA -s simCow_chr6.simCow.chr6 548227 16 - 602619 CCAATTACGCCCT-GTC -s simDog_chr6.simDog.chr6 546048 17 - 593897 GCATTCAAGCATGAGCA -s simHuman_chr6.simHuman.chr6 552581 17 - 601863 ATACTTGAGTGTAAGTA -s simRat_chr6.simRat.chr6 234952 17 - 647215 AAATTCAGAATTGGGTA - -a -s simMouse_chr6.simMouse.chr6 12843 21 + 636262 TGATATGATTGAAGCTGTTTT -s Anc0.Anc0refChr2 7511 21 + 17989 TGATATGAGTCAACCTaTTTT -s Anc1.Anc1refChr2 114587 21 - 144309 TGATATGAGTCAACCTATTTT -s Anc2.Anc2refChr0 5175 21 - 56053 TGATATGAGTCAACCTcTGTT -s mr.mrrefChr0 11660 21 + 130230 TGATATGAGTGAAGCTATTTT -s simCow_chr6.simCow.chr6 548277 21 - 602619 TGATAAGAgtggacatcagta -s simDog_chr6.simDog.chr6 546099 20 - 593897 TGACATGAATCACCCC-TGTT -s simHuman_chr6.simHuman.chr6 552631 21 - 601863 TGATATGAGTTAACCTATTTT -s simRat_chr6.simRat.chr6 234969 21 - 647215 TGATATGAGTGAAGCTATTTT - -a -s simMouse_chr6.simMouse.chr6 12864 8 + 636262 CAGATGGA -s Anc0.Anc0refChr2 7532 8 + 17989 CAGGTGAa -s Anc1.Anc1refChr2 114608 8 - 144309 CAGGTGAA -s Anc2.Anc2refChr0 5196 8 - 56053 CAGGTGAa -s mr.mrrefChr0 11681 8 + 130230 CAGATGGA -s simCow_chr6.simCow.chr6 548299 8 - 602619 catgtgaa -s simDog_chr6.simDog.chr6 546119 7 - 593897 CAGGTGA- -s simHuman_chr6.simHuman.chr6 552652 8 - 601863 CAGGTGAG -s simRat_chr6.simRat.chr6 234990 8 - 647215 TAGATGGA - -a -s simMouse_chr6.simMouse.chr6 12872 15 + 636262 CCACCCTAATGTCCG -s Anc0.Anc0refChr2 7540 14 + 17989 tc-TTCCATCCTCcg -s Anc1.Anc1refChr2 114616 14 - 144309 TC-TTCCATCCTCCG -s Anc2.Anc2refChr0 5204 14 - 56053 tt-TTCCATCCTCtg -s mr.mrrefChr0 11689 15 + 130230 CCACTCTAATGTCCG -s simCow_chr6.simCow.chr6 548324 14 - 602619 tt-ttactttaactg -s simDog_chr6.simDog.chr6 546126 10 - 593897 ---TTCCATCCTC-- -s simHuman_chr6.simHuman.chr6 552660 14 - 601863 TC-TTCCATCTTCCG -s simRat_chr6.simRat.chr6 234998 15 - 647215 CCACTCTACTATCCA - -a -s simMouse_chr6.simMouse.chr6 12887 7 + 636262 ATGGACC -s Anc0.Anc0refChr2 7584 7 + 17989 ATGGACT -s Anc1.Anc1refChr2 114660 7 - 144309 ATGGACT -s Anc2.Anc2refChr0 5248 7 - 56053 GTGGCCT -s mr.mrrefChr0 11704 7 + 130230 ATGGACC -s simCow_chr6.simCow.chr6 548369 7 - 602619 GTGGCCT -s simHuman_chr6.simHuman.chr6 552704 7 - 601863 ATGAATT -s simRat_chr6.simRat.chr6 235013 7 - 647215 ATGGACC - -a -s simMouse_chr6.simMouse.chr6 12894 4 + 636262 TCTC -s Anc0.Anc0refChr2 7591 4 + 17989 AACC -s Anc1.Anc1refChr2 114667 4 - 144309 AACC -s Anc2.Anc2refChr0 5255 4 - 56053 AACC -s mr.mrrefChr0 11711 4 + 130230 TCTC -s simCow_chr6.simCow.chr6 548440 4 - 602619 AACC -s simDog_chr6.simDog.chr6 546161 1 - 593897 ---T -s simHuman_chr6.simHuman.chr6 552711 4 - 601863 AGCC -s simRat_chr6.simRat.chr6 235020 4 - 647215 TCTC - -a -s simMouse_chr6.simMouse.chr6 12898 1 + 636262 A -s Anc0.Anc0refChr2 7596 1 + 17989 A -s Anc1.Anc1refChr2 114672 1 - 144309 A -s Anc2.Anc2refChr0 5260 1 - 56053 A -s mr.mrrefChr0 11715 1 + 130230 A -s simCow_chr6.simCow.chr6 548445 1 - 602619 C -s simDog_chr6.simDog.chr6 546163 1 - 593897 A -s simHuman_chr6.simHuman.chr6 552716 1 - 601863 A -s simRat_chr6.simRat.chr6 235024 1 - 647215 A - -a -s simMouse_chr6.simMouse.chr6 12899 2 + 636262 TT -s Anc0.Anc0refChr2 7604 2 + 17989 GT -s Anc1.Anc1refChr2 114680 2 - 144309 GT -s Anc2.Anc2refChr0 5268 2 - 56053 GT -s mr.mrrefChr0 11723 2 + 130230 GT -s simCow_chr6.simCow.chr6 548453 2 - 602619 GT -s simDog_chr6.simDog.chr6 546171 2 - 593897 GT -s simHuman_chr6.simHuman.chr6 552724 2 - 601863 GT -s simRat_chr6.simRat.chr6 235032 2 - 647215 GT - -a -s simMouse_chr6.simMouse.chr6 12901 50 + 636262 CATTCCTCCATCCCAAACAAAAGATAGGTTGTATTGATAAAGGACACTGG -s Anc0.Anc0refChr2 7606 50 + 17989 GAATCTTCCATCCTCTACAGGAGAAAGCTTGTATTGATAGATAACACTGA -s Anc1.Anc1refChr2 114682 50 - 144309 GAATCTTCCATCCTCTACAGGAGAAAGCTTGTATTGATAGATAACACTGA -s Anc2.Anc2refChr0 5270 50 - 56053 GAATCTTCCATCCTCTGCAGGAGAAAGCTTGTATTGATAGATAACACTGA -s mr.mrrefChr0 11725 50 + 130230 CATTCCTCCATCCTAAACAGAAGATAGCTTGTATTGATAAAGGACACTGG -s simCow_chr6.simCow.chr6 548461 50 - 602619 GAATTTTCCATCCTCAGCAGGAGAAAGCTTGTATTGATAGATAACACTGC -s simDog_chr6.simDog.chr6 546173 42 - 593897 --AGCTGCC------TGCAGAAGAAAGCTCGTATTGATACATAACACCAA -s simHuman_chr6.simHuman.chr6 552726 50 - 601863 GAATCTTCCATCTTCTACAGGGGAAAGCTTGCATTGATAGACAACACTGA -s simRat_chr6.simRat.chr6 235034 42 - 647215 CATTCCCCCCTCCTGAACAGAAGATATCT--------TAAAGGGCACTGG - -a -s simMouse_chr6.simMouse.chr6 12951 26 + 636262 TACCTTGCACAACAGGTTTTCAAACT -s Anc0.Anc0refChr2 7657 25 + 17989 TACTCTTCAC-ATACATTTTCAAAGT -s Anc1.Anc1refChr2 114733 26 - 144309 TACTCTTCACAATACATTTTCAAAGT -s Anc2.Anc2refChr0 5321 25 - 56053 TACTCTTCAC-ATACATTTTCAACGT -s mr.mrrefChr0 11775 26 + 130230 TACTCTTCACAACAGATTTTCAAACT -s simCow_chr6.simCow.chr6 548512 23 - 602619 TATTCT-CAC-ATACATTTTCAAC-T -s simDog_chr6.simDog.chr6 546216 25 - 593897 GGCTATTCAT-ACACATTTTCAACGT -s simHuman_chr6.simHuman.chr6 552777 26 - 601863 TACTCTTCACAATACATTTTCAAAAT -s simRat_chr6.simRat.chr6 235076 26 - 647215 TACTCTTCACAACATACTTCCAAACT - -a -s simMouse_chr6.simMouse.chr6 12977 44 + 636262 AAGGGACCTCTTCTAGCTTCTATGCCTCTATGACTGGTTGGTCT -s Anc0.Anc0refChr2 7682 19 + 17989 AA-------------------------CTATGACTGGTTGGCCT -s Anc1.Anc1refChr2 114759 19 - 144309 AA-------------------------CTATGACTGGTTGGCCT -s Anc2.Anc2refChr0 5346 19 - 56053 AA-------------------------TTATTACTAGTTGGCCT -s mr.mrrefChr0 11801 19 + 130230 AA-------------------------CTATGACTGGTTGGTCT -s simCow_chr6.simCow.chr6 548535 15 - 602619 AA-------------------------TTATCACT----GGCCT -s simDog_chr6.simDog.chr6 546242 19 - 593897 AA-------------------------TTATTACTAGTTGGCCT -s simHuman_chr6.simHuman.chr6 552803 19 - 601863 AG-------------------------CTATGACTGTTTGGCCC -s simRat_chr6.simRat.chr6 235102 19 - 647215 AA-------------------------CGATGACTGGATGGTCT - -a -s simMouse_chr6.simMouse.chr6 13021 34 + 636262 CGGTTGTTAATCATATACTAGAGGCAGGCTAAGG -s Anc0.Anc0refChr2 7701 30 + 17989 CTATAATTGATCACATACTGG----AAACTCAGG -s Anc1.Anc1refChr2 114778 30 - 144309 CTATAATTGATCACATACTGG----AAACTCAGG -s Anc2.Anc2refChr0 5365 30 - 56053 CTATAATTGATCACATACTGG----AAACTCAGG -s mr.mrrefChr0 11820 30 + 130230 CTGTTATTAATCATATACTAG----AGACTAAGG -s simCow_chr6.simCow.chr6 548553 30 - 602619 CTATAACTAATCACATACTGG----TACCTCTAC -s simDog_chr6.simDog.chr6 546261 30 - 593897 CTAAATTGGCTCACATATTGG----ACACTCAGG -s simHuman_chr6.simHuman.chr6 552822 30 - 601863 CTATAATTGATCACATACTGG----AAACTCAGG -s simRat_chr6.simRat.chr6 235121 29 - 647215 CTGTCA-TAATCAAATACTAG----AGACTAAGG - -a -s simMouse_chr6.simMouse.chr6 13055 32 + 636262 TCATATAACTTGATTCTTGTAGGGCTTAATAT -s Anc0.Anc0refChr2 7731 32 + 17989 CCATGTAACTTGATTCTTGTAGAGCTTACTCT -s Anc1.Anc1refChr2 114808 32 - 144309 CCATGTAACTTGATTCTTGTAGAGCTTACTCT -s Anc2.Anc2refChr0 5395 32 - 56053 CCATGTAACTTGATTCTTGTATAGCTTACTCT -s mr.mrrefChr0 11850 32 + 130230 CCATGTAACTTGATTCTTGTAGAGCTTAATAT -s simCow_chr6.simCow.chr6 548583 32 - 602619 CCATCTAAGCTGATCCTTGTACAGCTCACTAT -s simDog_chr6.simDog.chr6 546311 32 - 593897 TCATGTCACTTGATTCTTGTATAGCTTAGTCT -s simHuman_chr6.simHuman.chr6 552852 31 - 601863 CCATGTAACTT-AGTCTTGTAGAGCTTACTGT -s simRat_chr6.simRat.chr6 235150 32 - 647215 CCATGTGACTTGACTCTTGTAGAGCTTAATAT - -a -s simMouse_chr6.simMouse.chr6 13087 79 + 636262 TCTCATCTGTATCCTGTCAAGCATTGAGTTGCATTTACTAATAACCTATAATGTTGGTAATATGGAGATGGTAATAGAG -s Anc0.Anc0refChr2 7765 78 + 17989 TTCAATCTCAATCCTGTCAAGCATTTAATGTGATTT-CTGATTTCCTATGTTGTCGGTAATATGGACATGGTATCAAAA -s Anc1.Anc1refChr2 114842 78 - 144309 TTCAATCTCAATCCTGTCAAGCATTTAATGTGATTT-CTGATTTCCTATGTTGTCGGTAATATGGACATGGTATCAAAA -s Anc2.Anc2refChr0 5429 78 - 56053 TTCAATCTCAATCCTGTCAAGCATGTAATGTGATTT-ATGATTTCCTATGTTGTCAGTAATATGGCCATGGTATCAAAA -s mr.mrrefChr0 11882 79 + 130230 TCTCATCTGTATCCTGTCAAGCATTGAATGGCATTTACTGATAACCTATAATGTTGGTAATATGGAGATGGTAATAAAG -s simCow_chr6.simCow.chr6 548617 78 - 602619 CTCAATCTTAATCCTCTCAAGAATGTAATGTGATTA-ATGATTTCCTATGTTGTCAGTAACATGGTCATGGTATCAAAA -s simDog_chr6.simDog.chr6 546345 78 - 593897 TTCAATCTCAATCCTGTCAAGCATGTACTGTAATTT-ACAATTTCCTATGTTGTTAGTAATATGGCCATGGTGTCCAAA -s simHuman_chr6.simHuman.chr6 552885 72 - 601863 TTCAATCTCAATCCTGTCAAGTAGTCAAGGTGATTT-CTGATTTC------TGCCGGTAATATGGACATGGTATCAAGA -s simRat_chr6.simRat.chr6 235182 73 - 647215 TCTCACA---ATGCTGCCAAGCATTGAATGGCATTTACTGATAAGCTATAATGTTA--AATA-GGAGATGGTAATAAAG - -a -s simMouse_chr6.simMouse.chr6 13166 25 + 636262 AATGGACTGGCAAAGGTTAGTTAGT -s Anc0.Anc0refChr2 7848 22 + 17989 AACAAAATGATTCAGATTAGTT--- -s Anc1.Anc1refChr2 114925 22 - 144309 AACAAAATGATTCAGATTAGTT--- -s Anc2.Anc2refChr0 5512 22 - 56053 AACAAAATCATTCAGATTAGCT--- -s mr.mrrefChr0 11966 25 + 130230 AATGGACTGATAAAGATTAGTTAGT -s simCow_chr6.simCow.chr6 548700 20 - 602619 AAGAAAATTATTCAGGTTAG----- -s simDog_chr6.simDog.chr6 546428 21 - 593897 AACAAAATCAAT-AGATTAGCT--- -s simHuman_chr6.simHuman.chr6 552962 22 - 601863 AACAAAGCGATTCAGATCAATT--- -s simRat_chr6.simRat.chr6 235260 25 - 647215 AATGGACTGATGAAGATTGGTTAGT - -a -s simMouse_chr6.simMouse.chr6 13191 20 + 636262 TTTGTATCCAAAACCACCCT -s Anc0.Anc0refChr2 7870 20 + 17989 TTCCTGCCTCCAATCACCCT -s Anc1.Anc1refChr2 114947 20 - 144309 TTCCTGCCTCCAATCACCCT -s Anc2.Anc2refChr0 5534 20 - 56053 TTCCTGCCTCCAATCGCCCT -s mr.mrrefChr0 11991 20 + 130230 TTTGTATCTACAACCACCCT -s simCow_chr6.simCow.chr6 548720 20 - 602619 TTTCTGCATCCAATCCCCCT -s simDog_chr6.simDog.chr6 546451 20 - 593897 TTCCTGCCTCCATTTGCCCT -s simHuman_chr6.simHuman.chr6 552984 12 - 601863 TT--------CAAACACCCT -s simRat_chr6.simRat.chr6 235285 20 - 647215 TTTGTATCTGCAAGCGCCCT - -a -s simMouse_chr6.simMouse.chr6 13211 7 + 636262 GAATTGC -s Anc0.Anc0refChr2 7890 7 + 17989 AAGTTGT -s Anc1.Anc1refChr2 114967 7 - 144309 AAGTTGT -s Anc2.Anc2refChr0 5554 7 - 56053 AAGTTGT -s mr.mrrefChr0 12011 7 + 130230 AAATTGC -s simCow_chr6.simCow.chr6 548740 7 - 602619 AAGTTGC -s simDog_chr6.simDog.chr6 546471 7 - 593897 AAGTTGT -s simHuman_chr6.simHuman.chr6 552996 7 - 601863 AAGCTGT -s simRat_chr6.simRat.chr6 235306 7 - 647215 AAATTGC - -a -s simMouse_chr6.simMouse.chr6 13218 10 + 636262 TTCACAATTC -s Anc0.Anc0refChr2 7899 10 + 17989 CTCAAGATTC -s Anc1.Anc1refChr2 114976 10 - 144309 CTCAAGATTC -s Anc2.Anc2refChr0 5563 10 - 56053 CTCAAGATTC -s mr.mrrefChr0 12020 10 + 130230 TTCACAATTC -s simCow_chr6.simCow.chr6 548749 10 - 602619 CTCAAGATTC -s simDog_chr6.simDog.chr6 546480 10 - 593897 CACAAGATTC -s simHuman_chr6.simHuman.chr6 553005 10 - 601863 CTCAAGATGC -s simRat_chr6.simRat.chr6 235315 10 - 647215 TTCACAATTC - -a -s simMouse_chr6.simMouse.chr6 13228 31 + 636262 AGCTTGGAGCACATCGCAAGAACCTCTCAGC -s Anc0.Anc0refChr2 7921 31 + 17989 GGTTTGGGGCATATGGCAACAACCTTATAGT -s Anc1.Anc1refChr2 114998 31 - 144309 GGTTTGGGGCATATGGCAACAACCTTATAGT -s Anc2.Anc2refChr0 5585 31 - 56053 AGTTTGGGATATATGGCAACAACCTTATAGT -s mr.mrrefChr0 12042 31 + 130230 GGCTTGGAGCACATGGCAAGAACCTTACAGC -s simCow_chr6.simCow.chr6 548771 26 - 602619 AGTTAGGGAT-----GCTACAACCTTGTAGT -s simDog_chr6.simDog.chr6 546503 31 - 593897 AGTTTGGGATATATGGCAACAACCTTATAAT -s simHuman_chr6.simHuman.chr6 553027 31 - 601863 GGTTTGGGGCATATGGCAACAACCTTATAGT -s simRat_chr6.simRat.chr6 235337 31 - 647215 GGCTTGGAGCACATGGCAAGGTCTTTACAGC - -a -s simMouse_chr6.simMouse.chr6 13259 13 + 636262 AACTTTTCATGCT -s Anc0.Anc0refChr2 7963 13 + 17989 AATCTTTCAAAGC -s Anc1.Anc1refChr2 115040 13 - 144309 AATCTTTCAAAGC -s Anc2.Anc2refChr0 5627 13 - 56053 ATTCTTTCAAAGC -s mr.mrrefChr0 12073 13 + 130230 AATTTTTCAAGCT -s simCow_chr6.simCow.chr6 548811 13 - 602619 AGTCTTTATAAGC -s simDog_chr6.simDog.chr6 546545 13 - 593897 CTTTTTTCAGAAT -s simHuman_chr6.simHuman.chr6 553069 13 - 601863 AATCTTTCAAAGC -s simRat_chr6.simRat.chr6 235368 13 - 647215 GATTTTTGAAGCT - -a -s simMouse_chr6.simMouse.chr6 13272 76 + 636262 TGTTTCTATTCCTTGGTGTCCTTTCACTTCTAAACAGTGGTACTTGTTCTGGAGCAAATCAAGGTACTCCAATAGA -s Anc0.Anc0refChr2 7976 41 + 17989 TGTCTCCATTCCTTGGTGTCCTTTGCCTTCTAAACAGTG-----------------------------------GA -s Anc1.Anc1refChr2 115053 41 - 144309 TGTCTCCATTCCTTGGTGTCCTTTGCCTTCTAAACAGTG-----------------------------------GA -s Anc2.Anc2refChr0 5640 41 - 56053 TGTCTCCATTGCTTGGTGTCCTCTGCCTTCTAGACAGTG-----------------------------------AA -s mr.mrrefChr0 12086 69 + 130230 TGTTTCTATTCCTTGGTGTCCTTTCACTTCTAAACAGTG-------TTCTGGAGCAAATCAAGGTACTCCAATAGA -s simCow_chr6.simCow.chr6 548858 41 - 602619 GGTATCTATTACTTGGTGTTCTCGGCCTTCTGGAAGGTG-----------------------------------TG -s simDog_chr6.simDog.chr6 546558 41 - 593897 TATCTCCATTGCTTCACGTCCTCTGCCTTCCAGACAGTG-----------------------------------AA -s simHuman_chr6.simHuman.chr6 553082 41 - 601863 TGTGTCCATTCCTTGGTCTCTTTTACCTTCTAAACCGTG-----------------------------------GC -s simRat_chr6.simRat.chr6 235381 63 - 647215 TGTTTCTATTTCTTGGTATGCTTTCACTTTCAC-------------TTTTAAAAAAAATAAAGGTACTCCAATAAA - -a -s simMouse_chr6.simMouse.chr6 13348 2 + 636262 CC -s Anc0.Anc0refChr2 8017 2 + 17989 TC -s Anc1.Anc1refChr2 115094 2 - 144309 TC -s Anc2.Anc2refChr0 5681 2 - 56053 TC -s mr.mrrefChr0 12155 2 + 130230 CC -s simCow_chr6.simCow.chr6 548899 2 - 602619 TC -s simDog_chr6.simDog.chr6 546620 2 - 593897 CC -s simHuman_chr6.simHuman.chr6 553123 2 - 601863 TC -s simRat_chr6.simRat.chr6 235444 2 - 647215 CC - -a -s simMouse_chr6.simMouse.chr6 13350 38 + 636262 ATTGTCAACTACTCTATCAACTGCTAGATGAAGGACCC -s Anc0.Anc0refChr2 8019 32 + 17989 AGTTTCAACTACCCATCCAACTGCCCGATGAA------ -s Anc1.Anc1refChr2 115096 32 - 144309 AGTTTCAACTACCCATCCAACTGCCCGATGAA------ -s Anc2.Anc2refChr0 5683 32 - 56053 AGTTTCAACTACCCATCCAACTGCCCGATGAA------ -s mr.mrrefChr0 12157 38 + 130230 ATTGTCAACTACTCTACCAACTGCCAGATGAAGGACCC -s simCow_chr6.simCow.chr6 548918 32 - 602619 AAATTCAACTACCCATCCAACTGCCCAATGAG------ -s simDog_chr6.simDog.chr6 546622 32 - 593897 AGTTTCAATTAGCCATCCAACTGCCCGATGAA------ -s simHuman_chr6.simHuman.chr6 553125 32 - 601863 ACCTTCAGCTACCCGTCCAAGTGCCTGATGAA------ -s simRat_chr6.simRat.chr6 235446 36 - 647215 ATTGTCAACTACTCAACCAACTGCCAGC--AAGAATCC - -a -s simMouse_chr6.simMouse.chr6 13388 11 + 636262 AGCGAATCCTT -s Anc0.Anc0refChr2 8069 7 + 17989 ----AATCCTT -s Anc1.Anc1refChr2 115149 11 - 144309 AGCTAATCCTT -s Anc2.Anc2refChr0 5733 7 - 56053 ----ATTCATT -s mr.mrrefChr0 12216 11 + 130230 AGCGAATCCTT -s simCow_chr6.simCow.chr6 548967 7 - 602619 ----ATCCTTT -s simDog_chr6.simDog.chr6 546672 7 - 593897 ----GTTCACT -s simHuman_chr6.simHuman.chr6 553178 11 - 601863 AGCTAATCCTT -s simRat_chr6.simRat.chr6 235535 11 - 647215 AATGAATTCTC - -a -s simMouse_chr6.simMouse.chr6 13399 12 + 636262 TTTTTAACACAA -s Anc0.Anc0refChr2 8077 12 + 17989 TATTAGCCACAA -s Anc1.Anc1refChr2 115161 12 - 144309 TATTAGCCACAA -s Anc2.Anc2refChr0 5741 12 - 56053 TATTAGACACAA -s mr.mrrefChr0 12227 12 + 130230 TTTTAGCCACAA -s simCow_chr6.simCow.chr6 548975 12 - 602619 TATTAGTCACAA -s simDog_chr6.simDog.chr6 546680 12 - 593897 TATTAGAGATAA -s simHuman_chr6.simHuman.chr6 553190 12 - 601863 TCTTAGCCGCAA -s simRat_chr6.simRat.chr6 235546 12 - 647215 TTTTAGCCACAA - -a -s simMouse_chr6.simMouse.chr6 13411 26 + 636262 TTACCCTGTATGATGACTTAGGAGGC -s Anc0.Anc0refChr2 8089 18 + 17989 GTACCCTGTGTAATGAC--------C -s Anc1.Anc1refChr2 115173 18 - 144309 GTACCCTGTGTAATGAC--------C -s Anc2.Anc2refChr0 5753 18 - 56053 GTACCCTGTGTAATGAC--------C -s mr.mrrefChr0 12239 26 + 130230 TTACCCTGTATGATGACTTAGGAGGC -s simCow_chr6.simCow.chr6 548987 18 - 602619 GTACCCTGTGTAATGAC--------C -s simDog_chr6.simDog.chr6 546692 18 - 593897 GTACCGTATGTAATGAC--------T -s simHuman_chr6.simHuman.chr6 553203 18 - 601863 CTATCCTGTGTAATGAC--------C -s simRat_chr6.simRat.chr6 235558 26 - 647215 TTACCCTGTATGATGACTGAGGATGC - -a -s simMouse_chr6.simMouse.chr6 13437 8 + 636262 TCATACCT -s Anc0.Anc0refChr2 8107 8 + 17989 TCATCCCT -s Anc1.Anc1refChr2 115191 8 - 144309 TCATCCCT -s Anc2.Anc2refChr0 5771 8 - 56053 TCATCCCT -s mr.mrrefChr0 12265 8 + 130230 TCATACCT -s simDog_chr6.simDog.chr6 546718 8 - 593897 TCATCCCT -s simHuman_chr6.simHuman.chr6 553221 8 - 601863 TCACCCTT -s simRat_chr6.simRat.chr6 235584 8 - 647215 TCATATCT - -a -s simMouse_chr6.simMouse.chr6 13445 12 + 636262 CCATCACAAACT -s Anc0.Anc0refChr2 8115 12 + 17989 CTGTCAGAACCA -s Anc1.Anc1refChr2 115199 12 - 144309 CTGTCAGAACCA -s Anc2.Anc2refChr0 5779 12 - 56053 CTGTCAGAACCA -s mr.mrrefChr0 12273 12 + 130230 CCATCAGAAACT -s simCow_chr6.simCow.chr6 549005 10 - 602619 --ATCAGCAGCA -s simDog_chr6.simDog.chr6 546730 12 - 593897 CTGTCAGAACTA -s simHuman_chr6.simHuman.chr6 553229 12 - 601863 CTGTTAGAACCA -s simRat_chr6.simRat.chr6 235592 12 - 647215 CAATCAGACACT - -a -s simMouse_chr6.simMouse.chr6 13457 83 + 636262 GGCTTCATTCCTCCATTAGAAAACAAGCCTTATAGGTCAATATACAATCATCATTAATTAGCCTTCTCAACCACCAGCTCACC -s Anc0.Anc0refChr2 8127 71 + 17989 AGCTTTGTTCCTCCATCAGAAG-CAAGGTTTGTGGGTCAGCCTATTCCCCTCAGTAATCAGCTGTC-----------CTAACC -s Anc1.Anc1refChr2 115211 71 - 144309 AGCTTTGTTCCTCCATCAGAAG-CAAGGTTTGTGGGTCAGCCTATTCCCCTCAGTAATCAGCTGTC-----------CTAACC -s Anc2.Anc2refChr0 5792 71 - 56053 AGTTTTGTCCCTCCATAAGAAG-CAAGGTTTGTGGGTCAGCCTATTCCCCTCAGTAATCAGCTGTC-----------CCAACT -s mr.mrrefChr0 12285 79 + 130230 GGCTTCATTCCTCCATCAGAAAACAAGCCTTATAGGTCAACATACACTCATCATTAATTAGCCTTCTCAAC----AGCTCACC -s simCow_chr6.simCow.chr6 549016 71 - 602619 GGTTTCATCCCTCCATAAGAAG-CGAGGTATTTGGGTGAGCCTATGATCCTCAGGAATCATTTGTC-----------CCAACT -s simDog_chr6.simDog.chr6 546743 71 - 593897 AGTTTTGTCCCTCCATAAGAGG-CAGAGTTTGTGGGTCAGTCTATTCCCCTCAGTAATCAGCTGTC-----------CCAAGT -s simHuman_chr6.simHuman.chr6 553241 69 - 601863 CACTCA--TCCGCCATCAGAAG-CAAGGTTTGTGGGTCAGCCTATTCCCCTCTGTAAGCAGCTGCC-----------CTAGCC -s simRat_chr6.simRat.chr6 235604 67 - 647215 GGCTTCATTTCTCCATCAGAAAACAAGTCTTATAGGTCAACATACACTCATCAATAATT----------------GGATCACC - -a -s simMouse_chr6.simMouse.chr6 13540 96 + 636262 TGGGGGGCTGGTGGAGGAGTATGCTCCTCTGGCTGGGCTCAAAGGCCAGGAGGCACCTTAGTCGTGACTGACTTTAGATACATGCTGTTAGAAACT -s Anc0.Anc0refChr2 8198 4 + 17989 AGGG-------------------------------------------------------------------------------------------- -s Anc1.Anc1refChr2 115282 4 - 144309 AGGG-------------------------------------------------------------------------------------------- -s Anc2.Anc2refChr0 5863 4 - 56053 AGAG-------------------------------------------------------------------------------------------- -s mr.mrrefChr0 12364 96 + 130230 TGGGGGGCTGGTGGAGGAGTATGCTCCTCTGGCTGGGCTCAAAGGCCAGGAGGCACCTTAGTCGTGACTGACTTTAGATACATGCTGTTAGAAACT -s simCow_chr6.simCow.chr6 549088 4 - 602619 AGAG-------------------------------------------------------------------------------------------- -s simDog_chr6.simDog.chr6 546814 4 - 593897 ACAG-------------------------------------------------------------------------------------------- -s simHuman_chr6.simHuman.chr6 553310 4 - 601863 AGGG-------------------------------------------------------------------------------------------- -s simRat_chr6.simRat.chr6 235671 96 - 647215 TGGGGGGCTGGTGGAGGAGTATGCTCCTCTGGCTTGGCTGGAACGCTAGGGGAAACCCAAGTCATGACTGACTTTAGGTACATGCTGTTAGAAACT - -a -s simMouse_chr6.simMouse.chr6 13636 6 + 636262 GTGTGA -s Anc0.Anc0refChr2 9108 4 - 17989 --GGGA -s Anc1.Anc1refChr2 28330 4 + 144309 --GGGA -s Anc2.Anc2refChr0 49269 4 + 56053 --GGGG -s mr.mrrefChr0 12460 6 + 130230 GTGTGA -s simCow_chr6.simCow.chr6 52558 4 + 602619 --GAGG -s simDog_chr6.simDog.chr6 46104 4 + 593897 --GGGG -s simHuman_chr6.simHuman.chr6 47841 4 + 601863 --GGGA -s simRat_chr6.simRat.chr6 235786 6 - 647215 GTGGGA - -a -s simMouse_chr6.simMouse.chr6 13642 1 + 636262 A -s Anc0.Anc0refChr2 9112 1 - 17989 G -s Anc1.Anc1refChr2 28334 1 + 144309 G -s Anc2.Anc2refChr0 49274 1 + 56053 G -s mr.mrrefChr0 12466 1 + 130230 A -s simCow_chr6.simCow.chr6 52563 1 + 602619 G -s simDog_chr6.simDog.chr6 46109 1 + 593897 G -s simHuman_chr6.simHuman.chr6 47845 1 + 601863 G -s simRat_chr6.simRat.chr6 235792 1 - 647215 A - -a -s simMouse_chr6.simMouse.chr6 13643 30 + 636262 TTGTAATGAATGAAACTAGGACTCATACTA -s Anc0.Anc0refChr2 9114 25 - 17989 TTGTAATAACAC----TAGGAT-CCTACTG -s Anc1.Anc1refChr2 28336 26 + 144309 TTGTAATAACAC----TAGGATTCCTACTG -s Anc2.Anc2refChr0 49276 25 + 56053 TTGTGACAACAC----TAGGAT-CCTACAG -s mr.mrrefChr0 12467 26 + 130230 TTGTAATGAATG----TAGGACTCATACTA -s simCow_chr6.simCow.chr6 52565 25 + 602619 TTGTGTCAATGC----TAGGAC-TCTACAG -s simDog_chr6.simDog.chr6 46111 25 + 593897 TTGTGACAACAC----TAGGAT-CCTACAG -s simHuman_chr6.simHuman.chr6 47847 26 + 601863 TTGTAATAGCAC----TAGGATTCCTACTG -s simRat_chr6.simRat.chr6 235793 26 - 647215 TTGTAATGAAAG----TAGGACTCACACTG - -a -s simMouse_chr6.simMouse.chr6 13673 1 + 636262 T -s Anc0.Anc0refChr2 9139 1 - 17989 T -s Anc1.Anc1refChr2 28362 1 + 144309 T -s Anc2.Anc2refChr0 49446 1 + 56053 T -s mr.mrrefChr0 12493 1 + 130230 T -s simCow_chr6.simCow.chr6 52751 1 + 602619 C -s simDog_chr6.simDog.chr6 46293 1 + 593897 T -s simHuman_chr6.simHuman.chr6 47873 1 + 601863 T -s simRat_chr6.simRat.chr6 235819 1 - 647215 T - -a -s simMouse_chr6.simMouse.chr6 13674 35 + 636262 CATTAGTAAAGACCTGTGATTAAAAGGCAGTTACA -s Anc0.Anc0refChr2 9140 1 - 17989 T---------------------------------- -s Anc1.Anc1refChr2 28363 1 + 144309 T---------------------------------- -s Anc2.Anc2refChr0 49447 1 + 56053 T---------------------------------- -s mr.mrrefChr0 12494 35 + 130230 CATTAGTAAAGACCTGTGATTAAAAGGCAGTTACA -s simCow_chr6.simCow.chr6 52760 1 + 602619 T---------------------------------- -s simHuman_chr6.simHuman.chr6 47874 1 + 601863 T---------------------------------- -s simRat_chr6.simRat.chr6 235820 35 - 647215 CCTTAGTAAACACTCATGATTAAAAGGCAGTTATA - -a -s simMouse_chr6.simMouse.chr6 13709 56 + 636262 CGCATGCCAAATGTTGGTCATTTGCACTGTTAGTGTGCACTGGATGCATGGTAGGC -s mr.mrrefChr0 12529 56 + 130230 CGCATGCCAAATGTTGGTCATTTGCACTGTTAGTGTGCACTGGATGCATGGTAGGC -s simRat_chr6.simRat.chr6 235859 56 - 647215 CTCATGCTAAACGTTGGTCATTTTCACTGATTCTATGCACTGGGTGCGTGGTAGGC - -a -s simMouse_chr6.simMouse.chr6 13765 84 + 636262 TGCAGAGATGTACCATGCTTCAGAAATGGTTCAACTGCACCCAATGTTATCGTGGTCGTATGATGTCCAATATTTGAGTTTGTA -s Anc0.Anc0refChr2 9141 37 - 17989 --------------------------------------------TGTCACCGTGGTC--TTGATGTCTCACACCTGAGTTT-AG -s Anc1.Anc1refChr2 28364 37 + 144309 --------------------------------------------TGTCACCGTGGTC--TTGATGTCTCACACCTGAGTTT-AG -s Anc2.Anc2refChr0 49448 37 + 56053 --------------------------------------------CATCACAGTGGTC--TTGGGGCCTCACACCTGAGTTG-AG -s mr.mrrefChr0 12585 83 + 130230 TGCAGAGATGTACCATGCTTCAGAAATGGTTCAACTGCACCCAATGTTATCGTGGTCGTATGATGTCCAATACTTGAGTTT-TG -s simCow_chr6.simCow.chr6 52761 37 + 602619 --------------------------------------------CATCACAGTGGTC--TTGGGGCCTTGCACTTGAGTTC-AG -s simDog_chr6.simDog.chr6 46294 17 + 593897 ------------------------------------------------------------------CTCACACCTGAGTTG-AG -s simHuman_chr6.simHuman.chr6 47875 37 + 601863 --------------------------------------------TGTCACCGCAGTA--CTGATGTCTCACACCTGAGTTT-AG -s simRat_chr6.simRat.chr6 235916 83 - 647215 TGCAGGGATGTACCATGCTCCAGATCTGGCTCAACTACACCCAATGTTATTGTGGTCGTATAATGTCCAATACTTGAAGTT-TG - -a -s simMouse_chr6.simMouse.chr6 13849 22 + 636262 TATTATGAGTAGACTTTTGAAA -s Anc0.Anc0refChr2 9181 21 - 17989 AATTACAGGTAGAC-GTTGAAA -s Anc1.Anc1refChr2 28404 22 + 144309 AATTACAGGTAGACTGTTGAAA -s Anc2.Anc2refChr0 49488 21 + 56053 AATTACAGGTAGAC-GTTGAAA -s mr.mrrefChr0 12668 22 + 130230 AATTATGAGTAGACTTTTGAAA -s simCow_chr6.simCow.chr6 52801 21 + 602619 ATTTACAGGTAGAT-ACTAAAA -s simDog_chr6.simDog.chr6 46314 21 + 593897 AATTACACGTAGAC-GTTGAAA -s simHuman_chr6.simHuman.chr6 47915 22 + 601863 AATTACAGGTAGACTGGTGAAA -s simRat_chr6.simRat.chr6 235999 22 - 647215 AATTATGAGTAGACTTTTGAAA - -a -s simMouse_chr6.simMouse.chr6 13871 32 + 636262 CGATTATTATCCACGGGAGTCAGGTGGAGTCA -s Anc0.Anc0refChr2 9202 31 - 17989 CGAT-GTAATCCACAGGCGTCAGGTGTATCCA -s Anc1.Anc1refChr2 28426 31 + 144309 CGAT-GTAATCCACAGGCGTCAGGTGTATCCA -s Anc2.Anc2refChr0 49509 31 + 56053 CGAT-GTACTCCACAGGCGTCAGGTGTATCTA -s mr.mrrefChr0 12690 31 + 130230 CGAT-ATTATCCACAGGAGTCAGGTGTAGTCA -s simCow_chr6.simCow.chr6 52822 31 + 602619 TGGT-GTACTCTGCAGGTATCAGGTGTATCTA -s simDog_chr6.simDog.chr6 46381 31 + 593897 CTAT-GTACCCCACAGGCGTTAGGAGTATCTA -s simHuman_chr6.simHuman.chr6 47937 31 + 601863 CGAT-GCAATCCACAGGGGTCAGGTATACCCA -s simRat_chr6.simRat.chr6 236021 31 - 647215 TGAG-ATTACCCACAGGAGTCAGGTGTATTGA - -a -s simMouse_chr6.simMouse.chr6 13903 41 + 636262 TGTTCCCCCTCTGTAGCGTTTTAATCATTGAGTAGCTTAGC -s Anc0.Anc0refChr2 9233 40 - 17989 TGTTAC-CTTTTCTAGCATTCTACTCATTGAATACCTTAGA -s Anc1.Anc1refChr2 28457 40 + 144309 TGTTAC-CTTTTCTAGCATTCTACTCATTGAATACCTTAGA -s Anc2.Anc2refChr0 49546 40 + 56053 TGTTAC-CTTTTCTAGCATTCTAATCATTGAATACCTTAGA -s mr.mrrefChr0 12721 41 + 130230 TGTTCCCCCTCTGTAGCATTTTACTCATTGAGTAGCTTAGC -s simCow_chr6.simCow.chr6 52859 40 + 602619 TGATAC-CCTCTCTAGCATTCTAGTCATTGAATACCTAAGA -s simDog_chr6.simDog.chr6 46418 40 + 593897 TGTCAG-CTTTTCTAGCATCCTGATCATTAAATACCGTAGA -s simHuman_chr6.simHuman.chr6 47968 40 + 601863 TGTTTC-CATTTTTAGGATTGTACACACTGAATATATTAGA -s simRat_chr6.simRat.chr6 236052 41 - 647215 TGTTCCCCCTCTCAAGCATTTAACTCATTGAGCAGCTTAGC - -a -s simMouse_chr6.simMouse.chr6 13944 20 + 636262 TTTTAAGCTTTTAAGACTCC -s Anc0.Anc0refChr2 9274 18 - 17989 TTCTAAGACTTTTCTATT-- -s Anc1.Anc1refChr2 28498 20 + 144309 TTCTAAGACTTTTCTATTTC -s Anc2.Anc2refChr0 49587 18 + 56053 TTCTAAGGCTCCTCTATT-- -s mr.mrrefChr0 12762 20 + 130230 TTTTAAGATTTTAAGACTCC -s simCow_chr6.simCow.chr6 52900 16 + 602619 CTCAAAGTCTGCTGTA---- -s simDog_chr6.simDog.chr6 46459 18 + 593897 TACTAAGGCTCCTCAGTT-- -s simHuman_chr6.simHuman.chr6 48009 20 + 601863 TTCTAACACTTTTCTATTTC -s simRat_chr6.simRat.chr6 236093 20 - 647215 TTTTAAGATTTTAAAACCCC - -a -s simMouse_chr6.simMouse.chr6 13964 26 + 636262 CTTGAAGTGGGCTGGAATTTGCAATG -s Anc0.Anc0refChr2 9292 26 - 17989 CTTGAAGCGGGCAGGAATTCAAAATG -s Anc1.Anc1refChr2 28518 26 + 144309 CTTGAAGCGGGCAGGAATTCAAAATG -s Anc2.Anc2refChr0 49605 26 + 56053 CTTGTAGCGGGCAGGAATTCAAAATG -s mr.mrrefChr0 12782 26 + 130230 CTTGAAGTGGGCTGGAATTTGCAATG -s simCow_chr6.simCow.chr6 52916 26 + 602619 CTTATAAGTGGGTGGAATTTAAAATG -s simDog_chr6.simDog.chr6 46477 26 + 593897 CTTGTAGCGGGCAGGGATTCTAAATG -s simHuman_chr6.simHuman.chr6 48033 26 + 601863 CTTCAAGCAGGCAGGAATTCAACATG -s simRat_chr6.simRat.chr6 236113 26 - 647215 CTTGAAGTGGGCTGGAATTTGCAATG - -a -s simMouse_chr6.simMouse.chr6 13990 51 + 636262 AAGATATGTGGTGGTGAGCACATCTGTTGCAATGAAGATATGTGGTGGTGA -s Anc0.Anc0refChr2 9318 24 - 17989 AAGATATATGGTGAGGAATCCA---------------------------AA -s Anc1.Anc1refChr2 28544 24 + 144309 AAGATATATGGTGAGGAATCCA---------------------------AA -s Anc2.Anc2refChr0 49631 24 + 56053 AAGATATATGGTTAGGAATCTC---------------------------AG -s mr.mrrefChr0 12808 24 + 130230 AAGATATATGGTGGTGAGTCCA---------------------------GA -s simCow_chr6.simCow.chr6 52942 24 + 602619 AAAATATATAGTTAGGAATTTA---------------------------AG -s simDog_chr6.simDog.chr6 46503 24 + 593897 AAGATATAGGGTTAGGACTCTC---------------------------AG -s simDog_chr6.simDog.chr6 568027 24 + 593897 AAGATATATGATTAGGAGTCTC---------------------------AA -s simHuman_chr6.simHuman.chr6 48059 24 + 601863 AAGATAAAAGGTGAGGAATCCA---------------------------CA -s simRat_chr6.simRat.chr6 236139 24 - 647215 AAAACATATGGTGGTGATTCCA---------------------------GA - -a -s simMouse_chr6.simMouse.chr6 14041 7 + 636262 GCACATC -s Anc0.Anc0refChr2 9347 7 - 17989 GCATATC -s Anc1.Anc1refChr2 28573 7 + 144309 GCATATC -s Anc2.Anc2refChr0 49660 7 + 56053 GCACATC -s mr.mrrefChr0 12832 7 + 130230 GCATATC -s simCow_chr6.simCow.chr6 52971 7 + 602619 ACACGTC -s simDog_chr6.simDog.chr6 46532 7 + 593897 GTACACC -s simDog_chr6.simDog.chr6 568056 7 + 593897 GCACATC -s simHuman_chr6.simHuman.chr6 48088 7 + 601863 GCATATC -s simRat_chr6.simRat.chr6 236163 7 - 647215 GCATATC - -a -s simMouse_chr6.simMouse.chr6 14048 45 + 636262 TGTATTAGACTATGTACCACTGTACAGAAGAATGAAGCTTAGTTT -s Anc0.Anc0refChr2 9354 45 - 17989 TGTATTATGCTGTGTATCAATGTACAACAGAATGTAACCTGGATT -s Anc1.Anc1refChr2 28580 45 + 144309 TGTATTATGCTGTGTATCAATGTACAACAGAATGTAACCTGGATT -s Anc2.Anc2refChr0 49667 45 + 56053 TGTATTATGCTGTTTATCAATGCCCAACAGAATATAACCTGGATT -s mr.mrrefChr0 12839 45 + 130230 TGTATTAGACTATGTATCACTGTACAGAAGAATGTAGCTTAGTTT -s simCow_chr6.simCow.chr6 52978 45 + 602619 TGTGTTATGCTGCGTATCAATGCACAACAGAATATAACCTGGATT -s simDog_chr6.simDog.chr6 46539 45 + 593897 AGTATAAATCTGTTTATCAACGCCCAACAGAATATAACCTGGATT -s simDog_chr6.simDog.chr6 568063 45 + 593897 TGTATTATACTGTTTAGCAGTTCCCAACAGAATATAACCTGGATT -s simHuman_chr6.simHuman.chr6 48097 45 + 601863 TGTATTATGCTGTGCATCAATGTACAATACAATGTAACCTGGATT -s simRat_chr6.simRat.chr6 236170 41 - 647215 TGTATTAGACTATGTATCACTGTGCAGGAGAATATA----AGTTT - -a -s simMouse_chr6.simMouse.chr6 14093 22 + 636262 GCAGAGGGTGTTCGATGGCCGA -s Anc0.Anc0refChr2 9409 22 - 17989 GCAAAGCTTGTTAGATAGCTGT -s Anc1.Anc1refChr2 28635 22 + 144309 GCAAAGCTTGTTAGATAGCTGT -s Anc2.Anc2refChr0 49722 22 + 56053 TCAAAGCTTGTCAGATAGCTGT -s mr.mrrefChr0 12884 22 + 130230 GCAAAGGTTGTTAGATAGCCGT -s simCow_chr6.simCow.chr6 53033 22 + 602619 GCACATCTTGTTAGATAGCTGC -s simDog_chr6.simDog.chr6 46594 22 + 593897 TCAAAACTTGTCAGATAGCTGT -s simDog_chr6.simDog.chr6 568118 22 + 593897 TGAAAGCTCGTCAGATAGCTGT -s simHuman_chr6.simHuman.chr6 48152 22 + 601863 GCAAAGCTTGTTAGATAGCTGT -s simRat_chr6.simRat.chr6 236211 22 - 647215 GCAAAGTTTGTTAGATAGCCGT - -a -s simMouse_chr6.simMouse.chr6 14115 1 + 636262 A -s Anc0.Anc0refChr2 9431 1 - 17989 G -s Anc1.Anc1refChr2 28657 1 + 144309 G -s Anc2.Anc2refChr0 49744 1 + 56053 G -s mr.mrrefChr0 12906 1 + 130230 A -s simCow_chr6.simCow.chr6 53055 1 + 602619 A -s simDog_chr6.simDog.chr6 46616 1 + 593897 G -s simDog_chr6.simDog.chr6 568140 1 + 593897 G -s simHuman_chr6.simHuman.chr6 48174 1 + 601863 G -s simRat_chr6.simRat.chr6 236237 1 - 647215 A - -a -s simMouse_chr6.simMouse.chr6 14116 44 + 636262 ATGAAAGAATTATCATTACTACTTTCTTTCAGTAGGTATTTACT -s Anc0.Anc0refChr2 9432 44 - 17989 ATAAAAGAATTATCATTACCACCTTTTTACAGGAAGTAATAACT -s Anc1.Anc1refChr2 28658 44 + 144309 ATAAAAGAATTATCATTACCACCTTTTTACAGGAAGTAATAACT -s Anc2.Anc2refChr0 49745 44 + 56053 ATAAAAGGATGATCATTACCACCTTTCTACAGGAAGTTACAATT -s mr.mrrefChr0 12907 44 + 130230 ATGAAAGAATTATCATTACCACTTTCTTTCAGGAGGTATTTACT -s simCow_chr6.simCow.chr6 53056 44 + 602619 ATGAAAGGATGATCATTACCATCCTTCAATAGGAAGTACTGATT -s simDog_chr6.simDog.chr6 46617 44 + 593897 ATAAAAGGATTATCATTACCACCTTACTACAGGAAGTTACAATC -s simDog_chr6.simDog.chr6 568145 44 + 593897 ATAAAAAGATGATCACTACCACCTTGCTACAGGAAGTTACAACT -s simHuman_chr6.simHuman.chr6 48175 44 + 601863 ATAGAAGAATTATCATTACCACCTTTTTACAGGAAGTAATAACT -s simRat_chr6.simRat.chr6 236238 44 - 647215 ATGAAAGAATTATCATAGCCACTTTCTTTCTGGAGGTATTTACT - -a -s simMouse_chr6.simMouse.chr6 14160 31 + 636262 TTACATCATGAATGTGACTTTTCCTCTGATA -s Anc0.Anc0refChr2 9476 31 - 17989 TTACATCATGAAGGTGTCTTTCTGTCTAATA -s Anc1.Anc1refChr2 28702 31 + 144309 TTACATCATGAAGGTGTCTTTCTGTCTAATA -s Anc2.Anc2refChr0 49789 31 + 56053 TTACATTGTGAAGGTGTCTTTCTGTCTAATA -s mr.mrrefChr0 12951 31 + 130230 TTACATCATGAAGGTGACTTTTTCTCTGATA -s simCow_chr6.simCow.chr6 53100 31 + 602619 TCACAGTGTGAAGGTGCCTTGCCATCGAATA -s simDog_chr6.simDog.chr6 46661 31 + 593897 TTACATTGTGAAGGTGTTTTTCTGTCTAATA -s simDog_chr6.simDog.chr6 568233 31 + 593897 TGACATTGTGAAGACATCTTCCTGTCTAATA -s simHuman_chr6.simHuman.chr6 48219 31 + 601863 TTATATCATGAAGGCACCTTTCTGTATAATT -s simRat_chr6.simRat.chr6 236282 31 - 647215 TTACATCATCAAGGTGGCTTCTTCTCTGACA - -a -s simMouse_chr6.simMouse.chr6 14191 14 + 636262 AGCCTTCTCATCCA -s Anc0.Anc0refChr2 9508 14 - 17989 AGCCCTCCTATATA -s Anc1.Anc1refChr2 28734 14 + 144309 AGCCCTCCTATATA -s Anc2.Anc2refChr0 49821 14 + 56053 AGCTCTTCTGTATA -s mr.mrrefChr0 12983 14 + 130230 AGCCTTCTCATCCA -s simCow_chr6.simCow.chr6 53132 14 + 602619 AGCCCTTCTGTTTA -s simDog_chr6.simDog.chr6 46693 14 + 593897 AGCTCTTCTCTACA -s simDog_chr6.simDog.chr6 568265 14 + 593897 AACTCTTCTGTATG -s simHuman_chr6.simHuman.chr6 48251 14 + 601863 AGCCCTCATATTTA -s simRat_chr6.simRat.chr6 236314 14 - 647215 AGTCTTCTCATCCA - -a -s simMouse_chr6.simMouse.chr6 14205 13 + 636262 GTGAAGCTGTCCA -s Anc0.Anc0refChr2 9522 11 - 17989 AGTCCT--GCCCC -s Anc1.Anc1refChr2 28748 13 + 144309 AGTCCTCTGCCCC -s Anc2.Anc2refChr0 49835 11 + 56053 AGTCAT--GCCCC -s mr.mrrefChr0 12997 13 + 130230 GTGAAGCTGTCCA -s simCow_chr6.simCow.chr6 53146 11 + 602619 GGGCAT--GCCCC -s simDog_chr6.simDog.chr6 568279 11 + 593897 AGTCAG--GCCCC -s simHuman_chr6.simHuman.chr6 48265 13 + 601863 AGTCCTCTGGCCC -s simRat_chr6.simRat.chr6 236328 13 - 647215 GTGTAGCTGTCAG - -a -s simMouse_chr6.simMouse.chr6 14218 2 + 636262 CA -s Anc0.Anc0refChr2 9533 2 - 17989 TA -s Anc1.Anc1refChr2 28761 2 + 144309 TA -s Anc2.Anc2refChr0 49846 2 + 56053 TA -s mr.mrrefChr0 13010 2 + 130230 CA -s simCow_chr6.simCow.chr6 53157 2 + 602619 TA -s simDog_chr6.simDog.chr6 46707 2 + 593897 TG -s simDog_chr6.simDog.chr6 568290 2 + 593897 TA -s simHuman_chr6.simHuman.chr6 48278 2 + 601863 TA - -a -s simMouse_chr6.simMouse.chr6 14220 6 + 636262 TGAGCT -s Anc0.Anc0refChr2 9536 6 - 17989 TAAGCC -s Anc1.Anc1refChr2 28764 6 + 144309 TAAGCC -s Anc2.Anc2refChr0 49849 6 + 56053 TAAGTC -s mr.mrrefChr0 13012 6 + 130230 TGAGCT -s simCow_chr6.simCow.chr6 53160 6 + 602619 AAGGTC -s simDog_chr6.simDog.chr6 46710 3 + 593897 TCC--- -s simDog_chr6.simDog.chr6 568293 3 + 593897 TAA--- -s simHuman_chr6.simHuman.chr6 48281 6 + 601863 AAAGCC - -a -s simMouse_chr6.simMouse.chr6 14226 8 + 636262 CTAATACC -s Anc0.Anc0refChr2 9542 8 - 17989 CTAATACC -s Anc1.Anc1refChr2 28770 8 + 144309 CTAATACC -s Anc2.Anc2refChr0 49855 8 + 56053 CTAATACT -s mr.mrrefChr0 13018 8 + 130230 CTAATACC -s simCow_chr6.simCow.chr6 53234 6 + 602619 CTAAT--T -s simDog_chr6.simDog.chr6 46713 6 + 593897 --AATACT -s simDog_chr6.simDog.chr6 568296 6 + 593897 --AACACT -s simHuman_chr6.simHuman.chr6 48287 8 + 601863 CTAACACC - -a -s simMouse_chr6.simMouse.chr6 14234 32 + 636262 GGGTATATACATCAAAAAGTTGCACCAAAGTT -s Anc0.Anc0refChr2 9550 26 - 17989 GGGTATATATATTAAAA-GTGGCATTA----- -s Anc1.Anc1refChr2 28778 26 + 144309 GGGTATATATATTAAAA-GTGGCATTA----- -s Anc2.Anc2refChr0 49863 26 + 56053 GGGCATATATATTCGAA-GTGGCATCA----- -s mr.mrrefChr0 13026 31 + 130230 GGGTATATACATCAAAA-GTTGCACTAAAGTT -s simCow_chr6.simCow.chr6 53240 26 + 602619 GGGCATATATGTTCAAA-GTGGCATCA----- -s simDog_chr6.simDog.chr6 46719 23 + 593897 GGGCACATATATTCGAA-GTGGC---A----- -s simDog_chr6.simDog.chr6 568302 15 + 593897 GGACATATATATTAG----------------- -s simHuman_chr6.simHuman.chr6 48298 26 + 601863 GGGTATATATGTTAAAA-GCAGCATTA----- -s simRat_chr6.simRat.chr6 236341 27 - 647215 ----GTATACATCAAAA-GTTGCACTAAAGTT - -a -s simMouse_chr6.simMouse.chr6 14266 18 + 636262 CATCGTATTGTGCCCATA -s Anc0.Anc0refChr2 9576 13 - 17989 -----TATTGTGCCAATT -s Anc1.Anc1refChr2 28804 13 + 144309 -----TATTGTGCCAATT -s Anc2.Anc2refChr0 49889 13 + 56053 -----TATTGTGCCAATT -s mr.mrrefChr0 13057 18 + 130230 CATCGTATTGTGCCCATA -s simCow_chr6.simCow.chr6 53266 13 + 602619 -----TATTGTGCCAAGT -s simDog_chr6.simDog.chr6 46742 13 + 593897 -----TATTGTATCAATT -s simHuman_chr6.simHuman.chr6 48324 13 + 601863 -----TGTTGTGCCAATC -s simRat_chr6.simRat.chr6 236369 17 - 647215 TACCATATTGTGCCT-TG - -a -s simMouse_chr6.simMouse.chr6 14284 58 + 636262 TATTTGAGGGTTGGCCTTGTCAATTCAGGGTTGCCCTCAGGATCACCACTAGGCCACT -s Anc0.Anc0refChr2 9590 57 - 17989 TATTTATGGGTTGGCTTGTTAGTACCAGAGTTGCCTTGAAGATTGCCACAAGGCCAT- -s Anc1.Anc1refChr2 28818 58 + 144309 TATTTATGGGTTGGCTTGTTAGTACCAGAGTTGCCTTGAAGATTGCCACAAGGCCATT -s Anc2.Anc2refChr0 49903 57 + 56053 TATTTATGGGTTGGCTTGTAAGTACCAGAGTTGCCTTGAAGATTGCTATAAGGCCAT- -s mr.mrrefChr0 13075 58 + 130230 TATTTGAGGGTTGGCCTTGTCAATTCAGGGTTGCCCTGAGGATCACCACTAGGCCACT -s simCow_chr6.simCow.chr6 53280 52 + 602619 TATTTATGGGTT----TGTCAGT-CCAGAGTTGCCTTGAAGATTGGTATAAGGCCAT- -s simDog_chr6.simDog.chr6 46756 42 + 593897 TATTTATGGGTTGGCTTGTAGGTAGCAGA---------------GCTATAAGGCCAT- -s simHuman_chr6.simHuman.chr6 48338 58 + 601863 TATTTATGGGTTGGCTTATTAGTCCCAGAGTTGCCTTGATGACTGCCACAAGGCCATC -s simRat_chr6.simRat.chr6 236386 58 - 647215 TATGTGCAGGTTGGGCTTGTTAATTCAGGGTTGCCATGAGGATCACCACTAGGCCACT - -a -s simMouse_chr6.simMouse.chr6 14342 3 + 636262 CAC -s Anc0.Anc0refChr2 9647 3 - 17989 CAC -s Anc1.Anc1refChr2 28876 3 + 144309 CAC -s Anc2.Anc2refChr0 49960 3 + 56053 CAC -s mr.mrrefChr0 13133 3 + 130230 CAC -s simCow_chr6.simCow.chr6 53332 3 + 602619 CAC -s simDog_chr6.simDog.chr6 46798 3 + 593897 CAC -s simHuman_chr6.simHuman.chr6 48404 3 + 601863 CAC -s simRat_chr6.simRat.chr6 236444 3 - 647215 CGC - -a -s simMouse_chr6.simMouse.chr6 14345 14 + 636262 TGGATTACTATCAT -s Anc0.Anc0refChr2 9650 14 - 17989 TGGCTCACTACCAT -s Anc1.Anc1refChr2 28879 14 + 144309 TGGCTCACTACCAT -s Anc2.Anc2refChr0 49963 14 + 56053 TGGCTCACTCCCAT -s mr.mrrefChr0 13136 14 + 130230 TGGCTTACTATCAT -s simCow_chr6.simCow.chr6 53339 14 + 602619 TGGCTTAATCCTAT -s simDog_chr6.simDog.chr6 46801 14 + 593897 TGGCTCACTCCCAT -s simHuman_chr6.simHuman.chr6 48407 12 + 601863 TGGCTCACTA--AT -s simRat_chr6.simRat.chr6 236447 14 - 647215 TGGCTTACTATCAT - -a -s simMouse_chr6.simMouse.chr6 14359 16 + 636262 TGAGCATTGCTGCCTT -s Anc0.Anc0refChr2 9664 13 - 17989 T---CATTGCAGACTT -s Anc1.Anc1refChr2 28893 13 + 144309 T---CATTGCAGACTT -s Anc2.Anc2refChr0 49980 13 + 56053 T---CAATGCAGACTT -s mr.mrrefChr0 13150 16 + 130230 TGAGCATTGCTGCCTT -s simCow_chr6.simCow.chr6 53356 6 + 602619 T---TAG-------TT -s simDog_chr6.simDog.chr6 46818 13 + 593897 T---CAATGCAGACTT -s simHuman_chr6.simHuman.chr6 48419 13 + 601863 T---CATTGCAGTCTT -s simRat_chr6.simRat.chr6 236461 16 - 647215 GGAGCATTGCTCCCTT - -a -s simMouse_chr6.simMouse.chr6 14375 65 + 636262 TGATGTCTTATGTCTTTGATGGATGTTACAGCTGCAGGTGCACCCCACAAATGCTAGATTGTGGG -s Anc0.Anc0refChr2 9677 58 - 17989 GGCT---TGATGTGGACGATGCATGTTACAGCTAAAGTTGCACCCCACAAACTCTAG----TGGG -s Anc1.Anc1refChr2 28906 65 + 144309 GGCTAGCTGATGTGGACGATGCATGTTACAGCTAAAGTTGCACCCCACAAACTCTAGCGAGTGGG -s Anc2.Anc2refChr0 49993 58 + 56053 GGCT---TGATGTGGAAGATGCATGTTACAGCTAAAGTTGCACCCCACAAACTTCAG----TGGG -s mr.mrrefChr0 13166 65 + 130230 TGATGTCTTATGTCTTCGATGGATGTTACAGCTGCAGGTGCACCCCACAAACGCTAGATTGTGGG -s simCow_chr6.simCow.chr6 53362 44 + 602619 GGAC---TGACGTGGGATATGCATGTTACTGCTAAAGTTGCAACCCA------------------ -s simDog_chr6.simDog.chr6 46833 58 + 593897 GGCT---TGATATGGAAGAAGAAGGTTATAGCTAAAGTTAAACCCCACAAACTTCAG----TGGG -s simHuman_chr6.simHuman.chr6 48432 65 + 601863 GGTTAGCTGATGTGGCCGATACATGTTACCACTAAAGTTGCGTCCCACAAACTCTAGCGAGTCGG -s simRat_chr6.simRat.chr6 236477 65 - 647215 TGATGTCTCATGTCTTCGATGAATGTTATAGCTGCAGGTGCACCCCATAAACACTAGATTGTGGG - -a -s simMouse_chr6.simMouse.chr6 14440 25 + 636262 TGGAGTCACTACTCAACAGAAGTGT -s Anc0.Anc0refChr2 9737 25 - 17989 CGAAATTACTCCTCGACAGAAGTAT -s Anc1.Anc1refChr2 28973 25 + 144309 CGAAATTACTCCTCGACAGAAGTAT -s Anc2.Anc2refChr0 50053 25 + 56053 CAAAATTAGTCCTCGACAGAAGTAT -s mr.mrrefChr0 13231 25 + 130230 CGAAATCACTACTCAACAGAAGTGT -s simCow_chr6.simCow.chr6 53406 13 + 602619 ------------TCGACAGAAATAT -s simDog_chr6.simDog.chr6 46893 25 + 593897 CAAAATTAGTCCTCAACAGAAGTAT -s simHuman_chr6.simHuman.chr6 48499 25 + 601863 CGAAATTACTGCTTGACAGAAGTAT -s simRat_chr6.simRat.chr6 236542 25 - 647215 CGACATCACTACTCAACAGAAGTGT - -a -s simMouse_chr6.simMouse.chr6 14465 2 + 636262 CT -s Anc0.Anc0refChr2 9762 2 - 17989 CT -s Anc1.Anc1refChr2 28998 2 + 144309 CT -s Anc2.Anc2refChr0 50078 2 + 56053 CT -s mr.mrrefChr0 13256 2 + 130230 CT -s simCow_chr6.simCow.chr6 53419 2 + 602619 CT -s simDog_chr6.simDog.chr6 46963 2 + 593897 CT -s simHuman_chr6.simHuman.chr6 48524 2 + 601863 CT -s simRat_chr6.simRat.chr6 236567 2 - 647215 AT - -a -s simMouse_chr6.simMouse.chr6 14467 29 + 636262 TAGCATTGGACCACAGAGATCGCCTCCAA -s Anc0.Anc0refChr2 9764 14 - 17989 TGACACATGACCAC--------------- -s Anc1.Anc1refChr2 29000 14 + 144309 TGACACATGACCAC--------------- -s Anc2.Anc2refChr0 50080 14 + 56053 TGACACATGCCTAT--------------- -s mr.mrrefChr0 13258 29 + 130230 TAGCACTGGACCACAGAGATTGCCTCCAA -s simCow_chr6.simCow.chr6 53421 14 + 602619 TGACACAAGCCTAT--------------- -s simDog_chr6.simDog.chr6 46965 14 + 593897 TGACACATGCGTTT--------------- -s simHuman_chr6.simHuman.chr6 48526 14 + 601863 CTACACACGACCAC--------------- -s simRat_chr6.simRat.chr6 236571 29 - 647215 TGGCACCAGACCACAGTGATTGCCTCCAA - -a -s simMouse_chr6.simMouse.chr6 14496 5 + 636262 TTCTC -s Anc0.Anc0refChr2 8882 5 + 17989 ACCTC -s Anc1.Anc1refChr2 115980 5 - 144309 ACCTC -s Anc2.Anc2refChr0 6785 5 - 56053 ACCTC -s mr.mrrefChr0 13287 5 + 130230 TTCTC -s simCow_chr6.simCow.chr6 550062 5 - 602619 ACCTC -s simDog_chr6.simDog.chr6 547794 5 - 593897 ATCTC -s simHuman_chr6.simHuman.chr6 554023 5 - 601863 ACCTC -s simRat_chr6.simRat.chr6 236600 5 - 647215 TTCTC - -a -s simMouse_chr6.simMouse.chr6 14501 6 + 636262 CAGCAG -s Anc0.Anc0refChr2 8890 6 + 17989 CAGCAT -s Anc1.Anc1refChr2 115988 6 - 144309 CAGCAT -s Anc2.Anc2refChr0 6793 6 - 56053 CAGCAT -s mr.mrrefChr0 13295 6 + 130230 CAGCAG -s simCow_chr6.simCow.chr6 550070 6 - 602619 CAACAT -s simDog_chr6.simDog.chr6 547802 6 - 593897 TTGCAT -s simHuman_chr6.simHuman.chr6 554031 6 - 601863 CAGCAA -s simRat_chr6.simRat.chr6 236608 6 - 647215 CAACAG - -a -s simMouse_chr6.simMouse.chr6 14507 19 + 636262 AACCTGGTGCATGAACATG -s Anc0.Anc0refChr2 8896 19 + 17989 AACCTGCTGCATGAACATG -s Anc1.Anc1refChr2 115994 19 - 144309 AACCTGCTGCATGAACATG -s Anc2.Anc2refChr0 6799 19 - 56053 AACCTGCTGCATGAACATG -s mr.mrrefChr0 13301 19 + 130230 AACCTGGTGCATGAACATG -s simCow_chr6.simCow.chr6 550077 19 - 602619 AACCTGCTGTGTGAACTAG -s simDog_chr6.simDog.chr6 547808 19 - 593897 AACCTGATGCATGAATATA -s simHuman_chr6.simHuman.chr6 554037 17 - 601863 AACCC--TGCATGAACATG -s simRat_chr6.simRat.chr6 236614 19 - 647215 ACCCTGCGGCATGAACATG - -a -s simMouse_chr6.simMouse.chr6 14526 44 + 636262 GTTGTCTGCTGACCTCTCTACAGTCATTGACCATGGTTTGGCAT -s Anc0.Anc0refChr2 8919 44 + 17989 ATTGTCTGCTGACCTTTCTATAGTTGTGGATTATGAATTGTCAT -s Anc1.Anc1refChr2 116017 44 - 144309 ATTGTCTGCTGACCTTTCTATAGTTGTGGATTATGAATTGTCAT -s Anc2.Anc2refChr0 6822 44 - 56053 ATTGTCTGCTGACCTTTCTATAGTTGTGGATTATGAATTGTCAT -s mr.mrrefChr0 13324 44 + 130230 GTTGTCTGCTGACCTCTCTACAGTCATTGACCATGGTTTGGCAT -s simCow_chr6.simCow.chr6 550100 40 - 602619 ATTGTCTGCTGACCTCTCTATAGTTGCAGATTATGCA----CAT -s simDog_chr6.simDog.chr6 547831 44 - 593897 ATTGTCTGGTGACCTTTCTGTAGTTGTGGATTTTGAATTGTCGT -s simHuman_chr6.simHuman.chr6 554058 42 - 601863 ATTGGCTGCTGACCTTACTATAGTTGTA--TTATGTGTTTTTAT -s simRat_chr6.simRat.chr6 236637 44 - 647215 GTTGTCTGCTGACCTCTCTACAGTCATGGACCATGCTTTGGCAT - -a -s simMouse_chr6.simMouse.chr6 14570 51 + 636262 CTGGAGAAGTTACCTTGCCAGTTGCCAGTAAAACCCTTACTTGTAATAGTC -s Anc0.Anc0refChr2 8964 38 + 17989 TTGGACAAGTTATT-------T------TAAAGCCCTAAGTTGTAGTGTTC -s Anc1.Anc1refChr2 116062 39 - 144309 TTGGACAAGTTATT-------TC-----TAAAGCCCTAAGTTGTAGTGTTC -s Anc2.Anc2refChr0 6867 38 - 56053 TTGGACAAGTTATT-------T------TAAAGCCCTAAGTTGTAGTGTTC -s mr.mrrefChr0 13368 44 + 130230 CTGGAGAAGTTACC-------TTGCCAGTAAAACCCTAACTTGTAATAGTC -s simCow_chr6.simCow.chr6 550141 38 - 602619 TTGGACAAATTAAT-------T------TAAAGCCCAAAGTTGTAGTGTTC -s simDog_chr6.simDog.chr6 547876 38 - 593897 TTGGATAAGTTATT-------T------TAAAGCCCTAAGTTGTAGTATTC -s simHuman_chr6.simHuman.chr6 554101 39 - 601863 TTGGACAAGTTAAG-------TC-----TAAAGCCCTATGTTGCAGAGTTC -s simRat_chr6.simRat.chr6 236681 44 - 647215 CTTGATAGGTTACC-------TTGCCAGCAAATCCCAAACTTGTAATACTC - -a -s simMouse_chr6.simMouse.chr6 14621 6 + 636262 ATCCGC -s Anc0.Anc0refChr2 9004 6 + 17989 AGCCTC -s Anc1.Anc1refChr2 116103 6 - 144309 AGCCTC -s Anc2.Anc2refChr0 6907 6 - 56053 AGCCTC -s mr.mrrefChr0 13414 6 + 130230 ATCCTC -s simCow_chr6.simCow.chr6 550181 6 - 602619 AGACTC -s simDog_chr6.simDog.chr6 547916 6 - 593897 AGCCTC -s simHuman_chr6.simHuman.chr6 554142 6 - 601863 AGCATC -s simRat_chr6.simRat.chr6 236727 6 - 647215 ATCCTC - -a -s simMouse_chr6.simMouse.chr6 14627 29 + 636262 CAACCATTGGTAACTTGTATTTTCTTAAA -s Anc0.Anc0refChr2 9014 27 + 17989 --AGCTTTTGGGGCCCATATTTTCTCAAA -s Anc1.Anc1refChr2 116113 29 - 144309 CAAGCTTTTGGGGCCCATATTTTCTCAAA -s Anc2.Anc2refChr0 6917 27 - 56053 --AGCTTTTGGGGCCCATATTTTCTCAAA -s mr.mrrefChr0 13420 29 + 130230 CAACCATTGGTAACCTGTATTTTCTTAAA -s simCow_chr6.simCow.chr6 550191 27 - 602619 --AGCTTTTGGGGCCCATATTTTCTCAAA -s simDog_chr6.simDog.chr6 547926 27 - 593897 --AGCTTTCAGGGCCCATATTTTCTCAAA -s simHuman_chr6.simHuman.chr6 554152 29 - 601863 CAAGCTTTTGGGGCCCATGCTTTCTCAAA -s simRat_chr6.simRat.chr6 236733 29 - 647215 CAGCCATTGATAACCTGTATTGTTTTAAA - -a -s simMouse_chr6.simMouse.chr6 14656 1 + 636262 A -s Anc0.Anc0refChr2 9041 1 + 17989 A -s Anc1.Anc1refChr2 116142 1 - 144309 A -s Anc2.Anc2refChr0 6944 1 - 56053 A -s mr.mrrefChr0 13449 1 + 130230 A -s simCow_chr6.simCow.chr6 550220 1 - 602619 A -s simDog_chr6.simDog.chr6 547953 1 - 593897 A -s simHuman_chr6.simHuman.chr6 554181 1 - 601863 A -s simRat_chr6.simRat.chr6 236762 1 - 647215 C - -a -s simMouse_chr6.simMouse.chr6 14657 40 + 636262 CACTACAAACTGACCACACAGATTGAATTAATACCTATGG -s Anc0.Anc0refChr2 9042 40 + 17989 CACTGCAAATTCACCACACTGGTTGAATTAATACCTATTA -s Anc1.Anc1refChr2 116143 40 - 144309 CACTGCAAATTCACCACACTGGTTGAATTAATACCTATTA -s Anc2.Anc2refChr0 6950 40 - 56053 CACTGCAAATTCACCACATTGGTTGAATTAATACCTATTA -s mr.mrrefChr0 13450 40 + 130230 CACTACAAACTGACCACACAGGTTGAATTAATACCTATTA -s simCow_chr6.simCow.chr6 550226 39 - 602619 CATTACAAACTCATCACATTGGTTAAA-TAAAACCTATTA -s simDog_chr6.simDog.chr6 547959 40 - 593897 CACTGCGAATTCACCACATTGGCTGAATTAATACCTATTT -s simHuman_chr6.simHuman.chr6 554182 34 - 601863 ------AAATTCACTACACTAGTAGAATTATTACCTATTA -s simRat_chr6.simRat.chr6 236763 40 - 647215 TACTACGAGCTGACCACACAGGTCAAATTAATACCTATTA - -a -s simMouse_chr6.simMouse.chr6 14697 27 + 636262 AATTAAGGATGTTGTCCCTACTCTACT -s Anc0.Anc0refChr2 9083 27 + 17989 AAGTAAGAGTATTATTTCTACTCTACT -s Anc1.Anc1refChr2 116184 27 - 144309 AAGTAAGAGTATTATTTCTACTCTACT -s Anc2.Anc2refChr0 6991 27 - 56053 AGGTAAGAGTATTATCTCTACTGTACT -s mr.mrrefChr0 13491 27 + 130230 AATTAAGGATGTTGTTCCTACTCTACT -s simCow_chr6.simCow.chr6 550266 26 - 602619 AGGT-GGAGTATTATCTCTGCTGTACT -s simDog_chr6.simDog.chr6 548000 27 - 593897 AGATAAGGATCTTATCTCTACTGTACT -s simHuman_chr6.simHuman.chr6 554217 27 - 601863 AAGCAAGAGTATTATTGCTACTCTACT -s simRat_chr6.simRat.chr6 236804 27 - 647215 AATTCAGGATGTTGTTCCAACTCTACT - -a -s simMouse_chr6.simMouse.chr6 14724 2 + 636262 TT -s Anc0.Anc0refChr2 9110 2 + 17989 TT -s Anc1.Anc1refChr2 116211 2 - 144309 TT -s Anc2.Anc2refChr0 7018 2 - 56053 TT -s mr.mrrefChr0 13518 2 + 130230 TT -s simCow_chr6.simCow.chr6 550292 2 - 602619 TT -s simDog_chr6.simDog.chr6 548029 2 - 593897 TT -s simHuman_chr6.simHuman.chr6 554244 2 - 601863 TT -s simRat_chr6.simRat.chr6 236831 2 - 647215 TT - -a -s simMouse_chr6.simMouse.chr6 14726 18 + 636262 ATGTTCGGCCATTCACAA -s Anc0.Anc0refChr2 9113 18 + 17989 CTGTTTGCCCATCCCCAA -s Anc1.Anc1refChr2 116214 18 - 144309 CTGTTTGCCCATCCCCAA -s Anc2.Anc2refChr0 7021 18 - 56053 CTGTCTGCCCATCCCCAG -s mr.mrrefChr0 13520 18 + 130230 ATGTTTGGCCATTCACAA -s simCow_chr6.simCow.chr6 550295 18 - 602619 ATGTCTGCCCATCCCCAG -s simDog_chr6.simDog.chr6 548032 18 - 593897 CTGTCTGCCCATCCCCTG -s simHuman_chr6.simHuman.chr6 554247 18 - 601863 GGGTTTGCTCAGCCCCAA -s simRat_chr6.simRat.chr6 236833 18 - 647215 ATGTCTGGCCATTCACAA - -a -s simMouse_chr6.simMouse.chr6 14744 5 + 636262 TCACA -s Anc0.Anc0refChr2 9131 5 + 17989 TGGAA -s Anc1.Anc1refChr2 116232 5 - 144309 TGGAA -s Anc2.Anc2refChr0 7039 5 - 56053 TGGAA -s mr.mrrefChr0 13538 5 + 130230 TCACA -s simCow_chr6.simCow.chr6 550313 5 - 602619 TGGAA -s simDog_chr6.simDog.chr6 548050 5 - 593897 TGGAG -s simHuman_chr6.simHuman.chr6 554266 5 - 601863 TGGAA -s simRat_chr6.simRat.chr6 236851 5 - 647215 TCACT - -a -s simMouse_chr6.simMouse.chr6 14749 8 + 636262 GCTCAAAC -s Anc0.Anc0refChr2 9136 8 + 17989 GCTCAAAG -s Anc1.Anc1refChr2 116237 8 - 144309 GCTCAAAG -s Anc2.Anc2refChr0 7044 8 - 56053 GCTGAAAG -s mr.mrrefChr0 13543 8 + 130230 GCTCAAAC -s simCow_chr6.simCow.chr6 550322 8 - 602619 GTTTAAAG -s simDog_chr6.simDog.chr6 548055 8 - 593897 GCTGGAAG -s simHuman_chr6.simHuman.chr6 554271 8 - 601863 GCTCAAAG -s simRat_chr6.simRat.chr6 236856 8 - 647215 GTTCAAAT - -a -s simMouse_chr6.simMouse.chr6 14757 4 + 636262 ACTG -s Anc0.Anc0refChr2 9144 4 + 17989 TACC -s Anc1.Anc1refChr2 116245 4 - 144309 TACC -s Anc2.Anc2refChr0 7052 4 - 56053 CACC -s mr.mrrefChr0 13551 4 + 130230 TATG -s simCow_chr6.simCow.chr6 550335 4 - 602619 CATT -s simDog_chr6.simDog.chr6 548063 4 - 593897 CACC -s simHuman_chr6.simHuman.chr6 554279 4 - 601863 TACC -s simRat_chr6.simRat.chr6 236864 4 - 647215 TATG - -a -s simMouse_chr6.simMouse.chr6 14761 3 + 636262 AAT -s Anc0.Anc0refChr2 9148 3 + 17989 AAT -s Anc1.Anc1refChr2 116249 3 - 144309 AAT -s Anc2.Anc2refChr0 7061 3 - 56053 AAT -s mr.mrrefChr0 13555 3 + 130230 AAT -s simCow_chr6.simCow.chr6 550344 3 - 602619 ACT -s simDog_chr6.simDog.chr6 548072 3 - 593897 AAC -s simHuman_chr6.simHuman.chr6 554283 3 - 601863 AAT -s simRat_chr6.simRat.chr6 236868 3 - 647215 AAT - -a -s simMouse_chr6.simMouse.chr6 14764 34 + 636262 GACACAAGGAAATGATATAGAGATATTTAGTCCG -s Anc0.Anc0refChr2 9152 34 + 17989 GACACGAGTAGATGATATGTAGCTATTGAGTCAG -s Anc1.Anc1refChr2 116253 34 - 144309 GACACGAGTAGATGATATGTAGCTATTGAGTCAG -s Anc2.Anc2refChr0 7065 34 - 56053 GACACGAGTAGATGATATGTAACTATTGAGTCAG -s mr.mrrefChr0 13558 34 + 130230 GACACAAGTAAATGATATAGAGATATTTAGTCCG -s simCow_chr6.simCow.chr6 550348 34 - 602619 AACACATGTTAATGATATATAACTATTGAGCCGG -s simDog_chr6.simDog.chr6 548076 34 - 593897 GACACGAGTAGACAATATGTAACTATTGAGTCAG -s simHuman_chr6.simHuman.chr6 554287 34 - 601863 GACACGATTAGATGACACGTAGCTATTAAGTCAG -s simRat_chr6.simRat.chr6 236871 34 - 647215 GACACAAGTAAATGATATACAGAAATTTAGTCCG - -a -s simMouse_chr6.simMouse.chr6 14798 29 + 636262 ATGAGTTCTAAGTCACTAGTTTGAGCTGT -s Anc0.Anc0refChr2 9189 27 + 17989 ATAAGTTCTAA--GACTAGTGTGAACTGT -s Anc1.Anc1refChr2 116290 29 - 144309 ATAAGTTCTAAGCGACTAGTGTGAACTGT -s Anc2.Anc2refChr0 7102 27 - 56053 ATAAGTTCAAA--GACTAGTGTGAACTGT -s mr.mrrefChr0 13592 29 + 130230 ATGAGTTCTAAGTCACTAGTTTGAGCTGT -s simCow_chr6.simCow.chr6 550385 24 - 602619 AGAAGTTCAAA-----TATTGGAACCTGC -s simDog_chr6.simDog.chr6 548113 24 - 593897 ATAAGTTCAAA--GACTAGTATGA---CT -s simHuman_chr6.simHuman.chr6 554324 29 - 601863 ATAATTTCTAAGCGACTCGTGTGAACTGT -s simRat_chr6.simRat.chr6 236905 29 - 647215 ATGTGTTCTAAGTCACTAGTTTGAGCTGT - -a -s simMouse_chr6.simMouse.chr6 14827 44 + 636262 AGGGAGTAGAAGAGTGCTATTTCAATTCTATGTTCTATAATTTA -s Anc0.Anc0refChr2 9216 41 + 17989 AAGTAGTAGAAGGGTGCTATTTCA---TTATTTTAAACCAGTTA -s Anc1.Anc1refChr2 116319 41 - 144309 AAGTAGTAGAAGGGTGCTATTTCA---TTATTTTAAACCAGTTA -s Anc2.Anc2refChr0 7129 41 - 56053 AAGTAGCAGGAGGGTGCTATTTCA---ATATTCTAAAACACTTA -s mr.mrrefChr0 13621 44 + 130230 AGGTAGTAGAAGAGTGCTATTTCAATTCTATGTTCTACAATTTA -s simCow_chr6.simCow.chr6 550409 41 - 602619 AGGTAGCAGGAGGTTGCTACTTCA---ATGTTCTAAAACACTTA -s simDog_chr6.simDog.chr6 548137 41 - 593897 GAGTAGCAGGAAGCTGCTATTTCA---ATATTCTAAAACACTCT -s simHuman_chr6.simHuman.chr6 554353 41 - 601863 AAGTAGTGCAAGGGTGCTATTGCA---TTATTTTAAACCAGTTA -s simHuman_chr6.simHuman.chr6 57139 41 - 601863 AAGTAGTGCAAGGGTGCTATTGCA---TTATTTTAAACCAGTTA -s simRat_chr6.simRat.chr6 236934 44 - 647215 AGGTAGTAGAAGTGTGGTATTTCAATTCAATGTTCTACAATTCA - -a -s simMouse_chr6.simMouse.chr6 14871 20 + 636262 GGAAGCTAGCAGAATGTAAC -s Anc0.Anc0refChr2 9258 20 + 17989 AGAAGCTATAAAAATCTAAC -s Anc1.Anc1refChr2 116361 20 - 144309 AGAAGCTATAAAAATCTAAC -s Anc2.Anc2refChr0 7171 20 - 56053 AAAAGCTATAAACATCTAAA -s mr.mrrefChr0 13665 20 + 130230 AGAAGCTAGCAGAATGTAAC -s simCow_chr6.simCow.chr6 550450 20 - 602619 AAAAGCTAGAAACAGCTAAA -s simDog_chr6.simDog.chr6 548179 20 - 593897 GAAATTTATAAACATCTAAA -s simHuman_chr6.simHuman.chr6 554395 20 - 601863 AGAAGCGATAAAAATCCAAC -s simHuman_chr6.simHuman.chr6 57181 20 - 601863 AGAAGCGATAAAAATCCAAC -s simRat_chr6.simRat.chr6 236978 20 - 647215 AAAAGCTAGCAGAATGTAAC - -a -s simMouse_chr6.simMouse.chr6 14891 81 + 636262 ACAACCTGCATAGGATAACCCTTTAGAGGCTCCCTGATAGATAGTTAAGGTAGGTACAATGTCATGACTACTAAACACTTT -s Anc0.Anc0refChr2 9278 77 + 17989 GTGATCTGCATAGGATAATCCTCCAGAGGGCCTCTGATACATAGGCTAGGTAGGT----TGCCCTCATTTTTAACCACTTT -s Anc1.Anc1refChr2 116381 77 - 144309 GTGATCTGCATAGGATAATCCTCCAGAGGGCCTCTGATACATAGGCTAGGTAGGT----TGCCCTCATTTTTAACCACTTT -s Anc2.Anc2refChr0 7191 77 - 56053 GTGATCTGCATAGGATAATTCTCCAGAGGGCCTCTGATACATAGGCTAGGTAGGT----TGCCCTCACTTTTAACCACTTT -s mr.mrrefChr0 13685 81 + 130230 ACGACCTGCATAGGATAACCCTCCAGAGGCCCCCTGATAGATAGTTAAGGTAGGTACAATGTCATGATTACTAACCACTTT -s simCow_chr6.simCow.chr6 550472 77 - 602619 GTGACCTGCATAGAATAAGTCTCCAGAGGCTGTTTGATACAAATGCCAGGGAGAT----TGCCCTCACATTTAACCACTTT -s simDog_chr6.simDog.chr6 548199 77 - 593897 TTGAATTGCATAGGATACCTCTCCAAAGGGCATCTGATACATAGGTTAGCTAGGT----TGCCCTCACTTGTAACCAATTT -s simHuman_chr6.simHuman.chr6 554415 77 - 601863 GTGATCTGCATAGGATAATCCTCCAGAGGGCCTCTGATACATAGGCTAGGTAGGT----TGCCCCCATTTTGAACCACTCT -s simHuman_chr6.simHuman.chr6 57201 77 - 601863 GTGATCTGCATAGGATAATCCTCCAGAGGGCCTCTGATACATAGGCTAGGTAGGT----TGCCCCCATTTTGAACCACTCT -s simRat_chr6.simRat.chr6 236998 81 - 647215 ACGACCTGCATAGGATAACCCTCCAGAGGCCCCCTGATATATAGTTAAGGTAAGTACAATGTCATGATTACTAACCATTTT - -a -s simMouse_chr6.simMouse.chr6 14972 19 + 636262 GTTATCCAGATAAGAAAAC -s Anc0.Anc0refChr2 9355 19 + 17989 GTTATCCAGATAAGAAAAT -s Anc1.Anc1refChr2 116458 19 - 144309 GTTATCCAGATAAGAAAAT -s Anc2.Anc2refChr0 7268 19 - 56053 GTTATCCAGATAAGAAAAT -s mr.mrrefChr0 13766 19 + 130230 GTTATCCAGATAAGAAAAC -s simCow_chr6.simCow.chr6 550550 19 - 602619 GTGATCCAGATGAGGAAAT -s simDog_chr6.simDog.chr6 548276 19 - 593897 GTTATCCAGATTAGAAAAT -s simHuman_chr6.simHuman.chr6 554492 19 - 601863 GTTATCCATTTAAGAGAAT -s simHuman_chr6.simHuman.chr6 57278 19 - 601863 GTTATCCATTTAAGAGAAT -s simRat_chr6.simRat.chr6 237079 19 - 647215 GTTATCCAGATAAAAATAC - -a -s simMouse_chr6.simMouse.chr6 14991 26 + 636262 ACTCTATGGGTAGTGATTAAGCTATT -s Anc0.Anc0refChr2 9376 26 + 17989 ACTCTATGGGTAATGATTAGATCACT -s Anc1.Anc1refChr2 116479 26 - 144309 ACTCTATGGGTAATGATTAGATCACT -s Anc2.Anc2refChr0 7289 26 - 56053 ACTCTATGGGTAATGATTAGATCACT -s mr.mrrefChr0 13787 26 + 130230 ACTCTATGGGTAGTGATTAAGCTATT -s simCow_chr6.simCow.chr6 550571 26 - 602619 ACTTTATGGGTAATGGTTAGATCACT -s simDog_chr6.simDog.chr6 548297 20 - 593897 CCTCCATGCATAATGA------CACT -s simHuman_chr6.simHuman.chr6 554513 26 - 601863 ACTCTATGGGTAATGATTAGATCACT -s simHuman_chr6.simHuman.chr6 57299 26 - 601863 ACTCTATGGGTAATGATCAGATCACT -s simRat_chr6.simRat.chr6 237100 26 - 647215 CCTCTATGGGTAGTGATTAAGCTATT - -a -s simMouse_chr6.simMouse.chr6 15017 3 + 636262 CTA -s Anc0.Anc0refChr2 9402 3 + 17989 TTT -s Anc1.Anc1refChr2 116505 3 - 144309 TTT -s Anc2.Anc2refChr0 7315 3 - 56053 TTT -s mr.mrrefChr0 13813 3 + 130230 CTA -s simCow_chr6.simCow.chr6 550603 3 - 602619 TCT -s simDog_chr6.simDog.chr6 548317 3 - 593897 TTT -s simHuman_chr6.simHuman.chr6 554539 3 - 601863 TTT -s simHuman_chr6.simHuman.chr6 57325 3 - 601863 TTT -s simRat_chr6.simRat.chr6 237126 3 - 647215 CTA - -a -s simMouse_chr6.simMouse.chr6 15020 21 + 636262 ATATTAAGTCCAATATTATGA -s Anc0.Anc0refChr2 9405 21 + 17989 ATCTTAATCCCTATTTTGTGA -s Anc1.Anc1refChr2 116508 21 - 144309 ATCTTAATCCCTATTTTGTGA -s Anc2.Anc2refChr0 7319 21 - 56053 ATCTTAATCCCCATCTTGTGA -s mr.mrrefChr0 13816 21 + 130230 ATATTAAGTCCTATATTATGA -s simCow_chr6.simCow.chr6 550607 21 - 602619 ATCATAATCCCCATCTTGTGA -s simDog_chr6.simDog.chr6 548321 21 - 593897 ATCTTCATCCCCATCTCATGA -s simHuman_chr6.simHuman.chr6 554542 21 - 601863 ATCTTAATCCCTATTTTGTGA -s simHuman_chr6.simHuman.chr6 57328 21 - 601863 ATCTTAATCCCTATTTTGTGA -s simRat_chr6.simRat.chr6 237129 21 - 647215 ATATTAAATCCTACATTATGA - -a -s simMouse_chr6.simMouse.chr6 15041 2 + 636262 CC -s Anc0.Anc0refChr2 9426 2 + 17989 CC -s Anc1.Anc1refChr2 116529 2 - 144309 CC -s Anc2.Anc2refChr0 7340 2 - 56053 CC -s mr.mrrefChr0 13837 2 + 130230 CC -s simCow_chr6.simCow.chr6 550629 2 - 602619 CC -s simDog_chr6.simDog.chr6 548342 2 - 593897 CC -s simHuman_chr6.simHuman.chr6 554563 2 - 601863 CC -s simHuman_chr6.simHuman.chr6 57349 2 - 601863 CC -s simRat_chr6.simRat.chr6 237150 2 - 647215 CC - -a -s simMouse_chr6.simMouse.chr6 15043 2 + 636262 CT -s Anc0.Anc0refChr2 9438 2 + 17989 CC -s Anc1.Anc1refChr2 116541 2 - 144309 CC -s Anc2.Anc2refChr0 7352 2 - 56053 CC -s mr.mrrefChr0 13839 2 + 130230 CT -s simCow_chr6.simCow.chr6 550641 2 - 602619 CG -s simDog_chr6.simDog.chr6 548354 2 - 593897 CC -s simHuman_chr6.simHuman.chr6 554575 2 - 601863 CC -s simHuman_chr6.simHuman.chr6 57361 2 - 601863 CC -s simRat_chr6.simRat.chr6 237152 2 - 647215 CT - -a -s simMouse_chr6.simMouse.chr6 15045 172 + 636262 AATGGGTACTATGTCCAAGGTCTATGCTCGTAAATGTATGGACATAATATCATCCTACACTTATCACTGAGTGAACACCACCCATGCTGGATCCATCCTACCATATATGAGAGGCTGGCGAAACTTTCCAACCACAACCACTCAGGGAATTGCTAAGGATAGACTAGTTAAG -s Anc0.Anc0refChr2 9440 89 + 17989 AATGGGTATAATGC-----------------------------------------------------------AAAACCATCCACACTCGTTT----CTGCCGGAGACAAAAGATTGTAGCTAGTTTCCTGCTAC------TTAGTGAGT-GCTAAATA------------- -s Anc1.Anc1refChr2 116543 102 - 144309 AATGGGTATAATGC-----------------------------------------------------------AAAACCATCCACACTCGTTT----CTGCCGGAGACAAAAGATTGTAGCTAGTTTCCTGCTAC------TTAGTGAGT-GCTAAATATAGCCTGGTCAAG -s Anc2.Anc2refChr0 7354 89 - 56053 AATAGGTATAATGC-----------------------------------------------------------AAAACCATCCACACTCCTTT----CTGCCGCAGACAAAAGATTGTGGTTAATTTCCTGCTAC------TAAGAGAGT-GCTAAATA------------- -s mr.mrrefChr0 13841 103 + 130230 AATGGGTACTATGT-----------------------------------------------------------AAAACCATCCATGCTCGATC----CTACCATATACAAAAGGCTGTCGATACTTTCCAGCCAC------TCAGGGAATTGCTAAGGATAGACTAGTCAAG -s simCow_chr6.simCow.chr6 49867 89 + 602619 AATATGTATAATGC-----------------------------------------------------------AGAATCATCCACTCTCCTTT----CTGCCACAGACAAAAGATTTTGGTTAATTTGTCACTAC------TAAGAGAGA-GTTAAATG------------- -s simDog_chr6.simDog.chr6 548356 89 - 593897 AATAGGTAAGATCC-----------------------------------------------------------GAGACCATCTACGCCCCTTT----CTGCCGCATACAAAAGATTGTGGTTAATTTTCTCCTAC------TAAGAGAGT-GCTAAATA------------- -s simHuman_chr6.simHuman.chr6 554577 102 - 601863 AATGGGTATAATGC-----------------------------------------------------------AAAACCATCCACACTCGTTT----CTGCTGGAGACAAAAGATTGTAGCTAGTTTCCTGCTAC------TTAGTGTGT-GCTAAATATAGCCTGGTCAAG -s simHuman_chr6.simHuman.chr6 57363 102 - 601863 AATGGGTATAATGC-----------------------------------------------------------AAAACCATCCACACTCGTTT----CTGCTGGAGACAAAAGATTGTAGCTAGTTTCCTGCTAC------TTAGTGTGT-GCTAAATATAGCCTGGTCAAG -s simRat_chr6.simRat.chr6 237154 103 - 647215 AATGGGTACTGTGT-----------------------------------------------------------ACAACCATCCATGCTCCATC----CTACCATATGCAAAAGGCTGTCGATACATTCTAGCCAC------TCAGGCAATTGCTAAGGTTAGACTAGTCAAG - -a -s simMouse_chr6.simMouse.chr6 15217 34 + 636262 CTGCTGCACCAGCCCGGGTCAGATGTTGTGACCA -s Anc0.Anc0refChr2 9529 15 + 17989 ----------------GGTCAGATGTG---AATA -s Anc1.Anc1refChr2 116652 34 - 144309 CGGAGATTTAATTCTGGGTCAGATGTGGTAAATA -s Anc2.Anc2refChr0 7443 15 - 56053 ----------------GGTCAGATGTG---AATA -s mr.mrrefChr0 13944 34 + 130230 CTGCTGTACCAGTCCGGGTCAGATGTGGTGACCA -s simCow_chr6.simCow.chr6 49956 15 + 602619 ----------------GATCAAAGGTG---ATTT -s simDog_chr6.simDog.chr6 548445 15 - 593897 ----------------GGTCAGATGTG---AATA -s simHuman_chr6.simHuman.chr6 554686 34 - 601863 CGGAGATTTAATTCTGGGACAGATGTGGTAAATA -s simHuman_chr6.simHuman.chr6 57472 34 - 601863 CGGAGATTTAATTCTGGGACAGATGTGGTAAATA -s simRat_chr6.simRat.chr6 237257 34 - 647215 CTGCTGTACCAGTTGAGGTCAGATGTGGTGACCA - -a -s simMouse_chr6.simMouse.chr6 15251 25 + 636262 ACATCATTATCCCGTGCATAACCAT -s Anc0.Anc0refChr2 9544 25 + 17989 ATATCAATATGTCATACATAGCATT -s Anc1.Anc1refChr2 116686 25 - 144309 ATATCAATATGTCATACATAGCATT -s Anc2.Anc2refChr0 7459 25 - 56053 ATATCAGTATGTCATACTTAGCATT -s mr.mrrefChr0 13978 25 + 130230 ACATCATTATCCCATGCATAGCCAT -s simCow_chr6.simCow.chr6 49972 25 + 602619 ATATCAGTATGTCATGCTTCACATA -s simDog_chr6.simDog.chr6 548461 25 - 593897 ATATCAGTATGTCATACTTTGCATT -s simHuman_chr6.simHuman.chr6 554720 25 - 601863 ATATCAATATGTCATATATAGCATT -s simHuman_chr6.simHuman.chr6 57506 25 - 601863 ATATCAATATGTCATATATAGCATT -s simRat_chr6.simRat.chr6 237291 25 - 647215 ACATCATTATCCCATGAATAGCCAT - -a -s simMouse_chr6.simMouse.chr6 15276 34 + 636262 CTATGGGGGAGTAAATTCAACTTATAGGACCTGA -s Anc0.Anc0refChr2 9572 34 + 17989 CTACAGAGCATTAAATACAACTTATGAGACTTAA -s Anc1.Anc1refChr2 116714 34 - 144309 CTACAGAGCATTAAATACAACTTATGAGACTTAA -s Anc2.Anc2refChr0 7489 34 - 56053 CTACAGAGAATTAAATAGAACTTATGAGACTTAA -s mr.mrrefChr0 14003 34 + 130230 CTATGGGGGAGTAAATTCAACTTATAGGACTTGA -s simCow_chr6.simCow.chr6 50002 31 + 602619 CTACAGACAAGTAAATAGTACCTATGAGA---AA -s simDog_chr6.simDog.chr6 548491 34 - 593897 CTACAGCGAGATAAATAGGACTTCTGAAGCTTAG -s simHuman_chr6.simHuman.chr6 554748 34 - 601863 CTTCAGAGCATTGAATACAACTCATGAGACTTAA -s simHuman_chr6.simHuman.chr6 57534 34 - 601863 CTTCAGAGCATTGAATACAACTCATGAGACTTAA -s simRat_chr6.simRat.chr6 237354 34 - 647215 CTGTGGGGGAGTAAATTCAACTTATAGCATTTGA - -a -s simMouse_chr6.simMouse.chr6 15310 58 + 636262 TACATGTTAGGACTGTCTTATGTAATGCTACTTGGGACTTTGTGCTAGTTGGCAGACA -s Anc0.Anc0refChr2 9612 29 + 17989 TACATATTAGGACTGTTTGATCTGCTAAT----------------------------- -s Anc1.Anc1refChr2 116754 58 - 144309 TACATATTAGGACTGTTTGATCTGCTAATAATCAGGTCTTTGTGACAGTTAGATCAAA -s Anc2.Anc2refChr0 7529 29 - 56053 TACATATTAGGGCTGTTTGATCTGCTAGT----------------------------- -s mr.mrrefChr0 14037 58 + 130230 TACATATTAGGACTGTCTTATGTAATGCTACTTAGGACTTTGTGCTAGTTGGCTGAAA -s simCow_chr6.simCow.chr6 50039 22 + 602619 TACATGTTAGGGCTGTTTGT-------GA----------------------------- -s simDog_chr6.simDog.chr6 548531 29 - 593897 TACATATTAGGGCTGGTTGATCTATTAGT----------------------------- -s simHuman_chr6.simHuman.chr6 554788 58 - 601863 TACTCATTAGGACTGTTTGATCTGCTAATAATCAGGTCTTTGTGACAGTTAGATCAAA -s simHuman_chr6.simHuman.chr6 57574 58 - 601863 TACTCATTAGGACTGTTTGATCTGCTAATAATCAGGTCTTTGTGACAGTTAGATCAAA -s simRat_chr6.simRat.chr6 237388 58 - 647215 TACATATTAGGACTGTCTTATGTAATGCTACTTAAGACTTTGCGCTAGTTGGCTGAAA - -a -s simMouse_chr6.simMouse.chr6 15368 13 + 636262 GTTGAAACAGATT -s Anc0.Anc0refChr2 9641 8 + 17989 -----ATCAGATC -s Anc1.Anc1refChr2 116813 13 - 144309 ATTGAATCAGATC -s Anc2.Anc2refChr0 7558 8 - 56053 -----ATCAGATC -s mr.mrrefChr0 14095 13 + 130230 GTTGAAACAGATT -s simCow_chr6.simCow.chr6 50061 8 + 602619 -----ATCAGATC -s simDog_chr6.simDog.chr6 548560 8 - 593897 -----ATTAGATC -s simHuman_chr6.simHuman.chr6 554847 13 - 601863 ATTGAATCAGATC -s simHuman_chr6.simHuman.chr6 57633 13 - 601863 ATTGAATCAGATC -s simRat_chr6.simRat.chr6 237446 13 - 647215 GTTGAAGCAGATT - -a -s simMouse_chr6.simMouse.chr6 15381 13 + 636262 GGCAACTTACCTC -s Anc0.Anc0refChr2 9649 13 + 17989 AGCAACTACCCCC -s Anc1.Anc1refChr2 116826 13 - 144309 AGCAACTACCCCC -s Anc2.Anc2refChr0 7566 13 - 56053 AGCAACTACCCCC -s mr.mrrefChr0 14108 13 + 130230 GGCAACTTACCCC -s simCow_chr6.simCow.chr6 50071 13 + 602619 AGCAACTACCCCC -s simDog_chr6.simDog.chr6 548568 13 - 593897 AGTAACTACCCCC -s simHuman_chr6.simHuman.chr6 554860 13 - 601863 AGCAACTACACCC -s simHuman_chr6.simHuman.chr6 57646 13 - 601863 AGCAACTACACCC -s simRat_chr6.simRat.chr6 237459 13 - 647215 GCCAGCTTATCCC - -a -s simMouse_chr6.simMouse.chr6 15394 12 + 636262 CACACAGTAATT -s Anc0.Anc0refChr2 9662 7 + 17989 CATAC-----TA -s Anc1.Anc1refChr2 116839 7 - 144309 CATAC-----TA -s Anc2.Anc2refChr0 7588 7 - 56053 CATAC-----TA -s mr.mrrefChr0 14121 12 + 130230 CACACAGTAATA -s simCow_chr6.simCow.chr6 50093 7 + 602619 CATGC-----TA -s simDog_chr6.simDog.chr6 548590 7 - 593897 TGTAC-----TA -s simHuman_chr6.simHuman.chr6 554873 7 - 601863 CATAC-----TA -s simHuman_chr6.simHuman.chr6 57659 7 - 601863 CATAC-----TA -s simRat_chr6.simRat.chr6 237472 12 - 647215 CTAGCAGTAATA - -a -s simMouse_chr6.simMouse.chr6 15406 11 + 636262 GTATATGTGAT -s Anc0.Anc0refChr2 9669 11 + 17989 GTATATAGGAA -s Anc1.Anc1refChr2 116846 11 - 144309 GTATATAGGAA -s Anc2.Anc2refChr0 7595 11 - 56053 GTGTATAGGAA -s mr.mrrefChr0 14133 11 + 130230 GTATATGTGAT -s simCow_chr6.simCow.chr6 50100 11 + 602619 GTGTGTAGGAT -s simDog_chr6.simDog.chr6 548597 11 - 593897 GTGTATAGGAA -s simHuman_chr6.simHuman.chr6 554880 11 - 601863 ATATATAGGGA -s simHuman_chr6.simHuman.chr6 57666 11 - 601863 ATATATAGGGA -s simRat_chr6.simRat.chr6 237489 11 - 647215 GTATATGTGAT - -a -s simMouse_chr6.simMouse.chr6 15417 8 + 636262 AAGACATG -s Anc0.Anc0refChr2 9682 8 + 17989 AAGACACA -s Anc1.Anc1refChr2 116860 8 - 144309 AAGACACA -s Anc2.Anc2refChr0 7608 8 - 56053 AAGACACA -s mr.mrrefChr0 14146 8 + 130230 AAGACATG -s simCow_chr6.simCow.chr6 50113 8 + 602619 AAGACACA -s simDog_chr6.simDog.chr6 548610 8 - 593897 AAGATACA -s simHuman_chr6.simHuman.chr6 554894 8 - 601863 AAGGCACA -s simHuman_chr6.simHuman.chr6 57680 8 - 601863 AAGGCACA -s simRat_chr6.simRat.chr6 237502 8 - 647215 TAGACATT - -a -s simMouse_chr6.simMouse.chr6 15425 5 + 636262 CTTTT -s Anc0.Anc0refChr2 9690 5 + 17989 ATTTT -s Anc1.Anc1refChr2 116868 5 - 144309 ATTTT -s Anc2.Anc2refChr0 7616 5 - 56053 ATTTT -s mr.mrrefChr0 14154 5 + 130230 CTTTT -s simCow_chr6.simCow.chr6 50121 5 + 602619 CTTTT -s simDog_chr6.simDog.chr6 548618 5 - 593897 AGTTT -s simHuman_chr6.simHuman.chr6 554902 5 - 601863 ATTTT -s simHuman_chr6.simHuman.chr6 57688 5 - 601863 ATTTT -s simRat_chr6.simRat.chr6 237515 5 - 647215 TGTTT - -a -s simMouse_chr6.simMouse.chr6 15430 162 + 636262 GTTCTACTTCCATCAGCCGCTTCAGCCATTAAGTGGGCAGGCACGTTCTAGACTCAAAACAGGTGCCTGACATCACTTGACAGTGTGTGAATTGGACCCTGACAAACCTCTTGTGTGAGACAGACAGGCTCTGTGGTTGCTTGACATCTTGTCAAGCCGGGC -s Anc0.Anc0refChr2 9695 27 + 17989 CTTCTACCTCCACCAGCCCCTTCAGAT--------------------------------------------------------------------------------------------------------------------------------------- -s Anc1.Anc1refChr2 116873 27 - 144309 CTTCTACCTCCACCAGCCCCTTCAGAT--------------------------------------------------------------------------------------------------------------------------------------- -s Anc2.Anc2refChr0 7621 27 - 56053 CTTCTACCTCCAACAGCCCCTTCAGAT--------------------------------------------------------------------------------------------------------------------------------------- -s mr.mrrefChr0 14159 162 + 130230 GTTCTACTTCCACCAGCCGCTTCAGACATTAAGTGGGCAGGCACGTTCTAGACTCAAAACAGGTGCCTGACATCACTTGACAGTGTGTGAATTGGACCCTGACAAACCTCTTGTGTGAGACAGACAGGCTCTGTGGTTGCTTGACATCTTGTCAAGCCGGGC -s simCow_chr6.simCow.chr6 50126 27 + 602619 CTTCTATCTCTCACTGCCCCTTCTGAT--------------------------------------------------------------------------------------------------------------------------------------- -s simDog_chr6.simDog.chr6 548640 27 - 593897 CTCCTACCTCCGATGGCCCCTTCAGAC--------------------------------------------------------------------------------------------------------------------------------------- -s simHuman_chr6.simHuman.chr6 554907 27 - 601863 CTTCTACCTCCACCAGCCCCTTCAAAT--------------------------------------------------------------------------------------------------------------------------------------- -s simHuman_chr6.simHuman.chr6 57693 25 - 601863 --TCTACCTCCACCAGCCCCTTCAAAT--------------------------------------------------------------------------------------------------------------------------------------- -s simRat_chr6.simRat.chr6 237520 162 - 647215 GTTCTACTTCCACCGGCAGTTTTAGAGATTAAATGGACAGGCTCATTCTAGCCTCAAAATAGGTGCCTGTCATCACTTGACAGTGCGTGTATCAGGCCCTGACAAAACTCTTGTGTGAGCCGAACAGACTCTGTGACTGCTTGACATCTCGTCAAGCCGGGC - -a -s simMouse_chr6.simMouse.chr6 15592 147 + 636262 AGGCTCATAGCAAGGCACTAACCATGTGTACGTCGCTGTGTGGGGCAGGCTCATAGCCAAGCACTAACCATGTGTACATAGCCGCATTTGCCTTTTTTTGGAGCTTTGCACGAGGCACTATGAGAAATCTAAACAACGTTAAGGTAC -s Anc0.Anc0refChr2 9722 10 + 17989 -----------------------------------------------------------------------------------------------------------------------------------------GTTAAGATAC -s Anc1.Anc1refChr2 116900 10 - 144309 -----------------------------------------------------------------------------------------------------------------------------------------GTTAAGATAC -s Anc2.Anc2refChr0 7648 10 - 56053 -----------------------------------------------------------------------------------------------------------------------------------------GTTAAGTTAT -s mr.mrrefChr0 14321 121 + 130230 AGGCTCATAGCAAGGCACTAACCATGTGTACGT--------------------------AGCACTAACCATGTGTACATAGCCGCATTTGCCTTTTTTTGGAGCTTTGCACGAGGCACTATGAGAAATCTAAACAACGTTAAGGTAC -s simCow_chr6.simCow.chr6 50153 10 + 602619 -----------------------------------------------------------------------------------------------------------------------------------------ATTAAGTGAT -s simDog_chr6.simDog.chr6 548667 10 - 593897 -----------------------------------------------------------------------------------------------------------------------------------------TCTAAGTAAT -s simHuman_chr6.simHuman.chr6 554934 10 - 601863 -----------------------------------------------------------------------------------------------------------------------------------------GTTAAGATAC -s simHuman_chr6.simHuman.chr6 57718 10 - 601863 -----------------------------------------------------------------------------------------------------------------------------------------GTTAAGATAC -s simRat_chr6.simRat.chr6 237683 121 - 647215 AGGCTCATAGCCATACACTAACCATGTGAACAC--------------------------GGCACTAATCATGTGTATGTGGCTGCATTTGCCTTTTTTTGGAGCCTTGCATGAGGCACTGTGCGAAATCTAAACAATGTTAAGCTAC - -a -s simMouse_chr6.simMouse.chr6 15739 11 + 636262 TCTCTACAATC -s Anc0.Anc0refChr2 9740 9 + 17989 T-TATTG-ATC -s Anc1.Anc1refChr2 116918 10 - 144309 TGTATTG-ATC -s Anc2.Anc2refChr0 7666 9 - 56053 T-TATTG-ATC -s mr.mrrefChr0 14442 10 + 130230 TCTCTAC-ATC -s simCow_chr6.simCow.chr6 50171 6 + 602619 T-TTTT----C -s simDog_chr6.simDog.chr6 548685 9 - 593897 T-TATCT-ATC -s simHuman_chr6.simHuman.chr6 554952 10 - 601863 TGTATTG-ATC -s simHuman_chr6.simHuman.chr6 57736 10 - 601863 TGTATTG-ATC -s simRat_chr6.simRat.chr6 237804 10 - 647215 TCTCTAC-ATC - -a -s simMouse_chr6.simMouse.chr6 15750 26 + 636262 TCTTCAGATTCTATAAGTAACACTAA -s Anc0.Anc0refChr2 9749 26 + 17989 TCTCCAGATTATACATGTGACATCAA -s Anc1.Anc1refChr2 116928 26 - 144309 TCTCCAGATTATACATGTGACATCAA -s Anc2.Anc2refChr0 7676 26 - 56053 CCTCCAGATTATACATGTTAAATCAA -s mr.mrrefChr0 14452 26 + 130230 TCTTCAGATTCTATAAGTGACACTAA -s simCow_chr6.simCow.chr6 50178 26 + 602619 CTGTCTGATTATATATGTTAAATCAG -s simDog_chr6.simDog.chr6 548695 26 - 593897 CCTCCAGATTATAAATGTTAAATCAA -s simHuman_chr6.simHuman.chr6 554962 17 - 601863 TGTCC---------ATGTGACATCAA -s simHuman_chr6.simHuman.chr6 57746 17 - 601863 TGTCC---------ATGTGACATCAA -s simRat_chr6.simRat.chr6 237814 26 - 647215 TGTTTAGATTTTATTAGTGACATTAA - -a -s simMouse_chr6.simMouse.chr6 15776 23 + 636262 TAAAAGTTGTTGTCGCTGTTTTC -s Anc0.Anc0refChr2 9775 23 + 17989 TGCAAGTTGTTGTCACTGGTTTC -s Anc1.Anc1refChr2 116954 23 - 144309 TGCAAGTTGTTGTCACTGGTTTC -s Anc2.Anc2refChr0 7702 23 - 56053 GGCAAGTTGTTATCACTGGTTTC -s mr.mrrefChr0 14478 23 + 130230 TAAAAGTTGTTGTCGCTGTTTTC -s simCow_chr6.simCow.chr6 50207 23 + 602619 GGCAAGTTGTTATCACTGGTTTA -s simDog_chr6.simDog.chr6 548721 23 - 593897 GGTAAATTGTCAACACTGGTATC -s simHuman_chr6.simHuman.chr6 554979 23 - 601863 TGCAAGTTGTTGTCACTGGTTTC -s simHuman_chr6.simHuman.chr6 57763 23 - 601863 TGCAAGTTGTTGTCACTGGTTTC -s simRat_chr6.simRat.chr6 237840 23 - 647215 TATAAGTTGTTGTCAGTGTTTTC - -a -s simMouse_chr6.simMouse.chr6 15799 52 + 636262 ATAAAACGCGCATCAGGCACATCATGAAGACCTGAAAACTTTGGAAATGTGA -s Anc0.Anc0refChr2 9839 51 + 17989 ATAAGATGTACATGAGGCACATCATGAAGAACTAAAAATCTTGTAAAAGT-A -s Anc1.Anc1refChr2 117019 51 - 144309 ATAAGATGTACATGAGGCACATCATGAAGAACTAAAAATCTTGTAAAAGT-A -s Anc2.Anc2refChr0 7766 51 - 56053 ATAAGATGTACATGTGTCACATCATGATGAACTAAAAATCATGTAAAAGT-A -s mr.mrrefChr0 14501 52 + 130230 ATAAAACGCGCATCAGGCACATCATGAAGACCTGAAAACTTTGGAAATGTGA -s simCow_chr6.simCow.chr6 50297 51 + 602619 ATGAGATAAACATGTGTCTCATCATGATGAACTGGGAATCATGTAAAAGT-A -s simDog_chr6.simDog.chr6 548785 51 - 593897 ATAAAATGCACGTGTGTCACATCATGATGAACTAAAAATTATGTAAAAGT-A -s simHuman_chr6.simHuman.chr6 555044 47 - 601863 GTAAGATGTATAGGAGGAA----ATGAAGAACTAAAAGTCTTGTAGAAGT-A -s simHuman_chr6.simHuman.chr6 57829 47 - 601863 GTAAGATGTATAGGAGGAA----ATGAAGAACTAAAAGTCTTGTAGAAGT-A -s simRat_chr6.simRat.chr6 237863 52 - 647215 ATATGACTAAAATAAGCCACATCATGAAGAAGTGAAAATTTTGGAAATGTAA - -a -s simMouse_chr6.simMouse.chr6 15851 73 + 636262 CTTTGGGGTAGTTTGGTGTAGTTTTTGTCAGATTCCATGCATATCCTAGGCAGGCAACACATGACCAGTAAAC -s Anc0.Anc0refChr2 9890 67 + 17989 CTTTTGAGTAGCTGGGAGTAGTCTTTGTCTGAATACACTCATC--CTAGGCAGAACGTAC----TCAGCAGAC -s Anc1.Anc1refChr2 117070 67 - 144309 CTTTTGAGTAGCTGGGAGTAGTCTTTGTCTGAATACACTCATC--CTAGGCAGAACGTAC----TCAGCAGAC -s Anc2.Anc2refChr0 7817 67 - 56053 TTTTTAAGTAGCTGGGAGTAGTCTTTGTCTAAATACACTCATC--CTAGGCAGAACGTAC----TCAGCAGAC -s mr.mrrefChr0 14553 71 + 130230 CTTTGGGGTAGTTTGGTGTAGTTTTTGTCAGATTCCATGCATA--CTAGGCAGGCAACACATGACCAGTAAAC -s simCow_chr6.simCow.chr6 50349 63 + 602619 TTTTGAGATAGCTGTGA--AGTCTTT--CTAAATGCACTCATC--CTAGGCAGAACATAA----TCAGCAGAC -s simDog_chr6.simDog.chr6 548836 67 - 593897 TTTTAAAGTAGGTAGGAGTAGTCTGCATCTAAATATATTCATC--CTAGGCAGAATGTAC----CCAGCACAC -s simHuman_chr6.simHuman.chr6 555091 67 - 601863 CTTTTGAGTAGCTGGGAGTGGTCTTTGTCTGAACACACTTACC--CTTGGCAGAACGTAC----TCAGCAGAC -s simHuman_chr6.simHuman.chr6 57876 58 - 601863 CTTTTGAGTAGCTGGGAGTGGTCTTTGTCTGAACACACTTACC--CTTGGCAGAACGCCC------------- -s simRat_chr6.simRat.chr6 237915 71 - 647215 TTTTGGGGTAGTGTGGTGTAGTCTTTGCCAGCTTGTACCCATA--CTACGCTGGCAATAAGTAACTATTTAAC - -a -s simMouse_chr6.simMouse.chr6 15924 12 + 636262 TCCTTTTCTACT -s Anc0.Anc0refChr2 9959 10 + 17989 T--TTTTTTGCT -s Anc1.Anc1refChr2 117139 10 - 144309 T--TTTTTTGCT -s Anc2.Anc2refChr0 7886 10 - 56053 T--TTTTTTGCT -s mr.mrrefChr0 14624 10 + 130230 T--TTTTCTACT -s simCow_chr6.simCow.chr6 50414 10 + 602619 G--TTTCTTACT -s simDog_chr6.simDog.chr6 548905 10 - 593897 T--CTTTGTGCA -s simHuman_chr6.simHuman.chr6 555160 10 - 601863 T--TTTTTTGCT -s simRat_chr6.simRat.chr6 237986 10 - 647215 T--TTTTCTCCT - -a -s simMouse_chr6.simMouse.chr6 15936 49 + 636262 TCTGGACTGCACCACATATTCTATTCATTCCAGTCCCTTGCTCTTTCAT -s Anc0.Anc0refChr2 9969 49 + 17989 TTTAAACTCTAACATACCTCTTCTTCATTCCAGTGCCCAGCTCTTTCAT -s Anc1.Anc1refChr2 117149 49 - 144309 TTTAAACTCTAACATACCTCTTCTTCATTCCAGTGCCCAGCTCTTTCAT -s Anc2.Anc2refChr0 7896 49 - 56053 TTTAAACTCTAACATACCTCTTCTTCATTCCAGTGCCCAGCTCTTTCAT -s mr.mrrefChr0 14634 49 + 130230 TCTGGACTGCACCACATATTCTATTCATTCCAGTCCCTTGCTCTTTCAT -s simCow_chr6.simCow.chr6 50452 49 + 602619 TTTGAACTCTAACACATCTCTTATTCACTCCAGTGTCCAGCTCTTTAAT -s simDog_chr6.simDog.chr6 548915 49 - 593897 TTTAAACTCTAACATACCTCTTCTTCATTCCAGTGCCCAGCTATCTCAT -s simHuman_chr6.simHuman.chr6 555170 49 - 601863 GTTAAACACTAACATGCCTCTTCTTCGTTCCAGTGCCCAGCGCTTTCAT -s simRat_chr6.simRat.chr6 237996 49 - 647215 TTTGGACTGTGACACATATCCTGTCCATTCCAGTCCCTTGCTCTTTCAC - -a -s simMouse_chr6.simMouse.chr6 15985 12 + 636262 GGATACAAATTT -s Anc0.Anc0refChr2 10018 12 + 17989 GGATACCAATTT -s Anc1.Anc1refChr2 117198 12 - 144309 GGATACCAATTT -s Anc2.Anc2refChr0 7945 12 - 56053 GGATACCAATTC -s mr.mrrefChr0 14683 12 + 130230 GGATACAAATTT -s simCow_chr6.simCow.chr6 50501 12 + 602619 GGATACCAATTC -s simDog_chr6.simDog.chr6 548965 12 - 593897 GGATACCAAGTC -s simHuman_chr6.simHuman.chr6 555219 12 - 601863 GGATACCAATTT -s simRat_chr6.simRat.chr6 238045 12 - 647215 GGCTACAAATTT - -a -s simMouse_chr6.simMouse.chr6 15997 93 + 636262 AATCTCACCAACACATGTTGGGTAGGGCTCAAGACATGGGTGGGTGACAAGGCCTGAACCATACTACACATGATTATTACAAAGTCACATGGA -s Anc0.Anc0refChr2 10033 27 + 17989 AATCCCACCAATACATGTTGAGCAGG-----------------------------------------------------T------------- -s Anc1.Anc1refChr2 117213 39 - 144309 AATCCCACCAATACATGTTGAGCAGG-----------------------------------------------------TGAACTCAC-TAAA -s Anc2.Anc2refChr0 7960 27 - 56053 AATCCCATCAATACATGATGAGCAGG-----------------------------------------------------T------------- -s mr.mrrefChr0 14695 39 + 130230 AATCTCACCAACACATGTTGGGTAGG-----------------------------------------------------CAAAGTCAC-TGAA -s simCow_chr6.simCow.chr6 50516 27 + 602619 AATCCCATCAATACATGCTTAGTGAG-----------------------------------------------------T------------- -s simDog_chr6.simDog.chr6 548980 27 - 593897 AATCCCATCAATACATGATGAGCAGG-----------------------------------------------------T------------- -s simHuman_chr6.simHuman.chr6 555234 39 - 601863 AATCCCACCAATACATGTCATTGGGG-----------------------------------------------------AGAACTCAC-TAAA -s simRat_chr6.simRat.chr6 238057 39 - 647215 AATCTCACTAACACATGTTGGGTAGG-----------------------------------------------------CAAAGTCAC-TGAA - -a -s simMouse_chr6.simMouse.chr6 16090 24 + 636262 AAGGGCCTTGATCCTCGACATTGA -s Anc0.Anc0refChr2 10060 7 + 17989 ATGGGCA----------------- -s Anc1.Anc1refChr2 117252 7 - 144309 ATGGGCA----------------- -s Anc2.Anc2refChr0 7987 7 - 56053 ATTGGCA----------------- -s mr.mrrefChr0 14734 10 + 130230 ATGGGCATTG-------------- -s simCow_chr6.simCow.chr6 50546 7 + 602619 ATTGCCA----------------- -s simDog_chr6.simDog.chr6 549007 7 - 593897 ATTGGCA----------------- -s simHuman_chr6.simHuman.chr6 555273 7 - 601863 ATGGGCA----------------- -s simRat_chr6.simRat.chr6 238096 10 - 647215 ATGGGCATCG-------------- - -a -s simMouse_chr6.simMouse.chr6 16114 18 + 636262 TTGAGTCATCTTAGTCAC -s Anc0.Anc0refChr2 10067 17 + 17989 TTG-GTCACATTAGCCGC -s Anc1.Anc1refChr2 117259 18 - 144309 TTGAGTCACATTAGCCGC -s Anc2.Anc2refChr0 7994 17 - 56053 TTG-GTCACATTAGCCGA -s mr.mrrefChr0 14744 18 + 130230 TTGAGTCATCTTAGTCAC -s simCow_chr6.simCow.chr6 50560 17 + 602619 TGA-GTCGCATTAGCCAA -s simDog_chr6.simDog.chr6 549014 16 - 593897 TTG-GTCACATTAGCCG- -s simHuman_chr6.simHuman.chr6 555280 16 - 601863 TTGAGTCA--TTAGCTGC -s simRat_chr6.simRat.chr6 238106 18 - 647215 TTGAGTCACCTTAGACAC - -a -s simMouse_chr6.simMouse.chr6 16132 5 + 636262 TACCC -s Anc0.Anc0refChr2 10101 5 + 17989 TACAT -s Anc1.Anc1refChr2 117294 5 - 144309 TACAT -s Anc2.Anc2refChr0 8028 5 - 56053 TACAT -s mr.mrrefChr0 14777 5 + 130230 TACAC -s simCow_chr6.simCow.chr6 50591 5 + 602619 TACAT -s simDog_chr6.simDog.chr6 549046 5 - 593897 TACAT -s simHuman_chr6.simHuman.chr6 555313 5 - 601863 TACAT -s simRat_chr6.simRat.chr6 238139 5 - 647215 TACAC - -a -s simMouse_chr6.simMouse.chr6 16137 14 + 636262 CCAGACAAACCTAT -s Anc0.Anc0refChr2 10111 14 + 17989 CAGCACTGATTAAT -s Anc1.Anc1refChr2 117304 14 - 144309 CAGCACTGATTAAT -s Anc2.Anc2refChr0 8038 14 - 56053 CAGCACTGATTAAT -s mr.mrrefChr0 14787 14 + 130230 CCAGACAAATCAAT -s simCow_chr6.simCow.chr6 50601 14 + 602619 CAGCCCTGATTAAT -s simDog_chr6.simDog.chr6 549056 14 - 593897 CAGCACTGATTAAT -s simHuman_chr6.simHuman.chr6 555323 14 - 601863 CAGCAGTGATTAAT -s simRat_chr6.simRat.chr6 238149 14 - 647215 CCATACAAATCAAT - -a -s simMouse_chr6.simMouse.chr6 16151 48 + 636262 TGGCTTGTGTTGTTCACAGGTAAGCCCTGTTTGCAAGGTGTCTAGGGT -s Anc0.Anc0refChr2 10126 28 + 17989 TGGTTTGTCTAG--------------------ATGGAGTGACTAGGAC -s Anc1.Anc1refChr2 117319 28 - 144309 TGGTTTGTCTAG--------------------ATGGAGTGACTAGGAC -s Anc2.Anc2refChr0 8053 28 - 56053 TGGTTTGACTAT--------------------ATGAAGTAACCAGGAC -s mr.mrrefChr0 14801 28 + 130230 TGGCTTGTGTTG--------------------GCGGGGTGACTAGGGT -s simCow_chr6.simCow.chr6 50616 28 + 602619 TGGTTTGACTAT--------------------ATGAAGTAACCAGGAC -s simDog_chr6.simDog.chr6 549071 2 - 593897 TG---------------------------------------------- -s simHuman_chr6.simHuman.chr6 555338 28 - 601863 TGAATTGTTCAG--------------------ATGGAGTGACTAGTAC -s simRat_chr6.simRat.chr6 238163 28 - 647215 AAGTTTGTCTGG--------------------GGGGTGTGACTAAGGT - -a -s simMouse_chr6.simMouse.chr6 16199 1 + 636262 G -s Anc0.Anc0refChr2 10154 1 + 17989 G -s Anc1.Anc1refChr2 117347 1 - 144309 G -s Anc2.Anc2refChr0 8084 1 - 56053 G -s mr.mrrefChr0 14829 1 + 130230 G -s simDog_chr6.simDog.chr6 549075 1 - 593897 G -s simHuman_chr6.simHuman.chr6 555366 1 - 601863 G -s simRat_chr6.simRat.chr6 238191 1 - 647215 G - -a -s simMouse_chr6.simMouse.chr6 16200 7 + 636262 ACTCAAT -s Anc0.Anc0refChr2 10155 7 + 17989 CCCCAAT -s Anc1.Anc1refChr2 117348 7 - 144309 CCCCAAT -s Anc2.Anc2refChr0 8085 7 - 56053 CCCCAAT -s mr.mrrefChr0 14830 7 + 130230 CCCCAAT -s simCow_chr6.simCow.chr6 50645 7 + 602619 CCCCATA -s simDog_chr6.simDog.chr6 549076 7 - 593897 CCCCAAT -s simHuman_chr6.simHuman.chr6 555383 7 - 601863 CCCCAAT -s simRat_chr6.simRat.chr6 238192 7 - 647215 CCCCAAT - -a -s simMouse_chr6.simMouse.chr6 16207 13 + 636262 GATGCCCATTTCA -s Anc0.Anc0refChr2 10176 12 + 17989 -AGGCCTTGTCAT -s Anc1.Anc1refChr2 117369 13 - 144309 AAGGCCTTGTCAT -s Anc2.Anc2refChr0 8106 12 - 56053 -AGGCCTTGTCAT -s mr.mrrefChr0 14851 13 + 130230 AATGCCCTTTCCA -s simCow_chr6.simCow.chr6 50666 12 + 602619 -AGGCCTTGTCAA -s simDog_chr6.simDog.chr6 549097 12 - 593897 -AGTCCTTGTCAT -s simHuman_chr6.simHuman.chr6 555404 13 - 601863 AAGGCCTTGTCAT -s simRat_chr6.simRat.chr6 238213 13 - 647215 AAAGCCCTTTCCA - -a -s simMouse_chr6.simMouse.chr6 16220 11 + 636262 GTGACTTTGCC -s Anc0.Anc0refChr2 10188 11 + 17989 CAGGCTTTGTA -s Anc1.Anc1refChr2 117382 11 - 144309 CAGGCTTTGTA -s Anc2.Anc2refChr0 8118 11 - 56053 CAGGCCTTGTA -s mr.mrrefChr0 14864 11 + 130230 GTGACTTTGTA -s simCow_chr6.simCow.chr6 50678 11 + 602619 ATGGCCTTTTA -s simDog_chr6.simDog.chr6 549109 11 - 593897 CAGGCCTTGTA -s simHuman_chr6.simHuman.chr6 555417 11 - 601863 TAGGCTTTGTA -s simRat_chr6.simRat.chr6 238227 11 - 647215 ATGACTTTGTA - -a -s simMouse_chr6.simMouse.chr6 16231 1 + 636262 T -s Anc0.Anc0refChr2 10214 1 + 17989 T -s Anc1.Anc1refChr2 117409 1 - 144309 T -s Anc2.Anc2refChr0 8144 1 - 56053 T -s mr.mrrefChr0 14889 1 + 130230 T -s simCow_chr6.simCow.chr6 50704 1 + 602619 T -s simDog_chr6.simDog.chr6 549135 1 - 593897 G -s simHuman_chr6.simHuman.chr6 555444 1 - 601863 T -s simRat_chr6.simRat.chr6 238252 1 - 647215 T - -a -s simMouse_chr6.simMouse.chr6 16232 19 + 636262 ATAGAGCACTGCTTGATGC -s Anc0.Anc0refChr2 10265 17 + 17989 ACAGAGCACTGCTTG--AC -s Anc1.Anc1refChr2 117460 19 - 144309 ACAGAGCACTGCTTGCCAC -s Anc2.Anc2refChr0 8195 17 - 56053 ACACAACACTGCTTG--AT -s mr.mrrefChr0 14890 19 + 130230 ATAGAGCACTGCTTGCCAC -s simCow_chr6.simCow.chr6 50716 2 + 602619 -----------------AA -s simDog_chr6.simDog.chr6 549186 17 - 593897 ACACAACACTGCTTG--GT -s simHuman_chr6.simHuman.chr6 555744 19 - 601863 ACAGAGCACTGCTTGCCAC -s simRat_chr6.simRat.chr6 238253 19 - 647215 ATGGTTCAGGCCTTGCCAC - -a -s simMouse_chr6.simMouse.chr6 16251 74 + 636262 AAACACATGATAGAAAGGGTTGACAGGGCTAAAGTGTTGGGTAAAAAGTGACAAGGCCTGGAAGCATACTTATT -s Anc0.Anc0refChr2 10282 74 + 17989 AAACATAAGATAGAAAGGGTTGGTAGGGATAAAATGTTGGGTAAAAAGCAACATGGGCTGTAAGCATGCTGATT -s Anc1.Anc1refChr2 117479 74 - 144309 AAACATAAGATAGAAAGGGTTGGTAGGGATAAAATGTTGGGTAAAAAGCAACATGGGCTGTAAGCATGCTGATT -s Anc2.Anc2refChr0 8212 74 - 56053 AAATATAAGATAGAAAGGGTTGGTTGGGATAAAATGTTGGGTAAAAAGCAACATGGGCTGTAAGCATGCTGATT -s mr.mrrefChr0 14909 74 + 130230 AAACACATGATAGAAAGGGTTGACAGGGCTAAAGTGTTGGGTAAAAAGTGACAAGGCCTGGAAGCATACTTATT -s simCow_chr6.simCow.chr6 50718 65 + 602619 ACATATAAGATAGAA-----TGGTT--GATAAATTGTTGGGTAAAAAGCAA-ATGGGCTGT-ACCATATTGATT -s simDog_chr6.simDog.chr6 549203 74 - 593897 AAATATAAAATAGAAAGGGTTGGTTGGGATAGAATGTTGGGTAAAAGGCAACATAGGCTGTAAGCATGCTGCTT -s simHuman_chr6.simHuman.chr6 555763 74 - 601863 AAGCAAAAGATAGAAAGGGTTGTTAGGGTTAAAATGATGGGTAAAAAGAAAGATGGACTGTAAACATGCTGATT -s simRat_chr6.simRat.chr6 238291 74 - 647215 AAACACATGACAGAAAAAATTGACAGGGCTAAAGTGTTGGGTAAAAAGGGACAAAGCCTGGAAGCATACTTATT - -a -s simMouse_chr6.simMouse.chr6 16325 54 + 636262 TCAGACTGCAGCTTCATGTTCAATTGCTGGGCCTAATAACTGCTAAAGTATTCC -s Anc0.Anc0refChr2 10372 54 + 17989 TCAGATTCCAGTTTCTTGCCAACATTGTGTGCCTAATAACTGCTAAAAAATGAT -s Anc1.Anc1refChr2 117569 54 - 144309 TCAGATTCCAGTTTCTTGCCAACATTGTGTGCCTAATAACTGCTAAAAAATGAT -s Anc2.Anc2refChr0 8302 54 - 56053 TCAGATTCCAGTTTCTCGCCAACATTGGGTACCTAATAACTGCTAAAAGATGAT -s mr.mrrefChr0 14983 54 + 130230 TCAGACTGCAGCTTCATGTCCAATTTGTGGGCCTAATAACTGCTAAAGAATTCC -s simCow_chr6.simCow.chr6 50799 32 + 602619 T----------------GCCAAC------TTACTAATAATTGCCAAAAGATGAT -s simDog_chr6.simDog.chr6 549293 54 - 593897 CCAGATTCCAGTTTCTCGCTAACATTGGGCACCTAATAACTGCTGAAAGATGAT -s simHuman_chr6.simHuman.chr6 555853 54 - 601863 TCAGGTTATGGTTTCTTTCCAACGTTGTGTGGCTAATAACTTTTAAAAAAGGAT -s simRat_chr6.simRat.chr6 238365 54 - 647215 TCACACTGCAGCTTCATGGCTGATTTGTGGGCCTAATAGCTCCTAAAGAATTCC - -a -s simMouse_chr6.simMouse.chr6 16379 3 + 636262 ACA -s Anc0.Anc0refChr2 10436 3 + 17989 ACA -s Anc1.Anc1refChr2 117633 3 - 144309 ACA -s Anc2.Anc2refChr0 8366 3 - 56053 GCA -s mr.mrrefChr0 15037 3 + 130230 ACA -s simCow_chr6.simCow.chr6 50841 3 + 602619 GCA -s simDog_chr6.simDog.chr6 549357 3 - 593897 GCA -s simHuman_chr6.simHuman.chr6 555917 3 - 601863 ACA -s simRat_chr6.simRat.chr6 238419 3 - 647215 ACA - -a -s simMouse_chr6.simMouse.chr6 16382 1 + 636262 A -s Anc0.Anc0refChr2 10439 1 + 17989 A -s Anc1.Anc1refChr2 117636 1 - 144309 A -s Anc2.Anc2refChr0 8369 1 - 56053 A -s mr.mrrefChr0 15040 1 + 130230 A -s simCow_chr6.simCow.chr6 50844 1 + 602619 A -s simDog_chr6.simDog.chr6 549361 1 - 593897 A -s simHuman_chr6.simHuman.chr6 555920 1 - 601863 A -s simRat_chr6.simRat.chr6 238422 1 - 647215 A - -a -s simMouse_chr6.simMouse.chr6 16383 9 + 636262 GAATGATGT -s Anc0.Anc0refChr2 10445 9 + 17989 GAATAGTAC -s Anc1.Anc1refChr2 117642 9 - 144309 GAATAGTAC -s Anc2.Anc2refChr0 8375 9 - 56053 GGAGGGTAC -s mr.mrrefChr0 15041 9 + 130230 GAATAGTGT -s simCow_chr6.simCow.chr6 50850 9 + 602619 GGAGGGTAC -s simHuman_chr6.simHuman.chr6 555926 9 - 601863 GAGTAGTAC -s simRat_chr6.simRat.chr6 238423 9 - 647215 GAATAGTGT - -a -s simMouse_chr6.simMouse.chr6 16392 23 + 636262 TTAATATATTAGCCATTAACCAC -s Anc0.Anc0refChr2 10454 23 + 17989 TTGTGACTTTAACCATTGGCCAC -s Anc1.Anc1refChr2 117651 23 - 144309 TTGTGACTTTAACCATTGGCCAC -s Anc2.Anc2refChr0 8384 23 - 56053 TGGTGACTTTAACCATTGGCCAA -s mr.mrrefChr0 15050 23 + 130230 TTAATATATTAACCATTAACCAC -s simCow_chr6.simCow.chr6 50862 23 + 602619 TGGTGACTCTAACCACTGGCCAG -s simDog_chr6.simDog.chr6 549367 21 - 593897 --GTGACTTTCACCCTTTGCCAA -s simHuman_chr6.simHuman.chr6 555935 23 - 601863 TTGTGACTTTAACCATTGGCCAC -s simRat_chr6.simRat.chr6 238432 23 - 647215 TTAATATATTAACCATTATCCAC - -a -s simMouse_chr6.simMouse.chr6 16415 1 + 636262 T -s Anc0.Anc0refChr2 10477 1 + 17989 T -s Anc1.Anc1refChr2 117674 1 - 144309 T -s Anc2.Anc2refChr0 8407 1 - 56053 T -s mr.mrrefChr0 15073 1 + 130230 T -s simCow_chr6.simCow.chr6 50902 1 + 602619 T -s simDog_chr6.simDog.chr6 549388 1 - 593897 T -s simHuman_chr6.simHuman.chr6 555958 1 - 601863 T -s simRat_chr6.simRat.chr6 238455 1 - 647215 T - -a -s simMouse_chr6.simMouse.chr6 16416 24 + 636262 TGAAACAGACTACATTGTCTTGGA -s Anc0.Anc0refChr2 10484 22 + 17989 --AAACAGACTAGATTGTATTAGG -s Anc1.Anc1refChr2 117681 24 - 144309 TGAAACAGACTAGATTGTATTAGG -s Anc2.Anc2refChr0 8414 22 - 56053 --AAACAGACTAGATTATATTAAG -s mr.mrrefChr0 15074 24 + 130230 TGAAACAGACTACATTGTCTTGGA -s simCow_chr6.simCow.chr6 50909 22 + 602619 --TGACAGACTAGACTATATTGAG -s simDog_chr6.simDog.chr6 549395 22 - 593897 --AAACAGACTATATTATATTAAG -s simHuman_chr6.simHuman.chr6 555972 24 - 601863 TGAAACAGACTAGATTGTATTAGG -s simRat_chr6.simRat.chr6 238456 24 - 647215 TGAAACAGACTACATTGCCTTAAA - -a -s simMouse_chr6.simMouse.chr6 16440 5 + 636262 GGATG -s Anc0.Anc0refChr2 10506 4 + 17989 GGAC- -s Anc1.Anc1refChr2 117705 5 - 144309 GGACA -s Anc2.Anc2refChr0 8436 4 - 56053 GGAT- -s mr.mrrefChr0 15098 5 + 130230 GGACG -s simCow_chr6.simCow.chr6 50931 4 + 602619 GTAT- -s simDog_chr6.simDog.chr6 549417 4 - 593897 GGAC- -s simHuman_chr6.simHuman.chr6 555997 5 - 601863 GGTCA -s simRat_chr6.simRat.chr6 238480 5 - 647215 GGACG - -a -s simMouse_chr6.simMouse.chr6 16445 11 + 636262 TGTCTTTTCAC -s Anc0.Anc0refChr2 10510 10 + 17989 TGTCAT-TCAC -s Anc1.Anc1refChr2 117710 10 - 144309 TGTCAT-TCAC -s Anc2.Anc2refChr0 8440 10 - 56053 TGTCAT-TCAC -s mr.mrrefChr0 15103 11 + 130230 TGTCTTTTCAC -s simCow_chr6.simCow.chr6 50936 10 + 602619 TGACAT-TCAC -s simDog_chr6.simDog.chr6 549421 10 - 593897 TGTCAT-GCAC -s simHuman_chr6.simHuman.chr6 556002 10 - 601863 TGGCAT-TCAC -s simRat_chr6.simRat.chr6 238485 11 - 647215 TGTCTTCCCAC - -a -s simMouse_chr6.simMouse.chr6 16456 11 + 636262 TGAGAGGTTGT -s Anc0.Anc0refChr2 10524 11 + 17989 TTAGAGGATGC -s Anc1.Anc1refChr2 117724 11 - 144309 TTAGAGGATGC -s Anc2.Anc2refChr0 8454 11 - 56053 TTAGAAGATCC -s mr.mrrefChr0 15114 11 + 130230 TGAGAGGTTGT -s simCow_chr6.simCow.chr6 50950 11 + 602619 TTAGATGATCC -s simDog_chr6.simDog.chr6 549435 11 - 593897 TTTAAAAATCC -s simHuman_chr6.simHuman.chr6 556016 11 - 601863 TTAGAGGAGGC -s simRat_chr6.simRat.chr6 238496 11 - 647215 TGAGAGGTTGT - -a -s simMouse_chr6.simMouse.chr6 16467 9 + 636262 TCATTTTTT -s Anc0.Anc0refChr2 10535 9 + 17989 TTGTTTTTT -s Anc1.Anc1refChr2 117735 9 - 144309 TTGTTTTTT -s Anc2.Anc2refChr0 8465 9 - 56053 TTGTTTTTT -s mr.mrrefChr0 15125 9 + 130230 TCATTTTTT -s simCow_chr6.simCow.chr6 50973 9 + 602619 TTGTTTTTT -s simDog_chr6.simDog.chr6 549446 9 - 593897 CTGTATTTT -s simHuman_chr6.simHuman.chr6 556027 9 - 601863 TTTTTTTTT -s simRat_chr6.simRat.chr6 238507 9 - 647215 TCATTTTTT - -a -s simMouse_chr6.simMouse.chr6 16476 44 + 636262 GGAGGGTCTAATAGGCAAGTAGGCGAATCCATCTCTGATGTAAA -s Anc0.Anc0refChr2 10544 44 + 17989 GGAGGGTTTAATAGGCAACTAGGTGATCCCATGTCTGGCCTGAA -s Anc1.Anc1refChr2 117744 44 - 144309 GGAGGGTTTAATAGGCAACTAGGTGATCCCATGTCTGGCCTGAA -s Anc2.Anc2refChr0 8474 44 - 56053 GGAGGGTTTAATAGGCAACTAGGTAATCCGCTGTCTGGCTTGAA -s mr.mrrefChr0 15134 44 + 130230 GGAGGGTTTAATAGGCAAGTAGGTGAATCCATCTCTGATCTAAA -s simCow_chr6.simCow.chr6 50989 43 + 602619 GGAGGATTTGAT-GGCAACTAGGTAATCCCATGTCTGGCTTGAA -s simDog_chr6.simDog.chr6 549455 44 - 593897 GGAGGGTTTAATAGGCGACTAGACAATTTGCTGTGTGGCTTGAA -s simHuman_chr6.simHuman.chr6 556036 43 - 601863 GGAGGTTTTAATAGGCAACTAGGTGAT-CCATTTCTGGCCTGAG -s simRat_chr6.simRat.chr6 238516 44 - 647215 GGAGGGTTTAATTGGCAAATAGATGAGTCCATATCTGAGCTAAA - -a -s simMouse_chr6.simMouse.chr6 16520 14 + 636262 CAAAATAAGACACT -s Anc0.Anc0refChr2 10588 14 + 17989 CAAAATAAGACACT -s Anc1.Anc1refChr2 117788 14 - 144309 CAAAATAAGACACT -s Anc2.Anc2refChr0 8518 14 - 56053 CAAAATGAGACATT -s mr.mrrefChr0 15178 14 + 130230 CAAAATAAGACACT -s simCow_chr6.simCow.chr6 51040 14 + 602619 CAAAATGATACATC -s simDog_chr6.simDog.chr6 549499 14 - 593897 TAAAATGAGATATT -s simHuman_chr6.simHuman.chr6 556079 14 - 601863 CAAAATAAAACACT -s simRat_chr6.simRat.chr6 238560 14 - 647215 CAAAATAAGGCACT - -a -s simMouse_chr6.simMouse.chr6 16534 24 + 636262 GTATTCTACATTAGGGTGTCATTC -s Anc0.Anc0refChr2 10610 17 + 17989 ATAGTCTACATTAGA-------TA -s Anc1.Anc1refChr2 117810 17 - 144309 ATAGTCTACATTAGA-------TA -s Anc2.Anc2refChr0 8540 17 - 56053 AGAGTCTACATTAGG-------TA -s mr.mrrefChr0 15192 24 + 130230 GTATTCTACATTAGAGTGTCATTC -s simCow_chr6.simCow.chr6 51062 17 + 602619 GGAGTCTACATTAGG-------TA -s simDog_chr6.simDog.chr6 549521 17 - 593897 AGAGTCTAAATTAGG-------CA -s simHuman_chr6.simHuman.chr6 556101 17 - 601863 ATAGTCTACATCAGA-------TA -s simRat_chr6.simRat.chr6 238574 24 - 647215 GTTTTCTACATTACAGGCTCATTC - -a -s simMouse_chr6.simMouse.chr6 16558 25 + 636262 ACTAATTCACTGATGGATCAGGGCC -s Anc0.Anc0refChr2 10627 25 + 17989 GCCAATTCAATGATGGATCAGGGCT -s Anc1.Anc1refChr2 117827 25 - 144309 GCCAATTCAATGATGGATCAGGGCT -s Anc2.Anc2refChr0 8557 25 - 56053 GCCAATTCAATAATGGATCAGATCT -s mr.mrrefChr0 15216 25 + 130230 ACTAATTCACTGATGGATCAGGGCC -s simCow_chr6.simCow.chr6 51079 25 + 602619 CCCCATTAACTAAGGGATCAGATCT -s simDog_chr6.simDog.chr6 549539 15 - 593897 GGCAGCACAACAATG---------- -s simHuman_chr6.simHuman.chr6 556118 25 - 601863 GCCAATTCAGTGATGGATAAGGGCT -s simRat_chr6.simRat.chr6 238598 25 - 647215 ATTAAGTCACTGACGGATCAGGGCC - -a -s simMouse_chr6.simMouse.chr6 16583 59 + 636262 CAGCCCACAAGTTGGGAAATTCGCAGTACTTTACTGTAGTGTGGCATCACCACCATTTT -s Anc0.Anc0refChr2 10659 44 + 17989 CAGCACACCAATTGGAGAATTCGCAGTACTTTACTGTGGTGTGA--------------- -s Anc1.Anc1refChr2 117859 44 - 144309 CAGCACACCAATTGGAGAATTCGCAGTACTTTACTGTGGTGTGA--------------- -s Anc2.Anc2refChr0 8589 44 - 56053 CAGCACACCAATGGGAGAATTAGCAGTACTTTACTGTGGTATGA--------------- -s mr.mrrefChr0 15241 59 + 130230 CAGCACACAAATTGGGAAATTCGCAGTACTTTACTGTAGTGTGGCAGTGCCACCATTTT -s simCow_chr6.simCow.chr6 51110 44 + 602619 CAGCACACCAATAGGAGAATTAGCAATGTTTAACTACAGTACAA--------------- -s simDog_chr6.simDog.chr6 549558 44 - 593897 TAGCACACCAATGGCAGCCTTAGCAGCACTTTACTGTGGCATGA--------------- -s simHuman_chr6.simHuman.chr6 556150 44 - 601863 CAGCACACCAACTGGATAATTCATAGTCCGTTACTGTGGTGTGA--------------- -s simRat_chr6.simRat.chr6 238623 52 - 647215 CAGCACACAAATTCGGAAATTAGC-------TACCGTAGTGTGGCAGTGCCACCATATT - -a -s simMouse_chr6.simMouse.chr6 16642 126 + 636262 GATCTAACTAGAACTGTTTAACAGAATAGATAGTAAGCAAAAGTAGCTAAGGGTCTTGCAACTCAGATGAACATATTCTGGCAAGAACTATGGCAAGCAAGATACTATAGGAGTCAAGCAATTGCA -s mr.mrrefChr0 15300 126 + 130230 GATCTAACTAGAACTGTTTAACAGAATAGATAGTAAGCAAAAGTAGCTAAGGGTCTTGCAACTCAGATGAACATATTCTGGCAAGAACTATGGCAAGCAAGATACTATAGGAGTCAAGCAATTGCA -s simRat_chr6.simRat.chr6 238682 126 - 647215 GATCTAGCTAGAACTGTTTCAAAGACCAGATAGTGAGCAAAAGTAGCTAAGGGTCTTGCACCTCAGATGGACATATTCAGGCAGGAACTATGGTATTCAAGCTACTATAGGAGTCAAGCAATTACA - -a -s simMouse_chr6.simMouse.chr6 16768 54 + 636262 ATCCCAGTTAGGAATTAGCCTAACTTATGGATGAAAATATGAAGGGGTGTAAGG -s Anc0.Anc0refChr2 10703 21 + 17989 --------------------------------GGTATTCTGGA-GGGTCTTTTA -s Anc1.Anc1refChr2 117903 22 - 144309 --------------------------------GGTATTCTGGAGGGGTCTTTTA -s Anc2.Anc2refChr0 8633 21 - 56053 --------------------------------GGTATTCTGGA-GGGTCCTTTA -s mr.mrrefChr0 15426 54 + 130230 ATCCCAGTTAGGAATTAGCCTAACTTATGGATGAAAATATGAAGGGGTGTAAGG -s simCow_chr6.simCow.chr6 51154 21 + 602619 --------------------------------GATATTCTGGA-GGGTCCTTTA -s simDog_chr6.simDog.chr6 549602 21 - 593897 --------------------------------GGTATTCTGGG-CGGCCCTTTA -s simHuman_chr6.simHuman.chr6 556194 22 - 601863 --------------------------------GGTAGTCTGGAGGGTTCTTTTA -s simRat_chr6.simRat.chr6 238812 54 - 647215 ATCCCAGTTAGGAATTAACCTAACTTGTGGATGAAAATATGAAGGGGTGTTAGG - -a -s simMouse_chr6.simMouse.chr6 16822 82 + 636262 GAGAAGGTGGAGATGAGAGCCTCTCCTTTAGAGAAGTAATTAATGCACTACATGGAGGAACTTGTCACATCATCATGAGTGG -s Anc0.Anc0refChr2 10739 82 + 17989 GAGATGGTAGAGATGAGAACTTCTCCTTTAAAGAGGTAATTAACACATTACATGGTGAAACTTGTCTCATCCCTCAGAATGG -s Anc1.Anc1refChr2 117940 82 - 144309 GAGATGGTAGAGATGAGAACTTCTCCTTTAAAGAGGTAATTAACACATTACATGGTGAAACTTGTCTCATCCCTCAGAATGG -s Anc2.Anc2refChr0 8671 82 - 56053 GAGATGGTAGAGATGAGAACTTCTCCTTTAAAGAGGTAATCAACACATTACATGGTGAAACTTGTCTCATCCCTCAGAATGG -s mr.mrrefChr0 15492 82 + 130230 GAGAAGGTAGAGATGAGAACCTCTCCTTTAGAGAAGTAATTAATGCACTACATGGAGGAACTTGTCACATCACCCAGAATGG -s simCow_chr6.simCow.chr6 51192 82 + 602619 GAGATGGTGGAGATGAGAACCTCTCCTTTATATAGGTAATCAACACTTTATATGGAAACACTTGTCACATACCTGAGAATGG -s simDog_chr6.simDog.chr6 549640 81 - 593897 GATTTGGCAGCGGAGGTAACT-CTCCTCTAAAGAGGAACTCAACACATTACACGGTGAAATCTATTTCCTCCCTCAGTATGG -s simHuman_chr6.simHuman.chr6 556231 82 - 601863 GAGATGGTAGAGATGAGAACTCCTCTTTTAAAAAGGTGATTAACACATTACATGGGCAGACTTGCCGTATCTCTCAGAATAG -s simRat_chr6.simRat.chr6 238889 81 - 647215 GAGAAGGTAGAGATGCGAACCTCTCC-TTAGATAAGTAATTACTGCACTACATGGAGGAACTTATCACATCACCCAAAACGG - -a -s simMouse_chr6.simMouse.chr6 16904 39 + 636262 AAAAATAATATCTTAAGTGAGAGTAGTGAATCAAGCAGG -s Anc0.Anc0refChr2 10824 35 + 17989 GG----ATTACCATGAGTGCCAGCAGTGAATGAACCAGG -s Anc1.Anc1refChr2 118025 35 - 144309 GG----ATTACCATGAGTGCCAGCAGTGAATGAACCAGG -s Anc2.Anc2refChr0 8760 35 - 56053 GG----ATTACCATGAGTGCCAGCAGGCAATGAACCAGG -s mr.mrrefChr0 15574 35 + 130230 AA----AATATCTTGAGTGAGAGTAGTGAATCAAGCAGG -s simCow_chr6.simCow.chr6 51281 35 + 602619 GG----ATTACCATGAGTGTCAGCAGGTAATGAACCAGG -s simDog_chr6.simDog.chr6 549728 35 - 593897 GG----ATTACCATGAGTGCCATCAGGCAATGGACCAGG -s simHuman_chr6.simHuman.chr6 556316 32 - 601863 GG----ATTACCATGAGTG---GCAGTGAATGAACCAGG -s simRat_chr6.simRat.chr6 238970 35 - 647215 AA----AATATCTTGAGTGTGAGTAGTGAATTAAGCAGG - -a -s simMouse_chr6.simMouse.chr6 16943 2 + 636262 GT -s Anc0.Anc0refChr2 10860 2 + 17989 TT -s Anc1.Anc1refChr2 118061 2 - 144309 TT -s Anc2.Anc2refChr0 8796 2 - 56053 TG -s mr.mrrefChr0 15609 2 + 130230 GT -s simCow_chr6.simCow.chr6 51317 2 + 602619 TG -s simDog_chr6.simDog.chr6 549764 2 - 593897 TG -s simHuman_chr6.simHuman.chr6 556349 2 - 601863 TT -s simRat_chr6.simRat.chr6 239005 2 - 647215 GT - -a -s simMouse_chr6.simMouse.chr6 16945 12 + 636262 GAGGAGCCTGCG -s Anc0.Anc0refChr2 10862 12 + 17989 GAGGAACCTGCA -s Anc1.Anc1refChr2 118063 12 - 144309 GAGGAACCTGCA -s Anc2.Anc2refChr0 8798 12 - 56053 AAAGAACCTGTA -s mr.mrrefChr0 15611 12 + 130230 GAGGAACCTGCG -s simCow_chr6.simCow.chr6 51319 12 + 602619 TAAGACCCTATA -s simDog_chr6.simDog.chr6 549767 12 - 593897 AAAGAACCTGTG -s simHuman_chr6.simHuman.chr6 556351 12 - 601863 GGGGAACCTGCA -s simRat_chr6.simRat.chr6 239007 12 - 647215 GAGGAACCTGTG - -a -s simMouse_chr6.simMouse.chr6 16957 25 + 636262 TTGCTGAAATTACATGAATACCTTG -s Anc0.Anc0refChr2 10874 5 + 17989 TTGCT-------------------- -s Anc1.Anc1refChr2 118075 25 - 144309 TTGCTGAAACCACATTAGTGCCTTG -s Anc2.Anc2refChr0 8810 5 - 56053 TTTCC-------------------- -s mr.mrrefChr0 15623 25 + 130230 TTGCTGAAACTACATTAGTACCTTG -s simCow_chr6.simCow.chr6 51331 5 + 602619 TATCC-------------------- -s simDog_chr6.simDog.chr6 549779 5 - 593897 TTTCC-------------------- -s simHuman_chr6.simHuman.chr6 556668 25 - 601863 TTGCTGAAACCACATTAGTGCCTTG -s simRat_chr6.simRat.chr6 239019 25 - 647215 TTGCTGAAACTACACTAGCACCTTC - -a -s simMouse_chr6.simMouse.chr6 16982 3 + 636262 ACC -s Anc0.Anc0refChr2 10879 3 + 17989 ACC -s Anc1.Anc1refChr2 118100 3 - 144309 ACC -s Anc2.Anc2refChr0 8815 3 - 56053 ACC -s mr.mrrefChr0 15648 3 + 130230 ACC -s simDog_chr6.simDog.chr6 549784 3 - 593897 ACC -s simHuman_chr6.simHuman.chr6 556695 3 - 601863 ACC -s simRat_chr6.simRat.chr6 239044 3 - 647215 ACC - -a -s simMouse_chr6.simMouse.chr6 16985 15 + 636262 TAGGAGATTGGTAAT -s Anc0.Anc0refChr2 10884 13 + 17989 TAGTGACTTGG--AA -s Anc1.Anc1refChr2 118105 13 - 144309 TAGTGACTTGG--AA -s Anc2.Anc2refChr0 8820 13 - 56053 AAGTGACTTGG--AA -s mr.mrrefChr0 15651 15 + 130230 TAGGAGATTGGTAAT -s simCow_chr6.simCow.chr6 51336 11 + 602619 --TTATCTTGG--AA -s simDog_chr6.simDog.chr6 549789 13 - 593897 AAGTGACTTGG--AA -s simHuman_chr6.simHuman.chr6 556700 13 - 601863 TAGTGCTTTGG--AA -s simRat_chr6.simRat.chr6 239047 15 - 647215 TGTGGGATTGGTAAT - -a -s simMouse_chr6.simMouse.chr6 17000 9 + 636262 CTAATTGAT -s Anc0.Anc0refChr2 10897 9 + 17989 CCATTTGAT -s Anc1.Anc1refChr2 118118 9 - 144309 CCATTTGAT -s Anc2.Anc2refChr0 8833 9 - 56053 CCATTTGAT -s mr.mrrefChr0 15666 9 + 130230 CTAATTGAT -s simCow_chr6.simCow.chr6 51347 9 + 602619 GCATTTGAT -s simDog_chr6.simDog.chr6 549802 9 - 593897 CCATTTGAT -s simHuman_chr6.simHuman.chr6 556713 9 - 601863 CAATGTGAT -s simRat_chr6.simRat.chr6 239064 9 - 647215 CTAATTGAT - -a -s simMouse_chr6.simMouse.chr6 17009 63 + 636262 CAACTTAGACACATTTAGCAAAGTGTCCTATTCGTGGAAATGAGTGGGCTCAATTTGAGCTAC -s Anc0.Anc0refChr2 10906 37 + 17989 AGAGTTAGACACA------GGAGCATTATAT--------------------AAGTGTACCAAC -s Anc1.Anc1refChr2 118127 37 - 144309 AGAGTTAGACACA------GGAGCATTATAT--------------------AAGTGTACCAAC -s Anc2.Anc2refChr0 8842 37 - 56053 AGAGTTAGACATA------GGGCCATTATTT--------------------AAGTGTACCAAC -s mr.mrrefChr0 15675 62 + 130230 CAACTTAGACACATTTAGCAGAGTGTCCTATTCGTGGAAATGAGT-GACTCAATTTGACCTAC -s simCow_chr6.simCow.chr6 51357 37 + 602619 AAAGATAGACATA------GGGCCATTATTC--------------------AGGTGGGCTGAC -s simDog_chr6.simDog.chr6 549811 37 - 593897 AGAGTTAGACATA------GGGCCAAAATTT--------------------AAGTGTACCAAC -s simHuman_chr6.simHuman.chr6 556722 37 - 601863 ACAGTTAGACACA------GGAGCATTATAT--------------------AACTCAACCCAC -s simRat_chr6.simRat.chr6 239073 62 - 647215 CAACTTAAACACATTCAGCAGAGTGTCCTACTCATGGAAATAAGT-GACACAATTTGACCTAC - -a -s simMouse_chr6.simMouse.chr6 17072 37 + 636262 TCATGTAAATGGCTCGAAATAGATTAAGGCCAAGATT -s Anc0.Anc0refChr2 10943 27 + 17989 TCATGCAAATG----------ACTTAAGGCTAGGATT -s Anc1.Anc1refChr2 118164 27 - 144309 TCATGCAAATG----------ACTTAAGGCTAGGATT -s Anc2.Anc2refChr0 8879 27 - 56053 TCATGCAAACG----------ACTTAAGGCTAGGATT -s mr.mrrefChr0 15737 37 + 130230 TCATGTAAATGGCTCGAAATAGCTTAAGGCTAGGATT -s simCow_chr6.simCow.chr6 51394 27 + 602619 TTAGGGAAACG----------ACTTAAGACCACAATT -s simDog_chr6.simDog.chr6 549848 27 - 593897 TCATGCAAACG----------ACTTAAGGCTAGGATT -s simHuman_chr6.simHuman.chr6 556761 27 - 601863 TCATGCAAATG----------ACTTAAGGCTAGGATT -s simRat_chr6.simRat.chr6 239135 37 - 647215 TCATGGAAATGGCTCGAAATAGCTTAAGGTTAGGATT - -a -s simMouse_chr6.simMouse.chr6 17109 23 + 636262 TGTATTGTCCCAATAACTTATAA -s Anc0.Anc0refChr2 10974 23 + 17989 TGAGTTGTCCCAAGGCCTTATAA -s Anc1.Anc1refChr2 118195 23 - 144309 TGAGTTGTCCCAAGGCCTTATAA -s Anc2.Anc2refChr0 8910 23 - 56053 TAAGTTGTCCCAAGGGCTTTTAA -s mr.mrrefChr0 15774 23 + 130230 TGTATTGTCCCAAGGCCTTATAA -s simCow_chr6.simCow.chr6 51500 23 + 602619 TAAATTCTCCTGAGGTCTTCTAA -s simDog_chr6.simDog.chr6 549879 23 - 593897 TAGGTTGTCCCAAGTGTTATAAA -s simHuman_chr6.simHuman.chr6 556792 23 - 601863 TGACTGGTCCCAAGGCCTTATAA -s simRat_chr6.simRat.chr6 239172 23 - 647215 TGTGTTGTCCCAAGGCCTTATAA - -a -s simMouse_chr6.simMouse.chr6 17132 82 + 636262 AGTATTCATGCAACAAGAACAGGATTTGCTAGCATCAATCTACAACTGTGCCAGTGTTTAGATCACACTCTAGCACTAGAAG -s Anc0.Anc0refChr2 10997 81 + 17989 TGT-TCCATGCAACAACAATGGGATTTGCAAGCATCATTTTACAACTGTGGTTTTATTTAAATCATGCTCTATCACAAGAAG -s Anc1.Anc1refChr2 118218 81 - 144309 TGT-TCCATGCAACAACAATGGGATTTGCAAGCATCATTTTACAACTGTGGTTTTATTTAAATCATGCTCTATCACAAGAAG -s Anc2.Anc2refChr0 8933 81 - 56053 TGT-TCCATGGAACAACAATGAGATTTGTAAGCATCATTTTACAACGGAGGTTTTATTTAAATCATGCTCTATCACAAGAAG -s mr.mrrefChr0 15797 82 + 130230 AGTATTCATGCAACAAGAACAGGATTTGCTAGCATCAATCTACAACTGTGCCTGTGTTTAGATCACACTCTAGCACTAGAAG -s simCow_chr6.simCow.chr6 51525 80 + 602619 TGT-TGCAAGTAATAACAATATGATTTGTGAGCATCA-CATACAGCCAAGGTTTTATTTAAATCATACACTATTGCAAGAAG -s simDog_chr6.simDog.chr6 549902 80 - 593897 TGT-TCCATGGAACAACAATGATGATTGTAAGCATCATTTTACAACGGAGGTTATATTTAAATCATG-TCTATCACAAGTAG -s simHuman_chr6.simHuman.chr6 556815 81 - 601863 TGT-TACATGCAACAACAATGGGATTTGCAAGCACCCTTTTACAATTGTGATTTTACTTAAATCATGCTCTATCACAAGAAG -s simRat_chr6.simRat.chr6 239195 82 - 647215 AGTATTCATGCAACAAGAACAGGATTTGCTAGAATCAGCCTACAGCTGTACCTGGGGTTAGATCACACTATAGCACTGGAAG - -a -s simMouse_chr6.simMouse.chr6 17214 6 + 636262 CAAAGT -s Anc0.Anc0refChr2 11079 6 + 17989 CAAAAT -s Anc1.Anc1refChr2 118300 6 - 144309 CAAAAT -s Anc2.Anc2refChr0 9015 6 - 56053 CAAAAT -s mr.mrrefChr0 15879 6 + 130230 CAAAGT -s simCow_chr6.simCow.chr6 51606 6 + 602619 CAAAAT -s simDog_chr6.simDog.chr6 549983 6 - 593897 CAAAGT -s simHuman_chr6.simHuman.chr6 556897 6 - 601863 CAAAAT -s simRat_chr6.simRat.chr6 239277 6 - 647215 CAAAGT - -a -s simMouse_chr6.simMouse.chr6 17220 13 + 636262 GCCATTTTCTTGA -s Anc0.Anc0refChr2 11085 13 + 17989 GCCATTATCTAGA -s Anc1.Anc1refChr2 118306 13 - 144309 GCCATTATCTAGA -s Anc2.Anc2refChr0 9021 13 - 56053 GCCATTATCTAGA -s mr.mrrefChr0 15885 13 + 130230 GCCATTTTCTAGA -s simCow_chr6.simCow.chr6 51612 13 + 602619 GCCAGATTCTAGA -s simDog_chr6.simDog.chr6 549996 13 - 593897 GCCATTAGCTAGA -s simHuman_chr6.simHuman.chr6 556903 13 - 601863 GCCATTCTCTAGA -s simRat_chr6.simRat.chr6 239283 13 - 647215 GCCATTTTCTAGA - -a -s simMouse_chr6.simMouse.chr6 17233 8 + 636262 AATTTCTG -s Anc0.Anc0refChr2 11098 8 + 17989 AATTTCTA -s Anc1.Anc1refChr2 118319 8 - 144309 AATTTCTA -s Anc2.Anc2refChr0 9038 8 - 56053 TATTTCTA -s mr.mrrefChr0 15898 8 + 130230 AATTTCTG -s simCow_chr6.simCow.chr6 51629 8 + 602619 TATTTCTT -s simDog_chr6.simDog.chr6 550013 8 - 593897 TATTTCTA -s simHuman_chr6.simHuman.chr6 556916 8 - 601863 AATTTCTA -s simRat_chr6.simRat.chr6 239296 8 - 647215 AATTTTTG - -a -s simMouse_chr6.simMouse.chr6 17241 29 + 636262 GGACCAGAACTATTAAAAAGTGAAGATTT -s Anc0.Anc0refChr2 11107 29 + 17989 GAATTAGAGTTGTCAAAAAGTGAAGATTT -s Anc1.Anc1refChr2 118328 29 - 144309 GAATTAGAGTTGTCAAAAAGTGAAGATTT -s Anc2.Anc2refChr0 9047 29 - 56053 GAATTAGAGTTGTCAAAAAGTGAAGATTT -s mr.mrrefChr0 15906 29 + 130230 GGATCAGAACTATTAAAAAGTGAAGATTT -s simCow_chr6.simCow.chr6 51638 29 + 602619 GGATCAGACTTATCAATCAGAGAAGATTT -s simDog_chr6.simDog.chr6 550022 27 - 593897 GAATTAGAGTTGTCAAAAAGTG--GATTT -s simHuman_chr6.simHuman.chr6 556925 29 - 601863 GAATTAGAGTTTTCAAAAAGTGAAGATTT -s simRat_chr6.simRat.chr6 239304 29 - 647215 GGATCGGAACTATTAAAATGTGAAGATTT - -a -s simMouse_chr6.simMouse.chr6 17270 20 + 636262 ACATGGTAACTACCACTAGG -s Anc0.Anc0refChr2 11136 17 + 17989 AATTGCTGGCTACTGCT--- -s Anc1.Anc1refChr2 118357 20 - 144309 AATTGCTGGCTACTGCTAGG -s Anc2.Anc2refChr0 9079 17 - 56053 AATACCTGGATACTGCT--- -s mr.mrrefChr0 15935 20 + 130230 ACATGCTAGCTACCACTAGG -s simCow_chr6.simCow.chr6 51670 1 + 602619 A------------------- -s simDog_chr6.simDog.chr6 550052 17 - 593897 AATACCTGGATACTGCT--- -s simHuman_chr6.simHuman.chr6 556954 20 - 601863 AATTGCTGGCTACTCAGAGG -s simRat_chr6.simRat.chr6 239333 20 - 647215 ACAAGCTAGCTACCAGTGAG - -a -s simMouse_chr6.simMouse.chr6 17290 12 + 636262 GGCCACCAAGAC -s Anc0.Anc0refChr2 11153 10 + 17989 --CCACCAGGCC -s Anc1.Anc1refChr2 118377 12 - 144309 GGCCACCAGGCC -s Anc2.Anc2refChr0 9096 10 - 56053 --CCACGAGGCC -s mr.mrrefChr0 15955 12 + 130230 GGCCACCAGGAC -s simDog_chr6.simDog.chr6 550069 10 - 593897 --CCACGAGGCC -s simHuman_chr6.simHuman.chr6 556982 12 - 601863 GGCCACCAGGGC -s simRat_chr6.simRat.chr6 239353 12 - 647215 GACCACCAGGAT - -a -s simMouse_chr6.simMouse.chr6 17302 6 + 636262 TGCAGG -s Anc0.Anc0refChr2 11170 6 + 17989 TACAGG -s Anc1.Anc1refChr2 118396 6 - 144309 TACAGG -s Anc2.Anc2refChr0 9113 6 - 56053 TACCAG -s mr.mrrefChr0 15967 6 + 130230 TGCAGG -s simDog_chr6.simDog.chr6 550086 6 - 593897 TACCAG -s simHuman_chr6.simHuman.chr6 557001 6 - 601863 TATAGG -s simRat_chr6.simRat.chr6 239365 6 - 647215 TGCAGG - -a -s simMouse_chr6.simMouse.chr6 17308 74 + 636262 CTCTTTCACCCTGGACGCATGCCCTAAATATTATAAATCAAAGCCATAAAATGACCCCTGAGGACAGCTTATAG -s Anc0.Anc0refChr2 11176 25 + 17989 CTCCTTCACC-------------------------------------------------GAGTACAGCTTACAG -s Anc1.Anc1refChr2 118402 74 - 144309 CTCCTTCACCCTGGGCTCATGCCCCAAATACTATGAGTCTAAGCCCTATACTAACCTGAGAGTACAGCTTACAG -s Anc2.Anc2refChr0 9119 25 - 56053 CTCCCTCACC-------------------------------------------------GGGTACAGCTTACAG -s mr.mrrefChr0 15973 74 + 130230 CTCTTTCACCCTGGACTCATGCCCTAAATATTATAAATCTAAGCCATAAAATAACCTCTGAGGACAGCTTATAG -s simDog_chr6.simDog.chr6 550092 25 - 593897 CTCCCTCACC-------------------------------------------------GGGTACAGCTTACAG -s simHuman_chr6.simHuman.chr6 557007 71 - 601863 CCCCTTCAACCTGGGCTCATGCCCCAAATACTATGAGTCTAAGCCCTATACTAACCTGAGAGCA---CCTACAC -s simRat_chr6.simRat.chr6 239379 73 - 647215 CTTTTTCACCTTGGACTTATGCCCTAAATA-TATAAATCTAAGCCATAAAATAATCTAAGAGTACAGCTTAGAG - -a -s simMouse_chr6.simMouse.chr6 17382 8 + 636262 CTGGACAC -s Anc0.Anc0refChr2 11201 8 + 17989 CTGGATAG -s Anc1.Anc1refChr2 118476 8 - 144309 CTGGATAG -s Anc2.Anc2refChr0 9145 8 - 56053 CTGAAAAG -s mr.mrrefChr0 16047 8 + 130230 CTGGATAC -s simDog_chr6.simDog.chr6 550118 8 - 593897 CTGAAAAG -s simHuman_chr6.simHuman.chr6 557078 8 - 601863 TTGCATAT -s simRat_chr6.simRat.chr6 239452 8 - 647215 CTGGATAC - -a -s simMouse_chr6.simMouse.chr6 17390 16 + 636262 CTGTTGTACCATTATG -s Anc0.Anc0refChr2 11209 15 + 17989 CTGTTGTGGC-CTATG -s Anc1.Anc1refChr2 118484 16 - 144309 CTGTTGTGGCACTATG -s Anc2.Anc2refChr0 9153 15 - 56053 CAGATATAGC-CAATG -s mr.mrrefChr0 16055 16 + 130230 CTGTTGTGGCATTATG -s simDog_chr6.simDog.chr6 550126 15 - 593897 CAGATATAGC-CAATG -s simHuman_chr6.simHuman.chr6 557205 16 - 601863 CTGTTGTGGTACTATG -s simRat_chr6.simRat.chr6 239460 16 - 647215 CTGTTGTGGCAACGTG - -a -s simMouse_chr6.simMouse.chr6 17406 98 + 636262 TGGAGCAGGTGGAGGTTACAAGCATATTCAATTCTCAGGCTCTGACACCATATCCCTCCCCCTACCCCTAGCTTAGACATTCTATTCAAACAGGCACT -s Anc0.Anc0refChr2 11224 96 + 17989 TGTAATATGTAGAACTTGCAAGCATCCCCAATCCTCAGGTTCCAACACCAT-T-CTTTCCCCTCCTCCTAGCTTAAACATTCTATTCCAATGTGCACT -s Anc1.Anc1refChr2 118500 97 - 144309 TGTAATATGTAGAACTTGCAAGCATCCCCAATCCTCAGGTTCCAACACCATAT-CTTTCCCCTCCTCCTAGCTTAAACATTCTATTCCAATGTGCACT -s Anc2.Anc2refChr0 9169 96 - 56053 TGCACTATGTAGAACACGTAAGCAGCTCTAATCCTTAGGTTTCAGCACCAT-T-CTTTCCTCTCCTCCAAGCCTAAACATTATACTCCAATGTGCACT -s mr.mrrefChr0 16071 98 + 130230 TGGAGCAGGTGGAGGTTACAAGCATCCTCAATTCTCAGGCTCTGACACCATATCCCTCCCCCTACCCCTAGCTTAGACATTCTATTCAAACAGGCACT -s simCow_chr6.simCow.chr6 51671 58 + 602619 --------------------------------------GTTTCAGCACAAT-T-CTTTCCTTGGCCCTAAGCCTGAGCATTTTACTTCGATGTACGCT -s simDog_chr6.simDog.chr6 550142 87 - 593897 TGCACTATGTAGAACACGTAAGCAGCTCTAATCCTTAGGTT-CAGCACCAT----------CTCTTTCAAGCCTAAATGTTATACCCCAATGGGCACT -s simHuman_chr6.simHuman.chr6 557221 97 - 601863 TGTAATATGTAGGACTTGCAAGCATCCCCAATCCTCAGGTTCCAACTCCATAT-TTTTCCCCTCCTCCTAGCTTAAACATGCTATTCCAATGTGCACT -s simRat_chr6.simRat.chr6 239476 98 - 647215 TGGAGCAGGTGGAGGTTACAAGCATCCTCAATTCTCAGGCACTGATAACACATCCCTTCCCCTACCCCTAGCTTAGACATTCTACTCAAACAGGCACT - -a -s simMouse_chr6.simMouse.chr6 17504 39 + 636262 TGGTAAGCTCTGGTGAATCAACACAGATTGCTTACACAG -s Anc0.Anc0refChr2 11326 29 + 17989 TGGCGAGTTTTGGTGAATCAATACAGA----------AA -s Anc1.Anc1refChr2 118603 29 - 144309 TGGCGAGTTTTGGTGAATCAATACAGA----------AA -s Anc2.Anc2refChr0 9271 29 - 56053 TGGCGAGTTCTGGTGAATCAATACAGA----------AA -s mr.mrrefChr0 16169 35 + 130230 TGGTAAGCTTTGGTGAATCAACACAGATTGCTT----AG -s simCow_chr6.simCow.chr6 51735 26 + 602619 TGGCTAGTT---GTGCACCACTACAGA----------AA -s simDog_chr6.simDog.chr6 550235 29 - 593897 TGGCGGTTTCTGGTGAATCAATCCAGA----------AA -s simHuman_chr6.simHuman.chr6 557324 29 - 601863 TGGCCAGTTTTGGTGAATCAATACGGA----------AA -s simRat_chr6.simRat.chr6 239574 33 - 647215 TGGAAAGCTTTGGTAAATCAACACAGATTACTT------ - -a -s simMouse_chr6.simMouse.chr6 17543 58 + 636262 ATGACTTATGATTAACTGAAGGGGTTCTCACCCTGTTGTTGTATATGATAGTTGATAT -s Anc0.Anc0refChr2 11355 56 + 17989 ATGACTAAGAGTTATATGGACAGGTTCCTACTTTGTTGTTGTATAT--TTGTTAATAG -s Anc1.Anc1refChr2 118632 56 - 144309 ATGACTAAGAGTTATATGGACAGGTTCCTACTTTGTTGTTGTATAT--TTGTTAATAG -s Anc2.Anc2refChr0 9314 56 - 56053 ATGACTAGGAGTTGTATGGACAGGTGCCTACTTTGTTGCTGTATAT--TTGTTAATAG -s mr.mrrefChr0 16204 58 + 130230 ATGACTAAGAGTTAAATGAAGGGGTTCCCACCTTGTTGTTGTATATGATAGTTGATAT -s simCow_chr6.simCow.chr6 51775 52 + 602619 ATGATTAGGAGTTGTATTGACAGATCCCTAGTTTCTTG----ATAT--CTGTTAATAG -s simDog_chr6.simDog.chr6 550278 56 - 593897 ATGACTAGGAGTTGTGTGGACAGGTGCCTACTTTGTTGCTGTATAT--TTGTTAATGG -s simHuman_chr6.simHuman.chr6 557353 56 - 601863 AGGGGTAAGAGCTATATGGACAGGTTCCTACTTTGTTGTTGTATAT--TTTCTAATAG -s simRat_chr6.simRat.chr6 239607 58 - 647215 ATGAATAGGAGTTAAATGAAGGGGTTTCCACCTTATTGTTGTATATGATAGTTGATAT - -a -s simMouse_chr6.simMouse.chr6 17601 52 + 636262 TGGGCTCTGATTGAGGACTCAACATTCATAAGGTATTGGATCATACTCACAG -s Anc0.Anc0refChr2 11411 52 + 17989 TGGTCTTTAATTCAGAACTCCTCCTCTGTATGTTATGGGATGTAACTCACAG -s Anc1.Anc1refChr2 118688 52 - 144309 TGGTCTTTAATTCAGAACTCCTCCTCTGTATGTTATGGGATGTAACTCACAG -s Anc2.Anc2refChr0 9370 52 - 56053 TGGTCTTTAATTCAGAACTCCAACTCTGTATGTTATGGGATGTAACTCACAG -s mr.mrrefChr0 16262 52 + 130230 TGGGCTCTGATTCAGAACTCCTCATTCATAAGGTATGGGATCTTACTCACAG -s simCow_chr6.simCow.chr6 51835 52 + 602619 GGGTCCTTAATTCAGAACTCCATCTGTGTATGCTATGGGATGTAACTCACAG -s simDog_chr6.simDog.chr6 550334 41 - 593897 TGGTCTCTAATTTAGAACTCCAACTCTGTATGTTATGAAAT----------- -s simHuman_chr6.simHuman.chr6 557409 52 - 601863 TGGTCTTTAATTCATAGCTCCTCCTCTGTATGTTATGGGATGTCACCCACAG -s simRat_chr6.simRat.chr6 239665 52 - 647215 TGGGCTCTGATTCGGAACTGCTCATTCATACGGTATGGGATCTTACTCACAG - -a -s simMouse_chr6.simMouse.chr6 17653 2 + 636262 CA -s Anc0.Anc0refChr2 11468 2 + 17989 CA -s Anc1.Anc1refChr2 118745 2 - 144309 CA -s Anc2.Anc2refChr0 9427 2 - 56053 CA -s mr.mrrefChr0 16314 2 + 130230 CA -s simCow_chr6.simCow.chr6 51912 2 + 602619 CA -s simDog_chr6.simDog.chr6 550375 1 - 593897 -A -s simHuman_chr6.simHuman.chr6 557466 2 - 601863 CA -s simRat_chr6.simRat.chr6 239717 2 - 647215 CA - -a -s simMouse_chr6.simMouse.chr6 17655 18 + 636262 AGCATGACTTCTGGACTA -s Anc0.Anc0refChr2 11470 18 + 17989 AGCACAACATTTGGATTA -s Anc1.Anc1refChr2 118747 18 - 144309 AGCACAACATTTGGATTA -s Anc2.Anc2refChr0 9429 18 - 56053 AGCACAACATTTCGATTA -s mr.mrrefChr0 16316 18 + 130230 AGCACAACTTCTGGACTA -s simCow_chr6.simCow.chr6 51925 18 + 602619 AGCATAACATTTCAGTTA -s simDog_chr6.simDog.chr6 550376 18 - 593897 AGCACAATCTCTCGATGA -s simHuman_chr6.simHuman.chr6 557468 18 - 601863 AGCACAACATTTGGATTA -s simRat_chr6.simRat.chr6 239719 18 - 647215 AGCACAACCTCTGGGCTA - -a -s simMouse_chr6.simMouse.chr6 17673 6 + 636262 CTTATG -s Anc0.Anc0refChr2 11506 6 + 17989 CCTGTC -s Anc1.Anc1refChr2 118783 6 - 144309 CCTGTC -s Anc2.Anc2refChr0 9465 6 - 56053 CCTGCC -s mr.mrrefChr0 16334 6 + 130230 CTTATG -s simCow_chr6.simCow.chr6 51960 6 + 602619 CCTGCC -s simDog_chr6.simDog.chr6 550412 6 - 593897 CCTGCT -s simHuman_chr6.simHuman.chr6 557504 6 - 601863 TCTGTC -s simRat_chr6.simRat.chr6 239737 6 - 647215 CTTATG - -a -s simMouse_chr6.simMouse.chr6 17679 14 + 636262 GGGTTGAGTACTGA -s Anc0.Anc0refChr2 11513 14 + 17989 AGGGTGAAAACTCA -s Anc1.Anc1refChr2 118790 14 - 144309 AGGGTGAAAACTCA -s Anc2.Anc2refChr0 9472 14 - 56053 AGGGTGAAAACTCA -s mr.mrrefChr0 16341 14 + 130230 GGGTTGAGTACTGA -s simCow_chr6.simCow.chr6 51967 3 + 602619 AGG----------- -s simDog_chr6.simDog.chr6 550419 14 - 593897 AGGGTGAAAACTCA -s simHuman_chr6.simHuman.chr6 557511 14 - 601863 AGCATGAACACTCA -s simRat_chr6.simRat.chr6 239744 14 - 647215 GGGTTGAGTACTGA - -a -s simMouse_chr6.simMouse.chr6 17693 20 + 636262 TGTGATAGAGAATCATGGTG -s Anc0.Anc0refChr2 11527 20 + 17989 TACGTTAGAGAAACATAGAG -s Anc1.Anc1refChr2 118804 20 - 144309 TACGTTAGAGAAACATAGAG -s Anc2.Anc2refChr0 9486 20 - 56053 TACGTTAGAAAAACACAGAG -s mr.mrrefChr0 16355 20 + 130230 TGTGATAGAGAATCATGGTG -s simCow_chr6.simCow.chr6 552757 19 - 602619 AACGTTAGAAAAACA-GGAG -s simDog_chr6.simDog.chr6 550433 20 - 593897 TATGTTACAAACCCACAGGG -s simHuman_chr6.simHuman.chr6 557525 20 - 601863 TACATTTGAGAAACATAAAG -s simRat_chr6.simRat.chr6 239758 20 - 647215 TGTGATAGAGAATCATGGTG - -a -s simMouse_chr6.simMouse.chr6 17713 23 + 636262 AAAAGTAGCAAACCAGGCTTACC -s Anc0.Anc0refChr2 11548 23 + 17989 TAAAGTCACAAACCAGGCTTAAC -s Anc1.Anc1refChr2 118825 23 - 144309 TAAAGTCACAAACCAGGCTTAAC -s Anc2.Anc2refChr0 9507 23 - 56053 TAAAGTCACAAACCAGGCTTAAC -s mr.mrrefChr0 16375 23 + 130230 AAAAGTAGCAAACCAGGCTTAAC -s simCow_chr6.simCow.chr6 552777 23 - 602619 TAAAGCCGCAAACCAGGCTTAAC -s simDog_chr6.simDog.chr6 550454 23 - 593897 CAAAGTCACAAACCAGGCTTAAC -s simHuman_chr6.simHuman.chr6 557546 23 - 601863 TGAAGTCACAAACCATGCTTAAC -s simRat_chr6.simRat.chr6 239778 23 - 647215 AAAAGTTGCAAACCAGGCTTAAC - -a -s simMouse_chr6.simMouse.chr6 17736 58 + 636262 CTTAAATCCTCAGAAAAGGAAAAGTCTGATGTGCACAAGCCACGCCCTTCACGCCATT -s Anc0.Anc0refChr2 11571 52 + 17989 CTCTAATCTTTA------GAAAAGCTTGATGTGTACAAGTGGCTCCCATAAGGCCATT -s Anc1.Anc1refChr2 118848 52 - 144309 CTCTAATCTTTA------GAAAAGCTTGATGTGTACAAGTGGCTCCCATAAGGCCATT -s Anc2.Anc2refChr0 9542 52 - 56053 CTCTAATCTTTA------GAAAAGCTAGGTGTGTACAAGTGGCTCCCATAAGGCCATT -s mr.mrrefChr0 16398 52 + 130230 CTTAAATCCTTA------GAAAAGTTTGATGTGTACAAGTCACGCCCTTCACGCCATT -s simCow_chr6.simCow.chr6 552812 52 - 602619 CTCTAATCTTTA------GAAAAGTTAGCTGTGAAAAAGTCGCTCTCATAAGTCCAAT -s simDog_chr6.simDog.chr6 550489 49 - 593897 CTCTAATCTTTG------GAAAAGCTAGGTGTGTAC---TGGCTCCCATAAAGCCATT -s simHuman_chr6.simHuman.chr6 557569 52 - 601863 CTCTAATCTTTA------GAAAACCTTGATGTGTACAAGTTGCTCCCAAAAGGCCATT -s simRat_chr6.simRat.chr6 239801 52 - 647215 CTTAAATCCATA------GAAAAGTTTGATGTGTACAGGTCACACCCTTGACATCATT - -a -s simMouse_chr6.simMouse.chr6 17794 1 + 636262 A -s Anc0.Anc0refChr2 11623 1 + 17989 A -s Anc1.Anc1refChr2 118900 1 - 144309 A -s Anc2.Anc2refChr0 9594 1 - 56053 A -s mr.mrrefChr0 16450 1 + 130230 A -s simCow_chr6.simCow.chr6 552870 1 - 602619 A -s simDog_chr6.simDog.chr6 550538 1 - 593897 A -s simHuman_chr6.simHuman.chr6 557621 1 - 601863 A -s simRat_chr6.simRat.chr6 239853 1 - 647215 A - -a -s simMouse_chr6.simMouse.chr6 17795 36 + 636262 TTGGATTCATGGATAACAGCAATTGCACAGCTGCCG -s Anc0.Anc0refChr2 11625 17 + 17989 ------------------ACAACCACAC-GCAGTCG -s Anc1.Anc1refChr2 118902 36 - 144309 GTAAACTTGAGAAAAACAACAACCACACAGCAGTCG -s Anc2.Anc2refChr0 9596 17 - 56053 ------------------ACAACCACAC-GCAGTAG -s mr.mrrefChr0 16451 36 + 130230 GTGAACTCATGGATAACAGCAATCACACAGCTGTCG -s simCow_chr6.simCow.chr6 552872 17 - 602619 ------------------ACAGCCATCA-GCAGTAG -s simDog_chr6.simDog.chr6 550540 17 - 593897 ------------------ACAATCACAC-GCAGTAG -s simHuman_chr6.simHuman.chr6 557623 36 - 601863 GTAAACTTGAGAAAAACAACTACCACACATCAGTCA -s simRat_chr6.simRat.chr6 239854 36 - 647215 GTGAACTCATGGATAACATCAATCACACAGCTGTCG - -a -s simMouse_chr6.simMouse.chr6 17831 40 + 636262 GTCTTTCCATGGTAGCAAGCCAAGGAGGGTAACTGTGCTA -s Anc0.Anc0refChr2 11642 36 + 17989 ACCTTTCCACAGAAGAAA-TCAAGCAGGAAAACC---CTG -s Anc1.Anc1refChr2 118938 37 - 144309 ACCTTTCCACAGAAGAAAGTCAAGCAGGAAAACC---CTG -s Anc2.Anc2refChr0 9613 36 - 56053 ACCTTTCCACAGAAGAAA-TCAAGCAGGAAAACC---TTG -s mr.mrrefChr0 16487 37 + 130230 GTCTTTCCATAGTAGAAAGCCAAGGAGGGTAACT---CTA -s simCow_chr6.simCow.chr6 552895 36 - 602619 ACCTTTCCACAGAAGAGA-TCAAGCAGGCAAGCC---ATG -s simDog_chr6.simDog.chr6 550557 35 - 593897 ACCTTT-CATAGAAGAAA-TCAAGCAGGATAACC---TTG -s simHuman_chr6.simHuman.chr6 557659 37 - 601863 ACCCTTGCACAGCAGAAAGTCAAGCAGGAAAACC---CTG -s simRat_chr6.simRat.chr6 239890 37 - 647215 GTCTTTCCATAGTAGAAAGCCAAGGAGGGTAACT---CTA - -a -s simMouse_chr6.simMouse.chr6 17871 24 + 636262 TAAGCTGGGAGAGCCTGTTACCCC -s Anc0.Anc0refChr2 11683 24 + 17989 CAAGCTGGGAGAGTCTGTTCCCCT -s Anc1.Anc1refChr2 118980 24 - 144309 CAAGCTGGGAGAGTCTGTTCCCCT -s Anc2.Anc2refChr0 9654 24 - 56053 CAAGCTGGGAAAGTCTGTTCCCTT -s mr.mrrefChr0 16524 24 + 130230 TAAGCTGGGAGAGCCTGTTACCCC -s simCow_chr6.simCow.chr6 552936 24 - 602619 CAAGCTGGGAAAGCCTGTTTACTC -s simDog_chr6.simDog.chr6 550597 24 - 593897 CAAGCTGGGAAAGTCTGTTCCCTT -s simHuman_chr6.simHuman.chr6 557701 24 - 601863 CAAGCTAGAAGAGTCTATTCCCCT -s simRat_chr6.simRat.chr6 239927 24 - 647215 TAAGCTGGGATAGCCTGTTACCCC - -a -s simMouse_chr6.simMouse.chr6 17895 3 + 636262 TAA -s Anc0.Anc0refChr2 11707 3 + 17989 TAA -s Anc1.Anc1refChr2 119004 3 - 144309 TAA -s Anc2.Anc2refChr0 9679 3 - 56053 TAA -s mr.mrrefChr0 16548 3 + 130230 TAA -s simCow_chr6.simCow.chr6 552961 3 - 602619 TAA -s simDog_chr6.simDog.chr6 550622 3 - 593897 TAA -s simHuman_chr6.simHuman.chr6 557725 3 - 601863 TAG -s simRat_chr6.simRat.chr6 239951 3 - 647215 GAA - -a -s simMouse_chr6.simMouse.chr6 17898 105 + 636262 AAGTGGAATTGTAAAATGTTAAGATTAAGTATAGCAAAGGGTAAAGTGTAATGAGGTGTGTGCTGTTGCTATGTGCAATATCAGAAACCATCGAGGGTATGTCTG -s Anc0.Anc0refChr2 11711 38 + 17989 AAGGAGAAATGGGATTCATTAAAACTAAGTATAATGAA------------------------------------------------------------------- -s Anc1.Anc1refChr2 119008 90 - 144309 AAGGAGAAATGGGATTCATTAAAACTAAGTATAATGAAGAGTAGAGACTAGT---GTGTATGTGGCCATCATGGG-------GGAAG-----AAGGAAGTTTCCA -s Anc2.Anc2refChr0 9683 38 - 56053 AAGGAAAAATGGGATTCATTAAGACCAAGTAAGATGAG------------------------------------------------------------------- -s mr.mrrefChr0 16552 104 + 130230 AAGTAGAATTGTAATTCATTAAAATTAAGTATAATGAAGGGTAAAGTGTAATGAGGTGTATGCTGTTGCTATGTGCAATAGCGGAAA-CATCAAGGGAGTTTCTG -s simCow_chr6.simCow.chr6 552965 1 - 602619 A-------------------------------------------------------------------------------------------------------- -s simDog_chr6.simDog.chr6 550626 38 - 593897 TAGGAAAAATGGGATTCATTAAGACCAAGTAAGATGAG------------------------------------------------------------------- -s simHuman_chr6.simHuman.chr6 557729 90 - 601863 AAGCAGAAATGAGGTTCACTAAAACTAAGTATAATGAAGAGTAGAGACTAGT---GTGTATGTGGCCATCATGGG-------GGAAG-----AAGGAAGTTTCCA -s simRat_chr6.simRat.chr6 239955 104 - 647215 AAGTAGAACTGTAATTCATTAAAATTAAGTATAATGAAGGGTAACATGTAATGAAGCGTATGCTGTTGCTATGTGCATTAGTGGAAA-CATCAAGGGAGTTTCTG - -a -s simMouse_chr6.simMouse.chr6 18003 49 + 636262 TCATGAATTAGTGAACCTGAACACACGCTGTTAAGTTTAATACTGTGAT -s Anc0.Anc0refChr2 11749 44 + 17989 ----GAATCAACGATCCCTTACACTAGCC-ATAGTTTTAAAACAATGCT -s Anc1.Anc1refChr2 119098 48 - 144309 TGACGAATCAACGATCCCTTACACTAGCC-ATAGTTTTAAAACAATGCT -s Anc2.Anc2refChr0 9721 44 - 56053 ----GAATCAACAATCCCTTACACTAGCT-ATAGTTTTAAAACAATGCT -s mr.mrrefChr0 16656 48 + 130230 TCATGAATTAGTGAACCTGAACACAAGCC-TTAAGTTTAATACTATGAT -s simCow_chr6.simCow.chr6 552966 28 - 602619 -------------------TACACCAGCA-ATAGTTTTAAA-CAATGCT -s simDog_chr6.simDog.chr6 550664 44 - 593897 ----GAATCAACAATCCCTTACACTAGCT-ATATTTTGAAAAGAATGGT -s simHuman_chr6.simHuman.chr6 557820 48 - 601863 TGACAAATCAAAGAGCCATTACTTTATTC-ATAGTTTTAGAGCAACGCT -s simRat_chr6.simRat.chr6 240059 48 - 647215 TCATGAATTAGTGAACCTGAACACAAGCC-TTAAATAGAATACCATGAT - -a -s simMouse_chr6.simMouse.chr6 18052 63 + 636262 TATGGTATGCTGACTCAATTCCAATTGGGGTAAAATAAAGCCCAGATCAGGGTGAATTACAAC -s Anc0.Anc0refChr2 11798 27 + 17989 TATGGTATGCTGACTCAATTGCAATCG------------------------------------ -s Anc1.Anc1refChr2 119151 55 - 144309 TATGGTATGCTGACTCAATTGCAATCGGGGTAAGATTATGGTCAGGTTAGACTAA-------- -s Anc2.Anc2refChr0 9770 27 - 56053 GATGGTATGCTGACTCAATTGCAATCA------------------------------------ -s mr.mrrefChr0 16704 63 + 130230 TATGGTATGCTGACTCAATTGCAATTGGGGTAAGATTAAGGCCAGGTCAGGGTAAATTACAAC -s simCow_chr6.simCow.chr6 552999 27 - 602619 GATGGTATGCTGACTCAATTGCAATCA------------------------------------ -s simHuman_chr6.simHuman.chr6 557873 55 - 601863 TATGGTATGCTGACTCAATTGCGATGGGGGTAAGATTATGGTCAGGTTAGACTAA-------- -s simRat_chr6.simRat.chr6 240107 63 - 647215 GATTGTATGCTGACTCAATTGCAATTGGGGTATGATTAAGGCCAGGTCAGGGTAAATTGCAAC - -a -s simMouse_chr6.simMouse.chr6 18115 30 + 636262 ACTAAACACACAGCATTTCCATGCGTTCTT -s Anc0.Anc0refChr2 11825 19 + 17989 -----------ACTGTTTCCATGTGTTTTT -s Anc1.Anc1refChr2 119206 30 - 144309 AATAAGTACACACTGTTTCCATGTGTTTTT -s Anc2.Anc2refChr0 9797 19 - 56053 -----------ACTGTTTCTACATGTTTTG -s mr.mrrefChr0 16767 30 + 130230 ACTAAACACACACTATTTCCATGTGTTCTT -s simCow_chr6.simCow.chr6 553026 19 - 602619 -----------ACTGTTTCTACATGTTTTG -s simHuman_chr6.simHuman.chr6 557928 30 - 601863 AATAAGTACACACTGTTTCCATGTGTTTTT -s simRat_chr6.simRat.chr6 240174 30 - 647215 ACTAACCACACACTATTTCTATGTGTTCTT - -a -s simMouse_chr6.simMouse.chr6 18145 28 + 636262 GAGCTGAACTTGATCTAATCCATCATGT -s Anc0.Anc0refChr2 11848 24 + 17989 AAGATGGACTTT----AACCCAACATTT -s Anc1.Anc1refChr2 119240 24 - 144309 AAGATGGACTTT----AACCCAACATTT -s Anc2.Anc2refChr0 9820 24 - 56053 AAGATGGACTTT----AACCGAACATTC -s mr.mrrefChr0 16797 28 + 130230 GAGCTGAACTTGATCTAATCCATCATGT -s simCow_chr6.simCow.chr6 553049 24 - 602619 AAGATGGACTTT----AACCGAACATTC -s simHuman_chr6.simHuman.chr6 557962 24 - 601863 AAGATGGACTTT----AACCCAGCTTAT -s simRat_chr6.simRat.chr6 240204 28 - 647215 GAGCTGAACTTGATCTAATCCATCATGC - -a -s simMouse_chr6.simMouse.chr6 18173 10 + 636262 CATCCTGTTG -s Anc0.Anc0refChr2 11879 10 + 17989 CATCCTGTTG -s Anc1.Anc1refChr2 119271 10 - 144309 CATCCTGTTG -s Anc2.Anc2refChr0 9851 10 - 56053 CATCCAGTTG -s mr.mrrefChr0 16825 10 + 130230 CACCCTGTTG -s simCow_chr6.simCow.chr6 553080 10 - 602619 CATCCAGTTG -s simHuman_chr6.simHuman.chr6 557993 10 - 601863 CATGCTCTTG -s simRat_chr6.simRat.chr6 240232 10 - 647215 CACCCTGTTG - -a -s simMouse_chr6.simMouse.chr6 18183 21 + 636262 TCCGTAGTGCATGAATTGATA -s Anc0.Anc0refChr2 11895 21 + 17989 TCCGCCGTGCATGACTTGAGG -s Anc1.Anc1refChr2 119287 21 - 144309 TCCGCCGTGCATGACTTGAGG -s Anc2.Anc2refChr0 9867 21 - 56053 CCCACCGTGCATAACTTGAGG -s mr.mrrefChr0 16835 21 + 130230 TCCGTAGTGCATGAATTGATA -s simCow_chr6.simCow.chr6 553099 21 - 602619 CCCACCGTGCATAACTTGAGG -s simHuman_chr6.simHuman.chr6 558009 21 - 601863 TTTGCCATGCACGACACGGAG -s simRat_chr6.simRat.chr6 240242 3 - 647215 TCA------------------ - -a -s simMouse_chr6.simMouse.chr6 18204 5 + 636262 CAGTC -s Anc0.Anc0refChr2 11916 5 + 17989 ATGAT -s Anc1.Anc1refChr2 119308 5 - 144309 ATGAT -s Anc2.Anc2refChr0 9888 5 - 56053 ATGAT -s mr.mrrefChr0 16856 5 + 130230 CAGTC -s simCow_chr6.simCow.chr6 553149 5 - 602619 ATGAT -s simHuman_chr6.simHuman.chr6 558030 5 - 601863 ATGAT - -a -s simMouse_chr6.simMouse.chr6 18209 15 + 636262 ATTTTGAATAACCGA -s Anc0.Anc0refChr2 11921 14 + 17989 T-ACCAAGTATCCGA -s Anc1.Anc1refChr2 119313 14 - 144309 T-ACCAAGTATCCGA -s Anc2.Anc2refChr0 9893 14 - 56053 T-ACCAAGTATTGGG -s mr.mrrefChr0 16861 14 + 130230 A-TTTGAGTAACCGA -s simCow_chr6.simCow.chr6 553155 14 - 602619 T-ACCAAGTATTGGG -s simHuman_chr6.simHuman.chr6 558035 14 - 601863 C-ACCAAGTATCCAA -s simRat_chr6.simRat.chr6 240245 13 - 647215 --TTTGAGTAACCGA - -a -s simMouse_chr6.simMouse.chr6 18224 68 + 636262 ACCCCTATAATAGCAGTTATACAGCACAATATTGAATGTGGTTAATATGCTCTTTTACCCTAATGACT -s Anc0.Anc0refChr2 11935 59 + 17989 TCCTCTATAATAGGCAAGAGACAGCA-AAT--------TGCTGAACATGCTCTTATGCCGCAATAACA -s Anc1.Anc1refChr2 119327 60 - 144309 TCCTCTATAATAGGCAAGAGACAGCACAAT--------TGCTGAACATGCTCTTATGCCGCAATAACA -s Anc2.Anc2refChr0 9907 59 - 56053 TCCTCTATAATCAGCAAGAGAAAGCA-AAT--------TGCCAAACATGCTCTTATGCCGCAATAACA -s mr.mrrefChr0 16875 68 + 130230 ACCCCTATAATAGCAGTTATACAGCACAATATTGAATGTGCTGAATATGCTCTTTTACCCTAATGACA -s simCow_chr6.simCow.chr6 553170 57 - 602619 TCCTCTATAATCAGCAAGAGAAAGCA-AAT--------TGCCAAACAT--TCTTGTGCCAGAATAACA -s simDog_chr6.simDog.chr6 550713 20 - 593897 ------------------------------------------------GCTCTTAAGTCGCAATTACA -s simHuman_chr6.simHuman.chr6 558049 60 - 601863 CCCTGTATAGCAGTCAAGAGACAGCACCAT--------TACTGAACATGCTCTTCTGCTTCAATAACA -s simRat_chr6.simRat.chr6 240258 68 - 647215 ACCCCTGTAATAGCAGTTACACTGCACAATATTCAAGATGCTGAATATTGTCTTTTTCCCTAACGCCA - -a -s simMouse_chr6.simMouse.chr6 18292 1 + 636262 T -s Anc0.Anc0refChr2 11994 1 + 17989 T -s Anc1.Anc1refChr2 119387 1 - 144309 T -s Anc2.Anc2refChr0 9973 1 - 56053 T -s mr.mrrefChr0 16943 1 + 130230 T -s simCow_chr6.simCow.chr6 553234 1 - 602619 C -s simDog_chr6.simDog.chr6 550740 1 - 593897 T -s simHuman_chr6.simHuman.chr6 558109 1 - 601863 T -s simRat_chr6.simRat.chr6 240326 1 - 647215 T - -a -s simMouse_chr6.simMouse.chr6 18293 12 + 636262 GAACCTCTGTTC -s Anc0.Anc0refChr2 11996 12 + 17989 GAACATCTGTTC -s Anc1.Anc1refChr2 119389 12 - 144309 GAACATCTGTTC -s Anc2.Anc2refChr0 9975 12 - 56053 GAACAGCTGTTC -s mr.mrrefChr0 16944 12 + 130230 GAACCTCTGTTC -s simCow_chr6.simCow.chr6 553236 12 - 602619 GAACAACTGTTC -s simDog_chr6.simDog.chr6 550742 12 - 593897 GCACAGCAGCTC -s simHuman_chr6.simHuman.chr6 558111 12 - 601863 GAGTATGTGTTC -s simRat_chr6.simRat.chr6 240327 12 - 647215 GAACCTCTGTTT - -a -s simMouse_chr6.simMouse.chr6 18305 8 + 636262 ATTCTTGA -s Anc0.Anc0refChr2 12011 8 + 17989 ATTTTTGA -s Anc1.Anc1refChr2 119404 8 - 144309 ATTTTTGA -s Anc2.Anc2refChr0 9990 8 - 56053 TCTTTTGA -s mr.mrrefChr0 16956 8 + 130230 ATTCTTGA -s simCow_chr6.simCow.chr6 553251 8 - 602619 CCTTTGGA -s simDog_chr6.simDog.chr6 550757 8 - 593897 TCTGTTGA -s simHuman_chr6.simHuman.chr6 558126 8 - 601863 ATTTTTGA -s simRat_chr6.simRat.chr6 240339 8 - 647215 ATTCTTGA - -a -s simMouse_chr6.simMouse.chr6 18313 1 + 636262 A -s Anc0.Anc0refChr2 12019 1 + 17989 T -s Anc1.Anc1refChr2 119412 1 - 144309 T -s Anc2.Anc2refChr0 9998 1 - 56053 T -s mr.mrrefChr0 16964 1 + 130230 A -s simCow_chr6.simCow.chr6 553259 1 - 602619 T -s simDog_chr6.simDog.chr6 550768 1 - 593897 T -s simHuman_chr6.simHuman.chr6 558134 1 - 601863 T -s simRat_chr6.simRat.chr6 240347 1 - 647215 A - -a -s simMouse_chr6.simMouse.chr6 18314 1 + 636262 T -s Anc0.Anc0refChr2 12021 1 + 17989 T -s Anc1.Anc1refChr2 119414 1 - 144309 T -s Anc2.Anc2refChr0 10000 1 - 56053 C -s mr.mrrefChr0 16966 1 + 130230 T -s simCow_chr6.simCow.chr6 553261 1 - 602619 C -s simDog_chr6.simDog.chr6 550770 1 - 593897 C -s simHuman_chr6.simHuman.chr6 558136 1 - 601863 T -s simRat_chr6.simRat.chr6 240349 1 - 647215 T - -a -s simMouse_chr6.simMouse.chr6 18315 56 + 636262 TGGTGGAACTATTAATCTAGATGTTGTGTGTTTATGTCATCCCAAGGTAAATGACA -s Anc0.Anc0refChr2 12023 56 + 17989 TAATGGGACTATTAGTCTTGATGCTATGGATTTGTGTCAACTCATTGTAAATCATA -s Anc1.Anc1refChr2 119416 56 - 144309 TAATGGGACTATTAGTCTTGATGCTATGGATTTGTGTCAACTCATTGTAAATCATA -s Anc2.Anc2refChr0 10002 56 - 56053 TAATGGGACTATTAGTCTTGATGCTATGGATTTGTGTCAACTCATTGTAAATCATA -s mr.mrrefChr0 16967 56 + 130230 TGGTGGGACTATTAATCTTGATGTTGTGTGTTTATGTCATCCCATGGTAAATGACA -s simCow_chr6.simCow.chr6 553263 48 - 602619 TAATTGGATTATTAGTCTTG-----ATGGATTTGTGTTAACTCGTT-TAAA--ATA -s simDog_chr6.simDog.chr6 550772 56 - 593897 TAATGGAACTATTAGTCGTGATGCTATGGATTAGTGTCAACTCATTGTAAATCATA -s simHuman_chr6.simHuman.chr6 558138 56 - 601863 TAATGTGACTATTAGTTTTGATGCTATCGATTTGTGTCAACTCATTGTAAAGCATA -s simRat_chr6.simRat.chr6 240350 56 - 647215 TGGTGGGACTATAAATCTTGATGTTGTGTGTTTATGTCATCCCGTGGTAAATGACA - -a -s simMouse_chr6.simMouse.chr6 18371 3 + 636262 ATA -s Anc0.Anc0refChr2 12084 3 + 17989 AGG -s Anc1.Anc1refChr2 119477 3 - 144309 AGG -s Anc2.Anc2refChr0 10063 3 - 56053 AAG -s mr.mrrefChr0 17023 3 + 130230 AGA -s simCow_chr6.simCow.chr6 553316 3 - 602619 AAG -s simDog_chr6.simDog.chr6 550833 3 - 593897 AAG -s simHuman_chr6.simHuman.chr6 558199 3 - 601863 AGG -s simRat_chr6.simRat.chr6 240406 3 - 647215 AGA - -a -s simMouse_chr6.simMouse.chr6 18374 1 + 636262 C -s Anc0.Anc0refChr2 12087 1 + 17989 C -s Anc1.Anc1refChr2 119480 1 - 144309 C -s Anc2.Anc2refChr0 10073 1 - 56053 C -s mr.mrrefChr0 17026 1 + 130230 C -s simCow_chr6.simCow.chr6 553326 1 - 602619 T -s simDog_chr6.simDog.chr6 550843 1 - 593897 C -s simHuman_chr6.simHuman.chr6 558202 1 - 601863 G -s simRat_chr6.simRat.chr6 240409 1 - 647215 C - -a -s simMouse_chr6.simMouse.chr6 18375 8 + 636262 CAAAGGAG -s Anc0.Anc0refChr2 12088 8 + 17989 CCAAGGAG -s Anc1.Anc1refChr2 119481 8 - 144309 CCAAGGAG -s Anc2.Anc2refChr0 10074 8 - 56053 CCAAGGAG -s mr.mrrefChr0 17027 8 + 130230 CCAAGGAG -s simCow_chr6.simCow.chr6 553327 8 - 602619 CCAAGGAG -s simDog_chr6.simDog.chr6 550844 8 - 593897 CCAAAGAG -s simHuman_chr6.simHuman.chr6 558203 8 - 601863 CCAAGGAG -s simRat_chr6.simRat.chr6 240415 8 - 647215 CCAAGGAG - -a -s simMouse_chr6.simMouse.chr6 18383 88 + 636262 AGAGGCCAATACCTGTCCCAAGACAACCCTTAGCCTTTAGATCCATTCAGTGTTTAAAATCTAATAACATTGTGTCTGCAGAATCCAT -s Anc0.Anc0refChr2 12098 82 + 17989 AGGAGCAAAGACCTCACCCCAGACGACTTCTGGTCTTCAGATCTACACAATGTCTTAAATCTAA----ATCGTTTC--TAGGATCAAT -s Anc1.Anc1refChr2 119491 88 - 144309 AGGAGCAAAGACCTCACCCCAGACGACTTCTGGTCTTCAGATCTACACAATGTCTTAAATCTAATAACATCGTTTCTGTAGGATCAAT -s Anc2.Anc2refChr0 10084 82 - 56053 AGGGGCAAAGACCTCACCCCAGACGACTTCTGGTCTTCAGATCTACACCATGTCTTCAATCTAA----ATCATTTT--TAGGATCAAT -s mr.mrrefChr0 17037 88 + 130230 AGAAGCCAATACCTCTCCCCAGACGACCCCTAGTCTTTAGATCCATTCAGTGTTTAAAATCTAATAACATTGTGTCTGCAGGATCCAT -s simCow_chr6.simCow.chr6 553338 82 - 602619 AGGGGCAAAAACCTCTCCCCAGACAACTTCTGGTCTTCAAATCTACACCATGTCCTCCATCTAA----GGACTTTT--TAGGACAAAG -s simDog_chr6.simDog.chr6 550854 82 - 593897 AGGGGCAAGGACCTCACCCCAGACGACTTCTGGTCTTCAGATCTACACCATGTCTACAATCTAA----ATCATGTT--TGTTGTCAAT -s simHuman_chr6.simHuman.chr6 558213 88 - 601863 AGGAGCAAAGACCCCCTGCCTGATGACTTCTGGTCTTCAGATCTGCACAATATCTTAAATTGAATAACATCGTTTCAGTAGGATCAAT -s simRat_chr6.simRat.chr6 240425 88 - 647215 AGAAGCCAAAACCTCTCCCCAGGCGACACCAAGTCTTTGGATTCATTCAGTGTTTAAAATCTTATAACATTGGGTCTGCAAGATCCAT - -a -s simMouse_chr6.simMouse.chr6 18471 47 + 636262 ATATGCCTCTAATGTCCCTGCTATAGAACTGTACAATGTGTTGTGAT -s Anc0.Anc0refChr2 12237 10 + 17989 ATAATCCTCT------------------------------------- -s Anc1.Anc1refChr2 119636 46 - 144309 ATAATCCTCTATTCCATCTGCTATAAATCAGTAGAATG-GGTGTGAT -s Anc2.Anc2refChr0 10224 10 - 56053 ATAATCCTCT------------------------------------- -s mr.mrrefChr0 17125 47 + 130230 ATATGCCTCTAATGCACCTGCTATAGAACTGTACAATGTGGTGTGAT -s simCow_chr6.simCow.chr6 553491 10 - 602619 ACACTCATCT------------------------------------- -s simDog_chr6.simDog.chr6 550993 10 - 593897 ATTATCCTCT------------------------------------- -s simHuman_chr6.simHuman.chr6 558358 46 - 601863 ATAAACCTCTATTCCATCTGCTATAAATCAGTAGAATG-GGTGTGAT -s simRat_chr6.simRat.chr6 240513 46 - 647215 ACA-GCCTCTAATGCACATGCTTTAGAACTGTACCATGTGGTGTGAT - -a -s simMouse_chr6.simMouse.chr6 18518 18 + 636262 GATAGGTTGAAACTGGGG -s Anc0.Anc0refChr2 12247 1 + 17989 -----------------A -s Anc1.Anc1refChr2 119682 18 - 144309 GACAAGCTGAATTTGGAA -s Anc2.Anc2refChr0 10234 1 - 56053 -----------------A -s mr.mrrefChr0 17172 18 + 130230 GATAAGTTGAATCTGGAG -s simCow_chr6.simCow.chr6 553501 1 - 602619 -----------------C -s simDog_chr6.simDog.chr6 551003 1 - 593897 -----------------A -s simHuman_chr6.simHuman.chr6 558405 18 - 601863 GACAAGCTGAATTTGGAA -s simRat_chr6.simRat.chr6 240559 18 - 647215 GATAAGTTGAATCTGGAG - -a -s simMouse_chr6.simMouse.chr6 18536 32 + 636262 TCTTGCTGATGGAGAGCCATATAGCCCAGTAG -s Anc0.Anc0refChr2 12248 18 + 17989 TCTTGCCACTGGAAAGCT-------------- -s Anc1.Anc1refChr2 119700 32 - 144309 TCTTGCCACTGGAAAGCTAGTTTACTCTGCGA -s Anc2.Anc2refChr0 10235 18 - 56053 TCTACCCACTGTTAAACT-------------- -s mr.mrrefChr0 17190 32 + 130230 TCTTGCTAATGGAGAGCCAGATAGCTCAGTAG -s simCow_chr6.simCow.chr6 553502 3 - 602619 TCT----------------------------- -s simDog_chr6.simDog.chr6 551004 18 - 593897 TCTACCCACTGTTAAACT-------------- -s simHuman_chr6.simHuman.chr6 558425 32 - 601863 TCTTGCAACTGGAAAGCTAGTTTACTCTGCGA -s simRat_chr6.simRat.chr6 240577 32 - 647215 TCTTGCTAATGGAGAGCCGGATAGCTCAGTAG - -a -s simMouse_chr6.simMouse.chr6 18568 19 + 636262 CAATTGTCCAAAGGCAAGA -s Anc0.Anc0refChr2 12266 19 + 17989 CATTTGTCCAAAGGCAAGA -s Anc1.Anc1refChr2 119732 19 - 144309 CATTTGTCCAAAGGCAAGA -s Anc2.Anc2refChr0 10253 19 - 56053 TTTTTGTCCATAGGCAAGA -s mr.mrrefChr0 17222 19 + 130230 CATTTGTCCAAAGGCAAGA -s simDog_chr6.simDog.chr6 551022 19 - 593897 TTTTTGTCCATAGGCAAGA -s simHuman_chr6.simHuman.chr6 558457 16 - 601863 CAT---GCTGAAGGCAAGA -s simRat_chr6.simRat.chr6 240614 19 - 647215 GATTTGTCCAAAGGCAAGA - -a -s simMouse_chr6.simMouse.chr6 18587 1 + 636262 T -s Anc0.Anc0refChr2 12285 1 + 17989 T -s Anc1.Anc1refChr2 119751 1 - 144309 T -s Anc2.Anc2refChr0 10272 1 - 56053 T -s mr.mrrefChr0 17241 1 + 130230 T -s simDog_chr6.simDog.chr6 551044 1 - 593897 T -s simHuman_chr6.simHuman.chr6 558473 1 - 601863 T -s simRat_chr6.simRat.chr6 240633 1 - 647215 T - -a -s simMouse_chr6.simMouse.chr6 18588 62 + 636262 CATTGTTGGTTTTTCCCTAACTGTTGCCTAACGGTAATCAAATGTCTTTGAAACCAGTGTAA -s Anc0.Anc0refChr2 12290 61 + 17989 CATT-TTGGTTTTTCCCTAACTGATGGAAAACAGTAATTGAATGCATTTGAAACCAATATAA -s Anc1.Anc1refChr2 119756 62 - 144309 CATTGTTGGTTTTTCCCTAACTGATGGAAAACAGTAATTGAATGCATTTGAAACCAATATAA -s Anc2.Anc2refChr0 10277 61 - 56053 CCTT-TTAGTTTTGCCCTGACTGATGGAAGACAGTAATTGAATGCATTTAGAACCAACATGA -s mr.mrrefChr0 17242 62 + 130230 CATTGTTGGTTTTTCCCTAACTGTTGCATAACAGTAATCAAATGTCTTTGAAACCAATATAA -s simDog_chr6.simDog.chr6 551049 61 - 593897 CCTT-TTAGTTTTGCCCTGACTGATGGAAGACAGTAATTGAATGCATTTAGAACCAACATGA -s simHuman_chr6.simHuman.chr6 558478 62 - 601863 CATTGTTGGTTTTTCTCCAACTGATGAAAAATAGTAAATGAATGCTTTTGAAACCAATATAA -s simRat_chr6.simRat.chr6 240634 62 - 647215 CATTTTTGGTTTTTCCCTAACTGTTGCATAACAACAATCAAATGTCTTTGAGATGAATATAA - -a -s simMouse_chr6.simMouse.chr6 18650 18 + 636262 CCTTCGATAACCTTGACT -s Anc0.Anc0refChr2 12354 18 + 17989 TTTTTGATACCCTTAACT -s Anc1.Anc1refChr2 119821 18 - 144309 TTTTTGATACCCTTAACT -s Anc2.Anc2refChr0 10341 18 - 56053 TTTTGGATACTCTTAGCT -s mr.mrrefChr0 17304 18 + 130230 TTTTTGATAACCTTAACT -s simDog_chr6.simDog.chr6 551113 18 - 593897 TTTTGGATACTCTTAGCT -s simHuman_chr6.simHuman.chr6 558543 18 - 601863 TTTCTGGTACCCTTAACT -s simRat_chr6.simRat.chr6 240696 18 - 647215 TTTTTGATAACCTTAACT - -a -s simMouse_chr6.simMouse.chr6 18668 63 + 636262 GATGCTCTAATGCTCTGGGTTGCCTGATAGTAATTAACAAGCTAGTTGGTGCTACATCTTTAA -s Anc0.Anc0refChr2 12372 58 + 17989 GAGTCTCTAATGGTCTGAA--TCCTGATAGCAC-T-ACAAGGTAGTTGTCGTGACATCCTT-T -s Anc1.Anc1refChr2 119839 60 - 144309 GAGTCTCTAATGGTCTGAATTTCCTGATAGCAC-T-ACAAGGTAGTTGTCGTGACATCCTT-T -s Anc2.Anc2refChr0 10359 58 - 56053 GAGTCTCTACTGGTCTGAA--TCCTGACAGCAC-T-AAAAGGTACTTGTCGTGACATCCTT-T -s mr.mrrefChr0 17322 62 + 130230 GATGCTCTAATGCTCTGGATTGCCTGATAGCAA-TAACAAGGTAGTTGGTGCTACATCTTTAA -s simDog_chr6.simDog.chr6 551131 58 - 593897 GAGTCTCTACTGGTCTGAA--TCCTGACAGCAC-T-AAAAGGTACTTGTCGTGACATCCTT-T -s simHuman_chr6.simHuman.chr6 558561 60 - 601863 GAATCCCTGATGATCTGTATTTCGTGATAGCAG-T-ACAAGGTAGTTATCGTGACATCCTT-T -s simRat_chr6.simRat.chr6 240716 62 - 647215 GATGCTCTAATGCTCTGGATTGCCTGATAGCAA-TAGCGAGGCAGTTGGTGCTACATCTTACA - -a -s simMouse_chr6.simMouse.chr6 18731 55 + 636262 ACAATAGCTCACACAAGCAAACTAGACAATGCACAGCCACATATTTGCACTGATC -s Anc0.Anc0refChr2 12430 47 + 17989 GCGGTAGCACTCGCAATCAGACAAGATAAT--------CCGTGTTTGCTCTGACC -s Anc1.Anc1refChr2 119899 51 - 144309 GCGGTAGCACTCGCAATCAGACAAGATAATTCA----CCCGTGTTTGCTCTGACC -s Anc2.Anc2refChr0 10417 47 - 56053 GTGGTAGCATTCGCAATCAGACATGGTAAT--------CTGTGTTTATTCTGACC -s mr.mrrefChr0 17384 55 + 130230 GCAATAGCTCACACAAGCAAACAAGATAATGCACAGCCACGTATTTGCACTGACC -s simDog_chr6.simDog.chr6 551211 47 - 593897 GTGGTAGCATTCGCAATCAGACATGGTAAT--------CTGTGTTTATTCTGACC -s simHuman_chr6.simHuman.chr6 558621 51 - 601863 GCGCTAGCACTTGCAATCAGACAAGATAACTCA----CTCGTGTTTGCCATGACC -s simRat_chr6.simRat.chr6 240778 55 - 647215 GCAATACCTCACACAAACAAACAAGATAATGCACAGTCCTGTATTTGGACAGACC - -a -s simMouse_chr6.simMouse.chr6 18786 50 + 636262 AGGATCAACTATGTGATGGACCCGCCATCATGGAGCAGCATTATTCAGTC -s Anc0.Anc0refChr2 12477 46 + 17989 AGCATCGACTCTGTAATGG----GCCATAATGGGGAACCCTTATTGAGTC -s Anc1.Anc1refChr2 119950 50 - 144309 AGCATCGACTCTGTAATGGTATCGCCATAATGGGGAACCCTTATTGAGTC -s Anc2.Anc2refChr0 10464 46 - 56053 AGCATTGATTCTGTACTGG----GCTACAATGGGGAACCCTTATTGAGTC -s mr.mrrefChr0 17439 50 + 130230 AGCATCAACTATGTGATGGACCCGCCATAATGGGGCAGCATTATTCAGTC -s simCow_chr6.simCow.chr6 553505 10 - 602619 ----------------------------------------TTATTGAGTC -s simDog_chr6.simDog.chr6 551259 46 - 593897 AGCATTGATTCTGTACTGG----GCTACAATGGGGAACCCTTATTGGGTC -s simHuman_chr6.simHuman.chr6 558672 50 - 601863 AGCATCTACTCTGTAATGATATCCCCATAATGGGGAACCTTTATTGAGTC -s simRat_chr6.simRat.chr6 240833 50 - 647215 AGCATCAGCTATGTGATGGACCCGTCACAATGGGGCAGTGTTATTCAGAC - -a -s simMouse_chr6.simMouse.chr6 18836 20 + 636262 CAGGTAACATTGATGAGGCT -s Anc0.Anc0refChr2 12523 20 + 17989 CAGGTAATATTGATGATGCT -s Anc1.Anc1refChr2 120000 20 - 144309 CAGGTAATATTGATGATGCT -s Anc2.Anc2refChr0 10510 20 - 56053 CAGGTAATATTGATGGTGCT -s mr.mrrefChr0 17494 20 + 130230 CAGGTAACATTGATGAGGCT -s simCow_chr6.simCow.chr6 553515 17 - 602619 CAGA---TATTGATTGGGCT -s simDog_chr6.simDog.chr6 551305 20 - 593897 CATGTAAAATTGATGGTGCT -s simHuman_chr6.simHuman.chr6 558722 20 - 601863 CTGGTATTATTGATAATGCT -s simRat_chr6.simRat.chr6 11458 10 + 647215 ----TAATATTGAC------ - -a -s simMouse_chr6.simMouse.chr6 18856 51 + 636262 ACTCCCTCCCAAACCCAGCGGCAGCGCATGTTGACAGCCCAACTATAGTTC -s Anc0.Anc0refChr2 12543 47 + 17989 A----CTCCAAAACCCAGTGGTACAGGATGTTGGCAGCCTAACTATAGTTC -s Anc1.Anc1refChr2 120020 47 - 144309 A----CTCCAAAACCCAGTGGTACAGGATGTTGGCAGCCTAACTATAGTTC -s Anc2.Anc2refChr0 10530 47 - 56053 A----CTCCAAAACCCAGTAGTACAAGATGTTGGCAACCTAACTGTAGTTC -s mr.mrrefChr0 17514 48 + 130230 AC---CTCCCAAACCCAGCGGCAGCGCATGTTGACAGCCCAACTATAGTTC -s simCow_chr6.simCow.chr6 553532 47 - 602619 A----CTCCCAAACCCACTAGTATGAAATGTTGGGACCCTAACTGTAGTTC -s simDog_chr6.simDog.chr6 551326 47 - 593897 G----CTCCAAAACCCAGTAGGACAAGATGCTGGCAACCTAACTGTAGTTC -s simHuman_chr6.simHuman.chr6 558742 44 - 601863 A----CTCCTAAACCCAGTGGTAAAGGATCTT---AGACTGAAGATTGGTC - -a -s simMouse_chr6.simMouse.chr6 18907 15 + 636262 TATTATACTTATTTA -s Anc0.Anc0refChr2 12590 14 + 17989 TGTCATAACTACTC- -s Anc1.Anc1refChr2 120067 15 - 144309 TGTCATAACTACTCA -s Anc2.Anc2refChr0 11001 14 - 56053 TGTCATAACGGCTC- -s mr.mrrefChr0 17562 15 + 130230 TATTATACTTATTTA -s simCow_chr6.simCow.chr6 553815 14 - 602619 TGTCACAACAGCTC- -s simDog_chr6.simDog.chr6 552011 14 - 593897 TGTCATAACGGCTC- -s simHuman_chr6.simHuman.chr6 558786 15 - 601863 TGTCATAACTACTCA - -a -s simMouse_chr6.simMouse.chr6 18922 451 + 636262 TAGTTGTATACATATCAAGTATATTCATTATCCCAAACTACAATTCCCCTACTTTTGTTGTAAAAGTTGATTTTCTTCCCCCTGATGGGAGGATCTTTTGGCTCTTTTTTAGCTGCTGTGTACCAACTCATGTAATTGAGTATACATTCCGAACTGCCTAATGTGCCTGCAATCTATCAGTAGTGAAGCCTTGCCCATGCCTGAGGTAGCTCACAGGTCAGAGGAATATGCCCAGCACTTTAGGACATTATAGGATTCCCCAGCAAATCAACAATCATCCACTGGTGGACTAACAGGTCCACCCTTGTGTCAGTAGTAGAGGACCATTTGCTCAGCGTAAATGCCAATTAACTTGCTGTGTAATTTTATCTTGCACTCCTACTTTTGAAGGGATTGTGGAAATTGATCCAGTCAGACTATAAAGAAACCACTACAGAGAGAATTATGTTCA -s Anc1.Anc1refChr2 120632 17 - 144309 TAGTTATAAACATATCA-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- -s mr.mrrefChr0 17577 311 + 130230 TAGTTGTATACATATCAAGTATATTCATTATCCCAAACTACAATTCCCCTACTTTTGTTGTAAAAGTTGATTTTCTTCCCCCTGATGGGAGGATCTTTTGGCTCTTTTTTAGCTGCTGTGTACCAACT-ATGTAATTGAGTATACATTCCGAACTGCCTAATGTGCCTGCAATCTATCAGTAGTGAAGCCTTGCCCATGCCTGAGGTAGCTCACAGGTCAGAGGAATATGCCCAGCACTTTAGGACATTATAGGATTCCCCAGCAAATCAACAATCATCCACTGGTGGACT-------------------------------------------------------------------------------------------------------------------------------------------CTACAGAGAGAATTATGTTCA -s simHuman_chr6.simHuman.chr6 559482 17 - 601863 TAGTTATAAACATATCA-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- -s simRat_chr6.simRat.chr6 11468 11 + 647215 --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ACATATGTTCA - -a -s simMouse_chr6.simMouse.chr6 19373 27 + 636262 GTACTTAGTGCATGAAGGTGCCATTTT -s mr.mrrefChr0 17888 22 + 130230 GTACTTAGTGCAC-----TGCCACCTT -s simRat_chr6.simRat.chr6 11482 22 + 647215 GTACCAGCTGCAC-----TGCCACCTT - -a -s simMouse_chr6.simMouse.chr6 19400 17 + 636262 ATATAGACTTGAGGAGG -s Anc0.Anc0refChr2 13152 2 + 17989 ---------------GG -s Anc1.Anc1refChr2 120649 6 - 144309 -----------ATGTGG -s Anc2.Anc2refChr0 11587 2 - 56053 ---------------GG -s mr.mrrefChr0 17910 17 + 130230 ACTTAGGCTTGATGAGG -s simCow_chr6.simCow.chr6 554462 2 - 602619 ---------------GG -s simHuman_chr6.simHuman.chr6 559499 6 - 601863 -----------ATGTGG -s simRat_chr6.simRat.chr6 11511 17 + 647215 ACTCAGGGCTAATGAGG - -a -s simMouse_chr6.simMouse.chr6 19417 3 + 636262 AAG -s Anc0.Anc0refChr2 13620 3 + 17989 AGG -s Anc1.Anc1refChr2 121121 3 - 144309 AGG -s Anc2.Anc2refChr0 12075 3 - 56053 AGG -s mr.mrrefChr0 17927 3 + 130230 AAG -s simCow_chr6.simCow.chr6 555058 3 - 602619 AAA -s simDog_chr6.simDog.chr6 552432 3 - 593897 AGG -s simHuman_chr6.simHuman.chr6 560148 3 - 601863 AGG -s simRat_chr6.simRat.chr6 11528 3 + 647215 AAG - -a -s simMouse_chr6.simMouse.chr6 19420 17 + 636262 TCCTTTGATCCCTGGTG -s Anc0.Anc0refChr2 13623 7 + 17989 TCCTTCA---------- -s Anc1.Anc1refChr2 121124 17 - 144309 TCCTTCAACCTCTGGTG -s Anc2.Anc2refChr0 12078 7 - 56053 ATCGCCA---------- -s mr.mrrefChr0 17930 17 + 130230 TCCTTTAATTCCTGGTG -s simCow_chr6.simCow.chr6 555064 7 - 602619 ATCCCCA---------- -s simDog_chr6.simDog.chr6 552435 7 - 593897 ATCGCCA---------- -s simHuman_chr6.simHuman.chr6 560151 17 - 601863 TCCTTCAACCTCTGGTG -s simRat_chr6.simRat.chr6 11531 17 + 647215 TCCTTTAATTCACCGTC - -a -s simMouse_chr6.simMouse.chr6 19437 2 + 636262 TG -s Anc0.Anc0refChr2 13641 2 + 17989 TG -s Anc1.Anc1refChr2 121152 2 - 144309 TG -s Anc2.Anc2refChr0 12096 2 - 56053 TG -s mr.mrrefChr0 17947 2 + 130230 TG -s simCow_chr6.simCow.chr6 555082 2 - 602619 TG -s simDog_chr6.simDog.chr6 552453 2 - 593897 TG -s simHuman_chr6.simHuman.chr6 560184 2 - 601863 TG -s simRat_chr6.simRat.chr6 11548 2 + 647215 TA - -a -s simMouse_chr6.simMouse.chr6 19439 46 + 636262 TCCCTCTTTCACTACCTCAGCTCTTCTGTCATCTGCCAGACAGACT -s Anc0.Anc0refChr2 13643 37 + 17989 ACTGTCTTTCACTACCTTAGCTCTTCAGA-------CAGACAGA-- -s Anc1.Anc1refChr2 121154 37 - 144309 ACTGTCTTTCACTACCTTAGCTCTTCAGA-------CAGACAGA-- -s Anc2.Anc2refChr0 12098 37 - 56053 AATGTCTTTCACCACCTTAACTCCCCAGA-------CGGCTAAA-- -s mr.mrrefChr0 17949 46 + 130230 TCCCTCTTTCACTACCTCAGCTCTTCTGTCGTCTGCCAGACAGACT -s simCow_chr6.simCow.chr6 555084 7 - 602619 GGAGTCT--------------------------------------- -s simDog_chr6.simDog.chr6 552456 37 - 593897 AATCTCTTTCACCACCTTAACTCCCCAGA-------CGGCTAAA-- -s simHuman_chr6.simHuman.chr6 560186 37 - 601863 ACTGTCTTTCACTGTCTTAGCTTTTCAGC-------CAGACAGG-- -s simRat_chr6.simRat.chr6 11550 46 + 647215 TCTCTCTTTCACTACCTCAGCTCTTCTGCCGTCTGCCACAGAGACT - -a -s simMouse_chr6.simMouse.chr6 19485 40 + 636262 TTTTATGCTGAGTATAATGACTCGTCAAGCCTGGCAATAC -s Anc0.Anc0refChr2 13680 38 + 17989 TTTACTGCTGAGTATA-GGAGTTATC-AGCGTGTATCTCA -s Anc1.Anc1refChr2 121191 39 - 144309 TTTACTGCTGAGTATATGGAGTTATC-AGCGTGTATCTCA -s Anc2.Anc2refChr0 12135 38 - 56053 TTTACTGCTGAGTATA-GGAGTTATC-AGTGTGTATCACA -s mr.mrrefChr0 17995 40 + 130230 TTTTATGCTGAGTATAATGACTCATCAAGCCTGGCAATAC -s simDog_chr6.simDog.chr6 552496 38 - 593897 TTTACTGCTGAGTATA-GGAGTTATC-AGTGTGTATCACA -s simHuman_chr6.simHuman.chr6 560223 39 - 601863 TTTGCTGCAGAGTATATGGAGGTATC-AGCATGTGTCTCA -s simRat_chr6.simRat.chr6 11596 40 + 647215 TTTTATGCTGAGTATAATGACACATCAAGCCTGGCAATAC - -a -s simMouse_chr6.simMouse.chr6 19525 22 + 636262 TCACTGTTTTTTTGACTTGTTT -s Anc0.Anc0refChr2 13718 22 + 17989 TCAATGTTTTTTTTACTTGTTC -s Anc1.Anc1refChr2 121230 22 - 144309 TCAATGTTTTTTTTACTTGTTC -s Anc2.Anc2refChr0 12176 22 - 56053 TCAATGATTTTTTTACTTGTTC -s mr.mrrefChr0 18035 22 + 130230 TCACTGTTTTTTTGACTTGTTT -s simCow_chr6.simCow.chr6 555094 22 - 602619 CCAATAATATCCTTACTTGGAC -s simDog_chr6.simDog.chr6 552538 22 - 593897 TTAATGATTTTTTTACTTGTTC -s simHuman_chr6.simHuman.chr6 560262 22 - 601863 TCAATGTTTTTTTTGCTTGTTC -s simRat_chr6.simRat.chr6 11636 22 + 647215 TCACTGTTTTTTTGACCTGTTT - -a -s simMouse_chr6.simMouse.chr6 19547 6 + 636262 TCAATG -s Anc0.Anc0refChr2 13740 6 + 17989 CCAGCA -s Anc1.Anc1refChr2 121252 6 - 144309 CCAGCA -s Anc2.Anc2refChr0 12198 6 - 56053 CCAGCA -s mr.mrrefChr0 18057 6 + 130230 TCAATG -s simCow_chr6.simCow.chr6 555124 6 - 602619 CCAACA -s simDog_chr6.simDog.chr6 552560 6 - 593897 TCAGCA -s simHuman_chr6.simHuman.chr6 560284 6 - 601863 CCAGCA -s simRat_chr6.simRat.chr6 11658 6 + 647215 TCAATG - -a -s simMouse_chr6.simMouse.chr6 19553 1 + 636262 T -s Anc0.Anc0refChr2 13749 1 + 17989 C -s Anc1.Anc1refChr2 121261 1 - 144309 C -s Anc2.Anc2refChr0 12207 1 - 56053 C -s mr.mrrefChr0 18063 1 + 130230 T -s simCow_chr6.simCow.chr6 555133 1 - 602619 C -s simDog_chr6.simDog.chr6 552569 1 - 593897 T -s simHuman_chr6.simHuman.chr6 560293 1 - 601863 C -s simRat_chr6.simRat.chr6 11664 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 19554 4 + 636262 AAGT -s Anc0.Anc0refChr2 13750 4 + 17989 AAGT -s Anc1.Anc1refChr2 121262 4 - 144309 AAGT -s Anc2.Anc2refChr0 12208 4 - 56053 AAGT -s mr.mrrefChr0 18064 4 + 130230 AAGT -s simCow_chr6.simCow.chr6 555139 4 - 602619 AAGT -s simDog_chr6.simDog.chr6 552570 4 - 593897 AGGT -s simHuman_chr6.simHuman.chr6 560294 4 - 601863 AAGT -s simRat_chr6.simRat.chr6 11665 4 + 647215 AAGT - -a -s simMouse_chr6.simMouse.chr6 19558 33 + 636262 TTCAGGTGCTCCATTAGAAGAAGGACACTGTAA -s Anc0.Anc0refChr2 13754 30 + 17989 TTAAGGTGCTCTGTT---AGAAGGGCACTTTAA -s Anc1.Anc1refChr2 121266 30 - 144309 TTAAGGTGCTCTGTT---AGAAGGGCACTTTAA -s Anc2.Anc2refChr0 12212 30 - 56053 TTAAGGTGCTCTGCT---AGTAGGGCACCTTAA -s mr.mrrefChr0 18068 30 + 130230 TTCAGGTGCTCTGTT---AGAAGGACACTGTAA -s simCow_chr6.simCow.chr6 555145 30 - 602619 TTATAGTGCCCTTCT---AGCAGAGCACCTTAA -s simDog_chr6.simDog.chr6 552574 25 - 593897 ATAAGGTGCTCTGCT---AGTAGGCCTC----- -s simHuman_chr6.simHuman.chr6 560298 30 - 601863 TTGAGTTGTTCTGTA---AGAAGGGCACTATAA -s simRat_chr6.simRat.chr6 11669 30 + 647215 TTCAGGTCCTCTGTT---AGAAGGACACTGTGG - -a -s simMouse_chr6.simMouse.chr6 19591 31 + 636262 TCCCTTTTAGGTAAGCTATGCTAGTGTAATT -s Anc0.Anc0refChr2 13784 31 + 17989 TAACATTTCTGTAAGCCAGGCCAGTCTAGTT -s Anc1.Anc1refChr2 121296 31 - 144309 TAACATTTCTGTAAGCCAGGCCAGTCTAGTT -s Anc2.Anc2refChr0 12242 31 - 56053 GAACATTTCTATCCGCCAGGCCAGTCTAGTT -s mr.mrrefChr0 18098 31 + 130230 TCCCTCTTAGGTAAGCTATGCTAGTGTAATT -s simCow_chr6.simCow.chr6 555208 31 - 602619 GAACATTTCTATCCCCAAAAAAAGTCTGGCT -s simDog_chr6.simDog.chr6 552599 17 - 593897 --------------GACAGGCCAGTCCATTT -s simHuman_chr6.simHuman.chr6 560328 31 - 601863 TAACATTTCAGTAAGCCAGGCCAATCTAGTT -s simRat_chr6.simRat.chr6 11699 31 + 647215 TCCCTCTTTGGTAAGTCATGTTCGTATGATT - -a -s simMouse_chr6.simMouse.chr6 19622 6 + 636262 AATCAA -s Anc0.Anc0refChr2 13815 6 + 17989 AATGAT -s Anc1.Anc1refChr2 121327 6 - 144309 AATGAT -s Anc2.Anc2refChr0 12273 6 - 56053 AATGTT -s mr.mrrefChr0 18129 6 + 130230 AATCAA -s simCow_chr6.simCow.chr6 555245 6 - 602619 AGTGTT -s simDog_chr6.simDog.chr6 552616 6 - 593897 AATGTT -s simHuman_chr6.simHuman.chr6 560359 6 - 601863 AATGAT -s simRat_chr6.simRat.chr6 11730 6 + 647215 AATCAA - -a -s simMouse_chr6.simMouse.chr6 19628 9 + 636262 GCTACGAGG -s Anc0.Anc0refChr2 13821 9 + 17989 GTTATGGGG -s Anc1.Anc1refChr2 121333 9 - 144309 GTTATGGGG -s Anc2.Anc2refChr0 12279 9 - 56053 GTTATGGGG -s mr.mrrefChr0 18135 9 + 130230 GCTACGAGG -s simCow_chr6.simCow.chr6 555254 9 - 602619 GTTATGGAA -s simDog_chr6.simDog.chr6 552622 9 - 593897 GTTATGGGG -s simHuman_chr6.simHuman.chr6 560365 9 - 601863 GTTATGGGG -s simRat_chr6.simRat.chr6 11736 9 + 647215 GCTACGAGG - -a -s simMouse_chr6.simMouse.chr6 19637 11 + 636262 CATAGACCCTA -s Anc0.Anc0refChr2 13830 1 + 17989 C---------- -s Anc1.Anc1refChr2 121342 11 - 144309 CCTAGGCCCCA -s Anc2.Anc2refChr0 12288 1 - 56053 C---------- -s mr.mrrefChr0 18144 11 + 130230 CATAGACCCTA -s simCow_chr6.simCow.chr6 555268 1 - 602619 T---------- -s simDog_chr6.simDog.chr6 552631 1 - 593897 C---------- -s simHuman_chr6.simHuman.chr6 560374 11 - 601863 ACTAGGCCCCA -s simRat_chr6.simRat.chr6 11745 11 + 647215 CCTAGACCCTA - -a -s simMouse_chr6.simMouse.chr6 19648 10 + 636262 TGGAATTGCT -s Anc0.Anc0refChr2 13831 10 + 17989 TAGAAATAAC -s Anc1.Anc1refChr2 121353 10 - 144309 TAGAAATAAC -s Anc2.Anc2refChr0 12289 10 - 56053 TAGCAATAAC -s mr.mrrefChr0 18155 10 + 130230 TAGAATTGCT -s simCow_chr6.simCow.chr6 555269 10 - 602619 CATCAATAAC -s simDog_chr6.simDog.chr6 552632 3 - 593897 TAG------- -s simHuman_chr6.simHuman.chr6 560387 10 - 601863 TAGAAATATC -s simRat_chr6.simRat.chr6 11756 10 + 647215 CAGAATTGCT - -a -s simMouse_chr6.simMouse.chr6 19658 21 + 636262 GCTTCATTACCATCCGAATCT -s Anc0.Anc0refChr2 13845 15 + 17989 TCTTGGTTACC------AGCT -s Anc1.Anc1refChr2 121367 15 - 144309 TCTTGGTTACC------AGCT -s Anc2.Anc2refChr0 12303 15 - 56053 TCTTGGTTACC------TGCT -s mr.mrrefChr0 18165 15 + 130230 GCTTCATTACC------ATCT -s simCow_chr6.simCow.chr6 555283 15 - 602619 TCCTGTTTACT------TGCT -s simDog_chr6.simDog.chr6 552638 15 - 593897 TCTTGGTTCCC------TGCT -s simHuman_chr6.simHuman.chr6 560401 15 - 601863 TCTTGGTTACC------AGCT -s simRat_chr6.simRat.chr6 11766 15 + 647215 GCTTCATTACC------ATCT - -a -s simMouse_chr6.simMouse.chr6 19679 23 + 636262 ATTATGATTTATGCTAGGTGAAG -s Anc0.Anc0refChr2 13866 23 + 17989 ATTATAATTGACTCTATGTGAAG -s Anc1.Anc1refChr2 121388 23 - 144309 ATTATAATTGACTCTATGTGAAG -s Anc2.Anc2refChr0 12324 23 - 56053 ATTATAATTGACTCTATGTGAAG -s mr.mrrefChr0 18180 23 + 130230 ATTATGATTTATGCTAGGTGAAG -s simCow_chr6.simCow.chr6 555304 23 - 602619 ATTATAATTGACTCCATGTGAGG -s simDog_chr6.simDog.chr6 552659 23 - 593897 ATTACAATTCACACTATGTGAAG -s simHuman_chr6.simHuman.chr6 560422 16 - 601863 GTTATTACTGACTCT-------G -s simRat_chr6.simRat.chr6 11781 22 + 647215 ATTATGA-TTATGCTAGTTGAGG - -a -s simMouse_chr6.simMouse.chr6 19702 2 + 636262 AG -s Anc0.Anc0refChr2 13889 2 + 17989 GA -s Anc1.Anc1refChr2 121411 2 - 144309 GA -s Anc2.Anc2refChr0 12349 2 - 56053 GA -s mr.mrrefChr0 18203 2 + 130230 AG -s simDog_chr6.simDog.chr6 552684 2 - 593897 GA -s simHuman_chr6.simHuman.chr6 560438 2 - 601863 GA -s simRat_chr6.simRat.chr6 11803 2 + 647215 AG - -a -s simMouse_chr6.simMouse.chr6 19704 12 + 636262 TGTTGACTTAGT -s Anc0.Anc0refChr2 13897 12 + 17989 AGATAACTTAGT -s Anc1.Anc1refChr2 121419 12 - 144309 AGATAACTTAGT -s Anc2.Anc2refChr0 12357 12 - 56053 AGATAACTTAGC -s mr.mrrefChr0 18211 12 + 130230 TGTTAACTTAGT -s simCow_chr6.simCow.chr6 555334 12 - 602619 AGATAACATAGC -s simDog_chr6.simDog.chr6 552692 12 - 593897 ATATAACTCGGC -s simHuman_chr6.simHuman.chr6 560446 12 - 601863 AGATAACTTAGT -s simRat_chr6.simRat.chr6 11811 12 + 647215 TGGTAACTTAGT - -a -s simMouse_chr6.simMouse.chr6 19716 9 + 636262 TGAGCCTTA -s Anc0.Anc0refChr2 13911 9 + 17989 TGAGACTTA -s Anc1.Anc1refChr2 121433 9 - 144309 TGAGACTTA -s Anc2.Anc2refChr0 12371 9 - 56053 TGTGACTTA -s mr.mrrefChr0 18225 9 + 130230 TGAGCCTTA -s simCow_chr6.simCow.chr6 555348 9 - 602619 TGTGACTAA -s simDog_chr6.simDog.chr6 552706 7 - 593897 T--GACTTT -s simHuman_chr6.simHuman.chr6 560460 9 - 601863 TCAGACTTA -s simRat_chr6.simRat.chr6 11825 9 + 647215 TGAACCTTA - -a -s simMouse_chr6.simMouse.chr6 19725 7 + 636262 AGATAAA -s Anc0.Anc0refChr2 13921 7 + 17989 ATATATA -s Anc1.Anc1refChr2 121443 7 - 144309 ATATATA -s Anc2.Anc2refChr0 12381 7 - 56053 ATATATA -s mr.mrrefChr0 18234 7 + 130230 AGATAAA -s simCow_chr6.simCow.chr6 555358 7 - 602619 ATGTATA -s simDog_chr6.simDog.chr6 552714 7 - 593897 ATATATA -s simHuman_chr6.simHuman.chr6 560470 7 - 601863 ATATATA -s simRat_chr6.simRat.chr6 11834 7 + 647215 AGAGAAA - -a -s simMouse_chr6.simMouse.chr6 19732 10 + 636262 GACTTGCTCC -s Anc0.Anc0refChr2 13939 10 + 17989 GACAAGCTAC -s Anc1.Anc1refChr2 121461 10 - 144309 GACAAGCTAC -s Anc2.Anc2refChr0 12399 10 - 56053 GACAAGCTAC -s mr.mrrefChr0 18241 10 + 130230 GACTTGCTCC -s simCow_chr6.simCow.chr6 555376 10 - 602619 GACAAGCGAT -s simDog_chr6.simDog.chr6 552732 10 - 593897 GACAAGCTGC -s simHuman_chr6.simHuman.chr6 560488 10 - 601863 GACAAGCTAC -s simRat_chr6.simRat.chr6 11841 10 + 647215 GACTTGCTCC - -a -s simMouse_chr6.simMouse.chr6 19742 6 + 636262 ACTATA -s Anc0.Anc0refChr2 13959 6 + 17989 ACTATA -s Anc1.Anc1refChr2 121481 6 - 144309 ACTATA -s Anc2.Anc2refChr0 12419 6 - 56053 ACTATA -s mr.mrrefChr0 18251 6 + 130230 ACTATA -s simCow_chr6.simCow.chr6 555396 6 - 602619 ACTAAA -s simDog_chr6.simDog.chr6 552752 6 - 593897 ACTATA -s simHuman_chr6.simHuman.chr6 560508 6 - 601863 ACCATA -s simRat_chr6.simRat.chr6 11851 6 + 647215 ACTATA - -a -s simMouse_chr6.simMouse.chr6 19748 3 + 636262 GTA -s Anc0.Anc0refChr2 13965 3 + 17989 GTA -s Anc1.Anc1refChr2 121487 3 - 144309 GTA -s Anc2.Anc2refChr0 12425 3 - 56053 GTA -s mr.mrrefChr0 18257 3 + 130230 GTA -s simCow_chr6.simCow.chr6 555403 3 - 602619 GTA -s simDog_chr6.simDog.chr6 552758 3 - 593897 GTA -s simHuman_chr6.simHuman.chr6 560514 3 - 601863 GTA -s simRat_chr6.simRat.chr6 11857 3 + 647215 GTA - -a -s simMouse_chr6.simMouse.chr6 19751 19 + 636262 CATGATAGAGTGACATAAC -s Anc0.Anc0refChr2 13971 19 + 17989 CTTAATAGGGTGACATAAC -s Anc1.Anc1refChr2 121493 19 - 144309 CTTAATAGGGTGACATAAC -s Anc2.Anc2refChr0 12431 19 - 56053 CTTAATAGGGTGACCTAAC -s mr.mrrefChr0 18260 19 + 130230 CATGATAGAGTGACATAAC -s simCow_chr6.simCow.chr6 555409 19 - 602619 CTTAGTAGTGTGTCCTAAC -s simDog_chr6.simDog.chr6 552764 19 - 593897 CTTAATAGGGTGACCTAAC -s simHuman_chr6.simHuman.chr6 560520 19 - 601863 CTTAATAGGGTGACACAAT -s simRat_chr6.simRat.chr6 11860 19 + 647215 CATGGTAAAGTGACATAAC - -a -s simMouse_chr6.simMouse.chr6 19770 71 + 636262 TCAATTGGGGGCAGTAAGGACTCGGTCATCCATATCGTTAGAAGTTTAGTCACCCATAGCCTTAGAAATAA -s Anc0.Anc0refChr2 13991 46 + 17989 GTTGTTCGGAGGGGTAAGTACTTAGTCGTCCATAT------------------------CCTTA-AAACTA -s Anc1.Anc1refChr2 121513 46 - 144309 GTTGTTCGGAGGGGTAAGTACTTAGTCGTCCATAT------------------------CCTTA-AAACTA -s Anc2.Anc2refChr0 12451 46 - 56053 GTTGTTCAGAGGGGTAAGTACTTAGTTGTCCATAC------------------------TTTGG-AAACTA -s mr.mrrefChr0 18279 47 + 130230 TCAATTGGGGGCGGTAAGGACTTAGTCATCCATAT------------------------CCTTAGAGATAA -s simCow_chr6.simCow.chr6 555429 46 - 602619 GCTGTTCAGAGGGTTAAGCACTTAGTTATGCACAA------------------------TTTGT-AATCAA -s simDog_chr6.simDog.chr6 552784 46 - 593897 GTAGTTCAGTGAGGGAAGTCCTTAAATGTCCATAC------------------------TTTGG-AGACTA -s simHuman_chr6.simHuman.chr6 560540 46 - 601863 GTTGTTAGGAGGGATAAGTACTTAGTCCTCCATAT------------------------CCTTA-CAACTG -s simRat_chr6.simRat.chr6 11879 47 + 647215 TCAATTGGGGGCGGTAAGGACTTAGTCATCCATAT------------------------CCTTAGAGATAA - -a -s simMouse_chr6.simMouse.chr6 19841 89 + 636262 CCCCTCTCCCCCACCGGGATGTGACATAGACTGGAGTTCCTTTTAGTGAAACAATCAATTGTGTGAATGCAGGCCGACAAGAGCATATA -s Anc0.Anc0refChr2 14037 80 + 17989 CACCACTCCCCC-CCAGGATGTAGCATAATCTGGAGCTCCTGGTGGTGAAAGAATCA--------ACAATAGGCCAACAAGAGGCTATA -s Anc1.Anc1refChr2 121559 81 - 144309 CACCACTCCCCCGCCAGGATGTAGCATAATCTGGAGCTCCTGGTGGTGAAAGAATCA--------ACAATAGGCCAACAAGAGGCTATA -s Anc2.Anc2refChr0 12497 80 - 56053 CATTACTCCCCT-CCAGAATGTAGCATAATCTGGAGCTCCTGGTGGTGTAAGAATCA--------ACAATAGGCCAACAAAATGCTATT -s mr.mrrefChr0 18326 89 + 130230 CCCCTCTCCCCCACCAGGATGTGGCATAGACTGGAGTTCCTTTTAGTGAAACAATCAATTGTGTGACAGTAGGCCAACAAGAGCATATA -s simCow_chr6.simCow.chr6 555475 80 - 602619 CCTTACTTCCCT-CCACAAGATAGCATAGTCAGGGACTCCTGGCAGTGGAAGAATCA--------ACAATAGGCCGATAACATGCTGTG -s simDog_chr6.simDog.chr6 552830 80 - 593897 CATTACTCCACT-CCAGAATGTAGCATAATCTGGAGCTCCTGTTGTTATAAGAATAA--------ACAATAAGCCAACAAAATGCTATT -s simHuman_chr6.simHuman.chr6 560586 81 - 601863 CACCACTCCCTCGCCAGGATGTAGCATCATCTAGAGCTCCTAGTGGTGAAAGAATCA--------ACAATGGGCTAACAAGAGGTTATA -s simRat_chr6.simRat.chr6 11927 89 + 647215 CCCCTCTCCCCCACCAGGATTTGGCATAGAGTAGAGTTCCTTTTAGTGAAACAATCAATTGCATAACAGTAGGCCAGCAAGAGCTTATA - -a -s simMouse_chr6.simMouse.chr6 19930 60 + 636262 ATGCACCAAGCAGCTTGGTTGTTTGGCCATTGACATATCAGCAACTAGTGGCTCATCCAA -s Anc0.Anc0refChr2 14182 60 + 17989 ATGCACCAAGCAGGCTGTAAGTTAGACCATGGGCACTTCAGCAATTGGTGGCTAAACTAG -s Anc1.Anc1refChr2 121705 60 - 144309 ATGCACCAAGCAGGCTGTAAGTTAGACCATGGGCACTTCAGCAATTGGTGGCTAAACTAG -s Anc2.Anc2refChr0 12642 60 - 56053 GTGCATCAGGCAGGCTGTAAGTTAGAACATGGGCACTGCAACAATTGGTGGCTAAACTAG -s mr.mrrefChr0 18415 60 + 130230 ATGCACCAAGCAGCTTGGATGTTTGGCCATTGGCACATCAGCAACTGGTGGCTCACCCAA -s simCow_chr6.simCow.chr6 555620 60 - 602619 GTGCATCGGGCAGGTTGTAAGTTAGAACATGAGCACTGCAACAAGGGTTGGCTGAACTAA -s simDog_chr6.simDog.chr6 552984 60 - 593897 GTGCATCAGGTAGGCTGTAAGTTAGAACATAGGCACTGCAACAATTGGTGCCTAACCTAG -s simHuman_chr6.simHuman.chr6 560732 60 - 601863 ACGCACCAAGCAGGCTGTAAGTAAGACCATGGACACTTCAGCAGTTGATGGCTACACTAG -s simRat_chr6.simRat.chr6 12016 60 + 647215 ATGCACCAAGCAGCTTGCATGTTTGGCCATGAGCACATCAGTAACTGGTGGCTCACCCAA - -a -s simMouse_chr6.simMouse.chr6 19990 10 + 636262 TGGTATTAAC -s Anc0.Anc0refChr2 14242 10 + 17989 TGACATTTTC -s Anc1.Anc1refChr2 121765 10 - 144309 TGACATTTTC -s Anc2.Anc2refChr0 12702 10 - 56053 TGACATTTTC -s mr.mrrefChr0 18475 10 + 130230 TGGTATTGAC -s simCow_chr6.simCow.chr6 555680 10 - 602619 CAACATTTTT -s simDog_chr6.simDog.chr6 553044 10 - 593897 TGCCATTGCC -s simHuman_chr6.simHuman.chr6 560792 10 - 601863 TGACATTTTG -s simRat_chr6.simRat.chr6 12081 10 + 647215 TGGTACTGAA - -a -s simMouse_chr6.simMouse.chr6 20000 20 + 636262 AGGTTCAGTAAACACCTGTA -s Anc0.Anc0refChr2 14252 20 + 17989 AGGTACTGTAAACACTTGTA -s Anc1.Anc1refChr2 121775 20 - 144309 AGGTACTGTAAACACTTGTA -s Anc2.Anc2refChr0 12712 20 - 56053 AGGTACTGTAAACACTTGTA -s mr.mrrefChr0 18485 20 + 130230 AGGTTCAGTAAACACTTGTA -s simCow_chr6.simCow.chr6 555691 20 - 602619 AGGCACTGTAAACACTTGTA -s simDog_chr6.simDog.chr6 553054 20 - 593897 AGTTACTGTAAACACTTGTA -s simHuman_chr6.simHuman.chr6 560802 20 - 601863 AGGTACTGTAACCTCTTGTA -s simRat_chr6.simRat.chr6 12091 20 + 647215 AGGTTCGGTAAACACTTGTA - -a -s simMouse_chr6.simMouse.chr6 20020 9 + 636262 GGAACCAAG -s Anc0.Anc0refChr2 14272 9 + 17989 GGTACTGAG -s Anc1.Anc1refChr2 121795 9 - 144309 GGTACTGAG -s Anc2.Anc2refChr0 12732 9 - 56053 GGTAATGAG -s mr.mrrefChr0 18505 9 + 130230 GGAACCAAG -s simCow_chr6.simCow.chr6 555711 9 - 602619 GGTGATGAG -s simDog_chr6.simDog.chr6 553076 9 - 593897 GTTAATGAG -s simHuman_chr6.simHuman.chr6 560822 9 - 601863 GGTACTGAG -s simRat_chr6.simRat.chr6 12111 9 + 647215 GGAACCAAG - -a -s simMouse_chr6.simMouse.chr6 20029 85 + 636262 TCTATGCACCCAATATAGTAACTTTAATTCTTTGTTTAAGACCTAGTAACTATAGCCAATTGTTAAAGACCCACTTTGCAATCAG -s Anc0.Anc0refChr2 14296 59 + 17989 TTTATGAACCCCATATAGTA--------------------------TGACTATAGTCATTTGTTGAAGACCCACTTTGCAATTGG -s Anc1.Anc1refChr2 121819 59 - 144309 TTTATGAACCCCATATAGTA--------------------------TGACTATAGTCATTTGTTGAAGACCCACTTTGCAATTGG -s Anc2.Anc2refChr0 12756 59 - 56053 TTTATGAACCCCATATAATA--------------------------TGACTATAGTCATTTGTTGAAGACCTACTTTGCAATTGG -s mr.mrrefChr0 18528 85 + 130230 TTTATGAACCCAATATAGTAACTTTAATTCTTTGTTTAAGACCTAGTAACTATAGCCAATTGTTAAGGACCCACTTTGCAATCAG -s simCow_chr6.simCow.chr6 555735 59 - 602619 TCTATCGGCCCCACATAATA--------------------------GCACTATCATCCTTTGCTCAAGACCTACTTTGCAATTGG -s simDog_chr6.simDog.chr6 553101 58 - 593897 TTTATGAA-CTCATGTAATA--------------------------TGACTATAGTCAATTGTTGAGGACCTGCTTTGCAATCGG -s simHuman_chr6.simHuman.chr6 560846 59 - 601863 TTTGTGAACCCCATATAGTA--------------------------TGACTATAGTCATTAGTTGAAGACCCACTTTGCAATTGG -s simRat_chr6.simRat.chr6 12134 85 + 647215 TTTATGAACCCAATATAGCAACTATAGTGCTTTGTTTAAGACCCAGTAACTATAGCCAATTGTTAAGGACCCAATTTGCGATCAG - -a -s simMouse_chr6.simMouse.chr6 20114 169 + 636262 GGTGGATGTTAAGTGACTTATGTAATGGAGCACATAATTATGGTGGTCTATGAACCCAATATAGTAATTTCTTGTTTAAGACCCAGCAACTTATAGCCAATTTTCAAAGACCCAATTTGTAATTAGGGTGGATGTTAAGTGACCGATGTAATTGAGCATGATGTTAAGT -s Anc0.Anc0refChr2 14355 28 + 17989 GAT-GATGCTCCATGACTGATGTAATGTA-------------------------------------------------------------------------------------------------------------------------------------------- -s Anc1.Anc1refChr2 121878 29 - 144309 GATAGATGCTCCATGACTGATGTAATGTA-------------------------------------------------------------------------------------------------------------------------------------------- -s Anc2.Anc2refChr0 12815 28 - 56053 GAT-GATGCTCCATGGCTGATGTAATGTA-------------------------------------------------------------------------------------------------------------------------------------------- -s mr.mrrefChr0 18613 29 + 130230 GATGGATGTTAAATGACTGATGTAATGGA-------------------------------------------------------------------------------------------------------------------------------------------- -s simCow_chr6.simCow.chr6 555794 28 - 602619 GGT-AGAGCTCCATGGCTGATATGATGTA-------------------------------------------------------------------------------------------------------------------------------------------- -s simDog_chr6.simDog.chr6 553159 28 - 593897 GAT-GATGTTCCATGGCTGATGTAATGTA-------------------------------------------------------------------------------------------------------------------------------------------- -s simHuman_chr6.simHuman.chr6 560906 29 - 601863 GGTAGATTCTGCATGACAGATTTCGCGTA-------------------------------------------------------------------------------------------------------------------------------------------- -s simRat_chr6.simRat.chr6 12219 29 + 647215 GATAGATGTTAAATGACTGATGTAATAGA-------------------------------------------------------------------------------------------------------------------------------------------- - -a -s simMouse_chr6.simMouse.chr6 20283 101 + 636262 GACTGATGTAATTGAGCACATAATTTTGCACTTTTGAAACCATGGTTGTGAACATAATTGTGAGCTTATGAAGTCAAGCTAGCAAGACATAGGACTGGCTT -s Anc0.Anc0refChr2 14385 46 + 17989 ACCTGA---------------------------------------------------TAGTTAGCTTATGAAGTCAAGATGGCAAGACAC----ATGGATT -s Anc1.Anc1refChr2 121909 51 - 144309 ACCTGAT--------------------------------------------------TAGTTAGCTTATGAAGTCAAGATGGCAAGACACAGGAATGGATT -s Anc2.Anc2refChr0 12845 46 - 56053 ACATGA---------------------------------------------------TAATTAGCTTATGAAATTAAGATGGCAAGATAC----ATGGATT -s mr.mrrefChr0 18642 101 + 130230 GACTGATGTAATTGAGCACATAATTATGCACTTTTGAAACCAAGGTTGTGAACATAATTGTGAGCTTATGAAGTCAAGCTAGCAAGACATAGGACTGGCTT -s simCow_chr6.simCow.chr6 555824 31 - 602619 ATATGA---------------------------------------------------TAATTACCCCA------AAAGTTGGCAGGAT------------- -s simDog_chr6.simDog.chr6 553189 46 - 593897 ACATGA---------------------------------------------------TAATTTGCTTATGAAATTAAGATGGCAAGATAC----ATGGATT -s simHuman_chr6.simHuman.chr6 560937 51 - 601863 ACCTGAT--------------------------------------------------TAGTTAGCTTATGAAGTCAAGGAGGCACGACACAGGAATGGATT -s simRat_chr6.simRat.chr6 12248 101 + 647215 GACAGATGTAATGGAGCACATAATTATGCACTTTTGAAACCAAGGTTGCTAACATAATCGTGATCATATAGAGTCAAGCTAACAAGACATAGGACTGGCTT - -a -s simMouse_chr6.simMouse.chr6 20384 19 + 636262 GATGTTTTAAAGTTTAGTA -s Anc0.Anc0refChr2 14432 19 + 17989 GATGTTATAATGTTAAGTA -s Anc1.Anc1refChr2 121961 19 - 144309 GATGTTATAATGTTAAGTA -s Anc2.Anc2refChr0 12892 19 - 56053 GATGTAATAATGTTAAGTA -s mr.mrrefChr0 18743 19 + 130230 GATGTTTTAAAGTTTAGTA -s simCow_chr6.simCow.chr6 555855 19 - 602619 GATGTAACAAGTTTAAGTA -s simDog_chr6.simDog.chr6 553236 19 - 593897 AATGTAATGGTGTTAAGTA -s simHuman_chr6.simHuman.chr6 560989 19 - 601863 GATATTGTAATGTTAGGTA -s simRat_chr6.simRat.chr6 12349 19 + 647215 GATGTTTTAACATTTAGTA - -a -s simMouse_chr6.simMouse.chr6 20403 7 + 636262 AATGTAA -s Anc0.Anc0refChr2 14451 7 + 17989 AATGTCA -s Anc1.Anc1refChr2 121980 7 - 144309 AATGTCA -s Anc2.Anc2refChr0 12917 7 - 56053 AATGTCA -s mr.mrrefChr0 18762 7 + 130230 AATGTAA -s simCow_chr6.simCow.chr6 555881 7 - 602619 AATGTCA -s simDog_chr6.simDog.chr6 553261 7 - 593897 AATGTCA -s simHuman_chr6.simHuman.chr6 561008 7 - 601863 AATGTTA -s simRat_chr6.simRat.chr6 12368 7 + 647215 AATGTAA - -a -s simMouse_chr6.simMouse.chr6 20410 4 + 636262 ATTG -s Anc0.Anc0refChr2 14459 4 + 17989 ATAG -s Anc1.Anc1refChr2 121988 4 - 144309 ATAG -s Anc2.Anc2refChr0 12925 4 - 56053 TTAG -s mr.mrrefChr0 18769 4 + 130230 ATTG -s simCow_chr6.simCow.chr6 555889 4 - 602619 TTAG -s simDog_chr6.simDog.chr6 553269 4 - 593897 TTAG -s simHuman_chr6.simHuman.chr6 561016 4 - 601863 ATAG -s simRat_chr6.simRat.chr6 12375 4 + 647215 ATTG - -a -s simMouse_chr6.simMouse.chr6 20414 57 + 636262 TTTTTTTGTGATTCTATGTATCATGTGATGTCTCAGCTTGGAATTAAGGCATGGTTA -s Anc0.Anc0refChr2 14468 56 + 17989 CCTTTCAGTGGTTCCATCTATCATGTGACACCTCAGCTTGGAAGTAAGGCATGT-TA -s Anc1.Anc1refChr2 121997 56 - 144309 CCTTTCAGTGGTTCCATCTATCATGTGACACCTCAGCTTGGAAGTAAGGCATGT-TA -s Anc2.Anc2refChr0 12934 56 - 56053 CCTTTCAGTGGTTCCATCTATCATGTGACACCTCAGCTTGGAAGTAAGGCATGT-TA -s mr.mrrefChr0 18778 56 + 130230 TCTTTTTGTGGTTCCATCTATCATGTGATGTCTCAGCTTGGAATTAAGGCATGG-TA -s simCow_chr6.simCow.chr6 555898 56 - 602619 CCTTTCGGTGGTTCCATTTACCACGTGACATCTTTGCTGTGAAGTGAAGCATGT-TA -s simDog_chr6.simDog.chr6 553278 56 - 593897 TCTTTCAATAGTCCCATCTATCATGTGACACCTCAGCTTGGAATTAAGGCATGC-TA -s simHuman_chr6.simHuman.chr6 561025 50 - 601863 CCCTTCAGTGGATCCATCTATCATGTGA------AGCCTGGAAGTAAGGCATGT-TA -s simRat_chr6.simRat.chr6 12384 56 + 647215 TCTTTTTCTGGTTCCATCTACCATGTGATCTCTCAGCCTGGAGTTAAGGCATGG-TA - -a -s simMouse_chr6.simMouse.chr6 20471 22 + 636262 ACCTAAATGAAGTTACACCACG -s Anc0.Anc0refChr2 14530 22 + 17989 AAATAGAGGAAGTTATCCTATG -s Anc1.Anc1refChr2 122059 22 - 144309 AAATAGAGGAAGTTATCCTATG -s Anc2.Anc2refChr0 12996 22 - 56053 AAATGGAGAAAGTTATCCTATG -s mr.mrrefChr0 18834 22 + 130230 AACTAAATGAAGTTACACCATG -s simCow_chr6.simCow.chr6 555960 22 - 602619 AAAGGGAGAAAGTTATCCTATG -s simDog_chr6.simDog.chr6 553340 22 - 593897 AAATGGAGAGTGTTATCCTATG -s simHuman_chr6.simHuman.chr6 561081 22 - 601863 AAATAGAGGAAGTTATCCAATG -s simRat_chr6.simRat.chr6 12440 22 + 647215 AACTAAATAAAGTTACACCATG - -a -s simMouse_chr6.simMouse.chr6 20493 28 + 636262 ACCATCCTACTGAGTGCCTAGACTGGCT -s Anc0.Anc0refChr2 14552 28 + 17989 CCTTCCATACTGAGTGCCTAAACTACCT -s Anc1.Anc1refChr2 122081 28 - 144309 CCTTCCATACTGAGTGCCTAAACTACCT -s Anc2.Anc2refChr0 13018 28 - 56053 CCTTCCATACTGACTGCCTTAACTACCT -s mr.mrrefChr0 18856 28 + 130230 ACCATCCTACTGAGTGCCTAAACTGGCT -s simCow_chr6.simCow.chr6 555988 28 - 602619 TCCTCCATACTTAACACCTGTACCGCCT -s simDog_chr6.simDog.chr6 553362 28 - 593897 CCTTCCATACTGTCTGCTTTAACTAGCT -s simHuman_chr6.simHuman.chr6 561103 28 - 601863 CCTTCCATACCAAGTGCCTAAAGTCCCC -s simRat_chr6.simRat.chr6 12462 28 + 647215 ACCATCCTACTGAGTGCCTAAACTGGCT - -a -s simMouse_chr6.simMouse.chr6 20521 1 + 636262 A -s Anc0.Anc0refChr2 14580 1 + 17989 A -s Anc1.Anc1refChr2 122109 1 - 144309 A -s Anc2.Anc2refChr0 13046 1 - 56053 A -s mr.mrrefChr0 18884 1 + 130230 A -s simCow_chr6.simCow.chr6 556016 1 - 602619 A -s simDog_chr6.simDog.chr6 553390 1 - 593897 A -s simHuman_chr6.simHuman.chr6 561132 1 - 601863 A -s simRat_chr6.simRat.chr6 12490 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 20522 20 + 636262 ACTCCGGTTTAGCCTACCTG -s Anc0.Anc0refChr2 14581 9 + 17989 ACACTGGTT----------- -s Anc1.Anc1refChr2 122110 9 - 144309 ACACTGGTT----------- -s Anc2.Anc2refChr0 13050 9 - 56053 ACACTGGTT----------- -s mr.mrrefChr0 18885 20 + 130230 ACACTGGTTTAGCCTACATG -s simCow_chr6.simCow.chr6 556020 8 - 602619 ACACTGGT------------ -s simDog_chr6.simDog.chr6 553394 9 - 593897 ACACTGGTT----------- -s simHuman_chr6.simHuman.chr6 561133 9 - 601863 ACTCTGCTT----------- -s simRat_chr6.simRat.chr6 12491 19 + 647215 ACACTGGTTTAG-CTACATG - -a -s simMouse_chr6.simMouse.chr6 20542 7 + 636262 GCTACAC -s Anc0.Anc0refChr2 14590 7 + 17989 GCTAGAC -s Anc1.Anc1refChr2 122119 7 - 144309 GCTAGAC -s Anc2.Anc2refChr0 13059 7 - 56053 GCTAGAC -s mr.mrrefChr0 18905 7 + 130230 GCTACAC -s simCow_chr6.simCow.chr6 556028 7 - 602619 GCTATGC -s simDog_chr6.simDog.chr6 553414 7 - 593897 GCTAGAC -s simRat_chr6.simRat.chr6 12510 7 + 647215 GATACAC - -a -s simMouse_chr6.simMouse.chr6 20549 11 + 636262 AAATGTGGGCA -s Anc0.Anc0refChr2 14597 11 + 17989 AAATATGGACC -s Anc1.Anc1refChr2 122126 11 - 144309 AAATATGGACC -s Anc2.Anc2refChr0 13067 11 - 56053 AAATATGGACC -s mr.mrrefChr0 18912 11 + 130230 AAATGTGGGCA -s simCow_chr6.simCow.chr6 556036 11 - 602619 AAATGTGGGAC -s simDog_chr6.simDog.chr6 553426 11 - 593897 AAATATGGACC -s simRat_chr6.simRat.chr6 12517 11 + 647215 AAATGTGGGCA - -a -s simMouse_chr6.simMouse.chr6 20560 25 + 636262 CCCTTTAGATGTCAAGAGCTTACTA -s Anc0.Anc0refChr2 14608 25 + 17989 CCCTTCAGGTGACCAATGCTTACTA -s Anc1.Anc1refChr2 122137 25 - 144309 CCCTTCAGGTGACCAATGCTTACTA -s Anc2.Anc2refChr0 13083 25 - 56053 CCCTTCAAGTGACCAATACTCACTA -s mr.mrrefChr0 18923 25 + 130230 CCCTTCAGATGTCAAGAGCTTACTA -s simCow_chr6.simCow.chr6 556052 25 - 602619 CTCTCCAAGTGTCCAACACTCACTA -s simDog_chr6.simDog.chr6 553442 25 - 593897 CCCTTCAAGTGACCAATACTCACTA -s simHuman_chr6.simHuman.chr6 561142 23 - 601863 --CTTCAGGTCACCTATGCTTACTA -s simRat_chr6.simRat.chr6 12528 25 + 647215 ACCTTCAGATGTCTACAGCTTCCTA - -a -s simMouse_chr6.simMouse.chr6 20585 13 + 636262 TAACTGCCAGCCA -s Anc0.Anc0refChr2 14637 13 + 17989 TACCTCCCAACCA -s Anc1.Anc1refChr2 122166 13 - 144309 TACCTCCCAACCA -s Anc2.Anc2refChr0 13121 13 - 56053 TACCTCCCAATCA -s mr.mrrefChr0 18948 13 + 130230 TAACTGCCAACCA -s simCow_chr6.simCow.chr6 556091 13 - 602619 TACCTACCACTCT -s simDog_chr6.simDog.chr6 553480 13 - 593897 TACCTCCCAATCA -s simHuman_chr6.simHuman.chr6 561169 13 - 601863 TACCTCCTATCGA -s simRat_chr6.simRat.chr6 12553 13 + 647215 TAACTGCAAACCA - -a -s simMouse_chr6.simMouse.chr6 20598 6 + 636262 GCGGGC -s Anc0.Anc0refChr2 14650 6 + 17989 ATGGTC -s Anc1.Anc1refChr2 122179 6 - 144309 ATGGTC -s Anc2.Anc2refChr0 13134 6 - 56053 ATGGTC -s mr.mrrefChr0 18961 6 + 130230 GTGGGC -s simCow_chr6.simCow.chr6 556113 6 - 602619 ATGGTT -s simDog_chr6.simDog.chr6 553493 6 - 593897 ATGGTC -s simHuman_chr6.simHuman.chr6 561182 6 - 601863 AAGGTC -s simRat_chr6.simRat.chr6 12566 6 + 647215 GTGGGC - -a -s simMouse_chr6.simMouse.chr6 20604 44 + 636262 CAGAATCCACAGTGCAGCCCTCCCCATCCACCCACTAAATGGAA -s Anc0.Anc0refChr2 14656 38 + 17989 CAGGATTTGCAG------CTCCTATATCAACCTACTGAATGAAA -s Anc1.Anc1refChr2 122185 38 - 144309 CAGGATTTGCAG------CTCCTATATCAACCTACTGAATGAAA -s Anc2.Anc2refChr0 13140 38 - 56053 CAGGATTTGCAG------CTCATATATCAACCTACTGACTGAAA -s mr.mrrefChr0 18967 44 + 130230 CAGGATCTGCAGTGCAGCCCTCTCCATCCACCCACTGAATGGAA -s simCow_chr6.simCow.chr6 556134 38 - 602619 TAGGATTTGCAG------CTCATTTATCAAGCTACTGAGTGAGA -s simDog_chr6.simDog.chr6 553499 38 - 593897 CAGGATTTGCGG------CTCATATATCAACCTACTGACTGCAA -s simHuman_chr6.simHuman.chr6 561188 38 - 601863 CATGATATGCAG------CTCCTGTATTAACCTACTAAATGAAA -s simRat_chr6.simRat.chr6 12572 44 + 647215 CAGGATCTGCAGTGCAGCCCTCTCCATCCACTCACTGAATGGTA - -a -s simMouse_chr6.simMouse.chr6 20648 9 + 636262 TAAATGTTG -s Anc0.Anc0refChr2 14694 9 + 17989 TGAATGTTG -s Anc1.Anc1refChr2 122223 9 - 144309 TGAATGTTG -s Anc2.Anc2refChr0 13188 9 - 56053 TGACTGTTG -s mr.mrrefChr0 19011 9 + 130230 TGAATGTTG -s simCow_chr6.simCow.chr6 556182 9 - 602619 TGACTGTTG -s simDog_chr6.simDog.chr6 553547 9 - 593897 TGACTGTTG -s simHuman_chr6.simHuman.chr6 561226 9 - 601863 TGAATATTG -s simRat_chr6.simRat.chr6 12616 9 + 647215 TGAAAGTTG - -a -s simMouse_chr6.simMouse.chr6 20657 13 + 636262 ATGTCACCATCAC -s Anc0.Anc0refChr2 15001 13 + 17989 CTGACACCATCAC -s Anc1.Anc1refChr2 122530 13 - 144309 CTGACACCATCAC -s Anc2.Anc2refChr0 13502 13 - 56053 CTGACAACATCAC -s mr.mrrefChr0 19020 13 + 130230 ATGTCACCATCAC -s simCow_chr6.simCow.chr6 556466 13 - 602619 CTGACTTCAGCAC -s simDog_chr6.simDog.chr6 553840 13 - 593897 CCGACAACATCCC -s simHuman_chr6.simHuman.chr6 561536 13 - 601863 CTGACACCATCAC -s simRat_chr6.simRat.chr6 12625 13 + 647215 ATGCCACCATCAC - -a -s simMouse_chr6.simMouse.chr6 20670 8 + 636262 CCCTACTA -s Anc0.Anc0refChr2 15014 8 + 17989 CCCTACTA -s Anc1.Anc1refChr2 122543 8 - 144309 CCCTACTA -s Anc2.Anc2refChr0 13515 8 - 56053 CCCTACTA -s mr.mrrefChr0 19033 8 + 130230 CCCTACTA -s simCow_chr6.simCow.chr6 556479 8 - 602619 CCCTATTG -s simDog_chr6.simDog.chr6 553853 8 - 593897 CCCTACAA -s simHuman_chr6.simHuman.chr6 561549 8 - 601863 CCCTAATA -s simRat_chr6.simRat.chr6 12642 8 + 647215 CCCTACTA - -a -s simMouse_chr6.simMouse.chr6 20678 31 + 636262 TTGGTACACATGTAGATGAATTGCTTTTTAT -s Anc0.Anc0refChr2 15022 25 + 17989 CTGGTACACATATGGAT-AAGT-----TGAT -s Anc1.Anc1refChr2 122551 25 - 144309 CTGGTACACATATGGAT-AAGT-----TGAT -s Anc2.Anc2refChr0 13523 25 - 56053 CTGGTACACACATGGAT-AAGT-----TGAT -s mr.mrrefChr0 19041 26 + 130230 TTGGTACACATGTAGATGAATT-----TTAT -s simCow_chr6.simCow.chr6 556487 25 - 602619 TTGGTACACACATGCAT-AAGT-----TGCT -s simDog_chr6.simDog.chr6 553903 25 - 593897 CAGGTACACACAAAGAT-AAGG-----TGAT -s simHuman_chr6.simHuman.chr6 561557 25 - 601863 CTGATACACATATGTAC-AACT-----TGAT -s simRat_chr6.simRat.chr6 12650 26 + 647215 TTGATACACACTCTGACAAATT-----TTGA - -a -s simMouse_chr6.simMouse.chr6 20709 77 + 636262 GAGTATGTGCAATCCTGCATCGGTACACACGTAGATGAATTGGTTTTTATGAGTATGTGCCATCCTGCATGTGGGCA -s Anc0.Anc0refChr2 15065 21 + 17989 GAGCATATGGAATTC--------------------------------------------------------TGGGCA -s Anc1.Anc1refChr2 122594 21 - 144309 GAGCATATGGAATTC--------------------------------------------------------TGGGCA -s Anc2.Anc2refChr0 13566 21 - 56053 GAGCATATGGAATTC--------------------------------------------------------TGGGCA -s mr.mrrefChr0 19067 31 + 130230 GAGTATGTGCAATCCTGC----------------------------------------------CTGCATGTGGGCA -s simCow_chr6.simCow.chr6 556544 21 - 602619 GAGTATATGGAGTGC--------------------------------------------------------TGGGCA -s simDog_chr6.simDog.chr6 553942 21 - 593897 GAGCATATGGAATTC--------------------------------------------------------TGGACA -s simHuman_chr6.simHuman.chr6 561600 21 - 601863 GAGCATATGAAATAC--------------------------------------------------------TAGGCA -s simRat_chr6.simRat.chr6 12676 31 + 647215 TAGGATATGCAATCCTGC----------------------------------------------CTTCCTGGGCATC - -a -s simMouse_chr6.simMouse.chr6 20786 56 + 636262 CACATTGACAAAATATTGTCAATCACCCCTCTTGTCAAACATCAGGCACTGGCCAG -s Anc0.Anc0refChr2 15088 55 + 17989 CAAACTGACAGAATATTGTCAAATGCTCCCCCT-TCAAACATGAGGCTCAGGCTGG -s Anc1.Anc1refChr2 122617 55 - 144309 CAAACTGACAGAATATTGTCAAATGCTCCCCCT-TCAAACATGAGGCTCAGGCTGG -s Anc2.Anc2refChr0 13589 55 - 56053 CAAACTGACAGAATATTCACAAATGGTCCCCCT-TCAAACATGAGGCTCAGGCTGG -s mr.mrrefChr0 19098 56 + 130230 CACATTGACAAAATATTGTCAATCACCCCTCTTGTCAAACATCAGGCACTGGCCAG -s simCow_chr6.simCow.chr6 556567 55 - 602619 GAAACAGACAGAATATTAGCAAATATTCCCACT-TCAAACATGAGCCTCAGGCTGA -s simDog_chr6.simDog.chr6 553965 55 - 593897 CGTATTAACAGAATATTCACAAATGGTCCCCCT-TCAAAGAGGAGGCTCAGGCTGG -s simHuman_chr6.simHuman.chr6 561623 55 - 601863 CAAACGGACAGAATATTGTCAAAAGCTCCCCCT-TCAAGCATGAGATTCAGGCTGG -s simRat_chr6.simRat.chr6 12707 56 + 647215 CGCATTGACAGTATATTGTCAATAACTCCTCTTTTCAAACATGAGGCGCAGGCTAG - -a -s simMouse_chr6.simMouse.chr6 20842 1 + 636262 G -s Anc0.Anc0refChr2 15143 1 + 17989 G -s Anc1.Anc1refChr2 122672 1 - 144309 G -s Anc2.Anc2refChr0 13644 1 - 56053 G -s mr.mrrefChr0 19154 1 + 130230 G -s simCow_chr6.simCow.chr6 556622 1 - 602619 G -s simDog_chr6.simDog.chr6 554020 1 - 593897 G -s simHuman_chr6.simHuman.chr6 561678 1 - 601863 G -s simRat_chr6.simRat.chr6 12767 1 + 647215 G - -a -s simMouse_chr6.simMouse.chr6 20843 5 + 636262 ATCTT -s Anc0.Anc0refChr2 15144 5 + 17989 ATCTT -s Anc1.Anc1refChr2 122673 5 - 144309 ATCTT -s Anc2.Anc2refChr0 13645 5 - 56053 ATCTT -s mr.mrrefChr0 19155 5 + 130230 ATCTT -s mr.mrrefChr3 82836 5 + 181027 TACCT -s simCow_chr6.simCow.chr6 556623 5 - 602619 ATCTT -s simDog_chr6.simDog.chr6 554021 5 - 593897 ATCTT -s simHuman_chr6.simHuman.chr6 561679 5 - 601863 ATCTT -s simMouse_chr6.simMouse.chr6 531014 5 + 636262 CACCT -s simRat_chr6.simRat.chr6 542098 5 + 647215 TACCC -s simRat_chr6.simRat.chr6 12768 5 + 647215 ATCTT - -a -s simMouse_chr6.simMouse.chr6 20848 1 + 636262 A -s Anc0.Anc0refChr2 15156 1 + 17989 G -s Anc1.Anc1refChr2 122685 1 - 144309 G -s Anc2.Anc2refChr0 13657 1 - 56053 G -s mr.mrrefChr0 19160 1 + 130230 A -s mr.mrrefChr3 82841 1 + 181027 G -s simCow_chr6.simCow.chr6 556635 1 - 602619 A -s simDog_chr6.simDog.chr6 554032 1 - 593897 G -s simHuman_chr6.simHuman.chr6 561691 1 - 601863 G -s simMouse_chr6.simMouse.chr6 531019 1 + 636262 G -s simRat_chr6.simRat.chr6 542103 1 + 647215 A -s simRat_chr6.simRat.chr6 12773 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 20849 20 + 636262 AGCATTCTCTCTAGTCAGCA -s Anc0.Anc0refChr2 15157 20 + 17989 AGCATTCCCTCCAGTAAACA -s Anc1.Anc1refChr2 122686 20 - 144309 AGCATTCCCTCCAGTAAACA -s Anc2.Anc2refChr0 13658 20 - 56053 AGCATTCCCTCCAGTAAACA -s mr.mrrefChr0 19161 20 + 130230 AGCATTCTCTCTAGTCAGCA -s mr.mrrefChr3 86953 20 + 181027 AAATTTACCTCTAGTCAGCA -s simCow_chr6.simCow.chr6 556636 20 - 602619 AGAATCTCCTCCGGTAAACA -s simDog_chr6.simDog.chr6 554033 20 - 593897 AGCATTCCCTCTACTAAACA -s simHuman_chr6.simHuman.chr6 561692 20 - 601863 AGCATTCCCTCCAGTAAACA -s simMouse_chr6.simMouse.chr6 536345 20 + 636262 CAATTCACCTCTGGTCAGCA -s simRat_chr6.simRat.chr6 547139 20 + 647215 aagtttgccTCTAGTCAGCA -s simRat_chr6.simRat.chr6 12778 20 + 647215 AGCACTCCCTCTAGTCAGCA - -a -s simMouse_chr6.simMouse.chr6 20869 6 + 636262 GTCTAA -s Anc0.Anc0refChr2 15177 6 + 17989 CTCTAA -s Anc1.Anc1refChr2 122706 6 - 144309 CTCTAA -s Anc2.Anc2refChr0 13678 6 - 56053 CTCTAA -s mr.mrrefChr0 19181 6 + 130230 GTATAA -s mr.mrrefChr3 86973 6 + 181027 ATCTAA -s simCow_chr6.simCow.chr6 556656 6 - 602619 CTCTAT -s simDog_chr6.simDog.chr6 554055 6 - 593897 ACCTAA -s simHuman_chr6.simHuman.chr6 561712 6 - 601863 CTCTAG -s simMouse_chr6.simMouse.chr6 536365 6 + 636262 ATCCAA -s simRat_chr6.simRat.chr6 547159 6 + 647215 ATCTAA -s simRat_chr6.simRat.chr6 12798 6 + 647215 ATATAA - -a -s simMouse_chr6.simMouse.chr6 20875 15 + 636262 TTAGATTAGACTAAC -s Anc0.Anc0refChr2 15183 15 + 17989 TTAGATGAAACTGAC -s Anc1.Anc1refChr2 122712 15 - 144309 TTAGATGAAACTGAC -s Anc2.Anc2refChr0 13684 15 - 56053 TTAGATGAAACTGAC -s mr.mrrefChr0 19187 15 + 130230 TTAGATTAGACTGAC -s mr.mrrefChr3 86979 15 + 181027 TTAGACAAGACTGAC -s simCow_chr6.simCow.chr6 556662 15 - 602619 TTACATGAAACTGAC -s simDog_chr6.simDog.chr6 554061 15 - 593897 TTAGACGAAACTGAC -s simHuman_chr6.simHuman.chr6 561875 15 - 601863 TTAGATGAAATTGAC -s simMouse_chr6.simMouse.chr6 536371 15 + 636262 TTAGACAAGACTGAC -s simRat_chr6.simRat.chr6 547165 15 + 647215 TTAGATAAGACTGAC -s simRat_chr6.simRat.chr6 12804 15 + 647215 TTAGATAGGACTGAC - -a -s simMouse_chr6.simMouse.chr6 20890 25 + 636262 ACAATTTGTAATCTTGTGCTTTATA -s Anc0.Anc0refChr2 15198 24 + 17989 ACA-TTTCTAAGCTTATGCTTTATA -s Anc1.Anc1refChr2 122727 24 - 144309 ACA-TTTCTAAGCTTATGCTTTATA -s Anc2.Anc2refChr0 13699 24 - 56053 ACA-TTTCTGAGCTGATCCTTTATG -s mr.mrrefChr0 19202 24 + 130230 ACA-TTTGTAATCTTGTGCTTTATA -s mr.mrrefChr3 86994 24 + 181027 ACA-TTTGTAAGCTTGTTCTTTATA -s simCow_chr6.simCow.chr6 556677 24 - 602619 ACT-TTTCTGAGCTGACACTTTATG -s simDog_chr6.simDog.chr6 554076 24 - 593897 ACA-TCTCTGAGCTGGTCCTTTATG -s simHuman_chr6.simHuman.chr6 561890 24 - 601863 ACA-TTTCTAAGCTAATGCTTTATA -s simMouse_chr6.simMouse.chr6 536386 24 + 636262 ACA-TTTGTAAGCTTGTTCTTTATA -s simRat_chr6.simRat.chr6 547187 24 + 647215 ACA-CTTGTAATCTTGTGCTTTTTA -s simRat_chr6.simRat.chr6 12819 24 + 647215 ACA-TTTGTAATCTTGTGCCTAATA - -a -s simMouse_chr6.simMouse.chr6 20915 51 + 636262 ACAAAGGTGTGTGACATACATATAAATTGTGTAATGAGCTGCAGTATCAAC -s Anc0.Anc0refChr2 15222 50 + 17989 ACAG-GGTGTGTGACATACATATAACTTGCCTAAAGAACTGTAGTGTCAAC -s Anc1.Anc1refChr2 122751 51 - 144309 ACAGAGGTGTGTGACATACATATAACTTGCCTAAAGAACTGTAGTGTCAAC -s Anc2.Anc2refChr0 13723 50 - 56053 ACAG-GGTGTCTGACATACATATAACTTGCCCAAAGAACTGTAGTGTCAAG -s mr.mrrefChr0 19226 51 + 130230 ACAAAGGTGTGTGACGTACATATAAATTGTGTAATGAGCTGCAGTGTCAAC -s mr.mrrefChr3 87018 51 + 181027 ACAAAGGTGTGTGACATACATATAAATTGTGTAATGACCTGTAGTGTCAAC -s simCow_chr6.simCow.chr6 556707 50 - 602619 ACAG-GCTGTCTGGCATACATATAACTTGCTCAAAGAACTGTAATGTTGGG -s simDog_chr6.simDog.chr6 554100 50 - 593897 ACAG-GGTGTCTGACATACATATAACTTGCCCAATGAACTGTAGTGTCAAT -s simHuman_chr6.simHuman.chr6 561914 50 - 601863 ACTGCA-TGTTTGATGCACATGTAACTTGCCTAAAGAACTGCAGTGTCAAT -s simMouse_chr6.simMouse.chr6 536410 51 + 636262 ACAAAGTTATGTGACATACATATAAATTGTGTAATGACCTTTAGTGTCAAC -s simRat_chr6.simRat.chr6 547211 51 + 647215 ACAAAGGTGTATGTCATACATATAAATTGTGTGTTGACCTGTAGTGTCCAC -s simRat_chr6.simRat.chr6 12843 51 + 647215 GCAAAGGTGTGTGACGTACATCTAGATTGTGTAATGACCTGTAGTGTCAAC - -a -s simMouse_chr6.simMouse.chr6 20966 80 + 636262 CCCAATTGGGACCTCGTAACGCTTCAGTCTAGAATCAACTTATAAACTATGTGAAATCAATAATGTCAGACACATTGGTC -s Anc0.Anc0refChr2 15272 74 + 17989 C--AATTGGAAGCTTATAATGCTTCAGTTTAGAACCATTTTATGGACCATGTGAAATTAATAATGTCAGACACATT---- -s Anc1.Anc1refChr2 122802 78 - 144309 C--AATTGGAAGCTTATAATGCTTCAGTTTAGAACCATTTTATGGACCATGTGAAATTAATAATGTCAGACACATTGGTG -s Anc2.Anc2refChr0 13773 74 - 56053 C--AATTGGAAGCTTATAATGCTTCAGTTTAGGACCATTCTATGGACCATGTGAAATTAATATTGTCAGATGCTTT---- -s mr.mrrefChr0 19277 78 + 130230 C--AATTGGGACCTTATAATGCTTCAGTTTAGAATCATCTTATAAACCATGTGAAATCAATAATGTCAGACACATTGGTC -s mr.mrrefChr3 87069 78 + 181027 C--AATTGGGACCTTATAATGCTTCAGTCTAGAATCATCTTATGAACCATGTGAAATCAATAATGTCAGACCCATTGGTA -s simCow_chr6.simCow.chr6 556757 74 - 602619 C--AATTGGGAGCTTGTAATACTTCAGCTTAGGACCACTATATGTACCATGTGAAATCAATATTGTCAGATGCTTT---- -s simDog_chr6.simDog.chr6 554150 73 - 593897 C--AATTGGAAGTTTACACCGCTTCTGTGCAGGACCATTCTATGGA-CATGTGAGACTAATATTGTCAGATGCTTT---- -s simHuman_chr6.simHuman.chr6 561970 77 - 601863 C--AATCAAAAGCTTATGATGCTTCAGTTTAGA-CCATTGTATGGACCAGGTGCAAttaataatgtctgacaccttggtg -s simMouse_chr6.simMouse.chr6 536461 75 + 636262 C--AATTGGGTCCTTATAATGCTTCAG---AAAATCATCTTATGAACCATGTGAAATCAATAATGTCAGACCCATTGGTA -s simRat_chr6.simRat.chr6 547262 78 + 647215 C--AATTGGGACCTTATAATGTGTCCGTCTAGAAACATCTTATGAACCCCGTGAAATGAATTCTGTCAGACACATTGGTC -s simRat_chr6.simRat.chr6 12894 78 + 647215 C--AATTGGGATCTTATAATGCTTCAGTTTAGAAACATCTTATAAACCATGTGAAATCAATAATGTCAGACATATTGGTC - -a -s simMouse_chr6.simMouse.chr6 21046 1 + 636262 T -s Anc1.Anc1refChr2 122880 1 - 144309 t -s mr.mrrefChr0 19355 1 + 130230 T -s simHuman_chr6.simHuman.chr6 562047 1 - 601863 t -s simRat_chr6.simRat.chr6 12972 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 21047 21 + 636262 GTATATCTTAAAGTTATGTGT -s Anc1.Anc1refChr2 122881 21 - 144309 ATATATCTTAAAGTTATGTGC -s mr.mrrefChr0 19356 21 + 130230 ATATATCTTAAAGTTATGTGC -s mr.mrrefChr3 87147 21 + 181027 ATATCTCCCAAAGTTTTGTGT -s simHuman_chr6.simHuman.chr6 562048 20 - 601863 acatatc-taaaattatgtac -s simMouse_chr6.simMouse.chr6 536536 21 + 636262 ATATACCCTAAAGTTTTGTGT -s simRat_chr6.simRat.chr6 547341 21 + 647215 ATATCTTCCAAAGTTATGTGT -s simRat_chr6.simRat.chr6 12973 21 + 647215 ATATATCGTAAAGTTATGTGC - -a -s simMouse_chr6.simMouse.chr6 21068 14 + 636262 ATGTGACCCCTAAA -s Anc1.Anc1refChr2 122902 14 - 144309 ATGTGACCCCTCAA -s mr.mrrefChr0 19377 14 + 130230 ATGTGACCCCTCAA -s mr.mrrefChr3 87168 14 + 181027 ATATGACGCCTCAA -s simHuman_chr6.simHuman.chr6 562095 14 - 601863 ctgggatccatcaa -s simMouse_chr6.simMouse.chr6 536557 14 + 636262 ATATGACGCCTCAA -s simRat_chr6.simRat.chr6 547362 14 + 647215 ATGTGACCCTTCAA -s simRat_chr6.simRat.chr6 12994 14 + 647215 ATGTGACCCCTCGA - -a -s simMouse_chr6.simMouse.chr6 21082 6 + 636262 GTGTCT -s Anc0.Anc0refChr2 15346 3 + 17989 ---TCT -s Anc1.Anc1refChr2 122916 6 - 144309 GTGTCT -s Anc2.Anc2refChr0 13847 3 - 56053 ---TCT -s mr.mrrefChr0 19391 6 + 130230 GTGTCT -s mr.mrrefChr3 87182 6 + 181027 GTGTCT -s simCow_chr6.simCow.chr6 556831 3 - 602619 ---TCT -s simDog_chr6.simDog.chr6 554223 3 - 593897 ---TCT -s simHuman_chr6.simHuman.chr6 562110 6 - 601863 gggtCT -s simMouse_chr6.simMouse.chr6 536571 6 + 636262 GTGTCT -s simRat_chr6.simRat.chr6 547376 6 + 647215 GTGTCT -s simRat_chr6.simRat.chr6 13008 6 + 647215 GTGTCT - -a -s simMouse_chr6.simMouse.chr6 21088 2 + 636262 AC -s Anc0.Anc0refChr2 15349 2 + 17989 GC -s Anc1.Anc1refChr2 122922 2 - 144309 GC -s Anc2.Anc2refChr0 13850 2 - 56053 CC -s mr.mrrefChr0 19397 2 + 130230 GC -s mr.mrrefChr3 87188 2 + 181027 gc -s simCow_chr6.simCow.chr6 556834 2 - 602619 CC -s simDog_chr6.simDog.chr6 554227 2 - 593897 CC -s simHuman_chr6.simHuman.chr6 562116 2 - 601863 GC -s simMouse_chr6.simMouse.chr6 536577 2 + 636262 gc -s simRat_chr6.simRat.chr6 547382 2 + 647215 gc -s simRat_chr6.simRat.chr6 13014 2 + 647215 GC - -a -s simMouse_chr6.simMouse.chr6 21090 39 + 636262 ATTGCTGCATTAACATATATGTTAATCTTAGAATCTACA -s Anc0.Anc0refChr2 15351 38 + 17989 ATAGTTGGATTA-TATATAGGCTACTCCTAGAAGTTACA -s Anc1.Anc1refChr2 122924 38 - 144309 ATAGTTGGATTA-TATATAGGCTACTCCTAGAAGTTACA -s Anc2.Anc2refChr0 13852 38 - 56053 ATAGTTGGATAA-CATATAGGCCACTTCTAGCAGTTACA -s mr.mrrefChr0 19399 39 + 130230 ATTGCTGGATTAATATATATGTTAATCTTAGAATTTACA -s simCow_chr6.simCow.chr6 556836 38 - 602619 ACAGTTGGATAA-CATTTAGGCCACTTCAGAGAGTTACA -s simDog_chr6.simDog.chr6 554229 38 - 593897 ATAGTTGGATAA-CATATAGGCCACTTCTAGCAGATACA -s simHuman_chr6.simHuman.chr6 562118 38 - 601863 ATAGTTTGATTT-TATATAGGCTACTCCTCGAAGTTACA -s simRat_chr6.simRat.chr6 13016 39 + 647215 ATTGCTAGATTAATATATATGTTAATCTTAGAACTTACT - -a -s simMouse_chr6.simMouse.chr6 21129 26 + 636262 CATAAGAGGATCAGTGTACATCCCTT -s Anc0.Anc0refChr2 15390 26 + 17989 CCCAGGGGGATCAGCGGTCATTCCCC -s Anc1.Anc1refChr2 122963 26 - 144309 CCCAGGGGGATCAGCGGTCATTCCCC -s Anc2.Anc2refChr0 13891 26 - 56053 CCCAGGGGGATCAGCTGTCATTCCCC -s mr.mrrefChr0 19438 26 + 130230 CCTAAGAGGATCAGTGTACATCCCTT -s simCow_chr6.simCow.chr6 556875 26 - 602619 CCTAAGGGGATCAGCTGTCAGTCCCC -s simDog_chr6.simDog.chr6 554268 22 - 593897 CCCAGGG----CCGCTGTCTTTCTCC -s simHuman_chr6.simHuman.chr6 562157 26 - 601863 CCCAGGGGGATCAGCGATCATTCCCC -s simRat_chr6.simRat.chr6 13055 26 + 647215 CCTAAAAGGATCAGTGTACATCCCTT - -a -s simMouse_chr6.simMouse.chr6 21155 1 + 636262 A -s Anc0.Anc0refChr2 15417 1 + 17989 G -s Anc1.Anc1refChr2 122990 1 - 144309 G -s Anc2.Anc2refChr0 13918 1 - 56053 G -s mr.mrrefChr0 19465 1 + 130230 A -s simCow_chr6.simCow.chr6 556902 1 - 602619 G -s simDog_chr6.simDog.chr6 554291 1 - 593897 G -s simHuman_chr6.simHuman.chr6 562184 1 - 601863 G -s simRat_chr6.simRat.chr6 13082 1 + 647215 C - -a -s simMouse_chr6.simMouse.chr6 21156 6 + 636262 AATGTC -s Anc0.Anc0refChr2 15418 6 + 17989 AATGTC -s Anc1.Anc1refChr2 122991 6 - 144309 AATGTC -s Anc2.Anc2refChr0 13919 6 - 56053 AATGTC -s mr.mrrefChr0 19466 6 + 130230 AATGTC -s simCow_chr6.simCow.chr6 556903 6 - 602619 AATGTC -s simDog_chr6.simDog.chr6 554292 6 - 593897 AATCTC -s simHuman_chr6.simHuman.chr6 562185 6 - 601863 GGTGAC -s simRat_chr6.simRat.chr6 13088 6 + 647215 AATGTC - -a -s simMouse_chr6.simMouse.chr6 21162 71 + 636262 CCATGTATCTGCACTAGTCATTTATACAAAGTTCAATAGTTTCTATATCTTAGTATTTACTTGATATTGCA -s Anc0.Anc0refChr2 15434 69 + 17989 CCATGTATCTGCAGTCATCATTTATGTGTATGCCAGTAGTCCCTATATCTTAGTATTGACTTGAT--CGAA -s Anc1.Anc1refChr2 123007 69 - 144309 CCATGTATCTGCAGTCATCATTTATGTGTATGCCAGTAGTCCCTATATCTTAGTATTGACTTGAT--CGAA -s Anc2.Anc2refChr0 13935 69 - 56053 CCAAGTATCTACAGCCAGTATTTATGTATATGCCAGTAGTCCCTACATCTTAGCATTGACTAGAT--TGAA -s mr.mrrefChr0 19472 71 + 130230 CCATGTATCTGCACTAGTCATTTATACGTAGTTCAATAGTTCCTATATCTTAGTATTTACTTGATATCGCA -s simCow_chr6.simCow.chr6 556919 57 - 602619 AC---TATCTA---------TGTATGTATATGCCAGTAGTCTATACATCTCAGCATTGACTAGAT--TGAA -s simDog_chr6.simDog.chr6 554308 59 - 593897 CCAAGTAACTACAGCCAGTAGT---------CCCAGTAGTCCCTACATCTTAGCATTCA-TAGAT--TGAA -s simHuman_chr6.simHuman.chr6 562201 69 - 601863 CCATGTATCTGCAATCTTCATTTGTGTGTCAGCCAGTGGTCCCTTTATCTTACTATTGATTTGAT--CGAA -s simRat_chr6.simRat.chr6 13094 71 + 647215 CCATGTATCTGTACTAGTCTTTTAGACGTAGTTCAATAGTTCTTATATCTTAGTATTTACTTGATACCGCA - -a -s simMouse_chr6.simMouse.chr6 21233 24 + 636262 GGTTTTGAGCATGAGGCTCACATC -s Anc0.Anc0refChr2 15504 24 + 17989 TATTTTGAGCATAAGGGTCACATC -s Anc1.Anc1refChr2 123077 24 - 144309 TATTTTGAGCATAAGGGTCACATC -s Anc2.Anc2refChr0 14009 24 - 56053 TATTTTGAGCATAAGGGTCACATC -s mr.mrrefChr0 19543 24 + 130230 GATTTTGAGCATGAGGCTCACATC -s simCow_chr6.simCow.chr6 556981 24 - 602619 TATTGTGAGCTTAAGGGTCACATC -s simDog_chr6.simDog.chr6 554372 24 - 593897 TATTTTAAGCATAATGGTCAAATC -s simHuman_chr6.simHuman.chr6 562271 24 - 601863 TATTTTGAACATAAGGGTCACATC -s simRat_chr6.simRat.chr6 13165 24 + 647215 GATTTTGAGCATGAGGATCACATG - -a -s simMouse_chr6.simMouse.chr6 21257 31 + 636262 CAGTGGCTGTCCATCAACCAACCCATCCATA -s Anc0.Anc0refChr2 15528 31 + 17989 CAGTGGCTGTCCATTGAAAAACCTATCCACA -s Anc1.Anc1refChr2 123101 31 - 144309 CAGTGGCTGTCCATTGAAAAACCTATCCACA -s Anc2.Anc2refChr0 14033 31 - 56053 CAGTGGCAGTCCATTGTAAAACCTATCCACA -s mr.mrrefChr0 19567 31 + 130230 CAGTGGCTGTCCATCAACAAACCTATCCATA -s simCow_chr6.simCow.chr6 557005 31 - 602619 CAGTGGCAGTCCATTGGAAAACCTACCTATG -s simDog_chr6.simDog.chr6 554396 31 - 593897 CAGTGGCAGTCCATTGTAAAACCTATCCACA -s simHuman_chr6.simHuman.chr6 562309 31 - 601863 CAGTGGCTGCCCATTGAAAAACTTAGCCACA -s simRat_chr6.simRat.chr6 13189 31 + 647215 CAGTGGCTGTCCATCAACAAATCTATCCATA - -a -s simMouse_chr6.simMouse.chr6 21288 94 + 636262 GGTCATGAAAATACAGGTCTTTGCTTCCCTTGTCATGAGAATAATCTCTGAATACCACAGGTAAAAGGATATGGTTACAGCTAGGTCTTTTTTA -s Anc0.Anc0refChr2 15559 93 + 17989 ACTCATGGGAGTACATGCTTTTCCTTCCTTGTTCTTAATAGTGATCTCTCAATCCCCCATGCAAAAGGAAATGATTATA-CTAGTCCTCCTTTA -s Anc1.Anc1refChr2 123132 93 - 144309 ACTCATGGGAGTACATGCTTTTCCTTCCTTGTTCTTAATAGTGATCTCTCAATCCCCCATGCAAAAGGAAATGATTATA-CTAGTCCTCCTTTA -s Anc2.Anc2refChr0 14082 93 - 56053 ACTCATTGGAGTACATGCTTTTCCTTCCTGGTTCTCAATAGTGGTCTCTCAATCTCCCATGCAAAAGGAAATGATTATA-CTAGTCCTCCTTTA -s mr.mrrefChr0 19598 94 + 130230 GGTCATGAAAATACATGTCTTTGCTTCCCTTGTCTTGAGAATGATCTCTGAATACCACATGTAAAAGGATATGGTTACAGCTAGTCCTTTTTTA -s simCow_chr6.simCow.chr6 557054 77 - 602619 ACT-----GAGTACATGCCTTTCCTTGCTGCTTCTCAATAGTGGTCTCACAATCTTCCATG-----------GATTATA-CTACTCCTCCTTCA -s simDog_chr6.simDog.chr6 554445 93 - 593897 ACTCATTGGATTACATGCTTTTCCTTCCTGGTACCCAGTTGCAGTTTCTCAATCTCCCATGCAAAAGGAAATGATTATG-CTAGCCCTAGGTTA -s simHuman_chr6.simHuman.chr6 562340 93 - 601863 ACTCGTGCGAGTACATACTCTCCCTTCCTTGTTCTTCATACTGATCTCCAAACTCCCTATCCAGAAGGAAATAATTATA-CTAGTCGTCCTTTA -s simRat_chr6.simRat.chr6 13220 93 + 647215 GGTCATGGAA-TACATGTCTTTGCTTCCCTTGTCTTTAAGATGATCTCTGAATACCACATGTAAAAGGATATGGTTACAGCTAGTCATTTTTTA - -a -s simMouse_chr6.simMouse.chr6 21382 13 + 636262 CCGAAATTGTTTT -s Anc0.Anc0refChr2 15687 13 + 17989 CTGAGCTCATTTC -s Anc1.Anc1refChr2 123260 13 - 144309 CTGAGCTCATTTC -s Anc2.Anc2refChr0 14212 13 - 56053 CTAAGCTCATTTC -s mr.mrrefChr0 19692 13 + 130230 CCGAGCTTGTTTT -s simCow_chr6.simCow.chr6 557168 13 - 602619 CTAAGCTCCTTTC -s simDog_chr6.simDog.chr6 554645 13 - 593897 CCAAACTAACTTC -s simHuman_chr6.simHuman.chr6 562471 13 - 601863 CTGAGCTCATTTC -s simRat_chr6.simRat.chr6 13313 13 + 647215 CCGAGCTTGATTT - -a -s simMouse_chr6.simMouse.chr6 21395 43 + 636262 CTGCAGTTTATCCAACACACCTCCAGTTATGCAAATACTTGCA -s Anc0.Anc0refChr2 15711 43 + 17989 CTGCAGATAATACAGGACACTTCCAATTGAGTAAATACTTTCA -s Anc1.Anc1refChr2 123284 43 - 144309 CTGCAGATAATACAGGACACTTCCAATTGAGTAAATACTTTCA -s Anc2.Anc2refChr0 14236 43 - 56053 CTCCAGATAATACAGGACACTGCCAATTGAGTAAATACTTTCA -s mr.mrrefChr0 19705 43 + 130230 CTGCAGTTTATCCAACACACTTCCAGTTATGCAAATACTTGCA -s simCow_chr6.simCow.chr6 557192 43 - 602619 CACTAGATGATACACGACACTCCCAATTGAGTAAATACTTCCA -s simDog_chr6.simDog.chr6 554669 43 - 593897 CTCCAGAGAATACAGGATGCTGCGAATTGAGTAAATACTTTCA -s simHuman_chr6.simHuman.chr6 562495 43 - 601863 CTGAAGATAATAAAGGACACTTCCAAATGAGTAAATACATTCA -s simRat_chr6.simRat.chr6 13326 43 + 647215 CTGTACTTTATCCAACACACTCCCAGCTATGCAAATACTTGCA - -a -s simMouse_chr6.simMouse.chr6 21438 6 + 636262 TTTCTT -s Anc0.Anc0refChr2 15754 6 + 17989 TTTCTT -s Anc1.Anc1refChr2 123327 6 - 144309 TTTCTT -s Anc2.Anc2refChr0 14279 6 - 56053 TTTCTA -s mr.mrrefChr0 19748 6 + 130230 TTTCTT -s mr.mrrefChr3 179255 6 + 181027 TTGCTT -s simCow_chr6.simCow.chr6 557235 6 - 602619 TTTCTG -s simDog_chr6.simDog.chr6 554712 6 - 593897 TTTCAA -s simHuman_chr6.simHuman.chr6 562538 5 - 601863 TTACT- -s simMouse_chr6.simMouse.chr6 633161 6 + 636262 TTGCTT -s simRat_chr6.simRat.chr6 644335 6 + 647215 TCAGTC -s simRat_chr6.simRat.chr6 13369 6 + 647215 TTTCTT - -a -s simMouse_chr6.simMouse.chr6 21444 11 + 636262 CACTATGTAGA -s Anc0.Anc0refChr2 15760 10 + 17989 CACCATGTAT- -s Anc1.Anc1refChr2 123333 11 - 144309 CACCATGTATA -s Anc2.Anc2refChr0 14285 10 - 56053 CACCATGTCT- -s mr.mrrefChr0 19754 11 + 130230 CACTATGTAGA -s mr.mrrefChr3 179263 11 + 181027 CACCTTTTATC -s simCow_chr6.simCow.chr6 557241 10 - 602619 CACCATGAAT- -s simDog_chr6.simDog.chr6 554718 10 - 593897 CACCATGTCT- -s simHuman_chr6.simHuman.chr6 562543 7 - 601863 -ACTGTTT--- -s simMouse_chr6.simMouse.chr6 633169 11 + 636262 CACCTTTTATT -s simRat_chr6.simRat.chr6 644343 11 + 647215 CACCTTTTATC -s simRat_chr6.simRat.chr6 13375 11 + 647215 CATTATGTAGG - -a -s simMouse_chr6.simMouse.chr6 21455 14 + 636262 CGTGGAAGCCTTCT -s Anc0.Anc0refChr2 15770 14 + 17989 TCTGGAAACCTTCT -s Anc1.Anc1refChr2 123344 14 - 144309 TCTGGAAACCTTCT -s Anc2.Anc2refChr0 14295 14 - 56053 TCTGGAAACCTTCT -s mr.mrrefChr0 19765 14 + 130230 TGTGGAAGCCTTCT -s mr.mrrefChr3 179570 14 + 181027 TGTGTAGATCATCC -s simCow_chr6.simCow.chr6 557251 14 - 602619 TCTGGAAACCTTCT -s simDog_chr6.simDog.chr6 554728 14 - 593897 TCTGGAAATCATCC -s simHuman_chr6.simHuman.chr6 562550 14 - 601863 TCTGGAAACCTTCT -s simMouse_chr6.simMouse.chr6 633490 14 + 636262 TGTGTAGATCATCC -s simRat_chr6.simRat.chr6 644663 14 + 647215 CGTGTAGATCATCC -s simRat_chr6.simRat.chr6 13386 14 + 647215 TGTGGAAGCCTTCT - -a -s simMouse_chr6.simMouse.chr6 21469 7 + 636262 GAGAGCC -s Anc0.Anc0refChr2 15800 7 + 17989 AAGGGCC -s Anc1.Anc1refChr2 123374 7 - 144309 AAGGGCC -s Anc2.Anc2refChr0 14328 7 - 56053 AAGGGCC -s mr.mrrefChr0 19779 7 + 130230 GAGGGCC -s mr.mrrefChr3 179601 7 + 181027 AAGGGCA -s simCow_chr6.simCow.chr6 557286 7 - 602619 AAGGTCC -s simDog_chr6.simDog.chr6 554762 7 - 593897 AAGGGCC -s simHuman_chr6.simHuman.chr6 562580 7 - 601863 AAGGGCC -s simMouse_chr6.simMouse.chr6 633521 7 + 636262 AAGGGCA -s simRat_chr6.simRat.chr6 644694 7 + 647215 AAGGGCA -s simRat_chr6.simRat.chr6 13400 7 + 647215 GAGGACC - -a -s simMouse_chr6.simMouse.chr6 21476 33 + 636262 AAGCTTGTGCTAGCAAAATGGATGCAGGAAAAT -s Anc0.Anc0refChr2 15807 32 + 17989 AAGCT-GTGTTGGCTAAATAGATGCAAATTTAT -s Anc1.Anc1refChr2 123381 32 - 144309 AAGCT-GTGTTGGCTAAATAGATGCAAATTTAT -s Anc2.Anc2refChr0 14335 32 - 56053 AAGCT-GTGTTGGCTAAATAGATGCAAATTTAC -s mr.mrrefChr0 19786 32 + 130230 AAGCT-GTGCTGGCAAAATAGATGCAGGAAAAT -s mr.mrrefChr3 179608 32 + 181027 AACCT-GTGGCGGTTAAAAAGGCACTAATTTCT -s simCow_chr6.simCow.chr6 557293 32 - 602619 AAGCC-AACTTGGCTAAATAGATGCTAATTTAC -s simDog_chr6.simDog.chr6 554769 32 - 593897 AGGCT-GTGTTGGCTAAATAGATTCAAATTTAC -s simDog_chr6.simDog.chr6 591574 32 + 593897 AATCT-GTGATAGCTGGATAGATGTACATAAAG -s simHuman_chr6.simHuman.chr6 562587 29 - 601863 AAGCT-GTGTTGCCTAAATAGATGCAAAT---T -s simMouse_chr6.simMouse.chr6 633528 32 + 636262 AACCT-GTGGCGGTTAAAAAGGCACTAATTTCT -s simRat_chr6.simRat.chr6 644701 32 + 647215 AACCT-GTGGTGATTAAAAAGGCACTAATTTCT -s simRat_chr6.simRat.chr6 13407 31 + 647215 AAGCT-GTGATGGC-AAAGAGATGCTGGAAAAT - -a -s simMouse_chr6.simMouse.chr6 21509 1 + 636262 A -s Anc0.Anc0refChr2 15841 1 + 17989 A -s Anc1.Anc1refChr2 123415 1 - 144309 A -s Anc2.Anc2refChr0 14369 1 - 56053 A -s mr.mrrefChr0 19820 1 + 130230 A -s mr.mrrefChr3 179642 1 + 181027 A -s simCow_chr6.simCow.chr6 557327 1 - 602619 T -s simDog_chr6.simDog.chr6 554803 1 - 593897 A -s simDog_chr6.simDog.chr6 591608 1 + 593897 A -s simHuman_chr6.simHuman.chr6 562618 1 - 601863 A -s simMouse_chr6.simMouse.chr6 633562 1 + 636262 A -s simRat_chr6.simRat.chr6 644735 1 + 647215 A -s simRat_chr6.simRat.chr6 13440 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 21510 26 + 636262 ACAAAGTTGTCTGAGGCATAACTTCA -s Anc0.Anc0refChr2 15845 26 + 17989 ACAAAATTGTCTGACAGAAGACTTGG -s Anc1.Anc1refChr2 123419 26 - 144309 ACAAAATTGTCTGACAGAAGACTTGG -s Anc2.Anc2refChr0 14373 26 - 56053 ACAAAATTGTCTGACAGAAGTCTAGG -s mr.mrrefChr0 19821 26 + 130230 ACAAAGTTGTCTGAGGCATAACTTGA -s mr.mrrefChr3 179646 26 + 181027 ACAAAATTGTCTGATAGAAGGCTTAG -s simCow_chr6.simCow.chr6 557332 26 - 602619 ACATAATTGTCTGTCAGAAGTCTAGG -s simDog_chr6.simDog.chr6 554807 26 - 593897 AACCAATTGTCTTACAGAAGTTTTGG -s simDog_chr6.simDog.chr6 591612 26 + 593897 GCAAAATTGTCTGACAGAATACCAGA -s simHuman_chr6.simHuman.chr6 562619 26 - 601863 GCAAAATTGACTGGCAGATGACTTGG -s simMouse_chr6.simMouse.chr6 633566 26 + 636262 ACAAAATTGTCTGATAGAAGGCTTAG -s simRat_chr6.simRat.chr6 644739 26 + 647215 AAAAAATTGTCTGATAGAAGACTTCG -s simRat_chr6.simRat.chr6 13441 26 + 647215 AGAAAGTTGTCTGAGGAACAACTTGA - -a -s simMouse_chr6.simMouse.chr6 21536 25 + 636262 TCATGCCATATCACATACATGGGTA -s Anc0.Anc0refChr2 15871 23 + 17989 TCATGCATGATCA--TGCAAAGGTA -s Anc1.Anc1refChr2 123445 23 - 144309 TCATGCATGATCA--TGCAAAGGTA -s Anc2.Anc2refChr0 14399 23 - 56053 TCATACATGATCA--TGCAAAAGTA -s mr.mrrefChr0 19847 23 + 130230 TCATGCCATATCA--TACATGGGTA -s mr.mrrefChr3 179672 23 + 181027 TGATTCATGATTG--TGTAGAGGCA -s simCow_chr6.simCow.chr6 557358 14 - 602619 TCATACAGGATCA--T--------- -s simDog_chr6.simDog.chr6 554833 23 - 593897 TCACACATAATCA--TGCATATGTA -s simDog_chr6.simDog.chr6 591638 23 + 593897 TCATGCATGATAA--TGAAACAGGA -s simHuman_chr6.simHuman.chr6 562645 23 - 601863 TCATGCATGATCA--TCCAAAGGTA -s simMouse_chr6.simMouse.chr6 633592 23 + 636262 TGATTCATGATTG--TGTAGAGGCA -s simRat_chr6.simRat.chr6 644766 23 + 647215 TGATTCATGCTTG--TGTAAAGGCA -s simRat_chr6.simRat.chr6 13467 23 + 647215 TCATGCCATATGA--TGCAGGGGTA - -a -s simMouse_chr6.simMouse.chr6 21561 4 + 636262 GAAA -s Anc0.Anc0refChr2 15894 4 + 17989 AGCT -s Anc1.Anc1refChr2 123468 4 - 144309 AGCT -s Anc2.Anc2refChr0 14422 4 - 56053 AGCT -s mr.mrrefChr0 19870 4 + 130230 GAAA -s mr.mrrefChr3 179695 4 + 181027 GGAA -s simDog_chr6.simDog.chr6 554856 4 - 593897 GGCT -s simDog_chr6.simDog.chr6 591661 4 + 593897 ATCT -s simHuman_chr6.simHuman.chr6 562668 4 - 601863 AGCT -s simMouse_chr6.simMouse.chr6 633616 4 + 636262 GGAA -s simRat_chr6.simRat.chr6 644789 4 + 647215 GGCA -s simRat_chr6.simRat.chr6 13490 4 + 647215 GAAT - -a -s simMouse_chr6.simMouse.chr6 21565 1 + 636262 A -s mr.mrrefChr0 19874 1 + 130230 A -s simRat_chr6.simRat.chr6 13494 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 21566 33 + 636262 TATATGAAGGTTCTTGTTTTAGTGGTATGACCT -s Anc0.Anc0refChr2 15898 33 + 17989 TATAGGAATGTTCTGGTTCCAGGGGGATGACCC -s Anc1.Anc1refChr2 123472 33 - 144309 TATAGGAATGTTCTGGTTCCAGGGGGATGACCC -s Anc2.Anc2refChr0 14426 33 - 56053 TATAGGAATGTTCTGGTTCCAGGGGGATGACCC -s mr.mrrefChr0 19877 33 + 130230 TATATGAATGTTCTTGTTTTAGTGGTATGACCT -s mr.mrrefChr3 179699 33 + 181027 TATGGGAATGCTCTGATTTCATGGGGGAGGCTT -s simCow_chr6.simCow.chr6 557372 25 - 602619 --------TGTTCTGGCTCCAGGGGAATGACCC -s simDog_chr6.simDog.chr6 554860 33 - 593897 TATAGGAATGTCCAGGTTCTGGGGGGATCACCC -s simDog_chr6.simDog.chr6 591665 33 + 593897 CATAGGAATGTTCTGCTTCAAGGCATATGACCC -s simHuman_chr6.simHuman.chr6 562672 33 - 601863 TACAAAAATGTTTTGGTTCCAGCGGGGTGACCC -s simMouse_chr6.simMouse.chr6 633620 33 + 636262 TATGGGAATGCTCTGATTTCATGGGGGAGGCTT -s simRat_chr6.simRat.chr6 644793 33 + 647215 TATGGGGATGTTCTGGTTTCAGGGGGGAGGCTT -s simRat_chr6.simRat.chr6 13502 33 + 647215 TATATGAATGTCCTTGTTTTAGGGGTATGACCT - -a -s simMouse_chr6.simMouse.chr6 21599 7 + 636262 ATTGGTT -s Anc0.Anc0refChr2 15932 7 + 17989 ATTGGTT -s Anc1.Anc1refChr2 123506 7 - 144309 ATTGGTT -s Anc2.Anc2refChr0 14460 7 - 56053 ATTAGTT -s mr.mrrefChr0 19910 7 + 130230 ATTGGTT -s mr.mrrefChr3 179733 7 + 181027 ATTGGTT -s simCow_chr6.simCow.chr6 557398 7 - 602619 ATTAGTT -s simDog_chr6.simDog.chr6 554894 7 - 593897 GTCAGTT -s simDog_chr6.simDog.chr6 591699 7 + 593897 ATTGGTC -s simHuman_chr6.simHuman.chr6 562706 7 - 601863 ATTGGTT -s simMouse_chr6.simMouse.chr6 633654 7 + 636262 ATTGGTT -s simRat_chr6.simRat.chr6 644827 7 + 647215 ATTGGCT -s simRat_chr6.simRat.chr6 13535 7 + 647215 ATTGGTT - -a -s simMouse_chr6.simMouse.chr6 21606 4 + 636262 TTCT -s Anc0.Anc0refChr2 15939 4 + 17989 TTCC -s Anc1.Anc1refChr2 123513 4 - 144309 TTCC -s Anc2.Anc2refChr0 14467 4 - 56053 TTCC -s mr.mrrefChr0 19917 4 + 130230 TTCT -s mr.mrrefChr3 179740 4 + 181027 TTCC -s simCow_chr6.simCow.chr6 557405 4 - 602619 TTGC -s simDog_chr6.simDog.chr6 591706 4 + 593897 TTCC -s simHuman_chr6.simHuman.chr6 562713 4 - 601863 ATCC -s simMouse_chr6.simMouse.chr6 633661 4 + 636262 TTCC -s simRat_chr6.simRat.chr6 644834 4 + 647215 TTCA -s simRat_chr6.simRat.chr6 13542 4 + 647215 TTCT - -a -s simMouse_chr6.simMouse.chr6 21610 6 + 636262 TAGGCA -s Anc0.Anc0refChr2 15943 6 + 17989 TGGACA -s Anc1.Anc1refChr2 123517 6 - 144309 TGGACA -s Anc2.Anc2refChr0 14471 6 - 56053 TGGACA -s mr.mrrefChr0 19921 6 + 130230 TAGACA -s simCow_chr6.simCow.chr6 557409 6 - 602619 TGGACA -s simDog_chr6.simDog.chr6 591710 6 + 593897 TGGACA -s simHuman_chr6.simHuman.chr6 562717 6 - 601863 GGGACC -s simRat_chr6.simRat.chr6 13546 6 + 647215 TAGACA - -a -s simMouse_chr6.simMouse.chr6 21616 5 + 636262 TTTCA -s Anc0.Anc0refChr2 15949 5 + 17989 TTCCA -s Anc1.Anc1refChr2 123523 5 - 144309 TTCCA -s Anc2.Anc2refChr0 14477 5 - 56053 TTCCA -s mr.mrrefChr0 19927 5 + 130230 TTTCA -s simCow_chr6.simCow.chr6 557415 5 - 602619 GTTCA -s simDog_chr6.simDog.chr6 554901 5 - 593897 TTCCA -s simDog_chr6.simDog.chr6 591716 5 + 593897 TTCCA -s simHuman_chr6.simHuman.chr6 562723 5 - 601863 TTCCA -s simRat_chr6.simRat.chr6 13552 5 + 647215 TTTGA - -a -s simMouse_chr6.simMouse.chr6 21621 6 + 636262 GCCATT -s Anc0.Anc0refChr2 15954 6 + 17989 ATTCGG -s Anc1.Anc1refChr1 67673 6 + 69767 ATCCGG -s Anc1.Anc1refChr2 123528 6 - 144309 GTTCCT -s Anc2.Anc2refChr0 14482 6 - 56053 GTTCTC -s Anc2.Anc2refChr1 140742 6 + 142988 ACTTGG -s mr.mrrefChr0 19932 6 + 130230 GCCACT -s mr.mrrefChr3 179951 6 + 181027 ATCCGA -s simCow_chr6.simCow.chr6 599922 6 + 602619 ACTTGG -s simCow_chr6.simCow.chr6 557420 6 - 602619 GCTCTT -s simDog_chr6.simDog.chr6 554906 6 - 593897 ATTCTC -s simDog_chr6.simDog.chr6 591721 5 + 593897 GTCCT- -s simHuman_chr6.simHuman.chr6 599774 6 + 601863 GTCCTC -s simHuman_chr6.simHuman.chr6 562728 6 - 601863 GTTCCT -s simMouse_chr6.simMouse.chr6 633873 6 + 636262 ATCTGA -s simRat_chr6.simRat.chr6 645059 6 + 647215 ATCCAA -s simRat_chr6.simRat.chr6 13557 6 + 647215 GCCACT - -a -s simMouse_chr6.simMouse.chr6 21627 2 + 636262 TA -s Anc0.Anc0refChr2 15961 2 + 17989 TG -s Anc1.Anc1refChr1 67680 2 + 69767 AA -s Anc1.Anc1refChr2 123534 2 - 144309 TG -s Anc2.Anc2refChr0 14491 2 - 56053 TG -s Anc2.Anc2refChr1 140749 2 + 142988 TG -s mr.mrrefChr0 19938 2 + 130230 TA -s mr.mrrefChr3 179958 2 + 181027 AA -s simCow_chr6.simCow.chr6 599929 2 + 602619 TG -s simCow_chr6.simCow.chr6 557429 2 - 602619 TG -s simDog_chr6.simDog.chr6 554915 2 - 593897 TG -s simDog_chr6.simDog.chr6 591727 2 + 593897 CA -s simHuman_chr6.simHuman.chr6 599781 2 + 601863 AA -s simHuman_chr6.simHuman.chr6 562734 2 - 601863 TG -s simMouse_chr6.simMouse.chr6 633880 2 + 636262 AA -s simRat_chr6.simRat.chr6 645066 2 + 647215 AA -s simRat_chr6.simRat.chr6 13563 2 + 647215 TA - -a -s simMouse_chr6.simMouse.chr6 21629 2 + 636262 AT -s Anc0.Anc0refChr2 15965 2 + 17989 AT -s Anc1.Anc1refChr2 123538 2 - 144309 AT -s Anc2.Anc2refChr0 14495 2 - 56053 AT -s mr.mrrefChr0 19940 2 + 130230 AT -s simCow_chr6.simCow.chr6 557433 2 - 602619 TT -s simDog_chr6.simDog.chr6 554919 2 - 593897 AT -s simDog_chr6.simDog.chr6 591734 2 + 593897 AT -s simHuman_chr6.simHuman.chr6 562738 2 - 601863 AT -s simRat_chr6.simRat.chr6 13565 2 + 647215 AT - -a -s simMouse_chr6.simMouse.chr6 21631 3 + 636262 ATG -s Anc0.Anc0refChr2 15967 3 + 17989 ATA -s Anc1.Anc1refChr1 67683 3 + 69767 ATA -s Anc1.Anc1refChr2 123540 3 - 144309 ATG -s Anc2.Anc2refChr0 14497 3 - 56053 ATA -s Anc2.Anc2refChr1 140752 3 + 142988 ATA -s mr.mrrefChr0 19942 3 + 130230 ATG -s mr.mrrefChr3 179961 3 + 181027 ATA -s simCow_chr6.simCow.chr6 599932 3 + 602619 ATA -s simCow_chr6.simCow.chr6 557435 3 - 602619 ATA -s simDog_chr6.simDog.chr6 554921 3 - 593897 ATA -s simDog_chr6.simDog.chr6 591736 3 + 593897 ATG -s simHuman_chr6.simHuman.chr6 599784 3 + 601863 ATA -s simHuman_chr6.simHuman.chr6 562740 3 - 601863 GTG -s simMouse_chr6.simMouse.chr6 633883 3 + 636262 CTA -s simRat_chr6.simRat.chr6 645069 3 + 647215 ATA -s simRat_chr6.simRat.chr6 13567 3 + 647215 AGG - -a -s simMouse_chr6.simMouse.chr6 21634 3 + 636262 GTG -s Anc0.Anc0refChr2 15970 3 + 17989 ATG -s Anc1.Anc1refChr1 67686 3 + 69767 ATG -s Anc1.Anc1refChr2 123543 3 - 144309 ATG -s Anc2.Anc2refChr0 14500 3 - 56053 ATG -s Anc2.Anc2refChr1 140755 3 + 142988 ATG -s mr.mrrefChr0 19945 3 + 130230 GTG -s mr.mrrefChr3 179964 3 + 181027 ATA -s simCow_chr6.simCow.chr6 599936 3 + 602619 ATG -s simCow_chr6.simCow.chr6 557438 3 - 602619 ATG -s simDog_chr6.simDog.chr6 554924 3 - 593897 ATG -s simDog_chr6.simDog.chr6 591739 3 + 593897 ATG -s simHuman_chr6.simHuman.chr6 599787 3 + 601863 ATG -s simHuman_chr6.simHuman.chr6 562743 3 - 601863 ATG -s simMouse_chr6.simMouse.chr6 633886 3 + 636262 ATA -s simRat_chr6.simRat.chr6 645072 3 + 647215 ACA -s simRat_chr6.simRat.chr6 13570 3 + 647215 GTG - -a -s simMouse_chr6.simMouse.chr6 21637 8 + 636262 GGTTCTAA -s Anc0.Anc0refChr2 15973 8 + 17989 AGTCCTAC -s Anc1.Anc1refChr1 67694 8 + 69767 AGTCCTAC -s Anc1.Anc1refChr2 123546 8 - 144309 GGTCCTAC -s Anc2.Anc2refChr0 14503 8 - 56053 AGTCCTAC -s Anc2.Anc2refChr1 140758 8 + 142988 TAAACTAC -s mr.mrrefChr0 19948 8 + 130230 GGTCCTAC -s mr.mrrefChr3 179972 8 + 181027 AGTCCTAC -s simCow_chr6.simCow.chr6 599939 8 + 602619 TAAACTAC -s simCow_chr6.simCow.chr6 557441 7 - 602619 A-TCCTAC -s simDog_chr6.simDog.chr6 554927 8 - 593897 GGTCCTAC -s simDog_chr6.simDog.chr6 591742 8 + 593897 AGTCATAT -s simHuman_chr6.simHuman.chr6 599795 8 + 601863 AGTCCTAC -s simHuman_chr6.simHuman.chr6 562746 8 - 601863 GGTCCTAC -s simMouse_chr6.simMouse.chr6 633894 8 + 636262 AGTCCTCA -s simRat_chr6.simRat.chr6 645080 8 + 647215 AGTCCTAC -s simRat_chr6.simRat.chr6 13573 8 + 647215 GGTCGTAC - -a -s simMouse_chr6.simMouse.chr6 21645 5 + 636262 AAAGT -s Anc0.Anc0refChr2 15981 5 + 17989 AACAG -s Anc1.Anc1refChr1 67702 5 + 69767 AACAG -s Anc1.Anc1refChr2 123554 5 - 144309 AATAG -s Anc2.Anc2refChr0 14511 5 - 56053 GATAG -s Anc2.Anc2refChr1 140771 5 + 142988 AACGG -s mr.mrrefChr0 19956 5 + 130230 AAAGT -s mr.mrrefChr3 179980 5 + 181027 AAGAG -s simCow_chr6.simCow.chr6 599952 5 + 602619 AACGG -s simCow_chr6.simCow.chr6 557448 5 - 602619 AAGAG -s simDog_chr6.simDog.chr6 554935 5 - 593897 GATAG -s simDog_chr6.simDog.chr6 591750 5 + 593897 GAAAG -s simHuman_chr6.simHuman.chr6 599803 5 + 601863 AAAAG -s simHuman_chr6.simHuman.chr6 562754 5 - 601863 AATAG -s simMouse_chr6.simMouse.chr6 633902 5 + 636262 AAGAG -s simRat_chr6.simRat.chr6 645088 5 + 647215 AAGGG -s simRat_chr6.simRat.chr6 13581 5 + 647215 ACAGT - -a -s simMouse_chr6.simMouse.chr6 21650 3 + 636262 GCT -s Anc0.Anc0refChr2 15986 3 + 17989 GCC -s Anc1.Anc1refChr1 67707 3 + 69767 GCC -s Anc1.Anc1refChr2 123559 3 - 144309 GCT -s Anc2.Anc2refChr0 14516 1 - 56053 --C -s Anc2.Anc2refChr1 140776 3 + 142988 GCC -s mr.mrrefChr0 19961 3 + 130230 GCT -s mr.mrrefChr3 179985 3 + 181027 GCA -s simCow_chr6.simCow.chr6 599957 3 + 602619 ACC -s simCow_chr6.simCow.chr6 557453 1 - 602619 --C -s simDog_chr6.simDog.chr6 591755 3 + 593897 GCC -s simHuman_chr6.simHuman.chr6 599808 3 + 601863 GCG -s simHuman_chr6.simHuman.chr6 562759 3 - 601863 GCT -s simMouse_chr6.simMouse.chr6 633907 3 + 636262 GGA -s simRat_chr6.simRat.chr6 645093 3 + 647215 GCA -s simRat_chr6.simRat.chr6 13586 3 + 647215 GCT - -a -s simMouse_chr6.simMouse.chr6 21653 36 + 636262 CTCCCCAGTATGCCTTCCTTAAGGGCTAAGGTATAG -s Anc0.Anc0refChr2 15990 36 + 17989 TACCCCATTAGACCTTCCTTAGGAGATAAATCGTAG -s Anc1.Anc1refChr1 67711 36 + 69767 TACCCCATTAGGCCTTCCTTCGGAGATAAATCGTAG -s Anc1.Anc1refChr2 123563 36 - 144309 TACCCCATTAGACCTTCCTTAGGAGATAAAGCATAG -s Anc2.Anc2refChr0 14518 36 - 56053 TACCCCATTAGATCTTCCTTAGAAGACAAATCATAG -s Anc2.Anc2refChr1 140780 36 + 142988 TACCCCATTAGGCCTTCCTTTGGAGATAAATCGTAG -s mr.mrrefChr0 19965 36 + 130230 CTCCCCAGTATGCCTTCCTTAAGGGCTAAAGCATAG -s mr.mrrefChr3 179989 36 + 181027 TACACCATTAGACCCTCCTTCAGAGATAAATTATAA -s simCow_chr6.simCow.chr6 599961 36 + 602619 TACCCCATTAGACCTTCCATAGAAGATAAATCATTT -s simCow_chr6.simCow.chr6 557455 24 - 602619 TACCCCATTAGAACTTCCT------------CATAG -s simDog_chr6.simDog.chr6 591759 36 + 593897 TACTGCATGAAGCCTTCCTTTGGAGATAAATTGTAG -s simDog_chr6.simDog.chr6 554940 29 - 593897 -------CTAGATCTTCCCTAGAAGACAAATCATAG -s simHuman_chr6.simHuman.chr6 599812 36 + 601863 TACCCGATTAGGCCTTCCTTCGGAGATAAATCCTAG -s simHuman_chr6.simHuman.chr6 562763 36 - 601863 TACCTCATTGAACCTTCCTCAGGAGATAAAGCATAG -s simMouse_chr6.simMouse.chr6 633911 36 + 636262 TATACCATTAGACCCTCCTTAAGAGATAATTTATAA -s simRat_chr6.simRat.chr6 645097 36 + 647215 TACATCATTAGAGCCTCCTTCAGAGATAAATTATAA -s simRat_chr6.simRat.chr6 13590 36 + 647215 CTCCCAAGAATGTCTCCCTTAAGGGCTAAATCATAG - -a -s simMouse_chr6.simMouse.chr6 21689 4 + 636262 AGTA -s Anc0.Anc0refChr2 16026 4 + 17989 GGAG -s Anc1.Anc1refChr1 67747 4 + 69767 GGAG -s Anc1.Anc1refChr2 123599 4 - 144309 GGAG -s Anc2.Anc2refChr0 14554 4 - 56053 GGAG -s Anc2.Anc2refChr1 140816 4 + 142988 GGAG -s mr.mrrefChr0 20001 4 + 130230 AGTG -s mr.mrrefChr3 180025 4 + 181027 GTAG -s simCow_chr6.simCow.chr6 599997 4 + 602619 GGAG -s simCow_chr6.simCow.chr6 557479 4 - 602619 GGAG -s simDog_chr6.simDog.chr6 591795 4 + 593897 GGAG -s simDog_chr6.simDog.chr6 554969 4 - 593897 GGAA -s simHuman_chr6.simHuman.chr6 599848 4 + 601863 GGAG -s simHuman_chr6.simHuman.chr6 562799 4 - 601863 TGAG -s simMouse_chr6.simMouse.chr6 633947 4 + 636262 GTAG -s simRat_chr6.simRat.chr6 645136 4 + 647215 GTAG -s simRat_chr6.simRat.chr6 13626 4 + 647215 AGTG - -a -s simMouse_chr6.simMouse.chr6 21693 10 + 636262 CTGGTGCTGA -s Anc0.Anc0refChr2 16030 10 + 17989 CTTGTGATGA -s Anc1.Anc1refChr2 123603 10 - 144309 CTTGTGATGA -s Anc2.Anc2refChr0 14558 10 - 56053 CTTGTGATGA -s Anc2.Anc2refChr1 140820 10 + 142988 TTAGTGATGA -s mr.mrrefChr0 20005 10 + 130230 CTGGTGCTGA -s simCow_chr6.simCow.chr6 600001 10 + 602619 CTCACAACAA -s simCow_chr6.simCow.chr6 557483 10 - 602619 CTTATGATCA -s simDog_chr6.simDog.chr6 591799 10 + 593897 TTAGTGATGA -s simDog_chr6.simDog.chr6 554973 10 - 593897 TTTGTGATGG -s simHuman_chr6.simHuman.chr6 562803 10 - 601863 CTTGTGATGA -s simRat_chr6.simRat.chr6 13630 9 + 647215 CTG-TGCTGA - -a -s simMouse_chr6.simMouse.chr6 21703 5 + 636262 TACAG -s Anc0.Anc0refChr2 16040 5 + 17989 CTCAG -s Anc1.Anc1refChr1 67751 5 + 69767 CTCAG -s Anc1.Anc1refChr2 123613 5 - 144309 CTCAG -s Anc2.Anc2refChr0 14568 5 - 56053 CTCAG -s Anc2.Anc2refChr1 140830 5 + 142988 CTCAG -s mr.mrrefChr0 20015 5 + 130230 TACAG -s simCow_chr6.simCow.chr6 600011 5 + 602619 CTCAG -s simCow_chr6.simCow.chr6 557493 5 - 602619 GTCAG -s simDog_chr6.simDog.chr6 591809 5 + 593897 CTACA -s simDog_chr6.simDog.chr6 554983 5 - 593897 CTCAG -s simHuman_chr6.simHuman.chr6 599852 5 + 601863 CTCAG -s simHuman_chr6.simHuman.chr6 562813 5 - 601863 CTCAG -s simRat_chr6.simRat.chr6 13639 5 + 647215 TATAG - -a -s simMouse_chr6.simMouse.chr6 21708 9 + 636262 ATCATGTAT -s Anc0.Anc0refChr9 0 9 + 35212 AGCATGTTT -s Anc1.Anc1refChr2 123618 9 - 144309 AGCATGTTT -s Anc2.Anc2refChr0 14573 9 - 56053 AGCATGTTT -s mr.mrrefChr0 20020 9 + 130230 AGCATGTAT -s simCow_chr6.simCow.chr6 557498 9 - 602619 AGCATGTTT -s simDog_chr6.simDog.chr6 554988 9 - 593897 AGCACATTT -s simHuman_chr6.simHuman.chr6 562818 9 - 601863 GGCATGTCT -s simRat_chr6.simRat.chr6 13644 9 + 647215 AGCACGTAT - -a -s simMouse_chr6.simMouse.chr6 21717 4 + 636262 TGTA -s Anc0.Anc0refChr9 10 4 + 35212 TGTT -s Anc1.Anc1refChr2 123628 4 - 144309 TGTT -s Anc2.Anc2refChr0 14583 4 - 56053 TGTT -s mr.mrrefChr0 20029 4 + 130230 TGTA -s simCow_chr6.simCow.chr6 557508 4 - 602619 TGTT -s simDog_chr6.simDog.chr6 554998 4 - 593897 TGTT -s simHuman_chr6.simHuman.chr6 562828 4 - 601863 TGTT -s simRat_chr6.simRat.chr6 13653 4 + 647215 TGTA - -a -s simMouse_chr6.simMouse.chr6 21721 74 + 636262 TGTGAATAATGTGTATCTAATCCTCTTTCTCCACAAGTGTCTGTTATTACCTGAGAACTTCCCTTGTCATGTTT -s Anc0.Anc0refChr9 14 74 + 35212 TGTCAATGGTGTGTATTTAATTCTCTTCCTCCACAAATGTCTGTTAATACCTGGGGTCTTCCCTTGTTGTGAGT -s Anc1.Anc1refChr2 123632 74 - 144309 TGTCAATGGTGTGTATTTAATTCTCTTCCTCCACAAATGTCTGTTAATACCTGGGGTCTTCCCTTGTTGTGAGT -s Anc2.Anc2refChr0 14587 74 - 56053 TGTCAATGGTGTGTATTTAATTCTCTTCCCCCACAAATGTTTGTTAATACCTGGGGTCTTCCTTTGTTGTGAGT -s mr.mrrefChr0 20033 74 + 130230 TGTGAATAATGTGTATTTAATCCTCTTTCTCCACAAGTGTCTGTTATTACCTGGGATCTTCCCTTGTCATGTTT -s simCow_chr6.simCow.chr6 557512 74 - 602619 TGTCAATGGTGTGTATATAATTCTCTTCCCCCACAAATGTTTGTTAATACCTGAGGTCTTACTTTGCCGTGAGT -s simDog_chr6.simDog.chr6 555009 74 - 593897 TTTCAATGATGTGTATTTAATTCTCTTCCCCCATCAATGTTTGGTAATACATGGGGTCTTCCTTTGTTGTAAGT -s simHuman_chr6.simHuman.chr6 562832 74 - 601863 TGTTAATGGTGTGTATTTCATTCTGCTCCTCCACAGATGTCTGTTAATACCTGGGGTCTGCCCTTGTTGTGACT -s simRat_chr6.simRat.chr6 13657 74 + 647215 TGTGAATAATGTGTATTTAATCCTCTTGCTCCACAAGTGTCTGTTGTTCCCTGGGATCTTCCCTTGTCATGTTT - -a -s simMouse_chr6.simMouse.chr6 21795 27 + 636262 AACAAAAATGGTAAATTGCTACTAAAA -s Anc0.Anc0refChr9 88 27 + 35212 AACAAAAATATTAAATCTCAACTAAGA -s Anc1.Anc1refChr2 123706 27 - 144309 AACAAAAATATTAAATCTCAACTAAGA -s Anc2.Anc2refChr0 14661 27 - 56053 TGACAAACTATTAAATCTCAACTAAAA -s mr.mrrefChr0 20107 27 + 130230 AACAAAAATGGTAAATTGCTACTAAGA -s simCow_chr6.simCow.chr6 557586 27 - 602619 TGTTAAAGTGTTAAATCTCAACTGAGC -s simDog_chr6.simDog.chr6 555083 27 - 593897 TGACAAACTATTAAATCTCAACTAAAA -s simHuman_chr6.simHuman.chr6 562908 27 - 601863 AACAAGAATATTAAATCCCAACTAGGT -s simRat_chr6.simRat.chr6 13731 27 + 647215 AACCGAGATGGTAAATTGCTACTAAGG - -a -s simMouse_chr6.simMouse.chr6 21822 68 + 636262 TGCAAGTGCACAGGACATGTATGCAATACACATGTGTAATTGCAATATACATGTGTAATGAGATATAA -s Anc0.Anc0refChr9 115 10 + 35212 TTTA----------------------------------------------------------ATATTA -s Anc1.Anc1refChr2 123733 10 - 144309 TTTA----------------------------------------------------------ATATTA -s Anc2.Anc2refChr0 14697 10 - 56053 TTTT----------------------------------------------------------AGGGTG -s mr.mrrefChr0 20134 48 + 130230 TGTA--------------GTATGCAATACACATGTG------CAATATACATGTGTAATGAGATATAA -s simCow_chr6.simCow.chr6 557622 10 - 602619 TTTT----------------------------------------------------------ATGGTG -s simDog_chr6.simDog.chr6 555119 10 - 593897 TTTT----------------------------------------------------------AGGGAG -s simHuman_chr6.simHuman.chr6 562935 10 - 601863 TTTA----------------------------------------------------------ATATTA -s simRat_chr6.simRat.chr6 13758 48 + 647215 TGTG--------------GTATACTGTACACATAAG------CAATAAACAAGCGCAATGAGATATAA - -a -s simMouse_chr6.simMouse.chr6 21890 11 + 636262 ACTAACTAGAA -s Anc0.Anc0refChr9 127 11 + 35212 ACTGATTATGG -s Anc1.Anc1refChr2 123745 11 - 144309 ACTGATTATGG -s Anc2.Anc2refChr0 14709 11 - 56053 ACTGATGATGG -s mr.mrrefChr0 20184 11 + 130230 ACTAACTAGAA -s simCow_chr6.simCow.chr6 557634 11 - 602619 ACTGATAATGG -s simDog_chr6.simDog.chr6 555131 11 - 593897 ACTGTTGATGG -s simHuman_chr6.simHuman.chr6 562947 11 - 601863 ACTGATTATGG -s simRat_chr6.simRat.chr6 13808 11 + 647215 CCTAACAAGAC - -a -s simMouse_chr6.simMouse.chr6 21901 72 + 636262 CCCATTACATACAGACACTATACATCCTAGGGATTTATATTCTAATAAGGGGTTCTTGGCTGGCATGATTTG -s Anc0.Anc0refChr9 141 58 + 35212 TTCATTAAACGCCG-----------T---GACCTGTCTGCCTAATCAATGATGTATTGGCTGGCACAATTTG -s Anc1.Anc1refChr2 123759 58 - 144309 TTCATTAAACGCCG-----------T---GACCTGTCTGCCTAATCAATGATGTATTGGCTGGCACAATTTG -s Anc2.Anc2refChr0 14723 58 - 56053 TTTGTTAAACAACA-----------T---TACCTGTCTGCCTAATCAATGGTGTATTGGCTGGCACAACTTG -s mr.mrrefChr0 20195 68 + 130230 CCCATTACATGCAGACACTA-ACATT---GAGCTTTATATTCTAATAAGGAGTTCTTGGCTGGCATGATTTG -s simCow_chr6.simCow.chr6 557648 58 - 602619 TATGTTAAACAGAT-----------C---TACATGTCTGCTTGATCAACGGGGTATTGGCTGGCACAACTTG -s simDog_chr6.simDog.chr6 555145 52 - 593897 TTTGTTAAACAACA-----------T---TACCTGTCTGCCTAATCAATGGTG----GGCCGGCGCAA--TG -s simHuman_chr6.simHuman.chr6 562961 58 - 601863 TGCATTAAACGCGG-----------T---GACCTATCTGCCTAATCAATGATGTATTGGTTGGCACAATTTG -s simRat_chr6.simRat.chr6 13819 68 + 647215 ACCATTACATGCAGACACTA-ATATT---GAGCTTTGTATTCTAATGGGGACTTCTTGGCTGGCATGATTTG - -a -s simMouse_chr6.simMouse.chr6 21973 87 + 636262 TTAATACATTGATGTTGTGCCATTGCTGTTTTATTATTATGATTGCTATAGGTCTGACACTGCTATAGGTCTGTAAACTGTATTAGC -s Anc0.Anc0refChr9 199 70 + 35212 TTAATACATTGATGTTGTTCTATTGTTATTTCCCTATTGTAATTATTATAGGT----------------T-TGTAGACAGTATTACA -s Anc1.Anc1refChr2 123817 70 - 144309 TTAATACATTGATGTTGTTCTATTGTTATTTCCCTATTGTAATTATTATAGGT----------------T-TGTAGACAGTATTACA -s Anc2.Anc2refChr0 14781 70 - 56053 TTAATACATTGATGTTGTTCTATTGTTATTTCCCTATTGTACCTATTACAGGT----------------C-TGTGTACAAGCTTACA -s mr.mrrefChr0 20263 86 + 130230 TTAATACATTGATGTTGTGCCATTGCTGTTTTATTATTATGATTACTATAGGTCTGACACTGCTATAGGT-TGTAGACTGTATTAGC -s simCow_chr6.simCow.chr6 557706 65 - 602619 TTAGTTCAATGATGTTGTTCTATTACCATCTCCTCATTGCACTTATTACTGGT----------------C-AGTGTACA-----ACC -s simDog_chr6.simDog.chr6 555197 70 - 593897 TGAATACATTGATGTTGTTCTATTGTTATTTCCCTATTGTACCTATTACAGGT----------------C-TGTGTACAAGCTTCAA -s simHuman_chr6.simHuman.chr6 563019 50 - 601863 TTGATACATTGATGTTGTCCT--------------------ATTAGTATAGGT----------------T-TGTAGACAGTATTACA -s simRat_chr6.simRat.chr6 13897 86 + 647215 TTAATACATTGATGTTGTGCCATTGCTGTTCCTTTATTACACTTAACGTAGGCCTGACATTGCTGTAGGT-TGTAGCCTTTATTAGT - -a -s simMouse_chr6.simMouse.chr6 22060 10 + 636262 TTCAAAGAGA -s Anc0.Anc0refChr9 269 10 + 35212 TTTCGTGGGA -s Anc1.Anc1refChr2 123887 10 - 144309 TTTCGTGGGA -s Anc2.Anc2refChr0 14851 10 - 56053 TTTCGTGGGA -s mr.mrrefChr0 20349 10 + 130230 TTCAATGGGA -s simCow_chr6.simCow.chr6 557771 10 - 602619 TCTCGTGGTA -s simDog_chr6.simDog.chr6 555269 10 - 593897 TTTAGCAGGA -s simHuman_chr6.simHuman.chr6 563069 10 - 601863 TTTCGTGGGA -s simRat_chr6.simRat.chr6 13983 10 + 647215 TTCAATGGCA - -a -s simMouse_chr6.simMouse.chr6 22070 5 + 636262 CTCAT -s Anc0.Anc0refChr9 285 5 + 35212 GTCAT -s Anc1.Anc1refChr2 123903 5 - 144309 GTCAT -s Anc2.Anc2refChr0 14867 5 - 56053 GTCGT -s mr.mrrefChr0 20365 5 + 130230 CTCAT -s simCow_chr6.simCow.chr6 557787 5 - 602619 GTTGT -s simDog_chr6.simDog.chr6 555285 5 - 593897 GTCGT -s simHuman_chr6.simHuman.chr6 563085 5 - 601863 GTCAT -s simRat_chr6.simRat.chr6 13999 5 + 647215 CTCAT - -a -s simMouse_chr6.simMouse.chr6 22075 43 + 636262 TACTACAACTGCTGGCATCCTAAAAAAATGAGCCCCTCTAACA -s Anc0.Anc0refChr9 290 43 + 35212 TACTTCTAATGCTGACATCTTAAAAAAATGAGCCCCTCTATCA -s Anc1.Anc1refChr2 123908 43 - 144309 TACTTCTAATGCTGACATCTTAAAAAAATGAGCCCCTCTATCA -s Anc2.Anc2refChr0 14872 43 - 56053 TACTTCTAATGCTGACAGCTTAAAAAAATGAGCACATCTATCA -s mr.mrrefChr0 20370 43 + 130230 TACTACAACTGCTGGCATCCTAAAAAAATGAGCCCCTCTAACA -s simCow_chr6.simCow.chr6 557794 42 - 602619 TACGTGTAATGCTGACACCTT-AAAAGATGAGCACATCTATCA -s simDog_chr6.simDog.chr6 555291 43 - 593897 GACTTCTAACGCTGAGAGCTTAAAAAAATTAGCATATCTATCA -s simHuman_chr6.simHuman.chr6 563090 42 - 601863 TACTTCTAATACTGACTTCGTAAAAAAATGAG-CCCTATATCA -s simRat_chr6.simRat.chr6 14004 43 + 647215 TACTGCAACTGCTGGCATCCTAAAAAAATAAGCCCCTCTAACA - -a -s simMouse_chr6.simMouse.chr6 22118 44 + 636262 TAATACAGGATACCTCCGTGCTGAATGCTGGGCATCTTTAACTT -s Anc0.Anc0refChr9 333 41 + 35212 GCATAG--GCT-CCTTACTGTTGAATGGCTGGCATTTTCAACTT -s Anc1.Anc1refChr2 123951 41 - 144309 GCATAG--GCT-CCTTACTGTTGAATGGCTGGCATTTTCAACTT -s Anc2.Anc2refChr0 14916 41 - 56053 GCATAG--GTT-CCTTACTGTTGAATGGCTGGCATTTTCAACTT -s mr.mrrefChr0 20413 44 + 130230 TAATACAGGCTACCTCCCTGCTGAATGCTGGGCATTTTTAACTT -s simCow_chr6.simCow.chr6 557837 38 - 602619 ---TAA--GTT-CCCTACTTGTGAATGGCTAGCTTTTTCAACTT -s simDog_chr6.simDog.chr6 555338 41 - 593897 GCACAG--ATT-CCTCATTGTTGAGTAGCTGGCATCTTCAACTT -s simHuman_chr6.simHuman.chr6 563132 41 - 601863 GCATAT--GCT-CCTTGCTGTTGAATGGCCGGCATTTTCAACTT -s simRat_chr6.simRat.chr6 14047 44 + 647215 TAATACAGGCTACCTGACTGCTGAACACTGGGCACTTCTAATTT - -a -s simMouse_chr6.simMouse.chr6 22162 30 + 636262 TAGAAAAGACCATGTATTCAGCTACAGAGA -s Anc0.Anc0refChr9 374 30 + 35212 TAGACTAGCCCATGTTGTCAGCTACAGAGA -s Anc1.Anc1refChr2 123992 30 - 144309 TAGACTAGCCCATGTTGTCAGCTACAGAGA -s Anc2.Anc2refChr0 14957 30 - 56053 TAGGCTAGCCCATGTTGTCAGCTTCAGAGA -s mr.mrrefChr0 20457 30 + 130230 TAGAATAGACCATGTAGTCAGCTACAGAGA -s simCow_chr6.simCow.chr6 557875 30 - 602619 TTGTCTAGCCCATGTCTTCAGCTCCAGTGA -s simDog_chr6.simDog.chr6 555379 30 - 593897 TAGGCCAGTCCATGTTGTCAGCTTCAGAGA -s simHuman_chr6.simHuman.chr6 563175 30 - 601863 TAGATTTGCCCACGTTGTCGGCTACGGAGA -s simRat_chr6.simRat.chr6 14091 30 + 647215 TGGAATAGACCATGTAGTCAGCTTCAGAAA - -a -s simMouse_chr6.simMouse.chr6 22192 6 + 636262 GATAAT -s Anc0.Anc0refChr9 404 6 + 35212 GATGAT -s Anc1.Anc1refChr2 124022 6 - 144309 GATGAT -s Anc2.Anc2refChr0 14987 6 - 56053 GATGAT -s mr.mrrefChr0 20487 6 + 130230 GATAAT -s simCow_chr6.simCow.chr6 557905 6 - 602619 AACGGT -s simDog_chr6.simDog.chr6 555409 6 - 593897 GATGAT -s simHuman_chr6.simHuman.chr6 563207 6 - 601863 GATCCT -s simRat_chr6.simRat.chr6 14121 6 + 647215 GATAAT - -a -s simMouse_chr6.simMouse.chr6 22198 63 + 636262 GCATGTTGTAGCCTGGATCAGCTACAGTGGGACAATGAACTATATAGCCTGGCAAAGGTAAAA -s Anc0.Anc0refChr9 410 19 + 35212 G--------------------------------------------AGCCTGGCAGAGGCAAAA -s Anc1.Anc1refChr2 124028 19 - 144309 G--------------------------------------------AGCCTGGCAGAGGCAAAA -s Anc2.Anc2refChr0 15001 19 - 56053 T--------------------------------------------AGCCAGGCAGAGGCAAAA -s mr.mrrefChr0 20493 63 + 130230 GCATGTTGTAGCCTGGATCAGCTACAGTGGGACAATGAACTATATAGCCTGGCAAAGGCAAAA -s simCow_chr6.simCow.chr6 557919 15 - 602619 T--------------------------------------------A----GGCGGGGGTAAGG -s simDog_chr6.simDog.chr6 555423 19 - 593897 T--------------------------------------------AGCCAGGCAGAGGCAAAA -s simHuman_chr6.simHuman.chr6 563213 19 - 601863 G--------------------------------------------AGCCTGACACAAGCAAAA -s simRat_chr6.simRat.chr6 14127 63 + 647215 GCATGGTGTAGCCCGGATCAGCTACAGAGGGACAATGCACTATATAGTCTGGCAGAGGCAAAA - -a -s simMouse_chr6.simMouse.chr6 22261 16 + 636262 ACCACAGACTTTTTTT -s Anc0.Anc0refChr9 430 15 + 35212 GCCA-TGGCTTTTTTT -s Anc1.Anc1refChr2 124048 16 - 144309 GCCACTGGCTTTTTTT -s Anc2.Anc2refChr0 15021 15 - 56053 GCCA-TGGCTTTTTTT -s mr.mrrefChr0 20557 16 + 130230 GCCACAGACTTTTTTT -s simCow_chr6.simCow.chr6 557935 15 - 602619 GCCA-AGGCTTTTTTT -s simDog_chr6.simDog.chr6 555443 15 - 593897 GCCA-TGGGTTTTTTT -s simHuman_chr6.simHuman.chr6 563233 16 - 601863 GCCACTAGCTTCTTTC -s simRat_chr6.simRat.chr6 14191 16 + 647215 GGCACAGACTTTTTTT - -a -s simMouse_chr6.simMouse.chr6 22277 45 + 636262 TTGCTCACATATTTTATCATGTAAATCTCTTGTGATGCACTCGCC -s Anc0.Anc0refChr9 445 38 + 35212 TTGCCTGCATGTTTTGTCTTGTA-------TGTGAGGCATTTATC -s Anc1.Anc1refChr2 124064 44 - 144309 TTGCCTGCATGTTTTGTCTTGTACCCAAC-TGTGAGGCATTTATC -s Anc2.Anc2refChr0 15036 38 - 56053 TCACCTGCATGTTTTGTCTTGTA-------TGTGAGGCATTTATC -s mr.mrrefChr0 20573 45 + 130230 TTGCCCACATATTTTATCATGTACATCTCTTGTGATGCACTCGCC -s simCow_chr6.simCow.chr6 557950 38 - 602619 TCATCTGTATGTTTTGTCTTGAA-------TGTTAGGCATTGATC -s simDog_chr6.simDog.chr6 555458 37 - 593897 TCACCTGCCCGTTTTGTATTGTA-------TGTGAGGCATTTAT- -s simHuman_chr6.simHuman.chr6 563249 29 - 601863 TTGCCTGCATGTTTTGCCTTGTACCCAAC---------------- -s simRat_chr6.simRat.chr6 14210 45 + 647215 TTGCCCACATATTTTATCATGTACATCCCTCATGATGCACTAGTC - -a -s simMouse_chr6.simMouse.chr6 22322 22 + 636262 TCAACCTTGTAAAGCCTTCCAC -s Anc0.Anc0refChr9 483 22 + 35212 TCAACCTTGTAAAGCCTTTTAT -s Anc1.Anc1refChr2 124108 22 - 144309 TCAACCTTGTAAAGCCTTTTAT -s Anc2.Anc2refChr0 15078 22 - 56053 TCAACCTTATAAAGCCTTTTAT -s mr.mrrefChr0 20618 22 + 130230 TCAACCTTGTAAAGCCTTTTAT -s simCow_chr6.simCow.chr6 557992 17 - 602619 ACAA-----TAGCGCCTTTTAT -s simDog_chr6.simDog.chr6 555496 22 - 593897 TCAACCTTATAAAGCCTTTTAT -s simHuman_chr6.simHuman.chr6 563278 21 - 601863 -CAACCTTGTTAACCCTTTTAT -s simRat_chr6.simRat.chr6 14255 22 + 647215 TCTTCCCTTTGAATCCTTTTAT - -a -s simMouse_chr6.simMouse.chr6 22344 23 + 636262 CACAGGTGTGTGTGAATTTATCA -s Anc0.Anc0refChr9 505 19 + 35212 CA---TAG-GTGTGTATATCTCA -s Anc1.Anc1refChr2 124130 22 - 144309 CATAGTAG-GTGTGTATATCTCA -s Anc2.Anc2refChr0 15100 19 - 56053 GA---TAG-GTGTATATATCATC -s mr.mrrefChr0 20640 22 + 130230 CATAGGTG-GTGTGTATTTATCA -s simCow_chr6.simCow.chr6 558009 15 - 602619 CA---TAG-GTGTATAGTT---- -s simDog_chr6.simDog.chr6 555518 19 - 593897 GA---TAG-ACATATATACCATC -s simHuman_chr6.simHuman.chr6 563300 22 - 601863 CATAGTAG-GTGTGTATCTCTCA -s simRat_chr6.simRat.chr6 14277 22 + 647215 CATAGGTG-TTGTGTATTTACCA - -a -s simMouse_chr6.simMouse.chr6 22367 44 + 636262 GTGTGTGAGGACATAGAGGTGCTGGTTCGAATGATTGAAATTTG -s Anc0.Anc0refChr9 528 31 + 35212 GTAAGTGAGGGCTTAAAGGTGTCAGTTAGAA------------- -s Anc1.Anc1refChr2 124156 35 - 144309 GTAAGTGAGGGCTTAAAGGTGTCAGTTAGAATGAT--------- -s Anc2.Anc2refChr0 15123 31 - 56053 GTGAATAAGGGCTAAAAGGTTTCAGTAGGAA------------- -s mr.mrrefChr0 20662 44 + 130230 GTATGTGAGGGCATAAAGGTGCCAGTTAGAATGATTGAAATTTG -s simDog_chr6.simDog.chr6 555541 31 - 593897 GTGAATAAGGGCTAAAAGGTTTCAGTAGGAA------------- -s simHuman_chr6.simHuman.chr6 563326 35 - 601863 CTAAGTGATGGCTTAAAGGTGTCAGTTAGAATGAT--------- -s simRat_chr6.simRat.chr6 14299 44 + 647215 TTATGTCAGGGCATAAAAGTGACAGTTAGAATCATTGAAAGTTG - -a -s simMouse_chr6.simMouse.chr6 22411 39 + 636262 AACCATTGAAAGTTGGGGGTCAACGCTTCCTTGCTCATT -s Anc0.Anc0refChr9 559 5 + 35212 ----------------------------------TCATT -s Anc1.Anc1refChr2 124191 16 - 144309 -----------------------CCCTTCTTTGCTCATT -s Anc2.Anc2refChr0 15154 5 - 56053 ----------------------------------TCATG -s mr.mrrefChr0 20706 25 + 130230 AACCATTGA--------------CGCTTCCTTGCTCATT -s simDog_chr6.simDog.chr6 555572 5 - 593897 ----------------------------------TCATG -s simHuman_chr6.simHuman.chr6 563361 16 - 601863 -----------------------CCCTTCTTTGCTCATT -s simRat_chr6.simRat.chr6 14344 9 + 647215 AATCATTGG------------------------------ - -a -s simMouse_chr6.simMouse.chr6 22450 23 + 636262 TAAACACTGGCATCTGGCACATC -s Anc0.Anc0refChr9 570 18 + 35212 TAATCACTGTG-TC----ACTCA -s Anc1.Anc1refChr2 124213 19 - 144309 TAATCACTGTGATC----ACTCA -s Anc2.Anc2refChr0 15165 18 - 56053 TCATCTCTGTG-TC----ACTCA -s mr.mrrefChr0 20731 19 + 130230 TAAACACTGGCATC----ACATC -s simDog_chr6.simDog.chr6 555583 18 - 593897 TCATCTCTGTG-TC----ACTCA -s simHuman_chr6.simHuman.chr6 563383 19 - 601863 TAAGTACTGAGATC----ACCCA - -a -s simMouse_chr6.simMouse.chr6 22473 16 + 636262 AGGATATAAGTGCCTG -s Anc0.Anc0refChr9 588 14 + 35212 AGGCT-TAAATG-CTA -s Anc1.Anc1refChr2 124232 14 - 144309 AGGCT-TAAATG-CTA -s Anc2.Anc2refChr0 15183 14 - 56053 AGCCT-TTAATT-CCA -s mr.mrrefChr0 20750 15 + 130230 AGGAT-TAAGTGCCTA -s simDog_chr6.simDog.chr6 555606 14 - 593897 AGCCT-TTAATT-CCA -s simHuman_chr6.simHuman.chr6 563402 14 - 601863 AGGCT-TAAATG-CTA -s simRat_chr6.simRat.chr6 14353 5 + 647215 -----------GCGCA - -a -s simMouse_chr6.simMouse.chr6 22489 13 + 636262 ATATTGGGTGCAA -s Anc0.Anc0refChr9 602 12 + 35212 ATATT-GGTGCAG -s Anc1.Anc1refChr2 124246 13 - 144309 ATATTGGGTGCAG -s Anc2.Anc2refChr0 15197 12 - 56053 ATATT-GATGCAG -s mr.mrrefChr0 20765 13 + 130230 ATATTGGGTGCAA -s simDog_chr6.simDog.chr6 555621 12 - 593897 ATATT-GATGCAG -s simHuman_chr6.simHuman.chr6 563416 13 - 601863 ATATTGGGTGCAT -s simRat_chr6.simRat.chr6 14358 13 + 647215 TTGTCGGGTGCAA - -a -s simMouse_chr6.simMouse.chr6 22502 3 + 636262 TGT -s Anc0.Anc0refChr9 618 3 + 35212 TGT -s Anc1.Anc1refChr2 124263 3 - 144309 TGT -s Anc2.Anc2refChr0 15213 3 - 56053 TGT -s mr.mrrefChr0 20782 3 + 130230 TGT -s simDog_chr6.simDog.chr6 555642 3 - 593897 TGT -s simHuman_chr6.simHuman.chr6 563433 3 - 601863 TGT -s simRat_chr6.simRat.chr6 14375 3 + 647215 TGT - -a -s simMouse_chr6.simMouse.chr6 22505 5 + 636262 TGGAT -s Anc0.Anc0refChr9 621 5 + 35212 TACAT -s Anc1.Anc1refChr2 124266 5 - 144309 TACAT -s Anc2.Anc2refChr0 15216 5 - 56053 TTGAT -s mr.mrrefChr0 20785 5 + 130230 TACAT -s simDog_chr6.simDog.chr6 555645 5 - 593897 TTGAT -s simHuman_chr6.simHuman.chr6 563437 5 - 601863 TACAT -s simRat_chr6.simRat.chr6 14378 5 + 647215 TACAT - -a -s simMouse_chr6.simMouse.chr6 22510 8 + 636262 CTGCTCTT -s Anc0.Anc0refChr9 784 8 + 35212 CTGTTGTT -s Anc1.Anc1refChr2 124430 8 - 144309 CTGTTGTT -s Anc2.Anc2refChr0 18901 8 - 56053 TTGTAGTT -s mr.mrrefChr0 20948 8 + 130230 CTGCTCTT -s simCow_chr6.simCow.chr6 559389 8 - 602619 TTGTCGTT -s simDog_chr6.simDog.chr6 555810 7 - 593897 TAGTAGC- -s simHuman_chr6.simHuman.chr6 563628 8 - 601863 CTGTTGTC -s simRat_chr6.simRat.chr6 14560 8 + 647215 CTGCTCTT - -a -s simMouse_chr6.simMouse.chr6 22518 45 + 636262 ATATTTTGTGCATCCATAGGAGCAGGTGATCAGCATGACATCATA -s Anc0.Anc0refChr9 793 45 + 35212 ATATTGTGTGCAATAGAAGGGGCAACTGTTCAACATGTTATCATA -s Anc1.Anc1refChr2 124439 45 - 144309 ATATTGTGTGCAATAGAAGGGGCAACTGTTCAACATGTTATCATA -s Anc2.Anc2refChr0 18910 45 - 56053 GTATTGTGTGCAATAGAAGGGGCAACTGTTTGACATATTATCATA -s mr.mrrefChr0 20956 45 + 130230 ATATTTTGTGCATCCATAGGAGCAGGTGTTCAGCATGACATCATA -s simCow_chr6.simCow.chr6 559398 44 - 602619 -TAGTGTGTGCAATAGAACTGGCGACCATTTGACATTTTGTAATA -s simDog_chr6.simDog.chr6 555817 44 - 593897 GTGTTATGTGCAATAAAAGGGGCAACTGTTTGA-GCATTAGCATA -s simHuman_chr6.simHuman.chr6 563637 45 - 601863 ATATTGTGTGCAATAGAAGGGGCAATTGTTCAACATGTTATCATA -s simRat_chr6.simRat.chr6 14568 45 + 647215 ATATTTTGTGCACCTATAAGAGCAGGTGTTCAGCAGTACACCATA - -a -s simMouse_chr6.simMouse.chr6 22563 12 + 636262 GGGAGGAGCAGG -s Anc0.Anc0refChr9 838 12 + 35212 GGGAGGAGGAGG -s Anc1.Anc1refChr2 124484 12 - 144309 GGGAGGAGGAGG -s Anc2.Anc2refChr0 18955 12 - 56053 GGGAGGAGGAGG -s mr.mrrefChr0 21001 12 + 130230 GGGAGGAGCAGG -s simCow_chr6.simCow.chr6 559445 12 - 602619 GGGAGGAGGAGG -s simDog_chr6.simDog.chr6 555861 9 - 593897 ---AGGAGGATC -s simHuman_chr6.simHuman.chr6 563682 12 - 601863 GGGAGGAGGAGG -s simRat_chr6.simRat.chr6 14613 12 + 647215 GGGAGGAGCAGG - -a -s simMouse_chr6.simMouse.chr6 22575 9 + 636262 TAAGCTGTT -s Anc0.Anc0refChr9 851 9 + 35212 TATGCTATC -s Anc1.Anc1refChr2 124497 9 - 144309 TATGCTATC -s Anc2.Anc2refChr0 18968 9 - 56053 TATGCTATC -s mr.mrrefChr0 21013 9 + 130230 TAAGCTGTT -s simCow_chr6.simCow.chr6 559458 9 - 602619 TATGCTATC -s simDog_chr6.simDog.chr6 555871 9 - 593897 TATGCCATC -s simHuman_chr6.simHuman.chr6 563695 9 - 601863 TATGCTATC -s simRat_chr6.simRat.chr6 14625 9 + 647215 TACACTGTT - -a -s simMouse_chr6.simMouse.chr6 22584 14 + 636262 GTATAACAGGTTTG -s Anc0.Anc0refChr9 860 14 + 35212 GTATGACAATTTTG -s Anc1.Anc1refChr2 124506 14 - 144309 GTATGACAATTTTG -s Anc2.Anc2refChr0 18985 14 - 56053 GTATGACAATTTTG -s mr.mrrefChr0 21022 14 + 130230 GTATAACAGGTTTG -s simCow_chr6.simCow.chr6 559475 14 - 602619 ATATGACAATTTTG -s simDog_chr6.simDog.chr6 555888 14 - 593897 GTATGACAATTTTG -s simHuman_chr6.simHuman.chr6 563704 14 - 601863 GCATGACAACTTTA -s simRat_chr6.simRat.chr6 14634 14 + 647215 GTATAACAGGTTTG - -a -s simMouse_chr6.simMouse.chr6 22598 6 + 636262 TTCCAA -s Anc0.Anc0refChr9 874 6 + 35212 TGCCTA -s Anc1.Anc1refChr2 124520 6 - 144309 TGCCTA -s Anc2.Anc2refChr0 19435 6 - 56053 TGCCTA -s mr.mrrefChr0 21036 6 + 130230 TGCCAA -s simCow_chr6.simCow.chr6 559964 6 - 602619 TGCCTA -s simDog_chr6.simDog.chr6 556410 6 - 593897 CGTCTA -s simHuman_chr6.simHuman.chr6 563718 6 - 601863 TGCCTA -s simRat_chr6.simRat.chr6 14648 6 + 647215 TGCAAA - -a -s simMouse_chr6.simMouse.chr6 22604 7 + 636262 AACACAG -s Anc0.Anc0refChr9 883 5 + 35212 AACAC-- -s Anc1.Anc1refChr2 124529 7 - 144309 AACACGG -s Anc2.Anc2refChr0 19444 5 - 56053 AACAC-- -s mr.mrrefChr0 21042 7 + 130230 AACACAG -s simCow_chr6.simCow.chr6 559973 2 - 602619 CA----- -s simDog_chr6.simDog.chr6 556419 5 - 593897 AACAC-- -s simHuman_chr6.simHuman.chr6 563727 7 - 601863 AACATGG -s simRat_chr6.simRat.chr6 14654 7 + 647215 AACACAG - -a -s simMouse_chr6.simMouse.chr6 22611 23 + 636262 TGATTTAAAAGGGCACAGATACC -s Anc0.Anc0refChr9 888 19 + 35212 --ATCTGAACAGTTGC--ATACC -s Anc1.Anc1refChr2 124536 21 - 144309 TGATCTGAACAGTTGC--ATACC -s Anc2.Anc2refChr0 19449 19 - 56053 --ATCTGAACAGTTGC--ATAAC -s mr.mrrefChr0 21049 23 + 130230 TGATTTAAAAGGGTACAGATACC -s simCow_chr6.simCow.chr6 559975 19 - 602619 --ATCTGAACAGTTGC--ATAAC -s simDog_chr6.simDog.chr6 556424 3 - 593897 --------------------AAC -s simHuman_chr6.simHuman.chr6 563734 21 - 601863 TGATGTGAACAGTTGC--ATACC -s simRat_chr6.simRat.chr6 14666 23 + 647215 TGATTTAAAAGGGTACAGATACC - -a -s simMouse_chr6.simMouse.chr6 22634 11 + 636262 TTTGATCTTGG -s Anc0.Anc0refChr9 913 11 + 35212 TTTCATATTGG -s Anc1.Anc1refChr2 124563 11 - 144309 TTTCATATTGG -s Anc2.Anc2refChr0 19475 11 - 56053 TTTCATATTGG -s mr.mrrefChr0 21072 11 + 130230 TTTGATCTTGG -s simCow_chr6.simCow.chr6 560001 11 - 602619 TTTCATATTGG -s simDog_chr6.simDog.chr6 556434 11 - 593897 TCTCATATTGG -s simHuman_chr6.simHuman.chr6 563761 11 - 601863 TTTCATTTTGG -s simRat_chr6.simRat.chr6 14689 11 + 647215 TTTGATATGGG - -a -s simMouse_chr6.simMouse.chr6 22645 61 + 636262 AAAGCACCTAGATATCACATCATGAGGAGCGAACAGCATGAGATTTAATTTAGTGTATTGA -s Anc0.Anc0refChr9 925 56 + 35212 CTCCCAGCTGGTTTTCATATCATGAGGACAT-----CATGAGATTCAATCTATTGCATTGA -s Anc1.Anc1refChr2 124575 61 - 144309 CTCCCAGCTGGTTTTCATATCATGAGGACATAACAGCATGAGATTCAATCTATTGCATTGA -s Anc2.Anc2refChr0 19487 56 - 56053 CTCCTAGCTGGTTTTCATATCATGAGGACAT-----CATGAGGTTCAATCTATTGCATTGA -s mr.mrrefChr0 21084 61 + 130230 AAAGCACCTGGATATCATATCATGAGGAGCGAACAGCATGAGATTCAATTTATTGCATTGA -s simCow_chr6.simCow.chr6 560012 35 - 602619 -----GGATGGGTGTCATA---------------------AGGTTTGATATATTTCATTCA -s simDog_chr6.simDog.chr6 556446 55 - 593897 CTCCTAGCTGGTTTTCATATCATGAGGACAT-----CATGAG-TCCAATCTATTGCATTGA -s simHuman_chr6.simHuman.chr6 563773 61 - 601863 GTCCCAGCTGGTTTCCATATCACGAGGGCATAACAGCTTGAGATTCAATGTATCGCATTGA -s simRat_chr6.simRat.chr6 14701 60 + 647215 AAAGCACCTGCATCTTATATC-TGAGGAGCGAACAGCATGAGATTCGGTTTATTGCATTGA - -a -s simMouse_chr6.simMouse.chr6 22706 5 + 636262 ATCTG -s Anc0.Anc0refChr9 1021 4 + 35212 GTCT- -s Anc1.Anc1refChr2 124676 4 - 144309 GTCT- -s Anc2.Anc2refChr0 19583 4 - 56053 GTCT- -s mr.mrrefChr0 21145 5 + 130230 ATCTG -s simCow_chr6.simCow.chr6 560087 4 - 602619 GTCT- -s simDog_chr6.simDog.chr6 556513 4 - 593897 GTCT- -s simHuman_chr6.simHuman.chr6 563874 4 - 601863 GTCT- -s simRat_chr6.simRat.chr6 14761 5 + 647215 AGTTG - -a -s simMouse_chr6.simMouse.chr6 22711 14 + 636262 AAGACGGTTACTGT -s Anc0.Anc0refChr9 1025 9 + 35212 -----AGACATAAT -s Anc1.Anc1refChr2 124680 9 - 144309 -----AGACATAAT -s Anc2.Anc2refChr0 19587 9 - 56053 -----AGACATAAT -s mr.mrrefChr0 21150 14 + 130230 AAGACAGATATTGT -s simCow_chr6.simCow.chr6 560091 9 - 602619 -----TGACCTAAT -s simDog_chr6.simDog.chr6 556517 9 - 593897 -----AGACATAAT -s simHuman_chr6.simHuman.chr6 563878 9 - 601863 -----AGACATAAT -s simRat_chr6.simRat.chr6 14835 14 + 647215 AAGACAGATATTGT - -a -s simMouse_chr6.simMouse.chr6 22725 6 + 636262 AACACA -s Anc0.Anc0refChr9 1034 6 + 35212 AATCCA -s Anc1.Anc1refChr2 124689 6 - 144309 AATCCA -s Anc2.Anc2refChr0 19596 6 - 56053 CACCCA -s mr.mrrefChr0 21164 6 + 130230 AATACA -s simCow_chr6.simCow.chr6 560100 6 - 602619 CACTCA -s simDog_chr6.simDog.chr6 556539 6 - 593897 CACCAG -s simHuman_chr6.simHuman.chr6 563887 6 - 601863 AATCCA -s simRat_chr6.simRat.chr6 14849 6 + 647215 AATGCA - -a -s simMouse_chr6.simMouse.chr6 22731 9 + 636262 CAAATCTGT -s Anc0.Anc0refChr9 1075 9 + 35212 TGAATCTGT -s Anc1.Anc1refChr2 124730 9 - 144309 TGAATCTGT -s Anc2.Anc2refChr0 19637 9 - 56053 TGAATCTGT -s mr.mrrefChr0 21205 9 + 130230 CAAATCTGT -s simCow_chr6.simCow.chr6 560141 9 - 602619 TGGATCTGT -s simDog_chr6.simDog.chr6 556583 9 - 593897 TGAGTCTGC -s simHuman_chr6.simHuman.chr6 563928 9 - 601863 TGAATCTGT -s simRat_chr6.simRat.chr6 14891 9 + 647215 CTAATCTCT - -a -s simMouse_chr6.simMouse.chr6 22740 11 + 636262 TGTGATGATCC -s Anc0.Anc0refChr9 1085 11 + 35212 TATGTTGATCC -s Anc1.Anc1refChr2 124740 11 - 144309 TATGTTGATCC -s Anc2.Anc2refChr0 19647 11 - 56053 TATGTTGATCC -s mr.mrrefChr0 21214 11 + 130230 TGTGATGATCC -s simCow_chr6.simCow.chr6 560151 11 - 602619 TATGTCAATCG -s simDog_chr6.simDog.chr6 556593 11 - 593897 TATGTTGATCC -s simHuman_chr6.simHuman.chr6 563938 11 - 601863 TATGTTGATCC -s simRat_chr6.simRat.chr6 14900 11 + 647215 TGTGCTGATCC - -a -s simMouse_chr6.simMouse.chr6 22751 18 + 636262 TACTGAGTAATTGAGGTG -s Anc0.Anc0refChr9 1104 1 + 35212 T----------------- -s Anc1.Anc1refChr2 124759 4 - 144309 TTCA-------------- -s Anc2.Anc2refChr0 19666 1 - 56053 T----------------- -s mr.mrrefChr0 21225 18 + 130230 TACAAAGTAATTGAGGTG -s simDog_chr6.simDog.chr6 556612 1 - 593897 T----------------- -s simHuman_chr6.simHuman.chr6 563957 4 - 601863 TTCA-------------- -s simRat_chr6.simRat.chr6 14911 18 + 647215 TACAAAGTAATTGAGGTA - -a -s simMouse_chr6.simMouse.chr6 22769 69 + 636262 ACCCCCATCAATTAGCAAGTAAGTCACATCTAGTACTTACCAGAAGCAGACCAGTTGTATTAGTGTAGA -s Anc0.Anc0refChr9 1105 11 + 35212 ----------------------------------------------------------CTAAGTGCAGT -s Anc1.Anc1refChr2 124763 12 - 144309 ---------------------------------------------------------TCTAAGTGCAGT -s Anc2.Anc2refChr0 19812 11 - 56053 ----------------------------------------------------------TTGAATGCAGT -s mr.mrrefChr0 21243 58 + 130230 ACCCCCATCAATTAGCAAGTAAGTC-----------TTACCAGAAGCAGACCAGTTGTATTAGTGTAGA -s simCow_chr6.simCow.chr6 560310 11 - 602619 ----------------------------------------------------------TCAAATGCAAT -s simDog_chr6.simDog.chr6 556762 11 - 593897 ----------------------------------------------------------TTGAATGCAGT -s simHuman_chr6.simHuman.chr6 563961 10 - 601863 ---------------------------------------------------------TCTGAGTACA-- -s simRat_chr6.simRat.chr6 14968 58 + 647215 ACCCCCATTGATGAGCACGTAAGTC-----------TTACCGGAAGCAGACCAGCTGTGTTAGTGAAGA - -a -s simMouse_chr6.simMouse.chr6 22838 78 + 636262 ATATATGTAGGTGCTACTTGTCACTGACAACCACTTTTACCATTAAGAGCAGCTTAAATCTTCCAGTTTTACATCTAG -s Anc0.Anc0refChr9 1116 74 + 35212 A---ATGTAGACACAAATTGTCTCTGACAGCCTCCTT-ACCATTAGGGGAGGCTAAACTCATGTTTTTTTGTACCTAT -s Anc1.Anc1refChr2 124775 74 - 144309 A---ATGTAGACACAAATTGTCTCTGACAGCCTCCTT-ACCATTAGGGGAGGCTAAACTCATGTTTTTTTGTACCTAT -s Anc2.Anc2refChr0 19823 74 - 56053 A---ATGTAGACACAAATTGATTTTAATAGCCTCCTT-ACCATTAGGGGAGGATAAACTCATGTCTTTCTGTACTTAT -s mr.mrrefChr0 21301 78 + 130230 ATATATGTAGGTGCTACTTGTCACTGACAACCACTTTTACCATTAAGAGCAGCTAAAATCTTCCTGTTTTACATCTAG -s simCow_chr6.simCow.chr6 560321 41 - 602619 A---ATGTTGAGGCAAATTGACTTTGACGGCCCCCTT-ACCATTG--------------------------------- -s simDog_chr6.simDog.chr6 556779 74 - 593897 A---ATGTAGACACAAATTGATTTTAATAGCCTTCTT-AATATTAGGGGAGGATAAACTCATGTCTTTCTGTACTTAT -s simHuman_chr6.simHuman.chr6 563971 74 - 601863 A---AGTGAAAGAGGTTTAGTCTCTGACAGCCTCCTT-ACCATCAGGGGAGGCTAAATTCATGTTTTTTTGTACCTAT -s simRat_chr6.simRat.chr6 15026 69 + 647215 ATATATGTAGGTGCTACTTGTCAC-------CACTTGTA--ACTGACAGCAGCTAAAATCTTCCTGATTTACATCTAG - -a -s simMouse_chr6.simMouse.chr6 22916 100 + 636262 CTATGAATGTTCTCTCTTGGCATCGATAACCATTTGCAGTACTAGACACACAAAGGGCATCGCTTAGCATGTGCCAACCTTCAACTTCAATTTCTTACTC -s Anc0.Anc0refChr9 1190 48 + 35212 CTACCAATGTTC-----------------------------------------------TCTCTT----TCTTTCAACCACCAACTTCCATTTCTTACT- -s Anc1.Anc1refChr2 124849 54 - 144309 CTACCAATGTTCTCTCTC-----------------------------------------TCTCTT----TCTTTCAACCACCAACTTCCATTTCTTACT- -s Anc2.Anc2refChr0 19897 48 - 56053 CTGCCAAAGTGC-----------------------------------------------TCTCTT----TCTTTGAACCACCAATTTCCATTTCATATT- -s mr.mrrefChr0 21379 100 + 130230 CTATGAATGTTCTCTCTTGGCATCGATAACCATTTGCAGTACTAGACACACAAAGGGCATCGCTTAGCATGTGCCAACCTTCAACTTCAATTTCTTACTC -s simCow_chr6.simCow.chr6 560362 48 - 602619 CTGAAACTGTGC-----------------------------------------------ACTCTT----TCTGTGAATCACCAATTTCCATTTCATATT- -s simDog_chr6.simDog.chr6 556854 48 - 593897 CTGCCAAAGTGC-----------------------------------------------TCCCCT----TTTTTGAACCACCAATTTTCATTCCATGTT- -s simHuman_chr6.simHuman.chr6 564045 54 - 601863 CTACAAGTGTTCTTTCTC-----------------------------------------TCTCTT----TCTCTCAAGCACCAACTTCTATTTCTCACT- -s simRat_chr6.simRat.chr6 15095 99 + 647215 CTATGAACGTTCGCCCTTGGCATCACCAACCATTTGTAGTACTGGAGATAGGTAAGGCACTGCTTAGCATGAGCCAACCTTCAACCT-GATTTCTTACTC - -a -s simMouse_chr6.simMouse.chr6 23016 22 + 636262 TTTGACGAGTATATAACTTAAT -s Anc0.Anc0refChr9 1238 22 + 35212 TGTGATATGGATGTGTTTGTAT -s Anc1.Anc1refChr2 124903 22 - 144309 TGTGATATGGATGTGTTTGTAT -s Anc2.Anc2refChr0 19945 22 - 56053 TGTGATATGGATGTGTTTGTAT -s mr.mrrefChr0 21479 22 + 130230 TTTGACAAGTATATAACTTAAT -s simCow_chr6.simCow.chr6 560411 22 - 602619 TATCGAATGGATCTGTTTGTAT -s simDog_chr6.simDog.chr6 556935 22 - 593897 TGTGATATGGATGTGTTTGTAT -s simHuman_chr6.simHuman.chr6 564099 22 - 601863 TGTGATATGGATGTGTTTGTAT -s simRat_chr6.simRat.chr6 15194 22 + 647215 TTCGACAAGTATATAGCTTAAT - -a -s simMouse_chr6.simMouse.chr6 23038 4 + 636262 ATAC -s Anc0.Anc0refChr9 1267 4 + 35212 ATAC -s Anc1.Anc1refChr2 124932 4 - 144309 ATAC -s Anc2.Anc2refChr0 19976 4 - 56053 ATAT -s mr.mrrefChr0 21501 4 + 130230 ATAC -s simCow_chr6.simCow.chr6 560442 4 - 602619 CTAC -s simDog_chr6.simDog.chr6 556966 4 - 593897 ATAT -s simHuman_chr6.simHuman.chr6 564128 4 - 601863 ATAC -s simRat_chr6.simRat.chr6 15216 4 + 647215 ATAC - -a -s simMouse_chr6.simMouse.chr6 23042 41 + 636262 CTTACACTTCCAACCCTGTAACAGATAGCCGATTTGCTTCC -s Anc0.Anc0refChr9 1271 41 + 35212 CTTACACCTCCAATCCTCCAACAGTTGCCTAGCCAATTTCC -s Anc1.Anc1refChr2 124936 41 - 144309 CTTACACCTCCAATCCTCCAACAGTTGCCTAGCCAATTTCC -s Anc2.Anc2refChr0 19980 41 - 56053 CTTATACCTCCAATTCTCCAACATTAGCCCAGCCAATTTCT -s mr.mrrefChr0 21505 41 + 130230 CTTACACTTCCAACCCTGTAACAGATAGCTGATTTATTTCC -s simCow_chr6.simCow.chr6 560446 41 - 602619 TTTGTGCCTCCAATACTCCAACTATAATCCAGCCCATTTTT -s simDog_chr6.simDog.chr6 556970 41 - 593897 CTTATACTTCTAATTTGCCAACATTAGCCCAGCCAATGTCT -s simHuman_chr6.simHuman.chr6 564133 41 - 601863 CCTACAGCTCCAATCCTCCAGCAGTTGACTAGCCAATTCCC -s simRat_chr6.simRat.chr6 15220 30 + 647215 -----------AACCCTGTAACAGATAGCTGATTCATTTCC - -a -s simMouse_chr6.simMouse.chr6 23083 36 + 636262 CTGCCAGGTTTCCCTTCCATAATGTCTAGTCCCTGC -s Anc0.Anc0refChr9 1312 32 + 35212 TTGCC----TTAATCTCCAGCTTGTCTAGTCACTAA -s Anc1.Anc1refChr2 124977 32 - 144309 TTGCC----TTAATCTCCAGCTTGTCTAGTCACTAA -s Anc2.Anc2refChr0 20039 32 - 56053 TTGCC----TTAATCTCCAGCTTGTCTAGTGACTAA -s mr.mrrefChr0 21546 36 + 130230 CTGCCAGATTTCCTTTCCATAATGTCTAGTCCCTGC -s simCow_chr6.simCow.chr6 560505 30 - 602619 TTGCC----C--ATCTCCAGCTTGTCTAGTGAGTTA -s simDog_chr6.simDog.chr6 557030 32 - 593897 TTGCC----TTAATCTCTAGCTTATCTAGTGACTAA -s simHuman_chr6.simHuman.chr6 564174 32 - 601863 TTGCA----TTAATCACCAGCTTGTCTAGTCACTAA -s simRat_chr6.simRat.chr6 15250 36 + 647215 CTGTCAGATCTCCTTTCTGTAATGTCTAATCCCTGC - -a -s simMouse_chr6.simMouse.chr6 23119 4 + 636262 AGTA -s Anc0.Anc0refChr9 1344 4 + 35212 GGTG -s Anc1.Anc1refChr2 125009 4 - 144309 GGTG -s Anc2.Anc2refChr0 20071 4 - 56053 GGTG -s mr.mrrefChr0 21582 4 + 130230 AGTG -s simCow_chr6.simCow.chr6 560535 4 - 602619 GGTG -s simDog_chr6.simDog.chr6 557087 4 - 593897 GGTG -s simHuman_chr6.simHuman.chr6 564206 4 - 601863 GGTG -s simRat_chr6.simRat.chr6 15286 4 + 647215 AATG - -a -s simMouse_chr6.simMouse.chr6 23123 1 + 636262 T -s Anc0.Anc0refChr9 1352 1 + 35212 T -s Anc1.Anc1refChr2 125017 1 - 144309 T -s Anc2.Anc2refChr0 20079 1 - 56053 T -s mr.mrrefChr0 21586 1 + 130230 T -s simCow_chr6.simCow.chr6 560543 1 - 602619 T -s simDog_chr6.simDog.chr6 557095 1 - 593897 T -s simHuman_chr6.simHuman.chr6 564214 1 - 601863 T -s simRat_chr6.simRat.chr6 15290 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 23124 1 + 636262 T -s Anc0.Anc0refChr9 1353 1 + 35212 T -s Anc1.Anc1refChr2 125018 1 - 144309 T -s Anc2.Anc2refChr0 20080 1 - 56053 T -s mr.mrrefChr0 21587 1 + 130230 T -s simCow_chr6.simCow.chr6 560546 1 - 602619 T -s simDog_chr6.simDog.chr6 557096 1 - 593897 T -s simHuman_chr6.simHuman.chr6 564215 1 - 601863 T -s simRat_chr6.simRat.chr6 15291 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 23125 37 + 636262 GCATTTGTTGGGTAGCTAACTTAGCCCGCTATGCTGC -s Anc0.Anc0refChr9 1354 37 + 35212 TAGCTAGCTAGGTAGCTCACTTAGCCTGGTAAGATGC -s Anc1.Anc1refChr2 125019 37 - 144309 TAGCTAGCTAGGTAGCTCACTTAGCCTGGTAAGATGC -s Anc2.Anc2refChr0 20083 37 - 56053 TAGCTAGGTAGGTAGCTCACTTAGCCTGGTAAGATGC -s mr.mrrefChr0 21588 37 + 130230 TCGTTTGCTGGGTAGCTAACTTAGCCTGCTATGATGC -s simCow_chr6.simCow.chr6 560549 35 - 602619 TGGCTGGGAAGCT--CTCACTAAGCCAAGTGAGATGA -s simDog_chr6.simDog.chr6 557099 37 - 593897 TAATCAGGTAGGTAGTTCACTTAGCCTGGTAAGATGC -s simHuman_chr6.simHuman.chr6 564216 37 - 601863 TAGCTAGCCATGTAGCTTGCCTAGCCTGGTAAGAAGC -s simRat_chr6.simRat.chr6 15292 37 + 647215 TCGTTTGCTGGGTAGCAAACTTAGCCTGCTATGATGC - -a -s simMouse_chr6.simMouse.chr6 23162 10 + 636262 TGCCAATTAA -s Anc0.Anc0refChr9 1395 10 + 35212 TGCCAATTTG -s Anc1.Anc1refChr2 125060 10 - 144309 TGCCAATTTG -s Anc2.Anc2refChr0 20124 10 - 56053 TGCCTATTTG -s mr.mrrefChr0 21625 10 + 130230 TGCCAATTTA -s simCow_chr6.simCow.chr6 560588 10 - 602619 TGCCTATTTG -s simDog_chr6.simDog.chr6 557140 10 - 593897 TGCCTGTTCG -s simHuman_chr6.simHuman.chr6 564257 10 - 601863 CGCCAATTTG -s simRat_chr6.simRat.chr6 15329 10 + 647215 TGCCAATTTA - -a -s simMouse_chr6.simMouse.chr6 23172 3 + 636262 CAG -s Anc0.Anc0refChr9 1406 3 + 35212 AAG -s Anc1.Anc1refChr2 125071 3 - 144309 AAG -s Anc2.Anc2refChr0 20135 3 - 56053 AAC -s mr.mrrefChr0 21635 3 + 130230 CAG -s simDog_chr6.simDog.chr6 557151 3 - 593897 AAC -s simHuman_chr6.simHuman.chr6 564268 3 - 601863 AAG -s simRat_chr6.simRat.chr6 15339 3 + 647215 CAG - -a -s simMouse_chr6.simMouse.chr6 23175 23 + 636262 CAAACCTACCACATTGCCCCCTG -s Anc0.Anc0refChr9 1414 23 + 35212 CAAACCTGACACTTTCGCACCTA -s Anc1.Anc1refChr2 125079 23 - 144309 CAAACCTGACACTTTCGCACCTA -s Anc2.Anc2refChr0 20143 23 - 56053 CAAACTTGACACTTTCGCACTTA -s mr.mrrefChr0 21643 23 + 130230 CAAACCTAACACATTGCCCCCTA -s simCow_chr6.simCow.chr6 560598 8 - 602619 ---------------CGCACTTA -s simDog_chr6.simDog.chr6 557159 23 - 593897 CAAACTTGACACTTTTGTACTTA -s simHuman_chr6.simHuman.chr6 564276 23 - 601863 CAAGCCTGACACTTTCACTCCTA -s simRat_chr6.simRat.chr6 15347 23 + 647215 CAAACCTAACACATTGCTCCCTA - -a -s simMouse_chr6.simMouse.chr6 23198 9 + 636262 GACTTTGCT -s Anc0.Anc0refChr9 1439 9 + 35212 GATTCTGCC -s Anc1.Anc1refChr2 125104 9 - 144309 GATTCTGCC -s Anc2.Anc2refChr0 20168 9 - 56053 AATTCTGCC -s mr.mrrefChr0 21666 9 + 130230 GACTTTGCC -s simCow_chr6.simCow.chr6 560608 9 - 602619 AATCCTGCT -s simDog_chr6.simDog.chr6 557184 9 - 593897 AATTCTCTC -s simHuman_chr6.simHuman.chr6 564301 9 - 601863 GATTCTGCC -s simRat_chr6.simRat.chr6 15370 9 + 647215 GACTTTGCC - -a -s simMouse_chr6.simMouse.chr6 23207 2 + 636262 CA -s Anc0.Anc0refChr9 1448 2 + 35212 CA -s Anc1.Anc1refChr2 125113 2 - 144309 CA -s Anc2.Anc2refChr0 20179 2 - 56053 CA -s mr.mrrefChr0 21675 2 + 130230 CA -s simCow_chr6.simCow.chr6 560619 2 - 602619 CA -s simDog_chr6.simDog.chr6 557195 2 - 593897 CA -s simHuman_chr6.simHuman.chr6 564310 2 - 601863 CA -s simRat_chr6.simRat.chr6 15379 2 + 647215 CA - -a -s simMouse_chr6.simMouse.chr6 23209 15 + 636262 TGCCCTCGCATAGAG -s Anc0.Anc0refChr9 1450 12 + 35212 CACT---GTATAGAG -s Anc1.Anc1refChr2 125115 12 - 144309 CACT---GTATAGAG -s Anc2.Anc2refChr0 20181 12 - 56053 CACT---GTACAGAG -s mr.mrrefChr0 21677 15 + 130230 TACCCTCGTATAGAG -s simCow_chr6.simCow.chr6 560631 12 - 602619 CACT---CTACAGAG -s simDog_chr6.simDog.chr6 557197 12 - 593897 CACT---GTACAGAG -s simHuman_chr6.simHuman.chr6 564312 12 - 601863 GACT---GTATAGAG -s simRat_chr6.simRat.chr6 15381 15 + 647215 CACACTAGTAAAAAG - -a -s simMouse_chr6.simMouse.chr6 23224 48 + 636262 ACAGTCCAAGTGGTTTCGGTTTCTTGAATTTACTAATCTCTACACTCT -s Anc0.Anc0refChr9 1476 48 + 35212 ATAGTCGTAGTTGCCATGGTTTGCATAACTTGGAATGTTCAACACACT -s Anc1.Anc1refChr2 125141 48 - 144309 ATAGTCGTAGTTGCCATGGTTTGCATAACTTGGAATGTTCAACACACT -s Anc2.Anc2refChr0 20207 48 - 56053 ATAGCCGTAGTTGCCATGGTTTGCATAACTTGGAATGTTCAACATACT -s mr.mrrefChr0 21692 48 + 130230 ACAGTCCAAGTGGTTTCGGTTTCTTTAATTTAGTAATCTCTACACTCT -s simCow_chr6.simCow.chr6 560657 48 - 602619 ATTGCTGTAGTTGCCATAGTCTGCTTAAATTGGAATGTTCAATAAGCT -s simDog_chr6.simDog.chr6 557223 42 - 593897 ATAGCCGTAGTTGCCATGGTTTGCATAACTTGGAA------ACATACT -s simHuman_chr6.simHuman.chr6 564338 48 - 601863 ATAGTCATAGTTACGGTGGTGTGCCTGACCTGGAATGATCAACACCCT -s simRat_chr6.simRat.chr6 15396 48 + 647215 ACAGCCCAATTCGTTTCAGTTTCTTTAATTCAGTAGTCTCTACACTCT - -a -s simMouse_chr6.simMouse.chr6 23272 4 + 636262 TGTG -s Anc0.Anc0refChr9 1527 4 + 35212 GGTG -s Anc1.Anc1refChr2 125192 4 - 144309 GGTG -s Anc2.Anc2refChr0 20258 4 - 56053 CGTG -s mr.mrrefChr0 21743 4 + 130230 GGTG -s simCow_chr6.simCow.chr6 560708 4 - 602619 ATTG -s simDog_chr6.simDog.chr6 557268 4 - 593897 CGTG -s simHuman_chr6.simHuman.chr6 564389 4 - 601863 GGTG -s simRat_chr6.simRat.chr6 15447 4 + 647215 GGTG - -a -s simMouse_chr6.simMouse.chr6 23276 34 + 636262 CACTATACTAACAGGATGAAGGGGTCTCACATAC -s Anc0.Anc0refChr9 1534 34 + 35212 TGTTACAGAAACAGGATAGATCGGTCTCACTTAC -s Anc1.Anc1refChr2 125199 34 - 144309 TGTTACAGAAACAGGATAGATCGGTCTCACTTAC -s Anc2.Anc2refChr0 20265 34 - 56053 TGTTACAGAAACAGGATAGATCGGTCTCACTTAC -s mr.mrrefChr0 21747 34 + 130230 TGCTATACTAACAGGATGAAGGGGTCTCACATAC -s simCow_chr6.simCow.chr6 560727 33 - 602619 TGTTAGAGGAAAAGAATAGGACAGTCT-ACTTAA -s simDog_chr6.simDog.chr6 557275 33 - 593897 TGTTAC-GAAACAGGACGGATTGGTCCCATGTAC -s simHuman_chr6.simHuman.chr6 564396 34 - 601863 TGTTACAGAAACAGGATAGATCGGTCTCACTTAC -s simRat_chr6.simRat.chr6 15451 34 + 647215 TGCTAAACTAACAAGAAGAAGGGGTTTCACACAC - -a -s simMouse_chr6.simMouse.chr6 23310 18 + 636262 CAGGGGTTCCCCTTTGAG -s Anc0.Anc0refChr9 1568 18 + 35212 CAGGGTTTGCTTTTGGAG -s Anc1.Anc1refChr2 125233 18 - 144309 CAGGGTTTGCTTTTGGAG -s Anc2.Anc2refChr0 20299 18 - 56053 CAGGGTTTTCTTTAGGAG -s mr.mrrefChr0 21781 18 + 130230 CAGGGGTTGCCCTTTGAG -s simCow_chr6.simCow.chr6 560770 18 - 602619 CACTGTGACCTTGAGGAG -s simDog_chr6.simDog.chr6 557308 16 - 593897 AGGGATTTTCTTT--AAG -s simHuman_chr6.simHuman.chr6 564430 18 - 601863 CAGGGTTTGCTTTTGGAG -s simRat_chr6.simRat.chr6 15485 18 + 647215 CAGGGGTTGCCCTTTGAG - -a -s simMouse_chr6.simMouse.chr6 23328 9 + 636262 GTGATGAAA -s Anc0.Anc0refChr9 1586 9 + 35212 GTGCTAAAG -s Anc1.Anc1refChr2 125251 9 - 144309 GTGCTAAAG -s Anc2.Anc2refChr0 20317 9 - 56053 GTGCTAATG -s mr.mrrefChr0 21799 9 + 130230 GTGATAAAA -s simCow_chr6.simCow.chr6 560809 9 - 602619 GTGTTAGGG -s simDog_chr6.simDog.chr6 557324 9 - 593897 GTGCATATG -s simHuman_chr6.simHuman.chr6 564448 9 - 601863 GTGCTAAAG -s simRat_chr6.simRat.chr6 15503 9 + 647215 GTGATAAAA - -a -s simMouse_chr6.simMouse.chr6 23337 30 + 636262 CACTATGACTTTATATTTCATGGCAAAATT -s Anc0.Anc0refChr9 1595 30 + 35212 CACTATAGCCTCATATTTCATGACAAAATG -s Anc1.Anc1refChr2 125260 30 - 144309 CACTATAGCCTCATATTTCATGACAAAATG -s Anc2.Anc2refChr0 20326 30 - 56053 CACTATAGCCTCATATTTTATGACAAAATG -s mr.mrrefChr0 21808 30 + 130230 CACTATGACTTTATATTTCATGGCAAAATT -s simCow_chr6.simCow.chr6 560819 30 - 602619 CAGCATAGCATCATATTTTATTAAAAAATG -s simDog_chr6.simDog.chr6 557333 30 - 593897 CACTACAACCTCCTATTTTATGACAAAACA -s simHuman_chr6.simHuman.chr6 564457 30 - 601863 CACAATAGCGTCATATTGCATGACGAAATG -s simRat_chr6.simRat.chr6 15512 30 + 647215 CACTATGACTTTATATTTCATGGCAGAATT - -a -s simMouse_chr6.simMouse.chr6 23367 4 + 636262 TGAG -s Anc0.Anc0refChr9 1625 4 + 35212 TGAG -s Anc1.Anc1refChr2 125290 4 - 144309 TGAG -s Anc2.Anc2refChr0 20356 4 - 56053 TGAG -s mr.mrrefChr0 21838 4 + 130230 TGAG -s simCow_chr6.simCow.chr6 561047 4 - 602619 TGAG -s simDog_chr6.simDog.chr6 557363 4 - 593897 TGAG -s simHuman_chr6.simHuman.chr6 564487 4 - 601863 TGAG -s simRat_chr6.simRat.chr6 15542 4 + 647215 TGAG - -a -s simMouse_chr6.simMouse.chr6 23371 48 + 636262 ACAGAGCTGGTTGTCCCTATGGGCAGTAACTGACTTTGTTCAATCTGT -s Anc0.Anc0refChr9 1629 48 + 35212 ACAAATTTTGATGTGCCTATGGACAGGAACTGACATTGTTTGATCTGC -s Anc1.Anc1refChr2 125294 48 - 144309 ACAAATTTTGATGTGCCTATGGACAGGAACTGACATTGTTTGATCTGC -s Anc2.Anc2refChr0 20360 48 - 56053 ACAGATTTTGATGTGCCTATGGACTGGAACTGACATTGGTTGGTCTGC -s mr.mrrefChr0 21842 48 + 130230 ACAAAGCTGGTTGTCCCTATGGGCAGTAACTGACTTTGTTTGATCTGT -s simCow_chr6.simCow.chr6 561052 36 - 602619 ACAGATTTTGATCTTCCTA------GGGACTGACATT------TCTGC -s simDog_chr6.simDog.chr6 557367 48 - 593897 ACAGATGTTGATGTGCCTATGGACTGTAACTGACATTGGTTGGTCTGT -s simHuman_chr6.simHuman.chr6 564491 48 - 601863 ACAAATTTTGATGTGCCTGTGGATAGGAACTGACATTGTTTGATCTGC -s simRat_chr6.simRat.chr6 15546 48 + 647215 ACAAAGCTGGTTGTCCCTATGGGCAGTAACTGACTTTGTCTGATCTGT - -a -s simMouse_chr6.simMouse.chr6 23419 19 + 636262 ATTGTATGTGATCTGTCTC -s Anc0.Anc0refChr9 1683 7 + 35212 AT----CC--------CTT -s Anc1.Anc1refChr2 125348 11 - 144309 ATTGCACC--------CTT -s Anc2.Anc2refChr0 20414 7 - 56053 AT----CC--------GGT -s mr.mrrefChr0 21890 19 + 130230 ATTGTATGTGATCTGTCTC -s simDog_chr6.simDog.chr6 557421 7 - 593897 AT----CC--------GGT -s simHuman_chr6.simHuman.chr6 564545 11 - 601863 ATTGCACA--------CTT -s simRat_chr6.simRat.chr6 15594 14 + 647215 ATT-----TGATCTGTCTC - -a -s simMouse_chr6.simMouse.chr6 23438 19 + 636262 AATAGCACTTTTTATGAGT -s Anc0.Anc0refChr9 1690 19 + 35212 ATTAGTACCTTTTATGATG -s Anc1.Anc1refChr2 125359 19 - 144309 ATTAGTACCTTTTATGATG -s Anc2.Anc2refChr0 20421 19 - 56053 ATTATTACCTTTTATGATG -s mr.mrrefChr0 21909 19 + 130230 AATAGTACTTTTTATGATT -s simCow_chr6.simCow.chr6 561091 19 - 602619 ATTATTACCTTTTACGATG -s simDog_chr6.simDog.chr6 557428 19 - 593897 GCCATTATGTCTTATGATG -s simHuman_chr6.simHuman.chr6 564556 19 - 601863 ATTAGTACCTTTTATGATG -s simRat_chr6.simRat.chr6 15609 19 + 647215 AGTAATGCTTTTTATGATT - -a -s simMouse_chr6.simMouse.chr6 23457 2 + 636262 GT -s Anc0.Anc0refChr9 1709 2 + 35212 GT -s Anc1.Anc1refChr2 125378 2 - 144309 GT -s Anc2.Anc2refChr0 20442 2 - 56053 AT -s mr.mrrefChr0 21928 2 + 130230 GT -s simCow_chr6.simCow.chr6 561112 2 - 602619 AC -s simDog_chr6.simDog.chr6 557449 2 - 593897 AT -s simHuman_chr6.simHuman.chr6 564575 2 - 601863 GT -s simRat_chr6.simRat.chr6 15628 2 + 647215 GT - -a -s simMouse_chr6.simMouse.chr6 23459 8 + 636262 ATGTGTTA -s Anc0.Anc0refChr9 1729 8 + 35212 CTGTGTCA -s Anc1.Anc1refChr2 125398 8 - 144309 CTGTGTCA -s Anc2.Anc2refChr0 20462 8 - 56053 CTGTGTCA -s mr.mrrefChr0 21930 8 + 130230 ATGTGTTA -s simCow_chr6.simCow.chr6 561128 8 - 602619 CTGTGTTA -s simDog_chr6.simDog.chr6 557470 8 - 593897 CTGTATCA -s simHuman_chr6.simHuman.chr6 564595 8 - 601863 CTGTGTCA -s simRat_chr6.simRat.chr6 15630 8 + 647215 ATGTGTTA - -a -s simMouse_chr6.simMouse.chr6 23467 6 + 636262 ATGATC -s Anc0.Anc0refChr9 1738 6 + 35212 ATGATT -s Anc1.Anc1refChr2 125407 6 - 144309 ATGATT -s Anc2.Anc2refChr0 20471 6 - 56053 ATGATT -s mr.mrrefChr0 21938 6 + 130230 ATGATC -s simCow_chr6.simCow.chr6 561137 6 - 602619 ATGATT -s simDog_chr6.simDog.chr6 557479 6 - 593897 ATGATT -s simHuman_chr6.simHuman.chr6 564604 6 - 601863 ACGATT -s simRat_chr6.simRat.chr6 15638 6 + 647215 ATGATC - -a -s simMouse_chr6.simMouse.chr6 23473 17 + 636262 ATTCCAGAATCCGCTAA -s Anc0.Anc0refChr9 1776 17 + 35212 AGTCAGGATTATAATGA -s Anc1.Anc1refChr2 125445 17 - 144309 AGTCAGGATTATAATGA -s Anc2.Anc2refChr0 20520 17 - 56053 AGTCAGGATTATAATGA -s mr.mrrefChr0 21944 17 + 130230 ATTCAGGAATCCGCTGA -s simCow_chr6.simCow.chr6 561187 17 - 602619 AGTCAGGATTATAAAGA -s simDog_chr6.simDog.chr6 557528 17 - 593897 AGTCAGGATTATAGTGA -s simHuman_chr6.simHuman.chr6 564642 17 - 601863 AGTCAGGATTATAATGA -s simRat_chr6.simRat.chr6 15644 17 + 647215 ATTTAGGAATCAGCTGA - -a -s simMouse_chr6.simMouse.chr6 23490 6 + 636262 AAAATA -s Anc0.Anc0refChr9 1793 6 + 35212 AAGATA -s Anc1.Anc1refChr2 125462 6 - 144309 AAGATA -s Anc2.Anc2refChr0 20537 6 - 56053 AAGATA -s mr.mrrefChr0 21961 6 + 130230 AAGATA -s simCow_chr6.simCow.chr6 561204 6 - 602619 AAGATA -s simDog_chr6.simDog.chr6 557545 6 - 593897 GAGAAG -s simHuman_chr6.simHuman.chr6 564659 6 - 601863 AAGATA -s simRat_chr6.simRat.chr6 15664 6 + 647215 TGGACA - -a -s simMouse_chr6.simMouse.chr6 23496 7 + 636262 CCTGAGA -s Anc0.Anc0refChr9 1804 7 + 35212 TATGAAA -s Anc1.Anc1refChr2 125473 7 - 144309 TATGAAA -s Anc2.Anc2refChr0 20548 7 - 56053 TATGTAA -s mr.mrrefChr0 21972 7 + 130230 TCTGAGA -s simCow_chr6.simCow.chr6 561215 7 - 602619 TATATTA -s simDog_chr6.simDog.chr6 557556 7 - 593897 TATGTAA -s simHuman_chr6.simHuman.chr6 564670 7 - 601863 TATGAAA -s simRat_chr6.simRat.chr6 15675 7 + 647215 TCTGAGA - -a -s simMouse_chr6.simMouse.chr6 23503 57 + 636262 GGTGGCGAACTAAAGCATAGACAAGATACCTCAATACCTGAAGAGTGGTGGGTAGTT -s Anc0.Anc0refChr9 1822 49 + 35212 GGGAACCAACTAAAGCATGGACAA--------AATACCTGAAGAGTGTCAAGTATTT -s Anc1.Anc1refChr2 125491 49 - 144309 GGGAACCAACTAAAGCATGGACAA--------AATACCTGAAGAGTGTCAAGTATTT -s Anc2.Anc2refChr0 20566 49 - 56053 AGGAACCAACTAAAGCATGGACAA--------AATACCTGAAGAGAGTCAAGTATTT -s mr.mrrefChr0 21979 49 + 130230 GGTGGCGAACTAAAGCATAGACAA--------AATACCTGAAGAGTGGTGAGTAGTT -s simCow_chr6.simCow.chr6 561233 42 - 602619 AGGATCCAACTACAGAATGGACA---------------TGAAGAGAATCAAGTATTT -s simDog_chr6.simDog.chr6 557574 49 - 593897 AGGAACTAACTAAAACATGGACAA--------AATACCTGAAGAGAGTCAAGTATTT -s simHuman_chr6.simHuman.chr6 564688 48 - 601863 GGGAACCAACTGAAGTATGGACAA--------CATACCTGAAGAGTGTCAAGTA-TT -s simRat_chr6.simRat.chr6 15682 49 + 647215 AGTGGCAAACTAATGCTTAGACAA--------AATACCTGAAGACTGGTGAGTAGTT - -a -s simMouse_chr6.simMouse.chr6 23560 25 + 636262 CAATGAGGAAGCTCGCACTTAGCTG -s Anc0.Anc0refChr9 1886 25 + 35212 CAATGAAGAAGATAGCTCTTCAGTG -s Anc1.Anc1refChr2 125555 25 - 144309 CAATGAAGAAGATAGCTCTTCAGTG -s Anc2.Anc2refChr0 20630 25 - 56053 CAATGAAGTAGATAGCTATTCAGTG -s mr.mrrefChr0 22043 25 + 130230 CAATGAGGAAGCTCGCACTTCACTG -s simCow_chr6.simCow.chr6 561290 18 - 602619 CAG-------GATAGCTATTCAGTA -s simDog_chr6.simDog.chr6 557638 25 - 593897 CAATGAAGTAGATAGCTATTCAGTG -s simHuman_chr6.simHuman.chr6 564751 25 - 601863 CAATGAACAAGATAGCTCTTCAGTG -s simRat_chr6.simRat.chr6 15746 25 + 647215 CAATGAGGCAGCTGGCACTTCACTG - -a -s simMouse_chr6.simMouse.chr6 23585 40 + 636262 CAAGAGAACCTACTAAAAGCTATGATTAGTACAACCAAGA -s Anc0.Anc0refChr9 1918 40 + 35212 TGAAACACCCTCCTAAAAACATTGATGAGCATAACCAAAA -s Anc1.Anc1refChr2 125587 40 - 144309 TGAAACACCCTCCTAAAAACATTGATGAGCATAACCAAAA -s Anc2.Anc2refChr0 20662 40 - 56053 TGGAACACCCTCCTAAAAACATTGATGAGCATAACCAAAA -s mr.mrrefChr0 22068 40 + 130230 TAAGAGAACCTACTAAAAGCTATGATGAGTACAACCAAGA -s simCow_chr6.simCow.chr6 561315 40 - 602619 TGGGACGCCCTTCTAACCAGAATGACGAGCATAAGCAAAA -s simDog_chr6.simDog.chr6 557670 40 - 593897 CGGAACACCCCCCTGAAAGCATTGATGAGCATAACCAAAA -s simHuman_chr6.simHuman.chr6 564783 40 - 601863 TGAAACACCCTCCTAAAAACCTTGATGAGCATAACCAAAA -s simRat_chr6.simRat.chr6 15771 39 + 647215 TAAGAGAACCTACTAAAAGCTAT-ATGAGTACAATCAAGA - -a -s simMouse_chr6.simMouse.chr6 23625 5 + 636262 TTAAC -s Anc0.Anc0refChr9 1959 5 + 35212 TTGAC -s Anc1.Anc1refChr2 125628 5 - 144309 TTGAC -s Anc2.Anc2refChr0 20703 5 - 56053 TTGTC -s mr.mrrefChr0 22108 5 + 130230 TTGAC -s simCow_chr6.simCow.chr6 561356 5 - 602619 TTGTT -s simDog_chr6.simDog.chr6 557711 5 - 593897 TTGTC -s simHuman_chr6.simHuman.chr6 564824 5 - 601863 CTGAC -s simRat_chr6.simRat.chr6 15810 5 + 647215 TTGAC - -a -s simMouse_chr6.simMouse.chr6 23630 42 + 636262 CACTGGGCATGGATTGGAGTCTGACTAGAGCATATCTTATCT -s Anc0.Anc0refChr9 1974 42 + 35212 CACTGCCCATGGAATGGAGTGAGACTAGAAAAGATCTTGTTT -s Anc1.Anc1refChr2 125643 42 - 144309 CACTGCCCATGGAATGGAGTGAGACTAGAAAAGATCTTGTTT -s Anc2.Anc2refChr0 20718 42 - 56053 TGCTGCCCATGGAAAGGAGTGAGACTAGAAAAGATCTTGTTT -s mr.mrrefChr0 22113 42 + 130230 CACTGGGCATGGATTGGAGTCTGACTAGAGCATATCTTATCT -s simCow_chr6.simCow.chr6 561371 42 - 602619 TGCCCCCCATGAAAAGGAATTTGACTAGAAAAGATCTTGTTT -s simDog_chr6.simDog.chr6 557726 28 - 593897 TGCTGCCCATGGAAAAGAGGGATTTTAA-------------- -s simHuman_chr6.simHuman.chr6 564839 42 - 601863 CACTGCTCATGGAATGGAGTGAGACTAGAAAACATCTTGTTA -s simRat_chr6.simRat.chr6 15815 42 + 647215 CACTGGGCATGGATTGGAGTCTGGCTAGAGCGTATCTTATCT - -a -s simMouse_chr6.simMouse.chr6 23672 56 + 636262 TCAATTCTTACACATCTGTAGTATGTTATTCCTGGAAGTTTTAAAGCTAGTTTATG -s Anc0.Anc0refChr9 2024 53 + 35212 TCCACTCCCATGCATCTGTAGGGTGTTATTCCTGGGGCTTT--AAACTAGTT-TTG -s Anc1.Anc1refChr2 125693 55 - 144309 TCCACTCCCATGCATCTGTAGGGTGTTATTCCTGGGGCTTTCAAAACTAGTT-TTG -s Anc2.Anc2refChr0 20768 53 - 56053 TCCGCTCCCATGCATATGTAGGGTGTTATTCCTGGGGCCTT--AAACCAGTT-TTG -s mr.mrrefChr0 22155 56 + 130230 TCAATTCTCACACATCTGTAGTGTGTTATTCCTGGAAGTTTTAAAGCTAGTTTATG -s simCow_chr6.simCow.chr6 561423 53 - 602619 TCCGCTCCCATGCATATGTAGGGTGTTATTCCTGGGGCCTT--AAACCAGTT-TTG -s simHuman_chr6.simHuman.chr6 564889 55 - 601863 TCCACCCCCATGCATCAGTAGGGCGTTATACCTGGGGCTTTCAAAAGTGGTT-GTG -s simRat_chr6.simRat.chr6 15857 56 + 647215 TCAATTCTCACACCTCTGTTTTGTGTTATCCCTGGAAGTTTTAAAGCTAGCTTATG - -a -s simMouse_chr6.simMouse.chr6 23728 44 + 636262 TTTGACCTAATGCAGTTAAAGCCTCACTTATTTCAAAGCTAAGA -s Anc0.Anc0refChr9 2077 44 + 35212 TTTAATTTAATGCTGTTCAGGATCCACTTGTTTTAAAGCTAAAA -s Anc1.Anc1refChr2 125748 44 - 144309 TTTAATTTAATGCTGTTCAGGATCCACTTGTTTTAAAGCTAAAA -s Anc2.Anc2refChr0 20821 44 - 56053 TTCAATTGTATGTTGTTCAGGATCTATTTGTTTTATAACCAGAA -s mr.mrrefChr0 22211 44 + 130230 TTTGACCTAATGCAGTTAAAGCCCCACTTATTTTAAAGCTAAGA -s simCow_chr6.simCow.chr6 561479 44 - 602619 TTCAATTGTATGTTGTTCAGGATCTATTTGTTTTATAACCAGAA -s simHuman_chr6.simHuman.chr6 564944 44 - 601863 TGTTATTTAATGCTGTTCAGGATCCACTTGTTCTAAAGCTTAAA -s simRat_chr6.simRat.chr6 15913 42 + 647215 TTTAACCTAATCCAGTCAG-GCCCCACTTATTTTAGG-CCATGA - -a -s simMouse_chr6.simMouse.chr6 23772 27 + 636262 CATACCTGACAGTCTGGAGGCTAGGAC -s Anc0.Anc0refChr9 2121 19 + 35212 AA--------AATCTGGAGGCTAGAAC -s Anc1.Anc1refChr2 125792 19 - 144309 AA--------AATCTGGAGGCTAGAAC -s Anc2.Anc2refChr0 20865 19 - 56053 AA--------GATCTGGAAGTTAGAAC -s mr.mrrefChr0 22255 27 + 130230 CATAACTAACAGTCTGGAGGCTAGGAC -s simCow_chr6.simCow.chr6 561531 19 - 602619 AA--------GATCTGGAAGTTAGAAC -s simHuman_chr6.simHuman.chr6 564988 19 - 601863 AA--------ACTCTGCAGGCTAGCAC -s simRat_chr6.simRat.chr6 15955 27 + 647215 CATAACGAACAGTCTGGAGGCTAGTAC - -a -s simMouse_chr6.simMouse.chr6 23799 31 + 636262 TGATTTGGGGTTGCATAATCTTGCCACAGTT -s Anc0.Anc0refChr9 2140 31 + 35212 TGATTTGAGGTTGCATCATCTGTCCACACTA -s Anc1.Anc1refChr2 125811 31 - 144309 TGATTTGAGGTTGCATCATCTGTCCACACTA -s Anc2.Anc2refChr0 20884 31 - 56053 TGCTCTGAGGTGTTATCATCCGTGCACACTA -s mr.mrrefChr0 22282 31 + 130230 TGATTTGGGGTTGCATAATCTTGCCACACTT -s simCow_chr6.simCow.chr6 561551 31 - 602619 TGCTCTGAGGTGTTATCATCCGTGCACACTA -s simHuman_chr6.simHuman.chr6 565007 31 - 601863 TAATTTGAGGTTGCATGACCTGTCCATACTG -s simRat_chr6.simRat.chr6 15982 31 + 647215 TGATTTGTGGTTGCATAATCTTGCTACACTT - -a -s simMouse_chr6.simMouse.chr6 23830 11 + 636262 TACCTGTTTCC -s Anc0.Anc0refChr9 2171 11 + 35212 TGCTTGTATCC -s Anc1.Anc1refChr2 125842 11 - 144309 TGCTTGTATCC -s Anc2.Anc2refChr0 20915 11 - 56053 TGCTCCTATCC -s mr.mrrefChr0 22313 11 + 130230 TACCTGTTTCC -s simCow_chr6.simCow.chr6 561582 11 - 602619 TGCTCCTATCC -s simHuman_chr6.simHuman.chr6 565044 11 - 601863 TGTTTGTGCCT -s simRat_chr6.simRat.chr6 16013 11 + 647215 TACCTGTTTCC - -a -s simMouse_chr6.simMouse.chr6 23841 33 + 636262 TAACCTATCAAAAGGTGCTTCATAGCAACAATT -s Anc0.Anc0refChr9 2182 30 + 35212 TAAGTTGACCAAAAATGCTTCATGGCCA---TA -s Anc1.Anc1refChr2 125853 30 - 144309 TAAGTTGACCAAAAATGCTTCATGGCCA---TA -s Anc2.Anc2refChr0 20926 30 - 56053 CCAGTTGACCCAAAATGCTTCATGGCCA---TA -s mr.mrrefChr0 22324 30 + 130230 TAACCTATCAAAAGATGCTTCATAGCAA---TT -s simCow_chr6.simCow.chr6 561593 30 - 602619 CCAGTTGATTGAAAATGTTTCATGGCCA---TA -s simDog_chr6.simDog.chr6 557754 24 - 593897 ------GACCCTAAAGACTTCATGGCTA---TA -s simHuman_chr6.simHuman.chr6 565055 30 - 601863 TAAGTTGGCCAAGAATGCTTCATGGACA---TA -s simRat_chr6.simRat.chr6 16026 30 + 647215 TAACCTATCAAAAGATGCTTCCTTGCAA---GT - -a -s simMouse_chr6.simMouse.chr6 23874 19 + 636262 CCATGAGGACAGATAGGTA -s Anc0.Anc0refChr9 2212 19 + 35212 CCATGAGGACAGATAGGCG -s Anc1.Anc1refChr2 125883 19 - 144309 CCATGAGGACAGATAGGCG -s Anc2.Anc2refChr0 20956 19 - 56053 CCATGAGGACAGATAAGCG -s mr.mrrefChr0 22354 19 + 130230 CCATGAGGACAGATAGGTA -s simCow_chr6.simCow.chr6 561623 19 - 602619 CCATGAGGAAAGATAAGTG -s simDog_chr6.simDog.chr6 557786 19 - 593897 CCATGAGGGCAGATAAGCA -s simHuman_chr6.simHuman.chr6 565085 19 - 601863 CGATGAGAACAGATAGGAG -s simRat_chr6.simRat.chr6 16056 19 + 647215 CTGCAAGGACAGATAGGTA - -a -s simMouse_chr6.simMouse.chr6 23893 11 + 636262 ATTAAGGATAT -s Anc0.Anc0refChr9 2269 11 + 35212 ATTAAGTATAT -s Anc1.Anc1refChr2 125940 11 - 144309 ATTAAGTATAT -s Anc2.Anc2refChr0 21013 11 - 56053 ATTAAGTATAT -s mr.mrrefChr0 22373 11 + 130230 ATTAAGGATAT -s simCow_chr6.simCow.chr6 561680 11 - 602619 ATTAAGTTTAT -s simDog_chr6.simDog.chr6 557843 11 - 593897 ATTAAGTATGT -s simHuman_chr6.simHuman.chr6 565142 11 - 601863 ATCAAGTGTAT -s simRat_chr6.simRat.chr6 16075 10 + 647215 ATTTAG-ATAT - -a -s simMouse_chr6.simMouse.chr6 23904 60 + 636262 GAGAGCAAACACCTATTTGTAATAAAGTACACATCTAACTGATGAAGAGTCAGTTCTAAT -s Anc0.Anc0refChr9 2280 60 + 35212 GAGAGCAGTTACATTGTTGTTCTAAAGTATACATCTAATTGATCAAGGGCCAATTCTAAT -s Anc1.Anc1refChr2 125951 60 - 144309 GAGAGCAGTTACATTGTTGTTCTAAAGTATACATCTAATTGATCAAGGGCCAATTCTAAT -s Anc2.Anc2refChr0 21032 60 - 56053 GAGAGCAGTTACACTGTTGTTCTAAAGAATACATCTAATTAATGTAGGGCCAATTCTAGT -s mr.mrrefChr0 22384 60 + 130230 GAGAGCAGACACATATTTGTAATAAAGTACACATCTAACTGATCAAGGGCCAATTCTAAT -s simCow_chr6.simCow.chr6 561699 60 - 602619 AATAGCAGGTACATTGTCATTCTGTTGCATACATCTAATTTATACAGGGCAAAATCTACC -s simDog_chr6.simDog.chr6 557862 60 - 593897 GAGAGCAGTTACACTGTTGTCCTAAAAAATACATCTAACTAATGTATGTCCAATTCTAGT -s simHuman_chr6.simHuman.chr6 565153 58 - 601863 GAGAGCAGCTACAT-CTTGTTCTAAAGTAAA-ATCTAATTGATCAGGGGCCAATTCTGAT -s simRat_chr6.simRat.chr6 16085 60 + 647215 GAGAGCAGACACATATTTGTATTAAAGTACACATCTAACTAATCAAGGGCCAATTCTAGT - -a -s simMouse_chr6.simMouse.chr6 23964 9 + 636262 TTATTGCCT -s Anc0.Anc0refChr9 2340 8 + 35212 TTAT-GTCT -s Anc1.Anc1refChr2 126011 8 - 144309 TTAT-GTCT -s Anc2.Anc2refChr0 21093 8 - 56053 TTAT-GTCC -s mr.mrrefChr0 22444 9 + 130230 TTATTGCCT -s simCow_chr6.simCow.chr6 561760 8 - 602619 GTAT-GTTC -s simDog_chr6.simDog.chr6 557923 8 - 593897 TTCT-GTCC -s simHuman_chr6.simHuman.chr6 565211 8 - 601863 TTAT-GTCT -s simRat_chr6.simRat.chr6 16145 9 + 647215 TTATTGGCT - -a -s simMouse_chr6.simMouse.chr6 23973 118 + 636262 ATTTAGATCCCCAATTTAAATCCCTATATAGCAACTAGTCTCATCCCAAACATGCATGATATAGCACCTCTGCGATTTTAGTAACCTCTACTAGACCTAAGGACAATTTGTAGGTGTG -s Anc0.Anc0refChr9 2348 104 + 35212 ATTTACATCCC-------------TATGTAGAAATTAATCTGATCCCAAACACATCTGAAATGACACCTCTGCACCTGTAGTGACATCTCTTAGACC-AAAAACCGTCTTTAGGCAAG -s Anc1.Anc1refChr2 126019 107 - 144309 ATTTACATCCCTA-----------TATGTAGAAATTAATCTGATCCCAAACACATCTGAAATGACACCTCTGCACCTGTAGTGACATCTCTTAGACCAAAAAACCGTCTTTAGGCAAG -s Anc2.Anc2refChr0 21101 104 - 56053 ATTTACATCCT-------------TATGTAGAAATTAATCTGATCCCAAAAACATCTGGAGTGACACCTCTGCACCTGTAGTGACATCTCTTAGACC-AAAAACAGTCTTCAGGCAAG -s mr.mrrefChr0 22453 118 + 130230 ATTTAGATCCCCAATTTAAATCCCTATATAGCAACTAGTCTCATCCCAAACATGCATGATATAGCACCTCTGCGATTGTAGTAACCTCTACTAGACCTAAGGACCGTTTGTAGGCATG -s simCow_chr6.simCow.chr6 561768 95 - 602619 GTTCAC-CCCT-------------TACATAGAGATCAAT--GATCCCAAAAACTTCTGGAG--ACACCTCTGTACCCGTAGTGACATCTCTCAGTGC-AAGTATACT----AGGTAGG -s simDog_chr6.simDog.chr6 557931 104 - 593897 ATCTACATCCC-------------TAGGTAGAAATTAATGTGATCCCAAAAACATTTGGGATGATATCTGTGCACCTGTAGTGAGTTCTCTTAGACC-AAAAACAGTCTTCAGGCAAG -s simDog_chr6.simDog.chr6 314070 104 - 593897 ATAAACATCCT-------------TATGTAAAAATTAGTCTGATCCTAGAAACATCTCGAGTGGCACCCCTGCAAGTGTAGTGACATCTCTTAGACC-AAAAACAGTCTTCAGGCAAG -s simHuman_chr6.simHuman.chr6 565219 96 - 601863 GTTTACATCCCTA----------------------TGATCTTATCCCAAACACATCTAAAATGACACCCCTGCACATGTAGTGACATCTCTCAGACCAAAAAACCGTCTTTTGGCAAG -s simRat_chr6.simRat.chr6 16154 118 + 647215 ATTTAGATCTCCGATGTAAATCCTTAGATATAATCTAGTCTCATCCCAAACATGCTTGATATAGCACCTAAGTGACTGTAGTCACCTCTGCTAGACCTGAGGACCGTTTGTAGTCATG - -a -s simMouse_chr6.simMouse.chr6 24091 71 + 636262 GGGAGCAAATACTCATACCCATACTCAGTTGCTATTATAGTGATACAGTTCTCTTGGATAGCTTTCCATAA -s Anc0.Anc0refChr9 2454 30 + 35212 AG-----------------------------------------TGCAGTGTACTGGACTAGCTTTCCATAA -s Anc1.Anc1refChr2 126128 30 - 144309 AG-----------------------------------------TGCAGTGTACTGGACTAGCTTTCCATAA -s Anc2.Anc2refChr0 21207 30 - 56053 AA-----------------------------------------TGCAGAGTACTGGACTAGCTTTCCATAA -s mr.mrrefChr0 22573 71 + 130230 GGGAGCAAATACTCATACCCATACTCAGTTGCTATTATAGTGATACAGTTCTCTTGGCTAGCTTTCCATAA -s simCow_chr6.simCow.chr6 561865 29 - 602619 AC-----------------------------------------TGCAGTGTGTGGAGCTATCCTTC-ATAA -s simDog_chr6.simDog.chr6 558037 30 - 593897 AA-----------------------------------------TGCAGAGTACTGGACTAGCTTTACATAA -s simDog_chr6.simDog.chr6 314176 30 - 593897 AA-----------------------------------------TGAATAACACTGCAAAAGCTGTCCATAA -s simHuman_chr6.simHuman.chr6 565317 30 - 601863 AG-----------------------------------------TCCAGTGTGCTGGACTAGCTTTCCATAA -s simRat_chr6.simRat.chr6 16277 71 + 647215 AGGAGCAAATACTTGTACCCACACCTGGTTGCTATTGTAGTGATACTGTACACTTGGCTAGCTTTACATAA - -a -s simMouse_chr6.simMouse.chr6 24162 16 + 636262 TGTCAGCTGATAAGGC -s Anc0.Anc0refChr9 2484 16 + 35212 TGTGATTTTGTGAGGC -s Anc1.Anc1refChr2 126158 16 - 144309 TGTGATTTTGTGAGGC -s Anc2.Anc2refChr0 21237 16 - 56053 TGTGATTTTGTGAGGC -s mr.mrrefChr0 22644 16 + 130230 TGTCAGCTGGTGAGGC -s simCow_chr6.simCow.chr6 561894 16 - 602619 TGTGATTTTGTGATGC -s simDog_chr6.simDog.chr6 558067 16 - 593897 TGTGATCTTGTGAGGC -s simDog_chr6.simDog.chr6 314206 16 - 593897 TGTAATTGTGTGAGGC -s simHuman_chr6.simHuman.chr6 565348 16 - 601863 TGTGATATTGTGAGGC -s simRat_chr6.simRat.chr6 16348 16 + 647215 TGTCAGCTGGTGAGGC - -a -s simMouse_chr6.simMouse.chr6 24178 66 + 636262 CCACTTTAATGGTACAGTGTTCGCAACTGTAGCCTACACTCACCAGTGTATGTTGCTTGTGAGACT -s Anc0.Anc0refChr9 2501 66 + 35212 CCACTAGAATGAAACAGTATTCACAACTGTGGCCCACTTTCACTGGTGTAAATTGCTTGTGGGTCT -s Anc1.Anc1refChr2 126175 66 - 144309 CCACTAGAATGAAACAGTATTCACAACTGTGGCCCACTTTCACTGGTGTAAATTGCTTGTGGGTCT -s Anc2.Anc2refChr0 21254 66 - 56053 CCACTAGAATGAAATAGTATTCACAACTGTGGCCTACTTTCACTGTAGTAAATTGTTTGTAGCTCT -s mr.mrrefChr0 22660 66 + 130230 CCACTTTAATGATACAGTGTTCACAACTGTAGCCCACACTCACTGGTGTAAGTTGCTTGTGAGACT -s simCow_chr6.simCow.chr6 561911 64 - 602619 CCCTTAAAACATAATG--ATTCACAAATTCGGCCTACTTTCACTGTAGTTAATTGTTTGGAGCTGT -s simDog_chr6.simDog.chr6 558084 66 - 593897 CCACTAGAATGAAATAGTATTTGCAACGGTGGCCTACTCTCCTTGTAGTAAATTATATGTAACCCT -s simDog_chr6.simDog.chr6 314223 66 - 593897 CCACTAGGATGCAACAGTATTCACAACTGTGGTCTACTTTTACCATTGTAGATTGCTTGTGGCTCT -s simHuman_chr6.simHuman.chr6 565365 66 - 601863 CCACTAAAACAAATCACTATTCACAACCACGGCCCACTTTTACTGGTGTAAATTCCTTGTGTGTCT -s simRat_chr6.simRat.chr6 16364 66 + 647215 ACACTCTAATGATGCAGTGTTCACAACTGTAGCCCACACTCATTGGTGTAAGTTGCCTATGAGACT - -a -s simMouse_chr6.simMouse.chr6 24244 1 + 636262 G -s Anc0.Anc0refChr9 2567 1 + 35212 G -s Anc1.Anc1refChr2 126241 1 - 144309 G -s Anc2.Anc2refChr0 21320 1 - 56053 G -s mr.mrrefChr0 22726 1 + 130230 G -s simCow_chr6.simCow.chr6 561975 1 - 602619 G -s simDog_chr6.simDog.chr6 314289 1 - 593897 G -s simHuman_chr6.simHuman.chr6 565431 1 - 601863 G -s simRat_chr6.simRat.chr6 16430 1 + 647215 G - -a -s simMouse_chr6.simMouse.chr6 24245 52 + 636262 ACCATGCTCATGAACTCTGTCTCAACCTAGTCAGGAAGCCTGTCATTAATTA -s Anc0.Anc0refChr9 2568 52 + 35212 ACCACGCTTACGAACTCTATCTCAACTTGGTTAGCAAGTGTGTTATTCATTA -s Anc1.Anc1refChr2 126242 52 - 144309 ACCACGCTTACGAACTCTATCTCAACTTGGTTAGCAAGTGTGTTATTCATTA -s Anc2.Anc2refChr0 21321 52 - 56053 ACCACACTTATGAACTTTATCTCAACTTGGTTAGCAAGTGTGTTATTCATTA -s mr.mrrefChr0 22727 52 + 130230 ACCATGCTCACGAACTCTGTCTCAACCTAGTTAGCAAGCGTGTCATTAATTA -s simCow_chr6.simCow.chr6 561976 52 - 602619 GACACACTTATGGACTCTATCTAAACTTGGTTCGCAAGTGTGTTATTCATTA -s simDog_chr6.simDog.chr6 558150 52 - 593897 ACCCCACTTGTGAACTTTATCTCAACTTGGTTAGCATGTGTGCTACTTATGA -s simDog_chr6.simDog.chr6 314290 52 - 593897 ACCACACTTATGAACTTTGTCTCAACTTGGTTAGCAAGTGTGTTATTCATTA -s simHuman_chr6.simHuman.chr6 565432 51 - 601863 ACC-CGCTTACAAGCTCTCTCTCAAGTTGGTTATCACGAGCATTATTCATTA -s simRat_chr6.simRat.chr6 16431 52 + 647215 ACCATGCTCACGAACTCTGTCTCGTCGTAGTTAGCAAGTGTGTCATCAATTA - -a -s simMouse_chr6.simMouse.chr6 24297 37 + 636262 CCTTGGTAATATTAGTCAGAAGTAAGGGTTGTCACAG -s Anc0.Anc0refChr9 2620 37 + 35212 CCTAAGTAATATTAGTCAAAAGTGAAGGTTGTAGTAG -s Anc1.Anc1refChr2 126294 37 - 144309 CCTAAGTAATATTAGTCAAAAGTGAAGGTTGTAGTAG -s Anc2.Anc2refChr0 21373 37 - 56053 CTTAAGTAATGTTAGTCAAAATTGAAGGTAATAGTGG -s mr.mrrefChr0 22779 37 + 130230 CCTTAGTAATATTAGTCAGAAGTAAGGGTTGTCACAG -s simCow_chr6.simCow.chr6 562029 37 - 602619 CTTAAGTAATGTTAGTCAAAATTGAGGGTAATAGTGG -s simDog_chr6.simDog.chr6 558202 35 - 593897 CTTAAGCCATAATAGACACAATCAAAAGTACGAGT-- -s simDog_chr6.simDog.chr6 314342 34 - 593897 CCTGACTTATGTTAGTTGAAGTTGAAGGTAATGG--- -s simHuman_chr6.simHuman.chr6 565483 37 - 601863 CCTAAGTAATATTAGTCAATAGTTAAGGTTGTGGTAG -s simRat_chr6.simRat.chr6 16483 35 + 647215 TCTTAATAATATTAG--GGAAGTAAGAGTTGACACAG - -a -s simMouse_chr6.simMouse.chr6 24334 7 + 636262 GCAGCCA -s Anc0.Anc0refChr9 2700 7 + 35212 TTGATAC -s Anc1.Anc1refChr2 126374 7 - 144309 TTGATAC -s Anc2.Anc2refChr0 21453 7 - 56053 TTGATAC -s mr.mrrefChr0 22816 7 + 130230 GTGGCCA -s simCow_chr6.simCow.chr6 562110 7 - 602619 TCAATAC -s simDog_chr6.simDog.chr6 558277 7 - 593897 TTGAGGT -s simHuman_chr6.simHuman.chr6 565563 7 - 601863 TTGATAC -s simRat_chr6.simRat.chr6 16518 7 + 647215 ATGGCCA - -a -s simMouse_chr6.simMouse.chr6 24341 35 + 636262 GCATCACCTCCAAGAAGCAGTGTTCTGTGCACAAA -s Anc0.Anc0refChr9 2707 35 + 35212 GCATCACCTCCAATATGCAGTGTACTGTACACACA -s Anc1.Anc1refChr2 126381 35 - 144309 GCATCACCTCCAATATGCAGTGTACTGTACACACA -s Anc2.Anc2refChr0 21460 35 - 56053 GCATCACCTCCAATATGCAGTGTACTGTACACACA -s mr.mrrefChr0 22823 35 + 130230 GCATCACCTCCAAGAAGCAGTGTTCTGTGCACACA -s simCow_chr6.simCow.chr6 562117 35 - 602619 AAACCACCTGCAAGGTGCAGTGTACTGTACACATA -s simDog_chr6.simDog.chr6 558289 35 - 593897 GCATCACCTCCAATACGCAGTGTACAGTTCATACA -s simHuman_chr6.simHuman.chr6 565570 35 - 601863 GCATCACCCCCAAAATCCAGTGTACTGTACACACA -s simRat_chr6.simRat.chr6 16525 35 + 647215 CCAGCACCTCCAAGAAGCAGTATTCAGTGCACACA - -a -s simMouse_chr6.simMouse.chr6 24376 43 + 636262 ATGGGTACTGGATCTACAAGGAGCTAAACTTGCGGAAGAGGCC -s Anc0.Anc0refChr9 2748 9 + 35212 ATGGAT--TAA-------------------------------- -s Anc1.Anc1refChr2 126422 35 - 144309 ATGGAT--TAACTCTCCACATGACT------GCAGGACACATC -s Anc2.Anc2refChr0 21501 9 - 56053 TTGGAT--TAA-------------------------------- -s mr.mrrefChr0 22858 43 + 130230 ATGGATACTGGATCTACACGGAGCTAAACTTGCAGAAGAGGCC -s simCow_chr6.simCow.chr6 562158 9 - 602619 CTGGAT--TAA-------------------------------- -s simDog_chr6.simDog.chr6 558330 9 - 593897 TTGAAT--TAA-------------------------------- -s simHuman_chr6.simHuman.chr6 565611 35 - 601863 ATCGAT--TAACTCTCCACATGACT------GCAGGACACATC -s simRat_chr6.simRat.chr6 16560 43 + 647215 ATGGATACTGGATCTACACGGAGGTAAACTTGCAGAAGAGGCC - -a -s simMouse_chr6.simMouse.chr6 24419 39 + 636262 TCCAGTCCATGAGTTTCCTATTAAAGTGCCATTTTCGTG -s Anc0.Anc0refChr9 2757 20 + 35212 ---------------TCCAATTA--TAGCCGTTTTTG-- -s Anc1.Anc1refChr2 126457 37 - 144309 GTCAGACCAACCCATTCCAATTAATTAGCCGTTTTTG-- -s Anc2.Anc2refChr0 21510 20 - 56053 ---------------TCATATTA--TAGCCGGTATTG-- -s mr.mrrefChr0 22901 39 + 130230 TCCAGTCCATGAGTTTCCAATTAAAGTGCCATTTTTGTG -s simCow_chr6.simCow.chr6 562167 20 - 602619 ---------------ACAAATTA--CACCCAGTATTT-- -s simDog_chr6.simDog.chr6 558339 20 - 593897 ---------------TAATATTA--TAGCTGGTATTG-- -s simHuman_chr6.simHuman.chr6 565653 37 - 601863 GTCAGACCAACCCATTTCACCTCATTAGCCGTTTTTA-- -s simRat_chr6.simRat.chr6 16603 39 + 647215 TCCAGTCCATTAGTTTCCAATCAAAGTGCCATTTCTGTG - -a -s simMouse_chr6.simMouse.chr6 24458 37 + 636262 AATAACAACTCCAAGCAAAATCAAGGTGACAGTAATA -s Anc0.Anc0refChr9 2777 23 + 35212 --------------GCAAAATAAGGGTGATAGTAATA -s Anc1.Anc1refChr2 126494 27 - 144309 ----------CCTAGCAAAATAAGGGTGATAGTAATA -s Anc2.Anc2refChr0 21530 23 - 56053 --------------GCTAAATACGGGTGATAGCAATA -s mr.mrrefChr0 22940 37 + 130230 AATAACAACTCCAAGCAAAATCAGGGTGACAGTAATA -s simCow_chr6.simCow.chr6 562187 3 - 602619 --------------GCT-------------------- -s simDog_chr6.simDog.chr6 558359 23 - 593897 --------------GCTAAATACGGGTGATAGCAATA -s simHuman_chr6.simHuman.chr6 565690 27 - 601863 ----------CCTAAAAAAATTAGGGTGATAGTAATA -s simRat_chr6.simRat.chr6 16647 37 + 647215 GACAACCAGCTCAGGCACAGTCAGGGTGACAGCAATA - -a -s simMouse_chr6.simMouse.chr6 24495 34 + 636262 AAGTGTGCTAGTGGACCAGAATAGTCCGGGGAGC -s Anc0.Anc0refChr9 2800 33 + 35212 CAGTGTC-CAGTGCAACAGAAAAGTCAGGCTAGT -s Anc1.Anc1refChr2 126521 33 - 144309 CAGTGTC-CAGTGCAACAGAAAAGTCAGGCTAGT -s Anc2.Anc2refChr0 21553 33 - 56053 CAGTGTA-CAGTGCAACAGAAAAGTCAGGCTCGT -s mr.mrrefChr0 22977 34 + 130230 AAGTGTCCTAGTGGACCAGAATAGTCAGGCGAGT -s simCow_chr6.simCow.chr6 562190 19 - 602619 ---------------ACACAGAAGTCAGGCTTGT -s simDog_chr6.simDog.chr6 558412 33 - 593897 CAGTGTA-CAGTGCAACAGAAAAGTCCAGTTCAT -s simHuman_chr6.simHuman.chr6 565717 33 - 601863 TAGTGTC-GAGTGAAATAGAAAAGTCAGCCCAGT -s simRat_chr6.simRat.chr6 16684 34 + 647215 AAGTGTCCTAGTGGATCAGAATAGTCAGGCTAGT - -a -s simMouse_chr6.simMouse.chr6 24529 10 + 636262 TAGGCTGATA -s Anc0.Anc0refChr9 2833 2 + 35212 AC-------- -s Anc1.Anc1refChr2 126554 2 - 144309 AC-------- -s Anc2.Anc2refChr0 21586 2 - 56053 AC-------- -s mr.mrrefChr0 23011 10 + 130230 TAGGCTGATA -s simCow_chr6.simCow.chr6 562209 2 - 602619 CA-------- -s simDog_chr6.simDog.chr6 558448 2 - 593897 AC-------- -s simHuman_chr6.simHuman.chr6 565750 2 - 601863 AC-------- -s simRat_chr6.simRat.chr6 16718 10 + 647215 TAGGCCAATT - -a -s simMouse_chr6.simMouse.chr6 24539 4 + 636262 AATT -s Anc0.Anc0refChr9 2835 4 + 35212 AATT -s Anc1.Anc1refChr2 126556 4 - 144309 AATT -s Anc2.Anc2refChr0 21588 4 - 56053 AATT -s mr.mrrefChr0 23021 4 + 130230 AATT -s simCow_chr6.simCow.chr6 562211 4 - 602619 AGTT -s simDog_chr6.simDog.chr6 558454 4 - 593897 AATT -s simHuman_chr6.simHuman.chr6 565752 4 - 601863 AATT -s simRat_chr6.simRat.chr6 16728 4 + 647215 GATT - -a -s simMouse_chr6.simMouse.chr6 24543 24 + 636262 AGAGCTACAAGTAACAAGATTATT -s Anc0.Anc0refChr9 2839 23 + 35212 AGAGCTGCCAGCAGCGTAA-TACT -s Anc1.Anc1refChr2 126560 24 - 144309 AGAGCTGCCAGCAGCGTAATTACT -s Anc2.Anc2refChr0 21592 23 - 56053 AGAGCTGCCAGAAGCGTAA-TACT -s mr.mrrefChr0 23025 24 + 130230 AGAGCTGCAAGCAACAAAATTACT -s simCow_chr6.simCow.chr6 562215 18 - 602619 AGAGCTGCCAGAAGCAAA------ -s simDog_chr6.simDog.chr6 558458 23 - 593897 AAAACTGCCAGAAGTGTAA-TACT -s simHuman_chr6.simHuman.chr6 565756 24 - 601863 AGTGCTGCCAGCAGCGGAGTTACT -s simRat_chr6.simRat.chr6 16733 24 + 647215 AAAGCTGCAAGCAACAAAATTACT - -a -s simMouse_chr6.simMouse.chr6 24567 43 + 636262 GGAGTAGCAGAATTTGTGTCTGGCCCCTAATCCTGCTTAAATA -s Anc0.Anc0refChr9 2862 43 + 35212 GCAGTAGCAGGATTTGTGTCTGGCCTCTAATCCCTCTTAGATA -s Anc1.Anc1refChr2 126584 43 - 144309 GCAGTAGCAGGATTTGTGTCTGGCCTCTAATCCCTCTTAGATA -s Anc2.Anc2refChr0 21615 43 - 56053 GCAGTAGCAGGATTGGTGTCTGGCCTCTGATCCCTCTAAGATA -s mr.mrrefChr0 23049 43 + 130230 GGAGTAGCAGAATTTGTGTCTGGCCCCTAATCCTGCTTAAATA -s simCow_chr6.simCow.chr6 562233 35 - 602619 --------AGGACTCACATATGGCCTTTCATCTCTCTAAGATA -s simDog_chr6.simDog.chr6 558481 43 - 593897 GCAGTAGCAGGATTGGTGTCTGGCCTCTGATCCCTCTAAGATA -s simHuman_chr6.simHuman.chr6 565785 43 - 601863 GTAGTAGCAGGAATTGTGTCTGGCCACTAATCCCTCTTAGATA -s simRat_chr6.simRat.chr6 16757 42 + 647215 GGAGGAGCAGAATTCGTGT-TGGCCCCTAATCCTGCTTAAATG - -a -s simMouse_chr6.simMouse.chr6 24610 5 + 636262 ACAAC -s Anc0.Anc0refChr9 2906 5 + 35212 ACAAC -s Anc1.Anc1refChr2 126628 5 - 144309 ACAAC -s Anc2.Anc2refChr0 21659 5 - 56053 ACACC -s mr.mrrefChr0 23092 5 + 130230 ACAAC -s simCow_chr6.simCow.chr6 562271 5 - 602619 ACACC -s simDog_chr6.simDog.chr6 558525 5 - 593897 ACACC -s simHuman_chr6.simHuman.chr6 565829 5 - 601863 ACAAT -s simRat_chr6.simRat.chr6 16799 5 + 647215 ACAAC - -a -s simMouse_chr6.simMouse.chr6 24615 74 + 636262 GTGGAAGTTTATAGCAGGGGGAGATTCTGTTAGGCAAGAATTACAGAAGCTTCATAAATATAAATGGTTATACC -s Anc0.Anc0refChr9 2912 74 + 35212 CTGGGATTCTATAACAAGGGGAGATTATGCTGGACAAGAATTACGAGAGCTTCATGAATAAAAATGGCTATACC -s Anc1.Anc1refChr2 126634 74 - 144309 CTGGGATTCTATAACAAGGGGAGATTATGCTGGACAAGAATTACGAGAGCTTCATGAATAAAAATGGCTATACC -s Anc2.Anc2refChr0 21665 74 - 56053 CTGGGATTCCATAACAAGGGGAGATTATGCTGGACAAGAATTACGAGTGCTTCAGGAATTAAACTAGCGACACC -s mr.mrrefChr0 23097 74 + 130230 CTGGAAGTTTATAGCAGGGGGAGATTATGCTAGGCAAGAATTACAGGAGCTTCATAAATATAAATGGTTATACC -s simCow_chr6.simCow.chr6 562277 72 - 602619 CTGGGACTCTATAACAAACGGAGA--GTGCTGGACAAGAATTACAAGTGCTTTGGGAGTTAAATTAGCGACACC -s simDog_chr6.simDog.chr6 558531 73 - 593897 CTAAGATTCCACAACAAGGGGAGGTTATGTCGGACAGGGATTACGAATGC-TCAGGAATTAAACTAGCAACAGC -s simHuman_chr6.simHuman.chr6 565835 71 - 601863 CTGGGA---TATAACAAGTGGAGATTATGCTTGACAAGAATTACGAGAGCTTCCTGAATAAAAATGGCTATGAC -s simRat_chr6.simRat.chr6 16804 74 + 647215 CTGGAAGTTTATAGCAGGGGGAGATTATGCTGGGCTAGAATTACAGGAGCTTCATAAATATAAATGGTCATAGC - -a -s simMouse_chr6.simMouse.chr6 24689 26 + 636262 GTGAAATCTGCACAACTTTTAGTTGT -s Anc0.Anc0refChr9 2986 16 + 35212 -TAAAG---------CTTCCAGTTGT -s Anc1.Anc1refChr2 126708 17 - 144309 GTAAAG---------CTTCCAGTTGT -s Anc2.Anc2refChr0 21739 16 - 56053 -TAAAG---------GTTCCAATTGT -s mr.mrrefChr0 23171 22 + 130230 GTAAAATC----CAACTTTTAGTTGT -s simCow_chr6.simCow.chr6 562349 16 - 602619 -TAAAG---------GTTCCAATTGT -s simDog_chr6.simDog.chr6 558604 6 - 593897 -ACAAG---------G---------- -s simHuman_chr6.simHuman.chr6 565914 17 - 601863 GTAAAG---------CTTCCAGTCGG -s simRat_chr6.simRat.chr6 16878 8 + 647215 ATAAAATC------------------ - -a -s simMouse_chr6.simMouse.chr6 24715 14 + 636262 AGGTCCTATACCGG -s Anc0.Anc0refChr9 3002 14 + 35212 AGTTCCCTTCCTGG -s Anc1.Anc1refChr2 126725 14 - 144309 AGTTCCCTTCCTGG -s Anc2.Anc2refChr0 21755 14 - 56053 AGTTCCCTTCCTGG -s mr.mrrefChr0 23193 14 + 130230 AGGTCCTATACCGG -s simCow_chr6.simCow.chr6 562375 14 - 602619 AGTTCTCTTCCTGG -s simDog_chr6.simDog.chr6 558610 8 - 593897 -----CCTTCATG- -s simHuman_chr6.simHuman.chr6 565931 14 - 601863 AGTTCCCTTCCTGG - -a -s simMouse_chr6.simMouse.chr6 24729 15 + 636262 ATACAACTGAGTGGA -s Anc0.Anc0refChr9 3048 15 + 35212 ATAAAGCTAAGTAGA -s Anc1.Anc1refChr2 126771 15 - 144309 ATAAAGCTAAGTAGA -s Anc2.Anc2refChr0 21801 15 - 56053 ATAAAGCTAAGTAGA -s mr.mrrefChr0 23207 15 + 130230 ATACAACTGAGTGGA -s simCow_chr6.simCow.chr6 562452 15 - 602619 ATAGAGCTGAGTAGA -s simDog_chr6.simDog.chr6 558640 15 - 593897 ATAAAGCTAAGTAGA -s simHuman_chr6.simHuman.chr6 565977 15 - 601863 ATAAAGGCAAGTAGA - -a -s simMouse_chr6.simMouse.chr6 24744 6 + 636262 AAGACA -s Anc0.Anc0refChr9 3063 6 + 35212 AAGACA -s Anc1.Anc1refChr2 126786 6 - 144309 AAGACA -s Anc2.Anc2refChr0 21816 6 - 56053 AAGACA -s mr.mrrefChr0 23222 6 + 130230 AAGACA -s simCow_chr6.simCow.chr6 562467 6 - 602619 AAGACA -s simDog_chr6.simDog.chr6 558655 6 - 593897 GAGACA -s simHuman_chr6.simHuman.chr6 566124 6 - 601863 AAGACA -s simRat_chr6.simRat.chr6 16886 2 + 647215 ----CA - -a -s simMouse_chr6.simMouse.chr6 24750 46 + 636262 CAGACAAGGACAATAGATGTTATTATGTACAGATCCCCTGGCCCTC -s Anc0.Anc0refChr9 3073 46 + 35212 CAGGCCCGAACAAGAAATATTATTGTGTACAGATCCCCTGGTCCGC -s Anc1.Anc1refChr2 126796 46 - 144309 CAGGCCCGAACAAGAAATATTATTGTGTACAGATCCCCTGGTCCGC -s Anc2.Anc2refChr0 21826 46 - 56053 CAAGCCCGAACAAGAAATACTATTGTGTACAGATCCCCTGGTCTGC -s mr.mrrefChr0 23228 46 + 130230 CAGACAAGGACAATAAATGTTATTATGTACAGATCCCCTGGCCCTC -s simCow_chr6.simCow.chr6 562477 46 - 602619 CAAGTCCAAACAACAAACAATATTGTGTAGGGATCCCCTGGTCTTC -s simDog_chr6.simDog.chr6 558665 46 - 593897 GAAGCGCGGACCAGAAATGCTATTGTGCCCAGATCCCCTGGCCTGC -s simHuman_chr6.simHuman.chr6 566134 46 - 601863 CAGGCCGGAACAAGAAAAATTATTGTGTACAGATCCCCTGGTCCCC -s simRat_chr6.simRat.chr6 16888 46 + 647215 CAGACAAGGACAATAAATGTCATTCTGTACAGATTTCCTGACCCTC - -a -s simMouse_chr6.simMouse.chr6 24796 1 + 636262 C -s Anc0.Anc0refChr9 3123 1 + 35212 C -s Anc1.Anc1refChr2 126846 1 - 144309 C -s Anc2.Anc2refChr0 21876 1 - 56053 C -s mr.mrrefChr0 23274 1 + 130230 C -s simCow_chr6.simCow.chr6 562527 1 - 602619 C -s simDog_chr6.simDog.chr6 558715 1 - 593897 C -s simHuman_chr6.simHuman.chr6 566184 1 - 601863 C -s simRat_chr6.simRat.chr6 16934 1 + 647215 C - -a -s simMouse_chr6.simMouse.chr6 24797 29 + 636262 CCTGCCCAGGATACATAAGTTTACTGCAT -s Anc0.Anc0refChr9 3124 29 + 35212 CCTGCCCAGGATACATAGGTCTACTACAT -s Anc1.Anc1refChr2 126847 29 - 144309 CCTGCCCAGGATACATAGGTCTACTACAT -s Anc2.Anc2refChr0 21877 29 - 56053 CCTGTCTAGGATGCATAGGTCTACTACAT -s mr.mrrefChr0 23275 29 + 130230 CCTGCCCAGGATACATAAGCTTACTGCAT -s simCow_chr6.simCow.chr6 562528 29 - 602619 CCTGTCTAGGATCCATAAGCCTACTACAT -s simDog_chr6.simDog.chr6 558716 29 - 593897 TCTGTCTAGGATGCATAGGTTTACTGCAT -s simHuman_chr6.simHuman.chr6 566185 29 - 601863 CCTGCCCGGGATACACAGGTCTACTACAT -s simRat_chr6.simRat.chr6 16936 29 + 647215 CCTGCCCAGGAGGCATAGGCTTATTGCAT - -a -s simMouse_chr6.simMouse.chr6 24826 5 + 636262 TGGAT -s Anc0.Anc0refChr9 3153 5 + 35212 TAAAA -s Anc1.Anc1refChr2 126876 5 - 144309 TAAAA -s Anc2.Anc2refChr0 21914 5 - 56053 TAAAA -s mr.mrrefChr0 23304 5 + 130230 TGGAT -s simCow_chr6.simCow.chr6 562565 5 - 602619 TGGGA -s simDog_chr6.simDog.chr6 558753 5 - 593897 TAAAA -s simHuman_chr6.simHuman.chr6 566214 5 - 601863 GAAAA -s simRat_chr6.simRat.chr6 16965 5 + 647215 TGGAT - -a -s simMouse_chr6.simMouse.chr6 24831 15 + 636262 ATTTAAGATATCGCA -s Anc0.Anc0refChr9 3160 15 + 35212 ATTTGAGTTATCTGA -s Anc1.Anc1refChr2 126883 15 - 144309 ATTTGAGTTATCTGA -s Anc2.Anc2refChr0 21921 15 - 56053 ATTTGAGTTATCTGA -s mr.mrrefChr0 23310 15 + 130230 ATTTGAGATATCGCA -s simCow_chr6.simCow.chr6 562572 15 - 602619 ATTTGAAGTATCTCA -s simDog_chr6.simDog.chr6 558760 15 - 593897 ATATGAGTTATCTGA -s simHuman_chr6.simHuman.chr6 566221 15 - 601863 TTTTGAGTTATCTTA -s simRat_chr6.simRat.chr6 16971 15 + 647215 ATTTGAGCTATCACA - -a -s simMouse_chr6.simMouse.chr6 24846 10 + 636262 CACAGTATCT -s Anc0.Anc0refChr9 3176 10 + 35212 CGTAATATCT -s Anc1.Anc1refChr2 126899 10 - 144309 CGTAATATCT -s Anc2.Anc2refChr0 21937 10 - 56053 TGTAATACCT -s mr.mrrefChr0 23326 10 + 130230 CATAATATCT -s simCow_chr6.simCow.chr6 562588 10 - 602619 TATAATACCA -s simDog_chr6.simDog.chr6 558776 10 - 593897 TGTAATACCT -s simHuman_chr6.simHuman.chr6 566237 10 - 601863 CCATATGTCT -s simRat_chr6.simRat.chr6 16987 10 + 647215 CATAATATCT - -a -s simMouse_chr6.simMouse.chr6 24856 5 + 636262 TGATG -s Anc0.Anc0refChr9 3186 5 + 35212 GTATG -s Anc1.Anc1refChr2 126909 5 - 144309 GTATG -s Anc2.Anc2refChr0 21947 5 - 56053 GTATA -s mr.mrrefChr0 23336 5 + 130230 TGATG -s simCow_chr6.simCow.chr6 562598 5 - 602619 GTGCA -s simDog_chr6.simDog.chr6 558786 5 - 593897 GTATA -s simHuman_chr6.simHuman.chr6 566248 5 - 601863 CTATG -s simRat_chr6.simRat.chr6 16997 5 + 647215 TCATG - -a -s simMouse_chr6.simMouse.chr6 24861 23 + 636262 CACTCCATTTTTGGTCAATAAGG -s Anc0.Anc0refChr9 3191 23 + 35212 CACTTCAGTCTTGCTTGATCAGG -s Anc1.Anc1refChr2 126914 23 - 144309 CACTTCAGTCTTGCTTGATCAGG -s Anc2.Anc2refChr0 21956 23 - 56053 CACTTCAGTCTTGCTTGATCAGG -s mr.mrrefChr0 23341 23 + 130230 CACTCCATTTTTGGTCAATAAGG -s simCow_chr6.simCow.chr6 562607 23 - 602619 CACATCAGTCTTGCTCAATGAGG -s simDog_chr6.simDog.chr6 558795 23 - 593897 CACTTCAGTCTTGCTTGATCAAG -s simHuman_chr6.simHuman.chr6 566253 23 - 601863 CACTTTAGTCTTGCTTGATCAGG -s simRat_chr6.simRat.chr6 17002 23 + 647215 CACTCTATTTTGGGTCAATACTG - -a -s simMouse_chr6.simMouse.chr6 24884 2 + 636262 TC -s Anc0.Anc0refChr9 3214 1 + 35212 T- -s Anc1.Anc1refChr2 126937 2 - 144309 TC -s Anc2.Anc2refChr0 21979 1 - 56053 T- -s mr.mrrefChr0 23364 2 + 130230 TC -s simCow_chr6.simCow.chr6 562631 1 - 602619 C- -s simDog_chr6.simDog.chr6 558818 1 - 593897 T- -s simHuman_chr6.simHuman.chr6 566276 2 - 601863 TC -s simRat_chr6.simRat.chr6 17025 2 + 647215 TC - -a -s simMouse_chr6.simMouse.chr6 24886 39 + 636262 AGGCTGGCATGAGATTCTATGTGATTCAGCTCCTTGTTC -s Anc0.Anc0refChr9 3233 5 + 35212 AGGCC---------------------------------- -s Anc1.Anc1refChr2 126957 5 - 144309 AGGCC---------------------------------- -s Anc2.Anc2refChr0 21998 5 - 56053 AGAGC---------------------------------- -s mr.mrrefChr0 23366 39 + 130230 AGGCTGGCATGAGATCCTATGTGATTCAGCTCCTTGTTC -s simCow_chr6.simCow.chr6 562653 5 - 602619 AGATC---------------------------------- -s simDog_chr6.simDog.chr6 558837 5 - 593897 AGAGC---------------------------------- -s simHuman_chr6.simHuman.chr6 566361 5 - 601863 AGGCC---------------------------------- -s simRat_chr6.simRat.chr6 17027 39 + 647215 AGGCTGGCATGAGATCCTGTGTGATTTAGCTCCTTGTTC - -a -s simMouse_chr6.simMouse.chr6 24925 42 + 636262 AGTCAATTCCACCTTATTCCTGCAGTAGAGGGCTAAGGAGTT -s mr.mrrefChr0 23406 41 + 130230 AGTCAATTCCACCTTATTCCTGCAGTATAGG-CTAAGGAGTT -s simRat_chr6.simRat.chr6 17067 41 + 647215 AGCCAACTCCACCATATCCTTGCAGTATAGG-CTAGGGAATC - -a -s simMouse_chr6.simMouse.chr6 24967 19 + 636262 TTAGTGCACATTAATTTTG -s Anc0.Anc0refChr9 3238 13 + 35212 ------GATACTAACCTTG -s Anc1.Anc1refChr2 126962 13 - 144309 ------GATACTAACCTTG -s Anc2.Anc2refChr0 22003 13 - 56053 ------GATACTAACCTTG -s mr.mrrefChr0 23448 19 + 130230 TTAGTGCACATTAATTTTG -s simCow_chr6.simCow.chr6 562658 13 - 602619 ------AGTACTAATTTTG -s simDog_chr6.simDog.chr6 558842 13 - 593897 ------GAAACTAACCTTG -s simHuman_chr6.simHuman.chr6 566366 13 - 601863 ------TATCCTAACCTTA -s simRat_chr6.simRat.chr6 17114 19 + 647215 TTAGTTCACATTAATTTTG - -a -s simMouse_chr6.simMouse.chr6 24986 77 + 636262 TGATACCATAGTACATTTGAAATGTATTAATAGGTATATTCTTAACTCAATGTAACGGGTTATAAATTATTTCTTAT -s Anc0.Anc0refChr9 3252 77 + 35212 TGATGCCATGGTACAATTGAAATGCATTACAAAGTACATTTTTAACTCAGTGTGAGAGGTTACAAATTATTTCAAAT -s Anc1.Anc1refChr2 126976 77 - 144309 TGATGCCATGGTACAATTGAAATGCATTACAAAGTACATTTTTAACTCAGTGTGAGAGGTTACAAATTATTTCAAAT -s Anc2.Anc2refChr0 22017 77 - 56053 TGACGCCATGGTACAATTGAAATACATTGCAAAGTACATTTTTAACTCAGTTTGAGAGGTTACAAATTAGTTCAAAT -s mr.mrrefChr0 23468 77 + 130230 TGATGCCATAGTGCATTTGAAATGTATTAATAGGTATATTCTTAACTCAGTGTGACGGGTTATAAATTATTTCTTAT -s simCow_chr6.simCow.chr6 562672 75 - 602619 TGACGCCATGGTGCAGTTGAAATATACTGCAAAGTATATTTTCAACTCAGTTTGAGTGGATATAAATTAGTTCAA-- -s simDog_chr6.simDog.chr6 558856 65 - 593897 GGACGCCATGGCACAATTGAAATACATTGCAATGTACATTATTGACTTGGTTTGAGAGGTTAC------------AT -s simHuman_chr6.simHuman.chr6 566380 76 - 601863 TGGTGCCATTGTATGATTGAA-TGCATTATAAAGTACATTTTAAAATCAGTGTGAGAGGTTACGACTTATTTCAAAT -s simRat_chr6.simRat.chr6 17134 77 + 647215 GGATGCCATAGTGCCATTGTAATGAATTAATAGGTATATTCTTACCTCAGTGTGACAGGTTATAAATTATTTCTTAT - -a -s simMouse_chr6.simMouse.chr6 25063 4 + 636262 CATG -s Anc0.Anc0refChr9 3331 4 + 35212 CATG -s Anc1.Anc1refChr2 127055 4 - 144309 CATG -s Anc2.Anc2refChr0 22096 4 - 56053 CATG -s mr.mrrefChr0 23545 4 + 130230 CATG -s simCow_chr6.simCow.chr6 562749 4 - 602619 CATG -s simDog_chr6.simDog.chr6 558923 4 - 593897 CATA -s simHuman_chr6.simHuman.chr6 566458 4 - 601863 TATG -s simRat_chr6.simRat.chr6 17211 4 + 647215 CGTG - -a -s simMouse_chr6.simMouse.chr6 25067 16 + 636262 AAAGTGAAATACATAT -s Anc0.Anc0refChr9 3335 16 + 35212 GAAGAAAGATACATAT -s Anc1.Anc1refChr2 127059 16 - 144309 GAAGAAAGATACATAT -s Anc2.Anc2refChr0 22100 16 - 56053 GATGAAAGATAGGTAT -s mr.mrrefChr0 23549 16 + 130230 GAAGTAAAATACATAT -s simCow_chr6.simCow.chr6 562753 16 - 602619 GATGAAAGATAAGTCT -s simDog_chr6.simDog.chr6 558927 16 - 593897 GATGAAAGATAGGTAT -s simHuman_chr6.simHuman.chr6 566471 16 - 601863 AAAGAAAGATGCATAT -s simRat_chr6.simRat.chr6 17215 16 + 647215 GAAGTAAACTAGATTT - -a -s simMouse_chr6.simMouse.chr6 25083 32 + 636262 GTTTGGTGTGAAATACAAACCCCATTCTAACC -s Anc0.Anc0refChr9 3352 31 + 35212 GTTTGGTGTAAAATGCCAATTCAA-TCCAACC -s Anc1.Anc1refChr2 127076 31 - 144309 GTTTGGTGTAAAATGCCAATTCAA-TCCAACC -s Anc2.Anc2refChr0 22117 31 - 56053 ATTTGGTGTAAAATGCCAATTCAT-TCCAACC -s mr.mrrefChr0 23566 32 + 130230 GTTTGGTGTGAAATACAAACCCCATTCTAACC -s simCow_chr6.simCow.chr6 562770 31 - 602619 ATTTTGTGTAAAATGCCAACTCAT-TCCAAAC -s simDog_chr6.simDog.chr6 558944 31 - 593897 ATTTGGCGTATAATGCCAATTCAT-TTAAACT -s simHuman_chr6.simHuman.chr6 566488 31 - 601863 GATTGGTGTAACATGCCAATTCGA-TCCAACC -s simRat_chr6.simRat.chr6 17232 32 + 647215 GTTTGGCATGAAACACAAACCCCATTCTAACT - -a -s simMouse_chr6.simMouse.chr6 25115 19 + 636262 ACCTCTAAAGGAAGGAGAC -s Anc0.Anc0refChr9 3387 19 + 35212 GTCCATAAAGGAGGGAGAC -s Anc1.Anc1refChr2 127111 19 - 144309 GTCCATAAAGGAGGGAGAC -s Anc2.Anc2refChr0 22152 19 - 56053 GTGCATAAAGGAGGGAGAC -s mr.mrrefChr0 23598 19 + 130230 ACCCCTAAAGGAGGGAGAC -s simCow_chr6.simCow.chr6 562805 19 - 602619 GTGCATAAAGGAGTGAGAC -s simDog_chr6.simDog.chr6 558979 19 - 593897 GTGCATAAAGGAAGGAGAC -s simHuman_chr6.simHuman.chr6 566523 19 - 601863 GTCCATAAAGGAGGGAGAC -s simRat_chr6.simRat.chr6 17264 19 + 647215 ACCCCTAAAGGGGGCAGAC - -a -s simMouse_chr6.simMouse.chr6 25134 5 + 636262 TAACT -s Anc0.Anc0refChr9 3406 5 + 35212 TGCCT -s Anc1.Anc1refChr2 127130 5 - 144309 TGCCT -s Anc2.Anc2refChr0 22171 5 - 56053 TGCCT -s mr.mrrefChr0 23617 5 + 130230 TAACC -s simCow_chr6.simCow.chr6 562894 5 - 602619 TCCCC -s simDog_chr6.simDog.chr6 558998 5 - 593897 TGCCT -s simHuman_chr6.simHuman.chr6 566542 5 - 601863 TGTCT -s simRat_chr6.simRat.chr6 17283 5 + 647215 TAACC - -a -s simMouse_chr6.simMouse.chr6 25139 20 + 636262 TGTATTCCTCCCACTGCAAC -s Anc0.Anc0refChr9 3426 20 + 35212 TATATTCCTGCCCTTTCAAT -s Anc1.Anc1refChr2 127150 20 - 144309 TATATTCCTGCCCTTTCAAT -s Anc2.Anc2refChr0 22191 20 - 56053 TATATTCCTGCCCTTTCAAT -s mr.mrrefChr0 23622 20 + 130230 TGTATTCCTCCCACTGCAAC -s simCow_chr6.simCow.chr6 563007 19 - 602619 TATATT-CTGCCCTTTCAAG -s simDog_chr6.simDog.chr6 559018 20 - 593897 AATATTCTTGCCCTTTCAAT -s simHuman_chr6.simHuman.chr6 566562 20 - 601863 TATATTGCTTCCTGTTAAAT -s simRat_chr6.simRat.chr6 17288 20 + 647215 TGCATTCCTCCCTCTGTAAC - -a -s simMouse_chr6.simMouse.chr6 25159 8 + 636262 CATGCAGA -s Anc0.Anc0refChr9 3449 2 + 35212 ------GA -s Anc1.Anc1refChr2 127173 7 - 144309 C-CGCAGA -s Anc2.Anc2refChr0 22214 2 - 56053 ------GC -s mr.mrrefChr0 23642 7 + 130230 C-TGCAGA -s simCow_chr6.simCow.chr6 563029 2 - 602619 ------GC -s simDog_chr6.simDog.chr6 559041 2 - 593897 ------GC -s simHuman_chr6.simHuman.chr6 566585 7 - 601863 C-CGCATA -s simRat_chr6.simRat.chr6 17308 7 + 647215 C-TGCAGA - -a -s simMouse_chr6.simMouse.chr6 25167 34 + 636262 CAGAGAAACATGCATCATCAACACCTTTCACTAC -s Anc0.Anc0refChr9 3454 28 + 35212 CAGAGACACATGTATGATCAACACCTAT------ -s Anc1.Anc1refChr2 127183 32 - 144309 CAGAGACACATGTATGATCAACACCTATC--AAC -s Anc2.Anc2refChr0 22219 28 - 56053 TAGAGACACATGTATGATCAATACCTAT------ -s mr.mrrefChr0 23649 32 + 130230 CAGAGAAACATGCATCATCAACACCTTTC--TAC -s simCow_chr6.simCow.chr6 563033 23 - 602619 -----ATGCATGCATGGTCAATACTCAT------ -s simDog_chr6.simDog.chr6 559046 28 - 593897 TAGAGACACACATATGATCAATGCCTAT------ -s simHuman_chr6.simHuman.chr6 566595 32 - 601863 CTGAGACACATGTATGATTAACACCTATC--AAC -s simRat_chr6.simRat.chr6 17315 32 + 647215 CAGAGACACATGCATCATCAAAACCTTTC--TAC - -a -s simMouse_chr6.simMouse.chr6 25201 5 + 636262 AACAC -s Anc0.Anc0refChr9 3517 5 + 35212 AATGC -s Anc1.Anc1refChr2 127250 5 - 144309 AATGC -s Anc2.Anc2refChr0 22286 5 - 56053 AATGC -s mr.mrrefChr0 23681 5 + 130230 AACAC -s simCow_chr6.simCow.chr6 563094 5 - 602619 AATGC -s simDog_chr6.simDog.chr6 559113 5 - 593897 AATGC -s simHuman_chr6.simHuman.chr6 566665 5 - 601863 AATGC -s simRat_chr6.simRat.chr6 17347 5 + 647215 AACAC - -a -s simMouse_chr6.simMouse.chr6 25206 3 + 636262 TAT -s Anc0.Anc0refChr9 3522 2 + 35212 CA- -s Anc1.Anc1refChr2 127255 2 - 144309 CA- -s Anc2.Anc2refChr0 22309 2 - 56053 CA- -s mr.mrrefChr0 23686 2 + 130230 TA- -s simCow_chr6.simCow.chr6 563117 2 - 602619 CA- -s simDog_chr6.simDog.chr6 559137 2 - 593897 CA- -s simHuman_chr6.simHuman.chr6 566670 2 - 601863 CA- -s simRat_chr6.simRat.chr6 17352 2 + 647215 TA- - -a -s simMouse_chr6.simMouse.chr6 25209 13 + 636262 ATTTGCACATCAA -s Anc0.Anc0refChr9 3525 13 + 35212 GTTCACAAAACAA -s Anc1.Anc1refChr2 127258 13 - 144309 GTTCACAAAACAA -s Anc2.Anc2refChr0 22312 13 - 56053 GTTCACAAAACAA -s mr.mrrefChr0 23688 13 + 130230 ATTTGCACATCAA -s simCow_chr6.simCow.chr6 563120 13 - 602619 GTTCCACAAACAA -s simDog_chr6.simDog.chr6 559140 13 - 593897 CTTCACAAAATAA -s simHuman_chr6.simHuman.chr6 566673 13 - 601863 GCTGAGAAACCAA -s simRat_chr6.simRat.chr6 17354 13 + 647215 ATTCGCACATCCA - -a -s simMouse_chr6.simMouse.chr6 25222 7 + 636262 GACTATA -s Anc0.Anc0refChr9 3567 3 + 35212 ----ATA -s Anc1.Anc1refChr2 127300 7 - 144309 GCCTATA -s Anc2.Anc2refChr0 22354 3 - 56053 ----ATA -s mr.mrrefChr0 23701 7 + 130230 GACTATA -s simCow_chr6.simCow.chr6 563162 3 - 602619 ----ATA -s simDog_chr6.simDog.chr6 559180 3 - 593897 ----ATA -s simHuman_chr6.simHuman.chr6 566717 7 - 601863 GCCTACA -s simRat_chr6.simRat.chr6 17367 7 + 647215 GACTCTA - -a -s simMouse_chr6.simMouse.chr6 25229 16 + 636262 TTTACACATCAAAAAT -s Anc0.Anc0refChr9 3570 16 + 35212 TTTCCAAACCAAAAAT -s Anc1.Anc1refChr2 127307 16 - 144309 TTTCCAAACCAAAAAT -s Anc2.Anc2refChr0 22357 16 - 56053 TTGCCAAACCAAAAAT -s mr.mrrefChr0 23708 16 + 130230 TTTACACATCAAAAAT -s simCow_chr6.simCow.chr6 563167 12 - 602619 TTGCCAAACC----AT -s simDog_chr6.simDog.chr6 559183 13 - 593897 TT---AAACCAAAAAT -s simHuman_chr6.simHuman.chr6 566724 16 - 601863 TTTCCGAACCAAAAAT -s simRat_chr6.simRat.chr6 17374 16 + 647215 TTTGCAAATCAAAAAT - -a -s simMouse_chr6.simMouse.chr6 25245 4 + 636262 ATGA -s Anc0.Anc0refChr9 3605 4 + 35212 ATAA -s Anc1.Anc1refChr2 127342 4 - 144309 ATAA -s Anc2.Anc2refChr0 22392 4 - 56053 ATAA -s mr.mrrefChr0 23724 4 + 130230 ATGA -s simCow_chr6.simCow.chr6 563198 4 - 602619 GTAA -s simDog_chr6.simDog.chr6 559213 4 - 593897 ATAA -s simHuman_chr6.simHuman.chr6 566759 4 - 601863 ATAA -s simRat_chr6.simRat.chr6 17390 4 + 647215 ATGA - -a -s simMouse_chr6.simMouse.chr6 25249 8 + 636262 CAATTCTA -s Anc0.Anc0refChr9 3609 8 + 35212 CACTACTA -s Anc1.Anc1refChr2 127346 8 - 144309 CACTACTA -s Anc2.Anc2refChr0 22396 8 - 56053 CACTACTA -s mr.mrrefChr0 23728 8 + 130230 CAATTCTA -s simCow_chr6.simCow.chr6 563202 8 - 602619 ACCGGCTA -s simDog_chr6.simDog.chr6 559217 8 - 593897 CACTACTT -s simHuman_chr6.simHuman.chr6 566763 8 - 601863 CACTACTA -s simRat_chr6.simRat.chr6 17401 8 + 647215 CAATTCTC - -a -s simMouse_chr6.simMouse.chr6 25257 10 + 636262 AACTTGTCAG -s Anc0.Anc0refChr9 3623 10 + 35212 AATTTGGCAA -s Anc1.Anc1refChr2 127360 10 - 144309 AATTTGGCAA -s Anc2.Anc2refChr0 22410 10 - 56053 AATTTGGCAA -s mr.mrrefChr0 23736 10 + 130230 AACTTGTCAG -s simCow_chr6.simCow.chr6 563213 10 - 602619 AACTTAGCAA -s simDog_chr6.simDog.chr6 559231 10 - 593897 AATGTGGTAC -s simHuman_chr6.simHuman.chr6 566777 10 - 601863 AAATGGGCAA -s simRat_chr6.simRat.chr6 17409 10 + 647215 AACTTGACAG - -a -s simMouse_chr6.simMouse.chr6 25267 8 + 636262 TACCCCAG -s Anc0.Anc0refChr9 3633 8 + 35212 GGATCCAG -s Anc1.Anc1refChr2 127370 8 - 144309 GGATCCAG -s Anc2.Anc2refChr0 22420 8 - 56053 GGATCCAG -s mr.mrrefChr0 23746 8 + 130230 TACCCCAG -s simCow_chr6.simCow.chr6 563223 8 - 602619 GGATCCTG -s simDog_chr6.simDog.chr6 559245 8 - 593897 GGGTACAG -s simHuman_chr6.simHuman.chr6 566787 8 - 601863 GGATCCAG -s simRat_chr6.simRat.chr6 17419 8 + 647215 TACCCCAG - -a -s simMouse_chr6.simMouse.chr6 25275 2 + 636262 CC -s Anc0.Anc0refChr9 3641 2 + 35212 AC -s Anc1.Anc1refChr2 127378 2 - 144309 AC -s Anc2.Anc2refChr0 22428 2 - 56053 CC -s mr.mrrefChr0 23754 2 + 130230 AC -s simCow_chr6.simCow.chr6 563231 2 - 602619 CC -s simDog_chr6.simDog.chr6 559253 2 - 593897 CC -s simHuman_chr6.simHuman.chr6 566848 2 - 601863 AT -s simRat_chr6.simRat.chr6 17427 2 + 647215 AC - -a -s simMouse_chr6.simMouse.chr6 25277 35 + 636262 ACACAATCTTTCAATGAGTCACCAGTCATCTTTTT -s Anc0.Anc0refChr9 3643 35 + 35212 ACACAATCTTTTATTTAACCATCAGGCATCCTTTT -s Anc1.Anc1refChr2 127380 35 - 144309 ACACAATCTTTTATTTAACCATCAGGCATCCTTTT -s Anc2.Anc2refChr0 22430 35 - 56053 ACACAGTCTTTTATTTAACCATCAGGCAGCCATTT -s mr.mrrefChr0 23756 35 + 130230 ACACAATCTTTTATTGAGTCACCAGTCATCTTTTT -s simCow_chr6.simCow.chr6 563234 35 - 602619 ACACAGTTTATTATTTAACCATCAGGCAGGCCTTT -s simDog_chr6.simDog.chr6 559255 35 - 593897 ACACAGTCTTTTACTTAACCATCATGCAGCTATGT -s simHuman_chr6.simHuman.chr6 566850 35 - 601863 GCATAATCTTTTATTTAACCGTCAGGCATCCTGTT -s simRat_chr6.simRat.chr6 17429 35 + 647215 ACACAATCTTATATTGAGTCACCAGTTATCTTTCT - -a -s simMouse_chr6.simMouse.chr6 25312 13 + 636262 CACATACTGTCAT -s Anc0.Anc0refChr9 3678 13 + 35212 CACGTGCTCTTCT -s Anc1.Anc1refChr2 127415 13 - 144309 CACGTGCTCTTCT -s Anc2.Anc2refChr0 22465 13 - 56053 CACGTGCTCCTCT -s mr.mrrefChr0 23791 13 + 130230 CACATACTGTCAT -s simCow_chr6.simCow.chr6 563271 13 - 602619 CACATATTCCTCT -s simDog_chr6.simDog.chr6 559290 9 - 593897 CGTGTGCTC---- -s simHuman_chr6.simHuman.chr6 566885 13 - 601863 CACGTGCTCTTGT -s simRat_chr6.simRat.chr6 17464 13 + 647215 TACATACTGCCAT - -a -s simMouse_chr6.simMouse.chr6 25325 33 + 636262 GATTTCTGTATCCCATGCTTTTTATAATTCAAT -s Anc0.Anc0refChr9 3692 33 + 35212 GCTCTCTTGATCCTATGCTTCTTGTAAGTCAAT -s Anc1.Anc1refChr2 127429 33 - 144309 GCTCTCTTGATCCTATGCTTCTTGTAAGTCAAT -s Anc2.Anc2refChr0 22479 33 - 56053 GCTCTCTTGATCCTATACTTCTTGTATGTCAAT -s mr.mrrefChr0 23804 33 + 130230 GATTTCTGTATCCCATGCTTTTTGTAAGTCAAT -s simCow_chr6.simCow.chr6 563285 31 - 602619 GCTCTCTTCATCCTATTCTTC--TTAGGTCAAT -s simDog_chr6.simDog.chr6 559300 33 - 593897 GCTTTCTTGATCCTATATTTTTTGTATGTCAAC -s simHuman_chr6.simHuman.chr6 566899 33 - 601863 GCTCTCTTGATCCTATGCTTCTTGTAAGTCAAT -s simRat_chr6.simRat.chr6 17477 32 + 647215 CATTTCTGTATCCCATGCTTTT-GTAAGTCAAT - -a -s simMouse_chr6.simMouse.chr6 25358 26 + 636262 GCTTATATTTCTGTATATGGATGGAT -s Anc0.Anc0refChr9 3727 26 + 35212 GCTTATATCCCTGTATATGTGTGGAT -s Anc1.Anc1refChr2 127464 26 - 144309 GCTTATATCCCTGTATATGTGTGGAT -s Anc2.Anc2refChr0 22514 26 - 56053 GCTTATATCCCTGTATATGTGTGGAT -s mr.mrrefChr0 23837 26 + 130230 GCTTATATTTCTGTATATGGATGGAT -s simCow_chr6.simCow.chr6 563318 26 - 602619 GCTTTGATCCCTGTAAATGTGTGGCC -s simDog_chr6.simDog.chr6 559335 25 - 593897 GCTTATGT-CCTGTATATGTGTGGAT -s simHuman_chr6.simHuman.chr6 566934 25 - 601863 GCTTATATCCCTGTATATGT-TGGAT -s simRat_chr6.simRat.chr6 17509 26 + 647215 ACTTATATTTCTGTATCTGGATGGAT - -a -s simMouse_chr6.simMouse.chr6 25384 7 + 636262 TGCTAGT -s Anc0.Anc0refChr9 3753 7 + 35212 TGTTATT -s Anc1.Anc1refChr2 127490 7 - 144309 TGTTATT -s Anc2.Anc2refChr0 22555 7 - 56053 TCTTATT -s mr.mrrefChr0 23863 7 + 130230 TGCTATT -s simCow_chr6.simCow.chr6 563359 7 - 602619 TGTTACT -s simDog_chr6.simDog.chr6 559375 7 - 593897 TCTTATT -s simHuman_chr6.simHuman.chr6 566959 7 - 601863 TGTTATT -s simRat_chr6.simRat.chr6 17535 7 + 647215 TGGTATT - -a -s simMouse_chr6.simMouse.chr6 25391 30 + 636262 GCTGTAAACTTCAAACTCTAGTATGTGGCT -s Anc0.Anc0refChr9 3760 30 + 35212 GGTGCATACATCAAAATCCAGTGCTGAGCT -s Anc1.Anc1refChr2 127497 30 - 144309 GGTGCATACATCAAAATCCAGTGCTGAGCT -s Anc2.Anc2refChr0 22562 30 - 56053 GGGGCATACATCAAAATCCAATGCTGAGCT -s mr.mrrefChr0 23870 30 + 130230 GGTGTAAACTTCAAAATCTAGTGTGTGGCT -s simCow_chr6.simCow.chr6 563366 13 - 602619 GGTACATACAAGA----------------- -s simDog_chr6.simDog.chr6 559382 30 - 593897 GGGGCATGCATCAAAATCCAATGCTGAGCT -s simHuman_chr6.simHuman.chr6 566968 24 - 601863 GGTCCATACATCGAAATCCAGTGC------ -s simRat_chr6.simRat.chr6 17542 30 + 647215 GGTGTAAACTTCAAAAACTAGTGTGTGGCC - -a -s simMouse_chr6.simMouse.chr6 25421 2 + 636262 TC -s Anc0.Anc0refChr9 3790 2 + 35212 TT -s Anc1.Anc1refChr2 127527 2 - 144309 TT -s Anc2.Anc2refChr0 22595 2 - 56053 TT -s mr.mrrefChr0 23900 2 + 130230 TC -s simDog_chr6.simDog.chr6 559415 2 - 593897 TT -s simRat_chr6.simRat.chr6 17572 2 + 647215 TC - -a -s simMouse_chr6.simMouse.chr6 25423 6 + 636262 TCTGTG -s Anc0.Anc0refChr9 3792 6 + 35212 TCTATT -s Anc1.Anc1refChr2 127529 6 - 144309 TCTATT -s Anc2.Anc2refChr0 22597 6 - 56053 TCTATT -s mr.mrrefChr0 23902 6 + 130230 TCTATG -s simCow_chr6.simCow.chr6 563379 6 - 602619 TTTACT -s simDog_chr6.simDog.chr6 559418 6 - 593897 TCTATT -s simHuman_chr6.simHuman.chr6 566992 6 - 601863 TCTATT -s simRat_chr6.simRat.chr6 17574 6 + 647215 TCTATG - -a -s simMouse_chr6.simMouse.chr6 25429 4 + 636262 GTGT -s Anc0.Anc0refChr9 3798 4 + 35212 TTGT -s Anc1.Anc1refChr2 127535 4 - 144309 TTGT -s Anc2.Anc2refChr0 22621 4 - 56053 TTTT -s mr.mrrefChr0 23908 4 + 130230 GTGT -s simCow_chr6.simCow.chr6 563404 4 - 602619 TTTG -s simDog_chr6.simDog.chr6 559442 4 - 593897 TTTT -s simHuman_chr6.simHuman.chr6 566998 4 - 601863 CTGT -s simRat_chr6.simRat.chr6 17580 4 + 647215 GTTT - -a -s simMouse_chr6.simMouse.chr6 25433 49 + 636262 GGTTACCAGCATGTGATTTCTCCTGGGGCCAAAATACGTTAACTGGCTT -s Anc0.Anc0refChr9 3803 30 + 35212 GGGCCGCATCA-CAAAGGT------------------ATTGACTGGCTT -s Anc1.Anc1refChr2 127540 30 - 144309 GGGCCGCATCA-CAAAGGT------------------ATTGACTGGCTT -s Anc2.Anc2refChr0 22626 30 - 56053 GGGCCGCGTCA-CAAAGGT------------------ATTGACTGGCTT -s mr.mrrefChr0 23912 46 + 130230 GGTTACCAGCA-GAAATTTCCCCTGGGGCCAA--TACGTTAACTGGCTT -s simCow_chr6.simCow.chr6 563409 26 - 602619 GAGCCGCGGCA-CAAAG----------------------TGCCTAGCTT -s simDog_chr6.simDog.chr6 559447 30 - 593897 GGGCAGTGTTG-TAGAGGT------------------ATTCACTGGCTT -s simHuman_chr6.simHuman.chr6 567003 30 - 601863 GGGCCACATCA-CAAAGGT------------------ACCGACTGGCTT -s simRat_chr6.simRat.chr6 17584 46 + 647215 GGTTGCCAGCA-GAAATTCCCCCCAGGGCCAA--TACGTTTACTAGCTT - -a -s simMouse_chr6.simMouse.chr6 25482 14 + 636262 AGTGTACAAACACT -s Anc0.Anc0refChr9 3833 14 + 35212 AGCACCTAGATGTT -s Anc1.Anc1refChr2 127570 14 - 144309 AGCACCTAGATGTT -s Anc2.Anc2refChr0 22656 14 - 56053 AGCACCTAGATGTT -s mr.mrrefChr0 23958 14 + 130230 AGTGTACAAATGCT -s simCow_chr6.simCow.chr6 563435 14 - 602619 AGCACCTTGGTGTA -s simDog_chr6.simDog.chr6 559477 14 - 593897 AGCACCTAGATGTT -s simHuman_chr6.simHuman.chr6 567035 14 - 601863 AGCAAGTGGATGTT -s simRat_chr6.simRat.chr6 17630 14 + 647215 AGTGTACAAATGCT - -a -s simMouse_chr6.simMouse.chr6 25496 63 + 636262 GCTATAGAACATATGAATATCCGAATTGCTCCATGTTGACATCCCATGTGATTCTACCCACAT -s Anc0.Anc0refChr9 3847 63 + 35212 GCTAACTAATGTGTGGATATCCAAGGCACTCCATGTGGAGACTCCATGTGATTTAAACCACAC -s Anc1.Anc1refChr2 127584 63 - 144309 GCTAACTAATGTGTGGATATCCAAGGCACTCCATGTGGAGACTCCATGTGATTTAAACCACAC -s Anc2.Anc2refChr0 22670 63 - 56053 GCTATCTAATGTGTGGATCTGCATGGCACTCCATGTGGAGACTCCATGTGATTTAAACCACAC -s mr.mrrefChr0 23972 63 + 130230 GCTAAAGAACATATGAATATCCAAATTGCTCCATGTTGACATCCCATGTGATTTAACCCACAT -s simCow_chr6.simCow.chr6 563449 63 - 602619 GCTATCTAATGTGTGAATCTACATGGTGCTCCATGTGGAGACTCCATGTAGTTTAAACCATAC -s simDog_chr6.simDog.chr6 559491 57 - 593897 TCTATCTAATTTGTGGATCTGCATGCCATTCCATGTG------CCGTGAGATGTAAACCACAC -s simHuman_chr6.simHuman.chr6 567058 63 - 601863 GCTAACTAATGTGTGGATATCCAAGGAACTCCATGTGAGTGCTCCATGTGATTTAGATCACAC -s simRat_chr6.simRat.chr6 17644 63 + 647215 ACTAAAGAACATATCAATCTCCAAATTGCTCCATGTTGACATCCCATTTGATTTAACCCACAT - -a -s simMouse_chr6.simMouse.chr6 25559 23 + 636262 ACTTACCATCTCTTCCACTTAAT -s Anc0.Anc0refChr9 3910 23 + 35212 ACTTCCCACTTATCCCACTTTAT -s Anc1.Anc1refChr2 127647 23 - 144309 ACTTCCCACTTATCCCACTTTAT -s Anc2.Anc2refChr0 22733 23 - 56053 ACTTCCCACTTATCCCACTATAT -s mr.mrrefChr0 24035 23 + 130230 ACTTACCATCTCTTCCACTTAAT -s simCow_chr6.simCow.chr6 563843 23 - 602619 ACCTCTCACTTATCCCACTGAAT -s simDog_chr6.simDog.chr6 559548 23 - 593897 ACTTCCCACTTATCCCACTATAT -s simHuman_chr6.simHuman.chr6 567121 23 - 601863 ACTTCCTGATTATCCCACTTGAT -s simRat_chr6.simRat.chr6 17707 13 + 647215 ACCTACCATCC----------AT - -a -s simMouse_chr6.simMouse.chr6 25582 28 + 636262 GTTCAACATCTGAACCCAATGTAGCCCC -s Anc0.Anc0refChr9 3933 28 + 35212 GTTCAGCCTCTGATCTATGTGTGGTCCT -s Anc1.Anc1refChr2 127670 28 - 144309 GTTCAGCCTCTGATCTATGTGTGGTCCT -s Anc2.Anc2refChr0 22756 28 - 56053 GCCCAGCCTCTGATCTATGTAAGGTCCT -s mr.mrrefChr0 24058 28 + 130230 GTTCAACCTCTGAACCCAATGTGGTCCC -s simCow_chr6.simCow.chr6 563880 28 - 602619 GCGCAGTCTCCAAACTACGTAAGGTCCT -s simDog_chr6.simDog.chr6 559571 28 - 593897 GCCAAGCCTTTGATCTATGTAAGGACCT -s simHuman_chr6.simHuman.chr6 567144 28 - 601863 GTTCAGCCTCTGATTTGTGCGTGGTTCT -s simRat_chr6.simRat.chr6 17720 28 + 647215 GTGTGACCTATAAACCCAATGTGGTCCC - -a -s simMouse_chr6.simMouse.chr6 25610 27 + 636262 CTTGTGAGGGATTCCATGAGAACTCCT -s Anc0.Anc0refChr9 3961 27 + 35212 CTTGTGAGGGATTCTAGGAGAATTCAT -s Anc1.Anc1refChr2 127698 27 - 144309 CTTGTGAGGGATTCTAGGAGAATTCAT -s Anc2.Anc2refChr0 22784 27 - 56053 CTTGTGAGGGATTCTAGAAGAATTCAT -s mr.mrrefChr0 24086 27 + 130230 CTTGTGAGGGATTCCATGAGAATTCCT -s simCow_chr6.simCow.chr6 563944 25 - 602619 CTTGTGGGGGATTCTGGAGGAATTC-- -s simDog_chr6.simDog.chr6 559599 27 - 593897 CTTGTGAGGGCTTTGAGAAGAATTCAT -s simHuman_chr6.simHuman.chr6 567172 27 - 601863 CTTGTGATGGATTCTAGGAGAATTCAT -s simRat_chr6.simRat.chr6 17748 27 + 647215 CTTATGAGGGATTCCTTGAGAATTCCT - -a -s simMouse_chr6.simMouse.chr6 25637 8 + 636262 TTCAAATG -s Anc0.Anc0refChr9 3991 8 + 35212 TCTAAAAA -s Anc1.Anc1refChr2 127728 8 - 144309 TCTAAAAA -s Anc2.Anc2refChr0 22814 8 - 56053 TCTAAAAA -s mr.mrrefChr0 24113 8 + 130230 TTTAAAAG -s simCow_chr6.simCow.chr6 563969 8 - 602619 TCTCAAAA -s simDog_chr6.simDog.chr6 559629 8 - 593897 TCCAAACG -s simHuman_chr6.simHuman.chr6 567202 8 - 601863 TCTAAAAA -s simRat_chr6.simRat.chr6 17775 8 + 647215 TTTGAAAG - -a -s simMouse_chr6.simMouse.chr6 25645 40 + 636262 GGGTGTCAATCTTGCCAGTGGTAATGCCTTAATCCCTCCA -s Anc0.Anc0refChr9 3999 40 + 35212 GAATGTCAATCTTGCTATTGGTTTGACCTTGGTTGTATCA -s Anc1.Anc1refChr2 127736 40 - 144309 GAATGTCAATCTTGCTATTGGTTTGACCTTGGTTGTATCA -s Anc2.Anc2refChr0 22822 40 - 56053 GAATGTCAATCTTGCTATTGGTTTGACCTTGGTTGTATCA -s mr.mrrefChr0 24121 40 + 130230 GAGTGTCAATCTTGCCAGTGGTTATGCCTTAATCCCTCCA -s simCow_chr6.simCow.chr6 563980 40 - 602619 GAATGTCAATCTTGCTATTGGTTTGACCATGGTCGGATCA -s simDog_chr6.simDog.chr6 559637 40 - 593897 GAATGTCGATCTTGCCACCGGTTTCAGCTTAGTTGTATCA -s simHuman_chr6.simHuman.chr6 567210 40 - 601863 GAATGTCAATCTTGCTATTGGTTTGACCTTGGTAGTATCA -s simRat_chr6.simRat.chr6 17783 40 + 647215 GAGTGTCCATCTTGCCAGTGGTTGTGCCTTAATTCCTCCA - -a -s simMouse_chr6.simMouse.chr6 25685 41 + 636262 CCTAAGAGTTGCCCATGCAGCCAGTGTCAGTTAGTGTTTTG -s Anc0.Anc0refChr9 4039 24 + 35212 C-TGTGC---GCCCATACAGC-------------TGTTGTG -s Anc1.Anc1refChr2 127776 27 - 144309 C-TGTGCCTTGCCCATACAGC-------------TGTTGTG -s Anc2.Anc2refChr0 22862 24 - 56053 C-TGTGC---ACCCATACAGC-------------TGTTGTG -s mr.mrrefChr0 24161 41 + 130230 CCTGAGAGTTGCCCATGCAGCCAGTGTCAGTTAGTGTTTTG -s simCow_chr6.simCow.chr6 564020 24 - 602619 A-TGTGC---AGCGATACAGC-------------TGTTGTG -s simDog_chr6.simDog.chr6 559678 24 - 593897 C-TGTGC---ACCCATACAGC-------------TGTTGTG -s simHuman_chr6.simHuman.chr6 567250 15 - 601863 C-TGTGCCTTGCCCAT------------------------- -s simRat_chr6.simRat.chr6 17823 36 + 647215 CCTGAGG-----CTATGCAGCCAGTATTGGTTTTTGTTTTG - -a -s simMouse_chr6.simMouse.chr6 25726 76 + 636262 GTTGATGCCCCAGATTGATGCCCCACAGTATAGCAACCACAGTTTGCCAGCAATAATCTGAGTAAACTGGGTCAGG -s Anc0.Anc0refChr9 4063 65 + 35212 ATTTGT--------TTGTTGCCTCACACCATAGCA--ACTGGTTGGCCAGCAACCTTTTGAACATTATTGGT-AGG -s Anc1.Anc1refChr2 127803 67 - 144309 ATTTGT--------TTGTTGCCTCACACCATAGCACGACTGGTTGGCCAGCAACCTTTTGAACATTATTGGT-AGG -s Anc2.Anc2refChr0 22886 65 - 56053 ATTTGT--------TTGTTGCCTCACACCATAGCA--ACTGGTTGGCCAGCAATCTTTTGAACATTATTGGT-AGG -s mr.mrrefChr0 24202 76 + 130230 GTTGATGCCCCAGATTGATGCCCCACAGTATAGCAACCACAGTTTGCCAGCAACCATCTGAATAAACTGGGTCAGG -s simCow_chr6.simCow.chr6 564044 64 - 602619 ACCTGT--------TTGTTACCTCACAGCATAGCA--ACTGGTTGCCCAGCAATCTTTTGGA-ATTGTTGTC-AGT -s simDog_chr6.simDog.chr6 559703 65 - 593897 ATTTGT--------TTGTTGCCTCACACCATAGCA--ACTTGTTAGCCAATGATCTTTTGAACATTATTGGT-TCG -s simHuman_chr6.simHuman.chr6 567265 44 - 601863 -------------------------------AGCACGACTGGTTGGCCAGCAACCTTTCGAACATCATTGGG-AGG -s simRat_chr6.simRat.chr6 17859 76 + 647215 ATTGATGCCCCAGATTGATGCCCAACAGTATAGTAACCACAGTTCACCAGCGACCATCTGAATAAACTGGGTCAGG - -a -s simMouse_chr6.simMouse.chr6 25802 48 + 636262 AGCAACCACCTAGCCTTGCACCACAGGCAAGTCAATTAGAATTGAAGG -s Anc0.Anc0refChr9 4128 45 + 35212 AGCAACCACCTAGCACTTG-C-ACAGGTGTGTTGCT-ACTATTGATGG -s Anc1.Anc1refChr2 127870 46 - 144309 AGCAACCACCTAGCACTTG-C-ACAGGTGTGTTGCTCACTATTGATGG -s Anc2.Anc2refChr0 22953 45 - 56053 AGCAACCACCTAGCACTTG-C-ACTGGTGTGTTGCT-ACTATTGATGG -s mr.mrrefChr0 24278 47 + 130230 AGCAACCACCTAGCCTTGCAC-ACAGGTGAGTCAATTAGAATTGAAGG -s simCow_chr6.simCow.chr6 564110 45 - 602619 ACAGACCACCTGGCACTTG-C-TATGGTGTGTTGTT-ACTATTGATGG -s simDog_chr6.simDog.chr6 559770 45 - 593897 AGCAACTACCTAGTGCTTG-C-ACTGGTGTGTTGCT-AGTATTGACAG -s simHuman_chr6.simHuman.chr6 567309 46 - 601863 AGCAACCATCGAGCACTTT-C-ACAGGTGTGTTTCTCACTATTGATGG -s simRat_chr6.simRat.chr6 17935 47 + 647215 AGCAACCACCTAGGCTTGCAC-ACAGGTGAGTCAATTAGAATTGAAGG - -a -s simMouse_chr6.simMouse.chr6 25850 10 + 636262 ACGCTGAGGT -s Anc0.Anc0refChr9 4173 10 + 35212 ACTCTGAGGT -s Anc1.Anc1refChr2 127916 10 - 144309 ACTCTGAGGT -s Anc2.Anc2refChr0 23000 10 - 56053 ACTCTGAGGT -s mr.mrrefChr0 24325 10 + 130230 ACTCTGAGGT -s simCow_chr6.simCow.chr6 564156 9 - 602619 -CTCTGAGGT -s simDog_chr6.simDog.chr6 559817 10 - 593897 ACTCTGAGGT -s simHuman_chr6.simHuman.chr6 567355 10 - 601863 CCTCTCAGTG -s simRat_chr6.simRat.chr6 17982 10 + 647215 ACTCTGAGGT - -a -s simMouse_chr6.simMouse.chr6 25860 3 + 636262 GAG -s Anc0.Anc0refChr9 4183 3 + 35212 GAG -s Anc1.Anc1refChr2 127926 3 - 144309 GAG -s Anc2.Anc2refChr0 23011 3 - 56053 GAT -s mr.mrrefChr0 24335 3 + 130230 GAG -s simCow_chr6.simCow.chr6 564166 3 - 602619 GGT -s simDog_chr6.simDog.chr6 559828 3 - 593897 GAT -s simHuman_chr6.simHuman.chr6 567365 3 - 601863 GAG -s simRat_chr6.simRat.chr6 17992 3 + 647215 GAG - -a -s simMouse_chr6.simMouse.chr6 25863 25 + 636262 ATGAACTTTTGGGGGGACACTTGCC -s Anc0.Anc0refChr9 4190 24 + 35212 ATGGGCTTTTTGGGTGGCTCT-GCC -s Anc1.Anc1refChr2 127933 24 - 144309 ATGGGCTTTTTGGGTGGCTCT-GCC -s Anc2.Anc2refChr0 23018 24 - 56053 ATGGGCTTTTTGGGTGGCTCT-GCC -s mr.mrrefChr0 24338 24 + 130230 ATGAGCTTTTTGGGGGACACT-GCC -s simCow_chr6.simCow.chr6 564173 24 - 602619 ATGGGCCTTTTGGGTTGCTTT-GCC -s simDog_chr6.simDog.chr6 559835 23 - 593897 ATGGACTTTTTGGGGGGCTC--GCT -s simHuman_chr6.simHuman.chr6 567372 24 - 601863 ACGGGCTTTTTGAGTGGCTCT-GCC -s simRat_chr6.simRat.chr6 17995 21 + 647215 ATGAGCTTTTTGGGGGACACT---- - -a -s simMouse_chr6.simMouse.chr6 25888 18 + 636262 ATTTTGAGTTATATAGCA -s Anc0.Anc0refChr9 4214 18 + 35212 ATCTTGAGCTATATAGCA -s Anc1.Anc1refChr2 127957 18 - 144309 ATCTTGAGCTATATAGCA -s Anc2.Anc2refChr0 23042 18 - 56053 ATCTTGAGCTATATCATA -s mr.mrrefChr0 24362 18 + 130230 ATTTTGAGTTATATAGCA -s simCow_chr6.simCow.chr6 564208 18 - 602619 ATCTTGAACGATCTAAGA -s simDog_chr6.simDog.chr6 559858 18 - 593897 ATTTTGAGTTATATCATA -s simHuman_chr6.simHuman.chr6 567396 18 - 601863 ATCTTGAGCTATTTAGCA -s simRat_chr6.simRat.chr6 18016 18 + 647215 ATTTCGAGTTATATAGCA - -a -s simMouse_chr6.simMouse.chr6 25906 19 + 636262 TGTATCAGTGACCCCCGAA -s Anc0.Anc0refChr9 4232 19 + 35212 CGCAGTTGTGACCCTCTGA -s Anc1.Anc1refChr2 127975 19 - 144309 CGCAGTTGTGACCCTCTGA -s Anc2.Anc2refChr0 23060 19 - 56053 CACAGTTGTGACCCTCTGA -s mr.mrrefChr0 24380 19 + 130230 TGTATCAGTGACCCCCGAA -s simCow_chr6.simCow.chr6 564226 19 - 602619 CACACTTGTGACCTTCTGA -s simDog_chr6.simDog.chr6 559876 19 - 593897 CACAGTTGTGACCCTCTGA -s simHuman_chr6.simHuman.chr6 567416 6 - 601863 AGCGAT------------- -s simRat_chr6.simRat.chr6 18035 19 + 647215 TGTTTCAATGACCCTCCAA - -a -s simMouse_chr6.simMouse.chr6 25925 38 + 636262 TCAAAATTCCTTTGTAGTTTACCTTCAGAAATATAACA -s Anc0.Anc0refChr9 4251 38 + 35212 CCAAAATTCCTTTGTAGTCAATCTTCTGAAATAGAACA -s Anc1.Anc1refChr2 127994 38 - 144309 CCAAAATTCCTTTGTAGTCAATCTTCTGAAATAGAACA -s Anc2.Anc2refChr0 23079 38 - 56053 CCCCTTTTCCTTTGTAGTCAATCTTGTGAAATAGAACA -s mr.mrrefChr0 24399 38 + 130230 TCAAAATTCCTTTGTAGTTAATCTTCAGAAATATAACA -s simCow_chr6.simCow.chr6 564245 36 - 602619 CCAATATTCCTTTGTAGTCCAGC--GTAGAACAGAAGG -s simDog_chr6.simDog.chr6 559901 38 - 593897 CCCCTTGTCCTTTGTAGTTAATCTTGTGAGATAGAACA -s simHuman_chr6.simHuman.chr6 567422 37 - 601863 -CAAAATTCCTTTGTAATCAATCTTCTGAAATAGAACA -s simRat_chr6.simRat.chr6 18054 37 + 647215 TGTTATTTCCTTTGT-GTTAATTTTCGGAGATTTAACA - -a -s simMouse_chr6.simMouse.chr6 25963 7 + 636262 CAAGGCA -s Anc0.Anc0refChr9 4304 7 + 35212 CATAGTG -s Anc1.Anc1refChr2 128047 7 - 144309 CATAGTG -s Anc2.Anc2refChr0 23132 7 - 56053 AATAGTG -s mr.mrrefChr0 24437 7 + 130230 CAAGGCA -s simCow_chr6.simCow.chr6 564297 7 - 602619 ACTTGTG -s simDog_chr6.simDog.chr6 559954 7 - 593897 AATAGTG -s simHuman_chr6.simHuman.chr6 567479 7 - 601863 CATAGTG -s simRat_chr6.simRat.chr6 18091 7 + 647215 CAAGGCG - -a -s simMouse_chr6.simMouse.chr6 25970 27 + 636262 CATAGCTCTGCTGACTGCTGGCACACC -s Anc0.Anc0refChr9 4311 27 + 35212 CAAAATTCTGCCTACTTCTGGCAAAAT -s Anc1.Anc1refChr2 128054 27 - 144309 CAAAATTCTGCCTACTTCTGGCAAAAT -s Anc2.Anc2refChr0 23139 27 - 56053 CAAAATTCTGCCTACCTCTGGCAAAAT -s mr.mrrefChr0 24444 27 + 130230 CATAGCTCTGCTGACTGCTGGCAAAAC -s simCow_chr6.simCow.chr6 564304 15 - 602619 ------------TGGCATAAGTAAAGT -s simDog_chr6.simDog.chr6 559972 27 - 593897 CAAAATTCTGCCTACCTCTGCCAAGAT -s simHuman_chr6.simHuman.chr6 567486 27 - 601863 CAAGATTCTGCCTACTTCTTGCAAAAT -s simRat_chr6.simRat.chr6 18098 26 + 647215 CATA-CTCCAGTGACTGCTGGCAAGAC - -a -s simMouse_chr6.simMouse.chr6 25997 8 + 636262 CATTGGTA -s Anc0.Anc0refChr9 4338 8 + 35212 CCTGTGTA -s Anc1.Anc1refChr2 128081 8 - 144309 CCTGTGTA -s Anc2.Anc2refChr0 23166 8 - 56053 CCTGTATA -s mr.mrrefChr0 24471 8 + 130230 CATTGGTA -s simCow_chr6.simCow.chr6 564320 8 - 602619 ACTGTATA -s simDog_chr6.simDog.chr6 559999 8 - 593897 CCTGTAGA -s simHuman_chr6.simHuman.chr6 567513 8 - 601863 TTTGTGTA -s simRat_chr6.simRat.chr6 18124 8 + 647215 CATTGGTA - -a -s simMouse_chr6.simMouse.chr6 26005 41 + 636262 TATCCATTGGTATATCTCCACATGTGGTAGGGGGTCCAATG -s Anc0.Anc0refChr9 4347 29 + 35212 TATC------------TCTACATGTTGCAGAGTGACTAATG -s Anc1.Anc1refChr2 128090 29 - 144309 TATC------------TCTACATGTTGCAGAGTGACTAATG -s Anc2.Anc2refChr0 23175 29 - 56053 TATC------------TCTACATGTTGCAGAGTGACTAATG -s mr.mrrefChr0 24479 29 + 130230 TATC------------TCCACATGTTGTAGGGGGACCAATG -s simCow_chr6.simCow.chr6 564329 29 - 602619 CATC------------TCCACTTGTTACAGAGTGACTAATG -s simDog_chr6.simDog.chr6 560008 29 - 593897 TATC------------TCTGCATGTTGCAGAGTGACTAATA -s simHuman_chr6.simHuman.chr6 567523 28 - 601863 TATC------------TCAACATCATG-AGTGCGACTAATG -s simRat_chr6.simRat.chr6 18132 29 + 647215 TATC------------TCCACATGTTGTAGGGGGACCAATG - -a -s simMouse_chr6.simMouse.chr6 26046 24 + 636262 TGGCTGTGGATGAGGGATCTATAA -s Anc0.Anc0refChr9 4385 23 + 35212 CAGA-GTGAATGAGAGATCTATAA -s Anc1.Anc1refChr2 128128 23 - 144309 CAGA-GTGAATGAGAGATCTATAA -s Anc2.Anc2refChr0 23213 23 - 56053 CAGA-GTGAATGAGAGATCTATAA -s mr.mrrefChr0 24516 24 + 130230 TGGATGTGGATGAGGGATCTATAA -s simCow_chr6.simCow.chr6 564367 23 - 602619 CAGA-GTGAATGAGAGATCTAAAA -s simDog_chr6.simDog.chr6 560046 18 - 593897 CAGG-GTGAATGAG-----TATAA -s simHuman_chr6.simHuman.chr6 567560 23 - 601863 CAGA-GTGAATGAGAGATCTATAA -s simRat_chr6.simRat.chr6 18169 24 + 647215 TGGATGTGGATGAGGGATCTATAT - -a -s simMouse_chr6.simMouse.chr6 26070 22 + 636262 ACAAATCCTCCACTTATCTTTT -s Anc0.Anc0refChr9 4413 21 + 35212 AATGCCCCCCTGCTTGTCTTT- -s Anc1.Anc1refChr2 128156 22 - 144309 AATGCCCCCCTGCTTGTCTTTT -s Anc2.Anc2refChr0 23241 21 - 56053 AATGCCCCCCTGCCTGTCTTT- -s mr.mrrefChr0 24545 22 + 130230 ACTAATCCCCCACTTATCTTTT -s simCow_chr6.simCow.chr6 564395 18 - 602619 AATA---GCCTGCCTGTCTTT- -s simDog_chr6.simDog.chr6 560069 18 - 593897 AATGCCCCCCTACCCCTC---- -s simHuman_chr6.simHuman.chr6 567588 22 - 601863 AATTTCCCCCTGCTTGTCTTTT -s simRat_chr6.simRat.chr6 18198 22 + 647215 AGTAATCCCCCCCTTATCTTTA - -a -s simMouse_chr6.simMouse.chr6 26092 12 + 636262 CTATTTTTATGC -s Anc0.Anc0refChr9 4434 8 + 35212 ----TTTTATGT -s Anc1.Anc1refChr2 128178 12 - 144309 CTTATTTTATGT -s Anc2.Anc2refChr0 23262 8 - 56053 ----TTCTATGT -s mr.mrrefChr0 24567 12 + 130230 CTATTTTTATGC -s simCow_chr6.simCow.chr6 564413 8 - 602619 ----TTCTATGT -s simDog_chr6.simDog.chr6 560087 3 - 593897 ---------TGT -s simHuman_chr6.simHuman.chr6 567625 12 - 601863 CTTATTTTATGT -s simRat_chr6.simRat.chr6 18220 12 + 647215 TTATTTTTATGC - -a -s simMouse_chr6.simMouse.chr6 26104 29 + 636262 ATGTTAGGCTCCTGAGATAGGCTAGGTCA -s Anc0.Anc0refChr9 4447 29 + 35212 ACATTAGGCTTATGAAATATTTAAGGCCA -s Anc1.Anc1refChr2 128195 29 - 144309 ACATTAGGCTTATGAAATATTTAAGGCCA -s Anc2.Anc2refChr0 23275 29 - 56053 ACATTTGTCTTATGAAATATTTAAGGCCA -s mr.mrrefChr0 24584 29 + 130230 ATGTTAGGCTTATGAGATAGGTTAGGTCA -s simCow_chr6.simCow.chr6 564426 29 - 602619 ACATTGGTCTTATGGAATAGTTTAGGCCA -s simDog_chr6.simDog.chr6 560095 27 - 593897 ACAATTGTCTTATAAAATTTTCA--GCCG -s simHuman_chr6.simHuman.chr6 567642 29 - 601863 ACATTAGGCCTATGAAATATTTAGGGCCA -s simRat_chr6.simRat.chr6 18237 29 + 647215 ATGTTAGGCTTATGATGTAGGTTAGGTAA - -a -s simMouse_chr6.simMouse.chr6 26133 22 + 636262 TGTGATGGGTCTAAAGAACTGC -s Anc0.Anc0refChr9 4477 22 + 35212 TGTAGTAGACCTAAAAAACTGC -s Anc1.Anc1refChr2 128225 22 - 144309 TGTAGTAGACCTAAAAAACTGC -s Anc2.Anc2refChr0 23305 22 - 56053 TGTAGTAGACCTAAAAATCTGC -s mr.mrrefChr0 24613 22 + 130230 TGTGATGGATCTAAAGAACTGC -s simCow_chr6.simCow.chr6 564456 22 - 602619 TGTAGTAGACCTAAAATGCTGC -s simDog_chr6.simDog.chr6 560123 21 - 593897 TGTAGT-GACCTAAAAATCTGT -s simHuman_chr6.simHuman.chr6 567672 22 - 601863 TGCAGTAGACCTAAAAAACTTC -s simRat_chr6.simRat.chr6 18266 22 + 647215 TGTGATGGATCTAAATAACTGC - -a -s simMouse_chr6.simMouse.chr6 26155 40 + 636262 TCCAGTGAGGCACCGTTCTATGACACTGACTGACCTTCTT -s Anc0.Anc0refChr9 4504 40 + 35212 ACCAATGAGTCATTATTTTATGACGCTGACGGTTCTTCTC -s Anc1.Anc1refChr2 128252 40 - 144309 ACCAATGAGTCATTATTTTATGACGCTGACGGTTCTTCTC -s Anc2.Anc2refChr0 23333 40 - 56053 ACCAATGAGTCATTATTGTATGACGCTGACGGTTCTTCTC -s mr.mrrefChr0 24640 40 + 130230 TCCAATGAGTCATCATTTTATGACACTGACTGACCTTCTT -s simCow_chr6.simCow.chr6 564484 40 - 602619 ACCAATGAGTCGTCATTGTATGGCACTAGTGGTTCCTCTT -s simDog_chr6.simDog.chr6 560150 40 - 593897 AGCAATGGGTCATTATTGTATGATGCTGACAATGCTTCTC -s simHuman_chr6.simHuman.chr6 567699 40 - 601863 ACCAATGAGTCATTACCTTATGACTTTGACGGCTTTTTTC -s simRat_chr6.simRat.chr6 18294 40 + 647215 TCCAATGAGTCATCATTTTATGACACTGAGAGTCCTTCTT - -a -s simMouse_chr6.simMouse.chr6 26195 9 + 636262 AAGCAGGGC -s Anc0.Anc0refChr9 4544 8 + 35212 AATC-CAGC -s Anc1.Anc1refChr2 128292 8 - 144309 AATC-CAGC -s Anc2.Anc2refChr0 23373 8 - 56053 ATCC-CAGC -s mr.mrrefChr0 24680 9 + 130230 AATCACGGC -s simCow_chr6.simCow.chr6 564526 8 - 602619 TTCC-CAGC -s simDog_chr6.simDog.chr6 560190 8 - 593897 ATCC-CAAT -s simHuman_chr6.simHuman.chr6 567739 8 - 601863 AATC-CAGC -s simRat_chr6.simRat.chr6 18334 9 + 647215 AATCACGGC - -a -s simMouse_chr6.simMouse.chr6 26204 6 + 636262 TGTAGG -s Anc0.Anc0refChr9 4554 6 + 35212 TGTAAC -s Anc1.Anc1refChr2 128302 6 - 144309 TGTAAC -s Anc2.Anc2refChr0 23383 6 - 56053 TGTAAG -s mr.mrrefChr0 24689 6 + 130230 TGTAGC -s simCow_chr6.simCow.chr6 564536 6 - 602619 TGTAAT -s simDog_chr6.simDog.chr6 560200 6 - 593897 TGTAAG -s simHuman_chr6.simHuman.chr6 567753 6 - 601863 TGGAAC -s simRat_chr6.simRat.chr6 18343 6 + 647215 TATAGC - -a -s simMouse_chr6.simMouse.chr6 26210 23 + 636262 CTCTTAGTTAGAAATGCAACAGA -s Anc0.Anc0refChr9 4560 23 + 35212 CAGGTAGTTGGAAACATAACAGA -s Anc1.Anc1refChr2 128308 23 - 144309 CAGGTAGTTGGAAACATAACAGA -s Anc2.Anc2refChr0 23389 23 - 56053 CAGGTAGTTGGGAACATAACAGA -s mr.mrrefChr0 24695 23 + 130230 CTCTTAGTTAGAAATGCAACAGA -s simCow_chr6.simCow.chr6 564546 21 - 602619 CAGTTAGTTAG--ACATAACAGT -s simDog_chr6.simDog.chr6 560206 23 - 593897 CAGGTAGTTGGGAATGGAAGAGA -s simHuman_chr6.simHuman.chr6 567759 23 - 601863 CAGGTAGTTCAAAACATAACAGA -s simRat_chr6.simRat.chr6 18349 23 + 647215 CTCTTAGTTAGAAATGCAACAGA - -a -s simMouse_chr6.simMouse.chr6 26233 80 + 636262 CTGTGCCCATGTACCCAACCATTCATGAGGAAAGTTTCAAAACCATTTGACATCCAGAGCATCCGTTGTACAATCACCCA -s Anc0.Anc0refChr9 4583 71 + 35212 TCAT--------ATTTAGCCTTGCATAAG-ATAGTTTCACAACTATTTGACATGGAGAGCCCCTGACGTACAATCACCTA -s Anc1.Anc1refChr2 128331 71 - 144309 TCAT--------ATTTAGCCTTGCATAAG-ATAGTTTCACAACTATTTGACATGGAGAGCCCCTGACGTACAATCACCTA -s Anc2.Anc2refChr0 23412 71 - 56053 TCAT--------ATTTTGCCTTGCATAAG-ATAGTTTCACCACTATTTGACATGGAGAGCCCCTGACGTACAATCGCCTA -s mr.mrrefChr0 24718 72 + 130230 CTGT--------ACTCAACCATTCATAAGGAAAGTTTCAAAACCATTTGACATCCAGAGCACCCGTTGTACAATCACCCA -s simCow_chr6.simCow.chr6 564724 69 - 602619 TGAT--------AAGAAGGGTTCTACAAG-ATAGTTTCAC--CTATTTGACATGGAGAGCTCCTGATGTACAGTTGCCTC -s simCow_chr6.simCow.chr6 564567 69 - 602619 GCAG--------GTCTGGCCTTGCATAAG-ATAGTTTCAC--CCATTTGACATGGAGAGCCCCTTATATACAGTTAGGTA -s simDog_chr6.simDog.chr6 560229 71 - 593897 CCAC--------ATTTTACCTTGCATAGG-TTAGTTCTACCACTTTTTGACCTGGAGAGCCCCTCACGTACAATCGCCTA -s simHuman_chr6.simHuman.chr6 567782 70 - 601863 TGAT--------ATT-AGCCTTGCATAAG-ATAGTTTCACAGCTATCTGACGCGGAGAGCCCCTGACGTTCAATCACCTG -s simRat_chr6.simRat.chr6 18372 72 + 647215 CTGC--------ACTCAACAATTCGTAAGGAAGGTTTCAAAACCATTTGACATCCAGAGCACCCATTGTACAATCACTGA - -a -s simMouse_chr6.simMouse.chr6 26313 7 + 636262 TATAACA -s Anc0.Anc0refChr9 4678 7 + 35212 TATAACA -s Anc1.Anc1refChr2 128426 7 - 144309 TATAACA -s Anc2.Anc2refChr0 23507 7 - 56053 TATGACC -s mr.mrrefChr0 24790 7 + 130230 TATAACA -s simCow_chr6.simCow.chr6 564817 7 - 602619 TATGACC -s simCow_chr6.simCow.chr6 564660 7 - 602619 TATAACC -s simDog_chr6.simDog.chr6 560324 7 - 593897 TATGACC -s simHuman_chr6.simHuman.chr6 567876 7 - 601863 TATAACA -s simRat_chr6.simRat.chr6 18444 7 + 647215 TTGAACA - -a -s simMouse_chr6.simMouse.chr6 26320 23 + 636262 ATGTGAGGTACGGTGGGGCCAGA -s Anc0.Anc0refChr9 4685 16 + 35212 ATATGAA-----AT--AGTCAGG -s Anc1.Anc1refChr2 128433 21 - 144309 ATATGAAGTATGAT--AGTCAGG -s Anc2.Anc2refChr0 23514 16 - 56053 ATATGAA-----AT--ACTCATG -s mr.mrrefChr0 24797 23 + 130230 ATGTGAGGTATGGTGGAGCCAGA -s simCow_chr6.simCow.chr6 564824 16 - 602619 ATAAGAC-----AT--GCCCATG -s simCow_chr6.simCow.chr6 564667 16 - 602619 ATATGAA-----AT--GCTCCTG -s simDog_chr6.simDog.chr6 560331 10 - 593897 ATATGAA-----AT--A------ -s simHuman_chr6.simHuman.chr6 567883 21 - 601863 ATATGAAGTATGAT--AGTCAGG -s simRat_chr6.simRat.chr6 18453 23 + 647215 ATGCGAGGTATGGTGGAGCCAGA - -a -s simMouse_chr6.simMouse.chr6 26343 29 + 636262 ACTCCATGGGTCAGCCCGGGGTGTATTAT -s Anc0.Anc0refChr9 4702 28 + 35212 ACCCCTGAGTCCAGTCCAGG-TCCATTAC -s Anc1.Anc1refChr2 128455 28 - 144309 ACCCCTGAGTCCAGTCCAGG-TCCATTAC -s Anc2.Anc2refChr0 23531 28 - 56053 ACCCCTGAGTCCAGTCCAGG-TCCATTAC -s mr.mrrefChr0 24820 28 + 130230 ACTCCATGGGTCAGCCCGGG-TGTATTAC -s simCow_chr6.simCow.chr6 564841 28 - 602619 AGCCCAGGTTGCAGTACAGG-TCCATTAC -s simCow_chr6.simCow.chr6 564684 28 - 602619 AGTCCAGGTTGCAGTACAGG-CCCATTAC -s simDog_chr6.simDog.chr6 560341 27 - 593897 -CGCTTGAGTCCAGTCCCGG-TCCATTAT -s simHuman_chr6.simHuman.chr6 567905 27 - 601863 GCCCATGAGTCCAGTCC-AG-TCCATTAC -s simRat_chr6.simRat.chr6 18476 28 + 647215 ACTCCATGGGTCAGCCCAGG-TGTATTAC - -a -s simMouse_chr6.simMouse.chr6 26372 2 + 636262 CA -s Anc0.Anc0refChr9 4730 2 + 35212 CA -s Anc1.Anc1refChr2 128483 2 - 144309 CA -s Anc2.Anc2refChr0 23569 2 - 56053 TG -s mr.mrrefChr0 24848 2 + 130230 CA -s simCow_chr6.simCow.chr6 564879 2 - 602619 TG -s simCow_chr6.simCow.chr6 564722 2 - 602619 CA -s simHuman_chr6.simHuman.chr6 567932 2 - 601863 CA -s simRat_chr6.simRat.chr6 18504 2 + 647215 CA - -a -s simMouse_chr6.simMouse.chr6 26374 52 + 636262 TTAGCCTCAATTCCTTGAACCCCATTCTATGATATTATCTTTAACCCCTCCT -s Anc0.Anc0refChr9 4732 51 + 35212 TTAGACTCAATTCCT-GGCTGTCTTTTTGAAACAATATGCTTAACTCCTCCT -s Anc1.Anc1refChr2 128485 51 - 144309 TTAGACTCAATTCCT-GGCTGTCTTTTTGAAACAATATGCTTAACTCCTCCT -s Anc2.Anc2refChr0 23571 51 - 56053 TTAGACTCATTTCCT-GGCTGTATTCTTGAAACAATATGCTTAACTCCTCCT -s mr.mrrefChr0 24850 52 + 130230 TTAGCCTCAATTCCTTGGACCTCATTTTAAAATATTATCTTTAACCCCTCCT -s simCow_chr6.simCow.chr6 564924 51 - 602619 TTAGACTCATTTCCT-GGTTGCATTCTTTAAACAATGTGCTTTACTCCTCCC -s simDog_chr6.simDog.chr6 560370 44 - 593897 CTAGA-------CCT-GGCTGTAGTCTTGAAACAATAAGCCTAACTCCTCCT -s simHuman_chr6.simHuman.chr6 567934 51 - 601863 TTAGACTCAATTCCT-GGCTGTCTTTTTGAAACAATATGCTTAACACCTCTG -s simRat_chr6.simRat.chr6 18506 52 + 647215 TTAGCCTCAATTCCTTGGTCATGATTTTAAAATATTGTCTCTAACCCCTCCT - -a -s simMouse_chr6.simMouse.chr6 26426 50 + 636262 GTAATTACGAAAAACTAGAGCAGAGAAGGCAGGCAACCACAAGAATGTGT -s Anc0.Anc0refChr9 4783 48 + 35212 ATAATTAAGAAAAATTCGTGCAGAAGAGG--GGACAACTTTAGAATGTAT -s Anc1.Anc1refChr2 128536 48 - 144309 ATAATTAAGAAAAATTCGTGCAGAAGAGG--GGACAACTTTAGAATGTAT -s Anc2.Anc2refChr0 23622 48 - 56053 ATAATTAAGAAAGATTCGTGCAGAAGACC--GGACAACTTTAGAATGTAT -s mr.mrrefChr0 24902 48 + 130230 GTAATTACGAAAAATTAGAGCAGAGAAGG--GGCAACCACTAGAATGTAT -s simCow_chr6.simCow.chr6 564975 46 - 602619 ATAATTAAGAAACATTTGTGCAGAAGCCA--GGAGTA--TCAGAACGAAT -s simDog_chr6.simDog.chr6 560414 48 - 593897 GTAATTAAGAAAGATTCATGCAGAAGACC--AGACAACTTTAGAATGTAT -s simHuman_chr6.simHuman.chr6 567990 48 - 601863 ATAATAAAGACAAATTGGTGCAGAAGAGG--GGGCATCTTTAGAATGTAT -s simRat_chr6.simRat.chr6 18558 37 + 647215 GTAATTAGGAAAAATTAGAGAA-------------ACCACTGCAATGTAT - -a -s simMouse_chr6.simMouse.chr6 26476 14 + 636262 AAGTGGACAAGATT -s Anc0.Anc0refChr9 4866 14 + 35212 AAGTGGGTAACATG -s Anc1.Anc1refChr2 128619 14 - 144309 AAGTGGGTAACATG -s Anc2.Anc2refChr0 23705 14 - 56053 AAATGGGTGACATG -s mr.mrrefChr0 24950 14 + 130230 AAGTGGGCAAGATT -s simCow_chr6.simCow.chr6 565056 14 - 602619 AAATGGGTGACATG -s simDog_chr6.simDog.chr6 560472 4 - 593897 ----------CATC -s simHuman_chr6.simHuman.chr6 568073 14 - 601863 AAGCGGGTACCATG -s simRat_chr6.simRat.chr6 18595 14 + 647215 AAGTGGGCAAGATT - -a -s simMouse_chr6.simMouse.chr6 26490 3 + 636262 TAA -s Anc0.Anc0refChr9 4883 3 + 35212 TAA -s Anc1.Anc1refChr2 128636 3 - 144309 TAA -s Anc2.Anc2refChr0 23722 3 - 56053 TAT -s mr.mrrefChr0 24967 3 + 130230 TAA -s simDog_chr6.simDog.chr6 560479 3 - 593897 TAT -s simHuman_chr6.simHuman.chr6 568090 3 - 601863 TAA -s simRat_chr6.simRat.chr6 18612 3 + 647215 TCA - -a -s simMouse_chr6.simMouse.chr6 26493 32 + 636262 GAGATCTAATCACTTGCACTGGTGACAGGTTT -s Anc0.Anc0refChr9 4887 27 + 35212 GGGACCTAACCTATTGG-----TGATAGGTTT -s Anc1.Anc1refChr2 128640 32 - 144309 GGGACCTAACCTATTGGAATGATGATAGGTTT -s Anc2.Anc2refChr0 23726 27 - 56053 GAGACCTAACATATTGG-----TGATAGGTTT -s mr.mrrefChr0 24970 32 + 130230 GGGATCTAATCTCTTGCACTGGTGATAGGTTT -s simCow_chr6.simCow.chr6 565072 24 - 602619 ---ACCTGACATGTTGG-----TGATAGGTTT -s simDog_chr6.simDog.chr6 560483 27 - 593897 GAGACCTAGCATATTGG-----TGATAGGTTT -s simHuman_chr6.simHuman.chr6 568094 32 - 601863 GGGACCTAACCTATTGGAATGATGATAGGTTG -s simRat_chr6.simRat.chr6 18615 32 + 647215 GGGATTTGATCTCTCACACTGGTGATAGGTTT - -a -s simMouse_chr6.simMouse.chr6 26525 22 + 636262 CGGTTGGCTGATTGACTCACAG -s Anc0.Anc0refChr9 4915 22 + 35212 CTGGTGGTTAATTGACTCACAC -s Anc1.Anc1refChr2 128673 22 - 144309 CTGGTGGTTAATTGACTCACAC -s Anc2.Anc2refChr0 23754 22 - 56053 CTGGTGGTTAATTGACTCACAC -s mr.mrrefChr0 25003 22 + 130230 CGGTTGGCTAATTGACTCACAG -s simCow_chr6.simCow.chr6 565096 21 - 602619 -TGGTGGTTAATTGATTCACTC -s simDog_chr6.simDog.chr6 560511 22 - 593897 CTACTGGTTAATTGACTCACAC -s simHuman_chr6.simHuman.chr6 568127 22 - 601863 CCGGTGGTTAAGTAACTCACAC -s simRat_chr6.simRat.chr6 18648 22 + 647215 CTGTTGGCTAATTGACTAATAG - -a -s simMouse_chr6.simMouse.chr6 26547 50 + 636262 ACAAACAAATTGTCCCGGCTTAGCTGAATGTCTCCATTGGCTCCTACATG -s Anc0.Anc0refChr9 4940 50 + 35212 ACAAATCAATGGTCACTACTTAGCTAAATTTCTCCCCTACTTCCTACATC -s Anc1.Anc1refChr2 128698 50 - 144309 ACAAATCAATGGTCACTACTTAGCTAAATTTCTCCCCTACTTCCTACATC -s Anc2.Anc2refChr0 23779 50 - 56053 ACAAATCAATGCCCAATACTTAGCTAAATTTCTCCCCTACTTCCTACGTC -s mr.mrrefChr0 25025 50 + 130230 ACAAACAAATGGTCACGACTTAGCTGAATTTCTCCATTGGCTCCTACATG -s simCow_chr6.simCow.chr6 565120 50 - 602619 AAAATCCAATGCGCCACATGTGGCTAAATTTCTCCCCTACTTCCTATGTC -s simDog_chr6.simDog.chr6 560536 45 - 593897 -CAAATTAATGCCAAATACTTAGGTAAAGTTCT----CACAGCCTACGTC -s simHuman_chr6.simHuman.chr6 568152 50 - 601863 CCAAATCAATGGTCACTACTTAGCTAAGTTTCTACCCTATTTCCTACATC -s simRat_chr6.simRat.chr6 18670 49 + 647215 ACAAACA-ATGGTCACGACTTAGCTGAATTTCTCCTTTGGCTCTTACATT - -a -s simMouse_chr6.simMouse.chr6 26597 111 + 636262 TCCTCATATCACAAAAGAGGGTAAGCAGTGGCGCTCAGAAGACACAGAGCTGTCACCTGGGAGAGCAGATGTGGCCTGAGAGACCAGACTCAGTCATTTGATGGTGTAATG -s Anc0.Anc0refChr9 4990 90 + 35212 CATTCATC-CACAAAAGAGGGAAAGCAGCAGCACTCAGAAGACCCAGAGCAGTCACTTGAGAG--------------------CTAACTTGAACAATGTGGCAGTGTAATG -s Anc1.Anc1refChr2 128748 91 - 144309 CATTCATCTCACAAAAGAGGGAAAGCAGCAGCACTCAGAAGACCCAGAGCAGTCACTTGAGAG--------------------CTAACTTGAACAATGTGGCAGTGTAATG -s Anc2.Anc2refChr0 23829 90 - 56053 CATTCAGC-AACAAAAGACGAAAAGTTGCAGCACTCAGAACACCCAGAGCAGTCACTTGAGAG--------------------CTCACTTGAACAAGGTGGCAGTGTAATG -s mr.mrrefChr0 25075 111 + 130230 TCCTCATATCACAAAAGAGGGTAAGCAGTGGCACTCAGAAGACACAGAGCTGTCACCTGGGAGAGCAGATGTGGCCTGAGAGACCAGACTCAGTCATTTGATGGTGTAATG -s simCow_chr6.simCow.chr6 565170 89 - 602619 CACTTA-C-AACAAAAGACGAAAAGTTGCAGCACTCAGAACACCCAGAGTGGCAACCTGAGAG--------------------CTGCCTCAGACACAGAGGCAGTGTAATA -s simDog_chr6.simDog.chr6 560581 55 - 593897 TGTACAG------------------------------------CTGGACCAGTCACTTGAGAG--------------------CTCACTTGAAAAAGGTGGCAGTGTAATG -s simHuman_chr6.simHuman.chr6 568202 91 - 601863 CAGTCATCTCACCAAAGGGGGAAACCAGCAGCACTCAGAAGACCCAGAGCAGTCACTTGAGAG--------------------CTAACTTGAACAATGTGTCAGTGCAGTG -s simRat_chr6.simRat.chr6 18727 111 + 647215 TCCTCACGTTGCAAAGGAGGGTAAGCAGTGGCACTCAGAAGACTCAGAGGCAGCACCTGGGAGAGCAGATGTGACCTGAGAGACCAGACTTAGTCAATTGGTGGTGTAATG - -a -s simMouse_chr6.simMouse.chr6 26708 35 + 636262 GTTGGCCCTGATCATCAGGGACTGCATTGTCAACA -s Anc0.Anc0refChr9 5089 34 + 35212 GCTGGC-CTGATCCTCAGGGAGTGCAGTGCCAACA -s Anc1.Anc1refChr2 128848 34 - 144309 GCTGGC-CTGATCCTCAGGGAGTGCAGTGCCAACA -s Anc2.Anc2refChr0 23928 34 - 56053 CCTGAC-CTGATCCTCAGGGAGTGCAGTGCCAACC -s mr.mrrefChr0 25186 35 + 130230 GTTGGCCCTGATCATCAGGGACTGCAGTGTCAACA -s simCow_chr6.simCow.chr6 565268 34 - 602619 CCTGAC-CTGATCCACAGGTAGTGATGTGCCAGCC -s simDog_chr6.simDog.chr6 560643 33 - 593897 -CCGAC-CTGGTCCTCAGGGAATACAGGGTCAACC -s simHuman_chr6.simHuman.chr6 568302 34 - 601863 GCTGGC-CTGATCCTCAGGGAGTGCAGTGCCAACA -s simRat_chr6.simRat.chr6 18838 35 + 647215 CTTGGCTCTGATCATCAGGGACTGCAGTGTCAACA - -a -s simMouse_chr6.simMouse.chr6 26743 18 + 636262 AGATAAGTATTTAGTAAG -s Anc0.Anc0refChr9 5123 18 + 35212 AGATAGGTAATTAATAAG -s Anc1.Anc1refChr2 128882 18 - 144309 AGATAGGTAATTAATAAG -s Anc2.Anc2refChr0 24107 18 - 56053 AGATAGTCGACTAATAGG -s mr.mrrefChr0 25221 18 + 130230 AGATAAGTATTTAGTAAG -s simDog_chr6.simDog.chr6 560991 18 - 593897 AGATAGTCGACTAATAGG -s simHuman_chr6.simHuman.chr6 568336 18 - 601863 AGAGAGGTACTTAACAAG -s simRat_chr6.simRat.chr6 18873 18 + 647215 AGATAAGTATTTAGTAAG - -a -s simMouse_chr6.simMouse.chr6 26761 107 + 636262 CATAAGTACTTGGATGTGGGACTAGAGCCCCTAGGGTCCAGACAACCATGTAAGAGAGTTTGAATTCTGGCAAAAGTGTAATGTTCCCCATTGGCTGTCTTAGTTGT -s Anc0.Anc0refChr9 5142 105 + 35212 CACAAGTACCTGGATGTGTGGTCACAACC--TAGGTACCTAGCAACTACATAAAAGGGTCTTAGATCTGGTGAGAGTGTAATGTTCCCCCTTGGCTGTCTTTATCAT -s Anc1.Anc1refChr2 128901 105 - 144309 CACAAGTACCTGGATGTGTGGTCACAACC--TAGGTACCTAGCAACTACATAAAAGGGTCTTAGATCTGGTGAGAGTGTAATGTTCCCCCTTGGCTGTCTTTATCAT -s Anc2.Anc2refChr0 24126 105 - 56053 CACAAGTACCTGGATGTGTGGTCACAACC--TAGGTACCTAGCAACTACATAAAAGGGTCTTAGATCTGGTGAGAATGTAATGTTCCCCCTTGGCTGTCTTTATCAT -s mr.mrrefChr0 25239 107 + 130230 CATAAGTACCTGGATGTGGGGCTAGAGCCCCTAGGGTCCAGACAACTATGTAAGAGAGTTTGAGATCTGGCAAAAGTGTAATGTTCCCCATTGGCTGTCTTTGTTGT -s simCow_chr6.simCow.chr6 565452 105 - 602619 CACAAGTAGCTGGATGTGTTGTTGCCACC--TGGGTCCCGATCAACTGCATGGAAGGGTCTTAGATCTGGTGAGAATGTAATGTTCCCCCTTGGCTGTATTTATCTT -s simDog_chr6.simDog.chr6 561010 105 - 593897 CACAAGTACCTGAATGTGTGGTCACAACC--TAGGTACCTAGAAACTACATAAAAGGGTCTTAAATCTGGTGAGAATGTAATGTCCCCTCCTTGCTGTCTTCATCAT -s simHuman_chr6.simHuman.chr6 568355 90 - 601863 CACAAGTATCTGGATGTGTGGTCAT-----------------CAACTACCTCAAAGGCTCTTAGATCTGGAGAGAGCATAATGTTCCCCCTTGGCTGTCTTTATCAC -s simRat_chr6.simRat.chr6 18891 104 + 647215 CATAAGTACCCAGA---GGAGCTAGAACCCCTAGGGTCCAGACAACTATGTAAGAGAGTTTGGGACCTGGCAAATGTGTAATGCTCCCCATTGGCTGTCTGTGTTGT - -a -s simMouse_chr6.simMouse.chr6 26868 29 + 636262 TATCATCTAGATTTTTTCCCAGGGTTGGA -s Anc0.Anc0refChr9 5247 29 + 35212 CATCATCCAGATTTTTTGTCATGGTGGGA -s Anc1.Anc1refChr2 129006 29 - 144309 CATCATCCAGATTTTTTGTCATGGTGGGA -s Anc2.Anc2refChr0 24253 29 - 56053 CATCATCCACATTTTTTGTCATGGTGGGA -s mr.mrrefChr0 25346 29 + 130230 TATCATCTAGATTTTTTCTCATGGTGGGA -s simCow_chr6.simCow.chr6 565580 29 - 602619 CATCATCCCAATTTTTTGTAAGAGTGGGA -s simDog_chr6.simDog.chr6 561139 29 - 593897 CCTCATCTACATTTTTTGTCATGGTGTGA -s simHuman_chr6.simHuman.chr6 568445 29 - 601863 CATCATCCAGATTTTTTGTCATTGTGGGA -s simRat_chr6.simRat.chr6 18995 29 + 647215 TATCATCTAGATTTTTTCTCATGGTGGGA - -a -s simMouse_chr6.simMouse.chr6 26897 19 + 636262 CATTGATCCTTTAATCAAA -s Anc0.Anc0refChr9 5277 19 + 35212 CTTTGATCCTTTCACCAAA -s Anc1.Anc1refChr2 129036 19 - 144309 CTTTGATCCTTTCACCAAA -s Anc2.Anc2refChr0 24283 19 - 56053 ATTTGATCCTTTCACTAAA -s mr.mrrefChr0 25375 19 + 130230 CATTGATCCTTTAACCAAA -s simCow_chr6.simCow.chr6 565610 19 - 602619 ATTTGATGTTTTAACAAAA -s simDog_chr6.simDog.chr6 561169 19 - 593897 ATTTGATCCTCTCACTAAA -s simHuman_chr6.simHuman.chr6 568475 19 - 601863 CTTAGATCCTTTGACCAAA -s simRat_chr6.simRat.chr6 19024 19 + 647215 CATTGGTCCTTTAACTAAA - -a -s simMouse_chr6.simMouse.chr6 26916 14 + 636262 AACAAAGGTGTCTA -s Anc0.Anc0refChr9 5301 14 + 35212 AGCAAATGCATGTA -s Anc1.Anc1refChr2 129060 14 - 144309 AGCAAATGCATGTA -s Anc2.Anc2refChr0 24307 14 - 56053 AGCACATGCATGTA -s mr.mrrefChr0 25394 14 + 130230 AACAAAGGTATCTA -s simCow_chr6.simCow.chr6 565634 14 - 602619 AGCACATGCAAGTA -s simDog_chr6.simDog.chr6 561193 14 - 593897 AGCGCACGTGTGTA -s simHuman_chr6.simHuman.chr6 568499 14 - 601863 AGCAAGTGCATGTA -s simRat_chr6.simRat.chr6 19043 14 + 647215 AACAAAGGTATCTA - -a -s simMouse_chr6.simMouse.chr6 26930 39 + 636262 CTGCCAATCAAGTGTACATACTGCCCAGAGTACTTACTG -s Anc0.Anc0refChr9 5317 33 + 35212 CTGCTAACTAAGAGTACATACTGCC------TTAAACTG -s Anc1.Anc1refChr2 129076 33 - 144309 CTGCTAACTAAGAGTACATACTGCC------TTAAACTG -s Anc2.Anc2refChr0 24323 33 - 56053 CTGCTAACTAAGAGTACATACTACC------TTAAACAG -s mr.mrrefChr0 25408 33 + 130230 CTGCCAATCAAGAGTACATACTGCC------ACTTACTG -s simCow_chr6.simCow.chr6 565650 32 - 602619 CCGCTAACTAAG-GCACATTCTACC------TTAAACAG -s simDog_chr6.simDog.chr6 561209 33 - 593897 CTTCTAACTAACAGTACATACTACC------TTGAACAA -s simHuman_chr6.simHuman.chr6 568515 33 - 601863 CTGCTAACAAAGAGTACATACTGCC------CTAGACTG -s simRat_chr6.simRat.chr6 19057 33 + 647215 CTGCGAATCAAGAGCACATACTGCC------ACCTGCTG - -a -s simMouse_chr6.simMouse.chr6 26969 59 + 636262 CCTTAAACAGACCCTTTTCAAGAAGGCCCTATTCACTAAAATGTCAGTCAAGTTAATGT -s Anc0.Anc0refChr9 5350 45 + 35212 CT-----------CTCTCCAAGGAGGCCCTACTGATTAAAGTGTTAATGAAGTGTA--- -s Anc1.Anc1refChr2 129109 45 - 144309 CT-----------CTCTCCAAGGAGGCCCTACTGATTAAAGTGTTAATGAAGTGTA--- -s Anc2.Anc2refChr0 24357 45 - 56053 CT-----------CTCTCCAAGGAGACCCTACTGATTTTAGTGTTAATGAAGTGTA--- -s mr.mrrefChr0 25441 59 + 130230 CCTTAAACAGACCCTTTCCAAGAAGGCCCTACTCACTAAAATGTTAGTCAAGTTAATGT -s simCow_chr6.simCow.chr6 565683 38 - 602619 CT-----------TTTACCAAGCAGAGCCTACA-------GTGTTAATGAAGTCTG--- -s simDog_chr6.simDog.chr6 561243 41 - 593897 CT-----------CTCTTCAAGGAGACCCTACTGATTTTAG----AACGAAGTGTA--- -s simHuman_chr6.simHuman.chr6 568548 45 - 601863 CT-----------CTCTCCAAGGAGGCCCTACTTATTAAAGTGTTAATGAAGTGTA--- -s simRat_chr6.simRat.chr6 19090 59 + 647215 CCTTAAACAAACCCTTTCCAAGAAGGCCCTGCTCTCTAAACTGTTAGTCAGTTTAATGT - -a -s simMouse_chr6.simMouse.chr6 27028 72 + 636262 ACTTACTGAGTTGATCCCACTTCCACTAGAGGGAGTTACAATCATTTGAAAGTTTAGTAGTTATGGTCCTTT -s Anc0.Anc0refChr9 5395 43 + 35212 -----------------------------AGGTAGCTACAATAGTATGGAAGTTTAGTAGTTCTTGCCCTTT -s Anc1.Anc1refChr2 129154 43 - 144309 -----------------------------AGGTAGCTACAATAGTATGGAAGTTTAGTAGTTCTTGCCCTTT -s Anc2.Anc2refChr0 24402 43 - 56053 -----------------------------AGGCGGCTACAATAGTATGGAAGCTTAGTAGTTCTTGCCCTTT -s mr.mrrefChr0 25500 72 + 130230 ACTTACTGAGTTGATCCCACTTCCACTAGAGGTAGTTACAATCATATGGAAGTTTAGTAGTTATGGTCCTTT -s simCow_chr6.simCow.chr6 565721 43 - 602619 -----------------------------AGGCTGCCACAATAGTATGGAAGCTTAGTAATTCTCCATCCTT -s simDog_chr6.simDog.chr6 561284 43 - 593897 -----------------------------AGGCGACTACATTAGTATGGAAGCTTAGTAGTTCTTGCCCTTT -s simHuman_chr6.simHuman.chr6 568593 43 - 601863 -----------------------------ACATAGCTACAATGGTAGAGAAGTGTAGTAGTTCTTACCCTTT -s simRat_chr6.simRat.chr6 19152 72 + 647215 ACTTACTTGGTTGATCCCACTTTCACTAGAGGTAGTTATAATAATATGGAAATTTAGTGGTTATGGTCCTTT - -a -s simMouse_chr6.simMouse.chr6 27100 17 + 636262 AAGATTTATAATGTTTC -s Anc0.Anc0refChr9 5440 17 + 35212 AGTATCTGTAATATTTC -s Anc1.Anc1refChr2 129199 17 - 144309 AGTATCTGTAATATTTC -s Anc2.Anc2refChr0 24447 17 - 56053 AGTACCTGTAATATTTC -s mr.mrrefChr0 25572 17 + 130230 AAGATTTATAATGTTTC -s simCow_chr6.simCow.chr6 565766 17 - 602619 AGTACCTTTAATATTTC -s simDog_chr6.simDog.chr6 561329 17 - 593897 AGTACCTGTAATATTTC -s simHuman_chr6.simHuman.chr6 568638 17 - 601863 AGTATCAGTAATATTTC -s simRat_chr6.simRat.chr6 19224 17 + 647215 ACGACTTATAATGTTTC - -a -s simMouse_chr6.simMouse.chr6 27117 15 + 636262 TCCCCTTTCCCCCAT -s Anc0.Anc0refChr9 5457 15 + 35212 CCCCTTTTCCCCCGT -s Anc1.Anc1refChr2 129216 15 - 144309 CCCCTTTTCCCCCGT -s Anc2.Anc2refChr0 24464 15 - 56053 CCCCTTTCCCCCCGT -s mr.mrrefChr0 25589 15 + 130230 TCCCTTTTCCCCCAT -s simCow_chr6.simCow.chr6 565783 15 - 602619 ACCCTTTACCCCCAT -s simDog_chr6.simDog.chr6 561348 15 - 593897 CCCCTTCCCCCCTGT -s simHuman_chr6.simHuman.chr6 568655 15 - 601863 CTCCTTTTCCCCCGT -s simRat_chr6.simRat.chr6 19241 15 + 647215 TCCCTTTTCCCCCAT - -a -s simMouse_chr6.simMouse.chr6 27132 11 + 636262 ACTATCTGTCT -s Anc0.Anc0refChr9 5475 11 + 35212 ACTGTCTGTCC -s Anc1.Anc1refChr2 129234 11 - 144309 ACTGTCTGTCC -s Anc2.Anc2refChr0 24482 11 - 56053 ACTGTCTATCC -s mr.mrrefChr0 25604 11 + 130230 ACTATCTGTCC -s simCow_chr6.simCow.chr6 565801 11 - 602619 ACGGTCCTTCC -s simDog_chr6.simDog.chr6 561366 11 - 593897 AATGTCTATCC -s simHuman_chr6.simHuman.chr6 568673 11 - 601863 ACTGTCTGTCC -s simRat_chr6.simRat.chr6 19256 11 + 647215 ATTATGTGTTC - -a -s simMouse_chr6.simMouse.chr6 27143 28 + 636262 GTTGATTGGGGTCCTTTCCTTGGCAAAG -s Anc0.Anc0refChr9 5489 28 + 35212 GTAGATAGGGGTCCTTCCCATTGCCATG -s Anc1.Anc1refChr2 129248 28 - 144309 GTAGATAGGGGTCCTTCCCATTGCCATG -s Anc2.Anc2refChr0 24496 28 - 56053 GCAGGCAGGGGTCTATCTCATTGACATG -s mr.mrrefChr0 25618 28 + 130230 GTTGATTGGGGTCCTTTCCTTTGCCAAG -s simCow_chr6.simCow.chr6 565815 28 - 602619 GCAGGCAGGGGTCTATCACATTGACATC -s simDog_chr6.simDog.chr6 561379 11 - 593897 -----------------TTATTGAAATG -s simHuman_chr6.simHuman.chr6 568687 28 - 601863 GTAGATAGGGGTCCTTCCCATTACCATG -s simRat_chr6.simRat.chr6 19270 27 + 647215 GTTAATTGGGGTCCTTTCCTTTGACAA- - -a -s simMouse_chr6.simMouse.chr6 27171 15 + 636262 ACTCTTACCGAATAA -s Anc0.Anc0refChr9 5518 15 + 35212 ATTCCTACTGAATAA -s Anc1.Anc1refChr2 129277 15 - 144309 ATTCCTACTGAATAA -s Anc2.Anc2refChr0 24525 15 - 56053 ATTCCTATTGAATAA -s mr.mrrefChr0 25646 15 + 130230 ACTCTTACCGAATAA -s simCow_chr6.simCow.chr6 565844 15 - 602619 ATTCTTATTGAATGA -s simDog_chr6.simDog.chr6 561391 15 - 593897 ATTCCTATGGAGTAA -s simHuman_chr6.simHuman.chr6 568716 15 - 601863 ATTCCTACTGAATAA -s simRat_chr6.simRat.chr6 19297 13 + 647215 --TCTTACCAGATAA - -a -s simMouse_chr6.simMouse.chr6 27186 133 + 636262 CTTAGCGAGTGGGCATACAACCAAGCTGGTTTCTTTGGGTTTCAGAGGGAATCTCGTCCTGTGGGCTTTGAGTTGCGTTCCTTCAACTTCAGTACAGTTTTTTGGGCTATCTGTACATATAAGTCTGAACTCC -s Anc0.Anc0refChr9 5543 131 + 35212 ATTAGCTATTGGGCACATGATTGAGCTGGTATTTTTGTAGTTTAGTGGGAATCTCATCTTGTGGACTTTGATTTGGG--TTATCAATTTCAGCACAGTTCATCAGGCTATATTTGCCTATTTGGATGACCTCC -s Anc1.Anc1refChr2 129302 133 - 144309 ATTAGCTATTGGGCACATGATTGAGCTGGTATTTTTGTAGTTTAGTGGGAATCTCATCTTGTGGACTTTGATTTGGGTTTTATCAATTTCAGCACAGTTCATCAGGCTATATTTGCCTATTTGGATGACCTCC -s Anc2.Anc2refChr0 24550 131 - 56053 ATTAACTTTTGGGTACATGCTTGAGCTGGTATTTTCGTAGTTTAGTGGCAATCTCAACTTGTGGACTTTGATTTGGG--CTATCAATTTCAGCACAGTTTATCAGAATATATTTGCCTATTTAGATGACTGCC -s mr.mrrefChr0 25661 133 + 130230 CTTAGCTAGTGGGCATACAACCAAGCTGGTTTTTTTGGATTTCAGAGGGAATCTCGTCCTGTGGGCTTTGAGTTGCGTTCCTTCAACTTCAGTACAGTTCTTTGGGCTATCTGTACATATAAGTCTGAACTCC -s simCow_chr6.simCow.chr6 565869 96 - 602619 TTTAAGTTTTGGTAACATGGTTGAGCTGGTATGTTCATAGTTCAGCTG--------------GGATTTTAGTTTGGG--CTATCAATTTCAGCA-AATTTAT------ATATTTGCATA-------------- -s simDog_chr6.simDog.chr6 561419 131 - 593897 ATTAACTTTTGGGTACATGCTTGAGCTGGTATTTTCGTAGTTTAGTGACAATCTCAACTTGTGGACTTTGATTTAGG--CAATCAATACCAGTACAGTTTATCAGAATGTACTTGCCTATTTAGATGACTGCC -s simHuman_chr6.simHuman.chr6 568741 133 - 601863 ATTAGCTACTGGGCACATGATTGAGCTGGTGCTTTTGTAGTTTAGGGGGAGTCCCATCTTGTGAAATTTGATTTGGGTTTTATCAATTTCAGCACAGTTCATCAGGCCATATTTGCCTATCTGGATGACCTCC -s simRat_chr6.simRat.chr6 19310 114 + 647215 CTTAGCTAGTGGGCATACAACCAAGCTGGTTTTGTTGCATTTCAGAG---------TCCTGTTGGCTTTGAG----GTTCCTACAACTTCAGTACAGTTCTCTGGACTATCTGTA------AGTCTGAACTCC - -a -s simMouse_chr6.simMouse.chr6 27319 11 + 636262 TGCCCTCATAT -s Anc0.Anc0refChr9 5676 11 + 35212 TGCACACCTGT -s Anc1.Anc1refChr2 129437 11 - 144309 TGCACACCTGT -s Anc2.Anc2refChr0 24683 11 - 56053 TGAATACCTGT -s mr.mrrefChr0 25794 11 + 130230 TGCCCACATAT -s simCow_chr6.simCow.chr6 565965 8 - 602619 ---ATACCTGC -s simDog_chr6.simDog.chr6 561552 11 - 593897 TGAATTCCCAT -s simHuman_chr6.simHuman.chr6 568876 11 - 601863 TGCACACCTGT -s simRat_chr6.simRat.chr6 19424 11 + 647215 TACCCAGATAT - -a -s simMouse_chr6.simMouse.chr6 27330 46 + 636262 AAGGTAGAGATTAAATCTAATCTCATGACATTACTTCCTTTCCACT -s Anc0.Anc0refChr9 5695 38 + 35212 AGTGAACCTATTAGATCTAATGTC--------GTTTCCTTTCCAAT -s Anc1.Anc1refChr2 129456 39 - 144309 AGTGAACCTATTAGATCTAATGTC-------TGTTTCCTTTCCAAT -s Anc2.Anc2refChr0 24702 38 - 56053 AGTGAACCTATTAGATCTATTGCC--------GGTTCCTTTCCAAT -s mr.mrrefChr0 25805 46 + 130230 AAGGTACAGATTAAATCTAATCTCATGACATTACTTCCTTTCCAAT -s simCow_chr6.simCow.chr6 565981 36 - 602619 AGCGA--CTATTAGAACTAGTGCT--------GGTTCCTTTCTAAT -s simDog_chr6.simDog.chr6 561571 38 - 593897 AGTGAACCCATTAGATCTATTGCC--------GGTTCCTTTCCAAT -s simHuman_chr6.simHuman.chr6 568895 39 - 601863 AGTGAACCTATTAGATCTAATGTC-------TCTTTCATTTCCAAT -s simRat_chr6.simRat.chr6 19435 46 + 647215 AAGGTACACATTAAATCCAATCTCATGAACTTACTTCCTTTCCAAT - -a -s simMouse_chr6.simMouse.chr6 27376 2 + 636262 CT -s Anc0.Anc0refChr9 5735 2 + 35212 TC -s Anc1.Anc1refChr2 129497 2 - 144309 TC -s Anc2.Anc2refChr0 24742 2 - 56053 TC -s mr.mrrefChr0 25851 2 + 130230 CT -s simCow_chr6.simCow.chr6 566019 2 - 602619 TC -s simHuman_chr6.simHuman.chr6 568936 2 - 601863 TC -s simRat_chr6.simRat.chr6 19481 2 + 647215 CT - -a -s simMouse_chr6.simMouse.chr6 27378 39 + 636262 AAGTAGCAGTCACACTTATGTGAACTCACTCGCTTTCCA -s Anc0.Anc0refChr9 5737 24 + 35212 AAGTAGCAATCACAATTTTGTGAA--------------- -s Anc1.Anc1refChr2 129499 24 - 144309 AAGTAGCAATCACAATTTTGTGAA--------------- -s Anc2.Anc2refChr0 24744 24 - 56053 AAGTAGCAATTACAATTTTGTGAA--------------- -s mr.mrrefChr0 25853 39 + 130230 AAGTAGCAGTCACACTTATGTGAACTCACTCGCTTTCCA -s simCow_chr6.simCow.chr6 566026 24 - 602619 AAGTAGCAATTACACTTTTATGAA--------------- -s simDog_chr6.simDog.chr6 561609 10 - 593897 ------------CAA--TGGTCAA--------------- -s simHuman_chr6.simHuman.chr6 568938 24 - 601863 GAGTAGCACTCACAATTTTGTGAA--------------- -s simRat_chr6.simRat.chr6 19483 39 + 647215 AAGTAGCAGGCACGGTTATGTAAGTTCAATTGCTTTCCA - -a -s simMouse_chr6.simMouse.chr6 27417 131 + 636262 ATTTAAGTTGCAGTCTCACTTATAAGAATTTCAATGTCTTTCAGCCTTCATAATCAGTGTGATATAATCATAAGCCAACTGTCACAAGCACATGATTCCTCCCTCAGCACAGTCTGGAAGAACGAACAGCC -s Anc0.Anc0refChr9 5761 98 + 35212 -----------------------------GGTAATGTGTTTCATCCCTCCTAATTAGCCTGATACAATTGTGAGCCC----TCTCAAGCACATGATTCCCCCCCCAGCACATCCAGTACAATTGAGCAGCC -s Anc1.Anc1refChr2 129523 98 - 144309 -----------------------------GGTAATGTGTTTCATCCCTCCTAATTAGCCTGATACAATTGTGAGCCC----TCTCAAGCACATGATTCCCCCCCCAGCACATCCAGTACAATTGAGCAGCC -s Anc2.Anc2refChr0 24768 98 - 56053 -----------------------------GGTCCTGTGTTTTATCTCTCCTAATTAGCCTGATACACTTGTGAGCCC----TCTCAAGCACTTGACTCCCCTACCAGCATATCCAGTACAGTTGAGCAGCC -s mr.mrrefChr0 25892 127 + 130230 ATTTAAGTTGCAGTCTCACTTATAAGAATTTTAATGTGTTTCAGCCTTCATAATCAGCGTGATATAATCATAAGCCC----TCACAAGCACATGATTCCCCCCTCAGCACAGCCTGGACAAATGAACAGCC -s simCow_chr6.simCow.chr6 566050 91 - 602619 -----------------------------TATCCTGTGTCATATCTCTCCAAATTATCCTCATACTCTTATGAGCCC----TCGCAAGCACCTGACTCCC-------CATGTCCAGTACACTTGAGCAGCC -s simDog_chr6.simDog.chr6 561619 90 - 593897 -----------------------------GG--------TTTATTTCTCCTAATTAGCTTGATATACTTGTAACCCC----CCTCAAACACTTGACTCCCCTACCAGCATAACCAGTACAGTTGAGCAGCC -s simHuman_chr6.simHuman.chr6 568962 98 - 601863 -----------------------------GGTAATATGCTTCTCCCCTCCTTACTAGCCTGAGACAATTGTGAGCCC----TCTCAAGCACATGATTTCCCCCCCATCACATCCATTACAAGTGAGCAGCC -s simRat_chr6.simRat.chr6 19524 127 + 647215 ATCTAAGTAGCAGTCACACTTATATGAATTTTGATGTGTCTCATCTTTCATAATCAGCATGATGTAATCATAAGCCC----TCACAAGCACAAGACTCCCCCCTCAGCACAACCTGGACAAATGAACAACC - -a -s simMouse_chr6.simMouse.chr6 27548 35 + 636262 TGGAGTGGACACATGATTCTCCTTAGAATGAAATC -s Anc0.Anc0refChr9 5860 35 + 35212 TGGAGCAGACACATGATTCTCTTTAGTATGAAATC -s Anc1.Anc1refChr2 129622 35 - 144309 TGGAGCAGACACATGATTCTCTTTAGTATGAAATC -s Anc2.Anc2refChr0 24867 35 - 56053 TGGAGCAGACACATGATTCTCTTTAGTATGAAATC -s mr.mrrefChr0 26019 35 + 130230 TGGAGTAGACACATGATTCTCTTTAGAATGAAATC -s simCow_chr6.simCow.chr6 566142 35 - 602619 TGGAGCAAACACATGTGCCGACTTTGTATGAAACC -s simDog_chr6.simDog.chr6 561710 31 - 593897 TGGAGGAGGCA----ATTCTCTTTAGTATGAAATG -s simHuman_chr6.simHuman.chr6 569061 35 - 601863 TGGGGCAGACACATCATTCTCTTTAGTATAGAATC -s simRat_chr6.simRat.chr6 19651 34 + 647215 TGGAGTAG-CACATGATTCTCTCTATAATGACATC - -a -s simMouse_chr6.simMouse.chr6 27583 28 + 636262 ATAAGGTAATTCCTGTGCACAGTTATAT -s Anc0.Anc0refChr9 5896 28 + 35212 ATAAGTTTATTTTTGCACACAGATATGC -s Anc1.Anc1refChr2 129658 28 - 144309 ATAAGTTTATTTTTGCACACAGATATGC -s Anc2.Anc2refChr0 24903 28 - 56053 ATAAGTTTATTTTTGCACACAGACATGC -s mr.mrrefChr0 26054 28 + 130230 ATAAGGTTATTCCTGCGCACAGTTATAT -s simCow_chr6.simCow.chr6 566178 28 - 602619 ATAAGTTTATTTTTCCACACAGACATGC -s simDog_chr6.simDog.chr6 561742 17 - 593897 ATAAGTTTAAGTTTGTA----------- -s simHuman_chr6.simHuman.chr6 569097 28 - 601863 ATAAGTTTATTTTTGCACACATCTATGC -s simRat_chr6.simRat.chr6 19685 27 + 647215 ATAATGGTATTC-TGCGCACAGTTGCAT - -a -s simMouse_chr6.simMouse.chr6 27611 2 + 636262 GT -s Anc0.Anc0refChr9 5924 2 + 35212 AC -s Anc1.Anc1refChr2 129686 2 - 144309 AC -s Anc2.Anc2refChr0 24931 2 - 56053 AC -s mr.mrrefChr0 26082 2 + 130230 GC -s simCow_chr6.simCow.chr6 566220 2 - 602619 AA -s simDog_chr6.simDog.chr6 561759 2 - 593897 GC -s simHuman_chr6.simHuman.chr6 569125 2 - 601863 AC -s simRat_chr6.simRat.chr6 19712 2 + 647215 GC - -a -s simMouse_chr6.simMouse.chr6 27613 21 + 636262 CTTGCTTGTAATTATCATGGG -s Anc0.Anc0refChr9 5931 20 + 35212 CATGCTTGTAATCAT-ACGCG -s Anc1.Anc1refChr2 129693 20 - 144309 CATGCTTGTAATCAT-ACGCG -s Anc2.Anc2refChr0 24938 20 - 56053 CACGCTTGTGGTCAT-ACACA -s mr.mrrefChr0 26084 21 + 130230 CTTGCTTGTAATTATCATGGG -s simCow_chr6.simCow.chr6 566227 17 - 602619 CCCGCCGGTG---AC-ACACA -s simDog_chr6.simDog.chr6 561766 20 - 593897 CACGCTTGTGGTCAT-ACACA -s simHuman_chr6.simHuman.chr6 569132 20 - 601863 CATGCTTGTAATCAT-ACGTG -s simRat_chr6.simRat.chr6 19714 21 + 647215 CTTGCATGTAATTATCATAGG - -a -s simMouse_chr6.simMouse.chr6 27634 9 + 636262 CCTGGCCCT -s Anc0.Anc0refChr9 5964 9 + 35212 ACTAGCCAT -s Anc1.Anc1refChr2 129726 9 - 144309 ACTAGCCAT -s Anc2.Anc2refChr0 24971 9 - 56053 ACTAGCCAT -s mr.mrrefChr0 26105 9 + 130230 CCTAGCCCT -s simCow_chr6.simCow.chr6 566283 9 - 602619 AGTAGTCAT -s simDog_chr6.simDog.chr6 561798 9 - 593897 ACTAGCCAT -s simHuman_chr6.simHuman.chr6 569165 9 - 601863 ATTAACCAT -s simRat_chr6.simRat.chr6 19735 9 + 647215 CCTAGCCCT - -a -s simMouse_chr6.simMouse.chr6 27643 105 + 636262 CACAAGAACATTAAGCCATTCCTAATGTAAAAATACATCTATTTACATTGCTAGCTTGGTAATTAGTGTGATAGAACTAACCCTTGGTACTAAATGAATAGTCAT -s Anc0.Anc0refChr9 5974 101 + 35212 CCCAAGAACATT--GGCATCCCTAATGTACAAATACCTCTATTTACATTGCTAGCCTGGTAGGTAGGG-GGTAGGACTAACC-TTGATACTAGATGAATAGATGT -s Anc1.Anc1refChr2 129736 101 - 144309 CCCAAGAACATT--GGCATCCCTAATGTACAAATACCTCTATTTACATTGCTAGCCTGGTAGGTAGGG-GGTAGGACTAACC-TTGATACTAGATGAATAGATGT -s Anc2.Anc2refChr0 24981 101 - 56053 CCCAAGAACATT--GGCATCCCTAATGTACCAATTGCTCTATTTACATTACTAGCCTGGTAGGTAGGG-GGTAGGACTAGCC-TTGATACTAGATGAATAGATTT -s mr.mrrefChr0 26115 105 + 130230 CACAAGAACATTAAGCCATTCCTAATGTAAAAATACATCTATTTACATTGCTAGCTTGGTAATTAGTGTGATAGAACTAACCCTTGGTACTAAATGAATAGTCGT -s simCow_chr6.simCow.chr6 566293 97 - 602619 CCCAAAAACATT--GGCATCCCTAATGTACAAATCCATCTATTTACAGTTCTCACCTTGTAGGTGGGG-GGTTGGACTAGCC-TTGGTACAAAATGGAGAG---- -s simDog_chr6.simDog.chr6 561808 101 - 593897 GCCGAGAACATT--GGCATCCTTAATGTACCAGTTGCTCTATTTACATCACTAGCCCGGTAGGCAGGG-GGTAGGCCTAGCT-TTGATACTAGAAGACTAAATTT -s simHuman_chr6.simHuman.chr6 569175 100 - 601863 CCCAAGAACATT--GGCATCCCTAGGTAACAATTACTTCTATTTACAATGCTA-CCTGGTAGGTAGGG-GGTAGTACTAACC-TTATTACTAGATAAATAGGAGT -s simRat_chr6.simRat.chr6 19745 104 + 647215 CACAAGGACATTAAGC-GTTCCTAATGTAAAAATACATCTATTTACATTGCTAGCTTGGTAAATAGTGTGATAGAACTAACCCTTGGTACTACATGAATAGACGT - -a -s simMouse_chr6.simMouse.chr6 27748 5 + 636262 ATTAG -s Anc0.Anc0refChr9 6076 5 + 35212 ATAGG -s Anc1.Anc1refChr2 129838 5 - 144309 ATAGG -s Anc2.Anc2refChr0 25083 5 - 56053 TTAGG -s mr.mrrefChr0 26220 5 + 130230 ATTAG -s simCow_chr6.simCow.chr6 566391 5 - 602619 CTAGG -s simDog_chr6.simDog.chr6 561910 5 - 593897 TTTGA -s simHuman_chr6.simHuman.chr6 569276 5 - 601863 ATAGG -s simRat_chr6.simRat.chr6 19849 5 + 647215 ATCAG - -a -s simMouse_chr6.simMouse.chr6 27753 30 + 636262 TTTACATTCATTTAGCCATACTCTTTACTG -s Anc0.Anc0refChr9 6081 30 + 35212 TTAATATTCATTTAACCATGATCTTTACTG -s Anc1.Anc1refChr2 129843 30 - 144309 TTAATATTCATTTAACCATGATCTTTACTG -s Anc2.Anc2refChr0 25088 30 - 56053 TTAATATTAATTTAACCAAGATCTTTACTG -s mr.mrrefChr0 26225 30 + 130230 TTTACATTCATTTAGCCATACTCTTTACTG -s mr.mrrefChr0 26427 30 + 130230 CTATCATTCATTTAGCCATACTCTTTACTG -s simCow_chr6.simCow.chr6 566396 30 - 602619 TTAATATCAATGTAACCACGATCTTTGCCG -s simDog_chr6.simDog.chr6 561915 30 - 593897 TTAATGTTAGTTTTAACAAAATCTTCACTG -s simHuman_chr6.simHuman.chr6 569281 30 - 601863 TTAATATTTAGTTAACCATGATCTTTACTG -s simMouse_chr6.simMouse.chr6 27949 30 + 636262 CTATCATTCATTTAGCCATACTCTTTACTG -s simRat_chr6.simRat.chr6 20049 30 + 647215 CTATCATTCTTTTAGCCATACTCTTTACTG -s simRat_chr6.simRat.chr6 19854 30 + 647215 TTTAGATTCATTTAGCCATACTCTTTACTG - -a -s simMouse_chr6.simMouse.chr6 27783 25 + 636262 GTCTCCCAATCATCCTGCTGCAATG -s Anc0.Anc0refChr9 6128 25 + 35212 GTCTCCCAATTATCTTACTGAGATG -s Anc1.Anc1refChr2 129890 25 - 144309 GTCTCCCAATTATCTTACTGAGATG -s Anc2.Anc2refChr0 25135 25 - 56053 GTCTCGCAATTATCTCACTGAGATG -s mr.mrrefChr0 26257 25 + 130230 GTCTCCCAATCATCCTACTGCAATG -s mr.mrrefChr0 26459 23 + 130230 --CTCCCAATCATCCTACTGCAATG -s simCow_chr6.simCow.chr6 566443 25 - 602619 GTCCCACAATTGTCTCACTGAGCTG -s simDog_chr6.simDog.chr6 561962 25 - 593897 GTCTTGCAATTATCTCACTGGGATG -s simHuman_chr6.simHuman.chr6 569328 25 - 601863 GTCTCCCAATTATCTTACTTAGATG -s simMouse_chr6.simMouse.chr6 27981 23 + 636262 --CTCCCAATCATCCTACTGCAATG -s simRat_chr6.simRat.chr6 20081 23 + 647215 --CTCCCAATCATCCTACTGCAATG -s simRat_chr6.simRat.chr6 19886 17 + 647215 --------ATCACCCTACTGCAATG - -a -s simMouse_chr6.simMouse.chr6 27808 17 + 636262 GGATTAGATGTTGACAG -s Anc0.Anc0refChr9 6158 17 + 35212 GGATCAGATGTAGATAG -s Anc1.Anc1refChr2 129920 17 - 144309 GGATCAGATGTAGATAG -s Anc2.Anc2refChr0 25165 17 - 56053 GGATCAGATGTAGATCG -s mr.mrrefChr0 26287 17 + 130230 GGATTAGATGTTGACAG -s mr.mrrefChr0 26487 17 + 130230 GGATCAGGTGTGGACAG -s simCow_chr6.simCow.chr6 566473 17 - 602619 GGATCAGATGTTGCTGG -s simDog_chr6.simDog.chr6 561987 11 - 593897 ------GATGTAGATCG -s simHuman_chr6.simHuman.chr6 569358 17 - 601863 GGTTCATATGTAGATAC -s simMouse_chr6.simMouse.chr6 28009 17 + 636262 GGATCAGGTGTGGACAG -s simRat_chr6.simRat.chr6 20118 17 + 647215 GGGTCAGATGTGGACAG -s simRat_chr6.simRat.chr6 19908 17 + 647215 GGATGAGATGTGGACAG - -a -s simMouse_chr6.simMouse.chr6 27825 6 + 636262 ATCATG -s Anc0.Anc0refChr9 6175 6 + 35212 ATCATT -s Anc1.Anc1refChr2 129937 6 - 144309 ATCATT -s Anc2.Anc2refChr0 25182 6 - 56053 ATCATT -s mr.mrrefChr0 26304 6 + 130230 ATCATT -s mr.mrrefChr0 26504 6 + 130230 CTTACT -s simCow_chr6.simCow.chr6 566490 6 - 602619 ATTATT -s simDog_chr6.simDog.chr6 561998 6 - 593897 ATCATT -s simHuman_chr6.simHuman.chr6 569375 6 - 601863 ATCATT -s simMouse_chr6.simMouse.chr6 28026 6 + 636262 CTTACT -s simRat_chr6.simRat.chr6 20137 6 + 647215 TTTATT -s simRat_chr6.simRat.chr6 19925 6 + 647215 ATTACT - -a -s simMouse_chr6.simMouse.chr6 27831 10 + 636262 TTGAAGAGCC -s Anc0.Anc0refChr9 6181 10 + 35212 TTGAAGAGCC -s Anc1.Anc1refChr2 129943 10 - 144309 TTGAAGAGCC -s Anc2.Anc2refChr0 25188 10 - 56053 TTGAAGAGGC -s mr.mrrefChr0 26310 10 + 130230 TTGAAGAGCC -s mr.mrrefChr0 26516 10 + 130230 TTGAAGAGCC -s simCow_chr6.simCow.chr6 566496 10 - 602619 TTGAAGAGGC -s simDog_chr6.simDog.chr6 562004 10 - 593897 CAGAAGAGGC -s simHuman_chr6.simHuman.chr6 569381 10 - 601863 TTGAAGAGCC -s simMouse_chr6.simMouse.chr6 28032 10 + 636262 TTGAAGAGCC -s simRat_chr6.simRat.chr6 20168 10 + 647215 TTGAAGAGCC -s simRat_chr6.simRat.chr6 19931 10 + 647215 TTGAAGAGCC - -a -s simMouse_chr6.simMouse.chr6 27841 28 + 636262 TCAAGGGCTCTGCAGCTCAGATAAAACT -s Anc0.Anc0refChr9 6192 20 + 35212 TCAGG--------AGAGCAAATAGCACA -s Anc1.Anc1refChr2 129954 28 - 144309 TCAGGGGCTCAGCAGAGCAAATAGCACA -s Anc2.Anc2refChr0 25199 20 - 56053 TCAGG--------AGAGTAAATAGCACA -s mr.mrrefChr0 26321 28 + 130230 TCAAGGGCTCTGCATCTCAAATAGAACT -s mr.mrrefChr0 26527 28 + 130230 GCAAGGGCCTCGCAGCCCAAATAAAACA -s simCow_chr6.simCow.chr6 566507 20 - 602619 TTAGG--------AGAGTAAATAGCACA -s simDog_chr6.simDog.chr6 562015 20 - 593897 TCAGG--------AGGGTAAATAGCACA -s simHuman_chr6.simHuman.chr6 569392 28 - 601863 TCAGGGCCTCAGGATAACAAATGGCACC -s simMouse_chr6.simMouse.chr6 28043 28 + 636262 TCAAGGGCTCCTCAGCCCAAATAAAACA -s simRat_chr6.simRat.chr6 20179 28 + 647215 GCAAGGGCCTGGCAGCCCAAATAAAACA -s simRat_chr6.simRat.chr6 19942 28 + 647215 TCAAGGGCTTTGCATCCCAAAAAGAACA - -a -s simMouse_chr6.simMouse.chr6 27869 6 + 636262 ACTAAA -s Anc0.Anc0refChr9 6282 6 + 35212 ACTAAA -s Anc1.Anc1refChr2 130052 6 - 144309 ACTAAA -s Anc2.Anc2refChr0 25289 6 - 56053 AATCAA -s mr.mrrefChr0 26349 6 + 130230 ACTAAA -s mr.mrrefChr0 26555 6 + 130230 ACTAAA -s simCow_chr6.simCow.chr6 566586 6 - 602619 AGAGAA -s simDog_chr6.simDog.chr6 562105 6 - 593897 AATCAA -s simMouse_chr6.simMouse.chr6 28071 6 + 636262 ACTATA -s simRat_chr6.simRat.chr6 20207 6 + 647215 ACTAAA -s simRat_chr6.simRat.chr6 19970 6 + 647215 ACTAAA - -a -s simMouse_chr6.simMouse.chr6 27875 5 + 636262 GTAGT -s Anc0.Anc0refChr9 6288 5 + 35212 GTAGT -s Anc1.Anc1refChr2 130058 5 - 144309 GTAGT -s Anc2.Anc2refChr0 25310 5 - 56053 GTAAT -s mr.mrrefChr0 26355 5 + 130230 GTAGT -s mr.mrrefChr0 26561 5 + 130230 GTAGT -s simCow_chr6.simCow.chr6 566609 5 - 602619 TTAAT -s simDog_chr6.simDog.chr6 562126 5 - 593897 GTATT -s simMouse_chr6.simMouse.chr6 28077 5 + 636262 GTGGT -s simRat_chr6.simRat.chr6 20213 5 + 647215 GTAGT -s simRat_chr6.simRat.chr6 19976 5 + 647215 GTAGT - -a -s simMouse_chr6.simMouse.chr6 27880 10 + 636262 AAACATAGGC -s Anc0.Anc0refChr9 6294 9 + 35212 AA-CTTAGGC -s Anc1.Anc1refChr2 130064 9 - 144309 AA-CTTAGGC -s Anc2.Anc2refChr0 25316 9 - 56053 AA-CTTATGA -s mr.mrrefChr0 26360 9 + 130230 AA-CATAGGC -s mr.mrrefChr0 26567 9 + 130230 AG-CTTAGGC -s simCow_chr6.simCow.chr6 566615 8 - 602619 TA-CTTATG- -s simDog_chr6.simDog.chr6 562132 9 - 593897 AA-CTTATGA -s simHuman_chr6.simHuman.chr6 569499 8 - 601863 -A-CCAAGGC -s simMouse_chr6.simMouse.chr6 28083 9 + 636262 AG-CTTAGGC -s simRat_chr6.simRat.chr6 20219 9 + 647215 AG-CTTAGGG -s simRat_chr6.simRat.chr6 19981 9 + 647215 AC-CTTAGGC - -a -s simMouse_chr6.simMouse.chr6 27890 17 + 636262 CTATTATGAACATGTTA -s Anc0.Anc0refChr9 6303 11 + 35212 CTGTT----ACATG--A -s Anc1.Anc1refChr2 130073 17 - 144309 CTGTTATGAACATGTTA -s Anc2.Anc2refChr0 25325 11 - 56053 ATGTT----ACATG--G -s mr.mrrefChr0 26369 17 + 130230 CTATTATGAACATGTTA -s mr.mrrefChr0 26576 17 + 130230 TTATTATGAACATGTTA -s simCow_chr6.simCow.chr6 566623 11 - 602619 ATGTT----TTATG--G -s simDog_chr6.simDog.chr6 562142 11 - 593897 ATGTT----ACATG--G -s simHuman_chr6.simHuman.chr6 569507 17 - 601863 CTGTTATGAACATATCA -s simMouse_chr6.simMouse.chr6 28092 17 + 636262 TTATTATGAACATGTTA -s simRat_chr6.simRat.chr6 20228 17 + 647215 TCATTATGAATATGTTA -s simRat_chr6.simRat.chr6 19990 17 + 647215 CTATTATGAACCTGTTA - -a -s simMouse_chr6.simMouse.chr6 27907 6 + 636262 GTGTAC -s Anc0.Anc0refChr9 6315 6 + 35212 GTGGAC -s Anc1.Anc1refChr2 130091 6 - 144309 GTGGAC -s Anc2.Anc2refChr0 25337 6 - 56053 GTGGAC -s mr.mrrefChr0 26386 6 + 130230 GTGTAC -s mr.mrrefChr0 26594 6 + 130230 GTGCAC -s simCow_chr6.simCow.chr6 566635 6 - 602619 ACGGAC -s simDog_chr6.simDog.chr6 562154 6 - 593897 GTGGAC -s simHuman_chr6.simHuman.chr6 569525 6 - 601863 GTGGAC -s simMouse_chr6.simMouse.chr6 28110 6 + 636262 GTGCAC -s simRat_chr6.simRat.chr6 20246 6 + 647215 GTGCAC -s simRat_chr6.simRat.chr6 20008 6 + 647215 GTGTAT - -a -s simMouse_chr6.simMouse.chr6 27913 36 + 636262 ATAGGATAATAGATAGTGCTCTAGCAGTGCTAAAGA -s Anc0.Anc0refChr9 6321 30 + 35212 ACAG----TTATTTGGTCTAGTGCCAGTGGTAT--A -s Anc1.Anc1refChr2 130097 35 - 144309 ACAGAATATTATTTGGTCTAGTGCCAGTGGTAT-AA -s Anc2.Anc2refChr0 25343 30 - 56053 ACAG----TTGTTTGGCCTAGTGCCCTTGGTAT--A -s mr.mrrefChr0 26392 35 + 130230 ATAGGATAATAGATAGTGCTCTAGCAGTGCTAA-GA -s mr.mrrefChr0 26600 35 + 130230 ACAGAATAATATTTAGTTTGCTAGCAGTGGTAA-GA -s simCow_chr6.simCow.chr6 566641 30 - 602619 ACAG----TTGTTTGGCCTAATGCGATTGGTAT--A -s simDog_chr6.simDog.chr6 562160 30 - 593897 TCAG----TTGTATGGCCTTGTACCCTTGGTAT--A -s simHuman_chr6.simHuman.chr6 569531 30 - 601863 ACAG----TTATTTGGACTAGTGCCGATGGTAT-A- -s simMouse_chr6.simMouse.chr6 28117 33 + 636262 ACAGAATAATATTTAGTTTGCTAGTAGT--TAA-GA -s simRat_chr6.simRat.chr6 20252 35 + 647215 ATAGGATAATAATTAGCTCTCTAGCAGTGGTAA-GA -s simRat_chr6.simRat.chr6 20014 35 + 647215 ATGGAATAATAATTAGTTCTATAGTGGCAGTAA-GA - -a -s simMouse_chr6.simMouse.chr6 27979 1 + 636262 G -s Anc0.Anc0refChr9 6111 1 + 35212 G -s Anc1.Anc1refChr2 129873 1 - 144309 G -s Anc2.Anc2refChr0 25118 1 - 56053 A -s mr.mrrefChr0 26457 1 + 130230 G -s mr.mrrefChr0 26255 1 + 130230 G -s simCow_chr6.simCow.chr6 566426 1 - 602619 A -s simDog_chr6.simDog.chr6 561945 1 - 593897 A -s simHuman_chr6.simHuman.chr6 569311 1 - 601863 C -s simRat_chr6.simRat.chr6 19884 1 + 647215 G -s simRat_chr6.simRat.chr6 20079 1 + 647215 G - -a -s simMouse_chr6.simMouse.chr6 27980 1 + 636262 C -s Anc0.Anc0refChr9 6127 1 + 35212 T -s Anc1.Anc1refChr2 129889 1 - 144309 T -s Anc2.Anc2refChr0 25134 1 - 56053 T -s mr.mrrefChr0 26458 1 + 130230 C -s mr.mrrefChr0 26256 1 + 130230 T -s simCow_chr6.simCow.chr6 566442 1 - 602619 C -s simDog_chr6.simDog.chr6 561961 1 - 593897 T -s simHuman_chr6.simHuman.chr6 569327 1 - 601863 T -s simRat_chr6.simRat.chr6 19885 1 + 647215 T -s simRat_chr6.simRat.chr6 20080 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 28004 3 + 636262 TGT -s Anc0.Anc0refChr9 6153 3 + 35212 TGT -s Anc1.Anc1refChr2 129915 3 - 144309 TGT -s Anc2.Anc2refChr0 25160 3 - 56053 TGT -s mr.mrrefChr0 26482 3 + 130230 TGT -s mr.mrrefChr0 26282 3 + 130230 TGT -s simCow_chr6.simCow.chr6 566468 3 - 602619 TGT -s simHuman_chr6.simHuman.chr6 569353 3 - 601863 TGT -s simRat_chr6.simRat.chr6 19903 3 + 647215 TGT -s simRat_chr6.simRat.chr6 20104 3 + 647215 TGT - -a -s simMouse_chr6.simMouse.chr6 28007 2 + 636262 TG -s Anc0.Anc0refChr9 6156 2 + 35212 TG -s Anc1.Anc1refChr2 129918 2 - 144309 TG -s Anc2.Anc2refChr0 25163 2 - 56053 TG -s mr.mrrefChr0 26485 2 + 130230 TG -s mr.mrrefChr0 26285 2 + 130230 TG -s simCow_chr6.simCow.chr6 566471 2 - 602619 TG -s simHuman_chr6.simHuman.chr6 569356 2 - 601863 TG -s simRat_chr6.simRat.chr6 19906 2 + 647215 TG -s simRat_chr6.simRat.chr6 20116 2 + 647215 TG - -a -s simMouse_chr6.simMouse.chr6 28042 1 + 636262 C -s Anc0.Anc0refChr9 6191 1 + 35212 C -s Anc1.Anc1refChr2 129953 1 - 144309 C -s Anc2.Anc2refChr0 25198 1 - 56053 C -s mr.mrrefChr0 26526 1 + 130230 C -s mr.mrrefChr0 26320 1 + 130230 C -s simCow_chr6.simCow.chr6 566506 1 - 602619 C -s simDog_chr6.simDog.chr6 562014 1 - 593897 C -s simHuman_chr6.simHuman.chr6 569391 1 - 601863 C -s simRat_chr6.simRat.chr6 19941 1 + 647215 C -s simRat_chr6.simRat.chr6 20178 1 + 647215 C - -a -s simMouse_chr6.simMouse.chr6 28082 1 + 636262 A -s Anc0.Anc0refChr9 6293 1 + 35212 G -s Anc1.Anc1refChr2 130063 1 - 144309 G -s Anc2.Anc2refChr0 25315 1 - 56053 G -s mr.mrrefChr0 26566 1 + 130230 A -s simCow_chr6.simCow.chr6 566614 1 - 602619 G -s simDog_chr6.simDog.chr6 562131 1 - 593897 G -s simRat_chr6.simRat.chr6 20218 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 28109 1 + 636262 T -s Anc0.Anc0refChr9 6314 1 + 35212 T -s Anc1.Anc1refChr2 130090 1 - 144309 T -s Anc2.Anc2refChr0 25336 1 - 56053 T -s mr.mrrefChr0 26593 1 + 130230 T -s simCow_chr6.simCow.chr6 566634 1 - 602619 T -s simDog_chr6.simDog.chr6 562153 1 - 593897 T -s simHuman_chr6.simHuman.chr6 569524 1 - 601863 G -s simRat_chr6.simRat.chr6 20245 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 28116 1 + 636262 C - -a -s simMouse_chr6.simMouse.chr6 28150 14 + 636262 CTATCACCAGCACA -s Anc0.Anc0refChr9 6351 7 + 35212 -------CAGCTCC -s Anc1.Anc1refChr2 130132 7 - 144309 -------CAGCTCC -s Anc2.Anc2refChr0 25373 7 - 56053 -------CATCTGC -s mr.mrrefChr0 26635 14 + 130230 CTATCACCAGCACA -s simCow_chr6.simCow.chr6 566671 7 - 602619 -------CATCTTC -s simDog_chr6.simDog.chr6 562190 5 - 593897 -------CA--TGT -s simHuman_chr6.simHuman.chr6 569561 7 - 601863 -------CAGCTCC -s simRat_chr6.simRat.chr6 20287 14 + 647215 CTATCATTAGCACA - -a -s simMouse_chr6.simMouse.chr6 28164 10 + 636262 TTTGACCATG -s Anc0.Anc0refChr9 6358 10 + 35212 CTTAATCAAA -s Anc1.Anc1refChr2 130139 10 - 144309 CTTAATCAAA -s Anc2.Anc2refChr0 25380 10 - 56053 CTTAATCAAA -s mr.mrrefChr0 26649 10 + 130230 TTTGACCATG -s simCow_chr6.simCow.chr6 566679 10 - 602619 CTTAATCAAA -s simDog_chr6.simDog.chr6 562195 10 - 593897 CTCAATTGCG -s simHuman_chr6.simHuman.chr6 569568 10 - 601863 CTTAATCAAA -s simRat_chr6.simRat.chr6 20301 10 + 647215 TTTGACCATG - -a -s simMouse_chr6.simMouse.chr6 28174 24 + 636262 ATTAAGGGGGAGGCCTACCAACGG -s Anc0.Anc0refChr9 6368 20 + 35212 ATCAAATGG-G---CTGCTGATGA -s Anc1.Anc1refChr2 130149 20 - 144309 ATCAAATGG-G---CTGCTGATGA -s Anc2.Anc2refChr0 25390 20 - 56053 ATCAAATGG-G---CTGCTGATGA -s mr.mrrefChr0 26659 21 + 130230 ATTAAGGGGGA---CTACCAATGG -s simCow_chr6.simCow.chr6 566695 20 - 602619 ATCAAGTGG-G---CTACTGCTGA -s simDog_chr6.simDog.chr6 562205 20 - 593897 AGCAAATGA-G---ATGCTAATGA -s simHuman_chr6.simHuman.chr6 569578 20 - 601863 ATCAAAAAG-C---CTGATGATGA -s simRat_chr6.simRat.chr6 20311 21 + 647215 ATTAAGGGGGG---CAACCAATGG - -a -s simMouse_chr6.simMouse.chr6 28198 9 + 636262 CATGCGTCC -s Anc0.Anc0refChr9 6388 9 + 35212 TTCCCTTAC -s Anc1.Anc1refChr2 130169 9 - 144309 TTCCCTTAC -s Anc2.Anc2refChr0 25410 9 - 56053 TTCCCTTAC -s mr.mrrefChr0 26680 9 + 130230 CACGCGTCC -s simCow_chr6.simCow.chr6 566715 9 - 602619 GCTCCTTAC -s simDog_chr6.simDog.chr6 562226 9 - 593897 TTCCCTTAC -s simHuman_chr6.simHuman.chr6 569598 9 - 601863 TTCCCTTAC -s simRat_chr6.simRat.chr6 20332 9 + 647215 CACACGTCC - -a -s simMouse_chr6.simMouse.chr6 28207 14 + 636262 ACACAACATCCTCC -s Anc0.Anc0refChr9 6407 13 + 35212 A-TAAATATTGTCC -s Anc1.Anc1refChr2 130188 14 - 144309 ACTAAATATTGTCC -s Anc2.Anc2refChr0 25429 13 - 56053 G-TAATTATAGTCT -s mr.mrrefChr0 26689 14 + 130230 ACACAACATTGTCC -s simCow_chr6.simCow.chr6 566734 13 - 602619 C-TAATTATAGTTT -s simDog_chr6.simDog.chr6 562245 13 - 593897 G-TAATTATAATCT -s simHuman_chr6.simHuman.chr6 569617 14 - 601863 ACTAAATATTGTCC -s simRat_chr6.simRat.chr6 20341 14 + 647215 ACACAACATTGTCC - -a -s simMouse_chr6.simMouse.chr6 28221 27 + 636262 AGATTGAATACTAAAACTGGACCTTGG -s Anc0.Anc0refChr9 6427 20 + 35212 AGGTTGTATATTGAA-------CCTGG -s Anc1.Anc1refChr2 130209 20 - 144309 AGGTTGTATATTGAA-------CCTGG -s Anc2.Anc2refChr0 25449 20 - 56053 AGGTTGTATATTGAA-------CCTGG -s mr.mrrefChr0 26703 27 + 130230 AGATTGAATACTAAAACTGGACCTTGG -s simCow_chr6.simCow.chr6 566754 19 - 602619 AGGTCGTAC-TTGAA-------CCTGG -s simDog_chr6.simDog.chr6 562265 20 - 593897 AGGCTGTATATTGAA-------CCTGG -s simHuman_chr6.simHuman.chr6 569638 20 - 601863 AGGTTGGATATTGAA-------CCTGG -s simRat_chr6.simRat.chr6 20355 27 + 647215 AGTTTGTATACGAGAACTGGACCTTGG - -a -s simMouse_chr6.simMouse.chr6 28248 1 + 636262 G -s Anc0.Anc0refChr9 6447 1 + 35212 G -s Anc1.Anc1refChr2 130229 1 - 144309 G -s Anc2.Anc2refChr0 25469 1 - 56053 G -s mr.mrrefChr0 26730 1 + 130230 G -s simCow_chr6.simCow.chr6 566773 1 - 602619 G -s simDog_chr6.simDog.chr6 562286 1 - 593897 G -s simHuman_chr6.simHuman.chr6 569658 1 - 601863 G -s simRat_chr6.simRat.chr6 20382 1 + 647215 G - -a -s simMouse_chr6.simMouse.chr6 28249 19 + 636262 CGGAGCTGATAGTTCTCCT -s Anc0.Anc0refChr9 6448 10 + 35212 GGCT-------GTGC--CT -s Anc1.Anc1refChr2 130230 17 - 144309 GGCTGCTGGGGGTGC--CT -s Anc2.Anc2refChr0 25470 10 - 56053 GGCT-------GTGC--CT -s mr.mrrefChr0 26731 19 + 130230 GGGAGCTGATGGTTCTCCT -s simCow_chr6.simCow.chr6 566777 10 - 602619 TGCT-------GTGC--CT -s simDog_chr6.simDog.chr6 562287 10 - 593897 GGCT-------GTGC--CT -s simHuman_chr6.simHuman.chr6 569659 17 - 601863 GGCTGCTGGGGGTGC--CT -s simRat_chr6.simRat.chr6 20383 19 + 647215 GGAAGCTGATGGGTCTCCT - -a -s simMouse_chr6.simMouse.chr6 28268 8 + 636262 CTTTTTCT -s Anc0.Anc0refChr9 6458 8 + 35212 CTTTTACT -s Anc1.Anc1refChr2 130247 8 - 144309 CTTTTACT -s Anc2.Anc2refChr0 25480 8 - 56053 CTTTCACT -s mr.mrrefChr0 26750 8 + 130230 CTTTTTCT -s simCow_chr6.simCow.chr6 567156 8 - 602619 CTATCACG -s simCow_chr6.simCow.chr6 566787 8 - 602619 GTTTTGCT -s simDog_chr6.simDog.chr6 562297 8 - 593897 CTTTCACT -s simHuman_chr6.simHuman.chr6 569676 8 - 601863 CTTTTGTT -s simRat_chr6.simRat.chr6 20402 8 + 647215 CTTTTTCT - -a -s simMouse_chr6.simMouse.chr6 28276 3 + 636262 ATC -s Anc0.Anc0refChr9 6469 3 + 35212 ATT -s Anc1.Anc1refChr2 130258 3 - 144309 ATT -s Anc2.Anc2refChr0 25491 3 - 56053 ATT -s mr.mrrefChr0 26761 3 + 130230 ATC -s simCow_chr6.simCow.chr6 567167 3 - 602619 GCT -s simCow_chr6.simCow.chr6 566798 3 - 602619 TTT -s simDog_chr6.simDog.chr6 562308 3 - 593897 ATT -s simHuman_chr6.simHuman.chr6 569687 3 - 601863 ATT -s simRat_chr6.simRat.chr6 20413 3 + 647215 ATC - -a -s simMouse_chr6.simMouse.chr6 28279 7 + 636262 CTGCCCG -s Anc0.Anc0refChr9 6477 7 + 35212 CTGTATG -s Anc1.Anc1refChr2 130266 7 - 144309 CTGTATG -s Anc2.Anc2refChr0 25499 7 - 56053 CTGTATG -s mr.mrrefChr0 26764 7 + 130230 CTGCCTG -s simCow_chr6.simCow.chr6 566806 7 - 602619 CTGTATG -s simDog_chr6.simDog.chr6 562316 7 - 593897 CTGTGCA -s simHuman_chr6.simHuman.chr6 569695 7 - 601863 CTGTATG -s simRat_chr6.simRat.chr6 20416 7 + 647215 CTACCTG - -a -s simMouse_chr6.simMouse.chr6 28286 34 + 636262 TCATATCTGAAGAATTTTGTGACTACACTGCTTG -s Anc0.Anc0refChr9 6484 24 + 35212 TCCC----------TTTTATGGATGCACTTCTTA -s Anc1.Anc1refChr2 130273 24 - 144309 TCCC----------TTTTATGGATGCACTTCTTA -s Anc2.Anc2refChr0 25506 24 - 56053 TGCC----------TTTTATGGAAGCACTTCTTA -s mr.mrrefChr0 26771 34 + 130230 TCACATCTGAAGAATTTTGTGACTACACTGCTTG -s simCow_chr6.simCow.chr6 567172 24 - 602619 TGCC----------TTTTATGGAAGCACTTCTCT -s simCow_chr6.simCow.chr6 566813 24 - 602619 TGCC----------TTTTATGGAAGCACTACTTT -s simDog_chr6.simDog.chr6 562323 24 - 593897 TGCC----------TATTATGGAAACACTTATTA -s simHuman_chr6.simHuman.chr6 569702 24 - 601863 TCCC----------TTTTATGGGTGCTCTTCTTA -s simRat_chr6.simRat.chr6 20423 32 + 647215 --ACATCTGAAAAATTTTGTGATTACACTGCCTG - -a -s simMouse_chr6.simMouse.chr6 28320 11 + 636262 AGGAGAACACC -s Anc0.Anc0refChr9 6514 11 + 35212 AACAGAGTATC -s Anc1.Anc1refChr2 130303 11 - 144309 AACAGAGTATC -s Anc2.Anc2refChr0 25536 11 - 56053 AACGGAGTATC -s mr.mrrefChr0 26805 11 + 130230 AAGAGAGCATC -s simCow_chr6.simCow.chr6 567202 11 - 602619 ACCAGAGTACC -s simCow_chr6.simCow.chr6 566843 11 - 602619 AACGGAGTATC -s simDog_chr6.simDog.chr6 562353 11 - 593897 AATGGAGTATC -s simHuman_chr6.simHuman.chr6 569732 11 - 601863 AACAGAGTATC -s simRat_chr6.simRat.chr6 20455 11 + 647215 AAGGGAGCATC - -a -s simMouse_chr6.simMouse.chr6 28331 51 + 636262 TATTCGCCAGAGGTTGCTCTGCTCTAGTAGACCAGGTGGGGGTGACCAACT -s Anc0.Anc0refChr9 6526 33 + 35212 T-----CCA------------CTCTATTAAATCTTATGGGTGTG-CTGCCT -s Anc1.Anc1refChr2 130315 38 - 144309 TTCCCACCA------------CTCTATTAAATCTTATGGGTGTG-CTGCCT -s Anc2.Anc2refChr0 25548 33 - 56053 T-----CCA------------CATTATTAAATCTTATAGTTGTG-CTGCAT -s mr.mrrefChr0 26816 51 + 130230 TATTCACCAGAGGTTGCTCTGCTCTAGTAAACCAGATGGGGGTGACTAACT -s simCow_chr6.simCow.chr6 567214 33 - 602619 A-----CCT------------CATCATTAAATCTGATAGTTGTG-CTGCAT -s simCow_chr6.simCow.chr6 566855 33 - 602619 T-----CTA------------CATTATTAAGTCTTGTAGTTGTG-CTGCAT -s simDog_chr6.simDog.chr6 562365 33 - 593897 C-----TCA------------CATTATAAAATCTTATAGTTGTG-CTGCAT -s simHuman_chr6.simHuman.chr6 569744 38 - 601863 TTCCCACCA------------CTCCACCAAATCTTATGGGTGTA-CTGTCT -s simRat_chr6.simRat.chr6 20466 51 + 647215 TATTCACCAGAGGTTGCTCTGCACTAGTAAACCAGATGGGGGTGACTAACT - -a -s simMouse_chr6.simMouse.chr6 28382 18 + 636262 ACATAAATTATTGCACTA -s Anc0.Anc0refChr9 6559 18 + 35212 AGTTGAATAATTGGGGTG -s Anc1.Anc1refChr2 130353 18 - 144309 AGTTGAATAATTGGGGTG -s Anc2.Anc2refChr0 25591 18 - 56053 AGTTGAATAATTGGGGTG -s mr.mrrefChr0 26867 18 + 130230 AGATAAATTATTGCACTA -s simCow_chr6.simCow.chr6 567257 18 - 602619 AGTTGTATAATTGGGCTG -s simCow_chr6.simCow.chr6 566898 18 - 602619 AGTTGAATAAACAGGTTG -s simDog_chr6.simDog.chr6 562408 18 - 593897 AGCTGAGTAATTGGGGCA -s simHuman_chr6.simHuman.chr6 569782 4 - 601863 TGGT-------------- -s simRat_chr6.simRat.chr6 20517 18 + 647215 AGTTAAATAATTGGGCTA - -a -s simMouse_chr6.simMouse.chr6 28400 10 + 636262 TGAGACCTGG -s Anc0.Anc0refChr9 6577 4 + 35212 T------TAG -s Anc1.Anc1refChr2 130371 4 - 144309 T------TAG -s Anc2.Anc2refChr0 25615 4 - 56053 T------TAG -s mr.mrrefChr0 26885 4 + 130230 T------TGG -s simCow_chr6.simCow.chr6 566922 4 - 602619 T------GAG -s simDog_chr6.simDog.chr6 562432 4 - 593897 T------TGA -s simHuman_chr6.simHuman.chr6 569786 3 - 601863 -------TAG -s simRat_chr6.simRat.chr6 20535 1 + 647215 T--------- - -a -s simMouse_chr6.simMouse.chr6 28410 5 + 636262 TCAAG -s Anc0.Anc0refChr9 6581 5 + 35212 TCAAG -s Anc1.Anc1refChr2 130375 5 - 144309 TCAAG -s Anc2.Anc2refChr0 25619 5 - 56053 TTAAG -s mr.mrrefChr0 26889 5 + 130230 TCAAG -s simCow_chr6.simCow.chr6 567280 5 - 602619 TTAAG -s simCow_chr6.simCow.chr6 566926 5 - 602619 ATAAG -s simDog_chr6.simDog.chr6 562436 5 - 593897 CTGAG -s simHuman_chr6.simHuman.chr6 569789 5 - 601863 TCAAA -s simRat_chr6.simRat.chr6 20536 3 + 647215 --ATG - -a -s simMouse_chr6.simMouse.chr6 28415 6 + 636262 AAAAGA -s Anc0.Anc0refChr9 6586 6 + 35212 AGAAGA -s Anc1.Anc1refChr2 130380 6 - 144309 AGAAGA -s Anc2.Anc2refChr0 25624 6 - 56053 AGAAGA -s mr.mrrefChr0 26894 6 + 130230 AAAAGA -s simCow_chr6.simCow.chr6 567285 6 - 602619 AGAAGA -s simCow_chr6.simCow.chr6 566953 6 - 602619 AGCAGG -s simDog_chr6.simDog.chr6 562441 6 - 593897 ACAAGA -s simHuman_chr6.simHuman.chr6 569794 6 - 601863 ATAAGA -s simRat_chr6.simRat.chr6 20539 6 + 647215 AAAAGA - -a -s simMouse_chr6.simMouse.chr6 28421 21 + 636262 GGTGCCCACATCAATCCTGAC -s Anc0.Anc0refChr9 6592 21 + 35212 GGTAACCACCCCATACCCAAC -s Anc1.Anc1refChr2 130386 21 - 144309 GGTAACCACCCCATACCCAAC -s Anc2.Anc2refChr0 25630 21 - 56053 GGTAACCACCCTATACCCAAG -s mr.mrrefChr0 26900 21 + 130230 GGTGCCCACATCAATCCTAAC -s simCow_chr6.simCow.chr6 567292 21 - 602619 GGTAACCTCCCCAAGATCAGC -s simCow_chr6.simCow.chr6 566959 21 - 602619 CATAACCATCCTATACCCAAG -s simDog_chr6.simDog.chr6 562447 21 - 593897 TGTAACCACTCTATACCCAAG -s simHuman_chr6.simHuman.chr6 569800 21 - 601863 GATAACCACCCCATCACCAAC -s simRat_chr6.simRat.chr6 20545 21 + 647215 GGTGTCTACATCAATCCTAAC - -a -s simMouse_chr6.simMouse.chr6 28442 9 + 636262 TAGAATAAG -s Anc0.Anc0refChr9 6613 9 + 35212 CACAATAAT -s Anc1.Anc1refChr2 130407 9 - 144309 CACAATAAT -s Anc2.Anc2refChr0 25651 9 - 56053 CACATCAAT -s mr.mrrefChr0 26921 9 + 130230 CAGAATAAG -s simCow_chr6.simCow.chr6 566980 9 - 602619 GATGTAGAG -s simDog_chr6.simDog.chr6 562468 9 - 593897 CACATCAAT -s simHuman_chr6.simHuman.chr6 569821 6 - 601863 CA--ATCA- -s simRat_chr6.simRat.chr6 20566 9 + 647215 CAGAATAAG - -a -s simMouse_chr6.simMouse.chr6 28451 28 + 636262 CTGGCTCGAGACCTGTGGCTTAGACTTA -s Anc0.Anc0refChr9 6622 23 + 35212 TGG-----TGACCTGTAGCTAACTCTTT -s Anc1.Anc1refChr2 130416 23 - 144309 TGG-----TGACCTGTAGCTAACTCTTT -s Anc2.Anc2refChr0 25660 23 - 56053 TAG-----TGACCTATAGCTAACTTTCT -s mr.mrrefChr0 26930 23 + 130230 CGG-----AGACCTGTGGCTTACTCTTA -s simCow_chr6.simCow.chr6 567313 23 - 602619 TAG-----TGACCTATAGCCAGCTTTCT -s simCow_chr6.simCow.chr6 566989 23 - 602619 GTG-----TGACTTATAGTTGACTTTTT -s simDog_chr6.simDog.chr6 562477 23 - 593897 AAG-----TGACCTATAGCTAACTTTCT -s simHuman_chr6.simHuman.chr6 569827 23 - 601863 TGG-----TGACGTGTAGCTAACTCTTT -s simRat_chr6.simRat.chr6 20575 23 + 647215 CGG-----AAACCTATGGCTTACTCTTA - -a -s simMouse_chr6.simMouse.chr6 28479 15 + 636262 ATAGCAATGTTTGTT -s Anc0.Anc0refChr9 6646 15 + 35212 ACTGCAATGTTTGTT -s Anc1.Anc1refChr2 130440 15 - 144309 ACTGCAATGTTTGTT -s Anc2.Anc2refChr0 25684 15 - 56053 ACTGCAATGTTTGTT -s mr.mrrefChr0 26953 15 + 130230 ATAGCAATGTTTGTT -s simCow_chr6.simCow.chr6 567337 15 - 602619 ACCGCTGTGTTTGTT -s simCow_chr6.simCow.chr6 567013 15 - 602619 ACTTCACTGGCTGTT -s simDog_chr6.simDog.chr6 562501 15 - 593897 TCTACAATGTTTGCT -s simHuman_chr6.simHuman.chr6 569851 15 - 601863 ACGGCAATGTTTGTT -s simRat_chr6.simRat.chr6 20598 15 + 647215 ATAGCGATGTTTGTT - -a -s simMouse_chr6.simMouse.chr6 28494 21 + 636262 TACTAACCTCTTACATGGGGC -s Anc0.Anc0refChr9 6661 21 + 35212 TACTAATTAATTACATGGAGC -s Anc1.Anc1refChr2 130455 21 - 144309 TACTAATTAATTACATGGAGC -s Anc2.Anc2refChr0 25699 21 - 56053 TACTAATTAATTGCATGGAGG -s mr.mrrefChr0 26968 21 + 130230 TACTAATCTCTTACATGGGGC -s simCow_chr6.simCow.chr6 567361 21 - 602619 TACTAATTAATTACATGAAGC -s simCow_chr6.simCow.chr6 567028 20 - 602619 TAGTAATTAACTGCC-AAAGG -s simDog_chr6.simDog.chr6 562516 20 - 593897 TACTTATTAATTGCATGG-GG -s simHuman_chr6.simHuman.chr6 569866 21 - 601863 CACTAATAAATTACATGGAGC -s simRat_chr6.simRat.chr6 20613 21 + 647215 TACTAATCTCTTACATGGGGC - -a -s simMouse_chr6.simMouse.chr6 28515 1 + 636262 A -s Anc0.Anc0refChr9 6682 1 + 35212 A -s Anc1.Anc1refChr2 130476 1 - 144309 A -s Anc2.Anc2refChr0 25720 1 - 56053 T -s mr.mrrefChr0 26989 1 + 130230 A -s simCow_chr6.simCow.chr6 567048 1 - 602619 T -s simDog_chr6.simDog.chr6 562536 1 - 593897 T -s simHuman_chr6.simHuman.chr6 569887 1 - 601863 A -s simRat_chr6.simRat.chr6 20634 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 28516 23 + 636262 TTAACAGATTGCAAACTAGTAAC -s Anc0.Anc0refChr9 6684 23 + 35212 TTAGCAGACTGCAGACTGTTAAC -s Anc1.Anc1refChr2 130478 23 - 144309 TTAGCAGACTGCAGACTGTTAAC -s Anc2.Anc2refChr0 25722 23 - 56053 TTAGCAGACTGCAGACTGTTAAC -s mr.mrrefChr0 26990 23 + 130230 TTAACAGATTGCAAACTGTTAAC -s simCow_chr6.simCow.chr6 567383 23 - 602619 TTAACAGACTGCTTACTGATAAC -s simCow_chr6.simCow.chr6 567050 23 - 602619 TTAGCAGACCGCAGACCATTAAC -s simDog_chr6.simDog.chr6 562538 23 - 593897 TGAGCAGTCTGCAGTTTGCTAAC -s simHuman_chr6.simHuman.chr6 569889 23 - 601863 TCAGTAGACTGCATACTGTTAAC -s simRat_chr6.simRat.chr6 20635 23 + 647215 CTAACAGATTGCAAACTGTTAAC - -a -s simMouse_chr6.simMouse.chr6 28539 5 + 636262 TACCA -s Anc0.Anc0refChr9 6707 5 + 35212 TGCCA -s Anc1.Anc1refChr2 130501 5 - 144309 TGCCA -s Anc2.Anc2refChr0 25745 5 - 56053 TGCCA -s mr.mrrefChr0 27013 5 + 130230 TACCA -s simCow_chr6.simCow.chr6 567406 5 - 602619 TATTG -s simCow_chr6.simCow.chr6 567073 5 - 602619 TATCA -s simDog_chr6.simDog.chr6 562564 5 - 593897 TGCAT -s simHuman_chr6.simHuman.chr6 569912 5 - 601863 TGCCA -s simRat_chr6.simRat.chr6 20658 5 + 647215 TACCA - -a -s simMouse_chr6.simMouse.chr6 28544 23 + 636262 ACCCATTGAAATGTGTTCTATGG -s Anc0.Anc0refChr9 6713 23 + 35212 ATTTATTAAATTGTTTTGTATGG -s Anc1.Anc1refChr2 130507 23 - 144309 ATTTATTAAATTGTTTTGTATGG -s Anc2.Anc2refChr0 25751 23 - 56053 ATTTTTTAAGTTGTTTGGTATGG -s mr.mrrefChr0 27018 23 + 130230 ACCTATTGAAATGTGTTCTATGG -s simCow_chr6.simCow.chr6 567412 23 - 602619 ATTTATTAATTCCCTTTGTATGG -s simCow_chr6.simCow.chr6 567079 23 - 602619 ATTTTTTAAGTTGTGTGGTATGG -s simDog_chr6.simDog.chr6 562570 23 - 593897 ATTTTTTAAGATGTTTGGCATGG -s simHuman_chr6.simHuman.chr6 569918 23 - 601863 ATTTATTAAATTGTTTTGTATGG -s simRat_chr6.simRat.chr6 20663 23 + 647215 ACCTATTGAACTGTGTTCTATGG - -a -s simMouse_chr6.simMouse.chr6 28567 50 + 636262 TCTCATGTTATACCTGGAGTTATGTTAATAGTATTGACTGTCAAGTTTAT -s Anc0.Anc0refChr9 6736 49 + 35212 TTTCACATTGTGTCAGGAGTTGTGTCAATAGTAATGA-TCTCCAACTTAT -s Anc1.Anc1refChr2 130530 49 - 144309 TTTCACATTGTGTCAGGAGTTGTGTCAATAGTAATGA-TCTCCAACTTAT -s Anc2.Anc2refChr0 25774 49 - 56053 TCCCACATTGTGTCAGGAGGTGTGTCAATAGTAATGA-TCTCCAACTTAT -s mr.mrrefChr0 27041 50 + 130230 TTTCATGTTATACCTGGAGTTATGTCAATAGTATTGACTGTCAAGTTTAT -s simCow_chr6.simCow.chr6 567435 49 - 602619 TTTCACATTGAGTTAAGAGGTGTGTCTATAGTAATGA-TCTCCAATTTAT -s simCow_chr6.simCow.chr6 567102 49 - 602619 TCCCACATTTTGACAAGAGGTCTGTTAATGGTAATGA-TTTCCAACATAT -s simDog_chr6.simDog.chr6 562594 48 - 593897 TCCCACAATGTGTCGGGAGAT-TGTCAATTGTAATGA-TGTTGATATTAT -s simHuman_chr6.simHuman.chr6 569941 49 - 601863 TTTTACATTGTGTCAGGAGTTGCTTCAATAGCAATGA-TCTCCAACTTAT -s simRat_chr6.simRat.chr6 20686 50 + 647215 TTTCATGTTATACCTGGAGTTATGCCAATAGTAGTGACTATCAAGTTTAT - -a -s simMouse_chr6.simMouse.chr6 28617 16 + 636262 TTTATGGTAGTAGGGG -s Anc0.Anc0refChr9 6785 16 + 35212 TTTATGGTTGTAAGGA -s Anc1.Anc1refChr2 130579 16 - 144309 TTTATGGTTGTAAGGA -s Anc2.Anc2refChr0 25823 16 - 56053 TTTATGGTTGTAAGTA -s mr.mrrefChr0 27091 16 + 130230 TTTATGGTAGTAGGGG -s simCow_chr6.simCow.chr6 567484 16 - 602619 TTTATGGTTGTGAGCA -s simCow_chr6.simCow.chr6 567151 3 - 602619 TGC------------- -s simDog_chr6.simDog.chr6 562831 16 - 593897 TTTCTGGTTTTAAGTA -s simHuman_chr6.simHuman.chr6 569990 16 - 601863 TTTAATGTTGGAAGGA -s simRat_chr6.simRat.chr6 20736 16 + 647215 TTTATGGTTGTCGGGG - -a -s simMouse_chr6.simMouse.chr6 28633 24 + 636262 ACTTTTAGGGCACTTGTTTGGGGG -s Anc0.Anc0refChr9 6824 16 + 35212 ----TTAG----CATGTTGGGGGG -s Anc1.Anc1refChr2 130618 16 - 144309 ----TTAG----CATGTTGGGGGG -s Anc2.Anc2refChr0 25862 16 - 56053 ----TTAT----CATATTGGAGGC -s mr.mrrefChr0 27124 24 + 130230 ACTTTTAGGGCACTTGTTTGGGGG -s simCow_chr6.simCow.chr6 567523 16 - 602619 ----TTCT----CATATTGGAGAC -s simDog_chr6.simDog.chr6 562870 16 - 593897 ----TTAT----CACATTGGAGGC -s simHuman_chr6.simHuman.chr6 570029 16 - 601863 ----TTAG----CATGTTGGGGGG -s simRat_chr6.simRat.chr6 20772 24 + 647215 ACATTTAGGGCACTTGTTACGGGG - -a -s simMouse_chr6.simMouse.chr6 28657 21 + 636262 TCCACAGCCATCCCCCTCCAC -s Anc0.Anc0refChr9 6844 6 + 35212 CCAATG--------------- -s Anc1.Anc1refChr2 130638 6 - 144309 CCAATG--------------- -s Anc2.Anc2refChr0 25882 6 - 56053 CAAATG--------------- -s mr.mrrefChr0 27152 6 + 130230 TCCACA--------------- -s simCow_chr6.simCow.chr6 567543 6 - 602619 TAAATG--------------- -s simDog_chr6.simDog.chr6 562890 6 - 593897 CATATA--------------- -s simHuman_chr6.simHuman.chr6 570049 6 - 601863 CCAATG--------------- -s simRat_chr6.simRat.chr6 20800 6 + 647215 TCCACA--------------- - -a -s simMouse_chr6.simMouse.chr6 28678 87 + 636262 TAGTTAATAAGCTGTGTTGTGGAGCTATGGAGCAGGCATGAATTGTGGCTGGTTAATAAGGTGAGTTAGTCGGTTCCTCATAACCAG -s Anc0.Anc0refChr9 6851 56 + 35212 TAGTTA-----------------GCTATTAAGCAAGCAGATGTT--------------AGGTGAGCTAATTTTTTCCTTTTAGTTAG -s Anc1.Anc1refChr2 130645 64 - 144309 TAGTTAATAAGTTG---------GCTATTAAGCAAGCAGATGTT--------------AGGTGAGCTAATTTTTTCCTTTTAGTTAG -s Anc2.Anc2refChr0 25889 56 - 56053 CTCTTA-----------------GCTATTAAGCAAGCAGATGTT--------------AGGTGAGCTAATTTTTTCCTTTTAGTTAG -s mr.mrrefChr0 27158 87 + 130230 TAGTTAATAAGCTGTGTTGTGGAGCTATGGAGCAGGCATGAATTGTGGCTGGTTAATAAGGTGAGTTAGTCGGTTCCTCATAACCAG -s simCow_chr6.simCow.chr6 567555 56 - 602619 CTCTCA-----------------GCTAGTAAGTGACTGGATGTT--------------AAACAAGTTGATTTTTTCTCCTTAGTTTG -s simDog_chr6.simDog.chr6 562897 56 - 593897 CTCTTA-----------------GCTATTAAGCAAGCAGATGTT--------------AGGTGAGCTAATTTTTTCCTTTTAGTTAG -s simHuman_chr6.simHuman.chr6 570056 14 - 601863 TAGTTAATAAGTTG------------------------------------------------------------------------- -s simRat_chr6.simRat.chr6 20806 87 + 647215 TAGTTAATAAGCTGTGTTGGGCAGCTATGGAGCAGGCATGAATTATAGCTGGTTAATAAGGTGAGTTAGTCAGTACCTCATAACCAG - -a -s simMouse_chr6.simMouse.chr6 28765 4 + 636262 TTAT -s Anc0.Anc0refChr9 6907 4 + 35212 TCAG -s Anc1.Anc1refChr2 130709 4 - 144309 TCAG -s Anc2.Anc2refChr0 25950 4 - 56053 TCAG -s mr.mrrefChr0 27245 4 + 130230 TTAT -s simCow_chr6.simCow.chr6 567616 4 - 602619 TAAG -s simDog_chr6.simDog.chr6 562958 4 - 593897 TCAG -s simRat_chr6.simRat.chr6 20893 4 + 647215 CTAT - -a -s simMouse_chr6.simMouse.chr6 28769 15 + 636262 GTAGATATGAGTGCA -s Anc0.Anc0refChr9 6911 15 + 35212 GTGAATTGGCGTGAG -s Anc1.Anc1refChr2 130713 15 - 144309 GTGAATTGGCGTGAG -s Anc2.Anc2refChr0 25954 15 - 56053 GTGAATTGGCATGAG -s mr.mrrefChr0 27249 15 + 130230 GTAGATATGAGTGCA -s simCow_chr6.simCow.chr6 567620 15 - 602619 GTGAATTAGCATGAG -s simDog_chr6.simDog.chr6 562966 15 - 593897 GTGAATTGGCATGAG -s simHuman_chr6.simHuman.chr6 570070 7 - 601863 --------ACGTTAG -s simRat_chr6.simRat.chr6 20897 15 + 647215 GTTGGCACAATTGCA - -a -s simMouse_chr6.simMouse.chr6 28784 5 + 636262 TGCAG -s Anc0.Anc0refChr9 6926 5 + 35212 CACAT -s Anc1.Anc1refChr2 130728 5 - 144309 CACAT -s Anc2.Anc2refChr0 25969 5 - 56053 CACAT -s mr.mrrefChr0 27264 5 + 130230 TGCAT -s simCow_chr6.simCow.chr6 567823 5 - 602619 TACAT -s simCow_chr6.simCow.chr6 567154 1 - 602619 ----T -s simDog_chr6.simDog.chr6 562981 5 - 593897 CACAT -s simHuman_chr6.simHuman.chr6 570077 5 - 601863 AACAT -s simRat_chr6.simRat.chr6 20912 5 + 647215 CGCAT - -a -s simMouse_chr6.simMouse.chr6 28789 130 + 636262 TTTTTTCTTTATTGTCAATTTATGATTCTTACTCCGCAGATCCAGTGGGTGTGCTTTGTCATGAGTGAGAGACCTACTGGCTATTGAAATTGTAGATTGCACATTGCGCATTATGGTATTTGTTTACTTC -s Anc0.Anc0refChr9 6931 119 + 35212 TTTTCTCTTTTTTGTGAATTTAATAATATTACTTCCCTGAATCTATAGATGT-CTTTATCACAAGTAATATACTTAATGGCTATTTAGATTGAAAGCTGC-------TCATTATGGTATTTAA---CGGC -s Anc1.Anc1refChr2 130733 120 - 144309 TTTTCTCTTTTTTGTGAATTTAATAATATTACTTCCCTGAATCTATAGATGTCCTTTATCACAAGTAATATACTTAATGGCTATTTAGATTGAAAGCTGC-------TCATTATGGTATTTAA---CGGC -s Anc2.Anc2refChr0 25974 119 - 56053 TTTTCTCTTTTTAGTGACTTTCATTATATTACTTCCCTAAATCTATAGATGT-CTTTATCACAAGTAATATACTTAAGGGCTATTTAGATTGAAAGCTGC-------TAATTAGGGTATTTAA---CGGC -s mr.mrrefChr0 27269 123 + 130230 TTTTCTCTTTATTGTCAATTTATGATTCTTACTCCCCAGATCCAGTGGGTGTGCTTTGTCATGAGTGAGAGACCTACTGGCTATTTAAATTGTAGACTGC-------GCATTATGGTATTTGTTTACTTC -s simCow_chr6.simCow.chr6 567828 117 - 602619 TCCTCTCTTTTTAGTGATTTTTACTATGTTACCTTCATAAATCTATAGA--T-CATTCTCACAAGTGACATACTTAAGGGCTATTTAGATTGAAAGCTAC-------TAATTAAGGTATTTAA---CGGG -s simCow_chr6.simCow.chr6 567155 1 - 602619 C--------------------------------------------------------------------------------------------------------------------------------- -s simDog_chr6.simDog.chr6 562990 117 - 593897 TTTTCTCTTTTTAGTGACTGCCAT--CATTACTTCCCTAAATCATTAGATGT-CTTTATCACAAGTAATACACCTAAGGGCCCTTTAGATTGAAAGCTGC-------TAATTAGGGTATTTAA---TGGC -s simHuman_chr6.simHuman.chr6 570082 119 - 601863 TTTCCCCTTTTTTGTGAACTTAATAATATTACTTCCCTGGAACTATAGATGTCTTTTATCACAAGT-ATATACTTAATGGCTATTTAGATTGAAAGCTGC-------TCATTATGGTATTTTC---CAGC -s simRat_chr6.simRat.chr6 20917 123 + 647215 TGTTCTCCTTATTGTCAATTTATGATTCTTACTCTCCAGATCCAGTGGGTGTACTTTGTCATGAGTGAGAGACCTAGTGGATATTTGAATTGTAGACTGC-------ACGTTAAGGTATTTATTTACTCC - -a -s simMouse_chr6.simMouse.chr6 28919 69 + 636262 TAGTCCCTATATAGACTACCACTGTTGTGTACCTGGAGTCGTGTTCCAGTTTATATAGCGATGTCAGGC -s Anc0.Anc0refChr9 7050 52 + 35212 GGTTCATTGCATAG-CAATTACT----------------CATGCCCCAATACATAAAGCCATGCCAGGT -s Anc1.Anc1refChr2 130853 53 - 144309 GGTTCATTGCATAG-CAATTACT---------------CCATGCCCCAATACATAAAGCCATGCCAGGT -s Anc2.Anc2refChr0 26127 52 - 56053 GGTTCATTGCATAG-CAATTACT----------------CATGCCCCAATAAGTCAAGCCATGCCAGGT -s mr.mrrefChr0 27392 68 + 130230 TAGTCCCTGCATAG-CTACCACTGTTGTGTACCTGGAGTCATGTTCCAATACATATAGCGATGTCAGGC -s simCow_chr6.simCow.chr6 567982 52 - 602619 AGTCGATCACATAG-CAATTAAT----------------CATGCCCCAATAAGTGAAGCCATAATAGGT -s simDog_chr6.simDog.chr6 563141 51 - 593897 GATTCATTGTATAG-CA-TTACT----------------CATGCCCCAATAAGTCAAGCGATGCCAGGT -s simHuman_chr6.simHuman.chr6 570201 53 - 601863 GGTTCATTGCATAT-CAGTTACT---------------CCATCCCCCAATACATAAAGCCATGCCAGGT -s simRat_chr6.simRat.chr6 21040 68 + 647215 TAGTCCCTGCATAG-CTACCTCTGCTGTGTACATGGAGTCATGTTCCAATACATATAGTGATATCCGGA - -a -s simMouse_chr6.simMouse.chr6 28988 42 + 636262 ACCGCAGTGAGCCAAAGTGGGATGTAGTGAAAGAGTATACAG -s Anc0.Anc0refChr9 7102 40 + 35212 ACCACAGTGTGCCCACATGGG--ATAGTGAGCGAATATCCAG -s Anc1.Anc1refChr2 130906 42 - 144309 ACCACAGTGTGCCCACATGGGATATAGTGAGCGAATATCCAG -s Anc2.Anc2refChr0 26179 40 - 56053 ACCACGGTGTGCCCCCATGGG--ATAGTGAGCGAACATCCAA -s mr.mrrefChr0 27460 42 + 130230 ACCGCAGTGAGCCAAAGTGGGATGTAGTGAGAGAGTATCCAG -s simCow_chr6.simCow.chr6 568034 39 - 602619 ACCACTGTGTGCCCCCAGGGG--AT-GTGAGCAATCATCCAA -s simDog_chr6.simDog.chr6 563193 37 - 593897 ACCACGGAGTGC--CCATGGG--ATAGTGGGCGAACACCC-A -s simHuman_chr6.simHuman.chr6 570254 42 - 601863 ACCACAGTGTGCACATATGGGACATAGTGAGTGACTATCCAG -s simRat_chr6.simRat.chr6 21108 41 + 647215 ACTGCAGTGAGTCAA-GTAGGATGTAGTGAGAGAGTATCCAA - -a -s simMouse_chr6.simMouse.chr6 29030 28 + 636262 AATTAGGATATGCAAAACTGTATTGACT -s Anc0.Anc0refChr9 7143 26 + 35212 AATGAGAATATGCAGAACTGCACTG--C -s Anc1.Anc1refChr2 130949 26 - 144309 AATGAGAATATGCAGAACTGCACTG--C -s Anc2.Anc2refChr0 26220 26 - 56053 GATGAGAATATGCAGAACTGCACTG--C -s mr.mrrefChr0 27502 28 + 130230 AATTAGGATATGCAAAACTGTATTGACT -s simCow_chr6.simCow.chr6 568074 26 - 602619 GATGAGAAAATGCAGAACTGCTCTG--C -s simDog_chr6.simDog.chr6 563231 23 - 593897 GAAGAGAATATGCAGAACTGAAC----- -s simHuman_chr6.simHuman.chr6 570297 26 - 601863 AATGAGAATATGCAGAACTGCACTG--C -s simRat_chr6.simRat.chr6 21149 26 + 647215 AAGTAG--TATCCAAAACTATATTGACT - -a -s simMouse_chr6.simMouse.chr6 29058 32 + 636262 AAAGCTAGGTAGAACAAGGGGCCCTTAAGTGT -s Anc0.Anc0refChr9 7169 32 + 35212 AAAGATAGGTAAAACCAGGGACCCTCAAATGC -s Anc1.Anc1refChr2 130975 32 - 144309 AAAGATAGGTAAAACCAGGGACCCTCAAATGC -s Anc2.Anc2refChr0 26246 32 - 56053 ACAGACAGGTAAAACCAGGGATCCTCAAATGC -s mr.mrrefChr0 27530 32 + 130230 AAAGCTAGGTAGAACAAGGGACCCTTAAGTGT -s simCow_chr6.simCow.chr6 568102 32 - 602619 ACAGACTGGTAAGATCAGGGGTCCTCCAATGT -s simDog_chr6.simDog.chr6 563254 26 - 593897 ------AGGTAAAACCAAGGATCCTCAAATGC -s simHuman_chr6.simHuman.chr6 570323 29 - 601863 AAAGATAGGGAAAA---GGGACCCTAAAATGC -s simRat_chr6.simRat.chr6 21175 32 + 647215 AACACTAGGTAGACCAAGGGACCCTTGAGTGT - -a -s simMouse_chr6.simMouse.chr6 29090 53 + 636262 TAAGTATGTCCACCAGTCTCACTCCTTACTTTTGGCCTTCTCTGTAACATTGT -s Anc0.Anc0refChr9 7201 52 + 35212 GAAT-ATGTTCACTTGGTCTTAGACTATCTTTTGGCCTTAACTGTAACATTGT -s Anc1.Anc1refChr2 131007 52 - 144309 GAAT-ATGTTCACTTGGTCTTAGACTATCTTTTGGCCTTAACTGTAACATTGT -s Anc2.Anc2refChr0 26278 52 - 56053 GAAT-ATGTTCACTTGGTCTTAGACTATCTTTTGGCCTTAACTGTAACATTGT -s mr.mrrefChr0 27562 52 + 130230 TAAG-ATGTCCACTAGTCTTACTCCTAACTTTTGGCCTTCTCTGTAACATTGT -s simCow_chr6.simCow.chr6 568134 48 - 602619 G-----TGCCCACTTGGTCCCAGACTATCATTTGCCCTTGTGTGTAACATTGT -s simDog_chr6.simDog.chr6 563281 52 - 593897 GAAT-ATGTTCTTTAGGTCTTATACTATCTTTTGGCCTTAACTGTAAGGTTGC -s simHuman_chr6.simHuman.chr6 570352 52 - 601863 GAAT-ATGTTCACTTGGGCTTAGACTACCTCTTGGCCTCAACAGTACCATTGT -s simRat_chr6.simRat.chr6 21207 52 + 647215 TAAG-ATGTCCACTAGTCTTACTCCTATCTTTTGGCCTTGGATGTAACGCCGT - -a -s simMouse_chr6.simMouse.chr6 29143 25 + 636262 ACTTATCTTGAACGAGATTCATTTG -s Anc0.Anc0refChr9 7254 25 + 35212 GATGATCCTAAACAAGAGCCACTTG -s Anc1.Anc1refChr2 131060 25 - 144309 GATGATCCTAAACAAGAGCCACTTG -s Anc2.Anc2refChr0 26331 25 - 56053 GATGATCCTAAACAACAGCCACTTG -s mr.mrrefChr0 27614 25 + 130230 GCTTATCTTGAACGAGATCCATTTG -s simCow_chr6.simCow.chr6 568183 25 - 602619 TGTGATCCTAAACCACACCCACTTG -s simDog_chr6.simDog.chr6 563334 24 - 593897 GATGATCCTTAACAACTGCC-CTTT -s simHuman_chr6.simHuman.chr6 570405 25 - 601863 GATGATCCTAAACAAGAACCACTTG -s simRat_chr6.simRat.chr6 21259 25 + 647215 GCTTATCTTGAACGACAGCTATTTG - -a -s simMouse_chr6.simMouse.chr6 29168 12 + 636262 ATGTGTCCTCTT -s Anc0.Anc0refChr9 7279 11 + 35212 GTT-GTCCTCTT -s Anc1.Anc1refChr2 131085 11 - 144309 GTT-GTCCTCTT -s Anc2.Anc2refChr0 26356 11 - 56053 GTT-GTCCTCTT -s mr.mrrefChr0 27639 12 + 130230 ATTTGTCCTCTT -s simCow_chr6.simCow.chr6 568210 10 - 602619 GTT--TCCTCTT -s simDog_chr6.simDog.chr6 563358 11 - 593897 GTT-GTACTGTT -s simHuman_chr6.simHuman.chr6 570430 11 - 601863 GTT-GTCCTCTT -s simRat_chr6.simRat.chr6 21284 12 + 647215 ATTTGTCCTCTT - -a -s simMouse_chr6.simMouse.chr6 29180 13 + 636262 TCTAGAAGCCTGG -s Anc0.Anc0refChr9 7290 13 + 35212 TACGCAAGTCTGA -s Anc1.Anc1refChr2 131096 13 - 144309 TACGCAAGTCTGA -s Anc2.Anc2refChr0 26367 13 - 56053 TACGCAGATGTGA -s mr.mrrefChr0 27651 13 + 130230 TCTAGAAGCCTGG -s simCow_chr6.simCow.chr6 568222 13 - 602619 TACACATCTGGGA -s simDog_chr6.simDog.chr6 563369 13 - 593897 GGAGCAGATGTGA -s simHuman_chr6.simHuman.chr6 570441 13 - 601863 TACGCAAGACTGA -s simRat_chr6.simRat.chr6 21296 5 + 647215 TCT--------GG - -a -s simMouse_chr6.simMouse.chr6 29193 14 + 636262 GTCTATTCATTGAT -s Anc0.Anc0refChr9 7303 7 + 35212 C-------AATTGG -s Anc1.Anc1refChr2 131109 7 - 144309 C-------AATTGG -s Anc2.Anc2refChr0 26380 7 - 56053 C-------AATTGG -s mr.mrrefChr0 27664 14 + 130230 CTCTATTCAATGAT -s simCow_chr6.simCow.chr6 568235 7 - 602619 C-------AATTGT -s simDog_chr6.simDog.chr6 563399 7 - 593897 C-------AACTGG -s simHuman_chr6.simHuman.chr6 570454 7 - 601863 C-------AATTGG -s simRat_chr6.simRat.chr6 21301 14 + 647215 CCCATTTTAATGAT - -a -s simMouse_chr6.simMouse.chr6 29207 8 + 636262 TGTTCTGG -s Anc0.Anc0refChr9 7310 8 + 35212 TGTTCTAG -s Anc1.Anc1refChr2 131116 8 - 144309 TGTTCTAG -s Anc2.Anc2refChr0 26387 8 - 56053 TCTTCTAG -s mr.mrrefChr0 27678 8 + 130230 TGTTCTAG -s simCow_chr6.simCow.chr6 568242 8 - 602619 TACTCTAG -s simDog_chr6.simDog.chr6 563409 8 - 593897 TCTTCTAG -s simHuman_chr6.simHuman.chr6 570461 8 - 601863 TGTTCTAG -s simRat_chr6.simRat.chr6 21315 8 + 647215 TGTTCTAG - -a -s simMouse_chr6.simMouse.chr6 29215 56 + 636262 TCTGTTTATTGAGTTTCTTGTGTTGCAAGTAGTTACACACATCCATCATTATGAAA -s Anc0.Anc0refChr9 7318 29 + 35212 TTTGTTCTTCTAATCTCTTGTTTTA----CAGT----------------------- -s Anc1.Anc1refChr2 131124 32 - 144309 TTTGTTCTTCTAATCTCTTGTTTTACAT-CAGT----------------------- -s Anc2.Anc2refChr0 26395 29 - 56053 TTTGTTCTTCTAATCACTTGTTTTA----CAGT----------------------- -s mr.mrrefChr0 27686 56 + 130230 TCTGTTCATTTAGTTTCTTGTGTTGCATGTAGTTACACACACCCATCATTATGAAA -s simCow_chr6.simCow.chr6 568254 29 - 602619 TTTGTTCTTCTAAACCCTTGTTTTA----TAGT----------------------- -s simDog_chr6.simDog.chr6 563417 29 - 593897 TTTATTCTTCTGATCACTTGTTATA----CAGC----------------------- -s simHuman_chr6.simHuman.chr6 570469 32 - 601863 ATTGGTCCTGTAATATCTTGTTTTACAT-CAGT----------------------- -s simRat_chr6.simRat.chr6 21323 56 + 647215 TCTGTTCATCTAGTTTCTTGTGTTGCATGTAGTTACAAACACCCATCATTACAAAA - -a -s simMouse_chr6.simMouse.chr6 29271 103 + 636262 TAGAGTGAGGGACCCACCATCAGATAAGACCTTCTGGGGTAGAGTAAATAGAAGACATTTGAACCAAACCAATCCCTTCAGTTGCAAAAGAAGCTGGAAACCA -s Anc0.Anc0refChr9 7347 38 + 35212 ----------------------------------------------------------------CAAAC-AACACCCTAAGTTGCATGAGAAGGTGGCAACCA -s Anc1.Anc1refChr2 131156 38 - 144309 ----------------------------------------------------------------CAAAC-AACACCCTAAGTTGCATGAGAAGGTGGCAACCA -s Anc2.Anc2refChr0 26424 38 - 56053 ----------------------------------------------------------------CAAAC-AACACCCTAAGTGGCATGAGAGGGTAGCAACCA -s mr.mrrefChr0 27742 102 + 130230 TAGAGTGAGGGACCCACCATCAGATAAGACCTTCTGGGGTAGAGGAAATAGAAGGCATTTGGACCAAAC-AATCCCTTCAGTTGCAAAAGAAGCTGGAAACCA -s simCow_chr6.simCow.chr6 568283 38 - 602619 ----------------------------------------------------------------CAAAC-AGCCCCCTCAGTGGCATGAGAGGGTAGCAACTA -s simDog_chr6.simDog.chr6 563446 24 - 593897 ----------------------------------------------------------------CAAAG-AACACCCTA--------------GTAGCAACCA -s simHuman_chr6.simHuman.chr6 570501 38 - 601863 ----------------------------------------------------------------CAAAC-AACTCACCAGGTTGCAGGAGAAGGTGGCAACCA -s simRat_chr6.simRat.chr6 21395 102 + 647215 TAGAGTGGGGGACCCACCCTCAGATAAGACCTTCTGGGGTAGAGGAAATAGTGGGCATTTGGACCAAAC-AATCCCTTCAGTTGCAAGAGAAGCTGGATATCA - -a -s simMouse_chr6.simMouse.chr6 29374 12 + 636262 TAAGCTAATTAG -s Anc0.Anc0refChr9 7460 12 + 35212 CAAGATGAGTAG -s Anc1.Anc1refChr2 131269 12 - 144309 CAAGATGAGTAG -s Anc2.Anc2refChr0 26537 12 - 56053 TAAGATGAGTAG -s mr.mrrefChr0 27844 12 + 130230 CAAGCTAATTAG -s simCow_chr6.simCow.chr6 568397 10 - 602619 TGAG--GAGTAG -s simDog_chr6.simDog.chr6 563545 12 - 593897 TAAGATAAGTGG -s simHuman_chr6.simHuman.chr6 570614 12 - 601863 CAAGATGAATAG -s simRat_chr6.simRat.chr6 21497 12 + 647215 CAAGGTAATTAG - -a -s simMouse_chr6.simMouse.chr6 29386 2 + 636262 CC -s Anc0.Anc0refChr9 7473 2 + 35212 TT -s Anc1.Anc1refChr2 131282 2 - 144309 TT -s Anc2.Anc2refChr0 26559 2 - 56053 TT -s mr.mrrefChr0 27857 2 + 130230 CC -s simCow_chr6.simCow.chr6 568418 2 - 602619 TA -s simDog_chr6.simDog.chr6 563567 2 - 593897 CT -s simHuman_chr6.simHuman.chr6 570627 2 - 601863 TT -s simRat_chr6.simRat.chr6 21510 2 + 647215 CC - -a -s simMouse_chr6.simMouse.chr6 29388 48 + 636262 TTGCCTAGATGGACTATAAACTATAGTTATCATGACTTCAGGCATTTA -s Anc0.Anc0refChr9 7480 42 + 35212 TCACCCCACTATA---TACCCAACAATAGACACG---TTAGGCACTTT -s Anc1.Anc1refChr2 131289 42 - 144309 TCACCCCACTATA---TACCCAACAATAGACACG---TTAGGCACTTT -s Anc2.Anc2refChr0 26566 42 - 56053 TCACCCCACTATA---TACCCAACAATAGATCCC---TTAGGCACTTT -s mr.mrrefChr0 27859 45 + 130230 TTACCTAAATAGA---TAAACTATAATTATCATGACTTCAGGCATTTA -s simCow_chr6.simCow.chr6 568425 42 - 602619 CCTAACCACTATA---TACCCAACTATAGATCCC---TTAGGCACTTC -s simDog_chr6.simDog.chr6 563574 25 - 593897 TCACCCCCCTACA---CACCCAACAT--------------------TT -s simHuman_chr6.simHuman.chr6 570634 42 - 601863 TCACCCCACTATA---TACCTAACAATAGCCAAG---TGAAGCACTTG -s simRat_chr6.simRat.chr6 21512 45 + 647215 TTACTTAAATAGA---TAAACTATAATTATCATGACTTCAGGCGTTTC - -a -s simMouse_chr6.simMouse.chr6 29436 29 + 636262 GCCTTTCTTGTCTCCACCAATAGTTGACC -s Anc0.Anc0refChr9 7523 26 + 35212 GCCTTCCCTATATCCAACAATAGTTG--- -s Anc1.Anc1refChr2 131332 29 - 144309 GCCTTCCCTATATCCAACAATAGTTGACT -s Anc2.Anc2refChr0 26609 26 - 56053 GCCTTCCCTATATCCAACAATAGTTG--- -s mr.mrrefChr0 27905 29 + 130230 GCCTTTCTTGTATCCAACAATAGTTGACT -s simCow_chr6.simCow.chr6 568468 22 - 602619 GCCTTC----TACCCACCAATGGTTG--- -s simDog_chr6.simDog.chr6 563600 26 - 593897 GCCCTCCCTATATCCAATATGAGTTG--- -s simHuman_chr6.simHuman.chr6 570677 29 - 601863 GCCTTCCCTATATCCAACAATAGTTGACT -s simRat_chr6.simRat.chr6 21558 29 + 647215 GCCTCTCTTGTACCCAACAGTAGTTGACT - -a -s simMouse_chr6.simMouse.chr6 29465 18 + 636262 TGGCACTTAGATTTTCCA -s Anc0.Anc0refChr9 7549 10 + 35212 --------AGGCTTTCCA -s Anc1.Anc1refChr2 131362 18 - 144309 TGGCACTTAGGCTTTCCA -s Anc2.Anc2refChr0 26635 10 - 56053 --------AGGCTTTCCA -s mr.mrrefChr0 27935 18 + 130230 TGGCACTTAGATTTTCCA -s simCow_chr6.simCow.chr6 568490 10 - 602619 --------AGGCTTTCCA -s simDog_chr6.simDog.chr6 563626 10 - 593897 --------AGGCTTTCCA -s simHuman_chr6.simHuman.chr6 570707 18 - 601863 TGGCACTTAGGCCTTCCA -s simRat_chr6.simRat.chr6 21588 18 + 647215 CGGCACTTAGATTTTCCA - -a -s simMouse_chr6.simMouse.chr6 29483 3 + 636262 GCT -s Anc0.Anc0refChr9 7559 3 + 35212 TCT -s Anc1.Anc1refChr2 131380 3 - 144309 TCT -s Anc2.Anc2refChr0 26646 3 - 56053 TCT -s mr.mrrefChr0 27953 3 + 130230 GCT -s simCow_chr6.simCow.chr6 568501 3 - 602619 TTT -s simDog_chr6.simDog.chr6 563637 3 - 593897 CCT -s simHuman_chr6.simHuman.chr6 570725 3 - 601863 TCT -s simRat_chr6.simRat.chr6 21606 3 + 647215 GCT - -a -s simMouse_chr6.simMouse.chr6 29486 7 + 636262 CCGATAT -s Anc0.Anc0refChr9 7563 7 + 35212 CCTATAT -s Anc1.Anc1refChr2 131384 7 - 144309 CCTATAT -s Anc2.Anc2refChr0 26650 7 - 56053 CCTATAT -s mr.mrrefChr0 27956 7 + 130230 CCGATAT -s simCow_chr6.simCow.chr6 568505 7 - 602619 CCTATAT -s simDog_chr6.simDog.chr6 563641 7 - 593897 CCTATAT -s simHuman_chr6.simHuman.chr6 570729 7 - 601863 TCTATAT -s simRat_chr6.simRat.chr6 21609 7 + 647215 CTGATAA - -a -s simMouse_chr6.simMouse.chr6 29493 59 + 636262 GAGGTTCATGAATATAGCCCAAGATTTGGTTGCACTAGAACAATGCCAATGATTTCAAA -s Anc0.Anc0refChr9 7570 57 + 35212 GGGGTGGC--ATTCTATCACAAGGTATGCCTTTATTAGTGAGATGCCACTTATTCCAGA -s Anc1.Anc1refChr2 131391 57 - 144309 GGGGTGGC--ATTCTATCACAAGGTATGCCTTTATTAGTGAGATGCCACTTATTCCAGA -s Anc2.Anc2refChr0 26662 57 - 56053 ACGGGGGC--ATTCTATCACAAGGTATGCCTTTATTAGTGAGTTGCCACTTATTCCAGA -s mr.mrrefChr0 27963 57 + 130230 GAGGTTCA--AATATAGCCCAAGATTTGGCTTTACTAGAGAGATGCCAATGATTTCAAA -s simCow_chr6.simCow.chr6 568517 57 - 602619 ACAGGTGC--CTTTTATCACAAGGTATTGCTTTAATAGTGAGCAGCCACTCAGTCCAGA -s simDog_chr6.simDog.chr6 563653 57 - 593897 ACGGGGGC--ATTCTATCACAAGGTATGCTTTTATTAGTGAGTTACTACGTATTCCAGA -s simHuman_chr6.simHuman.chr6 570736 57 - 601863 TGAGTGAC--ATTCTATCATAAGGTATAACTTTATTAGCGAGATGCCACTTGTTGCTGA -s simRat_chr6.simRat.chr6 21616 57 + 647215 GAGATTCA--AAAATACCCCAAGATTTGGCTTTACAAGAGAGATGCCAATGATTCCAAG - -a -s simMouse_chr6.simMouse.chr6 29552 2 + 636262 GG -s Anc0.Anc0refChr9 7627 2 + 35212 GG -s Anc1.Anc1refChr2 131448 2 - 144309 GG -s Anc2.Anc2refChr0 26719 2 - 56053 GG -s mr.mrrefChr0 28020 2 + 130230 GG -s mr.mrrefChr0 28453 2 + 130230 GA -s simCow_chr6.simCow.chr6 568574 2 - 602619 AG -s simDog_chr6.simDog.chr6 563710 2 - 593897 GG -s simHuman_chr6.simHuman.chr6 570793 2 - 601863 GG -s simMouse_chr6.simMouse.chr6 29996 2 + 636262 GA -s simRat_chr6.simRat.chr6 22245 2 + 647215 GA -s simRat_chr6.simRat.chr6 21673 2 + 647215 GG - -a -s simMouse_chr6.simMouse.chr6 29554 13 + 636262 GTCTTAAGAATAG -s Anc0.Anc0refChr9 7629 13 + 35212 TTGTTAGGACTAG -s Anc1.Anc1refChr2 131450 13 - 144309 TTGTTAGGACTAG -s Anc2.Anc2refChr0 26721 13 - 56053 TTGGTAGGCCATG -s mr.mrrefChr0 28022 13 + 130230 GTGTTAAGAATAG -s mr.mrrefChr0 28455 13 + 130230 TTGTTATAAATAG -s simCow_chr6.simCow.chr6 568576 12 - 602619 GTG-TAGGCCATT -s simDog_chr6.simDog.chr6 563712 13 - 593897 TTTGTAGGCCATG -s simHuman_chr6.simHuman.chr6 570795 13 - 601863 CTGTTGGGACTGT -s simMouse_chr6.simMouse.chr6 29998 13 + 636262 TTGTTATAAATAG -s simRat_chr6.simRat.chr6 22255 13 + 647215 TGATTCCAAAGAA -s simRat_chr6.simRat.chr6 21675 13 + 647215 TTGTTAAGAATAG - -a -s simMouse_chr6.simMouse.chr6 29567 5 + 636262 GGATG -s Anc0.Anc0refChr9 7642 4 + 35212 G-ATG -s Anc1.Anc1refChr2 131463 4 - 144309 G-ATG -s Anc2.Anc2refChr0 26734 4 - 56053 G-GAG -s mr.mrrefChr0 28035 4 + 130230 G-ATG -s mr.mrrefChr0 28468 4 + 130230 G-ATG -s simCow_chr6.simCow.chr6 568588 4 - 602619 G-GAA -s simDog_chr6.simDog.chr6 563725 4 - 593897 G-GAG -s simHuman_chr6.simHuman.chr6 570808 4 - 601863 G-ATG -s simMouse_chr6.simMouse.chr6 30011 4 + 636262 G-ATG -s simRat_chr6.simRat.chr6 22275 4 + 647215 G-ATG -s simRat_chr6.simRat.chr6 21688 4 + 647215 T-ATG - -a -s simMouse_chr6.simMouse.chr6 29572 4 + 636262 TTGG -s Anc0.Anc0refChr9 7646 4 + 35212 TTGG -s Anc1.Anc1refChr2 131467 4 - 144309 TTGG -s Anc2.Anc2refChr0 26738 4 - 56053 CTGG -s mr.mrrefChr0 28039 4 + 130230 TTGG -s mr.mrrefChr0 28472 4 + 130230 TTGG -s simCow_chr6.simCow.chr6 568592 4 - 602619 CTGG -s simDog_chr6.simDog.chr6 563729 4 - 593897 CTGG -s simHuman_chr6.simHuman.chr6 570812 1 - 601863 ---G -s simMouse_chr6.simMouse.chr6 30015 4 + 636262 TTGG -s simRat_chr6.simRat.chr6 22279 4 + 647215 TTGG -s simRat_chr6.simRat.chr6 21807 4 + 647215 TTGG - -a -s simMouse_chr6.simMouse.chr6 29576 20 + 636262 GTGTTCATGTAATGTGAACA -s Anc0.Anc0refChr9 7654 20 + 35212 TTGTCTATTAGATGTAAACA -s Anc1.Anc1refChr2 131475 20 - 144309 TTGTCTATTAGATGTAAACA -s Anc2.Anc2refChr0 26746 20 - 56053 TTGTCTATTAGGTGTAAACA -s mr.mrrefChr0 28043 20 + 130230 GTGTTTATCTAATGTGAACA -s mr.mrrefChr0 28480 20 + 130230 TTATCTGTTAAATGTGAACA -s simCow_chr6.simCow.chr6 568600 20 - 602619 GTGTCTATTTTGTGTAAAGA -s simDog_chr6.simDog.chr6 563737 20 - 593897 TTGTCTTTTAGGTGCAAACA -s simHuman_chr6.simHuman.chr6 570817 20 - 601863 ATGTCTATTGGATGTAAACA -s simMouse_chr6.simMouse.chr6 30023 20 + 636262 TTATCTGTTAAATGTGAACA -s simRat_chr6.simRat.chr6 22287 20 + 647215 TTATCTGTTAGATGTGAACA -s simRat_chr6.simRat.chr6 21811 20 + 647215 GTGTTTATCTAATGAGAACA - -a -s simMouse_chr6.simMouse.chr6 29596 4 + 636262 GCCT -s Anc0.Anc0refChr9 7674 3 + 35212 A-CT -s Anc1.Anc1refChr2 131495 3 - 144309 A-CT -s Anc2.Anc2refChr0 26766 3 - 56053 G-CT -s mr.mrrefChr0 28063 4 + 130230 ACCT -s simCow_chr6.simCow.chr6 568620 3 - 602619 G-CT -s simDog_chr6.simDog.chr6 563757 3 - 593897 G-CT -s simHuman_chr6.simHuman.chr6 570837 3 - 601863 A-CT -s simRat_chr6.simRat.chr6 21831 4 + 647215 ACCT - -a -s simMouse_chr6.simMouse.chr6 29600 10 + 636262 AGACTGTCTG -s Anc0.Anc0refChr9 7677 10 + 35212 GGGCTGTCTG -s Anc1.Anc1refChr2 131498 10 - 144309 GGGCTGTCTG -s Anc2.Anc2refChr0 26769 10 - 56053 GGGCTGTCCG -s mr.mrrefChr0 28067 10 + 130230 AGACTGTCTG -s mr.mrrefChr0 28500 10 + 130230 GGGTTGCATT -s simCow_chr6.simCow.chr6 568623 10 - 602619 GGGCTGTCCG -s simDog_chr6.simDog.chr6 563760 10 - 593897 GGGCTGTCCG -s simHuman_chr6.simHuman.chr6 570840 10 - 601863 GGGCTGTCTG -s simMouse_chr6.simMouse.chr6 30043 10 + 636262 GGGTTGCATT -s simRat_chr6.simRat.chr6 22307 10 + 647215 GGGTTGTAAT -s simRat_chr6.simRat.chr6 21835 10 + 647215 AGACTGTACA - -a -s simMouse_chr6.simMouse.chr6 29610 13 + 636262 TTGGTCTTTGGCC -s Anc0.Anc0refChr9 7693 13 + 35212 TCTGTCTTTTCTC -s Anc1.Anc1refChr2 131514 13 - 144309 TCTGTCTTTTCTC -s Anc2.Anc2refChr0 26785 13 - 56053 CCTGTCTTTTCTC -s mr.mrrefChr0 28077 13 + 130230 TTGGTCTTTGGCC -s mr.mrrefChr0 28516 13 + 130230 TTTGTCTTTACTC -s simCow_chr6.simCow.chr6 568639 13 - 602619 CCTGTCTTTTCTC -s simDog_chr6.simDog.chr6 563775 1 - 593897 ------------C -s simHuman_chr6.simHuman.chr6 570856 13 - 601863 TCTTTCTTTCTTC -s simMouse_chr6.simMouse.chr6 30059 13 + 636262 TTTGTCTTTACTC -s simRat_chr6.simRat.chr6 22323 13 + 647215 TTTCTCTTTAGTC -s simRat_chr6.simRat.chr6 21845 13 + 647215 TTTTCCTTTGACC - -a -s simMouse_chr6.simMouse.chr6 29623 12 + 636262 TTACTGGGGCAT -s Anc0.Anc0refChr9 7709 12 + 35212 CCACTGGGGCTT -s Anc1.Anc1refChr2 131530 12 - 144309 CCACTGGGGCTT -s Anc2.Anc2refChr0 26801 12 - 56053 ACACTGGGGCTT -s mr.mrrefChr0 28090 12 + 130230 TTACTGGGGCAT -s mr.mrrefChr0 28532 12 + 130230 CTACTGGGGCCT -s simCow_chr6.simCow.chr6 568655 12 - 602619 ACATTGGGGCTT -s simDog_chr6.simDog.chr6 563779 12 - 593897 ACACTGGAGTTT -s simHuman_chr6.simHuman.chr6 570872 9 - 601863 CCACTGGGA--- -s simMouse_chr6.simMouse.chr6 30075 12 + 636262 CTACTGGGGCCT -s simRat_chr6.simRat.chr6 22339 12 + 647215 CTACTGGGGCCT -s simRat_chr6.simRat.chr6 21858 12 + 647215 TTACTGTAGCAC - -a -s simMouse_chr6.simMouse.chr6 29635 12 + 636262 AAGACTGGATCT -s Anc0.Anc0refChr9 7721 11 + 35212 -GGACTGGGTCT -s Anc1.Anc1refChr2 131542 12 - 144309 AGGACTGGGTCT -s Anc2.Anc2refChr0 26813 11 - 56053 -GGCCTGGGCCT -s mr.mrrefChr0 28102 12 + 130230 AAGACTGGATCT -s mr.mrrefChr0 28545 12 + 130230 AGGACTAGGTCT -s simCow_chr6.simCow.chr6 568667 11 - 602619 -GGCTTAGGTCT -s simDog_chr6.simDog.chr6 563793 11 - 593897 -GGCCTGGGCCT -s simMouse_chr6.simMouse.chr6 30088 12 + 636262 AGGACTAGGTCT -s simRat_chr6.simRat.chr6 22352 12 + 647215 AGGACTAGGTCT -s simRat_chr6.simRat.chr6 21870 12 + 647215 AAGGCTGGGGCT - -a -s simMouse_chr6.simMouse.chr6 29647 7 + 636262 CTTTTTT -s Anc0.Anc0refChr9 7732 7 + 35212 CACTCTT -s Anc1.Anc1refChr2 131554 7 - 144309 CACTCTT -s Anc2.Anc2refChr0 26824 7 - 56053 CACCCTT -s mr.mrrefChr0 28114 7 + 130230 CTTTTTT -s mr.mrrefChr0 28557 7 + 130230 GACTCTT -s simCow_chr6.simCow.chr6 568678 7 - 602619 TACTCAT -s simDog_chr6.simDog.chr6 563804 7 - 593897 CACCCTT -s simMouse_chr6.simMouse.chr6 30100 7 + 636262 GACTCTT -s simRat_chr6.simRat.chr6 22380 7 + 647215 GACTCTC -s simRat_chr6.simRat.chr6 21882 7 + 647215 CTTTTTT - -a -s simMouse_chr6.simMouse.chr6 29654 20 + 636262 GATTTATTGGTAGCCAAAGT -s Anc0.Anc0refChr9 7739 20 + 35212 GATTAATTGGTAGCCAAAGT -s Anc1.Anc1refChr2 131561 20 - 144309 GATTAATTGGTAGCCAAAGT -s Anc2.Anc2refChr0 26835 20 - 56053 GATTAATTGGTAGCTCATGC -s mr.mrrefChr0 28121 20 + 130230 GATTTATTGGTAGCCAAAGT -s mr.mrrefChr0 28564 20 + 130230 CATACACAGGTGGCCAAAGT -s simCow_chr6.simCow.chr6 568689 20 - 602619 AACTGATTCATAGCCCAAGC -s simDog_chr6.simDog.chr6 563815 20 - 593897 GATTAATTGGTAGCTCATGC -s simMouse_chr6.simMouse.chr6 30107 20 + 636262 CATACACAGGTGGCCAAAGT -s simRat_chr6.simRat.chr6 22387 20 + 647215 CATACATGGGTGGCCAACGT -s simRat_chr6.simRat.chr6 21889 20 + 647215 GAGTCATTGGTAGCCAAAGT - -a -s simMouse_chr6.simMouse.chr6 29674 8 + 636262 GGCAGAGG -s Anc0.Anc0refChr9 7759 8 + 35212 GGCAGAGT -s Anc1.Anc1refChr2 131581 8 - 144309 GGCAGAGT -s Anc2.Anc2refChr0 26855 8 - 56053 AGCAGAGT -s mr.mrrefChr0 28141 8 + 130230 GGCAGAGG -s mr.mrrefChr0 28584 8 + 130230 GGCAGCAA -s simCow_chr6.simCow.chr6 568709 8 - 602619 AGTAAAGT -s simDog_chr6.simDog.chr6 563835 8 - 593897 AGCAGAGT -s simMouse_chr6.simMouse.chr6 30127 8 + 636262 GGCAGCAA -s simRat_chr6.simRat.chr6 22407 8 + 647215 GGCAGCAG -s simRat_chr6.simRat.chr6 21933 8 + 647215 GGTAAAGA - -a -s simMouse_chr6.simMouse.chr6 29682 13 + 636262 TTCTTTTTGGACA -s Anc0.Anc0refChr9 7767 13 + 35212 TTCTTTTTGGACA -s Anc1.Anc1refChr2 131589 13 - 144309 TTCTTTTTGGACA -s Anc2.Anc2refChr0 26863 13 - 56053 TCCTCAATGGACA -s mr.mrrefChr0 28149 13 + 130230 TTCTTTTTGGACA -s mr.mrrefChr0 28592 13 + 130230 TTCTTTTTGGACA -s simCow_chr6.simCow.chr6 568717 13 - 602619 TTCTTAAGGGATA -s simDog_chr6.simDog.chr6 563861 13 - 593897 TCCTCAATGGACA -s simMouse_chr6.simMouse.chr6 30135 13 + 636262 TTCTTTTTGGACA -s simRat_chr6.simRat.chr6 22415 13 + 647215 TTCTTTTCAGACA -s simRat_chr6.simRat.chr6 21941 13 + 647215 ATCTTTTTGGACA - -a -s simMouse_chr6.simMouse.chr6 29695 27 + 636262 AAACCAAAGAAAAAACTGAACAAAGTA -s Anc0.Anc0refChr9 7780 27 + 35212 AAACCAGAGAAAAAGCTGAGAAAAGTA -s Anc1.Anc1refChr2 131602 27 - 144309 AAACCAGAGAAAAAGCTGAGAAAAGTA -s Anc2.Anc2refChr0 26877 27 - 56053 AAACAAGAGAAAAAGCAGTGAAAACTA -s mr.mrrefChr0 28162 27 + 130230 AAACCAAAGAAAAAACTGAAAAAAGTA -s mr.mrrefChr0 28605 27 + 130230 AAACCAAGGAAAAAACTGAAGAAAGTA -s simCow_chr6.simCow.chr6 568731 25 - 602619 CAACAAGAGAAAAAGCT--GAAAACTA -s simDog_chr6.simDog.chr6 563875 27 - 593897 AAACAAGGGAGTAAGGAGTGAAAACTA -s simHuman_chr6.simHuman.chr6 570881 23 - 601863 ----CAGAGAAAAAGCCAAGAAAAGTA -s simMouse_chr6.simMouse.chr6 30148 27 + 636262 AAACCAAGGAAAAAACTGAAGAAAGTA -s simRat_chr6.simRat.chr6 22428 27 + 647215 AAACAAAGGGAAAAACTGAAGAAAGTA -s simRat_chr6.simRat.chr6 21954 27 + 647215 AAACCAAAGAAAAAAATGAAAAAAGTA - -a -s simMouse_chr6.simMouse.chr6 29722 13 + 636262 AAATCAGGTCCCT -s Anc0.Anc0refChr9 7807 13 + 35212 AAGTCATGCCCCT -s Anc1.Anc1refChr2 131629 13 - 144309 AAGTCATGCCCCT -s Anc2.Anc2refChr0 26904 13 - 56053 AAGTCATGCCCCT -s mr.mrrefChr0 28189 13 + 130230 AAATCAGGTCCCT -s mr.mrrefChr0 28632 13 + 130230 AAATTGTGTCCTT -s simCow_chr6.simCow.chr6 568757 13 - 602619 GATTCATCCCCCT -s simDog_chr6.simDog.chr6 563902 13 - 593897 ATGTCACGCCCCT -s simHuman_chr6.simHuman.chr6 570904 13 - 601863 AAGTCATGCCCCT -s simMouse_chr6.simMouse.chr6 30175 13 + 636262 AAATTGTGTCCTT -s simRat_chr6.simRat.chr6 22455 13 + 647215 AGATCGTGTCCTT -s simRat_chr6.simRat.chr6 21981 13 + 647215 AACTCAGGTCCCT - -a -s simMouse_chr6.simMouse.chr6 29735 24 + 636262 TCCAGAATTTTAGACCCGGTTGGT -s Anc0.Anc0refChr9 7837 19 + 35212 TCCACAATTTTAGACCCAG----- -s Anc1.Anc1refChr2 131659 24 - 144309 TCCACAATTTTAGACCCAGTTAGT -s Anc2.Anc2refChr0 26943 19 - 56053 TACACAATTTTAGACCCTA----- -s mr.mrrefChr0 28202 24 + 130230 TCCAGAATTTTAGACCCGGTTGGT -s mr.mrrefChr0 28645 24 + 130230 TGCAGAATATTAGACCCAGTTAGT -s simCow_chr6.simCow.chr6 568794 19 - 602619 TACACAATTTTAGACCCTA----- -s simDog_chr6.simDog.chr6 563958 19 - 593897 TACACAATTTTAGACCCCA----- -s simHuman_chr6.simHuman.chr6 570934 21 - 601863 TCCACAATTTTAGCCCTATCT--- -s simMouse_chr6.simMouse.chr6 30188 24 + 636262 TGCAGAATATTAGACCCAGTTAGT -s simRat_chr6.simRat.chr6 22468 24 + 647215 TTCAGAATTTTAGACCCAGCTAGT -s simRat_chr6.simRat.chr6 21994 24 + 647215 TCCAGAATTTTAGACTGGGTTGGT - -a -s simMouse_chr6.simMouse.chr6 29759 13 + 636262 TTGTCACTAGGCT -s Anc0.Anc0refChr9 7856 13 + 35212 TTTTCACTAGGCT -s Anc1.Anc1refChr2 131683 13 - 144309 TTTTCACTAGGCT -s Anc2.Anc2refChr0 26962 13 - 56053 TCTTTCCTAGGCT -s mr.mrrefChr0 28226 13 + 130230 TTGTCACTAGGCT -s mr.mrrefChr0 28669 13 + 130230 TAGTCACTAGGCT -s simCow_chr6.simCow.chr6 568818 13 - 602619 TCTGTCCTACAAT -s simDog_chr6.simDog.chr6 563977 11 - 593897 CTGTTC--AGGCT -s simHuman_chr6.simHuman.chr6 570955 11 - 601863 --TTCACTAGGCT -s simMouse_chr6.simMouse.chr6 30212 13 + 636262 TAGTCACTAGGCT -s simRat_chr6.simRat.chr6 22492 13 + 647215 TAGTAACTAGGCT -s simRat_chr6.simRat.chr6 22018 13 + 647215 TTGTCACTAGGCT - -a -s simMouse_chr6.simMouse.chr6 29772 5 + 636262 TGAAA -s Anc0.Anc0refChr9 7878 5 + 35212 CAAAA -s Anc1.Anc1refChr2 131705 5 - 144309 CAAAA -s Anc2.Anc2refChr0 26984 5 - 56053 CAAAA -s mr.mrrefChr0 28239 5 + 130230 TGAAA -s mr.mrrefChr0 28682 5 + 130230 CAAAA -s simCow_chr6.simCow.chr6 568840 5 - 602619 CAAAA -s simDog_chr6.simDog.chr6 563997 5 - 593897 CAAAA -s simHuman_chr6.simHuman.chr6 570975 5 - 601863 CAAAA -s simMouse_chr6.simMouse.chr6 30225 5 + 636262 CAAAA -s simRat_chr6.simRat.chr6 22505 5 + 647215 TGAAA -s simRat_chr6.simRat.chr6 22031 5 + 647215 TGAAA - -a -s simMouse_chr6.simMouse.chr6 29777 13 + 636262 GTAGGTCTAAGTG -s Anc0.Anc0refChr9 7883 13 + 35212 GCAGGTATAAATG -s Anc1.Anc1refChr2 131710 13 - 144309 GCAGGTATAAATG -s Anc2.Anc2refChr0 26989 13 - 56053 TCAGGTATAAATG -s mr.mrrefChr0 28244 13 + 130230 GTAGGTCTAAGTG -s mr.mrrefChr0 28687 13 + 130230 ACAGCTATAAGTG -s simCow_chr6.simCow.chr6 568845 13 - 602619 TCAAGCAGAAATG -s simDog_chr6.simDog.chr6 564002 12 - 593897 TCAGGTAT-AATG -s simHuman_chr6.simHuman.chr6 570987 13 - 601863 GCAGGTATAAATG -s simMouse_chr6.simMouse.chr6 30230 13 + 636262 ACAGCTATAAGTG -s simRat_chr6.simRat.chr6 22510 13 + 647215 ACAGGTATAAGTG -s simRat_chr6.simRat.chr6 22036 13 + 647215 ATACGTCTACGTG - -a -s simMouse_chr6.simMouse.chr6 29790 1 + 636262 A -s Anc0.Anc0refChr9 7896 1 + 35212 G -s Anc1.Anc1refChr2 131723 1 - 144309 G -s Anc2.Anc2refChr0 27002 1 - 56053 G -s mr.mrrefChr0 28257 1 + 130230 A -s mr.mrrefChr0 28700 1 + 130230 G -s simCow_chr6.simCow.chr6 568858 1 - 602619 G -s simDog_chr6.simDog.chr6 564014 1 - 593897 G -s simHuman_chr6.simHuman.chr6 571001 1 - 601863 A -s simMouse_chr6.simMouse.chr6 30243 1 + 636262 G -s simRat_chr6.simRat.chr6 22523 1 + 647215 G -s simRat_chr6.simRat.chr6 22049 1 + 647215 G - -a -s simMouse_chr6.simMouse.chr6 29791 3 + 636262 CTC -s Anc0.Anc0refChr9 7899 3 + 35212 CTC -s Anc1.Anc1refChr2 131726 3 - 144309 CTC -s Anc2.Anc2refChr0 27005 3 - 56053 TTC -s mr.mrrefChr0 28258 3 + 130230 CTC -s mr.mrrefChr0 28703 3 + 130230 CTT -s simCow_chr6.simCow.chr6 568861 3 - 602619 ATC -s simDog_chr6.simDog.chr6 564017 3 - 593897 TTC -s simHuman_chr6.simHuman.chr6 571002 3 - 601863 CTT -s simMouse_chr6.simMouse.chr6 30246 3 + 636262 CTT -s simRat_chr6.simRat.chr6 22526 3 + 647215 CTC -s simRat_chr6.simRat.chr6 22050 3 + 647215 CTC - -a -s simMouse_chr6.simMouse.chr6 29794 3 + 636262 CTT -s Anc0.Anc0refChr9 7902 3 + 35212 CAT -s Anc1.Anc1refChr2 131729 3 - 144309 CAT -s Anc2.Anc2refChr0 27031 3 - 56053 CAC -s mr.mrrefChr0 28261 3 + 130230 CTT -s mr.mrrefChr0 28706 3 + 130230 CTT -s simCow_chr6.simCow.chr6 568887 3 - 602619 CAC -s simDog_chr6.simDog.chr6 564056 3 - 593897 CAC -s simHuman_chr6.simHuman.chr6 571005 3 - 601863 CAT -s simMouse_chr6.simMouse.chr6 30249 3 + 636262 CTT -s simRat_chr6.simRat.chr6 22529 3 + 647215 CTG -s simRat_chr6.simRat.chr6 22053 3 + 647215 CTT - -a -s simMouse_chr6.simMouse.chr6 29797 11 + 636262 GCATCTAAGAA -s Anc0.Anc0refChr9 7905 11 + 35212 GCATCTAAGAA -s Anc1.Anc1refChr2 131732 11 - 144309 GCATCTAAGAA -s Anc2.Anc2refChr0 27034 11 - 56053 GCATCTAAGAA -s mr.mrrefChr0 28264 11 + 130230 GCATCTAAGAA -s mr.mrrefChr0 28709 11 + 130230 GCATCTATGAA -s simCow_chr6.simCow.chr6 568890 11 - 602619 GCAGCTAAGTA -s simDog_chr6.simDog.chr6 564063 11 - 593897 GCATCTAAGAA -s simHuman_chr6.simHuman.chr6 571008 11 - 601863 CTGTGTGTCAA -s simMouse_chr6.simMouse.chr6 30252 11 + 636262 GCATCTATGAA -s simRat_chr6.simRat.chr6 22532 11 + 647215 GCATCTATGCA -s simRat_chr6.simRat.chr6 22056 11 + 647215 ACATCTAAGAG - -a -s simMouse_chr6.simMouse.chr6 29808 3 + 636262 GTC -s Anc0.Anc0refChr9 7916 3 + 35212 ATC -s Anc1.Anc1refChr2 131743 3 - 144309 ATC -s Anc2.Anc2refChr0 27045 3 - 56053 ATC -s mr.mrrefChr0 28275 3 + 130230 GTC -s mr.mrrefChr0 28720 3 + 130230 ATC -s simCow_chr6.simCow.chr6 568901 3 - 602619 ATC -s simDog_chr6.simDog.chr6 564074 3 - 593897 ATC -s simHuman_chr6.simHuman.chr6 571019 3 - 601863 ATC -s simMouse_chr6.simMouse.chr6 30383 3 + 636262 ATC -s simRat_chr6.simRat.chr6 22543 3 + 647215 ATC -s simRat_chr6.simRat.chr6 22067 3 + 647215 GTC - -a -s simMouse_chr6.simMouse.chr6 29811 77 + 636262 AGATGAAGAACCACAGTGCTTGTGATTAAGGCACCACCTGATTTTGGGAAGGCCCAGTACAGACAGAGTTCCCACCT -s Anc0.Anc0refChr9 7919 71 + 35212 AGATGAAGAACCATAGTGCTTGGGGCTAAGGCACCACTTGATTT-GAGAAGGCCAGTTACTGG----G-CCTCACTT -s Anc1.Anc1refChr2 131746 72 - 144309 AGATGAAGAACCATAGTGCTTGGGGCTAAGGCACCACTTGATTT-GAGAAGGCCAGTTACTGG----GTCCTCACTT -s Anc2.Anc2refChr0 27048 71 - 56053 AGATAAGGAACCATAGTGCTTGGGGCTAAGGCACCAATTGATGT-GAGAAGGCCAGTTACTGG----G-CCTATCTT -s mr.mrrefChr0 28278 72 + 130230 AGATGAAGAACCACAGTGCTTGTGATTAAGGCACCACCTGATTT-GGGAAGGCCCATTACTGA----GTCCCCACCT -s mr.mrrefChr0 28723 72 + 130230 AGATCAAGTAGCATGGTGCTTGTGGTTAAGGCACTACTTGATTT-GAGAAGTCCCACCACTAA----GTTCCCACTT -s simCow_chr6.simCow.chr6 568904 70 - 602619 AGACAATGAACCATGGTGCTTAGAGCTAAGGCACCACTTGA-GT-GAGCAGTCCAATTACTGG----A-ACTCTCTT -s simDog_chr6.simDog.chr6 564077 71 - 593897 AGATAAGGAACCATAATGCTTGGGGCTAGGGCACCAATTGATGT-GAGAGGGCCAGCTACTGG----G-CCCATCTG -s simHuman_chr6.simHuman.chr6 571029 66 - 601863 AGATGAAGAACCATAGTCCATGGGACTAAGGGACCAC-----AT-GAGAAGGGCAGTTTCTGG----G-TCTTACCT -s simMouse_chr6.simMouse.chr6 30386 72 + 636262 AGATCAAGTAGCATGGTGCTTGTGGTTAAGGCACTACTTGATTT-GAGAAGTCCCACCACTAA----GTTCCCACTT -s simRat_chr6.simRat.chr6 22546 72 + 647215 AGATCAAGTAGCATTGTGCTTAAGATTAAGGCACAACTTGATCT-GAGAAATCCCACCACTAA----ATTCCCACTT -s simRat_chr6.simRat.chr6 22070 72 + 647215 AGATGAAGAACCACAATGCTTGTGATTAAGGCACCACCTGATTT-GGGAAGCCCCATTACTGA----GTCCCCACCT - -a -s simMouse_chr6.simMouse.chr6 29888 16 + 636262 ACTTTTGTTCCCGCCT -s mr.mrrefChr0 28350 11 + 130230 ACTTTTGTTCC----- -s simRat_chr6.simRat.chr6 22142 11 + 647215 ACTTTTGTTCC----- - -a -s simMouse_chr6.simMouse.chr6 29904 7 + 636262 ACTTTTT -s Anc0.Anc0refChr9 7990 7 + 35212 AATTTTT -s Anc1.Anc1refChr2 131818 7 - 144309 AATTTTT -s Anc2.Anc2refChr0 27119 7 - 56053 AACTTTT -s mr.mrrefChr0 28361 7 + 130230 ACTTTTT -s mr.mrrefChr0 28795 7 + 130230 AATTTTT -s simCow_chr6.simCow.chr6 568974 7 - 602619 AACTTTT -s simDog_chr6.simDog.chr6 564148 7 - 593897 AACTTTT -s simHuman_chr6.simHuman.chr6 571095 6 - 601863 AATCTT- -s simMouse_chr6.simMouse.chr6 30458 7 + 636262 AATTTTT -s simRat_chr6.simRat.chr6 22618 7 + 647215 AATTTTT -s simRat_chr6.simRat.chr6 22153 7 + 647215 ACTTTAA - -a -s simMouse_chr6.simMouse.chr6 29911 9 + 636262 ACCAGGCTG -s Anc0.Anc0refChr9 7997 3 + 35212 ACT------ -s Anc1.Anc1refChr2 131825 9 - 144309 ACTAGGCAG -s Anc2.Anc2refChr0 27126 3 - 56053 AGT------ -s mr.mrrefChr0 28368 9 + 130230 ACCAGGCTG -s mr.mrrefChr0 28802 9 + 130230 ACTAGACAG -s simCow_chr6.simCow.chr6 568990 3 - 602619 AGT------ -s simDog_chr6.simDog.chr6 564155 3 - 593897 AGT------ -s simMouse_chr6.simMouse.chr6 30465 9 + 636262 ACTAGACAG -s simRat_chr6.simRat.chr6 22625 9 + 647215 ACTAGACAG -s simRat_chr6.simRat.chr6 22160 9 + 647215 ACCAAGCTG - -a -s simMouse_chr6.simMouse.chr6 29920 5 + 636262 CTTGC -s Anc0.Anc0refChr9 8000 5 + 35212 CTTGC -s Anc1.Anc1refChr2 131834 5 - 144309 CTTGC -s Anc2.Anc2refChr0 27129 5 - 56053 CCTGT -s mr.mrrefChr0 28377 5 + 130230 CTTGC -s mr.mrrefChr0 28814 5 + 130230 TTCAC -s simCow_chr6.simCow.chr6 568993 5 - 602619 CCTGT -s simDog_chr6.simDog.chr6 564158 5 - 593897 CCTGT -s simMouse_chr6.simMouse.chr6 30477 5 + 636262 TTCAC -s simRat_chr6.simRat.chr6 22637 5 + 647215 TTCAC -s simRat_chr6.simRat.chr6 22169 5 + 647215 ATTGC - -a -s simMouse_chr6.simMouse.chr6 29925 13 + 636262 TTTAGGAGAGTAC -s Anc0.Anc0refChr9 8005 13 + 35212 TTTTGGAGAGTAC -s Anc1.Anc1refChr2 131839 13 - 144309 TTTTGGAGAGTAC -s Anc2.Anc2refChr0 27134 13 - 56053 TTTTGATGAGTAC -s mr.mrrefChr0 28382 13 + 130230 TTTAGGAGAGTAC -s mr.mrrefChr0 28819 13 + 130230 CTTGGGAAAGTAT -s simCow_chr6.simCow.chr6 568998 13 - 602619 TTTTGCTGAGTAC -s simDog_chr6.simDog.chr6 564163 13 - 593897 TTTTGATGAGTAT -s simHuman_chr6.simHuman.chr6 571101 12 - 601863 -TTTGGAAGGTAC -s simMouse_chr6.simMouse.chr6 30482 13 + 636262 CTTGGGAAAGTAT -s simRat_chr6.simRat.chr6 22644 13 + 647215 CTTAGGTAAGTAT -s simRat_chr6.simRat.chr6 22174 13 + 647215 TTTAGGAGAGGAC - -a -s simMouse_chr6.simMouse.chr6 29938 19 + 636262 CTATAAACTAGGGGCTTCC -s Anc0.Anc0refChr9 8020 19 + 35212 CCAAAAACTTGGGGCTTCT -s Anc1.Anc1refChr2 131854 19 - 144309 CCAAAAACTTGGGGCTTCT -s Anc2.Anc2refChr0 27149 19 - 56053 CCAAAAACTTGGGGCTTCT -s mr.mrrefChr0 28395 19 + 130230 CTATAAACTTGGTGCTTCC -s mr.mrrefChr0 28832 19 + 130230 TCACAAATTTGAGGCTTCC -s simCow_chr6.simCow.chr6 569013 19 - 602619 CTAAAAACTTGGGACTTCC -s simDog_chr6.simDog.chr6 564178 19 - 593897 CCAAAAACTGAGGGCTTCT -s simHuman_chr6.simHuman.chr6 571115 19 - 601863 CCAATAACTTGGTGCTCCT -s simMouse_chr6.simMouse.chr6 30495 19 + 636262 TCACAAATTTGAGGCTTCC -s simRat_chr6.simRat.chr6 22657 19 + 647215 CCACAAACATGGGGCTCCC -s simRat_chr6.simRat.chr6 22187 19 + 647215 CTACGAACTTAGTGCTTCC - -a -s simMouse_chr6.simMouse.chr6 29957 4 + 636262 CCAT -s Anc0.Anc0refChr9 8039 4 + 35212 CTGT -s Anc1.Anc1refChr2 131873 4 - 144309 CTGT -s Anc2.Anc2refChr0 27168 4 - 56053 TTGT -s mr.mrrefChr0 28414 4 + 130230 CCAT -s mr.mrrefChr0 28851 4 + 130230 CTGT -s simCow_chr6.simCow.chr6 569032 4 - 602619 ATCT -s simDog_chr6.simDog.chr6 564198 4 - 593897 TTGT -s simHuman_chr6.simHuman.chr6 571134 4 - 601863 CTAT -s simMouse_chr6.simMouse.chr6 30514 4 + 636262 CTGT -s simRat_chr6.simRat.chr6 22676 4 + 647215 TTGT -s simRat_chr6.simRat.chr6 22206 4 + 647215 TCAT - -a -s simMouse_chr6.simMouse.chr6 29961 1 + 636262 G -s Anc0.Anc0refChr9 8043 1 + 35212 T -s Anc1.Anc1refChr2 131877 1 - 144309 T -s Anc2.Anc2refChr0 27172 1 - 56053 T -s mr.mrrefChr0 28418 1 + 130230 G -s simCow_chr6.simCow.chr6 569036 1 - 602619 T -s simDog_chr6.simDog.chr6 564202 1 - 593897 T -s simHuman_chr6.simHuman.chr6 571138 1 - 601863 T -s simRat_chr6.simRat.chr6 22210 1 + 647215 G - -a -s simMouse_chr6.simMouse.chr6 29962 1 + 636262 G -s Anc0.Anc0refChr9 8044 1 + 35212 G -s Anc1.Anc1refChr2 131878 1 - 144309 G -s Anc2.Anc2refChr0 27173 1 - 56053 G -s mr.mrrefChr0 28419 1 + 130230 G -s mr.mrrefChr0 28855 1 + 130230 G -s simCow_chr6.simCow.chr6 569037 1 - 602619 G -s simDog_chr6.simDog.chr6 564203 1 - 593897 G -s simHuman_chr6.simHuman.chr6 571139 1 - 601863 G -s simMouse_chr6.simMouse.chr6 30518 1 + 636262 G -s simRat_chr6.simRat.chr6 22680 1 + 647215 G -s simRat_chr6.simRat.chr6 22211 1 + 647215 G - -a -s simMouse_chr6.simMouse.chr6 29963 5 + 636262 TAAGT -s Anc0.Anc0refChr9 8045 5 + 35212 TAAGT -s Anc1.Anc1refChr2 131879 5 - 144309 TAAGT -s Anc2.Anc2refChr0 27174 5 - 56053 TAAGT -s mr.mrrefChr0 28420 5 + 130230 TAAGT -s mr.mrrefChr0 28856 5 + 130230 TAAGT -s simCow_chr6.simCow.chr6 569038 5 - 602619 TAAGT -s simDog_chr6.simDog.chr6 564204 5 - 593897 TAGGT -s simHuman_chr6.simHuman.chr6 571140 5 - 601863 TGAGT -s simMouse_chr6.simMouse.chr6 30520 5 + 636262 TAAGT -s simRat_chr6.simRat.chr6 22681 5 + 647215 TAAGT -s simRat_chr6.simRat.chr6 22212 5 + 647215 TAAGT - -a -s simMouse_chr6.simMouse.chr6 29968 10 + 636262 TTATATGATA -s Anc0.Anc0refChr9 8050 10 + 35212 TTGTATGATC -s Anc1.Anc1refChr2 131884 10 - 144309 TTGTATGATC -s Anc2.Anc2refChr0 27179 10 - 56053 TTGTATGATC -s mr.mrrefChr0 28425 10 + 130230 TTGTATGATA -s mr.mrrefChr0 28861 10 + 130230 ATGTATGTGA -s simCow_chr6.simCow.chr6 569046 10 - 602619 TTGTGTGACC -s simDog_chr6.simDog.chr6 564209 10 - 593897 TTGTATGATC -s simHuman_chr6.simHuman.chr6 571145 10 - 601863 TTGTATGATC -s simMouse_chr6.simMouse.chr6 30525 10 + 636262 CTGTATGCTA -s simRat_chr6.simRat.chr6 22686 10 + 647215 ATGTATGTGG -s simRat_chr6.simRat.chr6 22217 10 + 647215 CTGTAGAATA - -a -s simMouse_chr6.simMouse.chr6 29978 7 + 636262 GTCATCA -s Anc0.Anc0refChr9 8075 7 + 35212 GTCATCA -s Anc1.Anc1refChr2 131909 7 - 144309 GTCATCA -s Anc2.Anc2refChr0 27204 7 - 56053 GTCATCA -s mr.mrrefChr0 28435 7 + 130230 GTCATCA -s mr.mrrefChr0 28871 7 + 130230 GCCATCA -s simCow_chr6.simCow.chr6 569071 7 - 602619 GTCATCA -s simDog_chr6.simDog.chr6 564234 7 - 593897 GTCATCA -s simHuman_chr6.simHuman.chr6 571170 7 - 601863 GTGATCA -s simMouse_chr6.simMouse.chr6 30535 7 + 636262 GCCATCA -s simRat_chr6.simRat.chr6 22696 7 + 647215 GCCACCA -s simRat_chr6.simRat.chr6 22227 7 + 647215 GTCATCA - -a -s simMouse_chr6.simMouse.chr6 29985 5 + 636262 GGTTT -s mr.mrrefChr0 28442 5 + 130230 GGGTT -s simRat_chr6.simRat.chr6 22234 5 + 647215 GGGTT - -a -s simMouse_chr6.simMouse.chr6 29990 6 + 636262 ACTAGA -s Anc0.Anc0refChr9 8082 6 + 35212 ATTGGC -s Anc1.Anc1refChr2 131916 6 - 144309 ATTGGC -s Anc2.Anc2refChr0 27211 6 - 56053 ATTGGC -s mr.mrrefChr0 28447 6 + 130230 ACTAGA -s mr.mrrefChr0 28878 6 + 130230 ATCAGC -s simCow_chr6.simCow.chr6 569078 6 - 602619 ATCAAC -s simDog_chr6.simDog.chr6 564241 6 - 593897 ATTGGC -s simHuman_chr6.simHuman.chr6 571177 6 - 601863 GTAGGC -s simMouse_chr6.simMouse.chr6 30542 6 + 636262 ATCAGC -s simRat_chr6.simRat.chr6 22703 6 + 647215 ATCAGC -s simRat_chr6.simRat.chr6 22239 6 + 647215 CCTAGA - -a -s simMouse_chr6.simMouse.chr6 30019 4 + 636262 GTGT -s Anc0.Anc0refChr9 7650 4 + 35212 GTGT -s Anc1.Anc1refChr2 131471 4 - 144309 GTGT -s Anc2.Anc2refChr0 26742 4 - 56053 GTGT -s mr.mrrefChr0 28476 4 + 130230 GTGT -s simCow_chr6.simCow.chr6 568596 4 - 602619 GTGT -s simDog_chr6.simDog.chr6 563733 4 - 593897 GTGG -s simHuman_chr6.simHuman.chr6 570813 4 - 601863 GTAT -s simRat_chr6.simRat.chr6 22283 4 + 647215 GTAT - -a -s simMouse_chr6.simMouse.chr6 30053 6 + 636262 ATGTGC -s Anc0.Anc0refChr9 7687 6 + 35212 ATGTGC -s Anc1.Anc1refChr2 131508 6 - 144309 ATGTGC -s Anc2.Anc2refChr0 26779 6 - 56053 ATGTGC -s mr.mrrefChr0 28510 6 + 130230 ATGTGC -s simCow_chr6.simCow.chr6 568633 6 - 602619 ATGTAC -s simDog_chr6.simDog.chr6 563770 5 - 593897 ATATG- -s simHuman_chr6.simHuman.chr6 570850 6 - 601863 TTGTGG -s simRat_chr6.simRat.chr6 22317 6 + 647215 ATGTGC - -a -s simMouse_chr6.simMouse.chr6 30072 3 + 636262 CTG -s Anc0.Anc0refChr9 7706 3 + 35212 TTG -s Anc1.Anc1refChr2 131527 3 - 144309 TTG -s Anc2.Anc2refChr0 26798 3 - 56053 TTG -s mr.mrrefChr0 28529 3 + 130230 CTG -s simCow_chr6.simCow.chr6 568652 3 - 602619 TTG -s simDog_chr6.simDog.chr6 563776 3 - 593897 TTG -s simHuman_chr6.simHuman.chr6 570869 3 - 601863 TTG -s simRat_chr6.simRat.chr6 22336 3 + 647215 TCA - -a -s simMouse_chr6.simMouse.chr6 30087 1 + 636262 G -s mr.mrrefChr0 28544 1 + 130230 G -s simRat_chr6.simRat.chr6 22351 1 + 647215 G - -a -s simMouse_chr6.simMouse.chr6 30244 2 + 636262 AC -s Anc0.Anc0refChr9 7897 2 + 35212 AC -s Anc1.Anc1refChr2 131724 2 - 144309 AC -s Anc2.Anc2refChr0 27003 2 - 56053 AC -s mr.mrrefChr0 28701 2 + 130230 AC -s simCow_chr6.simCow.chr6 568859 2 - 602619 AC -s simDog_chr6.simDog.chr6 564015 2 - 593897 AC -s simRat_chr6.simRat.chr6 22524 2 + 647215 AC - -a -s simMouse_chr6.simMouse.chr6 30263 120 + 636262 TTCAGATCAACTAGCAGGGTGCTTGTGGTTAAGGCACTACTTGATTTGAGAAGTCCCGCCACTAAGTTCCGACTTAATTTTTACTAGACAGAATTTAGTGGACCTTCTTGCAGCTATGAA - -a -s simMouse_chr6.simMouse.chr6 30474 3 + 636262 GAT -s mr.mrrefChr0 28811 3 + 130230 GAT -s simRat_chr6.simRat.chr6 22634 3 + 647215 AAT - -a -s simMouse_chr6.simMouse.chr6 30519 1 + 636262 G - -a -s simMouse_chr6.simMouse.chr6 30548 7 + 636262 AGTATTT -s Anc0.Anc0refChr9 8088 7 + 35212 TGCATTT -s Anc1.Anc1refChr2 131922 7 - 144309 TGCATTT -s Anc2.Anc2refChr0 27217 7 - 56053 TGCATTT -s mr.mrrefChr0 28884 7 + 130230 TGTATTT -s simCow_chr6.simCow.chr6 569084 7 - 602619 TGCATTC -s simDog_chr6.simDog.chr6 564247 7 - 593897 TGCATTT -s simHuman_chr6.simHuman.chr6 571183 7 - 601863 TGCATTT -s simRat_chr6.simRat.chr6 22709 7 + 647215 TGTATTT - -a -s simMouse_chr6.simMouse.chr6 30555 14 + 636262 AGTCTTCGTAAGGA -s Anc0.Anc0refChr9 8095 14 + 35212 AGTCTTCTTAAGGA -s Anc1.Anc1refChr2 131929 14 - 144309 AGTCTTCTTAAGGA -s Anc2.Anc2refChr0 27224 14 - 56053 AGTCTTCTTAAGGA -s mr.mrrefChr0 28891 14 + 130230 AGTCTTCTTAAGGA -s simCow_chr6.simCow.chr6 569091 14 - 602619 AGTCCTCTTAAGGA -s simDog_chr6.simDog.chr6 564254 14 - 593897 ACTCTTCCTCAGGA -s simHuman_chr6.simHuman.chr6 571190 14 - 601863 AGTCTTCTTAAGGA -s simRat_chr6.simRat.chr6 22717 14 + 647215 AGTGTTCTTAAGGA - -a -s simMouse_chr6.simMouse.chr6 30569 36 + 636262 CAGCTGGCAGTTTAGGGTGTAAGTTCACTCTAATCA -s Anc0.Anc0refChr9 8110 36 + 35212 CAGCAGGTGGTGTGTGGTATAAGTTTACTCTAATCA -s Anc1.Anc1refChr2 131944 36 - 144309 CAGCAGGTGGTGTGTGGTATAAGTTTACTCTAATCA -s Anc2.Anc2refChr0 27239 36 - 56053 CAGCAGATGGTGTGTAGTATAAGTTCACTCTAATTA -s mr.mrrefChr0 28906 36 + 130230 CAGCTGGTAGTTTGGGGTGTAAGTTTACTCTAATCA -s simCow_chr6.simCow.chr6 569106 36 - 602619 CAGCAGATGCTGTGTAGTCTAAGTTCACTCTAATTA -s simDog_chr6.simDog.chr6 564269 35 - 593897 CATCAGATGGTGTGTAGTATAAA-TCACTCTAATTA -s simHuman_chr6.simHuman.chr6 571205 36 - 601863 CAGCAGGTGGTGTGTGATATAAGTTTACTATAATCA -s simRat_chr6.simRat.chr6 22732 36 + 647215 CAATTGGTAGCTCGGGGTGTAAGTTTACTCTAGTCA - -a -s simMouse_chr6.simMouse.chr6 30605 71 + 636262 CTCACTATAAAATGACCAGTGTTCTGTCCCTATGGTTGGCTACTACTCTTGACATACGCAGGATTAACAGC -s Anc0.Anc0refChr9 8146 71 + 35212 CTTACTAGCAAATTGACAATCTCCTGTCTCTTTGGTTGGTTACTTCTATTGATATAGGTAGGATTTATATC -s Anc1.Anc1refChr2 131980 71 - 144309 CTTACTAGCAAATTGACAATCTCCTGTCTCTTTGGTTGGTTACTTCTATTGATATAGGTAGGATTTATATC -s Anc2.Anc2refChr0 27275 71 - 56053 CTTACTAGCAAATTGACAATCTCCTGTCTCTTTGGTTGGTTACTTCTATGGGGATAGGTAGGATTTATATT -s mr.mrrefChr0 28942 71 + 130230 CTCACTATAAAATGACCAGTGTCCTGTCCCTATGGTTGGCTACTACTCTTGATATACGCAGGATTAACAGC -s simCow_chr6.simCow.chr6 569142 61 - 602619 CTTACTA-------GAAAACCTCCTATCTCTTTGTTTGGTTACTTCTATGGGCATA---AGGATCTATATT -s simDog_chr6.simDog.chr6 564305 66 - 593897 CTTGCCAGCAAATTGACAATCTCCTGTCTCATTGGTTGGTCACTTCTA----GAGAGGTGGTCTTCATAT- -s simHuman_chr6.simHuman.chr6 571241 71 - 601863 CTTACTAGGAAGTCGGCACTCTCCTGTCTCTTTGGTTGGTTACTTCTATTGATATAGGTAGGATTTATATC -s simRat_chr6.simRat.chr6 22768 71 + 647215 CTCACTATAAAATTACCGGTGTCTTGTCCCTATGCTTGGCTACTACTTATTATATACACAGGATTAACAGC - -a -s simMouse_chr6.simMouse.chr6 30676 11 + 636262 CAAAGGTTAGC -s Anc0.Anc0refChr9 8218 11 + 35212 CAAAAGTTAAC -s Anc1.Anc1refChr2 132052 11 - 144309 CAAAAGTTAAC -s Anc2.Anc2refChr0 27347 11 - 56053 CAGAAGTTAAC -s mr.mrrefChr0 29013 11 + 130230 CAAAGGTTAGC -s simCow_chr6.simCow.chr6 569204 11 - 602619 CAGGGGTTAAT -s simDog_chr6.simDog.chr6 564372 11 - 593897 CAGAAGTTGCC -s simHuman_chr6.simHuman.chr6 571313 11 - 601863 CAAAAGCTAAC -s simRat_chr6.simRat.chr6 22839 11 + 647215 CACAGGTTAGC - -a -s simMouse_chr6.simMouse.chr6 30687 100 + 636262 CGTTTCATTGGTATGCTAAGTCTGTAGCTACAACCTGATACACCTTGTATTATGGGGATATTAGACATCTTGCTTGCACTACATGATGGTGATGTACCAT -s Anc0.Anc0refChr9 8229 97 + 35212 CTTTCTGCTGGTATACCATGCCTATAGCTACAACCTGATATAGCT-GTATTATAGGGGTAGTAAACATCCT--TTACACCACAATGTCGGAATGTGGCAT -s Anc1.Anc1refChr2 132063 97 - 144309 CTTTCTGCTGGTATACCATGCCTATAGCTACAACCTGATATAGCT-GTATTATAGGGGTAGTAAACATCCT--TTACACCACAATGTCGGAATGTGGCAT -s Anc2.Anc2refChr0 27358 97 - 56053 CTTTCTGCAGGTATACCATCCCTATAGCTACCACCTGATATAGCT-GTATTATAGTGGTAGTAAACATCCT--TTACATCACACTGTCGGAATGTGGCAT -s mr.mrrefChr0 29024 99 + 130230 CGTTCCATTGGTATGCTATGTCTGTAGCTACAACCTGATACACCT-GTATTATAGGGATATTAGACATCCTGCTTGCACCACAAGGTGGTGATGCACCAT -s simCow_chr6.simCow.chr6 569215 97 - 602619 CTTGCTGCACGTACATCATCACTAGAGCTACCACCCGGTATGGTT-GTATTAGAGTGATAGTGAACATCCT--TCACATCGGACTGCCTGAATGTGGCAA -s simDog_chr6.simDog.chr6 564624 97 - 593897 CTTTACACAGATATACCATCCCTATAGCTCCCACCTGATATAGCT-GTATTATACTGGTAGTAGACATCCT--TTGCATCACCCTGTTGGGATACAGCAT -s simHuman_chr6.simHuman.chr6 571324 82 - 601863 CTTTCTGCTGGTATACCATGCCTATATCTACA-----------CT-GTACTATAGGGGTAGTAAATATCCT--TTAAACCACAATGGCAGAATGTG---- -s simRat_chr6.simRat.chr6 22850 95 + 647215 CCTCCCATTGGTATGCTATGTCTGTAGCTATAACCTGATACACCT-GTATTATAGGGATATTAGACATACTGC----ACCACAAGGTGGGGGTGCACGAT - -a -s simMouse_chr6.simMouse.chr6 30787 14 + 636262 GAGTGTACTAATGA -s Anc0.Anc0refChr9 8326 13 + 35212 GAGTCTACTCAC-A -s Anc1.Anc1refChr2 132160 13 - 144309 GAGTCTACTCAC-A -s Anc2.Anc2refChr0 27455 13 - 56053 CAGTCCACCCAC-A -s mr.mrrefChr0 29123 14 + 130230 GAGTCTACTAATGA -s simCow_chr6.simCow.chr6 569330 13 - 602619 AAATCCCCTCAC-A -s simDog_chr6.simDog.chr6 564721 13 - 593897 CAGTCCACCCAC-A -s simHuman_chr6.simHuman.chr6 571406 13 - 601863 GCGCTTACTGAC-A -s simRat_chr6.simRat.chr6 22945 14 + 647215 GAGTCTAGTAATGA - -a -s simMouse_chr6.simMouse.chr6 30801 132 + 636262 CCTGTTATCTCAATTGTTCCCGCACTCGCTTGAGGTTAGAAATCCCCACTGCCAGAAACGGTACAACACGTAACGGTACAACGCGTGCCTTTATTACCCTGAGAACTTGAGAAAATGTGGTAGCATGTGCCC -s Anc0.Anc0refChr9 8339 28 + 35212 CCAC-------------------------------------------------------------------------------------------------AGAAC------AAATTTGGCAGCA-GTGTGC -s Anc1.Anc1refChr2 132173 28 - 144309 CCAC-------------------------------------------------------------------------------------------------AGAAC------AAATTTGGCAGCA-GTGTGC -s Anc2.Anc2refChr0 27471 28 - 56053 CCTC-------------------------------------------------------------------------------------------------AGATT------GAACTTGGCAAGT-GTGTGG -s mr.mrrefChr0 29137 34 + 130230 CCAG-------------------------------------------------------------------------------------------------AGAACTTGAGAAAATGTGGTAGCA-GTGCCC -s simCow_chr6.simCow.chr6 569350 28 - 602619 CCTG-------------------------------------------------------------------------------------------------AGATT------GAGACTCGCAAGT-GCTTTG -s simDog_chr6.simDog.chr6 564737 28 - 593897 CCTC-------------------------------------------------------------------------------------------------AGATT------GAACTTGGCAAGT-GTGTGG -s simHuman_chr6.simHuman.chr6 571419 28 - 601863 CCAC-------------------------------------------------------------------------------------------------ACAAC------AATTTCCAGAGCA-GTATAC -s simRat_chr6.simRat.chr6 22959 33 + 647215 CCAA-------------------------------------------------------------------------------------------------AGAACTAGAGAAAATGTGGTTGC--GTGCCC - -a -s simMouse_chr6.simMouse.chr6 30933 128 + 636262 CTAATTGAGCAAATGTGTGATTATGTTGATGCCCATATCTTGTTGTGAAGATATGGCACATCTCCTGAAGACAGAGACCTGAGTGACAGGCTCTCCAGGCCTTCCCCAATTTCAATTTATATGCTGCT -s Anc0.Anc0refChr9 8367 21 + 35212 CTA-----------------------------------------------------------------------------------------------------------GTCAATATATATGCTTAT -s Anc1.Anc1refChr2 132201 21 - 144309 CTA-----------------------------------------------------------------------------------------------------------GTCAATATATATGCTTAT -s Anc2.Anc2refChr0 27499 21 - 56053 GAT-----------------------------------------------------------------------------------------------------------GCCCATATATATGCTTAT -s mr.mrrefChr0 29171 36 + 130230 CTA--------------------------------------------------------------------------------------------CAGGCCTTCCCCAATTTCAATTTATATGCTGCT -s simCow_chr6.simCow.chr6 569380 21 - 602619 GAT-----------------------------------------------------------------------------------------------------------GCCCGTACATTTGCTTAA -s simDog_chr6.simDog.chr6 564765 21 - 593897 GAT-----------------------------------------------------------------------------------------------------------GCCCATATATATGCTTAT -s simHuman_chr6.simHuman.chr6 571447 15 - 601863 CTA-----------------------------------------------------------------------------------------------------------GTCAGAGTATAA------ -s simRat_chr6.simRat.chr6 22992 36 + 647215 CTA--------------------------------------------------------------------------------------------CAGGCCTTCCCCAATTTCTATTTATATGCTGCT - -a -s simMouse_chr6.simMouse.chr6 31061 4 + 636262 ATTT -s Anc0.Anc0refChr9 8388 4 + 35212 ATCC -s Anc1.Anc1refChr2 132222 4 - 144309 ATCC -s Anc2.Anc2refChr0 27554 4 - 56053 ATCC -s mr.mrrefChr0 29207 4 + 130230 ATCC -s simCow_chr6.simCow.chr6 569435 4 - 602619 ATCC -s simDog_chr6.simDog.chr6 564820 4 - 593897 ATCC -s simHuman_chr6.simHuman.chr6 571462 4 - 601863 ATCC -s simRat_chr6.simRat.chr6 23028 4 + 647215 ATCC - -a -s simMouse_chr6.simMouse.chr6 31065 35 + 636262 ATACCAATAAGTAACTAAGCGTGATGTTTGTGTAG -s Anc0.Anc0refChr9 8392 3 + 35212 A--------------------------------AG -s Anc1.Anc1refChr2 132226 3 - 144309 A--------------------------------AG -s Anc2.Anc2refChr0 27558 3 - 56053 G--------------------------------AC -s mr.mrrefChr0 29211 3 + 130230 A--------------------------------AG -s simCow_chr6.simCow.chr6 569439 3 - 602619 G--------------------------------AC -s simDog_chr6.simDog.chr6 564830 3 - 593897 G--------------------------------AC -s simHuman_chr6.simHuman.chr6 571466 3 - 601863 A--------------------------------AA -s simRat_chr6.simRat.chr6 23032 3 + 647215 A--------------------------------AG - -a -s simMouse_chr6.simMouse.chr6 31100 6 + 636262 GTTAAC -s Anc0.Anc0refChr9 8395 6 + 35212 TTTGAC -s Anc1.Anc1refChr2 132229 6 - 144309 TTTGAC -s Anc2.Anc2refChr0 27561 6 - 56053 CTTGTC -s mr.mrrefChr0 29214 6 + 130230 GTTAAC -s simCow_chr6.simCow.chr6 569442 6 - 602619 CTTGTC -s simDog_chr6.simDog.chr6 564836 6 - 593897 CTTGTC -s simHuman_chr6.simHuman.chr6 571469 3 - 601863 CT---C -s simRat_chr6.simRat.chr6 23035 6 + 647215 TTTAAC - -a -s simMouse_chr6.simMouse.chr6 31106 13 + 636262 ATTAAGTTAGTTG -s Anc0.Anc0refChr9 8401 13 + 35212 ATACAAGTAGTTA -s Anc1.Anc1refChr2 132235 13 - 144309 ATACAAGTAGTTA -s Anc2.Anc2refChr0 27596 13 - 56053 CCATAGGTAACGA -s mr.mrrefChr0 29220 13 + 130230 ATTAAGTTAGTTA -s simCow_chr6.simCow.chr6 569481 13 - 602619 GTATAAGAATTGA -s simDog_chr6.simDog.chr6 564871 13 - 593897 CCATAGGTAACGA -s simHuman_chr6.simHuman.chr6 571472 13 - 601863 ATATAAATAGTTA -s simRat_chr6.simRat.chr6 23041 13 + 647215 ACTGAGTTAGTTA - -a -s simMouse_chr6.simMouse.chr6 31119 3 + 636262 GAT -s Anc0.Anc0refChr9 8414 3 + 35212 GCT -s Anc1.Anc1refChr2 132248 3 - 144309 GCT -s Anc2.Anc2refChr0 27641 3 - 56053 GCT -s mr.mrrefChr0 29233 3 + 130230 GAT -s simCow_chr6.simCow.chr6 569526 3 - 602619 GCT -s simDog_chr6.simDog.chr6 564917 3 - 593897 GCT -s simHuman_chr6.simHuman.chr6 571485 3 - 601863 GCT -s simRat_chr6.simRat.chr6 23054 3 + 647215 GAC - -a -s simMouse_chr6.simMouse.chr6 31122 17 + 636262 GTTGCTTGATTTTCAAA -s Anc0.Anc0refChr9 8422 15 + 35212 GTTGATTGACTTACA-- -s Anc1.Anc1refChr2 132256 15 - 144309 GTTGATTGACTTACA-- -s Anc2.Anc2refChr0 27649 15 - 56053 TTTGACTGACTTACA-- -s mr.mrrefChr0 29236 17 + 130230 GTTGCTTGATTTTCAAA -s simCow_chr6.simCow.chr6 569534 15 - 602619 TTTGACTCACTATTA-- -s simDog_chr6.simDog.chr6 564925 15 - 593897 TTTGACTGACCTACA-- -s simHuman_chr6.simHuman.chr6 571493 15 - 601863 GTTGATTGACTTACA-- -s simRat_chr6.simRat.chr6 23057 17 + 647215 GTTGCTTGATCCTTAAG - -a -s simMouse_chr6.simMouse.chr6 31139 38 + 636262 GCACCTGGATGTGCATATGATCAATGGAACATTTGCCT -s Anc0.Anc0refChr9 8446 38 + 35212 GTACTTAGATGTGCAGATGCTTGACTGAAGTTTTGCTA -s Anc1.Anc1refChr2 132280 38 - 144309 GTACTTAGATGTGCAGATGCTTGACTGAAGTTTTGCTA -s Anc2.Anc2refChr0 27673 38 - 56053 GTACTTAGATGTGCAGGTGCTTGACTTAAGTTTTGCTA -s mr.mrrefChr0 29262 38 + 130230 GCACTTGGATGTGCATATGATCGATGGAACATTTGCCA -s simCow_chr6.simCow.chr6 569558 38 - 602619 GTATTTAGATGTGTAGGTGCTTGACTTAAGTCTTGCTA -s simDog_chr6.simDog.chr6 564950 38 - 593897 GTACATAGATGTGCAGGTCCTTGACCTGAGTTTTGCTA -s simHuman_chr6.simHuman.chr6 571517 38 - 601863 GTACTTAGATGTCCACATGTTTGACTGAAGTTTTGCTA -s simRat_chr6.simRat.chr6 23099 38 + 647215 GCACTTGGATGTGCATATGCGCGATGGCACAAACGTCA - -a -s simMouse_chr6.simMouse.chr6 31177 7 + 636262 TCTGGGT -s Anc0.Anc0refChr9 8485 7 + 35212 TCTGCAC -s Anc1.Anc1refChr2 132319 7 - 144309 TCTGCAC -s Anc2.Anc2refChr0 27712 7 - 56053 TCTGCAC -s mr.mrrefChr0 29301 7 + 130230 TCTGCAT -s simCow_chr6.simCow.chr6 569599 7 - 602619 TCAGCAC -s simDog_chr6.simDog.chr6 564989 7 - 593897 TCTGCAC -s simHuman_chr6.simHuman.chr6 571556 7 - 601863 TCTGCAC -s simRat_chr6.simRat.chr6 23138 7 + 647215 TCTGCAT - -a -s simMouse_chr6.simMouse.chr6 31184 28 + 636262 AAGGGTAATTCTTATATATTCCTGAATA -s Anc0.Anc0refChr9 8492 15 + 35212 AGGAGCAATTCTT-TA------------ -s Anc1.Anc1refChr2 132326 27 - 144309 AGGAGCAATTCTT-TATATTCCTGAATT -s Anc2.Anc2refChr0 27719 15 - 56053 AGGAGCAATTCTT-TA------------ -s mr.mrrefChr0 29308 28 + 130230 AAGAGTAATTCTTATATATTCCTGAATA -s simCow_chr6.simCow.chr6 569606 15 - 602619 AGGTGCAATTCTT-TA------------ -s simDog_chr6.simDog.chr6 564997 15 - 593897 AGGAGCAATCCTT-TA------------ -s simHuman_chr6.simHuman.chr6 571563 27 - 601863 AGGAACAGTTTTT-AATATTCTTGAATT -s simRat_chr6.simRat.chr6 23145 28 + 647215 AAGAGTAATTCTTATATATTCATGGTTA - -a -s simMouse_chr6.simMouse.chr6 31212 49 + 636262 GAGATCATCAGTAGATAAATAGCACCATCCTAGCATCATGGAGAGCCAT -s Anc0.Anc0refChr9 8507 6 + 35212 ------------------------------------TATATA------- -s Anc1.Anc1refChr2 132356 42 - 144309 GAGATCAGCAGTACACAGCTGCTACCGTTCTGTTCTTATATA------- -s Anc2.Anc2refChr0 27734 6 - 56053 ------------------------------------TATATC------- -s mr.mrrefChr0 29336 49 + 130230 GAGATCATCAGTAGATAAATAGCACCATCCTAGCATCATGGAGAGCCAT -s simCow_chr6.simCow.chr6 569621 6 - 602619 ------------------------------------GATAGT------- -s simDog_chr6.simDog.chr6 565012 6 - 593897 ------------------------------------TATGTC------- -s simHuman_chr6.simHuman.chr6 571593 42 - 601863 GAGATCAGTGGTACACAGCTGCTACCGTTCTGTTCTTATATA------- -s simRat_chr6.simRat.chr6 23173 49 + 647215 GAGATCATCAGTAGATAATTAACAACATTCTAGCATGACAGAGGGCCAT - -a -s simMouse_chr6.simMouse.chr6 31261 47 + 636262 TAGTACTACGCTTTCTCCTTTTCTTCCCATAAGCTGTGTGTGAGTGC -s Anc0.Anc0refChr9 8513 32 + 35212 ---------------CCTGATTTTTGAGATCAGCAGTATACAAATAC -s Anc1.Anc1refChr2 132398 32 - 144309 ---------------CCTGATTTTTGAGATCAGCAGTATACAAATAC -s Anc2.Anc2refChr0 27740 32 - 56053 ---------------CCTGATTTTTGGGTTCAGCAGTATACAAATAC -s mr.mrrefChr0 29385 47 + 130230 TAGTACTACGCTTTCTCCTTTTCTTCCCATAAGCTGTGTGTGAGTGC -s simCow_chr6.simCow.chr6 569627 32 - 602619 ---------------CCTGAATTTTGTGGTCAGCACTACACAAATAC -s simDog_chr6.simDog.chr6 565018 32 - 593897 ---------------CCTGATTTATGGGTTCAGCAGTATACAAATAC -s simHuman_chr6.simHuman.chr6 571635 32 - 601863 ---------------CCTGATTTTTGAGATCAGCAGTATACAAATAC -s simRat_chr6.simRat.chr6 23250 47 + 647215 TAGTAGTATGCTTTCTCCTTTTCTTGCCATAAGCTGTATGTCAGTGT - -a -s simMouse_chr6.simMouse.chr6 31308 14 + 636262 CTGACTTACTTAAG -s Anc0.Anc0refChr9 8552 14 + 35212 CTAACATCAGTCAG -s Anc1.Anc1refChr2 132437 14 - 144309 CTAACATCAGTCAG -s Anc2.Anc2refChr0 27779 14 - 56053 CTAACATCAGTCGG -s mr.mrrefChr0 29432 14 + 130230 CTGACTTACTTAAG -s simCow_chr6.simCow.chr6 569666 14 - 602619 CTCACATAAGTTGG -s simDog_chr6.simDog.chr6 565057 13 - 593897 CTAACATCAATC-T -s simHuman_chr6.simHuman.chr6 571674 14 - 601863 CTAACATCAGTCAG -s simRat_chr6.simRat.chr6 23297 14 + 647215 TTGACTTACTTAAG - -a -s simMouse_chr6.simMouse.chr6 31322 14 + 636262 AGTTCTCCCCTTCC -s Anc0.Anc0refChr9 8570 14 + 35212 AGTGCAATTCTTCA -s Anc1.Anc1refChr2 132455 14 - 144309 AGTGCAATTCTTCA -s Anc2.Anc2refChr0 27797 14 - 56053 AGTGCAATTCTTTA -s mr.mrrefChr0 29446 14 + 130230 AGTTCTCCCCTTCC -s simCow_chr6.simCow.chr6 569684 14 - 602619 AGTGCAATTTTTTA -s simDog_chr6.simDog.chr6 565074 14 - 593897 AGTATAATTCTCTA -s simHuman_chr6.simHuman.chr6 571692 14 - 601863 AGTGCATTTCTTCA -s simRat_chr6.simRat.chr6 23311 14 + 647215 AGTTCTCCCTTTCC - -a -s simMouse_chr6.simMouse.chr6 31336 216 + 636262 CTGTACCATACCTGTGTGGTATGGGGGATGCCATCCTCTCTTATGAAAAGTAACTTAAAGTCCTGCCCACATGCAGCTGTTCAGAAATCCTATGGCTCTGTATAGCACCTCCTTGCATGGAAATCGGGTCAGCTACACCCCGTACTTGACCTTAGTACACACTACAGTGACTTTCTATACATGATAGCAACACTCCCATAATATTGCATTCATTAA -s Anc0.Anc0refChr9 8584 17 + 35212 C-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ATATCACATCCATCAG -s Anc1.Anc1refChr2 132469 17 - 144309 C-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ATATCACATCCATCAG -s Anc2.Anc2refChr0 27811 17 - 56053 C-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ATATCACATCCATCAG -s mr.mrrefChr0 29460 101 + 130230 CTGTACCATACCTGTGTGGTATGGGGGATGCCATCCTCTCTTATGAAAAGTAACTTAAAGTCCTGTCA------------------------------------------------------------------------------------------------------------------GATAGCA-CACTCCCATAATATTACATTCATTAA -s simCow_chr6.simCow.chr6 569698 15 - 602619 C-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ATACCACATCCA--AG -s simDog_chr6.simDog.chr6 565088 17 - 593897 C-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ATATCATATCCATCAG -s simHuman_chr6.simHuman.chr6 571706 17 - 601863 C-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ATATCACACCTATCAG -s simRat_chr6.simRat.chr6 23328 101 + 647215 CTGCACCATACCAGTGTGGTATGAGAAATGCCATCCTCTCTAATCAAAAGTAACTTAAAGTCTTGTCA------------------------------------------------------------------------------------------------------------------GATATCA-CACTCACATAATATTACATTCATTAA - -a -s simMouse_chr6.simMouse.chr6 31552 32 + 636262 GGTGAATATTAATTATCTCTGTGCATTTATGA -s Anc0.Anc0refChr9 8601 31 + 35212 GGTGAAGATTA-TTCTCTCTGAGCACACACGC -s Anc1.Anc1refChr2 132486 31 - 144309 GGTGAAGATTA-TTCTCTCTGAGCACACACGC -s Anc2.Anc2refChr0 27828 31 - 56053 AGTGAAGATTA-ATCTCTCCAAGCACACACGC -s mr.mrrefChr0 29561 32 + 130230 GGTGAATATTAATTATCTCTGTGCATTCATGA -s simCow_chr6.simCow.chr6 569713 31 - 602619 TGTGCAATTTA-ATTGCTTCTATCACCTGTGG -s simDog_chr6.simDog.chr6 565105 31 - 593897 AGTGAGGACTA-ATCTCTCCAAGCACACACAC -s simHuman_chr6.simHuman.chr6 571723 31 - 601863 GATGAACATTA-TTCTCTCTGAGCACACAGGC -s simRat_chr6.simRat.chr6 23431 32 + 647215 GGTGAATATTAATTATCTCTGTGCATTCATGG - -a -s simMouse_chr6.simMouse.chr6 31584 8 + 636262 TAGCGCAG -s Anc0.Anc0refChr9 8632 8 + 35212 CAGCACAA -s Anc1.Anc1refChr2 132517 8 - 144309 CAGCACAA -s Anc2.Anc2refChr0 27859 8 - 56053 CTGCACAA -s mr.mrrefChr0 29593 8 + 130230 TAGCACAG -s simCow_chr6.simCow.chr6 569744 8 - 602619 CTGCACAA -s simDog_chr6.simDog.chr6 565140 8 - 593897 TTGCACAA -s simHuman_chr6.simHuman.chr6 571754 8 - 601863 CAGCACAA -s simRat_chr6.simRat.chr6 23463 8 + 647215 TAGCAATG - -a -s simMouse_chr6.simMouse.chr6 31592 3 + 636262 TGG -s Anc0.Anc0refChr9 8640 3 + 35212 TGG -s Anc1.Anc1refChr2 132525 3 - 144309 TGG -s Anc2.Anc2refChr0 27867 3 - 56053 TGG -s mr.mrrefChr0 29601 3 + 130230 TGG -s simCow_chr6.simCow.chr6 569752 3 - 602619 TGG -s simDog_chr6.simDog.chr6 565148 3 - 593897 CTG -s simHuman_chr6.simHuman.chr6 571762 3 - 601863 TGG -s simRat_chr6.simRat.chr6 23479 3 + 647215 TGC - -a -s simMouse_chr6.simMouse.chr6 31595 21 + 636262 AACCTTTTCTGTGTACCAGCA -s Anc0.Anc0refChr9 8686 21 + 35212 AACTGCCTCTAGGAACTAACA -s Anc1.Anc1refChr2 132571 21 - 144309 AACTGCCTCTAGGAACTAACA -s Anc2.Anc2refChr0 27913 21 - 56053 AAATGCCACTAGAAACTAATA -s mr.mrrefChr0 29604 21 + 130230 AACTTTTTCTGTGTACCAGCA -s simCow_chr6.simCow.chr6 569800 21 - 602619 AATTGCTACTAGTAACTGATC -s simDog_chr6.simDog.chr6 565194 21 - 593897 AAATGCCACTAGAAACTAATA -s simHuman_chr6.simHuman.chr6 571809 21 - 601863 GACTCCCTCTAGGAACTACCA -s simRat_chr6.simRat.chr6 23482 21 + 647215 AACTTTTTCTGTGTACCAGCA - -a -s simMouse_chr6.simMouse.chr6 31616 11 + 636262 GTCAACTACAC -s Anc0.Anc0refChr9 8707 11 + 35212 GGCAACTAAAC -s Anc1.Anc1refChr2 132592 11 - 144309 GGCAACTAAAC -s Anc2.Anc2refChr0 27936 11 - 56053 GGCAACTAAAC -s mr.mrrefChr0 29625 11 + 130230 GGCAACTACAC -s simCow_chr6.simCow.chr6 569823 11 - 602619 GGTAACTACAC -s simDog_chr6.simDog.chr6 565217 11 - 593897 GGCAACTAAAC -s simHuman_chr6.simHuman.chr6 571830 11 - 601863 GGCAACTAAAC -s simRat_chr6.simRat.chr6 23503 8 + 647215 GGCAAC---AC - -a -s simMouse_chr6.simMouse.chr6 31627 1 + 636262 T -s Anc0.Anc0refChr9 8718 1 + 35212 A -s Anc1.Anc1refChr2 132603 1 - 144309 A -s Anc2.Anc2refChr0 27947 1 - 56053 A -s mr.mrrefChr0 29636 1 + 130230 C -s simCow_chr6.simCow.chr6 569835 1 - 602619 A -s simDog_chr6.simDog.chr6 565228 1 - 593897 A -s simHuman_chr6.simHuman.chr6 571841 1 - 601863 A -s simRat_chr6.simRat.chr6 23511 1 + 647215 C - -a -s simMouse_chr6.simMouse.chr6 31628 19 + 636262 TACATTTTAAGGGACTCTG -s Anc0.Anc0refChr9 8725 16 + 35212 TATCCTTTGG---ACTCTG -s Anc1.Anc1refChr2 132610 16 - 144309 TATCCTTTGG---ACTCTG -s Anc2.Anc2refChr0 27954 16 - 56053 TATCCTTTGG---ACACTG -s mr.mrrefChr0 29637 17 + 130230 TATATTTTGGG--ACTCTG -s simCow_chr6.simCow.chr6 569842 16 - 602619 TAGCATTCAT---ACACTG -s simDog_chr6.simDog.chr6 565235 16 - 593897 TATCCTTTGG---GCACTG -s simHuman_chr6.simHuman.chr6 571848 16 - 601863 TGTCCTTTGG---ACTCTG -s simRat_chr6.simRat.chr6 23512 15 + 647215 TATTTTTTGGG----TCTG - -a -s simMouse_chr6.simMouse.chr6 31647 14 + 636262 CTGCTCAACGGGTC -s Anc0.Anc0refChr9 8741 6 + 35212 CTGCTT-------- -s Anc1.Anc1refChr2 132626 6 - 144309 CTGCTT-------- -s Anc2.Anc2refChr0 27972 6 - 56053 TTGCTT-------- -s mr.mrrefChr0 29654 14 + 130230 CTGCTCAACGGGTC -s simCow_chr6.simCow.chr6 569860 6 - 602619 TTGATT-------- -s simDog_chr6.simDog.chr6 565253 6 - 593897 TTGCTT-------- -s simHuman_chr6.simHuman.chr6 571864 6 - 601863 CTGCTT-------- -s simRat_chr6.simRat.chr6 23527 14 + 647215 CTGCTCAATTGATC - -a -s simMouse_chr6.simMouse.chr6 31661 54 + 636262 CTTCTACCCATGAGTCGCTCTGTATGTTCCATTGTGGCCTTTATTGATACACCT -s Anc0.Anc0refChr9 8747 46 + 35212 CTTCTCTCC-TCAGACACTCTG-----TCCATTG--GCCTTTACTGTCCCTCTT -s Anc1.Anc1refChr2 132632 48 - 144309 CTTCTCTCCATCAGACACTCTGT----TCCATTG--GCCTTTACTGTCCCTCTT -s Anc2.Anc2refChr0 27978 46 - 56053 CTTCTCTCC-TCAGACACTCTG-----TCCATTC--CCCTTTATTGCCCCTTTT -s mr.mrrefChr0 29668 54 + 130230 CTTCTACCCATGAGTCGCTCTGTATGTTCCATTGTGGCCTTTACTGTTACACCT -s simCow_chr6.simCow.chr6 569867 46 - 602619 CTTTTCTCC-TTCAACACTCTG-----TCCATTC--CCCTTTATTGCACCTTTT -s simDog_chr6.simDog.chr6 565259 46 - 593897 CTTCTCTCA-TCAGACACTCTG-----AACATTC--CCCTTTATTGCCCCTTTT -s simHuman_chr6.simHuman.chr6 571870 40 - 601863 CTTCTCTCCATCAGG------------TCCATTG--GCCTTTACTGTCCCTCTT -s simRat_chr6.simRat.chr6 23541 54 + 647215 CCTCTACCCATGACTCACTTTGTATGTTCGATTGTGCCCTTTACTGTTACACCT - -a -s simMouse_chr6.simMouse.chr6 31715 9 + 636262 AAACTACTA -s Anc0.Anc0refChr9 8816 9 + 35212 AAACCACTC -s Anc1.Anc1refChr2 132703 9 - 144309 AAACCACTC -s Anc2.Anc2refChr0 28047 9 - 56053 AAACCACTC -s mr.mrrefChr0 29731 9 + 130230 AAACCACTA -s simCow_chr6.simCow.chr6 569936 9 - 602619 AAACCGCTC -s simDog_chr6.simDog.chr6 565328 9 - 593897 AACCCACTC -s simHuman_chr6.simHuman.chr6 571933 9 - 601863 AAACCACTC -s simRat_chr6.simRat.chr6 23604 9 + 647215 AAGCCACTA - -a -s simMouse_chr6.simMouse.chr6 31724 28 + 636262 GAGGCTTTTATTAAAGTGGTTGTTTGGA -s Anc0.Anc0refChr9 8826 28 + 35212 GAGGCAGATATTAAGGCAGATCTTTAGT -s Anc1.Anc1refChr2 132713 28 - 144309 GAGGCAGATATTAAGGCAGATCTTTAGT -s Anc2.Anc2refChr0 28057 28 - 56053 CAGGTAGATATTAAGGCAGATCTTTAGT -s mr.mrrefChr0 29740 28 + 130230 GAGGCTTTTATTAAAGTGGTTGTTTGGA -s simCow_chr6.simCow.chr6 569946 28 - 602619 CAGGTAGAGACCAAGGCAGATCTTTAGT -s simDog_chr6.simDog.chr6 565338 28 - 593897 CAGGTAGATATTAAGGCAGATCTTCAGT -s simHuman_chr6.simHuman.chr6 571943 28 - 601863 GAGGCAGATATTAAGACAGATCTTTAGG -s simRat_chr6.simRat.chr6 23613 28 + 647215 GAGGTGTTTATTAATGTTGCTGTTTGGT - -a -s simMouse_chr6.simMouse.chr6 31752 8 + 636262 TGGGTTTG -s Anc0.Anc0refChr9 8856 8 + 35212 TGGAATTG -s Anc1.Anc1refChr2 132743 8 - 144309 TGGAATTG -s Anc2.Anc2refChr0 28087 8 - 56053 GGGAATAG -s mr.mrrefChr0 29768 8 + 130230 TGGGTTTG -s simCow_chr6.simCow.chr6 569976 8 - 602619 GGGAGTAG -s simDog_chr6.simDog.chr6 565368 8 - 593897 GGGAATAG -s simHuman_chr6.simHuman.chr6 571973 8 - 601863 TGGACTTG -s simRat_chr6.simRat.chr6 23641 8 + 647215 TGAGTGTG - -a -s simMouse_chr6.simMouse.chr6 31760 3 + 636262 TCA -s Anc0.Anc0refChr9 8864 3 + 35212 TGG -s Anc1.Anc1refChr2 132751 3 - 144309 TGG -s Anc2.Anc2refChr0 28095 3 - 56053 TGG -s mr.mrrefChr0 29776 3 + 130230 TCA -s simCow_chr6.simCow.chr6 569984 3 - 602619 TGG -s simDog_chr6.simDog.chr6 565376 3 - 593897 TGG -s simHuman_chr6.simHuman.chr6 571981 3 - 601863 TGG -s simRat_chr6.simRat.chr6 23650 3 + 647215 CCA - -a -s simMouse_chr6.simMouse.chr6 31763 18 + 636262 GAATATTGGTGATGTTAC -s Anc0.Anc0refChr9 8870 18 + 35212 GAATATTGGAGAAATTAC -s Anc1.Anc1refChr2 132761 18 - 144309 GAATATTGGAGAAATTAC -s Anc2.Anc2refChr0 28101 18 - 56053 GAATATTGGAGAAATTAC -s mr.mrrefChr0 29779 18 + 130230 GAATATTGGTGAAGTTAC -s simCow_chr6.simCow.chr6 569990 18 - 602619 GAATACTGGAGAAGTTGC -s simDog_chr6.simDog.chr6 565382 18 - 593897 AATTATTGGAAAAATTAC -s simHuman_chr6.simHuman.chr6 571991 18 - 601863 GAATATTGGAGAAATTTC -s simRat_chr6.simRat.chr6 23653 18 + 647215 GAATATTGGTGAAGTTAC - -a -s simMouse_chr6.simMouse.chr6 31781 11 + 636262 ATTCTAGATAT -s Anc0.Anc0refChr9 8890 11 + 35212 CTTCTAGATAT -s Anc1.Anc1refChr2 132781 11 - 144309 CTTCTAGATAT -s Anc2.Anc2refChr0 28121 11 - 56053 CTTCTAGTTAT -s mr.mrrefChr0 29797 11 + 130230 ATTCTAGATAT -s simCow_chr6.simCow.chr6 570010 11 - 602619 CTTCGAGTTAT -s simDog_chr6.simDog.chr6 565402 11 - 593897 TTTCTAGTTAT -s simHuman_chr6.simHuman.chr6 572011 11 - 601863 CTACTAGATAT -s simRat_chr6.simRat.chr6 23671 11 + 647215 ATGCTAGATAG - -a -s simMouse_chr6.simMouse.chr6 31792 20 + 636262 AGTCTTTGTAGGATTCCCCT -s Anc0.Anc0refChr9 8902 20 + 35212 ATTCTCTGCAAAACACACTT -s Anc1.Anc1refChr2 132793 20 - 144309 ATTCTCTGCAAAACACACTT -s Anc2.Anc2refChr0 28133 20 - 56053 ATTCTCTACAAAACATATTT -s mr.mrrefChr0 29808 20 + 130230 AGTCTTTGTAGGATACCCCT -s simCow_chr6.simCow.chr6 570022 20 - 602619 ATTGTATACAAAACATATTT -s simDog_chr6.simDog.chr6 565414 16 - 593897 ACTCAC----GAACATATCT -s simHuman_chr6.simHuman.chr6 572023 20 - 601863 ATTTTCTGCAAAACACACTT -s simRat_chr6.simRat.chr6 23682 20 + 647215 AGTCTATGTAGGTTACCCCT - -a -s simMouse_chr6.simMouse.chr6 31812 1 + 636262 T -s Anc0.Anc0refChr9 8922 1 + 35212 T -s Anc1.Anc1refChr2 132813 1 - 144309 T -s Anc2.Anc2refChr0 28153 1 - 56053 T -s mr.mrrefChr0 29828 1 + 130230 T -s simCow_chr6.simCow.chr6 570042 1 - 602619 T -s simDog_chr6.simDog.chr6 565430 1 - 593897 T -s simHuman_chr6.simHuman.chr6 572043 1 - 601863 T -s simRat_chr6.simRat.chr6 23703 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 31813 60 + 636262 CAACTAATCCTTTCTCAGAGGCATACTGAACTCTCCAATGCCACCATTCTTGTTTTGTTG -s Anc0.Anc0refChr9 8926 60 + 35212 CAACCACACCTTTCTAAGAGGTCCCTTGCACACTCCAATATGGCCACTCTTGTTATGTTT -s Anc1.Anc1refChr2 132817 60 - 144309 CAACCACACCTTTCTAAGAGGTCCCTTGCACACTCCAATATGGCCACTCTTGTTATGTTT -s Anc2.Anc2refChr0 28157 60 - 56053 CAACCACACCTTTTTATGAGGTCCCTTGCACACTCCAATATGACCACTCCTGTTATGTTT -s mr.mrrefChr0 29829 60 + 130230 CAACTAATCCTTTCTAAGAGGCCTACTGAACTCTCCAATGTCGCCATTCTTGTTTTGTTG -s simCow_chr6.simCow.chr6 570046 60 - 602619 TGACCACACCTTTTGATGAAGTCCCTTGCACACTCCAAAATGACCACTCCTGTTTTGCCA -s simDog_chr6.simDog.chr6 565434 60 - 593897 CAACCACACCCTTTTATATGGTCCCTTGCACACTCTGATATGACCATTCCAGTTATGTTT -s simHuman_chr6.simHuman.chr6 572047 54 - 601863 CAACCACACTTTTCTAAGAGGTCCCTTGCACGCTCCAATATAG------TTGTCACGTTT -s simRat_chr6.simRat.chr6 23704 60 + 647215 CAACTAATCGTTTCTAAGGGGCCTACTGGACTCTCCGATGTTGCCATTCTTGTTTTGTTG - -a -s simMouse_chr6.simMouse.chr6 31873 13 + 636262 TTCTTAGATGTTG -s Anc0.Anc0refChr9 9028 13 + 35212 TTTTCAGAAATCA -s Anc1.Anc1refChr2 132919 13 - 144309 TTTTCAGAAATCA -s Anc2.Anc2refChr0 28260 13 - 56053 TTTTCAGAAATCA -s mr.mrrefChr0 29925 13 + 130230 TTCTTAGATGTTG -s simCow_chr6.simCow.chr6 570151 7 - 602619 TTTTCAG------ -s simDog_chr6.simDog.chr6 565540 13 - 593897 TTTTCATAAATCA -s simHuman_chr6.simHuman.chr6 572143 13 - 601863 TTTTCAGAAATCA -s simRat_chr6.simRat.chr6 23802 13 + 647215 CTCTTACATGTTG - -a -s simMouse_chr6.simMouse.chr6 31886 6 + 636262 TGTTTT -s Anc0.Anc0refChr9 9047 6 + 35212 GATTTT -s Anc1.Anc1refChr2 132938 6 - 144309 GATTTT -s Anc2.Anc2refChr0 28279 6 - 56053 GAGTTT -s mr.mrrefChr0 29938 6 + 130230 TATTTT -s simCow_chr6.simCow.chr6 570163 6 - 602619 AAGTAT -s simDog_chr6.simDog.chr6 565559 6 - 593897 GGGTTT -s simHuman_chr6.simHuman.chr6 572162 6 - 601863 CATTTT -s simRat_chr6.simRat.chr6 23815 6 + 647215 TATTTT - -a -s simMouse_chr6.simMouse.chr6 31892 37 + 636262 TTAAACAGGCTTCTCTTGTACAGCTATACCAACCAGT -s Anc0.Anc0refChr9 9055 36 + 35212 T-AAACAGGCTTCATTTGTGCAAGAATACATACCCAT -s Anc1.Anc1refChr2 132946 36 - 144309 T-AAACAGGCTTCATTTGTGCAAGAATACATACCCAT -s Anc2.Anc2refChr0 28287 36 - 56053 T-AAACAGGCTTCATTTATGGAAGAATACATACCCAT -s mr.mrrefChr0 29944 36 + 130230 T-AAACAGGCTTCTCTTGTACAGCTATACCAACCAGT -s simCow_chr6.simCow.chr6 570171 36 - 602619 C-AAACAAGCATGGCTCATCGAAGAATACATATGCGT -s simDog_chr6.simDog.chr6 565567 34 - 593897 T-AAACAGGCTTCATTTATGGAAGTACA--TACCCAT -s simHuman_chr6.simHuman.chr6 572170 36 - 601863 T-AAACAGGCTTCATTTGTGCAAGAATAGGTACTCAT -s simRat_chr6.simRat.chr6 23821 36 + 647215 T-AAATAGGCTCCTCTTATACAGCTATATTAATCAGT - -a -s simMouse_chr6.simMouse.chr6 31929 33 + 636262 CACTAACTTGTCAGGTGACGCCAGGGCTGCTGA -s Anc0.Anc0refChr9 9091 13 + 35212 CACTAACTTGTC--------------------A -s Anc1.Anc1refChr2 132982 33 - 144309 CACTAACTTGTCAGGTTAGTCCGGAGATGCTAA -s Anc2.Anc2refChr0 28323 13 - 56053 CACTAACTTGTC--------------------A -s mr.mrrefChr0 29980 33 + 130230 CACTAACTTGTCAGGTGACTCCAGGGCTGCTAA -s simCow_chr6.simCow.chr6 570208 13 - 602619 CATTATCTTATC--------------------A -s simDog_chr6.simDog.chr6 565601 13 - 593897 GGCTAACTTGTC--------------------A -s simHuman_chr6.simHuman.chr6 572206 33 - 601863 CACTAACTTGTCATGTTAGTCCGGAGATGCTAA -s simRat_chr6.simRat.chr6 23857 32 + 647215 CACTAACTTGTCAGG-GGCTCAAGGGCTGCTAA - -a -s simMouse_chr6.simMouse.chr6 31962 78 + 636262 GGGCTGTATCCCTTTCTAGGCCTGTATCAAGTCATTTAGGGTTACAGATAAAGTAGTATTCCAATTGGAATAGGGGTG -s Anc0.Anc0refChr9 9104 64 + 35212 GGGCTGCATGCCTTTCTAGGCCTGTACTCAGTTACTCAGCCTTATAGATAAAATAATCCTTCAA-------------- -s Anc1.Anc1refChr2 133015 78 - 144309 GGGCTGCATGCCTTTCTAGGCCTGTACTCAGTTACTCAGCCTTATAGATAAAATAATCCTTCAATTGGGGAAGGGAAG -s Anc2.Anc2refChr0 28336 64 - 56053 GTGCTGCATGCCTTTCTAGGCCTGTACTCAGTTACTCAGCCTTATACATAAAATTAGCCGTCAA-------------- -s mr.mrrefChr0 30013 78 + 130230 GGGCTGCATGCCTTTCTAGGCCTGTATCAAGTTATTCAGCGTTACAGATAAAGTAGTATTCCAATTGGAATAGGGGTG -s simCow_chr6.simCow.chr6 570226 64 - 602619 GCGCTGCATTCCTTTCTAAGCCTGTACTCAATTGCTCAGCCCTGTACATAAAATGAATAGTCAA-------------- -s simDog_chr6.simDog.chr6 565614 57 - 593897 GTGCTACATGCCTTTCTAGGCTTGTACTCAGTTAACTGGTCTTAT--ATAAAATTAGCC------------------- -s simHuman_chr6.simHuman.chr6 572239 78 - 601863 GGGCTGCATGCCGTTCAAGACCTGTACTCAGTTACTCAGCCTTATAGATAAAATAATCCTTCCGGTGGGGAAGGGAAG -s simRat_chr6.simRat.chr6 23889 77 + 647215 GGGCTGCATGCCTTTCTAGGCCTGTATCAAGTTATTCAGCGTCAGAGATAAAGTAGTATACCACTTGGAT-AGAGGTG - -a -s simMouse_chr6.simMouse.chr6 32040 102 + 636262 GTGTCTAACTCATTTTAGGGGCGAAGAAGTTTGTAGCAAATTTTGAAAAAATGTTAACTTAACCACCAACCATTAATAGAGATAATACTGGTGTCCTGTCCT -s Anc0.Anc0refChr9 9168 54 + 35212 -----------------------------------------TCAAAAAAA-----AACTCACTCAACAACTTTCGCTAGCGACC-TAGTCATG-ATTGTCGA -s Anc1.Anc1refChr2 133093 100 - 144309 GTGCCTGAGCCATTTAAAGGG-GAAAGGGTTTGTTGCACATTCAAAAAAAAATGTAACTCACTCAACAACTTTCGCTAGCGACC-TAGTCATGAATTGTCGA -s Anc2.Anc2refChr0 28400 54 - 56053 -----------------------------------------TCAAAAAAA-----AGCCCACTCAACAGCTTTCGCCACCAACC-TAGCCATG-ATCGTTGA -s mr.mrrefChr0 30091 101 + 130230 GTGTCTGACTCATTTTAGGGGCGAAGAAGTTTGTAGCAAATTTTGAAAAAATGTTAACTTAACCACCAACTATCAATAGAGATA-TACTGATGTCCTGTCCT -s simCow_chr6.simCow.chr6 570290 54 - 602619 -----------------------------------------TCAAAAAAA-----AGCCCACTCAACAGCTTTCGCCACCAACC-TAGCCATG-ATCGTTGA -s simHuman_chr6.simHuman.chr6 572329 100 - 601863 GTGCCTGAGCCATTTAAAGGG-GAAAGGGTTTGTTGCACATTCCAAAAAAGATGTAAATCACACAGCAACTCTCCCTAGTGACT-TGGTCATGAATTGTCAA -s simRat_chr6.simRat.chr6 23966 89 + 647215 GAGTCTGA---------GGGGCGAGGAAGTTTGTAACAACTTTTGAAAAAATGTTA---TAACCTCCAACTATCAATAGAGATA-TACTGATACTCACTCTT - -a -s simMouse_chr6.simMouse.chr6 32142 12 + 636262 AGTCCAAGTCTT -s Anc0.Anc0refChr9 9222 12 + 35212 TGTCCACAACCT -s Anc1.Anc1refChr2 133193 12 - 144309 TGTCCACAACCT -s Anc2.Anc2refChr0 28454 12 - 56053 TGTTCACAACCT -s mr.mrrefChr0 30192 12 + 130230 AGTCCAAGTCTT -s simCow_chr6.simCow.chr6 570392 12 - 602619 TGTTCACAACCT -s simHuman_chr6.simHuman.chr6 572429 12 - 601863 TGTCCACAACCC -s simRat_chr6.simRat.chr6 24055 9 + 647215 AGTT---GTCTT - -a -s simMouse_chr6.simMouse.chr6 32154 66 + 636262 GATGCCTAGATAGTGGGTAAAAACAAAATATGGTCACCAAAGGGAACTATATAATGAACCAGTGAA -s Anc0.Anc0refChr9 9266 61 + 35212 GAAGTCTAGTTTGTGGACAAAGACAAAATAGGGTTGCTGAAGGGAACTATAT-----AGGATTAAA -s Anc1.Anc1refChr2 133237 64 - 144309 GAAGTCTAGTTTGTGGACAAAGACAAAATAGGGTTGCTGAAGGGAACTATAT--TCAAGGATTAAA -s Anc2.Anc2refChr0 28507 61 - 56053 GAAGTCTAGTTTGTAGACAAAGACAAAATGGGGTTGCTGAGGGGTACTAAAT-----AGGATTTAA -s mr.mrrefChr0 30204 66 + 130230 GATGCCTAGATAGTGGGTAAAGACAAAATATGGTCACCAAAGGGAACTATATAATGAACCAGTAAA -s simCow_chr6.simCow.chr6 570445 61 - 602619 AAAGCCGAGGTTCTAGACAACAATAAACTGGGGTCACTGAGAGGTGCTAAAT-----AGGCTTTAA -s simDog_chr6.simDog.chr6 565695 60 - 593897 GAAGTCTAGTTTGTATACAAAGACAGAAT-GGGTTGCTGAGGGGTACTAAGT-----AGGATTTAA -s simHuman_chr6.simHuman.chr6 572473 53 - 601863 -----------GGTGGACAAAGACAAAATAAGGTTGCTGTAGGGAACTATAT--TCAAGGACTAAA -s simRat_chr6.simRat.chr6 24064 66 + 647215 GAAGTCTAGATTGTGGGTAAAGACAAAATATGGTCACCAAAGGGAACTATATAATGAACCAGTAAA - -a -s simMouse_chr6.simMouse.chr6 32220 3 + 636262 TAC -s Anc0.Anc0refChr9 9327 3 + 35212 TAC -s Anc1.Anc1refChr2 133301 3 - 144309 TAC -s Anc2.Anc2refChr0 28570 3 - 56053 TGA -s mr.mrrefChr0 30270 3 + 130230 TAC -s simCow_chr6.simCow.chr6 570508 3 - 602619 TGA -s simDog_chr6.simDog.chr6 565757 3 - 593897 TGC -s simHuman_chr6.simHuman.chr6 572526 3 - 601863 TAC -s simRat_chr6.simRat.chr6 24130 3 + 647215 TAC - -a -s simMouse_chr6.simMouse.chr6 32223 32 + 636262 AGAACATTTGGTATCAGTGTGGAAGTCTGTAT -s Anc0.Anc0refChr9 9330 27 + 35212 AGAACATTAGGTATCTGTGTGGAAGTC----- -s Anc1.Anc1refChr2 133304 27 - 144309 AGAACATTAGGTATCTGTGTGGAAGTC----- -s Anc2.Anc2refChr0 28573 27 - 56053 AGAACATTAGGTATCTGTGTGGAAGTC----- -s mr.mrrefChr0 30273 32 + 130230 AGAACATTTGGTATCAGTGTGGAAGTCTGTAT -s simCow_chr6.simCow.chr6 570511 27 - 602619 TGAACATTAGGTATCTGCGTGGAAGGT----- -s simDog_chr6.simDog.chr6 565760 27 - 593897 AGAAAATTTGGTATCTGTGTGGAAGTC----- -s simHuman_chr6.simHuman.chr6 572559 27 - 601863 AGAACATTAGGTATCTGTGTGGAAGTC----- -s simRat_chr6.simRat.chr6 24133 32 + 647215 AGAACATTCGGTATCAGTGTGGAAGTCTGTAT - -a -s simMouse_chr6.simMouse.chr6 32255 17 + 636262 CCCAGATTTCATGTATA -s Anc0.Anc0refChr9 9357 15 + 35212 --CAGATTTCGTGTATA -s Anc1.Anc1refChr2 133331 15 - 144309 --CAGATTTCGTGTATA -s Anc2.Anc2refChr0 28600 15 - 56053 --CAGACTTCGTGCATA -s mr.mrrefChr0 30305 17 + 130230 CCCAGATTTCATGTATA -s simCow_chr6.simCow.chr6 570538 15 - 602619 --CAGACTTTGTGCACA -s simDog_chr6.simDog.chr6 565787 14 - 593897 --CAAA-TTCGTGCATG -s simHuman_chr6.simHuman.chr6 572586 15 - 601863 --CAGATTTCGTGTATA -s simRat_chr6.simRat.chr6 24166 17 + 647215 CCCAGATTTCATGCATA - -a -s simMouse_chr6.simMouse.chr6 32272 38 + 636262 ATGTTGGGGCTCTTTCCCCATTCGTAGTAGTCAAGGGC -s Anc0.Anc0refChr9 9386 32 + 35212 ATGTTGGGTCTCTTTGCCCATGTGTAG------AGCGT -s Anc1.Anc1refChr2 133360 32 - 144309 ATGTTGGGTCTCTTTGCCCATGTGTAG------AGCGT -s Anc2.Anc2refChr0 28629 32 - 56053 ATGTTGGGTCTCTTTGTCCATGTGTAG------AGCAT -s mr.mrrefChr0 30336 38 + 130230 ATGTTGGGGCTCTTTCCCCATTCGTAGTAGTCAAGGGC -s simCow_chr6.simCow.chr6 570567 31 - 602619 ATGTTGGGTCTCTTTG-CCATGAGTAG------AGCTT -s simDog_chr6.simDog.chr6 565815 32 - 593897 ATGTTGGGACTCTTTGTCCACGTGTAG------AGCAT -s simHuman_chr6.simHuman.chr6 572615 32 - 601863 ATGTTGGGTCTCTTTGCCCATGTGTAG------AGTGT -s simRat_chr6.simRat.chr6 24197 38 + 647215 ATGTTGGGGCTCTTTCCCCACTCGTAGTACATAAGGTC - -a -s simMouse_chr6.simMouse.chr6 32310 12 + 636262 CGAAGATCATCC -s Anc0.Anc0refChr9 9418 12 + 35212 TGTATGTCTTCC -s Anc1.Anc1refChr2 133392 12 - 144309 TGTATGTCTTCC -s Anc2.Anc2refChr0 28667 12 - 56053 TGTATGTCTTCT -s mr.mrrefChr0 30374 12 + 130230 TGAAGATCATCC -s simCow_chr6.simCow.chr6 570604 12 - 602619 TGTATGTTTCCT -s simDog_chr6.simDog.chr6 565853 12 - 593897 TGTATGTCTTCT -s simHuman_chr6.simHuman.chr6 572647 12 - 601863 TGTTTGTCTTCC -s simRat_chr6.simRat.chr6 24235 12 + 647215 TGAAGATGATCT - -a -s simMouse_chr6.simMouse.chr6 32322 30 + 636262 ATCTCGCAACGATACTTGGAACATGACCTG -s Anc0.Anc0refChr9 9430 5 + 35212 A-------------------------CCAA -s Anc1.Anc1refChr2 133404 5 - 144309 A-------------------------CCAA -s Anc2.Anc2refChr0 28679 5 - 56053 G-------------------------CCAA -s mr.mrrefChr0 30386 30 + 130230 ATCTCGCAACGATACTTGGAACATGACCTG -s simCow_chr6.simCow.chr6 570616 5 - 602619 T-------------------------CCAC -s simDog_chr6.simDog.chr6 565865 5 - 593897 G-------------------------CCAA -s simHuman_chr6.simHuman.chr6 572659 5 - 601863 A-------------------------CCAA -s simRat_chr6.simRat.chr6 24560 30 + 647215 ATCTCGCAAGTCTACTTGGAACACGACCTG - -a -s simMouse_chr6.simMouse.chr6 32352 10 + 636262 TGGTCAGCCC -s Anc0.Anc0refChr9 9436 10 + 35212 TAGTTACCCC -s Anc1.Anc1refChr2 133410 10 - 144309 TAGTTACCCC -s Anc2.Anc2refChr0 28730 10 - 56053 TAGTTACCTC -s mr.mrrefChr0 30417 10 + 130230 TAGTCAGCCC -s simCow_chr6.simCow.chr6 570669 10 - 602619 TCGTTACCTA -s simDog_chr6.simDog.chr6 566179 10 - 593897 TAGTTACCTC -s simHuman_chr6.simHuman.chr6 572665 10 - 601863 TAGTTATCCC -s simRat_chr6.simRat.chr6 24591 10 + 647215 TAGTAACCCC - -a -s simMouse_chr6.simMouse.chr6 32362 49 + 636262 ACCTTGAAACAGCAGAGGAAGTATGAATTACTAACAAACATGACTATGA -s Anc0.Anc0refChr9 9446 38 + 35212 ATCCTTAAACAGCAGAGTAACTAGGAGTTAATGAACAA----------- -s Anc1.Anc1refChr2 133420 41 - 144309 ATCCTTAAACAGCAGAGTAACTAGGAGTTAATGAACAACAT-------- -s Anc2.Anc2refChr0 28740 38 - 56053 ATCCTTAAACAGCTGAGGAACTAGGAGTTAATCAACAA----------- -s mr.mrrefChr0 30427 49 + 130230 ACCTTGAAACAGCAGAGTAAGTATGAGTTACTGACAAACATGACTATGA -s simCow_chr6.simCow.chr6 570683 38 - 602619 ACCCCTAAACACCTGAGGAACGAGGAATTAATCACCAA----------- -s simDog_chr6.simDog.chr6 566189 38 - 593897 ATCCTTAAACAGCTGAGGGACTGGGAGTTAATCAATAA----------- -s simHuman_chr6.simHuman.chr6 572675 37 - 601863 ----TTAGACAGCAGAGTAACTAGGAGTTAGTGAACAGCAT-------- -s simRat_chr6.simRat.chr6 24601 49 + 647215 ACCTTGCAACAGCAGAGTAAGTCTGAGTTACTGACAAACATGACTCTGA - -a -s simMouse_chr6.simMouse.chr6 32411 106 + 636262 TTGATATAACAAGGGCAATTAACGCCAAGCATCAATGAGAAGATGGTCGATGCGGATGATATAAGGCGTTTTTAAATTACAGTAACTGTCACATAGAACGTTAAAT -s Anc0.Anc0refChr9 9484 22 + 35212 ------------------------------------------------------------------------------------ACATCAGTATGGAACACTAGAT -s Anc1.Anc1refChr2 133461 36 - 144309 ----------------------------------------------------------------------TTTCAATTATAGTGACATCAGTATGGAACACTAGAT -s Anc2.Anc2refChr0 28778 22 - 56053 ------------------------------------------------------------------------------------ACATCAGTATGGAGCACTAGAT -s mr.mrrefChr0 30476 106 + 130230 TTGATATAACAAGGGCAATTAACGCCAAGCATCAATGAGAAGATGGTCGATGCGGATGATATAAGGCGTTTTTAAATTACAGTAACTGTCACATAGAACGTTAAAT -s simCow_chr6.simCow.chr6 570721 22 - 602619 ------------------------------------------------------------------------------------ACAGTAATATGGAGCACTAGAT -s simDog_chr6.simDog.chr6 566227 22 - 593897 ------------------------------------------------------------------------------------ACATCAGTAAGAAGCACTAGAT -s simHuman_chr6.simHuman.chr6 572712 36 - 601863 ----------------------------------------------------------------------TTTCAATTATAGTGGCAAGAGTATGGAACACTAGAT -s simRat_chr6.simRat.chr6 24651 106 + 647215 TGGGTAGAACACAGGCAAATTAGGCCATGCATTGATGAGAAAATGGTAAACGCAGATGATATAAGATCTTGTTAAAAATCAGTCACTGTCACATAGAGTGTTAAAT - -a -s simMouse_chr6.simMouse.chr6 32517 14 + 636262 CAGGTTTTTCAGCA -s Anc0.Anc0refChr9 9508 14 + 35212 CAGGTTTTTCAAAT -s Anc1.Anc1refChr2 133499 14 - 144309 CAGGTTTTTCAAAT -s Anc2.Anc2refChr0 28802 14 - 56053 CAGGTTTTTCAAAT -s mr.mrrefChr0 30582 14 + 130230 CAGGTTTTTCAGCA -s simCow_chr6.simCow.chr6 570745 14 - 602619 CAGGTCTTTCAAAC -s simDog_chr6.simDog.chr6 566251 14 - 593897 CAGGTTTTTCAAAT -s simHuman_chr6.simHuman.chr6 572750 14 - 601863 CCGGTTTTCCAAAT -s simRat_chr6.simRat.chr6 24757 14 + 647215 CAGGTTTCTCAGTC - -a -s simMouse_chr6.simMouse.chr6 32531 252 + 636262 ACTCTCTCATATAATAATTCTATGGTGGACAAAAATTGGTTGAGGCCAGATCAGTTACTACAGGTTAATTAAATTCTAAGAATGTTTTAGTGCTCCAATGCTTTAGCCTGGTGGTTGGCAAATACAGGAGCACGCTAGGTAAACTTTCATGGAATGCTTAATAGGATATGATAGGCTCCTTTTGTTCCAATTTGAAAATTTACTACCAGTGATGCCTAGTACCATTCTACAGATCGCACAAGAACAAGGCAC -s Anc0.Anc0refChr9 9522 193 + 35212 ACACTTTCACATGATAATTCTGTGGTGAACAAAGAATGATTGAGGCTAGATCAGTTACTATAGGTTAATGAAATT-TTAGAATGTATTAGTGCTGGATTGCTTGATTCTAATTGTTGATGAACACAGAAGCACTATAAAAAAACTCTCACGGGATGCTTAATATGATATGATAGGCTCTTTTTGTGAC------AAGATT---------------------------------------------------- -s Anc1.Anc1refChr2 133513 199 - 144309 ACACTTTCACATGATAATTCTGTGGTGAACAAAGAATGATTGAGGCTAGATCAGTTACTATAGGTTAATGAAATT-TTAGAATGTATTAGTGCTGGATTGCTTGATTCTAATTGTTGATGAACACAGAAGCACTATAAAAAAACTCTCACGGGATGCTTAATATGATATGATAGGCTCTTTTTGTGACAATTCTAAGATT---------------------------------------------------- -s Anc2.Anc2refChr0 28816 193 - 56053 ACACTTTCACATGATAATTCTGTGGTGAACAAAGAATGATTGAGGTTAGATCCGTTACTATAGGTTAATGAAATT-TTAGAATGTATTAGTGCTGGATTGCCTGATTCTAATTGTTGAAAAACACAGAAGCACTATAAAAAAACTCTCACAGGATGCCTAACATGATATGATATGCTCTTTTTGTGAC------AAGATT---------------------------------------------------- -s mr.mrrefChr0 30596 252 + 130230 ACACTCTCATATAATAATTCTATGGTGGACAAAAAATGGTTGAGGCCAGATCAGTTACTACAGGTTAATTAAATTCTTAGAATGTTTTAGTGCTCCAATGCTTTATCCTGATTGTTGATGAATACAGGAGCACTATAGGAAAACTTTCACGGAATGCTTAATAGGATATGATAGGCTCCTTTTGTTCCAATTTGAAAATTTACTACCAGTGATGCCTAGTACCATTCTACAGATCGCACAAGAACAAGGCAC -s simCow_chr6.simCow.chr6 570764 192 - 602619 ACACTCTCATATAATAATTGTCTGATGGAAAAAGAATGATTGAGCTTGGATCTGTGGGTATATGATAATGAAATT-ATAGAAATTTTTAGTGCTGGATTGCCTGATCCTAATTATTGACATGCACAGAAGCGCTATGAAAAAGGTTTCACAGGATGCATAACATGATATGATATGC-CTCTTTGTGAC------AAGATT---------------------------------------------------- -s simDog_chr6.simDog.chr6 566265 191 - 593897 ACACTTTCACATGATAATTCTGTGGTGAACAGAGAATGATTGAGGTTAGATCCCTTACTGTAGGTTAATGAAATT-TTAGAATGTATTAGTGCTGGATTGCCTGATTGTAGTTGTAGAAAAACATAAAGGCAC--TAAAACAACTCTCATAGGGGGTCTAACATGAGATGATATGCTCTTTGTGTGAC------AAGATT---------------------------------------------------- -s simHuman_chr6.simHuman.chr6 572764 195 - 601863 ATAGTTTCG----ATAACTCTGAAGTGCCCAAAGAATGATTGAGGCTAGATGAGTTACTATAGGTTAATGAAATT-TTAGAATGTATTAGTACGGGATTGCTTCATTCTAATTGTTGATGAACACAGAAGCACTATAAAAAAACTGTCACGGGATGCTTCATATGATATGGTAGGCTCTTTTTGTCACAGTTCTAAGATC---------------------------------------------------- -s simRat_chr6.simRat.chr6 24771 251 + 647215 AGACTCTCACATAATAATTCTATGGTGGACAAAAAATGGTTGAGGCCACATCAATTAGTACAGGTTACTTAAATTCTTAGAATGTTTTAGTGCTCAAATGCTC-ATCCTGATTATTGATGAATACAGGAGCACTATGGGAAAACTTTCACAGAATGCTTAATAGGATACGATCAGCTCCTTTTGTTCTAATTTGAAGATTTACTACCAGTGCTGCCAAGAACCACCCTACAGATCATACAAGAACAAAGCAC - -a -s simMouse_chr6.simMouse.chr6 32783 67 + 636262 AGACATATGCTTAGGGCACTTCCAGGCTATGGCAATCTCTTTCTGTGGTAATTTGAAGCTTCACTAC -s Anc0.Anc0refChr9 9715 4 + 35212 ---------------------------------------------------------------CTCT -s Anc1.Anc1refChr2 133712 4 - 144309 ---------------------------------------------------------------CTCT -s Anc2.Anc2refChr0 29009 4 - 56053 ---------------------------------------------------------------CTCT -s mr.mrrefChr0 30848 67 + 130230 AGACATATGCTTAGGGCACTTCCAGGCTATGGCAATCTCTTTCTGTGGTAATTTGAAGCTTCACTAC -s simCow_chr6.simCow.chr6 570956 4 - 602619 ---------------------------------------------------------------CTCT -s simDog_chr6.simDog.chr6 566456 4 - 593897 ---------------------------------------------------------------CTCT -s simHuman_chr6.simHuman.chr6 572959 4 - 601863 ---------------------------------------------------------------CTCT -s simRat_chr6.simRat.chr6 25038 62 + 647215 AGAAATATGCCTAGGGCACTTCCAGGCTATGACAATCTCTTTCTGTGGGGACTTGAAGCT-----AC - -a -s simMouse_chr6.simMouse.chr6 32850 7 + 636262 CAGTGCT -s Anc0.Anc0refChr9 9719 7 + 35212 TGGAGCT -s Anc1.Anc1refChr2 133716 7 - 144309 TGGAGCT -s Anc2.Anc2refChr0 29015 7 - 56053 TGAAGCT -s mr.mrrefChr0 30915 7 + 130230 CAGTGCT -s simCow_chr6.simCow.chr6 570962 7 - 602619 TGAAGTT -s simDog_chr6.simDog.chr6 566462 7 - 593897 TAAAGCT -s simHuman_chr6.simHuman.chr6 572963 7 - 601863 TGGAGCT -s simRat_chr6.simRat.chr6 25100 7 + 647215 CAGTGGT - -a -s simMouse_chr6.simMouse.chr6 32857 26 + 636262 ACTTAATTACTACTCTCTGAATAACC -s Anc0.Anc0refChr9 9726 25 + 35212 ATTTAGTT-CTACTCTATGGATAATA -s Anc1.Anc1refChr2 133723 25 - 144309 ATTTAGTT-CTACTCTATGGATAATA -s Anc2.Anc2refChr0 29022 25 - 56053 ATTTGGTT-CTACTCTATAGATAATA -s mr.mrrefChr0 30922 26 + 130230 ATTTAATTACTACTCTATGAATAACC -s simCow_chr6.simCow.chr6 570969 25 - 602619 ATTTGGTG-CTGCTCTCTAGATACTA -s simDog_chr6.simDog.chr6 566469 23 - 593897 ACT--GCT-CTACTCCATAGATGATA -s simHuman_chr6.simHuman.chr6 572970 25 - 601863 ATTTAGTT-CTATTCTATGGATAATA -s simRat_chr6.simRat.chr6 25114 26 + 647215 GTTTAATTACTACTCTATGAATAACC - -a -s simMouse_chr6.simMouse.chr6 32883 25 + 636262 AAGAGCTAAGCGCTCTTATGCTGAC -s Anc0.Anc0refChr9 9752 22 + 35212 AAGAACAAAGCACTC---ATTCTTC -s Anc1.Anc1refChr2 133749 25 - 144309 AAGAACAAAGCACTCTAAATTCTTC -s Anc2.Anc2refChr0 29048 22 - 56053 AGGAACAAAGTACTC---ATTCTTC -s mr.mrrefChr0 30949 25 + 130230 AAGAGCTAAGCGCTCTTAAGTTTAC -s simCow_chr6.simCow.chr6 570995 22 - 602619 GGGAACCAAGTACCC---ATTCTTC -s simDog_chr6.simDog.chr6 566493 22 - 593897 AGGAACAAAGTACTC---ATCCTAC -s simHuman_chr6.simHuman.chr6 572996 23 - 601863 AAGAACAAAGC--TCTAAATTCTTC -s simRat_chr6.simRat.chr6 25141 25 + 647215 AAGAGCTAAGCACTCTCAAGTTTAC - -a -s simMouse_chr6.simMouse.chr6 32908 9 + 636262 TCCAGTCAT -s Anc0.Anc0refChr9 9777 9 + 35212 TCCGGTTAT -s Anc1.Anc1refChr2 133777 9 - 144309 TCCGGTTAT -s Anc2.Anc2refChr0 29073 9 - 56053 TCTGGTTAT -s mr.mrrefChr0 30974 9 + 130230 TCCAGTCAT -s simCow_chr6.simCow.chr6 571020 9 - 602619 TCTAGTTCT -s simDog_chr6.simDog.chr6 566518 9 - 593897 TCTGGTTAC -s simHuman_chr6.simHuman.chr6 573022 9 - 601863 TCCGGTTAT -s simRat_chr6.simRat.chr6 25166 9 + 647215 TTCATTCCT - -a -s simMouse_chr6.simMouse.chr6 32917 16 + 636262 ATTATTAAAGGCAATT -s Anc0.Anc0refChr9 9791 16 + 35212 ATCTTTATAGGCAATT -s Anc1.Anc1refChr2 133791 16 - 144309 ATCTTTATAGGCAATT -s Anc2.Anc2refChr0 29087 16 - 56053 ATCTTTATAAGCAATT -s mr.mrrefChr0 30983 16 + 130230 ATCATTAAAGGCAATT -s simCow_chr6.simCow.chr6 571034 12 - 602619 G----TATGAGCAATT -s simDog_chr6.simDog.chr6 566532 16 - 593897 ATCTTTTTAAGCAATT -s simHuman_chr6.simHuman.chr6 573036 16 - 601863 ATCTTTATAGGCAATT -s simRat_chr6.simRat.chr6 25175 16 + 647215 GTCATTAAAGGCAATT - -a -s simMouse_chr6.simMouse.chr6 32933 1 + 636262 C -s Anc0.Anc0refChr9 9807 1 + 35212 C -s Anc1.Anc1refChr2 133807 1 - 144309 C -s Anc2.Anc2refChr0 29104 1 - 56053 C -s mr.mrrefChr0 30999 1 + 130230 C -s simCow_chr6.simCow.chr6 571047 1 - 602619 C -s simDog_chr6.simDog.chr6 566549 1 - 593897 C -s simHuman_chr6.simHuman.chr6 573052 1 - 601863 C -s simRat_chr6.simRat.chr6 25191 1 + 647215 C - -a -s simMouse_chr6.simMouse.chr6 32934 12 + 636262 CAAGACTAAGTC -s Anc0.Anc0refChr9 9831 11 + 35212 CA-GACTAAGTT -s Anc1.Anc1refChr2 133831 11 - 144309 CA-GACTAAGTT -s Anc2.Anc2refChr0 29130 11 - 56053 CA-GGCTGAGCT -s mr.mrrefChr0 31000 11 + 130230 CA-GACTAAGTC -s simDog_chr6.simDog.chr6 566576 11 - 593897 CA-GGCTGAGCT -s simHuman_chr6.simHuman.chr6 573076 11 - 601863 CA-AAATAAGTT -s simRat_chr6.simRat.chr6 25192 11 + 647215 CA-GACTAAGTC - -a -s simMouse_chr6.simMouse.chr6 32946 61 + 636262 ACAACACAAATTTGAACCAGGTGGGGTAGAAGGAACCCTTTGTTAATTGTCTGATATTGTG -s Anc0.Anc0refChr9 9842 48 + 35212 AGCAGACTGATTT--ACAATGTGAGGT-----------TTTGTTGATTGTTCCATTTTGTG -s Anc1.Anc1refChr2 133842 48 - 144309 AGCAGACTGATTT--ACAATGTGAGGT-----------TTTGTTGATTGTTCCATTTTGTG -s Anc2.Anc2refChr0 29141 48 - 56053 AGCAGACTGAGTT--ACAATATGAGGC-----------TTTGTTGATTGTTCCATTTTGTG -s mr.mrrefChr0 31011 61 + 130230 ACAACACAAATTTGAACAAGGTGGGGTACAAGGGACCTTTTGTTAATTGTCTGATATTGTG -s simCow_chr6.simCow.chr6 571069 46 - 602619 -GCACATTGAGTT--ACAATATGAGAA-----------TTTGTT-ATTGTTCCATGTTGTG -s simDog_chr6.simDog.chr6 566654 48 - 593897 AACAGACTGAGCT--GCAATATGACGC-----------TTTGTTGATTGTTCCATTTTGTG -s simHuman_chr6.simHuman.chr6 573087 48 - 601863 AGCAAAGTGATTC--ACAAAGTGAGGT-----------TTTGTTGGTTGCTCAATTTTGTG -s simRat_chr6.simRat.chr6 25203 61 + 647215 ACAACATCAACTTGCACAGGGTGGCATACAAGGGACCTTTTGTTACTTGTCTGATATTGTG - -a -s simMouse_chr6.simMouse.chr6 33007 13 + 636262 GCATTATTTATAT -s Anc0.Anc0refChr9 9891 13 + 35212 GGATTACTCATAT -s Anc1.Anc1refChr2 133891 13 - 144309 GGATTACTCATAT -s Anc2.Anc2refChr0 29190 13 - 56053 GGATTACTCATAT -s mr.mrrefChr0 31073 13 + 130230 GGATTATTTATAT -s simCow_chr6.simCow.chr6 571116 13 - 602619 AGACTACTCAAAC -s simDog_chr6.simDog.chr6 566702 13 - 593897 GGATTACTCATAT -s simHuman_chr6.simHuman.chr6 573136 13 - 601863 GGATTACTCATAA -s simRat_chr6.simRat.chr6 25265 13 + 647215 GGGTTATCTGAAT - -a -s simMouse_chr6.simMouse.chr6 33020 32 + 636262 TCTCACATCGTTACTGCTGCCCAATTGCATAC -s Anc0.Anc0refChr9 9906 32 + 35212 TCTTACATGGTCCTTGCTGCCCAGTCACATAC -s Anc1.Anc1refChr2 133906 32 - 144309 TCTTACATGGTCCTTGCTGCCCAGTCACATAC -s Anc2.Anc2refChr0 29205 32 - 56053 TCTTACATGATCCTTGCTACCCAGTCACATAT -s mr.mrrefChr0 31088 32 + 130230 TCTTACATCGTTCCTGCTGCCCAATTGCATAC -s simCow_chr6.simCow.chr6 571140 32 - 602619 TCTTAAATCAATTTTGCTACCCAGTCACATAT -s simDog_chr6.simDog.chr6 566717 32 - 593897 TCTTACATGATCCATGCTACCCAGTCACATAT -s simHuman_chr6.simHuman.chr6 573151 31 - 601863 TCTTACATTGC-CTTGCTGCCCAGTCACATAC -s simRat_chr6.simRat.chr6 25280 32 + 647215 TCTTACATCATTCCGGCTGCCCAATTGCATAT - -a -s simMouse_chr6.simMouse.chr6 33052 96 + 636262 CTTTCAGCATAGCAGTCCTTGCCCACCACTCACATCCAAACACACTGGGGCATATATAAATGTAAACTGCACTCCACCAAACTAGAAGAGAAATGA -s Anc0.Anc0refChr9 9938 70 + 35212 CTTACATTGTAGTAGCCCTTGCTCCCCAGTCACATACAAACTTACTGGGGCATATACAACTGGAAACTAC-------------------------- -s Anc1.Anc1refChr2 133938 96 - 144309 CTTACATTGTAGTAGCCCTTGCTCCCCAGTCACATACAAACTTACTGGGGCATATACAACTGGAAACTACAATCCACCTAACTAAAAGAGTGATAT -s Anc2.Anc2refChr0 29237 70 - 56053 CTTACATTGTAGTAGCCCTTGCTACCCAGTCACATATAAACTTGCTGGGGCAGATACAACTGGAAACTAC-------------------------- -s mr.mrrefChr0 31120 96 + 130230 CTTTCAGCATAGTAGTCCTTGCTCCCCACTCACATACAAACACACTGGGGCATATATAAATGTAAACTACACTCCACCAAACTAGAAGAGTAATGA -s simCow_chr6.simCow.chr6 571172 56 - 602619 ATTACATCATGGTACCC--TGCGAC------------AAACTAGCTGGGGCAGATACAAGTGGAAAGTAC-------------------------- -s simDog_chr6.simDog.chr6 566749 65 - 593897 CGTACGTTGTAGTAGCCCTTGCTACCCAGTCACATATAAACTTGCTGGGGC-----CAACTGGAAACTAC-------------------------- -s simHuman_chr6.simHuman.chr6 573234 96 - 601863 CTTACATTGTAGTAGCCCTTGCTCCTCAGTAACATACAAACTTACTGGGGCATATACACCTGGAAACTACAATCCACCTAACTAAAAGAGTGATAT -s simRat_chr6.simRat.chr6 25312 86 + 647215 CTTTCAGCATAGTAGTCCCTATTCCCCACTCA-ATACAAACACACTGGGGCATTTAT---------TTACATTCCACCAATCTAGAAGAGTAATGC - -a -s simMouse_chr6.simMouse.chr6 33148 54 + 636262 CTCCACCTTTGATGGGAGCAACTCTACATATGTATGGTATTGCCTATAAGCTAG -s Anc0.Anc0refChr9 10008 45 + 35212 ---------CAAGGGGAACTGATAAACAGATGTATGGTAATCCTTATATGTCAG -s Anc1.Anc1refChr2 134039 54 - 144309 CCCCAGTCTCAAGGGGAACTGATAAACAGATGTATGGTAATCCTTATATGTCAG -s Anc2.Anc2refChr0 29307 45 - 56053 ---------CAAGGGGAACTGATAAACAGATGTATGGTAATCCTTATATGTCAG -s mr.mrrefChr0 31221 54 + 130230 CTCCACCTTCAATGGGAGCAACTCTACATATGTATGGTATTGCCTATATGCTAG -s simCow_chr6.simCow.chr6 571228 44 - 602619 ---------CAAGGGGAGCTGATAGACAGATGTAT-GTAATCTTTACATGTCTG -s simDog_chr6.simDog.chr6 566814 45 - 593897 ---------CAAAAGGAACCGATAAACAGATGTATGGTACTTCTTCTATGTCAG -s simHuman_chr6.simHuman.chr6 573335 54 - 601863 CCCCAGTCTCAAGGTGAACTGGTAAACAGATACATGGCAAACCTTATATGTCAG -s simRat_chr6.simRat.chr6 25403 54 + 647215 CTCCACCTTCACTGGGAGCAAATCTACATGTGTATGGTATTGCCTATATGCTCT - -a -s simMouse_chr6.simMouse.chr6 33202 63 + 636262 CCACACTACCTCAAAGCCAGGGCGAACTGGTTGTATGAAAGCTTCCTTTTAGTTTCAAGGACT -s Anc0.Anc0refChr9 10089 56 + 35212 -------TCCCCAAAGCAAGGGAGAACTCAGTGCATTCAATCCCCATTTTAGTTTCATAGTCC -s Anc1.Anc1refChr2 134133 63 - 144309 CAATGCATCCCCAAAGCAAGGGAGAACTCAGTGCATTCAATCCCCATTTTAGTTTCATAGTCC -s Anc2.Anc2refChr0 29388 56 - 56053 -------TCCCCAAAACAAGGGAGAACTCAGTACATTCAATCACCATTTTTGTTTCATAGTGC -s mr.mrrefChr0 31275 63 + 130230 CCACACTACCCCAAAGCAAGGGCGAACTGGTTGTATGAAAGCCTCCTTTTAGTTTCAAGGACT -s simCow_chr6.simCow.chr6 571308 56 - 602619 -------TCCCCAGACCAAGGTATAACACAGCAGGTTCGATCTTCATTTTGGTTTCATAATGC -s simDog_chr6.simDog.chr6 566895 56 - 593897 -------TTCCCAAAACAAGGGAGACTTCAGTACATTCAATCACCTTTTTTGTCTCATAGTGC -s simHuman_chr6.simHuman.chr6 573429 63 - 601863 CAATGCATCCCCAAAGCAAGGGACGACTCAGTGCAATCAATCCCTATTTTAGTTTCATAGTCC -s simRat_chr6.simRat.chr6 25457 61 + 647215 CCACACTGCCCCAAAGTAAGGGCTAACTTGTTGTACGAAAGCCTCCTTTTAGTT--GAGGACT - -a -s simMouse_chr6.simMouse.chr6 33265 1 + 636262 G -s Anc0.Anc0refChr9 10145 1 + 35212 A -s Anc1.Anc1refChr2 134196 1 - 144309 A -s Anc2.Anc2refChr0 29449 1 - 56053 A -s mr.mrrefChr0 31338 1 + 130230 G -s simCow_chr6.simCow.chr6 571369 1 - 602619 G -s simDog_chr6.simDog.chr6 566956 1 - 593897 A -s simHuman_chr6.simHuman.chr6 573492 1 - 601863 A -s simRat_chr6.simRat.chr6 25518 1 + 647215 G - -a -s simMouse_chr6.simMouse.chr6 33266 1 + 636262 A -s Anc0.Anc0refChr9 10150 1 + 35212 A -s Anc1.Anc1refChr2 134201 1 - 144309 A -s Anc2.Anc2refChr0 29454 1 - 56053 A -s mr.mrrefChr0 31339 1 + 130230 A -s simCow_chr6.simCow.chr6 571374 1 - 602619 A -s simDog_chr6.simDog.chr6 566961 1 - 593897 C -s simHuman_chr6.simHuman.chr6 573497 1 - 601863 A -s simRat_chr6.simRat.chr6 25519 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 33267 9 + 636262 CAAACATTA -s Anc0.Anc0refChr9 10151 9 + 35212 AAAACATTA -s Anc1.Anc1refChr2 134202 9 - 144309 AAAACATTA -s Anc2.Anc2refChr0 29455 9 - 56053 AAGAGATTA -s mr.mrrefChr0 31340 9 + 130230 CAAACATTA -s simCow_chr6.simCow.chr6 571375 9 - 602619 AAGAGGTCA -s simDog_chr6.simDog.chr6 566962 9 - 593897 AAGAGATTT -s simHuman_chr6.simHuman.chr6 573498 9 - 601863 AAAACATTA -s simRat_chr6.simRat.chr6 25521 9 + 647215 CAAACCTTA - -a -s simMouse_chr6.simMouse.chr6 33276 118 + 636262 AGTATAAGGGAGTCATTCTGCATTCTATGTACAGGTATGTCTATGCACCTAAGTGTACATAGCTGGGTTGCTCCAATATAGTAGTCTACCGTTACTCCAATATATCAGTTTATTAAAT -s Anc0.Anc0refChr9 10161 34 + 35212 AGTAAAAGGAAATAATTGTGATTTCTTTGTACAT------------------------------------------------------------------------------------ -s Anc1.Anc1refChr2 134212 94 - 144309 AGTAAAAGGAAATAATTGTGATTTCTTTGTACATGTCTGGTTATTACCTTAAGTGTAGATGGCAGGGCTACTTAAAAGCAGC------------------------ATTGTAACAAAG -s Anc2.Anc2refChr0 29465 34 - 56053 AGCAAGAGGAAATAACTGTGATTTCTTTGTACAT------------------------------------------------------------------------------------ -s mr.mrrefChr0 31349 116 + 130230 AGTAAAAGGGAGTCATTCTGCATTCTATGTACATGTATGTCTATGCACCTAAGTGTACATAGCTGGGCTGCTCCAATATAGC--TCTACCGTTACTCCAATATATCAGTTTATCAAAT -s simCow_chr6.simCow.chr6 571385 34 - 602619 AAAAAGCAGAAATAACTGTGGTTTCTTTGCACAT------------------------------------------------------------------------------------ -s simDog_chr6.simDog.chr6 566972 34 - 593897 GGCAAGAGCAAATATCTGTAATTTCGTTGTACCT------------------------------------------------------------------------------------ -s simHuman_chr6.simHuman.chr6 573508 94 - 601863 AGTAAAAGGAAATAATTGTGTTTTCTTAGTTCATGTCTGGTTATTACCTTAAGTGTAGATGGCAGGGCTACTTAAAAGCAGC------------------------ATTGTAACAAAG -s simRat_chr6.simRat.chr6 25530 111 + 647215 AGCAAAAG-----CACTTTGCATCCTCTCTACATGTATGAATCTGCACCTAGGTGTACATAGCTGGGCTGCTCCAATATAGC--TCTACCGTTACTCCAATATATCAGTATATCAAAT - -a -s simMouse_chr6.simMouse.chr6 33394 20 + 636262 CATGCAAAGTGAAATAACAC -s Anc0.Anc0refChr9 10195 1 + 35212 -------------------G -s Anc1.Anc1refChr2 134306 20 - 144309 CATGCATTGTGAAGTCACAG -s Anc2.Anc2refChr0 29499 1 - 56053 -------------------G -s mr.mrrefChr0 31465 20 + 130230 CATGCAAAGTGAAATAACAC -s simCow_chr6.simCow.chr6 571419 1 - 602619 -------------------G -s simDog_chr6.simDog.chr6 567006 1 - 593897 -------------------G -s simHuman_chr6.simHuman.chr6 573602 20 - 601863 CATGCATTGTGAAGTCACAG -s simRat_chr6.simRat.chr6 25643 4 + 647215 CATG---------------- - -a -s simMouse_chr6.simMouse.chr6 33414 34 + 636262 TAAATAGCTGGGTGATTTTCTCAAGACCTAGGGA -s Anc0.Anc0refChr9 10197 34 + 35212 TAAATTGTTGGATCTTTTTCTCAACACCTAGGGA -s Anc1.Anc1refChr2 134327 34 - 144309 TAAATTGTTGGATCTTTTTCTCAACACCTAGGGA -s Anc2.Anc2refChr0 29501 34 - 56053 TAAATTGTTGGATCTTTTTCTCAACACCTATGGA -s mr.mrrefChr0 31485 34 + 130230 TAAATTGCTGGGTGATTTTCTCAAGACCTAGGGA -s simCow_chr6.simCow.chr6 571421 34 - 602619 TAAATTGGTGTATCTTTTTCTGAACAGGTATGGA -s simDog_chr6.simDog.chr6 567008 34 - 593897 TAAATTGTTGGATCTATTTTTCAGCACCTGTGGA -s simHuman_chr6.simHuman.chr6 573625 34 - 601863 TAAATTGTTGGATCCTTTTCTCAACACCTAGGGA -s simRat_chr6.simRat.chr6 25647 34 + 647215 TAAATTGCTGGGTGATTATCGCCAAACCTAAGGA - -a -s simMouse_chr6.simMouse.chr6 33448 6 + 636262 GTCAAG -s Anc0.Anc0refChr9 10241 6 + 35212 GTCAAG -s Anc1.Anc1refChr2 134371 6 - 144309 GTCAAG -s Anc2.Anc2refChr0 29545 6 - 56053 CCCAAG -s mr.mrrefChr0 31519 6 + 130230 GTCAAG -s simCow_chr6.simCow.chr6 571460 6 - 602619 CGCAAA -s simDog_chr6.simDog.chr6 567052 6 - 593897 CCCAAG -s simHuman_chr6.simHuman.chr6 573669 6 - 601863 GTCAGC -s simRat_chr6.simRat.chr6 25681 6 + 647215 GTTGAG - -a -s simMouse_chr6.simMouse.chr6 33454 46 + 636262 AGTAAGCACATTGTGTTTATTTGTAGAGTTCTAAGCCCTAAGTTTA -s Anc0.Anc0refChr9 10247 46 + 35212 AGGGAGCGCATTGTATTTTTTAGTGGGGTTCTAAGCTCTGAGCTTA -s Anc1.Anc1refChr2 134377 46 - 144309 AGGGAGCGCATTGTATTTTTTAGTGGGGTTCTAAGCTCTGAGCTTA -s Anc2.Anc2refChr0 29552 46 - 56053 CAGGAGAACATTGTATTTTTTAGTGGGGTTCTAAGCTCTAAGCTTA -s mr.mrrefChr0 31525 46 + 130230 AGTAAGCGCATTGTGTTTATTTGTAGAGTTCTAAGCCCTGAGTTTA -s simCow_chr6.simCow.chr6 571467 45 - 602619 CAGGAGATTGTTGTATTTTTATAT-GGTTTCTATGCTCTAACATTA -s simDog_chr6.simDog.chr6 567059 46 - 593897 CAGAGGAACACTATATTTTTTAGTGGAGTTCCGAGCTCTAAGCTTA -s simHuman_chr6.simHuman.chr6 573675 45 - 601863 AGGGAGCGCATTGTATTTTTTGGTGGGGCTCTAAGCTCTGGGCTT- -s simRat_chr6.simRat.chr6 25687 44 + 647215 AG--ATCGCATTATGTTTCTTTGTAGAGTTCTAAGCCCTGACTTTA - -a -s simMouse_chr6.simMouse.chr6 33500 64 + 636262 CTCTGGTTTCCTTACTTTCTAATGTAACCAGTATGAATCCCCTTAGGTCTCCCCCCTTTTCTTT -s Anc0.Anc0refChr9 10293 58 + 35212 TTTTGATTTCCTTACTTTCTAATCTAACCCCCATTAACCTCCTTAGTTATCTCCC-TTC----- -s Anc1.Anc1refChr2 134423 58 - 144309 TTTTGATTTCCTTACTTTCTAATCTAACCCCCATTAACCTCCTTAGTTATCTCCC-TTC----- -s Anc2.Anc2refChr0 29601 58 - 56053 TTTTGATTTCCTTACTTTCTAGTCTAATTCCCATTAACCTCCTTAGTTATCTCCC-TTC----- -s mr.mrrefChr0 31571 63 + 130230 CTCTGATTTCCTTACTTTCTAATCTAACCAGCATGAATCCCCTTAGGTCTCTCCC-TTTTCTTT -s simCow_chr6.simCow.chr6 571515 56 - 602619 TTTTGACTTCCTTAGTCTCTAGTCTAA--CTCATTAACCCCCTTAGTTATCTCCC-TTC----- -s simDog_chr6.simDog.chr6 567108 56 - 593897 TTTTGATTTCCCTACTTTCT--TTTAATTCCCATTGACCTCCTTAGATATCTCCC-TTT----- -s simHuman_chr6.simHuman.chr6 573720 57 - 601863 -TTTGATTTCCTTACTTTCTAATCCAACCCCCTTTAACCTGTTTAGTTATCTCCC-TTC----- -s simRat_chr6.simRat.chr6 25731 62 + 647215 CTCTCATTTTCTTACTTTCTAATCTAAC-GGCATGAATCCCCTTAGGTCTCTCCC-TTTTCTTT - -a -s simMouse_chr6.simMouse.chr6 33564 45 + 636262 ATTATCTCGTTATCTTTATTAGCTGCTTCCATTCATCCCAGTTGA -s Anc0.Anc0refChr9 10351 39 + 35212 ATTAT---GTT-TCTTTGTTAACTGCTTTTATTCACCCCAGCT-- -s Anc1.Anc1refChr2 134481 42 - 144309 ATTAT---GTTGTCTTTGTTAACTGCTTTTATTCACCCCAGCTGG -s Anc2.Anc2refChr0 29659 39 - 56053 ATTTT---GTT-TATCTGTTAACTGCTTTTATTCACCCCAGCT-- -s mr.mrrefChr0 31634 45 + 130230 ATTATCTCGTTATCTTTATTAGCTGCTTCCATTCATCCCAGCTGA -s simCow_chr6.simCow.chr6 571587 37 - 602619 CTTTT---GTT-TGTCCTT--GTTGCTTCTATCTGCGTCAACC-- -s simDog_chr6.simDog.chr6 567164 39 - 593897 ATTTT---GAT-TATCTGTTAACTGCTTTTGTTCATCCCAGCT-- -s simHuman_chr6.simHuman.chr6 573777 42 - 601863 ATTAT---GTTGTCTTTGTTAACTGCTTTTATTCACCCCAGCAGG -s simRat_chr6.simRat.chr6 25793 45 + 647215 GTTAACTAGTTATCTTTATTAGGTGGTTCCATTCATCCCAGCTCA - -a -s simMouse_chr6.simMouse.chr6 33609 67 + 636262 TCTGCACAGCTCTTCAACTGGCTTAAGACTCCTACTAACCTATGGGCCAAGAAGTCACTCTAAGACT -s Anc0.Anc0refChr9 10404 64 + 35212 ACTGCACCTCTCCCCGGCTGA---TGGACCTATATTACCCTGTAGATCCAGAGGTCAATCTAAGACT -s Anc1.Anc1refChr2 134537 64 - 144309 ACTGCACCTCTCCCCGGCTGA---TGGACCTATATTACCCTGTAGATCCAGAGGTCAATCTAAGACT -s Anc2.Anc2refChr0 29712 64 - 56053 TCTGAGCCACTCCCCGGCTGA---TGGATCTATATTACCCTGTAGATCCAGAGGTCAATCTAAGACT -s mr.mrrefChr0 31679 67 + 130230 ACTGCACATCTCTTCAACTGACTTAAGACTCCTACTAACCTGTGGGCCCAGAAGTCACTCTAAGACT -s simCow_chr6.simCow.chr6 571635 56 - 602619 -------CCCTCCCCAGCTGA----GGATCTATATTACCCTGTAGATCCAGAGACCAATCTAAGACT -s simDog_chr6.simDog.chr6 567217 42 - 593897 TCTGAGCCAGTCTAAGACTAA---TG-------------CCGTTGTTACTGAGGTCAA--------- -s simHuman_chr6.simHuman.chr6 573842 64 - 601863 ACTGCACCTCTCCCCGGCTGA---GGGACCTATATTACCCTGTAGATCCAGAGGACATTCTAAGATT -s simRat_chr6.simRat.chr6 25838 67 + 647215 ACTGCAAATCTCTTCAACTGACTTAAGATTCCTACTAACCTGCGGGCCCAGAAGCCACTCTAAGACT - -a -s simMouse_chr6.simMouse.chr6 33676 67 + 636262 AGTGAACTTACTATCAGGATTATCCTCAAGACTTAATAACAGGCTCCTTTATATAGCCCTCCAAATG -s Anc0.Anc0refChr9 10468 37 + 35212 ACTGGA------------------------------CAAAGGGCTCCCTTCCATAGCCCTCCATATG -s Anc1.Anc1refChr2 134601 37 - 144309 ACTGGA------------------------------CAAAGGGCTCCCTTCCATAGCCCTCCATATG -s Anc2.Anc2refChr0 29783 37 - 56053 ACTGGC------------------------------CATAGGGCTCCCTTCCATAGCCCTCCATATG -s mr.mrrefChr0 31746 67 + 130230 AGTGAACTTACTATCAGGATTATCCTCAAGACTTAATAACAGGCTCCTTTCCATAGCCCTCCAAATG -s simCow_chr6.simCow.chr6 571705 37 - 602619 ACTGGC------------------------------TATAAGGCCCCCTTCCATTGCCTTTTGTCTG -s simDog_chr6.simDog.chr6 567266 37 - 593897 ACTGGC------------------------------CATAGGGCTCCTTTCCATAGTCCTCCATATA -s simHuman_chr6.simHuman.chr6 573906 37 - 601863 ATTGGA------------------------------CAAAGGGCTCTCTTCCATAGCCCTACATGCG -s simRat_chr6.simRat.chr6 25905 62 + 647215 AGTGAATTTATTACCAGGATTATCCTCAAGGCTGAATAACAGGCTCCTTTCCAT-GCCCTCCA---- - -a -s simMouse_chr6.simMouse.chr6 33743 37 + 636262 GCTATTGGTGATGAACTACTGCCCAACCAGACCAAGA -s Anc0.Anc0refChr9 10509 32 + 35212 GCCA-----GATGAACTACTGCTGAATCAGATCAATA -s Anc1.Anc1refChr2 134642 32 - 144309 GCCA-----GATGAACTACTGCTGAATCAGATCAATA -s Anc2.Anc2refChr0 29826 32 - 56053 GCCA-----GATGAACTATTGCTGAATCAGATCAATA -s mr.mrrefChr0 31813 32 + 130230 GCTA-----GATGAACTACTGCCCAACCAGATCAAGA -s simCow_chr6.simCow.chr6 571748 32 - 602619 GTCA-----GACGAGTTATTGTTGAATCAAATCATTA -s simDog_chr6.simDog.chr6 567309 32 - 593897 ACCA-----GATGAACTATTACTGAATCAGATCAATA -s simHuman_chr6.simHuman.chr6 573947 32 - 601863 GCCA-----GGTGACCTACTGCTAAGTCAGATCAGTA -s simRat_chr6.simRat.chr6 25967 11 + 647215 --------------------------CCTGATCAAGA - -a -s simMouse_chr6.simMouse.chr6 33780 11 + 636262 CTCCTGGAGAA -s Anc0.Anc0refChr9 10541 11 + 35212 CTCAGACTCAG -s Anc1.Anc1refChr2 134674 11 - 144309 CTCAGACTCAG -s Anc2.Anc2refChr0 29862 11 - 56053 CTCAGACTCAG -s mr.mrrefChr0 31845 11 + 130230 CTCCTAGTGAA -s simCow_chr6.simCow.chr6 571867 11 - 602619 TTCAGACTCAA -s simDog_chr6.simDog.chr6 567345 11 - 593897 CTCAGACTCAG -s simHuman_chr6.simHuman.chr6 573979 11 - 601863 CTCAGACTCAG -s simRat_chr6.simRat.chr6 25978 11 + 647215 CTCCCAATGGC - -a -s simMouse_chr6.simMouse.chr6 33791 45 + 636262 ACCTTGCCTATCATCCCAGTAGGGTTGCTGAAGACACCACCATGA -s Anc0.Anc0refChr9 10552 45 + 35212 GCCTTGCCTCTCATTTCAGCAGGTTTGCTGAAGACACCACCACAA -s Anc1.Anc1refChr2 134685 45 - 144309 GCCTTGCCTCTCATTTCAGCAGGTTTGCTGAAGACACCACCACAA -s Anc2.Anc2refChr0 29873 45 - 56053 GCATTGCCTTTCATTTCAGCAGATTTGCTGAAGACACCACCACAA -s mr.mrrefChr0 31856 45 + 130230 ACCTTGCCTCTCATCTCAGTAGGGTTGCTGAAGACACCACCACAA -s simCow_chr6.simCow.chr6 571879 45 - 602619 GTGTCGCCATTCATTTCAGCAGATTTGCTGACAAAACCACCTCTA -s simDog_chr6.simDog.chr6 567356 45 - 593897 CCATTGCCTTTCATTTCAGCAGATTTGCTGAAGACACCACTACAA -s simHuman_chr6.simHuman.chr6 573990 44 - 601863 GCCTTGCA-CTGATTTCAGCAGGTCTGCTATGGACACCACCACAA -s simRat_chr6.simRat.chr6 25989 44 + 647215 ACCTTGCCTCTTATCTCTGT-GGGTTGTTGAAAACACTACCACAA - -a -s simMouse_chr6.simMouse.chr6 33836 13 + 636262 GTGTTACTATAGT -s Anc0.Anc0refChr9 10597 13 + 35212 GTGATACTGTAGT -s Anc1.Anc1refChr2 134730 13 - 144309 GTGATACTGTAGT -s Anc2.Anc2refChr0 29918 13 - 56053 TTGATACTGTAGT -s mr.mrrefChr0 31901 13 + 130230 GTGATACTATAGT -s simCow_chr6.simCow.chr6 571924 13 - 602619 ACAATACTGTAGT -s simDog_chr6.simDog.chr6 567401 13 - 593897 TTGGTACTGTAGT -s simHuman_chr6.simHuman.chr6 574036 13 - 601863 GTGATACTGTAGT -s simRat_chr6.simRat.chr6 26033 13 + 647215 GTGATACTCTAGT - -a -s simMouse_chr6.simMouse.chr6 33849 82 + 636262 TATTGCAGATGTATTTTTAGATATGAACTGCTTTGAGTTTTTGAATCTGGACTACTAGACCCTTCTTTAGCGCTTCATGCAA -s Anc0.Anc0refChr9 10612 64 + 35212 TTTTG-ATATGTACTT-------T--CCTGCTATGA--------ATCTGGACTGCTAGACCCTTTTTAAGTGCTTTATGCAT -s Anc1.Anc1refChr2 134745 71 - 144309 TTTTG-ATATGTACTTTCAGATCT--CCTGCTATGA--------ATCTGGACTGCTAGACCCTTTTTAAGTGCTTTATGCAT -s Anc2.Anc2refChr0 29933 64 - 56053 TTTTG-ATATATACTT-------T--CCTGCTATGA--------ATCTGGACTGCTAGACCCTTTTTAAGTTCTTTATGCAT -s mr.mrrefChr0 31914 73 + 130230 TATTG-AGATGTACTTTCAGATATGAACTGCTTTGA--------ATCTGGACTACTAGACCCTTCTTTAGTGCTTCATGCAA -s simCow_chr6.simCow.chr6 571939 64 - 602619 TTTTG-ACATATATTT-------T--CCCGCTATGA--------ACCTGGAGTGCTAAACCCTTATTAAGTTGTTTATGCAT -s simDog_chr6.simDog.chr6 567416 64 - 593897 TTTAG-ATTTATACTT-------T--CCTGCTATGA--------ATCGGAACTGCTAGACCTCTTTTAAGTTCTTTATGCAT -s simHuman_chr6.simHuman.chr6 574051 71 - 601863 TTTTG-ATATGTACTTTCAGATCT--CCTGCTATGA--------ATCTAGACTGTGAGCCCCTTTTAAACTGCTTTACGCAT -s simRat_chr6.simRat.chr6 26046 66 + 647215 TATTA-AGCCGTACTTTCCGATATGAAGTACTTTGG---------------CTACTACACCCTTCTTTAGTGCTTCatggac - -a -s simMouse_chr6.simMouse.chr6 33931 41 + 636262 GTACATTCACTATGATTAGCCTTAGGCTCTCATACATTGAG -s Anc0.Anc0refChr9 10676 41 + 35212 GTACAGTCACTGTGATAAGCCTGAATCATTCATACATTGAA -s Anc1.Anc1refChr2 134816 41 - 144309 GTACAGTCACTGTGATAAGCCTGAATCATTCATACATTGAA -s Anc2.Anc2refChr0 29997 41 - 56053 GTACAGTCATTGTGCTAAGCCTGAATCATTCATACATTGGA -s mr.mrrefChr0 31987 41 + 130230 GTACATTCACTGTGATTAGCCTTAGGCTCTCATACATTGAG -s simCow_chr6.simCow.chr6 572003 41 - 602619 GTACAGTGATTATGCTATGCCTGAGCAATTTATACATTAGA -s simDog_chr6.simDog.chr6 567480 41 - 593897 GTACAGTCGTTGTGCAAAGCCTGAATCATTCATACACTGGA -s simHuman_chr6.simHuman.chr6 574122 41 - 601863 GTATACGCACTGCAATAAACCCGGCATCTTCATACATTCAA -s simRat_chr6.simRat.chr6 156489 41 + 647215 GTACATTCACTGTGTTTAGCTTTAGGCTCTCATACATTGAG - -a -s simMouse_chr6.simMouse.chr6 33972 65 + 636262 TGGTGGCACCCAGCTCGTTGAACATGATAACCTATGACACATTTCACCCTGTGAGATAGTGGTAT -s Anc0.Anc0refChr9 10718 65 + 35212 TAGTGCCACGCAACTGGGCAAAAGTGATCACCCATGACCCATTTTATTCTTTGAGATAGTGGAAT -s Anc1.Anc1refChr2 134858 65 - 144309 TAGTGCCACGCAACTGGGCAAAAGTGATCACCCATGACCCATTTTATTCTTTGAGATAGTGGAAT -s Anc2.Anc2refChr0 30039 65 - 56053 CAGTGCCATGCAACTGGGCAAAAGTAATCACCCACAACCCATTTTGTTCTTTGACATAGTGGAAT -s mr.mrrefChr0 32028 65 + 130230 TGGTGGCACCCAGCTGGTTGAACATGATCACCTATGACACATTTCACTCTGTGAGATAGTGGTAT -s simCow_chr6.simCow.chr6 572045 65 - 602619 CATCGCGATGCAACTGGACAAAAATAATGACCCACAACCCATTTTCGTCTTTGACATAGTGGAAT -s simDog_chr6.simDog.chr6 567522 60 - 593897 CGGTGCCTTGCAACTGGGCAAAAGTAATCACTCACAACCCATTTTGTTCTTTG-----GTAGAAT -s simHuman_chr6.simHuman.chr6 574164 65 - 601863 TAGTGCCACACAACTGGGCAAAAGTGATCATCCATGACCCATTTGATTTTTTGAGATAGTGGAAT -s simRat_chr6.simRat.chr6 156530 65 + 647215 TGGTGGCACCCAGCTGGTTGAACATGGTCACCTATGACACATTTAACTCTGTGAGATAGTGGTAT - -a -s simMouse_chr6.simMouse.chr6 34037 60 + 636262 GACATATCACAGGGGCTGGCTTGGGAGTCAATGTGGCTCCTTGTCCCGCAGATCAAGCAC -s Anc0.Anc0refChr9 10787 20 + 35212 GACATCTC--AGGGTATAGATG-------------------------------------- -s Anc1.Anc1refChr2 134927 20 - 144309 GACATCTC--AGGGTATAGATG-------------------------------------- -s Anc2.Anc2refChr0 30108 20 - 56053 GACATCTC--AGGGTATAGATG-------------------------------------- -s mr.mrrefChr0 32093 52 + 130230 GACATATCACAGGGGCTGGCTTGGGAGTCAATGTGGCTCCTTGTCCCGCAGA-------- -s simCow_chr6.simCow.chr6 572114 20 - 602619 AACATTTC--AGGGTGTAGATG-------------------------------------- -s simDog_chr6.simDog.chr6 567586 20 - 593897 GACAGCTC--AGGGTATAGACA-------------------------------------- -s simHuman_chr6.simHuman.chr6 574233 20 - 601863 GACATCTC--AGGGTATAGATG-------------------------------------- -s simRat_chr6.simRat.chr6 156595 48 + 647215 GAC----CACAGAGGCTAACCAGGGAGTCAATCTGGCTCCTTGTCCAGCAGA-------- - -a -s simMouse_chr6.simMouse.chr6 34097 49 + 636262 TAGGGGAGTAGCAAACAGTTTTAACGTATGGACACTAATCAGCCACTCA -s mr.mrrefChr0 32145 45 + 130230 taggggagtagcaa----ttttaacgtatggacactaatcagccactCA -s simRat_chr6.simRat.chr6 26198 45 + 647215 taggggggtaggaa----ttttgatgtctggacactaatcaggtgctCA - -a -s simMouse_chr6.simMouse.chr6 34146 9 + 636262 AATAGTTCA -s mr.mrrefChr0 32190 9 + 130230 AATAGTTCA -s simRat_chr6.simRat.chr6 26244 9 + 647215 AATAGTTTA - -a -s simMouse_chr6.simMouse.chr6 34155 27 + 636262 GGATTTGCAATCCAGTTGAGTGCTATT -s mr.mrrefChr0 32199 27 + 130230 GGATTTGCAATCCAGTTGAGTGCTATT -s simRat_chr6.simRat.chr6 26254 27 + 647215 GGATTTGCAACCCAGCTGAGTACTATT - -a -s simMouse_chr6.simMouse.chr6 34182 78 + 636262 AAACTTGTCTTGTCTCATGAGTCCCGTTGCAGAATTTTTCCATGACAGAGTAAATATCTACATTTTGTTATATCTAGA -s Anc0.Anc0refChr9 10807 53 + 35212 ---------CACCCTCATGTGTTCCCTTGTATAAATTTTCCATGACGGAGTGACTTTTTAT----------------A -s Anc1.Anc1refChr2 134947 53 - 144309 ---------CACCCTCATGTGTTCCCTTGTATAAATTTTCCATGACGGAGTGACTTTTTAT----------------A -s Anc2.Anc2refChr0 30128 53 - 56053 ---------CACCCTCATGTGTTCCCTTGTATAAATTTTCCAAGATGGAGTGACTTTTTAC----------------A -s mr.mrrefChr0 32226 62 + 130230 AAACTTGTCTTGTCTCATGAGTCCCCTTGCATAATTTTTCCATGACAGAGTAAATATCTAT----------------A -s simCow_chr6.simCow.chr6 572134 41 - 602619 ---------CACCCTTATGTGTTCCTTTCCATGA------------GGAGTGATCTTTTGC----------------A -s simDog_chr6.simDog.chr6 567606 48 - 593897 ---------C-----CATGAGTTCCCTTGTATAAATTTTCCAAGATGGAGCAACTTTTTAC----------------A -s simHuman_chr6.simHuman.chr6 574253 53 - 601863 ---------CCCCCTCATGTGTTCGCTAATATAAATTTTCCATGACGGAGTGACTCTTTCT----------------A -s simRat_chr6.simRat.chr6 26284 62 + 647215 AAACTTGTTTTGTCTTATGAGTCCCCTTGCATAATTTTCCCATGACAAAGTAAATATCTAT----------------A - -a -s simMouse_chr6.simMouse.chr6 34260 1 + 636262 T -s Anc0.Anc0refChr9 10860 1 + 35212 T -s Anc1.Anc1refChr2 135000 1 - 144309 T -s Anc2.Anc2refChr0 30181 1 - 56053 T -s mr.mrrefChr0 32288 1 + 130230 T -s simCow_chr6.simCow.chr6 572175 1 - 602619 T -s simDog_chr6.simDog.chr6 567654 1 - 593897 T -s simHuman_chr6.simHuman.chr6 574309 1 - 601863 T -s simRat_chr6.simRat.chr6 26346 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 34261 28 + 636262 TTTGTTGTAGGGAACCTACTTGATTGGA -s Anc0.Anc0refChr9 10861 28 + 35212 TGGGTCCTAGGAAACCAACTTATTTGGA -s Anc1.Anc1refChr2 135001 28 - 144309 TGGGTCCTAGGAAACCAACTTATTTGGA -s Anc2.Anc2refChr0 30183 28 - 56053 TGGGTCCTAGGAAACCAACTTATTTGGA -s mr.mrrefChr0 32289 28 + 130230 TTTGTTGTAGGGAACCTACTTAATTGGA -s simCow_chr6.simCow.chr6 572177 26 - 602619 TTGGTTATAGGAAACGGACTT--TTGGC -s simDog_chr6.simDog.chr6 567656 28 - 593897 TGGGTCCTAGGAAACCAACCTATTTGGA -s simHuman_chr6.simHuman.chr6 574310 28 - 601863 TAGGTCCTAGGAAACTAACTTACTTGGA -s simRat_chr6.simRat.chr6 26347 28 + 647215 TTTGTTGCAGTGAACCTACTTAATTCAA - -a -s simMouse_chr6.simMouse.chr6 34289 11 + 636262 AAGTCAATATG -s Anc0.Anc0refChr9 10889 11 + 35212 AATCCCTTATG -s Anc1.Anc1refChr2 135029 11 - 144309 AATCCCTTATG -s Anc2.Anc2refChr0 30211 11 - 56053 AATCCCTTATT -s mr.mrrefChr0 32317 11 + 130230 AAGTCATTATG -s simCow_chr6.simCow.chr6 572203 7 - 602619 AACCCCT---- -s simDog_chr6.simDog.chr6 567686 11 - 593897 AGTCCCTTATT -s simHuman_chr6.simHuman.chr6 574338 11 - 601863 AATACGTTTTG -s simRat_chr6.simRat.chr6 26375 11 + 647215 AAGTCATTATG - -a -s simMouse_chr6.simMouse.chr6 34300 2 + 636262 GG -s Anc0.Anc0refChr9 10900 2 + 35212 CA -s Anc1.Anc1refChr2 135040 2 - 144309 CA -s Anc2.Anc2refChr0 30248 2 - 56053 CA -s mr.mrrefChr0 32328 2 + 130230 GA -s simCow_chr6.simCow.chr6 572229 2 - 602619 AA -s simDog_chr6.simDog.chr6 567739 2 - 593897 CA -s simHuman_chr6.simHuman.chr6 574349 2 - 601863 CA -s simRat_chr6.simRat.chr6 26386 2 + 647215 GA - -a -s simMouse_chr6.simMouse.chr6 34302 4 + 636262 AGCA -s Anc0.Anc0refChr9 10903 4 + 35212 AGTT -s Anc1.Anc1refChr2 135043 4 - 144309 AGTT -s Anc2.Anc2refChr0 30251 4 - 56053 AGTT -s mr.mrrefChr0 32331 4 + 130230 AGTT -s simCow_chr6.simCow.chr6 572232 4 - 602619 AGTT -s simDog_chr6.simDog.chr6 567742 4 - 593897 AGTC -s simHuman_chr6.simHuman.chr6 574352 4 - 601863 AGTT -s simRat_chr6.simRat.chr6 26389 4 + 647215 AGTT - -a -s simMouse_chr6.simMouse.chr6 34306 13 + 636262 AGTGTGGCTGTGT -s Anc0.Anc0refChr9 10907 13 + 35212 AGTTTTGATGTGT -s Anc1.Anc1refChr2 135047 13 - 144309 AGTTTTGATGTGT -s Anc2.Anc2refChr0 30255 13 - 56053 GGTTTTGATGTGT -s mr.mrrefChr0 32335 13 + 130230 AGTGTTGCTGTGT -s simCow_chr6.simCow.chr6 572236 13 - 602619 GGTTTTGTTGTAT -s simDog_chr6.simDog.chr6 567746 13 - 593897 GGTTTTGATGTGT -s simHuman_chr6.simHuman.chr6 574358 13 - 601863 AGTTTTGATGTCT -s simRat_chr6.simRat.chr6 26393 13 + 647215 AGTGTTACTGCGT - -a -s simMouse_chr6.simMouse.chr6 34319 19 + 636262 GTGTGGTTTACATCCCCAT -s Anc0.Anc0refChr9 10923 19 + 35212 ATGTGGCTTCCACCCTCAT -s Anc1.Anc1refChr2 135063 19 - 144309 ATGTGGCTTCCACCCTCAT -s Anc2.Anc2refChr0 30271 19 - 56053 ATGTAGCTTCCATCCTTAT -s mr.mrrefChr0 32348 19 + 130230 GTGTGGCTTACACCCTCAT -s simCow_chr6.simCow.chr6 572252 19 - 602619 ATGTAGATTCCATCCTTAT -s simDog_chr6.simDog.chr6 567762 13 - 593897 ATGTAGCTTCCAT------ -s simHuman_chr6.simHuman.chr6 574374 19 - 601863 ATGTGGCTTCCACCCTCAT -s simRat_chr6.simRat.chr6 26406 19 + 647215 GCGTGGCTTACACCCTCAT - -a -s simMouse_chr6.simMouse.chr6 34338 2 + 636262 CT -s Anc0.Anc0refChr9 10945 2 + 35212 CT -s Anc1.Anc1refChr2 135085 2 - 144309 CT -s Anc2.Anc2refChr0 30293 2 - 56053 CT -s mr.mrrefChr0 32367 2 + 130230 CT -s simCow_chr6.simCow.chr6 572274 2 - 602619 CT -s simDog_chr6.simDog.chr6 567777 2 - 593897 CT -s simHuman_chr6.simHuman.chr6 574396 2 - 601863 CT -s simRat_chr6.simRat.chr6 26425 2 + 647215 CT - -a -s simMouse_chr6.simMouse.chr6 34340 1 + 636262 A -s Anc0.Anc0refChr9 10947 1 + 35212 A -s Anc1.Anc1refChr2 135087 1 - 144309 A -s Anc2.Anc2refChr0 30296 1 - 56053 A -s mr.mrrefChr0 32369 1 + 130230 A -s simDog_chr6.simDog.chr6 567780 1 - 593897 A -s simHuman_chr6.simHuman.chr6 574398 1 - 601863 A -s simRat_chr6.simRat.chr6 26427 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 34341 31 + 636262 CTAATTATGACAGGTGGAGATACAATAATAT -s Anc0.Anc0refChr9 10948 31 + 35212 CTAATTTTGATAGGTAAAAATACAGTAATAG -s Anc1.Anc1refChr2 135088 31 - 144309 CTAATTTTGATAGGTAAAAATACAGTAATAG -s Anc2.Anc2refChr0 30297 31 - 56053 CTAATTTTGATGGGTAAAAATACAGTAATAG -s mr.mrrefChr0 32370 31 + 130230 CTAATTATGATAGGTGGAGATACAATAATAT -s simCow_chr6.simCow.chr6 572277 28 - 602619 ---ATATTGATTTGTAAAACTACAGTAATAG -s simDog_chr6.simDog.chr6 567781 31 - 593897 CTAATTGTGATGGGTAAAAATACAGTAATAG -s simHuman_chr6.simHuman.chr6 574407 31 - 601863 CTAATTTTGATAGGTAAACATACAGTAATAA -s simRat_chr6.simRat.chr6 26428 28 + 647215 CTAATTATGATAGGTGGAAAT---ATAATAT - -a -s simMouse_chr6.simMouse.chr6 34372 19 + 636262 AGAATCCAAGCTTTAGAGG -s Anc0.Anc0refChr9 10979 17 + 35212 AGAAG--AAAGTTGATCGG -s Anc1.Anc1refChr2 135119 19 - 144309 AGAAGCCAAAGTTGATCGG -s Anc2.Anc2refChr0 30328 17 - 56053 AGAAG--AAAGTTTATCGG -s mr.mrrefChr0 32401 19 + 130230 AGAATCCAAGCTTGAGAGG -s simCow_chr6.simCow.chr6 572316 17 - 602619 AGGAG--ACGCTGTAATGG -s simDog_chr6.simDog.chr6 567812 17 - 593897 AGAAG--AAAGTTTATCGG -s simHuman_chr6.simHuman.chr6 574438 19 - 601863 AGAAGCCAAAGTTGACGCA -s simRat_chr6.simRat.chr6 26456 19 + 647215 AGAATCTGAGCTTGAGAGG - -a -s simMouse_chr6.simMouse.chr6 34391 51 + 636262 AAATGCTTCAATAGGTCAAGAGCAATACCAAATTGTGATACACTGTGGTGT -s Anc0.Anc0refChr9 10996 27 + 35212 AAAG-----AATAGG-------------------GTCAGTCACTGTGATGT -s Anc1.Anc1refChr2 135138 32 - 144309 AAAGGTCGCAATAGG-------------------GTCAGTCACTGTGATGT -s Anc2.Anc2refChr0 30345 27 - 56053 AAAG-----AAGATG-------------------GTCAGTCAGTGTGATGT -s mr.mrrefChr0 32420 51 + 130230 AAAGGTTTCAATAGGTCAAGAGCAATACCAAATTGTCATACACTGTGATGT -s simCow_chr6.simCow.chr6 572342 27 - 602619 AAAT-----AAAACA-------------------GGCAGTCAGTGTGTCAT -s simDog_chr6.simDog.chr6 567829 27 - 593897 AAAG-----ACGATG-------------------GTCAGTCAGTGTGATGT -s simHuman_chr6.simHuman.chr6 574457 32 - 601863 AAAGGTCGCAATGGG-------------------GTCAGGCACTGTGATGT -s simRat_chr6.simRat.chr6 26475 51 + 647215 GAAGGTTTCAATAGGTCAAGAGCAATATCAGATTGTCATACACTGTGATGT - -a -s simMouse_chr6.simMouse.chr6 34442 98 + 636262 GGATTATCTCTGCTTTCATCATGTACATTTATAAACTCACTTGTCCTTTCGCAGTGCCCGTGCTACTCCTACTCCTATTAACTTACATTCCTTATTTC -s Anc0.Anc0refChr9 11023 61 + 35212 GG--------------------GTACATTAATAAATTCACTGGTTCTCTTTCACTGCCCATA------CAAATCCTATTAA-----------TACTTC -s Anc1.Anc1refChr2 135170 82 - 144309 GGGTTAACTCTGCCTATGTTACGTACATTAATAAATTCACTGGTTCTCTTTCACTGCCCATA------CAAATCCTATTAA----------TTACTTC -s Anc2.Anc2refChr0 30372 61 - 56053 GG--------------------GTACATTAATAGATTCACTGGTTCTCTCTCACTGCCCATA------TAAATCCTATTAA-----------TACTTC -s mr.mrrefChr0 32471 92 + 130230 GGATTATCTCTGCTTTCATCATGTACATTTATAAACTCACTTGTCCTTTTGCAGTGCCCGTG------CTACTCCTATTAACTTACATTCCTTATTTC -s simCow_chr6.simCow.chr6 572382 61 - 602619 AT--------------------GTACATTCATAGTTTCACTGGTTCTCTCTCACTGCCCATA------TAAATCCTATAAA-----------TACTTC -s simDog_chr6.simDog.chr6 567856 61 - 593897 GG--------------------GTACATTAATAGATTCACTGGTTCTCTCTCATTGCCCATA------TAAATCCTATTAA-----------TACTTC -s simHuman_chr6.simHuman.chr6 574489 76 - 601863 GGGTTAACTCTGCCTATGTTACGTACATACGTAAATTCACTC------TTTCATTGCCCATA------CAAATACTGTTAA----------TTACTTC -s simRat_chr6.simRat.chr6 26526 92 + 647215 GGAATATCTCTGCTTTCATCATGTACATTTAAAAGCTCACTTGTCCGTTTGCAGTGCCCGTG------CTACTCCTATTACAGTACATTCCTTGTTCT - -a -s simMouse_chr6.simMouse.chr6 34540 20 + 636262 CCTCTAATTTTTCACTCAGT -s Anc0.Anc0refChr9 11086 20 + 35212 CCTCTAATTTTTCACTTATA -s Anc1.Anc1refChr2 135254 20 - 144309 CCTCTAATTTTTCACTTATA -s Anc2.Anc2refChr0 30435 20 - 56053 TCCCTAATTATACACTTATA -s mr.mrrefChr0 32563 20 + 130230 CCTCTAATTTTTCACTCATT -s simCow_chr6.simCow.chr6 572445 20 - 602619 TCCCTAATTTCTCAGTAATG -s simDog_chr6.simDog.chr6 567919 20 - 593897 TCCCTAATTATACACTTATA -s simHuman_chr6.simHuman.chr6 574567 17 - 601863 CCTCTAATTTCTCACTA--- -s simRat_chr6.simRat.chr6 26618 20 + 647215 CCCCTAATTTTTCACTCATT - -a -s simMouse_chr6.simMouse.chr6 34560 75 + 636262 GCCCTCATCTCAGTCAAGATACTGCTGGACCCCTCTCCAATTCCCTGAATGCTGGACCCTCCAACTCCTCGAATT -s Anc0.Anc0refChr9 11106 51 + 35212 GTTATTTTCTCAGTCATATTATTACTGGGCTTCTTTCCAATTTCTT------------------------AAATT -s Anc1.Anc1refChr2 135274 51 - 144309 GTTATTTTCTCAGTCATATTATTACTGGGCTTCTTTCCAATTTCTT------------------------AAATT -s Anc2.Anc2refChr0 30455 51 - 56053 GTTATTTTCTCAGTCATATTATTACTGGGCTTCTTTCCAATTTCTT------------------------AAATT -s mr.mrrefChr0 32583 51 + 130230 GCCCCCATCTCAGTCAAAATACTGCTGGACCCCTCTCCAATTCCCT------------------------GAATT -s simCow_chr6.simCow.chr6 572472 51 - 602619 GCTATGTTCAGAGATACACTACTAGTGGGCTTCTTTCCAATTTCTT------------------------AAAAT -s simDog_chr6.simDog.chr6 567939 51 - 593897 GTTATTTTCTCAGTCATATTATTACTGGGCTTCTTTCCAACTCCTT------------------------AAATT -s simHuman_chr6.simHuman.chr6 574584 22 - 601863 --------TACTTTCACATTGTAACCAGCC--------------------------------------------- -s simRat_chr6.simRat.chr6 26638 51 + 647215 GCCCCCATCTCAGTCAAAATACTGCTGGACCCCTCTCCAAGTCCCT------------------------GAATT - -a -s simMouse_chr6.simMouse.chr6 34635 8 + 636262 TGCACAAA -s Anc0.Anc0refChr9 11157 8 + 35212 TGAGGAGA -s Anc1.Anc1refChr2 135325 8 - 144309 TGAGGAGA -s Anc2.Anc2refChr0 30524 8 - 56053 TGAGGAGA -s mr.mrrefChr0 32634 8 + 130230 TGCAGAAA -s simCow_chr6.simCow.chr6 572541 8 - 602619 TGTGGAGA -s simDog_chr6.simDog.chr6 568011 8 - 593897 TGAGGAGA -s simRat_chr6.simRat.chr6 26689 8 + 647215 TGCAGAAA - -a -s simMouse_chr6.simMouse.chr6 34643 46 + 636262 GTTGGCCCCAATATCGCTATTACATTGCAAATTGTTATGACAAAGA -s Anc0.Anc0refChr9 11165 46 + 35212 ATTAGTTACATGCTTACTATTACATTGGAACTAGCCACAACAAAAG -s Anc1.Anc1refChr2 135333 46 - 144309 ATTAGTTACATGCTTACTATTACATTGGAACTAGCCACAACAAAAG -s Anc2.Anc2refChr0 30532 46 - 56053 ATTAGTTACATGCTTACTATTACATTGGAACTAGCCACAACAGAAG -s mr.mrrefChr0 32642 46 + 130230 GTTGGCCCCAATATCGCTATTACATTGCAAATTGTTATGACAAAGA -s simCow_chr6.simCow.chr6 572549 46 - 602619 ATTAGCTATATGATCACTGTTACATCGCAACTAGTCACAACAGAAA -s simDog_chr6.simDog.chr6 568021 46 - 593897 ATTAGTTACATGCTTACTATTACATTGGAACTAACCACAACAGAAG -s simHuman_chr6.simHuman.chr6 574606 10 - 601863 ------------------------------------ACAACAAAAG -s simRat_chr6.simRat.chr6 26697 43 + 647215 GTTGGCCCCAAGA---CTATTACAATGCAATTTGTTATGACAGAGA - -a -s simMouse_chr6.simMouse.chr6 34689 3 + 636262 TAG -s Anc0.Anc0refChr9 11211 3 + 35212 TAG -s Anc1.Anc1refChr2 135379 3 - 144309 TAG -s Anc2.Anc2refChr0 30578 3 - 56053 TAG -s mr.mrrefChr0 32688 3 + 130230 TAG -s simCow_chr6.simCow.chr6 572602 3 - 602619 TAG -s simDog_chr6.simDog.chr6 568067 3 - 593897 TAG -s simHuman_chr6.simHuman.chr6 574616 3 - 601863 TAA -s simRat_chr6.simRat.chr6 26740 3 + 647215 TAC - -a -s simMouse_chr6.simMouse.chr6 34692 24 + 636262 CTCCCCACAGTCCTTGAGTAACAT -s Anc0.Anc0refChr9 11255 21 + 35212 ATCC---CAATCCCAGAGCAACAA -s Anc1.Anc1refChr2 135423 21 - 144309 ATCC---CAATCCCAGAGCAACAA -s Anc2.Anc2refChr0 30622 21 - 56053 ATCC---CAATCCCAGATCAACAA -s mr.mrrefChr0 32691 21 + 130230 CTCC---CAGTCCTAGAGTAACAT -s simCow_chr6.simCow.chr6 572645 21 - 602619 ATCC---TGATTTCAGAACAACAA -s simDog_chr6.simDog.chr6 568111 21 - 593897 ATCC---CAATCCTAGATCAACAA -s simHuman_chr6.simHuman.chr6 574660 21 - 601863 ATCC---CAATCCCAGAGCGATAC -s simRat_chr6.simRat.chr6 26743 21 + 647215 CTCC---CAGGCCTAAAGTAACAT - -a -s simMouse_chr6.simMouse.chr6 34716 53 + 636262 GTTGTGGAGAACACCTCCTGTCCAGTGATCTCGACATCAACAGTTCTTACAGG -s Anc0.Anc0refChr9 11276 50 + 35212 GTTGTGGGCAATGCCTGCTGTCTTGTGATCTTACCATCAACTGTTCT---GGG -s Anc1.Anc1refChr2 135444 50 - 144309 GTTGTGGGCAATGCCTGCTGTCTTGTGATCTTACCATCAACTGTTCT---GGG -s Anc2.Anc2refChr0 30643 50 - 56053 GTTGTGGACAATGCCTTCTGTCTTGTAATCTTACCATCAATTGTTTT---GGG -s mr.mrrefChr0 32712 53 + 130230 GTTGTGGGCAATGCCTGCTGTCCAGTGATCTTGACATCAACAGTTCTTACGGG -s simCow_chr6.simCow.chr6 572666 50 - 602619 GTTATGGACAATACCTACTGTCTTGTAAACTTACCATCTGTTGTTAT---GGA -s simDog_chr6.simDog.chr6 568132 42 - 593897 GCTGTGGACAATGCCTTCTTTCTTGTAAT--------CAATTGTTTG---GGG -s simHuman_chr6.simHuman.chr6 574681 50 - 601863 ATTGTGGGCAATGCCTGCCGTCTTGTGATCTTTCCAGCAACTGTTCT---GGG -s simRat_chr6.simRat.chr6 26765 53 + 647215 GTTGTGGGCCATGCCTGCTGCCGAGTGATCTTGACTTCAACAGTTATCACGGC - -a -s simMouse_chr6.simMouse.chr6 34769 1 + 636262 A -s Anc0.Anc0refChr9 11328 1 + 35212 A -s Anc1.Anc1refChr2 135496 1 - 144309 A -s Anc2.Anc2refChr0 30695 1 - 56053 A -s mr.mrrefChr0 32765 1 + 130230 A -s simCow_chr6.simCow.chr6 572718 1 - 602619 A -s simDog_chr6.simDog.chr6 568176 1 - 593897 G -s simHuman_chr6.simHuman.chr6 574733 1 - 601863 A -s simRat_chr6.simRat.chr6 26818 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 34770 22 + 636262 GCACTTGTTGCCAATGGGAGGA -s Anc0.Anc0refChr9 11329 15 + 35212 GG-------ACCATGGGGAAGA -s Anc1.Anc1refChr2 135497 22 - 144309 GGACCTTATACCATGGGGAAGA -s Anc2.Anc2refChr0 30696 15 - 56053 GG-------ACAATGAAGAAGG -s mr.mrrefChr0 32766 22 + 130230 GCACTTGTTGCCATTGGGAGGA -s simCow_chr6.simCow.chr6 572719 4 - 602619 GG-------AA----------- -s simDog_chr6.simDog.chr6 568177 15 - 593897 GG-------ACAATGAAGAAGG -s simHuman_chr6.simHuman.chr6 574734 22 - 601863 GGACCTTATACCATGGGGAAGA -s simRat_chr6.simRat.chr6 26820 22 + 647215 GCATTTGGTGCCATTGGGAGGG - -a -s simMouse_chr6.simMouse.chr6 34792 9 + 636262 AGTTACCAT -s Anc0.Anc0refChr9 11344 9 + 35212 AGGAATCAT -s Anc1.Anc1refChr2 135519 9 - 144309 AGGAATCAT -s Anc2.Anc2refChr0 30711 9 - 56053 AGGACTCAT -s mr.mrrefChr0 32788 9 + 130230 AGGTATCAT -s simDog_chr6.simDog.chr6 568192 9 - 593897 AGGACTCAT -s simHuman_chr6.simHuman.chr6 574799 9 - 601863 AGGAATCAT -s simRat_chr6.simRat.chr6 26842 9 + 647215 AGGTATAAT - -a -s simMouse_chr6.simMouse.chr6 34801 44 + 636262 CAGATTAACAAGTTAATTCCCCAGGGCCAGAGGCTATAAATGGT -s Anc0.Anc0refChr9 11354 44 + 35212 CAGATTTACCTGCTAATTATTAGGGGCCACAGGTTATTAATGGT -s Anc1.Anc1refChr2 135529 44 - 144309 CAGATTTACCTGCTAATTATTAGGGGCCACAGGTTATTAATGGT -s Anc2.Anc2refChr0 30721 44 - 56053 CAAGTTTGCCTGCTAATTATTAGGGGCCACAGGTCAGTCATGGT -s mr.mrrefChr0 32797 44 + 130230 CAGATTAACAAGTTAATTCCCCAGGGCCAGAGGCTATAAATGGT -s simCow_chr6.simCow.chr6 572723 39 - 602619 -----TTGGTACCTGGGGATCAGGTGCCACAGGCCAGCCGTGGT -s simDog_chr6.simDog.chr6 568202 44 - 593897 CAAGTTTGCCTGCCAATTATTAAGGGCAACAGGTCAGTCATGGT -s simHuman_chr6.simHuman.chr6 574809 44 - 601863 CAGATTTACCTGCTAATTGTTAGAAGTCACAGGGTGTTAATGGT -s simRat_chr6.simRat.chr6 26851 27 + 647215 CAGGTTAACAAGTT-----------------GGCTATGAATGGT - -a -s simMouse_chr6.simMouse.chr6 34845 6 + 636262 AGTAGA -s Anc0.Anc0refChr9 11398 3 + 35212 GGT--- -s Anc1.Anc1refChr2 135573 6 - 144309 GGTAGA -s Anc2.Anc2refChr0 30765 3 - 56053 GGT--- -s mr.mrrefChr0 32841 6 + 130230 GGTAGA -s simCow_chr6.simCow.chr6 572764 3 - 602619 GGC--- -s simDog_chr6.simDog.chr6 568246 3 - 593897 AGT--- -s simHuman_chr6.simHuman.chr6 574853 6 - 601863 GGTAGA -s simRat_chr6.simRat.chr6 26878 6 + 647215 GGTAGA - -a -s simMouse_chr6.simMouse.chr6 34851 10 + 636262 CTGAAGAGAA -s Anc0.Anc0refChr9 11401 4 + 35212 ------AGGT -s Anc1.Anc1refChr2 135579 10 - 144309 TTCAAAAGGT -s Anc2.Anc2refChr0 30768 4 - 56053 ------CGGT -s mr.mrrefChr0 32847 10 + 130230 CTGAAGAGAA -s simCow_chr6.simCow.chr6 572767 4 - 602619 ------CAGT -s simDog_chr6.simDog.chr6 568249 4 - 593897 ------CGGT -s simHuman_chr6.simHuman.chr6 574859 10 - 601863 TTCAAAAGGT -s simRat_chr6.simRat.chr6 26890 10 + 647215 ACAAAGAGAA - -a -s simMouse_chr6.simMouse.chr6 34861 38 + 636262 GTTCATGTGTTGCACATCATCTGTACCTATGCTCAAAT -s Anc0.Anc0refChr9 11409 38 + 35212 GTTCATATGTTGCATACCAGCTGTACCTATTAACACCT -s Anc1.Anc1refChr2 135593 38 - 144309 GTTCATATGTTGCATACCAGCTGTACCTATTAACACCT -s Anc2.Anc2refChr0 30776 38 - 56053 GTTCATGTGTTGCATACCAGCTGTACCTATTAACTCCT -s mr.mrrefChr0 32857 38 + 130230 GTTCATATGTTGCACATCATCTGTACCTATGCTCAACT -s simCow_chr6.simCow.chr6 572775 38 - 602619 TCACATGTGTTGCACACCAGCTGGACCTATTATCTCCT -s simDog_chr6.simDog.chr6 568257 38 - 593897 GTTCATGTGTTGCATATAAGCTGTACCTATGAACTCCT -s simHuman_chr6.simHuman.chr6 574873 38 - 601863 GTTCATATGTTGCAAACCAGCTGTACCTATTAACACCT -s simRat_chr6.simRat.chr6 26900 38 + 647215 GTTCATATGAAGCACATCATTTGAATCTATGTTCGACT - -a -s simMouse_chr6.simMouse.chr6 34899 55 + 636262 GCACCTTTCCTGGAATTCCATTTTGAAGTGATGTGCTGGATTTTTTGAAATGCTG -s Anc0.Anc0refChr9 11473 54 + 35212 GCAACCTTCCAGGAGTGTCACCTCAAAGTGAAGTGACGAAT-TTTCGAAGTGCTG -s Anc1.Anc1refChr2 135657 54 - 144309 GCAACCTTCCAGGAGTGTCACCTCAAAGTGAAGTGACGAAT-TTTCGAAGTGCTG -s Anc2.Anc2refChr0 30841 54 - 56053 GCAACCTTCCAGGAGAGTCACCTCAAAGTTAAGTGACTAAT-TTTCAAAGTGCTG -s mr.mrrefChr0 32895 55 + 130230 GCACCTTTCCTGGAATTCCATTTTGAAGTGAAGTGCTGGATTTTTTGAAATGCTG -s simCow_chr6.simCow.chr6 572841 53 - 602619 ACAACCTTCCAGGAGAGCCACCACAAAGTTAAGTGAC-AAT-TTTCAAAGTGCTG -s simDog_chr6.simDog.chr6 568322 45 - 593897 GCAACCTTTCACAAGAGTC-ACTCAAAGC--------TAAT-TCTTATAGTGCTG -s simHuman_chr6.simHuman.chr6 574976 54 - 601863 GCAACCTTCCAGGAGTGTCTCCTCAAAGTGAAGTGAAGAAT-TTTCGAAGTACTG -s simRat_chr6.simRat.chr6 26938 55 + 647215 GCATCTCTCCTGGGATCCCATTTTTAAGTGAAGTGTCGGATTTTTTGAAAACCTG - -a -s simMouse_chr6.simMouse.chr6 34954 6 + 636262 CTAATA -s Anc0.Anc0refChr9 11531 6 + 35212 CTTATC -s Anc1.Anc1refChr2 135715 6 - 144309 CTTATC -s Anc2.Anc2refChr0 30899 6 - 56053 CTTATC -s mr.mrrefChr0 32954 6 + 130230 CTAATC -s simCow_chr6.simCow.chr6 572898 6 - 602619 CTTATC -s simDog_chr6.simDog.chr6 568371 6 - 593897 CTTATC -s simHuman_chr6.simHuman.chr6 575034 6 - 601863 CTTATC -s simRat_chr6.simRat.chr6 26997 6 + 647215 CTAATC - -a -s simMouse_chr6.simMouse.chr6 34960 10 + 636262 AAGATTAACA -s Anc0.Anc0refChr9 11537 10 + 35212 AGGATTAACA -s Anc1.Anc1refChr2 135721 10 - 144309 AGGATTAACA -s Anc2.Anc2refChr0 30905 10 - 56053 AGGATTCACA -s mr.mrrefChr0 32960 10 + 130230 AAGATTAACA -s simCow_chr6.simCow.chr6 572904 10 - 602619 AGGACTGACA -s simDog_chr6.simDog.chr6 568413 10 - 593897 TGGATTCACA -s simHuman_chr6.simHuman.chr6 575040 10 - 601863 AGGATTAACA -s simRat_chr6.simRat.chr6 27003 10 + 647215 AAGATGAACA - -a -s simMouse_chr6.simMouse.chr6 34970 55 + 636262 ATTCAGAATAAGTTTCTACTCATATAATAGGTTTCTCAGCTAGCTCAGTATTTCA -s Anc0.Anc0refChr9 11549 53 + 35212 GTTCGGAATAACTCATTACTTGTACAATTGGTGCC--AATAACCTTGGAACTTTA -s Anc1.Anc1refChr2 135733 53 - 144309 GTTCGGAATAACTCATTACTTGTACAATTGGTGCC--AATAACCTTGGAACTTTA -s Anc2.Anc2refChr0 30917 53 - 56053 GTTCGGATTAACTCATTACTTGTACAATTGGTGCC--AATAACCTTGGAACTTTA -s mr.mrrefChr0 32970 55 + 130230 ATTCAGAATAAGTTTCTACTTGTATAATAGGTTTCTCAGCTAGCTCAGTATTTCA -s simCow_chr6.simCow.chr6 572916 53 - 602619 GTTCAGATTAACTCATTACTTGTAAAATTGGTGCC--AGCTACCTTGGAACTTCA -s simDog_chr6.simDog.chr6 568425 53 - 593897 GTTCGGATTAGCTCATTACTTGTTCAATTGGTGCC--AATAACCTTGGAACTTTA -s simHuman_chr6.simHuman.chr6 575052 37 - 601863 GTTTGGAAAAACACATTACTTGTACAATTGA------------------ACTTTA -s simRat_chr6.simRat.chr6 27013 55 + 647215 ACTCAGAATAAGTTTCTACTTGCATAATCGGTTTGTCAACTCGCTTAGTATCTCA - -a -s simMouse_chr6.simMouse.chr6 35025 11 + 636262 TTTCCATCTAG -s Anc0.Anc0refChr9 11602 10 + 35212 TTTTTAACTA- -s Anc1.Anc1refChr2 135786 10 - 144309 TTTTTAACTA- -s Anc2.Anc2refChr0 30970 10 - 56053 TTTTTAACTA- -s mr.mrrefChr0 33025 11 + 130230 TTTCCATCTAG -s simCow_chr6.simCow.chr6 573053 10 - 602619 TTTTCAACTA- -s simDog_chr6.simDog.chr6 568478 10 - 593897 TTTTTAACTA- -s simHuman_chr6.simHuman.chr6 575089 10 - 601863 TTTTTTACTA- -s simRat_chr6.simRat.chr6 27068 11 + 647215 TTTCCATCTAG - -a -s simMouse_chr6.simMouse.chr6 35036 5 + 636262 TAAAT -s Anc0.Anc0refChr9 11612 5 + 35212 TAGCT -s Anc1.Anc1refChr2 135796 5 - 144309 TAGCT -s Anc2.Anc2refChr0 30980 5 - 56053 TAGCT -s mr.mrrefChr0 33036 5 + 130230 TAAAT -s simCow_chr6.simCow.chr6 573063 5 - 602619 TAGCT -s simDog_chr6.simDog.chr6 568488 5 - 593897 TAGCT -s simHuman_chr6.simHuman.chr6 575099 5 - 601863 TAGGT -s simRat_chr6.simRat.chr6 27099 5 + 647215 TAAAT - -a -s simMouse_chr6.simMouse.chr6 35041 27 + 636262 CTAGATTTTGTTAGAAAGGTCACTAAA -s Anc0.Anc0refChr9 11617 24 + 35212 T---ATTTAATCTGATAGATTTATAAT -s Anc1.Anc1refChr2 135801 24 - 144309 T---ATTTAATCTGATAGATTTATAAT -s Anc2.Anc2refChr0 30985 24 - 56053 T---ATTAAATCTGATAAATTTACATT -s mr.mrrefChr0 33041 27 + 130230 TTAGATTTTGTTAGAAAGGTCACTAAA -s simCow_chr6.simCow.chr6 573070 24 - 602619 T---ATTAAATGTAATGAGTTTACATT -s simDog_chr6.simDog.chr6 568493 23 - 593897 T---GTTAAATCTGATAAATTC-CATT -s simHuman_chr6.simHuman.chr6 575104 24 - 601863 T---ATTTAATATGATAGATTTATAAT -s simRat_chr6.simRat.chr6 27104 27 + 647215 TTAGATTTTGTCAGAAAGGTCACTAAA - -a -s simMouse_chr6.simMouse.chr6 35068 98 + 636262 TCTTAATGGCAACAAGTGGCACTGTTGGACTCCCATGTGAATCTAGAACAAGCCACTCACCGCTAAACAAAGGGATCATAGGAGCAAAGGGGGTTTCC -s Anc0.Anc0refChr9 11641 55 + 35212 T------GGCAGGAAATG-------------------------------------GTCAGCGCTAACCAAATGGACCAAAACAATGAAGAGGGTCTTC -s Anc1.Anc1refChr2 135825 55 - 144309 T------GGCAGGAAATG-------------------------------------GTCAGCGCTAACCAAATGGACCAAAACAATGAAGAGGGTCTTC -s Anc2.Anc2refChr0 31009 55 - 56053 T------GGTGGGAAATG-------------------------------------GTCAGTGCTAGCCAAATGCACCAAAACAATGAAGAGGGGCTTC -s mr.mrrefChr0 33068 98 + 130230 TCTTAATGGCAACAAGTGGCACTGTTGGACTCCCATGTGAATCTAGAACAAGCCACTCACCGCTAAACAAAGGGATCATAGGAGCAAAGAGGGTTTCC -s simCow_chr6.simCow.chr6 573095 55 - 602619 G------GGTGGGAAACA-------------------------------------GTCAGTACTAGCCAAATGAACCAAAGGAATGAAGAGGGCCTTC -s simDog_chr6.simDog.chr6 568516 55 - 593897 T------TTTGAGAAATG-------------------------------------TTCAGTGCTAGACAGATGCACCAATACAATAAGGAGGGGCTCC -s simHuman_chr6.simHuman.chr6 575128 55 - 601863 T------GGCAGGAAATG-------------------------------------GTCAGCTCCAACCAAACAGAACAAACAAATGAAGAGGGTCTTC -s simRat_chr6.simRat.chr6 27131 98 + 647215 CCTTAACGGCGACAAGTGGTAATGTTGCACTACTATATGACTCTAGAACAAGCCACTCACTCCTAAACAAAGGGACCATCGGTGCAAAGAGAGTTTCC - -a -s simMouse_chr6.simMouse.chr6 35166 34 + 636262 TGGAATGGGCTCAAACAGCACTTGCGTCAAATGA -s Anc0.Anc0refChr9 11696 32 + 35212 TTAAAT--TCTCTAATAACATTTAATTCAAATGA -s Anc1.Anc1refChr2 135880 34 - 144309 TTAAATGCTCTCTAATAACATTTAATTCAAATGA -s Anc2.Anc2refChr0 31064 32 - 56053 TTAAAT--TTTTTATTAACATTTAATTCAAATGA -s mr.mrrefChr0 33166 34 + 130230 TTGAATGGGCTCAAACAGCATTTGCGTCAAATGA -s simCow_chr6.simCow.chr6 573211 32 - 602619 TTAAAT--TATTCCTGGAAATTTAATTTAAACAA -s simDog_chr6.simDog.chr6 568571 32 - 593897 TTAAAT--TTCTTATTAACATTTAATTCAAATGA -s simHuman_chr6.simHuman.chr6 575183 34 - 601863 TTAAATGCTCTCTAATAACATTTAATTCAAATGA -s simRat_chr6.simRat.chr6 27229 34 + 647215 TTGAATGTGATTAAACAGTATTTGTGTCAAATGA - -a -s simMouse_chr6.simMouse.chr6 35200 18 + 636262 TTCACTCACAAAATAGAC -s Anc0.Anc0refChr9 11728 18 + 35212 TTAACTCACAAAATATAC -s Anc1.Anc1refChr2 135914 18 - 144309 TTAACTCACAAAATATAC -s Anc2.Anc2refChr0 31096 18 - 56053 GAATCCCACAAACTCTAC -s mr.mrrefChr0 33200 18 + 130230 TTCACTCACAAAATAGAC -s simCow_chr6.simCow.chr6 573243 18 - 602619 TAATCCCGCAACAACTAC -s simDog_chr6.simDog.chr6 568603 18 - 593897 GAATCCCACAAACTCTAC -s simHuman_chr6.simHuman.chr6 575224 18 - 601863 TTGATTCAAATGATAACC -s simRat_chr6.simRat.chr6 27263 17 + 647215 -TCACTCACAAAATAGAC - -a -s simMouse_chr6.simMouse.chr6 35218 25 + 636262 TTTGAATGTGTCATGAGACTTTTAA -s Anc0.Anc0refChr9 11746 25 + 35212 TATTAATGTGTCACGAGATTTTCAA -s Anc1.Anc1refChr2 135932 25 - 144309 TATTAATGTGTCACGAGATTTTCAA -s Anc2.Anc2refChr0 31117 25 - 56053 TATTAATGTGTCATGTGATTTTCAA -s mr.mrrefChr0 33218 25 + 130230 TTTGAATGTGTCACGAGACTTTTAA -s simCow_chr6.simCow.chr6 573264 25 - 602619 TATTAATGTGTCGTGTGAGTTTCAA -s simDog_chr6.simDog.chr6 568624 25 - 593897 TATTAATGTGTCATGAGATTTTCAA -s simHuman_chr6.simHuman.chr6 575242 11 - 601863 C----------CACGAAATCT---- -s simRat_chr6.simRat.chr6 27280 25 + 647215 TTTGAATGTGTCACGAGACTTTTAA - -a -s simMouse_chr6.simMouse.chr6 35243 2 + 636262 CT -s Anc0.Anc0refChr9 11771 2 + 35212 TA -s Anc1.Anc1refChr2 135957 2 - 144309 TA -s Anc2.Anc2refChr0 31146 2 - 56053 TA -s mr.mrrefChr0 33243 2 + 130230 CT -s simCow_chr6.simCow.chr6 573293 1 - 602619 T- -s simDog_chr6.simDog.chr6 568653 2 - 593897 TA -s simRat_chr6.simRat.chr6 27305 2 + 647215 CC - -a -s simMouse_chr6.simMouse.chr6 35245 69 + 636262 CGTTGGTCTAGGGGACATTAGTTTGCAACCTTGTTTAACGAACCCCCAACTAATTGAACTGGAATACTA -s Anc0.Anc0refChr9 11793 63 + 35212 TCTGAGT-TATGATCCTGAAGTATTCACTCTT-----AGGGGTCAGCAGCAATTTGAGGCGGACTAACA -s Anc1.Anc1refChr2 135980 63 - 144309 TCTGAGT-TATGATCCTGAAGTATTCACTCTT-----AGGGGTCAGCAGCAATTTGAGGCGGACTAACA -s Anc2.Anc2refChr0 31168 63 - 56053 TCTGAGT-TATGATCCTGAAGTATTCACTCTT-----AGGGGTCAGCAGCAATTTGAGGCGGACTAACA -s mr.mrrefChr0 33273 69 + 130230 CGTTGGTCTAGGGGACATTAGTTTGCAACCTTGTTTAACGAACCCCCAACTAATTGAACTGGAATACTA -s simCow_chr6.simCow.chr6 573314 63 - 602619 AATAAGT-TATGATTAGGGAATATTCTGTCTT-----AGGGGTTAGCACCAATTAGGAGAGGACTGACA -s simDog_chr6.simDog.chr6 568683 63 - 593897 TCTGAGT-TATGATCCTGAAGTATTCACTCTT-----AGGGGTCAGCAGCAATTTGAGGCGGACTAACA -s simRat_chr6.simRat.chr6 27556 69 + 647215 CGTTGGTCTGGGGGACATTAGATTGCAACCTTGTTTAATGAACCTCCAACTAATTGAACTGGAGCACTA - -a -s simMouse_chr6.simMouse.chr6 35314 8 + 636262 AGATGGAT -s Anc0.Anc0refChr9 11856 3 + 35212 GGA----- -s Anc1.Anc1refChr2 136043 8 - 144309 GGATGTAT -s Anc2.Anc2refChr0 31231 3 - 56053 GGA----- -s mr.mrrefChr0 33342 8 + 130230 AGATGGAT -s simCow_chr6.simCow.chr6 573383 3 - 602619 GCA----- -s simDog_chr6.simDog.chr6 568746 3 - 593897 GGA----- -s simHuman_chr6.simHuman.chr6 575265 6 - 601863 --GTGTAT -s simRat_chr6.simRat.chr6 27625 8 + 647215 AGATGGAT - -a -s simMouse_chr6.simMouse.chr6 35322 10 + 636262 TCCTCTGAAC -s Anc0.Anc0refChr9 11859 4 + 35212 ------AAAC -s Anc1.Anc1refChr2 136051 10 - 144309 TCTGCTAAAC -s Anc2.Anc2refChr0 31234 4 - 56053 ------AAAC -s mr.mrrefChr0 33350 10 + 130230 TCCTCTGAAC -s simCow_chr6.simCow.chr6 573386 4 - 602619 ------AAAC -s simDog_chr6.simDog.chr6 568749 4 - 593897 ------AAAC -s simHuman_chr6.simHuman.chr6 575273 10 - 601863 TCTGCTAAAC -s simRat_chr6.simRat.chr6 27633 10 + 647215 TCCCCTGAAC - -a -s simMouse_chr6.simMouse.chr6 35332 11 + 636262 AAGGAGACATG -s Anc0.Anc0refChr9 11869 11 + 35212 AAGGGGTTATG -s Anc1.Anc1refChr2 136067 11 - 144309 AAGGGGTTATG -s Anc2.Anc2refChr0 31249 11 - 56053 AAGGGGTTATG -s mr.mrrefChr0 33360 11 + 130230 AAGGAGACATG -s simCow_chr6.simCow.chr6 573401 11 - 602619 GAGGGGTTGTT -s simDog_chr6.simDog.chr6 568764 11 - 593897 AAGGGGGTATG -s simHuman_chr6.simHuman.chr6 575289 11 - 601863 AAGGGGTTATG -s simRat_chr6.simRat.chr6 27643 11 + 647215 AAGGAGACATG - -a -s simMouse_chr6.simMouse.chr6 35343 3 + 636262 CTA -s Anc0.Anc0refChr9 11897 3 + 35212 CTT -s Anc1.Anc1refChr2 136095 3 - 144309 CTT -s Anc2.Anc2refChr0 31277 3 - 56053 CTT -s mr.mrrefChr0 33371 3 + 130230 CTA -s simCow_chr6.simCow.chr6 573429 3 - 602619 CTT -s simDog_chr6.simDog.chr6 568792 3 - 593897 CCT -s simHuman_chr6.simHuman.chr6 575317 3 - 601863 CTT -s simRat_chr6.simRat.chr6 27654 3 + 647215 CTA - -a -s simMouse_chr6.simMouse.chr6 35346 14 + 636262 GATCCTTGCCAGCC -s Anc0.Anc0refChr9 11900 14 + 35212 GATGGTCAGCAGCA -s Anc1.Anc1refChr2 136098 14 - 144309 GATGGTCAGCAGCA -s Anc2.Anc2refChr0 31280 14 - 56053 AATGGTCAGCAACA -s mr.mrrefChr0 33374 14 + 130230 GATCCTTGCCAGCC -s simCow_chr6.simCow.chr6 573432 14 - 602619 AATGGTCAGCAACT -s simDog_chr6.simDog.chr6 568795 14 - 593897 AATGGTCAGTGACA -s simHuman_chr6.simHuman.chr6 575320 14 - 601863 GATGGTCAGCAGCA -s simRat_chr6.simRat.chr6 27662 14 + 647215 GATCCTTGCCAGCC - -a -s simMouse_chr6.simMouse.chr6 35360 69 + 636262 TAACAAGAGGACAGTACCACACCCCCTCCCAATAATGGGACTGAATCAACTGTAATCAACTATTGGCCA -s Anc0.Anc0refChr9 11915 67 + 35212 TAACAAGAGCATAGTCCAATATCCTTTGCTAAAACTGGAAAGGAATCCATAATAATAAACTATAGTC-- -s Anc1.Anc1refChr2 136113 67 - 144309 TAACAAGAGCATAGTCCAATATCCTTTGCTAAAACTGGAAAGGAATCCATAATAATAAACTATAGTC-- -s Anc2.Anc2refChr0 31295 67 - 56053 TAACAAGAGCATAGTCCAATATCCTTTGATAAAACTGGAAAGGAGTCCATAAAGATAAACTATAGTC-- -s mr.mrrefChr0 33388 67 + 130230 TAACAAGAGGACAGTACCACACCCCCTGCTAATAATGGGACTGAATCAACTATAATCAACTATTGGC-- -s simCow_chr6.simCow.chr6 573447 48 - 602619 AAACAAAAGCATAGTCCAAT-------------------AAGGGGTCCATAAAGATAAACTATACTC-- -s simDog_chr6.simDog.chr6 568810 66 - 593897 TAACAAGAGCATAGTCCAATATCCTTTGATAAAACTGGAAAGGAGTCCATGAAGATAAACT-TAGTC-- -s simHuman_chr6.simHuman.chr6 575335 67 - 601863 TAACAAGAGTATAGTCCAATATCATTTGCTAAAACTGGAAAGGAATCCATAATAATAAACTGTAGTC-- -s simRat_chr6.simRat.chr6 27676 67 + 647215 CAACAAGAGGACAGTACCACACCCCCTGCTAATAACAGGACTGAATCAGCCATAGTCAACTATTGGC-- - -a -s simMouse_chr6.simMouse.chr6 35429 68 + 636262 GATAAGTGATATCATAACTTTGTATAATTGATTAATAATCTTCTTACAGCCACAACAAGTTCCACAAT -s Anc0.Anc0refChr9 11984 65 + 35212 AATAAACCATATCATAATTTTGTATAATTGATTAACAATCTTATT---GCTATATGAAGTTTTGCATC -s Anc1.Anc1refChr2 136182 65 - 144309 AATAAACCATATCATAATTTTGTATAATTGATTAACAATCTTATT---GCTATATGAAGTTTTGCATC -s Anc2.Anc2refChr0 31364 65 - 56053 AATAAACCATATCATAATTTTGTGTGATTGATTAACGATCTTATT---GCTATATGAAGTTTTGCATC -s mr.mrrefChr0 33455 68 + 130230 AATAAGTGATATCATAATTTTGTATAATTGATTAACAATCTTCTTACAGCTATAACAAGTTCCACAAC -s simCow_chr6.simCow.chr6 573497 63 - 602619 AATTAACAACAT-GCAATTTTGTCTG-CTGATTAACCATCTTATT---GCTATGAGAAGTTTTGCATC -s simDog_chr6.simDog.chr6 568878 63 - 593897 AATAAACCATATCATAAGTGCGTGTGATTGATGTGCGATTTTATT---TCTATATGAAGTTTTGCA-- -s simHuman_chr6.simHuman.chr6 575404 65 - 601863 ACTAAACTATATCATACTTTTGTATAATCGATTAACAATCTTATT---GCTATACAGCGTTTTGCAGC -s simRat_chr6.simRat.chr6 27743 68 + 647215 AATAAGTGATATCATAATTTTATATAATTGAGAAACAATCTTCTTACAGGTATAACAAGTTCCACAAC - -a -s simMouse_chr6.simMouse.chr6 35497 37 + 636262 ACAATGATAGCAAAAGTACCCAGGGTGATAATTAGCC -s Anc0.Anc0refChr9 12049 36 + 35212 CCTATG-TACTTAAAGTACCCAGAGTAATAAGTAACC -s Anc1.Anc1refChr2 136247 36 - 144309 CCTATG-TACTTAAAGTACCCAGAGTAATAAGTAACC -s Anc2.Anc2refChr0 31429 36 - 56053 CATATG-ATCTTAAAGTACCTAAAGTAATAAGTAACC -s mr.mrrefChr0 33523 37 + 130230 ACAATGATAGCAAAAGTACCCAGGGTAATAAGTAACC -s simCow_chr6.simCow.chr6 573561 36 - 602619 CATGCG-GTCTTAAAGTACCTATAGTGATAAGTATTC -s simDog_chr6.simDog.chr6 568941 33 - 593897 ---ATT-ATATTAAAGTAGCTAAAGGAATTAGTGACC -s simHuman_chr6.simHuman.chr6 575469 36 - 601863 CCTATG-TACTGAAAGTACCCAGAGTAATAAGGAACC -s simRat_chr6.simRat.chr6 27811 37 + 647215 ACCATTATAGCAAAAGTACCCAGGGCAATAAGTAACC - -a -s simMouse_chr6.simMouse.chr6 35534 10 + 636262 ATATGATCAA -s Anc0.Anc0refChr9 12089 10 + 35212 ACATTAAAAC -s Anc1.Anc1refChr2 136287 10 - 144309 ACATTAAAAC -s Anc2.Anc2refChr0 31469 10 - 56053 ACATTAAAGC -s mr.mrrefChr0 33560 10 + 130230 ATATGATAAA -s simCow_chr6.simCow.chr6 573601 7 - 602619 ATCTTAA--- -s simDog_chr6.simDog.chr6 568978 10 - 593897 ACATCAAAGC -s simHuman_chr6.simHuman.chr6 575509 10 - 601863 ACATTAAAAC -s simRat_chr6.simRat.chr6 27848 10 + 647215 ATATGATAAA - -a -s simMouse_chr6.simMouse.chr6 35544 1 + 636262 G -s Anc0.Anc0refChr9 12099 1 + 35212 G -s Anc1.Anc1refChr2 136297 1 - 144309 G -s Anc2.Anc2refChr0 31479 1 - 56053 G -s mr.mrrefChr0 33570 1 + 130230 G -s simDog_chr6.simDog.chr6 568989 1 - 593897 G -s simHuman_chr6.simHuman.chr6 575519 1 - 601863 G -s simRat_chr6.simRat.chr6 27858 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 35545 4 + 636262 CAAG -s Anc0.Anc0refChr9 12111 4 + 35212 TATG -s Anc1.Anc1refChr2 136309 4 - 144309 TATG -s Anc2.Anc2refChr0 31491 4 - 56053 TATG -s mr.mrrefChr0 33573 4 + 130230 CAAG -s simCow_chr6.simCow.chr6 573617 4 - 602619 TATA -s simDog_chr6.simDog.chr6 569001 4 - 593897 TATG -s simHuman_chr6.simHuman.chr6 575539 4 - 601863 TATG -s simRat_chr6.simRat.chr6 27861 4 + 647215 CAAG - -a -s simMouse_chr6.simMouse.chr6 35549 46 + 636262 AACTGTACCGTTGCACACTCTTCCAGTTCGTCACGTGTCAAAAGCC -s Anc0.Anc0refChr9 12116 34 + 35212 AGCTTCACCATGTTGTACTCATCCAGTC------------AACCCC -s Anc1.Anc1refChr2 136314 34 - 144309 AGCTTCACCATGTTGTACTCATCCAGTC------------AACCCC -s Anc2.Anc2refChr0 31496 34 - 56053 AGGTTCACCATGTTGTACTCATCCAGTC------------AACCCC -s mr.mrrefChr0 33577 34 + 130230 AACTTAACCATTGCACACTCTTCCAGTT------------AAAGCC -s simCow_chr6.simCow.chr6 573622 34 - 602619 GATTTCGCTGTGTTGTGCTCATCCAGTC------------AACCCC -s simDog_chr6.simDog.chr6 569006 34 - 593897 AGGTTCAGCAAGTAGTACTCATCCAGTC------------AACCCC -s simHuman_chr6.simHuman.chr6 575544 34 - 601863 AGCTTCACCATGTTGTACTAATCCAGTC------------AGTCCC -s simRat_chr6.simRat.chr6 27865 34 + 647215 AATCTAACCATTGCACACTCTTCCAGTT------------AAAGCC - -a -s simMouse_chr6.simMouse.chr6 35595 4 + 636262 TGTG -s Anc0.Anc0refChr9 12151 4 + 35212 TGTG -s Anc1.Anc1refChr2 136349 4 - 144309 TGTG -s Anc2.Anc2refChr0 31531 4 - 56053 TGTG -s mr.mrrefChr0 33611 4 + 130230 TGTG -s simCow_chr6.simCow.chr6 573657 4 - 602619 TGTT -s simDog_chr6.simDog.chr6 569041 4 - 593897 TGAG -s simHuman_chr6.simHuman.chr6 575579 4 - 601863 TGTG -s simRat_chr6.simRat.chr6 27899 4 + 647215 TGTG - -a -s simMouse_chr6.simMouse.chr6 35599 7 + 636262 TATGATG -s Anc0.Anc0refChr9 12168 7 + 35212 TGTGAGA -s Anc1.Anc1refChr2 136366 7 - 144309 TGTGAGA -s Anc2.Anc2refChr0 31548 7 - 56053 TGTGAGA -s mr.mrrefChr0 33615 7 + 130230 TATGATG -s simCow_chr6.simCow.chr6 573674 7 - 602619 TGTGAAA -s simDog_chr6.simDog.chr6 569058 7 - 593897 TGCGAGA -s simHuman_chr6.simHuman.chr6 575596 7 - 601863 TGTGACA -s simRat_chr6.simRat.chr6 27903 7 + 647215 TATGATG - -a -s simMouse_chr6.simMouse.chr6 35606 10 + 636262 AATTACAAAT -s Anc0.Anc0refChr9 12175 10 + 35212 ATCTACACAT -s Anc1.Anc1refChr2 136373 10 - 144309 ATCTACACAT -s Anc2.Anc2refChr0 31557 10 - 56053 ATCTACCCAT -s mr.mrrefChr0 33622 10 + 130230 AATTACAAAT -s simCow_chr6.simCow.chr6 573683 10 - 602619 GTCTACCCAT -s simDog_chr6.simDog.chr6 569067 10 - 593897 ATCTATCCAT -s simHuman_chr6.simHuman.chr6 575603 10 - 601863 ATCTACACAT -s simRat_chr6.simRat.chr6 27910 10 + 647215 AGTTACAAAT - -a -s simMouse_chr6.simMouse.chr6 35616 49 + 636262 CCTCCAAAGTACAAAAGATTCTCTCGCCTGTGAGAACAACCACTACAGG -s Anc0.Anc0refChr9 12204 49 + 35212 TCTTCGGAGGACCATGGATTCTGTGGCCTGTGAGATTAACCCCTATAGG -s Anc1.Anc1refChr2 136402 49 - 144309 TCTTCGGAGGACCATGGATTCTGTGGCCTGTGAGATTAACCCCTATAGG -s Anc2.Anc2refChr0 31586 49 - 56053 TCTTCGGAGGACCATGGATTCTGTGGCCTGTGAGATTAACCCTTATAGG -s mr.mrrefChr0 33632 49 + 130230 CCTACAAAGGACAAAAGATTCTCTCGCCTGTGAGAACAACCCCTACAGG -s simCow_chr6.simCow.chr6 573712 49 - 602619 TCATCGGAGGACCATGAATTCGTTGGCCTGTGACATCAACCCTTCTAGG -s simDog_chr6.simDog.chr6 569096 49 - 593897 TCTTTAGAGGACCATCGATTCTGAGGCCCATGAGATTGACCATTATGGG -s simHuman_chr6.simHuman.chr6 575633 49 - 601863 TCTCCGGAGGATTATGGATTCTGTGGCCTGTGAGATTAACCCCTATAGG -s simRat_chr6.simRat.chr6 27920 49 + 647215 CCTACAAAGGACAAAAGATTCTCCTGCCTGTGAGAACAACCCCTGCAGG - -a -s simMouse_chr6.simMouse.chr6 35665 6 + 636262 GTTTTA -s Anc0.Anc0refChr9 12253 6 + 35212 GTTGTA -s Anc1.Anc1refChr2 136451 6 - 144309 GTTGTA -s Anc2.Anc2refChr0 31635 6 - 56053 GCTGCA -s mr.mrrefChr0 33681 6 + 130230 GTTTTA -s simCow_chr6.simCow.chr6 573768 6 - 602619 ACTGCA -s simDog_chr6.simDog.chr6 569145 6 - 593897 GCTGCA -s simHuman_chr6.simHuman.chr6 575682 6 - 601863 GTCATA -s simRat_chr6.simRat.chr6 27969 6 + 647215 GTTTTA - -a -s simMouse_chr6.simMouse.chr6 35671 57 + 636262 GCCCCTGAAGCTTTAGACTCTGTGTTCCCTTTTTATGAACAGAAAGTGCACACTCTG -s Anc0.Anc0refChr9 12259 57 + 35212 GCCCCTGAAGCCATATAATGGACCTACCTTAATCATAAACTGAAAGTGTGCACTCTG -s Anc1.Anc1refChr2 136457 57 - 144309 GCCCCTGAAGCCATATAATGGACCTACCTTAATCATAAACTGAAAGTGTGCACTCTG -s Anc2.Anc2refChr0 31643 57 - 56053 GCCCCTGAAGCCATGTAATGGACCTACCTTAATCCTATACTGAAAGTGTGCACTCTG -s mr.mrrefChr0 33687 57 + 130230 GCCCCTGAAGCTTTAGACTGTGCCTACCCTTATTATGAACAGAAAGTGCACACTCTG -s simCow_chr6.simCow.chr6 573776 57 - 602619 ACCACTGAAGCCTAGCACTGTACCTGCATTAACTGTATACTGAAAGTGCGCACTCTG -s simDog_chr6.simDog.chr6 569153 57 - 593897 GCCCCTGAAGCCATGTAATGGACCTACCTTAATCCTATCCTGAAAGTCTGCACTCTG -s simHuman_chr6.simHuman.chr6 575688 50 - 601863 GCCCCTGAAGCCCTAAA-------TACCTTAATCATAAACTCAGAGTGTGCACTCTG -s simRat_chr6.simRat.chr6 27975 57 + 647215 GCCCCTGGGTCATTAGGCTGTGCCAACCCTGATTATGAACAGAAAGTGCACACTCTG - -a -s simMouse_chr6.simMouse.chr6 35728 7 + 636262 CTTGACT -s Anc0.Anc0refChr9 12321 7 + 35212 CTTACCC -s Anc1.Anc1refChr2 136519 7 - 144309 CTTACCC -s Anc2.Anc2refChr0 31705 7 - 56053 CTTACCC -s mr.mrrefChr0 33749 7 + 130230 CTTAACT -s simCow_chr6.simCow.chr6 573838 7 - 602619 CTTAATC -s simDog_chr6.simDog.chr6 569215 7 - 593897 CTTACCC -s simHuman_chr6.simHuman.chr6 575743 7 - 601863 CTTATCC -s simRat_chr6.simRat.chr6 28037 7 + 647215 CTTAGTT - -a -s simMouse_chr6.simMouse.chr6 35735 15 + 636262 TAGGGCAACATGAAA -s Anc0.Anc0refChr9 12329 15 + 35212 TTGGGCAGCATGAGA -s Anc1.Anc1refChr2 136527 15 - 144309 TTGGGCAGCATGAGA -s Anc2.Anc2refChr0 31713 15 - 56053 TTGGGCAGCATGAAA -s mr.mrrefChr0 33756 15 + 130230 TAGGGCAGCATGAGA -s simCow_chr6.simCow.chr6 573846 15 - 602619 TTAGGCAGCATGAAA -s simDog_chr6.simDog.chr6 569223 15 - 593897 TTGGGCAGTATGAAA -s simHuman_chr6.simHuman.chr6 575751 15 - 601863 TTGGGCAGCATGAGA -s simRat_chr6.simRat.chr6 28044 15 + 647215 TAGGGCAGCCTGAGA - -a -s simMouse_chr6.simMouse.chr6 35750 16 + 636262 TTATGTTAATTGCTCG -s Anc0.Anc0refChr9 12344 16 + 35212 GCATGTTAATTCATTC -s Anc1.Anc1refChr2 136542 16 - 144309 GCATGTTAATTCATTC -s Anc2.Anc2refChr0 31728 16 - 56053 GCATGTTAATTCATTC -s mr.mrrefChr0 33771 16 + 130230 TCATGTTAATTGCTCA -s simCow_chr6.simCow.chr6 573863 16 - 602619 GTGTGTTAATTCATTC -s simDog_chr6.simDog.chr6 569238 16 - 593897 CCACGTTAATTCATTC -s simHuman_chr6.simHuman.chr6 575766 16 - 601863 GCATGTTAATGCATTC -s simRat_chr6.simRat.chr6 28059 16 + 647215 TCATGTTAGTTGCTCA - -a -s simMouse_chr6.simMouse.chr6 35766 40 + 636262 TAAAAGATGTATTGGCAATTTGAGGGTGGTATTCTTGCTT -s Anc0.Anc0refChr9 12360 39 + 35212 TAAAACATGTCTGGATTATTTCAAAGTGT-GTTCTTGCTT -s Anc1.Anc1refChr2 136558 39 - 144309 TAAAACATGTCTGGATTATTTCAAAGTGT-GTTCTTGCTT -s Anc2.Anc2refChr0 31745 39 - 56053 TAAAACAGATCTGGATTATTTCAAAGTGT-GTTCTTGCTT -s mr.mrrefChr0 33787 39 + 130230 TAAAAGATGTATTGACAATTTGAGGGTGT-ATTCTTGCTT -s simCow_chr6.simCow.chr6 573880 35 - 602619 TAAAA----TCTGGACTATTCCAAAGTGT-GTTCCTGCTC -s simDog_chr6.simDog.chr6 569255 39 - 593897 TAAAACAGATCTGGATTATTTCAAAGTGG-ATTCTTGGTT -s simHuman_chr6.simHuman.chr6 575782 39 - 601863 AGAAACATGTCTGGATTACTACAAAGTGT-GTTTTGCTTT -s simRat_chr6.simRat.chr6 28075 39 + 647215 TAAAAGATGTATTGACAATTTGAGGACGT-ATTCTTGCTT - -a -s simMouse_chr6.simMouse.chr6 35806 8 + 636262 TATGTGGT -s Anc0.Anc0refChr9 12399 8 + 35212 CATGTGGA -s Anc1.Anc1refChr2 136597 8 - 144309 CATGTGGA -s Anc2.Anc2refChr0 31785 8 - 56053 CATGTGGA -s mr.mrrefChr0 33826 8 + 130230 TATGTGGT -s simCow_chr6.simCow.chr6 573916 6 - 602619 CATGTT-- -s simDog_chr6.simDog.chr6 569294 3 - 593897 -----GGA -s simHuman_chr6.simHuman.chr6 575821 8 - 601863 AATGTGGC -s simRat_chr6.simRat.chr6 28114 8 + 647215 TATGTGGT - -a -s simMouse_chr6.simMouse.chr6 35814 6 + 636262 TGCCAT -s Anc0.Anc0refChr9 12410 6 + 35212 TGCCTT -s Anc1.Anc1refChr2 136608 6 - 144309 TGCCTT -s Anc2.Anc2refChr0 31796 6 - 56053 TGCCTT -s mr.mrrefChr0 33834 6 + 130230 TGCCAT -s simCow_chr6.simCow.chr6 573924 6 - 602619 TGCCTT -s simDog_chr6.simDog.chr6 569300 4 - 593897 TG--TT -s simHuman_chr6.simHuman.chr6 575832 6 - 601863 TGCCTT -s simRat_chr6.simRat.chr6 28122 6 + 647215 TGCCAT - -a -s simMouse_chr6.simMouse.chr6 35820 26 + 636262 CCATCTCAATGTAATACTCCCATCAG -s Anc0.Anc0refChr9 12418 26 + 35212 CCTTTTCAATGTTATACTTCCATAAG -s Anc1.Anc1refChr2 136616 26 - 144309 CCTTTTCAATGTTATACTTCCATAAG -s Anc2.Anc2refChr0 31804 26 - 56053 CCTTTTCACTGTTATGCTTGCTCAAG -s mr.mrrefChr0 33840 26 + 130230 CCATCTCAATGTCATACTTCCATCAG -s simCow_chr6.simCow.chr6 573932 26 - 602619 CCATCTCAGTGTTATGATTGCTCCAG -s simDog_chr6.simDog.chr6 569306 26 - 593897 CCTCTTTACCGTCATGCTTGCTCAAG -s simHuman_chr6.simHuman.chr6 575840 26 - 601863 CCTTTTCAATATTATACTTCCATTAG -s simRat_chr6.simRat.chr6 28128 26 + 647215 CCATGTCAGTCTCATATCTACATCAG - -a -s simMouse_chr6.simMouse.chr6 35846 67 + 636262 CGTGTGGCCTGTCCTGAGCCCTTTATCTCTATGCCCAAGGCTCCAAACCCAATTTTTGCATCTACAC -s Anc0.Anc0refChr9 12444 67 + 35212 CATGTAGCCTGTCCTCAGCCCTTTGTTTCTATGCCCAAAGTTCAGAACTCACTTGTAGCAGGTACAC -s Anc1.Anc1refChr2 136642 67 - 144309 CATGTAGCCTGTCCTCAGCCCTTTGTTTCTATGCCCAAAGTTCAGAACTCACTTGTAGCAGGTACAC -s Anc2.Anc2refChr0 31830 67 - 56053 CATGTAGCATATCCTCAGCCCTTTGTTTCTATGCCCAAAGTTCAGAACTCACTTGTAGCAGGTACAC -s mr.mrrefChr0 33866 67 + 130230 CATGTGGCCTGTCCTCAGCCCTTTATCTCTATGCCCAAAGCTCCAAACCCAATTTTTGCAGCTACAC -s simCow_chr6.simCow.chr6 573958 66 - 602619 TATGTAACACATCCTTGGCCCTTTGTTTTTATACCCAAAGTTCAGAATCCACCTGTTGCA-GCATAC -s simDog_chr6.simDog.chr6 569332 67 - 593897 CATGTAGCATATCCTCAGCCCTGTGTTCCTATGCCCAAAACTCGGGACTCCCTTGTAGCAGGTACAC -s simHuman_chr6.simHuman.chr6 575872 55 - 601863 GATGTAGCCTGTCCTCAGCCCTTTGCTTCTATGCCCAAAGTTCAGACCTGACT------------AC -s simRat_chr6.simRat.chr6 28154 67 + 647215 CATGTGGTCTGTCCTCAGCCCTTTCTCTCTATGCCCAAAGCTCAAAACCCAATTTTTGCAGCTACAC - -a -s simMouse_chr6.simMouse.chr6 35913 28 + 636262 CTACAACCTTAGTGAATCCTCTACATGG -s Anc0.Anc0refChr9 12517 26 + 35212 TTCCAG--TTAATGAATATATAGTTGGG -s Anc1.Anc1refChr2 136720 26 - 144309 TTCCAG--TTAATGAATATATAGTTGGG -s Anc2.Anc2refChr0 31903 26 - 56053 TTCCCG--TTAATTAATATATAGTTGGG -s mr.mrrefChr0 33945 28 + 130230 CTACAACCTTAGTGAATACTCTGCATGG -s simCow_chr6.simCow.chr6 574030 26 - 602619 CTCAGG--GCATGTAATATACTATGGGG -s simDog_chr6.simDog.chr6 569405 26 - 593897 TTCCCA--TTCATTAATATATAGTTGGG -s simHuman_chr6.simHuman.chr6 575938 26 - 601863 TTCCAG--TGAATGTCCAAATGGGTGGG -s simRat_chr6.simRat.chr6 28233 28 + 647215 CTATAACCTTAGTGAATACTCTGCATGG - -a -s simMouse_chr6.simMouse.chr6 35941 21 + 636262 CCACTACATGTTATGTAACAT -s Anc0.Anc0refChr9 12545 21 + 35212 CCACTGCTTGTAATTACACAT -s Anc1.Anc1refChr2 136748 21 - 144309 CCACTGCTTGTAATTACACAT -s Anc2.Anc2refChr0 31931 21 - 56053 CCACTGCTTGTAATTACATAT -s mr.mrrefChr0 33973 21 + 130230 CCACTACATGTTATGTCACAT -s simCow_chr6.simCow.chr6 574058 19 - 602619 --ACTGCGTGTAATTAGATAT -s simDog_chr6.simDog.chr6 569433 21 - 593897 CCGCGTCTTGTACTTACATGT -s simHuman_chr6.simHuman.chr6 575966 21 - 601863 CCACTGGTTGTAATTACACAT -s simRat_chr6.simRat.chr6 28261 21 + 647215 CCACTACATGTTATGTCACAT - -a -s simMouse_chr6.simMouse.chr6 35962 47 + 636262 ACCAGCTATGGATACTTTACAAAGTGACCAAGAGCAATGGGGTACAA -s Anc0.Anc0refChr9 12568 47 + 35212 ACCAGTTATGGAGAATTCACAGATTGATCAAGAGCACTGGGGGGAAA -s Anc1.Anc1refChr2 136771 47 - 144309 ACCAGTTATGGAGAATTCACAGATTGATCAAGAGCACTGGGGGGAAA -s Anc2.Anc2refChr0 31954 47 - 56053 ACCAGTTATGGAGAATTCCCAGATTGATCAAGTGCCCTGTGGGGAAA -s mr.mrrefChr0 33996 47 + 130230 ACCAGCTATGGATACTTTACAGAGTGATCAAGAGCAATGGGGTACAA -s simCow_chr6.simCow.chr6 574079 45 - 602619 ACTGGTGATGGAGAATACCCAGGTTGATCAAGTGCC--TAGGGGAAA -s simDog_chr6.simDog.chr6 569456 47 - 593897 ACCAGTTAAGGAGAATTCCCAGACTGATCAAGTGCCCTGTAGGAAAA -s simHuman_chr6.simHuman.chr6 575989 47 - 601863 ACCAGTTATGGAAAATTCACAGATTAATCAAGAGCAGTCGGGGGAAA -s simRat_chr6.simRat.chr6 28284 47 + 647215 ACCAGCTATGGATGGTTGGCTGAGTGGTCAAGAGTAATGGGGCAGAA - -a -s simMouse_chr6.simMouse.chr6 36009 1 + 636262 A -s Anc0.Anc0refChr9 12620 1 + 35212 G -s Anc1.Anc1refChr2 136823 1 - 144309 G -s Anc2.Anc2refChr0 32006 1 - 56053 G -s mr.mrrefChr0 34043 1 + 130230 A -s simCow_chr6.simCow.chr6 574129 1 - 602619 T -s simDog_chr6.simDog.chr6 569508 1 - 593897 G -s simHuman_chr6.simHuman.chr6 576041 1 - 601863 G -s simRat_chr6.simRat.chr6 28331 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 36010 1 + 636262 G -s Anc0.Anc0refChr9 12621 1 + 35212 G -s Anc1.Anc1refChr2 136824 1 - 144309 G -s Anc2.Anc2refChr0 32007 1 - 56053 G -s mr.mrrefChr0 34044 1 + 130230 G -s simCow_chr6.simCow.chr6 574130 1 - 602619 G -s simDog_chr6.simDog.chr6 569595 1 - 593897 G -s simHuman_chr6.simHuman.chr6 576042 1 - 601863 G -s simRat_chr6.simRat.chr6 28332 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 36011 105 + 636262 TGGAATGCACACTCAGTTAAGCCAAAGAATGTAAAGAGAATGTGTACACAGGATGTCTACATAGTCAATCATCTTGCTCTTTTTGCTTGGTCTTCGTTGCTTGCT -s Anc0.Anc0refChr9 12622 74 + 35212 TGGAATGCACACTCAATCAAGTGAAAAAGTGTATGGAACATGTTTGCACATATTAAGTA----------GATCTTGCTCTCGTA--------------------- -s Anc1.Anc1refChr2 136825 74 - 144309 TGGAATGCACACTCAATCAAGTGAAAAAGTGTATGGAACATGTTTGCACATATTAAGTA----------GATCTTGCTCTCGTA--------------------- -s Anc2.Anc2refChr0 32008 74 - 56053 TGAAAAGCACACTCAATCAAGTGAAAAAGTGTATGGAACATGTTCGCACATATTAAGTA----------GATCTTGCTCTCGTA--------------------- -s mr.mrrefChr0 34045 105 + 130230 TGGAATGCACACTCAATTAAGACAAAGAATGTAAAGAGAATGTATACACAGGGTGTCTACATAGTCAATGATCTTGCTCTTGTTGCTTGGTCTTCGTTGCTTGCT -s simCow_chr6.simCow.chr6 574135 73 - 602619 TAATAAGCACACT-AATCAACTGAAAAAGTGTATGGAACATGTTAGCACATATTAAGTA----------GGTCTTGCTCTCATA--------------------- -s simDog_chr6.simDog.chr6 569596 73 - 593897 TGAAAAGCACACTCAATCAAGTGAAAAAGTGTATGAAACATGTTCACACATATTAAGTA----------GATCTGGCTTTTGT---------------------- -s simHuman_chr6.simHuman.chr6 576043 74 - 601863 TGGAATGCACGCTCAATCAAGTGAAAAAGTGAATGGAACATGTTTGCACAAATTAAGTA----------GATCTTGGTCTCGTA--------------------- -s simRat_chr6.simRat.chr6 28333 105 + 647215 TGAAATGCACTCTAAATTAAAACAACGAATGTAAAGAGAATGTACACATAGGGTGTCTACATAGTCAATGTTTTTGCTCTTGTTGCTTGTTCTTTATTACTTGCT - -a -s simMouse_chr6.simMouse.chr6 36116 15 + 636262 CTTGTTGACAGTCAC -s Anc0.Anc0refChr9 12696 15 + 35212 CTCATTAACAGTCAC -s Anc1.Anc1refChr2 136899 15 - 144309 CTCATTAACAGTCAC -s Anc2.Anc2refChr0 32082 15 - 56053 CTCATTAATGGTCAG -s mr.mrrefChr0 34150 15 + 130230 CTTGTTGACAGTCAC -s simCow_chr6.simCow.chr6 574220 15 - 602619 CTCATTAATGGTGAA -s simDog_chr6.simDog.chr6 569669 12 - 593897 ---TTTAATGGTCAG -s simHuman_chr6.simHuman.chr6 576117 15 - 601863 CTCATTAACAGTTAC -s simRat_chr6.simRat.chr6 28438 15 + 647215 CTTGTTGACAGTCAT - -a -s simMouse_chr6.simMouse.chr6 36131 27 + 636262 ATTACATCTGAACAACGCATACCGGTA -s Anc0.Anc0refChr9 12711 24 + 35212 ATTGGGTCAGAAC---TTATACTGGTG -s Anc1.Anc1refChr2 136914 24 - 144309 ATTGGGTCAGAAC---TTATACTGGTG -s Anc2.Anc2refChr0 32097 24 - 56053 ATTGGGTCAGAAC---TTATACTGATG -s mr.mrrefChr0 34165 27 + 130230 ATTACATCTGAACAACGTATACTGGTG -s simCow_chr6.simCow.chr6 574235 24 - 602619 ATTGGCTCATAAC---CTGTACTGATG -s simCow_chr6.simCow.chr6 149666 24 + 602619 ACTGGCTCAGAAC---CTGAACTGATG -s simDog_chr6.simDog.chr6 569681 24 - 593897 ATTAGGTCAAAAC---TTATACTGCTG -s simHuman_chr6.simHuman.chr6 576132 24 - 601863 ATTGGGTCAGAAC---TTATACTGGTG -s simRat_chr6.simRat.chr6 28453 27 + 647215 ATTAAATCTGAACAACGTATACTGATG - -a -s simMouse_chr6.simMouse.chr6 36158 21 + 636262 CTTCAAGGCACACTCCCCTAG -s Anc0.Anc0refChr9 12746 21 + 35212 CCACAGAGTACACTCCCCTAG -s Anc1.Anc1refChr2 136949 21 - 144309 CCACAGAGTACACTCCCCTAG -s Anc2.Anc2refChr0 32132 21 - 56053 CCACAGAGTACACTACCCTAG -s mr.mrrefChr0 34192 21 + 130230 CTTCAAAGTACACTCCCCTAG -s simCow_chr6.simCow.chr6 574270 21 - 602619 CCACAGAGTACACTACCCTAG -s simCow_chr6.simCow.chr6 149701 21 + 602619 CCACAGAGTACACTACCCTAG -s simDog_chr6.simDog.chr6 569716 18 - 593897 CCATGGAGTAC---ACCCTAG -s simHuman_chr6.simHuman.chr6 576167 21 - 601863 CCGCAGAGTACCCTCTCCTAG -s simRat_chr6.simRat.chr6 28480 21 + 647215 CTTCAAAGTACACTTCTCTAG - -a -s simMouse_chr6.simMouse.chr6 36179 3 + 636262 GTA -s Anc0.Anc0refChr9 12767 3 + 35212 GCA -s Anc1.Anc1refChr2 136970 3 - 144309 GCA -s Anc2.Anc2refChr0 32153 3 - 56053 GCA -s mr.mrrefChr0 34213 3 + 130230 GTA -s simCow_chr6.simCow.chr6 574294 3 - 602619 GTA -s simCow_chr6.simCow.chr6 149722 3 + 602619 GGA -s simDog_chr6.simDog.chr6 569734 3 - 593897 GCA -s simHuman_chr6.simHuman.chr6 576188 3 - 601863 GCA -s simRat_chr6.simRat.chr6 28501 3 + 647215 GTA - -a -s simMouse_chr6.simMouse.chr6 36182 22 + 636262 GATAAACGGGCTGCAGACTGGA -s Anc0.Anc0refChr9 12770 22 + 35212 GATAAATAGGCTACAGGCTGAA -s Anc1.Anc1refChr2 136973 22 - 144309 GATAAATAGGCTACAGGCTGAA -s Anc2.Anc2refChr0 32197 22 - 56053 GATAAATAGGCTACGGGCTGAA -s mr.mrrefChr0 34216 22 + 130230 GATAAATAGGCTGCACACTGGA -s simCow_chr6.simCow.chr6 574338 22 - 602619 AATGGATGGGCCATGGGCTGAA -s simCow_chr6.simCow.chr6 149814 22 + 602619 GATGGATGGGCTATGGGCTGAA -s simDog_chr6.simDog.chr6 569737 22 - 593897 GATAAATAGGCTACGGGCAGAG -s simHuman_chr6.simHuman.chr6 576191 22 - 601863 GATAAGTAGGCTACAGGCTGAA -s simRat_chr6.simRat.chr6 28504 19 + 647215 GAT---TAGGCTGCACACTGGA - -a -s simMouse_chr6.simMouse.chr6 36204 59 + 636262 AGGCAATGAAAATCCATGACAATTTCTGCTAGTAGCTAGCAACTTTCTAGAGAAAGGTG -s Anc0.Anc0refChr9 12794 52 + 35212 AGTCCATGAAAGTCCATG-------ACACTTACAGTAAAGAACTTTCTAGAGAAAGGTG -s Anc1.Anc1refChr2 136997 56 - 144309 AGTCCATGAAAGTCCATGACA---AACACTTACAGTAAAGAACTTTCTAGAGAAAGGTG -s Anc2.Anc2refChr0 32221 52 - 56053 AGTCCATGCAAGTCCATG-------ACACTTACAGTAAAGGACTTTCTAGAGAAAGGAG -s mr.mrrefChr0 34238 59 + 130230 AGGCCATGAAAGTCCATGACAATTACTGCTAGTAGCTAGTAACTTTCTAGAGAAAGGTG -s simCow_chr6.simCow.chr6 574362 52 - 602619 AGTCCATGCGAGTCCATG-------ATACTTACAGCAAAGGGCATTTTAGAGAAAGGAG -s simCow_chr6.simCow.chr6 149838 52 + 602619 AGTCCATGTGAGTCCATG-------ATACTTATAGCAAAGGGCTTTTTAGAGAAAGGAG -s simDog_chr6.simDog.chr6 569761 52 - 593897 AGTCCACGCAAGTCCATG-------ACACTTGCGGTGAATGACTTTCTAGAGAAAGGGG -s simHuman_chr6.simHuman.chr6 576215 48 - 601863 AGTCCATGAAAGT-----------AACACTGACAGTCAAGAAATCTCTAGAGAAAGGTG -s simRat_chr6.simRat.chr6 28523 58 + 647215 AGG-CATGAAAGCCTGTGACAATTACTGCTCATTACTAGTAACTTTCTAGAGAAAGGTG - -a -s simMouse_chr6.simMouse.chr6 36263 25 + 636262 TTGGAGGATTGGACACACTGGTGGT -s Anc0.Anc0refChr9 12846 25 + 35212 TTGTACAATTGGACACATGGGTGGT -s Anc1.Anc1refChr2 137053 25 - 144309 TTGTACAATTGGACACATGGGTGGT -s Anc2.Anc2refChr0 32273 25 - 56053 TTGTACAATTGGACATATGGCTGGT -s mr.mrrefChr0 34297 25 + 130230 TTGGAGGATTGGACACACTGGTGGT -s simCow_chr6.simCow.chr6 574414 25 - 602619 TTGTACAATTGGACTTATGGCTAGT -s simCow_chr6.simCow.chr6 149890 25 + 602619 TTGTACAATTGGACTAATGGCTAGT -s simDog_chr6.simDog.chr6 569813 25 - 593897 TTGTACAACTGGACATATGGCTGAT -s simHuman_chr6.simHuman.chr6 576263 25 - 601863 TTGTGCAATTGGACACATAGGTGGT -s simRat_chr6.simRat.chr6 28589 25 + 647215 GTGGAGGATTGGACACACTGGTGGG - -a -s simMouse_chr6.simMouse.chr6 36288 1 + 636262 T -s Anc0.Anc0refChr9 12871 1 + 35212 T -s Anc1.Anc1refChr2 137078 1 - 144309 T -s Anc2.Anc2refChr0 32298 1 - 56053 T -s mr.mrrefChr0 34322 1 + 130230 T -s simCow_chr6.simCow.chr6 574439 1 - 602619 T -s simCow_chr6.simCow.chr6 149917 1 + 602619 T -s simDog_chr6.simDog.chr6 569838 1 - 593897 T -s simHuman_chr6.simHuman.chr6 576288 1 - 601863 T -s simRat_chr6.simRat.chr6 28614 1 + 647215 C - -a -s simMouse_chr6.simMouse.chr6 36289 1 + 636262 A -s Anc0.Anc0refChr9 12875 1 + 35212 A -s Anc1.Anc1refChr2 137082 1 - 144309 A -s Anc2.Anc2refChr0 32302 1 - 56053 A -s mr.mrrefChr0 34326 1 + 130230 A -s simCow_chr6.simCow.chr6 574443 1 - 602619 A -s simCow_chr6.simCow.chr6 149921 1 + 602619 A -s simDog_chr6.simDog.chr6 569842 1 - 593897 A -s simHuman_chr6.simHuman.chr6 576292 1 - 601863 A -s simRat_chr6.simRat.chr6 28618 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 36290 5 + 636262 CAAGC -s Anc0.Anc0refChr9 12879 5 + 35212 CACTG -s Anc1.Anc1refChr2 137086 5 - 144309 CACTG -s Anc2.Anc2refChr0 32306 5 - 56053 CACTG -s mr.mrrefChr0 34327 5 + 130230 CAAGC -s simCow_chr6.simCow.chr6 574447 5 - 602619 TGTTG -s simCow_chr6.simCow.chr6 149925 5 + 602619 CATGG -s simDog_chr6.simDog.chr6 569846 5 - 593897 CACTG -s simHuman_chr6.simHuman.chr6 576296 5 - 601863 TACTG -s simRat_chr6.simRat.chr6 28619 5 + 647215 TAAGC - -a -s simMouse_chr6.simMouse.chr6 36295 1 + 636262 C -s Anc0.Anc0refChr9 12884 1 + 35212 C -s Anc1.Anc1refChr2 137091 1 - 144309 C -s Anc2.Anc2refChr0 32311 1 - 56053 C -s mr.mrrefChr0 34332 1 + 130230 T -s simCow_chr6.simCow.chr6 149930 1 + 602619 C -s simDog_chr6.simDog.chr6 569851 1 - 593897 C -s simHuman_chr6.simHuman.chr6 576301 1 - 601863 A -s simRat_chr6.simRat.chr6 28624 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 36296 2 + 636262 AT -s Anc0.Anc0refChr9 12885 2 + 35212 AT -s Anc1.Anc1refChr2 137092 2 - 144309 AT -s Anc2.Anc2refChr0 32312 2 - 56053 AT -s mr.mrrefChr0 34333 2 + 130230 AT -s simCow_chr6.simCow.chr6 149931 2 + 602619 AT -s simDog_chr6.simDog.chr6 569873 2 - 593897 AT -s simHuman_chr6.simHuman.chr6 576302 2 - 601863 TT -s simRat_chr6.simRat.chr6 28625 2 + 647215 GT - -a -s simMouse_chr6.simMouse.chr6 36298 110 + 636262 CGAGGCCAGCATTGAAACAGAAGCAATTGACAGTCTAAACATGTGACATTAACATTGTTTAGATTACAGGCAAATGACGCACTGTCAAGCAATCACATGCACCTGTAGAA -s Anc0.Anc0refChr9 12887 44 + 35212 TGAGGCCAGCATTGAAACAGAAGCAATGGGTAGTCCAAACTAGT------------------------------------------------------------------ -s Anc1.Anc1refChr2 137094 44 - 144309 TGAGGCCAGCATTGAAACAGAAGCAATGGGTAGTCCAAACTAGT------------------------------------------------------------------ -s Anc2.Anc2refChr0 32314 44 - 56053 TGAGGCCAGCATTGATATAGAAGCAATGGGTAGTCCAAACTAGT------------------------------------------------------------------ -s mr.mrrefChr0 34335 104 + 130230 TGAGGCCAGCATTGAAACAGAAGCAATTGATAGTCCAAACATGTGACATTAACATTGTTTAGATTAC------ATGACGCACTGTCAAGCAATCACATGCACCTGTAGAA -s simCow_chr6.simCow.chr6 574452 44 - 602619 TGAGGCCAGCATTGATATAGAAGCAACACATAGTCCAAACTAAT------------------------------------------------------------------ -s simCow_chr6.simCow.chr6 149933 1 + 602619 T------------------------------------------------------------------------------------------------------------- -s simDog_chr6.simDog.chr6 569875 44 - 593897 TGAGGCCAGCTGTGATATAGAAGCAATGGGGAATCCAAACTAGT------------------------------------------------------------------ -s simHuman_chr6.simHuman.chr6 576304 44 - 601863 TGAAGTCAGCATGGAAACAGAAGCAATGGGTAGTCCTGACTAGT------------------------------------------------------------------ -s simRat_chr6.simRat.chr6 28627 104 + 647215 TGAGGCCAGCATTGAAACAGAAGAAATTGATGGTCCAAACATGTGACATTAACATTGTTTAGATTTT------GTGATGCACTGTCAAGCAATCACAGGCACCCTTAGAA - -a -s simMouse_chr6.simMouse.chr6 36408 30 + 636262 GCGCCTGCTTGCCTCATGTAAGAGGTTTGT -s mr.mrrefChr0 34439 30 + 130230 GCGCCTGCTTGCCTCATGTAAGAGGTTTGT -s simRat_chr6.simRat.chr6 28732 30 + 647215 GAGCCTGCTTGCCTCATGCCAGAGATTTGT - -a -s simMouse_chr6.simMouse.chr6 36438 77 + 636262 CATGTAACTCGCTGTGTATATTCTAGATCCCCTGTCCAACTCGCACACTGTTGAGTGATCATAGGCAGTTGTAGAAG -s mr.mrrefChr0 34469 77 + 130230 CATGTAACTCGCTGTGTATATTCTAGATCCCCTGTCCAACTCGCACACTGTTGAGTGATCATAGGCAGTTGTAGAAG -s simRat_chr6.simRat.chr6 28764 77 + 647215 CATGCAGCTCCCTGTGTATATTCTAGATCCCCTGTCTAACTTGCATGGTGTTGAGTGATCACAGGAAACTGTAGAAG - -a -s simMouse_chr6.simMouse.chr6 36515 83 + 636262 ACTCAGTACCCTTCACCTGTGGAAGAAGCCTGGATGATGACATCCGAACAACCTTAATGTACCAATAGTAAAGGCACATAAAA -s Anc0.Anc0refChr9 12931 16 + 35212 ------------------------------------------------------------CCCAACAGT-------CATAACA -s Anc1.Anc1refChr2 137138 16 - 144309 ------------------------------------------------------------CCCAACAGT-------CATAACA -s Anc2.Anc2refChr0 32358 16 - 56053 ------------------------------------------------------------CCCAACCAT-------CATAACA -s mr.mrrefChr0 34546 77 + 130230 ACTCAGTACCCTTCACCTGTGGAAGAAGCCTGGATGA------CCGAACAACCTTAATGTACCAATAGTAAAGGCACATAAAA -s simCow_chr6.simCow.chr6 574496 14 - 602619 ------------------------------------------------------------TCCACCC---------CATGACA -s simDog_chr6.simDog.chr6 569919 16 - 593897 ------------------------------------------------------------CCCAACCAT-------CACAACA -s simHuman_chr6.simHuman.chr6 576348 16 - 601863 ------------------------------------------------------------CCCAACAGT-------CATAACA -s simRat_chr6.simRat.chr6 28842 77 + 647215 ACTCAGTGCCCTTCATCTGTGGCAGGAGCCTGCCTGA------CCAAACAACCTTAATGTACCAATAGGAAAGGCACATAAAA - -a -s simMouse_chr6.simMouse.chr6 36598 5 + 636262 AGCAA -s Anc0.Anc0refChr9 12951 5 + 35212 AGCAA -s Anc1.Anc1refChr2 137158 5 - 144309 AGCAA -s Anc2.Anc2refChr0 32378 5 - 56053 AGCAA -s mr.mrrefChr0 34623 5 + 130230 AGCAA -s simCow_chr6.simCow.chr6 574514 5 - 602619 AGCAT -s simDog_chr6.simDog.chr6 569939 5 - 593897 AGCAA -s simHuman_chr6.simHuman.chr6 576368 5 - 601863 AGCAA -s simRat_chr6.simRat.chr6 28919 5 + 647215 AGCAA - -a -s simMouse_chr6.simMouse.chr6 36603 35 + 636262 GCTAGTCGGCCTGTCTAACTAGCCAAGTTTTTAGA -s Anc0.Anc0refChr9 12956 35 + 35212 GCTAGTCAGATGTCTTGATGTGCCCAATCTCTAAG -s Anc1.Anc1refChr2 137163 35 - 144309 GCTAGTCAGATGTCTTGATGTGCCCAATCTCTAAG -s Anc2.Anc2refChr0 32420 35 - 56053 GCTAGTCAGATGTCTAGATGTGCCCAACCTCTAAG -s mr.mrrefChr0 34628 35 + 130230 GCTAGTCGGCCTGTCTAACTAGCCAAGTTTTTAGA -s simCow_chr6.simCow.chr6 574556 35 - 602619 CCTAGTCAAGTGTCTAGATGTGCCCAACCTCTAAG -s simDog_chr6.simDog.chr6 569981 35 - 593897 GCTAGTCAGATGTCCAGATGTGCCCAACCTTTAAG -s simHuman_chr6.simHuman.chr6 576373 35 - 601863 CCTAAACAGATATCTTGATGTATGCAATCTCTGAT -s simRat_chr6.simRat.chr6 28924 35 + 647215 GCTAGTCAGCCTGTCTAACTAGCCAAGTTCTTAGG - -a -s simMouse_chr6.simMouse.chr6 36638 11 + 636262 CCAAACATGAT -s Anc0.Anc0refChr9 12991 11 + 35212 ACAGACATGAT -s Anc1.Anc1refChr2 137198 11 - 144309 ACAGACATGAT -s Anc2.Anc2refChr0 32455 11 - 56053 ATAGACATGAT -s mr.mrrefChr0 34663 11 + 130230 CCAAACATGAT -s simCow_chr6.simCow.chr6 574846 11 - 602619 ATCCACATGAT -s simDog_chr6.simDog.chr6 570016 11 - 593897 ATAGACATGAT -s simHuman_chr6.simHuman.chr6 576408 11 - 601863 ACAGACATGAT -s simRat_chr6.simRat.chr6 28959 11 + 647215 ACAATCATGAT - -a -s simMouse_chr6.simMouse.chr6 36649 10 + 636262 GTCCCCTTAT -s Anc0.Anc0refChr9 13004 10 + 35212 GTCCCCTTGC -s Anc1.Anc1refChr2 137211 10 - 144309 GTCCCCTTGC -s Anc2.Anc2refChr0 32468 10 - 56053 GCCCCTTTGC -s mr.mrrefChr0 34674 10 + 130230 GTCCCCTTAT -s simCow_chr6.simCow.chr6 574859 10 - 602619 GCCCCTTTGC -s simDog_chr6.simDog.chr6 570029 10 - 593897 GCCTTTTTGC -s simHuman_chr6.simHuman.chr6 576421 10 - 601863 GTCCCCCTGG -s simRat_chr6.simRat.chr6 28970 10 + 647215 GTCCCATCAT - -a -s simMouse_chr6.simMouse.chr6 36659 42 + 636262 GATCAATCACAAATCTTTCATTCATATTAGGAGCAATTAACT -s Anc0.Anc0refChr9 13014 28 + 35212 TCCTGATTACTAAGGTTTTATTCATAT------------A-- -s Anc1.Anc1refChr2 137221 30 - 144309 TCCTGATTACTAAGGTTTTATTCATAT------------ATT -s Anc2.Anc2refChr0 32478 28 - 56053 TCCTGGTTACTGAGGTTTTACTCATGT------------A-- -s mr.mrrefChr0 34684 42 + 130230 GACCAATCACTAATCTTTCATTCATATTAGGAGCAATTAACT -s simCow_chr6.simCow.chr6 574870 28 - 602619 TCCTGCTTACTGAGCTTCTACTCCTGT------------A-- -s simDog_chr6.simDog.chr6 570039 28 - 593897 TCCTGGTTACTGAGGTTTTACTCATGT------------G-- -s simHuman_chr6.simHuman.chr6 576431 30 - 601863 TCCTGATTATTAAGGTTTTATTTGTAT------------ATT -s simRat_chr6.simRat.chr6 28980 42 + 647215 GACCAATCACTAATCTTTAACTCATGTTAGGAGCAATTAACT - -a -s simMouse_chr6.simMouse.chr6 36701 32 + 636262 ATGTTAGCAGCAACTTGGTGACTTATGAGGCT -s Anc0.Anc0refChr9 13042 25 + 35212 ----TAGCGGCAATTTGGTGACCTA---GGCT -s Anc1.Anc1refChr2 137251 29 - 144309 AGGTTAGCGGCAATTTGGTGACCTA---GGCT -s Anc2.Anc2refChr0 32506 25 - 56053 ----TAGCGGCAATTTGGTGACCTA---AGCC -s mr.mrrefChr0 34726 32 + 130230 ATGTTAGCAGCAATTTGGTGACTTATGAGGCT -s simCow_chr6.simCow.chr6 574898 14 - 602619 ----TAGCAGCAGTTTGG-------------- -s simDog_chr6.simDog.chr6 570067 25 - 593897 ----AAGCGGCAATTTGGTGACCTA---AGCC -s simHuman_chr6.simHuman.chr6 576461 23 - 601863 AGGTT------AATTTGGTGACCTA---GGCT -s simRat_chr6.simRat.chr6 29023 32 + 647215 AAGTTAGCAGCAATTTGGTGACTTATGAGGCT - -a -s simMouse_chr6.simMouse.chr6 36733 70 + 636262 ACTACTGGTGACTCTGGACATGCAATATCATACTTTGCACACATGTCTTTATTTGCAGTAACAACAAACA -s Anc0.Anc0refChr9 13073 42 + 35212 ACCATTGGTG--TATGGACATGGAAATTAACACTTTGCACACA--------------------------G -s Anc1.Anc1refChr2 137286 44 - 144309 ACCATTGGTGTATATGGACATGGAAATTAACACTTTGCACACA--------------------------G -s Anc2.Anc2refChr0 32537 42 - 56053 ACCATTGGGG--TATGGACATTGAGATTAACACTTTGCACACA--------------------------G -s mr.mrrefChr0 34758 70 + 130230 ACTACTGGTGTCTCTGGACATGCAATATCACACTTTGCACACATGTCTTTATTTGCAGTAACAACAAACA -s simCow_chr6.simCow.chr6 574912 41 - 602619 ACCATTGGC---TATGGACACAGAGGTTAACACTTTACATGCA--------------------------G -s simDog_chr6.simDog.chr6 570098 42 - 593897 ACCATTGGGG--TCTGGACATTGAGATTAACACATTGAACAAA--------------------------G -s simHuman_chr6.simHuman.chr6 576490 44 - 601863 ACCATTGGTGTATATGGACATGGAAATTTACACTTTGCACACA--------------------------G -s simRat_chr6.simRat.chr6 29055 70 + 647215 ACTACTGGTGTCTCTAGACATGCAATGTCACACATTGCACACATGTCTTTATCTGCAGTAACAACAAACA - -a -s simMouse_chr6.simMouse.chr6 36803 41 + 636262 ATCTTGACATATTTCTAATTGGCCAGATCAGCACATGAATT -s Anc0.Anc0refChr9 13115 41 + 35212 ATCTTGTTATGTTTCAAACTGGTCAGATCAGTGCATAAGTC -s Anc1.Anc1refChr2 137330 41 - 144309 ATCTTGTTATGTTTCAAACTGGTCAGATCAGTGCATAAGTC -s Anc2.Anc2refChr0 32584 41 - 56053 ATCTTCTTATGTTTCAAACTGGTCAGATCAGTGCATAGGTC -s mr.mrrefChr0 34828 41 + 130230 ATCTTGATATATTTCTAATTGGCCAGATCAGCACATGAATT -s simCow_chr6.simCow.chr6 574979 36 - 602619 ATCTTCTTATGGTTTAAACTGGTCAGAT--GTG---AGGTC -s simDog_chr6.simDog.chr6 570145 41 - 593897 ATCTTCTTATTTTTCAAACTGGTCAGATCAGTGCATAGGTC -s simHuman_chr6.simHuman.chr6 576534 41 - 601863 ATTGTGCTATGTTTCAAACTGATCAGATCAGTGTCTAAGCC -s simRat_chr6.simRat.chr6 29125 41 + 647215 ATCTTTGTATATTTCTAATTGGCCAGATGAGCACATGAATT - -a -s simMouse_chr6.simMouse.chr6 36844 51 + 636262 ACTCACACCAATGGTGGTTTTGAAAAATGAATGCATCTCACATGCATTTGA -s Anc0.Anc0refChr9 13156 51 + 35212 ATAAGAGCCCACCGTGGTTTTGATAAATGAATGCATTTCACATGCATTTCA -s Anc1.Anc1refChr2 137371 51 - 144309 ATAAGAGCCCACCGTGGTTTTGATAAATGAATGCATTTCACATGCATTTCA -s Anc2.Anc2refChr0 32625 51 - 56053 ATAAGAGCCCACCTTGGTTTTGATAAATGAATGCATTTCACATGCATTACA -s mr.mrrefChr0 34869 51 + 130230 ATTCAAACCAATGGTGGTTTTGAAAAATGAATGCATCTCACATGCATTTGA -s simCow_chr6.simCow.chr6 575016 51 - 602619 ACAAGAGCACACTTTGGTTTTGATACGTGAATGCTTTTCACCTGCATTCAA -s simDog_chr6.simDog.chr6 570186 51 - 593897 ATAAGAGGCCGCCTTGGTTTTGATAAATAAATGCATTTCACATGCATTACA -s simHuman_chr6.simHuman.chr6 576575 51 - 601863 ATATGAGCTGACCGTGGTATTGATAAATGAATGCATTTAACATGCATTTCA -s simRat_chr6.simRat.chr6 29166 51 + 647215 ATTCAAAACAGTGGTGGTTTCCAACAATGAATGCACGTCACATACATTTGA - -a -s simMouse_chr6.simMouse.chr6 36895 5 + 636262 CATGA -s Anc0.Anc0refChr9 13207 4 + 35212 CATG- -s Anc1.Anc1refChr2 137422 4 - 144309 CATG- -s Anc2.Anc2refChr0 32676 4 - 56053 CATG- -s mr.mrrefChr0 34920 5 + 130230 CATGA -s simCow_chr6.simCow.chr6 575067 4 - 602619 TAGC- -s simDog_chr6.simDog.chr6 570237 4 - 593897 CATG- -s simHuman_chr6.simHuman.chr6 576679 4 - 601863 CATG- -s simRat_chr6.simRat.chr6 29217 5 + 647215 CATGA - -a -s simMouse_chr6.simMouse.chr6 36900 41 + 636262 TGTACATCAGTGGTATCTACATACGGGGTGACGATGTTGTT -s Anc0.Anc0refChr9 13256 35 + 35212 tGGACATCAGTGTCATCTCCATATTGGGCAAA------GTT -s Anc1.Anc1refChr2 137471 41 - 144309 tGGACATCAGTGTCATCTCCATATTGGGCAAAGTTGTTGTT -s Anc2.Anc2refChr0 32725 35 - 56053 tGGACATAAGGGCCAACTCCATACTGGACAGA------GTT -s mr.mrrefChr0 34947 41 + 130230 TGTACATCAGTGTCATCTACATATGGGGTGACGATGTTGTT -s simCow_chr6.simCow.chr6 575111 9 - 602619 --------------------------GATACA------GTT -s simDog_chr6.simDog.chr6 570286 35 - 593897 TGGACATAAGGGCCAACTCCATACTGGACAGA------GTC -s simHuman_chr6.simHuman.chr6 577007 41 - 601863 tGGGTACCAGTGTCATCCCCACATTAGGCCAAGTTGTTGTT -s simRat_chr6.simRat.chr6 29244 41 + 647215 TATACATCAGTGTCATCTACATATGCGGAGAGGATGTTGTT - -a -s simMouse_chr6.simMouse.chr6 36941 27 + 636262 AATGGTTATTCAAATAAAACTTTAAAT -s Anc0.Anc0refChr9 13291 27 + 35212 AATGGTCAATCACATAAGGCTTCGAAT -s Anc1.Anc1refChr2 137512 27 - 144309 AATGGTCAATCACATAAGGCTTCGAAT -s Anc2.Anc2refChr0 32760 27 - 56053 AATGGTCAAGCACATAAGGCTCTGAAT -s mr.mrrefChr0 34988 27 + 130230 AATGGTTATTCAAATAAAACTTCAAAT -s simCow_chr6.simCow.chr6 575120 27 - 602619 AATGATCAAGCAAATAAAGCTCTCAAT -s simCow_chr6.simCow.chr6 432254 27 - 602619 ACTCGTCAATCACATAGAGCTCTAAAT -s simDog_chr6.simDog.chr6 570321 27 - 593897 AATGGCGAAGCTCATAAGGCTCTGGAT -s simHuman_chr6.simHuman.chr6 577048 27 - 601863 AATGGTCAATTGCTTAAGGCTTCGAAT -s simRat_chr6.simRat.chr6 29285 26 + 647215 AA-GGTTATTCAGATGAAACTCCAAAT - -a -s simMouse_chr6.simMouse.chr6 36968 47 + 636262 CTACCACTGACATAAAGTGCTTCCTCATTTCACACTACCATATAGCC -s Anc0.Anc0refChr9 13319 40 + 35212 CTGCAACTGACATAAATT-------CCTTTCTCACTATCATGTAGCC -s Anc1.Anc1refChr2 137540 40 - 144309 CTGCAACTGACATAAATT-------CCTTTCTCACTATCATGTAGCC -s Anc2.Anc2refChr0 32788 40 - 56053 CTGAAACTGACATAAATT-------GCTTTCTCACTATCAGGTAACC -s mr.mrrefChr0 35015 47 + 130230 CTGCAACTGACATAAAGTGCTTCCTCATTTCACACTACCATGTAGCC -s simCow_chr6.simCow.chr6 575148 40 - 602619 CTGAGATTGGGGCAGATT-------GTGCTCTCACTATTAGGTGACC -s simCow_chr6.simCow.chr6 432282 40 - 602619 CTGAGACTGGCACAAACT-------GTGCTCTCACTATCAGGTAATC -s simDog_chr6.simDog.chr6 570349 40 - 593897 CTTAAACTGACATAAATT-------GCTTTCTCATTATCAGGAAACC -s simHuman_chr6.simHuman.chr6 577076 40 - 601863 CTGCAATTGACATAAACT-------CCTTTCTCACAATCATGTAGGC -s simRat_chr6.simRat.chr6 29311 47 + 647215 CTGCAACTGACATAAAGTGCTTCGCCATTTCATACTACCATGTAGCC - -a -s simMouse_chr6.simMouse.chr6 37015 26 + 636262 TGTTGACACGTACCCCCCCAGGTTCA -s Anc0.Anc0refChr9 13364 26 + 35212 TTTCAATGTGCACCTCCCCGGAGTCG -s Anc1.Anc1refChr2 137585 26 - 144309 TTTCAATGTGCACCTCCCCGGAGTCG -s Anc2.Anc2refChr0 32837 26 - 56053 TTTCAAGGTGCACCTCCCCGGAGTCG -s mr.mrrefChr0 35062 26 + 130230 TGTTGATGTGTACCCCCCCAGGTTCA -s simCow_chr6.simCow.chr6 575197 26 - 602619 TTCAAAGGGGTACCTCTCAGGAGTTG -s simCow_chr6.simCow.chr6 432331 26 - 602619 TTGGAAGGGGCACCTCTCCGGAGTTG -s simDog_chr6.simDog.chr6 570397 25 - 593897 TTTCAACATGCACTTCCCCAGAGTC- -s simHuman_chr6.simHuman.chr6 577121 26 - 601863 TTTCAATGTGCAGGTCCCTGGAGTCC -s simRat_chr6.simRat.chr6 29358 26 + 647215 TGTTGATGTGTACCCCTCCAGGTTCA - -a -s simMouse_chr6.simMouse.chr6 37041 24 + 636262 CTCATTCAATATGCTCCCTCAACC -s Anc0.Anc0refChr9 13390 24 + 35212 CTGATGCAATACATTCCCATACTC -s Anc1.Anc1refChr2 137611 24 - 144309 CTGATGCAATACATTCCCATACTC -s Anc2.Anc2refChr0 32865 24 - 56053 CTGATGCAATACATTCCCATACTC -s mr.mrrefChr0 35088 24 + 130230 CTCATTCAATATGTTCCCACACTC -s simCow_chr6.simCow.chr6 575225 24 - 602619 CCCATGCAATACAATCAAATACAA -s simCow_chr6.simCow.chr6 432359 24 - 602619 CCCATGCAATACAGTCGAATACAC -s simDog_chr6.simDog.chr6 570423 24 - 593897 GTGATGCAATGAATCCCCATACTT -s simHuman_chr6.simHuman.chr6 577147 24 - 601863 ATGATGCAATACATTGCCAAACTC -s simRat_chr6.simRat.chr6 29384 24 + 647215 GTCATTCAATATGTTCCAATACTC - -a -s simMouse_chr6.simMouse.chr6 37065 89 + 636262 ATCTAGCCCAATTTCCTGAGTTGGATTATACTTGAGGAAAGCCCTAGAAAATTTCCAACCTTCAATGACAAAATGGCATGATCCTTCTG -s Anc0.Anc0refChr9 13415 78 + 35212 ACCTAGCCCAATTTCCTGTGATGAATTATACT-----------CTAGAAAATTTCCCACTTTCAATGACAATATAGCATGATTTTTCTG -s Anc1.Anc1refChr2 137636 78 - 144309 ACCTAGCCCAATTTCCTGTGATGAATTATACT-----------CTAGAAAATTTCCCACTTTCAATGACAATATAGCATGATTTTTCTG -s Anc2.Anc2refChr0 32890 78 - 56053 ACCTAGCCTAATTTCCTGTGATGAAGTATACA-----------CAAGAAAATTTCCCACTTTCAATGACAATATAGCATGATTTTCCTG -s mr.mrrefChr0 35112 89 + 130230 ATCTAGCCCAATTTCCTGAGTTGGATTATACTTGAGGAAAGCCCTAGAAAATTTCCAACCTTCAATGACAAAATGGCATGATCCTTCTG -s simCow_chr6.simCow.chr6 575250 65 - 602619 ACTTAGCCAAGTTTC--CTGA----------------------CAAGAACATTTCCTAATGTCAATGTCAATATTGCATGATTTTCCTG -s simCow_chr6.simCow.chr6 432384 49 - 602619 ACTTAGCCTGATTTC--GTGA----------------------CAAGAACATTCCCCAATGTCAATGACAATA---------------- -s simDog_chr6.simDog.chr6 570448 78 - 593897 ATCTATCCTAATTTCCTGAGATGAAGTATACA-----------CCGGAAAATTTCCCACTTTCAATGACATTATAGCATGATTTGCTTG -s simHuman_chr6.simHuman.chr6 577172 78 - 601863 ACCTAGCCCAATTTCCTGTGATCAATTGTACT-----------CTAGAAAATTTCCCACTTTCAATGACAATATAACATGATTATTCTG -s simRat_chr6.simRat.chr6 29408 89 + 647215 ATCTAGCCCAATTTCCTGAGTTGGATTATACTTGCGAAAAGCCCTAGAAAATTTCTGACCTTTAATGACAAAATGGCATGATCCTTCTG - -a -s simMouse_chr6.simMouse.chr6 37154 36 + 636262 CAAAAAGTCTTAGTACACTCATAATAATTTCCCTAA -s Anc0.Anc0refChr9 13494 34 + 35212 CAAATAGT-TTGTTACACTTACAATAATTTCACTA- -s Anc1.Anc1refChr2 137715 35 - 144309 CAAATAGT-TTGTTACACTTACAATAATTTCACTAA -s Anc2.Anc2refChr0 32969 34 - 56053 CAAATAGT-TGGTTACACTTACAATAACTGCACCA- -s mr.mrrefChr0 35202 36 + 130230 CAAAAAGTCTTAGTACACTCATAATAATTTCCCTAA -s simCow_chr6.simCow.chr6 575316 34 - 602619 CAAATTGT-TGGTTACACTTACAATAACCACACCA- -s simDog_chr6.simDog.chr6 570527 34 - 593897 CAAATAGT-TGGTTACACATCCAAAGACTGCATCA- -s simHuman_chr6.simHuman.chr6 577251 35 - 601863 CAAATAGT-TTGTTACACTTAAAATAATTTCGCTAA -s simRat_chr6.simRat.chr6 29498 36 + 647215 CAAAAAGTCTCAGTACACTCACAATAATTTCCCTAG - -a -s simMouse_chr6.simMouse.chr6 37190 116 + 636262 GCAGTGCACTTATATGGGCTATGTGCACAGCCCAGTCACAGGATCGATAGAGGATCTCCTGGTAGTTATTGTGTATCTAGCATATATTGTGTATCTAGCACTGAGCACCATATTCT -s Anc0.Anc0refChr9 13528 96 + 35212 -TACTTCAATTCAAGGGGCTATGTACACAGCCATGTTGCAGGATCTATGGCGG-TCACATGATTGCCATTGTGTATCTAGCAT------------------TGACCACTTTACCTT -s Anc1.Anc1refChr2 137758 97 - 144309 GTACTTCAATTCAAGGGGCTATGTACACAGCCATGTTGCAGGATCTATGGCGG-TCACATGATTGCCATTGTGTATCTAGCAT------------------TGACCACTTTACCTT -s Anc2.Anc2refChr0 33003 96 - 56053 -TACTTCAATTCAAGGAGCTATATACACAGCCATGTTGCAGGATCTATGGCAG-TCAGATGATTGCCATTGTGTATCTAGCAT------------------TGACCACTTTACCTT -s mr.mrrefChr0 35246 98 + 130230 GCAGTTCACTTCTAGGGGCTATGTGCACAGCCCAGTCGCAGGATCGATGGAGGATCTCATGATAGCTATTGTGTATCTAGCAT------------------TGAGCACCTTATTCT -s simCow_chr6.simCow.chr6 575351 93 - 602619 -TACTTCTATTAGAGGAGTTATATAGACAGCCATGTTGGAGGATCTATG-TAC-TTCTATG--TACTATTGTGTATCTAGCAT------------------TGACAGCTTTACCTT -s simDog_chr6.simDog.chr6 570561 96 - 593897 -TACTTCAATTCAAGGAGCTATAAACACAGCCATATCACAGGGCCTATGGCAG-TCAGATGATTGCCATCATGTATCTAGCAC------------------TGACCACATTACATT -s simHuman_chr6.simHuman.chr6 577295 95 - 601863 GTACTTCGTTTCAGGGGGCTATGTACACCGCCGTGTTGCA--ATCTATGTGGG-TCACATGATTGCCATTGTGTATCTAGCAT------------------TAACCACTTCACCTT -s simRat_chr6.simRat.chr6 29542 98 + 647215 GCAGTTCACTTCTAGGGGCTCTGTGCACAGCCAAGTCGCAGGATCCATGGAAGATCTCATGATAGCTATTGTCTATCTAGCAT------------------TGAGCACCTTGTTCT - -a -s simMouse_chr6.simMouse.chr6 37306 3 + 636262 GGG -s Anc0.Anc0refChr9 13643 3 + 35212 GGG -s Anc1.Anc1refChr2 137874 3 - 144309 GGG -s Anc2.Anc2refChr0 33118 3 - 56053 AAG -s mr.mrrefChr0 35367 3 + 130230 GGG -s simCow_chr6.simCow.chr6 575463 3 - 602619 AAG -s simDog_chr6.simDog.chr6 570676 3 - 593897 AAG -s simHuman_chr6.simHuman.chr6 577420 3 - 601863 GGG -s simRat_chr6.simRat.chr6 29672 3 + 647215 GGG - -a -s simMouse_chr6.simMouse.chr6 37309 4 + 636262 GGTC -s Anc0.Anc0refChr9 13646 4 + 35212 GGTC -s Anc1.Anc1refChr2 137877 4 - 144309 GGTC -s Anc2.Anc2refChr0 33121 4 - 56053 AGTC -s mr.mrrefChr0 35370 4 + 130230 GGTC -s simCow_chr6.simCow.chr6 575489 4 - 602619 AGTC -s simDog_chr6.simDog.chr6 570679 4 - 593897 AGTC -s simHuman_chr6.simHuman.chr6 577423 4 - 601863 GGTC -s simRat_chr6.simRat.chr6 29675 4 + 647215 GGTC - -a -s simMouse_chr6.simMouse.chr6 37313 33 + 636262 AATTAGGAAAACGGCAGCTCCACTTGATTGGCA -s Anc0.Anc0refChr9 13650 22 + 35212 GATTAGGAA--CCGCAGTGACACT--------- -s Anc1.Anc1refChr2 137881 24 - 144309 GATTAGGAA--CCGCAGTGACACTCC------- -s Anc2.Anc2refChr0 33145 22 - 56053 GACTGGCAG--CCTCTATGACACT--------- -s mr.mrrefChr0 35374 33 + 130230 AATTAGGAAAACGGCAGTTCCACTTGATTGGCA -s simCow_chr6.simCow.chr6 575512 17 - 602619 GACTG-------CTCTTTAACTGA--------- -s simDog_chr6.simDog.chr6 570703 22 - 593897 CACTGGCAG--CCTCTATGATACT--------- -s simHuman_chr6.simHuman.chr6 577427 24 - 601863 GATTAGGAA--CTGCAGTGACACTCC------- -s simRat_chr6.simRat.chr6 29679 33 + 647215 AATTAGGAAAACCGCAGTTCCGCTAGATTAGCA - -a -s simMouse_chr6.simMouse.chr6 37346 232 + 636262 GTAAGAGTAAGTGGTGAAACTAGTAGTGACATAAGTAGTGTTGTCGGATCGAGACGTGGATTCCAAGGGTAGGGTTAAATGGTTCGAACTCTCATCGCGGGACTATATAGTAGTGCTGATGGGTCGAGACGTGGAATCTGGGGTTAGGACCATGCTGTCAACGGGTTCCATAGGAATTGTGCTACCTCCCAATTTCACTATTGACACCAATTACATATTCGGTCATATGTAG -s Anc0.Anc0refChr9 13672 53 + 35212 -----AGTAAGTGGC-CAACTAATAGTGACACAA-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------CAATTACATATTCGTTGATATGTAT -s Anc1.Anc1refChr2 137905 57 - 144309 -CACGAGTAAGTGGC-CAACTAATAGTGACACAA-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------CAATTACATATTCGTTGATATGTAT -s Anc2.Anc2refChr0 33167 53 - 56053 -----AGTAAGTGGC-CAACTAATAGGAAGACAA-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------CAAATGCATGATCTTTGAAATGTAT -s mr.mrrefChr0 35407 59 + 130230 GTAAGAGTAAGTGGTGAAACTAATAGTGACATAA-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------CAATTACATATTCGGTCATATGTAG -s simCow_chr6.simCow.chr6 575529 49 - 602619 -----AGTAAGTGGC-CAACTAATAACAAGTCAA-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------CAAATGC----TCTTTCCAATGTAT -s simDog_chr6.simDog.chr6 570725 53 - 593897 -----AGTAGGTGGC-CAACTTATAGGAAGACAA-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------CAAATGCATGATCTTTGAAATGTAT -s simHuman_chr6.simHuman.chr6 577451 52 - 601863 -CACGAGTAAGTGGC-CAACTAATAGTGACACAA-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------CAATTACATATT-GTTAATCT---- -s simRat_chr6.simRat.chr6 29718 59 + 647215 GTAAGAGTAAGTGGTGAAACTAATAGTGACAAAA-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------CAATTACATATTCCGTCATATGTAG - -a -s simMouse_chr6.simMouse.chr6 37578 44 + 636262 CCCAAACTTTGTTAACAATCAATCTTTTGGAGAGTATTTACATA -s Anc0.Anc0refChr9 13725 25 + 35212 CATCTACTTTTTTAACAATCAATTT------------------- -s Anc1.Anc1refChr2 137962 25 - 144309 CATCTACTTTTTTAACAATCAATTT------------------- -s Anc2.Anc2refChr0 33220 25 - 56053 CATCTATTTTTCTAACAATCAATTT------------------- -s mr.mrrefChr0 35466 44 + 130230 CCCAAACTTTTTTAACAATCAATCTTTTGAAGAATATTTACATA -s simCow_chr6.simCow.chr6 575581 25 - 602619 CATCTATTTCGCTAACAATCAATTT------------------- -s simDog_chr6.simDog.chr6 570778 25 - 593897 CACCTATTTTTCTAACAATCAATTT------------------- -s simHuman_chr6.simHuman.chr6 577503 20 - 601863 -----ACTTTTTTGACAATCAATTT------------------- -s simRat_chr6.simRat.chr6 29777 44 + 647215 CCCAAACTTTTTCAACAATTAATCTTTTGAAGAATAATTACATG - -a -s simMouse_chr6.simMouse.chr6 37622 83 + 636262 CCTCTATATTGCACTGTCTACTTTTCAGTTGATTTGCTGAGTGGCATTAGCATATGTAGTACCATTTACTTTGTAATCAATAC -s mr.mrrefChr0 35510 83 + 130230 CCTCTATATTGCACTGTCTACTTTTCAGTTGATTTGCTGAGTGGCATTAGCATATGTAGTACCATTTACTTTGTAATCAATAC -s simRat_chr6.simRat.chr6 29823 83 + 647215 CCTCTATATTGCACCATCTACTTTTCAGTTGATTTGCTGAGCGGCATAGGCATATGTAGTACCATGTACTTTTTAATCAATAT - -a -s simMouse_chr6.simMouse.chr6 37705 33 + 636262 GCTGAGTGGCCTAAGCAGCTTGAATATGAACAT -s Anc0.Anc0refChr9 13750 26 + 35212 GCTAAGAGGAATAAG---CTTGAACATAA---- -s Anc1.Anc1refChr2 137987 26 - 144309 GCTAAGAGGAATAAG---CTTGAACATAA---- -s Anc2.Anc2refChr0 33245 26 - 56053 GCTAAGAGGAATAAG---CTTGAACATAA---- -s mr.mrrefChr0 35593 31 + 130230 GCTGAGTGGCCTAAG--GCTTGAATATGAACAT -s simCow_chr6.simCow.chr6 575606 24 - 602619 GCCAAGAGGTATAAG---CTT--ACATAC---- -s simDog_chr6.simDog.chr6 570803 26 - 593897 GCTGAGTGGAACAAT---CTTGAACATAA---- -s simHuman_chr6.simHuman.chr6 577523 26 - 601863 GCTAAGAGGGATAAG---CTTGAAGATAA---- -s simRat_chr6.simRat.chr6 29907 31 + 647215 GCTGACTGGCGTAAG--GGATGAATTTGAGCAT - -a -s simMouse_chr6.simMouse.chr6 37738 17 + 636262 GGGTAATAAAATATTGT -s Anc0.Anc0refChr9 13776 16 + 35212 -GGTAATAAAATAATGT -s Anc1.Anc1refChr2 138013 16 - 144309 -GGTAATAAAATAATGT -s Anc2.Anc2refChr0 33271 16 - 56053 -GGCAATAAAATAATGT -s mr.mrrefChr0 35624 17 + 130230 GGGTAATAAAATATTGT -s simCow_chr6.simCow.chr6 575630 16 - 602619 -AGCAATAAAATAATGT -s simDog_chr6.simDog.chr6 570829 16 - 593897 -GGCAATAAAATAACGT -s simHuman_chr6.simHuman.chr6 577549 16 - 601863 -GGTAATAGAATAATGT -s simRat_chr6.simRat.chr6 29939 17 + 647215 GGGTAATAAAATATTGT - -a -s simMouse_chr6.simMouse.chr6 37755 17 + 636262 ACCATGCATGAATGATG -s Anc0.Anc0refChr9 13795 7 + 35212 A----------GTGCTG -s Anc1.Anc1refChr2 138032 8 - 144309 AG---------GTGCTG -s Anc2.Anc2refChr0 33290 7 - 56053 A----------GTGCTG -s mr.mrrefChr0 35641 8 + 130230 AC---------ATGATG -s simCow_chr6.simCow.chr6 575646 2 - 602619 ---------------TG -s simDog_chr6.simDog.chr6 570848 7 - 593897 A----------GTGCTG -s simHuman_chr6.simHuman.chr6 577568 8 - 601863 AG---------GTGCTG -s simRat_chr6.simRat.chr6 29956 8 + 647215 TT---------ACTATG - -a -s simMouse_chr6.simMouse.chr6 37772 228 + 636262 CATGAATGAGGTTCATATCTGCATATCATCTGCGTATTAATACAAAGGCTGATGTACACAACACCTTGAAAGTTGTGAACATCATGAAGCCTGAAAGGATGTCAGTCCAGTTTTGAGTATCAGGTGATAGATAGCCTGTTTTATGGGGTGAAGGGTGTTGAGTCCTTCTGCACGTGCCCGTGATCACTTGTCACCATGTGAGGCGGGCAGACCCCTTCTAGAGGTGCC -s Anc0.Anc0refChr9 13811 46 + 35212 CATGAAAAAGGTCCTTATCTCCATATGATTTGCATATTAATACAAA-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- -s Anc1.Anc1refChr2 138049 46 - 144309 CATGAAAAAGGTCCTTATCTCCATATGATTTGCATATTAATACAAA-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- -s Anc2.Anc2refChr0 33306 46 - 56053 CATGAAAAAGGTCCTTATCTCCATATGACTTGCATATTAATACATA-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- -s mr.mrrefChr0 35649 226 + 130230 CATGAATGAGGTTCATATCTGCATATCATCTGCGTATTAATACAAAGGCTGATGTACACAACACCTTGAAAGTTGTGAACATCATGAAGCCTGAAAGGATGTCAGTCCAGTTTTGAGTATCAGGTGATAGATAGCCTGTTTTATGGGGTGAAGGGTGTTGAGTCCTTCTGCACGTGCCCGTGATCACTTGTCACCA--TGAGGCGGGCAGACCCCTTCTAGAGGTGCC -s simCow_chr6.simCow.chr6 575657 45 - 602619 CATGAAAAAGGTCCTTATCTCCATATGACTTGTTTATTAATAAAT--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- -s simDog_chr6.simDog.chr6 570864 45 - 593897 TGT-AAAAAGGTCTTCATCTCCATAAGACTTGCAGATTAGTACATA-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- -s simHuman_chr6.simHuman.chr6 577585 46 - 601863 CATAAAAAAGACCCTTATCTCCATATGATTTACATACTAATACAAA-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- -s simRat_chr6.simRat.chr6 29964 226 + 647215 CATTAAAGAGGTTCATATCTCCATAGGATCTGCGTATTAATACAGAGGTTGATGTACACGACACCCTGAAAGTTGTGAACATCATGAAGCCTGAATGGATGTTAGTCCAATTATGAATGTCAGGTGATAGATAGCATGTTTTGCAGGGTGAAGGGTGTTGGGTCGTTCTGCACATGCCTATGATCATTTGTCACCA--TGAGTCAGGCATGACCCTTCTAGAGGTGCC - -a -s simMouse_chr6.simMouse.chr6 38000 129 + 636262 TGATTGTTTCACATCATGTGAAGCAGGGCAGGCTCAGCAGCCTGGTACTAACTGTGCCTGCATGACCATGCTTGCCTTTTAATGGAGCTTGGCATGAGGTACTGTATGAAATCTGAACAAGGTAAAGCA -s Anc0.Anc0refChr9 13857 20 + 35212 -------------------------------------------------------------------------------------------------------------AAAGTGGACATGGTACAACA -s Anc1.Anc1refChr2 138095 20 - 144309 -------------------------------------------------------------------------------------------------------------AAAGTGGACATGGTACAACA -s Anc2.Anc2refChr0 33352 20 - 56053 -------------------------------------------------------------------------------------------------------------AGAGTGGTCATGCTACAACA -s mr.mrrefChr0 35875 123 + 130230 TGATTGTTTCACATCATGTGAAGCAGGG-AGGCTCAGCAGCCTGGTACTAACTGTGCCTGCATGACCATGCTTGCCTTTTAATGGAGCT---CATGA--TACTGTATGAAATCTGAACAAGGTAAAGCA -s simCow_chr6.simCow.chr6 575702 17 - 602619 ----------------------------------------------------------------------------------------------------------------GTGCTCATGCGACAACA -s simDog_chr6.simDog.chr6 570909 19 - 593897 -------------------------------------------------------------------------------------------------------------AGAG-GGTCATGCTACTACA -s simHuman_chr6.simHuman.chr6 577631 20 - 601863 -------------------------------------------------------------------------------------------------------------AAAGTGGACATAGTACAACA -s simRat_chr6.simRat.chr6 30192 123 + 647215 TGATTGTCCAACATCATGTGAAACAGGG-AGGCTCAGCAGCCTGGTCCTAACCGTGTGCACATGACCATGCTTGCTCTTGATTGGAGCT---CATGA--CACTGTATGAAATCTAAATAAGGTTAAGCA - -a -s simMouse_chr6.simMouse.chr6 38129 16 + 636262 TAACCCATTTCAACCA -s Anc0.Anc0refChr9 13879 15 + 35212 TAACATATTACAC-CC -s Anc1.Anc1refChr2 138117 15 - 144309 TAACATATTACAC-CC -s Anc2.Anc2refChr0 33374 15 - 56053 TAACATATCACAC-CC -s mr.mrrefChr0 35998 15 + 130230 TAACCCATTTCAA-CA -s simCow_chr6.simCow.chr6 575721 15 - 602619 TAACATATCATAC-CA -s simDog_chr6.simDog.chr6 570930 15 - 593897 TAACATATCACGC-TC -s simHuman_chr6.simHuman.chr6 577653 15 - 601863 TAACATACTACAC-CC -s simRat_chr6.simRat.chr6 30315 15 + 647215 TAACCCATTTCAA-CA - -a -s simMouse_chr6.simMouse.chr6 38145 60 + 636262 TATTCTGATCCCCTCTGAGATACCTCAATATTTTCCACTTTTTGGTTTAATGGGTATGTT -s Anc0.Anc0refChr9 13894 59 + 35212 AATTCTGATATTCTGTGTGATGACCCAATATTTCCCACCTTTTATTATGATGGGTCTG-T -s Anc1.Anc1refChr2 138132 59 - 144309 AATTCTGATATTCTGTGTGATGACCCAATATTTCCCACCTTTTATTATGATGGGTCTG-T -s Anc2.Anc2refChr0 33390 59 - 56053 AATTCTGATATTCTGTGTGATGACCCAATGTTTCCCACCTTTTATTATGATGGATCTG-T -s mr.mrrefChr0 36013 59 + 130230 TATTCTGATCCCCTCTGAGATACCTCAATATTTTCCACTTTTTGGTTTAATGGGTATG-T -s simCow_chr6.simCow.chr6 575737 47 - 602619 AATTCTGATCTTCCGTGTGATGA-CCAATGTTTGACACC-----------TGGTACTG-T -s simDog_chr6.simDog.chr6 570946 58 - 593897 AATTCTGATATCCTGT-TGATGACCCAATGTTTCCCAGCTTTTATTATGATGGATTTG-T -s simHuman_chr6.simHuman.chr6 577668 59 - 601863 AATTCTGATTTTCTGTGTGATGAGCCCACATGTCCCACCTTTTATTGTGATGTGTCTG-T -s simRat_chr6.simRat.chr6 30330 59 + 647215 TAATTTGGTCTCCTCTGAGATACCTCAATATTTCCCACTTTTTTGTTTAATGGGTCTG-T - -a -s simMouse_chr6.simMouse.chr6 38205 30 + 636262 GGGAGGGTATCTTAGTCTAATAACTTGTCC -s Anc0.Anc0refChr9 13954 30 + 35212 GGGAAAGTATCCCAGTCTACTAACATGTGC -s Anc1.Anc1refChr2 138192 30 - 144309 GGGAAAGTATCCCAGTCTACTAACATGTGC -s Anc2.Anc2refChr0 33450 30 - 56053 GGGAAAGTATCCCAGTCTACTAATATGTGC -s mr.mrrefChr0 36072 30 + 130230 GGGAGGGTATCTTAGTCTAATAACTTGTCC -s simCow_chr6.simCow.chr6 575785 28 - 602619 GGGATGGTATCCCAGTCTGCTA--ATGTGA -s simDog_chr6.simDog.chr6 571005 27 - 593897 GGGGAAGTATCCAAGTCCACTAATGT---C -s simHuman_chr6.simHuman.chr6 577728 29 - 601863 GGAAAAGTAGCCCAGGCTC-TAACATGTGC -s simRat_chr6.simRat.chr6 30389 30 + 647215 GCAAGGGTAACCCAGTCTAATAACTTGTCC - -a -s simMouse_chr6.simMouse.chr6 38235 21 + 636262 TAGTGAATTTTCAAGGTTATA -s Anc0.Anc0refChr9 13986 20 + 35212 TACTG-GAGTTTAGGGTTATA -s Anc1.Anc1refChr2 138224 20 - 144309 TACTG-GAGTTTAGGGTTATA -s Anc2.Anc2refChr0 33482 20 - 56053 TACTG-GAGTCTAGGGTTATA -s mr.mrrefChr0 36102 20 + 130230 TAGTG-ATTTTCAAGGTTATA -s simCow_chr6.simCow.chr6 575815 20 - 602619 TACTG-GAGTCCAGGGTTATA -s simDog_chr6.simDog.chr6 571034 20 - 593897 TACTG-GGGTCTACGGTTATA -s simHuman_chr6.simHuman.chr6 577759 20 - 601863 TATTG-GAGTTTAGAGTTATA -s simRat_chr6.simRat.chr6 30419 20 + 647215 TGCTG-ATTTTCAAGGTTATA - -a -s simMouse_chr6.simMouse.chr6 38256 20 + 636262 TATCCCACACACACTATCTG -s Anc0.Anc0refChr9 14006 16 + 35212 GATCC----CTCATTATCTG -s Anc1.Anc1refChr2 138244 16 - 144309 GATCC----CTCATTATCTG -s Anc2.Anc2refChr0 33502 16 - 56053 GATCC----CTCATTATCAG -s mr.mrrefChr0 36122 16 + 130230 TATCC----CACACTATCTG -s simCow_chr6.simCow.chr6 575835 16 - 602619 GATCC----CTTATTATCAG -s simDog_chr6.simDog.chr6 571067 16 - 593897 GATCC----CCCATTATCAG -s simHuman_chr6.simHuman.chr6 577779 16 - 601863 GATGC----CTCATCATCTG -s simRat_chr6.simRat.chr6 30439 16 + 647215 GATCC----CACACCATTTG - -a -s simMouse_chr6.simMouse.chr6 38276 12 + 636262 AGGTGCCCACTT -s Anc0.Anc0refChr9 14023 12 + 35212 AGTTGCCCACTG -s Anc1.Anc1refChr2 138262 12 - 144309 AGTTGCCCACTG -s Anc2.Anc2refChr0 33519 12 - 56053 AGTTGCCCCCTG -s mr.mrrefChr0 36138 12 + 130230 AGGTGCCCACTT -s simCow_chr6.simCow.chr6 575852 12 - 602619 AGTTGCCCCCTG -s simDog_chr6.simDog.chr6 571084 12 - 593897 CGTTGCCCCCTG -s simHuman_chr6.simHuman.chr6 577799 9 - 601863 AGCTCCCTA--- -s simRat_chr6.simRat.chr6 30455 12 + 647215 AAGTTCCCACTT - -a -s simMouse_chr6.simMouse.chr6 38288 8 + 636262 ATTACCAC -s Anc0.Anc0refChr9 14035 8 + 35212 AGATTGCC -s Anc1.Anc1refChr2 138274 8 - 144309 AGATTGCC -s Anc2.Anc2refChr0 33531 8 - 56053 AGATTGCC -s mr.mrrefChr0 36150 8 + 130230 ATTACCAC -s simCow_chr6.simCow.chr6 575864 8 - 602619 TGACTGCC -s simDog_chr6.simDog.chr6 571096 8 - 593897 AGATTGCC -s simRat_chr6.simRat.chr6 30468 8 + 647215 GTTAGCGC - -a -s simMouse_chr6.simMouse.chr6 38296 7 + 636262 CAGCTCC -s Anc0.Anc0refChr9 14043 7 + 35212 TGGTCTT -s Anc1.Anc1refChr2 138282 7 - 144309 TGGTCTT -s Anc2.Anc2refChr0 33539 7 - 56053 TGGTCTT -s mr.mrrefChr0 36158 7 + 130230 CAGCTCC -s simCow_chr6.simCow.chr6 575946 7 - 602619 CTGTCTT -s simDog_chr6.simDog.chr6 571104 7 - 593897 TGGTCTT -s simRat_chr6.simRat.chr6 30476 7 + 647215 CCGCTCC - -a -s simMouse_chr6.simMouse.chr6 38303 7 + 636262 TAAAGTG -s Anc0.Anc0refChr9 14050 7 + 35212 TAAAGTA -s Anc1.Anc1refChr2 138289 7 - 144309 TAAAGTA -s Anc2.Anc2refChr0 33546 7 - 56053 TAAAGTA -s mr.mrrefChr0 36165 7 + 130230 TAAAGTG -s simCow_chr6.simCow.chr6 575953 7 - 602619 GAAGGTA -s simDog_chr6.simDog.chr6 571111 7 - 593897 TAAAGTA -s simRat_chr6.simRat.chr6 30499 7 + 647215 TAAAGTG - -a -s simMouse_chr6.simMouse.chr6 38310 7 + 636262 TGAGTTT -s Anc0.Anc0refChr9 14057 7 + 35212 AAAATTC -s Anc1.Anc1refChr2 138296 7 - 144309 AAAATTC -s Anc2.Anc2refChr0 33553 7 - 56053 AAAATTC -s mr.mrrefChr0 36172 7 + 130230 TGAGTTT -s simCow_chr6.simCow.chr6 575968 7 - 602619 ATAATCT -s simDog_chr6.simDog.chr6 571118 7 - 593897 AAAATTC -s simRat_chr6.simRat.chr6 30506 7 + 647215 TGAGTTT - -a -s simMouse_chr6.simMouse.chr6 38317 7 + 636262 TAACTCT -s Anc0.Anc0refChr9 14064 7 + 35212 CAATTGT -s Anc1.Anc1refChr2 138303 7 - 144309 CAATTGT -s Anc2.Anc2refChr0 33564 7 - 56053 CAATTGT -s mr.mrrefChr0 36179 7 + 130230 TAACTCT -s simCow_chr6.simCow.chr6 575979 7 - 602619 CAACTGT -s simDog_chr6.simDog.chr6 571129 7 - 593897 CAATTGT -s simRat_chr6.simRat.chr6 30513 7 + 647215 CAACTCC - -a -s simMouse_chr6.simMouse.chr6 38324 73 + 636262 TCACTTTGCCTAATCAATAACTGAGTATGTTCCTTTCTTATCTCATCACAATCTTATCCTCTGGGTAGCATTC -s Anc0.Anc0refChr9 14071 64 + 35212 TTACTTTGCCTCATAAATAGCTGGGTACGTTTCTT---------ATCAGAATCATATTATTTGGGCAGAAATC -s Anc1.Anc1refChr2 138310 64 - 144309 TTACTTTGCCTCATAAATAGCTGGGTACGTTTCTT---------ATCAGAATCATATTATTTGGGCAGAAATC -s Anc2.Anc2refChr0 33572 64 - 56053 TTACTTTAGCTCATAAATAGCTGGGTACGTTTCTC---------ATCAGAATCATATTATTTGGGCAGACAGC -s mr.mrrefChr0 36186 73 + 130230 TCACTTTGCCTAATCAATAACTGAGTATGTTCCTTTCTTATCTCATCACAATCTTATCCTCTGGGTAGCATTC -s simCow_chr6.simCow.chr6 575987 64 - 602619 TGACCTTAGCTTATAAATAGCTGGGTATGTTTCTC---------AACAGAATCATATTATTTGGGCAGACAGC -s simDog_chr6.simDog.chr6 571137 42 - 593897 TTACTTTAGCTCATAAATAGCTGGGGACGTTTCTC---------TTCACAA---------------------- -s simHuman_chr6.simHuman.chr6 577808 59 - 601863 -----TTGCTTCATAAATAGCTGGGTACATTTCTT---------ATCAGAATCCGATTATTCGGACAGAAATC -s simRat_chr6.simRat.chr6 30520 73 + 647215 ACACTTTGTCTAATCAATAACTGAAAATGCTCCTTACTTTTCTCATTACAACCTTATCCTCTGGGTAGCACTC - -a -s simMouse_chr6.simMouse.chr6 38397 81 + 636262 CTGAGGTCTATAACACATTATACCCAGACCAGAAACAATTCAAGTGAGAACATAGGCAACTGAACCAGTTAGTTCAGATAA -s Anc0.Anc0refChr9 14139 79 + 35212 CTGTATTCTATAACACATTATACCCA--CAAGAAATAATTTAAGTGATAACATAAGTGACGGAACCAACAAATTCAGGTAA -s Anc1.Anc1refChr2 138378 81 - 144309 CTGTATTCTATAACACATTATACCCAAGCAAGAAATAATTTAAGTGATAACATAAGTGACGGAACCAACAAATTCAGGTAA -s Anc2.Anc2refChr0 33640 79 - 56053 CTGTATGAAAGAAAACATTATTCTCA--CAAGCACTAATGTAAGTGATAACAAAAGTGACGAAATCAACAAATGCAGGTAA -s mr.mrrefChr0 36259 81 + 130230 CTGAGGTCTATAACACATTATACCCAGACCAGAAACAATTCAAGTGAGAACATAGGCAACTGAACCAGTTAGTTCAGATAA -s simCow_chr6.simCow.chr6 576058 79 - 602619 CTGTATGAAAGAAAACATTATTCTCA--CAAGCACTAATGTAAGTGATAACAAAAGTGACGAAATCAACAAATGCAGGTAA -s simHuman_chr6.simHuman.chr6 577871 81 - 601863 CTGCATTCTATAACAGATTATATCCAAGTTATAGATAATTTGAGTCATAGCATAAGTGACCGCACTGACGAATTTAGGTAA -s simRat_chr6.simRat.chr6 30593 81 + 647215 CTGAGGCCTATATCACATTATACACAGACCAGAAACCATTCAAGGGAGAACATAAGTGACTGAACCAGTGAGTTAAGATAA - -a -s simMouse_chr6.simMouse.chr6 38478 61 + 636262 CCAGAACTTGCTAGCTTTAATGTACTTGATCCATTTTCTCATAAATGAAAGGATAACAGAT -s Anc0.Anc0refChr9 14218 26 + 35212 CCAA--------------------------------TTTCTT---TGAAAGGATAACAGAT -s Anc1.Anc1refChr2 138459 29 - 144309 CCAA--------------------------------TTTCTTAGGTGAAAGGATAACAGAT -s Anc2.Anc2refChr0 33719 26 - 56053 CTAA--------------------------------TTTCTT---TGAAAGGAGAACAGAT -s mr.mrrefChr0 36340 61 + 130230 CCAGAACTTGCTAGCTTTAATGTACTTGATCCATTTTCTCATAAATGAAAGGATAACAGAT -s simCow_chr6.simCow.chr6 576167 26 - 602619 CTAA--------------------------------TTTCTT---TGAAAGGAGAACAGAT -s simDog_chr6.simDog.chr6 571179 2 - 593897 -----------------------------------------------------------AT -s simHuman_chr6.simHuman.chr6 577952 29 - 601863 CCAA--------------------------------TTTCTTAGGTGAAAGGGTAACATGT -s simRat_chr6.simRat.chr6 30674 61 + 647215 TTAAAACTTGCTAGCTCTATTGTCCTTGATTCATTTTCTCGTAGTCGAAAGGATAACAGAT - -a -s simMouse_chr6.simMouse.chr6 38539 44 + 636262 ATTCATTTATGCTCAATTTGGTATGCACTTGCACAAACCACTTG -s Anc0.Anc0refChr9 14244 35 + 35212 ACTCA---------AATTTGGTGTGCCATGGTACAAATTCCTTG -s Anc1.Anc1refChr2 138488 44 - 144309 ACTCATTTATGCCCAATTTGGTGTGCCATGGTACAAATTCCTTG -s Anc2.Anc2refChr0 33745 35 - 56053 GCTCA---------GATCTGGTGTGCCATGGTACAAATTCCCTA -s mr.mrrefChr0 36401 44 + 130230 ATTCATTTATGCTCAATTTGGTATGCACTTGCACAAACCACTTG -s simCow_chr6.simCow.chr6 576193 35 - 602619 GCACA---------GATATGGTGAGTCACTGCACAAATTATCTA -s simDog_chr6.simDog.chr6 571181 35 - 593897 GCTTA---------GATCTGGTGTGCCATGGTACAAATTCCCTA -s simHuman_chr6.simHuman.chr6 577981 42 - 601863 ACCCGTTTATGCCCAATTTGGTGTGC--TGATACAAATTGCTCG -s simRat_chr6.simRat.chr6 30738 44 + 647215 ATTCATTTATGTTCAATTTGGTGTGCAATGGTATAAACCACTTA - -a -s simMouse_chr6.simMouse.chr6 38583 16 + 636262 AGATGAAAACAATTTA -s Anc0.Anc0refChr9 14287 16 + 35212 AGATGGACATAATTTT -s Anc1.Anc1refChr2 138540 16 - 144309 AGATGGACATAATTTT -s Anc2.Anc2refChr0 33788 16 - 56053 AGATGGACATAACTTT -s mr.mrrefChr0 36445 16 + 130230 AGATGAAAACAATTTA -s simCow_chr6.simCow.chr6 576236 16 - 602619 AGATGAACATAACTTT -s simDog_chr6.simDog.chr6 571224 16 - 593897 AGATGGACACAACTTC -s simHuman_chr6.simHuman.chr6 578031 16 - 601863 AGTTGGACATGATTTT -s simRat_chr6.simRat.chr6 30782 16 + 647215 AGATGAACACAATTTA - -a -s simMouse_chr6.simMouse.chr6 38599 3 + 636262 CAG -s Anc0.Anc0refChr9 14310 3 + 35212 CAG -s Anc1.Anc1refChr2 138563 3 - 144309 CAG -s Anc2.Anc2refChr0 33811 3 - 56053 CAG -s mr.mrrefChr0 36461 3 + 130230 CAG -s simCow_chr6.simCow.chr6 576259 3 - 602619 AAG -s simDog_chr6.simDog.chr6 571247 3 - 593897 CAA -s simHuman_chr6.simHuman.chr6 578054 3 - 601863 CAG -s simRat_chr6.simRat.chr6 30798 3 + 647215 CAT - -a -s simMouse_chr6.simMouse.chr6 38602 2 + 636262 CA -s Anc0.Anc0refChr9 14313 2 + 35212 CA -s Anc1.Anc1refChr2 138566 2 - 144309 CA -s Anc2.Anc2refChr0 33814 2 - 56053 CA -s mr.mrrefChr0 36464 2 + 130230 CA -s simCow_chr6.simCow.chr6 576262 2 - 602619 CA -s simDog_chr6.simDog.chr6 571250 2 - 593897 CA -s simHuman_chr6.simHuman.chr6 578057 2 - 601863 CA -s simRat_chr6.simRat.chr6 30802 2 + 647215 CG - -a -s simMouse_chr6.simMouse.chr6 38604 14 + 636262 CCATTGTGGTTCTA -s Anc0.Anc0refChr9 14316 9 + 35212 CCATTGT-----GA -s Anc1.Anc1refChr2 138569 9 - 144309 CCATTGT-----GA -s Anc2.Anc2refChr0 33817 9 - 56053 TCATTGT-----GA -s mr.mrrefChr0 36466 9 + 130230 CCATTGT-----TA -s simCow_chr6.simCow.chr6 576265 9 - 602619 TGATGGT-----GA -s simDog_chr6.simDog.chr6 571253 9 - 593897 TCATTTT-----GA -s simHuman_chr6.simHuman.chr6 578060 9 - 601863 CCAGTGT-----CA -s simRat_chr6.simRat.chr6 30804 9 + 647215 CCATTGT-----CA - -a -s simMouse_chr6.simMouse.chr6 38618 29 + 636262 AATATTGGGGCTCACACACCTCAAGGTCT -s Anc0.Anc0refChr9 14344 29 + 35212 AATATTGGAGCTTATGGACCTCAAGGCCT -s Anc1.Anc1refChr2 138597 29 - 144309 AATATTGGAGCTTATGGACCTCAAGGCCT -s Anc2.Anc2refChr0 33845 29 - 56053 AACATTGGAGCTTATGGACCTCAAGGCCT -s mr.mrrefChr0 36475 29 + 130230 AATATTGGGGCTCACACACCTCAAGGTCT -s simCow_chr6.simCow.chr6 576294 29 - 602619 AACATTGGAGCTTATGCACCTCAAGGTCT -s simDog_chr6.simDog.chr6 571273 29 - 593897 AACATTGGAGCTTATAGACCTCAAGGCCT -s simHuman_chr6.simHuman.chr6 578088 22 - 601863 AGTATTGGAGCTTATGGATTTC------- -s simRat_chr6.simRat.chr6 30813 29 + 647215 AATATCGGAGCTTATGCACCTTAATGGTT - -a -s simMouse_chr6.simMouse.chr6 38647 46 + 636262 TCTTATTAGCAAGATGGCAGGTCCAGTCCTTTTATGAGCAGTATGA -s Anc0.Anc0refChr9 14373 16 + 35212 TC------------------------------TAGGAGCAAGATGG -s Anc1.Anc1refChr2 138626 19 - 144309 TCT---------------------------TTTAGGAGCAAGATGG -s Anc2.Anc2refChr0 33874 16 - 56053 TC------------------------------TAGGAGCAAGATAG -s mr.mrrefChr0 36504 41 + 130230 TCT-----GCAAGATGGCAGGTCCAGTCCTTTTATGAGCAGTATGA -s simCow_chr6.simCow.chr6 576324 16 - 602619 CC------------------------------TAGGAGCAAGACAG -s simDog_chr6.simDog.chr6 571302 16 - 593897 TC------------------------------TACAAACAAGATAG -s simHuman_chr6.simHuman.chr6 578110 16 - 601863 ------------------------------TTTAGGAGCAAGATGG -s simRat_chr6.simRat.chr6 30842 41 + 647215 TCT-----GCCAGATGGCAGGTCCAGTCCTCTTATGATCAGTCTGG - -a -s simMouse_chr6.simMouse.chr6 38693 50 + 636262 TAGGCCCATTATTTTAACGCTACATGTGAGCAGTATGGCACCATTATCTT -s Anc0.Anc0refChr9 14389 15 + 35212 TGAGCTCGTT-----------------------------------ATTAT -s Anc1.Anc1refChr2 138645 15 - 144309 TGAGCTCGTT-----------------------------------ATTAT -s Anc2.Anc2refChr0 33890 15 - 56053 GGAGCTCGTT-----------------------------------ATTAT -s mr.mrrefChr0 36545 15 + 130230 TAGGCCCATT-----------------------------------ATCTT -s simCow_chr6.simCow.chr6 576343 15 - 602619 GGAGCAAGTT-----------------------------------ATTAT -s simDog_chr6.simDog.chr6 571318 15 - 593897 GGAGCTCGTT-----------------------------------ATTAT -s simHuman_chr6.simHuman.chr6 578126 15 - 601863 TGAGCTTCTT-----------------------------------ATTCT -s simRat_chr6.simRat.chr6 30883 15 + 647215 CAGGCCCATT-----------------------------------ACATT - -a -s simMouse_chr6.simMouse.chr6 38743 14 + 636262 AATCCTACACAAAC -s Anc0.Anc0refChr9 14404 14 + 35212 AGTTCAACAAAGAA -s Anc1.Anc1refChr2 138660 14 - 144309 AGTTCAACAAAGAA -s Anc2.Anc2refChr0 33906 14 - 56053 AGTTCAACAAAGAA -s mr.mrrefChr0 36560 14 + 130230 AATCCTACACAAAC -s simCow_chr6.simCow.chr6 576359 14 - 602619 AGTTTGACAAAGAA -s simDog_chr6.simDog.chr6 571334 14 - 593897 GGTTCAACACAGAA -s simHuman_chr6.simHuman.chr6 578141 14 - 601863 AGTTCAACAAAGAA -s simRat_chr6.simRat.chr6 30898 14 + 647215 AATCCTACAATGAA - -a -s simMouse_chr6.simMouse.chr6 38757 5 + 636262 CTGCA -s Anc0.Anc0refChr9 14418 5 + 35212 CTGTC -s Anc1.Anc1refChr2 138674 5 - 144309 CTGTC -s Anc2.Anc2refChr0 33920 5 - 56053 CTGTC -s mr.mrrefChr0 36574 5 + 130230 CTGCA -s simCow_chr6.simCow.chr6 576374 5 - 602619 CTGTG -s simDog_chr6.simDog.chr6 571348 5 - 593897 TAATC -s simHuman_chr6.simHuman.chr6 578155 5 - 601863 CTGTC -s simRat_chr6.simRat.chr6 30912 5 + 647215 CTGTG - -a -s simMouse_chr6.simMouse.chr6 38762 46 + 636262 TAGTTGACTTTTATGTTTAACTAGTCCTGAACTGCATGTGCTGTTA -s Anc0.Anc0refChr9 14423 29 + 35212 AAGTTGACTTTTATCATTCACT---CCTGAAC-------------- -s Anc1.Anc1refChr2 138679 29 - 144309 AAGTTGACTTTTATCATTCACT---CCTGAAC-------------- -s Anc2.Anc2refChr0 33925 29 - 56053 AAGTTAACTTTTATCATTCATT---CCTGAAC-------------- -s mr.mrrefChr0 36579 32 + 130230 TAGTTGACTTTTATGTTTAACTAGTCCTGAAC-------------- -s simCow_chr6.simCow.chr6 576379 29 - 602619 GAGTTAACTTTTAGAATTCATT---CCTGGAT-------------- -s simDog_chr6.simDog.chr6 571357 29 - 593897 AAGTTAACTGTTCTCAATCATT---CCTGAAC-------------- -s simHuman_chr6.simHuman.chr6 578160 29 - 601863 AAGTTGACTTTTATCATTCACT---CCTGAAC-------------- -s simRat_chr6.simRat.chr6 30917 32 + 647215 TAGTTGACTTTTATGTTTAACTACTCCTGAAC-------------- - -a -s simMouse_chr6.simMouse.chr6 38808 2 + 636262 CA -s Anc0.Anc0refChr9 14452 2 + 35212 AG -s Anc1.Anc1refChr2 138708 2 - 144309 AG -s Anc2.Anc2refChr0 33954 2 - 56053 AG -s mr.mrrefChr0 36611 2 + 130230 CA -s simCow_chr6.simCow.chr6 576408 2 - 602619 GG -s simDog_chr6.simDog.chr6 571386 2 - 593897 AG -s simHuman_chr6.simHuman.chr6 578189 2 - 601863 AG -s simRat_chr6.simRat.chr6 31062 2 + 647215 CA - -a -s simMouse_chr6.simMouse.chr6 38810 19 + 636262 GTTCACAGCCTTTTGAGTT -s Anc0.Anc0refChr9 14468 19 + 35212 GTTCACAGCCTTTTGAGTT -s Anc1.Anc1refChr2 138724 19 - 144309 GTTCACAGCCTTTTGAGTT -s Anc2.Anc2refChr0 33970 19 - 56053 GTTCACAGCTTTTTGAGTT -s mr.mrrefChr0 36613 19 + 130230 GTTCACAGCCTTTTGAGTT -s simCow_chr6.simCow.chr6 576424 19 - 602619 GTTTGCAGCTTTTTGAGTT -s simDog_chr6.simDog.chr6 571403 19 - 593897 GTTCACAGCTTTTTGAGTC -s simHuman_chr6.simHuman.chr6 578205 19 - 601863 GTTCACAGCCTTTTGAGGT -s simRat_chr6.simRat.chr6 31064 19 + 647215 GTTTACAGCCTTTTGTGTT - -a -s simMouse_chr6.simMouse.chr6 38829 24 + 636262 GGTATAAATGTCCATGGACATCAT -s Anc0.Anc0refChr9 14491 24 + 35212 GGTATAAATATCATCAGACATCGA -s Anc1.Anc1refChr2 138747 24 - 144309 GGTATAAATATCATCAGACATCGA -s Anc2.Anc2refChr0 33993 24 - 56053 GGTGTAAACATCATCAGAAATCGA -s mr.mrrefChr0 36632 24 + 130230 GGTATAAATGTCCATGGACATCAT -s simCow_chr6.simCow.chr6 576447 24 - 602619 GATGTAAACGTCATCATATATCAA -s simDog_chr6.simDog.chr6 571426 24 - 593897 GGTGTAAACATCATCAGAAATCGA -s simHuman_chr6.simHuman.chr6 578228 14 - 601863 GTTATAAATAT-----GAC----- -s simRat_chr6.simRat.chr6 31083 24 + 647215 GGTATAAATGTCCTTGGACATCAT - -a -s simMouse_chr6.simMouse.chr6 38853 20 + 636262 ATGGCCTCTGGATGCCCCTC -s Anc0.Anc0refChr9 14515 19 + 35212 ATGGCCTCTGGATGCCCC-C -s Anc1.Anc1refChr2 138771 19 - 144309 ATGGCCTCTGGATGCCCC-C -s Anc2.Anc2refChr0 34017 19 - 56053 ATGGCCTCTGGATGCCCC-C -s mr.mrrefChr0 36656 19 + 130230 ATGGCCTCTGGATGCCCC-C -s simCow_chr6.simCow.chr6 576471 19 - 602619 ATGATCTCTGGATGCCCC-C -s simDog_chr6.simDog.chr6 571451 16 - 593897 ATGGCATCTGGATG---C-C -s simHuman_chr6.simHuman.chr6 578242 15 - 601863 ----CCTCTGGATGCCCC-C -s simRat_chr6.simRat.chr6 31107 19 + 647215 ATGGCCTCTGGATGCCCC-C - -a -s simMouse_chr6.simMouse.chr6 38873 32 + 636262 AGACAGTTGTGTGAGGACACAATATTGTGATC -s Anc0.Anc0refChr9 14535 32 + 35212 AAAGAGTTGTCCTTAGACTCAATATCTTTATC -s Anc1.Anc1refChr2 138791 32 - 144309 AAAGAGTTGTCCTTAGACTCAATATCTTTATC -s Anc2.Anc2refChr0 34037 32 - 56053 AAAGACTTGTCCTTAGACTCAATATCTTTATC -s mr.mrrefChr0 36675 32 + 130230 AGACAGTTGTGTGAGGACACAATATTGTGATC -s simCow_chr6.simCow.chr6 576491 32 - 602619 AAAGACTTGTCCTCAAACACAATATCTTCATC -s simDog_chr6.simDog.chr6 571468 31 - 593897 AAAGACTTGTATTT-GAATCAATATCTTTATC -s simHuman_chr6.simHuman.chr6 578258 28 - 601863 AAAGAGTTGGCCTTAGACTCAATATCTC---- -s simRat_chr6.simRat.chr6 31126 32 + 647215 AGACAGTTGTGTGAGCACACATTATTGTGATC - -a -s simMouse_chr6.simMouse.chr6 38905 20 + 636262 AAAAGCATTTGTCACACATG -s Anc0.Anc0refChr9 14567 18 + 35212 ACAAGAGT--GCCCAGCATG -s Anc1.Anc1refChr2 138823 18 - 144309 ACAAGAGT--GCCCAGCATG -s Anc2.Anc2refChr0 34069 18 - 56053 ACAAGAGT--GCCCAGCATG -s mr.mrrefChr0 36707 20 + 130230 AAAAGCATTTGTCACACATG -s simCow_chr6.simCow.chr6 576523 18 - 602619 ATAAGAGC--ACGCAGTACA -s simDog_chr6.simDog.chr6 571499 18 - 593897 ACAAGAGT--GCCCAGCATG -s simRat_chr6.simRat.chr6 31160 20 + 647215 AAGAGCATCTGTCACACATG - -a -s simMouse_chr6.simMouse.chr6 38925 2 + 636262 AA -s Anc0.Anc0refChr9 14585 2 + 35212 AA -s Anc1.Anc1refChr2 138841 2 - 144309 AA -s Anc2.Anc2refChr0 34091 2 - 56053 AA -s mr.mrrefChr0 36727 2 + 130230 AA -s simCow_chr6.simCow.chr6 576545 2 - 602619 GA -s simDog_chr6.simDog.chr6 571521 2 - 593897 AA -s simRat_chr6.simRat.chr6 31180 2 + 647215 GA - -a -s simMouse_chr6.simMouse.chr6 38927 78 + 636262 CCCAGCCTGAATTGGATTGATTGTGTCAATCATACCCTGGCCAAGTATGGGAGGGAATTGGTGATCAGGTTGACATAT -s Anc0.Anc0refChr9 14587 38 + 35212 CCCAATCTGAGCCTCCCTGACTGTGCCAATAAC----------------------------------------CATAT -s Anc1.Anc1refChr2 138843 38 - 144309 CCCAATCTGAGCCTCCCTGACTGTGCCAATAAC----------------------------------------CATAT -s Anc2.Anc2refChr0 34093 38 - 56053 CCCAATCTGAGCCTCCCTGACTGTGCCAATAAC----------------------------------------CATAT -s mr.mrrefChr0 36729 78 + 130230 CCCAGCCTGAATTGGATTGATTGTGTCAATCATACCCTGGCCAAGTATGGGAGGGAATTGGTGATCAGGTTGACATAT -s simCow_chr6.simCow.chr6 576547 38 - 602619 CACAATCTGAATTTGCCGGTTTGTGAGAATAAC----------------------------------------CATAT -s simDog_chr6.simDog.chr6 571547 38 - 593897 CCCAATCTGAGCCTCCCTGACTGTGCCAATAAC----------------------------------------TATAT -s simHuman_chr6.simHuman.chr6 578286 5 - 601863 -------------------------------------------------------------------------CATAT -s simRat_chr6.simRat.chr6 31182 78 + 647215 CCGAGCCTGAATTGGATTGATTGTGCCAATAATCCCCTGGCCAAGTACAAGAGGAAATTGTTGGTCAGGTTGACATAT - -a -s simMouse_chr6.simMouse.chr6 39005 21 + 636262 ACTCTGTTACCCAAAAGCAAG -s Anc0.Anc0refChr9 14633 21 + 35212 ACTCCAGTACAAACAAGCAAG -s Anc1.Anc1refChr2 138889 21 - 144309 ACTCCAGTACAAACAAGCAAG -s Anc2.Anc2refChr0 34139 21 - 56053 ACTCCAGTGTAAGCAAGCAAG -s mr.mrrefChr0 36807 21 + 130230 ACTCTGTTACCCAAAAGCAAG -s simCow_chr6.simCow.chr6 576589 21 - 602619 CCTCCAGAGTATGCAAGCAAG -s simDog_chr6.simDog.chr6 571593 21 - 593897 ATCTCAATGTAAGCAAGCAAG -s simHuman_chr6.simHuman.chr6 578299 21 - 601863 ACTCCAGTACAGACCAGCAAG -s simRat_chr6.simRat.chr6 31260 21 + 647215 ACTCTGTTACCCAAGAGCAAG - -a -s simMouse_chr6.simMouse.chr6 39026 3 + 636262 ACA -s Anc0.Anc0refChr9 14654 3 + 35212 TAA -s Anc1.Anc1refChr2 138910 3 - 144309 TAA -s Anc2.Anc2refChr0 34160 3 - 56053 TAA -s mr.mrrefChr0 36828 3 + 130230 ACA -s simCow_chr6.simCow.chr6 576612 3 - 602619 CAG -s simDog_chr6.simDog.chr6 571614 3 - 593897 TGA -s simHuman_chr6.simHuman.chr6 578320 3 - 601863 GAA -s simRat_chr6.simRat.chr6 31281 3 + 647215 ACA - -a -s simMouse_chr6.simMouse.chr6 39029 14 + 636262 GTCCACCATTTGTC -s Anc0.Anc0refChr9 14660 14 + 35212 GTCCACCATTTTCC -s Anc1.Anc1refChr2 138916 14 - 144309 GTCCACCATTTTCC -s Anc2.Anc2refChr0 34166 14 - 56053 GTCCACCATTTTCC -s mr.mrrefChr0 36834 14 + 130230 GTCCACCATTTGTC -s simCow_chr6.simCow.chr6 576618 14 - 602619 GACCACCAGTTTCC -s simDog_chr6.simDog.chr6 571620 14 - 593897 GTCCACCATTTTTT -s simHuman_chr6.simHuman.chr6 578326 14 - 601863 ATCCACCATATTCC -s simRat_chr6.simRat.chr6 31287 14 + 647215 GTCCACCATTTGTC - -a -s simMouse_chr6.simMouse.chr6 39043 3 + 636262 ACA -s Anc0.Anc0refChr9 14682 3 + 35212 ATA -s Anc1.Anc1refChr2 138938 3 - 144309 ATA -s Anc2.Anc2refChr0 34188 3 - 56053 ACA -s mr.mrrefChr0 36848 3 + 130230 ATA -s simCow_chr6.simCow.chr6 576640 3 - 602619 ACA -s simDog_chr6.simDog.chr6 571641 3 - 593897 ACA -s simHuman_chr6.simHuman.chr6 578348 3 - 601863 ATA -s simRat_chr6.simRat.chr6 31301 3 + 647215 ATC - -a -s simMouse_chr6.simMouse.chr6 39046 53 + 636262 TACTAAGCAGGCTTTGTTGAGGAGCATGAACAGGTACTAGATACCTCCTTGCC -s Anc0.Anc0refChr9 14685 40 + 35212 TATTAAGCATGC-TTGCTATTGAGCTTCACTGGGT------------CTTGCC -s Anc1.Anc1refChr2 138941 41 - 144309 TATTAAGCATGCTTTGCTATTGAGCTTCACTGGGT------------CTTGCC -s Anc2.Anc2refChr0 34191 40 - 56053 TATTAAGTTTGC-CTGCTGTTGAGTTTCACTGGGT------------CCTACC -s mr.mrrefChr0 36851 53 + 130230 TATTAAGCAGGCTTTGTTAAGGAGCATCAACAGGTACTAGATACCTCCTTGCC -s simCow_chr6.simCow.chr6 576643 38 - 602619 TATTAAGTTTAA---ACTGATGAGTTTCCCTGGGT------------CCCACC -s simDog_chr6.simDog.chr6 571644 40 - 593897 TATTAAGTTTGC-CTGCTGTTGAGTTTCAGTGGGT------------CCTACC -s simHuman_chr6.simHuman.chr6 578351 41 - 601863 TATTAAGCATGCTTTGCTAGTTAGCTTCACTGGGT------------TTTGCC -s simRat_chr6.simRat.chr6 31311 53 + 647215 CATTTGTCACTTATTGTTAAGGAGGAACAGCAGGTACTAGCTACCTGCCTGCT - -a -s simMouse_chr6.simMouse.chr6 39099 24 + 636262 ACCTGCCTCCTCGCACAGGGTTGC -s Anc0.Anc0refChr9 14726 24 + 35212 AACCACTTCCTTGTGCAGTGTTCC -s Anc1.Anc1refChr2 138983 24 - 144309 AACCACTTCCTTGTGCAGTGTTCC -s Anc2.Anc2refChr0 34232 24 - 56053 AACCACTTCCTTGTGCAGTGTTCC -s mr.mrrefChr0 36904 24 + 130230 ACCTGCCTCCTTGCACAGGGCTGC -s simCow_chr6.simCow.chr6 576682 24 - 602619 AACCACTTTCTTGTGCAGTGTTCC -s simDog_chr6.simDog.chr6 571685 24 - 593897 AACCACTTCCTTGTGCATTGTTCC -s simHuman_chr6.simHuman.chr6 578393 23 - 601863 AAGCACTTCTTTGTGCGGT-TTCA -s simRat_chr6.simRat.chr6 31364 24 + 647215 GCCTGCTTCCTTGCACAGGGCTGA - -a -s simMouse_chr6.simMouse.chr6 39123 4 + 636262 GGAG -s Anc0.Anc0refChr9 14754 4 + 35212 GTGG -s Anc1.Anc1refChr2 139011 4 - 144309 GTGG -s Anc2.Anc2refChr0 34260 4 - 56053 GTGG -s mr.mrrefChr0 36928 4 + 130230 GGAG -s simCow_chr6.simCow.chr6 576710 4 - 602619 GCAG -s simDog_chr6.simDog.chr6 571713 4 - 593897 GTGG -s simHuman_chr6.simHuman.chr6 578420 4 - 601863 GTGG -s simRat_chr6.simRat.chr6 31388 4 + 647215 GGAG - -a -s simMouse_chr6.simMouse.chr6 39127 14 + 636262 AGAAGATATGATGT -s Anc0.Anc0refChr9 14758 14 + 35212 TGAAGGTATAATGA -s Anc1.Anc1refChr2 139015 14 - 144309 TGAAGGTATAATGA -s Anc2.Anc2refChr0 34264 14 - 56053 TGAAGGTATAGTGA -s mr.mrrefChr0 36932 14 + 130230 AGAAGATATGATGT -s simCow_chr6.simCow.chr6 576714 14 - 602619 TGGAGGTATAGTGG -s simDog_chr6.simDog.chr6 571724 14 - 593897 TAAGGGTATAGTGA -s simHuman_chr6.simHuman.chr6 578424 14 - 601863 TGAAGGTATTATGA -s simRat_chr6.simRat.chr6 31392 14 + 647215 AGAAGATGTGATGG - -a -s simMouse_chr6.simMouse.chr6 39141 11 + 636262 GGTAACGGTGT -s Anc0.Anc0refChr9 14772 11 + 35212 GGTATTGGTGT -s Anc1.Anc1refChr2 139029 11 - 144309 GGTATTGGTGT -s Anc2.Anc2refChr0 34278 11 - 56053 GGTATTGGTGT -s mr.mrrefChr0 36946 11 + 130230 GGTAATGGTGT -s simCow_chr6.simCow.chr6 576728 11 - 602619 GGTGTTGGTAT -s simDog_chr6.simDog.chr6 571741 11 - 593897 GCTAATGGGGT -s simHuman_chr6.simHuman.chr6 578438 11 - 601863 GGTATTGCTGT -s simRat_chr6.simRat.chr6 31406 11 + 647215 GGTAATGGTGG - -a -s simMouse_chr6.simMouse.chr6 39152 149 + 636262 AGGGGTAGTGAGATTGGGATAGTAGTGTGCATGGTATATCACCTTACTGGACTGTTTCTTACATTGGTATAATGGAGTAGTCCAAAGGAACAACGACAAGTTCCAGGAGCAATGGTGGACATTCTAATTTTCCCTAGATTAGTTAAGAC -s Anc0.Anc0refChr9 14783 25 + 35212 TGG--------GCGTGAGATAGTAGTGTG--TGTT------------------------------------------------------------------------------------------------------------------ -s Anc1.Anc1refChr2 139040 131 - 144309 TGG--------GCGTGAGATAGTAGTGTG--TGTTTTATTAGCTTATTGTACTGTTTCTAATGTTGGCC--ATGGAGTGGTCTAGGGGAAAATGAACAAGTTCTAAGAGGAATGGT------TCCAATTGTCCCTAGGTATATAACTAC -s Anc2.Anc2refChr0 34289 25 - 56053 TGA--------GCGTGAGTTAGTAGTGTG--TGTT------------------------------------------------------------------------------------------------------------------ -s mr.mrrefChr0 36957 149 + 130230 TGGGGTAGTGAGATTGAGATAGTAGTGTGCATGGTATATCACCTTACTGGACTGTTTCTTACATTGGTATAATGGAGTAGTCCAAGGGAACAAGGACAAGTTCCAGGAGGAATGGTGGACATTCCAATTTTCCCTAGATTAGTTAAGAC -s simCow_chr6.simCow.chr6 576739 14 - 602619 TGA--------GC------TAGTC-------TGTT------------------------------------------------------------------------------------------------------------------ -s simDog_chr6.simDog.chr6 571753 25 - 593897 TTA--------ATGTGAGTTAGTAGTGTG--TGTT------------------------------------------------------------------------------------------------------------------ -s simHuman_chr6.simHuman.chr6 578449 131 - 601863 TGG--------GCGTGAAAGAATAGTGTG--TGTTGTATTAGCTTATTGTACTGTTTCTAATGTTGGCC--ATGGAGTGGTCTAGGGGAAAATGAACAAGTTCTAAGAGGAATGGT------TCCAATTGTCCCTAGGTATATAACTAC -s simRat_chr6.simRat.chr6 31417 149 + 647215 TGGGGTAGCAAGATTGAGCTAGTAGTGTGCATCGTATATGACCTTACTAAACTGTTTCTGACATTGGTATAATGGAGTAGTCCACGGGAACAAGGAAAAGTTCCAGAGGGAATGGTGGACGGTCCAATTTTCCCTAGATTAGTTAACAC - -a -s simMouse_chr6.simMouse.chr6 39301 136 + 636262 TACAAAGAGATACGAATGTGTTGATGTTAAAAAGTTCCAACTTCTGCCTGATTGCCTGATATCTATTAGAGGAGTTATTACATTACCATAACTAGAGAAGCCTTGTACGAAGTGGAAGGCACAGACTCCACACACC -s Anc0.Anc0refChr9 14808 84 + 35212 --------------------------------------------TCCCCGA--------TATTTATTAGAGGGGTTATTAGATTACCATGACTGGAGAGGCCTTGTATGAAGCAGGAGGGACAGATTCCAAACAAC -s Anc1.Anc1refChr2 139171 88 - 144309 T----------------------------------------CTCTCCCCGA--------TATTTATTAGAGGGGTTATTAGATTACCATGACTGGAGAGGCCTTGTATGAAGCAGGAGGGACAGATTCCAAACAAC -s Anc2.Anc2refChr0 34314 84 - 56053 --------------------------------------------TCCCTGA--------TATTTAATAGAGGGGTCATTAGACTACCATGACTGGAGAGGCCTTGTATGAAGCAGGAGGGACAGATTCCAAACAAC -s mr.mrrefChr0 37106 128 + 130230 TACAAAGAGATACGAATGTGTTGATGTTAAAAAGTTCCAACTTCTGCCTGA--------TATCTATTAGAGGAGTTATTACATTACCATAACTAGAGAAGCCTTGTATGAAGCGGAAGGCACAGACTCCACACACC -s simCow_chr6.simCow.chr6 576753 84 - 602619 --------------------------------------------TCGTTCA--------TATTTTATAGAGGGGTCATAATACTACCATAGCTGGAGAGGCCATGTATGGAGCAGGACGGACAGATTCCAAACTAC -s simDog_chr6.simDog.chr6 571778 84 - 593897 --------------------------------------------TCCCTGG--------TATTTAAGAGAAAGGTCATTAGACTACCATGACTGGAGAGGCTTTGAATGACATATGAGGGACAGGCTTTAAACAAC -s simHuman_chr6.simHuman.chr6 578580 88 - 601863 T----------------------------------------CTCTCCCCAA--------TATTGATTAGAGGGGTTCTTAGATTACCATGACTGAAGAGGCCTTGTATGAAGCAGGAGGGACAGATTCCATACAAC -s simRat_chr6.simRat.chr6 31567 128 + 647215 TACAAAGAGATAGAAATGCACTGTTGTTAAAAAGTTCCAACTTCTGCCTGA--------TGTCTATTGGAGGAGTTACTGCATTACCATATCTAGAGAAGCCTTGTGTGAAGCGGAAGGCACAGACTCCACACACC - -a -s simMouse_chr6.simMouse.chr6 39437 51 + 636262 TTGACAGACCAGAACTTTTACCTGGTTGGATGCTTCTAAATATGCACTTCC -s Anc0.Anc0refChr9 14895 46 + 35212 TTGGCAGGACAGAACCTTTATCTAGTTGGTTAC----AAAT-TGCAGTTCC -s Anc1.Anc1refChr2 139262 46 - 144309 TTGGCAGGACAGAACCTTTATCTAGTTGGTTAC----AAAT-TGCAGTTCC -s Anc2.Anc2refChr0 34401 46 - 56053 TTGGCAGGACAGAACCTTTATCTAGTAGCTTAT----AAAT-AACAGTTCT -s mr.mrrefChr0 37237 51 + 130230 TTGGCAGACCAGAACTTTTATCTGGTTGGTTGCTTCTAAATATGCACTTCC -s simCow_chr6.simCow.chr6 576838 1 - 602619 --------------------------------------------------G -s simDog_chr6.simDog.chr6 571865 46 - 593897 TTGGCAGGACAGAACCTTTATCTAGTAGCTTAT----AAAT-AACAGTTCT -s simHuman_chr6.simHuman.chr6 578671 46 - 601863 TTGGCAAGACAGGAACAGTATCTAGTTGGTTAC----AAAT-TGCAGTTCC -s simRat_chr6.simRat.chr6 31698 51 + 647215 TTGGTAGACCAAAGCTTTTATCTGGGTGATTGCTTCTAAATATGCACTTCC - -a -s simMouse_chr6.simMouse.chr6 39488 336 + 636262 TCCAGAATTATATTGGAACAGGTATAACCCAGATCGCAGTTAGGCGCATGAATCTGTGAGAGCAGCAGGGCCTTTGCTATCCCTTCGCAATTCAGATGGAATAGTACCATACAGTACCATTAATTGAGCCATTGGATGAGGTGATCTCCTGTCAGATGCTCCCAAAGTAGGCAGGTAACAATGAAGGCTGATTGCAGCATATCTAATGGAATAGATAACACTTGATGCCGGTCATAACAGGGAAGCTTCGGCTTCTTCCTTCTTCCTCAGCTGGCTAATGGAAGTAGGACTCCTAAGTAATGACTCTTAAGTGACTCCTAATTTACTACTTACCTC -s Anc0.Anc0refChr9 14953 78 + 35212 ACCAGAATAATATTTAAATAGCTAGAACCC----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CTAGAAGAAAGAGGAGTCCTGAGTCATTGCT--------------GATTCACTAGTTGCCTC -s Anc1.Anc1refChr2 139320 78 - 144309 ACCAGAATAATATTTAAATAGCTAGAACCC----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CTAGAAGAAAGAGGAGTCCTGAGTCATTGCT--------------GATTCACTAGTTGCCTC -s Anc2.Anc2refChr0 34459 78 - 56053 ACTAGAATAATATTTAAATAGCTAGGGCCC----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CTAGAAGAAAGGGGAGTCCTGAGTCATTCCT--------------GATTCACTAGTTGCCTC -s mr.mrrefChr0 37288 335 + 130230 TCCAGAATTATATTGAAACAGGTAGAACCCAGATCGCAGTTAGGCGCATGAATCTGTGAGAGCAGCAGGGCCTTTGCTATCCCTTCGCAATTCAGATGGAATAGTACCATACAGTACCATTAATTGAGCCATTGGATGAGGTGATCTCCTGTCAGATGCTCCCAAAGTAGGCAGGTAACAATGAAGGCTGATTGCAGCATATCTAATGGAATAGATAACACTTGATGCCGGTCATA-CAGGGAAGCTTCGGCTTCTTCCTTCTTCCTCAGCTGGCTAATAGAAAGAGGACTCCTAAGTAATGGCTCTTAAGTGACTCCTAATTTACTAGTTACCTC -s simCow_chr6.simCow.chr6 576852 78 - 602619 ACTGGAATTATATTTAAATACCTAGGGCCC----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CTAGAAGAAGGGGGAGTCCTGAGTCATTTCT--------------GATTCGCTAGTTACCTT -s simDog_chr6.simDog.chr6 571923 71 - 593897 ACTAGAATAA---TCAAATAGCTAGGG-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CTAGCAGAAAGGGAAGTCCTGAGTCATGCCT--------------GATTCAATAG-TGACCC -s simHuman_chr6.simHuman.chr6 578729 78 - 601863 GCCAGAATAATATTTAAGTAGCAAGAACCC----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CTGGAAGAAAGAGGAGTCCTGAGTCATTGCT--------------GATTCACTAGTTGCCTC -s simRat_chr6.simRat.chr6 31749 335 + 647215 TCCAGAATTGTATTGAAACAGATAGAACCCAGATCACAGCTAGGCACATAAGTCAGTATGATTAGCAGGGCCTTTGCTGCCCCTTAACAATTCAAATGAAACCGTGCCATATAGTACCATTAATTAGGCCATCAAATGAGACGATCTCCTGTCTGATGCTCCCAAAGTAGGTGGGGAACAATGAAGGCTGATCACAGAATATCTGATGGCATGGGTAACAATTAAGCTCGATCATA-CAGGAAAGCTTTGCCTTCTTCCTTCTTCCTCACCTGGCTAATAGAAAGAGGACTACTAAGTGATCGCTCCTAAGTGACTCCTAATTTACTAGTTACCTG - -a -s simMouse_chr6.simMouse.chr6 39824 15 + 636262 CTTTTATACCTGACC -s Anc0.Anc0refChr9 15031 15 + 35212 CTGTTATCCTTGACT -s Anc1.Anc1refChr2 139398 15 - 144309 CTGTTATCCTTGACT -s Anc2.Anc2refChr0 34537 15 - 56053 CTGTTATCCTTAACT -s mr.mrrefChr0 37623 15 + 130230 CTTTTATACCTGACC -s simCow_chr6.simCow.chr6 576935 15 - 602619 CTGTTATTCCTAACT -s simDog_chr6.simDog.chr6 571994 15 - 593897 ACATAATCCTGACCT -s simHuman_chr6.simHuman.chr6 578807 15 - 601863 CTGTTATCCTTGACT -s simRat_chr6.simRat.chr6 32084 15 + 647215 CTTTTATTCCTGACC - -a -s simMouse_chr6.simMouse.chr6 39839 154 + 636262 AGCTAATATTAGTGCTACTTGTTGATGGTTGAAGGCCCCATCCTTGACTCCCCTGCTTTAGTAGGTGGATAGGCTTCTACTTAACTAAGTCAATAGGCCCACCATTTGTACTTCATACAATGAATGAATACAAGCATATTTGATCTCCAAACAC -s Anc0.Anc0refChr9 15046 154 + 35212 AGTTAATATCATTCCTACTTGTAAATGGTTCAAAGCCCCACTTCTGACCACTCTGCTTAACTAGGTGGATAGATTCATACTTAACTAAGTCGATAGGTTCAAAATTTGAGTTTTATGCAATGAATGAATACAAGGGTCTATTTCTTCTAAACTC -s Anc1.Anc1refChr2 139413 154 - 144309 AGTTAATATCATTCCTACTTGTAAATGGTTCAAAGCCCCACTTCTGACCACTCTGCTTAACTAGGTGGATAGATTCATACTTAACTAAGTCGATAGGTTCAAAATTTGAGTTTTATGCAATGAATGAATACAAGGGTCTATTTCTTCTAAACTC -s Anc2.Anc2refChr0 34558 154 - 56053 AGTTAATATCATTCCTACTTGTAACTGGTTCAAAGCCCCAATTCTGACCACACTGACTAACTAGGTGGATAGATTCATACTTCACTAAGTCGATAGATTCAAAATTTGAGTTTTATGCGATGAATGAATACAAGGGTCTATTTCTTCTAAAATC -s mr.mrrefChr0 37638 154 + 130230 AGCTAATATTAGTCCTACTTGTTGATGGTTGAAGGCCCCACCCTTGACTCCTCTGCTTTAGTAGGTGGATAGGCTTCTACTTAACTAAGTCAATAGGTTCACCATTTGTACTTCATGCAATGAATGAATACAAGCATATTTTACTTCTAAACAC -s simCow_chr6.simCow.chr6 576956 139 - 602619 AGTTAATATCATTCCTGCTTCTAATTGGTTTAAAGGCCCATCTCTGACCAC-CTGGGTAACTAGGTGGACGGATCCATACATCACTAAGTCGATAGATTCAAAATTTATATTTT-----AGAAATG---ACAAGGGTTTATTGCCTA------C -s simDog_chr6.simDog.chr6 572015 154 - 593897 AGTTAATATCATTCCTACTTGTAGCTAGTTCAAAGCCTCGATTCTGACAAGACTGACTAACTAGGTGGATAGATTAATACTTCAATAAATTGGTAGATTTAAAATTTGAGCTTTATGCGATGAGTGAATACACGGGTCTATTTCTTCTAAAATT -s simHuman_chr6.simHuman.chr6 578822 139 - 601863 AGTTAACATCATTCATACTTTCCAATGCTACAGCACCCCACTTCTAACCACTCTGCTTAACTAGGTGGATCA-----CATTTAACTATGCCTATAGGTTC----------TTTTGTGCAATGAATGAATACAAGTGTCTATTTCTTTTAAACTC -s simRat_chr6.simRat.chr6 32099 154 + 647215 AGCTAATATTAGTCCTACTTGTTGATGGTTGAAAGCCCCACCCTTGACTGCTCTGCTTTAATAGGTGGATAGGCTTTTAATTAACTAAGTCAATAAGTTTGAAATTTGTACTTCATGCAATGAATGAATACAAGCACATTTTACTTCTAAGCAC - -a -s simMouse_chr6.simMouse.chr6 39993 36 + 636262 AGGTATGCTATTCTTGAAGAATAATGAGGGAGAGGA -s Anc0.Anc0refChr9 15200 36 + 35212 TAGTATGCTGTTCTTGAAGAGTAGTGAGTTAGAGGA -s Anc1.Anc1refChr2 139567 36 - 144309 TAGTATGCTGTTCTTGAAGAGTAGTGAGTTAGAGGA -s Anc2.Anc2refChr0 34712 36 - 56053 TAGTATGCTGTTCTTGAAGAGTAGTGAGTCAGAGGA -s mr.mrrefChr0 37792 36 + 130230 AAGTATGCTATTCTTGAAGAATAATGAGTTAGAGGA -s simCow_chr6.simCow.chr6 577095 34 - 602619 TAGTGTGCTGTTCTTAAAGAGTAGTGAGT--GAGGA -s simDog_chr6.simDog.chr6 572170 36 - 593897 TAGTATGCTGTTCTTGAAGAGTAGTGAGTCAGAGGA -s simHuman_chr6.simHuman.chr6 578961 36 - 601863 TAGTACACTCTTCTTGAAAAGTAGTGACTTAGAGGA -s simRat_chr6.simRat.chr6 32253 36 + 647215 AAGTATGCTATTCTTGAAGAATAATGAGTTAAAGGA - -a -s simMouse_chr6.simMouse.chr6 40029 20 + 636262 ATCATCTAGGGTCCATTTTC -s Anc0.Anc0refChr9 15239 20 + 35212 ATAAGATAAGGTCAACTCCT -s Anc1.Anc1refChr2 139606 20 - 144309 ATAAGATAAGGTCAACTCCT -s Anc2.Anc2refChr0 34751 20 - 56053 ATAAGATAAGATCAACTCCT -s mr.mrrefChr0 37828 20 + 130230 ATCAGCTAGGGTCAACTTTC -s simCow_chr6.simCow.chr6 577132 20 - 602619 ATAAGATAAGATCAACTCCT -s simDog_chr6.simDog.chr6 572209 20 - 593897 GTGAGATAAGATCAATTCCA -s simHuman_chr6.simHuman.chr6 579000 20 - 601863 AGAAGATGAGGGCAACTCCT -s simRat_chr6.simRat.chr6 32289 20 + 647215 ATCAGCTAGGGTCAGCTTGC - -a -s simMouse_chr6.simMouse.chr6 40049 52 + 636262 TTTTAAGTGATACATAAAATTTGGATAAGCATTAGCGTAGACTGGAGTTTAG -s Anc0.Anc0refChr9 15259 49 + 35212 TTGGAGATGACACATACAACCAGAAGGAGTGCTAGAGTAAGTTAGAGT---C -s Anc1.Anc1refChr2 139626 49 - 144309 TTGGAGATGACACATACAACCAGAAGGAGTGCTAGAGTAAGTTAGAGT---C -s Anc2.Anc2refChr0 34771 49 - 56053 TCGGAGATGACACATAGAACCAGAAGGAGTGCTAGAGTAAGTTAGAGT---C -s mr.mrrefChr0 37848 52 + 130230 TTGTAGGTGATACATACAATTTGGATAAGCATTAGCGTAAACTGGAGTTTAG -s simCow_chr6.simCow.chr6 577152 49 - 602619 CCGAAGATGGAACATAAAATCAGATGGTGTGTTAGAGTAAGTTAGAGT---T -s simDog_chr6.simDog.chr6 572252 49 - 593897 TCGGTGATGACACACAGAACCAGAATAAGTGCTAGAGTAAGTTAGAGT---C -s simHuman_chr6.simHuman.chr6 579020 49 - 601863 TTGGAGATGACGAATACAACCAGAGGGAGTGCTAGAGTAAGTTAGAGT---A -s simRat_chr6.simRat.chr6 32309 41 + 647215 TTGTAGGTGATACATAC-----------GCATTAGTGTAAACTGGAGTTTGG - -a -s simMouse_chr6.simMouse.chr6 40101 7 + 636262 ATCTTGA -s Anc0.Anc0refChr9 15308 7 + 35212 AGATCGA -s Anc1.Anc1refChr2 139675 7 - 144309 AGATCGA -s Anc2.Anc2refChr0 34820 7 - 56053 AGATCAA -s mr.mrrefChr0 37900 7 + 130230 ATCTTGA -s simCow_chr6.simCow.chr6 577209 7 - 602619 AATCAAA -s simDog_chr6.simDog.chr6 572301 7 - 593897 AGATCAA -s simHuman_chr6.simHuman.chr6 579069 7 - 601863 ACATCGA -s simRat_chr6.simRat.chr6 32350 7 + 647215 ATCTTAG - -a -s simMouse_chr6.simMouse.chr6 40108 11 + 636262 CAGGTGTGAGC -s Anc0.Anc0refChr9 15315 9 + 35212 AA--TATAATC -s Anc1.Anc1refChr2 139682 9 - 144309 AA--TATAATC -s Anc2.Anc2refChr0 34827 9 - 56053 AA--TATAATC -s mr.mrrefChr0 37907 11 + 130230 CAGGTGTGAGC -s simCow_chr6.simCow.chr6 577216 9 - 602619 AA--TATAATC -s simDog_chr6.simDog.chr6 572313 9 - 593897 AA--TAAAATC -s simHuman_chr6.simHuman.chr6 579076 9 - 601863 AA--TATAATC -s simRat_chr6.simRat.chr6 32357 11 + 647215 CAGGGGTGAGC - -a -s simMouse_chr6.simMouse.chr6 40119 4 + 636262 TACT -s Anc0.Anc0refChr9 15324 4 + 35212 CACT -s Anc1.Anc1refChr2 139691 4 - 144309 CACT -s Anc2.Anc2refChr0 34890 4 - 56053 CACT -s mr.mrrefChr0 37918 4 + 130230 TACT -s simCow_chr6.simCow.chr6 577279 4 - 602619 CTCT -s simDog_chr6.simDog.chr6 572376 4 - 593897 CACC -s simHuman_chr6.simHuman.chr6 579085 4 - 601863 CACT -s simRat_chr6.simRat.chr6 32368 4 + 647215 TACT - -a -s simMouse_chr6.simMouse.chr6 40123 10 + 636262 CAAAACATTT -s Anc0.Anc0refChr9 15328 10 + 35212 CAAAACATTT -s Anc1.Anc1refChr2 139695 10 - 144309 CAAAACATTT -s Anc2.Anc2refChr0 34894 10 - 56053 CAAAACATCT -s mr.mrrefChr0 37922 10 + 130230 CAAAACATTT -s simCow_chr6.simCow.chr6 577283 10 - 602619 CAAAACATCT -s simDog_chr6.simDog.chr6 572380 10 - 593897 CAAAACACCC -s simHuman_chr6.simHuman.chr6 579090 10 - 601863 CAAAACATTT -s simRat_chr6.simRat.chr6 32372 10 + 647215 CAAAACATTT - -a -s simMouse_chr6.simMouse.chr6 40133 33 + 636262 CTACCCAACTCAAAGAATAAGTAAGAAGTTCAT -s Anc0.Anc0refChr9 15338 33 + 35212 TTTTCCAGCTCAAAGAATAAGTAAGAAGCTAAC -s Anc1.Anc1refChr2 139705 33 - 144309 TTTTCCAGCTCAAAGAATAAGTAAGAAGCTAAC -s Anc2.Anc2refChr0 34904 33 - 56053 TTTTCCAGCTCAAAGAATAAGTAAGAAGCTAAC -s mr.mrrefChr0 37932 33 + 130230 CTACCCAACTCAAAGAATAAGTAAGAAGTTCAT -s simCow_chr6.simCow.chr6 577293 33 - 602619 TTTTTCAACATAAGGAACAAGTAAGATGCTAAC -s simDog_chr6.simDog.chr6 572391 32 - 593897 TTTTCCTGCTCAAAGAATAAG-AAGAAGTGAAC -s simHuman_chr6.simHuman.chr6 579100 33 - 601863 TTTTCCAGCTCAAAGAATAAGTAAGAAGCTAAC -s simRat_chr6.simRat.chr6 32382 33 + 647215 CTACCCAACTCAAAGAATAAGTAAGAAGTTTAT - -a -s simMouse_chr6.simMouse.chr6 40166 94 + 636262 GAGATTTCGTTAGCGGTTTTTCAGGTTCAGTGTGTCCTGGCACCCTAAACCTTAAGAGAATGAGTTAAATTGGGATACTTCATAGCTGCAAATA -s Anc0.Anc0refChr9 15371 92 + 35212 TATACTTCTTCAATAACTTTTTAAGTTTGAAGTGTGCTGCCACCCTCAATCTTAAGAGAATGGATCCAGAGA--ATACTTCATACCTGCAAATT -s Anc1.Anc1refChr2 139738 92 - 144309 TATACTTCTTCAATAACTTTTTAAGTTTGAAGTGTGCTGCCACCCTCAATCTTAAGAGAATGGATCCAGAGA--ATACTTCATACCTGCAAATT -s Anc2.Anc2refChr0 34937 92 - 56053 TATACTTCTTCAATAATTTTTTAAGTTTGAAGTGTGCTGCTACTCTCAATCTTAAGAGAATGGATCCAGAGA--ATGTTTGATCCCTGTAAATT -s mr.mrrefChr0 37965 94 + 130230 GAGATTTCGTTAGTGGCTTTTCAGGTTCAGTGTGTCCTGGCACCCTCAACCTTAAGAGAATGAGTTAAAATGGGATACTTCATAGCTGCAAATA -s simCow_chr6.simCow.chr6 577326 92 - 602619 TATAGTTCTACAATAATATTTTAAGTTTGAAGTGTGCTTGTATACCCAATCTTAAGGGATGGGATCCGGCTA--ATTTTTGATGCCTGAAAGTC -s simDog_chr6.simDog.chr6 572720 89 - 593897 TATACTTCTTCACTAATTTTTTCAGTTTGAAGTGTGCTGCTACTCTCAGTCTTAGGAGAATGGATTCAGAGA--ATG---GATCCCAATGAATT -s simHuman_chr6.simHuman.chr6 579133 92 - 601863 TACCCTTCTTCAATTCCTTCTTAAGCTTGAAGTGTACTGTCACCCACAATCCCAAGAGGATGGATCCAGACA--ATACTCCATACCTGCAAATT -s simRat_chr6.simRat.chr6 32415 73 + 647215 GAGATTTCATTAGTGGCTT---------------------CACCCTCAACCTTAAGAGAATGAGTTAAAATGGGATACTTCATAGGTGCAAATA - -a -s simMouse_chr6.simMouse.chr6 40260 142 + 636262 TTTCCAGGTATCTAGTTCTGTATCTAGTTGTACAGGTATGCCTAGATAGGATGCCAATCCATTATAGCAAGTGACTACAGTATAGAATGTATAACAATTGTGAGCAGCCCATCCCTCCTAGATTACACACCTATATTAGGTA -s Anc0.Anc0refChr9 15463 49 + 35212 TCTCAGAGAGT-------------------TCCAGGCATAGCTAAATATGAAGCAA--------------------------------------------------------------------------TTATATTGGTTA -s Anc1.Anc1refChr2 139830 49 - 144309 TCTCAGAGAGT-------------------TCCAGGCATAGCTAAATATGAAGCAA--------------------------------------------------------------------------TTATATTGGTTA -s Anc2.Anc2refChr0 35029 49 - 56053 TCTCAGAGAGA-------------------TCCAGGCATAGCTAAATATCAAGCAC--------------------------------------------------------------------------TTCTATTGGTTT -s mr.mrrefChr0 38059 130 + 130230 TTTCCAGGTATCTAGAT------------GTACAGGTATGCCTAAATATGATGCCAATCCATTATAGCAAGTGACTACAGTAGAGAATGTATAACAATTGTGAGCAGCCCATCCCTCCTAGATTACACACCTATATTAGGTA -s simCow_chr6.simCow.chr6 577419 49 - 602619 TCTCAGTGAGA-------------------TCCAGGCATAACTAAATATCAAGGAC--------------------------------------------------------------------------TTCTAATGGTAT -s simDog_chr6.simDog.chr6 572809 49 - 593897 TCTCAGATAGA-------------------TCCATGCATAGCTAAATATCAAGCAC--------------------------------------------------------------------------TTCTATCTATTT -s simHuman_chr6.simHuman.chr6 579225 49 - 601863 TCTTTGAGAGT-------------------TTCAGACATAGCTAAATATGAAGTAA--------------------------------------------------------------------------TTATATTGGTTA -s simRat_chr6.simRat.chr6 32488 130 + 647215 TTTCCAGATATCTAGAT------------GTCCAGGTATGCCTAAATCTGATGCCAATCCATTTTAGCAAGTTACTACAGTAGAGAATGTATGGCAATGGTGTGCAGTCCATCCCTCCGAGATTATACACCTATATTATATA - -a -s simMouse_chr6.simMouse.chr6 40402 15 + 636262 TAGTTACTTAGACTA -s Anc0.Anc0refChr9 15512 15 + 35212 TAATTACTTAATTAA -s Anc1.Anc1refChr2 139879 15 - 144309 TAATTACTTAATTAA -s Anc2.Anc2refChr0 35078 15 - 56053 TAATTACTTAATTGG -s mr.mrrefChr0 38189 15 + 130230 TAGTTACTTAGATAA -s simCow_chr6.simCow.chr6 577468 15 - 602619 TAATTACTCAATTGG -s simDog_chr6.simDog.chr6 572858 15 - 593897 TAATTACTTAATTGG -s simHuman_chr6.simHuman.chr6 579275 15 - 601863 TAATTACGTAATTAA -s simRat_chr6.simRat.chr6 32618 15 + 647215 TAGCTATTTAGATAA - -a -s simMouse_chr6.simMouse.chr6 40417 30 + 636262 ATTGGCCAAGCCTCCACCACAATGACTTTC -s Anc0.Anc0refChr9 15531 30 + 35212 ACTAAGCAAGTTTTCACCACAATGTCTTTC -s Anc1.Anc1refChr2 139898 30 - 144309 ACTAAGCAAGTTTTCACCACAATGTCTTTC -s Anc2.Anc2refChr0 35097 30 - 56053 CCTAAGCAAGTTTTCACGATAATGTATTTC -s mr.mrrefChr0 38204 30 + 130230 ATTAACCAAGCCTCCACCACAATGACTTTC -s simCow_chr6.simCow.chr6 577487 29 - 602619 CCTAAACAAGTCTTC-CTATAATGTATTTC -s simDog_chr6.simDog.chr6 572877 30 - 593897 CCTGAGCAAGTTTTCATGATAATGTATTCC -s simHuman_chr6.simHuman.chr6 579294 30 - 601863 ACCAAGAAAGTTTTCACCACAATGTCATTC -s simRat_chr6.simRat.chr6 32633 30 + 647215 ATTAACCAAGCCTCCACCACAATGACTTTC - -a -s simMouse_chr6.simMouse.chr6 40447 58 + 636262 TTGCTTCAGAGGATGTCTTCCTCTCATAGGTTATTAGAGTCCACCAAGAATATCGTAT -s Anc0.Anc0refChr9 15561 56 + 35212 ATAGTATAGAGTGTCCCCTCTGCTCCTAG--TGTTAGAGTCCACTAAGAATATCATAT -s Anc1.Anc1refChr2 139928 56 - 144309 ATAGTATAGAGTGTCCCCTCTGCTCCTAG--TGTTAGAGTCCACTAAGAATATCATAT -s Anc2.Anc2refChr0 35127 56 - 56053 ATAGTATAGAGTGTCCCCTCTGCTCCTGG--GGTTAGAGTCCACTAAGAATATCATAT -s mr.mrrefChr0 38234 58 + 130230 TTACTTCAGAGGGTGTCTTCTTCTCATAGGTTATTAGAGTCCACCAAGAATATCATAT -s simCow_chr6.simCow.chr6 577516 56 - 602619 ATAGTGTAGATTGTCCCCACTGATCCTGG--GGTCAGAGTCCCTTATGACTATCATAT -s simDog_chr6.simDog.chr6 572908 56 - 593897 ACAGCATAGAGTGTTTCATCTGCTCCTGG--GGTTAGAGCCCACCAAGAATATCATAT -s simHuman_chr6.simHuman.chr6 579324 56 - 601863 ATAGTATAGAGTGTCCCCTCTGCTCCCAG--TGTTAGAGTCCACTAAGAATATCATAT -s simRat_chr6.simRat.chr6 32663 58 + 647215 TTACTTCAGAGGGTTTCTTCTTTTCATAGTTTATTAGAGTCCACCAAGAATATCATAT - -a -s simMouse_chr6.simMouse.chr6 40505 22 + 636262 GGGTTCACATTTGGGGTCCTGT -s Anc0.Anc0refChr9 15617 22 + 35212 GGGTTCACAATTGGGGTCTAAA -s Anc1.Anc1refChr2 139984 22 - 144309 GGGTTCACAATTGGGGTCTAAA -s Anc2.Anc2refChr0 35195 22 - 56053 GGGTTCACAATTGGGGTGTATA -s mr.mrrefChr0 38292 22 + 130230 GGGTTCACATTTGGGGTCCTAT -s simCow_chr6.simCow.chr6 577584 21 - 602619 AGGTTCACAATTGGGGTATAT- -s simDog_chr6.simDog.chr6 572976 22 - 593897 GGGTTCACAAGTGGGGTGTATA -s simHuman_chr6.simHuman.chr6 579380 22 - 601863 GGGTACATAATCAGGTTCTAAA -s simRat_chr6.simRat.chr6 32721 22 + 647215 GGGTTCACATTTGGGATCCTAT - -a -s simMouse_chr6.simMouse.chr6 40527 28 + 636262 CTCTTGATGGTGTGCTATACGGAGGAAG -s Anc0.Anc0refChr9 15639 28 + 35212 CCATTTATGTTGTGCTAGATTCAGAAAT -s Anc1.Anc1refChr2 140006 28 - 144309 CCATTTATGTTGTGCTAGATTCAGAAAT -s Anc2.Anc2refChr0 35217 28 - 56053 CCATTTATGTTGTGCTAGATTCAAATAT -s mr.mrrefChr0 38314 28 + 130230 CTCTTGATGGTGTGCTAGATGGAGGAAG -s simCow_chr6.simCow.chr6 577605 28 - 602619 CCTTTTTTGTTGTGCTAGGTTCAAATCT -s simDog_chr6.simDog.chr6 573000 28 - 593897 CCATTTATCTTGTGCTATATTCAAATAT -s simHuman_chr6.simHuman.chr6 579402 28 - 601863 CCACTTATGTTGTGCTAGATTCAGAAAT -s simRat_chr6.simRat.chr6 32743 28 + 647215 CTGTTGATGGTACACTAGATGGAGGAAG - -a -s simMouse_chr6.simMouse.chr6 40555 1 + 636262 C -s Anc0.Anc0refChr9 15667 1 + 35212 C -s Anc1.Anc1refChr2 140034 1 - 144309 C -s Anc2.Anc2refChr0 35245 1 - 56053 C -s mr.mrrefChr0 38342 1 + 130230 C -s simCow_chr6.simCow.chr6 577633 1 - 602619 C -s simDog_chr6.simDog.chr6 573063 1 - 593897 C -s simHuman_chr6.simHuman.chr6 579430 1 - 601863 C -s simRat_chr6.simRat.chr6 32771 1 + 647215 C - -a -s simMouse_chr6.simMouse.chr6 40556 89 + 636262 TCATTTGATATTTGTAATGGATCACCACTCACTTAATGTGTTACAAACAAACATTGCTTCCTTTAAAGGGCAAAGAAGGAGAGAGTGCT -s Anc0.Anc0refChr9 15668 70 + 35212 AA-----------GTAGTAATTCACTGGTCAATTAATGTGTCAGAAACAAATGATGATTCCT--------CTAATAAGCAGAGATTGCT -s Anc1.Anc1refChr2 140035 70 - 144309 AA-----------GTAGTAATTCACTGGTCAATTAATGTGTCAGAAACAAATGATGATTCCT--------CTAATAAGCAGAGATTGCT -s Anc2.Anc2refChr0 35246 70 - 56053 AA-----------GTAGTAATTCACTGGTCAATTAATGTATCAGAAACAAATGATGATTCCT--------TTAATAAGCAGAGATTGCT -s mr.mrrefChr0 38343 85 + 130230 TAATTTGATATTTGTAATGGATCACCAGTCACTTAATGTGTCAGAAACAAACATTGCTTCCT----AGGGCTAAGAAGCAGAGAGTGCT -s simCow_chr6.simCow.chr6 577641 70 - 602619 AG-----------ATAGTAGATCATGGGTCATTTAATGCATGAGAAACAAAATACAATTCCT--------TTAATAAGTAGAGATTGCT -s simDog_chr6.simDog.chr6 573064 69 - 593897 AA-----------GTCATAATCCACTGGTCAATTAAT-TATCAGAAACAAATGATGATTCCC--------TTAATAAGCAGAATTTGCT -s simHuman_chr6.simHuman.chr6 579431 70 - 601863 CA-----------GTAGTAACTCACTGGTCAATTAATGTGTCCGAAAAAAATGATGATTCCT--------CTAATAAGCAGAGACTGCT -s simRat_chr6.simRat.chr6 32772 85 + 647215 TAATTTGGTATCTGTAATGGATCACCAGTCAGTTAATGTGTCAGAAACAAACACTGGTTCCT----AAGGCTAGAAAGCAGAGAGTGCT - -a -s simMouse_chr6.simMouse.chr6 40645 6 + 636262 TGTGCA -s Anc0.Anc0refChr9 15741 6 + 35212 TGCACA -s Anc1.Anc1refChr2 140108 6 - 144309 TGCACA -s Anc2.Anc2refChr0 35319 6 - 56053 TGCACG -s mr.mrrefChr0 38428 6 + 130230 TGCACA -s simCow_chr6.simCow.chr6 577714 6 - 602619 TACATC -s simDog_chr6.simDog.chr6 573136 6 - 593897 TGCACG -s simHuman_chr6.simHuman.chr6 579504 6 - 601863 TGCAGA -s simRat_chr6.simRat.chr6 32857 6 + 647215 TGCACA - -a -s simMouse_chr6.simMouse.chr6 40651 14 + 636262 AACACCTTAAACTG -s Anc0.Anc0refChr9 15747 14 + 35212 AACACCTCACACTG -s Anc1.Anc1refChr2 140114 14 - 144309 AACACCTCACACTG -s Anc2.Anc2refChr0 35325 14 - 56053 AACATCTCACACTG -s mr.mrrefChr0 38434 14 + 130230 AACACCTTAAACTG -s simCow_chr6.simCow.chr6 577732 14 - 602619 AACATCTCACACTG -s simDog_chr6.simDog.chr6 573142 14 - 593897 AACATCTCACACTC -s simHuman_chr6.simHuman.chr6 579510 14 - 601863 AACACCTCACACTG -s simRat_chr6.simRat.chr6 32863 14 + 647215 AACACCTTATACTG - -a -s simMouse_chr6.simMouse.chr6 40665 52 + 636262 TTGTTAGCCATATAttgtgttcctgaagttagtctctcattactgcctttct -s Anc0.Anc0refChr9 15761 12 + 35212 TTGGCAGCCATA---------------------------------------- -s Anc1.Anc1refChr2 140128 12 - 144309 TTGGCAGCCATA---------------------------------------- -s Anc2.Anc2refChr0 35346 12 - 56053 TTGGCAGCTATA---------------------------------------- -s mr.mrrefChr0 38448 52 + 130230 TTGTTAGCCATATAttgtgttcctgaagttagtctctcattactgcctttct -s simCow_chr6.simCow.chr6 577753 1 - 602619 T--------------------------------------------------- -s simDog_chr6.simDog.chr6 573163 12 - 593897 TTGGCAGCTATA---------------------------------------- -s simHuman_chr6.simHuman.chr6 579524 12 - 601863 TCGCCAGCCATA---------------------------------------- -s simRat_chr6.simRat.chr6 32877 51 + 647215 TTG-GAGCCATATAttgtgttcctgaagtaagtctctcaaaactgcctttct - -a -s simMouse_chr6.simMouse.chr6 40717 184 + 636262 tggacattctgtttacttaaagagcttgttagcatatggtcaatgtgcagaccctgaaattgctgcttaactccttagtgTACTTGACTgtaccttgtctgcatctacaaaagttgtttgctgatgcccctgttcctaagtgttacaccatcattactgaagaaaagagttatacagggtccag -s mr.mrrefChr0 38500 182 + 130230 tggacattctgtttacttaaagagcttgttagcatatggtcaatgtgcagaccctgaaattgctgcttaactccttagtgTACTTGACTgtaccttgtctgcatctacaaaagttgtttgctgatgcccctgttcctaagt--tacaccatcattactgaagaaaagagttatacagggtccag -s simRat_chr6.simRat.chr6 32929 182 + 647215 tctacattctgtttgtttaatgagcttgttagcgtatggtcggtgtgcagatcccaaaaatgttgctcaactccatagtgTACTTGACTgtaccttgtgaacatcttcacaaattgtttgctgataccccttttctcaaat--tgcaccaccattactggagaaaagagttatacagagtcaag - -a -s simMouse_chr6.simMouse.chr6 40901 67 + 636262 gaggactgacttggatcttcagcctCGACCAGTGGGCCCGTGACCAAACACTGTTGTCTGTGCCCTC -s Anc0.Anc0refChr9 15773 28 + 35212 ---------------------------------------GTGACCAGTCATCCGTGTCTGTTCTCTC -s Anc1.Anc1refChr2 140140 28 - 144309 ---------------------------------------GTGACCAGTCATCCGTGTCTGTTCTCTC -s Anc2.Anc2refChr0 35358 28 - 56053 ---------------------------------------TTGACCAGTCATCCGCATCTGTTCTCTC -s mr.mrrefChr0 38682 67 + 130230 gaggactgacttggatcttcagcctCGACCAGTGGGCCCGTGACCAAACACTGTTGTCTGTGCCCTC -s simDog_chr6.simDog.chr6 573175 28 - 593897 ---------------------------------------TTGACCAGTCATCCGCATCTGTTCTCTC -s simHuman_chr6.simHuman.chr6 579536 28 - 601863 ---------------------------------------GTGAGCAGTCATCCCTGTCTGTTCTCTC -s simRat_chr6.simRat.chr6 33113 67 + 647215 gaggagtgacctggatttctagcctTGACCAGTGGCTCCTTGGCTAAACACTGTTGTCTGTGCCCTC - -a -s simMouse_chr6.simMouse.chr6 40968 32 + 636262 CCTTTCATTCCTAGTCTCATGCACCTCCCTGT -s Anc0.Anc0refChr9 15801 32 + 35212 CCTCTTATTCCAAGTCTTATTCACCCCCCTTT -s Anc1.Anc1refChr2 140168 32 - 144309 CCTCTTATTCCAAGTCTTATTCACCCCCCTTT -s Anc2.Anc2refChr0 35386 32 - 56053 CCCCATATTCCAAGCCTTATTCACACCTGTTC -s mr.mrrefChr0 38749 32 + 130230 CCTTTCATTCCTAGTCTCATGCACCTCCCTGT -s simDog_chr6.simDog.chr6 573203 32 - 593897 CCCCATATTCCAAGCCTTATTCACACCTGTTC -s simHuman_chr6.simHuman.chr6 579564 32 - 601863 CCTCTTATTCGCAGTCTTAGCCACCCCCCTTT -s simRat_chr6.simRat.chr6 33202 32 + 647215 CCTCTCATTTCCAGTCTTATACACTGCCCTGT - -a -s simMouse_chr6.simMouse.chr6 41000 93 + 636262 AACAACTGCGGGCTCCCTGGAGTGTCCTCTTTGAGTGACCTCTTTGAGAGGGAGGTTTGTACTGACCATGTGTGAGTATGTTCCAATTCTGTC -s Anc0.Anc0refChr9 15833 50 + 35212 AACAA----GGACAACCTGGTGTATA-------------------------------------GAC-CTG-ATGATGATGTGCCTATCATGTC -s Anc1.Anc1refChr2 140200 50 - 144309 AACAA----GGACAACCTGGTGTATA-------------------------------------GAC-CTG-ATGATGATGTGCCTATCATGTC -s Anc2.Anc2refChr0 35418 50 - 56053 AGCAG----GGACAACCTGGTATATA-------------------------------------GAC-CTT-ATCATGATGTGCCTATCACATC -s mr.mrrefChr0 38781 92 + 130230 AACAACTGCGGGCTCCCTGGAGTGTCCTCTTTGAGTGACCTCTTTGAGAGGGAGGTTTGTACTGAC-ATGTGTGAGTATGTTCCAATTCTGTC -s simCow_chr6.simCow.chr6 577754 27 - 602619 -------------------GTATATA-------------------------------------GAC-CTC-A--------TGACAATCACATC -s simDog_chr6.simDog.chr6 573235 50 - 593897 AGCAG----GGACAACCTGGTATATA-------------------------------------GAT-TTT-ATCATGATGTGCCTATCACATC -s simHuman_chr6.simHuman.chr6 579598 50 - 601863 GACAA----GGACAACCTTGTGTATA-------------------------------------GAC-CTG-ATGTTGATGTGCTGATCATGTC -s simRat_chr6.simRat.chr6 33234 92 + 647215 ACCAACTGTGGGCTCCCTGGAGTATCCTCTTCGTGTGACCTCTTTGAGAGGGAGGTTTATACTGAC-ATATGTACGTATGTTATAATCTGGTC - -a -s simMouse_chr6.simMouse.chr6 41093 5 + 636262 AGCTT -s Anc0.Anc0refChr9 15883 5 + 35212 AGCTT -s Anc1.Anc1refChr2 140250 5 - 144309 AGCTT -s Anc2.Anc2refChr0 35468 5 - 56053 AGCTT -s mr.mrrefChr0 38873 5 + 130230 AGCTT -s simCow_chr6.simCow.chr6 577781 5 - 602619 AGCTT -s simDog_chr6.simDog.chr6 573285 5 - 593897 CACTT -s simHuman_chr6.simHuman.chr6 579648 5 - 601863 AGCCT -s simRat_chr6.simRat.chr6 33327 5 + 647215 AGCTT - -a -s simMouse_chr6.simMouse.chr6 41098 12 + 636262 CATCACTTTCCA -s Anc0.Anc0refChr9 15889 8 + 35212 CA-CAG---CCA -s Anc1.Anc1refChr2 140256 8 - 144309 CA-CAG---CCA -s Anc2.Anc2refChr0 35474 8 - 56053 CA-CAG---CCA -s mr.mrrefChr0 38878 8 + 130230 CA-CAC---CCA -s simCow_chr6.simCow.chr6 577787 8 - 602619 CA-CAG---CCA -s simDog_chr6.simDog.chr6 573291 2 - 593897 CA---------- -s simHuman_chr6.simHuman.chr6 579654 8 - 601863 CA-CAG---CCC -s simRat_chr6.simRat.chr6 33332 8 + 647215 CA-CAC---CCA - -a -s simMouse_chr6.simMouse.chr6 41110 33 + 636262 TAGTAAACCTGTCTTGCCCAACCCACACCATCT -s Anc0.Anc0refChr9 15898 33 + 35212 AATTTAACTTCTCTTACCCAACACGCACTTTCT -s Anc1.Anc1refChr2 140265 33 - 144309 AATTTAACTTCTCTTACCCAACACGCACTTTCT -s Anc2.Anc2refChr0 35483 33 - 56053 AATTTAAGTTCCCTTATTTAACACGCACTTAGT -s mr.mrrefChr0 38886 33 + 130230 TAGTAAACCTGTCTTGCCCAACCCACACCATCT -s simCow_chr6.simCow.chr6 577796 33 - 602619 AATTTAAGTTCCCTTATTTAACACGCACTTAGT -s simHuman_chr6.simHuman.chr6 579663 33 - 601863 GATTTAACTTTTCTTACCCCACATGTACTGTCT -s simRat_chr6.simRat.chr6 33340 33 + 647215 TAGTCAACTGGTCTTGCCTAAGCCACACCATCT - -a -s simMouse_chr6.simMouse.chr6 41143 7 + 636262 GCCCCGG -s Anc0.Anc0refChr9 15936 7 + 35212 GAACCTG -s Anc1.Anc1refChr2 140303 7 - 144309 GAACCTG -s Anc2.Anc2refChr0 35521 7 - 56053 GAACCTG -s mr.mrrefChr0 38919 7 + 130230 GCCCCGG -s simCow_chr6.simCow.chr6 577834 7 - 602619 GAACCTG -s simHuman_chr6.simHuman.chr6 579701 7 - 601863 GTACCTG -s simRat_chr6.simRat.chr6 33373 7 + 647215 GCTCTGT - -a -s simMouse_chr6.simMouse.chr6 41150 6 + 636262 CTTCAA -s Anc0.Anc0refChr9 15943 6 + 35212 TGTCAA -s Anc1.Anc1refChr2 140310 6 - 144309 TGTCAA -s Anc2.Anc2refChr0 35528 6 - 56053 TGTCAA -s mr.mrrefChr0 38926 6 + 130230 CTTCAA -s simCow_chr6.simCow.chr6 577841 6 - 602619 TGTCAA -s simHuman_chr6.simHuman.chr6 579712 6 - 601863 TGTCAA -s simRat_chr6.simRat.chr6 33380 6 + 647215 CTTCAA - -a -s simMouse_chr6.simMouse.chr6 41156 5 + 636262 TTTGT -s Anc0.Anc0refChr9 15949 5 + 35212 CTTAT -s Anc1.Anc1refChr2 140316 5 - 144309 CTTAT -s Anc2.Anc2refChr0 35534 5 - 56053 CTTAT -s mr.mrrefChr0 38932 5 + 130230 TTTGT -s simCow_chr6.simCow.chr6 577869 5 - 602619 CTTAT -s simHuman_chr6.simHuman.chr6 579718 5 - 601863 CATAT -s simRat_chr6.simRat.chr6 33386 5 + 647215 CATGT - -a -s simMouse_chr6.simMouse.chr6 41161 6 + 636262 CAAGAT -s Anc0.Anc0refChr9 15967 6 + 35212 CTAGAT -s Anc1.Anc1refChr2 140334 6 - 144309 CTAGAT -s Anc2.Anc2refChr0 35552 6 - 56053 CTTAAT -s mr.mrrefChr0 38937 6 + 130230 CAAGAT -s simCow_chr6.simCow.chr6 577891 6 - 602619 CTTAAT -s simHuman_chr6.simHuman.chr6 579736 6 - 601863 CTAGAT -s simRat_chr6.simRat.chr6 33391 6 + 647215 CAAGAT - -a -s simMouse_chr6.simMouse.chr6 41167 11 + 636262 GGTGCAAAGGC -s Anc0.Anc0refChr9 15978 11 + 35212 GCTGCCCAGGC -s Anc1.Anc1refChr2 140345 11 - 144309 GCTGCCCAGGC -s Anc2.Anc2refChr0 35563 11 - 56053 GCTGCCCAGGT -s mr.mrrefChr0 38943 11 + 130230 GGTGCAAAGGC -s simCow_chr6.simCow.chr6 577908 11 - 602619 GCTGCACAGGT -s simDog_chr6.simDog.chr6 573293 10 - 593897 -CAGCCCAGAT -s simHuman_chr6.simHuman.chr6 579747 11 - 601863 GCTGCTGGGGC -s simRat_chr6.simRat.chr6 33397 11 + 647215 GGTGTAAAGGT - -a -s simMouse_chr6.simMouse.chr6 41178 4 + 636262 AGTC -s Anc0.Anc0refChr9 15992 4 + 35212 ATTC -s Anc1.Anc1refChr2 140359 4 - 144309 ATTC -s Anc2.Anc2refChr0 35577 4 - 56053 ATTT -s mr.mrrefChr0 38954 4 + 130230 AGTC -s simCow_chr6.simCow.chr6 577922 4 - 602619 ATCT -s simDog_chr6.simDog.chr6 573306 4 - 593897 ACTT -s simHuman_chr6.simHuman.chr6 579761 4 - 601863 ATTC -s simRat_chr6.simRat.chr6 33408 4 + 647215 AACC - -a -s simMouse_chr6.simMouse.chr6 41182 7 + 636262 CTGGACA -s Anc0.Anc0refChr9 16002 7 + 35212 CTTGATA -s Anc1.Anc1refChr2 140369 7 - 144309 CTTGATA -s Anc2.Anc2refChr0 35587 7 - 56053 TTTGATA -s mr.mrrefChr0 38958 7 + 130230 CTGGACA -s simCow_chr6.simCow.chr6 577932 7 - 602619 GTTGATC -s simDog_chr6.simDog.chr6 573316 7 - 593897 TCTGACA -s simHuman_chr6.simHuman.chr6 579771 7 - 601863 CTTGATT -s simRat_chr6.simRat.chr6 33412 7 + 647215 CTGAACA - -a -s simMouse_chr6.simMouse.chr6 41189 6 + 636262 CATGTC -s Anc0.Anc0refChr9 16009 6 + 35212 CATATC -s Anc1.Anc1refChr2 140376 6 - 144309 CATATC -s Anc2.Anc2refChr0 35594 6 - 56053 CATATC -s mr.mrrefChr0 38965 6 + 130230 CATGTC -s simCow_chr6.simCow.chr6 577941 6 - 602619 CGTATC -s simDog_chr6.simDog.chr6 573323 6 - 593897 CACACT -s simHuman_chr6.simHuman.chr6 579778 6 - 601863 CATTTC -s simRat_chr6.simRat.chr6 33419 6 + 647215 CATGTC - -a -s simMouse_chr6.simMouse.chr6 41195 1 + 636262 A -s Anc0.Anc0refChr9 16015 1 + 35212 A -s Anc1.Anc1refChr2 140382 1 - 144309 A -s Anc2.Anc2refChr0 35600 1 - 56053 A -s mr.mrrefChr0 38971 1 + 130230 A -s simCow_chr6.simCow.chr6 577947 1 - 602619 A -s simDog_chr6.simDog.chr6 573329 1 - 593897 A -s simHuman_chr6.simHuman.chr6 579808 1 - 601863 A -s simRat_chr6.simRat.chr6 33425 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 41196 12 + 636262 GGAGCTGGATCC -s Anc0.Anc0refChr9 16016 12 + 35212 GGACCTGAACAC -s Anc1.Anc1refChr2 140383 12 - 144309 GGACCTGAACAC -s Anc2.Anc2refChr0 35609 12 - 56053 GAACCTGAACAC -s mr.mrrefChr0 38972 12 + 130230 GGAGCTGGATCC -s simCow_chr6.simCow.chr6 577956 12 - 602619 AATGTTGCTCCC -s simDog_chr6.simDog.chr6 573338 12 - 593897 GAACCTGAACAC -s simHuman_chr6.simHuman.chr6 579809 12 - 601863 GGACACGTACAC -s simRat_chr6.simRat.chr6 33428 12 + 647215 GGGGCTCAATCC - -a -s simMouse_chr6.simMouse.chr6 41208 11 + 636262 CTTATCTTTTT -s Anc0.Anc0refChr9 16028 11 + 35212 ATTATTTCTTC -s Anc1.Anc1refChr2 140395 11 - 144309 ATTATTTCTTC -s Anc2.Anc2refChr0 35621 11 - 56053 AGTAATTCATC -s mr.mrrefChr0 38984 11 + 130230 CTTATCTTTTT -s simCow_chr6.simCow.chr6 577968 10 - 602619 A-TAGTCACTC -s simDog_chr6.simDog.chr6 573350 11 - 593897 AGTAATTCATC -s simHuman_chr6.simHuman.chr6 579837 11 - 601863 TTTCTTTCTTC -s simRat_chr6.simRat.chr6 33440 11 + 647215 CATCTCTTTTT - -a -s simMouse_chr6.simMouse.chr6 41219 11 + 636262 TAACTTATCAA -s Anc0.Anc0refChr9 16039 11 + 35212 TTACTTAATAA -s Anc1.Anc1refChr2 140406 11 - 144309 TTACTTAATAA -s Anc2.Anc2refChr0 35632 11 - 56053 TTACTTAATAA -s mr.mrrefChr0 38995 11 + 130230 TAACTTATCAA -s simCow_chr6.simCow.chr6 577978 11 - 602619 TTGCTTAGTAA -s simDog_chr6.simDog.chr6 573363 11 - 593897 TTACTTAATAA -s simHuman_chr6.simHuman.chr6 579848 10 - 601863 TTACTGAATA- -s simRat_chr6.simRat.chr6 33451 11 + 647215 TAACTTATCAG - -a -s simMouse_chr6.simMouse.chr6 41230 36 + 636262 CGTGTCTTTGCCCTATCACTCCCACAGTTATGCGCC -s Anc0.Anc0refChr9 16050 34 + 35212 CATGGCCTTGCCTCATCACTCCGACAGTCA--CTCC -s Anc1.Anc1refChr2 140417 34 - 144309 CATGGCCTTGCCTCATCACTCCGACAGTCA--CTCC -s Anc2.Anc2refChr0 35643 34 - 56053 CATGGCCTTGCCTCATCACTCCGACAGTCA--CTCC -s mr.mrrefChr0 39006 36 + 130230 CGTGTCTTTGCCCTATCACTCCCACAGTTATGCGCC -s simCow_chr6.simCow.chr6 577989 34 - 602619 CCTGGCCTTGCCTTATCACCCCCATTGTCA--CTCC -s simDog_chr6.simDog.chr6 573377 34 - 593897 CATGGCCATGCCTCATGACTCCGACAGTCA--CTCC -s simHuman_chr6.simHuman.chr6 579858 34 - 601863 CATGGCCTTGCTTAATCATGCCTACAGTCC--CTCC -s simRat_chr6.simRat.chr6 33462 36 + 647215 CGTGTCCTTGTCCCATCACCACCACAGTATTGTCAC - -a -s simMouse_chr6.simMouse.chr6 41266 41 + 636262 AGTCACTCTGAGTAGCACAGACAACTCTATTTCGACATTCA -s Anc0.Anc0refChr9 16084 39 + 35212 AGTCACTCAGAGTAGTACAGACAACCCTACT--AAGGTCTA -s Anc1.Anc1refChr2 140451 39 - 144309 AGTCACTCAGAGTAGTACAGACAACCCTACT--AAGGTCTA -s Anc2.Anc2refChr0 35680 39 - 56053 AGTCACTTACGGTCATTCAGACAACCCTACC--AAGGTCTA -s mr.mrrefChr0 39042 41 + 130230 AGTCACTCTGAGTAGCACAGACAACTCTATTTCGACATTCA -s simCow_chr6.simCow.chr6 578026 39 - 602619 AGTCACTAATGGTAGTACATGCAACCCTACC--AAAGTCTA -s simDog_chr6.simDog.chr6 573414 39 - 593897 AGTCACTTACGGTCATTCAGACAACTTAACC--AAGGTTTA -s simHuman_chr6.simHuman.chr6 579892 39 - 601863 CACATCTCGGAAGAGTACAGACATTCCTACT--AAGGTCTA -s simRat_chr6.simRat.chr6 33498 41 + 647215 AGTTGCGCAGAGTAGCACAGACAACTCCATTTGGAAATCCA - -a -s simMouse_chr6.simMouse.chr6 41307 13 + 636262 ACATTCGAATTTG -s Anc0.Anc0refChr9 16123 13 + 35212 ATATTTCTATTTG -s Anc1.Anc1refChr2 140490 13 - 144309 ATATTTCTATTTG -s Anc2.Anc2refChr0 35719 13 - 56053 ATGTTTCTATGTG -s mr.mrrefChr0 39083 13 + 130230 ACATTCGAATTTG -s simCow_chr6.simCow.chr6 578065 13 - 602619 ATGTTTCTATGAG -s simDog_chr6.simDog.chr6 573455 13 - 593897 ATGTTTCTCTGTG -s simHuman_chr6.simHuman.chr6 579931 13 - 601863 ATATTTATATTTA -s simRat_chr6.simRat.chr6 33539 13 + 647215 ACAATCAAGCCTG - -a -s simMouse_chr6.simMouse.chr6 41320 117 + 636262 TATCTAGAACACAACACGTGGAATTGTTTTCAGACTTGTGGCCTGGCCTGTATTGAACAAAATTGAGGTACTGTCCTAAAAGCAGCATATTTTGTCTTGAAAGGGCTGAGTGTGGAA -s Anc0.Anc0refChr9 16149 19 + 35212 TATCTAACACA--------------------------------------------------------------------------------------------------GTGTTGCA -s Anc1.Anc1refChr2 140516 19 - 144309 TATCTAACACA--------------------------------------------------------------------------------------------------GTGTTGCA -s Anc2.Anc2refChr0 35745 19 - 56053 TATCTAACTCA--------------------------------------------------------------------------------------------------GTGTTGCT -s mr.mrrefChr0 39096 117 + 130230 TATCTAGAACACAACACGTGGAATTGTTTTCAGACTTGTGGCCTGGCCTGTATTGAACAAAATTGAGGTACTGTCCTAAAAGCAGCATATTTTGTCTTGAAAGGGCTGAGTGTGGAA -s simCow_chr6.simCow.chr6 578091 19 - 602619 TATCTAATTCA--------------------------------------------------------------------------------------------------CTGTTACT -s simDog_chr6.simDog.chr6 573481 19 - 593897 TCTCTAACTCA--------------------------------------------------------------------------------------------------GTGTTGCT -s simHuman_chr6.simHuman.chr6 579957 19 - 601863 TATCTAACACA--------------------------------------------------------------------------------------------------GTGTTGCA -s simRat_chr6.simRat.chr6 33552 117 + 647215 TATTCAAAACACAACACTTTGAATTGTTTTGAGACTTGTGGCCTGGCCTGTATTGAACAAAATTGAGGTACTGTCCTAAAGGCAGCATATTTTGTCTTGGAAGGGCTGAGTGTGGAG - -a -s simMouse_chr6.simMouse.chr6 41437 6 + 636262 CCAACA -s Anc0.Anc0refChr9 16169 6 + 35212 CCAACA -s Anc1.Anc1refChr2 140536 6 - 144309 CCAACA -s Anc2.Anc2refChr0 35765 6 - 56053 ACAACA -s mr.mrrefChr0 39213 6 + 130230 CCAACA -s simCow_chr6.simCow.chr6 578111 6 - 602619 GCAACA -s simDog_chr6.simDog.chr6 573501 6 - 593897 ACAACA -s simHuman_chr6.simHuman.chr6 579977 6 - 601863 CCAACA -s simRat_chr6.simRat.chr6 33669 6 + 647215 CCATCA - -a -s simMouse_chr6.simMouse.chr6 41443 9 + 636262 GTGTCTTGT -s Anc0.Anc0refChr9 16180 9 + 35212 GTGACTTGT -s Anc1.Anc1refChr2 140547 9 - 144309 GTGACTTGT -s Anc2.Anc2refChr0 35776 9 - 56053 GAGACTTGT -s mr.mrrefChr0 39219 9 + 130230 GTGACTTGT -s simCow_chr6.simCow.chr6 578122 9 - 602619 GGGACATGT -s simDog_chr6.simDog.chr6 573512 9 - 593897 GAGACTTGT -s simHuman_chr6.simHuman.chr6 579988 9 - 601863 GTGACTTGT -s simRat_chr6.simRat.chr6 33675 9 + 647215 GTGAGATGT - -a -s simMouse_chr6.simMouse.chr6 41452 13 + 636262 TCCTCTACTCTAG -s Anc0.Anc0refChr9 16190 13 + 35212 TCCTATACTGAAG -s Anc1.Anc1refChr2 140557 13 - 144309 TCCTATACTGAAG -s Anc2.Anc2refChr0 35786 13 - 56053 GCCTATATTGAAG -s mr.mrrefChr0 39228 13 + 130230 TCCTCTACTCTAG -s simCow_chr6.simCow.chr6 578132 13 - 602619 GCCTTTATAGAAA -s simDog_chr6.simDog.chr6 573522 13 - 593897 GCCTACATTGAAG -s simHuman_chr6.simHuman.chr6 579998 13 - 601863 TCCTGTACTGGAG -s simRat_chr6.simRat.chr6 33684 13 + 647215 TACTCTACTCTGG - -a -s simMouse_chr6.simMouse.chr6 41465 13 + 636262 CGTGGGGGTGTCA -s Anc0.Anc0refChr9 16206 13 + 35212 TGTGAGGGTGTCA -s Anc1.Anc1refChr2 140573 13 - 144309 TGTGAGGGTGTCA -s Anc2.Anc2refChr0 35802 13 - 56053 AGTGAGGGTGTCA -s mr.mrrefChr0 39241 13 + 130230 TGTGGGGGTGTCA -s simCow_chr6.simCow.chr6 578148 13 - 602619 GGTGAGGATGTCA -s simDog_chr6.simDog.chr6 573538 13 - 593897 ACTGAGGGTATCA -s simHuman_chr6.simHuman.chr6 580014 13 - 601863 TGTGAGGGTGTCA -s simRat_chr6.simRat.chr6 33697 13 + 647215 TGTGGGGGTGTCA - -a -s simMouse_chr6.simMouse.chr6 41478 27 + 636262 CAGGACAGATTGTACATATAGCAGGAA -s Anc0.Anc0refChr9 16219 27 + 35212 AGGCAATGAATAGATAACTAGCAGAAA -s Anc1.Anc1refChr2 140586 27 - 144309 AGGCAATGAATAGATAACTAGCAGAAA -s Anc2.Anc2refChr0 35820 27 - 56053 AGGCGATGAATAGATAACTAGCAGAAA -s mr.mrrefChr0 39254 27 + 130230 CAGGACAGATTATACATATAGCAGGAA -s simCow_chr6.simCow.chr6 578166 26 - 602619 AGGC-ATGAGTAGATAACTAGCAGGAA -s simDog_chr6.simDog.chr6 573556 18 - 593897 AGGCGATGCATAGAT---------AAA -s simHuman_chr6.simHuman.chr6 580027 27 - 601863 AGGCAATGAATAGAAGACCAGGACAAA -s simRat_chr6.simRat.chr6 33710 27 + 647215 CAGGACAGAGTATACATATAGCAGGAA - -a -s simMouse_chr6.simMouse.chr6 41505 5 + 636262 TAGAA -s Anc0.Anc0refChr9 16246 5 + 35212 TAAAA -s Anc1.Anc1refChr2 140613 5 - 144309 TAAAA -s Anc2.Anc2refChr0 35847 5 - 56053 TAAAA -s mr.mrrefChr0 39281 5 + 130230 TAGAA -s simCow_chr6.simCow.chr6 578192 5 - 602619 TAAAC -s simDog_chr6.simDog.chr6 573577 5 - 593897 TAAAA -s simHuman_chr6.simHuman.chr6 580054 5 - 601863 TAATA -s simRat_chr6.simRat.chr6 33737 5 + 647215 TAGAA - -a -s simMouse_chr6.simMouse.chr6 41510 65 + 636262 TTTAGACAGATGTTTGGCAGAATGTTATCTACAGATAACATTATCTGAGCTTGCTTGTGGGCCTT -s Anc0.Anc0refChr9 16252 48 + 35212 TTTGGACATACATCTGGCAGGTGGTTATTTATAGAGAATATTATCTG-----------------T -s Anc1.Anc1refChr2 140619 48 - 144309 TTTGGACATACATCTGGCAGGTGGTTATTTATAGAGAATATTATCTG-----------------T -s Anc2.Anc2refChr0 35853 48 - 56053 TTTGGACATACATCTGGCAATTGGTTATTTATAGAGAATATTGTCTG-----------------T -s mr.mrrefChr0 39287 48 + 130230 TTTAGACAGATGTTTGGCAGGATGTTATCTACAGATAATATTATCTG-----------------T -s simCow_chr6.simCow.chr6 578198 48 - 602619 CTTGAACATACCATTGGCAAGTGGTTATTTATAGCAAATATAGTCTG-----------------T -s simDog_chr6.simDog.chr6 573583 48 - 593897 TTTGGACATACATCTGGCAATTGGTTATTTATAGAGAATGTTGGCTG-----------------T -s simHuman_chr6.simHuman.chr6 580060 45 - 601863 TTTGGACACACATATGGCTGGGG---GTTCATAGAGAGTATTATCTG-----------------T -s simRat_chr6.simRat.chr6 33743 48 + 647215 TTTACATAGATGTTTGGCAGGATGTTATCTACAGATTATATTATCTG-----------------T - -a -s simMouse_chr6.simMouse.chr6 41575 40 + 636262 GCGGCAAGTTGCACTTCCCTTGTGTGTGCTGTCTTTTCTC -s Anc0.Anc0refChr9 16300 40 + 35212 GTGGCAAATAGCATTTCCCTTGTATTCACTGTTTTTTCCC -s Anc1.Anc1refChr2 140667 40 - 144309 GTGGCAAATAGCATTTCCCTTGTATTCACTGTTTTTTCCC -s Anc2.Anc2refChr0 35901 40 - 56053 GTGGCAAATAGCATTTCCCTTGTATTCACTGTTTTTTTCC -s mr.mrrefChr0 39335 40 + 130230 GCGGCAAGTTGCACTTCCCTTGTGTGTGCTGTCTTTTCTC -s simCow_chr6.simCow.chr6 578246 38 - 602619 GTGTGATATAGCATTTCCGTTGTATGCACTGTTTTTTT-- -s simDog_chr6.simDog.chr6 573631 40 - 593897 GTGGCAAATATCATTTCCCTTGTATTCACTGATTTCTTCC -s simHuman_chr6.simHuman.chr6 580155 40 - 601863 GTGGCAAATAGTATTTCCCTTGTATTCAATGCTTTTTCCC -s simRat_chr6.simRat.chr6 33791 40 + 647215 GCAATAAGTTGCACTTCCCTTGTGTGTGCTGTCTATTCTC - -a -s simMouse_chr6.simMouse.chr6 41615 4 + 636262 AAGC -s Anc0.Anc0refChr9 16340 4 + 35212 AAGC -s Anc1.Anc1refChr2 140707 4 - 144309 AAGC -s Anc2.Anc2refChr0 35960 4 - 56053 AAGC -s mr.mrrefChr0 39375 4 + 130230 AAGC -s simCow_chr6.simCow.chr6 578286 4 - 602619 AACC -s simDog_chr6.simDog.chr6 573690 4 - 593897 AAGC -s simHuman_chr6.simHuman.chr6 580195 4 - 601863 AAGC -s simRat_chr6.simRat.chr6 33831 4 + 647215 AAGC - -a -s simMouse_chr6.simMouse.chr6 41619 40 + 636262 AGATTGCTTGCCCACTAAGTTTGCAGCATACTAACAATTA -s Anc0.Anc0refChr9 16345 40 + 35212 GCATTGCTTGCCCATTAAGGTTACACCAAATTAACAATTA -s Anc1.Anc1refChr2 140712 40 - 144309 GCATTGCTTGCCCATTAAGGTTACACCAAATTAACAATTA -s Anc2.Anc2refChr0 35965 40 - 56053 GCATTGCTTCCCCATTAAGGTGACACCAAATTAACAATTA -s mr.mrrefChr0 39380 40 + 130230 AGATTGCTTGCCCACTAAGTTTGCACCATATTAACAATTA -s simCow_chr6.simCow.chr6 578291 39 - 602619 GCATTGCTTA-CCATTAAGGTGACACAAAATGAACAGTTA -s simDog_chr6.simDog.chr6 573695 40 - 593897 GCATTACTTCCCTATTATGATGACAACAAATTAACAATTG -s simHuman_chr6.simHuman.chr6 580200 40 - 601863 GCATTGCTTGCCCATAAAGGTTATACCAAATTAACAATTA -s simRat_chr6.simRat.chr6 33836 40 + 647215 ATATTGCTTGCCCACTAAGTTTGCACCAGATCAACAATAA - -a -s simMouse_chr6.simMouse.chr6 41659 1 + 636262 T -s Anc0.Anc0refChr9 16385 1 + 35212 G -s Anc1.Anc1refChr2 140752 1 - 144309 G -s Anc2.Anc2refChr0 36005 1 - 56053 G -s mr.mrrefChr0 39420 1 + 130230 T -s simCow_chr6.simCow.chr6 578330 1 - 602619 G -s simDog_chr6.simDog.chr6 573735 1 - 593897 G -s simHuman_chr6.simHuman.chr6 580240 1 - 601863 G -s simRat_chr6.simRat.chr6 33946 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 41660 25 + 636262 GAACTTACATACTTAGGGCTCCTGA -s Anc0.Anc0refChr9 16388 25 + 35212 GACCTTACATACTTTAGGTGCCTGA -s Anc1.Anc1refChr2 140755 25 - 144309 GACCTTACATACTTTAGGTGCCTGA -s Anc2.Anc2refChr0 36008 25 - 56053 AACCTTACATACTTTAGGTGCCTGA -s mr.mrrefChr0 39421 25 + 130230 GAACTTACATACTTAGGGTTCCTGA -s simCow_chr6.simCow.chr6 578333 25 - 602619 AACCTTACATGATTTAGGTGCCTGA -s simDog_chr6.simDog.chr6 573738 25 - 593897 AACGGTCCCTACCTCAAGTGCCTGA -s simHuman_chr6.simHuman.chr6 580243 25 - 601863 GGCCTTACATACTTTAGGTGCCTGA -s simRat_chr6.simRat.chr6 33947 25 + 647215 GAACTTACATACGTGGAGTTCGTGA - -a -s simMouse_chr6.simMouse.chr6 41685 14 + 636262 GTCTTTGAAGGAAT -s Anc0.Anc0refChr9 16414 14 + 35212 GTCTGTGAAGGAAG -s Anc1.Anc1refChr2 140781 14 - 144309 GTCTGTGAAGGAAG -s Anc2.Anc2refChr0 36034 14 - 56053 GTCTGTGAAGGAAG -s mr.mrrefChr0 39446 14 + 130230 GTCTTTGAAGGAAT -s simCow_chr6.simCow.chr6 578359 14 - 602619 ATCGGTGAAGTAAT -s simDog_chr6.simDog.chr6 573764 14 - 593897 GTCTGTGAAGGAAG -s simHuman_chr6.simHuman.chr6 580269 14 - 601863 GTTTATGAAGGAAG -s simRat_chr6.simRat.chr6 33972 14 + 647215 GTCTTTAAAGGAAT - -a -s simMouse_chr6.simMouse.chr6 41699 11 + 636262 CTGGTAGAAAA -s Anc0.Anc0refChr9 16428 11 + 35212 CTGGAAGAAAA -s Anc1.Anc1refChr2 140795 11 - 144309 CTGGAAGAAAA -s Anc2.Anc2refChr0 36048 11 - 56053 CTGGAAGAAAA -s mr.mrrefChr0 39460 11 + 130230 CTGGTAGAAAA -s simCow_chr6.simCow.chr6 578373 11 - 602619 ATGGAGGAAAA -s simDog_chr6.simDog.chr6 573778 11 - 593897 CTGGAAGAAAA -s simHuman_chr6.simHuman.chr6 580283 11 - 601863 CTGGAAGAAAA -s simRat_chr6.simRat.chr6 612973 11 - 647215 CTGGTAGAAAA - -a -s simMouse_chr6.simMouse.chr6 41710 28 + 636262 GCTAAAATGAACCTACCACAGGGCCACT -s Anc0.Anc0refChr9 16439 25 + 35212 GCCAAAATGGACCTGC---AGGGTGTTA -s Anc1.Anc1refChr2 140806 25 - 144309 GCCAAAATGGACCTGC---AGGGTGTTA -s Anc2.Anc2refChr0 36059 25 - 56053 GCCAAAATGGGCCTGC---AACGTGTTA -s mr.mrrefChr0 39471 28 + 130230 GCCAAAATGGACCTACCACAGGGCCACT -s simCow_chr6.simCow.chr6 578384 23 - 602619 GACAGAATAG--CTGC---AAAGTGTTA -s simDog_chr6.simDog.chr6 573790 23 - 593897 GCTAAAATGAGCCTG-----ACATGTTA -s simHuman_chr6.simHuman.chr6 580294 25 - 601863 GCCAAAAGGGACCTGC---AGGGTGtta -s simRat_chr6.simRat.chr6 612984 28 - 647215 GCCAAAATGGACCTACCACAGGGCTACT - -a -s simMouse_chr6.simMouse.chr6 41738 3 + 636262 TTA -s Anc0.Anc0refChr9 16464 3 + 35212 TTT -s Anc1.Anc1refChr2 140831 3 - 144309 TTT -s Anc2.Anc2refChr0 36084 3 - 56053 TTT -s mr.mrrefChr0 39499 3 + 130230 TTA -s simCow_chr6.simCow.chr6 578407 3 - 602619 TCT -s simDog_chr6.simDog.chr6 573813 3 - 593897 ATT -s simHuman_chr6.simHuman.chr6 580319 3 - 601863 ttt -s simRat_chr6.simRat.chr6 613017 3 - 647215 TTA - -a -s simMouse_chr6.simMouse.chr6 41741 15 + 636262 CTATAGGAGTGGAGG -s Anc0.Anc0refChr9 16467 15 + 35212 ATATATAATAAACTT -s Anc1.Anc1refChr2 140834 15 - 144309 ATATATAATAAACTT -s Anc2.Anc2refChr0 36108 15 - 56053 ATATATAATAAACTT -s mr.mrrefChr0 39502 15 + 130230 CTATAGGAGTAAAGG -s simCow_chr6.simCow.chr6 578459 15 - 602619 GTATATAATAAAGTT -s simDog_chr6.simDog.chr6 573837 15 - 593897 ATATATAATGAACTT -s simHuman_chr6.simHuman.chr6 580322 15 - 601863 atatataataaattt -s simRat_chr6.simRat.chr6 613020 15 - 647215 CTATAGGAACAAAGG - -a -s simMouse_chr6.simMouse.chr6 41756 6 + 636262 CAGAAA -s Anc0.Anc0refChr9 16482 6 + 35212 TAGAAG -s Anc1.Anc1refChr2 140849 6 - 144309 TAGAAG -s Anc2.Anc2refChr0 36123 6 - 56053 TAGAGG -s mr.mrrefChr0 39517 6 + 130230 CAGAAA -s simCow_chr6.simCow.chr6 578474 6 - 602619 TAGAGG -s simDog_chr6.simDog.chr6 573852 6 - 593897 GAGGGG -s simHuman_chr6.simHuman.chr6 580337 6 - 601863 taGAAG -s simRat_chr6.simRat.chr6 613038 6 - 647215 CTGAGA - -a -s simMouse_chr6.simMouse.chr6 41762 1 + 636262 T -s Anc0.Anc0refChr9 16488 1 + 35212 T -s Anc1.Anc1refChr2 140855 1 - 144309 T -s Anc2.Anc2refChr0 36129 1 - 56053 T -s mr.mrrefChr0 39523 1 + 130230 T -s simCow_chr6.simCow.chr6 578480 1 - 602619 C -s simDog_chr6.simDog.chr6 573936 1 - 593897 T -s simHuman_chr6.simHuman.chr6 580343 1 - 601863 T -s simRat_chr6.simRat.chr6 613044 1 - 647215 T - -a -s simMouse_chr6.simMouse.chr6 41763 31 + 636262 AAGCTATTAGGGAAAGCAAATAAACAAGAAA -s Anc0.Anc0refChr9 16489 8 + 35212 A-----------------------CAAAAAA -s Anc1.Anc1refChr2 140856 8 - 144309 A-----------------------CAAAAAA -s Anc2.Anc2refChr0 36132 8 - 56053 A-----------------------CAAAAAA -s mr.mrrefChr0 39524 30 + 130230 AAGCTATTA-GGAAAGCAAATAGACAATAAA -s simCow_chr6.simCow.chr6 578491 7 - 602619 A-----------------------CAAAAA- -s simDog_chr6.simDog.chr6 573939 8 - 593897 A-----------------------CAAAAAA -s simHuman_chr6.simHuman.chr6 580344 8 - 601863 A-----------------------CGAGAAA -s simRat_chr6.simRat.chr6 613045 30 - 647215 AAGCTATTA-GGAAAGCAAATAGATAATAAA - -a -s simMouse_chr6.simMouse.chr6 41794 16 + 636262 CTGTGGAAACCACACA -s Anc0.Anc0refChr9 16497 16 + 35212 GGCTGGAAAGTAGACG -s Anc1.Anc1refChr2 140864 16 - 144309 GGCTGGAAAGTAGACG -s Anc2.Anc2refChr0 36140 16 - 56053 GGCTGGAAAGTAGACG -s mr.mrrefChr0 39554 16 + 130230 CTGTGGAAACCACACA -s simCow_chr6.simCow.chr6 578498 16 - 602619 GGTTCGAGAGTAGACC -s simDog_chr6.simDog.chr6 573948 16 - 593897 GGCTGGCAAATAGATG -s simHuman_chr6.simHuman.chr6 580352 16 - 601863 AAATGGAAAGTAGACT -s simRat_chr6.simRat.chr6 613075 16 - 647215 CTGTGGAAACCCCCCA - -a -s simMouse_chr6.simMouse.chr6 41810 8 + 636262 TCTACAAG -s Anc0.Anc0refChr9 16518 8 + 35212 CCTTAAAA -s Anc1.Anc1refChr2 140885 8 - 144309 CCTTAAAA -s Anc2.Anc2refChr0 36161 8 - 56053 CATTAAAA -s mr.mrrefChr0 39570 8 + 130230 TCTACAAG -s simCow_chr6.simCow.chr6 578519 8 - 602619 TATTAAAA -s simDog_chr6.simDog.chr6 573969 8 - 593897 CATTATAA -s simHuman_chr6.simHuman.chr6 580373 8 - 601863 CCTTAAAA -s simRat_chr6.simRat.chr6 613091 8 - 647215 TCTACAAG - -a -s simMouse_chr6.simMouse.chr6 41818 5 + 636262 ATGAC -s Anc0.Anc0refChr9 16526 5 + 35212 ATGGA -s Anc1.Anc1refChr2 140893 5 - 144309 ATGGA -s Anc2.Anc2refChr0 36169 5 - 56053 ATGGA -s mr.mrrefChr0 39578 5 + 130230 ATGAC -s simCow_chr6.simCow.chr6 578528 5 - 602619 ATAGG -s simDog_chr6.simDog.chr6 573977 5 - 593897 ATGGA -s simHuman_chr6.simHuman.chr6 580381 5 - 601863 ATGCA -s simRat_chr6.simRat.chr6 613099 5 - 647215 ACAAC - -a -s simMouse_chr6.simMouse.chr6 41823 3 + 636262 TGC -s Anc0.Anc0refChr9 16531 3 + 35212 TTC -s Anc1.Anc1refChr2 140898 3 - 144309 TTC -s Anc2.Anc2refChr0 36197 3 - 56053 TTC -s mr.mrrefChr0 39583 3 + 130230 TGC -s simCow_chr6.simCow.chr6 578556 3 - 602619 CTC -s simDog_chr6.simDog.chr6 574005 3 - 593897 TTT -s simHuman_chr6.simHuman.chr6 580386 3 - 601863 TTC -s simRat_chr6.simRat.chr6 613104 3 - 647215 TGC - -a -s simMouse_chr6.simMouse.chr6 41826 4 + 636262 TAAG -s Anc0.Anc0refChr9 16550 4 + 35212 TTAG -s Anc1.Anc1refChr2 140917 4 - 144309 TTAG -s Anc2.Anc2refChr0 36216 4 - 56053 TTAT -s mr.mrrefChr0 39586 4 + 130230 TAAG -s simCow_chr6.simCow.chr6 578575 4 - 602619 TTAC -s simDog_chr6.simDog.chr6 574024 4 - 593897 ATAT -s simHuman_chr6.simHuman.chr6 580405 4 - 601863 TCAG -s simRat_chr6.simRat.chr6 613107 4 - 647215 TAAG - -a -s simMouse_chr6.simMouse.chr6 41830 23 + 636262 TGGAGTCTCTGATATGATATGTG -s Anc0.Anc0refChr9 16554 22 + 35212 TGGTGTATA-GAAATCATATCTG -s Anc1.Anc1refChr2 140921 22 - 144309 TGGTGTATA-GAAATCATATCTG -s Anc2.Anc2refChr0 36220 22 - 56053 TGGTATATA-TAAATCATATCTG -s mr.mrrefChr0 39590 23 + 130230 TGGAGTCTCTGAAATGATATGTG -s simCow_chr6.simCow.chr6 578579 15 - 602619 TGACATATA-TACATC------- -s simDog_chr6.simDog.chr6 574028 22 - 593897 TTGTATATA-TAAATCATATCTG -s simHuman_chr6.simHuman.chr6 580409 22 - 601863 TGGGGTATA-GGAATCATATCTT -s simRat_chr6.simRat.chr6 613146 23 - 647215 TGGAGTCCGTGAAATGATATGTG - -a -s simMouse_chr6.simMouse.chr6 41853 32 + 636262 ATATGTTTATCAATCATTTTTCCACATATGTG -s Anc0.Anc0refChr9 16584 23 + 35212 ACATGGTTACTTGTCGCTACTGC--------- -s Anc1.Anc1refChr2 140951 23 - 144309 ACATGGTTACTTGTCGCTACTGC--------- -s Anc2.Anc2refChr0 36250 23 - 56053 ACATGGTTACTTGTTGCTACTGC--------- -s mr.mrrefChr0 39613 32 + 130230 ATATGTTTACCAATCACTTTTCCACATATGTG -s simCow_chr6.simCow.chr6 578597 23 - 602619 ACGTGGTAACTTGTTACTACTGC--------- -s simDog_chr6.simDog.chr6 574058 23 - 593897 TCATGGTTACTTGTTGCTACTGC--------- -s simHuman_chr6.simHuman.chr6 580439 23 - 601863 ACATGGTCCCTTGTCGCTACAGC--------- -s simRat_chr6.simRat.chr6 613169 32 - 647215 ATATGTTTACCAATCACTTTTCTACAAACATA - -a -s simMouse_chr6.simMouse.chr6 41885 15 + 636262 TGATGCACTATAGGA -s Anc0.Anc0refChr9 16607 15 + 35212 TTATTCACTTTGGGA -s Anc1.Anc1refChr2 140974 15 - 144309 TTATTCACTTTGGGA -s Anc2.Anc2refChr0 36286 15 - 56053 CTATTCATATTGAAA -s mr.mrrefChr0 39645 15 + 130230 TGATGCACTATAGGA -s simCow_chr6.simCow.chr6 578634 10 - 602619 CTTTTCATAT----- -s simDog_chr6.simDog.chr6 574094 15 - 593897 CCATTCATATTGAAA -s simHuman_chr6.simHuman.chr6 580462 15 - 601863 TTTGTCGCTCTGGGC -s simRat_chr6.simRat.chr6 613201 15 - 647215 TGATGCACTATAGGA - -a -s simMouse_chr6.simMouse.chr6 41900 2 + 636262 GG -s Anc0.Anc0refChr9 16623 2 + 35212 GA -s Anc1.Anc1refChr2 140990 2 - 144309 GA -s Anc2.Anc2refChr0 36304 2 - 56053 GA -s mr.mrrefChr0 39661 2 + 130230 GA -s simCow_chr6.simCow.chr6 578645 2 - 602619 CA -s simDog_chr6.simDog.chr6 574114 2 - 593897 GA -s simHuman_chr6.simHuman.chr6 580478 2 - 601863 AG -s simRat_chr6.simRat.chr6 34243 2 + 647215 AA - -a -s simMouse_chr6.simMouse.chr6 41902 36 + 636262 TACTGTTCCTGTAAGTGCAGAGTACTAACCACCAGC -s Anc0.Anc0refChr9 16625 28 + 35212 TACTCGACATGCA--------GTACAAACCCCCAAT -s Anc1.Anc1refChr2 140992 28 - 144309 TACTCGACATGCA--------GTACAAACCCCCAAT -s Anc2.Anc2refChr0 36306 28 - 56053 TACTCGACATGCA--------GTAGAAGCCCCCAAT -s mr.mrrefChr0 39663 28 + 130230 TACTGGGCCTGTA--------GTACTAACCACCAAC -s simCow_chr6.simCow.chr6 578647 28 - 602619 TACTCGGCATGCT--------GTACAAGTCCCCAAT -s simDog_chr6.simDog.chr6 574116 28 - 593897 TACTCGACATGCA--------GTAGAAGCCCCCAAT -s simHuman_chr6.simHuman.chr6 580480 20 - 601863 CATTAGAC-TACT--------GTTCCAAC------- -s simRat_chr6.simRat.chr6 34246 28 + 647215 TGCTGGGTATGTA--------GTAACAACCACCAAC - -a -s simMouse_chr6.simMouse.chr6 41938 18 + 636262 ATGTGAGACATGGTGTGC -s Anc0.Anc0refChr9 16653 14 + 35212 ATGGGAAACATGGG---- -s Anc1.Anc1refChr2 141020 18 - 144309 ATGGGAAACATGGGTACT -s Anc2.Anc2refChr0 36334 14 - 56053 ATGGGAAACAAGGG---- -s mr.mrrefChr0 39691 18 + 130230 ATGTGAGACATGGTGAAC -s simCow_chr6.simCow.chr6 578675 14 - 602619 ATGGGAAACAAGGG---- -s simDog_chr6.simDog.chr6 574145 14 - 593897 ATGGGAAACAAGGG---- -s simHuman_chr6.simHuman.chr6 580500 11 - 601863 -------ACATTGATACT -s simRat_chr6.simRat.chr6 34274 18 + 647215 ATGTGCGCCATGGTGAAC - -a -s simMouse_chr6.simMouse.chr6 41956 8 + 636262 ATAAAAAG -s Anc0.Anc0refChr9 16667 8 + 35212 ATAAAAAG -s Anc1.Anc1refChr2 141038 8 - 144309 ATAAAAAG -s Anc2.Anc2refChr0 36348 8 - 56053 ATAAAAAG -s mr.mrrefChr0 39709 8 + 130230 ATAAAAAG -s simDog_chr6.simDog.chr6 574162 8 - 593897 ATAAAAAG -s simHuman_chr6.simHuman.chr6 580511 8 - 601863 ATAAAAAG -s simRat_chr6.simRat.chr6 34292 8 + 647215 ATCAAAAG - -a -s simMouse_chr6.simMouse.chr6 41964 45 + 636262 CCTGCGGTCACATTAGACTTTTGAAAACATAACCTAAGGAAAGCT -s Anc0.Anc0refChr9 16676 43 + 35212 CCTATGGTCACAGTCAACTTTTTAA--CATAAGCTAAATAAAGCC -s Anc1.Anc1refChr2 141047 43 - 144309 CCTATGGTCACAGTCAACTTTTTAA--CATAAGCTAAATAAAGCC -s Anc2.Anc2refChr0 36357 43 - 56053 CCTAGGGTCACAGGCAGTTTTGTAA--CATAAGTGAAATAAAGCC -s mr.mrrefChr0 39718 45 + 130230 CCTGTGGTCACAGTAAACTTTTGAAAACATAAGCTAAGGAAAGCT -s simCow_chr6.simCow.chr6 578689 11 - 602619 ----------------------------------GGTCTAAAGCC -s simDog_chr6.simDog.chr6 574171 43 - 593897 CCTAGGGTCACAGGCAGTTTTGTAA--CATAAGTGAAATAAAGCC -s simHuman_chr6.simHuman.chr6 580520 43 - 601863 CCTATAGTCCCCATTAACTTTTTAG--CATCAGCTAAATAAAGCC -s simRat_chr6.simRat.chr6 34301 45 + 647215 CCTGTGGTCACTGTAAACTCTTGAAAACATAAGCTAAGGAAAGCT - -a -s simMouse_chr6.simMouse.chr6 42009 24 + 636262 TTGCTCACACATGACTAAAGATCT -s Anc0.Anc0refChr9 16719 23 + 35212 T-GATCACACATGACTAGAGATAT -s Anc1.Anc1refChr2 141090 23 - 144309 T-GATCACACATGACTAGAGATAT -s Anc2.Anc2refChr0 36400 23 - 56053 T-GATCACACATGACTAGAGATAT -s mr.mrrefChr0 39763 24 + 130230 TTGCTCACACATGACTAGAGATAT -s simCow_chr6.simCow.chr6 578700 23 - 602619 T-GATCACACTTAACACGAGATCT -s simDog_chr6.simDog.chr6 574214 23 - 593897 T-ATTAACACATGGCTAGAGATAT -s simHuman_chr6.simHuman.chr6 580563 23 - 601863 T-GATCATACATGACTAGAGATAT -s simRat_chr6.simRat.chr6 34353 24 + 647215 TTGCTCACACATGACTAGAGACAT - -a -s simMouse_chr6.simMouse.chr6 42033 25 + 636262 ACCAACCATCCCAATAGGAGAATTG -s Anc0.Anc0refChr9 16744 22 + 35212 AGCAATAAAC---ACAATATAATTG -s Anc1.Anc1refChr2 141115 22 - 144309 AGCAATAAAC---ACAATATAATTG -s Anc2.Anc2refChr0 36425 22 - 56053 AGCATTAAAC---ACAATATAATTG -s mr.mrrefChr0 39787 25 + 130230 ACCAACCATCCCAATAAGATAATTG -s simCow_chr6.simCow.chr6 578725 22 - 602619 AGCATTAGAC---GCAAAACAATTT -s simDog_chr6.simDog.chr6 574239 20 - 593897 AGCATTAAGT---AC--TGTAGTTG -s simHuman_chr6.simHuman.chr6 580588 22 - 601863 AGCAATAAAC---ACAACATAACTG -s simRat_chr6.simRat.chr6 34377 25 + 647215 ACCAACCATCCCAATAAGATAATTG - -a -s simMouse_chr6.simMouse.chr6 42058 2 + 636262 CC -s Anc0.Anc0refChr9 16766 2 + 35212 TG -s Anc1.Anc1refChr2 141137 2 - 144309 TG -s Anc2.Anc2refChr0 36447 2 - 56053 TG -s mr.mrrefChr0 39812 2 + 130230 TG -s simCow_chr6.simCow.chr6 578747 2 - 602619 TG -s simDog_chr6.simDog.chr6 574259 2 - 593897 TG -s simHuman_chr6.simHuman.chr6 580610 2 - 601863 TG -s simRat_chr6.simRat.chr6 34404 2 + 647215 TG - -a -s simMouse_chr6.simMouse.chr6 42060 2 + 636262 AT -s Anc0.Anc0refChr9 16773 2 + 35212 AA -s Anc1.Anc1refChr2 141144 2 - 144309 AA -s Anc2.Anc2refChr0 36454 2 - 56053 AA -s mr.mrrefChr0 39814 2 + 130230 AT -s simCow_chr6.simCow.chr6 578754 2 - 602619 AA -s simDog_chr6.simDog.chr6 574266 2 - 593897 TA -s simHuman_chr6.simHuman.chr6 580617 2 - 601863 AG -s simRat_chr6.simRat.chr6 34406 2 + 647215 AT - -a -s simMouse_chr6.simMouse.chr6 42062 14 + 636262 CTAGCTGATGATAA -s Anc0.Anc0refChr9 16779 14 + 35212 CTAGTGGCTGTTAA -s Anc1.Anc1refChr2 141150 14 - 144309 CTAGTGGCTGTTAA -s Anc2.Anc2refChr0 36461 14 - 56053 CTAGTGGCTGTTAA -s mr.mrrefChr0 39820 14 + 130230 CTAGTTGATGATAA -s simCow_chr6.simCow.chr6 578761 14 - 602619 CTAGTAGCTATCAA -s simDog_chr6.simDog.chr6 574273 14 - 593897 CTAATGGCTGTTAA -s simHuman_chr6.simHuman.chr6 580623 14 - 601863 CTGGGGGCTGTTTG -s simRat_chr6.simRat.chr6 34412 14 + 647215 CTAGTTGATGATAT - -a -s simMouse_chr6.simMouse.chr6 42076 21 + 636262 TGCGGTATCAGACAAAAAGAC -s Anc0.Anc0refChr9 16797 21 + 35212 TGCAGTATCAGAAGAAAAGAA -s Anc1.Anc1refChr2 141168 21 - 144309 TGCAGTATCAGAAGAAAAGAA -s Anc2.Anc2refChr0 36479 21 - 56053 TGCCATACCAGAAGAAAAGAA -s mr.mrrefChr0 39834 21 + 130230 TGCAGTATCAGACAGAAAGAA -s simCow_chr6.simCow.chr6 578778 21 - 602619 CACCCGGCCAGGAGAAAAGAT -s simDog_chr6.simDog.chr6 574291 21 - 593897 TGCCATACCAGAAGAAAAAAA -s simHuman_chr6.simHuman.chr6 580641 21 - 601863 TGCAGTATAAGAAGAAAAGAA -s simRat_chr6.simRat.chr6 34426 21 + 647215 AGTAGTATCAGACAGAAAGAA - -a -s simMouse_chr6.simMouse.chr6 42097 55 + 636262 GGATTAACTTCATTACATTGCTTTGTAGTAAGGGTAATCCTGACCATGCTAGAGC -s Anc0.Anc0refChr9 16818 52 + 35212 GATGTAAATTTGTTACATCACTTTGTA---AAAGTGTAACTGCCCATGCTACAAC -s Anc1.Anc1refChr2 141189 52 - 144309 GATGTAAATTTGTTACATCACTTTGTA---AAAGTGTAACTGCCCATGCTACAAC -s Anc2.Anc2refChr0 36500 52 - 56053 GATGTAAATTTGTTACATCACTTTGTA---AAAGTGTAACTGCCCATGCTCCAAC -s mr.mrrefChr0 39855 55 + 130230 GGATTAACTTCATTACATCACTTTGTAGTAAGGGTATTCCTGACCATGCTAGAGC -s simCow_chr6.simCow.chr6 578799 52 - 602619 GATGTGAGTTTGTTACATCACTTCACG---GAGGTGTAACTGCCCATACTTCAAT -s simDog_chr6.simDog.chr6 574312 52 - 593897 GATGTAAATTTGTCACATCACTTTGTA---AGAATGTAACTGCCCATGCTCCAAC -s simHuman_chr6.simHuman.chr6 580679 52 - 601863 GATGTAAATTTTTTACATCACTTTGTA---AAAGTGTAGCTGCCCATGCTACAAC -s simRat_chr6.simRat.chr6 34447 49 + 647215 CGATTCACTTCATT-CATCACTTTGGAGTAAGGGTATTCCTGTCCATGC-----A - -a -s simMouse_chr6.simMouse.chr6 42152 41 + 636262 GTTTTGGACCACCTCTGGTTAAAGGCTCATTATATAATCCA -s Anc0.Anc0refChr9 16870 41 + 35212 CTTTTGGACCACCACAGGCCAAAGGCTTATTATATAATCCA -s Anc1.Anc1refChr2 141241 41 - 144309 CTTTTGGACCACCACAGGCCAAAGGCTTATTATATAATCCA -s Anc2.Anc2refChr0 36552 41 - 56053 CTTTTAGACCACCAAAGGCCAAAGGCTTATTATGTAATCCA -s mr.mrrefChr0 39910 41 + 130230 GTTTTGGACCACCTCTGGTTAAAGGCTCATTATATAATCCA -s simCow_chr6.simCow.chr6 578852 41 - 602619 TTTTTAGACCACCTTAGGCAAAAGCCCTATTATGTAATCCA -s simDog_chr6.simDog.chr6 574364 40 - 593897 CTTTTAGACCACCAAATGCCAAAAGCTTAGTATG-AATCCA -s simHuman_chr6.simHuman.chr6 580731 41 - 601863 ATTTTGGACCACCACAGGCCAAAGGCTTATTATATAATCCA -s simRat_chr6.simRat.chr6 34496 33 + 647215 TTTTCAGACCAT--------AAAGGCTCATTATACACTCCG - -a -s simMouse_chr6.simMouse.chr6 42193 42 + 636262 TAACTGCTGTCATGTCAGGTGTAAGTGGTTTAGACTCTACTG -s Anc0.Anc0refChr9 16926 42 + 35212 TAGCTGATGCCAGATCAGGTGTATGTAGCTTAAACTGTACTC -s Anc1.Anc1refChr2 141297 42 - 144309 TAGCTGATGCCAGATCAGGTGTATGTAGCTTAAACTGTACTC -s Anc2.Anc2refChr0 36608 42 - 56053 TAGCTGATGCCATATCATGTGTATGTAGCTTAAACTGTACCC -s mr.mrrefChr0 39951 42 + 130230 TAACTGCTGTCAGGTCAGGTGTAAGTGGTTTAGACTCTACTG -s simCow_chr6.simCow.chr6 578908 40 - 602619 -AGCTGAACCCTTATCACGCGT-TGTGACTTAATTTGTACCC -s simDog_chr6.simDog.chr6 574419 41 - 593897 TAACTGATGCCATATCATGTGTAT-CAGCCTACACTGTATCT -s simHuman_chr6.simHuman.chr6 580787 42 - 601863 CAGCTGGTGCCAGATCAGATTTATGTTGCTTTAGCCATACTC -s simRat_chr6.simRat.chr6 34529 33 + 647215 TAACTGCTGTCAGGTCAGGTGTA---------GGCTGTACTG - -a -s simMouse_chr6.simMouse.chr6 42235 13 + 636262 CATAGCTCATAGT -s Anc0.Anc0refChr9 16968 13 + 35212 AACATCTGATAGT -s Anc1.Anc1refChr2 141339 13 - 144309 AACATCTGATAGT -s Anc2.Anc2refChr0 36650 13 - 56053 AACATCTGGTACT -s mr.mrrefChr0 39993 13 + 130230 CATAGCTCATAGT -s simCow_chr6.simCow.chr6 578949 13 - 602619 AATATGTGGTAAT -s simDog_chr6.simDog.chr6 574460 13 - 593897 AACATCTGGTACT -s simHuman_chr6.simHuman.chr6 580829 13 - 601863 AACATCTGATAGT -s simRat_chr6.simRat.chr6 34562 13 + 647215 CAAAGCTCATAGT - -a -s simMouse_chr6.simMouse.chr6 42248 12 + 636262 TTTCAGCTGGTG -s Anc0.Anc0refChr9 16981 11 + 35212 CTCCAGCTGGT- -s Anc1.Anc1refChr2 141352 11 - 144309 CTCCAGCTGGT- -s Anc2.Anc2refChr0 36663 11 - 56053 CTCCAGCTGAT- -s mr.mrrefChr0 40006 12 + 130230 TTTCAGCTGGTG -s simCow_chr6.simCow.chr6 578962 11 - 602619 AGTCAGCTGAT- -s simDog_chr6.simDog.chr6 574477 5 - 593897 CTCCA------- -s simHuman_chr6.simHuman.chr6 580842 11 - 601863 CTCCAGCTGGT- -s simRat_chr6.simRat.chr6 34575 12 + 647215 TGTCAGCTGATG - -a -s simMouse_chr6.simMouse.chr6 42260 17 + 636262 CATAATTGGGTGCCAAT -s Anc0.Anc0refChr9 16992 17 + 35212 CTTGATCAGGTGTCAAT -s Anc1.Anc1refChr2 141363 17 - 144309 CTTGATCAGGTGTCAAT -s Anc2.Anc2refChr0 36674 17 - 56053 CTCGATCAGGTGTCAAT -s mr.mrrefChr0 40018 17 + 130230 CTTAATTGGGTGCCAAT -s simCow_chr6.simCow.chr6 578974 17 - 602619 CTCGATCACATGGCAAT -s simDog_chr6.simDog.chr6 574482 13 - 593897 ----ATCGGGTGTCAAT -s simHuman_chr6.simHuman.chr6 580853 17 - 601863 CTTGATCAGGTGTCAAT -s simRat_chr6.simRat.chr6 34587 17 + 647215 CTTAATTGGGCGCCAAT - -a -s simMouse_chr6.simMouse.chr6 42277 151 + 636262 CAACAGTATCCAATGAATTGTGGTCTTGCACTTGGTGCTTCACGAGCCACCATTACGGATCCACGAGAACATTATTCCATTGGGAATACTAGATGATTTACTAACACTTAAGGAGTTGGAGACAATATCACAGTGCTGACAGCCAAGATAA -s Anc0.Anc0refChr9 17014 87 + 35212 CAACTGTACCCAATATACTGTAATCCTGCACCTAGTATT----------------------------------------------------------------GCATCTAAGAGGTTGGAGGCAATATCACAGCACTTGCAGCCAAAATAA -s Anc1.Anc1refChr2 141385 87 - 144309 CAACTGTACCCAATATACTGTAATCCTGCACCTAGTATT----------------------------------------------------------------GCATCTAAGAGGTTGGAGGCAATATCACAGCACTTGCAGCCAAAATAA -s Anc2.Anc2refChr0 36696 87 - 56053 CAACTGTACCCACTATACTGTAATTCTGCATCCAGTATT----------------------------------------------------------------GCATCTAAGATGTCAGATGCAATATAACACCACTTGCATGTGAAGTAA -s mr.mrrefChr0 40035 137 + 130230 CAACTGTATCCAATGAACTGTAGTCTTGCACTTGGTGCTTCACGA--------------TCCACGAGAACATTATTCCATTGGGAATACTAGATGATTTACTAACACTTAAGGGGTTGGAGACAATATCACAGTACTGGCAGCCAAGATAA -s simCow_chr6.simCow.chr6 578996 76 - 602619 TAACTGTACCCAGTATACTATAATTTTGCATCCAATATG----------------------------------------------------------------GCACCTAAGAAGTCAGATGCAATATGACATCACCTGC----------- -s simDog_chr6.simDog.chr6 574500 87 - 593897 CAACTGTACTCACTATATTGTAATTCTGCATCCAGTATT----------------------------------------------------------------ACATCTAAGATGTCAAATGCAATATAACACTGCTTGCATGTGAAGTAA -s simHuman_chr6.simHuman.chr6 580875 87 - 601863 CAACTGTAGCCAATATACTGTAATCCTGCACCTAGTATT----------------------------------------------------------------GCATCTAAGAGGTTGGAGTCAATATCACAGCACTTGTAGCCAAAATAA -s simRat_chr6.simRat.chr6 34604 137 + 647215 CAACTGCATCCAATGAACTGTAGTCTTGCATTTGGTGCTGCACGA--------------TCCACGAGAACGTCATTCCATTGGGAGTACTAGATGAACTGCTAACACTTGAGGGGTTGGAGACAATATCTCAGTACTGGCAGCCAAGATAA - -a -s simMouse_chr6.simMouse.chr6 42428 1 + 636262 T -s Anc0.Anc0refChr9 17102 1 + 35212 T -s Anc1.Anc1refChr2 141473 1 - 144309 T -s Anc2.Anc2refChr0 36784 1 - 56053 T -s mr.mrrefChr0 40172 1 + 130230 T -s simDog_chr6.simDog.chr6 574588 1 - 593897 T -s simHuman_chr6.simHuman.chr6 580963 1 - 601863 T -s simRat_chr6.simRat.chr6 34741 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 42429 115 + 636262 TACACATGAGCCATCGAAAGTTGGAAGTTTGATTTAGTGGCAAAGGACTGGGAATGCTTTACAGCCAGAAAAATAGTGGAAGGCGCCTGGAGAACATTTGGAGAACATTAACAGT -s Anc0.Anc0refChr9 17103 63 + 35212 TACATATGAGCCATA--AACTGGGAAGTTTCATGTAGTGG--------------------------------------------------AGTATAGTTGGAAGATCTTAACAGC -s Anc1.Anc1refChr2 141474 63 - 144309 TACATATGAGCCATA--AACTGGGAAGTTTCATGTAGTGG--------------------------------------------------AGTATAGTTGGAAGATCTTAACAGC -s Anc2.Anc2refChr0 36785 63 - 56053 TACATGACAGCAATA--AACTGGGACGTTTCACATAGTGG--------------------------------------------------AATATAGTAGAAAGCTCTTAACAGC -s mr.mrrefChr0 40173 114 + 130230 TACACATGAGCCATCGAAAGTTGGGAGTTTGATGTAGTGGCAAAGGACTGGGAACTCTTTACAGCTAGAAAA-TAGTGGAAGGGGCCTGGAGAACATTTGGAGAACATTAACAGT -s simCow_chr6.simCow.chr6 579072 28 - 602619 -----------------------------------AGCCA--------------------------------------------------AATGCAGTCGAATACTCATAACA-- -s simDog_chr6.simDog.chr6 574590 63 - 593897 TACATGACAGCAATA--AACTGGGACGTTTCACATAGTGG--------------------------------------------------AATATGGTACAAAGCTCTTGACTGC -s simHuman_chr6.simHuman.chr6 580964 63 - 601863 TACAGATGAGCCATT--AACTATGAAGTTTCATGTAGTGG--------------------------------------------------AGGATAATTGGAAGATTTGAACAAC -s simRat_chr6.simRat.chr6 34742 114 + 647215 TACACATGAGCCATCGAAAGATGGGAGTTTGATGTAGTGGCAAAGGACTGGGAACTCTCTACAGCTATTAAA-TAGTGGAAGGGGTCTGGAGAACATTTGGATAACATCAACAGT - -a -s simMouse_chr6.simMouse.chr6 42544 40 + 636262 AATGAATAGTAGTGAATGGAACAACTTAGCAAGAAGGATT -s Anc0.Anc0refChr9 17166 40 + 35212 AGGGACTAGTAACAAAAGGAAGACCTTAGCAAGAATGATT -s Anc1.Anc1refChr2 141537 40 - 144309 AGGGACTAGTAACAAAAGGAAGACCTTAGCAAGAATGATT -s Anc2.Anc2refChr0 36848 40 - 56053 AGGACCCCATCACAAAAGAAAGACCTTAGCAAGAATGACT -s mr.mrrefChr0 40287 40 + 130230 AATGACTAGTAACAAATGGAAGAACTTAGCAAGAAGGATT -s simCow_chr6.simCow.chr6 579100 4 - 602619 ------------------------------------GTGT -s simDog_chr6.simDog.chr6 574654 40 - 593897 AGGACCCCATCACAAAAGAAAGACCTTAGCAAGAATGACC -s simHuman_chr6.simHuman.chr6 581027 40 - 601863 AGGGACTAGCAACAAAAGGAAGACCTCAACAAGAATGATT -s simRat_chr6.simRat.chr6 34856 39 + 647215 AATGACTAGTAACAAA-GGAAGAACTTAGTGAGAAACATT - -a -s simMouse_chr6.simMouse.chr6 42584 33 + 636262 GGTAGAAGATCTGCTACCTAGGGATTCTATTCC -s Anc0.Anc0refChr9 17206 10 + 35212 GGTAGAAGAT----------------------- -s Anc1.Anc1refChr2 141577 10 - 144309 GGTAGAAGAT----------------------- -s Anc2.Anc2refChr0 36888 10 - 56053 GGTAGAAAAT----------------------- -s mr.mrrefChr0 40327 33 + 130230 GGTAGAAGATCTGCTACCTAGGGATTCTATTCC -s simCow_chr6.simCow.chr6 579104 10 - 602619 GGTAGCAAAC----------------------- -s simDog_chr6.simDog.chr6 574695 10 - 593897 GGCAGAAACT----------------------- -s simHuman_chr6.simHuman.chr6 581067 10 - 601863 GGTAGAAGAT----------------------- -s simRat_chr6.simRat.chr6 34895 33 + 647215 GGTAGAAGATCTGCTACCTAGGGATTCTATGCC - -a -s simMouse_chr6.simMouse.chr6 42617 36 + 636262 TCTTGTTTGGTAGATTCCAGTATACAACTGTTAAGA -s Anc0.Anc0refChr9 17216 6 + 35212 ------------------------------GAATGA -s Anc1.Anc1refChr2 141587 6 - 144309 ------------------------------GAATGA -s Anc2.Anc2refChr0 36898 6 - 56053 ------------------------------GAATGA -s mr.mrrefChr0 40360 36 + 130230 TCTTGTTTGGTAGATTCCAGTATACGACTGTTAAGA -s simCow_chr6.simCow.chr6 579114 6 - 602619 ------------------------------GAATGA -s simDog_chr6.simDog.chr6 574705 6 - 593897 ------------------------------GAATGA -s simHuman_chr6.simHuman.chr6 581077 6 - 601863 ------------------------------GAATAA -s simRat_chr6.simRat.chr6 34933 36 + 647215 TCTGGTTGGGTGAATTCCAGTATATGACTGTTAAGA - -a -s simMouse_chr6.simMouse.chr6 42653 14 + 636262 GGCTGAGGACAAAC -s Anc0.Anc0refChr9 17222 14 + 35212 GGCTGAAAACAAAA -s Anc1.Anc1refChr2 141593 14 - 144309 GGCTGAAAACAAAA -s Anc2.Anc2refChr0 36915 14 - 56053 GACTGAAAACAAAA -s mr.mrrefChr0 40396 14 + 130230 GGCTGAGGACAAAC -s simCow_chr6.simCow.chr6 579131 9 - 602619 GGTT-----TTAAA -s simDog_chr6.simDog.chr6 574722 14 - 593897 GACTGAAAACAACA -s simHuman_chr6.simHuman.chr6 581083 14 - 601863 TGCTGAAAACAAAA -s simRat_chr6.simRat.chr6 34969 14 + 647215 GACGGAGGACAAAC - -a -s simMouse_chr6.simMouse.chr6 42667 5 + 636262 TAGGT -s Anc0.Anc0refChr9 17237 5 + 35212 TAGGT -s Anc1.Anc1refChr2 141608 5 - 144309 TAGGT -s Anc2.Anc2refChr0 36930 5 - 56053 TAGGT -s mr.mrrefChr0 40410 5 + 130230 TAGGT -s simCow_chr6.simCow.chr6 579141 5 - 602619 TAGGT -s simDog_chr6.simDog.chr6 574737 5 - 593897 TAGAT -s simHuman_chr6.simHuman.chr6 581098 5 - 601863 TAGGT -s simRat_chr6.simRat.chr6 34983 5 + 647215 TAGGT - -a -s simMouse_chr6.simMouse.chr6 42672 14 + 636262 TTACCATCTTAATA -s Anc0.Anc0refChr9 17242 14 + 35212 TTACTGTCTTAATA -s Anc1.Anc1refChr2 141613 14 - 144309 TTACTGTCTTAATA -s Anc2.Anc2refChr0 36935 14 - 56053 TTACTGTCTTAATA -s mr.mrrefChr0 40415 14 + 130230 TTACTTTCTTAATA -s simCow_chr6.simCow.chr6 579146 14 - 602619 CTATTGTCTTAATA -s simDog_chr6.simDog.chr6 574766 14 - 593897 TTACTTTCTTAATA -s simHuman_chr6.simHuman.chr6 581103 14 - 601863 TTACTGTCCTAATA -s simRat_chr6.simRat.chr6 34988 13 + 647215 T-CATTTCTTAATA - -a -s simMouse_chr6.simMouse.chr6 42686 19 + 636262 GACATCAAGCAGTTGAACT -s Anc0.Anc0refChr9 17256 19 + 35212 GACATAAAGCAACTAAACC -s Anc1.Anc1refChr2 141627 19 - 144309 GACATAAAGCAACTAAACC -s Anc2.Anc2refChr0 36949 19 - 56053 GACATAAAGCAACTAAACC -s mr.mrrefChr0 40429 19 + 130230 GACATCAAGCAGCTGAACT -s simCow_chr6.simCow.chr6 579160 19 - 602619 GACGTAAAGCAACTAAACC -s simDog_chr6.simDog.chr6 574780 19 - 593897 GACATAAAGCGACTAAACC -s simHuman_chr6.simHuman.chr6 581119 19 - 601863 GAGATAAAGCAACCAAACC -s simRat_chr6.simRat.chr6 35001 19 + 647215 GACATCAAGCAGCTGAACT - -a -s simMouse_chr6.simMouse.chr6 42705 28 + 636262 TAGAGAGGCTCTCTCACAGTGCACCATT -s Anc0.Anc0refChr9 17275 28 + 35212 TAGAGAGACTCTTTTACTGTGGCCCAAG -s Anc1.Anc1refChr2 141646 28 - 144309 TAGAGAGACTCTTTTACTGTGGCCCAAG -s Anc2.Anc2refChr0 36977 28 - 56053 CAGAGAGACTCTTTTACTGTGGCCCAAG -s mr.mrrefChr0 40448 28 + 130230 TAGAGAGGCTCTCTTACAGTGCACCATT -s simCow_chr6.simCow.chr6 579188 28 - 602619 CAAAAAGAGCCGTCTACTGTGGCCGAAG -s simDog_chr6.simDog.chr6 574808 28 - 593897 CAGAGAGACTCTTTTACTGTGGCCCCAG -s simHuman_chr6.simHuman.chr6 581138 15 - 601863 TA-------------ACTGTGGTACAAG -s simRat_chr6.simRat.chr6 35020 28 + 647215 TAGAGAGGCTCTCTTACAGTGCACCATT - -a -s simMouse_chr6.simMouse.chr6 42733 15 + 636262 TTGATCTATCTAAAA -s Anc0.Anc0refChr9 17303 11 + 35212 GAGATCAA----ACA -s Anc1.Anc1refChr2 141674 11 - 144309 GAGATCAA----ACA -s Anc2.Anc2refChr0 37005 11 - 56053 GAGCCCAG----ACA -s mr.mrrefChr0 40476 11 + 130230 TTGATCTA----AAA -s simCow_chr6.simCow.chr6 579219 11 - 602619 GAGCCCAG----ACA -s simDog_chr6.simDog.chr6 574836 1 - 593897 G-------------- -s simHuman_chr6.simHuman.chr6 581153 11 - 601863 GGGATCAA----ACA -s simRat_chr6.simRat.chr6 35048 11 + 647215 GCGACCTA----AGA - -a -s simMouse_chr6.simMouse.chr6 42748 6 + 636262 GCTTCA -s Anc0.Anc0refChr9 17314 6 + 35212 TGTGCA -s Anc1.Anc1refChr2 141685 6 - 144309 TGTGCA -s Anc2.Anc2refChr0 37016 6 - 56053 TGTGCA -s mr.mrrefChr0 40487 6 + 130230 GCTTCA -s simCow_chr6.simCow.chr6 579232 6 - 602619 TGTGCA -s simDog_chr6.simDog.chr6 574837 4 - 593897 --TGCA -s simHuman_chr6.simHuman.chr6 581164 6 - 601863 TATGCA -s simRat_chr6.simRat.chr6 35059 6 + 647215 GCTTCA - -a -s simMouse_chr6.simMouse.chr6 42754 38 + 636262 GGTGACCACATTAAGATTTAGAGCAGGACATCTGATTG -s Anc0.Anc0refChr9 17320 38 + 35212 GGTGCTCATATTAAGATGTAAAGCAGCACTTTTGTTTG -s Anc1.Anc1refChr2 141691 38 - 144309 GGTGCTCATATTAAGATGTAAAGCAGCACTTTTGTTTG -s Anc2.Anc2refChr0 37022 38 - 56053 GGGGCTCATATTAAGGTGTAAAGCAGCACTTTTGTTTG -s mr.mrrefChr0 40493 38 + 130230 GGTGACCACATTAAGATTTAAAGCAGGACATCTGATTG -s simCow_chr6.simCow.chr6 579244 38 - 602619 GGGGCCCATAGTAAGGTGTAAACCAGCATTTTTGATTG -s simDog_chr6.simDog.chr6 574841 38 - 593897 GGGGCTCATATTAAGGTGCAGAGCAGTGCTTTAGTCTG -s simHuman_chr6.simHuman.chr6 581170 38 - 601863 GGTGCTCATATTAAGATGTAAAGCAGCACTTTTGGTTG -s simRat_chr6.simRat.chr6 35065 38 + 647215 GGTGACCAAATTAAGATTTAAAGGAGAACATCTGATTG - -a -s simMouse_chr6.simMouse.chr6 42792 58 + 636262 CAAGCCTCACTGGTTATCCCAACTATTGTCCAGACTATAGCAGAAAGAGTATAAACCT -s Anc0.Anc0refChr9 17366 57 + 35212 CTGGCTTCACTGGTGGCCACAACTATTATC-AACCTGAAGCAGAAAGAGTATATACAC -s Anc1.Anc1refChr2 141737 57 - 144309 CTGGCTTCACTGGTGGCCACAACTATTATC-AACCTGAAGCAGAAAGAGTATATACAC -s Anc2.Anc2refChr0 37068 57 - 56053 CTGGCTTCACTGGTGGCCACAACTATTATC-AACCTGAAGCAGAAAGAGTATATATAC -s mr.mrrefChr0 40531 58 + 130230 CAGGCTTCACTGGTTATCCCAACTATTGTCCAGACTATAGCAGAAAGAGTATAAACCT -s simCow_chr6.simCow.chr6 579290 57 - 602619 CTGGCTTCACTGGTGGCTGCAACTATTATC-AACCTGAAGCAGTAAGAGTAAGTCCAC -s simDog_chr6.simDog.chr6 574887 57 - 593897 CTGGCCCCACTGGTGGCCACACCTATGATC-AACTTGAATCAGAAAGAGTATATATAC -s simHuman_chr6.simHuman.chr6 581216 50 - 601863 CTGACTTCACTGGGGGCCACAACTATT------CCTGAAGCAGAGAGTGTATAGCC-- -s simRat_chr6.simRat.chr6 35103 58 + 647215 CAGGCTTCACTGGTTATCCCAACTATTGTCCAGACTATAGCAGAAAGAGTATAAACCT - -a -s simMouse_chr6.simMouse.chr6 42850 16 + 636262 GAATTCCCGATGTATG -s Anc0.Anc0refChr9 17423 16 + 35212 GCCCTTCAGATGCATA -s Anc1.Anc1refChr2 141794 16 - 144309 GCCCTTCAGATGCATA -s Anc2.Anc2refChr0 37125 16 - 56053 GCCCTTCAGATGCGTA -s mr.mrrefChr0 40589 16 + 130230 GCACTTCAGATGTACG -s simCow_chr6.simCow.chr6 579347 16 - 602619 ACCATTCAGATAGTCA -s simDog_chr6.simDog.chr6 574950 16 - 593897 GCCCTTCAGATGCGTA -s simHuman_chr6.simHuman.chr6 581266 12 - 601863 ----TTCAGATGCATA -s simRat_chr6.simRat.chr6 35161 16 + 647215 GCACTTCAGATGTACG - -a -s simMouse_chr6.simMouse.chr6 42866 24 + 636262 TCCCTAAAGAACAGCTGAGACTGT -s Anc0.Anc0refChr9 17440 24 + 35212 TCACTAAAGAACAGCCATGACTCT -s Anc1.Anc1refChr2 141811 24 - 144309 TCACTAAAGAACAGCCATGACTCT -s Anc2.Anc2refChr0 37142 24 - 56053 TCATTAAAGAACAGCCATGACTCT -s mr.mrrefChr0 40605 24 + 130230 TCCCTAAAGAACAGCTAAGACTGT -s simCow_chr6.simCow.chr6 579364 24 - 602619 TCATTAAAGAACAGCCATGACTCT -s simHuman_chr6.simHuman.chr6 581279 24 - 601863 TCACTACAGAACAGCCATGACTTC -s simRat_chr6.simRat.chr6 35177 24 + 647215 TCCCTAAAGAACAGCTAAGTCTGT - -a -s simMouse_chr6.simMouse.chr6 42890 3 + 636262 AAT -s Anc0.Anc0refChr9 17469 1 + 35212 --T -s Anc1.Anc1refChr2 141840 1 - 144309 --T -s Anc2.Anc2refChr0 37171 1 - 56053 --T -s mr.mrrefChr0 40634 3 + 130230 AAT -s simCow_chr6.simCow.chr6 579393 1 - 602619 --T -s simHuman_chr6.simHuman.chr6 581308 1 - 601863 --T -s simRat_chr6.simRat.chr6 35208 3 + 647215 AAT - -a -s simMouse_chr6.simMouse.chr6 42893 16 + 636262 GTAAGCCAATAGTCCA -s Anc0.Anc0refChr9 17470 16 + 35212 GTAAACCAATAGTCCC -s Anc1.Anc1refChr2 141841 16 - 144309 GTAAACCAATAGTCCC -s Anc2.Anc2refChr0 37172 16 - 56053 GTCAGCCAATAGTCCC -s mr.mrrefChr0 40637 16 + 130230 GTAAACCAATAGTCCA -s simCow_chr6.simCow.chr6 579398 16 - 602619 GTCAGCCAATAGTCTC -s simDog_chr6.simDog.chr6 574966 6 - 593897 ----------GCTCCC -s simHuman_chr6.simHuman.chr6 581309 16 - 601863 GTAGACCATCAGTCCC -s simRat_chr6.simRat.chr6 35211 16 + 647215 GTAAACCAATAGTCCA - -a -s simMouse_chr6.simMouse.chr6 42909 12 + 636262 TCTACATCCTTA -s Anc0.Anc0refChr9 17486 12 + 35212 CCTATGTCCTTG -s Anc1.Anc1refChr2 141857 12 - 144309 CCTATGTCCTTG -s Anc2.Anc2refChr0 37188 12 - 56053 CCTAAGTCCTTT -s mr.mrrefChr0 40653 12 + 130230 TCTATATCCTTG -s simCow_chr6.simCow.chr6 579416 12 - 602619 CCTAAGTCCTTT -s simDog_chr6.simDog.chr6 574972 12 - 593897 CCTAAGTCCTTT -s simHuman_chr6.simHuman.chr6 581325 12 - 601863 ACTATGTCATTG -s simRat_chr6.simRat.chr6 35227 12 + 647215 TTTATATCCTTG - -a -s simMouse_chr6.simMouse.chr6 42921 31 + 636262 GAAGTTCAATCTCCTTTTCACATAGTTGGTA -s Anc0.Anc0refChr9 17506 31 + 35212 CAATTCTAATCTCCTTTTGACATGGTTGGTG -s Anc1.Anc1refChr2 141877 31 - 144309 CAATTCTAATCTCCTTTTGACATGGTTGGTG -s Anc2.Anc2refChr0 37208 31 - 56053 TAATTCTAATCTCCTCTTGACATGGTTGGTG -s mr.mrrefChr0 40665 31 + 130230 CAAGTTCAATCTCCTTTTCACATAGTTGGTA -s simCow_chr6.simCow.chr6 579436 30 - 602619 TAATTCTAATCTCCTATTGACAT-GTTGGTG -s simDog_chr6.simDog.chr6 574992 31 - 593897 TCACTCAAATCTCCCCTTGACATGGTTGGTG -s simHuman_chr6.simHuman.chr6 581345 31 - 601863 CAGTTCTCATCTCCTTTCGACATGGTGAGTG -s simRat_chr6.simRat.chr6 35239 30 + 647215 CTAGTTCAATCTCCTTTTCACACAGTTGAT- - -a -s simMouse_chr6.simMouse.chr6 42952 12 + 636262 ACTTGTATATAC -s Anc0.Anc0refChr9 17537 12 + 35212 ATTTGTATACAC -s Anc1.Anc1refChr2 141908 12 - 144309 ATTTGTATACAC -s Anc2.Anc2refChr0 37239 12 - 56053 ATTAGTATACAC -s mr.mrrefChr0 40696 12 + 130230 ACTTGTATATAC -s simCow_chr6.simCow.chr6 579466 12 - 602619 GCCAGTATACGC -s simDog_chr6.simDog.chr6 575047 12 - 593897 ATTAGTGTAAAC -s simHuman_chr6.simHuman.chr6 581376 12 - 601863 ATTTGTAATCAC -s simRat_chr6.simRat.chr6 35269 9 + 647215 ---TGTATATAC - -a -s simMouse_chr6.simMouse.chr6 42964 19 + 636262 CCTCAGGGTCAAACAGATT -s Anc0.Anc0refChr9 17551 19 + 35212 CCCCCAGATCAATCAAATT -s Anc1.Anc1refChr2 141922 19 - 144309 CCCCCAGATCAATCAAATT -s Anc2.Anc2refChr0 37253 19 - 56053 CCCCCAAATCAATCAAATT -s mr.mrrefChr0 40708 19 + 130230 CCTCAGGGTCAAACAGATC -s simCow_chr6.simCow.chr6 579480 19 - 602619 CCCCCAAAACAAACAAATT -s simDog_chr6.simDog.chr6 575061 19 - 593897 CCCCCAAATGAATCAAATT -s simHuman_chr6.simHuman.chr6 581390 19 - 601863 CCCCCAGATCAATCAAATT -s simRat_chr6.simRat.chr6 35278 19 + 647215 CCTCAGAGTCAAACAGATC - -a -s simMouse_chr6.simMouse.chr6 42983 33 + 636262 AACACTTTGGGAATAACTTGGCACATTGATTTT -s Anc0.Anc0refChr9 17596 33 + 35212 AGCACTTGGGGAATGATTTGGCATATCAATTTC -s Anc1.Anc1refChr2 141972 33 - 144309 AGCACTTGGGGAATGATTTGGCATATCAATTTC -s Anc2.Anc2refChr0 37298 33 - 56053 AGCACTTGGGGAATGATTTGGCATATCAATTTC -s mr.mrrefChr0 40738 33 + 130230 AACACTTGGGGAATGACTTGGCACATTGATTTT -s simCow_chr6.simCow.chr6 579525 33 - 602619 AGCACTTGGGAAATGATTTGGAACATCAGTTTT -s simDog_chr6.simDog.chr6 575106 33 - 593897 CGCACTTGGGGAATGATTTAACATATCAATTTC -s simHuman_chr6.simHuman.chr6 581547 30 - 601863 AGCACTCAGGGA-TGATTTGGCAAATCAATT-- -s simRat_chr6.simRat.chr6 35308 33 + 647215 AACACTTGGAGAATGACTTGGCAGGTTGATTTT - -a -s simMouse_chr6.simMouse.chr6 43016 26 + 636262 AATTCAGGTGAATGATGGCCTATTTT -s Anc0.Anc0refChr9 17629 26 + 35212 GATTTGGGTGAATGATGGTCTATTTT -s Anc1.Anc1refChr2 142005 26 - 144309 GATTTGGGTGAATGATGGTCTATTTT -s Anc2.Anc2refChr0 37331 26 - 56053 GATTTGGGTGAATGATGGTATATTTT -s mr.mrrefChr0 40771 26 + 130230 AATTCAGGTGAATGATGGCCTATTTT -s simCow_chr6.simCow.chr6 579558 26 - 602619 GATTTGGGCAAACGATGGTATATTTT -s simDog_chr6.simDog.chr6 575140 26 - 593897 GATTTGGATGAATGACAGTATATCTT -s simHuman_chr6.simHuman.chr6 581577 26 - 601863 GATTTTAGTGAATGATGGTCTATTTT -s simRat_chr6.simRat.chr6 35341 26 + 647215 AAACCAGGTGAATGATGGCCTATTTT - -a -s simMouse_chr6.simMouse.chr6 43042 9 + 636262 AGGGAAGCA -s Anc0.Anc0refChr9 17663 9 + 35212 GGAGAATAC -s Anc1.Anc1refChr2 142039 9 - 144309 GGAGAATAC -s Anc2.Anc2refChr0 37365 9 - 56053 GGAGAATAC -s mr.mrrefChr0 40797 9 + 130230 AGGGAATCC -s simCow_chr6.simCow.chr6 579592 9 - 602619 GGAGAACAC -s simDog_chr6.simDog.chr6 575174 9 - 593897 CGAGAATAC -s simHuman_chr6.simHuman.chr6 581611 9 - 601863 GGAGAATAC -s simRat_chr6.simRat.chr6 35367 9 + 647215 AGGGAATCC - -a -s simMouse_chr6.simMouse.chr6 43051 36 + 636262 TCAAGATCTTCTGTTCTGCCTTATGAAGAGCATATC -s Anc0.Anc0refChr9 17672 35 + 35212 T-GTGATTTCCTGTTCTGCCTAACAAGGGGCATATC -s Anc1.Anc1refChr2 142048 35 - 144309 T-GTGATTTCCTGTTCTGCCTAACAAGGGGCATATC -s Anc2.Anc2refChr0 37374 35 - 56053 T-GTGATTTCATGTTCTGCCTAACAAGGGGCATATC -s mr.mrrefChr0 40806 36 + 130230 TCAAGATCTTCTGTTCTGCCTTATGAAGGGCATATC -s simCow_chr6.simCow.chr6 579603 32 - 602619 T-GTGATT-CTTTTTC--CTAAAAAAGGGGCATATC -s simDog_chr6.simDog.chr6 575183 35 - 593897 T-ACTATTTCATGTTCTGCCTTACAAGGAGCATATC -s simHuman_chr6.simHuman.chr6 581620 35 - 601863 T-GTGATTGCCTGCTCTGCCTAACAAGGGGCATATC -s simRat_chr6.simRat.chr6 35376 36 + 647215 TCAAGATCTTCTGTTCTGCCTTATGAAGGGCATATC - -a -s simMouse_chr6.simMouse.chr6 43087 30 + 636262 GCTATTACCTCAATGCAGACTAACTACCTT -s Anc0.Anc0refChr9 17709 30 + 35212 GGTATTACTTGAATGCAAACTAGATACCTA -s Anc1.Anc1refChr2 142085 30 - 144309 GGTATTACTTGAATGCAAACTAGATACCTA -s Anc2.Anc2refChr0 37411 30 - 56053 GGTATTACTTGAATGCAAACTAGATACCTA -s mr.mrrefChr0 40844 30 + 130230 GCTATTACCTCAATGCAGACTAACTACCTT -s simCow_chr6.simCow.chr6 579637 30 - 602619 GGATTGACATGAATGCAAACTAGATACCTA -s simDog_chr6.simDog.chr6 575220 30 - 593897 GGTATTATTTGAATACAGACTTGATACTTA -s simHuman_chr6.simHuman.chr6 581657 29 - 601863 GGCATTACTTGAATGCAAACTACATACCT- -s simRat_chr6.simRat.chr6 35414 30 + 647215 GCTATGACCTCAATGCAGACTATCTATCTT - -a -s simMouse_chr6.simMouse.chr6 43117 11 + 636262 GTACATGTACA -s Anc0.Anc0refChr9 17739 11 + 35212 GTAGATGCAAA -s Anc1.Anc1refChr2 142115 11 - 144309 GTAGATGCAAA -s Anc2.Anc2refChr0 37441 11 - 56053 TTTGACACAAT -s mr.mrrefChr0 40874 11 + 130230 GTACATGTACA -s simCow_chr6.simCow.chr6 579675 11 - 602619 TTTGATGTAAT -s simDog_chr6.simDog.chr6 575250 11 - 593897 TTTGACACAAT -s simHuman_chr6.simHuman.chr6 581686 11 - 601863 GTAGATGCAAA -s simRat_chr6.simRat.chr6 35444 11 + 647215 GTACATATACA - -a -s simMouse_chr6.simMouse.chr6 43128 11 + 636262 ATCTGTCATAT -s Anc0.Anc0refChr9 17750 11 + 35212 ATCTGTCATAT -s Anc1.Anc1refChr2 142126 11 - 144309 ATCTGTCATAT -s Anc2.Anc2refChr0 37452 11 - 56053 GGTTTTCATAT -s mr.mrrefChr0 40885 11 + 130230 ATCTGTCATAT -s simCow_chr6.simCow.chr6 579686 11 - 602619 GGTTTCCATAT -s simDog_chr6.simDog.chr6 575261 11 - 593897 GGTTTTCATAT -s simHuman_chr6.simHuman.chr6 581703 11 - 601863 ATCTGGCATGT -s simRat_chr6.simRat.chr6 35455 11 + 647215 ATATGTCATAC - -a -s simMouse_chr6.simMouse.chr6 43139 8 + 636262 GTGGTACA -s Anc0.Anc0refChr9 17761 8 + 35212 TTGGTGCA -s Anc1.Anc1refChr2 142137 8 - 144309 TTGGTGCA -s Anc2.Anc2refChr0 37463 8 - 56053 TTGGTGCA -s mr.mrrefChr0 40896 8 + 130230 TTGGTACA -s simCow_chr6.simCow.chr6 579697 7 - 602619 TT-GTGCA -s simDog_chr6.simDog.chr6 575272 8 - 593897 TTGGTGCA -s simHuman_chr6.simHuman.chr6 581735 8 - 601863 TTGGCGCA -s simRat_chr6.simRat.chr6 35466 8 + 647215 TTGCTACA - -a -s simMouse_chr6.simMouse.chr6 43147 10 + 636262 TTTTAGGTTC -s Anc0.Anc0refChr9 17774 10 + 35212 TTTCAGGTTT -s Anc1.Anc1refChr2 142150 10 - 144309 TTTCAGGTTT -s Anc2.Anc2refChr0 37476 10 - 56053 TTTCAGGTTT -s mr.mrrefChr0 40909 10 + 130230 TTTCAGGTTC -s simCow_chr6.simCow.chr6 579709 10 - 602619 TTTCAGGATT -s simDog_chr6.simDog.chr6 575285 10 - 593897 TTTCAGGTTT -s simHuman_chr6.simHuman.chr6 581748 10 - 601863 TTTCAGGTTT -s simRat_chr6.simRat.chr6 35479 10 + 647215 TTTCAGGTTC - -a -s simMouse_chr6.simMouse.chr6 43157 10 + 636262 GCAAGAAGTG -s Anc0.Anc0refChr9 17789 6 + 35212 ATAGGA---- -s Anc1.Anc1refChr2 142165 10 - 144309 ATAGGAAGTG -s Anc2.Anc2refChr0 37491 6 - 56053 GTAGCA---- -s mr.mrrefChr0 40919 10 + 130230 ACAAGAAGTG -s simCow_chr6.simCow.chr6 579724 6 - 602619 TCAGCA---- -s simDog_chr6.simDog.chr6 575300 6 - 593897 GTAGCA---- -s simHuman_chr6.simHuman.chr6 581763 10 - 601863 ATAGGAAGTG -s simRat_chr6.simRat.chr6 35489 10 + 647215 ACAAGAAGTG - -a -s simMouse_chr6.simMouse.chr6 43167 30 + 636262 TCAAGGATATGACATGGTGTTTATGCCAAT -s Anc0.Anc0refChr9 17795 30 + 35212 TGAAGGAAATAACATGATCTTTGCTCCAGT -s Anc1.Anc1refChr2 142175 30 - 144309 TGAAGGAAATAACATGATCTTTGCTCCAGT -s Anc2.Anc2refChr0 37497 30 - 56053 CGAAGGGCATAACATGATCTTTGCTCCTGT -s mr.mrrefChr0 40929 30 + 130230 TCAAGGAAATAACATGGTGTTTATGCCAAT -s simCow_chr6.simCow.chr6 579730 30 - 602619 GGAAGGGTTGAACATGGTCTCTGACCCTGT -s simDog_chr6.simDog.chr6 575306 30 - 593897 CGAGGCGCATAACAGGAACTTCGCTCCTGT -s simHuman_chr6.simHuman.chr6 581792 30 - 601863 TGAAGGAAATAACATGATCTTTGCTCCAGC -s simRat_chr6.simRat.chr6 35499 30 + 647215 TCAAGCAAATAACATGGTATGTATGCCAAT - -a -s simMouse_chr6.simMouse.chr6 43197 41 + 636262 TGCCAAAAACTATCAAGAAAATAACCTGAGTACAATTACTT -s Anc0.Anc0refChr9 17825 41 + 35212 TGCCAAAAACTATCAATAAAGTCAGCTGAGTACAATTACTT -s Anc1.Anc1refChr2 142205 41 - 144309 TGCCAAAAACTATCAATAAAGTCAGCTGAGTACAATTACTT -s Anc2.Anc2refChr0 37527 41 - 56053 TGCCAAAAACTATCAATAAGGTCAGCTGAGTACAATTACTT -s mr.mrrefChr0 40959 41 + 130230 TGCCAAAAACTATCAAGAAAATAACCTGAGTACAATTACTT -s simCow_chr6.simCow.chr6 579781 41 - 602619 TGCCAAAAACTATCTATAAGGTCAGTTGTGTATAATTACTT -s simDog_chr6.simDog.chr6 575336 41 - 593897 CACCAAACACTATCAAAAAGGTCTCCTGAGTACAATTACTT -s simHuman_chr6.simHuman.chr6 581822 41 - 601863 TGACAAAAACTATCAATAAAGTCAGCAGATTACAATTACTT -s simRat_chr6.simRat.chr6 35529 40 + 647215 TGCCAAA-ACTATCAAGATCATAACCTGAGTACAGTTACTT - -a -s simMouse_chr6.simMouse.chr6 43238 11 + 636262 AATTCTATGGG -s Anc0.Anc0refChr9 17866 10 + 35212 AAAT-CATAGG -s Anc1.Anc1refChr2 142246 10 - 144309 AAAT-CATAGG -s Anc2.Anc2refChr0 37568 10 - 56053 AAAT-CATAGG -s mr.mrrefChr0 41000 11 + 130230 AATTTCATGGG -s simCow_chr6.simCow.chr6 579822 10 - 602619 AAGT-CATAGG -s simDog_chr6.simDog.chr6 575378 10 - 593897 AAAT-CATAGG -s simHuman_chr6.simHuman.chr6 581863 10 - 601863 AGAT-CATAGG -s simRat_chr6.simRat.chr6 35569 11 + 647215 CATCTCATGGG - -a -s simMouse_chr6.simMouse.chr6 43249 41 + 636262 GAAGCTGCCTGTCACCTTTATAGTTCAAGGTGGGTGGCTAC -s Anc0.Anc0refChr9 17876 41 + 35212 AAAGCTGGTTGTCATAATAACAGCTCAAGGTGGGCGGCCAC -s Anc1.Anc1refChr2 142256 41 - 144309 AAAGCTGGTTGTCATAATAACAGCTCAAGGTGGGCGGCCAC -s Anc2.Anc2refChr0 37578 41 - 56053 AAAGCTGGTTGTCATAATAGCAGCTCTAGGTGGGCAGCCAT -s mr.mrrefChr0 41011 41 + 130230 GAAGCTGGTTGTCACCTTTATAGTTCAAGGTGGGTGGCCAC -s simCow_chr6.simCow.chr6 579840 41 - 602619 AAAGCTGGATGTCATAATACCAGTTCCAGGTGGGCAGCCAG -s simDog_chr6.simDog.chr6 575388 41 - 593897 AAAGCTGGTTCATATAATGGCAGCTCTAGGAATGCAGCCAT -s simHuman_chr6.simHuman.chr6 581873 41 - 601863 AAAGCTAGTCGTCATGATAACAGCTCAAGATGGGCGGCCAC -s simRat_chr6.simRat.chr6 35580 41 + 647215 GAAGCTGGTTGTCACTTTTGTAGTTCAAGGTGAATGGCCAT - -a -s simMouse_chr6.simMouse.chr6 43290 4 + 636262 GCCA -s Anc0.Anc0refChr9 17917 4 + 35212 GGCA -s Anc1.Anc1refChr2 142297 4 - 144309 GGCA -s Anc2.Anc2refChr0 37620 4 - 56053 GGCA -s mr.mrrefChr0 41052 4 + 130230 GGCA -s simCow_chr6.simCow.chr6 579882 4 - 602619 GGTA -s simDog_chr6.simDog.chr6 575430 4 - 593897 GGCA -s simHuman_chr6.simHuman.chr6 581914 4 - 601863 ATCA -s simRat_chr6.simRat.chr6 35621 4 + 647215 GGCA - -a -s simMouse_chr6.simMouse.chr6 43294 24 + 636262 GACCCATTGTAAGTATGATCCATT -s Anc0.Anc0refChr9 17924 24 + 35212 AACCTTTTCTGATTCTGATCCATT -s Anc1.Anc1refChr2 142304 24 - 144309 AACCTTTTCTGATTCTGATCCATT -s Anc2.Anc2refChr0 37627 24 - 56053 AACCTTTTCTGATTCTGATTCATT -s mr.mrrefChr0 41056 24 + 130230 AACCCATTGTAAGTATGATCCATT -s simCow_chr6.simCow.chr6 579889 24 - 602619 AACCTATTCTGATTCTGATTGATT -s simDog_chr6.simDog.chr6 575437 24 - 593897 AACCTTTTCTGATTTTGATTCATT -s simHuman_chr6.simHuman.chr6 581921 24 - 601863 AACCTGTTCTGATTCTGATCCGTT -s simRat_chr6.simRat.chr6 35625 24 + 647215 AACCCATTGTAAGTATCATCTATT - -a -s simMouse_chr6.simMouse.chr6 43318 19 + 636262 CCTTCTGATGACACTCATA -s Anc0.Anc0refChr9 17961 19 + 35212 CATCCTTATGACAGTCATG -s Anc1.Anc1refChr2 142344 19 - 144309 CATCCTTATGACAGTCATG -s Anc2.Anc2refChr0 37664 19 - 56053 CATCCACATGACAGTCATG -s mr.mrrefChr0 41080 19 + 130230 CATCCTGATGACACTCATA -s simCow_chr6.simCow.chr6 579920 18 - 602619 -ATTTCCCTAACAGTCATG -s simDog_chr6.simDog.chr6 575474 18 - 593897 CATCCACATGACAGCCA-G -s simHuman_chr6.simHuman.chr6 581961 19 - 601863 CATCCTTTTGACAGTCATG -s simRat_chr6.simRat.chr6 35649 19 + 647215 CATCTTGATGACAATCATA - -a -s simMouse_chr6.simMouse.chr6 43337 45 + 636262 ATTACCCAAGTGTAAAGAATTTTTTTTGTCACTTGCTTTTTTAAC -s Anc0.Anc0refChr9 17980 45 + 35212 CTTACACAAGAGTAAAGATTTTATTTTGTGATTTGGTTTTTTAAC -s Anc1.Anc1refChr2 142363 45 - 144309 CTTACACAAGAGTAAAGATTTTATTTTGTGATTTGGTTTTTTAAC -s Anc2.Anc2refChr0 37683 45 - 56053 CTTACACAAGAGTAAAGATTTTATTTTGTGATATGGTTTTTTAAC -s mr.mrrefChr0 41099 45 + 130230 ATTACACAAGTGTAAAGAATTTATTTTGTCATTTGCTTTTTTGAC -s simCow_chr6.simCow.chr6 579938 44 - 602619 CTCACACAAGACTAAAGACTTTATACTATGGA-TGGTTTTTTACT -s simDog_chr6.simDog.chr6 575492 45 - 593897 CTTACATAAGAGTAAAGATTTTATTTTGTGATATGGTTTTTTAAC -s simHuman_chr6.simHuman.chr6 581980 45 - 601863 CTTACACAAGAGTAAAGAGTTTATTTTGTGATTTGGTTTTTTAAC -s simRat_chr6.simRat.chr6 35668 45 + 647215 ATTACAAGTGTGAGAAGAGTTTATTTTGTCATTTGCTATTCTGAC -s simRat_chr6.simRat.chr6 35798 45 + 647215 AGAACACAAGTGTAAAGAATTTATTTTGTCATTTGCTCTTTTGAC - -a -s simMouse_chr6.simMouse.chr6 43382 3 + 636262 ATT -s Anc0.Anc0refChr9 18025 3 + 35212 ATT -s Anc1.Anc1refChr2 142408 3 - 144309 ATT -s Anc2.Anc2refChr0 37728 3 - 56053 ATT -s mr.mrrefChr0 41144 3 + 130230 ATT -s simCow_chr6.simCow.chr6 579985 3 - 602619 ATT -s simDog_chr6.simDog.chr6 575537 3 - 593897 AGT -s simHuman_chr6.simHuman.chr6 582025 3 - 601863 ATT -s simRat_chr6.simRat.chr6 35713 3 + 647215 GTT -s simRat_chr6.simRat.chr6 35843 3 + 647215 ATT - -a -s simMouse_chr6.simMouse.chr6 43385 51 + 636262 GGATGGATCAATCCATTTTAAGGAATATGTCCTGGGTTGGCTACTCTAGCA -s Anc0.Anc0refChr9 18029 50 + 35212 GTACACATCAATGCATTTTAGGGAGTATGTTCTGGGTTG-CTACTCTAGCC -s Anc1.Anc1refChr2 142412 50 - 144309 GTACACATCAATGCATTTTAGGGAGTATGTTCTGGGTTG-CTACTCTAGCC -s Anc2.Anc2refChr0 37732 50 - 56053 GTACACACCAATGCATTTTAGGGAGTATATTCTAGGTTG-CTACTCCAGCC -s mr.mrrefChr0 41147 51 + 130230 GCAGGGATCAATGCATTTTAAGGACTATGTCCTGGGTTGGTTGCTCTAGCA -s simCow_chr6.simCow.chr6 579989 49 - 602619 GTACACACCAATTAATTTTTGGAAGCATTTTCT-GGTTG-CTACTCCAGCC -s simDog_chr6.simDog.chr6 575541 50 - 593897 ACACACACCAATGCATTTTAGGGAGTATATTCTAGGTTG-CTACTCCAGCC -s simHuman_chr6.simHuman.chr6 582029 50 - 601863 GTGCACATCAATGCATTTTAGGGAGTATGTTCTGGGTTG-CTACTCTAGCC -s simRat_chr6.simRat.chr6 35716 51 + 647215 GCAGGGATCAATGCATTTTAAGGACTATGTCCTGGGTTGGTTGCTCTAGCA -s simRat_chr6.simRat.chr6 35846 51 + 647215 GCAGGGATCAATGCATTTTAAGAACTATGTCATGGGTCGGTTGCTCTGGCA - -a -s simMouse_chr6.simMouse.chr6 43436 7 + 636262 TAGGCTA -s Anc0.Anc0refChr9 18080 7 + 35212 CAAGATA -s Anc1.Anc1refChr2 142463 7 - 144309 CAAGATA -s Anc2.Anc2refChr0 37783 7 - 56053 CAAGATA -s mr.mrrefChr0 41198 7 + 130230 CAGGCTA -s simCow_chr6.simCow.chr6 580039 7 - 602619 CAAGATA -s simDog_chr6.simDog.chr6 575592 7 - 593897 CAAGATA -s simHuman_chr6.simHuman.chr6 582080 7 - 601863 CAAGATA -s simRat_chr6.simRat.chr6 35767 7 + 647215 CAGGGTA -s simRat_chr6.simRat.chr6 35897 7 + 647215 CAGGTTA - -a -s simMouse_chr6.simMouse.chr6 43443 13 + 636262 ATGTTTCTCAGTT -s Anc0.Anc0refChr9 18088 13 + 35212 ATGGCACCCAGTT -s Anc1.Anc1refChr2 142471 13 - 144309 ATGGCACCCAGTT -s Anc2.Anc2refChr0 37791 13 - 56053 ATGGCATCCAGTC -s mr.mrrefChr0 41205 13 + 130230 ATGTTCCTCAGTT -s simCow_chr6.simCow.chr6 580047 12 - 602619 GTGGTATGCAGC- -s simDog_chr6.simDog.chr6 575599 13 - 593897 ATGGCATCCAGTC -s simHuman_chr6.simHuman.chr6 582088 13 - 601863 ATGGGGCCCAGAT -s simRat_chr6.simRat.chr6 35774 13 + 647215 ATGTTCCTCAGTT -s simRat_chr6.simRat.chr6 35904 13 + 647215 ATGTTCCTCAGTT - -a -s simMouse_chr6.simMouse.chr6 43456 11 + 636262 ATATTGGACTT -s Anc0.Anc0refChr9 18108 11 + 35212 ATATCTACACT -s Anc1.Anc1refChr2 142491 11 - 144309 ATATCTACACT -s Anc2.Anc2refChr0 37811 11 - 56053 ATATCTACACT -s mr.mrrefChr0 41218 11 + 130230 ATATTGGACTT -s simCow_chr6.simCow.chr6 580061 11 - 602619 ATATCTACACC -s simDog_chr6.simDog.chr6 575647 11 - 593897 ATGTCTATGCT -s simHuman_chr6.simHuman.chr6 582108 11 - 601863 ATACCTACACT -s simRat_chr6.simRat.chr6 35787 11 + 647215 ATATTGGACTT -s simRat_chr6.simRat.chr6 35917 11 + 647215 GTATTGGACTT - -a -s simMouse_chr6.simMouse.chr6 43467 10 + 636262 AGATTCAAAA -s Anc0.Anc0refChr9 18119 10 + 35212 AGAATAAAAA -s Anc1.Anc1refChr2 142502 10 - 144309 AGAATAAAAA -s Anc2.Anc2refChr0 37822 10 - 56053 AGAACAAATA -s mr.mrrefChr0 41229 10 + 130230 AGATTCAAAA -s simCow_chr6.simCow.chr6 580072 10 - 602619 GGAAGAAATA -s simDog_chr6.simDog.chr6 575658 10 - 593897 AGAACAAATA -s simHuman_chr6.simHuman.chr6 582119 10 - 601863 AGGGTGAAAA -s simRat_chr6.simRat.chr6 35928 10 + 647215 AGATTCAAAG - -a -s simMouse_chr6.simMouse.chr6 43477 21 + 636262 CCTGATAAATTGATCTATATT -s Anc0.Anc0refChr9 18131 21 + 35212 CCGCATAAATTGACCTAGTTT -s Anc1.Anc1refChr2 142514 21 - 144309 CCGCATAAATTGACCTAGTTT -s Anc2.Anc2refChr0 37834 21 - 56053 CAGCATAAATTGACCTAGTTT -s mr.mrrefChr0 41239 21 + 130230 CCTGATAAATTGATCTATATT -s simCow_chr6.simCow.chr6 580084 21 - 602619 CAGCATAAATTGACCGAGTTT -s simDog_chr6.simDog.chr6 575670 21 - 593897 CAGCATTAATCGACCTAGCTT -s simHuman_chr6.simHuman.chr6 582131 21 - 601863 CCGCATAAGGTGACCTAGTTT -s simRat_chr6.simRat.chr6 35938 20 + 647215 CCTGATAAA-TGATCTACATT - -a -s simMouse_chr6.simMouse.chr6 43498 19 + 636262 TGTTGGATTGATCACCTGC -s Anc0.Anc0refChr9 18152 11 + 35212 TCTT--------CACCTCC -s Anc1.Anc1refChr2 142535 11 - 144309 TCTT--------CACCTCC -s Anc2.Anc2refChr0 37862 11 - 56053 TCTT--------CACCCCC -s mr.mrrefChr0 41260 19 + 130230 TGTTGGATTGATCACCTGC -s simCow_chr6.simCow.chr6 580112 11 - 602619 TCTT--------CATTCCC -s simDog_chr6.simDog.chr6 575698 11 - 593897 TCTT--------CCCCCCC -s simHuman_chr6.simHuman.chr6 582152 11 - 601863 TCTT--------CAACTTC -s simRat_chr6.simRat.chr6 35958 19 + 647215 TGTTGGATTGATGCCCTGC - -a -s simMouse_chr6.simMouse.chr6 43517 34 + 636262 CATTTGTCATGTGAAACACAATCACAACTGTGGC -s Anc0.Anc0refChr9 18165 34 + 35212 CTTCTGTCATTTGACATACAATCTTAGCTGTGGC -s Anc1.Anc1refChr2 142548 34 - 144309 CTTCTGTCATTTGACATACAATCTTAGCTGTGGC -s Anc2.Anc2refChr0 37875 34 - 56053 TTTCTGTCAGTTGACATACAATCTTAGCTGTGGC -s mr.mrrefChr0 41279 34 + 130230 CATTTGTCATGTGAAACACAATCACAACTGTGGC -s simCow_chr6.simCow.chr6 580125 34 - 602619 TTGCTGTCAGTGGACATCCAATTATAGCTGTGGC -s simDog_chr6.simDog.chr6 575711 26 - 593897 TTTATGTCAGTTGACATACAACCT--------GT -s simHuman_chr6.simHuman.chr6 582165 34 - 601863 CTTCTGTGATTTGTCATACAATCTTTGCTGTGGC -s simRat_chr6.simRat.chr6 35977 34 + 647215 TTTTTGTCATGTGAGACACAATCACAAGTGCGGC - -a -s simMouse_chr6.simMouse.chr6 43551 32 + 636262 TAGTTTTGATGTTTAGATACTTCCCTGCTCTA -s Anc0.Anc0refChr9 18199 28 + 35212 C--TTCCCA--TTGGGATATTTCCTCACTATA -s Anc1.Anc1refChr2 142582 28 - 144309 C--TTCCCA--TTGGGATATTTCCTCACTATA -s Anc2.Anc2refChr0 37909 28 - 56053 C--CCTCCA--TTGGAATATTTCCTCTCTATA -s mr.mrrefChr0 41313 32 + 130230 TAGTTCCGATGTTTAGATATTTCCTTACTATA -s simCow_chr6.simCow.chr6 580163 23 - 602619 C--CCTCTG--TTGGAATAATT-----CTACA -s simDog_chr6.simDog.chr6 575737 28 - 593897 C--CCTCCA--TTGTAACATCCCCTCTCTATA -s simHuman_chr6.simHuman.chr6 582199 28 - 601863 C--TTCCCA--TTGGGATATTTCCTCACTATA -s simRat_chr6.simRat.chr6 36011 32 + 647215 TCGTTCCTAAGATTAGATATTTCTTTACTATA - -a -s simMouse_chr6.simMouse.chr6 43583 5 + 636262 AGCGA -s Anc0.Anc0refChr9 18227 5 + 35212 AGCTA -s Anc1.Anc1refChr2 142610 5 - 144309 AGCTA -s Anc2.Anc2refChr0 37937 5 - 56053 AGCTA -s mr.mrrefChr0 41345 5 + 130230 AGCGA -s simCow_chr6.simCow.chr6 580186 5 - 602619 ACCTA -s simDog_chr6.simDog.chr6 575770 5 - 593897 AGTTA -s simHuman_chr6.simHuman.chr6 582227 5 - 601863 AGCTA -s simRat_chr6.simRat.chr6 36043 5 + 647215 AGTGA - -a -s simMouse_chr6.simMouse.chr6 43588 19 + 636262 GTGCATGTTTGGTGGGCAC -s Anc0.Anc0refChr9 18232 19 + 35212 TATTAATTTTGTGGGGGGC -s Anc1.Anc1refChr2 142615 19 - 144309 TATTAATTTTGTGGGGGGC -s Anc2.Anc2refChr0 37943 19 - 56053 TATTCATGTTGTGGGGGGC -s mr.mrrefChr0 41350 19 + 130230 GTGCATGTTTGGTGGGCAC -s simCow_chr6.simCow.chr6 580192 19 - 602619 CATTCATCTTGGGGGGCAC -s simDog_chr6.simDog.chr6 575776 19 - 593897 TATTCATGTAGTGGGGGGC -s simHuman_chr6.simHuman.chr6 582232 19 - 601863 TATTAATTTTGTGGGGGGC -s simRat_chr6.simRat.chr6 36048 19 + 647215 GTGCATGTTTTGTGGGCAT - -a -s simMouse_chr6.simMouse.chr6 43607 2 + 636262 CC -s Anc0.Anc0refChr9 18251 2 + 35212 CC -s Anc1.Anc1refChr2 142634 2 - 144309 CC -s Anc2.Anc2refChr0 37962 2 - 56053 CC -s mr.mrrefChr0 41369 2 + 130230 CC -s simCow_chr6.simCow.chr6 580214 2 - 602619 CC -s simDog_chr6.simDog.chr6 575795 2 - 593897 CC -s simHuman_chr6.simHuman.chr6 582251 2 - 601863 CC -s simRat_chr6.simRat.chr6 36067 2 + 647215 CC - -a -s simMouse_chr6.simMouse.chr6 43609 2 + 636262 AG -s Anc0.Anc0refChr9 18260 2 + 35212 GA -s Anc1.Anc1refChr2 142643 2 - 144309 GA -s Anc2.Anc2refChr0 37971 2 - 56053 GA -s mr.mrrefChr0 41371 2 + 130230 AG -s simCow_chr6.simCow.chr6 580223 2 - 602619 GA -s simDog_chr6.simDog.chr6 575804 2 - 593897 GA -s simHuman_chr6.simHuman.chr6 582260 2 - 601863 GA -s simRat_chr6.simRat.chr6 36069 2 + 647215 AG - -a -s simMouse_chr6.simMouse.chr6 43611 22 + 636262 TCTTCTTGGCCCATATGTCAGA -s Anc0.Anc0refChr9 18262 22 + 35212 TCTCCTTGTGCATTATGTTAGA -s Anc1.Anc1refChr2 142645 22 - 144309 TCTCCTTGTGCATTATGTTAGA -s Anc2.Anc2refChr0 37975 22 - 56053 TCTCCGTGTGCATTATGTTAGA -s mr.mrrefChr0 41373 22 + 130230 TCTTCTTGGCCCATATGTTAGA -s simCow_chr6.simCow.chr6 580227 22 - 602619 TCTCCATGTGCAATATGGCAGA -s simDog_chr6.simDog.chr6 575808 22 - 593897 TCTCTGTGTGCATTATGTTAGA -s simHuman_chr6.simHuman.chr6 582262 22 - 601863 TCTCCTTGTGCTGTATTCTAGT -s simRat_chr6.simRat.chr6 36071 22 + 647215 TCTTCTTGGCCCATATGTTAGA - -a -s simMouse_chr6.simMouse.chr6 43633 2 + 636262 GG -s Anc0.Anc0refChr9 18290 2 + 35212 GG -s Anc1.Anc1refChr2 142673 2 - 144309 GG -s Anc2.Anc2refChr0 38003 2 - 56053 GG -s mr.mrrefChr0 41401 2 + 130230 GG -s simCow_chr6.simCow.chr6 580259 2 - 602619 GG -s simDog_chr6.simDog.chr6 575836 2 - 593897 GG -s simHuman_chr6.simHuman.chr6 582290 2 - 601863 GG -s simRat_chr6.simRat.chr6 36099 2 + 647215 GG - -a -s simMouse_chr6.simMouse.chr6 43635 4 + 636262 ACTA -s Anc0.Anc0refChr9 18293 3 + 35212 AC-A -s Anc1.Anc1refChr2 142676 4 - 144309 ACTA -s Anc2.Anc2refChr0 38006 3 - 56053 AC-A -s mr.mrrefChr0 41403 4 + 130230 ACTA -s simCow_chr6.simCow.chr6 580262 3 - 602619 AC-A -s simDog_chr6.simDog.chr6 575839 3 - 593897 AC-A -s simHuman_chr6.simHuman.chr6 582293 4 - 601863 ACTA -s simRat_chr6.simRat.chr6 36101 4 + 647215 ACTA - -a -s simMouse_chr6.simMouse.chr6 43639 3 + 636262 AAA -s Anc0.Anc0refChr9 18296 1 + 35212 A-- -s Anc1.Anc1refChr2 142680 1 - 144309 A-- -s Anc2.Anc2refChr0 38009 1 - 56053 A-- -s mr.mrrefChr0 41407 3 + 130230 AAA -s simCow_chr6.simCow.chr6 580268 1 - 602619 A-- -s simDog_chr6.simDog.chr6 575842 1 - 593897 A-- -s simHuman_chr6.simHuman.chr6 582297 1 - 601863 A-- -s simRat_chr6.simRat.chr6 36105 3 + 647215 AAA - -a -s simMouse_chr6.simMouse.chr6 43642 30 + 636262 CATATCCTTATGGTTGATCACATCTATCCC -s Anc0.Anc0refChr9 18297 28 + 35212 CAT-GCC-CATGGTTAATTGCAGCTATCCC -s Anc1.Anc1refChr2 142681 29 - 144309 CATGGCC-CATGGTTAATTGCAGCTATCCC -s Anc2.Anc2refChr0 38010 28 - 56053 CAT-GCC-CATGGTTACTTGCAGCTATCCC -s mr.mrrefChr0 41410 30 + 130230 CATATCCTCATGGTTGATCACAGCTATCCC -s simCow_chr6.simCow.chr6 580269 28 - 602619 CAT-GCC-CATGGTTAGTTACAGCTATTCC -s simDog_chr6.simDog.chr6 575843 28 - 593897 AAT-GCC-CATGGTTACTTGTATCTATCCC -s simHuman_chr6.simHuman.chr6 582298 26 - 601863 CATGGTC-CGTGGTTAATGGCAGCTAT--- -s simRat_chr6.simRat.chr6 36109 30 + 647215 CATACCCTCACGGTTGATCACAGCTATCCC - -a -s simMouse_chr6.simMouse.chr6 43672 42 + 636262 TTGGGCATGAAAGTAAACTTCATTTTTCTTTCATATAATGAA -s Anc0.Anc0refChr9 18325 42 + 35212 TGGGGCAGGAAAGTAGTCTTTGTTCTTCTTTCTTACAATTCA -s Anc1.Anc1refChr2 142710 42 - 144309 TGGGGCAGGAAAGTAGTCTTTGTTCTTCTTTCTTACAATTCA -s Anc2.Anc2refChr0 38044 42 - 56053 TGGGGCAGGAAAGTAGTCTTTGTTCTTCTTTTTTACAATTCA -s mr.mrrefChr0 41440 42 + 130230 TTGGGCAGGAAAGTAAACTTTATTTTTCTTTCATATAATGAA -s simCow_chr6.simCow.chr6 580303 36 - 602619 TAGGGTAAGAAAGTAGACTCTTTTCTTCTTTTTTG------A -s simDog_chr6.simDog.chr6 575877 42 - 593897 TGAGACAGGAAAGTAGTCCTTGTTCTTCTTTTTTACAATTCA -s simHuman_chr6.simHuman.chr6 582324 42 - 601863 TGGGGCAGGAAAGTAGCTTTTGTTCTTCTTTCTTACAATTCA -s simRat_chr6.simRat.chr6 36139 42 + 647215 TTGGGCAGGAAAGTAAACTTTATTTTTCTTTTCTATCATGAA - -a -s simMouse_chr6.simMouse.chr6 43714 34 + 636262 TTACTAATAGATTTTCTGCCCTCTTTCTTGGTTG -s Anc0.Anc0refChr9 18367 34 + 35212 TTACTAATAGAATTACTGCTTTCTTTTTTGGTAG -s Anc1.Anc1refChr2 142752 34 - 144309 TTACTAATAGAATTACTGCTTTCTTTTTTGGTAG -s Anc2.Anc2refChr0 38086 34 - 56053 TTTCTAATAGAATTACTGCTCTCTTATTTAGTAG -s mr.mrrefChr0 41482 34 + 130230 TTACTAATAGATTTTCTGCCTTCTTTCTTGGTTG -s simCow_chr6.simCow.chr6 580339 34 - 602619 GTTCTAATAGACTTACTGCTCTCTTATTTAGTGG -s simDog_chr6.simDog.chr6 575919 34 - 593897 TTTCTAATAGAATCACTGCTCTCTTATTTAGTAG -s simHuman_chr6.simHuman.chr6 582367 34 - 601863 TTACTTATAAAATTACTGCATGCTTTTTTGGTAG -s simRat_chr6.simRat.chr6 36181 34 + 647215 TTACTAATAGATTTCCTGTCTTCTTTCTTGGTTG - -a -s simMouse_chr6.simMouse.chr6 43748 31 + 636262 AGTAAGACAATGCATAAAAGGAGACTCAGGC -s Anc0.Anc0refChr9 18401 26 + 35212 AGTGACATAAGGCATAAAAGT-----CAGAC -s Anc1.Anc1refChr2 142786 26 - 144309 AGTGACATAAGGCATAAAAGT-----CAGAC -s Anc2.Anc2refChr0 38120 26 - 56053 AGTGAAATAAGGCATGAAAGT-----CAAAC -s mr.mrrefChr0 41516 31 + 130230 AGTAACACAATGCATAAAAGTAGACTCAGAC -s simCow_chr6.simCow.chr6 580373 26 - 602619 GGTGGAATAAGACTTGAAAAT-----CAAAC -s simDog_chr6.simDog.chr6 575953 26 - 593897 AGTGAAATAGGGCATGCAAGC-----CAAAC -s simHuman_chr6.simHuman.chr6 582411 26 - 601863 AGGGACAAAAGGCATAAAAGT-----CAGAC -s simRat_chr6.simRat.chr6 36215 31 + 647215 AGTAACACAATGCATAAAAGTAGACTCAAAC - -a -s simMouse_chr6.simMouse.chr6 43779 58 + 636262 TCAAGCAGATCGAACACCATACAAACTCAATCTGACGGAACATCATCCAATGCCTATG -s Anc0.Anc0refChr9 18427 33 + 35212 T---------------------AAAATCAAGCTGATGAAACATCA---A-CAACCATA -s Anc1.Anc1refChr2 142812 33 - 144309 T---------------------AAAATCAAGCTGATGAAACATCA---A-CAACCATA -s Anc2.Anc2refChr0 38147 33 - 56053 T---------------------AAAATCAAGCTGATGAGACATCT---A-CAACCATA -s mr.mrrefChr0 41547 57 + 130230 TCAAGCAGATCGAACACCATACAAACTCAATCTGATGGAACATCATCCA-TACCCATG -s simCow_chr6.simCow.chr6 580400 33 - 602619 T---------------------AAAATCAAGCGGATGAGGCAACT---A-GAACCATA -s simDog_chr6.simDog.chr6 575980 33 - 593897 C---------------------AACTTCAATCTGATGAGACATAT---A-CAACCTTC -s simHuman_chr6.simHuman.chr6 582437 33 - 601863 T---------------------AAAATCAAGGTGATGAAACATCA---A-CAACCATA -s simRat_chr6.simRat.chr6 36246 57 + 647215 TCAAGCAGATCGAACACCATACTAACACAATCTAATGGAACATTATCCA-TACCCATG - -a -s simMouse_chr6.simMouse.chr6 43837 50 + 636262 GCCATAAAGCACATTGATTTAAAGTGAACTGTCCCGAATGGCATTACAAG -s Anc0.Anc0refChr9 18460 49 + 35212 GCAT-GAAACATATTGATTGAAAGGGAGTTATACCAAAAGGCAATACAAC -s Anc1.Anc1refChr2 142845 49 - 144309 GCAT-GAAACATATTGATTGAAAGGGAGTTATACCAAAAGGCAATACAAC -s Anc2.Anc2refChr0 38180 49 - 56053 GCAA-GAAACATATTGATAGAAAGGGAGTTACACCAAAAGCCAATACAAC -s mr.mrrefChr0 41604 50 + 130230 GCCTTAAAGCACATTGATTTAAAGTGAATTGTCCCAAATGGCATTACAAG -s simCow_chr6.simCow.chr6 580435 44 - 602619 GTGA-TAGACATATTGATGGAATGGGAGT-----CATAAACAAGTACATC -s simDog_chr6.simDog.chr6 576013 49 - 593897 ACAA-GAAGCATGTTGATAGAAAGGGAGTTACACCAAAAGCCAATACAAC -s simHuman_chr6.simHuman.chr6 582470 49 - 601863 GCTT-GAAATATATTGATTGAAAGGGAGTTTTACCAAAAGGCACTACAAC -s simRat_chr6.simRat.chr6 36303 50 + 647215 GCCTTAGAGCACGTTGATTTAAAGAGAATTGTCGCAGATGGCATTACAAA - -a -s simMouse_chr6.simMouse.chr6 43887 30 + 636262 TTGTTGTCCATTGGCTGGCTAATCAATTCG -s Anc0.Anc0refChr9 18509 30 + 35212 TTGTTGTCCATTCACTGACCCATTAATTGG -s Anc1.Anc1refChr2 142894 30 - 144309 TTGTTGTCCATTCACTGACCCATTAATTGG -s Anc2.Anc2refChr0 38229 30 - 56053 TTGTTGTCCTTTCACTGGCCCATTAAATGG -s mr.mrrefChr0 41654 30 + 130230 TTGTTGTCCATTGGCTGACTAATTAATtcg -s simCow_chr6.simCow.chr6 580479 27 - 602619 GTGTTGTCCCTTCAC---ACCATTAAATGA -s simDog_chr6.simDog.chr6 576064 30 - 593897 TTGTTGTCCTCTCACTGGCCTATTAAATGG -s simHuman_chr6.simHuman.chr6 582519 30 - 601863 TTGTTGTCCATTTACTGACCCTTTAATTGG -s simRat_chr6.simRat.chr6 36353 30 + 647215 TTGTTGTCCATCGGCCTACTAattgattga - -a -s simMouse_chr6.simMouse.chr6 43917 41 + 636262 TTGGCTGACTAATTGATTCTTTCTACTGAGATGCCATCTAG -s Anc0.Anc0refChr9 18540 32 + 35212 TT----GTCACAGT-----TGCCTACTGAGACTCAATCTAT -s Anc1.Anc1refChr2 142925 36 - 144309 TTGTCAGTCACAGT-----TGCCTACTGAGACTCAATCTAT -s Anc2.Anc2refChr0 38260 32 - 56053 TT----TTCACAGT-----TGCCTACTGACACTCAATCTGT -s mr.mrrefChr0 41684 41 + 130230 tTGGCTGACTAATTGATTCTTTCTACTGAGACTCCATCTAG -s simCow_chr6.simCow.chr6 580507 32 - 602619 AT----TTTACAGT-----TGCCTGCTGAAACTCAATCTGT -s simDog_chr6.simDog.chr6 576095 32 - 593897 TT----TTCACAGT-----TGCCTACTGACACTCAATCTGT -s simHuman_chr6.simHuman.chr6 582550 36 - 601863 TTGTCAGTCACACT-----TGCCTACTGAGACTCAATCAAT -s simRat_chr6.simRat.chr6 36383 41 + 647215 ttggctgactgattgattCTTTCTACTGAGACTCCAGCTAG - -a -s simMouse_chr6.simMouse.chr6 43958 138 + 636262 GGGCGGTCTAGATTTGAACAATCCTCTGCATTTAAGCAATCCACCAGCCATTACCCTGCTTAGCTCCGAATATATATGTTATGGTTGATTAATCCCACACCCAGCACCATGGTGTCAGTGTGCATTAGGAACACAGAA -s Anc0.Anc0refChr9 18572 76 + 35212 GGCTTATGT------------------GCATTTTAACAATCCACTAACTATCACCCTGCATAGG-----------------------------------------ACCATG--GTCAGCGTTCATTAAGA-CATGGAC -s Anc1.Anc1refChr2 142961 78 - 144309 GGCTTATGT------------------GCATTTTAACAATCCACTAACTATCACCCTGCATAGG-----------------------------------------ACCATGGTGTCAGCGTTCATTAAGA-CATGGAC -s Anc2.Anc2refChr0 38292 76 - 56053 GGCTTAGGT------------------GCATTTTAACAATCCACTAACTGTCATCCTGCATAGG-----------------------------------------ACCATG--ATCAGCATTCATTAAGA-CATGGAC -s mr.mrrefChr0 41725 133 + 130230 GGCCTGTCTA-ATTTGAACAATCCTCTGCATTTAAGCAATCCACCAGCCATTACCCTGCTTAGCTCCGAATATATATGT----GTTGATTAATCCCACACCCAGCACCATGGTGTCAGTGTGCATTAGGAACACAGAA -s simCow_chr6.simCow.chr6 580539 70 - 602619 AGC-TAAGT------------------GCAT-TTAACAATCCACTAACTGTTATACTCCATATG-----------------------------------------AT------ATCAGCTATCATTAAGA-CATGAAT -s simDog_chr6.simDog.chr6 576127 76 - 593897 GGTTTAGCT------------------GCGCTTTAAAAATCCACAAACTGTCGTCCTGCATAGG-----------------------------------------ACCATG--ATCAGCATTCATTAAGA-AATGGAC -s simHuman_chr6.simHuman.chr6 582586 76 - 601863 GGCTTATGT------------------GCATCTTAACAATCCACTAA--ATCACCCTGTGTAGG-----------------------------------------ACCATGGTGTCAGCGTTAATTAAGA-CATTGAC -s simRat_chr6.simRat.chr6 36442 133 + 647215 GGCCTGTCTC-ATTAGAGCAACCCTTTGCATTTAAGCAATCCACCAGCCATTACCCTGCTCAACTCGGAATATATATAT----ATTGGTTACTCTGACACCCAGCACCATGGTGTAAGTGTCCATTTGGAACACAGAC - -a -s simMouse_chr6.simMouse.chr6 44096 1 + 636262 T -s Anc0.Anc0refChr9 18648 1 + 35212 T -s Anc1.Anc1refChr2 143039 1 - 144309 T -s Anc2.Anc2refChr0 38368 1 - 56053 C -s mr.mrrefChr0 41858 1 + 130230 T -s simCow_chr6.simCow.chr6 580609 1 - 602619 T -s simDog_chr6.simDog.chr6 576203 1 - 593897 C -s simHuman_chr6.simHuman.chr6 582662 1 - 601863 T -s simRat_chr6.simRat.chr6 36576 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 44097 1 + 636262 A -s Anc0.Anc0refChr9 18649 1 + 35212 A -s Anc1.Anc1refChr2 143040 1 - 144309 A -s Anc2.Anc2refChr0 38369 1 - 56053 A -s mr.mrrefChr0 41859 1 + 130230 A -s simCow_chr6.simCow.chr6 580610 1 - 602619 A -s simDog_chr6.simDog.chr6 576204 1 - 593897 A -s simHuman_chr6.simHuman.chr6 582669 1 - 601863 A -s simRat_chr6.simRat.chr6 36577 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 44098 12 + 636262 ACAAAATGGTCT -s Anc0.Anc0refChr9 18650 12 + 35212 CTTCCATGGCCT -s Anc1.Anc1refChr2 143041 12 - 144309 CTTCCATGGCCT -s Anc2.Anc2refChr0 38379 12 - 56053 CTTCCACAGCCT -s mr.mrrefChr0 41860 12 + 130230 ACAAAATGGTCT -s simCow_chr6.simCow.chr6 580620 12 - 602619 TTTCAGCAGGCT -s simDog_chr6.simDog.chr6 576214 12 - 593897 CTTCCACAGCTT -s simHuman_chr6.simHuman.chr6 582670 12 - 601863 GTTCCATGGCCT -s simRat_chr6.simRat.chr6 36578 8 + 647215 ACGAGATG---- - -a -s simMouse_chr6.simMouse.chr6 44110 31 + 636262 TGCAACCAGTTAAACCACTGCCTATTTATGC -s Anc0.Anc0refChr9 18665 31 + 35212 GATTATCAGTTCAGCCACTGCCTATTACTGG -s Anc1.Anc1refChr2 143056 31 - 144309 GATTATCAGTTCAGCCACTGCCTATTACTGG -s Anc2.Anc2refChr0 38394 31 - 56053 GATTATCAGTTCAGCCACTGCCTACTACCGG -s mr.mrrefChr0 41872 31 + 130230 TGCAACCAGTTAAGCCACTGCCTATTTATGC -s simCow_chr6.simCow.chr6 580635 31 - 602619 AATTATCAGTTCAGCCACTGCCTACTACCGG -s simDog_chr6.simDog.chr6 576229 31 - 593897 GATTATCAGTTCAACCACTGCCTACTACCAG -s simHuman_chr6.simHuman.chr6 582685 31 - 601863 GATTATCAGTCCAGCCACTGCCTATTGCTGG -s simRat_chr6.simRat.chr6 36586 28 + 647215 ---AACCAGTTTAGCCGCTGCCTATTTATGC - -a -s simMouse_chr6.simMouse.chr6 44141 2 + 636262 AG -s Anc0.Anc0refChr9 18696 2 + 35212 AG -s Anc1.Anc1refChr2 143087 2 - 144309 AG -s Anc2.Anc2refChr0 38430 2 - 56053 AG -s mr.mrrefChr0 41903 2 + 130230 AG -s simCow_chr6.simCow.chr6 580671 2 - 602619 AA -s simDog_chr6.simDog.chr6 576265 2 - 593897 AG -s simHuman_chr6.simHuman.chr6 582716 2 - 601863 AG -s simRat_chr6.simRat.chr6 36614 2 + 647215 AG - -a -s simMouse_chr6.simMouse.chr6 44143 2 + 636262 CC -s Anc0.Anc0refChr9 18698 2 + 35212 CC -s Anc1.Anc1refChr2 143089 2 - 144309 CC -s Anc2.Anc2refChr0 38432 2 - 56053 CC -s mr.mrrefChr0 41905 2 + 130230 CC -s simCow_chr6.simCow.chr6 580673 2 - 602619 CC -s simDog_chr6.simDog.chr6 576267 2 - 593897 CC -s simHuman_chr6.simHuman.chr6 582719 2 - 601863 CC -s simRat_chr6.simRat.chr6 36616 2 + 647215 CC - -a -s simMouse_chr6.simMouse.chr6 44145 8 + 636262 GTCTGTAC -s Anc0.Anc0refChr9 18701 8 + 35212 GTCCACCC -s Anc1.Anc1refChr2 143092 8 - 144309 GTCCACCC -s Anc2.Anc2refChr0 38459 8 - 56053 GTCCACCC -s mr.mrrefChr0 41908 8 + 130230 GTCCGTAC -s simCow_chr6.simCow.chr6 580700 8 - 602619 GCCCACCC -s simDog_chr6.simDog.chr6 576294 8 - 593897 GTCCACCC -s simHuman_chr6.simHuman.chr6 582722 8 - 601863 GTCCACCC -s simRat_chr6.simRat.chr6 36619 8 + 647215 GTCCTAAC - -a -s simMouse_chr6.simMouse.chr6 44153 2 + 636262 CT -s Anc0.Anc0refChr9 18712 2 + 35212 CC -s Anc1.Anc1refChr2 143103 2 - 144309 CC -s Anc2.Anc2refChr0 38470 2 - 56053 CC -s mr.mrrefChr0 41916 2 + 130230 CC -s simCow_chr6.simCow.chr6 580711 2 - 602619 CT -s simDog_chr6.simDog.chr6 576305 2 - 593897 TC -s simHuman_chr6.simHuman.chr6 582733 2 - 601863 CC -s simRat_chr6.simRat.chr6 36627 2 + 647215 CC - -a -s simMouse_chr6.simMouse.chr6 44155 28 + 636262 TTGCATACACTTTTGAAATTATGTGTAG -s Anc0.Anc0refChr9 18718 28 + 35212 CTTCACACAGTCTCGAGACTATTCATAC -s Anc1.Anc1refChr2 143109 28 - 144309 CTTCACACAGTCTCGAGACTATTCATAC -s Anc2.Anc2refChr0 38476 28 - 56053 CTTCACGCAGCCTCGAGACTATTCATAC -s mr.mrrefChr0 41922 28 + 130230 TTGCATACACTTTTGAAATTATGCATAG -s simCow_chr6.simCow.chr6 580717 28 - 602619 CTTCAAGTCGCCTCGAGATTATTCATAC -s simDog_chr6.simDog.chr6 576311 27 - 593897 CTTCACGCAGCCTTGAGACCATTAAGA- -s simHuman_chr6.simHuman.chr6 582739 27 - 601863 CTCCACACAGTCTC-AGACTATTCATAC -s simRat_chr6.simRat.chr6 36633 28 + 647215 TCACATACACTTTTGAAATTGTACATAG - -a -s simMouse_chr6.simMouse.chr6 44183 3 + 636262 AAT -s Anc0.Anc0refChr9 18746 3 + 35212 AAT -s Anc1.Anc1refChr2 143137 3 - 144309 AAT -s Anc2.Anc2refChr0 38510 3 - 56053 AAT -s mr.mrrefChr0 41950 3 + 130230 AAT -s simCow_chr6.simCow.chr6 580751 3 - 602619 GAT -s simDog_chr6.simDog.chr6 576344 3 - 593897 AAT -s simHuman_chr6.simHuman.chr6 582766 3 - 601863 AAT -s simRat_chr6.simRat.chr6 36661 3 + 647215 AAT - -a -s simMouse_chr6.simMouse.chr6 44186 10 + 636262 TCAGAACTGT -s Anc0.Anc0refChr9 18749 10 + 35212 TCAAAGCTAT -s Anc1.Anc1refChr2 143140 10 - 144309 TCAAAGCTAT -s Anc2.Anc2refChr0 38513 10 - 56053 TCAAATCCAT -s mr.mrrefChr0 41953 10 + 130230 TCAGAGCTGT -s simCow_chr6.simCow.chr6 580754 10 - 602619 TCAAAACCAT -s simDog_chr6.simDog.chr6 576347 10 - 593897 TCAAATCCAC -s simHuman_chr6.simHuman.chr6 582784 10 - 601863 TCAAAGCTAT -s simRat_chr6.simRat.chr6 36664 10 + 647215 TGAGAGCTGT - -a -s simMouse_chr6.simMouse.chr6 44196 10 + 636262 GAATTTGATC -s Anc0.Anc0refChr9 18759 7 + 35212 TATA---ATG -s Anc1.Anc1refChr2 143150 7 - 144309 TATA---ATG -s Anc2.Anc2refChr0 38650 7 - 56053 TGTG---GTG -s mr.mrrefChr0 41963 10 + 130230 GAATTTGATC -s simCow_chr6.simCow.chr6 580892 7 - 602619 TGCA---ATG -s simDog_chr6.simDog.chr6 576491 7 - 593897 TGTG---GTG -s simHuman_chr6.simHuman.chr6 582794 4 - 601863 T------ACT -s simRat_chr6.simRat.chr6 36674 10 + 647215 GAATTTGGTC - -a -s simMouse_chr6.simMouse.chr6 44206 13 + 636262 CAGTTGGGGCCTG -s Anc0.Anc0refChr9 18766 13 + 35212 CAATTGAATCATA -s Anc1.Anc1refChr2 143157 13 - 144309 CAATTGAATCATA -s Anc2.Anc2refChr0 38657 13 - 56053 GTATTGAATCACA -s mr.mrrefChr0 41973 13 + 130230 CAGTTGGGTCCTG -s simCow_chr6.simCow.chr6 580899 13 - 602619 CAATTGAATCACA -s simDog_chr6.simDog.chr6 576498 13 - 593897 GTATTGAATCACA -s simHuman_chr6.simHuman.chr6 582800 13 - 601863 CAATTACATCTTA -s simRat_chr6.simRat.chr6 36684 13 + 647215 CAGTTGTGTCATG - -a -s simMouse_chr6.simMouse.chr6 44219 15 + 636262 TGCTATGATGCATTT -s Anc0.Anc0refChr9 18779 15 + 35212 AGCTACGATGCACTT -s Anc1.Anc1refChr2 143170 15 - 144309 AGCTACGATGCACTT -s Anc2.Anc2refChr0 38670 15 - 56053 AGCTACGATGCACTT -s Anc2.Anc2refChr0 17403 15 + 56053 AGCTACAATGCACTT -s mr.mrrefChr0 41986 15 + 130230 TGCTATGATGCACTT -s simCow_chr6.simCow.chr6 21727 15 + 602619 AACAAGGATGTAGTT -s simCow_chr6.simCow.chr6 580912 15 - 602619 TGCTACGATGGACTT -s simDog_chr6.simDog.chr6 17406 15 + 593897 AGCTACAATGCACTT -s simDog_chr6.simDog.chr6 576511 15 - 593897 AGTTACAATGCACTT -s simHuman_chr6.simHuman.chr6 582813 15 - 601863 AGCTACGATGCACTT -s simRat_chr6.simRat.chr6 36697 15 + 647215 TGCTATGATGCACTT - -a -s simMouse_chr6.simMouse.chr6 44234 3 + 636262 GAA -s Anc0.Anc0refChr9 18794 2 + 35212 AA- -s Anc1.Anc1refChr2 143185 3 - 144309 AAA -s Anc2.Anc2refChr0 38685 2 - 56053 GA- -s Anc2.Anc2refChr0 17418 2 + 56053 AA- -s mr.mrrefChr0 42001 3 + 130230 GAA -s simCow_chr6.simCow.chr6 21743 2 + 602619 AA- -s simCow_chr6.simCow.chr6 580927 2 - 602619 GA- -s simDog_chr6.simDog.chr6 17421 2 + 593897 AA- -s simDog_chr6.simDog.chr6 576526 2 - 593897 GA- -s simHuman_chr6.simHuman.chr6 582828 3 - 601863 AAA -s simRat_chr6.simRat.chr6 36712 3 + 647215 GAA - -a -s simMouse_chr6.simMouse.chr6 44237 6 + 636262 CACCGT -s Anc0.Anc0refChr9 18796 6 + 35212 CACCAT -s Anc1.Anc1refChr2 143188 6 - 144309 CACCAT -s Anc2.Anc2refChr0 17420 6 + 56053 CACCAT -s mr.mrrefChr0 42004 6 + 130230 CACCAT -s simCow_chr6.simCow.chr6 21745 6 + 602619 CACCAT -s simDog_chr6.simDog.chr6 17423 6 + 593897 CACCAT -s simHuman_chr6.simHuman.chr6 582831 6 - 601863 CCCCAT -s simRat_chr6.simRat.chr6 36715 6 + 647215 CACCAT - -a -s simMouse_chr6.simMouse.chr6 44243 8 + 636262 ACAGAGCC -s Anc0.Anc0refChr9 18802 8 + 35212 GAAAGACT -s Anc1.Anc1refChr2 143194 8 - 144309 GAAAGACT -s Anc2.Anc2refChr0 38687 8 - 56053 GAAAGACT -s Anc2.Anc2refChr0 17426 8 + 56053 AAAAGACT -s mr.mrrefChr0 42010 8 + 130230 GCAGAGCC -s simCow_chr6.simCow.chr6 21751 8 + 602619 GAGAGATG -s simCow_chr6.simCow.chr6 580929 6 - 602619 AAAA--CT -s simDog_chr6.simDog.chr6 17429 8 + 593897 AAAAGACT -s simDog_chr6.simDog.chr6 576528 8 - 593897 GAAAGACA -s simHuman_chr6.simHuman.chr6 582837 8 - 601863 GAAAGCCT -s simRat_chr6.simRat.chr6 36721 8 + 647215 GCAGAGCA - -a -s simMouse_chr6.simMouse.chr6 44251 1 + 636262 A -s Anc0.Anc0refChr9 18810 1 + 35212 A -s Anc1.Anc1refChr2 143202 1 - 144309 A -s Anc2.Anc2refChr0 38695 1 - 56053 A -s Anc2.Anc2refChr0 17434 1 + 56053 A -s mr.mrrefChr0 42018 1 + 130230 A -s simCow_chr6.simCow.chr6 21759 1 + 602619 A -s simCow_chr6.simCow.chr6 581069 1 - 602619 A -s simDog_chr6.simDog.chr6 17437 1 + 593897 A -s simDog_chr6.simDog.chr6 576536 1 - 593897 T -s simHuman_chr6.simHuman.chr6 582845 1 - 601863 A -s simRat_chr6.simRat.chr6 36729 1 + 647215 G - -a -s simMouse_chr6.simMouse.chr6 44252 1 + 636262 A -s Anc0.Anc0refChr9 18812 1 + 35212 A -s Anc1.Anc1refChr2 143204 1 - 144309 A -s Anc2.Anc2refChr0 38697 1 - 56053 T -s mr.mrrefChr0 42019 1 + 130230 A -s simCow_chr6.simCow.chr6 581071 1 - 602619 T -s simDog_chr6.simDog.chr6 576538 1 - 593897 T -s simHuman_chr6.simHuman.chr6 582847 1 - 601863 A -s simRat_chr6.simRat.chr6 36730 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 44253 4 + 636262 TTTT -s Anc0.Anc0refChr9 18819 4 + 35212 CTTT -s Anc1.Anc1refChr2 143211 4 - 144309 CTTT -s Anc2.Anc2refChr0 38704 4 - 56053 CTTT -s Anc2.Anc2refChr0 17437 4 + 56053 CTTT -s mr.mrrefChr0 42020 4 + 130230 TTTT -s simCow_chr6.simCow.chr6 21762 4 + 602619 CTTT -s simCow_chr6.simCow.chr6 581078 4 - 602619 CTAT -s simDog_chr6.simDog.chr6 17446 4 + 593897 CTTT -s simDog_chr6.simDog.chr6 576545 4 - 593897 CTTT -s simHuman_chr6.simHuman.chr6 582854 4 - 601863 CTTT -s simRat_chr6.simRat.chr6 36731 4 + 647215 TTTT - -a -s simMouse_chr6.simMouse.chr6 44257 21 + 636262 CCAATTGCCTTTGTGGGATGA -s Anc0.Anc0refChr9 18823 21 + 35212 CCAATAGCCTTAGTGTGATAA -s Anc1.Anc1refChr2 143215 21 - 144309 CCAATAGCCTTAGTGTGATAA -s Anc2.Anc2refChr0 38708 21 - 56053 CCAATAACCTTAGTGTGATAA -s Anc2.Anc2refChr0 17441 21 + 56053 GGAGTAGCCTTGGTCTGATAA -s mr.mrrefChr0 42024 21 + 130230 CCAATTGCCTTAGTGGGATGA -s simCow_chr6.simCow.chr6 21766 21 + 602619 GGAATAGGCTTGGCATGATAA -s simCow_chr6.simCow.chr6 581082 21 - 602619 CCAATAAACTCAGTGAGATGA -s simDog_chr6.simDog.chr6 17451 21 + 593897 GGAGTAGCCTTGGTCTGATAA -s simDog_chr6.simDog.chr6 576549 21 - 593897 CCAATAACCTTGGTGTGATAA -s simHuman_chr6.simHuman.chr6 582858 21 - 601863 CCACTAGCCTTAATGTGATAA -s simRat_chr6.simRat.chr6 36735 21 + 647215 CCAATTGCCTTAGTGGGATGA - -a -s simMouse_chr6.simMouse.chr6 44278 5 + 636262 TTGTC -s Anc0.Anc0refChr9 18845 5 + 35212 TTGTT -s Anc1.Anc1refChr2 143237 5 - 144309 TTGTT -s Anc2.Anc2refChr0 38730 5 - 56053 TTGTC -s Anc2.Anc2refChr0 17463 5 + 56053 TTGCT -s mr.mrrefChr0 42045 5 + 130230 TTGTC -s simCow_chr6.simCow.chr6 21788 5 + 602619 TTGTT -s simCow_chr6.simCow.chr6 581104 5 - 602619 TTGTC -s simDog_chr6.simDog.chr6 17473 5 + 593897 TTGCT -s simDog_chr6.simDog.chr6 576571 5 - 593897 CTGTC -s simHuman_chr6.simHuman.chr6 582880 5 - 601863 TTGTT -s simRat_chr6.simRat.chr6 36756 5 + 647215 TTGTC - -a -s simMouse_chr6.simMouse.chr6 44283 24 + 636262 TCAGAATTTCCCCTGATGTTCGAC -s Anc0.Anc0refChr9 18850 24 + 35212 TAAGGATTCCTCCAGACATTCAAT -s Anc1.Anc1refChr2 143242 24 - 144309 TAAGGATTCCTCCAGACATTCAAT -s Anc2.Anc2refChr0 38735 24 - 56053 TAAGGATTCCTCCAGACATTCAAT -s Anc2.Anc2refChr0 17468 24 + 56053 TAAGAATTCATCCAGACTGACAAC -s mr.mrrefChr0 42050 24 + 130230 TCAGAATTTCTCCTGATGTTCAAC -s simCow_chr6.simCow.chr6 21793 24 + 602619 TAAGAATTTCTTCAGATCTGCAAC -s simCow_chr6.simCow.chr6 581109 23 - 602619 TAAGGATTCCTCCAAA-ACTCAAT -s simDog_chr6.simDog.chr6 17478 24 + 593897 TAAGAATTCATCCAGACTGACAAC -s simDog_chr6.simDog.chr6 576578 24 - 593897 TAAGAATTCCTCCAGACATTCAAC -s simHuman_chr6.simHuman.chr6 582885 24 - 601863 TAAAGATTCCTCCAGACATTCAAT -s simRat_chr6.simRat.chr6 36761 24 + 647215 TCTGAATTTCTCCTAATGTTCAAC - -a -s simMouse_chr6.simMouse.chr6 44307 10 + 636262 TAAGCCAATC -s Anc0.Anc0refChr9 18874 10 + 35212 TAAGCCAACC -s Anc1.Anc1refChr2 143266 10 - 144309 TAAGCCAACC -s Anc2.Anc2refChr0 38759 10 - 56053 TAAGCCAACC -s Anc2.Anc2refChr0 17492 10 + 56053 TGTGCCAACC -s mr.mrrefChr0 42074 10 + 130230 TAAGCCAATC -s simCow_chr6.simCow.chr6 21817 10 + 602619 TAGGCCAACT -s simCow_chr6.simCow.chr6 581134 10 - 602619 CAAGCCCACC -s simDog_chr6.simDog.chr6 17502 10 + 593897 TGTGCCAACC -s simDog_chr6.simDog.chr6 576602 10 - 593897 TGGGCCAACC -s simHuman_chr6.simHuman.chr6 582909 10 - 601863 TAAGCCAACC -s simRat_chr6.simRat.chr6 36785 10 + 647215 TAAGCCAATC - -a -s simMouse_chr6.simMouse.chr6 44317 9 + 636262 ACAGCTGAT -s Anc0.Anc0refChr9 18884 9 + 35212 AGAGCTGAG -s Anc1.Anc1refChr2 143276 9 - 144309 AGAGCTGAG -s Anc2.Anc2refChr0 38769 9 - 56053 AGAGCTGAG -s Anc2.Anc2refChr0 17502 9 + 56053 ACAACTTTG -s mr.mrrefChr0 42084 9 + 130230 ACAGCTGAG -s simCow_chr6.simCow.chr6 21827 9 + 602619 ACAATGTCA -s simCow_chr6.simCow.chr6 581144 9 - 602619 GGAGCAGAA -s simDog_chr6.simDog.chr6 17512 9 + 593897 ACAACTTTG -s simDog_chr6.simDog.chr6 576612 9 - 593897 ACAGCTGAG -s simHuman_chr6.simHuman.chr6 582919 9 - 601863 AGAGCTGAG -s simRat_chr6.simRat.chr6 36870 9 + 647215 ACTGCTGAG - -a -s simMouse_chr6.simMouse.chr6 44326 2 + 636262 TC -s Anc0.Anc0refChr9 18893 2 + 35212 TC -s Anc1.Anc1refChr2 143285 2 - 144309 TC -s Anc2.Anc2refChr0 38778 2 - 56053 TC -s Anc2.Anc2refChr0 17528 2 + 56053 TA -s mr.mrrefChr0 42093 2 + 130230 TC -s simCow_chr6.simCow.chr6 21853 2 + 602619 TA -s simCow_chr6.simCow.chr6 581153 2 - 602619 TC -s simDog_chr6.simDog.chr6 17538 2 + 593897 TA -s simDog_chr6.simDog.chr6 576621 2 - 593897 TG -s simHuman_chr6.simHuman.chr6 582928 2 - 601863 TC -s simRat_chr6.simRat.chr6 36879 2 + 647215 TC - -a -s simMouse_chr6.simMouse.chr6 44328 9 + 636262 AACTGCCAG -s Anc0.Anc0refChr9 18895 9 + 35212 AACAGCAAA -s Anc1.Anc1refChr2 143287 9 - 144309 AACAGCAAA -s Anc2.Anc2refChr0 38780 9 - 56053 AACAGCAAA -s mr.mrrefChr0 42095 9 + 130230 AACAGCCAA -s simCow_chr6.simCow.chr6 581155 9 - 602619 GCCAGCAAA -s simDog_chr6.simDog.chr6 576623 9 - 593897 AACAGCAAA -s simHuman_chr6.simHuman.chr6 582930 9 - 601863 AACAGCAGA -s simRat_chr6.simRat.chr6 36881 9 + 647215 AACAGCCAA - -a -s simMouse_chr6.simMouse.chr6 44337 105 + 636262 AGAGTAAATATGAGAGAGTGCTACTGATCAGAAATTAGCTTGTTAATACCATCAGAGGATGTAATACATGGATAGGCTGGGAGCATCATCAGTCAAGTGGCATAT -s Anc0.Anc0refChr9 18905 105 + 35212 AGAGTAAATATAACTGAGTGCTAGTGATCAGAAATTCTCTTGTTAATACCTTCAAACCATGTAATACATAGCTAGGCTGGGTGCTTCTTCAGACAGCTACTATAT -s Anc1.Anc1refChr2 143297 105 - 144309 AGAGTAAATATAACTGAGTGCTAGTGATCAGAAATTCTCTTGTTAATACCTTCAAACCATGTAATACATAGCTAGGCTGGGTGCTTCTTCAGACAGCTACTATAT -s Anc2.Anc2refChr0 38790 105 - 56053 AGAGTAAATGTAACTGAGTGCTAGTGATCAGAAATTCTCTTGTTAATACCTTCAAACCATGTAATACATAACCATGCTGGGTGCTCCCACAGACAGCTACTATAT -s mr.mrrefChr0 42104 105 + 130230 AGAGTAAATATAAGAGAGTGCTAGTGATCAGAAATTATCTTGTTAATACCATCAGAGGATGTAATACATGGATAGGCTGGGAGCATCTTCAGTCAAGTAGCATAT -s simCow_chr6.simCow.chr6 581165 99 - 602619 AGGGTAAATGTCA-TGAGTGCTAGTGATCAGAAATTCTCTTGTTAACACCTTCAAACCATTTAATACACAACCAAGCTGGGTGC-----CAGATAGCTACTAGAT -s simDog_chr6.simDog.chr6 576633 105 - 593897 AAAGTAAATGTAACTGAGTGTTAGTGATTAGAAATTCACTTGCCAATACCTTCAGATCATGTAGTACATAATCATGCTCTGTGCTCCCACAGGCAGCTACCCTGC -s simHuman_chr6.simHuman.chr6 582940 105 - 601863 AGAGTAAATAAAGTTGAGTGCTAGTGACCAGAAATTCTCTTGTTTATGGCTTCAAACCATGTAAAACATAGCTAGGCTGGGGACTTCTTCAGACAGCTACTATAT -s simRat_chr6.simRat.chr6 36890 105 + 647215 AGAGTAAATATAAGAGAGTGCTAGTGATCAGAGATTTTCTTGTTAATACCATCAGAGGATGTAATACATGGATAGGCTGGGACCATCTTCTGTCAAGTAGCATAT - -a -s simMouse_chr6.simMouse.chr6 44442 32 + 636262 TGATAATTGGGACGAACCCTCCATATCACGTA -s Anc0.Anc0refChr9 19015 32 + 35212 TGATAAATGAGGTGAACACTTCATATTATGCT -s Anc1.Anc1refChr2 143407 32 - 144309 TGATAAATGAGGTGAACACTTCATATTATGCT -s Anc2.Anc2refChr0 38900 32 - 56053 TGATAAATAAGGTGAAGACTTCATATTATGCT -s mr.mrrefChr0 42214 32 + 130230 TGATAATTGGGATGAACCCTTCATATCACGCA -s simCow_chr6.simCow.chr6 581269 30 - 602619 TGATACATCCTGTGA--ATTTAGTATTATGCT -s simDog_chr6.simDog.chr6 576743 32 - 593897 TGATAAACAAGGTGAAGACTTCATATTATGCT -s simHuman_chr6.simHuman.chr6 583050 32 - 601863 CAATAAATGAGGTGAACTCTTCACATTATGCT -s simRat_chr6.simRat.chr6 37000 32 + 647215 TGATAATTGCGATGAACCCTTCATTTCACACA - -a -s simMouse_chr6.simMouse.chr6 44474 27 + 636262 GTGTGTATATGTAGTTGAAAGAAGTGC -s Anc0.Anc0refChr9 19047 19 + 35212 GTGCCCACACGGAAT--------GTGC -s Anc1.Anc1refChr2 143439 19 - 144309 GTGCCCACACGGAAT--------GTGC -s Anc2.Anc2refChr0 38932 19 - 56053 GTTCCCACACGGAAT--------GTGA -s mr.mrrefChr0 42246 27 + 130230 GTGTGTATATGTAGTTGAAAGAAGTGC -s simCow_chr6.simCow.chr6 581301 19 - 602619 GTTCCCACACATAAC--------GTAA -s simDog_chr6.simDog.chr6 576775 19 - 593897 GCTCCCGCATGGAAT--------GTGA -s simHuman_chr6.simHuman.chr6 583082 9 - 601863 TTGCCCA------------------AC -s simRat_chr6.simRat.chr6 37032 27 + 647215 GTGTGTATATGTGATGGAAAGAAGCGC - -a -s simMouse_chr6.simMouse.chr6 44501 19 + 636262 ACAATCTAGTCATAAACAC -s Anc0.Anc0refChr9 19066 19 + 35212 ACCATCCAGTCATCAACAC -s Anc1.Anc1refChr2 143458 19 - 144309 ACCATCCAGTCATCAACAC -s Anc2.Anc2refChr0 38951 19 - 56053 ATCATTTAAACATCAACAC -s mr.mrrefChr0 42273 19 + 130230 ACAATCCAGTCATAAACAC -s simCow_chr6.simCow.chr6 581328 19 - 602619 AACATTTAAACAGTGATAT -s simDog_chr6.simDog.chr6 576794 19 - 593897 ATCATTTAAACATCAACAC -s simHuman_chr6.simHuman.chr6 583091 19 - 601863 ACGATCCAGTCATCAACAC -s simRat_chr6.simRat.chr6 37059 19 + 647215 CCAAACCAGTCACAAACGT - -a -s simMouse_chr6.simMouse.chr6 44520 30 + 636262 AGAGTAATGATTTGCGATTTGCTATTGCAC -s Anc0.Anc0refChr9 19085 22 + 35212 AGATTAATGAGTTGCCACA-GC-------C -s Anc1.Anc1refChr2 143477 23 - 144309 AGATTAATGAGTTGCCACA-GC------AC -s Anc2.Anc2refChr0 38970 22 - 56053 AGATTAATGAGTTGCCACT-GC-------C -s mr.mrrefChr0 42292 29 + 130230 AGAGTAATGATTTGCCATA-GCTATTGCAC -s simCow_chr6.simCow.chr6 581347 22 - 602619 AGGTTAATGGGTTTCTACT-GC-------C -s simDog_chr6.simDog.chr6 576815 22 - 593897 AGATTAATGAGTTGCCACT-GC-------A -s simHuman_chr6.simHuman.chr6 583110 23 - 601863 AGACTAATGAGTTGCCACA-CC------AC -s simRat_chr6.simRat.chr6 37078 29 + 647215 AGAGTAATAATTTGCCATA-GCACTTTCAC - -a -s simMouse_chr6.simMouse.chr6 44550 39 + 636262 TTCAACATGACTATGTTTGTGTTGGCATGTGAGATATGG -s Anc0.Anc0refChr9 19107 39 + 35212 TTTCAGATCACTAGAAATGTGTTGGCATGTAAGATATGT -s Anc1.Anc1refChr2 143500 39 - 144309 TTTCAGATCACTAGAAATGTGTTGGCATGTAAGATATGT -s Anc2.Anc2refChr0 38992 39 - 56053 ACCCTGATTACTAGAAATGTGTTGACATACAGGATATGT -s mr.mrrefChr0 42321 39 + 130230 TTTCACATCACTATGTATGTGTTGGCATGTGAGATATGG -s simCow_chr6.simCow.chr6 581369 39 - 602619 CCCCTGATTACTAGAAATGTGTTGACATACAGGACATGG -s simDog_chr6.simDog.chr6 576837 28 - 593897 A-----------AAGATTGTGTTGACATACAGGGTATGT -s simHuman_chr6.simHuman.chr6 583133 39 - 601863 TTTCATTACTCTAGAAATGTGTTGGCATGTAAGAGGTAT -s simRat_chr6.simRat.chr6 37113 38 + 647215 CTTCACATCA-CATGCATAGGCTTACACGCGAGATATGG - -a -s simMouse_chr6.simMouse.chr6 44589 9 + 636262 TCAGGCTGT -s Anc0.Anc0refChr9 19146 9 + 35212 TCCCATGGT -s Anc1.Anc1refChr2 143539 9 - 144309 TCCCATGGT -s Anc2.Anc2refChr0 39031 9 - 56053 TTCCATGGT -s mr.mrrefChr0 42360 9 + 130230 TCAGGCTGT -s simCow_chr6.simCow.chr6 581408 9 - 602619 ATCCACAGT -s simDog_chr6.simDog.chr6 576865 9 - 593897 TTCCATGGT -s simHuman_chr6.simHuman.chr6 583172 9 - 601863 CCCCATGGT -s simRat_chr6.simRat.chr6 37152 9 + 647215 TCTACCAGT - -a -s simMouse_chr6.simMouse.chr6 44598 9 + 636262 CTGGTCTGG -s Anc0.Anc0refChr9 19155 8 + 35212 TATGTC-AC -s Anc1.Anc1refChr2 143548 9 - 144309 TATGTCTAC -s Anc2.Anc2refChr0 39042 8 - 56053 TATGTC-AA -s mr.mrrefChr0 42369 9 + 130230 CTGGTCTGC -s simCow_chr6.simCow.chr6 581419 8 - 602619 TACGAG-GA -s simDog_chr6.simDog.chr6 576876 8 - 593897 TATGTC-AA -s simHuman_chr6.simHuman.chr6 583181 9 - 601863 GATATCTAC -s simRat_chr6.simRat.chr6 37161 9 + 647215 CTGGTCTGC - -a -s simMouse_chr6.simMouse.chr6 44607 113 + 636262 CACATTGGAGGGTGATATGCTAGGAGTCAATAAGAGTCAGCTGAGACACTATCAGGAGCCCAACTAGTTTTTTTAAAACCATATAATAATTGGCATAACTCCAAGGCAACAGG -s Anc0.Anc0refChr9 19163 111 + 35212 CCCACTAGGGAGTTGTATCCT-AGAGTGGGTAGGAAGCAGCTGAGATACTATGAGAGAGCCAACTAGTTTTTTCAAGACCGT-TATTAACTGGCATAACTCCAAGACAACAAA -s Anc1.Anc1refChr2 143557 111 - 144309 CCCACTAGGGAGTTGTATCCT-AGAGTGGGTAGGAAGCAGCTGAGATACTATGAGAGAGCCAACTAGTTTTTTCAAGACCGT-TATTAACTGGCATAACTCCAAGACAACAAA -s Anc2.Anc2refChr0 39050 111 - 56053 CCCACTAGGGAGTTGTATGCT-AGAGTGGGTAGGAAGCAGCTGAGATACTATGAGAGAGCCAACTAGTTCTATCAAGACCAT-TATTAACTGGCATAATGCCAAAACAGCAAA -s mr.mrrefChr0 42378 113 + 130230 CACACTGGAGGGTGATATCCTAGGAGTCAATAGGAGGCAGCTGAGACACTATCAGGGGGCCAACTAGTTTTTTCAAAACCGTATAATAATTGGCATAACTCCAAGACAACAGA -s simCow_chr6.simCow.chr6 581427 111 - 602619 CCCACTAGGGAGTCGCATGCT-AGAGCAAGTAAGAAGCAGCTGAGACACTATGACAGAGCCAACTAGTTCTATCAAGACTAC-CCTTGACTGGCATAGTGCCAAAACAGCAAA -s simDog_chr6.simDog.chr6 576884 103 - 593897 CCTACTAGGGTGTTATATGCT-AGAGTGGATAGGAAGCAGGTGGGATACTATGAGAGACCCAACCAGTCCTATTGAGACCAT-TATTAAGTGGCTTAATGCTA--------AA -s simHuman_chr6.simHuman.chr6 583191 111 - 601863 CCCTCTAGGAAGTTGGATCCT-TGAGTGTGTAGGAAGCAGCTGAGATACTGTTAGAGAGCCAACTAGTTTTTTCAATACCGT-TACTAACAGGCATAACTCCATGAGCACTAA -s simRat_chr6.simRat.chr6 37170 113 + 647215 CACACTGGAGGGTGATATCCTAGGAGGCCATAGGAGGCAGCTGAGACACTATCAGGGGGCTAACTAGCTTTTTCAAGACTGTATAATGAGTGGCATAACTCCAAGACAGCAGA - -a -s simMouse_chr6.simMouse.chr6 44720 16 + 636262 AAGTTATAACAGTATA -s Anc0.Anc0refChr9 19274 16 + 35212 AAATTATCACAGTATA -s Anc1.Anc1refChr2 143668 16 - 144309 AAATTATCACAGTATA -s Anc2.Anc2refChr0 39161 16 - 56053 AAATTATCACAGTATA -s mr.mrrefChr0 42491 16 + 130230 AAATTATAACAGTATA -s simCow_chr6.simCow.chr6 581538 16 - 602619 AAATCATAACAGTCTA -s simDog_chr6.simDog.chr6 576989 16 - 593897 AAATTATCACAGTATA -s simHuman_chr6.simHuman.chr6 583302 16 - 601863 AAATTATGCCAGTATA -s simRat_chr6.simRat.chr6 37283 16 + 647215 AAATTATAATAGTATA - -a -s simMouse_chr6.simMouse.chr6 44736 7 + 636262 ACTGGCC -s Anc0.Anc0refChr9 19294 7 + 35212 ACTAGTA -s Anc1.Anc1refChr2 143688 7 - 144309 ACTAGTA -s Anc2.Anc2refChr0 39181 7 - 56053 ACTAGTA -s mr.mrrefChr0 42507 7 + 130230 ACTGGCC -s simCow_chr6.simCow.chr6 581558 7 - 602619 ACTAACA -s simDog_chr6.simDog.chr6 577009 7 - 593897 ACTAGTC -s simHuman_chr6.simHuman.chr6 583322 7 - 601863 ACTAGAA -s simRat_chr6.simRat.chr6 37299 4 + 647215 ---GACC - -a -s simMouse_chr6.simMouse.chr6 44743 35 + 636262 TCACTCATTAAAGAACTGCAGCAACTGGGCCTGCC -s Anc0.Anc0refChr9 19301 35 + 35212 TCAGTAATTCAACAACTGCATTAATGGGGCCCACC -s Anc1.Anc1refChr2 143695 35 - 144309 TCAGTAATTCAACAACTGCATTAATGGGGCCCACC -s Anc2.Anc2refChr0 39188 35 - 56053 TCAGTAACAGAACAACTGCATTAATGGGGCCCACC -s mr.mrrefChr0 42514 35 + 130230 TCAGTCATTCAAGAACTGCAGCAACTGGGCCCACC -s simCow_chr6.simCow.chr6 581569 35 - 602619 ATATTGAACTAACAACCGCGTTAATGGAGTCCACC -s simDog_chr6.simDog.chr6 577016 35 - 593897 TCAGTAACAGAATGACTGAATTAATGGGGCCAACC -s simHuman_chr6.simHuman.chr6 583329 35 - 601863 TCAGTAATTCAACAACTGCATTAATGGGGCCCACC -s simRat_chr6.simRat.chr6 37303 35 + 647215 TCAGTCATTCAAAAACTGCAGCAACTGGGCCCATG - -a -s simMouse_chr6.simMouse.chr6 44778 2 + 636262 TA -s Anc0.Anc0refChr9 19336 2 + 35212 AA -s Anc1.Anc1refChr2 143730 2 - 144309 AA -s Anc2.Anc2refChr0 39225 2 - 56053 AA -s mr.mrrefChr0 42549 2 + 130230 TA -s simCow_chr6.simCow.chr6 581606 2 - 602619 AA -s simDog_chr6.simDog.chr6 577053 2 - 593897 AA -s simHuman_chr6.simHuman.chr6 583364 2 - 601863 AA -s simRat_chr6.simRat.chr6 37338 2 + 647215 TA - -a -s simMouse_chr6.simMouse.chr6 44780 38 + 636262 CCTGCTGTTTATCAATCTTTGATAGAGTACTGAATTTT -s Anc0.Anc0refChr9 19339 38 + 35212 CCTACAGGCTATCAATCTTTGACAGACTTCTAAGATTT -s Anc1.Anc1refChr2 143733 38 - 144309 CCTACAGGCTATCAATCTTTGACAGACTTCTAAGATTT -s Anc2.Anc2refChr0 39228 38 - 56053 CCTACAGGCTACCAATCTCTGACAGGCATTCTAAATTT -s mr.mrrefChr0 42551 38 + 130230 CCTGCTGTTTATCAATCTTTGATAGAGTACTGAATTTT -s simCow_chr6.simCow.chr6 581609 20 - 602619 CTTACAGATTACCAAT------------------ATTT -s simDog_chr6.simDog.chr6 577056 38 - 593897 CCTACAGGCTACCAACCTCTGACAGGCATTCTAACTTT -s simHuman_chr6.simHuman.chr6 583367 38 - 601863 CCTATAGGCTATCAATCTTTGACAGACTGTCCAGATTT -s simRat_chr6.simRat.chr6 37340 37 + 647215 CCTGCTGTTAATCAATCTTTGATAG-GTTCTGGACTTT - -a -s simMouse_chr6.simMouse.chr6 44818 31 + 636262 ACTAGATATAAAAAAACTATAGCCATTAAGT -s Anc0.Anc0refChr9 19377 29 + 35212 A--AGAAATATACAAACTATTAGCATCGAGC -s Anc1.Anc1refChr2 143771 29 - 144309 A--AGAAATATACAAACTATTAGCATCGAGC -s Anc2.Anc2refChr0 39266 29 - 56053 A--ATAAGCATACAAACTATTAGCATCGAAC -s mr.mrrefChr0 42589 31 + 130230 ACTAGATATAAAAAAACTATAGCCATTGAGC -s simCow_chr6.simCow.chr6 581629 29 - 602619 A--GTATGCATACAAACTATTAGCATCGAAC -s simDog_chr6.simDog.chr6 577096 29 - 593897 G--ATAAGCATAAAAACTCTTAGCATTGAAC -s simHuman_chr6.simHuman.chr6 583405 29 - 601863 A--AGAAATGTACAAACTATTTGCATCGAGC -s simRat_chr6.simRat.chr6 37377 25 + 647215 AGTAGATGTAAAAAAACTAT------TGAGC - -a -s simMouse_chr6.simMouse.chr6 44849 1 + 636262 A -s Anc0.Anc0refChr9 19406 1 + 35212 A -s Anc1.Anc1refChr2 143800 1 - 144309 A -s Anc2.Anc2refChr0 39305 1 - 56053 A -s mr.mrrefChr0 42620 1 + 130230 A -s simCow_chr6.simCow.chr6 581668 1 - 602619 A -s simDog_chr6.simDog.chr6 577135 1 - 593897 A -s simHuman_chr6.simHuman.chr6 583434 1 - 601863 A -s simRat_chr6.simRat.chr6 37402 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 44850 35 + 636262 AACTCATGCTATTCACTGATAAGAATCATATGGGT -s Anc0.Anc0refChr9 19409 35 + 35212 AACTCAAGAGATTTACTGATCAGGATCACATGGGT -s Anc1.Anc1refChr2 143803 35 - 144309 AACTCAAGAGATTTACTGATCAGGATCACATGGGT -s Anc2.Anc2refChr0 39308 35 - 56053 AACTCAAGAGATCTACTGATCAGGATCACATGGGT -s mr.mrrefChr0 42621 35 + 130230 AACTCATGCGATTCACTGATCAGAATCATATGGGT -s simCow_chr6.simCow.chr6 581671 35 - 602619 GACTCATAAGATGTACTGATCAAGACCACAGGGGT -s simDog_chr6.simDog.chr6 577138 34 - 593897 AACTCAAGAGACCTAC-GATCAGGCTTACATGGGT -s simHuman_chr6.simHuman.chr6 583437 35 - 601863 AACTCAAGAGATTTGCTGAGCAGGATCACATGGGA -s simRat_chr6.simRat.chr6 37403 35 + 647215 AACTCATGCGATTCACTGACCAGAATTATATGGGT - -a -s simMouse_chr6.simMouse.chr6 44885 31 + 636262 GGATGATATATTGTACTGGCTGTGATAATCT -s Anc0.Anc0refChr9 19447 31 + 35212 GAATTCTACATTACACTAGCTTTGATACTCA -s Anc1.Anc1refChr2 143841 31 - 144309 GAATTCTACATTACACTAGCTTTGATACTCA -s Anc2.Anc2refChr0 39346 31 - 56053 GAATTCTACATTGCACTAGCTTTGATACTCA -s mr.mrrefChr0 42656 31 + 130230 GAATGATACATTATACTGGCTGTGATACTCT -s simCow_chr6.simCow.chr6 581709 27 - 602619 GGATTCTATATTGCTCTAGCATTG----TGA -s simDog_chr6.simDog.chr6 577175 30 - 593897 TAATTCTACACTGAATTAGCTATGATAC-CA -s simHuman_chr6.simHuman.chr6 583475 31 - 601863 GAATTCTACATTACACTAGTTTTGATACTCA -s simRat_chr6.simRat.chr6 37438 31 + 647215 GAATGATACGTTATACTGGCGGTGATACTCT - -a -s simMouse_chr6.simMouse.chr6 44916 25 + 636262 GATCTAACATGTAATTTAACAAGAG -s Anc0.Anc0refChr9 19478 25 + 35212 AATCTAGCATGTAATCTGACAAGAG -s Anc1.Anc1refChr2 143872 25 - 144309 AATCTAGCATGTAATCTGACAAGAG -s Anc2.Anc2refChr0 39377 25 - 56053 AATCTAGCATATAATCTGAAAAGAA -s mr.mrrefChr0 42687 25 + 130230 GATCTAACATGTAATTTAACAAGAG -s simCow_chr6.simCow.chr6 581736 25 - 602619 TAAGAAACCAAAAATTTGAAAAGAA -s simDog_chr6.simDog.chr6 577205 17 - 593897 AGTCTAGCAT-TAGTCTG------- -s simHuman_chr6.simHuman.chr6 583506 25 - 601863 CATCTAGCATGTAATGCGACAAGAG -s simRat_chr6.simRat.chr6 37484 25 + 647215 GTTCTAATGTGTAATTTAACAAATA - -a -s simMouse_chr6.simMouse.chr6 44941 9 + 636262 ACTTAAGCT -s Anc0.Anc0refChr9 19503 6 + 35212 TCTGAA--- -s Anc1.Anc1refChr2 143897 9 - 144309 TCTGAATAT -s Anc2.Anc2refChr0 39402 6 - 56053 TCTGAA--- -s mr.mrrefChr0 42712 9 + 130230 ACTTAAGCT -s simCow_chr6.simCow.chr6 581762 6 - 602619 TCTGAA--- -s simHuman_chr6.simHuman.chr6 583531 9 - 601863 CCTGAACAT -s simRat_chr6.simRat.chr6 37509 9 + 647215 ACTTAAGCT - -a -s simMouse_chr6.simMouse.chr6 44950 34 + 636262 ATGCAACAGGCCTCTCATCAGGAGACCAGTAACT -s Anc0.Anc0refChr9 19509 25 + 35212 ---------TCCTATCATCAAGTAACTAGGAACT -s Anc1.Anc1refChr2 143906 34 - 144309 ACACACCAGTCCTATCATCAAGTAACTAGGAACT -s Anc2.Anc2refChr0 39408 25 - 56053 ---------TCCTATCATCAAGTAACTAGGAACT -s mr.mrrefChr0 42721 34 + 130230 ACGCAACAGGCCTCTCATCAGGAGACTAGTAACT -s simCow_chr6.simCow.chr6 581768 25 - 602619 ---------TCCTATCATCAAGTAACTAGGAACT -s simHuman_chr6.simHuman.chr6 583543 34 - 601863 ACACACCAGTTCTTTCATCAAGTAGCTAGGGACT -s simRat_chr6.simRat.chr6 37518 21 + 647215 AC-------------TATCAGGCGACTGCTAACT - -a -s simMouse_chr6.simMouse.chr6 44984 84 + 636262 GGGGCAGCGAGGGATTAGAAAGCTGTTTCTGATTGTCTGGTACCTCTGAATGAGCATGCTTCTACTGAGGGTTTATCAAGGTCT -s Anc0.Anc0refChr9 19534 23 + 35212 AGGG-----AAGGGTGAGAAAGCTGT----GA---------------------------------------------------- -s Anc1.Anc1refChr2 143940 75 - 144309 AGGG-----AAGGGTGAGAAAGCTGT----GAATCCCTGGTATCTATGAACGAGCTAGCTTCCACTGGGGGCATATCAAGATCC -s Anc2.Anc2refChr0 39433 23 - 56053 AGGG-----AGGGGTGACCAAGCAGT----GA---------------------------------------------------- -s mr.mrrefChr0 42755 84 + 130230 GGGGCAGCGAAGGATTAGAAAGCTGTTTCTGATTCTCTGGTACCTCTGAATGAGCATGCTTCTACTGAGGGTTTATCAAGGTCT -s simCow_chr6.simCow.chr6 581795 23 - 602619 AGGG-----AGGGGTGACCAAGCAGT----GA---------------------------------------------------- -s simHuman_chr6.simHuman.chr6 583577 75 - 601863 AGGG-----AATGTTGAGAAAGCTGT----GAATCCCTGGTATCTATGAACGAGCTAGCTTCCACTGGGGGCATATCAAGATCC -s simRat_chr6.simRat.chr6 37539 84 + 647215 TGAGCAGTGAAGGACTAGAAAGCTGTTTCTGATTCTCTGGTACCTCTGAATGAGCATACTTCTACTGAGGATTTACCAGGGTCT - -a -s simMouse_chr6.simMouse.chr6 45068 17 + 636262 ATGGGTGAAGTATATTG -s Anc0.Anc0refChr9 19618 17 + 35212 ATGGCTGAAGAATATTG -s Anc1.Anc1refChr2 144076 17 - 144309 ATGGCTGAAGAATATTG -s Anc2.Anc2refChr0 39551 17 - 56053 ATGGCTGAAGAATATCT -s mr.mrrefChr0 42839 17 + 130230 ATGGGTGAAGTATATTG -s simCow_chr6.simCow.chr6 581884 17 - 602619 ACGGCTGAAGAATATCA -s simDog_chr6.simDog.chr6 577333 17 - 593897 ATAGCTGAAGAATATCT -s simHuman_chr6.simHuman.chr6 583783 17 - 601863 ATGACTGAAGACTATTG -s simRat_chr6.simRat.chr6 37623 17 + 647215 GTGGGTGAAGTGTATTG - -a -s simMouse_chr6.simMouse.chr6 45085 34 + 636262 GAGGGACCTTTGCACTGGGAACTAAAGTGTGGTC -s Anc0.Anc0refChr9 19635 33 + 35212 TAAGGAC-TTTACACTAGGAACCAAAGTGTGGTC -s Anc1.Anc1refChr2 144093 33 - 144309 TAAGGAC-TTTACACTAGGAACCAAAGTGTGGTC -s Anc2.Anc2refChr0 39568 33 - 56053 TAAGGAC-TTTACACTAGGAATCAAAGTGTGGTC -s mr.mrrefChr0 42856 34 + 130230 GAGGGACCTTTGCACTGGGAACCAAAGTGTGGTC -s simCow_chr6.simCow.chr6 581901 33 - 602619 TAAGGAA-TTTGCACCAGGAATCAAAGTGTGGTC -s simDog_chr6.simDog.chr6 577350 33 - 593897 TAGGAAC-TTTACACTACAAATCAAAGTGTGGTA -s simHuman_chr6.simHuman.chr6 583800 33 - 601863 TAATGAC-TCTACACTAGGAACCAAAGTGTGGTC -s simHuman_chr6.simHuman.chr6 155581 33 - 601863 CGGCGAC-TTTGCACTAGGAACCAATGTATAGTC -s simRat_chr6.simRat.chr6 37640 34 + 647215 GAGGGACCTTTGCACTGGGAACCAGAGTATGGTC - -a -s simMouse_chr6.simMouse.chr6 45119 74 + 636262 CTCCCAATTATTAATAGTGATGCATGCCTGGAAGTCAATGCATTACAGAATCATATAATGATCCTCAATAGCAA -s Anc0.Anc0refChr9 19668 72 + 35212 CACCTAAT-ATTTGCAGTGATACCTACCTCGGAGACATTACATTACAGAGACATGTA-ATGATCACAATAGGGA -s Anc1.Anc1refChr2 144126 72 - 144309 CACCTAAT-ATTTGCAGTGATACCTACCTCGGAGACATTACATTACAGAGACATGTA-ATGATCACAATAGGGA -s Anc2.Anc2refChr0 39601 72 - 56053 CACCTAAT-GTTTGCAGTGATACCTACCTCGGAGACATTACATTACAGAGACATGTA-ATGATCACAATAGGGA -s mr.mrrefChr0 42890 72 + 130230 CTCCCAAT-ATTTATAGTGATGCATGCCTGGGAGTCAATGCATTACAGAATCATATA-TGATCTTCAATAGGGA -s simCow_chr6.simCow.chr6 582075 72 - 602619 TACCTAAT-GTTTGCAGTGATGCCACCTTTGTAGACATTACATTAAAAAGTCTTGTA-ATGGTCACGATAGAGA -s simDog_chr6.simDog.chr6 577383 72 - 593897 CACCTAAT-GTTTGCAGTGATACCTACCTCGAAGACATTACATTACAGAGACATGCA-ATGATCACAATAGGTA -s simHuman_chr6.simHuman.chr6 583833 72 - 601863 CGCCTAAT-ATCTCCAGCAATACTTACATCAGAAATGTTACATTACAGAGTCATATA-GGGAGTTCAATAGGGA -s simHuman_chr6.simHuman.chr6 155614 71 - 601863 CACTGAAT-ATTTGCAG-GGTACCTACCTGAGAGACATTACATTTCAGTGACATGTA-ATGATCACAATAGGGG -s simRat_chr6.simRat.chr6 37674 72 + 647215 CTCCCAAT-ATTTAGAGTGATGCATGCCTGGGGGTCAATGCACTACAGAATCATATA-TGATCTTCAATAGGGA - -a -s simMouse_chr6.simMouse.chr6 45193 37 + 636262 TTAGATGTAATATTGGCACAGTCACAGCATCCAGCAT -s Anc0.Anc0refChr9 19740 23 + 35212 TTAGAAGTAAGATCATTGCA-----------CAA--- -s Anc1.Anc1refChr2 144198 26 - 144309 TTAGAAGTAAGATCATTGCA-----------CAATAT -s Anc2.Anc2refChr0 39673 23 - 56053 TTAGAAGTAAGATCATTGCA-----------TAA--- -s mr.mrrefChr0 42962 26 + 130230 TTAGATGTAATATTGTTGCA-----------CAGCAT -s simCow_chr6.simCow.chr6 582147 21 - 602619 TTAGACGTAAGATCATTGCA-----------T----- -s simDog_chr6.simDog.chr6 577455 23 - 593897 CTAGAAGTAAGATCATTGCA-----------TAA--- -s simHuman_chr6.simHuman.chr6 583905 26 - 601863 TTAGAAGTAAGATCATTGCA-----------CACTGT -s simHuman_chr6.simHuman.chr6 155685 26 - 601863 TCAGTAGTTAGATCATTGCA-----------CAATAT -s simRat_chr6.simRat.chr6 37755 26 + 647215 TTAGATGTAATATTGTTGCA-----------CAGCAT - -a -s simMouse_chr6.simMouse.chr6 45230 27 + 636262 CCACTGAAGAGGTAACTGATTGCACTA -s Anc0.Anc0refChr9 19763 27 + 35212 CCACCGCAGAGGTAACTGCTTGTACTA -s Anc1.Anc1refChr2 144224 27 - 144309 CCACCGCAGAGGTAACTGCTTGTACTA -s Anc2.Anc2refChr0 39696 27 - 56053 CCACCGCAGATGTAGCCCCTTGTACTA -s mr.mrrefChr0 42988 27 + 130230 CCACTGAAGAGGTAACTGGTTGTACTA -s simCow_chr6.simCow.chr6 582168 27 - 602619 TCACTGCAGGTGTAGCCCCTTGTACTG -s simDog_chr6.simDog.chr6 577481 27 - 593897 CCACCGCAGATGTAGCCCCCTGTACTA -s simHuman_chr6.simHuman.chr6 583931 17 - 601863 ----------GGCCACTTGTTATGCTA -s simHuman_chr6.simHuman.chr6 155711 14 - 601863 ----------AG---CTGCTTGTACTA -s simRat_chr6.simRat.chr6 37781 27 + 647215 CCACTGAAGATGTAACTGGTTGTACTA - -a -s simMouse_chr6.simMouse.chr6 45257 53 + 636262 CACATGACATTAGAGGACCATTGCTTATGCAGAGATCTTATGGTCCACTACCC -s Anc0.Anc0refChr9 19795 43 + 35212 CA--TT--------GGACCATGGCTTACTAAATGATCTGGTTTTTCACTAGCT -s Anc1.Anc1refChr2 144256 43 - 144309 CA--TT--------GGACCATGGCTTACTAAATGATCTGGTTTTTCACTAGCT -s Anc2.Anc2refChr0 39728 43 - 56053 CC--TT--------GGACAATGGCTTACTAAATGGTCTGGCTTCTCACTAGCT -s mr.mrrefChr0 43015 51 + 130230 CA--TGACATTAGAGGACCATTGCTTATGCAAAGATCTTATGGTCCACTACCC -s simCow_chr6.simCow.chr6 582200 43 - 602619 TC--TT--------GGCCAATGGCTTACTAAATTGTTTGGCTTCTCACTAGCT -s simDog_chr6.simDog.chr6 577513 43 - 593897 CC--TT--------GGTCAACAGCTTACTAAATGGCCTGACTTCTCACTAGCT -s simHuman_chr6.simHuman.chr6 583948 43 - 601863 CA--TT--------GGACCATGGCTTACTAAATGATTTGGTATTTGACTAGCT -s simHuman_chr6.simHuman.chr6 155730 43 - 601863 CA--TT--------GCACCATGGCTTACCATATGATCTGGTCTTTCAATAAAG -s simRat_chr6.simRat.chr6 37808 51 + 647215 TA--TGACATCGGAGGACCATTGCTTATGCAAAGATCTTATGATCCACTACCC - -a -s simMouse_chr6.simMouse.chr6 45310 3 + 636262 TGT -s Anc0.Anc0refChr9 19845 2 + 35212 TG- -s Anc1.Anc1refChr2 144306 3 - 144309 TGT -s Anc2.Anc2refChr0 39778 2 - 56053 TG- -s mr.mrrefChr0 43066 3 + 130230 TGT -s simCow_chr6.simCow.chr6 582250 2 - 602619 TG- -s simDog_chr6.simDog.chr6 577563 2 - 593897 TG- -s simHuman_chr6.simHuman.chr6 583998 3 - 601863 TGC -s simHuman_chr6.simHuman.chr6 155780 3 - 601863 CGT -s simRat_chr6.simRat.chr6 37859 3 + 647215 TGT - -a -s simMouse_chr6.simMouse.chr6 45313 33 + 636262 TGATTTAGATTTGACTGACTATGATGCAGATAG -s Anc0.Anc0refChr9 19847 25 + 35212 --ATTCTGATTTGA------ATAATTTAAGTTG -s Anc1.Anc1refChr0 0 27 - 16026 TGATTCTGATTTGA------ATAATTTAAGTTG -s Anc2.Anc2refChr0 39783 25 - 56053 --ATGCTAATTTCA------GTAATTTAAGCTG -s mr.mrrefChr0 43069 33 + 130230 TGATTTAGATTTGACTGACTATGATGCAGGTAG -s simCow_chr6.simCow.chr6 582255 25 - 602619 --ATGTAGATTTAA------ATAATTTAAGCTG -s simDog_chr6.simDog.chr6 577565 23 - 593897 ----GCTAATTCCA------GTAACTTAAGCTG -s simHuman_chr6.simHuman.chr6 584001 27 - 601863 TGATTCGGGTTTGA------AAAATATAAGTTG -s simRat_chr6.simRat.chr6 37862 33 + 647215 TGGTTTAGATTTGACTGACTACGATGCATGTAG - -a -s simMouse_chr6.simMouse.chr6 45346 35 + 636262 TGTCTAGCAGTCCTAAGTCAACACATGGATACGTG -s Anc0.Anc0refChr9 19872 35 + 35212 TTTCTAGCAATGCTAAGTTGATGCGTGAGTGTGTG -s Anc1.Anc1refChr0 27 35 - 16026 TTTCTAGCAATGCTAAGTTGATGCGTGAGTGTGTG -s Anc2.Anc2refChr0 39815 35 - 56053 TTTCTAGCAATGTTAAGTTGATGCGTGAGCATGTG -s mr.mrrefChr0 43102 35 + 130230 TGTCTAGCAGTCCTAAGTCAACACATGGGTGTGTG -s simCow_chr6.simCow.chr6 582287 35 - 602619 TTTCTAGCAATCTTAAGTTGATGTGTGTTCATGCC -s simDog_chr6.simDog.chr6 577595 35 - 593897 TTTCTAGCAATGTTAGCTGGATGCATAAGCATGTG -s simHuman_chr6.simHuman.chr6 584028 32 - 601863 ---CAAGCAATTCTAAGATGATGGGAGAGTGTGTG -s simRat_chr6.simRat.chr6 37895 35 + 647215 CGCCTAGCATTCCCAAGTCAACTCATGGGTGTGTG - -a -s simMouse_chr6.simMouse.chr6 45381 8 + 636262 TAAACTAA -s Anc0.Anc0refChr9 19907 8 + 35212 TAAATTAA -s Anc1.Anc1refChr0 62 8 - 16026 TAAATTAA -s Anc2.Anc2refChr0 39854 8 - 56053 TAACTTAA -s mr.mrrefChr0 43137 8 + 130230 TAAACTAA -s simCow_chr6.simCow.chr6 582326 8 - 602619 TAGGGTAA -s simDog_chr6.simDog.chr6 577634 8 - 593897 TAACTTAA -s simHuman_chr6.simHuman.chr6 584060 8 - 601863 TAAATTGA -s simRat_chr6.simRat.chr6 37930 8 + 647215 TAAACTAA - -a -s simMouse_chr6.simMouse.chr6 45389 15 + 636262 TTGTTCTTTGGGTCC -s Anc0.Anc0refChr9 19922 15 + 35212 TCAATCTCTAGGGCT -s Anc1.Anc1refChr0 77 15 - 16026 TCAATCTCTAGGGCT -s Anc2.Anc2refChr0 39869 15 - 56053 CCAATCTCTAGTGCT -s mr.mrrefChr0 43145 15 + 130230 TTGTTCTTTAGGTCC -s simCow_chr6.simCow.chr6 582341 15 - 602619 GCAATCTTTAGTGCT -s simDog_chr6.simDog.chr6 577649 15 - 593897 CCATTCTCTAGTACT -s simHuman_chr6.simHuman.chr6 584075 15 - 601863 TCAATCTCTAGGGCT -s simRat_chr6.simRat.chr6 37938 15 + 647215 TTGTCCTGCAGGTCC - -a -s simMouse_chr6.simMouse.chr6 45404 56 + 636262 CTTGCATTCAGGCAATCACATGCCACACAATGGAGATGGCTGTAATGGGTGGAGAC -s Anc0.Anc0refChr9 19937 56 + 35212 CATGCATATAGGAAATCACATGAATCACAACAGTGATTGCCACAATGGCTGGAGAC -s Anc1.Anc1refChr0 92 56 - 16026 CATGCATATAGGAAATCACATGAATCACAACAGTGATTGCCACAATGGCTGGAGAC -s Anc2.Anc2refChr0 39884 56 - 56053 CATGCATATAGGACATCACATGAATCACAACAGTGATTGCCACAATGGCTGGAGAC -s mr.mrrefChr0 43160 56 + 130230 CTTGCATTCAGGCAATCACATGCCACACAATGGAGATGGCTGTAATGGGTGGAGAC -s simCow_chr6.simCow.chr6 582369 56 - 602619 CATTCATATAGTACATTACATGAATCACAACAGTAATTGCCACAATGGCTGGAGAC -s simDog_chr6.simDog.chr6 577664 56 - 593897 CCTGTATATAGGACATCACATGAATCATAACAGCGATTTTCACAATGGCTGGAGAT -s simHuman_chr6.simHuman.chr6 584090 56 - 601863 CATGCATATAGGAAATCAAATGAACCACAACAGTGATTGCCACAATGGCAGGAGAC -s simRat_chr6.simRat.chr6 37953 52 + 647215 CTTGCATTCAGGTAATCACATACCACACA---GAGATGGCTGTA-TGGATGGAGAC - -a -s simMouse_chr6.simMouse.chr6 45460 93 + 636262 TATGTGGCACTTGATGAAGATACATCAGCTTTAAGAAGAGGACAGCTGATCAGCAGTCTTTGTAACTAATGATGAACAAGCCTTGTGGTGCGG -s Anc0.Anc0refChr9 19993 88 + 35212 TA--TGGCATTTGATGAAGACACATAGGGTGTAAGAAAACTACAGC--A-CAGCAGACTTTGTAACTACTGATCAGCAAACCTTGTGGTGACA -s Anc1.Anc1refChr0 148 88 - 16026 TA--TGGCATTTGATGAAGACACATAGGGTGTAAGAAAACTACAGC--A-CAGCAGACTTTGTAACTACTGATCAGCAAACCTTGTGGTGACA -s Anc2.Anc2refChr0 39940 88 - 56053 TA--GGGCATTTGATGAAGTCACATAGGGTGTAAGAAAACTACCGA--T-CAGCAGACTTTGTAACTACTGCTCAGCAAACTTTGTGGTGACA -s mr.mrrefChr0 43216 92 + 130230 TATGTGGCACTTGATGAAGACACATCAGCTTTAAGAAGAGGACAGCTGA-CAGCAGTCTTTGTAACTAATGATGAACAAGCCTTGTGGTGAGG -s simCow_chr6.simCow.chr6 582427 88 - 602619 CA--GGGCATTTGACGAAGCCACATAGGGTGAAAGAACACTACTGA--C-CAGCAGACTTTGTAACTACTGGTCAGCAATCTTTGTGGCCCCA -s simDog_chr6.simDog.chr6 577720 85 - 593897 TA--GGAC--TTGATGAAGTCACATAGGGTGTAAGA-AACTCCCGA--T-CTGCAGCCTTTGTAACTACTGCTTAGCAAACTTTGGGGTGACA -s simHuman_chr6.simHuman.chr6 584146 88 - 601863 TA--TGGCATCCTATGAAGACACATTGGGTATATGAGAACTACAGC--A-CAGCATACTTTGTAACTACTAAACAGCAAACCTTGTGGTGACA -s simRat_chr6.simRat.chr6 38005 92 + 647215 TATGTGGTACTTGAAGAAGACACATCAGCTTCAAGAATAGCACAGCTGA-CAGCAGTCTTTTTACCTAATGATAAACAAGCCTGGTGGTGAAG - -a -s simMouse_chr6.simMouse.chr6 45553 26 + 636262 CTAGGCCCTATCCTGCCAAACTAGTG -s Anc0.Anc0refChr9 20081 26 + 35212 CCAGGCTCTATCCTGACAGACTAGTG -s Anc1.Anc1refChr0 236 26 - 16026 CCAGGCTCTATCCTGACAGACTAGTG -s Anc2.Anc2refChr0 40028 26 - 56053 CCAGGCTCTATCCTGACAGACTAGTG -s mr.mrrefChr0 43308 26 + 130230 CCAGGCCCTATCCTGACAAACTAGTG -s simCow_chr6.simCow.chr6 582516 26 - 602619 CCAGGATCTATCCTGACAGAGCAATG -s simDog_chr6.simDog.chr6 577805 26 - 593897 CCAGGCTCTATTATGAGAGACTAGCG -s simHuman_chr6.simHuman.chr6 584234 26 - 601863 CCCGGCTCTATCCTGACAGTTTAGTG -s simRat_chr6.simRat.chr6 38097 26 + 647215 CCAGGCCCTATCCTGACAAACTGGTG - -a -s simMouse_chr6.simMouse.chr6 45579 21 + 636262 TTCCCACTAAACTCACTATGG -s Anc0.Anc0refChr9 20110 21 + 35212 TTCCCACTACACTCACAACAG -s Anc1.Anc1refChr0 265 21 - 16026 TTCCCACTACACTCACAACAG -s Anc2.Anc2refChr0 40057 21 - 56053 TTTCCACTACACTCACAACAG -s mr.mrrefChr0 43334 21 + 130230 TTCCCACTAAACTCACAACAG -s simCow_chr6.simCow.chr6 582545 21 - 602619 TTTCCACTACCCTCACCACAA -s simDog_chr6.simDog.chr6 577834 21 - 593897 TTTCCACTACACTCACAACAG -s simHuman_chr6.simHuman.chr6 584263 21 - 601863 TTCCAACTACACTCACAACAG -s simRat_chr6.simRat.chr6 38123 21 + 647215 TTCCCACTAAACTCATACCAG - -a -s simMouse_chr6.simMouse.chr6 45600 10 + 636262 GATGGTGGGA -s Anc0.Anc0refChr9 20131 9 + 35212 GAC-ATTCAA -s Anc1.Anc1refChr0 286 9 - 16026 GAC-ATTCAA -s Anc2.Anc2refChr0 40078 9 - 56053 GAC-ACTCAA -s mr.mrrefChr0 43355 10 + 130230 GATGATTGGA -s simCow_chr6.simCow.chr6 582566 9 - 602619 GAC-GCTAAA -s simDog_chr6.simDog.chr6 577855 9 - 593897 GAT-ACTCAA -s simHuman_chr6.simHuman.chr6 584284 9 - 601863 GAC-ATTTAA -s simRat_chr6.simRat.chr6 38152 10 + 647215 GATGATTGGA - -a -s simMouse_chr6.simMouse.chr6 45610 53 + 636262 CAATGATGACTGTTGAGGCCTGGCCTACTTGCTATTACCAGTTTGTTTCTGTC -s Anc0.Anc0refChr9 20140 34 + 35212 CAATAAAGACCTGTGAAGCCT-----ACTTGTTATTGC--------------C -s Anc1.Anc1refChr0 295 34 - 16026 CAATAAAGACCTGTGAAGCCT-----ACTTGTTATTGC--------------C -s Anc2.Anc2refChr0 40087 34 - 56053 CAATAAAGACCTGTGAAGCCT-----AGTTGTTATTGC--------------C -s mr.mrrefChr0 43365 45 + 130230 CAATAATGACTGTTGAGGCCT-----ACTTGCTATTACCAGTTTGTT---GTC -s simCow_chr6.simCow.chr6 582575 34 - 602619 CAATAGAGGCCTATGAAACCT-----ATTTGTTATTTA--------------C -s simDog_chr6.simDog.chr6 577867 34 - 593897 TAACAAAGACCTGTGAAGACT-----AGTTGTTATTGC--------------C -s simHuman_chr6.simHuman.chr6 584293 34 - 601863 CAGTAAAGACCAGTGAAGCCT-----ACTTGTTATTGC--------------T -s simRat_chr6.simRat.chr6 38162 42 + 647215 CAATAATGACTGTTGAGGCCT-----ATATACCATTATCAGTTAGTT------ - -a -s simMouse_chr6.simMouse.chr6 45663 32 + 636262 GGCTCTGTTGGGAAAGCCAACAATTAATCCAC -s Anc0.Anc0refChr9 20174 31 + 35212 GGTTCTGTTGG-AGAGCCAACAATTGATCCAA -s Anc1.Anc1refChr0 329 32 - 16026 GGTTCTGTTGGAAGAGCCAACAATTGATCCAA -s Anc2.Anc2refChr0 40121 31 - 56053 AGTTCTGTTGG-AGAGCCAACAATTGATCCAA -s mr.mrrefChr0 43410 32 + 130230 GGCTCTGTTGGGAAAGCCAACAATTGATCCAC -s simCow_chr6.simCow.chr6 582609 31 - 602619 AGTTTGTTGGG-AGAGCCGATGATTGCTCCAA -s simDog_chr6.simDog.chr6 577901 31 - 593897 AGCTCTGTTGG-AAAGCCAACATTCGATCTAA -s simHuman_chr6.simHuman.chr6 584327 32 - 601863 GGTTCTGCCAGAAGAGCCCACAATTGGTCCAA -s simRat_chr6.simRat.chr6 38379 32 + 647215 AGAACTGTTGGGAAAGCCATCGATTGATATAC - -a -s simMouse_chr6.simMouse.chr6 45695 7 + 636262 AGCTAAG -s Anc0.Anc0refChr9 20206 7 + 35212 GGCAAAA -s Anc1.Anc1refChr0 362 7 - 16026 GGCAAAA -s Anc2.Anc2refChr0 40153 7 - 56053 GGCAAAA -s mr.mrrefChr0 43442 7 + 130230 AGCTAAG -s simCow_chr6.simCow.chr6 582641 7 - 602619 GGCAAAA -s simDog_chr6.simDog.chr6 577933 7 - 593897 GGCAACA -s simHuman_chr6.simHuman.chr6 584360 7 - 601863 GGCAAAT -s simRat_chr6.simRat.chr6 38411 7 + 647215 AGCTAAG - -a -s simMouse_chr6.simMouse.chr6 45702 22 + 636262 TAAACAAATGGCAATTAGGAAC -s Anc0.Anc0refChr9 20213 22 + 35212 TAAATACAGGGCAATTAGGAGC -s Anc1.Anc1refChr0 369 22 - 16026 TAAATACAGGGCAATTAGGAGC -s Anc2.Anc2refChr0 40160 22 - 56053 TAAATACAGGGCAATTAGGAGT -s mr.mrrefChr0 43449 22 + 130230 TAAACAAATGGCAATTAGGAGC -s simCow_chr6.simCow.chr6 582648 22 - 602619 TGAATACAGGGCAAATATGAGA -s simDog_chr6.simDog.chr6 577947 22 - 593897 CAAATACAGGGCAATTGGGAGT -s simHuman_chr6.simHuman.chr6 584367 22 - 601863 TAAATACAGGGCAATTAGGGGC -s simRat_chr6.simRat.chr6 38418 22 + 647215 TAAACAAATGGCAATTGGGAGC - -a -s simMouse_chr6.simMouse.chr6 45724 22 + 636262 ATAGCTTCAAATGCTAGAATGG -s Anc0.Anc0refChr9 20235 18 + 35212 A----TTCAAATGCTAGGGTGG -s Anc1.Anc1refChr0 391 22 - 16026 ATAGCTTCAAATGCTAGGGTGG -s Anc2.Anc2refChr0 40182 18 - 56053 A----TTCAAATGCTAGGGTGG -s mr.mrrefChr0 43471 22 + 130230 ATAGCTTCAAATGCTAGAATGG -s simCow_chr6.simCow.chr6 582674 18 - 602619 A----TTCAGATACTAGGGTGG -s simDog_chr6.simDog.chr6 577969 18 - 593897 T----TTCAAATGCTAGGGTGG -s simHuman_chr6.simHuman.chr6 584389 21 - 601863 ATAGCTTAAAA-TCTAGGGTGG -s simRat_chr6.simRat.chr6 38440 22 + 647215 ATAGCTTCAAATGCTAGAATGG - -a -s simMouse_chr6.simMouse.chr6 45746 2 + 636262 TC -s Anc0.Anc0refChr9 20257 2 + 35212 TC -s Anc1.Anc1refChr0 417 2 - 16026 TC -s Anc2.Anc2refChr0 40204 2 - 56053 CC -s mr.mrrefChr0 43497 2 + 130230 TC -s simCow_chr6.simCow.chr6 582696 2 - 602619 CC -s simDog_chr6.simDog.chr6 577992 2 - 593897 CC -s simHuman_chr6.simHuman.chr6 584414 2 - 601863 TC -s simRat_chr6.simRat.chr6 38466 2 + 647215 TC - -a -s simMouse_chr6.simMouse.chr6 45748 15 + 636262 TGTAGGTTACAGGGC -s Anc0.Anc0refChr9 20259 11 + 35212 TG----TTACAAGCC -s Anc1.Anc1refChr0 419 15 - 16026 TGTATATTACAAGCC -s Anc2.Anc2refChr0 40206 11 - 56053 TG----TTACAAGCC -s mr.mrrefChr0 43499 15 + 130230 TGTATGTTACAGGGC -s simCow_chr6.simCow.chr6 582698 11 - 602619 TG----TTACACGCC -s simDog_chr6.simDog.chr6 577997 11 - 593897 TG----CTACAAACC -s simHuman_chr6.simHuman.chr6 584416 15 - 601863 TGTATATCCCAAGCC -s simRat_chr6.simRat.chr6 38468 15 + 647215 TGTATGTTACAGGGC - -a -s simMouse_chr6.simMouse.chr6 45763 93 + 636262 CCATATTGTCTTGTGTAATGACCCAAGGTCTGTAATGACCCAAGGTATGTGCTACATATGCCATGCCACCATGTCCTATGTTCTGCACACCCC -s Anc0.Anc0refChr9 20270 70 + 35212 CCAAGTTG----------------------TGTGATCACCCCATGGTTGGGCTACATATGCCATTAAACCATGTCCTATATCCTACAC-TCCC -s Anc1.Anc1refChr0 434 70 - 16026 CCAAGTTG----------------------TGTGATCACCCCATGGTTGGGCTACATATGCCATTAAACCATGTCCTATATCCTACAC-TCCC -s Anc2.Anc2refChr0 40217 70 - 56053 CCAAGTTG----------------------TGTGATCACCCCATGGTTGGGCTACATATGCAATTAAACCATGTCCTATATTCCACAC-TCCC -s mr.mrrefChr0 43514 93 + 130230 CCATATTGTCTTGTGTAATGACCCAAGGTCTGTAATGACCCAAGGTATGTGCTACATATGCCATGCCACCATGTCCTATATCCTGCACACCCC -s simCow_chr6.simCow.chr6 582709 69 - 602619 CCATG-TG----------------------TGTAATTACCCCATGGTTGGGCTACATATGCAATTAAGCCATGTCCTATATTTCGCGC-TCCC -s simDog_chr6.simDog.chr6 578010 68 - 593897 CCAAGT------------------------TATGATCACCTCATGGTTGGGCTCCATGTGCAGTTAAACCATATCCTTCATTCCACAC-TTCC -s simHuman_chr6.simHuman.chr6 584431 70 - 601863 CTGAGTTG----------------------TGTGGTCACCCCATGCTTGGGCTATATATGCCATTAAACCATGTCCTATATCCTACAC-TCTG -s simRat_chr6.simRat.chr6 38483 76 + 647215 CCATTTTGTGTTGTATAATGACCCAAGGCT-----------------TTTGCTACATATGCCATGCCACCATGGCCTATATCCTGCACACCCC - -a -s simMouse_chr6.simMouse.chr6 45856 20 + 636262 CCCTAGAATAGTATTCTAGA -s Anc0.Anc0refChr9 20340 20 + 35212 CTCTAATACAGCATTATATG -s Anc1.Anc1refChr0 504 20 - 16026 CTCTAATACAGCATTATATG -s Anc2.Anc2refChr0 40289 20 - 56053 CTCTAATACAGCATTATATG -s mr.mrrefChr0 43607 20 + 130230 CCCTAGAACAGTATTCTAGA -s simCow_chr6.simCow.chr6 582780 20 - 602619 TACTACTACAACATTATATG -s simDog_chr6.simDog.chr6 578080 18 - 593897 CTCTAATA--GAATTATATG -s simHuman_chr6.simHuman.chr6 584501 20 - 601863 TACAATGACGGCATTATGTG -s simRat_chr6.simRat.chr6 38559 20 + 647215 CCCTAGAACAGTATTCTAGA - -a -s simMouse_chr6.simMouse.chr6 45876 3 + 636262 GCT -s Anc0.Anc0refChr9 20360 3 + 35212 GAT -s Anc1.Anc1refChr0 524 3 - 16026 GAT -s Anc2.Anc2refChr0 40309 3 - 56053 GAT -s mr.mrrefChr0 43627 3 + 130230 GCT -s simCow_chr6.simCow.chr6 582800 3 - 602619 GAT -s simDog_chr6.simDog.chr6 578099 3 - 593897 GCT -s simHuman_chr6.simHuman.chr6 584521 3 - 601863 GAT -s simRat_chr6.simRat.chr6 38579 3 + 647215 GCT - -a -s simMouse_chr6.simMouse.chr6 45879 1 + 636262 A -s Anc0.Anc0refChr9 20364 1 + 35212 A -s Anc1.Anc1refChr0 528 1 - 16026 A -s Anc2.Anc2refChr0 40313 1 - 56053 A -s mr.mrrefChr0 43630 1 + 130230 A -s simCow_chr6.simCow.chr6 582804 1 - 602619 A -s simDog_chr6.simDog.chr6 578103 1 - 593897 A -s simHuman_chr6.simHuman.chr6 584525 1 - 601863 A -s simRat_chr6.simRat.chr6 38582 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 45880 39 + 636262 GAGTTCTTAGTTTTATCCTTACTGTCACCTAGCTAGTTA -s Anc0.Anc0refChr9 20365 39 + 35212 GAGCTCTTAATTTTTCCCTTACTGTCTTCTAGTTAGTTG -s Anc1.Anc1refChr0 529 39 - 16026 GAGCTCTTAATTTTTCCCTTACTGTCTTCTAGTTAGTTG -s Anc2.Anc2refChr0 40314 39 - 56053 GAGCTCTTACTTTTTCCCTTACTGTCTTCTAGTTAGTTG -s mr.mrrefChr0 43631 39 + 130230 GAGCTCTTAATTTTATCCTTACTGTCATCTAGCTAGTTA -s simCow_chr6.simCow.chr6 582805 39 - 602619 GAGCTCTTACTTCTTCCCTTACTGCCTTCCAGTTAGCTG -s simDog_chr6.simDog.chr6 578104 39 - 593897 GAACTCTTACTTTTTTCCATACTGTCTTCTAGTTAGTTG -s simHuman_chr6.simHuman.chr6 584526 39 - 601863 GAGCTCTTAATTTTTCCCTTAGTGTCTTCTAGTTAGTTG -s simRat_chr6.simRat.chr6 38599 39 + 647215 GAGCTCTTAATTTTATCCTTACTGGCATCTAGCTAGTCA - -a -s simMouse_chr6.simMouse.chr6 45919 1 + 636262 T -s Anc0.Anc0refChr9 20404 1 + 35212 G -s Anc1.Anc1refChr0 568 1 - 16026 G -s Anc2.Anc2refChr0 40371 1 - 56053 G -s mr.mrrefChr0 43670 1 + 130230 G -s simCow_chr6.simCow.chr6 582862 1 - 602619 A -s simDog_chr6.simDog.chr6 578161 1 - 593897 G -s simHuman_chr6.simHuman.chr6 584565 1 - 601863 G -s simRat_chr6.simRat.chr6 38638 1 + 647215 G - -a -s simMouse_chr6.simMouse.chr6 45920 34 + 636262 ATTGCTCAGTTTTATTAGCCATACACAATCTGAG -s Anc1.Anc1refChr0 623 34 - 16026 ATACTGCAGTCTGAATAAACTTGCACAGTTTGTC -s mr.mrrefChr0 43725 34 + 130230 ATTGTTCAGTCTTAATAACCTTGCACAATCTGAC -s simHuman_chr6.simHuman.chr6 584623 34 - 601863 ATACTGCAGTCTGAATAAACTTGCACAGTTTGTC -s simRat_chr6.simRat.chr6 38702 34 + 647215 ATGGTATAGTCTTAACAATCTTGCACCATCTGAC - -a -s simMouse_chr6.simMouse.chr6 45954 143 + 636262 CCAGGCTGAACATCCCCTAGTACAACCCATTGGAGTGGTGTGAATGTGTCATGTGGGGTGAATCTGCTATGTGTGTTTGTTTACTCGCTGGCAAATGGATAGTGTGTTACGTAGGCAATACCTATGGACATGACTGATATCCA -s Anc0.Anc0refChr9 20455 17 + 35212 ------------------------------------------------------------------------------------------------------------------------------GATGTGACAGATATCCA -s Anc1.Anc1refChr0 657 115 - 16026 TAAAGTCAAACATACCCTAGTACAGTATATGAAAGTGGTATAGGTGTGGTATGCGCAG-G-------------------------CTCCAACAAATAGATG--ACATTAGGGAGCAGATATCTACTGATGTGACAGATATCCA -s Anc2.Anc2refChr0 40422 17 - 56053 ------------------------------------------------------------------------------------------------------------------------------GATGTGACAGATATCCA -s mr.mrrefChr0 43759 132 + 130230 TCAGGCTGAACATCCCCTAGTACAACCTATTGGAGTGGTGTGAATGTGTTATGTGGGG-GAATCTGCTATGTG--------TACTCTCTAGCAAATGGATA--GTGTTAGGTAGCCAATACCTATGGACGTGACTGATATCCA -s simCow_chr6.simCow.chr6 582917 17 - 602619 ------------------------------------------------------------------------------------------------------------------------------GATGTGACAGATATCCA -s simHuman_chr6.simHuman.chr6 584663 115 - 601863 TAAAGTCAAACATACCCTAGTACAGTATATGAAAGTGGTATAGGTGTGGTATGCGCAG-G-------------------------CTCCAACAAATAGATG--ACATTAGGGAGCAGATATCTACTGATGTGACAGATATCTA -s simRat_chr6.simRat.chr6 38736 132 + 647215 TGAGGCTGAATATCCCCTAGCACAACCTATTGGAGTGGTGTGAATGTGTTATGTGGTG-GAATCTGTTATGTG--------TACCCTGTAGTGAGTGGATA--GTGTTAGATAGCCAATACATATGGGCGTGACTGATATCCA - -a -s simMouse_chr6.simMouse.chr6 46097 29 + 636262 TGAAGTTAAAATAAATATAGGATGATTGG -s Anc0.Anc0refChr9 20474 18 + 35212 GAAAGCT-----------ATGATGATTGG -s Anc1.Anc1refChr0 774 29 - 16026 GAAAGCTACAGGGGATGCATGATGATTGG -s Anc2.Anc2refChr0 40441 18 - 56053 TAAAGCT-----------ATGATGAGTGT -s mr.mrrefChr0 43891 29 + 130230 GAAAGCTAAAATAAATATAGGATGATTGG -s simCow_chr6.simCow.chr6 582936 18 - 602619 TAAAGCT-----------ATGATGAGTGT -s simHuman_chr6.simHuman.chr6 584780 29 - 601863 GAAAGCTCCAGGGGATGCATCATGATTGG -s simRat_chr6.simRat.chr6 38868 29 + 647215 GAAAGCTAAAATAAATATAGAAAGATTGG - -a -s simMouse_chr6.simMouse.chr6 46126 141 + 636262 TAGGAACCAAGTTTTAGAGCCGTCTTAAGGTCCCTGAAGCATAGCAAACCAACAGCTGCTAATTGCAGCCTTAGGACTCCTCCCCATCAAGACTCCATCTGCAAGTTGCATGAGTACTCTGGTGGAAGTGTTGTGTGGCTT -s Anc0.Anc0refChr9 20494 125 + 35212 ----------------GAGCCGTCATAACATCCATAAGGAATAGCAAAGCAATGGCTGCTAATTGCAGTCCTAGGACTCCTCCCCATCAAAACTTCATCTGCAGGATGCATGGGTACCAAGGCCAAAGTGTTATATGGCCC -s Anc1.Anc1refChr0 805 141 - 16026 CAGGAACTTAGCTCATGAGCCGTCATAACATCCATAAGGAATAGCAAAGCAATGGCTGCTAATTGCAGTCCTAGGACTCCTCCCCATCAAAACTTCATCTGCAGGATGCATGGGTACCAAGGCCAAAGTGTTATATGGCCC -s Anc2.Anc2refChr0 40461 125 - 56053 ----------------GAGTTATCATGACAATCATAAGGAATAGCAAAGAAATGGCTGCTAATTGCATTCCTAGGACTCCTCCCCATTACAACTTCACCTGCAGGATGCCCAGGTACAAAGGCCTAAGTGTCATATGGCCC -s mr.mrrefChr0 43920 141 + 130230 CAGGAACCAAGTTTTAGAGCCGTCTTAAGGTCCCTGAGGCATAGCAAAGCAACAGCTGCTAATTGCAGTCTTAGGACTCCTCCCCATCAAGACTCCATCTGCAAGTTGCATGAGTACCCTGGTGAAAGTGTTGTGTGGCTC -s simCow_chr6.simCow.chr6 582956 119 - 602619 -----------------AGTGAGCAGGACCATCATAAGGAATAGCAGAGAAATGGCTGCTAATTGTTATCCTAGGACTCATCCCTATTACAACTCCACCTGCAGGCTGCCCAGGTACAAGGGC-----TGTCATATGGCCA -s simDog_chr6.simDog.chr6 578205 124 - 593897 ----------------GAATTATCATGACAATC-TAAGGGATAGCAAAGAAACAGCTGCTAATCACATCCTTAGGACTCCTCCTCCTTACAACATCACCTGTAAGATGGCCAGGTACAAAGGCCTAAGTGTCATATGGACC -s simHuman_chr6.simHuman.chr6 584811 141 - 601863 CAGGAACTTAGCTCATGAGCCGTCATAACATCCATAAGGAATAGCAAAGCATTGGCTGCTAATTGCAGTCCTAGGACTCCTCTCCAGCAAAACTTCATCTGCTGGATGCATGGGTACCAAGGCCAAAGTGTTATATGGCGC -s simRat_chr6.simRat.chr6 38897 141 + 647215 CAGGAACCAAGTTTTAGAGCCATCTTAAGGTCCCTGAGACATGGCAAGGCAACAGCTGCTAACTGTAGTCATAGGACTCCTCCCCATCAAGACTCCAGCTGCAAGTAGCATGAGCGCCCTAGTGAGAGTGTTGTGTGGCAC - -a -s simMouse_chr6.simMouse.chr6 46267 12 + 636262 AGTATCAAACGG -s Anc0.Anc0refChr9 20620 12 + 35212 AACACCAAGAGG -s Anc1.Anc1refChr0 947 12 - 16026 AACACCAAGAGG -s Anc2.Anc2refChr0 40587 12 - 56053 AACACCAAGAGG -s mr.mrrefChr0 44061 12 + 130230 AGCATCAAAAGG -s simCow_chr6.simCow.chr6 583076 12 - 602619 AGGACCAAGAGG -s simDog_chr6.simDog.chr6 578330 12 - 593897 AACACCAAGAGG -s simHuman_chr6.simHuman.chr6 584953 12 - 601863 AACACCAAGAGA -s simRat_chr6.simRat.chr6 39038 12 + 647215 AGCATCAAAAAG - -a -s simMouse_chr6.simMouse.chr6 46279 64 + 636262 TAAGTAGTATAGTTCACCTTTTGCTAGACTTGTTTATGCATATTTAGAAAGCCTGATTTTTGTT -s Anc0.Anc0refChr9 20632 63 + 35212 TAGGCACCATAATTCACCTTTAGCTAGACCTGTTTATGCATATATATAAGG-TTGATTATTGCT -s Anc1.Anc1refChr0 959 63 - 16026 TAGGCACCATAATTCACCTTTAGCTAGACCTGTTTATGCATATATATAAGG-TTGATTATTGCT -s Anc2.Anc2refChr0 40599 63 - 56053 TAGGCACCATAATTCACCTTTAGCTAGCCCTTTTTATGCATACATAGAAGC-TTGATTATTGTA -s mr.mrrefChr0 44073 64 + 130230 TAGGTAGTATAATTCACCTTTTGCTAGACTTGTTTATGCATATTTATAAAGCTTGATTATTGCT -s simCow_chr6.simCow.chr6 583089 63 - 602619 TAGGCATTATAATTTACCTTTAGCTAGCCCTTTTTATGCATACATAAAAAC-TTGGTTATTGTA -s simDog_chr6.simDog.chr6 578342 49 - 593897 TAGGCACCATAATTCACCTTTAGCTTGCCC--------------TAGAAGC-TTGATTACAGTA -s simHuman_chr6.simHuman.chr6 584965 63 - 601863 TAGGCACCATAATTCAACTCTAGCTAGACCTGTTTATGCATATGTATAAGG-TTGATCATTTCT -s simRat_chr6.simRat.chr6 39050 64 + 647215 TAGGTAATATAATTCACCTTTTTCTAGACTTGTTTATGCATATTTATAAAACTTAATTACTACA - -a -s simMouse_chr6.simMouse.chr6 46343 13 + 636262 TATTGAGAGGATG -s Anc0.Anc0refChr9 20695 13 + 35212 CCTTAAGAGGGTG -s Anc1.Anc1refChr0 1022 13 - 16026 CCTTAAGAGGGTG -s Anc2.Anc2refChr0 40662 13 - 56053 CCTTAAGAGGGTA -s mr.mrrefChr0 44137 13 + 130230 TCTTGAGAGGATG -s simCow_chr6.simCow.chr6 583155 13 - 602619 CCTTAAGAGGGTA -s simDog_chr6.simDog.chr6 578391 13 - 593897 CTCTAAGAGGCTA -s simHuman_chr6.simHuman.chr6 585028 13 - 601863 GCTTAAGAGGGTG -s simRat_chr6.simRat.chr6 39114 13 + 647215 TCTTGAGAAGATG - -a -s simMouse_chr6.simMouse.chr6 46356 21 + 636262 TGTTCTTAACATATTTATATC -s Anc0.Anc0refChr9 20708 18 + 35212 TA---CAAACATGTTTAAAGC -s Anc1.Anc1refChr0 1035 18 - 16026 TA---CAAACATGTTTAAAGC -s Anc2.Anc2refChr0 40675 18 - 56053 CA---CAAACATGTTTAAAGC -s mr.mrrefChr0 44150 21 + 130230 TGTTCTTAACATGTTTATAGC -s simCow_chr6.simCow.chr6 583171 18 - 602619 CC---CAAACATGTTTAAAGC -s simDog_chr6.simDog.chr6 578404 11 - 593897 CA----------GCCTAAACA -s simHuman_chr6.simHuman.chr6 585041 18 - 601863 TA---AAAACATGTTTAAAGC -s simRat_chr6.simRat.chr6 39127 21 + 647215 TGTTCTTAACATGTTTATAGC - -a -s simMouse_chr6.simMouse.chr6 46377 10 + 636262 ACATAATAAT -s Anc0.Anc0refChr9 20732 10 + 35212 ACAAAAGAAA -s Anc1.Anc1refChr0 1059 10 - 16026 ACAAAAGAAA -s Anc2.Anc2refChr0 40699 10 - 56053 ACAAAAGAAA -s mr.mrrefChr0 44171 10 + 130230 ACAAAATAAT -s simCow_chr6.simCow.chr6 583195 10 - 602619 ACTAAAGGAA -s simDog_chr6.simDog.chr6 578421 10 - 593897 ACAAAAGAAA -s simHuman_chr6.simHuman.chr6 585065 10 - 601863 ATGAAAGAAA -s simRat_chr6.simRat.chr6 39148 10 + 647215 ACAAAATAAT - -a -s simMouse_chr6.simMouse.chr6 46387 15 + 636262 TTATTATTGATTTGG -s Anc0.Anc0refChr9 20742 15 + 35212 CTAAAAATGATCTGA -s Anc1.Anc1refChr0 1069 15 - 16026 CTAAAAATGATCTGA -s Anc2.Anc2refChr0 40710 15 - 56053 CTAAAAACAATCTGA -s mr.mrrefChr0 44181 15 + 130230 TTATAATTGATTTGG -s simCow_chr6.simCow.chr6 583206 15 - 602619 CTAAAAACAATCCAA -s simDog_chr6.simDog.chr6 578432 15 - 593897 CTAAAAACAATTTGA -s simHuman_chr6.simHuman.chr6 585075 15 - 601863 CTAGAAATGATCTGA -s simRat_chr6.simRat.chr6 39158 15 + 647215 TTAAAATTGATTTGG - -a -s simMouse_chr6.simMouse.chr6 46402 3 + 636262 AAC -s Anc0.Anc0refChr9 20757 3 + 35212 AGC -s Anc1.Anc1refChr0 1084 3 - 16026 AGC -s Anc2.Anc2refChr0 40725 3 - 56053 GGC -s mr.mrrefChr0 44196 3 + 130230 AAC -s simCow_chr6.simCow.chr6 583222 3 - 602619 GGC -s simDog_chr6.simDog.chr6 578447 3 - 593897 GGC -s simHuman_chr6.simHuman.chr6 585090 3 - 601863 AGC -s simRat_chr6.simRat.chr6 39173 3 + 647215 AAC - -a -s simMouse_chr6.simMouse.chr6 46405 23 + 636262 TTCTAGACTTCTCACTCCTACAA -s Anc0.Anc0refChr9 20760 23 + 35212 TTCTAAACTTGTTCTTTCTACAA -s Anc1.Anc1refChr0 1087 23 - 16026 TTCTAAACTTGTTCTTTCTACAA -s Anc2.Anc2refChr0 40728 23 - 56053 TTCTAAACTTGTTCTTTCTACAA -s mr.mrrefChr0 44199 23 + 130230 TTCTAAACTTCTCACTCCTACAA -s simCow_chr6.simCow.chr6 583225 17 - 602619 TTCTAA------TCTTTCTACAA -s simDog_chr6.simDog.chr6 578450 23 - 593897 TTCTAAACTTGTTCTTTCTACAA -s simHuman_chr6.simHuman.chr6 585093 23 - 601863 TTCTGAAGTTTTTCTTTCAACAA -s simRat_chr6.simRat.chr6 39177 23 + 647215 TTCTAAACTTCTCACTCCTGCAA - -a -s simMouse_chr6.simMouse.chr6 46428 37 + 636262 TGGTGCAGTGTGTAAAAGGCACTAGAGATTTTAGATG -s Anc0.Anc0refChr9 20783 36 + 35212 T-CCGCAGTGCGTAGGAGGTACCAGCAATCTTAGAGA -s Anc1.Anc1refChr0 1110 36 - 16026 T-CCGCAGTGCGTAGGAGGTACCAGCAATCTTAGAGA -s Anc2.Anc2refChr0 40752 36 - 56053 T-CCGCAGTGCATAGGAAGTACCAGCAATCTTGGAGA -s mr.mrrefChr0 44222 37 + 130230 TGGTGCAGTGCGTAGAAGGCACCAGAGATTTTAGAGG -s simCow_chr6.simCow.chr6 583243 36 - 602619 T-GAGCAGTGTATATAAAGTACCGGGAATCGTGAAAA -s simDog_chr6.simDog.chr6 578474 36 - 593897 T-CCACAGTGCATAGGAAGTACTAGCAATCTTGGAGA -s simHuman_chr6.simHuman.chr6 585116 36 - 601863 T-CCGTTGTGCGTTGGAGGTACCCGTAATCTTAGAGA -s simRat_chr6.simRat.chr6 39200 37 + 647215 TAGTGCAATGCGTAGAAGGCACCAGAGATTTTAGAGG - -a -s simMouse_chr6.simMouse.chr6 46465 26 + 636262 TAAGACAAAAAACCAATATTGCTAGA -s Anc0.Anc0refChr9 20819 10 + 35212 CAAAACC----------------AGA -s Anc1.Anc1refChr0 1146 10 - 16026 CAAAACC----------------AGA -s Anc2.Anc2refChr0 40788 10 - 56053 CCAAACC----------------AGA -s mr.mrrefChr0 44259 26 + 130230 CAAGACAAAAAACCAATATTGCTAGA -s simCow_chr6.simCow.chr6 583279 10 - 602619 CCAGACC----------------AGA -s simDog_chr6.simDog.chr6 578511 10 - 593897 CCAAACC----------------AGA -s simHuman_chr6.simHuman.chr6 585152 10 - 601863 CAAAATG----------------AGA -s simRat_chr6.simRat.chr6 39237 26 + 647215 CAAGACAAAACACTAATATTGCTAGA - -a -s simMouse_chr6.simMouse.chr6 46491 7 + 636262 TGTGAAA -s Anc0.Anc0refChr9 20831 7 + 35212 TGGGATA -s Anc1.Anc1refChr0 1158 7 - 16026 TGGGATA -s Anc2.Anc2refChr0 40846 7 - 56053 TGGGATA -s mr.mrrefChr0 44287 7 + 130230 TGTGATA -s simCow_chr6.simCow.chr6 583337 7 - 602619 TGAGAGA -s simDog_chr6.simDog.chr6 578571 7 - 593897 TGGGATA -s simHuman_chr6.simHuman.chr6 585164 3 - 601863 T----TG -s simRat_chr6.simRat.chr6 39265 7 + 647215 TGTGATA - -a -s simMouse_chr6.simMouse.chr6 46498 42 + 636262 TATTCACAATGTGAACATAGACTTTATTGCCTATGTTAACCT -s Anc0.Anc0refChr9 20838 41 + 35212 TA-TTACAATTTGAACAAAGCCTGCAGCGCTTATTCTAAAAT -s Anc1.Anc1refChr0 1165 42 - 16026 TATTTACAATTTGAACAAAGCCTGCAGCGCTTATTCTAAAAT -s Anc2.Anc2refChr0 40853 41 - 56053 TA-TTACAATTTGAACAAACCCTGCAGTGCTTATTCTAAAAT -s mr.mrrefChr0 44294 42 + 130230 TATTCACAATTTGAACAAAGCCTGTATCGCCTATGTTAACCT -s simCow_chr6.simCow.chr6 583345 41 - 602619 TT-TTACAATTTGAACAAACCCTGCTGTGCTTAGTCTAATAT -s simDog_chr6.simDog.chr6 578578 41 - 593897 TA-TTACAATTCGAACAAACACTGTAGTGCTTATGCCAAAAT -s simHuman_chr6.simHuman.chr6 585167 42 - 601863 TATTTATATCTTTAACAAAGCCTGCAGCACTTCTTCTAAAAT -s simRat_chr6.simRat.chr6 39272 42 + 647215 TATTCACAATTTGAACAAAGCCTGTATCGCCTAAGTAGACCT - -a -s simMouse_chr6.simMouse.chr6 46540 5 + 636262 ATGGT -s Anc0.Anc0refChr9 20881 5 + 35212 ATGGT -s Anc1.Anc1refChr0 1209 5 - 16026 ATGGT -s Anc2.Anc2refChr0 40896 5 - 56053 GTGGT -s mr.mrrefChr0 44336 5 + 130230 ATGGT -s simCow_chr6.simCow.chr6 583388 5 - 602619 ATGGG -s simDog_chr6.simDog.chr6 578621 5 - 593897 GTGGT -s simHuman_chr6.simHuman.chr6 585211 5 - 601863 ATGGT -s simRat_chr6.simRat.chr6 39314 5 + 647215 ATGGT - -a -s simMouse_chr6.simMouse.chr6 46545 1 + 636262 A -s Anc0.Anc0refChr9 20886 1 + 35212 A -s Anc1.Anc1refChr0 1214 1 - 16026 A -s Anc2.Anc2refChr0 40901 1 - 56053 A -s mr.mrrefChr0 44341 1 + 130230 A -s simCow_chr6.simCow.chr6 583393 1 - 602619 A -s simDog_chr6.simDog.chr6 578626 1 - 593897 A -s simHuman_chr6.simHuman.chr6 585346 1 - 601863 A -s simRat_chr6.simRat.chr6 39319 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 46546 46 + 636262 TTCTTCCAACCTCGAAAAAGTAGAGTGGAAAACACATGTTGGAATT -s Anc0.Anc0refChr9 20887 46 + 35212 TTCTTACAACCTTAAAACAGCAGAGGGAAAAACACACTTTGGAGAT -s Anc1.Anc1refChr0 1215 46 - 16026 TTCTTACAACCTTAAAACAGCAGAGGGAAAAACACACTTTGGAGAT -s Anc2.Anc2refChr0 40903 46 - 56053 TTCTTACAACCATAAAACCACAGAGGGAAAAACACACTTTGGAGAT -s mr.mrrefChr0 44342 46 + 130230 TTCTTCCAACCTTGAAAAAGCAGAGTGGAAAACACATGTTGGAATT -s simCow_chr6.simCow.chr6 583395 38 - 602619 TTCTTACAACCATAAAAAGACAGAGCGAAAAACACCAT-------- -s simDog_chr6.simDog.chr6 578628 45 - 593897 TTCTTACAACTATAAAACCATAGGGGG-AAAGCATACTTTGGAGAT -s simHuman_chr6.simHuman.chr6 585347 46 - 601863 TTCTTACAACCTTAAAACAGCAGAGGGAAAAACACACTTTGTATGT -s simRat_chr6.simRat.chr6 39320 46 + 647215 TTCGTCCAACTATGGAAAAGCAGAGTGGTAAACACATGTTGGAATT - -a -s simMouse_chr6.simMouse.chr6 46592 15 + 636262 GCAAACGTGAAGCAT -s Anc0.Anc0refChr9 20942 15 + 35212 ACAAATAAGAAGCCT -s Anc1.Anc1refChr0 1270 15 - 16026 ACAAATAAGAAGCCT -s Anc2.Anc2refChr0 40958 15 - 56053 ACAAATAAGAAACCT -s mr.mrrefChr0 44388 15 + 130230 GCAAATGTGAAGCAT -s simDog_chr6.simDog.chr6 578682 15 - 593897 ACAAATAAGAAACCT -s simHuman_chr6.simHuman.chr6 585402 15 - 601863 ACAAATAAGAAGCCT -s simRat_chr6.simRat.chr6 39366 15 + 647215 GCAAGTCGGAAGCAT - -a -s simMouse_chr6.simMouse.chr6 46607 4 + 636262 ACAC -s Anc0.Anc0refChr9 20957 4 + 35212 ACAC -s Anc1.Anc1refChr0 1285 4 - 16026 ACAC -s Anc2.Anc2refChr0 40973 4 - 56053 CCAC -s mr.mrrefChr0 44403 4 + 130230 ACAC -s simDog_chr6.simDog.chr6 578697 4 - 593897 CCAC -s simHuman_chr6.simHuman.chr6 585422 4 - 601863 ATGA -s simRat_chr6.simRat.chr6 39381 4 + 647215 ACAC - -a -s simMouse_chr6.simMouse.chr6 46611 27 + 636262 ATCGGATCACACATTCTAACAAACCTA -s Anc0.Anc0refChr9 20961 27 + 35212 ATGGTAAACCATATTCCAACATACCCA -s Anc1.Anc1refChr0 1289 27 - 16026 ATGGTAAACCATATTCCAACATACCCA -s Anc2.Anc2refChr0 40981 27 - 56053 ATGGTAAACCATATTGCAACATACTCA -s mr.mrrefChr0 44407 27 + 130230 ATCAAATCACACATTCTAACAAACCCA -s simCow_chr6.simCow.chr6 583435 24 - 602619 ATGATAAACCATATTGGAACATAC--- -s simDog_chr6.simDog.chr6 578705 27 - 593897 GTGGTAAACCATATTGCAACATGTTCA -s simHuman_chr6.simHuman.chr6 585426 27 - 601863 ATGGCAAACCAAACTCCAATGTACCCA -s simRat_chr6.simRat.chr6 39385 27 + 647215 AACAAATCACACATTCTAACAAACCCA - -a -s simMouse_chr6.simMouse.chr6 46638 79 + 636262 ACTGATTTAATACACCAACATCATAATATTGACCATCATATTACAATCCTGTTGGAGGATGTCATATTAGAATCCTGTT -s Anc0.Anc0refChr9 20988 49 + 35212 A---ACCCAACAAAATGAAATCAAAATG--------------------------GA-ACTATCAAATTAGAAAGTTGGT -s Anc1.Anc1refChr0 1316 50 - 16026 A---ACCCAACAAAATGAAATCAAAATGA-------------------------GA-ACTATCAAATTAGAAAGTTGGT -s Anc2.Anc2refChr0 41008 49 - 56053 G---ACCCGACAAAATGAAATGAACATG--------------------------GA-ACTATCAAATTAGAAAGTTGGT -s mr.mrrefChr0 44434 54 + 130230 ACTGATTTAATACATCAACATCACAATAT-------------------------GAGACTATCATATTAGAATCCTGGT -s simCow_chr6.simCow.chr6 583459 45 - 602619 -------TGACAAAATAAAATGAAGACA--------------------------GA-ACTATCCAATTAGAAAGTTGGT -s simDog_chr6.simDog.chr6 578781 49 - 593897 G---ACCCGACAAAATGAAATGAACCTG--------------------------GG-ACTCTCAAATCAGAAAGTTGGT -s simHuman_chr6.simHuman.chr6 585453 50 - 601863 A---ACACATCAACATCAAATCAAAATGA-------------------------GA-ACTATCAAATTGGGAAGTTGGT -s simRat_chr6.simRat.chr6 39412 54 + 647215 ACTGGTTTTATACATCAACATCACAATAT-------------------------AAGACCATCATATTAGAATCCTGGT - -a -s simMouse_chr6.simMouse.chr6 46717 18 + 636262 GGAGGATGCCAGGTGGAT -s Anc0.Anc0refChr9 21037 18 + 35212 GGAGTGTGGCAGGTAGGT -s Anc1.Anc1refChr0 1366 18 - 16026 GGAGTGTGGCAGGTAGGT -s Anc2.Anc2refChr0 41058 18 - 56053 GGAGTGTGGCAGGTAGGT -s mr.mrrefChr0 44488 18 + 130230 GGAGGATGCCAGGTGGAT -s simCow_chr6.simCow.chr6 583505 18 - 602619 GGGGTGTGGCAGGTAGGT -s simDog_chr6.simDog.chr6 578831 18 - 593897 GGAGTGTGGCTGGTAGAT -s simHuman_chr6.simHuman.chr6 585503 16 - 601863 --AGTGTGGCAGACAGGT -s simRat_chr6.simRat.chr6 39466 18 + 647215 GGAAGACGCCAGGTGGAT - -a -s simMouse_chr6.simMouse.chr6 46735 31 + 636262 GTTTGCACACAGGATAATTAGATGAATCAGA -s Anc0.Anc0refChr9 21061 31 + 35212 GCTAACACACAGGATACTTAAAGGAACTGGA -s Anc1.Anc1refChr0 1390 31 - 16026 GCTAACACACAGGATACTTAAAGGAACTGGA -s Anc2.Anc2refChr0 41082 31 - 56053 GCTAACAAGTAGGATACATAAAGGAACCGAA -s mr.mrrefChr0 44506 31 + 130230 GTTTACACACAGGATAATTAGATGAATTAGA -s simCow_chr6.simCow.chr6 583529 31 - 602619 GCTAACAATGAGGACATATAAAGGTACCAAA -s simDog_chr6.simDog.chr6 578855 31 - 593897 GCTAACAAGTAGGATACATAAAGGAACCGAA -s simHuman_chr6.simHuman.chr6 585525 31 - 601863 GCTAAAACACAGGATACTTGATAGGTCTGGA -s simRat_chr6.simRat.chr6 39484 31 + 647215 GGTTACACACACGATAGTTAGATGAGTTAGA - -a -s simMouse_chr6.simMouse.chr6 46766 8 + 636262 CGATGGAA -s Anc0.Anc0refChr9 21092 8 + 35212 GCCTGTCA -s Anc1.Anc1refChr0 1421 8 - 16026 GCCTGTCA -s Anc2.Anc2refChr0 41113 8 - 56053 GCCTGTCA -s mr.mrrefChr0 44537 8 + 130230 CGATGGAA -s simCow_chr6.simCow.chr6 583560 8 - 602619 GCCTCTCA -s simDog_chr6.simDog.chr6 578887 8 - 593897 GCCTGTCA -s simHuman_chr6.simHuman.chr6 585556 8 - 601863 GCCTGTGA -s simRat_chr6.simRat.chr6 39515 8 + 647215 AGATGGAA - -a -s simMouse_chr6.simMouse.chr6 46774 53 + 636262 GCAACTAAGTCTTCTGCAGCTCTAACGCCTTATCCACAATTTCACCCTACTCT -s Anc0.Anc0refChr9 21100 26 + 35212 GCAACTGAGTCCTCCGAAG---------CTTATTC------------------ -s Anc1.Anc1refChr0 1429 26 - 16026 GCAACTGAGTCCTCCGAAG---------CTTATTC------------------ -s Anc2.Anc2refChr0 41121 26 - 56053 ACAACTAGGTCCTCCAAAG---------CTTATTC------------------ -s mr.mrrefChr0 44545 53 + 130230 GCAACTGAGTCCTCTGCAGCTCTAACGCCTTATTCACAATTTCACCCTACTCT -s simCow_chr6.simCow.chr6 583768 26 - 602619 ATAACTAGGTCCTCCAGAG---------CTCATTC------------------ -s simDog_chr6.simDog.chr6 578895 26 - 593897 ACAACTAGGTCCTCCAAAA---------CATATTT------------------ -s simHuman_chr6.simHuman.chr6 585564 26 - 601863 GCAACTGAGTGCTCCGAAG---------CTTATTC------------------ -s simRat_chr6.simRat.chr6 39523 53 + 647215 ACAACTGAGTCCTCTGGAGCTCTAACACCTTATTCACAATTTCACCCTACTCT - -a -s simMouse_chr6.simMouse.chr6 46827 1 + 636262 T -s Anc0.Anc0refChr9 21126 1 + 35212 T -s Anc1.Anc1refChr0 1455 1 - 16026 T -s Anc2.Anc2refChr0 41150 1 - 56053 C -s mr.mrrefChr0 44598 1 + 130230 T -s simCow_chr6.simCow.chr6 583797 1 - 602619 G -s simDog_chr6.simDog.chr6 578924 1 - 593897 C -s simHuman_chr6.simHuman.chr6 585590 1 - 601863 T -s simRat_chr6.simRat.chr6 39576 1 + 647215 C - -a -s simMouse_chr6.simMouse.chr6 46828 19 + 636262 GTATACAGACTAAGCCGAA -s Anc0.Anc0refChr9 21132 19 + 35212 GAATGTAGACCAGGCTGGG -s Anc1.Anc1refChr0 1461 19 - 16026 GAATGTAGACCAGGCTGGG -s Anc2.Anc2refChr0 41156 19 - 56053 GAATGTATACCAGGCTGGG -s mr.mrrefChr0 44604 19 + 130230 GTATACAGACTAAGCCGAG -s simCow_chr6.simCow.chr6 583803 18 - 602619 AAATGTAAACCAGGCTGG- -s simDog_chr6.simDog.chr6 578930 16 - 593897 GA---TATACCAGGCTGGG -s simHuman_chr6.simHuman.chr6 585596 19 - 601863 GAATGTAGACCAGGCTGGG -s simRat_chr6.simRat.chr6 39582 19 + 647215 GTATACAGACTAAGCCAAG - -a -s simMouse_chr6.simMouse.chr6 46847 4 + 636262 CTGG -s Anc0.Anc0refChr9 21152 4 + 35212 TTGG -s Anc1.Anc1refChr0 1481 4 - 16026 TTGG -s Anc2.Anc2refChr0 41176 4 - 56053 TTGG -s mr.mrrefChr0 44623 4 + 130230 CTGG -s simCow_chr6.simCow.chr6 583822 4 - 602619 TTGG -s simDog_chr6.simDog.chr6 578947 4 - 593897 TTGG -s simHuman_chr6.simHuman.chr6 585616 4 - 601863 TTGG -s simRat_chr6.simRat.chr6 39601 4 + 647215 CTGG - -a -s simMouse_chr6.simMouse.chr6 46851 70 + 636262 TATTACTGTGGCCAACTAGGCACTACTGTTTAGATGAGCCTGACATTTGCAAGCATACACAAGGTTAGTG -s Anc0.Anc0refChr9 21156 70 + 35212 TATTACTGTGGATAAACAGGCACTACTGTTTAGATGACCATGTCATAAACAACCATATTCATGATCATTG -s Anc1.Anc1refChr0 1485 70 - 16026 TATTACTGTGGATAAACAGGCACTACTGTTTAGATGACCATGTCATAAACAACCATATTCATGATCATTG -s Anc2.Anc2refChr0 41180 70 - 56053 TATTACTGTGGCTGAACAGGCACCACTGTTTAGGTGACTATGTTATAAACAACCATATTCATGATCCTTG -s mr.mrrefChr0 44627 70 + 130230 TATTACTGTGGACAACTAGGCACTACTGTTTAGATGAGCCTGACATTAGCAAGCATACACAAGGTTATTG -s simCow_chr6.simCow.chr6 583826 70 - 602619 TATTGCTGTGGCTGAACAGGCACCACTGTTCAGGTGATTATGTTATAATCAACCATATTCATGATCGTTG -s simDog_chr6.simDog.chr6 578952 70 - 593897 TATTACTGGGGCTGAACAGGCACCATTGTTTAGGTGGCTATGTTATAAACTATTATATTTAAGATCCTTG -s simHuman_chr6.simHuman.chr6 585620 70 - 601863 TATTACTGTGTATACAGAGGTACTACTTTTTAAATGACCATGTCATAAACAACCATAATCATCATCATTG -s simRat_chr6.simRat.chr6 39605 70 + 647215 TATTACTGTGGACAACTAGGCACCACTGTTAAGATGAGCCTGACACTAGCAAGCATGTACAAGGTTATTG - -a -s simMouse_chr6.simMouse.chr6 46921 5 + 636262 ATTGG -s Anc0.Anc0refChr9 21226 5 + 35212 ATTAG -s Anc1.Anc1refChr0 1555 5 - 16026 ATTAG -s Anc2.Anc2refChr0 41299 5 - 56053 ATTAG -s mr.mrrefChr0 44697 5 + 130230 ATTGG -s simCow_chr6.simCow.chr6 583945 5 - 602619 ATTAC -s simDog_chr6.simDog.chr6 579076 5 - 593897 ATTAG -s simHuman_chr6.simHuman.chr6 585690 5 - 601863 CTTAG -s simRat_chr6.simRat.chr6 39675 5 + 647215 ATTGG - -a -s simMouse_chr6.simMouse.chr6 46926 19 + 636262 AGCCTTCCAATAAGAATGG -s Anc0.Anc0refChr9 21238 19 + 35212 AGCTTTCCAATGGGAATGG -s Anc1.Anc1refChr0 1567 19 - 16026 AGCTTTCCAATGGGAATGG -s Anc2.Anc2refChr0 41311 19 - 56053 AGCTTTCCAATGGGAATGG -s mr.mrrefChr0 44702 19 + 130230 AGCCTTCCAATGAGAATGG -s simCow_chr6.simCow.chr6 583957 19 - 602619 AGCTTTCCAATGGGAATGG -s simDog_chr6.simDog.chr6 579088 19 - 593897 AGCTTTCCAATGGGAATGG -s simHuman_chr6.simHuman.chr6 585702 19 - 601863 AGCATTCCAAAGGGAATGG -s simRat_chr6.simRat.chr6 39680 19 + 647215 AGCTTTCCAATGAGAATGG - -a -s simMouse_chr6.simMouse.chr6 46945 30 + 636262 AGCAGTCACAGTGCATGCAAAAAAGTACAT -s Anc0.Anc0refChr9 21257 30 + 35212 CATGTATACAGTTCATGCAAAAGGGGAGAC -s Anc1.Anc1refChr0 1586 30 - 16026 CATGTATACAGTTCATGCAAAAGGGGAGAC -s Anc2.Anc2refChr0 41330 30 - 56053 CATGTATACAGTTCATGCAAAAGGGGAGAC -s mr.mrrefChr0 44721 30 + 130230 AGCAGTCACAGTGCATGCAAAAAAGTACAT -s simCow_chr6.simCow.chr6 583976 30 - 602619 CATGGATACTGTTCATCATGGGGGAGAGAC -s simDog_chr6.simDog.chr6 579107 30 - 593897 CATGTATACACTTCATGCAAAATGGGAGAT -s simHuman_chr6.simHuman.chr6 585721 30 - 601863 CATGAATAGAGTTCATGCAACAGGGAAGAC -s simRat_chr6.simRat.chr6 39701 30 + 647215 TGCAGTCATGGTACATGCATAAAAGTACAT - -a -s simMouse_chr6.simMouse.chr6 46975 6 + 636262 AAGGAC -s Anc0.Anc0refChr9 21287 6 + 35212 ATACAG -s Anc1.Anc1refChr0 1616 6 - 16026 ATACAG -s Anc2.Anc2refChr0 41360 6 - 56053 ATACAG -s mr.mrrefChr0 44751 6 + 130230 ATGGAC -s simCow_chr6.simCow.chr6 584039 6 - 602619 AGACAG -s simDog_chr6.simDog.chr6 579137 6 - 593897 ATACAG -s simHuman_chr6.simHuman.chr6 585751 6 - 601863 ATATCT -s simRat_chr6.simRat.chr6 39731 6 + 647215 ATGGAA - -a -s simMouse_chr6.simMouse.chr6 46981 14 + 636262 TTTAAGTGAGAGTG -s Anc0.Anc0refChr9 21293 14 + 35212 TTTAAATGGAAATG -s Anc1.Anc1refChr0 1622 14 - 16026 TTTAAATGGAAATG -s Anc2.Anc2refChr0 41366 14 - 56053 TTTAAATAGAAATG -s mr.mrrefChr0 44757 14 + 130230 TTTAAGTGAGAGTG -s simCow_chr6.simCow.chr6 584047 14 - 602619 TTTAAATCAAAATT -s simDog_chr6.simDog.chr6 579143 14 - 593897 TTTAAATAGAAATG -s simHuman_chr6.simHuman.chr6 585757 14 - 601863 CTTAAATGGAAATG -s simRat_chr6.simRat.chr6 39737 14 + 647215 TTTAAGTGAGAGTG - -a -s simMouse_chr6.simMouse.chr6 46995 51 + 636262 AGGCCCAAAATCTTCCAAGGTGGACAATCAGCATAGGCTAAGCTGCCTAAC -s Anc0.Anc0refChr9 21308 50 + 35212 AGGCTCAAGATCCTACAAGGTGGACAATCGAT-ATAGATAGACTGCCTAGC -s Anc1.Anc1refChr0 1637 50 - 16026 AGGCTCAAGATCCTACAAGGTGGACAATCGAT-ATAGATAGACTGCCTAGC -s Anc2.Anc2refChr0 41381 50 - 56053 AGGCTCAAGATCCTGCAAGGTAGACAATCGAT-ATAGATAGACTGCCTGGC -s mr.mrrefChr0 44771 51 + 130230 AGGCCCAAAATCTTACAAGGTGGACAATCAGCATAAGCTAAACTGCCTAAC -s simCow_chr6.simCow.chr6 584062 50 - 602619 AGGCTAAAGGTCCTGTGAAATAGACAATGAGT-ATTGCTAGACTGACTGGT -s simDog_chr6.simDog.chr6 579158 50 - 593897 AGGCTCAAGATCCTGCAAGGTAGACAATCGAT-ATAGATAGACTGCCTGGC -s simHuman_chr6.simHuman.chr6 585772 50 - 601863 AGGCTCAAGATCCTACAAGGTGGACAATCCTT-CGAGTTAGACTGCATAGC -s simRat_chr6.simRat.chr6 39751 51 + 647215 AGGCCCAAAACCTTACATGCTGGACAATCAGCATAAGCTGAACTGCCTAAC - -a -s simMouse_chr6.simMouse.chr6 47046 11 + 636262 CACCCTGTTGT -s Anc0.Anc0refChr9 21362 11 + 35212 TGGCCTGTTTT -s Anc1.Anc1refChr0 1691 11 - 16026 TGGCCTGTTTT -s Anc2.Anc2refChr0 41435 11 - 56053 TGGCCTGTTTT -s mr.mrrefChr0 44822 11 + 130230 CACCCTGTTGT -s simCow_chr6.simCow.chr6 584116 5 - 602619 TGGCC------ -s simDog_chr6.simDog.chr6 579212 10 - 593897 CG-CCTGTTTT -s simHuman_chr6.simHuman.chr6 585826 11 - 601863 TGGCCTGTTAT -s simRat_chr6.simRat.chr6 39802 11 + 647215 CTCCCTGTTGT - -a -s simMouse_chr6.simMouse.chr6 47057 48 + 636262 TGCAGGATTGCTAAACCAAGTGATGATGACCTAAGCTTCAGTGCAGAG -s Anc0.Anc0refChr9 21373 48 + 35212 TGCAGAATTGCTAGACCTAGTGATTATGACTTAAGCTTCAGAGTTGAG -s Anc1.Anc1refChr0 1702 48 - 16026 TGCAGAATTGCTAGACCTAGTGATTATGACTTAAGCTTCAGAGTTGAG -s Anc2.Anc2refChr0 41446 48 - 56053 TGTGGATTTGCTAGACCTAGTGATTAGGACTTAAGCTTCAGAGTTAGG -s mr.mrrefChr0 44833 48 + 130230 TGCAGGATTGCTAAACCTAGTGATTATGACCTAAGCTTCAGTGCTGAG -s simCow_chr6.simCow.chr6 584121 43 - 602619 -----AGTTGCTAGACATGGTGATTTGCACTCAAGCTGCAGAGAGAGT -s simDog_chr6.simDog.chr6 579222 48 - 593897 TGTGGATTTGCCCGAACTAGTGATTAGGACCTAAGCTTCAGTGTTAGG -s simHuman_chr6.simHuman.chr6 585847 48 - 601863 TACAGAATTACTAGACCTACTGATTATGACTTAAGCATCAGAGGTGAG -s simRat_chr6.simRat.chr6 39813 48 + 647215 TGCAGGGTTGCTAAATCTAATGATTGTGACCTAAGCTTCAGCACTGAG - -a -s simMouse_chr6.simMouse.chr6 47105 55 + 636262 AATTATTCTAACCCTAGTATTATATGGCAATTAGATTATATCCAACTGGATAGCA -s Anc0.Anc0refChr9 21421 54 + 35212 -ATTATTCTAGCACTAGCATTATCTGGCAATAAGATTATATGCAACTGAATAGTG -s Anc1.Anc1refChr0 1750 54 - 16026 -ATTATTCTAGCACTAGCATTATCTGGCAATAAGATTATATGCAACTGAATAGTG -s Anc2.Anc2refChr0 41494 54 - 56053 -ATTATTCTAGCACTAGCATTACCTGGCATTAAGATTACATGCAACTGAATAGTG -s mr.mrrefChr0 44881 55 + 130230 AATTATTCTAACACTAGCATTATATGGCAATTAGATTATATCCAACTGGATAGTA -s simCow_chr6.simCow.chr6 584165 54 - 602619 -GTTATTCAATCACTAGCATTACTTGGCATTAACATTACATGCAACTGAATAGTG -s simDog_chr6.simDog.chr6 579270 54 - 593897 -ATTAATCTAGCACCAGTGTTACCTGGCATTAAGATTACATGTAAGTGAATAGTC -s simHuman_chr6.simHuman.chr6 585895 54 - 601863 -ATCATTCTGGCACTAGCATTATCTGGCAATAAGATTATATGCAGCTCAATAGTG -s simRat_chr6.simRat.chr6 39864 55 + 647215 ATTTATTCTAACACTAGCATTACATGGCAATTAGATTTTATCCAACTGGATAGTA - -a -s simMouse_chr6.simMouse.chr6 47160 13 + 636262 ACTGATGGGATAT -s Anc0.Anc0refChr9 21476 13 + 35212 ATTTTAGGGACAC -s Anc1.Anc1refChr0 1805 13 - 16026 ATTTTAGGGACAC -s Anc2.Anc2refChr0 41549 13 - 56053 ACTTTAGGGACAG -s mr.mrrefChr0 44937 13 + 130230 ATTGATGGGATAC -s simCow_chr6.simCow.chr6 584220 13 - 602619 ACTCTTGGGACAG -s simDog_chr6.simDog.chr6 579325 13 - 593897 ACTTTAGGGGCAG -s simHuman_chr6.simHuman.chr6 585950 13 - 601863 ATTTGAGCGACAC -s simRat_chr6.simRat.chr6 39920 13 + 647215 ATTGATGTGATAC - -a -s simMouse_chr6.simMouse.chr6 47173 11 + 636262 GGGAGAAGCAC -s Anc0.Anc0refChr9 21492 11 + 35212 AGGAGGAGCAC -s Anc1.Anc1refChr0 1821 11 - 16026 AGGAGGAGCAC -s Anc2.Anc2refChr0 41565 11 - 56053 GGGAGGAGCAC -s mr.mrrefChr0 44950 11 + 130230 AGGAGGAGCAC -s simCow_chr6.simCow.chr6 584236 11 - 602619 GGGAGGGGCAT -s simDog_chr6.simDog.chr6 579341 11 - 593897 GGGAGGAGCAC -s simHuman_chr6.simHuman.chr6 585966 11 - 601863 ATGTGGAGCAC -s simRat_chr6.simRat.chr6 39933 11 + 647215 AGGAGGAGCAC - -a -s simMouse_chr6.simMouse.chr6 47184 19 + 636262 AAATCAAGACACTTCCAGT -s Anc0.Anc0refChr9 21507 19 + 35212 AAATCATTTCAATTCCAGT -s Anc1.Anc1refChr0 1836 19 - 16026 AAATCATTTCAATTCCAGT -s Anc2.Anc2refChr0 41580 19 - 56053 AAATCATTTCAATTCTAGT -s mr.mrrefChr0 44961 19 + 130230 AAATCAAGACAATTCCAGT -s simCow_chr6.simCow.chr6 584251 19 - 602619 AAATCATTGTGATTCTGGT -s simDog_chr6.simDog.chr6 579356 17 - 593897 AAATCATTTCAATT--AAT -s simHuman_chr6.simHuman.chr6 585981 19 - 601863 AAATCATACCAATTCCAGT -s simRat_chr6.simRat.chr6 39944 19 + 647215 AAATCAATGCAATTCCAGC - -a -s simMouse_chr6.simMouse.chr6 47203 16 + 636262 GATGTGTGGGCCTTAC -s Anc0.Anc0refChr9 21527 14 + 35212 GGTGTGA--GCCTTAT -s Anc1.Anc1refChr0 1856 14 - 16026 GGTGTGA--GCCTTAT -s Anc2.Anc2refChr0 41600 14 - 56053 AGTGTTA--GCTTTAT -s mr.mrrefChr0 44981 14 + 130230 GATGTGT--GCCTTAC -s simCow_chr6.simCow.chr6 584271 14 - 602619 AGAGTTA--GCTTTAG -s simDog_chr6.simDog.chr6 579374 14 - 593897 AGTGTTA--GTTTTGT -s simHuman_chr6.simHuman.chr6 586001 14 - 601863 GGGGTGA--GCCTTAT -s simRat_chr6.simRat.chr6 39964 14 + 647215 GATGTGT--GGCTCAA - -a -s simMouse_chr6.simMouse.chr6 47219 40 + 636262 ACTTTAGTAGGGCTAGATGAGAGAGGGCATAGACATGCAG -s Anc0.Anc0refChr9 21541 40 + 35212 ATTTTAGTAGGGCTAGATTGGAAAGGGCATATACATGCAG -s Anc1.Anc1refChr0 1870 40 - 16026 ATTTTAGTAGGGCTAGATTGGAAAGGGCATATACATGCAG -s Anc2.Anc2refChr0 41614 40 - 56053 ATTTTAGTAGGGCTAGACTGAAAAGGGTATATACATGCAA -s mr.mrrefChr0 44995 40 + 130230 ACTTTAGTAGGGCTAGATGAGAGAGGGCATAGACATGCAG -s simCow_chr6.simCow.chr6 584285 39 - 602619 ATTTTAGTAGCACTAGAATTCAAAGGGTATATACA-GCAA -s simDog_chr6.simDog.chr6 579393 40 - 593897 ATTTTAATGGGGCTAAACTGATAAGGGTATATTCATGCAA -s simHuman_chr6.simHuman.chr6 586015 40 - 601863 ATTTTAGTAGGGCTAGGTTGGAAAGGGCGTATACATGCAG -s simRat_chr6.simRat.chr6 39978 40 + 647215 ACCTTAGTAGGGCTAGATGAGAGAAGGCATAGACATGCAA - -a -s simMouse_chr6.simMouse.chr6 47259 8 + 636262 ACTACAAT -s Anc0.Anc0refChr9 21583 8 + 35212 ACCCCAAT -s Anc1.Anc1refChr0 1912 8 - 16026 ACCCCAAT -s Anc2.Anc2refChr0 41656 8 - 56053 ACCCCAAT -s mr.mrrefChr0 45035 8 + 130230 ACTACAAT -s simCow_chr6.simCow.chr6 584326 8 - 602619 ACTCCTAT -s simDog_chr6.simDog.chr6 579435 8 - 593897 ACCCCACT -s simHuman_chr6.simHuman.chr6 586057 8 - 601863 ACCCCAAT -s simRat_chr6.simRat.chr6 40018 8 + 647215 ACTACAAT - -a -s simMouse_chr6.simMouse.chr6 47267 54 + 636262 TGATAGCCCTTTGTCAGTCAGATTCAAGCACTTTGCAGCTGGGTCCATAATTAC -s Anc0.Anc0refChr9 21594 29 + 35212 TGATAATCCTTTGTCA-------------------------AGCTCGTGAGTAC -s Anc1.Anc1refChr0 1923 29 - 16026 TGATAATCCTTTGTCA-------------------------AGCTCGTGAGTAC -s Anc2.Anc2refChr0 41667 29 - 56053 TGATAATTCCCTGCCA-------------------------ACCTCCTGAGTAC -s mr.mrrefChr0 45046 54 + 130230 TGATAACCCTTTGTCAGTCAGATTCAAGCACTTTGCAGCTGGGTTCGTGATTAC -s simCow_chr6.simCow.chr6 584337 21 - 602619 TGATAAATCCCC---------------------------------CATGAGTAT -s simDog_chr6.simDog.chr6 579446 29 - 593897 TGAGAGTTCCCTGCCA-------------------------ACCTTCTGAGTCC -s simHuman_chr6.simHuman.chr6 586068 29 - 601863 TGATAATCCTTTGTCA-------------------------AGCTCGTGAGTAC -s simRat_chr6.simRat.chr6 40029 54 + 647215 TGATAACCCTTTGCCAGTCAGGTTCAAGCCCTTTGCAGTCAGGTTCGTGATTAT - -a -s simMouse_chr6.simMouse.chr6 47321 41 + 636262 CAGCTGTTGCAATGCCTAATGATGGTGTTTCAGGGCCTTCA -s Anc0.Anc0refChr9 21626 41 + 35212 CAGCATTTGCTATGTGTACTGACAGTGCTTTCTGGCCCTCA -s Anc1.Anc1refChr0 1955 41 - 16026 CAGCATTTGCTATGTGTACTGACAGTGCTTTCTGGCCCTCA -s Anc2.Anc2refChr0 41699 41 - 56053 CCACATTTGCTATGTGTACTGACAGTGCTTTCTGGCCCTCA -s mr.mrrefChr0 45100 41 + 130230 CAGCTTTTGCTATGCCTAATGATGGTGTTTCAGGGCCTTCA -s simCow_chr6.simCow.chr6 584361 40 - 602619 CCACATGTGCTATGTGTAGTG-CGGTATTTTCTGGCCCTCT -s simDog_chr6.simDog.chr6 579478 35 - 593897 TCACATTTGGTA------CTGACAGTGCTTTGTGGCCCTCA -s simHuman_chr6.simHuman.chr6 586100 41 - 601863 CAGTATTTGCTATGTTTACTGACAGTGCTTTCCAGCCCTCT -s simRat_chr6.simRat.chr6 40083 41 + 647215 CAGCCTTTGCTATGCCTAATGATGGTGTTTCAGGGCCTTCA - -a -s simMouse_chr6.simMouse.chr6 47362 5 + 636262 GAAGT -s Anc0.Anc0refChr9 21667 5 + 35212 GTACT -s Anc1.Anc1refChr0 1996 5 - 16026 GTACT -s Anc2.Anc2refChr0 41741 5 - 56053 GTACT -s mr.mrrefChr0 45141 5 + 130230 GAAGT -s simCow_chr6.simCow.chr6 584402 5 - 602619 TTACT -s simDog_chr6.simDog.chr6 579514 5 - 593897 GTACT -s simHuman_chr6.simHuman.chr6 586141 1 - 601863 A---- -s simRat_chr6.simRat.chr6 40124 5 + 647215 GAAGT - -a -s simMouse_chr6.simMouse.chr6 47367 31 + 636262 AGGCCAATCCTAGCAAGGTTAAATAGAAGAA -s Anc0.Anc0refChr9 21672 31 + 35212 AGGCAAATTCTAGTAAGGTTAATTACAAGAA -s Anc1.Anc1refChr0 2001 31 - 16026 AGGCAAATTCTAGTAAGGTTAATTACAAGAA -s Anc2.Anc2refChr0 41746 31 - 56053 AGGCAAATTCTAGTAAGGTTAATTACAAGAA -s mr.mrrefChr0 45146 31 + 130230 AGGCCAATCCTAGCAAGGTTAAATAGAAGAA -s simCow_chr6.simCow.chr6 584410 31 - 602619 AGGCATATTTTAGTGAAGTTAATGACACGAA -s simDog_chr6.simDog.chr6 579519 31 - 593897 AGGCAAATTCTAGTAAGGCTAAGTACAAGAA -s simHuman_chr6.simHuman.chr6 586142 31 - 601863 AGGCAAATTCTGTTAAGGTCAATTACAAGGA -s simRat_chr6.simRat.chr6 40129 24 + 647215 AGGCCAATC-------GTTTAAATCAAAGAA - -a -s simMouse_chr6.simMouse.chr6 47398 13 + 636262 AGGCTTAAAGATT -s Anc0.Anc0refChr9 21703 13 + 35212 AGGCTTAAAGACT -s Anc1.Anc1refChr0 2032 13 - 16026 AGGCTTAAAGACT -s Anc2.Anc2refChr0 41777 13 - 56053 AGGCTTAAAGACC -s mr.mrrefChr0 45177 13 + 130230 AGGCTTAAAGATT -s simCow_chr6.simCow.chr6 584441 13 - 602619 CAGCTTAAAGACC -s simDog_chr6.simDog.chr6 579550 13 - 593897 AGACATAAACACC -s simHuman_chr6.simHuman.chr6 586173 13 - 601863 AGGTTTAAGGACT -s simRat_chr6.simRat.chr6 40157 13 + 647215 AGGCTTAAACATT - -a -s simMouse_chr6.simMouse.chr6 47411 35 + 636262 TTCTCACTCTAACACAGGTGTTAGATCACACGTAC -s Anc0.Anc0refChr9 21716 35 + 35212 GGCACACTCCTCCAGAAGTGTTACCTTACATCTCC -s Anc1.Anc1refChr0 2045 35 - 16026 GGCACACTCCTCCAGAAGTGTTACCTTACATCTCC -s Anc2.Anc2refChr0 41790 35 - 56053 GGCACACTCCTCCAGAAGTGTTACCTTATATCTCC -s mr.mrrefChr0 45190 35 + 130230 TTCTCACTCTAACACAGGTGTTAGATCACATGTAC -s simCow_chr6.simCow.chr6 584455 35 - 602619 GGTTCACCCCTTCTCAAGGGTTACTTCATATCTCT -s simDog_chr6.simDog.chr6 579563 31 - 593897 GGCACACTCCTCCAGAAGTGTTACCTTA----TCC -s simHuman_chr6.simHuman.chr6 586186 35 - 601863 CACACACTCCCCCAGAAGTGTTACCTTACATCTCC -s simRat_chr6.simRat.chr6 40170 35 + 647215 TTCTAACCCTGACACAGGTGTTAGAACATATGTAC - -a -s simMouse_chr6.simMouse.chr6 47446 18 + 636262 AGGTTCTGTGCGTTAATA -s Anc0.Anc0refChr9 21751 18 + 35212 AGATTCAGTGGATTGTAA -s Anc1.Anc1refChr0 2080 18 - 16026 AGATTCAGTGGATTGTAA -s Anc2.Anc2refChr0 41825 18 - 56053 GGATTCAGTGGATTGTTG -s mr.mrrefChr0 45225 18 + 130230 AGATTCTGTGGATTAAAA -s simCow_chr6.simCow.chr6 584490 9 - 602619 GGATTCTGC--------- -s simDog_chr6.simDog.chr6 579606 18 - 593897 GGACTCAATGGATTGTTG -s simHuman_chr6.simHuman.chr6 586221 18 - 601863 AAATTCAGTGGATTGCAA -s simRat_chr6.simRat.chr6 40205 18 + 647215 AGATTATGTGGACTAAAA - -a -s simMouse_chr6.simMouse.chr6 47464 53 + 636262 AGGATCTCCAGGTAGTGTATGCACACAAATTGAGTCAAAGATAAAGGTCATGT -s Anc0.Anc0refChr9 21770 48 + 35212 TGGGGCTATAGGTAGTGCATA-----AAATTGAGTTAATAATACAGACTATGT -s Anc1.Anc1refChr0 2099 48 - 16026 TGGGGCTATAGGTAGTGCATA-----AAATTGAGTTAATAATACAGACTATGT -s Anc2.Anc2refChr0 41844 48 - 56053 TGGGGCTATAGGTAGTGCATA-----AAATTGAGTTAATAATACAGACTATGT -s mr.mrrefChr0 45243 53 + 130230 AGGAGCTACAGGTAGTGTATACACACAAATTGAGTCAAAAATAAAGATCATGT -s simCow_chr6.simCow.chr6 584499 40 - 602619 -----CGATGGGTAGGGGATG-----CAATTAG---AATAATAAAGGCTATGT -s simDog_chr6.simDog.chr6 579625 47 - 593897 TGGGGATACAAATAGTGCATA-----AA-CTGAGTTTATAATACAGACTATGT -s simHuman_chr6.simHuman.chr6 586240 48 - 601863 TGGGGCTATAGGTAGTGCATA-----AAATTGAGTTAAGAATATAGACTATGT -s simRat_chr6.simRat.chr6 40223 53 + 647215 AGGAGCTACAGGTAGTGTATACACACAAATTCAGTCAAAAATAAAGAGCATGT - -a -s simMouse_chr6.simMouse.chr6 47517 67 + 636262 AGATATGTGTTAAGATCCATGGCTAACATTGGCCCACTAGGATAGTCATAGTTTGAGGGGGTGGCAG -s Anc0.Anc0refChr9 21818 61 + 35212 AGATATGTATTAAGATTCATGGCTGGCATAGACCCACTAGGGTAGAGA------AAGGGGATGGCAG -s Anc1.Anc1refChr0 2147 61 - 16026 AGATATGTATTAAGATTCATGGCTGGCATAGACCCACTAGGGTAGAGA------AAGGGGATGGCAG -s Anc2.Anc2refChr0 41892 61 - 56053 AGAGATGGATTAAGATTCATGGCTGGCATAGACCCACTCGGGTAGAGA------AAGGAGATGGTGG -s mr.mrrefChr0 45296 67 + 130230 AGATATGTGTTAAGATCCATGGCTAGCATTGGCCCACTAGGATAGTCATAGTTTGAGGGGGTGGCAG -s simCow_chr6.simCow.chr6 584539 57 - 602619 AGACATAGATTAAGTTTCATGGCTGGCATAGACCCACTTGGTTAAAGT------TAGGAGATG---- -s simDog_chr6.simDog.chr6 579672 61 - 593897 AGAGCTGGATTAAGATTCGTGGCTGGCATAGACCCACTCAGGTAGAAA------ATAAAGATGGTGG -s simHuman_chr6.simHuman.chr6 586288 61 - 601863 AGGTATGTATTAAGATTCATGGCTGGCGTCGACCCACTAGGGCAGAGA------AAGGGGATGACAG -s simRat_chr6.simRat.chr6 40277 67 + 647215 GGATACGCGTTAAGATCCATGGCTAGCATTAGCCCACTAGGATAGTCATAGTCTGAGGGGGTGGCAG - -a -s simMouse_chr6.simMouse.chr6 47584 37 + 636262 ACCTAGACCTTGGGGAAAGAACCATACAGAATTAATA -s Anc0.Anc0refChr9 21879 24 + 35212 ACC-AAACCAGGTGGATAG-------GAGGA-----A -s Anc1.Anc1refChr0 2208 37 - 16026 ACCTAAACCAGGTGGATAGAACAATAGAGGATGCATA -s Anc2.Anc2refChr0 41953 24 - 56053 ATC-ACATCAGTTGGTTAG-------GGGGG-----A -s mr.mrrefChr0 45363 37 + 130230 ACCTAAACCTTGGGGAAAGAACAATAGAGAATTAATA -s simDog_chr6.simDog.chr6 579738 24 - 593897 ATC-ACATCAGTTGGTTAG-------GGGGG-----A -s simHuman_chr6.simHuman.chr6 586352 37 - 601863 ACCTGAACCAGGTGAATAGAACAATAGAGGATGCATA -s simRat_chr6.simRat.chr6 40344 37 + 647215 ACTTAATCCTTCAAGAAAGAACAATAGAGAATAAGTA - -a -s simMouse_chr6.simMouse.chr6 47621 20 + 636262 TACCAGGCTATCTTACCTAT -s Anc0.Anc0refChr9 21903 20 + 35212 TGCCAGACCATCTAAACCAT -s Anc1.Anc1refChr0 2245 20 - 16026 TGCCAGACCATCTAAACCAT -s Anc2.Anc2refChr0 41977 20 - 56053 TGACAGAGCATCTAAACCAT -s mr.mrrefChr0 45400 20 + 130230 TGCCAGGCTATCTTACCTAT -s simCow_chr6.simCow.chr6 584596 18 - 602619 --ACAGAGTATCTAAGCCAT -s simDog_chr6.simDog.chr6 579762 20 - 593897 TGACAGAGCATCTATACCAT -s simHuman_chr6.simHuman.chr6 586389 20 - 601863 GGCCAGACCATGTAAACCAT -s simRat_chr6.simRat.chr6 40384 17 + 647215 TGCCAGG---TCTTACCTAT - -a -s simMouse_chr6.simMouse.chr6 47641 18 + 636262 ATGTATGGAACAATAGAG -s Anc0.Anc0refChr9 21923 18 + 35212 GTGAATAGAACAATAGAG -s Anc1.Anc1refChr0 2265 18 - 16026 GTGAATAGAACAATAGAG -s Anc2.Anc2refChr0 41997 18 - 56053 GTGATTAGAATACTAGAG -s mr.mrrefChr0 45420 18 + 130230 ATGTATAGAACAATAGAG -s simCow_chr6.simCow.chr6 584614 18 - 602619 AAGAGTACAATATTAGCA -s simDog_chr6.simDog.chr6 579782 18 - 593897 GTGGTTAGAATTCTAGAG -s simHuman_chr6.simHuman.chr6 586409 18 - 601863 GCGAACAGAACAATAGAG -s simRat_chr6.simRat.chr6 40404 18 + 647215 TTGTATAGAACAATACAG - -a -s simMouse_chr6.simMouse.chr6 47659 45 + 636262 CAGGTAGACAAAACAATATTTTAGTTGATAATTCTTATATCTTTG -s Anc0.Anc0refChr9 21947 44 + 35212 TAGGCCCAT-AAGCAATATTTTAATAGATAATTCTTAGATTTTGG -s Anc1.Anc1refChr0 2289 45 - 16026 TAGGCCCATGAAGCAATATTTTAATAGATAATTCTTAGATTTTGG -s Anc2.Anc2refChr0 42021 44 - 56053 TAGGCCCAT-AAGCAATATCTTAATAGCTAGTTCTTAGATTTTGG -s mr.mrrefChr0 45438 45 + 130230 CAGGTACATAAAACAATATTTTAGTTGATAATTCTTAGATCTTTG -s simCow_chr6.simCow.chr6 584638 44 - 602619 TAGGCCTAT-AAGCAGTGTCTTAATAGTCAGTACTTAGATTTAAG -s simDog_chr6.simDog.chr6 579806 44 - 593897 TGGGCCCAT-AAGCAACATCTTAATAGCTAGTTCATACATTATGG -s simHuman_chr6.simHuman.chr6 586433 45 - 601863 TAGGCCCATGAAGCAATTTTTTACTCGATAATTCTTAGATTTTGG -s simRat_chr6.simRat.chr6 40422 45 + 647215 CAGGTACATATAACAATATTATAGTTGATAATTCTTCGTTCTTTG - -a -s simMouse_chr6.simMouse.chr6 47704 10 + 636262 TCTTTGCCCA -s Anc0.Anc0refChr9 22005 10 + 35212 TATGTTCTTC -s Anc1.Anc1refChr0 2348 10 - 16026 TATGTTCTTC -s Anc2.Anc2refChr0 42079 10 - 56053 AATGTTCTTC -s mr.mrrefChr0 45495 10 + 130230 TCTTTGCCCA -s simCow_chr6.simCow.chr6 584711 10 - 602619 AATGTTCTCC -s simDog_chr6.simDog.chr6 579862 10 - 593897 AATGATCTTC -s simHuman_chr6.simHuman.chr6 586492 10 - 601863 TATGTCCTTC -s simRat_chr6.simRat.chr6 40479 10 + 647215 TCTTTGCCCA - -a -s simMouse_chr6.simMouse.chr6 47714 53 + 636262 TGCACTGCTCCATGTTAAAGTGCTTGAAGAGGGCAGGAACCTCTTTCTAATCA -s Anc0.Anc0refChr9 22015 44 + 35212 TGCCCTTATCAGTT---------TTTAATGTGACAAAAACCTCTTTGTAATCA -s Anc1.Anc1refChr0 2358 44 - 16026 TGCCCTTATCAGTT---------TTTAATGTGACAAAAACCTCTTTGTAATCA -s Anc2.Anc2refChr0 42089 44 - 56053 TGCCCTTATCAGTT---------TTTAATGTGACAAAAATATCTCTGTAATCA -s mr.mrrefChr0 45505 53 + 130230 TGCACTGCTCCATGTTAAAGTGCTTGAAGAGGGCAAGAACCTCTTTCTAATCA -s simCow_chr6.simCow.chr6 584721 44 - 602619 TGCCCTTATTAGAT---------CTTAATATGGCAAAAATATCTCTGTAACCA -s simDog_chr6.simDog.chr6 579894 44 - 593897 TGCCTTCATCAGTT---------TGTAATGTAACAAAAGTATCTCCATAATTA -s simHuman_chr6.simHuman.chr6 586502 44 - 601863 TGCCCCTATCAGTT---------TTTAATTTGACAAAGACCTCCTTGTAATCA -s simRat_chr6.simRat.chr6 40489 53 + 647215 TGCACTGCACCATGTCATAGTGCTTGAAGAGCGCAAGAACCTCTTTCTAATCA - -a -s simMouse_chr6.simMouse.chr6 47767 29 + 636262 TAGGACCCATGATGTTATAATGGTTTTTA -s Anc0.Anc0refChr9 22064 15 + 35212 --------------TTATAATGATCTTCA -s Anc1.Anc1refChr0 2407 15 - 16026 --------------TTATAATGATCTTCA -s Anc2.Anc2refChr0 42138 15 - 56053 --------------TTATAATGATCTTTG -s mr.mrrefChr0 45563 29 + 130230 TAGGACCCATGATGTTATAATGATCTTCA -s simCow_chr6.simCow.chr6 584770 15 - 602619 --------------TTATGATGTTTTTTG -s simDog_chr6.simDog.chr6 579943 15 - 593897 --------------TTATAATGATCATTG -s simHuman_chr6.simHuman.chr6 586551 15 - 601863 --------------TTATAATGAGCTTCA -s simRat_chr6.simRat.chr6 40547 29 + 647215 TAGAATCAATAACATTATAATGATCTTCA - -a -s simMouse_chr6.simMouse.chr6 47796 35 + 636262 AGTGAAGCAGAAATTCCATTCATATTTATGCTTTG -s Anc0.Anc0refChr9 22079 31 + 35212 AGTTAAGTATAAGTTACATTCATTTTTATGA---- -s Anc1.Anc1refChr0 2422 31 - 16026 AGTTAAGTATAAGTTACATTCATTTTTATGA---- -s Anc2.Anc2refChr0 42153 31 - 56053 AGTTAAGTATAAGTCACATTCATTTTTATGA---- -s mr.mrrefChr0 45592 31 + 130230 AGTGAAGCAGAAATTCCATTCATATTTATGC---- -s simCow_chr6.simCow.chr6 584785 31 - 602619 GGTTTTATATAGGTGGCTATCATTCTTATGA---- -s simDog_chr6.simDog.chr6 579961 27 - 593897 AGTTAAGTATGACTCACATGCATTTTC-------- -s simHuman_chr6.simHuman.chr6 586566 31 - 601863 AGTTAAGTATAAGCTACATTCGTCTTTATGT---- -s simRat_chr6.simRat.chr6 40576 31 + 647215 AGTCAATCCAAAATTCCATTCATATTTATGG---- - -a -s simMouse_chr6.simMouse.chr6 47831 24 + 636262 ACAACCATGTACGCCCCAGAGAAA -s Anc0.Anc0refChr9 22110 22 + 35212 CCTTGCAT-TAC-CCTCAGAGAAG -s Anc1.Anc1refChr0 2453 22 - 16026 CCTTGCAT-TAC-CCTCAGAGAAG -s Anc2.Anc2refChr0 42184 22 - 56053 CCATGCAT-TAC-CCTCAGAGATG -s mr.mrrefChr0 45623 24 + 130230 ACTACCATGTACGCCCCAGAGAAA -s simCow_chr6.simCow.chr6 584824 22 - 602619 CCATACAT-TAA-CCTCAGGGAGG -s simDog_chr6.simDog.chr6 579988 22 - 593897 CCATGCAC-TAC-CCTCACAGATT -s simHuman_chr6.simHuman.chr6 586597 22 - 601863 CCTCGCAT-TAT-CCACTGAGAAG -s simRat_chr6.simRat.chr6 40607 24 + 647215 ACTACCATGTACACCTCAGAGAAA - -a -s simMouse_chr6.simMouse.chr6 47855 29 + 636262 CTGTCATATCTGACTAGGTTACATCGTGG -s Anc0.Anc0refChr9 22132 29 + 35212 TTCTAATAGCCTACTAGGTTACATAGCTA -s Anc1.Anc1refChr0 2475 29 - 16026 TTCTAATAGCCTACTAGGTTACATAGCTA -s Anc2.Anc2refChr0 42206 29 - 56053 TTCTAATAGCCTACTAGGTTACATAGCTA -s mr.mrrefChr0 45647 29 + 130230 TTCTCATATCTGACTAGGTTACATAGCTA -s simCow_chr6.simCow.chr6 584851 29 - 602619 TCCTCAGACCCTACTAGTTTACATAGCTA -s simDog_chr6.simDog.chr6 580010 29 - 593897 TTCTAATAGCCTACTAGGCTACATAGCTA -s simHuman_chr6.simHuman.chr6 586619 26 - 601863 TTC---TGGCCTATTAGGTCACATAGCTA -s simRat_chr6.simRat.chr6 40631 29 + 647215 TCCTCATTTCTGACTAGGCTACATAGCTA - -a -s simMouse_chr6.simMouse.chr6 47884 12 + 636262 TCATCTACTGGG -s Anc0.Anc0refChr9 22161 12 + 35212 TAGTCTACTGGG -s Anc1.Anc1refChr0 2504 12 - 16026 TAGTCTACTGGG -s Anc2.Anc2refChr0 42235 12 - 56053 TAGTCTACGGGA -s mr.mrrefChr0 45676 12 + 130230 TCGTCTACTGGG -s simCow_chr6.simCow.chr6 584880 12 - 602619 TAGTCTACAGGT -s simDog_chr6.simDog.chr6 580040 12 - 593897 TAGTCTACGGGA -s simHuman_chr6.simHuman.chr6 586645 12 - 601863 TAGTCTACTGGG -s simRat_chr6.simRat.chr6 40660 12 + 647215 TTGACTAATGGG - -a -s simMouse_chr6.simMouse.chr6 47896 51 + 636262 TTTAGTTCGGGGCAACCTTTTAATAAACTGATTCGATTACTATTGAGTGGA -s Anc0.Anc0refChr9 22173 50 + 35212 TTTAGTGCAGGA-AGAATCTTCATGTACTGAGTCAAGTGGTATTGAGTGCA -s Anc1.Anc1refChr0 2516 50 - 16026 TTTAGTGCAGGA-AGAATCTTCATGTACTGAGTCAAGTGGTATTGAGTGCA -s Anc2.Anc2refChr0 42247 50 - 56053 TTTAGTGCAGAA-AGAATCTTCATGTACTGAGTCAAGTAGCATTGAGTGCA -s mr.mrrefChr0 45688 51 + 130230 TTTAGTTCAGGGCAACCTTTTAATAAACTGATTCAATTGCTATTGAGTGCA -s simCow_chr6.simCow.chr6 584892 50 - 602619 TTTAGGACAGAA-AGAATCTTTATGTCCTGAGTCAGGTAACATTGAGTCCA -s simDog_chr6.simDog.chr6 580052 50 - 593897 TTTGGTGCAAAA-AGAATCTTCATGTACTGGATCGAGGAGCATTGATTGCA -s simHuman_chr6.simHuman.chr6 586658 50 - 601863 TTTAGTGCAGGA-AGAATGTCCATGTACTGAGTCACGTGGTGTTGAGTACA -s simRat_chr6.simRat.chr6 40672 51 + 647215 TTTAGTACAGGGCAACCTCTTAATACATTGATTTAATTGCTATTGAGTGCA - -a -s simMouse_chr6.simMouse.chr6 47947 4 + 636262 GAAA -s Anc0.Anc0refChr9 22224 4 + 35212 AGTC -s Anc1.Anc1refChr0 2567 4 - 16026 AGTC -s Anc2.Anc2refChr0 42298 4 - 56053 AATC -s mr.mrrefChr0 45739 4 + 130230 AGAA -s simCow_chr6.simCow.chr6 584943 4 - 602619 GATC -s simDog_chr6.simDog.chr6 580103 4 - 593897 AATC -s simHuman_chr6.simHuman.chr6 586709 4 - 601863 AGTC -s simRat_chr6.simRat.chr6 40723 4 + 647215 AGAA - -a -s simMouse_chr6.simMouse.chr6 47951 94 + 636262 TCACTGACAAACTTCTACTTCTGAATATTGAAGAAATCAGCTGTGGCTAGTTTGAGGGCAAGCCCTAATATCTGGTAAAATGGTTAGCCCCCCC -s Anc0.Anc0refChr9 22228 87 + 35212 TGACTGACAA------ACCACTGCAATTTGAATAATTCATCTGTGGTTAGTTTGAAGACAAACCCTTATATTTGGTG-AACAGTTAGTTCCTTG -s Anc1.Anc1refChr0 2571 87 - 16026 TGACTGACAA------ACCACTGCAATTTGAATAATTCATCTGTGGTTAGTTTGAAGACAAACCCTTATATTTGGTG-AACAGTTAGTTCCTTG -s Anc2.Anc2refChr0 42302 87 - 56053 TGACTGACAA------ATCACTGCAATTCCAATAATTCATCTGTGGTTAGTTTGAAGATAAACCCTTATATTTGCTG-AACAACTTGCTGCTTG -s mr.mrrefChr0 45743 87 + 130230 TCACTGACAA------ACCACTGAATATTGAAGAAATCAGCTGTGGCTAGTTTGAGGGCAAACCCTAATATCTGGTA-AATGGTTAGTCCCCTC -s simCow_chr6.simCow.chr6 584947 78 - 602619 TGACTGACAA------ATCACTGCAACTC---------ATCTTTGGTTAGTTTGAAGGTAAACCCTTATATCTGATG-AACAACTTGCTGCTTG -s simDog_chr6.simDog.chr6 580123 71 - 593897 TGACTGACAA------TTCACTGCAATTCCAATAATTCATTTGTAGTTAGTTTGAAGATAAATCCTTATATTTCCTG----------------- -s simHuman_chr6.simHuman.chr6 586713 87 - 601863 TGATTTACAT------ACCACCGCAATTTGAATAATTCATCTGTGATTAGTTTAAAGCCAAACCCTGATACTTGGTG-AACTGTTAGTACCTTT -s simRat_chr6.simRat.chr6 40727 87 + 647215 TCACTGACAA------ACCATTGAATGTTGAACAAATCAACTGTGGCTCGTTTGAGGGCAAACCCCAATTTCTGACA-AATGGTCAGTCCTCTC - -a -s simMouse_chr6.simMouse.chr6 48045 35 + 636262 TACTCATACAGGTATCCCCATCCCTATACACCACT -s Anc0.Anc0refChr9 22319 35 + 35212 TGTTCATACAGGCATACCCATCACTATACACCACT -s Anc1.Anc1refChr0 2662 35 - 16026 TGTTCATACAGGCATACCCATCACTATACACCACT -s Anc2.Anc2refChr0 42393 35 - 56053 TGTTCATACAGGCATACCTATCATTATACATCACT -s mr.mrrefChr0 45830 35 + 130230 TACTCATACAGGTATCCCCATCCCTATACACCACT -s simCow_chr6.simCow.chr6 585029 35 - 602619 TGTTGATACAGGCAAACCTATCATTAGATATCACT -s simDog_chr6.simDog.chr6 580195 35 - 593897 TGTTCATACAGGCATACCTATCGTTATACATCACT -s simHuman_chr6.simHuman.chr6 586804 35 - 601863 TTTTCATACAGGCATACCCATCACTATACACCACT -s simRat_chr6.simRat.chr6 40814 35 + 647215 TGCTCATACAGGTATCCCTATCCCTATACACCACT - -a -s simMouse_chr6.simMouse.chr6 48080 1 + 636262 A -s Anc0.Anc0refChr9 22355 1 + 35212 A -s Anc1.Anc1refChr0 2698 1 - 16026 A -s Anc2.Anc2refChr0 42429 1 - 56053 A -s mr.mrrefChr0 45866 1 + 130230 A -s simCow_chr6.simCow.chr6 585065 1 - 602619 A -s simDog_chr6.simDog.chr6 580231 1 - 593897 A -s simHuman_chr6.simHuman.chr6 586840 1 - 601863 A -s simRat_chr6.simRat.chr6 40850 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 48081 9 + 636262 CACCACAGA -s Anc0.Anc0refChr9 22357 9 + 35212 CACCACAGA -s Anc1.Anc1refChr0 2700 9 - 16026 CACCACAGA -s Anc2.Anc2refChr0 42431 9 - 56053 CACCACAGA -s mr.mrrefChr0 45867 9 + 130230 CACCACAGA -s simCow_chr6.simCow.chr6 585067 9 - 602619 CACCACAGA -s simDog_chr6.simDog.chr6 580233 9 - 593897 CACCATAGA -s simHuman_chr6.simHuman.chr6 586842 9 - 601863 CACCACAGA -s simRat_chr6.simRat.chr6 40851 9 + 647215 CACCACAGA - -a -s simMouse_chr6.simMouse.chr6 48090 15 + 636262 ACTACGCTCAGATAT -s Anc0.Anc0refChr9 22366 13 + 35212 ATTG--TTCAGATAT -s Anc1.Anc1refChr0 2709 13 - 16026 ATTG--TTCAGATAT -s Anc2.Anc2refChr0 42442 13 - 56053 ATTG--TTCACATAT -s mr.mrrefChr0 45876 13 + 130230 ACTA--CTCAGATAT -s simCow_chr6.simCow.chr6 585078 13 - 602619 ATTG--TTCACATAT -s simDog_chr6.simDog.chr6 580244 13 - 593897 ATTG--TTCACATAC -s simHuman_chr6.simHuman.chr6 586851 9 - 601863 G------TCAGATAT -s simRat_chr6.simRat.chr6 40860 13 + 647215 ACTA--CTAAGATAT - -a -s simMouse_chr6.simMouse.chr6 48105 2 + 636262 TA -s Anc0.Anc0refChr9 22380 2 + 35212 TA -s Anc1.Anc1refChr0 2723 2 - 16026 TA -s Anc2.Anc2refChr0 42456 2 - 56053 TA -s mr.mrrefChr0 45889 2 + 130230 TA -s simCow_chr6.simCow.chr6 585092 2 - 602619 TA -s simDog_chr6.simDog.chr6 580258 2 - 593897 TA -s simHuman_chr6.simHuman.chr6 586861 2 - 601863 TA -s simRat_chr6.simRat.chr6 40873 2 + 647215 TA - -a -s simMouse_chr6.simMouse.chr6 48107 19 + 636262 GAGTTACATCCATGGGGGC -s Anc0.Anc0refChr9 22383 19 + 35212 TAGTTACATATATATATGC -s Anc1.Anc1refChr0 2726 19 - 16026 TAGTTACATATATATATGC -s Anc2.Anc2refChr0 42459 19 - 56053 TAGTTACATATATATATAC -s mr.mrrefChr0 45892 19 + 130230 GAGTTACATCCATGTAGGC -s simCow_chr6.simCow.chr6 585095 19 - 602619 TAGATACATATATATATAC -s simDog_chr6.simDog.chr6 580261 18 - 593897 TAGT-ACATATATACATAC -s simHuman_chr6.simHuman.chr6 586864 19 - 601863 TAGTTATATATATATATGC -s simRat_chr6.simRat.chr6 40876 19 + 647215 GAGTTACATTCATGTAGGG - -a -s simMouse_chr6.simMouse.chr6 48126 56 + 636262 TAGCAATGTTTTTTAGTGCACCTGCACTTGGTTGCAGACAAGGTGTCATGCAGATG -s Anc0.Anc0refChr9 22405 50 + 35212 TACAAATATCTTTTAGTATTCCTGCCCCTATTTGCA------GTATAATACATGTT -s Anc1.Anc1refChr0 2748 50 - 16026 TACAAATATCTTTTAGTATTCCTGCCCCTATTTGCA------GTATAATACATGTT -s Anc2.Anc2refChr0 42481 50 - 56053 TACAAATGTCTTTTAGTATTCCTGCCCCTATTTGCA------GTATAACACATGTT -s mr.mrrefChr0 45911 56 + 130230 TAGCAATATTTTTTAGTACTCCTGCACTTGGTTGCAGACAAGGTGTCATACAGATT -s simCow_chr6.simCow.chr6 585117 50 - 602619 TACAAATGTCTTTTAGTATACCTGCACCCATTAGTA------GAATTCCACATGTT -s simDog_chr6.simDog.chr6 580282 47 - 593897 TACAAATGTTTTTAA---CTCTTGCCCCTCTGTGCA------TTATAACACATGTT -s simHuman_chr6.simHuman.chr6 586886 50 - 601863 TATAAATATCTTTTAGTATTCCTGCGCCTACTTGCA------GTATAATACATGTT -s simRat_chr6.simRat.chr6 40895 56 + 647215 TAACAATATTTTTTAGCACTCCTGCACTTGGCTGCGGACAAGGTGTCATACAGATT - -a -s simMouse_chr6.simMouse.chr6 48182 14 + 636262 TCATACTGACCTGG -s Anc0.Anc0refChr9 22465 14 + 35212 TCATACTGAACTGG -s Anc1.Anc1refChr0 2808 14 - 16026 TCATACTGAACTGG -s Anc2.Anc2refChr0 42541 14 - 56053 TCATACTGAACTGG -s mr.mrrefChr0 45967 14 + 130230 TCATACTGAACTGG -s simCow_chr6.simCow.chr6 585176 14 - 602619 TCATACCAAACTGG -s simDog_chr6.simDog.chr6 580339 14 - 593897 TCATACTGAACAGG -s simHuman_chr6.simHuman.chr6 586946 14 - 601863 TCTTACTGAACTGG -s simRat_chr6.simRat.chr6 40951 14 + 647215 TCATACTGGACTGG - -a -s simMouse_chr6.simMouse.chr6 48196 22 + 636262 ACCCTCTGTTTAGACTACGGGG -s Anc0.Anc0refChr9 22479 22 + 35212 ACCCTCTGTTTAGACTATGGGG -s Anc1.Anc1refChr0 2822 22 - 16026 ACCCTCTGTTTAGACTATGGGG -s Anc2.Anc2refChr0 42555 22 - 56053 ACCCTCTGTTTAGACTTTGGGG -s mr.mrrefChr0 45981 22 + 130230 ACCCTCTGTTTAGACTACGGGG -s simCow_chr6.simCow.chr6 585202 22 - 602619 GCCCTCTATTTAGACTTGGGGG -s simDog_chr6.simDog.chr6 580353 22 - 593897 ACCCTCTGTTTAGACTTTGGGG -s simHuman_chr6.simHuman.chr6 586960 22 - 601863 CCCCTTTGTCTAAACTATAGGG -s simRat_chr6.simRat.chr6 40965 22 + 647215 ACCCTCTGTTTAGACTAGGGTG - -a -s simMouse_chr6.simMouse.chr6 48218 28 + 636262 CTGACCTGTTAATATGTATCCTTAAAAA -s Anc0.Anc0refChr9 22501 24 + 35212 CT----TGTTAATATGTAGCCTTATAAA -s Anc1.Anc1refChr0 2844 24 - 16026 CT----TGTTAATATGTAGCCTTATAAA -s Anc2.Anc2refChr0 42578 24 - 56053 CT----TCTCAATATGTAGCCTTATAAT -s mr.mrrefChr0 46003 28 + 130230 CTGACCTGTTAATATGTATCCTTAAAAA -s simCow_chr6.simCow.chr6 585225 18 - 602619 ----------AATATGTAGCCTTATAAT -s simDog_chr6.simDog.chr6 580379 12 - 593897 CT----TCTCAATCTG------------ -s simHuman_chr6.simHuman.chr6 586982 24 - 601863 CT----TGTTAATATGTAACCTTACAGA -s simRat_chr6.simRat.chr6 40987 28 + 647215 CTAACCTGTTAATATGTAGCCTTATAAA - -a -s simMouse_chr6.simMouse.chr6 48246 20 + 636262 AATGGATTCAATCATTATTG -s Anc0.Anc0refChr9 22584 20 + 35212 AAAGTGTCCAATTGTTATAA -s Anc1.Anc1refChr0 2927 20 - 16026 AAAGTGTCCAATTGTTATAA -s Anc2.Anc2refChr0 42661 20 - 56053 AAAGTGGCCAATTGTTGTAA -s mr.mrrefChr0 46031 20 + 130230 AATGGATTCAATCATTATTG -s simCow_chr6.simCow.chr6 585304 18 - 602619 AAAGTG--CAATTGTTGTAA -s simDog_chr6.simDog.chr6 580450 20 - 593897 AAAGTTGCCAAGTGTAGTAA -s simHuman_chr6.simHuman.chr6 587065 20 - 601863 AAAGTGTGCAATTGTTATGA -s simRat_chr6.simRat.chr6 41015 13 + 647215 -------TCAATCATTATTG - -a -s simMouse_chr6.simMouse.chr6 48266 27 + 636262 GAGCAAAAAAATGGGCAAAGTCTTGAT -s Anc0.Anc0refChr9 22604 26 + 35212 GAAT-AAAAAACGTACAAGTATCTGGT -s Anc1.Anc1refChr0 2947 26 - 16026 GAAT-AAAAAACGTACAAGTATCTGGT -s Anc2.Anc2refChr0 42681 26 - 56053 GAAT-TAAAAACTGACAGGTATCTGGT -s mr.mrrefChr0 46051 26 + 130230 GAGC-AAAAAATGTACAAGTTCTTGAT -s simCow_chr6.simCow.chr6 585324 26 - 602619 GCAT-CAAAAATTCACAGGTATCTAGT -s simDog_chr6.simDog.chr6 580470 26 - 593897 GAAT-TAAAAACTGACAGGTATCTGGT -s simHuman_chr6.simHuman.chr6 587085 26 - 601863 GTAT-AGAATAAGTACAAGTATCTGGT -s simRat_chr6.simRat.chr6 41028 26 + 647215 GGGC-GAAGAATGTACAAGTTGTTGAT - -a -s simMouse_chr6.simMouse.chr6 48293 29 + 636262 TGTAGAAGTTAGAAGCATCATACATCGGA -s Anc0.Anc0refChr9 22632 25 + 35212 TGTGGGTTGTAGAAGCC----ACCTAAGA -s Anc1.Anc1refChr0 2975 25 - 16026 TGTGGGTTGTAGAAGCC----ACCTAAGA -s Anc2.Anc2refChr0 42709 25 - 56053 TGTGGGTTGGAGAAGCC----TCCTAAGA -s mr.mrrefChr0 46077 29 + 130230 TGTAGAAGGTAGAAGCATCATACATCAGA -s simCow_chr6.simCow.chr6 585352 25 - 602619 GGTGGATAGGAAAAGCC----TCATAAGG -s simDog_chr6.simDog.chr6 580498 25 - 593897 TGCGAGTTGGAGAAGCC----TTCTAAGA -s simHuman_chr6.simHuman.chr6 587113 25 - 601863 TGTGGCTTGTAGAAACC----ACCTAAGA -s simRat_chr6.simRat.chr6 41054 29 + 647215 TGTAGAAGGTAGAAGCATAGTACACGAAA - -a -s simMouse_chr6.simMouse.chr6 48322 24 + 636262 GAGATTGTGTCATCCTAATTCCCA -s Anc0.Anc0refChr9 22657 23 + 35212 GAAATTGTGTCATCCTAA-TCCCA -s Anc1.Anc1refChr0 3000 23 - 16026 GAAATTGTGTCATCCTAA-TCCCA -s Anc2.Anc2refChr0 42734 23 - 56053 GAAATTGTGTCATCCTAA-TCCCA -s mr.mrrefChr0 46106 24 + 130230 GAGATTGTGTCATCCTAATTCCCA -s simCow_chr6.simCow.chr6 585377 23 - 602619 GAAATTGTGTCATCCTAA-TCCCA -s simDog_chr6.simDog.chr6 580526 23 - 593897 GAAATTGTGTCATCCTAA-TCCCA -s simHuman_chr6.simHuman.chr6 587138 23 - 601863 GAAATTGTGTCATCCATA-TCTCA -s simRat_chr6.simRat.chr6 41083 24 + 647215 GAGATTGTGTCATTCTAATTCCCA - -a -s simMouse_chr6.simMouse.chr6 48346 22 + 636262 GAATATATTTCCAGTTTAACAG -s Anc0.Anc0refChr9 22680 22 + 35212 GAATCTATGTACAGTTTAGCAT -s Anc1.Anc1refChr0 3023 22 - 16026 GAATCTATGTACAGTTTAGCAT -s Anc2.Anc2refChr0 42758 22 - 56053 GAATCTATGTACAGTCTAGCAT -s mr.mrrefChr0 46130 22 + 130230 GAATATATTTCCAGTTTAACAG -s simCow_chr6.simCow.chr6 585401 22 - 602619 GAGTCCATGTTCAGTATAGCAT -s simDog_chr6.simDog.chr6 580550 22 - 593897 AAATCTATATACACCCTAGCAA -s simHuman_chr6.simHuman.chr6 587161 22 - 601863 GGATGTATGTACAGTTTAGCAT -s simRat_chr6.simRat.chr6 41107 22 + 647215 GAATATATTTCCAGTTTAACAC - -a -s simMouse_chr6.simMouse.chr6 48368 37 + 636262 TTGGCTCCAGGAGGATTGAATTGAAATAGTGCTTTTT -s Anc0.Anc0refChr9 22704 34 + 35212 TGTGTTCCAAGAA---TGCATGGAATTAGTGGTTTAT -s Anc1.Anc1refChr0 3047 34 - 16026 TGTGTTCCAAGAA---TGCATGGAATTAGTGGTTTAT -s Anc2.Anc2refChr0 42782 34 - 56053 GGTGTTCCTAGAA---TGCATGGAATTAGTTGTATAT -s mr.mrrefChr0 46152 37 + 130230 TTGGCTCCAGGAGGATTGAATGGAAATAGTGCTTTTT -s simCow_chr6.simCow.chr6 585425 34 - 602619 GGTGATCTCAGAA---TGCATGGAATTATTTGTATTT -s simDog_chr6.simDog.chr6 580574 25 - 593897 GGTGTTCCT------------GGAATAAGTTGTAAAT -s simHuman_chr6.simHuman.chr6 587185 34 - 601863 TGTGTTCCAAGAA---TGTATGGAATTACTGGTTTAT -s simRat_chr6.simRat.chr6 41129 37 + 647215 TCGGCTCCAGGAGGACTCAATGGAACTCGTAATTTTT - -a -s simMouse_chr6.simMouse.chr6 48405 3 + 636262 GGT -s Anc0.Anc0refChr9 22738 3 + 35212 GAA -s Anc1.Anc1refChr0 3081 3 - 16026 GAA -s Anc2.Anc2refChr0 42816 3 - 56053 GAA -s mr.mrrefChr0 46189 3 + 130230 GAT -s simCow_chr6.simCow.chr6 585465 3 - 602619 GAG -s simDog_chr6.simDog.chr6 580599 3 - 593897 GAA -s simHuman_chr6.simHuman.chr6 587219 3 - 601863 GAA -s simRat_chr6.simRat.chr6 41166 3 + 647215 GAG - -a -s simMouse_chr6.simMouse.chr6 48408 14 + 636262 CCTATCATAGACCA -s Anc0.Anc0refChr9 22741 7 + 35212 CCTAT-------AA -s Anc1.Anc1refChr0 3084 7 - 16026 CCTAT-------AA -s Anc2.Anc2refChr0 42819 7 - 56053 CCTAT-------AT -s mr.mrrefChr0 46192 7 + 130230 CCTAT-------CA -s simCow_chr6.simCow.chr6 585468 7 - 602619 CCTGT-------AC -s simDog_chr6.simDog.chr6 580602 7 - 593897 CCCAT-------AT -s simHuman_chr6.simHuman.chr6 587222 7 - 601863 CCTAT-------AA -s simRat_chr6.simRat.chr6 41171 7 + 647215 CCTAT-------CA - -a -s simMouse_chr6.simMouse.chr6 48422 11 + 636262 AAGTATTATGT -s Anc0.Anc0refChr9 22806 9 + 35212 AATCATTA--T -s Anc1.Anc1refChr0 3149 11 - 16026 AATCATTATTT -s Anc2.Anc2refChr0 42884 9 - 56053 AATCATTA--T -s mr.mrrefChr0 46199 11 + 130230 AATCATTATTT -s simCow_chr6.simCow.chr6 585529 9 - 602619 AACCACTA--T -s simDog_chr6.simDog.chr6 580665 9 - 593897 AATCATTA--T -s simHuman_chr6.simHuman.chr6 587287 11 - 601863 AATCATTCTTT -s simRat_chr6.simRat.chr6 41178 11 + 647215 AATCATTGTTT - -a -s simMouse_chr6.simMouse.chr6 48433 6 + 636262 ACCTAC -s Anc0.Anc0refChr9 22819 6 + 35212 ATCTAC -s Anc1.Anc1refChr0 3164 6 - 16026 ATCTAC -s Anc2.Anc2refChr0 42897 6 - 56053 ATCTAC -s mr.mrrefChr0 46210 6 + 130230 ACCTAC -s simCow_chr6.simCow.chr6 585541 6 - 602619 GCCTAC -s simDog_chr6.simDog.chr6 580678 6 - 593897 ATCTAC -s simHuman_chr6.simHuman.chr6 587306 6 - 601863 ATCTGC -s simRat_chr6.simRat.chr6 41189 6 + 647215 ACCTAC - -a -s simMouse_chr6.simMouse.chr6 48439 51 + 636262 ATATCCCCATATACTATGATGATAACGGTATCAGAAAAAGGGTTGCTATTA -s Anc0.Anc0refChr9 22828 51 + 35212 ACATCTCCATATGATCTGATGATAATGGTAGCAGAAACAGTGTTGCTATTG -s Anc1.Anc1refChr0 3173 51 - 16026 ACATCTCCATATGATCTGATGATAATGGTAGCAGAAACAGTGTTGCTATTG -s Anc2.Anc2refChr0 42906 51 - 56053 ACATCTCCTTATGAGCTGATGATAATGGTAGCAGACACAGTGTTGCTATTG -s mr.mrrefChr0 46216 51 + 130230 ATATCCCCATATACTATGATGATAACGGTAGCAGAAAAAGTGTTGCTATTG -s simCow_chr6.simCow.chr6 585550 51 - 602619 ACATCTCCTTATAACCTGATAATAATGGTAGCAGATACAGTGTTGCTATTG -s simDog_chr6.simDog.chr6 580687 50 - 593897 GCATCACCTTATGAGTTGA-GAGTATGGTAGCAGACACATTGTTGCTATTG -s simHuman_chr6.simHuman.chr6 587315 51 - 601863 ACATCTCCATATGATCTAACGATAAAGGTAGCAGAATCAGTGTTGCTATTG -s simRat_chr6.simRat.chr6 41195 51 + 647215 AAATCCCCATTTACTATGATAATAATGCTAGCTCAAATAGTGTTGCTATTG - -a -s simMouse_chr6.simMouse.chr6 48490 36 + 636262 GGAAGTAAGTATTGTCAACTTTTAGCCTCTTGTACT -s Anc0.Anc0refChr9 22891 34 + 35212 GGAAATATGCATCTTCCTCTTCTGGCCACT--TACT -s Anc1.Anc1refChr0 3236 34 - 16026 GGAAATATGCATCTTCCTCTTCTGGCCACT--TACT -s Anc2.Anc2refChr0 42969 34 - 56053 GGAAATATGCATCTTCCTCTTCTGGCCACT--AACT -s mr.mrrefChr0 46267 36 + 130230 GGAAGTAAGTATTGTCCACTTTTAGCCTCTTGTACT -s simCow_chr6.simCow.chr6 585613 34 - 602619 GTAAATACGGATTGTGCTCTTCTGGCCACT--GACT -s simDog_chr6.simDog.chr6 580749 34 - 593897 GGATGTATGCATCTTCCCCCTCTGGCCACT--AACT -s simHuman_chr6.simHuman.chr6 587378 34 - 601863 GGAAATATGCATCCTCCTCTACTGACCACT--TACT -s simRat_chr6.simRat.chr6 41246 36 + 647215 GGAGGTAAGTATTGTCCACTTATAGGCTCTTGTACT - -a -s simMouse_chr6.simMouse.chr6 48526 4 + 636262 TAAA -s Anc0.Anc0refChr9 22931 4 + 35212 TAAA -s Anc1.Anc1refChr0 3276 4 - 16026 TAAA -s Anc2.Anc2refChr0 43009 4 - 56053 TAAA -s mr.mrrefChr0 46303 4 + 130230 TAAA -s simCow_chr6.simCow.chr6 585653 4 - 602619 TAAA -s simDog_chr6.simDog.chr6 580789 4 - 593897 TAGA -s simHuman_chr6.simHuman.chr6 587418 4 - 601863 TAAT -s simRat_chr6.simRat.chr6 41282 4 + 647215 TAAG - -a -s simMouse_chr6.simMouse.chr6 48530 12 + 636262 CAGCAAGCTCAA -s Anc0.Anc0refChr9 22935 12 + 35212 CATAATGCTCAA -s Anc1.Anc1refChr0 3280 12 - 16026 CATAATGCTCAA -s Anc2.Anc2refChr0 43013 12 - 56053 CATAATGCTCAA -s mr.mrrefChr0 46307 12 + 130230 CAGCAAGCTCAA -s simCow_chr6.simCow.chr6 585658 12 - 602619 TACAGTGCTCAA -s simDog_chr6.simDog.chr6 580793 12 - 593897 CATAACACTCAA -s simHuman_chr6.simHuman.chr6 587422 12 - 601863 CATGATGATCAG -s simRat_chr6.simRat.chr6 41286 12 + 647215 CAGCGCACTCAA - -a -s simMouse_chr6.simMouse.chr6 48542 28 + 636262 GTCACATTCACAGTAAGCACCTAAGATC -s Anc0.Anc0refChr9 22948 28 + 35212 GTCACCCTAGCTCTAGTGACCGGAGATC -s Anc1.Anc1refChr0 3293 28 - 16026 GTCACCCTAGCTCTAGTGACCGGAGATC -s Anc2.Anc2refChr0 43026 28 - 56053 GTCAACCTAGCTCTAGTGACCGGAGATC -s mr.mrrefChr0 46320 28 + 130230 GTCACATTCACTGTAAGCACCTAAGATC -s simCow_chr6.simCow.chr6 585671 22 - 602619 GTCAACCTAGTTCTTTGGACCT------ -s simDog_chr6.simDog.chr6 580806 28 - 593897 GTCAACCTAGCTCGAGTGACCGGAGATC -s simHuman_chr6.simHuman.chr6 587435 28 - 601863 GTCACCCTAGCTCTAGAGATCCGAAATC -s simRat_chr6.simRat.chr6 41299 28 + 647215 GTCACGTTCACTGTAAGCACCTAAGATC - -a -s simMouse_chr6.simMouse.chr6 48570 89 + 636262 AATGTATATTGTTGCCATGGCAACAATTTAACAACTCGAGGTTGGTAGCAAAGAATGCTTACAGATCTGATGAACTGAATAACAGTCTT -s Anc0.Anc0refChr9 22977 89 + 35212 GTTATATACTTCTGCCACAGCAAGAAAATAAACACTCCAGGATGATAGCCAAGAATGCTGACAAAGCCCATAAAATTCTTAGCGGTTTG -s Anc1.Anc1refChr0 3322 89 - 16026 GTTATATACTTCTGCCACAGCAAGAAAATAAACACTCCAGGATGATAGCCAAGAATGCTGACAAAGCCCATAAAATTCTTAGCGGTTTG -s Anc2.Anc2refChr0 43055 89 - 56053 GTTATATACTTCTGCCACAGCAAGAAAATAAACACTCCAGGATGGTAGCCAAGAATGCTGACAAAGGCCATAAAATTTTTAGTGGTTTG -s mr.mrrefChr0 46349 89 + 130230 AATATATATTGCTGCCATGGCAACAAAATAAACACTCGAGGTTGATAGCAAAGAATGCTGACAGATCTGATGAACTGCATAACGGTCTT -s simCow_chr6.simCow.chr6 585693 85 - 602619 ----TATACTTCTGCCACAGCAAGAAAATAAACACTCCAGGATGGTAGCCAATAAAGTTGATAAAGTCACTAAAAGTTTAAGTGGTTTG -s simDog_chr6.simDog.chr6 580835 88 - 593897 GTTATATACTTCTACCA-AGCAAGAAATTAAACACTCCAGAACGGTAGCCAAGAATGCTGACAAAGGCCAGAAAGTTTCTAGTGGTTTG -s simHuman_chr6.simHuman.chr6 587464 89 - 601863 GCCATATACTTCTGCCAGAACAAGAAAAGAAACAGTCTAGGATGATCACCAAGAACACTGACAAAGCACATAAAATTCTTAGCGGTTTG -s simRat_chr6.simRat.chr6 41328 89 + 647215 AATACATATTGCTACAATGGCAACAAAATAAACCCTGCAGGGTGAATGCAAAGAATGCTGAGAGATCTGATGAACTGCATAATGGTCTT - -a -s simMouse_chr6.simMouse.chr6 48659 5 + 636262 AGCAG -s Anc0.Anc0refChr9 23067 5 + 35212 AGCTG -s Anc1.Anc1refChr0 3412 5 - 16026 AGCTG -s Anc2.Anc2refChr0 43145 5 - 56053 ATGTG -s mr.mrrefChr0 46438 5 + 130230 AGCAG -s simCow_chr6.simCow.chr6 585779 5 - 602619 ATATG -s simDog_chr6.simDog.chr6 580924 5 - 593897 GTGTG -s simHuman_chr6.simHuman.chr6 587554 5 - 601863 AGCTG -s simRat_chr6.simRat.chr6 41417 5 + 647215 AGCAG - -a -s simMouse_chr6.simMouse.chr6 48664 37 + 636262 GGCACTGATGCTACCTGGCTTCACCTATACAACTCTT -s Anc0.Anc0refChr9 23073 29 + 35212 GCCTCTGAAGCTGCCTGGATT---ATAGCCA-----C -s Anc1.Anc1refChr0 3418 29 - 16026 GCCTCTGAAGCTGCCTGGATT---ATAGCCA-----C -s Anc2.Anc2refChr0 43151 29 - 56053 GCCTCTGAAGCTGCCTGGATT---ATAGCCA-----C -s mr.mrrefChr0 46443 37 + 130230 GGCACTGATGCTACCTGGCTTCACATATCCAACTCTC -s simCow_chr6.simCow.chr6 585785 29 - 602619 GCCTCTGACGCTGCCTGGTTT---ATAGTCA-----C -s simDog_chr6.simDog.chr6 580930 29 - 593897 GCCTTTGAAGCTGCCTGGATT---ATAGCCA-----C -s simHuman_chr6.simHuman.chr6 587560 29 - 601863 GCCGCTAAAGCTGCTGGGGTT---ATAGCCA-----C -s simRat_chr6.simRat.chr6 41422 37 + 647215 GGCACTGATGCTACCTGGCTTCACATATCCAACTCTC - -a -s simMouse_chr6.simMouse.chr6 48701 65 + 636262 CATCTATGCAACTAGGGGCCATCAGGCCACATCAGTGCTTGGTGCTTTATTTTCAGCTGTTTGTG -s Anc0.Anc0refChr9 23102 16 + 35212 CATCC-------------------------------------------------AGCTGTTTGTC -s Anc1.Anc1refChr0 3447 16 - 16026 CATCC-------------------------------------------------AGCTGTTTGTC -s Anc2.Anc2refChr0 43216 16 - 56053 CATCC-------------------------------------------------AGCTGTTTCTC -s mr.mrrefChr0 46480 26 + 130230 CATCCATGCAACTAG---------------------------------------AGCTGTTTGTG -s simCow_chr6.simCow.chr6 585872 16 - 602619 TATCC-------------------------------------------------AGATTTTTCTC -s simDog_chr6.simDog.chr6 581012 16 - 593897 CATCC-------------------------------------------------AGCTGTCTCTC -s simHuman_chr6.simHuman.chr6 587589 16 - 601863 TATCC-------------------------------------------------AGCTGTTTGTA -s simRat_chr6.simRat.chr6 41459 26 + 647215 CAACCACACAATAAG---------------------------------------AACTGTTTTTG - -a -s simMouse_chr6.simMouse.chr6 48766 5 + 636262 TATGG -s Anc0.Anc0refChr9 23118 5 + 35212 TATGG -s Anc1.Anc1refChr0 3463 5 - 16026 TATGG -s Anc2.Anc2refChr0 43232 5 - 56053 TATGA -s mr.mrrefChr0 46506 5 + 130230 TATGG -s simCow_chr6.simCow.chr6 585898 5 - 602619 TAGTA -s simDog_chr6.simDog.chr6 581028 5 - 593897 TATGA -s simHuman_chr6.simHuman.chr6 587605 5 - 601863 TATGG -s simRat_chr6.simRat.chr6 41485 5 + 647215 TATGG - -a -s simMouse_chr6.simMouse.chr6 48771 12 + 636262 AACATTCTTGTT -s Anc0.Anc0refChr9 23123 12 + 35212 AACATTAATGTT -s Anc1.Anc1refChr0 3468 12 - 16026 AACATTAATGTT -s Anc2.Anc2refChr0 43237 12 - 56053 AACATTAATGTT -s mr.mrrefChr0 46511 12 + 130230 AACATTCTTGTT -s simCow_chr6.simCow.chr6 585903 12 - 602619 CTCATAGGTGTT -s simDog_chr6.simDog.chr6 581033 12 - 593897 AACAGTAATGTT -s simHuman_chr6.simHuman.chr6 587611 12 - 601863 AACATTAATGTT -s simRat_chr6.simRat.chr6 41490 12 + 647215 AACATTCTTGTC - -a -s simMouse_chr6.simMouse.chr6 48783 39 + 636262 TGTATTATTCTCACAGGTTGTGACATAAAAATCTTGAAG -s Anc0.Anc0refChr9 23135 3 + 35212 TGT------------------------------------ -s Anc1.Anc1refChr0 3480 3 - 16026 TGT------------------------------------ -s Anc2.Anc2refChr0 43249 3 - 56053 TGT------------------------------------ -s mr.mrrefChr0 46523 39 + 130230 TGTATTATTCTCACAGGTTGTGACACAAAAATCTTGAAG -s simCow_chr6.simCow.chr6 585928 3 - 602619 TGC------------------------------------ -s simDog_chr6.simDog.chr6 581045 2 - 593897 -GT------------------------------------ -s simHuman_chr6.simHuman.chr6 587623 3 - 601863 TGT------------------------------------ -s simRat_chr6.simRat.chr6 41502 39 + 647215 TGTATTATTGACATAAGTTGTAACACAAAAGTCTTGGAG - -a -s simMouse_chr6.simMouse.chr6 48822 51 + 636262 TACTATGTGCACATCTCCCAGATTGATTGACTGACACTCCAGAAACTGTTC -s Anc0.Anc0refChr9 23138 14 + 35212 -------------------------------------TATACAAACTGTAT -s Anc1.Anc1refChr0 3483 14 - 16026 -------------------------------------TATACAAACTGTAT -s Anc2.Anc2refChr0 43252 14 - 56053 -------------------------------------CATACAAACTGTAT -s mr.mrrefChr0 46562 51 + 130230 TACTATGTGCACATCTCCCAGATTGATTGACTGACACTCCAGAAACTGTTT -s simCow_chr6.simCow.chr6 585931 14 - 602619 -------------------------------------CACACAAACCGTTT -s simDog_chr6.simDog.chr6 581047 14 - 593897 -------------------------------------CTTAATACTTATAT -s simHuman_chr6.simHuman.chr6 587626 14 - 601863 -------------------------------------TATACAAACTGTGT -s simRat_chr6.simRat.chr6 41558 51 + 647215 TGCTATGTGCACATCTCCAGGATTGATGGACTGTCACTCCAGAGTGTGTTT - -a -s simMouse_chr6.simMouse.chr6 48873 66 + 636262 AGGAAGGAATTGCCCTGGTTGATTCTGTTTATAAGTCCGACCCACCTATTATGCACATGAACAGTC -s Anc0.Anc0refChr9 23152 66 + 35212 AGGAAGGAACTGCCCTTGTTAATTCTTTTTGAATGTCAGAAATGCCTATTATAGGCATGTATAGTC -s Anc1.Anc1refChr0 3497 66 - 16026 AGGAAGGAACTGCCCTTGTTAATTCTTTTTGAATGTCAGAAATGCCTATTATAGGCATGTATAGTC -s Anc2.Anc2refChr0 43266 66 - 56053 AGGAAGGAGCTGCCCTTGTTAATTCTTTTTGAATGTCAGAAATGCCTATTATAGGCATGTATAGTC -s mr.mrrefChr0 46613 66 + 130230 AGGAAGGAATTGCCCTGGTTGATTCTGTTTATAAGTCAGAACCACCTATTATACACATGAACAGTC -s simCow_chr6.simCow.chr6 585945 65 - 602619 AGGAAGGAGCTGGCCTTGTTAATTCTTTTTGAGT-TCAGAAGTGCCTATTATAGGCATGTACAGGC -s simDog_chr6.simDog.chr6 581064 66 - 593897 AGGAAGAAGCTGCCCTACTTTATTCTTTTTGAATGACAGAAATGCCTATCATCGGCATGTATAGTC -s simHuman_chr6.simHuman.chr6 587640 66 - 601863 AGGAAGGAACTGTCCCTGTTAACTCTTTTTGAATGTCAGAAATGCCTATTTTAGGCATGTGTCGTC -s simRat_chr6.simRat.chr6 41609 58 + 647215 AGGAAGGAGTTGCCCTGGTTGATTC--------AGTCAGAACCACCTATTATATACATGAACAGTC - -a -s simMouse_chr6.simMouse.chr6 48939 14 + 636262 TGTATTTATCAAAC -s Anc0.Anc0refChr9 23219 14 + 35212 TGTATTTTTCATCC -s Anc1.Anc1refChr0 3564 14 - 16026 TGTATTTTTCATCC -s Anc2.Anc2refChr0 43333 14 - 56053 TGTATCTTTCATCC -s mr.mrrefChr0 46680 14 + 130230 TGTATTTTTCAAAC -s simCow_chr6.simCow.chr6 586011 14 - 602619 TGTATCTTTCATCC -s simDog_chr6.simDog.chr6 581131 4 - 593897 TGCA---------- -s simHuman_chr6.simHuman.chr6 587707 14 - 601863 TGTATTTTTCATCC -s simRat_chr6.simRat.chr6 41668 14 + 647215 TATATTTTTCAAAC - -a -s simMouse_chr6.simMouse.chr6 48953 61 + 636262 CTTCGTGATGACAAAAATACAATAGTAGGACAGTGCAAGCATCTATTAGTGTCATCATTAA -s Anc0.Anc0refChr9 23233 61 + 35212 CTTCGTGATAACAAAAATATTATAGTAGGGCAGTGCATGAATTTATTAGTACCATCTTCAG -s Anc1.Anc1refChr0 3578 61 - 16026 CTTCGTGATAACAAAAATATTATAGTAGGGCAGTGCATGAATTTATTAGTACCATCTTCAG -s Anc2.Anc2refChr0 43347 61 - 56053 CTTCATGATAAGAAGTATATTATAGTTGAGCAGTGCATGAACTTATTAGCACCATCTTCAG -s mr.mrrefChr0 46694 61 + 130230 CTTCGTGATGACAAAAATACAATAGTAGGACAGTGCAAGCATCTATTAGTATCATCATTAA -s simCow_chr6.simCow.chr6 586053 61 - 602619 CTTCATGATAAGAAGTATATTATAGTTGAGCAGTGCATGAACTTATTAACACCATCTCCAG -s simDog_chr6.simDog.chr6 581135 22 - 593897 ---------------------------------------AACTTATTAGCACCATCTTCAG -s simHuman_chr6.simHuman.chr6 587721 61 - 601863 CTTTGTGATTACAGAAATATCATAGTAAGGTGGTGCAGGAATTCATTGGTACCATCTTCAT -s simRat_chr6.simRat.chr6 41682 61 + 647215 CTCCGTCATGACAAAAATACAATAGTTGGACAGTGCACGCATCTATTAGTATCATCATTAG - -a -s simMouse_chr6.simMouse.chr6 49014 30 + 636262 GTTTCTCCAGATATCTTGATGTTTCAACAA -s Anc0.Anc0refChr9 23294 30 + 35212 GTTTATACAGTTATCTTGATGTTTCAACAA -s Anc1.Anc1refChr0 3639 30 - 16026 GTTTATACAGTTATCTTGATGTTTCAACAA -s Anc2.Anc2refChr0 43408 30 - 56053 GTTTATACAGTTATCTTGCTGTTTCAACAG -s mr.mrrefChr0 46755 30 + 130230 GTTTCTCCAGATATCTTGATGTTTCAACAA -s simCow_chr6.simCow.chr6 586129 30 - 602619 GTTTATACAATCATCTTGCTGTGACCACAG -s simDog_chr6.simDog.chr6 581157 30 - 593897 GTTTATACAGCTATCTTGCTGTTTCAACAG -s simHuman_chr6.simHuman.chr6 587782 30 - 601863 GTTTTTACAGTTATCTTAATGTTTCAACAA -s simRat_chr6.simRat.chr6 41743 30 + 647215 ATTTCTCCACATATCTTGATGTTTCAACAA - -a -s simMouse_chr6.simMouse.chr6 49044 12 + 636262 GCTGGCTTTAAC -s Anc0.Anc0refChr9 23328 12 + 35212 GCTGGCATGATC -s Anc1.Anc1refChr0 3673 12 - 16026 GCTGGCATGATC -s Anc2.Anc2refChr0 43442 12 - 56053 ACTGGCATGATT -s mr.mrrefChr0 46785 12 + 130230 GCTGGCTTTAAC -s simCow_chr6.simCow.chr6 586163 12 - 602619 ACTGGCATGATT -s simDog_chr6.simDog.chr6 581191 12 - 593897 ACTGGTGTGATT -s simHuman_chr6.simHuman.chr6 587816 12 - 601863 GCTGGCATGATC -s simRat_chr6.simRat.chr6 41773 12 + 647215 GCTGGCCTTGAT - -a -s simMouse_chr6.simMouse.chr6 49056 59 + 636262 TCGTATTCGAAAAATTAGTCCGTCCAAGTTTAAGATGCGTGTTTTTTGGCAAGCATATG -s Anc0.Anc0refChr9 23341 58 + 35212 TTGTAACTGAGCTATTAATCTATACA-CTGAAAAAAGCATGCATTTTAGCTAGCATATG -s Anc1.Anc1refChr0 3686 58 - 16026 TTGTAACTGAGCTATTAATCTATACA-CTGAAAAAAGCATGCATTTTAGCTAGCATATG -s Anc2.Anc2refChr0 43455 58 - 56053 TTGTAACTAAGCTATTAAGCTATACA-CTGAGAAAAGTATTCATTTTAGCTAGCATATG -s mr.mrrefChr0 46797 58 + 130230 TTGTATTCGAAAAATTAGTCCGTCCA-GTTTAAAATGCGTGTTTTTTAGCAAGCATATG -s simCow_chr6.simCow.chr6 586176 55 - 602619 TTGTAACTAAGCTATT---CTATGCA-CTGATAAAAGTATTCAGTTTAGCTAGCATATG -s simDog_chr6.simDog.chr6 581204 58 - 593897 TTGTAACTAAGATATTAAGCTATACA-CTGAGAAAAGTAATCATTTTAGCTAGCATATG -s simHuman_chr6.simHuman.chr6 587829 58 - 601863 TTATAACTGAGCTATTATTCTATACA-ATGAAGAAATCATGCATTTTAGCTAGCATAAG -s simRat_chr6.simRat.chr6 41785 56 + 647215 TTGTATTCAAAAAATTAGTCCTTCCA-GTTTAAAATGC--GTTTTTCAGCAAGCATATG - -a -s simMouse_chr6.simMouse.chr6 49115 15 + 636262 TCCTTATTGCTTCTA -s Anc0.Anc0refChr9 23399 15 + 35212 TCTTTTTTGCTTCTG -s Anc1.Anc1refChr0 3744 15 - 16026 TCTTTTTTGCTTCTG -s Anc2.Anc2refChr0 43513 15 - 56053 TCTTGTTTGCTTCTG -s mr.mrrefChr0 46855 15 + 130230 TCTTTATTGCTTCTA -s simCow_chr6.simCow.chr6 586232 15 - 602619 TCTTCTTCAGTTTAG -s simDog_chr6.simDog.chr6 581262 14 - 593897 -CTTGTTTGCTTCTG -s simHuman_chr6.simHuman.chr6 587887 15 - 601863 TCTTTTTTGCTTCTG -s simRat_chr6.simRat.chr6 41841 15 + 647215 TCTTTGTTGCTTTTA - -a -s simMouse_chr6.simMouse.chr6 49130 9 + 636262 GGCTTGCAG -s Anc0.Anc0refChr9 23414 9 + 35212 TGTTTTTCT -s Anc1.Anc1refChr0 3759 9 - 16026 TGTTTTTCT -s Anc2.Anc2refChr0 43528 9 - 56053 TGTTCTTCT -s mr.mrrefChr0 46870 9 + 130230 GGTTTGCAG -s simCow_chr6.simCow.chr6 586255 9 - 602619 TGTTCTTCT -s simDog_chr6.simDog.chr6 581276 8 - 593897 TGTTCT-CT -s simHuman_chr6.simHuman.chr6 587902 9 - 601863 TGTTTTTCC -s simRat_chr6.simRat.chr6 41856 9 + 647215 GGTTTACAG - -a -s simMouse_chr6.simMouse.chr6 49139 27 + 636262 AAGGTTAAGCTGAGTCCTGACAATGCA -s Anc0.Anc0refChr9 23423 26 + 35212 AA-CTTAAGCTGAGTTGTGATGATGCA -s Anc1.Anc1refChr0 3768 26 - 16026 AA-CTTAAGCTGAGTTGTGATGATGCA -s Anc2.Anc2refChr0 43537 26 - 56053 GA-CTTAAGCTGAGTTGTGATGATGTA -s mr.mrrefChr0 46879 26 + 130230 AA-GTTAAGCTGAGTCCTGACAATGCA -s simCow_chr6.simCow.chr6 586286 26 - 602619 GG-CTTAAGCTGAGTTGTGATGGTGTA -s simDog_chr6.simDog.chr6 581284 26 - 593897 GA-GTTAAGCTGAGCTGGGTTGAGGTA -s simHuman_chr6.simHuman.chr6 587911 26 - 601863 AA-CTTAAGCTGAGTTGTGATGATGCA -s simRat_chr6.simRat.chr6 41865 26 + 647215 AA-GTTAAGGTGAGTCATGACAATGCA - -a -s simMouse_chr6.simMouse.chr6 49166 28 + 636262 GAGATCAATTCCCTGTCTAAGCACCCCA -s Anc0.Anc0refChr9 23451 27 + 35212 GAGATAAAATCCCTCTCTAAGCA-TCCA -s Anc1.Anc1refChr0 3796 27 - 16026 GAGATAAAATCCCTCTCTAAGCA-TCCA -s Anc2.Anc2refChr0 43565 27 - 56053 GAGATAAAATCCCTCTCCAAGCA-TCCA -s mr.mrrefChr0 46905 28 + 130230 GAGATAAATTCCCTGTCTAAGCACCCCA -s simCow_chr6.simCow.chr6 586314 27 - 602619 GAGATAAACTCCCTCCCCAAGCA-CACA -s simDog_chr6.simDog.chr6 581312 27 - 593897 CAGCTGGAATCCCTCTCCAGGCA-TCGA -s simHuman_chr6.simHuman.chr6 587939 27 - 601863 GAAATAAAATCCCTTTCTAAGCA-TCCA -s simRat_chr6.simRat.chr6 41891 28 + 647215 GAGATAAATTCTATGTCTAACCACCCCA - -a -s simMouse_chr6.simMouse.chr6 49194 1 + 636262 G -s Anc0.Anc0refChr9 23478 1 + 35212 G -s Anc1.Anc1refChr0 3823 1 - 16026 G -s Anc2.Anc2refChr0 43592 1 - 56053 G -s mr.mrrefChr0 46933 1 + 130230 G -s simCow_chr6.simCow.chr6 586347 1 - 602619 G -s simDog_chr6.simDog.chr6 581339 1 - 593897 G -s simHuman_chr6.simHuman.chr6 587966 1 - 601863 G -s simRat_chr6.simRat.chr6 41919 1 + 647215 C - -a -s simMouse_chr6.simMouse.chr6 49195 94 + 636262 AAGCAAACACCATCTATATTAGTTCCCTGGCCTCTATTCTGATTGGGAACTCAAATCTATAAAATATAGTATCTCCACATGAAACAGAACCCCT -s Anc0.Anc0refChr9 23479 94 + 35212 AAACAAACAACATCTATATTAGTTCCTTAGGCTATATACTGGTTGGGTACTCAAACCTATAAAATGTATTATTTCCACAGGAAACAGAGCCCCT -s Anc1.Anc1refChr0 3824 94 - 16026 AAACAAACAACATCTATATTAGTTCCTTAGGCTATATACTGGTTGGGTACTCAAACCTATAAAATGTATTATTTCCACAGGAAACAGAGCCCCT -s Anc2.Anc2refChr0 43593 94 - 56053 AAACAAACAACATCTATATTAGTTCCTTAGGCGACATACTTCTTGGGTACTTGAACCTATAAAATGTATCTTTTCCACAGGAAACAGAGCCCCT -s mr.mrrefChr0 46934 94 + 130230 AAGCAAACACCATCTATATTAGTTCCCTAGCCTCTATTCTGGTTGGGAACTCAAATCTATAAAATATAGTATCTCCACATGAAACAGAACCCCT -s simCow_chr6.simCow.chr6 586348 92 - 602619 AAGCAAGCACCATCTATATTAGTTCCTTAGGCGACATACTACTTGGGTACTTGAG--TATGAAATGTATCTTTTCCCCAGGAAACAGAGCCCCT -s simDog_chr6.simDog.chr6 581371 94 - 593897 GAACAAACGACATCTATATGAGTTCCTTAGGTGACATACTTCTCGGGCACTTGAACCCATAAAACGTATCTTTTCCACAGGAAACAGAGCACCC -s simHuman_chr6.simHuman.chr6 587967 94 - 601863 AAACAAACATCATTTATATTAGTTCCTTAGACTTTACAGTGGTTGTGTACTCAAACCTATAAAGTGTATTATTTCCACAGGAAACAGAGCCCCT -s simRat_chr6.simRat.chr6 41920 93 + 647215 AAGCAAACA-AATCTGTATTGGTTCCCTAGCCTCTATTCTGGTTGGGGACTCAAAGCTATAAAATACACTATCTCCACACGAAACAGACCCCCT - -a -s simMouse_chr6.simMouse.chr6 49289 18 + 636262 TTATGACGAGGACTCAAT -s Anc0.Anc0refChr9 23575 18 + 35212 TTATGACTAGAACACAAT -s Anc1.Anc1refChr0 3920 18 - 16026 TTATGACTAGAACACAAT -s Anc2.Anc2refChr0 43689 18 - 56053 TTATGACTAGAACACAAT -s mr.mrrefChr0 47028 18 + 130230 TTATGACGAGGACTCAAT -s simCow_chr6.simCow.chr6 586442 18 - 602619 TTATGACTTCACCATAAT -s simDog_chr6.simDog.chr6 581467 18 - 593897 TTATGACTAGAACACAAT -s simHuman_chr6.simHuman.chr6 588063 18 - 601863 TTATGACTAACACACAAT -s simRat_chr6.simRat.chr6 42013 18 + 647215 TTATGACAAGGACTTAAT - -a -s simMouse_chr6.simMouse.chr6 49307 14 + 636262 TAGAATAATTAGAA -s Anc0.Anc0refChr9 23600 14 + 35212 TTGCTTAAGTAGCA -s Anc1.Anc1refChr0 3945 14 - 16026 TTGCTTAAGTAGCA -s Anc2.Anc2refChr0 43714 14 - 56053 TTGCTTAAGTAGCA -s mr.mrrefChr0 47046 14 + 130230 TAGAATAATTAGAA -s simCow_chr6.simCow.chr6 586472 14 - 602619 TTGCTTTAGTAGCA -s simDog_chr6.simDog.chr6 581492 14 - 593897 TTGCTTAATTAGCA -s simHuman_chr6.simHuman.chr6 588088 14 - 601863 TTGCTTAAGTAGCA -s simRat_chr6.simRat.chr6 42031 14 + 647215 TGGAATAATTAGAA - -a -s simMouse_chr6.simMouse.chr6 49321 9 + 636262 TGTTGCTCC -s Anc0.Anc0refChr9 23624 9 + 35212 TGTTAATCA -s Anc1.Anc1refChr0 3969 9 - 16026 TGTTAATCA -s Anc2.Anc2refChr0 43738 9 - 56053 TGTTAATCA -s mr.mrrefChr0 47060 9 + 130230 TGTTGCTCA -s simCow_chr6.simCow.chr6 586496 9 - 602619 TGTTTATCA -s simDog_chr6.simDog.chr6 581516 9 - 593897 CATTAATCA -s simHuman_chr6.simHuman.chr6 588112 9 - 601863 TGTTAATCA -s simRat_chr6.simRat.chr6 42045 9 + 647215 TGTTGCTCA - -a -s simMouse_chr6.simMouse.chr6 49330 20 + 636262 AACAGTGGAGTATTTTATTG -s Anc0.Anc0refChr9 23644 20 + 35212 AACAGTAGAGTATTTTGCTG -s Anc1.Anc1refChr0 3989 20 - 16026 AACAGTAGAGTATTTTGCTG -s Anc2.Anc2refChr0 43758 20 - 56053 AACAGTAGAGTCGTTTGCTG -s mr.mrrefChr0 47069 20 + 130230 AACAGTGGAGTATTTTATTG -s simCow_chr6.simCow.chr6 586516 20 - 602619 TACAATAGAGTGGTTTGCTG -s simDog_chr6.simDog.chr6 581535 19 - 593897 ACCAGTAGAGTCGTTTGCT- -s simHuman_chr6.simHuman.chr6 588132 20 - 601863 AACAGTTGAGTATTTTGCTG -s simRat_chr6.simRat.chr6 42054 20 + 647215 AACACTGGAGTTTTTTATTG - -a -s simMouse_chr6.simMouse.chr6 49350 18 + 636262 CCATTTTTATTGCCTTGA -s Anc0.Anc0refChr9 23664 13 + 35212 TCTTGTTTGTTTC----- -s Anc1.Anc1refChr0 4009 13 - 16026 TCTTGTTTGTTTC----- -s Anc2.Anc2refChr0 43778 13 - 56053 TCTTGTTTGTTTT----- -s mr.mrrefChr0 47089 18 + 130230 CCATTTTTATTGCCTTGA -s simCow_chr6.simCow.chr6 586546 12 - 602619 TCT-GTTCATCTT----- -s simDog_chr6.simDog.chr6 581554 13 - 593897 TCTTATTTGTTTT----- -s simHuman_chr6.simHuman.chr6 588152 13 - 601863 TCTCGTTTGTTTC----- -s simRat_chr6.simRat.chr6 42074 18 + 647215 CCCTTTTTATTGCCTTGA - -a -s simMouse_chr6.simMouse.chr6 49368 102 + 636262 GATTATGCTCAAAGGTAAGGTCACGTCAAGTTAATCCAATTCCATTTTGTTGCTGTATTAATGTATCACCTTTGCTTTGAGCTTTGATATGGGGTATCTTTG -s Anc0.Anc0refChr9 23677 87 + 35212 AGTTAGACTCA-----AAGGTCATATCAAATGAACCTGAACCCATTTTGCT-CTGTCTCAACCTATCATCTCT---------TCTGATAGAGGGTTTGGTTG -s Anc1.Anc1refChr0 4022 87 - 16026 AGTTAGACTCA-----AAGGTCATATCAAATGAACCTGAACCCATTTTGCT-CTGTCTCAACCTATCATCTCT---------TCTGATAGAGGGTTTGGTTG -s Anc2.Anc2refChr0 43792 87 - 56053 AGTTAGACTCA-----CAGGCCATATTAAATGACCCTGAACCCACCTTGCT-CTGTCTCGACCTATCATCTCC---------ACTGATAGAAGGTTTGGTTG -s mr.mrrefChr0 47107 90 + 130230 GATTATGCTCA-----AAGGTCATGTCAAGTGAATCTGATTCCATTTTGTTGCTGTATTAATGTATCATCTTT-------GCTTTGATATAGGGTATCTTTG -s simCow_chr6.simCow.chr6 586559 81 - 602619 AGTCAGACTCA-----CAGGCCATATTAAAGGATCCTTAACTCACCTTGCT-CTGCCTC------TCATGTCG---------ACTGGTAGAAGGTGTGGTGG -s simDog_chr6.simDog.chr6 581568 87 - 593897 AATTAGACTCA-----CAGGCTGTATTAAATGACCCAGCATCCACCTTGAT-CTGTCTTGACCTATCATCTTC---------ACTGATAGAAGGTTTGGCTG -s simHuman_chr6.simHuman.chr6 588165 86 - 601863 AGTTAGACTTG-----AAGGTCATATCAAATGAACCTGAACCCATTTCACT-CTGTCTCAAACTATCATTTCT---------TCTGACAGAGGGT-TTGTTG -s simRat_chr6.simRat.chr6 42092 90 + 647215 AATTATGTTCA-----AAGGTCATGTTAAGAGAATCTGATTCCATTTTGTTGCTGTATTAATGTATCATCTTT-------GCTTTGATATAGGGTATCTTTG - -a -s simMouse_chr6.simMouse.chr6 49470 181 + 636262 ACAATTGGATGCCTCAAAATAACATATTAGCTGGTCCATATTAAAAAGCAACAGGGATAGACATTATCGGCTTATCCTCATTTAACTTGTATCACCTGCTCTATTATGTCTTCTCCTTGCCATAAGGGACCCAATTTTCACTGTGATGATCTTTCGAGGGGATTAGTCCCTCTCTGTTCCG -s Anc0.Anc0refChr9 23764 83 + 35212 ATAACCTAATGCCTTAGACTAACATATTGGTTGGTCCATAGTAGAAAGG------------------------GTCTGCAAATAACTTGATACTCAAGCTTT--------------------------------------------------------------------------TATAG -s Anc1.Anc1refChr0 4109 83 - 16026 ATAACCTAATGCCTTAGACTAACATATTGGTTGGTCCATAGTAGAAAGG------------------------GTCTGCAAATAACTTGATACTCAAGCTTT--------------------------------------------------------------------------TATAG -s Anc2.Anc2refChr0 43879 83 - 56053 ACAACCTGATGCCTTAGACTAGCATATTGGTTGGTCCATAGTAGAAAAG------------------------GTCTGCAAATAGTTTGATACTCAAGCTTT--------------------------------------------------------------------------TATAG -s mr.mrrefChr0 47197 83 + 130230 ATAACTTAATGCCTCAAAATAACATATTAGCTGGTCCATATTAAAAAGC------------------------ATCCTCATTTAACTTGTATCACCTGCTTT--------------------------------------------------------------------------TTCAG -s simCow_chr6.simCow.chr6 586640 74 - 602619 ACAACCTGATGCCTTAGACTACCATATCGCTTCGCCCATAGTAGAAAAG------------------------GTCTGCCA---------TAAGCTTGACCT--------------------------------------------------------------------------TACAG -s simDog_chr6.simDog.chr6 581655 81 - 593897 ACAACCTGATGCCTTAGAATAGCATATTGG--GGTCCATAGTAGAAAAG------------------------ATCTGCAAATAGTTTGACCCTCAAGCTTT--------------------------------------------------------------------------TATAG -s simHuman_chr6.simHuman.chr6 588251 83 - 601863 ATTACCTAATGCCTTAGACAAACATATTGGTTGGTCCATAGTAGAAAGG------------------------GTCTGGAAATCACTCGATACTCAGGCTTT--------------------------------------------------------------------------TGTAG -s simRat_chr6.simRat.chr6 42200 83 + 647215 ATAACATAATGCCTCAAAATAACATATTAGCTGGTCCATATTAAAAAGC------------------------ATCCACATTCAACTTGTACCACCTACTTT--------------------------------------------------------------------------TTAAG - -a -s simMouse_chr6.simMouse.chr6 49651 32 + 636262 TATACTTTGTTGACTTCAATACCTTATACTAA -s Anc0.Anc0refChr9 24087 31 + 35212 tttacttag-agacttcaatagcacctaatat -s Anc1.Anc1refChr0 4446 31 - 16026 tttacttag-agacttcaatagcacctaatat -s Anc2.Anc2refChr0 44202 31 - 56053 cttacttag-agacttcaatagcacctgatat -s mr.mrrefChr0 47514 32 + 130230 TATACTTTGTTGACTTCAATACCTTATACTAA -s simCow_chr6.simCow.chr6 586946 31 - 602619 cttacttag-agacttcaatagcacctgatat -s simHuman_chr6.simHuman.chr6 588628 31 - 601863 tgtacttag-cgacttcagtagcacttaattt -s simRat_chr6.simRat.chr6 42530 32 + 647215 TGTACTTTGTTGACTTCAATACATTTTACTAA - -a -s simMouse_chr6.simMouse.chr6 49683 12 + 636262 GATTATGTGTAT -s Anc0.Anc0refChr9 24118 10 + 35212 gtttacatag-- -s Anc1.Anc1refChr0 4477 12 - 16026 gtttacatagat -s Anc2.Anc2refChr0 44233 10 - 56053 gtttacatag-- -s mr.mrrefChr0 47546 12 + 130230 GATTATGTGTAT -s simCow_chr6.simCow.chr6 586977 10 - 602619 gtttacatag-- -s simHuman_chr6.simHuman.chr6 588659 12 - 601863 gtgtacctaaat -s simRat_chr6.simRat.chr6 42575 12 + 647215 GACCATGTGTAT - -a -s simMouse_chr6.simMouse.chr6 49695 14 + 636262 ATCTATACAACTGG -s Anc0.Anc0refChr9 24133 14 + 35212 atctatttgcttgc -s Anc1.Anc1refChr0 4494 14 - 16026 atctatttgcttgc -s Anc2.Anc2refChr0 44248 14 - 56053 atctatttgcttac -s mr.mrrefChr0 47558 14 + 130230 ATCTATACAACTGG -s simCow_chr6.simCow.chr6 586992 14 - 602619 atctatttgcttac -s simHuman_chr6.simHuman.chr6 588680 14 - 601863 accccagtgcttgc -s simRat_chr6.simRat.chr6 42587 14 + 647215 ATCTGTACAACCGG - -a -s simMouse_chr6.simMouse.chr6 49709 25 + 636262 TAGGCAGAGGTGTAGCAAATTGCAT -s Anc0.Anc0refChr9 24147 25 + 35212 gaggtgaaagtgtggaaacttggac -s Anc1.Anc1refChr0 4508 25 - 16026 gaggtgaaagtgtggaaacttggac -s Anc2.Anc2refChr0 44262 25 - 56053 gaggtgaaagtgtggaaactgggac -s mr.mrrefChr0 47572 25 + 130230 TAGGCAGAGGTGTAGCAAATTGCAT -s simCow_chr6.simCow.chr6 587051 25 - 602619 gaggtgaaagtgtggaaactgggac -s simHuman_chr6.simHuman.chr6 588694 25 - 601863 gacctgaaagtcttaaaactttaac -s simRat_chr6.simRat.chr6 42601 25 + 647215 TAGGCATAGGTGTAGCAAATTGCAT - -a -s simMouse_chr6.simMouse.chr6 49734 21 + 636262 TTGCATCATCAATCTGAAGTC -s Anc0.Anc0refChr9 24180 8 + 35212 ctg---ca------ca----c -s Anc1.Anc1refChr0 4541 11 - 16026 ctgtatca------ca----c -s Anc2.Anc2refChr0 44295 8 - 56053 ctg---ca------ca----c -s mr.mrrefChr0 47597 15 + 130230 TTGCATCA------TGAAGTC -s simCow_chr6.simCow.chr6 587084 8 - 602619 ctg---ca------ca----c -s simHuman_chr6.simHuman.chr6 588727 11 - 601863 ctctatca------ca----c -s simRat_chr6.simRat.chr6 42626 15 + 647215 TTGTATCA------TGAATTT - -a -s simMouse_chr6.simMouse.chr6 49755 10 + 636262 CTTAAAGACC -s Anc0.Anc0refChr9 24191 10 + 35212 cattgagact -s Anc1.Anc1refChr0 4555 10 - 16026 cattgagact -s Anc2.Anc2refChr0 44306 10 - 56053 aattgtgact -s mr.mrrefChr0 47612 10 + 130230 CTTAAAGACC -s simCow_chr6.simCow.chr6 587095 10 - 602619 aattgtgact -s simHuman_chr6.simHuman.chr6 588741 10 - 601863 catcgagact -s simRat_chr6.simRat.chr6 42641 10 + 647215 CTTAAAGACT - -a -s simMouse_chr6.simMouse.chr6 49765 12 + 636262 TCAATTCTAAAT -s Anc0.Anc0refChr9 24201 12 + 35212 gaaagtcaaaat -s Anc1.Anc1refChr0 4565 12 - 16026 gaaagtcaaaat -s Anc2.Anc2refChr0 44316 12 - 56053 gaaagtcaaact -s mr.mrrefChr0 47622 12 + 130230 TCAATTCTAAAT -s simCow_chr6.simCow.chr6 587106 12 - 602619 gaaagtcaaact -s simHuman_chr6.simHuman.chr6 588751 12 - 601863 gtaaatcaaaat -s simRat_chr6.simRat.chr6 42651 12 + 647215 TCAAGCCTAAAT - -a -s simMouse_chr6.simMouse.chr6 49777 18 + 636262 TCATTTGCCAACCGTGCA -s Anc0.Anc0refChr9 24213 15 + 35212 ccttt---caaccgtgca -s Anc1.Anc1refChr0 4577 15 - 16026 ccttt---caaccgtgca -s Anc2.Anc2refChr0 44328 15 - 56053 cttct---caagcatgta -s mr.mrrefChr0 47634 18 + 130230 TCATTTGCCAACCGTGCA -s simCow_chr6.simCow.chr6 587118 15 - 602619 cttct---caagcatgta -s simHuman_chr6.simHuman.chr6 588767 15 - 601863 ccctt---caactgtgca -s simRat_chr6.simRat.chr6 42663 18 + 647215 TCATTTGCCGATTGTGCA - -a -s simMouse_chr6.simMouse.chr6 49795 49 + 636262 TCACTTTGAGACAATTGATTTGCAATGATTGAGCTTTAAACTTCTAGCC -s Anc0.Anc0refChr9 24228 11 + 35212 cc--------------------------------------ctcataacc -s Anc1.Anc1refChr0 4592 11 - 16026 cc--------------------------------------ctcataacc -s Anc2.Anc2refChr0 44343 11 - 56053 cc--------------------------------------cacataacc -s mr.mrrefChr0 47652 35 + 130230 TCAC--------------TTTGCAATGATTGAGCTTTAAACTTCTAGCC -s simCow_chr6.simCow.chr6 587136 11 - 602619 cc--------------------------------------cacataacc -s simHuman_chr6.simHuman.chr6 588782 11 - 601863 cc--------------------------------------ctcataact -s simRat_chr6.simRat.chr6 42681 35 + 647215 GCAC--------------TTTGCAATGATTGCGCTTTAAAGCCGCAGCC - -a -s simMouse_chr6.simMouse.chr6 49844 34 + 636262 AGAATAGATGAGCAATGTGGAACCTTGCCTTAGA -s Anc0.Anc0refChr9 24239 34 + 35212 acactagatgagcgatatggaaaccaacctTATA -s Anc1.Anc1refChr0 4603 34 - 16026 acactagatgagcgatatggaaaccaacctTATA -s Anc2.Anc2refChr0 44354 34 - 56053 acaccagaagagcgacatggaaaccaacctTATC -s mr.mrrefChr0 47687 34 + 130230 AGAATAGATGAGCAATGTGGAACCTTGCCTTAGA -s simCow_chr6.simCow.chr6 587147 34 - 602619 acaccagaagagcgacatggaaaccaacctTATC -s simHuman_chr6.simHuman.chr6 588793 34 - 601863 gaattagatgagtgatatatgatccaacctTATA -s simRat_chr6.simRat.chr6 42731 34 + 647215 CAAATAGATGAGCAATGTGGAACCTTGCCCTGGA - -a -s simMouse_chr6.simMouse.chr6 49878 14 + 636262 TCTTGGCCTTGCTC -s Anc0.Anc0refChr9 24273 14 + 35212 TCTTGAACCTGCCT -s Anc1.Anc1refChr0 4637 14 - 16026 TCTTGAACCTGCCT -s Anc2.Anc2refChr0 44388 14 - 56053 TCTTGAATCTGCCT -s mr.mrrefChr0 47721 14 + 130230 TCTTGGCCTTGCTC -s simCow_chr6.simCow.chr6 587181 14 - 602619 TCTTGAATCTGCCT -s simHuman_chr6.simHuman.chr6 588829 14 - 601863 TCTCAAACCTGCCT -s simRat_chr6.simRat.chr6 42765 14 + 647215 TCTTGGTCTTGCTC - -a -s simMouse_chr6.simMouse.chr6 49892 4 + 636262 TTTC -s Anc0.Anc0refChr9 24412 4 + 35212 TCTT -s Anc1.Anc1refChr0 4776 4 - 16026 TCTT -s Anc2.Anc2refChr0 44527 4 - 56053 TCCT -s mr.mrrefChr0 47735 4 + 130230 TTTC -s simCow_chr6.simCow.chr6 587328 4 - 602619 TCCT -s simHuman_chr6.simHuman.chr6 588973 4 - 601863 TCTT -s simRat_chr6.simRat.chr6 42779 4 + 647215 TCTT - -a -s simMouse_chr6.simMouse.chr6 49896 12 + 636262 ACTGTGCAAAAT -s Anc0.Anc0refChr9 24416 12 + 35212 AATGGAAAAAAT -s Anc1.Anc1refChr0 4780 12 - 16026 AATGGAAAAAAT -s Anc2.Anc2refChr0 44531 12 - 56053 AATGGAAAAAAT -s mr.mrrefChr0 47739 12 + 130230 ACTGTGCAAAAT -s simCow_chr6.simCow.chr6 587339 12 - 602619 AATGGATAAAAT -s simDog_chr6.simDog.chr6 581845 9 - 593897 ---GGAACAGAT -s simHuman_chr6.simHuman.chr6 588977 12 - 601863 GATGGAGAAAAT -s simRat_chr6.simRat.chr6 42783 12 + 647215 GCTGCACAAAAT - -a -s simMouse_chr6.simMouse.chr6 49908 7 + 636262 GCTGTTT -s Anc0.Anc0refChr9 24428 7 + 35212 GATGTCT -s Anc1.Anc1refChr0 4792 7 - 16026 GATGTCT -s Anc2.Anc2refChr0 44543 7 - 56053 GATGTCT -s mr.mrrefChr0 47751 7 + 130230 GCTGTTT -s simCow_chr6.simCow.chr6 587351 7 - 602619 GCCACCC -s simDog_chr6.simDog.chr6 581859 7 - 593897 GATGTGT -s simHuman_chr6.simHuman.chr6 588989 7 - 601863 GGTGTCT -s simRat_chr6.simRat.chr6 42795 7 + 647215 GCAGTTT - -a -s simMouse_chr6.simMouse.chr6 49915 18 + 636262 CATGCTGTAATTTCAGGT -s Anc0.Anc0refChr9 24438 18 + 35212 TATCCTGACATTCGAGGG -s Anc1.Anc1refChr0 4802 18 - 16026 TATCCTGACATTCGAGGG -s Anc2.Anc2refChr0 44553 18 - 56053 TTTCCCGACATTCGAAGG -s mr.mrrefChr0 47758 18 + 130230 CATGCTGTAATTTCAGGT -s simCow_chr6.simCow.chr6 587361 9 - 602619 TT-------ATTCAAC-- -s simDog_chr6.simDog.chr6 581869 18 - 593897 TTTCCCGACATTTGAAGG -s simHuman_chr6.simHuman.chr6 588999 18 - 601863 TAACTTGCCATTCGAGGG -s simRat_chr6.simRat.chr6 42802 18 + 647215 CATGCTGTACTTTCAGGT - -a -s simMouse_chr6.simMouse.chr6 49933 46 + 636262 GATACCTACTATTTCAGGTGATACCTACTGGATTGTGACACTCTCA -s Anc0.Anc0refChr9 24456 33 + 35212 GATGCCTACT-----GGATGATCC--------TTACTACTCTCTCA -s Anc1.Anc1refChr0 4820 33 - 16026 GATGCCTACT-----GGATGATCC--------TTACTACTCTCTCA -s Anc2.Anc2refChr0 44571 33 - 56053 GATGCGTACT-----GGATGGTCC--------TTACTACTCTGTCA -s mr.mrrefChr0 47776 33 + 130230 GATACCTACT-----AGGTGATAC--------TTGTGACACTCTCA -s simCow_chr6.simCow.chr6 587370 12 - 602619 -----------------AAGGTCC--------TTCCT--------- -s simDog_chr6.simDog.chr6 581888 33 - 593897 GATGCGTACT-----GGGTGGTTC--------TTATGACTCTGTCA -s simHuman_chr6.simHuman.chr6 589017 33 - 601863 GGTGCCTACT-----GGATGATCC--------ATACTACTCCCTCA -s simRat_chr6.simRat.chr6 42820 33 + 647215 GTTACCTACT-----GGGTTGTAT--------TTATGTCACTCTCA - -a -s simMouse_chr6.simMouse.chr6 49979 50 + 636262 CTTAAAAATGACCAGTCACCCATGGTTTTGTAGCTTTGAATTAGATGTGT -s Anc0.Anc0refChr9 24489 50 + 35212 CGTGAAAATGATCAGTTTTCAATGGTATTGTAGCTCTATATTAGTTGTAC -s Anc1.Anc1refChr0 4853 50 - 16026 CGTGAAAATGATCAGTTTTCAATGGTATTGTAGCTCTATATTAGTTGTAC -s Anc2.Anc2refChr0 44604 50 - 56053 CGTGAAAAAAGTCAGTTTTCAATGGTATTATAGCTCTATTTTAGTTGTAC -s mr.mrrefChr0 47809 50 + 130230 CTTAAAAATGACCAGTCACCCATGGTTTTGTAGCTTTGAATTAGATGTGT -s simCow_chr6.simCow.chr6 587382 48 - 602619 --TGAAAAGACTCAGTTTGCAACAGTATTACAGTTCTATGTTTGTTGTAC -s simDog_chr6.simDog.chr6 581921 50 - 593897 CGCCAAAAAAGCCAGTGTTCAATGGTATTATAACTCTACTTTAGTTGTAC -s simHuman_chr6.simHuman.chr6 589050 50 - 601863 ACTGAAAATGATCAGTTTACAATGGTATTGTAGCTCTATATTAGTCTTAC -s simRat_chr6.simRat.chr6 42856 50 + 647215 CTTAATAATGACTAGCTACCCATGGTATCGTAGCTCTGTATTAGATATGA - -a -s simMouse_chr6.simMouse.chr6 50029 78 + 636262 ACAGAAGTAGATATTCTTCTTCCAGTAAATCAACTATAGCAGTATCGTCATTTCAGCCCTTGTGAGTCTCATAATTGC -s Anc0.Anc0refChr9 24541 76 + 35212 ACAGAAGTATATATTACTTTCCCAAAAAATTCCTTATAGCAGCATAGTCAATGCAGTCCTTTTG-GTCTTGTAGTT-C -s Anc1.Anc1refChr0 4905 76 - 16026 ACAGAAGTATATATTACTTTCCCAAAAAATTCCTTATAGCAGCATAGTCAATGCAGTCCTTTTG-GTCTTGTAGTT-C -s Anc2.Anc2refChr0 44656 76 - 56053 ACAGAAGTATATATTACTTTCCCAAAAAGTTCCTTATAGCAGCATAGTCAATGCAGTCCTTTTG-GTCTTGTAGTA-T -s mr.mrrefChr0 47859 77 + 130230 ACAGAAGTAGATATTCTTCTTCCAGTAAATCAACTATAGCAGTATCGTCATTTCAGCCCTTGTGAGTCTCATAATT-C -s simCow_chr6.simCow.chr6 587432 71 - 602619 ACAGAACTGGATATTACTTCCCCAAAAACTTACCTACA-----AGAGTCAATGCAGGCCTTTTA-GTTTGGTAGTA-T -s simDog_chr6.simDog.chr6 581973 73 - 593897 ACAGAAGCATATA---CCTTCCCAAAAAGTTCCTTATAGCAGCATAGTCAATCCAGTCCTTTCG-GTCTTGCAGTA-T -s simHuman_chr6.simHuman.chr6 589102 76 - 601863 ACAGAAGTATCTATTACTTTGTCAAAAAATTGCTTATGGCAGCATAGTCAAGGAAGTCCTTTTG-GTCTTGTCGTT-C -s simRat_chr6.simRat.chr6 42906 77 + 647215 ACAGAAGTAGATATTCTTCTTCCAGGAAATCATCTATAGCAATATGGTCATTTTAGCCCTTGTGAGTCTCATAACT-C - -a -s simMouse_chr6.simMouse.chr6 50107 73 + 636262 ATTGGTCTTGTAACCCTATAGCTTGTCAGCAAGGACAGAAATTACTTGTACACTCTTATACTTGCTGTAATAG -s Anc0.Anc0refChr9 24617 56 + 35212 A---------TAACTCTATG------CAAA-AGAACACAAATGACTTGGAGGCTACCATACATGTTGGAACA- -s Anc1.Anc1refChr0 4981 56 - 16026 A---------TAACTCTATG------CAAA-AGAACACAAATGACTTGGAGGCTACCATACATGTTGGAACA- -s Anc2.Anc2refChr0 44732 56 - 56053 A---------TAACTCTTTG------TAAA-AGAACACAAATGACTTGGAGGCTACCATACATGTTGGAACA- -s mr.mrrefChr0 47936 71 + 130230 ATTGGTCTTGTAACCCTATAGCTTGTCAGC-AGGACAGAAATTACTTGTACACTCTTATACTTGCTGTAATA- -s simCow_chr6.simCow.chr6 587504 56 - 602619 A---------TAACTCTTTG------TAAA-AGGACACAAATGACTTGAATGCTACCCTACTTGTTGGAACA- -s simDog_chr6.simDog.chr6 582046 54 - 593897 A---------TAATTCTTT--------AAA-AGAACACAAATCACTTGGAGGCTACCATACATGTTCGAACA- -s simHuman_chr6.simHuman.chr6 589178 56 - 601863 A---------TAACTCTATG------CACA-CAACCACAAATGGCTTGGAGGCTACCAAACCTGTGGGAACA- -s simRat_chr6.simRat.chr6 42983 71 + 647215 ATTGGTCCTTAAGCCCTGTAGTTTGTGGAC-AGGACAGAAATGACTGGTAGGCTATTATACGTGCTGGGATA- - -a -s simMouse_chr6.simMouse.chr6 50180 30 + 636262 TGAGTTTGACTTCTTGGCAGACTTATTCTG -s Anc0.Anc0refChr9 24674 26 + 35212 CTAGTTTGA----TTGGCAGTCTTATTCTG -s Anc1.Anc1refChr0 5038 27 - 16026 CTAGTTTGA---TTTGGCAGTCTTATTCTG -s Anc2.Anc2refChr0 44789 26 - 56053 CTGGTTTGA----TTGGCAGTCCCATTCTG -s mr.mrrefChr0 48007 27 + 130230 TGAGTTTGA---CTTGGCAGACTTATTCTG -s simCow_chr6.simCow.chr6 587561 26 - 602619 CTGGTTTGA----TTGGCAGTCCCATACTG -s simDog_chr6.simDog.chr6 582101 26 - 593897 CTGGTTTGA----TTGGCAGTCCCATTCTG -s simHuman_chr6.simHuman.chr6 589235 27 - 601863 CCAGTTTGA---TCTGGTAGTGTTATTGTG -s simRat_chr6.simRat.chr6 43054 27 + 647215 TTAGTTTGA---TTTGGCATACTCATTCTG - -a -s simMouse_chr6.simMouse.chr6 50210 5 + 636262 ATTGC -s Anc0.Anc0refChr9 24701 5 + 35212 AGGGC -s Anc1.Anc1refChr0 5066 5 - 16026 AGGGC -s Anc2.Anc2refChr0 44816 5 - 56053 AGGGC -s mr.mrrefChr0 48034 5 + 130230 ATTGC -s simCow_chr6.simCow.chr6 587588 5 - 602619 GGTGC -s simDog_chr6.simDog.chr6 582128 5 - 593897 AGGGC -s simHuman_chr6.simHuman.chr6 589263 5 - 601863 AGAGC -s simRat_chr6.simRat.chr6 43082 5 + 647215 ATTGC - -a -s simMouse_chr6.simMouse.chr6 50215 9 + 636262 CGGATGCCT -s Anc0.Anc0refChr9 24706 9 + 35212 AGGATGCTG -s Anc1.Anc1refChr0 5071 9 - 16026 AGGATGCTG -s Anc2.Anc2refChr0 44821 9 - 56053 AGGATCCTG -s mr.mrrefChr0 48039 9 + 130230 CGGATGCCT -s simCow_chr6.simCow.chr6 587594 9 - 602619 AGGGTCCTA -s simDog_chr6.simDog.chr6 582133 9 - 593897 AGGATCCTG -s simHuman_chr6.simHuman.chr6 589268 9 - 601863 AAGCTGCTG -s simRat_chr6.simRat.chr6 43087 9 + 647215 AGGACACCT - -a -s simMouse_chr6.simMouse.chr6 50224 11 + 636262 ACTCAGTAGCA -s Anc0.Anc0refChr9 24715 11 + 35212 ACTCACTAACA -s Anc1.Anc1refChr0 5080 11 - 16026 ACTCACTAACA -s Anc2.Anc2refChr0 44830 11 - 56053 ATTCACTAACA -s mr.mrrefChr0 48048 11 + 130230 ACTCAGTAGCA -s simCow_chr6.simCow.chr6 587603 11 - 602619 ATTCACTAATT -s simDog_chr6.simDog.chr6 582142 11 - 593897 GTTCACTAACA -s simHuman_chr6.simHuman.chr6 589277 11 - 601863 ACTCACTAACA -s simRat_chr6.simRat.chr6 43097 11 + 647215 GCTCAGTAACA - -a -s simMouse_chr6.simMouse.chr6 50235 5 + 636262 TTAAG -s Anc0.Anc0refChr9 24765 5 + 35212 TTAAG -s Anc1.Anc1refChr0 5130 5 - 16026 TTAAG -s Anc2.Anc2refChr0 44882 5 - 56053 CTAAA -s mr.mrrefChr0 48059 5 + 130230 TTAAG -s simDog_chr6.simDog.chr6 582194 5 - 593897 CTAAA -s simHuman_chr6.simHuman.chr6 589327 5 - 601863 TTAAG -s simRat_chr6.simRat.chr6 43108 5 + 647215 TTAAG - -a -s simMouse_chr6.simMouse.chr6 50240 2 + 636262 AT -s Anc0.Anc0refChr9 24773 2 + 35212 AT -s Anc1.Anc1refChr0 5138 2 - 16026 AT -s Anc2.Anc2refChr0 44890 2 - 56053 TA -s mr.mrrefChr0 48064 2 + 130230 AT -s simDog_chr6.simDog.chr6 582202 2 - 593897 TA -s simHuman_chr6.simHuman.chr6 589335 2 - 601863 AT -s simRat_chr6.simRat.chr6 43113 2 + 647215 TT - -a -s simMouse_chr6.simMouse.chr6 50242 12 + 636262 GTATTTGGTACA -s Anc0.Anc0refChr9 24775 12 + 35212 GTATTTGATGCA -s Anc1.Anc1refChr0 5140 12 - 16026 GTATTTGATGCA -s Anc2.Anc2refChr0 44892 12 - 56053 GTATTAGATGCA -s mr.mrrefChr0 48066 12 + 130230 GTATTTGGTACA -s simDog_chr6.simDog.chr6 582204 12 - 593897 GTATTAGATGCA -s simHuman_chr6.simHuman.chr6 589337 12 - 601863 GCATTTGATGCA -s simRat_chr6.simRat.chr6 43123 12 + 647215 TTATTTGATACA - -a -s simMouse_chr6.simMouse.chr6 50254 1 + 636262 T -s Anc0.Anc0refChr9 24790 1 + 35212 T -s Anc1.Anc1refChr0 5155 1 - 16026 T -s Anc2.Anc2refChr0 44907 1 - 56053 T -s mr.mrrefChr0 48078 1 + 130230 T -s simDog_chr6.simDog.chr6 582219 1 - 593897 T -s simHuman_chr6.simHuman.chr6 589352 1 - 601863 T -s simRat_chr6.simRat.chr6 43135 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 50255 4 + 636262 TGGC -s Anc0.Anc0refChr9 24791 4 + 35212 TAGC -s Anc1.Anc1refChr0 5156 4 - 16026 TAGC -s Anc2.Anc2refChr0 44908 4 - 56053 TAAT -s mr.mrrefChr0 48079 4 + 130230 TGGC -s simDog_chr6.simDog.chr6 582221 4 - 593897 TAAT -s simHuman_chr6.simHuman.chr6 589353 4 - 601863 TAGC -s simRat_chr6.simRat.chr6 43136 4 + 647215 TGGC - -a -s simMouse_chr6.simMouse.chr6 50259 1 + 636262 T -s Anc0.Anc0refChr9 24896 1 + 35212 T -s Anc1.Anc1refChr0 5261 1 - 16026 T -s Anc2.Anc2refChr0 45013 1 - 56053 T -s mr.mrrefChr0 48083 1 + 130230 T -s simCow_chr6.simCow.chr6 587706 1 - 602619 G -s simDog_chr6.simDog.chr6 582326 1 - 593897 T -s simHuman_chr6.simHuman.chr6 589462 1 - 601863 T -s simRat_chr6.simRat.chr6 43140 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 50260 2 + 636262 GT -s Anc0.Anc0refChr9 24935 2 + 35212 AT -s Anc1.Anc1refChr0 5300 2 - 16026 AT -s Anc2.Anc2refChr0 45052 2 - 56053 AT -s mr.mrrefChr0 48122 2 + 130230 GT -s simCow_chr6.simCow.chr6 587745 2 - 602619 AT -s simDog_chr6.simDog.chr6 582371 2 - 593897 GT -s simHuman_chr6.simHuman.chr6 589501 2 - 601863 AT -s simRat_chr6.simRat.chr6 43179 2 + 647215 GT - -a -s simMouse_chr6.simMouse.chr6 50262 68 + 636262 CTTTTTGCACCTTAGGCAAGTTGAAGTATCAAGACCTTCGTTATGATAATTCAAATCAAGTTGGTGTA -s Anc0.Anc0refChr9 24938 66 + 35212 CAATTTGTACAATAGTCAAGTGGAAGG-TCCAAGTCTTCATTCTGATGATTCAAATTAAATTGGT-TA -s Anc1.Anc1refChr0 5303 66 - 16026 CAATTTGTACAATAGTCAAGTGGAAGG-TCCAAGTCTTCATTCTGATGATTCAAATTAAATTGGT-TA -s Anc2.Anc2refChr0 45055 66 - 56053 CAATTTGTACAATAGTCTAGTGGAAGG-ATCAAGTCTTCATTCTCATGATTCAAATTAAATTGAC-TT -s mr.mrrefChr0 48124 68 + 130230 CTTTTTGCACCTTAGGCAAGTTGAAGTATCAAGACCTTCATTCTGATAATTCAAATTAAGTTGGTGTA -s simCow_chr6.simCow.chr6 587748 66 - 602619 CTATGTGTACAATAGTCTAGTGGAAGG-ATGAAGCCTTCATTCTCATGATTCAAATTAAATTGAC-TT -s simDog_chr6.simDog.chr6 582374 66 - 593897 CAATTTGTACCCTAGTCTAGTGGAAGG-ATCAGGTCTTCATTCTCATGATTCAAATTGAATTAAC-TT -s simHuman_chr6.simHuman.chr6 589504 66 - 601863 CCCTTTGTACAATAGTCATGTGGAAGA-TCCAAGTCTTCATTCTGATGATTCAAATTAAATTGGT-TA -s simRat_chr6.simRat.chr6 43181 68 + 647215 CTTTTTGCACCTTAGGCAAGTTGAAGTATCAAGACCTTCATTCTGATAATTTGAATTGAGTTGGGGTA - -a -s simMouse_chr6.simMouse.chr6 50330 27 + 636262 GGTAGATCATGGTCCTTGTCCTAGTAT -s Anc0.Anc0refChr9 25022 27 + 35212 GGTAGATCATGGACCCTACCCTAGTAT -s Anc1.Anc1refChr0 5387 27 - 16026 GGTAGATCATGGACCCTACCCTAGTAT -s Anc2.Anc2refChr0 45139 27 - 56053 GGTAGATCATGGACCCTACCCTAGTAT -s mr.mrrefChr0 48210 27 + 130230 GGTAGATCATGGTCCTTGTCCTAGTAT -s simCow_chr6.simCow.chr6 587832 27 - 602619 GGTAGATCATGGCTTCTACCCTAGTAT -s simDog_chr6.simDog.chr6 582456 27 - 593897 GGTAGATCATTCACCTTACCCTAGGAT -s simHuman_chr6.simHuman.chr6 589588 26 - 601863 TGTAGATCATGGACC-CAACGTAGTAT -s simRat_chr6.simRat.chr6 43271 27 + 647215 GGTAGATCATGGTCTTTGTCCTAGTAT - -a -s simMouse_chr6.simMouse.chr6 50357 25 + 636262 ACAGTAAAAAGTGAAAAACTTCCAA -s Anc0.Anc0refChr9 25050 25 + 35212 ACAGTAAAAAATAAGTAACTCCCAG -s Anc1.Anc1refChr0 5415 25 - 16026 ACAGTAAAAAATAAGTAACTCCCAG -s Anc2.Anc2refChr0 45167 25 - 56053 ACAGTATAGAATAAGTGATTCCCAG -s mr.mrrefChr0 48237 25 + 130230 ACAGTAAAAAGTGAGAAACTTCCAA -s simCow_chr6.simCow.chr6 587860 24 - 602619 GCAGTATAGAGTAAGT-ATTGTCAA -s simDog_chr6.simDog.chr6 582484 25 - 593897 ACAGTATAGTACAGGTGATTCCCAG -s simHuman_chr6.simHuman.chr6 589615 25 - 601863 ACAGTAAAAAATAAGTAACTCCCAG -s simRat_chr6.simRat.chr6 43298 25 + 647215 GCAGTAAAAAGTGCGAGACTGCAAA - -a -s simMouse_chr6.simMouse.chr6 50382 15 + 636262 TCAATGACTTTAAGG -s Anc0.Anc0refChr9 25077 15 + 35212 TCCAAGACTTTAAGG -s Anc1.Anc1refChr0 5442 15 - 16026 TCCAAGACTTTAAGG -s Anc2.Anc2refChr0 45194 15 - 56053 TCCAAGACTTTAAGG -s mr.mrrefChr0 48262 15 + 130230 TCAATGACTTTAAGG -s simCow_chr6.simCow.chr6 587886 15 - 602619 TCCAAGATTTTAAGG -s simDog_chr6.simDog.chr6 582511 15 - 593897 TCCATGACTCTAAAG -s simHuman_chr6.simHuman.chr6 589642 15 - 601863 TCCAAGACTTTAAGT -s simRat_chr6.simRat.chr6 43323 15 + 647215 TCAATGACTTTAAGG - -a -s simMouse_chr6.simMouse.chr6 50397 21 + 636262 TTACATTTTATCCTATTTTTT -s Anc0.Anc0refChr9 25092 21 + 35212 CTTTATTTTATCCCATCTTTT -s Anc1.Anc1refChr0 5457 21 - 16026 CTTTATTTTATCCCATCTTTT -s Anc2.Anc2refChr0 45209 21 - 56053 CTTTATTTTATCCCATCTTTT -s mr.mrrefChr0 48277 21 + 130230 TTACATTTTATCCTATCTTTT -s simCow_chr6.simCow.chr6 587901 21 - 602619 TTTCATTTTATCCCTTCTTTT -s simDog_chr6.simDog.chr6 582526 21 - 593897 CTGTATTTGATCCTAAATTTT -s simHuman_chr6.simHuman.chr6 589657 21 - 601863 CTTTATACTAAGCCATCCTTT -s simRat_chr6.simRat.chr6 43345 21 + 647215 TTACATTTCATCCTATCTTTT - -a -s simMouse_chr6.simMouse.chr6 50418 30 + 636262 TTCTCAATAACTCCTCAAGTGAGTTAATTT -s Anc0.Anc0refChr9 25113 29 + 35212 TAAT-GATGACTTCTCAAAGGAGTTAATGG -s Anc1.Anc1refChr0 5478 29 - 16026 TAAT-GATGACTTCTCAAAGGAGTTAATGG -s Anc2.Anc2refChr0 45231 29 - 56053 TAAT-GATGTCTTCTCAAAGGGGTTAATGG -s mr.mrrefChr0 48298 30 + 130230 TTCTCAATAACTCCTCAAGTGAGTTAATTT -s simCow_chr6.simCow.chr6 587923 24 - 602619 TAA------TCCTCTCAAAGGGGTTAGTGT -s simDog_chr6.simDog.chr6 582548 29 - 593897 TAAT-GATGTCTTCTCAAAGGGGTTAATGG -s simHuman_chr6.simHuman.chr6 589678 29 - 601863 TGAT-GATGACTGCCCAATGGAGTTAATGG -s simRat_chr6.simRat.chr6 43366 30 + 647215 TTCTCAATAACTACTCAGGTGAGTTAATTT - -a -s simMouse_chr6.simMouse.chr6 50448 9 + 636262 GTCTGGATG -s Anc0.Anc0refChr9 25142 9 + 35212 GTCTGTACT -s Anc1.Anc1refChr0 5507 9 - 16026 GTCTGTACT -s Anc2.Anc2refChr0 45260 9 - 56053 GTCTGTACT -s mr.mrrefChr0 48328 9 + 130230 GTCTGGACG -s simCow_chr6.simCow.chr6 591360 9 - 602619 ATCTGTACT -s simDog_chr6.simDog.chr6 582577 9 - 593897 GTATGAATT -s simHuman_chr6.simHuman.chr6 589707 9 - 601863 GTCTGTACT -s simRat_chr6.simRat.chr6 43396 9 + 647215 GTCTGGACG - -a -s simMouse_chr6.simMouse.chr6 50457 19 + 636262 ATTATAAGTGCTCTATACC -s Anc0.Anc0refChr9 25175 19 + 35212 ATTTTAGGTTCTCTATACC -s Anc1.Anc1refChr0 5540 19 - 16026 ATTTTAGGTTCTCTATACC -s Anc2.Anc2refChr0 45296 19 - 56053 ATTTTAGGTTCTCTATACC -s mr.mrrefChr0 48337 19 + 130230 ATTATAAGTGCTCTATACC -s simCow_chr6.simCow.chr6 591396 19 - 602619 ATTTTGGGTACTCTATGCC -s simDog_chr6.simDog.chr6 582613 19 - 593897 ATTTTAGGCTCTCCATACC -s simHuman_chr6.simHuman.chr6 589740 19 - 601863 ATTTTAGGTCCTCTATACC -s simRat_chr6.simRat.chr6 43405 19 + 647215 ATGGTAAGTGCTTTACACC - -a -s simMouse_chr6.simMouse.chr6 50476 62 + 636262 CTCACACTGCAATCTCAGCGTCTGGTGCAACATCTTAACTTATCAGTAAGGGTAATGACACC -s Anc0.Anc0refChr9 25195 59 + 35212 TTCACATTGCAATTCTAGAGTCTGCTGCAACTTCTTGGCTTACTAG---GGGTATTCATACC -s Anc1.Anc1refChr0 5560 59 - 16026 TTCACATTGCAATTCTAGAGTCTGCTGCAACTTCTTGGCTTACTAG---GGGTATTCATACC -s Anc2.Anc2refChr0 45316 59 - 56053 TCAACATTGCAATTCTAGAGTATGCTGCAACTTCTTGGCTTACTAG---GGGTATTCATACC -s mr.mrrefChr0 48356 62 + 130230 CTCACATTGCAATTTCAGCGTCTGCTGCAACATCTTAACTTACCAGTAAGGGTATTGACACC -s simCow_chr6.simCow.chr6 591416 59 - 602619 TCAACATTACAGTTCTAGAGTTTGCTGCAACTACTTGGCTTATTAG---CGGTATTTATACC -s simDog_chr6.simDog.chr6 582633 59 - 593897 TCACCATTGCAATTCTTGAGTATGCTGCAACTTCTTGGCTTACTAG---GGGTGGCCATACC -s simHuman_chr6.simHuman.chr6 589760 59 - 601863 TTCACATTGCAATTCTAGAGTCCACTGCAACCTCTTGGCTTACTAG---GGGTATTCATACC -s simRat_chr6.simRat.chr6 43424 62 + 647215 CTCACCTTACAATTTCAGTGTCTGCTGCAACATCTTAACTTACCAGTAAAGGTATTAACAAC - -a -s simMouse_chr6.simMouse.chr6 50538 79 + 636262 TCAGGCTGATTGATAGCATTTTAACTTACCAGTGAGGATTATGACACCTCAGGCTGATTGAGACAAACGATCACAGTGG -s Anc0.Anc0refChr9 25257 26 + 35212 TCAGGCTGG----T------------------------------------------------ACCAACCATG-TAGTGG -s Anc1.Anc1refChr0 5622 26 - 16026 TCAGGCTGG----T------------------------------------------------ACCAACCATG-TAGTGG -s Anc2.Anc2refChr0 45378 26 - 56053 CCAGGCTGG----T------------------------------------------------TCCAACCATG-TAGTAG -s mr.mrrefChr0 48418 31 + 130230 TCAGGCTGAGTGAT------------------------------------------------ACAAACAATGACAGTGG -s simCow_chr6.simCow.chr6 591478 26 - 602619 CCAGGTTGG----T------------------------------------------------TTCAACCATG-TAGTAG -s simDog_chr6.simDog.chr6 582695 26 - 593897 CAAAGCCTG----T------------------------------------------------TCCAACCATG-TAATAG -s simHuman_chr6.simHuman.chr6 589822 26 - 601863 TCAGGCTGG----T------------------------------------------------ACCGATCACG-TAGTGG -s simRat_chr6.simRat.chr6 43486 31 + 647215 TCAAGCTGAGTAAT------------------------------------------------ACAAACAATGTCAGTGG - -a -s simMouse_chr6.simMouse.chr6 50617 9 + 636262 GTCAAAGTA -s Anc0.Anc0refChr9 25287 9 + 35212 GTCAAAGAA -s Anc1.Anc1refChr0 5652 9 - 16026 GTCAAAGAA -s Anc2.Anc2refChr0 45408 9 - 56053 GCCAAAGAA -s mr.mrrefChr0 48449 9 + 130230 GTCAAAGTA -s simCow_chr6.simCow.chr6 591508 9 - 602619 CCTGAAGAA -s simDog_chr6.simDog.chr6 582725 9 - 593897 GCCAAACAA -s simHuman_chr6.simHuman.chr6 589852 9 - 601863 GTCAAAGAA -s simRat_chr6.simRat.chr6 43517 9 + 647215 GTCAAAAAA - -a -s simMouse_chr6.simMouse.chr6 50626 14 + 636262 ATCCTTACAACTTC -s Anc0.Anc0refChr9 25300 14 + 35212 ATTCTCCCAGGTTA -s Anc1.Anc1refChr0 5665 14 - 16026 ATTCTCCCAGGTTA -s Anc2.Anc2refChr0 45421 14 - 56053 ATTCTCCGAGGTTA -s mr.mrrefChr0 48458 14 + 130230 ATCCTTACAACTTA -s simCow_chr6.simCow.chr6 591520 13 - 602619 ATCCCTCAAGGTT- -s simDog_chr6.simDog.chr6 582738 14 - 593897 ATTCTCTGAGGTTA -s simHuman_chr6.simHuman.chr6 589865 14 - 601863 ATGCGCCCAGGTAA -s simRat_chr6.simRat.chr6 43526 14 + 647215 ACCCTTACAACTTA - -a -s simMouse_chr6.simMouse.chr6 50640 13 + 636262 CCCAATAGGTTGT -s Anc0.Anc0refChr9 25314 12 + 35212 TCCAATAGGTTG- -s Anc1.Anc1refChr0 5679 13 - 16026 TCCAATAGGTTGT -s Anc2.Anc2refChr0 45435 12 - 56053 CACAACAGGTTA- -s mr.mrrefChr0 48472 13 + 130230 TCCAATAGGTTGT -s simCow_chr6.simCow.chr6 591533 8 - 602619 ---AACAGGGT-- -s simDog_chr6.simDog.chr6 582752 12 - 593897 CACAACAGGTTA- -s simHuman_chr6.simHuman.chr6 589979 13 - 601863 TCTTTTGGGTTGT -s simHuman_chr6.simHuman.chr6 589879 13 - 601863 TCCAATGGGTTGT -s simRat_chr6.simRat.chr6 43540 13 + 647215 TCCAATAAGTTGT - -a -s simMouse_chr6.simMouse.chr6 50653 1 + 636262 T -s Anc0.Anc0refChr9 25326 1 + 35212 A -s Anc1.Anc1refChr0 5692 1 - 16026 A -s Anc2.Anc2refChr0 45447 1 - 56053 A -s mr.mrrefChr0 48485 1 + 130230 T -s simDog_chr6.simDog.chr6 582764 1 - 593897 A -s simHuman_chr6.simHuman.chr6 589892 1 - 601863 A -s simRat_chr6.simRat.chr6 43553 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 50654 13 + 636262 CAGCCACAATGCA -s Anc0.Anc0refChr9 25327 13 + 35212 CAGCCACAATGCT -s Anc1.Anc1refChr0 5693 13 - 16026 CAGCCACAATGCT -s Anc2.Anc2refChr0 45448 13 - 56053 AAGCTACAATGCC -s mr.mrrefChr0 48486 13 + 130230 CAGCCACAATGCA -s simCow_chr6.simCow.chr6 591541 6 - 602619 -------AATGCC -s simDog_chr6.simDog.chr6 582765 13 - 593897 AAGCTACAATGCC -s simHuman_chr6.simHuman.chr6 589992 13 - 601863 CAGCCACAATGCT -s simHuman_chr6.simHuman.chr6 589893 13 - 601863 CAGCCACAATACT -s simRat_chr6.simRat.chr6 43554 13 + 647215 CAGCCACAATGCA - -a -s simMouse_chr6.simMouse.chr6 50667 28 + 636262 ATTAAGTAAACCAAAGCTCATGATCATT -s Anc0.Anc0refChr9 25340 28 + 35212 ATTCAGTGAACCATAGTTCAAGATTATT -s Anc1.Anc1refChr0 5706 28 - 16026 ATTCAGTGAACCATAGTTCAAGATTATT -s Anc2.Anc2refChr0 45461 28 - 56053 ATTCAGTGAACCATAGTTCAAGATTATT -s mr.mrrefChr0 48499 28 + 130230 ATTAAGTAAACCAAAGTTCATGATCATT -s simCow_chr6.simCow.chr6 591551 28 - 602619 AATCATTCAATCTTAGTTTATGATTATT -s simDog_chr6.simDog.chr6 582778 28 - 593897 ATTCAGTGAACCATAATTCAAGATTATT -s simHuman_chr6.simHuman.chr6 590005 28 - 601863 AGTCAGACAACCACAGTTGTAGATTATT -s simHuman_chr6.simHuman.chr6 589906 28 - 601863 ATTCAGTGAACCATAGTTGATGATTATT -s simRat_chr6.simRat.chr6 43567 28 + 647215 ATTGAGTAAGCCAAAGTTCAGGACCCTT - -a -s simMouse_chr6.simMouse.chr6 50695 15 + 636262 GGTGATAGACCTTTC -s Anc0.Anc0refChr9 25368 15 + 35212 GACAATAGACCTCTC -s Anc1.Anc1refChr0 5734 15 - 16026 GACAATAGACCTCTC -s Anc2.Anc2refChr0 45489 15 - 56053 GACAACAGACCTCTT -s mr.mrrefChr0 48527 15 + 130230 GATGATAGACCTTTC -s simCow_chr6.simCow.chr6 591579 15 - 602619 GACAACAGACCTTTA -s simDog_chr6.simDog.chr6 582806 15 - 593897 GATGACAGACCTCTT -s simHuman_chr6.simHuman.chr6 590033 15 - 601863 GACAATAGACCCCTC -s simHuman_chr6.simHuman.chr6 589935 15 - 601863 GACTATGGACCTCTC -s simRat_chr6.simRat.chr6 43595 15 + 647215 GATGATAGACCTTCC - -a -s simMouse_chr6.simMouse.chr6 50710 1 + 636262 A -s Anc0.Anc0refChr9 25383 1 + 35212 A -s Anc1.Anc1refChr0 5749 1 - 16026 A -s Anc2.Anc2refChr0 45504 1 - 56053 A -s mr.mrrefChr0 48542 1 + 130230 A -s simCow_chr6.simCow.chr6 591594 1 - 602619 A -s simDog_chr6.simDog.chr6 582821 1 - 593897 A -s simHuman_chr6.simHuman.chr6 589950 1 - 601863 A -s simRat_chr6.simRat.chr6 43610 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 50711 21 + 636262 ATAATCAGAACCACATTGCCA -s Anc0.Anc0refChr9 25384 21 + 35212 TTGACCATGACTACAATGTTA -s Anc1.Anc1refChr0 5750 21 - 16026 TTGACCATGACTACAATGTTA -s Anc2.Anc2refChr0 45505 21 - 56053 TTGACCATGACTATGCTGTTA -s mr.mrrefChr0 48543 21 + 130230 TTAATCATGACTACATTGCTA -s simCow_chr6.simCow.chr6 591595 21 - 602619 TTGACCATAACTATGTTGTCA -s simDog_chr6.simDog.chr6 582822 21 - 593897 ATGAACATGACTCTGCTGTTA -s simHuman_chr6.simHuman.chr6 590048 21 - 601863 TTGACCATGACTACAATGTTA -s simHuman_chr6.simHuman.chr6 589951 16 - 601863 TTGGCCATGACTACAA----- -s simRat_chr6.simRat.chr6 43611 21 + 647215 TTAATCATGACTACACTGCTA - -a -s simMouse_chr6.simMouse.chr6 50732 22 + 636262 TATTAACCCTTTATTAACTCAG -s Anc0.Anc0refChr9 25406 22 + 35212 TATTATGCCTTTATTTCCCTGA -s Anc1.Anc1refChr0 5772 22 - 16026 TATTATGCCTTTATTTCCCTGA -s Anc2.Anc2refChr0 45527 22 - 56053 TATTATGCCTTTCTTTCTCTGA -s mr.mrrefChr0 48565 22 + 130230 TATTATCCCTTTATTTCCTTGG -s simCow_chr6.simCow.chr6 591617 22 - 602619 TATTATGCCTTTCTTTCTCAGA -s simDog_chr6.simDog.chr6 582844 22 - 593897 TATTATGCCTTTCTCTCTTTTA -s simHuman_chr6.simHuman.chr6 590070 22 - 601863 TATTATGCCTTTATTTCCCTGA -s simHuman_chr6.simHuman.chr6 589968 11 - 601863 TGGTATACCTT----------- -s simRat_chr6.simRat.chr6 43633 22 + 647215 TATTATCCCTTTTTTTCCTTGG - -a -s simMouse_chr6.simMouse.chr6 50754 8 + 636262 CCAGACCC -s Anc0.Anc0refChr9 25429 8 + 35212 TGAGACTC -s Anc1.Anc1refChr0 5795 8 - 16026 TGAGACTC -s Anc2.Anc2refChr0 45550 8 - 56053 TGAGACTC -s mr.mrrefChr0 48588 8 + 130230 TCAGACCC -s simCow_chr6.simCow.chr6 591640 8 - 602619 TGAGACTT -s simDog_chr6.simDog.chr6 582867 7 - 593897 T-CGGCTC -s simHuman_chr6.simHuman.chr6 590093 8 - 601863 TGAGACTC -s simRat_chr6.simRat.chr6 43656 8 + 647215 TTGGACCC - -a -s simMouse_chr6.simMouse.chr6 50762 24 + 636262 TGACTTATTCCTTTCAGTGTAGGT -s Anc0.Anc0refChr9 25443 24 + 35212 TGTCTTACTCCTTACGGTTTATGT -s Anc1.Anc1refChr0 5809 24 - 16026 TGTCTTACTCCTTACGGTTTATGT -s Anc2.Anc2refChr0 45564 24 - 56053 TGTTTTACTCCTTATGGTTTATGT -s mr.mrrefChr0 48596 24 + 130230 TGACTTATTCCTTTCAGTGTAGGT -s simCow_chr6.simCow.chr6 591654 24 - 602619 TGCTTTACTCCTTATGGTCTATGT -s simDog_chr6.simDog.chr6 582880 24 - 593897 TGTTTTACTCCTTATGATTTATGT -s simHuman_chr6.simHuman.chr6 590107 24 - 601863 TGGCTTAATCCTTACGGTTTATGT -s simRat_chr6.simRat.chr6 43664 24 + 647215 TGATTTATTCCTTCCAGTGTAGGT - -a -s simMouse_chr6.simMouse.chr6 50786 119 + 636262 CTACTCCTTTTACTGTATTTTAATTTTCTATGGCAGAACATTCCTTACCCATGAACCCATGCATAATCTATATTGCAGGAGTCACATGGAGATCCTGAGCCCGTTGGTTAATTGAACTG -s Anc0.Anc0refChr9 25467 45 + 35212 CTACTCCCTTCAGTGTATTCTGATTTTTTATGGCAGAGCTTCTTT-------------------------------------------------------------------------- -s Anc1.Anc1refChr0 5833 75 - 16026 CTACTCCCTTCAGTGTATTCTGATTTTTTATGGCAGAGCTTCTTTTATCAATCAACCCGCCCATAGTCAAGATAG-------------------------------------------- -s Anc2.Anc2refChr0 45588 45 - 56053 CTACTCCCTTCAGTGTATTCTGATTGTTTATGGCAGAGCTTCTTT-------------------------------------------------------------------------- -s mr.mrrefChr0 48620 116 + 130230 CTACTCCTTTTACTGTATTCTAATTTTCTATGGCAGAGCATTCCTTATCAATGAACCCACCCATAGTCTATATTGCAGGAGTCACATGGAGATCCTGAG-CCGTTGGTTAATTG--CTG -s simCow_chr6.simCow.chr6 591679 45 - 602619 CCACTCTGTTCAGTGTATTCTGATTGATGATGGCAGACCTTCTTT-------------------------------------------------------------------------- -s simDog_chr6.simDog.chr6 582904 45 - 593897 CTGCCCCCTTCAGTGTATTCTGATTGTTTATGGCAGAGCTTCTGT-------------------------------------------------------------------------- -s simHuman_chr6.simHuman.chr6 590131 67 - 601863 CTACTCC--------TATTCTGATTTTTTATGGAGGAGCTTCTTCTATCAATCAACCCGCCCATAGTCAAGATAG-------------------------------------------- -s simRat_chr6.simRat.chr6 43688 116 + 647215 CTACTCTTTTCACTGTGTTCTAATTTTGTCTGGCAGAGCATTGCTTATCAATGACCCCACCCATAGTCCGTATTCCTGGAGTTGCATGGTGATCTTGAG-CTGCTGGTTAGATG--CTG - -a -s simMouse_chr6.simMouse.chr6 50905 74 + 636262 GTGGAGTTAGACGGACATCACTGAACAAGGAGCTTCATAGCATGAGATCTCTAGCCAGTCTCTTCTATGGACAT -s Anc0.Anc0refChr9 25512 1 + 35212 -------------------------------------------------------------------------T -s Anc1.Anc1refChr0 5908 10 - 16026 ----------------------------------------------------------------CTACTAATAT -s Anc2.Anc2refChr0 45633 1 - 56053 -------------------------------------------------------------------------T -s mr.mrrefChr0 48736 30 + 130230 GTGG--------------------------------------------CTCTAGCCAGTCTCTTCTATTAACAT -s simCow_chr6.simCow.chr6 591724 1 - 602619 -------------------------------------------------------------------------T -s simDog_chr6.simDog.chr6 582949 1 - 593897 -------------------------------------------------------------------------T -s simHuman_chr6.simHuman.chr6 590198 10 - 601863 ----------------------------------------------------------------CTACTAATAT -s simRat_chr6.simRat.chr6 43805 30 + 647215 GTGG--------------------------------------------CTCACTTCATTCTCCTCGATTAGCAT - -a -s simMouse_chr6.simMouse.chr6 50979 6 + 636262 ATGTGG -s Anc0.Anc0refChr9 25513 5 + 35212 ACA-GG -s Anc1.Anc1refChr0 5918 5 - 16026 ACA-GG -s Anc2.Anc2refChr0 45634 5 - 56053 ACA-TG -s mr.mrrefChr0 48766 6 + 130230 ACGTGG -s simCow_chr6.simCow.chr6 591728 5 - 602619 ACA-TA -s simDog_chr6.simDog.chr6 582950 5 - 593897 ACA-TG -s simHuman_chr6.simHuman.chr6 590208 5 - 601863 ACA-GG -s simRat_chr6.simRat.chr6 43835 6 + 647215 GCGTGG - -a -s simMouse_chr6.simMouse.chr6 50985 27 + 636262 TCACCTTATAGTACATGAATACCTTGT -s Anc0.Anc0refChr9 25518 26 + 35212 TTACCTT-TTGTACATGGTCACCTTGT -s Anc1.Anc1refChr0 5923 26 - 16026 TTACCTT-TTGTACATGGTCACCTTGT -s Anc2.Anc2refChr0 45639 26 - 56053 TTGCCTT-ATGTACATGGTCACCTTCT -s mr.mrrefChr0 48772 27 + 130230 TCACCTTATAGTACATGAATACCTTGT -s simCow_chr6.simCow.chr6 591733 26 - 602619 CTTCCTT-ACATACATGGTCACCCTAT -s simDog_chr6.simDog.chr6 582956 26 - 593897 TTGCCTT-ATGTACATGGCCACCTTCC -s simHuman_chr6.simHuman.chr6 590213 26 - 601863 TAACCTT-TTGTACATGGTCGCCTTGT -s simRat_chr6.simRat.chr6 43841 27 + 647215 TCACTATATAGTACATGAATCCCTTGT - -a -s simMouse_chr6.simMouse.chr6 51012 102 + 636262 GCAATGATCACCTAATGCCATAAGGCCAGGAATCTATGTTAATCATGACTCAACCCTATGACTCAAGGGCTTAAATGATATATACACACCAGCCTTTTTACA -s Anc0.Anc0refChr9 25544 66 + 35212 G------------GGTGCAAAAAGGCCAGAAATCT--------------------CTATGACTCAA-GGCTCAAATGA---GTACAGGCCAGACTTTTCACG -s Anc1.Anc1refChr0 5949 69 - 16026 G------------GGTGCAAAAAGGCCAGAAATCT--------------------CTATGACTCAA-GGCTCAAATGACATGTACAGGCCAGACTTTTCACG -s Anc2.Anc2refChr0 45665 66 - 56053 G------------GGTCCAAAAAGCCCAGAAATCT--------------------CTGTGACTCAA-GGCTCAAATGA---GTACAGGCCAGACTTTTCATG -s mr.mrrefChr0 48799 102 + 130230 GCAATGATCACCTAATGCCATAAGGCCAGGAATCTATGTTAATCATGACTCAACCCTATGACTCAAGGGCTTAAATGATATATACACACCAGCCTTTTTACA -s simCow_chr6.simCow.chr6 591828 66 - 602619 G------------TGCACAAAAAGCCCAGAAATCT--------------------CGCGGACTCAA-GGCTTAAATGA---GTACAGGCCAAACTTTTCAAG -s simDog_chr6.simDog.chr6 582982 61 - 593897 A------------GTTCCAAAAAGCCTAGAAATCT--------------------CTGTGGCTACA-GGCTCA--------GTACAGGCCAGACCTATCATG -s simHuman_chr6.simHuman.chr6 590239 67 - 601863 G------------GGTGCA--AATGCCAGAATTCT--------------------CTATGACTCAA-GGCTCAAATGACATGTACAGGCTAGAATTTTCACG -s simRat_chr6.simRat.chr6 43868 99 + 647215 GCAATGATCACCTAATGCCATAAGGCCAGGAATCTATGTTAATCATGACTCAATCTTAT---TCAAGGGCTTGAATGATATATACACACAAGCCCTTCTACA - -a -s simMouse_chr6.simMouse.chr6 51114 24 + 636262 AAACACCAGCCTTTTCATAGATTT -s Anc0.Anc0refChr9 25610 13 + 35212 A-----------TTTAAGTGCTAT -s Anc1.Anc1refChr0 6018 13 - 16026 A-----------TTTAAGTGCTAT -s Anc2.Anc2refChr0 45732 13 - 56053 A-----------TTTAAGTGCTAT -s mr.mrrefChr0 48901 24 + 130230 AAACACCAGCCTTTTCATTGATTT -s simCow_chr6.simCow.chr6 591895 13 - 602619 A-----------TTTAAATGCTAT -s simDog_chr6.simDog.chr6 583044 13 - 593897 A-----------TTTAAGTGCGAT -s simHuman_chr6.simHuman.chr6 590306 13 - 601863 A-----------TTTAAGTGCTAT -s simRat_chr6.simRat.chr6 43967 24 + 647215 AAACACCAGCCTTTTCATTGATTA - -a -s simMouse_chr6.simMouse.chr6 51138 32 + 636262 ATGGATTTAAGTATACCTGTTTATGGGACGTT -s Anc0.Anc0refChr9 25627 31 + 35212 AAGTATTGGAA-ATACCTGTTTCTGGACTGTT -s Anc1.Anc1refChr0 6035 31 - 16026 AAGTATTGGAA-ATACCTGTTTCTGGACTGTT -s Anc2.Anc2refChr0 45749 31 - 56053 AAGCATCGGAA-ATACCTGGGTCTGTACTGTT -s mr.mrrefChr0 48929 32 + 130230 ATGTATTTAAGTATACCTGTTTATGGGATGTT -s simCow_chr6.simCow.chr6 591912 27 - 602619 AAGCATCAGAG-AGACCTGGGTATATAC---- -s simDog_chr6.simDog.chr6 583061 27 - 593897 AGG----GGAA-GTCCCTGGGTCTGTACTGTT -s simHuman_chr6.simHuman.chr6 590323 30 - 601863 AAGTATTGGAA-ATACCTGTTTCT-GTCTGTT -s simRat_chr6.simRat.chr6 43995 32 + 647215 ATTTATTTAAGTATACCCATTTATGGAATGTT - -a -s simMouse_chr6.simMouse.chr6 51170 32 + 636262 ATCAATAAAAGAAACTGTAATATCTTATAAAT -s Anc0.Anc0refChr9 25659 32 + 35212 ATCAATACAAGAAACTATAATATGTAATGATT -s Anc1.Anc1refChr0 6067 32 - 16026 ATCAATACAAGAAACTATAATATGTAATGATT -s Anc2.Anc2refChr0 45781 32 - 56053 TTCAATACAAGAAACTATAATATGTAACGACT -s mr.mrrefChr0 48961 32 + 130230 ATCAATAAAAGAAACTATAATATCTTATAATT -s simCow_chr6.simCow.chr6 591939 26 - 602619 ------ACAAGAAGCTATAATATGTAACAACT -s simDog_chr6.simDog.chr6 583089 31 - 593897 TTCAATACAAGAAACTATAATATGTAA-GACT -s simHuman_chr6.simHuman.chr6 590355 32 - 601863 ATCAATACAGGAAACTAAAATATGTAATGATT -s simRat_chr6.simRat.chr6 44027 32 + 647215 ATCAATAAAAGAAACTATAATATCTTATAATT - -a -s simMouse_chr6.simMouse.chr6 51202 58 + 636262 TTGTGATGCATTATGTTAGATCAGAGATACAGTTGCCTCTATAATTAGGCTGCCCTGT -s Anc0.Anc0refChr9 25692 58 + 35212 TTGAGATGAATTAGGTTAGACCTGAGGTATGTCTGATTCAATAATTAGAGCGACCCAT -s Anc1.Anc1refChr0 6100 58 - 16026 TTGAGATGAATTAGGTTAGACCTGAGGTATGTCTGATTCAATAATTAGAGCGACCCAT -s Anc2.Anc2refChr0 45814 58 - 56053 TTGAGATGAATTAGGTCAGACCTGGGGTATGTCTGATTCAATACTTAGAGTGACCCAT -s mr.mrrefChr0 48993 58 + 130230 TTGAGATGCATTATGTTAGATCAGAGATACAGCTGCTTCAATAATTAGGCCACCCTGT -s simCow_chr6.simCow.chr6 591966 54 - 602619 TTGAGATGAATTAGG-CAGGCCTGGGGTATGTACCGTT---TACTTAGAATGACCCAT -s simDog_chr6.simDog.chr6 583121 58 - 593897 TTGAGATGAATTAAGTCAAACCTGGGGTATACCTGATGCAATACTTGGAGTGACCCAT -s simHuman_chr6.simHuman.chr6 590388 56 - 601863 TTGAGATGAAT--GGTTAGACCTGAGGTATGTCTGATTCAATGATTAAAGCCACCCAT -s simRat_chr6.simRat.chr6 44059 57 + 647215 TTAAGATGCATTATGTTAGATCAGAGATACAGCTCCTTCAATAA-TAGCCCAACTTGT - -a -s simMouse_chr6.simMouse.chr6 51260 26 + 636262 TCATTTCAGCATTGTGCCAACTATTA -s Anc0.Anc0refChr9 25751 25 + 35212 TAATTAA-GCATTGAGTCAACTATTA -s Anc1.Anc1refChr0 6159 25 - 16026 TAATTAA-GCATTGAGTCAACTATTA -s Anc2.Anc2refChr0 45873 25 - 56053 TACTTAA-GCATCGAGTCAACTATTA -s mr.mrrefChr0 49051 25 + 130230 TCATTTC-GCATTGTGTCAACTATTA -s simCow_chr6.simCow.chr6 592021 25 - 602619 TACTTAA-GCATCAAGTCAACCATTA -s simDog_chr6.simDog.chr6 583180 25 - 593897 CACTTAA-GCATCGAGACAACTATTA -s simHuman_chr6.simHuman.chr6 590445 25 - 601863 TGATTAA-GCATTGAGTCAACTATTA -s simRat_chr6.simRat.chr6 44116 25 + 647215 TTATTTC-CCATTGTGTCAATGGTTA - -a -s simMouse_chr6.simMouse.chr6 51286 13 + 636262 ATAATTAGTAACT -s Anc0.Anc0refChr9 25776 12 + 35212 ACCATCTGTAAC- -s Anc1.Anc1refChr0 6184 12 - 16026 ACCATCTGTAAC- -s Anc2.Anc2refChr0 45898 12 - 56053 ACCATCTGTAGC- -s mr.mrrefChr0 49076 12 + 130230 ATAATTTGTAAC- -s simCow_chr6.simCow.chr6 592046 12 - 602619 ACCATCTGTAGC- -s simDog_chr6.simDog.chr6 583205 12 - 593897 ACCATCTGTAGG- -s simHuman_chr6.simHuman.chr6 590470 12 - 601863 AGCATCTACAAC- -s simRat_chr6.simRat.chr6 44143 12 + 647215 ATGATTTGTAAC- - -a -s simMouse_chr6.simMouse.chr6 51299 30 + 636262 GAACAAGGCCTATCCTATGCCACATCCCAA -s Anc0.Anc0refChr9 25788 30 + 35212 GAACATGGCCTCTCCTGTGTCCCATTCTAA -s Anc1.Anc1refChr0 6196 30 - 16026 GAACATGGCCTCTCCTGTGTCCCATTCTAA -s Anc2.Anc2refChr0 45911 30 - 56053 GAACATGGCCTCTCCTGTGTCCCATTCTAA -s mr.mrrefChr0 49088 30 + 130230 GAACAAGGCCTCTCCTGTGCCACATCCCAA -s simCow_chr6.simCow.chr6 592059 30 - 602619 GAACATGGCCTCTCCTGTATCCCACTCTAA -s simDog_chr6.simDog.chr6 583218 29 - 593897 GAACATAGCCTCTCCTGAG-CCCATTCTAA -s simHuman_chr6.simHuman.chr6 590482 30 - 601863 TGACATGGCCTCTCTTGTGTCCCGTTCGAC -s simRat_chr6.simRat.chr6 44155 30 + 647215 AAACAAGGTCTCTCCTGTGCCACATCACAA - -a -s simMouse_chr6.simMouse.chr6 51329 17 + 636262 CAATTGTAGGGCTTAGC -s Anc0.Anc0refChr9 25818 17 + 35212 GAGCTGTGGGGCTTACC -s Anc1.Anc1refChr0 6226 17 - 16026 GAGCTGTGGGGCTTACC -s Anc2.Anc2refChr0 45941 17 - 56053 TAGCTGTGGAGCTTACC -s mr.mrrefChr0 49118 17 + 130230 GAACTGTAGGGCTTAGC -s simCow_chr6.simCow.chr6 592089 17 - 602619 CAGCTGTAGAGCTTACC -s simDog_chr6.simDog.chr6 583247 17 - 593897 TAACTGTGGAGCTTACC -s simHuman_chr6.simHuman.chr6 590514 17 - 601863 GATTAGAGGGACCCATC -s simRat_chr6.simRat.chr6 44185 17 + 647215 GAACTGTGGAGCTTAGT - -a -s simMouse_chr6.simMouse.chr6 51346 17 + 636262 AAAATTGAAAAGGTTGT -s Anc0.Anc0refChr9 25835 17 + 35212 ATAATTGATGAGGGTGT -s Anc1.Anc1refChr0 6243 17 - 16026 ATAATTGATGAGGGTGT -s Anc2.Anc2refChr0 45958 17 - 56053 ATAATTAATGAGGGTGC -s mr.mrrefChr0 49135 17 + 130230 AAAATTGAAAAGGTTGT -s simCow_chr6.simCow.chr6 592106 17 - 602619 ACAAATAGAAAGGGTGC -s simDog_chr6.simDog.chr6 583264 17 - 593897 ATAATTAATGAGGGTGC -s simHuman_chr6.simHuman.chr6 590537 17 - 601863 AGCATTGAGTCACCTAT -s simRat_chr6.simRat.chr6 44202 17 + 647215 AAAATTAAAGAGGGTGT - -a -s simMouse_chr6.simMouse.chr6 51363 25 + 636262 TAGGACAAACTAGTATAGGTAATAC -s Anc0.Anc0refChr9 25852 25 + 35212 TAGGATGAACTAGTATAGATAATAC -s Anc1.Anc1refChr0 6260 25 - 16026 TAGGATGAACTAGTATAGATAATAC -s Anc2.Anc2refChr0 45976 25 - 56053 TAGGATGAACTAGTACACATACTAC -s mr.mrrefChr0 49152 25 + 130230 TAGGACAAACTAGTATAGGTAATAC -s simCow_chr6.simCow.chr6 592124 25 - 602619 TGGGATGGACTAGTACACAAAATAC -s simDog_chr6.simDog.chr6 583282 25 - 593897 TAGGACGAACTAGTACAGATGCTAC -s simHuman_chr6.simHuman.chr6 590554 23 - 601863 TAAGCATCTGTAGTATAG--AAAAA -s simRat_chr6.simRat.chr6 44219 25 + 647215 TAGGACAAGCTAGTATGGGTAATAC - -a -s simMouse_chr6.simMouse.chr6 51388 18 + 636262 AGTTCGAATGACTATCAG -s Anc0.Anc0refChr9 25877 15 + 35212 A---TGAATTAGTAGCAG -s Anc1.Anc1refChr0 6285 15 - 16026 A---TGAATTAGTAGCAG -s Anc2.Anc2refChr0 46008 15 - 56053 A---TTAATTAGAAGCAG -s mr.mrrefChr0 49177 15 + 130230 A---TGAATGAGTATCAG -s simCow_chr6.simCow.chr6 592156 15 - 602619 G---TAAACTAGGAGCAG -s simDog_chr6.simDog.chr6 583314 15 - 593897 A---GTAATTAGAAGCAG -s simHuman_chr6.simHuman.chr6 590577 15 - 601863 A---TGAATTAGTAGCAG -s simRat_chr6.simRat.chr6 44244 15 + 647215 A---TGAACCAGTATCAG - -a -s simMouse_chr6.simMouse.chr6 51406 22 + 636262 AGGCTAATACAAGAATTCCCAA -s Anc0.Anc0refChr9 25907 22 + 35212 AGACTAACCCATGATTTCCCAA -s Anc1.Anc1refChr0 6315 22 - 16026 AGACTAACCCATGATTTCCCAA -s Anc2.Anc2refChr0 46039 22 - 56053 AGACTAACCCATGATTTCCCAA -s mr.mrrefChr0 49192 22 + 130230 AGGCTAATACAAGAATTCCCAA -s simCow_chr6.simCow.chr6 592187 22 - 602619 AGACTAACCCATAGTTTCCCAA -s simDog_chr6.simDog.chr6 583345 22 - 593897 ACACTATCCCATGATTTCCTAA -s simHuman_chr6.simHuman.chr6 590607 22 - 601863 AGACTAACCCATGTCCTCCCAA -s simRat_chr6.simRat.chr6 44259 22 + 647215 AGGATAATACAAGAATTCCCAA - -a -s simMouse_chr6.simMouse.chr6 51428 15 + 636262 GATATGAGCAGCAGG -s Anc0.Anc0refChr9 25929 15 + 35212 GAAATGAGCAGCAGG -s Anc1.Anc1refChr0 6337 15 - 16026 GAAATGAGCAGCAGG -s Anc2.Anc2refChr0 46061 15 - 56053 GCAATGAGCAGCAGG -s mr.mrrefChr0 49214 15 + 130230 GATATGAGCAGCAGG -s simCow_chr6.simCow.chr6 592216 15 - 602619 GCAATGAGCAGTAGG -s simDog_chr6.simDog.chr6 583367 15 - 593897 GCAGTGAGCAGCAGG -s simHuman_chr6.simHuman.chr6 590629 15 - 601863 GAAATGAGTAGCAGG -s simRat_chr6.simRat.chr6 44281 15 + 647215 GATATGAGCAGCAGG - -a -s simMouse_chr6.simMouse.chr6 51443 15 + 636262 TATGGGTTGCGTGTG -s Anc0.Anc0refChr9 25944 13 + 35212 TATGGGTTT--GGTG -s Anc1.Anc1refChr0 6352 13 - 16026 TATGGGTTT--GGTG -s Anc2.Anc2refChr0 46076 13 - 56053 TATGGGTTT--GGTG -s mr.mrrefChr0 49229 15 + 130230 TATGGGTTTCGTGTG -s simCow_chr6.simCow.chr6 592231 13 - 602619 TATGAGTTT--GGTG -s simDog_chr6.simDog.chr6 583385 13 - 593897 TATGGGTTT--GGTT -s simHuman_chr6.simHuman.chr6 590644 13 - 601863 TACGGGTTT--GGTG -s simRat_chr6.simRat.chr6 44296 15 + 647215 TATGGGCTTTGTGTG - -a -s simMouse_chr6.simMouse.chr6 51458 10 + 636262 GCATTAATGG -s Anc0.Anc0refChr9 25957 10 + 35212 GTATTAATAG -s Anc1.Anc1refChr0 6365 10 - 16026 GTATTAATAG -s Anc2.Anc2refChr0 46089 10 - 56053 GTATTAATAG -s mr.mrrefChr0 49244 10 + 130230 GCATTAATGG -s simCow_chr6.simCow.chr6 592246 10 - 602619 GTAATAATGG -s simDog_chr6.simDog.chr6 583398 10 - 593897 GTATTAATAG -s simHuman_chr6.simHuman.chr6 590657 10 - 601863 GTATTAATAG -s simRat_chr6.simRat.chr6 44311 10 + 647215 GCACTAATGG - -a -s simMouse_chr6.simMouse.chr6 51468 15 + 636262 AATTAAACAGCTGAG -s Anc0.Anc0refChr9 25971 15 + 35212 GATTAAACAGCTGAG -s Anc1.Anc1refChr0 6379 15 - 16026 GATTAAACAGCTGAG -s Anc2.Anc2refChr0 46103 15 - 56053 GATTAGGCAGCTGAG -s mr.mrrefChr0 49254 15 + 130230 GATTAAACAGCTGAG -s simCow_chr6.simCow.chr6 592260 14 - 602619 GATTAGGCAG-TGAG -s simDog_chr6.simDog.chr6 583412 15 - 593897 GGTTAGGCAGCTGAG -s simHuman_chr6.simHuman.chr6 590672 15 - 601863 GATTAAAATGCTGCG -s simRat_chr6.simRat.chr6 44321 15 + 647215 GATTAAACAGCTGAG - -a -s simMouse_chr6.simMouse.chr6 51483 12 + 636262 TTCACAAATCCC -s Anc0.Anc0refChr9 25986 12 + 35212 TTCATAAATCAA -s Anc1.Anc1refChr0 6394 12 - 16026 TTCATAAATCAA -s Anc2.Anc2refChr0 46118 12 - 56053 TTCATAAATCAA -s mr.mrrefChr0 49269 12 + 130230 TTCACAAATCCA -s simCow_chr6.simCow.chr6 592274 12 - 602619 TTTAAAAATGAA -s simDog_chr6.simDog.chr6 583428 12 - 593897 TTCATAAATCAA -s simHuman_chr6.simHuman.chr6 590687 12 - 601863 TTCATAAATCAA -s simRat_chr6.simRat.chr6 44336 12 + 647215 TTCACACATACA - -a -s simMouse_chr6.simMouse.chr6 51495 23 + 636262 TTGGTCGTTTAACATGTGGTTCC -s Anc0.Anc0refChr9 25998 23 + 35212 CTGGTTGTTTAACATGTGGCTTC -s Anc1.Anc1refChr0 6406 23 - 16026 CTGGTTGTTTAACATGTGGCTTC -s Anc2.Anc2refChr0 46132 23 - 56053 CTGATTGTTTAACATGTGACTTC -s mr.mrrefChr0 49281 23 + 130230 CTGGTTGTTTAACATGTGGTTCC -s simCow_chr6.simCow.chr6 592288 23 - 602619 CTGATCGTTTAACATGTGACTTC -s simDog_chr6.simDog.chr6 583442 23 - 593897 CTGATTATTTCACATGTGATTTT -s simHuman_chr6.simHuman.chr6 590699 23 - 601863 CCTGGTGTTTAACATGTGGCTTC -s simRat_chr6.simRat.chr6 44348 23 + 647215 CTAGTTGTTTAACATGTGGTTCC - -a -s simMouse_chr6.simMouse.chr6 51518 14 + 636262 ATACAGCCTGGATG -s Anc0.Anc0refChr9 26021 10 + 35212 AT--TGCCTCA--C -s Anc1.Anc1refChr0 6429 12 - 16026 AT--TGCCTCACTC -s Anc2.Anc2refChr0 46155 10 - 56053 AT--TGCAGCA--C -s mr.mrrefChr0 49304 14 + 130230 ATACAGCCTGGATG -s simCow_chr6.simCow.chr6 592317 10 - 602619 AT--TGCAGTG--C -s simDog_chr6.simDog.chr6 583475 10 - 593897 AT--TGCAGCA--C -s simHuman_chr6.simHuman.chr6 590722 12 - 601863 AT--TGCCTTACTC -s simRat_chr6.simRat.chr6 44371 14 + 647215 ATACAGCCCAGATG - -a -s simMouse_chr6.simMouse.chr6 51532 34 + 636262 TTGTGAGTACAGTATCCATGTAAGCAGCAAAGAA -s Anc0.Anc0refChr9 26031 21 + 35212 TTG-------------CATGTAAGCAACAAAGAA -s Anc1.Anc1refChr0 6441 21 - 16026 TTG-------------CATGTAAGCAACAAAGAA -s Anc2.Anc2refChr0 46165 21 - 56053 TTG-------------CATGTAAGCAACAAAGAG -s mr.mrrefChr0 49318 34 + 130230 TTGTGAGTACAGTATCCATGTAAGCAGCAAAGAA -s simCow_chr6.simCow.chr6 592327 21 - 602619 TTG-------------CATGTAAGCAACAAAGAA -s simDog_chr6.simDog.chr6 583485 20 - 593897 TTG-------------C-CGTAAGCAACAAAGAG -s simHuman_chr6.simHuman.chr6 590734 21 - 601863 TTG-------------CATGTAAGCAACATTGAA -s simRat_chr6.simRat.chr6 44400 34 + 647215 TTATGATTGCAGTACTCATGTAAGCAGCAAAGAA - -a -s simMouse_chr6.simMouse.chr6 51566 63 + 636262 GATGATACTTTTGTATTCATATAGTTATGGATTATTATGCCTGCTGATTTTCATTATTGGTTG -s Anc0.Anc0refChr9 26052 49 + 35212 GATGATATTTTTGTATCTAT------TTTATTTTTAATGCTGACCAATCTTCAAC-------- -s Anc1.Anc1refChr0 6462 49 - 16026 GATGATATTTTTGTATCTAT------TTTATTTTTAATGCTGACCAATCTTCAAC-------- -s Anc2.Anc2refChr0 46186 49 - 56053 GATGATATTTTTGTATCTAT------TTTATTTTTAATGCTGACCAGTCTTCAAC-------- -s mr.mrrefChr0 49352 63 + 130230 GATGATACTTTTGTATTCATATAGTTATGGATTATTATGCCTGCTAATCTTCATTATTGGTTG -s simCow_chr6.simCow.chr6 592348 49 - 602619 GATGACATTTTTGTATCTAT------TTTATTCTTTCCAGTGACCAGACATCAAC-------- -s simDog_chr6.simDog.chr6 583505 49 - 593897 GATGATATTTTTGTAGCTAT------TTTATTTTTAATGCTGACCAGTCTTCAAC-------- -s simHuman_chr6.simHuman.chr6 590756 49 - 601863 GATGATATCTTTGTATCTAT------TTTAGTTTTCATGCTGACCAATCGTCAAC-------- -s simRat_chr6.simRat.chr6 44434 63 + 647215 GATGTTACTTTTGTATTCATATAGTTATGGATTATTACACCTGCTAATCTTCATTATTGGTTG - -a -s simMouse_chr6.simMouse.chr6 51629 53 + 636262 ATTCATATGATGAGCTCCACAGGTGAGCTAGTTTGAATACTGACTAATCATCA -s Anc0.Anc0refChr9 26101 32 + 35212 -----TATCATGTTTTTCCCAGGTTA---------CACCCTGTCTG------- -s Anc1.Anc1refChr0 6511 36 - 16026 -----TATCATGTTTTTCCCAGGTTA-----CTTTCACCCTGTCTG------- -s Anc2.Anc2refChr0 46235 32 - 56053 -----TACCGTGTCTTTCCCAGGTTA---------CACCCTTTCTG------- -s mr.mrrefChr0 49415 53 + 130230 ATTCATATGATGATCTCCACAGGTGAGCTAGTTTTAATACTGACTGATCATCA -s simCow_chr6.simCow.chr6 592397 31 - 602619 -----TGCCTTGTCTTTCTCAGGTTG---------CACCCTAGCC-------- -s simDog_chr6.simDog.chr6 583554 32 - 593897 -----CACCGTGTCCATCCCAGGTCA---------CACCCTTTCTG------- -s simHuman_chr6.simHuman.chr6 590805 28 - 601863 -----TATCATGCTTTGC-------------CTTTCACTCTGTCTG------- -s simRat_chr6.simRat.chr6 44508 53 + 647215 CTTCATATGATGATCTCCATAGGTGAGCTAATTTTAATCCTGACTGATCATCA - -a -s simMouse_chr6.simMouse.chr6 51682 6 + 636262 CCTTTC -s Anc0.Anc0refChr9 26133 6 + 35212 CTTTTC -s Anc1.Anc1refChr0 6547 6 - 16026 CTTTTC -s Anc2.Anc2refChr0 46267 6 - 56053 CTTTTC -s mr.mrrefChr0 49468 6 + 130230 CCTTTC -s simCow_chr6.simCow.chr6 592428 6 - 602619 TTTTTC -s simDog_chr6.simDog.chr6 583586 6 - 593897 CTTTTC -s simHuman_chr6.simHuman.chr6 590833 6 - 601863 CTTTTC -s simRat_chr6.simRat.chr6 44562 6 + 647215 CCTTTC - -a -s simMouse_chr6.simMouse.chr6 51688 106 + 636262 TTTCACCCTGTCCTTTTCTACCACCCACCACCAACTGTTTTATGTCCAGCTTCCATAAAGGAACCTGGGTGAGTAGGAGTTTGATGTCAATTCTGCAGAGTGGCAC -s Anc0.Anc0refChr9 26143 72 + 35212 CATC-CCCTCTTCCCTCCTG---------------------------------TACAGAGTAGCCTGGGTGTATAGGAACCTGATTTCTATTCAGCAGAATAGTAC -s Anc1.Anc1refChr0 6557 72 - 16026 CATC-CCCTCTTCCCTCCTG---------------------------------TACAGAGTAGCCTGGGTGTATAGGAACCTGATTTCTATTCAGCAGAATAGTAC -s Anc2.Anc2refChr0 46277 72 - 56053 CATC-CCCTCTTCCCTCCTG---------------------------------TACAGAGTCGCCTGGGTGTATAGGAACCTGATTTCTATGCAGCAGAATAGTAC -s mr.mrrefChr0 49478 73 + 130230 TTTCACCCTGTTCCCTCCTA---------------------------------TATAGAGGAACCTGGGTGTGTAGGAGCTTGATGTCAATTCTGCAGAGTAGTAC -s simCow_chr6.simCow.chr6 592438 67 - 602619 CATC-CCCTCTTTCCTCCTG---------------------------------TACAGAGTGGCCTGGGACTATGGGA-----ATTACAATGCAGCAGAATAGTAC -s simDog_chr6.simDog.chr6 583596 72 - 593897 CATC-CCCTCTTCCCTCCAG---------------------------------TACAGAATCGCCTGAGTGGATAGGTACCTGTTTTGTATGCAGCAGAATAGCAT -s simHuman_chr6.simHuman.chr6 590843 71 - 601863 CGTC-CCTCTTTCCCTCCTG---------------------------------TACAGAGTAG-CTGGGTGTATCGGACCCTTATTCCCATTCAGCAGAATAGTAC -s simRat_chr6.simRat.chr6 44572 73 + 647215 TTTCACCCTGTTCCCTCCTA---------------------------------TTTAGAGGAACCTGGGTGTGTAGGATCTTGATGTCAATCCTACAGAGTAATAG - -a -s simMouse_chr6.simMouse.chr6 51794 25 + 636262 ATTGCTGCTTCTGAATCCACTCAGA -s Anc0.Anc0refChr9 26218 25 + 35212 ATTGCTGCTTCCTAACTCACACAGA -s Anc1.Anc1refChr0 6632 25 - 16026 ATTGCTGCTTCCTAACTCACACAGA -s Anc2.Anc2refChr0 46352 25 - 56053 ATTGCTGCTTCCTAACTCATACAGA -s mr.mrrefChr0 49551 25 + 130230 ATTGCTGCTTCTGAATCCACTCAGA -s simCow_chr6.simCow.chr6 592508 25 - 602619 ATTATTGCTTCTGACCTCCTACAGA -s simDog_chr6.simDog.chr6 583671 25 - 593897 ATTGCTTCTTCCTAACTCATACAGG -s simHuman_chr6.simHuman.chr6 590917 25 - 601863 ATTGCTGCTTCCTAACTCACAGGGA -s simRat_chr6.simRat.chr6 44645 25 + 647215 ATTGCTGCTTCTGAATCCACGCAGA - -a -s simMouse_chr6.simMouse.chr6 51819 8 + 636262 TTTAATCT -s Anc0.Anc0refChr9 26244 8 + 35212 TTTAATCT -s Anc1.Anc1refChr0 6658 8 - 16026 TTTAATCT -s Anc2.Anc2refChr0 46378 8 - 56053 TTTATTTT -s mr.mrrefChr0 49577 8 + 130230 TTTAATCT -s simCow_chr6.simCow.chr6 592534 8 - 602619 CATACTTT -s simDog_chr6.simDog.chr6 583697 8 - 593897 TTTATTTT -s simHuman_chr6.simHuman.chr6 590943 8 - 601863 TTGAATCT -s simRat_chr6.simRat.chr6 44671 8 + 647215 TTTAATCT - -a -s simMouse_chr6.simMouse.chr6 51827 12 + 636262 CACCATCTAGGA -s Anc0.Anc0refChr9 26252 12 + 35212 CACCACATGTGA -s Anc1.Anc1refChr0 6666 12 - 16026 CACCACATGTGA -s Anc2.Anc2refChr0 46386 12 - 56053 CACCACATGTGA -s mr.mrrefChr0 49585 12 + 130230 CACCATCTAGGA -s simCow_chr6.simCow.chr6 592542 12 - 602619 CACCACATGTGG -s simDog_chr6.simDog.chr6 583706 12 - 593897 AACCACATGTGA -s simHuman_chr6.simHuman.chr6 590951 12 - 601863 CACCACATGTGA -s simRat_chr6.simRat.chr6 44679 12 + 647215 CAGCATCTAAGA - -a -s simMouse_chr6.simMouse.chr6 51839 10 + 636262 ACCACACTCC -s Anc0.Anc0refChr9 26272 10 + 35212 ATTGTGCTCC -s Anc1.Anc1refChr0 6686 10 - 16026 ATTGTGCTCC -s Anc2.Anc2refChr0 46406 10 - 56053 ATTGTGCTCA -s mr.mrrefChr0 49597 10 + 130230 ACCGTGCTCC -s simCow_chr6.simCow.chr6 592562 10 - 602619 ATGGTGCTCA -s simDog_chr6.simDog.chr6 583726 10 - 593897 ATTGCACTCA -s simHuman_chr6.simHuman.chr6 590971 10 - 601863 ATTGTGCTCC -s simRat_chr6.simRat.chr6 44691 10 + 647215 ACCGTGCTCC - -a -s simMouse_chr6.simMouse.chr6 51849 4 + 636262 TTGC -s Anc0.Anc0refChr9 26293 4 + 35212 TTGT -s Anc1.Anc1refChr0 6707 4 - 16026 TTGT -s Anc2.Anc2refChr0 46427 4 - 56053 TTGT -s mr.mrrefChr0 49607 4 + 130230 TTGC -s simCow_chr6.simCow.chr6 592583 4 - 602619 GAGT -s simDog_chr6.simDog.chr6 583747 4 - 593897 TTGT -s simHuman_chr6.simHuman.chr6 590992 4 - 601863 TTGT -s simRat_chr6.simRat.chr6 44701 4 + 647215 TTGG - -a -s simMouse_chr6.simMouse.chr6 51853 17 + 636262 TACTATTAATTTACACA -s Anc0.Anc0refChr9 26298 15 + 35212 --TTATTAATTTACACC -s Anc1.Anc1refChr0 6712 17 - 16026 TATTATTAATTTACACC -s Anc2.Anc2refChr0 46432 15 - 56053 --TTATTAATGTACACC -s mr.mrrefChr0 49611 17 + 130230 TACTATTAATTTACACA -s simCow_chr6.simCow.chr6 592588 10 - 602619 --TTA-----GTACACC -s simDog_chr6.simDog.chr6 583752 15 - 593897 --TTATTAATGTACAAC -s simHuman_chr6.simHuman.chr6 590997 17 - 601863 TATCATCAATTTACACC -s simRat_chr6.simRat.chr6 44705 17 + 647215 TACTACTAATTTACACA - -a -s simMouse_chr6.simMouse.chr6 51870 76 + 636262 CCTCTTTAAAATTTCTGTTATCACCCTTGTGGTCCATATCAATAATATCACCCTTTTACTTATAACTGAGCAGTAG -s Anc0.Anc0refChr9 26330 68 + 35212 TCTCTTCAATTTTTCTGTTATCCTCCTTGTTGTCTATAACAATTATACCACCCTTTTACTTA-CACTTA------- -s Anc1.Anc1refChr0 6746 69 - 16026 TCTCTTCAATTTTTCTGTTATCCTCCTTGTTGTCTATAACAATTATACCACCCTTTTACTTATCACTTA------- -s Anc2.Anc2refChr0 46464 68 - 56053 TCTCTTCACTTTTTCTGTTATCCTCCTTGTTCTCTATAATAATTATGCCACCCTTTTATTTG-CACTTC------- -s mr.mrrefChr0 49628 69 + 130230 CCTCTTTAAAATTTCTGTTATCACCCTTGTGGTCCATAACAATAATATCACCCTTTTACTTATAACTGA------- -s simCow_chr6.simCow.chr6 592615 68 - 602619 TTTCTACACTTTTTATATCATAATCCTTCTCATCTATAATAATTATTCCACCCTTGTAATTG-CACTTG------- -s simDog_chr6.simDog.chr6 583784 68 - 593897 TCTCTTCACTCTTTCTGTTATCCTCCCTGTTCTCTATCATAATTATGCTACCCTTTTATTTG-CTCTGC------- -s simHuman_chr6.simHuman.chr6 591031 69 - 601863 TCTCTTCAATTCTTCTGTAATCGTCCTTGTTGACTATAACAATTATAGCACCCTCTTACTTATCACCTA------- -s simRat_chr6.simRat.chr6 44722 69 + 647215 CCTCTTTAAAGTTTCTGTCATCACCCTTGTGGCCCATAACAATCATATCACCCTTTTACTTATTACTGA------- - -a -s simMouse_chr6.simMouse.chr6 51946 29 + 636262 CATCCTGTGAGCTGGAGGTTCTCAAGGCA -s Anc0.Anc0refChr9 26404 29 + 35212 TGGCCTGTGAGCTGGAGATTCTCAAGTCA -s Anc1.Anc1refChr0 6821 29 - 16026 TGGCCTGTGAGCTGGAGATTCTCAAGTCA -s Anc2.Anc2refChr0 46538 29 - 56053 AGGTGGGTGAGCTGGAGATTGTCAAGTCA -s mr.mrrefChr0 49697 29 + 130230 TGGCCTGTGAGCTGGAGGTTCTCAAGGCA -s simCow_chr6.simCow.chr6 592689 29 - 602619 AGCTGGGTGGGCCGGAGATTGTGAAGTTA -s simDog_chr6.simDog.chr6 583858 29 - 593897 AGGTGGGTGAGCTTCAGATTGTCAATTCA -s simHuman_chr6.simHuman.chr6 591106 29 - 601863 TGGCCTGAGAACTGGAGATTCTTAAGCCA -s simRat_chr6.simRat.chr6 44791 29 + 647215 TGGCCTGTGAGCTTGAGGTTCTCAAGGCA - -a -s simMouse_chr6.simMouse.chr6 51975 11 + 636262 ACAATTACTTA -s Anc0.Anc0refChr9 26437 11 + 35212 ACATCTACTTA -s Anc1.Anc1refChr0 6854 11 - 16026 ACATCTACTTA -s Anc2.Anc2refChr0 46571 11 - 56053 ACATCTACTTA -s mr.mrrefChr0 49726 11 + 130230 ACATTTACTTA -s simCow_chr6.simCow.chr6 592722 11 - 602619 ACATCTACTTA -s simDog_chr6.simDog.chr6 583891 11 - 593897 ACATCTACTTA -s simHuman_chr6.simHuman.chr6 591139 11 - 601863 ATATCTACTTA -s simRat_chr6.simRat.chr6 44820 11 + 647215 ACATTTACTTA - -a -s simMouse_chr6.simMouse.chr6 51986 68 + 636262 TGGTTCTGGTGCAATATCCAACTTGTATCTTTAATGTATTTTGTCTGGGGTCCTGCCCTTGATTTACA -s Anc0.Anc0refChr9 26448 68 + 35212 TGGTTCTGAAGTAATATCCGAACCATGTCTGGAATGTGTCTTGACTGGGGTTGGGTCTTCAATTTATA -s Anc1.Anc1refChr0 6865 68 - 16026 TGGTTCTGAAGTAATATCCGAACCATGTCTGGAATGTGTCTTGACTGGGGTTGGGTCTTCAATTTATA -s Anc2.Anc2refChr0 46582 68 - 56053 TGGTTCTGAAGTAATATCTGAACCATGTCTGGAATGTGTCTTGACTGGGGTTGGGTCTTCAATTTATA -s mr.mrrefChr0 49737 68 + 130230 TGGTTCTGGTGCAATATCCAACTTATGTCTTTAATGTATCTTGTCTGGGGTCGTGCCTTTGATTTACA -s simCow_chr6.simCow.chr6 592736 68 - 602619 TAGTTCTGATGCAATGTCAAAACCATGTCTTGAAGGCGTCTTGACTGGGGTTGGGCCTTCAATCTATA -s simDog_chr6.simDog.chr6 583902 68 - 593897 TGGTTCTGAAGTAAGATCTGAAGCATGTCTGGAATGTGTCTAGACTGGGGTTGGGTCTTCAATTTATA -s simHuman_chr6.simHuman.chr6 591150 68 - 601863 TGGTTTTGCCGAAATATCCGCACAATGTCCGGGGTGTGTCTTGCTTGGGGTTGGGTCTGCAATTTGTG -s simRat_chr6.simRat.chr6 44831 68 + 647215 TGATTCTGGTGCAATATCCAATTCATGTCTTTAATGGATCTTGTCTGGCGTGGTGCCTTTGATTTCCA - -a -s simMouse_chr6.simMouse.chr6 52054 32 + 636262 CTCACTTTTGTCAGTGTGCATAGTGCTATATG -s Anc0.Anc0refChr9 26525 32 + 35212 ATTACTTTTGTAAGTGGGTATAGTGCTATATG -s Anc1.Anc1refChr0 6942 32 - 16026 ATTACTTTTGTAAGTGGGTATAGTGCTATATG -s Anc2.Anc2refChr0 46659 32 - 56053 ATTACTTTTGTAAGTGGGTATAGTGCTATATG -s mr.mrrefChr0 49805 32 + 130230 ATCACTTTTGTCAGTGTGCATAGTGCTATATG -s simCow_chr6.simCow.chr6 592813 32 - 602619 ATTACTCGTGGAAGTGGGTAAGGTGCTATGTG -s simDog_chr6.simDog.chr6 583979 32 - 593897 ATTACTTTTGTATCTCGGTATAGTGCTATATG -s simHuman_chr6.simHuman.chr6 591227 32 - 601863 ATTACTTTTTTAAGTGCCTATAGTGCTATATG -s simRat_chr6.simRat.chr6 44899 32 + 647215 ATCACTTTTATCAGAGTGCACAGTGCTATATG - -a -s simMouse_chr6.simMouse.chr6 52086 30 + 636262 ATTTCAGAACTCTTATTTGGAGAAAATCAT -s Anc0.Anc0refChr9 26557 30 + 35212 ATGTCAAAACTTTTACTTGGAGATGCTCAT -s Anc1.Anc1refChr0 6974 30 - 16026 ATGTCAAAACTTTTACTTGGAGATGCTCAT -s Anc2.Anc2refChr0 46691 30 - 56053 ATGTCAAAACTTTTACTTGGACATGCTTAT -s mr.mrrefChr0 49837 30 + 130230 ATGTCAGAACTCTTACTTGGAGAAACTCAT -s simCow_chr6.simCow.chr6 592845 20 - 602619 ATGACAAAACAT----------ATGCTAGT -s simDog_chr6.simDog.chr6 584020 30 - 593897 ACATCAAAACTTTTACTTGGACATGCTTAT -s simHuman_chr6.simHuman.chr6 591259 30 - 601863 GTGTCAAAACTTTTACTTGGGGATGCTCAT -s simRat_chr6.simRat.chr6 44931 30 + 647215 ATGTCAGAACTCTTACTTGGAGAAACTCAT - -a -s simMouse_chr6.simMouse.chr6 52116 22 + 636262 TCATCAAGTAAATTTATCTGTC -s Anc0.Anc0refChr9 26588 18 + 35212 TTATCA-TCA---GTATCAGTC -s Anc1.Anc1refChr0 7005 22 - 16026 TTATCAGTCAAATGTATCAGTC -s Anc2.Anc2refChr0 46722 18 - 56053 GTATCA-TCG---GTATCAGTC -s mr.mrrefChr0 49868 22 + 130230 TCATCAAGTAAATGTATCTGTC -s simCow_chr6.simCow.chr6 592865 10 - 602619 ---------G---GTATCAGTC -s simDog_chr6.simDog.chr6 584051 8 - 593897 GTATCA-TC------------- -s simHuman_chr6.simHuman.chr6 591290 22 - 601863 TTATCAGTCAAATGTATCAGTC -s simRat_chr6.simRat.chr6 44962 22 + 647215 TCATCAACTAAATGTATCCGTC - -a -s simMouse_chr6.simMouse.chr6 52138 6 + 636262 TGAAGG -s Anc0.Anc0refChr9 26609 6 + 35212 TGAAGG -s Anc1.Anc1refChr0 7030 6 - 16026 TGAAGG -s Anc2.Anc2refChr0 46743 6 - 56053 TGAAGG -s mr.mrrefChr0 49893 6 + 130230 TGAAGG -s simCow_chr6.simCow.chr6 592878 6 - 602619 TGAAGA -s simDog_chr6.simDog.chr6 584059 6 - 593897 TGAAGG -s simHuman_chr6.simHuman.chr6 591315 6 - 601863 TAGAGG -s simRat_chr6.simRat.chr6 44987 6 + 647215 TGAAGG - -a -s simMouse_chr6.simMouse.chr6 52144 3 + 636262 GGA -s Anc0.Anc0refChr9 26616 3 + 35212 GGA -s Anc1.Anc1refChr0 7037 3 - 16026 GGA -s Anc2.Anc2refChr0 46750 3 - 56053 GAA -s mr.mrrefChr0 49899 3 + 130230 GGA -s simCow_chr6.simCow.chr6 592885 3 - 602619 AAG -s simDog_chr6.simDog.chr6 584066 3 - 593897 GAA -s simHuman_chr6.simHuman.chr6 591322 3 - 601863 GGA -s simRat_chr6.simRat.chr6 44993 3 + 647215 GGA - -a -s simMouse_chr6.simMouse.chr6 52147 135 + 636262 GGGGATATGCTGACTAACTACTCATCCATCAATGGACCTAACCCAAACCCAGGGTACCATGAAATATTCTTTAATTCTTGCTATTTCTCACAATGCACCACATAGAGTTCAGATGACTGGTGCTAGAGCATGATT -s Anc0.Anc0refChr9 26627 102 + 35212 AGGGACA---------------------------GGCCTGCCCTATACCCTG-----CATGAGTTACTTCTTCATTATTGCTACCTCTTGCATTGTACCACA-ATGGTCCAGAGGACTGGTGGTAGAGCAAGGTC -s Anc1.Anc1refChr0 7048 103 - 16026 AGGGACA---------------------------GGCCTGCCCTATACCCTG-----CATGAGTTACTTCTTCATTATTGCTACCTCTTGCATTGTACCACATATGGTCCAGAGGACTGGTGGTAGAGCAAGGTC -s Anc2.Anc2refChr0 46761 102 - 56053 AGGGACA---------------------------GGCTTGCCCTATACCCTG-----CATGAGTCACTTCTTCATTATTGCTACCTCATGCATTGTATCACA-ATGGTCCTGAGGACTGGTGGTAGAGCAAGGTC -s mr.mrrefChr0 49910 134 + 130230 GGGGATATGCTGAC-GACTACTCATCTGTCAATGGACCTAACCCAAACCTGGGGTACCATGAAATATTTTTTAATTCTTGCTATTTCTCACATTGCACCACATAGGGTTCAGATGACTGGTGGTAGAGCAAGATT -s simCow_chr6.simCow.chr6 592896 94 - 602619 AGGGA----------------------------------GCCCTACACCCTG-----CATGATTCGCTTCTTCATTATTGCTACCTCATGCATTGT-TCACA-ATGGTCCCAAGGACTGGTGGTAGAGCAAGGCC -s simDog_chr6.simDog.chr6 584077 102 - 593897 AGGAGCA---------------------------GGCTTGCCCAATACCCTA-----CTTGAGTCACTTCTTAATTATTGCTTCCTCATGCATTGCATCACA-ATGGTCCTGAGGACTGGTGGTAGAGCAAGGTC -s simHuman_chr6.simHuman.chr6 591333 103 - 601863 AGGGACA---------------------------GGCCTCCCTTATGCTCTG-----CATGAGGTACTTCTTCATTATTGCTACCACTTGCATTGTGCCACATACGGTCCAGAGGATCGATGGTAGGTCAAAGTC -s simRat_chr6.simRat.chr6 45004 134 + 647215 GGGGATACGTTGAC-GACTACTCATCTGTCAATGGACCAAACCCAGACCTGGGGCACCATGAAATATTTTTTAATTCTTGTTCTTTTTCATATTGCACCACATATGGTTCAGATGACTGGTGGTGGAGCAAGATT - -a -s simMouse_chr6.simMouse.chr6 52282 31 + 636262 AAGCCAGCTGAACAACTGGTCAGGATCAAAG -s Anc0.Anc0refChr9 26729 31 + 35212 TGGCCAGTTGACTGAATGTCCAGGATCTAAG -s Anc1.Anc1refChr0 7151 31 - 16026 TGGCCAGTTGACTGAATGTCCAGGATCTAAG -s Anc2.Anc2refChr0 46863 31 - 56053 TGGCCAATTGACTGAATGTCCAAGATCTAAG -s mr.mrrefChr0 50044 31 + 130230 AAGCCAGCTGAACAACTGTTCAGGATCTAAG -s simCow_chr6.simCow.chr6 592990 30 - 602619 TGGCCAATTGACTGCATATCCA-GATCTATG -s simDog_chr6.simDog.chr6 584242 31 - 593897 TGGCCAATTGACTGAATGTCCAAAATCTAAC -s simHuman_chr6.simHuman.chr6 591436 31 - 601863 TGGTCAGGTGACTGAGTGTCCAGGATTTAAG -s simRat_chr6.simRat.chr6 45138 31 + 647215 AAGCCATCTGAACAATTGTTCGGGATCTAAG - -a -s simMouse_chr6.simMouse.chr6 52313 7 + 636262 CCTCCCA -s Anc0.Anc0refChr9 26760 7 + 35212 TCTGCTA -s Anc1.Anc1refChr0 7182 7 - 16026 TCTGCTA -s Anc2.Anc2refChr0 46895 7 - 56053 CCTGCTA -s mr.mrrefChr0 50075 7 + 130230 TCTCCCA -s simCow_chr6.simCow.chr6 593021 7 - 602619 CTTACCG -s simDog_chr6.simDog.chr6 584274 7 - 593897 CCTGCTA -s simHuman_chr6.simHuman.chr6 591467 7 - 601863 TCTGCTA -s simRat_chr6.simRat.chr6 45169 7 + 647215 TCTCCCA - -a -s simMouse_chr6.simMouse.chr6 52320 15 + 636262 TCACCAAAGAGACCC -s Anc0.Anc0refChr9 26770 8 + 35212 CCACC-AAG------ -s Anc1.Anc1refChr0 7192 8 - 16026 CCACC-AAG------ -s Anc2.Anc2refChr0 46907 8 - 56053 CCACC-AAG------ -s mr.mrrefChr0 50082 14 + 130230 TCACC-AAGAGACCC -s simCow_chr6.simCow.chr6 593033 8 - 602619 CCACC-AAA------ -s simDog_chr6.simDog.chr6 584286 8 - 593897 CCACC-AAG------ -s simHuman_chr6.simHuman.chr6 591477 8 - 601863 CCACC-AAG------ -s simRat_chr6.simRat.chr6 45176 14 + 647215 TCACC-AAGGGACCC - -a -s simMouse_chr6.simMouse.chr6 52335 1 + 636262 T -s Anc0.Anc0refChr9 26778 1 + 35212 T -s Anc1.Anc1refChr0 7200 1 - 16026 T -s Anc2.Anc2refChr0 46915 1 - 56053 A -s mr.mrrefChr0 50096 1 + 130230 T -s simCow_chr6.simCow.chr6 593041 1 - 602619 C -s simDog_chr6.simDog.chr6 584300 1 - 593897 A -s simHuman_chr6.simHuman.chr6 591485 1 - 601863 T -s simRat_chr6.simRat.chr6 45190 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 52336 11 + 636262 CTCAGACATTA -s Anc0.Anc0refChr9 26779 11 + 35212 CTCAGACATTC -s Anc1.Anc1refChr0 7201 11 - 16026 CTCAGACATTC -s Anc2.Anc2refChr0 46916 11 - 56053 CTCAGATATTC -s mr.mrrefChr0 50097 11 + 130230 CTCAGACATTA -s simCow_chr6.simCow.chr6 593043 11 - 602619 CTCAGATATTC -s simDog_chr6.simDog.chr6 584301 11 - 593897 CGCAGATATTC -s simHuman_chr6.simHuman.chr6 591486 11 - 601863 CTCAGACATTC -s simRat_chr6.simRat.chr6 45191 11 + 647215 CTCAAATATTA - -a -s simMouse_chr6.simMouse.chr6 52347 20 + 636262 ACTGTCATTCACTGTAGGTG -s Anc0.Anc0refChr9 26792 19 + 35212 ACTG-CATTCACTGTAGGTG -s Anc1.Anc1refChr0 7214 19 - 16026 ACTG-CATTCACTGTAGGTG -s Anc2.Anc2refChr0 46929 19 - 56053 ATTA-CATTCACTGTAGGTG -s mr.mrrefChr0 50108 20 + 130230 ACTGTCATTCACTGTAGGTG -s simCow_chr6.simCow.chr6 593056 19 - 602619 ATTA-CATTCACTATAGGTA -s simDog_chr6.simDog.chr6 584314 15 - 593897 ATTA-CA----CTGTAGGTG -s simHuman_chr6.simHuman.chr6 591499 19 - 601863 ACTG-CACTCTCTGTGGATG -s simRat_chr6.simRat.chr6 45202 20 + 647215 ACTGTCAATCACTGTAGTTA - -a -s simMouse_chr6.simMouse.chr6 52367 10 + 636262 ATCCAGTAGT -s Anc0.Anc0refChr9 26868 10 + 35212 ACCCCGAACT -s Anc1.Anc1refChr0 7290 10 - 16026 ACCCCGAACT -s Anc2.Anc2refChr0 47005 10 - 56053 ACCCCGAACT -s mr.mrrefChr0 50128 10 + 130230 ATCCAGTAGT -s simCow_chr6.simCow.chr6 593130 10 - 602619 ACTTCTAACT -s simDog_chr6.simDog.chr6 584386 10 - 593897 ACCCTGAACT -s simHuman_chr6.simHuman.chr6 592471 10 - 601863 ACCCCCGACT - -a -s simMouse_chr6.simMouse.chr6 52377 10 + 636262 GGATGTAAAG -s Anc0.Anc0refChr9 26878 10 + 35212 TATTGTAAGG -s Anc1.Anc1refChr0 7300 10 - 16026 TATTGTAAGG -s Anc2.Anc2refChr0 47015 10 - 56053 TATTGTAAGG -s mr.mrrefChr0 50138 10 + 130230 GGATGTAAAG -s simCow_chr6.simCow.chr6 593142 10 - 602619 TATTGTAAGG -s simDog_chr6.simDog.chr6 584396 10 - 593897 TACTGCAAGG -s simHuman_chr6.simHuman.chr6 592481 10 - 601863 CATTGTAAGG - -a -s simMouse_chr6.simMouse.chr6 52387 50 + 636262 TAGTGCATGTTCATATACAAGCTCTATATGCAATGTGAATGCTGCCACTG -s Anc0.Anc0refChr9 26892 50 + 35212 TAGTGCATGTTCCTATGCGAACTCCATATGCTATGTGAATGCTGCAACTG -s Anc1.Anc1refChr0 7314 50 - 16026 TAGTGCATGTTCCTATGCGAACTCCATATGCTATGTGAATGCTGCAACTG -s Anc2.Anc2refChr0 47029 50 - 56053 TAGTGCATGTTCCTATGCGAACTCCATAAGCTATGGGAGTGCTGCAACTG -s mr.mrrefChr0 50148 50 + 130230 TAGTGCATGTTCATATACAAACTCTATATGCTATGTGAATGCTGCAACTG -s simCow_chr6.simCow.chr6 593156 27 - 602619 TAGTGCATGTTCCCACGCGAACTCCAT----------------------- -s simDog_chr6.simDog.chr6 584410 47 - 593897 TAGTACA---TCCTATGTGGACTCCGTAAGCTATGGGAGTGCTGCAACTG -s simHuman_chr6.simHuman.chr6 592495 50 - 601863 TAGTGCATGTTCCTATGCGAACCCCATATGCTATGTGAATGCTGCAACTG -s simRat_chr6.simRat.chr6 45222 39 + 647215 ----------TCTTATACAAACT-TATATGCTATTTGAATGCTGCAGCTG - -a -s simMouse_chr6.simMouse.chr6 52437 7 + 636262 AGAGCCC -s Anc0.Anc0refChr9 26944 7 + 35212 AGAGTCC -s Anc1.Anc1refChr0 7366 7 - 16026 AGAGTCC -s Anc2.Anc2refChr0 47081 7 - 56053 AGAATCC -s mr.mrrefChr0 50198 7 + 130230 AGAGTCC -s simDog_chr6.simDog.chr6 584459 7 - 593897 AGAATCC -s simHuman_chr6.simHuman.chr6 592548 7 - 601863 AGAGTCC -s simRat_chr6.simRat.chr6 45261 7 + 647215 AGAATCC - -a -s simMouse_chr6.simMouse.chr6 52444 41 + 636262 CTAAGGCATGGTTAACAATATCATTGATGTGACTGTAAGGT -s Anc0.Anc0refChr9 26951 39 + 35212 CTAAGGC-CAGTT-ACTATGTGAATGATGAAACTGTCAAGT -s Anc1.Anc1refChr0 7373 40 - 16026 CTAAGGC-CAGTTAACTATGTGAATGATGAAACTGTCAAGT -s Anc2.Anc2refChr0 47088 39 - 56053 CCAAGGC-CAGAT-ACTATGTGAAGCATGAAACTGTCAAGT -s mr.mrrefChr0 50205 41 + 130230 CTAAGGCATGGTTAACAATATCATTGATGTGACTGTCAAGT -s simCow_chr6.simCow.chr6 593183 16 - 602619 -------------------------CATGAGACTGTCAAGT -s simDog_chr6.simDog.chr6 584466 39 - 593897 CCAAGGC-CAGAT-ACTATGTGAAGCATGAAACTGTCAAGT -s simHuman_chr6.simHuman.chr6 592555 40 - 601863 CTAAGTC-CAGTTAACTAAGTGAATGAGGCAACTGTCGAGT -s simRat_chr6.simRat.chr6 45271 41 + 647215 CTAAGGCATGGTTAAGAATATCATTGATGTGACTGTCAAGT - -a -s simMouse_chr6.simMouse.chr6 52485 20 + 636262 GTCCCTAAGTCCCAGTTAAC -s Anc0.Anc0refChr9 26990 19 + 35212 GTCCCTAA-TTCCAGCTGAC -s Anc1.Anc1refChr0 7413 19 - 16026 GTCCCTAA-TTCCAGCTGAC -s Anc2.Anc2refChr0 47127 19 - 56053 GTCCCTAA-TTCCAATTAAC -s mr.mrrefChr0 50246 20 + 130230 GTCCCTAAGTCCCAGCTGAC -s simCow_chr6.simCow.chr6 593199 19 - 602619 GTACCTAA-TTCCAATTAAC -s simDog_chr6.simDog.chr6 584506 19 - 593897 GTCCCAAA-GTCCAATTAAC -s simHuman_chr6.simHuman.chr6 592595 19 - 601863 GTCCCTAA-TTCAAGCTGAC -s simRat_chr6.simRat.chr6 45312 20 + 647215 GTCCTTAAGTCCCAGCTGAC - -a -s simMouse_chr6.simMouse.chr6 52505 37 + 636262 AGTCCATATATTAATATGCTCAAATGACCCCATTGAA -s Anc0.Anc0refChr9 27009 24 + 35212 GGCACATATATTAGTATGCTCAAA------------- -s Anc1.Anc1refChr0 7432 24 - 16026 GGCACATATATTAGTATGCTCAAA------------- -s Anc2.Anc2refChr0 47146 24 - 56053 GACACATGTATTAGTATGCTCAGA------------- -s mr.mrrefChr0 50266 37 + 130230 AGTCCATATATTAATATGCTCAAATGACCCCATTGAA -s simCow_chr6.simCow.chr6 593218 24 - 602619 AATACATTTATTGACATGCTCAGA------------- -s simDog_chr6.simDog.chr6 584527 18 - 593897 GACACATGCATTAGTATG------------------- -s simHuman_chr6.simHuman.chr6 592614 24 - 601863 GGCTCATATATCAGTACACTCAAA------------- -s simRat_chr6.simRat.chr6 45332 37 + 647215 AGTCCATGTATTAATATGCTTAAATGACCCCATTGAA - -a -s simMouse_chr6.simMouse.chr6 52542 13 + 636262 GTCCTGATCACAC -s Anc0.Anc0refChr9 27033 5 + 35212 --------CGCAC -s Anc1.Anc1refChr0 7456 5 - 16026 --------CGCAC -s Anc2.Anc2refChr0 47170 5 - 56053 --------TGCAC -s mr.mrrefChr0 50303 13 + 130230 GTCCTGATCACAC -s simCow_chr6.simCow.chr6 593242 5 - 602619 --------TATGC -s simDog_chr6.simDog.chr6 584545 4 - 593897 ---------GCAC -s simHuman_chr6.simHuman.chr6 592638 5 - 601863 --------CGCAC -s simRat_chr6.simRat.chr6 45377 13 + 647215 GTCCTGATCACCC - -a -s simMouse_chr6.simMouse.chr6 52555 17 + 636262 TGCGTGGGTTAGGGAGT -s Anc0.Anc0refChr9 27039 17 + 35212 TGCATAAATATGAGACT -s Anc1.Anc1refChr0 7462 17 - 16026 TGCATAAATATGAGACT -s Anc2.Anc2refChr0 47176 17 - 56053 TGCATAAATATGAGACT -s mr.mrrefChr0 50316 17 + 130230 TGCATAGATTAGGGAGT -s simCow_chr6.simCow.chr6 593248 17 - 602619 TGCATCAATATGAGAGT -s simDog_chr6.simDog.chr6 584550 17 - 593897 AGGATAGATATCAGACT -s simHuman_chr6.simHuman.chr6 592644 17 - 601863 TGCATAAATATGACCAT -s simRat_chr6.simRat.chr6 45390 17 + 647215 TGCATATATTAGGGAGT - -a -s simMouse_chr6.simMouse.chr6 52572 40 + 636262 TAGTGGTGGGCGAACAGAAGAATCTTCATTCCCAATTCCC -s Anc0.Anc0refChr9 27057 37 + 35212 TGGTAGGAGGTGAAG---AAAACCTTCATTCCCCATCTCA -s Anc1.Anc1refChr0 7480 37 - 16026 TGGTAGGAGGTGAAG---AAAACCTTCATTCCCCATCTCA -s Anc2.Anc2refChr0 47194 37 - 56053 GGGTAGGAGGTGAAG---AAAACCTTCATTCCCCATCTTA -s mr.mrrefChr0 50334 40 + 130230 TAGTGGTGGGTGAAGAGAAGAATCTTCATTCCCAATTCCC -s simCow_chr6.simCow.chr6 593266 37 - 602619 GGGTACAAAGCGCAG---AAAACTTCCATTCCCCATCCTG -s simDog_chr6.simDog.chr6 584568 37 - 593897 GGGTAGGAGGTGAAG---AAAACCTTCTGTCCCCATCTTA -s simHuman_chr6.simHuman.chr6 592662 37 - 601863 TGGTAGCAGGTGAAG---AAAACCTTCATCCTCCATCTCA -s simRat_chr6.simRat.chr6 45408 33 + 647215 TAGTGGTTGATGAAGAGAAGAATCTT-------AATTCCT - -a -s simMouse_chr6.simMouse.chr6 52612 2 + 636262 AT -s Anc0.Anc0refChr9 27102 2 + 35212 AT -s Anc1.Anc1refChr0 7525 2 - 16026 AT -s Anc2.Anc2refChr0 47239 2 - 56053 AT -s mr.mrrefChr0 50374 2 + 130230 AT -s simCow_chr6.simCow.chr6 593311 2 - 602619 AT -s simDog_chr6.simDog.chr6 584613 2 - 593897 AT -s simHuman_chr6.simHuman.chr6 592707 2 - 601863 AT -s simRat_chr6.simRat.chr6 45441 2 + 647215 AT - -a -s simMouse_chr6.simMouse.chr6 52614 1 + 636262 C -s Anc0.Anc0refChr9 27104 1 + 35212 G -s Anc1.Anc1refChr0 7527 1 - 16026 G -s Anc2.Anc2refChr0 47241 1 - 56053 G -s mr.mrrefChr0 50376 1 + 130230 C -s simCow_chr6.simCow.chr6 593313 1 - 602619 G -s simDog_chr6.simDog.chr6 584735 1 - 593897 A -s simDog_chr6.simDog.chr6 584615 1 - 593897 G -s simHuman_chr6.simHuman.chr6 592709 1 - 601863 A -s simRat_chr6.simRat.chr6 45443 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 52615 5 + 636262 CCAAA -s Anc0.Anc0refChr9 27105 5 + 35212 ACAGT -s Anc1.Anc1refChr0 7528 5 - 16026 ACAGT -s Anc2.Anc2refChr0 47242 5 - 56053 ACAGT -s mr.mrrefChr0 50377 5 + 130230 CCAAA -s simCow_chr6.simCow.chr6 593314 5 - 602619 ACAGT -s simDog_chr6.simDog.chr6 584616 5 - 593897 ACATT -s simHuman_chr6.simHuman.chr6 592710 5 - 601863 ACAGT -s simRat_chr6.simRat.chr6 45444 5 + 647215 CCTAA - -a -s simMouse_chr6.simMouse.chr6 52620 5 + 636262 AGACT -s Anc0.Anc0refChr9 27110 5 + 35212 GGACT -s Anc1.Anc1refChr0 7533 5 - 16026 GGACT -s Anc2.Anc2refChr0 47247 5 - 56053 GAACT -s mr.mrrefChr0 50382 5 + 130230 AGACT -s simCow_chr6.simCow.chr6 593319 5 - 602619 GAGCT -s simDog_chr6.simDog.chr6 584736 5 - 593897 GAACT -s simDog_chr6.simDog.chr6 584621 5 - 593897 GAACT -s simHuman_chr6.simHuman.chr6 592715 5 - 601863 GGACT -s simRat_chr6.simRat.chr6 45449 5 + 647215 AGACT - -a -s simMouse_chr6.simMouse.chr6 52625 139 + 636262 CAGCAACTGTTTGTAAGTAATAATTCTCTTTACTAATGAACATCAATGGAAATGCAGGATACGGTACCCCTCGAGAAGCACAATCCGCCGGGCCTGAGGAACTATATTCAGGAAAGACTAGTTAAATGACACTGACAAA -s Anc0.Anc0refChr9 27115 93 + 35212 CAGCAATTGGTTGTATGTAACAATTACCTTTACTAATGAACATCAACAAAGACATGGAATACAGT----------------------------CTGAGGAGCTATATTCCAGAAAGATAAG------------------ -s Anc1.Anc1refChr0 7538 93 - 16026 CAGCAATTGGTTGTATGTAACAATTACCTTTACTAATGAACATCAACAAAGACATGGAATACAGT----------------------------CTGAGGAGCTATATTCCAGAAAGATAAG------------------ -s Anc2.Anc2refChr0 47252 93 - 56053 CAGCCATCAGTCGTATGTAACAATAACCTTTGCTAATGAACATCTACAAAGACATGGAATACAGT----------------------------CTGAGGAGCTATATTCCAGAAAGATAAG------------------ -s mr.mrrefChr0 50387 111 + 130230 CAGCAACTGTTTGTAAGTAACAATTCCCTTTACTAATGAACATCAATGAAAATGCAGGATACGGT----------------------------CTGAGGAACTATATTCAGGAAAGATTAGTTAGATGACACTGACAAA -s simCow_chr6.simCow.chr6 593325 92 - 602619 CAGCAATCAGTAGTATGTGACA-CTACCTTTACTAATGAGCATCAGCAAAGAGGCAGAATACAGT----------------------------TTGAGGAGTTATATTCCACCAAAATAAG------------------ -s simDog_chr6.simDog.chr6 584741 93 - 593897 CAGCCATCAGTCGTACGTAACAATAACCTTTGCTAATGAACATCTACAAAGACATGAAATACAGT----------------------------CTGAGGAGCTATATTCCAGAAAGATAAC------------------ -s simDog_chr6.simDog.chr6 584626 93 - 593897 CAGCCATGAATCGTATGTAATAATAACCTTTGCTAATGAACACCTCTAAAGACATGGAATACAGT----------------------------CTGAGGAGCTATATTCCAGAAAGATAAG------------------ -s simHuman_chr6.simHuman.chr6 592720 93 - 601863 CAGGAATTGGTTGGATGTAACAATTACCTTTACCAATGAGCATCAACAAAGACATGGAAGACCGT----------------------------CTGAGGAGCTATATTCCAGAAAGATAAG------------------ -s simRat_chr6.simRat.chr6 45454 111 + 647215 CAGCAACCGTTTGTAAGTAACAATTCCCTTTACTAATGAACATCAATGAAAATGCAGGATTCTAT----------------------------CTTAAGCACTATATTGGGGAAGGATTAGCTAGATGACAGTGGTAAA - -a -s simMouse_chr6.simMouse.chr6 52764 29 + 636262 TGAAGCATAAGCCTCCCATTTTAGTACAG -s Anc0.Anc0refChr9 7744 29 - 35212 TGAAGTGAAAGCCTACCATTTTAGTGCAG -s Anc1.Anc1refChr0 8135 29 + 16026 TGAAGTGAAAGCCTACCATTTTAGTGCAG -s Anc2.Anc2refChr0 8442 29 + 56053 TGAAGTGAAAGCCTACCATTTTAGTGCAA -s mr.mrrefChr0 50498 29 + 130230 TGAAGCAAAAGCCTCCCATTTTAGTACAG -s simCow_chr6.simCow.chr6 8935 29 + 602619 TGAAGAGAAAGCCTACCTTGCTAGTGCAA -s simDog_chr6.simDog.chr6 8799 23 + 593897 ---CATGAAAGCCTGCCATTTTAGTG--- -s simHuman_chr6.simHuman.chr6 8781 29 + 601863 TGAAGTGAAAGCCTACTATTTTAGTGCAG -s simRat_chr6.simRat.chr6 45565 29 + 647215 TGAAGCAAAAGCCTCCCAGTTTAATACAG - -a -s simMouse_chr6.simMouse.chr6 52793 85 + 636262 GCCTCTTTCGAGGGACCTAAGAAGGGTTCGGCATTTTAGGATTCCGTTCCATAATCTCCTAGTACTCCACTCCCAGCTCAACTAA -s Anc0.Anc0refChr9 7773 80 - 35212 TCCTCTTTCAGGTGATCTGACATAGGTTAGGCATTTCAGGAATCTGTTGCATAATCTCTTAGTTTACCCCTCTTGGCTCA----- -s Anc1.Anc1refChr0 8164 80 + 16026 TCCTCTTTCAGGTGATCTGACATAGGTTAGGCATTTCAGGAATCTGTTGCATAATCTCTTAGTTTACCCCTCTTGGCTCA----- -s Anc2.Anc2refChr0 8471 80 + 56053 TCCTCTTTCAGGTAATCTGACATAGGTTAGGCATTTCAGGAATCTGTTGCATAATCCTTTAGTTTACCCCTCTTGGCTCG----- -s mr.mrrefChr0 50527 85 + 130230 GCCTCTTTCGAGGGACCTAAGAAGGGTTAGGCATTTTAGGATTCTGTTCCATAATCTCTTAGTACACCACTCCTGGCTCAACTAA -s simCow_chr6.simCow.chr6 8964 80 + 602619 GCCTCTTTCAGGTAATCTGACATGGGTTAGGCAATTCAGGAATTGGTTATATAATTGATTAGTTTACCCCTCTTCGCTCC----- -s simDog_chr6.simDog.chr6 8822 80 + 593897 TCCTCTTTCAGGTAATGTTACATAGGTTAGGCATTTCAGGAATCTGTTGCATAATCCTTTAGTTTAGTCCTCTTGGCTTG----- -s simHuman_chr6.simHuman.chr6 8810 80 + 601863 TCCACGTTCAGGTGATCTGATATATGCTAGGCAGTCCAGGAATATGTTGCATAATCTCTTAGTTTACCCCTCATGGCTCA----- -s simRat_chr6.simRat.chr6 45596 66 + 647215 GC-------------------AAGGGTAAGGCATTTTAGGATTCTGTTCTATAATCTCTTAGTACACTGTTCCTGGCTCAACTAA - -a -s simMouse_chr6.simMouse.chr6 52878 13 + 636262 TAGCGTCATTATT -s Anc0.Anc0refChr9 7904 13 - 35212 GAGCAACATTATT -s Anc1.Anc1refChr0 8295 13 + 16026 GAGCAACATTATT -s Anc2.Anc2refChr0 8603 13 + 56053 GAGCAACATTATT -s mr.mrrefChr0 50664 13 + 130230 TAGCGTCATTATT -s simCow_chr6.simCow.chr6 9096 11 + 602619 A--CAACATTTTT -s simDog_chr6.simDog.chr6 8958 13 + 593897 GAGCAACGTTATT -s simHuman_chr6.simHuman.chr6 8943 8 + 601863 GAGCAAAA----- -s simRat_chr6.simRat.chr6 45933 13 + 647215 TAGCATCACTATT - -a -s simMouse_chr6.simMouse.chr6 52891 24 + 636262 GACTTGTTTCATGGCTTTTGCATC -s Anc0.Anc0refChr9 7917 24 - 35212 GACTTGTATTATGGCTTTTGCACC -s Anc1.Anc1refChr0 8308 24 + 16026 GACTTGTATTATGGCTTTTGCACC -s Anc2.Anc2refChr0 8616 24 + 56053 GACTCACATTATGGCTATTGCACC -s mr.mrrefChr0 50677 24 + 130230 GACTTGTTTCATGGCTTTTGCATC -s simCow_chr6.simCow.chr6 9108 24 + 602619 GATTCATTTTATTGCTATTGCACT -s simDog_chr6.simDog.chr6 8971 24 + 593897 GACTCACATTATGCCTATTGCACC -s simHuman_chr6.simHuman.chr6 8951 21 + 601863 ---TTGTCTTATGGCTTTTGCACC -s simRat_chr6.simRat.chr6 45946 24 + 647215 GACTCATTTTACTATTGACTCACT - -a -s simMouse_chr6.simMouse.chr6 52915 32 + 636262 TAAATTGTGCTTTACCTGCCCGTCCTGCCCAG -s Anc0.Anc0refChr9 7943 20 - 35212 TATATTACAACTTACCTCGC------------ -s Anc1.Anc1refChr0 8334 20 + 16026 TATATTACAACTTACCTCGC------------ -s Anc2.Anc2refChr0 8642 20 + 56053 TATATTACAACTCACCTCGC------------ -s mr.mrrefChr0 50701 20 + 130230 TAAATTGTGCTTTACCTGCC------------ -s simCow_chr6.simCow.chr6 9134 20 + 602619 TATGTTATGATGAACTTTGT------------ -s simDog_chr6.simDog.chr6 8997 20 + 593897 TATATCACAACTCATCTCAC------------ -s simHuman_chr6.simHuman.chr6 8974 20 + 601863 TACATTACAACTTACCTAGC------------ -s simRat_chr6.simRat.chr6 45970 20 + 647215 CATTTTATGTCTTTCATACC------------ - -a -s simMouse_chr6.simMouse.chr6 52947 31 + 636262 TATATAGTGCACGTCGATTGTGTGGACACAA -s Anc0.Anc0refChr9 7965 14 - 35212 TACCTAGTCTAC-----------------AA -s Anc1.Anc1refChr0 8356 14 + 16026 TACCTAGTCTAC-----------------AA -s Anc2.Anc2refChr0 8664 14 + 56053 TACCTAGTCTAC-----------------AA -s mr.mrrefChr0 50721 14 + 130230 TATATAGTGCAC-----------------AA -s simCow_chr6.simCow.chr6 9156 14 + 602619 TACCTAGTCTAC-----------------AA -s simDog_chr6.simDog.chr6 9019 14 + 593897 TACCTAGTCTAC-----------------AA -s simHuman_chr6.simHuman.chr6 8996 14 + 601863 TGCCTGCTCTAC-----------------AG -s simRat_chr6.simRat.chr6 45990 14 + 647215 TAAACACTGTAC-----------------AA - -a -s simMouse_chr6.simMouse.chr6 52978 1 + 636262 C -s Anc0.Anc0refChr9 27470 1 + 35212 C -s Anc1.Anc1refChr0 7893 1 - 16026 C -s Anc2.Anc2refChr0 47613 1 - 56053 T -s mr.mrrefChr0 50735 1 + 130230 C -s simCow_chr6.simCow.chr6 593686 1 - 602619 T -s simHuman_chr6.simHuman.chr6 593084 1 - 601863 C -s simRat_chr6.simRat.chr6 46004 1 + 647215 C - -a -s simMouse_chr6.simMouse.chr6 52979 15 + 636262 TGAATTTCAGCCAAT -s Anc0.Anc0refChr9 27471 15 + 35212 TGGATACAAGTGGTT -s Anc1.Anc1refChr0 7894 15 - 16026 TGGATACAAGTGGTT -s Anc2.Anc2refChr0 47614 15 - 56053 TGGACACAAGTGGTT -s mr.mrrefChr0 50736 15 + 130230 TGAATTTCAGCCAAT -s simCow_chr6.simCow.chr6 593698 15 - 602619 TGAACATGGGTGGCT -s simDog_chr6.simDog.chr6 585098 15 - 593897 TAGGCACAAGTGGTA -s simHuman_chr6.simHuman.chr6 593085 15 - 601863 TGGATACAAGGGGTT -s simRat_chr6.simRat.chr6 46005 15 + 647215 CGATTATTATGCAAT - -a -s simMouse_chr6.simMouse.chr6 52994 18 + 636262 GAGACCACCCACAGATAA -s Anc0.Anc0refChr9 27490 12 + 35212 GGG------CACAAATTA -s Anc1.Anc1refChr0 7913 12 - 16026 GGG------CACAAATTA -s Anc2.Anc2refChr0 47633 12 - 56053 GGC------AACAAATTA -s mr.mrrefChr0 50751 12 + 130230 GAG------CACAGATAA -s simCow_chr6.simCow.chr6 593717 12 - 602619 GGC------AACCAATTA -s simDog_chr6.simDog.chr6 585117 12 - 593897 GGC------ATCAAATTA -s simHuman_chr6.simHuman.chr6 593104 12 - 601863 GGG------CACAAATCA -s simRat_chr6.simRat.chr6 46020 12 + 647215 GAG------CACAGATAA - -a -s simMouse_chr6.simMouse.chr6 53012 8 + 636262 CATATAAG -s Anc0.Anc0refChr9 27507 7 + 35212 CATAT-TG -s Anc1.Anc1refChr0 7930 8 - 16026 CATATGTG -s Anc2.Anc2refChr0 47650 7 - 56053 TATAT-TG -s mr.mrrefChr0 50763 8 + 130230 CATATAAG -s simCow_chr6.simCow.chr6 593734 7 - 602619 GATGT-TA -s simDog_chr6.simDog.chr6 585134 7 - 593897 TATAT-TG -s simHuman_chr6.simHuman.chr6 593121 8 - 601863 CATATGTG -s simRat_chr6.simRat.chr6 46032 8 + 647215 CATGTAGG - -a -s simMouse_chr6.simMouse.chr6 53020 6 + 636262 AGCATG -s Anc0.Anc0refChr9 27515 6 + 35212 AGCATG -s Anc1.Anc1refChr0 7939 6 - 16026 AGCATG -s Anc2.Anc2refChr0 47658 6 - 56053 ACAGCG -s mr.mrrefChr0 50771 6 + 130230 AGCATG -s simCow_chr6.simCow.chr6 593742 4 - 602619 ACA--A -s simDog_chr6.simDog.chr6 585142 6 - 593897 ACAGCG -s simHuman_chr6.simHuman.chr6 593130 6 - 601863 AGCATG -s simRat_chr6.simRat.chr6 46040 6 + 647215 AGCATG - -a -s simMouse_chr6.simMouse.chr6 53026 6 + 636262 AGCCAT -s Anc0.Anc0refChr9 27531 6 + 35212 AGTCAT -s Anc1.Anc1refChr0 7955 6 - 16026 AGTCAT -s Anc2.Anc2refChr0 47674 6 - 56053 AGTCAT -s mr.mrrefChr0 50777 6 + 130230 AGCCAT -s simCow_chr6.simCow.chr6 593756 6 - 602619 AGTCAT -s simDog_chr6.simDog.chr6 585158 6 - 593897 AGTCTT -s simHuman_chr6.simHuman.chr6 593152 6 - 601863 AGTCAT -s simRat_chr6.simRat.chr6 46046 6 + 647215 AGCCAT - -a -s simMouse_chr6.simMouse.chr6 53032 9 + 636262 GCAATATAG -s Anc0.Anc0refChr9 27538 9 + 35212 GCAATAAAA -s Anc1.Anc1refChr0 7962 9 - 16026 GCAATAAAA -s Anc2.Anc2refChr0 47681 9 - 56053 GCAATGAAA -s mr.mrrefChr0 50783 9 + 130230 GCAATATAG -s simCow_chr6.simCow.chr6 593763 4 - 602619 ACAA----- -s simDog_chr6.simDog.chr6 585165 9 - 593897 GCAATGAAA -s simHuman_chr6.simHuman.chr6 593159 9 - 601863 GCAATAAAA -s simRat_chr6.simRat.chr6 46052 9 + 647215 GCAATATAG - -a -s simMouse_chr6.simMouse.chr6 53041 18 + 636262 TCAGAAGACAGGTGGGAG -s Anc0.Anc0refChr9 27547 18 + 35212 TCAGAAAACAGGCAGGAG -s Anc1.Anc1refChr0 7971 18 - 16026 TCAGAAAACAGGCAGGAG -s Anc2.Anc2refChr0 47690 18 - 56053 ACAGAAATCAGGCAGAAG -s mr.mrrefChr0 50792 18 + 130230 TCAGAAGACAGGTGGGAG -s simCow_chr6.simCow.chr6 593767 6 - 602619 ------------CAGAGG -s simDog_chr6.simDog.chr6 585174 18 - 593897 ACAGAAATCAGGTCGAAG -s simHuman_chr6.simHuman.chr6 593169 18 - 601863 TCAGAAAACAGGCAGGAG -s simRat_chr6.simRat.chr6 46061 18 + 647215 TATGGAGACAGGTGGGAT - -a -s simMouse_chr6.simMouse.chr6 53059 10 + 636262 TCATGAATTA -s Anc0.Anc0refChr9 27587 10 + 35212 ACATAGATTA -s Anc1.Anc1refChr0 8011 10 - 16026 ACATAGATTA -s Anc2.Anc2refChr0 47730 10 - 56053 ACATAGATTA -s mr.mrrefChr0 50810 10 + 130230 TCATGAATTA -s simCow_chr6.simCow.chr6 593796 10 - 602619 AGAAACGATA -s simDog_chr6.simDog.chr6 585214 10 - 593897 ACATAGATCA -s simHuman_chr6.simHuman.chr6 593209 10 - 601863 GCATAGATTA -s simRat_chr6.simRat.chr6 46079 10 + 647215 ACTCTAATTA - -a -s simMouse_chr6.simMouse.chr6 53069 2 + 636262 CT -s Anc0.Anc0refChr9 27597 2 + 35212 TT -s Anc1.Anc1refChr0 8021 2 - 16026 TT -s Anc2.Anc2refChr0 47740 2 - 56053 TT -s mr.mrrefChr0 50820 2 + 130230 CT -s simCow_chr6.simCow.chr6 593809 2 - 602619 TA -s simDog_chr6.simDog.chr6 585224 2 - 593897 TT -s simHuman_chr6.simHuman.chr6 593219 2 - 601863 TC -s simRat_chr6.simRat.chr6 46089 2 + 647215 CT - -a -s simMouse_chr6.simMouse.chr6 53071 31 + 636262 GGGATTCTCAATCAATCATTGGCTCTTGCAG -s Anc0.Anc0refChr9 27599 11 + 35212 GGGTTTTACAG-------------------- -s Anc1.Anc1refChr0 8023 11 - 16026 GGGTTTTACAG-------------------- -s Anc2.Anc2refChr0 47742 11 - 56053 GGGTGTTACTG-------------------- -s mr.mrrefChr0 50822 25 + 130230 GGGATTCTCAATCAATCATTGGCTC------ -s simCow_chr6.simCow.chr6 593811 11 - 602619 GAGACTGACCC-------------------- -s simDog_chr6.simDog.chr6 585242 11 - 593897 GGGTGTTACTG-------------------- -s simHuman_chr6.simHuman.chr6 593221 11 - 601863 GGGTTTTGCAG-------------------- -s simRat_chr6.simRat.chr6 46091 25 + 647215 GGGATTCTCAACAACTCATCAGCTC------ - -a -s simMouse_chr6.simMouse.chr6 53102 8 + 636262 GACACTGA -s Anc0.Anc0refChr9 27610 8 + 35212 GACACTGA -s Anc1.Anc1refChr0 8034 8 - 16026 GACACTGA -s Anc2.Anc2refChr0 47753 8 - 56053 GAAACTGA -s mr.mrrefChr0 50847 8 + 130230 GACACTGA -s simCow_chr6.simCow.chr6 593822 8 - 602619 GAAACTGA -s simDog_chr6.simDog.chr6 585262 8 - 593897 GAAACCAA -s simHuman_chr6.simHuman.chr6 593232 8 - 601863 GACACTGA -s simRat_chr6.simRat.chr6 46116 8 + 647215 GACACTGA - -a -s simMouse_chr6.simMouse.chr6 53110 120 + 636262 TGCAGGTCCAAGATGATATATAAGATTGTGACTCAACCAGGCACTCCCTGGAGAAAGATGGGATAGGTAGGCTTTCCTAGTTGTGAATAGAGAACGCATCATACTACTTGCACCTTGTCA -s Anc0.Anc0refChr9 27626 2 + 35212 TG---------------------------------------------------------------------------------------------------------------------- -s Anc1.Anc1refChr0 8050 2 - 16026 TG---------------------------------------------------------------------------------------------------------------------- -s Anc2.Anc2refChr0 47769 2 - 56053 CA---------------------------------------------------------------------------------------------------------------------- -s mr.mrrefChr0 50855 94 + 130230 TGCAGGTCCAAGATGATATATA--------------------------TGGAGAAAGATGGGATAGGTAGGCTTTCCTAGTTGTGAATAGAGAACGCATCATACTACTTGCACCTTGTCA -s simCow_chr6.simCow.chr6 593838 2 - 602619 CA---------------------------------------------------------------------------------------------------------------------- -s simDog_chr6.simDog.chr6 585278 2 - 593897 CA---------------------------------------------------------------------------------------------------------------------- -s simHuman_chr6.simHuman.chr6 593248 2 - 601863 TG---------------------------------------------------------------------------------------------------------------------- -s simRat_chr6.simRat.chr6 46124 94 + 647215 CACAGGTCCAATCTGATGCTTA--------------------------TGGAGAAAGATTAGATATGTAGGCTTCCCTATTTGTGAATCAAGAATGCATCATACTACTTGCACCATGTCA - -a -s simMouse_chr6.simMouse.chr6 53230 110 + 636262 TAACCTGACCTACTGGTTGCAAAATAATTGTGATCCTTATCACATTTCTTATTGACACATGTCTCTGGTAGACAAGACACATAGGGTTGCTAATGACTGCTTGTTGTGAG -s mr.mrrefChr0 50949 110 + 130230 TAACCTGACCTACTGGTTGCAAAATAATTGTGATCCTTATCACATTTCTTATTGACACATGTCTCTGGTAGACAAGACACATAGGGTTGCTAATGACTGCTTGTTGTGAG -s simRat_chr6.simRat.chr6 46349 110 + 647215 TAACCTGACCTATTGGTTGCACGATATTTGTGATCCATACCACATCTCTTATTTCCACATGTCTTTGGTAGACAAGACACGTGGGGTTGCTAATGACTGCTTGTTATGGG - -a -s simMouse_chr6.simMouse.chr6 53340 13 + 636262 TGATGACTGTAGA -s mr.mrrefChr0 51059 13 + 130230 TGATGACTGTAGA -s simRat_chr6.simRat.chr6 46502 13 + 647215 TGATAACTGTGAA - -a -s simMouse_chr6.simMouse.chr6 53353 34 + 636262 ACCTACTCACCGGGAGGGATCTCCTGTATGACGG -s mr.mrrefChr0 51072 34 + 130230 ACCTACTCACCGGGAGGGATCTCCTGTATGACGG -s simRat_chr6.simRat.chr6 46516 34 + 647215 ACCTGCTCACCGGGAGGGATCTCCTGTATTACGG - -a -s simMouse_chr6.simMouse.chr6 53387 166 + 636262 ACTTCCACATGATGGTGCATCCAGACATAGTGGTTGGACCTTGGTCTCACGTGGACTCTAAAGGTGGCCTtcactgggagggacctcctgtatgatagcacttccacacatcatatttggaccttgctttcacgtggacccttgaggtggcctagcccccactcag -s mr.mrrefChr0 51106 88 + 130230 ACTTCCACA----------------CATAGTGGTTGG--------------------CTAAAGGTGGCCTtcactgggagggacctcctgtatgatagc------------------------------------------ttgaggtggcctagcccccactcag -s simRat_chr6.simRat.chr6 46551 88 + 647215 AATTCTACA----------------CATCATGGTTGG--------------------CTAAAGGTGGCCTTCACTGGAAGGGATCTCCTGTATGTTGGC------------------------------------------TAGaggtggcctaccccccacttgg - -a -s simMouse_chr6.simMouse.chr6 53553 75 + 636262 tccctttgtttgttaccaggtgcactagcgttttctttggaaagtttccggtAGCTCATAAGTTAGAGGCCCAGT -s mr.mrrefChr0 51194 73 + 130230 tccctttgtttgttaccaggtgcactagcgttttctttggaaagtttccagtAGCTCATAAGt--gaggcccagt -s simRat_chr6.simRat.chr6 46640 73 + 647215 tccctgactttgctaccaggggcactagcgttttctttggaaagtttccagtagctcataagt--gagacccagt - -a -s simMouse_chr6.simMouse.chr6 53628 15 + 636262 AAAGGTGATCACTCA -s Anc0.Anc0refChr9 27628 13 + 35212 --GGGCAATTATGCA -s Anc1.Anc1refChr0 8052 13 - 16026 --GGGCAATTATGCA -s Anc2.Anc2refChr0 47771 13 - 56053 --AGGCACTTATGCA -s mr.mrrefChr0 51267 15 + 130230 AAGGGTGATCACACA -s simCow_chr6.simCow.chr6 593840 13 - 602619 --AAGAACTTATGCA -s simDog_chr6.simDog.chr6 585280 13 - 593897 --AGGCACGCATGCA -s simHuman_chr6.simHuman.chr6 593250 13 - 601863 --GGGGTATTATGTT -s simRat_chr6.simRat.chr6 46763 15 + 647215 AAGGGTGATCACACA - -a -s simMouse_chr6.simMouse.chr6 53643 45 + 636262 AATTAGCTCTCTATCTGGTCAATCTTTATCAAGTACCCAGTGTTT -s Anc0.Anc0refChr9 27641 26 + 35212 AATTCGCCCTGTATATAATTGAC-------------------ACC -s Anc1.Anc1refChr0 8065 26 - 16026 AATTCGCCCTGTATATAATTGAC-------------------ACC -s Anc2.Anc2refChr0 47784 26 - 56053 AATTCGCCCTGTGTATAATTGAC-------------------ACC -s mr.mrrefChr0 51282 26 + 130230 AATTAGCTCTCTATCTGGTCAAT-------------------TTT -s simCow_chr6.simCow.chr6 593863 26 - 602619 AATTTGCCCTCTGTCTAATTCAC-------------------AAC -s simDog_chr6.simDog.chr6 585293 26 - 593897 AATTCGCCCTGTGTACAAGTGAC-------------------ACC -s simHuman_chr6.simHuman.chr6 593263 20 - 601863 AGT--GCATGATA----ATTGAC-------------------AGC -s simRat_chr6.simRat.chr6 46778 26 + 647215 AATTAGCTTGCTATCGGGTCAAT-------------------GTT - -a -s simMouse_chr6.simMouse.chr6 53688 64 + 636262 TATCAAGTACCCAGTGTAAAGGGTCAGGTAGACTTGATTGTGCACTAATCATGTATTCATAGAG -s Anc0.Anc0refChr9 27667 64 + 35212 TATCAAGTACCCAGTGTAAAGGGCCAGGCAGAGTTGATTGAGGCCTAATAATGGATTCATAGAG -s Anc1.Anc1refChr0 8091 64 - 16026 TATCAAGTACCCAGTGTAAAGGGCCAGGCAGAGTTGATTGAGGCCTAATAATGGATTCATAGAG -s Anc2.Anc2refChr0 47811 64 - 56053 TATCAAGTACCCAGTGTAAAGGGCCAGGCAGAGTTGATTGAGGCCCAATAATGGATTCATAGAG -s mr.mrrefChr0 51308 64 + 130230 TATCAAGTACCCAGTGTAAAGGGTCAGGTAGACTTGATTGTGCCCTAATCATGCATTCATAGAG -s simCow_chr6.simCow.chr6 593894 64 - 602619 TATCAAGTACTCAGTGTGAAGGGTCCGGCAGAGATGATTGCCACCCAATCATGGTTTCTTAATG -s simDog_chr6.simDog.chr6 585320 64 - 593897 TAAACAGTACCCGGTGTAAAGGGCCAGACAGAGTTGATCGAGGCCCAATAATGGATTCATAGAG -s simHuman_chr6.simHuman.chr6 593283 56 - 601863 TATCAAGTACCCAGTGTAAAGGGCCAGGCAGATTTGATTGAGGCCTAAT--------CATACAG -s simRat_chr6.simRat.chr6 46804 64 + 647215 TATCAAGTACCCAGCGTAAAGGGTCAGGTAGACTTGATTGTGCCCTAATCATGCATTTATAGAG - -a -s simMouse_chr6.simMouse.chr6 53752 3 + 636262 GTC -s Anc0.Anc0refChr9 27733 3 + 35212 ATC -s Anc1.Anc1refChr0 8157 3 - 16026 ATC -s Anc2.Anc2refChr0 47877 3 - 56053 ATC -s mr.mrrefChr0 51372 3 + 130230 GTC -s simCow_chr6.simCow.chr6 593960 3 - 602619 ATG -s simDog_chr6.simDog.chr6 585386 3 - 593897 ATC -s simHuman_chr6.simHuman.chr6 593341 3 - 601863 ATC -s simRat_chr6.simRat.chr6 46868 3 + 647215 ATC - -a -s simMouse_chr6.simMouse.chr6 53755 6 + 636262 ACCAAA -s Anc0.Anc0refChr9 27738 6 + 35212 ACCATA -s Anc1.Anc1refChr0 8162 6 - 16026 ACCATA -s Anc2.Anc2refChr0 47882 6 - 56053 ACCATA -s mr.mrrefChr0 51375 6 + 130230 ACCAAA -s simCow_chr6.simCow.chr6 593965 6 - 602619 GCCATA -s simDog_chr6.simDog.chr6 585391 6 - 593897 ATCATA -s simHuman_chr6.simHuman.chr6 593346 6 - 601863 ACCATA -s simRat_chr6.simRat.chr6 46871 6 + 647215 ACCAAA - -a -s simMouse_chr6.simMouse.chr6 53761 74 + 636262 AGTATGCACACTGAGTTGCCATAGTTCAGCTCCAGAGGTAGTTAAGGGCGCTCAAATTTTATACAAAATAAGAC -s Anc0.Anc0refChr9 27745 74 + 35212 AGTACACATTCCAACTTAACTCTGCATAGCCCTACAGGTAGACAAGCATGCTCAAATTTTGTACAAAACAAGAC -s Anc1.Anc1refChr0 8169 74 - 16026 AGTACACATTCCAACTTAACTCTGCATAGCCCTACAGGTAGACAAGCATGCTCAAATTTTGTACAAAACAAGAC -s Anc2.Anc2refChr0 47889 74 - 56053 AGTACACATTCCAACTTAACTCTGTATAGCCCCACAGGCAGACAAGCATGCTCAAAGTTTGTACAAAACTAGAC -s mr.mrrefChr0 51382 74 + 130230 AGTATGCATACTAAGTTGACACTGCTTAGCTCTAGAGGTAGTTAAGGGCGCTCAAATTTTATACAAAATAAGAC -s simCow_chr6.simCow.chr6 593972 74 - 602619 AGTACACATTCCAATTTAGCTCTGTATAGCCTCAAAGGCAGATGAGCATGCTTAAAGTGTCTACAAAACCAAAC -s simDog_chr6.simDog.chr6 585398 74 - 593897 AATACACATTTCAACTTTACTCTGTATAACCCCACAGGCAGACAGGCATGCTCAAGGTTTGTACAAAACTAGAC -s simHuman_chr6.simHuman.chr6 593353 73 - 601863 AGTACATATTCCAGCTTAACTCTGCATAGCCCTA-AAGTAGACAAGCATGCTCAAATATTTTACAAAACAAGAC -s simRat_chr6.simRat.chr6 46878 74 + 647215 AGTATTCATACTAAGTTGACACTGCTTAGCTCTAGAGGTATTTGATGGATTTCAAATTTTCTATAAAATAAGAC - -a -s simMouse_chr6.simMouse.chr6 53835 87 + 636262 TATCAGAACTCCAATTTAGTTGATGTGCCAGCAACTGAGTTTGGCTACCTCTAGCAGTGCCCTTAAGGCACTTAAGTCCAGTGTGAT -s Anc0.Anc0refChr9 27829 83 + 35212 TTTTAGGATACCAATTCATTTGACAAG---CCAAA-GTGATTGGCTACACGTCCCAATGCATTTAAGGCTCCTATTTCCAATGTGAT -s Anc1.Anc1refChr0 8253 86 - 16026 TTTTAGGATACCAATTCATTTGACAAGCCACCAAA-GTGATTGGCTACACGTCCCAATGCATTTAAGGCTCCTATTTCCAATGTGAT -s Anc2.Anc2refChr0 47973 83 - 56053 TTTTAGGATATCAATTCATTTGACAAG---CCAAA-GTGATTGACTAGACGTCCCAATGCATTTAAGGCTCCTATTTCCAATGTGAT -s mr.mrrefChr0 51456 87 + 130230 TATCAGAACTCCAATTCAGTTGACAAGCCACCAACTGAGTTTGGCTACCTCTAGCAATGCCCTTAAGGCTCTTATGTCCAATGTGAT -s simCow_chr6.simCow.chr6 594056 81 - 602619 TTTCAGGACATCAGGTTATTCGACAAG---CCAAA-GTGGTTGACTATATGTTCTGGTGCATTTAAGGCTCC--TTGCCAATGTGAT -s simDog_chr6.simDog.chr6 585482 77 - 593897 TTTTAGGATGTCAATTCATTTGACCGG---CCAAA-ATAAGTGACTAGACGTCCCAATGTATTTAAGGCTCCTATTTC------CAC -s simHuman_chr6.simHuman.chr6 593436 86 - 601863 TTTTAAGATACCCATACATATGGCAAGCCACCAAA-GTGATTGGCCACACATGCCAATGCATTTCTGGCTCCTATCCCCAATATGAT -s simRat_chr6.simRat.chr6 46952 87 + 647215 TCTCAGAACTCCAATTCAGTTGACAAGCAACCAATCAAGTTTGGCTACCTCTAGCAATGTCCTTGAGGCTCTTATATTCAATGTGAT - -a -s simMouse_chr6.simMouse.chr6 53922 17 + 636262 TAATCTAATCATCATAA -s Anc0.Anc0refChr9 27914 11 + 35212 GA------TCAACATAA -s Anc1.Anc1refChr0 8341 11 - 16026 GA------TCAACATAA -s Anc2.Anc2refChr0 48058 11 - 56053 GA------GCAAAATAA -s mr.mrrefChr0 51545 17 + 130230 TAATCTAATCATCATAA -s simCow_chr6.simCow.chr6 594139 11 - 602619 GG------ATAAAATAA -s simDog_chr6.simDog.chr6 585561 11 - 593897 GA------GCAAAACAA -s simHuman_chr6.simHuman.chr6 593524 11 - 601863 AA------TCAACATAA -s simRat_chr6.simRat.chr6 47041 17 + 647215 TAATCTAAACATCATAG - -a -s simMouse_chr6.simMouse.chr6 53939 12 + 636262 TTTTCATTGACC -s Anc0.Anc0refChr9 27925 11 + 35212 GGCTC-TGATTT -s Anc1.Anc1refChr0 8352 11 - 16026 GGCTC-TGATTT -s Anc2.Anc2refChr0 48069 11 - 56053 GCCTC-TGATTT -s mr.mrrefChr0 51562 12 + 130230 TGTTCATTGACC -s simCow_chr6.simCow.chr6 594150 11 - 602619 GCCTC-TGATTT -s simDog_chr6.simDog.chr6 585578 11 - 593897 GCCTC-TGATTT -s simHuman_chr6.simHuman.chr6 593535 11 - 601863 GGCTC-TCATTT -s simRat_chr6.simRat.chr6 47058 12 + 647215 AGTTCATTGAGC - -a -s simMouse_chr6.simMouse.chr6 53951 10 + 636262 TCCAGGAGTT -s Anc0.Anc0refChr9 27936 10 + 35212 TCCAATAATT -s Anc1.Anc1refChr0 8363 10 - 16026 TCCAATAATT -s Anc2.Anc2refChr0 48091 10 - 56053 TCCAATAATT -s mr.mrrefChr0 51574 10 + 130230 TCCAGGAGTT -s simCow_chr6.simCow.chr6 594172 10 - 602619 TCCAGTAATT -s simDog_chr6.simDog.chr6 585600 10 - 593897 TCCAATAATC -s simHuman_chr6.simHuman.chr6 593546 10 - 601863 TCCAATAATT -s simRat_chr6.simRat.chr6 47070 10 + 647215 TCCAGGAGTT - -a -s simMouse_chr6.simMouse.chr6 53961 37 + 636262 TATTGTTTAATGATTAACTATTGAAATTTCCTATCTC -s Anc0.Anc0refChr9 27946 30 + 35212 CATTCTCTA-------ACTATCTAAACGTCTTATCTC -s Anc1.Anc1refChr0 8373 30 - 16026 CATTCTCTA-------ACTATCTAAACGTCTTATCTC -s Anc2.Anc2refChr0 48101 30 - 56053 CATTCTCTA-------ATAATCTAAACGTCTTATCTC -s mr.mrrefChr0 51584 37 + 130230 TATTGTTTAATGATTAACTATTTAAACTTCCTATCTC -s simCow_chr6.simCow.chr6 594182 27 - 602619 CATTCCCTA-------A---TCTAAACTTCTTATCTC -s simDog_chr6.simDog.chr6 585612 30 - 593897 TATTCTCTA-------ATAATGTAAGTGTCTTATTTC -s simHuman_chr6.simHuman.chr6 593556 28 - 601863 CATTTTCTA-------ACTGTCTAAACATCTTATC-- -s simRat_chr6.simRat.chr6 47080 37 + 647215 TATTGCTTGATGATTAAATATTTAAGCTTCCTACCTT - -a -s simMouse_chr6.simMouse.chr6 53998 5 + 636262 GTGAA -s Anc0.Anc0refChr9 27976 5 + 35212 ATGAA -s Anc1.Anc1refChr0 8403 5 - 16026 ATGAA -s Anc2.Anc2refChr0 48131 5 - 56053 ATGAA -s mr.mrrefChr0 51621 5 + 130230 GTGAA -s simCow_chr6.simCow.chr6 594209 5 - 602619 ATGAA -s simDog_chr6.simDog.chr6 585642 5 - 593897 ATGAA -s simHuman_chr6.simHuman.chr6 593900 5 - 601863 TACAA -s simRat_chr6.simRat.chr6 47117 5 + 647215 GTGAA - -a -s simMouse_chr6.simMouse.chr6 54003 33 + 636262 CTGTGTAAGACTGATTGCAGGGGTTGCTGCATC -s Anc0.Anc0refChr9 27981 31 + 35212 TTGTGTAGAGCTGACAGCAGGGGTTTTTGTA-- -s Anc1.Anc1refChr0 8408 31 - 16026 TTGTGTAGAGCTGACAGCAGGGGTTTTTGTA-- -s Anc2.Anc2refChr0 48137 31 - 56053 TTGTGCAGAGCTGACAGCAGGGGTTTTTGTA-- -s mr.mrrefChr0 51626 31 + 130230 CTGTGTAAGACTGATTGCAGGGGTTGCTGCA-- -s simCow_chr6.simCow.chr6 594215 30 - 602619 T-GTGCAGATCTGTGGGCAAGGGTCTTTGTA-- -s simDog_chr6.simDog.chr6 585648 31 - 593897 TTGTGCAGAGCTGACAGCAGGGGTTTTTGTA-- -s simHuman_chr6.simHuman.chr6 593905 28 - 601863 TTGTGTCGAGCAGACAGCAGGTGTTTTT----- -s simRat_chr6.simRat.chr6 47122 31 + 647215 CTGTGTAAGACTGATTGCAGGGGTTGCTGCA-- - -a -s simMouse_chr6.simMouse.chr6 54036 11 + 636262 TATAAGACAGA -s Anc0.Anc0refChr9 28012 10 + 35212 TATAAGAC-CA -s Anc1.Anc1refChr0 8439 11 - 16026 TATAAGACACA -s Anc2.Anc2refChr0 48170 10 - 56053 TATAAGAC-CC -s mr.mrrefChr0 51657 11 + 130230 TATAAGACAGA -s simCow_chr6.simCow.chr6 594247 10 - 602619 TTCGAGAC-CC -s simDog_chr6.simDog.chr6 585681 10 - 593897 TATAAGAC-CC -s simHuman_chr6.simHuman.chr6 593933 8 - 601863 ---ATGTTATA -s simRat_chr6.simRat.chr6 47153 11 + 647215 TATAAGACACA - -a -s simMouse_chr6.simMouse.chr6 54047 49 + 636262 CCCCCCACACTCTAGGAGCTTATTAAATCTACAGTGAATTTCTTCTGAG -s Anc0.Anc0refChr9 28022 49 + 35212 CCCCCCAGCCCCCAGGAGTCAGTTAAATATACAGTGGAATATTTCTAAG -s Anc1.Anc1refChr0 8450 49 - 16026 CCCCCCAGCCCCCAGGAGTCAGTTAAATATACAGTGGAATATTTCTAAG -s Anc2.Anc2refChr0 48180 49 - 56053 CCCCCCAGCCCCCAGGAGTCAGTTAAATATACAGTGGAATATTTCTAAG -s mr.mrrefChr0 51668 49 + 130230 CCCCCCACACTCTAGGAGCTTATTAAATCTACAGTGAATTTCTTCTGAG -s simCow_chr6.simCow.chr6 594258 49 - 602619 CCCCCCAGCTCCCAGGAGTTAGTGAAACATACAGTGGAATATTCTTAAG -s simDog_chr6.simDog.chr6 585691 49 - 593897 CCTCCTGGCCCCCAGGAGTCAATTAAATATACACTGGAATATTTCTAAG -s simHuman_chr6.simHuman.chr6 593941 49 - 601863 CCCCCCAGCCCCCAAGAGTCAGCTAAATATACAGTGGAGTATTTCTAAG -s simRat_chr6.simRat.chr6 47164 49 + 647215 CCCCCCATACTCTAGGAGCTTATTAGATCTACAGTGAATTTCTTCTGAG - -a -s simMouse_chr6.simMouse.chr6 54096 14 + 636262 CACTCAAGGGAGTG -s Anc0.Anc0refChr9 28088 14 + 35212 AACTCAAGGGGGTG -s Anc1.Anc1refChr0 8516 14 - 16026 AACTCAAGGGGGTG -s Anc2.Anc2refChr0 48246 14 - 56053 AGCCCAAGGGGGTG -s mr.mrrefChr0 51717 14 + 130230 CACTCAAGGGAGTG -s simCow_chr6.simCow.chr6 594324 14 - 602619 AGCCCCAGGGTGTG -s simDog_chr6.simDog.chr6 585758 14 - 593897 AGCCCAGGGGGGTG -s simHuman_chr6.simHuman.chr6 594007 14 - 601863 AACTCAAGGGGTTG -s simRat_chr6.simRat.chr6 47213 14 + 647215 CACCCAAGGGAGTG - -a -s simMouse_chr6.simMouse.chr6 54110 53 + 636262 TGGCAAGAAGGGAACAAGCCAATAAGAAAAGTACCCAGAGGTCACAGAAGAGT -s Anc0.Anc0refChr9 28106 45 + 35212 TGGCAAAAAGGCTATAAGACTATAGTAAAGA--------GGTTCCTAGGGGGT -s Anc1.Anc1refChr0 8534 52 - 16026 TGGCAAAAAGGCTATAAGACTATAGTAAAGATCTGCAG-GGTTCCTAGGGGGT -s Anc2.Anc2refChr0 48264 45 - 56053 TGGCAAAAAGGCTATAAAACTGTAGTAAAGA--------GGTTCCTAGGGGGT -s mr.mrrefChr0 51735 53 + 130230 TGGCAAGAAGGCAATAAGCCAATAAGAAAAGTCCCCAGAGGTCCCAGAAGAGT -s simCow_chr6.simCow.chr6 594342 44 - 602619 TGGCCAGAAGGCTATCAACCTGTAGGAAAG---------GGTTACACGGGAGT -s simDog_chr6.simDog.chr6 585776 42 - 593897 CAGCAAAAAGGCTACAAAACTGTGTTAGTGA-----------TCCTAGGGGGT -s simHuman_chr6.simHuman.chr6 594025 52 - 601863 TGGCTAAAGGGCCATAAGACTATAGTAAAGATCTGCAG-GGTTCCCAGGGGGT -s simRat_chr6.simRat.chr6 47231 53 + 647215 TGGCAAGAATGCTGTAACCCAATAAGAAAAGTCCCCAGTGGTCCCAGAAGAGT - -a -s simMouse_chr6.simMouse.chr6 54163 1 + 636262 C -s Anc0.Anc0refChr9 28159 1 + 35212 C -s Anc1.Anc1refChr0 8594 1 - 16026 C -s Anc2.Anc2refChr0 48317 1 - 56053 C -s mr.mrrefChr0 51796 1 + 130230 C -s simCow_chr6.simCow.chr6 594394 1 - 602619 C -s simDog_chr6.simDog.chr6 585826 1 - 593897 T -s simHuman_chr6.simHuman.chr6 594085 1 - 601863 C -s simRat_chr6.simRat.chr6 47292 1 + 647215 C - -a -s simMouse_chr6.simMouse.chr6 54164 57 + 636262 CCAGCAGTGCAATGGCTGTGACCATTTCACAGGTTAAGAGCTATCAAGGGAGATCAT -s Anc0.Anc0refChr9 28160 57 + 35212 CATGCAGAGCAATGTCTGTGACCATTTCACACAGTAAGAACTATTGCAGATGGTCAT -s Anc1.Anc1refChr0 8595 57 - 16026 CATGCAGAGCAATGTCTGTGACCATTTCACACAGTAAGAACTATTGCAGATGGTCAT -s Anc2.Anc2refChr0 48319 57 - 56053 CATGCAAAGTAATGTCTGTGACCATTTCACACAGTAAGAACTATTGCAGATGGTTAT -s mr.mrrefChr0 51797 57 + 130230 CCAGCAGTGCAATGGCTGTGACCATTTCACAGGTTAAGAGCTATCGAGGGAGATCAT -s simCow_chr6.simCow.chr6 594396 57 - 602619 CAGAGTAAGTAATGTCTGTGACCATTTTACACAGTCAGAACTACTGCAGATGGTAAA -s simDog_chr6.simDog.chr6 585828 57 - 593897 CGTGCAAAATAATGTTTGTGTCCATTTCACACTGTAAGAACTATCACAGATGGTTGT -s simHuman_chr6.simHuman.chr6 594086 57 - 601863 CATGCAGAGCAATGTCAGTGACCATCTCACACAGCGAGGAATATTGCAGATGGTCAC -s simRat_chr6.simRat.chr6 47293 51 + 647215 CCAGCAGTGCAA------TTACCATTTCACAGGTTAAGAGCCATCGAGGGAGATTAT - -a -s simMouse_chr6.simMouse.chr6 54221 48 + 636262 GATGGGGTCTTGACATATTGTATTTCAACAATCATTAAATTAGCAGGG -s Anc0.Anc0refChr9 28217 47 + 35212 GATGAGTTCTTGACATATTGTTTTTGAACAGTAATTAACCTAA-TGAG -s Anc1.Anc1refChr0 8652 47 - 16026 GATGAGTTCTTGACATATTGTTTTTGAACAGTAATTAACCTAA-TGAG -s Anc2.Anc2refChr0 48376 47 - 56053 GATGAGTTCTTGACATCTTGTTTTTGAATAGTAATTAACCTAA-TGAA -s mr.mrrefChr0 51854 48 + 130230 GATGGGGTCTTGACATATTGTATTTCAACAATCATTAAATTAGCTGGG -s simCow_chr6.simCow.chr6 594453 47 - 602619 GTTGAGTTCTTGGCATCTTGTTTTTGAATAGTAATTAACCTAA-TAAC -s simDog_chr6.simDog.chr6 585886 47 - 593897 GATGAGTTCTTCACCTCCTGTTTTCCAATAGTAACTAACCTGA-AGAA -s simHuman_chr6.simHuman.chr6 594143 47 - 601863 AATGAGTTCTTGACATATTGTTTTTGATCAGTAATTAACCTAA-TGTG -s simRat_chr6.simRat.chr6 47344 48 + 647215 GATGGGATCCTGATATACTTTATTTCAACAATCATTAGGTTAGCTGAG - -a -s simMouse_chr6.simMouse.chr6 54269 27 + 636262 GTTCGGGAGTCTGTGGGTTCATAAACC -s Anc0.Anc0refChr9 28264 27 + 35212 GTTGGGGGGGTTATAAGTTTATAAACC -s Anc1.Anc1refChr0 8699 27 - 16026 GTTGGGGGGGTTATAAGTTTATAAACC -s Anc2.Anc2refChr0 48424 27 - 56053 GTTGGGGGGGTTACAACTTTTTAAACC -s mr.mrrefChr0 51902 27 + 130230 GTTGGGGAGTTTGTGGGTTCATAAACC -s simCow_chr6.simCow.chr6 594501 27 - 602619 GTTGGAAGGGTTACAACTTTCTAAACC -s simDog_chr6.simDog.chr6 585934 27 - 593897 GTTGAGGGGGTTACAACTTTTCAAACG -s simHuman_chr6.simHuman.chr6 594190 27 - 601863 GTTGGGGGGGTTATAAGTTTATCAACC -s simRat_chr6.simRat.chr6 47392 27 + 647215 GTTGGGGAATTCGTGGGTCCATAGACC - -a -s simMouse_chr6.simMouse.chr6 54296 6 + 636262 ATTAGT -s Anc0.Anc0refChr9 28294 6 + 35212 ATTAGT -s Anc1.Anc1refChr0 8729 6 - 16026 ATTAGT -s Anc2.Anc2refChr0 48454 6 - 56053 ATCAGT -s mr.mrrefChr0 51929 6 + 130230 ATTAGT -s simCow_chr6.simCow.chr6 594531 6 - 602619 GTCAGT -s simDog_chr6.simDog.chr6 585964 6 - 593897 ATCAGT -s simHuman_chr6.simHuman.chr6 594220 6 - 601863 ATTAGT -s simRat_chr6.simRat.chr6 47419 6 + 647215 ATCATT - -a -s simMouse_chr6.simMouse.chr6 54302 2 + 636262 TA -s Anc0.Anc0refChr9 28300 2 + 35212 AA -s Anc1.Anc1refChr0 8735 2 - 16026 AA -s Anc2.Anc2refChr0 48460 2 - 56053 AA -s mr.mrrefChr0 51935 2 + 130230 TA -s simCow_chr6.simCow.chr6 594539 2 - 602619 AA -s simDog_chr6.simDog.chr6 585970 2 - 593897 AA -s simHuman_chr6.simHuman.chr6 594226 2 - 601863 AA -s simRat_chr6.simRat.chr6 47425 2 + 647215 TA - -a -s simMouse_chr6.simMouse.chr6 54304 29 + 636262 AGTCCTTAAATGGGTCAGGTGAATGAGAT -s Anc0.Anc0refChr9 28303 29 + 35212 ATTCCTTAAGTGGGTAGAGGGAATGACTT -s Anc1.Anc1refChr0 8738 29 - 16026 ATTCCTTAAGTGGGTAGAGGGAATGACTT -s Anc2.Anc2refChr0 48463 29 - 56053 ATTCCTTGAGTGGGTAGAGGGAATCACTT -s mr.mrrefChr0 51937 29 + 130230 AGTCCTTAAATGGGTCAGATGAATGAGAT -s simCow_chr6.simCow.chr6 594542 29 - 602619 ATTCCTTGAGTGGGTTGAGGGAATCACTT -s simDog_chr6.simDog.chr6 585973 29 - 593897 ATTGTTTGACTGGGTAGAGGGAGTCACTT -s simHuman_chr6.simHuman.chr6 594229 25 - 601863 ATTCCATAAGTAGT----CCAAATGGCTT -s simRat_chr6.simRat.chr6 47427 29 + 647215 AGTTCTGAAATGGATCAGATGAACAAAAT - -a -s simMouse_chr6.simMouse.chr6 54333 11 + 636262 AGGCTGCGCCG -s Anc0.Anc0refChr9 28333 11 + 35212 TGTCAGTGCAG -s Anc1.Anc1refChr0 8768 11 - 16026 TGTCAGTGCAG -s Anc2.Anc2refChr0 48493 11 - 56053 TGTCAGTGCAG -s mr.mrrefChr0 51966 11 + 130230 TGGCCGCGCCG -s simCow_chr6.simCow.chr6 594572 11 - 602619 CGTCAGTGCAG -s simDog_chr6.simDog.chr6 586003 11 - 593897 TGTCAGTGTAG -s simHuman_chr6.simHuman.chr6 594255 11 - 601863 TGTCAGTGCAG -s simRat_chr6.simRat.chr6 47456 11 + 647215 TAGCCGTGCCG - -a -s simMouse_chr6.simMouse.chr6 54344 25 + 636262 GCTGAGTAATAAATGATCATGATGC -s Anc0.Anc0refChr4 2334 24 - 45765 GCTGAGTC-AAAGAGATCTAGATGC -s Anc1.Anc1refChr2 33036 24 + 144309 GCTGAGTC-AAAGAGATCTAGATGC -s Anc2.Anc2refChr0 55358 24 + 56053 GCCAAGTC-AAAGAGATCTAGATGC -s mr.mrrefChr0 51977 25 + 130230 GCTGAGTGATAAATGATCATGATGC -s simCow_chr6.simCow.chr6 58966 24 + 602619 GTCAAGTT-TAAGAGCTCTAGATGC -s simDog_chr6.simDog.chr6 52909 24 + 593897 GCCAGGTC-AAATAGATCAGGATGC -s simHuman_chr6.simHuman.chr6 53210 24 + 601863 ACTGAGCA-CAAGAGATCTAGATGC -s simRat_chr6.simRat.chr6 47467 25 + 647215 GCTGAGTGATAAATGATCAGGATGC - -a -s simMouse_chr6.simMouse.chr6 54369 15 + 636262 ATGTTGATAAGTTTT -s Anc0.Anc0refChr4 2363 11 - 45765 ATA----AAAGTTGC -s Anc1.Anc1refChr2 33065 11 + 144309 ATA----AAAGTTGC -s Anc2.Anc2refChr0 55388 11 + 56053 ATA----AAGGGTGC -s mr.mrrefChr0 52002 11 + 130230 ATG----TAAGTTGC -s simCow_chr6.simCow.chr6 58996 11 + 602619 ATA----AGGAATGC -s simDog_chr6.simDog.chr6 52939 11 + 593897 ATA----AAGGGTGC -s simHuman_chr6.simHuman.chr6 53239 11 + 601863 ATA----AAAGTTGC -s simRat_chr6.simRat.chr6 47492 11 + 647215 ATG----TAAGTTGC - -a -s simMouse_chr6.simMouse.chr6 54384 3 + 636262 GGC -s Anc0.Anc0refChr4 2377 3 - 45765 TGC -s Anc1.Anc1refChr2 33079 3 + 144309 TGC -s Anc2.Anc2refChr0 55402 3 + 56053 TGC -s mr.mrrefChr0 52016 3 + 130230 GGC -s simCow_chr6.simCow.chr6 59010 3 + 602619 TGC -s simDog_chr6.simDog.chr6 52953 3 + 593897 AGC -s simHuman_chr6.simHuman.chr6 53253 3 + 601863 TGC -s simMouse_chr6.simMouse.chr6 54578 3 + 636262 GGC -s simRat_chr6.simRat.chr6 47506 3 + 647215 GGC - -a -s simMouse_chr6.simMouse.chr6 54387 51 + 636262 AATAAAAAGTGCTTAGGGTCCCAAGGGTTTGGTTTAAATCCTTCTTTTTGA -s Anc0.Anc0refChr4 2380 51 - 45765 AATGAAAAACACTAAAGGTCCCAAAGAATTGGTTTAGATCCTTCATTTTGG -s Anc1.Anc1refChr2 33082 51 + 144309 AATGAAAAACACTAAAGGTCCCAAAGAATTGGTTTAGATCCTTCATTTTGG -s Anc2.Anc2refChr0 55405 51 + 56053 AATGAAAAACACTAAAGGTCCCAAAGAATTGGTCAAGATCCTTCATTTTGG -s mr.mrrefChr0 52019 51 + 130230 AATGAAAAATGCTTAGGGTCCCAAGGGTTTGGTTTACATCCTTCTTTTTGG -s simCow_chr6.simCow.chr6 59013 51 + 602619 AATGAAAATCATTAAAGGTCCTGTAGAATTGGTCAAGATCCTTCTTTTTGG -s simDog_chr6.simDog.chr6 52976 51 + 593897 AATGAAAAACACTAAAGGTCCCAAGGAATTGGCCATGATCCTTCATTTTGG -s simHuman_chr6.simHuman.chr6 53256 45 + 601863 AATGAAAAAAACAC---TTCCCAAAGAATTGGTTTAGAACCTT---TTTAG -s simMouse_chr6.simMouse.chr6 54581 51 + 636262 AACGAAACATACTTAGTGTCCCAAGAGTTTTGTTTACATCCCTCTTTTTGG -s simRat_chr6.simRat.chr6 47509 51 + 647215 AATGAGAAATGCTTCGGGTCCCAAGGGTTTGGTTTACATCCTTCTTTTGGG - -a -s simMouse_chr6.simMouse.chr6 54438 7 + 636262 GGTTTAA -s Anc0.Anc0refChr4 2436 7 - 45765 GGATTAA -s Anc1.Anc1refChr2 33138 7 + 144309 GGATTAA -s Anc2.Anc2refChr0 55462 7 + 56053 GGATTAA -s mr.mrrefChr0 52070 7 + 130230 GGTTTAA -s simCow_chr6.simCow.chr6 59070 7 + 602619 GGTTTGA -s simDog_chr6.simDog.chr6 53033 7 + 593897 GGATTAA -s simMouse_chr6.simMouse.chr6 54632 7 + 636262 GGTTGAA -s simRat_chr6.simRat.chr6 47560 6 + 647215 GGAGTA- - -a -s simMouse_chr6.simMouse.chr6 54445 8 + 636262 AAGGACTG -s Anc0.Anc0refChr4 2443 8 - 45765 AAGTGTTA -s Anc1.Anc1refChr2 33145 8 + 144309 AAGTGTTA -s Anc2.Anc2refChr0 55472 8 + 56053 AAGTGTTA -s mr.mrrefChr0 52077 8 + 130230 AAGGACTG -s simCow_chr6.simCow.chr6 59080 8 + 602619 AAGTGTCA -s simDog_chr6.simDog.chr6 53043 8 + 593897 AAGTGTTA -s simHuman_chr6.simHuman.chr6 53306 1 + 601863 -------A -s simMouse_chr6.simMouse.chr6 54639 8 + 636262 AAGGAATG - -a -s simMouse_chr6.simMouse.chr6 54453 10 + 636262 CTGACATCCT -s Anc0.Anc0refChr4 2451 10 - 45765 CTGACATCCT -s Anc1.Anc1refChr2 33153 10 + 144309 CTGACATCCT -s Anc2.Anc2refChr0 55480 10 + 56053 CTAACATCCT -s mr.mrrefChr0 52085 10 + 130230 CTGACATCCT -s simCow_chr6.simCow.chr6 59088 7 + 602619 ---ACATCGT -s simDog_chr6.simDog.chr6 53055 10 + 593897 CTAACACCCT -s simHuman_chr6.simHuman.chr6 53307 10 + 601863 CTGACATCCT -s simMouse_chr6.simMouse.chr6 54647 10 + 636262 CTGACATCTT -s simRat_chr6.simRat.chr6 47566 4 + 647215 ------TCCT - -a -s simMouse_chr6.simMouse.chr6 54463 4 + 636262 AAAC -s Anc0.Anc0refChr4 2461 4 - 45765 AAAC -s Anc1.Anc1refChr2 33163 4 + 144309 AAAC -s Anc2.Anc2refChr0 55490 4 + 56053 AAAC -s mr.mrrefChr0 52095 4 + 130230 AAAC -s simCow_chr6.simCow.chr6 59095 4 + 602619 TAAC -s simDog_chr6.simDog.chr6 53065 4 + 593897 AAGC -s simHuman_chr6.simHuman.chr6 53317 4 + 601863 AAAC -s simMouse_chr6.simMouse.chr6 54658 4 + 636262 AAAC -s simRat_chr6.simRat.chr6 47570 4 + 647215 GAAC - -a -s simMouse_chr6.simMouse.chr6 54467 9 + 636262 TATTGTTGG -s Anc0.Anc0refChr4 2466 9 - 45765 TATTGTTGG -s Anc1.Anc1refChr2 33168 9 + 144309 TATTGTTGG -s Anc2.Anc2refChr0 55495 9 + 56053 TATTGTTGG -s mr.mrrefChr0 52100 9 + 130230 TATTGTTGG -s simCow_chr6.simCow.chr6 59100 9 + 602619 TATTGTGGA -s simDog_chr6.simDog.chr6 53070 9 + 593897 TACTGTTGG -s simHuman_chr6.simHuman.chr6 53322 9 + 601863 AATTGTTGG -s simMouse_chr6.simMouse.chr6 54663 9 + 636262 TATTGTTGG -s simRat_chr6.simRat.chr6 47575 9 + 647215 TATTATTGT - -a -s simMouse_chr6.simMouse.chr6 54476 12 + 636262 AGATATGAGGTG -s Anc0.Anc0refChr4 2475 12 - 45765 AGTTTTAAAACA -s Anc1.Anc1refChr2 33177 12 + 144309 AGTTTTAAAACA -s Anc2.Anc2refChr0 55504 12 + 56053 TGTTTTAAAACA -s mr.mrrefChr0 52109 12 + 130230 AGATATGAGATG -s simCow_chr6.simCow.chr6 59119 12 + 602619 TGTTTCAAAACA -s simDog_chr6.simDog.chr6 53079 12 + 593897 TGATTTGAAACA -s simHuman_chr6.simHuman.chr6 53331 12 + 601863 AGTTGTAAAACA -s simMouse_chr6.simMouse.chr6 54672 12 + 636262 AGATATGAGATG -s simRat_chr6.simRat.chr6 47584 12 + 647215 AGATATGAGATG - -a -s simMouse_chr6.simMouse.chr6 54488 4 + 636262 CTGT -s Anc0.Anc0refChr4 2487 4 - 45765 GTGT -s Anc1.Anc1refChr2 33189 4 + 144309 GTGT -s Anc2.Anc2refChr0 55516 4 + 56053 GTGC -s mr.mrrefChr0 52121 4 + 130230 CTGT -s simCow_chr6.simCow.chr6 59140 4 + 602619 ATGC -s simDog_chr6.simDog.chr6 53091 4 + 593897 GTGC -s simHuman_chr6.simHuman.chr6 53343 4 + 601863 GTGT -s simMouse_chr6.simMouse.chr6 54684 4 + 636262 CTGT -s simRat_chr6.simRat.chr6 47596 4 + 647215 CTGT - -a -s simMouse_chr6.simMouse.chr6 54492 3 + 636262 CCT -s Anc0.Anc0refChr4 2492 2 - 45765 -CC -s Anc1.Anc1refChr2 33194 3 + 144309 CCC -s Anc2.Anc2refChr0 55521 2 + 56053 -CC -s mr.mrrefChr0 52126 3 + 130230 CCT -s simCow_chr6.simCow.chr6 59145 2 + 602619 -CC -s simDog_chr6.simDog.chr6 53096 2 + 593897 -CC -s simHuman_chr6.simHuman.chr6 53348 3 + 601863 CCC -s simMouse_chr6.simMouse.chr6 54689 3 + 636262 CCT -s simRat_chr6.simRat.chr6 47601 3 + 647215 CCT - -a -s simMouse_chr6.simMouse.chr6 54495 12 + 636262 AAAGACTTTCCT -s Anc0.Anc0refChr4 2494 12 - 45765 AAAGACTCTGTT -s Anc1.Anc1refChr2 33197 12 + 144309 AAAGACTCTGTT -s Anc2.Anc2refChr0 55523 12 + 56053 AAAGACTCTGTC -s mr.mrrefChr0 52129 12 + 130230 AAAGACTTTCCT -s simCow_chr6.simCow.chr6 59149 12 + 602619 GAAGAACCTGTC -s simDog_chr6.simDog.chr6 53098 12 + 593897 AAAGACTCTGTC -s simHuman_chr6.simHuman.chr6 53351 12 + 601863 AAAGACTCTATT -s simMouse_chr6.simMouse.chr6 54692 12 + 636262 AAAGAATATCCT -s simRat_chr6.simRat.chr6 47604 12 + 647215 AAAGACTTTCCT - -a -s simMouse_chr6.simMouse.chr6 54507 3 + 636262 CGA -s Anc0.Anc0refChr4 2527 3 - 45765 CTA -s Anc1.Anc1refChr2 33230 3 + 144309 CTA -s Anc2.Anc2refChr0 55556 3 + 56053 CTA -s mr.mrrefChr0 52141 3 + 130230 CTA -s simCow_chr6.simCow.chr6 59182 3 + 602619 CTA -s simDog_chr6.simDog.chr6 53130 3 + 593897 CTG -s simHuman_chr6.simHuman.chr6 53384 3 + 601863 CTA -s simMouse_chr6.simMouse.chr6 54704 3 + 636262 CTA -s simRat_chr6.simRat.chr6 47616 3 + 647215 CTA - -a -s simMouse_chr6.simMouse.chr6 54510 61 + 636262 GGTAACAGTTATGTTGTTTGCTTTGCCCATATCATACTGGACCTAGGCACAGTTTGATTAT -s Anc0.Anc0refChr4 2530 60 - 45765 GGTTATAATCATGTTGTT-GTTTTGCCCATGCCATACTGGACCAAGGCACAATTTGATTAT -s Anc1.Anc1refChr2 33233 60 + 144309 GGTTATAATCATGTTGTT-GTTTTGCCCATGCCATACTGGACCAAGGCACAATTTGATTAT -s Anc2.Anc2refChr0 55559 60 + 56053 GGTTATAATCATGTTGTT-ATTTTGCCCATGCCATAATGAACCAAGGCACAATTTGATTCT -s mr.mrrefChr0 52144 61 + 130230 GGTAACCGTTATGTTGTTTGCTTTGCCCATACCATACTGGACCAAGGCACAGTTTGATTAT -s simCow_chr6.simCow.chr6 59196 60 + 602619 TGTTATTATTATGTTGTT-ATTTTGCCCATGCCATAATGAACCAAAGGGCAGTTTGAATCC -s simDog_chr6.simDog.chr6 53133 60 + 593897 GGCTATAGTCGTGTTGTT-ATTTTGCCCATGCCATAATGAACTGAGGCACAATTTAATTCT -s simHuman_chr6.simHuman.chr6 53387 60 + 601863 GGTCATGATCATGTTGTT-GTCTTGCCCATGCCATACTGGACCAAGGCACAATTTGATTAT -s simMouse_chr6.simMouse.chr6 54707 61 + 636262 GGTAACCATTATGTTGTTTGCTTTGCATGTACCATACTGGACCAAGGCACAGTTTGATTAG -s simRat_chr6.simRat.chr6 47619 60 + 647215 GGTAACCGTTATGTTGTTTGCTTTGCCCATGCTATACTGGACTAAGGCACAGTTTGATAA- - -a -s simMouse_chr6.simMouse.chr6 54571 2 + 636262 TG -s Anc0.Anc0refChr4 2590 2 - 45765 CA -s Anc1.Anc1refChr2 33293 2 + 144309 CA -s Anc2.Anc2refChr0 55619 2 + 56053 CA -s mr.mrrefChr0 52205 2 + 130230 TG -s simCow_chr6.simCow.chr6 59256 2 + 602619 CA -s simDog_chr6.simDog.chr6 53197 2 + 593897 CA -s simHuman_chr6.simHuman.chr6 53447 2 + 601863 CA -s simMouse_chr6.simMouse.chr6 54768 2 + 636262 TG - -a -s simMouse_chr6.simMouse.chr6 54573 3 + 636262 CAT -s mr.mrrefChr0 52236 3 + 130230 TAT -s simMouse_chr6.simMouse.chr6 54818 3 + 636262 TAT -s simRat_chr6.simRat.chr6 47708 3 + 647215 TAT - -a -s simMouse_chr6.simMouse.chr6 54576 2 + 636262 AG -s Anc0.Anc0refChr4 2375 2 - 45765 AG -s Anc1.Anc1refChr2 33077 2 + 144309 AG -s Anc2.Anc2refChr0 55400 2 + 56053 AG -s mr.mrrefChr0 52014 2 + 130230 AG -s simCow_chr6.simCow.chr6 59008 2 + 602619 AG -s simDog_chr6.simDog.chr6 52951 2 + 593897 AG -s simHuman_chr6.simHuman.chr6 53251 2 + 601863 AG -s simRat_chr6.simRat.chr6 47504 2 + 647215 AG - -a -s simMouse_chr6.simMouse.chr6 54657 1 + 636262 T - -a -s simMouse_chr6.simMouse.chr6 54662 1 + 636262 A -s Anc0.Anc0refChr4 2465 1 - 45765 A -s Anc1.Anc1refChr2 33167 1 + 144309 A -s Anc2.Anc2refChr0 55494 1 + 56053 A -s mr.mrrefChr0 52099 1 + 130230 A -s simCow_chr6.simCow.chr6 59099 1 + 602619 A -s simDog_chr6.simDog.chr6 53069 1 + 593897 A -s simHuman_chr6.simHuman.chr6 53321 1 + 601863 A -s simRat_chr6.simRat.chr6 47574 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 54688 1 + 636262 T -s Anc0.Anc0refChr4 2491 1 - 45765 T -s Anc1.Anc1refChr2 33193 1 + 144309 T -s Anc2.Anc2refChr0 55520 1 + 56053 T -s mr.mrrefChr0 52125 1 + 130230 T -s simCow_chr6.simCow.chr6 59144 1 + 602619 A -s simDog_chr6.simDog.chr6 53095 1 + 593897 T -s simHuman_chr6.simHuman.chr6 53347 1 + 601863 T -s simRat_chr6.simRat.chr6 47600 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 54770 48 + 636262 ATAGAATATGTGATAGGTGTCACACTTTGGTTATCACACAAATTTGGT -s Anc0.Anc0refChr4 2592 1 - 45765 -------------------T---------------------------- -s Anc1.Anc1refChr2 33295 1 + 144309 -------------------T---------------------------- -s Anc2.Anc2refChr0 55621 1 + 56053 -------------------G---------------------------- -s mr.mrrefChr0 52207 29 + 130230 -------------------TCACACTTTGGTTATCACACAAATTTGGT -s simCow_chr6.simCow.chr6 59258 1 + 602619 -------------------C---------------------------- -s simDog_chr6.simDog.chr6 53199 1 + 593897 -------------------G---------------------------- -s simHuman_chr6.simHuman.chr6 53449 1 + 601863 -------------------T---------------------------- -s simRat_chr6.simRat.chr6 47679 29 + 647215 -------------------TCACACTTTGATTATCACATAAGTTTGAT - -a -s simMouse_chr6.simMouse.chr6 54821 26 + 636262 TGCACAGCATCTTGTCATTGTCTAGA -s Anc0.Anc0refChr4 2593 23 - 45765 ---ACAGCATCTTGTCATTGTCTAGA -s Anc1.Anc1refChr2 33296 23 + 144309 ---ACAGCATCTTGTCATTGTCTAGA -s Anc2.Anc2refChr0 55622 23 + 56053 ---ACAGCACCTTGTCATTGTCTAGA -s mr.mrrefChr0 52239 26 + 130230 TGCACAGCATCTTGTCATTGTCTAGA -s simCow_chr6.simCow.chr6 59259 23 + 602619 ---ATGGTACCTTGTCATTGTCGAGA -s simDog_chr6.simDog.chr6 53200 23 + 593897 ---ACAGCACCTTGTCACTGTTTAGA -s simHuman_chr6.simHuman.chr6 53450 23 + 601863 ---ACAGCATCTTGTCGTTGTCTAGA -s simRat_chr6.simRat.chr6 47711 26 + 647215 TGCACACCACCTTGTCATTGTTGAGA - -a -s simMouse_chr6.simMouse.chr6 54847 5 + 636262 ATATG -s Anc0.Anc0refChr4 2617 5 - 45765 TTATG -s Anc1.Anc1refChr2 33320 5 + 144309 TTATG -s Anc2.Anc2refChr0 55646 5 + 56053 TTATG -s mr.mrrefChr0 52265 5 + 130230 TTATG -s simCow_chr6.simCow.chr6 59283 5 + 602619 TTATG -s simDog_chr6.simDog.chr6 53224 5 + 593897 TTATA -s simHuman_chr6.simHuman.chr6 53474 5 + 601863 TTATG -s simRat_chr6.simRat.chr6 47737 5 + 647215 TTATG - -a -s simMouse_chr6.simMouse.chr6 54852 18 + 636262 TCCAAGGACCCATAGGCA -s Anc0.Anc0refChr4 2624 17 - 45765 -CCAAGGTCTCATAATTA -s Anc1.Anc1refChr2 33327 17 + 144309 -CCAAGGTCTCATAATTA -s Anc2.Anc2refChr0 55653 17 + 56053 -CCAAGGTCTCATAATTA -s mr.mrrefChr0 52272 18 + 130230 TCCAAGGACCCATAGGCA -s simCow_chr6.simCow.chr6 59291 17 + 602619 -CCAAGGTCTCATAATTA -s simDog_chr6.simDog.chr6 53231 17 + 593897 -TCAAACTCTCATAAATC -s simHuman_chr6.simHuman.chr6 53481 17 + 601863 -CCAAGGTCTCATAATTA -s simRat_chr6.simRat.chr6 47744 18 + 647215 TCCAAGGACCCATAGGCA - -a -s simMouse_chr6.simMouse.chr6 54870 9 + 636262 TAAAATATA -s Anc0.Anc0refChr4 2645 9 - 45765 TAAAATATA -s Anc1.Anc1refChr2 33348 9 + 144309 TAAAATATA -s Anc2.Anc2refChr0 55674 9 + 56053 CAAAATAAG -s mr.mrrefChr0 52290 9 + 130230 TAAAATATA -s simCow_chr6.simCow.chr6 59312 9 + 602619 GAAAATAAG -s simDog_chr6.simDog.chr6 53252 9 + 593897 CAAAAAAAG -s simHuman_chr6.simHuman.chr6 53502 9 + 601863 TAAAATATA -s simRat_chr6.simRat.chr6 47762 9 + 647215 TGAAATATA - -a -s simMouse_chr6.simMouse.chr6 54879 21 + 636262 ACAACCAATAGGCAATGTGAG -s Anc0.Anc0refChr4 2658 21 - 45765 ACACCCAATAGATACTGTGAG -s Anc1.Anc1refChr2 33361 21 + 144309 ACACCCAATAGATACTGTGAG -s Anc2.Anc2refChr0 55687 21 + 56053 ACACCCAGCTGATACTGAGGG -s mr.mrrefChr0 52299 21 + 130230 ACAACCAATAGGCAATGTGAG -s simCow_chr6.simCow.chr6 59325 17 + 602619 GCCCCCAG----TAATGTTGG -s simDog_chr6.simDog.chr6 53265 21 + 593897 ACACTCAGCTGATACTGAGGG -s simHuman_chr6.simHuman.chr6 53515 21 + 601863 ATACCTAATAGTTACTGTTAG -s simRat_chr6.simRat.chr6 47771 21 + 647215 ACAACCAATAGGCAATGTCAG - -a -s simMouse_chr6.simMouse.chr6 54900 1 + 636262 A -s Anc0.Anc0refChr4 2686 1 - 45765 A -s Anc1.Anc1refChr2 33389 1 + 144309 A -s Anc2.Anc2refChr0 55729 1 + 56053 A -s mr.mrrefChr0 52320 1 + 130230 A -s simCow_chr6.simCow.chr6 59363 1 + 602619 G -s simDog_chr6.simDog.chr6 53307 1 + 593897 A -s simHuman_chr6.simHuman.chr6 53543 1 + 601863 A -s simRat_chr6.simRat.chr6 47792 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 54901 5 + 636262 ACAGG -s Anc0.Anc0refChr4 2687 5 - 45765 ACAGG -s Anc1.Anc1refChr2 33390 5 + 144309 ACAGG -s Anc2.Anc2refChr0 55733 5 + 56053 ATAGG -s mr.mrrefChr0 52321 5 + 130230 ACAGG -s simCow_chr6.simCow.chr6 59367 5 + 602619 GTGGG -s simDog_chr6.simDog.chr6 53311 5 + 593897 ATAAG -s simHuman_chr6.simHuman.chr6 53544 5 + 601863 ACAGG -s simRat_chr6.simRat.chr6 47824 5 + 647215 ACAGG - -a -s simMouse_chr6.simMouse.chr6 54906 49 + 636262 ACAGTAGTGAGTCACCTGGCACTAAATTGGTGCACCAGCTCAGATATAG -s Anc0.Anc0refChr4 2692 49 - 45765 ACCGTAAAGGACTGCTTGGCGCTAAACTGATGCACTAGTTCAGGTATAG -s Anc1.Anc1refChr2 33395 49 + 144309 ACCGTAAAGGACTGCTTGGCGCTAAACTGATGCACTAGTTCAGGTATAG -s Anc2.Anc2refChr0 55742 49 + 56053 ACCGTAAAGGACTGCTTGTGGCTAAACCAATGCACTAGTTTAGGTATAG -s mr.mrrefChr0 52326 49 + 130230 ACAGTAGTGAATCACCTGGCACTAAATTGGTGCACCAGCTCAGATATAG -s simCow_chr6.simCow.chr6 59376 49 + 602619 ACAGTAAAGGACTGCTTGAAGCTAAACCAATGCAATAGTTTCGATATGG -s simDog_chr6.simDog.chr6 53320 49 + 593897 ACCGTGAAGGACTGCTTGTGGCTAAGCCAATGCACTAGTTTAGGTAGAA -s simHuman_chr6.simHuman.chr6 53549 49 + 601863 ATTATAAGTGACTGCTTGGCGCTAAACTGATGCACTAGTTCAGGTATAG -s simRat_chr6.simRat.chr6 47829 49 + 647215 ACAGTAGTGAATCACCTGGTATTAAATTGGTGCACCAGCTCAGATATAG - -a -s simMouse_chr6.simMouse.chr6 54955 1 + 636262 G -s Anc0.Anc0refChr4 2754 1 - 45765 G -s Anc1.Anc1refChr2 33457 1 + 144309 G -s Anc2.Anc2refChr0 55804 1 + 56053 G -s mr.mrrefChr0 52375 1 + 130230 G -s simCow_chr6.simCow.chr6 59438 1 + 602619 G -s simDog_chr6.simDog.chr6 53392 1 + 593897 A -s simHuman_chr6.simHuman.chr6 53611 1 + 601863 G -s simRat_chr6.simRat.chr6 47878 1 + 647215 G - -a -s simMouse_chr6.simMouse.chr6 54956 23 + 636262 AAATTCGAGGACTATCATCATTA -s Anc0.Anc0refChr4 2755 15 - 45765 AAAACCAAGGACTAT-------- -s Anc1.Anc1refChr2 33458 15 + 144309 AAAACCAAGGACTAT-------- -s Anc2.Anc2refChr0 55805 15 + 56053 AAAACCAAGGACTAT-------- -s mr.mrrefChr0 52376 23 + 130230 AAATTCGAGGACTATCATCATTA -s simCow_chr6.simCow.chr6 59439 15 + 602619 AAAACCAGCGGCAAT-------- -s simDog_chr6.simDog.chr6 53393 15 + 593897 ATTGCCAAGGACTAT-------- -s simHuman_chr6.simHuman.chr6 53612 15 + 601863 AAAACCAAGGACTAC-------- -s simRat_chr6.simRat.chr6 48100 23 + 647215 AAATCTGAGGACTATCGTCATTA - -a -s simMouse_chr6.simMouse.chr6 54979 38 + 636262 TTTACTTCCTACTGAGTATGTGCCAGGCCTACATATTT -s Anc0.Anc0refChr4 2770 17 - 45765 ---------------------ACAAGGCAGAATGACTT -s Anc1.Anc1refChr2 33473 17 + 144309 ---------------------ACAAGGCAGAATGACTT -s Anc2.Anc2refChr0 55820 17 + 56053 ---------------------ACAAGGCAGAATGTCTT -s mr.mrrefChr0 52399 38 + 130230 TTTACTTCCTACTGAGTATGTGCCAGGCCTACATATTT -s simCow_chr6.simCow.chr6 59454 16 + 602619 ---------------------ACAAGGCA-AATGTCTT -s simDog_chr6.simDog.chr6 53408 17 + 593897 ---------------------ACAAAGTAGAATGTCCT -s simHuman_chr6.simHuman.chr6 53627 17 + 601863 ---------------------ACAAGGCAGAATGACTT -s simRat_chr6.simRat.chr6 48124 38 + 647215 TTTGCTTCACACTTAGTATGTGCCAGGTCTAAATCTGA - -a -s simMouse_chr6.simMouse.chr6 55017 30 + 636262 TTCCACTGAGTATGTACCAGGTGTGCAACT -s Anc0.Anc0refChr4 2787 5 - 45765 GTCTA------------------------- -s Anc1.Anc1refChr2 33490 5 + 144309 GTCTA------------------------- -s Anc2.Anc2refChr0 55839 5 + 56053 GTATA------------------------- -s mr.mrrefChr0 52437 30 + 130230 TTCCACTGAGTATGTACCAGGTGTGCAACT -s simCow_chr6.simCow.chr6 59472 5 + 602619 TTATA------------------------- -s simDog_chr6.simDog.chr6 53427 5 + 593897 GTATA------------------------- -s simHuman_chr6.simHuman.chr6 53644 5 + 601863 GTCTA------------------------- -s simRat_chr6.simRat.chr6 48162 30 + 647215 TTTCACTGAGTATGTGCTAGGCCTGCAACC - -a -s simMouse_chr6.simMouse.chr6 55047 1 + 636262 G -s Anc0.Anc0refChr4 2792 1 - 45765 G -s Anc1.Anc1refChr2 33495 1 + 144309 G -s Anc2.Anc2refChr0 55844 1 + 56053 G -s mr.mrrefChr0 52467 1 + 130230 G -s simCow_chr6.simCow.chr6 59484 1 + 602619 G -s simDog_chr6.simDog.chr6 53432 1 + 593897 G -s simHuman_chr6.simHuman.chr6 53649 1 + 601863 G -s simRat_chr6.simRat.chr6 48192 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 55048 155 + 636262 TTCCTTCATTACTAGTATAAAACAGCTCATGCCCCTGAAATTTTTGCCTGCCTGTATCAGGCCTAAAAATGGTATTAATCTTCAGGGACTGCTCGGCATACCTATCTTTTGCATTCATTAGGTAGAATTGGCACAATGTCCACTGAAGCTCCATA -s Anc0.Anc0refChr4 2793 101 - 45765 TTCTGTCATCAATGATATAAAACAGCTCTTAGCCCTCAAGTTTTTGCTATGCTATATAAGAGTTAAAAATGATATTAAGATTCTTGGACAGCTGGACATCC------------------------------------------------------ -s Anc1.Anc1refChr2 33496 101 + 144309 TTCTGTCATCAATGATATAAAACAGCTCTTAGCCCTCAAGTTTTTGCTATGCTATATAAGAGTTAAAAATGATATTAAGATTCTTGGACAGCTGGACATCC------------------------------------------------------ -s Anc2.Anc2refChr0 55845 101 + 56053 TTCTGTCATCAATGATATAAAACAGCTCTTAGCCTTCAAGTTTTTGCTATGCCATATAAGAGTTAAAAATGATATTAAGATACTTGGACAGCAGCACATCC------------------------------------------------------ -s mr.mrrefChr0 52468 155 + 130230 TTCCTTCATTACTAGTATAAAACAGCTCATGCCCCTGAAATTTTTGCCTGCCTGTATCAGGCCTAAAAATGGTATTAATCTTCAGGGACTGCTCGGCATACCTATCTTTTGCATTCATTAGGTAGAATTGGCACAATGTCCACTGAAGCTCCATA -s simCow_chr6.simCow.chr6 59485 86 + 602619 TTTAATCATCAATAATATACAACAGTCATTAGTCTTCAAGTTTTTGTTAAGGCATATAAGAGTTAAATATAATATTAGAATAC---------------TCC------------------------------------------------------ -s simDog_chr6.simDog.chr6 53436 98 + 593897 TTCTGTCATCAATGACATAAGACAGCTCCTAGCCTTCAAGTTTTTCCTTTGCCATATAAAAGTTAAAAATGATATTAAG---CTTGGACAGCAGCACATCC------------------------------------------------------ -s simHuman_chr6.simHuman.chr6 53650 101 + 601863 TTCTGTCATCAGTGATGTAAAACAGCTCTTAAACCTTAAGTTTTTGCTATGCTATATAAGAATTAAAAGTGAGATAAAGGTTCTTGGCCAGTTGGCTATCC------------------------------------------------------ -s simRat_chr6.simRat.chr6 48193 155 + 647215 TTTCTTCGTTACTAGTATAAAACAGCTCATGCCCTTGAAATTATTGCATTGATGTATCAGACCTAAAAATGGTATTAATCTTCAGGGACTGCTGGGCATACGTGTCTCTTGCATTCAGTAGGTATAATTAGAGTAATATGCACTGAGGCTCCATG - -a -s simMouse_chr6.simMouse.chr6 55203 99 + 636262 TGACATCTAACACAGTATGCCCCTTGTGATTGGCTCACCAGAAGATTGAGTTTAAATGCAATTGTGTGTCTATATACATTGAGCGGCCAACGTTGTATG -s mr.mrrefChr0 52623 99 + 130230 TGACATCTAACACAGTATGCCCCTTGTGATTGGCTCACCAGAAGATTGAGTTTAAATGCAATTGTGTGTCTATATACATTGAGCGGCCAACGTTGTATG -s simRat_chr6.simRat.chr6 48349 99 + 647215 TGACAACTAACACAGTATCTCCCGTGTGAATGGCCCACAAGAGGATTCAGTCGAAGAGCAATTGTGTGGCTGTATACAATGAATGGCCAACATTGAATG - -a -s simMouse_chr6.simMouse.chr6 55302 73 + 636262 CCATGAGTGCCTATTGGATCTCTTAACTTGGCGCGGGCAGGTTGCACCCCATGTAAGCTGAAACTACACTATT -s Anc0.Anc0refChr4 2894 8 - 45765 -----------------------------------------------------------------ACATTCTC -s Anc1.Anc1refChr2 33597 8 + 144309 -----------------------------------------------------------------ACATTCTC -s Anc2.Anc2refChr0 55946 8 + 56053 -----------------------------------------------------------------ACATTCTC -s mr.mrrefChr0 52722 73 + 130230 CCATGAGTGCCTATTGGATCTCTTAACTTGGCGCGGGCAGGTTGCACCCCATGTAAGCTGAAACTACACTATT -s simCow_chr6.simCow.chr6 59571 8 + 602619 -----------------------------------------------------------------ACATTCTT -s simDog_chr6.simDog.chr6 53534 8 + 593897 -----------------------------------------------------------------ACATTCAC -s simHuman_chr6.simHuman.chr6 53751 8 + 601863 -----------------------------------------------------------------ACATTCTC -s simRat_chr6.simRat.chr6 48487 73 + 647215 ACATAGGTGCCTATTGGATCTCTTAACTCGGCACGGGCAGGTTGTGCCCCATGTAAACCGAAGGCACATTATT - -a -s simMouse_chr6.simMouse.chr6 55375 7 + 636262 GCAATCA -s Anc0.Anc0refChr4 2902 7 - 45765 GGTAGTA -s Anc1.Anc1refChr2 33605 7 + 144309 GGTAGTA -s Anc2.Anc2refChr0 55964 7 + 56053 GGTTGTA -s mr.mrrefChr0 52795 7 + 130230 GCAATTA -s simCow_chr6.simCow.chr6 59589 5 + 602619 GG--GTA -s simDog_chr6.simDog.chr6 53552 7 + 593897 GGTTGTA -s simHuman_chr6.simHuman.chr6 53759 7 + 601863 GGTAGTA -s simRat_chr6.simRat.chr6 48560 7 + 647215 GCAATTA - -a -s simMouse_chr6.simMouse.chr6 55382 11 + 636262 GGCAGAGCCTG -s Anc0.Anc0refChr4 2910 11 - 45765 GGCAGAACCTG -s Anc1.Anc1refChr2 33613 11 + 144309 GGCAGAACCTG -s Anc2.Anc2refChr0 55972 11 + 56053 GGCAGAACCTG -s mr.mrrefChr0 52803 11 + 130230 GGCAGAGCCTG -s simCow_chr6.simCow.chr6 59595 11 + 602619 AGCAGAACCTG -s simDog_chr6.simDog.chr6 53560 11 + 593897 GGCAGTACCTG -s simHuman_chr6.simHuman.chr6 53767 11 + 601863 GGCAGAACCTT -s simRat_chr6.simRat.chr6 48568 11 + 647215 GGCAGGGCCTG - -a -s simMouse_chr6.simMouse.chr6 55393 13 + 636262 TAGATAACCTGCT -s Anc0.Anc0refChr4 2922 13 - 45765 TATACCACCTGTT -s Anc1.Anc1refChr2 33625 13 + 144309 TATACCACCTGTT -s Anc2.Anc2refChr0 55984 13 + 56053 TATACCAGACGTT -s mr.mrrefChr0 52815 13 + 130230 TAGACAACCTGCT -s simCow_chr6.simCow.chr6 59607 12 + 602619 TAT-CCATGTGCT -s simDog_chr6.simDog.chr6 53572 13 + 593897 TATACCAGACGTT -s simHuman_chr6.simHuman.chr6 53779 13 + 601863 TATACCACCTGAT -s simRat_chr6.simRat.chr6 48580 13 + 647215 TAAACAACCTGCT - -a -s simMouse_chr6.simMouse.chr6 55406 5 + 636262 GTAAT -s Anc0.Anc0refChr4 2935 5 - 45765 GTAAT -s Anc1.Anc1refChr2 33638 5 + 144309 GTAAT -s Anc2.Anc2refChr0 55997 5 + 56053 GTAAT -s mr.mrrefChr0 52828 5 + 130230 GTAAT -s simCow_chr6.simCow.chr6 59619 5 + 602619 GTAAT -s simDog_chr6.simDog.chr6 53585 5 + 593897 GCAAC -s simHuman_chr6.simHuman.chr6 53809 5 + 601863 GTAGT -s simRat_chr6.simRat.chr6 48593 5 + 647215 GTAAT - -a -s simMouse_chr6.simMouse.chr6 55411 9 + 636262 GACTGCTAT -s Anc0.Anc0refChr4 2940 9 - 45765 GACTGCTAT -s Anc1.Anc1refChr2 33643 9 + 144309 GACTGCTAT -s Anc2.Anc2refChr0 56002 9 + 56053 AACTGTTGT -s mr.mrrefChr0 52833 9 + 130230 GACTGCTAT -s simCow_chr6.simCow.chr6 59624 9 + 602619 AACTGTCTT -s simDog_chr6.simDog.chr6 53590 9 + 593897 AACCGTTGT -s simHuman_chr6.simHuman.chr6 53814 9 + 601863 GACTGCTAT -s simRat_chr6.simRat.chr6 48601 9 + 647215 GACTGCTAT - -a -s simMouse_chr6.simMouse.chr6 55420 3 + 636262 AGA -s Anc0.Anc0refChr4 2949 3 - 45765 GGA -s Anc1.Anc1refChr2 33652 3 + 144309 GGA -s Anc2.Anc2refChr0 56012 3 + 56053 GGA -s mr.mrrefChr0 52842 3 + 130230 AGA -s simCow_chr6.simCow.chr6 59634 3 + 602619 GGA -s simDog_chr6.simDog.chr6 53600 3 + 593897 GGA -s simHuman_chr6.simHuman.chr6 53823 3 + 601863 GGG -s simRat_chr6.simRat.chr6 48610 3 + 647215 AGA - -a -s simMouse_chr6.simMouse.chr6 55423 26 + 636262 GCATATCAAGGTTATGGCCAACAATG -s Anc0.Anc0refChr4 2952 26 - 45765 GTATGTAAAGGTTACTGCCAACATTG -s Anc1.Anc1refChr2 33655 26 + 144309 GTATGTAAAGGTTACTGCCAACATTG -s Anc2.Anc2refChr0 56015 26 + 56053 ATATGTAAACGTTACTGCCAACAATC -s mr.mrrefChr0 52845 26 + 130230 GCATATCAAGGTTATGGCCAACATTG -s simCow_chr6.simCow.chr6 59637 25 + 602619 ATA-GCAAATGTTACTGCCAACAATC -s simDog_chr6.simDog.chr6 53603 26 + 593897 ACATGTAAACATTACTGCCAATAATC -s simHuman_chr6.simHuman.chr6 53833 26 + 601863 GTATGTTAGGGTTACTGCCACCATTG -s simRat_chr6.simRat.chr6 48613 26 + 647215 GCATATCAAGGTTATGGCCAACATTG - -a -s simMouse_chr6.simMouse.chr6 55449 9 + 636262 AACTTGCAA -s Anc0.Anc0refChr4 2978 9 - 45765 CCTTTACAA -s Anc1.Anc1refChr2 33681 9 + 144309 CCTTTACAA -s Anc2.Anc2refChr0 56041 9 + 56053 CCTTTACAA -s mr.mrrefChr0 52871 9 + 130230 ACCTTGCAA -s simCow_chr6.simCow.chr6 59665 9 + 602619 CCTTTACAA -s simDog_chr6.simDog.chr6 53629 9 + 593897 CCTTTACAA -s simHuman_chr6.simHuman.chr6 53859 8 + 601863 -CTTTACAA -s simRat_chr6.simRat.chr6 48639 9 + 647215 ACCTTGCAA - -a -s simMouse_chr6.simMouse.chr6 55458 15 + 636262 CTATAAACTTAACTA -s Anc0.Anc0refChr4 2987 3 - 45765 TTA------------ -s Anc1.Anc1refChr2 33690 3 + 144309 TTA------------ -s Anc2.Anc2refChr0 56050 3 + 56053 TCA------------ -s mr.mrrefChr0 52880 3 + 130230 CTA------------ -s simCow_chr6.simCow.chr6 59837 3 + 602619 tgA------------ -s simDog_chr6.simDog.chr6 53638 3 + 593897 TCA------------ -s simHuman_chr6.simHuman.chr6 53867 3 + 601863 TTA------------ -s simRat_chr6.simRat.chr6 48648 3 + 647215 CTA------------ - -a -s simMouse_chr6.simMouse.chr6 55473 44 + 636262 TAAACTTTTGAGAGCACTGGATAGTTTACATGCCTCGATAGTAC -s Anc0.Anc0refChr4 2990 44 - 45765 TAGGCTTTTGAGAGCATTGGAACACTCTCATGCCTTAATAGTAC -s Anc1.Anc1refChr2 33693 44 + 144309 TAGGCTTTTGAGAGCATTGGAACACTCTCATGCCTTAATAGTAC -s Anc2.Anc2refChr4 0 44 + 10050 CAGGCTTTTGAGAGCGTTGGAACACTCTCATGCCTTATTAGTAC -s mr.mrrefChr0 52883 44 + 130230 TAAACTTTTGAGAGCATTGGATAGTTTACATGCCTCGATAGTAC -s simCow_chr6.simCow.chr6 59840 44 + 602619 CAGGCTTTTGAGAGCGTTGGAAAATTCTAATGCCTCATTATAAC -s simDog_chr6.simDog.chr6 56622 44 + 593897 CAGGCTCTTGATAGTGTTGGAACACTTTCATGCCTTATTAGTAT -s simHuman_chr6.simHuman.chr6 53870 37 + 601863 TAGGCTTTTGAGAGCATT-------TCTCATGCCTTAATAGGAC -s simRat_chr6.simRat.chr6 48651 44 + 647215 TAAATTTTTAAGAGCATTGGACAGTTTACATGCCTCGATAGTAC - -a -s simMouse_chr6.simMouse.chr6 55517 32 + 636262 TTAGAAACGTTTTCATAAGCATGAATTATTGA -s Anc0.Anc0refChr4 3034 32 - 45765 TTAGAAATGTTGTCATAAAAATAAATTATTGG -s Anc1.Anc1refChr2 33737 32 + 144309 TTAGAAATGTTGTCATAAAAATAAATTATTGG -s Anc2.Anc2refChr4 44 32 + 10050 TTAGGAATGTTGTCATAAAAATGAATTATTGG -s mr.mrrefChr0 52927 32 + 130230 TTAGAAATGTTTTCATAAGCATAAATTATTGG -s simCow_chr6.simCow.chr6 60048 32 + 602619 TTAGGAATGTTATCATAAAAATGAATTATTGG -s simDog_chr6.simDog.chr6 56666 32 + 593897 TTAGGCAAGTTGTCATAAGAATGAATTCTTGG -s simHuman_chr6.simHuman.chr6 53907 32 + 601863 TTAGAAATGTTGTCATAAAAGCAAATTAATCG -s simRat_chr6.simRat.chr6 48695 32 + 647215 TTAGAAATGCTTGCACAAGCATAAATTATTGG - -a -s simMouse_chr6.simMouse.chr6 55549 18 + 636262 TTTTTCGGGCTTTTCAAG -s Anc0.Anc0refChr4 3066 18 - 45765 ATTCTCTAGCTTTTCAAA -s Anc1.Anc1refChr2 33769 18 + 144309 ATTCTCTAGCTTTTCAAA -s Anc2.Anc2refChr4 76 18 + 10050 ATTCTCTAGCTTTTCAAA -s mr.mrrefChr0 52959 18 + 130230 TTTTTCTGGCTTTTCAAG -s simCow_chr6.simCow.chr6 60084 18 + 602619 ATTTTGCAGCCTTTCAAA -s simDog_chr6.simDog.chr6 56698 18 + 593897 ATTCTCTGGCTTTTCAAA -s simHuman_chr6.simHuman.chr6 53939 18 + 601863 ATTCTCTAGCTTTTAGAA -s simRat_chr6.simRat.chr6 48727 18 + 647215 TTTTTCTGGCTTTTCAAG - -a -s simMouse_chr6.simMouse.chr6 55567 6 + 636262 ATCATG -s Anc0.Anc0refChr4 3084 6 - 45765 ATCCTG -s Anc1.Anc1refChr2 33787 6 + 144309 ATCCTG -s Anc2.Anc2refChr4 94 6 + 10050 ATCCTG -s mr.mrrefChr0 52977 6 + 130230 ATCATG -s simCow_chr6.simCow.chr6 60104 6 + 602619 ATCCTG -s simDog_chr6.simDog.chr6 56716 6 + 593897 AAGCTG -s simHuman_chr6.simHuman.chr6 53957 6 + 601863 ATCCTG -s simRat_chr6.simRat.chr6 48745 6 + 647215 ATCATG - -a -s simMouse_chr6.simMouse.chr6 55573 3 + 636262 GGT -s Anc0.Anc0refChr4 3091 3 - 45765 GGT -s Anc1.Anc1refChr2 33794 3 + 144309 GGT -s Anc2.Anc2refChr4 101 3 + 10050 GGT -s mr.mrrefChr0 52983 3 + 130230 GGT -s simCow_chr6.simCow.chr6 60111 3 + 602619 GGT -s simDog_chr6.simDog.chr6 56723 3 + 593897 GGC -s simHuman_chr6.simHuman.chr6 53964 3 + 601863 GGT -s simRat_chr6.simRat.chr6 48751 3 + 647215 GAT - -a -s simMouse_chr6.simMouse.chr6 55576 75 + 636262 TCTAACTAACTACACCACTTGTTCTGAGGAATTAATACTAAGGGGGATGACATTTCCCTAGCTATCAGAGCATTG -s Anc0.Anc0refChr4 3101 61 - 45765 T--AATTA-CTGCT--ACTCGTTCTGAGGAAGTGACACAAGGGGGGAGGGCATTTCCAGATC---------TTTG -s Anc1.Anc1refChr2 33804 63 + 144309 T--AATTA-CTGCTCCACTCGTTCTGAGGAAGTGACACAAGGGGGGAGGGCATTTCCAGATC---------TTTG -s Anc2.Anc2refChr4 111 61 + 10050 T--AATTA-TTGCT--ACCCATTCTGAGGAAGTGACACAAGTGGTGAGGGCATTTCCAGATC---------TTTG -s mr.mrrefChr0 52993 75 + 130230 TCTAATTAACTACACCACTTGTTCTGAGGAATTAATACTAAGGGGGATGACATTTCCCTAGCTATCAGAGCATTG -s simCow_chr6.simCow.chr6 60121 60 + 602619 T--CATTG-GTC-T--ACCCCTTCTGAGGAAGTGACACAAGAGGTGAGGGCATTTCCAAATC---------TTCG -s simDog_chr6.simDog.chr6 56733 61 + 593897 T--AACTA-TTGCT--ACCCATCTTGAGGAAGTGACACGAGTGGTGGGGGCATTTCCAGATC---------CTTG -s simHuman_chr6.simHuman.chr6 53974 62 + 601863 T--AATTA-CTTCTCCTCT-GTTCTGATGAAGTGACACAAGGGGGGAGGGCATGTCCACATC---------TTTG -s simRat_chr6.simRat.chr6 48765 75 + 647215 TTTAATTAACTACACCACTTGTTCTGAGGAATTCATACTAAGGGAGATGACATTTTCCTAGCTATAGGGGCATTG - -a -s simMouse_chr6.simMouse.chr6 55651 45 + 636262 CCGGATGACATTGGTTGGCTTCCCGGGCCTGCAGAAGTACAAACC -s Anc0.Anc0refChr4 3162 25 - 45765 CGGAATGACCCATGCTG--------------------AACCAACC -s Anc1.Anc1refChr2 33867 25 + 144309 CGGAATGACCCATGCTG--------------------AACCAACC -s Anc2.Anc2refChr4 172 25 + 10050 GGGAATGACCCATGCTG--------------------CACCAACC -s mr.mrrefChr0 53068 45 + 130230 CCGGATGACATTGGTTGGCTTCCCGGACCTGCAGAAGAACAAACC -s simCow_chr6.simCow.chr6 60181 6 + 602619 AGGAGT--------------------------------------- -s simDog_chr6.simDog.chr6 56794 25 + 593897 GGAAATGACCCATGCTG--------------------CACCAACC -s simHuman_chr6.simHuman.chr6 54047 25 + 601863 CTGAATTATCCATGATG--------------------AACCAACC -s simRat_chr6.simRat.chr6 48840 44 + 647215 CTGGAGGGCATTGGTTGGCTTCCTGGACCTGCAGGAGAACAAAC- - -a -s simMouse_chr6.simMouse.chr6 55696 9 + 636262 ACCCAAGCA -s Anc0.Anc0refChr4 3187 9 - 45765 ACTAAAACA -s Anc1.Anc1refChr2 33892 9 + 144309 ACTAAAACA -s Anc2.Anc2refChr4 197 9 + 10050 ACTAAAACA -s mr.mrrefChr0 53113 9 + 130230 ACCCAAACA -s simDog_chr6.simDog.chr6 56820 9 + 593897 ACTAAAACA -s simHuman_chr6.simHuman.chr6 54072 9 + 601863 ACTAACACA -s simRat_chr6.simRat.chr6 48884 9 + 647215 GCCCAAACA - -a -s simMouse_chr6.simMouse.chr6 55705 6 + 636262 TGTTGT -s Anc0.Anc0refChr4 3196 6 - 45765 TGGTGC -s Anc1.Anc1refChr2 33901 6 + 144309 TGGTGC -s Anc2.Anc2refChr4 206 6 + 10050 TGGTGT -s mr.mrrefChr0 53122 6 + 130230 TGTTGC -s simDog_chr6.simDog.chr6 56843 6 + 593897 TGGTGT -s simHuman_chr6.simHuman.chr6 54081 6 + 601863 TGGTGC -s simRat_chr6.simRat.chr6 48893 6 + 647215 TGTTGC - -a -s simMouse_chr6.simMouse.chr6 55711 4 + 636262 GCCA -s Anc0.Anc0refChr4 3203 4 - 45765 ACTG -s Anc1.Anc1refChr2 33908 4 + 144309 ACTG -s Anc2.Anc2refChr4 213 4 + 10050 TCTG -s mr.mrrefChr0 53128 4 + 130230 ACTG -s simDog_chr6.simDog.chr6 56850 4 + 593897 TCTG -s simHuman_chr6.simHuman.chr6 54088 4 + 601863 ACTG -s simRat_chr6.simRat.chr6 48899 4 + 647215 ACTG - -a -s simMouse_chr6.simMouse.chr6 55715 11 + 636262 AAGATGGTTCT -s Anc0.Anc0refChr4 3207 11 - 45765 AAGGTGATGTT -s Anc1.Anc1refChr2 33912 11 + 144309 AAGGTGATGTT -s Anc2.Anc2refChr4 217 11 + 10050 AAGGTGATGTT -s mr.mrrefChr0 53132 11 + 130230 AAGATGATTCT -s simDog_chr6.simDog.chr6 56856 11 + 593897 AAGGTGATGTT -s simHuman_chr6.simHuman.chr6 54092 11 + 601863 AAGGTGATCTT -s simRat_chr6.simRat.chr6 48903 11 + 647215 AAGATAATTCT - -a -s simMouse_chr6.simMouse.chr6 55726 4 + 636262 GTTG -s Anc0.Anc0refChr4 3218 4 - 45765 TTTG -s Anc1.Anc1refChr2 33923 4 + 144309 TTTG -s Anc2.Anc2refChr4 228 4 + 10050 TCTG -s mr.mrrefChr0 53143 4 + 130230 GTTG -s simDog_chr6.simDog.chr6 56870 4 + 593897 TCTG -s simHuman_chr6.simHuman.chr6 54103 4 + 601863 TTTG -s simRat_chr6.simRat.chr6 48914 4 + 647215 GTTG - -a -s simMouse_chr6.simMouse.chr6 55730 62 + 636262 TCCTTCCACATGACAGCTTAAGGTAACAAAACACTCATTGGAAGGAGTGAAAGGGTGACTCA -s Anc0.Anc0refChr4 3229 47 - 45765 TCCTCCCAGATGACTGCTT-TGGTAAGAAAACCTTCATTGGAAGG--------------TCT -s Anc1.Anc1refChr2 33934 47 + 144309 TCCTCCCAGATGACTGCTT-TGGTAAGAAAACCTTCATTGGAAGG--------------TCT -s Anc2.Anc2refChr4 239 47 + 10050 TTCTCTCAGATGACTACTT-TGGAAAGAAAATCTTTATTGGGAAG--------------GTT -s mr.mrrefChr0 53147 62 + 130230 TCCTCCCACATGACAGCTTATGGTAACAAAACACTCATTGGAAGGAGTGAAAGGGTGACTCA -s simDog_chr6.simDog.chr6 56881 47 + 593897 TTCTCTCAGATGACTACTT-TGGAAAGAAAATCTTTATTGGGAAG--------------GTT -s simHuman_chr6.simHuman.chr6 54114 47 + 601863 TCCTCCCAGGTAGTGGCTT-TGGTAAGGAAGCCTTCATTGGAAGG--------------TCT -s simRat_chr6.simRat.chr6 48918 62 + 647215 CCCTCCCATATGACAGGTTATGGTAACAAAACACTCATTGGAATGAGTGAAACGGTGACTCA - -a -s simMouse_chr6.simMouse.chr6 55792 16 + 636262 CAGTCCACAGAGAGCG -s Anc0.Anc0refChr4 3276 16 - 45765 CACTCCACACACAAAG -s Anc1.Anc1refChr2 33981 16 + 144309 CACTCCACACACAAAG -s Anc2.Anc2refChr4 286 16 + 10050 CACTCCACACACAAAA -s mr.mrrefChr0 53209 16 + 130230 CAGTCCGCAGAGAGGG -s simCow_chr6.simCow.chr6 60187 11 + 602619 -----CTAATACAAAT -s simDog_chr6.simDog.chr6 56941 16 + 593897 CACTCCACACACAAAA -s simHuman_chr6.simHuman.chr6 54161 16 + 601863 CCCTCCACGCAAAAAG -s simRat_chr6.simRat.chr6 48980 14 + 647215 CAATGCGCT--GGAGC - -a -s simMouse_chr6.simMouse.chr6 55808 6 + 636262 AAAGGG -s Anc0.Anc0refChr4 3295 6 - 45765 ATGGGG -s Anc1.Anc1refChr2 34000 6 + 144309 ATGGGG -s Anc2.Anc2refChr4 305 6 + 10050 GTGTGG -s mr.mrrefChr0 53225 6 + 130230 AAGGGG -s simCow_chr6.simCow.chr6 60201 6 + 602619 CTATAA -s simDog_chr6.simDog.chr6 56960 6 + 593897 GGGTGG -s simHuman_chr6.simHuman.chr6 54180 6 + 601863 ATGGGG -s simRat_chr6.simRat.chr6 48994 6 + 647215 GAGTGG - -a -s simMouse_chr6.simMouse.chr6 55814 7 + 636262 CACTAAC -s Anc0.Anc0refChr4 3302 7 - 45765 CACAAAA -s Anc1.Anc1refChr2 34007 7 + 144309 CACAAAA -s Anc2.Anc2refChr4 312 7 + 10050 CACAAAA -s mr.mrrefChr0 53232 7 + 130230 CACAAAC -s simCow_chr6.simCow.chr6 60208 7 + 602619 CATAAGA -s simDog_chr6.simDog.chr6 56967 7 + 593897 TGCAAAA -s simHuman_chr6.simHuman.chr6 54187 7 + 601863 CACAAAT -s simRat_chr6.simRat.chr6 49001 7 + 647215 CACAAAC - -a -s simMouse_chr6.simMouse.chr6 55821 13 + 636262 CCATTATAGAGAT -s Anc0.Anc0refChr4 3309 13 - 45765 CGACTACTAAGGT -s Anc1.Anc1refChr2 34014 13 + 144309 CGACTACTAAGGT -s Anc2.Anc2refChr4 319 13 + 10050 TGACTACTAAGGT -s mr.mrrefChr0 53239 13 + 130230 CCACTATAGAGAT -s simCow_chr6.simCow.chr6 60215 13 + 602619 TGACTAATAAGGT -s simDog_chr6.simDog.chr6 56974 10 + 593897 TG---ACTAAGGT -s simHuman_chr6.simHuman.chr6 54196 13 + 601863 CAACCACTAAGGT -s simRat_chr6.simRat.chr6 49008 13 + 647215 CCGCTATAGAGAT - -a -s simMouse_chr6.simMouse.chr6 55834 4 + 636262 GTTC -s Anc0.Anc0refChr4 3325 4 - 45765 GTTC -s Anc1.Anc1refChr2 34030 4 + 144309 GTTC -s Anc2.Anc2refChr4 335 4 + 10050 GTTC -s mr.mrrefChr0 53252 4 + 130230 GTTC -s simCow_chr6.simCow.chr6 60231 4 + 602619 GTTC -s simDog_chr6.simDog.chr6 56987 4 + 593897 GTTC -s simHuman_chr6.simHuman.chr6 54212 4 + 601863 GTTC -s simRat_chr6.simRat.chr6 49021 4 + 647215 GTTC - -a -s simMouse_chr6.simMouse.chr6 55838 75 + 636262 TGGTACGCTCAATGATAAGGGCAAGGTCCCACCACTTAGGAGAGAGCAGCTTCAAAGTAGTCAGTAGTCATTAAA -s Anc0.Anc0refChr4 3338 50 - 45765 TAG-GCCCTCATTGGCAAGGGCAAGGCTCCACT-----------------TAAAGAATACTC-------ATAAAA -s Anc1.Anc1refChr2 34043 67 + 144309 TAG-GCCCTCATTGGCAAGGGCAAGGCTCCACTACTTAGGAGAGAGCAACTAAAGAATACTC-------ATAAAA -s Anc2.Anc2refChr4 348 50 + 10050 TAG-GCCCTCATTGGCAAGGGCAAGGCTCCACT-----------------TAAAACATACTC-------ACAAAA -s mr.mrrefChr0 53256 74 + 130230 TGG-GCCCTCAATGATAAGGGCAAGGCCCCACCACTTAGGAGAGAGCAACTTCAGAGTAGTCAGTAGTCATAAAA -s simCow_chr6.simCow.chr6 60244 40 + 602619 CGG-GCCCTCAAAAGCAAGGGCAAGGCCCCACT-----------------TA-----------------GCAGAA -s simDog_chr6.simDog.chr6 57000 50 + 593897 TAG-GTCCCCATTGGCAAGGGTAAGGCTCCACT-----------------TAAAACATACTC-------ACAAAA -s simHuman_chr6.simHuman.chr6 54225 61 + 601863 TAG-GCCCTCAGTGGCAAGGACGAGGC------ACTTAGGAGAGAGCAACTATAGACTAATC-------ATAAAA -s simRat_chr6.simRat.chr6 49025 74 + 647215 TGG-GCCCTCAATGCAAAGGGCAAGGCCCCACCACTTAGGAGAGAACAACTTCAGAGTAGTTAGTATTCATAAAA - -a -s simMouse_chr6.simMouse.chr6 55913 28 + 636262 AATTAGCTTAGCAAATTCAATTGGAAGT -s Anc0.Anc0refChr4 3388 28 - 45765 AATTTTCTTAGCAATCGTAATGGGGAGT -s Anc1.Anc1refChr2 34110 28 + 144309 AATTTTCTTAGCAATCGTAATGGGGAGT -s Anc2.Anc2refChr4 399 28 + 10050 AATTTTCTTAGCAATCTTAGTGGGGAGT -s mr.mrrefChr0 53330 28 + 130230 AATTAGCTTAGCAAATGCAATTGGAAGT -s simCow_chr6.simCow.chr6 60285 28 + 602619 AAAATTCTTAGGAATCTTGGTGGGGAGT -s simDog_chr6.simDog.chr6 57051 28 + 593897 AATTCCCTTAGCAAGCTCAGTGGGAAAT -s simHuman_chr6.simHuman.chr6 54286 28 + 601863 AATTTTCTCAGCAATCGTAATGGAGAGT -s simRat_chr6.simRat.chr6 49099 20 + 647215 ---TAGCTTAGCAAATG-----GGATGC - -a -s simMouse_chr6.simMouse.chr6 55941 43 + 636262 TATGAACAAGATGAAGTTGCTCACTATGAACATGCTTTATATA -s Anc0.Anc0refChr4 3417 43 - 45765 TAGGAACAGGATGAAGTTGCTCACTACCAAAATGCTATATCGA -s Anc1.Anc1refChr2 34139 43 + 144309 TAGGAACAGGATGAAGTTGCTCACTACCAAAATGCTATATCGA -s Anc2.Anc2refChr4 428 43 + 10050 TAGGAACAGGATGATGTTGCTCACTACCAAAATGCTATATCGA -s mr.mrrefChr0 53358 43 + 130230 TATGAACAGGATGAAGTTGCTCACTACGAACATGCTTTATATA -s simCow_chr6.simCow.chr6 60314 39 + 602619 T----ACAGGATTAGGCTGCACACTATCAACATGCTATATAGG -s simDog_chr6.simDog.chr6 57080 43 + 593897 TAGGAACACGATGATGTTGCTCACTACCCCAATGCTGTATCAA -s simHuman_chr6.simHuman.chr6 54315 43 + 601863 TAGGAGCAGGATGAAGTTGCTCACTACCAAGATACTATATGGA -s simRat_chr6.simRat.chr6 49119 43 + 647215 TAAGGACAGGATGAAGTGGCTCAGTACGAACGTGCTTTATACA - -a -s simMouse_chr6.simMouse.chr6 55984 22 + 636262 ATATGAGACATGTTAAATCGAT -s Anc0.Anc0refChr4 3461 22 - 45765 ACACGAGTCAAGTTCAAGTGTT -s Anc1.Anc1refChr2 34183 22 + 144309 ACACGAGTCAAGTTCAAGTGTT -s Anc2.Anc2refChr4 472 22 + 10050 ACACGAGTCAAGTTCAAGTATT -s mr.mrrefChr0 53401 22 + 130230 ATATGAGACATGTTAAATCGAT -s simCow_chr6.simCow.chr6 60354 22 + 602619 ATATGAGTCAAGTTTGTGCATT -s simDog_chr6.simDog.chr6 57124 22 + 593897 ACGCGAGCCAAGCTCAAGTATT -s simHuman_chr6.simHuman.chr6 54359 22 + 601863 AGACAAGTCAAGTTGAAGGGTT -s simRat_chr6.simRat.chr6 49162 22 + 647215 ATATGAGTCGTGTTGAATCGAT - -a -s simMouse_chr6.simMouse.chr6 56006 25 + 636262 ATGAGAAGTGATGGACTGAATACTT -s Anc0.Anc0refChr4 3483 25 - 45765 GCCAGGAGGAGTGGACTGAATAGAA -s Anc1.Anc1refChr2 34205 25 + 144309 GCCAGGAGGAGTGGACTGAATAGAA -s Anc2.Anc2refChr4 494 25 + 10050 GCCAGGAGGAATGGACTGAATAGAA -s mr.mrrefChr0 53423 25 + 130230 ATGAGAAGTGGTGGACTGAATAGTA -s simCow_chr6.simCow.chr6 60377 25 + 602619 GCCAGAAGCAATGGACCGAATTGAA -s simDog_chr6.simDog.chr6 57146 25 + 593897 GCCAGGGGGAATGGACTGTATAGAA -s simHuman_chr6.simHuman.chr6 54381 25 + 601863 GCCAGGAGAAGTAGACTGAATAGAA -s simRat_chr6.simRat.chr6 49184 17 + 647215 AT--------GTGGACGGAATTGTA - -a -s simMouse_chr6.simMouse.chr6 56031 13 + 636262 GTGCCTTCCCAAT -s Anc0.Anc0refChr4 3510 13 - 45765 GTGCCTTCTCAAT -s Anc1.Anc1refChr2 34232 13 + 144309 GTGCCTTCTCAAT -s Anc2.Anc2refChr4 521 13 + 10050 GTGCCTTCTAAAT -s mr.mrrefChr0 53448 13 + 130230 GTGCCTTCCCAAT -s simCow_chr6.simCow.chr6 60404 13 + 602619 ATGCCTTCTGAAC -s simDog_chr6.simDog.chr6 57173 13 + 593897 GTAACTTCCAAAT -s simHuman_chr6.simHuman.chr6 54408 13 + 601863 GTGCCTTCTCAAT -s simRat_chr6.simRat.chr6 49201 13 + 647215 GCGCCTTCATAAT - -a -s simMouse_chr6.simMouse.chr6 56044 2 + 636262 AC -s Anc0.Anc0refChr4 3523 2 - 45765 TC -s Anc1.Anc1refChr2 34245 2 + 144309 TC -s Anc2.Anc2refChr4 539 2 + 10050 TC -s mr.mrrefChr0 53461 2 + 130230 TC -s simCow_chr6.simCow.chr6 60422 2 + 602619 TT -s simDog_chr6.simDog.chr6 57191 2 + 593897 TC -s simHuman_chr6.simHuman.chr6 54421 2 + 601863 TC -s simRat_chr6.simRat.chr6 49214 2 + 647215 TC - -a -s simMouse_chr6.simMouse.chr6 56046 88 + 636262 TGTGGGTTCCTACCACAAGCAAACTTATAACTCTTGTAAAGTTAGAAAGTCTGCTTGGTACTACAGGGATTACTGAATAAGTTTGATA -s Anc0.Anc0refChr4 3526 71 - 45765 TTTATGTTCCAACCACAAGTCAACTCATAATGCTTGTAAAGTTAAAAAGTCTGACTGGTGT----GAATTCAC------------AT- -s Anc1.Anc1refChr2 34248 71 + 144309 TTTATGTTCCAACCACAAGTCAACTCATAATGCTTGTAAAGTTAAAAAGTCTGACTGGTGT----GAATTCAC------------AT- -s Anc2.Anc2refChr4 542 71 + 10050 ATTATGTTTCAACCACAAGTCAACTCATAATGCTTGTAAAGTTAAAAAGTCTGACTGGTGT----GAATTCAC------------AT- -s mr.mrrefChr0 53464 72 + 130230 TGTGGGTTCCTACCACAAGCAAACTTATAATTCTTGTAAAGTTAGAAAGTCTGCTTGGTAC----GGGATTAC------------ATA -s simCow_chr6.simCow.chr6 60425 71 + 602619 ATTGTGTTTCAACCACAAGTCAACACATATTTCTTGTAAATTTAGAACACCTAATCGGTGT----GGATTTAC------------AT- -s simDog_chr6.simDog.chr6 57194 71 + 593897 ATTATGTTTCAACCACAAGTCAACTCATAATGCTTGTGAGGCTAAAAAGTCTGACTGGTGT----GAATTCAC------------AT- -s simHuman_chr6.simHuman.chr6 54424 41 + 601863 T------TCC--CCACAAGTCAACTCATAATCCTTGTACAGTTAAAAAG--------------------------------------- -s simRat_chr6.simRat.chr6 49221 72 + 647215 CGTGCGTTCCTGCCACAAACAAACTTAAAATTCTTGCAAAGTTAGAAGGTCTGCTTGGTAT----GAGATTGC------------ATA - -a -s simMouse_chr6.simMouse.chr6 56134 20 + 636262 ATCACTGTGTAATTTCAATA -s Anc1.Anc1refChr2 34319 12 + 144309 --------AGTTTTTTGATA -s mr.mrrefChr0 53536 20 + 130230 ATCACTGTATAATTTTGATA -s simHuman_chr6.simHuman.chr6 54465 12 + 601863 --------AGTTTTTTGATA -s simRat_chr6.simRat.chr6 49294 20 + 647215 ATCACTGAATAATTTTGATA - -a -s simMouse_chr6.simMouse.chr6 56154 6 + 636262 AACTGG -s Anc0.Anc0refChr4 3597 1 - 45765 -----G -s Anc1.Anc1refChr2 34331 6 + 144309 AACAGG -s Anc2.Anc2refChr4 613 1 + 10050 -----G -s mr.mrrefChr0 53556 6 + 130230 AACTGG -s simCow_chr6.simCow.chr6 60496 1 + 602619 -----A -s simDog_chr6.simDog.chr6 57265 1 + 593897 -----G -s simHuman_chr6.simHuman.chr6 54478 6 + 601863 AACAGG -s simRat_chr6.simRat.chr6 49314 6 + 647215 AACTGG - -a -s simMouse_chr6.simMouse.chr6 56160 36 + 636262 TTCCCACTAAATGAGTTAAAAATTGGAGTGATCTAT -s Anc0.Anc0refChr4 3598 36 - 45765 TTCCCATTGTATAGGTCTAACACAGGAGGGTTCTAT -s Anc1.Anc1refChr2 34337 36 + 144309 TTCCCATTGTATAGGTCTAACACAGGAGGGTTCTAT -s Anc2.Anc2refChr4 614 36 + 10050 TTCTTATTGTATAGGTCTAACACAAGAGGCTTCTAT -s mr.mrrefChr0 53562 36 + 130230 TTCCCACTAAATAAGTTTAAAATTGGAGTGATCTAT -s simCow_chr6.simCow.chr6 60527 36 + 602619 TTCGTGTTGTATAGGTCTAACACAAGAGGCTTCTTT -s simDog_chr6.simDog.chr6 57266 24 + 593897 AGGTTAGTGTAGAGTTTTGAAA------------AT -s simHuman_chr6.simHuman.chr6 54484 36 + 601863 TTCCCATTGCATAGGCCTAACACAGCAGGGCTCCAT -s simRat_chr6.simRat.chr6 49320 36 + 647215 TTCCCACTAAATAAGTTTAAGATTGGAAAGATTTAT - -a -s simMouse_chr6.simMouse.chr6 56196 35 + 636262 GAGTCTGCATTTTGGTATGGACTTGTGCCACATCC -s Anc0.Anc0refChr4 3634 28 - 45765 GAG-------TTTGGTATGGATTTACGCCACATCC -s Anc1.Anc1refChr2 34373 35 + 144309 GAGTCCACATTTTGGTATGGATTTACGCCACATCC -s Anc2.Anc2refChr4 650 28 + 10050 GAG-------TTTGGTATGGATTTACCCCACATCC -s mr.mrrefChr0 53598 35 + 130230 GAGTCTGCATTTTGGTATGGATTTGTGCCACATCC -s simCow_chr6.simCow.chr6 60573 28 + 602619 GAG-------TTTGGTACGGATCTGGCCCACATCC -s simDog_chr6.simDog.chr6 57290 28 + 593897 GAG-------TTTGGTATGGATTTACCCCACATCC -s simHuman_chr6.simHuman.chr6 54520 35 + 601863 GAGTCCACATTTTGGTCTGAATTTAAGCTACATCC -s simRat_chr6.simRat.chr6 49356 35 + 647215 GAGCCTGCATTTTGGTATGGATTTGTGCCAGATCC - -a -s simMouse_chr6.simMouse.chr6 56231 16 + 636262 ACAACCAGGGCTCAAG -s Anc0.Anc0refChr4 3662 15 - 45765 A-AACCAGGGATTAAG -s Anc1.Anc1refChr2 34408 16 + 144309 ACAACCAGGGATTAAG -s Anc2.Anc2refChr4 678 15 + 10050 A-AACCAGGGATTAGG -s mr.mrrefChr0 53633 16 + 130230 ACAACCAGGGCTCAAG -s simCow_chr6.simCow.chr6 60602 15 + 602619 A-AACCAGGGATTCGG -s simDog_chr6.simDog.chr6 57318 15 + 593897 A-AACCAGGGATCAGA -s simHuman_chr6.simHuman.chr6 54555 13 + 601863 AC---CAGGGTCTAAG -s simRat_chr6.simRat.chr6 49391 16 + 647215 GCAACCAGGACGCAAG - -a -s simMouse_chr6.simMouse.chr6 56247 17 + 636262 ATGTAAGCAGTGGTGGT -s Anc0.Anc0refChr4 3684 17 - 45765 ACCTAAGCAGAGGTGAT -s Anc1.Anc1refChr2 34431 17 + 144309 ACCTAAGCAGAGGTGAT -s Anc2.Anc2refChr4 700 17 + 10050 ACCTAAGCAGAGGTGAT -s mr.mrrefChr0 53649 17 + 130230 ATGTAAGCAGTGGTGGT -s simCow_chr6.simCow.chr6 60624 17 + 602619 ATATAAGCAAAGGTGAC -s simDog_chr6.simDog.chr6 57340 17 + 593897 ACCTAAGCAGAGGTGAT -s simHuman_chr6.simHuman.chr6 54575 17 + 601863 ACTGAAGCAGAGTGATC -s simRat_chr6.simRat.chr6 49407 17 + 647215 ATGTAAGCAGTGGTGAT - -a -s simMouse_chr6.simMouse.chr6 56264 48 + 636262 GGTATAGGGTACCCCAATTAGTTTCAGGGATCAACATTTCTGTGTTAA -s Anc0.Anc0refChr4 3701 48 - 45765 GGTATCTGGTGTCCTGCTAGACTCCAGTGATCAACATTTCTTTGTTTA -s Anc1.Anc1refChr2 34448 48 + 144309 GGTATCTGGTGTCCTGCTAGACTCCAGTGATCAACATTTCTTTGTTTA -s Anc2.Anc2refChr4 718 48 + 10050 GGTATCTGGTGTCCTGCTAGACTCCAGTGATCGACATTTCTTTGTTTA -s mr.mrrefChr0 53666 48 + 130230 GGTATAGGGTATCCCACTTAGTTTCAGTGATCAACATTTCTTTGTTAA -s simCow_chr6.simCow.chr6 60642 46 + 602619 GGTATCTGATATCCTGCTAGACTCCAGTAATC--CATTTCTTTGATAA -s simDog_chr6.simDog.chr6 57358 48 + 593897 GGTATCTGGTGTCCTGCAAGACTCCGGTGATTGACATTTCTTTCTTTA -s simHuman_chr6.simHuman.chr6 54592 48 + 601863 GGTACCTTGTGTCCTGCTAGAATCCATTGATCAACATTTCTTAGTTTA -s simRat_chr6.simRat.chr6 49424 48 + 647215 GGTATTGGATATCCCACTTAGTTTCAGTGATCAAAATTTCTTTGTTAA - -a -s simMouse_chr6.simMouse.chr6 56312 7 + 636262 TATGAGT -s Anc0.Anc0refChr4 3749 6 - 45765 AATGAG- -s Anc1.Anc1refChr2 34496 7 + 144309 AATGAGT -s Anc2.Anc2refChr4 766 6 + 10050 AATTAG- -s mr.mrrefChr0 53714 7 + 130230 TATGAGT -s simCow_chr6.simCow.chr6 60688 6 + 602619 AGCAAG- -s simDog_chr6.simDog.chr6 57406 6 + 593897 TATTAG- -s simHuman_chr6.simHuman.chr6 54641 7 + 601863 GATGAGT -s simRat_chr6.simRat.chr6 49472 7 + 647215 TATGAGT - -a -s simMouse_chr6.simMouse.chr6 56319 10 + 636262 TTGTTCATAT -s Anc0.Anc0refChr4 3755 5 - 45765 -----TACAT -s Anc1.Anc1refChr2 34504 10 + 144309 TTGTATACAT -s Anc2.Anc2refChr4 772 5 + 10050 -----TACAC -s mr.mrrefChr0 53722 10 + 130230 TTGTATATAT -s simCow_chr6.simCow.chr6 60694 5 + 602619 -----TACTC -s simDog_chr6.simDog.chr6 57412 5 + 593897 -----TACAC -s simHuman_chr6.simHuman.chr6 54649 10 + 601863 TTGTATACAT -s simRat_chr6.simRat.chr6 49480 10 + 647215 TTGTATATAT - -a -s simMouse_chr6.simMouse.chr6 56329 6 + 636262 ATCATC -s Anc0.Anc0refChr4 3760 6 - 45765 AGCATT -s Anc1.Anc1refChr2 34514 6 + 144309 AGCATT -s Anc2.Anc2refChr4 777 6 + 10050 AGCATT -s mr.mrrefChr0 53732 6 + 130230 AGCATC -s simCow_chr6.simCow.chr6 60701 6 + 602619 TGCATA -s simDog_chr6.simDog.chr6 57417 6 + 593897 AGCATT -s simHuman_chr6.simHuman.chr6 54659 6 + 601863 AGCATT -s simRat_chr6.simRat.chr6 49490 6 + 647215 AGCATC - -a -s simMouse_chr6.simMouse.chr6 56335 5 + 636262 TGTAC -s Anc0.Anc0refChr4 3769 5 - 45765 TGGAC -s Anc1.Anc1refChr2 34523 5 + 144309 TGGAC -s Anc2.Anc2refChr4 786 5 + 10050 TGGAC -s mr.mrrefChr0 53741 5 + 130230 TGTAC -s simCow_chr6.simCow.chr6 60710 5 + 602619 TGGAA -s simDog_chr6.simDog.chr6 57426 5 + 593897 TGAAC -s simHuman_chr6.simHuman.chr6 54668 5 + 601863 TAGAC -s simRat_chr6.simRat.chr6 49499 5 + 647215 TGTAC - -a -s simMouse_chr6.simMouse.chr6 56340 14 + 636262 AGGTAGCATCAGAA -s Anc0.Anc0refChr4 3780 14 - 45765 AGGTAGCAGTAGGA -s Anc1.Anc1refChr2 34534 14 + 144309 AGGTAGCAGTAGGA -s Anc2.Anc2refChr4 797 14 + 10050 AGGTGGCAGTTGGA -s mr.mrrefChr0 53746 14 + 130230 AGGTAGCATCAGAA -s simCow_chr6.simCow.chr6 60721 14 + 602619 AGGTGGCAGTTGCA -s simDog_chr6.simDog.chr6 57437 14 + 593897 ATGTGGTGGTTGGA -s simHuman_chr6.simHuman.chr6 54679 14 + 601863 AGGTAGCAGTAGGA -s simRat_chr6.simRat.chr6 49504 12 + 647215 AGGTATCATCA--A - -a -s simMouse_chr6.simMouse.chr6 56354 31 + 636262 TCGGCATTGATGATAAAGGGTAACGGATCAC -s Anc0.Anc0refChr4 3794 20 - 45765 CTTGCATTAACTGT----------GCTTCA- -s Anc1.Anc1refChr2 34548 21 + 144309 CTTGCATTAACTGT----------GCTTCAG -s Anc2.Anc2refChr4 811 20 + 10050 CTTGCATTAACTGT----------GCTTTA- -s mr.mrrefChr0 53760 31 + 130230 CTGGCATTGATGATAAAGGGTAACGGATCAG -s simCow_chr6.simCow.chr6 60757 20 + 602619 CTTGCTTTAAGTGT----------GCTTTA- -s simDog_chr6.simDog.chr6 57451 14 + 593897 CTTGGATTGACTGT----------------- -s simHuman_chr6.simHuman.chr6 54693 21 + 601863 CTTGCATTAACTGT----------GCTTCAG -s simRat_chr6.simRat.chr6 49516 31 + 647215 CTGGCGTTGATGATAAAGGGTAACGGATCAG - -a -s simMouse_chr6.simMouse.chr6 56385 16 + 636262 CAAAGCTGTCAGGCAA -s Anc0.Anc0refChr4 3814 15 - 45765 -AAAGATATCAGGGTA -s Anc1.Anc1refChr2 34569 16 + 144309 CAAAGATATCAGGGTA -s Anc2.Anc2refChr4 831 15 + 10050 -CAAGATAGGAAGGTA -s mr.mrrefChr0 53791 16 + 130230 CAAAGCTGTCAGGCAA -s simCow_chr6.simCow.chr6 60777 15 + 602619 -CAAGATAGGAAGGTA -s simHuman_chr6.simHuman.chr6 54717 16 + 601863 CAAAGGTATCAGGTTA -s simRat_chr6.simRat.chr6 49547 13 + 647215 CAAAGCCG---GGCAA - -a -s simMouse_chr6.simMouse.chr6 56401 29 + 636262 CCACCACTTCCATAACTGAACTCTATTGA -s Anc0.Anc0refChr4 3829 28 - 45765 TCAGATTCTA-ATAACTGAATTCTATTAA -s Anc1.Anc1refChr2 34585 28 + 144309 TCAGATTCTA-ATAACTGAATTCTATTAA -s Anc2.Anc2refChr4 846 28 + 10050 TCAGATTCTA-TTAACTGAATTCTATTGA -s mr.mrrefChr0 53807 29 + 130230 CCACATCTTCCATAACTGAATTCTATTAA -s simCow_chr6.simCow.chr6 60792 28 + 602619 TCAGATTCTA-TTAACTGAAATTTAGTGA -s simDog_chr6.simDog.chr6 57465 11 + 593897 ------------------AATTCTATGGA -s simHuman_chr6.simHuman.chr6 54733 28 + 601863 TCTGATTCTA-ATAACTGAATTCTAATAA -s simRat_chr6.simRat.chr6 49561 29 + 647215 CCACATCTTCCATAACTGACTTATAGTAA - -a -s simMouse_chr6.simMouse.chr6 56430 37 + 636262 TTGAATGTTTAAAGATACAGAAAGCACTTGGTATTTC -s Anc0.Anc0refChr4 3857 37 - 45765 TTGAATGTTCAAAGATACAAAATGGCCATGATATATT -s Anc1.Anc1refChr2 34613 37 + 144309 TTGAATGTTCAAAGATACAAAATGGCCATGATATATT -s Anc2.Anc2refChr4 874 37 + 10050 TTGAATGTTCAAGGATACAAAATGGCCATGATATATT -s mr.mrrefChr0 53836 37 + 130230 TTGAATGTTTAAAGATACAGAAAGCACTTGGTATTTC -s simCow_chr6.simCow.chr6 60820 37 + 602619 TTGAATGTTCAAGGATAGAGGATGGCTATGATATATT -s simDog_chr6.simDog.chr6 57476 32 + 593897 CTGGATGTCCAAGGATACAAA-----CATGATATATT -s simHuman_chr6.simHuman.chr6 54761 37 + 601863 TTTAATGTTCAAAGATATAAAATTGCCATGATACATT -s simRat_chr6.simRat.chr6 49856 37 + 647215 TTAAATGTTTAAGGATACAGAAAGCACTTGGTATTTC - -a -s simMouse_chr6.simMouse.chr6 56467 9 + 636262 CATGGGATC -s Anc0.Anc0refChr4 3894 9 - 45765 CACAGGATT -s Anc1.Anc1refChr2 34650 9 + 144309 CACAGGATT -s Anc2.Anc2refChr4 911 9 + 10050 CACAGGTTT -s mr.mrrefChr0 53873 9 + 130230 CATAGGATC -s simCow_chr6.simCow.chr6 60857 9 + 602619 CACAGGTTT -s simDog_chr6.simDog.chr6 57508 9 + 593897 CAACGGTCT -s simHuman_chr6.simHuman.chr6 54798 9 + 601863 CACAGGATT -s simRat_chr6.simRat.chr6 49895 9 + 647215 CATAGGATC - -a -s simMouse_chr6.simMouse.chr6 56476 17 + 636262 AACATAGTCTTTACAGC -s Anc0.Anc0refChr4 3903 17 - 45765 ACCATAGTCTTGACACT -s Anc1.Anc1refChr2 34659 17 + 144309 ACCATAGTCTTGACACT -s Anc2.Anc2refChr4 920 17 + 10050 ACCATAGTCTTGACAAT -s mr.mrrefChr0 53882 17 + 130230 AACATAGTCTTTACACC -s simCow_chr6.simCow.chr6 60866 17 + 602619 ACTAGACTGTTGACAAT -s simDog_chr6.simDog.chr6 57517 17 + 593897 ACCATTGTCTCGACAAT -s simHuman_chr6.simHuman.chr6 54844 17 + 601863 GCCGTAGTCTTGACACT -s simRat_chr6.simRat.chr6 49904 17 + 647215 AACATAGTCTTTACACC - -a -s simMouse_chr6.simMouse.chr6 56493 9 + 636262 AACCCACTC -s Anc0.Anc0refChr4 3920 8 - 45765 AAACCAAT- -s Anc1.Anc1refChr2 34676 8 + 144309 AAACCAAT- -s Anc2.Anc2refChr4 937 8 + 10050 AAACCAAA- -s mr.mrrefChr0 53899 9 + 130230 AACCCACTC -s simCow_chr6.simCow.chr6 60883 8 + 602619 AAACCAAA- -s simDog_chr6.simDog.chr6 57536 8 + 593897 AAACCAAG- -s simHuman_chr6.simHuman.chr6 54861 8 + 601863 GAACCATT- -s simRat_chr6.simRat.chr6 49921 9 + 647215 AACCCACCC - -a -s simMouse_chr6.simMouse.chr6 56502 78 + 636262 AACTTTACTGTACAGGTGTATTAAGACTGTCTAGCTGTTCCGTCTCAAGTGCATGTGGTTAATGTTAGATCAGTGTTC -s Anc0.Anc0refChr4 3928 63 - 45765 AACTTTACTGAGCAGA---TTGAAGACT-----------TGTTCTCAAGTACTTGTGGT-AATGCCAGATCAGTGCCC -s Anc1.Anc1refChr2 34684 66 + 144309 AACTTTACTGAGCAGATGTTTGAAGACT-----------TGTTCTCAAGTACTTGTGGT-AATGCCAGATCAGTGCCC -s Anc2.Anc2refChr4 945 63 + 10050 AGATTTCCTTAGCGAA---TTGCCGTTT-----------TGTTCTCAAAAACTTGTGAT-AATGCCAGATCAGTGCCC -s mr.mrrefChr0 53908 77 + 130230 AACTTTACTGTACAGATGTATTAAGACTGTCTAGCTGTTTCTTCTCAAGTGCATGTGGT-AATGTTAGATCAGTGTCC -s simCow_chr6.simCow.chr6 60893 63 + 602619 AGTTTACCGTAGCGAA---TAACTGTTT-----------TGTTCTCAAAAACTTGTGAT-AATGCTAGAACAGTGTCC -s simDog_chr6.simDog.chr6 57544 33 + 593897 AGATTTCCTT-----A---TTGCC-------------------------------------ATGCCGGATCAGGTCTA -s simHuman_chr6.simHuman.chr6 54869 66 + 601863 AACTTTACTGGGAAGATGTTTCAAAACT-----------TGTTCTCAAGTACCTGAGGA-GATGCCAGATCAGTGCCC -s simRat_chr6.simRat.chr6 49930 77 + 647215 AACTCTACTGTACAGATGTATTAAGACTGACTAGTGGTTTCTTCTCAAGTCGTTGTGGT-AATGGAAGATCAATGTCC - -a -s simMouse_chr6.simMouse.chr6 56580 1 + 636262 A -s Anc0.Anc0refChr4 3991 1 - 45765 A -s Anc1.Anc1refChr2 34750 1 + 144309 A -s Anc2.Anc2refChr4 1008 1 + 10050 A -s mr.mrrefChr0 53985 1 + 130230 A -s simCow_chr6.simCow.chr6 60957 1 + 602619 A -s simDog_chr6.simDog.chr6 57577 1 + 593897 A -s simHuman_chr6.simHuman.chr6 54935 1 + 601863 A -s simRat_chr6.simRat.chr6 50007 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 56581 28 + 636262 CTAAATGTATGTCTTAAGGATTGTTCAT -s Anc0.Anc0refChr4 3992 28 - 45765 CTAAATATAAGTTTTTAGATTGGTTCAA -s Anc1.Anc1refChr2 34751 28 + 144309 CTAAATATAAGTTTTTAGATTGGTTCAA -s Anc2.Anc2refChr4 1011 28 + 10050 CTAAACATAAGTTTTTAGGTTGGTCCTA -s mr.mrrefChr0 53986 28 + 130230 CTAAATGTATGTCTTAAGAATTGTTCAT -s simCow_chr6.simCow.chr6 60960 28 + 602619 CTAAACATATGTTTTTAGGTTTATGCCA -s simDog_chr6.simDog.chr6 57580 28 + 593897 CTAAACATAAGTTTTTAAGTAGGACCTA -s simHuman_chr6.simHuman.chr6 54936 19 + 601863 ATAAAT---------CAGATTGGTTCAA -s simRat_chr6.simRat.chr6 50008 28 + 647215 CTAAATGTATGTTTTAAGAATTGGTCAC - -a -s simMouse_chr6.simMouse.chr6 56609 23 + 636262 TGGAGAGAGTGCATAAAGCATCC -s Anc0.Anc0refChr4 4021 23 - 45765 TGGAGTAAGTGCATACAGCCTCT -s Anc1.Anc1refChr2 34780 23 + 144309 TGGAGTAAGTGCATACAGCCTCT -s Anc2.Anc2refChr4 1040 23 + 10050 TGGAGTAAGTGCATACAGCCTCT -s mr.mrrefChr0 54014 23 + 130230 TGGAGAGAGTGCATAAAGCATCC -s simCow_chr6.simCow.chr6 60989 23 + 602619 AGGAGCAAGTGCATACAACCTCC -s simDog_chr6.simDog.chr6 57609 23 + 593897 TGTAGTAAGTGCATACAGCCTCT -s simHuman_chr6.simHuman.chr6 54956 23 + 601863 TGGAGTAAGTGCATACAGCCTCT -s simRat_chr6.simRat.chr6 50036 23 + 647215 TGGGGAGGGTGCATAAAGCATCG - -a -s simMouse_chr6.simMouse.chr6 56632 9 + 636262 TAGAACCTT -s Anc0.Anc0refChr4 4045 9 - 45765 GAGAAGATT -s Anc1.Anc1refChr2 34804 9 + 144309 GAGAAGATT -s Anc2.Anc2refChr4 1064 9 + 10050 GAGAAGATT -s mr.mrrefChr0 54037 9 + 130230 TAGAATCTT -s simCow_chr6.simCow.chr6 61013 9 + 602619 TTGAGTATT -s simDog_chr6.simDog.chr6 57633 9 + 593897 GAGAAGACT -s simHuman_chr6.simHuman.chr6 54980 9 + 601863 GAGAAAATT -s simRat_chr6.simRat.chr6 50059 9 + 647215 TAGAATCTT - -a -s simMouse_chr6.simMouse.chr6 56641 1 + 636262 A -s Anc0.Anc0refChr4 4054 1 - 45765 A -s Anc1.Anc1refChr2 34813 1 + 144309 A -s Anc2.Anc2refChr4 1073 1 + 10050 G -s mr.mrrefChr0 54046 1 + 130230 A -s simCow_chr6.simCow.chr6 61022 1 + 602619 G -s simDog_chr6.simDog.chr6 57642 1 + 593897 G -s simHuman_chr6.simHuman.chr6 54991 1 + 601863 A -s simRat_chr6.simRat.chr6 50068 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 56642 9 + 636262 GCCCAATAC -s Anc0.Anc0refChr4 4065 9 - 45765 GACCAATAC -s Anc1.Anc1refChr2 34824 9 + 144309 GACCAATAC -s Anc2.Anc2refChr4 1084 9 + 10050 AATCAATAC -s mr.mrrefChr0 54047 9 + 130230 GCCCAATAC -s simDog_chr6.simDog.chr6 57653 9 + 593897 AATCAATAC -s simHuman_chr6.simHuman.chr6 55002 9 + 601863 GACCAATAC -s simRat_chr6.simRat.chr6 50069 9 + 647215 GCCCAATAC - -a -s simMouse_chr6.simMouse.chr6 56651 4 + 636262 ATAT -s Anc0.Anc0refChr4 4076 4 - 45765 ATAT -s Anc1.Anc1refChr2 34835 4 + 144309 ATAT -s Anc2.Anc2refChr4 1095 4 + 10050 GTAT -s mr.mrrefChr0 54056 4 + 130230 ATAT -s simDog_chr6.simDog.chr6 57664 4 + 593897 GTAT -s simHuman_chr6.simHuman.chr6 55013 4 + 601863 ATAT -s simRat_chr6.simRat.chr6 50078 4 + 647215 ATAT - -a -s simMouse_chr6.simMouse.chr6 56655 6 + 636262 ACTAGA -s Anc0.Anc0refChr4 4080 6 - 45765 ATGATA -s Anc1.Anc1refChr2 34839 6 + 144309 ATGATA -s Anc2.Anc2refChr4 1099 6 + 10050 ACAATA -s mr.mrrefChr0 54060 6 + 130230 ATGAGA -s simDog_chr6.simDog.chr6 57688 6 + 593897 ACAATA -s simHuman_chr6.simHuman.chr6 55017 6 + 601863 ATGAAA -s simRat_chr6.simRat.chr6 50082 6 + 647215 ATGAGA - -a -s simMouse_chr6.simMouse.chr6 56661 169 + 636262 TATTCAGCTGGAGCCATAATTACATGACTTGACGGGTCGAGATGTGGATTCCGGGGTTAGGACCATGCTGTCAACGGGTTCCATAGGAACTGTGATACCTCCCAATTTCACTATGGCTCTAAACTCATTAACAAGAAATTCTTGGAGATCAATGGGTGCCGTTACCTGA -s Anc0.Anc0refChr4 4093 23 - 45765 TGG----------------------------------------------------------------------------------------------------------------------------------------TCTTGGGGTTC----------ACTGCCTGA -s Anc1.Anc1refChr2 34852 70 + 144309 TGGTAAACTGGATTCGTAATTACACAGCTTCACA---------------------------------------------------------------------------------------------------TTATAATCTTGGGGTTCACTGGGTGTTACTGCCTGA -s Anc2.Anc2refChr4 1112 23 + 10050 TGG----------------------------------------------------------------------------------------------------------------------------------------TTTTGCAGTTC----------ACTGCCTGA -s mr.mrrefChr0 54066 70 + 130230 TATTCAACTGGAGCCGTAATTACATGACTTGACG---------------------------------------------------------------------------------------------------AGAAATTCTTGGGGATCAATGGGTGTCATTGCCTGA -s simDog_chr6.simDog.chr6 57701 23 + 593897 TGG----------------------------------------------------------------------------------------------------------------------------------------TTTTGCAGTTC----------ACTGCCTGA -s simHuman_chr6.simHuman.chr6 55030 70 + 601863 TGGTAAACTGGATTCGTAATTACACAGCTTCACA---------------------------------------------------------------------------------------------------TTATAATCTTGGGTGTCACTGGGTGTTACTGCCTAA -s simRat_chr6.simRat.chr6 50088 70 + 647215 TATTCAACTGGGGCTGCAACTACATGACTTTGCG---------------------------------------------------------------------------------------------------ACAAATTCTAGGGGAGCAATTGATGTCATTGCCTGA - -a -s simMouse_chr6.simMouse.chr6 56830 39 + 636262 CTGACACTAGTTGATGGAGGTCTGCTGTCTAGGAAAGTT -s Anc0.Anc0refChr4 4130 39 - 45765 CTGACAATAGTTGAGGGAGGTCTGTTGTTTAAGTGAGTT -s Anc1.Anc1refChr2 34936 39 + 144309 CTGACAATAGTTGAGGGAGGTCTGTTGTTTAAGTGAGTT -s Anc2.Anc2refChr4 1149 39 + 10050 CTGACAATTGTTGAGAGGGGTCTGTAGTTTAAGTGAGCT -s mr.mrrefChr0 54136 39 + 130230 CTGACACTAGTTGATGGAGGTCTGCTGTCTAGGAAAGTT -s simDog_chr6.simDog.chr6 57738 39 + 593897 CTGACAATTGTTGAGAGGGGTCTGTAGTTTAAGTGAGCT -s simHuman_chr6.simHuman.chr6 55115 39 + 601863 TTGACAATAATTGAGGGAGGTGTGATGTATAACTGAGTT -s simRat_chr6.simRat.chr6 50158 39 + 647215 CTGACACTAGTTGATGGAGGTCTGCTATCTAGGAAAACT - -a -s simMouse_chr6.simMouse.chr6 56869 24 + 636262 ATAATATTTAAACTAGCTAGTAGC -s Anc0.Anc0refChr4 4169 24 - 45765 CTGAATATAAAGCTAGGTTATAGC -s Anc1.Anc1refChr2 34975 24 + 144309 CTGAATATAAAGCTAGGTTATAGC -s Anc2.Anc2refChr4 1188 24 + 10050 CTGTATACAAGGCTAAGTTATAGA -s mr.mrrefChr0 54175 24 + 130230 ATGATATTTAAACTAGGTTGTAGC -s simDog_chr6.simDog.chr6 57787 24 + 593897 CTGTATACAAGGCTAAGTTATAGA -s simHuman_chr6.simHuman.chr6 55154 24 + 601863 CTGAACATAAAGCTTGGTTATAGC -s simRat_chr6.simRat.chr6 50197 24 + 647215 ATGATATTTAAACTAGGTTGTAGT - -a -s simMouse_chr6.simMouse.chr6 56893 2 + 636262 GG -s Anc0.Anc0refChr4 4213 2 - 45765 AT -s Anc1.Anc1refChr2 35019 2 + 144309 AT -s Anc2.Anc2refChr4 1232 2 + 10050 AT -s mr.mrrefChr0 54199 2 + 130230 GG -s simDog_chr6.simDog.chr6 57831 2 + 593897 AT -s simHuman_chr6.simHuman.chr6 55198 2 + 601863 AC -s simRat_chr6.simRat.chr6 50221 2 + 647215 GG - -a -s simMouse_chr6.simMouse.chr6 56895 23 + 636262 ACTTGCATATCCATTTAGACTAG -s Anc0.Anc0refChr4 4218 20 - 45765 ACTTGCATTTCCATTTTGA---G -s Anc1.Anc1refChr2 35024 20 + 144309 ACTTGCATTTCCATTTTGA---G -s Anc2.Anc2refChr4 1237 20 + 10050 ACCAGCATTTCCATTTTAG---G -s mr.mrrefChr0 54204 20 + 130230 ACTTGCATATCCATTTAGA---G -s simDog_chr6.simDog.chr6 57836 20 + 593897 ACCAGCATTTCCATTTTAG---G -s simHuman_chr6.simHuman.chr6 55203 20 + 601863 ACTTGCATGTCCATTTTGA---G -s simRat_chr6.simRat.chr6 50226 20 + 647215 ACTTGCATTTCCATTTAGA---G - -a -s simMouse_chr6.simMouse.chr6 56918 8 + 636262 TATGTGCA -s Anc0.Anc0refChr4 4258 8 - 45765 TATATGCC -s Anc1.Anc1refChr2 35064 8 + 144309 TATATGCC -s Anc2.Anc2refChr4 1277 8 + 10050 TATATGCC -s mr.mrrefChr0 54224 8 + 130230 TATGTGCC -s simDog_chr6.simDog.chr6 57876 8 + 593897 TATATGCC -s simHuman_chr6.simHuman.chr6 55243 8 + 601863 TATATGTC -s simRat_chr6.simRat.chr6 50246 8 + 647215 TATGAGCC - -a -s simMouse_chr6.simMouse.chr6 56926 13 + 636262 TAATCCAGTCATT -s Anc0.Anc0refChr4 4269 13 - 45765 TTATCCTGTTATT -s Anc1.Anc1refChr2 35075 13 + 144309 TTATCCTGTTATT -s Anc2.Anc2refChr4 1288 13 + 10050 CTATCCTGTTATT -s mr.mrrefChr0 54232 13 + 130230 TAATCCAGTCATT -s simDog_chr6.simDog.chr6 57887 13 + 593897 CTATCCTGTTATT -s simHuman_chr6.simHuman.chr6 55254 13 + 601863 TCATCATGTTATT -s simRat_chr6.simRat.chr6 50254 13 + 647215 TAATCCAGTCATT - -a -s simMouse_chr6.simMouse.chr6 56939 13 + 636262 AAGAGTTTTGAAT -s Anc0.Anc0refChr4 4285 13 - 45765 AACACTCTTGAAT -s Anc1.Anc1refChr2 35091 13 + 144309 AACACTCTTGAAT -s Anc2.Anc2refChr4 1304 13 + 10050 AGCACTCATGAAT -s mr.mrrefChr0 54245 13 + 130230 AAGAGTTTTGAAT -s simDog_chr6.simDog.chr6 57903 13 + 593897 AGCACTCATGAAT -s simHuman_chr6.simHuman.chr6 55270 13 + 601863 AATAATCTTGGAC -s simRat_chr6.simRat.chr6 50267 13 + 647215 AAGAGTTTTGAAT - -a -s simMouse_chr6.simMouse.chr6 56952 18 + 636262 GTCATTTTGTCAATGACA -s Anc0.Anc0refChr4 4298 18 - 45765 GTCATTTTGTCAGTGGCA -s Anc1.Anc1refChr2 35104 18 + 144309 GTCATTTTGTCAGTGGCA -s Anc2.Anc2refChr4 1317 18 + 10050 ATCATTTTGTCAGTGGCA -s mr.mrrefChr0 54258 18 + 130230 GTCATTTTGTCAATGGCA -s simCow_chr6.simCow.chr6 61026 11 + 602619 -------TGTAAGTGGCA -s simDog_chr6.simDog.chr6 57932 18 + 593897 ATCATTTTGTCAGTGGCA -s simHuman_chr6.simHuman.chr6 55283 18 + 601863 GTTATTGTGTCTGTGGCA -s simRat_chr6.simRat.chr6 50280 18 + 647215 GTCATTTTGTCAATGGCA - -a -s simMouse_chr6.simMouse.chr6 56970 7 + 636262 CAGGGAT -s Anc0.Anc0refChr4 4320 7 - 45765 CAGAGAT -s Anc1.Anc1refChr2 35126 7 + 144309 CAGAGAT -s Anc2.Anc2refChr4 1339 7 + 10050 CAGTGAT -s mr.mrrefChr0 54276 7 + 130230 CAGAGAT -s simCow_chr6.simCow.chr6 61041 7 + 602619 CAGCGAT -s simDog_chr6.simDog.chr6 57954 7 + 593897 TAGTAAT -s simHuman_chr6.simHuman.chr6 55305 7 + 601863 CAGAGAT -s simRat_chr6.simRat.chr6 50298 7 + 647215 CAGAGAT - -a -s simMouse_chr6.simMouse.chr6 56977 35 + 636262 AGGGGCACTAGCAACAACCCCTTGACCACTCCAGG -s Anc0.Anc0refChr4 4329 35 - 45765 ATTGGCATTAGTAACAAGCCTTTGAACATTTCAAG -s Anc1.Anc1refChr2 35135 35 + 144309 ATTGGCATTAGTAACAAGCCTTTGAACATTTCAAG -s Anc2.Anc2refChr4 1348 35 + 10050 ATTGGCATTAGTAACAAGCCTTTGAATATTACAAC -s mr.mrrefChr0 54283 35 + 130230 AGGGGCACTAGCAACAACCCCTTGACCACTTCAGG -s simCow_chr6.simCow.chr6 61050 35 + 602619 ATTGGCATTAGTAACAAGCCTCTGAATAGTGTCAC -s simDog_chr6.simDog.chr6 57963 20 + 593897 GTGG-------TAACAAGATTT------TTACA-- -s simHuman_chr6.simHuman.chr6 55314 35 + 601863 ATTGGCATTATTAACAAGCCTTTGGTCATTTCAAG -s simRat_chr6.simRat.chr6 50305 35 + 647215 AGGGGCACTAGCAACAACCCCTTGAACACTTCAGC - -a -s simMouse_chr6.simMouse.chr6 57012 22 + 636262 GCATATTGCCAGTGATGGTGAA -s Anc0.Anc0refChr4 4365 22 - 45765 GAATATAAACAATGATCAGGAG -s Anc1.Anc1refChr2 35171 22 + 144309 GAATATAAACAATGATCAGGAG -s Anc2.Anc2refChr4 1384 22 + 10050 GAATATAAACAATGATCAGGAG -s mr.mrrefChr0 54318 22 + 130230 GCATATTGCCAGTGATGGGGAA -s simCow_chr6.simCow.chr6 61086 22 + 602619 GAATACAAGCAACAACAAAGAG -s simDog_chr6.simDog.chr6 57983 18 + 593897 ----ATAAACAATGATCGGGAG -s simHuman_chr6.simHuman.chr6 55350 22 + 601863 GAATATAATTAATGAGCAGGAG -s simRat_chr6.simRat.chr6 50340 22 + 647215 ACGTATTGCCAGTAATAGGGAA - -a -s simMouse_chr6.simMouse.chr6 57034 16 + 636262 GTAATCAATCTCCAAG -s Anc0.Anc0refChr4 4396 15 - 45765 -CACTGAATCTACAAG -s Anc1.Anc1refChr2 35202 16 + 144309 ACACTGAATCTACAAG -s Anc2.Anc2refChr4 1415 15 + 10050 -CACTGAATCTACAAG -s mr.mrrefChr0 54349 16 + 130230 GTAATCAATCTCCAAG -s simCow_chr6.simCow.chr6 61117 15 + 602619 -CACTGAGTGTCCAAG -s simDog_chr6.simDog.chr6 58010 15 + 593897 -CACTGAACCTACAAG -s simHuman_chr6.simHuman.chr6 55381 10 + 601863 ACACCGAATC------ -s simRat_chr6.simRat.chr6 50371 16 + 647215 GTAATCAATTTACAAG - -a -s simMouse_chr6.simMouse.chr6 57050 57 + 636262 GAGGTAAAATCAAGGAAGGGGCCACTCGTTTTGTAGATTAACCATCAATGTATTTAT -s Anc0.Anc0refChr4 4411 57 - 45765 GAGATAAACTCAAGGAAGGGGCCTCTGGTCTAATAAATTAACTATCAAGGCACTTAG -s Anc1.Anc1refChr2 35218 57 + 144309 GAGATAAACTCAAGGAAGGGGCCTCTGGTCTAATAAATTAACTATCAAGGCACTTAG -s Anc2.Anc2refChr4 1430 57 + 10050 GAGATAAACTCCAGGAAGAGGCCTCTGGTCTAATAAATTAACTATTAAGGCACTTAG -s mr.mrrefChr0 54365 57 + 130230 GAGGTAAACTCAAGGAAGGGGCCACTGGTCTTGTAGATTAACTATCAATGTATTTAT -s simCow_chr6.simCow.chr6 61135 57 + 602619 GAGATAAACTCCAGGAAGAGCTCCCTGGTCTAATAAATTAACTATTAAGGCCCTTAG -s simDog_chr6.simDog.chr6 58025 57 + 593897 GAGATAAACTCCAAGAAGAGGCCTCAGGTCTAACAAATTAACAATTAAAGCACTTAG -s simHuman_chr6.simHuman.chr6 55391 55 + 601863 --GATAGACTCAAGGAAGGGACCTCTGGTCACATAAATTCATTATCCAGGCACTTAG -s simRat_chr6.simRat.chr6 50387 57 + 647215 GAGGTAAACTCAAGGAGGCGGCCACCGATCTTGTAGATTAACTATCAATGTGTTTAT - -a -s simMouse_chr6.simMouse.chr6 57107 43 + 636262 ATATTTCACACCCACAGATGCTCAGCAAGTCTTTAGTAGTCTT -s Anc0.Anc0refChr4 4468 43 - 45765 GCATCTTACATGCAAGATCGCCCAGCAATCCTTTAGAAGTCGT -s Anc1.Anc1refChr2 35275 43 + 144309 GCATCTTACATGCAAGATCGCCCAGCAATCCTTTAGAAGTCGT -s Anc2.Anc2refChr4 1487 43 + 10050 GCATCTTACATGCAAGATCACCCAGCAGACCTTTAGAAGTTGT -s mr.mrrefChr0 54422 43 + 130230 ATATTTTACACCCACAGATGCTCAGCAATTCTTTAGTAGTCTT -s simCow_chr6.simCow.chr6 61310 43 + 602619 GTATCTAACATGCAAGATCACGCATTAGGCGTCTAAAAGTTGT -s simDog_chr6.simDog.chr6 58082 43 + 593897 CCATCTTACATGTGAGTTCACCCAGCAGACCTTTAGAAGTTGT -s simHuman_chr6.simHuman.chr6 55446 43 + 601863 GAATCTTACATGCAAGATAGTCAAGCAATCCTTTAGAAGTCCT -s simRat_chr6.simRat.chr6 50444 43 + 647215 TCATTTTACACCCACAGATGCTCAGCAATTCTTTAGGAGTCTA - -a -s simMouse_chr6.simMouse.chr6 57150 17 + 636262 GGGTCAACAATTCCATT -s Anc0.Anc0refChr4 4511 16 - 45765 GGGGCA-CAACCCTATG -s Anc1.Anc1refChr2 35318 16 + 144309 GGGGCA-CAACCCTATG -s Anc2.Anc2refChr4 1530 16 + 10050 GGGGCA-CAACCCTATG -s mr.mrrefChr0 54465 17 + 130230 GGGTCAACAACCCCATT -s simCow_chr6.simCow.chr6 61353 16 + 602619 GGGACA-CAACCATATG -s simDog_chr6.simDog.chr6 58126 16 + 593897 GGGGCA-CAACCCTATG -s simHuman_chr6.simHuman.chr6 55489 16 + 601863 GGGCCA-CAACCCTATA -s simRat_chr6.simRat.chr6 50487 17 + 647215 GGGTCAACGACCCCATT - -a -s simMouse_chr6.simMouse.chr6 57167 17 + 636262 GCTGTGTCAAACTACTC -s Anc0.Anc0refChr4 4527 12 - 45765 TCTATTT-----TACCC -s Anc1.Anc1refChr2 35334 12 + 144309 TCTATTT-----TACCC -s Anc2.Anc2refChr4 1546 12 + 10050 TCTATTT-----TACCC -s mr.mrrefChr0 54482 17 + 130230 GCTGTTTCAAACTACTC -s simCow_chr6.simCow.chr6 61403 12 + 602619 TCTATTT-----TACCC -s simDog_chr6.simDog.chr6 58142 12 + 593897 TCTATTT-----TACCC -s simHuman_chr6.simHuman.chr6 55505 12 + 601863 TCCATTC-----TACCC -s simRat_chr6.simRat.chr6 50504 17 + 647215 GTTGTTTCAAACTACTC - -a -s simMouse_chr6.simMouse.chr6 57184 2 + 636262 AG -s Anc0.Anc0refChr4 4539 2 - 45765 AT -s Anc1.Anc1refChr2 35346 2 + 144309 AT -s Anc2.Anc2refChr4 1560 2 + 10050 AT -s mr.mrrefChr0 54499 2 + 130230 AG -s simCow_chr6.simCow.chr6 61417 2 + 602619 AT -s simDog_chr6.simDog.chr6 58156 2 + 593897 AT -s simHuman_chr6.simHuman.chr6 55517 2 + 601863 AT -s simRat_chr6.simRat.chr6 50521 2 + 647215 AG - -a -s simMouse_chr6.simMouse.chr6 57186 45 + 636262 AAGCCTTCTGCTACATTAGAACACACAACCCTAGCCCTTCTTGAT -s Anc0.Anc0refChr4 4544 42 - 45765 AACCCTCCTGTTACCTTGAAACACAC---CCTTGTCCCTCTGGGT -s Anc1.Anc1refChr2 35351 42 + 144309 AACCCTCCTGTTACCTTGAAACACAC---CCTTGTCCCTCTGGGT -s Anc2.Anc2refChr4 1565 42 + 10050 AACCCTCCTGTTACCTTGAACCATGC---CCTTGTCCCTCCGGGT -s mr.mrrefChr0 54501 42 + 130230 AACCCTTCTGCTACATTAAAACACAC---CCTAGCCCTTCTTGAT -s simCow_chr6.simCow.chr6 61422 42 + 602619 AACCCTCCCATTATCTTGAGCCATGC---CCTTGTCTCTCCGGAT -s simDog_chr6.simDog.chr6 58161 40 + 593897 AACCATCCTGCGACCTTGAACCATGT---GCTAG--CCTCCGGGT -s simHuman_chr6.simHuman.chr6 55522 42 + 601863 AACCCGCCTGTTACCTTGAAACACAC---CCTTGTCCCTCTGGCT -s simRat_chr6.simRat.chr6 50523 19 + 647215 AACCATTCTGCTACATTAA-------------------------- - -a -s simMouse_chr6.simMouse.chr6 57231 16 + 636262 GACTCTAGGGTTTTCT -s Anc0.Anc0refChr4 4586 16 - 45765 GACCCCAGGGTTTTCT -s Anc1.Anc1refChr2 35393 16 + 144309 GACCCCAGGGTTTTCT -s Anc2.Anc2refChr4 1607 16 + 10050 GACCCCAGGATTTTCA -s mr.mrrefChr0 54543 16 + 130230 GACCCTAGGGTTTTCT -s simCow_chr6.simCow.chr6 61465 16 + 602619 GACCCCAGGATTTTCA -s simDog_chr6.simDog.chr6 58201 16 + 593897 GACCCCAAGATTTTCA -s simHuman_chr6.simHuman.chr6 55564 16 + 601863 GACCCCTGGGTTTTCT -s simRat_chr6.simRat.chr6 50542 13 + 647215 ---CCTAGGGTTTTCT - -a -s simMouse_chr6.simMouse.chr6 57247 10 + 636262 CATTCATAAG -s Anc0.Anc0refChr4 4605 10 - 45765 CCTGCATAAG -s Anc1.Anc1refChr2 35412 10 + 144309 CCTGCATAAG -s Anc2.Anc2refChr4 1626 10 + 10050 CCTGCATAAG -s mr.mrrefChr0 54559 10 + 130230 CATTCATAAG -s simCow_chr6.simCow.chr6 61484 10 + 602619 CCTACATAAG -s simDog_chr6.simDog.chr6 58220 10 + 593897 TCTGCATAAA -s simHuman_chr6.simHuman.chr6 55583 10 + 601863 CCTGTATAAG -s simRat_chr6.simRat.chr6 50555 10 + 647215 TATTCATAAG - -a -s simMouse_chr6.simMouse.chr6 57257 22 + 636262 ACATCACACCAGGTCCATGAGA -s Anc0.Anc0refChr4 4620 22 - 45765 ACATCACCCCAGGTTCATGACA -s Anc1.Anc1refChr2 35427 22 + 144309 ACATCACCCCAGGTTCATGACA -s Anc2.Anc2refChr4 1641 22 + 10050 ACGTCACCCCAGGTTCATGACA -s mr.mrrefChr0 54569 22 + 130230 ACATCACACCAGGTCCATGACA -s simCow_chr6.simCow.chr6 61499 22 + 602619 ATTTCATCCCAGGTTCATGACA -s simDog_chr6.simDog.chr6 58235 22 + 593897 ACGTTACCCTAGGTTCATGACA -s simHuman_chr6.simHuman.chr6 55598 22 + 601863 ACATCACCCCAGGTTCATGACA -s simRat_chr6.simRat.chr6 50565 22 + 647215 ACCTCATGCCAGGTCCATGACA - -a -s simMouse_chr6.simMouse.chr6 57279 23 + 636262 TTGATGAGCCTCCCTACTTTTGA -s Anc0.Anc0refChr4 4642 23 - 45765 CTAGTGAGGCTCCTTTCCTTTGA -s Anc1.Anc1refChr2 35449 23 + 144309 CTAGTGAGGCTCCTTTCCTTTGA -s Anc2.Anc2refChr4 1663 23 + 10050 CTAGTGAGGTTCCTTTCCTTTGA -s mr.mrrefChr0 54591 23 + 130230 CTGATGAGGCTCCCTACTTTTGA -s simCow_chr6.simCow.chr6 61521 18 + 602619 CCAGCAATATTCCTT-----TGA -s simDog_chr6.simDog.chr6 58257 23 + 593897 CTAGTGAGGTTCCCTTCCTTTGA -s simHuman_chr6.simHuman.chr6 55620 23 + 601863 CTAGTTAGGCTCCTTGCCTGTGA -s simRat_chr6.simRat.chr6 50591 23 + 647215 CTGAAGAGGCTCCCTATTCTTGT - -a -s simMouse_chr6.simMouse.chr6 57302 65 + 636262 GGAATGGCAATGCACTATTTTCTATTCCATACATTGTTTAGTATCAGTCATACCCTACAATCACA -s Anc0.Anc0refChr4 4668 64 - 45765 GGAAGGAAGATGCATTACCATCTATTCCACAGGGAGCTTAGTGTTAGTCATGCT-TACAATCATG -s Anc1.Anc1refChr2 35475 64 + 144309 GGAAGGAAGATGCATTACCATCTATTCCACAGGGAGCTTAGTGTTAGTCATGCT-TACAATCATG -s Anc2.Anc2refChr4 1689 64 + 10050 GGAAGAAAGGTGCATTACCATCTATTCCACAGGGAACTTAGTGTTAGCCATGCT-TACAATCATG -s mr.mrrefChr0 54614 65 + 130230 GGAATGAAGATGCATTACTTTCTATTCCATACGTTGTTTAGTGTCAGTCATGCCCTACAATCACA -s simCow_chr6.simCow.chr6 61542 64 + 602619 GGCAGAAGGGTGCATTACCATCTATTTCACATGGTAATTAGTGCTGGCAATACT-TATGAGCATG -s simDog_chr6.simDog.chr6 58283 64 + 593897 GGAAGAAAGGTGTATTACCGTTTATTCCACAGGGAACTTAGTGTTAGCCCTGTT-TACAATAAAG -s simHuman_chr6.simHuman.chr6 55646 64 + 601863 GAAAAGAAGACGCATTACCAGCTACTCTGCAGGGGGCTTAGTGATAGTCATGCT-TACCATCATG -s simRat_chr6.simRat.chr6 50614 65 + 647215 GGAACAAAGATGTGTTACTTTCTATTCCATGTGTTGTTTAGTGCCAGTTGTGCCCTACAATTACA - -a -s simMouse_chr6.simMouse.chr6 57367 59 + 636262 ATGACACAAGTTCAGTTTAACAGGGGTTATAGCTATATATCTATTTTCATTGTCCCATC -s Anc0.Anc0refChr4 4738 54 - 45765 CTGA---GAGTTCA--ATAACAGGGGTTAAAATTGTTTATCTACACTCATTGATCTTAT -s Anc1.Anc1refChr2 35545 54 + 144309 CTGA---GAGTTCA--ATAACAGGGGTTAAAATTGTTTATCTACACTCATTGATCTTAT -s Anc2.Anc2refChr4 1759 54 + 10050 CTGA---GAGTTTA--ATTACGAGAGTTAAAATTGTTTATCTACACTCATTAATCTTAT -s mr.mrrefChr0 54679 59 + 130230 CTGACACAAGTTCAGTTTAACAGGGGTTATAACTATATATCTACTTTCATTGTCCCAAT -s simCow_chr6.simCow.chr6 61612 54 + 602619 CTAA---GGGGTAA--TTTACGAGAGTTAATATTGTTTATCTACACTCATTAATCTTAT -s simDog_chr6.simDog.chr6 58354 42 + 593897 GAGA---GAGTTTA--AT------------AATTGTTTATCTACACTCATTAATCTGAT -s simHuman_chr6.simHuman.chr6 55716 54 + 601863 CTGA---GAGTTCA--CTAATAGTGGTTAAAATTGTTTAGCTACACTCATCGATCGTAT -s simRat_chr6.simRat.chr6 50679 59 + 647215 CTGACACAAGATCAGTTTAACAGGGGTTATAACTATATATCTACCTTCATTGTCTCAAT - -a -s simMouse_chr6.simMouse.chr6 57426 5 + 636262 AACTG -s Anc0.Anc0refChr4 4794 5 - 45765 AACTA -s Anc1.Anc1refChr2 35601 5 + 144309 AACTA -s Anc2.Anc2refChr4 1815 5 + 10050 AAATA -s mr.mrrefChr0 54738 5 + 130230 AACTG -s simCow_chr6.simCow.chr6 61668 5 + 602619 AAATA -s simDog_chr6.simDog.chr6 58398 5 + 593897 AAATA -s simHuman_chr6.simHuman.chr6 55772 5 + 601863 AACTA -s simRat_chr6.simRat.chr6 50738 5 + 647215 AACTG - -a -s simMouse_chr6.simMouse.chr6 57431 8 + 636262 ACCTATTT -s Anc0.Anc0refChr4 4800 8 - 45765 ACCAATTT -s Anc1.Anc1refChr2 35607 8 + 144309 ACCAATTT -s Anc2.Anc2refChr4 1821 8 + 10050 ACCAATTT -s mr.mrrefChr0 54743 8 + 130230 ACCTATTT -s simCow_chr6.simCow.chr6 61674 6 + 602619 ACTAAT-- -s simDog_chr6.simDog.chr6 58404 8 + 593897 ACCAAGTT -s simHuman_chr6.simHuman.chr6 55778 8 + 601863 ACCAATTT -s simRat_chr6.simRat.chr6 50743 8 + 647215 ACCTACTT - -a -s simMouse_chr6.simMouse.chr6 57439 15 + 636262 CAACAGATTCCCCTG -s Anc0.Anc0refChr4 4808 15 - 45765 CAACAGGTTCCCTTG -s Anc1.Anc1refChr2 35615 15 + 144309 CAACAGGTTCCCTTG -s Anc2.Anc2refChr4 1829 15 + 10050 CCACAGGTTCCCTTG -s mr.mrrefChr0 54751 15 + 130230 CAACAGATTCCCCTG -s simCow_chr6.simCow.chr6 61680 11 + 602619 ----AGGCTCCCTTG -s simDog_chr6.simDog.chr6 58412 12 + 593897 CCACAGATCCAC--- -s simHuman_chr6.simHuman.chr6 55786 15 + 601863 CAACAGGTTCCCTTG -s simRat_chr6.simRat.chr6 50759 15 + 647215 CATCAGATTTCCCTG - -a -s simMouse_chr6.simMouse.chr6 57454 35 + 636262 AAAAGTCTATCTTCTGGGTATTTTGGCCATGAACA -s Anc0.Anc0refChr4 4823 35 - 45765 AAAAGCCTATCTTCTGGGTATTTCAGCCATGACCA -s Anc1.Anc1refChr2 35630 35 + 144309 AAAAGCCTATCTTCTGGGTATTTCAGCCATGACCA -s Anc2.Anc2refChr4 1844 35 + 10050 AAAGGCTCATCATCTGGGTATTTCAGCCATGACCA -s mr.mrrefChr0 54766 35 + 130230 AAAAGTCTATCTTCTGGGTATTTTGGCCATGAACA -s simCow_chr6.simCow.chr6 61692 35 + 602619 AAAGGCTAAACAACTAGGTATTTCAGCCATGACCA -s simDog_chr6.simDog.chr6 58424 33 + 593897 --AGGCTCATCATCTGGATACAACAGGTATGACCG -s simHuman_chr6.simHuman.chr6 55801 35 + 601863 AAAAGCCTTCCTTCTGGGCATTTCAGCCATGACCA -s simRat_chr6.simRat.chr6 50774 35 + 647215 GAACGTCTATGTTCTGGGGATTTTGGCCATGAATA - -a -s simMouse_chr6.simMouse.chr6 57489 108 + 636262 TCAAATCAGTAGTGGATTCATAGTCATGTTCTGGGGGACATCAGTTTATGAGAGTGGTCATGCAGGCCCAAGAAGGACCAAGAGTCATTCTACCAGTGTCATCAGTCT -s Anc0.Anc0refChr4 4858 98 - 45765 TCAAATTTATAGGGGATTTATTATCATGTTCTGGGGGACACTAGTCTATGAGAATGATCATACTGA----------ACTAAAAGTGAGTCAGCAAATGCCATCAGTCT -s Anc1.Anc1refChr2 35665 98 + 144309 TCAAATTTATAGGGGATTTATTATCATGTTCTGGGGGACACTAGTCTATGAGAATGATCATACTGA----------ACTAAAAGTGAGTCAGCAAATGCCATCAGTCT -s Anc2.Anc2refChr4 1879 98 + 10050 TCAAATTTGTAAGGGATTTATTATCATGTTCTGGGGGACACTAGTCCATGCGAATGATCGTACTCA----------ACTACAAGTGAGTCAGCAAATGCCATCAGTCT -s mr.mrrefChr0 54801 108 + 130230 TCAAATCAATAGTGGATTCATAGTCATGTTCTGGGGGACATCAGTTTATGAGAATGGTCATGCAGGCCCAAGAAGGACCAAGAGTCATTCTGCCAATGTCATCAGTCT -s simCow_chr6.simCow.chr6 61727 77 + 602619 TCAAATCTGTAAGGGATTTATAAGCATGTTCTGGGGGACACTAGTTCATGGGAATG-------------------------------GTCAGCAAATGTCATTAGCCT -s simDog_chr6.simDog.chr6 58467 97 + 593897 TCAAACTGGTAAGGGATTTATTGTCAGGTTCTGGGGGACCCAAGTCCA-GCGAATGATCGTACTCA----------ACTACAAGTGAGCCAGCGATTGCCATCAGTCT -s simHuman_chr6.simHuman.chr6 55836 98 + 601863 TCAAATTTATAGGGGATTTGTCATGATGTTCTGGGGGACACTAGTATATGAGAATGATCATACTGA----------ACTAAAAGTAAGTCAGCAAATGCCATAAGTCT -s simRat_chr6.simRat.chr6 50809 107 + 647215 TCAAATCAATAGTGGATTCATAGTCATGTTCTGGAGGACATCAGTTTATGAGAATG-TGATGTAGGACCAAGAGGGACCAAGAGTGATTCTGCGAATTTCATCAGTCT - -a -s simMouse_chr6.simMouse.chr6 57597 25 + 636262 GGAGAATGTCCATGCTCTAGGGATA -s Anc0.Anc0refChr4 4956 25 - 45765 GGAGCATGTCCACACTCTAAAGATC -s Anc1.Anc1refChr2 35763 25 + 144309 GGAGCATGTCCACACTCTAAAGATC -s Anc2.Anc2refChr4 1977 25 + 10050 GAAGCATGTCCACACTCTAAAGATC -s mr.mrrefChr0 54909 25 + 130230 GGAGCATGTCCATGCTCTAGAGATA -s simCow_chr6.simCow.chr6 61806 25 + 602619 GAAGTGTGCCCACACTCTAAAAATC -s simDog_chr6.simDog.chr6 58564 25 + 593897 GATGCATGTCCACACTCTAAAGTTC -s simHuman_chr6.simHuman.chr6 55934 25 + 601863 GGAGCTTGTCCACAATCTAAATATT -s simRat_chr6.simRat.chr6 50916 25 + 647215 ATAGCATGTCCATGCTCCAGAGATA - -a -s simMouse_chr6.simMouse.chr6 57622 37 + 636262 CCCAATGACTGCCCTGCAGAAGCCAGCTTAACCAAAA -s Anc0.Anc0refChr4 4981 37 - 45765 CCCAATAGCTGCTTTGTACTAGCCTGCCTAAACAAAA -s Anc1.Anc1refChr2 35788 37 + 144309 CCCAATAGCTGCTTTGTACTAGCCTGCCTAAACAAAA -s Anc2.Anc2refChr4 2002 37 + 10050 CCCAATAGCTGCTTTGTACTATCCTGGCTAAACAAAG -s mr.mrrefChr0 54934 37 + 130230 CCCAATGACTGCCCTGCAGAAGCCAGCTTAACCAAAA -s simCow_chr6.simCow.chr6 61831 37 + 602619 ACCAACAGTTGCCTGATACTCTCCTGGCTAAACAAAG -s simDog_chr6.simDog.chr6 58589 37 + 593897 CCTAGTGGCTGCTTTGTACCATTCTGGCTAAACAAAG -s simHuman_chr6.simHuman.chr6 55961 37 + 601863 CACAATAGCGGCTTTGTACTAGCCTGCCCAAATAAAA -s simRat_chr6.simRat.chr6 50941 37 + 647215 CCCAATGACTGCCCTGCAGAAGCCAGCTTAAGCAAAA - -a -s simMouse_chr6.simMouse.chr6 57659 21 + 636262 ATCCATCCCTAGGGTGGTCCC -s Anc0.Anc0refChr4 5018 7 - 45765 ATTCAT--------------C -s Anc1.Anc1refChr2 35825 7 + 144309 ATTCAT--------------C -s Anc2.Anc2refChr4 2039 7 + 10050 ATTCAT--------------C -s mr.mrrefChr0 54971 14 + 130230 ATTCAT-------GTGGTCCC -s simCow_chr6.simCow.chr6 61869 7 + 602619 ATTCAT--------------C -s simDog_chr6.simDog.chr6 58626 7 + 593897 ATTCAT--------------C -s simHuman_chr6.simHuman.chr6 55998 7 + 601863 ATTCAT--------------C -s simRat_chr6.simRat.chr6 50978 14 + 647215 ATTTAT-------ATGGTCCC - -a -s simMouse_chr6.simMouse.chr6 57680 6 + 636262 TAGGGT -s Anc0.Anc0refChr4 5025 6 - 45765 TAGAGT -s Anc1.Anc1refChr2 35832 6 + 144309 TAGAGT -s Anc2.Anc2refChr4 2048 6 + 10050 TAGCAT -s mr.mrrefChr0 54985 6 + 130230 TAGAGT -s simCow_chr6.simCow.chr6 61878 6 + 602619 AAATAT -s simDog_chr6.simDog.chr6 58635 6 + 593897 TAGCAT -s simHuman_chr6.simHuman.chr6 56005 6 + 601863 TATAGT -s simRat_chr6.simRat.chr6 50992 6 + 647215 TAGAGT - -a -s simMouse_chr6.simMouse.chr6 57686 13 + 636262 GGTGCTTGAACCA -s Anc0.Anc0refChr4 5031 13 - 45765 GGTATCTTAATCA -s Anc1.Anc1refChr2 35838 13 + 144309 GGTATCTTAATCA -s Anc2.Anc2refChr4 2054 13 + 10050 GATATCTTAATCA -s mr.mrrefChr0 54991 13 + 130230 GGTGCCTGAACCA -s simCow_chr6.simCow.chr6 61884 13 + 602619 GAGATCTTAATCA -s simDog_chr6.simDog.chr6 58641 13 + 593897 GATATCTTAATCA -s simHuman_chr6.simHuman.chr6 56012 13 + 601863 GGTATCTTAATCA -s simRat_chr6.simRat.chr6 50998 13 + 647215 GGTGCCTGAACAA - -a -s simMouse_chr6.simMouse.chr6 57699 1 + 636262 G -s Anc0.Anc0refChr4 5044 1 - 45765 G -s Anc1.Anc1refChr2 35851 1 + 144309 G -s Anc2.Anc2refChr4 2067 1 + 10050 G -s mr.mrrefChr0 55004 1 + 130230 G -s simCow_chr6.simCow.chr6 61897 1 + 602619 G -s simDog_chr6.simDog.chr6 58656 1 + 593897 G -s simHuman_chr6.simHuman.chr6 56025 1 + 601863 G -s simRat_chr6.simRat.chr6 51011 1 + 647215 G - -a -s simMouse_chr6.simMouse.chr6 57700 22 + 636262 ACTGTTAACACAAACAAACAAG -s Anc0.Anc0refChr4 5045 21 - 45765 AC-ATTAACACAAACAAAAAAA -s Anc1.Anc1refChr2 35852 21 + 144309 AC-ATTAACACAAACAAAAAAA -s Anc2.Anc2refChr4 2068 21 + 10050 CC-ATTAACACAAACAAAAAAA -s mr.mrrefChr0 55005 22 + 130230 ACTGTTAACACAAACAAACAAG -s simCow_chr6.simCow.chr6 61899 21 + 602619 CC-ATGAACACAAACAAAAAAA -s simDog_chr6.simDog.chr6 58657 21 + 593897 CC-ATTACTACAAACAAAAAAA -s simHuman_chr6.simHuman.chr6 56026 21 + 601863 AC-ATTAACACAAACAAAAAAA -s simRat_chr6.simRat.chr6 51012 22 + 647215 ACTGTTCACACAAGCAGACAAG - -a -s simMouse_chr6.simMouse.chr6 57722 107 + 636262 ATGTTCTCATTCAGCTAACGCGGACGTGGATCATTGCAAAGTTAGGGCACAGGACCATGCGTCACTTTCTGGACACCTCTCTCTTAGACATTCCTAGATTTGAATAG -s Anc0.Anc0refChr4 5066 85 - 45765 ACACTCCCCTTCAACTGACT------TGGATAATTGCAAAATTAGGGCTCTGGATTATGCACTTTT----------------CTTAGACATTTCCGCATGTGAACAG -s Anc1.Anc1refChr2 35873 85 + 144309 ACACTCCCCTTCAACTGACT------TGGATAATTGCAAAATTAGGGCTCTGGATTATGCACTTTT----------------CTTAGACATTTCCGCATGTGAACAG -s Anc2.Anc2refChr4 2089 85 + 10050 GCACTCCCCTTCAACTGACT------TGGATAAATGCAAAACTAGGGCTCTGGATTATGCACTTTT----------------CTTAGACATTTCCGTGTTTACATGG -s mr.mrrefChr0 55027 100 + 130230 ATGTTCTCATTCAGCTAACG------TGGATCATTGCAAAATTAGGGCACAGGATCATGCGTCACTTT-TGGACACCTCTCTCTTAGACATTCCTACATGTGAACAG -s simCow_chr6.simCow.chr6 61920 57 + 602619 GTGGCCCCCTTCATCTAACA------TGGATAGACACAAAACTAGGGCTCTGATATTGGCAAT-------------------------------------------- -s simDog_chr6.simDog.chr6 58678 85 + 593897 GCACTCCCTTTCAAGTGACT------TGGATAATTGCAAAACTAGGGCTTTGGATTATGCACTTTT----------------CTTAGACATTTCCGTGTTTACATGG -s simHuman_chr6.simHuman.chr6 56048 84 + 601863 ACACTCCCCTTCGACTGTCT------TGGAATAT-GCAAAATTAAAGTTCTGGATTATACTCTTTT----------------CTTAGACATTTGCGCATGTGAACAG -s simRat_chr6.simRat.chr6 51034 100 + 647215 ATGTTCTCATTCAGTTAACA------TGGATGATTGCCAAATTAGGACACAGGATCACGCGTCACTTT-TAGATACCTCCCTTTTAAACATTGCTACGTGGGAACAG - -a -s simMouse_chr6.simMouse.chr6 57829 59 + 636262 GACCACATACATATTCCATTGCACCTGTTTGTACCTGGCCTGGGTAAACTGTATACCAC -s Anc0.Anc0refChr4 5155 56 - 45765 GACAACATAAGT--TCCCTTGCACCTATTTGTACCTGGC-TGGGTAAACTTCGCACCAC -s Anc1.Anc1refChr2 35962 56 + 144309 GACAACATAAGT--TCCCTTGCACCTATTTGTACCTGGC-TGGGTAAACTTCGCACCAC -s Anc2.Anc2refChr4 2178 56 + 10050 AACAACATAAGT--TTTCTTGCACCTATTTGTAGCTGGT-TGGGTGAACTTCGCACCAC -s mr.mrrefChr0 55127 57 + 130230 GACAACATACAT--TCCATTGCACCTGTTTGTACCTGGCCTGGGTAAACTGTATACCAC -s simCow_chr6.simCow.chr6 61979 56 + 602619 AACACCGTAAGT--TTTCTTACACCTGATTGTAGCTGGT-TGGGGGGACTTGGAGCTAC -s simDog_chr6.simDog.chr6 58767 56 + 593897 ATACACATAAGT--TTTCTTGCACCTATTTGCAGCTGGT-TGGGTGAACTTCGCACCAC -s simHuman_chr6.simHuman.chr6 56137 47 + 601863 GACAACATGAGT--TCCTTTGCACCTATTTGTACCTGGC-TGGGTAAGAT--------- -s simRat_chr6.simRat.chr6 51134 57 + 647215 GACAACATACAT--TCCATTGCACCTGTTTGTACCTAGCCTGGGTAAACTTTATACCAC - -a -s simMouse_chr6.simMouse.chr6 57888 7 + 636262 GGATAAC -s Anc0.Anc0refChr4 5211 2 - 45765 -----AC -s Anc1.Anc1refChr2 36018 2 + 144309 -----AC -s Anc2.Anc2refChr4 2234 2 + 10050 -----AC -s mr.mrrefChr0 55184 7 + 130230 GGATAAC -s simCow_chr6.simCow.chr6 62035 2 + 602619 -----AC -s simDog_chr6.simDog.chr6 58823 2 + 593897 -----AC -s simRat_chr6.simRat.chr6 51193 7 + 647215 GGATAAC - -a -s simMouse_chr6.simMouse.chr6 57895 102 + 636262 AGATCACTAACTTTTGCAGCATCTATGTGATAAATCTGTTTGGGTGAAAGTCTGATTGGGTGTCTGGATGCAATGTCAGTATGCTAATGACCTATGGGTGTA -s Anc0.Anc0refChr4 5213 26 - 45765 TGAT----------------------------------------------------------------------------ATGCTGGGGAATTATGGCTGTA -s Anc1.Anc1refChr2 36020 26 + 144309 TGAT----------------------------------------------------------------------------ATGCTGGGGAATTATGGCTGTA -s Anc2.Anc2refChr4 2236 26 + 10050 TGAT----------------------------------------------------------------------------ATGCTGGGGAATTATGGCTGTA -s mr.mrrefChr0 55191 102 + 130230 AGATCACTAACTTTTGCAGCATCTATGTGATAAATCTGTTTGGGTGAAAGTCTGATTGGGTGTCTGGATGCAATGTCAGTATGCTAATGACCTATGGGTGTA -s simCow_chr6.simCow.chr6 62037 26 + 602619 TGAT----------------------------------------------------------------------------ATGCTGAGGAATTAGGGTGGTA -s simDog_chr6.simDog.chr6 58896 26 + 593897 TGAT----------------------------------------------------------------------------ATGCTGGGGAATTATGGCTGTA -s simRat_chr6.simRat.chr6 51200 102 + 647215 CGATCACCAACTTTTGAAGCATCTATGTAATAAATCTGGTTGAGTGCAAGTCTGGATGGGTGCATGGATGCAATGTCAGTGTGCTAACGACCTATGGGTGAA - -a -s simMouse_chr6.simMouse.chr6 57997 34 + 636262 TTCTTGTTCAGTACTTTGTATGCACAAGACTATA -s Anc0.Anc0refChr4 5239 32 - 45765 TTCTGG--GTGTACTCCCTTTGCTCCAGACCATA -s Anc1.Anc1refChr2 36046 32 + 144309 TTCTGG--GTGTACTCCCTTTGCTCCAGACCATA -s Anc2.Anc2refChr4 2264 32 + 10050 CTCTGG--GTGTACTCCCTTTGCTCCAGGCCATA -s mr.mrrefChr0 55293 34 + 130230 TTCTTGTTCAGTACTTCCTATGCACAAGACCATA -s simCow_chr6.simCow.chr6 62065 31 + 602619 CTCTAG--GAGTACTCCCCTTGCTCCAGGCC-TA -s simDog_chr6.simDog.chr6 58924 28 + 593897 CTCTGG--GTATACGCCCTTTGCTC----CCATA -s simHuman_chr6.simHuman.chr6 56184 32 + 601863 TTCTGG--GGGTACTCCCTTTGCTCCAGACCATA -s simRat_chr6.simRat.chr6 51302 34 + 647215 TTCTTGGCCAACACTTCCTATGCACAGGATCATG - -a -s simMouse_chr6.simMouse.chr6 58031 23 + 636262 GTGCGCATCAAGCACTTCTTATA -s Anc0.Anc0refChr4 5273 23 - 45765 GGGCATATCAAGCACCTATTATA -s Anc1.Anc1refChr2 36080 23 + 144309 GGGCATATCAAGCACCTATTATA -s Anc2.Anc2refChr4 2298 23 + 10050 GGGCATATCAAGCACCCATTATA -s mr.mrrefChr0 55327 23 + 130230 GTGCACATCAAGCACTTCTTATA -s simCow_chr6.simCow.chr6 62098 23 + 602619 GAGCATCTCAAGCACCCATTATA -s simDog_chr6.simDog.chr6 58954 23 + 593897 GGGCATATCAAGTAACCATTATA -s simHuman_chr6.simHuman.chr6 56218 23 + 601863 GGGCATATCAAGCACCTATTATA -s simRat_chr6.simRat.chr6 51336 23 + 647215 GTGCACATCATGCACTCCTTATA - -a -s simMouse_chr6.simMouse.chr6 58054 12 + 636262 GACACTAATAAT -s Anc0.Anc0refChr4 5296 3 - 45765 GAC--------- -s Anc1.Anc1refChr2 36103 3 + 144309 GAC--------- -s Anc2.Anc2refChr4 2327 3 + 10050 GAC--------- -s mr.mrrefChr0 55350 12 + 130230 GACACTAATAAT -s simCow_chr6.simCow.chr6 62127 3 + 602619 GAC--------- -s simDog_chr6.simDog.chr6 58983 3 + 593897 GAC--------- -s simHuman_chr6.simHuman.chr6 56241 3 + 601863 CTC--------- -s simRat_chr6.simRat.chr6 51359 12 + 647215 GACACTGGCAAT - -a -s simMouse_chr6.simMouse.chr6 58066 84 + 636262 GATGACAAGAGCATTATTTGATACTTGTTAAGGGTGGATCAACTTGTATCCTCTCTGTTAGTTTTGGTCATCTGTGTCTATGCC -s Anc0.Anc0refChr4 5299 47 - 45765 ----------------------------------TGGATTAAATTGTGTCCTCTCCCTCATTCTTGATC---TGTGTCTATAGC -s Anc1.Anc1refChr2 36106 47 + 144309 ----------------------------------TGGATTAAATTGTGTCCTCTCCCTCATTCTTGATC---TGTGTCTATAGC -s Anc2.Anc2refChr4 2330 47 + 10050 ----------------------------------TGGATTAGATGATGTCGCCTTCCTCATCCTTGATC---TGTGTCCATAGT -s mr.mrrefChr0 55362 84 + 130230 GATGACAAGAGCATTATTTGATACTTGTTAAGGGTGGATCAACTTGTATCCTCTCTGTCAGTTTTGATCATCTGTGTCTATGCC -s simCow_chr6.simCow.chr6 62130 46 + 602619 ----------------------------------TGGATTATATCATGTCAACCTCCCTATCCTTGATC---AGTTTCCCCAG- -s simDog_chr6.simDog.chr6 58986 47 + 593897 ----------------------------------TGGATTGGGTGATGCTGCCTTTCTCATCCTTGATC---TGTGTTCATAGT -s simHuman_chr6.simHuman.chr6 56244 47 + 601863 ----------------------------------TAGATTAAATTGTCTCCTCTCCCTCATTCTTGATC---TGTGTCTATATC -s simRat_chr6.simRat.chr6 51372 84 + 647215 GATGACAAGATCATTATTTGATACTTGTCAAGGACGGATCAACTTGTATCCTCTCTGTCAGCTTTGATCATCTGTGTTTATGCC - -a -s simMouse_chr6.simMouse.chr6 58150 15 + 636262 ACATACCCAGACAAT -s Anc0.Anc0refChr4 5346 15 - 45765 ACATATCCACACACC -s Anc1.Anc1refChr2 36153 15 + 144309 ACATATCCACACACC -s Anc2.Anc2refChr4 2377 15 + 10050 ACACATCCACACACC -s mr.mrrefChr0 55446 15 + 130230 ACATACCCACACAAT -s simCow_chr6.simCow.chr6 62176 13 + 602619 --ACATCCACACACC -s simDog_chr6.simDog.chr6 59033 15 + 593897 ACACACCCACCCATC -s simHuman_chr6.simHuman.chr6 56291 15 + 601863 ACATATCCACACACC -s simRat_chr6.simRat.chr6 51457 15 + 647215 ACATACCCACACAAT - -a -s simMouse_chr6.simMouse.chr6 58165 37 + 636262 CTGTGTCCACACCACATATTACACATTCATTATTTAG -s Anc0.Anc0refChr4 5377 36 - 45765 TTGTTTTCTTACCCTAGATCACTCTAT-ATTATTTGG -s Anc1.Anc1refChr2 36184 36 + 144309 TTGTTTTCTTACCCTAGATCACTCTAT-ATTATTTGG -s Anc2.Anc2refChr4 2408 36 + 10050 TTGTTTTCTTACGCTAGATCACTTTAT-ATTATTTGG -s mr.mrrefChr0 55461 37 + 130230 CTGTGTCCATACCACATATTACACATTCATTATTTAG -s simCow_chr6.simCow.chr6 62200 35 + 602619 TTGCTTTCTTACACTAGATC-CTTTAT-ATTATTGGG -s simDog_chr6.simDog.chr6 59064 36 + 593897 TTGTTTTCTTATGCTAGATCAGTTTAT-ATTATTTGG -s simHuman_chr6.simHuman.chr6 56322 36 + 601863 TTGTTTTCTTTCCCTAGATCACTCCAT-ATTATCTGG -s simRat_chr6.simRat.chr6 51472 30 + 647215 CTGTCTCCATGCCACATATTACACATTCA-------G - -a -s simMouse_chr6.simMouse.chr6 58202 1 + 636262 A -s Anc0.Anc0refChr4 5413 1 - 45765 A -s Anc1.Anc1refChr2 36220 1 + 144309 A -s Anc2.Anc2refChr4 2444 1 + 10050 A -s mr.mrrefChr0 55498 1 + 130230 A -s simCow_chr6.simCow.chr6 62236 1 + 602619 A -s simDog_chr6.simDog.chr6 59100 1 + 593897 A -s simHuman_chr6.simHuman.chr6 56358 1 + 601863 A -s simRat_chr6.simRat.chr6 51502 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 58203 18 + 636262 TTAGATAATTTAAACAAT -s Anc0.Anc0refChr4 5422 18 - 45765 TGACTCAATTTGAGCTAT -s Anc1.Anc1refChr2 36229 18 + 144309 TGACTCAATTTGAGCTAT -s Anc2.Anc2refChr4 2453 18 + 10050 TGACTCAATTTGAGCTAC -s mr.mrrefChr0 55499 18 + 130230 TTAGATAATTTAAACAAT -s simCow_chr6.simCow.chr6 62245 18 + 602619 TGATGTAACCTGATCTAG -s simDog_chr6.simDog.chr6 59109 18 + 593897 TGACTCAATTTGAGCTAC -s simHuman_chr6.simHuman.chr6 56367 18 + 601863 TGACTCAATTTGAGCTAT -s simRat_chr6.simRat.chr6 51503 18 + 647215 TTAGATAATTTAGACAAT - -a -s simMouse_chr6.simMouse.chr6 58221 16 + 636262 CCTTGCCGCCACTGGG -s Anc0.Anc0refChr4 5453 16 - 45765 TTTTAGAGCCACTGGA -s Anc1.Anc1refChr2 36260 16 + 144309 TTTTAGAGCCACTGGA -s Anc2.Anc2refChr4 2484 16 + 10050 TTTTAGAGCCACTGAA -s mr.mrrefChr0 55517 16 + 130230 CCTTGCAGCCACTGGA -s simCow_chr6.simCow.chr6 62276 16 + 602619 TATTAGAGCCACTGAA -s simDog_chr6.simDog.chr6 59140 16 + 593897 TTTTAGAGCCACTGAA -s simHuman_chr6.simHuman.chr6 56398 16 + 601863 TTTTAAAGACACTGGA -s simRat_chr6.simRat.chr6 51521 16 + 647215 CCTTGCAGCCACTGGA - -a -s simMouse_chr6.simMouse.chr6 58237 12 + 636262 CACCTGATGCAC -s Anc0.Anc0refChr4 5470 9 - 45765 CACCTGTC---T -s Anc1.Anc1refChr2 36277 12 + 144309 CACCTGTCTCTT -s Anc2.Anc2refChr4 2501 9 + 10050 CACCTGTC---T -s mr.mrrefChr0 55534 12 + 130230 CACCTGATGCTT -s simCow_chr6.simCow.chr6 62293 9 + 602619 CACCTGTC---T -s simDog_chr6.simDog.chr6 59157 9 + 593897 CACCTGTC---T -s simHuman_chr6.simHuman.chr6 56415 12 + 601863 CACCTGTCTCTT -s simRat_chr6.simRat.chr6 51538 12 + 647215 CACCTCATGCTT - -a -s simMouse_chr6.simMouse.chr6 58249 20 + 636262 ACCATGCATGTGCCCTGCAT -s Anc0.Anc0refChr4 5479 20 - 45765 ACTATGCCTGTGGCCTCAAT -s Anc1.Anc1refChr2 36289 20 + 144309 ACTATGCCTGTGGCCTCAAT -s Anc2.Anc2refChr4 2510 20 + 10050 ACTATGCCTGTGGCTTCAGT -s mr.mrrefChr0 55546 20 + 130230 ACCATGCATGTGCCCTGCAT -s simCow_chr6.simCow.chr6 62305 20 + 602619 ACCATGCCTCTGGCTCCAGT -s simDog_chr6.simDog.chr6 59166 17 + 593897 ACTATGCCTGTGGCTTC--- -s simHuman_chr6.simHuman.chr6 56427 19 + 601863 ACTA-GCCTGTGGCCTCAAT -s simRat_chr6.simRat.chr6 51550 20 + 647215 ACCATGCATGTGCCATGCAT - -a -s simMouse_chr6.simMouse.chr6 58269 18 + 636262 GTGACTATAACTGATGCG -s Anc0.Anc0refChr4 5499 10 - 45765 ----CCATA----ATGGG -s Anc1.Anc1refChr2 36309 14 + 144309 GTTCCCATA----ATGGG -s Anc2.Anc2refChr4 2530 10 + 10050 ----CCATG----ATGGG -s mr.mrrefChr0 55566 18 + 130230 GTGACTATAATTGATGGG -s simCow_chr6.simCow.chr6 62325 10 + 602619 ----CCATT----ATGGA -s simDog_chr6.simDog.chr6 59183 6 + 593897 --------G----ATGGG -s simHuman_chr6.simHuman.chr6 56448 14 + 601863 GTTCCCATA----ATGGG -s simRat_chr6.simRat.chr6 51570 18 + 647215 GTGACTATAATTGATGGG - -a -s simMouse_chr6.simMouse.chr6 58287 16 + 636262 TAAAGATATTAAAATG -s Anc0.Anc0refChr4 5510 16 - 45765 TAAAGATAATAAAATG -s Anc1.Anc1refChr2 36324 16 + 144309 TAAAGATAATAAAATG -s Anc2.Anc2refChr4 2541 16 + 10050 TAAAGATAATAAAGTG -s mr.mrrefChr0 55585 16 + 130230 TAAAGATATTAAAATG -s simCow_chr6.simCow.chr6 62336 16 + 602619 TAAAGGTAATAAAGTG -s simDog_chr6.simDog.chr6 59190 16 + 593897 TGAGAACAATAAAGTG -s simHuman_chr6.simHuman.chr6 56463 16 + 601863 CAGAGATAATAAAATG -s simRat_chr6.simRat.chr6 51589 16 + 647215 TAAAGATATTAAAATG - -a -s simMouse_chr6.simMouse.chr6 58303 19 + 636262 TGGCCTTTATCATACTTCG -s Anc0.Anc0refChr4 5527 15 - 45765 GAACCTTCATTATAC---- -s Anc1.Anc1refChr2 36341 19 + 144309 GAACCTTCATTATACTATG -s Anc2.Anc2refChr4 2558 15 + 10050 GAACCCTCATTATAC---- -s mr.mrrefChr0 55602 19 + 130230 TGGCCTTTATCATACTTCG -s simCow_chr6.simCow.chr6 62353 15 + 602619 GAAACCTCACTATAC---- -s simDog_chr6.simDog.chr6 59207 15 + 593897 GAACCCTCATTATCC---- -s simHuman_chr6.simHuman.chr6 56480 19 + 601863 GCACATTCATTATACTATG -s simRat_chr6.simRat.chr6 51606 19 + 647215 TGGCCTTTATCATACTGCG - -a -s simMouse_chr6.simMouse.chr6 58322 4 + 636262 TGCA -s Anc0.Anc0refChr4 5542 2 - 45765 --TA -s Anc1.Anc1refChr2 36360 4 + 144309 AGTA -s Anc2.Anc2refChr4 2573 2 + 10050 --TA -s mr.mrrefChr0 55621 4 + 130230 TGTA -s simCow_chr6.simCow.chr6 62368 2 + 602619 --TC -s simDog_chr6.simDog.chr6 59222 2 + 593897 --TA -s simHuman_chr6.simHuman.chr6 56499 4 + 601863 AGTA -s simRat_chr6.simRat.chr6 51626 4 + 647215 TATA - -a -s simMouse_chr6.simMouse.chr6 58326 18 + 636262 ACTACACAGTTTGTTGAG -s Anc0.Anc0refChr4 5544 18 - 45765 ACTAAATGGTTTAAAGAG -s Anc1.Anc1refChr2 36364 18 + 144309 ACTAAATGGTTTAAAGAG -s Anc2.Anc2refChr4 2575 18 + 10050 ACTAAATGGTTCAAAGAG -s mr.mrrefChr0 55625 18 + 130230 ACTACACAGTTTAATGAG -s simCow_chr6.simCow.chr6 62376 18 + 602619 ACTAAAGGGCTCAAAGAG -s simDog_chr6.simDog.chr6 59224 18 + 593897 ACTAAATGGTTCAAAGGG -s simHuman_chr6.simHuman.chr6 56523 18 + 601863 ACTAAATGGTTTAAAGAG -s simRat_chr6.simRat.chr6 51630 18 + 647215 ACTACACAGTTCAATGGG - -a -s simMouse_chr6.simMouse.chr6 58344 7 + 636262 CATTGCA -s Anc0.Anc0refChr4 5562 7 - 45765 AATGCTG -s Anc1.Anc1refChr2 36382 7 + 144309 AATGCTG -s Anc2.Anc2refChr4 2594 7 + 10050 AATGTTG -s mr.mrrefChr0 55643 7 + 130230 CATTCCA -s simCow_chr6.simCow.chr6 62395 7 + 602619 AATGTTA -s simDog_chr6.simDog.chr6 59243 7 + 593897 AATGTTG -s simHuman_chr6.simHuman.chr6 56541 7 + 601863 AATGCTG -s simRat_chr6.simRat.chr6 51648 7 + 647215 CATCCCA - -a -s simMouse_chr6.simMouse.chr6 58351 25 + 636262 AGTGTCACACATATTCAGGTTGTTA -s Anc0.Anc0refChr4 5570 25 - 45765 ACTGTCTCATATATTCAGCTGATTA -s Anc1.Anc1refChr2 36390 25 + 144309 ACTGTCTCATATATTCAGCTGATTA -s Anc2.Anc2refChr4 2602 25 + 10050 GCTGTCTCATATATTCAGCTGATTA -s mr.mrrefChr0 55650 25 + 130230 AGTGTCACACATATTCAGTTTGTTA -s simCow_chr6.simCow.chr6 62403 25 + 602619 GCTGACACATATATCCAGCTGCTTA -s simDog_chr6.simDog.chr6 59251 25 + 593897 GCTGTTTCCTATATTCGGCTGATTA -s simHuman_chr6.simHuman.chr6 56549 25 + 601863 ACTGTCTCAGATATTCAACTGATTA -s simRat_chr6.simRat.chr6 51655 25 + 647215 GGTGTCACACATATTCAGTTTGCTA - -a -s simMouse_chr6.simMouse.chr6 58376 45 + 636262 TGTTTGATATTCAATCATTATATGTCTTACAGAAACCCTTGTAAG -s Anc0.Anc0refChr4 5596 45 - 45765 CCTGTAAGATTAAATCCTTGTGTCTCTTACAGAAACCCTTATAAG -s Anc1.Anc1refChr2 36416 45 + 144309 CCTGTAAGATTAAATCCTTGTGTCTCTTACAGAAACCCTTATAAG -s Anc2.Anc2refChr4 2628 45 + 10050 CCTGAAAGATTAATTCCTTGTGTCTCTTACAAAAACCCTTATAAA -s mr.mrrefChr0 55675 45 + 130230 TGTTTGATATTCAATCATTGTGTGTCTTACAGAAACCCTTGTAAG -s simCow_chr6.simCow.chr6 62429 45 + 602619 CCTGAGAGATTAATCCCTCGTGTCTCTTACACAAACCTTTATTAA -s simDog_chr6.simDog.chr6 59277 45 + 593897 CCTGAAAGATTAGTTCCTTGTGTCTCTTACAAAATGCCTTATAAA -s simHuman_chr6.simHuman.chr6 56575 45 + 601863 CCTGTAGGATTAAATCCTTGTGTCTCTTACAGAAACTCTTATAAG -s simRat_chr6.simRat.chr6 51680 40 + 647215 -----GATATTCATTCATTGTGTATCTTACAGAAACCTCTGTAAG - -a -s simMouse_chr6.simMouse.chr6 58421 66 + 636262 ATGTTTGACTGGTAGCAGCAATGCTAGGGAATATTCACTAACTTTATTCTTAAAGAAGTGTATGTA -s Anc0.Anc0refChr4 5641 2 - 45765 A----------------------------------------------------------------T -s Anc1.Anc1refChr2 36461 6 + 144309 AT------------------------------------------------------------TGTT -s Anc2.Anc2refChr4 2673 2 + 10050 A----------------------------------------------------------------T -s mr.mrrefChr0 55720 7 + 130230 AT-----------------------------------------------------------ATGTA -s simCow_chr6.simCow.chr6 62480 2 + 602619 C----------------------------------------------------------------T -s simDog_chr6.simDog.chr6 59322 2 + 593897 A----------------------------------------------------------------T -s simHuman_chr6.simHuman.chr6 56620 6 + 601863 AT------------------------------------------------------------TGTT -s simRat_chr6.simRat.chr6 51720 7 + 647215 AT-----------------------------------------------------------ATGTA - -a -s simMouse_chr6.simMouse.chr6 58487 29 + 636262 AACTACAATGATGCACTCTGACTCAATGC -s Anc0.Anc0refChr4 5665 29 - 45765 ATTCACAAATATCTCCCCTTACACAAAGT -s Anc1.Anc1refChr2 36489 29 + 144309 ATTCACAAATATCTCCCCTTACACAAAGT -s Anc2.Anc2refChr4 2697 29 + 10050 ATTCACAAATATCTCCCCCTACACAAAGT -s mr.mrrefChr0 55727 29 + 130230 AACTACAATGATGCGCTCTGACTCAATAC -s simCow_chr6.simCow.chr6 62508 28 + 602619 ATTCACACATATCTCCCAGT-CACAAAGT -s simDog_chr6.simDog.chr6 59346 29 + 593897 ATTGACAAATGTCTTCCCCTATACAAAGT -s simHuman_chr6.simHuman.chr6 56685 29 + 601863 ATTCATAAACACCTCCCCTTACACAAGGT -s simRat_chr6.simRat.chr6 51727 29 + 647215 AACTACAATGATGCGCTTTGACTCAATAC - -a -s simMouse_chr6.simMouse.chr6 58516 22 + 636262 TTAAATAACTGAGTCAAGACAA -s Anc0.Anc0refChr4 5715 22 - 45765 TTTGAAAGGTCATTCTAGAAAA -s Anc1.Anc1refChr2 36539 22 + 144309 TTTGAAAGGTCATTCTAGAAAA -s Anc2.Anc2refChr4 2747 22 + 10050 TTTGAAAGGTCATTCTAAAAAA -s mr.mrrefChr0 55756 22 + 130230 TTGTATAACTGAGTCAAGACAA -s simCow_chr6.simCow.chr6 62557 20 + 602619 TTTGAAAGCTCATTCTAAAA-- -s simDog_chr6.simDog.chr6 59396 22 + 593897 TTTGAAGGGGTGTCCTCAAAAA -s simHuman_chr6.simHuman.chr6 56735 22 + 601863 TTTGAAAGTTCATTTTAGAAAT -s simRat_chr6.simRat.chr6 51756 22 + 647215 TTGTGTAGATGAGTCAAGACAA - -a -s simMouse_chr6.simMouse.chr6 58538 8 + 636262 ATATTAGT -s Anc0.Anc0refChr4 5737 8 - 45765 ATATTTAG -s Anc1.Anc1refChr2 36561 8 + 144309 ATATTTAG -s Anc2.Anc2refChr4 2769 8 + 10050 AGATTTAG -s mr.mrrefChr0 55778 8 + 130230 ATATTAAC -s simCow_chr6.simCow.chr6 62577 2 + 602619 ------AG -s simDog_chr6.simDog.chr6 59418 8 + 593897 AGATTTAG -s simHuman_chr6.simHuman.chr6 56760 8 + 601863 GTATTCAG -s simRat_chr6.simRat.chr6 51778 8 + 647215 ATATTAAC - -a -s simMouse_chr6.simMouse.chr6 58546 2 + 636262 GT -s Anc0.Anc0refChr4 5745 2 - 45765 AT -s Anc1.Anc1refChr2 36569 2 + 144309 AT -s Anc2.Anc2refChr4 2780 2 + 10050 AT -s mr.mrrefChr0 55786 2 + 130230 AT -s simCow_chr6.simCow.chr6 62582 2 + 602619 AT -s simDog_chr6.simDog.chr6 59429 2 + 593897 AT -s simHuman_chr6.simHuman.chr6 56768 2 + 601863 AT -s simRat_chr6.simRat.chr6 51786 2 + 647215 AT - -a -s simMouse_chr6.simMouse.chr6 58548 20 + 636262 CTGCATGTATTCACATCACA -s Anc0.Anc0refChr4 5785 20 - 45765 ATACATGTGTTCACATCACT -s Anc1.Anc1refChr2 36609 20 + 144309 ATACATGTGTTCACATCACT -s Anc2.Anc2refChr4 2820 20 + 10050 ATATATGTGTTCACATCACT -s mr.mrrefChr0 55788 20 + 130230 CTGCATGTGTTCACATCACA -s simCow_chr6.simCow.chr6 62622 20 + 602619 ATATATGTGTTCACATAGCT -s simDog_chr6.simDog.chr6 59469 19 + 593897 ATA-ATGTGTTCATGTCACT -s simHuman_chr6.simHuman.chr6 56808 20 + 601863 ATACATGTGTTCACATCACT -s simRat_chr6.simRat.chr6 51788 20 + 647215 CTGCATGTGTTCACATCACA - -a -s simMouse_chr6.simMouse.chr6 58568 5 + 636262 AGGGA -s Anc0.Anc0refChr4 5805 4 - 45765 AGG-A -s Anc1.Anc1refChr2 36629 4 + 144309 AGG-A -s Anc2.Anc2refChr4 2840 4 + 10050 AGG-A -s mr.mrrefChr0 55808 4 + 130230 AGG-A -s simCow_chr6.simCow.chr6 62643 4 + 602619 AGG-A -s simDog_chr6.simDog.chr6 59488 4 + 593897 AGG-A -s simHuman_chr6.simHuman.chr6 56828 4 + 601863 AGG-G -s simRat_chr6.simRat.chr6 51808 4 + 647215 AGG-A - -a -s simMouse_chr6.simMouse.chr6 58573 39 + 636262 CTGTGAGTTTGCTAGAAGTGTGTCTTGGGGAAGATGTCT -s Anc0.Anc0refChr4 5816 39 - 45765 GCATAAATTTGCAAGGAGCATGTCTTAGGGAAGACATTC -s Anc1.Anc1refChr2 36640 39 + 144309 GCATAAATTTGCAAGGAGCATGTCTTAGGGAAGACATTC -s Anc2.Anc2refChr4 2851 39 + 10050 GCATAAATTTGGAATGAGCATGTCTTAGGGAAGACATTC -s mr.mrrefChr0 55812 39 + 130230 CTGTGAGTTTGCTAGGAGTGTGTCTTAGGGAAGACATCT -s simCow_chr6.simCow.chr6 62654 39 + 602619 GCATAAATCTGTAATGAGCATGTCTTAGGGAAGACATTT -s simDog_chr6.simDog.chr6 59499 38 + 593897 -CATGAATTGGGGATGAGCATGTCATAGGGAAGACGTTC -s simHuman_chr6.simHuman.chr6 56839 39 + 601863 TCATAAATTTGCAAGGAGCCTGTCTTAGGGAAGACATTC -s simRat_chr6.simRat.chr6 51812 39 + 647215 CTGTGAGTTTGCTAGGAGTGTGTCTTAGGGAAGACATCT - -a -s simMouse_chr6.simMouse.chr6 58612 19 + 636262 ATCAATTTAGGGTATTTTG -s Anc0.Anc0refChr4 5861 5 - 45765 AT--------------TGG -s Anc1.Anc1refChr2 36685 5 + 144309 AT--------------TGG -s Anc2.Anc2refChr4 2896 5 + 10050 AT--------------TGG -s mr.mrrefChr0 55857 19 + 130230 ATCAATTTAGGGTATTTTG -s simCow_chr6.simCow.chr6 62699 5 + 602619 AT--------------TGA -s simDog_chr6.simDog.chr6 59550 5 + 593897 TT--------------TTG -s simHuman_chr6.simHuman.chr6 56884 5 + 601863 AT--------------TGG -s simRat_chr6.simRat.chr6 51857 19 + 647215 CTCAATTTAGGGTATTTTG - -a -s simMouse_chr6.simMouse.chr6 58631 30 + 636262 TGAATAGTCACTATTCCGAAGTGAAGACAT -s Anc0.Anc0refChr4 5866 30 - 45765 TGAATAGTCACCATATGGAGGTGAAAACAT -s Anc1.Anc1refChr2 36690 30 + 144309 TGAATAGTCACCATATGGAGGTGAAAACAT -s Anc2.Anc2refChr4 2901 30 + 10050 TGAATAGTCACCATATGGAGGTGAAAACAT -s mr.mrrefChr0 55876 30 + 130230 TGAATAGTCACTATACCGAGGTGAAGACAT -s simCow_chr6.simCow.chr6 62718 30 + 602619 TGAATCGTTACCATATGGAGGTGAAAACAT -s simDog_chr6.simDog.chr6 59555 11 + 593897 TGAGTAGTCAT------------------- -s simHuman_chr6.simHuman.chr6 56889 30 + 601863 TGAACAGTCGCCCTGTGGAGATGAAAACAT -s simRat_chr6.simRat.chr6 51876 30 + 647215 TGAATAGTCACTTTACCGAGGTGAAGACAT - -a -s simMouse_chr6.simMouse.chr6 58661 42 + 636262 CAAAAAATTGCAGGTATCAAGCTCTTTAACATAAAGGGCAAT -s Anc0.Anc0refChr4 5904 35 - 45765 GAAAAAATTGTAGGTATCAGGCCCCTT-------AGGGAAAT -s Anc1.Anc1refChr2 36728 42 + 144309 GAAAAAATTGTAGGTATCAGGCCCCTTACAATGAAGGGAAAT -s Anc2.Anc2refChr4 2939 35 + 10050 GAAAAAATTTTGTGTATCAGGCCCCTT-------AGGGAGAT -s mr.mrrefChr0 55911 42 + 130230 GAAAAAATTGTAGGTATCAAGCCCTTTAACATAAAGGGAAAT -s simCow_chr6.simCow.chr6 62756 35 + 602619 TAAAAAATTATGTGTATCAGGCCGCTT-------AGAAAGAC -s simDog_chr6.simDog.chr6 59571 35 + 593897 GAAAAAATTTGGTCTATGAGGCCCCTC-------AGGGAGAT -s simHuman_chr6.simHuman.chr6 56927 42 + 601863 GAAAAAATTGTAGGTATCAGTCCCCTTTCAATGAAGGGAAAT -s simRat_chr6.simRat.chr6 51911 42 + 647215 GAAAAAATTGTAGGTATAAAGCCCTTTAACATAAATGGAAAT - -a -s simMouse_chr6.simMouse.chr6 58703 22 + 636262 ATAAGAATCAGCCTTGTACGGG -s Anc0.Anc0refChr4 5940 21 - 45765 AAGAGAATAGGCCCAAGACAA- -s Anc1.Anc1refChr2 36771 21 + 144309 AAGAGAATAGGCCCAAGACAA- -s Anc2.Anc2refChr4 2975 21 + 10050 AAGAGAAAAGGCCCAAGGGAT- -s mr.mrrefChr0 55953 22 + 130230 ATAAGAATAGGCCTTGTACGAG -s simCow_chr6.simCow.chr6 62792 19 + 602619 AAAAAAAAATGTCCAAGGG--- -s simDog_chr6.simDog.chr6 59607 21 + 593897 AAGTGAAAGGGCTCAAGGGAT- -s simHuman_chr6.simHuman.chr6 56970 21 + 601863 AAGAGAATAGGCCCAAAACAA- -s simRat_chr6.simRat.chr6 51953 22 + 647215 AGAAGAATAGGCCTTGTAGGAG - -a -s simMouse_chr6.simMouse.chr6 58725 27 + 636262 ACATGCCGGCACTGAGATGATGTCTTA -s Anc0.Anc0refChr4 5961 16 - 45765 ----------ACTCATATGGTGTCT-G -s Anc1.Anc1refChr2 36792 16 + 144309 ----------ACTCATATGGTGTCT-G -s Anc2.Anc2refChr4 2996 16 + 10050 ----------ACTCATATGGTGTCT-G -s mr.mrrefChr0 55980 27 + 130230 ACATGCCTGCACTGAGATGATGTCTTA -s simCow_chr6.simCow.chr6 62811 16 + 602619 ----------ACTTGTATGACATCT-G -s simDog_chr6.simDog.chr6 59628 16 + 593897 ----------ACCCATATAGTGTTT-G -s simHuman_chr6.simHuman.chr6 56991 16 + 601863 ----------ACTCATATGGTGTCT-G -s simRat_chr6.simRat.chr6 51980 26 + 647215 ACATGCCTGCACTGAG-TGATGTCTTA - -a -s simMouse_chr6.simMouse.chr6 58752 11 + 636262 AAGTAACCTGG -s Anc0.Anc0refChr4 5977 11 - 45765 ACTTGACTTAA -s Anc1.Anc1refChr2 36808 11 + 144309 ACTTGACTTAA -s Anc2.Anc2refChr4 3012 11 + 10050 ACTTGAATTAA -s mr.mrrefChr0 56007 11 + 130230 AAATAACTTGC -s simCow_chr6.simCow.chr6 62898 11 + 602619 AAATGAAGTAA -s simDog_chr6.simDog.chr6 59644 11 + 593897 ACTTGAATTAA -s simHuman_chr6.simHuman.chr6 57007 11 + 601863 ACCTGACTTAA -s simRat_chr6.simRat.chr6 52006 11 + 647215 AAAAAACTTGC - -a -s simMouse_chr6.simMouse.chr6 58763 36 + 636262 CTTTGGTCTAGAGCCATTAATATTTGATTGCCAACA -s Anc0.Anc0refChr4 5988 36 - 45765 AATAGGCCTGTGTCCATTAATATTTAATTGCAAACC -s Anc1.Anc1refChr2 36819 36 + 144309 AATAGGCCTGTGTCCATTAATATTTAATTGCAAACC -s Anc2.Anc2refChr4 3025 36 + 10050 AATAGGCCTGTGTTCATTAATATTTGATTGCAAACC -s mr.mrrefChr0 56018 36 + 130230 ATTTGGTCTGGGGCCATTAATATTTAATTGCAAACA -s simCow_chr6.simCow.chr6 62911 36 + 602619 AGTAGGCCTTGGTTTATTAATATTTGCTTACAAACT -s simDog_chr6.simDog.chr6 59657 36 + 593897 AACAGGCCTGTGTTCATTAATATTTGATTGCAACCC -s simHuman_chr6.simHuman.chr6 57018 36 + 601863 AATAGGCCTGAGCCCATTAATATTTAATTGCAAACC -s simRat_chr6.simRat.chr6 52017 36 + 647215 ATTTGGTTTGGGGCCATTAGTATTTAATTCCAGACA - -a -s simMouse_chr6.simMouse.chr6 58799 3 + 636262 ATG -s Anc0.Anc0refChr4 6024 3 - 45765 ATA -s Anc1.Anc1refChr2 36855 3 + 144309 ATA -s Anc2.Anc2refChr4 3061 3 + 10050 ATA -s mr.mrrefChr0 56054 3 + 130230 ATG -s simCow_chr6.simCow.chr6 62947 3 + 602619 ATA -s simDog_chr6.simDog.chr6 59694 3 + 593897 ATA -s simHuman_chr6.simHuman.chr6 57054 3 + 601863 ATA -s simRat_chr6.simRat.chr6 52053 3 + 647215 ATG - -a -s simMouse_chr6.simMouse.chr6 58802 12 + 636262 AGGTTGTCAACA -s Anc0.Anc0refChr4 6046 12 - 45765 AGTTTCCCAACA -s Anc1.Anc1refChr2 36877 12 + 144309 AGTTTCCCAACA -s Anc2.Anc2refChr4 3083 12 + 10050 TGTTTCCAAACA -s mr.mrrefChr0 56057 12 + 130230 AGGTTGTCAACA -s simCow_chr6.simCow.chr6 62969 12 + 602619 TGTCTCCTGAAA -s simDog_chr6.simDog.chr6 59707 12 + 593897 TGTTTCCAAACA -s simHuman_chr6.simHuman.chr6 57076 12 + 601863 AGTTTCCCAACA -s simRat_chr6.simRat.chr6 52056 12 + 647215 AGGTTGTCCACA - -a -s simMouse_chr6.simMouse.chr6 58814 1 + 636262 T -s Anc0.Anc0refChr4 6058 1 - 45765 T -s Anc1.Anc1refChr2 36889 1 + 144309 T -s Anc2.Anc2refChr4 3095 1 + 10050 T -s mr.mrrefChr0 56069 1 + 130230 T -s simCow_chr6.simCow.chr6 62981 1 + 602619 T -s simDog_chr6.simDog.chr6 59719 1 + 593897 T -s simHuman_chr6.simHuman.chr6 57092 1 + 601863 T -s simRat_chr6.simRat.chr6 52068 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 58815 40 + 636262 ATTCTTATAAGTCTGGGTAGAAAGGGACTGACTGATTCAG -s Anc0.Anc0refChr4 6059 40 - 45765 GATCTTATAAGTGAGGGTGGATAAAGACTGGCTAATTTGG -s Anc1.Anc1refChr2 36890 40 + 144309 GATCTTATAAGTGAGGGTGGATAAAGACTGGCTAATTTGG -s Anc2.Anc2refChr4 3096 40 + 10050 GATCTTATAAGTGAGGGTGGATAAAGACTGGCCAATTTGG -s mr.mrrefChr0 56070 40 + 130230 GTTCTTATAAGTGAGGGTAGAAAGAGACTGGCTGATTCAG -s simCow_chr6.simCow.chr6 62983 40 + 602619 GATCTTATAAGTGAGGGTGGATAGGGACTGGCCAATTTAG -s simDog_chr6.simDog.chr6 59720 35 + 593897 GATCTGAT-----AGGGCGGAAAAAGACTGGCCAGTTGGG -s simHuman_chr6.simHuman.chr6 57093 40 + 601863 GATCTTATATGTGAGGGTGAATGAAGGCTGGTTAATTTGG -s simRat_chr6.simRat.chr6 52069 40 + 647215 GCTCTTATAAGTGAGGGTAGAAAGAGACTGGCTGACTCAG - -a -s simMouse_chr6.simMouse.chr6 58855 3 + 636262 TAA -s Anc0.Anc0refChr4 6102 3 - 45765 TAA -s Anc1.Anc1refChr2 36933 3 + 144309 TAA -s Anc2.Anc2refChr4 3140 3 + 10050 TAA -s mr.mrrefChr0 56110 3 + 130230 TAA -s simCow_chr6.simCow.chr6 63027 3 + 602619 TGA -s simDog_chr6.simDog.chr6 59759 3 + 593897 TAA -s simHuman_chr6.simHuman.chr6 57136 3 + 601863 TAA -s simRat_chr6.simRat.chr6 52109 3 + 647215 TAA - -a -s simMouse_chr6.simMouse.chr6 58858 9 + 636262 TGTTACAGT -s Anc0.Anc0refChr4 6110 9 - 45765 TTCTACAAT -s Anc1.Anc1refChr2 36941 9 + 144309 TTCTACAAT -s Anc2.Anc2refChr4 3148 9 + 10050 TTCTACAAT -s mr.mrrefChr0 56114 9 + 130230 TGTTACAGT -s simCow_chr6.simCow.chr6 63043 9 + 602619 TTCTGCAAT -s simDog_chr6.simDog.chr6 59767 9 + 593897 TTTTACAGC -s simHuman_chr6.simHuman.chr6 57144 9 + 601863 TTCTACAAT -s simRat_chr6.simRat.chr6 52113 9 + 647215 TGTTACAGT - -a -s simMouse_chr6.simMouse.chr6 58867 19 + 636262 CCATAGTCCCATTGTTATG -s Anc0.Anc0refChr4 6119 19 - 45765 ACATAGTCTCAATGTTATG -s Anc1.Anc1refChr2 36950 19 + 144309 ACATAGTCTCAATGTTATG -s Anc2.Anc2refChr4 3157 19 + 10050 ACATTGTCTCAATGTTATG -s mr.mrrefChr0 56123 19 + 130230 ACATAGTCTCAATGTTATG -s simCow_chr6.simCow.chr6 63084 19 + 602619 ACAGTTTCTCAACATTATG -s simDog_chr6.simDog.chr6 59776 19 + 593897 ACATTGTCCCAATGTCATG -s simHuman_chr6.simHuman.chr6 57153 19 + 601863 ACATAGTCTCAATGTTTTG -s simRat_chr6.simRat.chr6 52122 19 + 647215 ATATAGTCTCAACGTTATG - -a -s simMouse_chr6.simMouse.chr6 58886 27 + 636262 CTTCTGAGGTACTTACAGTGCTAAATA -s Anc0.Anc0refChr4 6142 25 - 45765 CTCACTACGTGCT--CAGTGCTACATA -s Anc1.Anc1refChr2 36973 27 + 144309 CTCACTACGTGCTCACAGTGCTACATA -s Anc2.Anc2refChr4 3180 25 + 10050 CTCACTACGTGCT--CAGTGCTACATA -s mr.mrrefChr0 56146 27 + 130230 CTTCTGAGGTACTTACAGTGCTACATA -s simCow_chr6.simCow.chr6 63107 22 + 602619 CTTGCTA---GCT--CAGTGCTACATT -s simDog_chr6.simDog.chr6 59795 17 + 593897 --CATTACGT--------GGCTACAGA -s simHuman_chr6.simHuman.chr6 57176 27 + 601863 CTCACTATGTTCTCACAGTTCTAGATA -s simRat_chr6.simRat.chr6 52145 27 + 647215 CTTCTGAGATACTTACAGTGCTACATA - -a -s simMouse_chr6.simMouse.chr6 58913 87 + 636262 AAATTATTAACTTAATTCAACCATAGTTAATCTTAATTCAACTATTGCCTTTTTTGTTCCTATCAAAAGGTCGTTGTAAAAAAACCT -s Anc0.Anc0refChr4 6167 66 - 45765 AAACTACTCAGTTAACCCATATCTAGT---------------------TTTTTGTGTTCCTATCAGGAGGTTGTTGTAGAAAAGTCC -s Anc1.Anc1refChr2 37000 66 + 144309 AAACTACTCAGTTAACCCATATCTAGT---------------------TTTTTGTGTTCCTATCAGGAGGTTGTTGTAGAAAAGTCC -s Anc2.Anc2refChr4 3205 66 + 10050 AAGCTACTCAGTCAACCCATATCTAGT---------------------TTTTTGTGTTCCTATAAGGATGTTGTTGTAGAAAAGTCC -s mr.mrrefChr0 56173 87 + 130230 AAATTATTAAGTTAATTCAACCATAGTTAATCTTAATTCAACTATAGCCTTTTTTGTTCCTATCAAAAGGTTGTTGTAAAAAAACCC -s simCow_chr6.simCow.chr6 63129 66 + 602619 AAGCTAGTCAGTCAGCACATATCTAGT---------------------TTTTTGTCTTCCTATAAGGAAGTTGCTGTAAAAAAGTCC -s simDog_chr6.simDog.chr6 59812 60 + 593897 AAGCTACTCAAGCGACCTATATCTAGT---------------------TTTCTCAGTTGCTATAAGG-TGTTTTTGCAGAGA----- -s simHuman_chr6.simHuman.chr6 57203 66 + 601863 AGACTAATCAGTTAACCCATGTCTAGT---------------------TTTTTGTGTTCCTATCAGGAGGGTGTTGTGGAAAACTCC -s simRat_chr6.simRat.chr6 52179 87 + 647215 AAATTATCAAGATAATTCAACTATAGTTAATCTTAATTCAACTATAGCCTTTTTAATTCCTGTCATAAGATTGTTGTAAAAAAACCC - -a -s simMouse_chr6.simMouse.chr6 59000 1 + 636262 T -s Anc0.Anc0refChr4 6234 1 - 45765 T -s Anc1.Anc1refChr2 37067 1 + 144309 T -s Anc2.Anc2refChr4 3272 1 + 10050 T -s mr.mrrefChr0 56261 1 + 130230 T -s simCow_chr6.simCow.chr6 63196 1 + 602619 T -s simDog_chr6.simDog.chr6 59873 1 + 593897 T -s simHuman_chr6.simHuman.chr6 57270 1 + 601863 C -s simRat_chr6.simRat.chr6 52267 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 59001 8 + 636262 ATCCAGCG -s Anc0.Anc0refChr4 6235 8 - 45765 GTCCAGTG -s Anc1.Anc1refChr2 37068 8 + 144309 GTCCAGTG -s Anc2.Anc2refChr4 3273 8 + 10050 GTCCAGTG -s mr.mrrefChr0 56262 8 + 130230 GTCCAGCG -s simCow_chr6.simCow.chr6 63197 8 + 602619 GTCCAGCA -s simDog_chr6.simDog.chr6 59874 8 + 593897 GTCCAGTG -s simHuman_chr6.simHuman.chr6 57271 8 + 601863 GTCCAGTG -s simRat_chr6.simRat.chr6 52321 8 + 647215 GTCCAGCA - -a -s simMouse_chr6.simMouse.chr6 59009 33 + 636262 TGCAATTCACCTAATTCACCTTAACCATTGTAA -s Anc0.Anc0refChr4 6243 24 - 45765 TGCAATTCACCT---------TAACCATTGTAA -s Anc1.Anc1refChr2 37076 24 + 144309 TGCAATTCACCT---------TAACCATTGTAA -s Anc2.Anc2refChr4 3281 24 + 10050 TGCACTTCACCT---------GAACCATTATAA -s mr.mrrefChr0 56270 24 + 130230 TGCAATTCACCT---------TAACCATTGTAA -s simCow_chr6.simCow.chr6 63205 20 + 602619 TGCATTTCACCT---------GAGCTATT---- -s simDog_chr6.simDog.chr6 59886 24 + 593897 TTCACTTCTCCT---------GAACCATTATAA -s simHuman_chr6.simHuman.chr6 57279 24 + 601863 TGCAATTCACCT---------TGACCATTGTAA -s simRat_chr6.simRat.chr6 52329 24 + 647215 TGCAATTTACCT---------TAGCCATTGTAG - -a -s simMouse_chr6.simMouse.chr6 59042 10 + 636262 ATCAGTTGAT -s Anc0.Anc0refChr4 6343 10 - 45765 ATCAGTTGAT -s Anc1.Anc1refChr2 37176 10 + 144309 ATCAGTTGAT -s Anc2.Anc2refChr4 3381 10 + 10050 ATCAGGTAAT -s mr.mrrefChr0 56294 10 + 130230 ATCAGTTGAT -s simCow_chr6.simCow.chr6 63290 10 + 602619 ATCAGGTGAT -s simCow_chr6.simCow.chr6 216810 10 + 602619 ATCAGGTATT -s simDog_chr6.simDog.chr6 59986 10 + 593897 ATCAGGTAAT -s simHuman_chr6.simHuman.chr6 57382 10 + 601863 ATCAGTTGAT -s simRat_chr6.simRat.chr6 52353 10 + 647215 ATCAGTTGAT - -a -s simMouse_chr6.simMouse.chr6 59052 3 + 636262 TGC -s Anc0.Anc0refChr4 6353 3 - 45765 TGC -s Anc1.Anc1refChr2 37186 3 + 144309 TGC -s Anc2.Anc2refChr4 3391 3 + 10050 CCC -s mr.mrrefChr0 56304 3 + 130230 TGC -s simCow_chr6.simCow.chr6 216820 3 + 602619 CAC -s simDog_chr6.simDog.chr6 59996 3 + 593897 CCC -s simHuman_chr6.simHuman.chr6 57392 3 + 601863 TGC -s simRat_chr6.simRat.chr6 52363 3 + 647215 TAC - -a -s simMouse_chr6.simMouse.chr6 59055 63 + 636262 ACTTAATGACTGACACTGTATGGGGCTGGAGCAAATCACTTAGCTTTCGTTCTTTTTGTATAG -s Anc0.Anc0refChr4 6356 63 - 45765 TCTTACTGCCTGACACTGTATGGGGCTGCTTCAAATCACTTAGTTTTTGCTCTATCAGTACAG -s Anc1.Anc1refChr2 37189 63 + 144309 TCTTACTGCCTGACACTGTATGGGGCTGCTTCAAATCACTTAGTTTTTGCTCTATCAGTACAG -s Anc2.Anc2refChr4 3394 63 + 10050 TCTTACTTCCTGACACTGTATGGAGCTGCTTCAAATCACATAGTTTTTGCTCCACCAGTACAG -s mr.mrrefChr0 56307 63 + 130230 ACTTAATGACTGACACTGTATGGGGCTGGTGCAAATCACTTAGCTTTTGTTCTTTTTGTATAG -s simCow_chr6.simCow.chr6 63300 61 + 602619 TCTTACTTCC--ACACTGTATGGAGTTTCTTCAGATCACCTAGTTTTTGCTCTACCAGTACAG -s simCow_chr6.simCow.chr6 216823 60 + 602619 TCTTACTTCC--ACACTGTAT-GAGCTACTTCAAAACAAATAGCTCTTGCCCCACCAGTACAG -s simDog_chr6.simDog.chr6 59999 63 + 593897 TCTTACTTCCTGACACTGTATGGAGCTGCTTCAAATCACATAGTTTTTGCTCCACCAGTACAG -s simHuman_chr6.simHuman.chr6 57395 63 + 601863 TCTTACTGCTTGACACCGCATGGGGTTGCTTCAAATCACTTAATTCTTGCTTTGTCATTACAG -s simRat_chr6.simRat.chr6 52366 63 + 647215 ACTTAATTACTGACACTGTATGGGGCTCGTGCAAATTACTTGGCTTTTGTTCTTTTTGTATAG - -a -s simMouse_chr6.simMouse.chr6 59118 11 + 636262 TTAAAGGAAAA -s Anc0.Anc0refChr4 6419 11 - 45765 TTGACAGGAAG -s Anc1.Anc1refChr2 37252 11 + 144309 TTGACAGGAAG -s Anc2.Anc2refChr4 3458 11 + 10050 TTGACGGGAAG -s mr.mrrefChr0 56370 11 + 130230 TTAAAAGAAAG -s simCow_chr6.simCow.chr6 63362 11 + 602619 TAAAGGGGAAG -s simCow_chr6.simCow.chr6 216884 11 + 602619 TTTAAGGGAAG -s simDog_chr6.simDog.chr6 60063 11 + 593897 TGGACTGGAAG -s simHuman_chr6.simHuman.chr6 57458 11 + 601863 TTGATAGGAAG -s simRat_chr6.simRat.chr6 52429 11 + 647215 TTAAAAGAAAG - -a -s simMouse_chr6.simMouse.chr6 59129 3 + 636262 TTG -s Anc0.Anc0refChr4 6430 3 - 45765 TTT -s Anc1.Anc1refChr2 37263 3 + 144309 TTT -s Anc2.Anc2refChr4 3469 3 + 10050 TTT -s mr.mrrefChr0 56381 3 + 130230 TTG -s simCow_chr6.simCow.chr6 63374 3 + 602619 TTT -s simCow_chr6.simCow.chr6 216895 3 + 602619 TTA -s simDog_chr6.simDog.chr6 60074 3 + 593897 CTT -s simHuman_chr6.simHuman.chr6 57469 3 + 601863 TTA -s simRat_chr6.simRat.chr6 52440 3 + 647215 TTG - -a -s simMouse_chr6.simMouse.chr6 59132 27 + 636262 TGTGAAATGCAATTTTGAAAATTTGGT -s Anc0.Anc0refChr4 6433 27 - 45765 CGTGAAAGGAAATTCTTAAAATTTGGT -s Anc1.Anc1refChr2 37266 27 + 144309 CGTGAAAGGAAATTCTTAAAATTTGGT -s Anc2.Anc2refChr4 3472 27 + 10050 CGTGAAAGGAAATTCTCAAAGTTCAGT -s mr.mrrefChr0 56384 27 + 130230 TGTGAAATGCAATTTTTAAAATTTGGT -s simCow_chr6.simCow.chr6 63377 27 + 602619 TGTGAAAGGGAATTTGTCAAATTTGGT -s simCow_chr6.simCow.chr6 216912 4 + 602619 TATT----------------------- -s simDog_chr6.simDog.chr6 60077 27 + 593897 CGTGAAAGAAAATTCTCAAAGTTCAGT -s simHuman_chr6.simHuman.chr6 57472 27 + 601863 CCCCAAAGGTATTTAGTAACATTTGGG -s simRat_chr6.simRat.chr6 52443 27 + 647215 TGTGAAATGCAATTTTTGAAATTTGGT - -a -s simMouse_chr6.simMouse.chr6 59159 101 + 636262 GAAATTTGCTGAGGTTAGAGCAATGATCCTCCATGTGCATTTTAAGCATGAGAATTGACGTTTGTTACATATCCTGCGTCCTAAACATAGTTTGGATATGA -s Anc0.Anc0refChr4 6460 92 - 45765 GCATTTTGTTGAGTTTGGAGATATAATTTTCTGTATTGATTTCAAGTAAGAGAATTGATATTTGTTGC---------ATCCTAAATATTGTTTGGATGTGA -s Anc1.Anc1refChr2 37293 93 + 144309 GCATTTTGTTGAGTTTGGAGATATAATTTTCTGTATTGATTTCAAGTAAGAGAATTGATATTTGTTGCA--------ATCCTAAATATTGTTTGGATGTGA -s Anc2.Anc2refChr4 3500 92 + 10050 GCATTTTGTGGGGTGTGGAGATATAATTTTCTGTGTTGATTTCTAGTAAGAGAACTGATATTTGTTGC---------ATCCTAAATATTGTTTGGATGTGA -s mr.mrrefChr0 56411 101 + 130230 GAAATTTGCTGAGTTTAGAGCAATGATCCTCCATATTCATTTCAAGTATGAGAATTGACATTTGTTACATATCCTGCATCCTAAACATAGTTTGGATATGA -s simCow_chr6.simCow.chr6 63405 83 + 602619 GCATTTTGTTAGGTGTAGAGACATGATTTTTGATGTTGATTTCCAGTATGAGAACTGATATTTGGT------------------ATATGGTCTGCATGATA -s simDog_chr6.simDog.chr6 60105 92 + 593897 GCATTTTGTGGGGTGTGGAGATATAATTTTCTGTGTTGAGTTCTCGTAAGAGAACTGATATTTGTTGC---------ATCCTAAACATTGTTTTGATCTGA -s simHuman_chr6.simHuman.chr6 57499 75 + 601863 ------TGTTGAGCTTTA------------CTGTATTGATTTCAAGTAGGAGAATTGAAACTTGTTCCA--------ATCCTGAATATTGTGTGAATGTAA -s simRat_chr6.simRat.chr6 52470 98 + 647215 GAAACTTGCTGAGTTTAGAGCAAAAATCC---ATATTCATCTCAAGTATGATAATTGACATTTGTTTCATATCCTGCATCCTAAACTTAGTTTGGGTATGA - -a -s simMouse_chr6.simMouse.chr6 59260 5 + 636262 TATGA -s Anc0.Anc0refChr4 6552 5 - 45765 TATGA -s Anc1.Anc1refChr2 37386 5 + 144309 TATGA -s Anc2.Anc2refChr4 3592 5 + 10050 AATGA -s mr.mrrefChr0 56512 5 + 130230 TATGA -s simCow_chr6.simCow.chr6 63488 5 + 602619 AATGA -s simDog_chr6.simDog.chr6 60199 4 + 593897 A-TTA -s simHuman_chr6.simHuman.chr6 57574 5 + 601863 TATGA -s simRat_chr6.simRat.chr6 52568 5 + 647215 TATGA - -a -s simMouse_chr6.simMouse.chr6 59265 4 + 636262 TAAG -s Anc0.Anc0refChr4 6557 4 - 45765 GAAG -s Anc1.Anc1refChr2 37391 4 + 144309 GAAG -s Anc2.Anc2refChr4 3597 4 + 10050 GCAG -s mr.mrrefChr0 56517 4 + 130230 TAAG -s simCow_chr6.simCow.chr6 63493 3 + 602619 -CAG -s simDog_chr6.simDog.chr6 60203 4 + 593897 GCAG -s simHuman_chr6.simHuman.chr6 57579 4 + 601863 CAAG -s simRat_chr6.simRat.chr6 52580 4 + 647215 GAAG - -a -s simMouse_chr6.simMouse.chr6 59269 48 + 636262 CTAGTTCAACGAAGGCTATGGAACAATCCTGGCAACCCAAGACTTAAC -s Anc0.Anc0refChr4 6563 39 - 45765 CTGGTTCAACG---------GAACAGTGCTGCCAACTCAAGGGTTAAT -s Anc1.Anc1refChr2 37397 39 + 144309 CTGGTTCAACG---------GAACAGTGCTGCCAACTCAAGGGTTAAT -s Anc2.Anc2refChr4 3603 39 + 10050 CTGGTTCAACA---------GAACAGTGCTGCCAACTCAAGGGTTAAT -s mr.mrrefChr0 56521 48 + 130230 CTAGTTCAACGAAGGCTATGGAACAATGCTGGCAACCCAAGACTTAAC -s simCow_chr6.simCow.chr6 63498 39 + 602619 CTCGTTCAACA---------TAGCAGTGCTGTTAACTCAAGGGTCAAT -s simDog_chr6.simDog.chr6 60209 39 + 593897 CTGGTCCAACA---------GAACAGCGCTGCCAGCACAAGGGTTAGT -s simHuman_chr6.simHuman.chr6 57585 39 + 601863 CTGTTTCAGCG---------GAACAGTGCTGCCAACTCAAGGATTAAT -s simRat_chr6.simRat.chr6 52584 48 + 647215 CTAGTTTAAAGAAGGCTATGAAACAATGATGGTAATGCAAGATTTGAC - -a -s simMouse_chr6.simMouse.chr6 59317 23 + 636262 TAATCACTTTTATTACTCCACAG -s Anc0.Anc0refChr4 6608 23 - 45765 TAATAACTTGTATCACTCCACAG -s Anc1.Anc1refChr2 37442 23 + 144309 TAATAACTTGTATCACTCCACAG -s Anc2.Anc2refChr4 3648 23 + 10050 TAATAACTTGTATCACACCACAA -s mr.mrrefChr0 56575 23 + 130230 TAATCACTTTTATTACTCCACAG -s simCow_chr6.simCow.chr6 63543 13 + 602619 TAATATCTTGTAT---------- -s simDog_chr6.simDog.chr6 60254 23 + 593897 TAATAACTTATATCACACCACAA -s simHuman_chr6.simHuman.chr6 57629 23 + 601863 TAATAACATGTATCACTCCACAG -s simRat_chr6.simRat.chr6 52638 23 + 647215 TAATCACTTTTATTACTCCACAG - -a -s simMouse_chr6.simMouse.chr6 59340 9 + 636262 GCTGTGCGA -s Anc0.Anc0refChr4 6636 9 - 45765 GCTGTTCTT -s Anc1.Anc1refChr2 37470 9 + 144309 GCTGTTCTT -s Anc2.Anc2refChr4 3676 9 + 10050 ACTGTTCTT -s mr.mrrefChr0 56598 9 + 130230 GCTGTGCGT -s simCow_chr6.simCow.chr6 63559 9 + 602619 ACTGTTCTT -s simDog_chr6.simDog.chr6 60282 9 + 593897 ACTCGTCCT -s simHuman_chr6.simHuman.chr6 57657 9 + 601863 GCTGTTCTT -s simRat_chr6.simRat.chr6 52661 9 + 647215 GATGTGCAT - -a -s simMouse_chr6.simMouse.chr6 59349 2 + 636262 TC -s Anc0.Anc0refChr4 6648 2 - 45765 CC -s Anc1.Anc1refChr2 37482 2 + 144309 CC -s Anc2.Anc2refChr4 3688 2 + 10050 CC -s mr.mrrefChr0 56607 2 + 130230 TC -s simCow_chr6.simCow.chr6 63571 2 + 602619 AG -s simDog_chr6.simDog.chr6 60294 2 + 593897 CC -s simHuman_chr6.simHuman.chr6 57669 2 + 601863 CC -s simRat_chr6.simRat.chr6 52670 2 + 647215 TC - -a -s simMouse_chr6.simMouse.chr6 59351 5 + 636262 CACTC -s Anc0.Anc0refChr4 6680 5 - 45765 TACTT -s Anc1.Anc1refChr2 37514 5 + 144309 TACTT -s Anc2.Anc2refChr4 3720 5 + 10050 TACTT -s mr.mrrefChr0 56635 5 + 130230 CACTC -s simCow_chr6.simCow.chr6 63603 5 + 602619 TACTT -s simDog_chr6.simDog.chr6 60324 5 + 593897 TACTT -s simHuman_chr6.simHuman.chr6 57701 5 + 601863 TACTT -s simRat_chr6.simRat.chr6 52698 5 + 647215 CACTC - -a -s simMouse_chr6.simMouse.chr6 59356 11 + 636262 ATGCCAGCAAG -s Anc0.Anc0refChr4 6692 11 - 45765 ATGTCAGGATG -s Anc1.Anc1refChr2 37526 11 + 144309 ATGTCAGGATG -s Anc2.Anc2refChr4 3732 11 + 10050 ATGTCAGGCTG -s mr.mrrefChr0 56640 11 + 130230 ATGTCAGCAAG -s simCow_chr6.simCow.chr6 63615 11 + 602619 ATGTCAGGCTG -s simDog_chr6.simDog.chr6 60336 11 + 593897 ATGTCAGGCTG -s simHuman_chr6.simHuman.chr6 57716 11 + 601863 ATATCAGGATG -s simRat_chr6.simRat.chr6 52703 11 + 647215 ATGTCAGCAAG - -a -s simMouse_chr6.simMouse.chr6 59367 3 + 636262 TAT -s Anc0.Anc0refChr4 6703 3 - 45765 TAT -s Anc1.Anc1refChr2 37537 3 + 144309 TAT -s Anc2.Anc2refChr4 3751 3 + 10050 CAT -s mr.mrrefChr0 56651 3 + 130230 TAT -s simCow_chr6.simCow.chr6 63634 3 + 602619 CAT -s simDog_chr6.simDog.chr6 60355 3 + 593897 CAT -s simHuman_chr6.simHuman.chr6 57727 3 + 601863 TAT -s simRat_chr6.simRat.chr6 52714 3 + 647215 TAT - -a -s simMouse_chr6.simMouse.chr6 59370 3 + 636262 ACA -s Anc0.Anc0refChr4 6707 3 - 45765 TCA -s Anc1.Anc1refChr2 37541 3 + 144309 TCA -s Anc2.Anc2refChr4 3755 3 + 10050 TTA -s mr.mrrefChr0 56654 3 + 130230 ACA -s simCow_chr6.simCow.chr6 63638 3 + 602619 TTA -s simDog_chr6.simDog.chr6 60359 3 + 593897 TTA -s simHuman_chr6.simHuman.chr6 57731 3 + 601863 CCA -s simRat_chr6.simRat.chr6 52717 3 + 647215 ACA - -a -s simMouse_chr6.simMouse.chr6 59373 21 + 636262 GCCAGGGATTTACAGTCTGTA -s Anc0.Anc0refChr4 6710 15 - 45765 GCCC------TACTGTCTGTG -s Anc1.Anc1refChr2 37544 21 + 144309 GCCCGGGACTTACTGTCTGTG -s Anc2.Anc2refChr4 3758 15 + 10050 GCCC------CAATGTCAGGG -s mr.mrrefChr0 56657 21 + 130230 GCCAGGGACTTACAGTCTGTA -s simCow_chr6.simCow.chr6 63735 15 + 602619 GCAC------CAACTTGACGG -s simDog_chr6.simDog.chr6 60362 15 + 593897 GCCC------CAATGCCAGGG -s simHuman_chr6.simHuman.chr6 57734 21 + 601863 ACCCGGGACTTACTGTTTGTG -s simRat_chr6.simRat.chr6 52720 21 + 647215 GCCAGGGACTTACAGTATGTA - -a -s simMouse_chr6.simMouse.chr6 59394 27 + 636262 TAATTTGTCTGTATAATTTATTGTTGC -s Anc0.Anc0refChr4 6725 23 - 45765 TAAACTGTTGTTGCTTTTTCTTG---- -s Anc1.Anc1refChr2 37565 23 + 144309 TAAACTGTTGTTGCTTTTTCTTG---- -s Anc2.Anc2refChr4 3897 23 + 10050 TAAACCGTTGTTGCTTTTTCTCG---- -s mr.mrrefChr0 56678 27 + 130230 TAATTTGTCGTTGCTTTTTCTTGTGGC -s simCow_chr6.simCow.chr6 64467 22 + 602619 TAAACCATTGTTGTTTCTTGTC----- -s simDog_chr6.simDog.chr6 60510 23 + 593897 TAAACCGCTGCTCCTTTTTCTCG---- -s simHuman_chr6.simHuman.chr6 57755 23 + 601863 TAAACTGTTGTTGCTTTTTCTTG---- -s simRat_chr6.simRat.chr6 52741 27 + 647215 TAATTTACCGTTGCTTTTGCGTGAGGA - -a -s simMouse_chr6.simMouse.chr6 59421 58 + 636262 TTTATCACAAGGCAACAGAAGTCATCTGGCCAGTTCTCTCCTATGTTATAACTTAGAG -s Anc0.Anc0refChr4 6748 49 - 45765 ---------GGACAACAGAGATAATCTGCTCAGTTCTCTCCAATGTTATAACTTGGAG -s Anc1.Anc1refChr2 37588 49 + 144309 ---------GGACAACAGAGATAATCTGCTCAGTTCTCTCCAATGTTATAACTTGGAG -s Anc2.Anc2refChr4 3920 49 + 10050 ---------GGACAACAGAGACAATCTGCTCAATTCTCTCCAATGTTATAACTTGGAG -s mr.mrrefChr0 56726 58 + 130230 TTTATCACAAGGCAACAGAAGTCATCTGGCCAGTTCTCTCCTATGTTATAACTTAGAG -s simCow_chr6.simCow.chr6 64489 46 + 602619 -----------ACAACAGAAGCAATCTGCTCACTTCTCTCCAATGTCTTAACATAGA- -s simDog_chr6.simDog.chr6 60539 49 + 593897 ---------GGATAACAGGGACAATTTGCTCAATTCTCTCCAATGTTATAATTTGGTG -s simHuman_chr6.simHuman.chr6 57778 49 + 601863 ---------GGACAGCAGATATAATCTGCTCAGTTCTCTCCCATCTTATAGCTAGGAG -s simRat_chr6.simRat.chr6 52878 58 + 647215 TTTATCATGAGGGAACAGAAGTCATCTTGCCAGTCCTCTCCTATGTTATAACTTAGAG - -a -s simMouse_chr6.simMouse.chr6 59479 12 + 636262 GTGCTAAAGACT -s Anc0.Anc0refChr4 6798 12 - 45765 GTGCTTATGACA -s Anc1.Anc1refChr2 37638 12 + 144309 GTGCTTATGACA -s Anc2.Anc2refChr4 3970 12 + 10050 GTGCTTATGACA -s mr.mrrefChr0 56784 12 + 130230 GTGCTAAAGACT -s simCow_chr6.simCow.chr6 64535 12 + 602619 GTGCTTTTGACA -s simDog_chr6.simDog.chr6 60589 12 + 593897 GTGCTTATGACA -s simHuman_chr6.simHuman.chr6 57828 12 + 601863 GTGCCTATGACA -s simRat_chr6.simRat.chr6 52936 12 + 647215 GTGCTAAAGACT - -a -s simMouse_chr6.simMouse.chr6 59491 4 + 636262 GCAT -s Anc0.Anc0refChr4 6814 4 - 45765 GCAA -s Anc1.Anc1refChr2 37654 4 + 144309 GCAA -s Anc2.Anc2refChr4 3986 4 + 10050 TCAA -s mr.mrrefChr0 56796 4 + 130230 GCAT -s simCow_chr6.simCow.chr6 64551 4 + 602619 TCCA -s simDog_chr6.simDog.chr6 60605 4 + 593897 TCAA -s simHuman_chr6.simHuman.chr6 57845 4 + 601863 GCAA -s simRat_chr6.simRat.chr6 52948 4 + 647215 GCAC - -a -s simMouse_chr6.simMouse.chr6 59495 1 + 636262 G -s Anc0.Anc0refChr4 6818 1 - 45765 T -s Anc1.Anc1refChr2 37658 1 + 144309 T -s Anc2.Anc2refChr4 3990 1 + 10050 T -s mr.mrrefChr0 56800 1 + 130230 T -s simCow_chr6.simCow.chr6 64555 1 + 602619 T -s simDog_chr6.simDog.chr6 60617 1 + 593897 T -s simHuman_chr6.simHuman.chr6 57849 1 + 601863 T -s simRat_chr6.simRat.chr6 52952 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 59496 28 + 636262 CCCAAGGTCATTCTACCTACACTAGCAG -s Anc0.Anc0refChr4 6819 22 - 45765 TTCAAG--AA----TTATTCATTTGCAG -s Anc1.Anc1refChr2 37659 26 + 144309 TTCAAG--AATTGTTTATTCATTTGCAG -s Anc2.Anc2refChr4 3991 22 + 10050 TTCAAA--AA----TTATTCATGTGCAG -s mr.mrrefChr0 56801 28 + 130230 CCCAAGGTAATTCTACCTACACTAGCAG -s simCow_chr6.simCow.chr6 64560 22 + 602619 TTTAAA--TA----CTATCCACATGTGG -s simDog_chr6.simDog.chr6 60618 22 + 593897 TTCAAA--AA----TCATTCATGTGCAG -s simHuman_chr6.simHuman.chr6 57850 26 + 601863 TTCAAG--AATTGTTTGTTCAGTTGCAG -s simRat_chr6.simRat.chr6 52953 28 + 647215 CCCAAGGCAATTCTACCTACACGAGCAG - -a -s simMouse_chr6.simMouse.chr6 59524 8 + 636262 ATGGAATC -s Anc0.Anc0refChr4 6842 8 - 45765 AAAGAAGC -s Anc1.Anc1refChr2 37686 8 + 144309 AAAGAAGC -s Anc2.Anc2refChr4 4014 8 + 10050 GAAGAAGC -s mr.mrrefChr0 56829 8 + 130230 ATGGAATC -s simCow_chr6.simCow.chr6 64583 8 + 602619 GAAGGAGC -s simDog_chr6.simDog.chr6 60641 8 + 593897 GAAGAAGC -s simHuman_chr6.simHuman.chr6 57877 8 + 601863 AAAGAAGC -s simRat_chr6.simRat.chr6 52981 8 + 647215 ATGGAATC - -a -s simMouse_chr6.simMouse.chr6 59532 123 + 636262 AACTGCATCCTTTTCACTAAGTGTAATAATATTCTTTCAATTTGACTATCTGGTTGATTGTCCATACTAACATAGATGCCATAAGCTCTTTTTAGAAGGAAGCAGCCTTCATTCTGCTCTTGG -s Anc0.Anc0refChr4 6871 113 - 45765 AACTGTATCATTTTGACTAAGTAAACTGGTATTCTTTGTACTTGGCTATCTGGTTGGTTGCCTGTATTAGCATATATGCTATTAACTCTACTTAGG----------CTCCACCCTGGTCCTGG -s Anc1.Anc1refChr2 37715 113 + 144309 AACTGTATCATTTTGACTAAGTAAACTGGTATTCTTTGTACTTGGCTATCTGGTTGGTTGCCTGTATTAGCATATATGCTATTAACTCTACTTAGG----------CTCCACCCTGGTCCTGG -s Anc2.Anc2refChr4 4053 113 + 10050 AATTGTATCATTTTGACAAAGTAAACTGGTATTCTTTGTACTTGTCTATTTGGTTGGTTGCCTGTATTAGCATATCTGCTATTAACACTACTTAGT----------CTCCACCCTGGTCCTAG -s mr.mrrefChr0 56837 113 + 130230 AACTGCATCCTTTTCACTAAGTGAAATAATATTCTTTGAATTTGGCTATCTGGTTGATTGTCCATACTAACATAGATGCTATAAACTCTTTTTAGG----------CTTCATTCTGCTCTTGG -s simCow_chr6.simCow.chr6 64623 113 + 602619 AATTGTATCATTTTGACGAGTTAAACTGGTATTCTTTGTTCTTGTCTATGCAGTTGATTGCCTGCATTAGCATATCTCCTAATGACACGATTTAGA----------CTCCATACTGGTCGTAG -s simDog_chr6.simDog.chr6 60680 113 + 593897 AATTGTACCATTTTAACAAAGTACACTGGTACTCTTTGTACTTGTTAATTTGGTTGGTTGGTTGTATTAGCATATCTGCTATTAACACTACTAAAT----------CTCCACCCTGGTCCTAG -s simHuman_chr6.simHuman.chr6 57906 112 + 601863 AGCTGTATCATTGTGACTAAGTAACTTGGTGTTCTTTGCACCTGGCTACCTGGTTGGCTGCCTGTATAAGCATATAT-CTTTTAACTCAACTTAGG----------CTCCAGCCTGATCCTGG -s simRat_chr6.simRat.chr6 52989 110 + 647215 AACTGCATCCTTTTCACTAAGCGAAATAATATTCTTTGGATTTGGCTATCTGGGTGATTGACCATACTAATATAGATGCTATACACACTTTTTAGG----------CTTCATTCTGCA---AG - -a -s simMouse_chr6.simMouse.chr6 59655 1 + 636262 C -s Anc0.Anc0refChr4 6986 1 - 45765 T -s Anc1.Anc1refChr2 37830 1 + 144309 T -s Anc2.Anc2refChr4 4168 1 + 10050 T -s mr.mrrefChr0 56950 1 + 130230 T -s simCow_chr6.simCow.chr6 64738 1 + 602619 T -s simDog_chr6.simDog.chr6 60795 1 + 593897 T -s simHuman_chr6.simHuman.chr6 58020 1 + 601863 T -s simRat_chr6.simRat.chr6 53099 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 59656 13 + 636262 CACAATGCAAACC -s Anc0.Anc0refChr4 6987 13 - 45765 TAGACTGTAATTC -s Anc1.Anc1refChr2 37831 13 + 144309 TAGACTGTAATTC -s Anc2.Anc2refChr4 4177 13 + 10050 TAGACTATAACTC -s mr.mrrefChr0 56951 13 + 130230 TACAATGTAATTC -s simCow_chr6.simCow.chr6 64747 13 + 602619 GACACCTTAACTC -s simDog_chr6.simDog.chr6 60804 13 + 593897 TAGACTATAACTC -s simHuman_chr6.simHuman.chr6 58021 13 + 601863 TAGACTGTAATTC -s simRat_chr6.simRat.chr6 53100 13 + 647215 TAAAGTATAGTTC - -a -s simMouse_chr6.simMouse.chr6 59669 12 + 636262 TCACAGATGTGA -s Anc0.Anc0refChr4 7001 12 - 45765 TCACAGATGTGA -s Anc1.Anc1refChr2 37845 12 + 144309 TCACAGATGTGA -s Anc2.Anc2refChr4 4191 12 + 10050 TCACAGATGTGA -s mr.mrrefChr0 56965 12 + 130230 TCACAGATGTGA -s simCow_chr6.simCow.chr6 64761 11 + 602619 TGATACACGTG- -s simDog_chr6.simDog.chr6 60818 12 + 593897 TCACAGATGTGA -s simHuman_chr6.simHuman.chr6 58035 12 + 601863 TCACAGATGTTA -s simRat_chr6.simRat.chr6 53114 12 + 647215 CCACAGATGAGA - -a -s simMouse_chr6.simMouse.chr6 59681 3 + 636262 ATT -s Anc0.Anc0refChr4 7015 3 - 45765 ATT -s Anc1.Anc1refChr2 37859 3 + 144309 ATT -s Anc2.Anc2refChr4 4205 3 + 10050 GTT -s mr.mrrefChr0 56977 3 + 130230 ATT -s simCow_chr6.simCow.chr6 64772 3 + 602619 GTT -s simDog_chr6.simDog.chr6 60832 3 + 593897 GTT -s simHuman_chr6.simHuman.chr6 58049 3 + 601863 ATT -s simRat_chr6.simRat.chr6 53126 3 + 647215 GTT - -a -s simMouse_chr6.simMouse.chr6 59684 6 + 636262 GGTCAC -s Anc0.Anc0refChr4 7018 6 - 45765 GGGTAC -s Anc1.Anc1refChr2 37862 6 + 144309 GGGTAC -s Anc2.Anc2refChr4 4208 6 + 10050 GGGTAC -s mr.mrrefChr0 56980 6 + 130230 GGTCAC -s simCow_chr6.simCow.chr6 64775 6 + 602619 GGGCCC -s simDog_chr6.simDog.chr6 60869 6 + 593897 GGATAC -s simHuman_chr6.simHuman.chr6 58052 6 + 601863 GGGTAC -s simRat_chr6.simRat.chr6 53129 6 + 647215 GGTCAC - -a -s simMouse_chr6.simMouse.chr6 59690 15 + 636262 AGCACGTACAGGGCA -s Anc0.Anc0refChr4 7027 15 - 45765 AGAATGTCTAGCCCC -s Anc1.Anc1refChr2 37871 15 + 144309 AGAATGTCTAGCCCC -s Anc2.Anc2refChr4 4217 15 + 10050 AGAATGTCTAGCCCC -s mr.mrrefChr0 56986 15 + 130230 AGAATGTACAGGGCA -s simCow_chr6.simCow.chr6 64784 14 + 602619 -GATCGTCTAACCCT -s simDog_chr6.simDog.chr6 60878 15 + 593897 AAAATGTCCAGCCGC -s simHuman_chr6.simHuman.chr6 58061 15 + 601863 AGAATGTCTAGCCCC -s simRat_chr6.simRat.chr6 53135 15 + 647215 AGAATGTACAGGACT - -a -s simMouse_chr6.simMouse.chr6 59705 85 + 636262 ATGTGGTCCTGCCACTTTTAACAGCAAGTTACTCCCATGGGGAGAACTGCACCTGCTTGTACTGCTCTCACATATTCAAAGAGTA -s Anc0.Anc0refChr4 7042 61 - 45765 ATGTGGTCTTGCTGCCTTCACCACCAAGT----------------------TCAGCTTGTTCAGCTG--ACATGTTCAAAGAGTA -s Anc1.Anc1refChr2 37886 83 + 144309 ATGTGGTCTTGCTGCCTTCACCACCAAGTTACTCCCACACACAGGAGTCCATCAGCTTGTTCAGCTG--ACATGTTCAAAGAGTA -s Anc2.Anc2refChr4 4232 61 + 10050 ATGTAGTCTTGCTGCCTTCACCAATGAGT----------------------TCAGCTTGTTCAGCTG--ACATGTTCAAAGAGTA -s mr.mrrefChr0 57001 85 + 130230 ATGTGGTCCTGCTGCTTTTAACACCAAGTTACTCCCATGGGGAGAACTGCACCTGCTTGTACTGCTCTCACATATTCAAAGAGTA -s simCow_chr6.simCow.chr6 64801 59 + 602619 ATGTAGTCCTGCTGCTTTCACAAGAGAGT----------------------TCAGCGTGTCCAGCTC--ACATATTCCAAA--TG -s simDog_chr6.simDog.chr6 60893 61 + 593897 ATGTAGTCTTGCTGCCTTCACCAATGAGT----------------------TCTGTTTATTCAGCTG--ACATGTTCAAAGAGTA -s simHuman_chr6.simHuman.chr6 58076 80 + 601863 ATATGGTCTGGCTGTCTTCACCACCAAATTACTCCCACACACAGGAGTCCATCAGCTTGTTCAG-----ACATGTTCAAAGACTA -s simRat_chr6.simRat.chr6 53150 85 + 647215 ATGTGGTCCTTCTGCTTTGAACACCGAGTTACTTCCATGGGGATAATTGCTCCTGCTTGGACTGGTCCCACATATTCGACGAGTA - -a -s simMouse_chr6.simMouse.chr6 59790 24 + 636262 AACACTAATTGTATTAGGGGCTAA -s Anc0.Anc0refChr4 7108 24 - 45765 AACAACAACTGTACCAGGGGCCAG -s Anc1.Anc1refChr2 37974 24 + 144309 AACAACAACTGTACCAGGGGCCAG -s Anc2.Anc2refChr4 4298 24 + 10050 AAAAACAACTGTACCAGGGGCCAG -s mr.mrrefChr0 57091 24 + 130230 AACACTAATTGTATTAGGGGCCAA -s simCow_chr6.simCow.chr6 64865 24 + 602619 AGAAACGACTGTACCAGGCGCCAG -s simDog_chr6.simDog.chr6 60959 24 + 593897 AAAAGCAACTGTACCAGGGGCCAG -s simHuman_chr6.simHuman.chr6 58161 24 + 601863 AACAAGAGCTTAACCAGGGGCCAG -s simRat_chr6.simRat.chr6 53240 24 + 647215 AATACTAATTGTATTGGGGGCCAA - -a -s simMouse_chr6.simMouse.chr6 59814 23 + 636262 TGTACTGTCTAAAGAAAGGTTAA -s Anc0.Anc0refChr4 7138 23 - 45765 CATACCAGCTAAGGAAAGGTTAA -s Anc1.Anc1refChr2 38004 23 + 144309 CATACCAGCTAAGGAAAGGTTAA -s Anc2.Anc2refChr4 4328 23 + 10050 CATACCAGCTAAGAAAAGGTTAA -s mr.mrrefChr0 57115 23 + 130230 TGTACCATCTAAAGAAAGGTTAA -s simCow_chr6.simCow.chr6 64895 23 + 602619 CATACCAGCTAAGAAAAGGTTAA -s simDog_chr6.simDog.chr6 60989 19 + 593897 TATACCAGC----AGAAGATTAA -s simHuman_chr6.simHuman.chr6 58191 23 + 601863 CATATCACCTAAGGAAAGGTTAA -s simRat_chr6.simRat.chr6 53264 23 + 647215 TGTACCATCTATAGAAAGGTTAA - -a -s simMouse_chr6.simMouse.chr6 59837 5 + 636262 CAGCT -s Anc0.Anc0refChr4 7168 5 - 45765 CAGCT -s Anc1.Anc1refChr2 38034 5 + 144309 CAGCT -s Anc2.Anc2refChr4 4358 5 + 10050 AAGCT -s mr.mrrefChr0 57138 5 + 130230 CAGCT -s simCow_chr6.simCow.chr6 64925 5 + 602619 ACGCT -s simDog_chr6.simDog.chr6 61015 5 + 593897 AAGCT -s simHuman_chr6.simHuman.chr6 58223 5 + 601863 CAGCT -s simRat_chr6.simRat.chr6 53287 5 + 647215 CAGCT - -a -s simMouse_chr6.simMouse.chr6 59842 28 + 636262 TTGAGTTGCCAGTAACCCAAATACGTGT -s Anc0.Anc0refChr4 7184 28 - 45765 TTAAGTTGCCAGTAACCCAGCTGCATGA -s Anc1.Anc1refChr2 38050 28 + 144309 TTAAGTTGCCAGTAACCCAGCTGCATGA -s Anc2.Anc2refChr4 4374 28 + 10050 TTGAGTAGCAATTAACCCAGCTGCATGA -s mr.mrrefChr0 57154 28 + 130230 TTAAGTTGCCAGTAACCCAGCTACGTGT -s simCow_chr6.simCow.chr6 64941 28 + 602619 TTGAGTGGTAAATAACTTAGCTTTATGA -s simDog_chr6.simDog.chr6 61031 28 + 593897 TTGAGTAGCAATTAACCCAGCTGCATGA -s simHuman_chr6.simHuman.chr6 58239 28 + 601863 CTAAGTTGGCAGTAACCAAGCCGCTTGG -s simRat_chr6.simRat.chr6 53305 25 + 647215 TTAAGTTG---GTAACCCAGCTATGTAT - -a -s simMouse_chr6.simMouse.chr6 59870 36 + 636262 CTGGTCACAGGGAAATTTTGTATGCTTGCATGTTTT -s Anc0.Anc0refChr4 7214 35 - 45765 TAGGTCATAGGC-AATTGTGTATATCTGCATGTTTT -s Anc1.Anc1refChr2 38080 36 + 144309 TAGGTCATAGGCAAATTGTGTATATCTGCATGTTTT -s Anc2.Anc2refChr4 4404 35 + 10050 TAGGTCATAGGC-AATTGTCTATATCTGCATGTATT -s mr.mrrefChr0 57182 36 + 130230 CTGGTCACAGGGAAATTGTGTATGTTTGCATGTTTT -s simCow_chr6.simCow.chr6 64971 21 + 602619 CAGGTCAT-----GATTGT----------ATGTATC -s simDog_chr6.simDog.chr6 61061 35 + 593897 TGGGTCATAGGC-AATTGTCTATATCTGCATGAATT -s simHuman_chr6.simHuman.chr6 58269 36 + 601863 TAGGTCATAGGCAAATCGTGTATATCTGCATGTTTT -s simRat_chr6.simRat.chr6 53330 36 + 647215 GTGACCACAGGGAAATTGTGTATGTTTGCATGTTGT - -a -s simMouse_chr6.simMouse.chr6 59906 47 + 636262 GTGTGCACATTATTGAACTGTCTATGATTTCTAGTGAACATTGTAAG -s Anc0.Anc0refChr4 7249 44 - 45765 ---TATGCATTGTTAATCTATACACAACCTTTATTATGCTCTTTAAA -s Anc1.Anc1refChr2 38116 47 + 144309 GTATATGCATTGTTAATCTATACACAACCTTTATTATGCTCTTTAAA -s Anc2.Anc2refChr4 4439 44 + 10050 ---TATGGATTGTTAATCTATACACATCCTTTATTATGATCTTTAAA -s mr.mrrefChr0 57218 47 + 130230 GTGTATACATTATTAAACTGTCTATGATTTTTAGTGAACATTGTAAG -s simCow_chr6.simCow.chr6 64992 44 + 602619 ---TATGTACTATTAATCTCTACACATCATTTATTATGATCTTTAGA -s simDog_chr6.simDog.chr6 61096 44 + 593897 ---TATGGATTGTTAATCAATACACTTCCTTTATTGTGATCTTTAAA -s simHuman_chr6.simHuman.chr6 58306 47 + 601863 GTATATGCCTTGTTAATCTATACACAACCTTTAATATGCTCTTTAAA -s simRat_chr6.simRat.chr6 53366 47 + 647215 ATGTATACATTATCAGATTGTCTATCATTTTTAGTGAACATTATAAG - -a -s simMouse_chr6.simMouse.chr6 59953 10 + 636262 AGCTGTGCTT -s Anc0.Anc0refChr4 7295 10 - 45765 AGCCGTGCTT -s Anc1.Anc1refChr2 38165 10 + 144309 AGCCGTGCTT -s Anc2.Anc2refChr4 4485 10 + 10050 AGCCGTGCTA -s mr.mrrefChr0 57265 10 + 130230 AGCTGTGCTT -s simCow_chr6.simCow.chr6 65038 10 + 602619 AGCCGTGCTT -s simDog_chr6.simDog.chr6 61142 10 + 593897 AACCATGCTA -s simHuman_chr6.simHuman.chr6 58355 10 + 601863 AGCCGTGCCT -s simRat_chr6.simRat.chr6 53413 9 + 647215 AGCTAT-CTT - -a -s simMouse_chr6.simMouse.chr6 59963 20 + 636262 TGATTTACGTGGGGTTTAAA -s Anc0.Anc0refChr4 7305 20 - 45765 TGATTTACTTAAGAGCTAAA -s Anc1.Anc1refChr2 38175 20 + 144309 TGATTTACTTAAGAGCTAAA -s Anc2.Anc2refChr4 4495 20 + 10050 TTATTTAATTAAGAGCTAAA -s mr.mrrefChr0 57275 20 + 130230 TGATTTACGTGGGGTTTAAA -s simCow_chr6.simCow.chr6 65048 20 + 602619 TTATTAAGTTAAGATCTAAA -s simDog_chr6.simDog.chr6 61152 20 + 593897 TTACTTAATTAAGAGCTAAA -s simHuman_chr6.simHuman.chr6 58366 20 + 601863 TGATTTACTTAAGCGCCAAA -s simRat_chr6.simRat.chr6 53422 20 + 647215 TAATTTATGTGGGGCTTAAA - -a -s simMouse_chr6.simMouse.chr6 59983 1 + 636262 A -s Anc0.Anc0refChr4 7325 1 - 45765 A -s Anc1.Anc1refChr2 38195 1 + 144309 A -s Anc2.Anc2refChr4 4517 1 + 10050 A -s mr.mrrefChr0 57295 1 + 130230 A -s simCow_chr6.simCow.chr6 65070 1 + 602619 A -s simDog_chr6.simDog.chr6 61174 1 + 593897 A -s simHuman_chr6.simHuman.chr6 58386 1 + 601863 A -s simRat_chr6.simRat.chr6 53442 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 59984 51 + 636262 GAGTGTTCGAAATGAAGTGTTCTGGTTTGCCAGTTGCAAATGGTCTAGAGA -s Anc0.Anc0refChr4 7326 18 - 45765 GAGTACT-------------------------------AAT--TCTAGAGT -s Anc1.Anc1refChr2 38196 18 + 144309 GAGTACT-------------------------------AAT--TCTAGAGT -s Anc2.Anc2refChr4 4518 18 + 10050 GGGTACT-------------------------------AAG--TCTAGAGT -s mr.mrrefChr0 57296 18 + 130230 GAGTGCT-------------------------------AAT--TCTAGAGA -s simCow_chr6.simCow.chr6 65071 18 + 602619 GTGTACT-------------------------------AAG--CCTAGTGT -s simDog_chr6.simDog.chr6 61175 18 + 593897 GGGCATT-------------------------------AAG--TCAAGAGT -s simHuman_chr6.simHuman.chr6 58387 18 + 601863 GAGTCCC-------------------------------AAT--TCTCAAGT -s simRat_chr6.simRat.chr6 53444 7 + 647215 GAGTGCT-------------------------------------------- - -a -s simMouse_chr6.simMouse.chr6 60035 23 + 636262 CTATGGGAGTAAGTACAAAGCTG -s Anc0.Anc0refChr4 7344 19 - 45765 CTA----ATTGAGTACATAGCTG -s Anc1.Anc1refChr2 38214 19 + 144309 CTA----ATTGAGTACATAGCTG -s Anc2.Anc2refChr4 4536 19 + 10050 CTA----ATTGGGTACATATCTG -s mr.mrrefChr0 57314 19 + 130230 CTA----AGTAAGTACAAAGCTG -s simCow_chr6.simCow.chr6 65096 19 + 602619 CCA----ATTGGCTACATATCTG -s simDog_chr6.simDog.chr6 61193 18 + 593897 CT-----ATTGGGTACATATCTG -s simHuman_chr6.simHuman.chr6 58405 19 + 601863 CTA----ATTGAGTACATGGCTG - -a -s simMouse_chr6.simMouse.chr6 60058 51 + 636262 TCAGATCCCCTTCCAAAAGTTAAATGTAATGTCCAAACATTTTAGAAATAA -s Anc0.Anc0refChr4 7363 50 - 45765 TCAGACCACCTTCCACAAGTTGAATGTAATGCACAAACA-TTAAGAAACAA -s Anc1.Anc1refChr2 38233 50 + 144309 TCAGACCACCTTCCACAAGTTGAATGTAATGCACAAACA-TTAAGAAACAA -s Anc2.Anc2refChr4 4555 50 + 10050 TCAGACCACCTTCCACAAGTTGAATGTATTGCACATACA-CTAAGAAGCAA -s mr.mrrefChr0 57333 50 + 130230 TCAGATCCCCTTCCAAAAGTTAAATGTAATGTCCAAACA-TTTAGAAATAA -s simCow_chr6.simCow.chr6 65116 50 + 602619 TAAGACTACCTTCCGCAAGTTGATTGTATGGCAAAGACA-CAAAGAAGCAA -s simDog_chr6.simDog.chr6 61211 50 + 593897 TCAGATCACCTTCCACTAGTTGAATGTGTTGGACATACA-CTAAGAAGCAA -s simHuman_chr6.simHuman.chr6 58424 50 + 601863 TCAGACCACTTTCCACAACTTGAAGGTAATGCACAAATA-TGGAGAAACAA - -a -s simMouse_chr6.simMouse.chr6 60109 19 + 636262 CAGGTGTCTATGTGTAGGC -s Anc0.Anc0refChr4 7413 19 - 45765 TGGCAGTCTATATGTAGGC -s Anc1.Anc1refChr2 38283 19 + 144309 TGGCAGTCTATATGTAGGC -s Anc2.Anc2refChr4 4605 19 + 10050 TGGCAGTCGATATGTAGGC -s mr.mrrefChr0 57383 19 + 130230 CAGGTGTCTATGTGTAGGC -s simCow_chr6.simCow.chr6 65166 19 + 602619 TGGCAGTTGATATGTAGGT -s simDog_chr6.simDog.chr6 61262 19 + 593897 TGGCAGTCGATATGTAGGC -s simHuman_chr6.simHuman.chr6 58474 19 + 601863 GGGCAGTCTATATGTAGAC - -a -s simMouse_chr6.simMouse.chr6 60128 17 + 636262 CAGTAAAGGTCATTTTG -s Anc0.Anc0refChr4 7447 17 - 45765 CAGTGAGTGATTTCTTG -s Anc1.Anc1refChr2 38317 17 + 144309 CAGTGAGTGATTTCTTG -s Anc2.Anc2refChr4 4639 17 + 10050 TAGTGAGTGATTTCTTG -s mr.mrrefChr0 57402 17 + 130230 CAGTAAAGGTCATTTTG -s simCow_chr6.simCow.chr6 65200 16 + 602619 TAGTGGGTGATTTCTT- -s simDog_chr6.simDog.chr6 61296 17 + 593897 TAGTGAGTGATTTCTTG -s simHuman_chr6.simHuman.chr6 58508 17 + 601863 CAGTGAGTCATTTCTTA - -a -s simMouse_chr6.simMouse.chr6 60145 2 + 636262 TA -s Anc0.Anc0refChr4 7464 2 - 45765 TA -s Anc1.Anc1refChr2 38334 2 + 144309 TA -s Anc2.Anc2refChr4 4656 2 + 10050 TG -s mr.mrrefChr0 57419 2 + 130230 TA -s simDog_chr6.simDog.chr6 61314 2 + 593897 TG -s simHuman_chr6.simHuman.chr6 58525 2 + 601863 TA - -a -s simMouse_chr6.simMouse.chr6 60147 8 + 636262 CTTTCTTG -s Anc0.Anc0refChr4 7471 8 - 45765 TTTTCTTG -s Anc1.Anc1refChr2 38341 8 + 144309 TTTTCTTG -s Anc2.Anc2refChr4 4663 8 + 10050 TTTTCTTG -s mr.mrrefChr0 57421 8 + 130230 CTTTCTTG -s simDog_chr6.simDog.chr6 61321 8 + 593897 TTTTCTTG -s simHuman_chr6.simHuman.chr6 58532 8 + 601863 TGTTCTTG - -a -s simMouse_chr6.simMouse.chr6 60155 10 + 636262 GATGTCCTCT -s Anc0.Anc0refChr4 7479 10 - 45765 GAGGTCCTCT -s Anc1.Anc1refChr2 38349 10 + 144309 GAGGTCCTCT -s Anc2.Anc2refChr4 4671 10 + 10050 GAGGTCCCCT -s mr.mrrefChr0 57429 10 + 130230 GATGTCCTCT -s simDog_chr6.simDog.chr6 61329 10 + 593897 GAGGTCCCCT -s simHuman_chr6.simHuman.chr6 58541 10 + 601863 GAGGTCCTCT - -a -s simMouse_chr6.simMouse.chr6 60165 17 + 636262 AGAAAGAGGATATAGGT -s Anc0.Anc0refChr4 7489 17 - 45765 CCAAAGAGGATATAGGC -s Anc1.Anc1refChr2 38359 17 + 144309 CCAAAGAGGATATAGGC -s Anc2.Anc2refChr4 4687 17 + 10050 CCAAAGAGGGTATAGAC -s mr.mrrefChr0 57439 17 + 130230 AGAAAGAGGATATAGGT -s simCow_chr6.simCow.chr6 65222 17 + 602619 CCAAAGAGATTATAGAC -s simDog_chr6.simDog.chr6 61346 17 + 593897 CCGAGGGGGGTATGGAC -s simHuman_chr6.simHuman.chr6 58551 17 + 601863 TCAAAAAGGATACAGGC - -a -s simMouse_chr6.simMouse.chr6 60182 15 + 636262 AGGCTGGCTGCAACA -s Anc0.Anc0refChr4 7507 15 - 45765 AAGCTTGCCCCAGGA -s Anc1.Anc1refChr2 38377 15 + 144309 AAGCTTGCCCCAGGA -s Anc2.Anc2refChr4 4705 15 + 10050 AAGCTTGCCCCAGGA -s mr.mrrefChr0 57456 15 + 130230 AGGCTGGCTGCAACA -s simCow_chr6.simCow.chr6 65240 15 + 602619 AAGCTTGCTCCTGGA -s simDog_chr6.simDog.chr6 61364 15 + 593897 AAGCTTGCCCCAGTA -s simHuman_chr6.simHuman.chr6 58569 15 + 601863 AAGCTTGCGCCAGGA - -a -s simMouse_chr6.simMouse.chr6 60197 14 + 636262 TTACTAGAGATCCT -s Anc0.Anc0refChr4 7534 14 - 45765 TTACTAAACATTCT -s Anc1.Anc1refChr2 38404 14 + 144309 TTACTAAACATTCT -s Anc2.Anc2refChr4 4732 14 + 10050 TAACTAAACATTCT -s mr.mrrefChr0 57471 14 + 130230 TTACTAGAGATCCT -s simCow_chr6.simCow.chr6 65264 10 + 602619 ----TAAAGACTCT -s simDog_chr6.simDog.chr6 61392 14 + 593897 TAACTAAGCATTCT -s simHuman_chr6.simHuman.chr6 58596 14 + 601863 TTACCAAACATTCT - -a -s simMouse_chr6.simMouse.chr6 60211 4 + 636262 TCGG -s Anc0.Anc0refChr4 7548 4 - 45765 TTGG -s Anc1.Anc1refChr2 38418 4 + 144309 TTGG -s Anc2.Anc2refChr4 4767 4 + 10050 TTGG -s mr.mrrefChr0 57485 4 + 130230 TCGG -s simCow_chr6.simCow.chr6 65295 4 + 602619 GCAG -s simDog_chr6.simDog.chr6 61427 4 + 593897 TTGG -s simHuman_chr6.simHuman.chr6 58610 4 + 601863 GTGG - -a -s simMouse_chr6.simMouse.chr6 60215 37 + 636262 TAAGGACTTTTAAGGACTTTTATGATGGCCTGTGACC -s Anc0.Anc0refChr4 7555 33 - 45765 TAAGGATTTTTAGGAA----TAATTTTGCCTCTGACC -s Anc1.Anc1refChr2 38425 33 + 144309 TAAGGATTTTTAGGAA----TAATTTTGCCTCTGACC -s Anc2.Anc2refChr4 4774 33 + 10050 TAAGGATTTTTAGGAA----TTATTTTGCCTCTGACC -s mr.mrrefChr0 57489 33 + 130230 TAAGGACTTTTAAGGA----TATGATGGCCTGTGACC -s simCow_chr6.simCow.chr6 65302 33 + 602619 TAAGGATGTTTAGTAA----TCATTTCACCTCTGACC -s simDog_chr6.simDog.chr6 61434 33 + 593897 TGAGGGTTTTTAGGCA----TTATTTTGTCTGTGATC -s simHuman_chr6.simHuman.chr6 58617 33 + 601863 TATGGATCTTTAGGAA----TAATCTTGCCTCTGACC - -a -s simMouse_chr6.simMouse.chr6 60252 39 + 636262 TGTGTGAATGCATGCGTGTTCTTTACTCTTGGCTAGGGT -s Anc0.Anc0refChr4 7588 37 - 45765 TGTACAAGTGCACAAGTGTTCTTTGCTCTAG--TCGGGT -s Anc1.Anc1refChr2 38458 37 + 144309 TGTACAAGTGCACAAGTGTTCTTTGCTCTAG--TCGGGT -s Anc2.Anc2refChr4 4807 37 + 10050 TGCACAAGTGCACAAGTGTTCTTTGCTCTAG--TCAGGT -s mr.mrrefChr0 57522 37 + 130230 TGTGTGAATGCATGCGTGTTCTTTACTCTTG--TAGGGT -s simCow_chr6.simCow.chr6 65353 34 + 602619 TGCACAGGTGCACAAG---TCTTTGCCCTGC--TCAGGT -s simDog_chr6.simDog.chr6 61467 34 + 593897 TGCACAAGTGCA---GTGTTCTTTGCTCTAG--TCAGGT -s simHuman_chr6.simHuman.chr6 58650 37 + 601863 CATACAAGTGCACAAGTATTCTTTGCTCCAG--TGGGGT - -a -s simMouse_chr6.simMouse.chr6 60291 25 + 636262 ATACTGTATTAGTGGAAATTTCTCA -s Anc0.Anc0refChr4 7625 22 - 45765 ATACT---CTGGTGAGAATTTTTTG -s Anc1.Anc1refChr2 38495 22 + 144309 ATACT---CTGGTGAGAATTTTTTG -s Anc2.Anc2refChr4 4847 22 + 10050 ATGTT---CTGGTGAGAATTTTTTG -s mr.mrrefChr0 57559 22 + 130230 ATACT---TTAGTGGAAATTTCTCA -s simCow_chr6.simCow.chr6 65390 22 + 602619 ATGTT---CTGGTGAGAATTCTTTG -s simDog_chr6.simDog.chr6 61504 22 + 593897 ATGTT---TTGTTGGGAATATTTTG -s simHuman_chr6.simHuman.chr6 58687 22 + 601863 ATACT---CTGGTGAGAATTTTTTC - -a -s simMouse_chr6.simMouse.chr6 60316 7 + 636262 GGTACCC -s Anc0.Anc0refChr4 7647 7 - 45765 TCCACTC -s Anc1.Anc1refChr2 38517 7 + 144309 TCCACTC -s Anc2.Anc2refChr4 4872 7 + 10050 TCCACTC -s mr.mrrefChr0 57581 7 + 130230 GGTACCC -s simCow_chr6.simCow.chr6 65415 7 + 602619 TCCATTC -s simDog_chr6.simDog.chr6 61529 7 + 593897 TCCACTC -s simHuman_chr6.simHuman.chr6 58709 7 + 601863 TCCACGC - -a -s simMouse_chr6.simMouse.chr6 60323 96 + 636262 TTGGTGCCTCTCCATGGGCGCGCCAAGTGTATAAAGGCGGAGAGCTAGCCTAAGCGAGTCATCTAGGTCTATAACTTCACTAGACTTTTTCTATTC -s Anc0.Anc0refChr4 7654 48 - 45765 T--GTGCCTCTACAC------------------------------------------CTCATCTAAGTGTATCTATCTACTAACATTTTTCT---- -s Anc1.Anc1refChr2 38524 48 + 144309 T--GTGCCTCTACAC------------------------------------------CTCATCTAAGTGTATCTATCTACTAACATTTTTCT---- -s Anc2.Anc2refChr4 4880 48 + 10050 T--GTACCTCTACAC------------------------------------------CTCATCTAAGTGTATCTATCTACTAACATTTTTCT---- -s mr.mrrefChr0 57588 48 + 130230 T--GTGCCTCTCCAT------------------------------------------GTCATCTAGGTCTATAACTTCACTAGACTTTTTCT---- -s simCow_chr6.simCow.chr6 65423 48 + 602619 T--GCACCTCTACAC------------------------------------------CTTATCTAAGTCTATCTATCTACTAGCATCTTTCT---- -s simDog_chr6.simDog.chr6 61537 48 + 593897 T--TTACCTCTTCAC------------------------------------------CTCATGTAAGTGTATCAATTTACTAACATTTTTCC---- -s simHuman_chr6.simHuman.chr6 58716 48 + 601863 T--GTGCCTCTACAC------------------------------------------CTCATCGAAGTGTATCTATCTACCAACATTTTTCT---- - -a -s simMouse_chr6.simMouse.chr6 60419 98 + 636262 TTCTATTAGTCAAGTTGGTGGTTCATTCCATACTTATAGCAAGGGTAAACCCTATCCATGATTGCCAGGTGGGTTGCATGCCATCTGTCATTGCACCC -s Anc0.Anc0refChr4 7702 22 - 45765 TCCTA----TTAACAT-TTGGCTCAT--------------------------------T--------------------------------------- -s Anc1.Anc1refChr2 38572 26 + 144309 TCCTATTATTTAACAT-TTGGCTCAT--------------------------------T--------------------------------------- -s Anc2.Anc2refChr4 4930 22 + 10050 TCCGA----TTAACAT-TTTGCTCAT--------------------------------T--------------------------------------- -s mr.mrrefChr0 57636 65 + 130230 TTCTATTAGTCAAGTT-GTGGTTCAT--------------------------------TGATTGCCAGGTGGGTTGCATGCCATCTGTCATTGCACCC -s simCow_chr6.simCow.chr6 65473 20 + 602619 TCTGA----TC--CAT-TTTTCTCAT--------------------------------T--------------------------------------- -s simDog_chr6.simDog.chr6 61587 22 + 593897 TCCGA----TTAACAT-TTTGCTCAT--------------------------------T--------------------------------------- -s simHuman_chr6.simHuman.chr6 58764 26 + 601863 TCCTATGATTTAACAT-TTGGCTGAC--------------------------------T--------------------------------------- -s simRat_chr6.simRat.chr6 53469 40 + 647215 ----------------------------------------------------------TGATTGCCAGGTGGGTTGCAAGCCATTTGTCATCACATCC - -a -s simMouse_chr6.simMouse.chr6 60517 173 + 636262 TTAATACCCTGTAGGCATGGTTATGTCTCCCAAGAGAGCCTGCTAGATAGATGACAGTTCGATAGAATTGGTATCTAACTTGGAACCACTCTTGCCAATTTACTATTTGGTTCATGTTCCGCAGTATGCTCTTCGAGCTTTTATGCGTGTGGGTAAGAAGGGAGGGTTGAGTT -s mr.mrrefChr0 57701 173 + 130230 TTAATACCCTGTAGGCATGGTTATGTCTCCCAAGAGAGCCTGCTAGATAGATGACAGTTCGATAGAATTGGTATCTAACTTGGAACCACTCTTGCCAATTTACTATTTGGTTCATGTTCCGCAGTATGCTCTTCGAGCTTTTATGCGTGTGGGTAAGAAGGGAGGGTTGAGTT -s simRat_chr6.simRat.chr6 53511 173 + 647215 TCAATACCCTGTAGGCTGACCACTGTCTCCCAATAGGGCCTGATAGCTAGATGACAATTTGATAGAATTGGTATCTAACTTGGAACCAAATTTGGCAATTTACTATTTGGTTCATGTTCCACAGGATACTCCTCGAGCTTCTTCGCACGGGGGTAAGAAGGGAGGGTTGAGTT - -a -s simMouse_chr6.simMouse.chr6 60690 28 + 636262 GGATCTAAGCGGGAACTTATACCCATAT -s mr.mrrefChr0 57874 28 + 130230 GGATCTAAGCGGGAACTTATACCCATAT -s simRat_chr6.simRat.chr6 53689 28 + 647215 TGATCTAGACAGGAACTTATACCCATAT - -a -s simMouse_chr6.simMouse.chr6 60718 144 + 636262 ATCCTAGGTAGTGGGTAGGATTGGATTGAGCTAAAGGGTTACCAGTAAATTAATACAGTCTGTGCATGCAACATGACTTTTCAAACTGGCGCAAATAACCTATAGTATAAGGAATGGAAGTGTTAAAGGCCGAAATATCCTTCA -s mr.mrrefChr0 57902 135 + 130230 ATCCTAGGTAGTGGGTAGGATTGGATTGAGCTAAAGGGTTACCAGTAAATTAATACAGTCTGTGCATGCAACATGACTTTT---------GCAAATAACCTATAGTATAAGGAATGGAAGTGTTAAAGGCCGAAATATCCTTCA -s simRat_chr6.simRat.chr6 53718 135 + 647215 ATCCTAGGTAGTGGGTAGGATTGGATTAAGCTAAAGACTTACCAGTAAATTAATACAGTCTGTGGGATCAACATGACTTTT---------GGAAATAACCGTTAGTATAGGGGGTGGAAGTGTTAAAGGCCGAAATATCTTTCA - -a -s simMouse_chr6.simMouse.chr6 60862 114 + 636262 GTTCTCAGTTCAAAGAGGCATGGGTTAGATCCAGTGGTTTCTTTATCCTATGAGACTGGTAAAAGTAAAATTGAATAGGATTAGGATGTAACATTCATCTTTCTTAGTCTATGG -s Anc0.Anc0refChr4 7724 58 - 45765 --------------------------------------CTAT------------ACTGATAGGGAGGTAATTAAATAGGATGTAGAT-TAA-----ATCTTTCTGTGTAAATGG -s Anc1.Anc1refChr2 38598 58 + 144309 --------------------------------------CTAT------------ACTGATAGGGAGGTAATTAAATAGGATGTAGAT-TAA-----ATCTTTCTGTGTAAATGG -s Anc2.Anc2refChr4 4952 58 + 10050 --------------------------------------CTAT------------ACTGATAGGGAGGTAATTAAATAGGATGTAGCT-TAC-----ACCTTTCTGTGTAAATGG -s mr.mrrefChr0 58037 102 + 130230 GTTCTCAGTTCAAAGAGGCATGGGTTAGATCCAGTGGTTTCT------------ACTGGTAAAAGTAAAATTGAATAGGATTAGGATGTAACATTCATCTTTCTTAGTCTATGA -s simCow_chr6.simCow.chr6 65493 58 + 602619 --------------------------------------CTAT------------ATTGATAGGGAGGTTATTAAATAGGATGTAGCT-TAC-----ACCTTTCTATGTGAATGG -s simDog_chr6.simDog.chr6 61609 58 + 593897 --------------------------------------TAAT------------ACTGATAGGGAGCTAATTCAATAGGATGTAACT-TTC-----ACCTTTCTGTGTAAATGG -s simHuman_chr6.simHuman.chr6 58790 58 + 601863 --------------------------------------CTAC------------ACTGATAGGGAGGTAATTAGATAGAATGTAGAT-TAA-----ATCTTATTCTGTAAGTAG -s simRat_chr6.simRat.chr6 53857 101 + 647215 GTTCTCAGTTCAAGATGGAATGGATTAGTTCCACTGGTTTCT------------ACCGGTAAAAGTAAAATTGA-TAGGATTAGGATGTAACGTTCGATTTTCTTAGTGAATCA - -a -s simMouse_chr6.simMouse.chr6 60976 1 + 636262 A -s Anc0.Anc0refChr4 7782 1 - 45765 G -s Anc1.Anc1refChr2 38656 1 + 144309 G -s Anc2.Anc2refChr4 5011 1 + 10050 G -s mr.mrrefChr0 58139 1 + 130230 A -s simCow_chr6.simCow.chr6 65552 1 + 602619 G -s simDog_chr6.simDog.chr6 61668 1 + 593897 G -s simRat_chr6.simRat.chr6 53958 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 60977 43 + 636262 ATCACCCATTATGGTAAATCTTAGCCGAAAGTTGCATTCCAGG -s Anc0.Anc0refChr4 7783 43 - 45765 CTCAACCATTACAGTAAATCTTTCCCCTGAGTTGCATTTCAGT -s Anc1.Anc1refChr2 38657 43 + 144309 CTCAACCATTACAGTAAATCTTTCCCCTGAGTTGCATTTCAGT -s Anc2.Anc2refChr4 5012 43 + 10050 CTCAGCCATTACAGCAAAATTTTCCCCTGAGTTGCATTTCAGT -s mr.mrrefChr0 58140 43 + 130230 TTCAACCATTATGGTAAATCTTTCCCCAAAGTTGCATTCCAGG -s simCow_chr6.simCow.chr6 65560 42 + 602619 CTCAGCCATTTCAGCAAA-TCTTTCCCTGGGTTGTATTTCAGT -s simDog_chr6.simDog.chr6 61669 43 + 593897 CTCAGCCATTACCGCAAGATTTTCCCCTGAGTTGCACTTCAGT -s simHuman_chr6.simHuman.chr6 58848 40 + 601863 ---GATTATGACAGTTAATCTTTCCTCTGAGTTGCATTTCAGT -s simRat_chr6.simRat.chr6 53959 43 + 647215 TTCAACCATTATGATAAATCTTTCCCCAAAGTTGCATTCCAAG - -a -s simMouse_chr6.simMouse.chr6 61020 3 + 636262 GGT -s Anc0.Anc0refChr4 7826 3 - 45765 GGT -s Anc1.Anc1refChr2 38700 3 + 144309 GGT -s Anc2.Anc2refChr4 5056 3 + 10050 GGT -s mr.mrrefChr0 58183 3 + 130230 GGT -s simCow_chr6.simCow.chr6 65603 3 + 602619 GGT -s simDog_chr6.simDog.chr6 61713 3 + 593897 GGT -s simHuman_chr6.simHuman.chr6 58888 3 + 601863 GGC -s simRat_chr6.simRat.chr6 54002 3 + 647215 TGT - -a -s simMouse_chr6.simMouse.chr6 61023 11 + 636262 CCAGACTTCCT -s Anc0.Anc0refChr4 7829 11 - 45765 CTGGATGTCCT -s Anc1.Anc1refChr2 38703 11 + 144309 CTGGATGTCCT -s Anc2.Anc2refChr4 5059 11 + 10050 CTGGATGCCCT -s mr.mrrefChr0 58186 11 + 130230 CTGGATTTCCT -s simCow_chr6.simCow.chr6 65606 11 + 602619 CTGGATGGCCC -s simDog_chr6.simDog.chr6 61716 11 + 593897 CTGGATGCCCT -s simHuman_chr6.simHuman.chr6 58892 11 + 601863 CTGGCTGTCCT -s simRat_chr6.simRat.chr6 54005 11 + 647215 CTGGATTTCCT - -a -s simMouse_chr6.simMouse.chr6 61034 1 + 636262 A -s Anc0.Anc0refChr4 7840 1 - 45765 C -s Anc1.Anc1refChr2 38714 1 + 144309 C -s Anc2.Anc2refChr4 5070 1 + 10050 C -s mr.mrrefChr0 58197 1 + 130230 A -s simCow_chr6.simCow.chr6 65620 1 + 602619 C -s simDog_chr6.simDog.chr6 61727 1 + 593897 C -s simHuman_chr6.simHuman.chr6 58903 1 + 601863 C -s simRat_chr6.simRat.chr6 54016 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 61035 12 + 636262 TTAACTTTTGAA -s Anc0.Anc0refChr4 7841 12 - 45765 TTAACTTTTGAA -s Anc1.Anc1refChr2 38715 12 + 144309 TTAACTTTTGAA -s Anc2.Anc2refChr4 5071 12 + 10050 TTAACTTTTGAA -s mr.mrrefChr0 58198 12 + 130230 TTAACTTTTGAA -s simCow_chr6.simCow.chr6 65621 12 + 602619 TTAACTTTTGAA -s simDog_chr6.simDog.chr6 61729 12 + 593897 CTTACTGTTTAA -s simHuman_chr6.simHuman.chr6 58904 12 + 601863 TTAACTTTTGAA -s simRat_chr6.simRat.chr6 54017 12 + 647215 TTAACTTTTGAA - -a -s simMouse_chr6.simMouse.chr6 61047 6 + 636262 TATGCT -s Anc0.Anc0refChr4 7861 6 - 45765 TGCTCT -s Anc1.Anc1refChr2 38735 6 + 144309 TGCTCT -s Anc2.Anc2refChr4 5091 6 + 10050 TGCTCT -s mr.mrrefChr0 58218 6 + 130230 TATGCT -s simCow_chr6.simCow.chr6 65641 4 + 602619 TG--CT -s simDog_chr6.simDog.chr6 61749 6 + 593897 TGCTCT -s simHuman_chr6.simHuman.chr6 58924 6 + 601863 TGCTCT -s simRat_chr6.simRat.chr6 54037 6 + 647215 TATGCA - -a -s simMouse_chr6.simMouse.chr6 61053 69 + 636262 TCTACTACCCCAACTATATGAGAGATAGGCATCTACAATGGTGGTCAGGTTTGTAGACCCAATTGTGCT -s Anc0.Anc0refChr4 7868 68 - 45765 TCTACTACCCCTACTACACAA-AGAGGGATACTTGCAATGTTGGTCAGACCTGTAAAGTCAATTCTGCT -s Anc1.Anc1refChr2 38742 68 + 144309 TCTACTACCCCTACTACACAA-AGAGGGATACTTGCAATGTTGGTCAGACCTGTAAAGTCAATTCTGCT -s Anc2.Anc2refChr4 5098 68 + 10050 TCTACTACCCCTACTACATAA-AGAGGGGTGCTTGCAATGTTGGTCAGACTTGTAAAGTCAATTCTTCT -s mr.mrrefChr0 58224 69 + 130230 TCTACTACCCCAACTATACAAGAGATAGACATCTACAATGGTGGTCAGGTCTGTAGACCCAATTGTGCT -s simCow_chr6.simCow.chr6 65646 66 + 602619 TCTACTATTGCTACTATATAA-AGAGG--TGCATCCAATGTTGGTCAGACTTGTAAAGTAGATTCTTCC -s simDog_chr6.simDog.chr6 61756 68 + 593897 TCTACTACCCCTACTACATGA-AGAGAGGTGCTTGGAATGTTGGTCATACTTGTTAAGTCAATTCTTTT -s simHuman_chr6.simHuman.chr6 58931 68 + 601863 TCTACTACCCCCACTACACAA-AGAGGGATACTTGCAGTGTTTGTCAGACCCGTAAAGTTCATTCTGCT -s simRat_chr6.simRat.chr6 54043 69 + 647215 TCTACTACCCCAACTATACAAAAGATAGACGTCTAGAATTGTGGTCAGTTCTGTAGACCCAATTGTGCT - -a -s simMouse_chr6.simMouse.chr6 61122 1 + 636262 G -s Anc0.Anc0refChr4 7936 1 - 45765 G -s Anc1.Anc1refChr2 38810 1 + 144309 G -s Anc2.Anc2refChr4 5168 1 + 10050 G -s mr.mrrefChr0 58293 1 + 130230 G -s simCow_chr6.simCow.chr6 65714 1 + 602619 G -s simDog_chr6.simDog.chr6 61826 1 + 593897 G -s simHuman_chr6.simHuman.chr6 58999 1 + 601863 G -s simRat_chr6.simRat.chr6 54112 1 + 647215 G - -a -s simMouse_chr6.simMouse.chr6 61123 19 + 636262 GCTGTCCAATAGGCAGGGG -s Anc0.Anc0refChr4 7939 16 - 45765 GCTG---GGTAAGCAGGGG -s Anc1.Anc1refChr2 38813 16 + 144309 GCTG---GGTAAGCAGGGG -s Anc2.Anc2refChr4 5171 16 + 10050 CCTG---GGTAAGCAGGGG -s mr.mrrefChr0 58294 19 + 130230 GCTGTCCGATAGGCAGGGG -s simCow_chr6.simCow.chr6 65717 16 + 602619 TCTT---GGTTAGCAGGGG -s simDog_chr6.simDog.chr6 61829 16 + 593897 CCTG---GGTAAGCAGGGG -s simHuman_chr6.simHuman.chr6 59002 16 + 601863 GCTG---GTTAAGCAGGGG -s simRat_chr6.simRat.chr6 54113 19 + 647215 GCTGTCTGATAGGCAGGGG - -a -s simMouse_chr6.simMouse.chr6 61142 9 + 636262 TATCACTTT -s Anc0.Anc0refChr4 7956 9 - 45765 TATAATTTG -s Anc1.Anc1refChr2 38830 9 + 144309 TATAATTTG -s Anc2.Anc2refChr4 5188 9 + 10050 TATAATTTG -s mr.mrrefChr0 58313 9 + 130230 TATCATTTT -s simCow_chr6.simCow.chr6 65734 9 + 602619 TATAATTTG -s simDog_chr6.simDog.chr6 61846 9 + 593897 TATAATTTG -s simHuman_chr6.simHuman.chr6 59019 9 + 601863 TATTATTTG -s simRat_chr6.simRat.chr6 54132 9 + 647215 TATAATTTT - -a -s simMouse_chr6.simMouse.chr6 61151 45 + 636262 AACGGCTACCAACCAGCCCCATAGACACTGTCAGCTTTCCTAGCG -s Anc0.Anc0refChr4 7965 12 - 45765 AACCACTATGAA--------------------------------- -s Anc1.Anc1refChr2 38839 12 + 144309 AACCACTATGAA--------------------------------- -s Anc2.Anc2refChr4 5197 12 + 10050 CACCACTATGAA--------------------------------- -s mr.mrrefChr0 58322 45 + 130230 AACGACTACCAACCAGCCCCATAGACACTGTCAGCTTTCCTAGCG -s simCow_chr6.simCow.chr6 65799 12 + 602619 CACCACTATGAA--------------------------------- -s simDog_chr6.simDog.chr6 61855 12 + 593897 CACCACTAAGAA--------------------------------- -s simHuman_chr6.simHuman.chr6 59028 12 + 601863 AACCACTATGAA--------------------------------- -s simRat_chr6.simRat.chr6 54141 45 + 647215 AACGACTACTAATCAGCCCCCCAGACACTGCTATCTTTCCTAGGG - -a -s simMouse_chr6.simMouse.chr6 61196 11 + 636262 ATAGTAGAGCA -s Anc0.Anc0refChr4 7977 6 - 45765 ---ATAG--CA -s Anc1.Anc1refChr2 38851 6 + 144309 ---ATAG--CA -s Anc2.Anc2refChr4 5209 6 + 10050 ---ATAG--CA -s mr.mrrefChr0 58370 9 + 130230 ATAGTAG--CA -s simCow_chr6.simCow.chr6 65811 6 + 602619 ---ATGG--CA -s simDog_chr6.simDog.chr6 61867 6 + 593897 ---ACAG--CA -s simHuman_chr6.simHuman.chr6 59040 6 + 601863 ---ATAA--GA -s simRat_chr6.simRat.chr6 54205 9 + 647215 ATAGTAG--CA - -a -s simMouse_chr6.simMouse.chr6 61207 7 + 636262 TCTCATA -s Anc0.Anc0refChr4 7983 7 - 45765 TCTCATG -s Anc1.Anc1refChr2 38857 7 + 144309 TCTCATG -s Anc2.Anc2refChr4 5218 7 + 10050 CCTCACG -s mr.mrrefChr0 58379 7 + 130230 TCTCATA -s simCow_chr6.simCow.chr6 65820 7 + 602619 TCTCACA -s simDog_chr6.simDog.chr6 61876 7 + 593897 CCCCACG -s simHuman_chr6.simHuman.chr6 59046 7 + 601863 TCTGCTT -s simRat_chr6.simRat.chr6 54214 7 + 647215 ACTCATA - -a -s simMouse_chr6.simMouse.chr6 61214 53 + 636262 TATTACTGTGCCCAATTCTATGAACCACTTTTACTAAAAATTGTATGATTTTC -s Anc0.Anc0refChr4 7990 53 - 45765 TATCACCATGCATAACTCTGGAAAGTATTTTAGTTAAAAATTGTGTGATTCTC -s Anc1.Anc1refChr2 38864 53 + 144309 TATCACCATGCATAACTCTGGAAAGTATTTTAGTTAAAAATTGTGTGATTCTC -s Anc2.Anc2refChr4 5225 53 + 10050 TATCACCATGCATAACTTTGGAAAGTATTTTAGTTAAAAATTGTGTGATTCTC -s mr.mrrefChr0 58386 53 + 130230 TATTACTGTGCCTAATTCTATGAACCACTTTTACTAAAAATTGTATGATTTTC -s simCow_chr6.simCow.chr6 65828 53 + 602619 TATCACCATGCAGTGCTTTGGAAAGTATATTAGTTAAAAATTCTGTGATTCTG -s simDog_chr6.simDog.chr6 61883 53 + 593897 TATCACCATACATAACTTTGGAAAGTTGTTTAGTTAAATATGGCATGGTGCTC -s simHuman_chr6.simHuman.chr6 59053 53 + 601863 GCTCACCATGCATGACTCTGGAAAGTATGTTGGTTAAAAATTGTGTGATTCTC -s simRat_chr6.simRat.chr6 54221 52 + 647215 TATTACTG-GCCTAATTCTATTAACCACTTTAACTAAAAATTGTATGATTTTC - -a -s simMouse_chr6.simMouse.chr6 61267 8 + 636262 CTTAGCTG -s Anc0.Anc0refChr4 8049 8 - 45765 CTTAGCTG -s Anc1.Anc1refChr2 38923 8 + 144309 CTTAGCTG -s Anc2.Anc2refChr4 5284 8 + 10050 CTTGGCTG -s mr.mrrefChr0 58439 8 + 130230 CTTAGCTG -s simCow_chr6.simCow.chr6 65887 8 + 602619 CTCTGTTG -s simDog_chr6.simDog.chr6 61942 8 + 593897 TGTGGCTT -s simHuman_chr6.simHuman.chr6 59112 8 + 601863 CTTAGCTG -s simRat_chr6.simRat.chr6 54273 8 + 647215 CCTAGCCG - -a -s simMouse_chr6.simMouse.chr6 61275 13 + 636262 CTACATTCAGACA -s Anc0.Anc0refChr4 8058 10 - 45765 TTGCATTCA---G -s Anc1.Anc1refChr2 38932 13 + 144309 TTGCATTCAGTCG -s Anc2.Anc2refChr4 5293 10 + 10050 CTGCATTCA---G -s mr.mrrefChr0 58447 13 + 130230 TTACATTCAGACA -s simCow_chr6.simCow.chr6 65896 10 + 602619 CTGCATTCA---G -s simDog_chr6.simDog.chr6 61951 10 + 593897 CTGCATTCA---A -s simHuman_chr6.simHuman.chr6 59121 13 + 601863 TTGCATTCAGTCG -s simRat_chr6.simRat.chr6 54281 11 + 647215 TTA--TTCAGACA - -a -s simMouse_chr6.simMouse.chr6 61288 26 + 636262 ATGGCTAAATTTTATAGAAAGTACTA -s Anc0.Anc0refChr4 8072 26 - 45765 ATGGCTAAATTTTATAGAGAGCAATA -s Anc1.Anc1refChr2 38949 26 + 144309 ATGGCTAAATTTTATAGAGAGCAATA -s Anc2.Anc2refChr4 5307 26 + 10050 ATGGCTAAATTTTATAGAGAGCAATA -s mr.mrrefChr0 58460 26 + 130230 ATGGCTAAATTTTATAGAAAGTACTA -s simCow_chr6.simCow.chr6 65910 26 + 602619 ATGGCCAAATTTTATAGAAAGCAGTA -s simDog_chr6.simDog.chr6 61965 26 + 593897 AAGGCTAAATTTTATAGAGAGCAACA -s simHuman_chr6.simHuman.chr6 59139 26 + 601863 ATTGCTAAATTTTGTACACAGCAATA -s simRat_chr6.simRat.chr6 54292 26 + 647215 ATGGCTAAATTTTATAGAAAGTACTA - -a -s simMouse_chr6.simMouse.chr6 61314 106 + 636262 CTGGGGGCCACTAGAGGAACGCGAACCATTTCAGATGATAAGATGGCGTGCAACTCTGGCAGAATGCCCTGACCACTTTTTTCATTCATGCGGTCAGACCCTATAA -s Anc0.Anc0refChr4 8107 77 - 45765 -------CCAGCAAAGATAGGGGAACCACTTCTGAGGGCGAATTGGAGTTCTCCCTCT-CAGATTCACCAG--------------TCATGCAGTAAGAC------- -s Anc1.Anc1refChr2 38984 105 + 144309 CAGAGAACCAGCAAAGATAGGGGAACCACTTCTGAGGGCGAATTGGAGTTCTCCCTCTGCAGATTCACCAG-CCACATTTCTGATTCATGCAGTAAGACTCTATGA -s Anc2.Anc2refChr4 5342 77 + 10050 -------CCAGCAAAGATAGTGGAACCACTTCTGAGGGCGAATTGGAGTTCTCCCTCT-CAGATACAACAA--------------TGATACAGAGAGAC------- -s mr.mrrefChr0 58486 106 + 130230 CTGGGAGCCACTAAAGGAACGCGAACCATTTCAGATGATAAGATGGCGTGCAACTCTTGCAGAATGCCCTGACCACTTTTTTCATTCATGCGGTAAGACCCTATGA -s simCow_chr6.simCow.chr6 65945 60 + 602619 -------CCAGCAAAGAGTGAGGAACCACTTTTGAGGTCAGATTG-----CTTCCACC-CAG-TACTTTAA--------------TAA------------------ -s simDog_chr6.simDog.chr6 62000 73 + 593897 -------CCAGCAGAAGTAGTAGAACCAGTTCT----GCGAATTGGAGTTCTCCCTGT-CAGATACAACAA--------------TGATACAGAGAGAC------- -s simHuman_chr6.simHuman.chr6 59174 105 + 601863 CAGAGAACTAGCAAAGATAGGGGAACCACTTCCAAGGGCGAATTGGAATTTTCTCTCTGAAGACTCACCAG-CCACATTTCTGATTCCTGCTGTACAACTCTATGA -s simRat_chr6.simRat.chr6 54318 106 + 647215 CTGGGAGCCACTAAAAGGACGTGAACCATTTCTGACGATAAGATGGCGTACAACTATTGCAGATTGCCCTGACCACTTTTTTCATTTATGTGGTAGGACCCTATGA - -a -s simMouse_chr6.simMouse.chr6 61420 23 + 636262 AAAGCATTGAGTGCACTGATAAT -s Anc0.Anc0refChr4 8184 15 - 45765 --------AAGTGCACTGATAGC -s Anc1.Anc1refChr2 39089 23 + 144309 AAGGGATTAAGTGCACTGATAGC -s Anc2.Anc2refChr4 5419 15 + 10050 --------AAGTGCACTGATAGC -s mr.mrrefChr0 58592 23 + 130230 AAAGCATTGAGTGCACTGATAAC -s simDog_chr6.simDog.chr6 62073 15 + 593897 --------AAGTGCACTGATAGC -s simHuman_chr6.simHuman.chr6 59303 23 + 601863 AAGGGATTAAGTTTACTGATAGC -s simRat_chr6.simRat.chr6 54424 23 + 647215 TAAGCATTGAGTACACTGATAAC - -a -s simMouse_chr6.simMouse.chr6 61443 126 + 636262 TACCAATCCTCCACCATGGCCTGACCTCTAATAGAGAGTATAAAACAATCTCAACACTTAGTTTTAAAACTTAATATACACTCCATTCTTCTTAGTTTCTAAACTTAATATACACTCCATTGCTAC -s Anc0.Anc0refChr4 8199 66 - 45765 CTCT-------------GGACTGACCTCTAATGGCAAGTGTAAAACAGTATCAACACTTATTATCC-----------------------------------------------ACTCCACTTCTTC -s Anc1.Anc1refChr2 39112 95 + 144309 CTCTG------------GGACTGACCTCTAATGGCAAGTGTAAAACAGTATCAACACTTATTATCCAATC--------CACT----------ACCTCTGTATAAGTC-TGGATACTCCACTTCTTC -s Anc2.Anc2refChr4 5434 66 + 10050 CTCT-------------GGACTGACCTCTAATGGCAAATGTAAAACAGTATCAACAGTTGTCATCC-----------------------------------------------ACTCCACTTCTTC -s mr.mrrefChr0 58615 110 + 130230 TACCAATCC------ATGGCCTGACCTCTAATAGAGAGTATAAAACAATCTCAACACTTAGTTTTAAAACTTAATATACACT----------TAGTCTCTAAACTTAATATACACTCCATTGCTAC -s simCow_chr6.simCow.chr6 66005 56 + 602619 -------------------AATGACCTCTAATG----ATGTCAAACAATATCAACAGGTGACATTC-----------------------------------------------ACTCCACTTCTTT -s simDog_chr6.simDog.chr6 62101 66 + 593897 CTCT-------------GGACTGACTTCAAATAGCAAATACAAAACAGGATCAATAGTTGTCATCC-----------------------------------------------ACTCCACTTCTTC -s simHuman_chr6.simHuman.chr6 59326 94 + 601863 CTCTG------------GGACTGACCTCTAATGGGAAGTGTAAGACA-TTTCAACACTTACTGTCCAATC--------CACT----------ACCTCTGTATAAGTC-TGGATAATCCACTACCTC -s simRat_chr6.simRat.chr6 54447 110 + 647215 TACCAATCC------ACAGCCTGACCGCTAATAGAGAATATGAAACTATCTCAACACTTAGTTTTAAAACTTAATATACACT----------TAATCTCAAAACATAACATACATCCCATTGATAC - -a -s simMouse_chr6.simMouse.chr6 61569 78 + 636262 TATGCAACTTTGGAGCCTAAGGTCTCCATTGCTACTATGTGACTTTGGAGCCTAAGGTAGGAGACGTGCGTGGTTCCC -s Anc0.Anc0refChr4 8265 38 - 45765 TGT-----------------------------------ATAAGTCTGGA-CCCAAGGTGTTACACAT----GGTTACC -s Anc1.Anc1refChr2 39207 38 + 144309 TGT-----------------------------------ATAAGTCTGGA-CCCAAGGTGTTACACAT----GGTTACC -s Anc2.Anc2refChr4 5500 38 + 10050 TGT-----------------------------------ATAAGTCTGGA-TCCAAGGTGTTACACAT----GGTTAAC -s mr.mrrefChr0 58725 39 + 130230 TAT-----------------------------------GTGACTTTGGAGCCTAAGGTAGGAGACGT----GGTTCCC -s simCow_chr6.simCow.chr6 66061 38 + 602619 TGT-----------------------------------ATAAGTTAGGA-TCCAAAGTATTACATAT----GGTTAAC -s simDog_chr6.simDog.chr6 62173 31 + 593897 TAT-----------------------------------ATAAGTCTGGA-TCCAAGGTGTGACACAT----------- -s simHuman_chr6.simHuman.chr6 59420 38 + 601863 TGT-----------------------------------ATAAGTCTGGA-CCCAAGGTGTTACACAT----GGTTGCC -s simRat_chr6.simRat.chr6 54557 39 + 647215 TAT-----------------------------------GTGACTTTGGAGCCTAAGGTAGGAGATGT----GGTTCCC - -a -s simMouse_chr6.simMouse.chr6 61647 4 + 636262 AAAA -s Anc0.Anc0refChr4 8303 4 - 45765 AAAA -s Anc1.Anc1refChr2 39245 4 + 144309 AAAA -s Anc2.Anc2refChr4 5538 4 + 10050 AAAT -s mr.mrrefChr0 58764 4 + 130230 AAAA -s simCow_chr6.simCow.chr6 66101 4 + 602619 AAAT -s simHuman_chr6.simHuman.chr6 59458 4 + 601863 AAAA -s simRat_chr6.simRat.chr6 54596 4 + 647215 CAAA - -a -s simMouse_chr6.simMouse.chr6 61651 12 + 636262 AATTTTGCCTAT -s Anc0.Anc0refChr4 8314 12 - 45765 AATCTTGCCTAT -s Anc1.Anc1refChr2 39256 12 + 144309 AATCTTGCCTAT -s Anc2.Anc2refChr4 5549 12 + 10050 AATCTCACCTAT -s mr.mrrefChr0 58768 12 + 130230 AATTTTGCCTAT -s simCow_chr6.simCow.chr6 66112 12 + 602619 ACACTCACCTAT -s simDog_chr6.simDog.chr6 62204 12 + 593897 AATCTCACCTAT -s simHuman_chr6.simHuman.chr6 59469 12 + 601863 AATCTTGCCCAT -s simRat_chr6.simRat.chr6 54600 12 + 647215 AATTTTGCCTAT - -a -s simMouse_chr6.simMouse.chr6 61663 4 + 636262 ATCT -s Anc0.Anc0refChr4 8327 4 - 45765 ATCC -s Anc1.Anc1refChr2 39269 4 + 144309 ATCC -s Anc2.Anc2refChr4 5562 4 + 10050 TTCC -s mr.mrrefChr0 58780 4 + 130230 ATCT -s simCow_chr6.simCow.chr6 66125 4 + 602619 CTCT -s simDog_chr6.simDog.chr6 62217 4 + 593897 TGCC -s simHuman_chr6.simHuman.chr6 59482 4 + 601863 ATCC -s simRat_chr6.simRat.chr6 54612 4 + 647215 ATCT - -a -s simMouse_chr6.simMouse.chr6 61667 8 + 636262 GTTGTGTG -s Anc0.Anc0refChr4 8331 8 - 45765 AGCATGTG -s Anc1.Anc1refChr2 39273 8 + 144309 AGCATGTG -s Anc2.Anc2refChr4 5566 8 + 10050 AGCATGCC -s mr.mrrefChr0 58784 8 + 130230 GTTGTGTG -s simCow_chr6.simCow.chr6 66129 8 + 602619 AGCATGCA -s simDog_chr6.simDog.chr6 62223 8 + 593897 AGCGTGCC -s simHuman_chr6.simHuman.chr6 59486 8 + 601863 AGCATTTG -s simRat_chr6.simRat.chr6 54616 8 + 647215 GTGGTATG - -a -s simMouse_chr6.simMouse.chr6 61675 45 + 636262 TACAAGTTGAAAGTAAGGTTGCAAGTCATATGCAATGAGCACTGA -s Anc0.Anc0refChr4 8342 45 - 45765 CAGGAGTTGACAACAAGATTGCAGGTCAGGTGTGATATTCTTTGG -s Anc1.Anc1refChr2 39284 45 + 144309 CAGGAGTTGACAACAAGATTGCAGGTCAGGTGTGATATTCTTTGG -s Anc2.Anc2refChr4 5577 45 + 10050 CAGGAGTTGACAACAAGATTGCAAGTCAGGTGTGATATTCTTTGG -s mr.mrrefChr0 58792 45 + 130230 TAGAAGTTGAAAGTAAGATTGCAGGTCATATGCAATGATCATTGA -s simCow_chr6.simCow.chr6 66140 35 + 602619 CAGGAGTT----------TTGCGAGTCAAGTGTGAGACTCTGTGC -s simDog_chr6.simDog.chr6 62234 45 + 593897 CAGGAGTTGACAACAAGATTGCAAGTCAGGTGTGATATTCTTTGG -s simHuman_chr6.simHuman.chr6 59497 45 + 601863 CAGGCGTTGATAACAAGATTGCAGGTTAGGCGTGATATTCTTTGG -s simRat_chr6.simRat.chr6 54624 45 + 647215 TAGAGGTTGACAGTAAGATTGCAGGTCATTTGCAATGATCATTGA - -a -s simMouse_chr6.simMouse.chr6 61720 11 + 636262 GTTGAAATATA -s Anc0.Anc0refChr4 8387 11 - 45765 GTTGAAACATT -s Anc1.Anc1refChr2 39329 11 + 144309 GTTGAAACATT -s Anc2.Anc2refChr4 5622 11 + 10050 GTTGAAACATT -s mr.mrrefChr0 58837 11 + 130230 GTTGAAATATA -s simCow_chr6.simCow.chr6 66195 11 + 602619 GTTGAAACATC -s simDog_chr6.simDog.chr6 62279 11 + 593897 GTTGAAACATT -s simHuman_chr6.simHuman.chr6 59542 11 + 601863 GTTGAAACATG -s simRat_chr6.simRat.chr6 54669 10 + 647215 GTT-AAATATA - -a -s simMouse_chr6.simMouse.chr6 61731 75 + 636262 TCCTGGCCTTGTTGTGTCTATCATCGATTAATGATCTTAGTAAACAGACATTGTGCAAAGTAGACAGACACAATG -s Anc0.Anc0refChr4 8407 72 - 45765 TCTTGACATTGTTGTGGCTGTCATCTAAGATTGAAATTGGTAAACAGTCATTCTACAAAATAGACA-AGACA--G -s Anc1.Anc1refChr2 39351 73 + 144309 TCTTGACATTGTTGTGGCTGTCATCTAAGATTGAAATTGGTAAACAGTCATTCTACAAAATAGACACAGACA--G -s Anc2.Anc2refChr4 5642 72 + 10050 TCTTGACACTGTTGTGGATATGATCTAAGATTGAAAGTGGTAAACGGTCATTCCACAAAATAGACA-AGACA--G -s mr.mrrefChr0 58848 75 + 130230 TCTTGGCATTGTTGTGTCTGTCATCGAATAATGATCTTAGTAAACAGACATTGTGCAAAGTAGACAGACACAATG -s simCow_chr6.simCow.chr6 66215 70 + 602619 TCTTGACACTGTT--GAATATGATCTAATAATGATGACAGTAAATGGTCATTGCACAAAATAGATG-AGACA--G -s simDog_chr6.simDog.chr6 62299 68 + 593897 TTTTGGCACTGTTGTGGATATGATCTAAGATTGAAAGTGGTAAACGCT----CCACAAAATAGACA-AGACA--G -s simHuman_chr6.simHuman.chr6 59578 69 + 601863 TCTTGACATTGTTAAGGCTGTCATTTAACCGT----TTGGTAAACAGTAATCATAGACGATAGACTCAGACA--G -s simRat_chr6.simRat.chr6 54679 75 + 647215 TTTTTCCATTGTTGTGTCTGTCGTCGAATAATGGTCTTAGTAAACAGGCATTGTTCAAAGTAGACAGACACAATG - -a -s simMouse_chr6.simMouse.chr6 61806 67 + 636262 ACTCTTTTGAATCTCCCAGCAGGGATGTCTTGACAAAGCTTTCAAGATTCTATGATGCACTGTTGCA -s Anc0.Anc0refChr4 8479 67 - 45765 CCCCTTTTGCATCACCCAGCATGGATGCCTTGACAAAACTTGCATGATTTTATGATGCAGTGTTGCA -s Anc1.Anc1refChr2 39424 67 + 144309 CCCCTTTTGCATCACCCAGCATGGATGCCTTGACAAAACTTGCATGATTTTATGATGCAGTGTTGCA -s Anc2.Anc2refChr4 5715 67 + 10050 CCCCTTTTGCATGACCCAGCATGGTTGCCTTGACAAAACTTTCATCATTTTATGGTGCAGTGTTGCA -s mr.mrrefChr0 58923 67 + 130230 ACTCTTTTGAATCTCCCAGCAGGGATGTCTTGACAAAGCTTGCAAGATTCTATGATGCACTGTTGCA -s simCow_chr6.simCow.chr6 66286 67 + 602619 CCTCTTTTATATGACCCAGTATTGTTGCCTTGACAAAACTTTCATAACTTTATGCTGCAGTGTTGCT -s simDog_chr6.simDog.chr6 62368 67 + 593897 CCCCTTTTGCATGACCCAACATGGTTGCCTGGACAAAACTTTCATCATATTATGGTGCAGTGTTGCA -s simHuman_chr6.simHuman.chr6 59647 64 + 601863 CCCCCTTT---TCCCTCAGGATGGATGCGTTGACAAACCTAGCATGATTTTATAATGCAGTGTTGCA -s simRat_chr6.simRat.chr6 54754 67 + 647215 ACTATTTGGCATCTCCTAGCAGGGATGTCTTGACAAAGCTTGCAAGATTCAATGATGCACTGTTGCA - -a -s simMouse_chr6.simMouse.chr6 61873 8 + 636262 CCATTACT -s Anc0.Anc0refChr4 8547 8 - 45765 CTAGCACT -s Anc1.Anc1refChr2 39492 8 + 144309 CTAGCACT -s Anc2.Anc2refChr4 5783 8 + 10050 CTAGCACT -s mr.mrrefChr0 58991 8 + 130230 CCATCACT -s simCow_chr6.simCow.chr6 66354 8 + 602619 CTAGCACT -s simDog_chr6.simDog.chr6 62436 8 + 593897 CTATCACT -s simHuman_chr6.simHuman.chr6 59712 8 + 601863 TGAGCACT -s simRat_chr6.simRat.chr6 54822 8 + 647215 CCATCACT - -a -s simMouse_chr6.simMouse.chr6 61881 18 + 636262 GTTTTTCCATATCATTAA -s Anc0.Anc0refChr4 8557 18 - 45765 GTTTTTCCATATCATTGA -s Anc1.Anc1refChr2 39502 18 + 144309 GTTTTTCCATATCATTGA -s Anc2.Anc2refChr4 5795 18 + 10050 GTTTTTCCATATCATTGT -s mr.mrrefChr0 58999 18 + 130230 GTTTTTCCATATCATTAA -s simCow_chr6.simCow.chr6 66366 16 + 602619 GTTTTTTCACATCATT-- -s simDog_chr6.simDog.chr6 62448 18 + 593897 GTTTTTCCATATCATTGT -s simHuman_chr6.simHuman.chr6 59722 18 + 601863 GCTTTTCCATGTCATTGA -s simRat_chr6.simRat.chr6 54830 18 + 647215 ATTTTTCCATATCATTAA - -a -s simMouse_chr6.simMouse.chr6 61899 21 + 636262 TTTGGTATTTGTGGCCCTGTT -s Anc0.Anc0refChr4 8583 21 - 45765 TAAGGTATTCATAGCCCTGTT -s Anc1.Anc1refChr2 39528 21 + 144309 TAAGGTATTCATAGCCCTGTT -s Anc2.Anc2refChr4 5821 21 + 10050 TAATGTATTCGTAACCCTGTT -s mr.mrrefChr0 59025 21 + 130230 TATGGTATTCATGGCCCTGTT -s simCow_chr6.simCow.chr6 66382 8 + 602619 -------------ACCCTGTT -s simDog_chr6.simDog.chr6 62474 21 + 593897 TAATGTATTCGTAACCCTGTT -s simHuman_chr6.simHuman.chr6 59748 21 + 601863 TAAGGTGTTCATAGCCCGGTT -s simRat_chr6.simRat.chr6 54856 21 + 647215 TATGGTATGCATGACCCTGTT - -a -s simMouse_chr6.simMouse.chr6 61920 16 + 636262 CATACAACTAAAGTGC -s Anc0.Anc0refChr4 8605 16 - 45765 AGCACAACTAGAGTAT -s Anc1.Anc1refChr2 39550 16 + 144309 AGCACAACTAGAGTAT -s Anc2.Anc2refChr4 5843 16 + 10050 AGCACAACTAGAGTAT -s mr.mrrefChr0 59046 16 + 130230 CATACAACTAAAGTGC -s simCow_chr6.simCow.chr6 66391 16 + 602619 AGCACAACTTAAGTAT -s simDog_chr6.simDog.chr6 62496 16 + 593897 AGCACAACTAGAGTAT -s simHuman_chr6.simHuman.chr6 59770 16 + 601863 TGCAGATCTAGAGTAT -s simRat_chr6.simRat.chr6 54877 16 + 647215 AATACAACTAAAGTGC - -a -s simMouse_chr6.simMouse.chr6 61936 13 + 636262 AGTCTATCATTGT -s Anc0.Anc0refChr4 8625 13 - 45765 AGTGTGTTATTCT -s Anc1.Anc1refChr2 39570 13 + 144309 AGTGTGTTATTCT -s Anc2.Anc2refChr4 5863 13 + 10050 ATTGTGTTATTCT -s mr.mrrefChr0 59066 13 + 130230 AGTCTGTTATTGT -s simCow_chr6.simCow.chr6 66411 13 + 602619 ATTGTGTCATTCT -s simDog_chr6.simDog.chr6 62516 13 + 593897 ATTGTGTTAATCT -s simHuman_chr6.simHuman.chr6 59790 13 + 601863 AGTTTGTTATTCT -s simRat_chr6.simRat.chr6 54897 13 + 647215 GGTCTGTTATTGA - -a -s simMouse_chr6.simMouse.chr6 61949 43 + 636262 AATAGATGCCAGTGTGAGGGTGAATTGACAGATCATGTACCCA -s Anc0.Anc0refChr4 8638 43 - 45765 AACAAATGCAAATGTCATGGTGGTTTGTCAATTCATGAGTCCA -s Anc1.Anc1refChr2 39583 43 + 144309 AACAAATGCAAATGTCATGGTGGTTTGTCAATTCATGAGTCCA -s Anc2.Anc2refChr4 5880 43 + 10050 AACAAATGCAAATGTCATGGTGGTTTGTCAATTCATGAGTCGA -s mr.mrrefChr0 59079 43 + 130230 AATAGATGCAAGTGTGAGGGTGATTTGACAGATCATGTACCCA -s simCow_chr6.simCow.chr6 66428 43 + 602619 AGCAAATGCAAATGTCCGGGTGGCATATTGATTCACAAGTCAT -s simDog_chr6.simDog.chr6 62533 43 + 593897 AACAAATGCAAATGTGATGGTGGTTTGTCAATTCATGAATCGA -s simHuman_chr6.simHuman.chr6 59803 43 + 601863 AAAAAATGCAAAAGTCATGTTGGTTTGTCAATTCATGAGTCCA -s simRat_chr6.simRat.chr6 54910 43 + 647215 AGCAGATGCAAGTGTAAGGGTCTTCTGACAGGTCGTGTACCCA - -a -s simMouse_chr6.simMouse.chr6 61992 1 + 636262 T -s Anc0.Anc0refChr4 8681 1 - 45765 C -s Anc1.Anc1refChr2 39626 1 + 144309 C -s Anc2.Anc2refChr4 5927 1 + 10050 C -s mr.mrrefChr0 59122 1 + 130230 T -s simCow_chr6.simCow.chr6 66475 1 + 602619 C -s simDog_chr6.simDog.chr6 62580 1 + 593897 C -s simHuman_chr6.simHuman.chr6 59846 1 + 601863 C -s simRat_chr6.simRat.chr6 54953 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 61993 81 + 636262 GAGTCATTGCTAGTTTCGCAAGCTATTTGGAGATACATCTTCATAGTCCTGATGTCATGTGCTATGGGATCAGTTGACTGA -s Anc0.Anc0refChr4 8682 63 - 45765 CTGTCATTGCTA----------ATATTGGGAGCTACAATTTCCTGGTC--------ATATGCTATAAGATAATGGGTTTAA -s Anc1.Anc1refChr2 39627 64 + 144309 CTGTCATTGCTAG---------ATATTGGGAGCTACAATTTCCTGGTC--------ATATGCTATAAGATAATGGGTTTAA -s Anc2.Anc2refChr4 5928 63 + 10050 CTGTCATTGCTA----------ATATTGGGAGCTACAATTTCCTGGTC--------ATATGCTATAAGATAATGGGTTTAA -s mr.mrrefChr0 59123 81 + 130230 CAGTCATTGCTAGTTTCGCAAGCTATTTGGAGCTACATTTTCCTGGTCCTGATGTCATGTGCTATGAGATCAGTTGACTAA -s simCow_chr6.simCow.chr6 66549 61 + 602619 CTGTCATTGCTA----------TTATTGGGAGCTACAATTTCCTG--C--------CCAAGGTATAAGATAATGAGCTTAA -s simDog_chr6.simDog.chr6 62581 63 + 593897 CTGTCATTGCTA----------ATATTGGAAGCTACAATTTCCAGGTC--------ATATGCTATAAGATAATGGGTTTAA -s simHuman_chr6.simHuman.chr6 59847 64 + 601863 CCATCATTGCTAG---------ATATTAGGAGCTAGAATTTCCTGGTC--------ATATGCTATAAGATAATGGGTTTAA -s simRat_chr6.simRat.chr6 54954 81 + 647215 CAGTCATTACTAGCTTTGCAGGCTATTGGGAGCTACAGTTTCCTGGTCATGATGTCATGTGCTATGAGATGAGCTGGCTAA - -a -s simMouse_chr6.simMouse.chr6 62074 2 + 636262 TT -s Anc0.Anc0refChr4 8754 2 - 45765 TC -s Anc1.Anc1refChr2 39700 2 + 144309 TC -s Anc2.Anc2refChr4 6000 2 + 10050 TC -s mr.mrrefChr0 59204 2 + 130230 TT -s simCow_chr6.simCow.chr6 66619 2 + 602619 CC -s simDog_chr6.simDog.chr6 62652 2 + 593897 TC -s simHuman_chr6.simHuman.chr6 59920 2 + 601863 TC -s simRat_chr6.simRat.chr6 55035 2 + 647215 TT - -a -s simMouse_chr6.simMouse.chr6 62076 30 + 636262 AAGAGAGTGTGTTGTTTATAAAGGATCATT -s Anc0.Anc0refChr4 8756 30 - 45765 AAAAAAATGTCTTGTTAATAAAGGACTGTT -s Anc1.Anc1refChr2 39702 30 + 144309 AAAAAAATGTCTTGTTAATAAAGGACTGTT -s Anc2.Anc2refChr4 6002 30 + 10050 AAAAAAATGTCATGTTAATGAAGGGCTGTT -s mr.mrrefChr0 59206 30 + 130230 AAGAGAGTGTGTTGTTTATAAAGGATCGTT -s simCow_chr6.simCow.chr6 66690 30 + 602619 AAAAAAGTGGCATATTAATCAGAGGCTGTT -s simDog_chr6.simDog.chr6 62654 30 + 593897 TAAAAAATGTCATGTTAATGAAGGGCTGTT -s simHuman_chr6.simHuman.chr6 59922 30 + 601863 AAAAAAATGTCTTGTTAATAAAGGACTGTT -s simRat_chr6.simRat.chr6 55037 30 + 647215 GAGAGAGTGTGTTGTTTATAAAGGAGCGTT - -a -s simMouse_chr6.simMouse.chr6 62106 43 + 636262 TCCTGCTGATAGTTCACATTCTGAGGTAACAAGATGGATAGTG -s Anc0.Anc0refChr4 8787 25 - 45765 TTCTGCAGATAATTCACCTT------------------TAACG -s Anc1.Anc1refChr2 39733 25 + 144309 TTCTGCAGATAATTCACCTT------------------TAACG -s Anc2.Anc2refChr4 6033 25 + 10050 TTCTACAGATAATTCATCTT------------------TAATG -s mr.mrrefChr0 59236 43 + 130230 TCCTGCTGATAGTTCACATTCTGAGGTAACAAGATGGATAGCG -s simCow_chr6.simCow.chr6 66721 25 + 602619 TTCTACAGATAATTACTCTT------------------TAATG -s simDog_chr6.simDog.chr6 62685 24 + 593897 TTCTACAGGTAGTTCAT-TG------------------TAATG -s simHuman_chr6.simHuman.chr6 59953 25 + 601863 TTCTGCAGATCATTCACTTT------------------TAACC -s simRat_chr6.simRat.chr6 55067 43 + 647215 CACTGCTGATAGTTCACATTCTGAGGTAACAAGATGCATAGCG - -a -s simMouse_chr6.simMouse.chr6 62149 3 + 636262 AAG -s Anc0.Anc0refChr4 8812 3 - 45765 AGG -s Anc1.Anc1refChr2 39758 3 + 144309 AGG -s Anc2.Anc2refChr4 6074 3 + 10050 AGG -s mr.mrrefChr0 59279 3 + 130230 AAG -s simCow_chr6.simCow.chr6 66762 3 + 602619 AAG -s simDog_chr6.simDog.chr6 62726 3 + 593897 AGG -s simHuman_chr6.simHuman.chr6 59978 3 + 601863 AGG -s simRat_chr6.simRat.chr6 55110 3 + 647215 AAA - -a -s simMouse_chr6.simMouse.chr6 62152 21 + 636262 TAGTGCCGCAATTTAAGAAGC -s Anc0.Anc0refChr4 8815 21 - 45765 TGTTGCAGCATTTTAAGAAAA -s Anc1.Anc1refChr2 39761 21 + 144309 TGTTGCAGCATTTTAAGAAAA -s Anc2.Anc2refChr4 6077 21 + 10050 TGTTGCAGCATTTAAAGAAAA -s mr.mrrefChr0 59282 21 + 130230 TAGTGCCGCAATTTAAGAAGC -s simCow_chr6.simCow.chr6 66765 20 + 602619 C-CTGGAGCATTTGGAGAAAT -s simDog_chr6.simDog.chr6 62729 21 + 593897 TGTTGCAGCATTTAAAGAAGA -s simHuman_chr6.simHuman.chr6 59981 21 + 601863 TGTTGCAGCATTTTAAAAAAA -s simRat_chr6.simRat.chr6 55114 21 + 647215 TACTGTCGCAACTTAAGAAGC - -a -s simMouse_chr6.simMouse.chr6 62173 13 + 636262 TGAGGTGTTGTGT -s Anc0.Anc0refChr4 8846 8 - 45765 TGA-----CGTGC -s Anc1.Anc1refChr2 39792 8 + 144309 TGA-----CGTGC -s Anc2.Anc2refChr4 6108 8 + 10050 TTA-----CGTAC -s mr.mrrefChr0 59303 8 + 130230 TGA-----TGTGT -s simCow_chr6.simCow.chr6 66795 8 + 602619 TTA-----CATAC -s simDog_chr6.simDog.chr6 62760 8 + 593897 GTA-----TGTAT -s simHuman_chr6.simHuman.chr6 60012 8 + 601863 TGA-----CGAGC -s simRat_chr6.simRat.chr6 55135 8 + 647215 TGA-----TGTGG - -a -s simMouse_chr6.simMouse.chr6 62186 35 + 636262 TATCATGTATTGTAACATTTTAAAAAAAGAGCAAA -s Anc0.Anc0refChr4 8864 35 - 45765 TATCACTTACCAGACAACTTCCAGAGCAAGCCAGA -s Anc1.Anc1refChr2 39810 35 + 144309 TATCACTTACCAGACAACTTCCAGAGCAAGCCAGA -s Anc2.Anc2refChr4 6126 35 + 10050 TATCACTTACCAGACAACTTCCAGAGCAAGCCAGA -s mr.mrrefChr0 59311 35 + 130230 TATCATGTATTGTAACATTTTAAAAAAAGAGCAAA -s simCow_chr6.simCow.chr6 66813 34 + 602619 TAAGACTTACCAGTTCACTT-CAGAGCAAGCTAAA -s simDog_chr6.simDog.chr6 62778 35 + 593897 TATCATTTACCATACAACTTCTTGAGTGAGCCAGA -s simHuman_chr6.simHuman.chr6 60030 35 + 601863 TATCACTTACCAGACAACTTCCAGATCAAGTCGGA -s simRat_chr6.simRat.chr6 55143 35 + 647215 TATCATGTATTGTAACATTTTAAAAAATGAGCAAA - -a -s simMouse_chr6.simMouse.chr6 62221 16 + 636262 GGTGGAGTAAGCCAAA -s Anc0.Anc0refChr4 8918 13 - 45765 ---GGAGAAAACCAAA -s Anc1.Anc1refChr2 39864 16 + 144309 GGAGGAGAAAACCAAA -s Anc2.Anc2refChr4 6180 13 + 10050 ---GGAGAAAACCAGA -s mr.mrrefChr0 59346 16 + 130230 GGTGGAGAAAACCAAA -s simCow_chr6.simCow.chr6 66866 13 + 602619 ---AGAGTGGGCCCGA -s simDog_chr6.simDog.chr6 62832 13 + 593897 ---GGATAAAACCAGA -s simHuman_chr6.simHuman.chr6 60084 16 + 601863 GGAGGACAAGACAGAA -s simRat_chr6.simRat.chr6 55178 16 + 647215 GGTGGAGAAAACCCAA - -a -s simMouse_chr6.simMouse.chr6 62237 15 + 636262 ATCTAGGCAGTGTAA -s Anc0.Anc0refChr4 8931 15 - 45765 ATCTAGGGACTGTAA -s Anc1.Anc1refChr2 39880 15 + 144309 ATCTAGGGACTGTAA -s Anc2.Anc2refChr4 6193 15 + 10050 ATCTAGGGACTGTAA -s mr.mrrefChr0 59362 15 + 130230 ATCTAGGGAGTGTAA -s simCow_chr6.simCow.chr6 66879 15 + 602619 ATCTAGGGACTGTAA -s simDog_chr6.simDog.chr6 62845 15 + 593897 ATGTAAGGATTGTAA -s simHuman_chr6.simHuman.chr6 60107 15 + 601863 ATCTAGGGACTGTAA -s simRat_chr6.simRat.chr6 55194 15 + 647215 ATCCAGGGAGTGTAA - -a -s simMouse_chr6.simMouse.chr6 62252 23 + 636262 TGTCTTCTTTTAAGACACATTCA -s Anc0.Anc0refChr4 8947 23 - 45765 GATATTTTTATAAGAAACATTCA -s Anc1.Anc1refChr2 39896 23 + 144309 GATATTTTTATAAGAAACATTCA -s Anc2.Anc2refChr4 6209 23 + 10050 GATATTTAGATAAAAAACATTCA -s mr.mrrefChr0 59377 23 + 130230 TGTCTTCTTTTAAGACACATTCA -s simCow_chr6.simCow.chr6 66895 23 + 602619 GATATTTGGATAAAAAACATTCA -s simDog_chr6.simDog.chr6 62861 23 + 593897 GGTTTTTAGATCAAAAACATTCA -s simHuman_chr6.simHuman.chr6 60123 23 + 601863 CATATTTTTATAAGAAACGTTCA -s simRat_chr6.simRat.chr6 55209 22 + 647215 TGTCTTCTTTTAAGACAC-TTCA - -a -s simMouse_chr6.simMouse.chr6 62275 11 + 636262 GATAACATGGT -s Anc0.Anc0refChr4 8970 4 - 45765 GATA------- -s Anc1.Anc1refChr2 39919 11 + 144309 GATAATTTGGC -s Anc2.Anc2refChr4 6232 4 + 10050 GAAA------- -s mr.mrrefChr0 59400 11 + 130230 GATAACATGGT -s simCow_chr6.simCow.chr6 66918 4 + 602619 GAGA------- -s simDog_chr6.simDog.chr6 62884 4 + 593897 GAAA------- -s simHuman_chr6.simHuman.chr6 60160 11 + 601863 GGTAATTTGGC -s simRat_chr6.simRat.chr6 55231 11 + 647215 GAGAACATGGA - -a -s simMouse_chr6.simMouse.chr6 62286 2 + 636262 CA -s Anc0.Anc0refChr4 8974 1 - 45765 -A -s Anc1.Anc1refChr2 39930 2 + 144309 CA -s Anc2.Anc2refChr4 6236 1 + 10050 -G -s mr.mrrefChr0 59411 2 + 130230 CA -s simCow_chr6.simCow.chr6 66922 1 + 602619 -G -s simDog_chr6.simDog.chr6 62888 1 + 593897 -G -s simHuman_chr6.simHuman.chr6 60180 2 + 601863 CA -s simRat_chr6.simRat.chr6 55242 2 + 647215 CA - -a -s simMouse_chr6.simMouse.chr6 62288 11 + 636262 GAGCTGACTTG -s Anc0.Anc0refChr4 8975 11 - 45765 GAGCCTGCTTG -s Anc1.Anc1refChr2 39932 11 + 144309 GAGCCTGCTTG -s Anc2.Anc2refChr4 6237 11 + 10050 GAGTCTACTTA -s mr.mrrefChr0 59413 11 + 130230 GAGCTTGCTTG -s simCow_chr6.simCow.chr6 66927 11 + 602619 GAGTCTAATTA -s simDog_chr6.simDog.chr6 62889 11 + 593897 GAGTCTACTTA -s simHuman_chr6.simHuman.chr6 60182 11 + 601863 GGACCTGCACG -s simRat_chr6.simRat.chr6 55244 11 + 647215 GAGCTTGCTAG - -a -s simMouse_chr6.simMouse.chr6 62299 8 + 636262 TAGCATAA -s Anc0.Anc0refChr4 8986 8 - 45765 TATCAAAA -s Anc1.Anc1refChr2 39943 8 + 144309 TATCAAAA -s Anc2.Anc2refChr4 6248 8 + 10050 CTTCAATA -s mr.mrrefChr0 59424 8 + 130230 TAGCATAA -s simCow_chr6.simCow.chr6 66938 8 + 602619 TTACAATG -s simDog_chr6.simDog.chr6 62900 8 + 593897 CTTCAATA -s simHuman_chr6.simHuman.chr6 60199 8 + 601863 TACCGGAC -s simRat_chr6.simRat.chr6 55255 8 + 647215 TAGCATAA - -a -s simMouse_chr6.simMouse.chr6 62307 8 + 636262 GATTTGTT -s Anc0.Anc0refChr4 8994 8 - 45765 GATTAGTT -s Anc1.Anc1refChr2 39951 8 + 144309 GATTAGTT -s Anc2.Anc2refChr4 6256 8 + 10050 GGTTATTT -s mr.mrrefChr0 59432 8 + 130230 GATTAGTT -s simCow_chr6.simCow.chr6 66952 8 + 602619 GGTTATTT -s simDog_chr6.simDog.chr6 62908 8 + 593897 GGTTATTT -s simHuman_chr6.simHuman.chr6 60207 6 + 601863 CAT--GTT -s simRat_chr6.simRat.chr6 55263 8 + 647215 GATTACTT - -a -s simMouse_chr6.simMouse.chr6 62315 30 + 636262 GCAATGGGTTATCTGGCCAGTGTAGTAGAT -s Anc0.Anc0refChr4 9002 30 - 45765 GCCATAGGTTGTGAGCCAATCTTTGTAGCT -s Anc1.Anc1refChr2 39959 30 + 144309 GCCATAGGTTGTGAGCCAATCTTTGTAGCT -s Anc2.Anc2refChr4 6264 30 + 10050 GCCATAGGGTGTGAGCCAATCTTTGTAGCT -s mr.mrrefChr0 59440 30 + 130230 GCCATGGGTTATCTGCCCAGCTTAGTAGAT -s simCow_chr6.simCow.chr6 66960 30 + 602619 GCTATAGGGTATGTGCCAATCTTTGTAGCT -s simDog_chr6.simDog.chr6 62916 30 + 593897 GCCATATGGTGTGAGCCAATCTTTGTAGCT -s simHuman_chr6.simHuman.chr6 60216 30 + 601863 ACCATAGGTTTTGGGCCAATCTTTGTAAGT -s simRat_chr6.simRat.chr6 55271 30 + 647215 GCCATGGGTTATCTGCCCAGCTTAGTAGAT - -a -s simMouse_chr6.simMouse.chr6 62345 9 + 636262 AAGATTCCA -s Anc0.Anc0refChr4 9032 9 - 45765 AAGATGCAA -s Anc1.Anc1refChr2 39989 9 + 144309 AAGATGCAA -s Anc2.Anc2refChr4 6294 9 + 10050 AAGATTCAA -s mr.mrrefChr0 59470 9 + 130230 AAGATGCAA -s simCow_chr6.simCow.chr6 66990 9 + 602619 AAGATCCAG -s simDog_chr6.simDog.chr6 62947 9 + 593897 AAAATTCAA -s simHuman_chr6.simHuman.chr6 60246 9 + 601863 AAGATGCAA -s simRat_chr6.simRat.chr6 55301 9 + 647215 AAGATGCAA - -a -s simMouse_chr6.simMouse.chr6 62354 26 + 636262 AACTGTTGGCCTAAGCTTTTAATAAA -s Anc0.Anc0refChr4 9041 25 - 45765 A-CTCACAGCACAAGATACTATTAAA -s Anc1.Anc1refChr2 39998 25 + 144309 A-CTCACAGCACAAGATACTATTAAA -s Anc2.Anc2refChr4 6303 25 + 10050 A-CTCACAGTACAAGATACTATTACA -s mr.mrrefChr0 59479 25 + 130230 A-CTGTCAGCCTAAGCTTTTATTAAA -s simCow_chr6.simCow.chr6 66999 24 + 602619 G-CTCAC-GTACAATATACTATTACA -s simDog_chr6.simDog.chr6 62959 25 + 593897 A-CTCACAATTCAAGATACTAATACA -s simHuman_chr6.simHuman.chr6 60255 25 + 601863 A-CCTGCAGCACAAGACCCTATCAAA -s simRat_chr6.simRat.chr6 55310 25 + 647215 A-CTCTCAGCCTAAGCTGTTATTAAA - -a -s simMouse_chr6.simMouse.chr6 62380 7 + 636262 TGCTGGG -s Anc0.Anc0refChr4 9067 7 - 45765 TGCTGGG -s Anc1.Anc1refChr2 40024 7 + 144309 TGCTGGG -s Anc2.Anc2refChr4 6329 7 + 10050 TGCCAGG -s mr.mrrefChr0 59505 7 + 130230 TGCTGGG -s simCow_chr6.simCow.chr6 67024 7 + 602619 TGCCAGG -s simDog_chr6.simDog.chr6 62985 7 + 593897 TGCCAGG -s simHuman_chr6.simHuman.chr6 60281 7 + 601863 TGCTGGG -s simRat_chr6.simRat.chr6 55336 7 + 647215 TGCTGTG - -a -s simMouse_chr6.simMouse.chr6 62387 12 + 636262 AGTTTAGGATAG -s Anc0.Anc0refChr4 9075 12 - 45765 AGTCTAGCATAG -s Anc1.Anc1refChr2 40032 12 + 144309 AGTCTAGCATAG -s Anc2.Anc2refChr4 6337 12 + 10050 AGTCTAGCATAG -s mr.mrrefChr0 59512 12 + 130230 AGTTTAGGATAG -s simCow_chr6.simCow.chr6 67032 12 + 602619 AGTTTAGCATAG -s simDog_chr6.simDog.chr6 62993 12 + 593897 AGTCTAGCATAG -s simHuman_chr6.simHuman.chr6 60289 12 + 601863 AGTCTTGAATAG -s simRat_chr6.simRat.chr6 55343 12 + 647215 AGTTTAGGATAA - -a -s simMouse_chr6.simMouse.chr6 62399 21 + 636262 CCTGATATGCCTGAACTCTAT -s Anc0.Anc0refChr4 9089 21 - 45765 ATTGATGTGCATAAACTCTGT -s Anc1.Anc1refChr2 40046 21 + 144309 ATTGATGTGCATAAACTCTGT -s Anc2.Anc2refChr4 6351 21 + 10050 ATTGATGTACATAGACTCTGT -s mr.mrrefChr0 59524 21 + 130230 CTTGATATGCCTGAACTCTGT -s simCow_chr6.simCow.chr6 67046 21 + 602619 ATTGATGGATATAGACTCTGT -s simDog_chr6.simDog.chr6 63007 21 + 593897 ATTGATGTACATTGACTCTAT -s simHuman_chr6.simHuman.chr6 60303 21 + 601863 TTCGATGTGCACAAAATCTGT -s simRat_chr6.simRat.chr6 55355 21 + 647215 CTTGATATGCCTGCACTCTGT - -a -s simMouse_chr6.simMouse.chr6 62420 11 + 636262 GACAATAATCC -s Anc0.Anc0refChr4 9115 11 - 45765 GACAATAATCC -s Anc1.Anc1refChr2 40072 11 + 144309 GACAATAATCC -s Anc2.Anc2refChr4 6377 11 + 10050 GACAATAATCA -s mr.mrrefChr0 59545 11 + 130230 GACAATAATCC -s simCow_chr6.simCow.chr6 67072 11 + 602619 TACAGTAATCA -s simDog_chr6.simDog.chr6 63033 11 + 593897 GACTATAATGA -s simHuman_chr6.simHuman.chr6 60329 11 + 601863 GACAATACTCC -s simRat_chr6.simRat.chr6 55376 11 + 647215 GACAATAATCC - -a -s simMouse_chr6.simMouse.chr6 62431 95 + 636262 CAGTGCAGAGAGACACAGTTTTTAATGTCCCTTATTGATACTTAGACTTTGGTTGGATGCACCACGCCCTTTTATATTTCATAACCCTTGTCTGT -s Anc0.Anc0refChr4 9128 86 - 45765 CAGTGCAGAAAGATGCAGTCTTTAATGTTCTTTACTGATATCTAAGCCTCAGCTGGATG--CAATGCTCTTATATACATC-------TTATTCAT -s Anc1.Anc1refChr2 40085 88 + 144309 CAGTGCAGAAAGATGCAGTCTTTAATGTTCTTTACTGATATCTAAGCCTCAGCTGGATGCACAATGCTCTTATATACATC-------TTATTCAT -s Anc2.Anc2refChr4 6390 86 + 10050 CAGTGCAGCAAGATGCAGCCTTTAATGGTCTCTACTGATATCTAAGCCTCATCTGGATG--CAATGCTCTTATATACATC-------TGATTCAT -s mr.mrrefChr0 59556 95 + 130230 CAGTGCAGAGAGACGCAGTTTTTAATGTTCTTTACTGATACTTAGACTTTGGTTGGATGCACCACGCCCTTTTATATTTCATAACCCTTATTCGT -s simCow_chr6.simCow.chr6 67085 85 + 602619 TAGTGCGGCAAACTGCAACTTTTAATG-TCTCTACTCAAATCTAGGCCTCATCTGGTTG--CAATGCTCTTCTATACACC-------TGATTCAT -s simDog_chr6.simDog.chr6 63046 86 + 593897 CAGTGCAGCAAGACACAGCCTTTAATGGTCTCTATTGCTATCTAATCCTTGTCTGGATG--CAATGCCCTTATAGACATT-------TGTTTTAT -s simHuman_chr6.simHuman.chr6 60342 88 + 601863 CAGTGCAGAAAGATGCAGTGTTTAATGTTCTTTACTGATATCTAAGCCTCAGCTGGATGAACAATGCTCTTATATACATC-------TTATTCAT -s simRat_chr6.simRat.chr6 55387 95 + 647215 TAGTGCACAGAGGGGTGGGTTTTAGTGTTCTTAACTGATACTTATACTTTGGTTGGATGCACCAGGCCCTTTTATATTTCATAATCCTTATTCGT - -a -s simMouse_chr6.simMouse.chr6 62526 33 + 636262 AGTGAATCGCAGCAATTGTCAGTGCAAATCAAC -s Anc0.Anc0refChr4 9214 33 - 45765 ACTTCATTGTAGCAATTGTGAGTGCGCAATTAA -s Anc1.Anc1refChr2 40173 33 + 144309 ACTTCATTGTAGCAATTGTGAGTGCGCAATTAA -s Anc2.Anc2refChr4 6489 33 + 10050 ACTTCATTGTAGCAATTGTGAGTGCGCAATTAA -s mr.mrrefChr0 59651 33 + 130230 AGTGAATTGCAGCAATTGTCAGTGCAAATCAAC -s simCow_chr6.simCow.chr6 67183 33 + 602619 ACTTTCATGTAGCAATTGTGAGTGCGGAATTAA -s simDog_chr6.simDog.chr6 63145 33 + 593897 ACTCCATTGTAGCAACTGTGAATCCACCATAAA -s simHuman_chr6.simHuman.chr6 60430 33 + 601863 ACTTCATTGTAGTAGTTGTGAGTGTGCAATTAA -s simRat_chr6.simRat.chr6 55482 33 + 647215 AGTGAATTGCAGCAATTGTCAGTACAAATCAAC - -a -s simMouse_chr6.simMouse.chr6 62559 4 + 636262 CAAG -s Anc0.Anc0refChr4 9248 4 - 45765 CTAG -s Anc1.Anc1refChr2 40207 4 + 144309 CTAG -s Anc2.Anc2refChr4 6523 4 + 10050 TTAG -s mr.mrrefChr0 59685 4 + 130230 CAAG -s simCow_chr6.simCow.chr6 67217 4 + 602619 TTAG -s simDog_chr6.simDog.chr6 63179 4 + 593897 TTAG -s simHuman_chr6.simHuman.chr6 60464 4 + 601863 CTAG -s simRat_chr6.simRat.chr6 55516 4 + 647215 CAAG - -a -s simMouse_chr6.simMouse.chr6 62563 1 + 636262 G -s Anc0.Anc0refChr4 9252 1 - 45765 G -s Anc1.Anc1refChr2 40211 1 + 144309 G -s Anc2.Anc2refChr4 6527 1 + 10050 G -s mr.mrrefChr0 59689 1 + 130230 G -s simCow_chr6.simCow.chr6 67221 1 + 602619 G -s simDog_chr6.simDog.chr6 63183 1 + 593897 G -s simHuman_chr6.simHuman.chr6 60469 1 + 601863 G -s simRat_chr6.simRat.chr6 55520 1 + 647215 G - -a -s simMouse_chr6.simMouse.chr6 62564 66 + 636262 TCAGGGCATGCTAACAATAATGTACTTGTTATATTAACCAGTCCTCCTCTCTACCAGTAGTCAGAC -s Anc0.Anc0refChr4 9253 65 - 45765 TTTGTGCCTGATGACAGTATTGTACTCACTATGTTAAGCACTCTTGTTCTATAC-AGTTGTCATGC -s Anc1.Anc1refChr2 40212 65 + 144309 TTTGTGCCTGATGACAGTATTGTACTCACTATGTTAAGCACTCTTGTTCTATAC-AGTTGTCATGC -s Anc2.Anc2refChr4 6528 65 + 10050 TTTGTGCCTGATGTCAGTATTTTACTCACTGTGTTAAGCACTCTTGTTCTATAC-AGTTGTCATGC -s mr.mrrefChr0 59690 65 + 130230 TTAGTGCATGCTGACAATAATGTACTTACTATATTAACCAGTCCTCCTCTCTAC-AGTAGTCAGAC -s simCow_chr6.simCow.chr6 67222 65 + 602619 ATTGTGCCTGTTGGCAGTATTTTATTCACTGTGTTAAGCACTCTAGTTCTATAC-AATTGTTATGC -s simDog_chr6.simDog.chr6 63184 65 + 593897 TATTTGCCTGATATCAGTATTTTACTCACTGCGTTAAACACGTTTATTCTATAC-AGTTGTCATGC -s simHuman_chr6.simHuman.chr6 60470 64 + 601863 TTTGTGCCTGATGACAGTATTG-ACTCACTATGTTAAGCCATCATGTTCTTTTC-AGTTGCCATGC -s simRat_chr6.simRat.chr6 55523 64 + 647215 CTGGTGCACACTGACAATAATTTAATTACTAT-TTAACCAGTCTTCCTCTCTAC-AGTAGTCAGAC - -a -s simMouse_chr6.simMouse.chr6 62630 44 + 636262 TAACACCATCCCCCAATATCCTCTTTTTGAACTATGGATGGCAT -s Anc0.Anc0refChr4 9320 41 - 45765 T-TCCCCATTCCCTAACATCCTC-TTTTGA-CTAGGGATAGTTT -s Anc1.Anc1refChr2 40279 43 + 144309 TGTCCCCATTCCCTAACATCCTCTTTTTGA-CTAGGGATAGTTT -s Anc2.Anc2refChr4 6595 41 + 10050 T-TCCGCATTCCTTAACATCCTC-TTTTGA-CTAGAGACAGTTT -s mr.mrrefChr0 59755 44 + 130230 TAACACCATCCCCCAATATCCTCTTTTTGAACTATGGATGGCAT -s simCow_chr6.simCow.chr6 67289 41 + 602619 A-TCCTCCCTTCAGAATATTCTC-TTTTGA-CTATAGACAGCTT -s simDog_chr6.simDog.chr6 63251 41 + 593897 T-TCTGCATTCCTTAGCTTCCTC-TTTTAA-CTGGAAACAGTCT -s simHuman_chr6.simHuman.chr6 60536 43 + 601863 TGTCCCCATTACCTAACATCCTTTTGCTGA-CTAAGGATAGTTT -s simRat_chr6.simRat.chr6 55587 44 + 647215 CAATACCATCCCCGAATATCCTCTTTTTGAACTATGGATGGCAT - -a -s simMouse_chr6.simMouse.chr6 62674 1 + 636262 C -s Anc0.Anc0refChr4 9362 1 - 45765 C -s Anc1.Anc1refChr2 40323 1 + 144309 C -s Anc2.Anc2refChr4 6637 1 + 10050 C -s mr.mrrefChr0 59799 1 + 130230 C -s simCow_chr6.simCow.chr6 67331 1 + 602619 T -s simDog_chr6.simDog.chr6 63295 1 + 593897 C -s simHuman_chr6.simHuman.chr6 60580 1 + 601863 C -s simRat_chr6.simRat.chr6 55631 1 + 647215 C - -a -s simMouse_chr6.simMouse.chr6 62675 59 + 636262 TTTACCTGGGACTTGGCCAGCGCCTGTATACAACTGATTAGTAGATAGGTGGAAATACA -s Anc0.Anc0refChr4 9363 59 - 45765 TTTACCTAGGGCTTGGCAACCAACTGTATACAACTGATCAATGTTTGTGTAAGTAGTCA -s Anc1.Anc1refChr2 40324 59 + 144309 TTTACCTAGGGCTTGGCAACCAACTGTATACAACTGATCAATGTTTGTGTAAGTAGTCA -s Anc2.Anc2refChr4 6649 59 + 10050 TTTACCTAGGGCTTGGCAACTGACTGTATACAACTAATCAATGTTTGTGTATGTAGTCA -s mr.mrrefChr0 59800 59 + 130230 TTTACCTGGGACTTGGCCAGCACCTGTATACAACTGATCAGTGGATAGGTGAAAATACA -s simCow_chr6.simCow.chr6 67343 59 + 602619 TTTACGTAGGGCTTGGCAGGCAACTGTATACGACTAATCAATGTTTGGGTAGGTAGTCA -s simDog_chr6.simDog.chr6 63307 59 + 593897 TTTACCTGGGGCTTGGCAACTGCCTTTATACAACTAATTAATATATATGTATGTAGTCA -s simHuman_chr6.simHuman.chr6 60581 56 + 601863 TTTATCTAGGCCTTATGGTACA---GTATACAACCGATCTATGTTTGTGTAAGTAGTCA -s simRat_chr6.simRat.chr6 55632 59 + 647215 TTTACCTGGGACTTGGTCAGCACCTGTATACAACTAATCAGTGAATAGGTGAAGATACA - -a -s simMouse_chr6.simMouse.chr6 62734 10 + 636262 TATTGAAACT -s Anc0.Anc0refChr4 9425 10 - 45765 TATTAAGATT -s Anc1.Anc1refChr2 40386 10 + 144309 TATTAAGATT -s Anc2.Anc2refChr4 6711 10 + 10050 TATTAAGATT -s mr.mrrefChr0 59859 10 + 130230 TATTGAAACT -s simCow_chr6.simCow.chr6 67405 10 + 602619 TAGTATGAAA -s simDog_chr6.simDog.chr6 63369 10 + 593897 TATTAAGATT -s simHuman_chr6.simHuman.chr6 60640 10 + 601863 TATTAAGATT -s simRat_chr6.simRat.chr6 55691 10 + 647215 TATTGAACCT - -a -s simMouse_chr6.simMouse.chr6 62744 1 + 636262 A -s Anc0.Anc0refChr4 9446 1 - 45765 A -s Anc1.Anc1refChr2 40407 1 + 144309 A -s Anc2.Anc2refChr4 6733 1 + 10050 C -s mr.mrrefChr0 59869 1 + 130230 A -s simCow_chr6.simCow.chr6 67427 1 + 602619 C -s simDog_chr6.simDog.chr6 63391 1 + 593897 C -s simHuman_chr6.simHuman.chr6 60661 1 + 601863 A -s simRat_chr6.simRat.chr6 55701 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 62745 13 + 636262 ATGATGTGGTTGG -s Anc0.Anc0refChr4 9459 13 - 45765 AAGCTGTGTTAGG -s Anc1.Anc1refChr2 40420 13 + 144309 AAGCTGTGTTAGG -s Anc2.Anc2refChr4 6746 13 + 10050 AATCTGTGTTAGG -s mr.mrrefChr0 59882 13 + 130230 ATGCTGTGGTTGG -s simCow_chr6.simCow.chr6 67440 13 + 602619 AATCTGTGATAGG -s simDog_chr6.simDog.chr6 63404 13 + 593897 AATCTGTGTTAGG -s simHuman_chr6.simHuman.chr6 60674 13 + 601863 AAGCTGTGCTAGG -s simRat_chr6.simRat.chr6 55714 13 + 647215 AGGCTGTGGTTGG - -a -s simMouse_chr6.simMouse.chr6 62758 23 + 636262 GCAGCGCACAGCAAAGGGTTCTT -s Anc0.Anc0refChr4 9475 23 - 45765 ACACTGTAGAACACAGGTCTTTT -s Anc1.Anc1refChr2 40436 23 + 144309 ACACTGTAGAACACAGGTCTTTT -s Anc2.Anc2refChr4 6762 23 + 10050 ACACTGTAGAACACAGGTCTTTT -s mr.mrrefChr0 59895 23 + 130230 GCAGTGCACAGCAAAGGGTTCTT -s simCow_chr6.simCow.chr6 67456 23 + 602619 GCATTGTAGGACACAGATCTCTT -s simDog_chr6.simDog.chr6 63420 23 + 593897 ACACTGTAGAACACAGGTGTTTT -s simHuman_chr6.simHuman.chr6 60690 23 + 601863 ACACTGTAGAACATAGGTCTTTT -s simRat_chr6.simRat.chr6 55727 23 + 647215 GCAGTGGACAGCAACAGGTTCTT - -a -s simMouse_chr6.simMouse.chr6 62781 18 + 636262 TAAGAACTCCTGAGCAGC -s Anc1.Anc1refChr2 40498 17 + 144309 TGAGG-CTGCTCATCATC -s mr.mrrefChr0 59918 18 + 130230 TAAGAACTCCTGAGCAGC -s simHuman_chr6.simHuman.chr6 60763 17 + 601863 TGAGG-CTGCTCATCATC -s simRat_chr6.simRat.chr6 55750 18 + 647215 TAAGAACTCCTGAGCAGC - -a -s simMouse_chr6.simMouse.chr6 62799 18 + 636262 ACAACCGAGGGCCCTTGT -s Anc0.Anc0refChr4 9537 8 - 45765 --------ATGAG--TGT -s Anc1.Anc1refChr2 40515 18 + 144309 ACATCCTTATGAGCTTGT -s Anc2.Anc2refChr4 6847 8 + 10050 --------ATGAG--TGT -s mr.mrrefChr0 59936 18 + 130230 ACAACCTTGGGCCCTTGT -s simCow_chr6.simCow.chr6 67541 8 + 602619 --------ATAAC--TGT -s simDog_chr6.simDog.chr6 63505 8 + 593897 --------ATGAG--TGT -s simHuman_chr6.simHuman.chr6 60781 18 + 601863 ACATCCTTAAGAGCTTGT -s simRat_chr6.simRat.chr6 55768 18 + 647215 ACAATCTTGGGCCCTTAT - -a -s simMouse_chr6.simMouse.chr6 62817 11 + 636262 ACTAAATAAGA -s Anc0.Anc0refChr4 9550 11 - 45765 GGTACATTAAG -s Anc1.Anc1refChr2 40538 11 + 144309 GGTACATTAAG -s Anc2.Anc2refChr4 6860 11 + 10050 GGCACATTAAG -s mr.mrrefChr0 59954 11 + 130230 ACTAAATTAAA -s simCow_chr6.simCow.chr6 67554 11 + 602619 GGCACATTAAG -s simDog_chr6.simDog.chr6 63518 11 + 593897 GGCACATTAAG -s simHuman_chr6.simHuman.chr6 60804 11 + 601863 GGTACATTAAG -s simRat_chr6.simRat.chr6 55786 11 + 647215 TCTAAATTAAA - -a -s simMouse_chr6.simMouse.chr6 62828 21 + 636262 CAAAGCTTTGACAGACAGCTA -s Anc0.Anc0refChr4 9572 18 - 45765 CAAAATTTTG---GACAGCTA -s Anc1.Anc1refChr2 40560 18 + 144309 CAAAATTTTG---GACAGCTA -s Anc2.Anc2refChr4 6882 18 + 10050 CAAAATTTTG---GACAGCTA -s mr.mrrefChr0 59965 21 + 130230 CAAAGCTTTGACAGACAGCTA -s simCow_chr6.simCow.chr6 67576 17 + 602619 CAAAG-TTTG---GACAGCTA -s simDog_chr6.simDog.chr6 63540 18 + 593897 TGAAATTTTG---GACAGCTA -s simHuman_chr6.simHuman.chr6 60847 18 + 601863 CAAAATTTTG---GACAGCCG -s simRat_chr6.simRat.chr6 55797 21 + 647215 CAAAGCTTCATCAGACAACTA - -a -s simMouse_chr6.simMouse.chr6 62849 2 + 636262 GC -s Anc0.Anc0refChr4 9590 2 - 45765 GC -s Anc1.Anc1refChr2 40578 2 + 144309 GC -s Anc2.Anc2refChr4 6900 2 + 10050 GC -s mr.mrrefChr0 59986 2 + 130230 GC -s simCow_chr6.simCow.chr6 67595 2 + 602619 GC -s simDog_chr6.simDog.chr6 63558 2 + 593897 GC -s simHuman_chr6.simHuman.chr6 60865 2 + 601863 GC -s simRat_chr6.simRat.chr6 55818 2 + 647215 GC - -a -s simMouse_chr6.simMouse.chr6 62851 7 + 636262 TGTTGTG -s Anc0.Anc0refChr4 9593 7 - 45765 TGCTGTG -s Anc1.Anc1refChr2 40581 7 + 144309 TGCTGTG -s Anc2.Anc2refChr4 6903 7 + 10050 TGCTGTG -s mr.mrrefChr0 59989 7 + 130230 TGCTGTG -s simCow_chr6.simCow.chr6 67598 7 + 602619 TCCAGTG -s simDog_chr6.simDog.chr6 63561 7 + 593897 TGCTGTG -s simHuman_chr6.simHuman.chr6 60868 7 + 601863 TGCTGTG -s simRat_chr6.simRat.chr6 55821 7 + 647215 TGCTGTG - -a -s simMouse_chr6.simMouse.chr6 62858 26 + 636262 GTGTCCCTCAGGGGATAAACCCTTCC -s Anc0.Anc0refChr4 9603 26 - 45765 GTATCCCACAGGAGAAAAACTCTTTC -s Anc1.Anc1refChr2 40591 26 + 144309 GTATCCCACAGGAGAAAAACTCTTTC -s Anc2.Anc2refChr4 6913 26 + 10050 GTATCTCATGGGAGAAAAACTCTTTC -s mr.mrrefChr0 59996 26 + 130230 GTGTCCCTCAGGGGATAAACCCTTCC -s simCow_chr6.simCow.chr6 67608 26 + 602619 GTAACTCATGGGAGAGAAAATCTTTC -s simDog_chr6.simDog.chr6 63571 26 + 593897 GTGTCTGATGGGAACAAAGCTCTTTT -s simHuman_chr6.simHuman.chr6 60878 26 + 601863 ATATCCCACAGGAGAAAAATTCTCTC -s simRat_chr6.simRat.chr6 55828 23 + 647215 GTGTCCCTCAAGGGATAAACCCT--- - -a -s simMouse_chr6.simMouse.chr6 62884 64 + 636262 ACAATGCACTACCAAGAAATTACCACCCTGCCTTTATCTCAGACATGTGGAGTGTGGCAGCTCA -s Anc0.Anc0refChr4 9632 32 - 45765 GCAATGCAATACCA-GAGAGGAATA-------------------------------GCATCGCA -s Anc1.Anc1refChr2 40620 32 + 144309 GCAATGCAATACCA-GAGAGGAATA-------------------------------GCATCGCA -s Anc2.Anc2refChr4 6942 32 + 10050 GTAATGCAATACCA-GAGAGGAATA-------------------------------TCTTGGCT -s mr.mrrefChr0 60022 63 + 130230 ACAATGCACTACCA-GAAATTACCACCCTGCCTTTATCTCAGACATGTGGAGTGTGGCAGCTCA -s simCow_chr6.simCow.chr6 67637 30 + 602619 GTAAAGCAATACA---AAGGTAACA-------------------------------TCTAGTCT -s simDog_chr6.simDog.chr6 63600 32 + 593897 ATAATGCAATACCA-GAGAGGAATA-------------------------------TCTTGGCT -s simHuman_chr6.simHuman.chr6 60907 32 + 601863 GCAATGCAATACCA-GAGAGAAATA-------------------------------GCACCCCA -s simRat_chr6.simRat.chr6 55851 61 + 647215 --AGTGCACTACCG-GAAATTACCACCCTGCCTTTGTCTTAGACATGTGGCGTGTGGCAGCTCA - -a -s simMouse_chr6.simMouse.chr6 62948 7 + 636262 GGAGCTA -s Anc0.Anc0refChr4 9664 7 - 45765 TAAACTT -s Anc1.Anc1refChr2 40652 7 + 144309 TAAACTT -s Anc2.Anc2refChr4 6974 7 + 10050 TAAACTT -s mr.mrrefChr0 60085 7 + 130230 GGAGCTT -s simCow_chr6.simCow.chr6 67682 7 + 602619 TAAACTT -s simDog_chr6.simDog.chr6 63632 7 + 593897 TTGTCTT -s simHuman_chr6.simHuman.chr6 60939 7 + 601863 TAAACTT -s simRat_chr6.simRat.chr6 55912 7 + 647215 GGGGCTT - -a -s simMouse_chr6.simMouse.chr6 62955 6 + 636262 CTGTGC -s Anc0.Anc0refChr4 9671 6 - 45765 CTGTGC -s Anc1.Anc1refChr2 40659 6 + 144309 CTGTGC -s Anc2.Anc2refChr4 6981 6 + 10050 CTGTGA -s mr.mrrefChr0 60092 6 + 130230 CTGTGC -s simCow_chr6.simCow.chr6 67689 6 + 602619 CTGTGT -s simDog_chr6.simDog.chr6 63643 6 + 593897 CTGTGA -s simHuman_chr6.simHuman.chr6 60946 6 + 601863 CTGTGC -s simRat_chr6.simRat.chr6 55919 6 + 647215 CTGTGC - -a -s simMouse_chr6.simMouse.chr6 62961 33 + 636262 AACAGCCATGAATTAGTCAAGAAATAATTGCAC -s Anc0.Anc0refChr4 9677 31 - 45765 GGTCA--AGGCAACAGTTCAGAAGTAATTGAAT -s Anc1.Anc1refChr2 40665 31 + 144309 GGTCA--AGGCAACAGTTCAGAAGTAATTGAAT -s Anc2.Anc2refChr4 6987 31 + 10050 GGTCA--AGGCAACAATTCAGAAGTAATTGAAT -s mr.mrrefChr0 60098 32 + 130230 AATAGC-ATGAATTAGTCAAGAAATAATTGCAC -s simCow_chr6.simCow.chr6 67697 31 + 602619 GGTCA--AGGCAACAATTCAGAAGTAATTGAAT -s simDog_chr6.simDog.chr6 63649 10 + 593897 AGT-----------------------ATGGCAC -s simHuman_chr6.simHuman.chr6 60952 31 + 601863 GGTTA--AGGCAACAGTTCAGAAGTAATTGAAT -s simRat_chr6.simRat.chr6 55925 6 + 647215 AATGGC--------------------------- - -a -s simMouse_chr6.simMouse.chr6 62994 29 + 636262 ACTCTCAAATATGCCTGCTCACCAGCTGT -s Anc0.Anc0refChr4 9708 27 - 45765 GCT-TCAAAT-GAGTTGCCCACCCACTGT -s Anc1.Anc1refChr2 40696 27 + 144309 GCT-TCAAAT-GAGTTGCCCACCCACTGT -s Anc2.Anc2refChr4 7018 27 + 10050 GTT-TCAAAT-GAGTTGCCCACCCACTGC -s mr.mrrefChr0 60130 27 + 130230 ACT-TCAAAT-TGCCTGCTCACCAGCTGT -s simCow_chr6.simCow.chr6 67729 27 + 602619 GTT-TCAAAT-GAGTTGCCCACCCACTGA -s simDog_chr6.simDog.chr6 63659 18 + 593897 CTC-TCATA----------CACTCATTGC -s simHuman_chr6.simHuman.chr6 60983 27 + 601863 GCT-TCAAAT-CAATTGCCCACCCACTGT -s simRat_chr6.simRat.chr6 55931 1 + 647215 ----------------------------G - -a -s simMouse_chr6.simMouse.chr6 63023 32 + 636262 TACGGGTGCTAAGGACATTCCTCTCCTGTAGG -s Anc0.Anc0refChr4 9736 30 - 45765 TGGGG--GCTAAGGACATTCCTCTTTGAGAGA -s Anc1.Anc1refChr2 40724 32 + 144309 TGGGGGTGCTAAGGACATTCCTCTTTGAGAGA -s Anc2.Anc2refChr4 7046 30 + 10050 TGGGA--GCTAAGGACATTCCTCTTTGAGAGA -s mr.mrrefChr0 60157 32 + 130230 TACGGGTGCTAAGGACATTCCTCTCCTGTAGG -s simCow_chr6.simCow.chr6 67757 30 + 602619 TGGAT--TCCAAGGACATGCTGCTTTGGGGGA -s simDog_chr6.simDog.chr6 63678 30 + 593897 TGAGA--GCTAAGGACATTCCTTTTTGAGAAA -s simHuman_chr6.simHuman.chr6 61011 32 + 601863 TGGGGGTGCTAAAGACATTCCTCTTTGAGAGA -s simRat_chr6.simRat.chr6 55932 32 + 647215 TATGGGTGCTAAGGACATTCCTCTCATGTAGG - -a -s simMouse_chr6.simMouse.chr6 63055 61 + 636262 CTGAGGGTCCACTTCTTCACCTAACCCAAATGCTGCTTTATACTGGGTCTAATGGGATGAT -s Anc0.Anc0refChr4 9789 61 - 45765 CTGAGGGTCTGCATCTTCACTCAGCTTAAGTGCCGTTTTGTTCTGGGTTTAATGGGATCAC -s Anc1.Anc1refChr2 40779 61 + 144309 CTGAGGGTCTGCATCTTCACTCAGCTTAAGTGCCGTTTTGTTCTGGGTTTAATGGGATCAC -s Anc2.Anc2refChr4 7100 61 + 10050 CCAAATATTTGTATTTTCACCCAGCTTTAGTGCGATTTTGTTCTGGGTTTAATGGGCTCAC -s mr.mrrefChr0 60189 61 + 130230 CTGAGGGTCCACATCTTCACTTAACCCAAATGCCGCTTTATACTGGGTCTAATGGGATGAT -s simCow_chr6.simCow.chr6 67795 24 + 602619 -------------------------------------TTGTTCTGGGTCTAATGGGGTCAC -s simDog_chr6.simDog.chr6 63732 61 + 593897 CCAAATATTTGTATTTTCACCCAGCTTTAGTGCGATTCTTTCATGGACTTTACAGGCTCAC -s simHuman_chr6.simHuman.chr6 61066 61 + 601863 CTGAGGGTCTGCATCTTCACTCAGCTTAAGTTTCGTGTTGTTCAGGGTATAATGGCATCAC -s simRat_chr6.simRat.chr6 55964 58 + 647215 CTGAGGGTCCATATCTTCACTTAA---AAATACCACCTGATACTGGGTTTCATGGGTTTAT - -a -s simMouse_chr6.simMouse.chr6 63116 2 + 636262 AC -s Anc0.Anc0refChr4 9850 2 - 45765 AT -s Anc1.Anc1refChr2 40840 2 + 144309 AT -s Anc2.Anc2refChr4 7161 2 + 10050 AT -s mr.mrrefChr0 60250 2 + 130230 AC -s simCow_chr6.simCow.chr6 67821 2 + 602619 AT -s simDog_chr6.simDog.chr6 63793 2 + 593897 AT -s simHuman_chr6.simHuman.chr6 61127 2 + 601863 AT -s simRat_chr6.simRat.chr6 56022 2 + 647215 AC - -a -s simMouse_chr6.simMouse.chr6 63118 4 + 636262 AAGA -s Anc0.Anc0refChr4 9855 4 - 45765 CAGA -s Anc1.Anc1refChr2 40845 4 + 144309 CAGA -s Anc2.Anc2refChr4 7166 4 + 10050 CAGG -s mr.mrrefChr0 60252 4 + 130230 AAGA -s simCow_chr6.simCow.chr6 67826 4 + 602619 CAGG -s simDog_chr6.simDog.chr6 63798 4 + 593897 GAGG -s simHuman_chr6.simHuman.chr6 61132 4 + 601863 CATA -s simRat_chr6.simRat.chr6 56024 4 + 647215 AAGA - -a -s simMouse_chr6.simMouse.chr6 63122 22 + 636262 CTACAGCAAAGATGTGGCATAA -s Anc0.Anc0refChr4 9860 22 - 45765 TGACATCAATGCTGTGGCATAC -s Anc1.Anc1refChr2 40850 22 + 144309 TGACATCAATGCTGTGGCATAC -s Anc2.Anc2refChr4 7171 22 + 10050 TGACATCAATGCTGTGGCATAC -s mr.mrrefChr0 60257 22 + 130230 CAACAGCAATGATGTGGCATAA -s simCow_chr6.simCow.chr6 67831 21 + 602619 TG-CATCATTGATGGGGCATAC -s simDog_chr6.simDog.chr6 63803 22 + 593897 TGATATCAATGCTGTGGCATAC -s simHuman_chr6.simHuman.chr6 61137 22 + 601863 TGACATTAATGGTGTGGCATAC -s simRat_chr6.simRat.chr6 56029 22 + 647215 CAACAGCAATGATGTGGCATAA - -a -s simMouse_chr6.simMouse.chr6 63144 12 + 636262 AAAATTAGTTAG -s Anc0.Anc0refChr4 9882 12 - 45765 AAAATTAGTTAA -s Anc1.Anc1refChr2 40872 12 + 144309 AAAATTAGTTAA -s Anc2.Anc2refChr4 7193 12 + 10050 AAAATTAGTTAA -s mr.mrrefChr0 60279 12 + 130230 AAAATTAGTTAG -s simCow_chr6.simCow.chr6 67852 12 + 602619 ATAGTTAGTTGA -s simDog_chr6.simDog.chr6 63825 12 + 593897 AAAATTACTTAA -s simHuman_chr6.simHuman.chr6 61159 12 + 601863 CAAATGAGCTAA -s simRat_chr6.simRat.chr6 56054 12 + 647215 AAAATAAGTTAG - -a -s simMouse_chr6.simMouse.chr6 63156 32 + 636262 AGGGATAATGGGACATGAAAGTTAGAGGTCCC -s Anc0.Anc0refChr4 9895 32 - 45765 AGGAATGATGGAGCATGAAAGTCAGAAAAACC -s Anc1.Anc1refChr2 40885 32 + 144309 AGGAATGATGGAGCATGAAAGTCAGAAAAACC -s Anc2.Anc2refChr4 7206 32 + 10050 AGTAATGAATGAGCACGAATGTCAGAAAAACC -s mr.mrrefChr0 60292 32 + 130230 AGGAATAATGGAACATGAAAGTTAGAGATCCC -s simCow_chr6.simCow.chr6 67865 32 + 602619 AGTAATGAATGAGCACGAATGTCAGAAAAACC -s simDog_chr6.simDog.chr6 63838 2 + 593897 AG------------------------------ -s simHuman_chr6.simHuman.chr6 61172 32 + 601863 AGGAATGATGGAGCATGCAAGTGAGGAAAACC -s simRat_chr6.simRat.chr6 56067 32 + 647215 AGGAATAATGGAACATGAAAGTCAGAGATCCT - -a -s simMouse_chr6.simMouse.chr6 63188 3 + 636262 ATG -s Anc0.Anc0refChr4 9927 3 - 45765 CTA -s Anc1.Anc1refChr2 40917 3 + 144309 CTA -s Anc2.Anc2refChr4 7238 3 + 10050 CTA -s mr.mrrefChr0 60324 3 + 130230 ATG -s simCow_chr6.simCow.chr6 67898 3 + 602619 CTA -s simHuman_chr6.simHuman.chr6 61204 3 + 601863 CCA -s simRat_chr6.simRat.chr6 56099 3 + 647215 GCG - -a -s simMouse_chr6.simMouse.chr6 63191 28 + 636262 CACTTACTTCTGATATACAAGAAATAAA -s Anc0.Anc0refChr4 9931 28 - 45765 CACTTCCTTCTGATATAGAAGAAATAAA -s Anc1.Anc1refChr2 40921 28 + 144309 CACTTCCTTCTGATATAGAAGAAATAAA -s Anc2.Anc2refChr4 7242 28 + 10050 CACTTCCTTCTGATATCGAAGGAGTAAA -s mr.mrrefChr0 60327 28 + 130230 CACTTACTTCTGATATACAAGAAATAAA -s simCow_chr6.simCow.chr6 67902 28 + 602619 CACTTCCTTCTGATATCGAAGGAGTAAA -s simHuman_chr6.simHuman.chr6 61208 28 + 601863 CATTTCCCTCTGAGATAGAAGAAATAAA -s simRat_chr6.simRat.chr6 56102 27 + 647215 TACTTTCTTCTGATATA-AAGAAATAAA - -a -s simMouse_chr6.simMouse.chr6 63219 38 + 636262 CTTGACATGTCTCAAATAGTCACATTGTCACGAATACT -s Anc0.Anc0refChr4 9960 38 - 45765 CTTTACATGTCACAGATGATTACACAGTCACAAATACT -s Anc1.Anc1refChr2 40950 38 + 144309 CTTTACATGTCACAGATGATTACACAGTCACAAATACT -s Anc2.Anc2refChr4 7271 38 + 10050 CTTTATATGTCAGAGATGATTGAGCAGTCACAAATAGT -s mr.mrrefChr0 60355 38 + 130230 CTTTACATGTCTCAAATAGTCACATAGTCACAAATACT -s simCow_chr6.simCow.chr6 67931 38 + 602619 CTTTATATGTCAGAGATGAATGTGCAGTCACAAATAAT -s simDog_chr6.simDog.chr6 63840 21 + 593897 ---------------ATGATTGAGTGGTCAC--ATGGT -s simHuman_chr6.simHuman.chr6 61237 38 + 601863 CTTTACATGTTACGTATGACTACACAGTCACAAACACT -s simRat_chr6.simRat.chr6 56129 34 + 647215 CTTTACACATCTCAAATCTTC----AGTCACAAATACT - -a -s simMouse_chr6.simMouse.chr6 63257 10 + 636262 AGACATCCTT -s Anc0.Anc0refChr4 10047 6 - 45765 TA----TCAT -s Anc1.Anc1refChr2 41037 10 + 144309 TAACATTCAT -s Anc2.Anc2refChr4 7358 6 + 10050 TA----TCAT -s mr.mrrefChr0 60442 10 + 130230 AGACATCCTT -s simCow_chr6.simCow.chr6 68031 6 + 602619 AA----CCAT -s simDog_chr6.simDog.chr6 63919 6 + 593897 TA----TCAT -s simHuman_chr6.simHuman.chr6 61324 10 + 601863 TAACATTCAT -s simRat_chr6.simRat.chr6 56224 10 + 647215 AGACATCCTT - -a -s simMouse_chr6.simMouse.chr6 63267 9 + 636262 GACTGACAT -s Anc0.Anc0refChr4 10058 9 - 45765 AACTGGTAC -s Anc1.Anc1refChr2 41052 9 + 144309 AACTGGTAC -s Anc2.Anc2refChr4 7369 9 + 10050 AACTGGTAC -s mr.mrrefChr0 60452 9 + 130230 GACTGACAT -s simCow_chr6.simCow.chr6 68042 9 + 602619 ACCTAGTTT -s simDog_chr6.simDog.chr6 63930 9 + 593897 AACTGGTAC -s simHuman_chr6.simHuman.chr6 61339 9 + 601863 AGCTGGAAC -s simRat_chr6.simRat.chr6 56234 9 + 647215 GACTGATAT - -a -s simMouse_chr6.simMouse.chr6 63276 22 + 636262 TGTACACTCTTAAGCAACTAGG -s Anc0.Anc0refChr4 10079 22 - 45765 TTAACACTCTGTAATCACTAAG -s Anc1.Anc1refChr2 41073 22 + 144309 TTAACACTCTGTAATCACTAAG -s Anc2.Anc2refChr4 7390 22 + 10050 TTAACACTCTGTAATCACTAAG -s mr.mrrefChr0 60468 22 + 130230 TGTACACTCTTAAGCAACTAAG -s simCow_chr6.simCow.chr6 68063 22 + 602619 TTAACAATCTGAGATTAGTAAG -s simDog_chr6.simDog.chr6 63951 22 + 593897 TTAACTCACACTAACCTCTAAG -s simHuman_chr6.simHuman.chr6 61360 22 + 601863 TTAACACTCTGCAATGACTAAG -s simRat_chr6.simRat.chr6 56250 22 + 647215 TATGCACTCCTAAGCAATTGAG - -a -s simMouse_chr6.simMouse.chr6 63298 24 + 636262 GCTTGATGGAGGCATGTTGGTGCC -s Anc0.Anc0refChr4 10101 24 - 45765 CTTTGATGGAGGCATGTTGGGTCT -s Anc1.Anc1refChr2 41095 24 + 144309 CTTTGATGGAGGCATGTTGGGTCT -s Anc2.Anc2refChr4 7412 24 + 10050 CTTTGATTGAGGCATGGTGGGTCT -s mr.mrrefChr0 60490 24 + 130230 CCTTGATGGAGGCATGTTGGTGCC -s simCow_chr6.simCow.chr6 68085 24 + 602619 CCTTGATTCAGGCATGGTGGGTCT -s simDog_chr6.simDog.chr6 63974 24 + 593897 CTCTGAGTGAGGCATGGTGGGTCT -s simHuman_chr6.simHuman.chr6 61382 24 + 601863 CTTTGATGGAGGGATGTTGGATCT -s simRat_chr6.simRat.chr6 56272 23 + 647215 CCATGATGGAGGCA-GTTGGTGCC - -a -s simMouse_chr6.simMouse.chr6 63322 11 + 636262 TCAACAAGACA -s Anc0.Anc0refChr4 10125 11 - 45765 GTAGACAGAAA -s Anc1.Anc1refChr2 41119 11 + 144309 GTAGACAGAAA -s Anc2.Anc2refChr4 7436 11 + 10050 GTAGACAGAAA -s mr.mrrefChr0 60514 11 + 130230 TTAGCAAGACA -s simCow_chr6.simCow.chr6 68109 4 + 602619 GTGG------- -s simDog_chr6.simDog.chr6 64001 11 + 593897 GTAGACAGAAA -s simHuman_chr6.simHuman.chr6 61406 11 + 601863 GTAGACAGAAA -s simRat_chr6.simRat.chr6 56295 11 + 647215 TTAGCAAGACA - -a -s simMouse_chr6.simMouse.chr6 63333 3 + 636262 CAG -s Anc1.Anc1refChr2 41138 3 + 144309 CAG -s mr.mrrefChr0 60533 3 + 130230 CAG -s simHuman_chr6.simHuman.chr6 61449 3 + 601863 CAG -s simRat_chr6.simRat.chr6 56314 3 + 647215 CAT - -a -s simMouse_chr6.simMouse.chr6 63336 47 + 636262 TAGACAGTGAGTCATTTTTTGAACTAGTGTAAAATAGGTTCATACTA -s Anc0.Anc0refChr4 10140 46 - 45765 -AGACAGAAGGCCATTTTTAGAACTAGGGTAAAATAAATACAAAATA -s Anc1.Anc1refChr2 41141 47 + 144309 TAGACAGAAGGCCATTTTTAGAACTAGGGTAAAATAAATACAAAATA -s Anc2.Anc2refChr4 7451 46 + 10050 -AGACAGAAGGCCATTTTTAGACCTAGGGTAAAATAAATACAAAATA -s mr.mrrefChr0 60536 47 + 130230 TAGACAGTGGGTCATTTTTTGAACTAGTGTAAAATAAGTTCATACTA -s simCow_chr6.simCow.chr6 68114 46 + 602619 -AGATAGAAGGTCATCTTTAGACTTAGGGTGCAATAAATACAAAATA -s simDog_chr6.simDog.chr6 64016 46 + 593897 -AGACAGAAAGCCATTTTTGGACCCAGGCTAAAATAAATGCAAAATA -s simHuman_chr6.simHuman.chr6 61459 47 + 601863 TAGACAAAAGGCCATTTTTAGCACTAGGGTAAAATAAATACACAATA -s simRat_chr6.simRat.chr6 56317 47 + 647215 TAGACAGTGGGTCATATTTTGAACTAGTGTAAAATAAGTTCAAACTA - -a -s simMouse_chr6.simMouse.chr6 63383 1 + 636262 C -s Anc0.Anc0refChr4 10186 1 - 45765 C -s Anc1.Anc1refChr2 41188 1 + 144309 C -s Anc2.Anc2refChr4 7497 1 + 10050 C -s mr.mrrefChr0 60583 1 + 130230 C -s simCow_chr6.simCow.chr6 68160 1 + 602619 C -s simDog_chr6.simDog.chr6 64062 1 + 593897 C -s simHuman_chr6.simHuman.chr6 61506 1 + 601863 C -s simRat_chr6.simRat.chr6 56367 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 63384 62 + 636262 TTAATGTACCTGTACATCACTTGCTTGTCACAAGATATCCAATAGTGGTGTTGCAAATACTT -s Anc0.Anc0refChr4 10191 48 - 45765 TCATTGTAC-TGCCATTCATTTCTATCTCACTAGATTCCTGAT---GG----------ATTG -s Anc1.Anc1refChr2 41193 58 + 144309 TCATTGTAC-TGCCATTCATTTCTATCTCACTAGATTCCTGAT---GGTGTTATGAATATTG -s Anc2.Anc2refChr4 7502 48 + 10050 TCATTGTAC-TGCCATTCATTTCTATTCCACTATATTCTTGAC---TG----------ATTA -s mr.mrrefChr0 60584 62 + 130230 TTAATGTACCTGCAAATCATTTGCTTCTCACAAGATTCCCAATAGTGGTGTTACAAATATTG -s simCow_chr6.simCow.chr6 68165 42 + 602619 TCATTG-------CATTGATTTCTATTCCACTATATTCTTGAC---TG----------GTTT -s simDog_chr6.simDog.chr6 64067 34 + 593897 TCATTGTAC-TGCCAGTCATTTCTATTCCCC---------------------------ATTA -s simHuman_chr6.simHuman.chr6 61511 58 + 601863 TCATTGTAC-TACCATTCATTTCTATCTCACTAGGTTCCTGAT---GGTGTTATGAATATTG -s simRat_chr6.simRat.chr6 56368 62 + 647215 TTAATGTACCTGCAAATCATTTGCTTCTCACAAGATTCCCAATAGTGGTGTTACAAATATTG - -a -s simMouse_chr6.simMouse.chr6 63446 50 + 636262 AGAACTGACATAGGATCATGAGTCGGTGATAGCTTCATAAAGTTCACACC -s Anc0.Anc0refChr4 10239 50 - 45765 AGGGCTGATACAGGGACCTGGGTAGGTAACAACTTCATAATGCTGGTATC -s Anc1.Anc1refChr2 41251 50 + 144309 AGGGCTGATACAGGGACCTGGGTAGGTAACAACTTCATAATGCTGGTATC -s Anc2.Anc2refChr4 7550 50 + 10050 AGGGCTGATACAGGGAACTGGGTAGGTAACAACTTCATAATGCTGGTATC -s mr.mrrefChr0 60646 50 + 130230 AGAACTGACACAGGATCATGAGTCGGTAACAACTTCATAAAGTTCGCACC -s simCow_chr6.simCow.chr6 68207 49 + 602619 AGGGCTGATACAGGGAACTGGATA-GTAACAACCTCATAAAGCTGATATC -s simDog_chr6.simDog.chr6 64101 49 + 593897 AGGGCTAATACAGGGAACTGGGCAGGTAAGAACTTTATAAT-TTAGTATA -s simHuman_chr6.simHuman.chr6 61569 50 + 601863 AGGGCTGATACAGGGACCTGGTTAGGAAACAACTTCATAATGCTGGTAAC -s simRat_chr6.simRat.chr6 56431 50 + 647215 AGAACTGACACAAGATCGTGAGTCAGTAACAACTTCATAAAATATGCTCT - -a -s simMouse_chr6.simMouse.chr6 63496 9 + 636262 CTAATTAGC -s Anc0.Anc0refChr4 10289 8 - 45765 CTAAGC-GC -s Anc1.Anc1refChr2 41301 9 + 144309 CTAAGCAGC -s Anc2.Anc2refChr4 7600 8 + 10050 CATAGC-TC -s mr.mrrefChr0 60696 9 + 130230 CTAATTAGC -s simCow_chr6.simCow.chr6 68265 8 + 602619 CATAGC-TC -s simDog_chr6.simDog.chr6 64150 8 + 593897 CATAGC-TT -s simHuman_chr6.simHuman.chr6 61619 9 + 601863 CTAAACAGC -s simRat_chr6.simRat.chr6 56481 9 + 647215 CTAATAAGC - -a -s simMouse_chr6.simMouse.chr6 63505 4 + 636262 TTAA -s Anc0.Anc0refChr4 10301 4 - 45765 TTGG -s Anc1.Anc1refChr2 41314 4 + 144309 TTGG -s Anc2.Anc2refChr4 7612 4 + 10050 TTGG -s mr.mrrefChr0 60705 4 + 130230 TTAG -s simCow_chr6.simCow.chr6 68277 4 + 602619 TGGG -s simDog_chr6.simDog.chr6 64162 4 + 593897 TTGA -s simHuman_chr6.simHuman.chr6 61632 4 + 601863 TTGG -s simRat_chr6.simRat.chr6 56490 4 + 647215 CGAG - -a -s simMouse_chr6.simMouse.chr6 63509 2 + 636262 CA -s Anc0.Anc0refChr4 10305 2 - 45765 TT -s Anc1.Anc1refChr2 41318 2 + 144309 TT -s Anc2.Anc2refChr4 7616 2 + 10050 TT -s mr.mrrefChr0 60709 2 + 130230 CA -s simCow_chr6.simCow.chr6 68284 2 + 602619 TT -s simDog_chr6.simDog.chr6 64166 2 + 593897 TT -s simHuman_chr6.simHuman.chr6 61636 2 + 601863 TT -s simRat_chr6.simRat.chr6 56494 2 + 647215 CA - -a -s simMouse_chr6.simMouse.chr6 63511 10 + 636262 GAAGTACCAG -s Anc0.Anc0refChr4 10307 10 - 45765 GAGGTGCCAG -s Anc1.Anc1refChr2 41320 10 + 144309 GAGGTGCCAG -s Anc2.Anc2refChr4 7619 10 + 10050 GAGGTGCCAG -s mr.mrrefChr0 60711 10 + 130230 GAAGTGCCAG -s simCow_chr6.simCow.chr6 68287 9 + 602619 GATGTGCCA- -s simDog_chr6.simDog.chr6 64169 10 + 593897 GAGGTGCCAG -s simHuman_chr6.simHuman.chr6 61638 10 + 601863 AAGGTGCCAG -s simRat_chr6.simRat.chr6 56496 10 + 647215 GAAGCGCCAG - -a -s simMouse_chr6.simMouse.chr6 63521 31 + 636262 GTATTGGCACCTGGGCAAGTGACAACAACAG -s Anc0.Anc0refChr4 10317 29 - 45765 GTATGGGCACCTGGGTAGGTGACAAC--CCG -s Anc1.Anc1refChr2 41330 29 + 144309 GTATGGGCACCTGGGTAGGTGACAAC--CCG -s Anc2.Anc2refChr4 7629 29 + 10050 GTATGGGGATATGGGTAGGTGACAAC--CCG -s mr.mrrefChr0 60721 29 + 130230 GTATTGGCACCTGGGCAAGTGACAAC--CAG -s simCow_chr6.simCow.chr6 68296 29 + 602619 GTATGGGGAGATGGGTCCATGACAAC--CAG -s simDog_chr6.simDog.chr6 64180 29 + 593897 ATATGGGGATATAGGTAGGTGACCAC--CCG -s simHuman_chr6.simHuman.chr6 61648 29 + 601863 GTATGGGCACCTGGGGATGTGAGAAC--CTG -s simRat_chr6.simRat.chr6 56506 6 + 647215 TTATTG------------------------- - -a -s simMouse_chr6.simMouse.chr6 63552 6 + 636262 ATCAAG -s Anc0.Anc0refChr4 10346 6 - 45765 ATAAAG -s Anc1.Anc1refChr2 41359 6 + 144309 ATAAAG -s Anc2.Anc2refChr4 7658 6 + 10050 ATAAAG -s mr.mrrefChr0 60750 6 + 130230 ATCAAG -s simCow_chr6.simCow.chr6 68325 6 + 602619 ATAAAG -s simDog_chr6.simDog.chr6 64220 6 + 593897 ATAAAG -s simHuman_chr6.simHuman.chr6 61677 6 + 601863 ATAAAA - -a -s simMouse_chr6.simMouse.chr6 63558 5 + 636262 TGACA -s Anc0.Anc0refChr4 10353 5 - 45765 TGTCA -s Anc1.Anc1refChr2 41366 5 + 144309 TGTCA -s Anc2.Anc2refChr4 7665 5 + 10050 TGTCA -s mr.mrrefChr0 60756 5 + 130230 TGACA -s simCow_chr6.simCow.chr6 68332 5 + 602619 TGTCA -s simDog_chr6.simDog.chr6 64227 5 + 593897 TGTCA -s simHuman_chr6.simHuman.chr6 61684 5 + 601863 TCTTA - -a -s simMouse_chr6.simMouse.chr6 63563 35 + 636262 TTATAATTGACTCAGTATTCAACAATGGAGGTCCC -s Anc0.Anc0refChr4 10358 35 - 45765 TCCTAATTACCTCAGCATTGATCAAAAAAGGTCTC -s Anc1.Anc1refChr2 41371 35 + 144309 TCCTAATTACCTCAGCATTGATCAAAAAAGGTCTC -s Anc2.Anc2refChr4 7670 35 + 10050 TCCCAATTACCTCAGCATAGGTCAAAAAAGGTCTG -s mr.mrrefChr0 60761 35 + 130230 TTATAATTAACTCAGTATTCAACAATGGAGGTCCC -s simCow_chr6.simCow.chr6 68375 32 + 602619 TCCAAATTACCTCAGCA---GTCAAAGGAAGGCTG -s simDog_chr6.simDog.chr6 64232 35 + 593897 GTCCCATCACCTCAGCATAGGTCAAGAAAGGTCTG -s simHuman_chr6.simHuman.chr6 61689 35 + 601863 TCCTAATTAGCTCAGCATTGATCAAAAAAGGTCTC -s simRat_chr6.simRat.chr6 56512 29 + 647215 ------TTAACTCAGTATTCGACAATGGAAGTCCC - -a -s simMouse_chr6.simMouse.chr6 63598 25 + 636262 TCCCCTCCACCACCACCCGATGAAC -s Anc0.Anc0refChr4 10396 25 - 45765 TCCCCTTCCCCACCACTTGATGAAC -s Anc1.Anc1refChr2 41409 25 + 144309 TCCCCTTCCCCACCACTTGATGAAC -s Anc2.Anc2refChr4 7708 25 + 10050 CCCCCTTCCCCACCACTTGATGAAC -s mr.mrrefChr0 60796 25 + 130230 TCCCCTCCACCACCACTTGATGAAC -s simCow_chr6.simCow.chr6 68410 25 + 602619 CCCCTGTCCCCACCACTTGATGAAC -s simDog_chr6.simDog.chr6 64270 25 + 593897 CCTCCTTCCGCACCACTTGATGAGC -s simHuman_chr6.simHuman.chr6 61727 25 + 601863 TCCCCTTCCCCTCCCCTTGATGAAC -s simRat_chr6.simRat.chr6 56541 24 + 647215 TCCCC-CCACGACCACTTGATGAAC - -a -s simMouse_chr6.simMouse.chr6 63623 28 + 636262 TTTTGAGTTATTGTGGAGAATTTGTAGT -s Anc0.Anc0refChr4 10421 23 - 45765 C-----ATTGTGCTGAAAACTTTTCAGT -s Anc1.Anc1refChr2 41434 23 + 144309 C-----ATTGTGCTGAAAACTTTTCAGT -s Anc2.Anc2refChr4 7733 23 + 10050 C-----ATTGTGCTGAAAACTTTTCAGT -s mr.mrrefChr0 60821 28 + 130230 TTTTGAGTTATGGTGGAGAATTTTCAGT -s simCow_chr6.simCow.chr6 68440 23 + 602619 C-----ATTGTACTGTAAACTTCTCAGT -s simDog_chr6.simDog.chr6 64295 23 + 593897 T-----TTTGTGCCGAAAACTTTTCAGT -s simHuman_chr6.simHuman.chr6 61752 23 + 601863 C-----ATTTTGATGATAACTTTTCAGT -s simRat_chr6.simRat.chr6 56565 28 + 647215 TTTTGAGTTATGGTGGAGGATTTTCAGT - -a -s simMouse_chr6.simMouse.chr6 63651 3 + 636262 TGC -s Anc0.Anc0refChr4 10444 3 - 45765 TTC -s Anc1.Anc1refChr2 41457 3 + 144309 TTC -s Anc2.Anc2refChr4 7757 3 + 10050 TTT -s mr.mrrefChr0 60849 3 + 130230 TGC -s simCow_chr6.simCow.chr6 68464 1 + 602619 --T -s simDog_chr6.simDog.chr6 64323 3 + 593897 TTT -s simHuman_chr6.simHuman.chr6 61775 3 + 601863 TCC -s simRat_chr6.simRat.chr6 56593 3 + 647215 TGC - -a -s simMouse_chr6.simMouse.chr6 63654 28 + 636262 AGTTTCATTGTCAATTTAATGAATGAGT -s Anc0.Anc0refChr4 10448 28 - 45765 AATTTCAATGTCAATTTGATGAAAAAGT -s Anc1.Anc1refChr2 41461 28 + 144309 AATTTCAATGTCAATTTGATGAAAAAGT -s Anc2.Anc2refChr4 7761 28 + 10050 AATTTCAATGTCAATTTGATGAAAAAGT -s mr.mrrefChr0 60852 28 + 130230 AGTTTCATTGTCAATTTAATGAATGAGT -s simCow_chr6.simCow.chr6 68466 28 + 602619 AATTTCAGTATCAATCTAATAAAGAAGT -s simDog_chr6.simDog.chr6 64327 28 + 593897 AGTGTCAATGTCAATTTGATGAAAAAGA -s simHuman_chr6.simHuman.chr6 61779 28 + 601863 AATTTCAATGTCAGTTTGATGCAATAGT -s simRat_chr6.simRat.chr6 56596 28 + 647215 AGCTTCATTGTCAATCTAATGAATGACT - -a -s simMouse_chr6.simMouse.chr6 63682 17 + 636262 ACTCAGTTACAAGCGGG -s Anc0.Anc0refChr4 10476 17 - 45765 ACTCAATTAGAAGAAAA -s Anc1.Anc1refChr2 41489 17 + 144309 ACTCAATTAGAAGAAAA -s Anc2.Anc2refChr4 7789 17 + 10050 ACTCAATTAGAAAAAAA -s mr.mrrefChr0 60880 17 + 130230 ACTCAGTTACAAGCGAA -s simCow_chr6.simCow.chr6 68494 17 + 602619 ACTCAATTAGAAGAAAA -s simDog_chr6.simDog.chr6 64359 17 + 593897 AATTAATTAGAAAAAAA -s simHuman_chr6.simHuman.chr6 61807 17 + 601863 ACTCAATTAGAAGAAAA -s simRat_chr6.simRat.chr6 56624 17 + 647215 ACTCAGTTACAAGGGAA - -a -s simMouse_chr6.simMouse.chr6 63699 11 + 636262 TGATTTGGAAA -s Anc0.Anc0refChr4 10493 11 - 45765 TGATTAAGAAA -s Anc1.Anc1refChr2 41506 11 + 144309 TGATTAAGAAA -s Anc2.Anc2refChr4 7806 11 + 10050 TGATTAAGAAA -s mr.mrrefChr0 60897 11 + 130230 TGATTTGGAAA -s simCow_chr6.simCow.chr6 68511 11 + 602619 TGAGTAAGAAA -s simDog_chr6.simDog.chr6 64376 11 + 593897 TGATTAACAAA -s simHuman_chr6.simHuman.chr6 61826 11 + 601863 TGATTGAGAAA -s simRat_chr6.simRat.chr6 56641 11 + 647215 TGATTTGGAAA - -a -s simMouse_chr6.simMouse.chr6 63710 12 + 636262 AGCTATATCCTC -s Anc0.Anc0refChr4 10505 12 - 45765 AGCTATATCCTC -s Anc1.Anc1refChr2 41518 12 + 144309 AGCTATATCCTC -s Anc2.Anc2refChr4 7818 12 + 10050 AGCTATATCCTC -s mr.mrrefChr0 60908 12 + 130230 AGCTATATCCTC -s simCow_chr6.simCow.chr6 68523 12 + 602619 AGCCACATCTTC -s simDog_chr6.simDog.chr6 64388 12 + 593897 AGCTATATCCGC -s simHuman_chr6.simHuman.chr6 61838 12 + 601863 AGCTATATCCTC -s simRat_chr6.simRat.chr6 56652 12 + 647215 AGCTACATTCTC - -a -s simMouse_chr6.simMouse.chr6 63722 79 + 636262 AAACAGATGATTTGAGAATTGCTGACCTTATCCTTTCCTGTTGGCTATCATTATGACTTTGTTTGAAAGCCTATCATGA -s Anc0.Anc0refChr4 10517 79 - 45765 AAAAGGGTGAATCAAGAATTGATGAAACTATTTTTACCTGTTGACTATGATCATGGCTTTCTTTAAAAGTATATCATGA -s Anc1.Anc1refChr2 41530 79 + 144309 AAAAGGGTGAATCAAGAATTGATGAAACTATTTTTACCTGTTGACTATGATCATGGCTTTCTTTAAAAGTATATCATGA -s Anc2.Anc2refChr4 7830 79 + 10050 AAAAGGGTGAATCAAGAATTGAGGAAACTATTTTTACCTGTGGATAATGATCATGGCTTCCTTTAAAAGTATATCATGT -s mr.mrrefChr0 60920 79 + 130230 AAACGGATGATTTGAGAATTGCTGACCTTATCTTTACCTGTTGGCTATGATTATGACTTTGTTTGAAAGCCTATCATGA -s simCow_chr6.simCow.chr6 68535 79 + 602619 AAAAGGGTGAATCACGAATTGCAGAAACTATGTCTACCAGTGGATAATGACCATGGCTTCCTTTGAAAGTTTATCATGT -s simDog_chr6.simDog.chr6 64407 73 + 593897 AAAAGGGTGTATAAAGAATTTAGGAAATTATTTTCTCATG------ATGCTCATGGGTACCTTTAAAAGCATATCATGT -s simHuman_chr6.simHuman.chr6 61850 79 + 601863 AAAGGGGTGAATCAAGAATTGATGGAACTATATTTACCCGTTGACTATGATCATAGCTTTTTTTAGAAGTGTATCATGA -s simRat_chr6.simRat.chr6 56664 79 + 647215 AAATGGATGATTTGAGAATTGCTAAGCTTGTTTTTACCTCCTGGCTATGATTATGATTTTGTTTGAAAGCCTATCATGG - -a -s simMouse_chr6.simMouse.chr6 63801 140 + 636262 TAGTGCTCACTAGGCTTGTATCAAGCATTGATGTTGTGTAGGTTTAATTAAATTCAGTAGCTGTGTATGAAAGCCAAACATGCTAGAGCTTGCTAGGCTCATATCAAAAATGGATGTGTTACAGGCTTAATTAAATTCAC -s Anc0.Anc0refChr4 10596 34 - 45765 TAGAGCTCACTAGGCTCATGTCAAGCATTGA----------------------------------------------------------------------------------------------------------CAG -s Anc1.Anc1refChr2 41609 34 + 144309 TAGAGCTCACTAGGCTCATGTCAAGCATTGA----------------------------------------------------------------------------------------------------------CAG -s Anc2.Anc2refChr4 7909 34 + 10050 TAGAGCTCACTAGGCTCATGTCAAGCATTGA----------------------------------------------------------------------------------------------------------TGG -s mr.mrrefChr0 60999 140 + 130230 TAGTGCTCACTAGGCTCATATCAAGCATTGATGTTGTGTAGATTTAATTAAATTCAGTAGCTGTGTATGAAAGCCTAACATGCTAGAGCTTCCCAGGCTCATATCAAAGATGGATGTATTACAGGCTTAAATAAATTCAG -s simCow_chr6.simCow.chr6 68614 34 + 602619 GAGAGCTCACTAGGCTCGTGTCAGGTGTTGT----------------------------------------------------------------------------------------------------------TGG -s simDog_chr6.simDog.chr6 64480 34 + 593897 TAGAGCTGACTAGGCTCATACCAAGCATTGA----------------------------------------------------------------------------------------------------------TGG -s simHuman_chr6.simHuman.chr6 61936 34 + 601863 TAGAAGTCACAAGGCTCATGTCAAGCATTGA----------------------------------------------------------------------------------------------------------CAG -s simRat_chr6.simRat.chr6 56743 140 + 647215 TAGTGCTCACCAGGCTCATATCAAGCATTGATGTTTTATAGAGTTAATGAAATTCAGCAGCTATGTATGAAAGCCTACCATGCTGGACCTTCCCAGGCTCATATCAAGGATTGATGCATTACAGGCTTAAATAAACTAAG - -a -s simMouse_chr6.simMouse.chr6 63941 16 + 636262 TACTGGGAGGGAAGGA -s Anc0.Anc0refChr4 10674 16 - 45765 TAATGGTGGAGGAGGG -s Anc1.Anc1refChr2 41687 16 + 144309 TAATGGTGGAGGAGGG -s Anc2.Anc2refChr4 7987 16 + 10050 TAATGGTGGAGGAGCG -s mr.mrrefChr0 61139 16 + 130230 TACTGGGAGGGAAGGA -s simCow_chr6.simCow.chr6 68693 16 + 602619 TAACAGGTGAGAAGTG -s simDog_chr6.simDog.chr6 64556 16 + 593897 TAATGGTGGAGGAGCG -s simHuman_chr6.simHuman.chr6 62025 16 + 601863 TAATGGTGGAAGAGGG -s simRat_chr6.simRat.chr6 56883 16 + 647215 TACTGGGAGGAAAGGA - -a -s simMouse_chr6.simMouse.chr6 63957 81 + 636262 AACCAGAAGAATCATTGTTAAATATTTGTGACCCCGACACCCCTCTAGAGCATTCTTAATGCTGGATACCATCCAGCTTAA -s Anc0.Anc0refChr4 10696 47 - 45765 GAACACAACGA--ATATACAATTGATTGTTCCATTG-------------GCCTTCCCAATTC------------------- -s Anc1.Anc1refChr2 41709 47 + 144309 GAACACAACGA--ATATACAATTGATTGTTCCATTG-------------GCCTTCCCAATTC------------------- -s Anc2.Anc2refChr4 8009 47 + 10050 GAACACAACGA--ATATACAATTGATTGTTCCATTG-------------GCCTTCCCAATTC------------------- -s mr.mrrefChr0 61155 81 + 130230 AACCAGAAGAATCATTGTTAAATATTTGTGACCCCGACACCCCTCTAGAGCATTCTTAATGCTGGATACCATCCAGCTTAA -s simCow_chr6.simCow.chr6 68714 47 + 602619 GAACACAACGA--ATATACAGTTGATTGTTCCAATG-------------CCCTTTCCAATTC------------------- -s simDog_chr6.simDog.chr6 64578 47 + 593897 GAACACAACAA--ATATTCAATTGATTGTACCATCG-------------GCCTTCCCAATTC------------------- -s simHuman_chr6.simHuman.chr6 62047 47 + 601863 GAGCACAAAGA--ATCTACAATTGACTACTCCAGTG-------------GCCTTCCCAGTTC------------------- -s simRat_chr6.simRat.chr6 56899 81 + 647215 AATCAGAATAAACATCGTTTAATCTTTGTGACCCTCACACTCCTCTGGACCATTCTTAATACTGGATACCATCCAGCTTAC - -a -s simMouse_chr6.simMouse.chr6 64038 22 + 636262 GATAATTACTTTAATACCTGTA -s Anc0.Anc0refChr4 10743 20 - 45765 GAAATTTATTT--ATGCCTGTA -s Anc1.Anc1refChr2 41756 20 + 144309 GAAATTTATTT--ATGCCTGTA -s Anc2.Anc2refChr4 8056 20 + 10050 TGAATTTATTT--AGGCCTGTA -s mr.mrrefChr0 61236 22 + 130230 GATAATTACTTTAATACCTGTA -s simCow_chr6.simCow.chr6 68761 18 + 602619 TGAATTTATTT--AGCCCTG-- -s simDog_chr6.simDog.chr6 64625 20 + 593897 TGAAGTTATTT--AGGCCTGTA -s simHuman_chr6.simHuman.chr6 62094 20 + 601863 GAAATTTATTT--ATGCCTGTA -s simRat_chr6.simRat.chr6 56984 22 + 647215 GATTGGGACACTAATACCTGTA - -a -s simMouse_chr6.simMouse.chr6 64060 138 + 636262 CAGGCTAGCTAGTCTATTGCAGTACCAAGATTGTAGGTCTTCAAAGCCACACTCAGGGCACAACTGTTCTTGCGAAAATCTAGAGTAAAGCTGTGAGGGTTGGGTTATATAATCCTTAAGTACCCGATAAGTCACATC -s Anc0.Anc0refChr4 10770 73 - 45765 CAAGCTTGCAAGTCTATTGCAGTAC-----------------------------------------------------------------ACATGAGGCTTAAATTATATGCCCCTTAAGTTCTTGAAAAGTCACATC -s Anc1.Anc1refChr2 41783 73 + 144309 CAAGCTTGCAAGTCTATTGCAGTAC-----------------------------------------------------------------ACATGAGGCTTAAATTATATGCCCCTTAAGTTCTTGAAAAGTCACATC -s Anc2.Anc2refChr4 8083 73 + 10050 CAAGCCTGCAAGTCTATTGCAATAC-----------------------------------------------------------------ACATGACGCTTAAATTATATGCCCCTTAAGTTCTTGAAAAGTCACATC -s mr.mrrefChr0 61258 73 + 130230 CAGGCTAGCTAGTCTATTGCAGTAC-----------------------------------------------------------------CTGTGAGGGTTGGGTTATATAATCCTTAAGTACCCGATAAGTCACATC -s simCow_chr6.simCow.chr6 68779 53 + 602619 --------------------AATAC-----------------------------------------------------------------ACATGATGTTTAAATTAAATGCCCCTTAAGTCCTTGGAAAGTCACATC -s simDog_chr6.simDog.chr6 64652 73 + 593897 CAAGCCTGCAAGTCTATTGCTATAC-----------------------------------------------------------------ACATGACGCTCAATTTGTATGCTGCTCAAGTTCTTGAAAAGTAACATC -s simHuman_chr6.simHuman.chr6 62121 72 + 601863 CAAGCTTGCAAGTCTACTGAAGTAC-----------------------------------------------------------------ACATGAGGCTTAAATTACATGCCCCTTAAGT-CTTGAAAAGGCACATC -s simRat_chr6.simRat.chr6 57006 73 + 647215 CAAGCTAGCTATTCTACTGCAGTAC-----------------------------------------------------------------TTGTGAGGGTTGGGTTGTATGGTCTTTAAGTTCCTGATAAGTCGCATC - -a -s simMouse_chr6.simMouse.chr6 64198 36 + 636262 CGTGATTACTCTAAACAGTCGGAATGATCAAGTCTT -s Anc0.Anc0refChr4 10845 36 - 45765 CCTGAGTATTTTGAACAGTTGGAATGATCAAGTCTA -s Anc1.Anc1refChr2 41858 36 + 144309 CCTGAGTATTTTGAACAGTTGGAATGATCAAGTCTA -s Anc2.Anc2refChr4 8158 36 + 10050 CCTGAGTGTGTTGAACAGTTGGAATAAACAAGTCTA -s mr.mrrefChr0 61331 36 + 130230 CGTGATTACTCTAAACAGTCGGAATGATCAAGTCTT -s simCow_chr6.simCow.chr6 68834 36 + 602619 CCTGGGTGTGTGGAACAGTTGGCATAAACAAGTGTA -s simDog_chr6.simDog.chr6 64728 35 + 593897 ACTGAGTGTGTTGAACAGTAGGAATAA-CAAGTCTA -s simHuman_chr6.simHuman.chr6 62195 36 + 601863 CTTGAGTATTTTGAACAGTTGGGATGATCAAGTCTA -s simRat_chr6.simRat.chr6 57079 36 + 647215 TGTGAGTACTTTACACAGTTGGAGTGATCACGTCTT - -a -s simMouse_chr6.simMouse.chr6 64234 26 + 636262 TATTTGACACATTAATCGCTTAAAAG -s Anc0.Anc0refChr4 10884 25 - 45765 TATA-GACAAAATAATTCCTTAAAAA -s Anc1.Anc1refChr2 41897 25 + 144309 TATA-GACAAAATAATTCCTTAAAAA -s Anc2.Anc2refChr4 8197 25 + 10050 TATA-GACAAAATAATTCCTTGATAA -s mr.mrrefChr0 61367 26 + 130230 TATTTGACACATTAATCGCTTAAAAG -s simCow_chr6.simCow.chr6 68873 24 + 602619 TATA-GAC-AAATAATTCCTTGAAAA -s simDog_chr6.simDog.chr6 64766 25 + 593897 TATA-GACAAAATAATTCCTTGATAA -s simHuman_chr6.simHuman.chr6 62234 25 + 601863 TATA-GACAAAATAATTCCTTAAAAA -s simRat_chr6.simRat.chr6 57115 26 + 647215 TATTTGACACATTAATTACTTGAAAG - -a -s simMouse_chr6.simMouse.chr6 64260 21 + 636262 GTCCATTCAAAATGAGTACAA -s Anc0.Anc0refChr4 10909 21 - 45765 GTCAACTCAAAATAAGTATAT -s Anc1.Anc1refChr2 41922 21 + 144309 GTCAACTCAAAATAAGTATAT -s Anc2.Anc2refChr4 8222 21 + 10050 GTCAACTCAAAATAAGTATGT -s mr.mrrefChr0 61393 21 + 130230 GTCCATTCAAAATGAGTACAA -s simCow_chr6.simCow.chr6 68897 17 + 602619 GTCAACTCA----AAGTCTGT -s simDog_chr6.simDog.chr6 64791 21 + 593897 GTCAGCTCAAAATAAGCATGT -s simHuman_chr6.simHuman.chr6 62263 21 + 601863 GTCAACTCAGAATAAGTATAT -s simRat_chr6.simRat.chr6 57141 21 + 647215 GTCCACTCAGAATAAGTGCAT - -a -s simMouse_chr6.simMouse.chr6 64281 159 + 636262 GATTTAGGCTCAGCCTATCACAAGAACCTCCTTGGCCCCCCATCCAGTCAGGAAGGGAACTATGTCAATTTATGCGGCATGTGAATGTCCACCGAGTCAGTTAGAGGTTTTTTGATATTCAGTGTGTAGAGGATAAACAGCAGTTATACGTTGAATGAG -s Anc0.Anc0refChr4 10930 28 - 45765 GATCAAAG--------------------------------------------------------------------------------------------GTAGAGGATATT------------------------------------AGT---CTCAG -s Anc1.Anc1refChr2 41943 28 + 144309 GATCAAAG--------------------------------------------------------------------------------------------GTAGAGGATATT------------------------------------AGT---CTCAG -s Anc2.Anc2refChr4 8245 28 + 10050 GATCAAAG--------------------------------------------------------------------------------------------GTGGAGGATAGT------------------------------------AGT---CTCAG -s mr.mrrefChr0 61414 64 + 130230 GATTTAGG--------------------------------------------------------------------------------------------TTAGAGGTTTTTTGATATTCAGTGTGTAGAGGATAAACAGCAGTTATACGT---ATGAG -s simCow_chr6.simCow.chr6 68916 28 + 602619 GATAAAAG--------------------------------------------------------------------------------------------GTGGTGGATGGT------------------------------------GGT---CGCAG -s simDog_chr6.simDog.chr6 64814 28 + 593897 AATCAAAG--------------------------------------------------------------------------------------------GTGGAGGATAGT------------------------------------AGT---CTCAG -s simHuman_chr6.simHuman.chr6 62284 28 + 601863 GATCAGAG--------------------------------------------------------------------------------------------GCAGAGGATCTC------------------------------------AGT---CTCAG -s simRat_chr6.simRat.chr6 57162 64 + 647215 GATTTAGG--------------------------------------------------------------------------------------------TTAGAGGTTTGTTAATAAACAGTGTGTAGAGGATAAACAGTAATTATAAAT---ATGAG - -a -s simMouse_chr6.simMouse.chr6 64440 26 + 636262 ATTTGAGTGAGATTGGCTGATAGTAT -s Anc0.Anc0refChr4 10958 22 - 45765 GTTGGAGG----TGAGTTAATAGCAT -s Anc1.Anc1refChr2 41971 22 + 144309 GTTGGAGG----TGAGTTAATAGCAT -s Anc2.Anc2refChr4 8273 22 + 10050 GTTGGAGG----TGAGTTAATTGCAT -s mr.mrrefChr0 61478 22 + 130230 ATTTGAGT----TTGGCTGATAGTAT -s simCow_chr6.simCow.chr6 68944 22 + 602619 GTAGAAGG----TGAGTTAATGGCAT -s simDog_chr6.simDog.chr6 64842 22 + 593897 GATGGAGG----TGAGTTAATTGCAC -s simHuman_chr6.simHuman.chr6 62312 22 + 601863 GTTAGAGG----TGAGTTAATAACAT -s simMouse_chr6.simMouse.chr6 64726 22 + 636262 ATTTGAGT----TTGGCTGATAGTAT -s simRat_chr6.simRat.chr6 57226 22 + 647215 ATTTGAGT----TTGGCTGATAGCAT - -a -s simMouse_chr6.simMouse.chr6 64466 1 + 636262 G -s Anc0.Anc0refChr4 10980 1 - 45765 G -s Anc1.Anc1refChr2 41993 1 + 144309 G -s Anc2.Anc2refChr4 8295 1 + 10050 A -s mr.mrrefChr0 61500 1 + 130230 G -s simCow_chr6.simCow.chr6 68966 1 + 602619 A -s simDog_chr6.simDog.chr6 64864 1 + 593897 A -s simHuman_chr6.simHuman.chr6 62334 1 + 601863 G -s simMouse_chr6.simMouse.chr6 64748 1 + 636262 G -s simRat_chr6.simRat.chr6 57250 1 + 647215 G - -a -s simMouse_chr6.simMouse.chr6 64467 1 + 636262 T -s Anc0.Anc0refChr4 10983 1 - 45765 T -s Anc1.Anc1refChr2 41996 1 + 144309 T -s Anc2.Anc2refChr4 8298 1 + 10050 T -s mr.mrrefChr0 61501 1 + 130230 T -s simCow_chr6.simCow.chr6 68969 1 + 602619 T -s simDog_chr6.simDog.chr6 64867 1 + 593897 C -s simHuman_chr6.simHuman.chr6 62337 1 + 601863 T -s simMouse_chr6.simMouse.chr6 64749 1 + 636262 T -s simRat_chr6.simRat.chr6 57251 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 64468 8 + 636262 AAATCAAA -s Anc0.Anc0refChr4 10984 8 - 45765 GTATCCAG -s Anc1.Anc1refChr2 41997 8 + 144309 GTATCCAG -s Anc2.Anc2refChr4 8299 8 + 10050 GTATTCTG -s mr.mrrefChr0 61502 8 + 130230 AAATCAAA -s simCow_chr6.simCow.chr6 68999 8 + 602619 GCATTCTG -s simDog_chr6.simDog.chr6 64868 3 + 593897 TTA----- -s simHuman_chr6.simHuman.chr6 62338 8 + 601863 GTATCCAG -s simMouse_chr6.simMouse.chr6 64750 8 + 636262 AAATCATA -s simRat_chr6.simRat.chr6 57252 8 + 647215 ATATCAAA - -a -s simMouse_chr6.simMouse.chr6 64476 92 + 636262 GGAGGGACCTTGCAGATGCAATGGTATGTTGAGGGTAGACAATAATTGTATATTTAACATTTTAATCCAAGGTAGCGGGTTTTTGGGAGACA -s Anc0.Anc0refChr4 10993 87 - 45765 GGAGCG----TGCAGACACA-TTGTATGTAGAGGATACACAAAAATTATACAATTAAAACTTTAAGCCATGGTAGGAAGGTCTTGAGGGACA -s Anc1.Anc1refChr2 42006 87 + 144309 GGAGCG----TGCAGACACA-TTGTATGTAGAGGATACACAAAAATTATACAATTAAAACTTTAAGCCATGGTAGGAAGGTCTTGAGGGACA -s Anc2.Anc2refChr4 8308 87 + 10050 GGAGCA----TGTAGACACA-TTGTATGTAGAGGATACACAAAAATTATACAACTAAAACTTTAAGCCATGGTAGGAAGGTCTTAAGGGACA -s mr.mrrefChr0 61511 92 + 130230 GGAGGGACCTTGCAGACACAATGGTATGTTGAGGGTAGACAATAATTGTATATTTAACATTTTAATCCAAGGTAGCAGGTTTTTGGGGGACA -s simCow_chr6.simCow.chr6 69008 87 + 602619 GGAGCA----TGTAGACACA-TTGTATGTAGATGATACACAAGAATTATACAACTAAAACTTTAAGACATGGTAGGTACATCTTCAGGGACA -s simDog_chr6.simDog.chr6 64871 74 + 593897 -----------------ACA-TTGCAAGTACAGGAATAAAATAAGCTACACAACTAAAAGTTTAAGCCATGGTAGGAAGGTCTTAAGGGATG -s simHuman_chr6.simHuman.chr6 62347 87 + 601863 GGGCAG----TGCAGACACA-TTATATGCAGAGGATACGCAAAAATTATACAATGAAGACTTTAAGCTATGGTAGGAAGGACTTGAGAGACA -s simMouse_chr6.simMouse.chr6 64759 92 + 636262 GGAGGGACCTTGCAGACACAATGGTATGTTGAGGGTAGACAATAATTGTATATCTAAAATTTTAATCCAAGGTAGCAGGTTTTTGGGGGACA -s simRat_chr6.simRat.chr6 57261 92 + 647215 GGAGGGACCTTGCGGACACAATGGTATGCCGAGGGTAAACAATAACTATATATTAAACATTTTAATCCAAGGTAGCAGGTTTTTGGGGGACA - -a -s simMouse_chr6.simMouse.chr6 64568 158 + 636262 GGAGTGTGGCAACCGTAAAGAGGTTATTTGCGGAGACATGCGTGTAAACAAAGGATGCACCGATGTTGAACGCACACAACCTGGCTCCTTATTATGATCAGTGACTATATGAAACTGAGTTGGGAGAGATTATGCTACTCAACTATACGTTGAATGAG -s Anc0.Anc0refChr4 11080 14 - 45765 GGAGTGAGGCATTT------------------------------------------------------------------------------------------------------------------------------------------------ -s Anc1.Anc1refChr2 42093 14 + 144309 GGAGTGAGGCATTT------------------------------------------------------------------------------------------------------------------------------------------------ -s Anc2.Anc2refChr4 8396 14 + 10050 GGAGTGAGGCATTT------------------------------------------------------------------------------------------------------------------------------------------------ -s mr.mrrefChr0 61603 112 + 130230 GGAGTGTGGCAATCGTAAAGAGGTTATTTGCGGAGACCTTCGTGTAACCAAAGGATGCACC----------------------------------------------TTTGAAACTGAGTTGGGAGAGATTATGCTACTCAACTAGAAGGGCTACAAG -s simCow_chr6.simCow.chr6 69096 14 + 602619 GGAGCGAGGTAATC------------------------------------------------------------------------------------------------------------------------------------------------ -s simDog_chr6.simDog.chr6 64946 14 + 593897 GGAGTTGGGCATTT------------------------------------------------------------------------------------------------------------------------------------------------ -s simHuman_chr6.simHuman.chr6 62434 14 + 601863 GGAATGAGGCATTA------------------------------------------------------------------------------------------------------------------------------------------------ -s simMouse_chr6.simMouse.chr6 64851 112 + 636262 GGAGTGTGGCAATCGTAAAGAGGTTATTTGCGGAGACCTTCGTGTAACCAAAGGATGCACC----------------------------------------------TTTGAAACTGGGTTGGGAGAGATTATGCCACTCAACTAGAAGGGCTACAAG -s simRat_chr6.simRat.chr6 57353 111 + 647215 -GAGTGTTACAATCATAAACAGGTTATTTGTGGAGACCTTTGTGTAACCAGAGGATGCACC----------------------------------------------TTTAAAACTGAGTTGGAAGAGTTTATGCTGCTCAACTAGATGGGCTACAAG - -a -s simMouse_chr6.simMouse.chr6 64758 1 + 636262 G -s Anc0.Anc0refChr4 10992 1 - 45765 T -s Anc1.Anc1refChr2 42005 1 + 144309 T -s Anc2.Anc2refChr4 8307 1 + 10050 T -s mr.mrrefChr0 61510 1 + 130230 G -s simCow_chr6.simCow.chr6 69007 1 + 602619 T -s simHuman_chr6.simHuman.chr6 62346 1 + 601863 A -s simRat_chr6.simRat.chr6 57260 1 + 647215 G - -a -s simMouse_chr6.simMouse.chr6 64963 15 + 636262 GTATTACCGCCCAAT -s Anc0.Anc0refChr4 11094 4 - 45765 -----------ATAT -s Anc1.Anc1refChr2 42107 4 + 144309 -----------ATAT -s Anc2.Anc2refChr4 8410 4 + 10050 -----------ATAT -s mr.mrrefChr0 61715 15 + 130230 GTATTACCGCCAAAT -s simCow_chr6.simCow.chr6 69110 4 + 602619 -----------ATAT -s simDog_chr6.simDog.chr6 64960 4 + 593897 -----------ATCT -s simHuman_chr6.simHuman.chr6 62448 4 + 601863 -----------ACAT -s simRat_chr6.simRat.chr6 57464 15 + 647215 TTATTGCCACTATAT - -a -s simMouse_chr6.simMouse.chr6 64978 24 + 636262 AAAATGGGAAGGGGTAGTCAATTT -s Anc0.Anc0refChr4 11098 18 - 45765 AAAATGGG------CAGCCCATTT -s Anc1.Anc1refChr2 42111 18 + 144309 AAAATGGG------CAGCCCATTT -s Anc2.Anc2refChr4 8419 18 + 10050 AAAATGGG------CAGCCCATTT -s mr.mrrefChr0 61730 18 + 130230 AAAATGGG------TAGCCAATTT -s simCow_chr6.simCow.chr6 69119 18 + 602619 AGAGTGGG------CAGACCGTTT -s simDog_chr6.simDog.chr6 64969 18 + 593897 AAAATGGG------AAGCTAATTT -s simHuman_chr6.simHuman.chr6 62452 18 + 601863 AAAATGGG------CCACCCATTT -s simRat_chr6.simRat.chr6 57479 18 + 647215 AAAACGGG------TAGCCTATTT - -a -s simMouse_chr6.simMouse.chr6 65002 133 + 636262 CTTATTGTACTGGGACCAAATAGCAGAAAGTTATTTAGACAACTTAAACTTTTGATGATGAATGCGCATTGTCTGTTATTTGTCATGATCAAGTTGTGTCTGGTACCTGACAATGAAGCCCCATCTCGTAAGA -s Anc0.Anc0refChr4 11116 94 - 45765 CTTGTTGCACTGG-ATCATGGATCACAA--ATACTTAGACAACTTAATCTTATGATGATGACCCTGCATTATCTGATATCTGACATGATAAAG-------------------------CC-----------GA -s Anc1.Anc1refChr2 42129 105 + 144309 CTTGTTGCACTGG-ATCATGGATCACAA--ATACTTAGACAACTTAATCTTATGATGATGACCCTGCATTATCTGATATCTGACATGATAAAG-------------------------CCCCATTGTGTGAGA -s Anc2.Anc2refChr4 8437 94 + 10050 CTTGTTGCACTGG-ATCATGGCTGACAG--ATACTTAGACAACTTAATCTTATGATGATGACCCTGGGTTACCTGATATCTGACATGATAAAG-------------------------CC-----------GC -s mr.mrrefChr0 61748 133 + 130230 CTTATTGCACTGGGACCAAATAGCAGAAAGTTATTTAGACAACTTAATCTTTTGATGATGAATGTGCATTGTCTGTTATTTGTCATGATCAAGTTGTGTCTGGTACCTGACAATGAAGCCCCATCTCGTAAGA -s simCow_chr6.simCow.chr6 69137 94 + 602619 TGTGTTGCACTGG-GTCATAGCTGATAG--ATACTAAGACACCTTAATCTTATCATGATGACTCTGGGTTACCTGATATCTGACAGGATGAAG-------------------------TC-----------GC -s simDog_chr6.simDog.chr6 64988 86 + 593897 CTTATTGCACTGG-ATTGTGCCTGACAG--CTACTTTGACAACTTAGTCATATGATGATGACCCT--------TGATATCTGACATGACAAAG-------------------------CA-----------GC -s simHuman_chr6.simHuman.chr6 62470 105 + 601863 CTTGGTGCATTGG-ATCATGGATCAAAA--ATACTTAGGCAACTTAATCTTATGGTGATGACCCTGCATTATCTGAGATCTGACATGCTAAAG-------------------------CCCCATTGTGTGAGA -s simRat_chr6.simRat.chr6 57497 133 + 647215 CTTATTGCACCGGGACTAAACAGTGGAAAGTTATTTAGATAACTTAATCATGTGATGATGAGTGTGCATTGTCTGTTATTTGTCATGGTCAAGTTGTGTCTGGTACATGACAGTGAAGTCTCCTGTAGTAAGA - -a -s simMouse_chr6.simMouse.chr6 65135 60 + 636262 TATGTGCCTGATGATGGGGCAGAATCTGTGCTGTGACCCCCTGATAAGTATTCCTTCCCT -s Anc0.Anc0refChr4 11210 60 - 45765 TGTGTGGCTGACTCTGAGGCAAAATCAGTGATGTTGTCCCCTGATAATTATCCCTTTTCT -s Anc1.Anc1refChr2 42234 60 + 144309 TGTGTGGCTGACTCTGAGGCAAAATCAGTGATGTTGTCCCCTGATAATTATCCCTTTTCT -s Anc2.Anc2refChr4 8531 60 + 10050 TGTGTGGCTGACTCTGAGGCAAAATCAGTGATGTTGTCCCTTGATAATTACCACTTTTCT -s mr.mrrefChr0 61881 60 + 130230 TATGTGGCTGACGATGGGGCAGAATCTGTGCTGTGACCCCCTGATAAGTATTCCTTTCCT -s simCow_chr6.simCow.chr6 69237 60 + 602619 TGTGGGGCTGACTCTGAGGCGAAATCAGTGATGTTGGTCTATGCTAATTACCACTTTGCT -s simDog_chr6.simDog.chr6 65074 53 + 593897 TGTTTATCTGACTCTGGGGTAAAACTAGTGAAGTTGTCCCTTGATA-------CTTTTCT -s simHuman_chr6.simHuman.chr6 62575 60 + 601863 TGTGTGGCTGACTCTGAGGCAAGATCAGTGGTGTTGTCCCCTGATAATTGTCCCACTACT -s simRat_chr6.simRat.chr6 57630 60 + 647215 TATGTGGCTGACAATGGGGCAGAATCTCTGATGTGACCCCTTGATAAATATTCCTTTGCT - -a -s simMouse_chr6.simMouse.chr6 65195 49 + 636262 AAACACCGAAAGAATCATTAAATTCTTGGCCTAATCTCACCTTATCGGA -s Anc0.Anc0refChr4 11272 39 - 45765 CAAGGTCAAAGAAATAACTAAATTTCTAGCCTAACCTCA---------- -s Anc1.Anc1refChr2 42296 39 + 144309 CAAGGTCAAAGAAATAACTAAATTTCTAGCCTAACCTCA---------- -s Anc2.Anc2refChr4 8593 39 + 10050 CAAGGTCAAAGAAACACCTGAATTTCTAGCCTAACCTCA---------- -s mr.mrrefChr0 61941 41 + 130230 AAACACCAAAAGAATCATTAAATTCTTAGCCTAATCTCACC-------- -s simCow_chr6.simCow.chr6 69299 39 + 602619 CACTGTCAAAGAAACACTTGAATTTCTACCCTAACCTAA---------- -s simDog_chr6.simDog.chr6 65129 39 + 593897 CAAGGCCAAACAAACACCTGATTTTCTAGCTTAACCTCA---------- -s simHuman_chr6.simHuman.chr6 62637 39 + 601863 CAAGGTCAAGGAAATAACTAGATCTCTATCCTAACTTCA---------- -s simRat_chr6.simRat.chr6 57690 41 + 647215 AAACACCAAAAGAATCATTAAATTCTTAGCCTAATCTCACC-------- - -a -s simMouse_chr6.simMouse.chr6 65244 5 + 636262 GTCAA -s Anc0.Anc0refChr4 11311 5 - 45765 GTCAA -s Anc1.Anc1refChr2 42335 5 + 144309 GTCAA -s Anc2.Anc2refChr4 8632 5 + 10050 GTTAA -s mr.mrrefChr0 61982 5 + 130230 GTCAA -s simCow_chr6.simCow.chr6 69338 5 + 602619 GTTAA -s simDog_chr6.simDog.chr6 65169 5 + 593897 GTTAG -s simHuman_chr6.simHuman.chr6 62676 5 + 601863 GTCAA -s simRat_chr6.simRat.chr6 57731 5 + 647215 GTCAA - -a -s simMouse_chr6.simMouse.chr6 65249 4 + 636262 GAAT -s Anc0.Anc0refChr4 11319 4 - 45765 GAAT -s Anc1.Anc1refChr2 42343 4 + 144309 GAAT -s Anc2.Anc2refChr4 8640 4 + 10050 GAAT -s mr.mrrefChr0 61987 4 + 130230 GAAT -s simCow_chr6.simCow.chr6 69346 4 + 602619 GGAT -s simDog_chr6.simDog.chr6 65177 4 + 593897 GAAT -s simHuman_chr6.simHuman.chr6 62684 4 + 601863 GAAT -s simRat_chr6.simRat.chr6 57736 4 + 647215 GAAT - -a -s simMouse_chr6.simMouse.chr6 65253 30 + 636262 CAATATAATTGCTCTAGGTCACTATGGTTC -s Anc0.Anc0refChr4 11327 30 - 45765 CATCGAAATTGCCCTAGACCAATTTGGATC -s Anc1.Anc1refChr2 42351 30 + 144309 CATCGAAATTGCCCTAGACCAATTTGGATC -s Anc2.Anc2refChr4 8648 30 + 10050 CATCGAAATTGCCCTAGACCAATTTCGATC -s mr.mrrefChr0 61991 30 + 130230 CAATATAATTGCTCTAGGTCAATATGGTTC -s simCow_chr6.simCow.chr6 69354 25 + 602619 CGTTGGAATTGGCCTAGACCACTCT----- -s simDog_chr6.simDog.chr6 65185 30 + 593897 CATCAAGACTGCCCCAGAACAATTTCGATC -s simHuman_chr6.simHuman.chr6 62692 30 + 601863 CATAGAAATTGCCCTAGACCAATTTGGATC -s simRat_chr6.simRat.chr6 57740 30 + 647215 CAATATAATTGCTCTAGGTCAATCTGGTTC - -a -s simMouse_chr6.simMouse.chr6 65283 95 + 636262 GAGGTGCCGTGTTGATTTGATATAATTGCTCTAGGTCAATATGGTTCATGCTGCCATGCTGGGTCTGGCATTAATGGTTTAACTTGTGTCAAATG -s Anc0.Anc0refChr4 11357 73 - 45765 TTCTTGCAGT------------TAGTTCCTC------ACTGAG--TCCAGTTGA-ATG-TGGATTAGGTGTTAATGGTTTAACTTGTGTCCAATA -s Anc1.Anc1refChr2 42381 76 + 144309 TTCTTGCAGT------------TAGTTCCTC------ACTGAG-TTCCAGTTGACATGCTGGATTAGGTGTTAATGGTTTAACTTGTGTCCAATA -s Anc2.Anc2refChr4 8678 73 + 10050 TTCTTGCAGC------------TGGCTCCTC------ACTGAG--TCCAGTTGA-ATG-TGGATTAGGTGTTAATGGGTTAAGTTATATCCCACA -s mr.mrrefChr0 62021 94 + 130230 GTGGTGCCGTGTTGATTTGATATAATTGCTCTAGGTCAATATG-TTCATGCTGCCATGCTGGGTCTGGCGTTAATGGTTTAACTTGTGTCCAATG -s simCow_chr6.simCow.chr6 69379 71 + 602619 TTCTTGCATC------------TGGCTCGTC------ACTGAG--TCCAGCTGA-ATT-TGGACTAG--GTTAATGGGTTAAGTTATATCCCACA -s simDog_chr6.simDog.chr6 65219 59 + 593897 CTCTTGCAGC------------TGGCTCCTC------ACTGAG--TCTAGTTGA-GTG-TGAATTAGGTGTTAATGGGTTA-------------- -s simHuman_chr6.simHuman.chr6 62722 73 + 601863 TTCTTACAGT------------TAGTTCCTC------ACTGAG-TTCCAGTTGAC---CTGGATTAGGAGTCAGAGGTTCGACTTGTGTCCAATA -s simRat_chr6.simRat.chr6 57770 94 + 647215 GTGGTGCCAGGTTGAATCAGTATAATTGCTCTAGGTCAATATG-GTCATGGTGCCATGTTGGGTCTGGTGTTAACGATTTAACTTGGGTCCAATG - -a -s simMouse_chr6.simMouse.chr6 65378 44 + 636262 GCACTTCTGTACCATAGGTATCACAGCACACACTTGCTGCTAAG -s Anc0.Anc0refChr4 11434 39 - 45765 ACACTTTTGCATCATAGGAATGACAACAC----TTG-TGCTTAA -s Anc1.Anc1refChr2 42461 39 + 144309 ACACTTTTGCATCATAGGAATGACAACAC----TTG-TGCTTAA -s Anc2.Anc2refChr4 8755 39 + 10050 ACACTTTTGCATCAAAGGAATGACAACAC----TTG-TGTTTAA -s mr.mrrefChr0 62119 40 + 130230 ACACTTTTGTACCATAGGTATCACAGCAC----TTGCTGCTAAG -s simCow_chr6.simCow.chr6 69454 39 + 602619 ACACTTTTGCATGAAAGGAATGACAACAC----TTG-CATCTAA -s simDog_chr6.simDog.chr6 65279 38 + 593897 ACCCTTTTGCATCCAAGGAATGACAATAC----TTG-TG-TTAA -s simHuman_chr6.simHuman.chr6 62799 39 + 601863 ACACTTTTGAATCATAGTAATGACAACAC----TTG-TGCTTAA -s simRat_chr6.simRat.chr6 57868 40 + 647215 ACACTTTTGTACCAAAGGTATCACAGCAC----TTGCCTCTAAG - -a -s simMouse_chr6.simMouse.chr6 65422 100 + 636262 AGCTGCTGTGGTACTTATTTAGTTAATGATAGTGCCTGAGCTAGCAGAAAACCATGATATGGGCGGGAGCTCAGTAACTAGGTTGGGTAACTAATAACTA -s Anc0.Anc0refChr4 11473 7 - 45765 GGTCCCT--------------------------------------------------------------------------------------------- -s Anc1.Anc1refChr2 42500 7 + 144309 GGTCCCT--------------------------------------------------------------------------------------------- -s Anc2.Anc2refChr4 8799 7 + 10050 GGTCCAT--------------------------------------------------------------------------------------------- -s mr.mrrefChr0 62159 100 + 130230 AGCTGCTGTGGTACTTATTTAGTTAATGATAGTGCCTGAGCTAGCAGAAAACCATGATATGGGCGGGAGCTCAGTAACTAGGTTGGGTAACTAATAACTA -s simCow_chr6.simCow.chr6 69503 7 + 602619 GGTGCAC--------------------------------------------------------------------------------------------- -s simDog_chr6.simDog.chr6 65322 7 + 593897 GGTCCAT--------------------------------------------------------------------------------------------- -s simHuman_chr6.simHuman.chr6 62838 7 + 601863 GGTATCT--------------------------------------------------------------------------------------------- -s simRat_chr6.simRat.chr6 57908 100 + 647215 ACATGATGTAGAACTTATTTAGTTAATGATGGCGACTAAGCTAGCAGAAAGCCATGATATGGGAGGGAGCTCAGTAACTAGGTTGGATAACTAACAACTA - -a -s simMouse_chr6.simMouse.chr6 65522 153 + 636262 AATATTAACTACTTATCAAAATGAGTCCACTGAACCGTCACTGCCTATCCACCCACATGACTTGCCTCTCAATATGACTAGCCTTTACAATGAATAGACATGAAGGTTCAGTTTTCAAGCTAATCAGGGAGAGGATCCAGTTAAGTATGGACA -s Anc0.Anc0refChr4 11480 101 - 45765 AATACT----------------------------------------------------GAATTGCCTCTCAACAAGACAAGGCTTTCCAGTAAATAGGTATGAAGGTACAGTTCTCGAGCTAATCAGGGAAAAGATTCAATCAGGTATGGACA -s Anc1.Anc1refChr2 42507 101 + 144309 AATACT----------------------------------------------------GAATTGCCTCTCAACAAGACAAGGCTTTCCAGTAAATAGGTATGAAGGTACAGTTCTCGAGCTAATCAGGGAAAAGATTCAATCAGGTATGGACA -s Anc2.Anc2refChr4 8814 101 + 10050 AATACT----------------------------------------------------GAATTGTCTCTTGACAAGACAAGGCTTTCCAGTAAATAGGTGTGAAGGTACAGTTCTCGAGCTAATCAGGGAAAAGAATCAATCAGGTATGGACA -s mr.mrrefChr0 62259 101 + 130230 AATATT----------------------------------------------------GACTTGCCTCTCAATATGACAAGCCTTTACAGTGAATAGACATGAAGGTTCAGTTTTCAAGCTAATCAGGGAGAAGATCCAGTTAAGTATGGACA -s simCow_chr6.simCow.chr6 69518 96 + 602619 AATACT----------------------------------------------------GCATTGTCTCATG---AGATAA-GCTGTCCAGAAGATAGGTGCGAAGG-ACACCTTTCAAGTTAATCAGGGAAATGACTGAATCAGGTATTGACA -s simDog_chr6.simDog.chr6 65337 101 + 593897 AATACT----------------------------------------------------GAGTTGTCTCTTGACAATACAAGGCTTTCCAGTGAATAGGTGTTAAGATTCAGTTCTCGAGCTAATCAGGGAAAAGAATCAATCAGGTATGGACA -s simHuman_chr6.simHuman.chr6 62845 101 + 601863 AATACT----------------------------------------------------GAATTGCCTCTCAACAAGACAAGGCTTTCCAGTAAGTAGGTAAGAGGGTACTGTTCTCGAGCTAATCAGAGAAAATATTCAATCAGGTATGGACA -s simRat_chr6.simRat.chr6 58008 101 + 647215 AATATT----------------------------------------------------GAGTTGCCTCTCTATATGACAAACATTTACAGTGAATAAACATGAAGGTTCAGTTTTCAAGCTAAGCAGGGAGGAGATCCAGTTAAGTATGGACA - -a -s simMouse_chr6.simMouse.chr6 65675 33 + 636262 AGTCTTTAAATGATTACTAGTTCCCTACTGGTT -s Anc0.Anc0refChr4 11581 33 - 45765 AGCATTTAATTGATTACAAGTCCCCAATTTGTT -s Anc1.Anc1refChr2 42608 33 + 144309 AGCATTTAATTGATTACAAGTCCCCAATTTGTT -s Anc2.Anc2refChr4 8915 33 + 10050 AGCATTAAATTGATTACAAGTCCCCAACTTGAT -s mr.mrrefChr0 62360 33 + 130230 AGTCTTTAATTGATTACTAGTTCCCTATTGGTT -s simCow_chr6.simCow.chr6 69614 33 + 602619 GACATTAGATTGATTACAAGTCCCCAACTTGGT -s simDog_chr6.simDog.chr6 65438 33 + 593897 AGCATTAAATGGATTACAAGTCCCCAACTTGAT -s simHuman_chr6.simHuman.chr6 62948 33 + 601863 AGCATTTAATTGAGTAAAAGTCCCCAATTTGTT -s simRat_chr6.simRat.chr6 58109 33 + 647215 AGTTTACAATTGATTACTGGTTCCCTATTGGTT - -a -s simMouse_chr6.simMouse.chr6 65708 54 + 636262 CATTGTAGCTAAGCACTGACCGTCTGTACCTGCATATAGGCAATAGCTAAGCCA -s Anc0.Anc0refChr4 11623 29 - 45765 CACTTTGC-------------------------ATATGGGCAAAAGTGAAGCAG -s Anc1.Anc1refChr2 42650 29 + 144309 CACTTTGC-------------------------ATATGGGCAAAAGTGAAGCAG -s Anc2.Anc2refChr4 8957 29 + 10050 CACCTTGC-------------------------ATATGAGCAAAGGTGAAGTAG -s mr.mrrefChr0 62393 29 + 130230 CATTTTGG-------------------------ATATGGGCAATAGCTAAGCCA -s simCow_chr6.simCow.chr6 69656 29 + 602619 CACCTTGC-------------------------ATATGAGCAAAGGTGAAGTAG -s simHuman_chr6.simHuman.chr6 62995 29 + 601863 CACTTTGC-------------------------AGTTGGGGAAAAGTGAAGCAG -s simRat_chr6.simRat.chr6 58142 29 + 647215 CATTTTGG-------------------------ATATGGGCAATAACTGAGCCA - -a -s simMouse_chr6.simMouse.chr6 65762 8 + 636262 GTGAAGAG -s Anc0.Anc0refChr4 11655 8 - 45765 GTGAAGAA -s Anc1.Anc1refChr2 42682 8 + 144309 GTGAAGAA -s Anc2.Anc2refChr4 8989 8 + 10050 ATGATGAG -s mr.mrrefChr0 62422 8 + 130230 GTGAAGAA -s simCow_chr6.simCow.chr6 69688 8 + 602619 ATGATGAG -s simHuman_chr6.simHuman.chr6 63027 8 + 601863 GTGAAGAA -s simRat_chr6.simRat.chr6 58171 8 + 647215 GTGAAGAA - -a -s simMouse_chr6.simMouse.chr6 65770 4 + 636262 AGAT -s Anc0.Anc0refChr4 11669 4 - 45765 GGAT -s Anc1.Anc1refChr2 42696 4 + 144309 GGAT -s Anc2.Anc2refChr4 9003 4 + 10050 GGAT -s mr.mrrefChr0 62430 4 + 130230 AGAT -s simCow_chr6.simCow.chr6 69702 4 + 602619 GGAT -s simHuman_chr6.simHuman.chr6 63041 4 + 601863 GGAT -s simRat_chr6.simRat.chr6 58179 4 + 647215 AGAT - -a -s simMouse_chr6.simMouse.chr6 65774 29 + 636262 TCATCCAACAGCTAAGCATCATACTGTAA -s Anc0.Anc0refChr4 11687 22 - 45765 TAATGTAACAATCGAGTACCA-------A -s Anc1.Anc1refChr2 42714 22 + 144309 TAATGTAACAATCGAGTACCA-------A -s Anc2.Anc2refChr4 9021 22 + 10050 TACTGTAAACATCGAGTACCA-------A -s mr.mrrefChr0 62448 29 + 130230 TCATCTAACAGCTAAGTATCATACTGTAA -s simCow_chr6.simCow.chr6 69720 22 + 602619 TACTGTAAACATCGAGTACCA-------A -s simHuman_chr6.simHuman.chr6 63059 22 + 601863 TGATGTAACAATCGGGTACCA-------A -s simRat_chr6.simRat.chr6 58197 29 + 647215 TTATATAACAGCTTAGTATCATACTGTAG - -a -s simMouse_chr6.simMouse.chr6 65803 60 + 636262 TGCGTACCCCTTATGATTCCAAAACCATAACACAGCCTGTCCAAAGAGTCCCACAGAGAA -s Anc0.Anc0refChr4 11709 54 - 45765 T----ACCC--TATTGTTCCAAAAACATAAAacagcctgttaaaagaatgaatcagaaga -s Anc1.Anc1refChr2 42736 54 + 144309 T----ACCC--TATTGTTCCAAAAACATAAAACAGCCTGTTAAAAGAATGAATCAGAAGA -s Anc2.Anc2refChr4 9043 54 + 10050 T----ACCC--TAATGGTTCAAAGAAATGAAacagcctattaaaagaatgaatcagaaga -s mr.mrrefChr0 62477 56 + 130230 T----ACCCCTTATGATTCCAAAACCATAACACAGCCTGTTCAAAGAGTCACACAGAGAA -s simCow_chr6.simCow.chr6 69752 54 + 602619 T----ACCC--TAATGGTTCAAAGAAATGAAacagcctattaaaagaatgaatcagaaga -s simHuman_chr6.simHuman.chr6 63081 54 + 601863 T----ACCC--TGTAGTCCCAAAAACAAAAAACAGCCTGATAAAAGAATGATGCAAAATA -s simRat_chr6.simRat.chr6 58226 30 + 647215 T------------------------------ACAGCCTGTTCAAAGAGTCACACAGAGAA - -a -s simMouse_chr6.simMouse.chr6 65863 5 + 636262 GAACT -s Anc0.Anc0refChr4 11763 5 - 45765 caaca -s Anc1.Anc1refChr2 42790 5 + 144309 CAACA -s Anc2.Anc2refChr4 9097 5 + 10050 caaca -s mr.mrrefChr0 62533 5 + 130230 TAACT -s simCow_chr6.simCow.chr6 69807 5 + 602619 caaca -s simHuman_chr6.simHuman.chr6 63135 5 + 601863 CAATA -s simRat_chr6.simRat.chr6 58256 5 + 647215 TGACT - -a -s simMouse_chr6.simMouse.chr6 65868 9 + 636262 GTAGACATA -s Anc1.Anc1refChr2 42803 9 + 144309 GGAGAGCTC -s mr.mrrefChr0 62538 9 + 130230 GGAGACATA -s simHuman_chr6.simHuman.chr6 63148 9 + 601863 GGAGAGCTC -s simRat_chr6.simRat.chr6 58261 9 + 647215 GGAGACGTA - -a -s simMouse_chr6.simMouse.chr6 65877 57 + 636262 TTAAAGACTGAGCGCCAATTGACAATGGGGACATTCAGGACTACGTGCAAGCAATAG -s Anc0.Anc0refChr4 11783 57 - 45765 gtagagactatgggccaattgatagccagaacatgcaggactacatgctaacaatcc -s Anc1.Anc1refChr2 42819 57 + 144309 Gtagagactatgggccaattgatagccagaacatgcaggactacatgctaacaatcc -s Anc2.Anc2refChr4 9117 57 + 10050 gaagagcctatggaccaattgatagccagagcatgcaggaatacatgctaacaatcc -s mr.mrrefChr0 62547 57 + 130230 GTAAAGACTGAGCGCCAATTGACAATGGGGACATTCAGGACTACATGCAAGCAATAG -s simCow_chr6.simCow.chr6 69827 51 + 602619 gaagagcctatggaccaattgata-ccag-----tcaggaatacatgctaacaattc -s simDog_chr6.simDog.chr6 65473 40 + 593897 -----------------ATTCATTGCCAGAGCATgcaggaataaatactaacaatcc -s simHuman_chr6.simHuman.chr6 63175 57 + 601863 Gtagaaactaggggccaattgatagaaagaacatccaggcctgcatgctaataatcc -s simRat_chr6.simRat.chr6 58270 57 + 647215 GTAAATACTGAGCGCCAATTGACAATTGACACATTCAGGACTACATGCAAGCAATAG - -a -s simMouse_chr6.simMouse.chr6 65934 17 + 636262 AACAAGTTCGACGCAGA -s Anc0.Anc0refChr4 11842 17 - 45765 aatgagtttgacataga -s Anc1.Anc1refChr2 42878 17 + 144309 aatgagtttgacataga -s Anc2.Anc2refChr4 9176 17 + 10050 aatgagtttgacataga -s mr.mrrefChr0 62604 17 + 130230 AACAAGTTTGACGCAGA -s simCow_chr6.simCow.chr6 69880 17 + 602619 aataagtttgacataga -s simDog_chr6.simDog.chr6 65515 17 + 593897 aatgagtttgacataga -s simHuman_chr6.simHuman.chr6 63234 17 + 601863 aattagtttgacataga -s simRat_chr6.simRat.chr6 58327 17 + 647215 AACAAGTTTGGTGCAGA - -a -s simMouse_chr6.simMouse.chr6 65951 13 + 636262 ATTATTGCACTTT -s Anc0.Anc0refChr4 11864 13 - 45765 agtacttcaatgt -s Anc1.Anc1refChr2 42900 13 + 144309 agtacttcaatgt -s Anc2.Anc2refChr4 9198 13 + 10050 agtacttcaatgt -s mr.mrrefChr0 62621 13 + 130230 ATTATTGCACTGT -s simCow_chr6.simCow.chr6 69902 13 + 602619 agtatttccatgt -s simDog_chr6.simDog.chr6 65537 13 + 593897 ggtacctcagcgt -s simHuman_chr6.simHuman.chr6 63256 13 + 601863 agtaattcaatgt -s simRat_chr6.simRat.chr6 58344 13 + 647215 ATTATTGCACTGT - -a -s simMouse_chr6.simMouse.chr6 65964 48 + 636262 AGATTAATTTTTGATGGGATGATTTACAATATTATGCACCAATGGACA -s Anc0.Anc0refChr4 11881 47 - 45765 aggaaaatctatgagagtatgacttccaatctcata-gcaactggaca -s Anc1.Anc1refChr2 42917 47 + 144309 aggaaaatctatgagagtatgacttccaatctcata-gcaactggaca -s Anc2.Anc2refChr4 9215 47 + 10050 aggaaaacctatgtgagtatgacttccaatctcata-gtaactggata -s mr.mrrefChr0 62634 48 + 130230 AGGTTAATTTTTGATAGGATGATTTCCAATATTATGCACAAATGGACA -s simCow_chr6.simCow.chr6 69919 47 + 602619 aggaaaaattatggaagtatgacttccgatctcata-gtgaatggata -s simDog_chr6.simDog.chr6 65554 41 + 593897 aggaaaccccatgtggtt--gactgccaatctcata-gtaact----g -s simHuman_chr6.simHuman.chr6 63273 47 + 601863 gggacaatgtatgagagccaggcttccagtctcata-gcaagttggca -s simRat_chr6.simRat.chr6 58357 48 + 647215 AGGCTAATTTCTGAAAGGATGATTTCCAATATTATGCACAGATGGACA - -a -s simMouse_chr6.simMouse.chr6 66012 54 + 636262 CTGAAGCATATACTGCTCAAAGGGGAGCGTACGACCGAATACAACTAAATTTCT -s Anc0.Anc0refChr4 11932 47 - 45765 ctgaagtatattccccttagaggg-----tacaa--gaatacaacaatcattat -s Anc1.Anc1refChr2 42968 47 + 144309 ctgaagtatattccccttagaggg-----tacaa--gaatacaacaatcattat -s Anc2.Anc2refChr4 9266 47 + 10050 ttgaattatactgcccttagagag-----tacaa--gaatgcaacaatcattat -s mr.mrrefChr0 62682 52 + 130230 CTGAAGCATATACTGCTCAGAGGGGAGCGTAcga--gaatacaactaaatttct -s simDog_chr6.simDog.chr6 65600 47 + 593897 ttgaattatactgcccttagagag-----tacaa--gaatgcaacaatcattat -s simHuman_chr6.simHuman.chr6 63324 47 + 601863 ctgaagtatattcccctaagaggg-----tacaa--gaatataacaagggctat -s simRat_chr6.simRat.chr6 58405 31 + 647215 CTGAAGCATATACTGCTCAGAGGAGATCATA----------------------- - -a -s simMouse_chr6.simMouse.chr6 66066 3 + 636262 CTG -s Anc0.Anc0refChr4 11979 3 - 45765 ctg -s Anc1.Anc1refChr2 43015 3 + 144309 ctg -s Anc2.Anc2refChr4 9313 3 + 10050 ccg -s mr.mrrefChr0 62734 3 + 130230 ctg -s simCow_chr6.simCow.chr6 69968 1 + 602619 --g -s simDog_chr6.simDog.chr6 65651 3 + 593897 ccg -s simHuman_chr6.simHuman.chr6 63371 3 + 601863 ctg - -a -s simMouse_chr6.simMouse.chr6 66069 15 + 636262 TCATAAATCTAGTGC -s Anc0.Anc0refChr4 11989 14 - 45765 ccgttgatct-gtgc -s Anc1.Anc1refChr2 43025 14 + 144309 ccgttgatct-gtgc -s Anc2.Anc2refChr4 9344 14 + 10050 ctgttgatct-gtgc -s mr.mrrefChr0 62737 15 + 130230 tcataaaTCTAGTGC -s simCow_chr6.simCow.chr6 69997 14 + 602619 ttgccgatct-gtgc -s simDog_chr6.simDog.chr6 65682 14 + 593897 ctgttacttt-gtgc -s simHuman_chr6.simHuman.chr6 63381 14 + 601863 ccgttgatct-gtgc -s simRat_chr6.simRat.chr6 58436 8 + 647215 -------TCTACTGC - -a -s simMouse_chr6.simMouse.chr6 66084 43 + 636262 TCTTGTTTGTTTGTGCAATGCAACAAGAGGACAGTGATGAGTA -s Anc0.Anc0refChr4 12005 43 - 45765 tcatgtttgtctgtgcaatgcaacaagagaacggtgatgaaca -s Anc1.Anc1refChr2 43041 43 + 144309 tcatgtttgtctgtgcaatgcaacaagagaacggtgatgaaca -s Anc2.Anc2refChr4 9360 43 + 10050 tcatgttggcctgtttgatccaacggaagaacgtagatgaaca -s mr.mrrefChr0 62752 43 + 130230 TCTTGTTTGTCTGTGCAATGCAACAAGAGGACagTGATGAGTA -s simCow_chr6.simCow.chr6 70013 17 + 602619 tcat--------------------------atatagatgaagg -s simDog_chr6.simDog.chr6 65698 43 + 593897 tcttgttggcctgtttgatccaacggaagaacgtagatgagca -s simHuman_chr6.simHuman.chr6 63397 43 + 601863 tcatgtttgtccatgcaatgcaacaagagaccggtgatgaaca -s simRat_chr6.simRat.chr6 58444 41 + 647215 TCGCGTTGGTCTGGGCAATGCAACATGAGGAC--TGATGAGTA - -a -s simMouse_chr6.simMouse.chr6 66127 13 + 636262 ATTTTGATTAGAT -s Anc0.Anc0refChr4 12051 13 - 45765 tattcaatcagat -s Anc1.Anc1refChr2 43087 13 + 144309 tattcaatcagat -s Anc2.Anc2refChr4 9406 13 + 10050 gattcagtcagat -s mr.mrrefChr0 62795 13 + 130230 TTTTTGATTAGAT -s simCow_chr6.simCow.chr6 70033 10 + 602619 agttcactca--- -s simDog_chr6.simDog.chr6 65744 13 + 593897 gattcagttagat -s simHuman_chr6.simHuman.chr6 63443 13 + 601863 tattcaatcagat -s simRat_chr6.simRat.chr6 58485 13 + 647215 TTTCTGATTAGAT - -a -s simMouse_chr6.simMouse.chr6 66140 66 + 636262 AAGAACAGGTTCAAATATCCACCTTTTGCGGCTACATTGTGGTTTATCTAAGGATCCCTGATCCCT -s Anc0.Anc0refChr4 12065 59 - 45765 aagaacagtttaaactatccaccttttgtgattacatgatcatttacctggggaacctt------- -s Anc1.Anc1refChr2 43101 59 + 144309 aagaacagtttaaactatccaccttttgtgattacatgatcatttacctggggaacctt------- -s Anc2.Anc2refChr4 9420 59 + 10050 aagaacagtttaaactgtccacattttgtgattacatgatcatttacctggggaaccct------- -s mr.mrrefChr0 62809 59 + 130230 AAGAACAGgttcaaatATCCACCTTTTGCGGCTACATTATGGTTTATCTAAGGAACCTT------- -s simCow_chr6.simCow.chr6 70044 58 + 602619 tagatcaatttaaaatgtccacttttcgtgattacatgattatctacct-gggaaccct------- -s simDog_chr6.simDog.chr6 65758 59 + 593897 aaggacagtttaaactgtccacattttgcgattagatgatcatttatctgggtaaccct------- -s simHuman_chr6.simHuman.chr6 63457 59 + 601863 aagaaaacttttaattatccaccttttgtgattacaagatcttttacctggggaacctt------- -s simRat_chr6.simRat.chr6 58499 51 + 647215 AAGAACAA--------ATCCACCTTTTGCAGCTACATCATGGTTTATCTAAGGAACCTT------- - -a -s simMouse_chr6.simMouse.chr6 66206 5 + 636262 TTATG -s Anc0.Anc0refChr4 12124 5 - 45765 tggtg -s Anc1.Anc1refChr2 43160 5 + 144309 tggtg -s Anc2.Anc2refChr4 9480 5 + 10050 tggtg -s mr.mrrefChr0 62868 5 + 130230 TTATG -s simCow_chr6.simCow.chr6 70103 5 + 602619 tggtg -s simDog_chr6.simDog.chr6 65818 5 + 593897 tgatg -s simHuman_chr6.simHuman.chr6 63516 5 + 601863 tggtg -s simRat_chr6.simRat.chr6 58550 5 + 647215 TTATG - -a -s simMouse_chr6.simMouse.chr6 66211 63 + 636262 AGCACCTCCCCATACTGACTTGCTTTAAATGAAAGCATGTTAAGTAAGATCTCTGGCAACAAA -s Anc0.Anc0refChr4 12134 31 - 45765 -------------------------------aaagcaagttaagcaag-tctctggttataaa -s Anc1.Anc1refChr2 43170 50 + 144309 accacctactcatattga-------------aaagcaagttaagcaagctctctggttataaa -s Anc2.Anc2refChr4 9490 31 + 10050 -------------------------------aaagcaagttaagcaag-tctctggttataaa -s mr.mrrefChr0 62873 63 + 130230 AGCACCTACCCATACTGACTTGCTTTAAATGAaagcatgttaagtaaGATCTCTGGCTACAAA -s simCow_chr6.simCow.chr6 70113 31 + 602619 -------------------------------agaacaagtaacgcaag-cctctggtgacaaa -s simDog_chr6.simDog.chr6 65828 31 + 593897 -------------------------------aaagcaagttaagcaag-tttctggttataaa -s simHuman_chr6.simHuman.chr6 63528 50 + 601863 accacctactcatattga-------------aaagcaaactaaacaagctctgtgtttataaa -s simRat_chr6.simRat.chr6 58555 48 + 647215 AGCACCTAACCATCATGATTTGCTCCGAATGA---------------AGTCTCTGGCTACAAA - -a -s simMouse_chr6.simMouse.chr6 66274 25 + 636262 CAACATGCTGCAACCCAGCTACCTC -s Anc0.Anc0refChr4 12167 25 - 45765 caacatactgaaacccagatgcttc -s Anc1.Anc1refChr2 43222 25 + 144309 caacatactgaaacccagatgcttc -s Anc2.Anc2refChr4 9523 25 + 10050 caacatactgaaaccgcaatgcttc -s mr.mrrefChr0 62936 25 + 130230 CAACATGCTGCAACCCAGCTGCCTC -s simCow_chr6.simCow.chr6 70146 25 + 602619 caacatactgaaaccgcaatgcttc -s simDog_chr6.simDog.chr6 65861 2 + 593897 ca----------------------- -s simHuman_chr6.simHuman.chr6 63580 25 + 601863 caatatactcaaacccagatgtttt -s simRat_chr6.simRat.chr6 58603 25 + 647215 CAACATGCTGCAACCCAGCTGACTC - -a -s simMouse_chr6.simMouse.chr6 66299 37 + 636262 AAATCACTTTCAAGCACAAGTTCCAATCATAAAGTTA -s Anc0.Anc0refChr4 12229 37 - 45765 gaatcacattcaaccatcagttccaaacataaaatta -s Anc1.Anc1refChr2 43284 37 + 144309 gaatcacattcaaccatcagttccaaacataaaatta -s Anc2.Anc2refChr4 9585 37 + 10050 gaatgacattcaaccatcagttctgaacataaaatta -s mr.mrrefChr0 62961 37 + 130230 AAATCACTTTCAACCATCAGTTCCAATCATAAAGTTA -s simCow_chr6.simCow.chr6 70199 36 + 602619 gaattaca-tcaatcatcagttctgaacataaaagta -s simDog_chr6.simDog.chr6 65898 32 + 593897 ggatgacattcaactgtcagttctg-----acaatca -s simHuman_chr6.simHuman.chr6 63643 37 + 601863 gaatcacattggaccatcagttccaaacgtaaaattc -s simRat_chr6.simRat.chr6 58628 37 + 647215 CAATCACTTTCAGCCATCAGTTCCAATCATAAAGCTG - -a -s simMouse_chr6.simMouse.chr6 66336 5 + 636262 CTAGG -s Anc0.Anc0refChr4 12266 5 - 45765 ctagg -s Anc1.Anc1refChr2 43321 5 + 144309 ctagg -s Anc2.Anc2refChr4 9622 5 + 10050 ctagg -s mr.mrrefChr0 62998 5 + 130230 CTAGG -s simCow_chr6.simCow.chr6 70236 5 + 602619 ctagg -s simDog_chr6.simDog.chr6 65930 5 + 593897 ttagg -s simHuman_chr6.simHuman.chr6 63680 5 + 601863 ctagg -s simRat_chr6.simRat.chr6 58665 5 + 647215 CTAGG - -a -s simMouse_chr6.simMouse.chr6 66341 18 + 636262 ATATTACATACACTAGAT -s Anc0.Anc0refChr4 12277 18 - 45765 acatgacagacactagat -s Anc1.Anc1refChr2 43332 18 + 144309 acatgacagacactagat -s Anc2.Anc2refChr4 9633 18 + 10050 acatggcagacactaggt -s mr.mrrefChr0 63003 18 + 130230 ATATTACATACACTAGAT -s simCow_chr6.simCow.chr6 70247 18 + 602619 acacaactgacaccagct -s simDog_chr6.simDog.chr6 65941 18 + 593897 acatggcagacactaggc -s simHuman_chr6.simHuman.chr6 63691 13 + 601863 -----atagacactagat -s simRat_chr6.simRat.chr6 58670 18 + 647215 ATATGACATACACTAGAT - -a -s simMouse_chr6.simMouse.chr6 66359 2 + 636262 AC -s Anc0.Anc0refChr4 12295 2 - 45765 ac -s Anc1.Anc1refChr2 43350 2 + 144309 ac -s Anc2.Anc2refChr4 9651 2 + 10050 ac -s mr.mrrefChr0 63021 2 + 130230 AC -s simCow_chr6.simCow.chr6 70265 2 + 602619 ac -s simDog_chr6.simDog.chr6 65987 2 + 593897 aa -s simHuman_chr6.simHuman.chr6 63704 2 + 601863 ac -s simRat_chr6.simRat.chr6 58688 2 + 647215 AC - -a -s simMouse_chr6.simMouse.chr6 66361 5 + 636262 CCAAG -s Anc0.Anc0refChr8 14302 5 + 17196 CTGAC -s Anc1.Anc1refChr8 11474 5 + 57822 CTGAC -s Anc2.Anc2refChr10 1242 5 + 1800 CTGAC -s mr.mrrefChr5 151272 5 - 294540 TTCAC -s simCow_chr6.simCow.chr6 271001 5 + 602619 CTGAC -s simDog_chr6.simDog.chr6 333049 5 - 593897 CTGAC -s simHuman_chr6.simHuman.chr6 240894 5 + 601863 CTGAC -s simMouse_chr6.simMouse.chr6 343888 5 - 636262 TTCAC -s simRat_chr6.simRat.chr6 366120 5 - 647215 TTCAC - -a -s simMouse_chr6.simMouse.chr6 66366 16 + 636262 TGAGAGTAAACAAAGG -s Anc0.Anc0refChr8 14312 16 + 17196 TGGTTATGAATGGAGT -s Anc1.Anc1refChr8 11484 16 + 57822 TGGTTATGAATGGAGT -s Anc2.Anc2refChr10 1252 16 + 1800 TGGTTATGAATGGTGT -s mr.mrrefChr5 151277 16 - 294540 TGAAAGTAAACAAAGG -s simCow_chr6.simCow.chr6 271011 16 + 602619 TGGTTATAAACGGTAT -s simDog_chr6.simDog.chr6 333059 16 - 593897 TGACTATGGTTGGTGT -s simHuman_chr6.simHuman.chr6 240904 16 + 601863 TGGTTATGAATGGAGT -s simMouse_chr6.simMouse.chr6 343893 14 - 636262 --AAAGTAAACAAAGG -s simRat_chr6.simRat.chr6 366125 14 - 647215 --AAGGCAAATCAAGG - -a -s simMouse_chr6.simMouse.chr6 66382 97 + 636262 ATTATCTGTTATGCAATCCTATATTGGGTGTGCTGGAAACTACTGAGTAGGGATTTCTGAGATGAACAATTGTGCTTGTATTATGTGCAACACTTCA -s Anc0.Anc0refChr8 14425 96 + 17196 ACAATCTGTTGTGCAATTTCTTATTCCTTGCTACAGAAAATCCCAAGTGGGGGTTTTTAAGGTAAGAAATTGTAGTTCTACTATTTGCAACACTTC- -s Anc1.Anc1refChr8 11597 96 + 57822 ACAATCTGTTGTGCAATTTCTTATTCCTTGCTACAGAAAATCCCAAGTGGGGGTTTTTAAGGTAAGAAATTGTAGTTCTACTATTTGCAACACTTC- -s Anc2.Anc2refChr10 1375 96 + 1800 ACAATCTGTTGTGCAATTTCTTATTCCTTGCTACAGAAAATCCCAAGTGGGGGTTTTTAAGGTAAGAAATTGTAGTTCTACTATTTGCAACACTTC- -s mr.mrrefChr5 151293 97 - 294540 ATTATCTGTTATGCAATCCTATATTGGGTGTGCTGGAAACTACTGAGTAGGGATTTCTGAGATGAACAATTGTGCTTGTATTATGTGCAACACTTCA -s simCow_chr6.simCow.chr6 271125 96 + 602619 ATAGTCTCTTGTATGATTTTCTATTCATAGCTTCAGAAAATTCTGAGTGGGGATTTTAGAGATAAGAAATTGTATATCTTCTATTTACAGCGTGCC- -s simDog_chr6.simDog.chr6 333185 96 - 593897 CCAATCCGCTGTGCAGTTTCTTATTCCTTGCTACAGAAAATCCCAAGTGGGGGTTTTTAAGGTAAGAAATTGTAGTTCTACTATTTGCAACACTTC- -s simHuman_chr6.simHuman.chr6 241017 17 + 601863 ACAATCTGTTGTGCAAT-------------------------------------------------------------------------------- -s simMouse_chr6.simMouse.chr6 343907 97 - 636262 ATTATCTGTTATGCAATCCTATATTGGGTGTGCTGGAAACTACTGAGTAGGGATTTCTGAGATGAACAATTGTGCTTGTATTATGTGCAACACTTCA -s simRat_chr6.simRat.chr6 366139 82 - 647215 ATCGTCTGTTGCACAATTCTATATTGGGTATGCTGGAAACTACTGAGTAGGGGTTTCTGGAATA--TTG-------------ATTTGCAACACTTCA - -a -s simMouse_chr6.simMouse.chr6 66479 22 + 636262 GCAACAACCATACAGTTCAAGA -s Anc0.Anc0refChr8 14521 22 + 17196 TCAACAACCATGCTGGTCAATA -s Anc1.Anc1refChr8 11693 22 + 57822 TCAACAACCATGCTGGTCAATA -s Anc2.Anc2refChr10 1471 22 + 1800 TCAACAACCATGCTGGTCAATA -s mr.mrrefChr5 151390 22 - 294540 GCAACAACCATACAGTTCAAGA -s simCow_chr6.simCow.chr6 271222 22 + 602619 GCAACAGCTTTACAGGTCATTA -s simDog_chr6.simDog.chr6 333281 22 - 593897 TCAACAACCATGCTGGTCAATA -s simMouse_chr6.simMouse.chr6 344004 22 - 636262 GCAACAACCATACAGTTCAAGA -s simRat_chr6.simRat.chr6 366221 22 - 647215 GCAACAATTATGCAGTTCAAGA - -a -s simMouse_chr6.simMouse.chr6 66501 4 + 636262 GGAA -s Anc0.Anc0refChr8 14543 4 + 17196 GGAA -s Anc1.Anc1refChr8 11715 4 + 57822 GGAA -s Anc2.Anc2refChr10 1531 4 + 1800 GGAA -s mr.mrrefChr5 151412 4 - 294540 GGAA -s simCow_chr6.simCow.chr6 271283 4 + 602619 GAAA -s simDog_chr6.simDog.chr6 333341 4 - 593897 GGAA -s simMouse_chr6.simMouse.chr6 344026 4 - 636262 GGAA -s simRat_chr6.simRat.chr6 366243 4 - 647215 TGTG - -a -s simMouse_chr6.simMouse.chr6 66505 3 + 636262 TGC -s Anc0.Anc0refChr8 14547 3 + 17196 TGT -s Anc1.Anc1refChr8 11719 3 + 57822 TGT -s Anc2.Anc2refChr10 1544 3 + 1800 TGT -s mr.mrrefChr5 151416 3 - 294540 TGC -s simCow_chr6.simCow.chr6 271296 3 + 602619 CGT -s simDog_chr6.simDog.chr6 333354 3 - 593897 TGT -s simMouse_chr6.simMouse.chr6 344030 3 - 636262 TGC -s simRat_chr6.simRat.chr6 366247 3 - 647215 TGC - -a -s simMouse_chr6.simMouse.chr6 66508 120 + 636262 TGCCCCTCAGAATGATCATGATGTGGGATGAAACAGCCTCAGAACTCCTCTGCCTTAAGCACAATTCCCCCTGTGCAAGATGCCCACTTATCCCAGAAGAGTCCTAGGTGAGGAATGGGT -s Anc0.Anc0refChr8 14550 106 + 17196 TGCCCCCTGGGTAGATACTGATATACCAT------GTCTT---ACTGATATATCTATACAAT-ATTTCTCATGCGCAATATGCCCATTTGGCTCAGAAGAGTCCCAG----GTAAGGGGC -s Anc1.Anc1refChr8 11722 109 + 57822 TGCCCCCTGGGTAGATACTGATATACCAT------GTCTT---ACTGATATATCTATACAATAATTTCTCATGCGCAATATGCCCATTTGGCTCAGAAGAGTCCCAG--GAGTAAGGGGC -s Anc2.Anc2refChr10 1547 106 + 1800 TTCCCCCTGAGTACACACTGATATACCAT------GTCTT---CCTGAGATATCTATACAAT-ATCTCTCACACGCGATATCTCCATTTGGCTCAGGAGAGACCCAG----ATAAGGTGC -s mr.mrrefChr5 151419 120 - 294540 TGCCCCTCAGAATGATCATGATGTGGGATGAAACAGCCTCAGAACTCCTCTGCCTTAAGCACAATTCCCCCTGTGCAAGATGCCCACTTATCCCAGAAGAGTCCTAGGTGAGGAATGGGT -s simCow_chr6.simCow.chr6 271299 42 + 602619 ----------------------------T------GTCTT---CCTGAGTCATCTATACAAT-ATCTCCTAACCAC----------------------------------------TTGC -s simDog_chr6.simDog.chr6 333391 106 - 593897 TTCCCCCTGAGTACACACTGATATACCAT------GTCTC---CCTGAGATATCTATACAAT-ATCTCTCACATGCGATATCTCCATTTGGCTCAGGAGAGACCCAG----ATAAGGTGC -s simHuman_chr6.simHuman.chr6 241034 109 + 601863 TGCCCCCTGGGCAGATTTTGATATACAAT------GTCTT---ACTAATATATCTATACAATATTTTCTCATGCGCAACATGCCCATTTGGCACAGAAGAGTCCCAG--GAGTAAGGGGC -s simMouse_chr6.simMouse.chr6 344033 120 - 636262 TGCCCCTCAGAATGATCATGATGCGGGATGAAACAGCCTCAGAACTCCTCTGCCTTAAGCACAATTCCGCCTGTGCAAGATGCCCACTTATCCCAGAAGAGTCCTAGATGAGGAATGGGT -s simRat_chr6.simRat.chr6 366250 120 - 647215 TGCCTCTCAGGATGATCATGACATGGGATGAAACAGCCTCGGAAGTCCTCGGCCTTAGGCACAATACTCTTTGTGCAAGATGCCCACTTGTACCAGAGTAGCCCCAGGCGGGGAATGGGA - -a -s simMouse_chr6.simMouse.chr6 66628 68 + 636262 GATGCTATGGCCCCCTATAAAACGTTATTACATCAATGCAACTTATCCCCCAAGATGTGTTGAACATG -s Anc0.Anc0refChr8 14656 53 + 17196 AATGCCACGATTCCCTGTGAG--------ACATCAATACAATATATTCCACCAGA-------AGCATA -s Anc1.Anc1refChr8 11831 53 + 57822 AATGCCACGATTCCCTGTGAG--------ACATCAATACAATATATTCCACCAGA-------AGCATA -s Anc2.Anc2refChr10 1653 53 + 1800 AATGCCACGATTCCCTGTGAG--------ACATCAATACAATATATTACACCAGA-------AGTTTA -s mr.mrrefChr5 151539 68 - 294540 GATGCTATGGCCCCCTATAAAACGTTATTACATCAATGCAACTTATCCCCCAAGATGTGTTGAACATG -s simCow_chr6.simCow.chr6 271341 46 + 602619 AATGTCCTGATTTCCTGTTAG--------ACATCAATACAATATATCACA--------------GTGA -s simDog_chr6.simDog.chr6 333497 53 - 593897 AATGCTACAAGTCCCTGTGAG--------ACATCAATATACTATAGTACCCCAGA-------AGTTTT -s simHuman_chr6.simHuman.chr6 241144 52 + 601863 AATGCCAAGATTCCCTGTGAG--------ACATCAA-ACAATATATTCCACCAGA-------AGCATA -s simMouse_chr6.simMouse.chr6 344153 68 - 636262 GATGCCATGGCCCCCTATAAAACGTTATTACATCAATGCAACTTATCCCCCAAGATGTGTTGAACGTG -s simRat_chr6.simRat.chr6 366370 67 - 647215 GATGCTGTGGCCCCCTATAAAACATTATCACATCAATGCAATTTATCCTC-AAGATGTGTTGAACACG - -a -s simMouse_chr6.simMouse.chr6 66696 26 + 636262 CACTTTAAAGTTGGACATAACAATAT -s Anc0.Anc0refChr8 14717 25 + 17196 -ATTCAAAAGCTGCACATAACAGTGT -s Anc1.Anc1refChr8 11892 25 + 57822 -ATTCAAAAGCTGCACATAACAGTGT -s Anc2.Anc2refChr10 1714 25 + 1800 -ATTCATAAGCTGCACATAACAATAT -s mr.mrrefChr5 151629 26 - 294540 CACTTTAAAGTTGAACATAACAATAT -s simCow_chr6.simCow.chr6 271395 24 + 602619 -ATTC-TAAGCTGCACATAACAATAT -s simDog_chr6.simDog.chr6 333558 13 - 593897 -ATTCA--------ACACTACA---- -s simHuman_chr6.simHuman.chr6 241204 25 + 601863 -GTTCAAAAGCTTCACATAACAGTGT -s simMouse_chr6.simMouse.chr6 344221 26 - 636262 CACTTTAAAGTTAAACACAACAATAT -s simRat_chr6.simRat.chr6 366459 26 - 647215 CACTTGAAAGTTGAACATAAGAATAT - -a -s simMouse_chr6.simMouse.chr6 66722 20 + 636262 GAATATCAAATGCACATGCT -s Anc0.Anc0refChr8 14744 19 + 17196 GAATGTc-AATGGGCTCGCT -s Anc1.Anc1refChr8 11919 20 + 57822 GAATGTcAAATGGGCTCGCT -s Anc2.Anc2refChr10 1741 19 + 1800 GAATGTT-AGTGGGCTCATT -s mr.mrrefChr5 151655 20 - 294540 GAATATCAAATGCACATGCT -s simCow_chr6.simCow.chr6 271426 19 + 602619 AAATACT-AGTGAGCTTATT -s simDog_chr6.simDog.chr6 333573 19 - 593897 GAATGTT-AGTGGGATCATT -s simHuman_chr6.simHuman.chr6 241231 19 + 601863 GAATGT-AAATGGGCTCGCT -s simMouse_chr6.simMouse.chr6 344247 20 - 636262 GAATATCAAATGCACATGCT -s simRat_chr6.simRat.chr6 366485 20 - 647215 GAATATCAAATGCGTACGTT - -a -s simMouse_chr6.simMouse.chr6 66742 17 + 636262 TATTAATTATATTTGCA -s Anc0.Anc0refChr8 14763 10 + 17196 AATTT------TCTCC- -s Anc1.Anc1refChr8 11939 12 + 57822 AATTTa----aTCTCC- -s Anc2.Anc2refChr5 249 7 + 8386 aatct------tc---- -s Anc2.Anc2refChr10 1760 10 + 1800 AATTT------TCACC- -s mr.mrrefChr5 151675 17 - 294540 TATTAATTATATTTGCA -s simCow_chr6.simCow.chr6 271445 10 + 602619 AATTA------TCACC- -s simCow_chr6.simCow.chr6 271733 7 + 602619 GATTT------CA---- -s simDog_chr6.simDog.chr6 333592 10 - 593897 AATTT------TCACC- -s simDog_chr6.simDog.chr6 333913 7 - 593897 aatct------tc---- -s simHuman_chr6.simHuman.chr6 241250 10 + 601863 AATTT------TCTCC- -s simMouse_chr6.simMouse.chr6 344267 17 - 636262 CACTAATTATATCTGCA -s simRat_chr6.simRat.chr6 366505 17 - 647215 TGTTAATTATCTTTGCA - -a -s simMouse_chr6.simMouse.chr6 66759 7 + 636262 AACACAT -s Anc0.Anc0refChr8 14773 7 + 17196 AACACAT -s Anc1.Anc1refChr8 11951 7 + 57822 AACACAT -s Anc2.Anc2refChr5 256 7 + 8386 gacacac -s Anc2.Anc2refChr10 1770 7 + 1800 AATTCAT -s mr.mrrefChr5 151692 7 - 294540 AACACAT -s simCow_chr6.simCow.chr6 271455 7 + 602619 AATTCAT -s simCow_chr6.simCow.chr6 271740 7 + 602619 GATACCA -s simDog_chr6.simDog.chr6 333920 7 - 593897 gacacac -s simHuman_chr6.simHuman.chr6 241260 7 + 601863 AACACAT -s simMouse_chr6.simMouse.chr6 344284 7 - 636262 AACACAT -s simRat_chr6.simRat.chr6 366522 7 - 647215 AACACAT - -a -s simMouse_chr6.simMouse.chr6 66766 16 + 636262 CAATATCTGAGTCGAC -s Anc0.Anc0refChr8 14781 16 + 17196 CATTTTCTGACTGGAC -s Anc1.Anc1refChr8 11959 16 + 57822 CATTTTCTGACTGGAC -s Anc2.Anc2refChr5 264 4 + 8386 catt------------ -s Anc2.Anc2refChr10 1778 16 + 1800 CATTTTCTGGCTGGGC -s mr.mrrefChr5 151699 16 - 294540 CAATATCTGAGTGGAC -s simCow_chr6.simCow.chr6 271463 16 + 602619 TCTTATCTGGCTGGGT -s simCow_chr6.simCow.chr6 271748 4 + 602619 TGTT------------ -s simDog_chr6.simDog.chr6 333603 16 - 593897 CATTTTCTGGCTGGGC -s simDog_chr6.simDog.chr6 333928 4 - 593897 catt------------ -s simHuman_chr6.simHuman.chr6 241268 16 + 601863 CATTTTCTGACTGGAC -s simMouse_chr6.simMouse.chr6 344291 7 - 636262 CAATCTC--------- -s simRat_chr6.simRat.chr6 366529 16 - 647215 TATTATCTGAGTGGAC - -a -s simMouse_chr6.simMouse.chr6 66782 2 + 636262 TG -s Anc0.Anc0refChr8 14797 2 + 17196 TG -s Anc1.Anc1refChr8 11975 2 + 57822 TG -s Anc2.Anc2refChr5 268 2 + 8386 tg -s Anc2.Anc2refChr10 1794 2 + 1800 TG -s mr.mrrefChr5 151715 2 - 294540 TG -s simCow_chr6.simCow.chr6 271752 2 + 602619 TG -s simDog_chr6.simDog.chr6 333619 2 - 593897 TG -s simDog_chr6.simDog.chr6 333932 2 - 593897 tg -s simHuman_chr6.simHuman.chr6 241284 2 + 601863 TG -s simRat_chr6.simRat.chr6 366545 2 - 647215 TG - -a -s simMouse_chr6.simMouse.chr6 66784 4 + 636262 TAAT -s Anc0.Anc0refChr8 14799 4 + 17196 TAAA -s Anc1.Anc1refChr8 11977 4 + 57822 TAAA -s Anc2.Anc2refChr5 270 4 + 8386 tatt -s Anc2.Anc2refChr10 1796 4 + 1800 GAAA -s mr.mrrefChr5 151717 4 - 294540 TAAT -s simCow_chr6.simCow.chr6 271479 4 + 602619 GGAA -s simCow_chr6.simCow.chr6 271754 4 + 602619 AATC -s simDog_chr6.simDog.chr6 333621 4 - 593897 GAAA -s simDog_chr6.simDog.chr6 333934 4 - 593897 tatt -s simHuman_chr6.simHuman.chr6 241286 4 + 601863 TAAA -s simRat_chr6.simRat.chr6 366547 4 - 647215 CAAG - -a -s simMouse_chr6.simMouse.chr6 66788 9 + 636262 TCAGCTCAA -s Anc0.Anc0refChr8 14803 9 + 17196 CCAACACAA -s Anc1.Anc1refChr8 11981 9 + 57822 CCAACACAA -s Anc2.Anc2refChr5 274 9 + 8386 CCAACACTA -s mr.mrrefChr5 151721 9 - 294540 TCAGACCAA -s simDog_chr6.simDog.chr6 537878 9 - 593897 CCAACACTA -s simHuman_chr6.simHuman.chr6 241290 9 + 601863 CCAACACAG -s simMouse_chr6.simMouse.chr6 344298 1 - 636262 --------A -s simRat_chr6.simRat.chr6 366551 9 - 647215 TCAGACCAA - -a -s simMouse_chr6.simMouse.chr6 66797 4 + 636262 GACT -s Anc0.Anc0refChr8 14814 4 + 17196 AATT -s Anc1.Anc1refChr8 11992 4 + 57822 AATT -s Anc2.Anc2refChr5 285 4 + 8386 AATT -s mr.mrrefChr5 151730 4 - 294540 GACT -s simDog_chr6.simDog.chr6 537889 4 - 593897 AATT -s simHuman_chr6.simHuman.chr6 241301 4 + 601863 AGTT -s simMouse_chr6.simMouse.chr6 344299 4 - 636262 GACT -s simRat_chr6.simRat.chr6 366560 4 - 647215 GACT - -a -s simMouse_chr6.simMouse.chr6 66801 5 + 636262 AGTTA -s Anc0.Anc0refChr8 14827 5 + 17196 AGAAC -s Anc1.Anc1refChr8 12005 5 + 57822 AGAAC -s Anc2.Anc2refChr5 298 5 + 8386 AGAAC -s mr.mrrefChr5 151743 5 - 294540 AGGAC -s simDog_chr6.simDog.chr6 537903 5 - 593897 AGAAC -s simHuman_chr6.simHuman.chr6 241314 5 + 601863 AGAGC -s simMouse_chr6.simMouse.chr6 344311 5 - 636262 AGGAC -s simRat_chr6.simRat.chr6 366573 5 - 647215 ATGAC - -a -s simMouse_chr6.simMouse.chr6 66806 11 + 636262 GCTAATTGGAG -s Anc0.Anc0refChr4 12314 11 - 45765 agtaattggaa -s Anc1.Anc1refChr2 43369 11 + 144309 agtaattggaa -s Anc2.Anc2refChr4 9670 11 + 10050 agtaattggaa -s mr.mrrefChr0 63039 11 + 130230 GCTAATTGGAG -s simCow_chr6.simCow.chr6 70284 10 + 602619 agcgattgg-t -s simDog_chr6.simDog.chr6 66006 6 + 593897 agta-----aa -s simHuman_chr6.simHuman.chr6 63723 11 + 601863 attaattggaa -s simRat_chr6.simRat.chr6 58706 11 + 647215 GATAATTGGAG - -a -s simMouse_chr6.simMouse.chr6 66817 3 + 636262 ATT -s Anc0.Anc0refChr4 12331 2 - 45765 a-t -s Anc1.Anc1refChr2 43386 3 + 144309 att -s Anc2.Anc2refChr4 9687 2 + 10050 a-t -s mr.mrrefChr0 63056 3 + 130230 ATT -s simCow_chr6.simCow.chr6 70300 2 + 602619 a-t -s simDog_chr6.simDog.chr6 66018 2 + 593897 a-t -s simHuman_chr6.simHuman.chr6 63740 3 + 601863 atg -s simRat_chr6.simRat.chr6 58723 3 + 647215 ATT - -a -s simMouse_chr6.simMouse.chr6 66820 24 + 636262 TGTATTGCAACTAACAAGTAGCAC -s Anc0.Anc0refChr4 12333 24 - 45765 tgtactgaaatcaataaggggcac -s Anc1.Anc1refChr2 43389 24 + 144309 tgtactgaaatcaataaggggcac -s Anc2.Anc2refChr4 9689 24 + 10050 tgtactgaaatcaataaggggcac -s mr.mrrefChr0 63059 24 + 130230 TGTATTGCAACTAATAAGTAGCAC -s simCow_chr6.simCow.chr6 70303 24 + 602619 tgtactgaaggtaatgaagggcat -s simDog_chr6.simDog.chr6 66020 24 + 593897 tgtactgaaatcaagaaggagcac -s simHuman_chr6.simHuman.chr6 63743 19 + 601863 tgta-----atcaataaggggcac -s simRat_chr6.simRat.chr6 58726 24 + 647215 TTTATTGCAACTAATAAGTAGCAT - -a -s simMouse_chr6.simMouse.chr6 66844 34 + 636262 TCAATCTGAGTAAGACATATTATCTGTGGATTAT -s Anc0.Anc0refChr4 12357 19 - 45765 ttaaa---------------tatttgtgggttga -s Anc1.Anc1refChr2 43413 19 + 144309 ttaaa---------------tatttgtgggttga -s Anc2.Anc2refChr4 9723 19 + 10050 ttaaa---------------tgtttgtgggttga -s mr.mrrefChr0 63083 34 + 130230 TCAATCTGAGTAAGACATATTATCTGTGGATTAT -s simCow_chr6.simCow.chr6 70337 19 + 602619 ttaaa---------------tgtttgacggttga -s simDog_chr6.simDog.chr6 66059 19 + 593897 ttaaa---------------tgtttgtggcttga -s simHuman_chr6.simHuman.chr6 63762 19 + 601863 ttaaa---------------tatttgcgggttga -s simRat_chr6.simRat.chr6 58750 34 + 647215 CCAATCTGAGTCCGACACATTATCTGTGGATTAT - -a -s simMouse_chr6.simMouse.chr6 66878 8 + 636262 GGCCTCAG -s Anc0.Anc0refChr4 12378 7 - 45765 g-acttaa -s Anc1.Anc1refChr2 43434 8 + 144309 gaacttaa -s Anc2.Anc2refChr4 9744 7 + 10050 g-acttaa -s mr.mrrefChr0 63117 8 + 130230 GGCCTCAG -s simCow_chr6.simCow.chr6 70358 7 + 602619 g-aatcaa -s simDog_chr6.simDog.chr6 66080 7 + 593897 g-acttaa -s simHuman_chr6.simHuman.chr6 63783 8 + 601863 gaacttaa -s simRat_chr6.simRat.chr6 58784 8 + 647215 GGTCTCAG - -a -s simMouse_chr6.simMouse.chr6 66886 18 + 636262 TGTGTTAAGCTTGAACTC -s Anc0.Anc0refChr4 12385 18 - 45765 tgtgttaaaccagaaaat -s Anc1.Anc1refChr2 43442 18 + 144309 tgtgttaaaccagaaaat -s Anc2.Anc2refChr4 9751 18 + 10050 tgtgttaagacagaaaat -s mr.mrrefChr0 63125 18 + 130230 TGTGTTAAACTTGAACTC -s simCow_chr6.simCow.chr6 70365 18 + 602619 tgtgtcaagataaaaaat -s simDog_chr6.simDog.chr6 66087 16 + 593897 tgtgctaa--cggataat -s simHuman_chr6.simHuman.chr6 63791 18 + 601863 cgtgttaaaccagaaaat -s simRat_chr6.simRat.chr6 58795 18 + 647215 TGTGTTGAACTTGAATTC - -a -s simMouse_chr6.simMouse.chr6 66904 22 + 636262 ACTAGCTTCACTCAAAGGAGGA -s Anc0.Anc0refChr4 12403 22 - 45765 gttaatattactcaaaggaaga -s Anc1.Anc1refChr2 43460 22 + 144309 gttaatattactcaaaggaaga -s Anc2.Anc2refChr4 9769 22 + 10050 gttaatattactcaaaggaaga -s mr.mrrefChr0 63143 22 + 130230 ACTAGCTTTACTCAAAGGAAGA -s simCow_chr6.simCow.chr6 70383 21 + 602619 attaatattac-caaatgaaga -s simDog_chr6.simDog.chr6 66104 22 + 593897 gctaaaattactcaaaggaaga -s simHuman_chr6.simHuman.chr6 63809 22 + 601863 gttaatgttacggaaaggaaga -s simRat_chr6.simRat.chr6 58813 22 + 647215 ACTAGCTTTACTCAAGGGAAGA - -a -s simMouse_chr6.simMouse.chr6 66926 8 + 636262 TAGTCTAA -s Anc0.Anc0refChr4 12425 8 - 45765 taacaaaa -s Anc1.Anc1refChr2 43482 8 + 144309 taacaaaa -s Anc2.Anc2refChr4 9794 8 + 10050 taacaaaa -s mr.mrrefChr0 63165 8 + 130230 TAGTCAAA -s simCow_chr6.simCow.chr6 70407 8 + 602619 cagggaca -s simDog_chr6.simDog.chr6 66129 8 + 593897 taacaaaa -s simHuman_chr6.simHuman.chr6 63831 8 + 601863 taacaaaa -s simRat_chr6.simRat.chr6 58835 8 + 647215 TAGGCAAA - -a -s simMouse_chr6.simMouse.chr6 66934 1 + 636262 C -s Anc0.Anc0refChr4 12433 1 - 45765 c -s Anc1.Anc1refChr2 43490 1 + 144309 c -s Anc2.Anc2refChr4 9802 1 + 10050 c -s mr.mrrefChr0 63173 1 + 130230 C -s simCow_chr6.simCow.chr6 70426 1 + 602619 c -s simDog_chr6.simDog.chr6 66137 1 + 593897 c -s simHuman_chr6.simHuman.chr6 63839 1 + 601863 c -s simRat_chr6.simRat.chr6 58843 1 + 647215 C - -a -s simMouse_chr6.simMouse.chr6 66935 17 + 636262 AAGATCCTTACACCCCT -s Anc0.Anc0refChr4 12438 7 - 45765 aagacc----------t -s Anc1.Anc1refChr2 43495 7 + 144309 aagacc----------t -s Anc2.Anc2refChr4 9807 7 + 10050 aagacc----------c -s mr.mrrefChr0 63174 17 + 130230 AAGATCCTTACACCCCT -s simCow_chr6.simCow.chr6 70431 7 + 602619 aagacc----------c -s simDog_chr6.simDog.chr6 66142 7 + 593897 aagacc----------c -s simHuman_chr6.simHuman.chr6 63844 7 + 601863 aagacc----------t -s simRat_chr6.simRat.chr6 58844 17 + 647215 CAGATCCTTACACCCCT - -a -s simMouse_chr6.simMouse.chr6 66952 16 + 636262 CCCTTTCACTCTCTAC -s Anc0.Anc0refChr4 12445 16 - 45765 ccatggccccccttac -s Anc1.Anc1refChr2 43502 16 + 144309 ccatggcccCCCTTAC -s Anc2.Anc2refChr4 9814 16 + 10050 ccatggccctccttac -s mr.mrrefChr0 63191 16 + 130230 CCCTTTCACCCCCTAC -s simCow_chr6.simCow.chr6 70438 16 + 602619 ctatggccctcttgac -s simDog_chr6.simDog.chr6 66149 16 + 593897 tcaaggcccttcttac -s simHuman_chr6.simHuman.chr6 63851 16 + 601863 ccatggcccCCCATAC -s simRat_chr6.simRat.chr6 58876 16 + 647215 CCCTTCCATCCCCTAC - -a -s simMouse_chr6.simMouse.chr6 66968 59 + 636262 ATCATGGGTATGTACTAACCAGGAGATCTGAACCAAAGACAAGAGCTAAGGACCCAGGC -s Anc0.Anc0refChr4 12462 59 - 45765 ATTGTGGCATTATACTATCCAGGAGATCTGAACCATagACcagggcaatagaccagggc -s Anc1.Anc1refChr2 43519 59 + 144309 ATTGTGGCATTATACTATCCAGGAGATCTGAACCATAGACCAGGGCAatagaccagggc -s Anc2.Anc2refChr4 9831 59 + 10050 ATTGGGGCATTATACAATCCAGGGAATCTGAACCATagACcagggcaatagaccagggc -s mr.mrrefChr0 63207 59 + 130230 ATTATGGCTATGTACTAACCAGGAGATCTGAACCAAAGACAAGGGCAAAAGACCCGGGC -s simCow_chr6.simCow.chr6 70455 59 + 602619 ATTGGGGCATTATACAATCCAGGGAATCTGAACCATagaccgggacaacagaccagggt -s simDog_chr6.simDog.chr6 66166 36 + 593897 AATGGGGCATTGTAC-----------------------ACcagggcaatataccagggc -s simHuman_chr6.simHuman.chr6 63868 59 + 601863 ATTGTGGCATTACACTACCCAGGAGGTTTCAACCACAAACCAAGGCAatagaccaggac -s simRat_chr6.simRat.chr6 58892 56 + 647215 ATTATGGCTATGTAGTAACCAGGAGATCTGAACCCAGGAC---GGCATAAGACCTGGTC - -a -s simMouse_chr6.simMouse.chr6 67027 19 + 636262 CAATGAGTTCTCTGTACAA -s Anc0.Anc0refChr4 12521 19 - 45765 aaaagatggatctgtcaaa -s Anc1.Anc1refChr2 43578 19 + 144309 aaaagatggatctgtcaaa -s Anc2.Anc2refChr4 9891 19 + 10050 aaaaaatggatctgtcaaa -s mr.mrrefChr0 63266 19 + 130230 CAATGAGTTCTCTGTACAA -s simCow_chr6.simCow.chr6 70515 19 + 602619 aaagaatggacctgtcaca -s simDog_chr6.simDog.chr6 66203 19 + 593897 aaaaaatggatctgtcaaa -s simHuman_chr6.simHuman.chr6 63927 19 + 601863 aaaagatgaatttgtcaaa -s simRat_chr6.simRat.chr6 58948 19 + 647215 CAATGAGTTCTCCGTACAA - -a -s simMouse_chr6.simMouse.chr6 67046 10 + 636262 CATTACATAT -s Anc0.Anc0refChr4 12540 10 - 45765 gattatgtgt -s Anc1.Anc1refChr2 43597 10 + 144309 gattatgtgt -s Anc2.Anc2refChr4 9917 10 + 10050 gattatgtgt -s mr.mrrefChr0 63285 10 + 130230 CATTATGTGT -s simCow_chr6.simCow.chr6 70541 10 + 602619 gattatgtgt -s simDog_chr6.simDog.chr6 66229 10 + 593897 gattttgtga -s simHuman_chr6.simHuman.chr6 63946 10 + 601863 gataatgtgt -s simRat_chr6.simRat.chr6 58967 10 + 647215 CATTATGTGT - -a -s simMouse_chr6.simMouse.chr6 67056 4 + 636262 CCCT -s Anc0.Anc0refChr4 12553 4 - 45765 cctt -s Anc1.Anc1refChr2 43610 4 + 144309 cctt -s Anc2.Anc2refChr4 9930 4 + 10050 cctt -s mr.mrrefChr0 63295 4 + 130230 CCTT -s simCow_chr6.simCow.chr6 70554 4 + 602619 cctt -s simDog_chr6.simDog.chr6 66242 4 + 593897 cctt -s simHuman_chr6.simHuman.chr6 63959 4 + 601863 cctt -s simRat_chr6.simRat.chr6 58977 4 + 647215 CCTT - -a -s simMouse_chr6.simMouse.chr6 67060 21 + 636262 ACCTATCTATGTATCCCATTC -s Anc0.Anc0refChr4 12557 21 - 45765 acctttctatgtattccatct -s Anc1.Anc1refChr2 43614 21 + 144309 acctttctatgtattccatct -s Anc2.Anc2refChr4 9934 21 + 10050 acctttttaattataccatct -s mr.mrrefChr0 63299 21 + 130230 ACCTATCTATGTATTCCATTC -s simCow_chr6.simCow.chr6 70560 21 + 602619 accttcttaattatcccatct -s simDog_chr6.simDog.chr6 66246 21 + 593897 acctttttaattataacatgt -s simHuman_chr6.simHuman.chr6 63963 21 + 601863 acctttctatgtattccatct -s simRat_chr6.simRat.chr6 58981 21 + 647215 AAGCATCTAAGCACTTGATTG - -a -s simMouse_chr6.simMouse.chr6 67081 17 + 636262 TTAATAATTTGGCAAAA -s Anc0.Anc0refChr4 12578 17 - 45765 ttaatgattcaggaaga -s Anc1.Anc1refChr2 43635 17 + 144309 ttaatgattcaggaaga -s Anc2.Anc2refChr4 9955 17 + 10050 ttaataattcaagaaga -s mr.mrrefChr0 63320 17 + 130230 TTAATGATTTGGCAAGA -s simCow_chr6.simCow.chr6 70595 17 + 602619 ttaataattcaagaaga -s simDog_chr6.simDog.chr6 66267 17 + 593897 ttataaaatcaacaagg -s simHuman_chr6.simHuman.chr6 63984 17 + 601863 ttaatgattcaggtaga -s simRat_chr6.simRat.chr6 59002 17 + 647215 CTAATGATTTGGAAAGA - -a -s simMouse_chr6.simMouse.chr6 67098 13 + 636262 AACACTGAGTTCA -s Anc0.Anc0refChr4 12596 13 - 45765 aacactgggttaa -s Anc1.Anc1refChr2 43655 13 + 144309 aacactgggttaa -s Anc2.Anc2refChr4 9973 13 + 10050 aacactgggtcaa -s mr.mrrefChr0 63337 13 + 130230 AACACTGAGTTAA -s simCow_chr6.simCow.chr6 70613 13 + 602619 aacactgggtgga -s simDog_chr6.simDog.chr6 66285 13 + 593897 aacactgtgtcat -s simHuman_chr6.simHuman.chr6 64006 13 + 601863 aacgctgggttaa -s simRat_chr6.simRat.chr6 59019 13 + 647215 AACAGTGAGTTAA - -a -s simMouse_chr6.simMouse.chr6 67111 29 + 636262 CCTTCACTCTGTCCCATAAGTGGTACTGG -s Anc0.Anc0refChr4 12610 29 - 45765 cattcactccattcaacaggtggtgctgg -s Anc1.Anc1refChr2 43669 29 + 144309 cattcactccattcaacaggtggtgctgg -s Anc2.Anc2refChr4 9987 29 + 10050 cattcactccactcaacaggtggtgctgg -s mr.mrrefChr0 63351 29 + 130230 CCTTCACTCTGTCCCATAGGTGGTGCTGG -s simCow_chr6.simCow.chr6 70627 29 + 602619 cattcactccactcaacagatgatgctgg -s simDog_chr6.simDog.chr6 66299 24 + 593897 catccattccact-----tgtagtcctgg -s simHuman_chr6.simHuman.chr6 64020 29 + 601863 tgctcactccattaaacaggtggtgctgg -s simRat_chr6.simRat.chr6 59033 29 + 647215 CCTTCACTCTGTCCCATAGGTGGTGCTGG - -a -s simMouse_chr6.simMouse.chr6 67140 6 + 636262 TAATCA -s Anc0.Anc0refChr4 12641 6 - 45765 taatca -s Anc1.Anc1refChr2 43700 6 + 144309 taatca -s Anc2.Anc2refChr4 10018 6 + 10050 tctttg -s mr.mrrefChr0 63380 6 + 130230 TAATCA -s simCow_chr6.simCow.chr6 70658 6 + 602619 tctttg -s simDog_chr6.simDog.chr6 66325 6 + 593897 tctttg -s simHuman_chr6.simHuman.chr6 64051 6 + 601863 taatca -s simRat_chr6.simRat.chr6 59062 6 + 647215 TTTTCA - -a -s simMouse_chr6.simMouse.chr6 67146 2 + 636262 AG -s Anc0.Anc0refChr4 12664 2 - 45765 aa -s Anc1.Anc1refChr2 43723 2 + 144309 aa -s Anc2.Anc2refChr4 10041 2 + 10050 ca -s Anc2.Anc2refChr7 12310 2 + 32194 GT -s mr.mrrefChr0 63386 2 + 130230 AG -s simCow_chr6.simCow.chr6 70681 1 + 602619 -a -s simDog_chr6.simDog.chr6 66706 2 + 593897 GT -s simDog_chr6.simDog.chr6 444665 2 + 593897 GT -s simDog_chr6.simDog.chr6 120688 2 - 593897 GC -s simDog_chr6.simDog.chr6 66348 2 + 593897 cg -s simHuman_chr6.simHuman.chr6 64074 2 + 601863 aa -s simRat_chr6.simRat.chr6 59068 2 + 647215 AG - -a -s simMouse_chr6.simMouse.chr6 67148 1 + 636262 T -s Anc0.Anc0refChr4 12666 1 - 45765 c -s Anc1.Anc1refChr2 43725 1 + 144309 c -s Anc2.Anc2refChr4 10043 1 + 10050 c -s Anc2.Anc2refChr7 12312 1 + 32194 C -s mr.mrrefChr0 63388 1 + 130230 T -s simCow_chr6.simCow.chr6 70682 1 + 602619 c -s simDog_chr6.simDog.chr6 66708 1 + 593897 C -s simDog_chr6.simDog.chr6 444668 1 + 593897 C -s simDog_chr6.simDog.chr6 120690 1 - 593897 C -s simDog_chr6.simDog.chr6 66350 1 + 593897 c -s simHuman_chr6.simHuman.chr6 64076 1 + 601863 c -s simRat_chr6.simRat.chr6 59070 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 67149 7 + 636262 TAACATG -s Anc0.Anc0refChr4 12667 7 - 45765 agacatg -s Anc1.Anc1refChr2 43726 7 + 144309 tgacatg -s Anc2.Anc2refChr4 10046 4 + 10050 acac--- -s Anc2.Anc2refChr7 12313 7 + 32194 AAAGatg -s mr.mrrefChr0 63389 7 + 130230 TAACATG -s simCow_chr6.simCow.chr6 70685 7 + 602619 aaacatg -s simDog_chr6.simDog.chr6 66709 4 + 593897 AAGG--- -s simDog_chr6.simDog.chr6 305715 4 + 593897 AAAG--- -s simDog_chr6.simDog.chr6 444669 4 + 593897 ATAG--- -s simDog_chr6.simDog.chr6 120691 4 - 593897 ATAG--- -s simDog_chr6.simDog.chr6 66353 4 + 593897 acag--- -s simHuman_chr6.simHuman.chr6 64077 7 + 601863 tcacatg -s simRat_chr6.simRat.chr6 59071 7 + 647215 TAACATG - -a -s simMouse_chr6.simMouse.chr6 67156 18 + 636262 TTCTTCTCCTTCctcctt -s Anc0.Anc0refChr4 12676 16 - 45765 tcctt--tctcactcctt -s Anc1.Anc1refChr2 43735 16 + 144309 tcctt--tctcactcctt -s Anc2.Anc2refChr7 12322 16 + 32194 ccttt--tctcacccctt -s mr.mrrefChr0 63396 16 + 130230 TTCTT--ccttcctcctt -s simCow_chr6.simCow.chr6 70694 16 + 602619 ccttt--tctcacccctt -s simHuman_chr6.simHuman.chr6 64086 16 + 601863 tcctt--tctcagtcctt -s simRat_chr6.simRat.chr6 59078 11 + 647215 TTCTT-------CTCCTT - -a -s simMouse_chr6.simMouse.chr6 67174 20 + 636262 tgcccaagttaaacaccgga -s Anc0.Anc0refChr4 12693 15 - 45765 caccaaagtt-aacac---- -s Anc1.Anc1refChr2 43752 16 + 144309 caccaaagttaaacac---- -s Anc2.Anc2refChr7 12339 15 + 32194 caccaaagtt-agcac---- -s mr.mrrefChr0 63412 20 + 130230 tgcccaagttaaacaccgga -s simCow_chr6.simCow.chr6 70711 15 + 602619 caccaaagtt-agcac---- -s simHuman_chr6.simHuman.chr6 64103 16 + 601863 caccaaaattaaacac---- -s simRat_chr6.simRat.chr6 59089 20 + 647215 TGCCCAAGTTAAACACCAGG - -a -s simMouse_chr6.simMouse.chr6 67194 54 + 636262 tgctggtagaactctcaatcttcaaacagtgccagaaattaatagtaaaaacta -s Anc0.Anc0refChr4 12708 43 - 45765 tgctgatggaactctcaatc------aagagggaa-----gataataaaaacta -s Anc1.Anc1refChr2 43768 49 + 144309 tgctgatggaactctcaatctttaaaaagagggaa-----gataataaaaacta -s Anc2.Anc2refChr7 12354 43 + 32194 tactgaaggaactcttgatc------acgaaggaa-----gataagaaagacta -s mr.mrrefChr0 63432 54 + 130230 tgctgatagaactctcaatcttcaaacagtgccagaaattaatagtaaaaacta -s simCow_chr6.simCow.chr6 70730 43 + 602619 tactgaaggaactcttgatc------acgaaggaa-----gataagaaagacta -s simHuman_chr6.simHuman.chr6 64119 49 + 601863 tgccaatggagctctcaacctttaaaaagagttaa-----gataataaaaacta -s simRat_chr6.simRat.chr6 59109 45 + 647215 TGCTGACAGAAGTCTCAGTCTtc-aacagtgcaagaaaataatagt-------- - -a -s simMouse_chr6.simMouse.chr6 67248 151 + 636262 ttctagtctatacccttcaaagtactggtgcttagaaaatgcttatgtaacagagacttcagcacctgcattgaggctaacaactgatagcaggaattattgaataaaaggtgttatgtggacagtatccaacaaagcattgtattgttaa -s Anc0.Anc0refChr4 12751 60 - 45765 ttctagacaacaccaatcaaggtactggcactgaacagattgttatg-ttaagacactac------------------------------------------------------------------------------------------a -s Anc1.Anc1refChr2 43817 61 + 144309 ttctagacaacaccaatcaaggtactggcactgaacagattgttatgcttaagacactac------------------------------------------------------------------------------------------a -s Anc2.Anc2refChr7 12397 60 + 32194 atctcgacaacactaatcaaggtaatggcactgaactgattgtcatg-ttaagtcaccaa------------------------------------------------------------------------------------------a -s mr.mrrefChr0 63486 61 + 130230 ttctagtctatacccttcaaagtactggtgcttagaaaatgcttatgtaacagagacttc------------------------------------------------------------------------------------------a -s simCow_chr6.simCow.chr6 70773 60 + 602619 atctcgacaacactaatcaaggtaatggcactgaactgattgtcatg-ttaagtcaccaa------------------------------------------------------------------------------------------a -s simHuman_chr6.simHuman.chr6 64171 61 + 601863 ttctagacaactccactcaaggtactggcactgaagagattattatgcttaagacactac------------------------------------------------------------------------------------------a -s simRat_chr6.simRat.chr6 59154 1 + 647215 ------------------------------------------------------------------------------------------------------------------------------------------------------a - -a -s simMouse_chr6.simMouse.chr6 67399 7 + 636262 ttgcaaa -s Anc0.Anc0refChr4 12819 7 - 45765 ctgctaa -s Anc1.Anc1refChr2 43886 7 + 144309 ctgctaa -s Anc2.Anc2refChr7 12465 7 + 32194 cagctaa -s mr.mrrefChr0 63547 7 + 130230 ttgcaaa -s simCow_chr6.simCow.chr6 70841 7 + 602619 cagctaa -s simHuman_chr6.simHuman.chr6 64240 7 + 601863 ctgccaa -s simRat_chr6.simRat.chr6 59155 7 + 647215 tagcaaa - -a -s simMouse_chr6.simMouse.chr6 67406 11 + 636262 ctgcaaggcta -s Anc0.Anc0refChr4 12831 10 - 45765 c-accgagtta -s Anc1.Anc1refChr2 43898 11 + 144309 ctaccgagtta -s Anc2.Anc2refChr7 12477 10 + 32194 c-atcgagtta -s mr.mrrefChr0 63554 11 + 130230 ctgcaaggcta -s simCow_chr6.simCow.chr6 70853 9 + 602619 c-at-gagtaa -s simDog_chr6.simDog.chr6 66790 7 + 593897 ----CGAATTG -s simHuman_chr6.simHuman.chr6 64258 11 + 601863 ctactgagtta -s simRat_chr6.simRat.chr6 59162 11 + 647215 ccacaaagcta - -a -s simMouse_chr6.simMouse.chr6 67417 4 + 636262 taaa -s Anc0.Anc0refChr4 12841 4 - 45765 caaa -s Anc1.Anc1refChr2 43909 4 + 144309 caaa -s Anc2.Anc2refChr7 12487 4 + 32194 caga -s mr.mrrefChr0 63565 4 + 130230 taaa -s simCow_chr6.simCow.chr6 70863 4 + 602619 caga -s simDog_chr6.simDog.chr6 66797 4 + 593897 CAGT -s simHuman_chr6.simHuman.chr6 64269 4 + 601863 aaaa -s simRat_chr6.simRat.chr6 59173 4 + 647215 taaa - -a -s simMouse_chr6.simMouse.chr6 67421 13 + 636262 ttgggacaacata -s Anc0.Anc0refChr4 12862 13 - 45765 ttgaaacagcata -s Anc1.Anc1refChr2 43930 13 + 144309 ttgaaacagcata -s Anc2.Anc2refChr7 12508 13 + 32194 ttgaaacagcata -s mr.mrrefChr0 63569 13 + 130230 ttgggacaacata -s simCow_chr6.simCow.chr6 70883 13 + 602619 ttgaaacagtgta -s simDog_chr6.simDog.chr6 66821 13 + 593897 CTGAAACTGCATA -s simHuman_chr6.simHuman.chr6 64290 13 + 601863 ttgaaagagcata -s simRat_chr6.simRat.chr6 59177 13 + 647215 ttgggacaacata - -a -s simMouse_chr6.simMouse.chr6 67434 2 + 636262 ta -s Anc0.Anc0refChr4 12882 2 - 45765 ta -s Anc1.Anc1refChr2 43950 2 + 144309 ta -s Anc2.Anc2refChr7 12528 2 + 32194 ta -s mr.mrrefChr0 63582 2 + 130230 ta -s simCow_chr6.simCow.chr6 70903 2 + 602619 tg -s simDog_chr6.simDog.chr6 66841 2 + 593897 TA -s simHuman_chr6.simHuman.chr6 64310 2 + 601863 ta -s simRat_chr6.simRat.chr6 59190 2 + 647215 ta - -a -s simMouse_chr6.simMouse.chr6 67436 4 + 636262 tgcc -s Anc0.Anc0refChr4 12884 4 - 45765 tgac -s Anc1.Anc1refChr2 43952 4 + 144309 tgac -s Anc2.Anc2refChr7 12530 4 + 32194 tgac -s mr.mrrefChr0 63584 4 + 130230 tgcc -s simCow_chr6.simCow.chr6 70905 4 + 602619 tgat -s simDog_chr6.simDog.chr6 66844 4 + 593897 TAAC -s simHuman_chr6.simHuman.chr6 64312 4 + 601863 tgac -s simRat_chr6.simRat.chr6 59192 4 + 647215 tgcc - -a -s simMouse_chr6.simMouse.chr6 67440 1 + 636262 g -s Anc0.Anc0refChr4 12907 1 - 45765 a -s Anc1.Anc1refChr2 43975 1 + 144309 a -s Anc2.Anc2refChr7 12553 1 + 32194 a -s mr.mrrefChr0 63588 1 + 130230 g -s simCow_chr6.simCow.chr6 70930 1 + 602619 a -s simDog_chr6.simDog.chr6 66867 1 + 593897 A -s simHuman_chr6.simHuman.chr6 64335 1 + 601863 a -s simRat_chr6.simRat.chr6 59196 1 + 647215 g - -a -s simMouse_chr6.simMouse.chr6 67441 12 + 636262 tacttattcata -s Anc0.Anc0refChr4 12908 12 - 45765 cactgattcatc -s Anc1.Anc1refChr2 43976 12 + 144309 cactgattcatc -s Anc2.Anc2refChr7 12554 12 + 32194 cactgattcaac -s mr.mrrefChr0 63589 12 + 130230 tacttattcata -s simCow_chr6.simCow.chr6 70953 12 + 602619 catttattaacc -s simDog_chr6.simDog.chr6 66868 11 + 593897 -ACTGGGACAAC -s simHuman_chr6.simHuman.chr6 64336 12 + 601863 cactcattcatc -s simRat_chr6.simRat.chr6 59197 12 + 647215 tacttattccta - -a -s simMouse_chr6.simMouse.chr6 67453 9 + 636262 caaaggagg -s Anc0.Anc0refChr4 12920 9 - 45765 catgggagg -s Anc1.Anc1refChr2 43988 9 + 144309 catgggagg -s Anc2.Anc2refChr7 12566 9 + 32194 catgtgaca -s mr.mrrefChr0 63601 9 + 130230 caaaggagg -s simCow_chr6.simCow.chr6 70965 9 + 602619 caagagaca -s simDog_chr6.simDog.chr6 66880 9 + 593897 CATATGACA -s simHuman_chr6.simHuman.chr6 64348 9 + 601863 catgggagg -s simRat_chr6.simRat.chr6 59209 9 + 647215 caaaagagg - -a -s simMouse_chr6.simMouse.chr6 67462 12 + 636262 tgagacttccag -s Anc0.Anc0refChr4 12930 12 - 45765 ctagactcccag -s Anc1.Anc1refChr2 43998 12 + 144309 ctagactcccag -s Anc2.Anc2refChr7 12576 12 + 32194 ctagactcccag -s mr.mrrefChr0 63610 12 + 130230 tgagacttccag -s simCow_chr6.simCow.chr6 70975 12 + 602619 ctagactcccag -s simDog_chr6.simDog.chr6 66890 12 + 593897 ATAGACTCCCAG -s simHuman_chr6.simHuman.chr6 64358 12 + 601863 ctagactcccag -s simRat_chr6.simRat.chr6 59218 12 + 647215 TGAGACTTCCAG - -a -s simMouse_chr6.simMouse.chr6 67474 4 + 636262 ttca -s Anc0.Anc0refChr4 12954 4 - 45765 ttca -s Anc1.Anc1refChr2 44022 4 + 144309 ttca -s Anc2.Anc2refChr7 12600 4 + 32194 ttca -s mr.mrrefChr0 63622 4 + 130230 ttca -s simCow_chr6.simCow.chr6 70997 3 + 602619 -tgg -s simDog_chr6.simDog.chr6 66914 4 + 593897 TTCA -s simHuman_chr6.simHuman.chr6 64382 4 + 601863 ttca -s simRat_chr6.simRat.chr6 59230 4 + 647215 TTAA - -a -s simMouse_chr6.simMouse.chr6 67478 20 + 636262 acaTGCAATCGATAAGAAAA -s Anc0.Anc0refChr4 12959 13 - 45765 ac-------taataagaaaa -s Anc1.Anc1refChr2 44027 18 + 144309 acatgca--taataagaaaa -s Anc2.Anc2refChr7 12605 13 + 32194 ac-------taataagaaga -s mr.mrrefChr0 63626 20 + 130230 acaTGCAATCGATAAGAAAA -s simCow_chr6.simCow.chr6 71001 13 + 602619 ac-------taataagaaga -s simDog_chr6.simDog.chr6 66919 13 + 593897 AT-------CAAGAAGAAGA -s simHuman_chr6.simHuman.chr6 64387 18 + 601863 acatgca--taatatgaaaa -s simRat_chr6.simRat.chr6 59234 20 + 647215 GCAAGAGATCAATAAGAAAA - -a -s simMouse_chr6.simMouse.chr6 67498 1 + 636262 C -s Anc0.Anc0refChr4 12972 1 - 45765 c -s Anc1.Anc1refChr2 44045 1 + 144309 c -s Anc2.Anc2refChr7 12618 1 + 32194 c -s mr.mrrefChr0 63646 1 + 130230 C -s simCow_chr6.simCow.chr6 71014 1 + 602619 c -s simDog_chr6.simDog.chr6 66932 1 + 593897 C -s simHuman_chr6.simHuman.chr6 64405 1 + 601863 c -s simRat_chr6.simRat.chr6 59260 1 + 647215 C - -a -s simMouse_chr6.simMouse.chr6 67499 9 + 636262 CCACACTGC -s Anc0.Anc0refChr4 12973 9 - 45765 ccacagaac -s Anc1.Anc1refChr2 44046 9 + 144309 ccacagaac -s Anc2.Anc2refChr7 12619 9 + 32194 ccacagaat -s mr.mrrefChr0 63647 9 + 130230 CCACACTGC -s simCow_chr6.simCow.chr6 71017 7 + 602619 ccacaga-- -s simDog_chr6.simDog.chr6 66933 9 + 593897 CCATAGAAT -s simHuman_chr6.simHuman.chr6 64406 9 + 601863 ccacagaac -s simRat_chr6.simRat.chr6 59261 9 + 647215 CCACACTGT - -a -s simMouse_chr6.simMouse.chr6 67508 15 + 636262 ACCTCACCCTTTTAG -s Anc0.Anc0refChr4 12983 15 - 45765 acctaaagctcagag -s Anc1.Anc1refChr2 44056 15 + 144309 acctaaagctcagag -s Anc2.Anc2refChr7 12629 15 + 32194 acctaaagctcagag -s mr.mrrefChr0 63656 15 + 130230 ACCTCACCCTTTTAG -s simCow_chr6.simCow.chr6 71024 13 + 602619 --ctaaagataagta -s simDog_chr6.simDog.chr6 67225 15 + 593897 ACCTAAGTCTCGGAG -s simHuman_chr6.simHuman.chr6 64416 15 + 601863 atcaaaaggtcagag -s simRat_chr6.simRat.chr6 59270 15 + 647215 ACCTCACCCTTTTAG - -a -s simMouse_chr6.simMouse.chr6 67523 39 + 636262 CATTGTACTGAAGAAACTGTGTCATGTCAGGCAATATAG -s Anc0.Anc0refChr4 12998 35 - 45765 agatcta-tgaataggttctctcac---aggtaaaggag -s Anc1.Anc1refChr2 44071 35 + 144309 agatcta-tgaataggttctctcac---aggtaaaggag -s Anc2.Anc2refChr7 12644 35 + 32194 agaacca-tgaataggtactctcac---aggtaaagggg -s mr.mrrefChr0 63671 39 + 130230 CATTGTACTGAAGAAACTGTGTCATGTCAGGCAATATAG -s simCow_chr6.simCow.chr6 71037 35 + 602619 aggatca-ttaataggtactctcac---aggtgaagggg -s simDog_chr6.simDog.chr6 67242 34 + 593897 AAAACCA-TGAGTAGGT-CTGTCAC---AGGTAAAGGGG -s simHuman_chr6.simHuman.chr6 64431 35 + 601863 agatcta-tgaataggttccctcag---aggtaaaggag -s simRat_chr6.simRat.chr6 59285 39 + 647215 TGTTGTACTCGAGAATCCATGTCATGTTAGGCAATATAG - -a -s simMouse_chr6.simMouse.chr6 67562 17 + 636262 CGCACACCCAAGACTAG -s Anc0.Anc0refChr4 13033 2 - 45765 t---------------g -s Anc1.Anc1refChr2 44106 2 + 144309 t---------------g -s Anc2.Anc2refChr7 12689 2 + 32194 t---------------t -s mr.mrrefChr0 63710 17 + 130230 CGCACACCCAAGACTAG -s simCow_chr6.simCow.chr6 71082 2 + 602619 t---------------t -s simDog_chr6.simDog.chr6 67286 2 + 593897 T---------------T -s simHuman_chr6.simHuman.chr6 64466 2 + 601863 t---------------g -s simRat_chr6.simRat.chr6 59324 17 + 647215 CGCACACCTAAGACTCG - -a -s simMouse_chr6.simMouse.chr6 67579 9 + 636262 CACATTAAA -s Anc0.Anc0refChr4 13035 9 - 45765 tgagttaaa -s Anc1.Anc1refChr2 44108 9 + 144309 tgagttaaa -s Anc2.Anc2refChr7 12691 9 + 32194 tgagttaaa -s mr.mrrefChr0 63727 9 + 130230 CACATTAAA -s simCow_chr6.simCow.chr6 71084 5 + 602619 ----ttaaa -s simDog_chr6.simDog.chr6 67319 9 + 593897 TGAGTTACA -s simHuman_chr6.simHuman.chr6 64468 9 + 601863 tgtgtaagc -s simRat_chr6.simRat.chr6 59341 9 + 647215 CACATAAAA - -a -s simMouse_chr6.simMouse.chr6 67588 10 + 636262 CAACACCTGA -s Anc0.Anc0refChr4 13044 10 - 45765 cagcacctga -s Anc1.Anc1refChr2 44117 10 + 144309 cagcacctga -s Anc2.Anc2refChr7 12701 10 + 32194 cagcacctga -s mr.mrrefChr0 63736 10 + 130230 CAACACCTGA -s simCow_chr6.simCow.chr6 71090 10 + 602619 cagcacctga -s simDog_chr6.simDog.chr6 67329 10 + 593897 CAGCACTAGA -s simHuman_chr6.simHuman.chr6 64477 10 + 601863 cagcacctgg -s simRat_chr6.simRat.chr6 59350 10 + 647215 CAACACCTGA - -a -s simMouse_chr6.simMouse.chr6 67598 27 + 636262 CAAAGTGTACTTTCACATAGTTCATCT -s Anc0.Anc0refChr4 13054 27 - 45765 aaaagtgtactttctcctagctttttt -s Anc1.Anc1refChr2 44127 27 + 144309 aaaagtgtactttctcctagctttttt -s Anc2.Anc2refChr7 12711 27 + 32194 aaaaatgtactttctcctagctttttt -s mr.mrrefChr0 63746 27 + 130230 CAAAGTGTACTTTCACATAGTTCATCT -s simCow_chr6.simCow.chr6 71100 27 + 602619 aaacaagtactttctcccagctcattt -s simDog_chr6.simDog.chr6 67340 27 + 593897 AAAAATGTACCTTCTCCTAGTTTTTTC -s simHuman_chr6.simHuman.chr6 64487 27 + 601863 aaaagtgtaatttatcctagcttgttt -s simRat_chr6.simRat.chr6 59360 27 + 647215 AATAGCGTACTTTCACATAGCTCATCT - -a -s simMouse_chr6.simMouse.chr6 67625 4 + 636262 TAAC -s Anc0.Anc0refChr4 13081 4 - 45765 taat -s Anc1.Anc1refChr2 44154 4 + 144309 taat -s Anc2.Anc2refChr7 12738 4 + 32194 taat -s mr.mrrefChr0 63773 4 + 130230 TAAC -s simCow_chr6.simCow.chr6 71127 3 + 602619 caa- -s simDog_chr6.simDog.chr6 67367 4 + 593897 TAAT -s simHuman_chr6.simHuman.chr6 64517 4 + 601863 taat -s simRat_chr6.simRat.chr6 59387 4 + 647215 TAAC - -a -s simMouse_chr6.simMouse.chr6 67629 2 + 636262 AA -s Anc0.Anc0refChr4 13085 2 - 45765 AA -s Anc1.Anc1refChr2 44158 2 + 144309 AA -s Anc2.Anc2refChr7 12744 2 + 32194 AA -s mr.mrrefChr0 63777 2 + 130230 AA -s simCow_chr6.simCow.chr6 71131 2 + 602619 AA -s simDog_chr6.simDog.chr6 67373 2 + 593897 AA -s simHuman_chr6.simHuman.chr6 64521 2 + 601863 ag -s simRat_chr6.simRat.chr6 59391 2 + 647215 AA - -a -s simMouse_chr6.simMouse.chr6 67631 9 + 636262 GTGAGGACT -s Anc0.Anc0refChr4 13087 9 - 45765 GTGAGCACT -s Anc1.Anc1refChr2 44160 9 + 144309 GTGAGCACT -s Anc2.Anc2refChr7 12746 9 + 32194 GCGAGCACT -s mr.mrrefChr0 63779 9 + 130230 GTGAGGACT -s simCow_chr6.simCow.chr6 71133 9 + 602619 GCGAACACT -s simDog_chr6.simDog.chr6 67375 9 + 593897 GCAAGCACT -s simHuman_chr6.simHuman.chr6 64523 9 + 601863 gtgagcact -s simRat_chr6.simRat.chr6 59394 9 + 647215 GTGAGTACT - -a -s simMouse_chr6.simMouse.chr6 67640 2 + 636262 TC -s Anc0.Anc0refChr4 13099 2 - 45765 TC -s Anc1.Anc1refChr2 44172 2 + 144309 TC -s Anc2.Anc2refChr7 12758 2 + 32194 TC -s mr.mrrefChr0 63788 2 + 130230 TC -s simCow_chr6.simCow.chr6 71145 2 + 602619 TA -s simDog_chr6.simDog.chr6 67387 2 + 593897 TC -s simHuman_chr6.simHuman.chr6 64535 2 + 601863 tc -s simRat_chr6.simRat.chr6 59403 2 + 647215 TC - -a -s simMouse_chr6.simMouse.chr6 67642 14 + 636262 CCAGTCTCCTTAAA -s Anc0.Anc0refChr4 13101 14 - 45765 CTagtctacttaaa -s Anc1.Anc1refChr2 44174 14 + 144309 CTagtctacttaaa -s Anc2.Anc2refChr7 12760 14 + 32194 CTagtccacttaaa -s mr.mrrefChr0 63790 14 + 130230 CCAGTCTCCTTAAA -s simCow_chr6.simCow.chr6 71147 2 + 602619 CT------------ -s simDog_chr6.simDog.chr6 67389 14 + 593897 GTAGTCCACTTAAA -s simHuman_chr6.simHuman.chr6 64537 14 + 601863 ctagtctacttaaa -s simRat_chr6.simRat.chr6 59408 14 + 647215 CCAGTCTTCTTAGA - -a -s simMouse_chr6.simMouse.chr6 67656 3 + 636262 AAG -s Anc0.Anc0refChr4 13115 3 - 45765 AAG -s Anc1.Anc1refChr2 44188 3 + 144309 AAG -s Anc2.Anc2refChr7 12774 3 + 32194 AAG -s mr.mrrefChr0 63804 3 + 130230 AAG -s simCow_chr6.simCow.chr6 71149 2 + 602619 -AG -s simDog_chr6.simDog.chr6 67403 3 + 593897 AAG -s simHuman_chr6.simHuman.chr6 64551 3 + 601863 ATG -s simRat_chr6.simRat.chr6 59447 3 + 647215 AAG - -a -s simMouse_chr6.simMouse.chr6 67659 1 + 636262 C -s Anc0.Anc0refChr4 13145 1 - 45765 C -s Anc1.Anc1refChr2 44218 1 + 144309 C -s Anc2.Anc2refChr7 12807 1 + 32194 C -s mr.mrrefChr0 63807 1 + 130230 C -s simCow_chr6.simCow.chr6 71181 1 + 602619 C -s simDog_chr6.simDog.chr6 67436 1 + 593897 G -s simHuman_chr6.simHuman.chr6 64581 1 + 601863 C -s simRat_chr6.simRat.chr6 59450 1 + 647215 C - -a -s simMouse_chr6.simMouse.chr6 67660 15 + 636262 ACCGACTTGTCTTGA -s Anc0.Anc0refChr4 13146 15 - 45765 ATTTACTCAACTTAA -s Anc1.Anc1refChr2 44219 15 + 144309 ATTTACTCAACTTAA -s Anc2.Anc2refChr7 12808 15 + 32194 ATTTACTCAACTTAA -s mr.mrrefChr0 63808 15 + 130230 ACCGACTTGTCTTGA -s simCow_chr6.simCow.chr6 71182 15 + 602619 CCTGACTCAACTTAA -s simDog_chr6.simDog.chr6 67474 15 + 593897 ATATATTAACTTAAA -s simHuman_chr6.simHuman.chr6 64582 15 + 601863 ATTTACTCAACTTAA -s simRat_chr6.simRat.chr6 59451 15 + 647215 ACCTACTTGTGTTGA - -a -s simMouse_chr6.simMouse.chr6 67675 12 + 636262 AAGAGAGCTGGT -s Anc0.Anc0refChr4 13161 12 - 45765 AGGGGAGCTGGT -s Anc1.Anc1refChr2 44234 12 + 144309 AGGGGAGCTGGT -s Anc2.Anc2refChr7 12823 12 + 32194 AGAGAGGCTTGT -s mr.mrrefChr0 63823 12 + 130230 AAGAGAGCTGGT -s simCow_chr6.simCow.chr6 71198 12 + 602619 AAAAAGGGTTGT -s simDog_chr6.simDog.chr6 67489 12 + 593897 AGAGAGGCTTGT -s simHuman_chr6.simHuman.chr6 64597 12 + 601863 AGGGGAGCTGGT -s simRat_chr6.simRat.chr6 59466 12 + 647215 AAGAGAGCTGAT - -a -s simMouse_chr6.simMouse.chr6 67687 10 + 636262 ATTGTGACAC -s Anc0.Anc0refChr4 13179 4 - 45765 A------CAC -s Anc1.Anc1refChr2 44252 4 + 144309 A------CAC -s Anc2.Anc2refChr7 12841 4 + 32194 A------CAC -s mr.mrrefChr0 63835 4 + 130230 A------CAC -s simCow_chr6.simCow.chr6 71216 4 + 602619 A------CAC -s simDog_chr6.simDog.chr6 67507 4 + 593897 A------CAC -s simHuman_chr6.simHuman.chr6 64615 4 + 601863 A------CAC -s simRat_chr6.simRat.chr6 59478 4 + 647215 C------CAC - -a -s simMouse_chr6.simMouse.chr6 67697 50 + 636262 TAAAGAAGAGCTGGAAAGTCCAGAAGTAAAGCTGGTAAACACTGCATACT -s Anc0.Anc0refChr4 13184 44 - 45765 TAAAGAAGAG-TGGATGGTTAAGAAATAGAATTG--AAACACT---TACT -s Anc1.Anc1refChr2 44257 45 + 144309 TAAAGAAGAGTTGGATGGTTAAGAAATAGAATTG--AAACACT---TACT -s Anc2.Anc2refChr7 12846 44 + 32194 TAAAGAAGAG-GGGATGGTTAAGAAATAGAATTG--AAACACT---TACT -s mr.mrrefChr0 63839 50 + 130230 TAAAGAAGAGCTGGAAAGTCCAGAAGTAAAGCTGGTAAACACTGCATACT -s simCow_chr6.simCow.chr6 71221 44 + 602619 TAAAGAAGAG-CTGACGGTTGAGCAATTGAGGTC--AAACACT---TACT -s simDog_chr6.simDog.chr6 67512 44 + 593897 TAAAGAAGAG-GGGATAGTTAAGACATAGGATTG--AAACACT---TACT -s simHuman_chr6.simHuman.chr6 64620 45 + 601863 TAAAGATGCGTTGGATGGCTTAGAAATGGAATTG--AAACACT---CACT -s simRat_chr6.simRat.chr6 59482 50 + 647215 TAAAGAAGAGCTGGAAAGGCCAGAAATAAACCTGGTAAACACTGCATACT - -a -s simMouse_chr6.simMouse.chr6 67747 11 + 636262 GTTAACTTGTA -s Anc0.Anc0refChr4 13243 11 - 45765 GTTCACATGTA -s Anc1.Anc1refChr2 44317 11 + 144309 GTTCACATGTA -s Anc2.Anc2refChr7 12905 11 + 32194 GCTCACATGTA -s mr.mrrefChr0 63889 11 + 130230 GTTAACTTGTA -s simCow_chr6.simCow.chr6 71280 11 + 602619 GCCCACATGTA -s simDog_chr6.simDog.chr6 67571 11 + 593897 GCTCACATGTA -s simHuman_chr6.simHuman.chr6 64680 11 + 601863 GTTCACATGTA -s simRat_chr6.simRat.chr6 59532 11 + 647215 ATTGACTTTTA - -a -s simMouse_chr6.simMouse.chr6 67758 41 + 636262 ACTTAACACAGTTGACTTTTTAACTCAATCTAAGGGAGCTA -s Anc0.Anc0refChr4 13264 40 - 45765 GCTGGATGCAGTTGAC-TTTCAACTCAATTTAGGGGAGCAG -s Anc1.Anc1refChr2 44338 40 + 144309 GCTGGATGCAGTTGAC-TTTCAACTCAATTTAGGGGAGCAG -s Anc2.Anc2refChr7 12926 40 + 32194 GCTGGATGCAGTGCAG-TTACAGCTCAATTGAGATGAGTAG -s mr.mrrefChr0 63900 41 + 130230 ACTTAACACAGTTGACTTTTTAACTCAATCTAAGGGAGCTA -s simCow_chr6.simCow.chr6 71301 40 + 602619 GGTATATGCAGTGCAG-TTACAGCTCAATTGAGATGAGTAG -s simDog_chr6.simDog.chr6 67592 13 + 593897 GCTGGTTGCAATG---------------------------- -s simHuman_chr6.simHuman.chr6 64701 40 + 601863 GCTGGATGCAGTTGAC-TTTAAACCCAATATAGGGGGGCAG -s simRat_chr6.simRat.chr6 59543 41 + 647215 ACTTAACACAATTGACATTTTAACACAATTTAAGTGAGCAA - -a -s simMouse_chr6.simMouse.chr6 67799 22 + 636262 CCAAGCATGAAAGCCATTCTGA -s Anc0.Anc0refChr4 13304 21 - 45765 TCCACAG-AAAAGACACTTTGA -s Anc1.Anc1refChr2 44378 22 + 144309 TCCACAGTAAAAGACACTTTGA -s Anc2.Anc2refChr7 12966 21 + 32194 TGCACAG-AAAAGACACTTTGA -s mr.mrrefChr0 63941 22 + 130230 CCAAGCATGAAAGCCATTCTGA -s simCow_chr6.simCow.chr6 71341 21 + 602619 TGCACAG-GAGAGACACTTTGA -s simDog_chr6.simDog.chr6 67605 19 + 593897 --CACAG-AGAAGACACCTTGA -s simHuman_chr6.simHuman.chr6 64741 22 + 601863 ACCACAGTAAAAGACACTTTGA -s simRat_chr6.simRat.chr6 59585 22 + 647215 CCAAGTGTGAAGGCCATTTTGA - -a -s simMouse_chr6.simMouse.chr6 67821 71 + 636262 AAATGAGGACCATACCTTTCCAACTGAACCTACAGATGCTCCTAATCGAGCTATACCCTTCAAATTCAACC -s Anc0.Anc0refChr4 13326 29 - 45765 AAGTGTGTACCATATTTTTCTAA------------------------------------------TCAACC -s Anc1.Anc1refChr2 44401 29 + 144309 AAGTGTGTACCATATTTTTCTAA------------------------------------------TCAACC -s Anc2.Anc2refChr7 12988 29 + 32194 AAGTGTGTACCATATTTTTCTAA------------------------------------------TCAACC -s mr.mrrefChr0 63963 30 + 130230 AAATGAGGACCATACCTTTCCAA-----------------------------------------TTCAACC -s simCow_chr6.simCow.chr6 71363 29 + 602619 AAATGAATACCATACTTTCCTCA------------------------------------------TGAACC -s simDog_chr6.simDog.chr6 67625 29 + 593897 AAGAGTGTACTATATTGTTCAAA------------------------------------------TCGACC -s simHuman_chr6.simHuman.chr6 64764 29 + 601863 AAGTGGGTACCATATTTTTCTAA------------------------------------------TCAACC -s simRat_chr6.simRat.chr6 59607 30 + 647215 AAATGAGAACTATACCTTTCCAA-----------------------------------------TTCAACC - -a -s simMouse_chr6.simMouse.chr6 67892 25 + 636262 TACAGATGGTCCTAATCAAGGCAGA -s Anc0.Anc0refChr4 13355 25 - 45765 TGTAAATAATCCTAGTCAACTTAAA -s Anc1.Anc1refChr2 44430 25 + 144309 TGTAAATAATCCTAGTCAACTTAAA -s Anc2.Anc2refChr7 13017 25 + 32194 TGTAAATAATCCTAGTCAACTTAAA -s mr.mrrefChr0 63993 25 + 130230 TACAGATGGTCCTAATCAAGGCAGA -s simCow_chr6.simCow.chr6 71392 25 + 602619 CACACATCTTGCTAGTCAACTTAAG -s simDog_chr6.simDog.chr6 67659 25 + 593897 TGTGAACAATCCTAGTCAACTTAAA -s simHuman_chr6.simHuman.chr6 64793 25 + 601863 TGTAAATAAGCTTAGTCAACTTAAA -s simRat_chr6.simRat.chr6 59637 25 + 647215 TACAGATGGTCCTAGTTGAGGCAGA - -a -s simMouse_chr6.simMouse.chr6 67917 66 + 636262 AATGTCGTCAATGAGGAGGAGTATGTAATTGTTGCACATGTGTCTTCAACTTCAGCATGAAAGCTT -s Anc0.Anc0refChr4 13380 56 - 45765 GA-GTCATC--TG---AGGAGCATGT-ATTGTTGCACATGCAT-TACATACTCATCATG-CAGC-T -s Anc1.Anc1refChr2 44455 60 + 144309 GA-GTCATC--TGAGGAGGAGCATGT-ATTGTTGCACATGCAT-TACATACTCATCATG-CAGCTT -s Anc2.Anc2refChr7 13046 56 + 32194 GG-GTCATC--TG---AGGAGCATGT-ATCATTGCTCAAGCAT-TACATACTCATCAAG-CAGC-T -s mr.mrrefChr0 64018 66 + 130230 AATGTCGTCAATGAGGAGGAGTATGTAATTGTTGCACATGTGTCTTCAACTTCAGCATGAAAGCTT -s simCow_chr6.simCow.chr6 71421 56 + 602619 GG-GTCATC--TG---AGGGGCATGT-ATCATTGCTCAAACCT-TATATACTCATCAGG-CAGC-T -s simDog_chr6.simDog.chr6 67688 38 + 593897 GG-GTTATC----------AGC--------------CAAGCAT-TACATAATCACGAAG-CAGC-T -s simHuman_chr6.simHuman.chr6 64818 60 + 601863 GA-GTCATC--TGAGGAGGAGCATGT-ATTGTTGCATATGCAT-TACATACTCATCATG-CAGCTT -s simRat_chr6.simRat.chr6 59662 66 + 647215 AATGTTGTCAATGAGGAGGAGTATCTAATTATTGTACATGTGATTTCAACTTCACCATGAAAGCTT - -a -s simMouse_chr6.simMouse.chr6 67983 19 + 636262 AAGAGAGTTATAAGAAAGT -s Anc0.Anc0refChr4 13436 15 - 45765 AAGAGAGTT---AGAAG-T -s Anc1.Anc1refChr2 44515 15 + 144309 AAGAGAGTT---AGAAG-T -s Anc2.Anc2refChr7 13102 15 + 32194 AAGAGAGTT---AGAAG-T -s mr.mrrefChr0 64084 18 + 130230 AAGAGAGTTATAAGAAA-T -s simCow_chr6.simCow.chr6 71477 15 + 602619 ATGAAAGTT---AGAGG-T -s simDog_chr6.simDog.chr6 67726 15 + 593897 AAGAGAATT---AGTAG-T -s simHuman_chr6.simHuman.chr6 64878 15 + 601863 AAAAGAGTT---AGAAG-T -s simRat_chr6.simRat.chr6 59729 18 + 647215 AATAGAGTTATAAGAAC-T - -a -s simMouse_chr6.simMouse.chr6 68002 1 + 636262 T -s Anc0.Anc0refChr4 13451 1 - 45765 T -s Anc1.Anc1refChr2 44530 1 + 144309 T -s Anc2.Anc2refChr7 13117 1 + 32194 T -s mr.mrrefChr0 64102 1 + 130230 T -s simCow_chr6.simCow.chr6 71492 1 + 602619 T -s simDog_chr6.simDog.chr6 67822 1 + 593897 T -s simHuman_chr6.simHuman.chr6 64893 1 + 601863 T -s simRat_chr6.simRat.chr6 59747 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 68003 12 + 636262 GAGTGATTTGTG -s Anc0.Anc0refChr4 13452 12 - 45765 GGGTTATTTATG -s Anc1.Anc1refChr2 44531 12 + 144309 GGGTTATTTATG -s Anc2.Anc2refChr7 13118 12 + 32194 GGGTTATTTATG -s mr.mrrefChr0 64103 12 + 130230 GAGTGATTTGTG -s simCow_chr6.simCow.chr6 71498 12 + 602619 GGGTTATTTATG -s simDog_chr6.simDog.chr6 67823 12 + 593897 GGGTTATCTATG -s simHuman_chr6.simHuman.chr6 64894 12 + 601863 GGTTTATTTATG -s simRat_chr6.simRat.chr6 59748 12 + 647215 GGATGATTTGTT - -a -s simMouse_chr6.simMouse.chr6 68015 17 + 636262 TTAAATGCATGTATTAG -s Anc0.Anc0refChr4 13464 17 - 45765 TGAACCACATATATTAA -s Anc1.Anc1refChr2 44543 17 + 144309 TGAACCACATATATTAA -s Anc2.Anc2refChr7 13133 17 + 32194 GGAACCACTTATATTAA -s mr.mrrefChr0 64115 17 + 130230 TTAAATGCATGTATTAG -s simCow_chr6.simCow.chr6 71513 15 + 602619 GGAACCACT--TATTAA -s simDog_chr6.simDog.chr6 67838 11 + 593897 GGAACCACTTA------ -s simHuman_chr6.simHuman.chr6 64906 17 + 601863 TGAACCACACATATTAA -s simRat_chr6.simRat.chr6 59760 17 + 647215 TTAACCACATGTATTAG - -a -s simMouse_chr6.simMouse.chr6 68032 22 + 636262 TTTATGCTTTGAGTCCTAATCT -s Anc0.Anc0refChr4 13488 22 - 45765 TTTGTGCTTTGACACCTAATTC -s Anc1.Anc1refChr2 44567 22 + 144309 TTTGTGCTTTGACACCTAATTC -s Anc2.Anc2refChr7 13157 22 + 32194 TTTGTCCTTAGACACCTAATTC -s mr.mrrefChr0 64132 22 + 130230 TTTATGCTTTGAGTCCTAATCT -s simCow_chr6.simCow.chr6 71535 22 + 602619 ATTGCCTTTAGGCACCCAACTT -s simDog_chr6.simDog.chr6 67849 22 + 593897 TTTGTCCTCAGACACCTAATTC -s simHuman_chr6.simHuman.chr6 64931 22 + 601863 TTTGTGCTTTAACACCTAATTC -s simRat_chr6.simRat.chr6 59777 22 + 647215 TTTATGCTTTGACTCCTAATCC - -a -s simMouse_chr6.simMouse.chr6 68054 7 + 636262 CTGTATT -s Anc0.Anc0refChr4 13510 7 - 45765 CTCTATT -s Anc1.Anc1refChr2 44589 7 + 144309 CTCTATT -s Anc2.Anc2refChr7 13179 7 + 32194 CTCTATC -s mr.mrrefChr0 64154 7 + 130230 CTGTATT -s simCow_chr6.simCow.chr6 71557 7 + 602619 CTCCATC -s simDog_chr6.simDog.chr6 67878 7 + 593897 CCCTATC -s simHuman_chr6.simHuman.chr6 64953 7 + 601863 CTCTATT -s simRat_chr6.simRat.chr6 59799 7 + 647215 CTGTATT - -a -s simMouse_chr6.simMouse.chr6 68061 2 + 636262 GA -s Anc0.Anc0refChr4 13519 2 - 45765 GA -s Anc1.Anc1refChr2 44598 2 + 144309 GA -s Anc2.Anc2refChr7 13188 2 + 32194 GA -s mr.mrrefChr0 64161 2 + 130230 GA -s simDog_chr6.simDog.chr6 67887 2 + 593897 GA -s simHuman_chr6.simHuman.chr6 64962 2 + 601863 GA -s simRat_chr6.simRat.chr6 59806 2 + 647215 GA - -a -s simMouse_chr6.simMouse.chr6 68063 43 + 636262 ACTTGTTGCCCTGTCTGTGCATTTATTAACACCATTGACTTCT -s Anc0.Anc0refChr4 13521 33 - 45765 CCTTGTTGACATGTGAACCCA---------TCTATTGA-TACT -s Anc1.Anc1refChr2 44600 33 + 144309 CCTTGTTGACATGTGAACCCA---------TCTATTGA-TACT -s Anc2.Anc2refChr7 13190 33 + 32194 CCATGTTGACATGTGAACCCA---------TTTATTGT-TACT -s mr.mrrefChr0 64163 34 + 130230 ACTTGTTGCCCTGTCTGTGCA---------ACCATTGACTTCT -s simCow_chr6.simCow.chr6 71566 30 + 602619 ---TCTTGACGTGTCAACTCA---------TTTATTTG-TACC -s simDog_chr6.simDog.chr6 67889 33 + 593897 CCATGTTGACATGGGAACCCA---------TTTATTGT-TACT -s simHuman_chr6.simHuman.chr6 64964 33 + 601863 GCTTGTTAAAATGTTACCCCA---------TCTATTGA-TACT -s simRat_chr6.simRat.chr6 59810 34 + 647215 ACTTGTTGCCCTGCCAGTCCA---------GCTATTGACTGCT - -a -s simMouse_chr6.simMouse.chr6 68106 72 + 636262 AACAGATTCCTTGACTTCTAACAGATTCTGAGTTTGGTCCAAGGAGACACTCACACTATCTTCTAATCATTT -s Anc0.Anc0refChr4 13554 57 - 45765 A---------CTGACTTCTAACAGATTCAGAGTTA-G-CCAAGAAGATACTCACATCATCTTTT----ATTT -s Anc1.Anc1refChr2 44633 58 + 144309 A---------CTGACTTCTAACAGATTCAGAGTTAGG-CCAAGAAGATACTCACATCATCTTTT----ATTT -s Anc2.Anc2refChr7 13223 57 + 32194 A---------CTGACTTCTCACAGATTCAGAGTTA-G-CCAAGAAAATGCTCACATCATCTTTT----ATTT -s mr.mrrefChr0 64197 71 + 130230 AACAGATTCCTTGACTTCTAACAGATTCTGAGTTTGG-CCAAGGAGACACTCACACTATCTTCTAATCATTT -s simCow_chr6.simCow.chr6 71596 55 + 602619 A---------CTTAGTTTTCACAGATTCAGGGTTA-G-CTATGAAAATGCT--CATATTTATTT----ATTT -s simDog_chr6.simDog.chr6 67990 57 + 593897 A---------CTGACTTCTCACAAATTCAAAGTTA-G-TCAAAAAAATGCTCACCTCATCTTTT----ATTT -s simHuman_chr6.simHuman.chr6 64997 56 + 601863 A---------CTGACTTCTAACAGATTCAGAGTTAG---CCAGAAGATACTTGCATGACCTTTT----ATTT -s simRat_chr6.simRat.chr6 59844 71 + 647215 AATGGATTCCTTGACTTCTAACGGATTCCAAGTTTGA-CCAGGAAGAAGCTCACACTATCTTCTATCCACTT - -a -s simMouse_chr6.simMouse.chr6 68178 2 + 636262 AC -s Anc0.Anc0refChr4 13611 2 - 45765 GC -s Anc1.Anc1refChr2 44691 2 + 144309 GC -s Anc2.Anc2refChr7 13281 2 + 32194 GC -s mr.mrrefChr0 64268 2 + 130230 AC -s simCow_chr6.simCow.chr6 71652 2 + 602619 GC -s simDog_chr6.simDog.chr6 68048 2 + 593897 GC -s simHuman_chr6.simHuman.chr6 65053 2 + 601863 GC -s simRat_chr6.simRat.chr6 59915 2 + 647215 AC - -a -s simMouse_chr6.simMouse.chr6 68180 12 + 636262 CTACAAGCACTT -s Anc0.Anc0refChr4 13615 12 - 45765 CATCTATCCCTT -s Anc1.Anc1refChr2 44695 12 + 144309 CATCTATCCCTT -s Anc2.Anc2refChr7 13285 12 + 32194 CATCTATCCCTT -s mr.mrrefChr0 64270 12 + 130230 CTACAAGCACTT -s simCow_chr6.simCow.chr6 71656 9 + 602619 CAT---GCCCTT -s simDog_chr6.simDog.chr6 68052 12 + 593897 CCCCTATTCCTT -s simHuman_chr6.simHuman.chr6 65057 12 + 601863 CATCGATCCCTT -s simRat_chr6.simRat.chr6 59917 12 + 647215 CTACAACCACTT - -a -s simMouse_chr6.simMouse.chr6 68192 25 + 636262 GGGGGCATTCAATGTGCTATGGCTG -s Anc0.Anc0refChr4 13627 25 - 45765 GGGGGCATTTGATGTGCTATGAGTG -s Anc1.Anc1refChr2 44707 25 + 144309 GGGGGCATTTGATGTGCTATGAGTG -s Anc2.Anc2refChr7 13297 25 + 32194 AGAGGCATTTGATGTGCTAAGAGTG -s mr.mrrefChr0 64282 25 + 130230 GGGGGCATTCAATGTGCTATGGCTG -s simCow_chr6.simCow.chr6 71665 25 + 602619 AGACATATTTCACATGCTAAGATCA -s simDog_chr6.simDog.chr6 68064 25 + 593897 AGAGGCATTTGATGTGCCCAGAGTG -s simHuman_chr6.simHuman.chr6 65071 25 + 601863 GAGGGCATTTGATGTGCTATCAGTG -s simRat_chr6.simRat.chr6 59929 25 + 647215 AGGGACATTCAATGTGCTATGAGTC - -a -s simMouse_chr6.simMouse.chr6 68217 11 + 636262 ATTGAGGTCCT -s Anc0.Anc0refChr4 13661 11 - 45765 ATTTTGATCCC -s Anc1.Anc1refChr2 44741 11 + 144309 ATTTTGATCCC -s Anc2.Anc2refChr7 13331 11 + 32194 ATTTTGATCCC -s mr.mrrefChr0 64307 11 + 130230 ATTGAGGTCCT -s simCow_chr6.simCow.chr6 71697 11 + 602619 ATTGTGACCCC -s simDog_chr6.simDog.chr6 68113 11 + 593897 CTTTTGATGCC -s simHuman_chr6.simHuman.chr6 65105 11 + 601863 ATTTTGATCGC -s simRat_chr6.simRat.chr6 59954 11 + 647215 ATAGACAATCT - -a -s simMouse_chr6.simMouse.chr6 68228 4 + 636262 CTTT -s Anc0.Anc0refChr4 13672 4 - 45765 TTTC -s Anc1.Anc1refChr2 44752 4 + 144309 TTTC -s Anc2.Anc2refChr7 13342 4 + 32194 TTTC -s mr.mrrefChr0 64318 4 + 130230 CTTT -s simCow_chr6.simCow.chr6 71708 4 + 602619 TTTC -s simDog_chr6.simDog.chr6 68124 4 + 593897 TTTC -s simHuman_chr6.simHuman.chr6 65116 4 + 601863 TTTC -s simRat_chr6.simRat.chr6 59967 4 + 647215 TTTT - -a -s simMouse_chr6.simMouse.chr6 68232 40 + 636262 AGATATGTCCCAATGATAGAATCAATTGTGCTTGCTTCCA -s Anc0.Anc0refChr4 13676 36 - 45765 AGCTATA----AATAATAGAGTTATTTGTGCTCCCTTGCA -s Anc1.Anc1refChr2 44756 36 + 144309 AGCTATA----AATAATAGAGTTATTTGTGCTCCCTTGCA -s Anc2.Anc2refChr7 13351 36 + 32194 AGCTATA----AATAATAGAGTTATTTGTGCTCCCTTGCA -s mr.mrrefChr0 64322 40 + 130230 AGATATGTCCCAATGATAGAATCAATTGTGCTTGCTTCCA -s simCow_chr6.simCow.chr6 71717 36 + 602619 AGCTATA----AGCAATAGAATTAATTGTGCTCCCTTGTA -s simDog_chr6.simDog.chr6 68133 36 + 593897 AGCTCCA----AATGACAGAGTTGTTTGTGCTACCTTGCA -s simHuman_chr6.simHuman.chr6 65120 36 + 601863 AGCCATA----ACTAATAGAGTTAGTTGTGCACCCTTGCA -s simRat_chr6.simRat.chr6 59971 40 + 647215 GGGTATGTCACAAGGATAGAATCAATTGTGCTTGCTTTCA - -a -s simMouse_chr6.simMouse.chr6 68272 27 + 636262 TGCATACAATATATcagcaacaattga -s Anc0.Anc0refChr4 13714 20 - 45765 TGCAAGC-------CAGCAGCAAGTGG -s Anc1.Anc1refChr2 44794 20 + 144309 TGCAAGC-------CAGCAGCAAGTGG -s Anc2.Anc2refChr7 13389 20 + 32194 TGTAAGC-------CTTTGGCAAGTGG -s mr.mrrefChr0 64362 27 + 130230 TGCATACAATATATcagcaacaattga -s simCow_chr6.simCow.chr6 71755 20 + 602619 TGTAAGC-------CTTTGGCAAGTGG -s simHuman_chr6.simHuman.chr6 65158 20 + 601863 TGCAAGC-------CAGCAGCGAGCGG -s simRat_chr6.simRat.chr6 60011 27 + 647215 TGCATGCAATAGACCAGCAGCAATTAA - -a -s simMouse_chr6.simMouse.chr6 68299 14 + 636262 cttgaagcaaatga -s Anc0.Anc0refChr4 13736 10 - 45765 CTTGAAGCAA---- -s Anc1.Anc1refChr2 44816 10 + 144309 CTTGAAGCAA---- -s Anc2.Anc2refChr7 13411 10 + 32194 CTCAAAGCGG---- -s mr.mrrefChr0 64389 14 + 130230 cttgaagcaaatga -s simCow_chr6.simCow.chr6 71777 10 + 602619 CTCAAAGCCG---- -s simDog_chr6.simDog.chr6 68171 6 + 593897 ----AACCGG---- -s simHuman_chr6.simHuman.chr6 65180 10 + 601863 CATGAAGCAA---- -s simRat_chr6.simRat.chr6 60038 14 + 647215 GATGAAGCAAAGCA - -a -s simMouse_chr6.simMouse.chr6 68313 284 + 636262 tttcctagtaatacaagtggtggcagtcatcaagggcccacaaattaaggatcacaatccttgctgatcttggcattttataatggaagccactaatagttcaaaggttattagatgttcttggggcacactgttgtgaattcatttgtggacctcgaatttacttaagctaatatacagctttagcaggactgccactgagacactgatggccctgttcaccacatgtaaaaaaacctctgtggaattcacctgtaacaggaaaaggggacttgtgatagagt -s mr.mrrefChr0 64403 283 + 130230 tttcctagtaatacaagtggtggcagtcatcaagggcc-acaaattaaggatcacaatccttgctgatcttggcattttataatggaagccactaatagttcaaaggttattagatgttcttggggcacactgttgtgaattcatttgtggacctcgaatttacttaagctaatatacagctttagcaggactgccactgagacactgatggccctgttcaccacatgtaaaaaaacctctgtggaattcacctgtaacaggaaaaggggacttgtgatagagt -s simRat_chr6.simRat.chr6 60059 283 + 647215 Tttcataggcatacaagtggtggcagttgccaaggact-ataaattaaggttcacaacccttgcaattctcgacatttcataatagaagccactaatagttcaaagattattagaagttctcggggcttgatgttgtgaatttatttgtccacctcaaatttactttagcgaagatatagccttagcaggactgctactgaggtaccgatggccccaatcaccacatgtaaaaaaacctccgtggaattcacctctaaccaaaaaaggggacctgtggtaaggt - -a -s simMouse_chr6.simMouse.chr6 68597 63 + 636262 gattccgagttaaaaaaattggccagccgaataacattacctgatttcaggtttcacaatgtg -s mr.mrrefChr0 64686 60 + 130230 gattccgagttaaaaaaattggccagccgaataacattac--gatttcaggtttcacaat-tg -s simRat_chr6.simRat.chr6 60343 60 + 647215 gactctgagttaaaaaaattgaccagcaaaataacattac--gattttaggttccacagt-tg - -a -s simMouse_chr6.simMouse.chr6 68660 120 + 636262 caaccattgccgaaacaacactccactggtataaacagatcattactatacaatatgcgtataagatagaTCATTCTAGGGATACCCCACACCCTTAAGTAATTTGACACCTTAGGGTTT -s mr.mrrefChr0 64746 119 + 130230 caaccattgccgaaacaacactccactggtataaacagatcattactatacaatatgcgtataagatagaTCATTCTAGGGATACCC-ACACCCTTAAGTAATTTGACACCTTAGGGTTT -s simRat_chr6.simRat.chr6 60409 119 + 647215 caaccattaccgaaacaacactccactggtatataaacatcattactatacaatatgggtataagatggaTCACCCTAGGGATACCC-ACACCCTTAAGGAAATCGACTCCTCAGGGTTT - -a -s simMouse_chr6.simMouse.chr6 68780 169 + 636262 AGAAAGCTGTTGTCATGTATACAGCAGCAAGAAGACCACACCTgcttcaggttcaccccattgaaggtaactcatgcatgcaattgtcaattggtattgtccattggtcctccttgtcctgtgacttgagcatattaattttataaccagacacattctacaaccctca -s mr.mrrefChr0 64865 169 + 130230 AGAAAGCTGTTGTCATGTATACAGCAGCAAGAAGACCACACCTgcttcaggttcaccccattgaaggtaactcatgcatgcaattgtcaattggtattgtccattggtcctccttgtcctgtgacttgagcatattaattttataaccagacacattctacaaccctca -s simRat_chr6.simRat.chr6 60529 169 + 647215 ATAAAGCCGTTGTCATGTATACAGCAGCAAGAGGGCCACACCTGCTCGAGATTCACCCCACTGAGTGTgactcatgcatgcaattgtccattggtattgtccattggtcatccttatcttacaacttgagcacattaattttacaaccagatacatttgacaaccctca - -a -s simMouse_chr6.simMouse.chr6 68949 50 + 636262 ctgaggaatttgaggaggttactggattcctggatggtataggcttactt -s Anc0.Anc0refChr4 13746 8 - 45765 ------------------------------------GTCTATGC------ -s Anc1.Anc1refChr2 44826 13 + 144309 ------------------------------------GTCTATGCtca-tt -s Anc2.Anc2refChr7 13421 8 + 32194 ------------------------------------GTCTCTGC------ -s mr.mrrefChr0 65034 49 + 130230 ctgaggaatttgaggaggttactggattcctggatggtataggctta-tt -s simCow_chr6.simCow.chr6 71787 7 + 602619 ------------------------------------GCCTGTG------- -s simDog_chr6.simDog.chr6 68177 8 + 593897 ------------------------------------GTCTCTGC------ -s simHuman_chr6.simHuman.chr6 65190 13 + 601863 ------------------------------------GTCTATGCTCA-TT -s simRat_chr6.simRat.chr6 60703 49 + 647215 ctgatgaatttgacaaggttactggattcctggatggtataggctca-tt - -a -s simMouse_chr6.simMouse.chr6 68999 7 + 636262 tgggtgt -s Anc0.Anc0refChr4 13760 7 - 45765 TGGCTGT -s Anc1.Anc1refChr2 44845 7 + 144309 TGGCTGT -s Anc2.Anc2refChr7 13435 7 + 32194 TTGCTGT -s mr.mrrefChr0 65083 7 + 130230 tgggtgt -s simCow_chr6.simCow.chr6 71799 7 + 602619 CTGCTGT -s simDog_chr6.simDog.chr6 68191 7 + 593897 TTGCTGT -s simHuman_chr6.simHuman.chr6 65211 7 + 601863 TGGATGT -s simRat_chr6.simRat.chr6 60752 7 + 647215 tgggtgt - -a -s simMouse_chr6.simMouse.chr6 69006 23 + 636262 acgataatgtcatctgcaaatcc -s Anc0.Anc0refChr4 13775 23 - 45765 ATGAGAATGACTTTAGCAAATCC -s Anc1.Anc1refChr2 44860 23 + 144309 ATGAGAATGACTTTAGCAAATCC -s Anc2.Anc2refChr7 13450 23 + 32194 ATGAGAATAACTTTAGCAAATCC -s mr.mrrefChr0 65090 23 + 130230 acgataatgtcatctgcaaatcc -s simCow_chr6.simCow.chr6 71814 23 + 602619 ATGAGAGTAAATTTAGCATATCc -s simDog_chr6.simDog.chr6 68206 23 + 593897 ATGAGAATAACTTTAGCAAATCC -s simHuman_chr6.simHuman.chr6 65226 23 + 601863 ATGTGAATGGCTTTATCAAATCC -s simRat_chr6.simRat.chr6 60759 23 + 647215 acaatcctttcatctgcaaatcc - -a -s simMouse_chr6.simMouse.chr6 69029 1 + 636262 a -s Anc0.Anc0refChr4 13798 1 - 45765 T -s Anc1.Anc1refChr2 44883 1 + 144309 T -s Anc2.Anc2refChr7 13473 1 + 32194 T -s mr.mrrefChr0 65113 1 + 130230 a -s simCow_chr6.simCow.chr6 72042 1 + 602619 T -s simDog_chr6.simDog.chr6 68229 1 + 593897 T -s simHuman_chr6.simHuman.chr6 65249 1 + 601863 T -s simRat_chr6.simRat.chr6 60782 1 + 647215 a - -a -s simMouse_chr6.simMouse.chr6 69030 1 + 636262 a -s Anc0.Anc0refChr4 13799 1 - 45765 A -s Anc1.Anc1refChr2 44884 1 + 144309 A -s Anc2.Anc2refChr7 13474 1 + 32194 A -s mr.mrrefChr0 65114 1 + 130230 a -s simCow_chr6.simCow.chr6 72043 1 + 602619 A -s simDog_chr6.simDog.chr6 68230 1 + 593897 A -s simHuman_chr6.simHuman.chr6 65250 1 + 601863 A -s simRat_chr6.simRat.chr6 60786 1 + 647215 a - -a -s simMouse_chr6.simMouse.chr6 69031 25 + 636262 ccttaatctcctcttcatccagtca -s Anc0.Anc0refChr4 13803 20 - 45765 ACTTAA-CTTCTTTGGAT---GT-G -s Anc1.Anc1refChr2 44888 20 + 144309 ACTTAA-CTTCTTTGGAT---GT-G -s Anc2.Anc2refChr7 13478 20 + 32194 AGTTAA-CTTCTTTGGAA---AT-G -s mr.mrrefChr0 65115 22 + 130230 ccttaatctcctcttcat---gtca -s simCow_chr6.simCow.chr6 72047 20 + 602619 TGTTAA-CTTCTTTGGAA---AT-G -s simDog_chr6.simDog.chr6 68234 20 + 593897 AGTTAA-TCTCTTTGGAA---AT-G -s simHuman_chr6.simHuman.chr6 65254 20 + 601863 ACTTAA-CTTCTTTGGAT---GT-G -s simRat_chr6.simRat.chr6 60787 22 + 647215 gattaatctcctcttcat---gaca - -a -s simMouse_chr6.simMouse.chr6 69056 2 + 636262 cg -s Anc0.Anc0refChr4 13823 2 - 45765 GG -s Anc1.Anc1refChr2 44908 2 + 144309 GG -s Anc2.Anc2refChr7 13498 2 + 32194 GG -s mr.mrrefChr0 65137 2 + 130230 cg -s simCow_chr6.simCow.chr6 72068 2 + 602619 GG -s simDog_chr6.simDog.chr6 68254 2 + 593897 CG -s simHuman_chr6.simHuman.chr6 65274 2 + 601863 GG -s simRat_chr6.simRat.chr6 60809 2 + 647215 ca - -a -s simMouse_chr6.simMouse.chr6 69058 19 + 636262 catcttgcacctttcccct -s Anc0.Anc0refChr4 13825 7 - 45765 TATCTTG------------ -s Anc1.Anc1refChr2 44910 7 + 144309 TATCTTG------------ -s Anc2.Anc2refChr7 13504 7 + 32194 TATCTTG------------ -s mr.mrrefChr0 65139 19 + 130230 catcttgcacctttcccct -s simCow_chr6.simCow.chr6 72074 7 + 602619 TTCCTCG------------ -s simDog_chr6.simDog.chr6 68260 7 + 593897 TATGTTG------------ -s simHuman_chr6.simHuman.chr6 65276 7 + 601863 TATCTTG------------ -s simRat_chr6.simRat.chr6 60811 19 + 647215 cagcttgcaccttttccct - -a -s simMouse_chr6.simMouse.chr6 69077 24 + 636262 agcatattgTAACTTAAATTATAT -s Anc0.Anc0refChr4 13832 22 - 45765 AGAATG--GCAACATAAACCATGC -s Anc1.Anc1refChr2 44917 22 + 144309 AGAATG--GCAACATAAACCATGC -s Anc2.Anc2refChr7 13513 22 + 32194 AGAATG--GCCACATAAACCATGC -s mr.mrrefChr0 65158 24 + 130230 agcatattgTAACTTAAATTATAC -s simCow_chr6.simCow.chr6 72083 22 + 602619 AGAATG--GCCACCTAAACCATGC -s simDog_chr6.simDog.chr6 68269 22 + 593897 AGAATG--GCCACATAGACTATGC -s simHuman_chr6.simHuman.chr6 65283 22 + 601863 AGAATG--GCAACATAAACCCTGC -s simRat_chr6.simRat.chr6 60830 24 + 647215 agtatattgTAACTTGAATTATAC - -a -s simMouse_chr6.simMouse.chr6 69101 58 + 636262 GACACCCTATCAGGATACCATACAATGTAGTGTTGTGGCTTGATTGACATCCTATTCC -s Anc0.Anc0refChr4 13855 55 - 45765 GATAACCTATCAGAATACCCTACAATGTAAT-TTGTGGATTGTGT--TATTTTATTTC -s Anc1.Anc1refChr2 44940 57 + 144309 GATAACCTATCAGAATACCCTACAATGTAAT-TTGTGGATTGTGTGCTATTTTATTTC -s Anc2.Anc2refChr7 13536 55 + 32194 GATAACCTATCAGAATACCCTACAATGTAAT-TTGTGAATTGTGT--TACTTTGTTTT -s mr.mrrefChr0 65182 58 + 130230 GACACCCTATCAGGATACCATACAATGTAGTGTTGTGGCTTGTTTGACATCCTATTTC -s simCow_chr6.simCow.chr6 72106 55 + 602619 GGTGACCTATCAGAATACCCTACAATGTAAT-TCATAACTTGTAT--CACTTTGCTTT -s simDog_chr6.simDog.chr6 68292 55 + 593897 GATAATCTATCAGAATACCCTACAATGTAAT-TTGTGAATTGCGT--TACTTCGTTTT -s simHuman_chr6.simHuman.chr6 65306 56 + 601863 GTTAACCTATCAGTATACCCTACAATGTAAT-TTGTGGATT-TGTGCTGTTTTATTTC -s simRat_chr6.simRat.chr6 60854 57 + 647215 GACACCCCATCAGGATACCACACAATGTAGTATTGTGGC-TGTTTGACCTCCTATTTC - -a -s simMouse_chr6.simMouse.chr6 69159 14 + 636262 AGTGAGGTCACTTC -s Anc0.Anc0refChr4 13912 14 - 45765 AGTGAGATCATTCC -s Anc1.Anc1refChr2 44999 14 + 144309 AGTGAGATCATTCC -s Anc2.Anc2refChr7 13593 14 + 32194 AGCGAGATCATTCC -s mr.mrrefChr0 65240 14 + 130230 AATGAGGTCATTCC -s simCow_chr6.simCow.chr6 72163 14 + 602619 AGCGAGATCATTCC -s simDog_chr6.simDog.chr6 68349 14 + 593897 AGCAAGATCGTCCC -s simHuman_chr6.simHuman.chr6 65364 14 + 601863 AGTGAGATCATTCC -s simRat_chr6.simRat.chr6 60911 14 + 647215 AATGAGGTCTTTCC - -a -s simMouse_chr6.simMouse.chr6 69173 33 + 636262 TGTGTATGAGAGAAATACTTGAAAGTGTCTACA -s Anc0.Anc0refChr4 13947 33 - 45765 TGTGCAAGTGAGAAAAACTTGAAAACTTCGGCA -s Anc1.Anc1refChr2 45034 33 + 144309 TGTGCAAGTGAGAAAAACTTGAAAACTTCGGCA -s Anc2.Anc2refChr7 13628 33 + 32194 TGTGCAAGTGAGAAAAATTTGAAAACTTCGGCA -s mr.mrrefChr0 65254 33 + 130230 TGTGTAAGAGAGAAATACTTGAAAGTGTCTGCA -s simCow_chr6.simCow.chr6 72198 33 + 602619 TGTGCATGTGAGAGAAATTTGAAAACCTCAGCT -s simDog_chr6.simDog.chr6 68384 33 + 593897 TCTGGAAGTAAGGAAGATTTCAAAGCTTCGGCA -s simHuman_chr6.simHuman.chr6 65399 33 + 601863 TGTGCAAGTGGGAAAAACTTGGTGACTTCGGCA -s simRat_chr6.simRat.chr6 60925 33 + 647215 TGTGTAAGAGAGAAATACTTGAAAGTGTCTGCA - -a -s simMouse_chr6.simMouse.chr6 69206 80 + 636262 TGGTCTCTCTAGGACATGCATTTCCCCCCAAGTTGGTCCAGGTGCAGCTCAGAACTTGACACTTGGGATAGCTAGTTTCT -s Anc0.Anc0refChr4 13980 80 - 45765 CAGTTCCTTTAAAACTTGCGTTTGCCCTCAGGTTGGTACAGGTGCAGTTCAAAACTTGACACTTGGGATAACAGGTTCCC -s Anc1.Anc1refChr2 45067 80 + 144309 CAGTTCCTTTAAAACTTGCGTTTGCCCTCAGGTTGGTACAGGTGCAGTTCAAAACTTGACACTTGGGATAACAGGTTCCC -s Anc2.Anc2refChr7 13661 80 + 32194 CAGTTCCTTTAAAACTTGCGTTTGCCCTCAGCTTGGTACAGGTGCAGTTCAAAACTTGACACTTGAGATAACAAGTTCCC -s mr.mrrefChr0 65287 80 + 130230 TAGTTCCTCTAGAACATGCATTTCCCCTCAAGTTGGTACAGGTGCAGCTCAGAACTTGACACTTGGGATAACTGGTTTCT -s simCow_chr6.simCow.chr6 72236 80 + 602619 CCGTCCCTTTAAAACTTGCACTTGTCCTCAACTTAATGCAGGTGTAGTTCAACACTTGGCACTTGAGTTAACAAACTCTC -s simDog_chr6.simDog.chr6 68417 80 + 593897 TAGTTCCTTTAAAACTTGCGTTTGCCCTCAGCTTGGTACAGGTGCAGTTAAAAACTCAACACTTGAGAGACCGAGTTCCC -s simHuman_chr6.simHuman.chr6 65432 53 + 601863 CAGTTCCT-----------------------GTCAGTACAGGTACATTTCAAAAATTGACACCTGGGATAACAGGT---- -s simRat_chr6.simRat.chr6 60958 79 + 647215 TAGTTCCTCTAGAACA-GCATTTTCCCTCAAGTTGATACAGGAGCAGCTCAGAACTTGACACTTGCGATAACTGGTTTCT - -a -s simMouse_chr6.simMouse.chr6 69286 19 + 636262 GGAAGGTTTCTACCAAGGT -s Anc0.Anc0refChr4 14060 19 - 45765 AAAGGGTTCCTAAGAGGCA -s Anc1.Anc1refChr2 45147 19 + 144309 AAAGGGTTCCTAAGAGGCA -s Anc2.Anc2refChr7 13741 19 + 32194 AAAGGTTTCCTTAGAGGCA -s mr.mrrefChr0 65367 19 + 130230 GGAAGGCTTCTACCAGGGT -s simCow_chr6.simCow.chr6 72316 19 + 602619 AAAGGTTTCCTTAGAGGCA -s simDog_chr6.simDog.chr6 68498 19 + 593897 AAAGGTTTCCTTAAGGGCA -s simHuman_chr6.simHuman.chr6 65485 15 + 601863 ----GGTTCCTAAGAGGCA -s simRat_chr6.simRat.chr6 61037 19 + 647215 GGAAGGCTTCTACCAGGGT - -a -s simMouse_chr6.simMouse.chr6 69305 11 + 636262 GGAACACGACC -s Anc0.Anc0refChr4 14079 11 - 45765 AATTCACAACC -s Anc1.Anc1refChr2 45166 11 + 144309 AATTCACAACC -s Anc2.Anc2refChr7 13761 11 + 32194 AATTCACAACC -s mr.mrrefChr0 65386 11 + 130230 GGATCACAACC -s simCow_chr6.simCow.chr6 72336 11 + 602619 TATCCACTACT -s simDog_chr6.simDog.chr6 68518 11 + 593897 AATTCTCAACC -s simHuman_chr6.simHuman.chr6 65500 11 + 601863 AATGCACAACC -s simRat_chr6.simRat.chr6 61056 11 + 647215 GGATCACAACT - -a -s simMouse_chr6.simMouse.chr6 69316 11 + 636262 CAACAGTAAAT -s Anc0.Anc0refChr4 14090 11 - 45765 CAACAGCACAC -s Anc1.Anc1refChr2 45177 11 + 144309 CAACAGCACAC -s Anc2.Anc2refChr7 13772 11 + 32194 CAACAGCACAC -s mr.mrrefChr0 65397 11 + 130230 CAACAGTAAAC -s simCow_chr6.simCow.chr6 72347 11 + 602619 CAACGCCACAC -s simDog_chr6.simDog.chr6 68530 11 + 593897 CAACAGCACAT -s simHuman_chr6.simHuman.chr6 65511 11 + 601863 CAACAGCACAC -s simRat_chr6.simRat.chr6 61067 11 + 647215 TAAAAGTAAAC - -a -s simMouse_chr6.simMouse.chr6 69327 43 + 636262 GTTCTTCAAGAGACACATGGTAGTCCGCATTTGCTCTGACATG -s Anc0.Anc0refChr4 14139 39 - 45765 GTG----AAAAGACACTGAAAATTTTACCTTGGCTCAGAGATG -s Anc1.Anc1refChr2 45226 39 + 144309 GTG----AAAAGACACTGAAAATTTTACCTTGGCTCAGAGATG -s Anc2.Anc2refChr7 13827 39 + 32194 ATG----AAAAGACACTGAAAATTTTACCTTGGCCCAGAGATG -s mr.mrrefChr0 65408 39 + 130230 GTG----AAGAGACACAGAGTAGTTTGCATTTGCTCTGAGATG -s simCow_chr6.simCow.chr6 72402 39 + 602619 ATG----GAATGACACTGAAAATTTTACCTTGGCCAACAGATA -s simDog_chr6.simDog.chr6 68585 39 + 593897 ATG----AAAAGACACTGAAAATTTTATCTTGTCCCAGAGATG -s simHuman_chr6.simHuman.chr6 65561 39 + 601863 GTG----AAAAGACACTGAAAATTTTACCTTGGCTCAGAGATG -s simRat_chr6.simRat.chr6 61078 39 + 647215 GTG----AGGAGACACCGAGTAGTTTGGTTTTGCTCTGAGATG - -a -s simMouse_chr6.simMouse.chr6 69370 37 + 636262 CACCTCCGTTAACGTGAAGAAGTTCAAGCATTGCAGG -s Anc0.Anc0refChr4 14178 37 - 45765 CAACTCCGCTGGCATGAAGAAGTTTATGCATTCCAGG -s Anc1.Anc1refChr2 45265 37 + 144309 CAACTCCGCTGGCATGAAGAAGTTTATGCATTCCAGG -s Anc2.Anc2refChr7 13866 37 + 32194 TAACTTGGCTGGCACAAAGAAGTTTATGCATTCCAGG -s mr.mrrefChr0 65447 37 + 130230 CACCTCCGTTAGCATGAAGAAGTTCAAGCATTCCAGG -s simCow_chr6.simCow.chr6 72442 36 + 602619 TAACTTTGCTGGCACAAAGAAGTC-ATGCATTTCAGG -s simDog_chr6.simDog.chr6 68624 31 + 593897 ------GGCTGGCACAAAGTGGTTTATGCATACCAGG -s simHuman_chr6.simHuman.chr6 65600 37 + 601863 CAACTCCGCTGGCATGAAGAAGTTAATGCATTCCAGG -s simRat_chr6.simRat.chr6 61117 37 + 647215 CACCTCTGTTAGCATGAAGAAGTTCACACATCCCAGG - -a -s simMouse_chr6.simMouse.chr6 69407 5 + 636262 CATAT -s Anc0.Anc0refChr4 14298 5 - 45765 CATAT -s Anc1.Anc1refChr2 45385 5 + 144309 CATAT -s Anc2.Anc2refChr7 13986 5 + 32194 CTTAT -s mr.mrrefChr0 65484 5 + 130230 CATAT -s simCow_chr6.simCow.chr6 72561 5 + 602619 CGTAT -s simDog_chr6.simDog.chr6 68737 5 + 593897 CTTAT -s simHuman_chr6.simHuman.chr6 65724 5 + 601863 CATAT -s simRat_chr6.simRat.chr6 61154 5 + 647215 CACAT - -a -s simMouse_chr6.simMouse.chr6 69412 13 + 636262 TCATGCTTTACTT -s Anc0.Anc0refChr4 14303 13 - 45765 TATAGCTACAATA -s Anc1.Anc1refChr2 45390 13 + 144309 TATAGCTACAATA -s Anc2.Anc2refChr7 13991 13 + 32194 TATACCCACAACA -s mr.mrrefChr0 65489 13 + 130230 TCATGCTTCACTT -s simCow_chr6.simCow.chr6 72566 4 + 602619 TATA--------- -s simDog_chr6.simDog.chr6 68742 13 + 593897 TGTACCCACAACA -s simHuman_chr6.simHuman.chr6 65729 13 + 601863 TATAGCTACAATC -s simRat_chr6.simRat.chr6 61184 13 + 647215 TCATGCTTCACTT - -a -s simMouse_chr6.simMouse.chr6 69425 2 + 636262 AC -s Anc0.Anc0refChr4 14322 2 - 45765 AT -s Anc1.Anc1refChr2 45409 2 + 144309 AT -s Anc2.Anc2refChr7 14010 2 + 32194 AT -s mr.mrrefChr0 65508 2 + 130230 AT -s simDog_chr6.simDog.chr6 68761 2 + 593897 AT -s simHuman_chr6.simHuman.chr6 65748 2 + 601863 AT -s simRat_chr6.simRat.chr6 61203 2 + 647215 AT - -a -s simMouse_chr6.simMouse.chr6 69427 9 + 636262 TGAAGAAGC -s Anc0.Anc0refChr4 14325 9 - 45765 TCAAGATGC -s Anc1.Anc1refChr2 45412 9 + 144309 TCAAGATGC -s Anc2.Anc2refChr7 14013 9 + 32194 TCATGATGC -s mr.mrrefChr0 65510 9 + 130230 TGAAGAAGC -s simDog_chr6.simDog.chr6 68764 9 + 593897 TCATGATGC -s simHuman_chr6.simHuman.chr6 65751 9 + 601863 TCAAGATGC -s simRat_chr6.simRat.chr6 61205 9 + 647215 TAAAGAAGC - -a -s simMouse_chr6.simMouse.chr6 69436 23 + 636262 CTTGCACAAAAGGAAGGAATGGT -s Anc0.Anc0refChr4 14344 21 - 45765 --TGCACAAAAGGAGGTAATGGG -s Anc1.Anc1refChr2 45431 23 + 144309 ACTGCACAAAAGGAGGTAATGGG -s Anc2.Anc2refChr7 14032 21 + 32194 --TTCACAGAGGGGAGTAATGGG -s mr.mrrefChr0 65519 23 + 130230 CTTGCACAAAAGGAGGGAATGGT -s simDog_chr6.simDog.chr6 68785 21 + 593897 --TTCACAGAGGGGAGTAATGGG -s simHuman_chr6.simHuman.chr6 65772 23 + 601863 ACTGCACAAAAGGAGGTAATGAG -s simRat_chr6.simRat.chr6 61214 22 + 647215 TTGGCAC-AAAGGAGGAAATGGT - -a -s simMouse_chr6.simMouse.chr6 69459 18 + 636262 ATTACTTCATCTAGAATC -s Anc0.Anc0refChr4 14374 18 - 45765 ACTACTTCATCTTTTGCC -s Anc1.Anc1refChr2 45463 18 + 144309 ACTACTTCATCTTTTGCC -s Anc2.Anc2refChr7 14062 18 + 32194 ACCAATTCATCTTTTGCC -s mr.mrrefChr0 65542 18 + 130230 ATTACTTCATCTATAATC -s simCow_chr6.simCow.chr6 72572 18 + 602619 ACAAGGTCATCTTTTTTC -s simDog_chr6.simDog.chr6 68815 18 + 593897 ACCAATTCATCTTTTGCC -s simHuman_chr6.simHuman.chr6 65804 18 + 601863 ACTACTTCATCTTTTGCC -s simRat_chr6.simRat.chr6 61236 18 + 647215 ATCAGTTCATCTATGATC - -a -s simMouse_chr6.simMouse.chr6 69477 20 + 636262 CTTGCTGTTATGGCCTGCCT -s Anc0.Anc0refChr4 14392 16 - 45765 TTTGCTGCAATG----GACT -s Anc1.Anc1refChr2 45481 16 + 144309 TTTGCTGCAATG----GACT -s Anc2.Anc2refChr7 14080 16 + 32194 TTTGCTGCAATG----GACT -s mr.mrrefChr0 65560 16 + 130230 CTTGCTGTTATG----GCCT -s simCow_chr6.simCow.chr6 72590 16 + 602619 TCTGCTGCCATG----GACT -s simDog_chr6.simDog.chr6 68850 16 + 593897 TTTGCTGCAATG----GATT -s simHuman_chr6.simHuman.chr6 65822 16 + 601863 TTTGCTACAATA----GACT -s simRat_chr6.simRat.chr6 61254 16 + 647215 CTTGCTGTTATG----GCCT - -a -s simMouse_chr6.simMouse.chr6 69497 7 + 636262 AAGATTA -s Anc0.Anc0refChr4 14408 7 - 45765 GGGATTA -s Anc1.Anc1refChr2 45497 7 + 144309 GGGATTA -s Anc2.Anc2refChr7 14096 7 + 32194 GGGATTA -s mr.mrrefChr0 65576 7 + 130230 AAGATTA -s simCow_chr6.simCow.chr6 72606 7 + 602619 AGAATTA -s simDog_chr6.simDog.chr6 68867 7 + 593897 GAGATTA -s simHuman_chr6.simHuman.chr6 65838 7 + 601863 GGGATTA -s simRat_chr6.simRat.chr6 61270 7 + 647215 AAGATTA - -a -s simMouse_chr6.simMouse.chr6 69504 26 + 636262 GTGCTCAGAAAAATGCCCCACTGTTC -s Anc0.Anc0refChr4 14415 26 - 45765 GTAGTAGGAATAGTGCCAAAGTGGTC -s Anc1.Anc1refChr2 45504 26 + 144309 GTAGTAGGAATAGTGCCAAAGTGGTC -s Anc2.Anc2refChr7 14103 26 + 32194 GTAGTAGGATTAGTGCTAAGGTGGTC -s mr.mrrefChr0 65583 26 + 130230 GTACTCAGAAAAATGCCACACTGTTC -s simCow_chr6.simCow.chr6 72613 26 + 602619 GTACTAGGATTAGGGCTAGGGTGAAC -s simDog_chr6.simDog.chr6 68874 26 + 593897 GTAGTAGGCTACATGCTTAGATAGTC -s simHuman_chr6.simHuman.chr6 65845 26 + 601863 GTATTAGGAATAGTGTCAAAGTGGTC -s simRat_chr6.simRat.chr6 61278 26 + 647215 GTACTCAGAAAAATGCCACGCTGATA - -a -s simMouse_chr6.simMouse.chr6 69530 9 + 636262 TGGGCGGAC -s Anc0.Anc0refChr4 14441 9 - 45765 TGGGCAATC -s Anc1.Anc1refChr2 45530 9 + 144309 TGGGCAATC -s Anc2.Anc2refChr7 14129 9 + 32194 TGGGCAATC -s mr.mrrefChr0 65609 9 + 130230 TGGGCGGAC -s simCow_chr6.simCow.chr6 72640 9 + 602619 TGGGCAGCC -s simDog_chr6.simDog.chr6 68900 9 + 593897 TGGGCAATC -s simHuman_chr6.simHuman.chr6 65871 9 + 601863 TGACTAATC -s simRat_chr6.simRat.chr6 61304 9 + 647215 TGGGCGGCC - -a -s simMouse_chr6.simMouse.chr6 69539 43 + 636262 CCCCATAAAAAATATGACCTCTCTTTTTGGAGTTTTGAGAGTG -s Anc0.Anc0refChr4 14451 34 - 45765 CCCCATTAAAGATATGGCCTCTCTTCTGG---------GAGTG -s Anc1.Anc1refChr2 45540 34 + 144309 CCCCATTAAAGATATGGCCTCTCTTCTGG---------GAGTG -s Anc2.Anc2refChr7 14139 34 + 32194 CCCTATTAGAGATATGGCCTCTCTTCTGG---------GAGTG -s mr.mrrefChr0 65618 42 + 130230 CCCCATAAAAGATATGACCTCTCTTCTTGGAGTTTT-AGAGTG -s simCow_chr6.simCow.chr6 72650 34 + 602619 CCCTATTAGAGATATGAATTCTCTTCTGA---------GAGTG -s simDog_chr6.simDog.chr6 68910 34 + 593897 CCCTATTAGAGATATGGCCGCGCTTCTGG---------GAGTG -s simHuman_chr6.simHuman.chr6 65881 34 + 601863 CCCCATTAAAGATATGTCCTCTCTTCTGG---------GAGTG -s simRat_chr6.simRat.chr6 61313 42 + 647215 CCCCATAAAAGATATGACCTCTCTTCTTGGAGTTGT-AGAGTG - -a -s simMouse_chr6.simMouse.chr6 69582 41 + 636262 GTGACACTGTCTCCATCCTGTTGCTTCTCAGCTAAATGAAT -s Anc0.Anc0refChr4 14485 41 - 45765 GTGACACTGTGCCCATCCTTTTGCTGCTCAGCTAAATCAAG -s Anc1.Anc1refChr2 45574 41 + 144309 GTGACACTGTGCCCATCCTTTTGCTGCTCAGCTAAATCAAG -s Anc2.Anc2refChr7 14175 41 + 32194 GTGATACTGTGCCCATCCTTTTGCTGCTAGCCTAAATCAAG -s mr.mrrefChr0 65660 41 + 130230 GTGACACTGTCCCCATCCTGTTGCTTCTCAGCTAAATGAAT -s simCow_chr6.simCow.chr6 72686 12 + 602619 GCGATACTGTCC----------------------------- -s simDog_chr6.simDog.chr6 68946 41 + 593897 GTGGTACTGTGCCCATCCTTTTGCTGCTAGCCTAAATCAAG -s simHuman_chr6.simHuman.chr6 65915 41 + 601863 GTGACACTGTACCTATCCTTTTGCCGCTCAGCTAAATCAAG -s simRat_chr6.simRat.chr6 61355 37 + 647215 GT---TCTGTCCCCAACCTGTTGCTTCTCAGCTAAATGAT- - -a -s simMouse_chr6.simMouse.chr6 69623 41 + 636262 TAAATGAAACACATTTTATGTCAACGGACTCCAGTTTAACT -s Anc0.Anc0refChr4 14526 41 - 45765 AAAACAAAACTAATTTAATGGCAGCGGATCCCAACCTAACT -s Anc1.Anc1refChr2 45615 41 + 144309 AAAACAAAACTAATTTAATGGCAGCGGATCCCAACCTAACT -s Anc2.Anc2refChr7 14216 41 + 32194 AAAACAAACCTAATCCAATGGCAGTTGATCCCAACCTAACT -s mr.mrrefChr0 65701 41 + 130230 TAAATGAAACACATTTTATGTCAGCGGACTCCAATTTAACT -s simCow_chr6.simCow.chr6 72698 23 + 602619 ------------------TGGCAGTTGATTCCAACCTACAT -s simDog_chr6.simDog.chr6 68988 41 + 593897 AAAACAAACCTAATCCAATGGGAGTTGGGCCCAACCTAACT -s simHuman_chr6.simHuman.chr6 65956 41 + 601863 AAAACAAAACTGATTTAATAGCAGCGAATACCAACCTAACT -s simRat_chr6.simRat.chr6 61392 40 + 647215 -AAATGCAACACGTCTTATGTCAGCTGACTCCAATTTAACT - -a -s simMouse_chr6.simMouse.chr6 69664 29 + 636262 ATGGAGTATAAAAGTGACATTTCTCACAC -s Anc0.Anc0refChr4 14567 29 - 45765 AAGGAGTCTAAAAGTAGCATCTCTTACAT -s Anc1.Anc1refChr2 45656 29 + 144309 AAGGAGTCTAAAAGTAGCATCTCTTACAT -s Anc2.Anc2refChr7 14257 29 + 32194 AGGGAGTCTAAAAGGAGCACCGCTTACAT -s mr.mrrefChr0 65742 29 + 130230 AAGGAGTATAAAAGTGACATTTCTCACAC -s simCow_chr6.simCow.chr6 72722 29 + 602619 AGAGAGTCTACAAGGAGTACCCCTTACAT -s simDog_chr6.simDog.chr6 69029 29 + 593897 AGGGAGTCTAAAGGGGACACTGCTGACAT -s simHuman_chr6.simHuman.chr6 65997 29 + 601863 AAGACGTTTAAAAGTAGCATCTCTTTTGT -s simRat_chr6.simRat.chr6 61432 19 + 647215 AAGGA----------GATGTTTTTCACAC - -a -s simMouse_chr6.simMouse.chr6 69693 69 + 636262 CTTGCCAATCCCCTGGTACAAAGTTCCCGATGCAGGTACTCACACCAGTATACTTCTTCTTGCACCTGA -s Anc0.Anc0refChr4 14597 68 - 45765 CTTGCCAGTGCCATGCTAGAAATTTCCTTGAACATGTAGTCACACCAGCTTACTTCTTCTTGCA-CTGA -s Anc1.Anc1refChr2 45686 68 + 144309 CTTGCCAGTGCCATGCTAGAAATTTCCTTGAACATGTAGTCACACCAGCTTACTTCTTCTTGCA-CTGA -s Anc2.Anc2refChr7 14287 68 + 32194 CTTGCCAGTGCCATGCCAGAAATTTCCTTGAACATGTGGTCACACCAGCTTACCCCTTGTTGCA-CTGA -s mr.mrrefChr0 65772 69 + 130230 CTTGCCAATGCCCTGCTACAAATTTCCCTATGCAGGTACTCACACCAGTATACTTCTTCTTGCACCTGA -s simCow_chr6.simCow.chr6 72752 64 + 602619 CTTGCCAGTGCTATGCCA-AAATCTCCTTGAACATGTGGTCACACCAGCTTATCCCCTG---CA-CATA -s simDog_chr6.simDog.chr6 69059 68 + 593897 CTTGCCAGTGCCATGTCAGAAAATTCCTTGAACATGTGGTGATACCAGTTTGCCCCTTGTTGTA-CTGA -s simHuman_chr6.simHuman.chr6 66027 68 + 601863 ATTGCCAGTGCCATGCTAGAAATTCCCTTGAACATGTATCCACACCAGCTTAATTCTTCTTTCA-CTGC -s simRat_chr6.simRat.chr6 61452 69 + 647215 CTTGCCAATGCCCTGCTACAAATTTCCCTATGCAGGTACTCACACCAGTAGACTTCTTGTTGCGACTAA - -a -s simMouse_chr6.simMouse.chr6 69762 23 + 636262 AAACAGCTGGATGCATGTACACC -s Anc0.Anc0refChr4 14665 22 - 45765 AAACTCCTGGATCATTCTACA-T -s Anc1.Anc1refChr2 45754 23 + 144309 AAACTCCTGGATCATTCTACATT -s Anc2.Anc2refChr7 14355 22 + 32194 TAACTCCTGGATCATTCTACA-T -s mr.mrrefChr0 65841 23 + 130230 AAACAGCTGGATGAATGTACACC -s simCow_chr6.simCow.chr6 72818 22 + 602619 TAACTCCTGGATCTTCCTACA-T -s simDog_chr6.simDog.chr6 69127 22 + 593897 TAACTCATGGATCATTCTGAA-T -s simHuman_chr6.simHuman.chr6 66095 23 + 601863 AAGCTCCTGGATCATTTTACATT -s simRat_chr6.simRat.chr6 61521 23 + 647215 AAATGGCTAGATGAAACTATACC - -a -s simMouse_chr6.simMouse.chr6 69785 32 + 636262 TACCACAATCGCCAGCTGCTTATAATACCATG -s Anc0.Anc0refChr4 14687 31 - 45765 CACTGCCATAG-CAGATGCTTATAAGACCATG -s Anc1.Anc1refChr2 45777 31 + 144309 CACTGCCATAG-CAGATGCTTATAAGACCATG -s Anc2.Anc2refChr7 14377 31 + 32194 CATTGCCATAG-CAGATGCTCATAAGACCATG -s mr.mrrefChr0 65864 32 + 130230 CACCACAATAGCCAGCTGCTTATAATACCATG -s simCow_chr6.simCow.chr6 72847 31 + 602619 CATTGACATAG-CAGGTACTCAGAATACCATG -s simDog_chr6.simDog.chr6 69149 31 + 593897 CATTCCCACAG-GAGATGTGCATAAGACCATG -s simHuman_chr6.simHuman.chr6 66118 31 + 601863 CACTGCTGTAA-CAGATGCTTAAAACACAATG -s simRat_chr6.simRat.chr6 61544 32 + 647215 CACCACAATAGCCAGCTGCTTATAATACCATG - -a -s simMouse_chr6.simMouse.chr6 69817 54 + 636262 TGTTAGTTGTGTGCAACATTGACTTTAAAGGGATGAACACCCATTGAAGTCAGT -s Anc0.Anc0refChr4 14718 52 - 45765 TT--AGCTGTGAGCCACATTGGCTTTACAGGGATGAACATTTGTTGGAATCCGC -s Anc1.Anc1refChr2 45808 52 + 144309 TT--AGCTGTGAGCCACATTGGCTTTACAGGGATGAACATTTGTTGGAATCCGC -s Anc2.Anc2refChr7 14410 52 + 32194 TT--AGCTGTGAGCCACATTGGCTTTACAGGGATAAATATTTGTTGGTATCCGC -s mr.mrrefChr0 65896 52 + 130230 TG--AGTTGTGTGCAACATTGACTTTAAAGGGATGAACACCTGTTGAAGTCAGC -s simCow_chr6.simCow.chr6 72880 51 + 602619 TT--CGCTGTGCA-CACACTGACTTTAGAGGGATAAATGTTTGTTGGTATCCGC -s simDog_chr6.simDog.chr6 69182 52 + 593897 TT--AGCTGTGAGCAACATTGGAATTACAGGGATAAATATTTATTGGTATCTGA -s simHuman_chr6.simHuman.chr6 66149 49 + 601863 -----AATGAGCGCCACAGTGGCTTTTCAGGGATGGACATTTGTTGGAATCCAC -s simRat_chr6.simRat.chr6 61576 52 + 647215 TG--AGCTGTGTGCAACATTGACTTTAAAGGGATGAACACCTGTTGAAGTCAGC - -a -s simMouse_chr6.simMouse.chr6 69871 20 + 636262 GAAAGTATAAAACAACATTC -s Anc0.Anc0refChr4 14776 20 - 45765 AAAACTATAAGTTAACATTC -s Anc1.Anc1refChr2 45866 20 + 144309 AAAACTATAAGTTAACATTC -s Anc2.Anc2refChr7 14468 20 + 32194 AAAACTATAAGTTAACATTC -s mr.mrrefChr0 65954 20 + 130230 AAAAGTATAAAACAACATTC -s simCow_chr6.simCow.chr6 72937 20 + 602619 AAAAGTATAAGTTAACATTG -s simDog_chr6.simDog.chr6 69240 20 + 593897 AAAGCTATAAGTGAACATTC -s simHuman_chr6.simHuman.chr6 66204 19 + 601863 ATAA-TATAAGTTAACATTC -s simRat_chr6.simRat.chr6 61634 20 + 647215 AAAAGTATAAAACAACATTC - -a -s simMouse_chr6.simMouse.chr6 69891 46 + 636262 CTTTGCATGAAATTGCCTATAAAACCAGGAAAAGGCAGCCACATCC -s Anc0.Anc0refChr4 14797 42 - 45765 ---TGTATGAAATTGCCTGTAGAACTGATAAAAGGCAGCCAA-TAC -s Anc1.Anc1refChr2 45887 45 + 144309 ATTTGTATGAAATTGCCTGTAGAACTGATAAAAGGCAGCCAA-TAC -s Anc2.Anc2refChr7 14489 42 + 32194 ---TGTATGGAATTGCCTGTAGAACTGATAAAAGGCATGCAA-TAC -s mr.mrrefChr0 65974 46 + 130230 CTTTGCATGAAATTGCCTATAAAACCAGGAAAAGGCAGCCACATCC -s simCow_chr6.simCow.chr6 72960 42 + 602619 ---TGTATGGAATTACCTGTAGAACTGTTGAAAGGCATGCAA-AAC -s simDog_chr6.simDog.chr6 69261 42 + 593897 ---TGTATGGAATCGCCTGTAGAACTGATAAAAGGCATGACA-TCC -s simHuman_chr6.simHuman.chr6 66227 42 + 601863 ATTTGAGTGAAATTGTCT---GAACTCATAAAAAGCAGCCAT-TAC -s simRat_chr6.simRat.chr6 61654 45 + 647215 CATT-CATGAAATTACCCATAAAACCGGAAAAAGGCAGCCACATCC - -a -s simMouse_chr6.simMouse.chr6 69937 21 + 636262 TACCCTTACCTAACTGCGTAG -s Anc0.Anc0refChr4 14839 21 - 45765 TAACCCCACTTAATTGCGGAA -s Anc1.Anc1refChr2 45932 21 + 144309 TAACCCCACTTAATTGCGGAA -s Anc2.Anc2refChr7 14531 21 + 32194 TAACCCCACTTAATTTCAGAA -s mr.mrrefChr0 66020 21 + 130230 TACCCTTACTTAACTGCGTAG -s simCow_chr6.simCow.chr6 73003 21 + 602619 TAACTCAACATGATTTCAGCA -s simDog_chr6.simDog.chr6 69303 17 + 593897 TAACCCCACTTAA----AGAC -s simHuman_chr6.simHuman.chr6 66269 21 + 601863 TAACCCCACTCAGTTGCGGAA -s simRat_chr6.simRat.chr6 61699 21 + 647215 TACCCTTACTTAACTGCATAC - -a -s simMouse_chr6.simMouse.chr6 69958 30 + 636262 TGTTCTAATCCACCTAACATGGTTATGAAT -s Anc0.Anc0refChr4 14860 21 - 45765 TGTTTTTATCTGATTAG---------GAAT -s Anc1.Anc1refChr2 45953 21 + 144309 TGTTTTTATCTGATTAG---------GAAT -s Anc2.Anc2refChr7 14552 21 + 32194 TGTTTTTATCTGATTAA---------CAAT -s mr.mrrefChr0 66041 30 + 130230 TGTTTTAATCTACCTAGCATGGTTATGAAT -s simCow_chr6.simCow.chr6 73024 21 + 602619 TGTTTTTATCTGACTAC---------TAGT -s simDog_chr6.simDog.chr6 69320 16 + 593897 TGTT-----CTGATTAA---------CAAT -s simHuman_chr6.simHuman.chr6 66290 21 + 601863 TGTTTTTTCCTGTTTAG---------GAAG -s simRat_chr6.simRat.chr6 61723 29 + 647215 TGTTTTAATCTACCTAGTATGGTTATGAA- - -a -s simMouse_chr6.simMouse.chr6 69988 49 + 636262 GTTTTAGTCTGTGCAAGTGGAAAGCCCTTCCACCATTGCTTTCTTTAAT -s Anc0.Anc0refChr4 14881 48 - 45765 GTTTTAGTCTGCTCAA-TGAGGGCATGTTCCACTATTGATTTATTTAAT -s Anc1.Anc1refChr2 45974 48 + 144309 GTTTTAGTCTGCTCAA-TGAGGGCATGTTCCACTATTGATTTATTTAAT -s Anc2.Anc2refChr7 14588 48 + 32194 GTTTTAGTCTGCTCAA-TGAGGGCATGTTCCACAATTCATTTATTTAAT -s mr.mrrefChr0 66071 49 + 130230 GTTTTAGTCTGTGCAAGTGGAAAGCCCTTCCACTATTGCTTTCTTTAAT -s simCow_chr6.simCow.chr6 73060 48 + 602619 GCTTTAGTCTGCTCTG-TGGAGGCAGGTTCCACAAGCCAGTTGTTTAAC -s simDog_chr6.simDog.chr6 69351 48 + 593897 GTTTTAGTCTGCTCAA-TGAGGGCATTTTCCACCATTCATTTATTTGGT -s simHuman_chr6.simHuman.chr6 66311 34 + 601863 GTTTCAGTCTGATCA---------------CACTGAGGTTCTATTTAAT -s simRat_chr6.simRat.chr6 61752 38 + 647215 -----------TGCAAGTGAAGAGCCCTTCCACTATTGCTTTTTTTAAT - -a -s simMouse_chr6.simMouse.chr6 70037 28 + 636262 GGAACACTGTGCATTGAGCATAAGCCTG -s Anc0.Anc0refChr4 14930 9 - 45765 GGAACACTA------------------- -s Anc1.Anc1refChr2 46023 28 + 144309 GGAACACTACAAATCGTACTCAAGGCTG -s Anc2.Anc2refChr7 14637 9 + 32194 AGATCACTA------------------- -s mr.mrrefChr0 66121 28 + 130230 GGAACACTGTGAATTGAGCACAAGCCTG -s simCow_chr6.simCow.chr6 73109 9 + 602619 AGATCACTA------------------- -s simDog_chr6.simDog.chr6 69400 9 + 593897 AGATCACTA------------------- -s simHuman_chr6.simHuman.chr6 66347 28 + 601863 GGAATGTTACAAATCGTACTCAAGGCTG -s simRat_chr6.simRat.chr6 61791 28 + 647215 GGAACACTGTGAATTGAGGACAAGTCTG - -a -s simMouse_chr6.simMouse.chr6 70065 132 + 636262 CCAGTCCACGACACTATTGGTGCCTTGTCACTGGTCCAGCTTTTTTCTAAGTCCAAGAACTCTACGCCATCTTAACGCTAGATTCGATTCATGCATAGTTGGGTGTAAATGAGTTAGACCATACCCAGCATC -s Anc0.Anc0refChr4 14941 128 - 45765 TCAGTCCACGGCACTATTGGTG-CTTGACTCTGGTCCAGCTTTTTACTAAGTTCAGGGACTCTTGGCCAACTTGTCGCTAAACTCAGTTCATGCACGATCAGGTGCAATTGAGTTAGACTGTACCCAG---T -s Anc1.Anc1refChr2 46053 128 + 144309 TCAGTCCACGGCACTATTGGTG-CTTGACTCTGGTCCAGCTTTTTACTAAGTTCAGGGACTCTTGGCCAACTTGTCGCTAAACTCAGTTCATGCACGATCAGGTGCAATTGAGTTAGACTGTACCCAG---T -s Anc2.Anc2refChr7 14648 128 + 32194 TCAGTCCATGGCACTATTGGTG-CTTGACTCTGGTCCAGCTTTTTACTAAGTTTGGGGACTCTTGGCCAACCTGTCACTAAACTCAGTTCATACATGGTCAGGTACAGTTGAGTTAGACTGTACCCAG---T -s mr.mrrefChr0 66149 129 + 130230 CCAGTCCACGGCACTATTGGTGCCTTGTCACTGGTCCAGCTTTTTTCTAAGTTCAAGAACTCTACGCCATCTTAACGCTAGACTCAATTCATGCACAATTGGGTGTAAATGAGTTAGACCATACCCAG---C -s simCow_chr6.simCow.chr6 73137 120 + 602619 TCAGTCCATGGCACTATTGATG-CTTGACTCTAGCCCAGCTTTTTACTAAGTTTGGGGACTCTGGGCGAACCTGTCATTAAACTCAGTTCATACATGGTCAGGTATAGTTGAGTTCGACTG----------- -s simDog_chr6.simDog.chr6 69410 124 + 593897 -CAGTCCATGGCAGTATTGGTG-CTTAACTCTGGTCCAACTTTTTATTAAGTTT-GTGACTCTTGGACAACCTGCCACTAAACTTGGTTCACACATTGTCAAGTACA--TGAGTTAGACTGTACCCAG---T -s simHuman_chr6.simHuman.chr6 66383 128 + 601863 TCAGTCCACGGCACTATTGGTG-CTTGGCTCTGGTCCAGCTTTTTACTAAGTTCAGGGACCCTTGGCCAACTTTTTGCTAAGCTCAGTTTATGGACGATCAGGTGCAAGTGAGTTAGAGTGTACCCTG---T -s simRat_chr6.simRat.chr6 61819 112 + 647215 CCAGTACATGGTACTATTGGTGCCTTGTCACTGGTCCAGCTTTTTTCTAAGTTCAAGAACTCTGCGCCATCTTAACCCTAGACTCAATTCATGTGCAATTGGGTGTAAATGA-------------------- - -a -s simMouse_chr6.simMouse.chr6 70197 8 + 636262 TGCTGTAC -s Anc0.Anc0refChr4 15069 8 - 45765 TATTTGAC -s Anc1.Anc1refChr2 46181 8 + 144309 TATTTGAC -s Anc2.Anc2refChr7 14776 8 + 32194 TATTTGAC -s mr.mrrefChr0 66278 8 + 130230 TGCTGTAC -s simCow_chr6.simCow.chr6 73257 2 + 602619 ------AC -s simDog_chr6.simDog.chr6 69542 8 + 593897 TATTTGCC -s simHuman_chr6.simHuman.chr6 66511 8 + 601863 TATTACAC -s simRat_chr6.simRat.chr6 61931 3 + 647215 -----TAC - -a -s simMouse_chr6.simMouse.chr6 70205 2 + 636262 AT -s Anc0.Anc0refChr4 15077 2 - 45765 TT -s Anc1.Anc1refChr2 46189 2 + 144309 TT -s Anc2.Anc2refChr7 14784 2 + 32194 TT -s mr.mrrefChr0 66286 2 + 130230 TT -s simCow_chr6.simCow.chr6 73259 2 + 602619 TT -s simDog_chr6.simDog.chr6 69553 2 + 593897 TT -s simHuman_chr6.simHuman.chr6 66519 2 + 601863 TC -s simRat_chr6.simRat.chr6 61934 2 + 647215 TT - -a -s simMouse_chr6.simMouse.chr6 70207 11 + 636262 CAGTTAGTGCA -s Anc0.Anc0refChr4 15080 11 - 45765 CAGTTGGTGCA -s Anc1.Anc1refChr2 46192 11 + 144309 CAGTTGGTGCA -s Anc2.Anc2refChr7 14787 11 + 32194 CAGTTGGAGCA -s mr.mrrefChr0 66288 11 + 130230 CAGTTGGTGCA -s simCow_chr6.simCow.chr6 73262 10 + 602619 -AGTTGGGGCA -s simDog_chr6.simDog.chr6 69556 11 + 593897 CAGTTGGAGCA -s simHuman_chr6.simHuman.chr6 66522 11 + 601863 CCGTTGGTGCT -s simRat_chr6.simRat.chr6 61936 11 + 647215 CAGTTGGTGCA - -a -s simMouse_chr6.simMouse.chr6 70218 5 + 636262 GAGCA -s Anc0.Anc0refChr4 15092 5 - 45765 GAGCA -s Anc1.Anc1refChr2 46204 5 + 144309 GAGCA -s Anc2.Anc2refChr7 14799 5 + 32194 GAGCA -s mr.mrrefChr0 66300 5 + 130230 GAGCA -s simCow_chr6.simCow.chr6 73273 5 + 602619 GAGCA -s simDog_chr6.simDog.chr6 69568 5 + 593897 GAGTA -s simHuman_chr6.simHuman.chr6 66534 5 + 601863 GAGCA -s simRat_chr6.simRat.chr6 61948 5 + 647215 GAGCA - -a -s simMouse_chr6.simMouse.chr6 70223 4 + 636262 TTGT -s Anc0.Anc0refChr4 15098 4 - 45765 TTGT -s Anc1.Anc1refChr2 46210 4 + 144309 TTGT -s Anc2.Anc2refChr7 14805 4 + 32194 TTGT -s mr.mrrefChr0 66305 4 + 130230 TTGT -s simCow_chr6.simCow.chr6 73279 4 + 602619 TTGT -s simDog_chr6.simDog.chr6 69574 4 + 593897 TTGT -s simHuman_chr6.simHuman.chr6 66540 4 + 601863 TTGT -s simRat_chr6.simRat.chr6 61953 4 + 647215 TTGA - -a -s simMouse_chr6.simMouse.chr6 70227 4 + 636262 TAAC -s Anc0.Anc0refChr4 15102 4 - 45765 TAAC -s Anc1.Anc1refChr2 46214 4 + 144309 TAAC -s Anc2.Anc2refChr7 14811 4 + 32194 TAAC -s mr.mrrefChr0 66309 4 + 130230 TAAC -s simCow_chr6.simCow.chr6 73285 4 + 602619 TAAA -s simDog_chr6.simDog.chr6 69580 4 + 593897 TAAC -s simHuman_chr6.simHuman.chr6 66544 4 + 601863 AAAG -s simRat_chr6.simRat.chr6 61957 4 + 647215 TAAC - -a -s simMouse_chr6.simMouse.chr6 70231 24 + 636262 ACCGGGATTCAATGTCTGGTGCTC -s Anc0.Anc0refChr4 15106 24 - 45765 ACCCAGATTCAATGTCTGGAGCCC -s Anc1.Anc1refChr2 46218 24 + 144309 ACCCAGATTCAATGTCTGGAGCCC -s Anc2.Anc2refChr7 14815 24 + 32194 ACCCAGTTTCAATATCTGGAGCCC -s mr.mrrefChr0 66313 24 + 130230 ACCGGGATTCAATGTCTGGTGCTC -s simCow_chr6.simCow.chr6 73290 24 + 602619 AGCCAGTTTTAAATTCTGGAACTC -s simDog_chr6.simDog.chr6 69584 24 + 593897 ACCCAGTTTCAATATCTGAAGCCC -s simHuman_chr6.simHuman.chr6 66548 24 + 601863 ACCCAGATTCAATGGCTAGAGCAC -s simRat_chr6.simRat.chr6 61961 24 + 647215 ATCAGCATTCAATGTCTGGTGCTC - -a -s simMouse_chr6.simMouse.chr6 70255 74 + 636262 AGCATCTAGATTCTAGGACCAAGTGAGTCACAAGTTTGCAGTTGAAATGTGCAGGAAAGAAAGAAGCACTCACT -s Anc0.Anc0refChr4 15131 73 - 45765 TGCATCCAGGTAATAGGATGAAGTGTGACACAAGTTTGTGCCTGAAATGTGCAGGAAAGAAGAAAG-AAGCACT -s Anc1.Anc1refChr2 46243 73 + 144309 TGCATCCAGGTAATAGGATGAAGTGTGACACAAGTTTGTGCCTGAAATGTGCAGGAAAGAAGAAAG-AAGCACT -s Anc2.Anc2refChr7 14840 73 + 32194 TGCATCCAGGTAATTGGGTGAAGTGTGACACGAGTTTATGCCTGAAATGTGCAAGATAGAAGAAAG-AAGTACT -s mr.mrrefChr0 66337 74 + 130230 TGCATCTAGGTTCTAGGACCAAGTGAGACACAAGTTTGCAGTTGAAATGTGCAGGAAAGAAAGAAGCACTCACT -s simCow_chr6.simCow.chr6 73315 67 + 602619 TGCATCCAGGTAATCAGGTAAAGTGTGAC-----TTTCTACCTGAATTGTGAAAACTAGAAGGAAG-AAGTAT- -s simDog_chr6.simDog.chr6 69609 73 + 593897 TGGATCCAGGTAATTGGGTGAAGAGTGACACGAGTTTATGCCTGAAATGTGCAAGATAGAAGATAG-AAGTACT -s simHuman_chr6.simHuman.chr6 66573 73 + 601863 TGCATCCTGGTAGTAGAATGAAGTGCAACACAAGTTTGTGCCTGAAATGTGCAGGAAAGAAGAAAG-AGACACT -s simRat_chr6.simRat.chr6 61985 74 + 647215 TGCATCTAGGTTCTAGGACTGAGTGAGACACAAGTTTGCAGTTGAAATGTGAAAGAAAGAAAGGCACACTCACT - -a -s simMouse_chr6.simMouse.chr6 70329 14 + 636262 GTGTGTCATTGTAC -s Anc0.Anc0refChr4 15204 14 - 45765 CTGTGTCATTGTAT -s Anc1.Anc1refChr2 46316 14 + 144309 CTGTGTCATTGTAT -s Anc2.Anc2refChr7 14913 14 + 32194 CTGTGTCATTGTAC -s mr.mrrefChr0 66411 14 + 130230 GTGTGTCATTGTAT -s simCow_chr6.simCow.chr6 73382 9 + 602619 -----TCATTGTAC -s simDog_chr6.simDog.chr6 69684 14 + 593897 CTGTGTTGTTGTAC -s simHuman_chr6.simHuman.chr6 66646 14 + 601863 TTGTGTCATTGTAT -s simRat_chr6.simRat.chr6 62059 14 + 647215 GTGTGTCATTATAT - -a -s simMouse_chr6.simMouse.chr6 70343 29 + 636262 AGTTCCAAAAACATCAATTTGACTCTGGT -s Anc0.Anc0refChr4 15222 29 - 45765 AGTTCCAAATATGTATGGTCAGACCTGCT -s Anc1.Anc1refChr2 46334 29 + 144309 AGTTCCAAATATGTATGGTCAGACCTGCT -s Anc2.Anc2refChr7 14931 29 + 32194 ACTTCCAGATATGTATGGTCAGACCTACT -s mr.mrrefChr0 66425 29 + 130230 AGTTCCAAAAACATCAATTTGAACCTGGT -s simCow_chr6.simCow.chr6 73394 17 + 602619 ------------ATCTAGTCAGAGCTCCT -s simDog_chr6.simDog.chr6 69702 29 + 593897 ACTTCCAGATATGTACGACTGGACCCAAT -s simHuman_chr6.simHuman.chr6 66664 29 + 601863 AGTTCCCAATATGTTTGGTCAGACCTGCT -s simRat_chr6.simRat.chr6 62073 29 + 647215 AATTCCGAAAACATCAATTGGAACCTGGT - -a -s simMouse_chr6.simMouse.chr6 70372 7 + 636262 CAAATAC -s Anc0.Anc0refChr4 15251 5 - 45765 CAAAT-- -s Anc1.Anc1refChr2 46363 7 + 144309 CAAATAC -s Anc2.Anc2refChr7 14960 5 + 32194 CAAAT-- -s mr.mrrefChr0 66454 7 + 130230 CAAATAC -s simCow_chr6.simCow.chr6 73478 5 + 602619 CAATA-- -s simDog_chr6.simDog.chr6 69731 5 + 593897 CAGAT-- -s simHuman_chr6.simHuman.chr6 66693 7 + 601863 CAAATAC -s simRat_chr6.simRat.chr6 62102 7 + 647215 CAAATAC - -a -s simMouse_chr6.simMouse.chr6 70379 72 + 636262 ACAGAGTAGCCACTGTGTCAGGATACTCATCTGGGGTTGGAATGAACTTACTGCGGGTGTGAGTCAGGCCTG -s Anc0.Anc0refChr4 15281 68 - 45765 ACAGAGTAGGCA-TGTGACAGGATTTTTA---GGGGTCGGAATGAACTTACTGCTGGGCTGAATGAGACCTA -s Anc1.Anc1refChr2 46395 69 + 144309 ACAGAGTAGGCACTGTGACAGGATTTTTA---GGGGTCGGAATGAACTTACTGCTGGGCTGAATGAGACCTA -s Anc2.Anc2refChr7 14990 68 + 32194 ACAGCCTAGGCA-TGGGACAGGATTTTTA---GGGGTCGGGATGAACTCTCTATTGGGCTGAACGAGACTTA -s mr.mrrefChr0 66461 72 + 130230 ACAGAGTAGCCACTGTGTCAGGATATTCATCTGGGGTTGGAATGAACTTACTGCGGGTGTGAGTCAGGCCTG -s simCow_chr6.simCow.chr6 73509 56 + 602619 ACATCATAAATC-TGG----------TT-----GGGTGGGGCCTATATGTTTATTGGGCTGAGCCAAAAATG -s simDog_chr6.simDog.chr6 69755 68 + 593897 ACAGCCTAGGCA-TGGGACAGGATTTTTA---GGGGTCGGGATGAACTCTCTATTGGGCTGAACGAGACTTA -s simHuman_chr6.simHuman.chr6 66726 69 + 601863 ACAGAGTAGGCACTGTACCAGGATTTTTA---GGGGTCGGAATGGATTTACTGCAGGCTTGAATTAGACCTA -s simRat_chr6.simRat.chr6 62109 72 + 647215 ACAGAGTAGCCAAGGTGTTGGGATATTCATCAGGGCTTGGATTGAACTTACCGTGAGGGTTAGTAAGGCCTG - -a -s simMouse_chr6.simMouse.chr6 70451 11 + 636262 TATAATGATGT -s Anc0.Anc0refChr4 15349 11 - 45765 TATTATGATGG -s Anc1.Anc1refChr2 46464 11 + 144309 TATTATGATGG -s Anc2.Anc2refChr7 15058 11 + 32194 TATTATGAATG -s mr.mrrefChr0 66533 11 + 130230 TATAATGATGT -s simCow_chr6.simCow.chr6 73567 11 + 602619 TATGATTAGTG -s simDog_chr6.simDog.chr6 69823 11 + 593897 TGCTATGAATG -s simHuman_chr6.simHuman.chr6 66795 11 + 601863 TATTATGATGG -s simRat_chr6.simRat.chr6 62181 11 + 647215 TATGATGATGA - -a -s simMouse_chr6.simMouse.chr6 70462 11 + 636262 CCTTTTCCAAG -s Anc0.Anc0refChr4 15360 2 - 45765 CC--------- -s Anc1.Anc1refChr2 46475 2 + 144309 CC--------- -s Anc2.Anc2refChr7 15069 2 + 32194 AC--------- -s mr.mrrefChr0 66544 11 + 130230 CCTTTTCCAAG -s simCow_chr6.simCow.chr6 73578 2 + 602619 AG--------- -s simDog_chr6.simDog.chr6 69834 2 + 593897 AC--------- -s simHuman_chr6.simHuman.chr6 66806 2 + 601863 CC--------- -s simRat_chr6.simRat.chr6 62195 11 + 647215 TCTTTTCCAAG - -a -s simMouse_chr6.simMouse.chr6 70473 70 + 636262 ACGTGAAACTGGGGATTGAGAACGAGTGGCGTGCAAGGATTTTTACTTAATCTGCTGTCATTCAATCCTT -s Anc0.Anc0refChr4 15362 65 - 45765 ATCTGAAATAGTGGGTTGAGATTGAGTGGCGTG-CACGGATCACACTTAGTCTACCTTCCTTCATT---- -s Anc1.Anc1refChr2 46477 66 + 144309 ATCTGAAATAGTGGGTTGAGATTGAGTGGCGTGCCACGGATCACACTTAGTCTACCTTCCTTCATT---- -s Anc2.Anc2refChr7 15071 65 + 32194 ACCTGAAATAGTTGGTTGGGATGAGGTGGAGTG-TGCAGATCACACTTAGTCAACCTTCCTTTGTT---- -s mr.mrrefChr0 66555 66 + 130230 ATGTGAAATTGGGGATTGAGAATGAGTGGCGTGCAAGGATTTTTACTTAGTCTACTGTCATTCAAT---- -s simCow_chr6.simCow.chr6 73580 14 + 602619 GGGTGAAATAGGAG-------------------------------------------------------- -s simDog_chr6.simDog.chr6 69843 65 + 593897 ACCTGAAAGAGTTGGTTGGGATGAGGTGGAGTG-TGCAGATCACACTTAGTCAACCTTCCTTTGTT---- -s simHuman_chr6.simHuman.chr6 66808 66 + 601863 ATCTAAAATAGTGGCTTGAGATTGAGTGGCATGCCACGGAGCACACTTAGTCTACCATCCTTCAGT---- -s simRat_chr6.simRat.chr6 62206 65 + 647215 ATGTGAAATTGGGGATTGAGAATGAGTGG-GTGCAAGGATTTTTACTTAGTCTACTGTCATCCAAC---- - -a -s simMouse_chr6.simMouse.chr6 70543 9 + 636262 TAATCCTTG -s Anc0.Anc0refChr3 109133 7 + 222631 TGTTAGT-- -s Anc1.Anc1refChr6 142868 9 + 197743 TGTTAGTTG -s Anc2.Anc2refChr1 21074 7 + 142988 TGTTAGT-- -s mr.mrrefChr3 47113 9 + 181027 TATTAGTTG -s simCow_chr6.simCow.chr6 477439 7 + 602619 TGTTAGT-- -s simDog_chr6.simDog.chr6 467841 7 + 593897 TGTTAGT-- -s simHuman_chr6.simHuman.chr6 474745 9 + 601863 TGTTAGTTG -s simMouse_chr6.simMouse.chr6 492845 9 + 636262 TATTAGATG - -a -s simMouse_chr6.simMouse.chr6 70552 78 + 636262 AGATGGAAAAGTGGCCTTAAGGTCCCGATCTGCATTTATGACACCTTAGTTTAATGTTAAAGGCCTCTAGCCAGTTCT -s Anc0.Anc0refChr3 109140 75 + 222631 ---TGGAAGGGTGGCCTTAAGGTCCCGATCCACATCTATGTCACCTTACTTTAATATTGTAGGACTCTAGCCAGGTAT -s Anc1.Anc1refChr6 142877 78 + 197743 AGATGGAAGGGTGGCCTTAAGGTCCCGATCCACATCTATGTCACCTTACTTTAATATTGTAGGACTCTAGCCAGGTAT -s Anc2.Anc2refChr1 21081 75 + 142988 ---TGGAAGGGTGGCTTTAAGGTCCAGATCCACATCTATGTCACCTTACTTTAATATTGTAGGACTGTAGCTAGGTAT -s mr.mrrefChr3 47122 78 + 181027 AGATGGAAAAGTGGCCTTAAGGTCCCGATCTGCATTTATGACACCTTAGTTTAATGTTAAAGGCCTCTAGCCAGTTCT -s simCow_chr6.simCow.chr6 477446 68 + 602619 ---TGGAAGGGT-------AGGCCCTGATCCAAATCTATGTCTCTTTACTTTAAAATTGTAGGACTGTAGGTAGGTAT -s simDog_chr6.simDog.chr6 467848 75 + 593897 ---TGGTAAGGTGGCTTTAAGATCGAGATCCACATCTATGTCACCTTACTTTAATATTGTAGGGCTGTAGCTAGGTAT -s simHuman_chr6.simHuman.chr6 474756 78 + 601863 AGACAGTTGGGTGGTCTTGAGGTCCCAATCACTATATATGTCACCTTACTTTAGTATGGTAGGACTCTAGCCAGATGT -s simMouse_chr6.simMouse.chr6 492854 78 + 636262 AGATGGAAAAGTGGCCTTAAGGTCCCGATCTGCATTTATGACACCTTAGTTTAATGTTAAAGGCCTCTAGCCAGTTCT - -a -s simMouse_chr6.simMouse.chr6 70630 1 + 636262 A -s Anc0.Anc0refChr3 109234 1 + 222631 A -s Anc1.Anc1refChr6 142974 1 + 197743 A -s Anc2.Anc2refChr1 21175 1 + 142988 A -s mr.mrrefChr3 47200 1 + 181027 A -s simCow_chr6.simCow.chr6 477530 1 + 602619 G -s simDog_chr6.simDog.chr6 467942 1 + 593897 A -s simHuman_chr6.simHuman.chr6 474853 1 + 601863 A -s simMouse_chr6.simMouse.chr6 492932 1 + 636262 A - -a -s simMouse_chr6.simMouse.chr6 70631 1 + 636262 C -s Anc1.Anc1refChr2 46548 1 + 144309 T -s mr.mrrefChr0 66630 1 + 130230 C -s simHuman_chr6.simHuman.chr6 66879 1 + 601863 T -s simRat_chr6.simRat.chr6 62282 1 + 647215 C - -a -s simMouse_chr6.simMouse.chr6 70632 14 + 636262 ATGAACGGTCTGTC -s Anc1.Anc1refChr2 46549 14 + 144309 ATGAACTGTCTTAC -s mr.mrrefChr0 66631 14 + 130230 ATGAACTGTCTGTC -s simHuman_chr6.simHuman.chr6 66893 14 + 601863 ATGAACTGTCTTAC -s simRat_chr6.simRat.chr6 62283 14 + 647215 AAGAATTGTCTGTC - -a -s simMouse_chr6.simMouse.chr6 70646 127 + 636262 AATAATTTGGCATATATTGTCCTGTTGTGAATAGATGGTTATGTGCCCTAACTTAAATCTATCTTAGGATCTTTCACCCTCCACTAAGGATACTTATGTTTTACTAAGTCTAATGAAAAGTATATTA -s Anc0.Anc0refChr4 15431 99 - 45765 ---------------ATTGTCCTGTTTTGAATAGATGGAGATGTGCACTGACTTAAAGCCCTGTTAGGATATTTTTCCCTGCA-------------TTTTTGACTAAGTTTAATAAAAAGTACATTG -s Anc1.Anc1refChr2 46563 127 + 144309 TATAAGCAGGTGAATATTGTCCTGTTTTGAATAGATGGAGATGTGCACTGACTTAAAGCCCTGTTAGGATATTTTTCCCTGCATTAATGGTAATCCTTTTTGACTAAGTTTAATAAAAAGTACATTG -s Anc2.Anc2refChr7 15140 99 + 32194 ---------------ATTGCCCTGTTTTGAATAGATGGAGATGTGCACTGACTTAATGCTCTGTTAGGCTGATCTTGCCTGCA-------------TTTTTGACTAAGTTTAATAAAAAGTGCATGG -s mr.mrrefChr0 66645 127 + 130230 AATAATCTGGCATATATTGTCCTGTTGTGAATAGATGGTTATGTGCCCTAACTTAAATCCATCTTAGGATATTTCACCCTCCACTAAGGATAATCATGTTTTACTAAGTCTAATAAAAAGTATATTA -s simCow_chr6.simCow.chr6 73594 31 + 602619 ----------------------------------------------------------------------------------A-------------TTCCTAACAAAGCTTTAAGGCAAGTGCAT-G -s simDog_chr6.simDog.chr6 69912 99 + 593897 ---------------ATTGCCCTGTTTTGAATAGATGGAGATGTGCACTGACTTAATGCTCTGTTAGGCTGATCTTGCCTGCA-------------TCTTTGGCTCAGTTTAATAAACAGTGTATGG -s simHuman_chr6.simHuman.chr6 66908 127 + 601863 TATAAGCAGGTGAATACTGTTCTGTTTACAATATACGGAGATGTGCACTTACTTAAAGCCCTGTTAGGATATTTTGCCCCACATTAATGGTAATCCTTTTTGACTAAGTTAAATAAAAAGTACTTTG -s simRat_chr6.simRat.chr6 62297 127 + 647215 AATAATCTGGCATATATTGTCCCATTGTGAATAGATGGTTATGTGCCCTGATTTAAATCCATCTTAGGATATTTCCCCCTCCACTGAGGATAATCATGTTCTACTAAGTCTAATAGAAAGTATATCA - -a -s simMouse_chr6.simMouse.chr6 70773 15 + 636262 GCTCCAACCAGATTT -s Anc0.Anc0refChr4 15530 15 - 45765 CCCCCAACCAGATTT -s Anc1.Anc1refChr2 46690 15 + 144309 CCCCCAACCAGATTT -s Anc2.Anc2refChr7 15239 15 + 32194 CCCCCAACTAGATTT -s mr.mrrefChr0 66772 15 + 130230 GCTCCAACCAGATTT -s simCow_chr6.simCow.chr6 73625 10 + 602619 TCTCCATCTA----- -s simDog_chr6.simDog.chr6 70015 15 + 593897 CACCCAACTAGATTT -s simHuman_chr6.simHuman.chr6 67035 15 + 601863 CCCCTAACCAGACTT -s simRat_chr6.simRat.chr6 62424 15 + 647215 GCTCCAACCAGATTT - -a -s simMouse_chr6.simMouse.chr6 70788 50 + 636262 GATATGATAAATACATACATAGGTAGAAGGAACTATTCATGTCTAGGGAG -s Anc0.Anc0refChr4 15545 39 - 45765 GATGT----------AACATAGTTGGAAGGAA-TAACAATGTTTATGTAG -s Anc1.Anc1refChr2 46705 40 + 144309 GATGT----------AACATAGTTGGAAGGAACTAACAATGTTTATGTAG -s Anc2.Anc2refChr7 15267 39 + 32194 GATGG----------AACATAGTCGGAAGAAA-TAACAATATTTGTATAA -s mr.mrrefChr0 66787 49 + 130230 GATGTGATAAAT-CATACATAGGTAGAAGGAACTATTCATGTCTAGGGAG -s simCow_chr6.simCow.chr6 73648 39 + 602619 AATAC----------CAGTTTATGAGAAGAAT-TTACAAACATTTCATGA -s simDog_chr6.simDog.chr6 70049 39 + 593897 GATGG----------AACATAGTCGGAAGGAA-TAATGATATTTGTATAA -s simHuman_chr6.simHuman.chr6 67050 40 + 601863 GATGT----------GACATAGCTGGACAGAACTAACAATGTTTATGTAG -s simRat_chr6.simRat.chr6 62439 49 + 647215 GATGTGATAAAT-CATACATAGGTAGAAGGAATTATTCATCTCTGGGGAG - -a -s simMouse_chr6.simMouse.chr6 70838 22 + 636262 GCTCATGATATCAACTTCCTTG -s Anc0.Anc0refChr4 15585 22 - 45765 AAGTATCATAACAGCTTCCCTG -s Anc1.Anc1refChr2 46746 22 + 144309 AAGTATCATAACAGCTTCCCTG -s Anc2.Anc2refChr7 15307 22 + 32194 AAGTATCATAACAGCTTCCCTG -s mr.mrrefChr0 66836 22 + 130230 GCTCATGATATCAGCTTCCTTG -s simCow_chr6.simCow.chr6 73688 22 + 602619 AGTGGACTGAACTTCATCCCAG -s simDog_chr6.simDog.chr6 70089 22 + 593897 CAGTATCATAACAGCTTCCTTG -s simHuman_chr6.simHuman.chr6 67091 22 + 601863 AAGTATCGTAGTAGCTTCCCTG -s simRat_chr6.simRat.chr6 62488 22 + 647215 GCTCATGATATCAGCTTCCTTG - -a -s simMouse_chr6.simMouse.chr6 70860 5 + 636262 ATGTT -s Anc0.Anc0refChr4 15607 5 - 45765 ATGTT -s Anc1.Anc1refChr2 46768 5 + 144309 ATGTT -s Anc2.Anc2refChr7 15329 5 + 32194 ATGCT -s mr.mrrefChr0 66858 5 + 130230 ATGTT -s simCow_chr6.simCow.chr6 73711 5 + 602619 ATGCC -s simDog_chr6.simDog.chr6 70111 5 + 593897 ATGCT -s simHuman_chr6.simHuman.chr6 67113 5 + 601863 ACGTT -s simRat_chr6.simRat.chr6 62510 5 + 647215 AAATT - -a -s simMouse_chr6.simMouse.chr6 70865 60 + 636262 TATTACCCAGCCCACAAAATCCTTACAAAACTTTGGTCCCATTGGGCAGAACACGCAACT -s Anc0.Anc0refChr4 15612 58 - 45765 TCTCACTCATACCACAAGGTCCCTGCAAA--TTTGGATCCATCTGGTAGAATGTCTGACT -s Anc1.Anc1refChr2 46773 60 + 144309 TCTCACTCATACCACAAGGTCCCTGCAAAACTTTGGATCCATCTGGTAGAATGTCTGACT -s Anc2.Anc2refChr7 15352 58 + 32194 TCTCCATCATACCACAGGGTCCCTGCAAA--CTTGAATCCATCTGGTAGAATGTCTGACT -s mr.mrrefChr0 66863 60 + 130230 TATTACCCAGCCCACAAAATCCTTACAAAACTTTGGTCCCATTGGGCAGAACACCCAACT -s simCow_chr6.simCow.chr6 73750 52 + 602619 --TCCATCATTGTACAGGTCCCATGCAG------GATTCCACCCCCTAAAATTCCTGACT -s simDog_chr6.simDog.chr6 70137 55 + 593897 TCTC---CATACCACAGGGTCCCTGCAAA--CTTGAATCCATATGGAGGGATGTCAGACT -s simHuman_chr6.simHuman.chr6 67118 60 + 601863 TCTCACTCATGCCAAAAGGTCCCTGCGGAACTGTGGGTCCATCTGGTAGAATGTCTGAAT -s simRat_chr6.simRat.chr6 62515 60 + 647215 TATTACCTAGCCCACAAAATCCTTCCAAAACTTTGGTCCCATTGGGCAGAACACCCCACT - -a -s simMouse_chr6.simMouse.chr6 70925 9 + 636262 ATATCCAAA -s Anc0.Anc0refChr4 15670 9 - 45765 AGCTTCAGG -s Anc1.Anc1refChr2 46833 9 + 144309 AGCTTCAGG -s Anc2.Anc2refChr7 15410 9 + 32194 AGCTTCAGG -s mr.mrrefChr0 66923 9 + 130230 AGATCCAAA -s simCow_chr6.simCow.chr6 73858 9 + 602619 AGCTCCAAT -s simDog_chr6.simDog.chr6 70192 9 + 593897 AGCCTCAGG -s simHuman_chr6.simHuman.chr6 67178 9 + 601863 AGCTTCAGG -s simRat_chr6.simRat.chr6 62575 9 + 647215 TGATCTAAA - -a -s simMouse_chr6.simMouse.chr6 70934 37 + 636262 GTCTAATCTTCTAATGTGTGTTTCTTAGGGACAAGCC -s Anc0.Anc0refChr4 15679 37 - 45765 GTCCAATGTTCTCATCTGTGTATCTTAGGAACATGCC -s Anc1.Anc1refChr2 46842 37 + 144309 GTCCAATGTTCTCATCTGTGTATCTTAGGAACATGCC -s Anc2.Anc2refChr7 15419 37 + 32194 GTCCAATGTTCTCATCTGTGTATATTAAGAACATGCC -s mr.mrrefChr0 66932 37 + 130230 GTCTAATGTTCTAATGTGTGTTTCTTAGGGACAAGCC -s simCow_chr6.simCow.chr6 73875 37 + 602619 GTCCAAGGTTCTCGCCTGTGTATATTAAGGACAAGCC -s simDog_chr6.simDog.chr6 70201 37 + 593897 GTCCAATGTTCTCATCTGTCTATATTAAGAACATGCC -s simHuman_chr6.simHuman.chr6 67187 28 + 601863 GTCCAATGTTCTCATCTGTGTATCTCAG--------- -s simRat_chr6.simRat.chr6 62584 37 + 647215 TTCTAATGTTCTAATGTATGTTTCTTATGGACAAGCC - -a -s simMouse_chr6.simMouse.chr6 70971 66 + 636262 CAATTTGGTCTTCAGGCATTCATGGACTCTATAATGCACCCCTGGACACACATAAGGTACATAAGC -s Anc0.Anc0refChr4 15716 64 - 45765 CTAGTTG--CTTCAAGCTCTCATGGGCTCTATATTGCATCCCTGGGCACATGTAAGGTACACAAGT -s Anc1.Anc1refChr2 46879 64 + 144309 CTAGTTG--CTTCAAGCTCTCATGGGCTCTATATTGCATCCCTGGGCACATGTAAGGTACACAAGT -s Anc2.Anc2refChr7 15459 64 + 32194 CTAGTTA--TTTCAAGCTCTTATGGGCTCTATATTGCATCCCTGGGCACACATAAGGTACACAAGT -s mr.mrrefChr0 66969 66 + 130230 CAATTTGGTCTTCAAGCATTCATGGACTCTATAATGCACCCCTGGACACATGTAAGGTACATAAGC -s simCow_chr6.simCow.chr6 73915 60 + 602619 ATAGTTA--TTACAAGTTCTTATAGACTCTACA----ACCTCTGGGTACACATAAGGTACACAAGA -s simDog_chr6.simDog.chr6 70262 64 + 593897 CTAGTTA--TTTCAAGCTCTTATGGGCTTAATATTGCATCCCTCGGCACACATAAGGTACACAGGT -s simHuman_chr6.simHuman.chr6 67215 60 + 601863 ----TTG--CTTCAATCTGTCATGGGCTCTATACTGCATTCCTGGGCACCTGTAAGGTCCAGAAGT -s simRat_chr6.simRat.chr6 62621 66 + 647215 CCATCTGGCCTTCAAGCACTCGTGGACTCTATAATGCACCCCTGGACACATGGAAGGCACATAAGC - -a -s simMouse_chr6.simMouse.chr6 71037 57 + 636262 TTTTAAGCTTTGCCTGCTCCTCCCTAACTATGGCAAGTTAAGTTTCACCATATCATG -s Anc0.Anc0refChr4 15781 56 - 45765 TTTTAAACTACTCCCTATCTCCCCTGACTAT-GCAAGTTAAGTGCCACTGGATCACA -s Anc1.Anc1refChr2 46944 57 + 144309 TTTTAAACTACTCCCTATCTCCCCTGACTATGGCAAGTTAAGTGCCACTGGATCACA -s Anc2.Anc2refChr7 15524 56 + 32194 TTTTAAACCACTCCCTATCTCACCTGACTAT-GCAAGTTAAGTGCCACTGGATCACA -s mr.mrrefChr0 67035 57 + 130230 TTTTTAGCTTCTCCTGCTCCTCCCTAACTATGGCAAGTTAAGTTTCACCATATCATG -s simCow_chr6.simCow.chr6 73976 56 + 602619 TTTTAAGCCACTCCCTATCTCGTTATACTGT-GCAGGGTAAGTGCCACTATTTCGCA -s simDog_chr6.simDog.chr6 70327 56 + 593897 TCTCAAATCACTCCATGTCTCACCTGACTAT-GCAAGTTAAGTGCCACTGGATCACA -s simHuman_chr6.simHuman.chr6 67276 36 + 601863 TTTTAAACTGCTTCCTATCTGCCCTGACTAAGGGCA--------------------- -s simRat_chr6.simRat.chr6 62687 51 + 647215 TTATTAGCTTCTCCTGCTCCTCCCCAACTAT------TTAAGTATCACCATATCATG - -a -s simMouse_chr6.simMouse.chr6 71094 3 + 636262 TTT -s Anc0.Anc0refChr4 15837 3 - 45765 TTG -s Anc1.Anc1refChr2 47001 3 + 144309 TTG -s Anc2.Anc2refChr7 15580 3 + 32194 TTG -s mr.mrrefChr0 67092 3 + 130230 TTT -s simCow_chr6.simCow.chr6 74032 3 + 602619 TTG -s simDog_chr6.simDog.chr6 70384 3 + 593897 TTG -s simRat_chr6.simRat.chr6 62738 3 + 647215 CTT - -a -s simMouse_chr6.simMouse.chr6 71097 1 + 636262 A -s Anc0.Anc0refChr4 15840 1 - 45765 G -s Anc1.Anc1refChr2 47004 1 + 144309 G -s Anc2.Anc2refChr7 15583 1 + 32194 G -s mr.mrrefChr0 67095 1 + 130230 A -s simCow_chr6.simCow.chr6 74035 1 + 602619 T -s simDog_chr6.simDog.chr6 70387 1 + 593897 G -s simRat_chr6.simRat.chr6 62743 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 71098 9 + 636262 ATAAGAGTG -s Anc0.Anc0refChr4 15841 9 - 45765 ATAAGGGCG -s Anc1.Anc1refChr2 47005 9 + 144309 ATAAGGGCG -s Anc2.Anc2refChr7 15585 9 + 32194 ATAAGGGCA -s mr.mrrefChr0 67096 9 + 130230 ATAAGAGTG -s simCow_chr6.simCow.chr6 74037 9 + 602619 GTAAAGACA -s simDog_chr6.simDog.chr6 70389 9 + 593897 ATAAGGGCA -s simHuman_chr6.simHuman.chr6 67312 1 + 601863 --------G -s simRat_chr6.simRat.chr6 62744 9 + 647215 ATAAGAGCG - -a -s simMouse_chr6.simMouse.chr6 71107 8 + 636262 TAATGTTA -s Anc0.Anc0refChr4 15850 8 - 45765 AAATGCTA -s Anc1.Anc1refChr2 47014 8 + 144309 AAATGCTA -s Anc2.Anc2refChr7 15595 8 + 32194 AAATGCTA -s mr.mrrefChr0 67105 8 + 130230 TAATGTTA -s simCow_chr6.simCow.chr6 74047 8 + 602619 AGATGCTA -s simDog_chr6.simDog.chr6 70399 8 + 593897 AAGTCCTA -s simHuman_chr6.simHuman.chr6 67313 8 + 601863 AAATGCAA -s simRat_chr6.simRat.chr6 62753 8 + 647215 TACTGTTA - -a -s simMouse_chr6.simMouse.chr6 71115 11 + 636262 TTGATGGCATT -s Anc0.Anc0refChr4 15858 11 - 45765 TCAACAGCATC -s Anc1.Anc1refChr2 47022 11 + 144309 TCAACAGCATC -s Anc2.Anc2refChr7 15603 11 + 32194 TCAACAGCATC -s mr.mrrefChr0 67113 11 + 130230 TTGATGGCATC -s simCow_chr6.simCow.chr6 74056 11 + 602619 TCAACCACATC -s simDog_chr6.simDog.chr6 70407 11 + 593897 TGAACAGCATC -s simHuman_chr6.simHuman.chr6 67321 11 + 601863 TCAACAGCATC -s simRat_chr6.simRat.chr6 62761 11 + 647215 TTGATGGCACC - -a -s simMouse_chr6.simMouse.chr6 71126 33 + 636262 TCATTTTTGGAAGCCCAAGATGATCACAGGGAA -s Anc0.Anc0refChr4 15870 32 - 45765 TCATTTGTGGATG-CTGATACCATCACAGGTAT -s Anc1.Anc1refChr2 47034 32 + 144309 TCATTTGTGGATG-CTGATACCATCACAGGTAT -s Anc2.Anc2refChr7 15615 32 + 32194 TCATTTGTGGACA-CTGATACCATCACAGGTAT -s mr.mrrefChr0 67124 33 + 130230 TCATTTTTGGATGCCCAAGATGATCACAGGGTT -s simCow_chr6.simCow.chr6 74068 32 + 602619 CAATTAGTGAACA-CTGATATCATGACAGGTAT -s simDog_chr6.simDog.chr6 70419 32 + 593897 TCATTTGTGGACA-CTGATACCATCACAGGTAT -s simHuman_chr6.simHuman.chr6 67333 32 + 601863 TGGTTTGTGGATG-CTGATGCCTTCACAGGTAT -s simRat_chr6.simRat.chr6 62772 33 + 647215 TAATCTTTGGATGCCCAGGATGATCATAGGGTT - -a -s simMouse_chr6.simMouse.chr6 71159 25 + 636262 CGGCATGCCAAAAGTTTTTTGATTT -s Anc0.Anc0refChr4 15905 25 - 45765 CAGCATGAAGAAAGTCAATCATTTC -s Anc1.Anc1refChr2 47069 25 + 144309 CAGCATGAAGAAAGTCAATCATTTC -s Anc2.Anc2refChr7 15650 25 + 32194 CAGGATGAAGAAAGTCTATCATTTC -s mr.mrrefChr0 67157 25 + 130230 CGGCATGACAAAAGTTATTCAATTT -s simCow_chr6.simCow.chr6 74103 25 + 602619 CAAGATGAAAAAAATCTATCATTTC -s simDog_chr6.simDog.chr6 70454 25 + 593897 CAGGACAAAGATAGTCTATCAGTTC -s simHuman_chr6.simHuman.chr6 67368 25 + 601863 TAGCATGAAGAAAGGCAATCATATC -s simRat_chr6.simRat.chr6 62805 25 + 647215 CAACATGACAAAAGTTATTCAATTT - -a -s simMouse_chr6.simMouse.chr6 71184 23 + 636262 ATGCAGGTCTTTCAACTAGTATG -s Anc0.Anc0refChr4 15930 23 - 45765 TTCCAAGTTTTTCAATTAGTATT -s Anc1.Anc1refChr2 47094 23 + 144309 TTCCAAGTTTTTCAATTAGTATT -s Anc2.Anc2refChr7 15675 23 + 32194 TTCCAAGTTTTTCTATTAGTATT -s mr.mrrefChr0 67182 23 + 130230 TTGCAGGTCTTTCAACTAGTATT -s simCow_chr6.simCow.chr6 74128 23 + 602619 CTCCATGTCCTTCTAGTAGTATT -s simDog_chr6.simDog.chr6 70481 23 + 593897 TGCCAAGTTTTTCTATTTGTATT -s simHuman_chr6.simHuman.chr6 67393 23 + 601863 TTCCAAGTTTTTCAATTACTACT -s simRat_chr6.simRat.chr6 62830 23 + 647215 TTGCAGGTCTTTCGACTAGTATT - -a -s simMouse_chr6.simMouse.chr6 71207 7 + 636262 TTCAGCA -s Anc0.Anc0refChr4 15954 7 - 45765 TTCAGAG -s Anc1.Anc1refChr2 47118 7 + 144309 TTCAGAG -s Anc2.Anc2refChr7 15699 7 + 32194 TTCAGAG -s mr.mrrefChr0 67206 7 + 130230 TTCAGCA -s simCow_chr6.simCow.chr6 74152 7 + 602619 TTCAGAG -s simDog_chr6.simDog.chr6 70505 7 + 593897 TTCAGAG -s simHuman_chr6.simHuman.chr6 67417 7 + 601863 TTGGTAG -s simRat_chr6.simRat.chr6 62854 7 + 647215 TTCAGCA - -a -s simMouse_chr6.simMouse.chr6 71214 23 + 636262 TCTAAAATCCCTTACAGTCTTAT -s Anc0.Anc0refChr4 15962 23 - 45765 TTTAAAGTGCTTCACAGTCTTGT -s Anc1.Anc1refChr2 47126 23 + 144309 TTTAAAGTGCTTCACAGTCTTGT -s Anc2.Anc2refChr7 15707 23 + 32194 TTGAAAGTGCTTCACAGTATTGT -s mr.mrrefChr0 67213 23 + 130230 TCTAAAATCCTTTACAGTCTTAT -s simCow_chr6.simCow.chr6 74159 22 + 602619 -AGCAAATGCATCACAGTATTAT -s simDog_chr6.simDog.chr6 70513 23 + 593897 TTGAAAGTGCTTCATGGTATTGT -s simHuman_chr6.simHuman.chr6 67425 23 + 601863 TTTAAAGTGCTTCACAGTCTTGT -s simRat_chr6.simRat.chr6 62861 23 + 647215 TCTCAAATCCTTGACAGTCTTAT - -a -s simMouse_chr6.simMouse.chr6 71237 34 + 636262 CTCCACCCTCACAGTCTGATCTCCACCTGAATCT -s Anc0.Anc0refChr4 15986 13 - 45765 CTCTATC--------------------T-CACCT -s Anc1.Anc1refChr2 47150 14 + 144309 CTCTATC--------------------TGCACCT -s Anc2.Anc2refChr7 15731 13 + 32194 CTCTATC--------------------T-CACCT -s mr.mrrefChr0 67236 14 + 130230 CTCCACC--------------------TGAATCT -s simCow_chr6.simCow.chr6 74182 13 + 602619 TTCTATC--------------------T-CACCT -s simDog_chr6.simDog.chr6 70537 13 + 593897 CTCTGTC--------------------C-CACCT -s simHuman_chr6.simHuman.chr6 67449 14 + 601863 CTCTATC--------------------TGCACCT -s simRat_chr6.simRat.chr6 62884 14 + 647215 CTCCACC--------------------TGAATCT - -a -s simMouse_chr6.simMouse.chr6 71271 58 + 636262 CTTTGTTTGTTTTTAATGTAATGTGCATATAGGTAGCTGCATTAACTGAACTATAGTC -s Anc0.Anc0refChr4 16006 52 - 45765 TTCTCTTTGTTTTTACTA-----TGCAAGTAGGCAGCTGTGTTAACTGAGCTATAGT- -s Anc1.Anc1refChr2 47171 52 + 144309 TTCTCTTTGTTTTTACTA-----TGCAAGTAGGCAGCTGTGTTAACTGAGCTATAGT- -s Anc2.Anc2refChr7 15751 52 + 32194 TTCTCTATGTTTTTACTA-----TGCAAGTAGGCAGCTGTGTTAACTGAGCTATAAT- -s mr.mrrefChr0 67250 53 + 130230 CTTTGTTTGTTTTTAATG-----TGCATATAGGTAGCTGCATTAACTGAGCTATAGTC -s simCow_chr6.simCow.chr6 74202 52 + 602619 TCCTCTATGCCTTTACTG-----TGCTAGTAGGCAGCTGTGTTAACTGAGCTATGAT- -s simDog_chr6.simDog.chr6 70557 52 + 593897 ATCTTTATGTTTTTAGCA-----TGCAAGTAGGCAGCTGTATTAGCTGAGTTGTAAT- -s simHuman_chr6.simHuman.chr6 67470 51 + 601863 TTCT-CTTGTTTTTACTA-----TGCAAGTAGGCAGCTGTGTTAACTGAGCTATAGT- -s simRat_chr6.simRat.chr6 62898 53 + 647215 CTTTGTTTGTTTTTAATG-----TGTATTTAGGTAGCTTCATCAACTGAGCTATAGTC - -a -s simMouse_chr6.simMouse.chr6 71329 8 + 636262 ACACACCT -s Anc0.Anc0refChr4 16058 1 - 45765 -------T -s Anc1.Anc1refChr2 47223 1 + 144309 -------T -s Anc2.Anc2refChr7 15803 1 + 32194 -------T -s mr.mrrefChr0 67303 8 + 130230 ACACACCT -s simCow_chr6.simCow.chr6 74254 1 + 602619 -------T -s simDog_chr6.simDog.chr6 70609 1 + 593897 -------T -s simHuman_chr6.simHuman.chr6 67521 1 + 601863 -------T -s simRat_chr6.simRat.chr6 62952 8 + 647215 GCACACCT - -a -s simMouse_chr6.simMouse.chr6 71337 3 + 636262 CAT -s Anc0.Anc0refChr4 16059 3 - 45765 CTA -s Anc1.Anc1refChr2 47224 3 + 144309 CTA -s Anc2.Anc2refChr7 15807 3 + 32194 CTA -s mr.mrrefChr0 67311 3 + 130230 CAT -s simCow_chr6.simCow.chr6 74258 3 + 602619 CTA -s simDog_chr6.simDog.chr6 70613 3 + 593897 CTA -s simHuman_chr6.simHuman.chr6 67522 3 + 601863 CTG -s simRat_chr6.simRat.chr6 62960 3 + 647215 CAT - -a -s simMouse_chr6.simMouse.chr6 71340 166 + 636262 CGCAATCCTCCTATTTTTTCTCTGTCATGAGGCTTATAATGCCTTACGAGATGCAAGGGACGAAGACACTTCTGCACCATTGAATTTGTTATCAGGTCTATAATTCTGTGTGCATGAAAGGCAATGGAACTAAGAATTAAACCCCTCATTCTAGGTATCTACCCCT -s Anc0.Anc0refChr4 16063 102 - 45765 CCTGATTCTCCCATTTTGCCTTTATGATGAGGCCTATATTGCCT----------------------------------------------------------------TGTGCATGAAATGCAATGGACCTAAAGACAAAGGCCCTCATTCTAGGTTATTCCCCCT -s Anc1.Anc1refChr2 47228 102 + 144309 CCTGATTCTCCCATTTTGCCTTTATGATGAGGCCTATATTGCCT----------------------------------------------------------------TGTGCATGAAATGCAATGGACCTAAAGACAAAGGCCCTCATTCTAGGTTATTCCCCCT -s Anc2.Anc2refChr7 15811 102 + 32194 CCTGATTCTCCCATTTTGCCCTTATAATGAGGCCTATATTGCCT----------------------------------------------------------------TGTGCATGAAATGCAATGGACCTAAAGACAAAGGCCCTCATTCTAGGTTATTGCCCCT -s mr.mrrefChr0 67315 166 + 130230 CGCGATTCTCCTATTTTTCCTCTGTGATGAGGCTTATATTGCCTTACGAGATGCAAGGGACGAAGACACTTCTGCACCATTGAATTTGTTATCAGGTCTATAATTCTGTGTGCATGAAAGGCAATGGAACTAAGAATTAAACCCCTCATTCTAGGTAACTCCCCCT -s simCow_chr6.simCow.chr6 74262 102 + 602619 TCTGATTCTCTCATTCTGCCTTTGTAAAGAGGCCTACATGGCCT----------------------------------------------------------------TGTGCATAATATGCAATGGACTTAAAGACAGCGGCCCTGATTCTAGATTATTGCCCCT -s simDog_chr6.simDog.chr6 70617 102 + 593897 CCTCATTCTCCCATTTTGCCCTTATAATGAGGCCTATATTGCCT----------------------------------------------------------------TGCCCATGAAAGGCACTGGACCTAAAGACTAAGGCCCTCATCCTAGGTTATTGCCCCT -s simHuman_chr6.simHuman.chr6 67526 96 + 601863 CTTGATTCTCCCATTTTGCCT-TATGATGAGGCCTATATTGCCT----------------------------------------------------------------TGTGCACGAACTGCAATGTACCTAAAGACAAATATGGTCACTCCAGGTTATTC----- -s simRat_chr6.simRat.chr6 62964 166 + 647215 CCCGGTTCTCCTATTTTTCCTCTGTGATGAGGCTTATATTCCCTTATGAGACACAATTTACAAAAGGATTTCTGCACCATTGAATATGCTATCAGGCCTATATTTCTGTGTGCATGAAAGGCATTGGAGCTAACAGTTAAACCCCTCATTCTTGATAACTCCCCCT - -a -s simMouse_chr6.simMouse.chr6 71506 10 + 636262 TACATCAGTG -s Anc0.Anc0refChr4 16165 10 - 45765 TACCTGAGTG -s Anc1.Anc1refChr2 47330 10 + 144309 TACCTGAGTG -s Anc2.Anc2refChr7 15918 10 + 32194 TACCTGAGTG -s mr.mrrefChr0 67481 10 + 130230 TACATCAGTG -s simCow_chr6.simCow.chr6 74369 10 + 602619 TACTACAGTG -s simDog_chr6.simDog.chr6 70724 10 + 593897 TACCTGAGTG -s simHuman_chr6.simHuman.chr6 67622 10 + 601863 TGCCTTAGTG -s simRat_chr6.simRat.chr6 63130 10 + 647215 TACATCAGTG - -a -s simMouse_chr6.simMouse.chr6 71516 27 + 636262 ATTCATTATCTGTGCATGCAGATGGAT -s Anc0.Anc0refChr4 16177 27 - 45765 ATTCAGTATGTGTGCATGCAGGTGGAT -s Anc1.Anc1refChr2 47342 27 + 144309 ATTCAGTATGTGTGCATGCAGGTGGAT -s Anc2.Anc2refChr7 15930 27 + 32194 ATTCAGTATGTGTGCATGCAGGTGGAT -s mr.mrrefChr0 67491 27 + 130230 ATTCATTATCTGTGCATGCAGATGGAT -s simCow_chr6.simCow.chr6 74381 27 + 602619 ATCTAGTAGGCAAGCATGCAGTATAAT -s simDog_chr6.simDog.chr6 70736 25 + 593897 GTTCAGTATGTGTGCAGGT--GTGGGA -s simHuman_chr6.simHuman.chr6 67634 27 + 601863 AGTCAATATGGGTGGATCCTGGCGGAT -s simRat_chr6.simRat.chr6 63140 27 + 647215 ATTCATTATCTGTGCATGCAGATGGAT - -a -s simMouse_chr6.simMouse.chr6 71543 5 + 636262 ATGCA -s Anc0.Anc0refChr4 16207 5 - 45765 ATGCA -s Anc1.Anc1refChr2 47372 5 + 144309 ATGCA -s Anc2.Anc2refChr7 15960 5 + 32194 ATGCA -s mr.mrrefChr0 67518 5 + 130230 ATGCA -s simCow_chr6.simCow.chr6 74411 4 + 602619 ATGC- -s simDog_chr6.simDog.chr6 70764 5 + 593897 ATGCA -s simHuman_chr6.simHuman.chr6 67664 5 + 601863 AAGCA -s simRat_chr6.simRat.chr6 63167 5 + 647215 ATGCA - -a -s simMouse_chr6.simMouse.chr6 71548 78 + 636262 CATAGATTTACACTCATCGCATACACCTGATTTCTAAGGTGGTATTCCACCTCTTGACAGACCCTTATACAGATTTCT -s Anc0.Anc0refChr4 16213 55 - 45765 CATAGATTTCCACTCATTGCATAGGCCCCCT--------------------TCTTGCCACAGCCTTATACAGG---AC -s Anc1.Anc1refChr2 47378 75 + 144309 CATAGATTTCCACTCATTGCATAGGCCCCCTTTCCAGGTTTGTATCCCCCCTCTTGCCACAGCCTTATACAGG---AC -s Anc2.Anc2refChr7 15966 55 + 32194 CATATATTTCCCCTTATTGCATAGGCCCCCG--------------------TCTTGCCACAGCCTTATACCGG---AC -s mr.mrrefChr0 67523 78 + 130230 CATAGATTTCCACTCATTGCATACACCTGATTTCTAAGGTGGTATTCCACCTCTTGCCACACCCTTATACAGATTTCT -s simCow_chr6.simCow.chr6 74416 55 + 602619 CATGAATTTGCCCTTATTGCATAGGCATCCC--------------------TCTTGCCCTGAACCCATACGGG---AC -s simDog_chr6.simDog.chr6 70770 47 + 593897 AACATCTGCCC-----TTGCATGGATCCCTG--------------------TCTTGCCACAGCCTTATGCCG------ -s simHuman_chr6.simHuman.chr6 67670 75 + 601863 CATAGATTTCCACTCATTCTATAGGCCCCCTTTCCAGGTTTGTATCCCCCCCCTTGCCACAGCCTTATAAAGG---AC -s simRat_chr6.simRat.chr6 63172 78 + 647215 CATAGATTTCCACTCATTGCATACTCCTGATTTTTAAGGCGGTATTCCACCGCTTGCCACATCCTTATACAGAGTTCT - -a -s simMouse_chr6.simMouse.chr6 71626 44 + 636262 CCTGCCACATCCTTATACAATGTGTGGTTATGTGCACATGTGCC -s Anc0.Anc0refChr4 16268 20 - 45765 CTTGC------------------------ATGTGTGCATGTGCC -s Anc1.Anc1refChr2 47453 20 + 144309 CTTGC------------------------ATGTGTGCATGTGCC -s Anc2.Anc2refChr7 16021 20 + 32194 CTAGC------------------------ATGGGTGCATGCACC -s mr.mrrefChr0 67601 44 + 130230 CTTGCCACATCCTTATACAATGTGTGGTTATGTGCACATGTGCC -s simCow_chr6.simCow.chr6 74471 7 + 602619 -------------------------------------ATGCACC -s simDog_chr6.simDog.chr6 70817 20 + 593897 CTAGC------------------------ATGGGTGCATGCACC -s simHuman_chr6.simHuman.chr6 67745 20 + 601863 CTTGC------------------------ATGTGAGGATGTGCC -s simRat_chr6.simRat.chr6 63267 44 + 647215 CTTGCCACATCCTTATACAATAAGTACTTATGTGCACATGAGCC - -a -s simMouse_chr6.simMouse.chr6 71670 41 + 636262 ATGGTAATGACATCAATATAGCTGCCCAGTTTTGTGGCAGC -s Anc0.Anc0refChr4 16288 41 - 45765 AAGGCAATCAGATTTATATCATTGCTCAGTATTATTGCATC -s Anc1.Anc1refChr2 47473 41 + 144309 AAGGCAATCAGATTTATATCATTGCTCAGTATTATTGCATC -s Anc2.Anc2refChr7 16068 41 + 32194 AAGCCAATCAGATTTACATCATTGCTCAGTATTATTGCATC -s mr.mrrefChr0 67645 41 + 130230 ATGGTAATGACATCAATATAGTTGCCCAGTTTTGTTGCAGC -s simCow_chr6.simCow.chr6 74506 41 + 602619 ATGCCAATCAGATTTACATCATTGCCCAGTTTTATTGCATC -s simDog_chr6.simDog.chr6 70864 40 + 593897 AAGCCAATCAGATTATCATCATTATTCAATA-TATTACATC -s simHuman_chr6.simHuman.chr6 67765 41 + 601863 ACGGCAAACAGATTTATATCATTGCTCAGTATTATTGCGTC -s simRat_chr6.simRat.chr6 63311 41 + 647215 ATGGTAATGTCATCATCATAGTTGCCCAGTTTTGTTGCAGC - -a -s simMouse_chr6.simMouse.chr6 71711 115 + 636262 CCAATAGGTACATAACTGGAGAATCACTTGGACGTGGAGGATCACCTGGGAATATAAGACTAAGGCACTCAGATTTATAGGATGGCTTTATAGAGGATGGCTTGTGGGTTGGGGA -s Anc0.Anc0refChr4 16331 86 - 45765 CCAAGAGATACTTATTCAGGGA---------------AGGATCACCTGGAAATATAAGACTAAAGTACCCAGATTCATAGAATATCTTT--------------GTGGGCTGGGGG -s Anc1.Anc1refChr2 47516 86 + 144309 CCAAGAGATACTTATTCAGGGA---------------AGGATCACCTGGAAATATAAGACTAAAGTACCCAGATTCATAGAATATCTTT--------------GTGGGCTGGGGG -s Anc2.Anc2refChr7 16111 86 + 32194 ACAAGAGATACTTATTCAGGGA---------------AGAATCACCTGGAAATATAAGACTAAAGTACCCAGACTCATAGAACATCTTT--------------GTGGGCTTGGGG -s mr.mrrefChr0 67686 101 + 130230 CCAATAGGTACATAACTAGAGAATCACTTGGACGTGGAGGATCACCTGGGAATATAAGACTAAGGCACTCAGATTTATAGGATGGCTTT--------------GTGGGCTGGGGG -s simCow_chr6.simCow.chr6 74549 86 + 602619 TCAAGAGGTACTTATTTAGGGA---------------AGAATCACTTAGAAATATAAGACTAAAGGACCCAGACCCATAGAACATCTTT--------------GTGGTCTTAGGG -s simDog_chr6.simDog.chr6 70906 86 + 593897 ACACGAGAGACTTAGTCAGGGA---------------AGAATAACCTGGAAATATGAGACTAGATTACCCAGTCTAATAGCACATTTTT--------------GTGGGCTTGGGG -s simHuman_chr6.simHuman.chr6 67808 86 + 601863 CCAAGCGATACTTATTCAGGGA---------------AGGACCACCTGTAAATATATGACTAACGTACCCAGATTCATAGAATACCTCT--------------GTGGGCTGGGGG -s simRat_chr6.simRat.chr6 63352 101 + 647215 CCATTAGGTACATAAGTAGAGAATCCCCTGGGAGTGGAGACTTACCTGGGAATCTAAGACTAAGGCACTCAAATTTATACGATGGCTTT--------------GTGCGCTGGGAG - -a -s simMouse_chr6.simMouse.chr6 71826 9 + 636262 AGAAGGGGA -s Anc0.Anc0refChr4 16421 4 - 45765 AG-----GA -s Anc1.Anc1refChr2 47606 9 + 144309 AGCAGGAGA -s Anc2.Anc2refChr7 16201 4 + 32194 AG-----GT -s mr.mrrefChr0 67787 9 + 130230 AGAAGGAGA -s simCow_chr6.simCow.chr6 74639 4 + 602619 GG-----GT -s simDog_chr6.simDog.chr6 70996 4 + 593897 AG-----GT -s simHuman_chr6.simHuman.chr6 67898 9 + 601863 AGCAGGATA -s simRat_chr6.simRat.chr6 63453 9 + 647215 AGAAGGAGA - -a -s simMouse_chr6.simMouse.chr6 71835 60 + 636262 CTATCATAAGCATTCACAGGGTTTAGGTCACCCAGTGATAGCTTCCCCTAAGAGCAATTT -s Anc0.Anc0refChr4 16427 60 - 45765 GTATCAGTGGTATGTGCAGGCTTCAGGCCATCCAGTGATTGCTTCCCCTAGGAGCAATTT -s Anc1.Anc1refChr2 47617 60 + 144309 GTATCAGTGGTATGTGCAGGCTTCAGGCCATCCAGTGATTGCTTCCCCTAGGAGCAATTT -s Anc2.Anc2refChr7 16207 60 + 32194 GTATAAGTGGTATGTGCAGGCTTCAGGCCATCCAGTGGTTGCTTCCCCTAGGAGCGATTT -s mr.mrrefChr0 67796 60 + 130230 GTATCATAGGCATGCACAGGGTTCAGGCCATCCAGTGATAGCTTCCCCTAGGAGCAATTT -s simCow_chr6.simCow.chr6 74645 59 + 602619 G-GTAAGTGGTATGTGCAGGTGTTATGTCGTTCAATGGTTGCTTCCCCCAGGAGTGATTT -s simDog_chr6.simDog.chr6 71002 60 + 593897 GTATAAGTGGTACGTGCAGGCTTCAGGCCATCCAGTGGTTGCTTCCCCTAGGAGCGATTT -s simHuman_chr6.simHuman.chr6 67909 59 + 601863 GTATCAGTGGTATGTGCAGGCTTCAGGCCAT-GAGTGATTGCTTTGCCTAGGAGCAATTT -s simRat_chr6.simRat.chr6 63462 60 + 647215 GTATCATAGGCATGCACAGGGTTCAGGCCATCCAGTGATAGCTTCCCCTAGGAGAGATTT - -a -s simMouse_chr6.simMouse.chr6 71895 69 + 636262 CTGGAAAGCCCCAATTACCAAGTCCACTTCCAGTCCTAGACTTCAAAATAAATGGGCTATGCTATAGCC -s Anc0.Anc0refChr4 16487 63 - 45765 CCAGAAAGCCAGAATAAACAAGCCCAT------TCTTAGCTTTTAAGTTAGAGGAGCTAGGTCTAAGCC -s Anc1.Anc1refChr2 47677 63 + 144309 CCAGAAAGCCAGAATAAACAAGCCCAT------TCTTAGCTTTTAAGTTAGAGGAGCTAGGTCTAAGCC -s Anc2.Anc2refChr7 16273 63 + 32194 CCAGAACATCAGGATAAACAAGCCCAT------TCTTAGCTTTTTAGTTAGAGGAGCCAGGTCTAAGCC -s mr.mrrefChr0 67856 69 + 130230 CCAGAAAGCCCCAATAACCAAGTCCACTTCCAGTCTTAGACTTCAAAATAAATGGGCTATGCTTTAGCC -s simCow_chr6.simCow.chr6 74710 45 + 602619 CCAGAACATCA------------------------TTAGCTTTTTAGTTAGAGGAGTCAGGTCTAAGTC -s simDog_chr6.simDog.chr6 71068 63 + 593897 CCAGAACATTAGGATAAACAAGCCCAT------TCTTAACTTTTTAAACAGGGGAGCCATGTCTAAGCC -s simHuman_chr6.simHuman.chr6 67968 63 + 601863 CCAACAAGCCAGAATACACTAGCCCAT------TCTTTGCTTTTAAGTTAGAGGAGCTAGGTCTAAGCT -s simRat_chr6.simRat.chr6 63522 69 + 647215 CCAGAAAGCCCCAATAACCAAGTCCACTTCCCCTCTTAGACTTCAAAATATATGGGCTATACGTTAGCC - -a -s simMouse_chr6.simMouse.chr6 71964 9 + 636262 CATTTAGTG -s Anc0.Anc0refChr4 16552 9 - 45765 CGTGGAGCA -s Anc1.Anc1refChr2 47742 9 + 144309 CGTGGAGCA -s Anc2.Anc2refChr7 16338 9 + 32194 TGTGGAGCA -s mr.mrrefChr0 67925 9 + 130230 CATTTAGTA -s simCow_chr6.simCow.chr6 74757 9 + 602619 GGTGGAGAA -s simDog_chr6.simDog.chr6 71133 9 + 593897 TGAGGGGCA -s simHuman_chr6.simHuman.chr6 68033 9 + 601863 CGTGGAGCA -s simRat_chr6.simRat.chr6 63591 9 + 647215 CATTTAGTA - -a -s simMouse_chr6.simMouse.chr6 71973 13 + 636262 CATCCTGGTTGAA -s Anc0.Anc0refChr4 16561 13 - 45765 GTTACTTATTGTA -s Anc1.Anc1refChr2 47751 13 + 144309 GTTACTTATTGTA -s Anc2.Anc2refChr7 16360 13 + 32194 GTTACTTATGGTA -s mr.mrrefChr0 67934 13 + 130230 CATCCTGATTGAA -s simCow_chr6.simCow.chr6 74780 13 + 602619 ACTACTTTTGGCA -s simDog_chr6.simDog.chr6 71155 13 + 593897 GTCACTTATGGTA -s simHuman_chr6.simHuman.chr6 68042 13 + 601863 GTTACTTATTGTA -s simRat_chr6.simRat.chr6 63600 13 + 647215 CATCCTGATTGAA - -a -s simMouse_chr6.simMouse.chr6 71986 18 + 636262 AAATCAGATGGGGGGAAT -s Anc0.Anc0refChr4 16583 18 - 45765 GGACCCCCAGTGGTGAAT -s Anc1.Anc1refChr2 47773 18 + 144309 GGACCCCCAGTGGTGAAT -s Anc2.Anc2refChr7 16382 18 + 32194 GGACCCCCAGTGGTGAAT -s mr.mrrefChr0 67947 18 + 130230 GAATCAGCTGGGGGGAAT -s simCow_chr6.simCow.chr6 74802 18 + 602619 GGATCCCCAGGGGTGATT -s simDog_chr6.simDog.chr6 71177 18 + 593897 GGACCCCCAGTGGTGAAT -s simHuman_chr6.simHuman.chr6 68064 18 + 601863 GGAGCCCCAGAGGTGAAT -s simRat_chr6.simRat.chr6 63613 18 + 647215 GAATCAGCTGGGGGGAAT - -a -s simMouse_chr6.simMouse.chr6 72004 21 + 636262 TAGTCCAAGTTAGAACAGAAG -s Anc0.Anc0refChr4 16608 21 - 45765 TAGTATAAACTAGAACAGAAA -s Anc1.Anc1refChr2 47798 21 + 144309 TAGTATAAACTAGAACAGAAA -s Anc2.Anc2refChr7 16407 21 + 32194 AAGTATAAACTAGAACAGAAA -s mr.mrrefChr0 67965 21 + 130230 TAGTCCAAGTTAGAACAGAAG -s simCow_chr6.simCow.chr6 74827 21 + 602619 ATGTATAAATTAGAACGGAAG -s simDog_chr6.simDog.chr6 71202 21 + 593897 AAGGATAAACTAGAACAGAAA -s simHuman_chr6.simHuman.chr6 68089 21 + 601863 TAGTATAAAGTAGAACAGAAA -s simRat_chr6.simRat.chr6 63631 21 + 647215 TAGTCCAAGTTAATATGGAAG - -a -s simMouse_chr6.simMouse.chr6 72025 11 + 636262 TGTCAGAAGGG -s Anc0.Anc0refChr4 16629 11 - 45765 TAACAAAAGGA -s Anc1.Anc1refChr2 47819 11 + 144309 TAACAAAAGGA -s Anc2.Anc2refChr7 16428 11 + 32194 TAACAAAACGA -s mr.mrrefChr0 67986 11 + 130230 TGACAGAAGGG -s simCow_chr6.simCow.chr6 74848 11 + 602619 TAACAGAAAAA -s simDog_chr6.simDog.chr6 71238 11 + 593897 TGCTGAAACGA -s simHuman_chr6.simHuman.chr6 68110 11 + 601863 TAACAAAAGGA -s simRat_chr6.simRat.chr6 63652 11 + 647215 TGACAGAAGGG - -a -s simMouse_chr6.simMouse.chr6 72036 15 + 636262 AGCAATGTATATACA -s Anc0.Anc0refChr4 16640 15 - 45765 AACATTGGATATGCA -s Anc1.Anc1refChr2 47830 15 + 144309 AACATTGGATATGCA -s Anc2.Anc2refChr7 16439 15 + 32194 AACATTAGATATGTA -s mr.mrrefChr0 67997 15 + 130230 AACATTGTATATGCA -s simCow_chr6.simCow.chr6 74859 15 + 602619 AACACTATGTATGTA -s simDog_chr6.simDog.chr6 71302 15 + 593897 AAAATGAGATAGGTC -s simHuman_chr6.simHuman.chr6 68121 15 + 601863 AACATTGCAAGTGCA -s simRat_chr6.simRat.chr6 63663 15 + 647215 AACATTGGACATGCA - -a -s simMouse_chr6.simMouse.chr6 72051 7 + 636262 CCTTTAC -s Anc0.Anc0refChr4 16655 7 - 45765 CTGTTGA -s Anc1.Anc1refChr2 47845 7 + 144309 CTGTTGA -s Anc2.Anc2refChr7 16454 7 + 32194 CTGTTGA -s mr.mrrefChr0 68012 7 + 130230 CCTTTGC -s simCow_chr6.simCow.chr6 74875 7 + 602619 CTGTTGA -s simDog_chr6.simDog.chr6 71317 7 + 593897 AGGTTGA -s simHuman_chr6.simHuman.chr6 68136 7 + 601863 CTGTTGA -s simRat_chr6.simRat.chr6 63678 7 + 647215 CCATTGC - -a -s simMouse_chr6.simMouse.chr6 72058 28 + 636262 AGTTAGATCAAAGCATCATATAGGTTCA -s Anc0.Anc0refChr4 16666 24 - 45765 AGTTAGGTC----CATGATTTTGGTTTA -s Anc1.Anc1refChr2 47856 27 + 144309 AGTTAGGTC-AGTCATGATTTTGGTTTA -s Anc2.Anc2refChr7 16465 24 + 32194 AGATAGGTC----CATGACTCTTGTTTA -s mr.mrrefChr0 68019 28 + 130230 AGTTAGATCAAATCATCATATAGGTTCA -s simCow_chr6.simCow.chr6 74886 24 + 602619 GAATAGGTC----CATGACTCTAGTTTA -s simDog_chr6.simDog.chr6 71328 24 + 593897 AGATAGGTC----TATGACTCTTGTCTA -s simHuman_chr6.simHuman.chr6 68147 27 + 601863 AGTTAGGTC-AGTCATGATTTTGGTTTA -s simRat_chr6.simRat.chr6 63685 28 + 647215 AGTTAGATCAAATCATTATACAAGTTCA - -a -s simMouse_chr6.simMouse.chr6 72086 4 + 636262 CATA -s Anc0.Anc0refChr4 16693 4 - 45765 CTTA -s Anc1.Anc1refChr2 47886 4 + 144309 CTTA -s Anc2.Anc2refChr7 16493 4 + 32194 CTTA -s mr.mrrefChr0 68047 4 + 130230 CATA -s simCow_chr6.simCow.chr6 74914 4 + 602619 CTAA -s simDog_chr6.simDog.chr6 71356 4 + 593897 CTTG -s simHuman_chr6.simHuman.chr6 68177 4 + 601863 CTTA -s simRat_chr6.simRat.chr6 63713 4 + 647215 TATA - -a -s simMouse_chr6.simMouse.chr6 72090 65 + 636262 TACTCCTGCATGCCCAACCTCTAGGTAACTGTATAAATTAGTTTCATCCATGGAATAACGGCTGC -s Anc0.Anc0refChr4 16841 60 - 45765 ---TCCTACATGACCAATCTCTAGGTAACT--CTAATCGAGTTCCATCCATGGGATTAGAGCTGC -s Anc1.Anc1refChr2 48034 65 + 144309 TTCTCCTACATGACCAATCTCTAGGTAACTGCCTAATCGAGTTCCATCCATGGGATTAGAGCTGC -s Anc2.Anc2refChr7 16669 60 + 32194 ---TCCTACGTAACCAATCTCTAGGTAACT--CTAATCGAGTTCCATACATAGGAGTAGAGCTGT -s mr.mrrefChr0 68051 65 + 130230 TACTCCTGCATGCCCAACCTCTAGGTAACTGTATAAATTAGTTCCATCCATGGAATAACGGCTGC -s simCow_chr6.simCow.chr6 75103 60 + 602619 ---CCATGCTTCCCCAATCTCTAGGTAACT--CTAATTGAGATCCATGTATAGAACAAAAGCCGT -s simDog_chr6.simDog.chr6 71532 45 + 593897 ---TCCTAAGTAACCA-----------------TAATCTAGTTCCATACATAGGGGTGGAGTTGT -s simHuman_chr6.simHuman.chr6 68341 65 + 601863 TTCTCCTACATGACCAATCCCTAGGTGACTGCTTAATGGAGTTCCATCCTCGGGATGAGAGCTGC -s simRat_chr6.simRat.chr6 63717 65 + 647215 CACTCCTGCATACCCAACCTTTAGGTAACTGTATAAGTTAGTTCCGTCCATGAAATAATGGCTGC - -a -s simMouse_chr6.simMouse.chr6 72155 13 + 636262 GTAGTGGTTAGTG -s Anc0.Anc0refChr4 16902 13 - 45765 GTAGTGGTTAGTG -s Anc1.Anc1refChr2 48100 13 + 144309 GTAGTGGTTAGTG -s Anc2.Anc2refChr7 16730 13 + 32194 GTAGTGGTTAGTG -s mr.mrrefChr0 68116 13 + 130230 GTAGTGGTTAGTG -s simCow_chr6.simCow.chr6 75164 13 + 602619 GTAGTGGTTACTG -s simDog_chr6.simDog.chr6 71578 13 + 593897 GTAGTGGTTAGTG -s simHuman_chr6.simHuman.chr6 68407 13 + 601863 GTAGTGCTTGGTG -s simRat_chr6.simRat.chr6 63782 13 + 647215 ATAGTGGTTAGTG - -a -s simMouse_chr6.simMouse.chr6 72168 13 + 636262 AAGTGTTGTGCAA -s Anc0.Anc0refChr4 16916 13 - 45765 AAAGGTTGTCCAA -s Anc1.Anc1refChr2 48114 13 + 144309 AAAGGTTGTCCAA -s Anc2.Anc2refChr7 16744 13 + 32194 AAAGGTTGCCCAA -s mr.mrrefChr0 68129 13 + 130230 AAGTGTTGTGCAA -s simCow_chr6.simCow.chr6 75178 13 + 602619 AAGGATTGCACAA -s simDog_chr6.simDog.chr6 71591 12 + 593897 -GAGGTTGCCCAA -s simHuman_chr6.simHuman.chr6 68421 13 + 601863 AAAGGTTGTCCAA -s simRat_chr6.simRat.chr6 63795 11 + 647215 AAGTGTTGCGT-- - -a -s simMouse_chr6.simMouse.chr6 72181 89 + 636262 GGCTTGGCAGACAGTGCCAGAGTCAAGGTCTGGAAGTTCTGTGTCTGATAATAACAGATACTCCACTTTTAACGCCGTCTTTTTGGGAG -s Anc0.Anc0refChr4 16936 70 - 45765 TGCTTAGTGGTTAGTGCAAGAGT------------------TTTCTGATAATAACAGTTGTCTAACTTGTAATGATGTCTTTTTGCT-A -s Anc1.Anc1refChr2 48134 70 + 144309 TGCTTAGTGGTTAGTGCAAGAGT------------------TTTCTGATAATAACAGTTGTCTAACTTGTAATGATGTCTTTTTGCT-A -s Anc2.Anc2refChr7 16764 70 + 32194 TGCTTAGTGCTTAGTGGAAGAGT------------------TTTCTGATAATAACATTTGTCTTACTTGTAATGATATTTTTTTGCT-A -s mr.mrrefChr0 68142 89 + 130230 GGCTTAGCAGACAGTGCCAGAGTCAAGGTCTGGAAGTTCTGTTTCTGATAATAACAGATATTCAACTTTTAATGCCGTCTTTTTGGGAA -s simCow_chr6.simCow.chr6 75198 70 + 602619 TGCTTAGTACCTAGTGTAAGAGC------------------TTTCTGATAATAAGAATTGTCTTACTTGTCATGACATTTTATTGCT-A -s simDog_chr6.simDog.chr6 71610 61 + 593897 TGCTTAGCGCTTAGTGGAAGAGT------------------TTTCTGAT--TAACATTTG-------TGCAATGATATTTTTTTGCT-A -s simHuman_chr6.simHuman.chr6 68441 70 + 601863 TGCTTAGTGGTTAGTGCAAGTGT------------------TTTCTGATAATAACAGCTGTCTAGCTTGTAATGATGTCTCTTTGCT-A -s simRat_chr6.simRat.chr6 63806 84 + 647215 GTCTTAGCAGACAGTGCCAGAGCCAAGGTCTGGAAGTTCTGTTTCTAATAATAATACATATTCAACTTCTAATGTC-----TTTTGTAA - -a -s simMouse_chr6.simMouse.chr6 72270 21 + 636262 AATTAGCAGCTCACTCCACAT -s Anc0.Anc0refChr4 17006 21 - 45765 CATTGACAGCTCACTCCCCAT -s Anc1.Anc1refChr2 48204 21 + 144309 CATTGACAGCTCACTCCCCAT -s Anc2.Anc2refChr7 16834 21 + 32194 CCTTGACAGCTCACTCCCCAT -s mr.mrrefChr0 68231 21 + 130230 AATTAGCAGCTCACTCCACAT -s simCow_chr6.simCow.chr6 75268 21 + 602619 CCTTGACAACTCACTCCCCAT -s simDog_chr6.simDog.chr6 71672 21 + 593897 CCTTGACAGCTCACTCCTCAT -s simHuman_chr6.simHuman.chr6 68511 21 + 601863 CATTGACAGCTCAATCCCCAT -s simRat_chr6.simRat.chr6 63890 21 + 647215 GCTTCGCAGCCCACTCAACAT - -a -s simMouse_chr6.simMouse.chr6 72291 46 + 636262 TGCTCCAGAAGTACCTTCAGGAAACCACATTTGCCAATACATAGAC -s Anc0.Anc0refChr4 17028 41 - 45765 GCCTCCAGAA-----TTGAGTAAATTAAGTTTTTTGCTAAGTAGAC -s Anc1.Anc1refChr2 48226 46 + 144309 GCCTCCAGAAATATCTTGAGTAAATTAAGTTTTTTGCTAAGTAGAC -s Anc2.Anc2refChr7 16856 41 + 32194 GCCTCCAGAA-----TTTAGTAAATTAAGTTTTTTGCTAAGTAGAT -s mr.mrrefChr0 68252 46 + 130230 TCCTCCAGAAGTACCTTGAGGAAACTACATTTGCTGATACATAGAC -s simCow_chr6.simCow.chr6 75290 41 + 602619 ACATCTAGAT-----TTTAGTAAATAAAATTTTCTGCTACGTGGAT -s simDog_chr6.simDog.chr6 71694 39 + 593897 GCCCCCAGAA-----TTTAGTGAATTAAGGTTTTTGCTAAGTAG-- -s simHuman_chr6.simHuman.chr6 68533 46 + 601863 GCCTCCAGAAATATCGTGAGTAATTTAACTTTTTTGCTAAGCAGGC -s simRat_chr6.simRat.chr6 63911 46 + 647215 TCCACCAGAAGGACCTTGAGGAAACTACATTTGCTGATACCTAGAC - -a -s simMouse_chr6.simMouse.chr6 72337 46 + 636262 CCCCACTGTGCTGTTTAGTAACCAACCAGTACATTACGATGTAATA -s Anc0.Anc0refChr4 17071 46 - 45765 CCTAAATGCACTTTTTAGACACCAACCAGTACATAAAAATACAATA -s Anc1.Anc1refChr2 48274 46 + 144309 CCTAAATGCACTTTTTAGACACCAACCAGTACATAAAAATACAATA -s Anc2.Anc2refChr7 16899 46 + 32194 CCTACACGCACTTTTGAGACACCAACCAGTACATAAAAATACAATA -s mr.mrrefChr0 68300 46 + 130230 CCCCACTGTGCTGTTTAGTAACCAACCAGTACATAACAATGCAATA -s simCow_chr6.simCow.chr6 75333 46 + 602619 CCTACACACACTTTTCAGACACCACCCAGTACATAAAAATGCAATA -s simDog_chr6.simDog.chr6 71733 32 + 593897 -------GCACTTTTG-------AACCAGTCCCTAAAAATACAATA -s simHuman_chr6.simHuman.chr6 68581 46 + 601863 CCTAATTGCACTTTTTAGATACCAACCAGTACATAAAAATACAATA -s simRat_chr6.simRat.chr6 63959 46 + 647215 CCCCACTCTGCTCTTTCGGAACCAACCAGTACATAACAATGCAATA - -a -s simMouse_chr6.simMouse.chr6 72383 4 + 636262 TACC -s Anc0.Anc0refChr4 17120 4 - 45765 AACC -s Anc1.Anc1refChr2 48323 4 + 144309 AACC -s Anc2.Anc2refChr7 16948 4 + 32194 AACC -s mr.mrrefChr0 68349 4 + 130230 TACC -s simCow_chr6.simCow.chr6 75382 4 + 602619 AACC -s simDog_chr6.simDog.chr6 71768 4 + 593897 AACC -s simHuman_chr6.simHuman.chr6 68630 4 + 601863 AACC -s simRat_chr6.simRat.chr6 64008 4 + 647215 TATC - -a -s simMouse_chr6.simMouse.chr6 72387 6 + 636262 ACTCCC -s Anc0.Anc0refChr4 17124 6 - 45765 ACCTCC -s Anc1.Anc1refChr2 48327 6 + 144309 ACCTCC -s Anc2.Anc2refChr7 16952 6 + 32194 ACCTCC -s mr.mrrefChr0 68353 6 + 130230 ACTCCC -s simCow_chr6.simCow.chr6 75387 6 + 602619 ACCTTC -s simDog_chr6.simDog.chr6 71772 6 + 593897 ACCCCG -s simHuman_chr6.simHuman.chr6 68634 6 + 601863 ACCTCC -s simRat_chr6.simRat.chr6 64012 6 + 647215 ACTCCC - -a -s simMouse_chr6.simMouse.chr6 72393 7 + 636262 TTGGTTA -s Anc0.Anc0refChr4 17157 7 - 45765 TTAGTTC -s Anc1.Anc1refChr2 48360 7 + 144309 TTAGTTC -s Anc2.Anc2refChr7 16985 7 + 32194 CTAGTTC -s mr.mrrefChr0 68359 7 + 130230 TTGGTTA -s simCow_chr6.simCow.chr6 75406 7 + 602619 GTAATTC -s simDog_chr6.simDog.chr6 71823 7 + 593897 CTAGTTC -s simHuman_chr6.simHuman.chr6 68667 7 + 601863 TCAGCTC -s simRat_chr6.simRat.chr6 64018 7 + 647215 TTGGGTA - -a -s simMouse_chr6.simMouse.chr6 72400 3 + 636262 CCT -s Anc0.Anc0refChr4 17166 3 - 45765 TTT -s Anc1.Anc1refChr2 48369 3 + 144309 TTT -s Anc2.Anc2refChr7 16994 3 + 32194 TTT -s mr.mrrefChr0 68368 3 + 130230 TCT -s simCow_chr6.simCow.chr6 75415 3 + 602619 TTT -s simDog_chr6.simDog.chr6 71832 3 + 593897 TTT -s simHuman_chr6.simHuman.chr6 68676 3 + 601863 TTT -s simRat_chr6.simRat.chr6 64027 3 + 647215 TCT - -a -s simMouse_chr6.simMouse.chr6 72403 14 + 636262 CTTGACTATCCATT -s Anc0.Anc0refChr4 17175 14 - 45765 TTTGACTACCCATT -s Anc1.Anc1refChr2 48378 14 + 144309 TTTGACTACCCATT -s Anc2.Anc2refChr7 17003 14 + 32194 TTTGACTACCCATT -s mr.mrrefChr0 68371 14 + 130230 CTTGACTATCCATT -s simCow_chr6.simCow.chr6 75424 14 + 602619 TTTGACTACTCATT -s simDog_chr6.simDog.chr6 71841 14 + 593897 CGTGACTACCCATT -s simHuman_chr6.simHuman.chr6 68685 14 + 601863 TTTGACTACCCATT -s simRat_chr6.simRat.chr6 64030 14 + 647215 CCTGACTATCCCTT - -a -s simMouse_chr6.simMouse.chr6 72417 34 + 636262 ACCAATTGAAGGACCATGTTTTAGTAACCCAAGT -s Anc0.Anc0refChr4 17189 34 - 45765 GTTAATTGAGGGATCATGCCTGATTAAACTCAGT -s Anc1.Anc1refChr2 48392 34 + 144309 GTTAATTGAGGGATCATGCCTGATTAAACTCAGT -s Anc2.Anc2refChr7 17017 34 + 32194 GGTAATTGAGGGATCATGCTTGGTTAAACTCAGT -s mr.mrrefChr0 68385 34 + 130230 GTCAATTGAAGGACCATGTCTGAGTAACCCAAGT -s simCow_chr6.simCow.chr6 75438 34 + 602619 AGTAACTGAGGGATCATGCTTGGTTAAACTAAGT -s simDog_chr6.simDog.chr6 71855 34 + 593897 GGTAATTGAGGGATCGTGCTTGGTCAAACTCAGT -s simHuman_chr6.simHuman.chr6 68703 34 + 601863 GTTGATTGAGGGATGATGCCTGATTAAACTCAGT -s simRat_chr6.simRat.chr6 64044 34 + 647215 GTCAATTGAAGGACCATGTCTGGGTAACCCAAGC - -a -s simMouse_chr6.simMouse.chr6 72451 34 + 636262 GATAAGTGAAGCAACTAAGAAAGTCATGAAAATT -s Anc0.Anc0refChr4 17231 29 - 45765 GACA-----ACCAAACAAGAAAATCACTAAAGTT -s Anc1.Anc1refChr2 48434 31 + 144309 GACAA---CACCAAACAAGAAAATCACTAAAGTT -s Anc2.Anc2refChr7 17059 29 + 32194 GTCA-----ACCAAACAAGAAAATCACTAAAGTT -s mr.mrrefChr0 68419 34 + 130230 GATAAGTGAACCAAATAAGAAAGTCATGAAAATT -s simCow_chr6.simCow.chr6 75480 29 + 602619 GTCA-----ACCAAACAAGAAAATCTGGGAAGTT -s simDog_chr6.simDog.chr6 71897 29 + 593897 GTTA-----ACCAAACAAGAAGATCACTAAAGTT -s simHuman_chr6.simHuman.chr6 68745 31 + 601863 GACAA---CACCAAAGAAGAAAATCACTAAGGTT -s simRat_chr6.simRat.chr6 64078 34 + 647215 GGTAAGTTAACCAAATAAGAAAGTCATGAAAATT - -a -s simMouse_chr6.simMouse.chr6 72485 31 + 636262 AATAATGTTACTATCAAGAGTGGCCAATGGA -s Anc0.Anc0refChr4 17260 30 - 45765 AATTACCTTACTATTAATAGT-GCCCCTGGA -s Anc1.Anc1refChr2 48465 30 + 144309 AATTACCTTACTATTAATAGT-GCCCCTGGA -s Anc2.Anc2refChr7 17088 30 + 32194 AATCCCCTTGTTATTAGTGGT-GCCCCTGGA -s mr.mrrefChr0 68453 31 + 130230 AATTATGTTACTATTAAGAGTGGCCAATGGA -s simCow_chr6.simCow.chr6 75509 8 + 602619 AA-----------------------CATGGA -s simDog_chr6.simDog.chr6 71927 30 + 593897 AATCCCCTTGTTATTAGTGGT-GCCCCTGGA -s simHuman_chr6.simHuman.chr6 68776 30 + 601863 AATTACCTTACTATTAATAGT-ACCCTTGGA -s simRat_chr6.simRat.chr6 64112 31 + 647215 AATTATGCTGCTGTTAAGAGTGTCGGATGGA - -a -s simMouse_chr6.simMouse.chr6 72516 3 + 636262 CCA -s Anc0.Anc0refChr4 17291 3 - 45765 CCA -s Anc1.Anc1refChr2 48496 3 + 144309 CCA -s Anc2.Anc2refChr7 17119 3 + 32194 CCA -s mr.mrrefChr0 68485 3 + 130230 CCA -s simCow_chr6.simCow.chr6 75518 3 + 602619 CCA -s simDog_chr6.simDog.chr6 71958 3 + 593897 CCA -s simHuman_chr6.simHuman.chr6 68807 3 + 601863 CCA -s simRat_chr6.simRat.chr6 64144 3 + 647215 CCA - -a -s simMouse_chr6.simMouse.chr6 72519 2 + 636262 GC -s Anc0.Anc0refChr4 17307 2 - 45765 AC -s Anc1.Anc1refChr2 48512 2 + 144309 AC -s Anc2.Anc2refChr7 17135 2 + 32194 AC -s mr.mrrefChr0 68488 2 + 130230 GC -s simCow_chr6.simCow.chr6 75534 2 + 602619 AC -s simDog_chr6.simDog.chr6 71974 2 + 593897 AC -s simHuman_chr6.simHuman.chr6 68823 2 + 601863 AC -s simRat_chr6.simRat.chr6 64147 2 + 647215 GC - -a -s simMouse_chr6.simMouse.chr6 72521 62 + 636262 TCATCTCATGCGTTCAAATTATCAAGACTCACTCCTTGCTTGCCACCTACAATAGTGTGTTC -s Anc0.Anc0refChr4 17309 54 - 45765 CCATTTCACCTGTTTAAGCCATCCAGACTC----C----TTGCTACATACAATAGCATGCTC -s Anc1.Anc1refChr2 48514 54 + 144309 CCATTTCACCTGTTTAAGCCATCCAGACTC----C----TTGCTACATACAATAGCATGCTC -s Anc2.Anc2refChr7 17137 54 + 32194 CCATTCCACCTGTTTCAGCCATCCAGACCC----T----TTGCTACATACAATAGCATGCTC -s mr.mrrefChr0 68490 58 + 130230 CCATCTCATGCGTTTAAACTATCAAGACTC----CTTGCTTGCTACCTACAATAGTGTGCTC -s simCow_chr6.simCow.chr6 75537 54 + 602619 CCATTGGACCTGTTTCAGTCATCCAGACCC----T----CTGCTACATACGATAAAATGCTC -s simDog_chr6.simDog.chr6 71976 54 + 593897 TCATTCCTCCTGTTTCAGCCACCCAGACCC----T----TTGCTAGAGACAATAGCATGCTC -s simHuman_chr6.simHuman.chr6 68825 54 + 601863 CCATTTCACCTGTTTAAGCCATTCAGACTC----C----TTACTACATACACTGGCATGCTC -s simRat_chr6.simRat.chr6 64149 58 + 647215 CCATCTCATGCGTATAAACTATCAAGACGC----CTTGCTTGCTACCTACAATAGTGTGCTC - -a -s simMouse_chr6.simMouse.chr6 72583 19 + 636262 ATACTCCAACAAAGAGAGA -s Anc0.Anc0refChr4 17364 19 - 45765 ATACTCTAACAGGTAAAGC -s Anc1.Anc1refChr2 48569 19 + 144309 ATACTCTAACAGGTAAAGC -s Anc2.Anc2refChr7 17192 19 + 32194 ATACTCTAACAGGTAAAGC -s mr.mrrefChr0 68548 19 + 130230 ATACTCCAACAAAGAGAGC -s simCow_chr6.simCow.chr6 75592 15 + 602619 TTACTCTCGCAAGGA---- -s simDog_chr6.simDog.chr6 72031 19 + 593897 ATACTCTAACCGGTAAAGC -s simHuman_chr6.simHuman.chr6 68880 19 + 601863 ACACACTAACAGGCAAAGC -s simRat_chr6.simRat.chr6 64207 19 + 647215 ATACTCCAACAAAGAGAGC - -a -s simMouse_chr6.simMouse.chr6 72602 53 + 636262 TTAAGCTCCTATAGCAACTAAATCCATATAAAACCATGAGCTGGAGAAGCTAA -s Anc0.Anc0refChr4 17390 50 - 45765 TTAAGCCCTTATGGCAATTAAGTCCCTATAGAGGCAAGTAGTGG-GAAGC--A -s Anc1.Anc1refChr2 48595 50 + 144309 TTAAGCCCTTATGGCAATTAAGTCCCTATAGAGGCAAGTAGTGG-GAAGC--A -s Anc2.Anc2refChr7 17218 50 + 32194 TTAAGCCCTTATGGCAATTAAGTCCCTATAGAGGCAAGTAGCGG-GACTC--A -s mr.mrrefChr0 68567 53 + 130230 TTAAGCTCCTATAGCAACTAAGTCCCTATAAAACCATGAGCTGGTGAAGCTAA -s simCow_chr6.simCow.chr6 75613 47 + 602619 TTAAGCCCTTATGGCAATTAAGTCCCCATAGAAGTAAGTA---C-GGTAC--A -s simDog_chr6.simDog.chr6 72057 50 + 593897 TTTAGGCCATATGGCAATTAAGTCCCTATAGGGGCAAGTAGCGG-GACTC--A -s simHuman_chr6.simHuman.chr6 68906 50 + 601863 TTAAGCCCTTATGGCAATTGAGTCCCTATTGAGGCAAATAGTGG-GAAGC--A -s simRat_chr6.simRat.chr6 64226 53 + 647215 TTAAGCTCCTATAGCAACTAAGTCCCCATAAAACCTCTAGCTGGTGAAGCTAA - -a -s simMouse_chr6.simMouse.chr6 72655 25 + 636262 GTCGTATAGCCAGACTGTTGGAAAA -s Anc0.Anc0refChr4 17440 25 - 45765 GTAGTTAAATCAAGTTCCTGGCAAC -s Anc1.Anc1refChr2 48645 25 + 144309 GTAGTTAAATCAAGTTCCTGGCAAC -s Anc2.Anc2refChr7 17268 25 + 32194 TAAATTAAATCGAATTCCTGGCAAC -s mr.mrrefChr0 68620 25 + 130230 GTCGTATAACCAGGCTGTTGGCAAA -s simCow_chr6.simCow.chr6 75660 25 + 602619 TAATTCAGACCGAATTCCTGGCCAC -s simDog_chr6.simDog.chr6 72108 25 + 593897 TAAATTAAATTGAATTCCTGGCAAC -s simHuman_chr6.simHuman.chr6 68956 25 + 601863 GTAGTTGAATCAAGTTCCTAGCAAC -s simRat_chr6.simRat.chr6 64279 25 + 647215 GTTGTATAACCAGGCTGTTGGCAAA - -a -s simMouse_chr6.simMouse.chr6 72680 16 + 636262 GGTCATCCACTTTGTA -s Anc0.Anc0refChr4 17514 14 - 45765 GGTCA-CCA-TTTGTA -s Anc1.Anc1refChr2 48719 15 + 144309 GGTCATCCA-TTTGTA -s Anc2.Anc2refChr7 17342 14 + 32194 GGTCA-CCA-TTGGTA -s mr.mrrefChr0 68645 16 + 130230 GGTCATCCACTTTGTA -s simCow_chr6.simCow.chr6 75731 14 + 602619 TGGCT-CCT-TTAATC -s simDog_chr6.simDog.chr6 72182 14 + 593897 GTTCA-CCA-TTGGTA -s simHuman_chr6.simHuman.chr6 69082 15 + 601863 GGCCATTCA-TTTGTA -s simRat_chr6.simRat.chr6 64304 16 + 647215 GGTCATCCACTTTGTA - -a -s simMouse_chr6.simMouse.chr6 72696 38 + 636262 ATTGACTATCCTTTATGTCTCCCTGGGACAAGCCAGTT -s Anc0.Anc0refChr4 17528 9 - 45765 TT-----------------------------GATGGTA -s Anc1.Anc1refChr2 48734 9 + 144309 TT-----------------------------GATGGTA -s Anc2.Anc2refChr7 17356 9 + 32194 TT-----------------------------GATGGTA -s mr.mrrefChr0 68661 38 + 130230 ATTGACTATCCTTTATGTCTCCCTGTCACAAGTTGGTT -s simCow_chr6.simCow.chr6 75745 9 + 602619 AA-----------------------------AATGGTA -s simDog_chr6.simDog.chr6 72197 9 + 593897 TT-----------------------------GTCGATA -s simHuman_chr6.simHuman.chr6 69097 9 + 601863 CT-----------------------------GATGGTA -s simRat_chr6.simRat.chr6 64320 38 + 647215 ATTGACTATGCCTTATGACGACCTGTCACAAGTTGGTT - -a -s simMouse_chr6.simMouse.chr6 72734 11 + 636262 GTCAGTACAAT -s Anc0.Anc0refChr4 17537 11 - 45765 TTCATTAGAAC -s Anc1.Anc1refChr2 48743 11 + 144309 TTCATTAGAAC -s Anc2.Anc2refChr7 17365 11 + 32194 TTCACTAGAAC -s mr.mrrefChr0 68699 11 + 130230 GTCATTACAAC -s simCow_chr6.simCow.chr6 75754 11 + 602619 TTCCCTAGAAT -s simDog_chr6.simDog.chr6 72238 11 + 593897 TTCACTAGAAC -s simHuman_chr6.simHuman.chr6 69106 11 + 601863 TTCATTAGAGC -s simRat_chr6.simRat.chr6 64358 11 + 647215 GTTATTACTAC - -a -s simMouse_chr6.simMouse.chr6 72745 34 + 636262 GCTTCCTAGGTTACCTAAATTACTGGTGCAAATG -s Anc0.Anc0refChr4 17548 34 - 45765 CATCCCTAGGTTACCTGAAGGATTGGTGCAAACT -s Anc1.Anc1refChr2 48754 34 + 144309 CATCCCTAGGTTACCTGAAGGATTGGTGCAAACT -s Anc2.Anc2refChr7 17376 34 + 32194 CATCCCTTGGTTACCTGAAGGATTGGTCCAAACT -s mr.mrrefChr0 68710 34 + 130230 GATTCCTAGGTTACCTAAATTACTGGTGCAAACG -s simCow_chr6.simCow.chr6 75765 34 + 602619 CATCCCTTACTTACCTGAAGGAATGGTCAAAACA -s simDog_chr6.simDog.chr6 72251 33 + 593897 CATCCCTTGGTTACCTG-AGGATTGGTCCAAATT -s simHuman_chr6.simHuman.chr6 69117 34 + 601863 CATCCCCAGGTTATATGAAGGATTTGTGCACACC -s simRat_chr6.simRat.chr6 64369 34 + 647215 GATTCCTAGGTTACCTAAATTACTGGTGCAAACA - -a -s simMouse_chr6.simMouse.chr6 72779 4 + 636262 TAGG -s Anc0.Anc0refChr4 17582 4 - 45765 TAGC -s Anc1.Anc1refChr2 48788 4 + 144309 TAGC -s Anc2.Anc2refChr7 17410 4 + 32194 TAGC -s mr.mrrefChr0 68744 4 + 130230 TAGC -s simCow_chr6.simCow.chr6 75799 4 + 602619 TAGC -s simDog_chr6.simDog.chr6 72287 4 + 593897 CAGC -s simHuman_chr6.simHuman.chr6 69151 4 + 601863 TAGC -s simRat_chr6.simRat.chr6 64403 4 + 647215 TAGC - -a -s simMouse_chr6.simMouse.chr6 72783 51 + 636262 CCATGTCCAAACATTCAAAGCACACTATTATACTATTAAAAGTATACCAAC -s Anc0.Anc0refChr4 17587 48 - 45765 TCATAAACAAACATTGAAAACACA---CTATACTGTTTGAAGCATCCAAAC -s Anc1.Anc1refChr2 48793 48 + 144309 TCATAAACAAACATTGAAAACACA---CTATACTGTTTGAAGCATCCAAAC -s Anc2.Anc2refChr7 17415 48 + 32194 TCATAAACAAACACTGAAAACACA---CTATACTGTCTGAAGCATCCAAAC -s mr.mrrefChr0 68748 48 + 130230 CCATGTCCAAACATTCAAAGCACA---TTATACTATTAAAAGTATCCCAAC -s simCow_chr6.simCow.chr6 75804 48 + 602619 CCATGAACCAATACTAAAAACACA---CTATACTGTCTGCTGTGTCTTAAC -s simDog_chr6.simDog.chr6 72292 48 + 593897 TCACAAACAAACACTGACAGGAAA---CTATACTCTCTTAAGCATCCAAAC -s simHuman_chr6.simHuman.chr6 69156 48 + 601863 TCATCAACAAACATTGAACACACA---CTATACTGGTTGAAGCACCCAAAC -s simRat_chr6.simRat.chr6 64407 48 + 647215 CCATGTCCAAACATCCAAAGCACA---GTATACTAATCAAAATATCCCAAC - -a -s simMouse_chr6.simMouse.chr6 72834 17 + 636262 ACAGAATCTCAAATGCA -s Anc0.Anc0refChr4 17635 9 - 45765 ACAG--CA------ACA -s Anc1.Anc1refChr2 48841 15 + 144309 ACAG--CACCAACTACA -s Anc2.Anc2refChr7 17463 9 + 32194 ACTG--CA------ACA -s mr.mrrefChr0 68796 15 + 130230 ACAG--CATCAAATGCA -s simCow_chr6.simCow.chr6 75852 9 + 602619 AATG--CA------ACA -s simDog_chr6.simDog.chr6 72340 9 + 593897 ACTG--CA------ACA -s simHuman_chr6.simHuman.chr6 69205 15 + 601863 ACAG--CACCAACTACA -s simRat_chr6.simRat.chr6 64455 15 + 647215 ATAG--CATAAAATGCA - -a -s simMouse_chr6.simMouse.chr6 72851 4 + 636262 ACGG -s Anc0.Anc0refChr4 17644 4 - 45765 GTGT -s Anc1.Anc1refChr2 48856 4 + 144309 GTGT -s Anc2.Anc2refChr7 17472 4 + 32194 GTGT -s mr.mrrefChr0 68811 4 + 130230 ATGT -s simCow_chr6.simCow.chr6 75862 4 + 602619 GTGT -s simDog_chr6.simDog.chr6 72349 4 + 593897 GTGT -s simHuman_chr6.simHuman.chr6 69220 4 + 601863 GTGT -s simRat_chr6.simRat.chr6 64470 4 + 647215 ATGT - -a -s simMouse_chr6.simMouse.chr6 72855 13 + 636262 CTATTGTCCACTC -s Anc0.Anc0refChr4 17648 13 - 45765 CCATTGTCCAATT -s Anc1.Anc1refChr2 48860 13 + 144309 CCATTGTCCAATT -s Anc2.Anc2refChr7 17480 13 + 32194 CCATAGTCAAATT -s mr.mrrefChr0 68815 13 + 130230 CTATTGTCCACTC -s simCow_chr6.simCow.chr6 75870 13 + 602619 CCATCATCAAGTT -s simDog_chr6.simDog.chr6 72357 13 + 593897 CTGTAGTCAGATC -s simHuman_chr6.simHuman.chr6 69224 13 + 601863 CCATTGTCCAACT -s simRat_chr6.simRat.chr6 64474 13 + 647215 CTATTGTCCAGGC - -a -s simMouse_chr6.simMouse.chr6 72868 9 + 636262 CCAATTTCT -s Anc0.Anc0refChr4 17663 9 - 45765 ATAATATCT -s Anc1.Anc1refChr2 48875 9 + 144309 ATAATATCT -s Anc2.Anc2refChr7 17495 9 + 32194 ATAATATCT -s mr.mrrefChr0 68828 9 + 130230 CTAATTTCT -s simCow_chr6.simCow.chr6 75885 9 + 602619 ATAATATCT -s simDog_chr6.simDog.chr6 72372 8 + 593897 A-AATATTA -s simHuman_chr6.simHuman.chr6 69239 9 + 601863 ATAATATCT -s simRat_chr6.simRat.chr6 64487 9 + 647215 CTAATTTCT - -a -s simMouse_chr6.simMouse.chr6 72877 57 + 636262 TCTTACTGCGATGAACATGTACAGCCTTCTGACTGAATGGACCCCTACATGTTACAG -s Anc0.Anc0refChr4 17672 47 - 45765 C------GCAATGAACATGCACAGCTTTCTGGAT----GGATCCTTACGGGTGACCG -s Anc1.Anc1refChr2 48884 54 + 144309 CCATATGGCAATGAACATGCACAGCTTTCTGGATG---GGATCCTTACGGGTGACCG -s Anc2.Anc2refChr7 17504 47 + 32194 C------ACAATGAACATGCTCAGCTTTCTGGAT----GGATCCTTATGGGTGACCA -s mr.mrrefChr0 68837 57 + 130230 TCTTACTGCAATGAACATGTACAGCTTTCTGACTGAATGGATCCCTACATGTTACAG -s simCow_chr6.simCow.chr6 75895 47 + 602619 C------ACAATGAACATGCCCAGTGTTCTGGAT----GGAACTTTATGGGTGACAA -s simDog_chr6.simDog.chr6 72380 47 + 593897 C------ACGATGAATACACTCAACTCTCTGGAT----GGATCCTTATGGGTGATCA -s simHuman_chr6.simHuman.chr6 69248 54 + 601863 CCATATGGCAACAAACATGCACAGCTTTCTGGATG---GGATTATTACGGGTGACGG -s simRat_chr6.simRat.chr6 64496 57 + 647215 TTTTGCTGCAGTGAACATGTACAGCTTTCTGACTGGATGGATCCCTACATGTTATAA - -a -s simMouse_chr6.simMouse.chr6 72934 53 + 636262 TGACCACATTCGACTGTATTGTAAGTCATCAAACATATACCACTCAGAGAACG -s Anc0.Anc0refChr4 17720 53 - 45765 TGAACACAATTGACTGTATGGTATATTGACAAATATATACCACTTCGAGAACA -s Anc1.Anc1refChr2 48939 53 + 144309 TGAACACAATTGACTGTATGGTATATTGACAAATATATACCACTTCGAGAACA -s Anc2.Anc2refChr7 17552 53 + 32194 TGAACACAATGTATTGAATGGTGTATTGACAAATATATACCACTTCGAGAATA -s mr.mrrefChr0 68894 53 + 130230 TGACCACATTTGACTGTATTGTAAGTTGTCAAACATATACCACTCAGAGAACG -s simCow_chr6.simCow.chr6 75943 53 + 602619 TGAACACAATGTATGGAGTGGTGCACTGACAAACATCCACCATGTAGAGAATA -s simDog_chr6.simDog.chr6 72428 51 + 593897 TGAACACAATGTATTGAATGG--TGTTGACAAGTATATACTACTTCAAGAATA -s simHuman_chr6.simHuman.chr6 69303 53 + 601863 TGAACACAACTGACTGTATGGAAGATTGGCAAAGTTATACCACTTTGAGAACA -s simRat_chr6.simRat.chr6 64553 53 + 647215 CGACCACATTTCGTTGTACTGTAAGTTGTCAAACATATACTGCTCAGAGAATG - -a -s simMouse_chr6.simMouse.chr6 72987 18 + 636262 GGTTAATTAACCTCATAT -s Anc0.Anc0refChr4 17773 18 - 45765 GGTCAACTGACCTCATGT -s Anc1.Anc1refChr2 48992 18 + 144309 GGTCAACTGACCTCATGT -s Anc2.Anc2refChr7 17605 18 + 32194 GGTCAACTGACCTCATGT -s mr.mrrefChr0 68947 18 + 130230 GGTTAATTAACCTCATAT -s simCow_chr6.simCow.chr6 75997 18 + 602619 GGTCAACTGACCTCATGT -s simDog_chr6.simDog.chr6 72479 18 + 593897 AGACAACTGACTTCATGT -s simHuman_chr6.simHuman.chr6 69356 18 + 601863 GGTCAACTGACCTCAAGT -s simRat_chr6.simRat.chr6 64606 18 + 647215 TATTAATTAACCTCATAG - -a -s simMouse_chr6.simMouse.chr6 73005 44 + 636262 TAATTTTTATCACCTATCCTTGTCAACTGAGGCTAATAATCGGT -s Anc0.Anc0refChr4 17791 7 - 45765 TCATTTT------------------------------------- -s Anc1.Anc1refChr2 49010 7 + 144309 TCATTTT------------------------------------- -s Anc2.Anc2refChr7 17623 7 + 32194 TCATGTT------------------------------------- -s mr.mrrefChr0 68965 44 + 130230 TAATTTTTATCACCTATCCTTGTCAACTGAGGCTAATAATCGGT -s simCow_chr6.simCow.chr6 76015 7 + 602619 ACACCTT------------------------------------- -s simDog_chr6.simDog.chr6 72506 6 + 593897 TCATG-T------------------------------------- -s simHuman_chr6.simHuman.chr6 69374 7 + 601863 TCATTCT------------------------------------- -s simRat_chr6.simRat.chr6 64624 44 + 647215 TAATTTTTATCACTCGTCGATGTCAACTGAGACTAATGAGCAGT - -a -s simMouse_chr6.simMouse.chr6 73049 51 + 636262 GACATACTGCAAGTCAGGATACCAACCTTAGATTCCAAAAAAGATTTATTA -s Anc0.Anc0refChr4 17798 9 - 45765 ------------------------------------------GACCTACTA -s Anc1.Anc1refChr2 49017 9 + 144309 ------------------------------------------GACCTACTA -s Anc2.Anc2refChr7 17630 9 + 32194 ------------------------------------------GACCTACTA -s mr.mrrefChr0 69009 46 + 130230 GACATACTGCAAGTCAGGATACCAACCTTAGATTC-----AAGATTTATTA -s simCow_chr6.simCow.chr6 76022 9 + 602619 ------------------------------------------GTCCTACTA -s simDog_chr6.simDog.chr6 72512 9 + 593897 ------------------------------------------GACCTACAA -s simHuman_chr6.simHuman.chr6 69381 9 + 601863 ------------------------------------------GACCTACTA -s simRat_chr6.simRat.chr6 64669 46 + 647215 GACACACTGCAACTCAGGATACCAACTGTAAATTC-----AAGATTTATTA - -a -s simMouse_chr6.simMouse.chr6 73100 6 + 636262 CATACT -s Anc0.Anc0refChr4 17827 6 - 45765 CATATT -s Anc1.Anc1refChr2 49046 6 + 144309 CATATT -s Anc2.Anc2refChr7 17660 6 + 32194 CATATT -s mr.mrrefChr0 69075 6 + 130230 CATACT -s simCow_chr6.simCow.chr6 76052 6 + 602619 CATACT -s simDog_chr6.simDog.chr6 72542 6 + 593897 CATATT -s simHuman_chr6.simHuman.chr6 69410 6 + 601863 CATATT -s simRat_chr6.simRat.chr6 64736 6 + 647215 CATCCG - -a -s simMouse_chr6.simMouse.chr6 73106 7 + 636262 GAAGAAC -s Anc0.Anc0refChr4 17885 7 - 45765 AATGAAT -s Anc1.Anc1refChr2 49104 7 + 144309 AATGAAT -s Anc2.Anc2refChr7 17728 7 + 32194 AATGAAT -s mr.mrrefChr0 69081 7 + 130230 GAAGAAC -s simCow_chr6.simCow.chr6 76125 7 + 602619 GATGAGT -s simDog_chr6.simDog.chr6 72610 7 + 593897 AATGAAT -s simHuman_chr6.simHuman.chr6 69474 7 + 601863 AGCAAAT -s simRat_chr6.simRat.chr6 64742 7 + 647215 GAAGAAC - -a -s simMouse_chr6.simMouse.chr6 73113 11 + 636262 CCAGGACTTCC -s Anc0.Anc0refChr4 17892 9 - 45765 CTAT--CTTCC -s Anc1.Anc1refChr2 49111 9 + 144309 CTAT--CTTCC -s Anc2.Anc2refChr7 17735 9 + 32194 CTAT--CTTTT -s mr.mrrefChr0 69088 11 + 130230 CCAGGACTTCC -s simCow_chr6.simCow.chr6 76132 9 + 602619 CTAT--CTTTT -s simDog_chr6.simDog.chr6 72617 9 + 593897 GAAT--CTTTT -s simHuman_chr6.simHuman.chr6 69481 9 + 601863 CTAT--CTTCC -s simRat_chr6.simRat.chr6 64750 11 + 647215 CCAGGGCTTCC - -a -s simMouse_chr6.simMouse.chr6 73124 10 + 636262 TTTACATATT -s Anc0.Anc0refChr4 17901 4 - 45765 TTCA------ -s Anc1.Anc1refChr2 49120 4 + 144309 TTCA------ -s Anc2.Anc2refChr7 17744 4 + 32194 TTCA------ -s mr.mrrefChr0 69099 10 + 130230 TTTACATATT -s simCow_chr6.simCow.chr6 76141 4 + 602619 TTCA------ -s simDog_chr6.simDog.chr6 72630 4 + 593897 TTCA------ -s simHuman_chr6.simHuman.chr6 69490 4 + 601863 ATCA------ -s simRat_chr6.simRat.chr6 64761 10 + 647215 TCTGCATATT - -a -s simMouse_chr6.simMouse.chr6 73134 7 + 636262 TCATAGG -s Anc0.Anc0refChr4 17905 5 - 45765 TCATC-- -s Anc1.Anc1refChr2 49124 5 + 144309 TCATC-- -s Anc2.Anc2refChr7 17749 5 + 32194 TCATC-- -s mr.mrrefChr0 69109 7 + 130230 TCATAGG -s simCow_chr6.simCow.chr6 76146 5 + 602619 TCATC-- -s simDog_chr6.simDog.chr6 72635 5 + 593897 TCATC-- -s simHuman_chr6.simHuman.chr6 69494 3 + 601863 TCA---- -s simRat_chr6.simRat.chr6 64771 7 + 647215 TCATAGG - -a -s simMouse_chr6.simMouse.chr6 73141 5 + 636262 AACGT -s Anc0.Anc0refChr4 17910 5 - 45765 AATCT -s Anc1.Anc1refChr2 49129 5 + 144309 AATCT -s Anc2.Anc2refChr7 17754 5 + 32194 AATCT -s mr.mrrefChr0 69116 5 + 130230 AATGT -s simCow_chr6.simCow.chr6 76153 5 + 602619 AATCT -s simDog_chr6.simDog.chr6 72640 5 + 593897 AATCT -s simHuman_chr6.simHuman.chr6 69497 5 + 601863 GATCT -s simRat_chr6.simRat.chr6 64778 5 + 647215 AATGT - -a -s simMouse_chr6.simMouse.chr6 73146 27 + 636262 GGAGTGAGTTGAATCAATCCTCCAAGC -s Anc0.Anc0refChr4 17915 25 - 45765 GGGTTGAATACA--CACTCCTATAAAT -s Anc1.Anc1refChr2 49134 25 + 144309 GGGTTGAATACA--CACTCCTATAAAT -s Anc2.Anc2refChr7 17760 25 + 32194 GGGTTGAATACA--AGCGCCTATGAAT -s mr.mrrefChr0 69121 27 + 130230 GGAGTGAGTTGAATCAATCCTCCAAGC -s simCow_chr6.simCow.chr6 76160 25 + 602619 GGGCTGAATCCA--GGCACCTATTAAT -s simDog_chr6.simDog.chr6 72646 25 + 593897 GGGTTGAGTACA--AGCGTCTATGAAT -s simHuman_chr6.simHuman.chr6 69502 25 + 601863 GGGTTGAATACA--CACTCCTATAAAT -s simRat_chr6.simRat.chr6 64783 27 + 647215 GGAGTGAGTTGAATGAATTCTCCAAGC - -a -s simMouse_chr6.simMouse.chr6 73173 18 + 636262 GCATCCTGACTTTCTTAG -s Anc0.Anc0refChr4 17941 18 - 45765 GCATCCTGGCACAGCATA -s Anc1.Anc1refChr2 49160 18 + 144309 GCATCCTGGCACAGCATA -s Anc2.Anc2refChr7 17786 18 + 32194 GCATCCTGGCACAGCATA -s mr.mrrefChr0 69149 18 + 130230 GCATCCTGACTTACTTAA -s simCow_chr6.simCow.chr6 76186 8 + 602619 GCAACC----------GA -s simDog_chr6.simDog.chr6 72672 18 + 593897 GCATCCTGGCACAGCATG -s simHuman_chr6.simHuman.chr6 69528 18 + 601863 GGATCCTGGCACAGCATA -s simRat_chr6.simRat.chr6 64811 18 + 647215 GCATCCTGACTTACTTAA - -a -s simMouse_chr6.simMouse.chr6 73191 11 + 636262 GAACTGGAAGC -s Anc0.Anc0refChr4 17968 11 - 45765 GAACTGAAAGA -s Anc1.Anc1refChr2 49187 11 + 144309 GAACTGAAAGA -s Anc2.Anc2refChr7 17813 11 + 32194 GAACTGAAAGA -s mr.mrrefChr0 69167 11 + 130230 GAACTGGAAGC -s simCow_chr6.simCow.chr6 76198 11 + 602619 GAACTGAAAGA -s simDog_chr6.simDog.chr6 72699 11 + 593897 AAACTAAAAGA -s simHuman_chr6.simHuman.chr6 69555 11 + 601863 GAATAGAAGGA -s simRat_chr6.simRat.chr6 64829 11 + 647215 GAACTGGAAGC - -a -s simMouse_chr6.simMouse.chr6 73202 13 + 636262 CAGTCCTATCCAG -s Anc0.Anc0refChr4 17993 13 - 45765 TAGTCCTATTCAG -s Anc1.Anc1refChr2 49212 13 + 144309 TAGTCCTATTCAG -s Anc2.Anc2refChr7 17838 13 + 32194 TATTCCTATTTAT -s mr.mrrefChr0 69192 13 + 130230 TAGTCCTATCCAG -s simCow_chr6.simCow.chr6 76223 13 + 602619 TTTCCCTATTCAT -s simDog_chr6.simDog.chr6 72724 13 + 593897 TATTCCTATTTAT -s simHuman_chr6.simHuman.chr6 69570 13 + 601863 TGGTCCTATTCAG -s simRat_chr6.simRat.chr6 64854 13 + 647215 TAGTCCTATCCAG - -a -s simMouse_chr6.simMouse.chr6 73215 19 + 636262 ACATATATATGGTGAACTA -s Anc0.Anc0refChr4 18020 19 - 45765 GGATATAATTGTTGAACTA -s Anc1.Anc1refChr2 49239 19 + 144309 GGATATAATTGTTGAACTA -s Anc2.Anc2refChr7 17865 19 + 32194 GGATATAATTGTTGAACCA -s mr.mrrefChr0 69205 19 + 130230 GCATATATATGGTGAACTA -s simCow_chr6.simCow.chr6 76261 18 + 602619 AGATATAATTGCTTAACC- -s simDog_chr6.simDog.chr6 72751 19 + 593897 GGATATAACTGTTGAACCT -s simHuman_chr6.simHuman.chr6 69597 19 + 601863 GAATATAGTGGTCTAACTA -s simHuman_chr6.simHuman.chr6 531983 19 - 601863 GGATATAATGGCCGAACTA -s simRat_chr6.simRat.chr6 64867 19 + 647215 GCATATATATGATGAACTA - -a -s simMouse_chr6.simMouse.chr6 73234 2 + 636262 AC -s Anc0.Anc0refChr4 18039 2 - 45765 AC -s Anc1.Anc1refChr2 49258 2 + 144309 AC -s Anc2.Anc2refChr7 17884 2 + 32194 AC -s mr.mrrefChr0 69224 2 + 130230 AC -s simCow_chr6.simCow.chr6 76279 2 + 602619 AC -s simDog_chr6.simDog.chr6 72773 2 + 593897 AC -s simRat_chr6.simRat.chr6 64886 2 + 647215 AC - -a -s simMouse_chr6.simMouse.chr6 73236 2 + 636262 TG -s Anc0.Anc0refChr4 18041 2 - 45765 TG -s Anc1.Anc1refChr2 49260 2 + 144309 TG -s Anc2.Anc2refChr7 17887 2 + 32194 TG -s mr.mrrefChr0 69226 2 + 130230 TG -s simCow_chr6.simCow.chr6 76282 2 + 602619 TC -s simDog_chr6.simDog.chr6 72776 2 + 593897 TG -s simRat_chr6.simRat.chr6 64888 2 + 647215 TG - -a -s simMouse_chr6.simMouse.chr6 73238 10 + 636262 AGGTCTGATA -s Anc0.Anc0refChr4 18043 10 - 45765 AGATCCCATA -s Anc1.Anc1refChr2 49262 10 + 144309 AGATCCCATA -s Anc2.Anc2refChr7 17890 10 + 32194 AGATCCCATA -s mr.mrrefChr0 69228 10 + 130230 AGATCTGATA -s simCow_chr6.simCow.chr6 76285 10 + 602619 AGATCCCATA -s simDog_chr6.simDog.chr6 72779 10 + 593897 AAATCCCATA -s simHuman_chr6.simHuman.chr6 69616 10 + 601863 AGATCCCATA -s simHuman_chr6.simHuman.chr6 532002 10 - 601863 AGATCCTGTA -s simRat_chr6.simRat.chr6 64890 10 + 647215 AGATCTGATA - -a -s simMouse_chr6.simMouse.chr6 73248 4 + 636262 TTAA -s Anc0.Anc0refChr4 18054 4 - 45765 TTAA -s Anc1.Anc1refChr2 49273 4 + 144309 TTAA -s Anc2.Anc2refChr7 17901 4 + 32194 TTAA -s mr.mrrefChr0 69238 4 + 130230 TTAA -s simCow_chr6.simCow.chr6 76296 4 + 602619 TTAA -s simDog_chr6.simDog.chr6 72790 4 + 593897 TCAA -s simHuman_chr6.simHuman.chr6 69627 4 + 601863 TTAA -s simHuman_chr6.simHuman.chr6 532013 4 - 601863 TTAA -s simRat_chr6.simRat.chr6 64900 4 + 647215 TTAA - -a -s simMouse_chr6.simMouse.chr6 73252 5 + 636262 CCTGA -s Anc0.Anc0refChr4 18058 5 - 45765 TCTGG -s Anc1.Anc1refChr2 49277 5 + 144309 TCTGG -s Anc2.Anc2refChr7 17905 5 + 32194 TGTGG -s mr.mrrefChr0 69242 5 + 130230 CCTGA -s simCow_chr6.simCow.chr6 76300 5 + 602619 TAGGA -s simDog_chr6.simDog.chr6 72794 4 + 593897 TGT-G -s simHuman_chr6.simHuman.chr6 532017 5 - 601863 TCCAG -s simRat_chr6.simRat.chr6 64904 5 + 647215 CCTGA - -a -s simMouse_chr6.simMouse.chr6 73257 10 + 636262 AGTTGTTTTT -s Anc0.Anc0refChr4 18063 10 - 45765 GGTTGTTTGT -s Anc1.Anc1refChr2 49282 10 + 144309 GGTTGTTTGT -s Anc2.Anc2refChr7 17910 10 + 32194 GGTTGTCTGT -s mr.mrrefChr0 69247 10 + 130230 AGTTGTTTTT -s simCow_chr6.simCow.chr6 76305 10 + 602619 GGTTGTCTGT -s simDog_chr6.simDog.chr6 72798 10 + 593897 AGTTGTCTGT -s simHuman_chr6.simHuman.chr6 69631 10 + 601863 GGTTGTTTGT -s simHuman_chr6.simHuman.chr6 532022 10 - 601863 GGTTGTTTGT -s simRat_chr6.simRat.chr6 64909 10 + 647215 AGTTGTCTTT - -a -s simMouse_chr6.simMouse.chr6 73267 6 + 636262 ACCAAG -s Anc0.Anc0refChr4 18076 6 - 45765 ATCATA -s Anc1.Anc1refChr2 49295 6 + 144309 ATCATA -s Anc2.Anc2refChr7 17923 6 + 32194 ATCATA -s mr.mrrefChr0 69257 6 + 130230 ACCAAA -s simCow_chr6.simCow.chr6 76318 6 + 602619 ATCATA -s simDog_chr6.simDog.chr6 72810 4 + 593897 --CATA -s simHuman_chr6.simHuman.chr6 69644 6 + 601863 ATCATA -s simHuman_chr6.simHuman.chr6 532035 6 - 601863 ATCACA -s simRat_chr6.simRat.chr6 64919 6 + 647215 AACCAA - -a -s simMouse_chr6.simMouse.chr6 73273 5 + 636262 CCGTT -s Anc0.Anc0refChr4 18082 5 - 45765 TCACT -s Anc1.Anc1refChr2 49301 5 + 144309 TCACT -s Anc2.Anc2refChr7 17929 5 + 32194 TCACT -s mr.mrrefChr0 69263 5 + 130230 CCATT -s simCow_chr6.simCow.chr6 76324 5 + 602619 TCACC -s simDog_chr6.simDog.chr6 72814 5 + 593897 TCACT -s simHuman_chr6.simHuman.chr6 532041 5 - 601863 TCACT -s simRat_chr6.simRat.chr6 64925 5 + 647215 CCATC - -a -s simMouse_chr6.simMouse.chr6 73278 6 + 636262 TGTGCA -s Anc0.Anc0refChr4 18087 6 - 45765 TGTGCT -s Anc1.Anc1refChr2 49306 6 + 144309 TGTGCT -s Anc2.Anc2refChr7 17934 6 + 32194 TGTGCT -s mr.mrrefChr0 69268 6 + 130230 TGTGCA -s simCow_chr6.simCow.chr6 76329 6 + 602619 AGTGCT -s simDog_chr6.simDog.chr6 72819 6 + 593897 TGTGCT -s simHuman_chr6.simHuman.chr6 69650 6 + 601863 TGTTCT -s simHuman_chr6.simHuman.chr6 532046 6 - 601863 TGTGCT -s simRat_chr6.simRat.chr6 64930 6 + 647215 TGTGCA - -a -s simMouse_chr6.simMouse.chr6 73284 5 + 636262 GACTT -s Anc0.Anc0refChr4 18096 5 - 45765 GACTT -s Anc1.Anc1refChr2 49315 5 + 144309 GACTT -s Anc2.Anc2refChr7 17943 5 + 32194 GACTT -s mr.mrrefChr0 69277 5 + 130230 GACTT -s simCow_chr6.simCow.chr6 76338 5 + 602619 GACTT -s simDog_chr6.simDog.chr6 72828 5 + 593897 GACTT -s simHuman_chr6.simHuman.chr6 69659 5 + 601863 GACTT -s simHuman_chr6.simHuman.chr6 532055 5 - 601863 GACTT -s simRat_chr6.simRat.chr6 64939 5 + 647215 GACTT - -a -s simMouse_chr6.simMouse.chr6 73289 29 + 636262 TTTGAGGTTTACTTGATTATTCAACATAG -s Anc0.Anc0refChr4 18122 28 - 45765 TATAAGGCTTATTTGGTTAGACACCATA- -s Anc1.Anc1refChr2 49341 29 + 144309 TATAAGGCTTATTTGGTTAGACACCATAG -s Anc2.Anc2refChr7 17969 28 + 32194 TATAAGGCTTATTTGGTTAGAAGCCATA- -s mr.mrrefChr0 69282 29 + 130230 TATAAGGTTTACTTGATTATTCAACATAG -s simCow_chr6.simCow.chr6 76364 28 + 602619 TGTCTGGGTAATTTGGTTAAAAGCCATA- -s simDog_chr6.simDog.chr6 72854 28 + 593897 TATAAAGATTATTTGTTTAGAAGCCATA- -s simHuman_chr6.simHuman.chr6 69684 29 + 601863 TATAAGGCTTGCTTGGTTAGACAACATTG -s simHuman_chr6.simHuman.chr6 532081 29 - 601863 TATAATACTGGTTTGGTTAGACACCGTTA -s simRat_chr6.simRat.chr6 64944 29 + 647215 TATAAGTTCTATTTGATTATTCAATATGG - -a -s simMouse_chr6.simMouse.chr6 73318 10 + 636262 GCATACTTTC -s Anc0.Anc0refChr4 18154 10 - 45765 AGATATACTC -s Anc1.Anc1refChr2 49374 10 + 144309 AGATATACTC -s Anc2.Anc2refChr7 18001 10 + 32194 AGGCATACTC -s mr.mrrefChr0 69311 10 + 130230 GGATACTTTC -s simCow_chr6.simCow.chr6 76395 10 + 602619 AGGCATACCT -s simDog_chr6.simDog.chr6 72886 10 + 593897 AGGCATACTG -s simHuman_chr6.simHuman.chr6 69717 10 + 601863 AGATATACTC -s simHuman_chr6.simHuman.chr6 532110 4 - 601863 A------CTC -s simRat_chr6.simRat.chr6 64973 10 + 647215 GGATACTTTC - -a -s simMouse_chr6.simMouse.chr6 73328 11 + 636262 TTGTTTCTCTG -s Anc0.Anc0refChr4 18164 11 - 45765 TTGTTTATTTG -s Anc1.Anc1refChr2 49384 11 + 144309 TTGTTTATTTG -s Anc2.Anc2refChr7 18014 11 + 32194 TTGTTTATTTG -s mr.mrrefChr0 69321 11 + 130230 TTGTTTCTCTG -s simCow_chr6.simCow.chr6 76408 11 + 602619 TTGTTCATTTG -s simDog_chr6.simDog.chr6 72899 11 + 593897 TTGTTTATTTG -s simHuman_chr6.simHuman.chr6 69727 5 + 601863 CTGTT------ -s simHuman_chr6.simHuman.chr6 532114 5 - 601863 TTGTT------ -s simRat_chr6.simRat.chr6 64983 11 + 647215 TTGTTTCTTGG - -a -s simMouse_chr6.simMouse.chr6 73339 54 + 636262 CACGTAAGGAACCCAATACTGCTGACCAACTAGTCTTACCTCACTGGTAATTTC -s Anc0.Anc0refChr4 18175 54 - 45765 CACATATGGAACCCATTACTGCCAAACAACTGGCCCCCCCTGGCTGGTAATTTC -s Anc1.Anc1refChr2 49395 54 + 144309 CACATATGGAACCCATTACTGCCAAACAACTGGCCCCCCCTGGCTGGTAATTTC -s Anc2.Anc2refChr7 18025 54 + 32194 CACATATGGAACCCATTACTGCCAAACAACTGGCCCCCCCTAGTTGGTAATTTC -s mr.mrrefChr0 69332 54 + 130230 CATGTAAGGAACCCAATACTGCTGACCAACTAGTCTTCCCTGACTGGTAATTTC -s simCow_chr6.simCow.chr6 76419 54 + 602619 CAAATATGGGACCCATTACTGCCAAGGAACCGGCCCCCCCTTGTCGGAAATTTC -s simDog_chr6.simDog.chr6 72911 54 + 593897 CACATATGGACCCTGTTACTACTAAACAACTGGCCCTCCCTAGTTGGTAATTTA -s simHuman_chr6.simHuman.chr6 69897 49 + 601863 ---ATATGGAACCCATTACTGCCAAACAACTCACC--CCCTGGCTGGTAAATTC -s simRat_chr6.simRat.chr6 64994 54 + 647215 CATGTAAGGAACCCAATACCGCTGAGCAACTGGTCTTCCCTGACTGGTAATTTC - -a -s simMouse_chr6.simMouse.chr6 73393 7 + 636262 ACGATTG -s Anc0.Anc0refChr4 18229 7 - 45765 ATGATTA -s Anc1.Anc1refChr2 49449 7 + 144309 ATGATTA -s Anc2.Anc2refChr7 18079 7 + 32194 ATGATTA -s mr.mrrefChr0 69386 7 + 130230 ATGATTG -s simCow_chr6.simCow.chr6 76473 7 + 602619 AGGATTA -s simDog_chr6.simDog.chr6 72973 7 + 593897 ATGATGA -s simHuman_chr6.simHuman.chr6 69946 7 + 601863 ATGCTTA -s simRat_chr6.simRat.chr6 65048 7 + 647215 ATGATTG - -a -s simMouse_chr6.simMouse.chr6 73400 44 + 636262 TATATTGGGAAGGGAAGACTAATCAATGCCCTATGCTTCTCTTA -s Anc0.Anc0refChr4 18236 43 - 45765 TGTGTCGGGAAGGGAAGACTAAACATTA-CCTATGTTTCTCTAA -s Anc1.Anc1refChr2 49456 43 + 144309 TGTGTCGGGAAGGGAAGACTAAACATTA-CCTATGTTTCTCTAA -s Anc2.Anc2refChr7 18086 43 + 32194 TGTGGCGGGATGGGACGACTAAATATTA-CCTATGTTTCTCTAA -s mr.mrrefChr0 69393 44 + 130230 TATATTGGGAAGGGAAGACTAATCATTGCCCTATGTTTCTCTTA -s simCow_chr6.simCow.chr6 76491 43 + 602619 TCCGCCAGGTTGGGATGGCTAAATATTA-CCTATGCTTCCCCAG -s simDog_chr6.simDog.chr6 72980 43 + 593897 TGTGGTGGGATGGGACAACTCAATACTA-TCCGTGTTTCTCTGA -s simHuman_chr6.simHuman.chr6 69953 43 + 601863 TGTCTCGGGAAGGGGAGTCTAAACGTTA-CCTATGTTTTTCTAA -s simRat_chr6.simRat.chr6 65055 44 + 647215 TATATTGGGCTGGGAAGACTATTCATTGCCCTATGTTTCTCTTA - -a -s simMouse_chr6.simMouse.chr6 73444 29 + 636262 GGGGTTGCCTAACATTGAAATCCACCCAT -s Anc0.Anc0refChr4 18280 28 - 45765 GGGGGTGCCTCACCACAAGATGAACCCG- -s Anc1.Anc1refChr2 49500 29 + 144309 GGGGGTGCCTCACCACAAGATGAACCCGC -s Anc2.Anc2refChr7 18130 28 + 32194 GGGGGTGCCTCACCACTAGATGAACCTG- -s mr.mrrefChr0 69437 29 + 130230 GGGGTTGCCTAACATCAAAATCCACCCAT -s simCow_chr6.simCow.chr6 76535 28 + 602619 GAGGATGCCTCACTTCTAGATGAACCTG- -s simDog_chr6.simDog.chr6 73024 28 + 593897 AGAGGTGCTTCACCACTAGTTGAACCTG- -s simHuman_chr6.simHuman.chr6 69997 29 + 601863 GGGGGTGCCTCCCCACAAGATGAACCCGC -s simRat_chr6.simRat.chr6 65099 29 + 647215 GGGGTTGCCTAACATCAAAATTCACCGAT - -a -s simMouse_chr6.simMouse.chr6 73473 16 + 636262 CTAAATACACCAGGTC -s Anc0.Anc0refChr4 18308 16 - 45765 CAATATATATCAGGCC -s Anc1.Anc1refChr2 49529 16 + 144309 CAATATATATCAGGCC -s Anc2.Anc2refChr7 18158 16 + 32194 CAATATATATCAGGCC -s mr.mrrefChr0 69466 16 + 130230 CTAAATACACCAGGTC -s simCow_chr6.simCow.chr6 76563 16 + 602619 CAATATATATAAGGCC -s simDog_chr6.simDog.chr6 73052 16 + 593897 CAATATATAACATGCC -s simHuman_chr6.simHuman.chr6 70044 16 + 601863 CAATATATATCAGGCC -s simRat_chr6.simRat.chr6 65128 16 + 647215 CTAAATACACCAGGTC - -a -s simMouse_chr6.simMouse.chr6 73489 18 + 636262 TTTATCTACCTCAAATGA -s Anc0.Anc0refChr4 18324 17 - 45765 TTTATCCACTTAAA-CGG -s Anc1.Anc1refChr2 49545 17 + 144309 TTTATCCACTTAAA-CGG -s Anc2.Anc2refChr7 18174 17 + 32194 TTTATCCTCTTAGA-CAG -s mr.mrrefChr0 69482 18 + 130230 TTTATCTACCTCAAATGA -s simCow_chr6.simCow.chr6 76591 17 + 602619 TTTATCTTCTTATC-CAG -s simDog_chr6.simDog.chr6 73068 17 + 593897 TTTATCCTCTTAGA-CAG -s simHuman_chr6.simHuman.chr6 70060 17 + 601863 TTGATTCACTTAAA-CGG -s simRat_chr6.simRat.chr6 65144 18 + 647215 TTTATCTACCTCAAATGA - -a -s simMouse_chr6.simMouse.chr6 73507 29 + 636262 ATTTATAAGCAAAGTACTGTGCTCAGGTA -s Anc0.Anc0refChr4 18341 29 - 45765 AGTTATTAGCAAAGTACTGTGCTCTGATA -s Anc1.Anc1refChr2 49562 29 + 144309 AGTTATTAGCAAAGTACTGTGCTCTGATA -s Anc2.Anc2refChr7 18197 29 + 32194 AGTTAATCACAATGTGGTGTGCTGTGATA -s mr.mrrefChr0 69500 29 + 130230 ATTTATAAGCAAAGTACTGTGCTCAGGTA -s simCow_chr6.simCow.chr6 76614 21 + 602619 AGT-AATCACAAAATGCTGTG-------G -s simDog_chr6.simDog.chr6 73091 29 + 593897 AGATAATCACAATGTGGTGTGCTGTGATA -s simHuman_chr6.simHuman.chr6 70077 29 + 601863 AGTTCTTAGTAAAGCACTGTGCTCTGATA -s simRat_chr6.simRat.chr6 65162 21 + 647215 ATTTATAAGCAAA--------CTCAGGTA - -a -s simMouse_chr6.simMouse.chr6 73536 4 + 636262 ATTT -s Anc0.Anc0refChr4 18376 4 - 45765 ATTT -s Anc1.Anc1refChr2 49597 4 + 144309 ATTT -s Anc2.Anc2refChr7 18232 4 + 32194 ATTT -s mr.mrrefChr0 69529 4 + 130230 ATTT -s simCow_chr6.simCow.chr6 76641 4 + 602619 ATTT -s simDog_chr6.simDog.chr6 73129 4 + 593897 AGTT -s simHuman_chr6.simHuman.chr6 70112 4 + 601863 ATTT -s simRat_chr6.simRat.chr6 65183 4 + 647215 ACTT - -a -s simMouse_chr6.simMouse.chr6 73540 1 + 636262 C -s Anc0.Anc0refChr4 18383 1 - 45765 T -s Anc1.Anc1refChr2 49604 1 + 144309 T -s Anc2.Anc2refChr7 18239 1 + 32194 T -s mr.mrrefChr0 69533 1 + 130230 C -s simCow_chr6.simCow.chr6 76648 1 + 602619 T -s simDog_chr6.simDog.chr6 73136 1 + 593897 T -s simHuman_chr6.simHuman.chr6 70119 1 + 601863 T -s simRat_chr6.simRat.chr6 65187 1 + 647215 C - -a -s simMouse_chr6.simMouse.chr6 73541 4 + 636262 ACCC -s Anc0.Anc0refChr4 18384 4 - 45765 ATCT -s Anc1.Anc1refChr2 49605 4 + 144309 ATCT -s Anc2.Anc2refChr7 18241 4 + 32194 ATCT -s mr.mrrefChr0 69534 4 + 130230 ACCC -s simCow_chr6.simCow.chr6 76650 4 + 602619 ATCT -s simDog_chr6.simDog.chr6 73138 4 + 593897 ATCT -s simHuman_chr6.simHuman.chr6 70120 4 + 601863 ATCT -s simRat_chr6.simRat.chr6 65188 4 + 647215 AACC - -a -s simMouse_chr6.simMouse.chr6 73545 27 + 636262 CCCCTCATAGCATCCACTGAGCACAGG -s Anc0.Anc0refChr4 18388 27 - 45765 CCCTCTATAACACCCACTGAGCACAGG -s Anc1.Anc1refChr2 49609 27 + 144309 CCCTCTATAACACCCACTGAGCACAGG -s Anc2.Anc2refChr7 18245 27 + 32194 CCCTCTATAACACCCACTGAGCACTGG -s mr.mrrefChr0 69538 27 + 130230 CCCCTCATAGCATCCACTGAGCACAGG -s simCow_chr6.simCow.chr6 76655 27 + 602619 CCCTCTATAACAGCCACTGAGAAATGG -s simDog_chr6.simDog.chr6 73142 27 + 593897 CCCTCTATAGCACCCTCTGAGCACTGG -s simHuman_chr6.simHuman.chr6 70124 27 + 601863 CTCTCTATCATGCCCACTGAGCAGAGA -s simRat_chr6.simRat.chr6 65192 27 + 647215 CCCCTGAGAGCATCCACTGAGTACAGG - -a -s simMouse_chr6.simMouse.chr6 73572 59 + 636262 GGAGTGTTCTCAATTACTAATCAGGTGAACAGCATGCAAGCCTGGAGTCTAACCAAATA -s Anc0.Anc0refChr4 18415 33 - 45765 GGCCTATTTTCCATTACTTATCAGATACCCCAA-------------------------- -s Anc1.Anc1refChr2 49636 33 + 144309 GGCCTATTTTCCATTACTTATCAGATACCCCAA-------------------------- -s Anc2.Anc2refChr7 18272 33 + 32194 GGCCTATTTTCCATTACTTATCAGATACCTTAA-------------------------- -s mr.mrrefChr0 69565 33 + 130230 GGAGTGTTCTCAATTACTAATCAGGTACACCGC-------------------------- -s simCow_chr6.simCow.chr6 76682 33 + 602619 GGCCTGTTCCCCCTAACTTACCAAATACCTTAA-------------------------- -s simDog_chr6.simDog.chr6 73169 33 + 593897 GGCTTATTTTCCATTACTTATCAGATACCTTAA-------------------------- -s simHuman_chr6.simHuman.chr6 70151 33 + 601863 GGCCATTTTTCCATGACTTATCAGATACGCCAA-------------------------- -s simRat_chr6.simRat.chr6 65232 33 + 647215 GCAGTGTTCTCAATTACTAATCAGGTACCCCGC-------------------------- - -a -s simMouse_chr6.simMouse.chr6 73631 90 + 636262 AATGTTAGATAAAGTAGATGGATGCCTCCCCCTGGACTGTTATCACAACCACTAGGTATTAGTGAGCTCTCTTAACAAGTCATAAAACAT -s Anc0.Anc0refChr4 27022 88 + 45765 AATGTTAGACAAAGTAGATGAGTTCTTCCCTC--AACTAGTGTCACAACTACTAGATACTCTTAACCTCTGTAAACAAGTCATGAAATAT -s Anc1.Anc1refChr2 94285 88 - 144309 AATGTTAGACAAAGTAGATGAGTTCTTCCCTC--AACTAGTGTCACAACTACTAGATACTCTTAACCTCTGTAAACAAGTCATGAAATAT -s Anc2.Anc2refChr7 13578 88 - 32194 AATGTTAGACAAAGTAGATGAGTTCTTCCCTC--AATTAGTGTCAAAACTACTAGATACTCTTAACCTCTGTAAACAAGTCATGAAAAAT -s mr.mrrefChr0 60226 90 - 130230 AATGTTAGATAAAGTAGATGGGTGCCTCCCCCTGGACTGTTATCACAACCACTAGATATTAGTGAGCTCTCTTAACAAGTCATAAAATAT -s simCow_chr6.simCow.chr6 525587 87 - 602619 AATATAAGACAAAGTAGATGGGTCCTT-CCTA--AATTAGTATCATAACTATTAGCTATTCCTAACCTCTGGATAGAAGACATGGAAAAT -s simDog_chr6.simDog.chr6 520352 88 - 593897 AATGTTAGACAAAGTAGAAGAGTTCTTCCCTC--AATTAGTGTCAAGACTACAAGATACCATTAACCTCTGTAAACAAGTATTAAAAAAC -s simHuman_chr6.simHuman.chr6 531327 88 - 601863 AATGTTAGACTAAGCAGATGAGTACTTGCTTC--AACTAGTGTCACAACTACTAGATACTCTTAACCTCTGTAAACAAGGCATGAAATAT -s simRat_chr6.simRat.chr6 581538 90 - 647215 AATGCTAGATAAAGTAGATGGGTGCATCTCCCTTGAGTGTCCTCACAACCACTAGATATTAGTGAGCTCTCTTAACAAGTCATAAAATAT - -a -s simMouse_chr6.simMouse.chr6 73721 6 + 636262 TTATTG -s Anc0.Anc0refChr4 27111 6 + 45765 TTGTTA -s Anc1.Anc1refChr2 94374 6 - 144309 TTGTTA -s Anc2.Anc2refChr7 13667 6 - 32194 TTGCTA -s mr.mrrefChr0 60316 6 - 130230 TTATTG -s simCow_chr6.simCow.chr6 525675 6 - 602619 TTGCCA -s simDog_chr6.simDog.chr6 520441 6 - 593897 TTGCTA -s simHuman_chr6.simHuman.chr6 531416 6 - 601863 TTGTTA -s simRat_chr6.simRat.chr6 581628 6 - 647215 TTATTA - -a -s simMouse_chr6.simMouse.chr6 73727 64 + 636262 CACCATGCTTTAGAATGCTTATGTCGATCATGGCAAGATTCATTGCACACCAGGCTTTAAAACA -s Anc0.Anc0refChr4 27117 30 + 45765 CACCAGGCTTTAAAATGTTTGGGTTGATCA---------------------------------- -s Anc1.Anc1refChr2 94380 30 - 144309 CACCAGGCTTTAAAATGTTTGGGTTGATCA---------------------------------- -s Anc2.Anc2refChr7 13673 30 - 32194 CACCAGGCTTTAAAATGTTTGGGTTGATCA---------------------------------- -s mr.mrrefChr0 60322 62 - 130230 CACCATGCTTTAGAATGCTTATGTCGATCATGGCAAGATTCATT--ACACCAGGCTTTAAAACA -s simCow_chr6.simCow.chr6 525681 30 - 602619 CACCAGGCTTCAAAATGTTTGTGTTGATCA---------------------------------- -s simDog_chr6.simDog.chr6 520447 30 - 593897 CACTGGGCTTTAAATCATTTGGGTCGATCC---------------------------------- -s simHuman_chr6.simHuman.chr6 531422 30 - 601863 CACCACGCTTTAAAATGTTTGCGTTGATCA---------------------------------- -s simRat_chr6.simRat.chr6 581642 62 - 647215 TACCATTCTTTAAGATGGTTGTGTCAATTATGGAAAGATTCATT--ATACCAGGCTTTAAAACA - -a -s simMouse_chr6.simMouse.chr6 73791 25 + 636262 TCAGAGAGGAAACACACACACTTCT -s Anc0.Anc0refChr4 27147 22 + 45765 ---GGGAGGAAACATACAGGCTTCC -s Anc1.Anc1refChr2 94410 22 - 144309 ---GGGAGGAAACATACAGGCTTCC -s Anc2.Anc2refChr7 13703 22 - 32194 ---GGGAGGAAACATACAGGCTTCC -s mr.mrrefChr0 60394 25 - 130230 TCAGAGAGGAAACATACACACTTCT -s simCow_chr6.simCow.chr6 525711 22 - 602619 ---GGGAGAAAACATACAAGCTTCT -s simDog_chr6.simDog.chr6 520477 22 - 593897 ---GGGGGGAAACATATAGGCTTCC -s simHuman_chr6.simHuman.chr6 531452 22 - 601863 ---GGGAGGAAGCATACAGGCTTCC -s simRat_chr6.simRat.chr6 581714 25 - 647215 TCAGCGAGGAAACATACACACTTCG - -a -s simMouse_chr6.simMouse.chr6 73816 10 + 636262 TGAACAGCTC -s Anc0.Anc0refChr4 27169 6 + 45765 TGAACA---- -s Anc1.Anc1refChr2 94432 10 - 144309 TGAACAGCTC -s Anc2.Anc2refChr7 13733 6 - 32194 TGGAGA---- -s mr.mrrefChr0 60419 10 - 130230 TGAACAGCTC -s simCow_chr6.simCow.chr6 525741 6 - 602619 TGGCCA---- -s simDog_chr6.simDog.chr6 520507 6 - 593897 TGGAGA---- -s simHuman_chr6.simHuman.chr6 531474 10 - 601863 TGAACAGCTC -s simRat_chr6.simRat.chr6 581739 10 - 647215 TGAACAGCTC - -a -s simMouse_chr6.simMouse.chr6 73826 21 + 636262 TTTTTATTTAGATATCTGACT -s Anc0.Anc0refChr4 27175 19 + 45765 -TTCTGTTTAT-TATGTGACT -s Anc1.Anc1refChr2 94442 21 - 144309 TTTCTGTTTATGTATGTGACT -s Anc2.Anc2refChr7 13739 19 - 32194 -TTCTACTTGT-TAAATGACT -s mr.mrrefChr0 60429 21 - 130230 TTTCTGTTTAGGTATGTGACT -s simCow_chr6.simCow.chr6 525747 19 - 602619 -TTTCACTTTA-TGAAAGACT -s simDog_chr6.simDog.chr6 520513 19 - 593897 -TTCTACTTGT-TAAATGACT -s simHuman_chr6.simHuman.chr6 531485 21 - 601863 TTTCTGTTTATGTATGTGACT -s simRat_chr6.simRat.chr6 581749 21 - 647215 TCTCTGTTTAGGTATGTGACT - -a -s simMouse_chr6.simMouse.chr6 73847 4 + 636262 ATAT -s Anc0.Anc0refChr4 27194 4 + 45765 ATTC -s Anc1.Anc1refChr2 94463 4 - 144309 ATTC -s Anc2.Anc2refChr7 13764 4 - 32194 ATTC -s mr.mrrefChr0 60450 4 - 130230 ATAT -s simCow_chr6.simCow.chr6 525772 4 - 602619 ACTC -s simDog_chr6.simDog.chr6 520538 4 - 593897 ATTC -s simHuman_chr6.simHuman.chr6 531506 4 - 601863 ATTC -s simRat_chr6.simRat.chr6 581770 4 - 647215 ATCT - -a -s simMouse_chr6.simMouse.chr6 73851 6 + 636262 GGTCAT -s Anc0.Anc0refChr4 27198 6 + 45765 AGCAGT -s Anc1.Anc1refChr2 94467 6 - 144309 AGCAGT -s Anc2.Anc2refChr7 13768 6 - 32194 AGCAGT -s mr.mrrefChr0 60454 6 - 130230 GGTCAT -s simCow_chr6.simCow.chr6 525776 6 - 602619 AGCTGT -s simDog_chr6.simDog.chr6 520574 6 - 593897 AGCAGT -s simHuman_chr6.simHuman.chr6 531510 6 - 601863 ACGAGT -s simRat_chr6.simRat.chr6 581774 6 - 647215 GGTCAT - -a -s simMouse_chr6.simMouse.chr6 73857 41 + 636262 AACTATGGATCTGATTAATCATTTTAAAAGTAAAATCTCCA -s Anc0.Anc0refChr4 27204 13 + 45765 A----------------------------GTGAGTTATCCA -s Anc1.Anc1refChr2 94473 39 - 144309 AACCCTGGATGTGATCTATCTTTT--GATGTGAGTTATCCA -s Anc2.Anc2refChr7 13774 13 - 32194 A----------------------------GGGAGTTACCCA -s mr.mrrefChr0 60460 41 - 130230 AACTATGGATCTGATCAATCATTTTAAAAGTGAAATCTCCA -s simCow_chr6.simCow.chr6 525788 13 - 602619 A----------------------------GGAGGTAAACCA -s simDog_chr6.simDog.chr6 520580 13 - 593897 A----------------------------GGGAGTTACCCA -s simHuman_chr6.simHuman.chr6 531516 39 - 601863 AACCCTGGATGTGATCTATCTTTT--GATGTGATCTATCTT -s simRat_chr6.simRat.chr6 581780 40 - 647215 CACTAT-GATCTGTTCAATCATTTTAAAAGTGAAATCTCCA - -a -s simMouse_chr6.simMouse.chr6 73898 27 + 636262 ATTTGAAAGTATAATCTCCATAATAGG -s Anc0.Anc0refChr4 27217 3 + 45765 GTT------------------------ -s Anc1.Anc1refChr2 94512 27 - 144309 GTTAAAAAGAGAAATTTCCATAGTAAG -s Anc2.Anc2refChr7 13787 3 - 32194 GTT------------------------ -s mr.mrrefChr0 60501 27 - 130230 ATTTGAAAGTATAATCTCCATAATAGG -s simCow_chr6.simCow.chr6 525802 3 - 602619 ATT------------------------ -s simDog_chr6.simDog.chr6 520593 3 - 593897 GTT------------------------ -s simHuman_chr6.simHuman.chr6 531555 27 - 601863 TTTAAAAAGAGAAATTTCCATAGTAAG -s simRat_chr6.simRat.chr6 581820 27 - 647215 ATTTGAAAGTATACTCTCCATAATAGG - -a -s simMouse_chr6.simMouse.chr6 73925 33 + 636262 TTAGGACATAAGTTCAACTCAATGAAATTGAAA -s Anc0.Anc0refChr4 27220 27 + 45765 --GGGAGGGAAACT----GCATTGATGTTGTGG -s Anc1.Anc1refChr2 94541 29 - 144309 TTGGGAGGGAAACT----GCATTGATGTTGTGG -s Anc2.Anc2refChr7 13790 27 - 32194 --GGGAGGGAAACT----GCATTAATGTTGTGG -s mr.mrrefChr0 60530 33 - 130230 TTAGGAGATAAGTTCAACTCAATGAAATTGAAG -s simCow_chr6.simCow.chr6 525805 27 - 602619 --GATAGGGTGACT----GCATTAATGCTGTGG -s simDog_chr6.simDog.chr6 520596 27 - 593897 --GGGAGAGAAACC----GCAATAATTTTGTGG -s simHuman_chr6.simHuman.chr6 531584 29 - 601863 TTCGAAGGGAAACT----GCATTGATGTCGTGG -s simRat_chr6.simRat.chr6 581849 33 - 647215 TTAGGAGATAGTTACAACTCAATGAAACTGAAG - -a -s simMouse_chr6.simMouse.chr6 73958 8 + 636262 ATGGGACA -s Anc0.Anc0refChr4 27267 8 + 45765 ATGGGACA -s Anc1.Anc1refChr2 94590 8 - 144309 ATGGGACA -s Anc2.Anc2refChr7 13838 8 - 32194 ATGGGACA -s mr.mrrefChr0 60582 8 - 130230 ATGGGACA -s simCow_chr6.simCow.chr6 525853 8 - 602619 ATGGGACA -s simDog_chr6.simDog.chr6 520644 8 - 593897 ATTCGACA -s simHuman_chr6.simHuman.chr6 531633 5 - 601863 ATGGG--- -s simRat_chr6.simRat.chr6 581901 8 - 647215 ATAGGACA - -a -s simMouse_chr6.simMouse.chr6 73966 10 + 636262 CTCTCAGTCC -s Anc0.Anc0refChr4 27275 10 + 45765 CTGTCAGTCC -s Anc1.Anc1refChr2 94598 10 - 144309 CTGTCAGTCC -s Anc2.Anc2refChr7 13847 10 - 32194 CTGTCAGTCC -s mr.mrrefChr0 60590 10 - 130230 CTGTCAGTCC -s simCow_chr6.simCow.chr6 525862 10 - 602619 CTGTCAGTCC -s simDog_chr6.simDog.chr6 520653 10 - 593897 CTGTCGGGCT -s simHuman_chr6.simHuman.chr6 531638 9 - 601863 -TGTCAGTAC -s simRat_chr6.simRat.chr6 581909 10 - 647215 CTGTCAGTCC - -a -s simMouse_chr6.simMouse.chr6 73976 31 + 636262 TAGAAGCAAAGATGGTGTATGTCTTCTTTTT -s Anc0.Anc0refChr4 27286 31 + 45765 TAGAAGCACAGATGAAGCATCTTTTCTTTTT -s Anc1.Anc1refChr2 94609 31 - 144309 TAGAAGCACAGATGAAGCATCTTTTCTTTTT -s Anc2.Anc2refChr7 13858 31 - 32194 TAAAAGCACAGATGAAGCATCCTTACTTTTT -s mr.mrrefChr0 60601 31 - 130230 TAGAAGCAAAGATGGTGTATCTCTTCTTTTT -s simCow_chr6.simCow.chr6 525873 31 - 602619 TAAAAGCGCAGATGAATCTTCCTTCCTTTTT -s simDog_chr6.simDog.chr6 520664 31 - 593897 TAAAAGCACCGGTGAAGCATCCTTACTTTTT -s simHuman_chr6.simHuman.chr6 531648 31 - 601863 TAGAAGTACAGATGAAGGATCTTTTCTTTTT -s simRat_chr6.simRat.chr6 581920 30 - 647215 TAGCAGCGAA-ATGGTGTATCTCTTCTTTTT - -a -s simMouse_chr6.simMouse.chr6 74007 1 + 636262 T -s Anc0.Anc0refChr4 18743 1 - 45765 G -s Anc1.Anc1refChr2 50024 1 + 144309 G -s Anc2.Anc2refChr7 18616 1 + 32194 G -s mr.mrrefChr0 70004 1 + 130230 T -s simCow_chr6.simCow.chr6 77032 1 + 602619 G -s simDog_chr6.simDog.chr6 73545 1 + 593897 G -s simHuman_chr6.simHuman.chr6 70536 1 + 601863 G -s simRat_chr6.simRat.chr6 65677 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 74008 7 + 636262 TTGGGTA -s Anc0.Anc0refChr4 18745 7 - 45765 TTTGGTA -s Anc1.Anc1refChr2 50026 7 + 144309 TTTGGTA -s Anc2.Anc2refChr7 18618 7 + 32194 TTTGATA -s mr.mrrefChr0 70006 7 + 130230 TTTGGTA -s simCow_chr6.simCow.chr6 77034 7 + 602619 TTTGATA -s simDog_chr6.simDog.chr6 73547 7 + 593897 TTTAATA -s simHuman_chr6.simHuman.chr6 70539 7 + 601863 TTTGGTA -s simRat_chr6.simRat.chr6 65679 7 + 647215 TTTGGTA - -a -s simMouse_chr6.simMouse.chr6 74015 2 + 636262 AC -s Anc0.Anc0refChr4 18752 2 - 45765 TC -s Anc1.Anc1refChr2 50033 2 + 144309 TC -s Anc2.Anc2refChr7 18625 2 + 32194 TC -s mr.mrrefChr0 70017 2 + 130230 TC -s simCow_chr6.simCow.chr6 77045 2 + 602619 TC -s simDog_chr6.simDog.chr6 73625 2 + 593897 TC -s simHuman_chr6.simHuman.chr6 70546 2 + 601863 TC -s simRat_chr6.simRat.chr6 65690 2 + 647215 TC - -a -s simMouse_chr6.simMouse.chr6 74017 222 + 636262 TAACCCTACCAGATTACACAATGACGTATGGGAATCAGCTATTGTAGAGCTTGTCCCTTTTATAGCAGATGATCAAGTCCTTTATAGCAGATGATCAAGTCCAAGAGATAGCTATAGGGCCATTATTGGGAGCTACTGCATCTGAATTTTTGAACTTCAACACCATCTGCCACAGTGATGAGTGCCAAAGAGAAGCAAACCCTTGATATAAGATAGTCTATC -s Anc0.Anc0refChr4 18775 205 - 45765 TAACCTCACCAGATTTCTCACTGATGTTTAAGAGTCAGTTGTTGTAGGCCTTACCTCATTTGTTCCAAATGATCAAGTTGTATAT-----------------AAAAGAAAAATATCGGCTTGTAATAGGGAGCTACTGCATCTAAACTTATGAATGTCAACACCTTTTGACAGGGTGATGTGTTCCAAAACGGAATAAACCCTTGATGTGAGATAGTCTACC -s Anc1.Anc1refChr2 50056 205 + 144309 TAACCTCACCAGATTTCTCACTGATGTTTAAGAGTCAGTTGTTGTAGGCCTTACCTCATTTGTTCCAAATGATCAAGTTGTATAT-----------------AAAAGAAAAATATCGGCTTGTAATAGGGAGCTACTGCATCTAAACTTATGAATGTCAACACCTTTTGACAGGGTGATGTGTTCCAAAACGGAATAAACCCTTGATGTGAGATAGTCTACC -s Anc2.Anc2refChr7 18648 205 + 32194 CAACCTCTCCAGATTTCTCACTGATGTTTATGAGTTAGTTGTTGTAGGCGTTACTTAGTTTGCTCCAAATGATCAAGTTGTATAT-----------------AAAAGAAAAATATCTGCTTGTAATAAGGAGCTGCTGCATGTAAACTTATGAATGTCAACACCTTTAGACAGGGTGATGTGTTCCAAAACTGAATAAACCCTTGATGTGACATAGTCTACC -s mr.mrrefChr0 70040 222 + 130230 TAACCTTACCAGATTTCACAATGATGTTTGAGAGTCAGCTGTTGTAGAGCTTGTCTCATTTATAGCAGATGATCAAGTTGTTTATAGCAGATGATCAAGTGCAAAAGATAGTTATAGGGCCATTATTGGGAGCTACTGCATCTGAATTTTTGAACGTCAACACCATTTGCCAGAGTGATGAGTGCCAAAGAGGAGCAAACCCTTGATATAAGATAGTCTATC -s simCow_chr6.simCow.chr6 77068 205 + 602619 CAACCTTGCCAGATATCACACTGATGTTTAGGGGTTAGTTATTGTTGGCTTTGCTTAGTTTGCTCCAAATGATCAAGTTGTATAT-----------------AAAAGAAAAATATCCGCTGGTGATCAGAAGCTGCTGCATGAAAACTTAAGAATGTTAACGCCTCTAGATACAGTGATGTGTACCAAAACTGGACGAGCCCTCAATGGGAAATAGTCTACC -s simDog_chr6.simDog.chr6 73648 204 + 593897 CAGCCTCTCCGGATTTCTCATTGATGTTTATGAGTTACTTGTTGTAGGCGTCACTTAGTTTGCTCCAAATGATCCAGTTGTATAT-----------------AAAAGAAAAACATCTGCGTGTAATAATGAGCTGATGAATGTAAACTTATGAACTTCAACACCTTTAGACAGGGTGATGCATTCCAAAACTGAATAAACCCTTGATGTGACATAGCTCAC- -s simHuman_chr6.simHuman.chr6 70564 203 + 601863 TAATCTAACCAGATTTCGCACCGATG-TTAAGAGTCAGTTGTTGTAGGCCTTACCTCATTTGTTCCAAATGATCAAGTTGTATAT-----------------AAAAGACAAATATTGGCTTTCAATAGGGAGTTACTGCATCTAAACTCATGATTGTCAGCACC-TTTGACAGGGTGATGTGTTTCAAAATGGAATAAACCATTGATGTGAGATAGTCTACC -s simRat_chr6.simRat.chr6 65719 203 + 647215 TAACCTTACCAGACCTCACAATGATGTTTGAGAGTCAGCTGTTGTGGTGCTTGTCTCATTTATAGCAGATGATCAAGTTGT-----------------GTGCAAAAGATAGTTATAGGGCCATTATTAGGAGCTACTGCATCTGAATT--TGTACGTCAACACCATTTGCCAGAGTAATGAGTCCCAAAGAGGAGCAAACTCTTGGTATAAAATGGTCTATC - -a -s simMouse_chr6.simMouse.chr6 74239 17 + 636262 AAATCTTTTCTGGACAA -s Anc0.Anc0refChr4 18989 17 - 45765 AAATCTTTTCTAAACAA -s Anc1.Anc1refChr2 50270 17 + 144309 AAATCTTTTCTAAACAA -s Anc2.Anc2refChr7 18862 17 + 32194 AGATCTTTGCTAAATAA -s mr.mrrefChr0 70262 17 + 130230 AAATCTTTTCTGGACAA -s simCow_chr6.simCow.chr6 77286 17 + 602619 AGATCTTGACAAATTAA -s simDog_chr6.simDog.chr6 73856 17 + 593897 AGATCTTTGCTACATGA -s simHuman_chr6.simHuman.chr6 70776 17 + 601863 AAATCTTTTCTAAACAA -s simRat_chr6.simRat.chr6 65922 17 + 647215 GAATCTTGTCTGGACAA - -a -s simMouse_chr6.simMouse.chr6 74256 3 + 636262 CTG -s Anc0.Anc0refChr4 19006 3 - 45765 ATA -s Anc1.Anc1refChr2 50287 3 + 144309 ATA -s Anc2.Anc2refChr7 18879 3 + 32194 ATA -s mr.mrrefChr0 70279 3 + 130230 CTA -s simCow_chr6.simCow.chr6 77303 3 + 602619 ATG -s simDog_chr6.simDog.chr6 73907 3 + 593897 ATA -s simHuman_chr6.simHuman.chr6 70793 3 + 601863 ATA -s simRat_chr6.simRat.chr6 65939 3 + 647215 CTA - -a -s simMouse_chr6.simMouse.chr6 74259 42 + 636262 CATTTTTTCACAACATGCACGATGACAGACCTTTTCTGGTCA -s Anc0.Anc0refChr4 19015 42 - 45765 GATTTTTTCACAATATGCACAAGAACAAACCTTTCCCTATAT -s Anc1.Anc1refChr2 50296 42 + 144309 GATTTTTTCACAATATGCACAAGAACAAACCTTTCCCTATAT -s Anc2.Anc2refChr7 18888 42 + 32194 GATTTTTTCATAATATGCACAAGAACAAACCTTTCCCTATAT -s mr.mrrefChr0 70282 42 + 130230 GATTTTTTCACAATATGCACGATGACAAACCTTTTCTAGTCA -s simCow_chr6.simCow.chr6 77312 34 + 602619 GATCTTTTTATAATATGCACACGAACGAACC--------TGT -s simDog_chr6.simDog.chr6 73916 42 + 593897 GAATTTTTCATAATATGCACCAGAGCAAACCTTTCCCTATAT -s simHuman_chr6.simHuman.chr6 70802 42 + 601863 GATTTTTTCACAATATGCACAGGCACAAAGCATTCTCTATAT -s simRat_chr6.simRat.chr6 65942 42 + 647215 GATTCTTTCACAATATGCATGATGGCAAACCTTTTCTAGCCA - -a -s simMouse_chr6.simMouse.chr6 74301 63 + 636262 AGATTCAGAGTGTTTATACTGGCTCTGCTAAAAGGACGCTCTTGCCATGCCAAGGAAAAGAAA -s Anc0.Anc0refChr4 19057 53 - 45765 TGTTCCTAGGT----CTGCTGTCTCTGGTAAAGGCAGGCTCTTGCCAAGCCAAGG------AA -s Anc1.Anc1refChr2 50338 53 + 144309 TGTTCCTAGGT----CTGCTGTCTCTGGTAAAGGCAGGCTCTTGCCAAGCCAAGG------AA -s Anc2.Anc2refChr7 18951 53 + 32194 TGTACCTAGGT----CTGCTGTCTACAGTACAGGCAGGCTCTTGCCAAGCCAAGG------GA -s mr.mrrefChr0 70324 59 + 130230 AGATTCAAAGT----ATACTGGCTCTGGTAAAAGGAGGCTCTTGCCATGCCAAGGAAAAGAAA -s simCow_chr6.simCow.chr6 77367 53 + 602619 AGTACCTAGGT----CTGCTGTCTACACTATAGGCAGGGTCTTCCTAAGCCAATG------AA -s simDog_chr6.simDog.chr6 73979 53 + 593897 TGTACTTAGGT----CTGCTGTCTACAGTACAGGCAGGCTCTCGCCAAGCCAAGG------GA -s simHuman_chr6.simHuman.chr6 70844 53 + 601863 TATTCCCAGGT----CTGCTGTGTCTGGTAATGGCAGGTTGTTACCAAGCAAAGG------AA -s simRat_chr6.simRat.chr6 65984 59 + 647215 AGATTCAAAGT----ATACTGGCTCTGGTGAAAGGAGGCTCTTGCCATGCCAAAAGGAAGAAA - -a -s simMouse_chr6.simMouse.chr6 74364 25 + 636262 TGTACACATTAACTGTTAACCATTT -s Anc0.Anc0refChr4 19110 25 - 45765 TGCACACATTAAGTGTTGACCATTT -s Anc1.Anc1refChr2 50391 25 + 144309 TGCACACATTAAGTGTTGACCATTT -s Anc2.Anc2refChr7 19005 25 + 32194 TACACACATTAAGTGTTGACCATTT -s mr.mrrefChr0 70383 25 + 130230 TGTACACATTAACTGTTAACCATTT -s simCow_chr6.simCow.chr6 77421 25 + 602619 TTCACCCATCAAGTGTTGACCATTT -s simDog_chr6.simDog.chr6 74033 25 + 593897 TACACACATTAAGCGTTGGCTATTT -s simHuman_chr6.simHuman.chr6 70897 25 + 601863 TGCACACATTACGTGTTGACCATTT -s simRat_chr6.simRat.chr6 66043 25 + 647215 TGTAAGCATTAACTGTTAACCATTT - -a -s simMouse_chr6.simMouse.chr6 74389 19 + 636262 ACAACCACTGACCTAAATT -s Anc0.Anc0refChr4 19136 19 - 45765 ACACACACTCATATTAATT -s Anc1.Anc1refChr2 50417 19 + 144309 ACACACACTCATATTAATT -s Anc2.Anc2refChr7 19031 19 + 32194 CCACACATTCATATTAATC -s mr.mrrefChr0 70408 19 + 130230 ACAAACACTGACCTAAATT -s simCow_chr6.simCow.chr6 77447 19 + 602619 CTCCACATCCATATTAATC -s simDog_chr6.simDog.chr6 74059 19 + 593897 CCACACATTCATATTAATC -s simHuman_chr6.simHuman.chr6 70923 15 + 601863 ACACACACTCAT----ATT -s simRat_chr6.simRat.chr6 66068 19 + 647215 ACAAACGGTAACCTAAATT - -a -s simMouse_chr6.simMouse.chr6 74408 88 + 636262 AACTAATGCATGACTGCAGGGTACCCTGGATTCAGTGAATCATGCCTGTCCATGGTTAGTGTTAATATTGCCTTTCTGAAGCAATATT -s Anc0.Anc0refChr4 19155 83 - 45765 CATTA---AATGATTGCAGGGTAACATGACTTCTGTGAATTCTGTCTGCTCACAGGTAAAGCTAGTATTTCCTGGCAGAAGCAAT--T -s Anc1.Anc1refChr2 50436 83 + 144309 CATTA---AATGATTGCAGGGTAACATGACTTCTGTGAATTCTGTCTGCTCACAGGTAAAGCTAGTATTTCCTGGCAGAAGCAAT--T -s Anc2.Anc2refChr7 19050 83 + 32194 CATTA---AATGATTGCAGGGTAACATGACTTCTGTGAATTCTGTCTGCTCACAGGTAAAGCTATTATTTCCTGGCAGAAGCAGT--A -s mr.mrrefChr0 70427 86 + 130230 AAATAATGAATGACTGCAGGGTACCATGGATTCAGTGAATCATGCCTGCCCATGGGTAGTGTTAGTATTTCCTTGCTGAAGCAAT--T -s simCow_chr6.simCow.chr6 77466 81 + 602619 CATTA---AATGATTGCAGAGTAACATTACTTCTGTGAATTCTGTCTGCTTACAGGTAAAGCTAATATTTCGTAGCCAAAACAG---- -s simDog_chr6.simDog.chr6 74078 83 + 593897 CATTA---ATTGATTGCAGGGGAACATGACTTCTGTAAATTGTGTCTGCTCGCAGGTACAGCTATTATTTCCTGGTAGAAGCTGT--A -s simHuman_chr6.simHuman.chr6 70939 83 + 601863 CATCA---AATGATTAGAGGGTAACATGACTTCTGCGAATTCCGTCTGCTCACAGGTAAAGCTAGTATTTCCTGGCAGAAGCAAT--T -s simRat_chr6.simRat.chr6 66087 86 + 647215 AAATAATCAGTGACTGCAGGGTACTATAGATTCAGTGAATCTTGCCTGCCCATGGGTATTGTTAGTATTTCCCTGCTGAAGCAAT--T - -a -s simMouse_chr6.simMouse.chr6 74496 5 + 636262 TCATT -s Anc0.Anc0refChr4 19238 5 - 45765 TGAGT -s Anc1.Anc1refChr2 50519 5 + 144309 TGAGT -s Anc2.Anc2refChr7 19133 5 + 32194 TAAGT -s mr.mrrefChr0 70513 5 + 130230 TGATT -s simCow_chr6.simCow.chr6 77547 4 + 602619 -AGGT -s simDog_chr6.simDog.chr6 74161 5 + 593897 TAAGT -s simHuman_chr6.simHuman.chr6 71022 5 + 601863 TGAGT -s simRat_chr6.simRat.chr6 66179 5 + 647215 TGTAT - -a -s simMouse_chr6.simMouse.chr6 74501 13 + 636262 ATATCCACACACC -s Anc0.Anc0refChr4 19243 13 - 45765 ATATCCCGACACC -s Anc1.Anc1refChr2 50524 13 + 144309 ATATCCCGACACC -s Anc2.Anc2refChr7 19138 13 + 32194 GTATGCCTACACC -s mr.mrrefChr0 70518 13 + 130230 ATATCCTGACACC -s simCow_chr6.simCow.chr6 77551 13 + 602619 GTATGCCTACACC -s simDog_chr6.simDog.chr6 74166 12 + 593897 GCAT-CCTACACC -s simHuman_chr6.simHuman.chr6 71027 13 + 601863 ATAACCCGACACC -s simRat_chr6.simRat.chr6 66187 13 + 647215 ATAGCGTGAAACC - -a -s simMouse_chr6.simMouse.chr6 74514 29 + 636262 AAGGTTAGGGTGCCCAGGTGGCTAACTTG -s Anc0.Anc0refChr4 19260 25 - 45765 A----GGAGGTGCCCAGGTCGCTAGCTTG -s Anc1.Anc1refChr2 50541 25 + 144309 A----GGAGGTGCCCAGGTCGCTAGCTTG -s Anc2.Anc2refChr7 19155 25 + 32194 T----GGAGGTGCCCAAGTCGCCAGCTTC -s mr.mrrefChr0 70535 29 + 130230 AAGGTGGAGGTGCCCAGGTGGCTAACTTG -s simCow_chr6.simCow.chr6 77568 11 + 602619 T----GGGGGTGCAC-------------- -s simDog_chr6.simDog.chr6 74182 25 + 593897 T----GGATGTGCCCAAGTCGCCAGCTTC -s simHuman_chr6.simHuman.chr6 71044 25 + 601863 A----GGAGGTGCCCAGATTGCTTGCTTG -s simRat_chr6.simRat.chr6 66204 29 + 647215 AAGGTGGAAGTGCCCAAGTGGCTAACTTG - -a -s simMouse_chr6.simMouse.chr6 74543 63 + 636262 GCCTGTTCCTCTGATTGGGAATGTGCTACTGATACATGTTTGAGGTCTACATCCAAGCATGTC -s Anc0.Anc0refChr4 19285 63 - 45765 GGCTATTTATCAGATTAGGAATGTGTCACTGGTTGATGTTTGGGATCCACATCCAAGCAGGTC -s Anc1.Anc1refChr2 50566 63 + 144309 GGCTATTTATCAGATTAGGAATGTGTCACTGGTTGATGTTTGGGATCCACATCCAAGCAGGTC -s Anc2.Anc2refChr7 19180 63 + 32194 GGCTATTTATCAGGTTAGGAATGTGTCATTAGTTGATGTTTAGGATGCACATCCAAGCAGTTC -s mr.mrrefChr0 70564 63 + 130230 GCCTATTCCTCTGATTGGGAATGTGCCACTGATTCATGTTTGAGGTCTACATCCAAGCATGTC -s simDog_chr6.simDog.chr6 74207 63 + 593897 GGCTATTTATCAGGTTAGGAATGTGTCATTAGTTGATGTTTAGGATGCACATCCAAGCAGTTC -s simHuman_chr6.simHuman.chr6 71070 63 + 601863 GGCTATTTTTTGGATTAGGAATGTGTGACTGGTTGTTGTTTGGGATCAACATCAAAGCAAGTC -s simRat_chr6.simRat.chr6 66233 63 + 647215 GCCTATTCCTCTGATTGAGAATGTGCCACTGATTCATGTTTGAGGCCTACTTCCAAGCATTTC - -a -s simMouse_chr6.simMouse.chr6 74606 255 + 636262 TTAGTGTGCTGCACTGTTACTATCAATAGGTTTATCCATTCATTGTGATTAAGCATTATTTGTCATATGTACAATAATCTGTATTTCATGTTCTGGAATACCTCTCCTGTTTTTCTTAACCTGCACAGAGTTTAAACATGTACATGATCTGCACCTTATAATACATTGTCTGTCTAGGTAGACTGGCTTCACTTATAAGACACCAGCCTGTTCCCAAATTACCAAACTTTCATGGGTCAGTTGGCCTTTGCTTGA -s Anc0.Anc0refChr4 19348 21 - 45765 AGGG------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AGCAGGCCCTTGCATGA -s Anc1.Anc1refChr2 50629 21 + 144309 AGGG------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AGCAGGCCCTTGCATGA -s Anc2.Anc2refChr7 19243 21 + 32194 TGGG------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AGCAGGTCCTTTCATGA -s mr.mrrefChr0 70627 21 + 130230 ATAG------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AGCAGGCCCTTGCTTGA -s simDog_chr6.simDog.chr6 74271 21 + 593897 TGGG------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AGCAGGTCCTTTCATGA -s simHuman_chr6.simHuman.chr6 71133 21 + 601863 AGGG------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AGCACACCCTTGCACAA -s simRat_chr6.simRat.chr6 66296 21 + 647215 ATAG------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AGCAGGTCCTCGCTTGA - -a -s simMouse_chr6.simMouse.chr6 74861 12 + 636262 TGTGCTTACTTC -s Anc0.Anc0refChr4 19376 12 - 45765 TGGGTTGCCCCC -s Anc1.Anc1refChr2 50657 12 + 144309 TGGGTTGCCCCC -s Anc2.Anc2refChr7 19271 12 + 32194 TGGGCTGCCACC -s mr.mrrefChr0 70655 12 + 130230 TGTGTTGCCCCC -s simDog_chr6.simDog.chr6 74299 12 + 593897 TGGGCTGCCACC -s simHuman_chr6.simHuman.chr6 71161 12 + 601863 TGGGTTGCCCCC -s simRat_chr6.simRat.chr6 66324 12 + 647215 TGAATTGCCCCC - -a -s simMouse_chr6.simMouse.chr6 74873 2 + 636262 TG -s Anc0.Anc0refChr4 19388 2 - 45765 TA -s Anc1.Anc1refChr2 50669 2 + 144309 TA -s Anc2.Anc2refChr7 19283 2 + 32194 TA -s mr.mrrefChr0 70667 2 + 130230 TG -s simDog_chr6.simDog.chr6 74311 2 + 593897 TA -s simHuman_chr6.simHuman.chr6 71173 2 + 601863 TA -s simRat_chr6.simRat.chr6 66338 2 + 647215 TG - -a -s simMouse_chr6.simMouse.chr6 74875 20 + 636262 ATAGGCCCCTGCAAGTTGTT -s Anc0.Anc0refChr4 19396 17 - 45765 ATGATTTCATGCAACAT--- -s Anc1.Anc1refChr2 50677 17 + 144309 ATGATTTCATGCAACAT--- -s Anc2.Anc2refChr7 19291 17 + 32194 ATGATTCGATGGCACAT--- -s mr.mrrefChr0 70675 20 + 130230 ATGAGCTCATGCAAGTTGTT -s simCow_chr6.simCow.chr6 77579 3 + 602619 --------------CGT--- -s simDog_chr6.simDog.chr6 74321 17 + 593897 ATGATTCGATGGCACAT--- -s simHuman_chr6.simHuman.chr6 71181 17 + 601863 ATGATTTCATGCAACAT--- -s simRat_chr6.simRat.chr6 66360 20 + 647215 ATGAGCTCAGGCAAGTTGTT - -a -s simMouse_chr6.simMouse.chr6 74895 63 + 636262 CAATGCAAAGTAGGATTCTTACTTCTCCTATTGCCAGCAGCCACCCAGGCGTGTGGCCTAGTT -s Anc0.Anc0refChr4 19413 45 - 45765 -------AGGTGAAATCCTTATTTCTC-----------ACCTTGCCAGGTGTCTGGCCTAGTT -s Anc1.Anc1refChr2 50694 45 + 144309 -------AGGTGAAATCCTTATTTCTC-----------ACCTTGCCAGGTGTCTGGCCTAGTT -s Anc2.Anc2refChr7 19308 45 + 32194 -------AGGTGAAATCCTAATTTCTC-----------ACCTTGCCAGGTGTCTGCCCTGGTT -s mr.mrrefChr0 70695 63 + 130230 CAATGCAAAGTAGGATTCTTATTTCTCCTATTGCCAGCAGCCTCCCAGGTGTCTGGCCTAGTT -s simCow_chr6.simCow.chr6 77582 12 + 602619 -------AGGTGAAATCCT-------------------------------------------- -s simDog_chr6.simDog.chr6 74338 45 + 593897 -------AGGTGAAATCTTAATTTCTC-----------ACCTTGCCAGGTGTCTGCCCTGGTT -s simHuman_chr6.simHuman.chr6 71198 45 + 601863 -------AGGTGAAATCCTTATTTCCC-----------AACTTGCCAGGTGTCTGGCCTAGTT -s simRat_chr6.simRat.chr6 66400 63 + 647215 CAATGCAGTGTAGGATTCTTATTTTGCCTATTGCCATGAGTCTCCCAGGTGTCTGGCCCCAGT - -a -s simMouse_chr6.simMouse.chr6 74958 19 + 636262 AGGGATACTTTTGGGGATG -s Anc0.Anc0refChr4 19458 19 - 45765 AAGAGAATTCATGGGGATG -s Anc1.Anc1refChr2 50739 19 + 144309 AAGAGAATTCATGGGGATG -s Anc2.Anc2refChr7 19353 19 + 32194 AAGAGAATCCATGGGGATA -s mr.mrrefChr0 70758 19 + 130230 AGGGATATTTATGGGGATG -s simDog_chr6.simDog.chr6 74384 19 + 593897 AAGAGAATCCATGGGGATA -s simHuman_chr6.simHuman.chr6 71243 19 + 601863 AAGATGATTCATGAGGATG -s simRat_chr6.simRat.chr6 66463 19 + 647215 AGGGATATTTATGGGGATG - -a -s simMouse_chr6.simMouse.chr6 74977 2 + 636262 GG -s Anc0.Anc0refChr4 19477 2 - 45765 GG -s Anc1.Anc1refChr2 50758 2 + 144309 GG -s Anc2.Anc2refChr7 19372 2 + 32194 GG -s mr.mrrefChr0 70777 2 + 130230 GG -s simDog_chr6.simDog.chr6 74410 2 + 593897 GG -s simHuman_chr6.simHuman.chr6 71262 2 + 601863 GG -s simRat_chr6.simRat.chr6 66482 2 + 647215 GG - -a -s simMouse_chr6.simMouse.chr6 74979 21 + 636262 TTCACCTGAAAATTTGTAGCC -s Anc0.Anc0refChr4 19480 21 - 45765 CTTAACTGAAAATTAGTAGTT -s Anc1.Anc1refChr2 50761 21 + 144309 CTTAACTGAAAATTAGTAGTT -s Anc2.Anc2refChr7 19375 21 + 32194 CATAACTGGTAATTAGTAGTT -s mr.mrrefChr0 70779 21 + 130230 TTCACCTGAAAATTTGTAGCC -s simCow_chr6.simCow.chr6 77594 8 + 602619 -------------TAGTATCC -s simDog_chr6.simDog.chr6 74413 21 + 593897 CATAACTGGTAATTAGTAGTT -s simHuman_chr6.simHuman.chr6 71265 21 + 601863 CTTATCTGAAAGACAGTAGTT -s simRat_chr6.simRat.chr6 66484 21 + 647215 GTCACCTGAGAATTTGTAGCC - -a -s simMouse_chr6.simMouse.chr6 75000 14 + 636262 CAAGCTTTGCATAC -s Anc0.Anc0refChr4 19502 14 - 45765 CAATGACAGTTAAC -s Anc1.Anc1refChr2 50783 14 + 144309 CAATGACAGTTAAC -s Anc2.Anc2refChr7 19397 14 + 32194 CAATGACAGTTAAC -s mr.mrrefChr0 70800 14 + 130230 CAAGCACTGCATAC -s simCow_chr6.simCow.chr6 77603 14 + 602619 CCTTGCCAAGTGTC -s simDog_chr6.simDog.chr6 74435 14 + 593897 CAATGACAGTTAAC -s simHuman_chr6.simHuman.chr6 71287 14 + 601863 TGATGACAGTTAAC -s simRat_chr6.simRat.chr6 66505 14 + 647215 CAAGCACTGCATAC - -a -s simMouse_chr6.simMouse.chr6 75014 5 + 636262 ACCCC -s Anc0.Anc0refChr4 19516 5 - 45765 ATCTT -s Anc1.Anc1refChr2 50797 5 + 144309 ATCTT -s Anc2.Anc2refChr7 19411 5 + 32194 ATCTT -s mr.mrrefChr0 70814 5 + 130230 ACCTC -s simCow_chr6.simCow.chr6 77619 5 + 602619 ATTTT -s simDog_chr6.simDog.chr6 74449 5 + 593897 AACTT -s simHuman_chr6.simHuman.chr6 71301 5 + 601863 ATCTT -s simRat_chr6.simRat.chr6 66519 5 + 647215 ACCTC - -a -s simMouse_chr6.simMouse.chr6 75019 31 + 636262 CTTCTAGACCCATAAACTCGCCATTACCCCT -s Anc0.Anc0refChr4 19535 31 - 45765 CTTCTAGACCCACAACCCCACCCACAACCCC -s Anc1.Anc1refChr2 50816 31 + 144309 CTTCTAGACCCACAACCCCACCCACAACCCC -s Anc2.Anc2refChr7 19430 31 + 32194 CTCCTAGACCCACAACCCCACCCACAACCCC -s mr.mrrefChr0 70819 31 + 130230 CTTCTAGACCCATAAACTCACCATTAACCCT -s simCow_chr6.simCow.chr6 77638 31 + 602619 CTCCTAGTCCAACAACCCCATCCACAACCCT -s simDog_chr6.simDog.chr6 74468 25 + 593897 C------ACCCACAACCCCACCCACAGCCCC -s simHuman_chr6.simHuman.chr6 71320 31 + 601863 CCTCTCAGCCCACAACCCCACCTACAACCCC -s simRat_chr6.simRat.chr6 66524 31 + 647215 CTTCTAGAGCCATGAACTCACCATTAACCCT - -a -s simMouse_chr6.simMouse.chr6 75050 5 + 636262 ACCCC -s Anc0.Anc0refChr4 19570 5 - 45765 ACCCC -s Anc1.Anc1refChr2 50851 5 + 144309 ACCCC -s Anc2.Anc2refChr7 19465 5 + 32194 ACCCC -s mr.mrrefChr0 70850 5 + 130230 ACCCC -s simCow_chr6.simCow.chr6 77673 5 + 602619 ACCCC -s simDog_chr6.simDog.chr6 74497 5 + 593897 ACCCC -s simHuman_chr6.simHuman.chr6 71355 5 + 601863 ACCCC -s simRat_chr6.simRat.chr6 66555 5 + 647215 ACCCC - -a -s simMouse_chr6.simMouse.chr6 75055 2 + 636262 CC -s Anc0.Anc0refChr4 19575 2 - 45765 CC -s Anc1.Anc1refChr2 50856 2 + 144309 CC -s Anc2.Anc2refChr7 19470 2 + 32194 CT -s mr.mrrefChr0 70855 2 + 130230 CC -s simCow_chr6.simCow.chr6 77678 2 + 602619 CA -s simDog_chr6.simDog.chr6 74502 2 + 593897 CT -s simHuman_chr6.simHuman.chr6 71363 2 + 601863 CC -s simRat_chr6.simRat.chr6 66560 2 + 647215 CC - -a -s simMouse_chr6.simMouse.chr6 75057 46 + 636262 AAGTTGGTTTGGTTGCTCAACCAAACCCAGCTGAACTACAAAAGGC -s Anc0.Anc0refChr4 19577 36 - 45765 CATTTGATTAGATTG----------TTCAGCTGAACTACAACAGTT -s Anc1.Anc1refChr2 50858 36 + 144309 CATTTGATTAGATTG----------TTCAGCTGAACTACAACAGTT -s Anc2.Anc2refChr7 19476 36 + 32194 CATTTGATTAGATTG----------TTCAGCTGAATTACAACAGTT -s mr.mrrefChr0 70857 46 + 130230 AAATTGGTTCAGTTGCTCAACCGAACTCAGCTGAACTACAAAAGGT -s simCow_chr6.simCow.chr6 77684 35 + 602619 CATTTGATTAGGTTG----------TTCAGC-GAGTTACAGCAGTT -s simDog_chr6.simDog.chr6 74508 36 + 593897 CATTTGATTAGATTG----------TTCAGCTGAATTACAACTATT -s simHuman_chr6.simHuman.chr6 71365 36 + 601863 CATTGGATCAGACTG----------TTCAGCCAAACTACAAGAGTT -s simRat_chr6.simRat.chr6 66562 46 + 647215 AAATTGGTTCAGTTGCTTAACCGAACTCAGCTGAACTACAAATGGT - -a -s simMouse_chr6.simMouse.chr6 75103 33 + 636262 TAAAGCTGCTTGAATGATGATGACCTGTGGGTG -s Anc0.Anc0refChr4 19620 33 - 45765 TGAAGGTGATTAATCAACAGCAACCTGTGGATG -s Anc1.Anc1refChr2 50901 33 + 144309 TGAAGGTGATTAATCAACAGCAACCTGTGGATG -s Anc2.Anc2refChr7 19519 33 + 32194 TGAAGGTGATTAATCAACAGCAACCTATGGATG -s mr.mrrefChr0 70903 33 + 130230 TAAAGCTGATTGAATGATGATAACCTGTGGGTG -s simCow_chr6.simCow.chr6 77730 33 + 602619 TGAAGGTGTTTAATCAACAACAACCTATGGTTG -s simDog_chr6.simDog.chr6 74550 33 + 593897 TGAAGGTGACTAAGGAACAGCAACCTATGGATG -s simHuman_chr6.simHuman.chr6 71408 33 + 601863 TGAGGGTGATTAATCAACAGCAACCTGTGGACG -s simRat_chr6.simRat.chr6 66608 33 + 647215 TAAAGTTGATTGAATGATGATAACCTGTGAGTG - -a -s simMouse_chr6.simMouse.chr6 75136 4 + 636262 AGTC -s Anc0.Anc0refChr4 19653 4 - 45765 CTTT -s Anc1.Anc1refChr2 50934 4 + 144309 CTTT -s Anc2.Anc2refChr7 19552 4 + 32194 CTTT -s mr.mrrefChr0 70936 4 + 130230 AGTC -s simCow_chr6.simCow.chr6 77763 4 + 602619 CTTT -s simDog_chr6.simDog.chr6 74585 4 + 593897 TTTT -s simHuman_chr6.simHuman.chr6 71441 4 + 601863 CTTT -s simRat_chr6.simRat.chr6 66641 4 + 647215 AGTC - -a -s simMouse_chr6.simMouse.chr6 75140 7 + 636262 CTTTCAT -s Anc0.Anc0refChr4 19662 7 - 45765 TCTTTTT -s Anc1.Anc1refChr2 50943 7 + 144309 TCTTTTT -s Anc2.Anc2refChr7 19561 7 + 32194 TCTTTTT -s mr.mrrefChr0 70940 7 + 130230 CTTTCTT -s simCow_chr6.simCow.chr6 77772 7 + 602619 TTTCTTT -s simDog_chr6.simDog.chr6 74594 7 + 593897 TCTTTTT -s simHuman_chr6.simHuman.chr6 71450 7 + 601863 TGTTTTT -s simRat_chr6.simRat.chr6 66645 7 + 647215 CTTTCTT - -a -s simMouse_chr6.simMouse.chr6 75147 41 + 636262 GTTATTCCTCTCTATTTTGATTACAGCTTAGAAATCAAGGG -s Anc0.Anc0refChr4 19669 32 - 45765 GCCATTCCTGTCAA-TTCAATCACAGG--------TCAGGT -s Anc1.Anc1refChr2 50950 32 + 144309 GCCATTCCTGTCAA-TTCAATCACAGG--------TCAGGT -s Anc2.Anc2refChr7 19568 32 + 32194 GCCATTCCTGTCAA-TTCAGTCACAGG--------TCAAGT -s mr.mrrefChr0 70947 33 + 130230 GTTATTCCTCTCTATTTTGATTACAGC--------CAAGGT -s simCow_chr6.simCow.chr6 77779 32 + 602619 GCCATTTCTGTCAA-TTTGGACACATA--------TCAAAT -s simDog_chr6.simDog.chr6 74602 32 + 593897 GACATTCCTGTCAA-TTCAGTCACAGG--------TCAAGT -s simHuman_chr6.simHuman.chr6 71457 32 + 601863 GCCATTCCTGTCAA-ATCAATCACAGG--------TCAGTT -s simRat_chr6.simRat.chr6 66652 33 + 647215 GTTATTCCTCCGTATTTTGATTACAGC--------CAACGT - -a -s simMouse_chr6.simMouse.chr6 75188 7 + 636262 TCTTCTG -s Anc0.Anc0refChr4 19701 7 - 45765 CCCACTG -s Anc1.Anc1refChr2 50982 7 + 144309 CCCACTG -s Anc2.Anc2refChr7 19600 7 + 32194 CCCACTG -s mr.mrrefChr0 70980 7 + 130230 TCTTCTG -s simCow_chr6.simCow.chr6 77818 7 + 602619 CCCACTG -s simDog_chr6.simDog.chr6 74634 7 + 593897 CCCGCTG -s simHuman_chr6.simHuman.chr6 71489 7 + 601863 CCCACTG -s simRat_chr6.simRat.chr6 66685 7 + 647215 TTTTTTG - -a -s simMouse_chr6.simMouse.chr6 75195 19 + 636262 ATAGCTTTTCAGTAGGAAG -s Anc0.Anc0refChr4 19708 16 - 45765 CCAG---TGCTGTAAGAAG -s Anc1.Anc1refChr2 50989 16 + 144309 CCAG---TGCTGTAAGAAG -s Anc2.Anc2refChr7 19607 16 + 32194 CCAG---TGGTGTAAGGAG -s mr.mrrefChr0 70987 19 + 130230 ACAGCTTTTCAGTAGGAAG -s simCow_chr6.simCow.chr6 77825 16 + 602619 CCAG---TGGTGTAAGGAG -s simDog_chr6.simDog.chr6 74641 16 + 593897 CCAG---TGGTGTAAGGAG -s simHuman_chr6.simHuman.chr6 71496 16 + 601863 CCAG---TGCTGTAAGAAG -s simRat_chr6.simRat.chr6 66693 19 + 647215 ACAGATTTACGATAGGAAG - -a -s simMouse_chr6.simMouse.chr6 75214 5 + 636262 CAAAC -s Anc0.Anc0refChr4 19811 5 - 45765 CAGGC -s Anc1.Anc1refChr2 51092 5 + 144309 CAGGC -s Anc2.Anc2refChr7 19710 5 + 32194 CAGAC -s mr.mrrefChr0 71006 5 + 130230 CAAGC -s simCow_chr6.simCow.chr6 77929 5 + 602619 CAGTC -s simDog_chr6.simDog.chr6 74744 5 + 593897 GAGAC -s simHuman_chr6.simHuman.chr6 71601 5 + 601863 CAGGC -s simRat_chr6.simRat.chr6 66712 5 + 647215 CAAGC - -a -s simMouse_chr6.simMouse.chr6 75219 20 + 636262 GCCAGAAAAAACAACTTGTC -s Anc0.Anc0refChr4 19818 20 - 45765 GCAAATAGAAACAAATCAAC -s Anc1.Anc1refChr2 51099 20 + 144309 GCAAATAGAAACAAATCAAC -s Anc2.Anc2refChr7 19717 20 + 32194 CCAAGTAGAATCAAATCAAC -s mr.mrrefChr0 71011 20 + 130230 GCCAAAAAAAACAACTTGTC -s simCow_chr6.simCow.chr6 77936 20 + 602619 TCAAGTAAAAGCAGATCAAC -s simDog_chr6.simDog.chr6 74751 19 + 593897 CCAAGCAGAATCAAAT-AAC -s simHuman_chr6.simHuman.chr6 71608 20 + 601863 GCAAATAGAAACAAGTCAAC -s simRat_chr6.simRat.chr6 66717 20 + 647215 ACCAAAAAAATCAACTTGTC - -a -s simMouse_chr6.simMouse.chr6 75239 1 + 636262 A -s Anc0.Anc0refChr4 19838 1 - 45765 A -s Anc1.Anc1refChr2 51119 1 + 144309 A -s Anc2.Anc2refChr7 19737 1 + 32194 A -s mr.mrrefChr0 71031 1 + 130230 A -s simCow_chr6.simCow.chr6 77956 1 + 602619 A -s simDog_chr6.simDog.chr6 74770 1 + 593897 A -s simHuman_chr6.simHuman.chr6 71628 1 + 601863 A -s simRat_chr6.simRat.chr6 66977 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 75240 5 + 636262 AGATG -s Anc0.Anc0refChr4 19845 5 - 45765 AGACA -s Anc1.Anc1refChr2 51126 5 + 144309 AGACA -s Anc2.Anc2refChr7 19744 5 + 32194 AGGCA -s mr.mrrefChr0 71032 5 + 130230 AGATG -s simDog_chr6.simDog.chr6 74777 5 + 593897 AGGCA -s simHuman_chr6.simHuman.chr6 71635 5 + 601863 AGACA -s simRat_chr6.simRat.chr6 66978 5 + 647215 GGATG - -a -s simMouse_chr6.simMouse.chr6 75245 9 + 636262 GAGTTTTAC -s Anc0.Anc0refChr4 19850 9 - 45765 GAATTTTAT -s Anc1.Anc1refChr2 51131 9 + 144309 GAATTTTAT -s Anc2.Anc2refChr7 19758 9 + 32194 GAATCCTTT -s mr.mrrefChr0 71037 9 + 130230 GAGTTTTAC -s simCow_chr6.simCow.chr6 77958 9 + 602619 GAATTCTTT -s simDog_chr6.simDog.chr6 74799 9 + 593897 GAATCCTTT -s simHuman_chr6.simHuman.chr6 71640 9 + 601863 GGTTTTCAA -s simRat_chr6.simRat.chr6 66983 9 + 647215 GAGCTTTCC - -a -s simMouse_chr6.simMouse.chr6 75254 4 + 636262 GTGG -s Anc0.Anc0refChr4 19859 4 - 45765 AAGT -s Anc1.Anc1refChr2 51140 4 + 144309 AAGT -s Anc2.Anc2refChr7 19767 4 + 32194 AAGT -s mr.mrrefChr0 71046 4 + 130230 GTGG -s simCow_chr6.simCow.chr6 77967 4 + 602619 AAGG -s simDog_chr6.simDog.chr6 74808 4 + 593897 AAGT -s simRat_chr6.simRat.chr6 66994 4 + 647215 GTGG - -a -s simMouse_chr6.simMouse.chr6 75258 14 + 636262 CAGGGGATATGAAA -s Anc0.Anc0refChr4 19863 10 - 45765 CAGGGGAAGT---- -s Anc1.Anc1refChr2 51144 10 + 144309 CAGGGGAAGT---- -s Anc2.Anc2refChr7 19771 10 + 32194 CAGGGGAAGT---- -s mr.mrrefChr0 71050 10 + 130230 CAGGGGATAT---- -s simCow_chr6.simCow.chr6 77971 10 + 602619 CAGGGGATGT---- -s simDog_chr6.simDog.chr6 74814 10 + 593897 CAGGGGAAGT---- -s simHuman_chr6.simHuman.chr6 71649 8 + 601863 --GTGGCAGG---- -s simRat_chr6.simRat.chr6 66998 10 + 647215 CACAGGAGAT---- - -a -s simMouse_chr6.simMouse.chr6 75272 25 + 636262 AAAGGGGGGGGTATTTAGGTTTGAA -s Anc0.Anc0refChr4 19874 25 - 45765 AAAGAGAGAGGCATGTAAGATTGGA -s Anc1.Anc1refChr2 51155 25 + 144309 AAAGAGAGAGGCATGTAAGATTGGA -s Anc2.Anc2refChr7 19782 25 + 32194 AAAGAGAAAGGCATGTAAGATTGGA -s mr.mrrefChr0 71060 25 + 130230 AAAGGGAGGGGTATTTAAGTTTGAA -s simCow_chr6.simCow.chr6 77982 24 + 602619 AAGGAGA-AGGCATGTAAGATTAAA -s simDog_chr6.simDog.chr6 74825 25 + 593897 AAAGAGAAGGGTATGTAAGATTGGA -s simHuman_chr6.simHuman.chr6 71658 25 + 601863 AAAGAGAGAGGCACATAAGATTGGA -s simRat_chr6.simRat.chr6 67008 25 + 647215 AAAGGGAAGGGTATTTAAGTTTGAA - -a -s simMouse_chr6.simMouse.chr6 75297 35 + 636262 CCTGTTGAGGAATTTTTAAGTGGATGAACTTAGTG -s Anc0.Anc0refChr4 19899 32 - 45765 CC---TTAGGAACCTTCAACGAGATGAACTTTACA -s Anc1.Anc1refChr2 51180 32 + 144309 CC---TTAGGAACCTTCAACGAGATGAACTTTACA -s Anc2.Anc2refChr7 19807 32 + 32194 CC---TGAGGAACCTTCAACGAGATGAACTTTACA -s mr.mrrefChr0 71085 35 + 130230 CCTGTTTAGGAACCTTTAAGTGGATGAACTTAGTG -s simCow_chr6.simCow.chr6 78006 20 + 602619 CC---TAAGGA--CTT------GAGGAAC----CA -s simDog_chr6.simDog.chr6 74851 32 + 593897 CC---TGAGGAACCTTCAACGAGATGAATTTTATA -s simHuman_chr6.simHuman.chr6 71683 32 + 601863 CC---TTAGGTACCTGCAAAGAGAAAAACTTTACA -s simRat_chr6.simRat.chr6 67033 35 + 647215 CCTGTTTAGGAACCTTTAAGTGGTTGAACTTAGTG - -a -s simMouse_chr6.simMouse.chr6 75332 50 + 636262 CTGGGAATTTTCACATCATTTGTTCCCCCATCTGTTGCTATAATTGGTAT -s Anc0.Anc0refChr4 19932 35 - 45765 CAGAGGGTTTTCACATAGTTTGATTCCCCG---------------GATGT -s Anc1.Anc1refChr2 51213 50 + 144309 CAGAGGGTTTTCACATAGTTTGATTCCCCGTCCATTGCTGTAATTGATGT -s Anc2.Anc2refChr7 19840 35 + 32194 CAGAGGGATTTCAGATAGTTTGATTCCCCG---------------GATGT -s mr.mrrefChr0 71120 50 + 130230 CTGGGGATTTTCACATAATTTGTTCCCCCATCTGTTGCTATAATTGGTAT -s simCow_chr6.simCow.chr6 78027 35 + 602619 CAGAGCGACTTCAAATGGTTTGACTCCACA---------------GATGT -s simDog_chr6.simDog.chr6 74884 35 + 593897 CAGAAGGATTTTAGGTAGTTTGATTCCCCG---------------GATGT -s simHuman_chr6.simHuman.chr6 71716 50 + 601863 CCAAGGGTTTTCACATAGTTTGATTCCCTGTCCATTGCTGTAATTAATGT -s simRat_chr6.simRat.chr6 67068 50 + 647215 CTGGGGATTTTCACATAATTTGTGCCCCCATCTGTTGCTACAATTGGTAT - -a -s simMouse_chr6.simMouse.chr6 75382 28 + 636262 ATGATCAACCACTAGGGAGAGCCTGCTG -s Anc0.Anc0refChr4 19990 27 - 45765 CTCTTCAA-AACTAGAAAGCACCTGCCA -s Anc1.Anc1refChr2 51286 27 + 144309 CTCTTCAA-AACTAGAAAGCACCTGCCA -s Anc2.Anc2refChr7 19898 27 + 32194 CTCTTCAA-ACCTAGAAAGCACCTGCCA -s mr.mrrefChr0 71170 28 + 130230 ATCATCAACCACTAGGGAGAGCCTGCTG -s simCow_chr6.simCow.chr6 78082 25 + 602619 --CTTCAA-GTCTAGAAAGCACCTGCCA -s simDog_chr6.simDog.chr6 74942 27 + 593897 CTCTCCAG-ACCTAGATGGCACCTGCCG -s simHuman_chr6.simHuman.chr6 71789 27 + 601863 TTCTTCAA-AACTAGAAAGCACCTGCCA -s simRat_chr6.simRat.chr6 67118 28 + 647215 ATCATCAACCACTAGGGAGAGCCTACTC - -a -s simMouse_chr6.simMouse.chr6 75410 26 + 636262 AAACTTGCAAGTGCATCTCCACCATA -s Anc0.Anc0refChr4 20018 26 - 45765 AAACTTATAAGTGCATCTCCACCACA -s Anc1.Anc1refChr2 51314 26 + 144309 AAACTTATAAGTGCATCTCCACCACA -s Anc2.Anc2refChr7 19926 26 + 32194 AAACTTATAAGTGCATCTCCACTGCA -s mr.mrrefChr0 71198 26 + 130230 AAACTTGCAAGTGCATCTCCACCATA -s simCow_chr6.simCow.chr6 78108 26 + 602619 AAACTTATAATTGTATTTACCCTGCA -s simDog_chr6.simDog.chr6 74970 26 + 593897 AAACTTATAAGTGCATCTCCACTGCA -s simHuman_chr6.simHuman.chr6 71817 26 + 601863 AAACTTATAAGGGCATCTCCACCACA -s simRat_chr6.simRat.chr6 67146 26 + 647215 TAAGTCGCAGGTGCATCTCCACTATA - -a -s simMouse_chr6.simMouse.chr6 75436 35 + 636262 CTCAATCATTCTTGCCACATCACATCATGTGATCA -s Anc0.Anc0refChr4 20049 35 - 45765 CTCAATGATTTGTTCTATATAGAGACATGTGCCTA -s Anc1.Anc1refChr2 51345 35 + 144309 CTCAATGATTTGTTCTATATAGAGACATGTGCCTA -s Anc2.Anc2refChr7 19957 35 + 32194 CTCAATGATTTGCTGTATATAGAGACATGTGCCTA -s mr.mrrefChr0 71224 35 + 130230 CTCAATCATTCTTGCCATATAGCAACATGTGATCA -s simCow_chr6.simCow.chr6 78139 35 + 602619 ATCAATGATTTGCTGTATTTAGAAGCATGTGCTTA -s simDog_chr6.simDog.chr6 75001 35 + 593897 CTCAATAATTTGCTGGATATAGAGACATGTGCCCA -s simHuman_chr6.simHuman.chr6 71863 35 + 601863 CTCAATGATTTGTTCTATAAAGATACAAGTGCGTA -s simRat_chr6.simRat.chr6 67172 35 + 647215 GTCAGTCATTCTTGGCATATAGCAACATGTGATCA - -a -s simMouse_chr6.simMouse.chr6 75471 14 + 636262 TGTTGCTGAATAAT -s Anc0.Anc0refChr4 20084 14 - 45765 TTTTGATGTAAGAT -s Anc1.Anc1refChr2 51380 14 + 144309 TTTTGATGTAAGAT -s Anc2.Anc2refChr7 19992 14 + 32194 TTTTGATGTAAGAT -s mr.mrrefChr0 71259 14 + 130230 TTTTGCTGAATGAT -s simCow_chr6.simCow.chr6 78174 14 + 602619 TTTTGATGTAAGAT -s simDog_chr6.simDog.chr6 75037 14 + 593897 TTTTGATGTAAGAT -s simHuman_chr6.simHuman.chr6 71898 14 + 601863 TTTTGATGTAAGAT -s simRat_chr6.simRat.chr6 67207 14 + 647215 TTTTACTGAACGAT - -a -s simMouse_chr6.simMouse.chr6 75485 16 + 636262 TTGCTGCCAGTTTGGT -s Anc0.Anc0refChr4 20098 16 - 45765 ATACTGCCAGCTTGGT -s Anc1.Anc1refChr2 51394 16 + 144309 ATACTGCCAGCTTGGT -s Anc2.Anc2refChr7 20006 16 + 32194 ATACTGCCAGCATGGC -s mr.mrrefChr0 71273 16 + 130230 TTGCTGCCAGCTTGGT -s simCow_chr6.simCow.chr6 78188 12 + 602619 ATACTGCTAACA---- -s simDog_chr6.simDog.chr6 75051 16 + 593897 ATACTGCCAGGATGGC -s simHuman_chr6.simHuman.chr6 71915 16 + 601863 CTACTGCCAGCTTGGT -s simRat_chr6.simRat.chr6 67221 16 + 647215 TTGCTGCCAGCTTTGT - -a -s simMouse_chr6.simMouse.chr6 75501 13 + 636262 TATAAGCCTCTAA -s Anc0.Anc0refChr4 20114 13 - 45765 TATAAACCTTTGA -s Anc1.Anc1refChr2 51410 13 + 144309 TATAAACCTTTGA -s Anc2.Anc2refChr7 20022 13 + 32194 TATAACCCTTTGG -s mr.mrrefChr0 71289 13 + 130230 TATAAACCTCTAA -s simCow_chr6.simCow.chr6 78200 10 + 602619 --TAATTTTTTG- -s simDog_chr6.simDog.chr6 75067 13 + 593897 TACAGCCCTTTGG -s simHuman_chr6.simHuman.chr6 71933 13 + 601863 TATAAACCTTTGA -s simRat_chr6.simRat.chr6 67237 12 + 647215 TATAAACCT-TAA - -a -s simMouse_chr6.simMouse.chr6 75514 8 + 636262 GAAAAATC -s Anc0.Anc0refChr4 20129 8 - 45765 GAATAGTC -s Anc1.Anc1refChr2 51425 8 + 144309 GAATAGTC -s Anc2.Anc2refChr7 20037 8 + 32194 AAATAGTC -s mr.mrrefChr0 71302 8 + 130230 GAATAATC -s simCow_chr6.simCow.chr6 78212 8 + 602619 AAATAGGT -s simDog_chr6.simDog.chr6 75082 8 + 593897 AAACAATC -s simHuman_chr6.simHuman.chr6 71948 8 + 601863 GACTAGTC -s simRat_chr6.simRat.chr6 67249 8 + 647215 AAATAATC - -a -s simMouse_chr6.simMouse.chr6 75522 4 + 636262 ATCA -s Anc0.Anc0refChr4 20137 4 - 45765 ATGA -s Anc1.Anc1refChr2 51433 4 + 144309 ATGA -s Anc2.Anc2refChr7 20045 4 + 32194 ATGA -s mr.mrrefChr0 71310 4 + 130230 ATCA -s simCow_chr6.simCow.chr6 78220 4 + 602619 GTGA -s simDog_chr6.simDog.chr6 75090 4 + 593897 ATGA -s simHuman_chr6.simHuman.chr6 71964 4 + 601863 ATGA -s simRat_chr6.simRat.chr6 67257 4 + 647215 ATCA - -a -s simMouse_chr6.simMouse.chr6 75526 68 + 636262 TTGTCTCGCATATCGTTTTGAAGCCTAGTTTTGTATAGATTATTTGTGTGTAGCTGGTTGCAAAAGTG -s Anc0.Anc0refChr4 20141 52 - 45765 GTGTGTAATGTATC---------CTTACAATTG-------TATTTTTGTGTAGATAGCCTGAGATATG -s Anc1.Anc1refChr2 51437 52 + 144309 GTGTGTAATGTATC---------CTTACAATTG-------TATTTTTGTGTAGATAGCCTGAGATATG -s Anc2.Anc2refChr7 20049 52 + 32194 GTGTGTAATGTATC---------CTTACAATTG-------TATTTTTGTGTAGATAGCCTGAGATATG -s mr.mrrefChr0 71314 67 + 130230 TTGTCTCGCATATC-TATTGAAGCCTAGTTTTGTATAGATTATTTGTGTGTAGCTGGCTGGAAAAGTG -s simCow_chr6.simCow.chr6 78225 52 + 602619 GGGTCTGAAGCATC---------CTAACAATTT-------TATTTTTGTGTTGATAGCCAGAGATATG -s simDog_chr6.simDog.chr6 75094 52 + 593897 TTGTGTAATGTATC---------CTTACAATTG-------TATCTTTGTGTAGATGGCCTGAGATATG -s simHuman_chr6.simHuman.chr6 71968 40 + 601863 GTGTGT---------------------CAATTG-------CATTTTTGTGTAGATAGCCTGAGACATG -s simRat_chr6.simRat.chr6 67261 67 + 647215 TTGTCTCATGTATC-CATTGAAGCTTGGTTTCTTATAGATTATTTGTGTGTAGTTGGCTGGAAAAGTG - -a -s simMouse_chr6.simMouse.chr6 75594 8 + 636262 CTCATGAC -s Anc0.Anc0refChr4 20194 8 - 45765 TTTATGAA -s Anc1.Anc1refChr2 51490 8 + 144309 TTTATGAA -s Anc2.Anc2refChr7 20102 8 + 32194 TTTATGAA -s mr.mrrefChr0 71381 8 + 130230 CTCATGAC -s simCow_chr6.simCow.chr6 78278 8 + 602619 TTTATGAA -s simDog_chr6.simDog.chr6 75147 8 + 593897 CTTATGGA -s simHuman_chr6.simHuman.chr6 72009 8 + 601863 TTTATGAA -s simRat_chr6.simRat.chr6 67328 8 + 647215 CCCATGAC - -a -s simMouse_chr6.simMouse.chr6 75602 20 + 636262 GAAGGAGATATAGAGACTAT -s Anc0.Anc0refChr4 20204 20 - 45765 TATAAGTATTTAGAAACTTT -s Anc1.Anc1refChr2 51500 20 + 144309 TATAAGTATTTAGAAACTTT -s Anc2.Anc2refChr7 20112 20 + 32194 TATAAGTATTTAAAAATTTA -s mr.mrrefChr0 71389 20 + 130230 GAAAGAGATATAGAGACTAT -s simCow_chr6.simCow.chr6 78288 18 + 602619 TAGAGGTA--TAAAGACTTT -s simDog_chr6.simDog.chr6 75156 18 + 593897 --TAAGAATTCAAAAATTTA -s simHuman_chr6.simHuman.chr6 72019 20 + 601863 TATATGTATTTAGACTCAGT -s simRat_chr6.simRat.chr6 67336 20 + 647215 ACAAGAGATATAGAGACTTT - -a -s simMouse_chr6.simMouse.chr6 75622 38 + 636262 GTAGTGACTCCTTTGTCAGCTCCAAAACATTATGTGAT -s Anc0.Anc0refChr4 20224 38 - 45765 GTTGTGACCCTTTGATTAACTCAAAAACTTTCTTTGAT -s Anc1.Anc1refChr2 51520 38 + 144309 GTTGTGACCCTTTGATTAACTCAAAAACTTTCTTTGAT -s Anc2.Anc2refChr7 20132 38 + 32194 TTTGTGACCCTTTGATTGACTCAAAAACTTACTTTGAT -s mr.mrrefChr0 71409 38 + 130230 GTTGTGACTCCTTTGTCAGCTCCAAAACATTATTTGAT -s simCow_chr6.simCow.chr6 78306 38 + 602619 TTGGTGGCCCACTGATTGATTCAAAAACTTCATTTGAT -s simDog_chr6.simDog.chr6 75174 34 + 593897 TTTGTGACCCTTTG----ACTCAAAAACTTACTTTGAT -s simHuman_chr6.simHuman.chr6 72042 37 + 601863 GTTGTGACCCTTTGACTAACTCAAATAC-CTGTTTGAT -s simRat_chr6.simRat.chr6 67356 38 + 647215 GTTGTGACTCCTTTGTCAGCTCTAAAACATTATTTGAT - -a -s simMouse_chr6.simMouse.chr6 75660 29 + 636262 GATCTGCAATGACTTGCTTACCTCTGAGT -s Anc0.Anc0refChr4 20274 29 - 45765 GCTCTGGAGTGACTTGCTTGTGTCAGAGA -s Anc1.Anc1refChr2 51570 29 + 144309 GCTCTGGAGTGACTTGCTTGTGTCAGAGA -s Anc2.Anc2refChr7 20182 29 + 32194 GCTCTGGAGTGTCTTGCTTGTGTCAGAGA -s mr.mrrefChr0 71447 29 + 130230 GATCTGCAATGACTTGCTTACCTCTGAGT -s simCow_chr6.simCow.chr6 78356 29 + 602619 ACTGTGGAGTGTCTTGCTTATGCCTGAGA -s simDog_chr6.simDog.chr6 75220 29 + 593897 GCTCTGGAATGTCTTGCTTGTGTCAGGGA -s simHuman_chr6.simHuman.chr6 72091 29 + 601863 GCTCTGGAGTGACTTGCTTGTGGCCGAGA -s simRat_chr6.simRat.chr6 67427 29 + 647215 GATCTGCAATGACTAGCTTACTTTTGAAT - -a -s simMouse_chr6.simMouse.chr6 75689 1 + 636262 T -s Anc0.Anc0refChr4 20303 1 - 45765 T -s Anc1.Anc1refChr2 51599 1 + 144309 T -s Anc2.Anc2refChr7 20211 1 + 32194 G -s mr.mrrefChr0 71476 1 + 130230 T -s simCow_chr6.simCow.chr6 78385 1 + 602619 C -s simDog_chr6.simDog.chr6 75249 1 + 593897 G -s simHuman_chr6.simHuman.chr6 72120 1 + 601863 T -s simRat_chr6.simRat.chr6 67460 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 75690 16 + 636262 ATCAAGACATGGATCA -s Anc0.Anc0refChr4 20306 16 - 45765 AACAAGACATGGATCA -s Anc1.Anc1refChr2 51602 16 + 144309 AACAAGACATGGATCA -s Anc2.Anc2refChr7 20214 16 + 32194 CACAAGACATGGATCA -s mr.mrrefChr0 71477 16 + 130230 ATCAAGACATGGATCA -s simCow_chr6.simCow.chr6 78388 16 + 602619 CATAAGACATGGATCA -s simDog_chr6.simDog.chr6 75252 16 + 593897 CACAAGAGATGGATCA -s simHuman_chr6.simHuman.chr6 72123 16 + 601863 AACAAGACATGGATCA -s simRat_chr6.simRat.chr6 67461 16 + 647215 ATTAAGACACGGATCA - -a -s simMouse_chr6.simMouse.chr6 75706 26 + 636262 AAGGGGACGAGTGTCCCTTACAGGGC -s Anc0.Anc0refChr4 20322 26 - 45765 AAGGGGATGAGAGTCCCTTACAAGGC -s Anc1.Anc1refChr2 51618 26 + 144309 AAGGGGATGAGAGTCCCTTACAAGGC -s Anc2.Anc2refChr7 20230 26 + 32194 AAAGGGATGTGAGTCCCTTACAAGGC -s mr.mrrefChr0 71493 26 + 130230 AAGGGGATGAGTGTCCCTTACAGGGC -s simCow_chr6.simCow.chr6 78404 26 + 602619 AAAAGGATGCAAGTCCCTAACATGGC -s simDog_chr6.simDog.chr6 75268 26 + 593897 AAAGGGATGTGAGTCCCTTACAAGGC -s simHuman_chr6.simHuman.chr6 72140 26 + 601863 AAGGAGATGAGAGTCCCTTACAAGGC -s simRat_chr6.simRat.chr6 67477 26 + 647215 AAGGGGATGGGTGTCCCTTACACAGA - -a -s simMouse_chr6.simMouse.chr6 75732 5 + 636262 TGTAT -s Anc0.Anc0refChr4 20349 5 - 45765 TGTAC -s Anc1.Anc1refChr2 51645 5 + 144309 TGTAC -s Anc2.Anc2refChr7 20257 5 + 32194 TGTAC -s mr.mrrefChr0 71519 5 + 130230 TGTAT -s simCow_chr6.simCow.chr6 78431 5 + 602619 GGTAT -s simDog_chr6.simDog.chr6 75295 5 + 593897 TGTAC -s simHuman_chr6.simHuman.chr6 72167 5 + 601863 TGTAA -s simRat_chr6.simRat.chr6 67503 5 + 647215 TGTAT - -a -s simMouse_chr6.simMouse.chr6 75737 80 + 636262 GAGGCTCTCTTACTCTGGAGAGAATCCCCTCATTATCTGACCAAAATTGGGACATTTGGCTATATTGAGGGACACAATAA -s Anc0.Anc0refChr4 20354 71 - 45765 GAGGCCCTTTTACCCTGGAAAGACTCCTCACATGATCTAAGCA------GGACACTTGGCCATA---AGAGACACAATGA -s Anc1.Anc1refChr2 51650 77 + 144309 GAGGCCCTTTTACCCTGGAAAGACTCCTCACATGATCTAAGCAACACTGGGACACTTGGCCATA---AGAGACACAATGA -s Anc2.Anc2refChr7 20262 71 + 32194 GAGGCCCTTTTACCCTGGAAAGACTCCTCACATGATCTAAGCA------GAACACTTGGCCATA---ATAGACACAATGA -s mr.mrrefChr0 71524 80 + 130230 GAGGCTCTTTTACTCTGGAGAGAATCCCCTCATTATCTGACCAAAATTGGGACATTTGGCTATATTGAGGGACACAATAA -s simCow_chr6.simCow.chr6 78436 68 + 602619 GAGGCCCTTTTACTCTGGATAATCTCCTCGCATGATCTTAGCA------G---ATTAGGCTATA---GTAGACACAATGA -s simDog_chr6.simDog.chr6 75305 71 + 593897 GAGGCTCTTCTATCCCAGAATGACTCCTCACGGGATCTAAACA------GAACACTTGACCATG---ATGGACTCAATGT -s simHuman_chr6.simHuman.chr6 72172 77 + 601863 GAGGCCCTTTTACACTGGAAAGCCTCCTCACATGACCTAAGCAACACTGAGACACTTGGCGATA---AGAGACATAATGA -s simRat_chr6.simRat.chr6 67508 79 + 647215 TAAGCTGTTTTACTCTGGAG-GAATCCCCTCATTATCTGGCCAAAATTGGTACATGTGGCTATATTGTGGCACACAATAA - -a -s simMouse_chr6.simMouse.chr6 75817 11 + 636262 TCTTGGTTGAT -s Anc0.Anc0refChr4 20425 11 - 45765 TCTTGGTTGAT -s Anc1.Anc1refChr2 51727 11 + 144309 TCTTGGTTGAT -s Anc2.Anc2refChr7 20352 11 + 32194 TCTTGGTTGAT -s mr.mrrefChr0 71604 11 + 130230 TCTTGGTTGAT -s simCow_chr6.simCow.chr6 78523 11 + 602619 TTTTAGTTGAT -s simDog_chr6.simDog.chr6 75395 11 + 593897 TCGTGGTTAGT -s simHuman_chr6.simHuman.chr6 72249 11 + 601863 TATTGGTTGAT -s simRat_chr6.simRat.chr6 67587 11 + 647215 TCTTGGTTGAT - -a -s simMouse_chr6.simMouse.chr6 75828 6 + 636262 GGGCTT -s Anc0.Anc0refChr4 20436 6 - 45765 GAGCCC -s Anc1.Anc1refChr2 51738 6 + 144309 GAGCCC -s Anc2.Anc2refChr7 20363 6 + 32194 CAGCCC -s mr.mrrefChr0 71615 6 + 130230 GGGCTT -s simCow_chr6.simCow.chr6 78534 6 + 602619 TGGCAT -s simDog_chr6.simDog.chr6 75406 6 + 593897 CAGCCC -s simHuman_chr6.simHuman.chr6 72260 6 + 601863 GAACCC -s simRat_chr6.simRat.chr6 67761 6 + 647215 GGGCTT - -a -s simMouse_chr6.simMouse.chr6 75834 28 + 636262 AAATACATCAATTATGGAATGATTGTAC -s Anc0.Anc0refChr4 20442 25 - 45765 CTGTGCCGATAGCATGGAATGATTG--- -s Anc1.Anc1refChr2 51744 25 + 144309 CTGTGCCGATAGCATGGAATGATTG--- -s Anc2.Anc2refChr7 20369 25 + 32194 CTGCGCCGATAGCATGTAATGATTG--- -s mr.mrrefChr0 71621 28 + 130230 ATATACATCAATTATGGAATGATTGTGC -s simCow_chr6.simCow.chr6 78543 25 + 602619 CTGGGCTGATAGCATGAAATGATTA--- -s simDog_chr6.simDog.chr6 75412 24 + 593897 AGGC-CCAATAGCATGTTATGACTG--- -s simHuman_chr6.simHuman.chr6 72266 25 + 601863 CTGTGCCGATAGCATGGAATGGTTA--- -s simRat_chr6.simRat.chr6 67767 28 + 647215 ATATACATCAATTATGGAATGATTGTGT - -a -s simMouse_chr6.simMouse.chr6 75862 36 + 636262 TGCTGATGTCAAATGTTGAGTTTCCCTACAATTAGG -s Anc0.Anc0refChr4 20467 29 - 45765 TGTAGATGT-------AAAGGTTTTTTACAATCAGG -s Anc1.Anc1refChr2 51769 29 + 144309 TGTAGATGT-------AAAGGTTTTTTACAATCAGG -s Anc2.Anc2refChr7 20394 29 + 32194 TGTAGATGT-------AAAGGTTTTTTACAATCAGG -s mr.mrrefChr0 71649 29 + 130230 TGCTGATGT-------TGAGTTTCCCTACAATTAGG -s simCow_chr6.simCow.chr6 78568 27 + 602619 TGTAGATGT-------AAAAG--TTTTACAATCAGT -s simDog_chr6.simDog.chr6 75436 29 + 593897 TGTTGCTGG-------ACGGGTTTTTTGCAATCAGG -s simHuman_chr6.simHuman.chr6 72323 29 + 601863 TGTAGATGT-------AAAGATCTTTTACTAGCAGC -s simRat_chr6.simRat.chr6 67795 29 + 647215 TGCTGATGT-------GGAGTTTCCCCACAATTAGG - -a -s simMouse_chr6.simMouse.chr6 75898 32 + 636262 GAGCAGGATTACTGAAATGTAACAGTGCATAA -s Anc0.Anc0refChr4 20500 30 - 45765 --GCAGCATTAATGAGACTGAGCAGTGCAAAA -s Anc1.Anc1refChr2 51802 32 + 144309 GAGCAGCATTAATGAGACTGAGCAGTGCAAAA -s Anc2.Anc2refChr7 20427 30 + 32194 --GTAACATTAATGAGACTGAGCAATGCAACA -s mr.mrrefChr0 71678 32 + 130230 GAGCAGGATTACTGAAATGTAGCAGTGCATAA -s simCow_chr6.simCow.chr6 78599 30 + 602619 --GTAACACTACGGAGACAGAGTATTGAAACA -s simDog_chr6.simDog.chr6 75469 24 + 593897 --------TTAATGAGACTAAGCAATGCAACA -s simHuman_chr6.simHuman.chr6 72357 32 + 601863 GAGCAGCATTATTTGGACTGAGCAGTGCACAA -s simRat_chr6.simRat.chr6 67824 32 + 647215 AAGCAGGACTACTGAAATGTAGCAGTGTATAA - -a -s simMouse_chr6.simMouse.chr6 75930 20 + 636262 AGCCAACAATTCACAGAAGG -s Anc0.Anc0refChr4 20530 19 - 45765 AGTCAAAAAATTACAG-AGG -s Anc1.Anc1refChr2 51834 20 + 144309 AGTCAAAAAATTACAGAAGG -s Anc2.Anc2refChr7 20457 19 + 32194 AGTCAAAAAATTGCAG-AGA -s mr.mrrefChr0 71710 20 + 130230 GGCCAACAATTCACAGAAGG -s simCow_chr6.simCow.chr6 78629 18 + 602619 AGTCAAAGAAT-GCAG-AAA -s simDog_chr6.simDog.chr6 75493 19 + 593897 AGACTAGAAATTGTAG-AGG -s simHuman_chr6.simHuman.chr6 72407 12 + 601863 AGTC--------ACAAAAGG -s simRat_chr6.simRat.chr6 67856 20 + 647215 GGTCAACAATCCCCAGAGAG - -a -s simMouse_chr6.simMouse.chr6 75950 3 + 636262 AAA -s Anc0.Anc0refChr4 20549 3 - 45765 AAG -s Anc1.Anc1refChr2 51854 3 + 144309 AAG -s Anc2.Anc2refChr7 20476 3 + 32194 CAG -s mr.mrrefChr0 71730 3 + 130230 AAA -s simCow_chr6.simCow.chr6 78647 3 + 602619 AAG -s simDog_chr6.simDog.chr6 75512 3 + 593897 CAG -s simHuman_chr6.simHuman.chr6 72419 3 + 601863 AAG -s simRat_chr6.simRat.chr6 67884 3 + 647215 AAA - -a -s simMouse_chr6.simMouse.chr6 75953 30 + 636262 ATCCTGTCTCCTAGAACAACAGTAATATTG -s Anc0.Anc0refChr4 20590 30 - 45765 ATCCTGTTTCCCAGATCAAGAGTAACATTG -s Anc1.Anc1refChr2 51895 30 + 144309 ATCCTGTTTCCCAGATCAAGAGTAACATTG -s Anc2.Anc2refChr7 20517 30 + 32194 ATACTGTTTCCCAAATCATGAGCAACATTG -s mr.mrrefChr0 71733 30 + 130230 ATCCTGTCTCCTAGAACAACAGTAACATTG -s simCow_chr6.simCow.chr6 78688 30 + 602619 ATAATGTTTCCATAATCATGAGCAAAAATG -s simDog_chr6.simDog.chr6 75553 30 + 593897 ATACTGATTGCCAAATCATGAGCAACATTG -s simHuman_chr6.simHuman.chr6 72501 30 + 601863 ATCTTGTATCCCAGATCAAGAGTAACCTTG -s simRat_chr6.simRat.chr6 67887 30 + 647215 ATCCTGTCCCCTAGAACATCAGTAACATTG - -a -s simMouse_chr6.simMouse.chr6 75983 8 + 636262 ACCGTTGC -s Anc0.Anc0refChr4 20620 8 - 45765 AGCGTCTC -s Anc1.Anc1refChr2 51925 8 + 144309 AGCGTCTC -s Anc2.Anc2refChr7 20547 8 + 32194 AGCATCTA -s mr.mrrefChr0 71763 8 + 130230 AGCGTTGC -s simCow_chr6.simCow.chr6 78719 8 + 602619 AGCATCTG -s simDog_chr6.simDog.chr6 75583 8 + 593897 AGCATCTA -s simHuman_chr6.simHuman.chr6 72531 8 + 601863 AGTGTCTC -s simRat_chr6.simRat.chr6 67917 8 + 647215 AGCATTGC - -a -s simMouse_chr6.simMouse.chr6 75991 55 + 636262 AAATAGAGATAGATGTAAATCTTCTTGCACCAAGTCACTGTTCCTGGCTGAAGAA -s Anc0.Anc0refChr4 20631 54 - 45765 AAATAAAGACAGTTGCAAATCAACTTACACCATATCACTGCTTCCGGCC-AAGGA -s Anc1.Anc1refChr2 51936 55 + 144309 AAATAAAGACAGTTGCAAATCAACTTACACCATATCACTGCTTCCGGCCAAAGGA -s Anc2.Anc2refChr7 20558 54 + 32194 AAATAAAGACAGTTGCAAATCAACTTACACCATATCACTGCTTCCGGCC-AAGGA -s mr.mrrefChr0 71771 55 + 130230 AAATCAAGACAGATGTAAATCAACTTGCACCAAGTCACTGTTCCTGGCTGAAGAA -s simCow_chr6.simCow.chr6 78730 54 + 602619 AAGTAAAGACTATTGCAATTCAACTTACACCAAAACACCACTTTCTGCC-ATGGG -s simDog_chr6.simDog.chr6 75594 54 + 593897 AAATACAGACAGTTGCAAATCAACTTGCACCATATCACTGATTCCGGCC-AAGGA -s simHuman_chr6.simHuman.chr6 72542 55 + 601863 ACATAAAGTCAGTTGCAGATCAACGTACACCATATTACTGCTTACAGCAACAGGC -s simRat_chr6.simRat.chr6 67925 55 + 647215 AAAGCAAGACAGATGTAAATCAACTTGCACCAAGTCACTGTTCCTGGCTGATGAA - -a -s simMouse_chr6.simMouse.chr6 76046 20 + 636262 CCACAAAGATCCAAGAGAGT -s Anc0.Anc0refChr4 20696 20 - 45765 TCACAATGATCCAAGAGAGT -s Anc1.Anc1refChr2 52002 20 + 144309 TCACAATGATCCAAGAGAGT -s Anc2.Anc2refChr7 20623 20 + 32194 TCACAATGATCCAAGAGAGT -s mr.mrrefChr0 71826 20 + 130230 CCACAAAGATCCAAGAGAGT -s simCow_chr6.simCow.chr6 78795 20 + 602619 TTACAATAACCTAAGTGAGT -s simDog_chr6.simDog.chr6 75659 20 + 593897 TCATGATGATCCAAGAGAAT -s simHuman_chr6.simHuman.chr6 72608 20 + 601863 TCACAACGAACCAAGGGAGT -s simRat_chr6.simRat.chr6 67980 20 + 647215 CCATAAAGATCAAAGAGGCT - -a -s simMouse_chr6.simMouse.chr6 76066 15 + 636262 TTCCCATACTGCCAA -s Anc0.Anc0refChr4 20716 15 - 45765 TTGCCATACTGCCAA -s Anc1.Anc1refChr2 52022 15 + 144309 TTGCCATACTGCCAA -s Anc2.Anc2refChr7 20645 15 + 32194 TTGCCATACTGCCAA -s mr.mrrefChr0 71846 15 + 130230 TTCCCATACTGCCAA -s simCow_chr6.simCow.chr6 78817 15 + 602619 TTACTGTGCAGCGAA -s simDog_chr6.simDog.chr6 75681 15 + 593897 TTGCCATACTGTCAA -s simHuman_chr6.simHuman.chr6 72628 12 + 601863 TAT---TGCCGCCAA -s simRat_chr6.simRat.chr6 68001 15 + 647215 TTACTATACTGCCAA - -a -s simMouse_chr6.simMouse.chr6 76081 44 + 636262 AATTATTTATTCCCCTCCTGGTCCCCTGGCAGGGGAGGGATTGA -s Anc0.Anc0refChr4 20731 41 - 45765 AATTGTTGACTCCCTTTCTGGT---CTGGCAGGGGAGAGGTTGA -s Anc1.Anc1refChr2 52037 41 + 144309 AATTGTTGACTCCCTTTCTGGT---CTGGCAGGGGAGAGGTTGA -s Anc2.Anc2refChr7 20660 41 + 32194 AATTGTTGACTCCCTTTCTGGT---CTGGCAGGGGCAAGGTTGA -s mr.mrrefChr0 71861 44 + 130230 AATTATTGATTCCCTTCCTGGTCTCCTGGCAGGGGAGGGATTGA -s simCow_chr6.simCow.chr6 78835 41 + 602619 TATTGTTGACTCCCTTTCTGGT---CTGACAGGGGAAAGGTTGA -s simDog_chr6.simDog.chr6 75696 41 + 593897 ACTTGCTGACTCCCTTTCTAGT---CTGGCAGGTGCAAGGTCGC -s simHuman_chr6.simHuman.chr6 72640 38 + 601863 AATTGTTGACTCCATCACTGGT---CTAGCAGGGGAG---TTGA -s simRat_chr6.simRat.chr6 68016 44 + 647215 AATTAATGATTCCCTTCCTGGTCTTCTGGCAGGGGAGGGGTTGA - -a -s simMouse_chr6.simMouse.chr6 76125 43 + 636262 TCTTGCACTGAACAGTCTGCAGACCTTTACTCTCAGGTAAGAG -s Anc0.Anc0refChr4 20773 43 - 45765 TCTTGCACTGAACCATTGACAAACTTTAAGACCCAGGTAAGAG -s Anc1.Anc1refChr2 52079 43 + 144309 TCTTGCACTGAACCATTGACAAACTTTAAGACCCAGGTAAGAG -s Anc2.Anc2refChr7 20702 43 + 32194 TCTTGCACTGAACCATTGACAAACTTTAAGACCCAGGTAAGAG -s mr.mrrefChr0 71906 43 + 130230 TCTTGCACTGAACAGTTTACAGACCTTTACACTCAGGTAAGAG -s simCow_chr6.simCow.chr6 78877 43 + 602619 TCTTGCACTGGACCAATGACAAATTTTAAACCCCAGGTAAGAG -s simDog_chr6.simDog.chr6 75738 43 + 593897 TCCTGCACTGAACCATTGACAAACTTTAAGACCCAGGTAAGAG -s simHuman_chr6.simHuman.chr6 72679 43 + 601863 TCTTGCACCGAGCCATTCACAAACTTTAATACCCTGGTAAGAG -s simRat_chr6.simRat.chr6 68061 43 + 647215 TCTTGCACTCAACTGTTGATGGACCTTTACACTCAGGTAAGAG - -a -s simMouse_chr6.simMouse.chr6 76168 59 + 636262 CTGCTATCCTTGTGAGAAAAGATGAAAGATGGATTGCACAACCGAATTCTCCTGATACC -s Anc0.Anc0refChr4 20817 59 - 45765 CTGCCATCATTGTAATAGAAGATGAAAGTTGAGTAGCACACTTGAGTTCTACTGATAGC -s Anc1.Anc1refChr2 52123 59 + 144309 CTGCCATCATTGTAATAGAAGATGAAAGTTGAGTAGCACACTTGAGTTCTACTGATAGC -s Anc2.Anc2refChr7 20746 59 + 32194 CTGCCATCACTGCAATAGAAGATGAAATTAGAGTAGCACACTTGAGTTCTACTGGTAGC -s mr.mrrefChr0 71949 59 + 130230 CTGCTATCCTTGTGAGAAAAGATGAAAGATGGATAGCACAACCGAGTTCTCCTGATAGC -s simCow_chr6.simCow.chr6 78921 58 + 602619 CTGCCATC-CTGGGATAGAAGATGAAATTAGAGTAGCCCAATAAAGTTCTAATGGTCGC -s simDog_chr6.simDog.chr6 75782 59 + 593897 CTGCCATCACTGCAATAGAAGATGAAATTAGAGTAGCACACTTGAGTTCTACTGGTAGC -s simHuman_chr6.simHuman.chr6 72723 53 + 601863 CTGCCATCTTTAT------AGGTGAAAGCTTTGTAGCATGCTTGAGTTCTATTGATAGC -s simRat_chr6.simRat.chr6 68104 59 + 647215 CTGCTATCCTTGTGTGAAAAGATGAAAGATGAATAGCACAACCGAGTTCTCCTGATAGC - -a -s simMouse_chr6.simMouse.chr6 76227 17 + 636262 TGGCATATCTAGGGGGA -s Anc0.Anc0refChr4 20876 17 - 45765 TGTCATATCTAGTGAGA -s Anc1.Anc1refChr2 52182 17 + 144309 TGTCATATCTAGTGAGA -s Anc2.Anc2refChr7 20805 17 + 32194 TGTCATATCTAGTGAGA -s mr.mrrefChr0 72008 17 + 130230 TGGCATATCTAGGGGGA -s simCow_chr6.simCow.chr6 78979 17 + 602619 TGTCATATCTGGTGAGA -s simDog_chr6.simDog.chr6 75841 17 + 593897 TGTTTTATCTAGCATGA -s simHuman_chr6.simHuman.chr6 72776 17 + 601863 TGTCATATCTAGTGAGA -s simRat_chr6.simRat.chr6 68172 17 + 647215 TGCAAACTGCAGGGTGG - -a -s simMouse_chr6.simMouse.chr6 76244 4 + 636262 CTTA -s Anc0.Anc0refChr4 20893 4 - 45765 TGTA -s Anc1.Anc1refChr2 52199 4 + 144309 TGTA -s Anc2.Anc2refChr7 20822 4 + 32194 TGTA -s mr.mrrefChr0 72025 4 + 130230 TATA -s simCow_chr6.simCow.chr6 78996 4 + 602619 TGTA -s simDog_chr6.simDog.chr6 75858 4 + 593897 TGTA -s simHuman_chr6.simHuman.chr6 72806 4 + 601863 TGTA -s simRat_chr6.simRat.chr6 68249 4 + 647215 TACA - -a -s simMouse_chr6.simMouse.chr6 76248 6 + 636262 GGTCCA -s Anc0.Anc0refChr4 20897 6 - 45765 GCTCCA -s Anc1.Anc1refChr2 52203 6 + 144309 GCTCCA -s Anc2.Anc2refChr7 20826 6 + 32194 ACTCCA -s mr.mrrefChr0 72029 6 + 130230 GCTCTA -s simCow_chr6.simCow.chr6 79000 6 + 602619 ACTCCA -s simDog_chr6.simDog.chr6 75862 6 + 593897 ACTCCA -s simHuman_chr6.simHuman.chr6 72810 6 + 601863 GCTCCA -s simRat_chr6.simRat.chr6 68257 6 + 647215 GCGATA - -a -s simMouse_chr6.simMouse.chr6 76254 8 + 636262 ATCCTAAG -s Anc0.Anc0refChr4 20908 8 - 45765 AGCCGATG -s Anc1.Anc1refChr2 52214 8 + 144309 AGCCGATG -s Anc2.Anc2refChr7 20837 8 + 32194 AGCCGATG -s mr.mrrefChr0 72035 8 + 130230 ATCCAAAG -s simCow_chr6.simCow.chr6 79011 5 + 602619 A---GATG -s simDog_chr6.simDog.chr6 75873 8 + 593897 AGCCGATG -s simHuman_chr6.simHuman.chr6 72821 8 + 601863 AGGGGATA -s simRat_chr6.simRat.chr6 68263 8 + 647215 ATTCAAAA - -a -s simMouse_chr6.simMouse.chr6 76262 1 + 636262 A -s Anc0.Anc0refChr4 20924 1 - 45765 A -s Anc1.Anc1refChr2 52230 1 + 144309 A -s Anc2.Anc2refChr7 20855 1 + 32194 A -s mr.mrrefChr0 72043 1 + 130230 A -s simCow_chr6.simCow.chr6 79026 1 + 602619 A -s simDog_chr6.simDog.chr6 75891 1 + 593897 A -s simHuman_chr6.simHuman.chr6 72837 1 + 601863 A -s simRat_chr6.simRat.chr6 68271 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 76263 2 + 636262 TG -s Anc0.Anc0refChr4 20932 2 - 45765 AG -s Anc1.Anc1refChr2 52238 2 + 144309 AG -s Anc2.Anc2refChr7 20863 2 + 32194 AA -s mr.mrrefChr0 72051 2 + 130230 TG -s simCow_chr6.simCow.chr6 79034 2 + 602619 AA -s simDog_chr6.simDog.chr6 75899 2 + 593897 AA -s simHuman_chr6.simHuman.chr6 72845 2 + 601863 AG -s simRat_chr6.simRat.chr6 68334 2 + 647215 TG - -a -s simMouse_chr6.simMouse.chr6 76265 15 + 636262 ACATGAGGAACCAAT -s Anc0.Anc0refChr4 20935 15 - 45765 ATCTAAGGAACCAAT -s Anc1.Anc1refChr2 52241 15 + 144309 ATCTAAGGAACCAAT -s Anc2.Anc2refChr7 20866 15 + 32194 ATCTAAGGAACCAAT -s mr.mrrefChr0 72053 15 + 130230 ACATGAGGAACCAAT -s simCow_chr6.simCow.chr6 79037 13 + 602619 ATCTAAGGAAT--AT -s simDog_chr6.simDog.chr6 75902 15 + 593897 ATCTAAGGAACCAAT -s simHuman_chr6.simHuman.chr6 72848 15 + 601863 ATCTAAGGAACCAAT -s simRat_chr6.simRat.chr6 68336 15 + 647215 ACATGAGGAATTGAT - -a -s simMouse_chr6.simMouse.chr6 76280 11 + 636262 GACTACTTCTG -s Anc0.Anc0refChr4 20950 11 - 45765 AACCACATCAG -s Anc1.Anc1refChr2 52256 11 + 144309 AACCACATCAG -s Anc2.Anc2refChr7 20881 11 + 32194 AACCATATCAC -s mr.mrrefChr0 72068 11 + 130230 GACTACTTCAG -s simCow_chr6.simCow.chr6 79050 7 + 602619 AA----AGGAA -s simDog_chr6.simDog.chr6 75917 11 + 593897 GGCCATATCAC -s simHuman_chr6.simHuman.chr6 72863 11 + 601863 AACCACATCAG -s simRat_chr6.simRat.chr6 68351 9 + 647215 GAC--CTTCAG -s simRat_chr6.simRat.chr6 184512 9 + 647215 TGC--GTCCAG - -a -s simMouse_chr6.simMouse.chr6 76291 66 + 636262 AGAGACTGTTAAATGCAGCTGGTCAGTTTGACAGCCACACTATTTAATGGGCACACCCTAATGCAA -s Anc0.Anc0refChr4 20974 45 - 45765 AATGGTTGTTGAATGCAGCTGATCAGTTTGACGGCCACACTC---------------------CAT -s Anc1.Anc1refChr2 52280 45 + 144309 AATGGTTGTTGAATGCAGCTGATCAGTTTGACGGCCACACTC---------------------CAT -s Anc2.Anc2refChr7 20905 45 + 32194 AATGGTTGTTGAATGCAGCTGATCAGTTTGATGGCCACACTT---------------------TAT -s mr.mrrefChr0 72079 66 + 130230 AGAGACTATTAAAGGCAGCTGGTCAGTCTGACAGTCACACTCTTTAATAGCCACACCATAATGCAA -s simCow_chr6.simCow.chr6 79072 45 + 602619 AATGGTTGTTGAATGTAGCTGATCAGTTTGATGGCAATACTT---------------------TAT -s simDog_chr6.simDog.chr6 75940 45 + 593897 AATGGTTGTTGAATGCAACTTATCAGTCTGATGGGCACACTT---------------------TAT -s simHuman_chr6.simHuman.chr6 72887 44 + 601863 AATGGTTGTAGGATACAGCTGA-CAGTTTGACGGCCACACTC---------------------CAG -s simRat_chr6.simRat.chr6 68360 66 + 647215 AGAGACTATTAAAGGCAGCTGGTCAGTCTGACAGTCACACTCTTTAATAGCCACACCATAATGCAA -s simRat_chr6.simRat.chr6 184521 66 + 647215 AGAGACTATTAAAGGCAGCTGGTCAGTCTGACAGTCACACTCTTTAATAGCCACACCATAATGCAA - -a -s simMouse_chr6.simMouse.chr6 76357 26 + 636262 TGCTACTCCCCCTTTTTTAAACTTTA -s Anc0.Anc0refChr4 21019 26 - 45765 TGCCACTTCCCTTCTTTAAGGCTGTA -s Anc1.Anc1refChr2 52325 26 + 144309 TGCCACTTCCCTTCTTTAAGGCTGTA -s Anc2.Anc2refChr7 20950 26 + 32194 TGCCACTTCCCTTCTTGAAGGATGTA -s mr.mrrefChr0 72145 26 + 130230 TGCTACTCCCCCTTTTTAAAACTTTA -s simCow_chr6.simCow.chr6 79119 26 + 602619 AACAACTTCCCTTCTTGAAGGATGTA -s simDog_chr6.simDog.chr6 75985 26 + 593897 TGCCACTTCCCTTCTTGAAGTATGTA -s simHuman_chr6.simHuman.chr6 72931 26 + 601863 TGTGACTTGCCTTCTCTAAGGCTGTA -s simRat_chr6.simRat.chr6 68426 26 + 647215 TGCTTCTCCCCCTTTTTAAAACTTTA -s simRat_chr6.simRat.chr6 184587 26 + 647215 TGCTACTCCCCCTTTTTAAAACTTTA - -a -s simMouse_chr6.simMouse.chr6 76383 54 + 636262 GGGAGATGTCAAACACCATGAACCCTGGAGGATTTTAGTCACTATGAACCCATA -s Anc0.Anc0refChr4 21045 29 - 45765 -GGAAAGTACATTCACCAGGAATCCAGGGA------------------------ -s Anc1.Anc1refChr2 52351 30 + 144309 GGGAAAGTACATTCACCAGGAATCCAGGGA------------------------ -s Anc2.Anc2refChr7 20976 29 + 32194 -GGAAAGTACATTCACCAGGAATCCAGGGA------------------------ -s mr.mrrefChr0 72171 54 + 130230 TGGAGATTTCAAACACCATGGACCCAGGAAGATTTTGGCCACTATGAACCCATA -s simCow_chr6.simCow.chr6 79145 29 + 602619 -GGAAAATACATTCACCAAGAATCAAGGGA------------------------ -s simDog_chr6.simDog.chr6 76011 29 + 593897 -GGCAGGTACATTCACCAGGAGCCCAGTGC------------------------ -s simHuman_chr6.simHuman.chr6 72958 30 + 601863 GGGAAAGTACATCGATCAGGAATCCAGGGA------------------------ -s simRat_chr6.simRat.chr6 68452 54 + 647215 TGGAGATTTCAAACACGATGGACCCAGGAAGATTTTGGCCACTATGAACCCATA -s simRat_chr6.simRat.chr6 184613 54 + 647215 TGGAGATTTCAGACACTATGGGCCCAGGAAGATTTTGACCACTACGAACCCATA - -a -s simMouse_chr6.simMouse.chr6 76437 26 + 636262 GGTAGGCACCATATCAGTCTAGGAGG -s Anc0.Anc0refChr4 21074 6 - 45765 -ATAGGC------------------- -s Anc1.Anc1refChr2 52381 19 + 144309 -ATAGGCACCCTATCA------AAGG -s Anc2.Anc2refChr7 21005 6 + 32194 -ATAGGC------------------- -s mr.mrrefChr0 72225 26 + 130230 GGTAGGCACCCTATCAGTCTAGGAGG -s simCow_chr6.simCow.chr6 79174 6 + 602619 -ATAGGG------------------- -s simDog_chr6.simDog.chr6 76040 6 + 593897 -GTAAGC------------------- -s simHuman_chr6.simHuman.chr6 72988 19 + 601863 -ATAGGCACCCTATCA------AAGG -s simRat_chr6.simRat.chr6 68506 26 + 647215 GGTAGGCAGCCTATAAGTTTAAGAGG -s simRat_chr6.simRat.chr6 184668 10 + 647215 GGTAGGCACC---------------- - -a -s simMouse_chr6.simMouse.chr6 76463 33 + 636262 CAAGTCCTTCTGCCCTTTGCAGTTGTGCTTATT -s Anc0.Anc0refChr4 21080 31 - 45765 TAAGACC--CTGCCCTTTGCTGTTTTGCCCAAT -s Anc1.Anc1refChr2 52400 31 + 144309 TAAGACC--CTGCCCTTTGCTGTTTTGCCCAAT -s Anc2.Anc2refChr7 21011 31 + 32194 TAAGACC--TTGCCCTTTGCTGTTTTGCCCTAT -s mr.mrrefChr0 72251 33 + 130230 CAAGTCCTTCTGCCCTTTGCAGTTGTGCTTATT -s simCow_chr6.simCow.chr6 79180 31 + 602619 TAAGACC--TTACCCTTTGCTATTTTGCCCTTG -s simCow_chr6.simCow.chr6 79295 31 + 602619 ATATGCC--TTGCCCTTTGCTATTTTGCCCCTG -s simDog_chr6.simDog.chr6 76046 31 + 593897 TACGAAC--TTGCCCTTTGCTGTTTTGTCTTAT -s simHuman_chr6.simHuman.chr6 73007 31 + 601863 TGAGACC--CAGCCCTTTGCTGTATTGCCCAAT -s simRat_chr6.simRat.chr6 68532 33 + 647215 CAAGTCCTTCTGCCCTTTGCAGTTGTATTTATT - -a -s simMouse_chr6.simMouse.chr6 76496 28 + 636262 CACAAGCAAGAAACACCAATTCTCATGG -s Anc0.Anc0refChr4 21111 25 - 45765 CTTGAGTAAGAAATGATAGTTGC---AA -s Anc1.Anc1refChr2 52431 28 + 144309 CTTGAGTAAGAAATGATAGTTGCCATAA -s Anc2.Anc2refChr7 21042 25 + 32194 TTTGAGTAAGAAATGATAGTTGC---AA -s mr.mrrefChr0 72284 28 + 130230 CATAAGCAAGAAACACCAATTCTCATGA -s simCow_chr6.simCow.chr6 79211 25 + 602619 TTTGAGTAAGAATTGACAGTTCC---AA -s simCow_chr6.simCow.chr6 79326 25 + 602619 TTTGAGTAAGCAGTGACAGTTGC---AA -s simDog_chr6.simDog.chr6 76077 25 + 593897 TTTGAGTAAGAAATGATGGTTGC---AA -s simHuman_chr6.simHuman.chr6 73038 28 + 601863 CTTGAGTAAGGAATGATAGTTGCCATAA -s simRat_chr6.simRat.chr6 68566 28 + 647215 CATAAGAAAGAAACACCAATTATTGTGA - -a -s simMouse_chr6.simMouse.chr6 76524 11 + 636262 ATCAATGCTTC -s Anc0.Anc0refChr4 21136 2 - 45765 A---------T -s Anc1.Anc1refChr2 52459 11 + 144309 ATCAATTTATT -s Anc2.Anc2refChr7 21067 2 + 32194 A---------T -s mr.mrrefChr0 72312 11 + 130230 ATCAATGCTTC -s simCow_chr6.simCow.chr6 79236 2 + 602619 A---------T -s simCow_chr6.simCow.chr6 79351 2 + 602619 A---------A -s simDog_chr6.simDog.chr6 76102 2 + 593897 A---------T -s simHuman_chr6.simHuman.chr6 73067 11 + 601863 GACAATTTATT -s simRat_chr6.simRat.chr6 68594 11 + 647215 ATCAATGCTCC - -a -s simMouse_chr6.simMouse.chr6 76535 29 + 636262 TCCTAAGAAGAACTGGCAGCAAACCAGAT -s Anc0.Anc0refChr4 21138 14 - 45765 TCCCATGAAA---------------CAAT -s Anc1.Anc1refChr2 52470 14 + 144309 TCCCATGAAA---------------CAAT -s Anc2.Anc2refChr7 21069 14 + 32194 TCCCATGAGA---------------CAAT -s mr.mrrefChr0 72323 29 + 130230 TCCTAAGAAGAACTGGCAGCAAACCCGAT -s simCow_chr6.simCow.chr6 79238 14 + 602619 TCAGATGGGA---------------CAAC -s simCow_chr6.simCow.chr6 79353 14 + 602619 TCATATGAGA---------------CACT -s simDog_chr6.simDog.chr6 76104 14 + 593897 TCCCATGAGA---------------CAAT -s simHuman_chr6.simHuman.chr6 73078 14 + 601863 TCCCATGAAA---------------CAAT -s simRat_chr6.simRat.chr6 68609 29 + 647215 TTCAGAGGAGAACTGGCAGCAAACCCGAT - -a -s simMouse_chr6.simMouse.chr6 76564 11 + 636262 GCCCCTCCCCC -s Anc0.Anc0refChr4 21152 11 - 45765 GCCCTTACCCC -s Anc1.Anc1refChr2 52484 11 + 144309 GCCCTTACCCC -s Anc2.Anc2refChr7 21083 11 + 32194 GCCCTTACCCC -s mr.mrrefChr0 72352 11 + 130230 GCCCCTCCCCC -s simCow_chr6.simCow.chr6 79253 11 + 602619 GCCCTTATCCC -s simCow_chr6.simCow.chr6 79367 11 + 602619 GTCCTTACCCT -s simDog_chr6.simDog.chr6 76118 11 + 593897 GCACTTACCAC -s simHuman_chr6.simHuman.chr6 73092 11 + 601863 GACCTTTCCTC -s simRat_chr6.simRat.chr6 68638 5 + 647215 GCCC------C - -a -s simMouse_chr6.simMouse.chr6 76575 8 + 636262 AAAGATGA -s Anc0.Anc0refChr4 21163 8 - 45765 AGAGAAGG -s Anc1.Anc1refChr2 52495 8 + 144309 AGAGAAGG -s Anc2.Anc2refChr7 21094 8 + 32194 AGAGAAGG -s mr.mrrefChr0 72363 8 + 130230 AAAGATGA -s simCow_chr6.simCow.chr6 79266 8 + 602619 AGAGAGGG -s simCow_chr6.simCow.chr6 79378 8 + 602619 AGAGAGGG -s simDog_chr6.simDog.chr6 76129 8 + 593897 AGAGAAGA -s simHuman_chr6.simHuman.chr6 73103 8 + 601863 AGAGAAGG -s simRat_chr6.simRat.chr6 68643 8 + 647215 AAAGATGA - -a -s simMouse_chr6.simMouse.chr6 76583 10 + 636262 CAAGCTGTGG -s Anc0.Anc0refChr4 21171 10 - 45765 CAGGCAGTGA -s Anc1.Anc1refChr2 52503 10 + 144309 CAGGCAGTGA -s Anc2.Anc2refChr7 21102 10 + 32194 CTGGCAGTAA -s mr.mrrefChr0 72371 10 + 130230 CAAGCTGTGG -s simCow_chr6.simCow.chr6 79274 10 + 602619 GTGGCTGTAA -s simCow_chr6.simCow.chr6 79386 10 + 602619 CCGGCAGTAA -s simDog_chr6.simDog.chr6 76138 10 + 593897 CTGGCAGTAA -s simHuman_chr6.simHuman.chr6 73111 10 + 601863 CAGGTGGTGA -s simRat_chr6.simRat.chr6 68651 10 + 647215 CAAGCTGCAG - -a -s simMouse_chr6.simMouse.chr6 76593 18 + 636262 GTCTGGGAATGATACTAA -s Anc0.Anc0refChr4 21181 18 - 45765 GCCAAGGAATGACATTGA -s Anc1.Anc1refChr2 52513 18 + 144309 GCCAAGGAATGACATTGA -s Anc2.Anc2refChr7 21112 18 + 32194 GCCAAGGAATGACATTGA -s mr.mrrefChr0 72381 18 + 130230 GCCTGGGAATGATACTAA -s simCow_chr6.simCow.chr6 79284 11 + 602619 GCCAAGGAATG------- -s simCow_chr6.simCow.chr6 79396 7 + 602619 GCCAAGG----------- -s simDog_chr6.simDog.chr6 76149 18 + 593897 GCCAAGGAATGACATTGA -s simHuman_chr6.simHuman.chr6 73121 18 + 601863 GCCAAGGAAGGGCATTTC -s simRat_chr6.simRat.chr6 68661 18 + 647215 GCCTGGGAATGATACTAA - -a -s simMouse_chr6.simMouse.chr6 76611 2 + 636262 CC -s Anc0.Anc0refChr4 21199 2 - 45765 AA -s Anc1.Anc1refChr2 52531 2 + 144309 AA -s Anc2.Anc2refChr7 21130 2 + 32194 AA -s mr.mrrefChr0 72399 2 + 130230 CA -s simCow_chr6.simCow.chr6 79403 2 + 602619 AA -s simDog_chr6.simDog.chr6 76167 2 + 593897 GA -s simHuman_chr6.simHuman.chr6 73139 2 + 601863 AA -s simRat_chr6.simRat.chr6 68679 2 + 647215 CA - -a -s simMouse_chr6.simMouse.chr6 76613 27 + 636262 AAAGATATGCTCCTAGAAACTAGACAG -s Anc0.Anc0refChr4 21220 22 - 45765 -AAGATCTGTCCCCACAGGATTG---- -s Anc1.Anc1refChr2 52552 26 + 144309 -AAGATCTGTCCCCACAGGATTGTCCT -s Anc2.Anc2refChr7 21151 22 + 32194 -AAAATCTGTCTCCATAGGATTG---- -s mr.mrrefChr0 72421 27 + 130230 AAAGATATGCTCCTACAAACTAGACAT -s simCow_chr6.simCow.chr6 79424 22 + 602619 -AAAATCTGTCTCCATAGAATTG---- -s simDog_chr6.simDog.chr6 76188 22 + 593897 -AAAATCTGTCTGCATAAGATTG---- -s simHuman_chr6.simHuman.chr6 73160 26 + 601863 -AAGATCTGTCCCCACAGGATCGTCCT -s simRat_chr6.simRat.chr6 68702 27 + 647215 AAAGATATGCTCCTACAAACTTGACAT - -a -s simMouse_chr6.simMouse.chr6 76640 5 + 636262 AGTGT -s Anc0.Anc0refChr4 21290 5 - 45765 AGTGT -s Anc1.Anc1refChr2 52626 5 + 144309 AGTGT -s Anc2.Anc2refChr7 21221 5 + 32194 AGTGT -s mr.mrrefChr0 72448 5 + 130230 AGTGT -s simCow_chr6.simCow.chr6 79489 5 + 602619 ATTGT -s simDog_chr6.simDog.chr6 76259 5 + 593897 AGTGT -s simHuman_chr6.simHuman.chr6 73239 5 + 601863 AGTGT -s simRat_chr6.simRat.chr6 68729 5 + 647215 AGTTT - -a -s simMouse_chr6.simMouse.chr6 76645 1 + 636262 C -s Anc0.Anc0refChr4 21295 1 - 45765 C -s Anc1.Anc1refChr2 52631 1 + 144309 C -s Anc2.Anc2refChr7 21235 1 + 32194 C -s mr.mrrefChr0 72453 1 + 130230 C -s simCow_chr6.simCow.chr6 79503 1 + 602619 C -s simDog_chr6.simDog.chr6 76273 1 + 593897 C -s simHuman_chr6.simHuman.chr6 73244 1 + 601863 T -s simRat_chr6.simRat.chr6 68734 1 + 647215 C - -a -s simMouse_chr6.simMouse.chr6 76646 18 + 636262 CCATTGTAATTGAACATA -s Anc0.Anc0refChr4 21297 18 - 45765 CTATGGCAATCAAACAGA -s Anc1.Anc1refChr2 52633 18 + 144309 CTATGGCAATCAAACAGA -s Anc2.Anc2refChr7 21237 18 + 32194 CTATTGCAATCAAACAGA -s mr.mrrefChr0 72454 18 + 130230 CCATGGTAATCAAACATA -s simCow_chr6.simCow.chr6 79505 18 + 602619 CTATTGAAATCAAACAGA -s simDog_chr6.simDog.chr6 76275 18 + 593897 CTATTGCTATTGAACAGA -s simHuman_chr6.simHuman.chr6 73246 18 + 601863 CTATGGCAATCAACCTGA -s simRat_chr6.simRat.chr6 68735 18 + 647215 CCATGGGAATCAAACATA - -a -s simMouse_chr6.simMouse.chr6 76664 32 + 636262 TTACAGTCCTGCTAATCCTCTTTAACATGACC -s Anc0.Anc0refChr4 21317 32 - 45765 CCCCACTGCTGCTGATTCTCTTTAAAGTGAGC -s Anc1.Anc1refChr2 52653 32 + 144309 CCCCACTGCTGCTGATTCTCTTTAAAGTGAGC -s Anc2.Anc2refChr7 21257 32 + 32194 CTCCACTGCTGCTGATTCTCTTTAAAGTGAGC -s mr.mrrefChr0 72472 32 + 130230 TCACAGTCCTGCTGATCCTCTTTAACATGAGC -s simCow_chr6.simCow.chr6 79525 29 + 602619 CTCCACTGC---TAATTTTCTTTAAAGTGAGA -s simDog_chr6.simDog.chr6 76295 32 + 593897 CTCTACTCCTGCTGATTCCTTTTAAAGTGAGC -s simHuman_chr6.simHuman.chr6 73266 32 + 601863 CCCCACTGCTGTTGATTCTCTTTAAAGTGTGC -s simRat_chr6.simRat.chr6 68753 32 + 647215 TCACAGCCCTTCTGATCCTCTTTGACATGAGC - -a -s simMouse_chr6.simMouse.chr6 76696 22 + 636262 TGCTTGTCATAATCTGTCCCAT -s Anc0.Anc0refChr4 21351 17 - 45765 TGCTTATAACAATCCT-----T -s Anc1.Anc1refChr2 52687 22 + 144309 TGCTTATAACAATCCTTATCAT -s Anc2.Anc2refChr7 21292 17 + 32194 TGCTTATAACAATCCT-----T -s mr.mrrefChr0 72504 22 + 130230 TGCTTATAATAATCCGTACCAT -s simCow_chr6.simCow.chr6 79557 17 + 602619 TGCTTATAACAATCCT-----T -s simDog_chr6.simDog.chr6 76330 17 + 593897 CGCTTATAGTAATCTT-----T -s simHuman_chr6.simHuman.chr6 73300 22 + 601863 TGCTTATAACAATCCTTATCAT -s simRat_chr6.simRat.chr6 68785 22 + 647215 TGCTTATAGTAGTCCGTACCAT - -a -s simMouse_chr6.simMouse.chr6 76718 24 + 636262 TGTAGAACATTTCTCCCTTTGTTC -s Anc0.Anc0refChr4 21368 24 - 45765 TACAGGACTTCACTCCATTTGTCC -s Anc1.Anc1refChr2 52709 24 + 144309 TACAGGACTTCACTCCATTTGTCC -s Anc2.Anc2refChr7 21309 24 + 32194 TACAGGACTTCACCCCATTTGTCC -s mr.mrrefChr0 72526 24 + 130230 TGTAGAACATCTCTCCCTTTGTTC -s simCow_chr6.simCow.chr6 79578 24 + 602619 TACAGCACTTCACCCCATTTGTCA -s simDog_chr6.simDog.chr6 76347 15 + 593897 TGTATGACTTC---------GTCC -s simHuman_chr6.simHuman.chr6 73322 24 + 601863 TACAGGACTTCATTGCTTTTGTCC -s simRat_chr6.simRat.chr6 68807 24 + 647215 AGTAGAACATCTCTCACTCTGTTC - -a -s simMouse_chr6.simMouse.chr6 76742 9 + 636262 CACAAAACT -s Anc0.Anc0refChr4 21393 9 - 45765 CACAAAATT -s Anc1.Anc1refChr2 52734 9 + 144309 CACAAAATT -s Anc2.Anc2refChr7 21334 9 + 32194 CACAAAATT -s mr.mrrefChr0 72550 9 + 130230 CACAAAACT -s simCow_chr6.simCow.chr6 79603 9 + 602619 CACAAAATT -s simDog_chr6.simDog.chr6 76363 9 + 593897 CACAACACT -s simHuman_chr6.simHuman.chr6 73347 9 + 601863 CACAAAATT -s simRat_chr6.simRat.chr6 68831 9 + 647215 CACAAAACT - -a -s simMouse_chr6.simMouse.chr6 76751 2 + 636262 GT -s Anc0.Anc0refChr4 21409 2 - 45765 CT -s Anc1.Anc1refChr2 52750 2 + 144309 CT -s Anc2.Anc2refChr7 21350 2 + 32194 CT -s mr.mrrefChr0 72559 2 + 130230 CT -s simDog_chr6.simDog.chr6 76379 2 + 593897 CT -s simHuman_chr6.simHuman.chr6 73363 2 + 601863 CT -s simRat_chr6.simRat.chr6 68840 2 + 647215 CT - -a -s simMouse_chr6.simMouse.chr6 76753 54 + 636262 GCTATTTGCTATTTCTACAAATGTGTGGTGTTATTCACTTAGCATCAAGGCAAA -s Anc0.Anc0refChr4 21411 52 - 45765 G--ACTTGCTATTTCTACAAATGTCTGGTGTTACTCACTTATCATCTAGGTAAA -s Anc1.Anc1refChr2 52752 52 + 144309 G--ACTTGCTATTTCTACAAATGTCTGGTGTTACTCACTTATCATCTAGGTAAA -s Anc2.Anc2refChr7 21352 52 + 32194 G--ACTTGCTATTTCTACAAATGCCTGGTGTTACTCACTTATCATCTAGGTAAA -s mr.mrrefChr0 72561 54 + 130230 GCTATTTGCTATTTCTACAAATGTGTGGTGTTATTCACTTAGCATCAAGGCAAA -s simCow_chr6.simCow.chr6 79617 52 + 602619 G--ACTTCTTATCCCTACAAGTGCTTGGTGTTACTCACTCATTGTGTACATAAA -s simDog_chr6.simDog.chr6 76407 50 + 593897 A--ACTTGCTGTTT-TACAAATGCCTTGTGTCACTTA-TTATCATCTAGGTAAA -s simHuman_chr6.simHuman.chr6 73365 52 + 601863 G--ACTTGCTATTTCCCCAGATGTCTGCTGTTCCTCATTTATCATCTAGGTAAA -s simRat_chr6.simRat.chr6 68842 54 + 647215 GCAATTTGCTAGTTCTACAAATGTGTGGTGTTATTTACTCAGTACCGACACGAA - -a -s simMouse_chr6.simMouse.chr6 76807 37 + 636262 GCTGAAAGCGGGGCATGATGGGCCACTGCCAACAATG -s Anc0.Anc0refChr4 21463 37 - 45765 GCTGAAAGTGGGGTATGAGGGGTCACTGCAAACAATG -s Anc1.Anc1refChr2 52804 37 + 144309 GCTGAAAGTGGGGTATGAGGGGTCACTGCAAACAATG -s Anc2.Anc2refChr7 21409 37 + 32194 ACTGAAAATGGGGCATGAGGGGTCACTGCAAACAATA -s mr.mrrefChr0 72615 37 + 130230 GCTGAAAGTGGGGTATGATGGGTCACTGCCAACAATG -s simCow_chr6.simCow.chr6 79674 37 + 602619 ACTGAGGATGGGCCATGGGGAGTGACTGCAAACCATA -s simDog_chr6.simDog.chr6 76462 37 + 593897 ACTGGAAATGGGGCATGAAGGGTCATTGCAGGCAATA -s simHuman_chr6.simHuman.chr6 73417 37 + 601863 GCTGAAAGTGGGGTGTGAGGGGTCACTGCAAACAATG -s simRat_chr6.simRat.chr6 68896 37 + 647215 GCTGAAAGTGGGGTATGATGAGTCATTGCCAAGAATA - -a -s simMouse_chr6.simMouse.chr6 76844 24 + 636262 CTTATACACATCTGTGTAGAATCT -s Anc0.Anc0refChr4 21500 24 - 45765 CCTATACATACCGTTGTAGCTTCT -s Anc1.Anc1refChr2 52841 24 + 144309 CCTATACATACCGTTGTAGCTTCT -s Anc2.Anc2refChr7 21446 24 + 32194 CCTATACATACCGTTGTAGCTTCT -s mr.mrrefChr0 72652 24 + 130230 CCTATACACATCTGTGTAGAATCT -s simCow_chr6.simCow.chr6 79731 24 + 602619 TCTACACATACCGCTGTAGCTCCT -s simDog_chr6.simDog.chr6 76499 16 + 593897 CCTAT--------TTATAACTTCT -s simHuman_chr6.simHuman.chr6 73454 24 + 601863 CCAATACATACCCTTGTAGCTTCT -s simRat_chr6.simRat.chr6 68933 24 + 647215 CCTACACACATCTGTGTAGAATCT - -a -s simMouse_chr6.simMouse.chr6 76868 64 + 636262 AGCTAATATGCCCACCTAATACAGAGATGGTCATTGTCCCTCGTACTCAAACCCATCAAAGCTG -s Anc0.Anc0refChr4 21524 64 - 45765 AGTTGCTATGGCTTGCTAGAACAGAGATGATCATAGTCCTTCATACCCAAACCCACCCAAGCTC -s Anc1.Anc1refChr2 52865 64 + 144309 AGTTGCTATGGCTTGCTAGAACAGAGATGATCATAGTCCTTCATACCCAAACCCACCCAAGCTC -s Anc2.Anc2refChr7 21474 64 + 32194 AGTTGCTATGGCTTGCTAGAACAGAGATGATCATAGTCCTTTACACCCAAACCCACCCAAGATC -s mr.mrrefChr0 72676 64 + 130230 AGCTAATATGCCCACCTAATACAGAGATGGTCATTGTCCCTCATACTCAAACCCACCAAAGCTG -s simCow_chr6.simCow.chr6 79759 64 + 602619 ATTTGCTATGGGTTGCTGAAACAGAGATGTTCATAGCTCTTGACACCCAAACCCACCCAAGTGC -s simDog_chr6.simDog.chr6 76519 64 + 593897 AGTTGCTATGGCTTGCTAGGACAAGGATGATCGTTGTCCTTTACTCCCAAACCCGCCCAAAATC -s simHuman_chr6.simHuman.chr6 73478 64 + 601863 AGTTGCTGTGGCTTGCTAGAACAGATTTGAGCAAAGTCCTACATACCCAAACCTACCCAAGCTC -s simRat_chr6.simRat.chr6 68957 64 + 647215 AGCTAGCATGTCCACCCAAGACAGAGATGGTCATTGTCCCTCATACTCAAACCAACCAAGGCTG - -a -s simMouse_chr6.simMouse.chr6 76932 3 + 636262 GAT -s Anc0.Anc0refChr4 21588 3 - 45765 AAA -s Anc1.Anc1refChr2 52929 3 + 144309 AAA -s Anc2.Anc2refChr7 21538 3 + 32194 ATA -s mr.mrrefChr0 72740 3 + 130230 AAT -s simCow_chr6.simCow.chr6 79823 3 + 602619 AAA -s simDog_chr6.simDog.chr6 76583 3 + 593897 ATG -s simHuman_chr6.simHuman.chr6 73552 3 + 601863 AAA -s simRat_chr6.simRat.chr6 69021 3 + 647215 AAG - -a -s simMouse_chr6.simMouse.chr6 76935 42 + 636262 TACTGCAAGTTAGCTGTAAATATGTATGAATACACTCATCAG -s Anc0.Anc0refChr4 21591 40 - 45765 CACTG--GGTTAGCAATGAAAATGTATGAATTAACTGGTCAT -s Anc1.Anc1refChr2 52932 40 + 144309 CACTG--GGTTAGCAATGAAAATGTATGAATTAACTGGTCAT -s Anc2.Anc2refChr7 21543 40 + 32194 CTCTG--GGTTAGCAATGTAAATGTATGAATTCACTGGTCAT -s mr.mrrefChr0 72743 42 + 130230 TACTGCAAGTTAGCTATAAATATGTATGAATTAACTGGTCAG -s simCow_chr6.simCow.chr6 79828 40 + 602619 CACTG--GGTTAGCAATGGAAATGTTTGAATCCACTGGTCAT -s simDog_chr6.simDog.chr6 76588 36 + 593897 TTCTA--TGTT----ATGTAACTGTATGAATTCACTGGTCAT -s simHuman_chr6.simHuman.chr6 73555 40 + 601863 CACTG--GGTGAGCAATCAAAATGTAAGAAATAACTGGTCAT -s simRat_chr6.simRat.chr6 69024 42 + 647215 TCCTGCAAGTTAGCTATAAATATGTATTAATTAACTGGTCAG - -a -s simMouse_chr6.simMouse.chr6 76977 130 + 636262 ACACCAAGTCTAGCCAACTTATATAGGTCACAAGTGGACCAAAGACGCAGGATGTAAGACTGGTGGGGGGACCCCTAGTAGGTACCATTGTGGATCTATGGTAAATTAATTCCTTTATGACAGAGATGTG -s Anc0.Anc0refChr4 21632 45 - 45765 TCACCAAGCCAATGAAACTTACATAGATGAGAAGTGAACC-------------------------------------------------------------------------------------ATATG -s Anc1.Anc1refChr2 52973 45 + 144309 TCACCAAGCCAATGAAACTTACATAGATGAGAAGTGAACC-------------------------------------------------------------------------------------ATATG -s Anc2.Anc2refChr7 21584 45 + 32194 TCACCAAGCCAATGAAACTTACATAGAGGAGAAGTGAACC-------------------------------------------------------------------------------------ATAGG -s mr.mrrefChr0 72786 129 + 130230 ACACCAAGTCTAGCCAACTTATATAGGTCACAAGTGGACCAAAGACGCAGGATGTAAGACTGGTGGGGGGACCCCTAGTAGGTACCATTGTGGATCTATGGTAAATTAATTC-TTTATGACAGAGATGTG -s simCow_chr6.simCow.chr6 79869 27 + 602619 TCACCA------------------AGAGGACAAGTGAAGC-------------------------------------------------------------------------------------AAAAG -s simDog_chr6.simDog.chr6 76625 45 + 593897 TCACCAAGCCAATGAAACTTACATAGAGGAGGAGTGAACC-------------------------------------------------------------------------------------ATAGA -s simHuman_chr6.simHuman.chr6 73640 45 + 601863 CCACCATGCCAGTGAAACTTCAACAGATGATAACTGAATC-------------------------------------------------------------------------------------CTATG -s simRat_chr6.simRat.chr6 69067 129 + 647215 ACACCAAATCTAGTAGCCTTAAATAGGTCACAAATGGACCATACACACAGGATGTCAGACTGATTGGGGGACTCCTAGTAGGTACCATTGTGGACTTATAGTTAATTAATTC-TTCATGACAGAGATGTA - -a -s simMouse_chr6.simMouse.chr6 77107 25 + 636262 TACTTGTTCACTTCCCCATCATCTC -s Anc0.Anc0refChr4 21841 25 - 45765 TACCTGTTCATCTCCCCATCACGTC -s Anc1.Anc1refChr2 53182 25 + 144309 TACCTGTTCATCTCCCCATCACGTC -s Anc2.Anc2refChr7 21793 25 + 32194 TACCTGTTTATCTGCCCATCGCGTC -s mr.mrrefChr0 72915 25 + 130230 TACTTGTTCACTTCCCCATCATCTC -s simCow_chr6.simCow.chr6 80065 25 + 602619 TACCTGTAGATCTGTCCACCATGTC -s simDog_chr6.simDog.chr6 76837 25 + 593897 TACATGTTTATCGGCCCATCGCGTC -s simHuman_chr6.simHuman.chr6 73849 21 + 601863 TACCTGTTCATCTCCCCGTCA---- -s simRat_chr6.simRat.chr6 69196 25 + 647215 TACCTGTTCACATCCCCATCATCTC - -a -s simMouse_chr6.simMouse.chr6 77132 41 + 636262 TTACCTAGGATCACTCTGCCCATTTGTCAGCCACACTGTTT -s Anc0.Anc0refChr4 21866 31 - 45765 TTACCTAGG----------GCATTTATCCGTCATTCTGATT -s Anc1.Anc1refChr2 53207 31 + 144309 TTACCTAGG----------GCATTTATCCGTCATTCTGATT -s Anc2.Anc2refChr7 21826 31 + 32194 TTAACTAGG----------GCATTTATCCATCATTTTGATT -s mr.mrrefChr0 72940 41 + 130230 TTACCTAGGATCACTCTGCCCATTTGTCAGCCACACTGTTT -s simCow_chr6.simCow.chr6 80098 31 + 602619 TTATTTAGG----------GCATTTATCCATCTTTATAGTT -s simDog_chr6.simDog.chr6 76870 31 + 593897 TTAACTATG----------GCATTTGTCCACCATTTTGAGT -s simHuman_chr6.simHuman.chr6 73870 30 + 601863 -TACCTAGA----------GCATTTACCTGTCATCCTGCTT -s simRat_chr6.simRat.chr6 69221 41 + 647215 TTGCCTAGCATCTGTCTGCCCATGTGTCAGCCACCCTGTTT - -a -s simMouse_chr6.simMouse.chr6 77173 46 + 636262 ACCATCCATGGGCGGTTCTCTTTCCTCTGCGTTATGGGATGGCCCT -s Anc0.Anc0refChr4 21897 4 - 45765 ACCA------------------------------------------ -s Anc1.Anc1refChr2 53238 4 + 144309 ACCA------------------------------------------ -s Anc2.Anc2refChr7 21857 4 + 32194 ACCA------------------------------------------ -s mr.mrrefChr0 72981 46 + 130230 ACCATCCATGGGCGGTTCTCTTTCCTCTGCGTTATGGGATGGCCCT -s simCow_chr6.simCow.chr6 80129 4 + 602619 ACCA------------------------------------------ -s simDog_chr6.simDog.chr6 76902 4 + 593897 ACCA------------------------------------------ -s simHuman_chr6.simHuman.chr6 73900 4 + 601863 ACCA------------------------------------------ -s simRat_chr6.simRat.chr6 69262 46 + 647215 ACCATCCATGGGAGGTTCTCTTTCTTCTGTGTCTCGGATAGGACCT - -a -s simMouse_chr6.simMouse.chr6 77219 21 + 636262 TGGTACCATGGAGCTGATGCT -s Anc0.Anc0refChr4 21901 6 - 45765 ---------------GATATT -s Anc1.Anc1refChr2 53242 6 + 144309 ---------------GATATT -s Anc2.Anc2refChr7 21861 6 + 32194 ---------------GATATT -s mr.mrrefChr0 73027 21 + 130230 TGGTACCATGGAGCTGATGCT -s simCow_chr6.simCow.chr6 80133 6 + 602619 ---------------GATATC -s simDog_chr6.simDog.chr6 76906 6 + 593897 ---------------GATATT -s simHuman_chr6.simHuman.chr6 73904 6 + 601863 ---------------GATATT -s simRat_chr6.simRat.chr6 69558 21 + 647215 TGGTACCATGAAGCTGATGAT - -a -s simMouse_chr6.simMouse.chr6 77240 6 + 636262 TCTCAC -s Anc0.Anc0refChr4 21907 6 - 45765 TCTTAC -s Anc1.Anc1refChr2 53248 6 + 144309 TCTTAC -s Anc2.Anc2refChr7 21869 6 + 32194 TCTTAC -s mr.mrrefChr0 73048 6 + 130230 TCTCAC -s simCow_chr6.simCow.chr6 80141 6 + 602619 ACTTAC -s simDog_chr6.simDog.chr6 76914 6 + 593897 TCTTAC -s simHuman_chr6.simHuman.chr6 73910 6 + 601863 TATTAC -s simRat_chr6.simRat.chr6 69579 6 + 647215 TATCAC - -a -s simMouse_chr6.simMouse.chr6 77246 4 + 636262 ACAG -s Anc0.Anc0refChr4 21913 4 - 45765 ATAG -s Anc1.Anc1refChr2 53254 4 + 144309 ATAG -s Anc2.Anc2refChr7 21897 4 + 32194 ATGG -s mr.mrrefChr0 73054 4 + 130230 ACAG -s simCow_chr6.simCow.chr6 80169 4 + 602619 ATGG -s simDog_chr6.simDog.chr6 76942 4 + 593897 ATGG -s simHuman_chr6.simHuman.chr6 73916 4 + 601863 TTAG -s simRat_chr6.simRat.chr6 69585 4 + 647215 ACAG - -a -s simMouse_chr6.simMouse.chr6 77250 45 + 636262 AGAGTTTGAATCATCTATGAGTTCAACTAATGAAATAACACCTAG -s Anc0.Anc0refChr4 21942 43 - 45765 AG--TTTATATCATGCTTAAGTTCAACAAATGCAAAAACACCTAG -s Anc1.Anc1refChr2 53283 43 + 144309 AG--TTTATATCATGCTTAAGTTCAACAAATGCAAAAACACCTAG -s Anc2.Anc2refChr7 21991 43 + 32194 CA--TTCATATCATGCTTAAGTTCAACAAATGCAAAAACACCTAG -s mr.mrrefChr0 73058 43 + 130230 AG--TTTGAATCATCTATGAGTTCAACTAATGAAATAACACCTAG -s simCow_chr6.simCow.chr6 80276 43 + 602619 AC--TTCATATTATACTTAAGTTCAACAAATACAAAAACATCTAG -s simDog_chr6.simDog.chr6 77037 43 + 593897 CA--ATCAGATCATGCTTGAGTTCAACAAATGCAAAAACACCTAG -s simHuman_chr6.simHuman.chr6 73958 43 + 601863 AG--TTTATATCATGCTTAAGTTCAACAAATGCAGAAACACCTAG -s simRat_chr6.simRat.chr6 69589 43 + 647215 AG--TTTGAATCATGTATGAGTTCAACTAATGGAATAATACCTAG - -a -s simMouse_chr6.simMouse.chr6 77295 44 + 636262 TGACAACTGCCCAGCATATCTGTACCACAGTACACTCCAGGTTC -s Anc0.Anc0refChr4 21985 44 - 45765 TGACAGTTGCCTAGCGTATTTGTACCACAGCTCACTCCAGGCCC -s Anc1.Anc1refChr2 53326 44 + 144309 TGACAGTTGCCTAGCGTATTTGTACCACAGCTCACTCCAGGCCC -s Anc2.Anc2refChr7 22034 44 + 32194 TCACAGTTGCCTAGCGCACTTGTACCACAGCTCACTCCAGGCCC -s mr.mrrefChr0 73101 44 + 130230 TGACAACTGCCCAGCATATCTGTACCACAGTACACTCCAGGTTC -s simCow_chr6.simCow.chr6 80319 43 + 602619 TCACGGTCGCCCAGCACACTTGT-TGACTGCTCACTTCAGGCGC -s simDog_chr6.simDog.chr6 77080 43 + 593897 TCACAGTTAGGTAGTG-ACTTGTACCACAGCTTACTCGGGCCCC -s simHuman_chr6.simHuman.chr6 74002 44 + 601863 TGACTGTTGCCAATCGTATTTGTACCACAGCTCATTCCAGGCCC -s simRat_chr6.simRat.chr6 69632 44 + 647215 TGACAATTGCCCAGCATATTTGTACCACAGCACACTCCAGGTTC - -a -s simMouse_chr6.simMouse.chr6 77339 22 + 636262 ATAGGCCTCCATTTCTAGATAC -s Anc0.Anc0refChr4 22029 12 - 45765 A-GT-----TACTTC----CAC -s Anc1.Anc1refChr2 53370 21 + 144309 A-GTGCCTCTACTTCCCCACAC -s Anc2.Anc2refChr7 22078 12 + 32194 A-GT-----TGCTTC----CAC -s mr.mrrefChr0 73145 22 + 130230 ATAGGCCTCCATTTCTAGATAC -s simCow_chr6.simCow.chr6 80362 12 + 602619 A-GT-----TGCTTC----CAC -s simDog_chr6.simDog.chr6 77128 3 + 593897 A-GT------------------ -s simHuman_chr6.simHuman.chr6 74046 21 + 601863 A-GTGCCTCTACTTCCCCACAC -s simRat_chr6.simRat.chr6 69676 22 + 647215 ATATGTCTCCATTTCCACATAT - -a -s simMouse_chr6.simMouse.chr6 77361 23 + 636262 TAGAATAATTATGTGaggattga -s Anc0.Anc0refChr4 22051 23 - 45765 TAAGATGGTTATGAGGGTACCGA -s Anc1.Anc1refChr2 53401 23 + 144309 TAAGATGGTTATGAGGGTACCGA -s Anc2.Anc2refChr7 22100 23 + 32194 AAAGATGGTTTTCAGGATCCCTA -s mr.mrrefChr0 73167 23 + 130230 TAGAATAATTATGTGaggattga -s simCow_chr6.simCow.chr6 80384 23 + 602619 AAAGATGGTTTTCAGGATCCCTA -s simDog_chr6.simDog.chr6 77131 1 + 593897 ----------------------A -s simHuman_chr6.simHuman.chr6 74077 23 + 601863 TAAGATGGTTATGAGGGCACCGA -s simRat_chr6.simRat.chr6 69698 23 + 647215 TAAAACAGTTATGTGaggattga - -a -s simMouse_chr6.simMouse.chr6 77384 4 + 636262 gact -s Anc0.Anc0refChr4 22076 4 - 45765 GGCT -s Anc1.Anc1refChr2 53426 4 + 144309 GGCT -s Anc2.Anc2refChr7 22125 4 + 32194 GGGT -s mr.mrrefChr0 73190 4 + 130230 gact -s simCow_chr6.simCow.chr6 80409 4 + 602619 GGGT -s simDog_chr6.simDog.chr6 77134 4 + 593897 GGGT -s simHuman_chr6.simHuman.chr6 74102 4 + 601863 GGCT -s simRat_chr6.simRat.chr6 69721 4 + 647215 gact - -a -s simMouse_chr6.simMouse.chr6 77388 75 + 636262 tgaggttgatcttattgttcggtgtagttcacatcacacctccagttcagtttcattgctcagatctcaggtccc -s Anc0.Anc0refChr4 22081 6 - 45765 TGAGGC--------------------------------------------------------------------- -s Anc1.Anc1refChr2 53431 6 + 144309 TGAGGC--------------------------------------------------------------------- -s Anc2.Anc2refChr7 22130 6 + 32194 TGAAAC--------------------------------------------------------------------- -s mr.mrrefChr0 73194 75 + 130230 tgaggttgatcttattgttcggtgtagttcacatcacacctccagttcagtttcattgctcagatctcaggtccc -s simCow_chr6.simCow.chr6 80414 6 + 602619 TGAAAC--------------------------------------------------------------------- -s simDog_chr6.simDog.chr6 77139 6 + 593897 TGAAAG--------------------------------------------------------------------- -s simHuman_chr6.simHuman.chr6 74107 6 + 601863 TGGGGC--------------------------------------------------------------------- -s simRat_chr6.simRat.chr6 69725 75 + 647215 ccaggttgatctacttgcttggtgtagttcacataacacctccagtttagtttcgtggctcagatctcaggtcCC - -a -s simMouse_chr6.simMouse.chr6 77463 169 + 636262 ccagactgaaggctgcttggatatcaagaaggaagtttggagttgttacaaaatacccttgtagtgtctcatcttcaagacttaatatacaccaaatagaagacttttacggtatgagcactggggggtgggcaaacagcttcaggatcgccaccccaaccaagtgcca -s mr.mrrefChr0 73269 169 + 130230 ccagactgaaggctgcttggatatcaagaaggaagtttggagttgttacaaaatacccttgtagtgtctcatcttcaagacttaatatacaccaaatagaagacttttacggtatgagcactggggggtgggcaaacagcttcaggatcgccaccccaaccaagtgcca -s simRat_chr6.simRat.chr6 69804 169 + 647215 CCGGACTGAAGGCTGCTGGGATATCAAGAAGGATGTTCAGAGTTGTTACAAAATACCCGTGCAGTGTCTCAGCTTTAAGACTTAACATACACCAAATAAaagacttttatggtatgagcagtgaggagtgggcaaacaccttcaggattgccacaccatctaagtgcta - -a -s simMouse_chr6.simMouse.chr6 77632 43 + 636262 gcattctttaagtagactgactatagacagaatgcagtggtgt -s mr.mrrefChr0 73438 43 + 130230 gcattctttaagtagactgactatagacagaatgcagtggtgt -s simRat_chr6.simRat.chr6 69975 43 + 647215 gtattctttaagtagactgattatagacaagatgcagtgatgt - -a -s simMouse_chr6.simMouse.chr6 77675 95 + 636262 aacttcacaaacacaaTGTCCCCTCCAAGTCACAAAGTGACCTGGTAGATGGCACCCACCAGAGACAACACTGCTATGGAAAGTTGCTTGAATCA -s Anc0.Anc0refChr4 22087 14 - 45765 ---------------------------------------------------------------------------------AGTTGATTGAAACA -s Anc1.Anc1refChr2 53437 14 + 144309 ---------------------------------------------------------------------------------AGTTGATTGAAACA -s Anc2.Anc2refChr7 22136 14 + 32194 ---------------------------------------------------------------------------------AGTTGATTGGAACA -s mr.mrrefChr0 73481 50 + 130230 aacttcacaaacacaaTGTCCCCTCCAAGTC---------------------------------------------TGGAAAGTTGCTTGAATCA -s simCow_chr6.simCow.chr6 80420 14 + 602619 ---------------------------------------------------------------------------------AGTTGATTGTAACG -s simDog_chr6.simDog.chr6 77145 14 + 593897 ---------------------------------------------------------------------------------ACTTGATTGGAACA -s simHuman_chr6.simHuman.chr6 74113 14 + 601863 ---------------------------------------------------------------------------------AGTTGATTGAACCA -s simRat_chr6.simRat.chr6 70024 50 + 647215 aacttcacaaacacgaTGTCCCCTCCAAGTC---------------------------------------------TGGAAAGTTAGTTGAATCA - -a -s simMouse_chr6.simMouse.chr6 77770 67 + 636262 CCTGCTTGGTTCTCAAATAGTACTGTAAGGTTGCCTGCTATTATTCGGTCTTACAATGCTGTGGAAT -s Anc0.Anc0refChr4 22101 67 - 45765 TTTACTTGGCTCTTCAACAATGATGTAAGGATGATTGCTAATACTTTGGCTCTTAATGTTATGACAT -s Anc1.Anc1refChr2 53451 67 + 144309 TTTACTTGGCTCTTCAACAATGATGTAAGGATGATTGCTAATACTTTGGCTCTTAATGTTATGACAT -s Anc2.Anc2refChr7 22150 67 + 32194 TTTACTTGACTCTTCAACAATGATGTAAGGAGGATTGCTAATACCTTGGCTCTTAGTGTTATGACAT -s mr.mrrefChr0 73531 67 + 130230 CCTGCTTGGTTCTCAAATAGTACTGTAAGGTTGCCTGCTATTATTCGGTCTTACAATGCTGTGGAAT -s simCow_chr6.simCow.chr6 80434 67 + 602619 CTTGCTTGATCCTTCAATAATGATGTAGGGAAGATTGCTAAGATCATGGCTCCTAGCGTTATGACAT -s simDog_chr6.simDog.chr6 77159 67 + 593897 TTTACTTGACTCTTCAACAATGATGTAAGGAGGATTACTAATACCTTGGCTCTTAGTGCTATGACTT -s simHuman_chr6.simHuman.chr6 74127 67 + 601863 ATAACTTGGCTCTTCAAGCATGAGGTAAAGATGATTGCTAGTACTTTGACTCTTAATGTTATGACAT -s simRat_chr6.simRat.chr6 70075 67 + 647215 CCAGTATGATTCTAAAACAGTAATGTAAGGGTGCCTTCTACTATTTTGTTCTACAATGCTATGGAAT - -a -s simMouse_chr6.simMouse.chr6 77837 95 + 636262 TGTTACCCTACTGGGGATTGCTTTTTTAGATTCTATTGCTAATAATATTACAACATCAGGTGTTGGAAGATCGAATTAAAGGGTGAGGTGACGGG -s Anc0.Anc0refChr4 22168 32 - 45765 TGCTATC------------------------------------------------TCAGGTGTTGGGAGAT------AAAGGTTAA--------- -s Anc1.Anc1refChr2 53518 32 + 144309 TGCTATC------------------------------------------------TCAGGTGTTGGGAGAT------AAAGGTTAA--------- -s Anc2.Anc2refChr7 22218 32 + 32194 TGCGATC------------------------------------------------TCAGGTGTTGGGAGAT------ACAGGTTAA--------- -s mr.mrrefChr0 73598 88 + 130230 TGTTACCCTACTGGGGATTGCTTTTTTAGATTCTATTGCTA-TAATATTACAACATCAGGTGTTGGAAGAT------AAAGGGTGAGGTGACGGG -s simCow_chr6.simCow.chr6 80502 32 + 602619 TGTGACC------------------------------------------------TCAGGTGTAGGGAGAT------ACAGGTTAG--------- -s simDog_chr6.simDog.chr6 77227 32 + 593897 CACGATC------------------------------------------------TCAGGTGTTGGGAGAT------CCAGGGTAA--------- -s simHuman_chr6.simHuman.chr6 74194 32 + 601863 TGCTTTC------------------------------------------------TCAGGTGCCCGGAGAC------AAAGGTCAA--------- -s simRat_chr6.simRat.chr6 70142 88 + 647215 TGCTACCCTAGTGGGGATTGCTTTTTTAAGTTCTCAGGCTA-CAATATTACAACCTCAGGTGTTGGAAGAT------AAAGGGTGAGATGATGGG - -a -s simMouse_chr6.simMouse.chr6 77932 32 + 636262 TGGACTAGTTCCAGGAAATCCCCTTTCTGTGT -s Anc0.Anc0refChr4 22200 29 - 45765 ---ACTAGTACCAAGCATCCCCCTTTATGTGT -s Anc1.Anc1refChr2 53550 29 + 144309 ---ACTAGTACCAAGCATCCCCCTTTATGTGT -s Anc2.Anc2refChr7 22250 29 + 32194 ---ACTAGTACCAAGCATCCCTCTTTATGTGT -s mr.mrrefChr0 73686 32 + 130230 TGGACTAGTTCCAGGAAATCCCCTTTCTGTGT -s simCow_chr6.simCow.chr6 80534 29 + 602619 ---ACTGGAGCCATCCCTTCCTCTTTATGTGT -s simDog_chr6.simDog.chr6 77259 29 + 593897 ---CCTAGTACCAAGCAGCCCTCATTATGTAT -s simHuman_chr6.simHuman.chr6 74226 29 + 601863 ---ACTAGTACCAAGCGTCCCCATTTATGTGT -s simRat_chr6.simRat.chr6 70231 32 + 647215 TGAACTGGTTCCAGGAATCCCACTTTATGTGT - -a -s simMouse_chr6.simMouse.chr6 77964 38 + 636262 GTGTGTGGCATGCTGATTGACTGCTTTTTTCTGTCTGT -s Anc0.Anc0refChr4 22236 38 - 45765 GAATGTGCCATGCTGATTTATTGCTTTTTTCTGTCTGT -s Anc1.Anc1refChr2 53586 38 + 144309 GAATGTGCCATGCTGATTTATTGCTTTTTTCTGTCTGT -s Anc2.Anc2refChr7 22286 38 + 32194 GAATGTGCCATGCTGATTTGTTGCTTTTTTCTGTCTGT -s mr.mrrefChr0 73718 38 + 130230 GTGTGTGGCATGCTGATTGACTGCTTTTTTCTGTCTGT -s simCow_chr6.simCow.chr6 80570 38 + 602619 TAGTGTGCTATGCTGATTTGTTGCTTTCCTCTGTCTGT -s simDog_chr6.simDog.chr6 77295 36 + 593897 GAATGTGCCCTGCTGATT--TTGTTTTTTTCTCGCTGT -s simHuman_chr6.simHuman.chr6 74262 38 + 601863 GAATGTGCCATGCTGATTTATTGCTTTTTCCTGTCTGT -s simRat_chr6.simRat.chr6 70263 38 + 647215 GTGTGGGCCCTGCTGGTTGACTGCTCTTTTCTATCTGT - -a -s simMouse_chr6.simMouse.chr6 78002 2 + 636262 AA -s Anc0.Anc0refChr4 22278 2 - 45765 AA -s Anc1.Anc1refChr2 53628 2 + 144309 AA -s Anc2.Anc2refChr7 22328 2 + 32194 AA -s mr.mrrefChr0 73756 2 + 130230 AA -s simCow_chr6.simCow.chr6 80612 2 + 602619 GA -s simDog_chr6.simDog.chr6 77335 2 + 593897 AA -s simHuman_chr6.simHuman.chr6 74305 2 + 601863 AA -s simRat_chr6.simRat.chr6 70301 2 + 647215 AT - -a -s simMouse_chr6.simMouse.chr6 78004 3 + 636262 CTA -s Anc0.Anc0refChr4 22280 3 - 45765 CTG -s Anc1.Anc1refChr2 53630 3 + 144309 CTG -s Anc2.Anc2refChr7 22330 3 + 32194 CTG -s mr.mrrefChr0 73758 3 + 130230 CTA -s simCow_chr6.simCow.chr6 80614 3 + 602619 CTG -s simDog_chr6.simDog.chr6 77337 3 + 593897 CTG -s simHuman_chr6.simHuman.chr6 74307 3 + 601863 CTG -s simRat_chr6.simRat.chr6 70349 3 + 647215 CTA - -a -s simMouse_chr6.simMouse.chr6 78007 4 + 636262 GATA -s Anc0.Anc0refChr4 22284 4 - 45765 GATA -s Anc1.Anc1refChr2 53634 4 + 144309 GATA -s Anc2.Anc2refChr7 22334 4 + 32194 GATA -s mr.mrrefChr0 73761 4 + 130230 GATA -s simCow_chr6.simCow.chr6 80618 4 + 602619 AATA -s simDog_chr6.simDog.chr6 77341 4 + 593897 GACA -s simHuman_chr6.simHuman.chr6 74311 4 + 601863 GATA -s simRat_chr6.simRat.chr6 70352 4 + 647215 GATA - -a -s simMouse_chr6.simMouse.chr6 78011 1 + 636262 C -s Anc0.Anc0refChr4 22288 1 - 45765 T -s Anc1.Anc1refChr2 53638 1 + 144309 T -s Anc2.Anc2refChr7 22338 1 + 32194 T -s mr.mrrefChr0 73765 1 + 130230 C -s simCow_chr6.simCow.chr6 80623 1 + 602619 T -s simDog_chr6.simDog.chr6 77345 1 + 593897 T -s simHuman_chr6.simHuman.chr6 74315 1 + 601863 T -s simRat_chr6.simRat.chr6 70356 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 78012 33 + 636262 CTATGTATCAGATTTTATGCACTATCAGCATAT -s Anc0.Anc0refChr4 22294 33 - 45765 GTATCTAGCCCATTATAATGGCTAGTTTAGACA -s Anc1.Anc1refChr2 53644 33 + 144309 GTATCTAGCCCATTATAATGGCTAGTTTAGACA -s Anc2.Anc2refChr7 22344 33 + 32194 GAATCTAGTCCATTATAATGGGTAGTTTAGACA -s mr.mrrefChr0 73766 33 + 130230 CTATGTATCAGATTTTATGCACTATCAGCATAT -s simCow_chr6.simCow.chr6 80629 31 + 602619 GAGTCTAGTCCATTATAATGGATAGTTTTGA-- -s simDog_chr6.simDog.chr6 77351 33 + 593897 GAATCTGGTTTATTATACTGGGTAGTTCAGACA -s simHuman_chr6.simHuman.chr6 74321 33 + 601863 GTATCTAGCCCATGATAATGGCTAGTCTAGCTA -s simRat_chr6.simRat.chr6 70357 33 + 647215 CTATGTATCAGATTTGATGCACCCTCACAATAC - -a -s simMouse_chr6.simMouse.chr6 78045 11 + 636262 TCTATGCACTA -s Anc0.Anc0refChr4 22327 11 - 45765 TCTGTGCACTA -s Anc1.Anc1refChr2 53677 11 + 144309 TCTGTGCACTA -s Anc2.Anc2refChr7 22377 11 + 32194 TCTGGGCACCA -s mr.mrrefChr0 73799 11 + 130230 TCTATGCACTA -s simCow_chr6.simCow.chr6 80660 10 + 602619 -TTGCACACAG -s simDog_chr6.simDog.chr6 77405 11 + 593897 TCTGGGCACCA -s simHuman_chr6.simHuman.chr6 74354 11 + 601863 TCTGTGCACTA -s simRat_chr6.simRat.chr6 70391 11 + 647215 TCTACCCAATG - -a -s simMouse_chr6.simMouse.chr6 78056 9 + 636262 TCAGCAATC -s Anc0.Anc0refChr4 22338 9 - 45765 TCAGCAATA -s Anc1.Anc1refChr2 53688 9 + 144309 TCAGCAATA -s Anc2.Anc2refChr7 22388 9 + 32194 TCAGCAATA -s mr.mrrefChr0 73810 9 + 130230 TCAGCAATC -s simCow_chr6.simCow.chr6 80670 9 + 602619 TCAGCAACA -s simDog_chr6.simDog.chr6 77448 9 + 593897 TCAGCAATG -s simHuman_chr6.simHuman.chr6 74365 9 + 601863 TAAGCAATA -s simRat_chr6.simRat.chr6 70402 9 + 647215 ACAGTAAGC - -a -s simMouse_chr6.simMouse.chr6 78065 13 + 636262 CATCTACCCAATG -s Anc0.Anc0refChr4 22347 13 - 45765 TATCTACTCAATG -s Anc1.Anc1refChr2 53697 13 + 144309 TATCTACTCAATG -s Anc2.Anc2refChr7 22397 13 + 32194 TATCTACTCAATG -s mr.mrrefChr0 73819 13 + 130230 CATCTACCCAATG -s simCow_chr6.simCow.chr6 80683 13 + 602619 TATCTACTCATTG -s simDog_chr6.simDog.chr6 77457 13 + 593897 TATTTACTCAATG -s simHuman_chr6.simHuman.chr6 74374 13 + 601863 TATCCAATCTGTG -s simRat_chr6.simRat.chr6 70415 13 + 647215 CATCTACCCAATG - -a -s simMouse_chr6.simMouse.chr6 78078 10 + 636262 ATAATAAATA -s Anc0.Anc0refChr4 22365 10 - 45765 ACAATAAATA -s Anc1.Anc1refChr2 53715 10 + 144309 ACAATAAATA -s Anc2.Anc2refChr7 22415 10 + 32194 ACAATAAATA -s mr.mrrefChr0 73832 10 + 130230 ATAATAAATA -s simCow_chr6.simCow.chr6 80701 10 + 602619 GTAATAAGTA -s simDog_chr6.simDog.chr6 77475 5 + 593897 AC-----ATA -s simHuman_chr6.simHuman.chr6 74392 10 + 601863 ACAACAAATA -s simRat_chr6.simRat.chr6 70428 10 + 647215 ACAATAAATA - -a -s simMouse_chr6.simMouse.chr6 78088 27 + 636262 AGCTGCAACAGGCAGGAAGGTGGCCTG -s Anc0.Anc0refChr4 22376 27 - 45765 AGTTGCATGAGGCAGGCTGGAAGCCAT -s Anc1.Anc1refChr2 53726 27 + 144309 AGTTGCATGAGGCAGGCTGGAAGCCAT -s Anc2.Anc2refChr7 22426 27 + 32194 AATTGCATGAGCCAAGCTGGAAGCCAT -s mr.mrrefChr0 73842 27 + 130230 AGCTGCAACAGGCAGGAAGGTGGCCTG -s simCow_chr6.simCow.chr6 80711 25 + 602619 --TTGCATGAGCCCAGCTGGAAACCAG -s simDog_chr6.simDog.chr6 77481 27 + 593897 AATCGCATGAGCCAAGCTGGTAGCCAT -s simHuman_chr6.simHuman.chr6 74403 27 + 601863 AGTTGTATGAGGCAGGCTGGAAGCCAA -s simRat_chr6.simRat.chr6 70438 27 + 647215 AACTGCAACAGGCCGGAAGGTGGCCTG - -a -s simMouse_chr6.simMouse.chr6 78115 325 + 636262 TCCAAATAACAAATAAGCCTTCACACAATCCATCATGCTCAGCTCCAATATAAGGCAGATGTGGCCATGTACATGTGGTAGGTAGGTCGGCTCTGAGCTCCTCAGGTGGCCAATCACCATCTAGCTTCAGTGCAAATTCTAGTTGAGTAATAGATCCCCAACATCCTTTTAATGGGCCCGATAGCACCCCCCATTTGGATCCAGGGACTAGTGGGCAGTTAATCTTTTGCTCTAGCCCATGCGTATCAATAATTAGAAATTTCGGCAGCCTACCTTATTTATTGGGTCGGGAATATGATATAATCCGCCCTGCTCCACACTCCCA -s Anc0.Anc0refChr4 22475 20 - 45765 CCCATATAAC------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TT-----------------------------------------------------------TGCTTCTA -s Anc1.Anc1refChr2 53825 20 + 144309 CCCATATAAC------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TT-----------------------------------------------------------TGCTTCTA -s Anc2.Anc2refChr7 22525 20 + 32194 CAGATAGAAC------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TT-----------------------------------------------------------TGCTTCTA -s mr.mrrefChr0 73869 234 + 130230 TCCAAATAACAAATAAGCCTTCACACAATCCATCATGCTCAGCTCCAATATAAGGCAGATGTGGCCATGTACATGTGGTAGGTAG-TCGGCTCTGAGCTCCTCAGGTGGCCAATCACCATCTAGCTTCAGTGCAAATTCTAGTTGAGT-------------------------------GATAGCACCCCCCATTTGGATCCAGGGACTAGTGGGCAGTTAATCTTTTGCTCTAGCCCATGCGTATCAATAATTAGAA-----------------------------------------------------------TGCTTCCA -s simCow_chr6.simCow.chr6 80806 20 + 602619 CAGATAGCAC------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TT-----------------------------------------------------------TGCTTCTA -s simDog_chr6.simDog.chr6 77580 20 + 593897 CAGATAGAAC------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AT-----------------------------------------------------------TGCTTCTC -s simHuman_chr6.simHuman.chr6 74502 20 + 601863 CCCAGATAAC------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TT-----------------------------------------------------------TGCTTCTA -s simRat_chr6.simRat.chr6 70465 234 + 647215 TCTAAATAACAAGCAAGCTTTCACACAATGCATCATGCCAAGCTCCATTACAAGGCAAACATGGTCATGTACATGTGGTAAGTAC-TTGGCTCTGAGCCCCTCAGGTGGCCAATCACCATCTAGCTTCAGGGCAAATTCTAGCTAAGT-------------------------------TATAGCACCCCCCATTTGGATCCAGGCACAAAAGGGGAGTTTGTCTCTTGCTCTAGCCCATGTGTATCGAAAATTGGAA-----------------------------------------------------------TGCTTCCA - -a -s simMouse_chr6.simMouse.chr6 78440 6 + 636262 TGGGCA -s Anc0.Anc0refChr4 22500 6 - 45765 TGCACA -s Anc1.Anc1refChr2 53850 6 + 144309 TGCACA -s Anc2.Anc2refChr7 22550 6 + 32194 TGCACA -s mr.mrrefChr0 74103 6 + 130230 TGGGCA -s simCow_chr6.simCow.chr6 80831 6 + 602619 TGCCCA -s simDog_chr6.simDog.chr6 77605 6 + 593897 TGCACA -s simHuman_chr6.simHuman.chr6 74527 6 + 601863 TGCACA -s simRat_chr6.simRat.chr6 70699 6 + 647215 TGGGCA - -a -s simMouse_chr6.simMouse.chr6 78446 7 + 636262 TCACAAA -s Anc0.Anc0refChr4 22506 7 - 45765 TCACAAA -s Anc1.Anc1refChr2 53856 7 + 144309 TCACAAA -s Anc2.Anc2refChr7 22556 7 + 32194 TCACAAA -s mr.mrrefChr0 74109 7 + 130230 TCACAAA -s simCow_chr6.simCow.chr6 80839 7 + 602619 TCACAAG -s simDog_chr6.simDog.chr6 77611 7 + 593897 TCACAAA -s simHuman_chr6.simHuman.chr6 74533 7 + 601863 TCACAAA -s simRat_chr6.simRat.chr6 70705 7 + 647215 TCACAGA - -a -s simMouse_chr6.simMouse.chr6 78453 16 + 636262 TTATAAGACAAGTAAT -s Anc0.Anc0refChr4 22513 16 - 45765 TTATAAGACAAGTAGT -s Anc1.Anc1refChr2 53863 16 + 144309 TTATAAGACAAGTAGT -s Anc2.Anc2refChr7 22563 16 + 32194 TTATAGGACAAGCAAT -s mr.mrrefChr0 74116 16 + 130230 TTATAAGACAAGTAGT -s simCow_chr6.simCow.chr6 80847 12 + 602619 TTATAGGACAA----T -s simDog_chr6.simDog.chr6 77618 16 + 593897 TTATAGGACAAGCAAG -s simHuman_chr6.simHuman.chr6 74540 16 + 601863 TTATAAGACAAATGGT -s simRat_chr6.simRat.chr6 70712 16 + 647215 TTAGAAGACAAGTAGT - -a -s simMouse_chr6.simMouse.chr6 78469 3 + 636262 AGA -s Anc0.Anc0refChr4 22529 3 - 45765 TGA -s Anc1.Anc1refChr2 53879 3 + 144309 TGA -s Anc2.Anc2refChr7 22583 3 + 32194 TGA -s mr.mrrefChr0 74132 3 + 130230 AGA -s simCow_chr6.simCow.chr6 80863 3 + 602619 AAA -s simDog_chr6.simDog.chr6 77638 3 + 593897 TGA -s simHuman_chr6.simHuman.chr6 74556 3 + 601863 GGA -s simRat_chr6.simRat.chr6 70728 3 + 647215 AGA - -a -s simMouse_chr6.simMouse.chr6 78472 13 + 636262 ACTTATCTTGCCT -s Anc0.Anc0refChr4 22532 13 - 45765 GTTTATTTTTCCT -s Anc1.Anc1refChr2 53882 13 + 144309 GTTTATTTTTCCT -s Anc2.Anc2refChr7 22586 13 + 32194 GTTTATTTTTCCT -s mr.mrrefChr0 74135 13 + 130230 ACTTATCTTGCCT -s simCow_chr6.simCow.chr6 80866 13 + 602619 GCTTATTTTACCT -s simDog_chr6.simDog.chr6 77641 13 + 593897 GTTTATTTTTCCT -s simHuman_chr6.simHuman.chr6 74559 3 + 601863 G----------CT -s simRat_chr6.simRat.chr6 70751 13 + 647215 ACTTATCTTGCCT - -a -s simMouse_chr6.simMouse.chr6 78485 14 + 636262 CTACCCTAAAAAAA -s Anc0.Anc0refChr4 22547 14 - 45765 ACTCAGTTGAGCCA -s Anc1.Anc1refChr2 53897 14 + 144309 ACTCAGTTGAGCCA -s Anc2.Anc2refChr7 22601 14 + 32194 ACTCAGTTGAGCCA -s mr.mrrefChr0 74150 14 + 130230 ATACACTTAAACAA -s simCow_chr6.simCow.chr6 80881 14 + 602619 ACTCAGTTGAGTCA -s simDog_chr6.simDog.chr6 77656 14 + 593897 ACTCAGCTGCGCCA -s simHuman_chr6.simHuman.chr6 74564 14 + 601863 ACTCATTTGAGCCA -s simRat_chr6.simRat.chr6 70766 14 + 647215 ATACAGTTAGACAA - -a -s simMouse_chr6.simMouse.chr6 78499 77 + 636262 AAAAAAAGCCCAAGCCAAAAAAAGCTTAAAGGTAGTTATGTAGCTCTCAACAAGCACCTTTGGGCGAAGTGGTAAAC -s Anc0.Anc0refChr4 22573 58 - 45765 -------------ATCAAAGGAAGCTAAAAGGTAG-TCTGTAGCAGTTAATTA-----TTCAGGTGAAGTCATATGC -s Anc1.Anc1refChr2 53923 59 + 144309 -------------ATCAAAGGAAGCTAAAAGGTAGTTCTGTAGCAGTTAATTA-----TTCAGGTGAAGTCATATGC -s Anc2.Anc2refChr7 22631 58 + 32194 -------------CTCAAAGGAAGCTAAATGCTAG-TCTGTAGCAGTTAATTA-----TACAGGTGAAGTCATATGC -s mr.mrrefChr0 74176 77 + 130230 AAAAAAAGCCCAAACCAAAAAAAGCTTAAAGGTAGTTATGTAGCTGTCAACAAGCACCTTTGGGCGAAGTGGTAAAC -s simCow_chr6.simCow.chr6 80911 58 + 602619 -------------CTCAAAGTAAGCTAAATGCTAG-TCTTTAGCAAACAATTA-----TGCAGGTGCAGTCATATGC -s simDog_chr6.simDog.chr6 77686 49 + 593897 -------------CCCAAAGGAGGCTA----------CTGTAGTGGTTAATTA-----TACAGGTGAAAGAATATGC -s simHuman_chr6.simHuman.chr6 74590 59 + 601863 -------------ATCAAGTGAAGCTATCACGTAGTTCCGTAGCAGTTAATTA-----TTCAGGTGTAGTCTTATGC -s simRat_chr6.simRat.chr6 70795 77 + 647215 AAAAAAAGCCAAAACCAAAAAAAGCTTAAAGGTAGTTATGCAGCTGTCAACAAGCAACTGTGGTGAAAGTGGTAAAC - -a -s simMouse_chr6.simMouse.chr6 78576 2 + 636262 CA -s Anc0.Anc0refChr4 22639 2 - 45765 CT -s Anc1.Anc1refChr2 53990 2 + 144309 CT -s Anc2.Anc2refChr7 22697 2 + 32194 CT -s mr.mrrefChr0 74253 2 + 130230 CA -s simCow_chr6.simCow.chr6 80977 2 + 602619 CT -s simDog_chr6.simDog.chr6 77743 2 + 593897 CT -s simHuman_chr6.simHuman.chr6 74657 2 + 601863 CT -s simRat_chr6.simRat.chr6 70872 2 + 647215 CA - -a -s simMouse_chr6.simMouse.chr6 78578 78 + 636262 TGTTAACGATAAGGCAGCAGAGTTTGGTCCGGGTCTGTGCAGGGAAAGAATTGCTGGCTTAGACCAAAGTTTATCACA -s Anc0.Anc0refChr4 22641 29 - 45765 TGCTAA----------------------------------------------GCTG---TAGACTTGGCTTTATCATG -s Anc1.Anc1refChr2 53992 29 + 144309 TGCTAA----------------------------------------------GCTG---TAGACTTGGCTTTATCATG -s Anc2.Anc2refChr7 22699 29 + 32194 TGCTAA----------------------------------------------GCTG---TAGACTTGGCATTGCCATG -s mr.mrrefChr0 74255 72 + 130230 TGTTAACGA-----CAGCAGAGTTTGGTCCGGGTCTGTGCAGGGAAAGAATTGCTG-CTTAGACCAGAGTTTATCACA -s simCow_chr6.simCow.chr6 80981 29 + 602619 TGCTAA----------------------------------------------CCTC---TAGACTTGGGATTGCCATG -s simDog_chr6.simDog.chr6 77745 28 + 593897 TTCTAG----------------------------------------------GCTG---TAGACTTAGCATTGCCA-G -s simHuman_chr6.simHuman.chr6 74659 29 + 601863 TGCTAA----------------------------------------------GCTG---TAGACTTGGTTTTATGATG -s simRat_chr6.simRat.chr6 70874 72 + 647215 TGTTAGCAA-----CAGTAGAGTTTGGTTGGGGTGTGTGGAGGGAAAGAATTGCCG-CTTAGACCAGAGTTTACCACA - -a -s simMouse_chr6.simMouse.chr6 78656 8 + 636262 TGCTAGCT -s Anc0.Anc0refChr4 22673 8 - 45765 TGCTGGCT -s Anc1.Anc1refChr2 54024 8 + 144309 TGCTGGCT -s Anc2.Anc2refChr7 22731 8 + 32194 TGCTGCTT -s mr.mrrefChr0 74327 8 + 130230 TGCTAGCT -s simCow_chr6.simCow.chr6 81010 8 + 602619 CGCTGCTT -s simDog_chr6.simDog.chr6 77776 8 + 593897 TGCTGCTT -s simHuman_chr6.simHuman.chr6 74691 8 + 601863 TGCTTGCT -s simRat_chr6.simRat.chr6 70946 8 + 647215 TGCTAACT - -a -s simMouse_chr6.simMouse.chr6 78664 35 + 636262 GTAGCCTTGGTGCCTAGTCTGTGTGGAATGGCAAT -s Anc0.Anc0refChr4 22685 35 - 45765 GTAGCTTAGGTGCCTAGTCTGTTACTATTATGAAA -s Anc1.Anc1refChr2 54036 35 + 144309 GTAGCTTAGGTGCCTAGTCTGTTACTATTATGAAA -s Anc2.Anc2refChr7 22743 35 + 32194 GTAGCTTAGGTGCCCAGTGAATTACTATCATGAAA -s mr.mrrefChr0 74339 35 + 130230 GTAGCTTTGGTGCCTAGTCTGTGTCGAATGGCAAT -s simCow_chr6.simCow.chr6 81022 33 + 602619 GTAGCTCTGGTGAGCAGTTGAT--ATGTCATGAAA -s simDog_chr6.simDog.chr6 77788 35 + 593897 GTAGTTTAGGTGCCCAGTGAATTACTAACAGGAAA -s simHuman_chr6.simHuman.chr6 74704 35 + 601863 GTGGCTTCGGTGCCTAAACTGTTCCAATTATGAAA -s simRat_chr6.simRat.chr6 70958 35 + 647215 GTAGCTTTGGTGCCTAGCCTATGTCTAATGGCGTT - -a -s simMouse_chr6.simMouse.chr6 78699 82 + 636262 CCCACCATATCATTGTTGCACTGATGCTGTTTTCATATATTCTTTGTACATCCTATGCAACATAAATTTTTAGTTTGCTCAC -s Anc0.Anc0refChr4 22721 80 - 45765 CCCAATATATCACTGTAGCACCTATACTGTTTCCATACATTCTTTGAACATTTTATGCCTCTTAAA--TTTACCTTGCTCTC -s Anc1.Anc1refChr2 54072 80 + 144309 CCCAATATATCACTGTAGCACCTATACTGTTTCCATACATTCTTTGAACATTTTATGCCTCTTAAA--TTTACCTTGCTCTC -s Anc2.Anc2refChr7 22779 80 + 32194 CCCAATATATCACTGTAGCACCTATACTGTTTCCATGCATTCTTTGAACATTTTATGCCTCTGAAA--TTTACCTTGCTCTC -s mr.mrrefChr0 74375 82 + 130230 CCCACCATATCATTGTTGCACTTATGCTGTTTTCATACATTCTTTGTACATCTTATGCCACATAAATTTTTAGCTTGCTCAC -s simCow_chr6.simCow.chr6 81056 80 + 602619 CTCAATATATCACTGAAGCACCTATACTGTTTGTGTCCATTCTTTAAACATTTTATGCCTCTGAAA--TTCACCTTACTCTC -s simDog_chr6.simDog.chr6 77824 80 + 593897 CCCATTATATCACTGTAGCTCCTATACTGTTTCCATGCATTCTTCGAACATCTTATGCCTCTGAAC--CTTACCATGCTCCC -s simHuman_chr6.simHuman.chr6 74740 80 + 601863 CCCAATGTATCTCTATAGCACCTATACTGCTTCCACACTTTCTTTGAACACTTTATGCCTCTTAGA--TTTACCTTGCTCTC -s simRat_chr6.simRat.chr6 70994 82 + 647215 CCTACCATATCATTTTTGCACTTATGCTATTTTCATACATTCTTTGTACATCTTATGCCACACAAATTTTTAGCTTGTCTAC - -a -s simMouse_chr6.simMouse.chr6 78781 17 + 636262 TATCTAGTATATACAGT -s Anc0.Anc0refChr4 22801 17 - 45765 TATCCAGTATTTACAGT -s Anc1.Anc1refChr2 54152 17 + 144309 TATCCAGTATTTACAGT -s Anc2.Anc2refChr7 22860 17 + 32194 TATCCATTATTTACAGT -s mr.mrrefChr0 74457 17 + 130230 TATCTAGTATATACAGT -s simCow_chr6.simCow.chr6 81137 15 + 602619 TCTCCATTATTTACC-- -s simDog_chr6.simDog.chr6 77905 17 + 593897 TATCCATTAATTACAGT -s simHuman_chr6.simHuman.chr6 74820 17 + 601863 TATTCTGTGTTTACAGT -s simRat_chr6.simRat.chr6 71076 17 + 647215 TATCTAATATATACAGT - -a -s simMouse_chr6.simMouse.chr6 78798 27 + 636262 CTTACACCAACCGATAACAGCTGTTTC -s Anc0.Anc0refChr4 22818 27 - 45765 TTTATGCCAAGCAATCACAGATGTTTC -s Anc1.Anc1refChr2 54169 27 + 144309 TTTATGCCAAGCAATCACAGATGTTTC -s Anc2.Anc2refChr7 22877 27 + 32194 TTCAAGGCCAGTAATCACAGATGTCGG -s mr.mrrefChr0 74474 27 + 130230 TTTATACCAACCGATAACAGCTGTTTC -s simDog_chr6.simDog.chr6 77922 27 + 593897 TTCAAGGCCAGTAATCACAGATGTCGG -s simHuman_chr6.simHuman.chr6 74863 27 + 601863 TTTATGCCAAGCAATCATGGATGTTTC -s simRat_chr6.simRat.chr6 71093 27 + 647215 TTTATACCAAACGATGACAGCTGTTTC - -a -s simMouse_chr6.simMouse.chr6 78825 13 + 636262 TTTGAGACCAGTG -s Anc0.Anc0refChr4 22846 13 - 45765 ACAGGGTCCAGTG -s Anc1.Anc1refChr2 54197 13 + 144309 ACAGGGTCCAGTG -s Anc2.Anc2refChr7 22905 13 + 32194 ACAGGGTCCAGTG -s mr.mrrefChr0 74501 13 + 130230 TTTGAGACCAGTG -s simDog_chr6.simDog.chr6 77950 13 + 593897 ACAGGGTCCAGTG -s simHuman_chr6.simHuman.chr6 74891 13 + 601863 ACAAGTTCCAGTG -s simRat_chr6.simRat.chr6 71120 13 + 647215 TGTGAGACCAGTG - -a -s simMouse_chr6.simMouse.chr6 78838 170 + 636262 CTTTTGGAAGCCTTTCATTTATAATGTGGGTACAAGTAAGGTGCATTTCTCATCACTTTGCAGTTTTTGTAGCTTATATCATTTTCATAACATTAATTACATCATCTTAAAGTTTATACAGTTATGATGTTTTAACAGGCTGGCGTTGGCTTCGGCTTATGTCTAAGTGT -s Anc0.Anc0refChr4 22867 89 - 45765 CTTGGGGAGGCTTCTCTTTTATAACTTGGGTAGTTGTGTGGTGGATTTCTTATCACTCTGAGATTTGTGTAG--TGCATCAGATTTTTGAA------------------------------------------------------------------------------- -s Anc1.Anc1refChr2 54218 89 + 144309 CTTGGGGAGGCTTCTCTTTTATAACTTGGGTAGTTGTGTGGTGGATTTCTTATCACTCTGAGATTTGTGTAG--TGCATCAGATTTTTGAA------------------------------------------------------------------------------- -s Anc2.Anc2refChr7 22926 89 + 32194 TTTGGGAAGGCTTCTCTTTTATATCTTTGGTAGTCATGTGGTTGATTTCTTAACACTCTCAGATTTGTGTAG--AGCATCAGATTTTTGAA------------------------------------------------------------------------------- -s mr.mrrefChr0 74514 169 + 130230 CTTTTGGAAGCCTTTCATTTATAATGTGGGTACATGTGAGGTGGATTTCTTATCACTTTGCAGTTTTTGTAGCTTGTATCATTTTCATAACATTAATTACATCATCTTAAAGTTTATACAGT-ATGATGTTTTAACAGGCTGGCGTTGGCTTCGGCTTATGTCTAAGTGT -s simCow_chr6.simCow.chr6 81152 75 + 602619 --------------TCTTTTATATATCTGGGAGTCATGTGGTATATTTCTTACCACTTTAAAATTTGTGTAG--AGTATTAGCTTTCTGAC------------------------------------------------------------------------------- -s simDog_chr6.simDog.chr6 77971 88 + 593897 TTTGGGAAGGCTTCTCTTTTATATCTTTGGTAGTC-TGTGGTTGATTTCTTAACACTCCCAGATCTATGTAG--AGCATCTGATTTTTGAA------------------------------------------------------------------------------- -s simHuman_chr6.simHuman.chr6 74912 89 + 601863 CTTGCAGAGGTATCTGTTTTATAACTTGGGCAATTGTGTGGTGGATTTCCTATGACACTGAGATTTGTGCGG--TGCATCAGATTTTTGAA------------------------------------------------------------------------------- -s simRat_chr6.simRat.chr6 71133 169 + 647215 TTTTTGGAAGCCTTTCATTTGTAATGTGGGTACATGTGGGATGGATTTCTTATCACTTTGCAGTTTTTGTCACATGTACCATTTTCTTGGCCTTAATTACATCATCTTTAGGTTTATACAAT-ATGATGTTTTAACAGGCTGGCCTTGGCTTCAGCTTACATCTAAATGT - -a -s simMouse_chr6.simMouse.chr6 79008 11 + 636262 ACCTGTGTGGA -s Anc0.Anc0refChr4 22973 11 - 45765 AAGTATGTGGA -s Anc1.Anc1refChr2 54324 11 + 144309 AAGTATGTGGA -s Anc2.Anc2refChr7 23032 11 + 32194 AAGGATGTGGA -s mr.mrrefChr0 74700 11 + 130230 ACCTATGTGGA -s simCow_chr6.simCow.chr6 81244 11 + 602619 GACCATATGGA -s simDog_chr6.simDog.chr6 78076 11 + 593897 AAGGTTGTGGA -s simHuman_chr6.simHuman.chr6 75018 11 + 601863 AGATATGTGGA -s simRat_chr6.simRat.chr6 71321 11 + 647215 ACCCACGTGGA - -a -s simMouse_chr6.simMouse.chr6 79019 7 + 636262 CAGTACT -s Anc0.Anc0refChr4 22984 7 - 45765 CACTACT -s Anc1.Anc1refChr2 54335 7 + 144309 CACTACT -s Anc2.Anc2refChr7 23043 7 + 32194 CACTACT -s mr.mrrefChr0 74711 7 + 130230 CAGTACT -s simCow_chr6.simCow.chr6 81256 7 + 602619 CACTACT -s simDog_chr6.simDog.chr6 78087 7 + 593897 CACTACT -s simHuman_chr6.simHuman.chr6 75029 7 + 601863 TGCTACT -s simRat_chr6.simRat.chr6 71332 7 + 647215 CAGTACT - -a -s simMouse_chr6.simMouse.chr6 79026 4 + 636262 GACA -s Anc0.Anc0refChr4 22992 4 - 45765 GACA -s Anc1.Anc1refChr2 54343 4 + 144309 GACA -s Anc2.Anc2refChr7 23051 4 + 32194 AACA -s mr.mrrefChr0 74718 4 + 130230 GACA -s simCow_chr6.simCow.chr6 81264 4 + 602619 AACA -s simDog_chr6.simDog.chr6 78095 4 + 593897 AACA -s simHuman_chr6.simHuman.chr6 75038 4 + 601863 GCCA -s simRat_chr6.simRat.chr6 71339 4 + 647215 GACA - -a -s simMouse_chr6.simMouse.chr6 79030 24 + 636262 TTGCTTCACTGCCTGCTTCCTAAA -s Anc0.Anc0refChr4 22997 24 - 45765 TCACTTTACTGCCTGCTTCCTATA -s Anc1.Anc1refChr2 54348 24 + 144309 TCACTTTACTGCCTGCTTCCTATA -s Anc2.Anc2refChr7 23056 24 + 32194 TCACTTTACTGCCTGCTTCCTATA -s mr.mrrefChr0 74722 24 + 130230 TTGCTTCACTGCCTGCTTCCTATA -s simCow_chr6.simCow.chr6 81269 22 + 602619 TCACTTTACTGGCTGCTT--TATA -s simDog_chr6.simDog.chr6 78100 24 + 593897 TCACTTTACTGCCTGCTTCCTACG -s simHuman_chr6.simHuman.chr6 75043 24 + 601863 TCACTTTACTGCCTGCTTCCGATA -s simRat_chr6.simRat.chr6 71343 23 + 647215 TTGCT-CACTGCCTGCTTTCTATA - -a -s simMouse_chr6.simMouse.chr6 79054 25 + 636262 TATGTATATTTCTTTTAGGTGTTTA -s Anc0.Anc0refChr4 23021 25 - 45765 TACTATTATTTCTTCTATGAGTTTC -s Anc1.Anc1refChr2 54372 25 + 144309 TACTATTATTTCTTCTATGAGTTTC -s Anc2.Anc2refChr7 23080 25 + 32194 TACTATTATTTCTTCTATGAGTTTC -s mr.mrrefChr0 74746 25 + 130230 TATGTATATTTCTTTTAGGTGTTTA -s simCow_chr6.simCow.chr6 81291 25 + 602619 AACCAGTATTCCTTCTATGAGTTTC -s simDog_chr6.simDog.chr6 78136 25 + 593897 TACTATCATTTCTTCTATGAGTTTC -s simHuman_chr6.simHuman.chr6 75067 25 + 601863 TACTATTATTTCTTCTATGAGATTC -s simRat_chr6.simRat.chr6 71366 25 + 647215 TATGTATAATTCTTTTAGGTGTTTA - -a -s simMouse_chr6.simMouse.chr6 79079 10 + 636262 CATCCTCTCA -s Anc0.Anc0refChr4 23046 10 - 45765 CCTCCTGTCT -s Anc1.Anc1refChr2 54397 10 + 144309 CCTCCTGTCT -s Anc2.Anc2refChr7 23105 10 + 32194 CCTCCTGTCT -s mr.mrrefChr0 74771 10 + 130230 CATCCTGTCA -s simCow_chr6.simCow.chr6 81322 10 + 602619 CCTCTTGTCT -s simDog_chr6.simDog.chr6 78161 10 + 593897 CCTCCTGTCT -s simHuman_chr6.simHuman.chr6 75092 10 + 601863 ACACCTGCCT -s simRat_chr6.simRat.chr6 71391 10 + 647215 CATCCTGTCA - -a -s simMouse_chr6.simMouse.chr6 79089 10 + 636262 TCACACAGCG -s Anc0.Anc0refChr4 23056 10 - 45765 TCACTAAGAG -s Anc1.Anc1refChr2 54407 10 + 144309 TCACTAAGAG -s Anc2.Anc2refChr7 23115 10 + 32194 TCACTAAGAG -s mr.mrrefChr0 74781 10 + 130230 TCACAAAGCG -s simCow_chr6.simCow.chr6 81336 10 + 602619 TCACTAAGCA -s simDog_chr6.simDog.chr6 78171 10 + 593897 TCATGAAGAG -s simHuman_chr6.simHuman.chr6 75102 10 + 601863 TCACTAAGAG -s simRat_chr6.simRat.chr6 71401 10 + 647215 TCACAAAGGG - -a -s simMouse_chr6.simMouse.chr6 79099 36 + 636262 CCACACTGGTTACTTACTTCTAAAACACTAGCGATG -s Anc0.Anc0refChr4 23067 36 - 45765 CCACTCTGATTACTTATGTCTGAAACTTTAGCAATA -s Anc1.Anc1refChr2 54418 36 + 144309 CCACTCTGATTACTTATGTCTGAAACTTTAGCAATA -s Anc2.Anc2refChr7 23126 36 + 32194 CCTCTCTGATTACTTATGTCTGAAACTTTAGAAATA -s mr.mrrefChr0 74791 36 + 130230 CCACACTGATTACTTATTTCTAAAACACTAGCAATG -s simCow_chr6.simCow.chr6 81347 36 + 602619 CCTTTCTTACTACTTATGTCTGAAACCTTAGAAATA -s simDog_chr6.simDog.chr6 78182 36 + 593897 CCTCCCTGATTTCTTATGTCTGAAACTTTAGAAATA -s simHuman_chr6.simHuman.chr6 75113 36 + 601863 CCACTCTGATTACTTATGTCTGAAGCGTTGGCAATA -s simRat_chr6.simRat.chr6 71411 36 + 647215 GCACACTAATTACTTATTTTTAAAACACTAGCAACG - -a -s simMouse_chr6.simMouse.chr6 79135 7 + 636262 GCTCCAC -s Anc0.Anc0refChr4 23103 7 - 45765 GCAATAC -s Anc1.Anc1refChr2 54454 7 + 144309 GCAATAC -s Anc2.Anc2refChr7 23162 7 + 32194 GCAATAC -s mr.mrrefChr0 74827 7 + 130230 GCTCCAC -s simCow_chr6.simCow.chr6 81383 7 + 602619 GTCTGAC -s simDog_chr6.simDog.chr6 78221 7 + 593897 acaatac -s simHuman_chr6.simHuman.chr6 75149 7 + 601863 GCAATAC -s simRat_chr6.simRat.chr6 71447 7 + 647215 GCTCCAC - -a -s simMouse_chr6.simMouse.chr6 79142 10 + 636262 CTACAACTTT -s Anc0.Anc0refChr4 23110 9 - 45765 TTGCAA-TTT -s Anc1.Anc1refChr2 54461 9 + 144309 TTGCAA-TTT -s Anc2.Anc2refChr7 23169 9 + 32194 TTGCAA-TTT -s mr.mrrefChr0 74834 10 + 130230 CTACAACTTT -s simCow_chr6.simCow.chr6 81390 9 + 602619 ATGTGT-TTT -s simDog_chr6.simDog.chr6 78509 9 + 593897 tGTCAA-TCT -s simHuman_chr6.simHuman.chr6 75156 9 + 601863 TTGCAA-TTT -s simRat_chr6.simRat.chr6 71454 10 + 647215 CTAGAACTTT - -a -s simMouse_chr6.simMouse.chr6 79152 75 + 636262 TCTACTTTTTACTCCTAACTCTATCATCTGGGCTTTGTTAAACTCAACATGTGTTCTTTGCTTGCTGGCTTACTC -s Anc0.Anc0refChr4 23119 75 - 45765 TACAATCTTTACTGCGAATTCTATTATCTGGGTTTTTTTAAGTTCGACCTCTGTTCAATATTTTTATGCCTGCCC -s Anc1.Anc1refChr2 54470 75 + 144309 TACAATCTTTACTGCGAATTCTATTATCTGGGTTTTTTTAAGTTCGACCTCTGTTCAATATTTTTATGCCTGCCC -s Anc2.Anc2refChr7 23178 75 + 32194 TACAATCTTTACTGCGAATTCTATTATCTGGTTTTTTTTAAGTTCGACCTCTGTTCAATATCTTTATGCCTGCCC -s mr.mrrefChr0 74844 75 + 130230 TCTACTTTTTACTGCTAACTCTATCATCTGGGCTTTGTTAAACTCAACATGTGTTCTTTGCTTGTTGGCTTACTC -s simCow_chr6.simCow.chr6 81400 68 + 602619 TCTAATCTTTACTGCGAATTCTATCATCTGGATTTTTCCTAGTCCAACCCCTGTT-------TTGTTGCCTGCCT -s simDog_chr6.simDog.chr6 78518 65 + 593897 TACAACGT----------GTCTACTTTTCAGTTGTTTTTAAGATCGCCCTCTGTTCAATATCTTTATCCTTGCTC -s simHuman_chr6.simHuman.chr6 75165 75 + 601863 CAGGATCTTAACTGCAAATTCTATGATCTGGGTTTTTTTAAGTTCCACCTTTGTTCAATATTTTTATGCCTGCCC -s simRat_chr6.simRat.chr6 71464 66 + 647215 TCTACTTTGTACTGCTAACTCTATCAGCTGGGCTTTGTTAAACTCAGC---------TTGCTTGTTGGCTTACTC - -a -s simMouse_chr6.simMouse.chr6 79227 3 + 636262 TAA -s Anc0.Anc0refChr4 23194 3 - 45765 TAA -s Anc1.Anc1refChr2 54545 3 + 144309 TAA -s Anc2.Anc2refChr7 23253 3 + 32194 TAA -s mr.mrrefChr0 74919 3 + 130230 TAA -s simCow_chr6.simCow.chr6 81469 3 + 602619 TAA -s simDog_chr6.simDog.chr6 78583 3 + 593897 TAC -s simHuman_chr6.simHuman.chr6 75240 3 + 601863 TAA -s simRat_chr6.simRat.chr6 71530 3 + 647215 TAA - -a -s simMouse_chr6.simMouse.chr6 79230 29 + 636262 AAGGCTGAAACAGTTATGTCTATGTATGT -s Anc0.Anc0refChr4 23197 28 - 45765 AAGGCTGACATCATTGTGGCCATGTA-TG -s Anc1.Anc1refChr2 54548 29 + 144309 AAGGCTGACATCATTGTGGCCATGTATTG -s Anc2.Anc2refChr7 23256 28 + 32194 AAGGCTGACATCATGGTGGCCATGTG-TG -s mr.mrrefChr0 74922 29 + 130230 AAGGCTGAAATCATTGTGGCTATGTATGT -s simCow_chr6.simCow.chr6 81472 28 + 602619 AAGACTGACATCATAGTGGCCATGTG-TG -s simDog_chr6.simDog.chr6 78589 28 + 593897 AAGGCTGACATCCTGCTGGCCATGTG-TG -s simHuman_chr6.simHuman.chr6 75243 27 + 601863 AAGTCTG--ATCATTGTGGCCATGCATTG -s simRat_chr6.simRat.chr6 71533 29 + 647215 AAGGCTGTAATCATTGTGGCTTTGTATGT - -a -s simMouse_chr6.simMouse.chr6 79259 22 + 636262 GTTAAATCCATATCAGGGCTTC -s Anc0.Anc0refChr4 23227 21 - 45765 GTTAAAGCCTTATCA-GTCTTG -s Anc1.Anc1refChr2 54579 21 + 144309 GTTAAAGCCTTATCA-GTCTTG -s Anc2.Anc2refChr7 23286 21 + 32194 GTTCAAGCCTTTTCA-GTCTTG -s mr.mrrefChr0 74951 22 + 130230 GTTAAATCCATATCAGGGCTTC -s simCow_chr6.simCow.chr6 81502 21 + 602619 GTTGCAGTCTTTTCA-GTCTTG -s simDog_chr6.simDog.chr6 78619 21 + 593897 GCTCAAGCCTTTTCA-GTCTTG -s simHuman_chr6.simHuman.chr6 75272 21 + 601863 GTGAGAGCCTTATCC-GTCTTA -s simRat_chr6.simRat.chr6 71562 22 + 647215 GTTAAATCCATATCAGGGCTTC - -a -s simMouse_chr6.simMouse.chr6 79281 3 + 636262 ATA -s Anc0.Anc0refChr4 23248 3 - 45765 ATA -s Anc1.Anc1refChr2 54600 3 + 144309 ATA -s Anc2.Anc2refChr7 23307 3 + 32194 ATA -s mr.mrrefChr0 74973 3 + 130230 ATA -s simCow_chr6.simCow.chr6 81523 3 + 602619 ATG -s simDog_chr6.simDog.chr6 78640 3 + 593897 ATA -s simHuman_chr6.simHuman.chr6 75297 3 + 601863 ATA -s simRat_chr6.simRat.chr6 71584 3 + 647215 ATA - -a -s simMouse_chr6.simMouse.chr6 79284 7 + 636262 CATCTGG -s Anc0.Anc0refChr4 23251 7 - 45765 AGTGTAG -s Anc1.Anc1refChr2 54603 7 + 144309 AGTGTAG -s Anc2.Anc2refChr7 23310 7 + 32194 AGTGGAG -s mr.mrrefChr0 74976 7 + 130230 CATCTGG -s simCow_chr6.simCow.chr6 81554 7 + 602619 AGTGAAG -s simDog_chr6.simDog.chr6 78643 7 + 593897 ATTGGAG -s simHuman_chr6.simHuman.chr6 75300 7 + 601863 AGTGTAG -s simRat_chr6.simRat.chr6 71587 7 + 647215 CATTTCG - -a -s simMouse_chr6.simMouse.chr6 79291 35 + 636262 GCCCCCCTTGTTTTGGCAGAACTCTGACTCTCCCC -s Anc0.Anc0refChr4 23260 35 - 45765 CCCTCCCTTGTTTTGATGGAACTTTGTCACTCTTT -s Anc1.Anc1refChr2 54612 35 + 144309 CCCTCCCTTGTTTTGATGGAACTTTGTCACTCTTT -s Anc2.Anc2refChr7 23319 35 + 32194 CTCTCCCTTGTTTTGATGGAACTTTGTCACCCTTT -s mr.mrrefChr0 74983 35 + 130230 GCCTCCCTTGTTTTGGTAGAACTCTGACACTCTCC -s simCow_chr6.simCow.chr6 81563 33 + 602619 CTCCCCTGTGTCTTGCTGGAACTTTGGTA--CTTT -s simDog_chr6.simDog.chr6 78651 32 + 593897 ---TCCCTGGTTTTGATGGAGCTTTGTCACCCTTT -s simHuman_chr6.simHuman.chr6 75309 35 + 601863 TCCTCCCTTGTTTTAATGGAACTTTGTCACTCTTT -s simRat_chr6.simRat.chr6 71594 35 + 647215 GCCTCCCTTGTTTTGGTAGAGCTCTGGCAATATCC - -a -s simMouse_chr6.simMouse.chr6 79326 4 + 636262 ATGA -s Anc0.Anc0refChr4 23295 4 - 45765 TTGA -s Anc1.Anc1refChr2 54647 4 + 144309 TTGA -s Anc2.Anc2refChr7 23355 4 + 32194 TTGA -s mr.mrrefChr0 75018 4 + 130230 ATGA -s simCow_chr6.simCow.chr6 81597 4 + 602619 TTGA -s simDog_chr6.simDog.chr6 78684 4 + 593897 TTGG -s simHuman_chr6.simHuman.chr6 75344 4 + 601863 TTGA -s simRat_chr6.simRat.chr6 71629 4 + 647215 ATGT - -a -s simMouse_chr6.simMouse.chr6 79330 32 + 636262 TATACCGAACAGACTTGTTTCAATGAATGTTA -s Anc0.Anc0refChr4 23300 32 - 45765 TACATCCAATAAACTTGTATCAATGAATGTTA -s Anc1.Anc1refChr2 54652 32 + 144309 TACATCCAATAAACTTGTATCAATGAATGTTA -s Anc2.Anc2refChr7 23360 32 + 32194 TACATCCGATAAATTTGTATCAATAAATATTT -s mr.mrrefChr0 75022 32 + 130230 TATACCGAACAGACTTGTTTCAATGAATGTTA -s simCow_chr6.simCow.chr6 81602 31 + 602619 TACATCTGACATATTTGT-TCAATAAAAATTT -s simDog_chr6.simDog.chr6 78689 32 + 593897 TACACCCGATAACTTTGTATGAACAAATATTT -s simHuman_chr6.simHuman.chr6 75349 32 + 601863 TACATTAAATAAACCTGTATCAATGAATGTTA -s simRat_chr6.simRat.chr6 71633 32 + 647215 GATACCCAACGGGCTTGTCTCAACGAATGTTA - -a -s simMouse_chr6.simMouse.chr6 79362 12 + 636262 ATCTCAGCTTAA -s Anc0.Anc0refChr4 23337 11 - 45765 GTCTCAGCT-AA -s Anc1.Anc1refChr2 54689 11 + 144309 GTCTCAGCT-AA -s Anc2.Anc2refChr7 23397 11 + 32194 ATCTCAGCT-AA -s mr.mrrefChr0 75054 11 + 130230 GTCTCAGCT-AA -s simCow_chr6.simCow.chr6 81638 11 + 602619 ATCTCAGCT-CA -s simDog_chr6.simDog.chr6 78726 11 + 593897 ATCTCAGCT-AA -s simHuman_chr6.simHuman.chr6 75386 11 + 601863 GTCACAGCT-AA -s simRat_chr6.simRat.chr6 71665 11 + 647215 GTCTCAGCT-AA - -a -s simMouse_chr6.simMouse.chr6 79374 29 + 636262 GAGGCTGGTTTCTGAGAGGAATTGGCAGA -s Anc0.Anc0refChr4 23348 28 - 45765 CAGATGTGTTTTTGAGAC-AATAGGCAGA -s Anc1.Anc1refChr2 54700 28 + 144309 CAGATGTGTTTTTGAGAC-AATAGGCAGA -s Anc2.Anc2refChr7 23408 28 + 32194 CAGATGTGTTATGGAGAC-AATAGGCAGA -s mr.mrrefChr0 75065 28 + 130230 GAGGCTGGTTTCTGAGAG-AATTGGCAGA -s simCow_chr6.simCow.chr6 81649 28 + 602619 CAGATGTGTCATGGCAGC-AGTGGACAGA -s simDog_chr6.simDog.chr6 78737 28 + 593897 CAAGTGTGTTATGGAGAC-AATAGGAAGA -s simHuman_chr6.simHuman.chr6 75401 28 + 601863 CAGATGTGTTTTTGAGAC-AATAGGCAGA -s simRat_chr6.simRat.chr6 71676 28 + 647215 GAGGCTGGTTTCTGAGAG-AATTGACAGA - -a -s simMouse_chr6.simMouse.chr6 79403 17 + 636262 TTATACCATTGTGGTTC -s Anc0.Anc0refChr4 23376 17 - 45765 CCCTATCACTGTGATTA -s Anc1.Anc1refChr2 54728 17 + 144309 CCCTATCACTGTGATTA -s Anc2.Anc2refChr7 23436 17 + 32194 TCCTATCACTGTGATTA -s mr.mrrefChr0 75093 17 + 130230 CTATACCATTGTGATTC -s simCow_chr6.simCow.chr6 81677 17 + 602619 TTCTATCACTCTGATTA -s simDog_chr6.simDog.chr6 78765 17 + 593897 TCCTATCACTGAGATTC -s simHuman_chr6.simHuman.chr6 75430 17 + 601863 CCCTATCACTGTGATTA -s simRat_chr6.simRat.chr6 71704 17 + 647215 CTATACCATTGTGATCC - -a -s simMouse_chr6.simMouse.chr6 79420 8 + 636262 TTAATTAC -s Anc0.Anc0refChr4 23393 8 - 45765 TTAGCTAC -s Anc1.Anc1refChr2 54745 8 + 144309 TTAGCTAC -s Anc2.Anc2refChr7 23453 8 + 32194 TTAGCTAC -s mr.mrrefChr0 75110 8 + 130230 TTAATTAC -s simCow_chr6.simCow.chr6 81695 8 + 602619 TTAGCTTC -s simDog_chr6.simDog.chr6 78782 8 + 593897 TTAGCCAC -s simHuman_chr6.simHuman.chr6 75447 8 + 601863 TTAGCTAC -s simRat_chr6.simRat.chr6 71721 8 + 647215 TTAATTAC - -a -s simMouse_chr6.simMouse.chr6 79428 12 + 636262 ACATCCTGGGAC -s Anc0.Anc0refChr4 23402 12 - 45765 ACATCTCGGTCC -s Anc1.Anc1refChr2 54754 12 + 144309 ACATCTCGGTCC -s Anc2.Anc2refChr7 23462 12 + 32194 ACATCTCAGTCC -s mr.mrrefChr0 75118 12 + 130230 ACATCCTGGGAC -s simCow_chr6.simCow.chr6 81704 11 + 602619 ACACTC-AGTCC -s simDog_chr6.simDog.chr6 78791 12 + 593897 ACATCTCAGTTC -s simHuman_chr6.simHuman.chr6 75456 12 + 601863 ACATCTGGGCCC -s simRat_chr6.simRat.chr6 71729 12 + 647215 ACATCCTGGGAC - -a -s simMouse_chr6.simMouse.chr6 79440 22 + 636262 CTTCCTATCTGTGTTGGAGTAT -s Anc0.Anc0refChr4 23414 22 - 45765 TTCCCTATATGTGTTGGAGTTT -s Anc1.Anc1refChr2 54766 22 + 144309 TTCCCTATATGTGTTGGAGTTT -s Anc2.Anc2refChr7 23474 22 + 32194 TTCTCTATATGTGTTAGAGTTT -s mr.mrrefChr0 75130 22 + 130230 CTCCCTATCTGTGTTGGAGTTT -s simCow_chr6.simCow.chr6 81730 22 + 602619 TTCTTTATATGAATCAGAGTCT -s simDog_chr6.simDog.chr6 78803 22 + 593897 TTCTCTATATGTGTTAGAGTTT -s simHuman_chr6.simHuman.chr6 75468 21 + 601863 TTCCCTATGTGTGCTGGAGTT- -s simRat_chr6.simRat.chr6 71741 22 + 647215 CTCCCTATCTGTGTTGGAGTTT - -a -s simMouse_chr6.simMouse.chr6 79462 56 + 636262 GTCAGATTATGACTTTTAACAGCAACGGAGGGCAACTTTACTGTTCAGCACTCAGA -s Anc0.Anc0refChr4 23436 55 - 45765 GCCAGG-TGCTACCTTAGACTGCAACAGAGAGCAACTTTGCCTCTCATCACTTAGC -s Anc1.Anc1refChr2 54788 55 + 144309 GCCAGG-TGCTACCTTAGACTGCAACAGAGAGCAACTTTGCCTCTCATCACTTAGC -s Anc2.Anc2refChr7 23497 55 + 32194 GCCAAG-TGCTACCTTAGACTTAGACAGAGAGTAACTTTGCCTCTCATCACTTGGC -s mr.mrrefChr0 75152 56 + 130230 GTCAGATTGTGACCTTTAACAGCAACGGAGAGCAACTTTACTGCTCAGCACTCAGA -s simCow_chr6.simCow.chr6 81753 49 + 602619 TCCAAG-TGTTACC------TTAGACAGAGAGTAACTTGGCCTCTCATCACTTGTC -s simDog_chr6.simDog.chr6 78826 54 + 593897 GCCAAG-AGCTTCCTTAGACTTAGACAGAGAGTAACTTTGGCTC-CAGCACTTGGC -s simHuman_chr6.simHuman.chr6 75489 49 + 601863 -CCAGG-TGGTACCCTAGAT-GCA----GAAGCAACCTTCCCTCTCATCACTGAGC -s simRat_chr6.simRat.chr6 71763 56 + 647215 GTCAAAGTGTTACCTTTCACAGCAATGGGGAGCAACTTTACTGCTCAGCAATCTGA - -a -s simMouse_chr6.simMouse.chr6 79518 28 + 636262 TTTAATTAGTATTTATTGCAGTTGTGCC -s Anc0.Anc0refChr4 23491 28 - 45765 TCTGATTATTGTTTACTAGTGTTGTGCC -s Anc1.Anc1refChr2 54843 28 + 144309 TCTGATTATTGTTTACTAGTGTTGTGCC -s Anc2.Anc2refChr7 23552 28 + 32194 TCTGATTATTATTTACTAGTGTTGTGGC -s mr.mrrefChr0 75208 28 + 130230 TTTAATTAGTGTTTATTACAGTTGTGCC -s simCow_chr6.simCow.chr6 81803 28 + 602619 TCTGATCATTCTTCACTAGCCTTGTGGC -s simDog_chr6.simDog.chr6 78880 22 + 593897 GCTGATTATTATTTACTAGTG------C -s simHuman_chr6.simHuman.chr6 75538 28 + 601863 TCTGAGTATGGTTTACTAGTATTGTGCC -s simRat_chr6.simRat.chr6 71819 28 + 647215 TTTAATTAGTGTTTATTACAGTTGTGCC - -a -s simMouse_chr6.simMouse.chr6 79546 14 + 636262 TGCTTTGGAATCTA -s Anc0.Anc0refChr4 23520 14 - 45765 TGTCTTGCAATCTA -s Anc1.Anc1refChr2 54872 14 + 144309 TGTCTTGCAATCTA -s Anc2.Anc2refChr7 23581 14 + 32194 TGTCTTGCAATCTA -s mr.mrrefChr0 75236 14 + 130230 TGCCTTGGAATCTA -s simCow_chr6.simCow.chr6 81832 13 + 602619 TGTC-TGCGCTCTA -s simDog_chr6.simDog.chr6 78903 14 + 593897 TGTCTTGTAATCTA -s simHuman_chr6.simHuman.chr6 75567 14 + 601863 TGTCCAGCAATCTA -s simRat_chr6.simRat.chr6 71847 14 + 647215 TGCCTTGAAATCTA - -a -s simMouse_chr6.simMouse.chr6 79560 18 + 636262 CTCCTGTCATTCTTTCTA -s Anc0.Anc0refChr4 23536 18 - 45765 CACCTATCATACTCCTTA -s Anc1.Anc1refChr2 54888 18 + 144309 CACCTATCATACTCCTTA -s Anc2.Anc2refChr7 23597 18 + 32194 CACCTATCATACTCCTTA -s mr.mrrefChr0 75250 18 + 130230 CACCTATCATTCTCTCTA -s simCow_chr6.simCow.chr6 81847 18 + 602619 CATCTATCATACCCTTTA -s simDog_chr6.simDog.chr6 78919 18 + 593897 CCCCTATCATACTCCTTA -s simHuman_chr6.simHuman.chr6 75583 18 + 601863 CACCTATCATACTCCTTA -s simRat_chr6.simRat.chr6 71861 18 + 647215 CACCTAGCGTTCCCTCTA - -a -s simMouse_chr6.simMouse.chr6 79578 39 + 636262 CTGAAGAAGCAAAATCTGACCAATGCCCTCAAGCATTAT -s Anc0.Anc0refChr4 23555 39 - 45765 CTCAAAAAGGGAACCCTGATCACCACATTTCATCCCTTT -s Anc1.Anc1refChr2 54907 39 + 144309 CTCAAAAAGGGAACCCTGATCACCACATTTCATCCCTTT -s Anc2.Anc2refChr7 23616 39 + 32194 CTCAAAAAGGGAACCCTGATCACCACATTTCATCCCTTT -s mr.mrrefChr0 75269 39 + 130230 CTGAAGAAGCAAAATCTGATCACCACATTTCAGCATTAT -s simCow_chr6.simCow.chr6 81866 35 + 602619 CTC----AGGGAACCCTAATCACTACATTCCATCCCTTC -s simDog_chr6.simDog.chr6 78938 39 + 593897 CTCAAAAAGGGACCCCTGATCACCACATTTCAACCCTCT -s simHuman_chr6.simHuman.chr6 75602 39 + 601863 CTCAGAAAGGGAACCCTGATCACCACATTTCATCCCTTT -s simRat_chr6.simRat.chr6 71880 39 + 647215 CTGAAGAAGCAAAGTCTGATCACCACATTTCACCATTAT - -a -s simMouse_chr6.simMouse.chr6 79617 31 + 636262 CTCCCCCACTCTTCGCACTCTCTGGGTCTTA -s Anc0.Anc0refChr4 23594 31 - 45765 TGATCCTACTCTGCCCATCCTCTGAGTCTCC -s Anc1.Anc1refChr2 54946 31 + 144309 TGATCCTACTCTGCCCATCCTCTGAGTCTCC -s Anc2.Anc2refChr7 23655 31 + 32194 TGATCCTACTCTGCCCATCCTTTGAGTCTCC -s mr.mrrefChr0 75308 31 + 130230 CTCTCCCACTCTGCGCACTCTCTGAGTCTTA -s simCow_chr6.simCow.chr6 81901 31 + 602619 TGACCTTACTCTGCCCATCCTTTGAGTCCCC -s simDog_chr6.simDog.chr6 78979 30 + 593897 TCATCCTACTCTG-CCATCCTTTGAGCCTCC -s simHuman_chr6.simHuman.chr6 75641 31 + 601863 TGATCCTACTCTGCCCATACTCTGAGTCTCC -s simRat_chr6.simRat.chr6 71919 31 + 647215 CTCTCCCACTCTGAGTACCCTCTGAGTCTTG - -a -s simMouse_chr6.simMouse.chr6 79648 38 + 636262 TTGTGAAGGGCCAGTAGAGTTTTAAATCAACGAACCTC -s Anc0.Anc0refChr4 23630 38 - 45765 TTGAGAGGGGCCAATAGATTTTTAGATCAACAGACATT -s Anc1.Anc1refChr2 54982 38 + 144309 TTGAGAGGGGCCAATAGATTTTTAGATCAACAGACATT -s Anc2.Anc2refChr7 23691 38 + 32194 TTGAGAGGGGTCAATATATTTTCAGATCAACAGACACT -s mr.mrrefChr0 75339 38 + 130230 TTGTGAAGGGCCAATAGAGTTTTAGATCAACGAACCTC -s simCow_chr6.simCow.chr6 81937 38 + 602619 CTGAGAGGGGTCAATATATTTTAAGACCAATAGATACT -s simDog_chr6.simDog.chr6 79014 35 + 593897 TTGGGTGGGGTTAATATACTTTCAGATCAACAGAC--- -s simHuman_chr6.simHuman.chr6 75677 38 + 601863 TTGAGAGGGGCCAATAGCTCTTTAGATTAACAGACTTT -s simRat_chr6.simRat.chr6 71950 33 + 647215 TTGGGAAGGGC--ATAAAGTTTCAGATCAATGAAC--- - -a -s simMouse_chr6.simMouse.chr6 79686 36 + 636262 TAGCCCAATGCACCCGAACATTTATGAATACGGCCG -s Anc0.Anc0refChr4 23669 36 - 45765 TAGACCAATAGCCATGAGCATTTATGAATAAGGCCG -s Anc1.Anc1refChr2 55021 36 + 144309 TAGACCAATAGCCATGAGCATTTATGAATAAGGCCG -s Anc2.Anc2refChr7 23730 36 + 32194 TAGACTAATAGCCATGAGAATTTATGAATAAAGCCT -s mr.mrrefChr0 75377 36 + 130230 TAGCCCAATGCACCCGAGCATTTATGAATACGGCCG -s simCow_chr6.simCow.chr6 81976 36 + 602619 TAGACTAATAGCCACAAGGATTCATGAATACAGCAT -s simDog_chr6.simDog.chr6 183237 27 + 593897 ---------AGCCATGAGAATTTGTGAATAAAGCCT -s simHuman_chr6.simHuman.chr6 75716 36 + 601863 TAGGTCAACATCCATGAGCATTTATGAATATGGCTG -s simRat_chr6.simRat.chr6 71983 21 + 647215 ---------------AAGCATTTATGAATAGGGCCA - -a -s simMouse_chr6.simMouse.chr6 79722 30 + 636262 TTTGTGTATTCTGTACTTCCCATCCTGGAC -s Anc0.Anc0refChr4 23705 30 - 45765 TCTGTGAATTCTGTACTTCCAGTTCCGGAC -s Anc1.Anc1refChr2 55057 30 + 144309 TCTGTGAATTCTGTACTTCCAGTTCCGGAC -s Anc2.Anc2refChr7 23766 30 + 32194 TTTGTGAGTCCTGTACTTCCAGTTCCGGAC -s mr.mrrefChr0 75413 30 + 130230 TCTGTGTATTCTGTACTTCCAATCCTGGAC -s simCow_chr6.simCow.chr6 82012 30 + 602619 GTTGTGAGTCCTGTACTTCTAATTCCGGAC -s simDog_chr6.simDog.chr6 183264 30 + 593897 TTTGTGAGACCTGCGCTTCCAGTTCTGGAC -s simHuman_chr6.simHuman.chr6 75756 25 + 601863 TCAGTGAATTCTGTACTTCCACTTC----- -s simRat_chr6.simRat.chr6 72004 30 + 647215 TCTGTGTATTCTGTACTTCCAATGCTGGAC - -a -s simMouse_chr6.simMouse.chr6 79752 86 + 636262 ACCAGATGTCTCTTCAGTACAGGAAATGATAGTGGTTCTAAAAAGTTTGTGATTACAGCGATTTCTACTTTCATGTTCTTTAGCAA -s Anc0.Anc0refChr4 23735 85 - 45765 TTCAGATGTTCCTTCAGTACAGGAACTGCGACTAGTTCTGAAAATTTTTCGGTTCCAGTGA-CTCTGCTCTAGTGTTCTTTAGAAA -s Anc1.Anc1refChr2 55087 85 + 144309 TTCAGATGTTCCTTCAGTACAGGAACTGCGACTAGTTCTGAAAATTTTTCGGTTCCAGTGA-CTCTGCTCTAGTGTTCTTTAGAAA -s Anc2.Anc2refChr7 23799 85 + 32194 TTTAAATGTTCCTTCAGTAAAGGAACTGCGACTAGTTCTGAAAATTTTTCAGTTCCAGTGA-CTCTGCTCAAGTGTTCTTTAGAAA -s mr.mrrefChr0 75443 86 + 130230 ACCAGATGTCTCTTCAGTACAGGAAATGATAGTGGTTCTAAAAAGTTTGTGATTACAGTGATTTCTACTCTAGTGTTCTTTAGCAA -s simCow_chr6.simCow.chr6 82045 85 + 602619 CTTAAATGTTTCTTCATTAAAAGATCTGCGACTGGTTCTGAAACTTTACCAGTTCCAATAA-CTCTACTCAAGTGTCCTTTGTGAA -s simDog_chr6.simDog.chr6 183297 85 + 593897 TTTAAATGTCCCTTCCGTAAAGGAACAACGATTAGTTCTGAAGATTTTTCAGCTCCAGTGA-CTCTGCTCAAGTATTATTTAGAAA -s simHuman_chr6.simHuman.chr6 75781 80 + 601863 --CAGACTTTCCTTCAGTGCAGGAACTGTGACTTGTTC---AAATTTTTCGTTTCCAGTGA-CTCTGCTCTAGTGTACTTTAGAAA -s simRat_chr6.simRat.chr6 72034 81 + 647215 CATAGATGTCTCTTCAGTACA-----TGATATTGGTTCTAAAAAGTTTGTGATTACAGTGATTTCTACTCTAGTGTTCCTTCACAA - -a -s simMouse_chr6.simMouse.chr6 79838 43 + 636262 CTAAGTGCACAATTTTCGTTTTTAAGTTGAAAGTTTAGAAGTT -s Anc0.Anc0refChr4 23830 43 - 45765 CTGCGTACACAGTATTTATTTTTAAATTGAAAGTTGGAAAGTT -s Anc1.Anc1refChr2 55182 43 + 144309 CTGCGTACACAGTATTTATTTTTAAATTGAAAGTTGGAAAGTT -s Anc2.Anc2refChr7 23894 43 + 32194 CTGCATACACAGTATTTATTCTTGAATTGAAAGTTGGAAGGTT -s mr.mrrefChr0 75529 43 + 130230 CTAAGTGCACAATTTTTGTTTTTAAGTTGAAAGTTGAGAAGTT -s simCow_chr6.simCow.chr6 82140 36 + 602619 CTGCATACACAGTATTTATTCTTGAATTGAAAG-------ATG -s simDog_chr6.simDog.chr6 183392 43 + 593897 CTGCATACACAGTATTTACTCTTGAATTGACAGTTGGAAGGTT -s simHuman_chr6.simHuman.chr6 75871 43 + 601863 CTGTGTACACAGTACTTATTTTTAAATTGAAAGTGGGAAAGTT -s simRat_chr6.simRat.chr6 72115 40 + 647215 CTAAGTGCA---TCTTTGTTTTTAAGTTGAAAGTTGAGAAGTT - -a -s simMouse_chr6.simMouse.chr6 79881 49 + 636262 GATGTGCCTTGGACATCTGAGAATCTTGCCCTCCCACTGGGATTTGAGT -s Anc0.Anc0refChr4 23875 49 - 45765 GACACTCCTTTAATTCTTAAAAGCCTTTCTCTTCCACTAAGATTCAAAC -s Anc1.Anc1refChr2 55227 49 + 144309 GACACTCCTTTAATTCTTAAAAGCCTTTCTCTTCCACTAAGATTCAAAC -s Anc2.Anc2refChr7 23939 49 + 32194 GACACTCCTTTAATTCTAAAAGGCCTTTTTCTTCCACTAAGATTCAAAC -s mr.mrrefChr0 75572 49 + 130230 GATGCGCCTTGGAAATCTGAGAACCTTTCCCTCCCACTGGGATTTGAGT -s simCow_chr6.simCow.chr6 82178 49 + 602619 GTCGCTCCTTTAATTCTGAAAGGCCTCCTTCTTCGACTAATATTAAAAC -s simDog_chr6.simDog.chr6 183437 49 + 593897 AACACTCCTTTAGTGCTAAAAGGCATTTTTCTTCCGTTAAGATTCAAAC -s simHuman_chr6.simHuman.chr6 75916 40 + 601863 GACACTCCTTTAATTC-TAAAAGCCTTTCTCTTCCACTAAG-------- -s simRat_chr6.simRat.chr6 72155 49 + 647215 GATGCGCCTTAGAAGTCTGATGACCTTTCCCTCCCACTGGAATTCGAGC - -a -s simMouse_chr6.simMouse.chr6 79930 2 + 636262 AC -s Anc0.Anc0refChr4 23924 2 - 45765 AC -s Anc1.Anc1refChr2 55276 2 + 144309 AC -s Anc2.Anc2refChr7 23988 2 + 32194 AC -s mr.mrrefChr0 75621 2 + 130230 AC -s simCow_chr6.simCow.chr6 82237 2 + 602619 AC -s simDog_chr6.simDog.chr6 183486 2 + 593897 AC -s simRat_chr6.simRat.chr6 72204 2 + 647215 AC - -a -s simMouse_chr6.simMouse.chr6 79932 13 + 636262 ATAAATCTGACAC -s Anc0.Anc0refChr4 23926 13 - 45765 CTAAATGTGACAC -s Anc1.Anc1refChr2 55278 13 + 144309 CTAAATGTGACAC -s Anc2.Anc2refChr7 23992 13 + 32194 CTAAATGTGACAC -s mr.mrrefChr0 75623 13 + 130230 ATAAATCTGACAC -s simCow_chr6.simCow.chr6 82241 13 + 602619 TAAACTGTGACAC -s simDog_chr6.simDog.chr6 183490 13 + 593897 CTAAATGTGACAC -s simRat_chr6.simRat.chr6 72206 13 + 647215 ATAAACCTGAGAC - -a -s simMouse_chr6.simMouse.chr6 79945 14 + 636262 GTTCCATTCTCTCT -s Anc0.Anc0refChr4 23939 14 - 45765 GCTGCTCTATCTAC -s Anc1.Anc1refChr2 55291 14 + 144309 GCTGCTCTATCTAC -s Anc2.Anc2refChr7 24009 14 + 32194 GCTGCTCTATCTAC -s mr.mrrefChr0 75636 14 + 130230 GTTCCATTCTCTCT -s simCow_chr6.simCow.chr6 82258 14 + 602619 TCTTCACTATCCTC -s simDog_chr6.simDog.chr6 183507 14 + 593897 GCTGCTCTATCTAC -s simRat_chr6.simRat.chr6 72219 14 + 647215 ATTCCATCCTCTCT - -a -s simMouse_chr6.simMouse.chr6 79959 33 + 636262 CAATCACAATCTGTGTTACTTCTAGGACACTAC -s Anc0.Anc0refChr4 23957 33 - 45765 CGATCACAACCTCTGCTACTTCTTGGATGCTAC -s Anc1.Anc1refChr2 55309 33 + 144309 CGATCACAACCTCTGCTACTTCTTGGATGCTAC -s Anc2.Anc2refChr7 24027 33 + 32194 TTATCACAACCTCTGCTACTTCTTGGATGCTAC -s mr.mrrefChr0 75654 33 + 130230 CGATCACAATCTGTGTTACTTCTAGGACACTAC -s simCow_chr6.simCow.chr6 82276 33 + 602619 TTATCACAACTTCAGCTACTTACCAGATACTAC -s simDog_chr6.simDog.chr6 183525 33 + 593897 TTATCACAACCTGTGCTGCTTCTTGGATGCCAC -s simHuman_chr6.simHuman.chr6 75960 33 + 601863 CGATCATAACCTCTGCTACTTCTTCGATGCTAC -s simRat_chr6.simRat.chr6 72243 33 + 647215 TGATCACAATCCGTTTTACTTCTAGGACACTAC - -a -s simMouse_chr6.simMouse.chr6 79992 20 + 636262 AGCCTGGCAAGTATTCTGCC -s Anc0.Anc0refChr4 23990 18 - 45765 AGATTGGTGGGTAGTCTG-- -s Anc1.Anc1refChr2 55342 18 + 144309 AGATTGGTGGGTAGTCTG-- -s Anc2.Anc2refChr7 24060 18 + 32194 AAATTGGTGGGTAGTCTG-- -s mr.mrrefChr0 75687 20 + 130230 AGCCTGGCAAGTATTCTGCC -s simCow_chr6.simCow.chr6 82309 18 + 602619 AAATTGGGGGTCAGTCTG-- -s simDog_chr6.simDog.chr6 183558 18 + 593897 AAATTGGTGAGTAGTCTG-- -s simHuman_chr6.simHuman.chr6 75994 18 + 601863 AGTGTGGTGGGTAGTCTG-- -s simRat_chr6.simRat.chr6 72276 20 + 647215 AGCCCGGCAAGTATTCTGCC - -a -s simMouse_chr6.simMouse.chr6 80012 6 + 636262 CATCTT -s Anc0.Anc0refChr4 24008 6 - 45765 CATCTT -s Anc1.Anc1refChr2 55360 6 + 144309 CATCTT -s Anc2.Anc2refChr7 24081 6 + 32194 CATCTT -s mr.mrrefChr0 75707 6 + 130230 CATCTT -s simCow_chr6.simCow.chr6 82330 6 + 602619 TATTTT -s simDog_chr6.simDog.chr6 183579 6 + 593897 CATCTT -s simHuman_chr6.simHuman.chr6 76012 6 + 601863 CATCTC -s simRat_chr6.simRat.chr6 72296 6 + 647215 CATCTT - -a -s simMouse_chr6.simMouse.chr6 80018 4 + 636262 GAGA -s Anc0.Anc0refChr4 24015 4 - 45765 GAGA -s Anc1.Anc1refChr2 55367 4 + 144309 GAGA -s Anc2.Anc2refChr7 24088 4 + 32194 GAGA -s mr.mrrefChr0 75713 4 + 130230 GAGA -s simCow_chr6.simCow.chr6 82337 4 + 602619 GAGA -s simDog_chr6.simDog.chr6 183586 4 + 593897 GAGA -s simHuman_chr6.simHuman.chr6 76019 4 + 601863 GAGA -s simRat_chr6.simRat.chr6 72302 4 + 647215 GAAA - -a -s simMouse_chr6.simMouse.chr6 80022 17 + 636262 TAATCTGTAAAAATTCC -s Anc0.Anc0refChr4 24019 12 - 45765 TA-----TAAAAAATGC -s Anc1.Anc1refChr2 55371 12 + 144309 TA-----TAAAAAATGC -s Anc2.Anc2refChr7 24092 12 + 32194 TA-----CAACAAAAGT -s mr.mrrefChr0 75717 17 + 130230 TAATCTGTAAAAATTCC -s simCow_chr6.simCow.chr6 82368 12 + 602619 TG-----CAGCGAAAGG -s simDog_chr6.simDog.chr6 183590 12 + 593897 TA-----CAACAAATGT -s simHuman_chr6.simHuman.chr6 76023 12 + 601863 TA-----TGAAAAATGC -s simRat_chr6.simRat.chr6 72306 17 + 647215 TAATCTGTAAAAGTTCC - -a -s simMouse_chr6.simMouse.chr6 80039 150 + 636262 ATAAGGTGTCTGAATTATCTTAGATTTCCGAGAAAAGATGACTTGGTATAGAGAAGAGGGATCAGATGCCTCCAGCCAGTGGGTGGTTGGCCACCATGTAGGATCTTACCTCTAGTACTTGTGGGGCATTTCAGTACTGATGGTTTCCCT -s Anc0.Anc0refChr4 24040 116 - 45765 ATAAGAAGACCCAATGATCTTGGGTTTGCTAGAGGAGATAGCTTAGTATAGAGAAGATGGATCAGATGCCTCATG-AAGTAGGTGCTTGCCCACCATGCAGGGG---------------------------------TAACTGTCTCCTT -s Anc1.Anc1refChr2 55392 147 + 144309 ATAAGAAGACCCAATGATCTTGGGTTTGCTAGAGGAGATAGCTTAGTATAGAGAAGATGGATCAGATGCCTCATG-AAGTAGGTGCTTGCCCACCATGCAGGGGC--ACCTGTAGCCCTTGTCTTGCATATCAGTACTAACTGTCTCCTT -s Anc2.Anc2refChr7 24116 116 + 32194 ATAACAAGACCCAATGATCTTGGGTTGGCTAGAGGAGATAGCTTAGTATAGAGAAGATGGATCAGAATCATCATG-AAGTAGGTGCTTGCCGACCGTGCAGTGG---------------------------------TAACTGTCTCCTT -s mr.mrrefChr0 75734 150 + 130230 ATAAGATGTCTGAATTATCTTAGATTTGCGAGAAGAGATGACTTGGTATAGAGAAGAGGGATCAGATGCCTCCTGCCAGTGGGTGGTTGGCCACCATGCAGGATCTTACCTCTAGCACTTGTGGGGCATTTCAGTACTGACGGTTTCCCT -s simCow_chr6.simCow.chr6 82392 109 + 602619 ATAACAAGACCCAATGGGCTTGGGTTGGCTGGGAGAGATAGTCTGGTATAGATAAGATGGATCCAAATCATCATG-AAGTAGGTACTTGCCGACCCTGCAGTGG---------------------------------TA-------CCCT -s simDog_chr6.simDog.chr6 183611 116 + 593897 ATGGCAAGACCCAATGATCTTGAGTTGACTAGAGGAGATAGCTTAGTATAGAGAAGGTGGGTCAGAATCACCATG-CAGTAGGTGCTTGCCGATCGTGCAGTGA---------------------------------TAACTGTCTTTTT -s simHuman_chr6.simHuman.chr6 76044 147 + 601863 ATAAGAAGACCCAATGATCTTCGGTTTGCTAGAGGGGATAGCTTTGTATAGCGAAGATGGATCAGATGCCTCATG-AAGTAGGTGATTACCCACCATCCAGGGGC--ACCTGTAGCCCTTGTCTTGCATATCTGTACTAACTGCCTCCTT -s simRat_chr6.simRat.chr6 72323 150 + 647215 ATAAGACGTCTGAATTATCTTAGATTTGCAAGGAGAGATGACTTGGTATAGAGAAGGAGGATCAGATGCCTCCTGCCAGTGGGTGGCTGGCTACCGTGCAGGATCCTACCTCCAGCTCTTTTGGGGCATTTCAATACTGACAGTTCCTCT - -a -s simMouse_chr6.simMouse.chr6 80189 4 + 636262 AATG -s Anc0.Anc0refChr4 24156 4 - 45765 AATG -s Anc1.Anc1refChr2 55539 4 + 144309 AATG -s Anc2.Anc2refChr7 24232 4 + 32194 AATG -s mr.mrrefChr0 75884 4 + 130230 AATG -s simCow_chr6.simCow.chr6 82501 2 + 602619 AA-- -s simDog_chr6.simDog.chr6 183729 4 + 593897 AATG -s simHuman_chr6.simHuman.chr6 76191 4 + 601863 AATG -s simRat_chr6.simRat.chr6 72473 4 + 647215 AATG - -a -s simMouse_chr6.simMouse.chr6 80193 35 + 636262 AATGAGAGCACAAATCAATAATAAAGTGACCTGTC -s Anc0.Anc0refChr4 24164 35 - 45765 AGGCAAAGCACTCATCAATAATAAAATGATCTGTC -s Anc1.Anc1refChr2 55547 35 + 144309 AGGCAAAGCACTCATCAATAATAAAATGATCTGTC -s Anc2.Anc2refChr7 24240 35 + 32194 AGGCAAGGCACTCATCAATAATAAAATGATCTGTC -s mr.mrrefChr0 75888 35 + 130230 AATGAAAGCACAAATCAATAATAAAGTGACCTGTC -s simCow_chr6.simCow.chr6 82503 27 + 602619 --------CACTCATCAATAATGAAACGATTTGTC -s simDog_chr6.simDog.chr6 183737 35 + 593897 AGGCAAGGTTCTAATCAGTAACAAAATGATCCGTC -s simHuman_chr6.simHuman.chr6 76199 35 + 601863 AGACAAAGCACTCATCAAGAATAAAATGATCTGTC -s simRat_chr6.simRat.chr6 72477 35 + 647215 AATGAAAGCACAAATCACTAATAAAGTGACCTGTC - -a -s simMouse_chr6.simMouse.chr6 80228 21 + 636262 TCGATAATCATTAAAATACAC -s Anc0.Anc0refChr4 24200 21 - 45765 ATAATAATTATTGAAATACAT -s Anc1.Anc1refChr2 55583 21 + 144309 ATAATAATTATTGAAATACAT -s Anc2.Anc2refChr7 24276 21 + 32194 ATAATAATTATTGAAATACAT -s mr.mrrefChr0 75923 21 + 130230 TTAATAATCATTGAAATACAT -s simCow_chr6.simCow.chr6 82531 21 + 602619 TTAATAATTATTGAGATATGT -s simDog_chr6.simDog.chr6 183773 21 + 593897 ATAATAATTATTGTAGTCCAT -s simHuman_chr6.simHuman.chr6 76235 21 + 601863 CTAATCATTATTGAAATACAT -s simRat_chr6.simRat.chr6 72512 21 + 647215 TTAATAATCATTGAAATAGAT - -a -s simMouse_chr6.simMouse.chr6 80249 32 + 636262 TGTGTTATAGTTATTCCACATACATATGATTA -s Anc0.Anc0refChr4 24225 32 - 45765 CTGGTCGTAGATATGCCACGTAAGTATGATTG -s Anc1.Anc1refChr2 55608 32 + 144309 CTGGTCGTAGATATGCCACGTAAGTATGATTG -s Anc2.Anc2refChr7 24303 32 + 32194 CTGGTCGTCGATGTGCAAGGTAAGTATAATCA -s mr.mrrefChr0 75944 32 + 130230 TGTGTTATAGTTATTCCACATACATATGATTG -s simCow_chr6.simCow.chr6 82558 32 + 602619 ATGGTCATTGATGTTCAAATTAAGTATAATCA -s simDog_chr6.simDog.chr6 183800 32 + 593897 CTGGCCGTCTATGTGCAAGGTAAGTATAATCA -s simHuman_chr6.simHuman.chr6 76260 31 + 601863 CCAATCGTAGGTACACC-CGTGAGTAGGATTG -s simRat_chr6.simRat.chr6 72533 32 + 647215 TGTGTTATAATTATTCTACATACATATGATTG - -a -s simMouse_chr6.simMouse.chr6 80281 7 + 636262 CTAGGAA -s Anc0.Anc0refChr4 24258 7 - 45765 GTATGAA -s Anc1.Anc1refChr2 55641 7 + 144309 GTATGAA -s Anc2.Anc2refChr7 24336 7 + 32194 GTATGAA -s mr.mrrefChr0 75976 7 + 130230 GTATGAA -s simCow_chr6.simCow.chr6 82591 7 + 602619 GTATGAA -s simDog_chr6.simDog.chr6 183833 7 + 593897 GTATGAA -s simHuman_chr6.simHuman.chr6 76292 7 + 601863 GTATGAA -s simRat_chr6.simRat.chr6 72565 7 + 647215 GTATCAA - -a -s simMouse_chr6.simMouse.chr6 80288 2 + 636262 CA -s Anc0.Anc0refChr4 24267 2 - 45765 CA -s Anc1.Anc1refChr2 55650 2 + 144309 CA -s Anc2.Anc2refChr7 24345 2 + 32194 CT -s mr.mrrefChr0 75983 2 + 130230 CA -s simCow_chr6.simCow.chr6 82600 2 + 602619 CT -s simHuman_chr6.simHuman.chr6 76301 2 + 601863 CA -s simRat_chr6.simRat.chr6 72572 2 + 647215 TG - -a -s simMouse_chr6.simMouse.chr6 80290 20 + 636262 CTTTAAGGATGGCATAAACT -s Anc0.Anc0refChr4 24269 20 - 45765 CTATAAGCGTGACATGAGCT -s Anc1.Anc1refChr2 55652 20 + 144309 CTATAAGCGTGACATGAGCT -s Anc2.Anc2refChr7 24347 20 + 32194 TTATAAGCCTTACATGAGCT -s mr.mrrefChr0 75985 20 + 130230 CTATAAGGGTGGCATAAACT -s simCow_chr6.simCow.chr6 82618 20 + 602619 TTATAACCCTCATGTAGATT -s simDog_chr6.simDog.chr6 183842 16 + 593897 ----AAGCCTTACATGAGCT -s simHuman_chr6.simHuman.chr6 76303 20 + 601863 CTATAAGAGTGACAGGAGCT -s simRat_chr6.simRat.chr6 72574 20 + 647215 CTATAAGGGTGGCATAAACT - -a -s simMouse_chr6.simMouse.chr6 80310 5 + 636262 AAGAT -s Anc0.Anc0refChr4 24290 5 - 45765 AAGAT -s Anc1.Anc1refChr2 55673 5 + 144309 AAGAT -s Anc2.Anc2refChr7 24368 5 + 32194 AAGAA -s mr.mrrefChr0 76005 5 + 130230 AAGAT -s simCow_chr6.simCow.chr6 82639 5 + 602619 AATAA -s simDog_chr6.simDog.chr6 183859 5 + 593897 AAGAA -s simHuman_chr6.simHuman.chr6 76324 5 + 601863 AAGAT -s simRat_chr6.simRat.chr6 72594 5 + 647215 AAGAC - -a -s simMouse_chr6.simMouse.chr6 80315 52 + 636262 GTTCTACCTGACATCTTAAATCTCCCTATGAGATAACAGAATACTGAGTAGA -s Anc0.Anc0refChr4 24295 51 - 45765 ATTCTACCTGAAATCCTGGAT-TTCCTGTGGGTTCACAGGGTAATGAGTAGG -s Anc1.Anc1refChr2 55678 51 + 144309 ATTCTACCTGAAATCCTGGAT-TTCCTGTGGGTTCACAGGGTAATGAGTAGG -s Anc2.Anc2refChr7 24373 51 + 32194 ATTCTCCCTGAAATCCTGGAC-TTCCGGAGGGTTCACAGGGTAATGAGTGGG -s mr.mrrefChr0 76010 52 + 130230 GTTCTACCTGACATCTTAAATCTCCCTATGAGATAACAGAATAATGAGTAGA -s simCow_chr6.simCow.chr6 82698 49 + 602619 ATACTCCCTAAAATCCT--AC-TTTTGGGGGGAGAAAAGAGGAATGAGTGGG -s simDog_chr6.simDog.chr6 183864 51 + 593897 ATTTTCCCTGAAAGCATGGAC-TTCCGGAGGGTTCACTGGGTAATGAGTGGG -s simHuman_chr6.simHuman.chr6 76329 51 + 601863 ATTCTACGTGAAATCCTTTAT-TTCCTGTGGGTTCTGAGTGTAATGCGTAGG -s simRat_chr6.simRat.chr6 72599 52 + 647215 GTTCTACCTGACATCTCAGATCTCCCTCAGAGCTAACAGAATAATGAGTAGA - -a -s simMouse_chr6.simMouse.chr6 80367 1 + 636262 G -s Anc0.Anc0refChr4 24346 1 - 45765 G -s Anc1.Anc1refChr2 55729 1 + 144309 G -s Anc2.Anc2refChr7 24424 1 + 32194 A -s mr.mrrefChr0 76062 1 + 130230 G -s simCow_chr6.simCow.chr6 82750 1 + 602619 A -s simDog_chr6.simDog.chr6 183915 1 + 593897 A -s simHuman_chr6.simHuman.chr6 76380 1 + 601863 G -s simRat_chr6.simRat.chr6 72651 1 + 647215 G - -a -s simMouse_chr6.simMouse.chr6 80368 5 + 636262 GCATC -s Anc0.Anc0refChr4 24347 5 - 45765 GCTCA -s Anc1.Anc1refChr2 55730 5 + 144309 GCTCA -s Anc2.Anc2refChr7 24440 5 + 32194 ACTCA -s mr.mrrefChr0 76063 5 + 130230 GCATC -s simCow_chr6.simCow.chr6 82766 5 + 602619 ACTCA -s simDog_chr6.simDog.chr6 183931 5 + 593897 ACTCA -s simHuman_chr6.simHuman.chr6 76381 5 + 601863 GCCCA -s simRat_chr6.simRat.chr6 72652 5 + 647215 GCATC - -a -s simMouse_chr6.simMouse.chr6 80373 2 + 636262 CC -s Anc0.Anc0refChr4 24352 2 - 45765 TG -s Anc1.Anc1refChr2 55735 2 + 144309 TG -s Anc2.Anc2refChr7 24451 2 + 32194 TG -s mr.mrrefChr0 76068 2 + 130230 CC -s simCow_chr6.simCow.chr6 82777 1 + 602619 A- -s simDog_chr6.simDog.chr6 183942 2 + 593897 TG -s simHuman_chr6.simHuman.chr6 76386 2 + 601863 TG -s simRat_chr6.simRat.chr6 72657 2 + 647215 CC - -a -s simMouse_chr6.simMouse.chr6 80375 6 + 636262 ATCCAA -s Anc0.Anc0refChr4 24355 6 - 45765 ATCTAA -s Anc1.Anc1refChr2 55738 6 + 144309 ATCTAA -s Anc2.Anc2refChr7 24454 6 + 32194 ATCTAA -s mr.mrrefChr0 76071 6 + 130230 ATCCAA -s simCow_chr6.simCow.chr6 82778 4 + 602619 --CCAG -s simDog_chr6.simDog.chr6 183945 6 + 593897 ATCTAA -s simHuman_chr6.simHuman.chr6 76389 6 + 601863 TTCTAA -s simRat_chr6.simRat.chr6 72660 6 + 647215 ATCAAA - -a -s simMouse_chr6.simMouse.chr6 80381 29 + 636262 ACATGCTCATTACATGAAAGATGGGGGAT -s Anc0.Anc0refChr4 24361 29 - 45765 ATATCCTAATAAGGTGAGATATGGGGGGA -s Anc1.Anc1refChr2 55744 29 + 144309 ATATCCTAATAAGGTGAGATATGGGGGGA -s Anc2.Anc2refChr7 24467 29 + 32194 GTATCTCAAGAAGGATAGATATGAGGGGG -s mr.mrrefChr0 76077 29 + 130230 ACATGCTCATTACATGAAAGATGGGGGAA -s simCow_chr6.simCow.chr6 82789 29 + 602619 GTATCTCAAAAAAGACAGGTGTGAGGGGG -s simDog_chr6.simDog.chr6 183962 29 + 593897 GTATTTCAGGAAGGATGGATATTAATGAG -s simHuman_chr6.simHuman.chr6 76395 29 + 601863 ATATCCTGATAATGTGATATATGGGGGGA -s simRat_chr6.simRat.chr6 72666 29 + 647215 ACATGCTCATTACATGAAAGATTGGGGAA - -a -s simMouse_chr6.simMouse.chr6 80410 4 + 636262 CGCT -s Anc0.Anc0refChr4 24390 4 - 45765 CACA -s Anc1.Anc1refChr2 55773 4 + 144309 CACA -s Anc2.Anc2refChr7 24501 4 + 32194 CACA -s mr.mrrefChr0 76106 4 + 130230 CGCT -s simCow_chr6.simCow.chr6 82828 4 + 602619 TAAA -s simDog_chr6.simDog.chr6 183996 4 + 593897 CACA -s simHuman_chr6.simHuman.chr6 76424 4 + 601863 AACA -s simRat_chr6.simRat.chr6 72695 4 + 647215 GGCT - -a -s simMouse_chr6.simMouse.chr6 80414 8 + 636262 CCTTCTAT -s Anc0.Anc0refChr4 24394 8 - 45765 CCTCTTAT -s Anc1.Anc1refChr2 55777 8 + 144309 CCTCTTAT -s Anc2.Anc2refChr7 24505 8 + 32194 ATTCTCAT -s mr.mrrefChr0 76110 8 + 130230 CCTTTTAT -s simCow_chr6.simCow.chr6 82849 8 + 602619 ATCCTCAT -s simDog_chr6.simDog.chr6 184000 6 + 593897 ATTCTC-- -s simHuman_chr6.simHuman.chr6 76428 8 + 601863 CCTCTTAT -s simRat_chr6.simRat.chr6 72699 8 + 647215 CCTTTTAT - -a -s simMouse_chr6.simMouse.chr6 80422 22 + 636262 TCCTGCAATGGCACAATGGATC -s Anc0.Anc0refChr4 24403 22 - 45765 TCACTCAATGGCACATTGAAAA -s Anc1.Anc1refChr2 55786 22 + 144309 TCACTCAATGGCACATTGAAAA -s Anc2.Anc2refChr7 24514 22 + 32194 TCACTCATTGGCACATTGAAAA -s mr.mrrefChr0 76118 22 + 130230 TCATGCAATGGCACAATGAATC -s simCow_chr6.simCow.chr6 82858 21 + 602619 TCACTCATTGG-ACATTGAAAA -s simDog_chr6.simDog.chr6 184006 22 + 593897 AAGCTCATTGGCACATGGAAAA -s simHuman_chr6.simHuman.chr6 76437 22 + 601863 TCACTCAAAGGCACATTGAAAA -s simRat_chr6.simRat.chr6 72707 22 + 647215 TCATGCAATGGTGTTGTGAATT - -a -s simMouse_chr6.simMouse.chr6 80444 1 + 636262 G -s Anc0.Anc0refChr4 24471 1 - 45765 A -s Anc1.Anc1refChr2 55854 1 + 144309 A -s Anc2.Anc2refChr7 24582 1 + 32194 A -s mr.mrrefChr0 76140 1 + 130230 G -s simCow_chr6.simCow.chr6 82925 1 + 602619 A -s simDog_chr6.simDog.chr6 184074 1 + 593897 A -s simHuman_chr6.simHuman.chr6 76505 1 + 601863 A -s simRat_chr6.simRat.chr6 72729 1 + 647215 G - -a -s simMouse_chr6.simMouse.chr6 80445 12 + 636262 AATAGGCTCTGG -s Anc0.Anc0refChr4 24571 12 - 45765 ATTTGGCTCTGA -s Anc1.Anc1refChr2 55954 12 + 144309 ATTTGGCTCTGA -s Anc2.Anc2refChr7 24684 12 + 32194 ATTTGGCTCTGA -s mr.mrrefChr0 76141 12 + 130230 AATAGGCTCTGG -s mr.mrrefChr0 76535 12 + 130230 ACTAGGCTCTGG -s simCow_chr6.simCow.chr6 83027 12 + 602619 ATTTGACTCTGA -s simDog_chr6.simDog.chr6 184175 12 + 593897 ATATGGCTCTGA -s simHuman_chr6.simHuman.chr6 76605 12 + 601863 ATTTGGCTGTGA -s simMouse_chr6.simMouse.chr6 80861 12 + 636262 ACTAGGCTCTGG -s simRat_chr6.simRat.chr6 73126 12 + 647215 ACAAGGCTCTGG -s simRat_chr6.simRat.chr6 72730 12 + 647215 AATAGGCTCTGG - -a -s simMouse_chr6.simMouse.chr6 80457 19 + 636262 GTTCTCAGTTGCACAATGA -s Anc0.Anc0refChr4 24583 19 - 45765 ATTTTTAATTGCACAACGA -s Anc1.Anc1refChr2 55966 19 + 144309 ATTTTTAATTGCACAACGA -s Anc2.Anc2refChr7 24696 19 + 32194 GTTTTTAATTGCACAACGC -s mr.mrrefChr0 76153 19 + 130230 ATTCTCAGTTGCACAATGA -s mr.mrrefChr0 76547 19 + 130230 ATTCTCGGTTATACAATGA -s simCow_chr6.simCow.chr6 83039 19 + 602619 GTTTTTAATTGCACAACGA -s simDog_chr6.simDog.chr6 184187 19 + 593897 GTTTTTAATTGCACAATGC -s simHuman_chr6.simHuman.chr6 76620 19 + 601863 ATTTTTAATTGTGCAACAT -s simMouse_chr6.simMouse.chr6 80873 19 + 636262 ATTCTCGGTTATACAATGA -s simRat_chr6.simRat.chr6 73138 19 + 647215 ATTCTCAGTTACACAATGA -s simRat_chr6.simRat.chr6 72742 19 + 647215 ATTCTCAGTTGCACAATGA - -a -s simMouse_chr6.simMouse.chr6 80476 14 + 636262 CGATTGGTGTCCTT -s Anc0.Anc0refChr4 24606 14 - 45765 GGTTTGAGATTCAT -s Anc1.Anc1refChr2 55989 14 + 144309 GGTTTGAGATTCAT -s Anc2.Anc2refChr7 24719 14 + 32194 GGTTCCAGATTCAT -s mr.mrrefChr0 76172 14 + 130230 TGATTGGTGTCCTT -s mr.mrrefChr0 76570 14 + 130230 GATTTGGTACTCTT -s simCow_chr6.simCow.chr6 83062 14 + 602619 AGTTCTGGATCCAT -s simDog_chr6.simDog.chr6 184210 14 + 593897 GGTTCCAGATTCAT -s simHuman_chr6.simHuman.chr6 76643 14 + 601863 GATTTGAGACTCAT -s simMouse_chr6.simMouse.chr6 80896 14 + 636262 GATTTGGTACTCTT -s simRat_chr6.simRat.chr6 73161 14 + 647215 GATTTGGTATTCTT -s simRat_chr6.simRat.chr6 72761 14 + 647215 TGATTGGTGTTATT - -a -s simMouse_chr6.simMouse.chr6 80490 3 + 636262 ACG -s Anc0.Anc0refChr4 24620 3 - 45765 AAG -s Anc1.Anc1refChr2 56003 3 + 144309 AAG -s Anc2.Anc2refChr7 24733 3 + 32194 AAG -s mr.mrrefChr0 76186 3 + 130230 AAG -s mr.mrrefChr0 76584 3 + 130230 AAC -s simCow_chr6.simCow.chr6 83076 3 + 602619 GAG -s simDog_chr6.simDog.chr6 184224 3 + 593897 AGG -s simHuman_chr6.simHuman.chr6 76657 3 + 601863 AAG -s simMouse_chr6.simMouse.chr6 80910 3 + 636262 AAC -s simRat_chr6.simRat.chr6 73175 3 + 647215 AAC -s simRat_chr6.simRat.chr6 72776 3 + 647215 AAG - -a -s simMouse_chr6.simMouse.chr6 80493 10 + 636262 GTCCAATTAG -s Anc0.Anc0refChr4 24624 2 - 45765 TT-------- -s Anc1.Anc1refChr2 56007 10 + 144309 TTCCAATCAG -s Anc2.Anc2refChr7 24737 2 + 32194 TT-------- -s mr.mrrefChr0 76189 10 + 130230 GTCCAATTAG -s mr.mrrefChr0 76588 10 + 130230 GTCCAGTCAG -s simCow_chr6.simCow.chr6 83080 2 + 602619 TT-------- -s simDog_chr6.simDog.chr6 184228 2 + 593897 TC-------- -s simHuman_chr6.simHuman.chr6 76661 2 + 601863 TT-------- -s simMouse_chr6.simMouse.chr6 80914 10 + 636262 GTCCAGTCAG -s simRat_chr6.simRat.chr6 73179 10 + 647215 GTCCAATCAG -s simRat_chr6.simRat.chr6 72779 10 + 647215 GTCCAATTTG - -a -s simMouse_chr6.simMouse.chr6 80503 14 + 636262 TGTGGCTACAAATT -s Anc0.Anc0refChr4 24626 14 - 45765 TGTGGTTACAAATG -s Anc1.Anc1refChr2 56017 14 + 144309 TGTGGTTACAAATG -s Anc2.Anc2refChr7 24739 14 + 32194 TATGGTTGAAAATG -s mr.mrrefChr0 76199 14 + 130230 TGTGGCTACAAATT -s mr.mrrefChr0 76598 14 + 130230 TGTGGCTATAAACT -s simCow_chr6.simCow.chr6 83090 14 + 602619 TATGGTTGAAAAAG -s simDog_chr6.simDog.chr6 184230 3 + 593897 C-----------TG -s simHuman_chr6.simHuman.chr6 76663 14 + 601863 TGTGGTTACAAATG -s simMouse_chr6.simMouse.chr6 80924 14 + 636262 TGTGGCTATAAACT -s simRat_chr6.simRat.chr6 73189 14 + 647215 TGTGGCTATAAACT -s simRat_chr6.simRat.chr6 72789 14 + 647215 TGTGGCTACAAATT - -a -s simMouse_chr6.simMouse.chr6 80517 2 + 636262 GA -s Anc0.Anc0refChr4 24640 2 - 45765 GA -s Anc1.Anc1refChr2 56031 2 + 144309 GA -s Anc2.Anc2refChr7 24753 2 + 32194 GA -s mr.mrrefChr0 76213 2 + 130230 GA -s mr.mrrefChr0 76612 2 + 130230 GA -s simCow_chr6.simCow.chr6 83104 2 + 602619 GA -s simDog_chr6.simDog.chr6 184233 2 + 593897 GA -s simHuman_chr6.simHuman.chr6 76677 2 + 601863 GA -s simMouse_chr6.simMouse.chr6 80938 2 + 636262 GA -s simRat_chr6.simRat.chr6 73208 2 + 647215 GA -s simRat_chr6.simRat.chr6 72803 2 + 647215 GA - -a -s simMouse_chr6.simMouse.chr6 80519 14 + 636262 CATGAGTGAACATT -s Anc0.Anc0refChr4 24642 14 - 45765 CATGAGTGCAACTT -s Anc1.Anc1refChr2 56033 14 + 144309 CATGAGTGCAACTT -s Anc2.Anc2refChr7 24755 14 + 32194 CATGAGTGCAACTT -s mr.mrrefChr0 76215 14 + 130230 CATGAGTGAACATT -s simCow_chr6.simCow.chr6 83106 14 + 602619 CATGGGTGCAACTT -s simDog_chr6.simDog.chr6 184235 14 + 593897 CATGAGTGCAACTT -s simHuman_chr6.simHuman.chr6 76679 14 + 601863 CTTGAGTGTGACTT -s simRat_chr6.simRat.chr6 72805 14 + 647215 CACGAGTGAGCATT - -a -s simMouse_chr6.simMouse.chr6 80533 7 + 636262 ATGAAAA -s Anc0.Anc0refChr4 24656 7 - 45765 ATAAGAA -s Anc1.Anc1refChr2 56047 7 + 144309 ATAAGAA -s Anc2.Anc2refChr7 24769 7 + 32194 CTAAGAA -s mr.mrrefChr0 76229 7 + 130230 ATGAAAA -s mr.mrrefChr0 76614 7 + 130230 ATGAGCA -s simCow_chr6.simCow.chr6 83120 7 + 602619 TTAATAA -s simDog_chr6.simDog.chr6 184249 7 + 593897 CTGAGAC -s simHuman_chr6.simHuman.chr6 76693 7 + 601863 ATAAGCA -s simMouse_chr6.simMouse.chr6 80940 7 + 636262 ATGAGCA -s simRat_chr6.simRat.chr6 73210 7 + 647215 GTGATCA -s simRat_chr6.simRat.chr6 72819 7 + 647215 ATAATAA - -a -s simMouse_chr6.simMouse.chr6 80540 28 + 636262 ATTATCTTGTTTGTTCACCATCCATAAC -s Anc0.Anc0refChr4 24663 20 - 45765 ACTCTCTTGTTTGTT----ATCCA---- -s Anc1.Anc1refChr2 56054 28 + 144309 ACTCTCTTGTTTGTTCATCATCCATAAC -s Anc2.Anc2refChr7 24776 20 + 32194 ACTCTCTCAGTTGCT----ACCCA---- -s mr.mrrefChr0 76236 28 + 130230 ATTATCTTGTTTGTTCACCATCCATAAC -s mr.mrrefChr0 76622 28 + 130230 ATTCTCCTGTTTGTTTATCATCCATAAA -s simCow_chr6.simCow.chr6 83127 20 + 602619 ACTGGCTCACTTGTT----TCCCA---- -s simDog_chr6.simDog.chr6 184256 20 + 593897 ACTCTCTCAGTTGCT----ACCCA---- -s simHuman_chr6.simHuman.chr6 76700 5 + 601863 ACTCT----------------------- -s simMouse_chr6.simMouse.chr6 80948 28 + 636262 ATTCTCCTGTTTGTTTATCATCCATAAA -s simRat_chr6.simRat.chr6 73218 28 + 647215 ATTATCCTGTTTGTTTGCCATCAATAAC -s simRat_chr6.simRat.chr6 72826 28 + 647215 ATTTTCTAGTTTGTTTATCATCCATAAA - -a -s simMouse_chr6.simMouse.chr6 80568 16 + 636262 ATTGCAGGCAATACTA -s Anc0.Anc0refChr4 24683 16 - 45765 ATTGCAGGCAATACTA -s Anc1.Anc1refChr2 56082 16 + 144309 ATTGCAGGCAATACTA -s Anc2.Anc2refChr7 24796 16 + 32194 ATTGCAGGTGAAACCA -s mr.mrrefChr0 76264 16 + 130230 ATTGCAGGCAATACTA -s mr.mrrefChr0 76650 16 + 130230 ATTGCGGGCAATTCTA -s simCow_chr6.simCow.chr6 83155 16 + 602619 ATTGTAGGTGTGACCA -s simDog_chr6.simDog.chr6 184276 16 + 593897 ATTGCAGGTGAAACCA -s simMouse_chr6.simMouse.chr6 80976 16 + 636262 ATTGCGGGCAATTCTA -s simRat_chr6.simRat.chr6 73246 16 + 647215 ATTGCAGGCAATACCA -s simRat_chr6.simRat.chr6 72854 16 + 647215 ATTGCAAGCAATACCT - -a -s simMouse_chr6.simMouse.chr6 80584 21 + 636262 CAAATTGTAGTTTTACCTACC -s Anc0.Anc0refChr4 24699 21 - 45765 CAAATTGTGGTTTGGCTTATC -s Anc1.Anc1refChr2 56098 21 + 144309 CAAATTGTGGTTTGGCTTATC -s Anc2.Anc2refChr7 24813 21 + 32194 CAAATTGTGGTTCGGCTTATA -s mr.mrrefChr0 76280 21 + 130230 CAAATTGTAGTTTTACCTACC -s mr.mrrefChr0 76666 21 + 130230 CAGATTTCAGTTTGACATATC -s simCow_chr6.simCow.chr6 83172 20 + 602619 CAAAGTGTGGTTCTGCTTAT- -s simDog_chr6.simDog.chr6 184293 18 + 593897 CAAATTGTGGTTCG---CATA -s simHuman_chr6.simHuman.chr6 76705 19 + 601863 --GGTTGTGGTTTGGCTTATT -s simMouse_chr6.simMouse.chr6 80992 21 + 636262 CAGATTTCAGTTTGACATATC -s simRat_chr6.simRat.chr6 73262 21 + 647215 CAGATTTCAGTTTGACCTATC -s simRat_chr6.simRat.chr6 72870 21 + 647215 CAGATTTCAGTTTTATCTACC - -a -s simMouse_chr6.simMouse.chr6 80605 8 + 636262 TTCTTTAT -s Anc0.Anc0refChr4 24722 7 - 45765 TCCTT-AC -s Anc1.Anc1refChr2 56121 7 + 144309 TCCTT-AC -s Anc2.Anc2refChr7 24836 7 + 32194 TCCTT-AC -s mr.mrrefChr0 76301 7 + 130230 TTCTT-AT -s mr.mrrefChr0 76687 7 + 130230 TCCTT-AT -s simCow_chr6.simCow.chr6 83193 7 + 602619 CCCTT-AC -s simDog_chr6.simDog.chr6 184313 7 + 593897 TCCTT-AC -s simHuman_chr6.simHuman.chr6 76726 7 + 601863 TCCTT-GC -s simMouse_chr6.simMouse.chr6 81013 7 + 636262 TCCTT-AT -s simRat_chr6.simRat.chr6 73283 7 + 647215 TCCTT-AT -s simRat_chr6.simRat.chr6 72891 7 + 647215 TCCTT-AT - -a -s simMouse_chr6.simMouse.chr6 80613 26 + 636262 CTGCTCAGTTTTACCTAACTCATTAT -s mr.mrrefChr0 76308 16 + 130230 CTGCT---------CTAAC-CATTAT -s simRat_chr6.simRat.chr6 72898 16 + 647215 CTGTT---------CTAAC-CATTAT - -a -s simMouse_chr6.simMouse.chr6 80639 16 + 636262 ATGTAATGCAGCCAGG -s Anc0.Anc0refChr4 24729 16 - 45765 ATATAATTGGGCCAAG -s Anc1.Anc1refChr2 56128 16 + 144309 ATATAATTGGGCCAAG -s Anc2.Anc2refChr7 24843 16 + 32194 ATATAACTGGGCCAAG -s mr.mrrefChr0 76324 16 + 130230 ATGTAATGCAGCCAGG -s mr.mrrefChr0 76694 16 + 130230 CTGTAATTCAGTCAAG -s simCow_chr6.simCow.chr6 83200 16 + 602619 ATAAAACTGGGCCAAG -s simDog_chr6.simDog.chr6 184320 16 + 593897 ACATAACTAGGCCAGT -s simHuman_chr6.simHuman.chr6 76733 16 + 601863 CTATAATTGGGCTGAG -s simMouse_chr6.simMouse.chr6 81020 16 + 636262 CTGTAATTCAGTCAAG -s simRat_chr6.simRat.chr6 73290 16 + 647215 CTGTAATTCAGTCAAG -s simRat_chr6.simRat.chr6 72914 16 + 647215 CTGTAATTAAACCAAG - -a -s simMouse_chr6.simMouse.chr6 80655 13 + 636262 ATTCATCTGCATC -s Anc0.Anc0refChr4 24748 13 - 45765 ATTCATCGGCAGC -s Anc1.Anc1refChr2 56147 13 + 144309 ATTCATCGGCAGC -s Anc2.Anc2refChr7 24862 13 + 32194 ATTCATGGCCGGC -s mr.mrrefChr0 76340 13 + 130230 ATTCATCTGCATC -s mr.mrrefChr0 76710 13 + 130230 ATTCATCTGCATC -s simCow_chr6.simCow.chr6 83219 13 + 602619 ATTTATGGCCGGC -s simDog_chr6.simDog.chr6 184339 13 + 593897 ATTCATGGCTGGC -s simHuman_chr6.simHuman.chr6 76752 13 + 601863 GTTCACAGGCAGC -s simMouse_chr6.simMouse.chr6 81036 13 + 636262 ATTCATCTGCATC -s simRat_chr6.simRat.chr6 73306 13 + 647215 ACTTGTCTGCATC -s simRat_chr6.simRat.chr6 72930 13 + 647215 ATTCATTTTCATC - -a -s simMouse_chr6.simMouse.chr6 80668 1 + 636262 T -s Anc0.Anc0refChr4 24761 1 - 45765 G -s Anc1.Anc1refChr2 56160 1 + 144309 G -s Anc2.Anc2refChr7 24875 1 + 32194 A -s mr.mrrefChr0 76353 1 + 130230 T -s mr.mrrefChr0 76723 1 + 130230 G -s simCow_chr6.simCow.chr6 83232 1 + 602619 A -s simDog_chr6.simDog.chr6 184352 1 + 593897 A -s simHuman_chr6.simHuman.chr6 76765 1 + 601863 G -s simMouse_chr6.simMouse.chr6 81051 1 + 636262 G -s simRat_chr6.simRat.chr6 73319 1 + 647215 A -s simRat_chr6.simRat.chr6 72943 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 80669 1 + 636262 T -s Anc0.Anc0refChr4 24762 1 - 45765 C -s Anc1.Anc1refChr2 56161 1 + 144309 C -s Anc2.Anc2refChr7 24876 1 + 32194 C -s mr.mrrefChr0 76354 1 + 130230 T -s simCow_chr6.simCow.chr6 83233 1 + 602619 C -s simDog_chr6.simDog.chr6 184353 1 + 593897 C -s simRat_chr6.simRat.chr6 72944 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 80670 1 + 636262 C -s Anc0.Anc0refChr4 24763 1 - 45765 G -s Anc1.Anc1refChr2 56162 1 + 144309 G -s Anc2.Anc2refChr7 24877 1 + 32194 G -s mr.mrrefChr0 76355 1 + 130230 C -s simCow_chr6.simCow.chr6 83234 1 + 602619 G -s simDog_chr6.simDog.chr6 184359 1 + 593897 G -s simHuman_chr6.simHuman.chr6 76766 1 + 601863 G -s simRat_chr6.simRat.chr6 72945 1 + 647215 G - -a -s simMouse_chr6.simMouse.chr6 80671 3 + 636262 TAA -s Anc0.Anc0refChr4 24764 3 - 45765 TAA -s Anc1.Anc1refChr2 56163 3 + 144309 TAA -s Anc2.Anc2refChr7 24878 3 + 32194 TAA -s mr.mrrefChr0 76356 3 + 130230 TAA -s mr.mrrefChr0 76724 3 + 130230 TAA -s simCow_chr6.simCow.chr6 83235 3 + 602619 TGG -s simDog_chr6.simDog.chr6 184360 3 + 593897 TAA -s simHuman_chr6.simHuman.chr6 76767 3 + 601863 TAA -s simMouse_chr6.simMouse.chr6 81052 3 + 636262 TAA -s simRat_chr6.simRat.chr6 73320 3 + 647215 TAA -s simRat_chr6.simRat.chr6 72946 3 + 647215 TAA - -a -s simMouse_chr6.simMouse.chr6 80674 1 + 636262 T -s Anc0.Anc0refChr4 24772 1 - 45765 T -s Anc1.Anc1refChr2 56171 1 + 144309 T -s Anc2.Anc2refChr7 24886 1 + 32194 T -s mr.mrrefChr0 76359 1 + 130230 T -s mr.mrrefChr0 76732 1 + 130230 C -s simCow_chr6.simCow.chr6 83243 1 + 602619 G -s simDog_chr6.simDog.chr6 184368 1 + 593897 T -s simHuman_chr6.simHuman.chr6 76775 1 + 601863 T -s simMouse_chr6.simMouse.chr6 81060 1 + 636262 C -s simRat_chr6.simRat.chr6 73328 1 + 647215 T -s simRat_chr6.simRat.chr6 72949 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 80675 8 + 636262 TACGTGGC -s Anc0.Anc0refChr4 24773 8 - 45765 CATATGGC -s Anc1.Anc1refChr2 56172 8 + 144309 CATATGGC -s Anc2.Anc2refChr7 24887 8 + 32194 CATATGGC -s mr.mrrefChr0 76360 8 + 130230 TACGTGGC -s mr.mrrefChr0 76733 8 + 130230 CATATGGC -s simCow_chr6.simCow.chr6 83244 8 + 602619 CATGTGGT -s simDog_chr6.simDog.chr6 184369 8 + 593897 CATATGGC -s simHuman_chr6.simHuman.chr6 76776 8 + 601863 CACATGGC -s simMouse_chr6.simMouse.chr6 81061 8 + 636262 CATATGGC -s simRat_chr6.simRat.chr6 73329 8 + 647215 CACATGGC -s simRat_chr6.simRat.chr6 72951 8 + 647215 CACATGGC - -a -s simMouse_chr6.simMouse.chr6 80683 22 + 636262 CCCACTTGATATGCCCTCCTAA -s Anc0.Anc0refChr4 24781 22 - 45765 TCCACCTTATATGCCCTCTTAA -s Anc1.Anc1refChr2 56180 22 + 144309 TCCACCTTATATGCCCTCTTAA -s Anc2.Anc2refChr7 24895 22 + 32194 TCCACCTTGGTTGCCCTCTTAA -s mr.mrrefChr0 76368 22 + 130230 CCCACTTGATATGCCCTCCTAA -s mr.mrrefChr0 76741 22 + 130230 CCCACCTTATGTGCCCTCCCAA -s simCow_chr6.simCow.chr6 83256 22 + 602619 GCCGCCTTGGTTGTCCTCTTGA -s simDog_chr6.simDog.chr6 184377 21 + 593897 TCCACCTTGGTT-CCCTCTGAA -s simHuman_chr6.simHuman.chr6 76784 21 + 601863 TCCACCTTACATGCCCTCTTA- -s simMouse_chr6.simMouse.chr6 81069 22 + 636262 CCCACCTTATGTGCCCTCCCAA -s simRat_chr6.simRat.chr6 73337 22 + 647215 CCCACCTTATGTGCCTTCCCAA -s simRat_chr6.simRat.chr6 72959 22 + 647215 CCCACCTGATGCGCTCCCCCAA - -a -s simMouse_chr6.simMouse.chr6 80705 7 + 636262 ACATGGC -s Anc0.Anc0refChr4 24803 4 - 45765 TCTG--- -s Anc1.Anc1refChr2 56202 7 + 144309 TCTGGTC -s Anc2.Anc2refChr7 24917 4 + 32194 TTTG--- -s mr.mrrefChr0 76390 7 + 130230 ACATGGC -s mr.mrrefChr0 76763 7 + 130230 TCTGCTC -s simCow_chr6.simCow.chr6 83278 4 + 602619 TTTG--- -s simDog_chr6.simDog.chr6 184398 4 + 593897 TTTG--- -s simMouse_chr6.simMouse.chr6 81091 7 + 636262 TCTGCTC -s simRat_chr6.simRat.chr6 73360 7 + 647215 TCTGCCC -s simRat_chr6.simRat.chr6 72981 7 + 647215 ACATGGC - -a -s simMouse_chr6.simMouse.chr6 80712 38 + 636262 CCCACCTGAGGTCTCCTCCCAATTTTTTTGGGACTCAG -s Anc0.Anc0refChr4 24807 12 - 45765 --------------------------TTTGGGACTCAG -s Anc1.Anc1refChr2 56209 38 + 144309 CCCACTTTAGTTCCCCTCCCAATTTTTTTGGGACTCAG -s Anc2.Anc2refChr7 24921 12 + 32194 --------------------------TTTGGGATTCAA -s mr.mrrefChr0 76397 38 + 130230 CCCACCTGAGGTCTCCTCCCAATTTTTTTGGGACTCAG -s mr.mrrefChr0 76771 38 + 130230 CCCAATTTATTTGCCCTCCCAATTTATTTCGGACTCAG -s simCow_chr6.simCow.chr6 83282 12 + 602619 --------------------------TTTGGGAGTCAA -s simDog_chr6.simDog.chr6 184402 12 + 593897 --------------------------TTTGGGATTCAA -s simMouse_chr6.simMouse.chr6 81099 38 + 636262 CCCAATTTATTTGCCCTCCCAATTTATTTCGGACTCAG -s simRat_chr6.simRat.chr6 73368 38 + 647215 CCCAATTTATTTGACCTCACAATTTATTTGGGACTCAG -s simRat_chr6.simRat.chr6 72988 38 + 647215 CCGACCTGAGGTGCCCTCCCAATTTTTTTCAGACTCAG - -a -s simMouse_chr6.simMouse.chr6 80750 6 + 636262 GACCCC -s Anc0.Anc0refChr4 24819 6 - 45765 CAACTC -s Anc1.Anc1refChr2 56247 6 + 144309 CAACTC -s Anc2.Anc2refChr7 24933 6 + 32194 CAACTC -s mr.mrrefChr0 76435 6 + 130230 GACCCC -s simCow_chr6.simCow.chr6 83294 3 + 602619 CAA--- -s simDog_chr6.simDog.chr6 184414 6 + 593897 CAACTC -s simHuman_chr6.simHuman.chr6 76805 3 + 601863 ---CTC -s simRat_chr6.simRat.chr6 73026 6 + 647215 GACTGC - -a -s simMouse_chr6.simMouse.chr6 80756 1 + 636262 A -s Anc0.Anc0refChr4 24825 1 - 45765 A -s Anc1.Anc1refChr2 56253 1 + 144309 A -s Anc2.Anc2refChr7 24939 1 + 32194 A -s mr.mrrefChr0 76441 1 + 130230 A -s mr.mrrefChr0 76809 1 + 130230 G -s simDog_chr6.simDog.chr6 184420 1 + 593897 A -s simHuman_chr6.simHuman.chr6 76808 1 + 601863 A -s simMouse_chr6.simMouse.chr6 81137 1 + 636262 G -s simRat_chr6.simRat.chr6 73406 1 + 647215 G -s simRat_chr6.simRat.chr6 73032 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 80757 29 + 636262 TAGAGCAGAACAACCTTTGTGTCTTCTGT -s Anc0.Anc0refChr4 24826 25 - 45765 TAT---AGAACAACC-TTGTGTCTCACAT -s Anc1.Anc1refChr2 56254 25 + 144309 TAT---AGAACAACC-TTGTGTCTCACAT -s Anc2.Anc2refChr7 24940 25 + 32194 TAT---AAAACAACC-TTGTGTCTCACAT -s mr.mrrefChr0 76442 25 + 130230 TAG---AGAACAACC-TTGTGTCTTCTGT -s mr.mrrefChr0 76810 25 + 130230 TAG---AGGACAACC-TTCTGTCTTCTGT -s simCow_chr6.simCow.chr6 83297 12 + 602619 -----------------CGTGTCTCACAT -s simDog_chr6.simDog.chr6 184421 25 + 593897 TAT---AAAACAACC-TTGTGTCTCACAT -s simHuman_chr6.simHuman.chr6 76809 25 + 601863 TAT---AGGACAACC-TTGTGTCTCACAT -s simMouse_chr6.simMouse.chr6 81138 25 + 636262 TAG---AGGACAACC-TTCTGTCTTCTGT -s simRat_chr6.simRat.chr6 73413 25 + 647215 TAG---AGGACAACC-TTCTGTCTTCTGT -s simRat_chr6.simRat.chr6 73033 25 + 647215 TAA---GGAACAACC-TTGTGTCTTTTGT - -a -s simMouse_chr6.simMouse.chr6 80786 5 + 636262 TCCAG -s Anc0.Anc0refChr4 24852 5 - 45765 TCTCT -s Anc1.Anc1refChr2 56280 5 + 144309 TCTCT -s Anc2.Anc2refChr7 24966 5 + 32194 TATCT -s mr.mrrefChr0 76467 5 + 130230 TCCAG -s mr.mrrefChr0 76835 5 + 130230 TCCAG -s simCow_chr6.simCow.chr6 83310 5 + 602619 CATCT -s simDog_chr6.simDog.chr6 184447 5 + 593897 TATCT -s simHuman_chr6.simHuman.chr6 76835 5 + 601863 TCTCT -s simMouse_chr6.simMouse.chr6 81163 5 + 636262 TCCAG -s simRat_chr6.simRat.chr6 73438 5 + 647215 TCCAG -s simRat_chr6.simRat.chr6 73058 5 + 647215 TCCAT - -a -s simMouse_chr6.simMouse.chr6 80791 15 + 636262 CGGATTAATGGGGTT -s Anc0.Anc0refChr4 24857 15 - 45765 AGGTCTCCTGGCCCT -s Anc1.Anc1refChr2 56285 15 + 144309 AGGTCTCCTGGCCCT -s Anc2.Anc2refChr7 24971 15 + 32194 AGGTCTCCTGGCCCT -s mr.mrrefChr0 76472 15 + 130230 CGGATTAATGGGGTT -s mr.mrrefChr0 76840 15 + 130230 AGGATTATTGGGGCT -s simCow_chr6.simCow.chr6 83324 8 + 602619 AAGTATCT------- -s simDog_chr6.simDog.chr6 184452 15 + 593897 AGGTCTCCTGGCCCT -s simHuman_chr6.simHuman.chr6 76840 15 + 601863 AGTTCTCCTGGCCCT -s simMouse_chr6.simMouse.chr6 81168 15 + 636262 AGGATTATTGGGGCT -s simRat_chr6.simRat.chr6 73443 15 + 647215 AGGATTATTGGAGCT -s simRat_chr6.simRat.chr6 73063 15 + 647215 TGGATTAATGGGGTT - -a -s simMouse_chr6.simMouse.chr6 80806 1 + 636262 G -s Anc0.Anc0refChr4 24876 1 - 45765 G -s Anc1.Anc1refChr2 56304 1 + 144309 G -s Anc2.Anc2refChr7 24990 1 + 32194 G -s mr.mrrefChr0 76487 1 + 130230 G -s mr.mrrefChr0 76855 1 + 130230 G -s simDog_chr6.simDog.chr6 184473 1 + 593897 G -s simHuman_chr6.simHuman.chr6 76859 1 + 601863 A -s simMouse_chr6.simMouse.chr6 81183 1 + 636262 G -s simRat_chr6.simRat.chr6 73458 1 + 647215 G -s simRat_chr6.simRat.chr6 73078 1 + 647215 G - -a -s simMouse_chr6.simMouse.chr6 80807 2 + 636262 GT -s mr.mrrefChr0 76488 2 + 130230 GT -s simRat_chr6.simRat.chr6 73079 2 + 647215 GT - -a -s simMouse_chr6.simMouse.chr6 80809 23 + 636262 GAGTCTGCAGAACTCTGGATAAG -s Anc0.Anc0refChr4 24877 21 - 45765 GAGTCCTAAGGACTGTGACT--G -s Anc1.Anc1refChr2 56305 23 + 144309 GAGTCCTAAGGACTGTGACTAAG -s Anc2.Anc2refChr7 24991 21 + 32194 GTGTCCTAAGGACTGGGACT--G -s mr.mrrefChr0 76490 23 + 130230 GAGTCTGCAGAACTCTGGATAAG -s mr.mrrefChr0 76856 23 + 130230 GACTCTATAGAACTCTGGATAAG -s simDog_chr6.simDog.chr6 184474 21 + 593897 GTGTCCTAAGGACTGGGACT--G -s simHuman_chr6.simHuman.chr6 76860 21 + 601863 GAGTGCTGAGGACTGTGACT--G -s simMouse_chr6.simMouse.chr6 81184 23 + 636262 GACTCTATAGAACTCTGGATAAG -s simRat_chr6.simRat.chr6 73459 23 + 647215 GACTCTTCAGAACTCTGTATAAG -s simRat_chr6.simRat.chr6 73081 23 + 647215 GAATCTACAGAACTCTGCATAAA - -a -s simMouse_chr6.simMouse.chr6 80832 2 + 636262 GC -s Anc0.Anc0refChr4 24898 2 - 45765 GC -s Anc1.Anc1refChr2 56328 2 + 144309 GC -s Anc2.Anc2refChr7 25012 2 + 32194 GC -s mr.mrrefChr0 76513 2 + 130230 GC -s mr.mrrefChr0 76879 2 + 130230 GC -s simDog_chr6.simDog.chr6 184496 2 + 593897 GC -s simHuman_chr6.simHuman.chr6 76881 2 + 601863 GC -s simMouse_chr6.simMouse.chr6 81207 2 + 636262 GC -s simRat_chr6.simRat.chr6 73482 2 + 647215 GC -s simRat_chr6.simRat.chr6 73104 2 + 647215 GC - -a -s simMouse_chr6.simMouse.chr6 80834 23 + 636262 TATCCTGGCAACTAACTGTTGTT -s Anc0.Anc0refChr4 24549 16 - 45765 TATATTAA-------CTGTTGTA -s Anc1.Anc1refChr2 55932 16 + 144309 TATATTAA-------CTGTTGTA -s Anc2.Anc2refChr7 24662 16 + 32194 TATATTAA-------CTGCTGTA -s mr.mrrefChr0 76515 16 + 130230 TATCCTGG-------CTGTTGTT -s simCow_chr6.simCow.chr6 83005 16 + 602619 TATATTGC-------CTGCTGGA -s simDog_chr6.simDog.chr6 184153 16 + 593897 TATATTAA-------CTGCCGTA -s simHuman_chr6.simHuman.chr6 76583 16 + 601863 TATATTAA-------CTGTTGTA -s simRat_chr6.simRat.chr6 73106 16 + 647215 TATCCTTT-------GTGTTGTT - -a -s simMouse_chr6.simMouse.chr6 80857 4 + 636262 GGGA -s Anc0.Anc0refChr4 24567 4 - 45765 ATGA -s Anc1.Anc1refChr2 55950 4 + 144309 ATGA -s Anc2.Anc2refChr7 24680 4 + 32194 ATGA -s mr.mrrefChr0 76531 4 + 130230 GGGA -s simCow_chr6.simCow.chr6 83023 4 + 602619 GTGA -s simDog_chr6.simDog.chr6 184171 4 + 593897 ATCA -s simHuman_chr6.simHuman.chr6 76601 4 + 601863 ATGA -s simRat_chr6.simRat.chr6 73122 4 + 647215 GGAA - -a -s simMouse_chr6.simMouse.chr6 80892 4 + 636262 ATTA -s Anc0.Anc0refChr4 24602 4 - 45765 ATTT -s Anc1.Anc1refChr2 55985 4 + 144309 ATTT -s Anc2.Anc2refChr7 24715 4 + 32194 ATTT -s mr.mrrefChr0 76566 4 + 130230 ATTA -s simCow_chr6.simCow.chr6 83058 4 + 602619 ACTT -s simDog_chr6.simDog.chr6 184206 4 + 593897 ATTT -s simHuman_chr6.simHuman.chr6 76639 4 + 601863 TTTT -s simRat_chr6.simRat.chr6 73157 4 + 647215 ATTA - -a -s simMouse_chr6.simMouse.chr6 80913 1 + 636262 A -s Anc0.Anc0refChr4 24623 1 - 45765 A -s Anc1.Anc1refChr2 56006 1 + 144309 A -s Anc2.Anc2refChr7 24736 1 + 32194 A -s mr.mrrefChr0 76587 1 + 130230 A -s simCow_chr6.simCow.chr6 83079 1 + 602619 A -s simDog_chr6.simDog.chr6 184227 1 + 593897 G -s simHuman_chr6.simHuman.chr6 76660 1 + 601863 A -s simRat_chr6.simRat.chr6 73178 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 80947 1 + 636262 T -s mr.mrrefChr0 76621 1 + 130230 T -s simRat_chr6.simRat.chr6 73217 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 81049 2 + 636262 TT - -a -s simMouse_chr6.simMouse.chr6 81055 5 + 636262 ATGCC -s Anc0.Anc0refChr4 24767 5 - 45765 GAGCC -s Anc1.Anc1refChr2 56166 5 + 144309 GAGCC -s Anc2.Anc2refChr7 24881 5 + 32194 GAACT -s mr.mrrefChr0 76727 5 + 130230 ATGCC -s simCow_chr6.simCow.chr6 83238 5 + 602619 GAATG -s simDog_chr6.simDog.chr6 184363 5 + 593897 GCACT -s simHuman_chr6.simHuman.chr6 76770 5 + 601863 GAGCC -s simRat_chr6.simRat.chr6 73323 5 + 647215 ATGCC - -a -s simMouse_chr6.simMouse.chr6 81098 1 + 636262 T -s mr.mrrefChr0 76770 1 + 130230 T -s simRat_chr6.simRat.chr6 73367 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 81209 15 + 636262 CACTCTGACAACTCA -s Anc0.Anc0refChr4 24900 4 - 45765 ----CTAA------- -s Anc1.Anc1refChr2 56330 4 + 144309 ----CTAA------- -s Anc2.Anc2refChr7 25014 4 + 32194 ----CTAA------- -s mr.mrrefChr0 76881 15 + 130230 CACTCTGACAACTCA -s simDog_chr6.simDog.chr6 184498 4 + 593897 ----CTAA------- -s simHuman_chr6.simHuman.chr6 76883 4 + 601863 ----AGAA------- -s simRat_chr6.simRat.chr6 73484 15 + 647215 TATCCTGACAACTCA - -a -s simMouse_chr6.simMouse.chr6 81224 13 + 636262 CTTCTCTCATCTT -s Anc0.Anc0refChr4 24904 7 - 45765 ------TCATATT -s Anc1.Anc1refChr2 56334 7 + 144309 ------TCATATT -s Anc2.Anc2refChr7 25018 7 + 32194 ------CAGAATT -s mr.mrrefChr0 76896 13 + 130230 CTTCTCTCATCTT -s simDog_chr6.simDog.chr6 184502 7 + 593897 ------CAGAATT -s simHuman_chr6.simHuman.chr6 76887 7 + 601863 ------TCATATT -s simRat_chr6.simRat.chr6 73500 13 + 647215 TTTCCCTCATTTT - -a -s simMouse_chr6.simMouse.chr6 81237 33 + 636262 GTGTTGATGAAGTCCTCTTGAGCCACCCAAAGG -s Anc0.Anc0refChr4 24913 31 - 45765 GTGTTAATGAT-TTGTC-TGAGGCACATTAAAG -s Anc1.Anc1refChr2 56343 31 + 144309 GTGTTAATGAT-TTGTC-TGAGGCACATTAAAG -s Anc2.Anc2refChr7 25027 31 + 32194 TTGTTAGTGCT-TTGGC-TGAAGCACATTAAAG -s mr.mrrefChr0 76909 32 + 130230 GTGTTGATGAA-TCCTCTTGAGCCACCCAAAGG -s simCow_chr6.simCow.chr6 83332 9 + 602619 ------------------------ACACTAAAG -s simDog_chr6.simDog.chr6 184511 31 + 593897 TTGTTAGTGCT-TTGGC-TGAAGCACATTAAAG -s simHuman_chr6.simHuman.chr6 76896 31 + 601863 GCGGTCAGAAT-CTTTT-TGAGACACTTGAAAG -s simRat_chr6.simRat.chr6 73513 32 + 647215 GTGTTGTTGGA-TCCTCTTGAGCCACCTAAAGG - -a -s simMouse_chr6.simMouse.chr6 81270 6 + 636262 TATCAG -s Anc0.Anc0refChr4 24944 6 - 45765 TATCAG -s Anc1.Anc1refChr2 56374 6 + 144309 TATCAG -s Anc2.Anc2refChr7 25058 6 + 32194 TATCTG -s mr.mrrefChr0 76941 6 + 130230 TATCAG -s simCow_chr6.simCow.chr6 83341 6 + 602619 TATCTG -s simDog_chr6.simDog.chr6 184544 6 + 593897 TATCTG -s simHuman_chr6.simHuman.chr6 76927 6 + 601863 TATCAG -s simRat_chr6.simRat.chr6 616153 6 - 647215 TGACAG -s simRat_chr6.simRat.chr6 73545 6 + 647215 TATCAG - -a -s simMouse_chr6.simMouse.chr6 81276 1 + 636262 A -s Anc0.Anc0refChr4 24950 1 - 45765 A -s Anc1.Anc1refChr2 56380 1 + 144309 A -s Anc2.Anc2refChr7 25064 1 + 32194 A -s mr.mrrefChr0 76947 1 + 130230 A -s simCow_chr6.simCow.chr6 83347 1 + 602619 A -s simDog_chr6.simDog.chr6 184550 1 + 593897 A -s simHuman_chr6.simHuman.chr6 76933 1 + 601863 A -s simRat_chr6.simRat.chr6 616162 1 - 647215 A -s simRat_chr6.simRat.chr6 73551 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 81277 40 + 636262 TTGTATTACTAAGATCATCTCCAAACTTTGAGGCAGACCT -s Anc0.Anc0refChr4 24951 37 - 45765 CT---TTACGAAGGTCCTACCTAACCTTTCAGGAACACCT -s Anc1.Anc1refChr2 56381 37 + 144309 CT---TTACGAAGGTCCTACCTAACCTTTCAGGAACACCT -s Anc2.Anc2refChr7 25065 37 + 32194 CT---TTACGAAGGTCCTACCTAACCTTTCAGGAACACCT -s mr.mrrefChr0 76948 40 + 130230 TTGTATTACTATGATCATCTCCAAACTTTCAGGCACACCT -s simCow_chr6.simCow.chr6 83349 31 + 602619 CT---TCACTAGGGTTCCACCTAATCTT------ACACCT -s simDog_chr6.simDog.chr6 184551 37 + 593897 CT---TTACGAAGGGCCTACCTAACCTTTCAGGAACACCT -s simHuman_chr6.simHuman.chr6 76934 37 + 601863 CT---TTAGCTAGGTCCTACTTAACCTTTCATGAACACCC -s simRat_chr6.simRat.chr6 616163 40 - 647215 CTGTATTACTATGATCATCTCAAAACTTTCAGGCACACTT -s simRat_chr6.simRat.chr6 73552 40 + 647215 TTGTATTACTATGATCATCTCCAAACTTTCAGGCACACCT - -a -s simMouse_chr6.simMouse.chr6 81317 62 + 636262 TGCCTCTAGTCCAGAATAGCTACCTCAATTTTGTGATCTGTGTGTGTATACACATTGTTCTT -s Anc0.Anc0refChr4 24990 54 - 45765 TGCCTCCAGCCTGTAATAGCTACCCTTATTT--TGA------TATTTATACATATTGCTCCC -s Anc1.Anc1refChr2 56420 54 + 144309 TGCCTCCAGCCTGTAATAGCTACCCTTATTT--TGA------TATTTATACATATTGCTCCC -s Anc2.Anc2refChr7 25104 54 + 32194 TGCTTCCAACCTGTAATCACTACCCTTGTTT--TGA------TATTTATACATATTGCTCCC -s mr.mrrefChr0 76988 60 + 130230 TGCCTCTAGCCCAGAATAGCTACCTCAATTT--TGATCTGTGTATGTATACATATTGCTCTT -s simCow_chr6.simCow.chr6 83382 40 + 602619 C--------------ATGACTACCCTTGTTT--TGA------TATTTATACATATTGCTTCC -s simDog_chr6.simDog.chr6 184590 28 + 593897 TGCTTCCAACCTGTAATCA----------------------------------ATTGTTCTC -s simHuman_chr6.simHuman.chr6 76973 54 + 601863 TGCCTCCAGCCTGAAATAGCTACTCTGATCC--TGA------TATCTATACATATTGCTCCC -s simRat_chr6.simRat.chr6 616203 60 - 647215 TGCCTCTAGCCCAGAATAGCTACCTCAATTT--TGATCTGTCTATGTATACATATTGCTCTT -s simRat_chr6.simRat.chr6 73592 60 + 647215 TGTCTCTAGCCCAGAATAGCTACCTTAATTT--TGATCTGTGTATGTATACCTATTGCTCTT - -a -s simMouse_chr6.simMouse.chr6 81379 1 + 636262 C -s Anc0.Anc0refChr4 25044 1 - 45765 C -s Anc1.Anc1refChr2 56474 1 + 144309 C -s Anc2.Anc2refChr7 25158 1 + 32194 C -s mr.mrrefChr0 77048 1 + 130230 C -s simCow_chr6.simCow.chr6 83422 1 + 602619 C -s simDog_chr6.simDog.chr6 184618 1 + 593897 C -s simHuman_chr6.simHuman.chr6 77027 1 + 601863 C -s simRat_chr6.simRat.chr6 73652 1 + 647215 C - -a -s simMouse_chr6.simMouse.chr6 81380 3 + 636262 GTT -s Anc0.Anc0refChr4 25045 3 - 45765 AAT -s Anc1.Anc1refChr2 56475 3 + 144309 AAT -s Anc2.Anc2refChr7 25159 3 + 32194 AAT -s mr.mrrefChr0 77049 3 + 130230 ACT -s simCow_chr6.simCow.chr6 83423 3 + 602619 AAT -s simDog_chr6.simDog.chr6 184619 1 + 593897 A-- -s simHuman_chr6.simHuman.chr6 77028 3 + 601863 ATT -s simRat_chr6.simRat.chr6 616263 3 - 647215 ACT -s simRat_chr6.simRat.chr6 73653 3 + 647215 ACT - -a -s simMouse_chr6.simMouse.chr6 81383 34 + 636262 CTAACCATGTTCCTTAACCTAACCTGGAACAGTT -s Anc0.Anc0refChr4 25049 28 - 45765 CTAATGAGGTTGCTTTC------CTGGATTCGTT -s Anc1.Anc1refChr2 56479 28 + 144309 CTAATGAGGTTGCTTTC------CTGGATTCGTT -s Anc2.Anc2refChr7 25163 28 + 32194 CTAATGAGGTTGCTTTC------CCTGCTTCCTT -s mr.mrrefChr0 77052 34 + 130230 CTAACCATGTTCCTTAACCTAACCTGGAACAGTT -s simCow_chr6.simCow.chr6 83427 28 + 602619 CTAGTGAGGTTGCCTTC------TGTGCTTACCT -s simDog_chr6.simDog.chr6 184620 26 + 593897 --AATGAGGTTGCTTTA------CCTGCTTCCTT -s simHuman_chr6.simHuman.chr6 77032 28 + 601863 CTAATGAGGTTGCTTCC------CTGGATTGGTT -s simRat_chr6.simRat.chr6 73656 34 + 647215 CTAACCATGTTGTTCAACTTAACCTGGGACCGTT - -a -s simMouse_chr6.simMouse.chr6 81417 10 + 636262 GAATTTTACT -s Anc0.Anc0refChr4 25077 9 - 45765 AAA-TTGACT -s Anc1.Anc1refChr2 56507 9 + 144309 AAA-TTGACT -s Anc2.Anc2refChr7 25194 9 + 32194 AAA-TTGATC -s mr.mrrefChr0 77086 10 + 130230 GAATTTTACT -s simCow_chr6.simCow.chr6 83458 9 + 602619 AAA-TTGATA -s simDog_chr6.simDog.chr6 184649 9 + 593897 AAA-TTGATC -s simHuman_chr6.simHuman.chr6 77060 9 + 601863 AAA-TTAACT -s simRat_chr6.simRat.chr6 73690 10 + 647215 GAATTGTATG - -a -s simMouse_chr6.simMouse.chr6 81427 21 + 636262 TATAGTGGACTATAAATTAAT -s Anc0.Anc0refChr4 25095 16 - 45765 TATGGTTAATCA-----TGCT -s Anc1.Anc1refChr2 56525 16 + 144309 TATGGTTAATCA-----TGCT -s Anc2.Anc2refChr7 25212 16 + 32194 CATGGTTAATCA-----TGCT -s mr.mrrefChr0 77096 16 + 130230 TATAGTGGACTA-----TAAT -s simCow_chr6.simCow.chr6 83476 16 + 602619 CGTGGTTAATCA-----TGCT -s simDog_chr6.simDog.chr6 184667 16 + 593897 CATGGTTAATCA-----GGCT -s simHuman_chr6.simHuman.chr6 77078 16 + 601863 TATGGTATATCA-----TGCT -s simRat_chr6.simRat.chr6 73700 16 + 647215 CATAATGCACTG-----TAAT - -a -s simMouse_chr6.simMouse.chr6 81448 30 + 636262 CGTTGAACGGGTTACTATGAGGTGCTCTTT -s Anc0.Anc0refChr4 25114 30 - 45765 AGTTCAATGGCTTACTCTGAGGTGCTCACT -s Anc1.Anc1refChr2 56544 30 + 144309 AGTTCAATGGCTTACTCTGAGGTGCTCACT -s Anc2.Anc2refChr7 25231 30 + 32194 AGTTCCATGGCTTACTCTGAGGAGCTCACT -s mr.mrrefChr0 77112 30 + 130230 CGTTGAACGGGTTACTATGAGGTGCTCTTT -s simCow_chr6.simCow.chr6 83495 30 + 602619 AGTTCCATTGGTTACTCTGAGGAGCTCACT -s simDog_chr6.simDog.chr6 184686 30 + 593897 GGTTCCATGGCTTACCCTAACAAGCTTACT -s simHuman_chr6.simHuman.chr6 77097 30 + 601863 AGTTCAATGACTTACTCTGGGGTGCTCACT -s simRat_chr6.simRat.chr6 73716 30 + 647215 CATTGATCAGATTACTCCAAAGCGCTCCCT - -a -s simMouse_chr6.simMouse.chr6 81478 156 + 636262 CTTCCTCTTGAGTATTATGTGGTCCATATCCAACTGCTTAAACTTATGTCAGAAGGCTGCATGTCTTCCGCAAGGTGGCTGGAACCGACCTGTATACTGGTAAATCATCAGGCATACAGTTCGTGTCCTGTAGTCAAGAGCGGATTATGAATTTGT -s Anc0.Anc0refChr4 25151 65 - 45765 CCAACTCTTGATAATTATGTGCACCATATCTAAATGTTT----------------------------------------------------------------------------------------CCATTGTCAGTAGTAGATGG---ATTTGT -s Anc1.Anc1refChr2 56581 68 + 144309 CCAACTCTTGATAATTATGTGCACCATATCTAAATGTTT----------------------------------------------------------------------------------------CCATTGTCAGTAGTAGATGGTGTATTTGT -s Anc2.Anc2refChr7 25268 65 + 32194 CCAACTCTTGATAATTATGTGCACCACATCTCTATGTTT----------------------------------------------------------------------------------------CCATTGTATGTATTAGATGG---ATTTGT -s mr.mrrefChr0 77142 68 + 130230 CTTCCTCTTGAGTATTATGTGGTCCATATCCAACTGCTT----------------------------------------------------------------------------------------CTGTAGTCAAGAGCGGATTATGAATTTGT -s simCow_chr6.simCow.chr6 83532 49 + 602619 CCAACTCCTGACTATTATGTGCACTACACCTC-ATGTCT----------------------------------------------------------------------------------------CCATTGTAGGG------------------ -s simDog_chr6.simDog.chr6 184723 65 + 593897 CCAACTGTTGATAGTTATGTGCACCACATATCTATGTTT----------------------------------------------------------------------------------------CCATTGTATGTATTAGATGG---ATTTGT -s simHuman_chr6.simHuman.chr6 77134 68 + 601863 CCAACTCTTGAACATTATGTGCACCATATCTAAACATAT----------------------------------------------------------------------------------------CCATCATCAGTAGTAGATGGTGTTTTTGC -s simRat_chr6.simRat.chr6 73746 68 + 647215 CTTCCTGTTGATTAAAATGTGGACCATATCGAATTGCTT----------------------------------------------------------------------------------------TGGTAGCCAACAATAGATTTTGAATCTGC - -a -s simMouse_chr6.simMouse.chr6 81634 2 + 636262 GG -s Anc0.Anc0refChr4 25221 2 - 45765 GG -s Anc1.Anc1refChr2 56654 2 + 144309 GG -s Anc2.Anc2refChr7 25338 2 + 32194 GT -s mr.mrrefChr0 77210 2 + 130230 GG -s simCow_chr6.simCow.chr6 83584 2 + 602619 AC -s simDog_chr6.simDog.chr6 184793 2 + 593897 GT -s simHuman_chr6.simHuman.chr6 77207 2 + 601863 GG -s simRat_chr6.simRat.chr6 73814 2 + 647215 TG - -a -s simMouse_chr6.simMouse.chr6 81636 13 + 636262 CAGCCACACTCCC -s Anc0.Anc0refChr4 25225 2 - 45765 -----------CC -s Anc1.Anc1refChr2 56658 2 + 144309 -----------CC -s Anc2.Anc2refChr7 25342 2 + 32194 -----------CC -s mr.mrrefChr0 77215 13 + 130230 CAGCCACACTCCC -s simCow_chr6.simCow.chr6 83588 2 + 602619 -----------CC -s simDog_chr6.simDog.chr6 184797 2 + 593897 -----------CC -s simHuman_chr6.simHuman.chr6 77211 2 + 601863 -----------CA -s simRat_chr6.simRat.chr6 73819 13 + 647215 CAGCCACGTCCCC - -a -s simMouse_chr6.simMouse.chr6 81649 29 + 636262 CTAAAATAAATTCCTATCTATTATAAACT -s Anc0.Anc0refChr4 25227 29 - 45765 CTAAAAAAAATTCTTCTCTACAATAGAAT -s Anc1.Anc1refChr2 56660 29 + 144309 CTAAAAAAAATTCTTCTCTACAATAGAAT -s Anc2.Anc2refChr7 25344 29 + 32194 CTAGAAAAAATTCTTCTATACAATAGAAT -s mr.mrrefChr0 77228 29 + 130230 CTAAAATAAACTCTTATCTACTATAGACT -s simCow_chr6.simCow.chr6 83590 29 + 602619 CTAGAAAAAACTCTTCTATACAATAGAAT -s simDog_chr6.simDog.chr6 184807 29 + 593897 CTAGAAAAAATTCTTCTATACAATAGAAT -s simHuman_chr6.simHuman.chr6 77213 29 + 601863 CTAAATAAAATACTTCTCTGCAGTAGAAC -s simRat_chr6.simRat.chr6 73832 29 + 647215 TGAAAATAAACTCTTACCTACTATAGATT - -a -s simMouse_chr6.simMouse.chr6 81678 59 + 636262 TGTGCACCTATTAAGACTTGTGCCATTATTATTTACCATTTAAGGATGTTATAATCTAA -s Anc0.Anc0refChr4 25256 44 - 45765 TGTGCACTTATAATAAC---------------TCACTATTTAAGGATGTTACAACAAGG -s Anc1.Anc1refChr2 56689 44 + 144309 TGTGCACTTATAATAAC---------------TCACTATTTAAGGATGTTACAACAAGG -s Anc2.Anc2refChr7 25373 44 + 32194 CATGCACTTATAATAAC---------------TCACTATTCTAGGATGTTTCAACAAGG -s mr.mrrefChr0 77257 59 + 130230 TGTGCACCTATTAAGACTTGTGCCATTATTATTTACCATTTAAGGATGTTATAACCTAA -s simCow_chr6.simCow.chr6 83625 41 + 602619 CATACACTTACA---AC---------------TCACTCTTCTAGGATGTTGCAACATGG -s simDog_chr6.simDog.chr6 184836 40 + 593897 CATG----TATTATAAC---------------TCATTATTCTCGAATGTTTCAACAAAG -s simHuman_chr6.simHuman.chr6 77242 44 + 601863 TGTGCACTTATAATAAC---------------TGACTAATTAAGGATGATACAATAGGG -s simRat_chr6.simRat.chr6 73861 59 + 647215 TGTGCACTTATTAAGACTTGTGCCATTATTATTTACCATTTAAAGATGTTATAACCTAT - -a -s simMouse_chr6.simMouse.chr6 81737 9 + 636262 GCGCTGTGG -s Anc0.Anc0refChr4 25300 9 - 45765 GCCCTCTAG -s Anc1.Anc1refChr2 56733 9 + 144309 GCCCTCTAG -s Anc2.Anc2refChr7 25417 9 + 32194 GCCCTCTAG -s mr.mrrefChr0 77316 9 + 130230 GCGCTGTGG -s simCow_chr6.simCow.chr6 83671 9 + 602619 GCCCCCCAG -s simDog_chr6.simDog.chr6 184876 9 + 593897 GCCCTATGT -s simHuman_chr6.simHuman.chr6 77286 9 + 601863 GCCCTCTAG -s simRat_chr6.simRat.chr6 73920 9 + 647215 GCGCTGTGG - -a -s simMouse_chr6.simMouse.chr6 81746 69 + 636262 CATGTCTGTTGTCTGTTAGAACCTAATGTAGGATAACTGGTGCCAAGGTCAGTTCAGACTCAGCATGCA -s Anc0.Anc0refChr4 25311 61 - 45765 CA-------TGCCTGTCAAAACCTAATGTAGGAT-ACTAGAGCCAAGGTCAGTTTAGACTCTGCATTCC -s Anc1.Anc1refChr2 56744 61 + 144309 CA-------TGCCTGTCAAAACCTAATGTAGGAT-ACTAGAGCCAAGGTCAGTTTAGACTCTGCATTCC -s Anc2.Anc2refChr7 25428 61 + 32194 CA-------TGCCTGTCAAAACCTAATGTAGGAT-ACTAGAGCCAAGGTCAGTTTAGACTCTGCATTCC -s mr.mrrefChr0 77325 62 + 130230 CA-------TGTCTGTTAGAACCTAATGTGGGATAACTGGTGCCAAGGTCAGTTCAGACTCAGCATGCA -s simCow_chr6.simCow.chr6 83682 61 + 602619 TA-------TACTTGTCAAAACCTATTATGGGAT-AATAGATCCTAGGTCAATCTAGACTCTGCATTCC -s simDog_chr6.simDog.chr6 184887 61 + 593897 CA-------AGCCTGTTAAAACCTAATGTAGGAT-ACTAGAGCCAAGATCAGTTTAGACCCTGCATCCC -s simHuman_chr6.simHuman.chr6 77297 61 + 601863 CA-------TGCCTGTCAAAACCTAATGGAGGAT-ACTAGAGGCAAGGTCACTTTTGGCTGTGAATTCC -s simRat_chr6.simRat.chr6 73929 62 + 647215 CA-------TGTCTGTTAGGATCTAATGTGGGATAACTGGTGCCAAGGTCACTTCAGACTCAGCCTGGA - -a -s simMouse_chr6.simMouse.chr6 81815 6 + 636262 AACATG -s Anc0.Anc0refChr4 25372 6 - 45765 AACATG -s Anc1.Anc1refChr2 56805 6 + 144309 AACATG -s Anc2.Anc2refChr7 25489 6 + 32194 AACATG -s mr.mrrefChr0 77387 6 + 130230 AACATG -s simCow_chr6.simCow.chr6 83746 6 + 602619 AACAAG -s simDog_chr6.simDog.chr6 184948 6 + 593897 AACATG -s simHuman_chr6.simHuman.chr6 77358 6 + 601863 AACATG -s simRat_chr6.simRat.chr6 73991 6 + 647215 AATGTA - -a -s simMouse_chr6.simMouse.chr6 81821 1 + 636262 T -s Anc0.Anc0refChr4 25379 1 - 45765 T -s Anc1.Anc1refChr2 56812 1 + 144309 T -s Anc2.Anc2refChr7 25496 1 + 32194 G -s mr.mrrefChr0 77393 1 + 130230 T -s simCow_chr6.simCow.chr6 83753 1 + 602619 A -s simDog_chr6.simDog.chr6 184955 1 + 593897 G -s simHuman_chr6.simHuman.chr6 77365 1 + 601863 T -s simRat_chr6.simRat.chr6 73997 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 81822 19 + 636262 GACTTCTATAAACTCTATA -s Anc0.Anc0refChr4 25380 14 - 45765 GACTTCTACAAACT----- -s Anc1.Anc1refChr2 56813 14 + 144309 GACTTCTACAAACT----- -s Anc2.Anc2refChr7 25497 14 + 32194 GGTTTCTTCAAACT----- -s mr.mrrefChr0 77394 19 + 130230 GACTTCTATAAACTCTATA -s simCow_chr6.simCow.chr6 83754 12 + 602619 GGTTC--TCAAAGT----- -s simDog_chr6.simDog.chr6 184956 14 + 593897 GGTCTCTTCTAACT----- -s simHuman_chr6.simHuman.chr6 77366 14 + 601863 GACTTCTACAGACT----- -s simRat_chr6.simRat.chr6 73999 19 + 647215 GACTTCTATAAATTCTATA - -a -s simMouse_chr6.simMouse.chr6 81841 16 + 636262 AGGTTTGTCATTTTCT -s Anc0.Anc0refChr4 25394 13 - 45765 ---TTTGTCAATTTTT -s Anc1.Anc1refChr2 56827 13 + 144309 ---TTTGTCAATTTTT -s Anc2.Anc2refChr7 25511 13 + 32194 ---CTTGTCAATTTTT -s mr.mrrefChr0 77413 16 + 130230 AGGTTTGTCATTTTCT -s simCow_chr6.simCow.chr6 83766 13 + 602619 ---CTAGTCAACTTTT -s simDog_chr6.simDog.chr6 184970 13 + 593897 ---CTTGTCAATTTTC -s simHuman_chr6.simHuman.chr6 77380 13 + 601863 ---TTTGTCACTTTTT -s simRat_chr6.simRat.chr6 74019 16 + 647215 ATGTTTGTCATTCTCT - -a -s simMouse_chr6.simMouse.chr6 81857 8 + 636262 ACATATGG -s Anc0.Anc0refChr4 25409 8 - 45765 ATGTGCGG -s Anc1.Anc1refChr2 56842 8 + 144309 ATGTGCGG -s Anc2.Anc2refChr7 25526 8 + 32194 CTGTGCGG -s mr.mrrefChr0 77429 8 + 130230 ACATGTGG -s simCow_chr6.simCow.chr6 83781 8 + 602619 CTGTGCGG -s simDog_chr6.simDog.chr6 184985 8 + 593897 CTGTAGGG -s simHuman_chr6.simHuman.chr6 77395 8 + 601863 ATGTGCAG -s simRat_chr6.simRat.chr6 74035 8 + 647215 ACATGTGG - -a -s simMouse_chr6.simMouse.chr6 81865 58 + 636262 ACACTAGTGATTTGTACTTCTCTAGTGTCTGACAGGGCGGACAGCTCATGGTATGTTT -s Anc0.Anc0refChr4 25418 30 - 45765 AGGTTAGTGATTGGCACTTTCCTT----------------------------ATGTAT -s Anc1.Anc1refChr2 56851 30 + 144309 AGGTTAGTGATTGGCACTTTCCTT----------------------------ATGTAT -s Anc2.Anc2refChr7 25535 30 + 32194 AGGTGAGTGATTGGCACTTTGTCC----------------------------ATGTGT -s mr.mrrefChr0 77438 41 + 130230 ACACTAGTGATTTGCACTTCTCTTGT-----------------GCTCATGGTATGTTT -s simCow_chr6.simCow.chr6 83790 30 + 602619 AGGTCAGTGATTGGCACTTTGTCC----------------------------ATGTGT -s simDog_chr6.simDog.chr6 184994 10 + 593897 AAGTGAGTGA------------------------------------------------ -s simHuman_chr6.simHuman.chr6 77404 30 + 601863 GGGTTGGTGATTGACAATTTCCTT----------------------------ATGTAT -s simHuman_chr6.simHuman.chr6 115380 30 + 601863 TTAATGGTGATTGACAATTTCCTT----------------------------ATGTAT -s simRat_chr6.simRat.chr6 74044 41 + 647215 ACACTAATGATTTGCACTTTTCTTGT-----------------GCTCATGGTATGATT - -a -s simMouse_chr6.simMouse.chr6 81923 27 + 636262 GGGTGGGGAGTTCACAGGATTCTCTGT -s Anc0.Anc0refChr4 25448 18 - 45765 GGATAGGGAGTCCACGA---------T -s Anc1.Anc1refChr2 56885 27 + 144309 GGATAGGGAGTCCACGAGATCCTCTGT -s Anc2.Anc2refChr7 25565 18 + 32194 GGAATGGGGGTACCAGA---------T -s mr.mrrefChr0 77479 27 + 130230 GGGTGGGGAGTTCACAAGATTCTCTGT -s simCow_chr6.simCow.chr6 83820 18 + 602619 GGAATGGGGGTACCAGA---------T -s simHuman_chr6.simHuman.chr6 77438 27 + 601863 GGATAGGGAGTCCATGGGTTCCTCTGT -s simHuman_chr6.simHuman.chr6 115414 27 + 601863 GGATAGGGAGTCCATGGGTTCCTCTGT -s simRat_chr6.simRat.chr6 74085 27 + 647215 GGGTGGTGAGTTCACAAGTTTCTCTGT - -a -s simMouse_chr6.simMouse.chr6 81950 7 + 636262 GAAAAAT -s Anc0.Anc0refChr4 25466 7 - 45765 GGAAAAC -s Anc1.Anc1refChr2 56912 7 + 144309 GGAAAAC -s Anc2.Anc2refChr7 25583 7 + 32194 GGAAAAC -s mr.mrrefChr0 77506 7 + 130230 GAAAAAT -s simCow_chr6.simCow.chr6 83838 5 + 602619 G--AAAC -s simDog_chr6.simDog.chr6 185004 6 + 593897 -GAAAAC -s simHuman_chr6.simHuman.chr6 77465 7 + 601863 AGAATAC -s simHuman_chr6.simHuman.chr6 115441 7 + 601863 AGAATAC -s simRat_chr6.simRat.chr6 74113 7 + 647215 GAAAAAC - -a -s simMouse_chr6.simMouse.chr6 81957 27 + 636262 CCATCCTAGTTAGCTGATGCCAGTGTT -s Anc0.Anc0refChr4 25481 27 - 45765 CTATCACTGTTTGCTGATGCCAGTGTT -s Anc1.Anc1refChr2 56927 27 + 144309 CTATCACTGTTTGCTGATGCCAGTGTT -s Anc2.Anc2refChr7 25598 27 + 32194 CTATCACTGCTTGCTAATGCCAGTGTT -s mr.mrrefChr0 77513 27 + 130230 CCATCCTAGTTTGCTGATGCCAGTGTT -s simCow_chr6.simCow.chr6 83845 27 + 602619 CTATCACTGCCTGCTAATGTCAGAGTT -s simDog_chr6.simDog.chr6 185018 27 + 593897 TTATGACAGCTTGCTAATGCCAGTGTT -s simHuman_chr6.simHuman.chr6 77480 27 + 601863 CTATCACTGTTTTCTGATGCCAGTTCT -s simHuman_chr6.simHuman.chr6 115456 27 + 601863 CTATCACTGTATTCTGATGCCAGTTCT -s simRat_chr6.simRat.chr6 74120 27 + 647215 CCATCCTAGTTTGCTGATGCCAGCGCT - -a -s simMouse_chr6.simMouse.chr6 81984 60 + 636262 AATGAGGGAAATTTGACTTTGGTGTAAGATCGGTGTATGTTGTTTCTACAAACCAGGGAT -s Anc0.Anc0refChr4 25511 60 - 45765 AATGAGGGCAATTTGTCTGTTTTATGTAGATGGTGTGTATGAATCCTGTAAAACAGGGCT -s Anc1.Anc1refChr2 56957 60 + 144309 AATGAGGGCAATTTGTCTGTTTTATGTAGATGGTGTGTATGAATCCTGTAAAACAGGGCT -s Anc2.Anc2refChr7 25628 60 + 32194 AATGAGGGCAATTTGTCTGTTTTTTGTAGATGGTGTGTATGAATCCTGTAAAACAGGGCG -s mr.mrrefChr0 77540 60 + 130230 AATGAGGGAAATTTGACTTTTGTATAAGATCGGTGTGTGTTGTTTCTGCAAACCAGGGTT -s simCow_chr6.simCow.chr6 83876 58 + 602619 AATGAGGGC--TTTATCTGTTTTTTGTAGATGGTGTGTGTGTACTCTGTAAAATAGGGCA -s simDog_chr6.simDog.chr6 185048 60 + 593897 AATGAGGGTAACTTGTCTGTTTTTTGCACATGGTATGTATGAATCCTGTAACACAGGGAG -s simHuman_chr6.simHuman.chr6 77510 57 + 601863 AATGAGGGCAATTTGTCTGTTTTATGTAGATGGTGTACATGAGTCCTGAA---CAGGGCT -s simHuman_chr6.simHuman.chr6 115486 35 + 601863 AATGAGGGCAATTTGTCTGTTTTATGTAGATGGTG------------------------- -s simRat_chr6.simRat.chr6 74147 60 + 647215 AATGAGGGAAATTTAGCTTTTGTATAAGATCAGTGTGTATTATTTCTGCAAATCAAGGTT - -a -s simMouse_chr6.simMouse.chr6 82044 24 + 636262 TATGACTACAACAATCCTCCCATA -s Anc0.Anc0refChr4 25574 21 - 45765 TATGACT---ATAATCCTCCCATA -s Anc1.Anc1refChr2 57020 21 + 144309 TATGACT---ATAATCCTCCCATA -s Anc2.Anc2refChr7 25691 21 + 32194 TGCAACC---ATAATCCTTCCATA -s mr.mrrefChr0 77600 21 + 130230 TATGACT---ACAATCCTCCCATA -s simCow_chr6.simCow.chr6 83936 16 + 602619 -----CC---GTGACCCTTCCATA -s simDog_chr6.simDog.chr6 185111 21 + 593897 TGCAACC---ATAATTCTTCCATG -s simHuman_chr6.simHuman.chr6 77570 21 + 601863 TATGATT---ATAATCCCCCTAAA -s simRat_chr6.simRat.chr6 74207 21 + 647215 TATGACT---ATACTCCTCCCATA - -a -s simMouse_chr6.simMouse.chr6 82068 20 + 636262 CAATCTGTTGAATTTCCACT -s Anc0.Anc0refChr4 25597 20 - 45765 CAATCTGTTGATTCCCCAAT -s Anc1.Anc1refChr2 57043 20 + 144309 CAATCTGTTGATTCCCCAAT -s Anc2.Anc2refChr7 25714 20 + 32194 CAATCTGTTGATTCCCGAAT -s mr.mrrefChr0 77621 20 + 130230 CAATCTGTTGAATTTCCACT -s simCow_chr6.simCow.chr6 83954 20 + 602619 CAGTCTGTTGATCCCCTAAT -s simDog_chr6.simDog.chr6 185134 20 + 593897 TAATCCGTTGATTGTTGATT -s simHuman_chr6.simHuman.chr6 77593 14 + 601863 CAAGCTGCC------CCAAT -s simRat_chr6.simRat.chr6 74228 20 + 647215 CAATCTGTTGAATTTTCACT - -a -s simMouse_chr6.simMouse.chr6 82088 8 + 636262 AGCATTAG -s Anc0.Anc0refChr4 25617 8 - 45765 AGCATAAG -s Anc1.Anc1refChr2 57063 8 + 144309 AGCATAAG -s Anc2.Anc2refChr7 25734 8 + 32194 AGCATAAG -s mr.mrrefChr0 77641 8 + 130230 AACATTAG -s simCow_chr6.simCow.chr6 83974 8 + 602619 AACTTAAG -s simDog_chr6.simDog.chr6 185158 8 + 593897 AGCATAAG -s simHuman_chr6.simHuman.chr6 77607 8 + 601863 AGCATAAG -s simRat_chr6.simRat.chr6 74248 8 + 647215 TACATTAG - -a -s simMouse_chr6.simMouse.chr6 82096 7 + 636262 TGGTGAC -s Anc0.Anc0refChr4 25625 7 - 45765 TTTCGAT -s Anc1.Anc1refChr2 57071 7 + 144309 TTTCGAT -s Anc2.Anc2refChr7 25742 7 + 32194 TTTCATT -s mr.mrrefChr0 77649 7 + 130230 TGGTGAC -s simCow_chr6.simCow.chr6 83982 7 + 602619 TTTCAGG -s simDog_chr6.simDog.chr6 185167 7 + 593897 TTTGATT -s simHuman_chr6.simHuman.chr6 77615 7 + 601863 TTTCGAG -s simRat_chr6.simRat.chr6 74256 7 + 647215 TACTGAC - -a -s simMouse_chr6.simMouse.chr6 82103 61 + 636262 TTTAAGGCTGCTGAGTTTAATACCTAACGTTAATTTTAGAAGCGTTTTAATTACAGTAACT -s Anc0.Anc0refChr4 25632 30 - 45765 TTAAGGGCT--------------------TTAGTTT--AC---------AATACAGTAACC -s Anc1.Anc1refChr2 57078 32 + 144309 TTAAGGGCT--------------------TTAGTTTTAAC---------AATACAGTAACC -s Anc2.Anc2refChr7 25754 30 + 32194 TTAGGGGTT--------------------TTCGTTT--AC---------AATACAGTAACC -s mr.mrrefChr0 77656 61 + 130230 TTTAAGGCTGCTGAGTTTAATACCTCACGTTAATTTTAGAGGCGTTTTAATTACAGTAACT -s simCow_chr6.simCow.chr6 83994 26 + 602619 TTAGGGGT------------------------GTTT--AC---------AATACAATAATC -s simDog_chr6.simDog.chr6 185179 30 + 593897 TTAGGGGTT--------------------TTCATTT--AC---------AATACAGTAACC -s simHuman_chr6.simHuman.chr6 77622 32 + 601863 TTAATTGCT--------------------TTAGTTTTAAC---------AATACAGTAACC -s simRat_chr6.simRat.chr6 74263 61 + 647215 TCTAAGGCCACTGAGTTTAATACCTCAAGTTAATTTTAGAGGCATTTTAATTATAGTAACT - -a -s simMouse_chr6.simMouse.chr6 82164 24 + 636262 AACTATAGAGAGGAGCTCTAATTG -s Anc0.Anc0refChr4 25662 24 - 45765 AGATACAAAGAGGTGCTCTAATAA -s Anc1.Anc1refChr2 57110 24 + 144309 AGATACAAAGAGGTGCTCTAATAA -s Anc2.Anc2refChr7 25784 24 + 32194 AGATACAAAGAGGTGCTTTAACAA -s mr.mrrefChr0 77717 24 + 130230 AGCTACAGAGAGGAGCTCTAATTG -s simCow_chr6.simCow.chr6 84020 24 + 602619 AGACACATAGAGGTCTGTTAACGA -s simDog_chr6.simDog.chr6 185209 24 + 593897 AGATACAAAGAGGTGCTTTAACAA -s simHuman_chr6.simHuman.chr6 77654 24 + 601863 AGATTCAAAGGGGTTCTCCAATAA -s simRat_chr6.simRat.chr6 74387 24 + 647215 AGCTACAAAGAGGAGCTCTAATTG - -a -s simMouse_chr6.simMouse.chr6 82188 69 + 636262 ACACCAATCCTGATACAATTTTGATAATTGTCAAGTTAATGGCTAAGCCTTCATAGATGGCAATGTTGG -s Anc0.Anc0refChr4 25686 69 - 45765 ATACCAATCCTGACACACTTTTGAAGATTGTAAGGGTAATGACCAGACTCTTGAATATGAGAGTGGGGG -s Anc1.Anc1refChr2 57134 69 + 144309 ATACCAATCCTGACACACTTTTGAAGATTGTAAGGGTAATGACCAGACTCTTGAATATGAGAGTGGGGG -s Anc2.Anc2refChr7 25808 69 + 32194 ATACCAATCCTGACACTCTTTTCAAGGTTGTAAGGGTAATGACCAGACTCTTGAATATGAGAGTGGGGG -s mr.mrrefChr0 77741 69 + 130230 ACACCAATCCTGACACAATTTTGATAATTGTAAAGTTAATGGCTAAGCCTTCATAGATGGCAATGGTGG -s simCow_chr6.simCow.chr6 84044 69 + 602619 CTACCAATCCTGACACTCTTTTTGAGATTGCAAGGGTAAGAAGTAAGCTCACGTAGATGGGAGTGGTGG -s simDog_chr6.simDog.chr6 185236 69 + 593897 ATACCAATCGTGATACTCTTTTCAAGGTTGTAAGGGTAATGACCAGACTCTTGAATATGAGAGTGGGGG -s simHuman_chr6.simHuman.chr6 77678 30 + 601863 ATACCAATCCTGACACACTTTTGGCCACTG--------------------------------------- -s simRat_chr6.simRat.chr6 74411 69 + 647215 ACACCAATCCGGACTCAATTCTGAGAATCGTAAAGTTAATGGCTAAGCCTTCATATATGACAATGGTGG - -a -s simMouse_chr6.simMouse.chr6 82257 5 + 636262 GGTAT -s Anc0.Anc0refChr4 25755 3 - 45765 GGC-- -s Anc1.Anc1refChr2 57203 5 + 144309 GGCAT -s Anc2.Anc2refChr7 25882 3 + 32194 GGC-- -s mr.mrrefChr0 77810 5 + 130230 GGTAT -s simCow_chr6.simCow.chr6 84116 3 + 602619 GTC-- -s simDog_chr6.simDog.chr6 185310 3 + 593897 GGC-- -s simHuman_chr6.simHuman.chr6 77708 2 + 601863 ---AT -s simRat_chr6.simRat.chr6 74480 5 + 647215 GGTAT - -a -s simMouse_chr6.simMouse.chr6 82262 44 + 636262 AACCATGTCTTGTTAATATGGGTTTGTCAAGCCCATTAAGTATA -s Anc0.Anc0refChr4 25759 43 - 45765 AACCCTGTCTTAGCACTTAAAGTTTGGCCAGCC-ATTAAATATA -s Anc1.Anc1refChr2 57209 43 + 144309 AACCCTGTCTTAGCACTTAAAGTTTGGCCAGCC-ATTAAATATA -s Anc2.Anc2refChr7 25886 43 + 32194 AACCCTGTCTTAGCGCTTAAAGGTTGGCCAGCC-AATAAATATA -s mr.mrrefChr0 77815 44 + 130230 AACCATGTCTTGTTAATATGGGTTTGTCCAGCCCATTAAGTATA -s simCow_chr6.simCow.chr6 84120 33 + 602619 AACCCTGTCTTAGTGCTTGAA---TGGCCAGTC-CAT------- -s simDog_chr6.simDog.chr6 185314 42 + 593897 AACCCTGTCTGAGCG-TTAGAGGTGATCAGGCC-AACAAATATA -s simHuman_chr6.simHuman.chr6 77711 43 + 601863 AACCCTGTCTTAGCACTTAAAGTTTGGCCAGCC-ATTAAAGATA -s simRat_chr6.simRat.chr6 74485 44 + 647215 AACCATGTCTTGATAATATAGGTTTGTCCAGCCTGTCAAGTATA - -a -s simMouse_chr6.simMouse.chr6 82306 18 + 636262 GTCAATGTAAGGGGACTA -s Anc0.Anc0refChr4 25802 16 - 45765 GTGAATGTAAGAGGTT-- -s Anc1.Anc1refChr2 57252 16 + 144309 GTGAATGTAAGAGGTT-- -s Anc2.Anc2refChr7 25929 16 + 32194 GTGGGTGTAAGAGGTT-- -s mr.mrrefChr0 77859 16 + 130230 GTCAATGTAAGGGGAC-- -s simCow_chr6.simCow.chr6 84153 13 + 602619 ---GGTGTAAGAGGTT-- -s simDog_chr6.simDog.chr6 185358 16 + 593897 GTGGGTGTAAAAAGTG-- -s simHuman_chr6.simHuman.chr6 77754 16 + 601863 GTGAATGAAAGAGGTT-- -s simRat_chr6.simRat.chr6 74529 16 + 647215 GTCAATGTAAGGGGGC-- - -a -s simMouse_chr6.simMouse.chr6 82324 53 + 636262 TATGATGAACAGGTTACGACCTATATGTTAATGATCTAGAAGAAGTATGTTAC -s Anc0.Anc0refChr4 25819 52 - 45765 TTTAATGAAGAAATTATGATTTATATGTTAGTAATATAT-AGAAGCATATAAC -s Anc1.Anc1refChr2 57269 52 + 144309 TTTAATGAAGAAATTATGATTTATATGTTAGTAATATAT-AGAAGCATATAAC -s Anc2.Anc2refChr7 25946 52 + 32194 TTTAATGAGGAAATTATGATTTATATGTTAGTAATATAT-AGAAGCATATAAT -s mr.mrrefChr0 77875 53 + 130230 TGTGATGAACAGGTTATGATCTATATGTTAATGATCTAGAAGAAGCATGTTAC -s simCow_chr6.simCow.chr6 84167 52 + 602619 GTTAACGAGGAAGTTATGGTTTATATGTTAGGAATATAT-ATAAGCATTTCAC -s simDog_chr6.simDog.chr6 185375 52 + 593897 TTTAATGAGCAGATTATGATGTATATGTTAGTAATATAT-AGAAGCATATAAT -s simHuman_chr6.simHuman.chr6 77771 47 + 601863 TTTAATGAAGGATTTATGATTTATATGTTAGTAGTATAT-AGAAGC-----AC -s simRat_chr6.simRat.chr6 74545 53 + 647215 CGTGATGAACAGGCTATGATCTATATGTTAACGACTTAGAGGAAGCATGTTAC - -a -s simMouse_chr6.simMouse.chr6 82377 42 + 636262 CAAACACTGCCATCGCATTCAGATCCATAAGTAGACATCTAG -s Anc0.Anc0refChr4 25871 42 - 45765 CAAGTACTGCCATCGGATTCAGATCCATCAATAGACATCTAG -s Anc1.Anc1refChr2 57321 42 + 144309 CAAGTACTGCCATCGGATTCAGATCCATCAATAGACATCTAG -s Anc2.Anc2refChr7 25998 42 + 32194 GAAGTACTTCCATTGGATCCAGACCCATCAATACATATCAAG -s mr.mrrefChr0 77928 42 + 130230 CAAATACTGCCATCGCATTCAGATCCATAAATAGACATCTAG -s mr.mrrefChr3 166248 42 - 181027 CAAATGCTGCCATCAGGTTCAGTTCCAAAAATAGACACCTGG -s simCow_chr6.simCow.chr6 84219 41 + 602619 AGA-TACTTCCACTGGATCCAGGCCCATAAATAGACATCAAG -s simDog_chr6.simDog.chr6 185427 42 + 593897 GAAGTATCTCCATTGTATCCAGACCCATCAATGCATATCAAG -s simHuman_chr6.simHuman.chr6 77818 33 + 601863 AAAGTGCTCCCATCTGATTCAGATCCATCAATA--------- -s simMouse_chr6.simMouse.chr6 177199 42 - 636262 CAAATGCTGCCATCAGGTTCAGTTCCAAAAATAGACACCTGG -s simMouse_chr6.simMouse.chr6 177071 3 - 636262 CAA--------------------------------------- -s simRat_chr6.simRat.chr6 178761 42 - 647215 CAAATGCTGCCATCACATTCAGATCTAAAAATAGATCTCTAG -s simRat_chr6.simRat.chr6 74598 41 + 647215 CAAATG-TGCCATCAAATTCAGATCCATAAATAGACATCTAG - -a -s simMouse_chr6.simMouse.chr6 82419 1 + 636262 G -s Anc0.Anc0refChr4 25913 1 - 45765 G -s Anc1.Anc1refChr2 57363 1 + 144309 G -s Anc2.Anc2refChr7 26041 1 + 32194 G -s mr.mrrefChr0 77970 1 + 130230 G -s mr.mrrefChr3 166290 1 - 181027 A -s simCow_chr6.simCow.chr6 84261 1 + 602619 G -s simDog_chr6.simDog.chr6 185470 1 + 593897 G -s simHuman_chr6.simHuman.chr6 77851 1 + 601863 A -s simMouse_chr6.simMouse.chr6 177241 1 - 636262 A -s simRat_chr6.simRat.chr6 178803 1 - 647215 A -s simRat_chr6.simRat.chr6 74639 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 82420 13 + 636262 GCAAAGCACATAT -s Anc0.Anc0refChr4 25914 13 - 45765 GCAAAGTGTGCAT -s Anc1.Anc1refChr2 57364 13 + 144309 GCAAAGTGTGCAT -s Anc2.Anc2refChr7 26042 13 + 32194 GCAAAATGTGCAT -s mr.mrrefChr0 77971 13 + 130230 GCAAAGCACATAT -s mr.mrrefChr3 166291 13 - 181027 GCAAAGTGCATAT -s simCow_chr6.simCow.chr6 84262 12 + 602619 -CAAATTGTGCCT -s simDog_chr6.simDog.chr6 185472 13 + 593897 GCAAAATGTTTAT -s simHuman_chr6.simHuman.chr6 77852 13 + 601863 GCACACTGTGCAT -s simMouse_chr6.simMouse.chr6 177242 13 - 636262 GCAAAGTGCATAT -s simRat_chr6.simRat.chr6 178804 13 - 647215 GCAAAGCACATAT -s simRat_chr6.simRat.chr6 74640 13 + 647215 GCAGAGCACATAT - -a -s simMouse_chr6.simMouse.chr6 82433 6 + 636262 TCCTTT -s Anc0.Anc0refChr4 25928 6 - 45765 TACTAT -s Anc1.Anc1refChr2 57378 6 + 144309 TACTAT -s Anc2.Anc2refChr7 26056 6 + 32194 TACTAT -s mr.mrrefChr0 77984 6 + 130230 TACTTT -s mr.mrrefChr3 166304 6 - 181027 TACTTT -s simCow_chr6.simCow.chr6 84274 6 + 602619 TACTAT -s simDog_chr6.simDog.chr6 185486 6 + 593897 TACTAT -s simHuman_chr6.simHuman.chr6 77866 6 + 601863 TACTAT -s simMouse_chr6.simMouse.chr6 177255 6 - 636262 TACTTT -s simRat_chr6.simRat.chr6 178817 6 - 647215 TACTTT -s simRat_chr6.simRat.chr6 74653 6 + 647215 TACTTT - -a -s simMouse_chr6.simMouse.chr6 82439 1 + 636262 T -s Anc0.Anc0refChr4 25934 1 - 45765 T -s Anc1.Anc1refChr2 57384 1 + 144309 T -s Anc2.Anc2refChr7 26062 1 + 32194 T -s mr.mrrefChr0 77990 1 + 130230 T -s simCow_chr6.simCow.chr6 84280 1 + 602619 T -s simDog_chr6.simDog.chr6 185492 1 + 593897 T -s simHuman_chr6.simHuman.chr6 77872 1 + 601863 T -s simRat_chr6.simRat.chr6 74659 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 82440 1 + 636262 T -s Anc0.Anc0refChr4 25935 1 - 45765 T -s Anc1.Anc1refChr2 57385 1 + 144309 T -s Anc2.Anc2refChr7 26063 1 + 32194 T -s mr.mrrefChr0 77991 1 + 130230 T -s simCow_chr6.simCow.chr6 84281 1 + 602619 T -s simDog_chr6.simDog.chr6 185494 1 + 593897 T -s simHuman_chr6.simHuman.chr6 77873 1 + 601863 T -s simRat_chr6.simRat.chr6 74660 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 82441 8 + 636262 AACCATGC -s Anc0.Anc0refChr4 25936 8 - 45765 AACCACAC -s Anc1.Anc1refChr2 57386 8 + 144309 AACCACAC -s Anc2.Anc2refChr7 26064 8 + 32194 AACCACAC -s mr.mrrefChr0 77992 8 + 130230 AACCATGC -s mr.mrrefChr3 166310 8 - 181027 GGCCATCT -s simCow_chr6.simCow.chr6 84282 8 + 602619 AACCATAC -s simDog_chr6.simDog.chr6 185495 8 + 593897 AACCACAT -s simHuman_chr6.simHuman.chr6 77874 8 + 601863 AACCACAC -s simMouse_chr6.simMouse.chr6 177261 8 - 636262 GGCCATCT -s simRat_chr6.simRat.chr6 178823 8 - 647215 AACCATGT -s simRat_chr6.simRat.chr6 74661 8 + 647215 GACCGTGC - -a -s simMouse_chr6.simMouse.chr6 82449 26 + 636262 CACTTATCTTTCCTTAACCTGAGTAT -s Anc0.Anc0refChr4 25948 26 - 45765 CATGTATGTTTCCTTAGCCTGGGTAT -s Anc1.Anc1refChr2 57398 26 + 144309 CATGTATGTTTCCTTAGCCTGGGTAT -s Anc2.Anc2refChr7 26076 26 + 32194 GATGTATGTTTCCTTGGCCTGGGTGT -s mr.mrrefChr0 78000 26 + 130230 CACATATCTTTCCTTAACCTGAGTAT -s mr.mrrefChr3 166318 26 - 181027 CACATATCATTGCTTAGCCTGATCAT -s simCow_chr6.simCow.chr6 84294 26 + 602619 TATGTATGTTTCCTTGGCCTGGGTGA -s simDog_chr6.simDog.chr6 185507 26 + 593897 GATGCATGTTTCCTGGCTCTGGGTGT -s simHuman_chr6.simHuman.chr6 77886 26 + 601863 CATGTATGCTTCTTTAGCCTGGGTTT -s simMouse_chr6.simMouse.chr6 177269 26 - 636262 CACATATCATTGCTTAGCCTGATCAT -s simRat_chr6.simRat.chr6 178831 26 - 647215 CACATATCTTTCCATAACCTAAGCAT -s simRat_chr6.simRat.chr6 74669 26 + 647215 CACATATCTTTCCTTAACCTGAGTAT - -a -s simMouse_chr6.simMouse.chr6 82475 5 + 636262 CCAGC -s Anc0.Anc0refChr4 25975 5 - 45765 TCAGC -s Anc1.Anc1refChr2 57425 5 + 144309 TCAGC -s Anc2.Anc2refChr7 26103 5 + 32194 TCAGC -s mr.mrrefChr0 78026 5 + 130230 CCAGC -s mr.mrrefChr3 166345 5 - 181027 CCAGC -s simCow_chr6.simCow.chr6 84321 4 + 602619 TCAG- -s simDog_chr6.simDog.chr6 185534 5 + 593897 TCAGC -s simHuman_chr6.simHuman.chr6 77913 5 + 601863 TCAGC -s simMouse_chr6.simMouse.chr6 177296 5 - 636262 CCAGC -s simRat_chr6.simRat.chr6 178858 5 - 647215 CCAGC -s simRat_chr6.simRat.chr6 74695 5 + 647215 CCAGC - -a -s simMouse_chr6.simMouse.chr6 82480 2 + 636262 AT -s Anc0.Anc0refChr4 25983 2 - 45765 AT -s Anc1.Anc1refChr2 57433 2 + 144309 AT -s Anc2.Anc2refChr7 26111 2 + 32194 AT -s mr.mrrefChr0 78031 2 + 130230 AT -s mr.mrrefChr3 166353 2 - 181027 AT -s simCow_chr6.simCow.chr6 84328 2 + 602619 GT -s simDog_chr6.simDog.chr6 185542 2 + 593897 AT -s simHuman_chr6.simHuman.chr6 77921 2 + 601863 AT -s simMouse_chr6.simMouse.chr6 177304 2 - 636262 AT -s simRat_chr6.simRat.chr6 178866 2 - 647215 AT -s simRat_chr6.simRat.chr6 74700 2 + 647215 AT - -a -s simMouse_chr6.simMouse.chr6 82482 15 + 636262 ATAATAATAGGAACA -s Anc0.Anc0refChr4 25985 15 - 45765 GTAACATTGAGAATA -s Anc1.Anc1refChr2 57435 15 + 144309 GTAACATTGAGAATA -s Anc2.Anc2refChr7 26113 15 + 32194 GTAACATTGAGAATA -s mr.mrrefChr0 78033 15 + 130230 ATAATAATGGGAACA -s mr.mrrefChr3 166355 15 - 181027 ATAATAATGGGAACA -s simCow_chr6.simCow.chr6 84330 15 + 602619 GTAGGATTGAGAATC -s simDog_chr6.simDog.chr6 185544 15 + 593897 GTGACATTGAGAATA -s simHuman_chr6.simHuman.chr6 77924 15 + 601863 GTAACATTGAGAATG -s simMouse_chr6.simMouse.chr6 177306 15 - 636262 ATAATAATGGGAACA -s simRat_chr6.simRat.chr6 178868 15 - 647215 AGAATGATGGGAACA -s simRat_chr6.simRat.chr6 74702 15 + 647215 ATAATGATGGGAACA - -a -s simMouse_chr6.simMouse.chr6 82497 23 + 636262 AATCAAAGCTACTTGGGTACCTA -s Anc0.Anc0refChr4 26002 22 - 45765 AA-CAAAGCGGTTTGAGTGCCAA -s Anc1.Anc1refChr2 57452 23 + 144309 AATCAAAGCGGTTTGAGTGCCAA -s Anc2.Anc2refChr7 26130 22 + 32194 AA-CAAAGCGGTTTAAGTGTCAA -s mr.mrrefChr0 78050 23 + 130230 AATCAAAGCTACTTGGGTACCTA -s mr.mrrefChr3 166372 23 - 181027 AATCAAAGTTACTTGAGTACCAA -s simCow_chr6.simCow.chr6 84347 22 + 602619 AA-TAAAGCAGTTTAAGTGTCAA -s simDog_chr6.simDog.chr6 185561 22 + 593897 AA-CAAAGGGACTTAAGTGTCAA -s simHuman_chr6.simHuman.chr6 77941 18 + 601863 AA-----GCGGTTAGAATGCCAA -s simMouse_chr6.simMouse.chr6 177323 23 - 636262 AATCAAAGTTACTTGAGTACCAA -s simRat_chr6.simRat.chr6 178885 23 - 647215 AATCAAAGCTACTTGAGTACCAA -s simRat_chr6.simRat.chr6 74719 22 + 647215 AATCAAAGCTACTTGGGTAC-TA - -a -s simMouse_chr6.simMouse.chr6 82520 3 + 636262 ATG -s Anc0.Anc0refChr4 26024 3 - 45765 AGG -s Anc1.Anc1refChr2 57475 3 + 144309 AGG -s Anc2.Anc2refChr7 26152 3 + 32194 AGG -s mr.mrrefChr0 78073 3 + 130230 AGG -s simCow_chr6.simCow.chr6 84369 3 + 602619 AAA -s simDog_chr6.simDog.chr6 185583 3 + 593897 AGG -s simHuman_chr6.simHuman.chr6 77959 3 + 601863 AGG -s simRat_chr6.simRat.chr6 74741 3 + 647215 AGG - -a -s simMouse_chr6.simMouse.chr6 82523 1 + 636262 T -s Anc0.Anc0refChr4 26027 1 - 45765 T -s Anc1.Anc1refChr2 57478 1 + 144309 T -s Anc2.Anc2refChr7 26155 1 + 32194 T -s mr.mrrefChr0 78076 1 + 130230 T -s mr.mrrefChr3 166395 1 - 181027 T -s simCow_chr6.simCow.chr6 84372 1 + 602619 T -s simDog_chr6.simDog.chr6 185586 1 + 593897 T -s simHuman_chr6.simHuman.chr6 77962 1 + 601863 T -s simMouse_chr6.simMouse.chr6 177346 1 - 636262 T -s simRat_chr6.simRat.chr6 178908 1 - 647215 T -s simRat_chr6.simRat.chr6 74744 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 82524 5 + 636262 GATCG -s Anc0.Anc0refChr4 26033 5 - 45765 GATTG -s Anc1.Anc1refChr2 57484 5 + 144309 GATTG -s Anc2.Anc2refChr7 26161 5 + 32194 GATTG -s mr.mrrefChr0 78077 5 + 130230 GATCG -s mr.mrrefChr3 166396 5 - 181027 GCTCA -s simCow_chr6.simCow.chr6 84378 5 + 602619 GATTG -s simDog_chr6.simDog.chr6 185592 5 + 593897 GATTG -s simHuman_chr6.simHuman.chr6 77968 5 + 601863 GATTG -s simMouse_chr6.simMouse.chr6 177347 5 - 636262 GCTCA -s simRat_chr6.simRat.chr6 178909 5 - 647215 GCTGA - -a -s simMouse_chr6.simMouse.chr6 82529 29 + 636262 GTCTGCATGCTCAAATTCTTAGAGCTCAC -s Anc0.Anc0refChr4 26043 29 - 45765 GTCCACATGTTCATATCCCAAGAGTTCAG -s Anc1.Anc1refChr2 57494 29 + 144309 GTCCACATGTTCATATCCCAAGAGTTCAG -s Anc2.Anc2refChr7 26173 29 + 32194 GTCCACATGTTCATATCCCAAGAGTTCAG -s mr.mrrefChr0 78082 29 + 130230 GTCTGCATGCTCAAATTCTTAGAGCTCAC -s mr.mrrefChr3 166401 29 - 181027 TTCGGCATATTCAAATTCTGAGAGCCTTC -s simCow_chr6.simCow.chr6 84390 28 + 602619 GTCCACATGTCCATATCACAA-AGTACAA -s simDog_chr6.simDog.chr6 185604 29 + 593897 GTTGACATACTCAGATCCCAAGAGCTCAG -s simHuman_chr6.simHuman.chr6 77978 29 + 601863 GTCCACATGTTGATATCGCAAGAGTTCAG -s simMouse_chr6.simMouse.chr6 177363 29 - 636262 TTCGGCATATTCAAATTCTGAGAGCCTTC -s simRat_chr6.simRat.chr6 178914 29 - 647215 TTCTGTATGTTCAAATTCTGAGAGCTTAC -s simRat_chr6.simRat.chr6 74745 19 + 647215 ----------TCAAATTCTGAGAGCTTAC - -a -s simMouse_chr6.simMouse.chr6 82558 8 + 636262 TTACGTTT -s Anc0.Anc0refChr4 26073 8 - 45765 TCACCATT -s Anc1.Anc1refChr2 57524 8 + 144309 TCACCATT -s Anc2.Anc2refChr7 26203 8 + 32194 TCACCATT -s mr.mrrefChr0 78112 8 + 130230 TTACGTTT -s mr.mrrefChr3 166431 8 - 181027 TCATGTTT -s simCow_chr6.simCow.chr6 84419 8 + 602619 TCACCATT -s simDog_chr6.simDog.chr6 185634 8 + 593897 TCACCATT -s simHuman_chr6.simHuman.chr6 78008 8 + 601863 TTACCATT -s simMouse_chr6.simMouse.chr6 177393 8 - 636262 TCATGTTT -s simRat_chr6.simRat.chr6 178944 8 - 647215 TCATTTTT -s simRat_chr6.simRat.chr6 74765 8 + 647215 TCACGTTT - -a -s simMouse_chr6.simMouse.chr6 82566 9 + 636262 AACACCACT -s Anc0.Anc0refChr4 26081 9 - 45765 AAGACCATT -s Anc1.Anc1refChr2 57532 9 + 144309 AAGACCATT -s Anc2.Anc2refChr7 26211 9 + 32194 AAGACCATT -s mr.mrrefChr0 78120 9 + 130230 AACACCACT -s mr.mrrefChr3 166439 9 - 181027 AACACCACT -s simCow_chr6.simCow.chr6 84427 8 + 602619 A-GACAATC -s simDog_chr6.simDog.chr6 185642 9 + 593897 GAGTCCATT -s simHuman_chr6.simHuman.chr6 78016 9 + 601863 AAGACCATA -s simMouse_chr6.simMouse.chr6 177402 9 - 636262 AACACCACT -s simRat_chr6.simRat.chr6 178952 9 - 647215 AACACCACT -s simRat_chr6.simRat.chr6 74773 9 + 647215 AATACCACT - -a -s simMouse_chr6.simMouse.chr6 82575 1 + 636262 A -s Anc0.Anc0refChr4 26090 1 - 45765 A -s Anc1.Anc1refChr2 57541 1 + 144309 A -s Anc2.Anc2refChr7 26220 1 + 32194 A -s mr.mrrefChr0 78129 1 + 130230 A -s simCow_chr6.simCow.chr6 84435 1 + 602619 G -s simDog_chr6.simDog.chr6 185651 1 + 593897 A -s simHuman_chr6.simHuman.chr6 78025 1 + 601863 A -s simRat_chr6.simRat.chr6 74782 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 82576 5 + 636262 GGAAA -s Anc0.Anc0refChr4 26091 5 - 45765 GGAAA -s Anc1.Anc1refChr2 57542 5 + 144309 GGAAA -s Anc2.Anc2refChr7 26221 5 + 32194 AGATA -s mr.mrrefChr0 78130 5 + 130230 GGAAA -s mr.mrrefChr3 166448 5 - 181027 GGAAA -s simCow_chr6.simCow.chr6 84436 5 + 602619 ATAAA -s simDog_chr6.simDog.chr6 185652 5 + 593897 AGATA -s simHuman_chr6.simHuman.chr6 78026 5 + 601863 GGAGA -s simMouse_chr6.simMouse.chr6 177412 5 - 636262 GGAAA -s simRat_chr6.simRat.chr6 178961 5 - 647215 AGAAA -s simRat_chr6.simRat.chr6 74783 5 + 647215 GGAAA - -a -s simMouse_chr6.simMouse.chr6 82581 5 + 636262 AGTGA -s Anc0.Anc0refChr4 26097 5 - 45765 AGAAA -s Anc1.Anc1refChr2 57548 5 + 144309 AGAAA -s Anc2.Anc2refChr7 26227 5 + 32194 AGAAA -s mr.mrrefChr0 78135 5 + 130230 AGTGA -s mr.mrrefChr3 166453 5 - 181027 AGCAA -s simCow_chr6.simCow.chr6 84442 5 + 602619 AAAAA -s simDog_chr6.simDog.chr6 185658 5 + 593897 AGAAA -s simHuman_chr6.simHuman.chr6 78032 5 + 601863 AGAAA -s simMouse_chr6.simMouse.chr6 177417 5 - 636262 AGCAA -s simRat_chr6.simRat.chr6 178966 5 - 647215 ATCAA -s simRat_chr6.simRat.chr6 74788 5 + 647215 AGTGA - -a -s simMouse_chr6.simMouse.chr6 82586 2 + 636262 CT -s Anc0.Anc0refChr4 26102 2 - 45765 CT -s Anc1.Anc1refChr2 57553 2 + 144309 CT -s Anc2.Anc2refChr7 26232 2 + 32194 AT -s mr.mrrefChr0 78140 2 + 130230 CT -s mr.mrrefChr3 166458 2 - 181027 CT -s simCow_chr6.simCow.chr6 84447 2 + 602619 CT -s simDog_chr6.simDog.chr6 185663 2 + 593897 AT -s simHuman_chr6.simHuman.chr6 78037 2 + 601863 TT -s simMouse_chr6.simMouse.chr6 177422 2 - 636262 CT -s simRat_chr6.simRat.chr6 178976 2 - 647215 CT -s simRat_chr6.simRat.chr6 74793 2 + 647215 CT - -a -s simMouse_chr6.simMouse.chr6 82588 1 + 636262 A -s Anc0.Anc0refChr4 26104 1 - 45765 A -s Anc1.Anc1refChr2 57555 1 + 144309 A -s Anc2.Anc2refChr7 26234 1 + 32194 A -s mr.mrrefChr0 78142 1 + 130230 A -s simCow_chr6.simCow.chr6 84449 1 + 602619 A -s simDog_chr6.simDog.chr6 185665 1 + 593897 A -s simHuman_chr6.simHuman.chr6 78039 1 + 601863 A -s simRat_chr6.simRat.chr6 74795 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 82589 4 + 636262 GCCT -s Anc0.Anc0refChr4 26107 4 - 45765 GCCT -s Anc1.Anc1refChr2 57558 4 + 144309 GCCT -s Anc2.Anc2refChr7 26237 4 + 32194 GCTT -s mr.mrrefChr0 78143 4 + 130230 GCCT -s simCow_chr6.simCow.chr6 84452 4 + 602619 GCAT -s simDog_chr6.simDog.chr6 185668 4 + 593897 GCTT -s simHuman_chr6.simHuman.chr6 78042 4 + 601863 ACCT -s simRat_chr6.simRat.chr6 74796 4 + 647215 GCCT - -a -s simMouse_chr6.simMouse.chr6 82593 29 + 636262 GTCAGAAGGCGTCATGTCACTAATAATAT -s Anc0.Anc0refChr4 26111 29 - 45765 GTCAGAAAGTgttgtgtcactaatattat -s Anc1.Anc1refChr2 57562 29 + 144309 GTCAGAAAGTgttgtgtcactaatattat -s Anc2.Anc2refChr7 26241 29 + 32194 GTCAGAAAGTgttgtgtcactaatgttgt -s mr.mrrefChr0 78147 29 + 130230 GTCAGAAGGTGTCATGTCACTAATAATAT -s mr.mrrefChr3 166460 29 - 181027 GTTAGAAGGTGTTGTGTCACTGTTAATAT -s simCow_chr6.simCow.chr6 84456 29 + 602619 GTCAGAAAGTGTTCTGTCACTAAAGTTGT -s simDog_chr6.simDog.chr6 185672 28 + 593897 GACAGAAAgtgttgtgtcacta-tgttgc -s simHuman_chr6.simHuman.chr6 78046 29 + 601863 GTCAGAAAATgttgtgtcactaacattat -s simMouse_chr6.simMouse.chr6 177424 29 - 636262 GTTAGAAGGTGTTGTGTCACTGTTAATAT -s simRat_chr6.simRat.chr6 178978 29 - 647215 GTCAGAAGGTGTTGTGTCACTAATAATAT -s simRat_chr6.simRat.chr6 74800 29 + 647215 GTCAGAAGGTGTCATGTCACTAATAATAT - -a -s simMouse_chr6.simMouse.chr6 82622 30 + 636262 TCCTGATTTCATACACCCTATTGAATGTCA -s Anc0.Anc0refChr4 26140 30 - 45765 tccctctttcttgcaccataccaaatttca -s Anc1.Anc1refChr2 57591 30 + 144309 tccctctttcttgcaccataccaaatttca -s Anc2.Anc2refChr7 26270 30 + 32194 tccctctttctcgaaccatagcaaatttca -s mr.mrrefChr0 78176 30 + 130230 TCCTGCTTTCATACACCCTACTAAATGTCA -s mr.mrrefChr3 166489 30 - 181027 TCCTGCTTCCATACAACTTATTGAATAACA -s simCow_chr6.simCow.chr6 84485 30 + 602619 TCCCTCTTCCTGGAACTATAACAAACGTCA -s simDog_chr6.simDog.chr6 185700 30 + 593897 tccccctttgtcaaaccatagcaaatttca -s simHuman_chr6.simHuman.chr6 78075 30 + 601863 tccctctttcttgcaccataccaaatctca -s simMouse_chr6.simMouse.chr6 177453 30 - 636262 TCCTGCTTCCATACAACTTATTGAATAACA -s simRat_chr6.simRat.chr6 179007 30 - 647215 TCCTGCTGACATGCACTCTATTGAATGTCA -s simRat_chr6.simRat.chr6 74844 30 + 647215 TCCTGCTTCCATACACCCTACTAAGTGTCA - -a -s simMouse_chr6.simMouse.chr6 82652 55 + 636262 TTACTGTATAAGGTTATGTTGTTGATACTACTCCCTTTCCACTGCACATTTTTAA -s Anc0.Anc0refChr4 26170 50 - 45765 TCAcaccataaggttgtgc--ctgacattactccctcttcactgca---ttttTA -s Anc1.Anc1refChr2 57621 55 + 144309 TCAcaccataaggttgtgcTGctgacattactccctcttcactgcaCATttttTA -s Anc2.Anc2refChr7 26301 50 + 32194 TCCcaccataaggttgtcc--ctgacattactccctcttcactgca---ttttTA -s mr.mrrefChr0 78206 55 + 130230 TTACAGCATAAGGTTATGTTGTTGATATTACTCCCTTTCCACTGCACATTTTTAA -s mr.mrrefChr3 166519 55 - 181027 TTTCAGTATAAGCTTGTGCTGTTGACATTACTCCCTTTCCACTGGACATTTTTAA -s simCow_chr6.simCow.chr6 84516 39 + 602619 TCCCACCATAACTTCCTCA--CTGATATTCCTCCCTCTGCA-------------- -s simDog_chr6.simDog.chr6 185731 50 + 593897 ccccaccataaggttgtcc--ctgactttacttgctcgtcactgca---ttttTA -s simHuman_chr6.simHuman.chr6 78303 52 + 601863 TCAcaccataaggttatgatgctgacattactccctcttcactgca---ttttTA -s simMouse_chr6.simMouse.chr6 177483 55 - 636262 TTTCAGTATAAGCTTGTGCTGTTGACATTACTCCCTTTCCACTGGACATTTTTAA -s simRat_chr6.simRat.chr6 179037 55 - 647215 TTTCAGTATAAGGCTGTGCTGTTGACATTACTCCCTTTCCACTGCACATATTTAA -s simRat_chr6.simRat.chr6 74874 55 + 647215 TTACAGCATGAGGCTATGCTGTTGAGATTACTCCCTTCCCACTGCGCATTTTTAA - -a -s simMouse_chr6.simMouse.chr6 82707 10 + 636262 TTCTCAGTTT -s Anc0.Anc0refChr4 26220 10 - 45765 tccttaGttt -s Anc1.Anc1refChr2 57676 10 + 144309 TCCTTAGtTT -s Anc2.Anc2refChr7 26351 10 + 32194 tccttaAttt -s mr.mrrefChr0 78261 10 + 130230 TTCTCAGTTT -s mr.mrrefChr3 166574 10 - 181027 TTCTCAGTTT -s simCow_chr6.simCow.chr6 84555 4 + 602619 ------ATtt -s simDog_chr6.simDog.chr6 185782 10 + 593897 tccttaattt -s simHuman_chr6.simHuman.chr6 78355 8 + 601863 TCCTTCGt-- -s simMouse_chr6.simMouse.chr6 177538 10 - 636262 TTCTCAGTTT -s simRat_chr6.simRat.chr6 179092 10 - 647215 TCCTCAGTTT -s simRat_chr6.simRat.chr6 74929 10 + 647215 TTCTCTGTTT - -a -s simMouse_chr6.simMouse.chr6 82717 18 + 636262 TCAACTGACTCCCTAATG -s Anc0.Anc0refChr4 26231 18 - 45765 ttggctgactccctagag -s Anc1.Anc1refChr2 57687 18 + 144309 ttggctgactccctagag -s Anc2.Anc2refChr7 26362 18 + 32194 tttgctaaccccctagag -s mr.mrrefChr0 78272 18 + 130230 TTGACTGACTCCCTAATG -s mr.mrrefChr3 166585 18 - 181027 TTGACTGACTCCCTAATA -s simCow_chr6.simCow.chr6 84560 18 + 602619 tttgctaaccccctagag -s simDog_chr6.simDog.chr6 185793 18 + 593897 tttgctaaccccctagca -s simHuman_chr6.simHuman.chr6 78364 18 + 601863 ttggctcactccgtagag -s simMouse_chr6.simMouse.chr6 177549 18 - 636262 TTGACTGACTCCCTAATA -s simRat_chr6.simRat.chr6 179103 18 - 647215 TCAACTGACTCCGTAATG -s simRat_chr6.simRat.chr6 74940 18 + 647215 TTGACTGACTCCCTAATG - -a -s simMouse_chr6.simMouse.chr6 82735 20 + 636262 ACTACACATGCTTCAATAAT -s Anc0.Anc0refChr4 26252 20 - 45765 accctaaaagccttaaaact -s Anc1.Anc1refChr2 57708 20 + 144309 accctaaaagccttaaaact -s Anc2.Anc2refChr7 26385 20 + 32194 accctgaaagccttaaaact -s mr.mrrefChr0 78290 20 + 130230 actACACATGcttcaataat -s mr.mrrefChr3 166603 20 - 181027 ACCACACATGCCTCGATAAT -s simCow_chr6.simCow.chr6 84583 20 + 602619 accttgagagcctaaaaact -s simDog_chr6.simDog.chr6 185816 20 + 593897 accctgaaagccctaaaact -s simHuman_chr6.simHuman.chr6 78385 20 + 601863 actctaaaagtcttaaaact -s simMouse_chr6.simMouse.chr6 177567 20 - 636262 ACCACACATGCCTCGATAAT -s simRat_chr6.simRat.chr6 179121 20 - 647215 ATTATAGATGCCTCAATAAT -s simRat_chr6.simRat.chr6 74958 7 + 647215 ---ACACATG---------- - -a -s simMouse_chr6.simMouse.chr6 82755 24 + 636262 ATACTGCTCAAGAACTATCACATC -s Anc0.Anc0refChr4 26275 22 - 45765 --gctgctcaagctctatcacatc -s Anc1.Anc1refChr2 57731 24 + 144309 ctgctgctcaagctctatcacatc -s Anc2.Anc2refChr7 26408 22 + 32194 --gctcctccagctttatcacatc -s mr.mrrefChr0 78310 24 + 130230 atactgctcaagaacTATCACATC -s mr.mrrefChr3 166623 24 - 181027 CTACTGCTCAAGGTCCATCACATC -s simCow_chr6.simCow.chr6 84606 22 + 602619 --actccccttgctctatcacatc -s simDog_chr6.simDog.chr6 185839 22 + 593897 --gttccttcaactttatcacatc -s simHuman_chr6.simHuman.chr6 78408 24 + 601863 ccgcctctcaagctgtatcacatc -s simMouse_chr6.simMouse.chr6 177587 24 - 636262 CTACTGCTCAAGGTCCATCACATC -s simRat_chr6.simRat.chr6 179141 24 - 647215 GTACTGGTCAAGATCCATCACATC -s simRat_chr6.simRat.chr6 74965 9 + 647215 ---------------TATCACATC - -a -s simMouse_chr6.simMouse.chr6 82779 16 + 636262 CTAGTGATTGAACCCA -s Anc0.Anc0refChr4 26297 16 - 45765 ctagtaactgaactaa -s Anc1.Anc1refChr2 57755 16 + 144309 ctagtaactgaactaa -s Anc2.Anc2refChr7 26430 16 + 32194 ctagtaactgaactaa -s mr.mrrefChr0 78334 16 + 130230 CTAGTGACTGAACCCA -s simCow_chr6.simCow.chr6 84628 16 + 602619 ctagtacctgaaCAAA -s simDog_chr6.simDog.chr6 185861 11 + 593897 ctagtaac-----taa -s simHuman_chr6.simHuman.chr6 78432 16 + 601863 ctcataacctaactaa -s simRat_chr6.simRat.chr6 74974 16 + 647215 TTAGTGACTGAACCCA - -a -s simMouse_chr6.simMouse.chr6 82795 17 + 636262 ATGGGGGAAAGCAAAGT -s Anc0.Anc0refChr4 26313 17 - 45765 aagagagatatggAAGA -s Anc1.Anc1refChr2 57771 17 + 144309 aagagagatatggAAGA -s Anc2.Anc2refChr7 26446 17 + 32194 aagagagatatggAAGA -s mr.mrrefChr0 78350 17 + 130230 ATGGGGGAAAGGAAAGT -s simCow_chr6.simCow.chr6 84644 17 + 602619 AATAGAGATATGGAAGA -s simDog_chr6.simDog.chr6 185872 17 + 593897 aagagtgatatggCAGA -s simHuman_chr6.simHuman.chr6 78448 17 + 601863 cagaaagatatggaaGG -s simRat_chr6.simRat.chr6 74993 17 + 647215 ATGGGGGACAGGTAAGT - -a -s simMouse_chr6.simMouse.chr6 82812 45 + 636262 AAATCGCAGAGTTAACATCTCCAGACCATTTTTCTATAGATCATC -s Anc0.Anc0refChr4 26330 31 - 45765 AAGTATCAAAGT--------------CACTCTCTTCCAGATCAAC -s Anc1.Anc1refChr2 57788 31 + 144309 AAGTATCAAAGT--------------CACTCTCTTCCAGATCAAC -s Anc2.Anc2refChr7 26463 31 + 32194 AAGTATCAAAGT--------------CCCTCTCTTCCAGATCAAC -s mr.mrrefChr0 78367 45 + 130230 AAATCGCAGAGTTAACATCTCCAGACCATTTTTCTATAGATCATC -s simCow_chr6.simCow.chr6 84661 31 + 602619 AAGTATCAACAC--------------CTCTCTCTTCCAGATCAAC -s simDog_chr6.simDog.chr6 185894 31 + 593897 AAGTATTAGAGT--------------CCCTTTCTTCCAAATGAAC -s simHuman_chr6.simHuman.chr6 78465 31 + 601863 AAGTATCAAAGT--------------CACTCTCTTCCAGATCGAC -s simRat_chr6.simRat.chr6 75010 45 + 647215 AAATTGCAGAGTACACATCTTGAGACAATCTTTCCATAGATCATC - -a -s simMouse_chr6.simMouse.chr6 82857 22 + 636262 ATGCAAGTGGAGGCTGGGTCTA -s Anc0.Anc0refChr4 26365 18 - 45765 ATGCAAGA----GCTGGCCCTG -s Anc1.Anc1refChr2 57823 18 + 144309 ATGCAAGA----GCTGGCCCTG -s Anc2.Anc2refChr7 26498 18 + 32194 AGGCAAGA----GTAGGCCATG -s mr.mrrefChr0 78416 22 + 130230 ATGCAAGTGGAGGCTGGGTCTA -s simCow_chr6.simCow.chr6 84696 11 + 602619 A-----------GTAGGCCATG -s simDog_chr6.simDog.chr6 185929 18 + 593897 TGGCAAGA----GTAGGCCATG -s simHuman_chr6.simHuman.chr6 78500 18 + 601863 ATGCAAGA----GCTGGCCCTG -s simRat_chr6.simRat.chr6 75059 22 + 647215 ATGCAAGGGGAGGCTGGGTCTC - -a -s simMouse_chr6.simMouse.chr6 82879 1 + 636262 C -s Anc0.Anc0refChr4 26383 1 - 45765 C -s Anc1.Anc1refChr2 57841 1 + 144309 C -s Anc2.Anc2refChr7 26516 1 + 32194 G -s mr.mrrefChr0 78438 1 + 130230 C -s simCow_chr6.simCow.chr6 84711 1 + 602619 G -s simDog_chr6.simDog.chr6 185947 1 + 593897 G -s simHuman_chr6.simHuman.chr6 78518 1 + 601863 C -s simRat_chr6.simRat.chr6 75081 1 + 647215 C - -a -s simMouse_chr6.simMouse.chr6 82880 44 + 636262 TTGGTTAGATCCCAACTGACATCAGTTGGCATACCCAGCACGGT -s Anc0.Anc0refChr4 26392 8 - 45765 CTGTTTAT------------------------------------ -s Anc1.Anc1refChr2 57850 8 + 144309 CTGTTTAT------------------------------------ -s Anc2.Anc2refChr7 26527 8 + 32194 CTGTTTAT------------------------------------ -s mr.mrrefChr0 78439 44 + 130230 TTGGTTAGATCCCAACTGACATCAGTTGGCATACCCAGCACGGT -s simCow_chr6.simCow.chr6 84722 8 + 602619 CTGGTTTT------------------------------------ -s simDog_chr6.simDog.chr6 185958 8 + 593897 CTATTTAT------------------------------------ -s simHuman_chr6.simHuman.chr6 78527 8 + 601863 CTGTTTAA------------------------------------ -s simRat_chr6.simRat.chr6 75082 44 + 647215 TTGGTCAGAGTCAGACTGACATCAGTTGGCATACCCAGTATGGG - -a -s simMouse_chr6.simMouse.chr6 82924 90 + 636262 GCGGCCTTCTAAGTCCAACCATCCATGCAGACCCTTAGCCTCACAGGAGGTTAGCTTGGGACACCAAAGCATAGGGCATCAGGAACCTCT -s Anc0.Anc0refChr4 26400 82 - 45765 -------TCTAAATGGAACCATCCATGCAGACCC-TGTACTCAAAGGGGATTAGCTTGGGACATTAAAGTATTGGGTGTCATGAACAGCT -s Anc1.Anc1refChr2 57858 83 + 144309 -------TCTAAATGGAACCATCCATGCAGACCCGTGTACTCAAAGGGGATTAGCTTGGGACATTAAAGTATTGGGTGTCATGAACAGCT -s Anc2.Anc2refChr7 26535 82 + 32194 -------TCTAAATGGAACCATCCATGCAGACCC-TGTACTGAAAGGGGATTAGCTTGGGACATTAAAGTATTTGCTGTCATGAACAGCT -s mr.mrrefChr0 78483 90 + 130230 GCGGCCTTCTAAATCCAACCATCCATGCAGACCCTTATCCTCACAGGAGGTTAGCTTGGGACACCAAAGCATAGGGTATCAGGAACCTCT -s simCow_chr6.simCow.chr6 84730 78 + 602619 -------T----ATGGGAGCATCCATGTAGGCCC-TGTGCTGATAGGGGCTTAACCTGGGACATTAGAATAGTTGGTGTCATGAACAGCT -s simDog_chr6.simDog.chr6 185966 79 + 593897 -------TCTAAATGGAACCATCCATGCAGACCC-TGTACGGAAGGGGGATTAGCTCGGGACATGAAAGTATTTGCTGTCATGAACA--- -s simHuman_chr6.simHuman.chr6 78535 81 + 601863 -------TCTAAATGGAGCCATCCATGCAGACCCGTGTACTCAAAGGGGTTTAGCTTGGGGTATTAAAGTGTTGGGTCTC--TAACACCT -s simRat_chr6.simRat.chr6 75191 90 + 647215 GAGGCCTTCCAAATACAACCATCCATGCAGACCCTTATGCTCAGAGGATGCTAGCTTGGGACACCAAAGCACAGGGTGTCATGAACCCCT - -a -s simMouse_chr6.simMouse.chr6 83014 71 + 636262 GTCACCAGCCTCCGAACCCCGCACACTCTATAAAACACTATTCTCTCATCGTCCCAGAAATTATATAGTTT -s Anc0.Anc0refChr4 26485 41 - 45765 G------GTCTCAGAACCCAGGGCACTCTGTGGCATACTATTCT------------------------TTT -s Anc1.Anc1refChr2 57944 41 + 144309 G------GTCTCAGAACCCAGGGCACTCTGTGGCATACTATTCT------------------------TTT -s Anc2.Anc2refChr7 26620 41 + 32194 A------GTCTCAGCACCCAGGGCACTCTGTGGCATACTATTCT------------------------TTT -s mr.mrrefChr0 78573 65 + 130230 G------GCCTCCGAACCCAGGGCACTCTATGGAACACTATTCTCTCATCGTCCCAGAAATTATATAGTTT -s simCow_chr6.simCow.chr6 84811 40 + 602619 A------GTTTCAGC-TGCAGGGCACTGTGGGGTACACTATTCT------------------------TTT -s simDog_chr6.simDog.chr6 186045 28 + 593897 --------TCTCAGCACCCAAGACACTCTGTGGCAT----------------------------------- -s simHuman_chr6.simHuman.chr6 78619 41 + 601863 G------GTCTCAGAGCCCAGGGCACCCTGTGGCATATCATTCT------------------------TTG -s simRat_chr6.simRat.chr6 75281 65 + 647215 G------GCCTCCAAACCCAGGGCACTCTATGGGACACTATCCTCTCATCAACCTAGAAATTACATAGCAT - -a -s simMouse_chr6.simMouse.chr6 83085 44 + 636262 CTGAGCTTGTACTTCAAACTCATCCATAGGCAGGTCTAGTCAAT -s Anc0.Anc0refChr4 26526 42 - 45765 CTGAGCTTGTACTTCAAACTATTCCATAGGTATCTCCAGTT--T -s Anc1.Anc1refChr2 57985 44 + 144309 CTGAGCTTGTACTTCAAACTATTCCATAGGTATCTCCAGTTAGT -s Anc2.Anc2refChr7 26661 42 + 32194 CTGGGCTTGGACTTCAAACTATTGCATTTGTATCTCTAGTT--T -s mr.mrrefChr0 78638 44 + 130230 CTGAGCTTGTACTTCAAACTCATCCATAGGTAGGTCCAGTCAAT -s simCow_chr6.simCow.chr6 84875 41 + 602619 CTGGGCTTGGACTTCAAACTATTGCATTTGTATCTCTAGTT--- -s simDog_chr6.simDog.chr6 186073 1 + 593897 -------------------------------------------T -s simHuman_chr6.simHuman.chr6 78660 44 + 601863 CTGAGCTTGTACTTCAAACTATTCCATAGGTATCTCCAGTTAGT -s simRat_chr6.simRat.chr6 75346 44 + 647215 CTGAGCCGGTGCTTCAAACTCATACATAGGTAGGGCCAGTCTAT - -a -s simMouse_chr6.simMouse.chr6 83129 18 + 636262 TTCACCCCTCAAGCTGCT -s Anc0.Anc0refChr4 26568 18 - 45765 TTCAACTCTCAAACTTTT -s Anc1.Anc1refChr2 58029 18 + 144309 TTCAACTCTCAAACTTTT -s Anc2.Anc2refChr7 26703 18 + 32194 TTCCACTCTCAAACTTTT -s mr.mrrefChr0 78682 18 + 130230 TTCACCCCTCAAGCTGCT -s simCow_chr6.simCow.chr6 84916 10 + 602619 --------ACAAACTTTT -s simDog_chr6.simDog.chr6 186074 18 + 593897 TTCCACTCTCAGACTTTT -s simHuman_chr6.simHuman.chr6 78704 18 + 601863 TTCAAGTCTCAAATTCTT -s simRat_chr6.simRat.chr6 75391 18 + 647215 TTCACCCATCAAGCTGCT - -a -s simMouse_chr6.simMouse.chr6 83147 1 + 636262 T -s Anc0.Anc0refChr4 26586 1 - 45765 C -s Anc1.Anc1refChr2 58047 1 + 144309 C -s Anc2.Anc2refChr7 26721 1 + 32194 C -s mr.mrrefChr0 78700 1 + 130230 T -s simCow_chr6.simCow.chr6 84928 1 + 602619 C -s simDog_chr6.simDog.chr6 186092 1 + 593897 C -s simHuman_chr6.simHuman.chr6 78722 1 + 601863 C -s simRat_chr6.simRat.chr6 75409 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 83148 81 + 636262 TTTTTGTAAATGGGTAATGTAACGCCTGCCCAGTCGACATGGTCCATCTGATTGCTGTATAGAGATTCTTATTGCTGATAT -s Anc0.Anc0refChr4 26596 81 - 45765 ATTTTATGAATAGGTAATGTGGCGCCTGTACAATCTATATGGTCCAACTGGTTGTTGTTTAAGTATTCTTATTGCTTATAT -s Anc1.Anc1refChr2 58057 81 + 144309 ATTTTATGAATAGGTAATGTGGCGCCTGTACAATCTATATGGTCCAACTGGTTGTTGTTTAAGTATTCTTATTGCTTATAT -s Anc2.Anc2refChr7 26731 81 + 32194 ATTTTATGAATAGGTAATGTGACGCCTGTACAACCTGTATGGTCCAACTGGTTGTTGATTAAGTATTCTTATTGCTTATAT -s mr.mrrefChr0 78701 81 + 130230 ATTTTGTAAATAGGTAATGTAGCGCCTGTCCAGTCTACATGGTCCAACTGGTTGTTGTATAGAGATTCTTATTGCTGATAT -s simCow_chr6.simCow.chr6 84942 81 + 602619 ATTTTATGAATAGGTAATGAGACACCTTTACAACCTTTATGGTTCAATTGGTTGTTGATTAATTTTTCTTATTGCTTATAA -s simDog_chr6.simDog.chr6 186102 80 + 593897 ATTT-ATAAATAGGTAACGTGATGCCTGTACAACCTGCATGGTCCAACCAGTTGTTGATTAAGTACTCTTATTGCTTATAT -s simHuman_chr6.simHuman.chr6 78732 81 + 601863 ATTTTATGAATAGGTAATGTGGCGCCTGTGCTATCTATGTGGTCCAACTGGTTGTAGTTTAAGTATTCTTAGTGCTTATAT -s simRat_chr6.simRat.chr6 75410 81 + 647215 ATTTTGTAAATAGGTAATGCAGTGCCTGTCCAGCCTACATGGTCCAACTAGTTGTTGTATAGCAACTCTTATTGCTCATAT - -a -s simMouse_chr6.simMouse.chr6 83229 20 + 636262 TCCATGATCTAGCCATTGCT -s Anc0.Anc0refChr4 26677 16 - 45765 TC----ATCTTTGTAGTCTT -s Anc1.Anc1refChr2 58138 16 + 144309 TC----ATCTTTGTAGTCTT -s Anc2.Anc2refChr7 26814 16 + 32194 TC----ATTGTTGTAGTCTG -s mr.mrrefChr0 78782 20 + 130230 TCCATGATCTAGCCATTGTT -s simCow_chr6.simCow.chr6 85025 10 + 602619 TC----AT------AGTTTC -s simDog_chr6.simDog.chr6 186184 16 + 593897 TC----AGTGTTGTAGTCTG -s simHuman_chr6.simHuman.chr6 78813 16 + 601863 TC----ATCTTTGTAGTATT -s simRat_chr6.simRat.chr6 75491 20 + 647215 TCCATGATCTAGCCATTGTT - -a -s simMouse_chr6.simMouse.chr6 83249 29 + 636262 CTGTGGTACAATTATTACCCTTCTGCTCT -s Anc0.Anc0refChr4 26694 29 - 45765 TTGTGATGCAACTGTTGCTTTTTTGTGCC -s Anc1.Anc1refChr2 58155 29 + 144309 TTGTGATGCAACTGTTGCTTTTTTGTGCC -s Anc2.Anc2refChr7 26831 29 + 32194 TTGTGATGCATCTATTGCTTTTTTGTGCC -s mr.mrrefChr0 78802 29 + 130230 TTGTGGTACAATTGTTGCCCTTCTGCTCT -s simCow_chr6.simCow.chr6 85036 25 + 602619 TTGTGTTGCAGTTATTGCTTTTAT----C -s simDog_chr6.simDog.chr6 186201 29 + 593897 TTGTGATGCATCTATCGCTTTTTGGTGCC -s simHuman_chr6.simHuman.chr6 78830 29 + 601863 TCATAATGCAAATGTTGCTTTTTTGTGCC -s simRat_chr6.simRat.chr6 75511 29 + 647215 TTGTGGTACAATTGATGCCCTTCTGCACT - -a -s simMouse_chr6.simMouse.chr6 83278 5 + 636262 CAAAT -s Anc0.Anc0refChr4 26723 5 - 45765 CACAT -s Anc1.Anc1refChr2 58184 5 + 144309 CACAT -s Anc2.Anc2refChr7 26860 5 + 32194 CACAG -s mr.mrrefChr0 78831 5 + 130230 CAAAT -s simCow_chr6.simCow.chr6 85061 5 + 602619 CACAA -s simDog_chr6.simDog.chr6 186233 5 + 593897 CTCAG -s simHuman_chr6.simHuman.chr6 78859 5 + 601863 CACAT -s simRat_chr6.simRat.chr6 75540 5 + 647215 TAAAT - -a -s simMouse_chr6.simMouse.chr6 83283 24 + 636262 CAGAACCAAGAAACATTCGTAATA -s Anc0.Anc0refChr4 26731 24 - 45765 CAGAGCCTAGGAATGTCTGGACTA -s Anc1.Anc1refChr2 58192 24 + 144309 CAGAGCCTAGGAATGTCTGGACTA -s Anc2.Anc2refChr7 26868 24 + 32194 CAGAGCCTAGGAATGTCTGGACTA -s mr.mrrefChr0 78836 24 + 130230 CAGAACCAAGAAACATTCGTAATA -s simCow_chr6.simCow.chr6 85069 24 + 602619 CAGAGCCTAGGTGTGTCCAGAATA -s simDog_chr6.simDog.chr6 186244 24 + 593897 CAGAGTCTAGAAATGCCTGTACTA -s simHuman_chr6.simHuman.chr6 78867 24 + 601863 CCAGGCCTCAGAATGTCAGGACTA -s simRat_chr6.simRat.chr6 75545 24 + 647215 CAGAGCCAAGAAACATCTGTAATA - -a -s simMouse_chr6.simMouse.chr6 83307 10 + 636262 TGTAATTTTT -s Anc0.Anc0refChr4 26755 10 - 45765 TGAAAGTGTT -s Anc1.Anc1refChr2 58216 10 + 144309 TGAAAGTGTT -s Anc2.Anc2refChr7 26892 10 + 32194 TGAAAGTGTT -s mr.mrrefChr0 78860 10 + 130230 TGTAATTTTT -s simCow_chr6.simCow.chr6 85096 10 + 602619 TGGAAGTGTT -s simDog_chr6.simDog.chr6 186268 10 + 593897 TGAAAGTGTT -s simHuman_chr6.simHuman.chr6 78891 10 + 601863 TGAATGGGTT -s simRat_chr6.simRat.chr6 75569 10 + 647215 TGCAATTTTT - -a -s simMouse_chr6.simMouse.chr6 83317 2 + 636262 CA -s Anc0.Anc0refChr4 26765 2 - 45765 AA -s Anc1.Anc1refChr2 58226 2 + 144309 AA -s Anc2.Anc2refChr7 26902 2 + 32194 AA -s mr.mrrefChr0 78870 2 + 130230 CA -s simCow_chr6.simCow.chr6 517141 2 - 602619 aa -s simDog_chr6.simDog.chr6 186278 2 + 593897 AA -s simHuman_chr6.simHuman.chr6 78901 2 + 601863 AA -s simRat_chr6.simRat.chr6 75579 2 + 647215 CA - -a -s simMouse_chr6.simMouse.chr6 83319 49 + 636262 ATCTAGACAAGAAACTTAACGATGTTTAGATTTTGCGCTGTGCCTGGTG -s Anc0.Anc0refChr4 26767 9 - 45765 TTCACGGCA---------------------------------------- -s Anc1.Anc1refChr2 58228 9 + 144309 TTCACGGCA---------------------------------------- -s Anc2.Anc2refChr7 26904 9 + 32194 TTCACGGCA---------------------------------------- -s mr.mrrefChr0 78872 49 + 130230 ATCTAGACAAGAAACTTAACGATGTTTAGATTTTGCGCTGTGCCTGGTG -s simCow_chr6.simCow.chr6 517143 9 - 602619 tgcacGTAA---------------------------------------- -s simDog_chr6.simDog.chr6 186281 9 + 593897 TTTACAGCA---------------------------------------- -s simHuman_chr6.simHuman.chr6 78903 9 + 601863 TCCATGGTA---------------------------------------- -s simRat_chr6.simRat.chr6 75581 49 + 647215 ACCTAGACAAGAAACTTAACATTGTTGAGATTTCGCACAGCACCCTGTG - -a -s simMouse_chr6.simMouse.chr6 83368 113 + 636262 CAAAGCCCCAGAAAAAGGCAAATGTGGGTGTGGGTATGTACACACGGGTAGTGCTTGGCTATGACCATGTGCCACATCGCCATGTACAGACGGTTAGTGGCTGGGTATGAGCC -s mr.mrrefChr0 78921 107 + 130230 CAAAGCCCCAGAAAAAGGCAAA------TGTGGGTATGTACACACGGGTAGTGCTTGGCTATGACCATGTGCCACATCGCCATGTACAGACGGTTAGTGGCTGGGTATGAGCC -s simRat_chr6.simRat.chr6 75631 107 + 647215 CAGAGCTCCAAAAACAGGCAAA------CGTGGCTATGTACACACAGTTAGTGCTTGACTATGAGCCTGCCCTGTGTGCCCATGTACACATGGTTAGTGCCTGGCTATGAGCC - -a -s simMouse_chr6.simMouse.chr6 83481 31 + 636262 CACAGAGTCTGCCTGCCTCACACAAGAGGTT -s mr.mrrefChr0 79028 31 + 130230 CACAGAGTCTGCCTGCCTCACACAAGAGGTT -s simRat_chr6.simRat.chr6 75766 31 + 647215 CACAGAGTCTGTCAGCCTCATGCTTGAGGTT - -a -s simMouse_chr6.simMouse.chr6 83512 46 + 636262 TGCCAGGCGTAGTTCCCCACATTGTAGATCTCCTGTCCAATTCATG -s mr.mrrefChr0 79059 46 + 130230 TGCCAGGCGTAGTTCCCCACATTGTAGATCTCCTGTCCGATTCATG -s simRat_chr6.simRat.chr6 75809 46 + 647215 TGTCAGGCGAAGTCCCCCACTATGTAGAGCTCCTGTCCGATTCACA - -a -s simMouse_chr6.simMouse.chr6 83558 59 + 636262 GACAGGCACCGGCGTCATGTCCAGAATGAGCCTCCCCATAGTACTGTGACTGAGCTATA -s Anc0.Anc0refChr4 26776 25 - 45765 ----------------------------------GCAATAGTACTGTGGCCAGGCTATA -s Anc1.Anc1refChr2 58237 25 + 144309 ----------------------------------GCAATAGTACTGTGGCCAGGCTATA -s Anc2.Anc2refChr7 26913 25 + 32194 ----------------------------------GCAATAGTACTGTGGCCAGGCTATA -s mr.mrrefChr0 79105 59 + 130230 GATAGGCACCTACTTCATGTCCAGAATGAGCCTCCCCATAGTACTGTGACTGGGCTATA -s simCow_chr6.simCow.chr6 517152 25 - 602619 ----------------------------------ATTATAGTACTGTGGCAAAGCTCTA -s simDog_chr6.simDog.chr6 186290 25 + 593897 ----------------------------------GCAATTGTATTATGACCCGGCTATA -s simHuman_chr6.simHuman.chr6 78912 25 + 601863 ----------------------------------TCAATAGTACTGTGGCCAGGCTATA -s simRat_chr6.simRat.chr6 76185 58 + 647215 GATACGCACCTATTTCATGTCCAGAATGAGCCTCCGCACAGTATTGTG-CTGGGCTATC - -a -s simMouse_chr6.simMouse.chr6 83617 41 + 636262 CCGTCTGTGCCTATTAGTCTGATAGTTCTTATAGCAGGTAT -s Anc0.Anc0refChr4 26801 32 - 45765 CCCTCTGTGTTTATGGGTCTCAGAGT---------GGGTAT -s Anc1.Anc1refChr2 58262 32 + 144309 CCCTCTGTGTTTATGGGTCTCAGAGT---------GGGTAT -s Anc2.Anc2refChr7 26938 32 + 32194 CCCTCTGTTTTTATGGGTCTCAGAGT---------GGGTCT -s mr.mrrefChr0 79164 41 + 130230 CCGTCTGTGTCTATTAGTCTGATAGTTCTTATAGCAGGTAT -s simCow_chr6.simCow.chr6 517177 32 - 602619 CCCCCTGTTTTTATGAGTCTCAGAGT---------GGGTGC -s simDog_chr6.simDog.chr6 186319 32 + 593897 CCCTCTATTTTTCTGGGTCTCAGAGG---------TGGTCT -s simHuman_chr6.simHuman.chr6 78937 32 + 601863 CCCTCTGTGTTTATGGGTCTCAGAGT---------GGGTAT -s simRat_chr6.simRat.chr6 76243 41 + 647215 ACATCTGTGTCTATTGGTCTGATAGTTCCTATGGCAGGTAT - -a -s simMouse_chr6.simMouse.chr6 83658 2 + 636262 GG -s Anc0.Anc0refChr4 26833 2 - 45765 GG -s Anc1.Anc1refChr2 58294 2 + 144309 GG -s Anc2.Anc2refChr7 26970 2 + 32194 GG -s mr.mrrefChr0 79205 2 + 130230 GG -s simCow_chr6.simCow.chr6 517209 2 - 602619 GG -s simDog_chr6.simDog.chr6 186351 2 + 593897 GG -s simHuman_chr6.simHuman.chr6 78969 2 + 601863 GG -s simRat_chr6.simRat.chr6 76285 2 + 647215 GG - -a -s simMouse_chr6.simMouse.chr6 83660 6 + 636262 CAATAG -s Anc0.Anc0refChr4 26847 6 - 45765 CCATAA -s Anc1.Anc1refChr2 58308 6 + 144309 CCATAA -s Anc2.Anc2refChr7 26984 6 + 32194 CCATAA -s mr.mrrefChr0 79207 6 + 130230 CAATAG -s simCow_chr6.simCow.chr6 517223 6 - 602619 CCAAAA -s simDog_chr6.simDog.chr6 186365 6 + 593897 CCATAA -s simHuman_chr6.simHuman.chr6 78983 6 + 601863 CCACAA -s simRat_chr6.simRat.chr6 76287 6 + 647215 CCACTG - -a -s simMouse_chr6.simMouse.chr6 83666 10 + 636262 ACCTTGACAG -s Anc0.Anc0refChr4 26853 10 - 45765 TATTAGATTG -s Anc1.Anc1refChr2 58314 10 + 144309 TATTAGATTG -s Anc2.Anc2refChr7 26990 10 + 32194 TATTAGATTG -s mr.mrrefChr0 79213 10 + 130230 ACCTTGACAG -s simCow_chr6.simCow.chr6 517229 10 - 602619 TGTTAGATCG -s simDog_chr6.simDog.chr6 186371 10 + 593897 TATTAGATTG -s simHuman_chr6.simHuman.chr6 78989 10 + 601863 TATTAAATGG -s simRat_chr6.simRat.chr6 76295 10 + 647215 ACCCTGTAAG - -a -s simMouse_chr6.simMouse.chr6 83676 21 + 636262 AATTTTGTAATTTTTCTAGAG -s Anc0.Anc0refChr4 26863 21 - 45765 AGTTTTATGTTTGTTTTTGTG -s Anc1.Anc1refChr2 58324 21 + 144309 AGTTTTATGTTTGTTTTTGTG -s Anc2.Anc2refChr7 27000 21 + 32194 AGTTTTATGTTTGTTTTTGTG -s mr.mrrefChr0 79223 21 + 130230 AATTTTGTAATTTTTCTAGAG -s simCow_chr6.simCow.chr6 517239 21 - 602619 AGTTTTATGTCAGTTTTTATA -s simDog_chr6.simDog.chr6 186381 21 + 593897 AGTTTTATGTTTATTTTTGGG -s simHuman_chr6.simHuman.chr6 78999 21 + 601863 ACTTTTATGTTTGCTTTTTTG -s simRat_chr6.simRat.chr6 76308 21 + 647215 CATTTTGTAATTTTTCTAGAG - -a -s simMouse_chr6.simMouse.chr6 83697 2 + 636262 CA -s Anc0.Anc0refChr4 26885 2 - 45765 CA -s Anc1.Anc1refChr2 58346 2 + 144309 CA -s Anc2.Anc2refChr7 27022 2 + 32194 CA -s mr.mrrefChr0 79244 2 + 130230 CA -s simCow_chr6.simCow.chr6 517261 2 - 602619 CA -s simDog_chr6.simDog.chr6 186403 2 + 593897 CA -s simHuman_chr6.simHuman.chr6 79021 2 + 601863 CA -s simRat_chr6.simRat.chr6 76329 2 + 647215 CA - -a -s simMouse_chr6.simMouse.chr6 83699 5 + 636262 TAGTT -s Anc0.Anc0refChr4 26887 5 - 45765 TAGTA -s Anc1.Anc1refChr2 58348 5 + 144309 TAGTA -s Anc2.Anc2refChr7 27030 5 + 32194 TGGTA -s mr.mrrefChr0 79246 5 + 130230 TAGTT -s simCow_chr6.simCow.chr6 517271 5 - 602619 TGGCA -s simDog_chr6.simDog.chr6 186411 5 + 593897 TGGTA -s simHuman_chr6.simHuman.chr6 79023 5 + 601863 TAGTA -s simRat_chr6.simRat.chr6 76331 5 + 647215 TAGTT - -a -s simMouse_chr6.simMouse.chr6 83704 7 + 636262 AGTTGGC -s Anc0.Anc0refChr4 26892 5 - 45765 AG--GGT -s Anc1.Anc1refChr2 58353 7 + 144309 AGTTGGT -s Anc2.Anc2refChr7 27035 5 + 32194 AG--GGT -s mr.mrrefChr0 79251 7 + 130230 AGTTGGC -s simCow_chr6.simCow.chr6 517288 5 - 602619 AG--GGT -s simDog_chr6.simDog.chr6 186416 5 + 593897 AG--GGT -s simHuman_chr6.simHuman.chr6 79028 7 + 601863 AGTTGGT -s simRat_chr6.simRat.chr6 76336 7 + 647215 AGTTAGC - -a -s simMouse_chr6.simMouse.chr6 83711 1 + 636262 G -s Anc0.Anc0refChr4 26897 1 - 45765 G -s Anc1.Anc1refChr2 58360 1 + 144309 G -s Anc2.Anc2refChr7 27040 1 + 32194 G -s mr.mrrefChr0 79258 1 + 130230 G -s simCow_chr6.simCow.chr6 517294 1 - 602619 G -s simDog_chr6.simDog.chr6 186421 1 + 593897 G -s simHuman_chr6.simHuman.chr6 79035 1 + 601863 G -s simRat_chr6.simRat.chr6 76343 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 83712 10 + 636262 TTACAGTTAG -s Anc0.Anc0refChr4 26898 10 - 45765 TTACAGTCAA -s Anc1.Anc1refChr2 58361 10 + 144309 TTACAGTCAA -s Anc2.Anc2refChr7 27047 10 + 32194 TTACAGTCAA -s mr.mrrefChr0 79259 10 + 130230 TTACAGTTAG -s simCow_chr6.simCow.chr6 517301 10 - 602619 TTATTGTCAA -s simDog_chr6.simDog.chr6 186428 10 + 593897 TTACAGTCAA -s simHuman_chr6.simHuman.chr6 79036 4 + 601863 TTGC------ -s simRat_chr6.simRat.chr6 76344 10 + 647215 TTACAATTAG - -a -s simMouse_chr6.simMouse.chr6 83722 9 + 636262 TTGGCAGGT -s Anc0.Anc0refChr4 26908 9 - 45765 TTACCAGGT -s Anc1.Anc1refChr2 58371 9 + 144309 TTACCAGGT -s Anc2.Anc2refChr7 27060 9 + 32194 TTACCAGGC -s mr.mrrefChr0 79269 9 + 130230 TTGGCAGGT -s simCow_chr6.simCow.chr6 517314 9 - 602619 TTCCTGGGA -s simDog_chr6.simDog.chr6 186441 9 + 593897 TTACCAGGC -s simHuman_chr6.simHuman.chr6 79040 5 + 601863 ----CGGTT -s simRat_chr6.simRat.chr6 76354 9 + 647215 TTGGCAGGT - -a -s simMouse_chr6.simMouse.chr6 83731 11 + 636262 AGGAAAAATAG -s Anc0.Anc0refChr4 26917 11 - 45765 TAGACAAATAG -s Anc1.Anc1refChr2 58380 11 + 144309 TAGACAAATAG -s Anc2.Anc2refChr7 27072 11 + 32194 TAGACAAATAG -s mr.mrrefChr0 79278 11 + 130230 AGGAAAAATAG -s simCow_chr6.simCow.chr6 517326 11 - 602619 TTGACAAATAG -s simDog_chr6.simDog.chr6 186453 11 + 593897 TAGACAAATAG -s simHuman_chr6.simHuman.chr6 79045 11 + 601863 TAGAGGAATGG -s simRat_chr6.simRat.chr6 76363 11 + 647215 TAGGAAAATTA - -a -s simMouse_chr6.simMouse.chr6 83742 19 + 636262 CATGTCAAGGAAATGCCCA -s Anc0.Anc0refChr4 26928 9 - 45765 CATGTTA----------CA -s Anc1.Anc1refChr2 58391 9 + 144309 CATGTTA----------CA -s Anc2.Anc2refChr7 27084 9 + 32194 CATGGTG----------TA -s mr.mrrefChr0 79289 19 + 130230 CATGTCAAGGAAATGCCCA -s simCow_chr6.simCow.chr6 517338 9 - 602619 CATGGTG----------AG -s simDog_chr6.simDog.chr6 186465 9 + 593897 CATGGTG----------TA -s simHuman_chr6.simHuman.chr6 79056 9 + 601863 TATGTTA----------CA -s simRat_chr6.simRat.chr6 76374 19 + 647215 CATGTCAAGGAAACGCCCA - -a -s simMouse_chr6.simMouse.chr6 83761 49 + 636262 CTAAACTTACAACACAGGATTACAACCATGATACATCACCATATTTACA -s Anc0.Anc0refChr4 26937 6 - 45765 ttaaGA------------------------------------------- -s Anc1.Anc1refChr2 58400 6 + 144309 TTAAGA------------------------------------------- -s Anc2.Anc2refChr7 27109 6 + 32194 ttatGA------------------------------------------- -s mr.mrrefChr0 79308 6 + 130230 CTAAAC------------------------------------------- -s simCow_chr6.simCow.chr6 517368 6 - 602619 ctaaaa------------------------------------------- -s simDog_chr6.simDog.chr6 186490 6 + 593897 TTATGT------------------------------------------- -s simHuman_chr6.simHuman.chr6 79065 6 + 601863 TTCAGA------------------------------------------- -s simRat_chr6.simRat.chr6 76393 6 + 647215 CTAAGT------------------------------------------- - -a -s simMouse_chr6.simMouse.chr6 83810 28 + 636262 GTCCACACTATCTGTTGCTATCAATAAG -s mr.mrrefChr5 247967 28 + 294540 GTCCACACTATCTGTTGCTATCAATAAG -s simRat_chr6.simRat.chr6 394395 28 + 647215 GTCCACACCGTCTGGTACTATTGATAAA - -a -s simMouse_chr6.simMouse.chr6 83838 14 + 636262 TAACCAGGGTATAT -s mr.mrrefChr5 247995 14 + 294540 TAACCAGGGTATAT -s simRat_chr6.simRat.chr6 394449 14 + 647215 TAACCAGGGTAGAT - -a -s simMouse_chr6.simMouse.chr6 83852 25 + 636262 CACTGGTTCATCCACCTAGGGCATT -s mr.mrrefChr5 248009 24 + 294540 CACTGGTTCATCCAC-TAGGGCATT -s simRat_chr6.simRat.chr6 394464 24 + 647215 CACTAGTTCATCTAC-TAGGGTATT - -a -s simMouse_chr6.simMouse.chr6 83877 1 + 636262 T -s Anc0.Anc0refChr3 26588 1 + 222631 T -s Anc1.Anc1refChr6 56179 1 + 197743 T -s Anc2.Anc2refChr13 30070 1 + 96486 T -s mr.mrrefChr5 248033 1 + 294540 T -s mr.mrrefChr5 177263 1 - 294540 C -s simCow_chr6.simCow.chr6 386196 1 + 602619 T -s simDog_chr6.simDog.chr6 376671 1 + 593897 T -s simHuman_chr6.simHuman.chr6 380584 1 + 601863 T -s simHuman_chr6.simHuman.chr6 445438 1 + 601863 T -s simMouse_chr6.simMouse.chr6 371337 1 - 636262 C -s simRat_chr6.simRat.chr6 394488 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 83878 4 + 636262 ACTT -s Anc0.Anc0refChr3 26589 4 + 222631 ACTT -s Anc1.Anc1refChr6 56180 4 + 197743 ACTT -s Anc2.Anc2refChr13 30071 4 + 96486 ACTT -s mr.mrrefChr5 248034 4 + 294540 ACTT -s mr.mrrefChr5 177910 4 - 294540 actt -s simCow_chr6.simCow.chr6 386197 4 + 602619 ACTT -s simDog_chr6.simDog.chr6 376672 4 + 593897 TCTT -s simHuman_chr6.simHuman.chr6 380585 4 + 601863 ACAA -s simHuman_chr6.simHuman.chr6 445439 4 + 601863 ACAA -s simMouse_chr6.simMouse.chr6 372192 4 - 636262 actt -s simRat_chr6.simRat.chr6 393367 4 - 647215 actt -s simRat_chr6.simRat.chr6 394489 4 + 647215 ATTT - -a -s simMouse_chr6.simMouse.chr6 83882 7 + 636262 GTTGTAA -s Anc0.Anc0refChr3 26594 7 + 222631 GTTCTAG -s Anc1.Anc1refChr6 56185 7 + 197743 GTTCTAG -s Anc2.Anc2refChr13 30076 7 + 96486 GTTCTAG -s mr.mrrefChr5 248038 7 + 294540 GTTGTAA -s mr.mrrefChr5 177914 7 - 294540 gccataa -s simCow_chr6.simCow.chr6 386202 7 + 602619 GCTCTAG -s simDog_chr6.simDog.chr6 376677 2 + 593897 GT----- -s simHuman_chr6.simHuman.chr6 445444 7 + 601863 GTTCTAG -s simMouse_chr6.simMouse.chr6 372196 7 - 636262 gccataa -s simRat_chr6.simRat.chr6 393371 7 - 647215 gctgaaa -s simRat_chr6.simRat.chr6 394493 7 + 647215 GTTGTGA - -a -s simMouse_chr6.simMouse.chr6 83889 3 + 636262 ACA -s Anc0.Anc0refChr3 26601 3 + 222631 ATA -s Anc1.Anc1refChr6 56192 3 + 197743 ATA -s Anc2.Anc2refChr13 30083 3 + 96486 ATG -s mr.mrrefChr5 248045 3 + 294540 ACA -s mr.mrrefChr5 177921 3 - 294540 ata -s simCow_chr6.simCow.chr6 386209 3 + 602619 ATG -s simHuman_chr6.simHuman.chr6 380589 3 + 601863 ATA -s simHuman_chr6.simHuman.chr6 445451 3 + 601863 ATA -s simMouse_chr6.simMouse.chr6 372203 3 - 636262 ata -s simRat_chr6.simRat.chr6 393378 3 - 647215 aca -s simRat_chr6.simRat.chr6 394500 3 + 647215 ATA - -a -s simMouse_chr6.simMouse.chr6 83892 3 + 636262 GCC -s Anc0.Anc0refChr4 26943 3 - 45765 GCC -s Anc1.Anc1refChr2 58406 3 + 144309 GCC -s Anc2.Anc2refChr7 27115 3 + 32194 GCC -s mr.mrrefChr0 79314 3 + 130230 GCC -s simCow_chr6.simCow.chr6 517374 2 - 602619 ac- -s simDog_chr6.simDog.chr6 186496 3 + 593897 GCC -s simHuman_chr6.simHuman.chr6 79071 3 + 601863 GCC - -a -s simMouse_chr6.simMouse.chr6 83895 17 + 636262 TAGCTGTGTGTCTTTAT -s Anc0.Anc0refChr4 26946 16 - 45765 TAGCCATTTATC-ATAT -s Anc1.Anc1refChr2 58409 16 + 144309 TAGCCATTTATC-ATAT -s Anc2.Anc2refChr7 27118 16 + 32194 TAACCATTTATC-ATAT -s mr.mrrefChr0 79317 17 + 130230 TAGCTGTGTGTCTTTAT -s simCow_chr6.simCow.chr6 85641 16 + 602619 TGACCATTTGTG-ATCA -s simDog_chr6.simDog.chr6 186499 16 + 593897 TAACCGCTTATC-ATAT -s simHuman_chr6.simHuman.chr6 79074 16 + 601863 TAGCCATCTATC-ATAT -s simRat_chr6.simRat.chr6 76399 4 + 647215 -------------TTAC - -a -s simMouse_chr6.simMouse.chr6 83912 9 + 636262 AGGCTTACT -s Anc0.Anc0refChr4 26962 9 - 45765 AGGTTAACT -s Anc1.Anc1refChr2 58425 9 + 144309 AGGTTAACT -s Anc2.Anc2refChr7 27134 9 + 32194 AGGTTAACT -s mr.mrrefChr0 79334 9 + 130230 AGGTTTACT -s simCow_chr6.simCow.chr6 85657 9 + 602619 AAGCAAACT -s simDog_chr6.simDog.chr6 186517 9 + 593897 AGGTTGACT -s simHuman_chr6.simHuman.chr6 79090 9 + 601863 AGGTTAACT -s simRat_chr6.simRat.chr6 76403 9 + 647215 AACTTTTCA - -a -s simMouse_chr6.simMouse.chr6 83921 10 + 636262 TTACAATCAT -s Anc0.Anc0refChr4 26971 10 - 45765 TTACAATTAT -s Anc1.Anc1refChr2 58434 10 + 144309 TTACAATTAT -s Anc2.Anc2refChr7 27143 10 + 32194 TTACAATTAT -s mr.mrrefChr0 79343 10 + 130230 TTACAATCAT -s simCow_chr6.simCow.chr6 85666 10 + 602619 TAACAATCAT -s simDog_chr6.simDog.chr6 186526 10 + 593897 TTACAACTAT -s simHuman_chr6.simHuman.chr6 79099 10 + 601863 TTACAATTAT -s simRat_chr6.simRat.chr6 76419 10 + 647215 TTACAACCAT - -a -s simMouse_chr6.simMouse.chr6 83931 8 + 636262 CCACGTGG -s Anc0.Anc0refChr4 26981 8 - 45765 CAACATGG -s Anc1.Anc1refChr2 58444 8 + 144309 CAACATGG -s Anc2.Anc2refChr7 27153 8 + 32194 CAACATGG -s mr.mrrefChr0 79353 8 + 130230 CCACATGG -s simCow_chr6.simCow.chr6 85676 7 + 602619 CAACACA- -s simDog_chr6.simDog.chr6 186536 8 + 593897 CGACATGG -s simHuman_chr6.simHuman.chr6 79109 8 + 601863 CAACAAGG -s simRat_chr6.simRat.chr6 76430 8 + 647215 CTGCATCA - -a -s simMouse_chr6.simMouse.chr6 83939 74 + 636262 AAAATTAGCTCGGTCTTACTTTGCCTCTGTCATATATCCCTAGGCCGTTTGGCATTTGGGGTGATATCAACAGA -s Anc0.Anc0refChr4 27009 74 - 45765 AATATTAGCTTGTACTTCTGTTGCCCGTGTGATTTGTTCTTAGGTTGTTTGACATGGGAGGTAATTGCAACAAA -s Anc1.Anc1refChr2 58472 74 + 144309 AATATTAGCTTGTACTTCTGTTGCCCGTGTGATTTGTTCTTAGGTTGTTTGACATGGGAGGTAATTGCAACAAA -s Anc2.Anc2refChr7 27182 74 + 32194 AATATTAGCTTGTACCTCTGTTGCCCGTGTGATTTGTTCTTAGGTTGTTTGACATGGGAGGTAATTGCAACAAA -s mr.mrrefChr0 79361 74 + 130230 AAAATTAGCTCGGTCTTATTTTGCCTCTGTCATATATCCCTAGGTCGTTTGGCATTTGGGGTGATAGCAACAGA -s simCow_chr6.simCow.chr6 85704 74 + 602619 AATATTAGCTTGCACCTCTGTTGCCCTTCTAATTGGTTCTTAGATTGTTTGATGTGGGAGGTAACTGCAACAAA -s simDog_chr6.simDog.chr6 186565 74 + 593897 AATATTAGCCTTTATCTCTGATGCCTGTGTGATTTATTCTTGGGTTGTCCGACATGAGAAGTGATTACAACAAA -s simHuman_chr6.simHuman.chr6 79137 67 + 601863 AATATTAGGTTGTACTTTTGTTGTCCT-------TGTTGTTATGTTGTTTAACATGGGAGGCAATTGCACCAAA -s simRat_chr6.simRat.chr6 76438 74 + 647215 CCAATTAGCTCGGTCTTATTTCGCCTCTGTCATAAATTCCAAGGTCGTTTGGCATTTGGGGTGATAGCAACAGA - -a -s simMouse_chr6.simMouse.chr6 84013 16 + 636262 TTAATGCCACCAATGC -s Anc0.Anc0refChr4 27085 16 - 45765 CTAAAGCCACTGATCT -s Anc1.Anc1refChr2 58548 16 + 144309 CTAAAGCCACTGATCT -s Anc2.Anc2refChr7 27258 16 + 32194 CAAAAGCCACTGATCT -s mr.mrrefChr0 79435 16 + 130230 TTAATGCCACCAATGC -s simCow_chr6.simCow.chr6 85780 9 + 602619 CA-------CTAATTT -s simDog_chr6.simDog.chr6 186641 16 + 593897 CAAAAGCCACTGATCT -s simHuman_chr6.simHuman.chr6 79206 16 + 601863 CTAAAACCACTGATCT -s simRat_chr6.simRat.chr6 76512 16 + 647215 TTAATGCCACCAATGC - -a -s simMouse_chr6.simMouse.chr6 84029 21 + 636262 CCAACTCCCAGTTGCAAATGA -s Anc0.Anc0refChr4 27102 21 - 45765 GCAGGTTCCAGTTGCAAGTAA -s Anc1.Anc1refChr2 58565 21 + 144309 GCAGGTTCCAGTTGCAAGTAA -s Anc2.Anc2refChr7 27275 21 + 32194 GCAGGTTCCAGTTACAAGCAA -s mr.mrrefChr0 79451 21 + 130230 CCAACTCCCAGTTGCAAATGA -s simCow_chr6.simCow.chr6 85790 21 + 602619 GCAGGTTCCAGTTACAAGCAA -s simDog_chr6.simDog.chr6 186658 20 + 593897 -CAAGTTCCAGTTACAGGCAA -s simHuman_chr6.simHuman.chr6 79223 21 + 601863 GCAGGTAACAGTTGCAAGTAA -s simRat_chr6.simRat.chr6 76528 21 + 647215 CCACCTTCCAGTTACAAAGGA - -a -s simMouse_chr6.simMouse.chr6 84050 33 + 636262 GATCTAGCTTCTGGAGCATTGTCAACACCATGA -s Anc0.Anc0refChr4 27125 33 - 45765 AGTGTAGCTTCTGGAGCATTGTCAATGCCAACA -s Anc1.Anc1refChr2 58588 33 + 144309 AGTGTAGCTTCTGGAGCATTGTCAATGCCAACA -s Anc2.Anc2refChr7 27298 33 + 32194 AGTGTAGCTTCTGGGGCATTGTCAATGCCAACA -s mr.mrrefChr0 79472 33 + 130230 AATGTAGCTTCTGGAGCATTGTCAACACCAACA -s simCow_chr6.simCow.chr6 85813 32 + 602619 ACGGTAGCTT-TGAGAGATGTACTATGTCAACA -s simDog_chr6.simDog.chr6 186680 33 + 593897 TGTGTAGTTTCTGGGGCATTGTCAATGCCAACC -s simHuman_chr6.simHuman.chr6 79246 33 + 601863 AGTGTAGCTTCTTGAGCGTTATCAATGCCGACA -s simRat_chr6.simRat.chr6 76549 33 + 647215 AATGTAGCTTCTGGAGCATTGTAAACACCAACA - -a -s simMouse_chr6.simMouse.chr6 84083 14 + 636262 GGGAGGGTAACCTC -s Anc0.Anc0refChr4 27160 14 - 45765 CGCACCATAAGGTC -s Anc1.Anc1refChr2 58623 14 + 144309 CGCACCATAAGGTC -s Anc2.Anc2refChr7 27333 14 + 32194 CGCACCATAAAGTC -s mr.mrrefChr0 79505 14 + 130230 GGCAGCATAAGCTC -s simCow_chr6.simCow.chr6 85847 14 + 602619 CACACCTTAAAGTC -s simDog_chr6.simDog.chr6 186715 14 + 593897 TGCACCATAAAGCT -s simHuman_chr6.simHuman.chr6 79281 14 + 601863 CGCACCATAAGGTC -s simRat_chr6.simRat.chr6 76582 14 + 647215 GGCAGCATAAGCTC - -a -s simMouse_chr6.simMouse.chr6 84097 20 + 636262 AAATGGATATTGTATATGTT -s Anc0.Anc0refChr4 27175 20 - 45765 AAATGAAAAGTTTATGTGTT -s Anc1.Anc1refChr2 58638 20 + 144309 AAATGAAAAGTTTATGTGTT -s Anc2.Anc2refChr7 27348 20 + 32194 AAATGAAAAGTTTATGTGTT -s mr.mrrefChr0 79519 20 + 130230 AAATGAATATTGTATATGTT -s simCow_chr6.simCow.chr6 85862 20 + 602619 AAATGAAAAGTTAATAAGTC -s simDog_chr6.simDog.chr6 186730 20 + 593897 AAATGAAAAGCTTATGTGCT -s simHuman_chr6.simHuman.chr6 79296 20 + 601863 CAGTAAAAAGTCTATGTGTT -s simRat_chr6.simRat.chr6 76596 20 + 647215 AAATGACTATTTTATATGTT - -a -s simMouse_chr6.simMouse.chr6 84117 27 + 636262 ATACATAGCCCAAAATTACATTCATTT -s Anc0.Anc0refChr4 27197 26 - 45765 GTACATAGCCCAGAAATCCACTC-CAA -s Anc1.Anc1refChr2 58660 26 + 144309 GTACATAGCCCAGAAATCCACTC-CAA -s Anc2.Anc2refChr7 27370 26 + 32194 GTGCATAGCGCAGAAATCCACTC-CAA -s mr.mrrefChr0 79541 27 + 130230 ATACATAGCCCAAAAATACATTCATTT -s simCow_chr6.simCow.chr6 85884 26 + 602619 ATGCATAGCTCAGAAATCCACCC-TAT -s simDog_chr6.simDog.chr6 186752 26 + 593897 GTGCATAGTGCAGAAATCCACTC-CCA -s simHuman_chr6.simHuman.chr6 79318 26 + 601863 GTACATAGCCCAGAAATCCACTC-CAA -s simRat_chr6.simRat.chr6 76618 27 + 647215 ATCCATAGCCAAAAAATACATTCTTGT - -a -s simMouse_chr6.simMouse.chr6 84144 62 + 636262 ACCTATATGTGTTGTTGCTGTGGTCCAGGAGATCTATGTCACTGCATGGTACGGACCATTGG -s Anc0.Anc0refChr4 27223 48 - 45765 ACCTACA--------------GGTTCAAGAGGCCCATGTCACTGCATGTAACATACCATCAA -s Anc1.Anc1refChr2 58686 62 + 144309 ACCTACATGTGTTGTCGCTGTGGTTCAAGAGGCCCATGTCACTGCATGTAACATACCATCAA -s Anc2.Anc2refChr7 27397 48 + 32194 AACTACA--------------GGTTCAAGAGGCCCATGTCACTGCATGTAACATACCATCAA -s mr.mrrefChr0 79568 62 + 130230 ACCTATATGTGTTGTTGCTGTGGTCCAGGAGATCTATGTCACTGCATGGTACGTACCATTGG -s simCow_chr6.simCow.chr6 85911 48 + 602619 AACTACA--------------GGTTCAAGAGGGTTCTGTCACTGTAAGTAACATGTCATCAA -s simDog_chr6.simDog.chr6 186779 48 + 593897 AACTACA--------------GCTTCAAGAGCCCCATGTCACTACATGTAACATACCATTAA -s simHuman_chr6.simHuman.chr6 79344 61 + 601863 ACCTTCATGTGTTGTCGCTGTGGTTCAAGATGCCC-TGTCACTGCATGTAACATACCATCAA -s simRat_chr6.simRat.chr6 76645 62 + 647215 ATCTATATGTGTTGTTGCCATTGTACAGGAGATCTATGCCACTACATGGCATGTACCATTGG - -a -s simMouse_chr6.simMouse.chr6 84206 83 + 636262 AATGGATCACACATTTTGGCTTTGGCGTTAAGATCAAGACTCTGTCCAGGAAGACTATGGATCCATTGTCTCAGTCATAGCTG -s Anc0.Anc0refChr4 27285 43 - 45765 AATGGAACATATACTAAGGCTCTGG-AATAAAAGGGAG---------------------------------------AAGCTG -s Anc1.Anc1refChr2 58762 44 + 144309 AATGGAACATATACTAAGGCTCTGGCAATAAAAGGGAG---------------------------------------AAGCTG -s Anc2.Anc2refChr7 27459 43 + 32194 AATGGAACATATACTAAGACTCTGG-AATAAAAGGGAG---------------------------------------AATCCG -s mr.mrrefChr0 79630 83 + 130230 AATGGATCACACATTATGGCTTTGGCGTTAAGATCAAGACTCTGTCCAGGAAGACTATGGATCCATTGTCTCAGTCAAAGCTG -s simCow_chr6.simCow.chr6 85971 43 + 602619 GGAGGAACATATACTAAGACCCAGA-AATAAAAGGTCG---------------------------------------AACAGG -s simDog_chr6.simDog.chr6 186840 43 + 593897 AATGGAACATACACTAATACTCTGG-AGTAAAGAGGAT---------------------------------------GATCCG -s simHuman_chr6.simHuman.chr6 79419 43 + 601863 AATGGAACATATACTAAGG-TGTGGCCACAATAGGGAG---------------------------------------AAGCTG -s simRat_chr6.simRat.chr6 76707 83 + 647215 AATGGATCACACATTATGTCTTTGGCGGTGAGATCAAAACTCTTAACAGAAAGACTGCGGGTGCATTGTCTCAGTCAAAGCTG - -a -s simMouse_chr6.simMouse.chr6 84289 3 + 636262 CTG -s Anc0.Anc0refChr4 27328 3 - 45765 TTG -s Anc1.Anc1refChr2 58806 3 + 144309 TTG -s Anc2.Anc2refChr7 27502 3 + 32194 TTG -s mr.mrrefChr0 79713 3 + 130230 CTG -s simCow_chr6.simCow.chr6 86014 3 + 602619 TTG -s simDog_chr6.simDog.chr6 186887 3 + 593897 CTG -s simHuman_chr6.simHuman.chr6 79462 3 + 601863 TTG -s simRat_chr6.simRat.chr6 76790 3 + 647215 CTT - -a -s simMouse_chr6.simMouse.chr6 84292 9 + 636262 GTTGTGTTA -s Anc0.Anc0refChr4 27331 9 - 45765 GTTATATTA -s Anc1.Anc1refChr2 58809 9 + 144309 GTTATATTA -s Anc2.Anc2refChr7 27505 9 + 32194 GGCAAATTA -s mr.mrrefChr0 79716 9 + 130230 GTTGTGTTA -s simCow_chr6.simCow.chr6 86018 9 + 602619 GGATGAATA -s simDog_chr6.simDog.chr6 186890 9 + 593897 GGCAAATTA -s simHuman_chr6.simHuman.chr6 79465 9 + 601863 GTTATATTA -s simRat_chr6.simRat.chr6 76793 9 + 647215 GTTGTGTTA - -a -s simMouse_chr6.simMouse.chr6 84301 18 + 636262 CAGTGAGGTTGATCAAAA -s Anc0.Anc0refChr4 27340 18 - 45765 CATTGAGGTTGGTTGAAA -s Anc1.Anc1refChr2 58818 18 + 144309 CATTGAGGTTGGTTGAAA -s Anc2.Anc2refChr7 27514 18 + 32194 CATTGAGGTTGGTTGAAA -s mr.mrrefChr0 79725 18 + 130230 CAGTGAGGTTGATCAAAA -s simCow_chr6.simCow.chr6 86065 18 + 602619 CATCATGGTTGGTTGAAA -s simDog_chr6.simDog.chr6 186899 18 + 593897 CGATGAGGATCACTTAAG -s simHuman_chr6.simHuman.chr6 79474 18 + 601863 CATTGCGGTTGGTTGAAA -s simRat_chr6.simRat.chr6 76802 18 + 647215 AAATGTGGTTGATCAAAG - -a -s simMouse_chr6.simMouse.chr6 84319 5 + 636262 CCTGG -s Anc0.Anc0refChr4 27359 5 - 45765 ATTGG -s Anc1.Anc1refChr2 58837 5 + 144309 ATTGG -s Anc2.Anc2refChr7 27533 5 + 32194 AATGG -s mr.mrrefChr0 79743 5 + 130230 CTTGG -s simCow_chr6.simCow.chr6 86084 5 + 602619 AATGG -s simDog_chr6.simDog.chr6 186918 5 + 593897 AATGT -s simHuman_chr6.simHuman.chr6 79493 5 + 601863 ATTGG -s simRat_chr6.simRat.chr6 76820 5 + 647215 CTTGG - -a -s simMouse_chr6.simMouse.chr6 84324 42 + 636262 CGAGTTTTGAGGGACAGTCAGCTAATCAATTTTAAATGCTAG -s Anc0.Anc0refChr4 27369 40 - 45765 TGAGTTTTGAGAGAAAGTCACTTAATTG--TTTAAATGTTGG -s Anc1.Anc1refChr2 58847 42 + 144309 TGAGTTTTGAGAGAAAGTCACTTAATTGATTTTAAATGTTGG -s Anc2.Anc2refChr7 27543 40 + 32194 TGAGTTTTGAGAGAAAGTCACTTACTTG--TTTAAATGTTGG -s mr.mrrefChr0 79748 42 + 130230 CGAGTTTTGAGGGAAAGTCACCTAATCGATTTTAAATGCTAG -s simCow_chr6.simCow.chr6 86094 40 + 602619 TGAGTTTTGAGAGAAAGTCACTTAGATG--TTTAGACACTGG -s simDog_chr6.simDog.chr6 186929 24 + 593897 TTGGTCTT----------------CTTG--GTTAAATGTTGG -s simHuman_chr6.simHuman.chr6 79503 41 + 601863 AGAGTTTTGAGAGAAAGTCACTCAATTGATTTT-AATGTTGG -s simRat_chr6.simRat.chr6 76825 42 + 647215 CAAGTTTGGAGGGAAAGTCACCTAATCGATCTTCAATGCTAG - -a -s simMouse_chr6.simMouse.chr6 84366 18 + 636262 TCACCTATGGGTTGACAT -s Anc0.Anc0refChr4 27409 18 - 45765 TCTTCTAGGGGCTGCGAG -s Anc1.Anc1refChr2 58889 18 + 144309 TCTTCTAGGGGCTGCGAG -s Anc2.Anc2refChr7 27583 18 + 32194 TCTTCTAGGGGCTGCGAG -s mr.mrrefChr0 79790 18 + 130230 TCACCTATGGGTTGAGAT -s simCow_chr6.simCow.chr6 86135 18 + 602619 TCTGCTAGGGGCTAAGAG -s simDog_chr6.simDog.chr6 186953 18 + 593897 TCTTATTGCAGCTGCGAA -s simHuman_chr6.simHuman.chr6 79544 18 + 601863 GTGTCTAGGGCCTGTGAG -s simRat_chr6.simRat.chr6 76867 18 + 647215 TCACCTATGGGTTGAGAT - -a -s simMouse_chr6.simMouse.chr6 84384 11 + 636262 CTATGAAAGCT -s Anc0.Anc0refChr4 27429 11 - 45765 ATGTAAAAGCT -s Anc1.Anc1refChr2 58909 11 + 144309 ATGTAAAAGCT -s Anc2.Anc2refChr7 27603 11 + 32194 ATGTAAAAGCT -s mr.mrrefChr0 79808 11 + 130230 CTATGAAAGCT -s simCow_chr6.simCow.chr6 86155 11 + 602619 ATGAAAGAGCT -s simDog_chr6.simDog.chr6 186973 11 + 593897 ATGTAAAAGAT -s simHuman_chr6.simHuman.chr6 79564 11 + 601863 ATGTAAAAGCT -s simRat_chr6.simRat.chr6 76885 11 + 647215 CTATGAAAGCT - -a -s simMouse_chr6.simMouse.chr6 84395 52 + 636262 ATTGGATTATCTCCTCTCTATTGGTTTGATTAGTTTTTTGTGTTTCTAGTCA -s Anc0.Anc0refChr4 27445 42 - 45765 ATTGGTTGATATACTC----------TGATCAATTTTTTGGGTTTTTAGATG -s Anc1.Anc1refChr2 58925 42 + 144309 ATTGGTTGATATACTC----------TGATCAATTTTTTGGGTTTTTAGATG -s Anc2.Anc2refChr7 27619 42 + 32194 ATTGGTTGATATACTT----------TGATCAATTTTTAGGGTATTTAGATG -s mr.mrrefChr0 79821 52 + 130230 ATTGGATGATCTCCTCTCTATTGGTTTGATTAGTTTTTTGGGTTTTTAGTCA -s simCow_chr6.simCow.chr6 86169 42 + 602619 ATTAGATGGTATACTT----------TCATCAATTTTTAGGGTGTCCAGATG -s simDog_chr6.simDog.chr6 186989 42 + 593897 ATTGGTTGATATACTT----------TGATCAATCTTTAGGGCATTTAAATG -s simHuman_chr6.simHuman.chr6 79580 42 + 601863 ATTGGGTGATATGCTC----------TGATCAATTTTTTGGGTTTTTAGCTC -s simRat_chr6.simRat.chr6 76898 52 + 647215 ATTGAATGATCTCCTCTCCATTGGTTTGACTAGTTTTTTGGGTTTTTAGTCA - -a -s simMouse_chr6.simMouse.chr6 84447 50 + 636262 GAAATGCTAGCAACTCAAAGTATAGGCTTAGCGGTAGACTGTTGTGAGAC -s Anc0.Anc0refChr4 27487 48 - 45765 GAAATGCTAGTAATGCAAGATGTGGGCTAAACATTGGACTG--GTGGCAC -s Anc1.Anc1refChr2 58967 48 + 144309 GAAATGCTAGTAATGCAAGATGTGGGCTAAACATTGGACTG--GTGGCAC -s Anc2.Anc2refChr7 27661 48 + 32194 GAAATGCTAGTAATGCAAGATGTGGGCTAAACATTGGGCTG--GTGGCAC -s mr.mrrefChr0 79873 48 + 130230 GAAATGCTAGCAACTCAAAGTATGGGCTTAGCGTTAGACTG--GTGAGAC -s simCow_chr6.simCow.chr6 86219 48 + 602619 GAAATGCCAGTAATGCAAGATGTAGACTTAACATTGGGCTG--GTGGCAC -s simDog_chr6.simDog.chr6 187031 48 + 593897 GGAATGCTAGTATTGTGAGATGTGGGCTAATCATTGGGTTG--GAGGCAC -s simHuman_chr6.simHuman.chr6 79622 48 + 601863 GAAATGCTAATAATGCAAGAGGTGGGCTGAACATTGTACTG--GTGGCAC -s simRat_chr6.simRat.chr6 76950 42 + 647215 GAAATGCTAGAAACTTAAAGTATGGGGTCAGTGTTAGACT--------AC - -a -s simMouse_chr6.simMouse.chr6 84497 7 + 636262 AACACTA -s Anc0.Anc0refChr4 27535 7 - 45765 AGCACTA -s Anc1.Anc1refChr2 59015 7 + 144309 AGCACTA -s Anc2.Anc2refChr7 27711 7 + 32194 AGCACTG -s mr.mrrefChr0 79921 7 + 130230 AACACTA -s simCow_chr6.simCow.chr6 86269 7 + 602619 CACACTG -s simDog_chr6.simDog.chr6 187081 7 + 593897 AGCACTG -s simHuman_chr6.simHuman.chr6 79670 7 + 601863 ATCACCA -s simRat_chr6.simRat.chr6 76992 7 + 647215 AACACTA - -a -s simMouse_chr6.simMouse.chr6 84504 1 + 636262 C -s Anc0.Anc0refChr4 27542 1 - 45765 C -s Anc1.Anc1refChr2 59022 1 + 144309 C -s Anc2.Anc2refChr7 27718 1 + 32194 C -s mr.mrrefChr0 79928 1 + 130230 C -s simCow_chr6.simCow.chr6 86283 1 + 602619 T -s simDog_chr6.simDog.chr6 187088 1 + 593897 C -s simHuman_chr6.simHuman.chr6 79677 1 + 601863 C -s simRat_chr6.simRat.chr6 76999 1 + 647215 C - -a -s simMouse_chr6.simMouse.chr6 84505 4 + 636262 AAGA -s Anc0.Anc0refChr4 27543 4 - 45765 AATA -s Anc1.Anc1refChr2 59023 4 + 144309 AATA -s Anc2.Anc2refChr7 27719 4 + 32194 TATA -s mr.mrrefChr0 79929 4 + 130230 AAGA -s simCow_chr6.simCow.chr6 86284 4 + 602619 TACA -s simDog_chr6.simDog.chr6 187089 4 + 593897 TATA -s simHuman_chr6.simHuman.chr6 79678 1 + 601863 A--- -s simRat_chr6.simRat.chr6 77006 4 + 647215 ATGA - -a -s simMouse_chr6.simMouse.chr6 84509 12 + 636262 TATAACCATTTC -s Anc0.Anc0refChr4 27547 8 - 45765 TATGAT----TC -s Anc1.Anc1refChr2 59027 8 + 144309 TATGAT----TC -s Anc2.Anc2refChr7 27724 8 + 32194 TATGAT----AT -s mr.mrrefChr0 79933 8 + 130230 TATAAC----TC -s simCow_chr6.simCow.chr6 86289 8 + 602619 TGTGAT----AT -s simDog_chr6.simDog.chr6 187094 8 + 593897 TATGAT----AT -s simHuman_chr6.simHuman.chr6 79679 2 + 601863 ----------TC -s simRat_chr6.simRat.chr6 77010 6 + 647215 TATCAC------ - -a -s simMouse_chr6.simMouse.chr6 84521 15 + 636262 CAGAAGTAGTAATGA -s Anc0.Anc0refChr4 27555 15 - 45765 CAGAACTAGAAATGA -s Anc1.Anc1refChr2 59035 15 + 144309 CAGAACTAGAAATGA -s Anc2.Anc2refChr7 27732 15 + 32194 CAGATCTAGAAATGA -s mr.mrrefChr0 79941 15 + 130230 CAGAAGTAGTAATGA -s simCow_chr6.simCow.chr6 86306 15 + 602619 CAGATGAAGAAATGC -s simDog_chr6.simDog.chr6 187102 15 + 593897 CAGATCTGGAAATGA -s simHuman_chr6.simHuman.chr6 79681 15 + 601863 CAGAACTAGAATTGA -s simRat_chr6.simRat.chr6 77016 6 + 647215 ---------TAGCGA - -a -s simMouse_chr6.simMouse.chr6 84536 12 + 636262 TGGTCAGTAATA -s Anc0.Anc0refChr4 27572 12 - 45765 GGGTCAATCAGT -s Anc1.Anc1refChr2 59052 12 + 144309 GGGTCAATCAGT -s Anc2.Anc2refChr7 27749 12 + 32194 GGGTCAATCAGT -s mr.mrrefChr0 79956 12 + 130230 TGGTCAGTCATA -s simCow_chr6.simCow.chr6 86323 12 + 602619 GGATTCATCGGT -s simDog_chr6.simDog.chr6 187119 12 + 593897 GGGTCAACCAGT -s simHuman_chr6.simHuman.chr6 79698 12 + 601863 GGGGCAATCAGT -s simRat_chr6.simRat.chr6 77022 12 + 647215 TGGTCAGTCACA - -a -s simMouse_chr6.simMouse.chr6 84548 54 + 636262 TCATGGATATAGCAATCAATCTCTATCCAGCTACTTCTTTGTATTGGTACATGC -s Anc0.Anc0refChr4 27584 53 - 45765 TCATGGATATAACAATCATGCTCTATCTGGCTGCTTTCCCATATT-ATACACCC -s Anc1.Anc1refChr2 59064 53 + 144309 TCATGGATATAACAATCATGCTCTATCTGGCTGCTTTCCCATATT-ATACACCC -s Anc2.Anc2refChr7 27761 53 + 32194 TCATGGATATAACAATCATGCTCTATCTTGCTGCTTTCCCATATT-ACACACCC -s mr.mrrefChr0 79968 53 + 130230 TCATGGATATAGCAATCAATCTCTATCTGGCTACTTCTCCGTATT-GTACACGC -s simCow_chr6.simCow.chr6 86335 53 + 602619 TCATGAATACAGCAATCATGCTTTGTCTATCTGCTTTCCCATATT-ACACACTC -s simDog_chr6.simDog.chr6 187151 52 + 593897 TTATGGATATAACAATCATGC-CTATCTTGCTCATTTCCTACATT-ACACACCC -s simHuman_chr6.simHuman.chr6 79710 53 + 601863 TCATGGATATAACAATCATGCTCTATCTGGCTGCTTTCCCATATT-TTAAACCC -s simRat_chr6.simRat.chr6 77034 53 + 647215 TCATGGATATAGCCATCAATCTATATCTGGCTACTTCTCCGTATT-GTACACTC - -a -s simMouse_chr6.simMouse.chr6 84602 40 + 636262 CTGGGACATACTTTTATAAGGAGAATAAAGCTTTTCTAAA -s Anc0.Anc0refChr4 27638 40 - 45765 CTAACACATACATTTTTAGGCAGAATAAAGTTGTGAAAAG -s Anc1.Anc1refChr2 59118 40 + 144309 CTAACACATACATTTTTAGGCAGAATAAAGTTGTGAAAAG -s Anc2.Anc2refChr7 27815 40 + 32194 CTAACACATACATTTTTAGAGAGAATAAAGTTGTGAAAAG -s mr.mrrefChr0 80021 40 + 130230 CTGGGACATACATTTTTAAGCAGAATAAAGCTTTTCTAAA -s simCow_chr6.simCow.chr6 86389 40 + 602619 CCAACACATATATTTTTAGCAAAAATAAAGTTGTGAAAAC -s simDog_chr6.simDog.chr6 187204 40 + 593897 GTAACACATACATTTTTAGAGAGAATTAAGTTGCGAAAAG -s simHuman_chr6.simHuman.chr6 79764 40 + 601863 CTAACACATACATTTTTAGGCAGGATAAAGTTGTGAAAAG -s simRat_chr6.simRat.chr6 77087 40 + 647215 CTGGTACATACATTGTTACCCAGAATAAAGCTTTTGTAAA - -a -s simMouse_chr6.simMouse.chr6 84642 14 + 636262 TTTAGGAATCACAT -s Anc0.Anc0refChr4 27678 14 - 45765 TTTAGGAGTCATAT -s Anc1.Anc1refChr2 59158 14 + 144309 TTTAGGAGTCATAT -s Anc2.Anc2refChr7 27855 14 + 32194 TCTAAGAGTCATAT -s mr.mrrefChr0 80061 14 + 130230 TTTAGGAATCATAT -s simCow_chr6.simCow.chr6 86430 14 + 602619 TCCACATGTCACAT -s simDog_chr6.simDog.chr6 187244 14 + 593897 TCTAAGAGTTATAT -s simHuman_chr6.simHuman.chr6 79804 14 + 601863 TTTAGGAGCCATGT -s simRat_chr6.simRat.chr6 77127 14 + 647215 TCTAGGAATCATAT - -a -s simMouse_chr6.simMouse.chr6 84656 22 + 636262 GTATCACACCAAGATGGAGGTT -s Anc0.Anc0refChr4 27692 18 - 45765 G----AAATGAAAATGCAGGTT -s Anc1.Anc1refChr2 59172 22 + 144309 GTTTAAAATGAAAATGCAGGTT -s Anc2.Anc2refChr7 27869 18 + 32194 G----ACATGAAAATGCAGGTT -s mr.mrrefChr0 80075 22 + 130230 GTATAAAACGAAGATGGAGGTT -s simCow_chr6.simCow.chr6 86444 18 + 602619 G----ACACAATAATGCAGGTT -s simDog_chr6.simDog.chr6 187258 18 + 593897 G----ACATGAAAGTGTAGACA -s simHuman_chr6.simHuman.chr6 79822 22 + 601863 ATTTACACTGAATATGCAGGTT -s simRat_chr6.simRat.chr6 77141 22 + 647215 TTATAAAGCGAAGATGGAGGTT - -a -s simMouse_chr6.simMouse.chr6 84678 9 + 636262 AACTGCATC -s Anc0.Anc0refChr4 27711 9 - 45765 AACTGACGC -s Anc1.Anc1refChr2 59195 9 + 144309 AACTGACGC -s Anc2.Anc2refChr7 27888 9 + 32194 AACTGACGC -s mr.mrrefChr0 80097 9 + 130230 AACTGCATC -s simCow_chr6.simCow.chr6 86463 9 + 602619 AACTGCTGC -s simDog_chr6.simDog.chr6 187277 9 + 593897 AACTGACGC -s simHuman_chr6.simHuman.chr6 79845 9 + 601863 AACTGTCCC -s simRat_chr6.simRat.chr6 77163 9 + 647215 AACTGCGTC - -a -s simMouse_chr6.simMouse.chr6 84687 3 + 636262 AAC -s Anc0.Anc0refChr4 27720 3 - 45765 AAC -s Anc1.Anc1refChr2 59204 3 + 144309 AAC -s Anc2.Anc2refChr7 27897 3 + 32194 AAC -s mr.mrrefChr0 80106 3 + 130230 AAC -s simCow_chr6.simCow.chr6 86475 3 + 602619 AAC -s simDog_chr6.simDog.chr6 187286 3 + 593897 AAC -s simHuman_chr6.simHuman.chr6 79854 3 + 601863 AAC -s simRat_chr6.simRat.chr6 77172 3 + 647215 AAC - -a -s simMouse_chr6.simMouse.chr6 84690 18 + 636262 AGCACGTTTGTAATGTCT -s Anc0.Anc0refChr4 27723 18 - 45765 AACAACTTTGTGACTTCT -s Anc1.Anc1refChr2 59207 18 + 144309 AACAACTTTGTGACTTCT -s Anc2.Anc2refChr7 27900 18 + 32194 AACAACTTTATGACTTCT -s mr.mrrefChr0 80109 18 + 130230 AACAACTTTGTAATGTCT -s simCow_chr6.simCow.chr6 86478 18 + 602619 AACAACTTTGTAACTTTT -s simDog_chr6.simDog.chr6 187289 18 + 593897 AACAACTTTATGAATTCT -s simHuman_chr6.simHuman.chr6 79858 16 + 601863 AACAACCTTG--ACTTCT -s simHuman_chr6.simHuman.chr6 79983 16 + 601863 AACAACCTTG--ACTTCT -s simRat_chr6.simRat.chr6 77175 18 + 647215 AACAACTTTGTAAGATCT - -a -s simMouse_chr6.simMouse.chr6 84708 5 + 636262 CTATA -s Anc0.Anc0refChr4 27742 5 - 45765 CTAAA -s Anc1.Anc1refChr2 59226 5 + 144309 CTAAA -s Anc2.Anc2refChr7 27919 5 + 32194 CAAAA -s mr.mrrefChr0 80127 5 + 130230 CTATA -s simCow_chr6.simCow.chr6 86497 5 + 602619 CAAAA -s simDog_chr6.simDog.chr6 187308 5 + 593897 CAAAA -s simHuman_chr6.simHuman.chr6 79875 5 + 601863 CTAAA -s simHuman_chr6.simHuman.chr6 80000 5 + 601863 CTAAA -s simRat_chr6.simRat.chr6 77193 5 + 647215 CTATA - -a -s simMouse_chr6.simMouse.chr6 84713 62 + 636262 CATTGCATTGTGGCCCATCATGACTCTTGGGCTAGTATTGCTAGTCTATAGTGACTCCACCT -s Anc0.Anc0refChr4 27747 62 - 45765 CATTGCCTCCTGGCCTCCCATGACTCCTGGGCTAGTATCACTAATTTATAGCATCTCCAATT -s Anc1.Anc1refChr2 59231 62 + 144309 CATTGCCTCCTGGCCTCCCATGACTCCTGGGCTAGTATCACTAATTTATAGCATCTCCAATT -s Anc2.Anc2refChr7 27961 62 + 32194 CATTGCTTCCTGGCCTCCCATGACTCCTGGGCTAGCATCCCCAATTTATAGCATCTCCAATT -s mr.mrrefChr0 80132 62 + 130230 CATTGCATTGTGGCCCATCATGACTCTTGGGCTAGTATTGCTAGTTTATAGCAACTCCACAT -s simCow_chr6.simCow.chr6 86503 60 + 602619 -ATTGCATGCTGGACTCCCATGACTCCTGGTTTAGCATTCC-AATTCATTGCATCTCCAATT -s simDog_chr6.simDog.chr6 187350 61 + 593897 CCATGCTTCCTGGCCTCCCATGACTCCTGGGCTAGCATCCCCAATTTAAAGCAT-TCCATGT -s simHuman_chr6.simHuman.chr6 79880 62 + 601863 CATTGCCTCCTGGCCTCCCACAACTCCTGGGGTAGTACCACTAATTGATAGCATCTCCAATT -s simHuman_chr6.simHuman.chr6 80005 62 + 601863 CATTGCCTCCTGGCCTCCCACAACTCCTGGGATAGTAGCACTAATTGATAGCATCTCCAATT -s simRat_chr6.simRat.chr6 77198 62 + 647215 CATTGCATTGTGGCCCATGATGACTCTTGGGCGAGTATTGCCAGATTATAGCAACTCCACAT - -a -s simMouse_chr6.simMouse.chr6 84775 1 + 636262 G -s Anc0.Anc0refChr4 27818 1 - 45765 A -s Anc1.Anc1refChr2 59303 1 + 144309 A -s Anc2.Anc2refChr7 28032 1 + 32194 A -s mr.mrrefChr0 80194 1 + 130230 G -s simCow_chr6.simCow.chr6 86572 1 + 602619 G -s simDog_chr6.simDog.chr6 187420 1 + 593897 A -s simHuman_chr6.simHuman.chr6 79952 1 + 601863 A -s simHuman_chr6.simHuman.chr6 80077 1 + 601863 A -s simRat_chr6.simRat.chr6 77260 1 + 647215 G - -a -s simMouse_chr6.simMouse.chr6 84776 30 + 636262 TGAGTGAGACTGGAAGTGCCAAGAAGTCCT -s Anc0.Anc0refChr4 27819 30 - 45765 TGACTGAGTCTTGGGTTCCTAAGAAGGTCT -s Anc1.Anc1refChr2 59304 30 + 144309 TGACTGAGTCTTGGGTTCCTAAGAAGGTCT -s Anc2.Anc2refChr7 28033 30 + 32194 TCACTGAGTCTTGTCTTCTTCCGAAGGTCT -s mr.mrrefChr0 80195 30 + 130230 TGACTGAGACTGGAGGTGCTAAGAAGTCCT -s simCow_chr6.simCow.chr6 86573 26 + 602619 TTTCTGAGTCCTGCATT----GGAAGGTCT -s simDog_chr6.simDog.chr6 187421 29 + 593897 TCACTTAGTATTGTCTTCTTCC-ATGGTCT -s simHuman_chr6.simHuman.chr6 79953 30 + 601863 TTACAGAGTCATGGGTTCCTAAGAAGGTCT -s simHuman_chr6.simHuman.chr6 80078 30 + 601863 TGACAGAGTCGTGGGTTCCTAAGAAGGTCT -s simRat_chr6.simRat.chr6 77262 24 + 647215 CTACTAAGACTGGAGGTGCTAAGA------ - -a -s simMouse_chr6.simMouse.chr6 84806 56 + 636262 ACTGAGTATTATGGCGAGCAACTTGCAATAAGAACCTGGGATAGTAAAAAGTAAGG -s Anc0.Anc0refChr4 27849 48 - 45765 ACTAAGTATTTGGAC-TTCAATTT---ATAAGAAT----TAAGGTGACAAACATGG -s Anc1.Anc1refChr2 59334 48 + 144309 ACTAAGTATTTGGAC-TTCAATTT---ATAAGAAT----TAAGGTGACAAACATGG -s Anc2.Anc2refChr7 28063 48 + 32194 CCCAATTATTTGGAT-TTTAATTT---ATAAGGAT----TAAGGTGACCAACATGG -s mr.mrrefChr0 80225 56 + 130230 ACTGAGTATTATGGCGATCAACTTGCAATAAGAACCTGGTATAGTAAAAAGTAAGG -s simCow_chr6.simCow.chr6 86599 46 + 602619 CTAAATTATTTGGAT-ATTAATTT---ATAAGGAT----TAA--TGACCATTATGG -s simDog_chr6.simDog.chr6 187450 46 + 593897 CCCCGTTGTCTGGAT-TT--ATTC---ATAAGGTT----TGAGGTGACCAACACGG -s simHuman_chr6.simHuman.chr6 80108 48 + 601863 ACTAAGTATTTGGAC-CTCAATTT---AGAAGAAT----TACGGTGCTAAACATGG -s simRat_chr6.simRat.chr6 77286 56 + 647215 ACTGAGTATTATGGTGATCAACTTCCAATAAGAACCTGGTATAGTAAGAAgtaagg - -a -s simMouse_chr6.simMouse.chr6 84862 6 + 636262 CAACCT -s Anc0.Anc0refChr4 27899 6 - 45765 CAAGTG -s Anc1.Anc1refChr2 59384 6 + 144309 CAAGTG -s Anc2.Anc2refChr7 28113 6 + 32194 CAAGTG -s mr.mrrefChr0 80281 6 + 130230 CAACCT -s simCow_chr6.simCow.chr6 86647 6 + 602619 CAAGTG -s simDog_chr6.simDog.chr6 187498 6 + 593897 CAAGTG -s simHuman_chr6.simHuman.chr6 80158 6 + 601863 CGAGTA -s simRat_chr6.simRat.chr6 77342 6 + 647215 caacct - -a -s simMouse_chr6.simMouse.chr6 84868 5 + 636262 GTTAA -s Anc0.Anc0refChr4 27905 5 - 45765 TTGGA -s Anc1.Anc1refChr2 59390 5 + 144309 TTGGA -s Anc2.Anc2refChr7 28119 5 + 32194 TTGGA -s mr.mrrefChr0 80287 5 + 130230 GTTAA -s simCow_chr6.simCow.chr6 86659 5 + 602619 TTGGA -s simDog_chr6.simDog.chr6 187504 5 + 593897 TTTGA -s simHuman_chr6.simHuman.chr6 80164 5 + 601863 TTGGA -s simRat_chr6.simRat.chr6 77348 5 + 647215 gttaa - -a -s simMouse_chr6.simMouse.chr6 84873 76 + 636262 ATAAAAAGACTCACATGATCTTATTATGTGGACAATGATGAGGTGTCCGCAAAATAGAATTATGTACATCTGACCA -s Anc0.Anc0refChr4 27910 66 - 45765 AGACATAAACCCA----CGCTAATAAGGTAGACA------AATTGTTAGCCAAGCAGGATTAGGTGCATCTGAAAA -s Anc1.Anc1refChr2 59395 66 + 144309 AGACATAAACCCA----CGCTAATAAGGTAGACA------AATTGTTAGCCAAGCAGGATTAGGTGCATCTGAAAA -s Anc2.Anc2refChr7 28124 66 + 32194 AGACATAAACCCA----CGCTAATAAGCTAGACA------AATCATTAGCCAAGCAGGACTAGGTGCATCTGAAAA -s mr.mrrefChr0 80292 76 + 130230 ATAAAAAGACTCAcaTGATCTTAttATGTGGACAATGATGAGGTGTCCGCAAAATAGAATTATGTACATCTGACCA -s simCow_chr6.simCow.chr6 86664 64 + 602619 AAATATAAACACA----CGCTAATAAGCTAGACA------AAT--TTAGCCATGCAGGAGTAGGTGCATCCGAAAT -s simDog_chr6.simDog.chr6 187509 60 + 593897 TGACTTAGACC----------AATAAGCTAGACG------GATCATCGGGCAAGCAAAACTGGGTGCATCTGAAAA -s simHuman_chr6.simHuman.chr6 80169 66 + 601863 AGACATAAACCCA----GGGTAATAAGGTAGACA------AATTGTTAGCCAAGGAGGATGAGGGGCAACTGAAAA -s simRat_chr6.simRat.chr6 77360 76 + 647215 ataaaaagaatcacacgatcttattgtatggacaATCATCAGATATCGGCAAAATAGAATTATGCACATCTGACCA - -a -s simMouse_chr6.simMouse.chr6 84949 9 + 636262 ATCATGTGT -s Anc0.Anc0refChr4 27982 9 - 45765 ACAATGTGT -s Anc1.Anc1refChr2 59467 9 + 144309 ACAATGTGT -s Anc2.Anc2refChr7 28196 9 + 32194 ACAATGTGT -s mr.mrrefChr0 80368 9 + 130230 ATCATGTGT -s simCow_chr6.simCow.chr6 86734 9 + 602619 ACAATGCGT -s simDog_chr6.simDog.chr6 187575 9 + 593897 ACAATGTGT -s simHuman_chr6.simHuman.chr6 80241 9 + 601863 ACTATGTGT -s simRat_chr6.simRat.chr6 77436 9 + 647215 ATCATGTGA - -a -s simMouse_chr6.simMouse.chr6 84958 163 + 636262 TCCCCCACATGCCTTGCCTTTTTTACGATCAACGAAATGGCTGGAACTGTAAAGCCAGGCAACTTTATTACATCTCCTGACCGGGGGGGCACAACTCTATGGTATACACATCTTTACTAGCGCAAAAAACCAGGGTCTGACCCTAGGATGCAGATTTTACGAA -s Anc0.Anc0refChr4 27993 74 - 45765 TCCTCTACATGCATTGCCTTATTTACTA--AAATAACTGGC----------AAGCAA--CAACTTTGTTGCATCTCCTAATCGGGGGG--------------------------------------------------------------------------- -s Anc1.Anc1refChr2 59478 91 + 144309 TCCTCTACATGCATTGCCTTATTTACTA--AAATAACTGGC----------AAGCAA--CAACTTTGTTGCATCTCCTAATCGGGGGGGTAAAGCACCTGCGT----------------------------------------------------------GA -s Anc2.Anc2refChr7 28207 74 + 32194 TCCTCTACATGCATTGCCTTATTTAGTA--AAATAACTGGC----------AAGCAA--CAACTTTGTTGCATCTCCTAATTGGGGGG--------------------------------------------------------------------------- -s mr.mrrefChr0 80379 103 + 130230 TCCCCCACATGCCTTGCCTTTTTTACGA--AACGAAATGGCTGGAACTGTAAAGCCAGGCAACTTTATTGCATCTCCTGACCGGGGGGGCACAACTCTAGCGT----------------------------------------------------------AA -s simCow_chr6.simCow.chr6 86745 74 + 602619 AGCTCTGCATGCACTGCCTTATTTAGTA--AGATAATTGGC----------ACCCAA--CAACTATGTTGCATCTCCTAATGGGGGAG--------------------------------------------------------------------------- -s simDog_chr6.simDog.chr6 187586 74 + 593897 TCCTCCACATGTCTTGCCTTATTTAGTA--GAATAACTGGC----------AAGGGG--CAACTTTGTTGCACCTCCTAATTGGAAGG--------------------------------------------------------------------------- -s simHuman_chr6.simHuman.chr6 80252 91 + 601863 TCCTATACATGCATTGAATTATTTACTA--AAATAACTGGC----------AAGCAA--CAACTTTGTCGCATCTCCTAATCGGGGGGGTAAAGCACCTGCGT----------------------------------------------------------GA -s simRat_chr6.simRat.chr6 77451 98 + 647215 CCCCCCACATGCCTCGCCACTTT-------AACGAAATGGTTGGTACTGTAAAGCCAGGCAACTTTATTGCTTCTCCTGACTGAGGGGGCAGAACCCTAGCGT----------------------------------------------------------AA - -a -s simMouse_chr6.simMouse.chr6 85121 38 + 636262 AACAGAGTTGACTAGTGTGTTTGAAGATACTAAGAAGT -s Anc0.Anc0refChr4 28067 22 - 45765 ----------------GTGGTTAAAGCTACAAAGAAGT -s Anc1.Anc1refChr2 59569 38 + 144309 AACAGAGCTGCCTGGTGTGGTTAAAGCTACAAAGAAGT -s Anc2.Anc2refChr7 28281 22 + 32194 ----------------CTGGTTAAAGCCGCAAAGAAGT -s mr.mrrefChr0 80482 38 + 130230 AACAGAGTTGACTAGTGTGGTTGAAGATACTAAGAAGT -s simCow_chr6.simCow.chr6 86819 22 + 602619 ----------------CTGGTCAAATCAGCAACAAAGT -s simDog_chr6.simDog.chr6 187660 22 + 593897 ----------------CTGGTTAAAGCCGCAAAGAAGT -s simHuman_chr6.simHuman.chr6 80365 38 + 601863 AACAGAGCTGCCTGGTGTGGTTAAAGCTACAAAGAAGT -s simRat_chr6.simRat.chr6 77549 38 + 647215 AACAGAGTTGACTAGTGTGGTTGAAGATACTAAGAAGT - -a -s simMouse_chr6.simMouse.chr6 85159 114 + 636262 CTGCCACTGTTTAGTGCTCTTTTTGGGGACAGAACACTTATGGGCAAGCCAAGTTGTAAGAGAATGATAAGAAAGTACTCCGTGCTTCAAACTAATGGATATAGCAAATTGATA -s Anc0.Anc0refChr4 28089 109 - 45765 CTTCAGATAATTAATTTTGTTTTT-GGGACAGAGTTCTTGAGGCTAGGGCAAGTAGTA--AAA--AATAAGAAAGTTCTTGATGTCTCACACTATTGGAAAGAGTAAATTGATG -s Anc1.Anc1refChr2 59607 109 + 144309 CTTCAGATAATTAATTTTGTTTTT-GGGACAGAGTTCTTGAGGCTAGGGCAAGTAGTA--AAA--AATAAGAAAGTTCTTGATGTCTCACACTATTGGAAAGAGTAAATTGATG -s Anc2.Anc2refChr7 28303 109 + 32194 CCTTAGATAATTAATTTTGTTTTT-AGGATAGAGTTCTTGAGGCTAGGGCAAGTAGTG--AAA--AATAAGAAAGCTCTTGGTGTCTCACATTATTGGAAGGAGTAGTGTGCTG -s mr.mrrefChr0 80520 112 + 130230 CTGCCACTGTTTAATGTTCTTTTTGGGGACAGAACACTTATGGGCAAGCCAAGTTGTA--AGAATAATAAGAAAGTACTCCATGCCTCAAACTAATGGATATAGCAAATTGATA -s simCow_chr6.simCow.chr6 86841 85 + 602619 TCTTATATAATTAATTTTGTCTCC-AGGATAGAGTTCTTGGGGCTAGGACAAG-ACTG--AAA--CATAAGGAAACTCTTGGTATGT-----------------------GCTG -s simDog_chr6.simDog.chr6 187682 109 + 593897 CCCTAGATGGTTAATTTTGTTTTT-ATGGTGGAGTTCTTGAGGCCAGGGCAAGTAGTG--AAA--AATTAGACAGCACTTGGTGACTCACATTATTGGAAGGAGTAGTGTGCTG -s simHuman_chr6.simHuman.chr6 80449 109 + 601863 CTTCAGACAATTAATTTTGTTTTT-GGGACATTGGTCTTGAGGCTTGGGCCAGTAGTA--AAA--AATAAACAAGTTCTTGATGTCTCATACTGTTTGAAAAGGAAAATCAATG -s simRat_chr6.simRat.chr6 77587 112 + 647215 GTGCTGTTGTTTAATGTTCTTTTTGGGGGCAGAACACTTATGGGCAAGCCAAGTTGTA--AGAACAATAAGAAAGTACTCCATGCCTCAAACCAACGGAGATAGTAAATTGACA - -a -s simMouse_chr6.simMouse.chr6 85273 36 + 636262 CATGAAGGTGAAGAAGAGTCCGGTCTTGAAAAGTCT -s Anc0.Anc0refChr4 28198 18 - 45765 CATGATGGTGTTA------------------AGACC -s Anc1.Anc1refChr2 59716 18 + 144309 CATGATGGTGTTA------------------AGACC -s Anc2.Anc2refChr7 28412 18 + 32194 CACAATGGTGTTA------------------AGACC -s mr.mrrefChr0 80632 18 + 130230 CATGAAGGTGAAG------------------AGTCC -s simCow_chr6.simCow.chr6 86928 18 + 602619 CACAATTGTGAGG------------------AGTCC -s simDog_chr6.simDog.chr6 187791 18 + 593897 CACAATGGTGTTA------------------AGACC -s simHuman_chr6.simHuman.chr6 80558 18 + 601863 CATGATGGTGTTA------------------AGACC -s simRat_chr6.simRat.chr6 77699 18 + 647215 CATGAAGGTGAAG------------------AGTCC - -a -s simMouse_chr6.simMouse.chr6 85309 25 + 636262 GGTCTAGTCGTCATGTACTACAGTT -s Anc0.Anc0refChr4 28216 22 - 45765 AGTCTAGTGGTCAAGTGCT---GTT -s Anc1.Anc1refChr2 59734 22 + 144309 AGTCTAGTGGTCAAGTGCT---GTT -s Anc2.Anc2refChr7 28430 22 + 32194 AGTCTAGTGGTCAAGTGCT---ACT -s mr.mrrefChr0 80650 25 + 130230 AGTCTAGTGGTCATGTACTACAGTT -s simCow_chr6.simCow.chr6 86949 21 + 602619 AGTTAGGTGGCCAATAGC----ACT -s simDog_chr6.simDog.chr6 187809 22 + 593897 AGTCTATTGGTCAAGTGCT---ACT -s simHuman_chr6.simHuman.chr6 80576 22 + 601863 AATCTAGTGCTCACGTGCT---GTT -s simRat_chr6.simRat.chr6 77717 25 + 647215 AGTATAGTGGTCATGCACTACAGTG - -a -s simMouse_chr6.simMouse.chr6 85334 5 + 636262 TGCAG -s Anc0.Anc0refChr4 28238 5 - 45765 TGCGG -s Anc1.Anc1refChr2 59756 5 + 144309 TGCGG -s Anc2.Anc2refChr7 28452 5 + 32194 GGCTA -s mr.mrrefChr0 80675 5 + 130230 TGCGG -s simCow_chr6.simCow.chr6 86970 5 + 602619 GACCA -s simDog_chr6.simDog.chr6 187831 5 + 593897 GGCTA -s simHuman_chr6.simHuman.chr6 80603 5 + 601863 TGTGG -s simRat_chr6.simRat.chr6 77742 5 + 647215 TGCGG - -a -s simMouse_chr6.simMouse.chr6 85339 9 + 636262 CTTGGTTGA -s Anc0.Anc0refChr4 28243 9 - 45765 CTTATTTGA -s Anc1.Anc1refChr2 59761 9 + 144309 CTTATTTGA -s Anc2.Anc2refChr7 28457 9 + 32194 CTTAGTTCA -s mr.mrrefChr0 80680 9 + 130230 CTTGTTTGA -s simCow_chr6.simCow.chr6 86981 9 + 602619 TGGACTTAA -s simDog_chr6.simDog.chr6 187836 9 + 593897 CTTGGTTCA -s simHuman_chr6.simHuman.chr6 80608 9 + 601863 CTTATTTGA -s simRat_chr6.simRat.chr6 77747 6 + 647215 CTTTTT--- - -a -s simMouse_chr6.simMouse.chr6 85348 102 + 636262 GGGAATCCTTATGACTGTGTGCGGTACTGGTCCCTAGAAGGCAAGAGGTCTTATGCTGGAAACAAAAACATTAGCCTTTTAAAGCAAGTACCTAAAAGCACA -s Anc0.Anc0refChr4 28252 97 - 45765 GGGACTCCTCACAATTGTGTGCGGCAATAAT--CCAGGAGACATGAGATATTATGCT---AAGAAAAACACTACCTTTTTAAAGCAAGCATCTCAAAGTACA -s Anc1.Anc1refChr2 59770 99 + 144309 GGGACTCCTCACAATTGTGTGCGGCAATAATCCCCAGGAGACATGAGATATTATGCT---AAGAAAAACACTACCTTTTTAAAGCAAGCATCTCAAAGTACA -s Anc2.Anc2refChr7 28466 97 + 32194 GGGACTCCTCACAATTGTGTGCGGCAACAAT--CCAGGAGACATGAGATATTATGCT---ATGAAAAACACTACCTTTTAAAAGCAAGCATCTCAAAGTACA -s mr.mrrefChr0 80689 102 + 130230 GGGAATCCTTATGACTGTGTGCGGTACTGGTCCCTAGGAGGCAAGAGGTATTATGCTGGAAACAAAAACATTAGCCTTTTAAAGCAAGTACCTAAAAGCACA -s simCow_chr6.simCow.chr6 86991 77 + 602619 AGTACTGTTTCCAATAGTGTGAGTCATCAAT----AGGAGACATGAGAT---------------------CTGCCCTTGCAAAGCAACCATCTCAAAGATCA -s simDog_chr6.simDog.chr6 187845 97 + 593897 GGGACTCCCCAGAATTGGTTGCGGCAACAAT--CCAGGAGACATGAGATATTATGCT---ATGAAAAACACTACCTCTTAAAAGCAAGCATCTCAAAGTACA -s simHuman_chr6.simHuman.chr6 80617 99 + 601863 GGGACTCCTCACCATTGTGTGCAGCAATCATCCCCAGGAGTCATGAGATATTATGCC---AAGAAAAACACTACCTTTTTAAAGCAAGCATCTCAAAGTATA -s simRat_chr6.simRat.chr6 77753 101 + 647215 -GGGGCTCCTATGTATTTGTGGCGTATTAGTCCCTAGGAGACAGAAGGTATTATGCTGGAGACAAAAACATTAGCCTTCTAAAGCAAGTGCCTAGAAGCACA - -a -s simMouse_chr6.simMouse.chr6 85450 18 + 636262 GACAAGAGAATGAAGGAT -s Anc0.Anc0refChr4 28350 18 - 45765 AAAAAGAGAGTGCTAGAT -s Anc1.Anc1refChr2 59870 18 + 144309 AAAAAGAGAGTGCTAGAT -s Anc2.Anc2refChr7 28564 18 + 32194 AAAAAGAGAGTGCCAGAA -s mr.mrrefChr0 80791 18 + 130230 GACAAGAGAGTGCTGGAT -s simCow_chr6.simCow.chr6 87069 17 + 602619 -AAAAGAGAGTGCCAGAA -s simDog_chr6.simDog.chr6 187943 10 + 593897 AGAAAGTAAG-------- -s simHuman_chr6.simHuman.chr6 80717 18 + 601863 AAAAAGAGAGTGCTAGAT -s simRat_chr6.simRat.chr6 77854 18 + 647215 GATAAGGGAGTGCTGGAT - -a -s simMouse_chr6.simMouse.chr6 85468 13 + 636262 GACCATAGAGACT -s Anc0.Anc0refChr4 28370 13 - 45765 GACAATATTTACC -s Anc1.Anc1refChr2 59890 13 + 144309 GACAATATTTACC -s Anc2.Anc2refChr7 28584 13 + 32194 GAGACTGTTTACC -s mr.mrrefChr0 80811 13 + 130230 GACCATAGAGACC -s simCow_chr6.simCow.chr6 87088 13 + 602619 GAGAGTGCTGGCT -s simDog_chr6.simDog.chr6 187953 10 + 593897 ---ACTGTTTACC -s simHuman_chr6.simHuman.chr6 80737 13 + 601863 TACAATAATAACC -s simRat_chr6.simRat.chr6 77874 13 + 647215 GACCATAGAGACC - -a -s simMouse_chr6.simMouse.chr6 85481 2 + 636262 TT -s Anc0.Anc0refChr4 28383 2 - 45765 TC -s Anc1.Anc1refChr2 59903 2 + 144309 TC -s Anc2.Anc2refChr7 28597 2 + 32194 TC -s mr.mrrefChr0 80824 2 + 130230 TT -s simCow_chr6.simCow.chr6 87112 2 + 602619 TC -s simDog_chr6.simDog.chr6 187963 2 + 593897 TC -s simHuman_chr6.simHuman.chr6 80750 2 + 601863 TC -s simRat_chr6.simRat.chr6 77887 2 + 647215 TT - -a -s simMouse_chr6.simMouse.chr6 85483 63 + 636262 TGATGGATATGAAAATAGGCATAGAAAATAAGCATGAGATGATCTGATGGTTATGTCTAGTCA -s Anc0.Anc0refChr4 28387 48 - 45765 TGATAGAT---------------GACAAAGGGCATAAGATGGCCTGATGGTTATGCCTGGTCA -s Anc1.Anc1refChr2 59907 48 + 144309 TGATAGAT---------------GACAAAGGGCATAAGATGGCCTGATGGTTATGCCTGGTCA -s Anc2.Anc2refChr7 28601 48 + 32194 TGATAGAT---------------AACAAAGGGCATAAGATGGCCTGTTGGGCACGCCTGAGCA -s mr.mrrefChr0 80828 63 + 130230 TGATGGATATGAAAATAGGCATAGAAAATAAGCATGAGATGATCTGATGGTTATGCCTAGTCA -s simCow_chr6.simCow.chr6 87116 31 + 602619 TGGTAGAT---------------AACAAAGGGCATTAGATGGTTTG----------------- -s simDog_chr6.simDog.chr6 187967 48 + 593897 TGATAGAT---------------AACAAAGGGGATAAGATGTCCTGTTGGGCACGCCTGAGCA -s simHuman_chr6.simHuman.chr6 80754 48 + 601863 TGATAGAT---------------GACAAAGGGCATAATATGGAATAATGGTTATACCAGGTCA -s simRat_chr6.simRat.chr6 77891 62 + 647215 TGATGGATATGAAAATAGGCATAGAAAATAAGCATGAGTTGATCTGCTGG-TATGCCTAGTCA - -a -s simMouse_chr6.simMouse.chr6 85546 44 + 636262 CTAAGATCTGACATATACGGGATACAGTTTACTAACTCCGTTAG -s Anc0.Anc0refChr4 28453 35 - 45765 CTTAGATCCTACATAT-----CTGCAGTCTACTATC-CCAC--- -s Anc1.Anc1refChr2 59973 43 + 144309 CTTAGATCCTACATATGAGGGCTGCAGTCTACTATC-CCACTAG -s Anc2.Anc2refChr7 28667 35 + 32194 CTTAGATCCTACATAT-----CTGCAGTCTACTATC-CCAC--- -s mr.mrrefChr0 80891 43 + 130230 CTAAGATCTGACATATACGGGCTACAGTCTACTAAC-CCATTAG -s simCow_chr6.simCow.chr6 87155 34 + 602619 CTTAGATCCTACATCT------GGCAGTCTAATATC-CCAC--- -s simDog_chr6.simDog.chr6 188033 34 + 593897 CTTAGATTCTACATAT-----CTGTAGTCTCCTATC-CCA---- -s simHuman_chr6.simHuman.chr6 80820 43 + 601863 CTGAGATCCTACATACGAGGGCTGCAGTCTACTACC-CCACTAG -s simRat_chr6.simRat.chr6 77953 43 + 647215 GTAGGATTTGCCACATACGGGCTACAGTCCACCAAC-CCATTAG - -a -s simMouse_chr6.simMouse.chr6 85590 7 + 636262 CTTAGCT -s Anc0.Anc0refChr4 28496 7 - 45765 CTAAGTC -s Anc1.Anc1refChr2 60024 7 + 144309 CTAAGTC -s Anc2.Anc2refChr7 28710 7 + 32194 CTAAGTC -s mr.mrrefChr0 80934 7 + 130230 CTTAGCC -s simCow_chr6.simCow.chr6 87197 7 + 602619 CTAAGTA -s simDog_chr6.simDog.chr6 188067 2 + 593897 -----TC -s simHuman_chr6.simHuman.chr6 80872 7 + 601863 CTGAGTC -s simRat_chr6.simRat.chr6 77996 7 + 647215 CTTAGCC - -a -s simMouse_chr6.simMouse.chr6 85597 63 + 636262 GACCCTAAGATCATGACATCTCTAAGATTGCGATGACCTAACACGGGGCTAGGGACTATGCAA -s Anc0.Anc0refChr4 28503 63 - 45765 AATACTAAGATCATGACATCTGTGAGATTGAAATGACTTGACAAGGGGCCAGGGATAATGTAA -s Anc1.Anc1refChr2 60031 63 + 144309 AATACTAAGATCATGACATCTGTGAGATTGAAATGACTTGACAAGGGGCCAGGGATAATGTAA -s Anc2.Anc2refChr7 28717 63 + 32194 GATACTAAGATCATGACATCTGTGGGATTGAGGTGACTTGACAAGGGGCCAGGGATAATGTAA -s mr.mrrefChr0 80941 63 + 130230 AACCCTAAGATCATGACATCTCTAAGATTGCAATGACCTAACACGGGGCTAGGGATTATGCAA -s simCow_chr6.simCow.chr6 87299 61 + 602619 GGTACTAAAATCATGACATCTG--GGCTTGAGGTGACTTGATAATGTGGCAAGGATAATGTAA -s simDog_chr6.simDog.chr6 188069 62 + 593897 GACACTAAGA-AGTGACATCTGTGGGATTGAGGTGACTTGACAGGGGGCCAGAGATAATGCAA -s simHuman_chr6.simHuman.chr6 80879 63 + 601863 AATACTAGGATCATGCCATCTGTGAGATTGGAATGACTTGACAAGGGGCCGGGGATAATGTCA -s simRat_chr6.simRat.chr6 78003 62 + 647215 AACCCT-AGATCATGACATCTCTAAGATTGCAATGGCCTAACACACGGCTAGGGATTATGGAG - -a -s simMouse_chr6.simMouse.chr6 85660 61 + 636262 ATTGTCTAGCTAGTTTTCAGTTTTGGCACTGCCCCCCCCTTTTGTTTACCTCATCAGTCTT -s Anc0.Anc0refChr4 28566 58 - 45765 ACTATCTAGCTAGTTTTCAATTTTGGCACTGCCCCCACC---TACTTACCTCATTGGTCAT -s Anc1.Anc1refChr2 60094 58 + 144309 ACTATCTAGCTAGTTTTCAATTTTGGCACTGCCCCCACC---TACTTACCTCATTGGTCAT -s Anc2.Anc2refChr7 28780 58 + 32194 ACTATCTAGCTAGTTTTCGATTTTGGCACTGCCTCCACC---TACCTAGCTCACTGATCAT -s mr.mrrefChr0 81004 61 + 130230 ATTATCTAGCTAGTTTTCAGTTTTGGCACTGCCCCCCCCTTTTGTTTACCTCATCAGTCTT -s simCow_chr6.simCow.chr6 87360 53 + 602619 ACTATCTAGGTAGTTTTCTATGTTGG-TGTGCCTCCACC---TACCTTGC----TGTTCAG -s simDog_chr6.simDog.chr6 188131 57 + 593897 ATTATCTAGCTAGTTTTCGAATT-AGCACTGTCTCCACC---TACCTAGCTCACTGATCAT -s simHuman_chr6.simHuman.chr6 80942 54 + 601863 ACTATCTAGCTAGTTGTCAATTTTGGCACTGCCCC-------TACTTACCTCATTGGTCAT -s simRat_chr6.simRat.chr6 78066 61 + 647215 ATTACCTAGCCAGTTTTCTGTTCTGGCACTGCCCCCCCCTTTTGTTGATTTCATCAGTTTT - -a -s simMouse_chr6.simMouse.chr6 85721 15 + 636262 CCATAAAATTAGTTT -s Anc0.Anc0refChr4 28641 15 - 45765 CCATAAATTTGGTTT -s Anc1.Anc1refChr2 60169 15 + 144309 CCATAAATTTGGTTT -s Anc2.Anc2refChr7 28855 15 + 32194 CCATAAATTTGGTTT -s mr.mrrefChr0 81065 15 + 130230 CCATAAAATTAGTTT -s simCow_chr6.simCow.chr6 87428 11 + 602619 CCATAAATTTG---- -s simDog_chr6.simDog.chr6 188249 15 + 593897 CCACAAATTTGGTTT -s simHuman_chr6.simHuman.chr6 81013 15 + 601863 CCATAAATCTGGTTT -s simRat_chr6.simRat.chr6 78127 15 + 647215 CCGTAAAATTTGTTT - -a -s simMouse_chr6.simMouse.chr6 85736 31 + 636262 GGCAGTTTGGCTTTAAATAGCTCTCACAGGA -s Anc0.Anc0refChr4 28656 29 - 45765 CAGTTCACATGTT--GACAGCTCTCAGAGGC -s Anc1.Anc1refChr2 60184 31 + 144309 CAGTTCACATGTTGAGACAGCTCTCAGAGGC -s Anc2.Anc2refChr7 28870 29 + 32194 CAGTTCACATGTT--GACAGCTCTCAGAGGC -s mr.mrrefChr0 81080 31 + 130230 GGCAGTTCAGCTTGAAATAGCTCTCACAGGA -s simCow_chr6.simCow.chr6 87439 28 + 602619 -AGATCATGTGTT--GACCACTATCAGAGGT -s simDog_chr6.simDog.chr6 188266 29 + 593897 CAGTTCACATGTG--GGTAGCTCTCAGAGGC -s simHuman_chr6.simHuman.chr6 81028 31 + 601863 TAGCCCACATATTGACACACTTTTCAGAGGC -s simRat_chr6.simRat.chr6 78142 15 + 647215 AGCAGTTCAGCTTGA---------------- - -a -s simMouse_chr6.simMouse.chr6 85767 2 + 636262 TG -s Anc0.Anc0refChr4 28685 2 - 45765 TG -s Anc1.Anc1refChr2 60215 2 + 144309 TG -s Anc2.Anc2refChr7 28903 2 + 32194 TG -s mr.mrrefChr0 81111 2 + 130230 TG -s simCow_chr6.simCow.chr6 87471 2 + 602619 TG -s simDog_chr6.simDog.chr6 188299 2 + 593897 TG -s simHuman_chr6.simHuman.chr6 81059 2 + 601863 TG - -a -s simMouse_chr6.simMouse.chr6 85769 24 + 636262 TTGCAATATTGGATGCAAGGGTAG -s Anc0.Anc0refChr4 28695 19 - 45765 TTGTCCCATTTG-----AGTGTAG -s Anc1.Anc1refChr2 60225 19 + 144309 TTGTCCCATTTG-----AGTGTAG -s Anc2.Anc2refChr7 28913 19 + 32194 TTGTCCCTTTTG-----GGTGTAG -s mr.mrrefChr0 81113 19 + 130230 TTGCCCCATTTG-----AGGGTAG -s simCow_chr6.simCow.chr6 87481 19 + 602619 TTGACCCCTTTG-----CACATAG -s simDog_chr6.simDog.chr6 188309 19 + 593897 TTGTCTATTTTG-----GGTGTAG -s simHuman_chr6.simHuman.chr6 81070 19 + 601863 TTGTCCCATTTG-----AGAGCAG -s simRat_chr6.simRat.chr6 78157 19 + 647215 TTGCCCCATTTG-----AGGATAG - -a -s simMouse_chr6.simMouse.chr6 85793 3 + 636262 TGA -s Anc0.Anc0refChr4 28715 3 - 45765 TGA -s Anc1.Anc1refChr2 60245 3 + 144309 TGA -s Anc2.Anc2refChr7 28933 3 + 32194 TGA -s mr.mrrefChr0 81132 3 + 130230 TGA -s simCow_chr6.simCow.chr6 87501 3 + 602619 TTA -s simDog_chr6.simDog.chr6 188329 3 + 593897 TGG -s simHuman_chr6.simHuman.chr6 81090 3 + 601863 TGA -s simRat_chr6.simRat.chr6 78176 3 + 647215 TGA - -a -s simMouse_chr6.simMouse.chr6 85796 18 + 636262 CATTGTTATATTGAATAT -s Anc0.Anc0refChr4 28724 18 - 45765 CAATGGGGTATTGAAGAT -s Anc1.Anc1refChr2 60254 18 + 144309 CAATGGGGTATTGAAGAT -s Anc2.Anc2refChr7 28944 18 + 32194 CAATGGGGTATTGAAGTT -s mr.mrrefChr0 81141 18 + 130230 CAATGGTGTATTGAATAT -s simCow_chr6.simCow.chr6 87512 17 + 602619 -AATTGAATATTGAAGGT -s simDog_chr6.simDog.chr6 188340 18 + 593897 CAGTGGGGTACTGAAGTT -s simHuman_chr6.simHuman.chr6 81099 18 + 601863 CAATGGGGTATTGAAGAT -s simRat_chr6.simRat.chr6 78186 18 + 647215 CAATGGTGTATTGAAAAT - -a -s simMouse_chr6.simMouse.chr6 85814 47 + 636262 CTTAACTCTGGAAGACACAGAACACACACCCTTGAATAAGTTTCTCC -s Anc0.Anc0refChr4 28742 47 - 45765 CTTAACCCTGGAAGACACCAAATTTGCAGCCTTGAATCAGTTGTTCA -s Anc1.Anc1refChr2 60272 47 + 144309 CTTAACCCTGGAAGACACCAAATTTGCAGCCTTGAATCAGTTGTTCA -s Anc2.Anc2refChr7 28967 47 + 32194 CTTAACCCTCGAAAATACCAAATTTGCAGCCTTGAATCAGCTGTTCA -s mr.mrrefChr0 81159 47 + 130230 CTTAACTCTGGAAGACACAGAATACGCACCCTTGAATAAGTTTTTCC -s simCow_chr6.simCow.chr6 87534 47 + 602619 CTGAACCCTCGAAAATACCAAATTCGCAGCCTTAAATGAGCTGTTCA -s simDog_chr6.simDog.chr6 188363 34 + 593897 CTTAACCC-------------ATTTGCACCCTTGAATCAACTGTTCA -s simHuman_chr6.simHuman.chr6 81117 47 + 601863 CTTAACCCTGGAAGACACCAACTTTGCAGCCTTGAATTAGTTGTACA -s simRat_chr6.simRat.chr6 78204 47 + 647215 CCTAACTCTGGAAAACGTTGAATAAGCACCCTTGAATCAGTTTTTCC - -a -s simMouse_chr6.simMouse.chr6 85861 94 + 636262 TGAAATGGGGTATCAAAAATCTTAACTCTGGAAGACATAGAATCTGTATTCTTGAGTGAGCTTTTCATTTTTACAAGAAGGTAGGTGTTCCTTG -s Anc0.Anc0refChr4 28789 25 - 45765 TTA--------------------------------------------------------------------TACAAGAAGGCAGTCTTTCCGT- -s Anc1.Anc1refChr2 60319 25 + 144309 TTA--------------------------------------------------------------------TACAAGAAGGCAGTCTTTCCGT- -s Anc2.Anc2refChr7 29015 25 + 32194 TTA--------------------------------------------------------------------TACAAGAAGGCAGTCTTTCTGT- -s mr.mrrefChr0 81206 85 + 130230 TGAAATGGGGTATCAAAAATCTTAACTCTGGAAGACATAGAATCTGTATTCTTGAGTGAGCTT--------TACAAGAAGGTAGGTGTTCCTT- -s simCow_chr6.simCow.chr6 87582 25 + 602619 TTA--------------------------------------------------------------------TGCAAGAAGGCAGTCTTTATGT- -s simDog_chr6.simDog.chr6 188398 24 + 593897 TTA--------------------------------------------------------------------TACAAGAAGGC-GTCTTTCTTT- -s simHuman_chr6.simHuman.chr6 81164 25 + 601863 TTA--------------------------------------------------------------------TACAAGACGGCAGTCTTTCCGT- -s simRat_chr6.simRat.chr6 78251 63 + 647215 TGAAAGGGGGTATCAAAAATCTTAGCTCTGGAAAACATAGAATCTGTATTCTTGAATCAGCTT------------------------------- - -a -s simMouse_chr6.simMouse.chr6 85955 10 + 636262 TTCTAGTATC -s Anc0.Anc0refChr4 28814 10 - 45765 TTCTTGAATC -s Anc1.Anc1refChr2 60344 10 + 144309 TTCTTGAATC -s Anc2.Anc2refChr7 29041 10 + 32194 TTCTTGAGTG -s mr.mrrefChr0 81291 10 + 130230 TTCTAGTATC -s simCow_chr6.simCow.chr6 87608 8 + 602619 ATCTT--CTG -s simDog_chr6.simDog.chr6 188423 10 + 593897 TTCTTGAGTG -s simHuman_chr6.simHuman.chr6 81189 10 + 601863 TCCTTGGATC - -a -s simMouse_chr6.simMouse.chr6 85965 19 + 636262 AGATGGAAAGAGTGAACTC -s Anc0.Anc0refChr4 28835 19 - 45765 AGGCTGAAAGAGTGTACTA -s Anc1.Anc1refChr2 60365 19 + 144309 AGGCTGAAAGAGTGTACTA -s Anc2.Anc2refChr7 29062 19 + 32194 AGGCTGAAAGAGTGTACTA -s mr.mrrefChr0 81301 19 + 130230 AGATGGAAAGAGTGAACTC -s simCow_chr6.simCow.chr6 87627 19 + 602619 AGGCTAAGAGAGTTTACTG -s simDog_chr6.simDog.chr6 188444 19 + 593897 AGGTTGAAAGAGTGTAATA -s simHuman_chr6.simHuman.chr6 81210 19 + 601863 AGGCTGAAAGAGTGTACTA - -a -s simMouse_chr6.simMouse.chr6 85984 11 + 636262 ACATGTGAAAG -s Anc0.Anc0refChr4 28854 11 - 45765 ACATGGGATAT -s Anc1.Anc1refChr2 60384 11 + 144309 ACATGGGATAT -s Anc2.Anc2refChr7 29081 11 + 32194 ACATGGGATAT -s mr.mrrefChr0 81320 11 + 130230 ACATGTGAAAG -s simCow_chr6.simCow.chr6 87646 11 + 602619 GCATGGGATAG -s simDog_chr6.simDog.chr6 188466 11 + 593897 ACATGGGATAT -s simHuman_chr6.simHuman.chr6 81229 11 + 601863 ATATGGGATAT - -a -s simMouse_chr6.simMouse.chr6 85995 67 + 636262 TGCAGATGGGATTGTTGATGGAATGTTTAGATCCCCAATATTTGTCCCACCTCAGTCACCTACAAAA -s Anc0.Anc0refChr4 28865 67 - 45765 TGCATGTGGAAATGCTAATAGAATGACTAGTTCCCCAATATGTGTCCCACCTCAGTTTCCTCTATAA -s Anc1.Anc1refChr2 60395 67 + 144309 TGCATGTGGAAATGCTAATAGAATGACTAGTTCCCCAATATGTGTCCCACCTCAGTTTCCTCTATAA -s Anc2.Anc2refChr7 29093 67 + 32194 TGCATGTGGAAATGCCAATAGAATGACTAGTTCCCCAATATGTATTCCACCATGGTTTCCTCTATAA -s mr.mrrefChr0 81331 67 + 130230 TGCAGATGGGATTGTTGATGGAATGTTTAGATCCCCAATATTTGTCCCACCTCAGTCACCTACAAAA -s simCow_chr6.simCow.chr6 87658 67 + 602619 TGCATGTGAAAATTCCAATAGAATGATCAGTTCCCCAATATGTATTCCACCATGGTTTCCTCTAGAA -s simDog_chr6.simDog.chr6 188478 41 + 593897 TGCATGTGGAAATGCCAATATGATGACTAGCTC--------------------------CTCCATAA -s simHuman_chr6.simHuman.chr6 81240 67 + 601863 AGCATGTGGAAATGCTAATAGAATGACAAGTTCGTCAATACCTGTCCCACCTCAGCTGCCTCTATAA - -a -s simMouse_chr6.simMouse.chr6 86062 9 + 636262 TGTGATGCT -s Anc0.Anc0refChr4 28932 9 - 45765 CATTATGCT -s Anc1.Anc1refChr2 60462 9 + 144309 CATTATGCT -s Anc2.Anc2refChr7 29160 9 + 32194 CATTATACT -s mr.mrrefChr0 81398 9 + 130230 TGTGATGCT -s simCow_chr6.simCow.chr6 87726 9 + 602619 CATTACACT -s simDog_chr6.simDog.chr6 188519 9 + 593897 CATTATACT -s simHuman_chr6.simHuman.chr6 81307 9 + 601863 CATTGTGCT - -a -s simMouse_chr6.simMouse.chr6 86071 19 + 636262 ACTGGGCCTGATCGAGAAG -s Anc0.Anc0refChr4 28941 19 - 45765 ACTGGACTTGATGGAGCAA -s Anc1.Anc1refChr2 60471 19 + 144309 ACTGGACTTGATGGAGCAA -s Anc2.Anc2refChr7 29169 19 + 32194 ACTGGACTTGATGGAGCAA -s mr.mrrefChr0 81407 19 + 130230 ACTGGGCCTGATCGAGAAG -s simCow_chr6.simCow.chr6 87737 19 + 602619 ACTGTGCTTGATGGAACAA -s simDog_chr6.simDog.chr6 188528 19 + 593897 ACTGGACTTGATGGAGCAA -s simHuman_chr6.simHuman.chr6 81316 19 + 601863 ACTGGACTTGATGGTGTAA -s simRat_chr6.simRat.chr6 78314 1 + 647215 ------------------G - -a -s simMouse_chr6.simMouse.chr6 86090 11 + 636262 GGAGTTGTGAA -s Anc0.Anc0refChr4 28960 11 - 45765 GGAGCAATAAA -s Anc1.Anc1refChr2 60490 11 + 144309 GGAGCAATAAA -s Anc2.Anc2refChr7 29188 11 + 32194 GAAGCAATAAA -s mr.mrrefChr0 81426 11 + 130230 GGAGTTATGAA -s simCow_chr6.simCow.chr6 87763 10 + 602619 GAAGCAAGGA- -s simDog_chr6.simDog.chr6 188547 11 + 593897 GAAGTGATAAA -s simHuman_chr6.simHuman.chr6 81335 11 + 601863 GGAGCAATAAA -s simRat_chr6.simRat.chr6 78315 11 + 647215 GGAGTCATGAT - -a -s simMouse_chr6.simMouse.chr6 86101 38 + 636262 GTGTCCTTTGCCCCAATCCACCACCACACCCGGCCTTG -s Anc0.Anc0refChr4 28972 31 - 45765 CTTTTCTTTCCTCCAAT---TCA----AAACTGATTTC -s Anc1.Anc1refChr2 60502 31 + 144309 CTTTTCTTTCCTCCAAT---TCA----AAACTGATTTC -s Anc2.Anc2refChr7 29200 31 + 32194 CTTTTCTTTCCTCCAAT---TCA----AAACTGATTTC -s mr.mrrefChr0 81437 35 + 130230 GTGTCCTTTGCCCCAAT---CCACTACACCCGGCCTTG -s simCow_chr6.simCow.chr6 87773 31 + 602619 CTTTTCTATCCTCCAAG---TCA----AAACTGATTTC -s simDog_chr6.simDog.chr6 188559 31 + 593897 CTTTTCCTTCCTTCAAT---TCA----AAACTGATTTC -s simHuman_chr6.simHuman.chr6 81347 17 + 601863 CTTTTCTTTTTTCTCTT--------------------- -s simRat_chr6.simRat.chr6 78326 35 + 647215 GCATCCTTTGTCCCAAT---CCACTACACCTGGCCTCA - -a -s simMouse_chr6.simMouse.chr6 86139 5 + 636262 ATATG -s Anc0.Anc0refChr4 29003 5 - 45765 ACATG -s Anc1.Anc1refChr2 60533 5 + 144309 ACATG -s Anc2.Anc2refChr7 29231 5 + 32194 ACATG -s mr.mrrefChr0 81472 5 + 130230 ATATG -s simCow_chr6.simCow.chr6 87817 5 + 602619 ATATA -s simDog_chr6.simDog.chr6 188590 5 + 593897 ACATG -s simRat_chr6.simRat.chr6 78361 5 + 647215 ATATG - -a -s simMouse_chr6.simMouse.chr6 86144 15 + 636262 TGTCTGCAACCTGTA -s Anc0.Anc0refChr4 29008 15 - 45765 TGCCTTCAAACTGCA -s Anc1.Anc1refChr2 60538 15 + 144309 TGCCTTCAAACTGCA -s Anc2.Anc2refChr7 29238 15 + 32194 TGCCTTCAAACTGCA -s mr.mrrefChr0 81477 15 + 130230 TGTCTGCAACCTGTA -s simCow_chr6.simCow.chr6 87824 15 + 602619 TGTCAGCAAATTTGA -s simDog_chr6.simDog.chr6 188597 15 + 593897 TGCCTTCAAACTGCA -s simRat_chr6.simRat.chr6 78366 15 + 647215 TGTCTGCGACCTCTA - -a -s simMouse_chr6.simMouse.chr6 86159 18 + 636262 GGATGTACCCTGACCTGT -s Anc0.Anc0refChr4 29023 16 - 45765 GGATGTA--CTTACCTGT -s Anc1.Anc1refChr2 60553 18 + 144309 GGATGTACCCTTACCTGT -s Anc2.Anc2refChr7 29254 16 + 32194 GGATGCA--CTTACCTGT -s mr.mrrefChr0 81492 18 + 130230 GGATGTACCCTGACCTGT -s simCow_chr6.simCow.chr6 87840 9 + 602619 AGATCTA---------GT -s simDog_chr6.simDog.chr6 188613 16 + 593897 GGATGCA--CTTACCTGT -s simHuman_chr6.simHuman.chr6 81364 17 + 601863 -GACGTACCCTCACCTGT -s simRat_chr6.simRat.chr6 78381 18 + 647215 GGATGTACCCTGACCTGT - -a -s simMouse_chr6.simMouse.chr6 86177 95 + 636262 TAGATTTTCTTTATATTTTTTATGGTTAATGACTGGCATGTTCTGTACATTGATTGGGAGATTAATTGATTAGTTAACTAACTACTTTAGTTAGT -s Anc0.Anc0refChr4 29040 88 - 45765 TGGATGTTT-------TTTTTATAGTTAATAACTGGAATGTTCTGCATATTGATTGGTAGATTAATTGATTAGTTAACTGACTACTTTGCCTAGC -s Anc1.Anc1refChr2 60572 88 + 144309 TGGATGTTT-------TTTTTATAGTTAATAACTGGAATGTTCTGCATATTGATTGGTAGATTAATTGATTAGTTAACTGACTACTTTGCCTAGC -s Anc2.Anc2refChr7 29271 88 + 32194 TGGATGTTT-------TTTTTATAGTTAATAACTGGAATGTACTGCATATTGATTGGTAGATTAATTGATTAGTTAACTGACAACTTTGCCTAGC -s mr.mrrefChr0 81510 88 + 130230 TGGATTTTC-------TTTTTATAGTTAATGACTGGCATGTTCTGTACATTGATTGGGAGATTAATTGATTAGTTAACTGACTACTTTAGTTAGT -s simCow_chr6.simCow.chr6 87850 88 + 602619 TGTATGCTT-------TTTTTATAGTTAGAAACTGAAATGTCCTGCATAGCGATTGGTAGATTAATTGGATAGTTAACTGACAACGTTACTTAGA -s simDog_chr6.simDog.chr6 188631 87 + 593897 TGGATGTTT-------TTTTTGT-GCTAATGACTTGACTGTACTGTATGTTGTTTGGTAGATGAACTGATTAGTTAACTGACAACTTTGCCTAGC -s simHuman_chr6.simHuman.chr6 81382 88 + 601863 TGGATGTTT-------TTCTTATAGTTAATAACTGGAATGTTATTCTTATGGATTGGTTGATTAGTCGATCAGTTAACTGGCTACTATGCCTAGC -s simRat_chr6.simRat.chr6 78399 88 + 647215 TGCATTTTC-------TTTTTATAGTTAATGACCGGCATGTTCTGTACGTTGATCTGGAGATTAATTGATTAGTTAACTGACTACTTTAGTTGGT - -a -s simMouse_chr6.simMouse.chr6 86272 163 + 636262 GTTCTTTGTAGCTCCTCACTCACATGTCCCGGGGTTAGGACCATGCTGTCGACGGTTTCCATAGGAATTGTACTACCTCCCAATTTCACTATTGCTCTAAACTCAAAAATGCTTACGGAGCGGTCCCATATGATACTGTGCTTCCTGGCTTTCATCTAGGCGT -s Anc0.Anc0refChr4 29128 14 - 45765 AT-----------------------------------------------------------------------------------------------------------------------------------------------------TCATCTAGCCCT -s Anc1.Anc1refChr2 60660 14 + 144309 AT-----------------------------------------------------------------------------------------------------------------------------------------------------TCATCTAGCCCT -s Anc2.Anc2refChr7 29359 14 + 32194 AT-----------------------------------------------------------------------------------------------------------------------------------------------------TCATCTAGCCCT -s mr.mrrefChr0 81598 63 + 130230 GTTCTTTGTAGCTCCTCACTCACATGT---------------------------------------------------------------------------------------------------GATATGATACTGTGCTTCCT-GCTTTCATCTAGGCGT -s simCow_chr6.simCow.chr6 87942 14 + 602619 AT-----------------------------------------------------------------------------------------------------------------------------------------------------TCATCTAACCCT -s simDog_chr6.simDog.chr6 188718 14 + 593897 AT-----------------------------------------------------------------------------------------------------------------------------------------------------TCATCTAGCCTT -s simHuman_chr6.simHuman.chr6 81470 14 + 601863 AT-----------------------------------------------------------------------------------------------------------------------------------------------------TCACTTAGACCT -s simRat_chr6.simRat.chr6 78487 63 + 647215 GTTCTTTATAGTTCCTCACTCACATGT---------------------------------------------------------------------------------------------------GATATGATACTCTGCTTCCT-ACATTCATTTAGGCAT - -a -s simMouse_chr6.simMouse.chr6 86435 20 + 636262 GAGTTTCCTGTTCCATTAGA -s Anc0.Anc0refChr4 29142 11 - 45765 GA-----CTGTCC----ATA -s Anc1.Anc1refChr2 60674 11 + 144309 GA-----CTGTCC----ATA -s Anc2.Anc2refChr7 29373 11 + 32194 TA-----CTGTCC----ATA -s mr.mrrefChr0 81661 13 + 130230 GAGT---CTGTTC----ATA -s simCow_chr6.simCow.chr6 87960 11 + 602619 AA-----CTGTCT----ATA -s simDog_chr6.simDog.chr6 188732 11 + 593897 TA-----ATGTTC----ATA -s simHuman_chr6.simHuman.chr6 81484 11 + 601863 GA-----CCGTCC----ATA -s simRat_chr6.simRat.chr6 78550 13 + 647215 GAGT---CAGGTC----ATA - -a -s simMouse_chr6.simMouse.chr6 86455 15 + 636262 GAAGATGGGGAAGAT -s Anc0.Anc0refChr4 29165 1 - 45765 --------------C -s Anc1.Anc1refChr2 60697 15 + 144309 GAAGATATGGAAGGC -s Anc2.Anc2refChr7 29396 1 + 32194 --------------C -s mr.mrrefChr0 81674 15 + 130230 GGAGATGGGGAAGAT -s simCow_chr6.simCow.chr6 87983 1 + 602619 --------------T -s simDog_chr6.simDog.chr6 188755 1 + 593897 --------------C -s simHuman_chr6.simHuman.chr6 81508 15 + 601863 GAAGATATGGAAGGC -s simRat_chr6.simRat.chr6 78563 9 + 647215 GGAGAT------GAT - -a -s simMouse_chr6.simMouse.chr6 86470 57 + 636262 GGGAAGGCTGGCAGCATTGCGCCATAGTATGTCACTGCTGTGGTCCTAAACTAAGTT -s Anc0.Anc0refChr4 29173 57 - 45765 TGGAAGGCTGGTGGTATATTGCCGTAGTACATCACTGCTGTGGTACTGTACTTAGCT -s Anc1.Anc1refChr2 60719 57 + 144309 TGGAAGGCTGGTGGTATATTGCCGTAGTACATCACTGCTGTGGTACTGTACTTAGCT -s Anc2.Anc2refChr7 29404 57 + 32194 TGGAAGGCTGGTGGTGTATTGCAGTAGTACATCACTGCTGTGGCAATGTGCTTTGCT -s mr.mrrefChr0 81689 57 + 130230 GGGAAGGCTGGCAGTATTTCGCCATAGTATGTCACTGCTGTGGTCCTAAACTAAGTT -s simCow_chr6.simCow.chr6 87991 57 + 602619 TGGATGGCTGGTGGTGTATTGCTGCAGTACATCACTGCTGTGGCGATGTGCTTTTCT -s simDog_chr6.simDog.chr6 188763 38 + 593897 TGGAAGGCTGG----------CAGTAGTACATTACTGCTGTGGCA---------GCT -s simHuman_chr6.simHuman.chr6 81530 57 + 601863 TGGAAGGCTGGTGGTATATTGCCGTAATCCACCACTGACATGGTACTGCACTTAGCC -s simRat_chr6.simRat.chr6 78572 53 + 647215 GGGAAGGCTAGCAGTATCTCGCCATAGTATGATGTTGCTGCTGCT----ACTGAGTT - -a -s simMouse_chr6.simMouse.chr6 86527 8 + 636262 TTCACTTA -s Anc0.Anc0refChr4 29230 8 - 45765 TTCGCTTC -s Anc1.Anc1refChr2 60776 8 + 144309 TTCGCTTC -s Anc2.Anc2refChr7 29461 8 + 32194 TTCGCGTC -s mr.mrrefChr0 81746 8 + 130230 TTCACTTA -s simCow_chr6.simCow.chr6 88048 8 + 602619 TTTGCCTC -s simDog_chr6.simDog.chr6 188801 8 + 593897 GCCACGTT -s simHuman_chr6.simHuman.chr6 81587 8 + 601863 TTCGCTTC -s simRat_chr6.simRat.chr6 78626 8 + 647215 TCCACTTA - -a -s simMouse_chr6.simMouse.chr6 86535 37 + 636262 TGCTGCTGCCACCCACCCTATTGCTTGCTTTTTTTTT -s Anc0.Anc0refChr4 29239 37 - 45765 TGCTGCTGATACCTACTTAATTGCTTGCTTTTTTTTT -s Anc1.Anc1refChr2 60785 37 + 144309 TGCTGCTGATACCTACTTAATTGCTTGCTTTTTTTTT -s Anc2.Anc2refChr7 29470 37 + 32194 TGCTGCTGATACCTACTTAATTGCTCGCTTTTTTTTT -s mr.mrrefChr0 81754 37 + 130230 TGCTGCTGCCACCCACTCAATTGCTTGCTTTTTTTTT -s simCow_chr6.simCow.chr6 88057 37 + 602619 GGCTCCTTACACATACTTAATTGCTTGTTTGTTTTTT -s simDog_chr6.simDog.chr6 188810 37 + 593897 TACTGCTGATACCTACTTAATTGCTCGCTTTTTTTTT -s simHuman_chr6.simHuman.chr6 81596 33 + 601863 TGCTGCTGATACCTACTTAA----TTGCCTTTTTCTA -s simRat_chr6.simRat.chr6 78634 37 + 647215 TGCTGGTGCCACCCACTCAATTGCTTCCTCTTTTTTT - -a -s simMouse_chr6.simMouse.chr6 86572 26 + 636262 ATAGTTGTATGACCCCGGGCCATATG -s Anc0.Anc0refChr4 29276 10 - 45765 GTAATAATAT---------------- -s Anc1.Anc1refChr2 60822 10 + 144309 GTAATAATAT---------------- -s Anc2.Anc2refChr7 29508 10 + 32194 GTAATAATAT---------------- -s mr.mrrefChr0 81791 24 + 130230 ATAGTTGTAT--CCCCGGGCCATATG -s simCow_chr6.simCow.chr6 88095 10 + 602619 GTAATAATAT---------------- -s simDog_chr6.simDog.chr6 188848 10 + 593897 GTAATAATGT---------------- -s simHuman_chr6.simHuman.chr6 81629 10 + 601863 GTAATAATAT---------------- -s simRat_chr6.simRat.chr6 78671 24 + 647215 ATGGTTGTAT--CCCTGGGCCAGATG - -a -s simMouse_chr6.simMouse.chr6 86598 131 + 636262 GATTCATCCATCCTCTTCCTGATACCCCAGAAGTCGCACCAACTCCCAATGTAGCTGTCATAGTTGGTAGGTTACTCAAAGTATACGGCAGCCACATACTCCATACAGATGAGTACTAGGCCCACAAGTCC -s mr.mrrefChr0 81815 58 + 130230 GATTCATCCATCCTCTTCCTGATACCCCAGAA-------------------------------------------------------------------------CAGATGAGTACTAGGCCCACAAGTCC -s simRat_chr6.simRat.chr6 78706 58 + 647215 GATTTGTTGGTCCCCCTTCTGGCACCCCATGA-------------------------------------------------------------------------CAGATGAGTACTATGCCCATGAGTCC - -a -s simMouse_chr6.simMouse.chr6 86729 210 + 636262 AGTTCAATCTTATTCACAGCATCTGGGTGACGCTCCCAGTTTTTGTCAGATGATCTCCTAGGTTGTAGGAATGGGctcttcaaccacttggttaacaaaggtgcacatcaggatccccaaatccattagggtgtcagcaaataatcatggatgcaagcacaacttgaatggtcacagcttcaaaactttccatacacaaagtatgtcttg -s mr.mrrefChr0 81873 186 + 130230 AGTTCAATCTTATTCACAGCATctgggtgacgctc--------------------tcctaggttgt-ggaatgggctcttcaaccacttggttaacaaaggtgcacatcaggatccccaaatccattagggtgtcagcaaataatcatg-atgcaagcacaacttgaatggtcacagcttcaaaact--ccatacacaaagtatgtcttg -s simRat_chr6.simRat.chr6 78765 186 + 647215 AGCCCATTCTTATTCACAGCATttccgtgacgcct--------------------ttctaggttgt-tgaatgatcacttcaactatgtggttaacaaaggtgcacatcaggatctccaaacccattaaggtgtcagcaaataattatg-atgtaattacaatttgaatggtctcagcttgaaaact--ccatacacaaagtatgtcttg - -a -s simMouse_chr6.simMouse.chr6 86939 67 + 636262 ttggtcctagcttctggactaggactcttatgttctgagaacttggcgaatagcaaatagttctaga -s mr.mrrefChr0 82059 67 + 130230 ttggtcctagcttctggactaggactcttatgttctgagaacttggcgaatagcaaatagttctaga -s simRat_chr6.simRat.chr6 78952 67 + 647215 ttggtcatagtttcaggagtaggactcttatgttctgagtactgggggaatagcaaatagttctaga - -a -s simMouse_chr6.simMouse.chr6 87006 19 + 636262 cggtcgggtacctgagcac -s mr.mrrefChr0 82126 19 + 130230 cggtcgggtacctgagcac -s simRat_chr6.simRat.chr6 79021 19 + 647215 tgttctagaatttgcacac - -a -s simMouse_chr6.simMouse.chr6 87025 24 + 636262 aaccaagcaccttaaaactattta -s Anc0.Anc0refChr4 29286 6 - 45765 ------------------TATTCA -s Anc1.Anc1refChr2 60832 6 + 144309 ------------------TATTCA -s Anc2.Anc2refChr7 29518 6 + 32194 ------------------TATTCA -s mr.mrrefChr0 82145 22 + 130230 aaccaagcacct--aaactattta -s simCow_chr6.simCow.chr6 88105 6 + 602619 ------------------TATACA -s simDog_chr6.simDog.chr6 188858 6 + 593897 ------------------TATTCA -s simHuman_chr6.simHuman.chr6 81639 6 + 601863 ------------------GATTCA -s simRat_chr6.simRat.chr6 79041 22 + 647215 aactaagcacCT--AACATGTTCA - -a -s simMouse_chr6.simMouse.chr6 87049 19 + 636262 CTGTGCACTATTAGTTTTT -s Anc0.Anc0refChr4 29292 14 - 45765 TTGTGCATTGCTAA----- -s Anc1.Anc1refChr2 60838 14 + 144309 TTGTGCATTGCTAA----- -s Anc2.Anc2refChr7 29524 14 + 32194 TTGTGCATTGCTAA----- -s mr.mrrefChr0 82167 14 + 130230 CTGTGCACTATTAG----- -s simCow_chr6.simCow.chr6 88111 14 + 602619 TTATGCATTGCTAA----- -s simDog_chr6.simDog.chr6 188864 14 + 593897 TTGTGCATTGCTAA----- -s simHuman_chr6.simHuman.chr6 81645 14 + 601863 TAGTGCATTGCTAA----- -s simRat_chr6.simRat.chr6 79066 14 + 647215 CAGAGTATAATTAG----- - -a -s simMouse_chr6.simMouse.chr6 87068 22 + 636262 GGAGTTAATTGCACTAGTTATA -s Anc0.Anc0refChr4 29308 19 - 45765 GCCATTAATT---GCACTAATA -s Anc1.Anc1refChr2 60854 19 + 144309 GCCATTAATT---GCACTAATA -s Anc2.Anc2refChr7 29540 19 + 32194 GCCATTAATT---GCACTAATA -s mr.mrrefChr0 82181 19 + 130230 GGAGTTAATT---CTAGTTATA -s simCow_chr6.simCow.chr6 88127 19 + 602619 GCCTTTACGT---GCACTAATA -s simDog_chr6.simDog.chr6 188880 19 + 593897 GCCATTAATT---GCACCGATA -s simHuman_chr6.simHuman.chr6 81661 19 + 601863 GCCATTAATT---GCACTAATA -s simRat_chr6.simRat.chr6 79080 19 + 647215 GGCAACAATT---CCAAGTACA - -a -s simMouse_chr6.simMouse.chr6 87090 46 + 636262 CTTTGTCTGGACTGAACATGTTAACATCATAATTGTTGACCGGTAT -s Anc0.Anc0refChr4 29330 39 - 45765 CCTGGT-------TATAATGTTAACATTATGATTGCATGCTTGTTC -s Anc1.Anc1refChr2 60876 39 + 144309 CCTGGT-------TATAATGTTAACATTATGATTGCATGCTTGTTC -s Anc2.Anc2refChr7 29562 39 + 32194 CCTGGT-------TATAATATTAACATTATGATTGCATGCTTGTTC -s mr.mrrefChr0 82200 39 + 130230 CTTTGT-------GAACATGTTAACATCATAATTGTTGACCGGTAT -s simCow_chr6.simCow.chr6 88149 39 + 602619 CATGGT-------TATAATATCTACATTATGATTACATGCTTGTCT -s simDog_chr6.simDog.chr6 188902 39 + 593897 CCTGGC-------TATAATATTAACATTATCATTGCCTGCTTGTTC -s simHuman_chr6.simHuman.chr6 81683 37 + 601863 CCTGGT-------TATAATGTTAACATTATGTTTGCATGCTTGT-- -s simRat_chr6.simRat.chr6 79099 39 + 647215 CCATAT-------AAAGTTCTAAATATAGTGATTGTTGACTGGTAT - -a -s simMouse_chr6.simMouse.chr6 87136 106 + 636262 TCTAATGTGTGACAGTCAAACAGCTTGTATTTGGGACGGGTGCAACACTTACCGTGATGAAAGTACATAACAAAAGGCTACTGACTCACATACCCTAAAACTGTTC -s Anc0.Anc0refChr4 29369 64 - 45765 TCTTAAGTGTGACCATCAAGCAGCTATC-------------------------------AAAGTACGTATCCAGAAGTTCATAATACTCATACTC----------- -s Anc1.Anc1refChr2 60915 64 + 144309 TCTTAAGTGTGACCATCAAGCAGCTATC-------------------------------AAAGTACGTATCCAGAAGTTCATAATACTCATACTC----------- -s Anc2.Anc2refChr7 29601 64 + 32194 TCTTAAGTGTGACCATAAAGCCACTATC-------------------------------AAAGTACGTATCCAGAAGTTCATAATACTCATGCTC----------- -s mr.mrrefChr0 82239 64 + 130230 TCTAATGTGTGACAGTCAAACAGCTTGT-------------------------------AAAGTACATAACAAAAGGTTAATGATTCACATACCC----------- -s simCow_chr6.simCow.chr6 88188 57 + 602619 TCTAAAGGGTGACAGTTAGGTTCTTTTC-------------------------------AAAGTACATATCTGGAAATACACAACA-------TC----------- -s simDog_chr6.simDog.chr6 188946 64 + 593897 TCTTAAGTGTGACCATAAAGCCACTAGC-------------------------------AAAGTACGTATCCAGAAGTTCATAATACTCATGCTC----------- -s simHuman_chr6.simHuman.chr6 81720 49 + 601863 ---------------TCAAGCAGCCCTC-------------------------------AAAGTAAGTATCCTGAAGTTCATAATGCGCATACTC----------- -s simRat_chr6.simRat.chr6 79138 64 + 647215 TCTAACGTCTGACAATCAAACAGCTTCT-------------------------------AAAGTACATAACAAAACGTTAATTATTCACATACCC----------- - -a -s simMouse_chr6.simMouse.chr6 87242 2 + 636262 TG -s mr.mrrefChr0 47518 2 - 130230 TG -s simRat_chr6.simRat.chr6 567604 2 - 647215 TG - -a -s simMouse_chr6.simMouse.chr6 87244 37 + 636262 AACCGGTGTTAATATTTCCTTATGATCAGGCTGGTAA -s Anc0.Anc0refChr4 15933 1 + 45765 ------------------------------------A -s Anc1.Anc1refChr2 82929 1 - 144309 ------------------------------------A -s Anc2.Anc2refChr7 2106 1 - 32194 ------------------------------------A -s mr.mrrefChr0 47520 37 - 130230 AACCGGTGTTAATATTTCCTTATGTTCAGGCTGGTAA -s simCow_chr6.simCow.chr6 513947 1 - 602619 ------------------------------------A -s simDog_chr6.simDog.chr6 404458 1 - 593897 ------------------------------------G -s simHuman_chr6.simHuman.chr6 519676 1 - 601863 ------------------------------------A -s simRat_chr6.simRat.chr6 567607 37 - 647215 AACCTGTGTTAATGTTTCCTTATGTTCAGGCTGGTAA - -a -s simMouse_chr6.simMouse.chr6 87281 27 + 636262 ATGACAAACACCCACCTGAGGTTTTTT -s Anc0.Anc0refChr4 15934 27 + 45765 ATGATAAAAACCTACCTGAGGTTTTTC -s Anc1.Anc1refChr2 82930 27 - 144309 ATGATAAAAACCTACCTGAGGTTTTTC -s Anc2.Anc2refChr7 2107 27 - 32194 ATGATAAAAACCTATCTGAGGTTTTTC -s mr.mrrefChr0 47557 27 - 130230 ATGACAAACACCTACCTGAGGTTTTTT -s simCow_chr6.simCow.chr6 513948 27 - 602619 ATAGGGAAAACCTATTTGAGGTCTCTG -s simDog_chr6.simDog.chr6 404459 27 - 593897 ATGATAAAAACCTATCGGAGGTTTTTC -s simHuman_chr6.simHuman.chr6 519677 27 - 601863 ATGATAAAAACCTACCTGAGGTTTTTC -s simRat_chr6.simRat.chr6 567646 27 - 647215 ATGACAGATACCTACCTGAGGTTTCTT - -a -s simMouse_chr6.simMouse.chr6 87308 1 + 636262 C -s Anc0.Anc0refChr4 15980 1 + 45765 C -s Anc1.Anc1refChr2 82976 1 - 144309 C -s Anc2.Anc2refChr7 2153 1 - 32194 T -s mr.mrrefChr0 47603 1 - 130230 C -s simCow_chr6.simCow.chr6 513994 1 - 602619 G -s simDog_chr6.simDog.chr6 404503 1 - 593897 T -s simHuman_chr6.simHuman.chr6 519723 1 - 601863 C -s simRat_chr6.simRat.chr6 567692 1 - 647215 C - -a -s simMouse_chr6.simMouse.chr6 87309 34 + 636262 CATGAATAGTTGCCTCACAATGAAGACTATAGTT -s Anc0.Anc0refChr4 15986 34 + 45765 CATGAATGGTGGGCCCATAAAGTGGTCCCTGATT -s Anc1.Anc1refChr2 82982 34 - 144309 CATGAATGGTGGGCCCATAAAGTGGTCCCTGATT -s Anc2.Anc2refChr7 2159 34 - 32194 CATGAATGGTGGGCCCATAAAGTGGTCCCAGATT -s mr.mrrefChr0 47604 34 - 130230 CATGAATAGTTGCCCCACAAAGAAGTCTATGATT -s simCow_chr6.simCow.chr6 514000 34 - 602619 CATGGGTAGTGGGCCCACAAAGTGGTCCAAGAGT -s simDog_chr6.simDog.chr6 404509 34 - 593897 CATGAACGATGGGCCCTTAAAGTAGTCCCAGATT -s simHuman_chr6.simHuman.chr6 519729 34 - 601863 CATGAATGGAGGGACCATAAAGTGGTCCGTGATT -s simRat_chr6.simRat.chr6 567693 34 - 647215 CATGAATAGTTGACCCACAAAGAAGTCTATGATT - -a -s simMouse_chr6.simMouse.chr6 87343 50 + 636262 TGCAGAATATCTATATACTGGAGCACTCTACATATGCTGCTCACCTGTGA -s Anc0.Anc0refChr4 16025 49 + 45765 TGTAGA-TGCCAATGTATTAGAGCACTCTAGATATGCTGCTCCCAAATGT -s Anc1.Anc1refChr2 83021 50 - 144309 TGTAGAATGCCAATGTATTAGAGCACTCTAGATATGCTGCTCCCAAATGT -s Anc2.Anc2refChr7 2198 49 - 32194 TTTAGA-TGCCAATGTATTAGAGCACTCTAGATATGCTGCTCCCAAATGT -s mr.mrrefChr0 47638 50 - 130230 TGCAGAATATCTATATACTGGAGCACTCTAGATATGCTGCTCACCAGTGA -s simCow_chr6.simCow.chr6 514039 46 - 602619 TATGGA--GCCA--GTATTGTATCACTCTAGACATGCTGCTCCCACATGT -s simDog_chr6.simDog.chr6 404548 49 - 593897 TTTAGA-TGCCAATATGTAAGAGCACTCTAAATATGCTGTTCCCAAATGT -s simHuman_chr6.simHuman.chr6 519768 50 - 601863 TGTAGGATGCCAATGTATTAGAACACTCTTGATATGCTGCTTCCAAATGT -s simRat_chr6.simRat.chr6 567727 50 - 647215 TGCAGAATATCTATATACTGGAGCACTCTGGATATGCTGCTCACCAGTGC - -a -s simMouse_chr6.simMouse.chr6 87393 28 + 636262 ATCCAGATAATGCAAGCTGCTCTCTTTC -s Anc0.Anc0refChr4 16074 28 + 45765 ATCCAGTTGATCCAAGCATCTCTTCTTC -s Anc1.Anc1refChr2 83071 28 - 144309 ATCCAGTTGATCCAAGCATCTCTTCTTC -s Anc2.Anc2refChr7 2252 28 - 32194 ATCCATTTGATCTGAGCATCTTTTCTGC -s mr.mrrefChr0 47688 28 - 130230 ATCCAGTTAATGCAAGCAGCTCTTTTTC -s simCow_chr6.simCow.chr6 514090 25 - 602619 ATCCAATTTAT---AGCATCTGTTCTCC -s simDog_chr6.simDog.chr6 404602 28 - 593897 ATCCATTTGATCTGAGCGTATTTCCTGC -s simHuman_chr6.simHuman.chr6 519818 28 - 601863 AGCCAGTTGATTCAAGCATCTCTTCTTC -s simRat_chr6.simRat.chr6 567777 28 - 647215 ATCCAGTTAATGCAAGCAGCTCTTTTTT - -a -s simMouse_chr6.simMouse.chr6 87421 5 + 636262 TCCTG -s Anc0.Anc0refChr4 16103 5 + 45765 GGCTG -s Anc1.Anc1refChr2 83100 5 - 144309 GGCTG -s Anc2.Anc2refChr7 2281 5 - 32194 GGTTG -s mr.mrrefChr0 47716 5 - 130230 TCCTG -s simCow_chr6.simCow.chr6 514119 5 - 602619 GGTTG -s simHuman_chr6.simHuman.chr6 519847 5 - 601863 GGCTG -s simRat_chr6.simRat.chr6 567805 5 - 647215 TCCTG - -a -s simMouse_chr6.simMouse.chr6 87426 26 + 636262 GGTTGGGGGTTCTTGCCTGATGTTTT -s Anc0.Anc0refChr4 16110 26 + 45765 GTTTGGGTGTCCTTGCCTACTGTTTT -s Anc1.Anc1refChr2 83107 26 - 144309 GTTTGGGTGTCCTTGCCTACTGTTTT -s Anc2.Anc2refChr7 2288 26 - 32194 GTCTTAGTGCCCCTGCCTACTGTTTT -s mr.mrrefChr0 47721 26 - 130230 GGTTGGGGGTTCTTGCCTGATGTTTT -s simCow_chr6.simCow.chr6 514126 26 - 602619 GTCTTAGTGCCCCTGCCTACTGTTTC -s simDog_chr6.simDog.chr6 404631 2 - 593897 ------------------------TT -s simHuman_chr6.simHuman.chr6 519854 26 - 601863 GTTTGGGTGTCCTTGGTTACTGTTTT -s simRat_chr6.simRat.chr6 567810 26 - 647215 GGGTGGGGGATCTTACCTGATGTTTT - -a -s simMouse_chr6.simMouse.chr6 87452 9 + 636262 CCTTTGAAG -s Anc0.Anc0refChr4 16136 9 + 45765 CCTTCAAAG -s Anc1.Anc1refChr2 83133 9 - 144309 CCTTCAAAG -s Anc2.Anc2refChr7 2314 9 - 32194 CCTTCAAAG -s mr.mrrefChr0 47747 9 - 130230 CCTTTGAAG -s simCow_chr6.simCow.chr6 514152 9 - 602619 CCTTCAAAG -s simDog_chr6.simDog.chr6 404636 9 - 593897 CCTTCAAAG -s simHuman_chr6.simHuman.chr6 519880 9 - 601863 CCTCCAAAA -s simRat_chr6.simRat.chr6 567836 9 - 647215 CCTTTGAAG - -a -s simMouse_chr6.simMouse.chr6 87461 9 + 636262 ATTGGTATG -s Anc0.Anc0refChr4 16146 8 + 45765 ATTGCCAT- -s Anc1.Anc1refChr2 83143 8 - 144309 ATTGCCAT- -s Anc2.Anc2refChr7 2324 8 - 32194 ATTGCCAT- -s mr.mrrefChr0 47756 8 - 130230 ATTGGTAT- -s simCow_chr6.simCow.chr6 514162 8 - 602619 ACTACCAT- -s simDog_chr6.simDog.chr6 404646 8 - 593897 ATTGCCAT- -s simHuman_chr6.simHuman.chr6 519890 8 - 601863 ATTGCCAT- -s simRat_chr6.simRat.chr6 567845 8 - 647215 ATTGATAT- - -a -s simMouse_chr6.simMouse.chr6 87470 9 + 636262 ATGTACCAT -s Anc0.Anc0refChr4 16155 9 + 45765 CTATACCAT -s Anc1.Anc1refChr2 83152 9 - 144309 CTATACCAT -s Anc2.Anc2refChr7 2333 9 - 32194 CTATACCAT -s mr.mrrefChr0 47764 9 - 130230 CTGTACCAT -s simCow_chr6.simCow.chr6 514173 9 - 602619 ATATATCAT -s simDog_chr6.simDog.chr6 404655 9 - 593897 CTATACCAT -s simHuman_chr6.simHuman.chr6 519899 9 - 601863 CCATACCAT -s simRat_chr6.simRat.chr6 567853 9 - 647215 CTGTATCAT - -a -s simMouse_chr6.simMouse.chr6 87479 29 + 636262 TGGTCATAGGTCATTGCTATTGACCTGAC -s Anc0.Anc0refChr4 16164 22 + 45765 TGATTA-------TTCTTATTAAATCTAC -s Anc1.Anc1refChr2 83161 22 - 144309 TGATTA-------TTCTTATTAAATCTAC -s Anc2.Anc2refChr7 2342 22 - 32194 TGATTA-------TTCTTATTAAATCTAC -s mr.mrrefChr0 47773 29 - 130230 TGGTCATAGGTCATTGTTATTGACTTTAC -s simCow_chr6.simCow.chr6 514183 22 - 602619 CAATTA-------TTCTTACTAAATTTAC -s simDog_chr6.simDog.chr6 404701 22 - 593897 TGATTA-------TTCTCATTAACTCTAC -s simHuman_chr6.simHuman.chr6 519908 22 - 601863 TGACTC-------TTCTTATTAAATCTCC -s simRat_chr6.simRat.chr6 567862 29 - 647215 CAGTCATAGGTCATTGTTATTGAGTTTAC - -a -s simMouse_chr6.simMouse.chr6 87508 19 + 636262 CCAGAACTATACAGCTAGG -s Anc0.Anc0refChr4 16186 19 + 45765 CCAGAAGTATACAGCTAGG -s Anc1.Anc1refChr2 83183 19 - 144309 CCAGAAGTATACAGCTAGG -s Anc2.Anc2refChr7 2366 19 - 32194 CCAGAAGTATACAGCTAGG -s mr.mrrefChr0 47802 19 - 130230 CCAGAACTATACAGCTAGG -s simCow_chr6.simCow.chr6 514207 19 - 602619 CCAGAAGTGTTCAGCTAGG -s simDog_chr6.simDog.chr6 404725 18 - 593897 CCAG-AGTATACAGCTAGG -s simHuman_chr6.simHuman.chr6 519930 19 - 601863 CCAGAAGTATACAGCTAGG -s simRat_chr6.simRat.chr6 567891 19 - 647215 CCAGAACTCTACAGCTGGT - -a -s simMouse_chr6.simMouse.chr6 87527 68 + 636262 CGCATCCCACTATGAGATACCTATAGTGTTCAGAGTGACATGAGGAAAAGTATCATTACCAATTTATG -s Anc0.Anc0refChr4 16205 67 + 45765 CACATCCCACTATAAGATACCTGTAGTGTCCAAAGTGATATTGG-AACAGTATAAATAACAATTTATG -s Anc1.Anc1refChr2 83202 68 - 144309 CACATCCCACTATAAGATACCTGTAGTGTCCAAAGTGATATTGGCAACAGTATAAATAACAATTTATG -s Anc2.Anc2refChr7 2385 67 - 32194 CACATCCCAATATAAGATACCTGTAGTGTCCAAAGTGATATTGG-AACAGTATAAACAACAATTTATG -s mr.mrrefChr0 47821 68 - 130230 CGCATCCCACTATGAGATACCTATAGTGTTCAGAGTGATATGAGGAAAAGTATCATTACCAATTTATG -s simCow_chr6.simCow.chr6 514226 67 - 602619 CACATCCTGATACATGCTACCTGTAGTGTTTAATGTAACATTGG-AACAGTATAAACAACAATCTATG -s simDog_chr6.simDog.chr6 404743 67 - 593897 CACATCCCAATATAAGATACCAGTAGGGTCCTAAGTGATATTGG-AACAGTAGAAACAACAATTTCTG -s simHuman_chr6.simHuman.chr6 519959 68 - 601863 CACATCCCACTATAACATACCTGTAGTGTCCATCGTGATATTGGCAACAGTATAAATAGCAATTTATG -s simRat_chr6.simRat.chr6 567910 68 - 647215 TGCATCCCACTATGAGATACCTATAGTGTTCAGAGTGATATGTGGAATAGTGTTATTACCAATTTCAA - -a -s simMouse_chr6.simMouse.chr6 87595 7 + 636262 TAAGCAA -s Anc0.Anc0refChr4 16294 7 + 45765 TAAGCAA -s Anc1.Anc1refChr2 83292 7 - 144309 TAAGCAA -s Anc2.Anc2refChr7 2474 7 - 32194 TAAGCAA -s mr.mrrefChr0 47889 7 - 130230 TAAGCAA -s simCow_chr6.simCow.chr6 514315 7 - 602619 TAAGCAA -s simDog_chr6.simDog.chr6 404832 7 - 593897 TAAGCAA -s simHuman_chr6.simHuman.chr6 520049 7 - 601863 TAAGTAA -s simRat_chr6.simRat.chr6 567978 7 - 647215 TAAGCAA - -a -s simMouse_chr6.simMouse.chr6 87602 13 + 636262 TAAACATACCCCG -s Anc0.Anc0refChr4 16301 13 + 45765 GAAACATACTCCT -s Anc1.Anc1refChr2 83299 13 - 144309 GAAACATACTCCT -s Anc2.Anc2refChr7 2482 13 - 32194 GAAACAAACTCCT -s mr.mrrefChr0 47896 13 - 130230 TAAACATACTCCT -s simCow_chr6.simCow.chr6 514323 13 - 602619 AGAACAAACCTCT -s simDog_chr6.simDog.chr6 404840 13 - 593897 GAAACAAACTCGT -s simHuman_chr6.simHuman.chr6 520056 13 - 601863 GAAATGTGCTCCT -s simRat_chr6.simRat.chr6 567985 13 - 647215 CAAACATACTCCT - -a -s simMouse_chr6.simMouse.chr6 87615 1 + 636262 T -s Anc0.Anc0refChr4 16314 1 + 45765 T -s Anc1.Anc1refChr2 83312 1 - 144309 T -s Anc2.Anc2refChr7 2495 1 - 32194 T -s mr.mrrefChr0 47909 1 - 130230 T -s simCow_chr6.simCow.chr6 514336 1 - 602619 T -s simDog_chr6.simDog.chr6 404853 1 - 593897 T -s simHuman_chr6.simHuman.chr6 520075 1 - 601863 T -s simRat_chr6.simRat.chr6 567998 1 - 647215 T - -a -s simMouse_chr6.simMouse.chr6 87616 5 + 636262 GGTAC -s Anc0.Anc0refChr4 16315 5 + 45765 GATAC -s Anc1.Anc1refChr2 83313 5 - 144309 GATAC -s Anc2.Anc2refChr7 2512 5 - 32194 GAGAT -s mr.mrrefChr0 47910 5 - 130230 GGTAC -s simCow_chr6.simCow.chr6 514358 5 - 602619 GAGAT -s simDog_chr6.simDog.chr6 404870 5 - 593897 GAGAT -s simHuman_chr6.simHuman.chr6 520076 5 - 601863 GCTAC -s simRat_chr6.simRat.chr6 567999 3 - 647215 GGT-- - -a -s simMouse_chr6.simMouse.chr6 87621 9 + 636262 AGAGCAGGT -s Anc0.Anc0refChr4 16320 9 + 45765 AGACCATCT -s Anc1.Anc1refChr2 83318 9 - 144309 AGACCATCT -s Anc2.Anc2refChr7 2517 9 - 32194 AAACCATCT -s mr.mrrefChr0 47915 9 - 130230 AGAGCAGGT -s simCow_chr6.simCow.chr6 514363 8 - 602619 AT-CCATCT -s simDog_chr6.simDog.chr6 404875 9 - 593897 AAACAACCT -s simHuman_chr6.simHuman.chr6 520082 9 - 601863 AGATCATCT -s simRat_chr6.simRat.chr6 568002 8 - 647215 -GAACAGTT - -a -s simMouse_chr6.simMouse.chr6 87630 120 + 636262 CTCTAGTGCCAGCCTTCATATGGCTTTAACCTGCTACCGGGGCATCCAAGAGTCAAAAAGTAATACTGTAGCCATTCTGCAGGTACATGGGTCACATGTTACTCATAAAGCTATTATAGT -s Anc0.Anc0refChr4 29832 71 - 45765 ------------------------TGTACCC-------ATAGCAGTCAAAAGTCAAAAGCA-----TGTCA----TAC------AT---GGTCATTTGAGACTAATAAGGTTATTATAGT -s Anc1.Anc1refChr2 61380 76 + 144309 ------------------------TGTACCC-------ATAGCAGTCAAAAGTCAAAAGCAGAAGCTGTCA----TAC------AT---GGTCATTTGAGACTAATAAGGTTATTATAGT -s Anc2.Anc2refChr7 30088 71 + 32194 ------------------------TGTACCC-------ATAGCAGTCAAAAGTCAAAAGCA-----TGTCA----TAG------AT---GGGCATTTGAGACTAATAAGGTTATAATAGT -s mr.mrrefChr0 82712 106 + 130230 CTCTAGTGCCAGCCTTCATATGGCTTTAACC-------GGAGCATCCAAGAGTCAAAAAGTAAAACTGTAG----TACGCAGGTAC---GGTCACATGTTACTCATAAAGCTATTATAGT -s simCow_chr6.simCow.chr6 88672 71 + 602619 ------------------------TGTTCCC-------ATAGCAATCAAAGGTGATTATCA-----TGTAG----TAT------AT---GGGCATTTGGGATTAATAGGGTTATAATATT -s simDog_chr6.simDog.chr6 189439 67 + 593897 ------------------------TGTACCC-------ATATCAGAGGAAAGTCAAAAGCA-----TCTCA----TAG------AC---GGGCATTTGAGACTGGAAAGGTC----TAGT -s simHuman_chr6.simHuman.chr6 82187 76 + 601863 ------------------------TCTACAC-------ATAGCAGTCAAAAGTCAAAAGTAGAAGCTGTTA----TAC------AT---GGTCATTTGAGACTAATAAGGTTATTATAGT -s simRat_chr6.simRat.chr6 79619 106 + 647215 CCGTCACGATGGCCTTCATCTGGCTGTAACC-------GAAGCATCCAAGAGTCAAAAAGTAGAACTGTAG----TACACAACCAC---GGTCACATGGTACTCATAAAGCTATTATAGT - -a -s simMouse_chr6.simMouse.chr6 87750 6 + 636262 CCAGAC -s Anc0.Anc0refChr4 29903 6 - 45765 CCAAAC -s Anc1.Anc1refChr2 61456 6 + 144309 CCAAAC -s Anc2.Anc2refChr7 30159 6 + 32194 CCAAAG -s mr.mrrefChr0 82818 6 + 130230 CCAGAC -s simCow_chr6.simCow.chr6 88744 6 + 602619 CCAAAG -s simDog_chr6.simDog.chr6 189506 6 + 593897 CCAAAG -s simHuman_chr6.simHuman.chr6 82263 6 + 601863 CCAAAC -s simRat_chr6.simRat.chr6 79725 6 + 647215 CCAGAC - -a -s simMouse_chr6.simMouse.chr6 87756 2 + 636262 AA -s Anc0.Anc0refChr4 30138 2 - 45765 AA -s Anc1.Anc1refChr2 61756 2 + 144309 AA -s Anc2.Anc2refChr7 30400 2 + 32194 AA -s mr.mrrefChr0 83030 2 + 130230 AA -s simCow_chr6.simCow.chr6 89000 2 + 602619 AA -s simDog_chr6.simDog.chr6 189744 2 + 593897 AC -s simHuman_chr6.simHuman.chr6 82640 2 + 601863 AA -s simRat_chr6.simRat.chr6 79944 2 + 647215 AA - -a -s simMouse_chr6.simMouse.chr6 87758 15 + 636262 TCTTCTCTCCTGAAG -s Anc0.Anc0refChr4 30140 14 - 45765 TGTTCTCTTCT-AAG -s Anc1.Anc1refChr2 61758 15 + 144309 TGTTCTCTTCTAAAG -s Anc2.Anc2refChr7 30402 14 + 32194 TGTCCTCTTCT-ATT -s mr.mrrefChr0 83032 15 + 130230 TCTTCTCTCCTGAAG -s simCow_chr6.simCow.chr6 89003 14 + 602619 TGCCCTCTTCT-GTT -s simDog_chr6.simDog.chr6 189746 14 + 593897 TGTCCTCTTCT-ATT -s simHuman_chr6.simHuman.chr6 82642 15 + 601863 TGTTATCCTCTAAAG -s simRat_chr6.simRat.chr6 79946 15 + 647215 TCTTCTCTCCGGAAG - -a -s simMouse_chr6.simMouse.chr6 87773 72 + 636262 CCAACGCATGTGTAACCAAGTGTCTCTGTATGATTGACTTCCTCCAGACCAGCATTCTCAGCAAAGGCAGAT -s Anc0.Anc0refChr4 30154 68 - 45765 ACAATCCTTGTGTAACCAGGTGTCTCTGTATGAATGACTTTCTCCGGA-CAGCATTACTGTCGAAGTCA--- -s Anc1.Anc1refChr2 61773 68 + 144309 ACAATCCTTGTGTAACCAGGTGTCTCTGTATGAATGACTTTCTCCGGA-CAGCATTACTGTCGAAGTCA--- -s Anc2.Anc2refChr7 30416 68 + 32194 ACAATCCTTGTGTAACCAGGTGTCTCCGTAAGAATGACTTTTTCGGGA-AAGCATTGCTGTCGAAGTCA--- -s mr.mrrefChr0 83047 72 + 130230 CCAACCCATGTGTAACCAGGTGTCTCTGTATGATTGACTTCCTCCAGACCAGCATTATCAGCAAAGGCAGAT -s simCow_chr6.simCow.chr6 89031 63 + 602619 ACAATCCTTGTGCAACCATGT-----CATAGGAATGACTCTTTCTGGA-AAGCATTGTTGTCGAAGTCA--- -s simDog_chr6.simDog.chr6 189760 68 + 593897 ACAATCCTTGTGTAACCAGGGGTCTCCGTAAGAATAACCTTTAGGGGA-AAGCATTGCTGTCAAGGTCA--- -s simHuman_chr6.simHuman.chr6 82657 65 + 601863 ACAATCCTTGAGTAACCAGGTATCTCTGTATAAATGACTTTCTCCGGA-CAGCTTTACTGACGAAG------ -s simRat_chr6.simRat.chr6 79961 72 + 647215 CCAACCCATGTGTAAACAGATGTCTCTGTATGATTGACTTCCTCCAGACCAGCATTATCAGCCAAGTCAGAT - -a -s simMouse_chr6.simMouse.chr6 87845 47 + 636262 TCATTGCCAGGCCCTCAGCTGCAAATTGCTATAGTTAATTTCATGGC -s Anc0.Anc0refChr4 30222 47 - 45765 TTAATGCTATACCCACTGCAACAGTTCACAATAGTTAATTTCTTGTC -s Anc1.Anc1refChr2 61841 47 + 144309 TTAATGCTATACCCACTGCAACAGTTCACAATAGTTAATTTCTTGTC -s Anc2.Anc2refChr7 30484 47 + 32194 TTAATGCTATACCCACTGCAACAGTTCACAGTAGTTAATTTCTTGTC -s mr.mrrefChr0 83119 47 + 130230 TTATTGCCAGGCCCTCAGCTGCAAGTTGCTATAGTTAATTTCTTGTC -s simCow_chr6.simCow.chr6 89097 47 + 602619 TTAATGCTGCACCCTCTCCTACAGCACACAGTAGTTAATGTCTTCTT -s simDog_chr6.simDog.chr6 189828 47 + 593897 TTAATGCTATACCCACTGCAAGAGTTCACAGTAGTTAGTTTCCTGTC -s simHuman_chr6.simHuman.chr6 82722 34 + 601863 TTACT------------GTCACAGTTCAC-AGAGTTAATATCTTGTC -s simRat_chr6.simRat.chr6 80033 47 + 647215 TTATTACCATGCCCTCAGCTGCAAGTTGCAATAGTTAATTTCTTGTC - -a -s simMouse_chr6.simMouse.chr6 87892 19 + 636262 TCTGTGCCTCATCATTATT -s Anc0.Anc0refChr4 30269 19 - 45765 TGTGAGCCGCACCAGTATT -s Anc1.Anc1refChr2 61888 19 + 144309 TGTGAGCCGCACCAGTATT -s Anc2.Anc2refChr7 30531 19 + 32194 TGTGAGCCGCACCAGTATT -s mr.mrrefChr0 83166 19 + 130230 TCTGTGCCTCATCATTATT -s simCow_chr6.simCow.chr6 89146 19 + 602619 TATGAGCCATTCGAGTGAT -s simDog_chr6.simDog.chr6 189875 19 + 593897 TGTAAGCTGCATCATCATC -s simHuman_chr6.simHuman.chr6 82756 19 + 601863 TTTGAGCCGCACCAGTATT -s simRat_chr6.simRat.chr6 80080 19 + 647215 TCTACGCCTCATCATTATT - -a -s simMouse_chr6.simMouse.chr6 87911 3 + 636262 TTG -s Anc0.Anc0refChr4 30293 3 - 45765 TTG -s Anc1.Anc1refChr2 61912 3 + 144309 TTG -s Anc2.Anc2refChr7 30555 3 + 32194 TTG -s mr.mrrefChr0 83190 3 + 130230 TTG -s simCow_chr6.simCow.chr6 89170 3 + 602619 TTG -s simDog_chr6.simDog.chr6 189899 3 + 593897 TTG -s simHuman_chr6.simHuman.chr6 82780 3 + 601863 TTG -s simRat_chr6.simRat.chr6 80104 3 + 647215 ATG - -a -s simMouse_chr6.simMouse.chr6 87914 13 + 636262 TAGATTTCATGGT -s Anc0.Anc0refChr4 30296 13 - 45765 ACTTTTACATTGT -s Anc1.Anc1refChr2 61915 13 + 144309 ACTTTTACATTGT -s Anc2.Anc2refChr7 30558 13 + 32194 ACTTTTACATTGT -s mr.mrrefChr0 83193 13 + 130230 TCGATTTCATGGT -s simCow_chr6.simCow.chr6 89173 13 + 602619 ACTTGTGCTTGGT -s simDog_chr6.simDog.chr6 189909 13 + 593897 ACTTTGACATTGT -s simHuman_chr6.simHuman.chr6 82783 13 + 601863 ACCTTTATATTAT -s simRat_chr6.simRat.chr6 80107 13 + 647215 TCAATGTCATGGT - -a -s simMouse_chr6.simMouse.chr6 87927 14 + 636262 GGATGGTCGACGGG -s Anc0.Anc0refChr4 30309 3 - 45765 GT-----------G -s Anc1.Anc1refChr2 61928 14 + 144309 GTATGGTTATCAGG -s Anc2.Anc2refChr7 30571 3 + 32194 GT-----------G -s mr.mrrefChr0 83206 14 + 130230 GGATGGTCAACGGG -s simCow_chr6.simCow.chr6 89190 3 + 602619 AG-----------G -s simDog_chr6.simDog.chr6 189922 3 + 593897 GT-----------G -s simHuman_chr6.simHuman.chr6 82796 14 + 601863 GTATGGTTATCAGG -s simRat_chr6.simRat.chr6 80120 14 + 647215 GGATAATCAACGGA - -a -s simMouse_chr6.simMouse.chr6 87941 17 + 636262 TTTACTGGCGATTAGCA -s Anc0.Anc0refChr4 30312 17 - 45765 TTTACCTGAGGTTAGAA -s Anc1.Anc1refChr2 61942 17 + 144309 TTTACCTGAGGTTAGAA -s Anc2.Anc2refChr7 30574 17 + 32194 TTTGCCTGTGGTTAGAT -s mr.mrrefChr0 83220 17 + 130230 TTTACTGGAGATTAGCA -s simCow_chr6.simCow.chr6 89193 17 + 602619 TTTACCTAGACTCAGAT -s simDog_chr6.simDog.chr6 189925 17 + 593897 TTTGCCTGTGGTTAGAT -s simHuman_chr6.simHuman.chr6 82811 17 + 601863 TTTACCCAAGGTTGAAA -s simRat_chr6.simRat.chr6 80134 17 + 647215 TTTAATGGAGATTAGCG - -a -s simMouse_chr6.simMouse.chr6 87958 12 + 636262 AACTATATGACA -s Anc0.Anc0refChr4 30329 12 - 45765 AATTATGTGAAA -s Anc1.Anc1refChr2 61959 12 + 144309 AATTATGTGAAA -s Anc2.Anc2refChr7 30591 12 + 32194 AATTATGTGAAC -s mr.mrrefChr0 83237 12 + 130230 AATTATATGACA -s simCow_chr6.simCow.chr6 89210 11 + 602619 GATTGTGTGAA- -s simDog_chr6.simDog.chr6 189942 12 + 593897 AATTATGTGAAC -s simHuman_chr6.simHuman.chr6 82996 12 + 601863 AATTATGTGATA -s simRat_chr6.simRat.chr6 80151 12 + 647215 GATTATATGACA - -a -s simMouse_chr6.simMouse.chr6 87970 3 + 636262 CTA -s Anc0.Anc0refChr4 30343 3 - 45765 CTA -s Anc1.Anc1refChr2 61973 3 + 144309 CTA -s Anc2.Anc2refChr7 30605 3 + 32194 CTA -s mr.mrrefChr0 83249 3 + 130230 CTA -s simCow_chr6.simCow.chr6 89223 3 + 602619 ATA -s simDog_chr6.simDog.chr6 189956 3 + 593897 CTA -s simHuman_chr6.simHuman.chr6 83010 3 + 601863 CTA -s simRat_chr6.simRat.chr6 80163 3 + 647215 CTA - -a -s simMouse_chr6.simMouse.chr6 87973 3 + 636262 GCA -s Anc0.Anc0refChr4 30346 3 - 45765 GAC -s Anc1.Anc1refChr2 61976 3 + 144309 GAC -s Anc2.Anc2refChr7 30608 3 + 32194 GAC -s mr.mrrefChr0 83252 3 + 130230 GCA -s simCow_chr6.simCow.chr6 89226 3 + 602619 GGC -s simDog_chr6.simDog.chr6 189960 3 + 593897 GAC -s simHuman_chr6.simHuman.chr6 83013 3 + 601863 GAC -s simRat_chr6.simRat.chr6 80166 3 + 647215 GCA - -a -s simMouse_chr6.simMouse.chr6 87976 21 + 636262 GAACAATAGGAAGGTTCAGCT -s Anc0.Anc0refChr4 30349 21 - 45765 TAATAACAGGAAAGCCCAGCT -s Anc1.Anc1refChr2 61979 21 + 144309 TAATAACAGGAAAGCCCAGCT -s Anc2.Anc2refChr7 30611 21 + 32194 TAATAACAGGAAAGCCGAGCT -s mr.mrrefChr0 83255 21 + 130230 GAACAATAGGAAGGTTCAGCT -s simCow_chr6.simCow.chr6 89229 21 + 602619 AAGTAGTGGGAAAGTCGAGCT -s simDog_chr6.simDog.chr6 190004 19 + 593897 TAATAACACAAAAGCC--GTC -s simHuman_chr6.simHuman.chr6 83016 21 + 601863 TAAGAACAGGAAAGCCCAGCT -s simRat_chr6.simRat.chr6 80169 21 + 647215 GAACAATAGGAGGGTTCAGCT - -a -s simMouse_chr6.simMouse.chr6 87997 8 + 636262 GGAGAAAG -s Anc0.Anc0refChr4 30373 8 - 45765 TAAGAAAA -s Anc1.Anc1refChr2 62003 8 + 144309 TAAGAAAA -s Anc2.Anc2refChr7 30635 8 + 32194 TAAGAAAA -s mr.mrrefChr0 83276 8 + 130230 GGAGAAAG -s simCow_chr6.simCow.chr6 89253 7 + 602619 TA-TAGTA -s simDog_chr6.simDog.chr6 190026 8 + 593897 TAAGAAAA -s simHuman_chr6.simHuman.chr6 83040 8 + 601863 CAAGAAAA -s simRat_chr6.simRat.chr6 80190 8 + 647215 AGAGAAAG - -a -s simMouse_chr6.simMouse.chr6 88005 54 + 636262 ATCACAAGCTATAGTTGCCAAGACTCAAAGGTCAAAGGGGCTATAGCAGCATTA -s Anc0.Anc0refChr4 30381 46 - 45765 ATAACAAGCTACAGCTGGGGAAACTC--------AATGAGTGATAATAGCTTTA -s Anc1.Anc1refChr2 62011 47 + 144309 ATAACAAGCTACAGCTGGGGAAACTC-------AAATGAGTGATAATAGCTTTA -s Anc2.Anc2refChr7 30643 46 + 32194 ATAGCAAGTTATAGCTGGGGAAGTTT--------AATGAGTGATGATAGCTTTA -s mr.mrrefChr0 83284 47 + 130230 ATCACAAGCTACAGCTGCCAAGACTC-------AAATGGGTTATAGCAGCATCA -s simCow_chr6.simCow.chr6 89260 45 + 602619 ATAGCAAGTTATAGATGGGAAACTTG--------AATG-GTTATGATAGCTTTA -s simDog_chr6.simDog.chr6 190048 46 + 593897 ATCGCGAGTTATAGCTGGTGTGGTTT--------AATGAGTGATGGTAGCTTGC -s simHuman_chr6.simHuman.chr6 83048 47 + 601863 ATAACAAGCAACATCTGGGGAAACTC-------AATTGAGTGGTAATAGCTTTA -s simRat_chr6.simRat.chr6 80198 47 + 647215 GTCATGAGCTACAGCTGCCAAGACTC-------AACTGAATTATAGCAGCATCA - -a -s simMouse_chr6.simMouse.chr6 88059 54 + 636262 AACAAATAAGCTGACGGATGTAAGCTTGAGCTGAGAGAGAATTGAAAATTACCT -s Anc0.Anc0refChr4 30427 54 - 45765 AACAAATAGTCTAATGGGGATAAGCTCAAATTCAAAAAGAATTGAAGACTACCT -s Anc1.Anc1refChr2 62058 54 + 144309 AACAAATAGTCTAATGGGGATAAGCTCAAATTCAAAAAGAATTGAAGACTACCT -s Anc2.Anc2refChr7 30689 54 + 32194 TACAACAAGTTAAATGGGGATATGTTCAAATGCAAAAAGAATTGAAGACTACCT -s mr.mrrefChr0 83331 54 + 130230 AACAAATAAGCTGATGGATGTAAGCTTAAGCTGAAAGAGAATTGAAAATTACCT -s simCow_chr6.simCow.chr6 89305 54 + 602619 GACAAATAGATAAATGGGGATATGATCAAATGCAGGAAGACTACACAATTACCT -s simDog_chr6.simDog.chr6 190094 47 + 593897 TACAACAAGTTAAATGG-------TTCAAATGCAAAAGGAATTGAAGACTAGCT -s simHuman_chr6.simHuman.chr6 83098 54 + 601863 AACAAATAGTCTAATGGGGACAACCTCAAATTCAAAAAGAATTAAAGACTACCT -s simRat_chr6.simRat.chr6 80245 54 + 647215 AACAAATAAGCTTATGGATGTAAGCCTAAGCTGAAAGAGAATTGAAAATTACCT - -a -s simMouse_chr6.simMouse.chr6 88113 25 + 636262 CTCGCCAAAGAGGTGAAAGTACTTT -s Anc0.Anc0refChr4 30481 25 - 45765 CTAGCCAAAAAGGTGAAGGTGCTTT -s Anc1.Anc1refChr2 62112 25 + 144309 CTAGCCAAAAAGGTGAAGGTGCTTT -s Anc2.Anc2refChr7 30743 25 + 32194 CTAGCCAGAAAGGCAAAGGTGCTTT -s mr.mrrefChr0 83385 25 + 130230 CTCGCCAAAAAGGTGAAAGTACTTT -s simCow_chr6.simCow.chr6 89359 25 + 602619 CTAGCCAGAAAGGCATGGGTGCTTT -s simDog_chr6.simDog.chr6 190141 25 + 593897 CTACCCAGAAAGGCAAAGGTGCTTT -s simHuman_chr6.simHuman.chr6 83156 24 + 601863 CTAGCGAAAAA-GTGAAGGTGCTTT -s simRat_chr6.simRat.chr6 80299 25 + 647215 CTCACCAAAAAGGTGAAAGTACTTT - -a -s simMouse_chr6.simMouse.chr6 88138 1 + 636262 G -s Anc0.Anc0refChr4 30506 1 - 45765 C -s Anc1.Anc1refChr2 62137 1 + 144309 C -s Anc2.Anc2refChr7 30768 1 + 32194 C -s mr.mrrefChr0 83410 1 + 130230 G -s simCow_chr6.simCow.chr6 89384 1 + 602619 A -s simDog_chr6.simDog.chr6 190180 1 + 593897 C -s simHuman_chr6.simHuman.chr6 83180 1 + 601863 C -s simRat_chr6.simRat.chr6 80324 1 + 647215 G - -a -s simMouse_chr6.simMouse.chr6 88139 1 + 636262 T -s Anc0.Anc0refChr4 30507 1 - 45765 T -s Anc1.Anc1refChr2 62138 1 + 144309 T -s Anc2.Anc2refChr7 30769 1 + 32194 T -s mr.mrrefChr0 83411 1 + 130230 T -s simCow_chr6.simCow.chr6 89386 1 + 602619 C -s simDog_chr6.simDog.chr6 190181 1 + 593897 T -s simHuman_chr6.simHuman.chr6 83181 1 + 601863 T -s simRat_chr6.simRat.chr6 80325 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 88140 42 + 636262 CATTATCAGACTTTAGATCATACCAGAGAAAATTCTAATATG -s Anc0.Anc0refChr4 30515 42 - 45765 CAATATCAGACCTCGGCTAAGTTCACAGAAAATTCTAATATG -s Anc1.Anc1refChr2 62146 42 + 144309 CAATATCAGACCTCGGCTAAGTTCACAGAAAATTCTAATATG -s Anc2.Anc2refChr7 30777 42 + 32194 CAATATCTGACCTCAGCTGAGTTCACAGAAAATTCTAATATG -s mr.mrrefChr0 83419 42 + 130230 CAATATCAGACTTTGGCTAATTCCAGAGAAAATTCTAATATG -s simCow_chr6.simCow.chr6 89394 42 + 602619 CAATATCTGAGCCCAGTTCAGTTCACATACAACTCTAGTATG -s simDog_chr6.simDog.chr6 190207 42 + 593897 CAATATCTGCCATCAGCTGATCTCACAGAAAATTCTGATATA -s simHuman_chr6.simHuman.chr6 83189 42 + 601863 CAATACCAGACCTAGGCTAAGTTCACAAAACATTCTAATTTG -s simRat_chr6.simRat.chr6 80333 42 + 647215 CAATATCAGACTTTGGCTAATTCCAGAGAAAATTGGAATATG - -a -s simMouse_chr6.simMouse.chr6 88182 21 + 636262 AATATTAGCATGAATAGTAGA -s Anc0.Anc0refChr4 30558 21 - 45765 AACATAAGAGTGAACAGTAGA -s Anc1.Anc1refChr2 62189 21 + 144309 AACATAAGAGTGAACAGTAGA -s Anc2.Anc2refChr7 30820 21 + 32194 AACATAAGAGTGAACAGTAGA -s mr.mrrefChr0 83461 21 + 130230 AATATTAGCGTGAATAGTAGA -s simCow_chr6.simCow.chr6 89437 21 + 602619 TACAGAAGAGTGAACAGTAGA -s simDog_chr6.simDog.chr6 190250 21 + 593897 AACATAAGAGTGAACAGTGGA -s simHuman_chr6.simHuman.chr6 83232 21 + 601863 AACATAAGAGTGAACAGCAGA -s simRat_chr6.simRat.chr6 80375 21 + 647215 AATATCAGCGTGAATAGTAGA - -a -s simMouse_chr6.simMouse.chr6 88203 100 + 636262 AGGCGGTTAAATGCACAGAGGGGATAGGGCTCTACTGGGATCAGACAAACATGAAGCTAAGTAGTAGTTTAGGACAGTTGTAGCCCCAAGGGACCAATTG -s Anc0.Anc0refChr4 30579 93 - 45765 AGGGGGTTT--TGCCCAGAAGAGATAGGGCTCTACTA-ACTAGGACCCTCAGGAAGGT---CATGACTTCAGAAAGGTCATGGCTTCAAGGG-CCAATAT -s Anc1.Anc1refChr2 62210 96 + 144309 AGGGGGTTTAATGCCCAGAAGAGATAGGGCTCTACTAGACTAGGACCCTCAGGAAGGT---CATGACTTCAGAAAGGTCATGGCTTCAAGGG-CCAATAT -s Anc2.Anc2refChr7 30841 93 + 32194 AGGGGGTTT--TGCCCAGAAGAGCTAGGGCTCTACTA-ACTAGGACCCTCAGGAAGGT---CATGACTTCAGAAAGGTCATGGCTTCAAGGG-CCAATAT -s mr.mrrefChr0 83482 100 + 130230 AGGGGGTTAAATGCACAGAGGGGATAGGGCTCTACTGGGATCAGACAAACATGAAGCTAAGTAGTAGTTTAGGACAGTTGTAGCCCCAAGGGACCAATTG -s simCow_chr6.simCow.chr6 89469 89 + 602619 AGGGGGTTT--TGCCCAGAATGCGTGGGTCTCTAC----CTAGCAC-CTCAGGAAGGT---CACCATCTTAGGAAGGGCATTGCTTCAGGAG-ACAAGTT -s simDog_chr6.simDog.chr6 190271 93 + 593897 AGGGGGTTT--TGCCCAGAAGAGCTAGGGCTCTACTA-ACTAGGACCCTCAGGAAGGT---CATGACTTCAGAAAGGTCATGGCTTCAAGGG-CCAATAT -s simHuman_chr6.simHuman.chr6 83253 38 + 601863 AGGGGGTTTAATGCCCAGAACAGATATGGCTCTATTAG-------------------------------------------------------------- -s simRat_chr6.simRat.chr6 80396 100 + 647215 AGGGGATTGAATGCACAGAGGGTATAGGGCTCCACTGGGGTCAGACAAACACCAAGCTGACTTGTAGCTTAGGACAGTTGTAGCCTCAAAAGACAAATTG - -a -s simMouse_chr6.simMouse.chr6 88303 17 + 636262 TCATGTATCTGATACAC -s Anc0.Anc0refChr4 30672 17 - 45765 TCACATATCTGACACAT -s Anc1.Anc1refChr2 62306 17 + 144309 TCACATATCTGACACAT -s Anc2.Anc2refChr7 30934 17 + 32194 TCACATATAGGACACAT -s mr.mrrefChr0 83582 17 + 130230 TCATGTATCTGATACAC -s simCow_chr6.simCow.chr6 89559 17 + 602619 TCATGCATCAGACACAT -s simDog_chr6.simDog.chr6 190364 17 + 593897 TCACATATAGGACACAT -s simHuman_chr6.simHuman.chr6 83291 9 + 601863 --------CTGACACTT -s simRat_chr6.simRat.chr6 80496 17 + 647215 TCATGTATCTGATACAC - -a -s simMouse_chr6.simMouse.chr6 88320 37 + 636262 CGGTCCTGTCCTCATGGTCCCTGTCTTCATAAAACAA -s Anc0.Anc0refChr4 30689 6 - 45765 CAGA-------------------------------AG -s Anc1.Anc1refChr2 62323 6 + 144309 CAGA-------------------------------AG -s Anc2.Anc2refChr7 30963 6 + 32194 CATG-------------------------------AG -s mr.mrrefChr0 83599 37 + 130230 CGGACCTGTCCTCATGGTCCCTGTCTTCATAAAACAA -s simCow_chr6.simCow.chr6 89588 6 + 602619 GATG-------------------------------GG -s simDog_chr6.simDog.chr6 190393 6 + 593897 CATG-------------------------------AG -s simHuman_chr6.simHuman.chr6 83300 6 + 601863 CAGA-------------------------------AG -s simRat_chr6.simRat.chr6 80513 37 + 647215 TGGACCTGTCTTCATGGTCCCTGTCCTCATGAAGCAA - -a -s simMouse_chr6.simMouse.chr6 88357 133 + 636262 ATCTCAATATGGTAATGTGTCCTGAGAAACAAAGAATGAATAACCAAAGCATTACTTGACAAGGGATAGTTAACACATTGATAGTTAACACATTGTCTGAGCCTTCTGGTTGGCAGAGACTAGACAAGTCACC -s Anc0.Anc0refChr4 30695 101 - 45765 ATCTCAATACGATGATTAATCTTGAGAGG---------------CAAAGCATTACTTGACAAG---------------TGATAGTTAATACATTGTCAGTGTCTTCAGATTGGC--AGACCAGACAGTTCATC -s Anc1.Anc1refChr2 62329 101 + 144309 ATCTCAATACGATGATTAATCTTGAGAGG---------------CAAAGCATTACTTGACAAG---------------TGATAGTTAATACATTGTCAGTGTCTTCAGATTGGC--AGACCAGACAGTTCATC -s Anc2.Anc2refChr7 30969 101 + 32194 ATCTCAATATGATGATTAATCTTGAGAGG---------------CAAAACATTACTCGACAAG---------------TGATAGTTAATACATTGTCAGTGTCTTCAGATGGTC--AGACCAGACAGTTCATC -s mr.mrrefChr0 83636 116 + 130230 ATCTCAATACGGTAATTAATCCTGAGAAGCAAAGAATGAATAACCAAAGCATTACTTGACAAG---------------TGATAGTTAACACATTGTCTGAGCCTTCTGGTTGGC--AGACCAGACAATTCACC -s simCow_chr6.simCow.chr6 89595 101 + 602619 ATCTCAATATGATGATTAATCTCAAGAGT---------------CAAAACATTACTCAACAAA---------------TGAAAGTTAATGGATTGTCAGTGTCTTCAGATGGTC--TGACTGGATAGTTCATC -s simDog_chr6.simDog.chr6 190399 101 + 593897 ATCTCAATATGATGATTTATATTGTGAGG---------------CATAACATTACTCGACAAG---------------TGATGGTTAGTACATTATCAGAGTCTTCAGCGGGTC--AGAGCAGACAGTTCATC -s simHuman_chr6.simHuman.chr6 83306 101 + 601863 ATTTCAATACAATGATTAATCTTGAGAGG---------------CAAAGCATTACTTGACAAC---------------TGATAGTTAAAACATTGTCAGTGTATTCAGATTGGC--AGACCAGACAGTTCATC -s simRat_chr6.simRat.chr6 80550 116 + 647215 ATCTCAATACGGCAATTAATCCTGAGAAGCACAGTATTAATAAGCAAAGCATTACTTGGCAAG---------------TGATAGTTAACACATTGTCTGAGCCCTCTAGTTGTC--AGACCAGACAATTGACC - -a -s simMouse_chr6.simMouse.chr6 88490 23 + 636262 TTTTAGTGGTTGCATAATGCAAA -s Anc0.Anc0refChr4 30804 22 - 45765 TCTCAGTGGTAGCAT-ATGCAAA -s Anc1.Anc1refChr2 62438 23 + 144309 TCTCAGTGGTAGCATAATGCAAA -s Anc2.Anc2refChr7 31078 22 + 32194 TCTCAGTGGTAGCAT-ATGCAAA -s mr.mrrefChr0 83752 23 + 130230 TTTTAGTGGTTGCATAATGCAAA -s simCow_chr6.simCow.chr6 89703 22 + 602619 TCTCTGTGGTAGCAT-GTTCAGA -s simDog_chr6.simDog.chr6 190508 22 + 593897 TCTCAGTGGTAGCAC-ATGCAAA -s simHuman_chr6.simHuman.chr6 83415 23 + 601863 TCTCAGTGGTAGCATAATGCAAA -s simRat_chr6.simRat.chr6 80666 23 + 647215 TTTTAGTGGTTGCATAATGCAAA - -a -s simMouse_chr6.simMouse.chr6 88513 5 + 636262 CCATC -s Anc0.Anc0refChr4 30826 5 - 45765 CCAGC -s Anc1.Anc1refChr2 62461 5 + 144309 CCAGC -s Anc2.Anc2refChr7 31100 5 + 32194 CCAGC -s mr.mrrefChr0 83775 5 + 130230 CCATC -s simCow_chr6.simCow.chr6 89740 5 + 602619 CAAGC -s simDog_chr6.simDog.chr6 190530 5 + 593897 CCAGC -s simHuman_chr6.simHuman.chr6 83438 5 + 601863 CCTGC -s simRat_chr6.simRat.chr6 80689 5 + 647215 CTATC - -a -s simMouse_chr6.simMouse.chr6 88518 1 + 636262 A -s Anc0.Anc0refChr4 30831 1 - 45765 A -s Anc1.Anc1refChr2 62466 1 + 144309 A -s Anc2.Anc2refChr7 31105 1 + 32194 A -s mr.mrrefChr0 83780 1 + 130230 A -s simCow_chr6.simCow.chr6 89745 1 + 602619 A -s simDog_chr6.simDog.chr6 190535 1 + 593897 T -s simHuman_chr6.simHuman.chr6 83443 1 + 601863 A -s simRat_chr6.simRat.chr6 80695 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 88519 21 + 636262 ACTTCATCATTTACTATTGGA -s Anc0.Anc0refChr4 30834 21 - 45765 ACTCCATTATTTACTATCAGA -s Anc1.Anc1refChr2 62469 21 + 144309 ACTCCATTATTTACTATCAGA -s Anc2.Anc2refChr7 31108 21 + 32194 ACTCCATTATTTACTATCAAA -s mr.mrrefChr0 83781 21 + 130230 ACTCCATCATTTACTATTGGA -s simCow_chr6.simCow.chr6 89748 21 + 602619 CCTCAATTATTTACTATCAAA -s simDog_chr6.simDog.chr6 190538 21 + 593897 ACTCCATTATTTTCTATCAAA -s simHuman_chr6.simHuman.chr6 83446 21 + 601863 ACTCTATTAATTACTATAAGA -s simRat_chr6.simRat.chr6 80696 21 + 647215 ACTCCATCATTTACTATTGGA - -a -s simMouse_chr6.simMouse.chr6 88540 1 + 636262 A -s Anc0.Anc0refChr4 30855 1 - 45765 G -s Anc1.Anc1refChr2 62490 1 + 144309 G -s Anc2.Anc2refChr7 31129 1 + 32194 G -s mr.mrrefChr0 83802 1 + 130230 G -s simCow_chr6.simCow.chr6 89769 1 + 602619 G -s simDog_chr6.simDog.chr6 190559 1 + 593897 G -s simHuman_chr6.simHuman.chr6 83468 1 + 601863 G -s simRat_chr6.simRat.chr6 80717 1 + 647215 G - -a -s simMouse_chr6.simMouse.chr6 88541 29 + 636262 CAGTTAATTCTTCTTCCACCATTGAACAT -s Anc0.Anc0refChr4 30857 28 - 45765 CAGTAAA-TCTCATTCCACCAATGAACAT -s Anc1.Anc1refChr2 62492 28 + 144309 CAGTAAA-TCTCATTCCACCAATGAACAT -s Anc2.Anc2refChr7 31131 28 + 32194 CAGTAAA-TCTCATTCCACCAATGAACAT -s mr.mrrefChr0 83804 28 + 130230 CAGTTAA-TCTTCTTCCACCATTGAACAT -s simCow_chr6.simCow.chr6 89771 28 + 602619 CAGAAGA-TCTCATTACACCAGTGAACAT -s simDog_chr6.simDog.chr6 190561 28 + 593897 CAGTAAA-TCCCATTCCACCAACGAACAT -s simHuman_chr6.simHuman.chr6 83470 28 + 601863 GAGTCAA-TCTCATTCGACCAATAAACAT -s simRat_chr6.simRat.chr6 80719 28 + 647215 CAGTTAA-TCTTCTTCCACTATTGAATGT - -a -s simMouse_chr6.simMouse.chr6 88570 11 + 636262 TGCATTACTCA -s Anc0.Anc0refChr4 30886 8 - 45765 TA---GATTCA -s Anc1.Anc1refChr2 62521 8 + 144309 TA---GATTCA -s Anc2.Anc2refChr7 31160 8 + 32194 TA---GATTCA -s mr.mrrefChr0 83832 8 + 130230 TA---GACTCA -s simCow_chr6.simCow.chr6 89800 8 + 602619 TT---GATTCA -s simDog_chr6.simDog.chr6 190590 8 + 593897 TA---GACTCA -s simHuman_chr6.simHuman.chr6 83499 8 + 601863 TA---GATTTA -s simRat_chr6.simRat.chr6 80747 8 + 647215 TA---GACTCA - -a -s simMouse_chr6.simMouse.chr6 88581 22 + 636262 TCTTGTAAGTGTACCCCCCATA -s Anc0.Anc0refChr4 30897 9 - 45765 TCTTGTAGG------------- -s Anc1.Anc1refChr2 62532 22 + 144309 TCTTGTAGGTATAGCCCCATTA -s Anc2.Anc2refChr7 31171 9 + 32194 TCTTGTAGG------------- -s mr.mrrefChr0 83840 22 + 130230 TCTTGTAAGTATACCCCCCATA -s simCow_chr6.simCow.chr6 89811 9 + 602619 TCTTAAAGG------------- -s simDog_chr6.simDog.chr6 190601 9 + 593897 TCTTGTAGG------------- -s simHuman_chr6.simHuman.chr6 83510 22 + 601863 TCGTGTAGATATAGCCCCATTA -s simRat_chr6.simRat.chr6 80755 22 + 647215 TCTTGTAAGTATACCCCTCACA - -a -s simMouse_chr6.simMouse.chr6 88603 13 + 636262 CATGGGCTAAGAA -s Anc0.Anc0refChr4 30906 13 - 45765 TATAGGATAAGAA -s Anc1.Anc1refChr2 62554 13 + 144309 TATAGGATAAGAA -s Anc2.Anc2refChr7 31180 13 + 32194 TATAGGATAAGAG -s mr.mrrefChr0 83862 13 + 130230 CATAGGCTAAGAA -s simCow_chr6.simCow.chr6 89820 13 + 602619 TATAATAGGAGGG -s simDog_chr6.simDog.chr6 190610 13 + 593897 TATAGGATAAGAG -s simHuman_chr6.simHuman.chr6 83534 13 + 601863 TGTAGGGTAAGAA -s simRat_chr6.simRat.chr6 80777 12 + 647215 CATAGGCTAAG-A - -a -s simMouse_chr6.simMouse.chr6 88616 43 + 636262 TCCATTTCAGTCTGTGGTACGAAATTTAGTCTGTTAGGGGAAA -s Anc0.Anc0refChr4 30919 33 - 45765 TCTGCTTCATTCTGTGATACAAAA-TTAGTCTGT--------- -s Anc1.Anc1refChr2 62567 33 + 144309 TCTGCTTCATTCTGTGATACAAAA-TTAGTCTGT--------- -s Anc2.Anc2refChr7 31193 33 + 32194 TCTGCTTCATTCTGTGATACAAAA-TTAGTCTAT--------- -s mr.mrrefChr0 83875 43 + 130230 TCCATTTCAGTCTGTGGTACGAAATTTAGTCTGTTAGGGGAAA -s simCow_chr6.simCow.chr6 89841 33 + 602619 TCTGTTTCCTTCTATGATACAAAA-TTAGTCTAT--------- -s simDog_chr6.simDog.chr6 190623 27 + 593897 TCTGCTTCATTCTGT---ACAAAA----GTCTAT--------- -s simHuman_chr6.simHuman.chr6 83547 33 + 601863 ACTGCTTCACTCTGTGATACAAAA-TTAGTCTGC--------- -s simRat_chr6.simRat.chr6 80789 43 + 647215 TCCATTAAAGTCTGTGGTATGAAATTTAGACTATTAGGGGGAA - -a -s simMouse_chr6.simMouse.chr6 88659 26 + 636262 TTGATGAAATCCCAACCTATGGGATG -s Anc0.Anc0refChr4 30952 22 - 45765 ----TGTAATTGCAACCTCAGGGTAG -s Anc1.Anc1refChr2 62600 22 + 144309 ----TGTAATTGCAACCTCAGGGTAG -s Anc2.Anc2refChr7 31226 22 + 32194 ----TGTAATTGTAATCTCAGTATAG -s mr.mrrefChr0 83918 26 + 130230 TTGATGAAATCCCAACCTATGGGATG -s simCow_chr6.simCow.chr6 89874 21 + 602619 ----AGAAATTGTAATCTCAGT-TGT -s simDog_chr6.simDog.chr6 190650 21 + 593897 ----TGTTATT-TAATCTCAGTATAG -s simHuman_chr6.simHuman.chr6 83580 22 + 601863 ----TGTAATTGCAACAGCGGGGTAG -s simRat_chr6.simRat.chr6 80833 26 + 647215 TTTATGAAATCTCAACCAATGGGGTG - -a -s simMouse_chr6.simMouse.chr6 88685 13 + 636262 CAGACCAGGCAGA -s Anc0.Anc0refChr4 30974 12 - 45765 CTGATCTGACAG- -s Anc1.Anc1refChr2 62622 12 + 144309 CTGATCTGACAG- -s Anc2.Anc2refChr7 31253 12 + 32194 CTGATCTGATAA- -s mr.mrrefChr0 83944 13 + 130230 CAGATCTGGCAGA -s simCow_chr6.simCow.chr6 89901 12 + 602619 CTCATATGAGAT- -s simDog_chr6.simDog.chr6 190676 12 + 593897 CTGATCTGATAA- -s simHuman_chr6.simHuman.chr6 83602 10 + 601863 T--ATCTGACAG- -s simRat_chr6.simRat.chr6 80859 13 + 647215 CAGATCTGGCAGA - -a -s simMouse_chr6.simMouse.chr6 88698 102 + 636262 ATGGTAACAACAAAACTACTCACTTTAATAACACAAAAAAGCAATTGAATCACTGTGACCTCTACTGTATTCCCGTATTCCCAATGGTATCTCACCATGGTA -s Anc0.Anc0refChr4 30986 89 - 45765 AAGGAAACAAC-AAACCAGTGAATTTAATGACAGAAAAAAGAA--TGGGTAATTGTGTCCACTATC--------AAATCCCCAGTAGTTTACCACCATGG-- -s Anc1.Anc1refChr2 62634 91 + 144309 AAGGAAACAAC-AAACCAGTGAATTTAATGACAGAAAAAAGAAATTGGGTAATTGTGTCCACTATC--------AAATCCCCAGTAGTTTACCACCATGG-- -s Anc2.Anc2refChr7 31265 89 + 32194 AAGGAAACAAC-AAACCAGTGAATTTAATGACAGAAATAAGAA--TGGGTAATTGTGTCCACTATC--------ATATCCCCAGTAGTTTACCACCATGG-- -s mr.mrrefChr0 83957 91 + 130230 AAGGTAACAAC-AAACCACTCACTTTAATAACACAAAAAAGCAATTGAATCACTGTGTCCTCTACT--------GAATTCCCAATGGTATCCCACCATGG-- -s simCow_chr6.simCow.chr6 89913 87 + 602619 -AGGAAGCGAC-AAACTAGTGACTCTAATGCCAGAAAGAAGAA---GGGTAATTGTGTTAACTATC--------ATAACCCCAGTAGTTTCGCACCATGG-- -s simDog_chr6.simDog.chr6 190691 89 + 593897 AAGGAAACAAC-AAACCAGTTAATTTATTGACAGAAATAAGGA--TGGGTAATTGTTTCCACTATC--------ATATCTCCAGTAATTTACCACCATGG-- -s simHuman_chr6.simHuman.chr6 83612 90 + 601863 GAGGGAACAAC-AAACCAGTGAGTTTAATGAAAGGATAAAGATATTGGGTAATCGTGTCCACTATC--------AAAGCCCCCGTAGT-TACCACCATGA-- -s simRat_chr6.simRat.chr6 80872 86 + 647215 TAGGTAACAAC-ATACCCCTTATTTTAATAACACAGAAAAACAATCAAATCACTGTGTCCTCTACT--------GACTTCGCAATGGTATCCCAC------- - -a -s simMouse_chr6.simMouse.chr6 88800 7 + 636262 TCAAATT -s Anc0.Anc0refChr4 31075 7 - 45765 CAAAATC -s Anc1.Anc1refChr2 62725 7 + 144309 CAAAATC -s Anc2.Anc2refChr7 31354 7 + 32194 CAAAATC -s mr.mrrefChr0 84048 7 + 130230 TCAAATT -s simCow_chr6.simCow.chr6 90000 7 + 602619 CAAAATC -s simDog_chr6.simDog.chr6 190782 7 + 593897 CAAAAGC -s simHuman_chr6.simHuman.chr6 83702 5 + 601863 --AAGTC -s simRat_chr6.simRat.chr6 80958 7 + 647215 TCAAATT - -a -s simMouse_chr6.simMouse.chr6 88807 35 + 636262 ATGAGTTCATTAATGGAAGGACAGGGAACTTAACA -s Anc0.Anc0refChr4 31088 27 - 45765 ATGAG--------TGGGGAGATAATGAATTTAATA -s Anc1.Anc1refChr2 62738 27 + 144309 ATGAG--------TGGGGAGATAATGAATTTAATA -s Anc2.Anc2refChr7 31367 27 + 32194 ACAAG--------TGGGGAGATAATGACTTTAATA -s mr.mrrefChr0 84061 35 + 130230 ATGAGTTCATTAATGGAGGGATAGGGAATTTAACA -s simCow_chr6.simCow.chr6 90013 27 + 602619 ACTAG--------TGGGGAGATAGTGACTTTAATA -s simDog_chr6.simDog.chr6 190799 27 + 593897 ACAAG--------TGGGTAGATAATGGCCTCAATA -s simHuman_chr6.simHuman.chr6 83713 27 + 601863 ATGAG--------TGGGGAGATGATGAATCTAATT -s simRat_chr6.simRat.chr6 80971 35 + 647215 ATGAGGTCATTAATGGAGGAATAGAGAATTTAAGA - -a -s simMouse_chr6.simMouse.chr6 88842 42 + 636262 GGGTGACATAATCCAGGACAGTAGAGGTCTAGTGCCAATGCC -s Anc0.Anc0refChr4 31115 42 - 45765 TGGTAACACAATGCAGGGTGGTAAAAATTTAGTGTCAAGGCC -s Anc1.Anc1refChr2 62765 42 + 144309 TGGTAACACAATGCAGGGTGGTAAAAATTTAGTGTCAAGGCC -s Anc2.Anc2refChr7 31394 42 + 32194 TGGTAACACAATGCAGAGTGGTAAAAATTTAGTATCAAGGCC -s mr.mrrefChr0 84096 42 + 130230 GGGTAACATAATCCAGGACAGTAGAAGTCTAGTGTCAATGCC -s simCow_chr6.simCow.chr6 90040 42 + 602619 GGGTAACACAATGCAGATTGGTAGAAACTGAGTATCAATCCC -s simDog_chr6.simDog.chr6 190826 42 + 593897 TGGTAACACAACGCAAAGTGGTGAAAATTTTGTATCAAGGCC -s simHuman_chr6.simHuman.chr6 83740 42 + 601863 AGGTAACACAATGCAGGGTGGTATAAATTTAGTGTCAAATCC -s simRat_chr6.simRat.chr6 81169 42 + 647215 GAGTAACATAATCCAGGACAGTAGAAGTCTTGTGTCAGTGCC - -a -s simMouse_chr6.simMouse.chr6 88884 25 + 636262 TGCAATTCTGTTAGTAAGGTGCTAG -s Anc0.Anc0refChr4 31180 25 - 45765 TGCTAATTTAATAGTAAGGCACCAG -s Anc1.Anc1refChr2 62830 25 + 144309 TGCTAATTTAATAGTAAGGCACCAG -s Anc2.Anc2refChr7 31459 25 + 32194 TGCTAATTTAATAGTAAGGCACCAG -s mr.mrrefChr0 84138 25 + 130230 TGCAATTCTATTAGTAAGGTGCTAG -s simCow_chr6.simCow.chr6 90106 25 + 602619 TGCCAATTTAATAGTAAGGCACTAA -s simDog_chr6.simDog.chr6 190889 25 + 593897 TGCTAATTTAATTGTCTGGCATCAG -s simHuman_chr6.simHuman.chr6 83805 25 + 601863 TGCTAACGTAATAGTAAGACACCAG -s simRat_chr6.simRat.chr6 81211 24 + 647215 TGCAATTCTATTAGTAAGGTGCTA- - -a -s simMouse_chr6.simMouse.chr6 88909 47 + 636262 CTGTCATTGGCTGCAAATACCAATTTATGACAAGTACCCACTTGTGA -s Anc0.Anc0refChr4 31205 15 - 45765 CTT----------------CCAATTTGTGAC---------------- -s Anc1.Anc1refChr2 62855 47 + 144309 CTTTCATCTGCAACAAATACCAATTTGTGACAAGTACCAACCAGTGA -s Anc2.Anc2refChr7 31484 15 + 32194 CTT----------------CCAATTTGCAAC---------------- -s mr.mrrefChr0 84163 47 + 130230 CTGTCATTGGCTGCAAATACCAATTTATGACAAGTACCCACTTGTGA -s simCow_chr6.simCow.chr6 90135 15 + 602619 CTA----------------CCAACTCGTAGC---------------- -s simDog_chr6.simDog.chr6 190914 15 + 593897 CTT----------------CCAATTTCCAAC---------------- -s simHuman_chr6.simHuman.chr6 83830 47 + 601863 CTCTCATCTGCAACAAATACCAACTTGTGACAAGTACCAACCAGTGA -s simRat_chr6.simRat.chr6 81235 35 + 647215 ------------GCAAATACCAATTTATGACAAGTACCCACTTGGCA - -a -s simMouse_chr6.simMouse.chr6 88956 49 + 636262 CCTTGTTTTGTGCCATAACTCCCTTTCCTGCATGGAACCTCCATTCTTA -s Anc0.Anc0refChr4 31220 49 - 45765 CTCTATTTTACACCTTACCTTCCTTTCCTTCATGTAACCTACCTCCTCA -s Anc1.Anc1refChr2 62902 49 + 144309 CTCTATTTTACACCTTACCTTCCTTTCCTTCATGTAACCTACCTCCTCA -s Anc2.Anc2refChr7 31499 49 + 32194 CTCTATTTTAGGCCTTACCTTCCTTTCCTTCATGTAACCTACCTCCTCA -s mr.mrrefChr0 84210 49 + 130230 CCCTGTTTTGCACCATAACTTCCTTTCCTGCATGGAACCTCCATCCTTA -s simCow_chr6.simCow.chr6 90150 49 + 602619 TTTGATTTTAGGCCTTACCTTCCCTTCCTTCATGTAACCTACCTCTTCA -s simDog_chr6.simDog.chr6 190929 49 + 593897 CTCTAATGTAGGCCTTACCTTCCTTTCATTCATGTAATCCACATTCTTG -s simHuman_chr6.simHuman.chr6 83878 49 + 601863 CTCTATTTTACACCTTATCTTTCGTTCCTTCATGTAACCTACCTCCTCA -s simRat_chr6.simRat.chr6 81270 49 + 647215 CCCTGGTTTGCACCATAACTTCCTTTCCTGAATGGAACTACCATCCTTA - -a -s simMouse_chr6.simMouse.chr6 89005 35 + 636262 TTATTTATATCCTCATGAACTGACTCCTGTATCAG -s Anc0.Anc0refChr4 31269 34 - 45765 TGATTCCCTTCTTGA-GAACTGACTTTTGCATTAC -s Anc1.Anc1refChr2 62951 34 + 144309 TGATTCCCTTCTTGA-GAACTGACTTTTGCATTAC -s Anc2.Anc2refChr7 31548 34 + 32194 TGGTTCCCTTCTTGA-GAACTGACTTTTGCATTGC -s mr.mrrefChr0 84259 35 + 130230 TTATTCACATCTTCATGAACTGACTCTTGCATCAG -s simCow_chr6.simCow.chr6 90212 34 + 602619 TGGTTCCCAACCTGG-GAGCTGACTTTTTCATTGC -s simDog_chr6.simDog.chr6 190978 34 + 593897 TGGTTCCCTTCTTCA-GAACTGACTTCTGTACTGC -s simHuman_chr6.simHuman.chr6 83927 34 + 601863 TGACTCCCTTCTTGA-AAACTGGTTTTTCCGTGAC -s simRat_chr6.simRat.chr6 81319 35 + 647215 TTATTCACATGTTTATGAACTGACTCTTGCATTAG - -a -s simMouse_chr6.simMouse.chr6 89040 28 + 636262 GGATTTTACGATAGCAACCCTCCTGGCC -s Anc0.Anc0refChr4 31303 28 - 45765 AGTGTTTATAATAGCAACCCTCTGAACC -s Anc1.Anc1refChr2 62985 28 + 144309 AGTGTTTATAATAGCAACCCTCTGAACC -s Anc2.Anc2refChr7 31582 28 + 32194 AGTGTACATAATATCAACCCTCTGAACC -s mr.mrrefChr0 84294 28 + 130230 AGATTTTACGATAGCAACCCTCTTAGCC -s simCow_chr6.simCow.chr6 90246 18 + 602619 AGTGTAGA----------CCTCTGAGCC -s simDog_chr6.simDog.chr6 191017 28 + 593897 GGTGTACATAATATCAACCCTCTGAACC -s simHuman_chr6.simHuman.chr6 83961 28 + 601863 AGTGTTTATAATAGCTACCCCCTGAACC -s simRat_chr6.simRat.chr6 81354 28 + 647215 AGATTTTACTATAGCAACCTTCTTAGCC - -a -s simMouse_chr6.simMouse.chr6 89068 38 + 636262 TGCTTTTAAATATAAATAGATAGAAGGAATATTATAAT -s Anc0.Anc0refChr4 31332 31 - 45765 TCTCT-------TGGGTAGACAAAAGGAATATTATAAT -s Anc1.Anc1refChr2 63014 31 + 144309 TCTCT-------TGGGTAGACAAAAGGAATATTATAAT -s Anc2.Anc2refChr7 31611 31 + 32194 TCTCT-------TGGGTAGACAAAAGGGATATTATAAT -s mr.mrrefChr0 84322 31 + 130230 TGCCT-------TAAATAGACAGAAGGAATATTATAAT -s simCow_chr6.simCow.chr6 90265 31 + 602619 TCTCT-------TGGGTAGACAAAAGGGATATTTTAAT -s simDog_chr6.simDog.chr6 191046 30 + 593897 TCT-T-------TGGGTAGGCAAAAAGGATATTATAAT -s simHuman_chr6.simHuman.chr6 83990 31 + 601863 TATCT-------TGGTTACACAACAGGAATATTACAAT -s simRat_chr6.simRat.chr6 81382 31 + 647215 TGGCT-------TAAGTAGACAGAAGGAATACCGTAAT - -a -s simMouse_chr6.simMouse.chr6 89106 36 + 636262 ATATTCTGCTTAAGGTACCAATGCAGAGGTTTCTGT -s Anc0.Anc0refChr4 31363 32 - 45765 ATATTTCACTTAAG--ACCAATGGAAAGGTC--AGT -s Anc1.Anc1refChr2 63045 36 + 144309 ATATTTCACTTAAGTCACCAATGGAAAGGTCCAAGT -s Anc2.Anc2refChr7 31642 32 + 32194 ATATTTCACTTAGG--ACCAATAGGAAGGTC--AGT -s mr.mrrefChr0 84353 36 + 130230 ATATTTTGCTTAAGGTACCAATGCAGAGGTCCCTGT -s simCow_chr6.simCow.chr6 90302 6 + 602619 ATATGT------------------------------ -s simDog_chr6.simDog.chr6 191076 32 + 593897 GCATTTCACTTAGG--ACCAATAGGAAGGTC--AGT -s simHuman_chr6.simHuman.chr6 84021 35 + 601863 ATATTTCACAAAAGTCACTAACGGAAAGG-CCAAGT -s simRat_chr6.simRat.chr6 81413 36 + 647215 ATATTTTGCTTAGGGTACCAATGTAGAGGTCCCTGT - -a -s simMouse_chr6.simMouse.chr6 89142 18 + 636262 CCCCACACTATAGACTTT -s Anc0.Anc0refChr4 31403 18 - 45765 CCCCACACTAAAGACTTT -s Anc1.Anc1refChr2 63089 18 + 144309 CCCCACACTAAAGACTTT -s Anc2.Anc2refChr7 31682 18 + 32194 CTCCACAATAAAGACTTC -s mr.mrrefChr0 84389 18 + 130230 CCCCACACTATAGACTTT -s simDog_chr6.simDog.chr6 191116 18 + 593897 CTCCACAATAAAGACTTC -s simHuman_chr6.simHuman.chr6 84064 18 + 601863 CCCCACACTAAGGACCTT -s simRat_chr6.simRat.chr6 81449 18 + 647215 CCCCACTCTAGAGACTTT - -a -s simMouse_chr6.simMouse.chr6 89160 18 + 636262 TTGCTTCTGCCAAACCAC -s Anc0.Anc0refChr4 31424 18 - 45765 TTGTTGCTGCCAAACCAC -s Anc1.Anc1refChr2 63110 18 + 144309 TTGTTGCTGCCAAACCAC -s Anc2.Anc2refChr7 31703 18 + 32194 TCGTTACTGCCAAACCAC -s mr.mrrefChr0 84407 18 + 130230 TTGCTGCTGCCAAACCAC -s simDog_chr6.simDog.chr6 191137 18 + 593897 TCGTTACTGCCAAACCAC -s simHuman_chr6.simHuman.chr6 84085 18 + 601863 TTGTTGCTTCCAAGCTAC -s simRat_chr6.simRat.chr6 81467 18 + 647215 TTGCTGCTGCCAAACCAC - -a -s simMouse_chr6.simMouse.chr6 89178 4 + 636262 TCCT -s Anc0.Anc0refChr4 31443 4 - 45765 CCCA -s Anc1.Anc1refChr2 63129 4 + 144309 CCCA -s Anc2.Anc2refChr7 31722 4 + 32194 CCCA -s mr.mrrefChr0 84426 4 + 130230 TCCT -s simDog_chr6.simDog.chr6 191156 4 + 593897 CCCA -s simHuman_chr6.simHuman.chr6 84104 4 + 601863 CCCA -s simRat_chr6.simRat.chr6 81486 4 + 647215 TCCT - -a -s simMouse_chr6.simMouse.chr6 89182 31 + 636262 GTGGGTGATAGTAGCCCATCAAGACATTAGT -s Anc0.Anc0refChr4 31448 31 - 45765 GTGGGTGATAATAGCCCATCAAGACATTGGT -s Anc1.Anc1refChr2 63134 31 + 144309 GTGGGTGATAATAGCCCATCAAGACATTGGT -s Anc2.Anc2refChr7 31727 31 + 32194 GTAGGTGATAATAGACCATTGACACATTGGT -s mr.mrrefChr0 84431 31 + 130230 GTGGGTGATAATAGCCCATCAAGACATTAGT -s simDog_chr6.simDog.chr6 191161 31 + 593897 GTAGGTGATAATAGACCATTGACACATTGGT -s simHuman_chr6.simHuman.chr6 84109 31 + 601863 GTGGGTGATAATAGCCCATCAAGACATTGGT -s simRat_chr6.simRat.chr6 81491 31 + 647215 GTGGGTGATAATAGCCCACCAAGACATTAGT - -a -s simMouse_chr6.simMouse.chr6 89213 26 + 636262 AGCATGGTGTGTTCTTATAAGTTCTC -s Anc0.Anc0refChr4 31480 26 - 45765 AGCTGGGTGTGTTTCTGTAATTTTTC -s Anc1.Anc1refChr2 63166 26 + 144309 AGCTGGGTGTGTTTCTGTAATTTTTC -s Anc2.Anc2refChr7 31759 26 + 32194 AGCTGGGTGTGTTTATGTAATTTTTG -s mr.mrrefChr0 84462 26 + 130230 AGCATGGTGTGTTTCTGTAAGTTCTC -s simCow_chr6.simCow.chr6 90308 26 + 602619 AGCTGTGTGTGTTTATGTAATTTTTT -s simDog_chr6.simDog.chr6 191193 26 + 593897 AGCTGGGTGTGTTTATGTAATTTTAG -s simHuman_chr6.simHuman.chr6 84141 26 + 601863 AGCTGGGTCCATTTCGGTAACTTGTC -s simRat_chr6.simRat.chr6 81522 26 + 647215 AGCATGGTGTGTTTCTGTAAGTTCTC - -a -s simMouse_chr6.simMouse.chr6 89239 10 + 636262 CCATACTAAA -s Anc0.Anc0refChr4 31506 10 - 45765 CCATTCAAAA -s Anc1.Anc1refChr2 63192 10 + 144309 CCATTCAAAA -s Anc2.Anc2refChr7 31785 10 + 32194 CCATTCAAAA -s mr.mrrefChr0 84488 10 + 130230 CCATACTAAA -s simCow_chr6.simCow.chr6 90335 10 + 602619 CCATGCATAA -s simDog_chr6.simDog.chr6 191219 10 + 593897 TCCTTCAAAA -s simHuman_chr6.simHuman.chr6 84167 10 + 601863 CCATTCAAAA -s simRat_chr6.simRat.chr6 81548 10 + 647215 CCATACCAAA - -a -s simMouse_chr6.simMouse.chr6 89249 92 + 636262 GTTAGTTGCCAGTGATGTGTCATGTAATGCTCCTGTGGCACATGCTTCCGGCTAGAGCCATGCCTAATTCCCAATGAGAGCCCTTAGGTGTG -s Anc0.Anc0refChr4 31524 85 - 45765 GCTA-TTGCA------GCGTTATACAATGCTCCTGTGGAGCCTGGTTGTGACTACAGTCATGCCTAACTCCCTATATAAGCACTTAGGTGGC -s Anc1.Anc1refChr2 63210 85 + 144309 GCTA-TTGCA------GCGTTATACAATGCTCCTGTGGAGCCTGGTTGTGACTACAGTCATGCCTAACTCCCTATATAAGCACTTAGGTGGC -s Anc2.Anc2refChr7 31803 85 + 32194 GCTA-TTGCA------GCGTTATACAATGCTCCTGTGAAGCCTGGTTGTGACTACAATCATGCCTAACTCCCTATATAAGCAATTAGGTGTC -s mr.mrrefChr0 84506 92 + 130230 GCTAGTTGCCAGTGATGTGTCATACAATGCTCCTGTGGCACATGCTTGCGGCTAGAGCCATGCCTAACTCCCAATGAAAGCCCTTAGGTGGG -s simCow_chr6.simCow.chr6 90353 85 + 602619 GCTA-TTGCA------GTGTTATACAATGCTCCTGTGAAGCCTGGTTGTGCCTAATACCATGCCTAACTCCCTATATAAGTCGCTAAGTGTC -s simDog_chr6.simDog.chr6 191237 85 + 593897 GCTA-CCTCT------GCGTTATACTATGCTGTAGTGAAGCCTGGTTGTGACTACAATTATCCCTGACTTTCAACATAAGCAATTAGGTGTC -s simHuman_chr6.simHuman.chr6 84185 85 + 601863 GCTA-TTGCA------GAGTTACACAATACTCCTGTGGAGCCTGGTTGTGTCTATAGTCATGCCTAACTCCCTATATAAGCTCTTAGGTGGC -s simRat_chr6.simRat.chr6 81566 91 + 647215 GCTAGTTGGCGGTGATGTGCCATACAATGCT-CTGTGGCACATGCTTGCGGCTAGAGCCATGCCTAACTTCCAATGAAAGCCCTTAGGTGGG - -a -s simMouse_chr6.simMouse.chr6 89341 79 + 636262 CGAAATTGTCATCACAATATTTAAAAAGCCATCTTCCTTGCCTCAACAGTGATGAGCTAAAAACTTTGAGAATAAGTAA -s Anc0.Anc0refChr4 31609 30 - 45765 CA-------------------------------------------------ATAAGTTAAAAACTTTAAGTATAACTCT -s Anc1.Anc1refChr2 63295 30 + 144309 CA-------------------------------------------------ATAAGTTAAAAACTTTAAGTATAACTCT -s Anc2.Anc2refChr7 31889 30 + 32194 CA-------------------------------------------------ATAAGTTAAAAACTTTGACTATAACTCT -s mr.mrrefChr0 84598 79 + 130230 CAAAATTGTCATCACAATATTTAAAAAGCCATCTTCCTTGCCTCAACAGTGATGAGCTAAAAACTTTAAGAATAAGTAA -s simCow_chr6.simCow.chr6 90439 30 + 602619 GG-------------------------------------------------ATAAGTTAAAAACTTGGATGATAACCCA -s simDog_chr6.simDog.chr6 191323 30 + 593897 CA-------------------------------------------------ATAAATTGAAAACTTTGACTATAACTCT -s simHuman_chr6.simHuman.chr6 84270 30 + 601863 CA-------------------------------------------------ATAAGTTAAAAACTTCAAGTATAACTCC -s simRat_chr6.simRat.chr6 81657 78 + 647215 CAAAATTGTCATCACAATATTTAAAAAGCCATCTTCCTTGCCTTAACAGTGATGTTCTAAGAAC-CTAAGAAGATGTAA - -a -s simMouse_chr6.simMouse.chr6 89420 4 + 636262 AAAC -s Anc0.Anc0refChr4 31639 4 - 45765 ATCT -s Anc1.Anc1refChr2 63325 4 + 144309 ATCT -s Anc2.Anc2refChr7 31919 4 + 32194 GTCT -s mr.mrrefChr0 84677 4 + 130230 AAAC -s simCow_chr6.simCow.chr6 90469 4 + 602619 GTCT -s simDog_chr6.simDog.chr6 191353 4 + 593897 GTCT -s simHuman_chr6.simHuman.chr6 84300 4 + 601863 ATCT -s simRat_chr6.simRat.chr6 81736 4 + 647215 CAAA - -a -s simMouse_chr6.simMouse.chr6 89424 32 + 636262 CTTTCAACATTACGCTGTTTTGTAATAAGTAT -s Anc0.Anc0refChr4 31643 32 - 45765 GTAAAAGTACCAAAGATCACTCTCACTATTCT -s Anc1.Anc1refChr2 63329 32 + 144309 GTAAAAGTACCAAAGATCACTCTCACTATTCT -s Anc2.Anc2refChr7 31927 32 + 32194 GTAAATATATCAAGGATCACTCTCACTTTTCT -s mr.mrrefChr0 84681 32 + 130230 GTATCAGCACTACACTGCTTTGTAATAAGTAT -s simCow_chr6.simCow.chr6 90477 32 + 602619 GTAAATATATCATGGATTACTTGTGCTGTTCT -s simDog_chr6.simDog.chr6 191361 32 + 593897 GTAAATATATCAAGGATCACCCTCACTTGGCT -s simHuman_chr6.simHuman.chr6 84304 32 + 601863 GTAAAAGTACCAGAGATCACTCTCACCATTCT -s simRat_chr6.simRat.chr6 81740 28 + 647215 GAAGCAGCACTCCAATACTTTAT-GTAGG--- - -a -s simMouse_chr6.simMouse.chr6 89456 12 + 636262 ATCATCTGCTAA -s Anc0.Anc0refChr4 31675 12 - 45765 GCCTTCTGCTAA -s Anc1.Anc1refChr2 63361 12 + 144309 GCCTTCTGCTAA -s Anc2.Anc2refChr7 31959 12 + 32194 GCCTTCTGATAA -s mr.mrrefChr0 84713 12 + 130230 ATCATCTGCTAA -s simCow_chr6.simCow.chr6 90510 12 + 602619 TTCCTCTGATAG -s simDog_chr6.simDog.chr6 191393 12 + 593897 GCCTTCCGATTA -s simHuman_chr6.simHuman.chr6 84336 12 + 601863 CCCTTCTGCTAA -s simRat_chr6.simRat.chr6 81768 10 + 647215 --CGTCCCCCAG - -a -s simMouse_chr6.simMouse.chr6 89468 19 + 636262 GAAGATGTAGCCAAAGAAG -s Anc0.Anc0refChr4 31687 18 - 45765 AGATATGTAGCCA-AACAA -s Anc1.Anc1refChr2 63373 18 + 144309 AGATATGTAGCCA-AACAA -s Anc2.Anc2refChr7 31971 18 + 32194 AGATATGTAGCCA-AACAA -s mr.mrrefChr0 84725 19 + 130230 GAATATGTAGCCACAAAAG -s simCow_chr6.simCow.chr6 90522 18 + 602619 GGGTATATAGCCA-AAGGA -s simDog_chr6.simDog.chr6 191405 16 + 593897 AAATATGTAAA---AACAA -s simHuman_chr6.simHuman.chr6 84348 18 + 601863 AGTTATGAAGCCC-AACAA -s simRat_chr6.simRat.chr6 81780 19 + 647215 GAATAGTCAACTGCAAGAG - -a -s simMouse_chr6.simMouse.chr6 89487 41 + 636262 CATACTCATTCATAAAGCACCAGCTTATAGTAAGCCTTGCA -s Anc0.Anc0refChr4 31715 41 - 45765 CCTAATCATCCACTAAGCACCAGCTTGAAGTAAGTATTGCA -s Anc1.Anc1refChr2 63402 41 + 144309 CCTAATCATCCACTAAGCACCAGCTTGAAGTAAGTATTGCA -s Anc2.Anc2refChr7 31999 41 + 32194 CCTAATCATCCACTAAGCCCCAGCTTGAAGTAAGTATTGCA -s mr.mrrefChr0 84755 41 + 130230 CCTACTCATCCACAAAGCACCAGCTTATAGTAAGCCTTGCA -s simCow_chr6.simCow.chr6 90550 41 + 602619 CCTGATCATCCACCAAACGTCATCTTGAAGTAAATATTGCA -s simDog_chr6.simDog.chr6 191431 41 + 593897 CCTAATCATCCACTAAGCCCCAGCTTGGAGTAAGTATTGCA -s simHuman_chr6.simHuman.chr6 84377 41 + 601863 CCTAATCACCCACTGAGCACCAACTTGAAGCAAGTATTGCA -s simRat_chr6.simRat.chr6 81810 41 + 647215 TCTACTCATCCACAAAGCACCAGCTTACAGGAAGCCTTGAA - -a -s simMouse_chr6.simMouse.chr6 89528 38 + 636262 ACTTCAGACCAGTGCATTGCATACCCTGAATTATGAAC -s Anc0.Anc0refChr4 31756 33 - 45765 ACCCCAAAC-----TATTGCAAACCCTGAACTATCAAT -s Anc1.Anc1refChr2 63443 33 + 144309 ACCCCAAAC-----TATTGCAAACCCTGAACTATCAAT -s Anc2.Anc2refChr7 32040 33 + 32194 ACCCAAAAC-----TACTGCAAACCCTGAACTATCAAT -s mr.mrrefChr0 84796 38 + 130230 ACTTCAGACCAGTGTATTGCATACCCTGAACTATGAAT -s simCow_chr6.simCow.chr6 90591 31 + 602619 ACCCAATAC-----TACTGCAAACCCTGAACTAT--AT -s simDog_chr6.simDog.chr6 191509 33 + 593897 ACCCAAAAC-----TGCTGGCAACCCTGAACTATCAAT -s simHuman_chr6.simHuman.chr6 84418 33 + 601863 ACCACAAAC-----TATTGCAAACCCCGAACTATCACT -s simRat_chr6.simRat.chr6 81851 38 + 647215 ACTTCACAGCAGTGTGTTGCATACCCTGAACTATTAAT - -a -s simMouse_chr6.simMouse.chr6 89566 224 + 636262 GGATGTCAATGGACTAGCTTTCAAAAGTATCACATGGTGTCTTGGTCATGGGTACtaaagagttcaataggacttggttggagtgtgagtcccaaaactttatactttcccctcagcacttacaccctgagaaagaggctacgttccatgaggcgtcttATATAGTGGATTCCAGTTAACTCCTCTGGTTCACTTGACAAAGTTACACCCTCATATAGCCCAAA -s Anc0.Anc0refChr4 31789 52 - 45765 GGGTGTCAATTGATTGGCTATA--AAGTGTCATGTGATGTCTTGGATGTGGGTA-------------------------------------------------------------------------------------------------------------------------------------------------------------------------- -s Anc1.Anc1refChr2 63476 52 + 144309 GGGTGTCAATTGATTGGCTATA--AAGTGTCATGTGATGTCTTGGATGTGGGTA-------------------------------------------------------------------------------------------------------------------------------------------------------------------------- -s Anc2.Anc2refChr7 32083 52 + 32194 GGGTTTCAATTGATTGGCTATA--AAATGTCATGTGATGTCTTGGATGTGGGTA-------------------------------------------------------------------------------------------------------------------------------------------------------------------------- -s mr.mrrefChr0 84834 221 + 130230 GGGTGTCAATGGACTAGCTTTC--AAGTATCACATGGTGTCTTGGTCATGGGTACtaaagagttcaataggacttggttggagtgtgagtcccaaaactttatactttcccctcagcacttacaccctgagaaagaggctacgttccatgaggcgtcttATATAGTG-ATTCCAGTTAACTCCTCTGGTTCACTTGACAAAGTTACACCCTCATATAGCCCAAA -s simCow_chr6.simCow.chr6 90632 38 + 602619 GTGTCTCAATTGACTGGC---------TGTCATGTGTTGT-------GTGGGTA-------------------------------------------------------------------------------------------------------------------------------------------------------------------------- -s simDog_chr6.simDog.chr6 191552 52 + 593897 GGGTTCCAATTGATTGGCTATA--AAATGTCATGTGATATCTTGGATGAGGATA-------------------------------------------------------------------------------------------------------------------------------------------------------------------------- -s simHuman_chr6.simHuman.chr6 84451 52 + 601863 GGGTGTCAATTAATTGGCAGTT--AAGTGTCATGTGATGTCTTACATGTGGGCA-------------------------------------------------------------------------------------------------------------------------------------------------------------------------- -s simRat_chr6.simRat.chr6 81889 221 + 647215 GGGTGTCAATGGACTAGCTCTC--AAGTACCAGATACTGTCTTGGTCATGGGTACtaaagagttcaatagcacttggttggagtacaaatcccaaaactttctactttcccgtcagcacttactccctgagaAACAGGCTGCCTTCCATGTGCCTTCTTATATAGTG-ATTCCAGTTAACTGCTATAGCTCACTTGACAAAGTTGCACCCTCATATCACAAAAA - -a -s simMouse_chr6.simMouse.chr6 89790 79 + 636262 TCTTTTAGAGACCCCCCAAGATGCATTCTGTGAACGTCAAGATTTGGTGCTTTATCTACACCCAGAGCTGTGACCCCTT -s mr.mrrefChr0 85055 78 + 130230 TCTTTTAGAGACCCCCCAAGATGCATTCTGTGAACGTCAAGATTTGGTGCTTTATCTA-ACCCAGAGCTGTGACCCCTT -s simRat_chr6.simRat.chr6 82120 78 + 647215 TCTTTTAAAGACCCCCCAAGATGCATTTTGTGAACATTGAGATTTGGTACTTTATCTA-ACATAAAGTTCTGAGGCTGT - -a -s simMouse_chr6.simMouse.chr6 89869 60 + 636262 CAATCAGCCATTGGTCTGAGGCACCTGGGGTTACGCTCTCATTAAGTAAACTATGAAAGT -s mr.mrrefChr0 85133 60 + 130230 CAATCAGCCATTGGTCTGAGGCACCTGGGGTTACGCTCTCATTAAGTAAACTATGAAAGT -s simRat_chr6.simRat.chr6 82200 60 + 647215 CAATCAACCATTGGTGTGGGGGACCTGAGGTCACACTCCCATTAAGCAAACTATAAAAGT - -a -s simMouse_chr6.simMouse.chr6 89929 75 + 636262 ATAGGAGTCCACTGGACCAACAGCGAAGTGTGTCATGGTATTACCAGCTCATCCTGTTCCACTCCATCTTCTTGA -s Anc0.Anc0refChr4 31841 22 - 45765 -----------------------------------------------------CTGTCACACTTCATCTTCTTTC -s Anc1.Anc1refChr2 63528 22 + 144309 -----------------------------------------------------CTGTCACACTTCATCTTCTTTC -s Anc2.Anc2refChr7 32135 22 + 32194 -----------------------------------------------------CTGTCATGCGTCATCATATTTC -s mr.mrrefChr0 85193 67 + 130230 ATAGGAGTCCACTGGA--------GAAGTGTGTCATGGTATTACCAGCTCATCCTGTTCCACTCCATCTTCTTGC -s simCow_chr6.simCow.chr6 90670 1 + 602619 -----------------------------------------------------C--------------------- -s simDog_chr6.simDog.chr6 191604 22 + 593897 -----------------------------------------------------ATGTCATGCGTCATCATATTTC -s simHuman_chr6.simHuman.chr6 84503 22 + 601863 -----------------------------------------------------CGGTCACACTGCCTCTGCTTTC -s simRat_chr6.simRat.chr6 82261 67 + 647215 ATAGGAGTCCACTCAA--------GGAGTATTTCGTGGTATCCCCTGCTCATCTCATTCCACTTCATCTTCTTGC - -a -s simMouse_chr6.simMouse.chr6 90004 2 + 636262 TA -s Anc0.Anc0refChr4 31863 2 - 45765 TA -s Anc1.Anc1refChr2 63550 2 + 144309 TA -s Anc1.Anc1refChr4 17393 2 + 17549 TA -s Anc2.Anc2refChr2 574 2 + 27695 TA -s Anc2.Anc2refChr7 32157 2 + 32194 TA -s mr.mrrefChr0 85260 2 + 130230 TA -s mr.mrrefChr5 113108 2 - 294540 TC -s simDog_chr6.simDog.chr6 191626 2 + 593897 TA -s simDog_chr6.simDog.chr6 306155 2 + 593897 TA -s simHuman_chr6.simHuman.chr6 319539 2 + 601863 TG -s simHuman_chr6.simHuman.chr6 84525 2 + 601863 TA -s simMouse_chr6.simMouse.chr6 302363 2 - 636262 TC -s simRat_chr6.simRat.chr6 322244 2 - 647215 TC -s simRat_chr6.simRat.chr6 82328 2 + 647215 TA - -a -s simMouse_chr6.simMouse.chr6 90006 6 + 636262 GCACCA -s Anc0.Anc0refChr4 31868 6 - 45765 GCACCA -s Anc1.Anc1refChr2 63555 6 + 144309 GCACCA -s Anc1.Anc1refChr4 17398 6 + 17549 ACAACA -s Anc2.Anc2refChr2 579 6 + 27695 ACAACA -s Anc2.Anc2refChr7 32162 6 + 32194 GCACCA -s mr.mrrefChr0 85265 6 + 130230 GCACCA -s mr.mrrefChr5 113113 6 - 294540 ACGATA -s simDog_chr6.simDog.chr6 191631 6 + 593897 GCACCA -s simDog_chr6.simDog.chr6 306160 6 + 593897 ACAACA -s simHuman_chr6.simHuman.chr6 319544 6 + 601863 ACCACA -s simHuman_chr6.simHuman.chr6 84530 6 + 601863 ACACCA -s simMouse_chr6.simMouse.chr6 302368 6 - 636262 ACGATA -s simRat_chr6.simRat.chr6 322249 6 - 647215 ACTATA -s simRat_chr6.simRat.chr6 82334 6 + 647215 GCACCA - -a -s simMouse_chr6.simMouse.chr6 90012 1 + 636262 C -s Anc0.Anc0refChr4 31874 1 - 45765 G -s Anc1.Anc1refChr2 63561 1 + 144309 G -s Anc2.Anc2refChr7 32168 1 + 32194 G -s mr.mrrefChr0 85271 1 + 130230 G -s simDog_chr6.simDog.chr6 191637 1 + 593897 G -s simHuman_chr6.simHuman.chr6 84536 1 + 601863 G -s simRat_chr6.simRat.chr6 82340 1 + 647215 G - -a -s simMouse_chr6.simMouse.chr6 90013 12 + 636262 AAATCAGAGGCA -s Anc0.Anc0refChr4 31875 12 - 45765 CAAATTAATATA -s Anc1.Anc1refChr2 63562 12 + 144309 AAAATGGATACA -s Anc1.Anc1refChr4 17404 12 + 17549 CAAACTAAGATA -s Anc2.Anc2refChr2 585 12 + 27695 CAAATTAATATA -s Anc2.Anc2refChr7 32169 12 + 32194 AAGGTGGATACA -s mr.mrrefChr0 85272 12 + 130230 AAAACAGAGGCA -s mr.mrrefChr5 113119 12 - 294540 CAAACTGAGATA -s simCow_chr6.simCow.chr6 90671 4 + 602619 --------TGCA -s simDog_chr6.simDog.chr6 191638 12 + 593897 AAGGTGGATACA -s simDog_chr6.simDog.chr6 306166 12 + 593897 CAAATTAATATA -s simHuman_chr6.simHuman.chr6 319550 12 + 601863 CGAACTAAGATA -s simHuman_chr6.simHuman.chr6 84537 12 + 601863 AAAATGGATACA -s simMouse_chr6.simMouse.chr6 302374 12 - 636262 CAAACTGAGATA -s simRat_chr6.simRat.chr6 322255 12 - 647215 AAACCTGAGCTA -s simRat_chr6.simRat.chr6 82341 12 + 647215 AAAACAGAAGCA - -a -s simMouse_chr6.simMouse.chr6 90025 3 + 636262 GCA -s Anc0.Anc0refChr4 31887 3 - 45765 GCC -s Anc1.Anc1refChr2 63574 3 + 144309 GCT -s Anc1.Anc1refChr4 17416 3 + 17549 GGC -s Anc2.Anc2refChr2 597 3 + 27695 GGC -s Anc2.Anc2refChr7 32181 3 + 32194 GCT -s mr.mrrefChr0 85284 3 + 130230 GCA -s mr.mrrefChr5 113131 3 - 294540 AGG -s simCow_chr6.simCow.chr6 90675 3 + 602619 GTG -s simDog_chr6.simDog.chr6 191654 3 + 593897 GCT -s simDog_chr6.simDog.chr6 306178 3 + 593897 GGC -s simHuman_chr6.simHuman.chr6 319562 3 + 601863 GGA -s simHuman_chr6.simHuman.chr6 84549 3 + 601863 GCT -s simMouse_chr6.simMouse.chr6 302386 3 - 636262 AGG -s simRat_chr6.simRat.chr6 322267 3 - 647215 AGG -s simRat_chr6.simRat.chr6 82353 3 + 647215 GTA - -a -s simMouse_chr6.simMouse.chr6 90028 4 + 636262 TATT -s Anc0.Anc0refChr4 31890 4 - 45765 TAAT -s Anc1.Anc1refChr2 63577 4 + 144309 TAAT -s Anc1.Anc1refChr4 17419 4 + 17549 AATG -s Anc2.Anc2refChr2 600 4 + 27695 AGAT -s Anc2.Anc2refChr7 32184 4 + 32194 TAAT -s mr.mrrefChr0 85287 4 + 130230 TATT -s mr.mrrefChr5 113134 4 - 294540 GATG -s simCow_chr6.simCow.chr6 90678 4 + 602619 TCAT -s simDog_chr6.simDog.chr6 191657 4 + 593897 TAAT -s simDog_chr6.simDog.chr6 306181 4 + 593897 AGAT -s simHuman_chr6.simHuman.chr6 319566 4 + 601863 AATG -s simHuman_chr6.simHuman.chr6 84552 4 + 601863 TAAT -s simMouse_chr6.simMouse.chr6 302389 4 - 636262 GATG -s simRat_chr6.simRat.chr6 322270 4 - 647215 GATG -s simRat_chr6.simRat.chr6 82356 4 + 647215 TACT - -a -s simMouse_chr6.simMouse.chr6 90032 1 + 636262 T -s Anc0.Anc0refChr4 31894 1 - 45765 T -s Anc1.Anc1refChr2 63581 1 + 144309 T -s Anc1.Anc1refChr4 17423 1 + 17549 T -s Anc2.Anc2refChr2 604 1 + 27695 T -s Anc2.Anc2refChr7 32188 1 + 32194 T -s mr.mrrefChr0 85291 1 + 130230 T -s mr.mrrefChr5 113138 1 - 294540 T -s simCow_chr6.simCow.chr6 90682 1 + 602619 T -s simDog_chr6.simDog.chr6 306185 1 + 593897 T -s simHuman_chr6.simHuman.chr6 319570 1 + 601863 T -s simHuman_chr6.simHuman.chr6 84556 1 + 601863 T -s simMouse_chr6.simMouse.chr6 302393 1 - 636262 T -s simRat_chr6.simRat.chr6 322274 1 - 647215 T -s simRat_chr6.simRat.chr6 82360 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 90033 2 + 636262 GA -s Anc0.Anc0refChr4 31895 2 - 45765 CA -s Anc1.Anc1refChr2 63582 2 + 144309 CA -s Anc1.Anc1refChr4 17424 2 + 17549 AT -s Anc2.Anc2refChr2 605 2 + 27695 CA -s Anc2.Anc2refChr7 32189 2 + 32194 CA -s mr.mrrefChr0 85292 2 + 130230 GA -s mr.mrrefChr5 113139 2 - 294540 AT -s simCow_chr6.simCow.chr6 90683 2 + 602619 CA -s simDog_chr6.simDog.chr6 191661 2 + 593897 TA -s simDog_chr6.simDog.chr6 306186 2 + 593897 CA -s simHuman_chr6.simHuman.chr6 319571 2 + 601863 AT -s simHuman_chr6.simHuman.chr6 84557 2 + 601863 CA -s simMouse_chr6.simMouse.chr6 302394 2 - 636262 AT -s simRat_chr6.simRat.chr6 322275 2 - 647215 GT -s simRat_chr6.simRat.chr6 82361 2 + 647215 GA - -a -s simMouse_chr6.simMouse.chr6 90035 2 + 636262 AT -s Anc0.Anc0refChr4 31915 2 - 45765 AT -s Anc1.Anc1refChr2 63584 2 + 144309 AT -s Anc1.Anc1refChr4 17546 2 + 17549 TT -s Anc2.Anc2refChr2 625 2 + 27695 AG -s Anc2.Anc2refChr7 32191 2 + 32194 AT -s mr.mrrefChr0 85294 2 + 130230 AT -s mr.mrrefChr5 113264 2 - 294540 GT -s simCow_chr6.simCow.chr6 90685 2 + 602619 AA -s simDog_chr6.simDog.chr6 191663 2 + 593897 AT -s simDog_chr6.simDog.chr6 306217 2 + 593897 AG -s simHuman_chr6.simHuman.chr6 319695 2 + 601863 TT -s simHuman_chr6.simHuman.chr6 84559 2 + 601863 AT -s simMouse_chr6.simMouse.chr6 302510 2 - 636262 GT -s simRat_chr6.simRat.chr6 322400 2 - 647215 GT -s simRat_chr6.simRat.chr6 82363 2 + 647215 AT - -a -s simMouse_chr6.simMouse.chr6 90037 1 + 636262 G -s Anc0.Anc0refChr4 31917 1 - 45765 G -s Anc1.Anc1refChr2 63586 1 + 144309 G -s Anc2.Anc2refChr2 627 1 + 27695 G -s mr.mrrefChr0 85296 1 + 130230 G -s simDog_chr6.simDog.chr6 306219 1 + 593897 G -s simHuman_chr6.simHuman.chr6 84561 1 + 601863 C -s simRat_chr6.simRat.chr6 82365 1 + 647215 G - -a -s simMouse_chr6.simMouse.chr6 90038 15 + 636262 CCAGCTTGAACACAG -s Anc0.Anc0refChr4 31918 14 - 45765 ACAACTTG-AATTAG -s Anc1.Anc1refChr2 63587 15 + 144309 ACAACTTGAAATTAG -s Anc2.Anc2refChr2 628 14 + 27695 ACAACTTG-ACTTAG -s mr.mrrefChr0 85297 15 + 130230 CCAGCTTGAACATAG -s simCow_chr6.simCow.chr6 90688 14 + 602619 ACAACTGG-ACTAAG -s simCow_chr6.simCow.chr6 294664 14 - 602619 ACAACTGG-ACTAAG -s simDog_chr6.simDog.chr6 191666 14 + 593897 GCAATTTG-ACTTAT -s simHuman_chr6.simHuman.chr6 84562 15 + 601863 ACAACTTCTAATTAG -s simRat_chr6.simRat.chr6 82366 15 + 647215 CCAGCCCGAACATAA - -a -s simMouse_chr6.simMouse.chr6 90053 1 + 636262 C -s Anc0.Anc0refChr4 31932 1 - 45765 C -s Anc1.Anc1refChr2 63602 1 + 144309 C -s Anc1.Anc1refChr4 17548 1 + 17549 C -s Anc2.Anc2refChr2 642 1 + 27695 C -s Anc2.Anc2refChr7 32193 1 + 32194 C -s mr.mrrefChr0 85312 1 + 130230 C -s mr.mrrefChr5 113266 1 - 294540 C -s simCow_chr6.simCow.chr6 90687 1 + 602619 C -s simCow_chr6.simCow.chr6 90702 1 + 602619 C -s simCow_chr6.simCow.chr6 294678 1 - 602619 C -s simDog_chr6.simDog.chr6 191665 1 + 593897 C -s simDog_chr6.simDog.chr6 191680 1 + 593897 C -s simHuman_chr6.simHuman.chr6 319697 1 + 601863 C -s simHuman_chr6.simHuman.chr6 84577 1 + 601863 T -s simMouse_chr6.simMouse.chr6 302512 1 - 636262 T -s simRat_chr6.simRat.chr6 322402 1 - 647215 C -s simRat_chr6.simRat.chr6 82381 1 + 647215 C - -a -s simMouse_chr6.simMouse.chr6 90054 16 + 636262 AGGCAAGCGGGTGCAA -s Anc0.Anc0refChr4 31933 16 - 45765 AGGGAAGTGGATTCAA -s Anc1.Anc1refChr2 63603 16 + 144309 AGGGAAGTGGATTCAA -s Anc2.Anc2refChr2 643 16 + 27695 AGGGAAGTGGATTAAA -s mr.mrrefChr0 85313 16 + 130230 AGGCAAGCGGGTGCAA -s simCow_chr6.simCow.chr6 90703 16 + 602619 AGGGAAGGGGATTAAA -s simCow_chr6.simCow.chr6 294679 16 - 602619 AAGGAAGAGGATTAAA -s simDog_chr6.simDog.chr6 191681 16 + 593897 AGGGGAGTGCACTTAA -s simHuman_chr6.simHuman.chr6 84578 16 + 601863 AGGGAAGTGGATTCTA -s simRat_chr6.simRat.chr6 82382 16 + 647215 AGGCAAGCAGGTGCAA - -a -s simMouse_chr6.simMouse.chr6 90070 27 + 636262 GTATCCAAACTCATGTAGGGATAAAGC -s Anc0.Anc0refChr4 31949 27 - 45765 TGGTCCAAATTGGTGTAGAAATAAAGG -s Anc1.Anc1refChr2 63619 27 + 144309 TGGTCCAAATTGGTGTAGAAATAAAGG -s Anc2.Anc2refChr2 660 27 + 27695 TGGTCCAAATTGGTGTAGAAATAAAGG -s mr.mrrefChr0 85329 27 + 130230 TTGTCCAAACTCATGTAGAGATAAAGG -s simCow_chr6.simCow.chr6 90720 27 + 602619 TGGTCCGAGTTGGTGTAGAAATAAAGG -s simCow_chr6.simCow.chr6 294696 27 - 602619 TGGTCCAAGTTGGTGTAGAAATAAAGG -s simDog_chr6.simDog.chr6 191697 27 + 593897 TGGTCCAAATTGGTGTAGAAATAGAGG -s simHuman_chr6.simHuman.chr6 84594 27 + 601863 TGGTCCAAATTGGTATGGAAATAAAGG -s simRat_chr6.simRat.chr6 82398 27 + 647215 TTGTCCAGACTCATGTAGAGATGAAGG - -a -s simMouse_chr6.simMouse.chr6 90097 2 + 636262 TA -s Anc0.Anc0refChr4 31976 2 - 45765 TG -s Anc1.Anc1refChr2 63646 2 + 144309 TG -s Anc2.Anc2refChr2 687 2 + 27695 TG -s mr.mrrefChr0 85356 2 + 130230 TG -s simCow_chr6.simCow.chr6 90747 2 + 602619 TA -s simCow_chr6.simCow.chr6 294723 2 - 602619 TG -s simDog_chr6.simDog.chr6 191732 2 + 593897 TG -s simHuman_chr6.simHuman.chr6 84621 2 + 601863 TG -s simRat_chr6.simRat.chr6 82425 2 + 647215 TG - -a -s simMouse_chr6.simMouse.chr6 90099 30 + 636262 AGCCTAGGTCTGGTGTGTGGGATATACCTG -s Anc0.Anc0refChr4 32062 30 - 45765 AGCCTGTGTCTAATGTGTGGGATACACCTG -s Anc1.Anc1refChr2 63732 30 + 144309 AGCCTGTGTCTAATGTGTGGGATACACCTG -s Anc2.Anc2refChr2 775 30 + 27695 GGCTTGTCTCTAATGTGTGGGATACACCTG -s mr.mrrefChr0 85358 30 + 130230 AGCCTAGGTCTGGTGTGTGGGATATACCTG -s simCow_chr6.simCow.chr6 90825 30 + 602619 GACTTGTATATAATCTGTGGGTTACGCCTG -s simDog_chr6.simDog.chr6 191821 30 + 593897 GGCTTGTCCCTCATGTGTGGGATACACCTG -s simHuman_chr6.simHuman.chr6 84707 30 + 601863 ATCCTGTGTCTAATATGTGGGATACACCTG -s simRat_chr6.simRat.chr6 82427 30 + 647215 AGCCTAGGTATGGCGTGTGGGATAGACCTG - -a -s simMouse_chr6.simMouse.chr6 90129 56 + 636262 AATAATTGAGTGAATAGCAAACTGTGCATGGGTCCCACTGGTGCTGCCAAATACCC -s Anc0.Anc0refChr4 32092 56 - 45765 GCTAATTGAGTGAATACCAAGCTGTGGTAAGCTTTCACTAGTGTTGTCTAATCCCC -s Anc1.Anc1refChr2 63762 56 + 144309 GCTAATTGAGTGAATACCAAGCTGTGGTAAGCTTTCACTAGTGTTGTCTAATCCCC -s Anc2.Anc2refChr2 805 56 + 27695 GCTACTTGAGTGAATACCAAGCTGTGGTAAGCTTTCACTAGTGTTGTTTAATCTCC -s mr.mrrefChr0 85388 56 + 130230 GCTAATTGAGTGAATAGCAAACTGTGCAAAGGTCCCACTGGTGCTGCCAAATCCCC -s simCow_chr6.simCow.chr6 90855 55 + 602619 G-TACTAGGGTGAATACCAAGCTGTGGGAAGCTTTCACTAGTGTTGTTAAATCTCC -s simDog_chr6.simDog.chr6 191851 56 + 593897 GCTACTTGAGTTAATATCGAGCTGTGGTAAGGTTACACTAGTGTTGCTTGATTTGT -s simHuman_chr6.simHuman.chr6 84758 56 + 601863 CCTAATTGAGTGAACCCCAAGCTGTGGCAAGCTTTCACTAGTGTTGTCTAATCCCC -s simRat_chr6.simRat.chr6 82457 56 + 647215 GCTAATCGAGTGAATGGCAACCTGTGCAAAGGTCCCACTGGTGCTGCCAAATCCCC - -a -s simMouse_chr6.simMouse.chr6 90185 25 + 636262 CACTCATTCACTCACTCAACCCTAT -s Anc0.Anc0refChr4 32148 17 - 45765 CAGTCACTCAC--------CCTTAC -s Anc1.Anc1refChr2 63818 17 + 144309 CAGTCACTCAC--------CCTTAC -s Anc2.Anc2refChr2 861 17 + 27695 CAGTCACTCAC--------CATTAC -s mr.mrrefChr0 85444 25 + 130230 CACTCACTCACTCACTCAACCTTAT -s simCow_chr6.simCow.chr6 90928 17 + 602619 CATTCACACAC--------CATTAC -s simDog_chr6.simDog.chr6 191907 17 + 593897 GAGTCACTCAC--------CATCAC -s simHuman_chr6.simHuman.chr6 84814 17 + 601863 CAGTCACTCAC--------CCTTAC -s simRat_chr6.simRat.chr6 82513 17 + 647215 CACTCACTCGC--------ACTTAT - -a -s simMouse_chr6.simMouse.chr6 90210 6 + 636262 AACAGT -s Anc0.Anc0refChr4 32165 6 - 45765 TGGTGT -s Anc1.Anc1refChr2 63835 6 + 144309 TGGTGT -s Anc2.Anc2refChr2 878 6 + 27695 TGGTGT -s mr.mrrefChr0 85469 6 + 130230 AACAGT -s simCow_chr6.simCow.chr6 90953 6 + 602619 TGGTTT -s simDog_chr6.simDog.chr6 191924 6 + 593897 TTATGT -s simHuman_chr6.simHuman.chr6 84831 6 + 601863 TGGGGT -s simRat_chr6.simRat.chr6 82530 6 + 647215 GACAGT - -a -s simMouse_chr6.simMouse.chr6 90216 10 + 636262 ATTTTATCAG -s Anc0.Anc0refChr4 32171 10 - 45765 GTTTTGTAAG -s Anc1.Anc1refChr2 63841 10 + 144309 GTTTTGTAAG -s Anc2.Anc2refChr2 896 10 + 27695 TTTTTGTAAG -s mr.mrrefChr0 85475 10 + 130230 GTTTTATCAG -s simCow_chr6.simCow.chr6 90971 10 + 602619 TTTTTGTATG -s simDog_chr6.simDog.chr6 191945 10 + 593897 TTTTTGTAAG -s simHuman_chr6.simHuman.chr6 84837 10 + 601863 GTCTATCTTA -s simRat_chr6.simRat.chr6 82536 10 + 647215 GTTTTATCAG - -a -s simMouse_chr6.simMouse.chr6 90226 2 + 636262 TA -s Anc0.Anc0refChr4 32181 2 - 45765 TA -s Anc1.Anc1refChr2 63851 2 + 144309 TA -s Anc2.Anc2refChr2 906 2 + 27695 TA -s mr.mrrefChr0 85485 2 + 130230 TA -s simCow_chr6.simCow.chr6 90983 2 + 602619 TA -s simDog_chr6.simDog.chr6 191955 2 + 593897 TA -s simHuman_chr6.simHuman.chr6 84847 2 + 601863 AA -s simRat_chr6.simRat.chr6 82546 2 + 647215 TA - -a -s simMouse_chr6.simMouse.chr6 90228 37 + 636262 AGTAGTATTTGTGTGTAGCATATGTCACAGTCCATCC -s Anc0.Anc0refChr4 32183 37 - 45765 CCTGTTACTTGTATGTAACTGCTGTCACACTCCATCC -s Anc1.Anc1refChr2 63853 37 + 144309 CCTGTTACTTGTATGTAACTGCTGTCACACTCCATCC -s Anc2.Anc2refChr2 911 37 + 27695 CCTGTTTCTTGTATGTAACTGCTGTCACACTCCATAC -s mr.mrrefChr0 85487 37 + 130230 AGTAGTACTTGTGTGTAACTTATGTCACAGTCCATCC -s simCow_chr6.simCow.chr6 90988 36 + 602619 GCCGTTTTTTGTATGTAACTTCTGTTACA-TCTATTC -s simDog_chr6.simDog.chr6 191960 37 + 593897 CCTGTTTCTTGTATGTAACCGCTGTCACACTCCATAC -s simHuman_chr6.simHuman.chr6 84849 37 + 601863 CCTGCTACTTATATGTAACTGCAATCACACTCCATCC -s simRat_chr6.simRat.chr6 82548 37 + 647215 AGGCGTGCTTGTGCGTAACTTTTGTCACAGTCTGTCC - -a -s simMouse_chr6.simMouse.chr6 90265 25 + 636262 CAGCATGAGGACCTATCAGGGAGGC -s Anc0.Anc0refChr4 32222 22 - 45765 AAGCATGAAAAGCTCTCAGGGA--- -s Anc1.Anc1refChr2 63892 22 + 144309 AAGCATGAAAAGCTCTCAGGGA--- -s Anc2.Anc2refChr2 950 22 + 27695 GAGCATGAAAAGCTCTCAGGGA--- -s mr.mrrefChr0 85524 25 + 130230 AAGCATGAGGAGCTATCAGGGAGGC -s simCow_chr6.simCow.chr6 91026 22 + 602619 GAGAATCAGAGGCTCTCAGGGA--- -s simDog_chr6.simDog.chr6 191999 22 + 593897 GAGCATGAAAAACTCTCAGTGA--- -s simHuman_chr6.simHuman.chr6 84888 22 + 601863 AGGCATAAACAGCTCTCCAGGA--- -s simRat_chr6.simRat.chr6 82585 25 + 647215 AAGCATGAGGAGCTATCAGGGAGGC - -a -s simMouse_chr6.simMouse.chr6 90290 20 + 636262 CCTTGGTCAGTTCTTCTTGT -s Anc0.Anc0refChr4 32244 19 - 45765 CCTCAGT-GGCTCTTCTCAT -s Anc1.Anc1refChr2 63914 19 + 144309 CCTCAGT-GGCTCTTCTCAT -s Anc2.Anc2refChr2 972 19 + 27695 CATCAGT-GGCTCGACTCAT -s mr.mrrefChr0 85549 20 + 130230 CCTCGGTCAGTTCTTCTTTT -s simCow_chr6.simCow.chr6 91048 19 + 602619 TGTCAGT-GGCTCAGCTAGT -s simDog_chr6.simDog.chr6 192023 19 + 593897 CACCAGT-GGCCCGATTCAT -s simHuman_chr6.simHuman.chr6 84910 19 + 601863 CCTCAGT-GGCTCTTCTCAT -s simRat_chr6.simRat.chr6 82610 20 + 647215 CCTCGATCAGTTCTTCTTTT - -a -s simMouse_chr6.simMouse.chr6 90310 56 + 636262 ATCAGAGTTTTTGCCATGGATACAGGTACCTTTAATTGTATCAGCCATAGCCATAA -s Anc0.Anc0refChr4 32268 36 - 45765 ATCAGAATTTCTGCATTGA--------------AATGACAG------TAGCCATAA -s Anc1.Anc1refChr2 63938 36 + 144309 ATCAGAATTTCTGCATTGA--------------AATGACAG------TAGCCATAA -s Anc2.Anc2refChr2 996 36 + 27695 CTCAGAATTTCTGCATTGA--------------AATGACAG------TAGCCAGAA -s mr.mrrefChr0 85574 50 + 130230 ATCAGAGTTTTTGCCATGGATACAGGTACCTTTAATGGTAT------TAGCCATAA -s simCow_chr6.simCow.chr6 91072 35 + 602619 CTCAGAATTT-TACATTGG--------------AACAAGGA------TAGCCTTTA -s simDog_chr6.simDog.chr6 192047 36 + 593897 CCCAGAATTTCTGCATTGA--------------AATGACAG------TAGCCAGAA -s simHuman_chr6.simHuman.chr6 84934 15 + 601863 ATCAGAAT-----------------------------------------GCCTTCA -s simRat_chr6.simRat.chr6 82635 50 + 647215 CTTAGAGTTTTTGCCCTGGGCACAGGTATCTTTAATGGTAT------TAGCCATAA - -a -s simMouse_chr6.simMouse.chr6 90366 33 + 636262 ATGGTACTGGGTTGAGCAGGTGTTAGACTGAGG -s Anc0.Anc0refChr4 32304 30 - 45765 A---AACTGGGCAGAGCAAATGTTAGACTAAGG -s Anc1.Anc1refChr2 63974 30 + 144309 A---AACTGGGCAGAGCAAATGTTAGACTAAGG -s Anc2.Anc2refChr2 1034 30 + 27695 A---AACTGGGCAGAGCAAATGGTAGACTAAGG -s mr.mrrefChr0 85624 33 + 130230 ATGGTACTGGGCAGAGCAGGTGTTAGACTAAGG -s simCow_chr6.simCow.chr6 91109 27 + 602619 A---TACTGGGCAGAGCAAA---TAGACTAAGG -s simDog_chr6.simDog.chr6 192085 23 + 593897 A---AACTGGGCAGAGCAAATGGTAG------- -s simHuman_chr6.simHuman.chr6 84949 30 + 601863 A---AAATGGGCAGAGCAAATGTTAGACTAAGG -s simRat_chr6.simRat.chr6 82685 29 + 647215 ATGGTACCGGACAGAGCAGGT----GACTAATG - -a -s simMouse_chr6.simMouse.chr6 90399 5 + 636262 TTGTC -s Anc0.Anc0refChr4 32346 5 - 45765 TTGTC -s Anc1.Anc1refChr2 64016 5 + 144309 TTGTC -s Anc2.Anc2refChr2 1076 5 + 27695 TTGTC -s mr.mrrefChr0 85657 5 + 130230 TTGTC -s simCow_chr6.simCow.chr6 91149 5 + 602619 TTGTC -s simHuman_chr6.simHuman.chr6 84991 5 + 601863 TTGCC -s simRat_chr6.simRat.chr6 82714 5 + 647215 TCGTC - -a -s simMouse_chr6.simMouse.chr6 90404 73 + 636262 AAACATTTGTCAAGCAAGGTAATACATACCAGAAGTGCTCTGGCAACACTATTGGAGCCTCATTTTCTTCTAA -s Anc0.Anc0refChr4 32351 52 - 45765 AACCCTTTGTCAAGCAA--------ATGACA-------------AATACTGTTGGAGCCAAATGTTCTTCCAA -s Anc1.Anc1refChr2 64021 52 + 144309 AACCCTTTGTCAAGCAA--------ATGACA-------------AATACTGTTGGAGCCAAATGTTCTTCCAA -s Anc2.Anc2refChr2 1081 52 + 27695 AAACCTTGGTCGCCCAA--------ATTACA-------------AATGCTGTTGGAGCCAAATGTTCTCCCAA -s mr.mrrefChr0 85662 71 + 130230 AACCATTTGTCAAGCAAGGTAAT--ATGCCAGAAGTGCTCTGGCAACACTGTTGGAGCCACATTTTCTTCTAA -s simCow_chr6.simCow.chr6 91154 52 + 602619 AAACCTTGGTCGCCCAA--------GTTATA-------------ATTTGTGTTGGAGCCAAATGTTCTCCCAA -s simDog_chr6.simDog.chr6 192108 35 + 593897 -------------------------ATTACA-------------AATGCTGCTGGAGCCAAATGTTCTCCTAA -s simHuman_chr6.simHuman.chr6 84996 52 + 601863 AACCTCTTGTCAAGCAA--------ATGACA-------------CATACTGTTGGATCCAAATGTTCTTCCAA -s simRat_chr6.simRat.chr6 82720 71 + 647215 AACCATTTGTCAAGCATGGTAAT--ATGCCAGAAGCGCTGTGGCAACACTGTAGGAGCCACATTTTCTTCTAA - -a -s simMouse_chr6.simMouse.chr6 90477 37 + 636262 CCCAAAGGGGGATCGTGAAGTGGGTCTAATGTTATCA -s Anc0.Anc0refChr4 32404 37 - 45765 CCCAGAAGGAGGGTTCTAGATGGGTTTAATGTTATCA -s Anc1.Anc1refChr2 64074 37 + 144309 CCCAGAAGGAGGGTTCTAGATGGGTTTAATGTTATCA -s Anc2.Anc2refChr2 1134 37 + 27695 CCCAGAAGGAGGGTTCTAGATGAGTTTAATGCTATCA -s mr.mrrefChr0 85733 37 + 130230 CCCAGAGGGGGGTTGTGAAGTGGGTTTAATGTTATCA -s simCow_chr6.simCow.chr6 91207 37 + 602619 CCCAAAAGCAAGGGTCTAGGTGAATTTAATGCTATTG -s simDog_chr6.simDog.chr6 192144 37 + 593897 TACAGAAGGGGGGTTCCATATCAGTATAATGCTTTCA -s simHuman_chr6.simHuman.chr6 85049 37 + 601863 CCCAGAAGGAGGGTTCTAGATGGGTTTAATGTTATCA -s simRat_chr6.simRat.chr6 82791 37 + 647215 CCCAGATGGGGGTTGTGAAGTGGGTTTAATGTTATCA - -a -s simMouse_chr6.simMouse.chr6 90514 17 + 636262 GGATAGGTGGTGCATTG -s Anc0.Anc0refChr4 32441 17 - 45765 GGATAGGTGGTGCATTG -s Anc1.Anc1refChr2 64111 17 + 144309 GGATAGGTGGTGCATTG -s Anc2.Anc2refChr2 1171 17 + 27695 GGATAGGTGGTGCAGTG -s mr.mrrefChr0 85770 17 + 130230 GGATAGGTGGTGCATTG -s simCow_chr6.simCow.chr6 91244 17 + 602619 GGATAGGCAGTGCGGTG -s simDog_chr6.simDog.chr6 192181 17 + 593897 GGATAGGTGGTGCAGAG -s simHuman_chr6.simHuman.chr6 85087 17 + 601863 GGATAGATGGTGCATTG -s simRat_chr6.simRat.chr6 82828 17 + 647215 GGATAGGTGATGCATTT - -a -s simMouse_chr6.simMouse.chr6 90531 17 + 636262 AGAACCTCTAATCGATC -s Anc0.Anc0refChr4 32458 17 - 45765 AGAATCTATAGTTAATC -s Anc1.Anc1refChr2 64128 17 + 144309 AGAATCTATAGTTAATC -s Anc2.Anc2refChr2 1188 17 + 27695 AGAATCTATAGTTCATC -s mr.mrrefChr0 85787 17 + 130230 AGAACCTATAATCAATC -s simCow_chr6.simCow.chr6 91261 17 + 602619 AGAACCTACAATCCATC -s simDog_chr6.simDog.chr6 192200 17 + 593897 AGAATCTTTAGTTCATC -s simHuman_chr6.simHuman.chr6 85104 17 + 601863 AGAAACCATAGTTAATC -s simRat_chr6.simRat.chr6 82845 17 + 647215 TGAACCTATAATCAATC - -a -s simMouse_chr6.simMouse.chr6 90548 20 + 636262 CAAAATTAAAAGGTTAGTCA -s Anc0.Anc0refChr4 32475 20 - 45765 TATGGTTAAAAGGTAAGTGC -s Anc1.Anc1refChr2 64145 20 + 144309 TATGGTTAAAAGGTAAGTGC -s Anc2.Anc2refChr2 1205 20 + 27695 TATTGTTAAAAGGTAAGTGC -s mr.mrrefChr0 85804 20 + 130230 CAAGGTTAAAAGGTTAGTCA -s simCow_chr6.simCow.chr6 91280 20 + 602619 TATTATTAAAAGGTAAATGC -s simDog_chr6.simDog.chr6 192217 20 + 593897 AATTGTTGAAAGGTAAGCGC -s simHuman_chr6.simHuman.chr6 85121 20 + 601863 TATGGTTAAAAGGTAAGTTC -s simRat_chr6.simRat.chr6 82862 20 + 647215 CAAGGTTAAAAGGCTAGTCA - -a -s simMouse_chr6.simMouse.chr6 90568 22 + 636262 GGACAATACTGATGCCAGTATT -s Anc0.Anc0refChr4 32499 22 - 45765 GAGTAACATTAATGCCAGTACA -s Anc1.Anc1refChr2 64169 22 + 144309 GAGTAACATTAATGCCAGTACA -s Anc2.Anc2refChr2 1229 22 + 27695 GAGTTACATTAATGCTAGTACA -s mr.mrrefChr0 85824 22 + 130230 GAACAATACTGATGCCAGTATT -s simCow_chr6.simCow.chr6 91304 22 + 602619 GAGTTGCATTAATGCGAGTACA -s simDog_chr6.simDog.chr6 192241 21 + 593897 GAGGTACATTGATGCTGGTAT- -s simHuman_chr6.simHuman.chr6 85145 22 + 601863 GAGTAACATTAATGCCAGTACA -s simRat_chr6.simRat.chr6 82882 22 + 647215 GAACAATACTGATGCTGGCATT - -a -s simMouse_chr6.simMouse.chr6 90590 3 + 636262 TGG -s Anc0.Anc0refChr4 32526 3 - 45765 TGA -s Anc1.Anc1refChr2 64196 3 + 144309 TGA -s Anc2.Anc2refChr2 1256 3 + 27695 TGA -s mr.mrrefChr0 85851 3 + 130230 TGG -s simCow_chr6.simCow.chr6 91331 3 + 602619 TGA -s simDog_chr6.simDog.chr6 192267 3 + 593897 TGA -s simHuman_chr6.simHuman.chr6 85172 3 + 601863 TGA -s simRat_chr6.simRat.chr6 82909 3 + 647215 TGG - -a -s simMouse_chr6.simMouse.chr6 90593 35 + 636262 GCCGGTAATAATGTCCAAACGACGGGATGGTCATA -s Anc0.Anc0refChr4 32533 33 - 45765 GCAGGTGGTAAC-TCCAATC-ATGGAAGAAACATA -s Anc1.Anc1refChr2 64203 33 + 144309 GCAGGTGGTAAC-TCCAATC-ATGGAAGAAACATA -s Anc2.Anc2refChr2 1263 33 + 27695 GCAGGTGGTAAC-TCCAATC-ATGGAAGAAACATA -s mr.mrrefChr0 85854 35 + 130230 GCCGGTAGTAATGTCCAAACGACGGGATGATCATA -s simCow_chr6.simCow.chr6 91340 33 + 602619 GCAGGTGGTAAC-TCCAATC-ATGGAAGACACATA -s simDog_chr6.simDog.chr6 192274 33 + 593897 GCAGGTGGTAAT-TACAATC-ACACAAGAAACATA -s simHuman_chr6.simHuman.chr6 85179 33 + 601863 GCAGGTGGTAAC-TCCAATC-ATGGAACAGCCGTA -s simRat_chr6.simRat.chr6 82912 35 + 647215 GCTGCTCGTAATGTCCAAACAATGGGATGATCATA - -a -s simMouse_chr6.simMouse.chr6 90628 16 + 636262 GGTGCTCTATCCAGGT -s Anc0.Anc0refChr4 32566 15 - 45765 GGTGCCCATCC-AGGC -s Anc1.Anc1refChr2 64236 15 + 144309 GGTGCCCATCC-AGGC -s Anc2.Anc2refChr2 1296 15 + 27695 GGTGCCCATCC-AGGC -s mr.mrrefChr0 85889 15 + 130230 GGTGCTCTATC-AGGT -s simCow_chr6.simCow.chr6 91373 15 + 602619 GGTATTCATCC-AGGC -s simDog_chr6.simDog.chr6 192307 15 + 593897 GGTGCCAATTG-AGGC -s simHuman_chr6.simHuman.chr6 85212 7 + 601863 GGc-----tcc-a--- -s simRat_chr6.simRat.chr6 82990 15 + 647215 GGTGCTCTATC-AGGT - -a -s simMouse_chr6.simMouse.chr6 90644 10 + 636262 ACTTATTTGG -s Anc0.Anc0refChr4 32581 10 - 45765 ACTTACTTGG -s Anc1.Anc1refChr2 64251 10 + 144309 ACTTACTTGG -s Anc2.Anc2refChr2 1311 10 + 27695 ACTTACTTGG -s mr.mrrefChr0 85904 10 + 130230 ACTTACTTGG -s simCow_chr6.simCow.chr6 91388 10 + 602619 AATTACACGG -s simDog_chr6.simDog.chr6 192326 10 + 593897 ACTTACTTGG -s simHuman_chr6.simHuman.chr6 85219 10 + 601863 actgtcaggg -s simRat_chr6.simRat.chr6 83005 10 + 647215 AATTACTTGG - -a -s simMouse_chr6.simMouse.chr6 90654 31 + 636262 GTACTACTCTTCTGGCTATGCACTACAATGA -s Anc1.Anc1refChr2 64271 31 + 144309 gtgccacaaaacagccaatccactaagaaga -s mr.mrrefChr0 85914 31 + 130230 GTACTACTCTTCTGGCTATGCACTACAATGA -s simHuman_chr6.simHuman.chr6 85253 31 + 601863 gtgccacaaaacagccaatccactaagaaga -s simRat_chr6.simRat.chr6 83015 31 + 647215 GTACTACTCTCCTGGTTATCCACTACAATGA - -a -s simMouse_chr6.simMouse.chr6 90685 42 + 636262 TGCAGATATGATAGGTCCCTTTCCTTTGGAATTACAAAAGAC -s Anc1.Anc1refChr2 64302 36 + 144309 tgcaggtatgat-ggtaactat-----gcaaaaaaagaaggc -s mr.mrrefChr0 85945 37 + 130230 TGCAGATATGATAGGTCCCTTT-----GGAATTACAAAAGAC -s simHuman_chr6.simHuman.chr6 85314 36 + 601863 tgcaggtatgat-ggtaactat-----gcaaaaaaagaaggc -s simRat_chr6.simRat.chr6 83046 37 + 647215 TGCAGATATGATGGGTCCCTTT-----GGAATTACAAAAGAC - -a -s simMouse_chr6.simMouse.chr6 90727 9 + 636262 ATGCATATT -s Anc1.Anc1refChr2 64338 9 + 144309 ataccaatt -s mr.mrrefChr0 85982 9 + 130230 ATGCATATT -s simHuman_chr6.simHuman.chr6 85361 9 + 601863 ataccaatt -s simRat_chr6.simRat.chr6 83083 9 + 647215 GTGCATATT - -a -s simMouse_chr6.simMouse.chr6 90736 11 + 636262 ATTGGGGAGAC -s Anc1.Anc1refChr2 64347 11 + 144309 ataggtcaggt -s mr.mrrefChr0 85991 11 + 130230 ATTGGGGAGAC -s simHuman_chr6.simHuman.chr6 85373 11 + 601863 ataggtcaggt -s simRat_chr6.simRat.chr6 83092 11 + 647215 TTTGGAGAGAA - -a -s simMouse_chr6.simMouse.chr6 90747 12 + 636262 GTACTATAAGTA -s Anc1.Anc1refChr2 64358 12 + 144309 atgctgtaagca -s mr.mrrefChr0 86002 12 + 130230 GTACTATAAGTA -s simHuman_chr6.simHuman.chr6 85390 12 + 601863 atgctgtaagca -s simRat_chr6.simRat.chr6 83103 12 + 647215 GTACTATAAGGA - -a -s simMouse_chr6.simMouse.chr6 90759 17 + 636262 AGCATTTTAACCTCAAC -s Anc0.Anc0refChr4 32607 16 - 45765 AGCATTTTAACC-CTGC -s Anc1.Anc1refChr2 64376 16 + 144309 AGCATTTTAACC-CTGC -s Anc2.Anc2refChr2 1337 16 + 27695 AGTATTTTAACC-CTGC -s mr.mrrefChr0 86014 17 + 130230 AGCATTTTAACCTCAAC -s simCow_chr6.simCow.chr6 91414 16 + 602619 AGTATTTTAACC-CTGT -s simDog_chr6.simDog.chr6 192352 15 + 593897 AA-ATTTTAACC-TTGC -s simHuman_chr6.simHuman.chr6 85461 16 + 601863 AGCATTTTAAGC-CTGC -s simRat_chr6.simRat.chr6 83115 17 + 647215 AAACTTTTTAACTCCAC - -a -s simMouse_chr6.simMouse.chr6 90776 3 + 636262 AGT -s Anc0.Anc0refChr4 32623 3 - 45765 TGA -s Anc1.Anc1refChr2 64392 3 + 144309 TGA -s Anc2.Anc2refChr2 1353 3 + 27695 TGA -s mr.mrrefChr0 86031 3 + 130230 AGT -s simCow_chr6.simCow.chr6 91430 3 + 602619 TGA -s simDog_chr6.simDog.chr6 192389 3 + 593897 TGA -s simHuman_chr6.simHuman.chr6 85477 3 + 601863 CGA -s simRat_chr6.simRat.chr6 83132 3 + 647215 AGG - -a -s simMouse_chr6.simMouse.chr6 90779 10 + 636262 GATGAGGAAA -s Anc0.Anc0refChr4 32627 10 - 45765 CATGAGGAAA -s Anc1.Anc1refChr2 64396 10 + 144309 CATGAGGAAA -s Anc2.Anc2refChr2 1357 10 + 27695 CATGAGGAAA -s mr.mrrefChr0 86035 10 + 130230 GATGAGGAAA -s simCow_chr6.simCow.chr6 91434 10 + 602619 CATGAGGGAG -s simDog_chr6.simDog.chr6 192393 10 + 593897 CATGAGGAAA -s simHuman_chr6.simHuman.chr6 85481 10 + 601863 CATGGGGAAA -s simRat_chr6.simRat.chr6 83136 10 + 647215 GATGAGGAAA - -a -s simMouse_chr6.simMouse.chr6 90789 32 + 636262 TGCAGGACCAAGATGGGGAAATACAGGACTAT -s Anc0.Anc0refChr4 32637 27 - 45765 ACCAGA--CACATTAA---GACAAAGGATTGT -s Anc1.Anc1refChr2 64406 27 + 144309 ACCAGA--CACATTAA---GACAAAGGATTGT -s Anc2.Anc2refChr2 1367 27 + 27695 ACCAGA--CACATTAA---GACAAAGGATTGT -s mr.mrrefChr0 86045 27 + 130230 TGCAGG--CAAGATGG---AACATAGGACTAT -s simCow_chr6.simCow.chr6 91444 27 + 602619 ACCGGA--AATATTAA---GACAAAGGATTGT -s simDog_chr6.simDog.chr6 192403 21 + 593897 ACCAGA--CACATTAA---GATAATG------ -s simHuman_chr6.simHuman.chr6 85492 27 + 601863 CATAGA--CACATTAA---GGCAAAGGGTTTT -s simRat_chr6.simRat.chr6 83146 27 + 647215 CGCAAG--CAAGATGG---AACATAGGACTAT - -a -s simMouse_chr6.simMouse.chr6 90821 58 + 636262 TGAGAACTCCAAGGCGAGGAGGCTGGTGCAATAAGGCTCTCACTGCATAAAAGAGATA -s Anc0.Anc0refChr4 32670 55 - 45765 TGAGAACTGCAAGGAGAGGA---TAGGGTAAGGTATCTCTCCCTGCACAGAAGAGAGA -s Anc1.Anc1refChr2 64439 55 + 144309 TGAGAACTGCAAGGAGAGGA---TAGGGTAAGGTATCTCTCCCTGCACAGAAGAGAGA -s Anc2.Anc2refChr2 1400 55 + 27695 TGAGAAATGCAAGGAGAGGA---TAGGGTAAGGTATCCATCCCTGCACAGAAGAGAGA -s mr.mrrefChr0 86072 58 + 130230 TGAGAACTCCAAGGCGAGGGGGCTGGTGCAATAAAGCTCTCACTGCATAGAAGAGATA -s simCow_chr6.simCow.chr6 91477 54 + 602619 TGAGAAATGCAAGGAGAGGA---TAGAGCATGCAACCTATGCC-GAACAGAAGGCAGA -s simDog_chr6.simDog.chr6 192428 55 + 593897 TGAGAAATGCAAGGGGAGGA---TAGGGTAAGGTATCCATCCCTGCACAGAAGAGAGA -s simHuman_chr6.simHuman.chr6 85525 36 + 601863 TGATAAC---AAGGA-------------------AACTCTAGTTTCACAGAAGAGAGA -s simRat_chr6.simRat.chr6 83173 58 + 647215 TGATAACTCCAACGTGAGGGGGCTCGTGCAACAAAGCTCTCACTGCATAGGAGAGATA - -a -s simMouse_chr6.simMouse.chr6 90879 206 + 636262 GGGTGGCAATGCTCCCCAATAGAAAATAATCCAGCATAGACCCATTGGGTTGCAGGAGTGGGGGACCACAGTCAATTGGCAGTGCCTGGAAAAGTCTAAACTCTATCTAGGAAAGTCATCTGCACTTAGAAACCTAGATGGGGGTTGCAACAACGGGGGACCACTGTCAGTTGGTGGCTATGCCTATAGATGGTCTAAATTCTAGC -s Anc0.Anc0refChr4 32725 110 - 45765 AGGTAATAATAGACCTGAGTAAAAAATAATCCAGATTAGACTCATTAGGTTGCAGGAATGGAGGACCACAATCAGTTGGCA-------------------------------------------------------------------------------------TCAGT---G---TAT-----TGAAAAGTCTAAAGTCTAGC -s Anc1.Anc1refChr2 64494 113 + 144309 AGGTAATAATAGACCTGAGTAAAAAATAATCCAGATTAGACTCATTAGGTTGCAGGAATGGAGGACCACAATCAGTTGGCA-------------------------------------------------------------------------------------TCAGT---GAATTAT-----TGAAAAGTCTAAAGTCTAGC -s Anc2.Anc2refChr2 1455 110 + 27695 AGGTAATAATAGACCTGAGTAAAAAATAATCCAAATTAGACTCAACAGGTTGTAGGAATGGAGGACCACAATCTGTTGGCA-------------------------------------------------------------------------------------AGAGT---G---CAT-----TGAAAAGTCCAAAGTGTAGC -s mr.mrrefChr0 86130 202 + 130230 GGGTGGCAATACTCCCCAATAGAAAATAATCCAGCATAGACTCATTGGGTTGCAGGAGTGGGGGACCACAGTCAATTGGCAGTGCCTGGAAAAGTCTAAACTCTATCTAGGAAAGTCATCTGCACTTAGAAACCTAGATGGGGGTTGCAACAACGGGGGACCAC-GTCAGT---TGACTATGCCTATAAATGGTCTAAATTCTAGC -s simCow_chr6.simCow.chr6 91531 92 + 602619 AGATACTAATAGAATTGA-TATAAAATCATCCAAATTAGACTCAACTGCCTGTAGGGATGGAGGACCACA------------------------------------------------------------------------------------------------------------CAT-----TGAAAAGTCAAAAGTTTATC -s simDog_chr6.simDog.chr6 192485 108 + 593897 AGGTAATAATAGACCATAGTAAAAAACAATCCAAATCAGACTCAACAGGTTGT--TAATGGAGAACCTCAATCTGTTGGCA-------------------------------------------------------------------------------------AGAGT---G---CAT-----TCGAAAGTCCAGAGTGTAGC -s simHuman_chr6.simHuman.chr6 85561 113 + 601863 AGGTAATAACAGATCTGAGTAAAATATAATGCAGATTAGATTTATTAGGTTGCAGGAATGGAGGACTACAATCATTTAGCA-------------------------------------------------------------------------------------TCAGT---GAATTAT-----TGAAAAGTCTAAACTCTAAC -s simRat_chr6.simRat.chr6 83231 199 + 647215 GGGTGGCAAAACCCC---ATAGAAATTCATCTAGCCTAGACTAATTGGGTCGCAGGAGTGGGGGACCACAGTAAGCTGGCAGTGCCTGGAAAAGTCTAAACTCCAGCTAGGAAAGTCATCTGCACTTAGAAGAGAGTCTGTAGGTTGCAACAATCGGGGACCAC-GTTAGT---TGACTATGCCTAGAAATGTACTAAATTCTAGC - -a -s simMouse_chr6.simMouse.chr6 91085 58 + 636262 TAAAAAAGTCAGCTACATTTAGGACTTGCTAATATACATAAGAGTACCCACAATGGAC -s Anc0.Anc0refChr4 32837 56 - 45765 TAAAAATGGCAACCACACTT--AACTTGATTTTATACCTGAGATTGCCTAGCATGCGT -s Anc1.Anc1refChr2 64609 58 + 144309 TAAAAATGGCAACCACACTTAAAACTTGATTTTATACCTGAGATTGCCTAGCATGCGT -s Anc2.Anc2refChr2 1567 56 + 27695 TAAAAATGGCAACCACACTT--AACTTGATTTTATACCTGAGATTGCCTAGCATGCGT -s mr.mrrefChr0 86332 58 + 130230 TAAAAAAGTCAACTACATTTAGGACTTGCTAATATACATAAGAGTACCCACAATGGAC -s simCow_chr6.simCow.chr6 91625 54 + 602619 GAAAAATAGCAAAC-CACCT--AACTTGATTTC-TACCTGAGATTGCTTACCATGTAC -s simDog_chr6.simDog.chr6 192595 56 + 593897 TAAAAATGGCAACCACACTT--AGCTTGATTTTATACCCGAGATTGCCTTGCATGCGT -s simHuman_chr6.simHuman.chr6 85676 56 + 601863 TAAAAATGACAAC--CACTTAAAACTTGATTTTATACCTGAGATTGCCTATCATGACT -s simRat_chr6.simRat.chr6 83430 49 + 647215 TAAAAAAGTCCAATACATTTAGGACTTGCTAATATACATAAG---------AATGGAG - -a -s simMouse_chr6.simMouse.chr6 91143 44 + 636262 CTTGTGTAGTCTGTGACAAAACTATCAAAGACTTAGTGACTCTG -s Anc0.Anc0refChr4 32893 40 - 45765 C---TGTAGTCTGTAAGGAAAATATC-AAGACTTAGTGGTTCTG -s Anc1.Anc1refChr2 64667 44 + 144309 CTGGTGTAGTCTGTAAGGAAAATATCAAAGACTTAGTGGTTCTG -s Anc2.Anc2refChr2 1623 40 + 27695 C---TGTACTCTGTAATGAAAATAAC-GAGACTTAGTGGTTCTG -s mr.mrrefChr0 86390 44 + 130230 CTGGTGTAGTCTGTGAGAAAACTATCAAAGACTTAGTGGCTCTG -s simCow_chr6.simCow.chr6 91687 36 + 602619 T---TGTGCGCTGTAATGAAAATAAC-----TTCAGTGCTTCTG -s simDog_chr6.simDog.chr6 192651 40 + 593897 C---TGTACTCTGTAATGAGAATAAC-GAGACTTAGCAGTCCTG -s simHuman_chr6.simHuman.chr6 85732 44 + 601863 CTGGAGTAGTCTGTAAGGAAAATATCAAAGGCTTAGTGGTTCTG -s simRat_chr6.simRat.chr6 83479 44 + 647215 CTGGTGTAGTCTGTGAGAGAACTATATGAGACTTAGTGGCTCCG - -a -s simMouse_chr6.simMouse.chr6 91187 24 + 636262 GGGTTGAAGATATCTGATAAGATG -s Anc0.Anc0refChr4 32934 23 - 45765 GAGTTGAAGATAT-TACTAAGATG -s Anc1.Anc1refChr2 64712 23 + 144309 GAGTTGAAGATAT-TACTAAGATG -s Anc2.Anc2refChr2 1664 23 + 27695 GAGTTGAAGGTAT-TACTAAGATG -s mr.mrrefChr0 86434 24 + 130230 GGGTTGAAGATATCTGATAAGATG -s simCow_chr6.simCow.chr6 91725 23 + 602619 GATTTGAAGGTAT-TACTAAGATA -s simDog_chr6.simDog.chr6 192692 23 + 593897 GAGTTGAAGGTAT-TACTAAGATG -s simHuman_chr6.simHuman.chr6 85777 23 + 601863 GAAGTGAAGATAT-TACTAACGTG -s simRat_chr6.simRat.chr6 83523 24 + 647215 GGGTTGAAGATATCTGATAAGAGG - -a -s simMouse_chr6.simMouse.chr6 91211 2 + 636262 GT -s Anc0.Anc0refChr4 32957 2 - 45765 CT -s Anc1.Anc1refChr2 64735 2 + 144309 CT -s Anc2.Anc2refChr2 1687 2 + 27695 CT -s mr.mrrefChr0 86458 2 + 130230 GT -s simCow_chr6.simCow.chr6 91748 2 + 602619 GT -s simDog_chr6.simDog.chr6 192716 2 + 593897 CT -s simHuman_chr6.simHuman.chr6 85800 2 + 601863 CT -s simRat_chr6.simRat.chr6 83547 2 + 647215 GT - -a -s simMouse_chr6.simMouse.chr6 91213 17 + 636262 CAAATAATATATTAATC -s Anc0.Anc0refChr4 32959 17 - 45765 CAAGTAATATGCTGATC -s Anc1.Anc1refChr2 64737 17 + 144309 CAAGTAATATGCTGATC -s Anc2.Anc2refChr2 1689 17 + 27695 CAAATAATATGCTGATC -s mr.mrrefChr0 86460 17 + 130230 CAAGTAATATATTAATC -s simCow_chr6.simCow.chr6 91750 17 + 602619 CAACTAATATGCTGATA -s simDog_chr6.simDog.chr6 192718 13 + 593897 CAAACAATAAG----CC -s simHuman_chr6.simHuman.chr6 85802 17 + 601863 CAAGTAATATGATGATC -s simRat_chr6.simRat.chr6 83551 17 + 647215 CAAGTAATAGATTATTC - -a -s simMouse_chr6.simMouse.chr6 91230 73 + 636262 TCCACCTTGCATAAAGATGACCCACGCCATGGCAAAATTTAATTGGGTTCCATGTCCTATGGTACCTCTAATT -s Anc0.Anc0refChr4 32977 10 - 45765 TCACCATTGC--------------------------------------------------------------- -s Anc1.Anc1refChr2 64755 10 + 144309 TCACCATTGC--------------------------------------------------------------- -s Anc2.Anc2refChr2 1707 10 + 27695 TCACCATTGC--------------------------------------------------------------- -s mr.mrrefChr0 86478 73 + 130230 TCCACCTTGCATAAAGGTGACCCACGCCATGGCAAAATTTAATTGGGTTCCATGTGCTATGGTACCTCCAATT -s simCow_chr6.simCow.chr6 91768 10 + 602619 CCACCATTGC--------------------------------------------------------------- -s simDog_chr6.simDog.chr6 192732 10 + 593897 TCACCATTGT--------------------------------------------------------------- -s simHuman_chr6.simHuman.chr6 85820 10 + 601863 TTGCCATTGC--------------------------------------------------------------- -s simRat_chr6.simRat.chr6 83569 73 + 647215 TCCACCTTGCATAAAGGTGAACCAGGCCATGGCAAAACATAATTGGACTCCATGTGCTATGATACCTCCAAGC - -a -s simMouse_chr6.simMouse.chr6 91303 86 + 636262 AATCTGGTCACAGTAACTTGGGAAAAATAAATCAAGACAAGGGTGGCTGTTTCATAAAGATGACCCACGCCATGGCAAAATTTAAA -s Anc0.Anc0refChr4 32987 1 - 45765 -------------------------------------------------------------------------------------T -s Anc1.Anc1refChr2 64765 1 + 144309 -------------------------------------------------------------------------------------T -s Anc2.Anc2refChr2 1717 1 + 27695 -------------------------------------------------------------------------------------T -s mr.mrrefChr0 86551 52 + 130230 AATCTGGTCATAGTAGCTTGGGAAAAATAAATCAAGACAAGGGT----------------------------------AATTTAAA -s simCow_chr6.simCow.chr6 91778 1 + 602619 -------------------------------------------------------------------------------------T -s simDog_chr6.simDog.chr6 192742 1 + 593897 -------------------------------------------------------------------------------------T -s simHuman_chr6.simHuman.chr6 85830 1 + 601863 -------------------------------------------------------------------------------------T -s simRat_chr6.simRat.chr6 83644 25 + 647215 GGCAGGGTCATAGTAGC-------------------------------------------------------------ACACTAAC - -a -s simMouse_chr6.simMouse.chr6 91389 5 + 636262 TGGGT -s Anc0.Anc0refChr4 32988 5 - 45765 tggat -s Anc1.Anc1refChr2 64766 5 + 144309 TGGAT -s Anc2.Anc2refChr2 1751 5 + 27695 tagat -s mr.mrrefChr0 86603 5 + 130230 TGGGT -s simCow_chr6.simCow.chr6 91814 5 + 602619 tcgac -s simDog_chr6.simDog.chr6 192799 5 + 593897 taagt -s simHuman_chr6.simHuman.chr6 85831 5 + 601863 TGGAT -s simRat_chr6.simRat.chr6 83669 5 + 647215 TGTGT - -a -s simMouse_chr6.simMouse.chr6 91394 24 + 636262 TCCATGTCCTATGGTACCTCTAAT -s Anc0.Anc0refChr4 32993 18 - 45765 accatgtc-----actcctct-at -s Anc1.Anc1refChr2 64771 18 + 144309 ACCATGTC-----ACTCCTCT-AT -s Anc2.Anc2refChr2 1756 18 + 27695 accatctc-----actcttct-at -s mr.mrrefChr0 86608 22 + 130230 TCCATGTCC-ATGGTACCTCT-AT -s simCow_chr6.simCow.chr6 91819 18 + 602619 tccatctc-----actcttct-ct -s simDog_chr6.simDog.chr6 192804 18 + 593897 actatctc-----actcttct-ag -s simHuman_chr6.simHuman.chr6 85836 18 + 601863 GCCATGTC-----ACGCCTCT-AT -s simRat_chr6.simRat.chr6 83675 22 + 647215 TACATGGCC-ATGTGAAGTCT-AT - -a -s simMouse_chr6.simMouse.chr6 91418 45 + 636262 TAATCTGGTCACAGTAACTTGGGAAAAATAAATCAAGACAAGGGT -s Anc0.Anc0refChr4 33198 45 - 45765 TAATCTGGTCACAGAGACTTGGGAAAAAAAAGTGTAGACAAGGGT -s Anc1.Anc1refChr2 64976 45 + 144309 TAATCTGGTCACAGAGACTTGGGAAAAAAAAGTGTAGACAAGGGT -s Anc2.Anc2refChr2 1996 45 + 27695 TAATCTGGTCACAGAGACTTGGAAAAAAAAAGTGTAGGCAAGGGT -s mr.mrrefChr0 86630 45 + 130230 TAATCTGGTCACAGTAACTTGGGAAAAAATAATTAAGACAAGGGT -s simCow_chr6.simCow.chr6 92057 45 + 602619 TAATCTGGTCACAGGTACTTGGAAGAAAAAAGCATGGTCAAGGGT -s simDog_chr6.simDog.chr6 193045 45 + 593897 TAATCTGGTCACAGAGACTTGGAAAAAAAAAGTGTAGGCAAGGGT -s simHuman_chr6.simHuman.chr6 86042 45 + 601863 TAATCTGGTCCTAGAGGCTTGGGAAAAAAAAGTGTAGACAAGGGC -s simRat_chr6.simRat.chr6 83697 45 + 647215 TAATCTGGTCGCAGTAACTTGGGAAAAAATAATTGAGATAAGGGT - -a -s simMouse_chr6.simMouse.chr6 91463 5 + 636262 GGCTG -s Anc0.Anc0refChr4 33257 5 - 45765 GGCTG -s Anc1.Anc1refChr2 65035 5 + 144309 GGCTG -s Anc2.Anc2refChr2 2055 5 + 27695 AGCTG -s mr.mrrefChr0 86675 5 + 130230 GGCTG -s simCow_chr6.simCow.chr6 92116 5 + 602619 AGCTG -s simDog_chr6.simDog.chr6 193104 5 + 593897 AGCTG -s simHuman_chr6.simHuman.chr6 86101 5 + 601863 GGCCG -s simRat_chr6.simRat.chr6 83742 5 + 647215 AGGTG - -a -s simMouse_chr6.simMouse.chr6 91468 2 + 636262 TT -s Anc0.Anc0refChr4 33266 2 - 45765 TT -s Anc1.Anc1refChr2 65044 2 + 144309 TT -s Anc2.Anc2refChr2 2064 2 + 27695 TT -s mr.mrrefChr0 86680 2 + 130230 TT -s simCow_chr6.simCow.chr6 92125 2 + 602619 TC -s simDog_chr6.simDog.chr6 193113 2 + 593897 TT -s simHuman_chr6.simHuman.chr6 86110 2 + 601863 TG -s simRat_chr6.simRat.chr6 83747 2 + 647215 TT - -a -s simMouse_chr6.simMouse.chr6 91470 10 + 636262 TATTATGTGA -s Anc0.Anc0refChr4 33268 10 - 45765 GGTAATGGGA -s Anc1.Anc1refChr2 65046 10 + 144309 GGTAATGGGA -s Anc2.Anc2refChr2 2066 10 + 27695 GGAAATGGGA -s mr.mrrefChr0 86682 10 + 130230 TATTATGTGA -s simCow_chr6.simCow.chr6 92136 9 + 602619 GGAAATGGG- -s simDog_chr6.simDog.chr6 487518 6 - 593897 ----CTGGGA -s simHuman_chr6.simHuman.chr6 86112 10 + 601863 GGTAATGGGA -s simRat_chr6.simRat.chr6 83749 10 + 647215 AAATATGTGG - -a -s simMouse_chr6.simMouse.chr6 91480 25 + 636262 GGATAGAACAGTGTCTAGATTATCT -s Anc0.Anc0refChr4 33279 25 - 45765 GCCCTGGACAATATCTAGTTTATCT -s Anc1.Anc1refChr2 65057 25 + 144309 GCCCTGGACAATATCTAGTTTATCT -s Anc2.Anc2refChr2 2077 25 + 27695 ACCCTTGACAATATCTAGTTCATCT -s mr.mrrefChr0 86692 25 + 130230 GGCTAGAACAGTGTCTAGATTATCT -s simCow_chr6.simCow.chr6 92146 25 + 602619 ACCCTTGACAATATCTAGTTCATCT -s simHuman_chr6.simHuman.chr6 86123 25 + 601863 GTCCTGGACAATATCTGGTTTATGT -s simRat_chr6.simRat.chr6 83759 25 + 647215 GGCTAGCACAGTGTCTAGATTATCT - -a -s simMouse_chr6.simMouse.chr6 91505 32 + 636262 CTACTTGGTATACTCTCACTACATGTGGTGGG -s Anc0.Anc0refChr4 33304 24 - 45765 CTAATGACTATACCCCCCCAACAT-------- -s Anc1.Anc1refChr2 65082 24 + 144309 CTAATGACTATACCCCCCCAACAT-------- -s Anc2.Anc2refChr2 2102 24 + 27695 CTAATGACAATATCCCCCCAACAC-------- -s mr.mrrefChr0 86717 32 + 130230 CTACTTAGTATACTCTCACTACATGTGGTGGG -s simCow_chr6.simCow.chr6 92171 24 + 602619 CTAATGACAATATCCCCCCAACAC-------- -s simDog_chr6.simDog.chr6 487524 3 - 593897 ---------------------AAC-------- -s simHuman_chr6.simHuman.chr6 86149 24 + 601863 CTGATAACTATACACCCCCAACAT-------- -s simRat_chr6.simRat.chr6 83784 32 + 647215 TGACTCAATATACTCTCACTACATGGGGTGGG - -a -s simMouse_chr6.simMouse.chr6 91537 9 + 636262 GACAGATTA -s Anc0.Anc0refChr4 33328 9 - 45765 GACAAGTCA -s Anc1.Anc1refChr2 65106 9 + 144309 GACAAGTCA -s Anc2.Anc2refChr2 2126 9 + 27695 GACAAGTCT -s mr.mrrefChr0 86749 9 + 130230 GACAGATTA -s simCow_chr6.simCow.chr6 92203 9 + 602619 GACAGGTCT -s simDog_chr6.simDog.chr6 487527 9 - 593897 GACAAGTCT -s simHuman_chr6.simHuman.chr6 86173 9 + 601863 TACAAGTGA -s simRat_chr6.simRat.chr6 83816 9 + 647215 GACAGTTTA - -a -s simMouse_chr6.simMouse.chr6 91546 58 + 636262 TCCTCAATTAATATTGTTGGGATTATCCCTGAACCATCAATATATTCTTTATCTTAGG -s Anc0.Anc0refChr4 33337 58 - 45765 TCCTTAGCTGATCTTCTTGGGACTGTCCCTGAAACATCAATATGCCCTTTACCTAGGA -s Anc1.Anc1refChr2 65115 58 + 144309 TCCTTAGCTGATCTTCTTGGGACTGTCCCTGAAACATCAATATGCCCTTTACCTAGGA -s Anc2.Anc2refChr2 2135 58 + 27695 TCCTTAGCTGATCTTCTTGGGACTCACCCAGAAACATTAGTATGCCCTCAACCCAGGA -s mr.mrrefChr0 86758 58 + 130230 TCCTCAATTAATATTGTTGGGACTGTCCCTGAACCATCAATATATTCTTTATCTTAGG -s simCow_chr6.simCow.chr6 92216 41 + 602619 TCTTTAGCTTATCTTGGTGGTACTCCCTCAGAAACCTTGGT----------------- -s simDog_chr6.simDog.chr6 487536 58 - 593897 TCCTTAGCTGATCTTCTTGGGACTCACCCAGAGACATTAGTATGCCCTCAACCCAGGA -s simHuman_chr6.simHuman.chr6 86182 57 + 601863 TCCTAAGCGGATCTT-TCGGGACTGTCCCTGAAACATCAATAGGCCCCTTACCTAGGA -s simRat_chr6.simRat.chr6 83825 58 + 647215 CCCTCAATCAATATTGTTGGGACTGTCACTGTATCATCAATATATTCTTTATCTTAGG - -a -s simMouse_chr6.simMouse.chr6 91604 44 + 636262 GCCACCCAACACAACCGTCAACTAATCTAACATGGATGCCTATA -s Anc0.Anc0refChr4 33399 44 - 45765 CTTGCCTGATACAACCTACAACTAATATAATAAAGATGCCCTCA -s Anc1.Anc1refChr2 65177 44 + 144309 CTTGCCTGATACAACCTACAACTAATATAATAAAGATGCCCTCA -s Anc2.Anc2refChr2 2197 44 + 27695 CTTATCTGATACAACCTACAACTAATATAATAAAGATACCCTCA -s mr.mrrefChr0 86816 44 + 130230 GTTGCCCGATACAACCGTCAACTAATATAATATGGATGCCTATA -s simCow_chr6.simCow.chr6 92257 38 + 602619 ------AGATACAAGCTACAACAAAGATAATATAGATACCTTTA -s simDog_chr6.simDog.chr6 487598 42 - 593897 CTTATCTGATACAACCTACAACTAATATATTAAA--TACCCTCA -s simHuman_chr6.simHuman.chr6 86243 44 + 601863 CTTGCCGGATACGACCTACAACTAATATGATAGAGGTGCCCTCA -s simRat_chr6.simRat.chr6 83883 44 + 647215 GTTGCCTGATACAACCGTCAACTAATATAATATTGATGCCTATA - -a -s simMouse_chr6.simMouse.chr6 91648 77 + 636262 ACTTGATGCCCTCAGGTCAATGTATGGAGAGCAAGAAGTAAACATGATTCTTCAATAGCAGCACACTTCAACCATAT -s Anc0.Anc0refChr4 33444 69 - 45765 GGTCAATGTCCCTA--TTGCTGTATGGAGAATTAGAAG-TAACATGATTGTTGAATAGCAGCATACT-----TGGAA -s Anc1.Anc1refChr2 65222 70 + 144309 GGTCAATGTCCCTA--TTGCTGTATGGAGAATTAGAAGTTAACATGATTGTTGAATAGCAGCATACT-----TGGAA -s Anc2.Anc2refChr2 2242 69 + 27695 GGTCAATATCTCTG--ATGCTGTATGGAGAATTAGATG-TAGCATGATTGTTGAATAGCAGCATACT-----TGGAA -s mr.mrrefChr0 86860 76 + 130230 ACTTGATGCCCTCAGGTCAATGTATGGAGAGCAAGAAGTAAACATGATTCTTCAATAGCAGCACACTTCAA-TATAT -s simCow_chr6.simCow.chr6 92296 68 + 602619 GGCCAATATCTCTG--ATGCTGTATGACAAGCTAGATG-TAGCATAATTATTGA-CATCAGCATAAT-----TGGAA -s simDog_chr6.simDog.chr6 487641 69 - 593897 GGTCAATATCTCTG--AAACCGTATGGAGAATTAGATG-TAGCATGAGTGTTGAATAGCAGCATACT-----TGGAA -s simHuman_chr6.simHuman.chr6 86288 63 + 601863 GGTCACTGTCCCTA--TTGCTGTATGGAG-------ACTTTAGATGATTGTTGAATAGCAGCAGCCC-----TGGAA -s simRat_chr6.simRat.chr6 83927 76 + 647215 ACATTGTGCCCTCAGGTCAATGTATGGAGAGCAAGATGAAAGCATGATTCGTCAATAGCAGTGCACTTCAA-TATAT - -a -s simMouse_chr6.simMouse.chr6 91725 7 + 636262 TACCAAC -s Anc0.Anc0refChr4 33513 7 - 45765 TATCATC -s Anc1.Anc1refChr2 65292 7 + 144309 TATCATC -s Anc2.Anc2refChr2 2311 7 + 27695 CATCATC -s mr.mrrefChr0 86936 7 + 130230 TATCAAC -s simCow_chr6.simCow.chr6 92364 7 + 602619 CATCATC -s simDog_chr6.simDog.chr6 487711 7 - 593897 CATCATC -s simHuman_chr6.simHuman.chr6 86351 7 + 601863 TATCAGC -s simRat_chr6.simRat.chr6 84003 7 + 647215 TATCAAC - -a -s simMouse_chr6.simMouse.chr6 91732 12 + 636262 CCAGAGCTTCGC -s Anc0.Anc0refChr4 33520 12 - 45765 CCAGAGCATAGC -s Anc1.Anc1refChr2 65299 12 + 144309 CCAGAGCATAGC -s Anc2.Anc2refChr2 2322 12 + 27695 CCAGAGCACAGC -s mr.mrrefChr0 86943 12 + 130230 CCAGAGCTTCGC -s simCow_chr6.simCow.chr6 92375 12 + 602619 CCAGAGCACAGC -s simDog_chr6.simDog.chr6 487722 12 - 593897 CCAGAGCACAGC -s simHuman_chr6.simHuman.chr6 86358 11 + 601863 TT-GAGCATAGC -s simRat_chr6.simRat.chr6 84010 12 + 647215 CCGGAGCTTGGC - -a -s simMouse_chr6.simMouse.chr6 91744 13 + 636262 AGGCTAATACCCA -s Anc0.Anc0refChr4 33533 13 - 45765 AGGCTAGTACCAA -s Anc1.Anc1refChr2 65312 13 + 144309 AGGCTAGTACCAA -s Anc2.Anc2refChr2 2335 13 + 27695 AGGCTAATACCAT -s mr.mrrefChr0 86955 13 + 130230 AGGCTAGTACCCA -s simCow_chr6.simCow.chr6 92388 13 + 602619 AGGCTAATACCAT -s simDog_chr6.simDog.chr6 487735 12 - 593897 AGGCTGATAT-AT -s simHuman_chr6.simHuman.chr6 86370 13 + 601863 AGGCTAGTACCAA -s simRat_chr6.simRat.chr6 84022 12 + 647215 CGG-TAGAACTGA - -a -s simMouse_chr6.simMouse.chr6 91757 121 + 636262 CTCTTATATCAGATAGGCAGCGCCAGCACTGTCCAGCACTGTGGAAACAAACAATTATAAACTATGGGAAGGTGTAAAAACTGTATAGATCTATTGTGTTCTGTACCACTTTGGAGTTCCA -s Anc0.Anc0refChr4 33549 108 - 45765 CCCACATATCAGATAGGTA-------------CCAGCATTGTGAAAGAGAACAATTATAAGGTACTCAAAGGTATAAAAACAGTATGAATCAATAGGGTTCTGTCCCACTGTGGAGTTCCA -s Anc1.Anc1refChr2 65328 108 + 144309 CCCACATATCAGATAGGTA-------------CCAGCATTGTGAAAGAGAACAATTATAAGGTACTCAAAGGTATAAAAACAGTATGAATCAATAGGGTTCTGTCCCACTGTGGAGTTCCA -s Anc2.Anc2refChr2 2351 108 + 27695 CCTACATATAAGATAGGTA-------------CCAGCATTTAGAAAGAGAACAATTATAAGGTACTCAGAGGTATAAAAACAGTATGAATCATGAGGTTTCTGTCCCATTGTGGGGTTCCA -s mr.mrrefChr0 86968 115 + 130230 CCCTTATATCAGATAGGCAGCGCCAG------CCAGCACTGTGGAAACAAACAATTATAAACTATGGGAAGGTGTAAAAACTGTATAGATCTATTGTGTTCTGTACCACTTTGGAGTTCCA -s simCow_chr6.simCow.chr6 92404 105 + 602619 CCTACATACTAGATGGCTA----------------GCAATTCAAAAGAGAGCAATTATAAGGTATGCAGAGGTATAAAAACAGTATGTATCAGAAGGATTCTTTCCAATTCTAGGGTTCGG -s simDog_chr6.simDog.chr6 487750 104 - 593897 C--ACATATAAGATAGGGA-------------CCAGGATGTAGCAAAAAAACAATTATAGGGTACT--GAAGTATAAAAACAGTATGAGTCATGAGGTTCCTGTCCCATTGTGGGGTTCCA -s simHuman_chr6.simHuman.chr6 86386 108 + 601863 CCCACATATCAGATAGGTA-------------CCAACATTGTGAAAGGGAACAATTACAAGGTACTCTAAGGTCTAAAGACCGTATGAATCAATGGGGTTCTGTCCCACTGTGGAGTTCCA -s simRat_chr6.simRat.chr6 84034 52 + 647215 CCCTATTATCAGATAG---ACGCCAG------------------------------------------------------------------ATTATGTTCGGTATCATTATGGAGTCCCA - -a -s simMouse_chr6.simMouse.chr6 91878 3 + 636262 TTG -s Anc0.Anc0refChr4 33657 3 - 45765 TTG -s Anc1.Anc1refChr2 65436 3 + 144309 TTG -s Anc2.Anc2refChr2 2459 3 + 27695 TTG -s mr.mrrefChr0 87083 3 + 130230 TTG -s simCow_chr6.simCow.chr6 92509 3 + 602619 TTG -s simDog_chr6.simDog.chr6 487854 3 - 593897 TTG -s simHuman_chr6.simHuman.chr6 86495 3 + 601863 TTG -s simRat_chr6.simRat.chr6 84086 3 + 647215 TTG - -a -s simMouse_chr6.simMouse.chr6 91881 30 + 636262 GCCTATCATCTGGACATGTTAATGGTAGTT -s Anc0.Anc0refChr4 33661 30 - 45765 GCTTGTGGTCAGGACATCCTAGTAATAGTT -s Anc1.Anc1refChr2 65440 30 + 144309 GCTTGTGGTCAGGACATCCTAGTAATAGTT -s Anc2.Anc2refChr2 2463 30 + 27695 CCTTGTGGTCAGGACATCCTAGTAATAGTT -s mr.mrrefChr0 87086 30 + 130230 GCCTATCATCAGGACATGTTAGTGGTAGTT -s simCow_chr6.simCow.chr6 92513 27 + 602619 ACTTGTGGTCAGG---TCCTAGTAATAGTT -s simDog_chr6.simDog.chr6 487858 30 - 593897 CCTTGTGGTCGGGACATACTATTAATAATT -s simHuman_chr6.simHuman.chr6 86499 30 + 601863 GCTTGTAGTCAGGACATCCTGGTAATAGTT -s simRat_chr6.simRat.chr6 84089 30 + 647215 GTCTATCATCAGGACATGTTAGTGGTAGTT - -a -s simMouse_chr6.simMouse.chr6 91911 30 + 636262 GTCATGGAGAGTTAGCCAGACCTGAGCTTG -s Anc0.Anc0refChr4 33691 24 - 45765 GC--TGTGGGGTTAGACAGCCCTG----TC -s Anc1.Anc1refChr2 65470 24 + 144309 GC--TGTGGGGTTAGACAGCCCTG----TC -s Anc2.Anc2refChr2 2493 24 + 27695 GC--TGTGGGGTTGGACAGCCCTG----AC -s mr.mrrefChr0 87116 30 + 130230 GTCATGTGGAGTTAGCCAGACCTGAGCTTG -s simCow_chr6.simCow.chr6 92542 24 + 602619 GA--TGCAGGGTTGGATTCCCCGG----AC -s simDog_chr6.simDog.chr6 487898 24 - 593897 GC--TGTGGGCTTGGACAGCCCTG----AC -s simHuman_chr6.simHuman.chr6 86529 24 + 601863 GC--TGTGGGGTTAGACAGCCCTG----TC -s simRat_chr6.simRat.chr6 84119 30 + 647215 GTCATGTGGAGTTAGCCAGACCTGAGCTCG - -a -s simMouse_chr6.simMouse.chr6 91941 28 + 636262 TTCAGATCTGATTCAGGTGCCACTCTTA -s Anc0.Anc0refChr4 33715 23 - 45765 CTCAGATTTG-----GACACCACTCTTG -s Anc1.Anc1refChr2 65494 23 + 144309 CTCAGATTTG-----GACACCACTCTTG -s Anc2.Anc2refChr2 2517 23 + 27695 CTCAGATTTG-----GACAACACTCTTG -s mr.mrrefChr0 87146 28 + 130230 TTCAGATTTGATTCAGATACCACTCTTG -s simCow_chr6.simCow.chr6 92566 23 + 602619 CTCAGATTTG-----GACATCCCTCTTG -s simDog_chr6.simDog.chr6 487922 23 - 593897 CACAGATTTG-----GACAACACTCTTG -s simHuman_chr6.simHuman.chr6 86553 23 + 601863 CTCAGATTTG-----GACACCACTCTTG -s simRat_chr6.simRat.chr6 84160 28 + 647215 TTCAGATTTGATTCATATACCAGTATTG - -a -s simMouse_chr6.simMouse.chr6 91969 18 + 636262 AACCCCTAGAAACATTTG -s Anc0.Anc0refChr4 33739 18 - 45765 AATCTCTTGAAGCATTTG -s Anc1.Anc1refChr2 65518 18 + 144309 AATCTCTTGAAGCATTTG -s Anc2.Anc2refChr2 2541 18 + 27695 AATCTCTTGAAGCATTTG -s mr.mrrefChr0 87174 18 + 130230 AACCTCTAGAAACATTTG -s simCow_chr6.simCow.chr6 92590 18 + 602619 AATCTCATGAAGCATTTG -s simDog_chr6.simDog.chr6 487946 18 - 593897 TATCTCTCGAAGCATTTA -s simHuman_chr6.simHuman.chr6 86577 18 + 601863 AATCTCTTGAAGCCTTTG -s simRat_chr6.simRat.chr6 84188 18 + 647215 AACCTCTGGAAACATACA - -a -s simMouse_chr6.simMouse.chr6 91987 21 + 636262 CTGTACTGAGAGGTAAGTATG -s Anc0.Anc0refChr4 33757 16 - 45765 CTGTGTTGAGAAGGA-----A -s Anc1.Anc1refChr2 65536 20 + 144309 CTGTGTTGAGAAGGAA-TATA -s Anc2.Anc2refChr2 2560 16 + 27695 CTGTGTTGAGAAGGA-----A -s mr.mrrefChr0 87192 21 + 130230 CTGTACTGAGAGGTAAGTATG -s simCow_chr6.simCow.chr6 92609 16 + 602619 CTGTGAGGAGAGGGA-----A -s simDog_chr6.simDog.chr6 487965 16 - 593897 CTGTGTTGAGAAGGA-----A -s simHuman_chr6.simHuman.chr6 86595 11 + 601863 ATG----GAGA------TATA -s simRat_chr6.simRat.chr6 84206 21 + 647215 TTGTCCTGCGAGGTAAGTATG - -a -s simMouse_chr6.simMouse.chr6 92008 11 + 636262 TTGCTCTCTCA -s Anc0.Anc0refChr4 33773 11 - 45765 TTACTCCCTCT -s Anc1.Anc1refChr2 65556 11 + 144309 TTACTCCCTCT -s Anc2.Anc2refChr2 2576 11 + 27695 TTACTCCCTGT -s mr.mrrefChr0 87213 11 + 130230 TTACTCCCTCA -s simCow_chr6.simCow.chr6 92631 11 + 602619 TTACTCTCTGT -s simDog_chr6.simDog.chr6 487981 11 - 593897 CTACTCCCTGT -s simHuman_chr6.simHuman.chr6 86606 11 + 601863 TTACCCCCTCT -s simRat_chr6.simRat.chr6 84227 11 + 647215 TTACTCCCTCG - -a -s simMouse_chr6.simMouse.chr6 92019 9 + 636262 TCAACAAGT -s Anc0.Anc0refChr4 33784 9 - 45765 TCAATGGGT -s Anc1.Anc1refChr2 65567 9 + 144309 TCAATGGGT -s Anc2.Anc2refChr2 2587 9 + 27695 TCAATGCAT -s mr.mrrefChr0 87224 9 + 130230 TCAACAGGT -s simCow_chr6.simCow.chr6 92644 9 + 602619 TCAATGCAT -s simDog_chr6.simDog.chr6 487992 9 - 593897 TCAATGCAT -s simHuman_chr6.simHuman.chr6 86617 9 + 601863 TCAAAGGGT -s simRat_chr6.simRat.chr6 84238 9 + 647215 TCGACAGGT - -a -s simMouse_chr6.simMouse.chr6 92028 20 + 636262 GCAGTATACTGTGTTGCAGA -s Anc0.Anc0refChr4 33793 20 - 45765 tCaatgcattgtgttgctaa -s Anc1.Anc1refChr2 65576 20 + 144309 TCAATGCATTGTGTTGCTAA -s Anc2.Anc2refChr2 2599 20 + 27695 tCaatgcattgtgttgctaa -s mr.mrrefChr0 87233 20 + 130230 GCAATGCACTGTGTTGCAGA -s simCow_chr6.simCow.chr6 92656 20 + 602619 CTaatgcatggtgttgctca -s simDog_chr6.simDog.chr6 488004 20 - 593897 tcaatgcattgtgtcgctaa -s simHuman_chr6.simHuman.chr6 86626 20 + 601863 TCAATGCATTGTGTTGTTTA -s simRat_chr6.simRat.chr6 84247 20 + 647215 GCAATGCACCATGTTGCAGA - -a -s simMouse_chr6.simMouse.chr6 92048 6 + 636262 CTACAG -s Anc0.Anc0refChr4 33813 6 - 45765 atcccg -s Anc1.Anc1refChr2 65596 6 + 144309 ATCCCG -s Anc2.Anc2refChr2 2623 6 + 27695 agcccc -s mr.mrrefChr0 87253 6 + 130230 ATACAG -s simCow_chr6.simCow.chr6 92680 6 + 602619 agtacc -s simDog_chr6.simDog.chr6 488028 6 - 593897 agcccc -s simHuman_chr6.simHuman.chr6 86646 6 + 601863 ATCCCG -s simRat_chr6.simRat.chr6 84267 6 + 647215 AATCAG - -a -s simMouse_chr6.simMouse.chr6 92054 26 + 636262 TCCTTGCATCATAACAGATTTCATCT -s Anc0.Anc0refChr4 33822 18 - 45765 tccttgcaccgtaacaaa-------- -s Anc1.Anc1refChr2 65605 26 + 144309 TCCTTGCACCGTAACAAACTGTGACC -s Anc2.Anc2refChr2 2632 18 + 27695 tccttgcaccgtaacaaa-------- -s mr.mrrefChr0 87259 26 + 130230 TCCTTGCATCATAACAGATTTTGTCT -s simCow_chr6.simCow.chr6 92689 18 + 602619 tccttgcacggtaacaaa-------- -s simDog_chr6.simDog.chr6 488037 17 - 593897 tccttg-cccgtaataaa-------- -s simHuman_chr6.simHuman.chr6 86658 26 + 601863 TCCTTGGACTGTGACACACTGTGACC -s simRat_chr6.simRat.chr6 84273 26 + 647215 TCCCTGCATCATACTAAATTTTGTCT - -a -s simMouse_chr6.simMouse.chr6 92080 5 + 636262 GGTTG -s Anc0.Anc0refChr4 33857 5 - 45765 ggttg -s Anc1.Anc1refChr2 65648 5 + 144309 GGTTG -s Anc2.Anc2refChr2 2667 5 + 27695 ggttg -s mr.mrrefChr0 87285 5 + 130230 GGTTG -s simCow_chr6.simCow.chr6 92735 5 + 602619 ggttg -s simDog_chr6.simDog.chr6 488083 5 - 593897 ggttg -s simHuman_chr6.simHuman.chr6 86701 5 + 601863 GGTTG -s simRat_chr6.simRat.chr6 84299 5 + 647215 GGTTG - -a -s simMouse_chr6.simMouse.chr6 92085 14 + 636262 CCCAAACCCCTAGC -s Anc0.Anc0refChr4 33862 14 - 45765 cccaaacccccagt -s Anc1.Anc1refChr2 65653 14 + 144309 CCCAAACCCCCAGT -s Anc2.Anc2refChr2 2724 14 + 27695 tgcaacccctcagt -s mr.mrrefChr0 87290 14 + 130230 CCCAAACCCCTAGC -s simCow_chr6.simCow.chr6 92791 14 + 602619 tgtaacccctctgc -s simDog_chr6.simDog.chr6 488140 14 - 593897 tccaaccccccagt -s simHuman_chr6.simHuman.chr6 86706 14 + 601863 CCTAAACCCCCAGT -s simRat_chr6.simRat.chr6 84304 14 + 647215 CCCAAACCCCTAGC - -a -s simMouse_chr6.simMouse.chr6 92099 5 + 636262 ACTTG -s Anc0.Anc0refChr4 33876 5 - 45765 acttg -s Anc1.Anc1refChr2 65667 5 + 144309 ACTTG -s Anc2.Anc2refChr2 2738 5 + 27695 gcgtg -s mr.mrrefChr0 87304 5 + 130230 ACTTG -s simCow_chr6.simCow.chr6 92805 5 + 602619 acttg -s simDog_chr6.simDog.chr6 488154 5 - 593897 gcgtg -s simHuman_chr6.simHuman.chr6 86737 5 + 601863 ACTTA -s simRat_chr6.simRat.chr6 84318 5 + 647215 ACTGG - -a -s simMouse_chr6.simMouse.chr6 92104 9 + 636262 AGCTGAGAG -s Anc0.Anc0refChr4 33881 9 - 45765 aacctggaa -s Anc1.Anc1refChr2 65672 9 + 144309 AACCTGGAA -s Anc2.Anc2refChr2 2744 9 + 27695 aacctgaaa -s mr.mrrefChr0 87309 9 + 130230 AGCTGAGAA -s simCow_chr6.simCow.chr6 92811 9 + 602619 gatctgaaa -s simDog_chr6.simDog.chr6 488160 9 - 593897 aacctgaaa -s simHuman_chr6.simHuman.chr6 86742 9 + 601863 AACCTGGGA -s simRat_chr6.simRat.chr6 84323 6 + 647215 ---TGTGAA - -a -s simMouse_chr6.simMouse.chr6 92113 7 + 636262 TCCTCAG -s Anc0.Anc0refChr4 33890 7 - 45765 tcttaag -s Anc1.Anc1refChr2 65681 7 + 144309 TCTTAAG -s Anc2.Anc2refChr2 2753 7 + 27695 ttttaaa -s mr.mrrefChr0 87318 7 + 130230 TCCTCAG -s simCow_chr6.simCow.chr6 92821 7 + 602619 tttttaa -s simDog_chr6.simDog.chr6 488169 7 - 593897 ttttaga -s simHuman_chr6.simHuman.chr6 86751 7 + 601863 CCATTAG -s simRat_chr6.simRat.chr6 84329 5 + 647215 TCCTC-- - -a -s simMouse_chr6.simMouse.chr6 92120 74 + 636262 ACGGGCGCCCAAGAAGCTGTGTCACATAGGATTACTCAAGCTTGAGCAGTGATATTGTATGCACCAGGTTTTGA -s Anc0.Anc0refChr4 33897 74 - 45765 aatgggaccccataagctgtgttacatcctaatagctgagctggaagagggatatggtatccagcTGGTGTGTC -s Anc1.Anc1refChr2 65688 74 + 144309 aatgggaccccataagctgtgttacatcctaatagctgagctggaagagggatatggtatccagcTGGTGTGTC -s Anc2.Anc2refChr2 2760 74 + 27695 gatgggaccccatgagcaatatcacatcctaatagctgaactacaagagggatatggtatccagcTGGTGTGTC -s mr.mrrefChr0 87325 74 + 130230 ACTGGCACCCAAGAAGCTGTGTTACATAGTATTACTCAAGCTGGAGCAGTGATATTGTATGCACCAGGTTTGGC -s simCow_chr6.simCow.chr6 92828 58 + 602619 gatgggatgccacga----------------ATAACTGACCTACAAAAATGATATGGTATCCAGCTGGTGTGTC -s simDog_chr6.simDog.chr6 488176 74 - 593897 gatgggaccccttgagcaatatcacatcctaataggcaaaccacatgagggatatggtgtccagcTGCTAAGTC -s simHuman_chr6.simHuman.chr6 86767 74 + 601863 attgggacctcataagctgtgttacaacctaatatctgggctggaagggcgatatggtatccaacTGGTGTGTC -s simRat_chr6.simRat.chr6 84334 73 + 647215 ACTGGCACCCGGGAAGCTGTGTTGCACAGTATTACTCAAACTGGAGTAGTTATATTATATGCACCAAG-CTGGC - -a -s simMouse_chr6.simMouse.chr6 92194 35 + 636262 TTCGGCTTTATGTTTATAGCTGCTCGAATAATAAA -s Anc0.Anc0refChr4 33972 28 - 45765 TTTGGCTTAGTGTATATAGCCGATG-------AAA -s Anc1.Anc1refChr2 65763 28 + 144309 TTTGGCTTAGTGTATATAGCCGATG-------AAA -s Anc2.Anc2refChr2 2835 28 + 27695 TGTGGCTTAGTGTATATAGCCCATG-------AAA -s mr.mrrefChr0 87399 28 + 130230 TTCGGCTTTATGTTTATAGCTGCTC-------AAA -s simCow_chr6.simCow.chr6 92887 28 + 602619 TGTGGCTGAGTGTATATAGCCCATG-------AAA -s simDog_chr6.simDog.chr6 488251 15 - 593897 TGTGGCTTGGTGTAT-------------------- -s simHuman_chr6.simHuman.chr6 86842 28 + 601863 TTTGGCTTAGTGTATATAGCCGATG-------AAA -s simRat_chr6.simRat.chr6 84407 28 + 647215 TTCAGCTTTATGTTTATAGCTGCTT-------AAA - -a -s simMouse_chr6.simMouse.chr6 92229 88 + 636262 TGATTATAATTTACTTATGATTACAGATTATGCCTAAACAGATTTAGATGTGGGTAAGTAAATTATAGACTAATGTTTAAGCATCAGG -s Anc0.Anc0refChr4 34000 87 - 45765 CCTTTTTTATTCTAATTGGTCTACAAACGAGGCCCAAACAGATTTAGGTTTGGGGAAGTGGATTATAGACTAAAGTTTATTGATT-AG -s Anc1.Anc1refChr2 65791 87 + 144309 CCTTTTTTATTCTAATTGGTCTACAAACGAGGCCCAAACAGATTTAGGTTTGGGGAAGTGGATTATAGACTAAAGTTTATTGATT-AG -s Anc2.Anc2refChr2 2863 87 + 27695 CCTGATTTGTCCTAATTGCTCTACAAACAAGGCCCAATCAAATTTAGGTTTGGGGAAGTGGATTATAGACTAAAGTTTATTGACT-AG -s mr.mrrefChr0 87427 87 + 130230 TGATTATAATTTACTTATGTTTACAGATGATGCCTAAACAGATTTAGATGTGGGTAAGTGAATTATAGACTAATGTTTAAGCATT-GG -s simCow_chr6.simCow.chr6 92916 86 + 602619 CCTGATTTGTACTAATCGCTCTACAAGCAAGGCC-AATCAAAGGTTGGTTTGGGGTATTGGATCATAGACCGAAGTTTATTGACT-AG -s simDog_chr6.simDog.chr6 488266 76 - 593897 ----------CCTAATTGCTCTCCAAACAAGGCCCAATCAAATTTAGGTTTGACAAAGTGTATTATAGAGTAAAATTTG-TGACT-AG -s simHuman_chr6.simHuman.chr6 86870 87 + 601863 CCTTTTTGACTCCAGTTGGTCCACATACGAGTCCCAAAGAGATTTAGGTTCGGGGAAGTGGATTATACACTATAGTTCACTGATT-AG -s simRat_chr6.simRat.chr6 84435 73 + 647215 TAACT-----------GTGTTTACAGATGAT---TAAACAGATTTAGATATGGGTAAGTGAATTATGGACTAATGTTTATGCATT-GG - -a -s simMouse_chr6.simMouse.chr6 92317 13 + 636262 TGGATACCCATAC -s Anc0.Anc0refChr4 34089 13 - 45765 TGGGTTCCCAAAC -s Anc1.Anc1refChr2 65880 13 + 144309 TGGGTTCCCAAAC -s Anc2.Anc2refChr2 2952 13 + 27695 TGGGTTCCCAAAC -s mr.mrrefChr0 87514 13 + 130230 TGGATACCCATAC -s simCow_chr6.simCow.chr6 93004 13 + 602619 TGGGTTCCCAAAC -s simDog_chr6.simDog.chr6 488344 13 - 593897 TGGGTACCCAAGC -s simHuman_chr6.simHuman.chr6 86959 13 + 601863 TGGGTTCCCAGAT -s simRat_chr6.simRat.chr6 84508 13 + 647215 CAGATACCCAACC - -a -s simMouse_chr6.simMouse.chr6 92330 9 + 636262 CTGCTAGCA -s Anc0.Anc0refChr4 34102 9 - 45765 TCTCTAGCA -s Anc1.Anc1refChr2 65893 9 + 144309 TCTCTAGCA -s Anc2.Anc2refChr2 2965 9 + 27695 TCTCTAGCA -s mr.mrrefChr0 87527 9 + 130230 CTGCTAGCA -s simCow_chr6.simCow.chr6 93018 9 + 602619 TGTCTAACA -s simDog_chr6.simDog.chr6 488357 9 - 593897 TCTCTAGCA -s simHuman_chr6.simHuman.chr6 86972 9 + 601863 GCTCGAGCA -s simRat_chr6.simRat.chr6 84521 9 + 647215 CTACTAGCA - -a -s simMouse_chr6.simMouse.chr6 92339 108 + 636262 GGCATGGCTACACAAGTCCCAAATAAGTATGATATGATCTGCTGTGCAATGCTCCTCCCTGCATAGAATGTCTATGATCAAATAAGAGCCAATTTAGTACATAGTACT -s Anc0.Anc0refChr4 34120 107 - 45765 GCCATGGCTGTGCAAGCCCCCACGAGTCAT-ACATTATCTGCCATGCAATGCTCCTCCCTGCGTAGAATTGCTATAAACAAATAAAAGCCACCTTAGTGCATAGTACT -s Anc1.Anc1refChr2 65911 108 + 144309 GCCATGGCTGTGCAAGCCCCCACGAGTCATAACATTATCTGCCATGCAATGCTCCTCCCTGCGTAGAATTGCTATAAACAAATAAAAGCCACCTTAGTGCATAGTACT -s Anc2.Anc2refChr2 2983 107 + 27695 GCCATGGCTGTGCAAGTCCCCACGAGTCAC-ACATTACCTGCCATGCAATGCACCTCCCTGTGTAGAATTGCTATAAACAAATACAAGGCACCTTAGTGCATAGTACT -s mr.mrrefChr0 87545 108 + 130230 GGCATGGCTACACAAGCCCCCAATAAGTATGACATGATCTGCTGTGCAATGCTCCTCCCTGCATAGAATGGCTATGATCAAATAAGAGCCAATTTAGTACATAGTACT -s simCow_chr6.simCow.chr6 93035 106 + 602619 GCTATGGCTGTGCGAGTCCACCCGTGACA--ACATGACCTGCCATGCAGTGCACCTCTCTGTGTAGAATTTCAATAAACAAATACAACGCACTTTAGTGCATAGTGCT -s simDog_chr6.simDog.chr6 488375 107 - 593897 ACCATGGCTCTGCAAGTCCCCACCAGTTGC-GCATTACTTGTCATGCAATGCACTTCCTTGTGAAGGATTGCTATAAACAAGTGCAAGGCACCTTAGTGCATGGTACT -s simHuman_chr6.simHuman.chr6 86990 108 + 601863 GCCATGGCTGTGCAAGCCCCCATGAGTCATACCATTATCTGCCCTGCAATGCTACTCCCCGCTTATAACTGCTATAAGCAAATAAAAGCCACCTTAGTGCATAGAATA -s simRat_chr6.simRat.chr6 84539 98 + 647215 GGTGTGGCTTCAGAAGCCCCC----------ACATAATCTGCTGTGCAATGCTCCTCCCTGCATAGAATGGCTATGATCAAGTAAGAGTCAATTTAGTACATAGTAAT - -a -s simMouse_chr6.simMouse.chr6 92447 3 + 636262 AGT -s Anc0.Anc0refChr4 34227 3 - 45765 AAT -s Anc1.Anc1refChr2 66019 3 + 144309 AAT -s Anc2.Anc2refChr2 3091 3 + 27695 AAT -s mr.mrrefChr0 87653 3 + 130230 AGT -s simCow_chr6.simCow.chr6 93142 3 + 602619 CAT -s simDog_chr6.simDog.chr6 488483 3 - 593897 AAT -s simHuman_chr6.simHuman.chr6 87098 3 + 601863 AAT -s simRat_chr6.simRat.chr6 84637 3 + 647215 AGT - -a -s simMouse_chr6.simMouse.chr6 92450 6 + 636262 GCTTTG -s Anc0.Anc0refChr4 34231 6 - 45765 GCCTTG -s Anc1.Anc1refChr2 66023 6 + 144309 GCCTTG -s Anc2.Anc2refChr2 3095 6 + 27695 ACTTTG -s mr.mrrefChr0 87656 6 + 130230 GCCTTG -s simCow_chr6.simCow.chr6 93146 6 + 602619 ACTCTA -s simDog_chr6.simDog.chr6 488487 6 - 593897 ACTTTG -s simHuman_chr6.simHuman.chr6 87102 6 + 601863 GTCTTG -s simRat_chr6.simRat.chr6 84640 6 + 647215 GCCTTG - -a -s simMouse_chr6.simMouse.chr6 92456 145 + 636262 ATACTGCCTAACATTGTTTAGATTTTGCACAGTGCCTCGTGCAAAGCTCCAATTAAAGGCAAATGCGTGCATTCCCATTTAGTACTTGACATGCTGTCGAGCACTCATAGGTGCCTATAGAAGGAGCCTGCCCTCCTCATGCAAG -s Anc0.Anc0refChr4 34238 8 - 45765 ATACTGG-----------------------------------------------------------------------------------------------------------------------------------------G -s Anc1.Anc1refChr2 66030 8 + 144309 ATACTGG-----------------------------------------------------------------------------------------------------------------------------------------G -s Anc2.Anc2refChr2 3102 8 + 27695 ATACTAG-----------------------------------------------------------------------------------------------------------------------------------------G -s mr.mrrefChr0 87663 145 + 130230 ATACTGCCTAACATTGTTTAGATTTTGCACAGTGCCTCGTGCAAAGCTCCAATTAAAGGCAAATGCGTGCATTCCCATTTAGTACTTGACATGCTGTCGAGCACTCATAGGTGCCTATAGAAGGAGCCTGCCCTCCTCATGCAAG -s simCow_chr6.simCow.chr6 93153 8 + 602619 ATACTTG-----------------------------------------------------------------------------------------------------------------------------------------G -s simDog_chr6.simDog.chr6 488494 8 - 593897 ATACTAG-----------------------------------------------------------------------------------------------------------------------------------------G -s simHuman_chr6.simHuman.chr6 87109 8 + 601863 AGACTGT-----------------------------------------------------------------------------------------------------------------------------------------G -s simRat_chr6.simRat.chr6 84647 145 + 647215 ATACTGCCTAACTTTGTTCAGATTTTGCGCAGCAGTTCGTGCAAAGCTCCAATAAAAGGCAAATGTCTGTATACACATTTAGCACTTGACACGCTATCAAGCAGTCAAAGGCACCCATCGAAGGAGCCTGCCCACCTCATGCAAA - -a -s simMouse_chr6.simMouse.chr6 92601 75 + 636262 CACCCTAATGGTCCAAAATGTCACTGCCATTCAAAGTACTATAAACCTTGTAATATTTTACAAGCATAGTTGTCA -s Anc0.Anc0refChr4 34246 75 - 45765 CAGTCTAATAGGCCAAAATATCCCTGTTATTCAAAATACTACAAACTATTTAGAATTTTACAAACATAGGTGTCA -s Anc1.Anc1refChr2 66038 75 + 144309 CAGTCTAATAGGCCAAAATATCCCTGTTATTCAAAATACTACAAACTATTTAGAATTTTACAAACATAGGTGTCA -s Anc2.Anc2refChr2 3110 75 + 27695 CAGTCTAATAGGCCAAAATATCCCTATTATTCAAAATACTACAAACTATTTAGAATTTTACAAACATAGGTGTCA -s mr.mrrefChr0 87808 75 + 130230 CACCCTAATGGTCCAAAATGTCACTGCTATTCAAAGTACTATAAACCTTGTAAAATTTTACAAACATAGTTGTCA -s simCow_chr6.simCow.chr6 93161 74 + 602619 CAGTCTAATAGGCCAAAATGTCCCT-TTATACAGAATACTACAATCTAGTTAAAATTTTACAAACATAAGTGGCA -s simDog_chr6.simDog.chr6 488542 75 - 593897 CAACCTAATGGGCCAAAACATCCATATTATTCAAAATACTATAGACTATTTAGAGCTTTACAGACATAGGTATCA -s simHuman_chr6.simHuman.chr6 87117 74 + 601863 CAGTCTAACAGGCCAAAATATCCCTGTTATTCAAAATACTACAAACTATTTAGAATTTT-CAAACATAGGTGACA -s simRat_chr6.simRat.chr6 84792 75 + 647215 CACCCTACTGGTCCAAAATGTCACTTCTATTCAAAGTACTATAAACCTTGTAAAACTCTACAAACATGATTGTCA - -a -s simMouse_chr6.simMouse.chr6 92676 26 + 636262 CTATGACATTGAATGCTAGAAAGAAC -s Anc0.Anc0refChr4 34321 22 - 45765 CTGGGATAGGCAATGCT----AAAAC -s Anc1.Anc1refChr2 66113 22 + 144309 CTGGGATAGGCAATGCT----AAAAC -s Anc2.Anc2refChr2 3185 22 + 27695 CTGGGTCAGCCAATGCT----AAACC -s mr.mrrefChr0 87883 22 + 130230 CTATGATATGGAATGCT----AGAAC -s simCow_chr6.simCow.chr6 93235 22 + 602619 CTAGGTCAGCCAATGCT----AAACC -s simDog_chr6.simDog.chr6 488617 22 - 593897 CTGGGTCAGCCAATGAT----AAACC -s simHuman_chr6.simHuman.chr6 87191 22 + 601863 CTGCGATAGGCAATGCT----AAAAC -s simRat_chr6.simRat.chr6 84868 22 + 647215 GTATGATGTGTGATGAC----AGAAC - -a -s simMouse_chr6.simMouse.chr6 92702 64 + 636262 TTAAAAGAAGAACATCACAAGCTTAAGAGTTTTTCAGCCAAATAATCTTCAATGGAAGAAGCTG -s Anc0.Anc0refChr4 34344 64 - 45765 CTAAAAAAAGAACATCAGAAGACTAAGAATTTTCCAGCCAAATGATCTTTGATAGAAGAAGCTT -s Anc1.Anc1refChr2 66136 64 + 144309 CTAAAAAAAGAACATCAGAAGACTAAGAATTTTCCAGCCAAATGATCTTTGATAGAAGAAGCTT -s Anc2.Anc2refChr2 3208 64 + 27695 CTGGAAAAAGAACGTCAGAAGACTAAGAATTTTCCAGCCAAATGATCTTTGATAGAAAAAGCTT -s mr.mrrefChr0 87905 64 + 130230 TTAAAAGAAGAACATCACAAGCTTAAGAGTTTTTCAGCCAAATAATCTTTGATGGAAGAAGCTG -s simCow_chr6.simCow.chr6 93258 64 + 602619 GAGGAACAAGAACGTCAGAAGGCTAAGAATTTTCCAGCCAAATAATCTTTGATAGAAAAAGCTT -s simDog_chr6.simDog.chr6 488640 63 - 593897 CTGGACAAGGAATGTCAGAAGACTAAGAATTT-ACAGCCAAATGATCTATGATAAAAAAAGCTT -s simHuman_chr6.simHuman.chr6 87214 64 + 601863 CTAACAAAAGAACATCAGAACACTAAGAATTTTCCAGCCAAATGATCTTTGATAGAAGAAGCTT -s simRat_chr6.simRat.chr6 84890 63 + 647215 TTAAAAGAAGAACATCACAAGCTTAAGAGTTCTTCAGCCAAATAATCTCTGATGGAA-AAGCTG - -a -s simMouse_chr6.simMouse.chr6 92766 1 + 636262 A -s Anc0.Anc0refChr4 34408 1 - 45765 A -s Anc1.Anc1refChr2 66200 1 + 144309 A -s Anc2.Anc2refChr2 3272 1 + 27695 A -s mr.mrrefChr0 87969 1 + 130230 A -s simCow_chr6.simCow.chr6 93503 1 + 602619 A -s simDog_chr6.simDog.chr6 488703 1 - 593897 A -s simHuman_chr6.simHuman.chr6 87278 1 + 601863 A -s simRat_chr6.simRat.chr6 84953 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 92767 7 + 636262 AGAGATT -s Anc0.Anc0refChr4 34409 7 - 45765 GGAGATT -s Anc1.Anc1refChr2 66201 7 + 144309 GGAGATT -s Anc2.Anc2refChr2 3274 7 + 27695 GGAGACT -s mr.mrrefChr0 87970 7 + 130230 AGAGATT -s simCow_chr6.simCow.chr6 93505 7 + 602619 GGATACT -s simDog_chr6.simDog.chr6 488705 7 - 593897 GGAGACT -s simHuman_chr6.simHuman.chr6 87279 7 + 601863 TAAGATT -s simRat_chr6.simRat.chr6 84954 7 + 647215 GGAGATT - -a -s simMouse_chr6.simMouse.chr6 92774 112 + 636262 ACTGACAACTACTTACACGCCTTGTTGACCACTCATTCCCTTGGAAACAGCATTATGGGAAGGAGTAACAGGTTTCCCTTGGAAACAGCATTATGCGAAGGAGTAACAGGTG -s Anc0.Anc0refChr4 34416 54 - 45765 ATGGAAA--------------------ACCGCATATGCACTTGGTGACAGCAATATGG--------------------------------------GAGGAGGAAACAGGTG -s Anc1.Anc1refChr2 66208 54 + 144309 ATGGAAA--------------------ACCGCATATGCACTTGGTGACAGCAATATGG--------------------------------------GAGGAGGAAACAGGTG -s Anc2.Anc2refChr2 3281 54 + 27695 ATGGAAA--------------------ACCGCATATGCACTTGGTGACAGCAATATGG--------------------------------------GAGGAGGAAACAGGTG -s mr.mrrefChr0 87977 74 + 130230 ACTGACAACTACTTACACGCCTTGTTGACCACTCATTCCCTTGGAAACAGCATTATGG--------------------------------------GAAGGAGTAACAGGTG -s simCow_chr6.simCow.chr6 93512 54 + 602619 ATGCAAA--------------------ACTACCTACGCACTTGGCAACAGCAATATGG--------------------------------------GAGGAGGAAATAGGTG -s simDog_chr6.simDog.chr6 98589 54 + 593897 ATGGAAA--------------------ACCGCATATGCACTTGGTGACAGCAATATGG--------------------------------------GAGGCGCAAACAAGTG -s simHuman_chr6.simHuman.chr6 87286 28 + 601863 ----------------------------------------------ATAGCAATATGG--------------------------------------AAGGACGAAACAGGTG -s simRat_chr6.simRat.chr6 84961 74 + 647215 ACTGACAACTACTTACACACCCTGTAAACCGCTAATTCCCTTGGAAAGAGCCTTATAG--------------------------------------GAAAGAACATCAGGTG - -a -s simMouse_chr6.simMouse.chr6 92886 19 + 636262 CCTGGGAAGACCTAGTCCC -s Anc0.Anc0refChr4 34470 19 - 45765 CCTAAGAAGACCTGGTCCC -s Anc1.Anc1refChr2 66262 19 + 144309 CCTAAGAAGACCTGGTCCC -s Anc2.Anc2refChr2 3335 19 + 27695 CGTAAAGAGGCCTGGTCCC -s mr.mrrefChr0 88051 19 + 130230 CCTAGGAAGACCTAGTCCC -s simCow_chr6.simCow.chr6 93566 10 + 602619 -----AGAGG----GTCCT -s simDog_chr6.simDog.chr6 98643 18 + 593897 CGTAA-GAGGCCTGGTCCC -s simHuman_chr6.simHuman.chr6 87321 19 + 601863 CCTAAGAGGAACTGGGCTC -s simRat_chr6.simRat.chr6 85035 19 + 647215 CCTAGGAAGACCTAGTCCC - -a -s simMouse_chr6.simMouse.chr6 92905 34 + 636262 TCTGATGCACCCTTTATGAGTTCAGCAGTGAAAA -s Anc0.Anc0refChr4 34500 34 - 45765 TCTGACATATCCTTTATAAGTTCAGCAATGAAAA -s Anc1.Anc1refChr2 66292 34 + 144309 TCTGACATATCCTTTATAAGTTCAGCAATGAAAA -s Anc2.Anc2refChr2 3365 34 + 27695 TCTGACATATCCTTTATAAATTCAGCAATGAAAA -s mr.mrrefChr0 88070 34 + 130230 TCTGATGCATCCTTTATGAGTTCAGCAGTGAAAA -s simCow_chr6.simCow.chr6 93587 34 + 602619 CCTGATATATCCTTAGTAAATTCAGCGACGGAAA -s simDog_chr6.simDog.chr6 98672 34 + 593897 TCCAACATATCCTTTATAAATTCAGCAATGAAAA -s simHuman_chr6.simHuman.chr6 87351 34 + 601863 TCTGACATATCCTTCATAAGTTCAGCAATGAAAA -s simRat_chr6.simRat.chr6 85054 33 + 647215 TCTGATGCATCC-TTAAGAGTTCAGCGGTGAAAA - -a -s simMouse_chr6.simMouse.chr6 92939 61 + 636262 GTATTTGAGATCCATAGGACAGAAAGCATATAAGTACAAACACTAGTATGATTTGTCCATG -s Anc0.Anc0refChr4 34535 49 - 45765 GCATTAAAGT-----A----ATAAG--ATATAAGTAAAAGCACTATTATGATTTGATC-TG -s Anc1.Anc1refChr2 66327 55 + 144309 GCATTAAAGT-----AGGACATAAGGTATATAAGTAAAAGCACTATTATGATTTGATC-TG -s Anc2.Anc2refChr2 3400 49 + 27695 GCGTTAAAGT-----G----ATAAG--ATATAAGTAAAAGCACTGTTATGATGTGATC-TG -s mr.mrrefChr0 88105 61 + 130230 GTATTTGAGATCCATAGGACAGAAAGCATATAAGTACAAACACTAGTATGATTTGTCCATG -s simCow_chr6.simCow.chr6 93622 49 + 602619 GCCTTAAAGT-----G----ATAAG--ATATAAGCGGGACCACTGTTATGATGTGATC-TG -s simDog_chr6.simDog.chr6 98707 47 + 593897 ATGTTAAAGT-----G----ACAAG--ATGTAAGTAAAAGCACTGTTAAAAATTGACC--- -s simHuman_chr6.simHuman.chr6 87386 39 + 601863 GCAATAAAGG-----AGGACATAAGGTGGATAA-----------AATATAGTT------AA -s simRat_chr6.simRat.chr6 85088 61 + 647215 GTATTTTAAATCCAAAAGACAGATAGCATATAAGTGAAAACAGTAGTATGATCTGCCCATG - -a -s simMouse_chr6.simMouse.chr6 93000 5 + 636262 ACTTG -s Anc0.Anc0refChr4 34584 5 - 45765 AATTG -s Anc1.Anc1refChr2 66382 5 + 144309 AATTG -s Anc2.Anc2refChr2 3449 5 + 27695 AATAG -s mr.mrrefChr0 88166 5 + 130230 ACTTG -s simCow_chr6.simCow.chr6 93672 5 + 602619 AATAG -s simDog_chr6.simDog.chr6 98754 5 + 593897 AATAG -s simHuman_chr6.simHuman.chr6 87425 5 + 601863 AATTA -s simRat_chr6.simRat.chr6 85149 5 + 647215 ACTTG - -a -s simMouse_chr6.simMouse.chr6 93005 8 + 636262 TGATGTGA -s Anc0.Anc0refChr4 34589 8 - 45765 TGATGGAA -s Anc1.Anc1refChr2 66387 8 + 144309 TGATGGAA -s Anc2.Anc2refChr2 3456 8 + 27695 TAACAGAC -s mr.mrrefChr0 88171 8 + 130230 TGATGTGA -s simCow_chr6.simCow.chr6 93679 8 + 602619 TAACAGAC -s simDog_chr6.simDog.chr6 98761 8 + 593897 TAACAGAC -s simHuman_chr6.simHuman.chr6 87430 8 + 601863 TGATGGAA -s simRat_chr6.simRat.chr6 85154 8 + 647215 TGATGTGA - -a -s simMouse_chr6.simMouse.chr6 93013 3 + 636262 ATG -s Anc0.Anc0refChr4 34597 3 - 45765 CTG -s Anc1.Anc1refChr2 66395 3 + 144309 CTG -s Anc2.Anc2refChr2 3464 3 + 27695 ATT -s mr.mrrefChr0 88179 3 + 130230 CTG -s simCow_chr6.simCow.chr6 93687 3 + 602619 AGT -s simDog_chr6.simDog.chr6 98769 3 + 593897 ATT -s simHuman_chr6.simHuman.chr6 87439 3 + 601863 CTG -s simRat_chr6.simRat.chr6 85162 3 + 647215 CTG - -a -s simMouse_chr6.simMouse.chr6 93016 6 + 636262 TTCCAG -s Anc0.Anc0refChr4 34600 6 - 45765 TAACAG -s Anc1.Anc1refChr2 66398 6 + 144309 TAACAG -s Anc2.Anc2refChr2 3467 6 + 27695 TAACAG -s mr.mrrefChr0 88182 6 + 130230 TTCCAG -s simCow_chr6.simCow.chr6 93696 6 + 602619 TAACAG -s simHuman_chr6.simHuman.chr6 87442 6 + 601863 TAACAG -s simRat_chr6.simRat.chr6 85165 6 + 647215 TTCCAG - -a -s simMouse_chr6.simMouse.chr6 93022 10 + 636262 ACACCAGGTC -s Anc0.Anc0refChr4 34607 10 - 45765 AAATTAGGTC -s Anc1.Anc1refChr2 66405 10 + 144309 AAATTAGGTC -s Anc2.Anc2refChr2 3474 10 + 27695 AAGTTGGGCC -s mr.mrrefChr0 88188 10 + 130230 ACACTAGGTC -s simCow_chr6.simCow.chr6 93703 10 + 602619 CAGCTGGGCC -s simDog_chr6.simDog.chr6 98772 8 + 593897 AAGTTG--CC -s simHuman_chr6.simHuman.chr6 87449 10 + 601863 AAATTAAGTC -s simRat_chr6.simRat.chr6 85171 10 + 647215 ACACTAGGTC - -a -s simMouse_chr6.simMouse.chr6 93032 42 + 636262 TCCTTGCTGGATGCACTATACGACCTGTTAAATCCTGCCCAG -s Anc0.Anc0refChr4 34618 42 - 45765 TCCTTGTTGCTTGCACTATGCAACCTGTTGAATCTTGTCCAG -s Anc1.Anc1refChr2 66416 42 + 144309 TCCTTGTTGCTTGCACTATGCAACCTGTTGAATCTTGTCCAG -s Anc2.Anc2refChr2 3485 42 + 27695 TCTTTGTTGCTTACACAATGCAACCTGTCCAATCTTGTCCAA -s mr.mrrefChr0 88198 42 + 130230 TCCTTGCTGCATGCACTATGCGACCTGTTGAATCCTGCCCAG -s simCow_chr6.simCow.chr6 93714 42 + 602619 TCTTTATCACCCACACAATGCAGCCTATCAACTCTTGTCCAA -s simDog_chr6.simDog.chr6 98781 42 + 593897 TCTTTGTTGCTTACACACTGCAACCTGTCCAATCTTGTCTAA -s simHuman_chr6.simHuman.chr6 87460 42 + 601863 GCCTTGTTGCTTGCACTATGCAACCTGTTGAATCATCTCCAG -s simRat_chr6.simRat.chr6 85181 42 + 647215 TCCTTGCTGCCTGCATAATGTTACCTGTTGAATCCTGCCCTG - -a -s simMouse_chr6.simMouse.chr6 93074 64 + 636262 TTAAAGATATTGTTGGAACAAATTCTGTCTTCTGATTTTTGATAGACCAGATCTTGTCCTCCGC -s Anc0.Anc0refChr4 34660 49 - 45765 GAAAATAATCTGTCAAAATATGTTC--------------TGATAGACCAGATCTGATCCTCCA- -s Anc1.Anc1refChr2 66458 49 + 144309 GAAAATAATCTGTCAAAATATGTTC--------------TGATAGACCAGATCTGATCCTCCA- -s Anc2.Anc2refChr2 3527 49 + 27695 GAAAATAATCTGTCAAAATATGTTC--------------TGATCGACTGGATCTGATCCTCCA- -s mr.mrrefChr0 88240 64 + 130230 TTAAATATATTGTTGAAATAAATTCTGTCTTCTGATTTTTGATAGACCAGATCTTGTCCTCCAC -s simCow_chr6.simCow.chr6 93756 49 + 602619 GCAAATAATCTGCCAAGATATGTTC--------------TGATGGACTGAATATGGTTCTCCA- -s simDog_chr6.simDog.chr6 98930 49 + 593897 GAAAATAATCTATCAAAGTATATTC--------------TGATCTACTGGATCTGATCCTCCA- -s simHuman_chr6.simHuman.chr6 87502 49 + 601863 GAAAATAATCTGACAAAATATGTTC--------------TGATAGACCAGATCTCATCCTCCA- -s simRat_chr6.simRat.chr6 85223 64 + 647215 TTAAATATGTTGTTGAAATAAATTCCGACTTCTGACTTTTGCTAGACCAGATTTTGTCCTCCAC - -a -s simMouse_chr6.simMouse.chr6 93138 25 + 636262 AGGTGATAGGGCAAGGATACAAAAA -s Anc0.Anc0refChr4 34715 25 - 45765 AGGTGATGGGGCAAGGGTACAATAA -s Anc1.Anc1refChr2 66513 25 + 144309 AGGTGATGGGGCAAGGGTACAATAA -s Anc2.Anc2refChr2 3582 25 + 27695 AGTTGATGGGGCTGGGGTACACTAA -s mr.mrrefChr0 88310 25 + 130230 AGGTGATGGGGCAAGGGTACAATAA -s simCow_chr6.simCow.chr6 93810 20 + 602619 -----ATGGGATTGCAGTACACCAA -s simDog_chr6.simDog.chr6 98985 25 + 593897 AGTTGATGGAGCTGGGGTACACTAA -s simHuman_chr6.simHuman.chr6 87557 25 + 601863 AGGTGACGGGGCAAGGGTGCAATAA -s simRat_chr6.simRat.chr6 85293 25 + 647215 AGGTGATGGGGCAAGGGTATAATAA - -a -s simMouse_chr6.simMouse.chr6 93163 24 + 636262 TGAAAGGGAACGCCGGCCCTACTA -s Anc0.Anc0refChr4 34741 24 - 45765 CAAACATGAACGCAAATCCTACTA -s Anc1.Anc1refChr2 66539 24 + 144309 CAAACATGAACGCAAATCCTACTA -s Anc2.Anc2refChr2 3608 24 + 27695 CAAACATGAAAGCAAATCCTACTA -s mr.mrrefChr0 88336 24 + 130230 TGAAAGGGAACGCCGACCCTACTA -s simCow_chr6.simCow.chr6 93831 24 + 602619 CAAAAGTTAAAGCAAATCCTACTA -s simDog_chr6.simDog.chr6 99011 24 + 593897 CGAACATGAAAGCAAATCCTACGA -s simHuman_chr6.simHuman.chr6 87583 19 + 601863 CAA-----AACGCAAATGCTACTA -s simRat_chr6.simRat.chr6 85319 24 + 647215 TGAAAGGGAAAGCGGACCTTACTA - -a -s simMouse_chr6.simMouse.chr6 93187 37 + 636262 AAAGGATAGACAGTGTTAAACCGCCTTCAGTTGTAAA -s Anc0.Anc0refChr4 34765 32 - 45765 AAAGGATAGGGAG-----AATAGCCTTCAGTTACAAA -s Anc1.Anc1refChr2 66563 32 + 144309 AAAGGATAGGGAG-----AATAGCCTTCAGTTACAAA -s Anc2.Anc2refChr2 3632 32 + 27695 AAAGGATAGGGAT-----AATAGGTTTCAGTTACAAA -s mr.mrrefChr0 88360 37 + 130230 AAAGGATAGACAGTGTTAAACCGCCTTCAGTTACAAA -s simCow_chr6.simCow.chr6 93855 32 + 602619 AAAGGATAGAGAC-----AATAAGTTTCAGTTATAAA -s simDog_chr6.simDog.chr6 99267 27 + 593897 AAGGGGGAGGGAT-----AAAAG-----AATTACAAA -s simHuman_chr6.simHuman.chr6 87602 32 + 601863 AAAGGATAGGAAG-----AATATCCTTCAGTTACGAG -s simRat_chr6.simRat.chr6 85343 34 + 647215 AAAGGATAGACAGAGTTAAACCACCTTTAGTTAC--- - -a -s simMouse_chr6.simMouse.chr6 93224 17 + 636262 TGTTTGAATTGGTGATT -s Anc0.Anc0refChr4 34802 17 - 45765 AGCTTGAATTGGTGCTT -s Anc1.Anc1refChr2 66600 17 + 144309 AGCTTGAATTGGTGCTT -s Anc2.Anc2refChr2 3674 17 + 27695 AGCTTGAATTAGTGCTC -s mr.mrrefChr0 88397 17 + 130230 TGTTTGAATTGGTGATT -s simCow_chr6.simCow.chr6 93897 17 + 602619 AGGTTTAATTAGTGCTG -s simDog_chr6.simDog.chr6 99304 17 + 593897 TGCGTGAATTAGTGCAC -s simHuman_chr6.simHuman.chr6 87639 17 + 601863 AGCTTAAATTGATGCTT - -a -s simMouse_chr6.simMouse.chr6 93241 29 + 636262 GGGATTGATAACATAATGCCGGTAGTTGC -s Anc0.Anc0refChr4 34820 27 - 45765 GGGATTGAT--CATAACTTAGATAGTTAC -s Anc1.Anc1refChr2 66618 27 + 144309 GGGATTGAT--CATAACTTAGATAGTTAC -s Anc2.Anc2refChr2 3692 27 + 27695 GGGATTGAT--AATAACTGAGATAGTTAC -s mr.mrrefChr0 88414 29 + 130230 GGGATTGATAACATAACGTAGGTAGTTGC -s simCow_chr6.simCow.chr6 93915 27 + 602619 GAGCTTGAT--TGTAACTGGGGTATTCAC -s simDog_chr6.simDog.chr6 99322 27 + 593897 GGGATTGGT--AATAACTGAGATAGTTGT -s simHuman_chr6.simHuman.chr6 87657 23 + 601863 GGGATCGAT--CATAACTT----AGTTAC -s simRat_chr6.simRat.chr6 85377 20 + 647215 ----TTCATGACATAACATAGGTA----- - -a -s simMouse_chr6.simMouse.chr6 93270 15 + 636262 TTTTAGCATAGCATT -s Anc0.Anc0refChr4 34852 15 - 45765 TTGCAGTGAGGCATT -s Anc1.Anc1refChr2 66650 15 + 144309 TTGCAGTGAGGCATT -s Anc2.Anc2refChr2 3724 15 + 27695 CTGCAGTGAGTTATT -s mr.mrrefChr0 88443 15 + 130230 TTTTAGCATAGCATT -s simCow_chr6.simCow.chr6 93949 15 + 602619 CTACAGTGAGTTATT -s simDog_chr6.simDog.chr6 99354 15 + 593897 CTGCAGCAAGTTACT -s simHuman_chr6.simHuman.chr6 87685 15 + 601863 TTCCAGTGAGGCATT -s simRat_chr6.simRat.chr6 85397 4 + 647215 -----------TGAT - -a -s simMouse_chr6.simMouse.chr6 93285 6 + 636262 ATGACA -s Anc0.Anc0refChr4 34869 6 - 45765 ATAACA -s Anc1.Anc1refChr2 66667 6 + 144309 ATAACA -s Anc2.Anc2refChr2 3744 6 + 27695 ATAGCA -s mr.mrrefChr0 88458 6 + 130230 ATAACA -s simCow_chr6.simCow.chr6 93969 6 + 602619 ATAACA -s simDog_chr6.simDog.chr6 99374 6 + 593897 ATAGCA -s simHuman_chr6.simHuman.chr6 87702 6 + 601863 ACAATA -s simRat_chr6.simRat.chr6 85401 6 + 647215 ATAACA - -a -s simMouse_chr6.simMouse.chr6 93291 83 + 636262 CAGGTACCCTAATAATCACAAACTAGATATAAGATGCAATGGTGAACCATCTTTTTAAAGCGCACAAGCAGGCTTGAGATTGG -s Anc0.Anc0refChr4 34875 77 - 45765 TAGTTACACTAATATTCAGAAGCTAGATCAAGGGCAAAGTGGTGTAACATCTCTCTA------ATGAGCAGGCTTGAGCTCGG -s Anc1.Anc1refChr2 66673 77 + 144309 TAGTTACACTAATATTCAGAAGCTAGATCAAGGGCAAAGTGGTGTAACATCTCTCTA------ATGAGCAGGCTTGAGCTCGG -s Anc2.Anc2refChr2 3750 77 + 27695 TAGTCACATTAACATTCAGAAGCTAGATCAAGGGCAAAGTGAACTAACATCTCTCTA------ATGAGCAGGCTTGAGCCCAG -s mr.mrrefChr0 88464 83 + 130230 CAGGTACCCTAATAATCAGAAACTAGATCTAAGATGCAATGGTGAACCATCTTTTTAAAGCGCATAAGCAGGCTTGAGCTTGG -s simCow_chr6.simCow.chr6 94020 77 + 602619 TAGTCACATTAACATTCCAAAGCTAGATCTAGGTCAAAATGGAGTAGCATCCCTCTA------CAGAGCAGGCTTGAGCATAG -s simDog_chr6.simDog.chr6 99380 77 + 593897 TAGTCACATTAACATTCAGGAGCTAGATTAAGGGCAAAGTGAACTAACATCTCTCTA------ATAAGCAGGCCTGAGCCCAG -s simHuman_chr6.simHuman.chr6 87708 65 + 601863 TAGTTACACTAATATTCAGAAGCTAGATCAAG--------GGTGTT----CTATCTG------ATGAGCAGGCTTAAGCTCGG -s simRat_chr6.simRat.chr6 85407 83 + 647215 CAGGTACCTTAATAATCAGGAATTAGATCTAAGGCGCAATGGTCAACCACCTTTTTGAAGAGCATAAGCAGGCTTGATCTTGG - -a -s simMouse_chr6.simMouse.chr6 93374 2 + 636262 GT -s Anc0.Anc0refChr4 34952 2 - 45765 TG -s Anc1.Anc1refChr2 66750 2 + 144309 TG -s Anc2.Anc2refChr2 3827 2 + 27695 TG -s mr.mrrefChr0 88547 2 + 130230 GT -s simCow_chr6.simCow.chr6 94097 2 + 602619 GC -s simDog_chr6.simDog.chr6 99461 2 + 593897 TG -s simHuman_chr6.simHuman.chr6 87773 2 + 601863 TG -s simRat_chr6.simRat.chr6 85490 2 + 647215 GT - -a -s simMouse_chr6.simMouse.chr6 93376 48 + 636262 GTTAAAACAGCATAAGTGCCCAGTGGAGTCATCCCAGTGCCCTGAATT -s Anc0.Anc0refChr4 34954 37 - 45765 GCCGAAACAGC-----------GTAGAGCTCCGCCAGTACCCTAAATT -s Anc1.Anc1refChr2 66752 37 + 144309 GCCGAAACAGC-----------GTAGAGCTCCGCCAGTACCCTAAATT -s Anc2.Anc2refChr2 3829 37 + 27695 GCCAAAACAGC-----------ATAGTGCTCCGCAGGTACTCTAAATT -s mr.mrrefChr0 88549 48 + 130230 GCTGAAACAGCATAAGTGCCCAGTGGAGTCATCCCAGTGCCCTGAATT -s simCow_chr6.simCow.chr6 94099 35 + 602619 ATCAAGACATC-----------ATAGTGCTC--TAGGTACTCTAAATT -s simDog_chr6.simDog.chr6 99481 37 + 593897 GCCAAAACAGC-----------ATAGTGCTCCGCAGATATTCTAGAGG -s simHuman_chr6.simHuman.chr6 87775 37 + 601863 GCCGAAACAGT-----------GCAGAGCTCCACCAGTACCCAAAATT -s simRat_chr6.simRat.chr6 85492 48 + 647215 GCTGAAACAGCTTAGGTGCCCAGTGGAGTAATCCTGGTGCCCTGAATT - -a -s simMouse_chr6.simMouse.chr6 93424 1 + 636262 T -s Anc0.Anc0refChr4 34991 1 - 45765 G -s Anc1.Anc1refChr2 66789 1 + 144309 G -s Anc2.Anc2refChr2 3866 1 + 27695 G -s mr.mrrefChr0 88597 1 + 130230 T -s simCow_chr6.simCow.chr6 94134 1 + 602619 G -s simDog_chr6.simDog.chr6 99520 1 + 593897 G -s simHuman_chr6.simHuman.chr6 87812 1 + 601863 G -s simRat_chr6.simRat.chr6 85540 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 93425 105 + 636262 AGCAGGGAAGCACCACTGAGGGTCCTGTTTGGCAGGGAAGCACTACTGAAGGTCCTAAACATATCCCTATCCCCACTCACCGGTAGTGATTGGATCAAAAGTAGA -s Anc0.Anc0refChr4 34992 36 - 45765 GGAAAGACTGCACCAATGCAGGTTC---------------------------------------------------------------------TCAAAGGTTGA -s Anc1.Anc1refChr2 66790 36 + 144309 GGAAAGACTGCACCAATGCAGGTTC---------------------------------------------------------------------TCAAAGGTTGA -s Anc2.Anc2refChr2 3867 36 + 27695 GGACAGACTGCACCAATGCATGTTC---------------------------------------------------------------------TCAAAGGTTGA -s mr.mrrefChr0 88598 75 + 130230 GGCAAGGAAGCACCACTGAAGGTCCTG------------------------------AACATATCCCTATCCCCACTCACCGGTAGTGATTGGATCAAAAGTAGA -s simCow_chr6.simCow.chr6 94139 36 + 602619 GGACAGGCTGTACCAAAGCGATTTC---------------------------------------------------------------------TCGAAGGTAGA -s simDog_chr6.simDog.chr6 99521 36 + 593897 GGACAAACTGCACCAATGCATGTTC---------------------------------------------------------------------TGAAAGGTTGA -s simHuman_chr6.simHuman.chr6 87813 36 + 601863 GGTAAGACTGCACCAATGCAGGTTC---------------------------------------------------------------------TCAAAGGTTGA -s simRat_chr6.simRat.chr6 85541 75 + 647215 GGCAAGGAAGCACCACTGAAGGTCCTG------------------------------AACACATTCCTATCCCTAGCCACCGGTAGGGATTGGATCAAAAATAGG - -a -s simMouse_chr6.simMouse.chr6 93530 15 + 636262 AGGACTTGCAATTGT -s Anc0.Anc0refChr4 35028 15 - 45765 ACTTCTAATAGCAGT -s Anc1.Anc1refChr2 66826 15 + 144309 ACTTCTAATAGCAGT -s Anc2.Anc2refChr2 3903 15 + 27695 ACTTCTAATAGCAGT -s mr.mrrefChr0 88673 15 + 130230 AGGACTTGCAATTGT -s simCow_chr6.simCow.chr6 94175 15 + 602619 ACTTTTAATAACAAT -s simDog_chr6.simDog.chr6 99557 15 + 593897 ACTTCTAATAGAAGT -s simHuman_chr6.simHuman.chr6 87849 15 + 601863 ACTTCTAAGAGCAGT -s simRat_chr6.simRat.chr6 85618 15 + 647215 AGAACTTGTAATTGT - -a -s simMouse_chr6.simMouse.chr6 93545 38 + 636262 TCCTCTCTTGGCCAGCCAATTTTCCAATATCTGGTAAT -s Anc0.Anc0refChr4 35045 36 - 45765 -CC-CTCTGTGCCAGCCAATTTTTCAATATTTGGTAAT -s Anc1.Anc1refChr2 66843 37 + 144309 TCC-CTCTGTGCCAGCCAATTTTTCAATATTTGGTAAT -s Anc2.Anc2refChr2 3920 36 + 27695 -CC-CTCTGTGCCAGCCAATTTTTCAATACTTGGTAAT -s mr.mrrefChr0 88688 37 + 130230 TCC-CTCTTGGCCAGCCAATTTTCCAATATCTGGTAAT -s simCow_chr6.simCow.chr6 94192 36 + 602619 -CC-CTCTGGGCCAGCCAATTTTTCAATACATTGTAAT -s simDog_chr6.simDog.chr6 99574 36 + 593897 -CC-CTCTGTGTCACCCACTTTTTCAATACTTGGTAAT -s simHuman_chr6.simHuman.chr6 87866 37 + 601863 TCC-CTCTCAGCCAGCCAATTTTTCAATATGTGGTAAT -s simRat_chr6.simRat.chr6 85633 37 + 647215 TCC-CTCTTGGACAGCCAATTTTCCAATATCTGGTAAT - -a -s simMouse_chr6.simMouse.chr6 93583 3 + 636262 AGG -s Anc0.Anc0refChr4 35083 3 - 45765 ATG -s Anc1.Anc1refChr2 66882 3 + 144309 ATG -s Anc2.Anc2refChr2 3958 3 + 27695 ATG -s mr.mrrefChr0 88725 3 + 130230 AGG -s simCow_chr6.simCow.chr6 94230 3 + 602619 ATG -s simDog_chr6.simDog.chr6 99612 3 + 593897 ATG -s simHuman_chr6.simHuman.chr6 87905 3 + 601863 ATG -s simRat_chr6.simRat.chr6 85670 3 + 647215 AGG - -a -s simMouse_chr6.simMouse.chr6 93586 30 + 636262 CAGTACAACCTCCTCTGTGAAGGCATTAGA -s Anc0.Anc0refChr4 35086 30 - 45765 CAGAACCTCTTTTACTGTGAAGGCATTAGA -s Anc1.Anc1refChr2 66885 30 + 144309 CAGAACCTCTTTTACTGTGAAGGCATTAGA -s Anc2.Anc2refChr2 3981 30 + 27695 CAGAATGTCTTTGACTGTGACAGCATTAGG -s mr.mrrefChr0 88728 30 + 130230 CAGAACCACCTCTTCTGTGAAGGCATTAGA -s simCow_chr6.simCow.chr6 94264 30 + 602619 CAAAATGTCAGTGACTGTGAGAGCATTAGC -s simDog_chr6.simDog.chr6 99635 30 + 593897 CAGAATGTCTTTGACTGTGACAGCATTAGG -s simHuman_chr6.simHuman.chr6 87908 29 + 601863 CAGAACCTCGTTTACTGTAAAGACATT-GA -s simRat_chr6.simRat.chr6 85673 26 + 647215 CAGAACCACCTCTTCTG----GGCATCAGA - -a -s simMouse_chr6.simMouse.chr6 93616 11 + 636262 TTCCAATATAA -s Anc0.Anc0refChr4 35116 11 - 45765 TTTCAAGATGG -s Anc1.Anc1refChr2 66915 11 + 144309 TTTCAAGATGG -s Anc2.Anc2refChr2 4013 11 + 27695 TTTCAAGATGG -s mr.mrrefChr0 88758 11 + 130230 TTCCAATATAA -s simCow_chr6.simCow.chr6 94296 11 + 602619 TTATTAGATGG -s simDog_chr6.simDog.chr6 99667 11 + 593897 TTTCAAGATGG -s simHuman_chr6.simHuman.chr6 87937 11 + 601863 TCTCAAGATGG -s simRat_chr6.simRat.chr6 85699 11 + 647215 TTCCAACGTAA - -a -s simMouse_chr6.simMouse.chr6 93627 21 + 636262 TGGAGGATGTCGATTCCTCTG -s Anc0.Anc0refChr4 35127 21 - 45765 GGAAAGATGTCAATTCATTTG -s Anc1.Anc1refChr2 66926 21 + 144309 GGAAAGATGTCAATTCATTTG -s Anc2.Anc2refChr2 4025 21 + 27695 GGAAAGATATCAATTCATTTG -s mr.mrrefChr0 88769 21 + 130230 TGGAGGATGTCGATTCCTCTG -s simCow_chr6.simCow.chr6 94308 16 + 602619 GGAAGAATC-----ACATTTG -s simDog_chr6.simDog.chr6 99679 21 + 593897 GGGGAGATATCAATTCATCTG -s simHuman_chr6.simHuman.chr6 87948 21 + 601863 GGAATGATGTCAATTCATTTG -s simRat_chr6.simRat.chr6 85710 21 + 647215 TGGAGGATGTTGATTCCTCTG - -a -s simMouse_chr6.simMouse.chr6 93648 5 + 636262 AATGT -s Anc0.Anc0refChr4 35148 5 - 45765 AAAGT -s Anc1.Anc1refChr2 66947 5 + 144309 AAAGT -s Anc2.Anc2refChr2 4071 5 + 27695 ACAGT -s mr.mrrefChr0 88790 5 + 130230 AATGT -s simCow_chr6.simCow.chr6 94351 5 + 602619 CCAGT -s simDog_chr6.simDog.chr6 99738 5 + 593897 ACATT -s simHuman_chr6.simHuman.chr6 87969 5 + 601863 AAGGT -s simRat_chr6.simRat.chr6 85731 5 + 647215 AATGT - -a -s simMouse_chr6.simMouse.chr6 93653 44 + 636262 GCACTGAAGTGAGATTCCTGGGTTAGTTTCACATCCAATGTCAG -s Anc0.Anc0refChr4 35153 42 - 45765 G--CTTAAATGAGATTCATGGGTTAGTCTCACATTCATTAGTAG -s Anc1.Anc1refChr2 66952 42 + 144309 G--CTTAAATGAGATTCATGGGTTAGTCTCACATTCATTAGTAG -s Anc2.Anc2refChr2 4076 42 + 27695 A--ATTAAATGAGATTCATGGGTTAGTCCTACATTCATTACTAG -s mr.mrrefChr0 88795 44 + 130230 GCACTGAAGTGAGATTCCTGGGTTAGTTTCACATTCAATGGCAG -s simCow_chr6.simCow.chr6 94356 42 + 602619 A--TTGATATGGGATTAATGGGTTAGACAGACATTCATTACTGG -s simDog_chr6.simDog.chr6 99743 37 + 593897 A--ATTAACTGAGACCCATGGGTTAGTTCTACGTTCA-----AG -s simHuman_chr6.simHuman.chr6 87974 42 + 601863 G--CTAAAATGAAATTCATGGGTTAGTCTCATATTCATCAGTAA -s simRat_chr6.simRat.chr6 85779 44 + 647215 GCACTGAAGTGAGATTCCAGGGTTAGTTATACATTCAATGGCAG - -a -s simMouse_chr6.simMouse.chr6 93697 29 + 636262 TGGGTCAATGTAGCTACGTCAACTTGTCA -s Anc0.Anc0refChr4 35196 29 - 45765 TGGGTCAATATAGCATTGTCAATCTTCTA -s Anc1.Anc1refChr2 66995 29 + 144309 TGGGTCAATATAGCATTGTCAATCTTCTA -s Anc2.Anc2refChr2 4119 29 + 27695 TGGGTCAATATAGCATCTTCAATCTTCTA -s mr.mrrefChr0 88839 29 + 130230 TGGGTCAATGTAGCAATGTCAACTTTTCA -s simCow_chr6.simCow.chr6 94399 29 + 602619 TGGGTCAACATAGTAGCTTGAACCTTTTG -s simDog_chr6.simDog.chr6 99781 29 + 593897 TGGGCCAATATAGCATCTTCAATTTTCCA -s simHuman_chr6.simHuman.chr6 88017 29 + 601863 TTGGTCAATATAGCATTGTCAAACTTCTA -s simRat_chr6.simRat.chr6 85823 29 + 647215 TGGGTCAATGTGGCAATGTCAACTTTTGA - -a -s simMouse_chr6.simMouse.chr6 93726 58 + 636262 GTTATACTACTCTCCTCTATCAACAATATTGGGGTCAGTAGAGCCAGTGTGCATAATG -s Anc0.Anc0refChr4 35225 57 - 45765 TCTATACCACTTTCAACTATCAAGAAAAATGGGGTCAAATAAGCCAGGATGCAT-ATG -s Anc1.Anc1refChr2 67024 57 + 144309 TCTATACCACTTTCAACTATCAAGAAAAATGGGGTCAAATAAGCCAGGATGCAT-ATG -s Anc2.Anc2refChr2 4148 57 + 27695 TCTATACCACTTTCAAGTATCAAGAAAAACAGGATCAAATAAGCCAGGATGCAT-ATG -s mr.mrrefChr0 88868 58 + 130230 GCTATACTACTCTCCACTATCAACAATATTGGGGTCAGTTGAGCCAGGGTGCATAATG -s simCow_chr6.simCow.chr6 94434 57 + 602619 TCGATACCCCTTTCAAGTCTCAAGAAAAACTGGATCAAATGAGCCAGGATGCAC-ATG -s simDog_chr6.simDog.chr6 99810 57 + 593897 TCTATATCACCTCCTAGTATCAAGAAAAACAGGACCAAAAAAGCCAGGATACAT-ATG -s simHuman_chr6.simHuman.chr6 88046 55 + 601863 TCTATACCACTTTCAACTATCATGAAGAATGGAGTCAAATAAGCCAGGATGC---ATG -s simRat_chr6.simRat.chr6 85852 58 + 647215 GCTATACTACTCTCCACTATTAACAATATTGGGATCAGTTGGGCCAGGGTGCATAATG - -a -s simMouse_chr6.simMouse.chr6 93784 94 + 636262 GAGGCACAACTTGTCCAGTCAGGAAGGATAGACATGCACATTGACTGTCGGGGCAATGCCAGCTAATATTCTAAAGATCTGCCTGAGGGGGGAA -s Anc0.Anc0refChr4 35282 90 - 45765 TAGTCACATCTTGTTTAGTCAGGAAGAATAGACCTGCACATAAGCTGTTGGGACA----CAGCTAATATTATAAAGATCCCCCTGAGGGTGGAG -s Anc1.Anc1refChr2 67081 90 + 144309 TAGTCACATCTTGTTTAGTCAGGAAGAATAGACCTGCACATAAGCTGTTGGGACA----CAGCTAATATTATAAAGATCCCCCTGAGGGTGGAG -s Anc2.Anc2refChr2 4205 90 + 27695 TTGTCACATCTTGCTTAGTCAAGAAGAATAGACCTGCACATAAGCTGTTGGGACA----GAGCTAATATTATAAAAATCCCCCTGAGGGTGGAG -s mr.mrrefChr0 88926 94 + 130230 GAGGCACAACTTGTCCAGTCAGGAAGGATAGACATGCACATTGACTGTTGGGGCAATGCCAGCTAATATTATAAAGATCTGCCTGAGGGTGGAA -s simCow_chr6.simCow.chr6 94491 90 + 602619 TCGTCACAACTTGCTGAGTCAAGAAAAATAGACCTGCACATAAGCTGTTGGGACA----AAGCTATTGTTGTAAAAATCCTCCTGAGAGTGGAG -s simDog_chr6.simDog.chr6 99870 85 + 593897 TTGCCACATC-----TAGTCAAGAAGAATAGACCACCGCGTAAGTTGTTGGTACA----GAGCTAATATCACAAAAATCCCTCTGAAGGTGGAG -s simHuman_chr6.simHuman.chr6 88101 90 + 601863 CAGTCACATCTTGTTTAGTCAGGAATAATAAATGTGTAAATAAGCTGTTGGGACA----CGGCTAACAGTATAAAGATCCCCCTGAGGGTAGAG -s simRat_chr6.simRat.chr6 85910 94 + 647215 GAGGCATAACTTGTCCCGTCAGGAGGGATAGACATGCACATTGACTGTTGGAGCAATGCTCGCTAATATTATAAAGACCTGCCTGAGGGTGGAA - -a -s simMouse_chr6.simMouse.chr6 93878 31 + 636262 AACTAGCATTCCCAAACTAATGTCCTAGAAA -s Anc0.Anc0refChr4 35377 31 - 45765 TACTAGTATTGCCAAACTAATGCCCTAGAGA -s Anc1.Anc1refChr2 67176 31 + 144309 TACTAGTATTGCCAAACTAATGCCCTAGAGA -s Anc2.Anc2refChr2 4300 31 + 27695 TAATAGTATTGCCAAATTAATGCCCTAAAGA -s mr.mrrefChr0 89020 31 + 130230 AACTAGCATTCCCAAACTAATGTCCTAGAGA -s simCow_chr6.simCow.chr6 94586 20 + 602619 TAATAATATTGCCAAATTAA----------- -s simDog_chr6.simDog.chr6 99960 31 + 593897 TAATTGTAGTGCCAAATTAATGCCCTAAAGA -s simHuman_chr6.simHuman.chr6 88196 31 + 601863 TACTAGTATTGCCAAACTAATGGCCTAGTGA -s simRat_chr6.simRat.chr6 86004 31 + 647215 AACTAGGATTCCCAAACTAATGCCCTAGAGA - -a -s simMouse_chr6.simMouse.chr6 93909 18 + 636262 TTTTTATGGGTACAGATG -s Anc0.Anc0refChr4 35408 17 - 45765 TTTCT-TAGGTCTGGGTG -s Anc1.Anc1refChr2 67207 17 + 144309 TTTCT-TAGGTCTGGGTG -s Anc2.Anc2refChr2 4331 17 + 27695 TTTCT-TAGGTCTGGGTG -s mr.mrrefChr0 89051 18 + 130230 TTTTTATGGGTACAGATG -s simCow_chr6.simCow.chr6 94606 13 + 602619 ----T-TAGGTCTGGGTG -s simDog_chr6.simDog.chr6 99992 17 + 593897 TTTCT-TATGTCTATTTG -s simHuman_chr6.simHuman.chr6 88227 17 + 601863 TTTCT-TTGGTCTGGGTG -s simRat_chr6.simRat.chr6 86035 18 + 647215 TTTTTGTGGGTACAGATG - -a -s simMouse_chr6.simMouse.chr6 93927 22 + 636262 AGCCACAAGGACCCTTTCAGCT -s Anc0.Anc0refChr4 35431 22 - 45765 AGTCACAAAGACACTTCTAGGT -s Anc1.Anc1refChr2 67230 22 + 144309 AGTCACAAAGACACTTCTAGGT -s Anc2.Anc2refChr2 4354 22 + 27695 AGTCATAGAGATACTTCTCGGT -s mr.mrrefChr0 89075 22 + 130230 AGTCACAAGGACCCTTTCAGCT -s simCow_chr6.simCow.chr6 94635 12 + 602619 GGGAAAGTAAAT---------- -s simDog_chr6.simDog.chr6 100015 22 + 593897 AGTCATAGAGATACTTCTCGGT -s simHuman_chr6.simHuman.chr6 88250 22 + 601863 AGTCACAAAGACTCTTATAGGT -s simRat_chr6.simRat.chr6 86059 22 + 647215 AGTCACAAGGACCCTTTGAGCT - -a -s simMouse_chr6.simMouse.chr6 93949 13 + 636262 CTATCAGGAGGAA -s Anc0.Anc0refChr4 35453 11 - 45765 CTGGGTGGAGC-- -s Anc1.Anc1refChr2 67252 13 + 144309 CTGGGTGGAGCAA -s Anc2.Anc2refChr2 4376 11 + 27695 CTGGGTGGAGC-- -s mr.mrrefChr0 89097 13 + 130230 CTATGAGGAGGAA -s simDog_chr6.simDog.chr6 100038 11 + 593897 CTGGGTGGAGC-- -s simHuman_chr6.simHuman.chr6 88272 13 + 601863 CTGGGTGGAGCAA -s simRat_chr6.simRat.chr6 86081 13 + 647215 CTATGGGGAGGAA - -a -s simMouse_chr6.simMouse.chr6 93962 30 + 636262 GAATTGAGGGGCAAGTAAATACATGGCAGA -s Anc0.Anc0refChr4 35464 9 - 45765 --------------------ACATGGCAG- -s Anc1.Anc1refChr2 67265 22 + 144309 GAATCGAGAG-------ATAACATGGCAG- -s Anc2.Anc2refChr2 4387 9 + 27695 --------------------ACTTGGCAG- -s mr.mrrefChr0 89110 30 + 130230 GAATTGAGGGGCAAGTAATTACATGGCAGA -s simCow_chr6.simCow.chr6 94647 9 + 602619 --------------------ACTTGGCAG- -s simDog_chr6.simDog.chr6 100049 3 + 593897 --------------------------CAA- -s simHuman_chr6.simHuman.chr6 88288 22 + 601863 GAATCGAGAG-------ATAACATGGCTG- -s simRat_chr6.simRat.chr6 86094 30 + 647215 GAATTGAGGGTCGAGTAATTACATGGCGGA - -a -s simMouse_chr6.simMouse.chr6 93992 24 + 636262 GAAGGAACACAAATCGGAAACTTG -s Anc0.Anc0refChr4 35473 24 - 45765 GAAGGAACACAAATTGTAAACTTG -s Anc1.Anc1refChr2 67287 24 + 144309 GAAGGAACACAAATTGTAAACTTG -s Anc2.Anc2refChr2 4396 24 + 27695 GAAGGCATGCAATTTGTAAGGATG -s mr.mrrefChr0 89140 24 + 130230 GAAGGAACACAAATTGGAAACTTG -s simCow_chr6.simCow.chr6 94657 24 + 602619 GAAGGGATGCAATTTGTAAGTCTG -s simDog_chr6.simDog.chr6 100052 24 + 593897 AAAGGCTTGAAATCTCTATGGATC -s simHuman_chr6.simHuman.chr6 88310 24 + 601863 GAAGGAACACAAATTGAAAACTTG -s simRat_chr6.simRat.chr6 86124 24 + 647215 GAAGGAATACAAATTGGAAACTTG - -a -s simMouse_chr6.simMouse.chr6 94016 5 + 636262 TGCCC -s Anc0.Anc0refChr4 35497 5 - 45765 TGTCC -s Anc1.Anc1refChr2 67311 5 + 144309 TGTCC -s Anc2.Anc2refChr2 4420 5 + 27695 TGTCC -s mr.mrrefChr0 89164 5 + 130230 TGCCC -s simCow_chr6.simCow.chr6 94681 5 + 602619 GGTCC -s simDog_chr6.simDog.chr6 100165 5 + 593897 TGTCC -s simHuman_chr6.simHuman.chr6 88334 5 + 601863 TGTTC -s simRat_chr6.simRat.chr6 86148 5 + 647215 TGCCC - -a -s simMouse_chr6.simMouse.chr6 94021 36 + 636262 ATGACAATGGTACCAAGTCAAATAGATTAATATATA -s Anc0.Anc0refChr4 35502 36 - 45765 AAGTGGATTGTTTCAAGTGGGATAGATTAATATATC -s Anc1.Anc1refChr2 67316 36 + 144309 AAGTGGATTGTTTCAAGTGGGATAGATTAATATATC -s Anc2.Anc2refChr2 4426 36 + 27695 CAGTGGATTGTTTCAAGTGGGATAGATTAATAAATC -s mr.mrrefChr0 89169 36 + 130230 ATGACAATGGTATCAAGTCAAATAGATTAATATATA -s simCow_chr6.simCow.chr6 94687 35 + 602619 CAGTGGATT-TTTCAAGTGGCATAGATTAATAAATT -s simDog_chr6.simDog.chr6 100171 36 + 593897 CAGTGGATTGTTTCAAGTGGGATAGATTGCTAAATC -s simHuman_chr6.simHuman.chr6 88339 36 + 601863 AAGTAGATTATTTCAAGTGGGATAGACTAATATATG -s simRat_chr6.simRat.chr6 86153 36 + 647215 ATGACAATGGTGTCAAGTCAAATAGATTAATATATA - -a -s simMouse_chr6.simMouse.chr6 94057 17 + 636262 AAAAGTTCAACAATATA -s Anc0.Anc0refChr4 35547 14 - 45765 ATAAGCT---TACTATA -s Anc1.Anc1refChr2 67361 14 + 144309 ATAAGCT---TACTATA -s Anc2.Anc2refChr2 4471 14 + 27695 ATAATCT---CACTGTG -s mr.mrrefChr0 89205 14 + 130230 ATAAGCT---TAATATA -s simCow_chr6.simCow.chr6 94731 12 + 602619 AT--TCT---CACTGTG -s simDog_chr6.simDog.chr6 100216 4 + 593897 ATAA------------- -s simHuman_chr6.simHuman.chr6 88384 14 + 601863 ATAAGCT---TACTATA -s simRat_chr6.simRat.chr6 86189 14 + 647215 ATAAGCT---TAATATA - -a -s simMouse_chr6.simMouse.chr6 94074 10 + 636262 CAATAATTAG -s Anc0.Anc0refChr4 35561 10 - 45765 TGATAATTAT -s Anc1.Anc1refChr2 67375 10 + 144309 TGATAATTAT -s Anc2.Anc2refChr2 4485 10 + 27695 TGATAATTAT -s mr.mrrefChr0 89219 10 + 130230 CAATAATTAG -s simCow_chr6.simCow.chr6 94796 10 + 602619 TGATAATTAT -s simHuman_chr6.simHuman.chr6 88398 10 + 601863 TGATAATTAT -s simRat_chr6.simRat.chr6 86203 10 + 647215 CAATACTTAG - -a -s simMouse_chr6.simMouse.chr6 94084 31 + 636262 ATGCAAAATTGACTAAGCATCTGTGTGGACA -s Anc0.Anc0refChr4 35613 31 - 45765 ATGCTAAATGGACAAAGCATAAATGTTGATG -s Anc1.Anc1refChr2 67427 31 + 144309 ATGCTAAATGGACAAAGCATAAATGTTGATG -s Anc2.Anc2refChr2 4537 31 + 27695 ATGCTAATTGGACAAGGCATAAATGTTGAAT -s mr.mrrefChr0 89229 31 + 130230 ATGCAAAATTGACTAAGCATCTGTGTGGACA -s simCow_chr6.simCow.chr6 94843 31 + 602619 ATGTTAACTGGACAAGGCATAAATTTTGAGT -s simDog_chr6.simDog.chr6 100242 31 + 593897 ATGCTAATTGAATGAGGCATAAATGGTGAAG -s simHuman_chr6.simHuman.chr6 88457 31 + 601863 ATCCTAAATGGACAAAGCTTACATGTAGATG -s simRat_chr6.simRat.chr6 86213 31 + 647215 ATGCAAAATTGATAAAGCATTTGTGTCAACA - -a -s simMouse_chr6.simMouse.chr6 94115 7 + 636262 TGTGCTG -s Anc0.Anc0refChr4 35644 1 - 45765 T------ -s Anc1.Anc1refChr2 67458 1 + 144309 T------ -s Anc2.Anc2refChr2 4568 1 + 27695 T------ -s mr.mrrefChr0 89260 7 + 130230 TGTGCTG -s simCow_chr6.simCow.chr6 94875 1 + 602619 T------ -s simDog_chr6.simDog.chr6 100273 1 + 593897 T------ -s simHuman_chr6.simHuman.chr6 88488 1 + 601863 T------ -s simRat_chr6.simRat.chr6 86244 7 + 647215 TGTGCTG - -a -s simMouse_chr6.simMouse.chr6 94122 2 + 636262 AT -s Anc0.Anc0refChr4 35645 2 - 45765 AT -s Anc1.Anc1refChr2 67459 2 + 144309 AT -s Anc2.Anc2refChr2 4569 2 + 27695 GT -s mr.mrrefChr0 89267 2 + 130230 AT -s simCow_chr6.simCow.chr6 94876 2 + 602619 GT -s simDog_chr6.simDog.chr6 100281 2 + 593897 GT -s simRat_chr6.simRat.chr6 86251 2 + 647215 AT - -a -s simMouse_chr6.simMouse.chr6 94124 18 + 636262 TGTTATATTAACTGCCTG -s Anc1.Anc1refChr6 56112 18 - 197743 TGTAATTTCAAAAAGTTG -s mr.mrrefChr0 89269 18 + 130230 TGTTATATTAACTGCCTG -s simHuman_chr6.simHuman.chr6 88716 18 + 601863 TGTAATTTCAAAAAGTTG -s simRat_chr6.simRat.chr6 86253 18 + 647215 AGTAATATTAACTACCTG - -a -s simMouse_chr6.simMouse.chr6 94142 15 + 636262 TGCCAAAGCATATTG -s Anc1.Anc1refChr6 56130 14 - 197743 TGCC-AAGCATATCA -s mr.mrrefChr0 89287 14 + 130230 TGCC-AAGCATATTG -s simHuman_chr6.simHuman.chr6 88736 14 + 601863 TGCC-AAGCATATCA -s simRat_chr6.simRat.chr6 86271 14 + 647215 TGCC-AAGCATATTG - -a -s simMouse_chr6.simMouse.chr6 94157 2 + 636262 AC -s Anc0.Anc0refChr3 114706 2 - 222631 AC -s Anc1.Anc1refChr6 56144 2 - 197743 AC -s Anc2.Anc2refChr1 123194 2 - 142988 AC -s Anc2.Anc2refChr2 4602 2 + 27695 AC -s mr.mrrefChr0 89301 2 + 130230 AC -s simCow_chr6.simCow.chr6 94909 2 + 602619 AT -s simCow_chr6.simCow.chr6 126316 2 - 602619 AC -s simDog_chr6.simDog.chr6 100314 2 + 593897 GC -s simHuman_chr6.simHuman.chr6 88750 2 + 601863 AC -s simRat_chr6.simRat.chr6 86285 2 + 647215 AC - -a -s simMouse_chr6.simMouse.chr6 94159 2 + 636262 AT -s Anc0.Anc0refChr3 114708 2 - 222631 AT -s Anc1.Anc1refChr6 56146 2 - 197743 AT -s Anc2.Anc2refChr1 123196 2 - 142988 AT -s Anc2.Anc2refChr2 4604 2 + 27695 AT -s mr.mrrefChr0 89303 2 + 130230 AT -s mr.mrrefChr3 135234 2 - 181027 AT -s simCow_chr6.simCow.chr6 94911 2 + 602619 GT -s simCow_chr6.simCow.chr6 126318 2 - 602619 AT -s simDog_chr6.simDog.chr6 100316 2 + 593897 AT -s simHuman_chr6.simHuman.chr6 89061 2 + 601863 AT -s simHuman_chr6.simHuman.chr6 128418 2 - 601863 AT -s simMouse_chr6.simMouse.chr6 144656 2 - 636262 AT -s simRat_chr6.simRat.chr6 147481 2 - 647215 AT -s simRat_chr6.simRat.chr6 86287 2 + 647215 TT - -a -s simMouse_chr6.simMouse.chr6 94161 3 + 636262 ATA -s Anc0.Anc0refChr3 114710 3 - 222631 GTC -s Anc1.Anc1refChr6 56148 3 - 197743 GTC -s Anc2.Anc2refChr1 123198 3 - 142988 GCA -s Anc2.Anc2refChr2 4606 3 + 27695 CTC -s mr.mrrefChr0 89305 3 + 130230 ATA -s mr.mrrefChr3 135236 3 - 181027 GTC -s simCow_chr6.simCow.chr6 126320 3 - 602619 GCA -s simDog_chr6.simDog.chr6 100318 3 + 593897 CTC -s simHuman_chr6.simHuman.chr6 89063 3 + 601863 GTC -s simHuman_chr6.simHuman.chr6 128420 3 - 601863 GTC -s simMouse_chr6.simMouse.chr6 144658 3 - 636262 GTC -s simRat_chr6.simRat.chr6 147483 3 - 647215 GTC -s simRat_chr6.simRat.chr6 86289 3 + 647215 GTA - -a -s simMouse_chr6.simMouse.chr6 94164 5 + 636262 CTATG -s Anc0.Anc0refChr3 114713 5 - 222631 TTATA -s Anc1.Anc1refChr6 56151 5 - 197743 TTATA -s Anc2.Anc2refChr1 123201 5 - 142988 TTATA -s Anc2.Anc2refChr2 4609 5 + 27695 TTATG -s mr.mrrefChr0 89308 5 + 130230 CTATG -s mr.mrrefChr3 135239 5 - 181027 TTATT -s simCow_chr6.simCow.chr6 126323 5 - 602619 TTATA -s simDog_chr6.simDog.chr6 100321 5 + 593897 TTATG -s simHuman_chr6.simHuman.chr6 89073 5 + 601863 TTATA -s simHuman_chr6.simHuman.chr6 128423 5 - 601863 TTATA -s simMouse_chr6.simMouse.chr6 144661 5 - 636262 TTATT -s simRat_chr6.simRat.chr6 147486 5 - 647215 TTATT -s simRat_chr6.simRat.chr6 86292 5 + 647215 CTATG - -a -s simMouse_chr6.simMouse.chr6 94169 2 + 636262 AC -s Anc0.Anc0refChr3 114718 2 - 222631 AC -s Anc1.Anc1refChr6 56156 2 - 197743 AC -s Anc2.Anc2refChr1 123206 2 - 142988 AC -s Anc2.Anc2refChr2 4614 2 + 27695 AC -s mr.mrrefChr0 89313 2 + 130230 AC -s mr.mrrefChr3 135244 2 - 181027 AC -s simCow_chr6.simCow.chr6 126328 2 - 602619 AC -s simDog_chr6.simDog.chr6 100326 2 + 593897 AC -s simHuman_chr6.simHuman.chr6 89078 2 + 601863 AC -s simHuman_chr6.simHuman.chr6 128428 2 - 601863 AC -s simMouse_chr6.simMouse.chr6 144666 2 - 636262 AC -s simRat_chr6.simRat.chr6 86297 2 + 647215 AC - -a -s simMouse_chr6.simMouse.chr6 94171 2 + 636262 AT -s Anc0.Anc0refChr3 114720 2 - 222631 AT -s Anc1.Anc1refChr6 56158 2 - 197743 AT -s Anc2.Anc2refChr1 123208 2 - 142988 AT -s Anc2.Anc2refChr2 4616 2 + 27695 AT -s mr.mrrefChr0 89315 2 + 130230 AT -s mr.mrrefChr3 135246 2 - 181027 AT -s simCow_chr6.simCow.chr6 94913 2 + 602619 AT -s simCow_chr6.simCow.chr6 126330 2 - 602619 AT -s simDog_chr6.simDog.chr6 100328 2 + 593897 AT -s simHuman_chr6.simHuman.chr6 89080 2 + 601863 AT -s simHuman_chr6.simHuman.chr6 128430 2 - 601863 AT -s simMouse_chr6.simMouse.chr6 144668 2 - 636262 AT -s simRat_chr6.simRat.chr6 86299 2 + 647215 AT - -a -s simMouse_chr6.simMouse.chr6 94173 2 + 636262 GC -s Anc0.Anc0refChr3 114724 2 - 222631 GC -s Anc1.Anc1refChr6 56162 2 - 197743 GC -s Anc2.Anc2refChr1 123212 2 - 142988 GC -s Anc2.Anc2refChr2 4620 2 + 27695 GC -s mr.mrrefChr0 89317 2 + 130230 GC -s mr.mrrefChr3 135250 2 - 181027 CT -s simCow_chr6.simCow.chr6 94917 2 + 602619 GC -s simCow_chr6.simCow.chr6 126334 2 - 602619 GC -s simDog_chr6.simDog.chr6 100332 2 + 593897 GC -s simHuman_chr6.simHuman.chr6 89084 2 + 601863 GC -s simHuman_chr6.simHuman.chr6 128434 2 - 601863 GC -s simMouse_chr6.simMouse.chr6 144672 2 - 636262 CT -s simRat_chr6.simRat.chr6 147491 2 - 647215 CA -s simRat_chr6.simRat.chr6 86301 2 + 647215 GC - -a -s simMouse_chr6.simMouse.chr6 94175 9 + 636262 TTAACTCTC -s Anc0.Anc0refChr3 114726 9 - 222631 TTAACTTTC -s Anc1.Anc1refChr6 56164 9 - 197743 TTAACTCTC -s Anc2.Anc2refChr1 123214 9 - 142988 TTAATTTTT -s Anc2.Anc2refChr2 4622 9 + 27695 TTAACTTTC -s mr.mrrefChr0 89319 9 + 130230 TTAACTCTC -s mr.mrrefChr3 135252 9 - 181027 TTAACTCTT -s simCow_chr6.simCow.chr6 94919 9 + 602619 TTATCTTTT -s simCow_chr6.simCow.chr6 126337 9 - 602619 TTAATTTTT -s simDog_chr6.simDog.chr6 100334 9 + 593897 TTAACCTTC -s simHuman_chr6.simHuman.chr6 89086 9 + 601863 TTAACTTTC -s simHuman_chr6.simHuman.chr6 128436 9 - 601863 TTAGCTCTC -s simMouse_chr6.simMouse.chr6 144674 8 - 636262 TTAACTC-T -s simRat_chr6.simRat.chr6 147493 9 - 647215 TTAACTCTT -s simRat_chr6.simRat.chr6 86303 9 + 647215 TCGACTCTC - -a -s simMouse_chr6.simMouse.chr6 94184 5 + 636262 TTACT -s Anc0.Anc0refChr3 114741 5 - 222631 TTGTT -s Anc1.Anc1refChr6 56179 5 - 197743 TTGTT -s Anc2.Anc2refChr1 123229 5 - 142988 TTGTT -s Anc2.Anc2refChr2 4637 5 + 27695 ATGTT -s mr.mrrefChr0 89328 5 + 130230 TTACT -s mr.mrrefChr3 135267 5 - 181027 TTGTT -s simCow_chr6.simCow.chr6 94934 5 + 602619 ATGTT -s simCow_chr6.simCow.chr6 126352 5 - 602619 TTGTT -s simDog_chr6.simDog.chr6 100349 5 + 593897 ACGTT -s simHuman_chr6.simHuman.chr6 89102 5 + 601863 TTGTT -s simHuman_chr6.simHuman.chr6 128451 5 - 601863 TTGTA -s simMouse_chr6.simMouse.chr6 144688 5 - 636262 TTGTT -s simRat_chr6.simRat.chr6 147508 5 - 647215 TTGAT -s simRat_chr6.simRat.chr6 86312 5 + 647215 TTACT - -a -s simMouse_chr6.simMouse.chr6 94189 4 + 636262 TACA -s Anc0.Anc0refChr3 114746 4 - 222631 TACA -s Anc1.Anc1refChr6 56184 4 - 197743 TACA -s Anc2.Anc2refChr1 123234 4 - 142988 TAAA -s Anc2.Anc2refChr2 4642 4 + 27695 AACA -s mr.mrrefChr0 89333 4 + 130230 TACA -s mr.mrrefChr3 135272 4 - 181027 TACA -s simCow_chr6.simCow.chr6 94939 4 + 602619 CACA -s simCow_chr6.simCow.chr6 126357 4 - 602619 TGTA -s simDog_chr6.simDog.chr6 100354 4 + 593897 AACA -s simDog_chr6.simDog.chr6 127235 4 - 593897 TAAA -s simHuman_chr6.simHuman.chr6 89107 4 + 601863 TACA -s simHuman_chr6.simHuman.chr6 128456 4 - 601863 TACA -s simMouse_chr6.simMouse.chr6 144693 4 - 636262 TGCA -s simRat_chr6.simRat.chr6 147513 4 - 647215 TACA -s simRat_chr6.simRat.chr6 86317 4 + 647215 TACA - -a -s simMouse_chr6.simMouse.chr6 94193 1 + 636262 A -s Anc0.Anc0refChr3 114750 1 - 222631 A -s Anc1.Anc1refChr6 56188 1 - 197743 A -s Anc2.Anc2refChr1 123238 1 - 142988 A -s Anc2.Anc2refChr2 4646 1 + 27695 A -s mr.mrrefChr0 89337 1 + 130230 A -s mr.mrrefChr3 135276 1 - 181027 A -s simCow_chr6.simCow.chr6 126361 1 - 602619 A -s simDog_chr6.simDog.chr6 100358 1 + 593897 A -s simDog_chr6.simDog.chr6 127239 1 - 593897 A -s simHuman_chr6.simHuman.chr6 89111 1 + 601863 A -s simHuman_chr6.simHuman.chr6 128460 1 - 601863 A -s simMouse_chr6.simMouse.chr6 144697 1 - 636262 A -s simRat_chr6.simRat.chr6 147517 1 - 647215 A -s simRat_chr6.simRat.chr6 86321 1 + 647215 G - -a -s simMouse_chr6.simMouse.chr6 94194 4 + 636262 GCCA -s Anc0.Anc0refChr3 114751 4 - 222631 GACA -s Anc1.Anc1refChr6 56189 4 - 197743 GACA -s Anc2.Anc2refChr1 123239 4 - 142988 GACA -s Anc2.Anc2refChr2 4647 4 + 27695 GACA -s mr.mrrefChr0 89338 4 + 130230 GCCA -s mr.mrrefChr3 135277 4 - 181027 GACA -s simCow_chr6.simCow.chr6 94943 4 + 602619 GACA -s simCow_chr6.simCow.chr6 126362 4 - 602619 GGCA -s simDog_chr6.simDog.chr6 100359 4 + 593897 GACA -s simDog_chr6.simDog.chr6 127240 4 - 593897 GACA -s simHuman_chr6.simHuman.chr6 89112 4 + 601863 CACA -s simHuman_chr6.simHuman.chr6 128461 4 - 601863 GACA -s simMouse_chr6.simMouse.chr6 144698 4 - 636262 GACA -s simRat_chr6.simRat.chr6 147518 4 - 647215 GACA -s simRat_chr6.simRat.chr6 86322 4 + 647215 GCCG - -a -s simMouse_chr6.simMouse.chr6 94198 3 + 636262 AGA -s Anc0.Anc0refChr3 114755 3 - 222631 AAG -s Anc1.Anc1refChr6 56193 3 - 197743 AAG -s Anc2.Anc2refChr1 123243 3 - 142988 AAG -s Anc2.Anc2refChr2 4651 3 + 27695 TAA -s mr.mrrefChr0 89342 3 + 130230 AGG -s mr.mrrefChr3 135281 3 - 181027 AAG -s simCow_chr6.simCow.chr6 94947 3 + 602619 TAA -s simCow_chr6.simCow.chr6 126366 3 - 602619 GGG -s simDog_chr6.simDog.chr6 127244 3 - 593897 AAG -s simHuman_chr6.simHuman.chr6 89116 3 + 601863 AGG -s simHuman_chr6.simHuman.chr6 128465 3 - 601863 AAG -s simMouse_chr6.simMouse.chr6 144702 3 - 636262 AAG -s simRat_chr6.simRat.chr6 147522 3 - 647215 AAG -s simRat_chr6.simRat.chr6 86326 3 + 647215 AGG - -a -s simMouse_chr6.simMouse.chr6 94201 7 + 636262 TTCCTTA -s Anc0.Anc0refChr3 114758 7 - 222631 TTCCCTA -s Anc1.Anc1refChr6 56196 7 - 197743 TTCCCTA -s Anc2.Anc2refChr1 123246 7 - 142988 TTCCCTA -s Anc2.Anc2refChr2 4654 7 + 27695 TCCCCTA -s mr.mrrefChr0 89345 7 + 130230 TTCCCTA -s mr.mrrefChr3 135284 7 - 181027 GCCCCTA -s simCow_chr6.simCow.chr6 94950 7 + 602619 TCCCCTA -s simCow_chr6.simCow.chr6 126369 7 - 602619 TTCACTA -s simDog_chr6.simDog.chr6 100363 7 + 593897 TCCCACA -s simDog_chr6.simDog.chr6 127247 7 - 593897 TTCCCTA -s simHuman_chr6.simHuman.chr6 89119 7 + 601863 TTCCCTA -s simHuman_chr6.simHuman.chr6 128468 7 - 601863 ACCCCTG -s simMouse_chr6.simMouse.chr6 144705 7 - 636262 GCCCCTA -s simRat_chr6.simRat.chr6 147525 7 - 647215 GCCCCTA -s simRat_chr6.simRat.chr6 86329 7 + 647215 TTCCCTA - -a -s simMouse_chr6.simMouse.chr6 94208 10 + 636262 TTTTGCTTAA -s Anc0.Anc0refChr3 114765 10 - 222631 TTTTCCTTAT -s Anc1.Anc1refChr6 56203 10 - 197743 TTTTCCTTAT -s Anc2.Anc2refChr1 123253 9 - 142988 TT-TTCTTAT -s Anc2.Anc2refChr2 4661 10 + 27695 TTGTCCTTAT -s mr.mrrefChr0 89352 10 + 130230 TTTTGCTTAT -s mr.mrrefChr3 135293 10 - 181027 TACTTCTGAT -s simCow_chr6.simCow.chr6 94957 10 + 602619 TTTCCCTTTT -s simCow_chr6.simCow.chr6 126376 9 - 602619 TT-TTATTAT -s simDog_chr6.simDog.chr6 100370 10 + 593897 TTGTGCCCAT -s simDog_chr6.simDog.chr6 127254 9 - 593897 TT-TTCTTAT -s simHuman_chr6.simHuman.chr6 89126 10 + 601863 TCCTCCTTAT -s simHuman_chr6.simHuman.chr6 128475 9 - 601863 TTTTCAT-AT -s simMouse_chr6.simMouse.chr6 144714 10 - 636262 CACTTCTGAT -s simRat_chr6.simRat.chr6 147534 10 - 647215 TGCTTCTGAT -s simRat_chr6.simRat.chr6 86336 10 + 647215 TTTTGCTCGT - -a -s simMouse_chr6.simMouse.chr6 94218 1 + 636262 A -s Anc0.Anc0refChr3 114775 1 - 222631 G -s Anc1.Anc1refChr6 56213 1 - 197743 G -s Anc2.Anc2refChr1 123262 1 - 142988 G -s Anc2.Anc2refChr2 4671 1 + 27695 G -s mr.mrrefChr0 89362 1 + 130230 A -s simCow_chr6.simCow.chr6 94967 1 + 602619 G -s simCow_chr6.simCow.chr6 126385 1 - 602619 A -s simDog_chr6.simDog.chr6 100380 1 + 593897 G -s simDog_chr6.simDog.chr6 127263 1 - 593897 G -s simHuman_chr6.simHuman.chr6 89136 1 + 601863 G -s simHuman_chr6.simHuman.chr6 128484 1 - 601863 G -s simRat_chr6.simRat.chr6 86346 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 94219 1 + 636262 C -s Anc0.Anc0refChr3 114776 1 - 222631 G -s Anc1.Anc1refChr6 56214 1 - 197743 G -s Anc2.Anc2refChr1 123263 1 - 142988 G -s Anc2.Anc2refChr2 4672 1 + 27695 G -s mr.mrrefChr0 89363 1 + 130230 C -s simCow_chr6.simCow.chr6 94968 1 + 602619 G -s simCow_chr6.simCow.chr6 126386 1 - 602619 G -s simDog_chr6.simDog.chr6 100382 1 + 593897 G -s simDog_chr6.simDog.chr6 127264 1 - 593897 G -s simHuman_chr6.simHuman.chr6 89137 1 + 601863 G -s simHuman_chr6.simHuman.chr6 128485 1 - 601863 A -s simRat_chr6.simRat.chr6 86347 1 + 647215 C - -a -s simMouse_chr6.simMouse.chr6 94220 8 + 636262 CTCACAGT -s Anc0.Anc0refChr3 114777 8 - 222631 CTCTCAGT -s Anc1.Anc1refChr6 56215 8 - 197743 CTCTCAGT -s Anc2.Anc2refChr1 123264 8 - 142988 CACTAGTT -s Anc2.Anc2refChr2 4673 8 + 27695 CTCTTAGC -s mr.mrrefChr0 89364 8 + 130230 CTCACAGT -s mr.mrrefChr3 135303 8 - 181027 CACCTAGT -s simCow_chr6.simCow.chr6 94969 8 + 602619 CTTTTAGC -s simCow_chr6.simCow.chr6 126387 8 - 602619 CACTAGTT -s simDog_chr6.simDog.chr6 100383 5 + 593897 CTCTT--- -s simDog_chr6.simDog.chr6 127265 1 - 593897 C------- -s simHuman_chr6.simHuman.chr6 89138 8 + 601863 CTCTTAGT -s simHuman_chr6.simHuman.chr6 128486 8 - 601863 CTCTCACT -s simMouse_chr6.simMouse.chr6 144724 8 - 636262 CACCTAGT -s simRat_chr6.simRat.chr6 147544 8 - 647215 CACCTAGT -s simRat_chr6.simRat.chr6 86348 8 + 647215 CTCACAGC - -a -s simMouse_chr6.simMouse.chr6 94228 2 + 636262 GA -s Anc0.Anc0refChr3 114786 2 - 222631 GG -s Anc1.Anc1refChr6 56224 2 - 197743 GG -s Anc2.Anc2refChr1 123273 2 - 142988 GG -s Anc2.Anc2refChr2 4682 2 + 27695 GG -s mr.mrrefChr0 89372 2 + 130230 GA -s mr.mrrefChr3 135312 2 - 181027 GG -s simCow_chr6.simCow.chr6 94978 2 + 602619 GG -s simCow_chr6.simCow.chr6 126396 2 - 602619 GG -s simHuman_chr6.simHuman.chr6 89147 2 + 601863 GG -s simHuman_chr6.simHuman.chr6 128495 2 - 601863 GG -s simMouse_chr6.simMouse.chr6 144733 2 - 636262 GG -s simRat_chr6.simRat.chr6 147553 2 - 647215 GG -s simRat_chr6.simRat.chr6 86356 2 + 647215 GA - -a -s simMouse_chr6.simMouse.chr6 94230 9 + 636262 TCCAGATTG -s Anc0.Anc0refChr3 114788 9 - 222631 TCCAGATGG -s Anc1.Anc1refChr6 56226 9 - 197743 TCCAGATGG -s Anc2.Anc2refChr1 123275 9 - 142988 TCCAGATGG -s Anc2.Anc2refChr2 4684 9 + 27695 TCCGGATGG -s mr.mrrefChr0 89374 9 + 130230 TCCAGATTG -s mr.mrrefChr3 135314 9 - 181027 GCCAGATGG -s simCow_chr6.simCow.chr6 94980 9 + 602619 TCCGGATGG -s simCow_chr6.simCow.chr6 126398 9 - 602619 TCCAGATGG -s simHuman_chr6.simHuman.chr6 89150 9 + 601863 GCTGAATGA -s simHuman_chr6.simHuman.chr6 128497 9 - 601863 TTCAGAAGG -s simMouse_chr6.simMouse.chr6 144735 9 - 636262 GCCAGATGG -s simRat_chr6.simRat.chr6 147555 9 - 647215 GCCTGATGG -s simRat_chr6.simRat.chr6 86358 9 + 647215 TCCAGATTG - -a -s simMouse_chr6.simMouse.chr6 94239 2 + 636262 GC -s Anc0.Anc0refChr3 114797 2 - 222631 GC -s Anc1.Anc1refChr6 56235 2 - 197743 GC -s Anc2.Anc2refChr1 123284 2 - 142988 GC -s Anc2.Anc2refChr2 4693 2 + 27695 AC -s mr.mrrefChr0 89383 2 + 130230 GC -s mr.mrrefChr3 135323 2 - 181027 GC -s simCow_chr6.simCow.chr6 94989 2 + 602619 AC -s simCow_chr6.simCow.chr6 126407 2 - 602619 GC -s simDog_chr6.simDog.chr6 127266 1 - 593897 -C -s simHuman_chr6.simHuman.chr6 128506 2 - 601863 GC -s simMouse_chr6.simMouse.chr6 144744 2 - 636262 AC -s simRat_chr6.simRat.chr6 147564 2 - 647215 GC -s simRat_chr6.simRat.chr6 86367 2 + 647215 GC - -a -s simMouse_chr6.simMouse.chr6 94241 1 + 636262 C -s Anc0.Anc0refChr3 114799 1 - 222631 C -s Anc1.Anc1refChr6 56237 1 - 197743 C -s Anc2.Anc2refChr1 123286 1 - 142988 T -s Anc2.Anc2refChr2 4695 1 + 27695 C -s mr.mrrefChr0 89385 1 + 130230 C -s mr.mrrefChr3 135325 1 - 181027 C -s simCow_chr6.simCow.chr6 94991 1 + 602619 C -s simCow_chr6.simCow.chr6 126409 1 - 602619 T -s simDog_chr6.simDog.chr6 127267 1 - 593897 T -s simHuman_chr6.simHuman.chr6 89159 1 + 601863 C -s simHuman_chr6.simHuman.chr6 128508 1 - 601863 C -s simMouse_chr6.simMouse.chr6 144746 1 - 636262 C -s simRat_chr6.simRat.chr6 147566 1 - 647215 C -s simRat_chr6.simRat.chr6 86369 1 + 647215 C - -a -s simMouse_chr6.simMouse.chr6 94242 1 + 636262 C -s Anc0.Anc0refChr3 114800 1 - 222631 A -s Anc1.Anc1refChr6 56238 1 - 197743 A -s Anc2.Anc2refChr1 123287 1 - 142988 G -s mr.mrrefChr0 89386 1 + 130230 C -s mr.mrrefChr3 135326 1 - 181027 A -s simCow_chr6.simCow.chr6 126410 1 - 602619 G -s simDog_chr6.simDog.chr6 127268 1 - 593897 G -s simHuman_chr6.simHuman.chr6 89160 1 + 601863 A -s simHuman_chr6.simHuman.chr6 128509 1 - 601863 T -s simMouse_chr6.simMouse.chr6 144747 1 - 636262 A -s simRat_chr6.simRat.chr6 147567 1 - 647215 A -s simRat_chr6.simRat.chr6 86370 1 + 647215 C - -a -s simMouse_chr6.simMouse.chr6 94243 15 + 636262 ATGAGTTCATGTGGA -s Anc0.Anc0refChr3 114801 13 - 222631 ATGAGTTCATGTG-- -s Anc1.Anc1refChr6 56239 15 - 197743 ATGAGTTCATGTGTA -s Anc2.Anc2refChr1 123288 10 - 142988 ATGAGTTCAT----- -s Anc2.Anc2refChr2 4696 13 + 27695 ATGAGTTCATGTG-- -s mr.mrrefChr0 89387 15 + 130230 ATGAGTTCATGTGAA -s mr.mrrefChr3 135327 15 - 181027 TTGAGGTCATGTGTA -s simCow_chr6.simCow.chr6 94993 13 + 602619 ATGAGTTCATGTG-- -s simCow_chr6.simCow.chr6 126411 10 - 602619 CTGAGTTCAT----- -s simDog_chr6.simDog.chr6 127269 10 - 593897 ATGAGTTCAT----- -s simHuman_chr6.simHuman.chr6 89161 15 + 601863 ATGAGATGATGTGAG -s simHuman_chr6.simHuman.chr6 128510 15 - 601863 ATGAGTTCATTTGTA -s simMouse_chr6.simMouse.chr6 144748 15 - 636262 TTTAGGTCATGTGCA -s simRat_chr6.simRat.chr6 147568 15 - 647215 TTGAGGTCATGGGTG -s simRat_chr6.simRat.chr6 86371 15 + 647215 ATGAGTTCATGTAAA - -a -s simMouse_chr6.simMouse.chr6 94258 3 + 636262 AGG -s Anc0.Anc0refChr3 114814 3 - 222631 GTG -s Anc1.Anc1refChr6 56254 3 - 197743 GGG -s Anc2.Anc2refChr1 123298 3 - 142988 ATG -s Anc2.Anc2refChr2 4709 3 + 27695 GTG -s mr.mrrefChr0 89402 3 + 130230 AGG -s mr.mrrefChr3 135342 3 - 181027 GGG -s simCow_chr6.simCow.chr6 126421 3 - 602619 GCA -s simDog_chr6.simDog.chr6 100388 3 + 593897 GTG -s simDog_chr6.simDog.chr6 127279 3 - 593897 ATG -s simHuman_chr6.simHuman.chr6 89176 3 + 601863 ATG -s simHuman_chr6.simHuman.chr6 128525 3 - 601863 GAG -s simMouse_chr6.simMouse.chr6 144763 3 - 636262 GGG -s simRat_chr6.simRat.chr6 147583 3 - 647215 CGG -s simRat_chr6.simRat.chr6 86386 3 + 647215 AGA - -a -s simMouse_chr6.simMouse.chr6 94261 1 + 636262 T -s Anc0.Anc0refChr3 114817 1 - 222631 T -s Anc1.Anc1refChr6 56257 1 - 197743 T -s Anc2.Anc2refChr1 123301 1 - 142988 C -s Anc2.Anc2refChr2 4712 1 + 27695 T -s mr.mrrefChr0 89405 1 + 130230 T -s mr.mrrefChr3 135345 1 - 181027 T -s simCow_chr6.simCow.chr6 95006 1 + 602619 T -s simCow_chr6.simCow.chr6 126424 1 - 602619 C -s simDog_chr6.simDog.chr6 100391 1 + 593897 T -s simDog_chr6.simDog.chr6 127282 1 - 593897 C -s simHuman_chr6.simHuman.chr6 89179 1 + 601863 T -s simHuman_chr6.simHuman.chr6 128528 1 - 601863 T -s simMouse_chr6.simMouse.chr6 144766 1 - 636262 T -s simRat_chr6.simRat.chr6 147586 1 - 647215 T -s simRat_chr6.simRat.chr6 86389 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 94262 11 + 636262 TACATTAATCT -s Anc0.Anc0refChr3 114818 11 - 222631 AGGGTTGTTTG -s Anc1.Anc1refChr6 56258 11 - 197743 AGTGTTGTTTG -s Anc2.Anc2refChr1 123302 11 - 142988 AGGGTTGTTTA -s Anc2.Anc2refChr2 4713 11 + 27695 AGGGTTGTTTG -s mr.mrrefChr0 89406 11 + 130230 TACATTAATCT -s mr.mrrefChr3 135346 11 - 181027 AGTTTCAATTG -s simCow_chr6.simCow.chr6 95007 11 + 602619 AGGGTTGCTTG -s simCow_chr6.simCow.chr6 126425 11 - 602619 AGGGTGGTTTA -s simDog_chr6.simDog.chr6 100392 11 + 593897 AGGGTTGTTCG -s simDog_chr6.simDog.chr6 127283 10 - 593897 -GGGTTGTTTA -s simHuman_chr6.simHuman.chr6 89182 11 + 601863 AGTGTTGTTTG -s simHuman_chr6.simHuman.chr6 128529 6 - 601863 -----TGTTTG -s simMouse_chr6.simMouse.chr6 144767 11 - 636262 AGTTTTGATGG -s simRat_chr6.simRat.chr6 147587 11 - 647215 AGTTTCAACTG -s simRat_chr6.simRat.chr6 86390 11 + 647215 CACATTACTCC - -a -s simMouse_chr6.simMouse.chr6 94273 37 + 636262 ATGTGCTATCAACACCTGTGGAAGGAGTGTGCCCACC -s mr.mrrefChr0 89417 37 + 130230 ATGTGCTATTAACACCTGTGGAAGGAGTGTGCCCACC -s simRat_chr6.simRat.chr6 86401 37 + 647215 ATGCACTATTGACACCTGTGGAAGGAGCATGCCCGCC - -a -s simMouse_chr6.simMouse.chr6 94310 3 + 636262 CAC -s mr.mrrefChr0 89454 3 + 130230 CAC -s simRat_chr6.simRat.chr6 86439 3 + 647215 TAC - -a -s simMouse_chr6.simMouse.chr6 94313 5 + 636262 TCACT -s Anc0.Anc0refChr3 114829 5 - 222631 CAGAT -s Anc1.Anc1refChr6 56269 5 - 197743 CAGAT -s Anc2.Anc2refChr1 123313 5 - 142988 CAGAT -s Anc2.Anc2refChr2 4724 5 + 27695 TAGAT -s mr.mrrefChr0 89457 5 + 130230 TCACT -s mr.mrrefChr3 135357 5 - 181027 TAAAC -s simCow_chr6.simCow.chr6 95018 5 + 602619 TAGAT -s simCow_chr6.simCow.chr6 126436 5 - 602619 CAGGT -s simDog_chr6.simDog.chr6 100403 5 + 593897 TGGAT -s simDog_chr6.simDog.chr6 127293 5 - 593897 CAGAT -s simHuman_chr6.simHuman.chr6 89193 5 + 601863 CAGAT -s simHuman_chr6.simHuman.chr6 128535 5 - 601863 CAGAT -s simMouse_chr6.simMouse.chr6 144778 5 - 636262 AAAAC -s simRat_chr6.simRat.chr6 147598 5 - 647215 TGAAC -s simRat_chr6.simRat.chr6 86442 5 + 647215 TCACC - -a -s simMouse_chr6.simMouse.chr6 94318 2 + 636262 GT -s Anc0.Anc0refChr3 114834 2 - 222631 AT -s Anc1.Anc1refChr6 56274 2 - 197743 AT -s Anc2.Anc2refChr1 123318 2 - 142988 AT -s Anc2.Anc2refChr2 4729 2 + 27695 GT -s mr.mrrefChr0 89462 2 + 130230 GT -s simCow_chr6.simCow.chr6 95023 2 + 602619 GT -s simCow_chr6.simCow.chr6 126441 2 - 602619 AT -s simDog_chr6.simDog.chr6 100408 2 + 593897 GT -s simDog_chr6.simDog.chr6 127298 2 - 593897 AT -s simHuman_chr6.simHuman.chr6 89198 2 + 601863 CT -s simHuman_chr6.simHuman.chr6 128540 2 - 601863 AT -s simRat_chr6.simRat.chr6 86447 2 + 647215 AT - -a -s simMouse_chr6.simMouse.chr6 94320 9 + 636262 CAAGGAATC -s Anc0.Anc0refChr3 114836 9 - 222631 CAAGTGGTG -s Anc1.Anc1refChr6 56276 9 - 197743 CAAGTGGTG -s Anc2.Anc2refChr1 123320 9 - 142988 CAAGTGGTG -s Anc2.Anc2refChr2 4731 9 + 27695 CAAGTGATG -s mr.mrrefChr0 89464 9 + 130230 CAAGGAATC -s simCow_chr6.simCow.chr6 95035 9 + 602619 CAAGTGATG -s simCow_chr6.simCow.chr6 126443 9 - 602619 CAAATGGTG -s simDog_chr6.simDog.chr6 100410 9 + 593897 CAAGTCATG -s simDog_chr6.simDog.chr6 127300 9 - 593897 CGAGTGGTA -s simHuman_chr6.simHuman.chr6 89200 9 + 601863 CAAGGGGTT -s simHuman_chr6.simHuman.chr6 128542 9 - 601863 CAAGTGGTG -s simRat_chr6.simRat.chr6 86449 9 + 647215 CAAGGAACC - -a -s simMouse_chr6.simMouse.chr6 94329 18 + 636262 ACACTTGTATATCATAAG -s Anc0.Anc0refChr3 114848 17 - 222631 ACACAT-TATTTCATAAC -s Anc1.Anc1refChr6 56288 17 - 197743 ACACAT-TATTTCATAAC -s Anc2.Anc2refChr1 123332 17 - 142988 ACACAT-TATTTCATAAC -s Anc2.Anc2refChr2 4743 17 + 27695 ATACAT-TATTTCATAAG -s mr.mrrefChr0 89473 18 + 130230 ACACTTGTATATCATAAG -s simCow_chr6.simCow.chr6 95047 17 + 602619 ATACAT-TATCTCATAGG -s simCow_chr6.simCow.chr6 126455 17 - 602619 ACACCT-TATTTCATAAC -s simDog_chr6.simDog.chr6 100422 17 + 593897 ATACAG-AAGTTCAGAAC -s simDog_chr6.simDog.chr6 127312 17 - 593897 TCACAT-TATTGCATATC -s simHuman_chr6.simHuman.chr6 89212 17 + 601863 ACACAT-TCTTTCATGAG -s simHuman_chr6.simHuman.chr6 128554 17 - 601863 ACACAT-CATTTCATAAC -s simRat_chr6.simRat.chr6 86458 18 + 647215 ACACCTGTATATCATAAG - -a -s simMouse_chr6.simMouse.chr6 94347 4 + 636262 CTGA -s Anc0.Anc0refChr3 114865 4 - 222631 ATGA -s Anc1.Anc1refChr6 56305 4 - 197743 ATGA -s Anc2.Anc2refChr1 123349 4 - 142988 ATGA -s Anc2.Anc2refChr2 4760 4 + 27695 ATGG -s mr.mrrefChr0 89491 4 + 130230 ATGA -s simCow_chr6.simCow.chr6 126472 4 - 602619 ATTA -s simDog_chr6.simDog.chr6 100439 4 + 593897 ATGG -s simDog_chr6.simDog.chr6 127329 4 - 593897 ATGA -s simHuman_chr6.simHuman.chr6 89229 4 + 601863 ACTA -s simHuman_chr6.simHuman.chr6 128571 4 - 601863 ATGA -s simRat_chr6.simRat.chr6 86476 4 + 647215 ATGA - -a -s simMouse_chr6.simMouse.chr6 94351 4 + 636262 TCTA -s Anc0.Anc0refChr3 114869 4 - 222631 TCTC -s Anc1.Anc1refChr6 56309 4 - 197743 TCTC -s Anc2.Anc2refChr1 123353 4 - 142988 TCTC -s Anc2.Anc2refChr2 4764 4 + 27695 TCTA -s mr.mrrefChr0 89495 4 + 130230 TCTA -s simCow_chr6.simCow.chr6 95064 4 + 602619 CCTA -s simCow_chr6.simCow.chr6 126476 4 - 602619 TCTC -s simDog_chr6.simDog.chr6 100443 4 + 593897 TCTA -s simDog_chr6.simDog.chr6 127333 4 - 593897 TCTC -s simHuman_chr6.simHuman.chr6 89233 4 + 601863 TCTA -s simHuman_chr6.simHuman.chr6 128575 4 - 601863 TCTC -s simRat_chr6.simRat.chr6 86480 4 + 647215 CCTA - -a -s simMouse_chr6.simMouse.chr6 94355 21 + 636262 GCACCACACTCACAGTGATGC -s Anc0.Anc0refChr3 114873 21 - 222631 ACTCCACACTCACAGTGATAT -s Anc1.Anc1refChr6 56313 21 - 197743 ACTCCACACTCACAGTGATAT -s Anc2.Anc2refChr1 123357 21 - 142988 ACTCCAGACCCACAGTGATAT -s Anc2.Anc2refChr2 4768 21 + 27695 ACTCCACACTTGTAGTGATGT -s mr.mrrefChr0 89499 21 + 130230 GCACCACACTGACAGTGATGT -s simCow_chr6.simCow.chr6 95068 21 + 602619 ACACCACACTCACAGTGATGT -s simCow_chr6.simCow.chr6 126480 20 - 602619 ACTCCAGACAAACA-TGATAT -s simDog_chr6.simDog.chr6 100447 21 + 593897 ACTCCACACTTGTTGTGATGT -s simDog_chr6.simDog.chr6 127337 21 - 593897 ACTCCAGATCCACAGTGATAT -s simHuman_chr6.simHuman.chr6 89238 21 + 601863 GCCCCTCACAGTGAATGATGT -s simHuman_chr6.simHuman.chr6 128579 21 - 601863 ACTCCACACTCACAGTGATAT -s simRat_chr6.simRat.chr6 86484 21 + 647215 GTACCACACTGACAGTGATGT - -a -s simMouse_chr6.simMouse.chr6 94376 6 + 636262 CTAGTT -s Anc0.Anc0refChr3 114902 6 - 222631 CTAGGG -s Anc1.Anc1refChr6 56342 6 - 197743 CTAGGG -s Anc2.Anc2refChr1 123386 6 - 142988 CTAGGG -s Anc2.Anc2refChr2 4797 6 + 27695 CTAGGG -s mr.mrrefChr0 89520 6 + 130230 CTAGTT -s simCow_chr6.simCow.chr6 95097 6 + 602619 CTAGGG -s simCow_chr6.simCow.chr6 126508 6 - 602619 CTAAGG -s simDog_chr6.simDog.chr6 100476 6 + 593897 TTAGGG -s simDog_chr6.simDog.chr6 127366 6 - 593897 CTAGGG -s simHuman_chr6.simHuman.chr6 89267 6 + 601863 CTAGTG -s simHuman_chr6.simHuman.chr6 128608 5 - 601863 -TAGGG -s simRat_chr6.simRat.chr6 86505 6 + 647215 GTAGTT - -a -s simMouse_chr6.simMouse.chr6 94382 10 + 636262 AGACATCTAA -s Anc0.Anc0refChr3 114912 10 - 222631 AGGCATCTGA -s Anc1.Anc1refChr6 56352 10 - 197743 AGGCATCTGA -s Anc2.Anc2refChr1 123396 7 - 142988 AGTCATC--- -s Anc2.Anc2refChr2 4807 10 + 27695 AGGTATCTGA -s mr.mrrefChr0 89526 10 + 130230 AGACATCTAA -s simCow_chr6.simCow.chr6 95107 10 + 602619 AGGTATCTGA -s simCow_chr6.simCow.chr6 126518 7 - 602619 AGCCTTC--- -s simDog_chr6.simDog.chr6 100486 10 + 593897 AGGTATCTGA -s simDog_chr6.simDog.chr6 127376 7 - 593897 TGTCATC--- -s simHuman_chr6.simHuman.chr6 89277 10 + 601863 AGGTATCTGA -s simHuman_chr6.simHuman.chr6 128617 8 - 601863 AGGTATCT-- -s simRat_chr6.simRat.chr6 86511 10 + 647215 AGACACCTAA - -a -s simMouse_chr6.simMouse.chr6 94392 2 + 636262 TG -s Anc0.Anc0refChr3 114922 2 - 222631 TA -s Anc1.Anc1refChr6 56362 2 - 197743 TA -s Anc2.Anc2refChr1 123403 2 - 142988 TA -s Anc2.Anc2refChr2 4817 2 + 27695 TA -s mr.mrrefChr0 89536 2 + 130230 TG -s mr.mrrefChr3 135362 2 - 181027 TA -s simCow_chr6.simCow.chr6 95117 2 + 602619 CA -s simCow_chr6.simCow.chr6 126525 2 - 602619 TA -s simDog_chr6.simDog.chr6 100496 2 + 593897 TT -s simDog_chr6.simDog.chr6 127383 2 - 593897 TG -s simHuman_chr6.simHuman.chr6 89287 2 + 601863 TA -s simHuman_chr6.simHuman.chr6 128625 1 - 601863 -A -s simMouse_chr6.simMouse.chr6 144783 2 - 636262 TA -s simRat_chr6.simRat.chr6 147603 2 - 647215 TA -s simRat_chr6.simRat.chr6 86521 2 + 647215 TG - -a -s simMouse_chr6.simMouse.chr6 94394 2 + 636262 CC -s Anc0.Anc0refChr3 114924 2 - 222631 CA -s Anc1.Anc1refChr6 56364 2 - 197743 CA -s Anc2.Anc2refChr1 123405 2 - 142988 CA -s Anc2.Anc2refChr2 4819 2 + 27695 CA -s mr.mrrefChr0 89538 2 + 130230 CC -s mr.mrrefChr3 135364 2 - 181027 GA -s simCow_chr6.simCow.chr6 95122 2 + 602619 CA -s simCow_chr6.simCow.chr6 126527 2 - 602619 CT -s simDog_chr6.simDog.chr6 100498 2 + 593897 CT -s simDog_chr6.simDog.chr6 127385 2 - 593897 CA -s simHuman_chr6.simHuman.chr6 89289 2 + 601863 CA -s simHuman_chr6.simHuman.chr6 128626 2 - 601863 CG -s simMouse_chr6.simMouse.chr6 144785 2 - 636262 GA -s simRat_chr6.simRat.chr6 147605 2 - 647215 GA -s simRat_chr6.simRat.chr6 86523 2 + 647215 CC - -a -s simMouse_chr6.simMouse.chr6 94396 5 + 636262 CATGT -s Anc0.Anc0refChr3 114926 5 - 222631 CATGT -s Anc1.Anc1refChr6 56366 5 - 197743 CATGT -s Anc2.Anc2refChr1 123407 5 - 142988 CATCT -s Anc2.Anc2refChr2 4821 5 + 27695 CATGT -s mr.mrrefChr0 89540 5 + 130230 CATGT -s mr.mrrefChr3 135366 5 - 181027 CATGT -s simCow_chr6.simCow.chr6 95124 5 + 602619 CATGT -s simCow_chr6.simCow.chr6 126529 5 - 602619 CACCT -s simDog_chr6.simDog.chr6 100500 5 + 593897 TATGC -s simDog_chr6.simDog.chr6 127391 5 - 593897 TATCT -s simHuman_chr6.simHuman.chr6 89291 5 + 601863 CATGT -s simHuman_chr6.simHuman.chr6 128628 5 - 601863 CATGT -s simMouse_chr6.simMouse.chr6 144787 5 - 636262 CATGT -s simRat_chr6.simRat.chr6 147607 5 - 647215 CATGT -s simRat_chr6.simRat.chr6 86525 5 + 647215 CAGGT - -a -s simMouse_chr6.simMouse.chr6 94401 9 + 636262 TGAACTATT -s Anc0.Anc0refChr3 114931 9 - 222631 TGAACTCTT -s Anc1.Anc1refChr6 56371 9 - 197743 TGAACTCTT -s Anc2.Anc2refChr1 123412 9 - 142988 TGGACTCTC -s Anc2.Anc2refChr2 4826 9 + 27695 TGAACTGAT -s mr.mrrefChr0 89545 9 + 130230 TGAACTATT -s mr.mrrefChr3 135371 9 - 181027 TGAACTGGT -s simCow_chr6.simCow.chr6 95129 9 + 602619 TAGACTGCT -s simCow_chr6.simCow.chr6 126540 9 - 602619 TGGACTATC -s simDog_chr6.simDog.chr6 100505 9 + 593897 TGACCTGAT -s simDog_chr6.simDog.chr6 127396 9 - 593897 CGGACTCTT -s simHuman_chr6.simHuman.chr6 89296 9 + 601863 TGAACTGTT -s simHuman_chr6.simHuman.chr6 128633 9 - 601863 TGAACTCTC -s simMouse_chr6.simMouse.chr6 144792 9 - 636262 TGAACTGGT -s simRat_chr6.simRat.chr6 147612 9 - 647215 TGAACTGGT -s simRat_chr6.simRat.chr6 86530 9 + 647215 TGAACTGTT - -a -s simMouse_chr6.simMouse.chr6 94410 2 + 636262 TC -s Anc0.Anc0refChr3 114940 2 - 222631 TC -s Anc1.Anc1refChr6 56380 2 - 197743 TC -s Anc2.Anc2refChr1 123421 2 - 142988 TC -s Anc2.Anc2refChr2 4835 2 + 27695 TC -s mr.mrrefChr0 89554 2 + 130230 TC -s mr.mrrefChr3 135380 2 - 181027 TC -s simCow_chr6.simCow.chr6 126549 2 - 602619 TC -s simDog_chr6.simDog.chr6 100514 2 + 593897 TC -s simDog_chr6.simDog.chr6 127405 2 - 593897 TC -s simHuman_chr6.simHuman.chr6 89305 2 + 601863 TC -s simHuman_chr6.simHuman.chr6 128642 2 - 601863 TC -s simMouse_chr6.simMouse.chr6 144801 2 - 636262 TG -s simRat_chr6.simRat.chr6 147621 2 - 647215 TC -s simRat_chr6.simRat.chr6 86539 2 + 647215 TC - -a -s simMouse_chr6.simMouse.chr6 94412 5 + 636262 ACACC -s Anc0.Anc0refChr3 114942 5 - 222631 TCACC -s Anc1.Anc1refChr6 56382 5 - 197743 TCACC -s Anc2.Anc2refChr1 123423 5 - 142988 TCACC -s Anc2.Anc2refChr2 4837 5 + 27695 TCACC -s mr.mrrefChr0 89556 5 + 130230 ACACC -s mr.mrrefChr3 135382 5 - 181027 TCACC -s simCow_chr6.simCow.chr6 95138 5 + 602619 TCACC -s simCow_chr6.simCow.chr6 126551 5 - 602619 TCTCC -s simDog_chr6.simDog.chr6 100516 5 + 593897 TCACC -s simDog_chr6.simDog.chr6 127407 5 - 593897 TCACC -s simHuman_chr6.simHuman.chr6 89307 5 + 601863 TCACC -s simHuman_chr6.simHuman.chr6 128644 3 - 601863 TCA-- -s simMouse_chr6.simMouse.chr6 144803 5 - 636262 TCATC -s simRat_chr6.simRat.chr6 147623 5 - 647215 TCACT -s simRat_chr6.simRat.chr6 86541 5 + 647215 ACACC - -a -s simMouse_chr6.simMouse.chr6 94417 12 + 636262 ACCATCTGGCAT -s Anc0.Anc0refChr3 114947 12 - 222631 ATTCCTTGTCAT -s Anc1.Anc1refChr6 56387 12 - 197743 ATTCCTTGTCAT -s Anc2.Anc2refChr1 123428 12 - 142988 ATTCCTTGTCAT -s Anc2.Anc2refChr2 4842 12 + 27695 ACTGCTTGTCAT -s mr.mrrefChr0 89561 12 + 130230 ACCATCTGGCAT -s mr.mrrefChr3 135387 12 - 181027 ATTCCTTGTCGG -s simCow_chr6.simCow.chr6 95143 12 + 602619 ACAGCTTAACAT -s simCow_chr6.simCow.chr6 126557 12 - 602619 AGTCCTTACTGC -s simDog_chr6.simDog.chr6 100521 12 + 593897 ACTGGTTGTCCT -s simDog_chr6.simDog.chr6 127412 12 - 593897 ATTCCTGGTCAT -s simHuman_chr6.simHuman.chr6 89312 12 + 601863 ACTGCTTGTCAT -s simHuman_chr6.simHuman.chr6 128647 11 - 601863 -TTCTTTGTCAG -s simMouse_chr6.simMouse.chr6 144808 12 - 636262 ATCCCTTGTCGG -s simRat_chr6.simRat.chr6 147628 12 - 647215 ATTCCTTGTCGG -s simRat_chr6.simRat.chr6 86546 12 + 647215 ACTACCTGGCAT - -a -s simMouse_chr6.simMouse.chr6 94429 14 + 636262 ATAAATATAAGTAG -s Anc0.Anc0refChr3 114961 14 - 222631 ATAAATGTATGCAC -s Anc1.Anc1refChr6 56401 14 - 197743 ATAAATGTATGCAC -s Anc2.Anc2refChr1 123442 14 - 142988 ATAAATGTATGCAC -s mr.mrrefChr0 89573 14 + 130230 ATAAATATAAGTAG -s mr.mrrefChr3 135401 14 - 181027 GTAAAGATATAGAC -s simCow_chr6.simCow.chr6 95155 14 + 602619 ATAGATGAGTGCTC -s simCow_chr6.simCow.chr6 126571 14 - 602619 ATAAATGTATGCAC -s simDog_chr6.simDog.chr6 127426 14 - 593897 AGAGATGTGTGCAC -s simHuman_chr6.simHuman.chr6 89324 14 + 601863 ATAAATGTAAGCAT -s simHuman_chr6.simHuman.chr6 128660 14 - 601863 ATAAATGTATGCAC -s simMouse_chr6.simMouse.chr6 144822 14 - 636262 GTAAAGATATAGAA -s simRat_chr6.simRat.chr6 147642 14 - 647215 GTAAAGATATAGAC -s simRat_chr6.simRat.chr6 86558 14 + 647215 ATACATGTAAGTAC - -a -s simMouse_chr6.simMouse.chr6 94443 1 + 636262 A -s Anc0.Anc0refChr3 114975 1 - 222631 A -s Anc1.Anc1refChr6 56415 1 - 197743 A -s Anc2.Anc2refChr1 123456 1 - 142988 A -s mr.mrrefChr0 89587 1 + 130230 A -s simCow_chr6.simCow.chr6 95169 1 + 602619 A -s simCow_chr6.simCow.chr6 126585 1 - 602619 A -s simDog_chr6.simDog.chr6 127440 1 - 593897 T -s simHuman_chr6.simHuman.chr6 89338 1 + 601863 A -s simHuman_chr6.simHuman.chr6 128674 1 - 601863 A -s simRat_chr6.simRat.chr6 86572 1 + 647215 G - -a -s simMouse_chr6.simMouse.chr6 94444 4 + 636262 CATC -s Anc0.Anc0refChr3 114976 4 - 222631 CATC -s Anc1.Anc1refChr6 56416 4 - 197743 CATC -s Anc2.Anc2refChr1 123457 4 - 142988 GATC -s mr.mrrefChr0 89588 4 + 130230 CATC -s mr.mrrefChr3 135415 4 - 181027 CGTT -s simCow_chr6.simCow.chr6 95170 4 + 602619 CATC -s simCow_chr6.simCow.chr6 126586 4 - 602619 GGTC -s simDog_chr6.simDog.chr6 127441 4 - 593897 GATC -s simHuman_chr6.simHuman.chr6 89339 4 + 601863 CATA -s simHuman_chr6.simHuman.chr6 128675 4 - 601863 GGTT -s simMouse_chr6.simMouse.chr6 144836 4 - 636262 CGTC -s simRat_chr6.simRat.chr6 147656 4 - 647215 GGTT -s simRat_chr6.simRat.chr6 86573 4 + 647215 CATC - -a -s simMouse_chr6.simMouse.chr6 94448 6 + 636262 TGCATC -s Anc0.Anc0refChr3 114980 6 - 222631 TGCAAT -s Anc1.Anc1refChr6 56420 6 - 197743 TGCAAT -s Anc2.Anc2refChr1 123461 6 - 142988 TGCAAT -s mr.mrrefChr0 89592 6 + 130230 TGCATC -s mr.mrrefChr3 135419 6 - 181027 TACATT -s simCow_chr6.simCow.chr6 95181 6 + 602619 TGTAAT -s simCow_chr6.simCow.chr6 126590 6 - 602619 TGTAAT -s simDog_chr6.simDog.chr6 127445 6 - 593897 TGCAAT -s simHuman_chr6.simHuman.chr6 89343 6 + 601863 TGCAAT -s simHuman_chr6.simHuman.chr6 128679 6 - 601863 TGCAGT -s simMouse_chr6.simMouse.chr6 144840 6 - 636262 TACATT -s simRat_chr6.simRat.chr6 147660 6 - 647215 TACACT -s simRat_chr6.simRat.chr6 86577 6 + 647215 TGCATT - -a -s simMouse_chr6.simMouse.chr6 94454 2 + 636262 AT -s Anc0.Anc0refChr3 114986 2 - 222631 GT -s Anc1.Anc1refChr6 56426 2 - 197743 GT -s Anc2.Anc2refChr1 123467 2 - 142988 GT -s mr.mrrefChr0 89598 2 + 130230 AT -s simCow_chr6.simCow.chr6 95187 2 + 602619 GT -s simCow_chr6.simCow.chr6 126596 2 - 602619 GT -s simDog_chr6.simDog.chr6 127451 2 - 593897 GT -s simHuman_chr6.simHuman.chr6 89349 2 + 601863 GC -s simHuman_chr6.simHuman.chr6 128685 2 - 601863 GT -s simRat_chr6.simRat.chr6 86583 2 + 647215 AT - -a -s simMouse_chr6.simMouse.chr6 94456 14 + 636262 ATGACAGCTGAAAC -s Anc0.Anc0refChr3 114988 14 - 222631 ATGACAGCTGGTGC -s Anc1.Anc1refChr6 56428 14 - 197743 ATGACAGCTGGTGC -s Anc2.Anc2refChr1 123469 14 - 142988 ATGACAGCTGGTGC -s mr.mrrefChr0 89600 14 + 130230 ATGACAGCTGAAAC -s mr.mrrefChr3 135425 14 - 181027 ATGACAGCTGGTAC -s simCow_chr6.simCow.chr6 95189 14 + 602619 ATGACAGCTGGGGC -s simCow_chr6.simCow.chr6 126598 14 - 602619 GGGACAACTGGTGC -s simDog_chr6.simDog.chr6 127453 14 - 593897 GTGACAGCTGGTGC -s simHuman_chr6.simHuman.chr6 89351 14 + 601863 ATGACATCTGGTGC -s simHuman_chr6.simHuman.chr6 128687 14 - 601863 ATGTCAGCTGGTGA -s simMouse_chr6.simMouse.chr6 144846 14 - 636262 ACAACAGCTGGTAC -s simRat_chr6.simRat.chr6 147666 14 - 647215 CTGACAGCCGGTAC -s simRat_chr6.simRat.chr6 86585 14 + 647215 AGGACAGCTGGCGC - -a -s simMouse_chr6.simMouse.chr6 94470 6 + 636262 TAGTCT -s Anc0.Anc0refChr3 115002 6 - 222631 TAGTCT -s Anc1.Anc1refChr6 56442 6 - 197743 TAGTCT -s Anc2.Anc2refChr1 123483 6 - 142988 TATTCT -s mr.mrrefChr0 89614 6 + 130230 TAGTCT -s mr.mrrefChr3 135439 6 - 181027 TAGTCT -s simCow_chr6.simCow.chr6 126612 6 - 602619 TAGTCA -s simDog_chr6.simDog.chr6 127467 6 - 593897 TATTCT -s simHuman_chr6.simHuman.chr6 89365 6 + 601863 TAGTCT -s simHuman_chr6.simHuman.chr6 128701 6 - 601863 TATTCT -s simMouse_chr6.simMouse.chr6 144860 6 - 636262 TAGTAT -s simRat_chr6.simRat.chr6 147680 6 - 647215 CAGTCC -s simRat_chr6.simRat.chr6 86599 6 + 647215 TAGTCT - -a -s simMouse_chr6.simMouse.chr6 94476 1 + 636262 G -s Anc0.Anc0refChr3 115008 1 - 222631 A -s Anc1.Anc1refChr6 56448 1 - 197743 A -s Anc2.Anc2refChr1 123489 1 - 142988 A -s mr.mrrefChr0 89620 1 + 130230 G -s simCow_chr6.simCow.chr6 126618 1 - 602619 A -s simDog_chr6.simDog.chr6 127473 1 - 593897 A -s simHuman_chr6.simHuman.chr6 89371 1 + 601863 G -s simHuman_chr6.simHuman.chr6 128707 1 - 601863 A -s simRat_chr6.simRat.chr6 86605 1 + 647215 G - -a -s simMouse_chr6.simMouse.chr6 94477 16 + 636262 AGCAAAAGCATGTCCT -s Anc0.Anc0refChr3 115009 16 - 222631 AGTGAATGCATGTCCT -s Anc1.Anc1refChr6 56449 16 - 197743 AGTGAATGCATGTCCT -s Anc2.Anc2refChr1 123490 16 - 142988 AGTGAAGGCATGTCCT -s mr.mrrefChr0 89621 16 + 130230 AGCAAAAGCATGTCCT -s mr.mrrefChr3 135445 16 - 181027 AGTGAATGCTTATCCT -s simCow_chr6.simCow.chr6 126619 16 - 602619 AGTGGAGACATGTCCT -s simDog_chr6.simDog.chr6 127474 16 - 593897 AGTGAAGGCATGTCCT -s simHuman_chr6.simHuman.chr6 89372 16 + 601863 AGTGAAAGCCTGTCCT -s simHuman_chr6.simHuman.chr6 128708 16 - 601863 AGTGAATGCCTGTCCT -s simMouse_chr6.simMouse.chr6 144866 16 - 636262 AGTGAATGCTTATCCT -s simRat_chr6.simRat.chr6 147686 16 - 647215 ATTGAATGCTCATTCA -s simRat_chr6.simRat.chr6 86606 16 + 647215 AGGAAAAGCATTTCCT - -a -s simMouse_chr6.simMouse.chr6 94493 1 + 636262 G -s Anc0.Anc0refChr3 115025 1 - 222631 G -s Anc1.Anc1refChr6 56465 1 - 197743 G -s Anc2.Anc2refChr1 123506 1 - 142988 G -s mr.mrrefChr0 89637 1 + 130230 G -s mr.mrrefChr3 135461 1 - 181027 G -s simCow_chr6.simCow.chr6 95203 1 + 602619 A -s simCow_chr6.simCow.chr6 126635 1 - 602619 G -s simDog_chr6.simDog.chr6 127490 1 - 593897 G -s simHuman_chr6.simHuman.chr6 89388 1 + 601863 G -s simHuman_chr6.simHuman.chr6 128724 1 - 601863 A -s simMouse_chr6.simMouse.chr6 144882 1 - 636262 G -s simRat_chr6.simRat.chr6 147702 1 - 647215 G -s simRat_chr6.simRat.chr6 86622 1 + 647215 G - -a -s simMouse_chr6.simMouse.chr6 94494 24 + 636262 AGATGCGAGTATAGAAGTACCATC -s Anc0.Anc0refChr3 115026 24 - 222631 AGATACAAGTGTAGAAACACCAAG -s Anc1.Anc1refChr6 56466 24 - 197743 AGATACAAGTGTAGAAACACCAAG -s Anc2.Anc2refChr1 123507 24 - 142988 AGATACAAGTGCAGAAACACCAAG -s mr.mrrefChr0 89638 24 + 130230 AGATGCGAGTATAGAAGTACCATC -s mr.mrrefChr3 135462 24 - 181027 TGATTCAAGTATAGAAACACCAAG -s simCow_chr6.simCow.chr6 95204 24 + 602619 AGATGCAAGTGGAGAAATACCAAG -s simCow_chr6.simCow.chr6 126639 24 - 602619 AAGCACAAGGGCAGAAACATCAAG -s simDog_chr6.simDog.chr6 127491 24 - 593897 AGATACAATTGCAGAAACACCAAG -s simHuman_chr6.simHuman.chr6 89389 24 + 601863 AGATGCAGGTGTAGAAATACCTAG -s simHuman_chr6.simHuman.chr6 128725 24 - 601863 AGATACACATCTAGAAACACCACA -s simMouse_chr6.simMouse.chr6 144883 24 - 636262 TGATTCTAGCATAGAAACATGAAG -s simRat_chr6.simRat.chr6 147703 24 - 647215 TGATTGAAGTATGGAAACACCAAG -s simRat_chr6.simRat.chr6 86623 24 + 647215 AGATGTAAGTTTATAAGCACCATC - -a -s simMouse_chr6.simMouse.chr6 94518 9 + 636262 CAGTAAAAA -s Anc0.Anc0refChr3 115050 9 - 222631 CAGTACAAG -s Anc1.Anc1refChr6 56490 9 - 197743 CAGTACAAG -s Anc2.Anc2refChr1 123531 9 - 142988 CAGTACAAG -s mr.mrrefChr0 89662 9 + 130230 CAGTAAAAA -s simCow_chr6.simCow.chr6 95228 9 + 602619 CGGTACAAT -s simCow_chr6.simCow.chr6 126663 9 - 602619 CAGTACAAG -s simDog_chr6.simDog.chr6 127515 9 - 593897 CTGTCCAGG -s simHuman_chr6.simHuman.chr6 89413 9 + 601863 CAGTATGAA -s simHuman_chr6.simHuman.chr6 128749 9 - 601863 CAGTACAAG -s simRat_chr6.simRat.chr6 86647 9 + 647215 CAGCAAAAA - -a -s simMouse_chr6.simMouse.chr6 94527 9 + 636262 GCACCTAAA -s Anc0.Anc0refChr3 115059 9 - 222631 GTACCTAAA -s Anc1.Anc1refChr6 56499 9 - 197743 GTACCTAAA -s Anc2.Anc2refChr1 123540 9 - 142988 GTACCTAAA -s mr.mrrefChr0 89671 9 + 130230 GCACCTAAA -s mr.mrrefChr3 135486 9 - 181027 GTATCAAAA -s simCow_chr6.simCow.chr6 95237 9 + 602619 GTACCTAGA -s simCow_chr6.simCow.chr6 126672 9 - 602619 GTATCTGAA -s simDog_chr6.simDog.chr6 127524 9 - 593897 GTACTTAAA -s simHuman_chr6.simHuman.chr6 89422 9 + 601863 GTACCTAAA -s simHuman_chr6.simHuman.chr6 128758 9 - 601863 GTATCTAAA -s simMouse_chr6.simMouse.chr6 144907 9 - 636262 GTATCAAAA -s simRat_chr6.simRat.chr6 147727 9 - 647215 GTATCAAAT -s simRat_chr6.simRat.chr6 86656 9 + 647215 GCACCTAAA - -a -s simMouse_chr6.simMouse.chr6 94536 10 + 636262 TATCATAGCA -s Anc0.Anc0refChr3 115069 10 - 222631 CATCCTATCA -s Anc1.Anc1refChr6 56509 10 - 197743 CATCCTATCA -s Anc2.Anc2refChr1 123550 10 - 142988 CATCCTATCA -s mr.mrrefChr0 89680 10 + 130230 TATCATAGCA -s mr.mrrefChr3 135496 10 - 181027 CACCCTAACA -s simCow_chr6.simCow.chr6 95247 10 + 602619 CATCTTATAA -s simCow_chr6.simCow.chr6 126682 10 - 602619 CATCTTGTCA -s simDog_chr6.simDog.chr6 127534 10 - 593897 TATCCTATCA -s simHuman_chr6.simHuman.chr6 89432 10 + 601863 CCTCCTATCA -s simHuman_chr6.simHuman.chr6 128768 10 - 601863 CATCCTATCA -s simMouse_chr6.simMouse.chr6 144917 10 - 636262 CACCCTAACA -s simRat_chr6.simRat.chr6 147737 10 - 647215 CACGCTAACA -s simRat_chr6.simRat.chr6 86671 10 + 647215 TATCATAGGA - -a -s simMouse_chr6.simMouse.chr6 94546 5 + 636262 ATAGA -s Anc0.Anc0refChr3 115084 5 - 222631 ATAGC -s Anc1.Anc1refChr6 56524 5 - 197743 ATAGC -s Anc2.Anc2refChr1 123565 5 - 142988 ATCGC -s mr.mrrefChr0 89690 5 + 130230 ATAGA -s mr.mrrefChr3 135511 5 - 181027 ATAAC -s simCow_chr6.simCow.chr6 95262 5 + 602619 ATAGC -s simCow_chr6.simCow.chr6 126697 5 - 602619 ATCAC -s simDog_chr6.simDog.chr6 127549 4 - 593897 AT-GC -s simHuman_chr6.simHuman.chr6 89447 5 + 601863 ATAGT -s simHuman_chr6.simHuman.chr6 128783 5 - 601863 CTAAC -s simMouse_chr6.simMouse.chr6 144932 5 - 636262 ATAAC -s simRat_chr6.simRat.chr6 147752 5 - 647215 ATAAC -s simRat_chr6.simRat.chr6 86681 5 + 647215 GTAGA - -a -s simMouse_chr6.simMouse.chr6 94551 5 + 636262 ATCAA -s Anc0.Anc0refChr3 115089 5 - 222631 CTTGA -s Anc1.Anc1refChr6 56529 5 - 197743 CTTGA -s Anc2.Anc2refChr1 123570 5 - 142988 CTTGA -s mr.mrrefChr0 89695 5 + 130230 ATCAA -s mr.mrrefChr3 135516 5 - 181027 TTTGG -s simCow_chr6.simCow.chr6 95267 5 + 602619 TTCGA -s simCow_chr6.simCow.chr6 126702 2 - 602619 CT--- -s simDog_chr6.simDog.chr6 127553 5 - 593897 CTTGA -s simHuman_chr6.simHuman.chr6 89452 5 + 601863 CTTGA -s simHuman_chr6.simHuman.chr6 128796 5 - 601863 CTTGG -s simMouse_chr6.simMouse.chr6 144937 5 - 636262 TTTGG -s simRat_chr6.simRat.chr6 147757 5 - 647215 TTTGG -s simRat_chr6.simRat.chr6 86686 5 + 647215 ATTGA - -a -s simMouse_chr6.simMouse.chr6 94556 2 + 636262 AC -s Anc0.Anc0refChr3 115094 2 - 222631 TC -s Anc1.Anc1refChr6 56534 2 - 197743 TC -s Anc2.Anc2refChr1 123575 2 - 142988 TT -s mr.mrrefChr0 89700 2 + 130230 AC -s simCow_chr6.simCow.chr6 95272 2 + 602619 TT -s simDog_chr6.simDog.chr6 127558 2 - 593897 TT -s simHuman_chr6.simHuman.chr6 89457 2 + 601863 TA -s simHuman_chr6.simHuman.chr6 128801 2 - 601863 CC -s simRat_chr6.simRat.chr6 86691 2 + 647215 AA - -a -s simMouse_chr6.simMouse.chr6 94558 13 + 636262 AGAATGTGGTTGA -s Anc0.Anc0refChr3 115096 13 - 222631 AGCATATGGTTGA -s Anc1.Anc1refChr6 56536 13 - 197743 AGCATATGGTTGA -s Anc2.Anc2refChr1 123577 13 - 142988 AGCATATGGTTGA -s mr.mrrefChr0 89702 13 + 130230 AGAATGTGGTTGA -s mr.mrrefChr3 135521 13 - 181027 AGTACATGGTCAA -s simCow_chr6.simCow.chr6 95274 13 + 602619 AGCCTGTGGTTGA -s simCow_chr6.simCow.chr6 126704 13 - 602619 AGCATATGATAGC -s simDog_chr6.simDog.chr6 127560 13 - 593897 AGCATGTGGTCTG -s simHuman_chr6.simHuman.chr6 89459 13 + 601863 AGCACATGGCTGA -s simHuman_chr6.simHuman.chr6 128803 13 - 601863 AGCATACAGTTGT -s simMouse_chr6.simMouse.chr6 144942 13 - 636262 AGTACATGGTCAA -s simRat_chr6.simRat.chr6 147762 13 - 647215 AGTAGATGATCAA -s simRat_chr6.simRat.chr6 86693 13 + 647215 AGGATGTGGTTGA - -a -s simMouse_chr6.simMouse.chr6 94571 18 + 636262 AGGCCTGACATGCCAACT -s Anc0.Anc0refChr3 115110 18 - 222631 ATGCCTGACCCGCCCACT -s Anc1.Anc1refChr6 56550 18 - 197743 ATGCCTGACCCGCCCACT -s Anc2.Anc2refChr1 123591 18 - 142988 ATACCTGACCCGCCCACT -s mr.mrrefChr0 89715 18 + 130230 AGGCCTGACATGCCAACT -s mr.mrrefChr3 135535 18 - 181027 AGGCCCAACCTGCCCACT -s simCow_chr6.simCow.chr6 95288 18 + 602619 ATATCTTATCCGCCTACT -s simCow_chr6.simCow.chr6 126718 18 - 602619 ATTCCTGACCCACCCACT -s simDog_chr6.simDog.chr6 127574 18 - 593897 AAACCTGACCTGCCCATT -s simHuman_chr6.simHuman.chr6 89473 18 + 601863 ATGTTTGACCCACCCACT -s simHuman_chr6.simHuman.chr6 128817 18 - 601863 ATGCCTAACCCGCCCACT -s simMouse_chr6.simMouse.chr6 144956 18 - 636262 AGGCCCAACCTGCCCACT -s simRat_chr6.simRat.chr6 147776 18 - 647215 AGGCCCAACCTGCCCACT -s simRat_chr6.simRat.chr6 86706 18 + 647215 TGGTCTGACATGCCCACT - -a -s simMouse_chr6.simMouse.chr6 94589 4 + 636262 ACCC -s Anc0.Anc0refChr3 115129 4 - 222631 ACTC -s Anc1.Anc1refChr6 56569 4 - 197743 ACTC -s Anc2.Anc2refChr1 123610 4 - 142988 ACTC -s mr.mrrefChr0 89733 4 + 130230 ACCC -s mr.mrrefChr3 135554 4 - 181027 ACTC -s simCow_chr6.simCow.chr6 95307 4 + 602619 ACTC -s simCow_chr6.simCow.chr6 126737 4 - 602619 ACTT -s simDog_chr6.simDog.chr6 127593 4 - 593897 ACTC -s simHuman_chr6.simHuman.chr6 89492 4 + 601863 GCCC -s simHuman_chr6.simHuman.chr6 128836 4 - 601863 ACTC -s simMouse_chr6.simMouse.chr6 144975 4 - 636262 ACTC -s simRat_chr6.simRat.chr6 147795 4 - 647215 ACTC -s simRat_chr6.simRat.chr6 86724 4 + 647215 ACCC - -a -s simMouse_chr6.simMouse.chr6 94593 4 + 636262 TTTG -s Anc0.Anc0refChr3 115133 4 - 222631 TTTT -s Anc1.Anc1refChr6 56573 4 - 197743 TTTT -s Anc2.Anc2refChr1 123614 4 - 142988 TTTT -s mr.mrrefChr0 89737 4 + 130230 TTTG -s mr.mrrefChr3 135558 4 - 181027 TTTT -s simCow_chr6.simCow.chr6 126741 4 - 602619 TTTT -s simDog_chr6.simDog.chr6 127597 4 - 593897 TTTT -s simHuman_chr6.simHuman.chr6 89496 4 + 601863 TTGT -s simHuman_chr6.simHuman.chr6 128840 4 - 601863 TTTT -s simMouse_chr6.simMouse.chr6 144979 4 - 636262 TTTT -s simRat_chr6.simRat.chr6 147799 4 - 647215 TTTC -s simRat_chr6.simRat.chr6 86728 4 + 647215 TTTG - -a -s simMouse_chr6.simMouse.chr6 94597 32 + 636262 GCTATTATGACCGCTCCTCCCTCCTTTGGCCC -s Anc0.Anc0refChr3 115137 32 - 222631 GCCATTTTAATCCCTCCTCCCTGATTTGATCC -s Anc1.Anc1refChr6 56577 32 - 197743 GCCATTTTAATCCCTCCTCCCTGATTTGATCC -s Anc2.Anc2refChr1 123618 32 - 142988 GCCATTTTAATCCCTCCTCCCTGATTTGATCC -s mr.mrrefChr0 89741 32 + 130230 GCTATTATGACCGCTCCTCCCTCCTTTGGCCC -s mr.mrrefChr3 135562 32 - 181027 GCCATTTTAATCCCTCCTCCTTGATTTGATCC -s simCow_chr6.simCow.chr6 95311 32 + 602619 ACCGGTTTAATCCTTCCCCCCTACTTTGGCCT -s simCow_chr6.simCow.chr6 126745 32 - 602619 GCCATTTTAGTCCCTCCTCCCTAATTTGATCC -s simDog_chr6.simDog.chr6 127601 32 - 593897 GCCATTTTAGACCCTCCTCCCTGATTTGATCC -s simHuman_chr6.simHuman.chr6 89500 32 + 601863 GCTATTTTTATCCCTCCTCCCTGCTTTGGCCT -s simHuman_chr6.simHuman.chr6 128844 32 - 601863 GCCATTTTAATCCCTCCTCCCTGATTTGATCC -s simMouse_chr6.simMouse.chr6 144983 32 - 636262 GCCATTTTAATCCCTCCTCCTTGATTTGATCC -s simRat_chr6.simRat.chr6 147803 32 - 647215 GCCATTTTAATCCCTCCTCCTTGATTTGATCC -s simRat_chr6.simRat.chr6 86732 32 + 647215 GCCATTATCACCACTCCTCCCTCATTTGGCCC - -a -s simMouse_chr6.simMouse.chr6 94629 12 + 636262 CAAGCTATCAGT -s Anc0.Anc0refChr3 115169 12 - 222631 CAATCTATTAGT -s Anc1.Anc1refChr6 56609 12 - 197743 CAATCTATTAGT -s Anc2.Anc2refChr1 123650 12 - 142988 CAATCTATTAGT -s mr.mrrefChr0 89773 12 + 130230 CAAGCTATCAGT -s mr.mrrefChr3 135594 12 - 181027 CAATCTATTAGT -s simCow_chr6.simCow.chr6 126777 12 - 602619 CAATCTATTAGT -s simDog_chr6.simDog.chr6 127633 12 - 593897 CAATCTATTAGT -s simHuman_chr6.simHuman.chr6 89532 12 + 601863 CAAGGGATTAGT -s simHuman_chr6.simHuman.chr6 128876 12 - 601863 CAATCTATTAGT -s simMouse_chr6.simMouse.chr6 145015 12 - 636262 CAATCTATTAGT -s simRat_chr6.simRat.chr6 147835 12 - 647215 CAATCTATTAGT -s simRat_chr6.simRat.chr6 86764 12 + 647215 CGAGCTATCAGT - -a -s simMouse_chr6.simMouse.chr6 94641 2 + 636262 GG -s Anc0.Anc0refChr3 115181 2 - 222631 GG -s Anc1.Anc1refChr6 56621 2 - 197743 GG -s Anc2.Anc2refChr1 123662 2 - 142988 GG -s mr.mrrefChr0 89785 2 + 130230 GG -s mr.mrrefChr3 135606 2 - 181027 GG -s simCow_chr6.simCow.chr6 126789 2 - 602619 GG -s simDog_chr6.simDog.chr6 127645 2 - 593897 GG -s simHuman_chr6.simHuman.chr6 89544 2 + 601863 GG -s simHuman_chr6.simHuman.chr6 128888 2 - 601863 GG -s simMouse_chr6.simMouse.chr6 145027 2 - 636262 GG -s simRat_chr6.simRat.chr6 86776 2 + 647215 AG - -a -s simMouse_chr6.simMouse.chr6 94643 4 + 636262 ACAC -s Anc0.Anc0refChr3 115183 4 - 222631 TTGC -s Anc1.Anc1refChr6 56623 4 - 197743 TTGC -s Anc2.Anc2refChr1 123664 4 - 142988 TTGC -s mr.mrrefChr0 89787 4 + 130230 ACAC -s mr.mrrefChr3 135608 4 - 181027 TTGC -s simCow_chr6.simCow.chr6 95343 4 + 602619 GTAT -s simCow_chr6.simCow.chr6 126791 4 - 602619 TGGT -s simDog_chr6.simDog.chr6 127647 4 - 593897 TTGC -s simHuman_chr6.simHuman.chr6 89546 4 + 601863 TTGC -s simHuman_chr6.simHuman.chr6 128890 4 - 601863 TTGC -s simMouse_chr6.simMouse.chr6 145029 4 - 636262 TTGC -s simRat_chr6.simRat.chr6 86778 4 + 647215 ATGC - -a -s simMouse_chr6.simMouse.chr6 94647 6 + 636262 TTTGCT -s Anc0.Anc0refChr3 115187 6 - 222631 TGCCCT -s Anc1.Anc1refChr6 56627 6 - 197743 TGCCCT -s Anc2.Anc2refChr1 123668 6 - 142988 TGCCCT -s mr.mrrefChr0 89791 6 + 130230 TTTGCT -s mr.mrrefChr3 135612 6 - 181027 TGGCCT -s simCow_chr6.simCow.chr6 95347 6 + 602619 AGTCTT -s simCow_chr6.simCow.chr6 126795 6 - 602619 TGCCCT -s simDog_chr6.simDog.chr6 127651 6 - 593897 TGCCCT -s simHuman_chr6.simHuman.chr6 89550 6 + 601863 TTCCCT -s simHuman_chr6.simHuman.chr6 128894 6 - 601863 TGTCCT -s simMouse_chr6.simMouse.chr6 145033 6 - 636262 TGGCCT -s simRat_chr6.simRat.chr6 147847 6 - 647215 TGGCCT -s simRat_chr6.simRat.chr6 86782 6 + 647215 TTTGCT - -a -s simMouse_chr6.simMouse.chr6 94653 6 + 636262 GAGCTG -s Anc0.Anc0refChr3 115193 6 - 222631 GAGATA -s Anc1.Anc1refChr6 56633 6 - 197743 GAGATA -s Anc2.Anc2refChr1 123674 6 - 142988 GAGATA -s mr.mrrefChr0 89797 6 + 130230 GAGCTG -s mr.mrrefChr3 135618 6 - 181027 GAGATA -s simCow_chr6.simCow.chr6 126801 6 - 602619 GAGATA -s simDog_chr6.simDog.chr6 127657 6 - 593897 GAGATA -s simHuman_chr6.simHuman.chr6 89556 6 + 601863 GAGATG -s simHuman_chr6.simHuman.chr6 128900 6 - 601863 GAGACA -s simMouse_chr6.simMouse.chr6 145039 6 - 636262 GAGATA -s simRat_chr6.simRat.chr6 147853 6 - 647215 GAGATA -s simRat_chr6.simRat.chr6 86788 6 + 647215 GAGATT - -a -s simMouse_chr6.simMouse.chr6 94659 15 + 636262 ATATAACAACCTGTA -s Anc0.Anc0refChr3 115199 13 - 222631 ACATTATTATC--TG -s Anc1.Anc1refChr6 56639 13 - 197743 ACATTATTATC--TG -s Anc2.Anc2refChr1 123680 13 - 142988 ACATTATTATC--TG -s Anc2.Anc2refChr2 4856 13 + 27695 GCATTATTTTT--AG -s mr.mrrefChr0 89803 13 + 130230 ATATAACAACC--TA -s mr.mrrefChr3 135624 13 - 181027 ACATTATTATC--TG -s simCow_chr6.simCow.chr6 126807 13 - 602619 ATATTATTATC--TG -s simDog_chr6.simDog.chr6 100639 13 + 593897 GCATTATTTTT--AG -s simDog_chr6.simDog.chr6 127663 13 - 593897 ACATTATTATC--TG -s simHuman_chr6.simHuman.chr6 89562 13 + 601863 ACATTACTATC--TG -s simHuman_chr6.simHuman.chr6 128906 13 - 601863 ACATTATTATC--TG -s simMouse_chr6.simMouse.chr6 145045 13 - 636262 ACATTGTTATC--TG -s simRat_chr6.simRat.chr6 147859 13 - 647215 ACGTTATTGTC--TG -s simRat_chr6.simRat.chr6 86794 13 + 647215 ACATGACAAAC--AA - -a -s simMouse_chr6.simMouse.chr6 94674 8 + 636262 CTGCCATA -s Anc0.Anc0refChr3 115214 8 - 222631 CTTCCATC -s Anc1.Anc1refChr6 56655 8 - 197743 CTTCCATC -s Anc2.Anc2refChr1 123695 8 - 142988 CTCCCATC -s Anc2.Anc2refChr2 4871 8 + 27695 TTTCTGTC -s mr.mrrefChr0 89816 8 + 130230 CTGCCATA -s mr.mrrefChr3 135642 8 - 181027 CTTCCATC -s simCow_chr6.simCow.chr6 126822 8 - 602619 CTCCCATC -s simDog_chr6.simDog.chr6 100654 8 + 593897 TTTCTGTC -s simDog_chr6.simDog.chr6 127678 8 - 593897 CTCCCATC -s simHuman_chr6.simHuman.chr6 89578 7 + 601863 -TTCCATC -s simHuman_chr6.simHuman.chr6 128922 7 - 601863 -TTCCATC -s simMouse_chr6.simMouse.chr6 145063 8 - 636262 CTTCCATC -s simRat_chr6.simRat.chr6 147877 8 - 647215 CTTCCATC -s simRat_chr6.simRat.chr6 86807 8 + 647215 TCTCCATA - -a -s simMouse_chr6.simMouse.chr6 94682 8 + 636262 TTTCCAAT -s Anc0.Anc0refChr3 115223 8 - 222631 TTTCCAAT -s Anc1.Anc1refChr6 56664 8 - 197743 TTTCCAAT -s Anc2.Anc2refChr1 123704 8 - 142988 TTTCCAAT -s Anc2.Anc2refChr2 4879 8 + 27695 TTTCTAAT -s mr.mrrefChr0 89824 8 + 130230 TTTCCAAT -s mr.mrrefChr3 135651 8 - 181027 TTTCCAGT -s simCow_chr6.simCow.chr6 126831 8 - 602619 TTTCCAAC -s simDog_chr6.simDog.chr6 100662 8 + 593897 TTTCTAAT -s simDog_chr6.simDog.chr6 127687 8 - 593897 TTCCCAAT -s simHuman_chr6.simHuman.chr6 89585 8 + 601863 TTTCCAAT -s simHuman_chr6.simHuman.chr6 128930 8 - 601863 TTTCCAAT -s simMouse_chr6.simMouse.chr6 145072 8 - 636262 TTTCCAGT -s simRat_chr6.simRat.chr6 147886 8 - 647215 TTACCAGT -s simRat_chr6.simRat.chr6 86815 8 + 647215 TTCCCAAA - -a -s simMouse_chr6.simMouse.chr6 94690 4 + 636262 TGGT -s Anc0.Anc0refChr3 115231 4 - 222631 TGGT -s Anc1.Anc1refChr6 56672 4 - 197743 TGGT -s Anc2.Anc2refChr1 123712 4 - 142988 GGGC -s Anc2.Anc2refChr2 4887 4 + 27695 CAGG -s mr.mrrefChr0 89832 4 + 130230 TGGT -s mr.mrrefChr3 135659 4 - 181027 TGGT -s simCow_chr6.simCow.chr6 126851 4 - 602619 GGGC -s simDog_chr6.simDog.chr6 100670 4 + 593897 CAGG -s simDog_chr6.simDog.chr6 127695 4 - 593897 GGAC -s simHuman_chr6.simHuman.chr6 89593 4 + 601863 TGGT -s simHuman_chr6.simHuman.chr6 128938 4 - 601863 TGGT -s simMouse_chr6.simMouse.chr6 145080 4 - 636262 TGGT -s simRat_chr6.simRat.chr6 147894 4 - 647215 TGGT -s simRat_chr6.simRat.chr6 86823 4 + 647215 TGGT - -a -s simMouse_chr6.simMouse.chr6 94694 36 + 636262 GACAGGATTATGGACTCTCTCTACGCACTGTTCCTG -s Anc0.Anc0refChr4 35647 4 - 45765 GACT-------------------------------- -s Anc1.Anc1refChr2 67461 4 + 144309 GACT-------------------------------- -s Anc2.Anc2refChr2 4571 4 + 27695 AATT-------------------------------- -s mr.mrrefChr0 89836 4 + 130230 GACA-------------------------------- -s simCow_chr6.simCow.chr6 94878 4 + 602619 AATT-------------------------------- -s simDog_chr6.simDog.chr6 100283 4 + 593897 AATC-------------------------------- -s simHuman_chr6.simHuman.chr6 89597 4 + 601863 GGCT-------------------------------- -s simRat_chr6.simRat.chr6 86827 4 + 647215 GACA-------------------------------- - -a -s simMouse_chr6.simMouse.chr6 94730 90 + 636262 CTTCAAAGTGTATTAACATCTGGGTCCAACTGAGCAGACTACTTCCTGTAGGCGACGGGACTCAGAGACAGAAAATTGGAGCTATATAAA -s Anc0.Anc0refChr4 35812 54 - 45765 CTTCAATGTGTCTTGATATCT------------------------------------GAACTAAGAGGCAAAAAACTGGGCCTATTTAAT -s Anc1.Anc1refChr2 67634 54 + 144309 CTTCAATGTGTCTTGATATCT------------------------------------GAACTAAGAGGCAAAAAACTGGGCCTATTTAAT -s Anc2.Anc2refChr2 5064 54 + 27695 CTTCAATGTCCCTTGATATCT------------------------------------GAACTAAGAGGCAAGAAACTGAGCCTACTTGAT -s mr.mrrefChr0 89840 54 + 130230 CTTCAAAGTGTATTAACATCT------------------------------------GGACTCAGAGACAGAAAATTGGAGCTATATAAA -s simDog_chr6.simDog.chr6 100847 54 + 593897 CTTCAATGTCCCTTGATATCT------------------------------------GAACTAAGAGGCAAGAAACTGAGCCTACTTGAT -s simHuman_chr6.simHuman.chr6 89777 54 + 601863 CTTCAATGTGTCTTTATATCT------------------------------------GAATTAAGAGGCAAAAAACTGGGACCCTCTAAG -s simRat_chr6.simRat.chr6 86831 46 + 647215 TTTCAAAGTACATTAAGACCT------------------------------------GGACTC-GAGACACAA------ATCTGTAT-GA - -a -s simMouse_chr6.simMouse.chr6 94820 69 + 636262 ATATTGTATTTCATAGCAAAATGAAACACTGACGGAATGGGCAGTCATGTGTGGTACACCCAAAAAGAA -s Anc0.Anc0refChr4 35868 48 - 45765 ATATTGCATCCCATAGCCAAACTAAAAGGCAAAGCACTGGGAC----------------TGA-----AA -s Anc1.Anc1refChr2 67690 64 + 144309 ATATTGCATCCCATAGCCAAACTAAAAGGCAAAGCACTGGGACGCCTTGAACAATACACTGA-----AA -s Anc2.Anc2refChr2 5120 48 + 27695 ATATTGCATCCCATAGCCACACTTAGAGGCCAAACACTGAGAC----------------TGA-----AA -s mr.mrrefChr0 89894 69 + 130230 ATATTGTATTCCATAGCCAAATGAAACAGTAACGGAATGGGCAGTCATGTGTGGTACACCCAAAAAGAA -s simDog_chr6.simDog.chr6 100903 48 + 593897 ATATTGCATCCCATAGCCACACTTAGAGGCCAAACACTGAGAC----------------TGA-----AA -s simHuman_chr6.simHuman.chr6 89833 64 + 601863 ATATTGCCTCCTATAGCCAATCAAAAAGGCAAAGCACTGGGACGCCTTGAACAATACACTGA-----AA -s simRat_chr6.simRat.chr6 86877 69 + 647215 ATATTGTATTCCATAGCCCAATGAAACAGTAATGGAATGGGCAGTCACACTTGGTACACCTGAAAAGAA - -a -s simMouse_chr6.simMouse.chr6 94889 11 + 636262 AATCTCAGGAA -s Anc0.Anc0refChr4 35916 11 - 45765 AATCTCTGGGC -s Anc1.Anc1refChr2 67754 11 + 144309 AATCTCTGGGC -s Anc2.Anc2refChr2 5168 11 + 27695 AATCTCTGGGC -s mr.mrrefChr0 89963 11 + 130230 AATCTCAGGAC -s simDog_chr6.simDog.chr6 100952 11 + 593897 AATCTCTGGGC -s simHuman_chr6.simHuman.chr6 89897 11 + 601863 AATTTCTGGGC -s simRat_chr6.simRat.chr6 86946 11 + 647215 AATCTCAGGAC - -a -s simMouse_chr6.simMouse.chr6 94900 2 + 636262 GA -s Anc0.Anc0refChr4 35927 2 - 45765 TA -s Anc1.Anc1refChr2 67765 2 + 144309 TA -s Anc2.Anc2refChr2 5180 2 + 27695 TA -s mr.mrrefChr0 89974 2 + 130230 GA -s simDog_chr6.simDog.chr6 100964 2 + 593897 TA -s simHuman_chr6.simHuman.chr6 89908 2 + 601863 TA -s simRat_chr6.simRat.chr6 86957 2 + 647215 CA - -a -s simMouse_chr6.simMouse.chr6 94902 12 + 636262 TTGCTATTGGTA -s Anc0.Anc0refChr4 35929 5 - 45765 TCGTT------- -s Anc1.Anc1refChr2 67767 12 + 144309 TCGTTTTCAGTG -s Anc2.Anc2refChr2 5182 5 + 27695 TCTTT------- -s mr.mrrefChr0 89976 12 + 130230 TTGTTATTGGTG -s simDog_chr6.simDog.chr6 100966 5 + 593897 TCTTT------- -s simHuman_chr6.simHuman.chr6 89914 12 + 601863 TCGTTTTCAGTG -s simRat_chr6.simRat.chr6 86959 9 + 647215 TTGTTAT---TG - -a -s simMouse_chr6.simMouse.chr6 94914 19 + 636262 TTGTAACCAAAAGTGTGAA -s Anc0.Anc0refChr4 35934 16 - 45765 --GCAACTAAAAGAG-TGT -s Anc1.Anc1refChr2 67779 19 + 144309 TTGCAACTAAAAGAGGTGT -s Anc2.Anc2refChr2 5187 16 + 27695 --ACAACTAAAAGAG-TGT -s mr.mrrefChr0 89988 19 + 130230 TTGTAACCAAAAGAGTGAA -s simDog_chr6.simDog.chr6 100971 16 + 593897 --ACAACTAAAAGAG-TGT -s simHuman_chr6.simHuman.chr6 89926 18 + 601863 CTGCGA-AGAAACAGCTGT -s simRat_chr6.simRat.chr6 86969 19 + 647215 TTATAACCAAAAGAGTGAA - -a -s simMouse_chr6.simMouse.chr6 94933 21 + 636262 GGTAGACACTAAAACTCTGAT -s Anc0.Anc0refChr4 35950 19 - 45765 GGTAGACACTAAAACTCC--C -s Anc1.Anc1refChr2 67798 19 + 144309 GGTAGACACTAAAACTCC--C -s Anc2.Anc2refChr2 5203 19 + 27695 GGTAGACACTTAAACTTC--C -s mr.mrrefChr0 90007 21 + 130230 GGTAGACACTAAAACTCCGAT -s simDog_chr6.simDog.chr6 100992 19 + 593897 GGTAGACACTTAAACTTC--C -s simHuman_chr6.simHuman.chr6 89944 19 + 601863 GATAGACACTAAAATGCC--C -s simRat_chr6.simRat.chr6 86988 21 + 647215 GGTAGACACTAAAACTCCGAT - -a -s simMouse_chr6.simMouse.chr6 94954 5 + 636262 CTCAG -s Anc0.Anc0refChr4 35969 5 - 45765 TTCAG -s Anc1.Anc1refChr2 67817 5 + 144309 TTCAG -s Anc2.Anc2refChr2 5222 5 + 27695 TTCCA -s mr.mrrefChr0 90028 5 + 130230 CTCAG -s simDog_chr6.simDog.chr6 101016 5 + 593897 TTCCA -s simHuman_chr6.simHuman.chr6 89963 5 + 601863 TTTAG -s simRat_chr6.simRat.chr6 87009 5 + 647215 CTCAG - -a -s simMouse_chr6.simMouse.chr6 94959 38 + 636262 TATGATTTACATACAGTCAAGGTTGGTTTTATCGACAT -s Anc0.Anc0refChr4 35983 37 - 45765 TTTGCTTCAGATATAGTTTAGACT-GCTTTATCAATAT -s Anc1.Anc1refChr2 67831 37 + 144309 TTTGCTTCAGATATAGTTTAGACT-GCTTTATCAATAT -s Anc2.Anc2refChr2 5236 37 + 27695 CTTGCTTCAGATATAGTTTGGACT-GCTTTATCAATAC -s mr.mrrefChr0 90042 38 + 130230 TATGATTTACATACAGTCAAGGTTGGTTTTATCAACAT -s simCow_chr6.simCow.chr6 95353 18 + 602619 -------------------GGACT-GCTTTATCCATCC -s simDog_chr6.simDog.chr6 101030 37 + 593897 CTTGCTTCAGATATAGTTTGGACC-ACTTTATCAATAC -s simHuman_chr6.simHuman.chr6 89977 37 + 601863 TTTGCCTCATCTATATCTCAGACT-GCTGTATCAATAT -s simRat_chr6.simRat.chr6 87023 38 + 647215 CCTGATTTACATACAATCAAGGTTGGTTTTATCAACAT - -a -s simMouse_chr6.simMouse.chr6 94997 1 + 636262 A -s Anc0.Anc0refChr4 36020 1 - 45765 A -s Anc1.Anc1refChr2 67868 1 + 144309 A -s Anc2.Anc2refChr2 5273 1 + 27695 A -s mr.mrrefChr0 90080 1 + 130230 A -s simCow_chr6.simCow.chr6 95371 1 + 602619 A -s simDog_chr6.simDog.chr6 101067 1 + 593897 A -s simHuman_chr6.simHuman.chr6 90014 1 + 601863 A -s simRat_chr6.simRat.chr6 87079 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 94998 23 + 636262 CCAATTAAAAACCATATTGCTGT -s Anc0.Anc0refChr4 36022 23 - 45765 CCAGTTAAAAACTATACTATTGG -s Anc1.Anc1refChr2 67870 23 + 144309 CCAGTTAAAAACTATACTATTGG -s Anc2.Anc2refChr2 5275 23 + 27695 TCAGTCAAAAACTGTAATATTAG -s mr.mrrefChr0 90081 23 + 130230 CCAATTAAAAACCATACTGTTGT -s simCow_chr6.simCow.chr6 95372 20 + 602619 ---GTCAAAAAGGGTAATATTAG -s simDog_chr6.simDog.chr6 101069 21 + 593897 TCAGTCAA--ACTGTAATATTAG -s simHuman_chr6.simHuman.chr6 90016 23 + 601863 CCAGTTAAAGACTACACTATTGG -s simRat_chr6.simRat.chr6 87080 23 + 647215 CCAATTAAAATCCATACTGTCGT - -a -s simMouse_chr6.simMouse.chr6 95021 9 + 636262 GAGTTTTTT -s Anc0.Anc0refChr4 36045 9 - 45765 GAGTTTATG -s Anc1.Anc1refChr2 67893 9 + 144309 GAGTTTATG -s Anc2.Anc2refChr2 5298 9 + 27695 GAGTTTATG -s mr.mrrefChr0 90104 9 + 130230 GAGTTTTTT -s simCow_chr6.simCow.chr6 95399 9 + 602619 GAGTTTATT -s simDog_chr6.simDog.chr6 101090 9 + 593897 GGCTTCATG -s simHuman_chr6.simHuman.chr6 90039 9 + 601863 GAGTTTAAG -s simRat_chr6.simRat.chr6 87103 9 + 647215 TAGTTTTTT - -a -s simMouse_chr6.simMouse.chr6 95030 22 + 636262 TTCTGTCTGCCACATAAAGGAG -s Anc0.Anc0refChr4 36057 10 - 45765 TTCTGCCT------------AG -s Anc1.Anc1refChr2 67905 10 + 144309 TTCTGCCT------------AG -s Anc2.Anc2refChr2 5310 10 + 27695 TTTTTCCT------------AA -s mr.mrrefChr0 90116 22 + 130230 TTCTGTCTGCCACATAAAGGAG -s simCow_chr6.simCow.chr6 95418 10 + 602619 TTTTTCCT------------AA -s simDog_chr6.simDog.chr6 101102 10 + 593897 TTTTTCTT------------AA -s simHuman_chr6.simHuman.chr6 90051 10 + 601863 TTCTGCCT------------AG -s simRat_chr6.simRat.chr6 87115 22 + 647215 TTCTGTCTGCCACATAAAGGAG - -a -s simMouse_chr6.simMouse.chr6 95052 9 + 636262 TTCAACTCC -s Anc0.Anc0refChr4 36067 6 - 45765 TT---GTGC -s Anc1.Anc1refChr2 67915 6 + 144309 TT---GTGC -s Anc2.Anc2refChr2 5320 6 + 27695 TT---GTGC -s mr.mrrefChr0 90138 9 + 130230 TTCAAGTCC -s simCow_chr6.simCow.chr6 95428 6 + 602619 TA---GTGT -s simDog_chr6.simDog.chr6 101112 6 + 593897 TT---GTGC -s simHuman_chr6.simHuman.chr6 90061 6 + 601863 TT---GTGC -s simRat_chr6.simRat.chr6 87138 9 + 647215 TTCAGGCCC - -a -s simMouse_chr6.simMouse.chr6 95061 64 + 636262 CAATAAAAAGGAGTTTAGAAGAATAATGGTACAGCAGGTAGAAGGAAGGCATTACCAGGCGCTA -s Anc0.Anc0refChr4 36073 50 - 45765 CAATATAAGGGGGTTGAGCAGAATAATGGCACACTAGTTAGAAG--------------GTACTA -s Anc1.Anc1refChr2 67921 50 + 144309 CAATATAAGGGGGTTGAGCAGAATAATGGCACACTAGTTAGAAG--------------GTACTA -s Anc2.Anc2refChr2 5328 50 + 27695 CAATATAAGGGGGTTGAGCAGAACAATGGCACACTAGTTAGAAG--------------GTACTA -s mr.mrrefChr0 90147 52 + 130230 CAATATAAAGGAGTTTAGCAGAATAATGGCACAGCAGGTAGAAGGA------------GCACTA -s simCow_chr6.simCow.chr6 95436 49 + 602619 CAGTGT-AGGGGATTGAGCAGGACAATGGCACACGCGTTTGAAG--------------GCACTA -s simDog_chr6.simDog.chr6 101120 50 + 593897 CAATATAGGGGGGTTGAGCAAAACAATGACACACTAGTTAGAAG--------------GTACTA -s simHuman_chr6.simHuman.chr6 90067 50 + 601863 TGTGATAAGGGGGTTGACCAGCATTATGGCACAATAGTTACAAG--------------GTACTA -s simRat_chr6.simRat.chr6 87147 52 + 647215 CAATATAAAGGAGTTTAGCGGAATAATGCCATAGCTCGTAGATAGA------------GCACTA - -a -s simMouse_chr6.simMouse.chr6 95125 35 + 636262 CCTGAATGGGTGGGTTGAGTCTTTCTTACTGAGCA -s Anc0.Anc0refChr4 36124 34 - 45765 CATGCAATGGTA-GTCAAGGATTTCATACAGAGCA -s Anc1.Anc1refChr2 67972 34 + 144309 CATGCAATGGTA-GTCAAGGATTTCATACAGAGCA -s Anc2.Anc2refChr2 5379 34 + 27695 CACACAATGGTA-GTCAAGTATCTCATACAGAGAA -s mr.mrrefChr0 90199 35 + 130230 CCTGCATTGGTAGGTTGAGGCTTTCTTACTGAGCA -s simCow_chr6.simCow.chr6 95486 34 + 602619 CACAAAATGGGA-GTTGAGTATCTCATACAGAGAG -s simDog_chr6.simDog.chr6 101171 34 + 593897 CACACAATGGTA-GTCAAGTATCTCATACAAAGAA -s simHuman_chr6.simHuman.chr6 90118 34 + 601863 CATGCAATGGTA-GTCAAGGAATGTATACAGAGCT -s simRat_chr6.simRat.chr6 87199 35 + 647215 CCCGCATTGGTAGATTGAGGCTTTCTTACTGAGAA - -a -s simMouse_chr6.simMouse.chr6 95160 6 + 636262 CCCTCC -s Anc0.Anc0refChr4 36159 6 - 45765 CACTCC -s Anc1.Anc1refChr2 68007 6 + 144309 CACTCC -s Anc2.Anc2refChr2 5414 6 + 27695 CACTTC -s mr.mrrefChr0 90235 6 + 130230 CCCTCC -s simCow_chr6.simCow.chr6 95521 5 + 602619 CACT-C -s simDog_chr6.simDog.chr6 101206 6 + 593897 CTCTTC -s simHuman_chr6.simHuman.chr6 90153 6 + 601863 GACTCC -s simRat_chr6.simRat.chr6 87235 6 + 647215 CCCTCC - -a -s simMouse_chr6.simMouse.chr6 95166 38 + 636262 TTGGTCTTGGCTATGGCCACGGACTGGACATGTCAAGA -s Anc0.Anc0refChr4 36173 38 - 45765 TTGTCCTTTGCAATGGACACTGACTGCACATGCAAAGA -s Anc1.Anc1refChr2 68021 38 + 144309 TTGTCCTTTGCAATGGACACTGACTGCACATGCAAAGA -s Anc2.Anc2refChr2 5428 38 + 27695 CTGTCCTTTGCAATGAATACTAACTGCGTGTGCAGAGA -s mr.mrrefChr0 90241 38 + 130230 TTGGCCTTTGCAATGGCCACTGACTGGACATGTCAAGA -s simCow_chr6.simCow.chr6 95534 38 + 602619 CTATCCTTTGCAATCAATACTAACTGTCTCTGCAGTGA -s simDog_chr6.simDog.chr6 101220 38 + 593897 CTGTCCCTTGGAATGAGTACTAACTGCGTGTGCAGATG -s simHuman_chr6.simHuman.chr6 90167 38 + 601863 TTGACCTTTGCAATGGACGCTGACTGAACATGCAAAGA -s simRat_chr6.simRat.chr6 87241 38 + 647215 TTGGCCTTTGGAATGGCCACTGACTGGGCATGTCAAGA - -a -s simMouse_chr6.simMouse.chr6 95204 4 + 636262 AATG -s Anc0.Anc0refChr4 36213 4 - 45765 AATG -s Anc1.Anc1refChr2 68061 4 + 144309 AATG -s Anc2.Anc2refChr2 5468 4 + 27695 AATG -s mr.mrrefChr0 90279 4 + 130230 AATG -s simCow_chr6.simCow.chr6 95574 4 + 602619 AATG -s simDog_chr6.simDog.chr6 101260 4 + 593897 AATG -s simHuman_chr6.simHuman.chr6 90207 4 + 601863 AATG -s simRat_chr6.simRat.chr6 87279 4 + 647215 AATG - -a -s simMouse_chr6.simMouse.chr6 95208 36 + 636262 AGGGCTTCAAGCAAGATCAGGACGCAAGGTTGTTAT -s Anc0.Anc0refChr4 36217 35 - 45765 ATGGTTCCAAGCCAGATAGGGGCACTAGG-TGTTCT -s Anc1.Anc1refChr2 68065 35 + 144309 ATGGTTCCAAGCCAGATAGGGGCACTAGG-TGTTCT -s Anc2.Anc2refChr2 5472 35 + 27695 ATGGCTCCAAGCCAGGTAGGGGTGCTAGG-TGGTCT -s mr.mrrefChr0 90283 36 + 130230 ATGGTTTCAAGCAAGATAGGGACACAAGGTTGTTAT -s simCow_chr6.simCow.chr6 95578 28 + 602619 ATGGGTTAATGCC----AAGGATTCCATT-TGG--- -s simDog_chr6.simDog.chr6 101264 35 + 593897 ACAGCTCCAAGCCAGGTAGGGGTGCTAGG-TGGTCT -s simHuman_chr6.simHuman.chr6 90211 35 + 601863 ATGGTTCCAAGTGAGATAGGGGCATTCGG-TGTTGT -s simRat_chr6.simRat.chr6 87285 36 + 647215 ATGGTCTCAAGCTAGATAGGGACACAAGGTTGTTAT - -a -s simMouse_chr6.simMouse.chr6 95244 4 + 636262 ACCA -s Anc0.Anc0refChr4 36255 4 - 45765 ATCA -s Anc1.Anc1refChr2 68103 4 + 144309 ATCA -s Anc2.Anc2refChr2 5510 4 + 27695 ATCG -s mr.mrrefChr0 90322 4 + 130230 ACCA -s simDog_chr6.simDog.chr6 101302 4 + 593897 ATCG -s simHuman_chr6.simHuman.chr6 90249 4 + 601863 ATAA -s simRat_chr6.simRat.chr6 87324 4 + 647215 ACCA - -a -s simMouse_chr6.simMouse.chr6 95248 5 + 636262 GCAAT -s Anc0.Anc0refChr4 36259 5 - 45765 GGGAT -s Anc1.Anc1refChr2 68107 5 + 144309 GGGAT -s Anc2.Anc2refChr2 5514 5 + 27695 GGGAT -s mr.mrrefChr0 90326 5 + 130230 GCAAT -s simDog_chr6.simDog.chr6 101334 5 + 593897 GGGAT -s simHuman_chr6.simHuman.chr6 90253 5 + 601863 GATAT -s simRat_chr6.simRat.chr6 87328 5 + 647215 GCAGT - -a -s simMouse_chr6.simMouse.chr6 95253 6 + 636262 GTACTA -s Anc0.Anc0refChr4 36266 6 - 45765 AGACTA -s Anc1.Anc1refChr2 68114 6 + 144309 AGACTA -s Anc2.Anc2refChr2 5521 6 + 27695 AGACAA -s mr.mrrefChr0 90331 6 + 130230 GTACTA -s simCow_chr6.simCow.chr6 95608 6 + 602619 AGACAA -s simDog_chr6.simDog.chr6 101341 6 + 593897 AGACAA -s simHuman_chr6.simHuman.chr6 90260 6 + 601863 AGACTA -s simRat_chr6.simRat.chr6 87333 6 + 647215 GTACTC - -a -s simMouse_chr6.simMouse.chr6 95259 7 + 636262 ATGGAAA -s Anc0.Anc0refChr4 36280 7 - 45765 ATGATCT -s Anc1.Anc1refChr2 68128 7 + 144309 ATGATCT -s Anc2.Anc2refChr2 5535 7 + 27695 ATGATCT -s mr.mrrefChr0 90337 7 + 130230 ATGGAAA -s simCow_chr6.simCow.chr6 95622 7 + 602619 ATGATCT -s simDog_chr6.simDog.chr6 101355 7 + 593897 ATGATCT -s simHuman_chr6.simHuman.chr6 90274 7 + 601863 ATGATCT -s simRat_chr6.simRat.chr6 87339 7 + 647215 ATGCAAA - -a -s simMouse_chr6.simMouse.chr6 95266 1 + 636262 G -s Anc0.Anc0refChr4 36287 1 - 45765 A -s Anc1.Anc1refChr2 68135 1 + 144309 A -s Anc2.Anc2refChr2 5542 1 + 27695 A -s mr.mrrefChr0 90344 1 + 130230 G -s simCow_chr6.simCow.chr6 95633 1 + 602619 G -s simDog_chr6.simDog.chr6 101362 1 + 593897 A -s simHuman_chr6.simHuman.chr6 90281 1 + 601863 A -s simRat_chr6.simRat.chr6 87346 1 + 647215 G - -a -s simMouse_chr6.simMouse.chr6 95267 66 + 636262 ACAGCACTTAGTTTATGTATTGACTCCTGTAGGAGTGCTGTGGGAGGTTGGTGTGATCATTACAAA -s Anc0.Anc0refChr4 36302 66 - 45765 ACAACATTTAGCATATGTATTAACTCCTATGGGAGTGCTTTTTGAGGTAGGAGTCATCCTTACAGA -s Anc1.Anc1refChr2 68150 66 + 144309 ACAACATTTAGCATATGTATTAACTCCTATGGGAGTGCTTTTTGAGGTAGGAGTCATCCTTACAGA -s Anc2.Anc2refChr2 5557 66 + 27695 ACAACATTTAGCATATGTATTAACTCCTATGAGAGTGGTTCTTGAGGTAGGAGTCATTCATACAGA -s mr.mrrefChr0 90359 66 + 130230 ACAGCACTTAGTTTATGTATTGACTCCTGTAGGAGTGCTGTGTGAGGTTGGTGTGATCATTACAAA -s simCow_chr6.simCow.chr6 95648 56 + 602619 ACAACATTTAGCACGTGTATCAACTCCCATGA---------TTGAGGTAGAAGTCAT-CCTTGAGA -s simDog_chr6.simDog.chr6 101388 66 + 593897 ACAACACGTAGCATATGTATTGCCTCCTATGAGAGTGGTTCTTGAGGTAAGAGTTCATCATACAAA -s simHuman_chr6.simHuman.chr6 90296 66 + 601863 ACAACATTAAGCAGATGTATTAACTCCTATGGGAGGGCTTTTTGAGGTAGGGATCATCCTCATAGA -s simRat_chr6.simRat.chr6 87361 66 + 647215 ACAGCACTTAGTTTATGTACTGACTGCTTTATGAGTGCTGTGTGAGGGTGGTGTAATCGTTACAAG - -a -s simMouse_chr6.simMouse.chr6 95333 22 + 636262 TAGTGGACTGAGCACTCGGCAA -s Anc0.Anc0refChr4 36368 20 - 45765 GAGTGTAGTGAGCACCCTAC-- -s Anc1.Anc1refChr2 68216 20 + 144309 GAGTGTAGTGAGCACCCTAC-- -s Anc2.Anc2refChr2 5623 20 + 27695 GGGTGTAGTGAGCCCCCTAC-- -s mr.mrrefChr0 90425 20 + 130230 TAGTGGACTGAGCACTCGGC-- -s simCow_chr6.simCow.chr6 95705 20 + 602619 ATATGGAGTGAGCCTCCTAT-- -s simDog_chr6.simDog.chr6 101454 18 + 593897 GGGAGTAATGA--CCCCTAC-- -s simHuman_chr6.simHuman.chr6 90362 20 + 601863 CAGTGTAGTGAGCACCCCAC-- -s simRat_chr6.simRat.chr6 87427 20 + 647215 TAGTGGACTGAGCACTCGGC-- - -a -s simMouse_chr6.simMouse.chr6 95355 11 + 636262 AAGTAATTCAA -s Anc0.Anc0refChr4 36388 3 - 45765 A--------AA -s Anc1.Anc1refChr2 68236 3 + 144309 A--------AA -s Anc2.Anc2refChr2 5644 3 + 27695 A--------AA -s mr.mrrefChr0 90445 11 + 130230 AAGTAATTCAA -s simCow_chr6.simCow.chr6 95726 3 + 602619 A--------AA -s simDog_chr6.simDog.chr6 101473 3 + 593897 A--------AA -s simHuman_chr6.simHuman.chr6 90382 3 + 601863 A--------AA -s simRat_chr6.simRat.chr6 87447 11 + 647215 AAGTAATCCAA - -a -s simMouse_chr6.simMouse.chr6 95366 1 + 636262 A -s Anc0.Anc0refChr4 36399 1 - 45765 G -s Anc1.Anc1refChr2 68247 1 + 144309 G -s Anc2.Anc2refChr2 5655 1 + 27695 G -s mr.mrrefChr0 90464 1 + 130230 G -s simCow_chr6.simCow.chr6 95737 1 + 602619 G -s simDog_chr6.simDog.chr6 101484 1 + 593897 G -s simHuman_chr6.simHuman.chr6 90393 1 + 601863 G -s simRat_chr6.simRat.chr6 87466 1 + 647215 G - -a -s simMouse_chr6.simMouse.chr6 95367 21 + 636262 ATCTGCCTGTCTGCATACTGA -s Anc0.Anc0refChr4 36400 21 - 45765 TACTACCTGTATGCATACTGT -s Anc1.Anc1refChr2 68248 21 + 144309 TACTACCTGTATGCATACTGT -s Anc2.Anc2refChr2 5657 21 + 27695 TATTACCTGTATGCATACTGT -s mr.mrrefChr0 90465 21 + 130230 ATCTACCTGTCTGCATACTGA -s simCow_chr6.simCow.chr6 95739 21 + 602619 TAGTACCTTTATGCATCCTGA -s simDog_chr6.simDog.chr6 101486 21 + 593897 TATGACCTGTATGCAAACTGT -s simHuman_chr6.simHuman.chr6 90394 21 + 601863 TACTACTTGTATGCATACTAC -s simRat_chr6.simRat.chr6 87467 21 + 647215 ATCTACCTGTCTGCATACTGA - -a -s simMouse_chr6.simMouse.chr6 95388 17 + 636262 TACCGCATGGTGATTTC -s Anc0.Anc0refChr4 36421 4 - 45765 AG-------------TC -s Anc1.Anc1refChr2 68269 4 + 144309 AG-------------TC -s Anc2.Anc2refChr2 5678 4 + 27695 AG-------------TC -s mr.mrrefChr0 90486 17 + 130230 TGCCGCATGGTGATTTC -s simCow_chr6.simCow.chr6 95760 4 + 602619 AC-------------TC -s simDog_chr6.simDog.chr6 101508 4 + 593897 AG-------------TC -s simHuman_chr6.simHuman.chr6 90415 4 + 601863 AG-------------TC -s simRat_chr6.simRat.chr6 87488 17 + 647215 TGCCATAAGGTGATTTC - -a -s simMouse_chr6.simMouse.chr6 95405 6 + 636262 CGGGGA -s Anc0.Anc0refChr4 36425 6 - 45765 CCAGAT -s Anc1.Anc1refChr2 68273 6 + 144309 CCAGAT -s Anc2.Anc2refChr2 5687 6 + 27695 CCAGAT -s mr.mrrefChr0 90503 6 + 130230 CGGGGA -s simCow_chr6.simCow.chr6 95770 6 + 602619 CCAGTT -s simDog_chr6.simDog.chr6 101517 6 + 593897 CCAGAT -s simHuman_chr6.simHuman.chr6 90419 6 + 601863 CCAGAT -s simRat_chr6.simRat.chr6 87505 6 + 647215 CAGATA - -a -s simMouse_chr6.simMouse.chr6 95411 21 + 636262 TTTAAAATAATATCAGTAGCG -s Anc0.Anc0refChr4 36431 21 - 45765 TTTAAAATAACAAAAGTACTT -s Anc1.Anc1refChr2 68279 21 + 144309 TTTAAAATAACAAAAGTACTT -s Anc2.Anc2refChr2 5695 21 + 27695 TTTAAAATAACAAAAGTACTT -s mr.mrrefChr0 90509 21 + 130230 TTTAAAATAACATAAGTACTG -s simCow_chr6.simCow.chr6 95777 21 + 602619 TTTAAAATAGCGAAAGTAGTG -s simDog_chr6.simDog.chr6 101527 21 + 593897 CTTAAAATAACAAAAGTACTT -s simHuman_chr6.simHuman.chr6 90425 21 + 601863 TTTAAAATGACAAAAGTACTC -s simRat_chr6.simRat.chr6 87511 21 + 647215 TTTAAAATAACATAAATACTG - -a -s simMouse_chr6.simMouse.chr6 95432 7 + 636262 TGTGTGT -s Anc0.Anc0refChr4 36452 7 - 45765 TGTGTGT -s Anc1.Anc1refChr2 68300 7 + 144309 TGTGTGT -s Anc2.Anc2refChr2 5716 7 + 27695 TGTGTGT -s mr.mrrefChr0 90530 7 + 130230 TGTGTGT -s simCow_chr6.simCow.chr6 95798 7 + 602619 TGTGTGT -s simDog_chr6.simDog.chr6 101549 6 + 593897 TGTGT-T -s simHuman_chr6.simHuman.chr6 90446 7 + 601863 TGTGTGT -s simRat_chr6.simRat.chr6 87532 7 + 647215 TGTGTCT - -a -s simMouse_chr6.simMouse.chr6 95439 10 + 636262 AGCCTTGTCC -s Anc0.Anc0refChr4 36459 10 - 45765 TGCCTTGTCC -s Anc1.Anc1refChr2 68307 10 + 144309 TGCCTTGTCC -s Anc2.Anc2refChr2 5723 10 + 27695 TGACTTGTCC -s mr.mrrefChr0 90537 10 + 130230 AGCCTTGTCC -s simCow_chr6.simCow.chr6 95806 10 + 602619 TGATATGTTC -s simDog_chr6.simDog.chr6 101555 10 + 593897 TGACTTGTCC -s simHuman_chr6.simHuman.chr6 90453 10 + 601863 TGCCTTGTCC -s simRat_chr6.simRat.chr6 87539 10 + 647215 AGCCTTGTCC - -a -s simMouse_chr6.simMouse.chr6 95449 15 + 636262 TAAAACTTGCTGGTG -s Anc0.Anc0refChr4 36469 13 - 45765 T--ACCGTGCTGTTG -s Anc1.Anc1refChr2 68317 13 + 144309 T--ACCGTGCTGTTG -s Anc2.Anc2refChr2 5733 13 + 27695 T--ACAGTGCTGTCG -s mr.mrrefChr0 90547 15 + 130230 TAAAACTTGCTGGTG -s simCow_chr6.simCow.chr6 95816 11 + 602619 T--A--GTGCTGTAG -s simDog_chr6.simDog.chr6 101566 13 + 593897 T--ACAGCGCTGTCA -s simHuman_chr6.simHuman.chr6 90463 13 + 601863 T--GCCGTGCTGTTG -s simRat_chr6.simRat.chr6 87549 11 + 647215 TAGAA----GTGGTG - -a -s simMouse_chr6.simMouse.chr6 95464 1 + 636262 G -s Anc0.Anc0refChr4 36484 1 - 45765 A -s Anc1.Anc1refChr2 68332 1 + 144309 A -s Anc2.Anc2refChr2 5748 1 + 27695 A -s mr.mrrefChr0 90562 1 + 130230 G -s simCow_chr6.simCow.chr6 95829 1 + 602619 G -s simDog_chr6.simDog.chr6 101581 1 + 593897 A -s simHuman_chr6.simHuman.chr6 90478 1 + 601863 A -s simRat_chr6.simRat.chr6 87560 1 + 647215 G - -a -s simMouse_chr6.simMouse.chr6 95465 31 + 636262 TCTACATAGTTACATAGCAATAATTGCATGT -s Anc0.Anc0refChr4 36485 30 - 45765 CTTGT-TTTTCATGTGGCAACAATGCCACTT -s Anc1.Anc1refChr2 68333 31 + 144309 CTTGTATTTTCATGTGGCAACAATGCCACTT -s Anc2.Anc2refChr2 5750 30 + 27695 CTTGT-TTTTCATGTGGCAACAATGCCACTT -s mr.mrrefChr0 90563 31 + 130230 TCTATATAGTTACATGGCAATAATGGCATTT -s simCow_chr6.simCow.chr6 95831 30 + 602619 CCTGT-CTCCTATATTGCAATAATGCCTCTT -s simDog_chr6.simDog.chr6 101583 30 + 593897 CTTGT-TTTTCATGTGGCACCAGTGCCACTT -s simHuman_chr6.simHuman.chr6 90479 31 + 601863 CTTGTATTTTCATGTGGCAACAATGCTGCTT -s simRat_chr6.simRat.chr6 87561 30 + 647215 T-GATATAGTTACATGGCAATAATGGCAATT - -a -s simMouse_chr6.simMouse.chr6 95496 23 + 636262 TCTATGAAGAATGTGAGGGAGGT -s Anc0.Anc0refChr4 36515 7 - 45765 TCTATGA---------------- -s Anc1.Anc1refChr2 68364 7 + 144309 TCTATGA---------------- -s Anc2.Anc2refChr2 5782 7 + 27695 TCTATGA---------------- -s mr.mrrefChr0 90594 23 + 130230 TCTATGAAGAATGTGAGGGAGGT -s simCow_chr6.simCow.chr6 95863 7 + 602619 TATATGA---------------- -s simDog_chr6.simDog.chr6 101615 7 + 593897 TCTATGA---------------- -s simHuman_chr6.simHuman.chr6 90510 7 + 601863 TCTATAA---------------- -s simRat_chr6.simRat.chr6 87591 23 + 647215 GCTATGATGAATGTGAGGGAGGT - -a -s simMouse_chr6.simMouse.chr6 95519 48 + 636262 CATTGGCCACCTCCTGCTTCTGGCATAGCTTCCAGCTTGGTGTAGGTA -s Anc0.Anc0refChr4 36522 2 - 45765 ----------------------------------------------TA -s Anc1.Anc1refChr2 68371 2 + 144309 ----------------------------------------------TA -s Anc2.Anc2refChr2 5789 2 + 27695 ----------------------------------------------TG -s mr.mrrefChr0 90617 36 + 130230 CATTGGCCACCTCCTGCTTCTGGCATAGCTTC------------GGTA -s simCow_chr6.simCow.chr6 95870 2 + 602619 ----------------------------------------------TG -s simDog_chr6.simDog.chr6 101622 2 + 593897 ----------------------------------------------TG -s simHuman_chr6.simHuman.chr6 90517 2 + 601863 ----------------------------------------------TA -s simRat_chr6.simRat.chr6 87615 36 + 647215 CACTGGCCACCCCCTGCCTCTGGCATAGCTTC------------AGTA - -a -s simMouse_chr6.simMouse.chr6 95567 148 + 636262 GACATGGCAAGTACCAGTAAATGGACACAAGTATAAGCTACATATAGGACCATGACAAACAATAAAGTCAGTTAATGACAACTCTTCTCAGAGGATCAAAACAAAAGGCAAATGCAGTCTACTTAGATAGGAACGGCAATTAAAATAT -s Anc0.Anc0refChr4 36524 148 - 45765 GACCTGATAAGTACCAGTAAATAGACACTAGTAAAAGGTGCATCTGGTACTATAACCAGCAGTTAAATGTATTAATGACAACCCTTTTCAGAGAATTAAATGGAGACAGAATTTCAGTCCTCTTAGATAAGAACAGCAATTAAAATAC -s Anc1.Anc1refChr2 68373 148 + 144309 GACCTGATAAGTACCAGTAAATAGACACTAGTAAAAGGTGCATCTGGTACTATAACCAGCAGTTAAATGTATTAATGACAACCCTTTTCAGAGAATTAAATGGAGACAGAATTTCAGTCCTCTTAGATAAGAACAGCAATTAAAATAC -s Anc2.Anc2refChr2 5791 148 + 27695 GACCTGATAAATTCCAGTGAATAGACACTAGTAAAAGGTGCATCTGGTACTATAACCAGCAGTTACATGTATTAATGACAACCCTTTTCAGAGAAGTGAATGGAGACAGAATTTCACTCCTCTTGGATAAGAACAGCAAGTAAAATAC -s mr.mrrefChr0 90653 148 + 130230 GACCTGGTAAGTACCAGTAAATGGACACAAGTATAAGCTACATATAGGACCATGACAAACAATAAAGTCAGTTAATGACAACTCTTTTCAGAGAATCAAAAGAAAAGGCAAATGCAGTCTACTTAGATAGGAACGGCAATTAAAATAT -s simCow_chr6.simCow.chr6 95886 146 + 602619 GA-CTGATAAATGCTAGTGAATAGACACAAG-AAGAGGTGCATATGGTACTATAACCAGCAATTACATATAATAGTAAAAACCCTTTCTGGAAAAGTGAATGTGGACGGAATTCTACTCCTCTTGGATAACAACATCAAGTAAAATTT -s simDog_chr6.simDog.chr6 101624 147 + 593897 GACCTGATAAATTCCAGTGAATAGGAACTAGTAAAGGGAGCATCTAGAACCATAACCATCAGTTACATGAATTAATGACAACCATTTTCAGAGAAGT-AATAGAGACAGAGTTTCACTTCTCTTGGATAAGAGCAGCAAGTAACAAAC -s simHuman_chr6.simHuman.chr6 90519 148 + 601863 AACCAGATAAGTACCAGCAAATAGACACGAATAAAAGGTGCATGCGGTGCTCTATCCAGGAGTTAAATGTATTCATGACAACCCTTTTCAGAGAATTAAAGGGAGACAGAATGTCAGTCCTCTTAGATAAGAACAGCAATTAAAATAC -s simRat_chr6.simRat.chr6 87651 130 + 647215 GAGCTGGTGAGTACTATTAAATGGAC-CAAGTATAATATACATATAGGACCATGGGAAATAATACAGTCAGTCAATGACAACTCTTTTCAGAGAATCAAAAGTAAAGGTGAACGCAGTCTACTTAGATAGA----------------- - -a -s simMouse_chr6.simMouse.chr6 95715 21 + 636262 GCCAAACTCCCAAAATTATTG -s Anc0.Anc0refChr4 36677 15 - 45765 GGCAA------CAGGTTATGG -s Anc1.Anc1refChr2 68526 15 + 144309 GGCAA------CAGGTTATGG -s Anc2.Anc2refChr2 5944 15 + 27695 GGCAA------CAGGTTATGG -s mr.mrrefChr0 90801 15 + 130230 GCCAA------AAAATTATTG -s simCow_chr6.simCow.chr6 96037 15 + 602619 AGCAA------AAGGGCATAG -s simDog_chr6.simDog.chr6 101776 15 + 593897 GGCAA------CAGTTTATGG -s simHuman_chr6.simHuman.chr6 90672 15 + 601863 GACAA------GAGGTTATGG -s simRat_chr6.simRat.chr6 87781 8 + 647215 -------------AATCATTG - -a -s simMouse_chr6.simMouse.chr6 95736 25 + 636262 TTGGTGCTAATAATTTATAGAAAAT -s Anc0.Anc0refChr4 36692 5 - 45765 ------------A--------AAAT -s Anc1.Anc1refChr2 68541 13 + 144309 ------------AGTTATGGAAAAT -s Anc2.Anc2refChr2 5959 5 + 27695 ------------A--------AAAT -s mr.mrrefChr0 90816 25 + 130230 TTGGTGCTAATAATTTATGGAAAAT -s simCow_chr6.simCow.chr6 96052 5 + 602619 ------------A--------CAAC -s simDog_chr6.simDog.chr6 101791 5 + 593897 ------------G--------AAAT -s simHuman_chr6.simHuman.chr6 90687 13 + 601863 ------------AGTTATGGAAAAT -s simRat_chr6.simRat.chr6 87790 25 + 647215 TTGGTGCCAATAGTTTATGGCAAAT - -a -s simMouse_chr6.simMouse.chr6 95761 51 + 636262 TAAAGTAGACAACATTCCCGTTACTAGCTTTCTGAAGTACCAACAAGTTCA -s Anc0.Anc0refChr4 36698 50 - 45765 TTAAGCAGATGCCATTTTCATCACTAGCTTGCCG-ATTACCATTAAGAAAG -s Anc1.Anc1refChr2 68555 50 + 144309 TTAAGCAGATGCCATTTTCATCACTAGCTTGCCG-ATTACCATTAAGAAAG -s Anc2.Anc2refChr2 5965 50 + 27695 TTAAGCAGATGCCATTTTCATCACTAGCTTGCCC-ATTACCATTAAGAAAG -s mr.mrrefChr0 90841 50 + 130230 TAAAGTAGACAACATTCCCGTTACTAGCTTTCTG-AGTACCAATAAGTTCA -s simCow_chr6.simCow.chr6 96058 50 + 602619 TTAAGCAGATGCCATTTTCATTATTAGCTTTGTA-ATTACCATTAGGAAAG -s simDog_chr6.simDog.chr6 101797 50 + 593897 TTAAGCAGATGTCATTTTCATCACTAAAACGCCC-TTGCCCGTGAAGTGAG -s simHuman_chr6.simHuman.chr6 90701 50 + 601863 TCAAGCAGATGCAATTTTCATCACTAGCTTCCAG-ATTACCATTAAGAAAG -s simRat_chr6.simRat.chr6 87815 9 + 647215 ------------------------------------------ATAAAGTCA - -a -s simMouse_chr6.simMouse.chr6 95812 29 + 636262 TAAGGAACAAGGGGCGGGACTAACCATAG -s Anc0.Anc0refChr4 36748 27 - 45765 CCAAGA--AAGTGTTGAGGGTAACCATCA -s Anc1.Anc1refChr2 68605 27 + 144309 CCAAGA--AAGTGTTGAGGGTAACCATCA -s Anc2.Anc2refChr2 6015 27 + 27695 CCAACA--ATGTATTTAGGGTAGCTTTCA -s mr.mrrefChr0 90891 27 + 130230 TAAAGA--AAGGGGCGGGACTAACCATAG -s simCow_chr6.simCow.chr6 96127 22 + 602619 CCAACC--ATGTATTTAGAGTGGG----- -s simDog_chr6.simDog.chr6 101848 27 + 593897 CCAACA--ATGTATTTAGGGTAGCTTTCA -s simHuman_chr6.simHuman.chr6 90751 27 + 601863 CTAAGA--AAGTGTGGCGGATTACCATTA -s simRat_chr6.simRat.chr6 87824 27 + 647215 TAAAGA--AAGCGGTGGGACTAACCATAG - -a -s simMouse_chr6.simMouse.chr6 95841 3 + 636262 TGT -s Anc0.Anc0refChr4 36775 3 - 45765 GGT -s Anc1.Anc1refChr2 68632 3 + 144309 GGT -s Anc2.Anc2refChr2 6042 3 + 27695 GGT -s mr.mrrefChr0 90918 3 + 130230 TGT -s simDog_chr6.simDog.chr6 101875 3 + 593897 GGT -s simHuman_chr6.simHuman.chr6 90813 3 + 601863 AAT -s simRat_chr6.simRat.chr6 87851 3 + 647215 TGT - -a -s simMouse_chr6.simMouse.chr6 95844 24 + 636262 GTGTTATTATCCACATTCTTACCC -s Anc0.Anc0refChr4 36779 18 - 45765 AGGGTA------GCTTTCTTGTTC -s Anc1.Anc1refChr2 68636 18 + 144309 AGGGTA------GCTTTCTTGTTC -s Anc2.Anc2refChr2 6046 18 + 27695 AGGGGA------GCTTTCTTGTTC -s mr.mrrefChr0 90922 24 + 130230 GTGTTATTATCCACATTCTTACTC -s simCow_chr6.simCow.chr6 96149 10 + 602619 --------------TCTCTTGTTC -s simDog_chr6.simDog.chr6 101879 18 + 593897 AGGGGA------GCTTTCAGGCTC -s simHuman_chr6.simHuman.chr6 90817 18 + 601863 AAGGTA------GCTTTCTTGTCC -s simRat_chr6.simRat.chr6 87855 24 + 647215 GTGTTATTATCTACATTAATCCTC - -a -s simMouse_chr6.simMouse.chr6 95868 18 + 636262 TATACCTCTTAAAGATGG -s Anc0.Anc0refChr4 36810 18 - 45765 CATGCCTCTTACTTTTTG -s Anc1.Anc1refChr2 68667 18 + 144309 CATGCCTCTTACTTTTTG -s Anc2.Anc2refChr2 6077 18 + 27695 CATGCCTCTTACTTTTTG -s mr.mrrefChr0 90946 18 + 130230 TATGCCTCTTAAAGATTG -s simCow_chr6.simCow.chr6 96172 18 + 602619 GATGCCTCTTACTGTTTG -s simDog_chr6.simDog.chr6 101910 18 + 593897 CATGCCTCTTACTTTCTG -s simHuman_chr6.simHuman.chr6 90848 18 + 601863 AATGCCTCTTACTATTTG -s simRat_chr6.simRat.chr6 87879 18 + 647215 TATGCCTCTTAAAGATTG - -a -s simMouse_chr6.simMouse.chr6 95886 28 + 636262 CTCCTGGCCACATGACACTGGATTCATG -s Anc0.Anc0refChr4 36828 28 - 45765 CTCCTACCCACCCCTTACTGGCTTCTCA -s Anc1.Anc1refChr2 68685 28 + 144309 CTCCTACCCACCCCTTACTGGCTTCTCA -s Anc2.Anc2refChr2 6095 28 + 27695 CTCTTACCCACCCCTTACTGGCTTCTCA -s mr.mrrefChr0 90964 28 + 130230 CTCCTGGCCACATGTCACTGGATTCATG -s simCow_chr6.simCow.chr6 96191 28 + 602619 CCCTCACCCACCTCTTACCGGCCCCTCA -s simDog_chr6.simDog.chr6 101928 23 + 593897 CTCTTATCC-CCCCTTACTGGCTT---- -s simHuman_chr6.simHuman.chr6 90866 28 + 601863 CTCCTACCCACCCATTACTGGTTTTGCA -s simRat_chr6.simRat.chr6 87897 28 + 647215 CTCCTTGCCACATGTCATTGGGTTGATG - -a -s simMouse_chr6.simMouse.chr6 95914 22 + 636262 AGTCTGATAAGTTTTGGCTGTA -s Anc0.Anc0refChr4 36856 22 - 45765 AGCCTCATAAGTTTTGCCTCTA -s Anc1.Anc1refChr2 68713 22 + 144309 AGCCTCATAAGTTTTGCCTCTA -s Anc2.Anc2refChr2 6123 22 + 27695 AGTCTCATAAGTTTCACCTCTA -s mr.mrrefChr0 90992 22 + 130230 AGCCTGATAAGTTTTGGCTGTA -s simCow_chr6.simCow.chr6 96233 22 + 602619 AGTCTCGTAAATTTCACCCCTA -s simDog_chr6.simDog.chr6 101951 15 + 593897 ---CTGATGAGT----CCTCTC -s simHuman_chr6.simHuman.chr6 90894 22 + 601863 AGCCTCATAATTTTTGTCTCTA -s simRat_chr6.simRat.chr6 87925 22 + 647215 AGCGCGATGAGTTTGGGCTGCA - -a -s simMouse_chr6.simMouse.chr6 95936 46 + 636262 GGGAACATTAATAGCATTGATGTACACGGATTGGGTGTGATATAGT -s Anc0.Anc0refChr4 36878 46 - 45765 AGTACTATTGATAGTATTGATGCACATGGATTAGGCATGATATAAC -s Anc1.Anc1refChr2 68735 46 + 144309 AGTACTATTGATAGTATTGATGCACATGGATTAGGCATGATATAAC -s Anc2.Anc2refChr2 6145 46 + 27695 AGTACTATTGATACTATGGATACACATGGATTAGGCATGATAAAAC -s mr.mrrefChr0 91014 46 + 130230 GGGAACATTAATAGCATTGATGTACATGGATTAGGTGTGATATAAC -s simCow_chr6.simCow.chr6 96255 46 + 602619 AGTAATATTGATACTATCTAGACACATGGATTAGGAATGATACAAC -s simDog_chr6.simDog.chr6 101966 46 + 593897 AGGCCCATTGTTACCATGGATACACATGGTTTAGACATGATGAAAC -s simHuman_chr6.simHuman.chr6 90916 46 + 601863 AGTACTATTGATAGTATTGATGCACATGGATTAGGCATGATATAAC -s simRat_chr6.simRat.chr6 87949 46 + 647215 GGGAGCATTAATAGCATTGATGTACATGGATTAGGTGTGATATAAC - -a -s simMouse_chr6.simMouse.chr6 95982 32 + 636262 CTGAGGAATAATAATGCATCTCAAGTGATGAT -s Anc0.Anc0refChr4 36924 32 - 45765 CTAAGTAATAATAATGCATCTCTAGTGATAAT -s Anc1.Anc1refChr2 68781 32 + 144309 CTAAGTAATAATAATGCATCTCTAGTGATAAT -s Anc2.Anc2refChr2 6191 32 + 27695 CCCAATAATAATAATGCATCTCTAGAAATAAT -s mr.mrrefChr0 91060 32 + 130230 CTAAGGAATAATAATGCATCTCAAGTGATGAT -s simCow_chr6.simCow.chr6 96310 30 + 602619 CCCCATAGTAATAATG--TCTCTGGTGATGAT -s simDog_chr6.simDog.chr6 102012 32 + 593897 CCCAATAATAACAACACATCTCTACAAATAAT -s simHuman_chr6.simHuman.chr6 90962 32 + 601863 CTAAGTAGTAATAATGCATTGATAGTGATAAT -s simRat_chr6.simRat.chr6 87995 32 + 647215 CTAAGGAATAACAATGCATCTCAAGTGATGAT - -a -s simMouse_chr6.simMouse.chr6 96014 6 + 636262 ATATTC -s Anc0.Anc0refChr4 36956 6 - 45765 ATATTC -s Anc1.Anc1refChr2 68813 6 + 144309 ATATTC -s Anc2.Anc2refChr2 6223 6 + 27695 GCATTC -s mr.mrrefChr0 91092 6 + 130230 ATATTC -s simCow_chr6.simCow.chr6 96340 6 + 602619 GCATTC -s simDog_chr6.simDog.chr6 102044 6 + 593897 GCATTC -s simHuman_chr6.simHuman.chr6 91052 6 + 601863 ATGCTC -s simRat_chr6.simRat.chr6 88027 6 + 647215 ACATTC - -a -s simMouse_chr6.simMouse.chr6 96020 19 + 636262 ATCACCTTTGTTTAAGATA -s Anc0.Anc0refChr4 36962 16 - 45765 A---CTTTTGTTTAGGATA -s Anc1.Anc1refChr2 68819 19 + 144309 ATCACTTTTGTTTAGGATA -s Anc2.Anc2refChr2 6229 16 + 27695 A---CTTTTATTTAGGATA -s mr.mrrefChr0 91098 19 + 130230 ATCACCTTTGTTTAGGATA -s simCow_chr6.simCow.chr6 96349 16 + 602619 A---CTTTTATTCAGGATA -s simDog_chr6.simDog.chr6 102050 16 + 593897 A---CTCTTATTTAGGATA -s simHuman_chr6.simHuman.chr6 91058 19 + 601863 ATCACTTCTGTTTAGGGTA -s simRat_chr6.simRat.chr6 88033 19 + 647215 ATCACCTTTGTTTAGGATA - -a -s simMouse_chr6.simMouse.chr6 96039 10 + 636262 AAGAGCTGCA -s Anc0.Anc0refChr4 36986 10 - 45765 AAGAACTACA -s Anc1.Anc1refChr2 68846 10 + 144309 AAGAACTACA -s Anc2.Anc2refChr2 6253 10 + 27695 AAGAACTACG -s mr.mrrefChr0 91117 10 + 130230 AAGAGCTGCA -s simCow_chr6.simCow.chr6 96369 10 + 602619 AAGGACTATG -s simDog_chr6.simDog.chr6 102074 10 + 593897 TAGAAGTACG -s simHuman_chr6.simHuman.chr6 91086 10 + 601863 AAGAACTACA -s simRat_chr6.simRat.chr6 88052 10 + 647215 TAGAGCTGTA - -a -s simMouse_chr6.simMouse.chr6 96049 57 + 636262 AACTGAAAAATGACATATGACTTGTTAATGTTGTTTGGCTGGCTGTGGAACCCAGCA -s Anc0.Anc0refChr4 37000 37 - 45765 AACTG-TCAA-------------------GCAGTTTGGGTGGCTCTGAGACCCAGGA -s Anc1.Anc1refChr2 68860 56 + 144309 AACTG-TCAATAACATATGAACTGTCATTGCAGTTTGGGTGGCTCTGAGACCCAGGA -s Anc2.Anc2refChr2 6267 37 + 27695 AACTG-TCAG-------------------GCATTTTGTGTGGCCCTGAGACCCAGGA -s mr.mrrefChr0 91127 57 + 130230 AACTGAAAAATGACATATGAACTGTTAATGTTGTTTGGCTGGCTGTGGGACCCAGCA -s simCow_chr6.simCow.chr6 96383 37 + 602619 AAGTG-TCAG-------------------GCATTTAGCATGGCCCTGAGACCCAGGA -s simDog_chr6.simDog.chr6 102088 37 + 593897 ACCTG-TCAG-------------------GCATTTTGTGTTGCCTTGAGACTCAGGA -s simHuman_chr6.simHuman.chr6 91100 56 + 601863 AACTG-TCAATAACATATGAACTGTCATTGCAGTTTGGGTGGCTCTGAGATCCAGGA -s simRat_chr6.simRat.chr6 88062 57 + 647215 AACTGAAAAACTGCATATGAACTGTTAATGTTGTTTGGCTGGCTGTGGGACCCAGAA - -a -s simMouse_chr6.simMouse.chr6 96106 28 + 636262 CTTTTTATGGATCTTGACCAATCACAGC -s Anc0.Anc0refChr4 37037 28 - 45765 CTTTTTTTAGCTTTTTACCAATTTTAAC -s Anc1.Anc1refChr2 68916 28 + 144309 CTTTTTTTAGCTTTTTACCAATTTTAAC -s Anc2.Anc2refChr2 6305 28 + 27695 CCCTTTTTAGCTTTTTATCAATTTTAAC -s mr.mrrefChr0 91184 28 + 130230 CTTTTTATGGATCTTGACCAATCACAGC -s simCow_chr6.simCow.chr6 96421 28 + 602619 CCCTTTTTAGCTCTTTAGCAATTTCAAC -s simDog_chr6.simDog.chr6 102126 28 + 593897 CCCGTTTTAGCTTTTTATCAATTTTAAC -s simHuman_chr6.simHuman.chr6 91156 22 + 601863 CTTTTTTTCGCTTTTCACTGAT------ -s simRat_chr6.simRat.chr6 88119 28 + 647215 CTTTTTATGGATCTTGACCTATCACAGC - -a -s simMouse_chr6.simMouse.chr6 96134 9 + 636262 TCTGCATGC -s Anc0.Anc0refChr4 37065 9 - 45765 TTTGCAAAC -s Anc1.Anc1refChr2 68944 9 + 144309 TTTGCAAAC -s Anc2.Anc2refChr2 6333 9 + 27695 TCTGCAAAT -s mr.mrrefChr0 91212 9 + 130230 TTTGCATGC -s simCow_chr6.simCow.chr6 96468 9 + 602619 TGTGCAGAT -s simDog_chr6.simDog.chr6 102154 9 + 593897 TCTGTAAAT -s simHuman_chr6.simHuman.chr6 91178 9 + 601863 TTTGCAAAC -s simRat_chr6.simRat.chr6 88147 9 + 647215 TTTGCATGC - -a -s simMouse_chr6.simMouse.chr6 96143 7 + 636262 AAATACA -s Anc0.Anc0refChr4 37076 7 - 45765 AAATGCA -s Anc1.Anc1refChr2 68955 7 + 144309 AAATGCA -s Anc2.Anc2refChr2 6344 7 + 27695 TGGTGCA -s mr.mrrefChr0 91222 7 + 130230 AAATACA -s simCow_chr6.simCow.chr6 96479 7 + 602619 TGGTGCA -s simDog_chr6.simDog.chr6 102165 7 + 593897 TGGTGCA -s simHuman_chr6.simHuman.chr6 91189 7 + 601863 AAATGCA -s simRat_chr6.simRat.chr6 88157 7 + 647215 AAATACA - -a -s simMouse_chr6.simMouse.chr6 96150 15 + 636262 ACTGCCATCTACATA -s Anc0.Anc0refChr4 37083 15 - 45765 ATGGTCATCTACACA -s Anc1.Anc1refChr2 68962 15 + 144309 ATGGTCATCTACACA -s Anc2.Anc2refChr2 6351 15 + 27695 ATGGTCATCTACACC -s mr.mrrefChr0 91229 15 + 130230 ACTGCCATCTACATA -s simCow_chr6.simCow.chr6 96486 15 + 602619 ATAGTTGTTTACACC -s simDog_chr6.simDog.chr6 102173 15 + 593897 ATGTTCATCTACATC -s simHuman_chr6.simHuman.chr6 91196 15 + 601863 TTGGTCATCTACACA -s simRat_chr6.simRat.chr6 88164 15 + 647215 ACTGCCTTCTACATT - -a -s simMouse_chr6.simMouse.chr6 96165 1 + 636262 C -s Anc0.Anc0refChr4 37098 1 - 45765 C -s Anc1.Anc1refChr2 68977 1 + 144309 C -s Anc2.Anc2refChr2 6366 1 + 27695 C -s mr.mrrefChr0 91244 1 + 130230 C -s simCow_chr6.simCow.chr6 96501 1 + 602619 C -s simDog_chr6.simDog.chr6 102188 1 + 593897 A -s simHuman_chr6.simHuman.chr6 91220 1 + 601863 C -s simRat_chr6.simRat.chr6 88179 1 + 647215 C - -a -s simMouse_chr6.simMouse.chr6 96166 40 + 636262 TTCATGTCAAATATACAATTGATGGATTGAGCACTGTCAT -s Anc0.Anc0refChr4 37099 36 - 45765 TACATGTTAAGTTCTCAATTGGTGGAT----AACTGTGAT -s Anc1.Anc1refChr2 68978 36 + 144309 TACATGTTAAGTTCTCAATTGGTGGAT----AACTGTGAT -s Anc2.Anc2refChr2 6368 36 + 27695 TACATGTTAAGTTCTCAATTGGTGGAT----AACTGTGAT -s mr.mrrefChr0 91245 40 + 130230 TTCATGTCAAATACACAATTGATGGATTGAGCACTGTCAT -s simCow_chr6.simCow.chr6 96503 36 + 602619 TACATGTTTAGTTCTCAATTGGTGGAC----AACTGTGAT -s simDog_chr6.simDog.chr6 102190 36 + 593897 CACGTGTTAATTTCTTGATTCGTGGAT----AACCGTGAT -s simHuman_chr6.simHuman.chr6 91221 36 + 601863 TACATGTTAAGTTCTCAATTGGTGGAT----AACTATGAT -s simRat_chr6.simRat.chr6 88180 40 + 647215 TGCATATCAATTACATGATTAATGGATTGAGCACTGTCAT - -a -s simMouse_chr6.simMouse.chr6 96206 15 + 636262 GTATACGTAAGTTGT -s Anc0.Anc0refChr4 37136 4 - 45765 GCAT----------- -s Anc1.Anc1refChr2 69015 11 + 144309 GCATAT----GCTGT -s Anc2.Anc2refChr2 6405 4 + 27695 CCAC----------- -s mr.mrrefChr0 91285 11 + 130230 GTATAT----GTTGT -s simDog_chr6.simDog.chr6 102227 4 + 593897 CCAC----------- -s simHuman_chr6.simHuman.chr6 91258 11 + 601863 GCATAT----GCTGT -s simRat_chr6.simRat.chr6 88220 11 + 647215 GTTTAT----GTTGT - -a -s simMouse_chr6.simMouse.chr6 96221 1 + 636262 G -s Anc0.Anc0refChr4 37284 1 - 45765 G -s Anc1.Anc1refChr2 69170 1 + 144309 G -s Anc2.Anc2refChr2 6553 1 + 27695 G -s mr.mrrefChr0 91296 1 + 130230 G -s simCow_chr6.simCow.chr6 96691 1 + 602619 G -s simDog_chr6.simDog.chr6 102375 1 + 593897 G -s simHuman_chr6.simHuman.chr6 91414 1 + 601863 G -s simRat_chr6.simRat.chr6 88231 1 + 647215 G - -a -s simMouse_chr6.simMouse.chr6 96222 4 + 636262 GTGG -s Anc0.Anc0refChr4 37285 4 - 45765 ATGG -s Anc1.Anc1refChr2 69171 4 + 144309 ATGG -s Anc2.Anc2refChr2 6554 4 + 27695 ATGG -s mr.mrrefChr0 91297 4 + 130230 ATGG -s simCow_chr6.simCow.chr6 96697 4 + 602619 ATGG -s simDog_chr6.simDog.chr6 102376 4 + 593897 CTGT -s simHuman_chr6.simHuman.chr6 91415 4 + 601863 ATGG -s simRat_chr6.simRat.chr6 88232 4 + 647215 ATGG - -a -s simMouse_chr6.simMouse.chr6 96226 13 + 636262 TTGTGTCTTCAAT -s Anc0.Anc0refChr4 37290 13 - 45765 TTGTGCCTTCAAT -s Anc1.Anc1refChr2 69176 13 + 144309 TTGTGCCTTCAAT -s Anc2.Anc2refChr2 6559 13 + 27695 TTGTGCCTTGAAC -s mr.mrrefChr0 91301 13 + 130230 TTGTGTCTTCAAT -s simCow_chr6.simCow.chr6 96702 13 + 602619 TTGCCCCTTGAGG -s simDog_chr6.simDog.chr6 102381 13 + 593897 TTTTGCCTTGAAC -s simHuman_chr6.simHuman.chr6 91420 13 + 601863 TTGTGCCTTCAAT -s simRat_chr6.simRat.chr6 88236 13 + 647215 TTGTGTCTTCAAT - -a -s simMouse_chr6.simMouse.chr6 96239 4 + 636262 CTGC -s Anc0.Anc0refChr4 37306 4 - 45765 CCAC -s Anc1.Anc1refChr2 69192 4 + 144309 CCAC -s Anc2.Anc2refChr2 6575 4 + 27695 CCAC -s mr.mrrefChr0 91315 4 + 130230 CTGC -s simCow_chr6.simCow.chr6 96718 4 + 602619 CCAC -s simDog_chr6.simDog.chr6 102397 4 + 593897 CCAC -s simHuman_chr6.simHuman.chr6 91436 4 + 601863 CCAC -s simRat_chr6.simRat.chr6 88250 4 + 647215 CTGT - -a -s simMouse_chr6.simMouse.chr6 96243 35 + 636262 TAATTGTTCTGTATTAAGCCATTAGCCTTGAAGCC -s Anc0.Anc0refChr4 37310 20 - 45765 TAA--------------ACCATAATGCCTGATG-C -s Anc1.Anc1refChr2 69196 34 + 144309 TAATTATCCTGTATTGGACCATAATGCCTGATG-C -s Anc2.Anc2refChr2 6579 20 + 27695 TAA--------------ACCATAATGCCTGATG-C -s mr.mrrefChr0 91319 34 + 130230 TAATTGTTCTGTATTAAGCCATTAGCCTTGAAG-C -s simCow_chr6.simCow.chr6 96736 20 + 602619 TGA--------------ATCATCAAGCCTCAAG-C -s simDog_chr6.simDog.chr6 102401 20 + 593897 TAA--------------ACCATAATGCCTGATG-C -s simHuman_chr6.simHuman.chr6 91440 19 + 601863 TAATTATCCTGTATTGGAC---------------- -s simRat_chr6.simRat.chr6 88254 34 + 647215 TACTTGTTCTGTATTAAGCCATGAGCCTTGAGG-C - -a -s simMouse_chr6.simMouse.chr6 96278 10 + 636262 ATATTTATGC -s Anc0.Anc0refChr4 37330 10 - 45765 ATGCTTGTGA -s Anc1.Anc1refChr2 69230 10 + 144309 ATGCTTGTGA -s Anc2.Anc2refChr2 6600 10 + 27695 ATGCTTGTGA -s mr.mrrefChr0 91353 10 + 130230 ATATTTATGC -s simCow_chr6.simCow.chr6 96757 10 + 602619 CCACTTGTGA -s simDog_chr6.simDog.chr6 102422 10 + 593897 ATGCTTGTGA -s simRat_chr6.simRat.chr6 88288 10 + 647215 ATATTTATGA - -a -s simMouse_chr6.simMouse.chr6 96288 15 + 636262 CTAATGGGGTACTGA -s Anc0.Anc0refChr4 37340 15 - 45765 CTCATGGGGTATTGA -s Anc1.Anc1refChr2 69240 15 + 144309 CTCATGGGGTATTGA -s Anc2.Anc2refChr2 6613 15 + 27695 CTCATGGGATATTGA -s mr.mrrefChr0 91363 15 + 130230 CTAATGGGGTACTGA -s simCow_chr6.simCow.chr6 96770 15 + 602619 CTCATAGGATATTAA -s simDog_chr6.simDog.chr6 102435 15 + 593897 CTCATGGGATAATGA -s simHuman_chr6.simHuman.chr6 91459 12 + 601863 ---ATGGTGTGTTGA -s simRat_chr6.simRat.chr6 88301 15 + 647215 CTAATGGGGTACTGA - -a -s simMouse_chr6.simMouse.chr6 96303 11 + 636262 CCTCTGATCCT -s Anc0.Anc0refChr4 37357 11 - 45765 CCTCTGGTTTC -s Anc1.Anc1refChr2 69257 11 + 144309 CCTCTGGTTTC -s Anc2.Anc2refChr2 6630 11 + 27695 CCTCTGGTTTC -s mr.mrrefChr0 91378 11 + 130230 CCTCTGATCCT -s simCow_chr6.simCow.chr6 96790 11 + 602619 CCTCCAGTTTC -s simDog_chr6.simDog.chr6 102452 11 + 593897 ACTGTGGGTTC -s simHuman_chr6.simHuman.chr6 91473 11 + 601863 CCTCTGGTTTC -s simRat_chr6.simRat.chr6 88316 11 + 647215 CCTCTGATCCT - -a -s simMouse_chr6.simMouse.chr6 96314 32 + 636262 TAACATCTACAGAAGGGCTGCTTGCCCCTGGC -s Anc0.Anc0refChr4 37368 32 - 45765 TAAAATCTACAGGAGGGCTGCCTGCCTCTGGC -s Anc1.Anc1refChr2 69268 32 + 144309 TAAAATCTACAGGAGGGCTGCCTGCCTCTGGC -s Anc2.Anc2refChr2 6641 32 + 27695 TGAAATCTACAGGAGGGCTGCCTGCCTCTGGC -s mr.mrrefChr0 91389 32 + 130230 TAACATCTACAGAAGGGCTGCTTGCCTCTGGC -s simCow_chr6.simCow.chr6 96801 32 + 602619 TGAACTCTACAGGAGGGCTGCTTGCCTTTGGC -s simDog_chr6.simDog.chr6 102463 32 + 593897 TGAAAACTACAGAGCTACTGCCTGCCTCTGGC -s simHuman_chr6.simHuman.chr6 91484 32 + 601863 CAAAATCTACAGGAGGGCTCCCTGCCTCTGAA -s simRat_chr6.simRat.chr6 88408 28 + 647215 TTACGTCTACA----GGCTGCTTGCCTCTGGC - -a -s simMouse_chr6.simMouse.chr6 96346 6 + 636262 TCATAG -s Anc0.Anc0refChr4 37400 6 - 45765 TCATAG -s Anc1.Anc1refChr2 69300 6 + 144309 TCATAG -s Anc2.Anc2refChr2 6673 6 + 27695 TCATAG -s mr.mrrefChr0 91421 6 + 130230 TCATAG -s simCow_chr6.simCow.chr6 96833 6 + 602619 TCATGG -s simDog_chr6.simDog.chr6 102495 6 + 593897 TCAGAG -s simHuman_chr6.simHuman.chr6 91516 6 + 601863 TCATAG -s simRat_chr6.simRat.chr6 88441 6 + 647215 TCATAG - -a -s simMouse_chr6.simMouse.chr6 96352 132 + 636262 GATGGTGCTGTTACATTTCTCACCCATGGTTCCTAGCTTTTTTGTGATGTTGTTGTGCTGGCAGTATACACCATGGTGCAGAATACAGCATGTTTCAACCAGTCTAGCTAAAACTGTCAGTGGGTAAGCACA -s Anc0.Anc0refChr4 37409 41 - 45765 GGTGGTGCTGGTGCACTTATTTTC--------CTAGGTTCTTT---------CTATCA-------------------------------------------------------------------------- -s Anc1.Anc1refChr2 69309 49 + 144309 GGTGGTGCTGGTGCACTTATTTTCTTAGCTTCCTAGGTTCTTT---------CTATCA-------------------------------------------------------------------------- -s Anc2.Anc2refChr2 6686 41 + 27695 GGTGGTGCTGGTGCACTTATTTTC--------CTAGGTTCTTC---------CCATCA-------------------------------------------------------------------------- -s mr.mrrefChr0 91427 132 + 130230 GATGGTGCTGTTACACTTCTCATCCATGGTTCCTAGCTTTTTTGTGATGTTGCTGTGCTTGCAGTATACACCATGGTGCAGTATACACCATGTTTCAACTGGTCTAGCTAAAATTGTCAGTGGGTAAGCACA -s simCow_chr6.simCow.chr6 96846 41 + 602619 GGTGGTGCTGATCCATTTTGGTTC--------CTAGGTTCTTC---------CCATCA-------------------------------------------------------------------------- -s simDog_chr6.simDog.chr6 102508 24 + 593897 GGTGGTACTGGTGAACTTATTTCC------------------------------------------------------------------------------------------------------------ -s simHuman_chr6.simHuman.chr6 91525 49 + 601863 GTTGGTGCTAGTGCACTTATTGTCTTAGCTTCCTAGGTTCTTT---------CTATCA-------------------------------------------------------------------------- -s simRat_chr6.simRat.chr6 88447 132 + 647215 GATGGTGCAGTTACACTTTTCATCCCTGGTTCCTAGCTTTTTTGTGGTGTTGCTGTGCTTGCAATATACACCATGGTGCAGTATACACCATGGTTCAGCTGGTCTAGCTAAAATTGTAAGCTGGTAAGCACA - -a -s simMouse_chr6.simMouse.chr6 96484 7 + 636262 ACTACAA -s mr.mrrefChr0 91559 7 + 130230 AATACAA -s simRat_chr6.simRat.chr6 88582 7 + 647215 AATACAA - -a -s simMouse_chr6.simMouse.chr6 96491 4 + 636262 TATA -s mr.mrrefChr0 91566 4 + 130230 TATA -s simRat_chr6.simRat.chr6 88596 4 + 647215 TATA - -a -s simMouse_chr6.simMouse.chr6 96495 57 + 636262 ACTAATGAAAACTGATAAAGATGTTGGAGCTCAGATAATTGTATTTCGTCTGGATCA -s mr.mrrefChr0 91571 57 + 130230 ACTAATGAAAACTGATAAAGATGTTGGAGCTCAGATAATTGTATTTCGTCTGGATCA -s simRat_chr6.simRat.chr6 88601 57 + 647215 GTTAATGAAAACCGATAAGGACGTGGCAACCCAGATAATCGCATTACGCCTGGAACA - -a -s simMouse_chr6.simMouse.chr6 96552 7 + 636262 TACACAG -s mr.mrrefChr0 91628 7 + 130230 TACACAG -s simRat_chr6.simRat.chr6 88662 7 + 647215 TATGCAA - -a -s simMouse_chr6.simMouse.chr6 96559 102 + 636262 ATACTGTGGGGGCCATGTAATTGCAGTTACAGTGAGGGACTAGCTTAACTCATACACCAGGATATGGGTGCACCAGGATATGGAGGGATATGCAAGATACTG -s mr.mrrefChr0 91635 102 + 130230 ATACTGTGGGGGCCATGTAATTGCAGTTACAGTGAGGGACTAGCTTAACTCATACACCAGGATATGGGTGCACCAGGATATGGAGGGATATGCAAGATACTG -s simRat_chr6.simRat.chr6 88670 102 + 647215 ATACTATAGGAGTCATGCAATTGCAATCACAGTGAGGGACTGGCTTAACTTGTGCACCTGGATATGGGTGCACCAGGATATGTAGGGGTATGGGAGATACTG - -a -s simMouse_chr6.simMouse.chr6 96661 22 + 636262 ATTGCAACAACATTAAGATTGC -s Anc0.Anc0refChr4 37450 19 - 45765 -TTGCAAAAACATT--GCATGA -s Anc1.Anc1refChr2 69358 19 + 144309 -TTGCAAAAACATT--GCATGA -s Anc2.Anc2refChr2 6727 19 + 27695 -TTAAAAAAACATT--GCATAA -s mr.mrrefChr0 91737 22 + 130230 ATTGCAACAACATTAAGATTGC -s simCow_chr6.simCow.chr6 96887 19 + 602619 -TTAAAAAAACATT--GCATCA -s simDog_chr6.simDog.chr6 102532 10 + 593897 ----------CAAT--GCATAA -s simHuman_chr6.simHuman.chr6 91574 19 + 601863 -TTGCAAAAACATT--GTATGA -s simRat_chr6.simRat.chr6 88777 22 + 647215 ATTGCAAAAACATTAAGATTGC - -a -s simMouse_chr6.simMouse.chr6 96683 12 + 636262 ATCAAACATTAA -s Anc0.Anc0refChr4 37469 12 - 45765 ACCAATTATTCA -s Anc1.Anc1refChr2 69377 12 + 144309 ACCAATTATTCA -s Anc2.Anc2refChr2 6746 12 + 27695 ACCAATTATTCA -s mr.mrrefChr0 91759 12 + 130230 ATCAAACATTAA -s simCow_chr6.simCow.chr6 96906 12 + 602619 GCCAATTGTACA -s simDog_chr6.simDog.chr6 102546 12 + 593897 ACCAATTACTCA -s simHuman_chr6.simHuman.chr6 91593 12 + 601863 ACCAAGTATTCA -s simRat_chr6.simRat.chr6 88799 12 + 647215 AACAAACATTAA - -a -s simMouse_chr6.simMouse.chr6 96695 42 + 636262 TTTATTGGCCTTAAAAATTGATTTCCCCACTCCTAAGGTTGT -s Anc0.Anc0refChr4 37481 31 - 45765 --------CCAT---GACTGGTTTCCTTGCTACTAAGGTTGC -s Anc1.Anc1refChr2 69389 42 + 144309 ATTATTGTCCATATTGACTGGTTTCCTTGCTACTAAGGTTGC -s Anc2.Anc2refChr2 6758 31 + 27695 --------CCAT---GACTGGTTTCCTTGCTACTAAGGTTAC -s mr.mrrefChr0 91771 42 + 130230 TTTATTGGCCTTAAAAATTGATTTCCCCACTCCTAAGGTTGT -s simCow_chr6.simCow.chr6 96918 30 + 602619 --------TAAT----ACTGGTCTCCTAACAAGTAAGGTTAC -s simDog_chr6.simDog.chr6 102558 27 + 593897 --------CCAT---GATGTTTTTCCTTGCTACTAAGG---- -s simHuman_chr6.simHuman.chr6 91605 42 + 601863 ATTATTGTCCATATTTACTGGTTTCCTTGTTATTAAGGTTGC -s simRat_chr6.simRat.chr6 88812 42 + 647215 TTTATTGGCCATAAAAATTGAGTTCACTGCTCCTAAGGTTAT - -a -s simMouse_chr6.simMouse.chr6 96737 25 + 636262 TGACAAATTTGTAAGAAACACCAGG -s Anc0.Anc0refChr4 37514 24 - 45765 TGGCAAAATT-TAATACAACATAGA -s Anc1.Anc1refChr2 69433 25 + 144309 TGGCAAAATTGTAATACAACATAGA -s Anc2.Anc2refChr2 6791 24 + 27695 AGGCAGAATT-TAATGCAACATAGA -s mr.mrrefChr0 91813 25 + 130230 TGACAAATTTGTAAGAAACACCAGG -s simCow_chr6.simCow.chr6 96950 24 + 602619 AGGCAGAATT-TAATGCAACATAGA -s simHuman_chr6.simHuman.chr6 91649 25 + 601863 TAGCAAAATCGGAACACAACATAGA -s simRat_chr6.simRat.chr6 88856 25 + 647215 TGACAAAATTGTAGGAAGCACAAGG - -a -s simMouse_chr6.simMouse.chr6 96762 1 + 636262 T -s Anc0.Anc0refChr4 37538 1 - 45765 T -s Anc1.Anc1refChr2 69458 1 + 144309 T -s Anc2.Anc2refChr2 6815 1 + 27695 T -s mr.mrrefChr0 91838 1 + 130230 T -s simCow_chr6.simCow.chr6 96974 1 + 602619 T -s simHuman_chr6.simHuman.chr6 91681 1 + 601863 T -s simRat_chr6.simRat.chr6 88881 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 96763 100 + 636262 GAGCAGGTTCATATGATTTCAATCCAATTCGCAGATCCTACTTTGTGTCATTTAGTCCTGCTATATACATAATCCTGGCTTAGCTAAATGACCTTTCTGC -s Anc0.Anc0refChr4 37539 86 - 45765 GAGCAGGTTCAAACGATTCT--------------CTTCTATTTAACATCATTTTGTACTGCTATATGCATAATTCTTACCTAACCCTATGACATTTATGC -s Anc1.Anc1refChr2 69459 86 + 144309 GAGCAGGTTCAAACGATTCT--------------CTTCTATTTAACATCATTTTGTACTGCTATATGCATAATTCTTACCTAACCCTATGACATTTATGC -s Anc2.Anc2refChr2 6817 86 + 27695 GTGCAGGTCCAAACGACTCT--------------CTTCTATTTAACATCATTTTGTACTGCTATATGTGTAATTCTTACCTAACCCTATGACATTTATGT -s mr.mrrefChr0 91839 100 + 130230 GAGCAGGTTCATATGATTTCAATCCAATTCGCAGATCCTACTTTGCATCATTTAGTACTGCTATATGCATAATCCTGGCTTAGCCCAATGACCTTTCTGC -s simCow_chr6.simCow.chr6 96976 86 + 602619 GTGCAGGTCCAAACAACTCC--------------CTTCTACTTTACATCATTTTGTCTGGCTATATGTGTCATTCTTACCTAACCCTATGATATTTATGT -s simDog_chr6.simDog.chr6 102585 77 + 593897 ---------CAAATGACTCT--------------CTTCTATTTAACATCATTCTGTACTGCTGTATGTGCAATTTTGACTCGGCCCTCTGACATTTATGT -s simHuman_chr6.simHuman.chr6 91682 86 + 601863 GAGCAGGTTCAAACGATTCT--------------CTTCTATTTAACATCATTTTGTACTGCTATGTACATGATTCTTACCTAACCTTATGACATTTATGC -s simRat_chr6.simRat.chr6 88882 100 + 647215 GAACAGGTTCATATGATTCAATCCTATTTTGCAAATCTTACTTTGCATCATTTAGTACTGCTATATGCATAGTCCTGGCTTAGCCCAATGACCTTTCTGC - -a -s simMouse_chr6.simMouse.chr6 96863 20 + 636262 TGGAAGCCACTTCCCACGAT -s Anc0.Anc0refChr4 37625 20 - 45765 AGAAAGCCATTTACAGTGAT -s Anc1.Anc1refChr2 69545 20 + 144309 AGAAAGCCATTTACAGTGAT -s Anc2.Anc2refChr2 6903 20 + 27695 AAAAAGCCATTTACAGTGAT -s mr.mrrefChr0 91939 20 + 130230 TGAAAGCCACTTCCCACGAT -s simCow_chr6.simCow.chr6 97062 20 + 602619 AGAAAACCATTTATGGATGT -s simDog_chr6.simDog.chr6 102662 20 + 593897 GAAAAGCCATTTGCAGTGAT -s simHuman_chr6.simHuman.chr6 91769 20 + 601863 AGAAAGCCATTTACAGTGAT -s simRat_chr6.simRat.chr6 88982 20 + 647215 TGAAAGCCACTTCCCACAAT - -a -s simMouse_chr6.simMouse.chr6 96883 6 + 636262 TAAAGG -s Anc0.Anc0refChr4 38331 6 - 45765 TATGGG -s Anc1.Anc1refChr2 70251 6 + 144309 TATGGG -s Anc2.Anc2refChr2 7616 6 + 27695 TATGGG -s mr.mrrefChr0 91959 6 + 130230 TATAGG -s simCow_chr6.simCow.chr6 97537 6 + 602619 TATGGG -s simDog_chr6.simDog.chr6 103470 6 + 593897 TATGGG -s simHuman_chr6.simHuman.chr6 92826 6 + 601863 TATGGG -s simRat_chr6.simRat.chr6 89002 6 + 647215 TATCGG - -a -s simMouse_chr6.simMouse.chr6 96889 18 + 636262 GACACTCAGCCCTCCCAT -s Anc0.Anc0refChr4 38344 10 - 45765 AATGTTCAG--------T -s Anc1.Anc1refChr2 70264 18 + 144309 AATGTTCAGATGTTTAAT -s Anc2.Anc2refChr2 7629 10 + 27695 AATGTTTAG--------T -s mr.mrrefChr0 91972 18 + 130230 GACACTCAGATCTCCCAT -s simCow_chr6.simCow.chr6 97550 9 + 602619 AATTTTT-G--------T -s simDog_chr6.simDog.chr6 103483 10 + 593897 AATGTTTAG--------T -s simHuman_chr6.simHuman.chr6 92839 18 + 601863 AATGTTCAAATGTTTAAT -s simRat_chr6.simRat.chr6 89015 18 + 647215 GACACTCAGATGTCCCAT - -a -s simMouse_chr6.simMouse.chr6 96907 9 + 636262 CCTCTTTTG -s Anc0.Anc0refChr4 38354 9 - 45765 CCTTGATCA -s Anc1.Anc1refChr2 70282 9 + 144309 CCTTGATCA -s Anc2.Anc2refChr2 7639 9 + 27695 TCTTGATCA -s mr.mrrefChr0 91990 9 + 130230 CCTCTTTTG -s simCow_chr6.simCow.chr6 97559 9 + 602619 TTTAGATCA -s simDog_chr6.simDog.chr6 103493 9 + 593897 TCTTTATCA -s simHuman_chr6.simHuman.chr6 92857 9 + 601863 CCTTGATCA -s simRat_chr6.simRat.chr6 89034 9 + 647215 CCTCTTTTG - -a -s simMouse_chr6.simMouse.chr6 96916 5 + 636262 GCTAG -s Anc0.Anc0refChr4 38364 5 - 45765 GCTAG -s Anc1.Anc1refChr2 70292 5 + 144309 GCTAG -s Anc2.Anc2refChr2 7649 5 + 27695 GCCAG -s mr.mrrefChr0 91999 5 + 130230 GCTAG -s simCow_chr6.simCow.chr6 97569 5 + 602619 GCCAG -s simDog_chr6.simDog.chr6 103503 5 + 593897 GCCAG -s simHuman_chr6.simHuman.chr6 92867 5 + 601863 GCTGG -s simRat_chr6.simRat.chr6 89043 5 + 647215 ACTAG - -a -s simMouse_chr6.simMouse.chr6 96921 8 + 636262 TCAGGTCA -s Anc0.Anc0refChr4 38371 8 - 45765 TCAGGTAA -s Anc1.Anc1refChr2 70299 8 + 144309 TCAGGTAA -s Anc2.Anc2refChr2 7656 8 + 27695 GCACATAC -s mr.mrrefChr0 92004 8 + 130230 TCAGGTCA -s simCow_chr6.simCow.chr6 97575 7 + 602619 -CACATGC -s simDog_chr6.simDog.chr6 103510 8 + 593897 GCACATAC -s simHuman_chr6.simHuman.chr6 92874 8 + 601863 TCAGGTAA -s simRat_chr6.simRat.chr6 89048 8 + 647215 CCAGGTCA - -a -s simMouse_chr6.simMouse.chr6 96929 6 + 636262 CACCCT -s Anc0.Anc0refChr4 38645 6 - 45765 CATCCT -s Anc1.Anc1refChr2 70573 6 + 144309 CATCCT -s Anc2.Anc2refChr2 7955 6 + 27695 GATCCT -s mr.mrrefChr0 92012 6 + 130230 CACCCT -s simCow_chr6.simCow.chr6 97893 6 + 602619 AATCCT -s simDog_chr6.simDog.chr6 103800 6 + 593897 GATCCT -s simHuman_chr6.simHuman.chr6 93299 6 + 601863 CATCCT -s simRat_chr6.simRat.chr6 89056 6 + 647215 CAGCCT - -a -s simMouse_chr6.simMouse.chr6 96935 36 + 636262 TTAAATTGTTTAATGATGTCTACACATTTCTAGTCT -s Anc0.Anc0refChr4 38651 23 - 45765 TT-------------CATTCTACACCTATTTAGTCT -s Anc1.Anc1refChr2 70579 36 + 144309 TTAACCCACTTTATGCATTCTACACCTATTTAGTCT -s Anc2.Anc2refChr2 7961 23 + 27695 TT-------------CATTCTACACCTAGTTGGTCT -s mr.mrrefChr0 92018 36 + 130230 TTAAATTGTTTAATGATGTCTACACATTTCTAGTCT -s simCow_chr6.simCow.chr6 97899 23 + 602619 TT-------------CATTCTACACCTGATTGGTCT -s simDog_chr6.simDog.chr6 103806 20 + 593897 TT-------------AATTCTA---TTAGATGGTCT -s simHuman_chr6.simHuman.chr6 93305 36 + 601863 TTAACCCACTTTATGCACTCTACACCTATTGAGTCT -s simRat_chr6.simRat.chr6 89067 36 + 647215 TTGAATTGTTCAATGAAGTCTACACATTTCTAGTCT - -a -s simMouse_chr6.simMouse.chr6 96971 11 + 636262 AAACATTTCTA -s Anc0.Anc0refChr4 38707 11 - 45765 AAACATTCCTA -s Anc1.Anc1refChr2 70648 11 + 144309 AAACATTCCTA -s Anc2.Anc2refChr2 8017 11 + 27695 AAACATTCCTA -s mr.mrrefChr0 92054 11 + 130230 AAACATTTCTA -s simCow_chr6.simCow.chr6 97955 10 + 602619 AAGCATT-CTA -s simDog_chr6.simDog.chr6 103859 11 + 593897 GAACATTCCCA -s simHuman_chr6.simHuman.chr6 93378 11 + 601863 AAACATTCCTA -s simRat_chr6.simRat.chr6 89103 11 + 647215 AAACAATTCGA - -a -s simMouse_chr6.simMouse.chr6 96982 6 + 636262 ATGTTC -s Anc0.Anc0refChr4 38777 6 - 45765 ATGATC -s Anc1.Anc1refChr2 70718 6 + 144309 ATGATC -s Anc2.Anc2refChr2 8087 6 + 27695 ATCATC -s mr.mrrefChr0 92065 6 + 130230 ATGTTC -s simCow_chr6.simCow.chr6 98040 6 + 602619 ATCATT -s simDog_chr6.simDog.chr6 103927 6 + 593897 ATCATC -s simHuman_chr6.simHuman.chr6 93448 6 + 601863 ATGCTC -s simRat_chr6.simRat.chr6 89114 6 + 647215 ATGTTT - -a -s simMouse_chr6.simMouse.chr6 96988 1 + 636262 A -s Anc0.Anc0refChr4 38783 1 - 45765 C -s Anc1.Anc1refChr2 70724 1 + 144309 C -s Anc2.Anc2refChr2 8106 1 + 27695 C -s mr.mrrefChr0 92071 1 + 130230 A -s simCow_chr6.simCow.chr6 98059 1 + 602619 C -s simDog_chr6.simDog.chr6 103946 1 + 593897 T -s simHuman_chr6.simHuman.chr6 93454 1 + 601863 C -s simRat_chr6.simRat.chr6 89120 1 + 647215 G - -a -s simMouse_chr6.simMouse.chr6 96989 1 + 636262 C -s Anc0.Anc0refChr4 38784 1 - 45765 C -s Anc1.Anc1refChr2 70725 1 + 144309 C -s Anc2.Anc2refChr2 8107 1 + 27695 C -s mr.mrrefChr0 92072 1 + 130230 C -s simCow_chr6.simCow.chr6 98062 1 + 602619 C -s simDog_chr6.simDog.chr6 103947 1 + 593897 C -s simHuman_chr6.simHuman.chr6 93455 1 + 601863 C -s simRat_chr6.simRat.chr6 89121 1 + 647215 C - -a -s simMouse_chr6.simMouse.chr6 96990 35 + 636262 AAAATTAACAAGAACACCTGTAAGTATAAGCCTAG -s Anc0.Anc0refChr4 38785 35 - 45765 AAATTTAGCAAGAACACCTGCTAGTACAGGCCTAG -s Anc1.Anc1refChr2 70726 35 + 144309 AAATTTAGCAAGAACACCTGCTAGTACAGGCCTAG -s Anc2.Anc2refChr2 8108 35 + 27695 AAATTTAGCAAGTACACCTGCTAGTACAGGGCTAG -s mr.mrrefChr0 92073 35 + 130230 AAATTTAACAAGAACACCTGTAAGTATAAGCCTAG -s simCow_chr6.simCow.chr6 98063 35 + 602619 AAGCTTAGCAAGTACGTTTGCTAGTAGAGGTCTAG -s simDog_chr6.simDog.chr6 103948 35 + 593897 AAATTTATCATATACACCTGCTAGTACAGGGTTAG -s simHuman_chr6.simHuman.chr6 93457 35 + 601863 GAATTTAGCGAGAACCCCAGCTAGTACAGGCCTAG -s simRat_chr6.simRat.chr6 89122 35 + 647215 AAATTTATCAAGAACACCCATAAGTATAAGCCTTG - -a -s simMouse_chr6.simMouse.chr6 97025 47 + 636262 TATTGTGTGCATGGTGTGGAATTGTGCTCTTTTATTCATGTCATAGC -s Anc0.Anc0refChr4 38822 47 - 45765 TATCTTGCACATGGTGGGGAATGCTGCTATTTTGTTGATGTCATAGC -s Anc1.Anc1refChr2 70763 47 + 144309 TATCTTGCACATGGTGGGGAATGCTGCTATTTTGTTGATGTCATAGC -s Anc2.Anc2refChr2 8145 47 + 27695 TATCTTGCACATGGTGGAGCATGCTGCTATTTTGTTGATGTTGTGGC -s mr.mrrefChr0 92108 47 + 130230 TATTGTGTGCATGGTGTGGAATTGTGCTCTTTTATTCATGTCATAGC -s simCow_chr6.simCow.chr6 98100 47 + 602619 TATTATGCACATTGTGTAGCAGGGGACTATTCTGTTCATGTAGTGAC -s simDog_chr6.simDog.chr6 103985 47 + 593897 TATCTTGCACATGGTAGAGTATGCTGCTATTTTGTTGATGTTGTGGC -s simHuman_chr6.simHuman.chr6 93494 30 + 601863 TATATTGCACATAGTGGGCA----TGC-----------TGCCATA-- -s simRat_chr6.simRat.chr6 89157 47 + 647215 TATTGTGTGCATGGTGTGGAATTGTGCTCTTTTATTTATGTCATAGC - -a -s simMouse_chr6.simMouse.chr6 97072 16 + 636262 TGACATCCCCATAAAG -s Anc0.Anc0refChr4 38869 16 - 45765 TGATATCCCCACAAAG -s Anc1.Anc1refChr2 70810 16 + 144309 TGATATCCCCACAAAG -s Anc2.Anc2refChr2 8196 16 + 27695 CAATACCTCCACAAAG -s mr.mrrefChr0 92155 16 + 130230 TGACATCCCCATAAAG -s simCow_chr6.simCow.chr6 98151 16 + 602619 CAATACCTCCACAGAG -s simDog_chr6.simDog.chr6 104036 16 + 593897 CAATACCTCCACAAAG -s simHuman_chr6.simHuman.chr6 93524 13 + 601863 TGGTGTACC---ATGG -s simRat_chr6.simRat.chr6 89204 16 + 647215 TGACATCCCCATAAAG - -a -s simMouse_chr6.simMouse.chr6 97088 11 + 636262 AATCCTCTGAT -s Anc0.Anc0refChr4 38885 11 - 45765 TGTCCTTTGAT -s Anc1.Anc1refChr2 70826 11 + 144309 TGTCCTTTGAT -s Anc2.Anc2refChr2 8213 11 + 27695 TGTCCTTTGAT -s mr.mrrefChr0 92171 11 + 130230 AATCCTCTGAT -s simCow_chr6.simCow.chr6 98168 11 + 602619 TTGCCTCTGGT -s simDog_chr6.simDog.chr6 104053 11 + 593897 TGTCCTTTGAT -s simHuman_chr6.simHuman.chr6 93537 11 + 601863 TGCCATTTTGC -s simRat_chr6.simRat.chr6 89220 11 + 647215 AATCCTCTGAT - -a -s simMouse_chr6.simMouse.chr6 97099 3 + 636262 GGA -s Anc0.Anc0refChr4 38896 3 - 45765 CAA -s Anc1.Anc1refChr2 70837 3 + 144309 CAA -s Anc2.Anc2refChr2 8224 3 + 27695 CAG -s mr.mrrefChr0 92182 3 + 130230 GGA -s simCow_chr6.simCow.chr6 98181 3 + 602619 CAG -s simDog_chr6.simDog.chr6 104064 3 + 593897 CAG -s simHuman_chr6.simHuman.chr6 93548 3 + 601863 ACA -s simRat_chr6.simRat.chr6 89231 3 + 647215 GGA - -a -s simMouse_chr6.simMouse.chr6 97102 28 + 636262 AGCCCAGTGTAAGTCTTAACTGGTACTT -s Anc0.Anc0refChr4 38899 24 - 45765 AGG----TATGACTCTTAGCTGGGGCTA -s Anc1.Anc1refChr2 70840 24 + 144309 AGG----TATGACTCTTAGCTGGGGCTA -s Anc2.Anc2refChr2 8227 24 + 27695 AGG----TATGACTCTTAGCTGGGGCTA -s mr.mrrefChr0 92185 28 + 130230 AGCCCAGTGTAAGTCTTAACTGGTACTT -s simCow_chr6.simCow.chr6 98184 24 + 602619 AGG----TGTGACTCTGAGATGGGGCTA -s simDog_chr6.simDog.chr6 104068 24 + 593897 AGG----CATCACTGTTAGCTGGGGCTA -s simHuman_chr6.simHuman.chr6 93551 24 + 601863 TGT----TATGGCTCTTAGCTAGAGCTA -s simRat_chr6.simRat.chr6 89234 22 + 647215 AGCCCAGTGTAAATCTT-ACTGG----- - -a -s simMouse_chr6.simMouse.chr6 97130 27 + 636262 GTTCATACGCTGGATAGAGAAGAGAAT -s Anc0.Anc0refChr4 38923 27 - 45765 TTTTATGGGCTGGATAGAGAGGAGAAC -s Anc1.Anc1refChr2 70864 27 + 144309 TTTTATGGGCTGGATAGAGAGGAGAAC -s Anc2.Anc2refChr2 8251 27 + 27695 TTTTATGGGCTGGATAGAGAGGTGAAC -s mr.mrrefChr0 92213 27 + 130230 GTTCATAGGCTGGATAGAGAAGAGAAC -s simCow_chr6.simCow.chr6 98210 27 + 602619 TTTTATGGACTGGATAGAGAGGGGAAC -s simDog_chr6.simDog.chr6 104092 27 + 593897 TTTTATGGGCTGGATAGGGATGTGAAC -s simHuman_chr6.simHuman.chr6 93575 27 + 601863 TTTTATGGGCTCAGTAGAAAGGAGAAC -s simRat_chr6.simRat.chr6 89256 21 + 647215 ------AGGCTGGATAGAGAAGAGAAC - -a -s simMouse_chr6.simMouse.chr6 97157 48 + 636262 CACGGTCTAAATTGGATTCCAAAGCTGTAACAAAATAGATTCCAAAAC -s Anc0.Anc0refChr4 38951 48 - 45765 CTTGAGCTGAAGTGGATTCCAAAGCAGTAATAAAATAGATTCCAAAAC -s Anc1.Anc1refChr2 70892 48 + 144309 CTTGAGCTGAAGTGGATTCCAAAGCAGTAATAAAATAGATTCCAAAAC -s Anc2.Anc2refChr2 8279 48 + 27695 CTTGAGCTAAAGTGGATTCCAAAGCAGTAATAAAATAGATTCCAAAGC -s mr.mrrefChr0 92241 48 + 130230 CATGGTCTGAATTGGATTCCAAAGCAGTAACAAAATAGATTCCAAAAC -s simCow_chr6.simCow.chr6 98238 48 + 602619 CTTAAGCTAAAGTGGATCCCAAAGCAGTAATAAACTAGATTCCAAAGT -s simDog_chr6.simDog.chr6 104120 48 + 593897 CTTGAGCTAAAGTGAAATTCACAACAGTAATAAAATAGATTCCAAAGC -s simHuman_chr6.simHuman.chr6 93603 48 + 601863 CTTGAGTTGAAGTGGATTCCAAAGCAGTAATAAAATAGATTCCTATAG -s simRat_chr6.simRat.chr6 89278 48 + 647215 CATGGTCTGGATTGGAGTCCAAAGCAGTAACAAAATAGATACTAAAAC - -a -s simMouse_chr6.simMouse.chr6 97205 12 + 636262 AGCAGTGTATCT -s Anc0.Anc0refChr4 39002 12 - 45765 AGCAGTCTATAT -s Anc1.Anc1refChr2 70943 12 + 144309 AGCAGTCTATAT -s Anc2.Anc2refChr2 8330 12 + 27695 AACAACCTATAT -s mr.mrrefChr0 92289 12 + 130230 AGCAGTGTATCT -s simCow_chr6.simCow.chr6 98289 12 + 602619 AACAAACTATAT -s simDog_chr6.simDog.chr6 104171 12 + 593897 AATAACTTATAA -s simHuman_chr6.simHuman.chr6 93654 12 + 601863 AGCAGTCTATAT -s simRat_chr6.simRat.chr6 89326 12 + 647215 AGCGGTGTATCT - -a -s simMouse_chr6.simMouse.chr6 97217 36 + 636262 AGATATGGTTCTATTCATGTTTTCAAATTAGAATGC -s Anc0.Anc0refChr4 39017 36 - 45765 GGATTTGGTTCTATTCATGTTTTCAAATTGGTATGT -s Anc1.Anc1refChr2 70958 36 + 144309 GGATTTGGTTCTATTCATGTTTTCAAATTGGTATGT -s Anc2.Anc2refChr2 8345 36 + 27695 GAATTTGGGTCCATCCATGTTTTCAAATTTGTATGT -s mr.mrrefChr0 92301 36 + 130230 AGATATGGTTCTATTCATGTTTTCAAATTGGAATGC -s simCow_chr6.simCow.chr6 98304 32 + 602619 GAATTTGGGTACATCTGTGTTGTCAAG----TATGG -s simDog_chr6.simDog.chr6 104186 36 + 593897 GAATTTAGGTCCATCCATGTTTTCAAATTTGGATAT -s simHuman_chr6.simHuman.chr6 93669 36 + 601863 GGATTTGGTTCTGTTCATGTCTCCAAATTGGTATGT -s simRat_chr6.simRat.chr6 89338 36 + 647215 AGAGATGGTTCTATTCATGTTTTCAAATAGGAGTGC - -a -s simMouse_chr6.simMouse.chr6 97253 27 + 636262 ATCAAAAATTCTGAATAGCCTAGTGTG -s Anc0.Anc0refChr4 39053 27 - 45765 ATCAAAATCTATAAATAGCCTAGTGTG -s Anc1.Anc1refChr2 70994 27 + 144309 ATCAAAATCTATAAATAGCCTAGTGTG -s Anc2.Anc2refChr2 8381 27 + 27695 ATCAAAATCTATAAATAGGCTAGTGTG -s mr.mrrefChr0 92337 27 + 130230 ATCAAAAATTATGAATAGCCTAGTGTG -s simCow_chr6.simCow.chr6 98336 27 + 602619 ATCAGCATTTATAAATAGGCTAGTGTG -s simDog_chr6.simDog.chr6 104222 27 + 593897 ATCAAAATCTATAAATAGGCTGGTGGA -s simHuman_chr6.simHuman.chr6 93705 27 + 601863 ATCAAAATCTATAAATAGCCTAGTGTT -s simRat_chr6.simRat.chr6 89375 27 + 647215 ATCAAAAATTATGAACAGCCTAGTGTA - -a -s simMouse_chr6.simMouse.chr6 97280 1 + 636262 G -s Anc0.Anc0refChr4 39080 1 - 45765 A -s Anc1.Anc1refChr2 71021 1 + 144309 A -s Anc2.Anc2refChr2 8408 1 + 27695 C -s mr.mrrefChr0 92364 1 + 130230 A -s simCow_chr6.simCow.chr6 98363 1 + 602619 C -s simDog_chr6.simDog.chr6 104249 1 + 593897 C -s simHuman_chr6.simHuman.chr6 93777 1 + 601863 A -s simRat_chr6.simRat.chr6 89402 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 97281 20 + 636262 TTGATGCATATGAGATTAAA -s Anc0.Anc0refChr4 39081 20 - 45765 TTGATGCATATGAATTTAAA -s Anc1.Anc1refChr2 71022 20 + 144309 TTGATGCATATGAATTTAAA -s Anc2.Anc2refChr2 8428 20 + 27695 TTGATGCATATGAATTTAAA -s mr.mrrefChr0 92365 20 + 130230 TTGATGCATATGAGATTAAA -s simCow_chr6.simCow.chr6 98383 20 + 602619 TTAATGCATATGGATTTCAA -s simDog_chr6.simDog.chr6 104269 20 + 593897 TTGATGCATTTGAATTTAAA -s simHuman_chr6.simHuman.chr6 93778 20 + 601863 TTGGTGTATAAGAATTTAAA -s simRat_chr6.simRat.chr6 89403 20 + 647215 TTGCTGCATATGAGATTGGA - -a -s simMouse_chr6.simMouse.chr6 97301 36 + 636262 ACAGAGCCCACTTCACTACAAATTGGTTGTAAACAT -s Anc0.Anc0refChr4 39108 36 - 45765 ATGGATCACAATTCATGACAAATAGGTTGTTAATAC -s Anc1.Anc1refChr2 71049 36 + 144309 ATGGATCACAATTCATGACAAATAGGTTGTTAATAC -s Anc2.Anc2refChr2 8455 36 + 27695 ATGGATCACAAGTCATGACAAATAGGTAGGTAATAC -s mr.mrrefChr0 92385 36 + 130230 ACAGAGCCCACTTCACTACAAATTGGTTGTAAACAT -s simCow_chr6.simCow.chr6 98410 36 + 602619 ATGGATCACAAGTTATGACAAATAGGTGTGTCACAC -s simDog_chr6.simDog.chr6 104296 36 + 593897 ATGTATCCCAAGTCATGACAAATAAGTAGGTAATAC -s simHuman_chr6.simHuman.chr6 93805 36 + 601863 ATGGATCATAATTCATAACAAATAGGTTGTTAATAC -s simRat_chr6.simRat.chr6 89423 36 + 647215 ACAGAGTGCACTGCACTACAAATGGGTTGTAAACAT - -a -s simMouse_chr6.simMouse.chr6 97337 21 + 636262 ATCAGACAATATTTTACTAAT -s Anc0.Anc0refChr4 39144 21 - 45765 TTTGGAATCTATTTTATTACT -s Anc1.Anc1refChr2 71085 21 + 144309 TTTGGAATCTATTTTATTACT -s Anc2.Anc2refChr2 8491 21 + 27695 TTTGGAATCTATTTTATTACT -s mr.mrrefChr0 92421 21 + 130230 ATCAGACTATATTTTACTAAT -s simCow_chr6.simCow.chr6 98458 21 + 602619 CTTGAGATCTACTTTATTAAT -s simDog_chr6.simDog.chr6 104332 21 + 593897 TTTAGAAACTATTTCATTACT -s simHuman_chr6.simHuman.chr6 93841 21 + 601863 TTTGGAGTCCAGTCTATTACA -s simRat_chr6.simRat.chr6 89459 21 + 647215 ATCAGACTATATTTTACTAAT - -a -s simMouse_chr6.simMouse.chr6 97358 19 + 636262 GTTTTGGGATCGACTTTTG -s Anc0.Anc0refChr4 39165 19 - 45765 GCTTTGGTACCTACTTTAG -s Anc1.Anc1refChr2 71106 19 + 144309 GCTTTGGTACCTACTTTAG -s Anc2.Anc2refChr2 8512 19 + 27695 GCTTTGGTACTTACTCTAG -s mr.mrrefChr0 92442 19 + 130230 GCTTTGGGATCGACTTTTG -s simCow_chr6.simCow.chr6 98480 19 + 602619 GCTTTGGCCTGTACTCCAG -s simDog_chr6.simDog.chr6 104353 19 + 593897 GCATTGCTACTTACTCTGA -s simHuman_chr6.simHuman.chr6 93862 19 + 601863 GCTTTGGTACCTACTTTAG -s simRat_chr6.simRat.chr6 89480 19 + 647215 TCTTTGGGATTGACTCTTG - -a -s simMouse_chr6.simMouse.chr6 97377 12 + 636262 TTCTATCATACC -s Anc0.Anc0refChr4 39184 3 - 45765 T---------CC -s Anc1.Anc1refChr2 71125 3 + 144309 T---------CC -s Anc2.Anc2refChr2 8531 3 + 27695 T---------CC -s mr.mrrefChr0 92461 12 + 130230 TTCTATCATACC -s simCow_chr6.simCow.chr6 98499 3 + 602619 A---------CC -s simDog_chr6.simDog.chr6 104378 3 + 593897 T---------CC -s simHuman_chr6.simHuman.chr6 93881 3 + 601863 T---------CC -s simRat_chr6.simRat.chr6 89499 12 + 647215 TTCTATCACCTC - -a -s simMouse_chr6.simMouse.chr6 97389 3 + 636262 CTC -s Anc0.Anc0refChr4 39187 3 - 45765 TTC -s Anc1.Anc1refChr2 71128 3 + 144309 TTC -s Anc2.Anc2refChr2 8534 3 + 27695 TTC -s mr.mrrefChr0 92473 3 + 130230 CTC -s simCow_chr6.simCow.chr6 98505 3 + 602619 TTC -s simDog_chr6.simDog.chr6 104381 3 + 593897 TTC -s simHuman_chr6.simHuman.chr6 93884 3 + 601863 GTC -s simRat_chr6.simRat.chr6 89511 3 + 647215 CAC - -a -s simMouse_chr6.simMouse.chr6 97392 164 + 636262 CCGATAATCATATACTTAGATGAGGCCCCCTCTGTGAAACAATAAATGTTTCATGAACTGGCCCTCTCTTCAACAGTAGGCAAGCTCCCCTAGGTATTGTCTGTCCACATTTCTTGAGCTAAGCATATTTGTATGAATCACTCTACAAAGAGCCAAGTGGTTTT -s Anc0.Anc0refChr4 39190 70 - 45765 CCCCTGATGAC---CTAAGTTGCTTCCCTCTGCT-GAAATA-----------ATGAACTA-----------------------------------------------------------------------------TCACTC--CAGTGAGCTAAGTCACTTG -s Anc1.Anc1refChr2 71131 72 + 144309 CCCCTGATGAC---CTAAGTTGCTTCCCTCTGCT-GAAATA-----------ATGAACTA-----------------------------------------------------------------------------TCACTCTACAGTGAGCTAAGTCACTTG -s Anc2.Anc2refChr2 8538 70 + 27695 CCCCTGATGAC---CTAAATTGCTTCCCTCTGCT-GAAATT-----------ATAAACTA-----------------------------------------------------------------------------TCACTC--AAGTGAGATAAGTCACTTG -s mr.mrrefChr0 92476 163 + 130230 CCGATAATCATATACTTAGATGAGGCCCCCTCTG-GAAACAATAAATGTTTCATGAACTGGCCCTCTCTTCAACAGTAGGCAAGCTCCCCTAGGTATTGTCTGTCCACATTTCTTGAGCTAAGCATATTTGTATGAATCACTCTACAAAGAGCCAAGTGGTTTT -s simCow_chr6.simCow.chr6 98509 65 + 602619 CCCCCAATGAC---CTTAATTGGTCCCCCATGCC-AAAATT-----------ATAAACTA-----------------------------------------------------------------------------TCACTT--GA-----ATATGTCACTTG -s simDog_chr6.simDog.chr6 104385 70 + 593897 CCCCTGATGGC---TGAAATTGCTTCCCTCTGTT-GAAGTT-----------AAAAACAG-----------------------------------------------------------------------------TTGCTC--AAGTGAGATAAGTCACTTG -s simHuman_chr6.simHuman.chr6 93887 72 + 601863 TCTCTGATGAC---CTCTGTTGTTACCCTTTGCT-GAAATA-----------ATGACCTA-----------------------------------------------------------------------------TCATTCTACAGCGACCTAAGCTACTTG -s simRat_chr6.simRat.chr6 89514 163 + 647215 CCGAGAATCACATACTCTGATGTGCTCCGCTCTG-AAAGCAATAACTGATTCATGAACTGGCCCTCTCTTTAGCAGTAGGCATGCTTCCCTAGGTATTGTATGTTGACATTTCTGGAGCTAAGCATATTTGCATGTATCACTCTACAGTGTGCTAAGTAACTTG - -a -s simMouse_chr6.simMouse.chr6 97556 12 + 636262 TCTGGTCAACAT -s Anc0.Anc0refChr4 39260 12 - 45765 GGTTGTTAACAT -s Anc1.Anc1refChr2 71203 12 + 144309 GGTTGTTAACAT -s Anc2.Anc2refChr2 8608 12 + 27695 GGTTGTTAACAT -s mr.mrrefChr0 92639 12 + 130230 TCTGGTCAACAT -s simCow_chr6.simCow.chr6 98574 12 + 602619 GGTCAATACCAT -s simDog_chr6.simDog.chr6 104461 12 + 593897 GGTTGTTGACAT -s simHuman_chr6.simHuman.chr6 93959 12 + 601863 GGTTGTTAACAT -s simRat_chr6.simRat.chr6 89677 12 + 647215 TCTTACTAACAT - -a -s simMouse_chr6.simMouse.chr6 97568 19 + 636262 AAATTCTAGATGTCATCTT -s Anc0.Anc0refChr4 39272 19 - 45765 AACTTATGGGTGTCATCTG -s Anc1.Anc1refChr2 71215 19 + 144309 AACTTATGGGTGTCATCTG -s Anc2.Anc2refChr2 8620 19 + 27695 AACTTATGGGTGTCATCTG -s mr.mrrefChr0 92651 19 + 130230 AAATTCTAGATGTCATCTT -s simCow_chr6.simCow.chr6 98592 19 + 602619 AACTTATGGGTGTCATCTG -s simDog_chr6.simDog.chr6 104473 19 + 593897 AACTTATGCATGCCATCTT -s simHuman_chr6.simHuman.chr6 93971 19 + 601863 AACTTGTGGGTGTCACTTG -s simRat_chr6.simRat.chr6 89689 19 + 647215 AACTTCTAGGTGTCATCTT - -a -s simMouse_chr6.simMouse.chr6 97587 24 + 636262 AATGTAGGGTTATATGCCTGCCAT -s Anc0.Anc0refChr4 39291 21 - 45765 GATGTACAATCAAAAGCCT---TT -s Anc1.Anc1refChr2 71234 24 + 144309 GATGTACAATCAAAAGCCTATTTT -s Anc2.Anc2refChr2 8639 21 + 27695 GATGTCCAATCAATAGCCT---TC -s mr.mrrefChr0 92670 24 + 130230 AATGTAGGGTTATATGCCTGCCAT -s simCow_chr6.simCow.chr6 98611 14 + 602619 CATGTTCACACA----------TC -s simDog_chr6.simDog.chr6 104511 19 + 593897 GTTATCCAATCAATAGCCT----- -s simHuman_chr6.simHuman.chr6 93990 24 + 601863 GATGTACAATCAAAAGCTTATTTT -s simRat_chr6.simRat.chr6 89708 24 + 647215 AATGTGAGGCTATGTGCCTGCCAT - -a -s simMouse_chr6.simMouse.chr6 97611 27 + 636262 TGAGAATGTATTTCTGCGGAAGCAATT -s Anc0.Anc0refChr4 39313 27 - 45765 TAAGGACCAATTTCTGATAAACCAATC -s Anc1.Anc1refChr2 71259 27 + 144309 TAAGGACCAATTTCTGATAAACCAATC -s Anc2.Anc2refChr2 8661 27 + 27695 TAAGGACCAATTTCTGATAAACCAATC -s mr.mrrefChr0 92694 27 + 130230 TGAGAATGTATTTCTGCGGAAGCAATT -s simCow_chr6.simCow.chr6 98626 27 + 602619 TAAGGATCGATTGCTGATACACCAATC -s simDog_chr6.simDog.chr6 104530 27 + 593897 TAAGGACCAATTTCTGTTGAACCCATC -s simHuman_chr6.simHuman.chr6 94015 27 + 601863 TAAAGGCCAATTTCGGATAAACAACTA -s simRat_chr6.simRat.chr6 89732 27 + 647215 TAAGAGTATATTGCTGCAGCAGCAATT - -a -s simMouse_chr6.simMouse.chr6 97638 10 + 636262 GGACTTACTG -s Anc0.Anc0refChr4 39340 10 - 45765 AGACATATTG -s Anc1.Anc1refChr2 71286 10 + 144309 AGACATATTG -s Anc2.Anc2refChr2 8688 10 + 27695 AGACATATTG -s mr.mrrefChr0 92721 10 + 130230 GGACTTACTG -s simCow_chr6.simCow.chr6 98653 8 + 602619 AGACATTT-- -s simDog_chr6.simDog.chr6 104557 10 + 593897 AGATGTACTG -s simHuman_chr6.simHuman.chr6 94042 10 + 601863 AGACATATTG -s simRat_chr6.simRat.chr6 89760 10 + 647215 GGACTTACTG - -a -s simMouse_chr6.simMouse.chr6 97648 19 + 636262 AGCTTAACTTTGTTCTGAT -s Anc0.Anc0refChr4 39354 16 - 45765 AGCATGCCA---TCTTTCC -s Anc1.Anc1refChr2 71300 19 + 144309 AGCATGCCACTTTCTTTCC -s Anc2.Anc2refChr2 8702 16 + 27695 GGCATGCCA---TCTTTCC -s mr.mrrefChr0 92731 19 + 130230 AGCTTAACTTTGTTCTGAT -s simCow_chr6.simCow.chr6 98661 9 + 602619 -------CT---TCTTTCC -s simDog_chr6.simDog.chr6 104571 16 + 593897 GGCATGCCA---ATTCTCC -s simHuman_chr6.simHuman.chr6 94056 19 + 601863 AGTATGCCACTTTCTTACC -s simRat_chr6.simRat.chr6 89770 19 + 647215 AATTTAACTTTATTTAGAT - -a -s simMouse_chr6.simMouse.chr6 97667 42 + 636262 TTAACACAGTGCCTCATGCAACACCCCAGTAAAAGACAAACA -s Anc0.Anc0refChr4 39370 14 - 45765 TTAATAGAATACCT---------------------------- -s Anc1.Anc1refChr2 71319 14 + 144309 TTAATAGAATACCT---------------------------- -s Anc2.Anc2refChr2 8718 14 + 27695 TTAATAGAATACCT---------------------------- -s mr.mrrefChr0 92750 42 + 130230 TTAACACAGTGCCTCATGCAACACCCCAGTAAAAGACAAACA -s simCow_chr6.simCow.chr6 98670 14 + 602619 TTAATAGAGTATCT---------------------------- -s simDog_chr6.simDog.chr6 104587 14 + 593897 TTAACAGAATACCT---------------------------- -s simHuman_chr6.simHuman.chr6 94075 14 + 601863 TTAATGGAATACCT---------------------------- -s simRat_chr6.simRat.chr6 89805 42 + 647215 TTCACACAGTGCCTCATGCAACACTCCAATAAAACGCAAAAA - -a -s simMouse_chr6.simMouse.chr6 97709 62 + 636262 CATCCGGGTATATGAGGCTAGTGCTTGGAGCTATACCAATGTAATACTATACTTCATGATCT -s Anc0.Anc0refChr4 39384 18 - 45765 -------------------------------------------ATAATA-ACTTCATGTACT -s Anc1.Anc1refChr2 71333 18 + 144309 -------------------------------------------ATAATA-ACTTCATGTACT -s Anc2.Anc2refChr2 8732 18 + 27695 -------------------------------------------ATTATA-AGTTCATGTACT -s mr.mrrefChr0 92792 62 + 130230 CATCCGGGTATATGAGGCTAGTGCTTGGAGCTATACCAATGTAATACTATACTTCATGATCT -s simCow_chr6.simCow.chr6 98684 18 + 602619 -------------------------------------------ACTACA-AGTTCATATATT -s simDog_chr6.simDog.chr6 104601 18 + 593897 -------------------------------------------ATTATG-GGTTCATGTACT -s simHuman_chr6.simHuman.chr6 94089 18 + 601863 -------------------------------------------ATATTA-ACTTCATGTACT -s simRat_chr6.simRat.chr6 89854 62 + 647215 CGGCCAGGTATGTGCAGTTAGGGTTTTGAGCTATAACAATTTAATACTATATTTCACAGCCT - -a -s simMouse_chr6.simMouse.chr6 97771 2 + 636262 CT -s Anc0.Anc0refChr4 39402 2 - 45765 CT -s Anc1.Anc1refChr2 71351 2 + 144309 CT -s Anc2.Anc2refChr2 8751 2 + 27695 CT -s mr.mrrefChr0 92854 2 + 130230 CT -s simCow_chr6.simCow.chr6 98703 2 + 602619 TT -s simDog_chr6.simDog.chr6 104620 2 + 593897 CT -s simHuman_chr6.simHuman.chr6 94107 2 + 601863 CT -s simRat_chr6.simRat.chr6 89916 2 + 647215 CT - -a -s simMouse_chr6.simMouse.chr6 97773 1 + 636262 C -s Anc0.Anc0refChr4 39412 1 - 45765 C -s Anc1.Anc1refChr2 71361 1 + 144309 C -s Anc2.Anc2refChr2 8761 1 + 27695 T -s mr.mrrefChr0 92856 1 + 130230 C -s simCow_chr6.simCow.chr6 98713 1 + 602619 T -s simDog_chr6.simDog.chr6 104630 1 + 593897 T -s simHuman_chr6.simHuman.chr6 94117 1 + 601863 C -s simRat_chr6.simRat.chr6 89918 1 + 647215 C - -a -s simMouse_chr6.simMouse.chr6 97774 4 + 636262 TGAT -s Anc0.Anc0refChr4 39413 4 - 45765 TGAT -s Anc1.Anc1refChr2 71362 4 + 144309 TGAT -s Anc2.Anc2refChr2 8763 4 + 27695 TGAT -s mr.mrrefChr0 92857 4 + 130230 TGAT -s simCow_chr6.simCow.chr6 98715 4 + 602619 TGAT -s simDog_chr6.simDog.chr6 104632 4 + 593897 TGAT -s simHuman_chr6.simHuman.chr6 94118 4 + 601863 TGAT -s simRat_chr6.simRat.chr6 89919 4 + 647215 CTGT - -a -s simMouse_chr6.simMouse.chr6 97778 70 + 636262 ATGAGCCTTTATATCTTCTTCTGCTTTGGCAATGGATCTGTAATGTTGTAAAACATCTGCCTAAACAGTT -s Anc0.Anc0refChr4 39417 64 - 45765 ATTA---TGTAT-TCT--TTTGCCCATGGTTGTGGAGCTGTCATGTTGGAAAATCTCAGCCTACACAATT -s Anc1.Anc1refChr2 71366 64 + 144309 ATTA---TGTAT-TCT--TTTGCCCATGGTTGTGGAGCTGTCATGTTGGAAAATCTCAGCCTACACAATT -s Anc2.Anc2refChr2 8767 64 + 27695 TTTA---TGTAT-TCT--TGTGCCCATGGTTGTGGAGCTGTCATGGTGGAAAATCTCAGCCCACATAATT -s mr.mrrefChr0 92861 69 + 130230 ATGAGCCTTTAT-TCTTCTTCTGCTTTGGCAATGGATCTGTAATGTTGTAAAACATCTGCCTAAACAGTT -s simCow_chr6.simCow.chr6 98719 64 + 602619 TTTA---TAAAT-TCT--TGCGCCCATGGTCGTGGCACAGGTATGCTGGAAAATCTCAGCCCACATGATT -s simDog_chr6.simDog.chr6 104636 64 + 593897 TTTA---TGTAC-TCT--TGTGCACATGGATGTGTAGCTGTCATGGTGGAAAATCTCAGCCCACATAATT -s simHuman_chr6.simHuman.chr6 94122 61 + 601863 ATTA---TGGAT-TCT--TTTGACCATAGTGGTGGAGCTGACATATTGGAAAAACTGAACCTACAC---T -s simRat_chr6.simRat.chr6 89925 69 + 647215 ATGTGCCTTTAT-TCTTCTTCTGACTTGGCAATGGACCTGTAATGTTGTAAAACACCTGCCTAAATAATT - -a -s simMouse_chr6.simMouse.chr6 97848 59 + 636262 TATACCGCCCTAAGCCTTATTTAAGAGAAGCAGCTTTGCAAAGCTATGCTTGGTCATGC -s Anc0.Anc0refChr4 39481 37 - 45765 TAT---------AGCCTTATCTAAGAG-------------AAGTTACCCTTGGTTATGT -s Anc1.Anc1refChr2 71430 37 + 144309 TAT---------AGCCTTATCTAAGAG-------------AAGTTACCCTTGGTTATGT -s Anc2.Anc2refChr2 8835 37 + 27695 TAT---------AGCCTTATCTAAGAG-------------AAGTTACCCTTGATTATGT -s mr.mrrefChr0 92930 57 + 130230 TATAC--CCCTAAGCCTTATTTAAGAGAAGCAGCTTTGCAAAGCTATGCTTGGTCATGC -s simCow_chr6.simCow.chr6 98785 36 + 602619 -AT---------AGCCTTATCTGTGAG-------------AAGTTACCCTTCTTTATAT -s simDog_chr6.simDog.chr6 104707 37 + 593897 TAT---------AGCCTTACCTAAGAG-------------AAGTTACCCTTGATGATGT -s simHuman_chr6.simHuman.chr6 94183 37 + 601863 TAT---------AGCCTTATCTAAGAG-------------AAGTTACCCATAGTTATGT -s simRat_chr6.simRat.chr6 89994 57 + 647215 TATAC--CCACTATCCTTATTTGAGAGAAGCAACTTTGCAAAGCTACACTTGGTCATGC - -a -s simMouse_chr6.simMouse.chr6 97907 95 + 636262 CCGCCAGTTAATTTGTTTATATTGTGTTCTTCGGAGATGTATTTTCTATGATCAGGATCGGTTTGGTATGTATGCCATGACTGCTAACAAAGAAT -s Anc0.Anc0refChr4 39519 93 - 45765 CTACCGGTTAATTTATTTACATTATGTTCAAGGGCGATGCACTCTCTATGACCATAATCAG-TAGGTATGTGTGCCATAACCCCTAACAAAGAA- -s Anc1.Anc1refChr2 71468 93 + 144309 CTACCGGTTAATTTATTTACATTATGTTCAAGGGCGATGCACTCTCTATGACCATAATCAG-TAGGTATGTGTGCCATAACCCCTAACAAAGAA- -s Anc2.Anc2refChr2 8873 93 + 27695 CTACCGGTTAATTTATTTACATTATGTTAAAGGGCGATCCACTCTCTATGACCATAATCAA-TAGGTATGTGTGCCACAACCCCTAACAAAGAA- -s mr.mrrefChr0 92987 95 + 130230 CCGCCAGTTAATTTGTTTATATTGTGTTCTTCGGAGATGTATTTTCTATGATCAGGATCGGTTTGGTATGTATGCCATGACTGCTAACAAAGAAT -s simCow_chr6.simCow.chr6 98822 90 + 602619 CTACAGGTGAGTTTATTTATGTTCT-TTGAAAGGTGATCTACTCTCTATGATCATAATCAC-TATGTATGTGG--CACAACCCCTAACAAAGAA- -s simDog_chr6.simDog.chr6 104745 76 + 593897 ATACCAGTTAACTTATTTACAATATGTTAAAGGGCGGTCCAC-CTCTATGACCATAATCAA-TAGGTATGTATGC----------------ACA- -s simHuman_chr6.simHuman.chr6 94221 93 + 601863 CTACTGGTTAATTGATTTACATTATGCTCGAGGGGCACGCACTCCCTATGACCATCATCAG-TAGGTATGTGTGCCATAGCCACTAGCAATGAA- -s simRat_chr6.simRat.chr6 90051 95 + 647215 CTGCCAGTTAATTTGTTTATATTGTGTTTGCGGGAGATGTATTCTCAATGATTAGGATCGGATTGGTATGTGTGCCACAATTGTTAACAAAGAGT - -a -s simMouse_chr6.simMouse.chr6 98002 35 + 636262 TTAACAGGTTCAAAGGAGAAATCAATGCCCAGGTA -s Anc0.Anc0refChr4 39612 34 - 45765 TTAACACACTTAAGGGAG-AATCACTGCACAGATA -s Anc1.Anc1refChr2 71561 35 + 144309 TTAACACACTTAAGGGAGGAATCACTGCACAGATA -s Anc2.Anc2refChr2 8966 34 + 27695 TTTGCACACTTCAGGGAG-AACCACTATATAGATA -s mr.mrrefChr0 93082 35 + 130230 TTAACAGGTTCAAAGGAGAAATCAATGCCCAGGTA -s simCow_chr6.simCow.chr6 98913 34 + 602619 TTTTCATACTACAGGGAG-AACCACACTGTAGATA -s simDog_chr6.simDog.chr6 104821 22 + 593897 TTTGCGCTCTT-------------CTATATTGATA -s simHuman_chr6.simHuman.chr6 94314 35 + 601863 TTAACAAACTTAAGGGAAGTGTCACTGCACAGATA -s simRat_chr6.simRat.chr6 90146 35 + 647215 TGAACAGATTCAAGGGAGAACTCAACATCCAGGGA - -a -s simMouse_chr6.simMouse.chr6 98037 6 + 636262 GACTGG -s Anc0.Anc0refChr4 39646 6 - 45765 GACTGA -s Anc1.Anc1refChr2 71596 6 + 144309 GACTGA -s Anc2.Anc2refChr2 9000 6 + 27695 GCCTGA -s mr.mrrefChr0 93117 6 + 130230 GACTGG -s simCow_chr6.simCow.chr6 98947 5 + 602619 G-CTGT -s simDog_chr6.simDog.chr6 104844 6 + 593897 GCCCGA -s simHuman_chr6.simHuman.chr6 94349 6 + 601863 GACTGA -s simRat_chr6.simRat.chr6 90181 6 + 647215 GACTGG - -a -s simMouse_chr6.simMouse.chr6 98043 1 + 636262 T -s Anc0.Anc0refChr4 39652 1 - 45765 T -s Anc1.Anc1refChr2 71602 1 + 144309 T -s Anc2.Anc2refChr2 9006 1 + 27695 T -s mr.mrrefChr0 93123 1 + 130230 T -s simCow_chr6.simCow.chr6 98952 1 + 602619 T -s simDog_chr6.simDog.chr6 104851 1 + 593897 T -s simHuman_chr6.simHuman.chr6 94355 1 + 601863 T -s simRat_chr6.simRat.chr6 90187 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 98044 1 + 636262 G -s Anc0.Anc0refChr4 39653 1 - 45765 G -s Anc1.Anc1refChr2 71603 1 + 144309 G -s Anc2.Anc2refChr2 9007 1 + 27695 A -s mr.mrrefChr0 93124 1 + 130230 G -s simCow_chr6.simCow.chr6 98953 1 + 602619 A -s simDog_chr6.simDog.chr6 104852 1 + 593897 A -s simHuman_chr6.simHuman.chr6 94356 1 + 601863 G -s simRat_chr6.simRat.chr6 90189 1 + 647215 G - -a -s simMouse_chr6.simMouse.chr6 98045 71 + 636262 GCACCTCCTAACCTGGTGATGAGTACTTTTCCTAGTCCTAGCTGAGGTTGTGTATGTGACTTTACTGCTTA -s Anc0.Anc0refChr4 39655 62 - 45765 GCACCTTCTAACCTG--GATGAATACTTTT------CCCAGCTGAGCTCGTGTATATGACTTCACTGCTC- -s Anc1.Anc1refChr2 71605 62 + 144309 GCACCTTCTAACCTG--GATGAATACTTTT------CCCAGCTGAGCTCGTGTATATGACTTCACTGCTC- -s Anc2.Anc2refChr2 9009 62 + 27695 GCACCATCTAACCTG--GATGAATACTTTT------CCCAGCTGAGCTCGTGTATATTACGTCACTGCCC- -s mr.mrrefChr0 93125 64 + 130230 GCACCTCCTAACCTGGTGATGAGTACTTTT------CCTAGCTGAGGTTGTGTATGTGACTTTACTGCTT- -s simCow_chr6.simCow.chr6 98955 56 + 602619 GCACCATCTAACCTG--G----ATGCTCTT------CCTAGCTGGG--CCAGCATGGTACGCTGCCACCC- -s simDog_chr6.simDog.chr6 104854 58 + 593897 GGTCCACCTAAC-----AATGAATACATTT------CCCAGCTGAGCTAGTGTACATTAC-TCAATGCCC- -s simHuman_chr6.simHuman.chr6 94358 62 + 601863 GCACCTTCTAACCTG--GATGAAGACTTTC------TCCACCTAAGTTCATGTATTTGACTTCACTGCTC- -s simRat_chr6.simRat.chr6 90190 64 + 647215 GCACCACCTAACCTGGTGATCAATACCTTT------CTAAGCTGAGTTTGTGTATGTGACTTTACTACTT- - -a -s simMouse_chr6.simMouse.chr6 98116 29 + 636262 AGCTCACAGTAGGTGTGCTTCTCACTCCC -s Anc0.Anc0refChr4 39718 28 - 45765 AGCTCATATAAAGTGTGCTTCTCAAACA- -s Anc1.Anc1refChr2 71668 29 + 144309 AGCTCATATAAAGTGTGCTTCTCAAACAC -s Anc2.Anc2refChr2 9072 28 + 27695 AGCTCATATAAAGTGTGCTTCTCAAACA- -s mr.mrrefChr0 93189 29 + 130230 AGCTCACAGTAGGTGTGCTTCTCACTCCC -s simCow_chr6.simCow.chr6 99012 26 + 602619 AGCTCAGATAAAGTGTGCTTCT--AACA- -s simDog_chr6.simDog.chr6 104913 24 + 593897 AGCTCATATAAAGTGCGCTTCTCA----- -s simHuman_chr6.simHuman.chr6 94421 29 + 601863 AGGTCATACAAAGTGTGCTTCTCATCCAC -s simRat_chr6.simRat.chr6 90254 29 + 647215 AGCTCACAATAAGTGTGCTTCTCACTCCC - -a -s simMouse_chr6.simMouse.chr6 98145 6 + 636262 CTGGGA -s Anc0.Anc0refChr4 39753 5 - 45765 ATAGT- -s Anc1.Anc1refChr2 71704 5 + 144309 ATAGT- -s Anc2.Anc2refChr2 9107 5 + 27695 ACAGT- -s mr.mrrefChr0 93218 6 + 130230 CTGGGA -s simCow_chr6.simCow.chr6 99045 5 + 602619 GCAGT- -s simDog_chr6.simDog.chr6 104938 5 + 593897 ACAAC- -s simHuman_chr6.simHuman.chr6 94460 5 + 601863 ATAGT- -s simRat_chr6.simRat.chr6 90283 6 + 647215 CTGGGA - -a -s simMouse_chr6.simMouse.chr6 98151 38 + 636262 GAACATATAGATTCAAGGCAACACACTCTCTATGGGTA -s Anc0.Anc0refChr4 39758 38 - 45765 GAACATATAGGTTTAAAGGAACACACTCTTAAAGGGAA -s Anc1.Anc1refChr2 71709 38 + 144309 GAACATATAGGTTTAAAGGAACACACTCTTAAAGGGAA -s Anc2.Anc2refChr2 9112 38 + 27695 AAACATATAGGTTTAAAGGAACACACTCTTAAAGACAA -s mr.mrrefChr0 93224 38 + 130230 GAACATATAGATTCAAGGCAACACACTCTCTATGGGTA -s simCow_chr6.simCow.chr6 99050 28 + 602619 AAACATATAGGTCTAAAGGGACTC----------ACAG -s simDog_chr6.simDog.chr6 104943 38 + 593897 AAATATATGGGTTTAAAGGAACAAACTCTTAAAGACCA -s simHuman_chr6.simHuman.chr6 94465 38 + 601863 GAACAAATAGGTTTAAAGGAACACCCCCCAAAAGGGAA -s simRat_chr6.simRat.chr6 90292 38 + 647215 AAACATATAGTCCCAAGGCAGCACCCTCTCTATGGGTA - -a -s simMouse_chr6.simMouse.chr6 98189 34 + 636262 TGGAAATATCAAAGTAAATTGGTTATGTGCATCA -s Anc0.Anc0refChr4 39797 30 - 45765 TGTAAATATCA--AGTGATTTGTTCTGTGCAC-- -s Anc1.Anc1refChr2 71748 34 + 144309 TGTAAATATCACAAGTGATTTGTTCTGTGCACCA -s Anc2.Anc2refChr2 9151 30 + 27695 TGTAAATATCA--AGTGATTTGTTCTGTGGGC-- -s mr.mrrefChr0 93262 34 + 130230 TGGAAATATCAAAGTAAATTGGTTATGTGCATCA -s simCow_chr6.simCow.chr6 99079 30 + 602619 CCTAAATATGA--AGTGATTTGTTCTGTGGGC-- -s simDog_chr6.simDog.chr6 104982 30 + 593897 TGTAGAAATCA--GGTGATTTGTTCTGTGGGC-- -s simHuman_chr6.simHuman.chr6 94504 34 + 601863 TGTAAATATCACAAGTGCTTTGTCCCATGCACCA -s simRat_chr6.simRat.chr6 90330 34 + 647215 TGGAAATATCAAAGTAAAATTGTTAGGTTCACCA - -a -s simMouse_chr6.simMouse.chr6 98223 76 + 636262 CATTTTATTGCAAGTCTGTCAAAACTTGCTACGTCTGGGATTATCTTTGGTTCCCACCGACACAATGGTGTTACAG -s Anc1.Anc1refChr2 71782 19 + 144309 CATTGAAGGGCAAA---------------------------------------------------------TGCTC -s mr.mrrefChr0 93296 76 + 130230 CATTTTATTGCAAGTCTGTCAAAACTTGCTACGTCTGGGATTATCTTTGGTTCCCACCGACACAATGGTGTTACAG -s simHuman_chr6.simHuman.chr6 94540 19 + 601863 CATTGAAGGGCAAA---------------------------------------------------------TGCTC -s simRat_chr6.simRat.chr6 90364 76 + 647215 CATTCTATTACAAGACTGTCAAATCTTGCTACTTCTGGGACTTTCGCTGGCTCCTACCAACACAAAGGTGTTGTAG - -a -s simMouse_chr6.simMouse.chr6 98299 4 + 636262 AATG -s Anc0.Anc0refChr4 39827 4 - 45765 AATG -s Anc1.Anc1refChr2 71801 4 + 144309 AATG -s Anc2.Anc2refChr2 9181 4 + 27695 AATG -s mr.mrrefChr0 93372 4 + 130230 AATG -s mr.mrrefChr0 93541 4 + 130230 CATA -s simCow_chr6.simCow.chr6 99109 4 + 602619 AATG -s simDog_chr6.simDog.chr6 105012 4 + 593897 AATG -s simHuman_chr6.simHuman.chr6 94559 4 + 601863 AATG -s simMouse_chr6.simMouse.chr6 98471 4 + 636262 CATA -s simRat_chr6.simRat.chr6 90618 4 + 647215 CATA -s simRat_chr6.simRat.chr6 90440 4 + 647215 AATG - -a -s simMouse_chr6.simMouse.chr6 98303 2 + 636262 TA -s Anc0.Anc0refChr4 39831 2 - 45765 CC -s Anc1.Anc1refChr2 71805 2 + 144309 CC -s Anc2.Anc2refChr2 9185 2 + 27695 CC -s mr.mrrefChr0 93376 2 + 130230 TA -s simCow_chr6.simCow.chr6 99113 2 + 602619 CC -s simDog_chr6.simDog.chr6 105016 2 + 593897 CC -s simHuman_chr6.simHuman.chr6 94563 2 + 601863 CC -s simRat_chr6.simRat.chr6 90444 2 + 647215 TA - -a -s simMouse_chr6.simMouse.chr6 98305 15 + 636262 TTTAGTGACAATTAA -s Anc0.Anc0refChr4 39833 15 - 45765 TTGAAGGGCAATTAC -s Anc1.Anc1refChr2 71807 15 + 144309 TTGAAGGGCAATTAC -s Anc2.Anc2refChr2 9187 15 + 27695 CTGAAGGGCAATTAC -s mr.mrrefChr0 93378 15 + 130230 TTTAGTGACAATTAA -s mr.mrrefChr0 93545 15 + 130230 TTGAATGACTATTAA -s simCow_chr6.simCow.chr6 99115 15 + 602619 CTAAAGGGTGATTAC -s simDog_chr6.simDog.chr6 105018 15 + 593897 CCGAAGGACAATTAC -s simHuman_chr6.simHuman.chr6 94565 15 + 601863 TTGAAGAGCAAATGC -s simMouse_chr6.simMouse.chr6 98475 15 + 636262 TTGAATGACTATTAA -s simRat_chr6.simRat.chr6 90622 15 + 647215 TTGAAGGACCATTAA -s simRat_chr6.simRat.chr6 90446 15 + 647215 TTGAAGGACAATTAA - -a -s simMouse_chr6.simMouse.chr6 98320 17 + 636262 TCACTTTTTGAGGTCTG -s Anc0.Anc0refChr4 39848 17 - 45765 TCATTTTTTGTGGTCTA -s Anc1.Anc1refChr2 71822 17 + 144309 TCATTTTTTGTGGTCTA -s Anc2.Anc2refChr2 9202 17 + 27695 TCATTATGTGTGGTGTA -s mr.mrrefChr0 93393 17 + 130230 TCACTTTTTGAGGTCTG -s mr.mrrefChr0 93560 17 + 130230 TCGTTTTCTGAGTCCTG -s simCow_chr6.simCow.chr6 99130 17 + 602619 TCATTATGTGTGGTTAA -s simDog_chr6.simDog.chr6 105033 12 + 593897 TCATTATGG-----GTA -s simHuman_chr6.simHuman.chr6 94580 17 + 601863 TCATCGATTATGGTATA -s simMouse_chr6.simMouse.chr6 98490 17 + 636262 TCGTTTTCTGAGTCCTG -s simRat_chr6.simRat.chr6 90639 17 + 647215 TCATATTCTCAGGCCTG -s simRat_chr6.simRat.chr6 90461 17 + 647215 TCATTTTTTAAAGTCTG - -a -s simMouse_chr6.simMouse.chr6 98337 8 + 636262 CATGACCT -s Anc0.Anc0refChr4 39867 8 - 45765 CATGATCT -s Anc1.Anc1refChr2 71841 8 + 144309 CATGATCT -s Anc2.Anc2refChr2 9221 8 + 27695 CATGATCT -s mr.mrrefChr0 93410 8 + 130230 CATGACCT -s mr.mrrefChr0 93577 8 + 130230 CACGACCT -s simCow_chr6.simCow.chr6 99149 8 + 602619 GCTGCTCT -s simDog_chr6.simDog.chr6 105047 8 + 593897 CATGACCT -s simHuman_chr6.simHuman.chr6 94599 8 + 601863 CAGGATCT -s simMouse_chr6.simMouse.chr6 98507 8 + 636262 CACGACCT -s simRat_chr6.simRat.chr6 90656 8 + 647215 CCTGACCT -s simRat_chr6.simRat.chr6 90478 8 + 647215 CATGACCC - -a -s simMouse_chr6.simMouse.chr6 98345 4 + 636262 CTAA -s Anc0.Anc0refChr4 39876 4 - 45765 CTAG -s Anc1.Anc1refChr2 71850 4 + 144309 CTAG -s Anc2.Anc2refChr2 9230 4 + 27695 CTAG -s mr.mrrefChr0 93418 4 + 130230 CTAA -s mr.mrrefChr0 93585 4 + 130230 CTAT -s simCow_chr6.simCow.chr6 99158 4 + 602619 CTAG -s simDog_chr6.simDog.chr6 105056 4 + 593897 TATA -s simHuman_chr6.simHuman.chr6 94608 4 + 601863 CTAG -s simMouse_chr6.simMouse.chr6 98515 4 + 636262 CTAT -s simRat_chr6.simRat.chr6 90664 4 + 647215 CTAT -s simRat_chr6.simRat.chr6 90486 4 + 647215 CAAA - -a -s simMouse_chr6.simMouse.chr6 98349 8 + 636262 AATATCAG -s Anc0.Anc0refChr4 39880 6 - 45765 AGTAT--G -s Anc1.Anc1refChr2 71854 8 + 144309 AGTATCAG -s Anc2.Anc2refChr2 9234 6 + 27695 AGTAT--G -s mr.mrrefChr0 93422 8 + 130230 AATATCAG -s mr.mrrefChr0 93589 8 + 130230 AATATCAA -s simCow_chr6.simCow.chr6 99162 6 + 602619 AGTAT--G -s simDog_chr6.simDog.chr6 495342 6 - 593897 AGTAC--G -s simHuman_chr6.simHuman.chr6 94612 6 + 601863 AGTAT--G -s simMouse_chr6.simMouse.chr6 98519 8 + 636262 AATATCAA -s simRat_chr6.simRat.chr6 90668 8 + 647215 AATATCAG -s simRat_chr6.simRat.chr6 90490 8 + 647215 AATATCAG - -a -s simMouse_chr6.simMouse.chr6 98357 1 + 636262 T -s mr.mrrefChr0 93430 1 + 130230 T -s simRat_chr6.simRat.chr6 90498 1 + 647215 C - -a -s simMouse_chr6.simMouse.chr6 98358 1 + 636262 T -s Anc0.Anc0refChr4 39886 1 - 45765 G -s Anc1.Anc1refChr2 71862 1 + 144309 G -s Anc2.Anc2refChr2 9240 1 + 27695 G -s mr.mrrefChr0 93431 1 + 130230 T -s mr.mrrefChr0 93597 1 + 130230 C -s simCow_chr6.simCow.chr6 99168 1 + 602619 G -s simDog_chr6.simDog.chr6 495348 1 - 593897 G -s simHuman_chr6.simHuman.chr6 94618 1 + 601863 G -s simMouse_chr6.simMouse.chr6 98527 1 + 636262 C -s simRat_chr6.simRat.chr6 90676 1 + 647215 C -s simRat_chr6.simRat.chr6 90499 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 98359 5 + 636262 TTCCA -s Anc0.Anc0refChr4 39887 5 - 45765 CACCA -s Anc1.Anc1refChr2 71863 5 + 144309 CACCA -s Anc2.Anc2refChr2 9241 5 + 27695 CACTG -s mr.mrrefChr0 93432 5 + 130230 TTCCA -s mr.mrrefChr0 93598 5 + 130230 TACCA -s simCow_chr6.simCow.chr6 99169 5 + 602619 CAATG -s simDog_chr6.simDog.chr6 495349 5 - 593897 CACTG -s simHuman_chr6.simHuman.chr6 94619 5 + 601863 CACCA -s simMouse_chr6.simMouse.chr6 98528 5 + 636262 TACCA -s simRat_chr6.simRat.chr6 90678 5 + 647215 TAACG -s simRat_chr6.simRat.chr6 90500 5 + 647215 TACCA - -a -s simMouse_chr6.simMouse.chr6 98364 9 + 636262 ACTAGCATT -s Anc0.Anc0refChr4 39892 9 - 45765 ATTAGCATT -s Anc1.Anc1refChr2 71868 9 + 144309 ATTAGCATT -s Anc2.Anc2refChr2 9246 9 + 27695 ATTAGCATT -s mr.mrrefChr0 93437 9 + 130230 ACTAGCATT -s mr.mrrefChr0 93603 9 + 130230 ACTAGCATT -s simCow_chr6.simCow.chr6 99174 9 + 602619 ATTAGCGTT -s simDog_chr6.simDog.chr6 495354 9 - 593897 ACTGGCATC -s simHuman_chr6.simHuman.chr6 94624 9 + 601863 ATTAGCATT -s simMouse_chr6.simMouse.chr6 98533 9 + 636262 ACTAACATT -s simRat_chr6.simRat.chr6 90683 9 + 647215 GCTAGCATT -s simRat_chr6.simRat.chr6 90513 9 + 647215 ACTAACATT - -a -s simMouse_chr6.simMouse.chr6 98373 1 + 636262 C -s Anc0.Anc0refChr4 39901 1 - 45765 T -s Anc1.Anc1refChr2 71877 1 + 144309 T -s Anc2.Anc2refChr2 9255 1 + 27695 T -s mr.mrrefChr0 93446 1 + 130230 C -s mr.mrrefChr0 93612 1 + 130230 C -s simCow_chr6.simCow.chr6 99183 1 + 602619 G -s simDog_chr6.simDog.chr6 495363 1 - 593897 T -s simHuman_chr6.simHuman.chr6 94633 1 + 601863 T -s simMouse_chr6.simMouse.chr6 98542 1 + 636262 C -s simRat_chr6.simRat.chr6 90522 1 + 647215 C - -a -s simMouse_chr6.simMouse.chr6 98374 14 + 636262 AACCAGACAGTTTT -s Anc0.Anc0refChr4 39902 14 - 45765 AACCATACAATTCG -s Anc1.Anc1refChr2 71878 14 + 144309 AACCATACAATTCG -s Anc2.Anc2refChr2 9256 14 + 27695 AACCATACAATGCG -s mr.mrrefChr0 93447 14 + 130230 AACCAGACAGTTTT -s mr.mrrefChr0 93613 14 + 130230 AACCATACAGTTCT -s simCow_chr6.simCow.chr6 99184 14 + 602619 CAACATACAATCCC -s simDog_chr6.simDog.chr6 495364 14 - 593897 AACCATATAATGCG -s simHuman_chr6.simHuman.chr6 94634 14 + 601863 AACCATACAATTCG -s simMouse_chr6.simMouse.chr6 98543 14 + 636262 AACCAGACAGTTCT -s simRat_chr6.simRat.chr6 90692 14 + 647215 ACTCCTTCAGTTGT -s simRat_chr6.simRat.chr6 90523 14 + 647215 AACCAGACAGTTCT - -a -s simMouse_chr6.simMouse.chr6 98388 1 + 636262 T -s Anc0.Anc0refChr4 39916 1 - 45765 C -s Anc1.Anc1refChr2 71892 1 + 144309 C -s Anc2.Anc2refChr2 9270 1 + 27695 C -s mr.mrrefChr0 93461 1 + 130230 T -s mr.mrrefChr0 93627 1 + 130230 C -s simCow_chr6.simCow.chr6 99198 1 + 602619 C -s simDog_chr6.simDog.chr6 495462 1 - 593897 C -s simHuman_chr6.simHuman.chr6 94648 1 + 601863 C -s simMouse_chr6.simMouse.chr6 98557 1 + 636262 C -s simRat_chr6.simRat.chr6 90706 1 + 647215 C -s simRat_chr6.simRat.chr6 90537 1 + 647215 C - -a -s simMouse_chr6.simMouse.chr6 98389 12 + 636262 TACTGGTTAGGA -s Anc0.Anc0refChr4 39917 10 - 45765 TAGCAGTTA--A -s Anc1.Anc1refChr2 71893 10 + 144309 TAGCAGTTA--A -s Anc2.Anc2refChr2 9271 10 + 27695 TAGCAGTTA--A -s mr.mrrefChr0 93462 12 + 130230 TACTGGTTAGGA -s simCow_chr6.simCow.chr6 99199 10 + 602619 TAGCAATTA--A -s simDog_chr6.simDog.chr6 495463 10 - 593897 TAGCAGTTA--A -s simHuman_chr6.simHuman.chr6 94649 10 + 601863 TAGCAGTTA--A -s simRat_chr6.simRat.chr6 90538 12 + 647215 TACCAGTTAGGA - -a -s simMouse_chr6.simMouse.chr6 98401 6 + 636262 CTATCC -s Anc0.Anc0refChr4 39927 6 - 45765 CTAAAC -s Anc1.Anc1refChr2 71903 6 + 144309 CTAAAC -s Anc2.Anc2refChr2 9281 6 + 27695 CTTAAC -s mr.mrrefChr0 93474 6 + 130230 CTATCC -s mr.mrrefChr0 93628 6 + 130230 CTATCC -s simCow_chr6.simCow.chr6 99209 6 + 602619 CTTAGC -s simDog_chr6.simDog.chr6 495473 6 - 593897 CTTAAC -s simHuman_chr6.simHuman.chr6 94659 6 + 601863 CTGAAC -s simMouse_chr6.simMouse.chr6 98558 6 + 636262 CTATCC -s simRat_chr6.simRat.chr6 90707 6 + 647215 CTATCC -s simRat_chr6.simRat.chr6 90550 6 + 647215 CTAGCC - -a -s simMouse_chr6.simMouse.chr6 98407 18 + 636262 ATCCTTTCCCACAAGATG -s Anc0.Anc0refChr4 39934 18 - 45765 ATTCCTTTTCATAAGATA -s Anc1.Anc1refChr2 71910 18 + 144309 ATTCCTTTTCATAAGATA -s Anc2.Anc2refChr2 9288 18 + 27695 ATTCCTGTTCATAAGATA -s mr.mrrefChr0 93480 18 + 130230 ATCCTTTCCCACAAGATG -s mr.mrrefChr0 93635 18 + 130230 ATTGTTTCTCATAAGATG -s simCow_chr6.simCow.chr6 99216 18 + 602619 ATTCCTGCCCATAAGATA -s simDog_chr6.simDog.chr6 495480 17 - 593897 ATTCTT-TTCATAAGATA -s simHuman_chr6.simHuman.chr6 94666 18 + 601863 ATCCCTATTTATAAGATA -s simMouse_chr6.simMouse.chr6 98565 18 + 636262 ACTGTTTCCCATCAGATG -s simRat_chr6.simRat.chr6 90714 18 + 647215 ATTGTTTCTCACAAGATG -s simRat_chr6.simRat.chr6 90557 18 + 647215 ATCCTGTCCCACAAGATG - -a -s simMouse_chr6.simMouse.chr6 98425 6 + 636262 CCGACC -s Anc0.Anc0refChr4 39952 6 - 45765 CATAGC -s Anc1.Anc1refChr2 71928 6 + 144309 CATAGC -s Anc2.Anc2refChr2 9306 6 + 27695 CATAGG -s mr.mrrefChr0 93498 6 + 130230 CCGACC -s mr.mrrefChr0 93653 6 + 130230 GACCCC -s simCow_chr6.simCow.chr6 99234 6 + 602619 CTTAGC -s simDog_chr6.simDog.chr6 495497 6 - 593897 CATATG -s simHuman_chr6.simHuman.chr6 94684 6 + 601863 CATAGT -s simMouse_chr6.simMouse.chr6 98583 6 + 636262 GACCCC -s simRat_chr6.simRat.chr6 90734 6 + 647215 GACTAC -s simRat_chr6.simRat.chr6 90575 6 + 647215 CAGACC - -a -s simMouse_chr6.simMouse.chr6 98431 3 + 636262 CTG -s Anc0.Anc0refChr4 39958 3 - 45765 TTG -s Anc1.Anc1refChr2 71934 3 + 144309 TTG -s Anc2.Anc2refChr2 9312 3 + 27695 TTG -s mr.mrrefChr0 93504 3 + 130230 CTG -s mr.mrrefChr0 93659 3 + 130230 TTG -s simCow_chr6.simCow.chr6 99240 3 + 602619 TTG -s simDog_chr6.simDog.chr6 495503 3 - 593897 TTG -s simHuman_chr6.simHuman.chr6 94690 3 + 601863 TTG -s simMouse_chr6.simMouse.chr6 98589 3 + 636262 TTG -s simRat_chr6.simRat.chr6 90743 3 + 647215 TTG -s simRat_chr6.simRat.chr6 90581 3 + 647215 TTG - -a -s simMouse_chr6.simMouse.chr6 98434 2 + 636262 TA -s Anc0.Anc0refChr4 39961 2 - 45765 CA -s Anc1.Anc1refChr2 71937 2 + 144309 CA -s Anc2.Anc2refChr2 9315 2 + 27695 CA -s mr.mrrefChr0 93507 2 + 130230 TA -s mr.mrrefChr0 93662 2 + 130230 CA -s simCow_chr6.simCow.chr6 99243 2 + 602619 CA -s simDog_chr6.simDog.chr6 495506 2 - 593897 CA -s simHuman_chr6.simHuman.chr6 94693 2 + 601863 TA -s simMouse_chr6.simMouse.chr6 98592 2 + 636262 CA -s simRat_chr6.simRat.chr6 90584 2 + 647215 TA - -a -s simMouse_chr6.simMouse.chr6 98436 3 + 636262 AGA -s Anc0.Anc0refChr4 39963 3 - 45765 AAA -s Anc1.Anc1refChr2 71939 3 + 144309 AAA -s Anc2.Anc2refChr2 9317 3 + 27695 AAA -s mr.mrrefChr0 93509 3 + 130230 AGA -s mr.mrrefChr0 93664 3 + 130230 AGG -s simCow_chr6.simCow.chr6 99245 3 + 602619 GAA -s simDog_chr6.simDog.chr6 495508 3 - 593897 AGA -s simHuman_chr6.simHuman.chr6 94695 3 + 601863 AAA -s simMouse_chr6.simMouse.chr6 98594 3 + 636262 AGG -s simRat_chr6.simRat.chr6 90746 3 + 647215 AGG -s simRat_chr6.simRat.chr6 90586 3 + 647215 AGG - -a -s simMouse_chr6.simMouse.chr6 98439 32 + 636262 TATTAAGCCTTTTTTTTACTGATTTTGCAGGT -s mr.mrrefChr0 93512 29 + 130230 TATTAA---TTTTTTTTACTGATTTTGCAGGT -s simRat_chr6.simRat.chr6 90589 29 + 647215 TTTAAA---TACATCCCACTGGCTTTGCAGAT - -a -s simMouse_chr6.simMouse.chr6 98564 1 + 636262 G -s Anc0.Anc0refChr4 39933 1 - 45765 T -s Anc1.Anc1refChr2 71909 1 + 144309 T -s Anc2.Anc2refChr2 9287 1 + 27695 T -s mr.mrrefChr0 93634 1 + 130230 T -s simCow_chr6.simCow.chr6 99215 1 + 602619 T -s simDog_chr6.simDog.chr6 495479 1 - 593897 T -s simHuman_chr6.simHuman.chr6 94665 1 + 601863 T -s simRat_chr6.simRat.chr6 90713 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 98597 5 + 636262 TTTAA -s Anc0.Anc0refChr4 39966 5 - 45765 TTTAA -s Anc1.Anc1refChr2 71942 5 + 144309 TTTAA -s Anc2.Anc2refChr2 9320 5 + 27695 TTTAA -s mr.mrrefChr0 93667 5 + 130230 TTTAA -s simCow_chr6.simCow.chr6 99248 5 + 602619 TTTAA -s simDog_chr6.simDog.chr6 495511 5 - 593897 TTTAA -s simHuman_chr6.simHuman.chr6 94698 5 + 601863 TTTAA -s simRat_chr6.simRat.chr6 90749 5 + 647215 TTGTA - -a -s simMouse_chr6.simMouse.chr6 98602 10 + 636262 GCATCTCTCC -s Anc0.Anc0refChr4 39971 4 - 45765 G------TCT -s Anc1.Anc1refChr2 71947 10 + 144309 GAACCTTTCT -s Anc2.Anc2refChr2 9325 4 + 27695 G------TCT -s mr.mrrefChr0 93672 10 + 130230 GCATCTCTCC -s simCow_chr6.simCow.chr6 99253 4 + 602619 G------TCA -s simDog_chr6.simDog.chr6 495516 4 - 593897 G------TCT -s simHuman_chr6.simHuman.chr6 94708 10 + 601863 AAACCTTTCT -s simRat_chr6.simRat.chr6 90754 2 + 647215 GC-------- - -a -s simMouse_chr6.simMouse.chr6 98612 2 + 636262 AT -s Anc0.Anc0refChr4 39976 2 - 45765 AT -s Anc1.Anc1refChr2 71958 2 + 144309 AT -s Anc2.Anc2refChr2 9330 2 + 27695 AT -s mr.mrrefChr0 93682 2 + 130230 AT -s simCow_chr6.simCow.chr6 99258 2 + 602619 CT -s simDog_chr6.simDog.chr6 495521 2 - 593897 AT -s simHuman_chr6.simHuman.chr6 94719 2 + 601863 AT - -a -s simMouse_chr6.simMouse.chr6 98614 1 + 636262 C -s Anc0.Anc0refChr4 39978 1 - 45765 C -s Anc1.Anc1refChr2 71960 1 + 144309 C -s Anc2.Anc2refChr2 9332 1 + 27695 C -s mr.mrrefChr0 93684 1 + 130230 C -s simCow_chr6.simCow.chr6 99261 1 + 602619 C -s simDog_chr6.simDog.chr6 495523 1 - 593897 C -s simHuman_chr6.simHuman.chr6 94721 1 + 601863 C - -a -s simMouse_chr6.simMouse.chr6 98615 36 + 636262 TGGCTACAATACCTTGTTCTAGGAGGACTGCAGGGT -s Anc0.Anc0refChr4 39981 22 - 45765 TGGCTGCAAT---TTGTTAA--------GAC---AA -s Anc1.Anc1refChr2 71963 22 + 144309 TGGCTGCAAT---TTGTTAA--------GAC---AA -s Anc2.Anc2refChr2 9335 22 + 27695 AGGCTGCAAT---CACTCAA--------GAC---AA -s mr.mrrefChr0 93685 27 + 130230 TGGCTACAAT-CCTTGTTCT--------TACAGGGT -s simCow_chr6.simCow.chr6 99264 14 + 602619 AGGCTGTGAT---CACT------------------- -s simDog_chr6.simDog.chr6 495526 22 - 593897 AGGCTGCAAT---CACTCAA--------GAC---AA -s simHuman_chr6.simHuman.chr6 94724 22 + 601863 TGGCTGCAAT---TTGTTAA--------CAC---AG -s simRat_chr6.simRat.chr6 90756 17 + 647215 -----------CCTTGTCCT--------TACAGGGT - -a -s simMouse_chr6.simMouse.chr6 98651 6 + 636262 GTGGTC -s Anc0.Anc0refChr4 40003 6 - 45765 GTGGTC -s Anc1.Anc1refChr2 71985 6 + 144309 GTGGTC -s Anc2.Anc2refChr2 9357 6 + 27695 GGGGCC -s mr.mrrefChr0 93712 6 + 130230 GTGGTC -s simDog_chr6.simDog.chr6 495548 6 - 593897 GGGGCC -s simHuman_chr6.simHuman.chr6 94755 6 + 601863 GTGGTC -s simRat_chr6.simRat.chr6 90774 6 + 647215 CTGGTC - -a -s simMouse_chr6.simMouse.chr6 98657 30 + 636262 TAATTTGTAGGAAGGCTAGGATATGTTTGC -s Anc0.Anc0refChr4 40009 29 - 45765 CAATTTGTGGGG-GCCTAGAATATGTTTGC -s Anc1.Anc1refChr2 71991 30 + 144309 CAATTTGTGGGGAGCCTAGAATATGTTTGC -s Anc2.Anc2refChr2 9365 29 + 27695 CAATTTGTGGTG-GCCTAGAATATGTTTGC -s mr.mrrefChr0 93718 30 + 130230 TAATTTGTGGGAAGCCTAGGATATGTTTGC -s simCow_chr6.simCow.chr6 99280 29 + 602619 CAACTTTTGTTG-GCCTAAAGTATGTTTGC -s simDog_chr6.simDog.chr6 495556 26 - 593897 CACTTTGGGGTA-GGCTAGAACATGC---C -s simHuman_chr6.simHuman.chr6 94761 30 + 601863 CAATTCGTGGGGAGCCTAGAATATGTGTGC -s simRat_chr6.simRat.chr6 90780 28 + 647215 TAATTTGTGGGAAGCCTAGG--ATGTTTGT - -a -s simMouse_chr6.simMouse.chr6 98687 43 + 636262 CAAACTCTCTCACCAGCAAAACACCTGCAAAACTTGCCCCAGA -s Anc0.Anc0refChr4 40038 30 - 45765 A------TCTCATCACCAAAGCTTCA-------TGCACCTAGA -s Anc1.Anc1refChr2 72021 34 + 144309 AAAG--CTCTCATCACCAAAGCTTCA-------TGCACCTAGA -s Anc2.Anc2refChr2 9394 30 + 27695 A------CCTCATAACCAAAGCTTCA-------TGCACCTAGA -s mr.mrrefChr0 93748 43 + 130230 CAAACTCTCTCACCAGCAAAACACCAGCAAAACTTGACCCAGA -s simCow_chr6.simCow.chr6 99315 30 + 602619 A------CCTCATGACCAAAACTTCA-------TGCACCCAGG -s simDog_chr6.simDog.chr6 495582 30 - 593897 A------CCTCATAACCAATGTGTTG-------TGCACCTAGA -s simHuman_chr6.simHuman.chr6 94791 34 + 601863 AAAG--CTCTCATCACCAAAGCTTCA-------TGCACCTGGA -s simRat_chr6.simRat.chr6 90808 43 + 647215 CAAACTCTCTCACCAGCAAAACACCAGCAAAACTTGACCAAGA - -a -s simMouse_chr6.simMouse.chr6 98730 5 + 636262 ATCTT -s Anc0.Anc0refChr4 40068 5 - 45765 ATAGT -s Anc1.Anc1refChr2 72055 5 + 144309 ATAGT -s Anc2.Anc2refChr2 9424 5 + 27695 ATAGT -s mr.mrrefChr0 93791 5 + 130230 ATCTT -s simCow_chr6.simCow.chr6 99370 5 + 602619 ATTGT -s simDog_chr6.simDog.chr6 495612 5 - 593897 ATAAT -s simHuman_chr6.simHuman.chr6 94825 5 + 601863 ATAGT -s simRat_chr6.simRat.chr6 90851 5 + 647215 ATCCT - -a -s simMouse_chr6.simMouse.chr6 98735 64 + 636262 GTTTTAAGTTGTAATAGTTATCAGATTACATTAACTCTTAAAATACAATTAGATAATTGTTGTA -s Anc0.Anc0refChr4 40073 64 - 45765 GGTTTAAGTTGTGACTGCTATCAGGTTATTTTAACTCTTTGATTACAATTATATAATTGTAATG -s Anc1.Anc1refChr2 72060 64 + 144309 GGTTTAAGTTGTGACTGCTATCAGGTTATTTTAACTCTTTGATTACAATTATATAATTGTAATG -s Anc2.Anc2refChr2 9429 64 + 27695 GGTTTAAATTGTGACTGCTATCATGTTATTTTAACTTTTAGATTACAATTATATAATTGTAATG -s mr.mrrefChr0 93796 64 + 130230 GTTTTAAGTTGTAATAGTTATCAGATTATATTAACTCTTTAAATACAATTAGATAATTGTTGTA -s simCow_chr6.simCow.chr6 99375 64 + 602619 AACCTTGCTTGTAACTGCTACTCAGTTATTATAACCTTTAGATTATAATTATATAATTGTGCTG -s simDog_chr6.simDog.chr6 495617 64 - 593897 GGTTCAAATTGTGAATCCTATCATGGTATTTCCACTTTTAGATCACACTTATATGATTGTAATG -s simHuman_chr6.simHuman.chr6 94830 64 + 601863 GGTTTAAGTTGTTACTGATATCAGGTCTTTTTAACTCTTTGACTACAATTATATACCTTTATTG -s simRat_chr6.simRat.chr6 90859 64 + 647215 CTTTTAAGTTGTAATATTTATCAGATTATCTTAACTCCTTAGGTACAATTAGATAATTGTTGTA - -a -s simMouse_chr6.simMouse.chr6 98799 8 + 636262 ATAATACA -s Anc0.Anc0refChr4 40137 8 - 45765 GTAAAACA -s Anc1.Anc1refChr2 72124 8 + 144309 GTAAAACA -s Anc2.Anc2refChr2 9493 8 + 27695 GTAAAACA -s mr.mrrefChr0 93860 8 + 130230 GTAATACA -s simCow_chr6.simCow.chr6 99445 8 + 602619 GTAAAACA -s simDog_chr6.simDog.chr6 495681 3 - 593897 -----CCA -s simHuman_chr6.simHuman.chr6 94894 8 + 601863 GCAAAACA -s simRat_chr6.simRat.chr6 90923 8 + 647215 GTATTAGA - -a -s simMouse_chr6.simMouse.chr6 98807 1 + 636262 A -s Anc0.Anc0refChr4 40158 1 - 45765 A -s Anc1.Anc1refChr2 72145 1 + 144309 A -s Anc2.Anc2refChr2 9514 1 + 27695 A -s mr.mrrefChr0 93868 1 + 130230 A -s simCow_chr6.simCow.chr6 99466 1 + 602619 A -s simDog_chr6.simDog.chr6 495697 1 - 593897 A -s simHuman_chr6.simHuman.chr6 94915 1 + 601863 A -s simRat_chr6.simRat.chr6 90931 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 98808 16 + 636262 AATAATTAAATCAGCA -s Anc0.Anc0refChr4 40159 16 - 45765 AATGGTTAAATAAGAA -s Anc1.Anc1refChr2 72146 16 + 144309 AATGGTTAAATAAGAA -s Anc2.Anc2refChr2 9521 16 + 27695 ATTGGTTAAATAAGAA -s mr.mrrefChr0 93869 16 + 130230 AATAATTAAATAAGCA -s simCow_chr6.simCow.chr6 99473 16 + 602619 AGTGCTTAAATAATAA -s simDog_chr6.simDog.chr6 495704 16 - 593897 ATTGGCTAAATAAGAA -s simHuman_chr6.simHuman.chr6 94916 16 + 601863 AATGGTTAAATAAGAA -s simRat_chr6.simRat.chr6 90932 16 + 647215 AATAATTAAATAGGCA - -a -s simMouse_chr6.simMouse.chr6 98824 1 + 636262 G -s Anc0.Anc0refChr4 40179 1 - 45765 G -s Anc1.Anc1refChr2 72166 1 + 144309 G -s Anc2.Anc2refChr2 9541 1 + 27695 G -s mr.mrrefChr0 93885 1 + 130230 G -s simCow_chr6.simCow.chr6 99493 1 + 602619 G -s simDog_chr6.simDog.chr6 495724 1 - 593897 G -s simHuman_chr6.simHuman.chr6 94936 1 + 601863 G -s simRat_chr6.simRat.chr6 90948 1 + 647215 G - -a -s simMouse_chr6.simMouse.chr6 98825 47 + 636262 CAAGTGCCTCAAACTTCTTGTCACATCAGTCTAACAACTCCTACACA -s Anc0.Anc0refChr4 40180 45 - 45765 CAAATGCCTGAATCTACTTGTCAA--CAGTCTAACAGCTCCTACACA -s Anc1.Anc1refChr2 72167 45 + 144309 CAAATGCCTGAATCTACTTGTCAA--CAGTCTAACAGCTCCTACACA -s Anc2.Anc2refChr2 9542 45 + 27695 TAGATGCCTGAATCTACTTGTCAA--GAGTCTAACAGCTCCTACACA -s mr.mrrefChr0 93886 47 + 130230 CAAGTGCCTCAAACTTCTTGTCACATCAGTCTAACAACTCCTACACA -s simCow_chr6.simCow.chr6 99494 45 + 602619 TAGGTGCCTGAATCTACTTGTCAA--GTGTCTAACAGCTCTTACACA -s simDog_chr6.simDog.chr6 495744 45 - 593897 TAGATACCTGAATCTACTTGTCAA--GAGTCTAAGAGCTCCTATACA -s simHuman_chr6.simHuman.chr6 94937 45 + 601863 CAATTGCCTGAATCTACCTGTCAA--CAGTCTAACAGCACCTACACA -s simRat_chr6.simRat.chr6 90949 46 + 647215 CAAGTACC-CAAACTTCTTGTTACATCAATCTGACAACTCCCACACA - -a -s simMouse_chr6.simMouse.chr6 98872 6 + 636262 AATACA -s Anc0.Anc0refChr4 40225 6 - 45765 AATACA -s Anc1.Anc1refChr2 72212 6 + 144309 AATACA -s Anc2.Anc2refChr2 9587 6 + 27695 AGTACA -s mr.mrrefChr0 93933 6 + 130230 AATACA -s simCow_chr6.simCow.chr6 99539 6 + 602619 ACCACA -s simDog_chr6.simDog.chr6 96845 6 + 593897 AGTAGG -s simHuman_chr6.simHuman.chr6 94982 6 + 601863 AATACA -s simRat_chr6.simRat.chr6 90995 6 + 647215 ATTACA - -a -s simMouse_chr6.simMouse.chr6 98878 44 + 636262 CAATGCCATTATTGTTGCCATCTAGGCCACAAGAAGCTTGCCGA -s Anc0.Anc0refChr4 40236 44 - 45765 CAATGTCATTTTTGTTGCCATCCAAGCCACACCAAGTTTGACAA -s Anc1.Anc1refChr2 72223 44 + 144309 CAATGTCATTTTTGTTGCCATCCAAGCCACACCAAGTTTGACAA -s Anc2.Anc2refChr2 9598 44 + 27695 CAATGTCATTTCTGTTGCCATCCAAGCCACACCAAGTTTGAGTC -s mr.mrrefChr0 93939 44 + 130230 CAATGCCATTTTTGTTGCCATCCAGGCCACAAGAAGCTTGCCAA -s simCow_chr6.simCow.chr6 99550 43 + 602619 CAATGTTATTACTGTTGCCGTCTAAGCCACACCAAGTCTGATG- -s simDog_chr6.simDog.chr6 96856 44 + 593897 TAATGTCATTTCTGTTGCCATCCAAGCCACATCAAGTTTGAGTC -s simHuman_chr6.simHuman.chr6 94993 44 + 601863 CAATCTCATTTTTGTTGCCATGCTTGCCATACCAAGGTTGACAA -s simRat_chr6.simRat.chr6 91001 44 + 647215 TAATGCCATTTTTGTTCCTATCCAGGCCACAAGGAGTTTGCCAA - -a -s simMouse_chr6.simMouse.chr6 98922 9 + 636262 CCCCACATA -s Anc0.Anc0refChr4 40280 9 - 45765 CCCCACAAA -s Anc1.Anc1refChr2 72267 9 + 144309 CCCCACAAA -s Anc2.Anc2refChr2 9642 9 + 27695 CCCCACAAA -s mr.mrrefChr0 93983 9 + 130230 CCCCACAAA -s simCow_chr6.simCow.chr6 99593 9 + 602619 CCCCACAAA -s simDog_chr6.simDog.chr6 96900 9 + 593897 CTTAACAAA -s simHuman_chr6.simHuman.chr6 95037 9 + 601863 CCCCACAAA -s simRat_chr6.simRat.chr6 91046 9 + 647215 CCCCACAAG - -a -s simMouse_chr6.simMouse.chr6 98931 4 + 636262 AACG -s Anc0.Anc0refChr4 40289 4 - 45765 AACA -s Anc1.Anc1refChr2 72276 4 + 144309 AACA -s Anc2.Anc2refChr2 9654 4 + 27695 AACA -s mr.mrrefChr0 93992 4 + 130230 AACA -s simCow_chr6.simCow.chr6 99605 4 + 602619 AACA -s simDog_chr6.simDog.chr6 96911 3 + 593897 -ACA -s simHuman_chr6.simHuman.chr6 95046 4 + 601863 AACA -s simRat_chr6.simRat.chr6 91055 4 + 647215 AACA - -a -s simMouse_chr6.simMouse.chr6 98935 58 + 636262 TGGATCATTCCAGCTTACTACTAACTTGCTAGGCTCGAAATTTGTCAATTTATGAGCA -s Anc0.Anc0refChr4 40293 58 - 45765 GGAATCACTCAAGCCTACTACCAACTTGCTAAGCTTAGAATTTCTTTATTTATTAACA -s Anc1.Anc1refChr2 72280 58 + 144309 GGAATCACTCAAGCCTACTACCAACTTGCTAAGCTTAGAATTTCTTTATTTATTAACA -s Anc2.Anc2refChr2 9658 58 + 27695 TGAGTCACTCAAGCCTGCTCTCAACTTGCTAAGCTTAGAATTTCTTTATTTATTAACA -s mr.mrrefChr0 93996 58 + 130230 GGAATCATTCCAGCTTACTACTAACTTGCTAGGCTCAAAATTTGTCAATTTATGAGCA -s simCow_chr6.simCow.chr6 99610 58 + 602619 AGAGTCACTCAAGCTTGCTCTCAACTTGCTAAGCTTAAAATTTCTCCATTTATTAACA -s simDog_chr6.simDog.chr6 96914 58 + 593897 TGAGTCACTCAAGCCCGCTCTTGACTTGCTAGGCTTTGCATTCCTTTAATTATTAACA -s simHuman_chr6.simHuman.chr6 95050 58 + 601863 GGAATCCCTCTGGCCTACTACCAACTTGCTAAGCTTAGAACTTCTGGATTTACTAACA -s simRat_chr6.simRat.chr6 91059 58 + 647215 GGAATCATTCCAGCTTACTATTAGCTTTCCAGGCTCAAAATTTGTCAATTCATGAGCA - -a -s simMouse_chr6.simMouse.chr6 98993 28 + 636262 GCTGGAATGTGGGGTTGGTAAATACCAT -s Anc0.Anc0refChr4 40351 28 - 45765 TCTAGAACTTGCTATTGGCAAGTATCAC -s Anc1.Anc1refChr2 72338 28 + 144309 TCTAGAACTTGCTATTGGCAAGTATCAC -s Anc2.Anc2refChr2 9729 28 + 27695 TCTAGAACTTGCTATTGGCAAGTATCAC -s mr.mrrefChr0 94054 28 + 130230 GCTGGAATGTGGGGTTGGTAAATACCAT -s simCow_chr6.simCow.chr6 99681 28 + 602619 TCTAGAATTTTTGATTGGCAAATATCAT -s simDog_chr6.simDog.chr6 96985 28 + 593897 TCTAGAACTTGCTATTGGCAAGTATCAC -s simHuman_chr6.simHuman.chr6 95108 3 + 601863 -------------------------CAC -s simRat_chr6.simRat.chr6 91117 28 + 647215 GCTGGAATGTGGGGTTGGCAAATACTAT - -a -s simMouse_chr6.simMouse.chr6 99021 47 + 636262 ATTTAGGTGGAATGTGGGGTTGGTAAATACCATATTTAGGTTTATTA -s Anc0.Anc0refChr4 40379 29 - 45765 ATAC--------------GGTGGTGAA-G---GCATTAGATTTATTC -s Anc1.Anc1refChr2 72366 32 + 144309 ATAC--------------GGTGGTGAA-GAGAGCATTAGATTTATTC -s Anc2.Anc2refChr2 9757 29 + 27695 ATAC--------------GGTGGTAAG-G---GCATTAGATTTATTC -s mr.mrrefChr0 94082 32 + 130230 ATTT--------------GTTGGTGAA-ACGATCATTAGGTTTATTA -s simCow_chr6.simCow.chr6 99711 29 + 602619 TTAT--------------GGTGAACAG-G---GCATCAGATGGATTC -s simDog_chr6.simDog.chr6 97013 29 + 593897 ATAC--------------GGTGGTAAG-G---ACTTTAAATTTATTC -s simHuman_chr6.simHuman.chr6 95111 24 + 601863 A----------------------TGAA-GAGAGCATTAGATTTATTC -s simRat_chr6.simRat.chr6 91145 32 + 647215 ATAT--------------GATGGTGAA-ACGAACATTAGGTTTAATT - -a -s simMouse_chr6.simMouse.chr6 99068 49 + 636262 GGACCAGTAGGCTTTTGCCATTAGGCTTTGGGCAAATGAACCATTGACT -s Anc0.Anc0refChr4 40414 33 - 45765 GGA--------------ACATTAAGCT--AGGCACATGAACCATTTACT -s Anc1.Anc1refChr2 72404 35 + 144309 GGA--------------ACATTAAGCTTTAGGCACATGAACCATTTACT -s Anc2.Anc2refChr2 9792 33 + 27695 GCA--------------ACATTAAGCT--AGGCACATGAACCATTTACT -s mr.mrrefChr0 94114 35 + 130230 GGA--------------CCATTAGGCTTTGGGCACATGAACCATTGACT -s simCow_chr6.simCow.chr6 99746 32 + 602619 G-A--------------ACATTAAGCT--AAGTGCAAGAACCATTTGCT -s simDog_chr6.simDog.chr6 97048 33 + 593897 GCA--------------ATGTTAAGCC--AGGCACATGAACCATTTACT -s simHuman_chr6.simHuman.chr6 95141 35 + 601863 GGA--------------ACATTAAGGTTTCGGCACATGACCCATTTACT -s simRat_chr6.simRat.chr6 91177 35 + 647215 GGA--------------CCACTGGGCTTTGGGCACATGAACCATTCACT - -a -s simMouse_chr6.simMouse.chr6 99117 40 + 636262 TTAGTGAAAAGCCTGTAGTTTAGTTCAGAATTCCTTAATT -s Anc0.Anc0refChr4 40447 36 - 45765 GTAGTGAAAAGTCTGTAGCCTAGT----AACTTCACAAAC -s Anc1.Anc1refChr2 72439 36 + 144309 GTAGTGAAAAGTCTGTAGCCTAGT----AACTTCACAAAC -s Anc2.Anc2refChr2 9825 36 + 27695 GTAGTGAAAAGTCTGTACGCTAGT----AACTTCACAAAC -s mr.mrrefChr0 94149 40 + 130230 TTAGTGAAAAGCCTGTAGCCTAGTTCAGAATTCCTTAATT -s simCow_chr6.simCow.chr6 99778 36 + 602619 GTAGTGAAAAGTCTGTTTGCTAGT----AGCTTCACTAAC -s simDog_chr6.simDog.chr6 97081 36 + 593897 GTAGTGAAAAGTCTATACGCTAGT----CACTTCACAAAG -s simHuman_chr6.simHuman.chr6 95181 36 + 601863 GTAGTGAAAAGTCGGTAGCCTACT----AACTTAACAAAC -s simRat_chr6.simRat.chr6 91212 38 + 647215 TTAGTG--AAGCCTGTAGCCTAGTTCAAGATTCCTCCGTC - -a -s simMouse_chr6.simMouse.chr6 99157 31 + 636262 CACTAGCCCGGCTCACACCCCATATAATGAC -s Anc0.Anc0refChr4 40483 31 - 45765 TATTGGTGTTGCTGACAATCAATATAGGTGC -s Anc1.Anc1refChr2 72475 31 + 144309 TATTGGTGTTGCTGACAATCAATATAGGTGC -s Anc2.Anc2refChr2 9861 31 + 27695 TATTGGTGTTGCTGACAATCAATATAGGTGC -s mr.mrrefChr0 94189 31 + 130230 CACTAGCCCGGCTCACACCCCATATAATGAC -s simCow_chr6.simCow.chr6 99821 31 + 602619 TACTGGCCTGTCTGACAACCAGTATAACTGC -s simDog_chr6.simDog.chr6 97117 31 + 593897 TATTGGTGTTGCTGACAATCAATATAGGTGC -s simHuman_chr6.simHuman.chr6 95217 2 + 601863 TA----------------------------- -s simRat_chr6.simRat.chr6 91250 31 + 647215 GACTAGGCCGGCTCACACCCCATATAACAAC - -a -s simMouse_chr6.simMouse.chr6 99188 46 + 636262 TGTCCGTCTAGTAAACTCCTAAAATGGATGTGCAGCAACCCCTTAA -s Anc0.Anc0refChr4 40514 23 - 45765 CTTACACTT-----------------------TAGTGACCCTTTAA -s Anc1.Anc1refChr2 72506 23 + 144309 CTTACACTT-----------------------TAGTGACCCTTTAA -s Anc2.Anc2refChr2 9892 23 + 27695 CTTACACTT-----------------------TAGTGACCCTCTAA -s mr.mrrefChr0 94220 44 + 130230 TGTCCGTCTAG--AACTCCTAAAATGGATGTGCAGCAACCCCTTAA -s simCow_chr6.simCow.chr6 99856 23 + 602619 CTTACACTC-----------------------TGGCAACCCGCTAA -s simDog_chr6.simDog.chr6 97148 23 + 593897 CTTACACTT-----------------------TAGTGACCCTCTAA -s simHuman_chr6.simHuman.chr6 95219 4 + 601863 ------------------------------------------TTGA -s simRat_chr6.simRat.chr6 91281 44 + 647215 CTTCCATTTAG--AACCTCCTAAATGGATCTGCAGCAACCCCCTAA - -a -s simMouse_chr6.simMouse.chr6 99234 38 + 636262 CAGGAAAATAGGATATAGGACAGTTTCCAGAGAGGACC -s Anc0.Anc0refChr4 40537 38 - 45765 CAGGGATGTAGGATATAAGACAGTTAAGAGAAAGGACT -s Anc1.Anc1refChr2 72529 38 + 144309 CAGGGATGTAGGATATAAGACAGTTAAGAGAAAGGACT -s Anc2.Anc2refChr2 9915 38 + 27695 CAAGGATGTAGGATATAAGGCAATCAAGAGAAAGGACT -s mr.mrrefChr0 94264 38 + 130230 CAGGAAAATAGGATATAGGACAGTTTCCAGAGAGGACC -s simCow_chr6.simCow.chr6 99879 37 + 602619 CAAGG-TGTAGGACATAAGGCAATCAAGAGATATGACT -s simDog_chr6.simDog.chr6 97171 38 + 593897 CAAGGATATAGGCTATAGGGCCATCAAGAGAAAGGGCT -s simHuman_chr6.simHuman.chr6 95223 38 + 601863 CAGGGATGTCAAAGATAAGATAGTTAAGAGAAAGAACT -s simRat_chr6.simRat.chr6 91326 38 + 647215 CCGGGAGATAGGATATAGGAGAGTTTCCAGAGAGGACC - -a -s simMouse_chr6.simMouse.chr6 99272 17 + 636262 CTTTGGTAATTTACATC -s Anc0.Anc0refChr4 40630 16 - 45765 CTCTGTGAATTTGCAA- -s Anc1.Anc1refChr2 72645 16 + 144309 CTCTGTGAATTTGCAA- -s Anc2.Anc2refChr2 10008 16 + 27695 CTCTGTGAATTTGCAA- -s mr.mrrefChr0 94340 17 + 130230 CTTTGGGAATTTGCATC -s simCow_chr6.simCow.chr6 99920 16 + 602619 CTCTGTGTATTTGAAT- -s simDog_chr6.simDog.chr6 97262 9 + 593897 -------AGCATGCCA- -s simHuman_chr6.simHuman.chr6 95363 16 + 601863 CTCTGTGAATTTGCAG- -s simRat_chr6.simRat.chr6 91406 17 + 647215 CTTTGGGAATTTGCACC - -a -s simMouse_chr6.simMouse.chr6 99289 35 + 636262 CGCTTGCTTCAGCTCATTGATGAAGATATGGAACA -s Anc0.Anc0refChr4 40646 35 - 45765 AGCTTGTGTCAGCTTATTGATAAAGATATGGAAGA -s Anc1.Anc1refChr2 72661 35 + 144309 AGCTTGTGTCAGCTTATTGATAAAGATATGGAAGA -s Anc2.Anc2refChr2 10024 35 + 27695 AGCTTGTGTCAGCTTATTGATAAAGATACAGAAGA -s mr.mrrefChr0 94357 35 + 130230 CGCTTGCTTCAGCTCATTGATGAAGATATGGAACA -s simCow_chr6.simCow.chr6 99937 35 + 602619 GGCTTGTCTCAGCTCATTGCTAAAGATACAGAAAA -s simDog_chr6.simDog.chr6 97271 35 + 593897 AGCTAGTGTGAGCTTATTGATATAGATGCAGAAGA -s simHuman_chr6.simHuman.chr6 95379 35 + 601863 AGCTTGTGCCAGCTTGTTGATAAAGATATGGAATA -s simRat_chr6.simRat.chr6 91423 34 + 647215 CACTCGCTTGAGCCCATTGATGAA-ACAGGCAGCA - -a -s simMouse_chr6.simMouse.chr6 99324 1 + 636262 T -s Anc0.Anc0refChr4 40681 1 - 45765 A -s Anc1.Anc1refChr2 72696 1 + 144309 A -s Anc2.Anc2refChr2 10059 1 + 27695 A -s mr.mrrefChr0 94392 1 + 130230 T -s simCow_chr6.simCow.chr6 99972 1 + 602619 A -s simDog_chr6.simDog.chr6 97307 1 + 593897 A -s simHuman_chr6.simHuman.chr6 95414 1 + 601863 A -s simRat_chr6.simRat.chr6 91457 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 99325 39 + 636262 GTAGAATATGCGGGCAGGCAATTCCTAGGATTTCTCAAT -s Anc0.Anc0refChr4 40682 28 - 45765 CCAGCATAAATAGGCAGGCAA----TAGGCTT------- -s Anc1.Anc1refChr2 72697 32 + 144309 CCAGCATAAATAGGCAGGCAACTCCTAGGCTT------- -s Anc2.Anc2refChr2 10060 28 + 27695 CCAGCATAAACAGGCAGGCAA----TAGGCTT------- -s mr.mrrefChr0 94393 39 + 130230 GCAGCATATGTGGGCAGGCAATTCCTAGGATTTCTCAAT -s simCow_chr6.simCow.chr6 99973 28 + 602619 GCAGCATAAACAGTCAGGCAG----TAAGCTT------- -s simDog_chr6.simDog.chr6 97308 18 + 593897 CTA----------GCAGGCAA----TAGAGTT------- -s simHuman_chr6.simHuman.chr6 95415 32 + 601863 CCAGCATAGATAGGCAGGCTACTCCTAGGCTT------- -s simRat_chr6.simRat.chr6 91463 39 + 647215 GCAGCATTTGTGGGCAGGTAATTCCTAGGATATCTCAAT - -a -s simMouse_chr6.simMouse.chr6 99364 22 + 636262 TCAACTTAGACAGATCAGATTC -s Anc0.Anc0refChr4 4665 21 + 45765 TCA-GGTAAACAAATAAGATTT -s Anc1.Anc1refChr2 71155 21 - 144309 TCA-GGTAAACAAATAAGATTT -s Anc2.Anc2refChr2 17212 21 - 27695 TCA-GGCAAACGAGTAAGATTT -s mr.mrrefChr0 94432 21 + 130230 TCA-CTTAGACAAATCAGATTC -s simCow_chr6.simCow.chr6 502235 21 - 602619 TCA-GGCAAACTACTAAGACTC -s simDog_chr6.simDog.chr6 496091 21 - 593897 CCA-GGCAAACGAGTAAGCTTT -s simHuman_chr6.simHuman.chr6 505981 21 - 601863 TCA-GCTGAACAAATTAGATCT -s simRat_chr6.simRat.chr6 91502 21 + 647215 TCA-CTTATACAAATCAGAATC - -a -s simMouse_chr6.simMouse.chr6 99386 13 + 636262 ATACACCAAGAAC -s Anc0.Anc0refChr4 4690 13 + 45765 ATGTAAGTAAAAC -s Anc1.Anc1refChr2 71180 13 - 144309 ATGTAAGTAAAAC -s Anc2.Anc2refChr2 17237 13 - 27695 ATGTAAGTAAAAC -s mr.mrrefChr0 94453 13 + 130230 ATGCACCAAGAAC -s simCow_chr6.simCow.chr6 502260 13 - 602619 ATGTTTGTAGAAC -s simDog_chr6.simDog.chr6 496116 13 - 593897 ATGTAAGTAAGAC -s simHuman_chr6.simHuman.chr6 506006 13 - 601863 ATGTAAGCAAAAC -s simRat_chr6.simRat.chr6 91523 12 + 647215 ATGCAC-AAGAAC - -a -s simMouse_chr6.simMouse.chr6 99399 9 + 636262 TAACCAAAC -s Anc0.Anc0refChr4 4703 9 + 45765 TAACTAAGC -s Anc1.Anc1refChr2 71193 9 - 144309 TAACTAAGC -s Anc2.Anc2refChr2 17250 9 - 27695 CAACTAAGC -s mr.mrrefChr0 94466 9 + 130230 TAACCAAAC -s simCow_chr6.simCow.chr6 502273 9 - 602619 CAGCTAAGC -s simDog_chr6.simDog.chr6 496130 9 - 593897 CAACTAAGC -s simHuman_chr6.simHuman.chr6 506019 9 - 601863 TAACTAAGC -s simRat_chr6.simRat.chr6 91535 9 + 647215 TAACCAAAT - -a -s simMouse_chr6.simMouse.chr6 99408 19 + 636262 CCCCTTCTTGGGAATGTGA -s Anc0.Anc0refChr4 4713 19 + 45765 CCTCTTCAAGGGAGTGTCC -s Anc1.Anc1refChr2 71203 19 - 144309 CCTCTTCAAGGGAGTGTCC -s Anc2.Anc2refChr2 17260 19 - 27695 CCTCTTCAAGGGAGTGCCC -s mr.mrrefChr0 94476 19 + 130230 CCTCTTCTTGGGAATGTGA -s simCow_chr6.simCow.chr6 502283 19 - 602619 CCTATTTGATGGAGTGCCC -s simDog_chr6.simDog.chr6 496140 19 - 593897 CCTCTTCAAGGGAGTGCCC -s simHuman_chr6.simHuman.chr6 506029 19 - 601863 CCTCTTCAAGGGAGTGTTC -s simRat_chr6.simRat.chr6 91545 19 + 647215 CCTCCTCTTGGGAATGTGA - -a -s simMouse_chr6.simMouse.chr6 99427 79 + 636262 AATGGCGACATGCGGAACAATAAATTCTGTCCAAAGTCCTCATGTCCGGAGTCCTCAATGCTTTTGTCAAGGGTAGAGT -s Anc0.Anc0refChr4 4732 20 + 45765 AATG--------------------------------------------------TCA---CTTTCTCTAAGGA------ -s Anc1.Anc1refChr2 71222 29 - 144309 AATG--------------------------------------------------TCACTGCTTTCTCTAAGGATAGATT -s Anc2.Anc2refChr2 17279 20 - 27695 AATG--------------------------------------------------TCC---CTCTCAGTAAGGA------ -s mr.mrrefChr0 94495 64 + 130230 AATGGCGACATGCGGAACAATAAATTC---------------TGTCCGGAGTCCTCAATGCTTTCTCCAAGGGTAGAGT -s simCow_chr6.simCow.chr6 502303 15 - 602619 AATG--------------------------------------------------TGC---CCCTCATT----------- -s simDog_chr6.simDog.chr6 496159 20 - 593897 AGAT--------------------------------------------------CCC---CTCTCAGTAAGGA------ -s simHuman_chr6.simHuman.chr6 506048 29 - 601863 AATG--------------------------------------------------TTACTGTGTTCTCTAAGGATAGATT -s simRat_chr6.simRat.chr6 91564 64 + 647215 AATGGTGACATGCAGAACATTAAATCC---------------TGTCTGAAGTCCTCAATGCTTTCTCCAAGGGTAGAGT - -a -s simMouse_chr6.simMouse.chr6 99506 19 + 636262 CCTTAGTGCTTTTTTGAAG -s Anc1.Anc1refChr2 71251 17 - 144309 CCT--GCGCTCCTTTGGAG -s mr.mrrefChr0 94559 19 + 130230 CCTTAGTGCTTTTTTGAAG -s simHuman_chr6.simHuman.chr6 506089 17 - 601863 CCT--GCGCTCCTTTGGAG -s simRat_chr6.simRat.chr6 91628 19 + 647215 CCTTAGTGCTTGTTTGAAG - -a -s simMouse_chr6.simMouse.chr6 99525 25 + 636262 AGACCTTTGTGTATGCAGACTGTTG -s Anc0.Anc0refChr4 4752 14 + 45765 -----------TACACAGAGTGTGG -s Anc1.Anc1refChr2 71268 22 - 144309 GGGCCT---TCTACACAGAGTGTGG -s Anc2.Anc2refChr2 17299 14 - 27695 -----------TCCACAGAGTGTGG -s mr.mrrefChr0 94578 25 + 130230 AGGCCTCTGTGTATGCAGACTGTTG -s simCow_chr6.simCow.chr6 502318 13 - 602619 ------------CTACAGGGTTTGG -s simDog_chr6.simDog.chr6 496179 14 - 593897 -----------TCCACAGAATGAGG -s simHuman_chr6.simHuman.chr6 506108 22 - 601863 GGGCCT---TCTACACAGAGTGTGG -s simRat_chr6.simRat.chr6 91647 25 + 647215 AGGCCTCTGTATATGCAGACTGTTG - -a -s simMouse_chr6.simMouse.chr6 99550 9 + 636262 TAATGCCAT -s Anc0.Anc0refChr4 4766 9 + 45765 CAATGTCAT -s Anc1.Anc1refChr2 71290 9 - 144309 CAATGTCAT -s Anc2.Anc2refChr2 17313 9 - 27695 CAACATCAT -s mr.mrrefChr0 94603 9 + 130230 TAATGTCAT -s simCow_chr6.simCow.chr6 502331 9 - 602619 TGACATCAT -s simDog_chr6.simDog.chr6 496196 9 - 593897 CAACATCAT -s simHuman_chr6.simHuman.chr6 506130 9 - 601863 CAATGTCAT -s simRat_chr6.simRat.chr6 91672 9 + 647215 TGATGTCAG - -a -s simMouse_chr6.simMouse.chr6 99559 48 + 636262 TGCCAATGGAAAATACCACCAACACACAGAACACACAGTATTGAGTCA -s Anc0.Anc0refChr4 4775 39 + 45765 TGCCAATGGAAAATACCACCAACACA-AGA--------CATTAAGTCA -s Anc1.Anc1refChr2 71299 39 - 144309 TGCCAATGGAAAATACCACCAACACA-AGA--------CATTAAGTCA -s Anc2.Anc2refChr2 17322 39 - 27695 TGCCAATGCAAAGTACAACCAACACA-AGA--------CATTAAGTCA -s mr.mrrefChr0 94612 39 + 130230 TGCCAATGGAAAATACCACCAACACA-AGA--------TATTAAGTCA -s simCow_chr6.simCow.chr6 502340 39 - 602619 TGCCAACGCAAAGTATAACCAACACA-AGA--------CATTAAGTCA -s simDog_chr6.simDog.chr6 496205 39 - 593897 TGCCAATGCGAAGTACAACCAACACA-GTA--------CATTAAGTTA -s simHuman_chr6.simHuman.chr6 506139 39 - 601863 TGCCAATAGAATATACCACTAATGCA-AGA--------CATGAAGTCA -s simRat_chr6.simRat.chr6 91682 39 + 647215 TGCCAATGGAAAATACCACCATCACA-AGA--------TATCAAGTCA - -a -s simMouse_chr6.simMouse.chr6 99607 8 + 636262 CAGAACAG -s Anc0.Anc0refChr4 4814 8 + 45765 CAGCACAG -s Anc1.Anc1refChr2 71338 8 - 144309 CAGCACAG -s Anc2.Anc2refChr2 17362 8 - 27695 CAGCACAA -s mr.mrrefChr0 94651 8 + 130230 CAGAACAG -s simCow_chr6.simCow.chr6 502380 8 - 602619 AAGCAAAA -s simDog_chr6.simDog.chr6 496245 8 - 593897 CAGCACAA -s simHuman_chr6.simHuman.chr6 506178 8 - 601863 CAGGACAG -s simRat_chr6.simRat.chr6 91721 8 + 647215 CAGACCAG - -a -s simMouse_chr6.simMouse.chr6 99615 9 + 636262 TGGAGTGAT -s Anc0.Anc0refChr4 4822 9 + 45765 TGGGGTGAC -s Anc1.Anc1refChr2 71346 9 - 144309 TGGGGTGAC -s Anc2.Anc2refChr2 17370 9 - 27695 TGGGGTGAC -s mr.mrrefChr0 94659 9 + 130230 TGGAGTGAT -s simCow_chr6.simCow.chr6 502389 9 - 602619 TGGGGTGAC -s simDog_chr6.simDog.chr6 496253 9 - 593897 TGCGGTGAC -s simHuman_chr6.simHuman.chr6 506186 9 - 601863 TTGGGTGAC -s simRat_chr6.simRat.chr6 91729 9 + 647215 TGGAGTGAT - -a -s simMouse_chr6.simMouse.chr6 99624 28 + 636262 TCAGAAGCCTCCCATCATCAGGGTTAAT -s Anc0.Anc0refChr4 4831 28 + 45765 TCTGGGTCCTCCCATCACCAGGACTAGT -s Anc1.Anc1refChr2 71355 28 - 144309 TCTGGGTCCTCCCATCACCAGGACTAGT -s Anc2.Anc2refChr2 17379 28 - 27695 TCTGGGTCCTCCCATCATCAGGAGTAGT -s mr.mrrefChr0 94668 28 + 130230 TCAGAAGCCTCCCATCACCAGGACTAAT -s simCow_chr6.simCow.chr6 502398 28 - 602619 TCTGGGTGCTTCCATCATCAGAATTAGT -s simDog_chr6.simDog.chr6 496263 28 - 593897 TCCGGGTCCTCCCATCATTAGGAGTAAA -s simHuman_chr6.simHuman.chr6 506195 28 - 601863 TCTGGGCCCTCCCATCACCAGGACTAGT -s simRat_chr6.simRat.chr6 91738 28 + 647215 TCAGAAGCCTCCCAGCACCAGTACTAAT - -a -s simMouse_chr6.simMouse.chr6 99652 2 + 636262 CA -s Anc0.Anc0refChr4 4904 2 + 45765 CC -s Anc1.Anc1refChr2 71428 2 - 144309 CC -s Anc2.Anc2refChr2 17452 2 - 27695 CC -s mr.mrrefChr0 94741 2 + 130230 CA -s simCow_chr6.simCow.chr6 502468 2 - 602619 CA -s simDog_chr6.simDog.chr6 496336 2 - 593897 CC -s simHuman_chr6.simHuman.chr6 506265 2 - 601863 CC -s simRat_chr6.simRat.chr6 91811 2 + 647215 TA - -a -s simMouse_chr6.simMouse.chr6 99654 1 + 636262 T -s Anc0.Anc0refChr4 4906 1 + 45765 C -s Anc1.Anc1refChr2 71430 1 - 144309 C -s Anc2.Anc2refChr2 17454 1 - 27695 C -s mr.mrrefChr0 94743 1 + 130230 T -s simCow_chr6.simCow.chr6 502470 1 - 602619 C -s simDog_chr6.simDog.chr6 496339 1 - 593897 C -s simHuman_chr6.simHuman.chr6 506267 1 - 601863 C -s simRat_chr6.simRat.chr6 91813 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 99655 20 + 636262 GTGACCATCACAGACTAAGG -s Anc0.Anc0refChr4 4908 19 + 45765 -TGGCCAACAAAAACTAAGG -s Anc1.Anc1refChr2 71432 20 - 144309 TTGGCCAACAAAAACTAAGG -s Anc2.Anc2refChr2 17456 19 - 27695 -TGGCCAACAAAAACTAAGG -s mr.mrrefChr0 94744 20 + 130230 TTGGCCATCACAAACTAAGG -s simCow_chr6.simCow.chr6 502472 19 - 602619 -TGGTCATCAAAAGCTAAGG -s simDog_chr6.simDog.chr6 496341 19 - 593897 -TGGCCAACAAACACTCAGG -s simHuman_chr6.simHuman.chr6 506269 20 - 601863 TGGGCCACCAAAAACCAAGG -s simRat_chr6.simRat.chr6 91814 20 + 647215 TTGGCCATCACAAACTAAGG - -a -s simMouse_chr6.simMouse.chr6 99675 61 + 636262 TTTCACATGGGACTTAAACCATGACTACTTCCGCAGGACATAACCTCTATCATGGGGTTGA -s Anc0.Anc0refChr4 4927 61 + 45765 GTTCACATAGGACTTAAACAATGACAACTTCCAGAGGATGTGACTTCTCTCCTGGGGTTAG -s Anc1.Anc1refChr2 71452 61 - 144309 GTTCACATAGGACTTAAACAATGACAACTTCCAGAGGATGTGACTTCTCTCCTGGGGTTAG -s Anc2.Anc2refChr2 17475 61 - 27695 GTTCACATAGGACTTAAATGATGACATTTTCCAGAGGATGTAACTTCTCTCCTGGGGTTAG -s mr.mrrefChr0 94764 61 + 130230 TTTCACATGGGACTTAAACAATGACAACTTCCAGAGGACATGACCTCTATCATGGGGTTGG -s simCow_chr6.simCow.chr6 502493 55 - 602619 GTTTAGATTGGACCGAAATGAC------TTCCAGAGAATGTAGCTTCTCTCCTGGGCATAG -s simDog_chr6.simDog.chr6 496360 61 - 593897 GTTCACATAAGACTTAGATGATGACATTTTCCAGAGGATGTAACTTCTCTCCTGGGGTTGG -s simHuman_chr6.simHuman.chr6 506289 60 - 601863 GTTCACATAGGACTTAAACAAGGACGACATCCAGCGGATGTG-CTTCTCTCCTGGGGTTAG -s simRat_chr6.simRat.chr6 91834 61 + 647215 TTTCACATGGGACTTAAACAGTGACAACTTCCAGAGGACATGTCCTCCATCACGGGGTTGG - -a -s simMouse_chr6.simMouse.chr6 99736 21 + 636262 TGCAAGCACCACCTTGACCTG -s Anc0.Anc0refChr4 4988 18 + 45765 TGGATATGTCAG---GACTTG -s Anc1.Anc1refChr2 71513 18 - 144309 TGGATATGTCAG---GACTTG -s Anc2.Anc2refChr2 17536 18 - 27695 TGGATATGTCAG---GACTTG -s mr.mrrefChr0 94825 21 + 130230 TGCATACACCAACTTGACCTG -s simCow_chr6.simCow.chr6 502548 18 - 602619 TGTATGTGTCAG---GACTTG -s simDog_chr6.simDog.chr6 496421 17 - 593897 TGGATATCGCAG----ACTTG -s simHuman_chr6.simHuman.chr6 506349 18 - 601863 TCAATATGTCAG---GACTGA -s simRat_chr6.simRat.chr6 91896 21 + 647215 TGCATACACCGATTTGACCTG - -a -s simMouse_chr6.simMouse.chr6 99757 4 + 636262 TTTC -s Anc0.Anc0refChr4 5006 4 + 45765 TATC -s Anc1.Anc1refChr2 71531 4 - 144309 TATC -s Anc2.Anc2refChr2 17558 4 - 27695 GATC -s mr.mrrefChr0 94846 4 + 130230 TTTC -s simCow_chr6.simCow.chr6 502570 4 - 602619 GATA -s simDog_chr6.simDog.chr6 496442 4 - 593897 GTTC -s simHuman_chr6.simHuman.chr6 506367 4 - 601863 TATT -s simRat_chr6.simRat.chr6 91917 4 + 647215 TTTA - -a -s simMouse_chr6.simMouse.chr6 99761 25 + 636262 GATGGCGGTGGGATACTTCACACAA -s Anc0.Anc0refChr4 5010 25 + 45765 GATGGTCCTGGGATACTTCATACAT -s Anc1.Anc1refChr2 71535 25 - 144309 GATGGTCCTGGGATACTTCATACAT -s Anc2.Anc2refChr2 17562 25 - 27695 GATAGACCTTGGATACTTCATACAT -s mr.mrrefChr0 94850 25 + 130230 GATGGTGCTGGGATACTTCATACAA -s simCow_chr6.simCow.chr6 502574 25 - 602619 GATAGGTCTAGGATACTTCATGCAT -s simDog_chr6.simDog.chr6 496447 25 - 593897 GATAGACCTTGGATACTGTGTACTC -s simHuman_chr6.simHuman.chr6 506371 25 - 601863 AGTGTTCCTGAGATACATCATACAT -s simRat_chr6.simRat.chr6 91921 25 + 647215 CATGGTGCTCGGATGCTTCATGCAA - -a -s simMouse_chr6.simMouse.chr6 99786 41 + 636262 CAGATATAATGTATCAAGATAGAATACATCAGGTCTGCAAA -s Anc0.Anc0refChr4 5035 20 + 45765 TTAGTATAGTGAATTAAGAT--------------------- -s Anc1.Anc1refChr2 71560 20 - 144309 TTAGTATAGTGAATTAAGAT--------------------- -s Anc2.Anc2refChr2 17587 20 - 27695 TTAGTATGGTGAATTGAGAT--------------------- -s mr.mrrefChr0 94875 41 + 130230 CAGATATAGTGTATCAAGATAGCCTACATCAGGTCTGCAAA -s simCow_chr6.simCow.chr6 502599 19 - 602619 ATGGTATGGTGAGTTGCGG---------------------- -s simDog_chr6.simDog.chr6 496551 20 - 593897 TTAGTATGGTGAATTGAGAT--------------------- -s simHuman_chr6.simHuman.chr6 506396 20 - 601863 TCAGTATAGTGCATTAAGAT--------------------- -s simRat_chr6.simRat.chr6 91946 41 + 647215 CAGTTATAGTGTACCAAGCTAGCCTACATCAGGTATGCAAA - -a -s simMouse_chr6.simMouse.chr6 99827 12 + 636262 CGTATATTAAAG -s Anc0.Anc0refChr4 41100 12 - 45765 CCTATATCAAAG -s Anc1.Anc1refChr2 73154 12 + 144309 CCTATATCAAAG -s Anc2.Anc2refChr2 10483 12 + 27695 CCTATATCTAAA -s mr.mrrefChr0 94916 12 + 130230 CCTATATCAAAG -s simCow_chr6.simCow.chr6 100384 12 + 602619 CCTCTATCTAAA -s simDog_chr6.simDog.chr6 97806 12 + 593897 CCTATATCTAAA -s simHuman_chr6.simHuman.chr6 95882 12 + 601863 CCTATATCAAAG -s simRat_chr6.simRat.chr6 91987 12 + 647215 CCTACATCAAAG - -a -s simMouse_chr6.simMouse.chr6 99839 8 + 636262 TTTAATGA -s Anc0.Anc0refChr4 41112 8 - 45765 TTTTTTGA -s Anc1.Anc1refChr2 73166 8 + 144309 TTTTTTGA -s Anc2.Anc2refChr2 10495 8 + 27695 TTTTTTGA -s mr.mrrefChr0 94928 8 + 130230 TTTAATGA -s simCow_chr6.simCow.chr6 100399 8 + 602619 TTTTTTGA -s simDog_chr6.simDog.chr6 97818 8 + 593897 TTTTTTCA -s simHuman_chr6.simHuman.chr6 95894 8 + 601863 TTTTTTGA -s simRat_chr6.simRat.chr6 91999 1 + 647215 T------- - -a -s simMouse_chr6.simMouse.chr6 99847 15 + 636262 ATGGGTTACCATAGC -s Anc0.Anc0refChr4 41124 15 - 45765 ACTAATTACAACATC -s Anc1.Anc1refChr2 73178 15 + 144309 ACTAATTACAACATC -s Anc2.Anc2refChr2 10507 15 + 27695 GCTAATTACAACATC -s mr.mrrefChr0 94936 15 + 130230 ATGGGTTACAATAGC -s simCow_chr6.simCow.chr6 100411 15 + 602619 GCTGATTACAACATA -s simDog_chr6.simDog.chr6 97830 15 + 593897 GCTAATTCGAACATC -s simHuman_chr6.simHuman.chr6 95906 15 + 601863 ACTAATTACACAATC -s simRat_chr6.simRat.chr6 92000 14 + 647215 -TAGGTTACAATAGC - -a -s simMouse_chr6.simMouse.chr6 99862 27 + 636262 TTGCATTGGATTGTCACGTACATACAC -s Anc0.Anc0refChr4 41142 27 - 45765 CAACAAGGGATAATCACTTACATTCAC -s Anc1.Anc1refChr2 73196 27 + 144309 CAACAAGGGATAATCACTTACATTCAC -s Anc2.Anc2refChr2 10525 27 + 27695 CAACAAGGGATAATCACTTACATTCAC -s mr.mrrefChr0 94954 27 + 130230 TTGCATTGGATAGTCACGTACATACAC -s simCow_chr6.simCow.chr6 100429 27 + 602619 CAACAAGGGATAATCACTTGCACTCAT -s simDog_chr6.simDog.chr6 97848 12 + 593897 CAA---------------TACATTCAC -s simHuman_chr6.simHuman.chr6 95924 27 + 601863 CAACAAGGGATAATCACCTACATTCAC -s simRat_chr6.simRat.chr6 92017 27 + 647215 TTGCATTGGATAGTCACATATGTACAC - -a -s simMouse_chr6.simMouse.chr6 99889 12 + 636262 ATAATTAATGAA -s Anc0.Anc0refChr4 41170 12 - 45765 ACTACTAATCAA -s Anc1.Anc1refChr2 73224 12 + 144309 ACTACTAATCAA -s Anc2.Anc2refChr2 10553 12 + 27695 ACTACTAATCAA -s mr.mrrefChr0 94981 12 + 130230 ATAATTAATGAA -s simCow_chr6.simCow.chr6 100457 12 + 602619 ATTGCAAATTAA -s simDog_chr6.simDog.chr6 97861 12 + 593897 ACTATTAATCAA -s simHuman_chr6.simHuman.chr6 95952 12 + 601863 ACTACTATTCAA -s simRat_chr6.simRat.chr6 92044 12 + 647215 ATGATTAATAAG - -a -s simMouse_chr6.simMouse.chr6 99901 23 + 636262 GGCCACCGACACTGGTATGAGCA -s Anc0.Anc0refChr4 41182 23 - 45765 GGATACCTACACTGGTATGGGGA -s Anc1.Anc1refChr2 73236 23 + 144309 GGATACCTACACTGGTATGGGGA -s Anc2.Anc2refChr2 10569 23 + 27695 GGATACCTACACTGCTATGGGGA -s mr.mrrefChr0 94993 23 + 130230 GGCCACCGACACTGGTATGAGCA -s simCow_chr6.simCow.chr6 100473 22 + 602619 GCATACCTACACTGATA-GGGGG -s simDog_chr6.simDog.chr6 97877 23 + 593897 GGATATCTACACCACTATGGGGA -s simHuman_chr6.simHuman.chr6 95964 23 + 601863 TAATACCTGCACTGGTATGGGGA -s simRat_chr6.simRat.chr6 92056 23 + 647215 GGTGACCCACATCGGTATGACCA - -a -s simMouse_chr6.simMouse.chr6 99924 14 + 636262 AAGTAGGCTTTACC -s Anc0.Anc0refChr4 41206 14 - 45765 AAGTAGGCTTTTTT -s Anc1.Anc1refChr2 73260 14 + 144309 AAGTAGGCTTTTTT -s Anc2.Anc2refChr2 10593 14 + 27695 AAGTAGGCTTTTTT -s mr.mrrefChr0 95016 14 + 130230 AAGTAGGCTTTTCC -s simCow_chr6.simCow.chr6 100496 14 + 602619 GAGTAGGCTTTTTT -s simDog_chr6.simDog.chr6 97901 14 + 593897 AAATAGGCGTTTTT -s simHuman_chr6.simHuman.chr6 95988 14 + 601863 AAGTATGCTTTCTT -s simRat_chr6.simRat.chr6 92079 14 + 647215 AAGTAGGCTTTTCC - -a -s simMouse_chr6.simMouse.chr6 99938 17 + 636262 ATGCAACCCCCACATCT -s Anc0.Anc0refChr4 41220 17 - 45765 CCTCTAACCCCTCATCT -s Anc1.Anc1refChr2 73274 17 + 144309 CCTCTAACCCCTCATCT -s Anc2.Anc2refChr2 10607 17 + 27695 CCTCTAACCCTTCATTT -s mr.mrrefChr0 95030 17 + 130230 ATGCAACCCCCACATCT -s simCow_chr6.simCow.chr6 100510 17 + 602619 CCTCTAACCCTCCATAT -s simDog_chr6.simDog.chr6 97922 17 + 593897 ACTCTAACCCTTCATTT -s simHuman_chr6.simHuman.chr6 96002 13 + 601863 CCTGTAACGCC----CT -s simRat_chr6.simRat.chr6 92093 17 + 647215 TTGCAACCTCCACATCT - -a -s simMouse_chr6.simMouse.chr6 99955 42 + 636262 ATGCTCCCTCCCTCGATACTATACTTGTCCAGTCACACAGCT -s Anc0.Anc0refChr4 41237 42 - 45765 ATGCTCTCTCCTTCCATACTAAACATGTTCAGCCATGCAGGT -s Anc1.Anc1refChr2 73291 42 + 144309 ATGCTCTCTCCTTCCATACTAAACATGTTCAGCCATGCAGGT -s Anc2.Anc2refChr2 10627 42 + 27695 ATGCACTCCCCTTCCATACTAAACATGTTCAGCCATGCAGGT -s mr.mrrefChr0 95047 42 + 130230 ATGCTCCCTCCCTCCATACTATACTTGTCCAGCCATGCAGGT -s simCow_chr6.simCow.chr6 100530 41 + 602619 CT-CACTACCCATATATACTAGGCTTGTTCAGCCAGGCAGGT -s simDog_chr6.simDog.chr6 97942 42 + 593897 ATGCACTCCCCTTCCATATTAAACATGTTCAGGCTTGCAGGT -s simHuman_chr6.simHuman.chr6 96015 42 + 601863 TTGCTTTTTCCTTCCATGCTAAATGCCTTCAGCCATGCAGGT -s simRat_chr6.simRat.chr6 92110 42 + 647215 ATGCTCCCTCCCTCCACACTATCCCTGTCCAGCCATGCAGGT - -a -s simMouse_chr6.simMouse.chr6 99997 73 + 636262 GATTATGACTAACCACTCTGCCCATCACTGCTAGGCAAGTATACCACCAACACTTGTACTGTCCGCTGGGTTA -s Anc0.Anc0refChr4 41279 64 - 45765 TTTTATGTAAAACTGCTTTGCCCATCACTATTAGGTAAGTGGACCACTTA---------TGTTCATTGGGTTA -s Anc1.Anc1refChr2 73333 73 + 144309 TTTTATGTAAAACTGCTTTGCCCATCACTATTAGGTAAGTGGACCACTTACCCTTTCTTTGTTCATTGGGTTA -s Anc2.Anc2refChr2 10669 64 + 27695 TTTTATGTAAAACTGCTTTGCCAATCACTATTAGGTAAGTGGTCCACTTA---------TGTTCATTGGGTTC -s mr.mrrefChr0 95089 73 + 130230 GATTATGACTAACCACTCTGCCCATCACTGTTAGGCAAGTATACCACCAACACTTGTACTGTCCGCTGGGTTA -s simCow_chr6.simCow.chr6 100572 64 + 602619 TTTTATGTAAAACTGCTCAGCCAATCACTATTAAGTAAGTGGGCCACTTA---------TGTTCATTGGGTTA -s simDog_chr6.simDog.chr6 97984 64 + 593897 TTTTATATATAACTACTTTGCGAATCACTATTAGGTAAGTGGTCCACTTA---------TGTTCATTAAGTTC -s simHuman_chr6.simHuman.chr6 96057 73 + 601863 TTTTATGTAAAACTGCTTCGCCCATCACTATTAGGTAAGTGGATCATATGCCCTTTCTTTGTTCATTGGGTTA -s simRat_chr6.simRat.chr6 92152 72 + 647215 GATTATGACTAACCATTCTGCCCAT-ACTGTTAGGCAAGTATACCACCAACACTTGTACTGTCTGCTGGGTCA - -a -s simMouse_chr6.simMouse.chr6 100070 47 + 636262 TCTAAGGCCTAATTAATGTAGTATTGATAGAACAAATAGTTGACACC -s Anc0.Anc0refChr4 41343 45 - 45765 TCTATGACAGAAATGAATTAATATTAGTAGAACAAGTAGTTGACA-- -s Anc1.Anc1refChr2 73406 45 + 144309 TCTATGACAGAAATGAATTAATATTAGTAGAACAAGTAGTTGACA-- -s Anc2.Anc2refChr2 10733 45 + 27695 TCTATGACAGAAATGAATTAATATGAGTAGATCAAGTAGTTGACA-- -s mr.mrrefChr0 95162 47 + 130230 TCTAAGGCATAATTAATGTAGTATTGGTAGAACAAATAGTTGACACC -s simCow_chr6.simCow.chr6 100636 45 + 602619 TCTATGACAGCAGTGAATTAATATGAGTAGATAAAGTAGTAGACA-- -s simDog_chr6.simDog.chr6 98048 45 + 593897 TCTATGACAGAAATGAACTATTATGAGTAGTTCAAGTAGTTGACA-- -s simHuman_chr6.simHuman.chr6 96132 41 + 601863 TCTGTGACACAAAT----CAATATTAGTAGAATAAGTAGTTGACA-- -s simRat_chr6.simRat.chr6 92224 47 + 647215 TCTAAGGCATAATTAATGTAGTATTCGTAGAACTAATAGTTGACACC - -a -s simMouse_chr6.simMouse.chr6 100117 15 + 636262 CAAGAGGGCTTACCT -s Anc0.Anc0refChr4 41388 8 - 45765 AGA-------TACTT -s Anc1.Anc1refChr2 73451 15 + 144309 AGAAATCCTTTACTT -s Anc2.Anc2refChr2 10778 8 + 27695 AGA-------TGCCT -s mr.mrrefChr0 95209 15 + 130230 CAAGATGGCTTACTT -s simCow_chr6.simCow.chr6 100685 8 + 602619 AGA-------TGCCT -s simHuman_chr6.simHuman.chr6 96173 15 + 601863 AGAAATCCTTTATTT -s simRat_chr6.simRat.chr6 92271 15 + 647215 CAAGATGGCTTACTG - -a -s simMouse_chr6.simMouse.chr6 100132 18 + 636262 TGTCCACAGGACCGATTC -s Anc0.Anc0refChr4 41396 17 - 45765 TATCAAAAGGG-TGATTC -s Anc1.Anc1refChr2 73466 17 + 144309 TATCAAAAGGG-TGATTC -s Anc2.Anc2refChr2 10786 17 + 27695 TATTAAAAAGG-TAATCG -s mr.mrrefChr0 95224 17 + 130230 TGTCCACAGGA-TGATTC -s simCow_chr6.simCow.chr6 100697 17 + 602619 TATTAAAAAGG-TAATCG -s simHuman_chr6.simHuman.chr6 96188 17 + 601863 TATCAGAAGGG-TGCTTC -s simRat_chr6.simRat.chr6 92286 13 + 647215 T----ACAGGA-TGATTC - -a -s simMouse_chr6.simMouse.chr6 100150 25 + 636262 GACAATTTCTCTTATCAGGCTTGCG -s Anc0.Anc0refChr4 41421 25 - 45765 GAGATTTTTTCCTGACATGCTTTTG -s Anc1.Anc1refChr2 73491 25 + 144309 GAGATTTTTTCCTGACATGCTTTTG -s Anc2.Anc2refChr2 10811 25 + 27695 GAGATTTTTTCCTGACATGCTTCTG -s mr.mrrefChr0 95241 25 + 130230 GACAATTTCTCTTGACAGGCTTTTG -s simCow_chr6.simCow.chr6 100722 25 + 602619 GAGATTTCTTCCCGACATGATTGTG -s simDog_chr6.simDog.chr6 497078 25 - 593897 GAGTATTTGTCCTGACATGCTGCTA -s simHuman_chr6.simHuman.chr6 96213 25 + 601863 AAAATATTTTCCTGACATGCTTTTG -s simRat_chr6.simRat.chr6 92299 25 + 647215 GACAATTTCTCTTGAGAGGCTTTTG - -a -s simMouse_chr6.simMouse.chr6 100175 6 + 636262 AAACTA -s Anc0.Anc0refChr4 41446 6 - 45765 AAGCTA -s Anc1.Anc1refChr2 73516 6 + 144309 AAGCTA -s Anc2.Anc2refChr2 10836 6 + 27695 AAGCTA -s mr.mrrefChr0 95266 6 + 130230 AAACTA -s simCow_chr6.simCow.chr6 100752 6 + 602619 AAGGTA -s simDog_chr6.simDog.chr6 497103 6 - 593897 AAGCTA -s simHuman_chr6.simHuman.chr6 96238 6 + 601863 AAGCTA -s simRat_chr6.simRat.chr6 92324 6 + 647215 AAACTA - -a -s simMouse_chr6.simMouse.chr6 100181 12 + 636262 ACTAAGTTTTGG -s Anc0.Anc0refChr4 41452 6 - 45765 ACTA------GG -s Anc1.Anc1refChr2 73522 6 + 144309 ACTA------GG -s Anc2.Anc2refChr2 10842 6 + 27695 ACTA------GG -s mr.mrrefChr0 95272 12 + 130230 ACTAAGTTTTGG -s simCow_chr6.simCow.chr6 100774 6 + 602619 ATTA------GT -s simDog_chr6.simDog.chr6 497109 6 - 593897 ACTA------GG -s simHuman_chr6.simHuman.chr6 96244 6 + 601863 ACTA------GG -s simRat_chr6.simRat.chr6 92330 12 + 647215 ACTAAGTTGTGG - -a -s simMouse_chr6.simMouse.chr6 100193 55 + 636262 TGACATCTAGAGCCATGTCAAGTGCCACTAACACAATGTTCCATTTACTTAACCA -s Anc0.Anc0refChr4 41458 41 - 45765 TGACATATA--------------GCCATTTGGATCATAGACCATTTGCATGACGG -s Anc1.Anc1refChr2 73528 41 + 144309 TGACATATA--------------GCCATTTGGATCATAGACCATTTGCATGACGG -s Anc2.Anc2refChr2 10848 41 + 27695 TGACATATA--------------GCCATTTGGATCATAGACCATTTGCATGACGG -s mr.mrrefChr0 95284 55 + 130230 TGACATCTAGAGCCATGTCAAGTGCCACTTACACAATGTTCCATTTACTTAACCA -s simCow_chr6.simCow.chr6 100780 41 + 602619 TGACATATA--------------GCCATTTGGATCATAGACCATTTGCACAACTG -s simDog_chr6.simDog.chr6 497121 41 - 593897 CACCATATA--------------GCCATTTGGATCATAGACCATTTGCATGACGG -s simHuman_chr6.simHuman.chr6 96250 31 + 601863 TGATATATA--------------GCCATATGGATCATAGACCATT---------- -s simRat_chr6.simRat.chr6 92342 55 + 647215 TGACATCTAGAGCCATGTCAAGTGCCACTTACACGATGTTCCATTTACTTAATCA - -a -s simMouse_chr6.simMouse.chr6 100248 24 + 636262 ACGTGTGGCCAGAATATCATTTCT -s Anc0.Anc0refChr4 41499 24 - 45765 ATGTGTGGTGAAAATATCATTTCT -s Anc1.Anc1refChr2 73569 24 + 144309 ATGTGTGGTGAAAATATCATTTCT -s Anc2.Anc2refChr2 10907 24 + 27695 ATGCATGGTGAAAATATCATTTCT -s mr.mrrefChr0 95339 24 + 130230 ACGTGTGGCCAAAATATCATTTCT -s simCow_chr6.simCow.chr6 100881 24 + 602619 GTGCATCTTTAAAATATAATTTCT -s simDog_chr6.simDog.chr6 497183 24 - 593897 ATGCATGGTGAAAATATCAATTCT -s simHuman_chr6.simHuman.chr6 96281 19 + 601863 ---TGTAG--AAAATACCATTTTT -s simRat_chr6.simRat.chr6 92397 24 + 647215 ATGTATGGCCAAAAAATCATTTCT - -a -s simMouse_chr6.simMouse.chr6 100272 2 + 636262 AG -s Anc0.Anc0refChr4 41523 2 - 45765 CA -s Anc1.Anc1refChr2 73593 2 + 144309 CA -s Anc2.Anc2refChr2 10931 2 + 27695 CA -s mr.mrrefChr0 95363 2 + 130230 AA -s simCow_chr6.simCow.chr6 100907 2 + 602619 CA -s simDog_chr6.simDog.chr6 497207 2 - 593897 CA -s simHuman_chr6.simHuman.chr6 96300 2 + 601863 CA -s simRat_chr6.simRat.chr6 92421 2 + 647215 AA - -a -s simMouse_chr6.simMouse.chr6 100274 12 + 636262 CAGACCAGCATA -s Anc0.Anc0refChr4 41525 10 - 45765 --CTCCAGCATG -s Anc1.Anc1refChr2 73596 12 + 144309 CACTCCAGCATG -s Anc2.Anc2refChr2 10933 10 + 27695 --CTCCAGAGTA -s mr.mrrefChr0 95366 12 + 130230 CAGACCAGCATG -s simCow_chr6.simCow.chr6 100909 10 + 602619 --CACCAGGGTA -s simDog_chr6.simDog.chr6 497209 10 - 593897 --CTCCAGAGTA -s simHuman_chr6.simHuman.chr6 96303 12 + 601863 CACTCCAGCATG -s simRat_chr6.simRat.chr6 92424 12 + 647215 CAGACCAGTGTG - -a -s simMouse_chr6.simMouse.chr6 100286 5 + 636262 TCAAC -s Anc0.Anc0refChr4 41535 5 - 45765 GCAAC -s Anc1.Anc1refChr2 73608 5 + 144309 GCAAC -s Anc2.Anc2refChr2 10943 5 + 27695 GCAAA -s mr.mrrefChr0 95378 5 + 130230 GCAAC -s simCow_chr6.simCow.chr6 100919 5 + 602619 GCAAG -s simDog_chr6.simDog.chr6 497219 5 - 593897 GTGAA -s simHuman_chr6.simHuman.chr6 96315 5 + 601863 GCAAC -s simRat_chr6.simRat.chr6 92438 5 + 647215 GCAAC - -a -s simMouse_chr6.simMouse.chr6 100291 15 + 636262 AGTGCAATATCTGGC -s Anc0.Anc0refChr4 41540 15 - 45765 TATACAACATCTAGC -s Anc1.Anc1refChr2 73613 15 + 144309 TATACAACATCTAGC -s Anc2.Anc2refChr2 10948 15 + 27695 TATACAACATCTAGC -s mr.mrrefChr0 95383 15 + 130230 TGTACAATATCTGGC -s simCow_chr6.simCow.chr6 100924 15 + 602619 TATACAACATCTAGT -s simDog_chr6.simDog.chr6 497224 15 - 593897 TAGATAATATCGAAC -s simHuman_chr6.simHuman.chr6 96321 15 + 601863 TATACAACATCTAGC -s simRat_chr6.simRat.chr6 92443 15 + 647215 TGTACAAAATCTGGC - -a -s simMouse_chr6.simMouse.chr6 100306 80 + 636262 TCCTGCAATTGGTAGGGTATTCATGGTATACTTTTTGTTAGTTGTTAAGGTCCTAGAAAAGCTAAGCTATACCCTTCCAG -s Anc0.Anc0refChr4 41555 21 - 45765 TCCAGCAATTTGTA--GCATTCA--------------------------------------------------------- -s Anc1.Anc1refChr2 73628 21 + 144309 TCCAGCAATTTGTA--GCATTCA--------------------------------------------------------- -s Anc2.Anc2refChr2 10963 21 + 27695 TCCAGCAATTTGTA--GCTTGCA--------------------------------------------------------- -s mr.mrrefChr0 95398 71 + 130230 TCCTGCAATTGGTAGGGCATTCATGGTATACTT----TTAGTTGTTAAGGTCCTAGAA-----AAGCTATACTCTTCTAG -s simCow_chr6.simCow.chr6 100939 21 + 602619 TCCAGCAGGTTATA--GCTTGCA--------------------------------------------------------- -s simDog_chr6.simDog.chr6 497239 21 - 593897 TACAGCAATCTGTA--GCTAGCA--------------------------------------------------------- -s simHuman_chr6.simHuman.chr6 96336 21 + 601863 TCCAGCATTTTGTA--TCATTCA--------------------------------------------------------- -s simRat_chr6.simRat.chr6 92463 71 + 647215 CCCTGTAATTGGTAGTGCATTCATGGTATGTTT----TTAGTTGCCCAGGTTTTAGGA-----AAGCTATACTCTTCTAA - -a -s simMouse_chr6.simMouse.chr6 100386 2 + 636262 GG -s Anc0.Anc0refChr4 41576 2 - 45765 GC -s Anc1.Anc1refChr2 73649 2 + 144309 GC -s Anc2.Anc2refChr2 10984 2 + 27695 GC -s mr.mrrefChr0 95469 2 + 130230 GG -s simCow_chr6.simCow.chr6 100960 2 + 602619 AC -s simDog_chr6.simDog.chr6 497261 2 - 593897 GT -s simHuman_chr6.simHuman.chr6 96357 2 + 601863 GC -s simRat_chr6.simRat.chr6 92534 2 + 647215 GG - -a -s simMouse_chr6.simMouse.chr6 100388 28 + 636262 CTATTAAGCCAAGAATTTAGGAGTCTTG -s Anc0.Anc0refChr4 41578 27 - 45765 ATAGTAATCCTTTAATTTAGGGGTCTT- -s Anc1.Anc1refChr2 73651 28 + 144309 ATAGTAATCCTTTAATTTAGGGGTCTTG -s Anc2.Anc2refChr2 10986 27 + 27695 ATAGTAATCCTTTACTTTAGGGGTCTT- -s mr.mrrefChr0 95471 28 + 130230 CTATTAAGCCAAGAATTTAGGGGTCTTG -s simCow_chr6.simCow.chr6 100962 25 + 602619 C--GGAATCCTTTACTTTAGGGGTCTA- -s simDog_chr6.simDog.chr6 497263 27 - 593897 ATAGTAATCTGCCACTTTAGGATTCTT- -s simHuman_chr6.simHuman.chr6 96359 28 + 601863 ATAGTAATCCTTTAAGTTAGGGGTTTTG -s simRat_chr6.simRat.chr6 92537 27 + 647215 CTATTGAGCCCAGAGTTTAGGGGTCCT- - -a -s simMouse_chr6.simMouse.chr6 100416 89 + 636262 AGGGTTTCCCCATGGAAATACTCTCCATAAGAACCTGGATTGTATACACTGTCTCACTTAAGTTTTTCTTAATAGTCCGACATGCTTTG -s Anc0.Anc0refChr4 41605 85 - 45765 AGGATCTCTCTAGGGAAATAATCTCTTTGATAACC-AGACACCAC---CTATCTCACTCAAGTTTCTCTTAGTAGTCTGACATGCTTTT -s Anc1.Anc1refChr2 73679 88 + 144309 AGGATCTCTCTAGGGAAATAATCTCTTTGATAACC-AGACACCACTTACTATCTCACTCAAGTTTCTCTTAGTAGTCTGACATGCTTTT -s Anc2.Anc2refChr2 11013 85 + 27695 AGGATCTTTCTAGGGAAATAGTCTATTTGATACCC-AGACACCAC---CTATCTCACTCAAGTTTCTCTTAGTAGTCTAACATGCTTTT -s mr.mrrefChr0 95499 89 + 130230 AGGGTTTCTCCATGGAAATAATCTCCATAAGAACCTGGATTGTATTCACTGTCTCACTTAAGTTTTTCTTAATAGTCTGACATGCTTTG -s simCow_chr6.simCow.chr6 100988 55 + 602619 AGGATCTTTTTATGGAAATGGTCAATT----------------------------------ATTGCTCTTAGTAGTCTAACATGTGTTT -s simDog_chr6.simDog.chr6 497290 85 - 593897 AGGATCTTTCTAGGGGAATAGTGTATTTGATACCC-AGACACCAC---CTATCTCACTCAAGTTTTTCTTAGTAGTCTAACATGCTTTG -s simHuman_chr6.simHuman.chr6 96387 84 + 601863 AGG----CTCTAAGGAAATAATCTCTTTGATAACC-AGCCACCACTTATCATCTCAGTCATGTTTCTCTTAGTAATTTGACATGCCTTT -s simRat_chr6.simRat.chr6 92564 86 + 647215 ---GTCTTTCCATGGAAATAATTTCCCTAAGAACCTGGATTGTATTCACTGTCGCACTTGAGTTTTTCTTAATAGTCTGACATGCTCTG - -a -s simMouse_chr6.simMouse.chr6 100505 15 + 636262 CAAGTCTATTTCAGA -s Anc0.Anc0refChr4 41690 15 - 45765 CAGGTCTATTTCAGA -s Anc1.Anc1refChr2 73767 15 + 144309 CAGGTCTATTTCAGA -s Anc2.Anc2refChr2 11098 15 + 27695 CAGGTCTATTTCAGA -s mr.mrrefChr0 95588 15 + 130230 CAAGTCTATTTCAGA -s simCow_chr6.simCow.chr6 101171 15 + 602619 TAGGGGTTTGCCAGA -s simDog_chr6.simDog.chr6 497375 14 - 593897 CAG-TCTATTTCAGC -s simHuman_chr6.simHuman.chr6 96471 15 + 601863 CAGGTCCATTTCAGA -s simRat_chr6.simRat.chr6 92650 15 + 647215 CAAGTCTATTGCAGA - -a -s simMouse_chr6.simMouse.chr6 100520 93 + 636262 TATAGGTCCAGTCCTAGAGTAGACAAGTCCTAGAATAGACATGGCTTATGCTAGGCTGCCGAGAAGAGATCAGCAAGTTGAATGCTGCATATA -s Anc0.Anc0refChr4 41705 76 - 45765 CATAGGTCC-------------ACA---CCTAGAGTAGAGATTCCTCATCCTAGCCCACCGAGAACACATTAGCAAGTTAAATG-TGCATTAA -s Anc1.Anc1refChr2 73782 76 + 144309 CATAGGTCC-------------ACA---CCTAGAGTAGAGATTCCTCATCCTAGCCCACCGAGAACACATTAGCAAGTTAAATG-TGCATTAA -s Anc2.Anc2refChr2 11113 76 + 27695 CATAGGTTC-------------AGA---CATAGAGTATAGATTCCTCATCCTAGCACACCAAGAACACATCAGCAAGTTAAATG-TGCATTAA -s mr.mrrefChr0 95603 93 + 130230 TATAGGTCCAGTCCTAGAGTAGACAAGTCCTAGAATAGACATGGCTTATGCTAGCCTGCCGAGAAGAGATTAGCAAGTTGAATGCTGCATATA -s simCow_chr6.simCow.chr6 101190 74 + 602619 CATAGGTTC-------------AGA---TATAGAGTATAGATTTCTCATCCTAGCTCACCAAGAAGACATCTGCAAGTTAA--G-TGGACTAA -s simDog_chr6.simDog.chr6 497389 76 - 593897 TATGGGTTC-------------AGA---CATAGAGTATAAATTCCCCGTCCTAGCACACCAAGAACACTTCAGCAAGTTAAATG-TTCATTAA -s simHuman_chr6.simHuman.chr6 96486 72 + 601863 CATAGGTCA-------------ACA---CCTAGACTAGAGATTCCTCATCCTTGCCCACCGAGAGAACAGTGGCAAAATA-----TGCATTAA -s simRat_chr6.simRat.chr6 92665 93 + 647215 TATAAGTCCAGTCCTAGAGTAGATAAGTTCTATAATAGGCATGGCTTATGCTAGCCTGCCGAGAAGAGGTTATTAGGTTGAATGCTGCATATG - -a -s simMouse_chr6.simMouse.chr6 100613 18 + 636262 CTGGATTCACTGCAATAA -s Anc0.Anc0refChr4 41787 18 - 45765 CTGAATTCACTGCAATAA -s Anc1.Anc1refChr2 73864 18 + 144309 CTGAATTCACTGCAATAA -s Anc2.Anc2refChr2 11195 18 + 27695 CTGAATTCACTGCAATAA -s mr.mrrefChr0 95702 18 + 130230 CTGAATTCACTGCAATAA -s simCow_chr6.simCow.chr6 101269 18 + 602619 TTGACCTCACTGTGACAA -s simDog_chr6.simDog.chr6 497473 18 - 593897 CTGAATTCACTGCAGTAA -s simHuman_chr6.simHuman.chr6 96564 18 + 601863 CTGAATTCACTGCAATAA -s simRat_chr6.simRat.chr6 92764 18 + 647215 CTGAATTCACTGAAATAA - -a -s simMouse_chr6.simMouse.chr6 100631 32 + 636262 GGCCATGATTATATGTAATGCATAGAGGAAGA -s Anc0.Anc0refChr4 41806 32 - 45765 GGCTATTATTATATGTAACACATACGGCAAGG -s Anc1.Anc1refChr2 73883 32 + 144309 GGCTATTATTATATGTAACACATACGGCAAGG -s Anc2.Anc2refChr2 11214 32 + 27695 GGCTATTATTATATGTAACACATACAGCAAGG -s mr.mrrefChr0 95720 32 + 130230 GGCCATTATTATATGTAACACATAGGGGAAGG -s simCow_chr6.simCow.chr6 101288 30 + 602619 G--CAACATGATTTGAAACAAATATAGCAAGG -s simDog_chr6.simDog.chr6 497492 32 - 593897 GGCTATTATTATATGTAGCACATACAGCAAGG -s simHuman_chr6.simHuman.chr6 96583 32 + 601863 GACTATTTTTATATGTAACACATAAGGCAAGG -s simRat_chr6.simRat.chr6 92782 32 + 647215 GGCCATTACTATATGTAACACGTAGGGGAAGG - -a -s simMouse_chr6.simMouse.chr6 100663 91 + 636262 ATGGCTCCATGTGAAGAGGCGAGACCCTTTACAGTTCAGTCTACCCTCTCTCTAACGTACCTTTATGGTTCATTCTACCCTCTCTCCAACC -s Anc0.Anc0refChr4 41840 34 - 45765 ----------------------GAATCTGTATGATTCATACTACCCTTTCTAT-----------------------------------ATC -s Anc1.Anc1refChr2 73917 34 + 144309 ----------------------GAATCTGTATGATTCATACTACCCTTTCTAT-----------------------------------ATC -s Anc2.Anc2refChr2 11248 34 + 27695 ----------------------GAATCTGTATGATTCATACTGCCATTTCTAT-----------------------------------ATT -s mr.mrrefChr0 95754 91 + 130230 ATGGCTCCATGTGAAGAGGCGAGAACCTTTATGGTTCATTCTACCCTCTCTCTAACGTACCTTTATGGTTCATTCTACCCTCTCTCCAACC -s simCow_chr6.simCow.chr6 101320 34 + 602619 ----------------------GAACTTGTATGATTCATACTTCCATTTCTAT-----------------------------------ATT -s simDog_chr6.simDog.chr6 497526 25 - 593897 ----------------------AAATCGGCGTAATTAATACTGC--------------------------------------------ATT -s simHuman_chr6.simHuman.chr6 96617 34 + 601863 ----------------------GAATCTCTATGATTCATACTACCCTTTCTAT-----------------------------------ATC -s simRat_chr6.simRat.chr6 92816 91 + 647215 ATGGGTCCATGTGAAAGGGCATGAACCTTTATGGTTCATTCTACCCTCTCTCTAACATACCATTATGATTCATTCTGCCCTCTCTCTGACT - -a -s simMouse_chr6.simMouse.chr6 100754 10 + 636262 TAATGATGGT -s Anc0.Anc0refChr4 41874 9 - 45765 TAAT-ATGAT -s Anc1.Anc1refChr2 73951 9 + 144309 TAAT-ATGAT -s Anc2.Anc2refChr2 11282 9 + 27695 TAAG-ATGAT -s mr.mrrefChr0 95845 10 + 130230 TAATGATGGT -s simCow_chr6.simCow.chr6 101354 9 + 602619 TAAG-ATGAC -s simDog_chr6.simDog.chr6 497551 9 - 593897 TAAG-ATGAT -s simHuman_chr6.simHuman.chr6 96651 9 + 601863 TAAT-ATGAT -s simRat_chr6.simRat.chr6 92908 10 + 647215 GAATGATGTT - -a -s simMouse_chr6.simMouse.chr6 100764 4 + 636262 GATG -s Anc0.Anc0refChr4 41883 4 - 45765 GATG -s Anc1.Anc1refChr2 73960 4 + 144309 GATG -s Anc2.Anc2refChr2 11294 4 + 27695 GATT -s mr.mrrefChr0 95855 4 + 130230 GATG -s simCow_chr6.simCow.chr6 101366 4 + 602619 GATG -s simDog_chr6.simDog.chr6 497563 4 - 593897 GATT -s simHuman_chr6.simHuman.chr6 96660 4 + 601863 GTTG -s simRat_chr6.simRat.chr6 92918 4 + 647215 GATG - -a -s simMouse_chr6.simMouse.chr6 100768 10 + 636262 AAATGGTCAT -s Anc0.Anc0refChr4 41887 10 - 45765 AAGGGGTTAT -s Anc1.Anc1refChr2 73964 10 + 144309 AAGGGGTTAT -s Anc2.Anc2refChr2 11298 10 + 27695 AGGGGGTTAC -s mr.mrrefChr0 95859 10 + 130230 AAATGGTCAT -s simCow_chr6.simCow.chr6 101370 10 + 602619 AGATGATTAC -s simDog_chr6.simDog.chr6 497567 10 - 593897 AGGGGGTTAC -s simHuman_chr6.simHuman.chr6 96665 10 + 601863 AACAGTTACT -s simRat_chr6.simRat.chr6 92922 10 + 647215 AAATGGTCAT - -a -s simMouse_chr6.simMouse.chr6 100778 42 + 636262 CGAAAACACAACGATAGACCTAACTCATGTGGATTAGATGGT -s Anc0.Anc0refChr4 41897 14 - 45765 T-------------------AAAATGATGT---------GGT -s Anc1.Anc1refChr2 73974 23 + 144309 T-------------------AAAATGATGTAGGTCTGATGGT -s Anc2.Anc2refChr2 11308 14 + 27695 T-------------------AAAATGATGT---------GGT -s mr.mrrefChr0 95869 24 + 130230 T------------------CAAACTCATGTGGATTAGATGGT -s simCow_chr6.simCow.chr6 101482 12 + 602619 T-------------------AAAATAATGT---------G-- -s simDog_chr6.simDog.chr6 497577 14 - 593897 T-------------------AAAGTGATGT---------GGT -s simHuman_chr6.simHuman.chr6 96675 23 + 601863 T-------------------AAAATGATGTAGGTCTGATGGT -s simRat_chr6.simRat.chr6 92932 24 + 647215 T------------------CAAACTCATGTGGATTATATGGT - -a -s simMouse_chr6.simMouse.chr6 100820 1 + 636262 G -s Anc0.Anc0refChr4 41912 1 - 45765 G -s Anc1.Anc1refChr2 73998 1 + 144309 G -s Anc2.Anc2refChr2 11323 1 + 27695 G -s mr.mrrefChr0 95893 1 + 130230 G -s simDog_chr6.simDog.chr6 497592 1 - 593897 G -s simHuman_chr6.simHuman.chr6 96699 1 + 601863 G -s simRat_chr6.simRat.chr6 92956 1 + 647215 G - -a -s simMouse_chr6.simMouse.chr6 100821 2 + 636262 TT -s Anc0.Anc0refChr4 41914 2 - 45765 TT -s Anc1.Anc1refChr2 74000 2 + 144309 TT -s Anc2.Anc2refChr2 11325 2 + 27695 TT -s mr.mrrefChr0 95895 2 + 130230 TT -s simCow_chr6.simCow.chr6 101495 2 + 602619 TC -s simDog_chr6.simDog.chr6 497594 2 - 593897 AT -s simHuman_chr6.simHuman.chr6 96701 2 + 601863 TT -s simRat_chr6.simRat.chr6 92958 2 + 647215 TT - -a -s simMouse_chr6.simMouse.chr6 100823 9 + 636262 AATCAGGAG -s Anc0.Anc0refChr4 41916 9 - 45765 AATCAGGAT -s Anc1.Anc1refChr2 74002 9 + 144309 AATCAGGAT -s Anc2.Anc2refChr2 11327 9 + 27695 AATCAGAAT -s mr.mrrefChr0 95897 9 + 130230 AATCAGGAG -s simCow_chr6.simCow.chr6 101497 9 + 602619 AATCAGAAT -s simDog_chr6.simDog.chr6 497604 9 - 593897 AATGAGAAT -s simHuman_chr6.simHuman.chr6 96703 9 + 601863 AATCAGGAT -s simRat_chr6.simRat.chr6 92960 9 + 647215 AATAAGGAG - -a -s simMouse_chr6.simMouse.chr6 100832 12 + 636262 ACACACATAATG -s Anc0.Anc0refChr4 41928 12 - 45765 GTTCCACTCATG -s Anc1.Anc1refChr2 74014 12 + 144309 GTTCCACTCATG -s Anc2.Anc2refChr2 11339 12 + 27695 GTTCCACTCATG -s mr.mrrefChr0 95909 12 + 130230 GTACACATAATG -s simCow_chr6.simCow.chr6 101509 12 + 602619 GTTCCACTCAAG -s simDog_chr6.simDog.chr6 497616 12 - 593897 ATTCCACTCATG -s simHuman_chr6.simHuman.chr6 96715 12 + 601863 GTTCCACTCATG -s simRat_chr6.simRat.chr6 92972 12 + 647215 GTAAACATGACG - -a -s simMouse_chr6.simMouse.chr6 100844 1 + 636262 T -s Anc0.Anc0refChr4 41940 1 - 45765 T -s Anc1.Anc1refChr2 74026 1 + 144309 T -s Anc2.Anc2refChr2 11352 1 + 27695 T -s mr.mrrefChr0 95921 1 + 130230 T -s simCow_chr6.simCow.chr6 101522 1 + 602619 T -s simDog_chr6.simDog.chr6 497629 1 - 593897 C -s simHuman_chr6.simHuman.chr6 96727 1 + 601863 T -s simRat_chr6.simRat.chr6 92984 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 100845 11 + 636262 CCACAACCTTC -s Anc0.Anc0refChr4 41943 11 - 45765 CCACAACCTCC -s Anc1.Anc1refChr2 74029 11 + 144309 CCACAACCTCC -s Anc2.Anc2refChr2 11355 11 + 27695 CCACTACCTCC -s mr.mrrefChr0 95922 11 + 130230 CCACAACCTTC -s simCow_chr6.simCow.chr6 101525 11 + 602619 TCGCTACCTCC -s simDog_chr6.simDog.chr6 497632 11 - 593897 CCATTACCTCG -s simHuman_chr6.simHuman.chr6 96730 11 + 601863 CCACAACCTCC -s simRat_chr6.simRat.chr6 92985 11 + 647215 CCACAACCTAC - -a -s simMouse_chr6.simMouse.chr6 100856 52 + 636262 TTTAATGATGTCTACAACCTTTTTTATCTTCAGGATCACCTCTTTAGCAAGA -s Anc0.Anc0refChr4 41956 28 - 45765 CA------------------------TCTTCAGGATCACCTCTTTACAGAGA -s Anc1.Anc1refChr2 74042 28 + 144309 CA------------------------TCTTCAGGATCACCTCTTTACAGAGA -s Anc2.Anc2refChr2 11368 28 + 27695 AA------------------------TCTTCAAGATCACCTCTTTACAGTGA -s mr.mrrefChr0 95933 28 + 130230 CT------------------------TCTTCAGGATCACCTCTTTAGCAAGA -s simCow_chr6.simCow.chr6 101538 28 + 602619 AA------------------------TCTTCAAGAGCATCTCACTACAGTGA -s simDog_chr6.simDog.chr6 497645 28 - 593897 AG------------------------TCTTCAAGATCACCTATTTACAGTGA -s simHuman_chr6.simHuman.chr6 96743 27 + 601863 CA------------------------TCTTCAGGATC-CCTCTTTACATAGA -s simRat_chr6.simRat.chr6 92996 28 + 647215 CT------------------------TCTTCAGGATGTCCTCTTTAGCAAGA - -a -s simMouse_chr6.simMouse.chr6 100908 73 + 636262 GCACCAAAATGACATGCACCTGGTCTTGATCACTCACAGGATGTGAGTATCTCACAGGAGGGATCTACACTAT -s Anc0.Anc0refChr4 41984 29 - 45765 A------------A--------------------------------GCATGTCACAGGTGGGATCTACATTAC -s Anc1.Anc1refChr2 74070 56 + 144309 A------------ATGCAGCTGGTCTAAATCACTCACAG-----AAGCATGTCACAGGTGGGATCTACATTAC -s Anc2.Anc2refChr2 11396 29 + 27695 A------------A--------------------------------GCATGTCACAGGTGGGATCTACATCAC -s mr.mrrefChr0 95961 73 + 130230 GCACCAAAATGACATGCACCTGGTCTTGATCACTCACAGGATGTGAGTATCTCACAGGAGGGATCTACACTAT -s simCow_chr6.simCow.chr6 101566 29 + 602619 A------------A--------------------------------GCATGTCACTGATGAAAGCTACAACAA -s simDog_chr6.simDog.chr6 497673 29 - 593897 A------------A--------------------------------GCATGTCACAGGTGGGATCTATATCAC -s simHuman_chr6.simHuman.chr6 96770 56 + 601863 A------------ATGCAGCTGGTCTAAATCACTCACAG-----AAGCATGTTGCAGGTGGGATCTACATTAC -s simRat_chr6.simRat.chr6 93027 73 + 647215 GCACCAAAATGACATGCATCTGGTCTTGATCACTCACAGGGTGTGAGTATCTCACAGAAGGGATCTACACTAT - -a -s simMouse_chr6.simMouse.chr6 100981 23 + 636262 TGCAGAATGCACCTGTACTAGCC -s Anc0.Anc0refChr4 42013 21 - 45765 TACACA-TACACATATAAT-TAC -s Anc1.Anc1refChr2 74126 22 + 144309 TACACAATACACATATAAT-TAC -s Anc2.Anc2refChr2 11425 21 + 27695 TACACA-TACACATATAAT-TAC -s mr.mrrefChr0 96034 23 + 130230 TACAGAATGCACCTGTACTATCC -s simCow_chr6.simCow.chr6 101595 21 + 602619 TACACA-TATGCATATAAC-TGC -s simDog_chr6.simDog.chr6 497957 21 - 593897 TACACA-TACACATATAAT-TAT -s simHuman_chr6.simHuman.chr6 96826 22 + 601863 TACATACTACATTTACGAT-TAC -s simRat_chr6.simRat.chr6 93100 23 + 647215 TACAGAATGCACCTGTACTATCC - -a -s simMouse_chr6.simMouse.chr6 101004 7 + 636262 TGGATTC -s Anc0.Anc0refChr4 42034 7 - 45765 TGGATTC -s Anc1.Anc1refChr2 74148 7 + 144309 TGGATTC -s Anc2.Anc2refChr2 11448 7 + 27695 TGTATTC -s mr.mrrefChr0 96057 7 + 130230 TGGATTC -s simCow_chr6.simCow.chr6 101618 7 + 602619 TATATTC -s simDog_chr6.simDog.chr6 497980 7 - 593897 TGTGTTC -s simHuman_chr6.simHuman.chr6 96848 7 + 601863 TGGATTC -s simRat_chr6.simRat.chr6 93123 7 + 647215 TGGATCC - -a -s simMouse_chr6.simMouse.chr6 101011 17 + 636262 TCACAACACATTTGCAG -s Anc0.Anc0refChr4 42041 17 - 45765 CCACAACACCTTCACAG -s Anc1.Anc1refChr2 74155 17 + 144309 CCACAACACCTTCACAG -s Anc2.Anc2refChr2 11455 17 + 27695 CCACAACACCTTCACAG -s mr.mrrefChr0 96064 17 + 130230 TCACAACACATTTGCAG -s simCow_chr6.simCow.chr6 101661 17 + 602619 CCACAATACTTTCACAG -s simDog_chr6.simDog.chr6 497987 17 - 593897 CTACAACACCTCCACAG -s simHuman_chr6.simHuman.chr6 96855 17 + 601863 CCACAACACCTTCACAG -s simRat_chr6.simRat.chr6 93130 17 + 647215 GCACAACACATTTGCAG - -a -s simMouse_chr6.simMouse.chr6 101028 4 + 636262 TGAT -s Anc0.Anc0refChr4 42058 4 - 45765 CTAT -s Anc1.Anc1refChr2 74172 4 + 144309 CTAT -s Anc2.Anc2refChr2 11472 4 + 27695 CTCT -s mr.mrrefChr0 96081 4 + 130230 CGAT -s simCow_chr6.simCow.chr6 101680 4 + 602619 ATCT -s simDog_chr6.simDog.chr6 498004 4 - 593897 CTCT -s simHuman_chr6.simHuman.chr6 96872 4 + 601863 CTAT -s simRat_chr6.simRat.chr6 93147 4 + 647215 CCAT - -a -s simMouse_chr6.simMouse.chr6 101032 83 + 636262 CAAGGAGCTTCAAATACACATTATGAACCTGGATTCTTGCAAAACATCTGCGGCTAGCAAGGAGCACCGCAACAATATTTTGA -s Anc0.Anc0refChr4 42062 22 - 45765 GAAAG--------------T--------------------------------------------CATTACATC---ATCATGA -s Anc1.Anc1refChr2 74176 22 + 144309 GAAAG--------------T--------------------------------------------CATTACATC---ATCATGA -s Anc2.Anc2refChr2 11476 22 + 27695 GAAAG--------------T--------------------------------------------CATCACATA---AACATGA -s mr.mrrefChr0 96085 39 + 130230 CAAGGAGCTTCAAATACACA--------------------------------------------CATTGCAACAATATTTTGA -s simCow_chr6.simCow.chr6 101684 22 + 602619 GAAAG--------------T--------------------------------------------CATCACATG---AACATAA -s simDog_chr6.simDog.chr6 498147 22 - 593897 GAATG--------------C--------------------------------------------CATCACATA---AACATGA -s simHuman_chr6.simHuman.chr6 96876 22 + 601863 GAAAG--------------T--------------------------------------------CATTATACC---ATCATGA -s simRat_chr6.simRat.chr6 93151 39 + 647215 CAAGGAGCATCAAGTGCACA--------------------------------------------CATTGCATTAATATTTTGA - -a -s simMouse_chr6.simMouse.chr6 101115 18 + 636262 ACCCCATAGACTTTAATA -s Anc0.Anc0refChr4 42084 17 - 45765 CCCTAAT-GAATCTTATC -s Anc1.Anc1refChr2 74198 17 + 144309 CCCTAAT-GAATCTTATC -s Anc2.Anc2refChr2 11498 17 + 27695 CCCTAAT-GGATTTTAGC -s mr.mrrefChr0 96124 18 + 130230 ACCCCATAGACTCTTATA -s simCow_chr6.simCow.chr6 101712 17 + 602619 CCCTCAT-GGATTTTAGC -s simDog_chr6.simDog.chr6 498169 8 - 593897 TCCTAAT-G--------- -s simHuman_chr6.simHuman.chr6 96898 17 + 601863 CCCTGTT-GAGTCTTATT -s simRat_chr6.simRat.chr6 93190 18 + 647215 ACCTCATATAATCTTATA - -a -s simMouse_chr6.simMouse.chr6 101133 64 + 636262 GATGGCCTACAAACAGTGCGAGATCCACTACTTGAACACCGTATGCCTGCTTAGATAGCATAAT -s Anc0.Anc0refChr4 42101 64 - 45765 GATCAATTACAAACAGTGAGAAACTCCCTACTTGGACACTGTGCACATGCTTAGATAACACACC -s Anc1.Anc1refChr2 74215 64 + 144309 GATCAATTACAAACAGTGAGAAACTCCCTACTTGGACACTGTGCACATGCTTAGATAACACACC -s Anc2.Anc2refChr2 11515 64 + 27695 GATCAATTACAAACAATGATAAACTCCCTACTTGGCCACTGTGCACATGCTTAGATAACACACC -s mr.mrrefChr0 96142 64 + 130230 GATGGCCTACAAACAGTGCGAAATCCACTACTTGGACACTGTATGCCTGCTTAGATAGCACACT -s simCow_chr6.simCow.chr6 101730 64 + 602619 GGTGAGTTATAAACAATGACCAACCCACTACTCAGCCAATGTGCACCTGCTTAGATACTACACC -s simDog_chr6.simDog.chr6 498177 63 - 593897 GATCAATTACAAACAATGATAAA-TCCATATTTGGCCACTGTGCACATGCTTGGCTAACACACC -s simHuman_chr6.simHuman.chr6 96915 64 + 601863 GATCAATTACAAATAGTGAGAAACTGTCTGCTTGGACACTCTGCACTTGCTTAGATAACGCACC -s simRat_chr6.simRat.chr6 93208 64 + 647215 GATGGCCTACCAACAGTGCAAAATCCACTACTTGGACACTGCATGCCTGCTTAGATAGCACACT - -a -s simMouse_chr6.simMouse.chr6 101197 11 + 636262 TGCTTTATATC -s Anc0.Anc0refChr4 42165 11 - 45765 TGCTTTATATC -s Anc1.Anc1refChr2 74279 11 + 144309 TGCTTTATATC -s Anc2.Anc2refChr2 11579 11 + 27695 TGCTTTATATC -s mr.mrrefChr0 96206 11 + 130230 TGCTTTATATC -s simCow_chr6.simCow.chr6 101794 11 + 602619 TGCTTTATATC -s simDog_chr6.simDog.chr6 498243 11 - 593897 TGCTTTATACC -s simHuman_chr6.simHuman.chr6 96979 11 + 601863 TCCTTAATATC -s simRat_chr6.simRat.chr6 93272 11 + 647215 TGCTTTGTACC - -a -s simMouse_chr6.simMouse.chr6 101208 160 + 636262 GGTGATGACACATACTGGCTAGTATTCCCATAGGAATGAAACAATTGCTCAGTGCAACTGACTACAAATTAGAAGCTCATACCAAGTGCTACAGGAACTAGGAGGTGTGGTTGCATGATTAAGTTTTTAGATTGTAGGTATGCCAATCAAATCAGGGGTT -s Anc0.Anc0refChr4 42177 92 - 45765 AGTGATAACACATATTGGCTATTGTTCATATAGCAATGAAACTATTGTCCAGTGCCA-----AA--------------------------------------------------------------TTAGACAGTAAGTGTGCCAATCAAATTTGGTG-T -s Anc1.Anc1refChr2 74291 97 + 144309 AGTGATAACACATATTGGCTATTGTTCATATAGCAATGAAACTATTGTCCAGTGCCAGTCTAAA--------------------------------------------------------------TTAGACAGTAAGTGTGCCAATCAAATTTGGTG-T -s Anc2.Anc2refChr2 11591 92 + 27695 AGTGATGACACATATTGGTGATTGTTCATATAGCAATGAAACCATTGTCCAGTGCCA-----AA--------------------------------------------------------------TTAGACAGCAAGTGGCCCAATCAAATTTGGTG-T -s mr.mrrefChr0 96217 159 + 130230 GGTGATAACACATTATTGCTAATATTCCCATAGGAATGAAACTATTGCTCAGTGCCACTGACAACAAATTAGAAGCTCATACCAAGTGCTACAGGAACTAGGAGGTGTGGTTGCATGATTAAGTTTTTAGACTGTAGGTATGCCAATCAAATCAGGTG-T -s simCow_chr6.simCow.chr6 101806 83 + 602619 AGTGATGACACATATTGGTAATTGT---------AATGAAATCACTGTCCAGTGCCA-----AA--------------------------------------------------------------TTTGACAGCAAGTGCCCTAAGCGAATTTGGTC-T -s simDog_chr6.simDog.chr6 498255 92 - 593897 AGTGATGACACATATTGTTGATTGTTCATATAGCAATGAAACCATTGTTCAGTGCCA-----AA--------------------------------------------------------------TCAAACAGCAAGTGGCCCTATCAAATATGGTG-T -s simHuman_chr6.simHuman.chr6 96993 91 + 601863 AGAGATAAC------TGGCTATTGTTCATACAATAATGAAACTATTGTCCAGTGCCGGTCTAAA--------------------------------------------------------------TTAGACAGTAAGTGTGCCAATCAAATTTGGTG-T -s simRat_chr6.simRat.chr6 93283 159 + 647215 AGTGATAACACATTATTGCCTATATTCCAATAGGAAGGTAAATTATCCAGAGTGCCACTGACAACAAGTTAGAAGATCATACCTAGTGCTAAAGGAACAAGTAGGTGTGGTTGCATGAATAATTTTTTAGACTGCAGGTATGCCAACCACATCAGGTG-T - -a -s simMouse_chr6.simMouse.chr6 101368 17 + 636262 TTGGTCAACTATTACCT -s Anc0.Anc0refChr4 42271 17 - 45765 TTGGTCAACTATTATCT -s Anc1.Anc1refChr2 74390 17 + 144309 TTGGTCAACTATTATCT -s Anc2.Anc2refChr2 11685 17 + 27695 TCAGTCAACCATTATCT -s mr.mrrefChr0 96376 17 + 130230 TTGGTCAACTATTACCT -s simCow_chr6.simCow.chr6 101891 17 + 602619 TCAGCCAACCATTATCT -s simDog_chr6.simDog.chr6 498349 17 - 593897 CCAGTCAACCATTGTCT -s simHuman_chr6.simHuman.chr6 97086 17 + 601863 TTGATAAGCTATTATCT -s simRat_chr6.simRat.chr6 93442 17 + 647215 TTGGCTAACTATTACTT - -a -s simMouse_chr6.simMouse.chr6 101385 7 + 636262 CATACTA -s Anc0.Anc0refChr4 42288 7 - 45765 CATGCTA -s Anc1.Anc1refChr2 74407 7 + 144309 CATGCTA -s Anc2.Anc2refChr2 11704 7 + 27695 CATGACT -s mr.mrrefChr0 96393 7 + 130230 CATACTA -s simCow_chr6.simCow.chr6 101910 7 + 602619 CAGGACT -s simDog_chr6.simDog.chr6 498368 7 - 593897 CATGACT -s simHuman_chr6.simHuman.chr6 97104 7 + 601863 TCGGCTA -s simRat_chr6.simRat.chr6 93459 7 + 647215 CATACTA - -a -s simMouse_chr6.simMouse.chr6 101392 14 + 636262 ATATTCTGTGGGCT -s Anc0.Anc0refChr4 42295 14 - 45765 ATATTCTGCAGGCT -s Anc1.Anc1refChr2 74414 14 + 144309 ATATTCTGCAGGCT -s Anc2.Anc2refChr2 11711 14 + 27695 ATATTCTGCAGGAT -s mr.mrrefChr0 96400 14 + 130230 ATATTCTGTGGGCT -s simCow_chr6.simCow.chr6 101917 14 + 602619 ATATTCTGCAGGCT -s simDog_chr6.simDog.chr6 498375 14 - 593897 ATATTCTGCAGGAC -s simHuman_chr6.simHuman.chr6 97111 8 + 601863 GTGCC------GCT -s simRat_chr6.simRat.chr6 93468 14 + 647215 ATATTCTGTAGACT - -a -s simMouse_chr6.simMouse.chr6 101406 17 + 636262 ATAAATGACTTGCAAAC -s Anc0.Anc0refChr4 42322 17 - 45765 ATCAATGACTGACAAAT -s Anc1.Anc1refChr2 74441 17 + 144309 ATCAATGACTGACAAAT -s Anc2.Anc2refChr2 11738 17 + 27695 ATCAATGACTGACAAAT -s mr.mrrefChr0 96414 17 + 130230 ATCAATGACTGGCAAAC -s simCow_chr6.simCow.chr6 101944 17 + 602619 ATCTATGATTGACAAAA -s simDog_chr6.simDog.chr6 498402 17 - 593897 ATCAATGACTTACAAAT -s simHuman_chr6.simHuman.chr6 97132 17 + 601863 ATCCATGACTGACAAAT -s simRat_chr6.simRat.chr6 93482 17 + 647215 ATCAATGACTGGCAAAC - -a -s simMouse_chr6.simMouse.chr6 101423 11 + 636262 TTGCAGTGAGC -s Anc0.Anc0refChr4 42340 11 - 45765 TTGTAGAGAAC -s Anc1.Anc1refChr2 74459 11 + 144309 TTGTAGAGAAC -s Anc2.Anc2refChr2 11756 11 + 27695 TTGTAGAGAAC -s mr.mrrefChr0 96432 11 + 130230 TTGCAGTGAAC -s simCow_chr6.simCow.chr6 101962 11 + 602619 TTGCAGAGAAC -s simDog_chr6.simDog.chr6 498420 11 - 593897 TCATGGAGAAC -s simHuman_chr6.simHuman.chr6 97150 11 + 601863 ATGTAGAGAAC -s simRat_chr6.simRat.chr6 93500 11 + 647215 TTGCATGAAAC - -a -s simMouse_chr6.simMouse.chr6 101434 8 + 636262 GGTGCTTG -s Anc0.Anc0refChr4 42352 8 - 45765 GGTGCCTG -s Anc1.Anc1refChr2 74471 8 + 144309 GGTGCCTG -s Anc2.Anc2refChr2 11768 8 + 27695 GGTGCCTG -s mr.mrrefChr0 96443 8 + 130230 GGTGCTTG -s simCow_chr6.simCow.chr6 101974 8 + 602619 GGTGCCTG -s simDog_chr6.simDog.chr6 498432 8 - 593897 GGTGCGTG -s simHuman_chr6.simHuman.chr6 97162 8 + 601863 GGTGCCTG -s simRat_chr6.simRat.chr6 93511 8 + 647215 AGTGCTTG - -a -s simMouse_chr6.simMouse.chr6 101442 194 + 636262 CTAAGTTAGATGTCTAGGGCATGCTTGTTGTTAGGTAAGGAAGGAGCCTAATGTTGTGATAAAAAAAAAAAACCCCACTAGGACAAAAAAAAGACAACTAGAACAATACCGAACCTACATTGATTATTCCAGTCGAAGGTGCTCAAAAAAATTAAATCTCCTGTTAATCCGATATCACCAGGGAGGAAAGACCC -s Anc0.Anc0refChr4 42360 174 - 45765 TTGAGTCAGATGTGTAGGGGAAGTTCATTTATAGATAGAGGAGGGGCCTGATGCAGTGTTCAATAAAAAAAGCCCCACTTGAACAATGTAAAACCTATAA--------------------TGATCCTTCCAGTGGGAGATTCTTGACAGAATTAAGTCTCTTCTTGATTCAATAGTGCAGGGGAAAAAAGACTG -s Anc1.Anc1refChr2 74479 174 + 144309 TTGAGTCAGATGTGTAGGGGAAGTTCATTTATAGATAGAGGAGGGGCCTGATGCAGTGTTCAATAAAAAAAGCCCCACTTGAACAATGTAAAACCTATAA--------------------TGATCCTTCCAGTGGGAGATTCTTGACAGAATTAAGTCTCTTCTTGATTCAATAGTGCAGGGGAAAAAAGACTG -s Anc2.Anc2refChr2 11776 174 + 27695 TTGAGTCAGATGTGAAGGGAAAGTTCATTTATCGATGGAGAAGGGGCCTGATGCAATGTTCAATACAAAAAGCCTCACTTGAACTTTGTAAAACTTACAA--------------------TGATCCTTCCAGTGGGAGATTATTGACAGAATTAAGTCTCTTCTTGATTCAATAGTGAAGGGGAAAAAAGACTG -s mr.mrrefChr0 96451 189 + 130230 CTAAGTTAGATGTCTAGGGGATGCTTGTTGATAGGTAAGGGAGGAGCCTAATGTTGTGATAAAAAAAAAAAACCCCACTAGGACAAAGAAAAGCCAATTAGAACAATACCGAA-----ATTGATTATTCCAGTGGAAGATGCTTGAAAAAATTAAATCTCCTGTTGATCCGATATCGCCAGGGAAGAAAGACCC -s simCow_chr6.simCow.chr6 101982 162 + 602619 TTTAGTCCGATGTAAAGGGAAAATTCTTTTATCAATGGGGTAGGGGCCTGACACAATGCTCAG---AAGAAGACTCA----AATTCTGCTAAGCTTGCAA--------------------TGAACCTTCCAGTGGGAGATTTATGACAGAATTAAGTCTCTTTTTGGTTCGATGGTGAAGGGAAAAAAA----- -s simDog_chr6.simDog.chr6 498440 170 - 593897 CTGAGTTAGATGTGAAGGGAATGCTCATTTATCGATGCAGAAGCGTCTCAATGCAATGTTCCATACAAAAAGCCTCACTTGAGCTTTGTAAAACTTACAA--------------------CCATGCTTCCA--GGTAGGAGATTAACAGAATCAAGTCTCTTCTTGATTAAATAAC--AGGGGGAAAAAGACTG -s simHuman_chr6.simHuman.chr6 97170 172 + 601863 TTGAGTCAGATGTGTAGGGGAATTTCATTCATAGATAGAGGAAGGGCCTGATGCAGCG--CAATAACAAGAGCCCCACTTGAACAATGTAAAACCTATGA--------------------TGATCCTTCCCACGGGGGATTCTTGCCAGAATTAAGTCTCTTCTTGATTCAATAGTGCAGGGGAAAAAAAACTG -s simRat_chr6.simRat.chr6 93526 186 + 647215 CCTAGTTAGATGTCTAGGGGATGCTTGTTGATATGTAATGGAGGAGCCTAATGTTGTGATAAAAAAAAAAAATCCCACTAGGACAAAGAAAAGCCCATTAGAACAATACTGAA-----ATTG--TACTTCAGTGGAAGATACTTG-GAAAATTAAATCTTCAATTGATCTGATATCGCCAAGGAAGAAAGACCA - -a -s simMouse_chr6.simMouse.chr6 101636 42 + 636262 CGGAGAGGATGCTTTCTGGAGATGCTCAAAAACTCATGTGTC -s Anc0.Anc0refChr4 42534 42 - 45765 TCAAGAGGGTGCTTTCTGGAGTTGCTCAAAAACTCATGTGTA -s Anc1.Anc1refChr2 74653 42 + 144309 TCAAGAGGGTGCTTTCTGGAGTTGCTCAAAAACTCATGTGTA -s Anc2.Anc2refChr2 11950 42 + 27695 TCCAGAGGGTGCTCTCTGGAGTTGCCTAAAAACTCTTGTGTA -s mr.mrrefChr0 96640 42 + 130230 TGAAGAGGGTGCTTTCTGGAGATGCTCAAAAACTCATGTGTT -s simCow_chr6.simCow.chr6 102144 36 + 602619 ------GGGTGCTCTCTGGAGTTGCCTAAAAACTCCTGTATT -s simDog_chr6.simDog.chr6 498613 42 - 593897 TCCAGAGGATGCTCTCTGGAGTTGCCTGAAAACTCTTGTGTA -s simHuman_chr6.simHuman.chr6 97342 42 + 601863 TCAAGAGGGTGCTTTCTCGAGGTGCTCAAAAACTCATGTGTA -s simRat_chr6.simRat.chr6 93712 42 + 647215 TGAAGAGAGTGCTTTCTGGAGATGCTCAAAAACTCATGTGTT - -a -s simMouse_chr6.simMouse.chr6 101678 32 + 636262 TACCTCACAAATAGTTATCACTTGTCAACATT -s Anc0.Anc0refChr4 42576 32 - 45765 TACTTAACAAAGAGCTATCACTTGTTAACATC -s Anc1.Anc1refChr2 74695 32 + 144309 TACTTAACAAAGAGCTATCACTTGTTAACATC -s Anc2.Anc2refChr2 11992 32 + 27695 TACTTAACAAAGAGCTATCACTTGTTAACATT -s mr.mrrefChr0 96682 32 + 130230 TACCTCACAAATAGTTATCACTTGTTAACATC -s simCow_chr6.simCow.chr6 102180 32 + 602619 AACTAAACAAAGAGCTATCACTAGTTGTAATT -s simDog_chr6.simDog.chr6 498655 32 - 593897 TACTTTATACAGAGATATCACTTGTTAACATT -s simHuman_chr6.simHuman.chr6 97388 32 + 601863 TAGTTAACAAAGAGCTATCACTTGTTAACATC -s simRat_chr6.simRat.chr6 93754 32 + 647215 TATGTCACAAATGATTATCAATTGTTAATGTC - -a -s simMouse_chr6.simMouse.chr6 101710 5 + 636262 GCTGA -s Anc0.Anc0refChr4 42609 5 - 45765 GCTGA -s Anc1.Anc1refChr2 74728 5 + 144309 GCTGA -s Anc2.Anc2refChr2 12025 5 + 27695 ACTGA -s mr.mrrefChr0 96714 5 + 130230 GCTGA -s simCow_chr6.simCow.chr6 102213 5 + 602619 ACTGA -s simDog_chr6.simDog.chr6 498688 1 - 593897 ----A -s simHuman_chr6.simHuman.chr6 97421 5 + 601863 GCTGA -s simRat_chr6.simRat.chr6 93786 5 + 647215 GCTGA - -a -s simMouse_chr6.simMouse.chr6 101715 12 + 636262 CCCTGGAGCCAG -s Anc0.Anc0refChr4 42615 12 - 45765 CCCTCAACCCTG -s Anc1.Anc1refChr2 74734 12 + 144309 CCCTCAACCCTG -s Anc2.Anc2refChr2 12031 12 + 27695 CCACCAACCCTG -s mr.mrrefChr0 96719 12 + 130230 CCCTGGACCCAG -s simCow_chr6.simCow.chr6 102219 11 + 602619 CC-CCAACCCTG -s simDog_chr6.simDog.chr6 498690 12 - 593897 CCACTAACCTTG -s simHuman_chr6.simHuman.chr6 97427 12 + 601863 CCCTCTACCCTG -s simRat_chr6.simRat.chr6 93791 12 + 647215 TGCTGGACCCAG - -a -s simMouse_chr6.simMouse.chr6 101727 20 + 636262 TGATGTGTATAGATGATTTC -s Anc0.Anc0refChr4 42665 20 - 45765 TTATGAGTATAGATAAATTC -s Anc1.Anc1refChr2 74784 20 + 144309 TTATGAGTATAGATAAATTC -s Anc2.Anc2refChr2 12081 20 + 27695 TTATGAGTATAGATAAATTC -s mr.mrrefChr0 96765 20 + 130230 TGATGTGTATAGATGAATTC -s simCow_chr6.simCow.chr6 102249 19 + 602619 GTATCAGTATAGATAAAT-C -s simDog_chr6.simDog.chr6 498740 20 - 593897 TTGTGGGTATAGATGGAATC -s simHuman_chr6.simHuman.chr6 97480 20 + 601863 TTATGAGTATAGATAAATTC -s simRat_chr6.simRat.chr6 93837 20 + 647215 TGGTGTGTATAGATGAATTT - -a -s simMouse_chr6.simMouse.chr6 101747 8 + 636262 ATTGATCA -s Anc0.Anc0refChr4 42691 7 - 45765 GTTGATC- -s Anc1.Anc1refChr2 74810 7 + 144309 GTTGATC- -s Anc2.Anc2refChr2 12107 7 + 27695 GTTGATC- -s mr.mrrefChr0 96785 8 + 130230 ATTGATCA -s simCow_chr6.simCow.chr6 102274 7 + 602619 GTTGATC- -s simDog_chr6.simDog.chr6 498764 7 - 593897 GTTGATT- -s simHuman_chr6.simHuman.chr6 97506 7 + 601863 GTTAATC- -s simRat_chr6.simRat.chr6 93857 8 + 647215 CTTGATCA - -a -s simMouse_chr6.simMouse.chr6 101755 22 + 636262 CCACTTGGCTACCCACTGGATA -s Anc0.Anc0refChr4 42698 22 - 45765 CCACCTGTCTGTCACCTGGATG -s Anc1.Anc1refChr2 74817 22 + 144309 CCACCTGTCTGTCACCTGGATG -s Anc2.Anc2refChr2 12114 22 + 27695 CCACCTGTCTGCCACTTGGATG -s mr.mrrefChr0 96793 22 + 130230 CCACTTGGCTATCAACTGGATA -s simCow_chr6.simCow.chr6 102282 22 + 602619 CCATCTGTCTGCCAATTGGATG -s simDog_chr6.simDog.chr6 498783 22 - 593897 CCACCTGTCTGCCACTTGGATG -s simHuman_chr6.simHuman.chr6 97513 22 + 601863 CCACCTGTCTGTCACCTGGATG -s simRat_chr6.simRat.chr6 93865 22 + 647215 CCACTTGGCTATCAGCTGGATA - -a -s simMouse_chr6.simMouse.chr6 101777 18 + 636262 TGATTGTTTTTATTTTTG -s Anc0.Anc0refChr4 42720 16 - 45765 GA--TTTTCTCACTTTTG -s Anc1.Anc1refChr2 74839 16 + 144309 GA--TTTTCTCACTTTTG -s Anc2.Anc2refChr2 12138 16 + 27695 GA--ATCTCTCATTCTTG -s mr.mrrefChr0 96815 18 + 130230 GGATTGTTTTCACTTTTG -s simCow_chr6.simCow.chr6 102306 16 + 602619 GA--ATCTTTGATGCTTG -s simDog_chr6.simDog.chr6 498807 16 - 593897 GA--ATCTCTCATTCTTG -s simHuman_chr6.simHuman.chr6 97535 16 + 601863 GA--TCTTGTCACTTGTG -s simRat_chr6.simRat.chr6 93887 18 + 647215 GGATTGTTTTCACTTTTG - -a -s simMouse_chr6.simMouse.chr6 101795 23 + 636262 GGGTGTAACAAGCTTTTAAGTGT -s Anc0.Anc0refChr4 42736 23 - 45765 GGGTTTGACAAGCTTTGAACTAT -s Anc1.Anc1refChr2 74855 23 + 144309 GGGTTTGACAAGCTTTGAACTAT -s Anc2.Anc2refChr2 12154 23 + 27695 GGGTTTGACAAGCTTTGAACTAT -s mr.mrrefChr0 96833 23 + 130230 GGGTGTAACAAGCTTTTAAGTGT -s simCow_chr6.simCow.chr6 102322 21 + 602619 GGGTTTGACA--CTTTGATGTAT -s simDog_chr6.simDog.chr6 498823 23 - 593897 GGGTTTGGCAAGCTTTGAACTAT -s simHuman_chr6.simHuman.chr6 97551 23 + 601863 TGGTTTGACAAGTGTTGAACTAT -s simRat_chr6.simRat.chr6 93906 23 + 647215 GAGTGTAACAAGCTGTTAAGTGT - -a -s simMouse_chr6.simMouse.chr6 101818 3 + 636262 CTT -s Anc0.Anc0refChr4 42759 3 - 45765 CTT -s Anc1.Anc1refChr2 74878 3 + 144309 CTT -s Anc2.Anc2refChr2 12177 3 + 27695 CTT -s mr.mrrefChr0 96856 3 + 130230 CTT -s simCow_chr6.simCow.chr6 102343 3 + 602619 CAT -s simDog_chr6.simDog.chr6 498846 3 - 593897 CTG -s simHuman_chr6.simHuman.chr6 97574 3 + 601863 CTT -s simRat_chr6.simRat.chr6 93930 3 + 647215 TTT - -a -s simMouse_chr6.simMouse.chr6 101821 17 + 636262 AGTAAGGAAACTAATGG -s Anc0.Anc0refChr4 42764 17 - 45765 AGTAAGGAAACAAATGC -s Anc1.Anc1refChr2 74883 17 + 144309 AGTAAGGAAACAAATGC -s Anc2.Anc2refChr2 12182 17 + 27695 AGTAAGGAAACAAATGG -s mr.mrrefChr0 96859 17 + 130230 AGTAAGGAAACTAATGC -s simCow_chr6.simCow.chr6 102348 17 + 602619 AGTAAGAAAACAAATGG -s simDog_chr6.simDog.chr6 498851 17 - 593897 AGTAAGGAAACAAATGG -s simHuman_chr6.simHuman.chr6 97579 17 + 601863 AGTAAGGAAACAAAAGC -s simRat_chr6.simRat.chr6 93933 17 + 647215 AGTAAGGGAACTAACGC - -a -s simMouse_chr6.simMouse.chr6 101838 1 + 636262 G -s Anc0.Anc0refChr4 42781 1 - 45765 G -s Anc1.Anc1refChr2 74900 1 + 144309 G -s Anc2.Anc2refChr2 12210 1 + 27695 G -s mr.mrrefChr0 96876 1 + 130230 G -s simCow_chr6.simCow.chr6 102376 1 + 602619 G -s simDog_chr6.simDog.chr6 498879 1 - 593897 G -s simHuman_chr6.simHuman.chr6 97596 1 + 601863 G -s simRat_chr6.simRat.chr6 93950 1 + 647215 G - -a -s simMouse_chr6.simMouse.chr6 101839 1 + 636262 A -s Anc0.Anc0refChr4 42782 1 - 45765 A -s Anc1.Anc1refChr2 74901 1 + 144309 A -s Anc2.Anc2refChr2 12211 1 + 27695 A -s mr.mrrefChr0 96877 1 + 130230 A -s simCow_chr6.simCow.chr6 102377 1 + 602619 A -s simDog_chr6.simDog.chr6 498880 1 - 593897 A -s simHuman_chr6.simHuman.chr6 97640 1 + 601863 A -s simRat_chr6.simRat.chr6 93951 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 101840 33 + 636262 TGTTGTGTGCTCCTGGAATGCAACAATTGTTGT -s Anc0.Anc0refChr4 42783 33 - 45765 TGTGGTGTGCTCAGGTAACCTCACAAGTGTTGT -s Anc1.Anc1refChr2 74902 33 + 144309 TGTGGTGTGCTCAGGTAACCTCACAAGTGTTGT -s Anc2.Anc2refChr2 12212 33 + 27695 TGTGTTGTGCTCAGGTAACCCCACAAGTGTTGT -s mr.mrrefChr0 96878 33 + 130230 TGTTGTGTGCTCATGGAATGTAACAATTGTTGT -s simCow_chr6.simCow.chr6 102378 33 + 602619 TGCATTGTGTTCAGGTAACGCCACAATTCCCGT -s simDog_chr6.simDog.chr6 498881 30 - 593897 TGTGTTGTGCTTATG---CCCCACAAGTGTTGT -s simHuman_chr6.simHuman.chr6 97641 33 + 601863 TGTGGTGTCCTCAGGAAACCTCATGAGTGTTGT -s simRat_chr6.simRat.chr6 93953 33 + 647215 TGTTGTATGCTCATAGAATGTGACAATTGTGGT - -a -s simMouse_chr6.simMouse.chr6 101873 5 + 636262 AGTGC -s Anc0.Anc0refChr4 42825 5 - 45765 AGTGT -s Anc1.Anc1refChr2 74944 5 + 144309 AGTGT -s Anc2.Anc2refChr2 12254 5 + 27695 AGTGT -s mr.mrrefChr0 96911 5 + 130230 AGTGC -s simCow_chr6.simCow.chr6 102420 5 + 602619 AGTGC -s simDog_chr6.simDog.chr6 498920 5 - 593897 AGTGT -s simHuman_chr6.simHuman.chr6 97683 5 + 601863 AGTGT -s simRat_chr6.simRat.chr6 93986 5 + 647215 AGTGC - -a -s simMouse_chr6.simMouse.chr6 101878 49 + 636262 ACATCATGAGCCGTATGAGTCACCAGGCCTTCCATAGCTTGCCACAGAC -s Anc0.Anc0refChr4 42833 49 - 45765 ACACCATGAGAGATAAGTGTTAGCAGGCTTTGACTAGATGGCCATAGAC -s Anc1.Anc1refChr2 74952 49 + 144309 ACACCATGAGAGATAAGTGTTAGCAGGCTTTGACTAGATGGCCATAGAC -s Anc2.Anc2refChr2 12268 49 + 27695 ATGCCATGAGAGACAAGTGTTAGCAGGCTTTGACTAAATGGGTATAGAC -s mr.mrrefChr0 96916 49 + 130230 ACATCATGAGCCGTATGAGTCAGCAGGCCTTCAATAGATGGCCACAGAC -s simCow_chr6.simCow.chr6 102436 49 + 602619 ATGCCTTGACAGAGAAGTGTTAGCAGGCTTTGACTAAACGGGAATACTC -s simDog_chr6.simDog.chr6 498934 49 - 593897 ATGCCACAAGAGACAGATGTTAGCAGGCATTGACTAAATGGGTATAGAC -s simHuman_chr6.simHuman.chr6 97691 49 + 601863 ACACCATGATATATAAGTGCTGGCAGGCTTTGACTAGATGGCCATAGAC -s simRat_chr6.simRat.chr6 93991 49 + 647215 ACATCATGAGCAGAATGAGTCAGCAGGCCCTAAATAGATGGGCACAGAC - -a -s simMouse_chr6.simMouse.chr6 101927 43 + 636262 TCTTGATTAACAGGCTTTGTGATTTCAGGAGTAGGAAGAATCA -s Anc0.Anc0refChr4 42883 43 - 45765 GCTTTTCTATCAGACTTGATAATGTCAGGAAAAGAATGTATCA -s Anc1.Anc1refChr2 75002 43 + 144309 GCTTTTCTATCAGACTTGATAATGTCAGGAAAAGAATGTATCA -s Anc2.Anc2refChr2 12318 43 + 27695 GGTTTTCTATCAGACTTGATAATGTCAGGAAAAGAATGTATCA -s mr.mrrefChr0 96965 43 + 130230 TCTTGACTAACAGACTTTGTGATGTCAGGAGTAGGAAGTATCA -s simCow_chr6.simCow.chr6 102486 43 + 602619 GTTTTCATATCAGACTCGATAATGTCAGGGAAAGAGTGTATCA -s simDog_chr6.simDog.chr6 498984 43 - 593897 AGTTGTCTATCAGACTTGATAATGTATGGAATAGAATGTATCA -s simHuman_chr6.simHuman.chr6 97741 43 + 601863 GCCATTCTATCAGATTTGATAATGTCATGACAAGAATGTATCA -s simRat_chr6.simRat.chr6 94040 43 + 647215 TCTTGACTAACAGACTTTGTGATGTCAGGAATAGGAAGTATCA - -a -s simMouse_chr6.simMouse.chr6 101970 18 + 636262 AAGAATCATGTCGGCAAG -s Anc0.Anc0refChr4 42929 18 - 45765 AAGCATCGTGCTAACAGG -s Anc1.Anc1refChr2 75050 18 + 144309 AAGCATCGTGCTAACAGG -s Anc2.Anc2refChr2 12364 18 + 27695 TAGCATTGAGCCAACAGG -s mr.mrrefChr0 97008 18 + 130230 AAGAATCATGTTGGCAAG -s simCow_chr6.simCow.chr6 102532 18 + 602619 CAGCAGTGGGCCAACAGG -s simDog_chr6.simDog.chr6 499030 18 - 593897 TGGCATTGAGCCAACAGA -s simHuman_chr6.simHuman.chr6 97789 18 + 601863 AAGCATCGTGCTAACAGG -s simRat_chr6.simRat.chr6 94083 18 + 647215 AAGAATCATGTTGGTAAA - -a -s simMouse_chr6.simMouse.chr6 101988 8 + 636262 TTGTAGCC -s Anc0.Anc0refChr4 42948 8 - 45765 TTGTCGCT -s Anc1.Anc1refChr2 75069 8 + 144309 TTGTCGCT -s Anc2.Anc2refChr2 12383 8 + 27695 TTATCACT -s mr.mrrefChr0 97026 8 + 130230 TTGTAGCC -s simCow_chr6.simCow.chr6 102551 8 + 602619 TTATCACT -s simDog_chr6.simDog.chr6 499049 8 - 593897 TTATCACT -s simHuman_chr6.simHuman.chr6 97808 8 + 601863 TTGTCGCT -s simRat_chr6.simRat.chr6 94101 8 + 647215 TTGTAGCC - -a -s simMouse_chr6.simMouse.chr6 101996 102 + 636262 TATTTCAACCTCTCACATGTGATCTGAGATTTAACGATCTCATAGGGGACTCTGTTATGTCTGCAATAAATTACCTAAATGTCATTTGGATCATTGGTGCTG -s Anc0.Anc0refChr4 42956 102 - 45765 TATTTGAATCTCCCACATGTTCTCTGAGATGTAACCACCATATAGGGCACCCTGTGATGTCTGCAATAAGTTACCCAGATGTCATGTGCATCGTTGGTGGTA -s Anc1.Anc1refChr2 75077 102 + 144309 TATTTGAATCTCCCACATGTTCTCTGAGATGTAACCACCATATAGGGCACCCTGTGATGTCTGCAATAAGTTACCCAGATGTCATGTGCATCGTTGGTGGTA -s Anc2.Anc2refChr2 12391 102 + 27695 TATTTGAATCTCCCACATGTTCTCTGCGCTGTAACCACCATATAGGGCACCTTGCGATGTCTGGAGTAAGTTACCCAGATGTCATGTGCATCGCTGGTGGTA -s mr.mrrefChr0 97034 102 + 130230 TATTTGAACCTCTCACATGTGATCTGAGATTTAACGATCTTATAGGGGACTCTGTGATGTCTGCAATAAATTACCTAGATGTCATTTGCATCATTGGTGCTG -s simCow_chr6.simCow.chr6 102559 102 + 602619 TATTTGATCCTGCTGGATGTTATCTGTGCTGTAAACACCATATATGGTCCCTTACCACATCTGAGGTAGCTTACCCATATGTGATGTGTGTCACTGGTGGTA -s simDog_chr6.simDog.chr6 499058 102 - 593897 TATCTGCATCTCCCACATAGTCTTTGCGCTGTAACCACCATATAGAGCACCTTGCGATGTCTAGAGTAAGTTAACCGGATGTCATGTACATTGCTGGTAGTA -s simHuman_chr6.simHuman.chr6 97816 102 + 601863 TGTTTGAATCTCCCACATGTTCTCTAAGATGTAACCACCATATAGGACACCCTGTGATGTCTGCAATAAGTTGCCCAGATGTCGTATGCATCTTTGGTGGTA -s simRat_chr6.simRat.chr6 94109 102 + 647215 TATTTGAACCTCTCGCATGTGACCTGAGATTTGATGATCTTATAGGGGACTCTGTGGTGTCTGCAATAAATTACCTAGATGTCATTTCCATCATTGGTGCTG - -a -s simMouse_chr6.simMouse.chr6 102098 66 + 636262 CTGACACTTTTTGGTAAGTGGCTGCATTCTGCAATGGCACTAATGTTTAACAGGCTTGGTTTGAGC -s Anc0.Anc0refChr4 43058 63 - 45765 CTCTCACTTTCTGGTAAGTAGCTACATTCTGAGATAAAACCAATGTTTACCAGGTTTGGTTTG--- -s Anc1.Anc1refChr2 75179 66 + 144309 CTCTCACTTTCTGGTAAGTAGCTACATTCTGAGATAAAACCAATGTTTACCAGGTTTGGTTTGGCC -s Anc2.Anc2refChr2 12493 63 + 27695 CTTTCACTTTCTTGTAGGTAGCTACATTCTGAGATAAAACCAATGTTTACCAGGTTTGGTTTG--- -s mr.mrrefChr0 97136 66 + 130230 CTCACACTTTTTGGTAAGTGGCTGCATTCTGAGATGACACCAATGTTTAACAGGCTTGGTTTGAGC -s simCow_chr6.simCow.chr6 102661 61 + 602619 CTTTCATTTTCTTGTAGGTAGCTACATTC--AGATAAAGCTAGTGTTCAGCAGGCTTGGTTTG--- -s simDog_chr6.simDog.chr6 499164 63 - 593897 CTTCCACTTTCTTGTAGGTAGCCACATTCTGAGATAAAACCAATGTTTGCCAGGTTTGGTTTG--- -s simHuman_chr6.simHuman.chr6 97918 66 + 601863 TTCTCAGTTTCTGGTAAGTAGCTACACTCTGAGATAATACCAATGTTTACCAGGGTCGGTCAGGCC -s simRat_chr6.simRat.chr6 94211 66 + 647215 CCCACACTCTTTGATAAGTGGCTGCATTCTGAGATGACACCAATATTTAACAGGTTTGGTTTGAGC - -a -s simMouse_chr6.simMouse.chr6 102164 6 + 636262 ATGGCA -s Anc0.Anc0refChr4 43132 6 - 45765 ATGGCA -s Anc1.Anc1refChr2 75259 6 + 144309 ATGGCA -s Anc2.Anc2refChr2 12575 6 + 27695 ATGGCA -s mr.mrrefChr0 97216 6 + 130230 ATGGCA -s simCow_chr6.simCow.chr6 102743 6 + 602619 ATGGCA -s simDog_chr6.simDog.chr6 499247 6 - 593897 ATGGCA -s simHuman_chr6.simHuman.chr6 98030 6 + 601863 ATGGCA -s simRat_chr6.simRat.chr6 94291 6 + 647215 ATGGCA - -a -s simMouse_chr6.simMouse.chr6 102170 4 + 636262 AACA -s Anc0.Anc0refChr4 43138 4 - 45765 AACA -s Anc1.Anc1refChr2 75265 4 + 144309 AACA -s Anc2.Anc2refChr2 12582 4 + 27695 AGCC -s mr.mrrefChr0 97222 4 + 130230 AACA -s simCow_chr6.simCow.chr6 102750 4 + 602619 ACCC -s simDog_chr6.simDog.chr6 499254 4 - 593897 AGCC -s simHuman_chr6.simHuman.chr6 98036 4 + 601863 AATA -s simRat_chr6.simRat.chr6 94297 4 + 647215 AACA - -a -s simMouse_chr6.simMouse.chr6 102174 1 + 636262 A -s Anc0.Anc0refChr4 43142 1 - 45765 A -s Anc1.Anc1refChr2 75269 1 + 144309 A -s Anc2.Anc2refChr2 12586 1 + 27695 T -s mr.mrrefChr0 97226 1 + 130230 A -s simCow_chr6.simCow.chr6 102754 1 + 602619 T -s simDog_chr6.simDog.chr6 499258 1 - 593897 C -s simHuman_chr6.simHuman.chr6 98040 1 + 601863 A -s simRat_chr6.simRat.chr6 94302 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 102175 3 + 636262 AAG -s Anc0.Anc0refChr4 43149 3 - 45765 AGA -s Anc1.Anc1refChr2 75276 3 + 144309 AGA -s Anc2.Anc2refChr2 12594 3 + 27695 AGA -s mr.mrrefChr0 97227 3 + 130230 AAG -s simCow_chr6.simCow.chr6 102762 3 + 602619 AGA -s simDog_chr6.simDog.chr6 499266 3 - 593897 AGA -s simHuman_chr6.simHuman.chr6 98047 3 + 601863 ATA -s simRat_chr6.simRat.chr6 94303 3 + 647215 AAG - -a -s simMouse_chr6.simMouse.chr6 102178 77 + 636262 AGTCAAACATTAAGAATCATCCTGGAGGTATCCGACCATTCGTACACTCACAGAAGTTTTAGCGCACATGCTAAGGA -s Anc0.Anc0refChr4 43152 77 - 45765 AGGCAAACAATGAGAATCATCTTTGAGGCATCAGACCATTCATATACTCTAAGAAATTTTTGCTTGTATGGAATGGG -s Anc1.Anc1refChr2 75279 77 + 144309 AGGCAAACAATGAGAATCATCTTTGAGGCATCAGACCATTCATATACTCTAAGAAATTTTTGCTTGTATGGAATGGG -s Anc2.Anc2refChr2 12597 77 + 27695 AGGCAAACAATGAGAATCATCTTTGAGGCATCAGCCCATTCATATACTCTAAGAAATTTTTGCTTGTATGGAATGGG -s mr.mrrefChr0 97230 77 + 130230 AGTCAAACATTAAGAATCATCCTGGAGGTATCCGACCATTCGTACACTCACAGAAGTTTTAGCGCGCATGCAAAGGA -s simCow_chr6.simCow.chr6 102765 64 + 602619 AGGGAAACGAGGAGGAACATCCCTGAGGCATTG-----TTCACATACTCTAGGAAGTTTTT--------GCAATGGG -s simDog_chr6.simDog.chr6 499271 77 - 593897 ACACAAACAATAAGAATCATCTTTGAGGCGCCAGCCCATTTATATACGCCAAGAGAGCACTGCTTGTATGGAATGAG -s simHuman_chr6.simHuman.chr6 98050 77 + 601863 TGGCAAACCATGAGTGTCATCTTTGAGGCATCAGACCATTCATATACTCTAAGAAATTTTTGCCTGTATAAAATGGG -s simRat_chr6.simRat.chr6 94306 77 + 647215 AATCCAACATTAAGCATCATCCCAGAGGTATCCAACCATTCGTACACTCACAGAAGTTTTAGCTCGCATGTAAAGGA - -a -s simMouse_chr6.simMouse.chr6 102255 4 + 636262 AAAT -s Anc0.Anc0refChr4 43229 4 - 45765 AAAT -s Anc1.Anc1refChr2 75356 4 + 144309 AAAT -s Anc2.Anc2refChr2 12674 4 + 27695 AAAT -s mr.mrrefChr0 97307 4 + 130230 AAAT -s simCow_chr6.simCow.chr6 102830 4 + 602619 AAAT -s simDog_chr6.simDog.chr6 499348 4 - 593897 AAAT -s simHuman_chr6.simHuman.chr6 98127 4 + 601863 AAAT -s simRat_chr6.simRat.chr6 94383 4 + 647215 AAAT - -a -s simMouse_chr6.simMouse.chr6 102259 54 + 636262 GACCTCCTCCCCATATGGTTTTGTCTATATGGTTTTATTTAATCTTTAACCTAA -s Anc0.Anc0refChr4 43233 45 - 45765 GGTTCCCTCTGTATACGGTTTTATCTATATTGTTCTACTTAATCT--------- -s Anc1.Anc1refChr2 75360 45 + 144309 GGTTCCCTCTGTATACGGTTTTATCTATATTGTTCTACTTAATCT--------- -s Anc2.Anc2refChr2 12678 45 + 27695 AATTCCCTATGTATACGGTTCTATCTATATTGTTCTACTTAATCT--------- -s mr.mrrefChr0 97311 54 + 130230 GGCCTCCTCTCCATATGGTTTTGTCTATATGGTTCTACTTAATCTTTAACCTAA -s simCow_chr6.simCow.chr6 102840 45 + 602619 AATGGGCTTCGTATATGGTTGGATCTATATTGTTCTCCTTGATCT--------- -s simDog_chr6.simDog.chr6 499352 45 - 593897 AATTCCCTATCTATACGGTACTATCTATATGGTTGTATCTAATCT--------- -s simHuman_chr6.simHuman.chr6 98131 45 + 601863 GGTTCCCTCTGTATACGGTTTTATATATATTGTTCTACTCACTCT--------- -s simRat_chr6.simRat.chr6 94387 54 + 647215 GGGCTTCTATCCATATAGTTTTGTCTATCCGGTTCTACTTAATCTTTAGTGTAA - -a -s simMouse_chr6.simMouse.chr6 102313 3 + 636262 GAA -s mr.mrrefChr0 97365 3 + 130230 GAA -s simRat_chr6.simRat.chr6 94458 3 + 647215 GAA - -a -s simMouse_chr6.simMouse.chr6 102316 18 + 636262 TTCTTAATCAAGTTGGCA -s Anc0.Anc0refChr4 43278 15 - 45765 ---TTAATCAAATTGGGC -s Anc1.Anc1refChr2 75405 15 + 144309 ---TTAATCAAATTGGGC -s Anc2.Anc2refChr2 12723 15 + 27695 ---TTAATCAAATTGAGC -s mr.mrrefChr0 97368 18 + 130230 TTCTTAATCAAGTTGGCA -s simCow_chr6.simCow.chr6 102885 13 + 602619 ---TTGATCAAATAG--C -s simDog_chr6.simDog.chr6 499397 15 - 593897 ---TTAATCAAATTGAGC -s simHuman_chr6.simHuman.chr6 98176 15 + 601863 ---TTAATCAAATTGGTC -s simRat_chr6.simRat.chr6 94464 18 + 647215 TTCTTAATCAAGTTGGCA - -a -s simMouse_chr6.simMouse.chr6 102334 29 + 636262 TTTGCCAATGGCACCTCAAGTGACATCAA -s Anc0.Anc0refChr4 43295 29 - 45765 TTTTCCCATGACACTTCAAGTGACCGCCA -s Anc1.Anc1refChr2 75422 29 + 144309 TTTTCCCATGACACTTCAAGTGACCGCCA -s Anc2.Anc2refChr2 12740 29 + 27695 CTTTCACATGACATTTCAAGTGTTCGCCA -s mr.mrrefChr0 97388 29 + 130230 TTTGCCCATGGCACCTCAAGTGACATCAA -s simCow_chr6.simCow.chr6 102900 8 + 602619 GTTT---------------------GACA -s simDog_chr6.simDog.chr6 499414 29 - 593897 CTTTCACATGACATTTCAAGTGTTCACCA -s simHuman_chr6.simHuman.chr6 98193 29 + 601863 TCTTCCCATAACACTTCAAGTGACTGCCA -s simRat_chr6.simRat.chr6 94484 29 + 647215 TTTGCCCCTGGCGCCTCAAGTGACATCAA - -a -s simMouse_chr6.simMouse.chr6 102363 7 + 636262 CTCTAAC -s Anc0.Anc0refChr4 43324 5 - 45765 C--TGAC -s Anc1.Anc1refChr2 75451 7 + 144309 CCCTGAC -s Anc2.Anc2refChr2 12769 5 + 27695 C--TGAC -s mr.mrrefChr0 97417 7 + 130230 CTCTAAC -s simCow_chr6.simCow.chr6 102908 5 + 602619 C--TGAT -s simDog_chr6.simDog.chr6 499443 5 - 593897 C--TAAC -s simHuman_chr6.simHuman.chr6 98225 7 + 601863 CCCTGAC -s simRat_chr6.simRat.chr6 94513 7 + 647215 CTCCCGG - -a -s simMouse_chr6.simMouse.chr6 102370 15 + 636262 GTTGGCATTGTGCTC -s Anc0.Anc0refChr4 43346 15 - 45765 GTAGAAAGTGTGCTT -s Anc1.Anc1refChr2 75475 15 + 144309 GTAGAAAGTGTGCTT -s Anc2.Anc2refChr2 12791 15 + 27695 GTAGAAAGTGTGCTT -s mr.mrrefChr0 97424 15 + 130230 GTTGACATTGTGCTT -s simCow_chr6.simCow.chr6 102930 14 + 602619 G-AGAAAGTGTGCTT -s simDog_chr6.simDog.chr6 499465 3 - 593897 GTA------------ -s simHuman_chr6.simHuman.chr6 98249 15 + 601863 GCAGATAGTGTGATT -s simRat_chr6.simRat.chr6 94520 15 + 647215 GTTGACATTGTGCTT - -a -s simMouse_chr6.simMouse.chr6 102385 14 + 636262 TCCTGATGGTTGCA -s Anc0.Anc0refChr4 43361 14 - 45765 ACCTGAagaTTGCA -s Anc1.Anc1refChr2 75490 14 + 144309 ACCTGAagaTTGCA -s Anc2.Anc2refChr2 12806 14 + 27695 ACCCGAagaACACC -s mr.mrrefChr0 97439 14 + 130230 ACCTGATGGTTGCA -s simCow_chr6.simCow.chr6 102944 14 + 602619 ACCCGAAGAACACC -s simHuman_chr6.simHuman.chr6 98269 14 + 601863 Acctggcgcttgca -s simRat_chr6.simRat.chr6 94535 14 + 647215 ACCTTATGGTTGCA - -a -s simMouse_chr6.simMouse.chr6 102399 54 + 636262 GCATGATCTGGTATAGATGGCTTCTCACAAAAGATGCCCCGCAAGGAAACAGTG -s Anc0.Anc0refChr4 43375 53 - 45765 GCATGACCCTGTATAGAACCCTCCTCATAAAAGAT-CCTTGCAAAGAAACAGTA -s Anc1.Anc1refChr2 75504 54 + 144309 GCATGACCCTGTATAGAACCCTCCTCATAAAAGATGCCTTGCAAAGAAACAGTA -s Anc2.Anc2refChr2 12826 53 + 27695 GCATGACCCTATATAGAACCCTCCTCATAAAGGCT-CCTCAAAAAGACATAGTA -s mr.mrrefChr0 97453 54 + 130230 GCATGATCTTGTATAGATGGCTTCTCACAAAAGATGCCTTGCAAGGAAACAGTA -s simCow_chr6.simCow.chr6 102964 48 + 602619 GCATCATCCAATATAGATGTCTCCCCACAAAGGGC-TTGCAAACA-----AGTG -s simDog_chr6.simDog.chr6 499468 50 - 593897 ---TGTCCCTACATAGAACCCTCCTCATAAAGGCT-CCTCAAAAAGACATAGTA -s simHuman_chr6.simHuman.chr6 98510 37 + 601863 GCATGACCCTGTAT-----------------AGATGCCTTGCAAAGAAACAGTA -s simRat_chr6.simRat.chr6 94549 54 + 647215 GCATGATCTTGTATAAATGGCTTCTCACAAAAGGTGCCTTTCAAGGAAACAGTA - -a -s simMouse_chr6.simMouse.chr6 102453 29 + 636262 CTACCATGGGTGCTTTTGTTTAAGCGGAG -s Anc0.Anc0refChr4 43430 29 - 45765 TTACCATGGATGCTTTTGTTTGTACGGAG -s Anc1.Anc1refChr2 75560 29 + 144309 TTACCATGGATGCTTTTGTTTGTACGGAG -s Anc2.Anc2refChr2 12881 29 + 27695 TTACCATGGATGCTTTTGTTCGTACAGAG -s mr.mrrefChr0 97509 29 + 130230 TTACCATGGATGCTTTTGTTTAAACGGAG -s simCow_chr6.simCow.chr6 103014 29 + 602619 TAACCATGGATCCTTTTGTTCGTACAGAG -s simDog_chr6.simDog.chr6 499520 27 - 593897 TTACCACGGATG--TTTGTACATGCAGAG -s simHuman_chr6.simHuman.chr6 98549 29 + 601863 TTACCATCGACGCCTTTGTTTGTACGGTG -s simRat_chr6.simRat.chr6 94605 29 + 647215 TTACTATGGATGCTTTTGTATAAACAGAG - -a -s simMouse_chr6.simMouse.chr6 102482 93 + 636262 TTATACCTGAGTGTTGATTCTCTGTATCTATGTCAACAAGCTCTGTATATACAATGGAACTTACATGGGTTTTAACAGCTTGTATGTCATCAA -s Anc0.Anc0refChr4 43460 80 - 45765 TTATGCATGAATGTTAT-CCTCTATATCTATGTCAACAAACTGTGTCAAGACAAGGGAACCTGCATGGA-GTTGACGTCTC-----------A -s Anc1.Anc1refChr2 75590 82 + 144309 TTATGCATGAATGTTATTCCTCTATATCTATGTCAACAAACTGTGTCAAGACAAGGGAACCTGCATGGATGTTGACGTCTC-----------A -s Anc2.Anc2refChr2 12911 80 + 27695 TTATGCATGAATATTAT-CCAACATATCTATGTCAACAAACTGCATCAAGACCAGGTAACCTGCATGGA-GTTGAGGTCTC-----------G -s mr.mrrefChr0 97538 93 + 130230 TTATACATGAGTGTTATTTCTCTGTATCTATGTCAACAAGCTCTGTATATACAATGGAACTTGCATGGGTTTTGACGGCTCGTATGTCATCAA -s simCow_chr6.simCow.chr6 103044 56 + 602619 TTATGCATGAATTTTAT-CCTCCCTATCTGAGTCAACAAGCTGCATCAAGACTGG-------------------------C-----------C -s simDog_chr6.simDog.chr6 499548 80 - 593897 TCCTGTATGAATATCAT-CCAACATATCTATGTCAACAAACTGCATCAGGATCAGGTAACCTGCATGGA-GTTGAGGTCTT-----------G -s simHuman_chr6.simHuman.chr6 98579 82 + 601863 TTATGCATTAATGTTATTCCTCTATATCTATGTCATCAATCTATGTCAAAGCAAGGGAACCTGTATGGATGTTGACGTCTC-----------A -s simRat_chr6.simRat.chr6 94634 93 + 647215 TTATATATGATTGTCATTTCTCTGTATCTATGTCAACAAGCTCCCTGTACACAAAGGAACTTGCATGGGTTTTGTTGGCTCATATGTCATCAA - -a -s simMouse_chr6.simMouse.chr6 102575 46 + 636262 ATATGATGTCTAAGTTGGGATACCATCCAGAAGGGGAGGACATTAC -s Anc0.Anc0refChr4 43540 35 - 45765 ATATTAT-----------GATACTGTCCAGAGGGGGGGGAAATGAT -s Anc1.Anc1refChr2 75672 35 + 144309 ATATTAT-----------GATACTGTCCAGAGGGGGGGGAAATGAT -s Anc2.Anc2refChr2 12991 35 + 27695 ATATTAT-----------GATATTGTCCAGGGGTTGGGGAAATGAT -s mr.mrrefChr0 97631 46 + 130230 ATATGATGTCTAAGTTGGGATACCATCCAGAAGGGGAGGACATTAC -s simCow_chr6.simCow.chr6 103100 35 + 602619 ATGTTAT-----------GATATTTGCCAGGGAAAGGGGAGATGAT -s simDog_chr6.simDog.chr6 499659 35 - 593897 ATATTAT-----------GGTATTGTCCAGGGGTTGGGGAAACAAT -s simHuman_chr6.simHuman.chr6 98661 35 + 601863 ATATTAT-----------GATCCTGTCCAGAGGGGGGGGAAATGAT -s simRat_chr6.simRat.chr6 94727 45 + 647215 ATATGATGCATAAGTTGGGATACCA-CCAGACGGGGAGGACGTTGC - -a -s simMouse_chr6.simMouse.chr6 102621 2 + 636262 CA -s Anc0.Anc0refChr4 43575 2 - 45765 GA -s Anc1.Anc1refChr2 75707 2 + 144309 GA -s Anc2.Anc2refChr2 13034 2 + 27695 GA -s mr.mrrefChr0 97677 2 + 130230 CA -s simCow_chr6.simCow.chr6 103143 2 + 602619 GA -s simDog_chr6.simDog.chr6 499720 2 - 593897 GG -s simHuman_chr6.simHuman.chr6 98696 2 + 601863 GA -s simRat_chr6.simRat.chr6 94772 2 + 647215 TA - -a -s simMouse_chr6.simMouse.chr6 102623 12 + 636262 GCTCCTCAGTTT -s Anc0.Anc0refChr4 43583 12 - 45765 GCTCACAAATTA -s Anc1.Anc1refChr2 75715 12 + 144309 GCTCACAAATTA -s Anc2.Anc2refChr2 13042 12 + 27695 GGCCACAAATTA -s mr.mrrefChr0 97679 12 + 130230 GCTCCTCAATTT -s simCow_chr6.simCow.chr6 103151 12 + 602619 AGCCACAAATTG -s simDog_chr6.simDog.chr6 499728 12 - 593897 GGCCACAAATTA -s simHuman_chr6.simHuman.chr6 98704 12 + 601863 GCTCACACATTC -s simRat_chr6.simRat.chr6 94774 12 + 647215 GCTCCTCAATTT - -a -s simMouse_chr6.simMouse.chr6 102635 13 + 636262 AACACTAAGAAGA -s Anc0.Anc0refChr4 43595 13 - 45765 AACACCAGGAAGA -s Anc1.Anc1refChr2 75727 13 + 144309 AACACCAGGAAGA -s Anc2.Anc2refChr2 13054 13 + 27695 AACACCAGGATGA -s mr.mrrefChr0 97691 13 + 130230 AACACTAGGAAGA -s simCow_chr6.simCow.chr6 103163 13 + 602619 AACACCAGGATGA -s simDog_chr6.simDog.chr6 499740 13 - 593897 AACACCAAGGTAA -s simHuman_chr6.simHuman.chr6 98716 13 + 601863 AACACCAGGAAGT -s simRat_chr6.simRat.chr6 94788 13 + 647215 AACACTAGGAAAA - -a -s simMouse_chr6.simMouse.chr6 102648 7 + 636262 TAATAGT -s Anc0.Anc0refChr4 43608 7 - 45765 TAACAGT -s Anc1.Anc1refChr2 75740 7 + 144309 TAACAGT -s Anc2.Anc2refChr2 13067 7 + 27695 TAACAGC -s mr.mrrefChr0 97704 7 + 130230 TAACAGT -s simCow_chr6.simCow.chr6 103177 7 + 602619 TATTAGC -s simDog_chr6.simDog.chr6 499753 6 - 593897 TAACAG- -s simHuman_chr6.simHuman.chr6 98729 7 + 601863 TAACAGT -s simRat_chr6.simRat.chr6 94801 7 + 647215 TAGCATC - -a -s simMouse_chr6.simMouse.chr6 102655 30 + 636262 AGTTTTTGCTTATGCCACCCTAAAGAATAT -s Anc0.Anc0refChr4 43619 30 - 45765 TATTTTTGCTTATGACACCCTATAGAATAT -s Anc1.Anc1refChr2 75751 30 + 144309 TATTTTTGCTTATGACACCCTATAGAATAT -s Anc2.Anc2refChr2 13078 30 + 27695 TATTTTTGCTTATGATACCCTATGGAATAT -s mr.mrrefChr0 97711 30 + 130230 AGTTTTTGCTTATGCCACCCTAAAGAATAT -s simCow_chr6.simCow.chr6 103188 30 + 602619 TGTTTTCGGTTAAGATACCATATGGACTAT -s simDog_chr6.simDog.chr6 499763 25 - 593897 TATTTTTGCTTAT-----CCTATGGAACAT -s simHuman_chr6.simHuman.chr6 98740 30 + 601863 CATTTTTGCTTATGACACCCCATAGAGTAT -s simRat_chr6.simRat.chr6 94808 30 + 647215 AGTTTTTATTTATTCCACCCTAAAGAATAT - -a -s simMouse_chr6.simMouse.chr6 102685 9 + 636262 ATTTATTCT -s Anc0.Anc0refChr4 43650 9 - 45765 ATTTAATTT -s Anc1.Anc1refChr2 75782 9 + 144309 ATTTAATTT -s Anc2.Anc2refChr2 13109 9 + 27695 ATTTAATTT -s mr.mrrefChr0 97741 9 + 130230 ATTTATTTT -s simCow_chr6.simCow.chr6 103219 9 + 602619 ATTTAATTT -s simDog_chr6.simDog.chr6 499789 9 - 593897 ATTTAACTT -s simHuman_chr6.simHuman.chr6 98771 9 + 601863 ATTTAATTT -s simRat_chr6.simRat.chr6 94838 9 + 647215 ATTTATTTT - -a -s simMouse_chr6.simMouse.chr6 102694 56 + 636262 CTTTGACCTATTGATTGCCCTATGGGTACTCTGCCACAGTTCACTTTTACTGATTT -s Anc0.Anc0refChr4 43660 44 - 45765 CTTTGACCCAT------------GGATGCTCTGTCACAGTTCACTTTTGTGGATTT -s Anc1.Anc1refChr2 75792 56 + 144309 CTTTGACCCATGGATTGGCCCATGGATGCTCTGTCACAGTTCACTTTTGTGGATTT -s Anc2.Anc2refChr2 13119 44 + 27695 CTTTGACCCAT------------GGATGCTTTGTGACAGTTCACTTTTGTGGATTT -s mr.mrrefChr0 97750 56 + 130230 CTTTGACCTATTGATTGCCCTATGGATGCTCTGCCACAGTTCACTTTTATTGATTT -s simCow_chr6.simCow.chr6 103229 44 + 602619 CCTTGATCCAT------------GGATGCTGTGTGACAGTTCACTTCTGTGTATTT -s simDog_chr6.simDog.chr6 499799 42 - 593897 CTTTAACCCAT------------GGGTGCCTTG--ACAATTCACTTTTGTGGATTT -s simHuman_chr6.simHuman.chr6 98781 56 + 601863 CTTTGACCCATGGATTGGCCCATGGATGCTCTGTCATAGTCCATTTTTGTGGATTT -s simRat_chr6.simRat.chr6 94847 56 + 647215 CTCTGACCTATTGATTGCCCTATTGATGCTCCGCCACAGTTCACTTCTATAGACTT - -a -s simMouse_chr6.simMouse.chr6 102750 12 + 636262 AACATTGCTAAG -s Anc0.Anc0refChr4 43704 10 - 45765 AACATTGCTA-- -s Anc1.Anc1refChr2 75848 10 + 144309 AACATTGCTA-- -s Anc2.Anc2refChr2 13163 10 + 27695 AACATTGCTA-- -s mr.mrrefChr0 97806 12 + 130230 AACATTGCTAAG -s simCow_chr6.simCow.chr6 103273 10 + 602619 AACATTGCTA-- -s simDog_chr6.simDog.chr6 499841 10 - 593897 AACATTGCTA-- -s simHuman_chr6.simHuman.chr6 98837 10 + 601863 AACATCACTA-- -s simRat_chr6.simRat.chr6 94914 12 + 647215 AACATTGCTAAT - -a -s simMouse_chr6.simMouse.chr6 102762 12 + 636262 TACATGTGTGTG -s Anc0.Anc0refChr4 43714 12 - 45765 CACACATGGGTG -s Anc1.Anc1refChr2 75858 12 + 144309 CACACATGGGTG -s Anc2.Anc2refChr2 13173 12 + 27695 CACACATGGGTG -s mr.mrrefChr0 97818 12 + 130230 TACATGTGTGTG -s simCow_chr6.simCow.chr6 103285 12 + 602619 CATACAAGGATG -s simDog_chr6.simDog.chr6 499894 12 - 593897 AGCACATGGGTG -s simHuman_chr6.simHuman.chr6 98847 12 + 601863 CACAGATAGGTG -s simRat_chr6.simRat.chr6 94926 2 + 647215 TA---------- - -a -s simMouse_chr6.simMouse.chr6 102774 13 + 636262 TAGTTTTACATAT -s Anc0.Anc0refChr4 43726 13 - 45765 AAGTCTTAGATAT -s Anc1.Anc1refChr2 75870 13 + 144309 AAGTCTTAGATAT -s Anc2.Anc2refChr2 13185 13 + 27695 AAGTCTTAGATAT -s mr.mrrefChr0 97830 13 + 130230 TAGTCTTACATAT -s simCow_chr6.simCow.chr6 103310 13 + 602619 AGACCTAAAATAT -s simDog_chr6.simDog.chr6 499906 13 - 593897 AAGTTGTAGATAT -s simHuman_chr6.simHuman.chr6 98859 13 + 601863 AAGTCTTGGATGT -s simRat_chr6.simRat.chr6 94928 10 + 647215 ---TCTTCCATAT - -a -s simMouse_chr6.simMouse.chr6 102787 66 + 636262 TTTAGCCAGTAGTAAGCTTTATAACTTTCATGTACTGTAAGGCACATCAAATAATCACCCTCATCT -s Anc0.Anc0refChr4 43739 66 - 45765 TTTATCCATTGGCAAGCTCTATAACTTTCAGGTACAGCAAGGCACATTAAATAATCAACCTCACTG -s Anc1.Anc1refChr2 75883 66 + 144309 TTTATCCATTGGCAAGCTCTATAACTTTCAGGTACAGCAAGGCACATTAAATAATCAACCTCACTG -s Anc2.Anc2refChr2 13199 66 + 27695 TTTATCAATTGGCAAGCTCTATAACTTTCAGGTACAGCAAGGCACAGTAAATGATCAACCTCACTG -s mr.mrrefChr0 97843 66 + 130230 TTTATCCAGTAGTAAGCTTTATAACTTTCATGTACAGTAAGGCACATCAAATAATCACCCTCATCT -s simCow_chr6.simCow.chr6 103333 66 + 602619 TTTATCTGTTGACAAGCTCTATAACTTTCAGGTACAGCAAGGCACAGTAAATGGTCAACCTCACAG -s simDog_chr6.simDog.chr6 499920 65 - 593897 TTTATCAATTGGCAAGTTCTATAACTTTCAGATACAGCAAGGTATAGTATATGACCAATGTCACT- -s simHuman_chr6.simHuman.chr6 98872 66 + 601863 CTAATACATTGGCAAGCTCTTTAACTTCCAGGTACAGCAGGACACATTAATTACTCAACCTCAATC -s simRat_chr6.simRat.chr6 94938 66 + 647215 TTTCTCCAGTAGGGAGTTTTATAACCATCATGTACAGAAAGGCACAGCAAATAATAACCCTCATCT - -a -s simMouse_chr6.simMouse.chr6 102853 16 + 636262 GGAGAGATAATCATCC -s Anc0.Anc0refChr4 43805 16 - 45765 GGAGAGATATTAATCC -s Anc1.Anc1refChr2 75949 16 + 144309 GGAGAGATATTAATCC -s Anc2.Anc2refChr2 13265 16 + 27695 GGAGAGATGTTAATCC -s mr.mrrefChr0 97909 16 + 130230 GGAGAGATAATCATCC -s simCow_chr6.simCow.chr6 103399 16 + 602619 GGAGAGATGTTAATCC -s simDog_chr6.simDog.chr6 499985 7 - 593897 ---------TTAATCC -s simHuman_chr6.simHuman.chr6 98943 16 + 601863 GGAGGGATATTAAGCC -s simRat_chr6.simRat.chr6 95004 16 + 647215 GGAGAGATAATCATCC - -a -s simMouse_chr6.simMouse.chr6 102869 16 + 636262 TTGCATTTGTATATAC -s Anc0.Anc0refChr4 43821 16 - 45765 TTGTATTTGTATATAT -s Anc1.Anc1refChr2 75965 16 + 144309 TTGTATTTGTATATAT -s Anc2.Anc2refChr2 13281 16 + 27695 TTGTATTCATATATAT -s mr.mrrefChr0 97925 16 + 130230 TTGCATTTGTATATAT -s simCow_chr6.simCow.chr6 103415 16 + 602619 TTGTATTCATATACAC -s simDog_chr6.simDog.chr6 499992 16 - 593897 TTGTATTCATATATAT -s simHuman_chr6.simHuman.chr6 98970 16 + 601863 TTGTATTTGTATAAGT -s simRat_chr6.simRat.chr6 95020 16 + 647215 TTGCATCTGTATATAT - -a -s simMouse_chr6.simMouse.chr6 102885 2 + 636262 GT -s Anc0.Anc0refChr4 43837 2 - 45765 GT -s Anc1.Anc1refChr2 75981 2 + 144309 GT -s Anc2.Anc2refChr2 13297 2 + 27695 GT -s mr.mrrefChr0 97941 2 + 130230 GT -s simCow_chr6.simCow.chr6 103431 2 + 602619 TT -s simDog_chr6.simDog.chr6 500008 2 - 593897 GT -s simHuman_chr6.simHuman.chr6 98986 2 + 601863 GT -s simRat_chr6.simRat.chr6 95073 2 + 647215 GT - -a -s simMouse_chr6.simMouse.chr6 102887 7 + 636262 TTAAATG -s Anc0.Anc0refChr4 43844 7 - 45765 CTGAATG -s Anc1.Anc1refChr2 75988 7 + 144309 CTGAATG -s Anc2.Anc2refChr2 13304 7 + 27695 CTGAATG -s mr.mrrefChr0 97943 7 + 130230 CTAAATG -s simCow_chr6.simCow.chr6 103438 7 + 602619 CTGGATG -s simDog_chr6.simDog.chr6 500015 7 - 593897 CTGAATG -s simHuman_chr6.simHuman.chr6 98993 7 + 601863 CTGAATA -s simRat_chr6.simRat.chr6 95075 7 + 647215 CTAAATG - -a -s simMouse_chr6.simMouse.chr6 102894 58 + 636262 ATACAGTAGTTGCCCTCCCATTAATAACTGTTCATAGAACTTTCTCTTGCAGTTGTGT -s Anc0.Anc0refChr4 43853 57 - 45765 ATATAGTAGTATCTTACCCACTAATAACTATTTAATGCACTTTATCTTAGTGATAC-T -s Anc1.Anc1refChr2 75997 58 + 144309 ATATAGTAGTATCTTACCCACTAATAACTATTTAATGCACTTTATCTTAGTGATACAT -s Anc2.Anc2refChr2 13313 57 + 27695 ATATAGTAGTATCTTACCCACAAATGACTATTCAATGCACTTTATTCTAGTGATAC-T -s mr.mrrefChr0 97952 58 + 130230 ATACAGTAGTTGCCCTCCCATTAATAACTGTTTATAGAACTTTCTCTTGGAGTTGTGT -s simCow_chr6.simCow.chr6 103447 57 + 602619 ATATAGTAGTGTCTTACCCATAAATCACTATTCAATGCAATTTATTCTAAGGATAT-T -s simDog_chr6.simDog.chr6 500024 57 - 593897 ACCTGGTAGTATCCTGCTCACAAATGACTATTCAACGCACTTTATTCACGTGATAC-T -s simHuman_chr6.simHuman.chr6 99002 58 + 601863 ATATAGTAGTATCTTACCTCCTTACAACTATTTAATGCACGCTATCTTAGCGACACAT -s simRat_chr6.simRat.chr6 95084 58 + 647215 ATACAGTAGTTGCCCTCCCATAAATAACTGTTTATAGTACTTTGTCTTGGTGTTGTGT - -a -s simMouse_chr6.simMouse.chr6 102952 8 + 636262 TGCACATG -s Anc0.Anc0refChr4 43910 8 - 45765 TATGCATG -s Anc1.Anc1refChr2 76055 8 + 144309 TATGCATG -s Anc2.Anc2refChr2 13370 8 + 27695 TATGCATG -s mr.mrrefChr0 98010 8 + 130230 TGTGCATG -s simCow_chr6.simCow.chr6 103506 8 + 602619 TATGCATG -s simDog_chr6.simDog.chr6 500081 8 - 593897 TATGCATG -s simHuman_chr6.simHuman.chr6 99060 8 + 601863 TTTGCATG -s simRat_chr6.simRat.chr6 95142 8 + 647215 TGTGCATG - -a -s simMouse_chr6.simMouse.chr6 102960 6 + 636262 TGATGC -s Anc0.Anc0refChr4 43918 6 - 45765 TGATGC -s Anc1.Anc1refChr2 76063 6 + 144309 TGATGC -s Anc2.Anc2refChr2 13378 6 + 27695 TGATGT -s mr.mrrefChr0 98018 6 + 130230 TGATGC -s simCow_chr6.simCow.chr6 103519 6 + 602619 TGATGT -s simDog_chr6.simDog.chr6 500089 6 - 593897 TGATGT -s simHuman_chr6.simHuman.chr6 99068 6 + 601863 TGATGC -s simRat_chr6.simRat.chr6 95150 6 + 647215 TGATGC - -a -s simMouse_chr6.simMouse.chr6 102966 40 + 636262 CTGTCTTGATTAGTGCAAAGTCTACTCCAAAAACCTTGGG -s Anc0.Anc0refChr4 43946 33 - 45765 CTGTCTTGATTGATGTAGCATGAATT----CATCCAT--- -s Anc1.Anc1refChr2 76091 33 + 144309 CTGTCTTGATTGATGTAGCATGAATT----CATCCAT--- -s Anc2.Anc2refChr2 13406 33 + 27695 CTGTCTTGATTGATGTAGCATGAATT----CATCCAT--- -s mr.mrrefChr0 98024 40 + 130230 CTGTCTTGATTAGTGCAAAGTCTACTCCAAAAACCTTGGG -s simCow_chr6.simCow.chr6 103547 32 + 602619 CTGTATTTATC-ATGTAGCATGGATA----CTCCCAT--- -s simDog_chr6.simDog.chr6 500117 33 - 593897 CTACCTTGTTTGATGTAGCATGAATT----CATCCAT--- -s simHuman_chr6.simHuman.chr6 99096 33 + 601863 CTGTCTTCATTGATGTAGCATGAATT----GATCCAT--- -s simRat_chr6.simRat.chr6 95156 40 + 647215 TTGCCTTGATTGGTGTAAAGTCTACTCCGAAACCTTTGGG - -a -s simMouse_chr6.simMouse.chr6 103006 18 + 636262 TACACACCGATAACACTG -s Anc0.Anc0refChr4 811 17 + 45765 TACA-ACATATTCTGTTT -s Anc1.Anc1refChr2 67200 17 - 144309 TACA-ACATATTCTGTTT -s Anc2.Anc2refChr2 13040 17 - 27695 TACC-TCATGTTCTGTTT -s mr.mrrefChr0 98064 18 + 130230 TACACACCGATAACACTG -s simDog_chr6.simDog.chr6 92506 17 + 593897 TACC-TCATGTTCTGTTT -s simHuman_chr6.simHuman.chr6 501642 17 - 601863 TACA-ACACATTCTGTTT -s simRat_chr6.simRat.chr6 95196 18 + 647215 TATACCCCAATAACACTG - -a -s simMouse_chr6.simMouse.chr6 103024 42 + 636262 CAATTGACCAATCTGGCTCATCCGAGTGTAGATCATATACCT -s Anc0.Anc0refChr4 828 40 + 45765 CAATTGACCAACCTGACTTGCCAAA--GTAGATCATATACCT -s Anc1.Anc1refChr2 67217 40 - 144309 CAATTGACCAACCTGACTTGCCAAA--GTAGATCATATACCT -s Anc2.Anc2refChr2 13057 40 - 27695 TAATTGACCAACTTGACTTGCCAAA--GTAGTTTATACACCC -s mr.mrrefChr0 98082 42 + 130230 CAATTGACCAATCTGGCTCATCCGAGTGTAGATCATATACCT -s simCow_chr6.simCow.chr6 497757 27 - 602619 -------------TGACTTACCAAG--GTAGATCATACACCC -s simDog_chr6.simDog.chr6 92529 40 + 593897 TAATTGACCAACTTGACTTGCCCGA--GTAGTTTATACACCC -s simHuman_chr6.simHuman.chr6 501659 36 - 601863 CAATTGACAAACCTGACTTGCCAAA--ATAGATC---TA-CT -s simRat_chr6.simRat.chr6 95214 42 + 647215 CAATTGACCAATCTGGCTTTTCCCAGTGTAGATCAAATACCT - -a -s simMouse_chr6.simMouse.chr6 103066 2 + 636262 GA -s Anc0.Anc0refChr4 868 2 + 45765 GA -s Anc1.Anc1refChr2 67257 2 - 144309 GA -s Anc2.Anc2refChr2 13098 2 - 27695 GA -s mr.mrrefChr0 98124 2 + 130230 GA -s simCow_chr6.simCow.chr6 497785 2 - 602619 TA -s simDog_chr6.simDog.chr6 92570 2 + 593897 GA -s simHuman_chr6.simHuman.chr6 501695 2 - 601863 GA -s simRat_chr6.simRat.chr6 95256 2 + 647215 TA - -a -s simMouse_chr6.simMouse.chr6 103068 18 + 636262 GCCTAGTTCCTATCTGTC -s Anc0.Anc0refChr4 870 10 + 45765 GCATAGTTA--------G -s Anc1.Anc1refChr2 67259 10 - 144309 GCATAGTTA--------G -s Anc2.Anc2refChr2 13100 10 - 27695 GAACAGTTA--------G -s mr.mrrefChr0 98126 18 + 130230 GCCTAGTTCCTATCTGTC -s simCow_chr6.simCow.chr6 497788 10 - 602619 TTCCAGTTA--------G -s simDog_chr6.simDog.chr6 92572 10 + 593897 GAACAGTTA--------G -s simHuman_chr6.simHuman.chr6 501697 5 - 601863 GCATA------------- -s simRat_chr6.simRat.chr6 95258 18 + 647215 GCCTAGTTACTAGCTCTC - -a -s simMouse_chr6.simMouse.chr6 103086 21 + 636262 CTAACTAATTTTTAATTGCTG -s Anc0.Anc0refChr4 880 16 + 45765 CTAACCAATTTTTCAT----- -s Anc1.Anc1refChr2 67269 16 - 144309 CTAACCAATTTTTCAT----- -s Anc2.Anc2refChr2 13110 16 - 27695 CTAACCAATTTTTCAT----- -s mr.mrrefChr0 98144 21 + 130230 CTAACTAATTTTTAATTGCTG -s simCow_chr6.simCow.chr6 497798 16 - 602619 CCAACCTATTTTTTAT----- -s simDog_chr6.simDog.chr6 92583 16 + 593897 CTAACCAATTTTTCAT----- -s simRat_chr6.simRat.chr6 95276 21 + 647215 CTAACTAATTTTTAATTGCCA - -a -s simMouse_chr6.simMouse.chr6 103107 11 + 636262 TAGTTTACATA -s Anc0.Anc0refChr4 896 11 + 45765 AAGTTTGAATA -s Anc1.Anc1refChr2 67285 11 - 144309 AAGTTTGAATA -s Anc2.Anc2refChr2 13126 11 - 27695 AAGTTTGAGTG -s mr.mrrefChr0 98165 11 + 130230 TAGTTTACATA -s simCow_chr6.simCow.chr6 497821 11 - 602619 AAGGCTGAGAG -s simDog_chr6.simDog.chr6 92599 11 + 593897 GAATTTGAGTG -s simHuman_chr6.simHuman.chr6 501702 10 - 601863 -AGTTTGAACA -s simRat_chr6.simRat.chr6 95297 11 + 647215 TAGTCCACATA - -a -s simMouse_chr6.simMouse.chr6 103118 31 + 636262 CATACTGAGCATAGGACTGAGTAAACATTAT -s Anc0.Anc0refChr4 907 31 + 45765 AAAACTGAGCATAGGATTGAATAAACAATAT -s Anc1.Anc1refChr2 67296 31 - 144309 AAAACTGAGCATAGGATTGAATAAACAATAT -s Anc2.Anc2refChr2 13137 31 - 27695 AAAAGTGAGCATAGGATTGAATAAACAATAT -s mr.mrrefChr0 98176 31 + 130230 CATACTGAGCATAGGACTGAGTAAACATTAT -s simCow_chr6.simCow.chr6 497832 31 - 602619 AAAAGAGAGCATAGGATTGAATAAAGAATAC -s simDog_chr6.simDog.chr6 92611 31 + 593897 AAAAGTGAGCACAGGATTGAATAAACAATAT -s simHuman_chr6.simHuman.chr6 501712 31 - 601863 GAAACTGAGCATATGATCGAATGAATAATGT -s simRat_chr6.simRat.chr6 95308 31 + 647215 CATACTGAGCACAGGACTGAGTAAACATTAT - -a -s simMouse_chr6.simMouse.chr6 103149 5 + 636262 TGGGC -s Anc0.Anc0refChr4 938 5 + 45765 TGGTC -s Anc1.Anc1refChr2 67327 5 - 144309 TGGTC -s Anc2.Anc2refChr2 13168 5 - 27695 TTGTG -s mr.mrrefChr0 98207 5 + 130230 TGGGC -s simCow_chr6.simCow.chr6 497863 5 - 602619 TTATG -s simDog_chr6.simDog.chr6 92642 5 + 593897 TTGTG -s simHuman_chr6.simHuman.chr6 501749 5 - 601863 TGTTC -s simRat_chr6.simRat.chr6 95339 5 + 647215 TGTGC - -a -s simMouse_chr6.simMouse.chr6 103154 8 + 636262 TAAAGGAC -s Anc0.Anc0refChr4 943 8 + 45765 TTGAGGAC -s Anc1.Anc1refChr2 67332 8 - 144309 TTGAGGAC -s Anc2.Anc2refChr2 13173 8 - 27695 TTGCGGAC -s mr.mrrefChr0 98212 8 + 130230 TAAAGGAC -s simCow_chr6.simCow.chr6 497868 8 - 602619 TTTGGGAT -s simDog_chr6.simDog.chr6 92647 8 + 593897 TTGCGGAC -s simHuman_chr6.simHuman.chr6 501756 8 - 601863 TTGAGTAC -s simRat_chr6.simRat.chr6 95344 8 + 647215 TTAAGCAC - -a -s simMouse_chr6.simMouse.chr6 103162 16 + 636262 AGAGAGTTAGGTCACT -s Anc0.Anc0refChr4 953 16 + 45765 AAAGAGTTAGGTCGCC -s Anc1.Anc1refChr2 67342 16 - 144309 AAAGAGTTAGGTCGCC -s Anc2.Anc2refChr2 13183 16 - 27695 AAAGAGTTAGGGCGTC -s mr.mrrefChr0 98220 16 + 130230 AGAGAGTTAGGTCACT -s simCow_chr6.simCow.chr6 497878 16 - 602619 AAATTGTTAGGACATC -s simDog_chr6.simDog.chr6 92657 16 + 593897 AAAGACTTAGAGCGTC -s simHuman_chr6.simHuman.chr6 501766 16 - 601863 AAAGAGTTAGGTCGCG -s simRat_chr6.simRat.chr6 95352 16 + 647215 AGAGAGTTAGGTCAGA - -a -s simMouse_chr6.simMouse.chr6 103178 11 + 636262 TTGGACAGTTG -s Anc0.Anc0refChr4 969 8 + 45765 TTG---AATTA -s Anc1.Anc1refChr2 67358 8 - 144309 TTG---AATTA -s Anc2.Anc2refChr2 13205 8 - 27695 TTA---AATTA -s mr.mrrefChr0 98236 11 + 130230 TTGGACAGTTG -s simCow_chr6.simCow.chr6 497900 8 - 602619 TTA---CATGA -s simDog_chr6.simDog.chr6 92679 8 + 593897 TCA---AATTT -s simHuman_chr6.simHuman.chr6 501782 8 - 601863 GTG---AATAA -s simRat_chr6.simRat.chr6 95368 11 + 647215 TTAGAGAGTTG - -a -s simMouse_chr6.simMouse.chr6 103189 1 + 636262 C -s Anc0.Anc0refChr4 977 1 + 45765 C -s Anc1.Anc1refChr2 67366 1 - 144309 C -s Anc2.Anc2refChr2 13213 1 - 27695 C -s mr.mrrefChr0 98247 1 + 130230 C -s simCow_chr6.simCow.chr6 497909 1 - 602619 C -s simDog_chr6.simDog.chr6 92687 1 + 593897 A -s simHuman_chr6.simHuman.chr6 501790 1 - 601863 C -s simRat_chr6.simRat.chr6 95379 1 + 647215 C - -a -s simMouse_chr6.simMouse.chr6 103190 28 + 636262 CGCATTTTGTATGTTAGAGGTGTCTACC -s Anc0.Anc0refChr4 978 28 + 45765 ATCATGTTGAATGTGAAAAGTGTCAGTC -s Anc1.Anc1refChr2 67367 28 - 144309 ATCATGTTGAATGTGAAAAGTGTCAGTC -s Anc2.Anc2refChr2 13214 28 - 27695 ATCATGTTGAATGTGAACAGTGTCAGTC -s mr.mrrefChr0 98248 28 + 130230 CGCATTTTGTATGTTAGAGGTGTCTACC -s simCow_chr6.simCow.chr6 497910 28 - 602619 ATCATGTTGCATGTGTACAATGTCAGCC -s simDog_chr6.simDog.chr6 92688 28 + 593897 ATCGTGTTTAATGTGAACAGCGTTGGTT -s simHuman_chr6.simHuman.chr6 501791 28 - 601863 ATCATGTTGAATGTGAAAAGTGTCAGTC -s simRat_chr6.simRat.chr6 95381 28 + 647215 CATATTTTGTATGTTTGAGGTGTCCACC - -a -s simMouse_chr6.simMouse.chr6 103218 16 + 636262 TGATCTAGTGCCGGCA -s Anc0.Anc0refChr4 1009 4 + 45765 TTA------T------ -s Anc1.Anc1refChr2 67398 10 - 144309 TTA------TCCGGTA -s Anc2.Anc2refChr2 13245 4 - 27695 TTA------T------ -s mr.mrrefChr0 98276 10 + 130230 TGA------GCCGGCA -s simCow_chr6.simCow.chr6 497941 4 - 602619 TGA------T------ -s simDog_chr6.simDog.chr6 92719 4 + 593897 TTA------T------ -s simHuman_chr6.simHuman.chr6 501822 10 - 601863 TTA------CCCGGTA -s simRat_chr6.simRat.chr6 95409 10 + 647215 TGA------GCCTGCA - -a -s simMouse_chr6.simMouse.chr6 103234 10 + 636262 AACAGGCTGA -s Anc0.Anc0refChr4 1013 9 + 45765 A-TGGTTTGA -s Anc1.Anc1refChr2 67408 9 - 144309 A-TGGTTTGA -s Anc2.Anc2refChr2 13249 9 - 27695 A-TGGTTTGA -s mr.mrrefChr0 98286 9 + 130230 A-CAGGCTGA -s simCow_chr6.simCow.chr6 497945 9 - 602619 A-TGTCTTAA -s simDog_chr6.simDog.chr6 92723 9 + 593897 A-TGGTGTGA -s simHuman_chr6.simHuman.chr6 501833 9 - 601863 A-TGGTTTGA -s simRat_chr6.simRat.chr6 95419 9 + 647215 G-CAGGTTGA - -a -s simMouse_chr6.simMouse.chr6 103244 14 + 636262 CATTAGCTTGATAG -s Anc0.Anc0refChr4 1024 14 + 45765 CATTGCAGTGACTG -s Anc1.Anc1refChr2 67419 14 - 144309 CATTGCAGTGACTG -s Anc2.Anc2refChr2 13260 14 - 27695 CACTGCAGTGTCTG -s mr.mrrefChr0 98295 14 + 130230 CATTAGCTTGATAG -s simCow_chr6.simCow.chr6 497956 14 - 602619 TTCCGAAGTGTTTG -s simDog_chr6.simDog.chr6 92734 14 + 593897 CACTTCAGTGTCTG -s simHuman_chr6.simHuman.chr6 501844 14 - 601863 CATTGCACTGACTG -s simRat_chr6.simRat.chr6 95428 14 + 647215 CATTAACTTGAGAG - -a -s simMouse_chr6.simMouse.chr6 103258 78 + 636262 TATTTCTAACTGGCATGCCAAATGTTTAAACTTATAACAGGAGGTAGGTCAAGTGGGACAACATATCTTTGCAATATC -s Anc0.Anc0refChr4 1039 78 + 45765 TGGTTGTAATGAACATGCCGGATATCTAAGATTGCAACAGGAGGTAAGTGGAGTGGAATAACAAATCCCAGCAATGCC -s Anc1.Anc1refChr2 67434 78 - 144309 TGGTTGTAATGAACATGCCGGATATCTAAGATTGCAACAGGAGGTAAGTGGAGTGGAATAACAAATCCCAGCAATGCC -s Anc2.Anc2refChr2 13275 78 - 27695 TGGTTGTAATGAACATGCTGGATACCTAAGATTGCAACCGGAGGTAAGTGGAGTGGAATAACAAATCCCAGCAATGCC -s mr.mrrefChr0 98309 78 + 130230 TATTTCTAACTGGCATGCCAAATGTTTAAACTTATAACAGGAGGTAGGTCAAGTGGGACAACATATCTTTGCAATATC -s simCow_chr6.simCow.chr6 497971 78 - 602619 TGGTAGTAATGAACATGCTAGATACTTAAGATTGCAATGGGAGGGAAGGGGAGTGGAACAACAATTCCCAACAATGCC -s simDog_chr6.simDog.chr6 92749 74 + 593897 TGGCTGTTATCAACATGCTGG----CTAAGACTGCAACCGGAGGTAAGTGGAGTGGAATATCTGATTTCAGCACTGTC -s simHuman_chr6.simHuman.chr6 501859 78 - 601863 TGGTTGTAATGAACATACCGGATATCTAACATTGCAACAGGAAGTAAGTGGAGTGGAATGACAAATCCCAGCAATGCC -s simRat_chr6.simRat.chr6 95442 78 + 647215 TATTCCTGACTGACATGCCAAACATTCAAAATTATAACAGGGGATACGTGAAGTGGATCAACAAATCTTTGCAGTACC - -a -s simMouse_chr6.simMouse.chr6 103336 2 + 636262 TT -s Anc0.Anc0refChr4 1117 2 + 45765 TT -s Anc1.Anc1refChr2 67512 2 - 144309 TT -s Anc2.Anc2refChr2 13353 2 - 27695 CT -s mr.mrrefChr0 98387 2 + 130230 TT -s simCow_chr6.simCow.chr6 498049 2 - 602619 GT -s simDog_chr6.simDog.chr6 92823 2 + 593897 CT -s simHuman_chr6.simHuman.chr6 502036 2 - 601863 TC -s simRat_chr6.simRat.chr6 95520 2 + 647215 CT - -a -s simMouse_chr6.simMouse.chr6 103338 14 + 636262 ATAGACACACATGG -s Anc0.Anc0refChr4 1119 14 + 45765 ATCAAAACATACAG -s Anc1.Anc1refChr2 67514 14 - 144309 ATCAAAACATACAG -s Anc2.Anc2refChr2 13371 14 - 27695 ATCAAAACATACAG -s mr.mrrefChr0 98389 14 + 130230 ATAGACACACATGG -s simCow_chr6.simCow.chr6 498072 14 - 602619 ATTAACACATATGG -s simDog_chr6.simDog.chr6 92841 14 + 593897 ATCAAAACATACAG -s simHuman_chr6.simHuman.chr6 502038 14 - 601863 GTTCGAACATACAG -s simRat_chr6.simRat.chr6 95522 14 + 647215 ATGGGCACAAATAG - -a -s simMouse_chr6.simMouse.chr6 103352 42 + 636262 TCCATAAAAAGTGGTTCACCACTGATGGAAGTCACATGAGGA -s Anc0.Anc0refChr4 1133 41 + 45765 T-CATAGAAAGTGTTTCATCACTGATGGAAATCACAAGAGGA -s Anc1.Anc1refChr2 67528 41 - 144309 T-CATAGAAAGTGTTTCATCACTGATGGAAATCACAAGAGGA -s Anc2.Anc2refChr2 13385 41 - 27695 T-CATAGAACGTGTTTCATCACTGATGGAAATCACAAGGGGA -s mr.mrrefChr0 98403 42 + 130230 TCCATAAAAAGTGGTTCACCACTGATGGAAGTCACATGAGGA -s simCow_chr6.simCow.chr6 498090 34 - 602619 T-CATAGAAGGAGTTTCACCACTGATGGCAATCAC------- -s simDog_chr6.simDog.chr6 92855 41 + 593897 T-CATTGAACGTGTTTCATCATTGTTGGAAATCACAAGGGGA -s simHuman_chr6.simHuman.chr6 502052 41 - 601863 T-AATAGAAAGTGTTTCATCACTGATGGAAATCACAAGAAGA -s simRat_chr6.simRat.chr6 95536 42 + 647215 TCCACACAAAGTGGTTCACCACTGATGGAAGTCACATGAGGA - -a -s simMouse_chr6.simMouse.chr6 103394 22 + 636262 GGATATCAAGAAGGTTAGCCCA -s Anc0.Anc0refChr4 1174 19 + 45765 GGGCACT---AATGTCATACTA -s Anc1.Anc1refChr2 67569 19 - 144309 GGGCACT---AATGTCATACTA -s Anc2.Anc2refChr2 13426 19 - 27695 AGGCACT---AATGTCATGCTA -s mr.mrrefChr0 98445 19 + 130230 GGGTATC---AAGGTTAGACCA -s simCow_chr6.simCow.chr6 498124 19 - 602619 AGGCATT---AATGTCATGCTA -s simDog_chr6.simDog.chr6 92896 12 + 593897 AAGCACT---AGTAC------- -s simHuman_chr6.simHuman.chr6 502112 19 - 601863 GGGCTGT---AATGTCATACTA -s simRat_chr6.simRat.chr6 95578 19 + 647215 GGGTATC---AAGGTTAGACCA - -a -s simMouse_chr6.simMouse.chr6 103416 67 + 636262 TGTGTGCTACAATGCAACAGATGGGGCTTCCACATCCAGGGAAGAATAATTGACTAAGAATGCATTA -s Anc0.Anc0refChr4 1193 67 + 45765 TGTGTGCTACAACTCAATAGATGGGGCTCCTACATCCAGGAAAGTATAATTGTCTAATACTACATCA -s Anc1.Anc1refChr2 67588 67 - 144309 TGTGTGCTACAACTCAATAGATGGGGCTCCTACATCCAGGAAAGTATAATTGTCTAATACTACATCA -s Anc2.Anc2refChr2 13445 67 - 27695 TGTGTGCTGCAACTCAATAGGTGGGGCTCCTACATCCAGAAAAGTATAATTGTCTAATACTACATCA -s mr.mrrefChr0 98464 67 + 130230 TGTGTGCTACAATGCAACAGATGGGGCTTCCACATCCAGGGAAGAATAATTGACTAAGACTGCATTA -s simCow_chr6.simCow.chr6 498144 66 - 602619 TGTGTGCTG-AACTACATAGGTGGGGTACCTATATCCCGAAAAGTGTGAATGTCTAATACTACAACA -s simDog_chr6.simDog.chr6 92908 57 + 593897 ---------CAACTCAGT-GGTGGGGCTCCTACATCCAGAGAAGGACAATTGTCTAAAGCTACATCA -s simHuman_chr6.simHuman.chr6 502131 67 - 601863 TGTGTGCCACAGCTCAATCGATGGGGCCCCTAATTTCAGGAAAGTCTAATCACTTGATACTACCTCA -s simRat_chr6.simRat.chr6 95597 39 + 647215 TGTGTGCT----------------------------CAGGGAAGAATAATTGACTAAGACAGCATTG - -a -s simMouse_chr6.simMouse.chr6 103483 70 + 636262 ATAGTAGCCTAGCCCATTTACCAGTGTGACCACACCACACTTGGTACAGTGGGTCAGTACATATCATACT -s Anc0.Anc0refChr4 1264 70 + 45765 ACAGTAGCATAGCCCATTTGTGATCCTAACTAAGACTTAATCTGTACAGTAGGTCAGAAGATATCACACT -s Anc1.Anc1refChr2 67659 70 - 144309 ACAGTAGCATAGCCCATTTGTGATCCTAACTAAGACTTAATCTGTACAGTAGGTCAGAAGATATCACACT -s Anc2.Anc2refChr2 13517 70 - 27695 ACAGTAGCATAGCCCATTTGTGATCCTGAATAAGACTTAATCTGTACAGTAGGTCAGAAGATATCACACT -s mr.mrrefChr0 98535 70 + 130230 ATAGTAGCCTAGCCCATTTGCCAGTGTAACCACACCTCACTCGGTACAGTAGGTCAGAACATATCATACT -s simCow_chr6.simCow.chr6 498215 55 - 602619 ACAGTAGCATAGTCCATTTG--------GATC------AACCTGTACAG-AGTTCAGCAGACATCACACT -s simDog_chr6.simDog.chr6 92970 70 + 593897 ACAGTAGCAAAGCCCATGAGTGATCCTGAATAAGACTTACTCAGTACAGTAGGTCAGAAGATATCACACT -s simHuman_chr6.simHuman.chr6 502208 70 - 601863 ACAGTAGCATAGCCTATTTGTGATGCTAACAAAGACTTAATCTGTACCGAAGGTCACAAGATATTAGACT -s simRat_chr6.simRat.chr6 95640 70 + 647215 ATAGTAGCCTAGTCCATTTGCCAATGTAACCACACCTCACCCGGTACAGTAGGTCAGAACATATCATACT - -a -s simMouse_chr6.simMouse.chr6 103553 1 + 636262 C -s Anc0.Anc0refChr4 1346 1 + 45765 C -s Anc1.Anc1refChr2 67741 1 - 144309 C -s Anc2.Anc2refChr2 13599 1 - 27695 C -s mr.mrrefChr0 98605 1 + 130230 C -s simCow_chr6.simCow.chr6 498282 1 - 602619 C -s simDog_chr6.simDog.chr6 93052 1 + 593897 C -s simHuman_chr6.simHuman.chr6 502290 1 - 601863 C -s simRat_chr6.simRat.chr6 95710 1 + 647215 C - -a -s simMouse_chr6.simMouse.chr6 103554 76 + 636262 TCCAATAGTGTGAAGAAGCAGGTCACCTAGATTAAGTTAACTGCTCATAGTAGTCACAGGCTAAAGAGCGCTTATC -s Anc0.Anc0refChr4 1362 70 + 45765 CACACTAGTGTGAAGGAGTGGTTCATCTAGA-----TTAACTGCTCATAGTTGTTACAGGCTT-AGTCCAAAATTA -s Anc1.Anc1refChr2 67757 71 - 144309 CACACTAGTGTGAAGGAGTGGTTCATCTAGA-----TTAACTGCTCATAGTTGTTACAGGCTTAAGTCCAAAATTA -s Anc2.Anc2refChr2 13615 70 - 27695 CATACTAGTGTGATGGAGTGGTTCATCTGGA-----TTAACTGCTCACAGTTGTTACAGGATT-AGTCTAAAATTA -s mr.mrrefChr0 98621 71 + 130230 TACAATAGTGTGAAGGAGCAGGTCACCTAGA-----TTAACTGCTCATAGTAGTTACAGGCTAAAGAGCGCTTATC -s simCow_chr6.simCow.chr6 498304 70 - 602619 CATACTAGTGTGATAGAGTGGTTCGTCTGGA-----TTAATCGCTCACAGTTGGTACAGGTGT-AGTCTAGGATTA -s simDog_chr6.simDog.chr6 93068 70 + 593897 CATACAAACATAATGGAGTGGTTTATCTGGA-----CGAACTGCTCACAGTTGTTATAGGATC-AGTCTAAAATTA -s simHuman_chr6.simHuman.chr6 502306 71 - 601863 CACACTAGTGTGTAGGAGTGGTTCAACCAGG-----TTAACTGTGCATAGTTGTTACAGGCTTAAGTTCAAAATTA -s simRat_chr6.simRat.chr6 95726 71 + 647215 TACAATAGTGTGAAGGAGCAGGTCATCTAGA-----CTAACTGCTCATAGTAGTTGCTGGCTCAAAAGTGCTAATC - -a -s simMouse_chr6.simMouse.chr6 103630 11 + 636262 ATTGTCCAGTG -s Anc0.Anc0refChr4 1432 11 + 45765 AGCAGCCAGTC -s Anc1.Anc1refChr2 67828 11 - 144309 AGCAGCCAGTC -s Anc2.Anc2refChr2 13694 11 - 27695 AGCAGCCAGTC -s mr.mrrefChr0 98692 11 + 130230 ATTGTCCAGTG -s simCow_chr6.simCow.chr6 498383 11 - 602619 ATCATCCAGTT -s simDog_chr6.simDog.chr6 93147 11 + 593897 AGCAGCCAGTC -s simHuman_chr6.simHuman.chr6 502377 11 - 601863 AACAGCTAACA -s simRat_chr6.simRat.chr6 95797 11 + 647215 ATTGTCCAAGG - -a -s simMouse_chr6.simMouse.chr6 103641 7 + 636262 AGGGATT -s Anc0.Anc0refChr4 1443 7 + 45765 AGTGAGT -s Anc1.Anc1refChr2 67839 7 - 144309 AGTGAGT -s Anc2.Anc2refChr2 13705 7 - 27695 AGTGAGT -s mr.mrrefChr0 98703 7 + 130230 AGTGATT -s simCow_chr6.simCow.chr6 498395 7 - 602619 AGTGAGT -s simDog_chr6.simDog.chr6 93158 7 + 593897 AGTGAGT -s simHuman_chr6.simHuman.chr6 502388 7 - 601863 TGTGAGT -s simRat_chr6.simRat.chr6 95808 7 + 647215 CTTGATT - -a -s simMouse_chr6.simMouse.chr6 103648 22 + 636262 GTTTCAGCAATTTAACAAGACA -s Anc0.Anc0refChr4 1450 21 + 45765 ACTTCAGCAATTTAACAGTA-A -s Anc1.Anc1refChr2 67846 21 - 144309 ACTTCAGCAATTTAACAGTA-A -s Anc2.Anc2refChr2 13712 21 - 27695 ACTTCAGCCATTTAACAGTA-A -s mr.mrrefChr0 98710 22 + 130230 GCTTCAGCAATTTAACAAGACA -s simCow_chr6.simCow.chr6 498403 21 - 602619 ACCTCAGCCATTTAACAGTA-A -s simDog_chr6.simDog.chr6 93165 12 + 593897 ACTTCAGCCATT---------- -s simHuman_chr6.simHuman.chr6 502395 21 - 601863 ACTTCAGCAATTTAACAGTA-A -s simRat_chr6.simRat.chr6 95815 22 + 647215 GCTTCAGCAATTTAACAAGACA - -a -s simMouse_chr6.simMouse.chr6 103670 59 + 636262 ACCATGAAGTAAACAGTGGAATCCTTGCTAGTATAGGCAATGCATTGTTTATAACTTCT -s Anc0.Anc0refChr4 1471 59 + 45765 ACTAAGATGTAAATAGTGGTATCCTTACCCCTAAGGGCAATGCGTGGTTTATGACTTCC -s Anc1.Anc1refChr2 67867 59 - 144309 ACTAAGATGTAAATAGTGGTATCCTTACCCCTAAGGGCAATGCGTGGTTTATGACTTCC -s Anc2.Anc2refChr2 13733 59 - 27695 CCTAAGATGTTAATAGTGGTATCCTTACCCCTAAGGGCAATGTGTGGTTTATGACTTTC -s mr.mrrefChr0 98732 59 + 130230 ACCATGAAGTAAACAGTGGAATCCTTACTAGTATAGGCAATGCATTGTTTATAACTTCC -s simCow_chr6.simCow.chr6 498424 58 - 602619 CCCAAGAAGTTAATAGTGGTATCC-TACTTCCAAAGCCAGGTTGTGGTTTACAACCTTC -s simDog_chr6.simDog.chr6 93177 57 + 593897 --TAAGATATTAATAATGGTATCATTATCCTTAAGGGCAATGTGTGGTTTATGACTTTC -s simHuman_chr6.simHuman.chr6 502416 59 - 601863 ACTAAGAGGTAAATAGTGATATCCACACCCCTAAGGGTAATGCGTAGTATATTACTTCC -s simRat_chr6.simRat.chr6 95862 59 + 647215 ACCATGAATTAAACAATGGAATCCTTACTTGTATAGGCATTGCATTGTTTATAACTTCC - -a -s simMouse_chr6.simMouse.chr6 103729 1 + 636262 G -s Anc0.Anc0refChr4 1536 1 + 45765 A -s Anc1.Anc1refChr2 67932 1 - 144309 A -s Anc2.Anc2refChr2 13798 1 - 27695 A -s mr.mrrefChr0 98791 1 + 130230 A -s simCow_chr6.simCow.chr6 498488 1 - 602619 A -s simDog_chr6.simDog.chr6 93250 1 + 593897 A -s simHuman_chr6.simHuman.chr6 502481 1 - 601863 A -s simRat_chr6.simRat.chr6 95921 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 103730 1 + 636262 C -s Anc0.Anc0refChr4 1537 1 + 45765 G -s Anc1.Anc1refChr2 67933 1 - 144309 G -s Anc2.Anc2refChr2 13799 1 - 27695 G -s mr.mrrefChr0 98792 1 + 130230 C -s simCow_chr6.simCow.chr6 498489 1 - 602619 G -s simDog_chr6.simDog.chr6 93273 1 + 593897 A -s simHuman_chr6.simHuman.chr6 502482 1 - 601863 G -s simRat_chr6.simRat.chr6 95922 1 + 647215 C - -a -s simMouse_chr6.simMouse.chr6 103731 75 + 636262 CAAGATACTCCTCTAGTTAGGCTATATAGGATGAAAAGCCTTAACCTGTAGGATGTATCCAAATGTAGGGGGCAA -s Anc0.Anc0refChr4 1538 75 + 45765 CGAGATACTTCTTTAGTTGGACTATATAGAATGAGAAGCGTTAACCTGTAGAATGTATCTGAATGTGATGAGCAA -s Anc1.Anc1refChr2 67934 75 - 144309 CGAGATACTTCTTTAGTTGGACTATATAGAATGAGAAGCGTTAACCTGTAGAATGTATCTGAATGTGATGAGCAA -s Anc2.Anc2refChr2 13800 75 - 27695 CGAGATACTTCTTTAGTTGGACTGTATAGAATGAGAAGCGTTAGCCTGTAGAATGTATCTGGATGTGATGAGCAA -s mr.mrrefChr0 98793 75 + 130230 CAAGATACTCCTTTAGTTAGGCTATATAGGATGAAAAGCCTTAACCTGTAGGATGTATCCAAATGTAGGGGGCAA -s simCow_chr6.simCow.chr6 498532 74 - 602619 CCAGA-ACTTCTTTAGTTGGGCACTATAAAATCAGAAGCATTAGCCTGTAAGAAGTATCTGGATGTGAGGAGCAA -s simDog_chr6.simDog.chr6 93274 75 + 593897 CGAGATATTTCTTTAGTTGGACTGTATAGAAGGAGAGGCGTTAGCCTGTAGAATGCATCTGGATGTGATGAGAAA -s simHuman_chr6.simHuman.chr6 502483 75 - 601863 CGAGATACTTCTTTAGTTGTATCATATGGAATGAGAAGCGGTAACCTGTATAACGTATTTGAACATGATGAGCAA -s simRat_chr6.simRat.chr6 95923 75 + 647215 CAAGATACTCCTTTAGTTAGGCAGCATAGGATGAAAGGCCCTAACCTGTAGGATGGATCCAAATGTAGGGGGCAA - -a -s simMouse_chr6.simMouse.chr6 103806 21 + 636262 GCCATGAGTGTGCTGGACAGA -s Anc0.Anc0refChr4 1613 19 + 45765 GCCTGGAGTGTGCTGGA-C-A -s Anc1.Anc1refChr2 68009 20 - 144309 GCCTGGAGTGTGCTGGACC-A -s Anc2.Anc2refChr2 13875 19 - 27695 CCCTGGAGAGTGCTGGA-C-A -s mr.mrrefChr0 98868 21 + 130230 GCCAGGAGTGTGCTGGACAGA -s simCow_chr6.simCow.chr6 498606 19 - 602619 CCCTGCAGAGCACTGGA-C-A -s simDog_chr6.simDog.chr6 93351 19 + 593897 CCCTTGAGACTGCTGGA-C-A -s simHuman_chr6.simHuman.chr6 502558 19 - 601863 GCT-GGAGTGTGCTGGACC-A -s simRat_chr6.simRat.chr6 95998 21 + 647215 GCCAGGAGTGTGCTGGACAGA - -a -s simMouse_chr6.simMouse.chr6 103827 8 + 636262 AAGGTTTT -s Anc0.Anc0refChr4 1632 8 + 45765 ACAACTCT -s Anc1.Anc1refChr2 68029 8 - 144309 ACAACTCT -s Anc2.Anc2refChr2 13894 8 - 27695 ACAACTCT -s mr.mrrefChr0 98889 8 + 130230 AAGGTTTT -s simCow_chr6.simCow.chr6 498631 8 - 602619 ACAACTAC -s simDog_chr6.simDog.chr6 93370 8 + 593897 GAAGCTCT -s simHuman_chr6.simHuman.chr6 502577 8 - 601863 ACAACTCT -s simRat_chr6.simRat.chr6 96019 8 + 647215 TAGGTCTT - -a -s simMouse_chr6.simMouse.chr6 103835 19 + 636262 CGTCACACAGACAGTCAGA -s Anc0.Anc0refChr4 1640 19 + 45765 CATACCACACACAGCCAGA -s Anc1.Anc1refChr2 68037 19 - 144309 CATACCACACACAGCCAGA -s Anc2.Anc2refChr2 13903 19 - 27695 CATACCACACACAGCCAGA -s mr.mrrefChr0 98897 19 + 130230 CGTCACACAGACAGTCAGA -s simCow_chr6.simCow.chr6 498640 19 - 602619 CACACCACACACAACCAGA -s simDog_chr6.simDog.chr6 93379 19 + 593897 CATACTACACACAGCCAGA -s simHuman_chr6.simHuman.chr6 502585 19 - 601863 CCTACCACACACAGCCAGT -s simRat_chr6.simRat.chr6 96027 19 + 647215 CGTCACACATACAGTCAGA - -a -s simMouse_chr6.simMouse.chr6 103854 42 + 636262 AACAGGTGGATGGCAAAGAACGCTACAACAATCCTAACTAAG -s Anc0.Anc0refChr4 1659 39 + 45765 ATCAGGTGGAGGATAAAGAATGTTA---CAAGCAGAACTAAG -s Anc1.Anc1refChr2 68056 39 - 144309 ATCAGGTGGAGGATAAAGAATGTTA---CAAGCAGAACTAAG -s Anc2.Anc2refChr2 13922 39 - 27695 ATCAGGTGGAGGATACAGAATGCTA---CAAGCAGAACTAAA -s mr.mrrefChr0 98916 42 + 130230 AACAGGTGGATGGCAAAGAATGTTACAACAATCATAACTAAG -s simCow_chr6.simCow.chr6 498659 39 - 602619 ATCAGATGGAAGATAGAGAATGCTA---CAAGCAGAACTAAA -s simDog_chr6.simDog.chr6 93412 39 + 593897 ATCAGGTGGAGGTTACAGAATGCCA---CAATCAGAACTAAA -s simHuman_chr6.simHuman.chr6 502604 39 - 601863 ATCAAGTAGAGGATAAAGAATGTTG---CAAGGAAAACTAAG -s simRat_chr6.simRat.chr6 96046 42 + 647215 AACAGGTGGATGGCAAAGAATGTCATAACAATCATGACTAAC - -a -s simMouse_chr6.simMouse.chr6 103896 6 + 636262 GTCAAA -s Anc0.Anc0refChr4 1698 6 + 45765 GAGAAA -s Anc1.Anc1refChr2 68095 6 - 144309 GAGAAA -s Anc2.Anc2refChr2 14152 6 - 27695 TAGATA -s mr.mrrefChr0 98958 6 + 130230 GTCAAA -s simCow_chr6.simCow.chr6 498948 6 - 602619 TATATA -s simDog_chr6.simDog.chr6 93643 6 + 593897 TAGATC -s simHuman_chr6.simHuman.chr6 502643 6 - 601863 GAGAAA -s simRat_chr6.simRat.chr6 96088 2 + 647215 AT---- - -a -s simMouse_chr6.simMouse.chr6 103902 12 + 636262 TTATGTCCATAT -s Anc0.Anc0refChr4 1718 9 + 45765 TA---TCCACAT -s Anc1.Anc1refChr2 68115 9 - 144309 TA---TCCACAT -s Anc2.Anc2refChr2 14172 9 - 27695 TA---TCCACTT -s mr.mrrefChr0 98964 9 + 130230 TT---TCCACAT -s simCow_chr6.simCow.chr6 498968 6 - 602619 TA---TCCA--- -s simDog_chr6.simDog.chr6 93663 9 + 593897 TA---TCCGCTT -s simHuman_chr6.simHuman.chr6 502663 9 - 601863 TA---GCCACAT -s simRat_chr6.simRat.chr6 96090 5 + 647215 -------CACAT - -a -s simMouse_chr6.simMouse.chr6 103914 3 + 636262 TGA -s Anc0.Anc0refChr4 1729 3 + 45765 GGA -s Anc1.Anc1refChr2 68126 3 - 144309 GGA -s Anc2.Anc2refChr2 14183 3 - 27695 GGA -s mr.mrrefChr0 98973 3 + 130230 TGA -s simDog_chr6.simDog.chr6 93674 3 + 593897 GGA -s simHuman_chr6.simHuman.chr6 502674 3 - 601863 GGA -s simRat_chr6.simRat.chr6 96095 3 + 647215 TGA - -a -s simMouse_chr6.simMouse.chr6 103917 72 + 636262 ATTGATCAACATTATGACACCACACATGGTTGGTGTTTCTTTAAGTACCACTGTCACACTAAGTAACACACT -s Anc0.Anc0refChr4 1732 29 + 45765 TTTGAAGA-------------------GGGTTG-------------ACCACTTACAAAATA----------- -s Anc1.Anc1refChr2 68129 29 - 144309 TTTGAAGA-------------------GGGTTG-------------ACCACTTACAAAATA----------- -s Anc2.Anc2refChr2 14196 29 - 27695 TTTGAAGA-------------------GGGTTG-------------ACCACTTACAAAACA----------- -s mr.mrrefChr0 98976 53 + 130230 ATTGATCA-------------------GGTTGGTGTTTCTTTAAGTACCACTGTCACACTAAGTAACACACT -s simCow_chr6.simCow.chr6 498983 29 - 602619 TTTGAAGG-------------------GGGTTG-------------ACCACTTACAAAACA----------- -s simDog_chr6.simDog.chr6 93687 29 + 593897 TTAGCAGA-------------------GGGTTG-------------ACCAGCTACAATACT----------- -s simHuman_chr6.simHuman.chr6 502677 29 - 601863 TTTGAAGA-------------------GGATTG-------------ACCACTAACAAAATA----------- -s simRat_chr6.simRat.chr6 96098 53 + 647215 ATTGATTA-------------------GGTTGGTGTTTCTTCAAGTACCACTGTCACACTAAGCAACACACG - -a -s simMouse_chr6.simMouse.chr6 103989 29 + 636262 AGGGAGAGTGAGAATAGCTTGACGTGTTA -s mr.mrrefChr0 99029 29 + 130230 AGGGAGAGTGAGAATAGCTTGACGTGTTA -s simRat_chr6.simRat.chr6 96170 29 + 647215 AAGGAAAGCGAGAATAGCTATATGTATTA - -a -s simMouse_chr6.simMouse.chr6 104018 27 + 636262 CATGGTCCTGTCCCCTTGTTCAATGTA -s Anc0.Anc0refChr4 1761 12 + 45765 ---------------TTGGTACATGGA -s Anc1.Anc1refChr2 68158 14 - 144309 -------------TCTTGGTACATGGA -s Anc2.Anc2refChr2 14225 12 - 27695 ---------------TTGGTACTTGGA -s mr.mrrefChr0 99058 27 + 130230 CATGGTCCTGTCCCCTTGTTCAATGTA -s simCow_chr6.simCow.chr6 499012 8 - 602619 ---------------TTGGAAC----A -s simDog_chr6.simDog.chr6 93716 12 + 593897 ---------------TTGGTACTTGGA -s simHuman_chr6.simHuman.chr6 502706 14 - 601863 -------------TCTTGCGACATGGA -s simRat_chr6.simRat.chr6 96205 27 + 647215 CGTGGCCCTGTCCCCTTATTCAATGTA - -a -s simMouse_chr6.simMouse.chr6 104045 4 + 636262 TCTA -s Anc0.Anc0refChr4 45011 4 - 45765 TCTA -s Anc1.Anc1refChr2 77166 4 + 144309 TCTA -s Anc2.Anc2refChr2 14712 4 + 27695 TATA -s mr.mrrefChr0 99085 4 + 130230 TCTA -s simCow_chr6.simCow.chr6 104919 4 + 602619 TGTA -s simDog_chr6.simDog.chr6 501455 4 - 593897 TATA -s simHuman_chr6.simHuman.chr6 100278 4 + 601863 TCTA -s simRat_chr6.simRat.chr6 96232 4 + 647215 TGTA - -a -s simMouse_chr6.simMouse.chr6 104049 15 + 636262 CCTCTCGTCCCTTAT -s Anc0.Anc0refChr4 45018 15 - 45765 CCTTTTGTCCCTTCT -s Anc1.Anc1refChr2 77173 15 + 144309 CCTTTTGTCCCTTCT -s Anc2.Anc2refChr2 14719 15 + 27695 CCTTTTGTCCCTTCC -s mr.mrrefChr0 99089 15 + 130230 CCTCTCGTCCCTTAT -s simCow_chr6.simCow.chr6 104926 15 + 602619 CTTTTTGCCCTGTCC -s simDog_chr6.simDog.chr6 501462 15 - 593897 CCTTTTGTCCCTTCC -s simHuman_chr6.simHuman.chr6 100287 15 + 601863 CCTTTTGTCCCCTCT -s simRat_chr6.simRat.chr6 96236 15 + 647215 CCTCTCGTCCCTTTT - -a -s simMouse_chr6.simMouse.chr6 104064 29 + 636262 CATTGCGTGTATCTATGCCCATCACCTGT -s Anc0.Anc0refChr4 45033 28 - 45765 CATTGCCTGTATCCTT-CCCATTGCCTGT -s Anc1.Anc1refChr2 77188 28 + 144309 CATTGCCTGTATCCTT-CCCATTGCCTGT -s Anc2.Anc2refChr2 14734 28 + 27695 CATTGCCTATGTCCTT-CCCTTTGCCTGT -s mr.mrrefChr0 99104 29 + 130230 CATTGCGTGTATCTTTGCCCATCACCTGT -s simCow_chr6.simCow.chr6 104941 28 + 602619 CATTGCCTCTGTCCTT-CCCGTTGCCTGT -s simDog_chr6.simDog.chr6 501477 28 - 593897 CATTGCCTACGTGCCT-CCCTTTGCCTGT -s simHuman_chr6.simHuman.chr6 100302 28 + 601863 CATTGCCTGTATCCTT-CCCACTGCCCGT -s simRat_chr6.simRat.chr6 96255 29 + 647215 CATTGTGTGTATTTTTACCCATCATATGT - -a -s simMouse_chr6.simMouse.chr6 104093 16 + 636262 TAGGTGATGCCAAGTT -s Anc0.Anc0refChr4 45062 16 - 45765 TAGGTGATACCAAGTA -s Anc1.Anc1refChr2 77217 16 + 144309 TAGGTGATACCAAGTA -s Anc2.Anc2refChr2 14763 16 + 27695 TAGGTAATACCAAGTA -s mr.mrrefChr0 99133 16 + 130230 TAGGTGATGCCAAGTT -s simCow_chr6.simCow.chr6 104970 16 + 602619 TAGGTAATACCAAGTA -s simDog_chr6.simDog.chr6 501506 16 - 593897 AAGGCAATAGCAAGTA -s simHuman_chr6.simHuman.chr6 100331 16 + 601863 TAGGTGTTACCAGGTA -s simRat_chr6.simRat.chr6 96284 16 + 647215 TATGTGATGACAAGTT - -a -s simMouse_chr6.simMouse.chr6 104109 4 + 636262 TACG -s Anc0.Anc0refChr4 45078 4 - 45765 GCAG -s Anc1.Anc1refChr2 77233 4 + 144309 GCAG -s Anc2.Anc2refChr2 14779 4 + 27695 GCAG -s mr.mrrefChr0 99149 4 + 130230 TAAG -s simCow_chr6.simCow.chr6 105001 4 + 602619 GTAG -s simDog_chr6.simDog.chr6 501522 4 - 593897 GCAG -s simHuman_chr6.simHuman.chr6 100347 4 + 601863 CCAG -s simRat_chr6.simRat.chr6 96300 4 + 647215 TAAG - -a -s simMouse_chr6.simMouse.chr6 104113 4 + 636262 GGTG -s Anc0.Anc0refChr4 45082 4 - 45765 GGTG -s Anc1.Anc1refChr2 77237 4 + 144309 GGTG -s Anc2.Anc2refChr2 14805 4 + 27695 GGTG -s mr.mrrefChr0 99153 4 + 130230 GGTG -s simCow_chr6.simCow.chr6 105036 4 + 602619 GGTT -s simDog_chr6.simDog.chr6 501548 4 - 593897 GGTG -s simHuman_chr6.simHuman.chr6 100351 4 + 601863 GGTA -s simRat_chr6.simRat.chr6 96304 4 + 647215 GCTG - -a -s simMouse_chr6.simMouse.chr6 104117 7 + 636262 ACACCTC -s Anc0.Anc0refChr4 45093 7 - 45765 AAACTTT -s Anc1.Anc1refChr2 77248 7 + 144309 AAACTTT -s Anc2.Anc2refChr2 14816 7 + 27695 AAACTTT -s mr.mrrefChr0 99157 7 + 130230 ACACCTC -s simCow_chr6.simCow.chr6 105047 7 + 602619 AAACTTT -s simDog_chr6.simDog.chr6 501559 7 - 593897 GAACTCT -s simHuman_chr6.simHuman.chr6 100362 7 + 601863 AAAATTT -s simRat_chr6.simRat.chr6 96308 6 + 647215 ACACCT- - -a -s simMouse_chr6.simMouse.chr6 104124 28 + 636262 TTGATAGATCACAATTTTTATCCTCCAA -s Anc0.Anc0refChr4 45100 28 - 45765 TTTATAGTTCACAGTTTTTGTTTAGCCA -s Anc1.Anc1refChr2 77255 28 + 144309 TTTATAGTTCACAGTTTTTGTTTAGCCA -s Anc2.Anc2refChr2 14823 28 + 27695 TTTATAGTTCACAGTTTTTGTTTAGCCA -s mr.mrrefChr0 99164 28 + 130230 TTGATAGATCACAATTTTTATCCTCCAA -s simCow_chr6.simCow.chr6 105054 28 + 602619 TGTATAAATCACAGTTTTTGTTTAGTAA -s simDog_chr6.simDog.chr6 501566 28 - 593897 TTTATAGTCCACAGTTTTTGTTTAGCCA -s simHuman_chr6.simHuman.chr6 100370 28 + 601863 GTTCTAGTTTAGAGTTTTTGTTTAGCCA - -a -s simMouse_chr6.simMouse.chr6 104152 9 + 636262 AACGAATGA -s Anc0.Anc0refChr4 45128 9 - 45765 AAGGGATGA -s Anc1.Anc1refChr2 77283 9 + 144309 AAGGGATGA -s Anc2.Anc2refChr2 14851 9 + 27695 AAGGGGTGA -s mr.mrrefChr0 99192 9 + 130230 AACGAATGA -s simCow_chr6.simCow.chr6 105083 9 + 602619 AGGGGGTGA -s simDog_chr6.simDog.chr6 501594 9 - 593897 AAGGGGTGA -s simHuman_chr6.simHuman.chr6 100398 9 + 601863 AATGGATGA - -a -s simMouse_chr6.simMouse.chr6 104161 1 + 636262 A -s Anc0.Anc0refChr4 45147 1 - 45765 A -s Anc1.Anc1refChr2 77302 1 + 144309 A -s Anc2.Anc2refChr2 14870 1 + 27695 A -s mr.mrrefChr0 99201 1 + 130230 A -s simCow_chr6.simCow.chr6 105102 1 + 602619 A -s simDog_chr6.simDog.chr6 501613 1 - 593897 C -s simHuman_chr6.simHuman.chr6 100417 1 + 601863 A - -a -s simMouse_chr6.simMouse.chr6 104162 6 + 636262 CTCAGT -s Anc0.Anc0refChr4 45148 6 - 45765 CATTGT -s Anc1.Anc1refChr2 77303 6 + 144309 CATTGT -s Anc2.Anc2refChr2 14871 6 + 27695 CATTGT -s mr.mrrefChr0 99202 6 + 130230 CTCAGT -s simCow_chr6.simCow.chr6 105131 6 + 602619 CATGGT -s simDog_chr6.simDog.chr6 501614 6 - 593897 CATTGA -s simHuman_chr6.simHuman.chr6 100418 6 + 601863 CATTGT - -a -s simMouse_chr6.simMouse.chr6 104168 10 + 636262 ACTCTATTTC -s Anc0.Anc0refChr4 45154 10 - 45765 ACTCTATTCC -s Anc1.Anc1refChr2 77309 10 + 144309 ACTCTATTCC -s Anc2.Anc2refChr2 14877 10 + 27695 ACTATATACC -s mr.mrrefChr0 99208 10 + 130230 ACTCTATTTC -s simCow_chr6.simCow.chr6 105137 10 + 602619 ACTATATACC -s simDog_chr6.simDog.chr6 501620 10 - 593897 ACTATGTACC -s simHuman_chr6.simHuman.chr6 100430 10 + 601863 ACCCTATTGT -s simRat_chr6.simRat.chr6 96314 2 + 647215 --------TC - -a -s simMouse_chr6.simMouse.chr6 104178 2 + 636262 AA -s Anc0.Anc0refChr4 45164 2 - 45765 AG -s Anc1.Anc1refChr2 77319 2 + 144309 AG -s Anc2.Anc2refChr2 14892 2 + 27695 AG -s mr.mrrefChr0 99218 2 + 130230 AA -s simCow_chr6.simCow.chr6 105152 2 + 602619 AG -s simDog_chr6.simDog.chr6 501635 2 - 593897 AG -s simHuman_chr6.simHuman.chr6 100440 2 + 601863 AG -s simRat_chr6.simRat.chr6 96316 2 + 647215 AA - -a -s simMouse_chr6.simMouse.chr6 104180 59 + 636262 TCACTTTTTACAATGTTCAAGCGACTTCAGCCAATGTCATCCCAAGGTTATTCAACTGA -s Anc0.Anc0refChr4 45166 46 - 45765 TCACCTTT-----------ACCAACTTCAGACAATTTCA--CCAAATCTTTCCAAATAA -s Anc1.Anc1refChr2 77321 48 + 144309 TCACCTTT-----------ACCAACTTCAGACAATTTCATCCCAAATCTTTCCAAATAA -s Anc2.Anc2refChr2 14894 46 + 27695 TCTCCCTT-----------ACCAAATTCAGACAACTTCA--CCAAATCTTTCCAAATAA -s mr.mrrefChr0 99220 48 + 130230 TCACTTTT-----------AGCGACTTCAGCCAATGTCATCCCAAGGTTATTCAACTGA -s simCow_chr6.simCow.chr6 105154 46 + 602619 TCTCCTTT-----------AGCAAATCCAGACAACATCA--CCAAATCTGTGCGAAGAA -s simDog_chr6.simDog.chr6 501637 46 - 593897 TCTCCCTT-----------ACCAAATTCAGACAACTTCA--CCAAATCTTTCCAAATAA -s simHuman_chr6.simHuman.chr6 100442 24 + 601863 TCACATT--------------CTACTATGGT---TATCATC------------------ -s simRat_chr6.simRat.chr6 96321 48 + 647215 TCTCTTTT-----------AGCAAAGTCAGCCAATGTCATTCCAAGTTTATTCAACTGA - -a -s simMouse_chr6.simMouse.chr6 104239 1 + 636262 G -s Anc0.Anc0refChr4 45212 1 - 45765 G -s Anc1.Anc1refChr2 77369 1 + 144309 G -s Anc2.Anc2refChr2 14945 1 + 27695 G -s mr.mrrefChr0 99268 1 + 130230 G -s simCow_chr6.simCow.chr6 105205 1 + 602619 G -s simDog_chr6.simDog.chr6 501688 1 - 593897 G -s simRat_chr6.simRat.chr6 96369 1 + 647215 G - -a -s simMouse_chr6.simMouse.chr6 104240 16 + 636262 GTGGCCACAGTGAAGT -s Anc0.Anc0refChr4 45213 16 - 45765 ATACCCACAATGGATT -s Anc1.Anc1refChr2 77370 16 + 144309 ATACCCACAATGGATT -s Anc2.Anc2refChr2 14946 16 + 27695 ATACCCACAATGGATT -s mr.mrrefChr0 99269 16 + 130230 GTGGCCACAGTGAAGT -s simCow_chr6.simCow.chr6 105206 16 + 602619 GCGCCCATAACGGATT -s simDog_chr6.simDog.chr6 501690 16 - 593897 ATACCCACAATGGATT -s simRat_chr6.simRat.chr6 96370 16 + 647215 GTGGCCACAGTGAATC - -a -s simMouse_chr6.simMouse.chr6 104256 6 + 636262 GCTTTT -s Anc0.Anc0refChr4 45229 6 - 45765 ACTTTT -s Anc1.Anc1refChr2 77386 6 + 144309 ACTTTT -s Anc2.Anc2refChr2 14966 6 + 27695 ACTTTT -s mr.mrrefChr0 99285 6 + 130230 GCTTTT -s simCow_chr6.simCow.chr6 105226 6 + 602619 CTTCTT -s simDog_chr6.simDog.chr6 501710 6 - 593897 ACTTTT -s simRat_chr6.simRat.chr6 96386 6 + 647215 GCTTTT - -a -s simMouse_chr6.simMouse.chr6 104262 32 + 636262 TCTTGGAAACCTCTTTTGTGAACCTCCTTTTC -s Anc0.Anc0refChr4 45235 24 - 45765 T------AGCCTC--TTGTGGACCTCTTTGCC -s Anc1.Anc1refChr2 77392 24 + 144309 T------AGCCTC--TTGTGGACCTCTTTGCC -s Anc2.Anc2refChr2 14972 24 + 27695 T------AGCCTC--TTGTGGACTTCTTTGCC -s mr.mrrefChr0 99291 32 + 130230 TCTTGGAAACCTCTTTTGTGAACCTCCTTTTC -s simCow_chr6.simCow.chr6 105235 24 + 602619 T------AGCCCC--TTGTGGACTTCTTTGCC -s simDog_chr6.simDog.chr6 501716 24 - 593897 T------AGCCTC--TTGTAGACTTCGTTGCC -s simHuman_chr6.simHuman.chr6 100466 17 + 601863 ---------------TTGTGTTTCCCTATACC -s simRat_chr6.simRat.chr6 96392 32 + 647215 TTTTGTCAACCTCTTTTGCAAACTGCCTTTTC - -a -s simMouse_chr6.simMouse.chr6 104294 32 + 636262 TGGCTATCCAAGCTTTCATTCAGGTCCAATGT -s Anc0.Anc0refChr4 45259 32 - 45765 TGGGTAGGCACCCTTTCATTCAGGTTTAATGT -s Anc1.Anc1refChr2 77416 32 + 144309 TGGGTAGGCACCCTTTCATTCAGGTTTAATGT -s Anc2.Anc2refChr2 14996 32 + 27695 TGGGTAGGCACCCTTTCATTCAGGTTTAAGGT -s mr.mrrefChr0 99323 32 + 130230 TGGCTATCCAAGCTTTCATTCAGGTCTAATGT -s simCow_chr6.simCow.chr6 105260 32 + 602619 TGGGTAGTCACCCCTTCATTCTGATCTAAGGT -s simDog_chr6.simDog.chr6 501740 32 - 593897 TGGGTATGCTTCCTTTCATTCAGGTTTAAGGT -s simHuman_chr6.simHuman.chr6 100483 32 + 601863 TGGGCAGGTACTCTTTTATTCCGGTTTAATGT -s simRat_chr6.simRat.chr6 96424 32 + 647215 TGGCTATCCAAGCTATCATTCAGGTCTAATGT - -a -s simMouse_chr6.simMouse.chr6 104326 2 + 636262 CT -s Anc0.Anc0refChr4 45291 2 - 45765 CT -s Anc1.Anc1refChr2 77448 2 + 144309 CT -s Anc2.Anc2refChr2 15028 2 + 27695 CT -s mr.mrrefChr0 99355 2 + 130230 CT -s simCow_chr6.simCow.chr6 105292 2 + 602619 CT -s simDog_chr6.simDog.chr6 501772 2 - 593897 CT -s simHuman_chr6.simHuman.chr6 100515 2 + 601863 CT -s simRat_chr6.simRat.chr6 96460 2 + 647215 CT - -a -s simMouse_chr6.simMouse.chr6 104328 12 + 636262 GACCCATGACTA -s Anc0.Anc0refChr4 45293 12 - 45765 GACCCATGAATA -s Anc1.Anc1refChr2 77450 12 + 144309 GACCCATGAATA -s Anc2.Anc2refChr2 15030 12 + 27695 GATCCATTAATA -s mr.mrrefChr0 99357 12 + 130230 GACCCATGACTA -s simCow_chr6.simCow.chr6 105294 12 + 602619 AATGCATAAATA -s simDog_chr6.simDog.chr6 501779 12 - 593897 GGTCCATTAATA -s simHuman_chr6.simHuman.chr6 100517 12 + 601863 GACCCATGAATA -s simRat_chr6.simRat.chr6 96462 9 + 647215 GACCCATGA--- - -a -s simMouse_chr6.simMouse.chr6 104340 18 + 636262 CCAAGATATCAGATAGTT -s Anc0.Anc0refChr4 45305 18 - 45765 CCAAGATATCATATGGTT -s Anc1.Anc1refChr2 77462 18 + 144309 CCAAGATATCATATGGTT -s Anc2.Anc2refChr2 15048 18 + 27695 CCTAGAAATCATATGGTT -s mr.mrrefChr0 99369 18 + 130230 CCAAGATATCATATAGTT -s simCow_chr6.simCow.chr6 105330 14 + 602619 CCTAGAAATCATGT---- -s simDog_chr6.simDog.chr6 501797 18 - 593897 CCTAGAAATCACATGGTT -s simHuman_chr6.simHuman.chr6 100529 18 + 601863 ACAAGATATCATATTGTT -s simRat_chr6.simRat.chr6 96471 13 + 647215 -----ATACCATATATTG - -a -s simMouse_chr6.simMouse.chr6 104358 24 + 636262 ATGCCTCCTAATTCCAGTCCTGGG -s Anc0.Anc0refChr4 45323 24 - 45765 ATGCCTCCAATTTCCAGTCCTGGG -s Anc1.Anc1refChr2 77480 24 + 144309 ATGCCTCCAATTTCCAGTCCTGGG -s Anc2.Anc2refChr2 15066 24 + 27695 ATGCCTACAATTTCCAGTCCTGGG -s mr.mrrefChr0 99387 24 + 130230 ATGCCTCCAAATTCCAGTCCTGGG -s simCow_chr6.simCow.chr6 495292 24 - 602619 AAGCCTTCGATTTCCAGTCCTGGG -s simDog_chr6.simDog.chr6 501815 24 - 593897 GTGCCTACAATTTTCAGGGCTGGG -s simHuman_chr6.simHuman.chr6 100547 20 + 601863 A----TCCAATTTCCAGTCCTGGG -s simRat_chr6.simRat.chr6 96484 24 + 647215 ATGCCTCCAAATTCCAGTCCTGGG - -a -s simMouse_chr6.simMouse.chr6 104382 64 + 636262 CTTCGCTCCGTGGAGTTTCAGGCCGCTGCTTTTGTCTTTTATTTACAATACATAAATGGGGGAC -s Anc0.Anc0refChr4 45348 60 - 45765 CTTTGCTCCCCCGATTTTCAGTCCTGGGTTTTTGTTT----TTTACGGTTCATAAACAGGGGAC -s Anc1.Anc1refChr2 77505 60 + 144309 CTTTGCTCCCCCGATTTTCAGTCCTGGGTTTTTGTTT----TTTACGGTTCATAAACAGGGGAC -s Anc2.Anc2refChr2 15091 60 + 27695 TTTTGCTCCCCCTATTTTCAGTCCTGGGTTTTTGCTT----TTTATGGTTCATAAACAGGGGAC -s mr.mrrefChr0 99411 60 + 130230 CTTTGCTCCCTGGAGTTTCAGGCCTCGGCTTTTGTCT----TTTACAATACATAAATGGGGGAC -s simCow_chr6.simCow.chr6 495317 60 - 602619 TTTTGCTCCCCCAATCGTCGGTTCTGTGTCTTTACTT----TTTATGGCTCATAAACAGGGGAT -s simDog_chr6.simDog.chr6 501840 60 - 593897 TTTAACTCCCCCTTTTTTCAGTCCTGGATTTTTGCTT----TTTATGGTTCGTAAACAAGGAAC -s simHuman_chr6.simHuman.chr6 100568 58 + 601863 CTTTGCTCCCCTGATTTTCACTCCTGGGGTTTTGTTT----TTCAC--TGCATAAACAGATGAC -s simRat_chr6.simRat.chr6 96508 60 + 647215 CTTTGCTGCCTGAAGTTTCAGGCCTCGATTTTTGTCT----TTTACAATACATAAATGGGGGAC - -a -s simMouse_chr6.simMouse.chr6 104446 15 + 636262 CTTTTTAAAAGTGTC -s Anc0.Anc0refChr4 45409 15 - 45765 CTTTTTGAAAATATC -s Anc1.Anc1refChr2 77566 15 + 144309 CTTTTTGAAAATATC -s Anc2.Anc2refChr2 15152 15 + 27695 TTCTGTGAAAATATA -s mr.mrrefChr0 99471 15 + 130230 CTTTTTAAAAGTGTC -s simCow_chr6.simCow.chr6 495378 15 - 602619 TTCTAAAAACATATT -s simDog_chr6.simDog.chr6 501901 14 - 593897 TTCTGTGATAA-ATA -s simHuman_chr6.simHuman.chr6 100627 15 + 601863 CTTTTTGAAAATATC -s simRat_chr6.simRat.chr6 96568 15 + 647215 CTTTTTAAAAGTGTC - -a -s simMouse_chr6.simMouse.chr6 104461 42 + 636262 ATTAAATCACACAACCTATTATTAGCCATGTGTGGAAGAAGA -s Anc0.Anc0refChr4 45425 34 - 45765 AGTATACCATGAGACCTATCTTTGGTCATGTGTG-------- -s Anc1.Anc1refChr2 77582 34 + 144309 AGTATACCATGAGACCTATCTTTGGTCATGTGTG-------- -s Anc2.Anc2refChr2 15168 34 + 27695 AGTATACCATGAGATCTATCTTTGGTCATGTCCG-------- -s mr.mrrefChr0 99486 42 + 130230 ATTAAATCATGCAACCTATTATTAGCCATGTGTGGAAGAAGA -s simCow_chr6.simCow.chr6 495394 34 - 602619 AGCATCCCATTAGATCTCTCTCTGGTCATGCCCG-------- -s simDog_chr6.simDog.chr6 501916 31 - 593897 GGTATATCAGGTGATCTACCTTTGGTCATGT----------- -s simHuman_chr6.simHuman.chr6 100643 34 + 601863 AATATACCGTGAGACCTATCTTTGGTCATGTGTA-------- -s simRat_chr6.simRat.chr6 96583 42 + 647215 ATTACATCATGCAGCCTATAATTCACTATGTGTGGAAGAAGA - -a -s simMouse_chr6.simMouse.chr6 104503 14 + 636262 GAAGAAGGTGGAGC -s Anc0.Anc0refChr4 45459 14 - 45765 GAAGAAGGCAAAGC -s Anc1.Anc1refChr2 77616 14 + 144309 GAAGAAGGCAAAGC -s Anc2.Anc2refChr2 15202 14 + 27695 GAAGAAGGCAAAGC -s mr.mrrefChr0 99528 14 + 130230 GAAGAAGGTGAAGC -s simCow_chr6.simCow.chr6 495428 14 - 602619 GAAGAAGGCAAAGC -s simHuman_chr6.simHuman.chr6 100687 14 + 601863 GAAGAAGGCAAAGC -s simRat_chr6.simRat.chr6 96625 14 + 647215 GAAGAAGGTGAAGT - -a -s simMouse_chr6.simMouse.chr6 104517 8 + 636262 TTTCTTTT -s Anc0.Anc0refChr4 45474 8 - 45765 TTTCTTTT -s Anc1.Anc1refChr2 77631 8 + 144309 TTTCTTTT -s Anc2.Anc2refChr2 15217 8 + 27695 TTTCTTTT -s mr.mrrefChr0 99542 8 + 130230 TTTCTTTT -s simCow_chr6.simCow.chr6 495443 8 - 602619 TTTCTTTT -s simDog_chr6.simDog.chr6 501947 7 - 593897 -TTCCGGT -s simHuman_chr6.simHuman.chr6 100702 8 + 601863 TTTCTTTT -s simRat_chr6.simRat.chr6 96639 8 + 647215 TTTCTTTT - -a -s simMouse_chr6.simMouse.chr6 104525 62 + 636262 ATGATTGAGCTCATTTCTTACCCATTCATATCAGATATTCTATGATAAGCCTGAATTGTTAC -s Anc0.Anc0refChr4 45482 18 - 45765 TTGATTT----------TTACCCTCTCA---------------------------------- -s Anc1.Anc1refChr2 77639 18 + 144309 TTGATTT----------TTACCCTCTCA---------------------------------- -s Anc2.Anc2refChr2 15225 18 + 27695 TTGATTT----------TTACCCTCTCT---------------------------------- -s mr.mrrefChr0 99550 62 + 130230 TTGATTGAGCTCATTTCTTACCCATTCATATCAGATATTCTATGATAAGCCTGAATTGTTAC -s simCow_chr6.simCow.chr6 495460 18 - 602619 TTTATTG----------TTAACCACTCT---------------------------------- -s simDog_chr6.simDog.chr6 501954 18 - 593897 GAGTTTT----------GTACCCTCTCT---------------------------------- -s simHuman_chr6.simHuman.chr6 100710 18 + 601863 TTGATTA----------TTACCTGCTCA---------------------------------- -s simRat_chr6.simRat.chr6 96647 62 + 647215 TGGATTGGGCTCATTTGTTACCCATTCGTGTCAGATATAGTATGATAAGCCTGAATTGTTAC - -a -s simMouse_chr6.simMouse.chr6 104587 79 + 636262 CTAGCAGTCCCTTTGGGAGTATCAGAAAAGAAATCGAGATAGTCACCCTCCATAAGCCTAATTGATGCTACAGGTCCAT -s Anc0.Anc0refChr4 45500 62 - 45765 ----------CATTAGGAGTATCAGAGAA------GAGATAGTCCAACTCCAG-GGGCTAATTATTACTACTGCTTCAT -s Anc1.Anc1refChr2 77657 62 + 144309 ----------CATTAGGAGTATCAGAGAA------GAGATAGTCCAACTCCAG-GGGCTAATTATTACTACTGCTTCAT -s Anc2.Anc2refChr2 15243 62 + 27695 ----------GATTAGGTCTATCAGAGAA------GAGATAGTCCAACCCCAG-GGGCTAGTTATTACTACTGCTTCAC -s mr.mrrefChr0 99633 78 + 130230 CTAGCAGTCCCATTGGGAGTATCAGAGAAGAAATCGAGATAGTCCCCCTCCAT-AGCCTAATTAATGCTACAGGTCCAT -s simCow_chr6.simCow.chr6 495478 52 - 602619 ----------TATCAGGCCTGTCCAAGTA------GAGAGAGTCCTTCCCCAG-GG----------ACTACTGATTCAC -s simDog_chr6.simDog.chr6 501972 62 - 593897 ----------GATTAGGTCTATCAGAGAA------GAGATAGTCCAACCCCAG-GGGCTAGTTATTACTACTGCTTCAC -s simHuman_chr6.simHuman.chr6 100728 62 + 601863 ----------CATTAGGAGTCTTTGAGAA------GAGATAGACCAACTCCAG-GGGCCAATTATTACTACTGCTTCAT -s simRat_chr6.simRat.chr6 96732 76 + 647215 CTAGCAGTTACATTGGGAGTATCAGAGAAGATATCGAGATAATCCCCTTCCAT-AGCCTAATTAATGCTCCA--TCCAC - -a -s simMouse_chr6.simMouse.chr6 104666 39 + 636262 TTTGATTGCTGAGGCTACTTTTGTAAAGTTTGGATCTCT -s Anc0.Anc0refChr4 45568 16 - 45765 TT----------------------AAAGCTTGTAG-TCT -s Anc1.Anc1refChr2 77725 39 + 144309 TTCCATCGCTAGAGGCATTTTTATAAAGCTTGTAGCTCT -s Anc2.Anc2refChr2 15311 16 + 27695 TT----------------------AGAGATTGTAG-TGT -s mr.mrrefChr0 99711 39 + 130230 TTTGATTGCTTAGGCTACTTTTGTAAAGCTTGTATCTCT -s simCow_chr6.simCow.chr6 495536 3 - 602619 TT----------------------A-------------- -s simDog_chr6.simDog.chr6 502040 16 - 593897 GT----------------------AGAGATTGTAG-TGT -s simHuman_chr6.simHuman.chr6 100796 39 + 601863 TTCCATCGCTAGAGGCATTTTTAGAAAGCTTGTAACTCT -s simRat_chr6.simRat.chr6 96808 39 + 647215 TTTGATTGCCTAGGCTACTTTTGTAAAACTTGTATCTCT - -a -s simMouse_chr6.simMouse.chr6 104705 16 + 636262 AAGCCCTCTGACTATC -s Anc0.Anc0refChr4 45585 16 - 45765 GAGCTCTCTGACTATC -s Anc1.Anc1refChr2 77765 16 + 144309 GAGCTCTCTGACTATC -s Anc2.Anc2refChr2 15328 16 + 27695 GAGCTCTCTGGCCATC -s mr.mrrefChr0 99751 16 + 130230 AAGCCCTCTGACTATC -s simDog_chr6.simDog.chr6 502057 16 - 593897 GAGCTCTCTGGCCATC -s simHuman_chr6.simHuman.chr6 100836 16 + 601863 GAGCTCTCTGACTATC -s simRat_chr6.simRat.chr6 96848 16 + 647215 AAGGCCTCTGACTATC - -a -s simMouse_chr6.simMouse.chr6 104721 10 + 636262 ACATACAGTC -s Anc0.Anc0refChr4 45601 9 - 45765 ACATATGGT- -s Anc1.Anc1refChr2 77781 10 + 144309 ACATATGGTC -s Anc2.Anc2refChr2 15344 9 + 27695 ACATATGGT- -s mr.mrrefChr0 99767 10 + 130230 ACATATGGTC -s simDog_chr6.simDog.chr6 502073 9 - 593897 ACATATGGT- -s simHuman_chr6.simHuman.chr6 100857 10 + 601863 ACATATGATC -s simRat_chr6.simRat.chr6 96864 10 + 647215 ACATATGGTC - -a -s simMouse_chr6.simMouse.chr6 104731 65 + 636262 AGGGTGGGGACAGCCCTGTTGCTCTCATAGAGTTATGTGCTTGGCTGCATTTAGATGTGCCATCA -s Anc0.Anc0refChr4 45610 63 - 45765 --GGTGGGCACAGCCCCATTGCTTTCACAGAGTTATCTGCATAACTGCTTTTAGATATGCCATTA -s Anc1.Anc1refChr2 77791 65 + 144309 GGGGTGGGCACAGCCCCATTGCTTTCACAGAGTTATCTGCATAACTGCTTTTAGATATGCCATTA -s Anc2.Anc2refChr2 15353 63 + 27695 --GGTGGGCACAGCCCCATTGATTTCACAGAGTTATCTGCATAACTGCTTTTAGATATGCCTTTG -s mr.mrrefChr0 99777 65 + 130230 GGGGTGGGGACAGCCCTGTTGCTCTCATAGAGTTATGTGCTTAGCTGCATTTAGATGTGCCATCA -s simCow_chr6.simCow.chr6 495539 30 - 602619 -----------------------------------TTTGCATTGCTGCTTTTAGATATGCCCTTG -s simDog_chr6.simDog.chr6 502082 63 - 593897 --GGTGGGCACAGCCCCATTGATTTCACAGAGTTATCTGCCTAACTGCTTTTAGATATGCTTCCG -s simHuman_chr6.simHuman.chr6 100868 65 + 601863 GGGGTCAGCAACGCTCCATTGCTTTCACAGAGTTATCTGCATAACTGCTTTTAGATCCACCATTA -s simRat_chr6.simRat.chr6 96874 65 + 647215 GGGGTGGGGACAGCCATCTTGCTCTCATAGAGTTATGTGCTTAGCTACATTTAGACGTGCCATCA - -a -s simMouse_chr6.simMouse.chr6 104796 14 + 636262 TATGTGGTTCCATG -s Anc0.Anc0refChr4 45673 14 - 45765 TATTTGGCTCCATG -s Anc1.Anc1refChr2 77856 14 + 144309 TATTTGGCTCCATG -s Anc2.Anc2refChr2 15416 14 + 27695 TATTTGGCTCCATG -s Anc2.Anc2refChr13 23479 14 - 96486 TACTTGGTTCCATG -s mr.mrrefChr0 99842 14 + 130230 TATTTGGTTCCATG -s simCow_chr6.simCow.chr6 172645 14 - 602619 TATTTGTCTCCATG -s simCow_chr6.simCow.chr6 495569 14 - 602619 TATTTGATTCCATA -s simDog_chr6.simDog.chr6 172767 14 - 593897 TACTTGGTTCCATG -s simDog_chr6.simDog.chr6 502145 14 - 593897 TATTTGGCTCCGTG -s simHuman_chr6.simHuman.chr6 100933 14 + 601863 TATTTGGCTCTATG -s simRat_chr6.simRat.chr6 96939 14 + 647215 TCTTTGGTACCATG - -a -s simMouse_chr6.simMouse.chr6 104810 6 + 636262 AAATAG -s Anc0.Anc0refChr4 45688 6 - 45765 AAATAG -s Anc1.Anc1refChr2 77871 6 + 144309 AAATAG -s Anc2.Anc2refChr2 15431 6 + 27695 AAATAG -s Anc2.Anc2refChr13 23494 6 - 96486 AAACAG -s mr.mrrefChr0 99856 6 + 130230 AAATAG -s simCow_chr6.simCow.chr6 172660 6 - 602619 AAATAG -s simCow_chr6.simCow.chr6 495584 6 - 602619 AACTAG -s simDog_chr6.simDog.chr6 172782 6 - 593897 AAACAG -s simDog_chr6.simDog.chr6 502160 6 - 593897 AAATAG -s simHuman_chr6.simHuman.chr6 100948 6 + 601863 AAACAG -s simRat_chr6.simRat.chr6 96953 6 + 647215 AAGTAG - -a -s simMouse_chr6.simMouse.chr6 104816 6 + 636262 TTGTTG -s Anc0.Anc0refChr4 45694 6 - 45765 GTGTAG -s Anc1.Anc1refChr2 77877 6 + 144309 GTGTAG -s Anc2.Anc2refChr2 15437 6 + 27695 GTGTAG -s Anc2.Anc2refChr13 23500 6 - 96486 GTGCAG -s mr.mrrefChr0 99862 6 + 130230 TTGTTG -s simCow_chr6.simCow.chr6 172668 6 - 602619 GTGCAG -s simCow_chr6.simCow.chr6 495590 6 - 602619 GTGCAC -s simDog_chr6.simDog.chr6 172788 6 - 593897 GTGCAG -s simDog_chr6.simDog.chr6 502166 6 - 593897 GCGTAG -s simHuman_chr6.simHuman.chr6 100954 6 + 601863 GTGTAG -s simRat_chr6.simRat.chr6 96959 6 + 647215 TTGTTG - -a -s simMouse_chr6.simMouse.chr6 104822 4 + 636262 TTTA -s Anc0.Anc0refChr4 45700 4 - 45765 TTAA -s Anc1.Anc1refChr2 77883 4 + 144309 TTTA -s Anc2.Anc2refChr2 15443 4 + 27695 TTAA -s Anc2.Anc2refChr13 23506 4 - 96486 TTAA -s mr.mrrefChr0 99868 4 + 130230 TTTA -s simCow_chr6.simCow.chr6 172674 4 - 602619 TTAA -s simCow_chr6.simCow.chr6 495596 4 - 602619 TTAA -s simDog_chr6.simDog.chr6 172794 4 - 593897 TTAA -s simDog_chr6.simDog.chr6 502172 4 - 593897 TTGG -s simHuman_chr6.simHuman.chr6 100970 4 + 601863 TTTA -s simRat_chr6.simRat.chr6 96965 4 + 647215 TCTA - -a -s simMouse_chr6.simMouse.chr6 104826 1 + 636262 A -s Anc0.Anc0refChr4 45704 1 - 45765 T -s Anc1.Anc1refChr2 77887 1 + 144309 A -s Anc2.Anc2refChr2 15447 1 + 27695 T -s Anc2.Anc2refChr13 23510 1 - 96486 T -s mr.mrrefChr0 99872 1 + 130230 A -s simCow_chr6.simCow.chr6 172678 1 - 602619 T -s simCow_chr6.simCow.chr6 495600 1 - 602619 T -s simDog_chr6.simDog.chr6 172923 1 - 593897 T -s simDog_chr6.simDog.chr6 502176 1 - 593897 T -s simHuman_chr6.simHuman.chr6 100974 1 + 601863 A -s simRat_chr6.simRat.chr6 96969 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 104827 47 + 636262 TGACATAATGAGGAATAGCCTCACCATCACTACTACCCCATGATCAC -s Anc0.Anc0refChr4 45705 41 - 45765 TAACATAATCAGAACTGGCCTTGC------TACTCTCCCATGAGCTC -s Anc1.Anc1refChr2 77888 43 + 144309 TAACATAATCAGGACTGGCCTTGCTA----TACTCTCCCATGAGCTC -s Anc2.Anc2refChr2 15448 41 + 27695 TAACATAATCAGAACTGGCCTTGC------TACTCTCCCACGAGCTC -s Anc2.Anc2refChr13 23511 41 - 96486 AAACATAGTAAGAACTGGCCTTGC------CATTCTTTCATGATCTC -s mr.mrrefChr0 99873 47 + 130230 TGACATAATGAGGAATAGCCTCACCATCACTACTACCCCATGATCTC -s simCow_chr6.simCow.chr6 172679 41 - 602619 GAATATAATAAGAACTGGCCTTGT------TATTCTTCCTTGATCTC -s simCow_chr6.simCow.chr6 495601 41 - 602619 TAACATAATTAATGCTAGCATCTC------TACTCTCCCACAATCTC -s simDog_chr6.simDog.chr6 172924 41 - 593897 AAACATAGTAAGAACTGGCCTTGC------CATTCTTTCATGATCTC -s simDog_chr6.simDog.chr6 502177 41 - 593897 TTACATAATCAGAACTGGCCTTGC------TTCTCTCTCACGAGCTC -s simHuman_chr6.simHuman.chr6 100976 43 + 601863 TAACATAATAAGGACTGGCCTTGCTA----TATTCTCCCATGAGCTC -s simRat_chr6.simRat.chr6 96970 47 + 647215 TATCATAACGAGGAATAGCCTCACCATCACTACTACCCCATGATCTC - -a -s simMouse_chr6.simMouse.chr6 104874 4 + 636262 ACTG -s Anc0.Anc0refChr4 45746 4 - 45765 ACTA -s Anc1.Anc1refChr2 77931 4 + 144309 ACTA -s Anc2.Anc2refChr2 15489 4 + 27695 ACTA -s Anc2.Anc2refChr13 23552 4 - 96486 ACTA -s mr.mrrefChr0 99920 4 + 130230 ACTG -s simCow_chr6.simCow.chr6 172772 4 - 602619 ATTA -s simCow_chr6.simCow.chr6 495642 2 - 602619 AC-- -s simDog_chr6.simDog.chr6 172965 4 - 593897 ACTA -s simDog_chr6.simDog.chr6 502218 4 - 593897 ACTA -s simHuman_chr6.simHuman.chr6 101019 4 + 601863 ACTA -s simRat_chr6.simRat.chr6 97017 4 + 647215 ACTG - -a -s simMouse_chr6.simMouse.chr6 104878 6 + 636262 CTTTAG -s Anc0.Anc0refChr4 45753 6 - 45765 CTCTAA -s Anc1.Anc1refChr2 77938 6 + 144309 CTCTAA -s Anc2.Anc2refChr2 15496 6 + 27695 CCCCAA -s mr.mrrefChr0 99924 6 + 130230 CTTTAG -s simCow_chr6.simCow.chr6 495644 2 - 602619 ----AT -s simDog_chr6.simDog.chr6 502225 6 - 593897 CCCCAA -s simHuman_chr6.simHuman.chr6 101026 6 + 601863 CTCTGC -s simRat_chr6.simRat.chr6 97021 6 + 647215 CTTATG - -a -s simMouse_chr6.simMouse.chr6 104884 4 + 636262 CATG -s Anc0.Anc0refChr4 45759 4 - 45765 TGTA -s Anc1.Anc1refChr2 77944 4 + 144309 CGTA -s Anc2.Anc2refChr2 15503 4 + 27695 TGTA -s Anc2.Anc2refChr13 23559 4 - 96486 TACA -s mr.mrrefChr0 99930 4 + 130230 CGTG -s simCow_chr6.simCow.chr6 172779 4 - 602619 TACA -s simCow_chr6.simCow.chr6 495647 4 - 602619 TATA -s simDog_chr6.simDog.chr6 172972 4 - 593897 TACA -s simDog_chr6.simDog.chr6 502232 4 - 593897 TGTA -s simHuman_chr6.simHuman.chr6 101032 4 + 601863 CGTA -s simRat_chr6.simRat.chr6 97027 4 + 647215 CGTG - -a -s simMouse_chr6.simMouse.chr6 104888 2 + 636262 GG -s Anc0.Anc0refChr4 45763 2 - 45765 GG -s Anc1.Anc1refChr2 77948 2 + 144309 GG -s Anc2.Anc2refChr2 15507 2 + 27695 GG -s Anc2.Anc2refChr13 23563 2 - 96486 TT -s mr.mrrefChr0 99934 2 + 130230 GG -s simCow_chr6.simCow.chr6 172787 2 - 602619 TT -s simCow_chr6.simCow.chr6 495651 2 - 602619 GG -s simDog_chr6.simDog.chr6 172976 2 - 593897 TT -s simDog_chr6.simDog.chr6 502236 2 - 593897 GG -s simHuman_chr6.simHuman.chr6 101036 2 + 601863 GG -s simRat_chr6.simRat.chr6 97031 2 + 647215 GG - -a -s simMouse_chr6.simMouse.chr6 104890 2 + 636262 GA -s Anc0.Anc0refChr1 0 2 - 62388 GA -s Anc1.Anc1refChr2 77950 2 + 144309 GA -s Anc2.Anc2refChr2 15509 2 + 27695 GA -s mr.mrrefChr0 99936 2 + 130230 GA -s simCow_chr6.simCow.chr6 495653 2 - 602619 GA -s simDog_chr6.simDog.chr6 502239 2 - 593897 GA -s simHuman_chr6.simHuman.chr6 101038 2 + 601863 GA -s simRat_chr6.simRat.chr6 97033 2 + 647215 GA - -a -s simMouse_chr6.simMouse.chr6 104892 17 + 636262 TTAGGGCATTCCAGAAC -s Anc0.Anc0refChr1 7 17 - 62388 ATATGGCAGCCCAGCAC -s Anc1.Anc1refChr2 77957 17 + 144309 ATATGGCAGCCCAGCAC -s Anc2.Anc2refChr2 15516 17 + 27695 ATATGGCAGCCCAGCAA -s mr.mrrefChr0 99943 17 + 130230 TTAGGGCATCCCAGAAC -s simCow_chr6.simCow.chr6 495660 17 - 602619 AAATGGCAGCAAAGCAT -s simDog_chr6.simDog.chr6 502246 17 - 593897 ATATGGCAGCCCAGTAA -s simHuman_chr6.simHuman.chr6 101045 17 + 601863 CTATGGCAACCGAGCAC -s simRat_chr6.simRat.chr6 97040 17 + 647215 TTAGGGCATCCCAGAAC - -a -s simMouse_chr6.simMouse.chr6 104909 9 + 636262 CAAGAGACA -s Anc0.Anc0refChr1 28 9 - 62388 CAAGTGAGA -s Anc1.Anc1refChr2 77978 9 + 144309 CAAGTGAGA -s Anc2.Anc2refChr2 15537 9 + 27695 CAAGTGAGA -s mr.mrrefChr0 99964 9 + 130230 CAAGAGAGA -s simCow_chr6.simCow.chr6 495681 9 - 602619 AGAGCGGGA -s simDog_chr6.simDog.chr6 502267 9 - 593897 CAAGTGAGA -s simHuman_chr6.simHuman.chr6 101066 9 + 601863 CAAGTGAGA -s simRat_chr6.simRat.chr6 97061 9 + 647215 CAATAGAGA - -a -s simMouse_chr6.simMouse.chr6 104918 12 + 636262 AAACTCATCTTT -s Anc0.Anc0refChr1 38 8 - 62388 AA----ATCATT -s Anc1.Anc1refChr2 77988 8 + 144309 AA----ATCATT -s Anc2.Anc2refChr2 15547 8 + 27695 AA----ATCATC -s mr.mrrefChr0 99973 8 + 130230 AA----ATCATT -s simCow_chr6.simCow.chr6 495691 8 - 602619 AA----ATCATC -s simDog_chr6.simDog.chr6 502277 8 - 593897 CA----GCTATC -s simHuman_chr6.simHuman.chr6 101076 8 + 601863 AA----ATCATT -s simRat_chr6.simRat.chr6 97070 8 + 647215 AA----ATCATT - -a -s simMouse_chr6.simMouse.chr6 104930 31 + 636262 TTTAGGATTATGGGCAATACAAGCACTATAA -s Anc0.Anc0refChr1 55 31 - 62388 ATTATGATTATGGAAGAGGCGAACACTACAA -s Anc1.Anc1refChr2 78005 31 + 144309 ATTATGATTATGGAAGAGGCGAACACTACAA -s Anc2.Anc2refChr2 15564 31 + 27695 ATTATGACTATGGAAGAGGCGAACACTACAA -s mr.mrrefChr0 99981 31 + 130230 TCTAGGATTATGGACGAGGCAAGCACTACAA -s simCow_chr6.simCow.chr6 495708 31 - 602619 ATTAAGACTATGGAAGAGGTGAACACTATAA -s simDog_chr6.simDog.chr6 502294 31 - 593897 ATTATTCCTATGAAAGACGCAACTATTACAG -s simHuman_chr6.simHuman.chr6 101093 31 + 601863 ATTATGATTATGGAAGCGGCGAACACTACAA -s simRat_chr6.simRat.chr6 97078 31 + 647215 TCTAAGATTATAGATGAGGCAAGCACTACAA - -a -s simMouse_chr6.simMouse.chr6 104961 4 + 636262 AAGT -s Anc0.Anc0refChr1 92 4 - 62388 AAGC -s Anc1.Anc1refChr2 78042 4 + 144309 AAGC -s Anc2.Anc2refChr2 15601 4 + 27695 AAGC -s mr.mrrefChr0 100018 4 + 130230 AAGT -s simCow_chr6.simCow.chr6 495745 4 - 602619 AAGC -s simDog_chr6.simDog.chr6 502331 4 - 593897 AAGC -s simHuman_chr6.simHuman.chr6 101130 4 + 601863 AAGC -s simRat_chr6.simRat.chr6 97115 4 + 647215 AAGT - -a -s simMouse_chr6.simMouse.chr6 104965 16 + 636262 ATGCAACACCATTGCA -s Anc0.Anc0refChr1 101 16 - 62388 ATGCACCACCATTGCA -s Anc1.Anc1refChr2 78051 16 + 144309 ATGCACCACCATTGCA -s Anc2.Anc2refChr2 15610 16 + 27695 ATGCACCACCATTGCA -s mr.mrrefChr0 100022 16 + 130230 ATGCAACACCATTGCA -s simCow_chr6.simCow.chr6 495754 16 - 602619 ATGTCCCACCATTGCA -s simDog_chr6.simDog.chr6 502340 16 - 593897 ACACACCATTATTGCA -s simHuman_chr6.simHuman.chr6 101139 16 + 601863 ATGAACCACCATTGCA -s simRat_chr6.simRat.chr6 97119 16 + 647215 ATGCAACATCATTGCA - -a -s simMouse_chr6.simMouse.chr6 104981 33 + 636262 CATAGGAACCTCTATGTGAAGCCAATATTCTTG -s Anc0.Anc0refChr1 117 33 - 62388 TATAGGTACACCTACATGAAGTAGATATTCTAT -s Anc1.Anc1refChr2 78067 33 + 144309 TATAGGTACACCTACATGAAGTAGATATTCTAT -s Anc2.Anc2refChr2 15626 33 + 27695 TATAGGTACACCTACATCAAGTAGATATTCTAT -s mr.mrrefChr0 100038 33 + 130230 CATAGGTACCTCTATATGAAGCCAATATTCTTG -s simCow_chr6.simCow.chr6 495770 33 - 602619 TAGAGGTACACCTGCATAAAGTAAATCTTCTAT -s simDog_chr6.simDog.chr6 502356 33 - 593897 TATATGTACACCTACATCAAGCAGATATTCTAT -s simHuman_chr6.simHuman.chr6 101156 33 + 601863 TATAGGTACACCTACATGAAGTAGACATTCTAT -s simRat_chr6.simRat.chr6 97135 33 + 647215 CATAGGTACCTCTATATGAAGCCAATATTCTTG - -a -s simMouse_chr6.simMouse.chr6 105014 1 + 636262 T -s Anc0.Anc0refChr1 169 1 - 62388 T -s Anc1.Anc1refChr2 78119 1 + 144309 T -s Anc2.Anc2refChr2 15678 1 + 27695 T -s mr.mrrefChr0 100090 1 + 130230 T -s simCow_chr6.simCow.chr6 495822 1 - 602619 T -s simDog_chr6.simDog.chr6 502408 1 - 593897 T -s simHuman_chr6.simHuman.chr6 101208 1 + 601863 T -s simRat_chr6.simRat.chr6 97191 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 105015 88 + 636262 AAAATTCAATATGTCAAATTTCCACAAGTGACCATCCGTAACCAAGAGACCACAGTGACAAATCGATCTTTCGAGATCTTTTGATTCA -s Anc0.Anc0refChr1 170 65 - 62388 TCA------------AAATTTCCACTAGCCCTGCTCCTTCACCTAG-GATAACATCAACAAGTT----------GATCTTCTGTTTCA -s Anc1.Anc1refChr2 78120 65 + 144309 TCA------------AAATTTCCACTAGCCCTGCTCCTTCACCTAG-GATAACATCAACAAGTT----------GATCTTCTGTTTCA -s Anc2.Anc2refChr2 15679 65 + 27695 TCA------------AAATTTCTACTAGCCCTGCACCTTCACCTAG-GATAACATCAACAAGTT----------GATCTTCTGTTTCA -s mr.mrrefChr0 100091 78 + 130230 ACAATTCAATATGTCAAATTTCCACAAGTGACCATCCGTAACCAAGAGATCACAGTGACAAATT----------GATCTTTTGATTCA -s simCow_chr6.simCow.chr6 495823 64 - 602619 TCA------------AAACTT-TGCTAGCTATGCACCTTCACCCAG-GATAACATCAACAAGTT----------GATCTCTTGTTTCA -s simDog_chr6.simDog.chr6 502409 62 - 593897 ACA------------AAATTTCTACTAGCCCT---CCTTCACCTAA-GGTAACATCATCAAGGT----------GACCTTCTGTTTCG -s simHuman_chr6.simHuman.chr6 101209 65 + 601863 TCA------------AAATTACCATTAGCCTTGGTCCTTCCCCGAG-GATAACGTCCACAAGTT----------GATCTACTGTTTCA -s simRat_chr6.simRat.chr6 97197 78 + 647215 ACAATTCAATATGTCAAATTTCCACAAGTGATCATCCATAACCAAGAGATCACAGTGACAAATT----------GACCCTTTGATTCA - -a -s simMouse_chr6.simMouse.chr6 105103 18 + 636262 TTTGAGACCTGTTTCCAG -s Anc0.Anc0refChr1 235 18 - 62388 TTTGAGACCTGGTTGCGA -s Anc1.Anc1refChr2 78185 18 + 144309 TTTGAGACCTGGTTGCGA -s Anc2.Anc2refChr2 15744 18 + 27695 TTTGAGACCTGGTTGCGA -s mr.mrrefChr0 100169 18 + 130230 TTTGAGACCTGTTTCCAG -s simCow_chr6.simCow.chr6 495887 18 - 602619 TTTAAGACTTGGTTGCGA -s simDog_chr6.simDog.chr6 502471 18 - 593897 TGTGAGATCTGGCCAAGA -s simHuman_chr6.simHuman.chr6 101275 18 + 601863 TTTGGGACCCGGTTGCCA -s simRat_chr6.simRat.chr6 97275 18 + 647215 CTTGAGACCTGTTTCCAG - -a -s simMouse_chr6.simMouse.chr6 105121 1 + 636262 G -s Anc0.Anc0refChr1 253 1 - 62388 G -s Anc1.Anc1refChr2 78203 1 + 144309 G -s Anc2.Anc2refChr2 15762 1 + 27695 G -s mr.mrrefChr0 100187 1 + 130230 G -s simCow_chr6.simCow.chr6 495907 1 - 602619 G -s simDog_chr6.simDog.chr6 502489 1 - 593897 G -s simHuman_chr6.simHuman.chr6 101293 1 + 601863 G -s simRat_chr6.simRat.chr6 97293 1 + 647215 G - -a -s simMouse_chr6.simMouse.chr6 105122 8 + 636262 TGGACTTA -s Anc0.Anc0refChr1 254 8 - 62388 TGGACCTG -s Anc1.Anc1refChr2 78204 8 + 144309 TGGACCTG -s Anc2.Anc2refChr2 15767 8 + 27695 TGGACCTG -s mr.mrrefChr0 100188 8 + 130230 TGGACTTG -s simCow_chr6.simCow.chr6 495912 8 - 602619 TGGAACTG -s simDog_chr6.simDog.chr6 502494 8 - 593897 TGGACCCG -s simHuman_chr6.simHuman.chr6 101294 8 + 601863 TGGACCTG -s simRat_chr6.simRat.chr6 97294 8 + 647215 TGGACTTG - -a -s simMouse_chr6.simMouse.chr6 105130 9 + 636262 ATAGGTCCT -s Anc0.Anc0refChr1 262 9 - 62388 ATAGGTCAT -s Anc1.Anc1refChr2 78212 9 + 144309 ATAGGTCAT -s Anc2.Anc2refChr2 15775 9 + 27695 ATAGCTCAC -s mr.mrrefChr0 100196 9 + 130230 ATAGGTCCT -s simCow_chr6.simCow.chr6 495921 9 - 602619 ATTGCTCAA -s simDog_chr6.simDog.chr6 502502 8 - 593897 ACAGCTC-C -s simHuman_chr6.simHuman.chr6 101302 9 + 601863 ATAGGTCAT -s simRat_chr6.simRat.chr6 97302 9 + 647215 ATAGGTCCC - -a -s simMouse_chr6.simMouse.chr6 105139 27 + 636262 ATGTAATAGACACTCCCACATGCACCA -s Anc0.Anc0refChr1 272 25 - 62388 AGGTAAGGG--ATTATTAACTCCCAGT -s Anc1.Anc1refChr2 78222 25 + 144309 AGGTAAGGG--ATTATTAACTCCCAGT -s Anc2.Anc2refChr2 15785 25 + 27695 AGGTAGGGG--ATTATTAACTCCCAGT -s mr.mrrefChr0 100206 25 + 130230 ATGTAATAG--ACTCCCACATGCACCA -s simCow_chr6.simCow.chr6 495931 24 - 602619 ACATAGGG---ATCATCAACTCCCAGT -s simDog_chr6.simDog.chr6 502511 16 - 593897 GGGTAGGGG--ATTATTA--------- -s simHuman_chr6.simHuman.chr6 101312 25 + 601863 AGGTAAGGC--ATTATTAACTCCCAGT -s simRat_chr6.simRat.chr6 97312 25 + 647215 ATGTAATAG--ACTCCCCCATGCACCA - -a -s simMouse_chr6.simMouse.chr6 105166 16 + 636262 ATGAATTCTACTACAA -s Anc0.Anc0refChr1 299 16 - 62388 ACGGATCCTAACATAA -s Anc1.Anc1refChr2 78249 16 + 144309 ACGGATCCTAACATAA -s Anc2.Anc2refChr2 15812 16 + 27695 ACGGATCCTAACATAA -s mr.mrrefChr0 100233 16 + 130230 ATGATTTCTACTACAA -s simCow_chr6.simCow.chr6 495957 16 - 602619 ACGGATCTTGACATAA -s simDog_chr6.simDog.chr6 502527 10 - 593897 ------CCTAAGACAG -s simHuman_chr6.simHuman.chr6 101339 16 + 601863 TCTGATCCTAACATAA -s simRat_chr6.simRat.chr6 97339 16 + 647215 ATGATTTCTGCTACAA - -a -s simMouse_chr6.simMouse.chr6 105182 2 + 636262 AA -s Anc0.Anc0refChr1 991 2 - 62388 GA -s Anc1.Anc1refChr2 78941 2 + 144309 GA -s Anc2.Anc2refChr2 16511 2 + 27695 GA -s mr.mrrefChr0 100249 2 + 130230 AA -s simCow_chr6.simCow.chr6 496613 2 - 602619 GA -s simDog_chr6.simDog.chr6 503189 2 - 593897 CA -s simHuman_chr6.simHuman.chr6 102075 2 + 601863 GA -s simRat_chr6.simRat.chr6 97355 2 + 647215 AA - -a -s simMouse_chr6.simMouse.chr6 105184 10 + 636262 ACAAGTCTAC -s Anc0.Anc0refChr1 993 10 - 62388 ACAATGCTAC -s Anc1.Anc1refChr2 78943 10 + 144309 ACAATGCTAC -s Anc2.Anc2refChr2 16513 10 + 27695 CTAATGATAC -s mr.mrrefChr0 100251 10 + 130230 ACAAGTCTAC -s simCow_chr6.simCow.chr6 496617 10 - 602619 CTGATGACAC -s simDog_chr6.simDog.chr6 503191 10 - 593897 CTAATGATAC -s simHuman_chr6.simHuman.chr6 102077 10 + 601863 ACAAAGCTAC -s simRat_chr6.simRat.chr6 97357 10 + 647215 ACAAGTTCAC - -a -s simMouse_chr6.simMouse.chr6 105194 11 + 636262 TGGTGATCCCA -s Anc0.Anc0refChr1 1007 11 - 62388 GGGTATGTACA -s Anc1.Anc1refChr2 78957 11 + 144309 GGGTATGTACA -s Anc2.Anc2refChr2 16527 11 + 27695 GGGTATGTACA -s mr.mrrefChr0 100261 11 + 130230 TGGTGATTCCA -s simCow_chr6.simCow.chr6 496631 11 - 602619 GGGTATGTACA -s simDog_chr6.simDog.chr6 503205 11 - 593897 GGATCTGTACA -s simHuman_chr6.simHuman.chr6 102091 11 + 601863 CGGTATGTGCA -s simRat_chr6.simRat.chr6 97367 11 + 647215 TGGTGATTCCA - -a -s simMouse_chr6.simMouse.chr6 105205 25 + 636262 TCTACCATCTTGTGTATAAGTACAC -s Anc0.Anc0refChr1 1025 25 - 62388 TCTACTCTATTGTGCATAAGTACAC -s Anc1.Anc1refChr2 78975 25 + 144309 TCTACTCTATTGTGCATAAGTACAC -s Anc2.Anc2refChr2 16545 25 + 27695 TCTACTCTATTGTGCATAAGTACAC -s mr.mrrefChr0 100279 25 + 130230 TCTACCATCTTGTGTATAAGTACAC -s simCow_chr6.simCow.chr6 496649 25 - 602619 TCTACTCTGTTGTACATAAGTATAT -s simDog_chr6.simDog.chr6 503223 25 - 593897 TCTACCCTATTGTGCATAAGTACAC -s simHuman_chr6.simHuman.chr6 102109 25 + 601863 TGTACTCTTATGCTAAGAAGTACAC -s simRat_chr6.simRat.chr6 97385 25 + 647215 TCTACCTTCCTGTGTATAGGTACAC - -a -s simMouse_chr6.simMouse.chr6 105230 13 + 636262 TGACCATAGCAAG -s Anc0.Anc0refChr1 1054 13 - 62388 TGACCACAGCAAG -s Anc1.Anc1refChr2 79004 13 + 144309 TGACCACAGCAAG -s Anc2.Anc2refChr2 16574 13 + 27695 TGATCACAGCAAG -s mr.mrrefChr0 100304 13 + 130230 TGACCATAGCAAG -s simCow_chr6.simCow.chr6 496678 13 - 602619 TGAGCACAGTAAA -s simDog_chr6.simDog.chr6 503252 13 - 593897 TAATCACAGCAGG -s simHuman_chr6.simHuman.chr6 102138 13 + 601863 TGACCACAGCAAG -s simRat_chr6.simRat.chr6 97410 13 + 647215 TGACCATAGCAAG - -a -s simMouse_chr6.simMouse.chr6 105243 33 + 636262 TCTATTTTGAAATCTATTAGGTGTGGCTGCTTA -s Anc0.Anc0refChr1 1067 32 - 62388 TCTATTCTGAAATTTATTAGATAT-GCTGCCGT -s Anc1.Anc1refChr2 79017 32 + 144309 TCTATTCTGAAATTTATTAGATAT-GCTGCCGT -s Anc2.Anc2refChr2 16587 32 + 27695 TCTATTCTGAAATTTATTAGATAT-GCTGCCAT -s mr.mrrefChr0 100317 33 + 130230 TCTATTTTGAAATCTATTAGATGTGGCTGCTGA -s simCow_chr6.simCow.chr6 496695 32 - 602619 TCTATTCTGAAGTTTATTAGATAT-GCTTCCAT -s simDog_chr6.simDog.chr6 503265 32 - 593897 TCTATTCTGAAATTTATTAGAGAT-GCTGTCAG -s simHuman_chr6.simHuman.chr6 102151 32 + 601863 TCTATTCTGAAAATTATTAAATAT-GTTACCGT -s simRat_chr6.simRat.chr6 97423 33 + 647215 TTTATCTTGAAATCTATTAGATGTGGCTGCTGA - -a -s simMouse_chr6.simMouse.chr6 105276 14 + 636262 GTGCTCAACTGTTT -s Anc0.Anc0refChr1 1111 14 - 62388 GTGTTCATCTTTTT -s Anc1.Anc1refChr2 79061 14 + 144309 GTGTTCATCTTTTT -s Anc2.Anc2refChr2 16631 14 + 27695 GTGTTCATCTTTTT -s mr.mrrefChr0 100362 14 + 130230 GTGCTCATCTGTTT -s simCow_chr6.simCow.chr6 496739 14 - 602619 GGGCTCATCTTTTT -s simDog_chr6.simDog.chr6 503317 14 - 593897 GTGTTCATTTTTTT -s simHuman_chr6.simHuman.chr6 102195 14 + 601863 GTGTTCATCTTTTT -s simRat_chr6.simRat.chr6 97468 14 + 647215 GTGCTCATCTGTTT - -a -s simMouse_chr6.simMouse.chr6 105290 22 + 636262 GCATTCTGTAGATTGAAGTATC -s Anc0.Anc0refChr1 1126 21 - 62388 GTA-CCTATAGATTGCAACCTG -s Anc1.Anc1refChr2 79076 22 + 144309 GTAACCTATAGATTGCAACCTG -s Anc2.Anc2refChr2 16646 21 + 27695 GTA-CCTATAGATTGCCACCTG -s mr.mrrefChr0 100376 22 + 130230 GCATTCTGTAGATTGAAGTATC -s simCow_chr6.simCow.chr6 496754 13 - 602619 GTG-CCTATAGATT-------- -s simDog_chr6.simDog.chr6 503332 21 - 593897 GTA-CCTAAAAACTGCCACCTG -s simHuman_chr6.simHuman.chr6 102210 22 + 601863 GTAAACTATAGATTGTAACCTG -s simRat_chr6.simRat.chr6 97482 22 + 647215 GCATTCTGTAGATTGAAGTATC - -a -s simMouse_chr6.simMouse.chr6 105312 17 + 636262 ATACTTCCATTCCTGTA -s Anc0.Anc0refChr1 1147 12 - 62388 ATACTTCAATTC----- -s Anc1.Anc1refChr2 79098 12 + 144309 ATACTTCAATTC----- -s Anc2.Anc2refChr2 16667 12 + 27695 ATAATTCAATTC----- -s mr.mrrefChr0 100398 17 + 130230 ATACTTCCATTCCTGTA -s simCow_chr6.simCow.chr6 496767 5 - 602619 -------AATTC----- -s simDog_chr6.simDog.chr6 503355 12 - 593897 ATAATTCAATTC----- -s simHuman_chr6.simHuman.chr6 102232 10 + 601863 ATACTTCAAT------- -s simRat_chr6.simRat.chr6 97504 17 + 647215 ATACTGCCGTTCCTGCA - -a -s simMouse_chr6.simMouse.chr6 105329 38 + 636262 AATTTCTGTAAGGAGATCACCCCCCTCCTGCACTTCAA -s Anc0.Anc0refChr1 1159 33 - 62388 -----CCGAGAGAAGCTCATCCCCCTTTGGCACTTTAA -s Anc1.Anc1refChr2 79110 33 + 144309 -----CCGAGAGAAGCTCATCCCCCTTTGGCACTTTAA -s Anc2.Anc2refChr2 16679 33 + 27695 -----CCGAGAGAAGCTCATCCCCCTTTGGCACTTTAT -s mr.mrrefChr0 100415 38 + 130230 AATTTCTGTAAGGAGATCACCCCCCTCCTGCACTTCAA -s simCow_chr6.simCow.chr6 496772 33 - 602619 -----CTGAGAGAAAGTCGTCCCTCTTCTGCACCTTGT -s simDog_chr6.simDog.chr6 503367 33 - 593897 -----CCGAGAGAAGCTCATCCCCCTTTGGCACTTTAT -s simHuman_chr6.simHuman.chr6 102242 1 + 601863 -------------------------------------A -s simRat_chr6.simRat.chr6 97531 38 + 647215 AATTTCTGCAAGAAGAGCACCCCCCTCCTGCACTTCAA - -a -s simMouse_chr6.simMouse.chr6 105367 39 + 636262 CTTCCTTCTTTTAGACCATTCGGAATGTAACTTGTCTGT -s Anc0.Anc0refChr1 1192 39 - 62388 CTTCACTTTTTTACACAGCTCAGAATGTTATTTGGCTGT -s Anc1.Anc1refChr2 79143 39 + 144309 CTTCACTTTTTTACACAGCTCAGAATGTTATTTGGCTGT -s Anc2.Anc2refChr2 16735 39 + 27695 CTTCACCTCTTTACACAGCTCAGAATGTTATTTGGCTGT -s mr.mrrefChr0 100453 39 + 130230 CTTCCTTCTTTTACACAATTCAGAATGTAACTTGTCTGT -s simCow_chr6.simCow.chr6 496828 35 - 602619 CCTCAA----TTTCCCAGCTCATAATATTACTTGTTTAC -s simDog_chr6.simDog.chr6 503423 39 - 593897 CTTCACCTCTTTACACAGGTCAGCATGTTATTTGGCTGT -s simHuman_chr6.simHuman.chr6 102243 39 + 601863 CTTCACTGTTTTGCAGAGCTCAGAATGTTATTTAACTGG -s simRat_chr6.simRat.chr6 97569 39 + 647215 CTTTCTTTTTCTACACAATTCAGAATGTAACTTGTCTGT - -a -s simMouse_chr6.simMouse.chr6 105406 2 + 636262 TG -s Anc0.Anc0refChr1 1231 2 - 62388 TG -s Anc1.Anc1refChr2 79182 2 + 144309 TG -s Anc2.Anc2refChr2 16774 2 + 27695 TG -s mr.mrrefChr0 100492 2 + 130230 TG -s simCow_chr6.simCow.chr6 496863 2 - 602619 TG -s simDog_chr6.simDog.chr6 503462 2 - 593897 TG -s simHuman_chr6.simHuman.chr6 102292 2 + 601863 TA -s simRat_chr6.simRat.chr6 97608 2 + 647215 TG - -a -s simMouse_chr6.simMouse.chr6 105408 45 + 636262 GGGCCATGCTTGTCCTCCAATCTAAATACAGAGTGCTCTTCAGCC -s Anc0.Anc0refChr1 1233 44 - 62388 GGGGCAAGCTGGTCCTGAAATCCAAGTACAGAAT-CTCTTCAGCA -s Anc1.Anc1refChr2 79184 44 + 144309 GGGGCAAGCTGGTCCTGAAATCCAAGTACAGAAT-CTCTTCAGCA -s Anc2.Anc2refChr2 16778 44 + 27695 AGAGCAAGCTGGGCCTGAAATCCAAGTACCGAAT-CTCTTCAGCA -s mr.mrrefChr0 100494 44 + 130230 GGGGCATGCTTGTCCTCCAATCTAAATACAGAAT-CTCTTCAGCC -s simCow_chr6.simCow.chr6 496867 44 - 602619 AGACCATGTAGGACCTGACATGTAGGTACTGAAT-CCCTTAAGCA -s simDog_chr6.simDog.chr6 503466 44 - 593897 AGGGCAAGCTGGGCCTGAAATCCAAGTACCTAAA-TTATTCAGCA -s simHuman_chr6.simHuman.chr6 102294 35 + 601863 GAGGAGCGCTGGTCCT---------GAACAGAAT-CTCTTCAGCA -s simRat_chr6.simRat.chr6 97610 42 + 647215 GGGGCATGCTTGTTGTCCAATCTAAATACGGAA---TTTCCAGCC - -a -s simMouse_chr6.simMouse.chr6 105453 45 + 636262 TGTGCACTCCACTCTCCCACTCAGGTTTATTAGCACTCACAGTAG -s Anc0.Anc0refChr1 1277 40 - 62388 TGGACACTC-----TCCCACTCAGGTGCATTAGTGTCCACAATAG -s Anc1.Anc1refChr2 79228 42 + 144309 TGGACACTCC---CTCCCACTCAGGTGCATTAGTGTCCACAATAG -s Anc2.Anc2refChr2 16822 40 + 27695 TGGACACTC-----TCCCACTCAGGTGCATTAGTGTCCACAATAG -s mr.mrrefChr0 100538 45 + 130230 TGTGCACTCCACTCTCCCACTCAGGTTTATTAGCATTCACAGTAG -s simCow_chr6.simCow.chr6 496912 38 - 602619 TGGACACTC-----TCCCACTCA--TGCATTAGTGTCCACAATGC -s simDog_chr6.simDog.chr6 503510 40 - 593897 TGGACACTG-----TCTCACTCAGGTGCATTAGTACCCCCAATAG -s simHuman_chr6.simHuman.chr6 102329 42 + 601863 TGGATACCCC---CCCACACTCAGGTGCAGTAGTGTCCACAAAAG -s simRat_chr6.simRat.chr6 97652 45 + 647215 TGCGCATTCCACTCTCCCACTCAGGTTTAATAGCATTCTGAGTAG - -a -s simMouse_chr6.simMouse.chr6 105498 38 + 636262 GAGCATACTGTACCCAGTCGACGATTCTCAATGGTGGT -s Anc0.Anc0refChr1 1317 34 - 62388 TAGTATAGTGTTCCTACTTGATGAATCCCAATGG---- -s Anc1.Anc1refChr2 79270 34 + 144309 TAGTATAGTGTTCCTACTTGATGAATCCCAATGG---- -s Anc2.Anc2refChr2 16869 34 + 27695 TAGTATGGTGTTCCTACTCGATGAATCCCACTGG---- -s mr.mrrefChr0 100583 34 + 130230 GAGCATACTGTTCCCAGTTGATGATTCCCAATGG---- -s simCow_chr6.simCow.chr6 496957 34 - 602619 AACTATGGTGTTCCTAATGGATGACTCCCACTGG---- -s simDog_chr6.simDog.chr6 503557 34 - 593897 TAGTATGATGTTCCTACTCAATACATCCCACTGG---- -s simHuman_chr6.simHuman.chr6 102371 34 + 601863 TAGTATAGTGTTCCGGCTTGATGAGTCCCAATGG---- -s simRat_chr6.simRat.chr6 97697 34 + 647215 GAGCATACTATTTCCAGTTGATGATTCCCAATGC---- - -a -s simMouse_chr6.simMouse.chr6 105536 43 + 636262 TGGTTTACTCTTGGATGTTCACTTCCAATTAGGTAAATTCTGA -s Anc0.Anc0refChr1 1351 42 - 62388 ATGTTTACTTCCAGATGTTCACTTCCA-TTTGCTTAATTCTGG -s Anc1.Anc1refChr2 79304 43 + 144309 ATGTTTACTTCCAGATGTTCACTTCCAATTTGCTTAATTCTGG -s Anc2.Anc2refChr2 16903 42 + 27695 ATGTTTACTTCCAGATGTTCACTTCTA-TTTGCTTAATTCTGG -s mr.mrrefChr0 100617 43 + 130230 TGGTTTACTCTTGGATGTTCACTTCCAATTAGCTAAATTCTGA -s simCow_chr6.simCow.chr6 497001 42 - 602619 ATGTTTATTTCCATATGTTCACTTCTA-TTTGGTTAATTCTAG -s simDog_chr6.simDog.chr6 503591 42 - 593897 ATGTTTACTTCCAGATGTTCACTGCTA-TTTGCTTAATTCTGG -s simHuman_chr6.simHuman.chr6 102405 39 + 601863 ATATTCACTTCAAGATGTCCACTTCCAATTGCCTTAATT---- -s simRat_chr6.simRat.chr6 97731 43 + 647215 TGGTTTACTCTTGAATATTCACTTCCAATTAGCTAAATTCTGA - -a -s simMouse_chr6.simMouse.chr6 105579 35 + 636262 TAGGCCCTTCCAAGTTCCCATTAGCTAGCAAGGTC -s Anc0.Anc0refChr1 1393 29 - 62388 GGGGCT------AGTCTCCATTAGCCAGCCAGGTC -s Anc1.Anc1refChr2 79347 35 + 144309 GGGGCTTTTTCCAGTCTCCATTAGCCAGCCAGGTC -s Anc2.Anc2refChr2 16945 29 + 27695 GGGGCT------ATACTCCATTGGCCAGCCATGTT -s mr.mrrefChr0 100660 35 + 130230 TAGGCCCTTCCAAGTCTCCATTAGCCAGCAAGGTC -s simCow_chr6.simCow.chr6 497043 28 - 602619 GGGGCT------ATATTCCATTG-CCAGCTGAGTT -s simDog_chr6.simDog.chr6 503633 29 - 593897 GGGGCT------ATACTCCATTGGCCAGCCATGTT -s simHuman_chr6.simHuman.chr6 102444 31 + 601863 ----CATTTTCCAGTCTCCTTTAGCCAGCCAGGTC -s simRat_chr6.simRat.chr6 97791 35 + 647215 GAGGCCCTTCCAAGCCTCCATTACCCAGCAAGGTC - -a -s simMouse_chr6.simMouse.chr6 105614 19 + 636262 TACTGAAATCTGCTGGTGA -s Anc0.Anc0refChr1 1427 19 - 62388 TGCTGAAATCTGCTGGTGA -s Anc1.Anc1refChr2 79387 19 + 144309 TGCTGAAATCTGCTGGTGA -s Anc2.Anc2refChr2 16979 19 + 27695 TGCTGAAATCTGCTGGTAA -s mr.mrrefChr0 100695 19 + 130230 TGCTGAAATCTGCTGGTGA -s simCow_chr6.simCow.chr6 497076 19 - 602619 TACTAAAATCTGGTGGTAA -s simDog_chr6.simDog.chr6 503667 19 - 593897 TGCTGAAATCTGCTGGTAA -s simHuman_chr6.simHuman.chr6 102480 19 + 601863 TGCTGAAATCTGCTGGTGA -s simRat_chr6.simRat.chr6 97826 19 + 647215 TGCTGAAATCTGCTGGTGA - -a -s simMouse_chr6.simMouse.chr6 105633 205 + 636262 TGATAGAAAAGGATTAACTTTAACTTTGGTCCATATTACCTCAAGAATCGCTGTAAGTCCCAGTAAGTGCAAACAGCAACATATGTAGAAATGTCATTTACCACCCCTTACTACTATTTGTGTATAATTTGGAAGGTAACACTTTGGCAGGGCTTTGAAGTTTCAATGAATTTAGTTATCGTGATCCTTTTCTCAGAGTCATTAT -s Anc0.Anc0refChr1 1450 186 - 62388 TCAAAAATAGG-CTACAGTTCAACTTTGTTCCATTTTGCCCCAAGAATAGTTGTAGGTTCCAGGAAGAATAGACAGTATTA--------TATGTCATTTA-CACCCTTAATTCCTATTTGCACATAATTCAG-AGGTAATACTTTGGAAGGGTTTTGAAGTTTCAAAGAATTTGGTTATTTTGACCCTTATCTCAGG-------- -s Anc1.Anc1refChr2 79410 188 + 144309 TCAAAAATAGGGCTACAGTTCAACTTTGTTCCATTTTGCCCCAAGAATAGTTGTAGGTTCCAGGAAGAATAGACAGTATTA--------TATGTCATTTA-CACCCTTAATTCCTATTTGCACATAATTCAGCAGGTAATACTTTGGAAGGGTTTTGAAGTTTCAAAGAATTTGGTTATTTTGACCCTTATCTCAGG-------- -s Anc2.Anc2refChr2 17002 186 + 27695 TCAAAAATAGA-CTACAGTTCAACTTTGTTCCATTTTGCCCCAAGAATCATTGTAGGTTCCAGGAAGAGTAGACATTATTA--------TAAGTCATTTA-CACCCTTAATTCCTATTTGCACATAATCCAG-AGGTAATACTTTGGAGGGGTTTTGAAGTTTCAAAGACTTTGGTCATTTTGTCCCTTATCTCAGG-------- -s mr.mrrefChr0 100714 205 + 130230 TCATAGAAAGGGATTAACTTTAACTTTGTTCCATATTACCTCAAGAATAGCTGTAGGTCCCAGTAAGTACAAACAGTAACATATGTAGATATGTCATTTACCACCCCTTATTACTATTTGTGTATAATTTGGAAGGTAATACTTTGGCAGGGCTTTGAAGTTTCAATGAATTTAGTTATCGTGACCCTTTTCTCAGAGTCATTAT -s simCow_chr6.simCow.chr6 497099 164 - 602619 TCAAACACAGA-C-ACAATTCATCTTCATTCTGGTTT--------------------TTCCAGGGATGGTAGGCATTATCA--------TAGGTCCTTTG-CACCCTTAACTCTGATTTGCACATAATCCAA-ACGTTTTAATTTGGAGGGGTTCTGAAGTTTCAGAGACTTTGGTCA-TTTGTCCCTTATCTCAGG-------- -s simDog_chr6.simDog.chr6 503690 178 - 593897 TTAAAAATAGA-CTACAGTTCAACTGTGCTCCATTTTGCCCCAAGAATCATTGTAGGGTCTAAGAAGAGTAGACA-CATTA--------TCAGGCATTCA-TGCCCTTAATTCCTATTTGC-------CCAG-AGGTAATACTTTGGAGGGGTTTTGAAGTTTCAAAGTCCTTGGTCATTTTGTCCCTTATCTCAAG-------- -s simHuman_chr6.simHuman.chr6 102503 188 + 601863 TCCAAAATAGGGGTACAGAGCAACTTTGTTCCATTTTGCCCCACGAATAGGTGTCGGTTCCAGGAAGCATATACAGTATTG--------TATGTCATTTA-CATGCTTAATTCCCATTTTCACTTAATTCAGCAGATGCTACTTCGGAAGAGTCTTGAAGTTTCAAAGAATTTGGTTATGCTGACCCTCATCTCAGG-------- -s simRat_chr6.simRat.chr6 97845 205 + 647215 TCATAGAAAGCGATTAACTTTAACTTTGTTCCATATTACCTCAAGAGTAGTTGTAGGTCCCAGTAAGTACAAACAGTAAGATATGAAGATATGTCATTTACCACCCCTTATTACTCTTTATTTGTATTTTGAAAGGTAGTACTTTAACAGGGCTTCAAGGGTTCAATGAATTTAGTCATCATGACCCTTTTGTCAAAGTCTTTAT - -a -s simMouse_chr6.simMouse.chr6 105838 10 + 636262 ATTTTGTGCC -s Anc0.Anc0refChr1 1636 10 - 62388 ATTTTGTGCC -s Anc1.Anc1refChr2 79598 10 + 144309 ATTTTGTGCC -s Anc2.Anc2refChr2 17188 10 + 27695 ATTCTGTACC -s mr.mrrefChr0 100919 10 + 130230 ATTTTGTGCC -s simCow_chr6.simCow.chr6 497266 9 - 602619 ATTATATAC- -s simDog_chr6.simDog.chr6 504328 10 - 593897 ATTCTGTACC -s simHuman_chr6.simHuman.chr6 102691 10 + 601863 ATTTTGTGCC -s simRat_chr6.simRat.chr6 98050 10 + 647215 ATTTTGTGCC - -a -s simMouse_chr6.simMouse.chr6 105848 160 + 636262 CTCCCTATTTCTTTCATCTGTTTTAATTGCAATGATGGTAGTCAGAATGTGTAGTGATTATCAGTATGGCAGTAATTTTAATCACTGATGGTTACAAGGCACATGGGTGTATTACGGTGTTTGATCAGGTACAAGATGACATCTTCCACTTCCATACCTA -s Anc0.Anc0refChr1 1646 34 - 62388 CTCCTTATTGCTGTCATCTATATTTTTT------------------------------------------------------------------------------------------------------------------------------TACGTA -s Anc1.Anc1refChr2 79608 34 + 144309 CTCCTTATTGCTGTCATCTATATTTTTT------------------------------------------------------------------------------------------------------------------------------TACGTA -s Anc2.Anc2refChr2 17198 34 + 27695 CTCCTTATAGCTGTCATCTATATTTTTT------------------------------------------------------------------------------------------------------------------------------TAAGTA -s mr.mrrefChr0 100929 155 + 130230 CTCCCTATTTCTTTCATCTGTTTTCATTGGAATGATGGTAGTCAGAATGTGTAGTGATTATCAGTATGGCAGTAATTTTAATCACTGATGGTTACAAGGCACATGGGTGTATTA-----TTTGATCAGGTACAAGATGACATCTTCCACTTCCATACCTA -s simCow_chr6.simCow.chr6 107333 34 + 602619 CTCCTTATTCCTTTCATCTATGTCTATT------------------------------------------------------------------------------------------------------------------------------TGAGTA -s simDog_chr6.simDog.chr6 504338 34 - 593897 CTCCTTATAGCTGTCATCTGTATTTTTG------------------------------------------------------------------------------------------------------------------------------TAAGTA -s simHuman_chr6.simHuman.chr6 102701 29 + 601863 TTCCTTATT-----CATCTACAATTTTT------------------------------------------------------------------------------------------------------------------------------TCCTTA -s simRat_chr6.simRat.chr6 98060 155 + 647215 CTCCCTACTTCTTTCACCTGCGTTCATTGGAATTATGGTAGGCAGAACGTTTAGTATTTATCACTATGACATTAATTTTAATTACTGATGGTTACCATGCATGTGAGTGTATTA-----TTTGATCAGGTACATGATGGCATCTTCCACTTCCATACTTA - -a -s simMouse_chr6.simMouse.chr6 106008 24 + 636262 AGTCTTGCATATAATTGTCCCACA -s Anc0.Anc0refChr1 1686 24 - 62388 AGTCTCGCATTTCACTCTCCCATG -s Anc1.Anc1refChr2 79648 24 + 144309 AGTCTCGCATTTCACTCTCCCATG -s Anc2.Anc2refChr2 17238 24 + 27695 AGTCTCATGTTTCACTCTCCCATG -s mr.mrrefChr0 101084 24 + 130230 AGTCTTGCATATCACTCTCCCATA -s simCow_chr6.simCow.chr6 107373 24 + 602619 AGTCTTATGTCTAACTCTCCCATC -s simDog_chr6.simDog.chr6 504378 24 - 593897 AGTCTCATGTTACACTCTCCCATG -s simHuman_chr6.simHuman.chr6 102736 24 + 601863 AGTCTCGCATGTCACTCTCCCATG -s simRat_chr6.simRat.chr6 98215 24 + 647215 AGTCTTGCATATCACACTCCCATA - -a -s simMouse_chr6.simMouse.chr6 106032 5 + 636262 AAAGC -s Anc0.Anc0refChr1 1710 5 - 62388 ATAGC -s Anc1.Anc1refChr2 79672 5 + 144309 ATAGC -s Anc2.Anc2refChr2 17262 5 + 27695 ATGGC -s mr.mrrefChr0 101108 5 + 130230 AAAGC -s simCow_chr6.simCow.chr6 107397 5 + 602619 ATGGC -s simDog_chr6.simDog.chr6 504403 5 - 593897 ATGGC -s simHuman_chr6.simHuman.chr6 102760 5 + 601863 ATAGC -s simRat_chr6.simRat.chr6 98239 5 + 647215 CAAGC - -a -s simMouse_chr6.simMouse.chr6 106037 53 + 636262 TCTTGTATGTTGATTGGTGTGCTGCTGTAACCACTGCAGCGGGGTACCCAGTG -s Anc0.Anc0refChr1 1715 53 - 62388 TCTTGTATGCTCACTGGTGTCTTGCTCTAACCATTGTAGCTGGTTGCTCTATG -s Anc1.Anc1refChr2 79677 53 + 144309 TCTTGTATGCTCACTGGTGTCTTGCTCTAACCATTGTAGCTGGTTGCTCTATG -s Anc2.Anc2refChr2 17267 53 + 27695 TGTTGTATGCTCACTGGTCTCTTGCTCCAACCATTGTAGCTGGTTGCTCTATG -s mr.mrrefChr0 101113 53 + 130230 TCTTGTATGTTGATTGGTGTGCTGCTGTAACCATTGCAGCTGGGTACCCAGTG -s simCow_chr6.simCow.chr6 107462 52 + 602619 TGTTGTGTGCTCACTGGTATCTT-CTCCAACCATTGTAGCTGGCTGCTCTATG -s simDog_chr6.simDog.chr6 504408 53 - 593897 TGTTGTATGCTCACTGGTCTCTTGCTTCAGTTGTTGTAGCTAGTAGCATTATT -s simHuman_chr6.simHuman.chr6 102765 53 + 601863 TCTTGTATGCTCACTGGTGTCTTGCTCTAACCATTGTAGCTGGTTGCTCTATG -s simRat_chr6.simRat.chr6 98244 49 + 647215 TCTTGTATGGTAATTGGTGTG-TGCTAAA---ATTGCAGCTGGGTTGCCATTA - -a -s simMouse_chr6.simMouse.chr6 106090 43 + 636262 CAGTAATTGTCTTCTTGTTAACAACCTTTGCAACTGAATTTAG -s Anc0.Anc0refChr1 1790 38 - 62388 CAATAATTGTCTCCTTCTTA-----ATTTGGAACTGAAGTTAG -s Anc1.Anc1refChr2 79752 38 + 144309 CAATAATTGTCTCCTTCTTA-----ATTTGGAACTGAAGTTAG -s Anc2.Anc2refChr2 17342 38 + 27695 CTATAATTGTCTTCTTCTTA-----ACTTGGGACTGAAGTTAG -s mr.mrrefChr0 101166 43 + 130230 CAGTAATTGTCTCCTTGTTAACAACATTTGCAACTGAATTTAG -s simCow_chr6.simCow.chr6 107536 38 + 602619 CGATAATAGTCTTCTTCTTA-----ACTTGGGACTGAAGTTAG -s simDog_chr6.simDog.chr6 504476 38 - 593897 CTATGATTTTCTTCCTCTTT-----GCTTGGGACTGAAGTTAG -s simHuman_chr6.simHuman.chr6 102842 38 + 601863 CAATAATTGTCTCCTTCTTA-----ATTTGGAACTGAAGCTAG -s simRat_chr6.simRat.chr6 98293 43 + 647215 CAGTAATTTTCTCCTTGTTAACAACATTTACAACTAAATTTAG - -a -s simMouse_chr6.simMouse.chr6 106133 8 + 636262 TTGCAACA -s Anc0.Anc0refChr1 1828 8 - 62388 TTACAGTA -s Anc1.Anc1refChr2 79790 8 + 144309 TTACAGTA -s Anc2.Anc2refChr2 17380 8 + 27695 TTATAGTA -s mr.mrrefChr0 101209 8 + 130230 TTACAACA -s simCow_chr6.simCow.chr6 107711 8 + 602619 TTATAGTA -s simDog_chr6.simDog.chr6 504514 8 - 593897 TTATAGTG -s simHuman_chr6.simHuman.chr6 102880 8 + 601863 TTACACTA -s simRat_chr6.simRat.chr6 98336 8 + 647215 TTACAACA - -a -s simMouse_chr6.simMouse.chr6 106141 33 + 636262 TTGTTGCTTTGTCTAGCACATCCATATGTTTGG -s Anc0.Anc0refChr1 1836 30 - 62388 TTT-TGCCT--GTTGACATATCCATATATTTGG -s Anc1.Anc1refChr2 79798 31 + 144309 TTTGTGCCT--GTTGACATATCCATATATTTGG -s Anc2.Anc2refChr2 17388 30 + 27695 TTT-CACCT--GTTGACATATCCTTATATTTGG -s mr.mrrefChr0 101217 33 + 130230 TTGTTGCTTTGTTTAGCACATCCATATGTTTGG -s simCow_chr6.simCow.chr6 107720 30 + 602619 TTT-CCCTT--ATAGCCATATCCTTATATTTAA -s simDog_chr6.simDog.chr6 504522 30 - 593897 TTT-CACCT--GCTGACATATCCTTATGATTGG -s simHuman_chr6.simHuman.chr6 102888 31 + 601863 TTTGTGCCT--GTTGACAAATCCATAGATGCGG -s simRat_chr6.simRat.chr6 98344 33 + 647215 TTGTCAGTTTGTTTAGCATATCTGTATGTTTGA - -a -s simMouse_chr6.simMouse.chr6 106174 17 + 636262 GACATAGCTAATAAAAA -s Anc0.Anc0refChr1 1869 17 - 62388 GACAAGACCACTAGAAA -s Anc1.Anc1refChr2 79832 17 + 144309 GACAAGACCACTAGAAA -s Anc2.Anc2refChr2 17421 17 + 27695 GACAAGATCACTAGAAA -s mr.mrrefChr0 101250 17 + 130230 GACATAACCAATAAAAA -s simCow_chr6.simCow.chr6 107753 17 + 602619 GACAAGGTTGCTAGAAA -s simDog_chr6.simDog.chr6 504555 17 - 593897 GACAAGATCACTAGAAG -s simHuman_chr6.simHuman.chr6 102922 17 + 601863 GACAAGACCACAAGAAA -s simRat_chr6.simRat.chr6 98377 17 + 647215 GACATAACCAATAAAAA - -a -s simMouse_chr6.simMouse.chr6 106191 16 + 636262 CCTTCAAGGGGCCTGT -s Anc0.Anc0refChr1 1892 16 - 62388 CTTTCAAGGGGCCTGT -s Anc1.Anc1refChr2 79855 16 + 144309 CTTTCAAGGGGCCTGT -s Anc2.Anc2refChr2 17444 16 + 27695 CTTTTAAGGGGCCTGT -s mr.mrrefChr0 101267 16 + 130230 CTTTCAAGGGGCCTGT -s simCow_chr6.simCow.chr6 107776 16 + 602619 CTTTTAAGGGGCCTTT -s simDog_chr6.simDog.chr6 504578 16 - 593897 CTTTTAAGGGGCCTGT -s simHuman_chr6.simHuman.chr6 102945 16 + 601863 CTTTCAAGGGGTCTAT -s simRat_chr6.simRat.chr6 98394 16 + 647215 CTCTCAAGGGGCCTGT - -a -s simMouse_chr6.simMouse.chr6 106207 3 + 636262 GGA -s Anc0.Anc0refChr1 1908 3 - 62388 GTA -s Anc1.Anc1refChr2 79871 3 + 144309 GTA -s Anc2.Anc2refChr2 17460 3 + 27695 GTA -s mr.mrrefChr0 101283 3 + 130230 GGA -s simCow_chr6.simCow.chr6 107793 3 + 602619 GCA -s simDog_chr6.simDog.chr6 504594 3 - 593897 TTA -s simHuman_chr6.simHuman.chr6 102961 3 + 601863 GTA -s simRat_chr6.simRat.chr6 98410 3 + 647215 GGA - -a -s simMouse_chr6.simMouse.chr6 106210 5 + 636262 TATGA -s Anc0.Anc0refChr1 1912 5 - 62388 TATAA -s Anc1.Anc1refChr2 79875 5 + 144309 TATAA -s Anc2.Anc2refChr2 17464 5 + 27695 TATAA -s mr.mrrefChr0 101286 5 + 130230 TATGA -s simCow_chr6.simCow.chr6 107797 5 + 602619 TATAA -s simDog_chr6.simDog.chr6 504602 5 - 593897 TATAC -s simHuman_chr6.simHuman.chr6 102965 5 + 601863 TATAA -s simRat_chr6.simRat.chr6 98413 5 + 647215 TATGA - -a -s simMouse_chr6.simMouse.chr6 106215 60 + 636262 CCTTGTTTAACTATAGTGGTAGTCACATTTAATGTGAAACATCTTTTTCTGGATACCTGG -s Anc0.Anc0refChr1 1917 33 - 62388 CC---------------------------CAGTGGCAGACATCTTTTTTTGGATACCTGA -s Anc1.Anc1refChr2 79880 60 + 144309 CCTTTTTTAGGTTTAGTGGCATTTGTATACAGTGGCAGACATCTTTTTTTGGATACCTGA -s Anc2.Anc2refChr2 17469 33 + 27695 CT---------------------------CAGTGGCAGACATCTTATTTTGGATACCTGA -s mr.mrrefChr0 101291 60 + 130230 CCTTGTTTAACTATAGTGGTAGTTGCATTTAATGTGAAACATCTTTTTCTGGATACCTGG -s simCow_chr6.simCow.chr6 107803 33 + 602619 CT---------------------------CAGGGGCAGAGATCTTATTTTGGATACCTGA -s simDog_chr6.simDog.chr6 504607 31 - 593897 CT---------------------------CAGTGGCAGTCA--TTATTTTGGATAACCAA -s simHuman_chr6.simHuman.chr6 102970 60 + 601863 CCTTTTTTAGGTTTAGTGGCATTTGTATACAGTGGCAGACACCTTTTTTTGAATACCTGA -s simRat_chr6.simRat.chr6 98418 60 + 647215 CCTTGTTTAACTATAGTGGTAGTTGCATTTATTGTGGAACCTCTTCTTCTGGACACCTGG - -a -s simMouse_chr6.simMouse.chr6 106275 10 + 636262 AACAACATGA -s Anc0.Anc0refChr1 1950 10 - 62388 TACATGGCTG -s Anc1.Anc1refChr2 79940 10 + 144309 TACATGGCTG -s Anc2.Anc2refChr2 17503 10 + 27695 TACATGGCTG -s mr.mrrefChr0 101351 10 + 130230 AACAACATGA -s simCow_chr6.simCow.chr6 107837 10 + 602619 TACATGGCTT -s simDog_chr6.simDog.chr6 504639 10 - 593897 TATATGGCTG -s simHuman_chr6.simHuman.chr6 103030 10 + 601863 TACATGGCTC -s simRat_chr6.simRat.chr6 98478 10 + 647215 AACAACATGG - -a -s simMouse_chr6.simMouse.chr6 106285 7 + 636262 CATCATG -s Anc0.Anc0refChr1 1960 7 - 62388 CATCTTG -s Anc1.Anc1refChr2 79950 7 + 144309 CATCTTG -s Anc2.Anc2refChr2 17513 7 + 27695 CATATTC -s mr.mrrefChr0 101361 7 + 130230 CATCATG -s simCow_chr6.simCow.chr6 107847 1 + 602619 C------ -s simCow_chr6.simCow.chr6 108028 1 + 602619 C------ -s simDog_chr6.simDog.chr6 504649 7 - 593897 CATATTC -s simHuman_chr6.simHuman.chr6 103040 7 + 601863 CATCTTG -s simRat_chr6.simRat.chr6 98488 7 + 647215 TGTCATG - -a -s simMouse_chr6.simMouse.chr6 106292 24 + 636262 TTCTAGTGGGTCTAAGGCATTCAC -s Anc0.Anc0refChr1 1967 21 - 62388 TTT---TTGATTTAAGGGATTTGG -s Anc1.Anc1refChr2 79957 21 + 144309 TTT---TTGATTTAAGGGATTTGG -s Anc2.Anc2refChr2 17520 21 + 27695 TAT---TTGATTTAAGTGATTTGG -s mr.mrrefChr0 101368 24 + 130230 TTCTAGTGGGTCTAAGGCATTCAC -s simCow_chr6.simCow.chr6 107849 21 + 602619 TAT---TTGATTTAAGGGATTGGG -s simCow_chr6.simCow.chr6 108029 21 + 602619 TAT---CACATAAAAATGCTATGG -s simDog_chr6.simDog.chr6 504656 21 - 593897 TAT---TTAATTTAAGTGATTTGG -s simHuman_chr6.simHuman.chr6 103047 21 + 601863 TTT---TTGTCATAAGGGATTTCG -s simRat_chr6.simRat.chr6 98495 24 + 647215 TTCTAATGGGTCTAAGGCTTTCAC - -a -s simMouse_chr6.simMouse.chr6 106316 4 + 636262 AGTT -s Anc0.Anc0refChr1 1989 4 - 62388 ATTT -s Anc1.Anc1refChr2 79979 4 + 144309 ATTT -s Anc2.Anc2refChr2 17542 4 + 27695 ATTT -s mr.mrrefChr0 101393 4 + 130230 AGTT -s simCow_chr6.simCow.chr6 107871 4 + 602619 ATTT -s simCow_chr6.simCow.chr6 108051 4 + 602619 ATTT -s simDog_chr6.simDog.chr6 504678 4 - 593897 ATTC -s simHuman_chr6.simHuman.chr6 103069 4 + 601863 ATTT -s simRat_chr6.simRat.chr6 98520 4 + 647215 ACTT - -a -s simMouse_chr6.simMouse.chr6 106320 45 + 636262 TGGAGAACACCATCCCGGTGGTCAAAATGCCTATCTGTCCCATAC -s Anc0.Anc0refChr1 1993 45 - 62388 TGCATAACACCAACTGGGTAGCCAAAAAACCTATCTGCCCCATTT -s Anc1.Anc1refChr2 79983 45 + 144309 TGCATAACACCAACTGGGTAGCCAAAAAACCTATCTGCCCCATTT -s Anc2.Anc2refChr2 17546 45 + 27695 TGCATAACAACAACTGGGTTGCCAAAAAACCTATCTGCCACATTT -s mr.mrrefChr0 101397 45 + 130230 TGGAGAACACCATCCGGGTAGTCAAAATGCCTATCTGTCCCATAC -s simCow_chr6.simCow.chr6 107875 45 + 602619 TGCACAACAACAGCTGGATTGTAGAAAAACCTGTCTGCCACATTT -s simCow_chr6.simCow.chr6 108058 45 + 602619 TGCAGAACAACAGGTGGGTTGTGGAAAAACCTATCTGCTACATAT -s simDog_chr6.simDog.chr6 504682 43 - 593897 TGCATACCAACAACTGGGATGCCAAGTAACCTATCTGCCACAT-- -s simHuman_chr6.simHuman.chr6 103073 45 + 601863 TGAATAACACCAACTGGGTAGCCAAAGAACCTATCTGCCCCATCT -s simRat_chr6.simRat.chr6 98524 45 + 647215 TGGAGAACACCATCCGGGAAGTCAAAATGCCTATATGTCCGACAC - -a -s simMouse_chr6.simMouse.chr6 106365 10 + 636262 GATGGGAGGT -s Anc0.Anc0refChr1 2038 10 - 62388 ATTGGAGGTT -s Anc1.Anc1refChr2 80028 10 + 144309 ATTGGAGGTT -s Anc2.Anc2refChr2 17593 10 + 27695 ATTGGAGGTT -s mr.mrrefChr0 101442 10 + 130230 GATGGGAGGT -s simCow_chr6.simCow.chr6 107922 10 + 602619 ATTGGGGGTT -s simCow_chr6.simCow.chr6 108105 10 + 602619 ATTGGAGGTT -s simDog_chr6.simDog.chr6 504726 10 - 593897 ATTGGAGGGT -s simHuman_chr6.simHuman.chr6 103118 10 + 601863 ATTGGAGCAT -s simRat_chr6.simRat.chr6 98569 10 + 647215 GCTGGGAGGT - -a -s simMouse_chr6.simMouse.chr6 106375 20 + 636262 CTGCATTAACTTGGTAGAGG -s Anc0.Anc0refChr1 2048 5 - 62388 CT---------------AGG -s Anc1.Anc1refChr2 80038 20 + 144309 CTTAGTTGCCATGGTAGAGG -s Anc2.Anc2refChr2 17603 5 + 27695 CT---------------AAG -s mr.mrrefChr0 101452 20 + 130230 CTGCATTAACTTGGTAGAGG -s simCow_chr6.simCow.chr6 107932 5 + 602619 TT---------------GAG -s simCow_chr6.simCow.chr6 108115 5 + 602619 CT---------------AAG -s simDog_chr6.simDog.chr6 504736 5 - 593897 CT---------------AAT -s simHuman_chr6.simHuman.chr6 103130 20 + 601863 CTTAGTTGCCATGGTAGAGG -s simRat_chr6.simRat.chr6 98579 20 + 647215 CTGCATTAACTTGGCAGAGG - -a -s simMouse_chr6.simMouse.chr6 106395 5 + 636262 TCTAG -s Anc0.Anc0refChr1 2068 5 - 62388 TCTAA -s Anc1.Anc1refChr2 80073 5 + 144309 TCTAA -s Anc2.Anc2refChr2 17623 5 + 27695 TCTAA -s mr.mrrefChr0 101472 5 + 130230 TCTAG -s simCow_chr6.simCow.chr6 107951 5 + 602619 TCTAA -s simCow_chr6.simCow.chr6 108135 4 + 602619 TCTA- -s simDog_chr6.simDog.chr6 504755 5 - 593897 TCTAA -s simHuman_chr6.simHuman.chr6 103165 5 + 601863 TCTAA -s simRat_chr6.simRat.chr6 98599 5 + 647215 CCTAG - -a -s simMouse_chr6.simMouse.chr6 106400 33 + 636262 AGGTCAGCTATTCACCAACTACGATGGGAGTGA -s Anc0.Anc0refChr1 2078 33 - 62388 AGGTCATCGATTAATCAATCACAAGGAGAATGA -s Anc1.Anc1refChr2 80083 33 + 144309 AGGTCATCGATTAATCAATCACAAGGAGAATGA -s Anc2.Anc2refChr2 17633 33 + 27695 AGGTTGTTGATTAATCAATCACAAGGAGAATGG -s mr.mrrefChr0 101477 33 + 130230 AGGTCATCTATTCACCAACCACAATGGGAGTGA -s simCow_chr6.simCow.chr6 107961 33 + 602619 AGGTTGTTGATTAATCAATTCGAAGGAGAACAG -s simCow_chr6.simCow.chr6 108143 33 + 602619 AGGTTGTTATTTAATCCATCCTAAGCAGAAGGG -s simDog_chr6.simDog.chr6 504765 33 - 593897 ATGTTGTTGATTAATTAATAACCAGGAGAATTG -s simHuman_chr6.simHuman.chr6 103175 33 + 601863 AGGTCATCCATTAATCAATCACAAGGATAATGA -s simRat_chr6.simRat.chr6 98604 33 + 647215 AGGTCATCTATTTACCAACCACAATGGAAGAGA - -a -s simMouse_chr6.simMouse.chr6 106433 114 + 636262 GCCAAAGCAAGCCGGTGACAGGCCTAATGGGATATTCCTTCTTGTTCAATGGGGTCCATCTTAGGCCCCCAGTGTGATTAATAGGGGCTTCGATAACCTAGGGTGTGACATAAT -s Anc0.Anc0refChr1 2111 3 - 62388 ACT--------------------------------------------------------------------------------------------------------------- -s Anc1.Anc1refChr2 80116 3 + 144309 ACT--------------------------------------------------------------------------------------------------------------- -s Anc2.Anc2refChr2 17667 3 + 27695 ACT--------------------------------------------------------------------------------------------------------------- -s mr.mrrefChr0 101510 114 + 130230 GCCAAAGCAAGCTGGTGACTGGCCAAATGGGATATTCCTTCTTGTTCAATGGGGTCCATCTTAGGCCCCCAGTGTGATTAATAGGGGCTTCGATAACCTAGGGTGTGACATAAT -s simCow_chr6.simCow.chr6 107995 3 + 602619 TGT--------------------------------------------------------------------------------------------------------------- -s simCow_chr6.simCow.chr6 108177 3 + 602619 ACT--------------------------------------------------------------------------------------------------------------- -s simDog_chr6.simDog.chr6 504799 3 - 593897 GCC--------------------------------------------------------------------------------------------------------------- -s simHuman_chr6.simHuman.chr6 103208 3 + 601863 ACA--------------------------------------------------------------------------------------------------------------- -s simRat_chr6.simRat.chr6 98637 89 + 647215 TCCAGGGCAAGCTGGTGACTGGTCAA-------------------------GGGTCCATCTTAGGTCTCCAGTGTGATTAATGGGGGCTTCAATAACCAAGGGTGTGACCTAAT - -a -s simMouse_chr6.simMouse.chr6 106547 40 + 636262 TTCGCCAGCCCAATTGCCAGCTCAAATAGCACCAGCTGTA -s mr.mrrefChr0 101624 40 + 130230 TTCGCCAGCCCAATTGCCAGCTCAAATAGCACCAGCTGTA -s simRat_chr6.simRat.chr6 98727 40 + 647215 TCCCCCAGCCCAATTGCCAGCTCACATGGATCTGGTTGTA - -a -s simMouse_chr6.simMouse.chr6 106587 14 + 636262 TGTACACATCATTC -s mr.mrrefChr0 101664 14 + 130230 TGTACACATCATTC -s simRat_chr6.simRat.chr6 98785 14 + 647215 TATACACATCGCTC - -a -s simMouse_chr6.simMouse.chr6 106601 69 + 636262 GGCCAACGGCCAGTGCAATGAGGTCAAGTCTTACTTAATGTATGCAACAAAGATCAGATGGGCTCATTG -s Anc0.Anc0refChr1 2114 9 - 62388 -----------------------------------------------------------GAGCTT-TTC -s Anc1.Anc1refChr2 80119 9 + 144309 -----------------------------------------------------------GAGCTT-TTC -s Anc2.Anc2refChr2 17670 9 + 27695 -----------------------------------------------------------GAGCAT-TTC -s mr.mrrefChr0 101678 69 + 130230 GGCCAACGGCCAGTGCAATGAGGTCAAGTCTTACTTAATGTATGCAACAAAGATCAGATGGGCTCATTG -s simCow_chr6.simCow.chr6 107998 9 + 602619 -----------------------------------------------------------GAGCAT-TTC -s simCow_chr6.simCow.chr6 108180 9 + 602619 -----------------------------------------------------------GAGCAT-TTC -s simDog_chr6.simDog.chr6 504802 9 - 593897 -----------------------------------------------------------AAGTAT-TTT -s simHuman_chr6.simHuman.chr6 103211 9 + 601863 -----------------------------------------------------------GAGCTT-TTC -s simRat_chr6.simRat.chr6 98800 69 + 647215 GGTCAATGGCCAGTGCAAAGAGCTCATGTCATACTTTATGCATGCAACAAAGATCAGATGGGCGGATTT - -a -s simMouse_chr6.simMouse.chr6 106670 6 + 636262 ACTGTC -s Anc0.Anc0refChr1 2123 6 - 62388 ATTGTC -s Anc1.Anc1refChr2 80128 6 + 144309 ATTGTC -s Anc2.Anc2refChr2 17679 6 + 27695 ATTGTC -s mr.mrrefChr0 101747 6 + 130230 ACTGTC -s simCow_chr6.simCow.chr6 108189 6 + 602619 ATTGTC -s simDog_chr6.simDog.chr6 504811 6 - 593897 GTTGTC -s simHuman_chr6.simHuman.chr6 103220 6 + 601863 AATGTC -s simRat_chr6.simRat.chr6 98870 6 + 647215 ACTGTC - -a -s simMouse_chr6.simMouse.chr6 106676 21 + 636262 ATAGATTGATTCTAGGTAGGT -s Anc0.Anc0refChr1 2129 21 - 62388 ATAGGTTTATTCTATACAAGT -s Anc1.Anc1refChr2 80134 21 + 144309 ATAGGTTTATTCTATACAAGT -s Anc2.Anc2refChr2 17685 21 + 27695 ATAGGTTTATTCTATACGAGT -s mr.mrrefChr0 101753 21 + 130230 ATAGATTGATTCTAGGTAGGT -s simCow_chr6.simCow.chr6 108007 21 + 602619 ATAGTCTCATTCTATGCGAGT -s simCow_chr6.simCow.chr6 108195 21 + 602619 ATTGGATTACTCTATACAAGT -s simDog_chr6.simDog.chr6 504817 21 - 593897 ATAGGTCTATTATATATGAGT -s simHuman_chr6.simHuman.chr6 103226 21 + 601863 ATAGGTTTGTTCTATACAAGT -s simRat_chr6.simRat.chr6 98876 21 + 647215 ATAGATCTGTTCTAGGTAGGT - -a -s simMouse_chr6.simMouse.chr6 106697 44 + 636262 TTGCCATGTAAAAATGTTACAACACTTTGATGTCTTAGTATGTC -s Anc0.Anc0refChr1 2150 42 - 62388 CTATCACATAAACAAGTAACAGCACTTTGATGTGTCA--AGATG -s Anc1.Anc1refChr2 80155 42 + 144309 CTATCACATAAACAAGTAACAGCACTTTGATGTGTCA--AGATG -s Anc2.Anc2refChr2 17706 42 + 27695 CTATCACATAAACAAGTAACAGCACTTTGACCTGTCA--AGAAG -s mr.mrrefChr0 101774 42 + 130230 TTGCCATGTAAAAATGTTACAACACTTTGATGTCTTA--ATGTC -s simCow_chr6.simCow.chr6 108216 42 + 602619 CTATCAAATAACAATGCATGGACACCTTGACCTGTCA--AGGAG -s simDog_chr6.simDog.chr6 504838 42 - 593897 CTATTACGTGAACAAGTAACAGCAGTTCAACCTATGA--AGAAG -s simHuman_chr6.simHuman.chr6 103247 42 + 601863 CTATCACATAAAGACCTGACAGCACTCTGATGTGTCA--AAATA -s simRat_chr6.simRat.chr6 98897 42 + 647215 TTGCCATGTAAAGATGTAACAACACTTTGATCTCTTA--ATTGC - -a -s simMouse_chr6.simMouse.chr6 106741 17 + 636262 TTAGTGACCAGAAACCT -s Anc0.Anc0refChr1 2194 17 - 62388 GTAGTGACTAGCAACTT -s Anc1.Anc1refChr2 80199 17 + 144309 GTAGTGACTAGCAACTT -s Anc2.Anc2refChr2 17750 17 + 27695 GTAGTGACTAGCAACTT -s mr.mrrefChr0 101816 17 + 130230 TTAGTGACCAGAAACCT -s simCow_chr6.simCow.chr6 108260 17 + 602619 GTAGCGATTACCAACTT -s simDog_chr6.simDog.chr6 504882 17 - 593897 GTAGTGACTAGCCACTT -s simHuman_chr6.simHuman.chr6 103291 17 + 601863 GTAGTGACTAGCAACTT -s simRat_chr6.simRat.chr6 98939 17 + 647215 TTAGTGACCAGAAATCT - -a -s simMouse_chr6.simMouse.chr6 106758 234 + 636262 CAGATTTACTCATAGATAATTAAAATAAAATGTCACATGAACCTGTGCGGCTGTAGGTTATTAGATCAAAGAGGCCTGTCTAGATGCCGAAGAGTGTAATGGAGATTGTGTACCGGAGTGGTTTCTTTTCAGTGACTTTTCTGACTATCATCATTAATGTTTGTTGTCCCTAACCCTTTTGTCGCCAATCCTTCCTATCCATGTTCAATGAGGCTATAAGTTGATTCCAACTCA -s Anc0.Anc0refChr1 2212 51 - 62388 CAGATTTACTCATAGGTGATCACAATGAGA---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CTGTAAGTTGATCACAACTAG -s Anc1.Anc1refChr2 80217 51 + 144309 CAGATTTACTCATAGGTGATCACAATGAGA---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CTGTAAGTTGATCACAACTAG -s Anc2.Anc2refChr2 17768 51 + 27695 CAGATTTACTCATAGGTGATCACAATGAGA---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CGGTAAGTTGATCACAACTAG -s mr.mrrefChr0 101833 188 + 130230 CAGATTTACTCATAGATAATTAAAATAAAATGTCACATGAACCTGTGCGGCTGTAGGTTATTAGATCAAAGAGGCCTGTCTAGATGCCGAAGAGTGTAATGGAGATTGTGTACCGGAGTGGTTTCTTTTCAGTGACTTTTCTGACTATCATCATTAATGTTTGTTGT----------------------------------------------CTATAAGTTGATCCCAACTCA -s simCow_chr6.simCow.chr6 108278 50 + 602619 CAGAT-TACTCATAGGTGATCACAAAAGGA---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CCGTAAGCTGATCAAAACAAG -s simDog_chr6.simDog.chr6 504900 48 - 593897 TGGATTTACTAGTA---GATCACAGTGAAA---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CGATAAGTTGGTCACAACTAG -s simHuman_chr6.simHuman.chr6 103309 51 + 601863 CAGATCTACTCATAGGTGATCCCAACGAGA---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CTGTAAGTTGATCACAACTAG -s simRat_chr6.simRat.chr6 98956 188 + 647215 CAGATTTACTCATCGATAATTAAAAAAAAAGGTGACATAAACCTGTGTAGCTGTCGGTTATTAGATCAAAGAAGCCTGTGTATATGCAGAAGAATGTAGTGGAAATTGTGTACCCAAGTGGTTTCTTTTCAGTGTCTTTTCTGACTATCATCATTAAGGTTTGTTCT----------------------------------------------CTACAAGTTGATCCCAAATCA - -a -s simMouse_chr6.simMouse.chr6 106992 52 + 636262 TGCAACCGCTCCGTAAGCATTTTTGAGTTTAGGGCAATAGTGAAATTGTGTT -s Anc0.Anc0refChr1 2263 6 - 62388 TA----------------------------------------------TGGT -s Anc1.Anc1refChr2 80268 6 + 144309 TA----------------------------------------------TGGT -s Anc2.Anc2refChr2 17819 6 + 27695 TA----------------------------------------------TGGT -s mr.mrrefChr0 102021 6 + 130230 TG----------------------------------------------TGTT -s simCow_chr6.simCow.chr6 108331 5 + 602619 TA----------------------------------------------TGG- -s simDog_chr6.simDog.chr6 504948 6 - 593897 TT----------------------------------------------TGTT -s simHuman_chr6.simHuman.chr6 103360 6 + 601863 TA----------------------------------------------TGGT -s simRat_chr6.simRat.chr6 99144 6 + 647215 CA----------------------------------------------TGTT - -a -s simMouse_chr6.simMouse.chr6 107044 10 + 636262 TGGTGGTCAT -s Anc0.Anc0refChr1 2276 10 - 62388 CAGGAACTAT -s Anc1.Anc1refChr2 80281 10 + 144309 CAGGAACTAT -s Anc2.Anc2refChr2 17832 10 + 27695 CAGGAACTGT -s mr.mrrefChr0 102034 10 + 130230 TGGTGGTTAT -s simCow_chr6.simCow.chr6 108343 10 + 602619 CAGGAGCTGT -s simDog_chr6.simDog.chr6 504961 10 - 593897 CAAGTACTGT -s simHuman_chr6.simHuman.chr6 103373 10 + 601863 GAGGAACTAC -s simRat_chr6.simRat.chr6 99157 10 + 647215 TGGTAGTTAT - -a -s simMouse_chr6.simMouse.chr6 107054 77 + 636262 GTGAAATTTTTAAACACACCTCATATTACGCAAACATCCCACAGATGTGCAGACTAACCTAACTTAGTTTTTAGTAC -s Anc0.Anc0refChr1 2286 68 - 62388 ATAAAATTT---------CCACATACTGCCTGGACCTCCCACGGAAGTTCAGACCAAACTCACTTACTTTTTGGTAC -s Anc1.Anc1refChr2 80291 75 + 144309 ATAAAATTTTTACACA--CCACATACTGCCTGGACCTCCCACGGAAGTTCAGACCAAACTCACTTACTTTTTGGTAC -s Anc2.Anc2refChr2 17842 68 + 27695 ATAAAATTC---------CCATATACTGCCTGGACCTCCCAGGGAAGTTCAGGCCACACTCACTTACTTTTTGGTAC -s mr.mrrefChr0 102044 77 + 130230 GTGAAATTTTTAAACACACCACATATTACCCAAACCTCCCACAGATGTGCAGACTAACCTCACTTACTTTTTAGTAC -s simCow_chr6.simCow.chr6 108381 68 + 602619 GTAGAATTC---------TCATATACTGCCTAGACCTCCCGGGGAAGTTTAGGCTCCCTTCACTCACTTTTTGGTAT -s simDog_chr6.simDog.chr6 504971 64 - 593897 ATAAAATTC---------CCATGTATTGCCTGGGCCTCCCAGAGAAGTCCAAGCCACACT----TGCTTCTTGGTAC -s simHuman_chr6.simHuman.chr6 103383 72 + 601863 ATAA--TCTTTACACA---TACATACTGATTGGACCTCCCACGAAAGTTCGGACCAAACTCACATACTTTCTGGTAC -s simRat_chr6.simRat.chr6 99167 77 + 647215 GTGAAATTTTTAAATACACCACATACTACCCAAACCTGCCACAGATTTGCAGACTAAACTCACTTACTTTTTAATCC - -a -s simMouse_chr6.simMouse.chr6 107131 6 + 636262 TTTACC -s Anc0.Anc0refChr1 2357 6 - 62388 TTAACC -s Anc1.Anc1refChr2 80369 6 + 144309 TTAACC -s Anc2.Anc2refChr2 17913 6 + 27695 TTAACC -s mr.mrrefChr0 102121 6 + 130230 TTTGCC -s simCow_chr6.simCow.chr6 108452 6 + 602619 TTTACC -s simDog_chr6.simDog.chr6 505038 6 - 593897 TTAATA -s simHuman_chr6.simHuman.chr6 103458 6 + 601863 TTCACC -s simRat_chr6.simRat.chr6 99244 6 + 647215 TTTGCC - -a -s simMouse_chr6.simMouse.chr6 107137 25 + 636262 AGCGTGAGGCAACAATAAAATCTAG -s Anc0.Anc0refChr1 2363 18 - 62388 AGCTGCAAGCAATAATA-------T -s Anc1.Anc1refChr2 80375 18 + 144309 AGCTGCAAGCAATAATA-------T -s Anc2.Anc2refChr2 17919 18 + 27695 AGCTGCAAGCAATAATA-------T -s mr.mrrefChr0 102127 18 + 130230 AGCGTGAAGCAACAATA-------T -s simCow_chr6.simCow.chr6 108458 18 + 602619 AGCTGCAAGCAATAATA-------T -s simDog_chr6.simDog.chr6 505050 18 - 593897 GGCTGCAAGCAATAATA-------T -s simHuman_chr6.simHuman.chr6 103464 18 + 601863 AGCTGCAAGTGATGATA-------T -s simRat_chr6.simRat.chr6 99250 18 + 647215 AGCTTGAAGCAACGGTA-------T - -a -s simMouse_chr6.simMouse.chr6 107162 54 + 636262 AGGATGAGCATAAATAAATCGAGAATTAGGCTAATCCTTTGAAGTTTGGCATCT -s Anc0.Anc0refChr1 2388 53 - 62388 AGGGTAAGTACAAATCAATAGGAAATGAAGCTAGTC-TTTGGAGTTTAGTATCT -s Anc1.Anc1refChr2 80400 54 + 144309 AGGGTAAGTACAAATCAATAGGAAATGAAGCTAGTCCTTTGGAGTTTAGTATCT -s Anc2.Anc2refChr2 17944 53 + 27695 AGGGTAAATCCAAATCAACAGAACATGGAACTAGTC-TTTGGAGTTTAGTATCT -s mr.mrrefChr0 102145 54 + 130230 AGGATGAGCATAAATAAATAGGGAATTAGGCTAATCCTTTGAAGTTTGGCATCT -s simCow_chr6.simCow.chr6 108483 53 + 602619 AGGGTAAATCCAAATCAACAGAACATGGAACTAGTC-TGTACAATTTAGTATTT -s simDog_chr6.simDog.chr6 505075 22 - 593897 AGGGGA--------------------------------TTGGAGTTTAGTATCT -s simHuman_chr6.simHuman.chr6 103489 54 + 601863 AGAGTAAGTACAAAATAATAGGAAATGAAGCTAGTCCTTTGTGGTTTAGATTCT -s simRat_chr6.simRat.chr6 99268 54 + 647215 AGGATGAGCACAAATAAATAGGGAATTAAGCTAGTCCTTTGAAGTTTGGCATCC - -a -s simMouse_chr6.simMouse.chr6 107216 22 + 636262 GAGAGCACATATGCTCCAATGC -s Anc0.Anc0refChr1 2448 22 - 62388 CAGAGAACATCTGATCCAATGA -s Anc1.Anc1refChr2 80461 22 + 144309 CAGAGAACATCTGATCCAATGA -s Anc2.Anc2refChr2 18004 22 + 27695 CAGAGAACATCTGATCCAATGA -s mr.mrrefChr0 102199 22 + 130230 GAGAGCACATCTGCTCCAATGC -s simCow_chr6.simCow.chr6 108543 22 + 602619 CAGAGAACATCTGATCCAATGA -s simDog_chr6.simDog.chr6 505104 21 - 593897 CAGAGAAT-TCTGAACCAATGC -s simHuman_chr6.simHuman.chr6 103550 22 + 601863 CAGAGAACATCTCATCCAATGA -s simRat_chr6.simRat.chr6 99322 22 + 647215 CAGACAAGATCTGGTCTGATGC - -a -s simMouse_chr6.simMouse.chr6 107238 5 + 636262 ATACC -s Anc0.Anc0refChr1 2475 5 - 62388 ATAGA -s Anc1.Anc1refChr2 80488 5 + 144309 ATAGA -s Anc2.Anc2refChr2 18031 5 + 27695 CTAGA -s mr.mrrefChr0 102221 5 + 130230 ATACC -s simCow_chr6.simCow.chr6 108570 5 + 602619 CTAGA -s simDog_chr6.simDog.chr6 505130 5 - 593897 CTAGG -s simHuman_chr6.simHuman.chr6 103577 5 + 601863 ATTGA -s simRat_chr6.simRat.chr6 99344 5 + 647215 ATACC - -a -s simMouse_chr6.simMouse.chr6 107243 10 + 636262 TATACTGGTT -s Anc0.Anc0refChr1 2480 10 - 62388 TATACTGGTT -s Anc1.Anc1refChr2 80493 10 + 144309 TATACTGGTT -s Anc2.Anc2refChr2 18036 10 + 27695 TATACTGGTT -s mr.mrrefChr0 102226 10 + 130230 TATACTGGTT -s simCow_chr6.simCow.chr6 108584 10 + 602619 TTTACTGATT -s simDog_chr6.simDog.chr6 505135 10 - 593897 TATACTGGTT -s simHuman_chr6.simHuman.chr6 103582 10 + 601863 TACACTGGTT -s simRat_chr6.simRat.chr6 99349 10 + 647215 TATACTGGTT - -a -s simMouse_chr6.simMouse.chr6 107253 21 + 636262 TGTGGTGCCTTGTGTATATAC -s Anc0.Anc0refChr1 2490 21 - 62388 TGTGGTGCCCTGTGTATATGC -s Anc1.Anc1refChr2 80503 21 + 144309 TGTGGTGCCCTGTGTATATGC -s Anc2.Anc2refChr2 18046 21 + 27695 TGCAGTGCTCTGTGTATATGC -s mr.mrrefChr0 102236 21 + 130230 TGTGGTGCCCTGTGTATATAC -s simCow_chr6.simCow.chr6 108594 21 + 602619 TGCAGTTCACTGTGTATATGC -s simDog_chr6.simDog.chr6 505145 21 - 593897 TGCAGTGCTCTTTGTATATGC -s simHuman_chr6.simHuman.chr6 103592 21 + 601863 TGTGGTGCCCAGTGTATATGC -s simRat_chr6.simRat.chr6 99377 21 + 647215 TGTGGTGCCCTGCGTATATAC - -a -s simMouse_chr6.simMouse.chr6 107274 19 + 636262 ATTTCTAGTACATACCACA -s Anc0.Anc0refChr1 2512 19 - 62388 AACTATAGTACAAACCAAA -s Anc1.Anc1refChr2 80525 19 + 144309 AACTATAGTACAAACCAAA -s Anc2.Anc2refChr2 18068 19 + 27695 AACTATAGTACAAACTAAA -s mr.mrrefChr0 102257 19 + 130230 ATCTCTAGTACATACCACA -s simCow_chr6.simCow.chr6 108616 19 + 602619 TACTATAGTACAAACAAAA -s simDog_chr6.simDog.chr6 505167 18 - 593897 A-CTATAGTACAGACTAAA -s simHuman_chr6.simHuman.chr6 103614 19 + 601863 AACTATAGTACAAACCAAA -s simRat_chr6.simRat.chr6 99398 19 + 647215 ACCTCTAGTACATAGCAGA - -a -s simMouse_chr6.simMouse.chr6 107293 29 + 636262 ATTCAAGGCCTTGCACAGATAGCTTGTGG -s Anc0.Anc0refChr1 2534 25 - 62388 ATTCATGGCTTTGCATGGATG----GTGG -s Anc1.Anc1refChr2 80547 25 + 144309 ATTCATGGCTTTGCATGGATG----GTGG -s Anc2.Anc2refChr2 18090 25 + 27695 AGCCATGGCTTTGCATGGATG----GTGG -s mr.mrrefChr0 102276 29 + 130230 ATTCATGGCCCTGCACAGATAGCTTGTGG -s simCow_chr6.simCow.chr6 108638 25 + 602619 CCCCATGGATTTTCATGGATG----GTGG -s simDog_chr6.simDog.chr6 505188 25 - 593897 AGCCATGGCTCTGCATGGATA----GTGG -s simHuman_chr6.simHuman.chr6 103636 25 + 601863 ATTCATGGCTTGGCTTGGATG----GTGG -s simRat_chr6.simRat.chr6 99417 29 + 647215 ACTCATGACCCTGCACAGATAATTTGTGG - -a -s simMouse_chr6.simMouse.chr6 107322 13 + 636262 CCTAGTTTGTTCC -s Anc0.Anc0refChr1 2560 13 - 62388 TCCAGTTTCTTCC -s Anc1.Anc1refChr2 80573 13 + 144309 TCCAGTTTCTTCC -s Anc2.Anc2refChr2 18116 13 + 27695 TCCAGTTTCTTCC -s mr.mrrefChr0 102305 13 + 130230 TCTAGTTTGTTCC -s simCow_chr6.simCow.chr6 108664 13 + 602619 TACAGTTGGTTTC -s simDog_chr6.simDog.chr6 505214 13 - 593897 TCTAGTTTCTTCC -s simHuman_chr6.simHuman.chr6 103662 13 + 601863 TCCAGTTTCTTCC -s simRat_chr6.simRat.chr6 99446 13 + 647215 TGCAGTTTGTTCC - -a -s simMouse_chr6.simMouse.chr6 107335 13 + 636262 CCAATGTTCCCTC -s Anc0.Anc0refChr1 2574 13 - 62388 CCAATCTTTTCTT -s Anc1.Anc1refChr2 80587 13 + 144309 CCAATCTTTTCTT -s Anc2.Anc2refChr2 18130 13 + 27695 CCAATCTTTTGTT -s mr.mrrefChr0 102318 13 + 130230 CCAATGTTCCCTC -s simCow_chr6.simCow.chr6 108678 13 + 602619 CCAATTATTCATT -s simDog_chr6.simDog.chr6 505228 13 - 593897 CCAATCTTATGTT -s simHuman_chr6.simHuman.chr6 103676 13 + 601863 CCAATCCTTTCTT -s simRat_chr6.simRat.chr6 99459 13 + 647215 CCAATGTTCACTC - -a -s simMouse_chr6.simMouse.chr6 107348 18 + 636262 TTTTACCCCACAGCCACA -s Anc0.Anc0refChr1 2588 11 - 62388 TTCTACCCCAC------- -s Anc1.Anc1refChr2 80601 11 + 144309 TTCTACCCCAC------- -s Anc2.Anc2refChr2 18144 11 + 27695 TTCTATCCCAC------- -s mr.mrrefChr0 102331 18 + 130230 TTTTACCCCACAGCCACA -s simCow_chr6.simCow.chr6 108692 11 + 602619 TTTTATGCCAC------- -s simDog_chr6.simDog.chr6 505242 11 - 593897 TTCTATCCCAA------- -s simHuman_chr6.simHuman.chr6 103690 11 + 601863 TTCTACCACAC------- -s simRat_chr6.simRat.chr6 99472 18 + 647215 TCATACCAAACAGCCACA - -a -s simMouse_chr6.simMouse.chr6 107366 8 + 636262 ACCAAGAC -s Anc0.Anc0refChr1 2599 8 - 62388 ACCAAGAC -s Anc1.Anc1refChr2 80612 8 + 144309 ACCAAGAC -s Anc2.Anc2refChr2 18155 8 + 27695 ACCAAGAC -s mr.mrrefChr0 102349 8 + 130230 ACCAAGAC -s simCow_chr6.simCow.chr6 108704 8 + 602619 ACCAAGAC -s simDog_chr6.simDog.chr6 505253 8 - 593897 ACCCAGAT -s simHuman_chr6.simHuman.chr6 103701 8 + 601863 ACCAAGCC -s simRat_chr6.simRat.chr6 99490 8 + 647215 ACCAAGAC - -a -s simMouse_chr6.simMouse.chr6 107374 1 + 636262 A -s Anc0.Anc0refChr1 2607 1 - 62388 A -s Anc1.Anc1refChr2 80620 1 + 144309 A -s Anc2.Anc2refChr2 18164 1 + 27695 A -s mr.mrrefChr0 102357 1 + 130230 A -s simCow_chr6.simCow.chr6 108713 1 + 602619 T -s simDog_chr6.simDog.chr6 505262 1 - 593897 A -s simHuman_chr6.simHuman.chr6 103709 1 + 601863 A -s simRat_chr6.simRat.chr6 99498 1 + 647215 C - -a -s simMouse_chr6.simMouse.chr6 107375 29 + 636262 AAATACTTATGGAATGTAGCTATAGCATA -s Anc0.Anc0refChr1 2612 25 - 62388 AGTTACTTAT----TGTAGTTGCAGTATA -s Anc1.Anc1refChr2 80625 25 + 144309 AGTTACTTAT----TGTAGTTGCAGTATA -s Anc2.Anc2refChr2 18169 25 + 27695 AGTTACTTCC----TGTAGTTGCAGTATA -s mr.mrrefChr0 102358 29 + 130230 AATTACTTATGGAATGTAGCTATAGCATA -s simCow_chr6.simCow.chr6 108718 25 + 602619 GATTACCTCC----TGTAATTGCAGCATA -s simDog_chr6.simDog.chr6 505267 25 - 593897 AGTTACTGCC----TGTAGTTGCAGTATA -s simHuman_chr6.simHuman.chr6 103714 25 + 601863 TCTTATTTAT----TGTAGTTGCAGTGTC -s simRat_chr6.simRat.chr6 99499 29 + 647215 AGTTACTTATAGAATGCAACTATAGCATA - -a -s simMouse_chr6.simMouse.chr6 107404 31 + 636262 TTATATTGTCAGGGGTCATAGTGTGATGAAC -s Anc0.Anc0refChr1 2637 26 - 62388 TT-----GTCAGAGGTTAAGGTGACAAAAAC -s Anc1.Anc1refChr2 80650 26 + 144309 TT-----GTCAGAGGTTAAGGTGACAAAAAC -s Anc2.Anc2refChr2 18195 26 + 27695 TT-----GTCAGAGGTTAAGGTGACAAAAAC -s mr.mrrefChr0 102387 26 + 130230 TT-----GTCAGGGGTCATGGTGTGATGAAC -s simCow_chr6.simCow.chr6 108744 26 + 602619 TT-----GCCACGGGTCAAGGTGAAAAAAAC -s simDog_chr6.simDog.chr6 505293 26 - 593897 TT-----GTCAGAGGTTGAGGTGACAAAAAC -s simHuman_chr6.simHuman.chr6 103739 26 + 601863 CT-----GTCAGAGGTGAAGGTGACGAAAAC -s simRat_chr6.simRat.chr6 99528 26 + 647215 TT-----GTCAGGGGTCACGGTGTGATGAAC - -a -s simMouse_chr6.simMouse.chr6 107435 17 + 636262 TAATAAGTGGACTAGGA -s Anc0.Anc0refChr1 2663 17 - 62388 CCAGGTGTGGACTAGGA -s Anc1.Anc1refChr2 80676 17 + 144309 CCAGGTGTGGACTAGGA -s Anc2.Anc2refChr2 18222 17 + 27695 CCAGGTGTGAACTGGGG -s mr.mrrefChr0 102413 17 + 130230 TAAGGTGTGGACTAGGA -s simCow_chr6.simCow.chr6 108771 17 + 602619 CTAGGCATGAACTGGGG -s simDog_chr6.simDog.chr6 505320 15 - 593897 CCAGGTGTGAG--GGGG -s simHuman_chr6.simHuman.chr6 103765 17 + 601863 CCAGGTGTGGACCAGGA -s simRat_chr6.simRat.chr6 99554 17 + 647215 TAAGGTGTGGACTAGGA - -a -s simMouse_chr6.simMouse.chr6 107452 25 + 636262 CATGGCTGGCAGGTAACTGCATATG -s Anc0.Anc0refChr1 2683 25 - 62388 CATAGCTAAATTGTAACTGCATAGA -s Anc1.Anc1refChr2 80696 25 + 144309 CATAGCTAAATTGTAACTGCATAGA -s Anc2.Anc2refChr2 18242 25 + 27695 TATAGCTAAATTGTAACTACACAGA -s mr.mrrefChr0 102430 25 + 130230 CATAGCTGGATGGTAACTGCATATG -s simCow_chr6.simCow.chr6 108791 25 + 602619 TTTGGCTAAATTGTAAATACACCCA -s simDog_chr6.simDog.chr6 505338 25 - 593897 TATAGCTACATTGTAACTACCCAGA -s simHuman_chr6.simHuman.chr6 103785 22 + 601863 CATAGCTAAGTTGT---TGCATACA -s simRat_chr6.simRat.chr6 99571 25 + 647215 CATAGCTGAATGGCAACTGCATATA - -a -s simMouse_chr6.simMouse.chr6 107477 4 + 636262 GCTT -s Anc0.Anc0refChr1 2708 4 - 62388 GCCT -s Anc1.Anc1refChr2 80721 4 + 144309 GCCT -s Anc2.Anc2refChr2 18301 4 + 27695 GCCT -s mr.mrrefChr0 102455 4 + 130230 GCTT -s simCow_chr6.simCow.chr6 108853 4 + 602619 GCCT -s simDog_chr6.simDog.chr6 505397 4 - 593897 GCCT -s simHuman_chr6.simHuman.chr6 103807 4 + 601863 GCCT -s simRat_chr6.simRat.chr6 99596 4 + 647215 GCTT - -a -s simMouse_chr6.simMouse.chr6 107481 84 + 636262 TCTCCCAGCTACCTAACCTTACAGTAAGACAGAACCTAAGCACTAGCTATTTAATATCTCATGGTGATAAATGTGGGTGACAAT -s Anc0.Anc0refChr1 2713 74 - 62388 TCACCCAGCTACCCCACCTTTCAGTAAGTCAGAACTTAAGCACTAGATGTTGAATAAATTGTGGTGA--CA--------ATAAT -s Anc1.Anc1refChr2 80726 74 + 144309 TCACCCAGCTACCCCACCTTTCAGTAAGTCAGAACTTAAGCACTAGATGTTGAATAAATTGTGGTGA--CA--------ATAAT -s Anc2.Anc2refChr2 18306 74 + 27695 TCACCCAGCTACCCCACCTTTCAGTAGGTCAAAACTTAAGCACTAGATGTTGAATAAATTGTGGTGA--CA--------ATGAT -s mr.mrrefChr0 102459 82 + 130230 TCACCCAGCTACCTAACCTTACAGTAAGACAGAACCTAAGCACTAGCTATTTAATATCTCATGGTGA--AACATGGGTGACAAT -s simCow_chr6.simCow.chr6 108858 72 + 602619 TCACCCAGCTACTCCACCTTACATTATGTCAAAACTT--GCACTAGATGTTCAATAAATTGTGGTGC--CA--------ATGAT -s simDog_chr6.simDog.chr6 505402 69 - 593897 TCACCCAGCTACCCCACCTTTCAGTAGGTCAAAACCTAAGCACTAGATGTTGAATAAATTGTGGTGA--CA------------- -s simHuman_chr6.simHuman.chr6 103812 74 + 601863 TCATCCAGCTACCCCACTTTGCAGCAAGTCGGAACTCAAGCACTTGATGTTAAGTAAATTGTGGTAA--CA--------ATAAT -s simRat_chr6.simRat.chr6 99600 31 + 647215 TCACCTAGCTACCTGA-----------------------------------------------------ATCATAGGTGACGAT - -a -s simMouse_chr6.simMouse.chr6 107565 2 + 636262 GC -s Anc0.Anc0refChr1 2787 2 - 62388 GT -s Anc1.Anc1refChr2 80800 2 + 144309 GT -s Anc2.Anc2refChr2 18380 2 + 27695 GT -s mr.mrrefChr0 102541 2 + 130230 GC -s simCow_chr6.simCow.chr6 108930 2 + 602619 GT -s simHuman_chr6.simHuman.chr6 103886 2 + 601863 AT -s simRat_chr6.simRat.chr6 99632 2 + 647215 AC - -a -s simMouse_chr6.simMouse.chr6 107567 74 + 636262 AAGCATATACAACAGACATAGCTTGAGCACCAAAAAACCAGTCTTGAGGCGAATGTGTCCCTTATGTCTGGAGT -s Anc0.Anc0refChr1 2789 60 - 62388 TAACAAAAATGGAGAA----ACA---------GAAAATCAGTCTTGAGGCAAAAGTGT-CTTTATGAGTGAAGT -s Anc1.Anc1refChr2 80802 60 + 144309 TAACAAAAATGGAGAA----ACA---------GAAAATCAGTCTTGAGGCAAAAGTGT-CTTTATGAGTGAAGT -s Anc2.Anc2refChr2 18382 60 + 27695 TAACAAAAATGGAGAC----ACA---------GAAATTCAGTCGTGAGGCAAAAGTGT-CTCCATGAGTGAAGT -s mr.mrrefChr0 102543 61 + 130230 AAGCATATACAACAGA----GCT---------AAAAATCAATCTTGAGGCGAAAGTGTCCCTTATGTCTGGAGT -s simCow_chr6.simCow.chr6 108933 60 + 602619 TAACAAAAATGGAGAT----TCA---------AAAAGTCAGTCCCATGGCAAAGGTGT-CTCCATGAGTGAAGT -s simDog_chr6.simDog.chr6 505471 35 - 593897 ---------TGGGGAC----ATT---------GATATACAGTAGTGAATCAAAAA-----------------AT -s simHuman_chr6.simHuman.chr6 103888 60 + 601863 CAACAAAGCTGGAGAA----CCA---------GAATATCAGTCTTGAGGCAAAAGTGT-CTTTGTGGGTGATGT -s simRat_chr6.simRat.chr6 99634 61 + 647215 AAGCGTATACAACAGA----GCT---------AAAAATCAATCTTGAGGTGAAAGTGTCCCTTATGTCTGAAGT - -a -s simMouse_chr6.simMouse.chr6 107641 15 + 636262 TTCACTCCATATATA -s Anc0.Anc0refChr1 2852 15 - 62388 TTTATCACATACATG -s Anc1.Anc1refChr2 80865 15 + 144309 TTTATCACATACATG -s Anc2.Anc2refChr2 18445 15 + 27695 TTTATCACACACATG -s mr.mrrefChr0 102604 15 + 130230 TTCATTCCATATATG -s simCow_chr6.simCow.chr6 108996 15 + 602619 TTTATCACACACATG -s simDog_chr6.simDog.chr6 505509 15 - 593897 TTTATCACACACATG -s simHuman_chr6.simHuman.chr6 103951 15 + 601863 TTTATCACCTACATG -s simRat_chr6.simRat.chr6 99695 15 + 647215 TTCATTCCATATACG - -a -s simMouse_chr6.simMouse.chr6 107656 4 + 636262 TAGA -s Anc0.Anc0refChr1 2867 4 - 62388 TAGA -s Anc1.Anc1refChr2 80880 4 + 144309 TAGA -s Anc2.Anc2refChr2 18460 4 + 27695 TAGA -s mr.mrrefChr0 102619 4 + 130230 TAGA -s simCow_chr6.simCow.chr6 109011 4 + 602619 TAGA -s simDog_chr6.simDog.chr6 505524 4 - 593897 TAGA -s simHuman_chr6.simHuman.chr6 103966 4 + 601863 TGGA -s simRat_chr6.simRat.chr6 99718 4 + 647215 TAGA - -a -s simMouse_chr6.simMouse.chr6 107660 17 + 636262 GGCCATCATAAAATTGT -s Anc0.Anc0refChr1 2877 17 - 62388 TGCCATCATAAGATCAT -s Anc1.Anc1refChr2 80890 17 + 144309 TGCCATCATAAGATCAT -s Anc2.Anc2refChr2 18470 17 + 27695 TGCCATCATAAGATCAT -s mr.mrrefChr0 102623 17 + 130230 GGCCATCATAAGATTGT -s simCow_chr6.simCow.chr6 109021 17 + 602619 TGTCATCATAATATTGT -s simDog_chr6.simDog.chr6 505534 17 - 593897 TGCCATGATAAGATCAT -s simHuman_chr6.simHuman.chr6 103976 17 + 601863 TGCCATCATATGGTCAT -s simRat_chr6.simRat.chr6 99722 17 + 647215 GGCCATCATAAGATTGT - -a -s simMouse_chr6.simMouse.chr6 107677 8 + 636262 ACTCAACA -s Anc0.Anc0refChr1 2894 8 - 62388 ACTCAACA -s Anc1.Anc1refChr2 80907 8 + 144309 ACTCAACA -s Anc2.Anc2refChr2 18487 8 + 27695 ACTCAACA -s mr.mrrefChr0 102640 8 + 130230 ACTCAACA -s simCow_chr6.simCow.chr6 109038 8 + 602619 TCTCAACA -s simDog_chr6.simDog.chr6 505551 8 - 593897 ACTCAACA -s simHuman_chr6.simHuman.chr6 103994 8 + 601863 AATCAACT -s simRat_chr6.simRat.chr6 99739 8 + 647215 AGTCATCA - -a -s simMouse_chr6.simMouse.chr6 107685 1 + 636262 A -s Anc0.Anc0refChr1 2902 1 - 62388 A -s Anc1.Anc1refChr2 80915 1 + 144309 A -s Anc2.Anc2refChr2 18497 1 + 27695 A -s mr.mrrefChr0 102648 1 + 130230 A -s simCow_chr6.simCow.chr6 109048 1 + 602619 A -s simDog_chr6.simDog.chr6 505561 1 - 593897 A -s simHuman_chr6.simHuman.chr6 104002 1 + 601863 A -s simRat_chr6.simRat.chr6 99747 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 107686 32 + 636262 ACATCACCACCCCTCCTTCATCATGTCTGGTT -s Anc0.Anc0refChr1 2903 29 - 62388 ACATCACCACCGCTGCTTTCCTTTCTC---TT -s Anc1.Anc1refChr2 80916 29 + 144309 ACATCACCACCGCTGCTTTCCTTTCTC---TT -s Anc2.Anc2refChr2 18498 29 + 27695 ACATCAACACTGCCGCTTTCCTTTCTT---TG -s mr.mrrefChr0 102649 32 + 130230 ACATCACCACCCCTGCTTTATCTTGTCTGGTT -s simCow_chr6.simCow.chr6 109066 29 + 602619 GCATCAGCACTGCCGCATTCCTTTCTA---TG -s simDog_chr6.simDog.chr6 505562 29 - 593897 ACATCAACACTGCCGCTTTCCTTTCTT---TG -s simHuman_chr6.simHuman.chr6 104003 24 + 601863 ATATCACCACCTCTG-----CTTTCTC---TT -s simRat_chr6.simRat.chr6 99748 32 + 647215 CCATCACCACCCCTGCTTTGTCTTATCTAGTT - -a -s simMouse_chr6.simMouse.chr6 107718 37 + 636262 ACAACACAGTTACCTTCTTGGAGGTAAAGACTACTTC -s Anc0.Anc0refChr1 2932 37 - 62388 GCAATACAGTTACCTTCTAGCTGTACTGTACTACGCC -s Anc1.Anc1refChr2 80945 37 + 144309 GCAATACAGTTACCTTCTAGCTGTACTGTACTACGCC -s Anc2.Anc2refChr2 18527 37 + 27695 GCAATACAGTTACCTTCTAGCTGTACTGTACTATGCC -s mr.mrrefChr0 102681 37 + 130230 ACAACACAGTTACCTTCTTGGTGGTAAAGACTACTTC -s simCow_chr6.simCow.chr6 109095 36 + 602619 -CAATACAGTGACTTTCGAGCAGTACCGAGCCTTGCC -s simDog_chr6.simDog.chr6 505594 37 - 593897 GCAAGACAGTTAGCTTCTAGCTGTACTATACTATACC -s simHuman_chr6.simHuman.chr6 104027 37 + 601863 GCAATGCAGTTACCTTCTGGTGGTACTGTACTACGCC -s simRat_chr6.simRat.chr6 99780 37 + 647215 ACAACTCAGTTATCTTCTTAGTGGTAAAGGCTACTTC - -a -s simMouse_chr6.simMouse.chr6 107755 26 + 636262 TTTGTCTCAAAAAGTAATCATCAGGC -s Anc0.Anc0refChr1 2970 23 - 62388 TCTATTTCAAAAAGTAATCGTG---C -s Anc1.Anc1refChr2 80983 23 + 144309 TCTATTTCAAAAAGTAATCGTG---C -s Anc2.Anc2refChr2 18565 23 + 27695 TCTATTTCAAAAAGTAATCGTG---C -s mr.mrrefChr0 102719 26 + 130230 TCTGTCTCAAAAAGTAATCATCAGGC -s simCow_chr6.simCow.chr6 109132 23 + 602619 TGTACTCCAAAAAGTAATCGTC---A -s simDog_chr6.simDog.chr6 505632 23 - 593897 TCACTTTCAAAAAGCAATCATG---C -s simHuman_chr6.simHuman.chr6 104065 23 + 601863 TCTATTTCAAGAGGTAATCGTT---C -s simRat_chr6.simRat.chr6 99818 26 + 647215 TCTGTCTCAAAAAGTAATCATCAGGG - -a -s simMouse_chr6.simMouse.chr6 107781 57 + 636262 AATGAGAGGTCAAGCATTTGGATAGTACCTACTTATCAGGGACTAGCTCAAAGTGAA -s Anc0.Anc0refChr1 2993 57 - 62388 AATGAAGGGTCAAACAAGTGGATAGCACCTACCCATCAGGGATTAGCTTAAAGTTAT -s Anc1.Anc1refChr2 81006 57 + 144309 AATGAAGGGTCAAACAAGTGGATAGCACCTACCCATCAGGGATTAGCTTAAAGTTAT -s Anc2.Anc2refChr2 18588 57 + 27695 AATGAAGGGTCAAACAAGTGGATAACACCTACCCATCAGGCATCAGCTTAAAGTTAT -s mr.mrrefChr0 102745 57 + 130230 AATGAGAGGTCAAGCATTTGGATAGTACCTACTTATCAGGGATTAGCTCAAAGTGAA -s simCow_chr6.simCow.chr6 109155 55 + 602619 GA--AAGGGTCAAACATTTGGATAGAACCTACTCATCAGGAATCAGCTCAAAGTTAT -s simDog_chr6.simDog.chr6 505658 57 - 593897 AGTGAAATGTCAAACAAGTGGATAACACCTATCCATCATGCATCAGCTTAAAATTAT -s simHuman_chr6.simHuman.chr6 104088 49 + 601863 AATGTAGGGTCAAAC--------AGAACCTACCCATCAGGGACTAGCTTAAAGTTAC -s simRat_chr6.simRat.chr6 99844 56 + 647215 AATGAGAGGTCAAGCATTTCGTTAGATCCTACTTATCAGGGATTCACTCAAAGT-AA - -a -s simMouse_chr6.simMouse.chr6 107838 26 + 636262 ACTGAATAACAGGTTGAAGGTGCTAA -s Anc0.Anc0refChr1 3050 26 - 62388 TCTTATTCACAATTCTAAGGCCCTGA -s Anc1.Anc1refChr2 81063 26 + 144309 TCTTATTCACAATTCTAAGGCCCTGA -s Anc2.Anc2refChr2 18645 26 + 27695 TCTTATTCACAATTCTAATCCCCTGA -s mr.mrrefChr0 102802 26 + 130230 ACTGAATAACAAGTTGAAGGTGCTAA -s simCow_chr6.simCow.chr6 109221 21 + 602619 GCTTATCTACAGTATGA-----CTGA -s simDog_chr6.simDog.chr6 505715 26 - 593897 TCTTAATCATGATTCTAATCCCCTGA -s simHuman_chr6.simHuman.chr6 104137 26 + 601863 TCTTATTGACAATCCAAAGGCACTGG -s simRat_chr6.simRat.chr6 99900 26 + 647215 ACCGAATAACAAGTTGAAGGTGCCAA - -a -s simMouse_chr6.simMouse.chr6 107864 72 + 636262 GCTTATTGATAGCACAAAATGGCTCCACGTACAATACTGAGAAAGGAATGCAAACAGGAACGCAAAAGGGCA -s Anc0.Anc0refChr1 3077 22 - 62388 GCTTATCGATGGCACAAAATTA-------------------------------------------------- -s Anc1.Anc1refChr2 81090 22 + 144309 GCTTATCGATGGCACAAAATTA-------------------------------------------------- -s Anc2.Anc2refChr2 18672 22 + 27695 GCTTATCGATGGTACAAAATTA-------------------------------------------------- -s mr.mrrefChr0 102829 72 + 130230 GCTTATTGATAGCACAAAATGATTCCACGTACAATACTGAGAAAGGAATGCAAACAGGAACGCAAAAGGGCA -s simCow_chr6.simCow.chr6 109243 22 + 602619 GTCTATCTACGGTACAAAATTA-------------------------------------------------- -s simDog_chr6.simDog.chr6 505742 22 - 593897 GCTTATCGATGGTATAGAATCA-------------------------------------------------- -s simHuman_chr6.simHuman.chr6 104176 22 + 601863 GCTTATCCATGGCACAATACTA-------------------------------------------------- -s simRat_chr6.simRat.chr6 99927 72 + 647215 GCTTATTGATAGCACAAAAGGATTCCACGTACAATACTGTGATGGGAATGGAAATGGGAATGCAAAAGGACA - -a -s simMouse_chr6.simMouse.chr6 107936 397 + 636262 GTAATCTATCAATACAGTAAATCCTAATATTGATCTCACATGTAACTCATAAGTGATTAAGGACATTAAAAAGTAAAGCAGCAGTTACTGTCTGTCAGTTGATGCTTGGCTATGACCCTTCCCTGCGCAGCCATGTACACACGGTCAGTACATGGCTACAACTGCCCCGCATGGCATGTACACACAGCATCAGGGCTTGGAGTCTGCCCTGCGTGCGAAATGTCAATTAACGTGTGATTCTTTGTAAAGTATCCCACTCGTCGGCAGGTGCCAAGAGTATGCTGGGGTATGGAGGTTGCCTGGGCGAATGTGGAAAATTATGAGGGGCAAAATTTGTCCTACAATAAATCTTGGCTTAGTGGCCTGACACAATAGCCCTTTGGACTTGTCATGTGAA -s Anc0.Anc0refChr1 3099 11 - 62388 --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TGTTCTATGAA -s Anc1.Anc1refChr2 81112 11 + 144309 --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TGTTCTATGAA -s Anc2.Anc2refChr2 18694 11 + 27695 --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TGTTCTATAAA -s mr.mrrefChr0 102901 267 + 130230 GTAATCTATCAATACAGTAAATCCTAATATTGATCTCACATGTAACTCATAAGTGATTAAGGACATTAAAAAGTAAAGCAGCAGTTACTGTCTGTCA----------------------------------------------------------------------------------------------------------------------------------TAACGTGTGGTTCTTTGTAAAGTATCCCACTCGTCGGCAGGTGCCAAGAGTATGCTGGGGTATGGAGGTTGCCTGGGCGAATGTGGAAAATTATGAGGGGCAAAATTTGTCCTACAATAAATCTTGGCTTAGTGGCCTGACACAATAGCCCTTTGGACTTGTCATGTGAA -s simCow_chr6.simCow.chr6 109265 11 + 602619 --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GGTTGTATAAA -s simDog_chr6.simDog.chr6 505764 11 - 593897 --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TGTTCTATAAA -s simHuman_chr6.simHuman.chr6 104198 11 + 601863 --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TGTTCTATGAA -s simRat_chr6.simRat.chr6 100008 267 + 647215 GTAATCTATCCAAATATTAAATAATAACATTGATCTCACATGTGACTCACATGTGATCAAGGACATTAAAAAGTAAATCAGCAGTTACTGTCTGTAA----------------------------------------------------------------------------------------------------------------------------------TAATGTGTGGTTCTTTGTAAGGTATCCCTCTCATTGGGAGGTGCCAAGAGTATGCTAGGGTATAGAGCTCGCCTAGGCAAATGTGGAAATTTATGAGGTACAAAATTTGTCCTACTATACATCTTGGCTCATTGGCCTGATGCAGTAGACCTTTGGACTTGTCATGTGGA - -a -s simMouse_chr6.simMouse.chr6 108333 40 + 636262 TGTAGTATAGTAATATACAGTTGTATTTAGGGCATCAATC -s Anc0.Anc0refChr1 3244 40 - 62388 TGTAGCATATGCATAGATCATAGCATTTAGGGAGTCAACC -s Anc1.Anc1refChr2 81257 40 + 144309 TGTAGCATATGCATAGATCATAGCATTTAGGGAGTCAACC -s Anc2.Anc2refChr2 18857 40 + 27695 AGTAGCATATGCATAGGTCATAGCATTTAGGGAGCCACCC -s mr.mrrefChr0 103168 40 + 130230 TGTAGTATAGTAATATACAGTTGTATTTAGGGCATCAATC -s simCow_chr6.simCow.chr6 109442 38 + 602619 GGTGGACTATGCACAGGTCA--GAATTTGGGGCCCCACCT -s simDog_chr6.simDog.chr6 505904 40 - 593897 AGCAGCATATGCATAGGACATATCATTCAGGGAGCCATTC -s simHuman_chr6.simHuman.chr6 104355 40 + 601863 TTTAGCATACGCATACATCATAGCATTTAGAGAGTGAACC -s simRat_chr6.simRat.chr6 100275 40 + 647215 CGTAATATACTAATATACAGTTGGCTTTAGGGCGCCATTC - -a -s simMouse_chr6.simMouse.chr6 108373 29 + 636262 ATAATATTGTTACAGTGGGTGTTAGATCA -s Anc0.Anc0refChr1 3284 29 - 62388 ATCAAATGGTAACAGTGGGTGTTAGATCA -s Anc1.Anc1refChr2 81297 29 + 144309 ATCAAATGGTAACAGTGGGTGTTAGATCA -s Anc2.Anc2refChr2 18897 29 + 27695 ATCAAATGGTAACAGTAGGTCTTAGATAA -s mr.mrrefChr0 103208 29 + 130230 ATAATATTGTTACAGTGGGTGTTAGATCA -s simCow_chr6.simCow.chr6 109551 12 + 602619 ACCAAATGGTAA----------------- -s simDog_chr6.simDog.chr6 505944 29 - 593897 ATCAGATGGTAACAGTAGGTCTTAGATAA -s simHuman_chr6.simHuman.chr6 104473 29 + 601863 ATCAAATGGTAACAGTGGGAGTTAGGTCA -s simRat_chr6.simRat.chr6 100315 28 + 647215 ATAATATTGTTACAGGGCCTGTTAGATC- - -a -s simMouse_chr6.simMouse.chr6 108402 30 + 636262 TTTTTGGCTTGGGTGACTTTGCTTCTGCAG -s Anc0.Anc0refChr1 3315 30 - 62388 TTTAGGGTTTGTGCAACTTTGGTTCAACAG -s Anc1.Anc1refChr2 81328 30 + 144309 TTTAGGGTTTGTGCAACTTTGGTTCAACAG -s Anc2.Anc2refChr2 18928 30 + 27695 TTTAGGGTTTGTGCAACTTTGGTTCAACAG -s mr.mrrefChr0 103237 30 + 130230 TTTTGGGTTTGTGCAACTTTGCTTCTGCAG -s simCow_chr6.simCow.chr6 109563 30 + 602619 TTGAGGGTTTGTGCAACTTTGGTTCAACCA -s simDog_chr6.simDog.chr6 505975 30 - 593897 TTTAGGGTTTGTGCAACTTTGGTACAACAG -s simHuman_chr6.simHuman.chr6 104504 30 + 601863 TTTAGGATTTGTGCAACTTTGGTTCAACAG -s simRat_chr6.simRat.chr6 100343 27 + 647215 ---TGGGTTTGTGCAGCTTTGCCTCTGCAT - -a -s simMouse_chr6.simMouse.chr6 108432 23 + 636262 CCCATTCACTCAAATCTATTGTT -s Anc0.Anc0refChr1 3349 23 - 62388 CACATTCACTCAAGCCTATTTTT -s Anc1.Anc1refChr2 81362 23 + 144309 CACATTCACTCAAGCCTATTTTT -s Anc2.Anc2refChr2 18962 23 + 27695 CATGTCTTTTCAAGCCTATTTTT -s mr.mrrefChr0 103267 23 + 130230 CACATTCACTCAAATCTATTGTT -s simCow_chr6.simCow.chr6 109597 21 + 602619 CATGTCTTT--AAGCCTATTTTC -s simDog_chr6.simDog.chr6 506009 17 - 593897 CATGTCTTTTCA------TCTTT -s simHuman_chr6.simHuman.chr6 104538 23 + 601863 CACATTCACTCAAGCCTATTTTT -s simRat_chr6.simRat.chr6 100370 22 + 647215 CACATTCATTCAAATTCGTTGA- - -a -s simMouse_chr6.simMouse.chr6 108455 9 + 636262 ATACCATAC -s Anc0.Anc0refChr1 3372 9 - 62388 ATACCTTAT -s Anc1.Anc1refChr2 81385 9 + 144309 ATACCTTAT -s Anc2.Anc2refChr2 18985 9 + 27695 ATAGCTTAT -s mr.mrrefChr0 103290 9 + 130230 ATACCATAC -s simCow_chr6.simCow.chr6 109619 9 + 602619 ATAGCTTAT -s simDog_chr6.simDog.chr6 506026 9 - 593897 GTAGCTTAC -s simHuman_chr6.simHuman.chr6 104561 9 + 601863 ATACCTCAT -s simRat_chr6.simRat.chr6 100392 9 + 647215 ATACCATGC - -a -s simMouse_chr6.simMouse.chr6 108464 20 + 636262 TTACAAGACAAGATGGTGGA -s Anc0.Anc0refChr1 3401 20 - 62388 TAACAAGACAAAACTCTGCA -s Anc1.Anc1refChr2 81414 20 + 144309 TAACAAGACAAAACTCTGCA -s Anc2.Anc2refChr2 19014 20 + 27695 CAAGAAGATAAAACTCTGCA -s mr.mrrefChr0 103299 20 + 130230 TTACAAGACAAGATGGTGGA -s simCow_chr6.simCow.chr6 109648 20 + 602619 CAAGAAGATAAAACTCTGCA -s simDog_chr6.simDog.chr6 506055 19 - 593897 CAAGAAGATGAA-CTCTGGA -s simHuman_chr6.simHuman.chr6 104590 20 + 601863 TGACAAGGCATAACTCTGCA -s simRat_chr6.simRat.chr6 100401 20 + 647215 TTACAAGACAAGATGGTGGA - -a -s simMouse_chr6.simMouse.chr6 108484 21 + 636262 AGAGGAGCTATAGATGGTTCT -s Anc0.Anc0refChr1 3421 21 - 62388 GGAAGGGCTAAAAATGGTTCT -s Anc1.Anc1refChr2 81434 21 + 144309 GGAAGGGCTAAAAATGGTTCT -s Anc2.Anc2refChr2 19034 21 + 27695 GGAAGGGCTAAAAATGGTTCC -s mr.mrrefChr0 103319 21 + 130230 AGAGGAGCTAAAGATGGTTCT -s simCow_chr6.simCow.chr6 109669 21 + 602619 GGGCGGGCTAAAAATGGTCCC -s simDog_chr6.simDog.chr6 506074 21 - 593897 GGAAGGGCTAAAAATGATTCC -s simHuman_chr6.simHuman.chr6 104610 21 + 601863 TGAAGGGCTAAAAATGGTTCT -s simRat_chr6.simRat.chr6 100421 21 + 647215 GGAGGAGATAAAGCTGGTTCC - -a -s simMouse_chr6.simMouse.chr6 108505 80 + 636262 ATCCATTTATGGACGGATTATGGATGATCTATAACTTGAATTTCGGGACCATTAGTAGTGTACACATAACTTTCTGCTGT -s Anc0.Anc0refChr1 3442 68 - 62388 GTCCAGTTATGGACAGATTAAGATTAATTTATAACTTGAATTCTGTGCCC---ATTAGTGCAAACACATCT--------- -s Anc1.Anc1refChr2 81455 71 + 144309 GTCCAGTTATGGACAGATTAAGATTAATTTATAACTTGAATTCTGTGCCC---ATTAGTGCAAACACATCTTT------T -s Anc2.Anc2refChr2 19055 68 + 27695 ATCCAGTTATGGACAGATTAAGATTAATTTATAACTTGGATTCTGTGCTC---ATTAGTGCAAACACATCT--------- -s mr.mrrefChr0 103340 80 + 130230 GTCCATTTATGGACAGATTATGGATGATCTATAACTTGAATTCTGTGCCCATTAGTAGTGTACACACAACTTTCTGCTGT -s simCow_chr6.simCow.chr6 109690 40 + 602619 ATCCAATTATGGACAGAATAAGATTAATTTGTAACTCGGA---------------------------------------- -s simDog_chr6.simDog.chr6 506095 68 - 593897 ATCCAGTGATGGACAGATTAAAACTAACTTATAACTTGGATTCTGTGCTC---ATTAGTGCAAACACATCT--------- -s simHuman_chr6.simHuman.chr6 104631 71 + 601863 GTCCAGTTATGGACAGATTAGGATTAATTTATAACTTGAATTCTGTGCCC---AATAGTGCAAACACAGCTTT------T -s simRat_chr6.simRat.chr6 100443 80 + 647215 GTCCATTTATGGACAGACTATGGGTGATCTATGACTTGAATTCTGTACCTATTAGTAGTGTACACACAACTGTCAGCTGT - -a -s simMouse_chr6.simMouse.chr6 108585 45 + 636262 ACTACATATCACTTTACCATTACCCTGCAATGAACAATCTGTATA -s Anc0.Anc0refChr1 3510 40 - 62388 -----GTGTCACTTAGCCATTACCCTACCTTAAACAAGCTGTATA -s Anc1.Anc1refChr2 81526 45 + 144309 ACTATGTGTCACTTAGCCATTACCCTACCTTAAACAAGCTGTATA -s Anc2.Anc2refChr2 19123 40 + 27695 -----GTGTCACTTAGCCATTACCCTACCTTCAACAAGCTGTATA -s mr.mrrefChr0 103420 45 + 130230 ACTATATATCACTTTGCCATTACCCTGCCATAAACAATCTGTATA -s simCow_chr6.simCow.chr6 109730 38 + 602619 -------GTCACTTAGCCATTACCCTACCTTGACCAAGATGTATG -s simDog_chr6.simDog.chr6 506163 40 - 593897 -----GTGTCGCCTAGCTATTGCCCTACCTTCAACAAGCTGTATA -s simHuman_chr6.simHuman.chr6 104702 45 + 601863 ACTATGTGTCACTTAGCCATTACCCTATCTTAAACAAGCTGTACA -s simRat_chr6.simRat.chr6 100524 42 + 647215 ACTATATATCACTTTGC---TACCCTGCCATAAACAATCTGTATA - -a -s simMouse_chr6.simMouse.chr6 108630 24 + 636262 ATCATTTTATCTCCTGTTTGTTTG -s Anc0.Anc0refChr1 3550 20 - 62388 ATCATGTTTTTTCC----TGTTTA -s Anc1.Anc1refChr2 81571 20 + 144309 ATCATGTTTTTTCC----TGTTTA -s Anc2.Anc2refChr2 19163 20 + 27695 ATCATGTTTTTTCC----TGTTTA -s mr.mrrefChr0 103465 24 + 130230 ATCATTTTATCTCCTGTTTGTTTG -s simCow_chr6.simCow.chr6 109768 20 + 602619 ATCACGTTTTTTCC----TGTTTA -s simDog_chr6.simDog.chr6 506203 20 - 593897 ATCATGTTTTTGCC----TGTTTA -s simHuman_chr6.simHuman.chr6 104811 20 + 601863 ATCATGTTTCTTCC----TGTCTA -s simRat_chr6.simRat.chr6 100566 24 + 647215 ATCATTTTATCTCCTGTTTGTTTG - -a -s simMouse_chr6.simMouse.chr6 108654 30 + 636262 GAACTGCTTTTTTGATGCACTCCTACAGCA -s Anc0.Anc0refChr1 3570 28 - 62388 GAGTTGCTTTTTTGATGCACTCC--AAGTA -s Anc1.Anc1refChr2 81591 30 + 144309 GAGTTGCTTTTTTGATGCACTCCTAAAGTA -s Anc2.Anc2refChr2 19183 28 + 27695 GAGTTTCTCTTTTGGTGCACTCT--AAGTA -s mr.mrrefChr0 103489 30 + 130230 GAACTGCTTTTTTGATGCACTCCTACAGCA -s simCow_chr6.simCow.chr6 109790 28 + 602619 GAGCTTCTCTATTGGTGCACTTT--AAGTT -s simDog_chr6.simDog.chr6 506223 23 - 593897 GAGTT-----TCTGGTGCACTCT--AACTA -s simHuman_chr6.simHuman.chr6 104831 30 + 601863 GAGTTGCTTTTTTGATGCACCTCTAAGGTG -s simRat_chr6.simRat.chr6 100590 30 + 647215 GAAATGCTTTTTTGATGCACTCCTACACCA - -a -s simMouse_chr6.simMouse.chr6 108684 12 + 636262 GAGGTAAACCCT -s Anc0.Anc0refChr1 3600 12 - 62388 AATGTAAACTCT -s Anc1.Anc1refChr2 81623 12 + 144309 AATGTAAACTCT -s Anc2.Anc2refChr2 19213 12 + 27695 AATGTAAACTCT -s mr.mrrefChr0 103521 12 + 130230 GATGTAAACCCT -s simCow_chr6.simCow.chr6 109820 12 + 602619 GACATGCACTCT -s simDog_chr6.simDog.chr6 506248 12 - 593897 AATGTAAGCTCT -s simHuman_chr6.simHuman.chr6 104863 12 + 601863 AATGTAAACTCT -s simRat_chr6.simRat.chr6 100622 12 + 647215 GATTTAAACCCT - -a -s simMouse_chr6.simMouse.chr6 108696 27 + 636262 GTCATCAATAAGTTATTGGTTACTTTT -s Anc0.Anc0refChr1 3612 14 - 62388 GTC----ATAAT---------TCCTCT -s Anc1.Anc1refChr2 81635 14 + 144309 GTC----ATAAT---------TCCTCT -s Anc2.Anc2refChr2 19225 14 + 27695 GTC----ATAAT---------TCCTCC -s mr.mrrefChr0 103533 27 + 130230 GTCATCAATAAGTTATTGGTTACTTCT -s simCow_chr6.simCow.chr6 109835 14 + 602619 GTC----CTAAT---------TCGTCC -s simDog_chr6.simDog.chr6 506260 14 - 593897 GCC----ATAAT---------TCCTCC -s simHuman_chr6.simHuman.chr6 104875 13 + 601863 GT-----ATAAA---------GCCTCT -s simRat_chr6.simRat.chr6 100634 27 + 647215 ATCATCAATAAGTCATCGGTTACTTCT - -a -s simMouse_chr6.simMouse.chr6 108723 23 + 636262 AAAATACCCAAAAAGAGCCATAT -s Anc0.Anc0refChr1 3626 23 - 62388 AAAGTTCTTAAAAAGTGCTATTT -s Anc1.Anc1refChr2 81649 23 + 144309 AAAGTTCTTAAAAAGTGCTATTT -s Anc2.Anc2refChr2 19239 23 + 27695 AAAATTCTTAAAAAGTGCTATTT -s mr.mrrefChr0 103560 23 + 130230 AAAGTACTTAAAAAGAGCCATAT -s simCow_chr6.simCow.chr6 109850 23 + 602619 AAAACTCTTAAAAAGTGCTATAT -s simDog_chr6.simDog.chr6 506274 23 - 593897 AAAATTCTTAAATAGTGCCATTT -s simHuman_chr6.simHuman.chr6 104888 23 + 601863 AAAGTTCTTAAAAAGTGCTATGT -s simRat_chr6.simRat.chr6 100661 23 + 647215 AAAGTACTTAAATAAAGCCATAT - -a -s simMouse_chr6.simMouse.chr6 108746 27 + 636262 TTGTTTGCCCTTTCAAGGTAGATTAGG -s Anc0.Anc0refChr1 3649 27 - 62388 ATGCTTACCTTGTGAAGATGGATTAGA -s Anc1.Anc1refChr2 81672 27 + 144309 ATGCTTACCTTGTGAAGATGGATTAGA -s Anc2.Anc2refChr2 19262 27 + 27695 ATGCTTTCCTTGTGAAGATGGATTAGA -s mr.mrrefChr0 103583 27 + 130230 TTGTTTACCTTGTCAAGGTAGATTAGG -s simCow_chr6.simCow.chr6 109873 27 + 602619 AGGCTTTCCTTGTAAAGATGGATTAGA -s simDog_chr6.simDog.chr6 506297 26 - 593897 ATGCTTTCCTTGTGTTG-TGGATTAGA -s simHuman_chr6.simHuman.chr6 104911 27 + 601863 ATGCTGACCTTGTGAAGATGGATTAGA -s simRat_chr6.simRat.chr6 100686 27 + 647215 TTGTTTACCTGGTCAAGGTAGATTAGG - -a -s simMouse_chr6.simMouse.chr6 108773 5 + 636262 ATAAC -s Anc0.Anc0refChr1 3676 5 - 62388 CTAAA -s Anc1.Anc1refChr2 81699 5 + 144309 CTAAA -s Anc2.Anc2refChr2 19289 5 + 27695 CTAAA -s mr.mrrefChr0 103610 5 + 130230 ATAAC -s simCow_chr6.simCow.chr6 109902 5 + 602619 CTAGA -s simDog_chr6.simDog.chr6 506323 5 - 593897 CTAAA -s simHuman_chr6.simHuman.chr6 104938 5 + 601863 GTAAA -s simRat_chr6.simRat.chr6 100713 5 + 647215 TTAAC - -a -s simMouse_chr6.simMouse.chr6 108778 20 + 636262 ACACATGTTTCTCATGCTAA -s Anc0.Anc0refChr1 3681 14 - 62388 ATACTTGTTTTC--TG---- -s Anc1.Anc1refChr2 81704 18 + 144309 ATACTTGTTTTC--TGCTAA -s Anc2.Anc2refChr2 19294 14 + 27695 ATGCTTGTTCTC--TG---- -s mr.mrrefChr0 103615 20 + 130230 ACACATGTTTCTCATGCTAA -s simCow_chr6.simCow.chr6 109912 14 + 602619 ATGCTTGTTCTC--TG---- -s simDog_chr6.simDog.chr6 506328 14 - 593897 TTGCTTGTTCTC--TG---- -s simHuman_chr6.simHuman.chr6 104943 18 + 601863 ATACCTGTTTGC--TGCTAA -s simRat_chr6.simRat.chr6 100718 20 + 647215 ACACTTGTCTCTCATGCTAA - -a -s simMouse_chr6.simMouse.chr6 108798 36 + 636262 ATGGCTTTTCTCTAAATCACTTTTGTTCCAGAGTGT -s Anc0.Anc0refChr1 3695 27 - 62388 -GGGCTT--------GTTACTTTTGTGACAGAGCAT -s Anc1.Anc1refChr2 81722 36 + 144309 GGGGCTTTTCCTTAAGTTACTTTTGTGACAGAGCAT -s Anc2.Anc2refChr2 19308 27 + 27695 -GGGTTT--------GTTCCTTTTGTGACAGAGCAT -s mr.mrrefChr0 103635 36 + 130230 ATGGCTTTTCTCTAAATCACTTTTGTTCCAGAGTGT -s simCow_chr6.simCow.chr6 109926 18 + 602619 -G-----------------CTTTTGTGACAAAGCAT -s simDog_chr6.simDog.chr6 506342 17 - 593897 -GGGTTT--------GTTC----------AGAGCAT -s simHuman_chr6.simHuman.chr6 104963 36 + 601863 GGGGCTTTTCCTTAAGTTACTTTTGTCACAGAGCAT -s simRat_chr6.simRat.chr6 100738 35 + 647215 ATAGCTTTTCTCTAAATCAATTTTGTTCC-GAGTGT - -a -s simMouse_chr6.simMouse.chr6 108834 14 + 636262 TCATTATTGTATAT -s Anc0.Anc0refChr1 3722 14 - 62388 ACATTTTGCAGTAT -s Anc1.Anc1refChr2 81758 14 + 144309 ACATTTTGCAGTAT -s Anc2.Anc2refChr2 19335 14 + 27695 ACATTTTGCAGTAT -s mr.mrrefChr0 103671 14 + 130230 TCATTATTGTATAT -s simCow_chr6.simCow.chr6 109944 14 + 602619 ACATTTTGCAGTAT -s simDog_chr6.simDog.chr6 506359 14 - 593897 ACATCTTGCAGTAG -s simHuman_chr6.simHuman.chr6 105042 14 + 601863 CCATTTTCCAGTAT -s simRat_chr6.simRat.chr6 100773 14 + 647215 TCATTATTGTATAT - -a -s simMouse_chr6.simMouse.chr6 108848 2 + 636262 AG -s Anc0.Anc0refChr1 3736 2 - 62388 AG -s Anc1.Anc1refChr2 81772 2 + 144309 AG -s Anc2.Anc2refChr2 19349 2 + 27695 AG -s mr.mrrefChr0 103685 2 + 130230 AG -s simCow_chr6.simCow.chr6 109958 2 + 602619 AG -s simDog_chr6.simDog.chr6 506381 2 - 593897 AG -s simHuman_chr6.simHuman.chr6 105056 2 + 601863 AG -s simRat_chr6.simRat.chr6 100787 2 + 647215 AG - -a -s simMouse_chr6.simMouse.chr6 108850 66 + 636262 TAGAGCTTTAGGAGGCTGACCAATATCTACTTGCTACTGATGCCTGTCTGCTGGGTGTCTGAATAC -s Anc0.Anc0refChr1 3738 65 - 62388 AAGAGCAGTGGGAAGCTGA-CAATATCTGCTCCCCATTGGTGTCTGTCCCCTCAGCACCTGTACAC -s Anc1.Anc1refChr2 81774 65 + 144309 AAGAGCAGTGGGAAGCTGA-CAATATCTGCTCCCCATTGGTGTCTGTCCCCTCAGCACCTGTACAC -s Anc2.Anc2refChr2 19351 65 + 27695 AAGAGCAGTGGGAAGCTCA-CAATATCTGCTTCCCATTGGTGTCTACCCCCTCAGCACCTGTACAC -s mr.mrrefChr0 103687 66 + 130230 TAGAGCTTTAGGAGGCTGACCAATATCTACTCCCCACTGATGCCTGTCTGCTGGGTATCTGTATAC -s simCow_chr6.simCow.chr6 109963 61 + 602619 AAGAGCAGTGGGAAGCTAA-CAATGTTTGCTTCCCATT----CCTCCCGCCTCAGCATCTGTACAC -s simDog_chr6.simDog.chr6 506383 64 - 593897 AAGAGCAAAGGGAAGCTCA-CAATATCTGCTTCCCATGGGTGTCTACCCCCTCAGCACCTGCTTA- -s simHuman_chr6.simHuman.chr6 105058 65 + 601863 AAGAGCAGTGGGAAGCTGA-CAACATCTGCTCCCCATTGGTGTCTGTCCCCCCAGCACCTGTACAC -s simRat_chr6.simRat.chr6 100789 62 + 647215 TAGAGCTATAGGATGCTGACCAATATCTACTCCACACTGATGCCTGGCTGCTTTG-ATCTGTG--- - -a -s simMouse_chr6.simMouse.chr6 108916 66 + 636262 TATAACCGCATGTAAGCCAAAACCCCAACACAAAGGCCAAAAATCCAAAGAATTGAGGTGTTCCCC -s Anc0.Anc0refChr1 3806 14 - 62388 T-------------------ATCCCCTA---------------------------------TTCCC -s Anc1.Anc1refChr2 81842 14 + 144309 T-------------------ATCCCCTA---------------------------------TTCCC -s Anc2.Anc2refChr2 19419 14 + 27695 T-------------------GTCCCCTA---------------------------------TTCCC -s mr.mrrefChr0 103753 45 + 130230 T-------------------AACCCCAACACAAAGGCCAAAAATCCAAAGAATT--GGTGTTCCCC -s simCow_chr6.simCow.chr6 110027 14 + 602619 T-------------------TTCCCCTA---------------------------------TTCTC -s simDog_chr6.simDog.chr6 506449 14 - 593897 T-------------------GTCCTCTA---------------------------------TGCCT -s simHuman_chr6.simHuman.chr6 105126 14 + 601863 T-------------------ATCCCCTA---------------------------------TTCCC -s simRat_chr6.simRat.chr6 100851 37 + 647215 --------------------AACTCCAACACAGAGGCAAAAGATCCAAAGAATT--------CCC- - -a -s simMouse_chr6.simMouse.chr6 108982 17 + 636262 CCAGGAATTGCTCTGCT -s Anc0.Anc0refChr1 3820 17 - 62388 CAAGAAATTGGTCCGCT -s Anc1.Anc1refChr2 81856 17 + 144309 CAAGAAATTGGTCCGCT -s Anc2.Anc2refChr2 19434 17 + 27695 CAAGAAATTGGTCCGCT -s mr.mrrefChr0 103798 17 + 130230 CCAGGAATTGCTCTGCT -s simCow_chr6.simCow.chr6 110042 17 + 602619 GAAGAAATCAGTCTACT -s simDog_chr6.simDog.chr6 506464 17 - 593897 CAAGAAATTGCTCCGCT -s simHuman_chr6.simHuman.chr6 105140 17 + 601863 TAAGAAATTGGTCCGCT -s simRat_chr6.simRat.chr6 100888 11 + 647215 ------ATTGCTCTGCT - -a -s simMouse_chr6.simMouse.chr6 108999 10 + 636262 AGAGAATTTA -s Anc0.Anc0refChr1 3840 10 - 62388 AGGGGATTTG -s Anc1.Anc1refChr2 81876 10 + 144309 AGGGGATTTG -s Anc2.Anc2refChr2 19454 10 + 27695 TGGGGATTTA -s mr.mrrefChr0 103815 10 + 130230 AGAGGATTTG -s simCow_chr6.simCow.chr6 110062 10 + 602619 GGAGGATTTA -s simDog_chr6.simDog.chr6 506484 10 - 593897 TGGGGAGTTA -s simHuman_chr6.simHuman.chr6 105160 10 + 601863 AGCAGATTTG -s simRat_chr6.simRat.chr6 100899 10 + 647215 AGAGGATTTG - -a -s simMouse_chr6.simMouse.chr6 109009 17 + 636262 ACTTACTCATAGTATCT -s Anc0.Anc0refChr1 3850 17 - 62388 ACTTACTAATTCTGTCA -s Anc1.Anc1refChr2 81886 17 + 144309 ACTTACTAATTCTGTCA -s Anc2.Anc2refChr2 19464 17 + 27695 CCTTACTAATTCTGTCA -s mr.mrrefChr0 103825 17 + 130230 ACTTACTCATACTATCT -s simCow_chr6.simCow.chr6 110072 17 + 602619 GCTTAGCAATTTTGCAA -s simDog_chr6.simDog.chr6 506494 17 - 593897 CCTTACTAATTCAGTCA -s simHuman_chr6.simHuman.chr6 105174 17 + 601863 ACTTACTGATTCTGTCA -s simRat_chr6.simRat.chr6 100909 17 + 647215 GCTTACTCATGCTATCT - -a -s simMouse_chr6.simMouse.chr6 109026 60 + 636262 CGCATAGCACTTGTGTCCTATGGCAGCAAACATGCCAGTACTTTTCCTACTCTCCCTGCT -s Anc0.Anc0refChr1 3867 59 - 62388 TGCACAGCATGTGTATTCTATGGCAGCAATCATTCCAGTTCTTTTTC-ACTATCTGTGCA -s Anc1.Anc1refChr2 81903 60 + 144309 TGCACAGCATGTGTATTCTATGGCAGCAATCATTCCAGTTCTTTTTCTACTATCTGTGCA -s Anc2.Anc2refChr2 19481 59 + 27695 TGCACAGCATGCATATTCTATAGCAGCAATCATTCCAGTTCTTTTTC-ACTATCCATGCA -s mr.mrrefChr0 103842 60 + 130230 TGCATAGCACTTGTGTCCTATGGCAGCAAACATGCCAGTACTTTTCCTACTCTCTGTGCA -s simCow_chr6.simCow.chr6 110089 54 + 602619 TGCACAGCATGCATATTCTATAACAGCAATCATTCTAGTACTTCTAT-TCTACCC----- -s simDog_chr6.simDog.chr6 506512 59 - 593897 TGCACAGCATGCATATTCTGTAGCAGCAGTCATTCCAGTTCTTTTTC-ACCCTCCATGCA -s simHuman_chr6.simHuman.chr6 105191 60 + 601863 TGCACAGCATCTGTATTCTATGGCTGCAATCATTCCAGTCCTCTTGCTACTATCTGCACA -s simRat_chr6.simRat.chr6 100926 60 + 647215 TGCATAGCACGTGTGTCCTATGGCAGCAAACGTGTCGGTACTTTTCCTACTGTCTGTGCA - -a -s simMouse_chr6.simMouse.chr6 109086 45 + 636262 ACCTTATTCATCTCTCACTTGCAAGTATGCACAATTTTAGGCTTT -s Anc0.Anc0refChr1 3927 44 - 62388 TTCTTTCTCATCTCTCACTAGCCATTATACACAC-ATTAAACTTT -s Anc1.Anc1refChr2 81964 44 + 144309 TTCTTTCTCATCTCTCACTAGCCATTATACACAC-ATTAAACTTT -s Anc2.Anc2refChr2 19541 44 + 27695 TTCTTTCTCATCTCTCACTAGCCATTATACACAC-ATTGAACTTT -s mr.mrrefChr0 103902 45 + 130230 ATCTTATTCATCTCTCACTAGCAAGTATGCACAATTTTAGGCTTT -s simCow_chr6.simCow.chr6 110143 42 + 602619 --CTTTCTCATCATTCACCAGCCATTATGCACAA-TATTGACATT -s simDog_chr6.simDog.chr6 506572 44 - 593897 TTCCTTTACACTTCTCACTAACCATTACACATTC-ATTGAGCTGT -s simHuman_chr6.simHuman.chr6 105252 44 + 601863 TTCTTTCTCATCTCTCACTAGCCATTATTCACAG-GTTAAACTTT -s simRat_chr6.simRat.chr6 100986 45 + 647215 ATCTTATTCATCTCTCACTAGCAAGTATGCACTAATTTCGGTCTT - -a -s simMouse_chr6.simMouse.chr6 109131 8 + 636262 TCACAACT -s Anc0.Anc0refChr1 3971 8 - 62388 TCGAGAGT -s Anc1.Anc1refChr2 82008 8 + 144309 TCGAGAGT -s Anc2.Anc2refChr2 19585 8 + 27695 TCGAGAGT -s mr.mrrefChr0 103947 8 + 130230 TCACAACT -s simCow_chr6.simCow.chr6 110190 8 + 602619 TCCAGAGT -s simDog_chr6.simDog.chr6 506616 8 - 593897 TTGAGACT -s simHuman_chr6.simHuman.chr6 105296 8 + 601863 TCTAGAGT -s simRat_chr6.simRat.chr6 101031 8 + 647215 TCACAACT - -a -s simMouse_chr6.simMouse.chr6 109139 26 + 636262 GCTTTTGTGTCATGTAGTTTTTTAAT -s Anc0.Anc0refChr1 3979 18 - 62388 GCTTTTATGTTA------TTTTT--T -s Anc1.Anc1refChr2 82016 18 + 144309 GCTTTTATGTTA------TTTTT--T -s Anc2.Anc2refChr2 19593 18 + 27695 GCTGAAATGTTA------TTTTT--T -s mr.mrrefChr0 103955 26 + 130230 GCTTTTGTGTCATGTAGTTTTTTAAT -s simCow_chr6.simCow.chr6 113374 18 + 602619 GCTGAAATGTCA------TTTGT--T -s simDog_chr6.simDog.chr6 506624 18 - 593897 GCTGAAATGTTA------TTATT--T -s simHuman_chr6.simHuman.chr6 105304 18 + 601863 TCTTTTATGTTA------TTTTT--C -s simRat_chr6.simRat.chr6 101039 26 + 647215 GCTTTTGTGCCATGTAATTTTTTAAT - -a -s simMouse_chr6.simMouse.chr6 109165 14 + 636262 AAGGTAATGGCTGA -s Anc0.Anc0refChr1 3997 14 - 62388 AAGGTGATGGCTGA -s Anc1.Anc1refChr2 82034 14 + 144309 AAGGTGATGGCTGA -s Anc2.Anc2refChr2 19611 14 + 27695 AAGGTGATGGCTGA -s mr.mrrefChr0 103981 14 + 130230 AAGGTAATGGCTGA -s simCow_chr6.simCow.chr6 113392 14 + 602619 AAGGTGATAGCTGA -s simDog_chr6.simDog.chr6 506642 14 - 593897 GAGGTGATGTCTGA -s simHuman_chr6.simHuman.chr6 105322 14 + 601863 AGGGTGCTGGCTGA -s simRat_chr6.simRat.chr6 101073 14 + 647215 AAGGCAATAGCTGA - -a -s simMouse_chr6.simMouse.chr6 109179 17 + 636262 GGAGGTCTTCTCACGTT -s Anc0.Anc0refChr1 4013 16 - 62388 AAAGGTCTCCTCA-GTT -s Anc1.Anc1refChr2 82050 16 + 144309 AAAGGTCTCCTCA-GTT -s Anc2.Anc2refChr2 19627 16 + 27695 ATAGGTCTCCTAA-GTT -s mr.mrrefChr0 103995 16 + 130230 GAAGGTCTTCTCA-GTT -s simCow_chr6.simCow.chr6 113408 16 + 602619 ACAGGTCTCCTAA-GAT -s simDog_chr6.simDog.chr6 506658 16 - 593897 ATAGGTCTCCTAA-GTT -s simHuman_chr6.simHuman.chr6 105338 16 + 601863 AAAGGTCCCCACA-GTT -s simRat_chr6.simRat.chr6 101087 16 + 647215 GAAGGTTTTCTAA-CTT - -a -s simMouse_chr6.simMouse.chr6 109196 42 + 636262 ACTTATGCTTAGAGACAGATCTAACTAAGAACTAAGTGCCAA -s Anc0.Anc0refChr1 4040 35 - 62388 ACCTATGCATTAAGACAGATCTAAC-------GAAGTGCCAA -s Anc1.Anc1refChr2 82077 35 + 144309 ACCTATGCATTAAGACAGATCTAAC-------GAAGTGCCAA -s Anc2.Anc2refChr2 19654 35 + 27695 ACCTATACACTAAGACAGATCTAAC-------GAAGTGCCAA -s mr.mrrefChr0 104011 42 + 130230 ACTTATGCTTAGAGACACATCTAACTAAGAACTAAGTGCTAA -s simCow_chr6.simCow.chr6 113435 35 + 602619 ACCTATACAATGAGACAAATTCAGT-------GTGGGGCTAG -s simDog_chr6.simDog.chr6 506685 35 - 593897 ACCTAAACACAAAGACAGACCTGAC-------GAAGTACCAA -s simHuman_chr6.simHuman.chr6 105366 35 + 601863 ACCCATGCATTTATAAAGATCTATC-------CAAGTGCCAA -s simRat_chr6.simRat.chr6 101103 42 + 647215 AAGTATACTTAGAGACACATCTAACCAAGAACTAAGCGCTAG - -a -s simMouse_chr6.simMouse.chr6 109238 21 + 636262 CCATGACCCTTGACTGTATAT -s Anc0.Anc0refChr1 4075 20 - 62388 CCATAACACGT-ACTGTACAT -s Anc1.Anc1refChr2 82112 21 + 144309 CCATAACACGTGACTGTACAT -s Anc2.Anc2refChr2 19689 20 + 27695 AAATTACAAGT-ACTATGCAT -s mr.mrrefChr0 104053 21 + 130230 CCATAACCCTTGACTGTATAT -s simCow_chr6.simCow.chr6 113470 18 + 602619 ACATTA--AGT-TCTGTGCAT -s simDog_chr6.simDog.chr6 506720 20 - 593897 AAATTACAAGT-ACTATGCAT -s simHuman_chr6.simHuman.chr6 105406 21 + 601863 CCCTAGCACCTGACAGCACTC -s simRat_chr6.simRat.chr6 101145 21 + 647215 CCATAACCTTCAACTGTATAT - -a -s simMouse_chr6.simMouse.chr6 109259 17 + 636262 TTCTATGTATTCATTCT -s Anc0.Anc0refChr1 4095 17 - 62388 TTCAATATCCACATAAT -s Anc1.Anc1refChr2 82133 17 + 144309 TTCAATATCCACATAAT -s Anc2.Anc2refChr2 19709 17 + 27695 TTCAGTGTCCACATAAT -s mr.mrrefChr0 104074 17 + 130230 TTCAATATCTTCATTCT -s simCow_chr6.simCow.chr6 113488 17 + 602619 TTCACTGTCCACATAAT -s simDog_chr6.simDog.chr6 506740 17 - 593897 TTCAGTGTTCGCATAAT -s simHuman_chr6.simHuman.chr6 105463 17 + 601863 CTCAATATCCACACAAT -s simRat_chr6.simRat.chr6 101166 17 + 647215 ATCAATATCTGCGTTCT - -a -s simMouse_chr6.simMouse.chr6 109276 19 + 636262 ATTAAAGACTATAGAGTAG -s Anc0.Anc0refChr1 4113 19 - 62388 AGTAAAGACTATAGATCAG -s Anc1.Anc1refChr2 82151 19 + 144309 AGTAAAGACTATAGATCAG -s Anc2.Anc2refChr2 19727 19 + 27695 GGTGAAGACCATAGATTGG -s mr.mrrefChr0 104091 19 + 130230 ATTAAAGACTATAGAGCAG -s simCow_chr6.simCow.chr6 113506 16 + 602619 TG---AGACAATAGATTGG -s simDog_chr6.simDog.chr6 506758 19 - 593897 GGTGAAGACCAGAGATTGG -s simHuman_chr6.simHuman.chr6 105481 19 + 601863 AGCAAAAGCTATAGATCAG -s simRat_chr6.simRat.chr6 101183 19 + 647215 ATTAAAGACTATAGACCAG - -a -s simMouse_chr6.simMouse.chr6 109295 23 + 636262 ACATCGTGGAAGAAGGGTGTAGC -s Anc0.Anc0refChr1 4140 23 - 62388 ACCTTGTAGTGGAAGGGTGTAGC -s Anc1.Anc1refChr2 82178 23 + 144309 ACCTTGTAGTGGAAGGGTGTAGC -s Anc2.Anc2refChr2 19754 23 + 27695 GCCTTGCAGTGGAAGGGTGCAGC -s mr.mrrefChr0 104110 23 + 130230 ACATCGTGGAAGAAGGGTGTAGC -s simCow_chr6.simCow.chr6 113530 23 + 602619 GCATCAAAGTAGAAGGGAGCAGT -s simDog_chr6.simDog.chr6 506785 23 - 593897 GCCTTGCAGTGGAAGGGTACAGC -s simHuman_chr6.simHuman.chr6 105508 23 + 601863 ACCTTGTACTGGAAGGGTGTAGT -s simRat_chr6.simRat.chr6 101202 22 + 647215 AC-TCATGGGAGAAGGGTGTAGC - -a -s simMouse_chr6.simMouse.chr6 109318 20 + 636262 TCTCTTGTGGCCACTACTGT -s Anc0.Anc0refChr1 4163 20 - 62388 TCTCTTGGGGCCCCTGCTGT -s Anc1.Anc1refChr2 82201 20 + 144309 TCTCTTGGGGCCCCTGCTGT -s Anc2.Anc2refChr2 19792 20 + 27695 TCTCTTAGGGCCCCTGCTGT -s mr.mrrefChr0 104133 20 + 130230 TCTCTTGTGGCCCCTACTGT -s simCow_chr6.simCow.chr6 113568 18 + 602619 TCTATTAG--CCCCTGCTCT -s simDog_chr6.simDog.chr6 506823 20 - 593897 TCTCTTAGGGCCCTTGGTGT -s simHuman_chr6.simHuman.chr6 105531 20 + 601863 TCTCTTGGGCCCCCTGCTGT -s simRat_chr6.simRat.chr6 101224 20 + 647215 TCTCTTGTGGCTCCTACTGT - -a -s simMouse_chr6.simMouse.chr6 109338 13 + 636262 CAAGATATATCAA -s Anc0.Anc0refChr1 4184 13 - 62388 CAGGTTATATCAT -s Anc1.Anc1refChr2 82222 13 + 144309 CAGGTTATATCAT -s Anc2.Anc2refChr2 19813 13 + 27695 CAGATTATATCCT -s mr.mrrefChr0 104153 13 + 130230 CAAGATATATCAT -s simCow_chr6.simCow.chr6 113587 13 + 602619 TGGATTATATCTA -s simDog_chr6.simDog.chr6 506844 13 - 593897 CAGATGCTATCCT -s simHuman_chr6.simHuman.chr6 105552 13 + 601863 CAGGTTATATCAT -s simRat_chr6.simRat.chr6 101244 13 + 647215 CAAGATATATCAT - -a -s simMouse_chr6.simMouse.chr6 109351 5 + 636262 GAGAT -s Anc0.Anc0refChr1 4220 5 - 62388 GAGAT -s Anc1.Anc1refChr2 82258 5 + 144309 GAGAT -s Anc2.Anc2refChr2 19869 5 + 27695 GAGAT -s mr.mrrefChr0 104188 5 + 130230 GAGAT -s simCow_chr6.simCow.chr6 113643 5 + 602619 GAGAG -s simDog_chr6.simDog.chr6 506897 5 - 593897 GAGAT -s simHuman_chr6.simHuman.chr6 105588 5 + 601863 GAGTT -s simRat_chr6.simRat.chr6 101279 5 + 647215 GAGCC - -a -s simMouse_chr6.simMouse.chr6 109356 4 + 636262 CTAT -s Anc0.Anc0refChr1 4245 4 - 62388 CTGT -s Anc1.Anc1refChr2 82283 4 + 144309 CTGT -s Anc2.Anc2refChr2 19899 4 + 27695 CTGT -s mr.mrrefChr0 104193 4 + 130230 CTAT -s simCow_chr6.simCow.chr6 113674 4 + 602619 CTGC -s simDog_chr6.simDog.chr6 506933 4 - 593897 CTTT -s simHuman_chr6.simHuman.chr6 105613 4 + 601863 CTGT -s simRat_chr6.simRat.chr6 101284 4 + 647215 TCAG - -a -s simMouse_chr6.simMouse.chr6 109360 32 + 636262 CAGTGGGGATCATAATAAACAAAAATACCTTA -s Anc0.Anc0refChr1 4249 32 - 62388 TGGTGGGGATCTTAATAAAGAAAACCAGCTCA -s Anc1.Anc1refChr2 82287 32 + 144309 TGGTGGGGATCTTAATAAAGAAAACCAGCTCA -s Anc2.Anc2refChr2 19903 32 + 27695 TGGTGGGGATCTTAATACTGAAAACCAGCTCA -s mr.mrrefChr0 104197 32 + 130230 CAGTGGGGATCATAATAAACAAAAATACCTCA -s simCow_chr6.simCow.chr6 113678 31 + 602619 TGGTGGTGAATGTAG-ACTGGAAACCTCCTCA -s simDog_chr6.simDog.chr6 506938 32 - 593897 TGGTGGGGATCTTAATACTGAAAGCCAGTTCA -s simHuman_chr6.simHuman.chr6 105617 32 + 601863 TGATGAGGAGCTCAATCAATAAAACCAGCTCA -s simRat_chr6.simRat.chr6 101288 32 + 647215 CAGTGGGGATCATAATAAACAAAAATACCTCA - -a -s simMouse_chr6.simMouse.chr6 109392 10 + 636262 CTGCTCTATA -s Anc0.Anc0refChr1 4290 10 - 62388 CTGCTTTATA -s Anc1.Anc1refChr2 82328 10 + 144309 CTGCTTTATA -s Anc2.Anc2refChr2 19944 10 + 27695 CTGCTTTATA -s mr.mrrefChr0 104229 10 + 130230 CTGCTTTATA -s simCow_chr6.simCow.chr6 113718 10 + 602619 CTGCTTCATA -s simDog_chr6.simDog.chr6 506979 10 - 593897 CTGTTTTGTA -s simHuman_chr6.simHuman.chr6 105658 10 + 601863 CTGCCTTATA -s simRat_chr6.simRat.chr6 101320 10 + 647215 ATGATTTGTA - -a -s simMouse_chr6.simMouse.chr6 109402 27 + 636262 ATGCACTATCTCATTGAGTGACCTATG -s Anc0.Anc0refChr1 4300 27 - 62388 ATGTACTACCTCTCTGAGTGACCTATA -s Anc1.Anc1refChr2 82338 27 + 144309 ATGTACTACCTCTCTGAGTGACCTATA -s Anc2.Anc2refChr2 19955 27 + 27695 ATGTACTACCTCTCTGAGTGACCCATA -s mr.mrrefChr0 104239 27 + 130230 ATGCACTATCTCATTGAGTGACCTATG -s simCow_chr6.simCow.chr6 113729 27 + 602619 AGATACTACCTCTCTGAGTGACCCATA -s simDog_chr6.simDog.chr6 506990 27 - 593897 GTGTACTACCTCTCTGAGTGACCCACA -s simHuman_chr6.simHuman.chr6 105668 27 + 601863 ATGTACTACCTCTCTGAGTGACCTATA -s simRat_chr6.simRat.chr6 101331 27 + 647215 ATGCATTATCTTGTTGAGTGAACTATG - -a -s simMouse_chr6.simMouse.chr6 109429 20 + 636262 CCCAGCAGCAATGTTTGTGG -s Anc0.Anc0refChr1 4327 20 - 62388 TATAGTGGCAAAGTTTTTGA -s Anc1.Anc1refChr2 82365 20 + 144309 TATAGTGGCAAAGTTTTTGA -s Anc2.Anc2refChr2 19982 20 + 27695 TATAGTGTCAAAGTTTTTGA -s mr.mrrefChr0 104266 20 + 130230 CGCAGCAGCAATGTTTGTGC -s simCow_chr6.simCow.chr6 113756 20 + 602619 TTCAGTGACAACATTTTTGG -s simDog_chr6.simDog.chr6 507017 20 - 593897 CATAGAGTGATAGATTTTGA -s simHuman_chr6.simHuman.chr6 105695 20 + 601863 TAGTGTGGCAAAGTTTTTGA -s simRat_chr6.simRat.chr6 101358 20 + 647215 CGCAGCAGTAATGTATGTGC -s simRat_chr6.simRat.chr6 101501 20 + 647215 CGCAGCAGCAATGTTTGTGC - -a -s simMouse_chr6.simMouse.chr6 109449 13 + 636262 TAGTGTAATTAAT -s Anc0.Anc0refChr1 4347 12 - 62388 TAAATTTTTTAA- -s Anc1.Anc1refChr2 82385 13 + 144309 TAAATTTTTTAAA -s Anc2.Anc2refChr2 20006 12 + 27695 TAAATTTTTTAA- -s mr.mrrefChr0 104286 13 + 130230 TGATGTGATTTAA -s simCow_chr6.simCow.chr6 113780 12 + 602619 TAAATTTTTTAA- -s simDog_chr6.simDog.chr6 507041 12 - 593897 TAAATTTTTTAA- -s simHuman_chr6.simHuman.chr6 105715 13 + 601863 TAAATTTTTTAAA -s simRat_chr6.simRat.chr6 101378 13 + 647215 TGATGTGATTTAA -s simRat_chr6.simRat.chr6 101521 13 + 647215 TGATGTGATTTAA - -a -s simMouse_chr6.simMouse.chr6 109462 10 + 636262 AAGTTTTGTG -s Anc1.Anc1refChr2 82398 10 + 144309 AATTTTTGTC -s mr.mrrefChr0 104299 10 + 130230 AATTTTTGTG -s simHuman_chr6.simHuman.chr6 105734 10 + 601863 AATTTTTGTC -s simRat_chr6.simRat.chr6 101391 10 + 647215 AATTTTTGTG -s simRat_chr6.simRat.chr6 101534 10 + 647215 AATTTTTGTG - -a -s simMouse_chr6.simMouse.chr6 109472 6 + 636262 ATGACT -s Anc0.Anc0refChr1 4359 5 - 62388 -TGCCC -s Anc1.Anc1refChr2 82411 6 + 144309 ATGCCC -s Anc2.Anc2refChr2 20018 5 + 27695 -TGCCC -s mr.mrrefChr0 104312 6 + 130230 ATGACT -s simCow_chr6.simCow.chr6 113792 5 + 602619 -TTGCC -s simDog_chr6.simDog.chr6 507053 5 - 593897 -TGCTT -s simHuman_chr6.simHuman.chr6 105747 6 + 601863 TGTCCC -s simRat_chr6.simRat.chr6 101404 6 + 647215 ATGACT -s simRat_chr6.simRat.chr6 101547 6 + 647215 ATGACC - -a -s simMouse_chr6.simMouse.chr6 109478 6 + 636262 TTTGAA -s Anc0.Anc0refChr1 4364 6 - 62388 TTTGAA -s Anc1.Anc1refChr2 82417 6 + 144309 TTTGAA -s Anc2.Anc2refChr2 20023 6 + 27695 TTTGAA -s mr.mrrefChr0 104318 6 + 130230 TTTGAA -s simCow_chr6.simCow.chr6 113799 6 + 602619 TTTGCA -s simDog_chr6.simDog.chr6 507058 6 - 593897 TTTCAC -s simHuman_chr6.simHuman.chr6 105753 6 + 601863 TTTGAA -s simRat_chr6.simRat.chr6 101410 6 + 647215 TTTGAA -s simRat_chr6.simRat.chr6 101553 6 + 647215 TATGAA - -a -s simMouse_chr6.simMouse.chr6 109484 19 + 636262 ACATGCAATCCAACCATAT -s Anc0.Anc0refChr1 4372 19 - 62388 ACATGCAATCCCACCAGAT -s Anc1.Anc1refChr2 82425 19 + 144309 ACATGCAATCCCACCAGAT -s Anc2.Anc2refChr2 20031 19 + 27695 ACATCCAATCCCACCAGAT -s mr.mrrefChr0 104324 19 + 130230 ACATGCAATCCACCCACAT -s simCow_chr6.simCow.chr6 113807 19 + 602619 ACATCCAATCCCACCAGAT -s simDog_chr6.simDog.chr6 507066 16 - 593897 ACAACCAATCCTACTA--- -s simHuman_chr6.simHuman.chr6 105761 19 + 601863 ACATGCAATCCCACCAGAT -s simRat_chr6.simRat.chr6 101416 19 + 647215 ACATGCAATCCACCCACAT -s simRat_chr6.simRat.chr6 101559 19 + 647215 ACATGCAATCCACCCACAT - -a -s simMouse_chr6.simMouse.chr6 109503 68 + 636262 TATCCAGTGACCACCTTGTCTCGTTTACTCTGTTTATATATTAAAAAATCCACTATGCAGCACTTCGG -s Anc0.Anc0refChr1 4395 53 - 62388 TCTCCACTAGCTGCCTTG---------TTCTGAT----TCTCAAGAAATCTACTATTCAGAGCT--AG -s Anc1.Anc1refChr2 82448 53 + 144309 TCTCCACTAGCTGCCTTG---------TTCTGAT----TCTCAAGAAATCTACTATTCAGAGCT--AG -s Anc2.Anc2refChr2 20054 53 + 27695 TCTCCACTAGCTGCCTTG---------CTCTGAT----TCTCAAGAATTTTACTATTCAGAGCT--AG -s mr.mrrefChr0 104343 64 + 130230 TGTCCAGTGACTGCCTTGTATTATTTATTCTGTT----TATTAAAAAATCCATTGTGCAACACTTCTG -s simCow_chr6.simCow.chr6 113839 52 + 602619 TTTCCACTTGCTGCCTTC---------ATCT-AT----TCAGAAGAAGTTTACTATTCAGAACT--TA -s simDog_chr6.simDog.chr6 507083 53 - 593897 TCTCCACTAGCTGCCTTG---------CTATGAT----TCTCAAGAATTTTTCTATTAAGAGCT--AG -s simHuman_chr6.simHuman.chr6 105784 53 + 601863 TCTCAATGAGATGCCTTG---------TTCTGAT----CCTCAAGAAATCTACTCTTCAGAGCT--AG -s simRat_chr6.simRat.chr6 101435 64 + 647215 TGTCCAGTGACTGCCTTGTATTATTTATTCTGTT----TATTAAAAAATCCATTGTGCAACACCTCTG -s simRat_chr6.simRat.chr6 101578 64 + 647215 TGTCCAGTGACTGCCTTGTATTATTTATTCCGTT----TATTAAAAAATCCATTGTGCAACACTTCTG - -a -s simMouse_chr6.simMouse.chr6 109571 3 + 636262 TGA -s Anc1.Anc1refChr2 82501 3 + 144309 AGA -s mr.mrrefChr0 104407 3 + 130230 AGA -s simHuman_chr6.simHuman.chr6 105837 3 + 601863 AGA -s simRat_chr6.simRat.chr6 101642 3 + 647215 AGA - -a -s simMouse_chr6.simMouse.chr6 109574 2 + 636262 CT -s Anc1.Anc1refChr2 82504 2 + 144309 TT -s mr.mrrefChr0 104410 2 + 130230 CT -s simHuman_chr6.simHuman.chr6 105840 2 + 601863 TT -s simRat_chr6.simRat.chr6 101499 2 + 647215 TG -s simRat_chr6.simRat.chr6 101645 2 + 647215 CT - -a -s simMouse_chr6.simMouse.chr6 109576 38 + 636262 GCCTCATTTTTAGAAAATGCAGCATCATTGGTTTATTG -s Anc0.Anc0refChr1 4448 37 - 62388 -CTTGATTTTTGGAAAGTTCAGCACTATTGTTTTCCTT -s Anc1.Anc1refChr2 82506 38 + 144309 GCTTGATTTTTGGAAAGTTCAGCACTATTGTTTTCCTT -s Anc2.Anc2refChr2 20107 37 + 27695 -CTTAATTTCTGGAAAGTTCAACACTATTGTTTTCCTA -s mr.mrrefChr0 104412 38 + 130230 GCCTGATTTTTAGAAAATGCAGCACCATTGGTTTATTT -s simCow_chr6.simCow.chr6 113891 37 + 602619 -CTTAATTTATGCAAAGTTCAACACTATTGTTTGCCAA -s simDog_chr6.simDog.chr6 507136 37 - 593897 -CTTAATCTCTGGAAAGTTCAACATGATTGTATTCCTA -s simHuman_chr6.simHuman.chr6 105842 38 + 601863 GCTTGATTATTGGAAAGTTGAGCACTCTTGTTTTCCCT -s simRat_chr6.simRat.chr6 101647 38 + 647215 GGCTGATTGTTAGAAAATGCGGCACCATTTGTTTATTT - -a -s simMouse_chr6.simMouse.chr6 109614 17 + 636262 AAATTAAAACCTGCGAG -s Anc0.Anc0refChr1 4486 17 - 62388 AAGTTAAAACCCGCAAG -s Anc1.Anc1refChr2 82545 17 + 144309 AAGTTAAAACCCGCAAG -s Anc2.Anc2refChr2 20145 17 + 27695 AAGTTAAAACCCGCAAG -s mr.mrrefChr0 104451 17 + 130230 AAATTAAAACCCGCGAG -s simCow_chr6.simCow.chr6 113929 17 + 602619 AAATTAAAACCCACGAG -s simDog_chr6.simDog.chr6 507174 17 - 593897 AAGTTAAAACCCGCAAG -s simHuman_chr6.simHuman.chr6 105881 17 + 601863 AAGTTAAGACCCGCAAG -s simRat_chr6.simRat.chr6 101686 17 + 647215 AAATTAAATCCCGCGAT - -a -s simMouse_chr6.simMouse.chr6 109631 14 + 636262 CAAAATCATTTGGT -s Anc0.Anc0refChr1 4505 14 - 62388 CTAAATGCTTCGGC -s Anc1.Anc1refChr2 82564 14 + 144309 CTAAATGCTTCGGC -s Anc2.Anc2refChr2 20164 14 + 27695 CCAAATGCTTCGGC -s mr.mrrefChr0 104468 14 + 130230 CTAAATCATTTGGT -s simCow_chr6.simCow.chr6 113948 14 + 602619 CCAAATGCTTCGGC -s simDog_chr6.simDog.chr6 507193 13 - 593897 C-AACTGCCTTGGC -s simHuman_chr6.simHuman.chr6 105900 14 + 601863 CTAAATGCTTCGTC -s simRat_chr6.simRat.chr6 101703 14 + 647215 GTAAACCATTTGGT - -a -s simMouse_chr6.simMouse.chr6 109645 2 + 636262 GA -s Anc0.Anc0refChr1 4519 2 - 62388 GA -s Anc1.Anc1refChr2 82578 2 + 144309 GA -s Anc2.Anc2refChr2 20180 2 + 27695 GA -s mr.mrrefChr0 104482 2 + 130230 GA -s simCow_chr6.simCow.chr6 113964 2 + 602619 GA -s simDog_chr6.simDog.chr6 507208 2 - 593897 GA -s simHuman_chr6.simHuman.chr6 105914 2 + 601863 GA -s simRat_chr6.simRat.chr6 101717 2 + 647215 GA - -a -s simMouse_chr6.simMouse.chr6 109647 6 + 636262 CTTAAA -s Anc0.Anc0refChr1 4529 6 - 62388 TTTAGA -s Anc1.Anc1refChr2 82588 6 + 144309 TTTAGA -s Anc2.Anc2refChr2 20190 6 + 27695 TTTAGA -s mr.mrrefChr0 104484 6 + 130230 CTTAAA -s simCow_chr6.simCow.chr6 113974 6 + 602619 TTTAGA -s simDog_chr6.simDog.chr6 507218 6 - 593897 TTCAGA -s simHuman_chr6.simHuman.chr6 105924 6 + 601863 TTTAGA -s simRat_chr6.simRat.chr6 101719 6 + 647215 CTTAAG - -a -s simMouse_chr6.simMouse.chr6 109653 4 + 636262 TACT -s Anc0.Anc0refChr1 4535 4 - 62388 AGGT -s Anc1.Anc1refChr2 82594 4 + 144309 AGGT -s Anc2.Anc2refChr2 20196 4 + 27695 AGGT -s mr.mrrefChr0 104490 4 + 130230 CACT -s simCow_chr6.simCow.chr6 113994 4 + 602619 AGGT -s simDog_chr6.simDog.chr6 507224 4 - 593897 AGGT -s simHuman_chr6.simHuman.chr6 105930 4 + 601863 GGAT -s simRat_chr6.simRat.chr6 101725 4 + 647215 CACC - -a -s simMouse_chr6.simMouse.chr6 109657 6 + 636262 CTTCGG -s Anc0.Anc0refChr1 4541 6 - 62388 AACCGG -s Anc1.Anc1refChr2 82600 6 + 144309 AACCGG -s Anc2.Anc2refChr2 20202 6 + 27695 AACACG -s mr.mrrefChr0 104496 6 + 130230 CTTCGG -s simCow_chr6.simCow.chr6 114000 6 + 602619 AAAACG -s simDog_chr6.simDog.chr6 507230 6 - 593897 AACACG -s simHuman_chr6.simHuman.chr6 105936 6 + 601863 ACGCGG -s simRat_chr6.simRat.chr6 101731 6 + 647215 CTTCGG - -a -s simMouse_chr6.simMouse.chr6 109663 10 + 636262 AGCATAGACG -s Anc0.Anc0refChr1 4547 10 - 62388 GGCATAGACG -s Anc1.Anc1refChr2 82606 10 + 144309 GGCATAGACG -s Anc2.Anc2refChr2 20208 10 + 27695 GGCACAGATG -s mr.mrrefChr0 104502 10 + 130230 AGCATAGACG -s simCow_chr6.simCow.chr6 114012 10 + 602619 GGCGCAGATG -s simDog_chr6.simDog.chr6 507236 5 - 593897 AGCA-----G -s simHuman_chr6.simHuman.chr6 105942 10 + 601863 GGCATAGACG -s simRat_chr6.simRat.chr6 101737 10 + 647215 AGCATAGACG - -a -s simMouse_chr6.simMouse.chr6 109673 3 + 636262 GTG -s Anc0.Anc0refChr1 4559 3 - 62388 AAG -s Anc1.Anc1refChr2 82618 3 + 144309 AAG -s Anc2.Anc2refChr2 20220 3 + 27695 AAG -s mr.mrrefChr0 104512 3 + 130230 AGG -s simCow_chr6.simCow.chr6 114022 3 + 602619 AAG -s simDog_chr6.simDog.chr6 507243 3 - 593897 AAG -s simHuman_chr6.simHuman.chr6 105954 3 + 601863 AAG -s simRat_chr6.simRat.chr6 101747 3 + 647215 AGG - -a -s simMouse_chr6.simMouse.chr6 109676 10 + 636262 CTCGGGGTTC -s Anc0.Anc0refChr1 4562 10 - 62388 CTCGGGGCTC -s Anc1.Anc1refChr2 82621 10 + 144309 CTCGGGGCTC -s Anc2.Anc2refChr2 20223 10 + 27695 CTCGGAGCTC -s mr.mrrefChr0 104515 10 + 130230 CTCGGGGTTC -s simCow_chr6.simCow.chr6 114025 10 + 602619 CTCGGTGCTC -s simDog_chr6.simDog.chr6 507247 10 - 593897 CTCGGAACTC -s simHuman_chr6.simHuman.chr6 105957 10 + 601863 CTCGGGGCTC -s simRat_chr6.simRat.chr6 101750 10 + 647215 CTCAGGGTTC - -a -s simMouse_chr6.simMouse.chr6 109686 80 + 636262 GTGCGACGGGTCTAATTCACCCAGTAGTTAGTCGGCCCTGCCGGAGATCTACTCCCTATCCTAGACAGATCGGCTAACAG -s Anc0.Anc0refChr1 4572 77 - 62388 TAACGAGGAGTCTAGTTCACCGAG-AGTTATTCTGTCGT--CGAGATTTTATTCCCTCACCTCCACAGATCGGCTAACAG -s Anc1.Anc1refChr2 82631 77 + 144309 TAACGAGGAGTCTAGTTCACCGAG-AGTTATTCTGTCGT--CGAGATTTTATTCCCTCACCTCCACAGATCGGCTAACAG -s Anc2.Anc2refChr2 20242 77 + 27695 TAACGAGGAGTCTAGTCCACCGAG-AGTTATTCTATCGT--CGAGATTTTGTTCCCTCACCTCCACAGATCGGATAACAG -s mr.mrrefChr0 104525 80 + 130230 GTACGAGGGGTCTAATTCACCCAGTAGTTAGTCGGCCCTGCCGGAGATCTATTCCCTATCCTACACAGATCGGCTAACAG -s simCow_chr6.simCow.chr6 114044 71 + 602619 TAACAAGGGGTCTAGTACACCCAG-AGTTATTTTATCGT--CGAGATCTTG------CACCTGCACACATCGGTTAACAG -s simDog_chr6.simDog.chr6 507266 69 - 593897 AAACGAGGAGTCTAGTCCACCGAA-AGTTATTC----------AGATTTCGTTCCCTCACCTCCACAGATGGGATAACAT -s simHuman_chr6.simHuman.chr6 105967 75 + 601863 TAACGAGGAGATTAGTTCACCAAG-AGTTATTCTGTCTT--TGATATTTTATTCCCTCACC--CACAGATCGGCTAACAG -s simRat_chr6.simRat.chr6 101760 77 + 647215 GTACGAGGGGTCTAACTCACCCGGTAGTTAGTCGACCCTGCAAGAGAT---TTCCCTATCCTACACAGATCGGCTATCAG - -a -s simMouse_chr6.simMouse.chr6 109766 26 + 636262 CTTCGAACGCTTAATCCTCGTCTCTT -s Anc0.Anc0refChr1 4655 26 - 62388 CTCTGCATGCTGAGTCCTCGTCTCTT -s Anc1.Anc1refChr2 82714 26 + 144309 CTCTGCATGCTGAGTCCTCGTCTCTT -s Anc2.Anc2refChr2 20325 26 + 27695 CTCTTCATGCTGAGTTCTCGTTTCTT -s mr.mrrefChr0 104605 26 + 130230 CTTCGCACGCTTAGTCCTCGTCTCTT -s simCow_chr6.simCow.chr6 114126 26 + 602619 CACTAGATGCTGAGCTCCTGTTTCTG -s simDog_chr6.simDog.chr6 507335 26 - 593897 CTCTTCATGCTTAGTTCTCGTTTCTT -s simHuman_chr6.simHuman.chr6 106048 26 + 601863 CTCTGCGTGCTGAGTCCTCATCTCTT -s simRat_chr6.simRat.chr6 101837 26 + 647215 CTTCCCACGCTTAGTCCTTGTCTTTT - -a -s simMouse_chr6.simMouse.chr6 109792 13 + 636262 GGTCTCTCTTAAA -s Anc0.Anc0refChr1 4688 13 - 62388 GCTATCTCCTAGG -s Anc1.Anc1refChr2 82747 13 + 144309 GCTATCTCCTAGG -s Anc2.Anc2refChr2 20358 13 + 27695 GCTATCTCCTAGG -s mr.mrrefChr0 104638 13 + 130230 GGTATCTCTTAGA -s simCow_chr6.simCow.chr6 114159 13 + 602619 GCTATCTCCAACA -s simDog_chr6.simDog.chr6 507368 13 - 593897 GCTATGGCCTAGG -s simHuman_chr6.simHuman.chr6 106081 13 + 601863 GCTATCTTCTTGG -s simRat_chr6.simRat.chr6 101870 13 + 647215 GGTATCTCTTAGA - -a -s simMouse_chr6.simMouse.chr6 109805 8 + 636262 GCGGTTGG -s Anc0.Anc0refChr1 4702 8 - 62388 GCGGCTAG -s Anc1.Anc1refChr2 82761 8 + 144309 GCGGCTAG -s Anc2.Anc2refChr2 20372 8 + 27695 GCTGCTAA -s mr.mrrefChr0 104652 8 + 130230 GCGGTTGG -s simCow_chr6.simCow.chr6 114173 1 + 602619 G------- -s simDog_chr6.simDog.chr6 507382 8 - 593897 GCTGCTAA -s simHuman_chr6.simHuman.chr6 106095 8 + 601863 GCGGCTAG -s simRat_chr6.simRat.chr6 101884 8 + 647215 GCGGTTGG - -a -s simMouse_chr6.simMouse.chr6 109813 11 + 636262 CGGCTTTCAGT -s Anc0.Anc0refChr1 4710 11 - 62388 CAGCTTTCCTC -s Anc1.Anc1refChr2 82769 11 + 144309 CAGCTTTCCTC -s Anc2.Anc2refChr2 20380 11 + 27695 TAGCTTTCCTC -s mr.mrrefChr0 104660 11 + 130230 CAGCTTTCCTT -s simCow_chr6.simCow.chr6 114174 9 + 602619 --GCTTTCCTC -s simDog_chr6.simDog.chr6 507396 11 - 593897 TATCTTTCCCC -s simHuman_chr6.simHuman.chr6 106103 11 + 601863 CAGCTCTCCTC -s simRat_chr6.simRat.chr6 101892 11 + 647215 CAGCTTTTCTT - -a -s simMouse_chr6.simMouse.chr6 109824 2 + 636262 AC -s Anc0.Anc0refChr1 4721 2 - 62388 AC -s Anc1.Anc1refChr2 82780 2 + 144309 AC -s Anc2.Anc2refChr2 20391 2 + 27695 TC -s mr.mrrefChr0 104671 2 + 130230 AC -s simCow_chr6.simCow.chr6 114183 2 + 602619 TC -s simDog_chr6.simDog.chr6 507407 2 - 593897 TC -s simHuman_chr6.simHuman.chr6 106149 2 + 601863 AC -s simRat_chr6.simRat.chr6 101903 2 + 647215 AC - -a -s simMouse_chr6.simMouse.chr6 109826 22 + 636262 CCCACCAGGAGAGGCGTGCTCT -s Anc0.Anc0refChr1 4723 21 - 62388 T-TACCAGGAGAGGCGTGTTCT -s Anc1.Anc1refChr2 82782 22 + 144309 TGTACCAGGAGAGGCGTGTTCT -s Anc2.Anc2refChr2 20393 21 + 27695 T-TACCAGGAGAGACGTGTTCT -s mr.mrrefChr0 104673 22 + 130230 CGCACCAGGAGAGGCGTGTTCT -s simCow_chr6.simCow.chr6 114186 20 + 602619 T-TACCGGGAGAGACGTGCTC- -s simDog_chr6.simDog.chr6 507409 21 - 593897 T-TACCAGGAGAGACGTGTTCT -s simHuman_chr6.simHuman.chr6 106151 22 + 601863 TGTACCAGGAGAGGCGTGTTCT -s simRat_chr6.simRat.chr6 101905 8 + 647215 CGC--------------GTTCT - -a -s simMouse_chr6.simMouse.chr6 109848 46 + 636262 GGCCCAAGGCATAGGGATAGCCGGTTAAATTCGGAGAGCAAGGCGC -s Anc0.Anc0refChr1 4753 46 - 62388 GGCCCAAGGCGTAGGGACATCCCGTTCATGTTGGAGAGCAGGGCGC -s Anc1.Anc1refChr2 82813 46 + 144309 GGCCCAAGGCGTAGGGACATCCCGTTCATGTTGGAGAGCAGGGCGC -s Anc2.Anc2refChr2 20423 46 + 27695 GGCCCAAGGCGTAGGGCCATTCCGTCCATGTTGGAAAGCAGGGGGC -s mr.mrrefChr0 104695 46 + 130230 GGCCCAAGGCATAGGGATATCCGGTTAAATTCGGAGAGCAAGGCGC -s simCow_chr6.simCow.chr6 114209 46 + 602619 GGCCCAAGGCGTAGGGCCATTCCGTCAGTGTTGGATAACAGGGAGC -s simDog_chr6.simDog.chr6 507436 20 - 593897 --------------------------CATGTTGGAAAGCAAGGGGC -s simHuman_chr6.simHuman.chr6 106188 46 + 601863 GGTCCAAGGCGTAGGCACATCCTGTTCATGTTGGAGAGCAGGGCGT -s simRat_chr6.simRat.chr6 101913 46 + 647215 GACCCAAGGCATAGGGATATCCCGTAAACTTCGGAGGACATGGCGC - -a -s simMouse_chr6.simMouse.chr6 109894 10 + 636262 TTATAGTGCG -s Anc0.Anc0refChr1 4801 10 - 62388 TTATTGTTTG -s Anc1.Anc1refChr2 82861 10 + 144309 TTATTGTTTG -s Anc2.Anc2refChr2 20471 10 + 27695 TCATTGTTTG -s mr.mrrefChr0 104743 10 + 130230 TTATAGTTCG -s simCow_chr6.simCow.chr6 114257 10 + 602619 TCATTGTGTG -s simDog_chr6.simDog.chr6 507458 10 - 593897 TTACTGTTTG -s simHuman_chr6.simHuman.chr6 106240 10 + 601863 ttactgtttg -s simRat_chr6.simRat.chr6 101961 10 + 647215 TTATAGTTCG - -a -s simMouse_chr6.simMouse.chr6 109904 6 + 636262 AGCGAC -s Anc0.Anc0refChr1 4811 6 - 62388 AGCGAC -s Anc1.Anc1refChr2 82871 6 + 144309 AGCGAC -s Anc2.Anc2refChr2 20481 6 + 27695 AGCGAC -s mr.mrrefChr0 104753 6 + 130230 AGCGAC -s simCow_chr6.simCow.chr6 114267 6 + 602619 AGCGAC -s simDog_chr6.simDog.chr6 507468 6 - 593897 AGCGCC -s simHuman_chr6.simHuman.chr6 106893 6 + 601863 aaCGAC -s simRat_chr6.simRat.chr6 101971 6 + 647215 AGCGGT - -a -s simMouse_chr6.simMouse.chr6 109910 55 + 636262 CAGAGTTATATTAGGCGCACGTGACAGTATAATTTTAGGGTTCAAAGCTCAACCC -s Anc0.Anc0refChr1 4820 55 - 62388 CAGAGTAATATCCGGTGCACGCGGTAGTAAGCCTCTACGGTGGGAATCTCGGGCC -s Anc1.Anc1refChr2 82880 55 + 144309 CAGAGTAATATCCGGTGCACGCGGTAGTAAGCCTCTACGGTGGGAATCTCGGGCC -s Anc2.Anc2refChr2 20490 55 + 27695 CAGAGTAATATCCGGCGCACGCGGTAGCGAGCCTCTCCGGTGGGAATCTCGGGCC -s mr.mrrefChr0 104759 55 + 130230 CAGAGTTATATTAGGTGCACGTGGCAGTATAATTTTAGGGTTCAAAGCTCAACCC -s simCow_chr6.simCow.chr6 114276 55 + 602619 CACAGTATTGTTCAGATTAACCGGTAGCGCGCCTCTCTGGTCGGAATCTCAGGCT -s simDog_chr6.simDog.chr6 507477 55 - 593897 TAGAGTAATACCAGGCGCACGCGGTAGCGAACATCTCCGGCGGGAATCCCGAGCC -s simHuman_chr6.simHuman.chr6 106902 55 + 601863 CAGAGTAATATCCGGTACACGCGGTAGTAAGCCTCTACAGTGGGAATCTCGGGCC -s simRat_chr6.simRat.chr6 101977 55 + 647215 CAGAGTTATATTAGGTGCATGTTGCAGTATAATTTTAGGGTTAAAAGCTCAACCC - -a -s simMouse_chr6.simMouse.chr6 109965 10 + 636262 ACGGGCGTGC -s Anc0.Anc0refChr1 4875 10 - 62388 ACGGGCCTTC -s Anc1.Anc1refChr2 82935 10 + 144309 ACGGGCCTTC -s Anc2.Anc2refChr2 20546 10 + 27695 ACGGGCCTTC -s mr.mrrefChr0 104814 10 + 130230 ACGGGCGTGC -s simCow_chr6.simCow.chr6 114332 10 + 602619 ACGGGCCTTC -s simDog_chr6.simDog.chr6 507533 10 - 593897 ACGGGACTCA -s simHuman_chr6.simHuman.chr6 106957 10 + 601863 ACGCGCCTTC -s simRat_chr6.simRat.chr6 102032 10 + 647215 ACGGGCGTGC - -a -s simMouse_chr6.simMouse.chr6 109975 29 + 636262 CAAACTCCCGAATGGGGGGGCTGGTGTTA -s Anc0.Anc0refChr1 4891 29 - 62388 CAAACTCTTGAATTGGAGAGCTTGTGTTA -s Anc1.Anc1refChr2 82951 29 + 144309 CAAACTCTTGAATTGGAGAGCTTGTGTTA -s Anc2.Anc2refChr2 20562 29 + 27695 CAAACTCTTGAATTGGAGAGCTTGTGTTA -s mr.mrrefChr0 104824 29 + 130230 CAAACTCCCGAATGGGGGGGCTTGTGTTA -s simCow_chr6.simCow.chr6 114348 29 + 602619 TAAACTCTTGTATTGGAGAGCTTGTGTTA -s simDog_chr6.simDog.chr6 507549 29 - 593897 CAAACTCTTGAATTGGGGGTCTTGTGGTA -s simHuman_chr6.simHuman.chr6 106973 29 + 601863 CAAACTCTTGAATTGTAGAGCTCGTGTTA -s simRat_chr6.simRat.chr6 102042 29 + 647215 CAAACTCCCAAATGGGGGGGTCTGTCTTA - -a -s simMouse_chr6.simMouse.chr6 110004 4 + 636262 TTGT -s Anc0.Anc0refChr1 4920 4 - 62388 TTGT -s Anc1.Anc1refChr2 82980 4 + 144309 TTGT -s Anc2.Anc2refChr2 20591 4 + 27695 TTGT -s mr.mrrefChr0 104853 4 + 130230 TTGT -s simCow_chr6.simCow.chr6 114377 4 + 602619 TTAC -s simDog_chr6.simDog.chr6 507578 4 - 593897 TTGT -s simHuman_chr6.simHuman.chr6 107003 4 + 601863 TTGT -s simRat_chr6.simRat.chr6 102071 4 + 647215 TTGT - -a -s simMouse_chr6.simMouse.chr6 110008 62 + 636262 GGTGGCTTTGCACTGGCTAAACTTGAGCACTAGGATGTAGAAAAGTTAGCTGGCTGCTGTGA -s Anc0.Anc0refChr1 4924 57 - 62388 GGTGGTCTTGTACTGGCTACACTTGAGCACTA----GTTGAAAGGTCAGCCAGGTGCTG-GG -s Anc1.Anc1refChr2 82984 57 + 144309 GGTGGTCTTGTACTGGCTACACTTGAGCACTA----GTTGAAAGGTCAGCCAGGTGCTG-GG -s Anc2.Anc2refChr2 20595 57 + 27695 GGTGGTCTTGTACTGGCTACACTTGAGCACTA----GTTAATAGGGCAGCCAGGTGTTG-GG -s mr.mrrefChr0 104857 62 + 130230 GGTGGCTTTGCACTGGCTAAACTTGAGCACTAGGATGTAGAAAGGTTAGCTAGCTGCTGTGA -s simCow_chr6.simCow.chr6 114393 57 + 602619 GATGGTCTTGTACTCACTACACTTGAGCACTA----GTTAATAGGGCAGCCAGGTGTTG-GG -s simDog_chr6.simDog.chr6 507582 57 - 593897 GGTGGTATTGCACTGGCTACACTTGACCACTA----GTTAATAGGGCAGCCGGGTGTGG-AA -s simHuman_chr6.simHuman.chr6 107007 57 + 601863 GGTGGTCTTGTGTTGCTTACACTTGAGCACTA----GTTGAAAGGTCAGCCAAGTACTG-GG -s simRat_chr6.simRat.chr6 102075 62 + 647215 GGTGGCTTTGCACTGGCTAAAACTGAGCACTAAGATGTCAAAAGGTTAGCTACCTGCCATGA - -a -s simMouse_chr6.simMouse.chr6 110070 27 + 636262 AGCAGATTCCTGATTTTGACTTTCCCA -s Anc0.Anc0refChr1 4981 27 - 62388 AGAGGGTTCCTGACTTTTTCTTACCCA -s Anc1.Anc1refChr2 83041 27 + 144309 AGAGGGTTCCTGACTTTTTCTTACCCA -s Anc2.Anc2refChr2 20652 27 + 27695 GGAGGGTTCCTGGCTTTTTCTTACCCA -s mr.mrrefChr0 104919 27 + 130230 AGCAGGTTCCTGACTTTTACTTTCCCA -s simCow_chr6.simCow.chr6 114451 27 + 602619 TGAAGGTGCCTCGCTTCTTCTTACCCA -s simDog_chr6.simDog.chr6 507639 23 - 593897 GGAGGGCTCCAGGCTGTT----ACCCA -s simHuman_chr6.simHuman.chr6 107064 27 + 601863 AGAGGGTTCCTGACTTTTTTTGGCCCA -s simRat_chr6.simRat.chr6 102137 27 + 647215 AGCAGGTTCTTGACTTTTACTTTCCCA - -a -s simMouse_chr6.simMouse.chr6 110097 21 + 636262 ACTCCCCACACTATTGGTACA -s Anc0.Anc0refChr1 5016 20 - 62388 ACTCCCCCCACTATC-ATTCA -s Anc1.Anc1refChr2 83076 20 + 144309 ACTCCCCCCACTATC-ATTCA -s Anc2.Anc2refChr2 20687 20 + 27695 ACTCCCCCCACTATC-ATTGA -s mr.mrrefChr0 104946 21 + 130230 GCTCCCCACACTATTGATGCA -s simCow_chr6.simCow.chr6 114486 20 + 602619 ACTACCCACACTATT-ATTGG -s simDog_chr6.simDog.chr6 507670 20 - 593897 ACTCCTCCCACTATC-AATGA -s simHuman_chr6.simHuman.chr6 107099 20 + 601863 ACTCCCCCCAATATC-ATTCA -s simRat_chr6.simRat.chr6 102164 21 + 647215 GCTTCCCACACTATTGATGCA - -a -s simMouse_chr6.simMouse.chr6 110118 1 + 636262 T -s Anc0.Anc0refChr1 5036 1 - 62388 T -s Anc1.Anc1refChr2 83096 1 + 144309 T -s Anc2.Anc2refChr2 20707 1 + 27695 T -s mr.mrrefChr0 104967 1 + 130230 T -s simCow_chr6.simCow.chr6 114506 1 + 602619 T -s simDog_chr6.simDog.chr6 507691 1 - 593897 T -s simHuman_chr6.simHuman.chr6 107119 1 + 601863 T -s simRat_chr6.simRat.chr6 102185 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 110119 17 + 636262 CCTTGATCATAGGGCAG -s Anc0.Anc0refChr1 5037 17 - 62388 CCTTGACCATGAGGTAG -s Anc1.Anc1refChr2 83097 17 + 144309 CCTTGACCATGAGGTAG -s Anc2.Anc2refChr2 20708 17 + 27695 CCTTGACCATGAGGTAG -s mr.mrrefChr0 104968 17 + 130230 CCTTGATCATAGGGTAG -s simCow_chr6.simCow.chr6 114509 17 + 602619 CCTTGACCATGAGGTAA -s simDog_chr6.simDog.chr6 507692 17 - 593897 CCTTGACATGGAGGTAG -s simHuman_chr6.simHuman.chr6 107120 17 + 601863 CTTTGACCATGAGTTAG -s simRat_chr6.simRat.chr6 102186 17 + 647215 TCTTGATTATAGGGTAG - -a -s simMouse_chr6.simMouse.chr6 110136 6 + 636262 CTGTCT -s Anc0.Anc0refChr1 5056 6 - 62388 CTGGCT -s Anc1.Anc1refChr2 83116 6 + 144309 CTGGCT -s Anc2.Anc2refChr2 20727 6 + 27695 CTGGCT -s mr.mrrefChr0 104985 6 + 130230 CTGTCT -s simCow_chr6.simCow.chr6 114528 6 + 602619 CTGGCT -s simDog_chr6.simDog.chr6 507711 3 - 593897 TTG--- -s simHuman_chr6.simHuman.chr6 107139 6 + 601863 CCGGTT -s simRat_chr6.simRat.chr6 102203 6 + 647215 CTGTCT - -a -s simMouse_chr6.simMouse.chr6 110142 48 + 636262 TTGAAAGTTTATGCACAAGTAGTTGCACTACTTCTTAAGCTCGGCCCA -s Anc0.Anc0refChr1 5062 1 - 62388 T----------------------------------------------- -s Anc1.Anc1refChr2 83122 1 + 144309 T----------------------------------------------- -s Anc2.Anc2refChr2 20733 1 + 27695 T----------------------------------------------- -s mr.mrrefChr0 104991 48 + 130230 TTGAAAGTTTATGCATCAGTAGTTGCACTACTTCTTAAGCTCGGCCCA -s simCow_chr6.simCow.chr6 114612 1 + 602619 T----------------------------------------------- -s simHuman_chr6.simHuman.chr6 107145 1 + 601863 T----------------------------------------------- -s simRat_chr6.simRat.chr6 102209 48 + 647215 TTGAAAGTTTATGCATCAGTAGTTGCACTATTTCATAAGCTCAGCCAA - -a -s simMouse_chr6.simMouse.chr6 110190 84 + 636262 TCACATGGATTGTCAATCAAATCACTCACTGATCTCAACAAGCTGTTCAGTCTTCCTGTGTGTCCTTGGCATGATCCATTTGGG -s Anc0.Anc0refChr1 5063 45 - 62388 -----------------CAAAGTGCTAGCTGCTCTC-GCAGGCTGTTA---------------------CATGACTCTTTTGGG -s Anc1.Anc1refChr2 83123 67 + 144309 -----------------CAAAGTGCTAGCTGCTCTCAGCAGGCTGTTAGAAATTCCTGTGTCTCCTTGTCATGACTCTTTTGGG -s Anc2.Anc2refChr2 20734 45 + 27695 -----------------CAGAGTAGCAGCTGCTCTT-GCCGGCTAATA---------------------CACAACCCTTCCAGG -s mr.mrrefChr0 105039 84 + 130230 TCACATGGATTGTCAATCAAAGTGCTCACTGATCTCAACAGGCTGTTCAGTCTTCCTGTGTGTCCTTGTCATGATTCATTTGGG -s simCow_chr6.simCow.chr6 114613 45 + 602619 -----------------CAGAGTAGCAGCTGCTCTT-GCCGGCTAATA---------------------CACAACCCTTCCAGG -s simHuman_chr6.simHuman.chr6 107146 67 + 601863 -----------------CAAAGTGCTGGCTGCTCTCAGCAGGTTGTTAGAAATTCCTGTGTCTCCTTGTTGTGACTCCTTTGAG -s simRat_chr6.simRat.chr6 102258 84 + 647215 TCACATGGATTGTCAATTAAAGTGCTCACTGATCTCAACAGACTGTTCAGTCTTCCTGTGTGTTCTTGTCATGATTTATTTGGG - -a -s simMouse_chr6.simMouse.chr6 110274 31 + 636262 ACATCTTGTGTTGGTGCTGCACCTCTGGCTT -s Anc0.Anc0refChr1 5108 30 - 62388 ATGCCTTGTGT-GTTGCTGTAGCCCTGAATC -s Anc1.Anc1refChr2 83190 31 + 144309 ATGCCTTGTGTTGTTGCTGTAGCCCTGAATC -s Anc2.Anc2refChr2 20779 30 + 27695 GTGTCTTGTGT-GTTGTGGTAGCCTTGAATC -s mr.mrrefChr0 105123 31 + 130230 ACACCTTGTGTTGTTGCTGCACCTCTGGCTT -s simCow_chr6.simCow.chr6 114658 30 + 602619 GTGTCTTGTGT-GTTGTGGTACCCTTGAATC -s simDog_chr6.simDog.chr6 507714 10 - 593897 ---------------------GCTTTGAAAG -s simHuman_chr6.simHuman.chr6 107213 31 + 601863 ATGCCTTGTGTTTTTTCTGTAGCCCTGAATC -s simRat_chr6.simRat.chr6 102348 31 + 647215 ACACAGTGAAGTATTGCTACCAATGTTGTCT - -a -s simMouse_chr6.simMouse.chr6 110305 9 + 636262 CAGCCATGT -s Anc0.Anc0refChr1 5138 9 - 62388 CTACCACAT -s Anc1.Anc1refChr2 83221 9 + 144309 CTACCACAT -s Anc2.Anc2refChr2 20809 9 + 27695 CTACCACAT -s mr.mrrefChr0 105154 9 + 130230 CAGCCATGT -s simCow_chr6.simCow.chr6 114688 9 + 602619 CTACCATAT -s simDog_chr6.simDog.chr6 507724 9 - 593897 TTTACACTT -s simHuman_chr6.simHuman.chr6 107244 9 + 601863 CTACCACAT -s simRat_chr6.simRat.chr6 102381 9 + 647215 CAGCTATGT - -a -s simMouse_chr6.simMouse.chr6 110314 44 + 636262 CAATGATCATAAGCAACACAGTGAAATATTGCTGGCCCAACCAA -s Anc0.Anc0refChr1 5176 44 - 62388 CACAGATCACTAATATTACAGACAAAGCACTGTGACCAATATAA -s Anc1.Anc1refChr2 83259 44 + 144309 CACAGATCACTAATATTACAGACAAAGCACTGTGACCAATATAA -s Anc2.Anc2refChr2 20847 44 + 27695 CACAGATCACTAATATTACAGACAAAGCACTGTGACCAATATAA -s mr.mrrefChr0 105163 44 + 130230 CAATGATCATAAGCAACACAGTGAAAGCATGCTGGCCCAACCAA -s simCow_chr6.simCow.chr6 114725 43 + 602619 CACAGATCACCAACATCACAGAGAAAGC-CTGCCACCAATATAG -s simDog_chr6.simDog.chr6 507762 44 - 593897 CACAGATCACTAATGTTACAGTCAAGGCACTGTGACCAATATCA -s simHuman_chr6.simHuman.chr6 107283 44 + 601863 CACAGATCACTAATATGACAGACAAAGCTGTGTTACCAATATAA -s simRat_chr6.simRat.chr6 102390 33 + 647215 ------TGATTAGCAACCTATTGTAAGCAT-----CCCAACCAA - -a -s simMouse_chr6.simMouse.chr6 110358 18 + 636262 ATAAATTGGTATCATAAG -s Anc0.Anc0refChr1 5234 18 - 62388 ATAAATTGGGATCGTAAG -s Anc1.Anc1refChr2 83317 18 + 144309 ATAAATTGGGATCGTAAG -s Anc2.Anc2refChr2 20919 18 + 27695 ATAAATTGGGATTGTAAG -s mr.mrrefChr0 105207 18 + 130230 ATAAATTGGTATCATAAG -s simCow_chr6.simCow.chr6 114791 18 + 602619 ATAAATTGGGATTGAAAG -s simDog_chr6.simDog.chr6 507836 18 - 593897 ATAAATTGGGGTTGTTAG -s simHuman_chr6.simHuman.chr6 107341 18 + 601863 ATAGATTGGGATCGTAAG -s simRat_chr6.simRat.chr6 102423 18 + 647215 GTCAATTTGTATCTTAAG - -a -s simMouse_chr6.simMouse.chr6 110376 52 + 636262 CCAAATTTGCCTTGCAGTTACATGTCAATCAGCTGTGTCTGGCAAGTTGCAA -s Anc0.Anc0refChr1 5252 50 - 62388 CCAAACTTGCCTTGGGGTTACCTGCCAATAAGC--TGTCCGGCCAGTTGCAA -s Anc1.Anc1refChr2 83335 50 + 144309 CCAAACTTGCCTTGGGGTTACCTGCCAATAAGC--TGTCCGGCCAGTTGCAA -s Anc2.Anc2refChr2 20937 50 + 27695 CCAAACTTGTCTTGGGGTCACCTGCCAATAAGC--TGTCCGGCCAGTTGTGA -s mr.mrrefChr0 105225 52 + 130230 CCAAATTTGCCTTGCAGTTACCTGTCAATCAGCTGTGTCTGGCCAGTTGCAA -s simCow_chr6.simCow.chr6 114809 50 + 602619 CCAAACTTGTCTTGGGGACACCTGCCAATCAGC--TGCCTGGTCAGTTGTGA -s simDog_chr6.simDog.chr6 507854 50 - 593897 CCAAACTTGTCAGAGGGTCATCTCCCAATAAGC--TGTCCAGCCAGTAGTGG -s simHuman_chr6.simHuman.chr6 107364 50 + 601863 CAAAGCTCACCTTGGGGTTGCCTGCCAATTAGC--CGTCCGGCCCATTGCAA -s simRat_chr6.simRat.chr6 102441 49 + 647215 CCAAATCTGCCTCGCAGTTACCCGTCAGTCAGCTGTGT---GCCAGTGGCTA - -a -s simMouse_chr6.simMouse.chr6 110428 6 + 636262 TAACTT -s Anc0.Anc0refChr1 5302 6 - 62388 TAGCAT -s Anc1.Anc1refChr2 83385 6 + 144309 TAGCAT -s Anc2.Anc2refChr2 20987 6 + 27695 TAGCAT -s mr.mrrefChr0 105277 6 + 130230 TAACTT -s simCow_chr6.simCow.chr6 114859 6 + 602619 CAGCAT -s simDog_chr6.simDog.chr6 507905 6 - 593897 TAGTCT -s simHuman_chr6.simHuman.chr6 107414 6 + 601863 TAGCAT -s simRat_chr6.simRat.chr6 102490 6 + 647215 TAACTT - -a -s simMouse_chr6.simMouse.chr6 110434 5 + 636262 GTGGT -s Anc0.Anc0refChr1 5308 5 - 62388 AGGGT -s Anc1.Anc1refChr2 83391 5 + 144309 AGGGT -s Anc2.Anc2refChr2 20993 5 + 27695 AGGTT -s mr.mrrefChr0 105283 5 + 130230 GTGGT -s simCow_chr6.simCow.chr6 114912 5 + 602619 AGATT -s simDog_chr6.simDog.chr6 507911 5 - 593897 AGGTT -s simHuman_chr6.simHuman.chr6 107420 5 + 601863 AAGGT -s simRat_chr6.simRat.chr6 102496 5 + 647215 TTGGT - -a -s simMouse_chr6.simMouse.chr6 110439 29 + 636262 GGACATATATAACATCATCTATGCCCACT -s Anc0.Anc0refChr1 5313 29 - 62388 AGACACATATAACAGCATACAGGCCCTCT -s Anc1.Anc1refChr2 83396 29 + 144309 AGACACATATAACAGCATACAGGCCCTCT -s Anc2.Anc2refChr2 20999 29 + 27695 AGATGCAGATAACAGCATACAGGCCCTCT -s mr.mrrefChr0 105288 29 + 130230 AGACATATATAACATCATCTATGCCCACT -s simCow_chr6.simCow.chr6 114918 29 + 602619 ATATGAAAATAACGGCATACAGGCCCTCT -s simDog_chr6.simDog.chr6 507917 29 - 593897 GGATGCAGGTAATAGCATACAGGCCCTTT -s simHuman_chr6.simHuman.chr6 107425 29 + 601863 AGACACATATAACAGTATACAGGCCCTCT -s simRat_chr6.simRat.chr6 102501 29 + 647215 AGACATAGATAACTACTGCTACACCCACT - -a -s simMouse_chr6.simMouse.chr6 110468 108 + 636262 GGGTTCTAATTTAATGGTTTGCTTGTCACTCCCTATCCACCAATATTTggtaacctccccaagctaattaataatctgagtgacatccctggttacaaagttaatgtg -s Anc0.Anc0refChr1 5343 31 - 62388 AGGTTCTAATTTGCTAATTTGCTTGACACTA----------------------------------------------------------------------------- -s Anc1.Anc1refChr2 83426 31 + 144309 AGGTTCTAATTTGCTAATTTGCTTGACACTA----------------------------------------------------------------------------- -s Anc2.Anc2refChr2 21029 31 + 27695 AGTTTATACTTTGCTAATTTGCTTGACACTA----------------------------------------------------------------------------- -s mr.mrrefChr0 105318 108 + 130230 GGGTTCTAATTTAATAGTTTGCTTGTCACTCCCTATCCACCAATATTTggtaacctccccaagctaattaataatctgagtgacatccctggttacaaagttaatgtg -s simCow_chr6.simCow.chr6 114948 31 + 602619 AGTTTATACTTTGCTAATTTGGTTGACACTA----------------------------------------------------------------------------- -s simDog_chr6.simDog.chr6 507947 31 - 593897 ACTTTATACTTTGATAATTTGCTTGACACTA----------------------------------------------------------------------------- -s simHuman_chr6.simHuman.chr6 107455 31 + 601863 AGGTTCTGATTTGCTAATTTGCTTAACACTA----------------------------------------------------------------------------- -s simRat_chr6.simRat.chr6 102531 108 + 647215 GGGTTCTAATTTAATAGTTTTCTTGACACTGACTATCCACCAGTATTTggtaacctccccaggctaattaatactttgagtgacatcactggttacaaagttaatgtg - -a -s simMouse_chr6.simMouse.chr6 110576 102 + 636262 ctctctcaaaattattaagggaagccgctagtaattcacaaaatactagatgttcatgggttggcctgcagaaagttttgaatctgagaattttaatcttac -s mr.mrrefChr0 105426 102 + 130230 ctctctcaaaattattaagggaagccgctagtaattcacaaaatactagatgttcatgggttggcctgcagaaagttttgaatctgagaattttaatcttac -s simRat_chr6.simRat.chr6 102783 102 + 647215 ctttttcaagattaataagggaagccactagtaatacaaaaaataccagatgttcatgggttgacttgcagaaagttttgaatctgagaattttgatcttgc - -a -s simMouse_chr6.simMouse.chr6 110678 47 + 636262 gactgataacaaatctaatTCAaagttaaaaaaattgagcaagcaga -s mr.mrrefChr0 105528 47 + 130230 gactgataacaaatctaattcaaagttaaaaaaattgagcaagcaga -s simRat_chr6.simRat.chr6 102989 47 + 647215 gactcatagcaaatccaatttaaagtcaaaaaaattgggccagcaaa - -a -s simMouse_chr6.simMouse.chr6 110725 96 + 636262 tcaggttactatgaatgagttttaccaccaagttacctttgcaaagccggcactactggtatgaaagtgtgaataacagtcttttcactagttcaa -s mr.mrrefChr0 105575 89 + 130230 tcaggttactatgaatgagttttaccaccaagttacc-------agccggcactactggtatgaaagtgtgaataacagtcttttcactagttcaa -s simRat_chr6.simRat.chr6 103037 89 + 647215 tcaggatatagtaaataatttttactgccaagttacc-------acccagcactactggtatgaaagtgtgaataacggtcttttcactagttcaa - -a -s simMouse_chr6.simMouse.chr6 110821 189 + 636262 atggagccatcaacaaatagttttgtacgccagccaattgagattgcttaatgtttcacatcttggcatgaaatcctaagggagccagggatccattaatcaataagtggtgttggacaaatgtgttatctatccacaaagaattaaagcttgactctttcctaacttcttatatcagctgcaatggga -s mr.mrrefChr0 105664 154 + 130230 atggagccatcaacaaatagttttgtacgccagccaattga--ttgcttaatgtt--------------------------gagccagggatccattaatcaataagtggtgttggacaaatgtgttatctatccacaaagaattaaagctt-------tcctaacttcttatatcagctgcaatggga -s simRat_chr6.simRat.chr6 103142 154 + 647215 atagggcgctgtacaaatagtttgattccccagccaactga--ttgcttaatgtt--------------------------gaaccaaggatacacgaattaataagtattactggggaaatgtgttatctatccacagaaagtaaaggctt-------tcctaaggtcttatataagctgtgagggga - -a -s simMouse_chr6.simMouse.chr6 111010 75 + 636262 acaaccaagaattaaaacttgactttttcttcactccttatgtgaactgtaacaggactacaaatcagaactcct -s mr.mrrefChr0 105818 71 + 130230 acaaccaagaattaaaacttgactttttcttcactccttatgtgaactgta----gactacaaatcagaactcct -s simRat_chr6.simRat.chr6 103298 71 + 647215 acaaccaagaattaaaacatgactttttcataacactttgtgtgaactgta----gaccacagatcagaattcct - -a -s simMouse_chr6.simMouse.chr6 111085 430 + 636262 gccaaaaaaaacattgtaaaatgccacctaacatttggcacggggaaaatatatatctgaaggcaccaaaaacaactacagccaaacctaaaattgtgtggagtgaaagaaaagatgtctgcgggcatggtgaactccaggcctagaattttggacaaaaccgtcacctcctatgcccccaaaaggggtcgagcctcccgggttcggaaggaacccacaaagccacatccaaaaagaatgccaatgcactaatcagaagatggactagaaacattaacagtctgtcagtgtttggccaaagaattgccagaggaagtgtgcttcttccccatcAGCTCATTGGATGGGCAAGTcaccaggggaagtaagacttttcctgaggcctatcgtgcaggtattggtggtaggacaacactatgttgtgtcaggc -s mr.mrrefChr0 105889 415 + 130230 gccaaaaaaaacattgtaaaatgccacctaacatttggcacggggaaaatatatatctgaaggcaccaaaaacaa-tacagccaaacctaaaattgtgtggagtgaaagaaaagatgtctgcgggcatggtgaactccaggcctagaattttggacaaaaccgtcacctcctatgcccc-aaaaggggtcgagcctcccgggttcggaaggaacccacaaag-----tccaaaaagaatgccaatgcactaatcagaagatggactagaaacattaacagtctgtcagtgtttgg-------attgccagaggaagtgtgcttcttccccatcagctcattggatgggcaag-caccaggggaagtaagacttttcctgaggcctatcgtgcaggtattggtggtaggacaacactatgttgtgtcaggc -s simRat_chr6.simRat.chr6 103370 415 + 647215 gtcaaaaaaaacattgtaaaacaccactgaacatttggcacagggaaaatatgtatctgaaggcgctaaaaacaa-tacacctaaacctaaaattgtgtggagtgaaagtaaagacatctgtgggtatggtgaactccaggcttagaaatttggacaaaatcgtcaccacttatatccc-aagaggggactagtcccccggtttcagaaggaacccacaaag-----tccaaaaagagaaccaatgccacaatcagaagatggactagagacattaatagtcggtcagtgttttg-------agtgccagaggaagtctgcttcttcctcatcagcccattgcacagccaag-caccaggggaagtgagacttttcctgaggcctatcatgcaggtattggtggtaggacaacgccatgctgtgctatgc - -a -s simMouse_chr6.simMouse.chr6 111515 38 + 636262 aatgagtaacgatggagaaacctttttctaatatCCAT -s mr.mrrefChr0 106304 38 + 130230 aatgagtaacgatggagaaacctttttctaatatCCAT -s simRat_chr6.simRat.chr6 103786 38 + 647215 aatgagtaacaatcgagaaacctttttctaatatCTAT - -a -s simMouse_chr6.simMouse.chr6 111553 124 + 636262 ACAAGCATAATAAAAATGGTGACCTTATACAAAGGCAACACGTTTGAGTAATGGGAACCAGAAAGCCCTTTTTCCTTGCCACAAGCTATCCACAGGTTTGACTACACTTTGACTACATGATAAA -s Anc0.Anc0refChr1 5374 53 - 62388 -----------------------------------------------------------------------TTCACTGCTACTAGTTGCCCAAAGGTGCAACTGCACTTTAACTGTATGATAAA -s Anc1.Anc1refChr2 83457 53 + 144309 -----------------------------------------------------------------------TTCACTGCTACTAGTTGCCCAAAGGTGCAACTGCACTTTAACTGTATGATAAA -s Anc2.Anc2refChr2 21060 53 + 27695 -----------------------------------------------------------------------TTCACTGCTACTTGTTGCCCAAAGGTGCAACTGCACTTTAACTGTACGATAAA -s mr.mrrefChr0 106342 96 + 130230 ACAAGCATAATAAAAATGGTGACCTTATACAAA----------------------------AAAGCCCTTTTTCCTTGCCACAAGCTACCCACAGGTTTAACTGCACTTTAACTACATGATAAA -s simCow_chr6.simCow.chr6 114979 53 + 602619 -----------------------------------------------------------------------TTCACTGCTACTTGTTGCCTAAAGTTGCAACAGTAGCTTAGCTGTACAATAAG -s simDog_chr6.simDog.chr6 507978 50 - 593897 -----------------------------------------------------------------------GGCACTGCTACTTGTTACGCAAAGG---AACTGCACTTTAACTGTACGATAAA -s simHuman_chr6.simHuman.chr6 107486 50 + 601863 -----------------------------------------------------------------------TTCAGTGCT---AGTTGCCCAAAGGCACAACTGCACTTTAATTGTATGATAGA -s simRat_chr6.simRat.chr6 103851 96 + 647215 ACCAACATAAGAAAGATGGTGGCCTTATACAGC----------------------------AAGGCCCTTTTCCCTTGCCACAAGCTACCCACAGGTCTAACTGCAGTTTAACTACCTGATAAA - -a -s simMouse_chr6.simMouse.chr6 111677 15 + 636262 ATATAGCTGTGCACC -s Anc0.Anc0refChr1 5427 15 - 62388 ATATAGCATGGCACC -s Anc1.Anc1refChr2 83510 15 + 144309 ATATAGCATGGCACC -s Anc2.Anc2refChr2 21113 15 + 27695 ATATAGCATGGCACC -s mr.mrrefChr0 106438 15 + 130230 ATATAGCTGTGCACC -s simCow_chr6.simCow.chr6 115033 13 + 602619 ATATAACA--GCACT -s simDog_chr6.simDog.chr6 508028 15 - 593897 GCATAGAATGGCACC -s simHuman_chr6.simHuman.chr6 107536 15 + 601863 ATTTAGCATCGAACC -s simRat_chr6.simRat.chr6 103947 15 + 647215 ATATAGCCGTGCACC - -a -s simMouse_chr6.simMouse.chr6 111692 37 + 636262 AATATTGCTGGGCTTATTAGAGTATCAATATTACAGT -s Anc0.Anc0refChr1 5442 37 - 62388 AACATAGTGGGGCTAGGTAGTGTAACAGTATAACAGT -s Anc1.Anc1refChr2 83525 37 + 144309 AACATAGTGGGGCTAGGTAGTGTAACAGTATAACAGT -s Anc2.Anc2refChr2 21128 37 + 27695 ATCATAGTGGGGCTAGGTAGTATTACAGTATAACAGT -s mr.mrrefChr0 106453 37 + 130230 AACATTGCTGGGCTTGTTAGAGTATCAATATTACAGT -s simCow_chr6.simCow.chr6 115046 37 + 602619 ATTGTAGTGGGGCTAAGTAGTATTACACTATAACAGA -s simDog_chr6.simDog.chr6 508043 37 - 593897 ATCATAGTGGGGCTAGGTGGTATTACAGTATAACACT -s simHuman_chr6.simHuman.chr6 107553 37 + 601863 GACATAGTAAGGCTAGGTAGTGTAACAGTATAACAGT -s simRat_chr6.simRat.chr6 103962 27 + 647215 AACATTGCT-GGCTGGTTAGAGTATC---------GT - -a -s simMouse_chr6.simMouse.chr6 111729 16 + 636262 AGTAATTGGATGGTAT -s Anc0.Anc0refChr1 5479 16 - 62388 ACTAATTGAATGGTAT -s Anc1.Anc1refChr2 83562 16 + 144309 ACTAATTGAATGGTAT -s Anc2.Anc2refChr2 21165 16 + 27695 GCTAATTGAATGGTAT -s mr.mrrefChr0 106490 16 + 130230 AGTAATTGGATGGTAT -s simCow_chr6.simCow.chr6 115083 13 + 602619 GCTAATTGA---GTGT -s simDog_chr6.simDog.chr6 508080 16 - 593897 GCTAATTGAATGGTAT -s simHuman_chr6.simHuman.chr6 107599 16 + 601863 ATTAATGGAATAGCAT -s simRat_chr6.simRat.chr6 103989 16 + 647215 AGTAATTGGATGGTAT - -a -s simMouse_chr6.simMouse.chr6 111745 62 + 636262 GTGTGGCACCAAAATCCCTTTATGCCAAAGGGTACTATCCATGTATTACAACCCACAATGCC -s Anc0.Anc0refChr1 5495 62 - 62388 GTGGGTCTCTAAAGTTCTTTTATGGTAAAGGGTACTACTCATGTATTACAACATAAAATGGC -s Anc1.Anc1refChr2 83578 62 + 144309 GTGGGTCTCTAAAGTTCTTTTATGGTAAAGGGTACTACTCATGTATTACAACATAAAATGGC -s Anc2.Anc2refChr2 21183 62 + 27695 GTGGGTCTCTAAAGTTCTTTTATGGTAAAGGGAACTACTCATGTATTACAACATAAAATGGC -s mr.mrrefChr0 106506 62 + 130230 GTGGGTCACCAAAATCCCTTTATGCCAAAGGGTACTATTCATGTATTACAACCCACAATGCC -s simCow_chr6.simCow.chr6 115098 59 + 602619 GTGGGTTTCTAAAGTTATTTTATGGTAGAGGGAA--ATTCATGTATTACATGATAAAAT-GC -s simDog_chr6.simDog.chr6 508098 62 - 593897 GTGAGTCTCTAAAGTTCTTTTATGGGAAAGGGAACTACTCATGTATTACAACATAAAGTGGG -s simHuman_chr6.simHuman.chr6 107615 62 + 601863 GTGGGTCTCTAAAGTTCTTTTATGTTAAAGGGTACTCCTCATGTATTACAACATAGAATGGC -s simRat_chr6.simRat.chr6 104005 62 + 647215 GCGGGTCACAAAAATCCCTTTATGCCGTAGGGTACTATTCATGTATTACAACCCACAATGCT - -a -s simMouse_chr6.simMouse.chr6 111807 32 + 636262 CTCTGAAAGTAAGATGTTGCCAGAGTTCTAAC -s Anc0.Anc0refChr1 5562 29 - 62388 TTCAGATAGTAAGAAGTTACCAGAG---CAAC -s Anc1.Anc1refChr2 83645 32 + 144309 TTCAGATAGTAAGAAGTTACCAGAGTTTCAAC -s Anc2.Anc2refChr2 21250 29 + 27695 TTTAGATAGTAAGAAGCTGCCAGAG---CCAT -s mr.mrrefChr0 106573 32 + 130230 CTCTGAAAGTAAGATGTTACCAGAGTTCTAAC -s simCow_chr6.simCow.chr6 115162 29 + 602619 GATAGCTAGTGAGAATCAACCAGAG---CCAT -s simDog_chr6.simDog.chr6 508165 26 - 593897 TT---ATAGCAAGAAGCTGCCAGGG---CCAT -s simHuman_chr6.simHuman.chr6 107682 27 + 601863 TTCAGATAGTA-----TTAGTGGCATTTCAAC -s simRat_chr6.simRat.chr6 104072 32 + 647215 CTCCGAAAGTAAGAAGTTATCAGAGTTGTAAC - -a -s simMouse_chr6.simMouse.chr6 111839 1 + 636262 A -s Anc0.Anc0refChr1 5591 1 - 62388 A -s Anc1.Anc1refChr2 83677 1 + 144309 A -s Anc2.Anc2refChr2 21279 1 + 27695 A -s mr.mrrefChr0 106605 1 + 130230 A -s simCow_chr6.simCow.chr6 115191 1 + 602619 A -s simDog_chr6.simDog.chr6 508191 1 - 593897 A -s simHuman_chr6.simHuman.chr6 107723 1 + 601863 A -s simRat_chr6.simRat.chr6 104104 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 111840 88 + 636262 ATTCATAATGTAGATGGAGTTGCCTGACAATGTCATGGAGGACATATGTCCATCTGGCATGATCATTTGTGTATTTTTTAGTGGTTAC -s Anc0.Anc0refChr1 5592 61 - 62388 ATTGAGAGTACATATG----TTCCTTTCAAC---ATACTGAAAATACT------TGGC-CA-------------ATCATAGTTCTTAT -s Anc1.Anc1refChr2 83678 62 + 144309 ATTGAGAGTACATATG----TTCCTTTCAAC---ATACTGAAAATACT------TGGCACA-------------ATCATAGTTCTTAT -s Anc2.Anc2refChr2 21280 61 + 27695 ATTGCGAGTACATATG----TTCCTCTCAAC---ATGCTGAGAATACT------TTGC-TA-------------ATCATAGTTCTTAT -s mr.mrrefChr0 106606 69 + 130230 ATTCATAATGTAGATGTAGTTGCCTTACAATGTCATAGAGGACATATG------TGGCACA-------------TTTTTAGTGGTTAT -s simCow_chr6.simCow.chr6 115284 61 + 602619 ATTGCGAGTGCATATG----CTTCCCTCAAC---ATGCTGGGGATTCT------TCAC-TA-------------ATCATAGTGTTTAT -s simDog_chr6.simDog.chr6 508192 54 - 593897 ACT---AGTACATATG----TTCCT----AC---ATGCCGAGAATAGC------TTGC-TA-------------ATCACAGTTCTTAT -s simHuman_chr6.simHuman.chr6 107724 62 + 601863 ATTGAGAGTACATATG----TTCCTTTTAAC---ATACTGAAAATACT------TGGCACA-------------ATCATAGTCCTTTT -s simRat_chr6.simRat.chr6 104105 65 + 647215 ATTCATAATGAAGATGTAGATGCCTTACAATCTCATAGAGTGCATATG------T----CA-------------TTTTTAGTGGGTAT - -a -s simMouse_chr6.simMouse.chr6 111928 6 + 636262 GCCATT -s Anc0.Anc0refChr1 5653 6 - 62388 GCCGTT -s Anc1.Anc1refChr2 83740 6 + 144309 GCCGTT -s Anc2.Anc2refChr2 21351 6 + 27695 GCCGTT -s mr.mrrefChr0 106675 6 + 130230 GCCATT -s simCow_chr6.simCow.chr6 115356 6 + 602619 GAAGTT -s simDog_chr6.simDog.chr6 508256 6 - 593897 GCCATT -s simHuman_chr6.simHuman.chr6 107786 6 + 601863 ATCGTT -s simRat_chr6.simRat.chr6 104170 6 + 647215 GCCATT - -a -s simMouse_chr6.simMouse.chr6 111934 15 + 636262 TGTTCATTCCACGTG -s Anc0.Anc0refChr1 5662 15 - 62388 TATTCATTCCAAGAG -s Anc1.Anc1refChr2 83749 15 + 144309 TATTCATTCCAAGAG -s Anc2.Anc2refChr2 21360 15 + 27695 TATTCGTTCCAAGAG -s mr.mrrefChr0 106681 15 + 130230 TGTTCATTCCAAGAG -s simCow_chr6.simCow.chr6 115362 15 + 602619 TATTTTTTCCAAGGG -s simDog_chr6.simDog.chr6 508265 11 - 593897 ----CGTTCCAAGAG -s simHuman_chr6.simHuman.chr6 107795 15 + 601863 TATTCATTCCAATAG -s simRat_chr6.simRat.chr6 104176 15 + 647215 TGTTCATTCCAAGAG - -a -s simMouse_chr6.simMouse.chr6 111949 1 + 636262 A -s Anc0.Anc0refChr1 5677 1 - 62388 G -s Anc1.Anc1refChr2 83764 1 + 144309 G -s Anc2.Anc2refChr2 21375 1 + 27695 G -s mr.mrrefChr0 106696 1 + 130230 G -s simCow_chr6.simCow.chr6 115377 1 + 602619 G -s simDog_chr6.simDog.chr6 508321 1 - 593897 G -s simHuman_chr6.simHuman.chr6 107810 1 + 601863 G -s simRat_chr6.simRat.chr6 104191 1 + 647215 G - -a -s simMouse_chr6.simMouse.chr6 111950 67 + 636262 AACAGCCCTCTTATTGTTCACCAACATAAGTTTAGGATATAAAGCTTGTATTTTGTTACAAGCTCCT -s Anc0.Anc0refChr1 5678 48 - 62388 AAAAG-------------------GACAAGCTTAGGATATAAAGCTTATAATTCTTAACATACTCCT -s Anc1.Anc1refChr2 83765 48 + 144309 AAAAG-------------------GACAAGCTTAGGATATAAAGCTTATAATTCTTAACATACTCCT -s Anc2.Anc2refChr2 21376 48 + 27695 TGAGG-------------------GACAAGCTCAGGATATAAAGCTTATAATTCTTTACATATTCCT -s mr.mrrefChr0 106697 67 + 130230 AACAGCCCTCTTATTGTTCACCAACACAAGTTTAGGATATAAAGCTTATATTTTGTAACATGCTCCT -s simCow_chr6.simCow.chr6 115391 48 + 602619 TGAGG-------------------GACAAACTGAGGATATAAAGCTTGTCATTCTTTACAATTTCCT -s simDog_chr6.simDog.chr6 508322 48 - 593897 TGAGG-------------------GACAAGCTCAGGATATATAGCTTATAACTCTTTACATATCCCT -s simHuman_chr6.simHuman.chr6 107811 48 + 601863 AAAAG-------------------GACAAGCTTAAGACATTAAGCTTATAGTTCTTAACATACTCCT -s simRat_chr6.simRat.chr6 104192 67 + 647215 AACAGCCTTCTTATTGTTCACCAAAACAAGTTTAGGATATAAAGCGTATAATCTGTAACATGCTCCT - -a -s simMouse_chr6.simMouse.chr6 112017 88 + 636262 TTCCATTTAGGATATAAAGCCTATAATCTGTAACATGCTCCTGTCCTATCCATTATGGGCATTATCTCTATTCATTATAGGTATTGTG -s Anc0.Anc0refChr1 5726 24 - 62388 TT----------------------------------------------------------------TCTACTCATTGTGGGCATCATG -s Anc1.Anc1refChr2 83813 24 + 144309 TT----------------------------------------------------------------TCTACTCATTGTGGGCATCATG -s Anc2.Anc2refChr2 21424 24 + 27695 TT----------------------------------------------------------------TCTACTCATTGTGGACATCATG -s mr.mrrefChr0 106764 88 + 130230 TTCCATTTAGGATATAAAGCCTATAATCTGTAACATGCTCCTGTCCTATTCATTATGGGCATTATCTCTATTCATTATGGGCATTGTG -s simCow_chr6.simCow.chr6 115439 24 + 602619 TT----------------------------------------------------------------TCTATTGATGGTGGACATCATG -s simDog_chr6.simDog.chr6 508370 24 - 593897 TT----------------------------------------------------------------TCTACTCATTGTGGACATCATG -s simHuman_chr6.simHuman.chr6 107859 24 + 601863 TT----------------------------------------------------------------TCTACTCATTGTGGGCATCATG -s simRat_chr6.simRat.chr6 104264 88 + 647215 TTCCGTTTAGGATATAAAGCCTCTAACGTGTAGATTGCTCCTATTGTATTCATTATGGGCATTATCTCTATTCATTATGGGCATTGTG - -a -s simMouse_chr6.simMouse.chr6 112105 4 + 636262 AGTC -s Anc0.Anc0refChr1 5750 4 - 62388 AGTT -s Anc1.Anc1refChr2 83837 4 + 144309 AGTT -s Anc2.Anc2refChr2 21451 4 + 27695 AGTT -s mr.mrrefChr0 106852 4 + 130230 AGTC -s simCow_chr6.simCow.chr6 115466 4 + 602619 AGTT -s simDog_chr6.simDog.chr6 508397 4 - 593897 AGTT -s simHuman_chr6.simHuman.chr6 107883 4 + 601863 AGTT -s simRat_chr6.simRat.chr6 104352 4 + 647215 AGTC - -a -s simMouse_chr6.simMouse.chr6 112109 13 + 636262 TGAGTGAGAGGTG -s Anc0.Anc0refChr1 5755 13 - 62388 GGGGCCAGAGGTG -s Anc1.Anc1refChr2 83842 13 + 144309 GGGGCCAGAGGTG -s Anc2.Anc2refChr2 21456 13 + 27695 GGGGCCAGAGGTG -s mr.mrrefChr0 106856 13 + 130230 TGAGTGAGAGGTG -s simCow_chr6.simCow.chr6 115471 13 + 602619 AGGGCCAGAGGTG -s simDog_chr6.simDog.chr6 508402 6 - 593897 GGGGCC------- -s simHuman_chr6.simHuman.chr6 107888 13 + 601863 GGGGCCAAAGGTA -s simRat_chr6.simRat.chr6 104356 13 + 647215 TGAGTAAGAGATG - -a -s simMouse_chr6.simMouse.chr6 112122 10 + 636262 AGTAACTTGT -s Anc0.Anc0refChr1 5769 10 - 62388 AGTAATTTGT -s Anc1.Anc1refChr2 83856 10 + 144309 AGTAATTTGT -s Anc2.Anc2refChr2 21470 10 + 27695 AGTAATCTGT -s mr.mrrefChr0 106870 10 + 130230 AGTAACTTGT -s simCow_chr6.simCow.chr6 115485 10 + 602619 AGTAATCTGT -s simHuman_chr6.simHuman.chr6 107902 10 + 601863 AACGATTTAT -s simRat_chr6.simRat.chr6 104370 10 + 647215 AGTAACTTGT - -a -s simMouse_chr6.simMouse.chr6 112132 3 + 636262 TGA -s Anc0.Anc0refChr1 5779 3 - 62388 TTA -s Anc1.Anc1refChr2 83866 3 + 144309 TTA -s Anc2.Anc2refChr2 21480 3 + 27695 TTA -s mr.mrrefChr0 106880 3 + 130230 TGA -s simCow_chr6.simCow.chr6 115496 3 + 602619 TTT -s simDog_chr6.simDog.chr6 508408 2 - 593897 -TA -s simHuman_chr6.simHuman.chr6 107912 3 + 601863 TTA -s simRat_chr6.simRat.chr6 104380 3 + 647215 CAA - -a -s simMouse_chr6.simMouse.chr6 112135 32 + 636262 AAGAAGTCAGAGACAAGTTCTTCCTGAGGACG -s Anc0.Anc0refChr1 5788 32 - 62388 AATAGGTCAGAGACAAGTTCTGGCTGAGAACG -s Anc1.Anc1refChr2 83875 32 + 144309 AATAGGTCAGAGACAAGTTCTGGCTGAGAACG -s Anc2.Anc2refChr2 21489 32 + 27695 AATAGATCAGAGACAAGTTCTGGTTGAGAAAG -s mr.mrrefChr0 106883 32 + 130230 AAGAAGTCAGAGACAAGTTCTTCCTGAGGACG -s simCow_chr6.simCow.chr6 115505 32 + 602619 GTTAGATCAGAGAAAAGCTCTGCTCAATAAAG -s simDog_chr6.simDog.chr6 508416 28 - 593897 AATAGATTAGAGGCAAGTTCTGGTTGAG---- -s simHuman_chr6.simHuman.chr6 107921 32 + 601863 AATAGGTCAGAGACAAGTTCTGTCTGAGAACG -s simRat_chr6.simRat.chr6 104383 32 + 647215 AAGGAGTCAGAGACAAGTTCCTCATGAGGATG - -a -s simMouse_chr6.simMouse.chr6 112167 5 + 636262 ATTAA -s Anc0.Anc0refChr1 5820 5 - 62388 ATTAA -s Anc1.Anc1refChr2 83907 5 + 144309 ATTAA -s Anc2.Anc2refChr2 21521 5 + 27695 ATCAA -s mr.mrrefChr0 106915 5 + 130230 ATTAA -s simCow_chr6.simCow.chr6 115537 5 + 602619 ATCAA -s simHuman_chr6.simHuman.chr6 107953 5 + 601863 ATTAA -s simRat_chr6.simRat.chr6 104418 5 + 647215 ATTAA - -a -s simMouse_chr6.simMouse.chr6 112172 6 + 636262 CTCCCA -s Anc0.Anc0refChr1 5829 6 - 62388 TTCCCA -s Anc1.Anc1refChr2 83916 6 + 144309 TTCCCA -s Anc2.Anc2refChr2 21530 6 + 27695 TATCCA -s mr.mrrefChr0 106920 6 + 130230 TTCCCA -s simCow_chr6.simCow.chr6 115546 6 + 602619 TATCCA -s simHuman_chr6.simHuman.chr6 107962 6 + 601863 TTCCCA -s simRat_chr6.simRat.chr6 104423 6 + 647215 TTCCCA - -a -s simMouse_chr6.simMouse.chr6 112178 17 + 636262 GGAGAGGACCATGTGGG -s Anc0.Anc0refChr1 5835 6 - 62388 CAA-----------GGG -s Anc1.Anc1refChr2 83922 6 + 144309 CAA-----------GGG -s Anc2.Anc2refChr2 21536 6 + 27695 CAA-----------GGG -s mr.mrrefChr0 106926 17 + 130230 GGAGAGGACCATGTGGG -s simCow_chr6.simCow.chr6 115568 6 + 602619 CAA-----------GGG -s simHuman_chr6.simHuman.chr6 107968 6 + 601863 CAA-----------GGG -s simRat_chr6.simRat.chr6 104429 17 + 647215 GGAGAGGACCAAGGTGG - -a -s simMouse_chr6.simMouse.chr6 112195 15 + 636262 GAGGTTCTATCTTAG -s Anc0.Anc0refChr1 5842 15 - 62388 GGGGTGCTACCTGAG -s Anc1.Anc1refChr2 83929 15 + 144309 GGGGTGCTACCTGAG -s Anc2.Anc2refChr2 21543 15 + 27695 GGGATGCCACATGAG -s mr.mrrefChr0 106943 15 + 130230 GAGGTGCTATCTTAG -s simCow_chr6.simCow.chr6 115575 15 + 602619 GGGATGCCACATGAG -s simDog_chr6.simDog.chr6 508444 4 - 593897 -----------TGAG -s simHuman_chr6.simHuman.chr6 107975 15 + 601863 GTGGTGCTACCTGAG -s simRat_chr6.simRat.chr6 104446 15 + 647215 GAGGTGCTATCTTAC - -a -s simMouse_chr6.simMouse.chr6 112210 14 + 636262 CCTTACATCATAGA -s Anc0.Anc0refChr1 5857 14 - 62388 CCCCATATCATAGA -s Anc1.Anc1refChr2 83944 14 + 144309 CCCCATATCATAGA -s Anc2.Anc2refChr2 21558 14 + 27695 CCCCATATCATATA -s mr.mrrefChr0 106958 14 + 130230 CCTCACATCATAGA -s simCow_chr6.simCow.chr6 115608 14 + 602619 CCAGATCTCATAAA -s simDog_chr6.simDog.chr6 508448 14 - 593897 CCCCATATCACATA -s simHuman_chr6.simHuman.chr6 107990 14 + 601863 CCCCATATCATAGA -s simRat_chr6.simRat.chr6 104461 14 + 647215 TGTCACGTCACAGA - -a -s simMouse_chr6.simMouse.chr6 112224 12 + 636262 GTTATTGCAAAG -s Anc0.Anc0refChr1 5871 12 - 62388 GTTATTGCTTAT -s Anc1.Anc1refChr2 83958 12 + 144309 GTTATTGCTTAT -s Anc2.Anc2refChr2 21572 12 + 27695 GTTATTGCTTAT -s mr.mrrefChr0 106972 12 + 130230 GTTATTGCAAAT -s simCow_chr6.simCow.chr6 115622 12 + 602619 GTTATGGTGTAC -s simDog_chr6.simDog.chr6 508462 12 - 593897 GTTATTGCTTTT -s simHuman_chr6.simHuman.chr6 108005 12 + 601863 GTTATTGCTTAT -s simRat_chr6.simRat.chr6 104475 12 + 647215 GTTATTGCACAT - -a -s simMouse_chr6.simMouse.chr6 112236 14 + 636262 CTTTTTCATACCTG -s Anc0.Anc0refChr1 5883 14 - 62388 CTTTTTCATATCTG -s Anc1.Anc1refChr2 83970 14 + 144309 CTTTTTCATATCTG -s Anc2.Anc2refChr2 21585 14 + 27695 CTTTTTTATATTTG -s mr.mrrefChr0 106984 14 + 130230 CTTTTTCATACCTG -s simCow_chr6.simCow.chr6 115635 14 + 602619 CTCTTTTGCGTTGG -s simDog_chr6.simDog.chr6 508475 14 - 593897 CTTTTTTATATTTG -s simHuman_chr6.simHuman.chr6 108017 14 + 601863 CTGTTTCATATCTG -s simRat_chr6.simRat.chr6 104487 14 + 647215 CTTTTTTATACCTG - -a -s simMouse_chr6.simMouse.chr6 112250 23 + 636262 CAGATTAACCTGGCATAGATAGC -s Anc0.Anc0refChr1 5898 20 - 62388 CAAAAAAACCTGGCATAGAC--- -s Anc1.Anc1refChr2 83985 23 + 144309 CAAAAAAACCTGGCATAGACTGC -s Anc2.Anc2refChr2 21600 20 + 27695 CAAAAAAACCTGGCATAGAC--- -s mr.mrrefChr0 106999 23 + 130230 CAGAAAAACCTGGCATAGATAGC -s simCow_chr6.simCow.chr6 115650 14 + 602619 CAAAAAAA------ATCTAG--- -s simDog_chr6.simDog.chr6 508490 20 - 593897 CACAAAAACCTGGCATAGAC--- -s simHuman_chr6.simHuman.chr6 108032 23 + 601863 CAAAAAAACCTGGCATAGACTGC -s simRat_chr6.simRat.chr6 104502 23 + 647215 CAGAAAAACCTGGCATAGATAGT - -a -s simMouse_chr6.simMouse.chr6 112273 65 + 636262 TAAAGTCAGAGATGTCAGCTCAATCTAAGGATCACAAATGTCATCACAATTTCAGGGATATGTCT -s Anc0.Anc0refChr1 5918 35 - 62388 ---ATTCAGATATGTCGGCTCAATC---------------------------CTAAGCTATGTTT -s Anc1.Anc1refChr2 84008 38 + 144309 TAAATTCAGATATGTCGGCTCAATC---------------------------CTAAGCTATGTTT -s Anc2.Anc2refChr2 21620 35 + 27695 ---ATTCAGATATGTCGGATCGATC---------------------------TTAAGCTATGTTT -s mr.mrrefChr0 107022 45 + 130230 TAAAGTCAGAGATGTCAGCTCAATCTAAGGA--------------------TCAGAGATATGTCT -s simCow_chr6.simCow.chr6 115664 34 + 602619 ---ATTCAAGTATGCCAATTT-AAC---------------------------GTAGGCTATGTCT -s simDog_chr6.simDog.chr6 508510 35 - 593897 ---ATTCAGATATGTCGGAGCGATC---------------------------TTAAGCTATGTTT -s simHuman_chr6.simHuman.chr6 108057 38 + 601863 TAAATCCAGACATGTCGGCTCAATC---------------------------CTAAGGTATGGTT -s simRat_chr6.simRat.chr6 104525 45 + 647215 TAAAGTCAGAGGCATCAGCTCAATCTAAGGA--------------------TCAGAGACATGTCC - -a -s simMouse_chr6.simMouse.chr6 112338 31 + 636262 GCCCAGTCTTAAGTATAATTCAATTTATTCT -s Anc0.Anc0refChr1 5953 31 - 62388 GCCCAGTCTTAGATATAATTTAATTTGTTAT -s Anc1.Anc1refChr2 84046 31 + 144309 GCCCAGTCTTAGATATAATTTAATTTGTTAT -s Anc2.Anc2refChr2 21655 31 + 27695 GCCCAGTTTTAGATATAATTTCATTTGTTAT -s mr.mrrefChr0 107067 31 + 130230 GCCCAGTCTTAAGTATAATTCAATTTATTCT -s simCow_chr6.simCow.chr6 115699 31 + 602619 GCCCAGTATGTGATATACTTTTAGTCGCTAT -s simDog_chr6.simDog.chr6 508545 31 - 593897 GCCCAGTTTTAGATATAATCTCATTTGTTAT -s simHuman_chr6.simHuman.chr6 108095 31 + 601863 GCCCGATCTTAGATACAATTTAATTTGTTAT -s simRat_chr6.simRat.chr6 104570 31 + 647215 GGCCAGTCTTGAGTATAATTGAATTTACTCT - -a -s simMouse_chr6.simMouse.chr6 112369 14 + 636262 CTCTGCAGAGATAA -s Anc0.Anc0refChr1 5985 14 - 62388 CTCTTCAAAGAGAA -s Anc1.Anc1refChr2 84078 14 + 144309 CTCTTCAAAGAGAA -s Anc2.Anc2refChr2 21687 14 + 27695 CTTTTCAAAGAGAA -s mr.mrrefChr0 107098 14 + 130230 CTCTGCAGAGATAA -s simCow_chr6.simCow.chr6 115731 14 + 602619 CTTATCTAAGAGAA -s simDog_chr6.simDog.chr6 508577 12 - 593897 CTTTTCAAAGGG-- -s simHuman_chr6.simHuman.chr6 108127 14 + 601863 CTCTTCAAGGAGAA -s simRat_chr6.simRat.chr6 104601 14 + 647215 CTCTGCAGAGATAA - -a -s simMouse_chr6.simMouse.chr6 112383 11 + 636262 TTCCCATGTCC -s Anc0.Anc0refChr1 6002 11 - 62388 TTCACATGTGC -s Anc1.Anc1refChr2 84095 11 + 144309 TTCACATGTGC -s Anc2.Anc2refChr2 21704 11 + 27695 TGCACCTGTGC -s mr.mrrefChr0 107112 11 + 130230 TTCCCATGTCC -s simCow_chr6.simCow.chr6 115748 11 + 602619 TGCTCGTGAGC -s simDog_chr6.simDog.chr6 508589 9 - 593897 --CACCTGTGC -s simHuman_chr6.simHuman.chr6 108144 11 + 601863 TTCACATGTGC -s simRat_chr6.simRat.chr6 104615 11 + 647215 TTCCCATGTCC - -a -s simMouse_chr6.simMouse.chr6 112394 1 + 636262 C -s Anc0.Anc0refChr1 6015 1 - 62388 C -s Anc1.Anc1refChr2 84108 1 + 144309 C -s Anc2.Anc2refChr2 21717 1 + 27695 C -s mr.mrrefChr0 107125 1 + 130230 C -s simCow_chr6.simCow.chr6 115761 1 + 602619 C -s simDog_chr6.simDog.chr6 508600 1 - 593897 C -s simHuman_chr6.simHuman.chr6 108157 1 + 601863 C -s simRat_chr6.simRat.chr6 104628 1 + 647215 C - -a -s simMouse_chr6.simMouse.chr6 112395 3 + 636262 ACA -s Anc0.Anc0refChr1 6016 2 - 62388 -CA -s Anc1.Anc1refChr2 84109 3 + 144309 ACA -s Anc2.Anc2refChr2 21718 2 + 27695 -CT -s mr.mrrefChr0 107126 3 + 130230 ACA -s simCow_chr6.simCow.chr6 115762 1 + 602619 -C- -s simDog_chr6.simDog.chr6 508601 2 - 593897 -CT -s simHuman_chr6.simHuman.chr6 108174 3 + 601863 ACA -s simRat_chr6.simRat.chr6 104629 3 + 647215 ATA - -a -s simMouse_chr6.simMouse.chr6 112398 18 + 636262 ATAAATTCAACTTAGATC -s Anc0.Anc0refChr1 6018 18 - 62388 ATAAATTTTATTTATATC -s Anc1.Anc1refChr2 84112 18 + 144309 ATAAATTTTATTTATATC -s Anc2.Anc2refChr2 21720 18 + 27695 GTAAATTTTATTTATAAC -s mr.mrrefChr0 107129 18 + 130230 ATAAATTTAACTTAGATC -s simCow_chr6.simCow.chr6 115763 12 + 602619 ATGAATTTGATT------ -s simDog_chr6.simDog.chr6 508603 18 - 593897 GTAAATTTTGTTTATAAC -s simHuman_chr6.simHuman.chr6 108182 18 + 601863 ATAAATTTTATTTGTATC -s simRat_chr6.simRat.chr6 104632 18 + 647215 ATAAATTTCACTTAGATC - -a -s simMouse_chr6.simMouse.chr6 112416 15 + 636262 TCATTCCTAATGGAT -s Anc0.Anc0refChr1 6036 15 - 62388 TGATTACTCAGGGAT -s Anc1.Anc1refChr2 84130 15 + 144309 TGATTACTCAGGGAT -s Anc2.Anc2refChr2 21738 15 + 27695 TGATTAATCAGGGAT -s mr.mrrefChr0 107147 15 + 130230 TCATTACTCATGGAT -s simCow_chr6.simCow.chr6 115775 6 + 602619 -------TCAG--AT -s simDog_chr6.simDog.chr6 508621 15 - 593897 TGATTAATCAGGGTT -s simHuman_chr6.simHuman.chr6 108200 15 + 601863 TTGTTACTCAGGAAT -s simRat_chr6.simRat.chr6 104695 15 + 647215 TCATTACTCATGGAT - -a -s simMouse_chr6.simMouse.chr6 112431 4 + 636262 AAAT -s Anc0.Anc0refChr1 6060 4 - 62388 AAAT -s Anc1.Anc1refChr2 84154 4 + 144309 AAAT -s Anc2.Anc2refChr2 21762 4 + 27695 GAGT -s mr.mrrefChr0 107162 4 + 130230 AAAT -s simCow_chr6.simCow.chr6 115790 3 + 602619 -AGT -s simDog_chr6.simDog.chr6 508645 4 - 593897 GAGT -s simHuman_chr6.simHuman.chr6 108224 4 + 601863 AAAT -s simRat_chr6.simRat.chr6 104710 4 + 647215 AAAC - -a -s simMouse_chr6.simMouse.chr6 112435 1 + 636262 T -s Anc0.Anc0refChr1 6065 1 - 62388 T -s Anc1.Anc1refChr2 84159 1 + 144309 T -s Anc2.Anc2refChr2 21767 1 + 27695 T -s mr.mrrefChr0 107166 1 + 130230 T -s simCow_chr6.simCow.chr6 115794 1 + 602619 T -s simDog_chr6.simDog.chr6 508650 1 - 593897 T -s simHuman_chr6.simHuman.chr6 108229 1 + 601863 T -s simRat_chr6.simRat.chr6 104714 1 + 647215 C - -a -s simMouse_chr6.simMouse.chr6 112436 6 + 636262 GAACTT -s Anc0.Anc0refChr1 6066 6 - 62388 GAACTT -s Anc1.Anc1refChr2 84160 6 + 144309 GAACTT -s Anc2.Anc2refChr2 21768 6 + 27695 GAATTT -s mr.mrrefChr0 107167 6 + 130230 GAACTT -s simCow_chr6.simCow.chr6 115795 6 + 602619 GAATTT -s simDog_chr6.simDog.chr6 508651 6 - 593897 GAATCT -s simHuman_chr6.simHuman.chr6 108230 6 + 601863 AAACTT -s simRat_chr6.simRat.chr6 104747 6 + 647215 GAACTT - -a -s simMouse_chr6.simMouse.chr6 112442 66 + 636262 CTTTGATCCTGTAGGCAAGTAAAAGAAGTTAAGGAGACTGGGTTTTTAAAAGGCCCTCAGTGTTGC -s Anc0.Anc0refChr1 6072 66 - 62388 CTTTGTGCCTGTAGGCAATTAAAATCAGTTAAGGAGCCTGGCGTAATTAATTGCCCTCAATCTTGG -s Anc1.Anc1refChr2 84166 66 + 144309 CTTTGTGCCTGTAGGCAATTAAAATCAGTTAAGGAGCCTGGCGTAATTAATTGCCCTCAATCTTGG -s Anc2.Anc2refChr2 21774 66 + 27695 TTTTGTGCCTGTAGGCAATTAAAATCAGTTGAGAAGCCTGGCGTAATTAATTGCCCTCAATCTTGG -s mr.mrrefChr0 107173 66 + 130230 CTTTGAGCCTGTAGGCAATTAAAAGAAGTTAAGGAGACTGGTTTTTTAAAAGGCCCTCAGTGTTGC -s simCow_chr6.simCow.chr6 115831 66 + 602619 TTTTGTGCCTGTAAGCAATTAAAGTCAGTTGAGGAGACTGATGTAATTTATTACCCCTAATCTTGG -s simDog_chr6.simDog.chr6 508657 66 - 593897 TTTTGGGACTGTAGGCAATTAAAATCAGTTGAGAAGCCTGGCATCATTAACTGCCATCAATCCTGG -s simHuman_chr6.simHuman.chr6 108236 52 + 601863 CTATGTGCCTATAGGT-GTTGCAA----TCAATG---------TAATCGATTGCCCTCAATCTTGT -s simRat_chr6.simRat.chr6 104753 66 + 647215 CTTTGAGCCTGTAGGCAATTAAAAGAAGTTGAGGAGACGGGTTTTGTAAAAAGTCCTCAGTGTTGC - -a -s simMouse_chr6.simMouse.chr6 112508 10 + 636262 ATTAGTCATA -s Anc0.Anc0refChr1 6138 10 - 62388 ATTAGGCATA -s Anc1.Anc1refChr2 84232 10 + 144309 ATTAGGCATA -s Anc2.Anc2refChr2 21840 10 + 27695 ATTAGGCATA -s mr.mrrefChr0 107239 10 + 130230 ATTAGTCATA -s simCow_chr6.simCow.chr6 115898 10 + 602619 ATTAGGTAGA -s simDog_chr6.simDog.chr6 508723 10 - 593897 ATTAGGCGTA -s simHuman_chr6.simHuman.chr6 108288 10 + 601863 GTTAGGCAAA -s simRat_chr6.simRat.chr6 104819 10 + 647215 ATCAGTCATA - -a -s simMouse_chr6.simMouse.chr6 112518 57 + 636262 AACCTCAAGAGCAAGGTGGTGGACTCCTAGAAATGTGTCAACCCATAAGCTTCAGTA -s Anc0.Anc0refChr1 6149 57 - 62388 AACCTCAAGTTGAGGGTAGTGGACTCCTGGGAATGTGTCAGACTATAACATTCCATA -s Anc1.Anc1refChr2 84243 57 + 144309 AACCTCAAGTTGAGGGTAGTGGACTCCTGGGAATGTGTCAGACTATAACATTCCATA -s Anc2.Anc2refChr2 21851 57 + 27695 AACCTCAAGTGGAGGGTAGTGCACTCCTGGGAATGTGTCAGACTATAACATTCCATA -s mr.mrrefChr0 107249 57 + 130230 AACCTCAAGATGAAGGTGGTGGACTCCTAGAAATGTGTCAACCTATAACCTTCAGTA -s simCow_chr6.simCow.chr6 115909 49 + 602619 AACCTCAAGTAGAAGGTGAGGAACTCCTTTAAATTTG-----CCGTGACGTTCC--- -s simDog_chr6.simDog.chr6 508734 57 - 593897 AACCTCAACCGTAGTGTAGTACACTCCTGGGAATGTGTCAGACTATAACATTCAATA -s simHuman_chr6.simHuman.chr6 108299 57 + 601863 AACCTCAAGTTGAGGGTATTGGACTCCTCCGAATGTGTCAGACTATAACATTCCATC -s simRat_chr6.simRat.chr6 104829 57 + 647215 AACCTCAAGCTGAAGGTGGTGGACTCCTAGAAGTGTGTCAACTTATAGCCTTCAGTG - -a -s simMouse_chr6.simMouse.chr6 112575 40 + 636262 TTCATTGTTAAGACTTATACTATTTCATCTCAGGTGAATG -s Anc0.Anc0refChr1 6207 37 - 62388 TTTATCGTTAAAACTTATGCCATTTCATTGT---TGGACA -s Anc1.Anc1refChr2 84301 37 + 144309 TTTATCGTTAAAACTTATGCCATTTCATTGT---TGGACA -s Anc2.Anc2refChr2 21909 37 + 27695 ATTATCGTTAAAGCTTATGTCATTTCAGTGT---TGGACA -s mr.mrrefChr0 107306 37 + 130230 TTCATTGTTAAAACTTATACTATTTCATTTC---TGGATG -s simCow_chr6.simCow.chr6 115959 37 + 602619 ATTATCGTTAAAGCTTATGTCATTACAGTGT---TGGACA -s simDog_chr6.simDog.chr6 508792 18 - 593897 ATCAT---------TTGTCTCATTTCA------------- -s simHuman_chr6.simHuman.chr6 108357 37 + 601863 TTTATCAGTAAAACTTATGCCACTGCATTGT---TGGACA -s simRat_chr6.simRat.chr6 104886 34 + 647215 TTCATTGTTAAAACTTATATTGTT---CTAG---TGGGTC - -a -s simMouse_chr6.simMouse.chr6 112615 22 + 636262 TTGTTGTAGTCTAGGACGCACA -s Anc0.Anc0refChr1 6246 20 - 62388 CCATA--TGTCTGGGACACAGA -s Anc1.Anc1refChr2 84340 22 + 144309 CCATACTTGTCTGGGACACAGA -s Anc2.Anc2refChr2 21948 20 + 27695 CCACA--TGTCTGGGACATAGA -s mr.mrrefChr0 107343 22 + 130230 TTGTTGTAGTCTAGGACACACA -s simCow_chr6.simCow.chr6 115999 17 + 602619 CCA-----GTCTGGGACATGGA -s simDog_chr6.simDog.chr6 508810 6 - 593897 ---CA--T-----------AGA -s simHuman_chr6.simHuman.chr6 108396 22 + 601863 CCATCATGGTCTGGGATACAAG -s simRat_chr6.simRat.chr6 104920 22 + 647215 TTGTTGTAGTCTAGAACACCCA - -a -s simMouse_chr6.simMouse.chr6 112637 10 + 636262 ATCCTAAGTT -s Anc0.Anc0refChr1 6266 10 - 62388 ATCCTTAGTT -s Anc1.Anc1refChr2 84362 10 + 144309 ATCCTTAGTT -s Anc2.Anc2refChr2 21968 10 + 27695 ATCTTTAGTT -s mr.mrrefChr0 107365 10 + 130230 ATCCTTAGTT -s simCow_chr6.simCow.chr6 116016 10 + 602619 ATCTTTAGTT -s simDog_chr6.simDog.chr6 508816 10 - 593897 ATCTTTGGTT -s simHuman_chr6.simHuman.chr6 108419 10 + 601863 ATCCTTAGTT -s simRat_chr6.simRat.chr6 104942 10 + 647215 ATCTTTAGTT - -a -s simMouse_chr6.simMouse.chr6 112647 16 + 636262 CATAAATTTCATGCAT -s Anc0.Anc0refChr1 6276 16 - 62388 CATGAATCTTATGCAT -s Anc1.Anc1refChr2 84372 16 + 144309 CATGAATCTTATGCAT -s Anc2.Anc2refChr2 21978 16 + 27695 CATGAACCTTATGCAT -s mr.mrrefChr0 107375 16 + 130230 CATAAATTTCATGCAT -s simCow_chr6.simCow.chr6 116026 15 + 602619 GAGGGG-CTTATGCAT -s simDog_chr6.simDog.chr6 508830 16 - 593897 CATGAACCTTATGCAT -s simHuman_chr6.simHuman.chr6 108429 16 + 601863 CATGAATCCTATGCAT -s simRat_chr6.simRat.chr6 104952 16 + 647215 CACAAATTTCATGCAT - -a -s simMouse_chr6.simMouse.chr6 112663 8 + 636262 TGTCTTCT -s Anc0.Anc0refChr1 6292 7 - 62388 ACT-TCAT -s Anc1.Anc1refChr2 84388 7 + 144309 ACT-TCAT -s Anc2.Anc2refChr2 21995 7 + 27695 ACT-TCAT -s mr.mrrefChr0 107391 8 + 130230 TGTCTTCT -s simCow_chr6.simCow.chr6 116042 7 + 602619 ACT-CTAT -s simDog_chr6.simDog.chr6 508847 7 - 593897 GCT-TCAT -s simHuman_chr6.simHuman.chr6 108445 7 + 601863 ACT-TCAT -s simRat_chr6.simRat.chr6 104968 8 + 647215 TGCCTTCT - -a -s simMouse_chr6.simMouse.chr6 112671 51 + 636262 TGCAGGGTCGCCTTTACTGCCAAGACTTGCTGTTGTTATATGAAAGACTAT -s Anc0.Anc0refChr1 6299 51 - 62388 TCAAGGGTGGACTTCACTTTCAGGACTAAATGTGGCTATATGAAAAAATAT -s Anc1.Anc1refChr2 84395 51 + 144309 TCAAGGGTGGACTTCACTTTCAGGACTAAATGTGGCTATATGAAAAAATAT -s Anc2.Anc2refChr2 22002 51 + 27695 TCAAGGGTGGACTTCACTTTCAGGACTAAATGTGGCTATATGAAAAAATAT -s mr.mrrefChr0 107399 51 + 130230 TGCAGGGTGGCCTTCACTGCCAAGACTTGCTGTTGTTATATGAAAGACTAT -s simCow_chr6.simCow.chr6 116098 51 + 602619 TCGAGGGTGGACTTCACATTGAGGCCTAGATGTGGCTATATGAAAAAATAT -s simDog_chr6.simDog.chr6 508854 51 - 593897 TCAAGAGTGGAATTCACTCTCAGGACTAAATGTAGCTACAAGAAAAAATAT -s simHuman_chr6.simHuman.chr6 108452 51 + 601863 ACAAGGGAGGACTTCACTTTTAGGACTACATGTGGGTATATGAAGAAATAC -s simRat_chr6.simRat.chr6 104976 51 + 647215 TGCAGGGTGGCCTTCACTGCCAAGATTTGCTCTTATTATATGAAATACTAT - -a -s simMouse_chr6.simMouse.chr6 112722 7 + 636262 GTGCTGA -s Anc0.Anc0refChr1 6351 7 - 62388 ATGCTGA -s Anc1.Anc1refChr2 84447 7 + 144309 ATGCTGA -s Anc2.Anc2refChr2 22054 7 + 27695 ATGCAGA -s mr.mrrefChr0 107451 7 + 130230 GTGCTGA -s simCow_chr6.simCow.chr6 116150 4 + 602619 AC---GA -s simDog_chr6.simDog.chr6 508906 7 - 593897 ATGCAGA -s simHuman_chr6.simHuman.chr6 108504 7 + 601863 ATGTTGA -s simRat_chr6.simRat.chr6 105028 7 + 647215 GTGCTGA - -a -s simMouse_chr6.simMouse.chr6 112729 23 + 636262 ACTAACCCACCGGCAGCCAGGGG -s Anc0.Anc0refChr1 6361 23 - 62388 TATGGTGTACCTGCAGCCAGGTT -s Anc1.Anc1refChr2 84457 23 + 144309 TATGGTGTACCTGCAGCCAGGTT -s Anc2.Anc2refChr2 22064 23 + 27695 TATGGTGTACCTGCAGCCAGGTT -s mr.mrrefChr0 107459 23 + 130230 ACTGACCCACCGGCAGCCAGGGG -s simCow_chr6.simCow.chr6 116157 23 + 602619 TATATTGTACCTGCAGCTGGGTT -s simDog_chr6.simDog.chr6 508916 23 - 593897 TATGGTGTACTTGAAGCCAGGTT -s simHuman_chr6.simHuman.chr6 108514 23 + 601863 TATGGTGTACCTGCAGAAATGCT -s simRat_chr6.simRat.chr6 105036 23 + 647215 ACTGACCAACCAGCAGCCAGGGG - -a -s simMouse_chr6.simMouse.chr6 112752 3 + 636262 CCC -s Anc0.Anc0refChr1 6384 3 - 62388 CAA -s Anc1.Anc1refChr2 84480 3 + 144309 CAA -s Anc2.Anc2refChr2 22087 3 + 27695 CAA -s mr.mrrefChr0 107482 3 + 130230 CTC -s simCow_chr6.simCow.chr6 116180 3 + 602619 GTC -s simDog_chr6.simDog.chr6 508949 3 - 593897 CAA -s simHuman_chr6.simHuman.chr6 108537 3 + 601863 CAT -s simRat_chr6.simRat.chr6 105059 3 + 647215 GTC - -a -s simMouse_chr6.simMouse.chr6 112755 40 + 636262 CTTTTCTCACGTTGCCTGCTATAACCTTCTTGTTTAACTG -s Anc0.Anc0refChr1 6397 36 - 62388 TTTTTCTCATTTTGCC--ATATGACCTTCTAGTTAAAC-- -s Anc1.Anc1refChr2 84493 36 + 144309 TTTTTCTCATTTTGCC--ATATGACCTTCTAGTTAAAC-- -s Anc2.Anc2refChr2 22100 36 + 27695 TTTTTCACATTTTGCC--GTATGACCTTCTAGTCAAAC-- -s mr.mrrefChr0 107485 40 + 130230 CTTTTCTCACGTTGCCTGATATAACCTTCTTGTTAAACTG -s simCow_chr6.simCow.chr6 116193 31 + 602619 CTTCTGAAA-----CC--CCATGCCCTTCTAGTCTAAC-- -s simDog_chr6.simDog.chr6 508962 36 - 593897 TTTTTCACCTTTTGGT--GTACAACCTTCCAGTCAAAC-- -s simHuman_chr6.simHuman.chr6 108550 36 + 601863 TTTTTCTCAATTTCCC--AGATGACCTTCTAGTTAATC-- -s simRat_chr6.simRat.chr6 105062 40 + 647215 CTTTTCTCACCTCGCCTGATATAACCTTCTTGTTAAACTA - -a -s simMouse_chr6.simMouse.chr6 112795 6 + 636262 TAACTA -s Anc0.Anc0refChr1 6433 6 - 62388 TAACTA -s Anc1.Anc1refChr2 84529 6 + 144309 TAACTA -s Anc2.Anc2refChr2 22136 6 + 27695 TAACTA -s mr.mrrefChr0 107525 6 + 130230 TAACTA -s simCow_chr6.simCow.chr6 116226 6 + 602619 TAACTA -s simHuman_chr6.simHuman.chr6 108586 6 + 601863 TAACTA -s simRat_chr6.simRat.chr6 105102 6 + 647215 TAACTA - -a -s simMouse_chr6.simMouse.chr6 112801 74 + 636262 CTAAAGATCTATCATGGATTTATCCTACCCTGCAGCAACTATGTTGCATAGTCAGCCAAAGAGTACAATACAAG -s Anc0.Anc0refChr1 6440 74 - 62388 CTAAATGTCAATCATTCATTTATCCTACCCTACAGTAACTGAGTTGAATAGTCAGCAACTGAGTATGATACAGG -s Anc1.Anc1refChr2 84536 74 + 144309 CTAAATGTCAATCATTCATTTATCCTACCCTACAGTAACTGAGTTGAATAGTCAGCAACTGAGTATGATACAGG -s Anc2.Anc2refChr2 22143 74 + 27695 CTAAATGTTACTCATTCATCTAATCTGCCCTACAGTAACTGAGTTGAATAGGCAGCAACTGAGTATGATACAGG -s mr.mrrefChr0 107531 74 + 130230 CTAAAGATCTATCATGGATTTATCCTACCCTGCAGCAACTATGTTGCATAGTCAGCAAATGAGTATAATACAAG -s simCow_chr6.simCow.chr6 116233 70 + 602619 TCGAATTTTGTTCATGC----CAGCTTCACTATAGTAATTGAGTTGATCAGGTAGCAACTGAGCATGCTACAAG -s simDog_chr6.simDog.chr6 508999 74 - 593897 CTAAATGTTACTCATTTATCTAATCTGCCCTACAGTAACTAAGTTGTATATGCAACAACTAATTATGATACAGG -s simHuman_chr6.simHuman.chr6 108593 74 + 601863 CTCAGTGTCAATCATACATTTATCCTACCCTACAGTACCTGAGTTGAATAGTCAGCAACTGAGTATGATACAGA -s simRat_chr6.simRat.chr6 105108 72 + 647215 CTAA--ATTTATCATGGATTTATTCTACCCTGCTGCAACTATGTTGCATACTCAGCAGTTGAGTATAGTACAAG - -a -s simMouse_chr6.simMouse.chr6 112875 70 + 636262 TAGATTGTACATTTGTTTATTTGGAGTAGAAAACTGAGTTTGATACCAGTACATATGTAACATTTGTTCA -s Anc0.Anc0refChr1 6514 19 - 62388 TAGATTC---AT-----------------------------------------------A-ATTTATTCA -s Anc1.Anc1refChr2 84610 20 + 144309 TAGATTC---AT-----------------------------------------------ACATTTATTCA -s Anc2.Anc2refChr2 22217 19 + 27695 TAGATTC---AT-----------------------------------------------A-GGTTATACA -s mr.mrrefChr0 107605 63 + 130230 TAGATTG---ATTTGTTTATTTGGAGTAG-AAACTGAGTTTGATACCAGTACAT---TAACATTTGTTCA -s simCow_chr6.simCow.chr6 116304 19 + 602619 TAGATTC---AC-----------------------------------------------A-GATCATGCA -s simDog_chr6.simDog.chr6 509073 19 - 593897 TAGACTC---AT-----------------------------------------------A-GGCTATACA -s simHuman_chr6.simHuman.chr6 108667 20 + 601863 TCGATTC---AT-----------------------------------------------ACATTTATTCA -s simRat_chr6.simRat.chr6 105180 63 + 647215 AAGATAG---GTTTGTTTATTTTGAGTAG-CAACTGAGTTTAATTCTGGTCGAT---TAACATTTGTTCA - -a -s simMouse_chr6.simMouse.chr6 112945 28 + 636262 TTTCAGCCCTGGAACAAAAGTAGTGCAA -s Anc0.Anc0refChr1 6533 28 - 62388 TTTTGGCCACGCAACAAAAGTAAGGCAA -s Anc1.Anc1refChr2 84630 28 + 144309 TTTTGGCCACGCAACAAAAGTAAGGCAA -s Anc2.Anc2refChr2 22236 28 + 27695 TTTTGGCCACGCTACAAAAGTAAGGCAA -s mr.mrrefChr0 107668 28 + 130230 TTTCAGCCATGGAACAAAAGTAGTGCAA -s simCow_chr6.simCow.chr6 116324 28 + 602619 TTTTGGCTGTGCTACAAAAGTAAGGCAA -s simDog_chr6.simDog.chr6 509092 28 - 593897 TTTTAGCCACGCTGCAAAAGTAAGGCAA -s simHuman_chr6.simHuman.chr6 108687 28 + 601863 TATTGGCCAGGTAACAAAAGTAAGGCAA -s simRat_chr6.simRat.chr6 105243 28 + 647215 TTTCAGTCACGGAACAATGGTAGTGCAA - -a -s simMouse_chr6.simMouse.chr6 112973 6 + 636262 TACAAA -s Anc0.Anc0refChr1 6561 6 - 62388 TACAAA -s Anc1.Anc1refChr2 84658 6 + 144309 TACAAA -s Anc2.Anc2refChr2 22265 6 + 27695 CAGAAA -s mr.mrrefChr0 107696 6 + 130230 TACAAA -s simCow_chr6.simCow.chr6 116353 6 + 602619 TACAAA -s simDog_chr6.simDog.chr6 509121 6 - 593897 CAGAAA -s simHuman_chr6.simHuman.chr6 108715 4 + 601863 TAC--A -s simRat_chr6.simRat.chr6 105271 6 + 647215 TAAAAA - -a -s simMouse_chr6.simMouse.chr6 112979 18 + 636262 ATTGTGTTCTTGGTGAGT -s Anc0.Anc0refChr1 6567 18 - 62388 ATTGTGTTTTTCCAGAGT -s Anc1.Anc1refChr2 84664 18 + 144309 ATTGTGTTTTTCCAGAGT -s Anc2.Anc2refChr2 22271 18 + 27695 ATTGTGTCTTTCCAGGGT -s mr.mrrefChr0 107702 18 + 130230 ATTGTGTTCTTGGTGAGT -s simCow_chr6.simCow.chr6 116359 18 + 602619 ATTGTGCCTTTCCAGGAC -s simDog_chr6.simDog.chr6 509127 18 - 593897 GTTGTGTCTTTCCAGGGT -s simHuman_chr6.simHuman.chr6 108719 18 + 601863 ATTGTGTTTTTTTGAAGA -s simRat_chr6.simRat.chr6 105281 18 + 647215 ATTGTCTTCTTGATGAGT - -a -s simMouse_chr6.simMouse.chr6 112997 67 + 636262 TAACTTGTCGCAAAACCCATAAATAACAAAGGGTGACAGGTAAGTGGAGACGATAACCCCCCCTATC -s Anc0.Anc0refChr1 6585 65 - 62388 TGAATTGCCACACAATCTATAAATGACAAA-GGTGACAGGTAATCAGAGGCAATACCCCCCCCTAC- -s Anc1.Anc1refChr2 84682 65 + 144309 TGAATTGCCACACAATCTATAAATGACAAA-GGTGACAGGTAATCAGAGGCAATACCCCCCCCTAC- -s Anc2.Anc2refChr2 22290 65 + 27695 TGAATAGCCACACAATTTATAAATGACAGA-GGTAACAGGTAATCAGGGGCAATACCCCCCCCTAC- -s mr.mrrefChr0 107720 67 + 130230 TGACTTGTCACAAAACCCATAAATAACAAAGGGTGACAGGTAATTAGAGACGATAACCCCCCCTATC -s simCow_chr6.simCow.chr6 116378 65 + 602619 TAAATCACCTCACACTTTATAAAGGACACT-GGTAACAGGTAATTAGTGGCAATGCCGCCCCCTAC- -s simDog_chr6.simDog.chr6 509146 65 - 593897 GGAATAGCCACACAATTTATTAATGACAGA-GGTAGCAGGTAGTCGGGGGCAACACCCCCCCCTAC- -s simHuman_chr6.simHuman.chr6 108737 62 + 601863 TGAATTGCCACACAATCTATAAATGACAAA----GACAGGTAATCAGAAGCAATACCCCCCCCCAC- -s simRat_chr6.simRat.chr6 105299 66 + 647215 TGACTTGTCACAAAACCCATAAATAAT-AAGGGTGATAGGTAATTAGAGACCATAGCCCCCCCTATC - -a -s simMouse_chr6.simMouse.chr6 113064 2 + 636262 AA -s Anc0.Anc0refChr1 6650 1 - 62388 -A -s Anc1.Anc1refChr2 84747 1 + 144309 -A -s Anc2.Anc2refChr2 22355 1 + 27695 -A -s mr.mrrefChr0 107787 2 + 130230 AA -s simCow_chr6.simCow.chr6 116445 1 + 602619 -A -s simDog_chr6.simDog.chr6 509211 1 - 593897 -C -s simHuman_chr6.simHuman.chr6 108799 1 + 601863 -A -s simRat_chr6.simRat.chr6 105367 2 + 647215 AA - -a -s simMouse_chr6.simMouse.chr6 113066 80 + 636262 ATTGAAGCAACTGTAGTAAGACTATAGTGGCTGGATAAGCAGCAAACCATTGTGGGTCTCCCTCTAGGAGGGGAATTGGG -s Anc0.Anc0refChr1 6651 79 - 62388 ATTAAAGCACCTAGGGTAAGAGA-TAGTTGGTGGTAGACCAGTAGACCATCAGGAATATCCCAATAGTAGGGAAATTGGA -s Anc1.Anc1refChr2 84748 80 + 144309 ATTAAAGCACCTAGGGTAAGAGACTAGTTGGTGGTAGACCAGTAGACCATCAGGAATATCCCAATAGTAGGGAAATTGGA -s Anc2.Anc2refChr2 22356 79 + 27695 ATTAAAGCACGTAGGGTAAGAGA-TAGTTGGTGGTAGACCAGTAGACCATCAGGAATATCACAATAGTAGGGAAATTGGA -s mr.mrrefChr0 107789 80 + 130230 ATTGAAGCACCTGTAGTAAGACTATAGTGGCTGGTTGACCAGTAAACCATTGTGGGTCTCCCTCTAGGAGGGGAATTGGG -s simCow_chr6.simCow.chr6 116446 78 + 602619 ATTAAAGCACATGGGGCAAGAAT-TATTTGGTGGTTGACCAGTTGACTATCAGAAATATC-CACTAGAAGGGAAGTTGGA -s simDog_chr6.simDog.chr6 509213 79 - 593897 ATTAAGGCATGTAGCGTAAGAGA-TAGTTGCTGGTAGCCCAGTAGACCATCAGGAATATCACAAAAATGGGGAAATTGCA -s simHuman_chr6.simHuman.chr6 108800 79 + 601863 ATTAAAGTGCCTAGGATTAGAGGCTAGTTGGT-GTAGACCTGTATACCTTCAGGAATATCCCAATAGTAGGGAAATTGGA -s simRat_chr6.simRat.chr6 105369 80 + 647215 ATTGAAGCACCTGCAGCAAGAATATAGGGGCTGGTGGACCAGTACACCAATGTGGGTCTCCCTCTAGGGGGGGAATTGGG - -a -s simMouse_chr6.simMouse.chr6 113146 92 + 636262 GCACACATGGTTGCCAAGGAAAGGGGCAGAGCAGGGTGAAGGGGCAGAGCAGAGTATAGTTGGGCAGGTAAACAAATAGTCCCACACATGTA -s Anc0.Anc0refChr1 6732 72 - 62388 AGATACATGGTTACTAAGGAAA--------------------GACAAACTAGAGTGTAGTTGAAAAGGTAAACAAATAGTCTCACACAATTG -s Anc1.Anc1refChr2 84830 72 + 144309 AGATACATGGTTACTAAGGAAA--------------------GACAAACTAGAGTGTAGTTGAAAAGGTAAACAAATAGTCTCACACAATTG -s Anc2.Anc2refChr2 22437 72 + 27695 AGATACATAGTTACTGAGGAAA--------------------GACAAACTAGGATGTAGTTGAAAAGGTGAACAAACAGTCTCACACAATTG -s mr.mrrefChr0 107869 92 + 130230 GCATACATGGTTGCCAAGGAAAGGGGCAGAGCAGGGTGAAGGGGCAGAGCAGAGTATAGTTGGGCAGGTAAACAAATAGTCCCACACATGTA -s simCow_chr6.simCow.chr6 116526 72 + 602619 AGATACATAGTTACTCAGGAAA--------------------GACCAGGTAGCTTGTAGTTGAGAAGGTGAACATACAGTCCCACACAAGTG -s simDog_chr6.simDog.chr6 509294 72 - 593897 AAACACATAATTACTGTGGAAA--------------------GACAAACTAAGATCTAGTTGAAAAGGTGAACAAACAGTCTCACACAATTG -s simHuman_chr6.simHuman.chr6 108881 61 + 601863 AGATACATGGTTAGTAAGGAAA--------------------GACATACTAGAGTGTAGTTGAAAAGGTAAACAAATGGTC----------- -s simRat_chr6.simRat.chr6 105449 92 + 647215 GCATACATGGTTGCCATGGAAAGGGGCAGAGCAGGGGAAAGGGGCACAGCAAGGTATAGTTGGGCAGGTAAACAAATAGTCCCACACATGTG - -a -s simMouse_chr6.simMouse.chr6 113238 4 + 636262 TCTA -s Anc0.Anc0refChr1 6804 4 - 62388 ACTA -s Anc1.Anc1refChr2 84902 4 + 144309 ACTA -s Anc2.Anc2refChr2 22509 4 + 27695 ACTA -s mr.mrrefChr0 107961 4 + 130230 TCTA -s simCow_chr6.simCow.chr6 116598 4 + 602619 ACTA -s simDog_chr6.simDog.chr6 509366 4 - 593897 ACTA -s simHuman_chr6.simHuman.chr6 108942 1 + 601863 ---A -s simRat_chr6.simRat.chr6 105543 4 + 647215 TCTA - -a -s simMouse_chr6.simMouse.chr6 113242 2 + 636262 AA -s Anc0.Anc0refChr1 6808 2 - 62388 AA -s Anc1.Anc1refChr2 84906 2 + 144309 AA -s Anc2.Anc2refChr2 22513 2 + 27695 AA -s mr.mrrefChr0 107965 2 + 130230 AA -s simCow_chr6.simCow.chr6 116602 2 + 602619 AG -s simDog_chr6.simDog.chr6 509371 2 - 593897 AA -s simHuman_chr6.simHuman.chr6 108943 2 + 601863 AA -s simRat_chr6.simRat.chr6 105547 2 + 647215 AC - -a -s simMouse_chr6.simMouse.chr6 113244 21 + 636262 CTGTGGTGAGGGAAGTACAGA -s Anc0.Anc0refChr1 6810 21 - 62388 CTACAGTGAGGGTAGTACAAC -s Anc1.Anc1refChr2 84908 21 + 144309 CTACAGTGAGGGTAGTACAAC -s Anc2.Anc2refChr2 22518 21 + 27695 CTACAGCAAGGGTAGTACAAC -s mr.mrrefChr0 107967 21 + 130230 CTGTGGTGAGGGTAGTACAGA -s simCow_chr6.simCow.chr6 116607 21 + 602619 CTACAGCAAGGGTAGTTCAAT -s simDog_chr6.simDog.chr6 509376 20 - 593897 CTAC-GCAAAGGTAGTACAAC -s simHuman_chr6.simHuman.chr6 108945 21 + 601863 CTACAGTGAGGGTAGTAGAAG -s simRat_chr6.simRat.chr6 105549 21 + 647215 CTGTGGTGAGGGTAGTACAGA - -a -s simMouse_chr6.simMouse.chr6 113265 6 + 636262 CCTCAT -s Anc0.Anc0refChr1 6832 6 - 62388 TAGGGT -s Anc1.Anc1refChr2 84930 6 + 144309 TAGGGT -s Anc2.Anc2refChr2 22540 6 + 27695 TAGGGT -s mr.mrrefChr0 107989 6 + 130230 CCGGGT -s simCow_chr6.simCow.chr6 116629 6 + 602619 CACGGT -s simDog_chr6.simDog.chr6 509397 6 - 593897 TAGGGT -s simHuman_chr6.simHuman.chr6 108967 6 + 601863 TTGGGT -s simRat_chr6.simRat.chr6 105571 6 + 647215 CAGGGT - -a -s simMouse_chr6.simMouse.chr6 113271 28 + 636262 GTCATAGCTCTTTGCAAAGGTTCTCTAT -s Anc0.Anc0refChr1 6838 28 - 62388 ATGGTAACTTTTTGCAAAGGTACTCTAT -s Anc1.Anc1refChr2 84936 28 + 144309 ATGGTAACTTTTTGCAAAGGTACTCTAT -s Anc2.Anc2refChr2 22546 28 + 27695 ATGGTAATTTTTCACCAAGGTACTCCAT -s mr.mrrefChr0 107995 28 + 130230 GTCATAGCTCTTTGCAAAGGTTCTCTAT -s simCow_chr6.simCow.chr6 116635 28 + 602619 ATTGTAATCTTTCACCAAGATATTCCAT -s simDog_chr6.simDog.chr6 509403 28 - 593897 ACGGTGATTTTTCACCAAGGTACTCCAG -s simHuman_chr6.simHuman.chr6 108973 22 + 601863 ATGGTAACT--TTGCA----TACTCTAT -s simRat_chr6.simRat.chr6 105587 28 + 647215 GTCATAGCTATTTGCAGAGGTTCTCAAC - -a -s simMouse_chr6.simMouse.chr6 113299 18 + 636262 CACAAGCTTCAGATTGAG -s Anc0.Anc0refChr1 6866 18 - 62388 CACAAGCTTCAGAATCAG -s Anc1.Anc1refChr2 84964 18 + 144309 CACAAGCTTCAGAATCAG -s Anc2.Anc2refChr2 22574 18 + 27695 CACAAGCTTCAGAATCAT -s mr.mrrefChr0 108023 18 + 130230 CACAAGCTTCAGATTGAG -s simCow_chr6.simCow.chr6 116668 18 + 602619 CACAAGCTTCAAAATCAT -s simDog_chr6.simDog.chr6 509431 18 - 593897 GACAGGCCCCAGAATGAT -s simHuman_chr6.simHuman.chr6 108995 18 + 601863 CACAAGTTTCAGAATCAG -s simRat_chr6.simRat.chr6 105615 18 + 647215 CACAAGCTTCAGATCAAG - -a -s simMouse_chr6.simMouse.chr6 113317 29 + 636262 GTTTTGTATGCTGCAAATGGGATATATAC -s Anc0.Anc0refChr1 6889 24 - 62388 GTTTTGTGTGCTGTG-----GACATATCC -s Anc1.Anc1refChr2 84987 27 + 144309 GTTTTGTGTGCTGTGCA--GGACATATCC -s Anc2.Anc2refChr2 22597 24 + 27695 GTTTTGTGTGCTGTG-----GACATACCC -s mr.mrrefChr0 108041 29 + 130230 GTTTTGTATGCTGCAAATGGGATATATAC -s simCow_chr6.simCow.chr6 116691 24 + 602619 ATTTTGCCCGTTGTA-----CACGTACGC -s simDog_chr6.simDog.chr6 509454 24 - 593897 GTTTTTTGTGCTGTG-----GACATACCC -s simHuman_chr6.simHuman.chr6 109018 21 + 601863 GTTTTGTGTGCTGTGCA--------ATCC -s simRat_chr6.simRat.chr6 105633 29 + 647215 GTTTTGTATGCTGCAGACAGGACAACTTC - -a -s simMouse_chr6.simMouse.chr6 113346 31 + 636262 TTAGAAGTATGGGTCTGGGCACACATCCCTA -s Anc0.Anc0refChr1 6913 31 - 62388 TTAGAAGCAGGGGTTTGGGCACACATCCCTA -s Anc1.Anc1refChr2 85014 31 + 144309 TTAGAAGCAGGGGTTTGGGCACACATCCCTA -s Anc2.Anc2refChr2 22628 31 + 27695 TTAGAAGCAGGGGTTATGGCACACATTCCTA -s mr.mrrefChr0 108070 31 + 130230 TTAGAAGTATGGGTTTGGGCACACATCCCTA -s simCow_chr6.simCow.chr6 116722 31 + 602619 TTAGAGGTAAGGGATATAGCACACGTTCCTA -s simDog_chr6.simDog.chr6 509485 31 - 593897 TTAGAAGCAGGGGTTATGGCACACATTCCTA -s simHuman_chr6.simHuman.chr6 109039 19 + 601863 T------------TTTGCTTACACATCCCTA -s simRat_chr6.simRat.chr6 105662 31 + 647215 TTGGAAGTACGGATTTGGGCACACTTTCCCA - -a -s simMouse_chr6.simMouse.chr6 113377 29 + 636262 GTCTGAAAGAAATTTCTCACAGGAGTGTA -s Anc0.Anc0refChr1 6944 29 - 62388 GTCTGAAAGGAGTCTCTCACCAGATTCCA -s Anc1.Anc1refChr2 85045 29 + 144309 GTCTGAAAGGAGTCTCTCACCAGATTCCA -s Anc2.Anc2refChr2 22659 29 + 27695 GTCTGAAAGGAGTCTCTCACCAAATGCCA -s mr.mrrefChr0 108101 29 + 130230 GTCTGAAAGAAGTTTCTCACAAGAGTCTA -s simCow_chr6.simCow.chr6 116753 28 + 602619 GTGTGAAAGGAGTTTCTCATCAAAT-CCA -s simDog_chr6.simDog.chr6 509516 29 - 593897 GCCTGAAAGGAGTCTCTCACCAAGTGCAA -s simHuman_chr6.simHuman.chr6 109059 29 + 601863 GTCTGAAAGGAGTATCTCACTAGATTCCA -s simRat_chr6.simRat.chr6 105693 29 + 647215 GTCTGAAAGAAGTTTCTCACAAGAGTCTA - -a -s simMouse_chr6.simMouse.chr6 113406 22 + 636262 ATTAATTATGTGACTGACAGAC -s Anc0.Anc0refChr1 6974 22 - 62388 GTCAATTATATGACTGAGAGAT -s Anc1.Anc1refChr2 85075 22 + 144309 GTCAATTATATGACTGAGAGAT -s Anc2.Anc2refChr2 22689 22 + 27695 GTTAATTATATGACTGAGGGAT -s mr.mrrefChr0 108131 22 + 130230 GTCAATTATGTGACTGACAGAT -s simCow_chr6.simCow.chr6 116782 22 + 602619 GTTAGTTATATGACTGAGTGAT -s simDog_chr6.simDog.chr6 509546 22 - 593897 ATTAATGATATGACTGAGGGAT -s simHuman_chr6.simHuman.chr6 109089 22 + 601863 GTCAATTCTATGACTGAGAGAT -s simRat_chr6.simRat.chr6 105723 22 + 647215 GTCAATTATGTGACTGACAGAT - -a -s simMouse_chr6.simMouse.chr6 113428 46 + 636262 GAGACTCTGTCTAGGGGAACGCGGCCCTGGATGGCGGGTATGTTAT -s Anc0.Anc0refChr1 6996 46 - 62388 GAGACTATGTCTAGGGGAATTCAAGCCTCTATAGCAGTTTTGTTGC -s Anc1.Anc1refChr2 85097 46 + 144309 GAGACTATGTCTAGGGGAATTCAAGCCTCTATAGCAGTTTTGTTGC -s Anc2.Anc2refChr2 22711 46 + 27695 GAGACTCTGTCTAGGGGAATTCAAGCCTCTATAGCAGTTTTGTTGC -s mr.mrrefChr0 108153 46 + 130230 GAGACTATGTCTAGGGGAATGCAGCCCTGGATGGCGGGTATGTTAT -s simCow_chr6.simCow.chr6 116804 46 + 602619 GAGACTCTGTCTAGGGGAATGCAGACCTCCATAGCTGTTTTGTTGC -s simDog_chr6.simDog.chr6 509568 46 - 593897 AAGGCTCTGTCTTGGGGAATTCAAGCCTCTATTGCAATTCTGTTGT -s simHuman_chr6.simHuman.chr6 109111 43 + 601863 GAGACTATGTCAAGGGGAATTTCAGACT---TAGCAGTCTTATTGC -s simRat_chr6.simRat.chr6 105751 40 + 647215 GAGACTATGTCTAGG---ATGCAGCCCTTGGTGGTGAGTA---TAT - -a -s simMouse_chr6.simMouse.chr6 113474 2 + 636262 GT -s Anc0.Anc0refChr1 7058 2 - 62388 GT -s Anc1.Anc1refChr2 85159 2 + 144309 GT -s Anc2.Anc2refChr2 22773 2 + 27695 GT -s mr.mrrefChr0 108199 2 + 130230 GT -s simCow_chr6.simCow.chr6 116866 2 + 602619 GT -s simDog_chr6.simDog.chr6 509630 2 - 593897 GT -s simHuman_chr6.simHuman.chr6 109170 2 + 601863 GT -s simRat_chr6.simRat.chr6 105791 2 + 647215 GC - -a -s simMouse_chr6.simMouse.chr6 113476 28 + 636262 ATCATCAAGAGATCCAGTTCACTAGCAA -s Anc0.Anc0refChr1 7060 26 - 62388 GTTATCAGGAGATATAGTAGACCA--AG -s Anc1.Anc1refChr2 85161 26 + 144309 GTTATCAGGAGATATAGTAGACCA--AG -s Anc2.Anc2refChr2 22775 26 + 27695 GTTATCAGGAGATATAGTAGACCA--AG -s mr.mrrefChr0 108201 28 + 130230 ATTATCAGGAGATCCAGTTCACTAGCAA -s simCow_chr6.simCow.chr6 116868 26 + 602619 GTTGTCAGGAGACCTAGTAGATGA--AG -s simDog_chr6.simDog.chr6 509634 26 - 593897 GTTATTGGGAGGTATAGTAGACCA--AG -s simHuman_chr6.simHuman.chr6 109172 11 + 601863 GTTATCAGGAG----------------- -s simRat_chr6.simRat.chr6 105793 28 + 647215 ATTATCAGGAGATACAGTTCACTACCAA - -a -s simMouse_chr6.simMouse.chr6 113504 28 + 636262 ACCTGACAAGTATATAAACATAAGAGCC -s Anc0.Anc0refChr1 7086 28 - 62388 ACATGACCAATATGCAGCCATAAACGCT -s Anc1.Anc1refChr2 85187 28 + 144309 ACATGACCAATATGCAGCCATAAACGCT -s Anc2.Anc2refChr2 22801 28 + 27695 ACATGACCAATATGCAGCCTGAAAAGCA -s mr.mrrefChr0 108229 28 + 130230 ACCTGACAAGTATATAAACATAAACGCT -s simCow_chr6.simCow.chr6 116894 28 + 602619 GCTTGATGAATGTGCAGCCCAGAATGCA -s simDog_chr6.simDog.chr6 509662 28 - 593897 ACATGACCAATATGCAGCCTGAAAAGCA -s simHuman_chr6.simHuman.chr6 109183 9 + 601863 -------------------ATAAACGCT -s simRat_chr6.simRat.chr6 105821 28 + 647215 ACCTGCCACATGTATCAACATAAACGCT - -a -s simMouse_chr6.simMouse.chr6 113532 23 + 636262 CAGAACACATTTCAGAGGCATAT -s Anc0.Anc0refChr1 7114 19 - 62388 T----CTCCTGTGGGGGGAACAT -s Anc1.Anc1refChr2 85215 19 + 144309 T----CTCCTGTGGGGGGAACAT -s Anc2.Anc2refChr2 22829 19 + 27695 T----CTCCTGTGGGGGCAACAT -s mr.mrrefChr0 108257 23 + 130230 CAGAACACATTTCGGAGGCATAT -s simCow_chr6.simCow.chr6 116925 19 + 602619 T----CTCCTGTGGGGGCAACAT -s simDog_chr6.simDog.chr6 509690 19 - 593897 T----CTCCTATGGGAGCGGCAT -s simHuman_chr6.simHuman.chr6 109192 19 + 601863 T----CTCCTGTGGTGGGAACAT -s simRat_chr6.simRat.chr6 105849 21 + 647215 CAGAATAC--TTAGGAGGCATAT - -a -s simMouse_chr6.simMouse.chr6 113555 10 + 636262 ATCAGGATAC -s Anc0.Anc0refChr1 7133 10 - 62388 AGTAGAGTAT -s Anc1.Anc1refChr2 85234 10 + 144309 AGTAGAGTAT -s Anc2.Anc2refChr2 22848 10 + 27695 AGTAGAGTAT -s mr.mrrefChr0 108280 10 + 130230 ATCAGGGTAC -s simCow_chr6.simCow.chr6 116966 10 + 602619 AGTAGAGTAT -s simDog_chr6.simDog.chr6 509709 9 - 593897 AGTAG-GTAT -s simHuman_chr6.simHuman.chr6 109211 10 + 601863 ACTAGAGTAT -s simRat_chr6.simRat.chr6 105870 10 + 647215 ATCAGGGTAC - -a -s simMouse_chr6.simMouse.chr6 113565 37 + 636262 TTTACAGGTTTTGGAAGCAATGCACCATGTATTGTTG -s Anc0.Anc0refChr1 7148 1 - 62388 T------------------------------------ -s Anc1.Anc1refChr2 85249 37 + 144309 TTGGAGGGTTTTGAAATGGAGGAGACATGCGTTGTCG -s Anc2.Anc2refChr2 22863 1 + 27695 T------------------------------------ -s mr.mrrefChr0 108290 37 + 130230 TTTACAGGTTTTGGAAGCAATGCGCCATGCATTGTTG -s simCow_chr6.simCow.chr6 116981 1 + 602619 T------------------------------------ -s simDog_chr6.simDog.chr6 509723 1 - 593897 T------------------------------------ -s simHuman_chr6.simHuman.chr6 109226 37 + 601863 TTGGAGGGTTTTGAAATGGAGGAGACATGCGTTGTCG -s simRat_chr6.simRat.chr6 105880 37 + 647215 TTTACAAGTCTTGGAACCAATGCGCCATGCATTGTTG - -a -s simMouse_chr6.simMouse.chr6 113602 28 + 636262 GATATTCTATAATCACATGCAGGGCATA -s Anc1.Anc1refChr2 85286 27 + 144309 GATAAATTAT-ATCATACTCATGTTACA -s mr.mrrefChr0 108327 27 + 130230 GATAATCTAT-ATCATATGCAGGTCACA -s simHuman_chr6.simHuman.chr6 109263 27 + 601863 GATAAATTAT-ATCATACTCATGTTACA -s simRat_chr6.simRat.chr6 105974 24 + 647215 GATAATCTAT----ATATGCAGGTCACA - -a -s simMouse_chr6.simMouse.chr6 113630 40 + 636262 TGTCCATAAACATTTTCCATAGACACTTCCACGTAAAGAG -s Anc0.Anc0refChr1 7149 22 - 62388 ---CCATCAACATT---------------CACATAAAAGG -s Anc1.Anc1refChr2 85324 25 + 144309 TGTCCATCAACATT---------------CACATAAAAGG -s Anc2.Anc2refChr2 22864 22 + 27695 ---CCATCATTATT---------------CATGTGGAAGG -s mr.mrrefChr0 108365 40 + 130230 TGTCCATAAACATTTTCCATAAACATTTCCACATAAAGAG -s simCow_chr6.simCow.chr6 116982 22 + 602619 ---CCATCAATATA---------------TACTTAGGAGG -s simDog_chr6.simDog.chr6 509724 22 - 593897 ---CCATCATTATT---------------CATGTGTAAGG -s simHuman_chr6.simHuman.chr6 109301 21 + 601863 TGTCTGTCAACATT---------------CACACAA---- -s simRat_chr6.simRat.chr6 106009 40 + 647215 CGTCCATAAACATTTTCCATAAACATTTCCACATAAAGAA - -a -s simMouse_chr6.simMouse.chr6 113670 65 + 636262 TTCATCTAGGAAAGATTATGCAAAGTGCCTACTATGGAAATTTTGACAACAGAAAGAAGTGAACT -s Anc0.Anc0refChr1 7171 64 - 62388 TTCATC-AAAAAGGGTCATTCAAAATGCCTACTAGGGAAGTTTTGACAGCAGAAAGAAGGGAACT -s Anc1.Anc1refChr2 85349 64 + 144309 TTCATC-AAAAAGGGTCATTCAAAATGCCTACTAGGGAAGTTTTGACAGCAGAAAGAAGGGAACT -s Anc2.Anc2refChr2 22886 64 + 27695 TTCTTC-AAAAAGCGTCATTGAAAACACCTACTAGGAAAGGTTTGACAGCAGAAAGAAGGGAACT -s mr.mrrefChr0 108405 65 + 130230 TTCATCTAGGAAAGGTTATGCAAAATGCCTACTATGGAAATTTTGACAACAGAAAGAAGTGAACT -s simCow_chr6.simCow.chr6 117007 60 + 602619 TCCTTC-AAAGAGAGTAATTTAAAGCACCTACTAGGAAAG----GACGATAGAAAGAAGGGAACT -s simDog_chr6.simDog.chr6 509746 64 - 593897 TTCTTC-AAAAACCGTCATTGAAAACACCTATTAGGAAAGGTTTGACAGCAGAAAGAATGGAACT -s simHuman_chr6.simHuman.chr6 109322 62 + 601863 --CATC-AAAAAGGGTGATTCAAAATGCATGCTAGAGAAGTTTTGACAGCAGAAAGAAGGAAACT -s simRat_chr6.simRat.chr6 106049 65 + 647215 TTCATCTAGGAAAGGTTACGCAAAATACCTACTATGGAAATATTGACAACAGAAAGAAGTGGACT - -a -s simMouse_chr6.simMouse.chr6 113735 15 + 636262 AGGACACCAAACAAT -s Anc0.Anc0refChr1 7301 15 - 62388 AAGACACCAACCAAT -s Anc1.Anc1refChr2 85479 15 + 144309 AAGACACCAACCAAT -s Anc2.Anc2refChr2 23016 15 + 27695 AAGACACCAACCAAT -s mr.mrrefChr0 108470 15 + 130230 AAGACACCAAACAAT -s simCow_chr6.simCow.chr6 117133 15 + 602619 AAGACACCAACCAAT -s simDog_chr6.simDog.chr6 509876 15 - 593897 AAGACACCGGCCAAC -s simHuman_chr6.simHuman.chr6 109450 15 + 601863 AAGACAACAACCAAT -s simRat_chr6.simRat.chr6 106114 15 + 647215 AAGACACCAGTCAAT - -a -s simMouse_chr6.simMouse.chr6 113750 84 + 636262 AACATTTAACCAGCAAGCAATTTGGCTTAGAAATAGATCCTGAATCCTGGCCCTCGCCAGCCCTCGACGTGGGCTATTCATTGC -s Anc0.Anc0refChr1 7317 35 - 62388 AATATTTGAACAGCAA-------------------------------------------------GCCATGGGCTAATCATAAC -s Anc1.Anc1refChr2 85495 35 + 144309 AATATTTGAACAGCAA-------------------------------------------------GCCATGGGCTAATCATAAC -s Anc2.Anc2refChr2 23032 35 + 27695 AATATTTGAACATGAA-------------------------------------------------GCCATGGGCTAATCATAAC -s mr.mrrefChr0 108486 35 + 130230 AACATTTAAACAGCAA-------------------------------------------------GACATGGGCTAATCATTGC -s simCow_chr6.simCow.chr6 117149 35 + 602619 AGTATTCGAACTTGTA-------------------------------------------------GCCATGGGCTAATCATAAT -s simDog_chr6.simDog.chr6 509892 35 - 593897 AATCTTTGAACATGAG-------------------------------------------------GCCATGGGCTCATTATACC -s simHuman_chr6.simHuman.chr6 109466 35 + 601863 AATATTTGAACAGCAA-------------------------------------------------GCTACAGGCTAATCATAAC -s simRat_chr6.simRat.chr6 106130 35 + 647215 AACATTCAAACAGTAA-------------------------------------------------GACATGGGTTAATCATCGC - -a -s simMouse_chr6.simMouse.chr6 113834 1 + 636262 A -s Anc0.Anc0refChr1 7352 1 - 62388 A -s Anc1.Anc1refChr2 85530 1 + 144309 A -s Anc2.Anc2refChr2 23067 1 + 27695 A -s mr.mrrefChr0 108521 1 + 130230 A -s simCow_chr6.simCow.chr6 117186 1 + 602619 A -s simDog_chr6.simDog.chr6 509927 1 - 593897 A -s simHuman_chr6.simHuman.chr6 109501 1 + 601863 A -s simRat_chr6.simRat.chr6 106165 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 113835 3 + 636262 TAA -s Anc0.Anc0refChr1 7353 3 - 62388 TCA -s Anc1.Anc1refChr2 85531 3 + 144309 TCA -s Anc2.Anc2refChr2 23068 3 + 27695 TCA -s mr.mrrefChr0 108522 3 + 130230 TAA -s simCow_chr6.simCow.chr6 117187 3 + 602619 TCA -s simDog_chr6.simDog.chr6 509931 3 - 593897 TCA -s simHuman_chr6.simHuman.chr6 109502 3 + 601863 TCA -s simRat_chr6.simRat.chr6 106166 3 + 647215 TAA - -a -s simMouse_chr6.simMouse.chr6 113838 17 + 636262 TAATGCCAAGAATGAAG -s Anc0.Anc0refChr1 7356 17 - 62388 TAATCCCAAGAATGAGT -s Anc1.Anc1refChr2 85534 17 + 144309 TAATCCCAAGAATGAGT -s Anc2.Anc2refChr2 23071 17 + 27695 TAATCCCAATAATGGGT -s mr.mrrefChr0 108525 17 + 130230 TAATGCCAAGAATGAAT -s simCow_chr6.simCow.chr6 117190 17 + 602619 TAATGCCAAAAATGGGC -s simDog_chr6.simDog.chr6 509935 17 - 593897 TAATCCCACTTAGTGGT -s simHuman_chr6.simHuman.chr6 109505 17 + 601863 TAATACCAAGAATGAGT -s simRat_chr6.simRat.chr6 106169 16 + 647215 TAAAGCC-AGAATGAAT - -a -s simMouse_chr6.simMouse.chr6 113855 5 + 636262 TACCA -s Anc0.Anc0refChr1 7373 5 - 62388 TAATA -s Anc1.Anc1refChr2 85551 5 + 144309 TAATA -s Anc2.Anc2refChr2 23088 5 + 27695 TAATA -s mr.mrrefChr0 108542 5 + 130230 TACCA -s simCow_chr6.simCow.chr6 117207 5 + 602619 TAGCA -s simDog_chr6.simDog.chr6 509958 5 - 593897 TGATC -s simHuman_chr6.simHuman.chr6 109522 5 + 601863 TAATA -s simRat_chr6.simRat.chr6 106185 5 + 647215 TGCCA - -a -s simMouse_chr6.simMouse.chr6 113860 10 + 636262 AGAAAGAATA -s Anc0.Anc0refChr1 7384 10 - 62388 ACAAGAAATA -s Anc1.Anc1refChr2 85562 10 + 144309 ACAAGAAATA -s Anc2.Anc2refChr2 23099 10 + 27695 ACAAGAAATA -s mr.mrrefChr0 108547 10 + 130230 AGAAAGAATA -s simCow_chr6.simCow.chr6 117217 10 + 602619 ACAAGAAGCA -s simDog_chr6.simDog.chr6 509969 10 - 593897 CCAAATAATA -s simHuman_chr6.simHuman.chr6 109533 10 + 601863 ACAAGAAATA -s simRat_chr6.simRat.chr6 106190 10 + 647215 AGACAGAAGA - -a -s simMouse_chr6.simMouse.chr6 113870 27 + 636262 ACCATAATAGTTCCATGATATGGTGGT -s Anc0.Anc0refChr1 7394 27 - 62388 AGATCAACAGTGCCATAATATGGCAGT -s Anc1.Anc1refChr2 85572 27 + 144309 AGATCAACAGTGCCATAATATGGCAGT -s Anc2.Anc2refChr2 23109 27 + 27695 AGATCAACAGTGACATAATATGGCAGT -s mr.mrrefChr0 108557 27 + 130230 ACCTTAATAGTTCCATGATATGGTGGT -s simCow_chr6.simCow.chr6 117227 27 + 602619 AGATTAACAATTTCATAATATGCCAGT -s simDog_chr6.simDog.chr6 509983 23 - 593897 AGACCACTAGTGACCTG----CGAATT -s simHuman_chr6.simHuman.chr6 109543 27 + 601863 AAATCAACAGTCCCATAGTATGGCAGT -s simRat_chr6.simRat.chr6 106200 27 + 647215 GGCTTAATAGTTCCGTGATATGGTGGT - -a -s simMouse_chr6.simMouse.chr6 113897 3 + 636262 AGG -s Anc0.Anc0refChr1 7424 3 - 62388 GGG -s Anc1.Anc1refChr2 85602 3 + 144309 GGG -s Anc2.Anc2refChr2 23139 3 + 27695 GGG -s mr.mrrefChr0 108584 3 + 130230 GGG -s simCow_chr6.simCow.chr6 117257 3 + 602619 GAG -s simDog_chr6.simDog.chr6 510009 3 - 593897 AGG -s simHuman_chr6.simHuman.chr6 109573 3 + 601863 GGG -s simRat_chr6.simRat.chr6 106227 3 + 647215 GTG - -a -s simMouse_chr6.simMouse.chr6 113900 13 + 636262 GAAATCAGAACAC -s Anc0.Anc0refChr1 7427 13 - 62388 GAAATTAGACCAT -s Anc1.Anc1refChr2 85605 13 + 144309 GAAATTAGACCAT -s Anc2.Anc2refChr2 23142 13 + 27695 GAAATTAGACCAT -s mr.mrrefChr0 108587 13 + 130230 GAAATCAGACCAT -s simCow_chr6.simCow.chr6 117260 13 + 602619 GTAATTGGACCAC -s simDog_chr6.simDog.chr6 510016 11 - 593897 GAGAGTAG--TGT -s simHuman_chr6.simHuman.chr6 109576 13 + 601863 GAAATTAGACCAT -s simRat_chr6.simRat.chr6 106230 13 + 647215 GAAGTCAGACCAT - -a -s simMouse_chr6.simMouse.chr6 113913 17 + 636262 TAGTGATCTACCACCAT -s Anc0.Anc0refChr1 7440 17 - 62388 TAGTGACACAGTACCAA -s Anc1.Anc1refChr2 85618 17 + 144309 TAGTGACACAGTACCAA -s Anc2.Anc2refChr2 23155 17 + 27695 TAGTGTCACAGTGTCAA -s mr.mrrefChr0 108600 17 + 130230 TAGTGATCTACCACCAT -s simCow_chr6.simCow.chr6 117304 15 + 602619 TAGTGTCACA--GTCAA -s simDog_chr6.simDog.chr6 510027 17 - 593897 TAATGTCACAGTGTCAA -s simHuman_chr6.simHuman.chr6 109589 14 + 601863 TAGTGA---GTTACCAC -s simRat_chr6.simRat.chr6 106243 17 + 647215 TAGTGAACTATCTCCAT - -a -s simMouse_chr6.simMouse.chr6 113930 10 + 636262 CTTATTGTGC -s Anc0.Anc0refChr1 7460 10 - 62388 CATATTATGC -s Anc1.Anc1refChr2 85638 10 + 144309 CATATTATGC -s Anc2.Anc2refChr2 23175 10 + 27695 AATATCATGC -s mr.mrrefChr0 108617 10 + 130230 CTTATTGTGC -s simCow_chr6.simCow.chr6 117322 10 + 602619 AATATCATAC -s simDog_chr6.simDog.chr6 510047 10 - 593897 ATTATCATGC -s simHuman_chr6.simHuman.chr6 109606 10 + 601863 CATATTATGC -s simRat_chr6.simRat.chr6 106260 10 + 647215 CTTAGTGTGC - -a -s simMouse_chr6.simMouse.chr6 113940 4 + 636262 CACA -s Anc0.Anc0refChr1 7470 4 - 62388 TGCA -s Anc1.Anc1refChr2 85648 4 + 144309 TGCA -s Anc2.Anc2refChr2 23185 4 + 27695 TGCA -s mr.mrrefChr0 108627 4 + 130230 CACA -s simCow_chr6.simCow.chr6 117332 4 + 602619 AGCA -s simDog_chr6.simDog.chr6 510061 4 - 593897 TACA -s simHuman_chr6.simHuman.chr6 109616 4 + 601863 TGCA -s simRat_chr6.simRat.chr6 106270 4 + 647215 CACA - -a -s simMouse_chr6.simMouse.chr6 113944 13 + 636262 TTAAAATGGAGGG -s Anc0.Anc0refChr1 7478 13 - 62388 ATACAAAGGGGGG -s Anc1.Anc1refChr2 85656 13 + 144309 ATACAAAGGGGGG -s Anc2.Anc2refChr2 23193 13 + 27695 ATACAAAGGGGGG -s mr.mrrefChr0 108631 13 + 130230 TTAAAATGGAGGG -s simCow_chr6.simCow.chr6 117340 13 + 602619 CTACAAAGGGTGG -s simDog_chr6.simDog.chr6 510069 13 - 593897 ATACAAAGGGGGA -s simHuman_chr6.simHuman.chr6 109624 13 + 601863 GTACAAAGGGGGG -s simRat_chr6.simRat.chr6 106274 13 + 647215 TTAAAATGGAAGG - -a -s simMouse_chr6.simMouse.chr6 113957 4 + 636262 GAGG -s Anc0.Anc0refChr1 7491 4 - 62388 GGTG -s Anc1.Anc1refChr2 85669 4 + 144309 GGTG -s Anc2.Anc2refChr2 23206 4 + 27695 GGTG -s mr.mrrefChr0 108644 4 + 130230 GGGG -s simCow_chr6.simCow.chr6 117353 4 + 602619 TGTG -s simDog_chr6.simDog.chr6 510084 4 - 593897 GGTG -s simHuman_chr6.simHuman.chr6 109637 4 + 601863 GGTG -s simRat_chr6.simRat.chr6 106287 4 + 647215 GGGG - -a -s simMouse_chr6.simMouse.chr6 113961 56 + 636262 CACAAAATGGACTCAATTATTGTAATGACAATATTTTGGCAGTAGGTTTAATCCTT -s Anc0.Anc0refChr1 7495 53 - 62388 CGAAAAAAG---TCGATTATTATGATGACAATGCTATGGTGGTAGGTTAAATCTTC -s Anc1.Anc1refChr2 85673 55 + 144309 CGAAAAAAG-GGTCGATTATTATGATGACAATGCTATGGTGGTAGGTTAAATCTTC -s Anc2.Anc2refChr2 23210 53 + 27695 TGAAAAAAG---TCGTTTATTATGATAATAGTGCTATGATGGTAAGTTAAATCTAC -s mr.mrrefChr0 108648 56 + 130230 CACAAAATGGACTCAATTATTGTAATGACAATACTTTGGTGGTAGGTTTAATCTTT -s simCow_chr6.simCow.chr6 117360 53 + 602619 TATAAACAA---TCTTTTATCTTGATAATAGTGCTATCCTGGTAAGTTCAATATCC -s simDog_chr6.simDog.chr6 510088 39 - 593897 TGAAAAAAG---CAGTCTACTA--------------TGACAGTAAGTTAAATCCAC -s simHuman_chr6.simHuman.chr6 109641 47 + 601863 C---------GGTCCATTATTATGATGACAAAGCTCTGGTGGCAGGTTAAATCTTC -s simRat_chr6.simRat.chr6 106291 56 + 647215 CACAAAGTGGACTCAATTATTGTAACAATAATCCTTTGGTGGTGGGTTTAATCTTT - -a -s simMouse_chr6.simMouse.chr6 114017 3 + 636262 AGC -s Anc0.Anc0refChr1 7548 3 - 62388 GAA -s Anc1.Anc1refChr2 85728 3 + 144309 GAA -s Anc2.Anc2refChr2 23264 3 + 27695 GAG -s mr.mrrefChr0 108704 3 + 130230 AGA -s simCow_chr6.simCow.chr6 117414 3 + 602619 GAG -s simDog_chr6.simDog.chr6 510128 3 - 593897 GAG -s simHuman_chr6.simHuman.chr6 109688 3 + 601863 GAA -s simRat_chr6.simRat.chr6 106347 3 + 647215 AGA - -a -s simMouse_chr6.simMouse.chr6 114020 10 + 636262 ACTGCTGAAG -s Anc0.Anc0refChr1 7556 5 - 62388 A-----AGAA -s Anc1.Anc1refChr2 85736 5 + 144309 A-----AGAA -s Anc2.Anc2refChr2 23272 5 + 27695 A-----AGAA -s mr.mrrefChr0 108707 5 + 130230 A-----GAAG -s simCow_chr6.simCow.chr6 117422 5 + 602619 A-----AGAG -s simDog_chr6.simDog.chr6 510136 5 - 593897 A-----AGAA -s simHuman_chr6.simHuman.chr6 109696 5 + 601863 A-----AGAA -s simRat_chr6.simRat.chr6 106350 5 + 647215 A-----GATG - -a -s simMouse_chr6.simMouse.chr6 114030 12 + 636262 TATTCCTAAAAA -s Anc0.Anc0refChr1 7561 11 - 62388 TAT-CCTAAAGA -s Anc1.Anc1refChr2 85741 12 + 144309 TATTCCTAAAGA -s Anc2.Anc2refChr2 23277 11 + 27695 TAC-CCTAAAGA -s mr.mrrefChr0 108712 12 + 130230 TATTCCTAAAAA -s mr.mrrefChr0 108883 12 + 130230 TATTCCCAAACA -s simCow_chr6.simCow.chr6 117427 11 + 602619 TAC-CCTAAAGA -s simDog_chr6.simDog.chr6 510141 11 - 593897 TTC-CCTAAAGA -s simHuman_chr6.simHuman.chr6 109701 11 + 601863 TAT-ACTAAAGT -s simMouse_chr6.simMouse.chr6 114184 12 + 636262 TATTCCCAAACA -s simRat_chr6.simRat.chr6 106541 12 + 647215 TATTCCCAAGGA -s simRat_chr6.simRat.chr6 106355 12 + 647215 TCTTCCTAGAAG - -a -s simMouse_chr6.simMouse.chr6 114042 2 + 636262 GA -s mr.mrrefChr0 108724 2 + 130230 GA -s simRat_chr6.simRat.chr6 106367 2 + 647215 AA - -a -s simMouse_chr6.simMouse.chr6 114044 29 + 636262 ATAAGCACTCTTCTGTCTAAGCTTGGCTG -s Anc0.Anc0refChr1 7572 29 - 62388 AAAATCATTCTTCATTCTGATCTTGGCTG -s Anc1.Anc1refChr2 85753 29 + 144309 AAAATCATTCTTCATTCTGATCTTGGCTG -s Anc2.Anc2refChr2 23288 29 + 27695 AAAATCATACTTAATTCTGATCTTGGCTG -s mr.mrrefChr0 108726 29 + 130230 ATAAGCACTCTTCTGTCTGAGCTTGGCTG -s mr.mrrefChr0 108895 29 + 130230 AGAAGTCCTCTCTATTTTGATCTTGGCTG -s simCow_chr6.simCow.chr6 117438 29 + 602619 CAAATAATTCTTAATTTTGTTCTTGTCTA -s simDog_chr6.simDog.chr6 510152 29 - 593897 AAAATCATACTTAATTCTGATTTTGGCTG -s simHuman_chr6.simHuman.chr6 109712 29 + 601863 GAAATCATCCTTCGCTCTGCTCTTGGCTG -s simMouse_chr6.simMouse.chr6 114196 29 + 636262 AGAAGTCCTCTCTATTTTGATCTTGGCTG -s simRat_chr6.simRat.chr6 106553 29 + 647215 AAAAGTACTCTCTATTTTGATCTTGGCTG -s simRat_chr6.simRat.chr6 106369 29 + 647215 ACAAGCACTCTTTAGTCTGAGCTTGGCTG - -a -s simMouse_chr6.simMouse.chr6 114073 1 + 636262 C -s Anc0.Anc0refChr1 7601 1 - 62388 C -s Anc1.Anc1refChr2 85782 1 + 144309 C -s Anc2.Anc2refChr2 23317 1 + 27695 G -s mr.mrrefChr0 108755 1 + 130230 C -s simCow_chr6.simCow.chr6 117467 1 + 602619 G -s simDog_chr6.simDog.chr6 510181 1 - 593897 G -s simHuman_chr6.simHuman.chr6 109741 1 + 601863 C -s simRat_chr6.simRat.chr6 106398 1 + 647215 C - -a -s simMouse_chr6.simMouse.chr6 114074 17 + 636262 CCAAGGCTTTGATAGGC -s Anc0.Anc0refChr1 7602 17 - 62388 CTAAGGCTTTGAGAGGC -s Anc1.Anc1refChr2 85783 17 + 144309 CTAAGGCTTTGAGAGGC -s Anc2.Anc2refChr2 23318 17 + 27695 CTAAGGCTTTGAGAGGC -s mr.mrrefChr0 108756 17 + 130230 CCAAGGCTTTGATAGGC -s mr.mrrefChr0 108924 17 + 130230 CTAAGGCTTTGATAGAC -s simCow_chr6.simCow.chr6 117468 17 + 602619 CTAGGTCTTTGAGAGGC -s simDog_chr6.simDog.chr6 510182 17 - 593897 CTAAGGCTTTGAGAGGC -s simHuman_chr6.simHuman.chr6 109742 17 + 601863 ATAAGGCTTTGAGGGGC -s simMouse_chr6.simMouse.chr6 114225 17 + 636262 CTAAGGCTTTGATAGAC -s simRat_chr6.simRat.chr6 106607 17 + 647215 CTAAGACTTTGATAAGC -s simRat_chr6.simRat.chr6 106399 17 + 647215 CCAAGGCTTTGATAGGC - -a -s simMouse_chr6.simMouse.chr6 114091 6 + 636262 AAAGGA -s Anc0.Anc0refChr1 7620 6 - 62388 CAGGAA -s Anc1.Anc1refChr2 85801 6 + 144309 CAGGAA -s Anc2.Anc2refChr2 23336 6 + 27695 CAGGAA -s mr.mrrefChr0 108774 6 + 130230 AAAGGA -s mr.mrrefChr0 108942 6 + 130230 CTGCAT -s simCow_chr6.simCow.chr6 117486 6 + 602619 CATGAT -s simDog_chr6.simDog.chr6 510200 6 - 593897 TAGGGA -s simHuman_chr6.simHuman.chr6 109760 6 + 601863 CACGAA -s simMouse_chr6.simMouse.chr6 114243 6 + 636262 CTGCAT -s simRat_chr6.simRat.chr6 106625 6 + 647215 CTGCAT -s simRat_chr6.simRat.chr6 106417 6 + 647215 AAAGGA - -a -s simMouse_chr6.simMouse.chr6 114097 14 + 636262 CACAGGTTGAGGGC -s Anc0.Anc0refChr1 7626 14 - 62388 CAGAGGTCGAGGGC -s Anc1.Anc1refChr2 85807 14 + 144309 CAGAGGTCGAGGGC -s Anc2.Anc2refChr2 23342 14 + 27695 CAGAGGTCGAGGGC -s mr.mrrefChr0 108780 14 + 130230 CACAGGTTGAGGGC -s mr.mrrefChr0 108948 14 + 130230 CACAGGTTGACATC -s simCow_chr6.simCow.chr6 117492 14 + 602619 CAGAAACTGAGGGC -s simDog_chr6.simDog.chr6 510207 14 - 593897 CAGAGGTCGGGGGC -s simHuman_chr6.simHuman.chr6 109766 14 + 601863 CAGAGGTCAAGGGC -s simMouse_chr6.simMouse.chr6 114249 14 + 636262 CACAGGTTGACATC -s simRat_chr6.simRat.chr6 106631 14 + 647215 CACAGGTTGGCAGC -s simRat_chr6.simRat.chr6 106423 12 + 647215 TACAGGAT--AGGC - -a -s simMouse_chr6.simMouse.chr6 114111 8 + 636262 ACAAAGTT -s Anc0.Anc0refChr1 7640 8 - 62388 ACAGAGCT -s Anc1.Anc1refChr2 85821 8 + 144309 ACAGAGCT -s Anc2.Anc2refChr2 23356 8 + 27695 ACAGAGCT -s mr.mrrefChr0 108794 8 + 130230 ACAAAGTT -s simCow_chr6.simCow.chr6 117506 8 + 602619 GCAGAGCT -s simDog_chr6.simDog.chr6 510221 8 - 593897 ACAGAGCT -s simHuman_chr6.simHuman.chr6 109780 8 + 601863 TCAGAGCC -s simRat_chr6.simRat.chr6 106435 8 + 647215 ACAAGGTT - -a -s simMouse_chr6.simMouse.chr6 114119 13 + 636262 ACTTACAGGAGTG -s Anc0.Anc0refChr1 7648 9 - 62388 AAGT----GGGTA -s Anc1.Anc1refChr2 85829 9 + 144309 AAGT----GGGTA -s Anc2.Anc2refChr2 23364 9 + 27695 AAGT----GGGTA -s mr.mrrefChr0 108802 13 + 130230 ACTTACAGGAGTG -s simCow_chr6.simCow.chr6 117514 9 + 602619 AAGA----GAGTA -s simDog_chr6.simDog.chr6 510229 9 - 593897 AAGT----GGGCA -s simHuman_chr6.simHuman.chr6 109788 9 + 601863 AAGT----GGGTA -s simRat_chr6.simRat.chr6 106451 13 + 647215 ACTTTCAGGAGTG - -a -s simMouse_chr6.simMouse.chr6 114132 3 + 636262 TCA -s Anc0.Anc0refChr1 7657 3 - 62388 CCT -s Anc1.Anc1refChr2 85838 3 + 144309 CCT -s Anc2.Anc2refChr2 23373 3 + 27695 CCT -s mr.mrrefChr0 108815 3 + 130230 TCA -s simCow_chr6.simCow.chr6 117523 3 + 602619 TCT -s simDog_chr6.simDog.chr6 510242 3 - 593897 CCT -s simHuman_chr6.simHuman.chr6 109797 3 + 601863 CCT -s simRat_chr6.simRat.chr6 106464 3 + 647215 TCA - -a -s simMouse_chr6.simMouse.chr6 114135 1 + 636262 A -s Anc0.Anc0refChr1 7660 1 - 62388 C -s Anc1.Anc1refChr2 85841 1 + 144309 C -s Anc2.Anc2refChr2 23376 1 + 27695 T -s mr.mrrefChr0 108818 1 + 130230 A -s mr.mrrefChr0 108962 1 + 130230 C -s simCow_chr6.simCow.chr6 117526 1 + 602619 T -s simDog_chr6.simDog.chr6 510245 1 - 593897 T -s simHuman_chr6.simHuman.chr6 109800 1 + 601863 C -s simMouse_chr6.simMouse.chr6 114263 1 + 636262 C -s simRat_chr6.simRat.chr6 106645 1 + 647215 T -s simRat_chr6.simRat.chr6 106467 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 114136 12 + 636262 TGGGGATGTTGA -s Anc0.Anc0refChr1 7661 12 - 62388 CAGGAGTGTTGA -s Anc1.Anc1refChr2 85842 12 + 144309 CAGGAGTGTTGA -s Anc2.Anc2refChr2 23377 12 + 27695 CAGGAGTGTTGA -s mr.mrrefChr0 108819 12 + 130230 TGGGGATGTTGA -s mr.mrrefChr0 108963 12 + 130230 TGGGAATGTCAA -s simCow_chr6.simCow.chr6 117527 12 + 602619 TAGGATTGTCAA -s simDog_chr6.simDog.chr6 510246 12 - 593897 CATGAGTGTTGA -s simHuman_chr6.simHuman.chr6 109801 12 + 601863 CAGGAGTGTTGG -s simMouse_chr6.simMouse.chr6 114273 12 + 636262 TGGGAATGTCAA -s simRat_chr6.simRat.chr6 106646 12 + 647215 TGGCACCTTTAT -s simRat_chr6.simRat.chr6 106468 12 + 647215 TGGAGATGTCAA - -a -s simMouse_chr6.simMouse.chr6 114148 24 + 636262 TCTTCTGAAACCTGGCTTTTGACC -s Anc0.Anc0refChr1 7682 24 - 62388 TCTTATTGAACCTTGCTTTTGTCC -s Anc1.Anc1refChr2 85863 24 + 144309 TCTTATTGAACCTTGCTTTTGTCC -s Anc2.Anc2refChr2 23398 24 + 27695 TCGTATTGAACCTTGCTTTTGTCC -s mr.mrrefChr0 108840 24 + 130230 TCTTCTTGAACCTGGCTTTTGACC -s mr.mrrefChr0 108984 24 + 130230 TATTATTGGACCATACTTTTTTCA -s simCow_chr6.simCow.chr6 117548 24 + 602619 TCCTATTGAACCTTGCCTTTGTTC -s simDog_chr6.simDog.chr6 510267 24 - 593897 TTGTATTAGACCTTGCTTTTGGCC -s simHuman_chr6.simHuman.chr6 109822 24 + 601863 TCTTATTGAACTTCGCTCTTGTCT -s simMouse_chr6.simMouse.chr6 114294 24 + 636262 TATTATTGGACCATACTTTTTTCA -s simRat_chr6.simRat.chr6 106670 24 + 647215 TATTATTGAGCCGTACTGTTGTCA -s simRat_chr6.simRat.chr6 106489 24 + 647215 TCTTCTTGGACCTGGCTTTTGACC - -a -s simMouse_chr6.simMouse.chr6 114172 1 + 636262 A -s Anc0.Anc0refChr1 7708 1 - 62388 A -s Anc1.Anc1refChr2 85889 1 + 144309 A -s Anc2.Anc2refChr2 23424 1 + 27695 A -s mr.mrrefChr0 108864 1 + 130230 A -s mr.mrrefChr0 109008 1 + 130230 T -s simCow_chr6.simCow.chr6 117573 1 + 602619 A -s simDog_chr6.simDog.chr6 510293 1 - 593897 A -s simHuman_chr6.simHuman.chr6 109848 1 + 601863 A -s simMouse_chr6.simMouse.chr6 114318 1 + 636262 T -s simRat_chr6.simRat.chr6 106694 1 + 647215 T -s simRat_chr6.simRat.chr6 106513 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 114173 11 + 636262 TGCTATTGGAT -s Anc0.Anc0refChr1 7728 11 - 62388 TGCTATTGGAC -s Anc1.Anc1refChr2 85909 11 + 144309 TGCTATTGGAC -s Anc2.Anc2refChr2 23444 11 + 27695 TGCTATTGGAC -s mr.mrrefChr0 108872 11 + 130230 TGCTATTGGAT -s mr.mrrefChr0 109031 11 + 130230 TGCTACTTGAT -s simCow_chr6.simCow.chr6 117593 11 + 602619 TGCTATTGGAC -s simDog_chr6.simDog.chr6 510313 11 - 593897 TGCTATTGGAC -s simHuman_chr6.simHuman.chr6 109868 11 + 601863 TGCTATGGAAC -s simMouse_chr6.simMouse.chr6 114341 11 + 636262 TGCTGCTTGAT -s simRat_chr6.simRat.chr6 106717 11 + 647215 TGTTACTTGAT -s simRat_chr6.simRat.chr6 106530 11 + 647215 TGCTATTGACT - -a -s simMouse_chr6.simMouse.chr6 114242 1 + 636262 A -s Anc0.Anc0refChr1 7619 1 - 62388 T -s Anc1.Anc1refChr2 85800 1 + 144309 T -s Anc2.Anc2refChr2 23335 1 + 27695 T -s mr.mrrefChr0 108941 1 + 130230 A -s mr.mrrefChr0 108773 1 + 130230 A -s simCow_chr6.simCow.chr6 117485 1 + 602619 T -s simDog_chr6.simDog.chr6 510199 1 - 593897 T -s simHuman_chr6.simHuman.chr6 109759 1 + 601863 T -s simRat_chr6.simRat.chr6 106416 1 + 647215 A -s simRat_chr6.simRat.chr6 106624 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 114264 9 + 636262 AGAGCCAAG - -a -s simMouse_chr6.simMouse.chr6 114285 3 + 636262 TGG -s Anc0.Anc0refChr1 7673 3 - 62388 TGG -s Anc1.Anc1refChr2 85854 3 + 144309 TGG -s Anc2.Anc2refChr2 23389 3 + 27695 TGG -s mr.mrrefChr0 108975 3 + 130230 TGG -s mr.mrrefChr0 108831 3 + 130230 TCG -s simCow_chr6.simCow.chr6 117539 3 + 602619 TGG -s simDog_chr6.simDog.chr6 510258 3 - 593897 TGG -s simHuman_chr6.simHuman.chr6 109813 3 + 601863 TGG -s simRat_chr6.simRat.chr6 106480 3 + 647215 TCG -s simRat_chr6.simRat.chr6 106658 3 + 647215 TGG - -a -s simMouse_chr6.simMouse.chr6 114288 6 + 636262 GGAAGG -s Anc0.Anc0refChr1 7676 6 - 62388 GGGAGG -s Anc1.Anc1refChr2 85857 6 + 144309 GGGAGG -s Anc2.Anc2refChr2 23392 6 + 27695 GGGAGG -s mr.mrrefChr0 108978 6 + 130230 GGAAGG -s mr.mrrefChr0 108834 6 + 130230 GGGAAG -s simCow_chr6.simCow.chr6 117542 6 + 602619 GGGGGT -s simDog_chr6.simDog.chr6 510261 6 - 593897 GGGAGG -s simHuman_chr6.simHuman.chr6 109816 6 + 601863 GGGAGG -s simRat_chr6.simRat.chr6 106483 6 + 647215 GGGAAG -s simRat_chr6.simRat.chr6 106664 6 + 647215 GGAAGG - -a -s simMouse_chr6.simMouse.chr6 114319 5 + 636262 CTATG -s Anc0.Anc0refChr1 7709 5 - 62388 AGATG -s Anc1.Anc1refChr2 85890 5 + 144309 AGATG -s Anc2.Anc2refChr2 23425 5 + 27695 AGATG -s mr.mrrefChr0 109009 5 + 130230 CTATG -s mr.mrrefChr0 108865 5 + 130230 AGATG -s simCow_chr6.simCow.chr6 117574 5 + 602619 AGCTG -s simDog_chr6.simDog.chr6 510294 5 - 593897 AGATA -s simHuman_chr6.simHuman.chr6 109849 5 + 601863 AGATG -s simRat_chr6.simRat.chr6 106514 5 + 647215 AGATG -s simRat_chr6.simRat.chr6 106695 5 + 647215 CTAGG - -a -s simMouse_chr6.simMouse.chr6 114324 15 + 636262 ATTATCTCAAGCCAT -s Anc0.Anc0refChr1 7714 12 - 62388 ATGAT---GAGTCTG -s Anc1.Anc1refChr2 85895 12 + 144309 ATGAT---GAGTCTG -s Anc2.Anc2refChr2 23430 12 + 27695 ATGAT---GAGTCTG -s mr.mrrefChr0 109014 15 + 130230 ATTATCTCAAGTCAT -s simCow_chr6.simCow.chr6 117579 12 + 602619 GTTAT---GAGTCTG -s simDog_chr6.simDog.chr6 510299 12 - 593897 ATGAT---GAGTCTG -s simHuman_chr6.simHuman.chr6 109854 12 + 601863 ATGAT---GAGTCTG -s simRat_chr6.simRat.chr6 106700 15 + 647215 ATTATCACAAGTCAT - -a -s simMouse_chr6.simMouse.chr6 114339 2 + 636262 AT -s Anc0.Anc0refChr1 7726 2 - 62388 AT -s Anc1.Anc1refChr2 85907 2 + 144309 AT -s Anc2.Anc2refChr2 23442 2 + 27695 AT -s mr.mrrefChr0 109029 2 + 130230 AT -s mr.mrrefChr0 108870 2 + 130230 AT -s simCow_chr6.simCow.chr6 117591 2 + 602619 AT -s simDog_chr6.simDog.chr6 510311 2 - 593897 AT -s simHuman_chr6.simHuman.chr6 109866 2 + 601863 AT -s simRat_chr6.simRat.chr6 106519 2 + 647215 AT -s simRat_chr6.simRat.chr6 106715 2 + 647215 AT - -a -s simMouse_chr6.simMouse.chr6 114352 7 + 636262 TAGAGTA -s Anc0.Anc0refChr1 7739 7 - 62388 TCTAGTA -s Anc1.Anc1refChr2 85920 7 + 144309 TCTAGTA -s Anc2.Anc2refChr2 23455 7 + 27695 TCTAGTA -s mr.mrrefChr0 109042 7 + 130230 TATAGTA -s simCow_chr6.simCow.chr6 117604 7 + 602619 TCTAGTA -s simDog_chr6.simDog.chr6 510324 7 - 593897 CCTAGGA -s simHuman_chr6.simHuman.chr6 109879 7 + 601863 TCTAGTA -s simRat_chr6.simRat.chr6 106728 7 + 647215 TATAATA - -a -s simMouse_chr6.simMouse.chr6 114359 46 + 636262 AGGGATCCTCCTCACATACTTATTGGTACTTCAAATCCTAATACTA -s Anc0.Anc0refChr1 7754 44 - 62388 AAGAATCCTCCTCACACACTTACTGGTACTCCAAATCCTGAAAC-- -s Anc1.Anc1refChr2 85935 44 + 144309 AAGAATCCTCCTCACACACTTACTGGTACTCCAAATCCTGAAAC-- -s Anc2.Anc2refChr2 23470 44 + 27695 AAGAATCCTCCTCACACACTCACCAGTACTCCAAATCCTGAAAC-- -s mr.mrrefChr0 109049 46 + 130230 AGGAATCCTCCTCACATACTTATTGGTACTTCAAATCCTAATACTA -s simCow_chr6.simCow.chr6 117619 44 + 602619 AAGAATCCGCCTCACACACTGACCAATATACCAGATCATGAAAG-- -s simDog_chr6.simDog.chr6 510339 44 - 593897 AAGAAACCTCCTCACACACTCAACAGTACTCCAAATCCTGAAAC-- -s simHuman_chr6.simHuman.chr6 109894 44 + 601863 AAGAATCCTCCTCACACACTTGCTGGTACTCCAAATCCAGAAAC-- -s simRat_chr6.simRat.chr6 106735 45 + 647215 AGGAAG-CTCCTCACAAACTTATTGGTACTTCACAACTTAACACTA - -a -s simMouse_chr6.simMouse.chr6 114405 5 + 636262 TGGAA -s Anc0.Anc0refChr1 7798 5 - 62388 TGGAA -s Anc1.Anc1refChr2 85979 5 + 144309 TGGAA -s Anc2.Anc2refChr2 23514 5 + 27695 TGGAA -s mr.mrrefChr0 109095 5 + 130230 TGGAA -s simCow_chr6.simCow.chr6 117665 5 + 602619 TGGAA -s simDog_chr6.simDog.chr6 510383 5 - 593897 TGGAA -s simHuman_chr6.simHuman.chr6 109938 5 + 601863 TGGAA -s simRat_chr6.simRat.chr6 106780 5 + 647215 TGGAA - -a -s simMouse_chr6.simMouse.chr6 114410 26 + 636262 GCCAAGTACTGGGGCTCTCTGAGATA -s Anc0.Anc0refChr1 7803 26 - 62388 GTCAAGCACTCGGGCTCTCTAGGATG -s Anc1.Anc1refChr2 85984 26 + 144309 GTCAAGCACTCGGGCTCTCTAGGATG -s Anc2.Anc2refChr2 23519 26 + 27695 GTAAGGCACTCAGGCTCTCTAGGATG -s mr.mrrefChr0 109100 26 + 130230 GCCAAGTACTGGGGCTCTCTGAGATA -s simCow_chr6.simCow.chr6 117670 26 + 602619 TTTAGGCACTCAGGCTCTCAAGGATG -s simDog_chr6.simDog.chr6 510390 26 - 593897 GTAAGCCACTCAAGCTCTCTAGGATG -s simHuman_chr6.simHuman.chr6 109943 26 + 601863 ATCAAGCACTTGGGCTCTCTAGGATG -s simRat_chr6.simRat.chr6 106785 26 + 647215 GCAAAGTACTGGGGCTCTCTGAGATA - -a -s simMouse_chr6.simMouse.chr6 114436 17 + 636262 GCAGGCCTTAAGCTATT -s Anc0.Anc0refChr1 7831 17 - 62388 ACAGGTCTTGACCCATT -s Anc1.Anc1refChr2 86012 17 + 144309 ACAGGTCTTGACCCATT -s Anc2.Anc2refChr2 23547 17 + 27695 ACAGGTCTTGAGCCATT -s mr.mrrefChr0 109126 17 + 130230 GCAGGCCTTAACCTATT -s simCow_chr6.simCow.chr6 117698 17 + 602619 ACAGGTCTTAAACCATT -s simDog_chr6.simDog.chr6 510418 17 - 593897 ACAGGTCTTGAGCCATT -s simHuman_chr6.simHuman.chr6 109971 15 + 601863 ACAGGTCTTGAC--ATT -s simRat_chr6.simRat.chr6 106811 17 + 647215 GCAGGCCTTAACCTATT - -a -s simMouse_chr6.simMouse.chr6 114453 43 + 636262 TATCGAATGGATTAGTTATTTTCTGGCTGCCATTTTGGACAGA -s Anc0.Anc0refChr1 7848 40 - 62388 TAAACAATGGTGTAGTTGTCCCCTGTCTGGCACCT---GCACA -s Anc1.Anc1refChr2 86029 40 + 144309 TAAACAATGGTGTAGTTGTCCCCTGTCTGGCACCT---GCACA -s Anc2.Anc2refChr2 23585 40 + 27695 TAAACAGTGGTGTGGTTGTCCCCTGTCTGGCACCT---GCACA -s mr.mrrefChr0 109143 43 + 130230 TATCCAATGGTTTAGTTATCTCCTGGCTGCCATTTTGGACAGA -s simCow_chr6.simCow.chr6 117736 35 + 602619 TAAACAGTGGTGTGGATA-----TGTCTGGCATCT---GCGCA -s simDog_chr6.simDog.chr6 510456 40 - 593897 TAAATAGTGGTGTGGTTGTCCCCCATCTGGCACCT---GCACT -s simHuman_chr6.simHuman.chr6 109986 40 + 601863 TAGACAATTGTGTAGTCGTCCCCTGTCTGGCACCT---GCACA -s simRat_chr6.simRat.chr6 106828 43 + 647215 TAACCAATGGTTTAGTTATCTCCTGGCTGCCTTTCTGGACAGT - -a -s simMouse_chr6.simMouse.chr6 114496 52 + 636262 TGTTAATCAGATCATAAGGCTAGAGTATCTTGTACGTGACATTTTGGGGGAG -s Anc0.Anc0refChr1 7888 52 - 62388 CGTTAATCAAATCATAGGACTATAGTACTTAGTAAGTGACATTTTAGGGGAG -s Anc1.Anc1refChr2 86069 52 + 144309 CGTTAATCAAATCATAGGACTATAGTACTTAGTAAGTGACATTTTAGGGGAG -s Anc2.Anc2refChr2 23627 52 + 27695 CGTTGATCAAATCATTGGACTATAGTACTTAGTAAGTTACATTCTAGGGGAG -s mr.mrrefChr0 109186 52 + 130230 TGTTAATCAGATCATAAGACTAGAGTACCTTGTAAGTGACATTTTGGGGGAG -s simCow_chr6.simCow.chr6 117773 52 + 602619 TGTCTCTCAAATCAGTGGACTGAAGTACTTAGTAAGTTTCATTCTAGGGGAG -s simDog_chr6.simDog.chr6 510498 52 - 593897 CGTTGACCAAGTCATTGGTCTATAGCATTTAGTGAGTTACATTCTAGGGGAG -s simHuman_chr6.simHuman.chr6 110026 50 + 601863 GCTTAGTCAAATCATAGGACTATAGTACTTAGTAAG-GTCACTTTAGTGG-G -s simRat_chr6.simRat.chr6 106871 52 + 647215 TGTTAATCAGATCATAAGACTAGAGTACCTTGTAAGTGACATTTTGGAGGAG - -a -s simMouse_chr6.simMouse.chr6 114548 4 + 636262 AAAA -s Anc0.Anc0refChr1 7942 4 - 62388 AAAA -s Anc1.Anc1refChr2 86123 4 + 144309 AAAA -s Anc2.Anc2refChr2 23683 4 + 27695 AAAA -s mr.mrrefChr0 109240 4 + 130230 AAAA -s simCow_chr6.simCow.chr6 117829 4 + 602619 AAAA -s simDog_chr6.simDog.chr6 510554 4 - 593897 AAAA -s simHuman_chr6.simHuman.chr6 110078 4 + 601863 GATA -s simRat_chr6.simRat.chr6 106925 4 + 647215 AAAA - -a -s simMouse_chr6.simMouse.chr6 114552 4 + 636262 AACT -s Anc0.Anc0refChr1 7946 4 - 62388 AACT -s Anc1.Anc1refChr2 86127 4 + 144309 AACT -s Anc2.Anc2refChr2 23687 4 + 27695 AATT -s mr.mrrefChr0 109244 4 + 130230 ACCT -s simCow_chr6.simCow.chr6 117833 4 + 602619 AATT -s simDog_chr6.simDog.chr6 510573 4 - 593897 AATT -s simHuman_chr6.simHuman.chr6 110082 4 + 601863 ATCT -s simRat_chr6.simRat.chr6 106929 3 + 647215 AC-T - -a -s simMouse_chr6.simMouse.chr6 114556 3 + 636262 ACA -s Anc0.Anc0refChr1 7950 3 - 62388 AAA -s Anc1.Anc1refChr2 86131 3 + 144309 AAA -s Anc2.Anc2refChr2 23692 3 + 27695 AAA -s mr.mrrefChr0 109248 3 + 130230 ACA -s simCow_chr6.simCow.chr6 117838 3 + 602619 AAA -s simDog_chr6.simDog.chr6 510578 3 - 593897 AAA -s simHuman_chr6.simHuman.chr6 110086 3 + 601863 TGA -s simRat_chr6.simRat.chr6 106932 3 + 647215 ACA - -a -s simMouse_chr6.simMouse.chr6 114559 20 + 636262 AAGACAAAGAAGTGAGCTCA -s Anc0.Anc0refChr1 7954 20 - 62388 AAGACAGATAAGCGTGCTCA -s Anc1.Anc1refChr2 86135 20 + 144309 AAGACAGATAAGCGTGCTCA -s Anc2.Anc2refChr2 23696 20 + 27695 ATGACAGATAAGCGTGATTA -s mr.mrrefChr0 109251 20 + 130230 AAGACAAAGAAGTGAGCTCA -s simCow_chr6.simCow.chr6 117842 20 + 602619 ATGACAGATGAGCGGGGTAA -s simDog_chr6.simDog.chr6 510582 20 - 593897 ATGACAGGTAAGTGTGATTA -s simHuman_chr6.simHuman.chr6 110090 20 + 601863 AATCTCGACAAACATTCTCA -s simRat_chr6.simRat.chr6 106935 20 + 647215 AAGACAAAGATGTGAGCTCA - -a -s simMouse_chr6.simMouse.chr6 114579 29 + 636262 AGCATGCAATTGACTTACCTTTTGTCTGA -s Anc0.Anc0refChr1 7974 20 - 62388 AACAAGAAATT--------TTCT-TCCAT -s Anc1.Anc1refChr2 86155 20 + 144309 AACAAGAAATT--------TTCT-TCCAT -s Anc2.Anc2refChr2 23718 20 + 27695 AATAAGAAATT--------TTGT-TCCAT -s mr.mrrefChr0 109271 28 + 130230 AACATGCAATTGACTTACCTTCT-TCTGA -s simCow_chr6.simCow.chr6 117864 18 + 602619 --TAGGACACT--------TAAT-TCCAT -s simDog_chr6.simDog.chr6 510604 20 - 593897 AATGACAACTT--------TTGT-CCTGT -s simHuman_chr6.simHuman.chr6 110110 20 + 601863 AACAAGAAATT--------TCCT-TCCAT -s simRat_chr6.simRat.chr6 106955 28 + 647215 AACATGCAACCGACTTACTTTCT-TCTGA - -a -s simMouse_chr6.simMouse.chr6 114608 26 + 636262 GTTCTGGAAAGGAAATTTCTAGTTAG -s Anc0.Anc0refChr1 7994 25 - 62388 ATTGTGGAAG-GAAATTTCTAGTGAC -s Anc1.Anc1refChr2 86175 25 + 144309 ATTGTGGAAG-GAAATTTCTAGTGAC -s Anc2.Anc2refChr2 23738 25 + 27695 ATTGTGGGAG-GGAATTTCTTTTTAG -s mr.mrrefChr0 109299 25 + 130230 GTTCTGGAAA-GAAATTCCTAGTGAC -s simCow_chr6.simCow.chr6 117887 25 + 602619 ATGGTGGCAG-GGAATTTCTTTTTAG -s simDog_chr6.simDog.chr6 510624 25 - 593897 ATTGTGGGAG-GGAATGTCTTTTTAG -s simHuman_chr6.simHuman.chr6 110130 23 + 601863 AATGCAGAAC-TAAACTA--AGTGTC -s simRat_chr6.simRat.chr6 106983 25 + 647215 GTTCGGGAAA-GAAATTCCTAGTGAC - -a -s simMouse_chr6.simMouse.chr6 114634 23 + 636262 TTATCCTACTGCACTACAAAATG -s Anc0.Anc0refChr1 8019 23 - 62388 TTACCCTACCACACCTCCACATG -s Anc1.Anc1refChr2 86200 23 + 144309 TTACCCTACCACACCTCCACATG -s Anc2.Anc2refChr2 23763 23 + 27695 TTACCCTACCACACCTCCACATG -s mr.mrrefChr0 109324 23 + 130230 TTATCCTACTGCACTACAAAATG -s simCow_chr6.simCow.chr6 117912 23 + 602619 TTACCCTACTGCACCTCCACATG -s simDog_chr6.simDog.chr6 510649 23 - 593897 CTACCCTACCACACCTCCACATG -s simHuman_chr6.simHuman.chr6 110157 14 + 601863 TTGATCTCACTTAT--------- -s simRat_chr6.simRat.chr6 107008 23 + 647215 TTATCCTACTACACTGCGACATG - -a -s simMouse_chr6.simMouse.chr6 114657 17 + 636262 AGAGTGTTTCTTTGCAA -s Anc0.Anc0refChr1 8042 10 - 62388 AAA-------TCTTTTA -s Anc1.Anc1refChr2 86223 16 + 144309 AAA-CTTTCATCTTTTA -s Anc2.Anc2refChr2 23786 10 + 27695 AAA-------TGTTTTA -s mr.mrrefChr0 109347 17 + 130230 AGAGTTTTTCTCTGTAA -s simCow_chr6.simCow.chr6 117936 7 + 602619 AAA-------TGTG--- -s simDog_chr6.simDog.chr6 510672 10 - 593897 AAA-------TGTTTTA -s simHuman_chr6.simHuman.chr6 110171 13 + 601863 ----CTTTCATCTTTCA -s simRat_chr6.simRat.chr6 107031 17 + 647215 AGAGTTTCTCTCTGTAG - -a -s simMouse_chr6.simMouse.chr6 114674 1 + 636262 A -s Anc0.Anc0refChr1 8052 1 - 62388 A -s Anc1.Anc1refChr2 86239 1 + 144309 A -s Anc2.Anc2refChr2 23796 1 + 27695 G -s mr.mrrefChr0 109364 1 + 130230 A -s simDog_chr6.simDog.chr6 510684 1 - 593897 G -s simHuman_chr6.simHuman.chr6 110184 1 + 601863 A -s simRat_chr6.simRat.chr6 107048 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 114675 1 + 636262 A -s Anc0.Anc0refChr1 8054 1 - 62388 T -s Anc1.Anc1refChr2 86241 1 + 144309 T -s Anc2.Anc2refChr2 23798 1 + 27695 T -s mr.mrrefChr0 109365 1 + 130230 A -s simDog_chr6.simDog.chr6 510686 1 - 593897 T -s simHuman_chr6.simHuman.chr6 110186 1 + 601863 T -s simRat_chr6.simRat.chr6 107049 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 114676 16 + 636262 ATACAAGTGTTCACTT -s Anc0.Anc0refChr1 8055 16 - 62388 ATACAAGTGTTTGCTT -s Anc1.Anc1refChr2 86242 16 + 144309 ATACAAGTGTTTGCTT -s Anc2.Anc2refChr2 23799 16 + 27695 ATACAAGTGTTTGCCT -s mr.mrrefChr0 109366 16 + 130230 ATACAAGTGTTCACTT -s simCow_chr6.simCow.chr6 117943 12 + 602619 ----AAGTATTCACCT -s simDog_chr6.simDog.chr6 510691 16 - 593897 ATACAACTGTTTGCCT -s simHuman_chr6.simHuman.chr6 110187 16 + 601863 CTACAAGTGTGTGCTT -s simRat_chr6.simRat.chr6 107050 16 + 647215 ACACAAGTGTTCACTT - -a -s simMouse_chr6.simMouse.chr6 114692 36 + 636262 GCTATTAGCATGATACTTGAATGACAATACTAGCCA -s Anc0.Anc0refChr1 8071 36 - 62388 GCAATTAATGTGATATTCAAATTACCATACTAATCA -s Anc1.Anc1refChr2 86258 36 + 144309 GCAATTAATGTGATATTCAAATTACCATACTAATCA -s Anc2.Anc2refChr2 23815 36 + 27695 GCAATTAATGTGATATCCAAATTACCATCCTAATCA -s mr.mrrefChr0 109382 36 + 130230 GCTATTAGCATGATATTTGAATGACAATACTAGCCA -s mr.mrrefChr0 20665 36 - 130230 GCAGTTAGTAAGATATTCAATTGGACATGCTAGCCA -s simCow_chr6.simCow.chr6 117955 36 + 602619 GCAAATAATACGATATCCAGAATACCATCCTAATCA -s simDog_chr6.simDog.chr6 510707 36 - 593897 GCAATTAGTGTAATATCCAAGTTACCATCCCAATCA -s simHuman_chr6.simHuman.chr6 110203 36 + 601863 GCAAGTAATGTGATATTTGAATTACCATATTAATCA -s simMouse_chr6.simMouse.chr6 521387 36 - 636262 GCAGTTAGTAAGATATTCAATTGGACATGCTAGCCA -s simRat_chr6.simRat.chr6 539969 36 - 647215 GCAGTTAGTAGGATATTCGATTGAACAGGCTAGCCA -s simRat_chr6.simRat.chr6 107066 36 + 647215 ACTGCTAGCATGATATCTGGATGGCAATTCTAGCCA - -a -s simMouse_chr6.simMouse.chr6 114728 1 + 636262 C -s Anc0.Anc0refChr1 8107 1 - 62388 G -s Anc1.Anc1refChr2 86294 1 + 144309 G -s Anc2.Anc2refChr2 23851 1 + 27695 G -s mr.mrrefChr0 109418 1 + 130230 C -s simCow_chr6.simCow.chr6 117991 1 + 602619 G -s simDog_chr6.simDog.chr6 510743 1 - 593897 G -s simHuman_chr6.simHuman.chr6 110239 1 + 601863 G -s simRat_chr6.simRat.chr6 107102 1 + 647215 C - -a -s simMouse_chr6.simMouse.chr6 114729 8 + 636262 TTTCACAT -s Anc0.Anc0refChr1 8108 8 - 62388 TGTTACAG -s Anc1.Anc1refChr2 86295 8 + 144309 TGTTACAG -s Anc2.Anc2refChr2 23852 8 + 27695 TGTTACAA -s mr.mrrefChr0 109419 8 + 130230 TTTCACAT -s mr.mrrefChr0 20701 8 - 130230 GTTAACAG -s simCow_chr6.simCow.chr6 117992 8 + 602619 TATCATAA -s simDog_chr6.simDog.chr6 510744 8 - 593897 TGTTACAA -s simHuman_chr6.simHuman.chr6 110240 8 + 601863 TGTTACAG -s simMouse_chr6.simMouse.chr6 521423 8 - 636262 GTTAACAG -s simRat_chr6.simRat.chr6 540005 8 - 647215 GTTGACAG -s simRat_chr6.simRat.chr6 107103 8 + 647215 TTCCATAT - -a -s simMouse_chr6.simMouse.chr6 114737 14 + 636262 TCACAGTTAGATAT -s Anc0.Anc0refChr1 8116 14 - 62388 ACATACTTAGATAT -s Anc1.Anc1refChr2 86303 14 + 144309 ACATACTTAGATAT -s Anc2.Anc2refChr2 23860 14 + 27695 ACATACTTGGATAT -s mr.mrrefChr0 109427 14 + 130230 TCACAGTTAGATAT -s mr.mrrefChr0 20709 14 - 130230 GCACACTTAGATAT -s simCow_chr6.simCow.chr6 118000 14 + 602619 ACATCCCTAGATAT -s simDog_chr6.simDog.chr6 510773 14 - 593897 ACATACTTGGATAT -s simHuman_chr6.simHuman.chr6 110248 14 + 601863 ACATACTTAGATAT -s simMouse_chr6.simMouse.chr6 521431 14 - 636262 GCACACTTAGATAT -s simRat_chr6.simRat.chr6 540013 14 - 647215 GCACACTTAGATAT -s simRat_chr6.simRat.chr6 107111 14 + 647215 GCACAGTTAGATAT - -a -s simMouse_chr6.simMouse.chr6 114751 4 + 636262 TCGA -s Anc0.Anc0refChr1 8130 4 - 62388 TTGA -s Anc1.Anc1refChr2 86317 4 + 144309 TTGA -s Anc2.Anc2refChr2 23895 4 + 27695 TTGC -s mr.mrrefChr0 109441 4 + 130230 TCGA -s mr.mrrefChr0 20723 4 - 130230 TTGA -s simCow_chr6.simCow.chr6 118040 4 + 602619 TTGG -s simDog_chr6.simDog.chr6 510808 4 - 593897 TTGC -s simHuman_chr6.simHuman.chr6 110262 4 + 601863 TTGA -s simMouse_chr6.simMouse.chr6 521445 4 - 636262 TTGA -s simRat_chr6.simRat.chr6 540027 4 - 647215 TTGA -s simRat_chr6.simRat.chr6 107125 4 + 647215 TCAA - -a -s simMouse_chr6.simMouse.chr6 114755 23 + 636262 CTAGGTGTTATGGGATGGGAACC -s Anc0.Anc0refChr1 8134 23 - 62388 TTAGGGGTTATGGGTTGGAAGCC -s Anc1.Anc1refChr2 86321 23 + 144309 TTAGGGGTTATGGGTTGGAAGCC -s Anc2.Anc2refChr2 23899 23 + 27695 TTGGGGGTTAGGGGTTGGAAGCC -s mr.mrrefChr0 109445 23 + 130230 CTAGGTGTTATGGGATAGGAACC -s mr.mrrefChr0 20727 23 - 130230 TAAGGGAATATGGGTTGTAAGCC -s simCow_chr6.simCow.chr6 118044 23 + 602619 TGGCGGGGTAGGGGTTGGAAGCC -s simDog_chr6.simDog.chr6 510813 23 - 593897 TTGGGGGTTAGGGGTTGGAAGCC -s simHuman_chr6.simHuman.chr6 110266 23 + 601863 TTAGGGGTTATGGGTCAGAAGCC -s simMouse_chr6.simMouse.chr6 521449 23 - 636262 TAAGGGAATATGGGTTGTAAGCC -s simRat_chr6.simRat.chr6 540031 23 - 647215 TAGGGGAATGTGAGTTGCAAGCC -s simRat_chr6.simRat.chr6 107129 23 + 647215 CTAGGTGTTATGGGATAGGAACC - -a -s simMouse_chr6.simMouse.chr6 114778 12 + 636262 TGCTTCAATTCA -s Anc0.Anc0refChr1 54219 12 + 62388 TACCATCAGTCA -s Anc1.Anc1refChr2 57953 12 - 144309 TACCATCAGTCA -s Anc2.Anc2refChr2 3761 12 - 27695 TATCATCAGTCA -s mr.mrrefChr0 109468 12 + 130230 TGCCTCAATTCA -s simCow_chr6.simCow.chr6 484540 12 - 602619 TATCATCATTCT -s simDog_chr6.simDog.chr6 83049 12 + 593897 TATCATCTGTCA -s simHuman_chr6.simHuman.chr6 491562 12 - 601863 TTCCATCAGTCA -s simRat_chr6.simRat.chr6 107152 9 + 647215 TGCCT---TTCA - -a -s simMouse_chr6.simMouse.chr6 114875 74 + 636262 AGCTGCAGGAAAACACTTCTATTTCTGTGATAGGTCCATGTCAGGAACAGTGCTGGCAAAACTAGTAATTGCCG -s Anc0.Anc0refChr1 8169 42 - 62388 --------------------------------GGTCCCTCTAGGAGACAATGCTGGCAAAGCTAGTAATTGCTG -s Anc1.Anc1refChr2 86356 42 + 144309 --------------------------------GGTCCCTCTAGGAGACAATGCTGGCAAAGCTAGTAATTGCTG -s Anc2.Anc2refChr2 23934 42 + 27695 --------------------------------GGTCCCTCTAGGAGACAATGCTGGCAAAACTAGTACTTGCTG -s mr.mrrefChr0 109565 74 + 130230 AGCTGCAGGAAAACACTTCTATTTCTGTGATAGGTCCATGTCAGGAACAGTGCTGGCAAAGCTAGTAATTGCCG -s simCow_chr6.simCow.chr6 118079 41 + 602619 --------------------------------GAT-CCTCTAGGAGACAAAGCTGGCAAAACTAGTACTTGCTG -s simDog_chr6.simDog.chr6 510848 26 - 593897 --------------------------------GGTCCCTCTAGGAGACAATGCTAGCA---------------- -s simHuman_chr6.simHuman.chr6 110301 42 + 601863 --------------------------------GGTTCCTATAGGAGACACTGCTGGCACAGATAGTGATTTGTG -s simRat_chr6.simRat.chr6 107246 74 + 647215 AGCTGCAGGAAAACACTTGTATTTCTATGATAGTTCCATGTCAGGAACAGCGCTGGCAAAGTTAGTAACTGCCA - -a -s simMouse_chr6.simMouse.chr6 114949 26 + 636262 CTTTACTTTGCAATTTGCCCGAGCAA -s Anc0.Anc0refChr1 8211 26 - 62388 CTTTACTTTTCAATTTGCTTGATCAA -s Anc1.Anc1refChr2 86398 26 + 144309 CTTTACTTTTCAATTTGCTTGATCAA -s Anc2.Anc2refChr2 23976 26 + 27695 CTTTGCTTTTCAATTTGCTTGATCAA -s mr.mrrefChr0 109639 26 + 130230 CTTTACTTTGCAATTTGCTCGATCAA -s simCow_chr6.simCow.chr6 118121 26 + 602619 CTTTGCTTTTTAATTTGCTTGATCAA -s simDog_chr6.simDog.chr6 510874 13 - 593897 ---------TCAACTGG---GATCA- -s simHuman_chr6.simHuman.chr6 110343 26 + 601863 CTTTACTTTTCAATTTGCTTGATCAA -s simRat_chr6.simRat.chr6 107320 26 + 647215 CTTTACTTTGAAATTTGCTCGATCAA - -a -s simMouse_chr6.simMouse.chr6 114975 40 + 636262 ATGTGTGCTACACGTGAGATCAATATTACAATTTATTAAA -s Anc0.Anc0refChr1 8237 17 - 62388 A-----------------------ATTACAATTTATTATA -s Anc1.Anc1refChr2 86424 17 + 144309 A-----------------------ATTACAATTTATTATA -s Anc2.Anc2refChr2 24002 17 + 27695 A-----------------------ATTACAATTTATTATA -s mr.mrrefChr0 109665 40 + 130230 ATGTGTGCTACACGTGAGATCAATATTACAATTTATTATA -s simCow_chr6.simCow.chr6 118151 17 + 602619 A-----------------------ATTACAGTTTATTAAA -s simDog_chr6.simDog.chr6 510887 12 - 593897 ----------------------------CAATTTATTATA -s simHuman_chr6.simHuman.chr6 110369 17 + 601863 A-----------------------ATTGCAATTTATTATA -s simRat_chr6.simRat.chr6 107346 40 + 647215 ATGTGTGTCGCATGTAAGATCATTATTACAATTTATTATA - -a -s simMouse_chr6.simMouse.chr6 115015 11 + 636262 ATGGGTGACTT -s Anc0.Anc0refChr1 8254 9 - 62388 TC--ATGACTT -s Anc1.Anc1refChr2 86441 9 + 144309 TC--ATGACTT -s Anc2.Anc2refChr2 24019 9 + 27695 TC--ATGACTT -s mr.mrrefChr0 109705 11 + 130230 ATGGGTGACTT -s simCow_chr6.simCow.chr6 118168 9 + 602619 TC--ATGACTT -s simDog_chr6.simDog.chr6 510899 9 - 593897 TC--ATGGCTT -s simHuman_chr6.simHuman.chr6 110386 9 + 601863 TC--TTGACTT -s simRat_chr6.simRat.chr6 107441 11 + 647215 ATAGGTGGCTT - -a -s simMouse_chr6.simMouse.chr6 115026 46 + 636262 ATTCAGGGCTTACACTCTTTGTCCTGAACGTGAAATTTGTGACATT -s Anc0.Anc0refChr1 8264 46 - 62388 ATCCAGTGCTTCCACTCTATATCCTAAAAGTGAAGAGTGCAGCATT -s Anc1.Anc1refChr2 86451 46 + 144309 ATCCAGTGCTTCCACTCTATATCCTAAAAGTGAAGAGTGCAGCATT -s Anc2.Anc2refChr2 24029 46 + 27695 ATCCAGTTCTTCCACTCTATATCCTAAAAGTGAAGAGTGCAGCATT -s mr.mrrefChr0 109716 46 + 130230 ATTCAGGGCTTACACTCTTTGTCCTGAACGTGAAATTTGTGACATT -s simCow_chr6.simCow.chr6 118178 46 + 602619 ATCCAGTTTTTCAACACTGTAGTCTAAAAGCAAAGAGTGCAGCATT -s simDog_chr6.simDog.chr6 510909 46 - 593897 ACTTTGTTCTTCCACTCAATATCCTAAAAGTGAAAAGTGCAGCATT -s simHuman_chr6.simHuman.chr6 110396 23 + 601863 ATCCAGTGATTCCATGTTATATC----------------------- -s simRat_chr6.simRat.chr6 107452 46 + 647215 ATTCAGGGCTTGCACTCTTTGTCCTGGACGTTAAATTTATGACCTT - -a -s simMouse_chr6.simMouse.chr6 115072 14 + 636262 ACAATTATATCATG -s Anc0.Anc0refChr1 8310 14 - 62388 ACAATTGTGTCATG -s Anc1.Anc1refChr2 86497 14 + 144309 ACAATTGTGTCATG -s Anc2.Anc2refChr2 24075 14 + 27695 ACAATTGTGTCATG -s mr.mrrefChr0 109762 14 + 130230 ACAATTATATCATG -s simCow_chr6.simCow.chr6 118239 14 + 602619 ACAATCATTTCATG -s simDog_chr6.simDog.chr6 510955 14 - 593897 ACAATTGTGTCATG -s simRat_chr6.simRat.chr6 107498 14 + 647215 ACAATTATATCTTG - -a -s simMouse_chr6.simMouse.chr6 115086 14 + 636262 TGAAGTAAGACTCT -s Anc0.Anc0refChr1 8324 14 - 62388 TATGACAAGACTCT -s Anc1.Anc1refChr2 86511 14 + 144309 TATGACAAGACTCT -s Anc2.Anc2refChr2 24096 14 + 27695 TATGACAAGACTCT -s mr.mrrefChr0 109776 14 + 130230 TGAAGTAAGACTCT -s simCow_chr6.simCow.chr6 118260 9 + 602619 CATGATAAG----- -s simDog_chr6.simDog.chr6 510976 14 - 593897 TATGACAAGACTCT -s simRat_chr6.simRat.chr6 107513 14 + 647215 TGAAATAAGACTCT - -a -s simMouse_chr6.simMouse.chr6 115100 16 + 636262 AGCTAGTTAGATGTGG -s Anc0.Anc0refChr1 8338 16 - 62388 AGCCAGGAAGGGGTGG -s Anc1.Anc1refChr2 86525 16 + 144309 AGCCAGGAAGGGGTGG -s Anc2.Anc2refChr2 24113 16 + 27695 AGCCAGGAAGGGGTGG -s mr.mrrefChr0 109790 16 + 130230 AGCTAGTTAGATGTGG -s simCow_chr6.simCow.chr6 118269 16 + 602619 AGCCAGTAAGGGGTGG -s simDog_chr6.simDog.chr6 510995 16 - 593897 AGCCAGGAAGGGGTGG -s simRat_chr6.simRat.chr6 107532 16 + 647215 AGCCAGTTAGATGTGG - -a -s simMouse_chr6.simMouse.chr6 115116 74 + 636262 GTCAAGCAAAGTACAAAAAGTGGTGAGAACTGAACTGAGGTTTGGAATTGAAGTTGGGTACCAAGTAGAGAAAG -s Anc0.Anc0refChr1 8354 17 - 62388 GT----------------------------------------------------AGGGTATTA-----AGAGAA -s Anc1.Anc1refChr2 86541 24 + 144309 GT--------------------------------------------------GTAGGGTATTATGTGGAGAGAA -s Anc2.Anc2refChr2 24129 17 + 27695 GT----------------------------------------------------AGGGCATAA-----GCAAGA -s mr.mrrefChr0 109806 61 + 130230 GTCAAGCAAAGTACAAAAAGTGGTGAGAACTGAA-------------TTGAAGTTGGGTACCAAGTAGAGAAAG -s simCow_chr6.simCow.chr6 118333 17 + 602619 GT----------------------------------------------------ACAGCATCA-----TCTAGA -s simDog_chr6.simDog.chr6 511011 17 - 593897 GT----------------------------------------------------AGGGCATAA-----GCAAGA -s simHuman_chr6.simHuman.chr6 110419 22 + 601863 ----------------------------------------------------GTAGGGTATTATGTGGAGAGAA -s simRat_chr6.simRat.chr6 107548 61 + 647215 GACAAGCAAAGTACAAAATGTGGTAAGAACTGAG-------------TTTAAGTTGGGCACCACGTAAAGAAAG - -a -s simMouse_chr6.simMouse.chr6 115190 53 + 636262 TAGCAAAAAACAGGAGATTGTGTGGAAGGACATCTTTGACAGTGATTTGAGAC -s Anc0.Anc0refChr1 8371 23 - 62388 TAGCAAAGGATGTGAACTTGTGC------------------------------ -s Anc1.Anc1refChr2 86565 52 + 144309 TAGCAAAGGATGTGAACTTGTGCAAAAGAAC-TCATTAATAGTGCACTGGCAC -s Anc2.Anc2refChr2 24146 23 + 27695 TAGCAAAAAATGGGAACTTGTGT------------------------------ -s mr.mrrefChr0 109867 53 + 130230 TAGCAAAAGACAGGAGATTGTGTGGAAGGACATCTTTGACAGTGATCTGAGAC -s simCow_chr6.simCow.chr6 118355 23 + 602619 TAGCCAAAAATGGGAACTTGTGT------------------------------ -s simDog_chr6.simDog.chr6 511028 23 - 593897 TAGCAAAAAATGGGAACTTGTGT------------------------------ -s simHuman_chr6.simHuman.chr6 110441 52 + 601863 TAGCAAAGGATGTGAACTTGTGCAAAAGAAC-TCATTAATAGTGTACTGGCGC -s simRat_chr6.simRat.chr6 107609 53 + 647215 TAGCAAAAGACCGGAGATTGTGTGGAAGGACATCCGTGACAGTTATCCAATAC - -a -s simMouse_chr6.simMouse.chr6 115243 4 + 636262 ATCC -s Anc1.Anc1refChr2 86618 4 + 144309 ATGC -s mr.mrrefChr0 109920 4 + 130230 ATCC -s simHuman_chr6.simHuman.chr6 110494 4 + 601863 ATGC -s simRat_chr6.simRat.chr6 107662 4 + 647215 ATCC - -a -s simMouse_chr6.simMouse.chr6 115247 1 + 636262 A -s Anc1.Anc1refChr2 86623 1 + 144309 A -s mr.mrrefChr0 109925 1 + 130230 A -s simHuman_chr6.simHuman.chr6 110499 1 + 601863 A -s simRat_chr6.simRat.chr6 107667 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 115248 10 + 636262 TCTGCCCTTT -s Anc0.Anc0refChr1 8408 10 - 62388 GCTGATGTTT -s Anc1.Anc1refChr2 86642 10 + 144309 GCTGATGTTT -s Anc2.Anc2refChr2 24183 10 + 27695 GCTGATGTTT -s mr.mrrefChr0 109926 10 + 130230 TCTGACCTTT -s simCow_chr6.simCow.chr6 118432 10 + 602619 ACTGATGTTT -s simDog_chr6.simDog.chr6 511068 10 - 593897 GCTGATGTTT -s simHuman_chr6.simHuman.chr6 110518 10 + 601863 GCTGATGTGT -s simRat_chr6.simRat.chr6 107668 10 + 647215 CCTAACCTTT - -a -s simMouse_chr6.simMouse.chr6 115258 3 + 636262 ATC -s Anc0.Anc0refChr1 8418 3 - 62388 CTT -s Anc1.Anc1refChr2 86652 3 + 144309 CTT -s Anc2.Anc2refChr2 24193 3 + 27695 CTT -s mr.mrrefChr0 109936 3 + 130230 CTC -s simCow_chr6.simCow.chr6 118443 3 + 602619 CTT -s simDog_chr6.simDog.chr6 511078 3 - 593897 CTT -s simHuman_chr6.simHuman.chr6 110528 3 + 601863 CTT -s simRat_chr6.simRat.chr6 107678 3 + 647215 CTC - -a -s simMouse_chr6.simMouse.chr6 115261 43 + 636262 TATTGCACACCACAGAAATGGTGTAAGATTTTTCCCTCTTTAT -s Anc0.Anc0refChr1 8421 43 - 62388 AATTGAGTACCACAGAAATGGTGTAAGACTGTTGCTTCTTTAT -s Anc1.Anc1refChr2 86655 43 + 144309 AATTGAGTACCACAGAAATGGTGTAAGACTGTTGCTTCTTTAT -s Anc2.Anc2refChr2 24196 43 + 27695 AATTGAGTAGCAAGGAAATGGTGTAAATCTGTTGCTTCTTTAT -s mr.mrrefChr0 109939 43 + 130230 TATTGCATACCACAGAAATGGTGTAAGATTGTTCCTTCTTTAT -s simCow_chr6.simCow.chr6 118446 43 + 602619 AACCAACTATCATGGAAATGGTGCCAAGCTGGTGCTTCTTTAT -s simDog_chr6.simDog.chr6 511086 43 - 593897 AATTGAGTAGCAAGGAAATGGTGTAAATCTGTTGCTTCCTTAT -s simHuman_chr6.simHuman.chr6 110531 43 + 601863 AATTGAGTACCACAGAAATGGTGTAAGACTGTTGCTTCTTTAC -s simRat_chr6.simRat.chr6 107681 43 + 647215 TATTGCATACCACAGAAATGGTGTAAGATTGTACCTTCTTTAT - -a -s simMouse_chr6.simMouse.chr6 115304 14 + 636262 CAGTTGCATAATCT -s Anc0.Anc0refChr1 8464 14 - 62388 TGGGTACATAATTT -s Anc1.Anc1refChr2 86698 14 + 144309 TGGGTACATAATTT -s Anc2.Anc2refChr2 24239 14 + 27695 TGGGTACATAGTTT -s mr.mrrefChr0 109982 14 + 130230 CGGTTGCATAATCT -s simCow_chr6.simCow.chr6 118680 14 + 602619 TGGGTACATATTTT -s simDog_chr6.simDog.chr6 511129 14 - 593897 TGGTTACATAGTTT -s simHuman_chr6.simHuman.chr6 110574 14 + 601863 TGGGTACACAATTT -s simRat_chr6.simRat.chr6 107724 14 + 647215 CGGATGCATAATCT - -a -s simMouse_chr6.simMouse.chr6 115318 24 + 636262 CAGAGAACACATCACAATTTTTGC -s Anc0.Anc0refChr1 8478 24 - 62388 CAGAGAACACATCATAATTCTTGA -s Anc1.Anc1refChr2 86712 24 + 144309 CAGAGAACACATCATAATTCTTGA -s Anc2.Anc2refChr2 24253 24 + 27695 CAGAAAAGACATCATAATTCTTGA -s mr.mrrefChr0 109996 24 + 130230 CAGAGAACACATCATAATTTTTGC -s simCow_chr6.simCow.chr6 118694 24 + 602619 CAGAAAAGATATCATAATTCTTGA -s simDog_chr6.simDog.chr6 511143 23 - 593897 CAGAAAAGACAT-ATAATTCTTGG -s simHuman_chr6.simHuman.chr6 110589 24 + 601863 CAGAGAACACCTCATAATTCTTGA -s simRat_chr6.simRat.chr6 107738 24 + 647215 CAGAGAACCCACCATAATGTTTGC - -a -s simMouse_chr6.simMouse.chr6 115342 23 + 636262 ATAACTATTAGGGTCCACATCTG -s Anc0.Anc0refChr1 8502 23 - 62388 ATATCTATTATTGCCCACAGTAG -s Anc1.Anc1refChr2 86736 23 + 144309 ATATCTATTATTGCCCACAGTAG -s Anc2.Anc2refChr2 24327 23 + 27695 ATCTATATTATTGCCCACAGTAG -s mr.mrrefChr0 110020 23 + 130230 ATAACTATTAGGGTCCACATCTG -s simCow_chr6.simCow.chr6 118768 23 + 602619 GTCTATATTATTGCACACAGTAG -s simDog_chr6.simDog.chr6 511222 21 - 593897 ATC--TATTACTACCAACAGTAG -s simHuman_chr6.simHuman.chr6 110613 23 + 601863 ATATCAATTGTTGCCCGCAGTAG -s simRat_chr6.simRat.chr6 107762 23 + 647215 ATAACTATTAGGGTCCACATCTG - -a -s simMouse_chr6.simMouse.chr6 115365 31 + 636262 ATGATTAGTATGGTGAGTACGGCATGTTGTT -s Anc0.Anc0refChr1 8525 29 - 62388 ATAGATAGTTTGGTAAATATGGCACGT--TT -s Anc1.Anc1refChr2 86759 29 + 144309 ATAGATAGTTTGGTAAATATGGCACGT--TT -s Anc2.Anc2refChr2 24350 29 + 27695 ATAGAAAGTTTGGTAAATATGGCACGT--TT -s mr.mrrefChr0 110043 29 + 130230 ATGATTAGTATGGTGAGTACGGCATGT--TT -s simCow_chr6.simCow.chr6 118791 29 + 602619 ATGGAAAGTTTGGTAAGTAGGGCACTG--TC -s simDog_chr6.simDog.chr6 511245 29 - 593897 ATAGAAAGTTGGGTAGATATGGCATGT--TT -s simHuman_chr6.simHuman.chr6 110636 29 + 601863 ATAGATAGTTTGGTAAATATGGCACAT--TT -s simRat_chr6.simRat.chr6 107785 29 + 647215 ATGATTAGTAGGGTGAGTGCGGCTTGT--TT - -a -s simMouse_chr6.simMouse.chr6 115396 30 + 636262 TTATAACCCCCACGGATAAGACTAAGGCAG -s Anc0.Anc0refChr1 8558 30 - 62388 CCATAACCCCCACAGATTAGACTAAGATGG -s Anc1.Anc1refChr2 86792 30 + 144309 CCATAACCCCCACAGATTAGACTAAGATGG -s Anc2.Anc2refChr2 24383 30 + 27695 TCATAACCCCCACAGATTAGACTAAGATGA -s mr.mrrefChr0 110072 30 + 130230 CTATAACCCCCACAGATAAGACTAAGGTGG -s simCow_chr6.simCow.chr6 118824 30 + 602619 ACATAACCCCCACAAAGTAGAGTAAGATGA -s simDog_chr6.simDog.chr6 511278 28 - 593897 TCATAA--CTCACAGATTAGACAAAGCTGA -s simHuman_chr6.simHuman.chr6 110669 30 + 601863 CCATTACCCCCACAGATTAGGCTAAGATGG -s simRat_chr6.simRat.chr6 107814 29 + 647215 CTATAACACCCA-AGATAAGACTAAGGTGG - -a -s simMouse_chr6.simMouse.chr6 115426 18 + 636262 GCCCCCATATGCAGTCGC -s Anc0.Anc0refChr1 8589 18 - 62388 GCTCCTATCCAAAAGCTC -s Anc1.Anc1refChr2 86823 18 + 144309 GCTCCTATCCAAAAGCTC -s Anc2.Anc2refChr2 24414 18 + 27695 GCTCCTATCCAAAAGCTC -s mr.mrrefChr0 110102 18 + 130230 GCCCCTATCTGCAGTCGC -s simCow_chr6.simCow.chr6 118855 18 + 602619 GCTCCACTCAAAAATCTC -s simDog_chr6.simDog.chr6 511307 18 - 593897 ACCTTTATCCAAAAGCTC -s simHuman_chr6.simHuman.chr6 110700 18 + 601863 GCTCCTATCCAAAAGATC -s simRat_chr6.simRat.chr6 107843 17 + 647215 GCCCCTATCGGCA-CCGC - -a -s simMouse_chr6.simMouse.chr6 115444 2 + 636262 AA -s Anc0.Anc0refChr1 8608 2 - 62388 AA -s Anc1.Anc1refChr2 86842 2 + 144309 AA -s Anc2.Anc2refChr2 24433 2 + 27695 AA -s mr.mrrefChr0 110120 2 + 130230 AA -s simCow_chr6.simCow.chr6 118874 2 + 602619 GA -s simDog_chr6.simDog.chr6 511326 2 - 593897 AA -s simHuman_chr6.simHuman.chr6 110719 2 + 601863 AA -s simRat_chr6.simRat.chr6 107860 2 + 647215 AA - -a -s simMouse_chr6.simMouse.chr6 115446 26 + 636262 TTCTATCCTGCTGAGAGCTGGTGAAC -s Anc0.Anc0refChr1 8613 26 - 62388 ATCTAATCTGTTGGAAGCTGACAAAC -s Anc1.Anc1refChr2 86847 26 + 144309 ATCTAATCTGTTGGAAGCTGACAAAC -s Anc2.Anc2refChr2 24438 26 + 27695 ATCTAATCTGTTGGAAGGTGACAAAC -s mr.mrrefChr0 110125 26 + 130230 TTCTATCCTGTTGGGAGCTGGTGAAC -s simCow_chr6.simCow.chr6 118879 26 + 602619 ATCCAATCCATTGAAAGGTATCAAAA -s simDog_chr6.simDog.chr6 511331 26 - 593897 GTCTAAACTGTTGGAAGGTGACAAAC -s simHuman_chr6.simHuman.chr6 110724 26 + 601863 ATTTACTCTGTTGGAAGCTGACATAC -s simRat_chr6.simRat.chr6 107865 26 + 647215 TTCTATCCTGTTGGGAGCTGGTGAAC - -a -s simMouse_chr6.simMouse.chr6 115472 7 + 636262 ATCGCTC -s Anc0.Anc0refChr1 8640 7 - 62388 GTTGCTC -s Anc1.Anc1refChr2 86874 7 + 144309 GTTGCTC -s Anc2.Anc2refChr2 24465 7 + 27695 GTTGCTC -s mr.mrrefChr0 110151 7 + 130230 GTTGCTC -s simCow_chr6.simCow.chr6 118906 7 + 602619 GTTACTC -s simDog_chr6.simDog.chr6 511358 7 - 593897 GTTGATC -s simHuman_chr6.simHuman.chr6 110751 7 + 601863 GTTGCTC -s simRat_chr6.simRat.chr6 107891 7 + 647215 GTTGCTC - -a -s simMouse_chr6.simMouse.chr6 115479 2 + 636262 AT -s Anc0.Anc0refChr1 8647 2 - 62388 AC -s Anc1.Anc1refChr2 86881 2 + 144309 AC -s Anc2.Anc2refChr2 24472 2 + 27695 AC -s mr.mrrefChr0 110158 2 + 130230 AC -s simCow_chr6.simCow.chr6 118924 2 + 602619 AC -s simDog_chr6.simDog.chr6 511365 2 - 593897 AT -s simHuman_chr6.simHuman.chr6 110758 2 + 601863 AC -s simRat_chr6.simRat.chr6 107898 2 + 647215 AC - -a -s simMouse_chr6.simMouse.chr6 115481 15 + 636262 GCGAAGTAAGGGAGA -s Anc0.Anc0refChr1 8655 15 - 62388 GTAAAGTAAGAGAGT -s Anc1.Anc1refChr2 86889 15 + 144309 GTAAAGTAAGAGAGT -s Anc2.Anc2refChr2 24480 15 + 27695 GTAAAGTAAGAGAGT -s mr.mrrefChr0 110160 15 + 130230 GTAAAGTAAGAGAGA -s simCow_chr6.simCow.chr6 118934 15 + 602619 GGAAAGGAAGAGAGT -s simDog_chr6.simDog.chr6 511373 15 - 593897 GTAAAGTAAGCGGAC -s simHuman_chr6.simHuman.chr6 110766 15 + 601863 GTAAAGTAAGAGAGT -s simRat_chr6.simRat.chr6 107900 15 + 647215 ATAAAGTAAGAAAGG - -a -s simMouse_chr6.simMouse.chr6 115496 13 + 636262 ACTCCTTGCTACA -s Anc0.Anc0refChr1 8678 12 - 62388 ACTCATTGCTGC- -s Anc1.Anc1refChr2 86912 12 + 144309 ACTCATTGCTGC- -s Anc2.Anc2refChr2 24503 12 + 27695 ACTCATTGCTGC- -s mr.mrrefChr0 110183 13 + 130230 ACTCCTTGCTGCA -s simCow_chr6.simCow.chr6 118957 12 + 602619 GCTAATTGCTGC- -s simDog_chr6.simDog.chr6 511396 11 - 593897 ACTCATTG-GAA- -s simHuman_chr6.simHuman.chr6 110789 12 + 601863 ACTCATTGCTGC- -s simRat_chr6.simRat.chr6 107923 13 + 647215 ACGTCTTACTGCA - -a -s simMouse_chr6.simMouse.chr6 115509 36 + 636262 AATCCTTTGACCTGACTAGGAGACTGCATAGAACAA -s Anc0.Anc0refChr1 8690 36 - 62388 AATCCTATGAGTTAGCTGGAGGACTGCATAGAAAAA -s Anc1.Anc1refChr2 86924 36 + 144309 AATCCTATGAGTTAGCTGGAGGACTGCATAGAAAAA -s Anc2.Anc2refChr2 24515 36 + 27695 GATCCTATGAGTTAGCTAGAGGACTGCATAGAAAAA -s mr.mrrefChr0 110196 36 + 130230 AATCCTATGACTTGACTGGGAGACTGCATAGAAAAA -s simCow_chr6.simCow.chr6 118971 36 + 602619 GATTGTATGAGTTAGCTAGAGGACTGCATAGAAAAA -s simDog_chr6.simDog.chr6 511407 36 - 593897 GATCCTATGAGTCCGTTAGAGGACTCCATAGAAGAA -s simHuman_chr6.simHuman.chr6 110801 36 + 601863 AATCCTATGAGTTAGCTGGAGGACTGCATCCAAAGA -s simRat_chr6.simRat.chr6 107936 36 + 647215 AATCCTACGACTGGACTGGGAGACTGCATAGAAAAA - -a -s simMouse_chr6.simMouse.chr6 115545 13 + 636262 GATACAAGGTGAT -s Anc0.Anc0refChr1 8726 13 - 62388 GACATAAAATATT -s Anc1.Anc1refChr2 86960 13 + 144309 GACATAAAATATT -s Anc2.Anc2refChr2 24551 13 + 27695 GACATAAAATATT -s mr.mrrefChr0 110232 13 + 130230 GATATAAGGTGAT -s simCow_chr6.simCow.chr6 119007 13 + 602619 GACATAAAATATT -s simDog_chr6.simDog.chr6 511443 13 - 593897 GATATAAAATATT -s simDog_chr6.simDog.chr6 249540 12 + 593897 GAGG-GAAATATT -s simHuman_chr6.simHuman.chr6 110837 11 + 601863 GACATAATAT--T -s simRat_chr6.simRat.chr6 107972 13 + 647215 GATTTGAGCTGAT - -a -s simMouse_chr6.simMouse.chr6 115558 10 + 636262 AAAGAAAGTC -s Anc0.Anc0refChr1 8744 10 - 62388 AAAGAAAGAC -s Anc1.Anc1refChr2 86978 10 + 144309 AAAGAAAGAC -s Anc2.Anc2refChr2 24569 10 + 27695 AAAGAAAGAT -s mr.mrrefChr0 110250 10 + 130230 AAAGAAAGTC -s simCow_chr6.simCow.chr6 119025 10 + 602619 ACCGAAAGAT -s simDog_chr6.simDog.chr6 511461 10 - 593897 AAAGAAGGAT -s simDog_chr6.simDog.chr6 249557 10 + 593897 AAAGACTGAC -s simHuman_chr6.simHuman.chr6 110853 10 + 601863 AAACAAAGAC -s simRat_chr6.simRat.chr6 107990 10 + 647215 AAAGAAAGTC - -a -s simMouse_chr6.simMouse.chr6 115568 1 + 636262 A -s Anc0.Anc0refChr1 8754 1 - 62388 A -s Anc1.Anc1refChr2 86988 1 + 144309 A -s Anc2.Anc2refChr2 24579 1 + 27695 A -s mr.mrrefChr0 110260 1 + 130230 A -s simCow_chr6.simCow.chr6 119035 1 + 602619 A -s simDog_chr6.simDog.chr6 249567 1 + 593897 A -s simHuman_chr6.simHuman.chr6 110863 1 + 601863 A -s simRat_chr6.simRat.chr6 108000 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 115569 15 + 636262 CAAAAGCAACACTTG -s Anc0.Anc0refChr1 8755 14 - 62388 CAAAAGC-ACACTTA -s Anc1.Anc1refChr2 86989 14 + 144309 CAAAAGC-ACACTTA -s Anc2.Anc2refChr2 24580 14 + 27695 CAAAAGC-ACACTTA -s mr.mrrefChr0 110261 15 + 130230 CAAAAGCAACACTTG -s simCow_chr6.simCow.chr6 119036 14 + 602619 CAAAAGC-ACACTTA -s simDog_chr6.simDog.chr6 511471 14 - 593897 CAAACGC-ACACTTA -s simDog_chr6.simDog.chr6 249568 14 + 593897 CAAAAGC-AGACTTA -s simHuman_chr6.simHuman.chr6 110864 14 + 601863 CAAAAGC-ACACTTA -s simRat_chr6.simRat.chr6 108001 15 + 647215 AAAAAGCAACGCTTC - -a -s simMouse_chr6.simMouse.chr6 115584 12 + 636262 AAAGGGAACTGG -s Anc0.Anc0refChr1 8769 12 - 62388 AAAGAGAAATGG -s Anc1.Anc1refChr2 87003 12 + 144309 AAAGAGAAATGG -s Anc2.Anc2refChr2 24594 12 + 27695 AAAGAGAAATGG -s mr.mrrefChr0 110276 12 + 130230 AAAGGGAAATGG -s simCow_chr6.simCow.chr6 119087 12 + 602619 AAACAGTAATGG -s simDog_chr6.simDog.chr6 511485 12 - 593897 AAAGAGAAATGG -s simDog_chr6.simDog.chr6 249582 12 + 593897 AAAGAGAAATGG -s simHuman_chr6.simHuman.chr6 110878 12 + 601863 CAAGAGAAATGG -s simRat_chr6.simRat.chr6 108016 12 + 647215 AAAGGGAAATAG - -a -s simMouse_chr6.simMouse.chr6 115596 16 + 636262 CTATACTGTTTTAAAA -s Anc0.Anc0refChr1 8782 16 - 62388 CAATACTATGTTATGA -s Anc1.Anc1refChr2 87016 16 + 144309 CAATACTATGTTATGA -s Anc2.Anc2refChr2 24607 16 + 27695 CAATACTATGTCATGA -s mr.mrrefChr0 110288 16 + 130230 CTATACTGTTTTAAAA -s simCow_chr6.simCow.chr6 119100 16 + 602619 CAAAATTATGTCATAA -s simDog_chr6.simDog.chr6 511498 16 - 593897 CAATACTAGGTTATGA -s simDog_chr6.simDog.chr6 249595 16 + 593897 CAATACTATGTCATGA -s simHuman_chr6.simHuman.chr6 110891 16 + 601863 CAGTACTATGTTATGA -s simRat_chr6.simRat.chr6 108028 16 + 647215 CTATACTGTTTTAAAA - -a -s simMouse_chr6.simMouse.chr6 115612 65 + 636262 CACTGCTAGTTTGCACTTTTATCATTACTGATAAGTGTTTCTTTTGTGAGCTGGATCATATCGTA -s Anc0.Anc0refChr1 8798 64 - 62388 CACTGCTAATTTGCACTATTATCATTATTTACAAGTGTAT-TTCTGAGAGGGGTACCATGTTGTA -s Anc1.Anc1refChr2 87032 64 + 144309 CACTGCTAATTTGCACTATTATCATTATTTACAAGTGTAT-TTCTGAGAGGGGTACCATGTTGTA -s Anc2.Anc2refChr2 24623 64 + 27695 CCCTGTTAATTTCCACTATTATCATTACCTACAAGTGTAT-TTCTGAGAGGGATACCATGTCCTA -s mr.mrrefChr0 110304 65 + 130230 CACTGCTAGTTTGCACTTTTATCATTATTTATAAGTGTATCTTTTGAGAGCTGGATCATATTGTA -s simCow_chr6.simCow.chr6 119116 60 + 602619 TC----TAATTTCCACTATTATTGTTACCTACAAGTGTAT-TTCCCAGAGGGATCCCAAGTCCTA -s simDog_chr6.simDog.chr6 511514 64 - 593897 CCCTGATAATTTCCACTATTACCATTACTTACAAGTGTAT-TTCTGAGAGGGATACTATGTCCTA -s simDog_chr6.simDog.chr6 249611 53 + 593897 CCCTGTTAATTTGCACCATCATCATTACCTACAAGTGTAT-TT---------ATACCAGGTCC-- -s simHuman_chr6.simHuman.chr6 110907 62 + 601863 CACTACTAATTTGCACTATGATA--TATTTACAAGTGTAT-TTCTGAGGGGGGTACCATCTTGTA -s simRat_chr6.simRat.chr6 108045 65 + 647215 CACTGCTACTTTGCATTTTTACTATTATCTATAAGTGTAGCCTTCGAGAGCAGGATGATATTGTA - -a -s simMouse_chr6.simMouse.chr6 115677 8 + 636262 CCTTGGCA -s Anc0.Anc0refChr1 8863 8 - 62388 CTTGAATG -s Anc1.Anc1refChr2 87097 8 + 144309 CTTGAATG -s Anc2.Anc2refChr2 24688 8 + 27695 CTTGAATG -s mr.mrrefChr0 110370 8 + 130230 CTTTGACA -s simCow_chr6.simCow.chr6 119177 8 + 602619 CTTAAAAG -s simDog_chr6.simDog.chr6 511579 8 - 593897 CTGGAAGG -s simDog_chr6.simDog.chr6 249664 6 + 593897 --TGAATG -s simHuman_chr6.simHuman.chr6 110970 8 + 601863 CTTGAATG -s simRat_chr6.simRat.chr6 108111 8 + 647215 TTTTGACA - -a -s simMouse_chr6.simMouse.chr6 115685 11 + 636262 TGACGCTTTGT -s Anc0.Anc0refChr1 8873 11 - 62388 AGACTTTTTGG -s Anc1.Anc1refChr2 87107 11 + 144309 AGACTTTTTGG -s Anc2.Anc2refChr2 24698 11 + 27695 AGTGTATCTAG -s mr.mrrefChr0 110378 11 + 130230 TGACGTTTTGT -s simCow_chr6.simCow.chr6 119187 10 + 602619 AGTGTATCT-G -s simDog_chr6.simDog.chr6 511589 5 - 593897 ------TCTAG -s simDog_chr6.simDog.chr6 249674 5 + 593897 ------TCTAG -s simHuman_chr6.simHuman.chr6 110980 11 + 601863 AGACCTTTTGG -s simRat_chr6.simRat.chr6 108119 11 + 647215 CAACTTTTTCT - -a -s simMouse_chr6.simMouse.chr6 115696 7 + 636262 TAATAAG -s Anc0.Anc0refChr1 8887 7 - 62388 AAGTTAG -s Anc1.Anc1refChr2 87121 7 + 144309 AAGTTAG -s Anc2.Anc2refChr2 24712 7 + 27695 AAGTTAG -s mr.mrrefChr0 110389 7 + 130230 TAATAAG -s simCow_chr6.simCow.chr6 119200 7 + 602619 AAGTTAA -s simDog_chr6.simDog.chr6 511597 7 - 593897 AAGTTAG -s simDog_chr6.simDog.chr6 249682 7 + 593897 AAGTTAG -s simHuman_chr6.simHuman.chr6 110994 7 + 601863 AAGTTAG -s simRat_chr6.simRat.chr6 108130 7 + 647215 TAATAAA - -a -s simMouse_chr6.simMouse.chr6 115703 9 + 636262 GCCAGTGCC -s Anc0.Anc0refChr1 8894 9 - 62388 TCCAGTACC -s Anc1.Anc1refChr2 87128 9 + 144309 TCCAGTACC -s Anc2.Anc2refChr2 24719 9 + 27695 TCCAGTACC -s mr.mrrefChr0 110396 9 + 130230 GCCAGTGCC -s simCow_chr6.simCow.chr6 119207 6 + 602619 ---AATACC -s simDog_chr6.simDog.chr6 249689 9 + 593897 TCCAGCGCC -s simHuman_chr6.simHuman.chr6 111001 9 + 601863 TCCAGTACT -s simRat_chr6.simRat.chr6 108137 9 + 647215 GCCAGTGCC - -a -s simMouse_chr6.simMouse.chr6 115712 77 + 636262 AGAGAGTGCACATTTGCCGATTAGTGCATACTAACTAAAACTTCAGTGTATGCTAACTCCTACTAATACTCTTCACT -s Anc0.Anc0refChr1 8903 53 - 62388 AGACAATGCACATTTGCCAGACAATGCATATTAA-------------------TCATTACTATCA-----CTTCACT -s Anc1.Anc1refChr2 87137 53 + 144309 AGACAATGCACATTTGCCAGACAATGCATATTAA-------------------TCATTACTATCA-----CTTCACT -s Anc2.Anc2refChr2 24728 53 + 27695 AGACAATGCAAATTTGCCAGACAATGCATATTAA-------------------CCATTACTATCG-----CTTCACT -s mr.mrrefChr0 110405 77 + 130230 AGAGAATGCACATTTGCCAATCAATGCATACTAACTAAAACTTCAGTGTATGCTAACTACTACTAATACTCTTCACT -s simCow_chr6.simCow.chr6 119213 53 + 602619 AGACAATGTATATCTGCCAGCCTATGTATATTAA-------------------CCATAACTTCCT-----CCTCATT -s simDog_chr6.simDog.chr6 249698 53 + 593897 AGACAGTTCTAATTCGCCAGACAAGGCATATCAA-------------------CCATTACCATAG-----CTCCACC -s simHuman_chr6.simHuman.chr6 111011 53 + 601863 GGACAAAGCACATTTGTCAGGCAATGCATATTGA-------------------TGATTACTATCA-----CTTCACT -s simRat_chr6.simRat.chr6 108146 74 + 647215 AGAGAATGCATATTCGCCAATCAAT---TACTAACTAACACTTCAGTACACACTAACTACTGCTAATACTCTTCACT - -a -s simMouse_chr6.simMouse.chr6 115789 9 + 636262 GTCTTGTGT -s Anc0.Anc0refChr1 8956 9 - 62388 ATCTTGCAT -s Anc1.Anc1refChr2 87190 9 + 144309 ATCTTGCAT -s Anc2.Anc2refChr2 24781 9 + 27695 ATCTTGCAT -s mr.mrrefChr0 110482 9 + 130230 GTCTTGTGT -s simCow_chr6.simCow.chr6 119266 9 + 602619 GTCTTATGT -s simDog_chr6.simDog.chr6 511604 9 - 593897 ATCTTGCAT -s simDog_chr6.simDog.chr6 249751 9 + 593897 ATCTTGCAT -s simHuman_chr6.simHuman.chr6 111064 9 + 601863 ATCTTGCAT -s simRat_chr6.simRat.chr6 108220 9 + 647215 GTCTTGTGT - -a -s simMouse_chr6.simMouse.chr6 115798 51 + 636262 CACAACTGGCAGTGAGCCAGAAGATGAGGCCCAACGACACTAAAAGTTATT -s Anc0.Anc0refChr1 8965 11 - 62388 AACAAGTAAC----------------------------------------T -s Anc1.Anc1refChr2 87199 11 + 144309 AACAAGTAAC----------------------------------------T -s Anc2.Anc2refChr2 24790 11 + 27695 AACAAGTAAC----------------------------------------T -s mr.mrrefChr0 110491 27 + 130230 CACAACTGACAGTGAGC------------------------AAAAGTTATT -s simCow_chr6.simCow.chr6 119276 11 + 602619 AATAAGTAAC----------------------------------------T -s simDog_chr6.simDog.chr6 511613 11 - 593897 AACAAGTAAT----------------------------------------T -s simDog_chr6.simDog.chr6 249760 11 + 593897 AGCAAGTAAC----------------------------------------T -s simHuman_chr6.simHuman.chr6 111073 11 + 601863 TACACATAAC----------------------------------------T -s simRat_chr6.simRat.chr6 108229 27 + 647215 CACAACTGACAGTGAGC------------------------AAAAGTTATT - -a -s simMouse_chr6.simMouse.chr6 115849 23 + 636262 GGTGGAGAAAGTAGCTGTCAGCA -s Anc0.Anc0refChr1 8976 23 - 62388 GTTGGAAAAAGTAGCTGTCATCG -s Anc1.Anc1refChr2 87210 23 + 144309 GTTGGAAAAAGTAGCTGTCATCG -s Anc2.Anc2refChr2 24801 23 + 27695 GTTGGAAAAAGTAACTGTCATGG -s mr.mrrefChr0 110518 23 + 130230 GGTGGAGAAAGTAGCTGTCATCA -s simCow_chr6.simCow.chr6 119287 23 + 602619 GCTGGAAAAAGTAACTGTCATGG -s simDog_chr6.simDog.chr6 511624 23 - 593897 GTTGGAAAAAGTAACTGTCATGG -s simDog_chr6.simDog.chr6 249771 23 + 593897 GTTGGAAACAGTGGCTGTCATGG -s simHuman_chr6.simHuman.chr6 111084 23 + 601863 GTTGGACCAAGTAGCTGTCATCG -s simRat_chr6.simRat.chr6 108258 22 + 647215 GGTGGAGACAGTAG-TGTCATCA - -a -s simMouse_chr6.simMouse.chr6 115872 2 + 636262 GA -s Anc0.Anc0refChr1 8999 2 - 62388 GA -s Anc1.Anc1refChr2 87233 2 + 144309 GA -s Anc2.Anc2refChr2 24824 2 + 27695 GA -s mr.mrrefChr0 110541 2 + 130230 GA -s simCow_chr6.simCow.chr6 119310 2 + 602619 GA -s simDog_chr6.simDog.chr6 249794 2 + 593897 AA -s simHuman_chr6.simHuman.chr6 111107 2 + 601863 GA -s simRat_chr6.simRat.chr6 108280 2 + 647215 GA - -a -s simMouse_chr6.simMouse.chr6 115874 13 + 636262 CTTTGGATGTTAC -s Anc0.Anc0refChr1 9001 13 - 62388 CTTAGGGTGATTT -s Anc1.Anc1refChr2 87235 13 + 144309 CTTAGGGTGATTT -s Anc2.Anc2refChr2 24826 13 + 27695 CTTAGGGTGATCT -s mr.mrrefChr0 110543 13 + 130230 CTTTGGATGTTTC -s simCow_chr6.simCow.chr6 119312 13 + 602619 CTTATGGTGATCT -s simDog_chr6.simDog.chr6 249797 13 + 593897 CGTAGGCTGATCC -s simHuman_chr6.simHuman.chr6 111109 13 + 601863 CTTAGGGCGATTT -s simRat_chr6.simRat.chr6 108282 13 + 647215 CTTTGGATGTCTC - -a -s simMouse_chr6.simMouse.chr6 115887 83 + 636262 ATGCCAAGCTGGACTTATCAATGCGAGGCAAGCCAAGCTGATGGTCTTCCAGGCGTAGCAGACCTTATAAGGGAATATCAGCA -s Anc0.Anc0refChr1 9014 27 - 62388 ATGCCTAGCTGAACTTATAAGT------------------------------------------------GGAAG-------- -s Anc1.Anc1refChr2 87248 27 + 144309 ATGCCTAGCTGAACTTATAAGT------------------------------------------------GGAAG-------- -s Anc2.Anc2refChr2 24839 27 + 27695 ATCCCTAGCTGAACTTATAAGT------------------------------------------------GGAAG-------- -s mr.mrrefChr0 110556 83 + 130230 ATGCCAAGCTGGACTTATCAATGCGAGGCAAGCCAAGCTGATGGTCTTCCAGGCGTAGCAGACCTTATAAGGGAATATCAGCA -s simCow_chr6.simCow.chr6 119325 27 + 602619 ATGCCTTGTTGAACTTATAAAT------------------------------------------------AGACA-------- -s simDog_chr6.simDog.chr6 511647 27 - 593897 ATCCCTAGCTGAGCTTATATGT------------------------------------------------GGAAG-------- -s simDog_chr6.simDog.chr6 249810 22 + 593897 ATCCCCAGCTGAAC---TAGGT------------------------------------------------GGA---------- -s simHuman_chr6.simHuman.chr6 111122 27 + 601863 ATGCCCAGCTGAGCTTATAAGT------------------------------------------------GGAAG-------- -s simRat_chr6.simRat.chr6 108295 83 + 647215 ATGCCAAGCTGGACTTATCAATGTGATGCAAGCCAAGCTGAAGGTCTTCCAGGTGCAGTGGACCTTATAAGTGAACATGAGCA - -a -s simMouse_chr6.simMouse.chr6 115970 4 + 636262 TTAG -s Anc0.Anc0refChr1 9041 4 - 62388 TAAG -s Anc1.Anc1refChr2 87275 4 + 144309 TAAG -s Anc2.Anc2refChr2 24866 4 + 27695 TAAG -s mr.mrrefChr0 110639 4 + 130230 TTAG -s simCow_chr6.simCow.chr6 119352 4 + 602619 TAAG -s simDog_chr6.simDog.chr6 511674 4 - 593897 CAAG -s simHuman_chr6.simHuman.chr6 111149 4 + 601863 TATG -s simHuman_chr6.simHuman.chr6 232074 4 - 601863 TAAG -s simRat_chr6.simRat.chr6 108378 4 + 647215 TTAG - -a -s simMouse_chr6.simMouse.chr6 115974 68 + 636262 TAGATGTCCAAAAGTGAATCCCACTACTATGGTGACTGAAAACAGTCCGGTTCCAGTAAGTGTATCCA -s Anc0.Anc0refChr1 9048 68 - 62388 TAGATGTCCAGAAGTGGATCACAAACCTATGGTGATTGAAAACAATGCAGTCACAGTAAGTGTCTTTA -s Anc1.Anc1refChr2 87282 68 + 144309 TAGATGTCCAGAAGTGGATCACAAACCTATGGTGATTGAAAACAATGCAGTCACAGTAAGTGTCTTTA -s Anc2.Anc2refChr2 24873 68 + 27695 TAGATGTCCAGAAGTGGATCACAAGCCTATGGTGATTGAAAACAATGCAGTCACAGTAAGTGTCTTTA -s mr.mrrefChr0 110643 68 + 130230 TAGATGTCCAAAAGTGAATCCCACTACTATGGTGACTGAAAACAGTCCGGTTCCAGTAAGTGTATCTA -s simCow_chr6.simCow.chr6 119359 68 + 602619 TAGATGTCAAGAAGTGGACCCCAAGCCTATGGTAATTGCAAACAATGTGATCATAGTAAGTGTCCCTA -s simDog_chr6.simDog.chr6 511681 68 - 593897 TGGATGTGTTGAAGTGGATCACAAGCCGATGGTGATTGAAAAAAATACAGGGACAGCAAGTGTTTTTA -s simHuman_chr6.simHuman.chr6 111156 68 + 601863 TAGATGTACAGGAGTGGGTCCCAAACCCATGGTGATTGAAAACAACGCGGTCACAGTAAGTGTCTTTA -s simHuman_chr6.simHuman.chr6 232081 68 - 601863 TCGATGTCCGGGAGTGGATCACAAACCTATAGTGATTGAAAACAGTGCAGTCACAGTAAGTGTCTCTA -s simRat_chr6.simRat.chr6 108382 65 + 647215 TAGATGTCCAAAAGTAAATCCCA---CCATGGTGACTGAAAACAGTCTGGTTGCAGTAAGAGCATCTA - -a -s simMouse_chr6.simMouse.chr6 116042 25 + 636262 TCATTTTCTGACTATAGCCTTTTAA -s Anc0.Anc0refChr1 9116 25 - 62388 CCATATTCTGTCCTTAGCCTTATGA -s Anc1.Anc1refChr2 87357 25 + 144309 CCATATTCTGTCCTTAGCCTTATGA -s Anc2.Anc2refChr2 24941 25 + 27695 CCATATGCTGTCCTTAGCCCTATGA -s mr.mrrefChr0 110711 25 + 130230 TCATTTTCTGTCCATAGCCTTATGA -s simCow_chr6.simCow.chr6 119427 25 + 602619 CCTTATGCTGTCCTTGGCCCTATGA -s simDog_chr6.simDog.chr6 511749 25 - 593897 CCATACGCTGTCCTCAGCCCTATGA -s simHuman_chr6.simHuman.chr6 111232 25 + 601863 CCATATTTTTTCCTTAGCCTTACGG -s simHuman_chr6.simHuman.chr6 232156 25 - 601863 CCATATTCTGTCCTTAGCCTTATGC -s simRat_chr6.simRat.chr6 108447 25 + 647215 TTATTTTCTGTCCATAGGCTCATGT - -a -s simMouse_chr6.simMouse.chr6 116067 1 + 636262 T -s Anc0.Anc0refChr1 9141 1 - 62388 C -s Anc1.Anc1refChr2 87382 1 + 144309 C -s Anc2.Anc2refChr2 24966 1 + 27695 C -s mr.mrrefChr0 110736 1 + 130230 T -s simCow_chr6.simCow.chr6 119452 1 + 602619 C -s simDog_chr6.simDog.chr6 511774 1 - 593897 C -s simHuman_chr6.simHuman.chr6 232181 1 - 601863 A -s simRat_chr6.simRat.chr6 108472 1 + 647215 C - -a -s simMouse_chr6.simMouse.chr6 116068 3 + 636262 AAC -s Anc0.Anc0refChr1 9142 3 - 62388 TAT -s Anc1.Anc1refChr2 87383 3 + 144309 TAT -s Anc2.Anc2refChr2 24967 3 + 27695 TGT -s mr.mrrefChr0 110737 3 + 130230 TAC -s simCow_chr6.simCow.chr6 119453 3 + 602619 TGG -s simDog_chr6.simDog.chr6 511775 3 - 593897 TGT -s simHuman_chr6.simHuman.chr6 111257 3 + 601863 TAT -s simHuman_chr6.simHuman.chr6 232182 3 - 601863 TAT -s simRat_chr6.simRat.chr6 108473 3 + 647215 TAC - -a -s simMouse_chr6.simMouse.chr6 116071 14 + 636262 TCTGTCTCTGTGCT -s Anc0.Anc0refChr1 9145 14 - 62388 TTCATCTCTATCCT -s Anc1.Anc1refChr2 87386 14 + 144309 TTCATCTCTATCCT -s Anc2.Anc2refChr2 24970 14 + 27695 TTCATCTCTATCCT -s mr.mrrefChr0 110740 14 + 130230 TTTGTCTCTATGCT -s simCow_chr6.simCow.chr6 119461 14 + 602619 TTCATCTCTTTCCT -s simDog_chr6.simDog.chr6 511778 14 - 593897 TTTATCTCTATCCT -s simHuman_chr6.simHuman.chr6 111260 14 + 601863 TTCGTCCCTATTTT -s simHuman_chr6.simHuman.chr6 232185 14 - 601863 TTCATCCCTATCTT -s simRat_chr6.simRat.chr6 108476 14 + 647215 TTTGTCTCTATACT - -a -s simMouse_chr6.simMouse.chr6 116085 6 + 636262 GTGAAC -s Anc0.Anc0refChr1 9159 6 - 62388 CTGAAC -s Anc1.Anc1refChr2 87400 6 + 144309 CTGAAC -s Anc2.Anc2refChr2 24984 6 + 27695 CTGAAC -s mr.mrrefChr0 110754 6 + 130230 CTGAAC -s simCow_chr6.simCow.chr6 119483 6 + 602619 CTGAAC -s simDog_chr6.simDog.chr6 511792 6 - 593897 CTGAAC -s simHuman_chr6.simHuman.chr6 111274 6 + 601863 CTGCAC -s simHuman_chr6.simHuman.chr6 232199 6 - 601863 CTGCAC -s simRat_chr6.simRat.chr6 108490 6 + 647215 CTGAAG - -a -s simMouse_chr6.simMouse.chr6 116091 3 + 636262 GAT -s Anc0.Anc0refChr1 9168 3 - 62388 GGT -s Anc1.Anc1refChr2 87409 3 + 144309 GGT -s Anc2.Anc2refChr2 24993 3 + 27695 GGT -s mr.mrrefChr0 110763 3 + 130230 GAT -s simCow_chr6.simCow.chr6 119492 3 + 602619 GTT -s simDog_chr6.simDog.chr6 511801 3 - 593897 GGT -s simHuman_chr6.simHuman.chr6 111283 3 + 601863 GGG -s simHuman_chr6.simHuman.chr6 232208 3 - 601863 GGT -s simRat_chr6.simRat.chr6 108499 3 + 647215 GAT - -a -s simMouse_chr6.simMouse.chr6 116094 6 + 636262 GCAATG -s Anc0.Anc0refChr1 9171 6 - 62388 GCAATG -s Anc1.Anc1refChr2 87412 6 + 144309 GCAATG -s Anc2.Anc2refChr2 24996 6 + 27695 ACAATG -s mr.mrrefChr0 110766 6 + 130230 GCAATG -s simCow_chr6.simCow.chr6 119495 6 + 602619 ATAATG -s simDog_chr6.simDog.chr6 511804 6 - 593897 ACAGTG -s simHuman_chr6.simHuman.chr6 111286 6 + 601863 GCAATG -s simHuman_chr6.simHuman.chr6 232211 6 - 601863 GCAATG -s simRat_chr6.simRat.chr6 108505 6 + 647215 GCAATG - -a -s simMouse_chr6.simMouse.chr6 116100 14 + 636262 TTTATACACTTATG -s Anc0.Anc0refChr1 9178 12 - 62388 TTTATGCACCTA-- -s Anc1.Anc1refChr2 87419 14 + 144309 TTTATGCACCTATG -s Anc2.Anc2refChr2 25003 12 + 27695 TTTATACATCTA-- -s mr.mrrefChr0 110773 14 + 130230 TTTATGCACGTATG -s simCow_chr6.simCow.chr6 119502 12 + 602619 TTTATATATTGA-- -s simDog_chr6.simDog.chr6 511811 12 - 593897 TTCATACATCTA-- -s simHuman_chr6.simHuman.chr6 111293 14 + 601863 TTTATGCACGTATG -s simHuman_chr6.simHuman.chr6 232218 14 - 601863 TTTATCCACCTATG -s simRat_chr6.simRat.chr6 108512 14 + 647215 ATTATGCATGTATG - -a -s simMouse_chr6.simMouse.chr6 116114 2 + 636262 GT -s Anc0.Anc0refChr1 9191 2 - 62388 GC -s Anc1.Anc1refChr2 87434 2 + 144309 GC -s Anc2.Anc2refChr2 25016 2 + 27695 GC -s mr.mrrefChr0 110787 2 + 130230 GT -s simCow_chr6.simCow.chr6 119515 2 + 602619 CC -s simDog_chr6.simDog.chr6 511824 2 - 593897 GC -s simHuman_chr6.simHuman.chr6 232237 2 - 601863 GC -s simRat_chr6.simRat.chr6 108526 2 + 647215 GT - -a -s simMouse_chr6.simMouse.chr6 116116 32 + 636262 CATGCTAATTAGTTAAATAAATATTGAGATTC -s Anc0.Anc0refChr1 9193 20 - 62388 AACGCTAACCAGT----TAAATGT-------- -s Anc1.Anc1refChr2 87436 20 + 144309 AACGCTAACCAGT----TAAATGT-------- -s Anc2.Anc2refChr2 25018 20 + 27695 AACGCTTACAAGT----TAAGTGT-------- -s mr.mrrefChr0 110789 28 + 130230 CATGCTAACTAGT----TAAATATTGAGATAC -s simCow_chr6.simCow.chr6 119517 20 + 602619 AATGCTTACAAGT----AATGTCT-------- -s simDog_chr6.simDog.chr6 511826 20 - 593897 AGCACATATAGGT----TAAGTGC-------- -s simHuman_chr6.simHuman.chr6 111308 20 + 601863 CACGCTAACCAGT----TGAAGCT-------- -s simHuman_chr6.simHuman.chr6 232239 20 - 601863 AACGCTAACCAGG----TAAAGGT-------- -s simRat_chr6.simRat.chr6 108528 28 + 647215 AGTGGTGCCTAGT----TAAATATTGAGATAC - -a -s simMouse_chr6.simMouse.chr6 116148 76 + 636262 TATCTTCAACACTCTTCTAGGCATATCTTGGTGGGTGTGGAGTCAAGGCATAATGTTCCAGTCAGGGGTACCCTTA -s Anc0.Anc0refChr1 9319 72 - 62388 TGTCTTAAACAGTCTTCTAAGCTTGTCTTGGTA----TGAAGTCATGACATGATGTTCTAGTCAAATGTGCCCCTA -s Anc1.Anc1refChr2 87563 72 + 144309 TGTCTTAAACAGTCTTCTAAGCTTGTCTTGGTA----TGAAGTCATGACATGATGTTCTAGTCAAATGTGCCCCTA -s Anc2.Anc2refChr2 25154 72 + 27695 AGTCTTAAACAGTCTTCTAAGCTTGTTTGAGCA----TGAAGTCATGACATGATGTTCTAGTCTAATATGCCCCTT -s mr.mrrefChr0 110817 76 + 130230 TATCTTCAACACTCTTCTAAGCATATCTTGGTGGGTGTGGAGTCAAGGCATGATGTTCTAGTCAGGGGTACCCTTA -s simCow_chr6.simCow.chr6 119642 70 + 602619 AGTCTTAAACAGTCTGCTAAGCTTATT--AGAA----TGAAGTCATAACATGAAGCTCTAGTCTAATAGACCCCTG -s simDog_chr6.simDog.chr6 511978 67 - 593897 AGTCTTAAACAGTCTTCCAAGCTTGTTTGAGCA----TGAAGTCATGACGGGATGTTCTAG-----CATGCCCTAT -s simHuman_chr6.simHuman.chr6 111428 72 + 601863 TGTCTTAAACAGTCTCTTAAGCCCGTCTTGGTA----TGAACTCATGACATGACTTTCTAGTCAAATGTGCCACTA -s simRat_chr6.simRat.chr6 108556 76 + 647215 TATCTTGAACACTCTACTAAGCATATCTTGGTGGGTGTGGAGTCAAGGCATGTTGTTCTAGTCAGGGGTACCCTTG - -a -s simMouse_chr6.simMouse.chr6 116224 29 + 636262 GTCTCAGAAGGTGCTCTTCATACTCTATC -s Anc0.Anc0refChr1 9393 29 - 62388 GTCTCAAAAGTTACTCTTCAGACTCTATC -s Anc1.Anc1refChr2 87637 29 + 144309 GTCTCAAAAGTTACTCTTCAGACTCTATC -s Anc2.Anc2refChr2 25228 29 + 27695 GTTTCAAAAGTCACTCTTCAGACTCTATC -s mr.mrrefChr0 110893 29 + 130230 GTCTCAGAAGGTACTCTTCATACTCTATC -s simCow_chr6.simCow.chr6 119714 29 + 602619 GTTTCGGAAGTCACTATTCGGACTCTATC -s simDog_chr6.simDog.chr6 512047 29 - 593897 GTTTCAAGAGTCACTCTTCAGACTCTATC -s simHuman_chr6.simHuman.chr6 111502 29 + 601863 GTCTCAAAAATTACTCTTCAGACTCCATC -s simRat_chr6.simRat.chr6 108632 29 + 647215 GTCTCAGAAGGTACCCTTCATACTCTATG - -a -s simMouse_chr6.simMouse.chr6 116253 14 + 636262 CCTCAGCTTAAGCA -s Anc0.Anc0refChr1 9424 13 - 62388 CCTAAGCTCAAG-A -s Anc1.Anc1refChr2 87668 13 + 144309 CCTAAGCTCAAG-A -s Anc2.Anc2refChr2 25259 13 + 27695 CCTAAGATCAAG-A -s mr.mrrefChr0 110922 14 + 130230 CCTAAGCTTAAGCA -s simCow_chr6.simCow.chr6 119745 13 + 602619 CCTAGGATCAAG-A -s simDog_chr6.simDog.chr6 512078 13 - 593897 CCTAAGATCAGG-A -s simHuman_chr6.simHuman.chr6 111533 13 + 601863 CCTAAACTCAAG-A -s simRat_chr6.simRat.chr6 108661 14 + 647215 ACTAGGCTTAAGCG - -a -s simMouse_chr6.simMouse.chr6 116267 18 + 636262 AGTGAAAATAAAGCTGAG -s Anc0.Anc0refChr1 9437 18 - 62388 AGTGGATGTGAAGGTGAG -s Anc1.Anc1refChr2 87681 18 + 144309 AGTGGATGTGAAGGTGAG -s Anc2.Anc2refChr2 25272 18 + 27695 AGTAGATGTGAAGGTTAG -s mr.mrrefChr0 110936 18 + 130230 AGTGGAAATAAAGCTGAG -s simCow_chr6.simCow.chr6 119758 18 + 602619 ACCAAATGTGAAGGATAG -s simDog_chr6.simDog.chr6 512096 18 - 593897 AGTAGATGTGAAGGTTAA -s simHuman_chr6.simHuman.chr6 111546 18 + 601863 GGTGGATGTGAAGGTGAG -s simRat_chr6.simRat.chr6 108675 18 + 647215 AGTAGAATTAAAGCTGAG - -a -s simMouse_chr6.simMouse.chr6 116285 49 + 636262 ACATTCTGTAAAGAATAAACAGTTGTTGGGTATATAAAAGTATATGAAA -s Anc0.Anc0refChr1 9487 46 - 62388 ---TTGTGTAAAGATTAAATAGTTGTTGGGCATATAACAATATACAGAA -s Anc1.Anc1refChr2 87731 49 + 144309 ATATTGTGTAAAGATTAAATAGTTGTTGGGCATATAACAATATACAGAA -s Anc2.Anc2refChr2 25322 46 + 27695 ---TTGTGTAAAGATTATATAATAGTTGGGCATATAACAATATACAGAA -s mr.mrrefChr0 110954 49 + 130230 ATATTCTGTAAAGAATAAACAGTTGTTGGGTATATAAAAGTATATGAAA -s simCow_chr6.simCow.chr6 119811 46 + 602619 ---TTGTGTAAATATTATGTAGTAGTTGGGCATATAACAATATACAGAA -s simDog_chr6.simDog.chr6 512117 46 - 593897 ---CTGCGTAAAGATTATATAATAGTTGGGCATATAACATTATGCAGAT -s simHuman_chr6.simHuman.chr6 111605 46 + 601863 ATATTGTGCAAGCATTAAATAGGT---GGACATATAACAACATACAGAA -s simRat_chr6.simRat.chr6 108693 49 + 647215 ATATTCAGTAAAGAGTAAACAGTTGTTGTGTATATAAGAGTATAAGAAA - -a -s simMouse_chr6.simMouse.chr6 116334 61 + 636262 ACACTTACTGTTACCTGGGATTAGTCTAGAATTGATGTGGCTATATGTTGTCCCTCTCCAA -s Anc0.Anc0refChr1 9534 49 - 62388 ATACCCACACTTGCCTGAGATTATTCTAGAATTGATGAGGCTTTTT--TG----------A -s Anc1.Anc1refChr2 87781 49 + 144309 ATACCCACACTTGCCTGAGATTATTCTAGAATTGATGAGGCTTTTT--TG----------A -s Anc2.Anc2refChr2 25369 49 + 27695 ATACCTACACTTGCCTGATATTATCCGTAAATGGAGGAGGCTTTTT--TG----------A -s mr.mrrefChr0 111004 51 + 130230 ACACTCACTGTTACCTGGGATTAGTCTAGAATTGATGAGGCTATATGTTG----------A -s simCow_chr6.simCow.chr6 119858 48 + 602619 ATACCTACAC-CACCTGACATTATCCGTCAATGAAGGAGGATTTAT--TG----------A -s simDog_chr6.simDog.chr6 512164 42 - 593897 ATACCTGCTCTTGCCTGATAT-------AGATGGGGGAGGCTTTTT--TC----------A -s simHuman_chr6.simHuman.chr6 111652 49 + 601863 ATACCCACACTTGCCTGAGATTACTCTAGAATTCATGAGGCTTTCT--TG----------A -s simRat_chr6.simRat.chr6 108743 51 + 647215 ACACTCACTGTTACCTGGGATTAGTCTAGAATGGATGAGACTATATTTTG----------A - -a -s simMouse_chr6.simMouse.chr6 116395 17 + 636262 CCCTCTCCAATAGGGAT -s Anc0.Anc0refChr1 9583 17 - 62388 CCCACTCCAAACGGGAT -s Anc1.Anc1refChr2 87830 17 + 144309 CCCACTCCAAACGGGAT -s Anc2.Anc2refChr2 25419 17 + 27695 CCCATTCCAAACAGGAT -s mr.mrrefChr0 111055 17 + 130230 CCCTCTCCAATAGGGAT -s simCow_chr6.simCow.chr6 119907 17 + 602619 CCCAATCTAAACAGGAT -s simDog_chr6.simDog.chr6 512207 17 - 593897 CCCCTTCCAAACAGGAT -s simHuman_chr6.simHuman.chr6 111701 17 + 601863 CCCACTCCATGCGGGAT -s simRat_chr6.simRat.chr6 108794 17 + 647215 CCCCCTCCAATAGGAAT - -a -s simMouse_chr6.simMouse.chr6 116412 3 + 636262 GGG -s Anc1.Anc1refChr2 87862 3 + 144309 GAG -s mr.mrrefChr0 111072 3 + 130230 GGG -s simHuman_chr6.simHuman.chr6 111737 3 + 601863 GAG -s simRat_chr6.simRat.chr6 108811 3 + 647215 AGG - -a -s simMouse_chr6.simMouse.chr6 116415 7 + 636262 TCATCTA -s Anc0.Anc0refChr1 9615 3 - 62388 ----TTA -s Anc1.Anc1refChr2 87865 7 + 144309 TCAATTA -s Anc2.Anc2refChr2 25451 3 + 27695 ----TTA -s mr.mrrefChr0 111075 7 + 130230 TCATCTA -s simCow_chr6.simCow.chr6 119935 3 + 602619 ----TCA -s simDog_chr6.simDog.chr6 512239 3 - 593897 ----TTA -s simHuman_chr6.simHuman.chr6 111748 7 + 601863 TCAATTA -s simRat_chr6.simRat.chr6 108814 7 + 647215 TTATCTG - -a -s simMouse_chr6.simMouse.chr6 116422 39 + 636262 TTCTTTCATGACGACTATGGAGTTATTGATCATGATCCT -s Anc0.Anc0refChr1 9618 39 - 62388 TCCTTTTATGAGAGTTATGGAGTTATTAAGCATGGTCCC -s Anc1.Anc1refChr2 87872 39 + 144309 TCCTTTTATGAGAGTTATGGAGTTATTAAGCATGGTCCC -s Anc2.Anc2refChr2 25454 39 + 27695 TCCTTTTATTAGAGTTATGGAGTTATTAAGCATAGTCCC -s mr.mrrefChr0 111082 39 + 130230 TTCTTTCATGACGACTATGGAGTTATTGATCATGATCCT -s simCow_chr6.simCow.chr6 119987 39 + 602619 TCCTTTTAGTAGCGTCATAGAGTTATTGAATATCGTCCC -s simDog_chr6.simDog.chr6 512242 39 - 593897 TCCTTTTATTAGAGTTATGGAGTTATCAAGCACAGTCCA -s simHuman_chr6.simHuman.chr6 111755 39 + 601863 TCCTTCTGTGAGAGTTATGGAGTTATTAAGCATGGTCCC -s simRat_chr6.simRat.chr6 108821 39 + 647215 TTCTTTCATGGAGACCATGGAGTTATTCATCATGATCCT - -a -s simMouse_chr6.simMouse.chr6 116461 3 + 636262 GGG -s Anc0.Anc0refChr1 9675 3 - 62388 GTG -s Anc1.Anc1refChr2 87929 3 + 144309 GTG -s Anc2.Anc2refChr2 25511 3 + 27695 GTG -s mr.mrrefChr0 111121 3 + 130230 GGG -s simCow_chr6.simCow.chr6 120044 3 + 602619 GGG -s simDog_chr6.simDog.chr6 512299 3 - 593897 CTA -s simHuman_chr6.simHuman.chr6 111812 3 + 601863 GAG -s simRat_chr6.simRat.chr6 108860 3 + 647215 GGG - -a -s simMouse_chr6.simMouse.chr6 116464 44 + 636262 TTTTATTGGGCACCCCAATGTCCAGGCGCACACCCTAAATTTGC -s Anc0.Anc0refChr1 9693 43 - 62388 TTATCTTGG-CACCCTAATGTCCAGCAGGACACCCTTAATCTAC -s Anc1.Anc1refChr2 87947 43 + 144309 TTATCTTGG-CACCCTAATGTCCAGCAGGACACCCTTAATCTAC -s Anc2.Anc2refChr2 25529 43 + 27695 TTATCTTGG-CACCCTAATGTCAAGCAGGACACTGCTAATCTAC -s mr.mrrefChr0 111139 44 + 130230 TTTTATTGGGCACCCCAATGTCCAGGAGCACACCCTAAATTTGC -s simCow_chr6.simCow.chr6 120062 41 + 602619 TTATCTT---CACCCTAACGTCGAGCAAGACGCTGCTAATTTAC -s simDog_chr6.simDog.chr6 512317 43 - 593897 TCATCTTGG-CATCCTACTGTTAAGCAGGACACTGCTAATCTAC -s simHuman_chr6.simHuman.chr6 111830 43 + 601863 TTATCTTGT-CACCTTAATGTCCAGAAGGACACCCTTAATCTAC -s simRat_chr6.simRat.chr6 108878 43 + 647215 TTTTATTGGCCACCCCAATGTTCAGGAGTACACCGTAA-TTTGC - -a -s simMouse_chr6.simMouse.chr6 116508 23 + 636262 ATCTGGGGGAGGTTGAGGCCATA -s Anc0.Anc0refChr1 9738 20 - 62388 -TCTAGGAGGGGTTT--GCCCTT -s Anc1.Anc1refChr2 87992 21 + 144309 ATCTAGGAGGGGTTT--GCCCTT -s Anc2.Anc2refChr2 25574 20 + 27695 -TTTAGGAGGGGTTT--GCCCTT -s mr.mrrefChr0 111183 23 + 130230 ATCTGGGGGAGGTTGAGGCCATA -s simCow_chr6.simCow.chr6 120105 20 + 602619 -TTTAGCAGGGTTCT--GCCCTT -s simDog_chr6.simDog.chr6 512362 15 - 593897 ---TAGGTTCAGGTT--GCT--- -s simHuman_chr6.simHuman.chr6 111875 21 + 601863 ATCTAGTAGGGGTTT--GCCCTC -s simRat_chr6.simRat.chr6 108921 23 + 647215 ATCTGAGGGAGGTTGAGGCCACA - -a -s simMouse_chr6.simMouse.chr6 116531 7 + 636262 GTTTACC -s Anc0.Anc0refChr1 9768 3 - 62388 ----ACT -s Anc1.Anc1refChr2 88023 7 + 144309 GTTTACT -s Anc2.Anc2refChr2 25604 3 + 27695 ----ACT -s mr.mrrefChr0 111206 7 + 130230 GTTTACC -s simCow_chr6.simCow.chr6 120135 3 + 602619 ----ACT -s simHuman_chr6.simHuman.chr6 111909 7 + 601863 GTTTACT -s simRat_chr6.simRat.chr6 108944 7 + 647215 GTTTACC - -a -s simMouse_chr6.simMouse.chr6 116538 20 + 636262 AACATGCAAGCTTGCCTTCA -s Anc0.Anc0refChr1 9773 14 - 62388 AACCTGCAT------CCTCA -s Anc1.Anc1refChr2 88032 14 + 144309 AACCTGCAT------CCTCA -s Anc2.Anc2refChr2 25609 14 + 27695 AACCTGCTT------TCTGA -s mr.mrrefChr0 111213 20 + 130230 AACATGCAAGCTTGCCTTCA -s simCow_chr6.simCow.chr6 120141 14 + 602619 AACCTGCTT------TCTGA -s simHuman_chr6.simHuman.chr6 111918 14 + 601863 AACCTGCAG------CCTCA -s simRat_chr6.simRat.chr6 108951 20 + 647215 AACATGCAAGTTTGCCTTCA - -a -s simMouse_chr6.simMouse.chr6 116558 16 + 636262 TTTCTTGTGTGTCCCC -s Anc0.Anc0refChr1 9787 16 - 62388 TATATTGTCTGACCAC -s Anc1.Anc1refChr2 88046 16 + 144309 TATATTGTCTGACCAC -s Anc2.Anc2refChr2 25623 16 + 27695 TAGATTGTCCGTCCAC -s mr.mrrefChr0 111233 16 + 130230 TTTCTTGTCTGACCCC -s simCow_chr6.simCow.chr6 120156 16 + 602619 TAGATTGTCCGTCCAC -s simHuman_chr6.simHuman.chr6 111932 16 + 601863 TGTATTGGCTGACCAC -s simRat_chr6.simRat.chr6 108971 16 + 647215 TTTCTTGTCCGATCCC - -a -s simMouse_chr6.simMouse.chr6 116574 113 + 636262 CATCATGTGTAAAAATAACAATATTTTTGAAAAACGCCAGGGTGTACCTAGTGATCTAAAAATGAAAAAACAAATACTTTTATGCTTGTTGTGATGTAGGAATATTCAGAACA -s Anc0.Anc0refChr1 9803 107 - 62388 CTCCATGTGCTGGGATAACAATATTTTTGAAAAACATTAGGTAGTATGTGGCGGTACAAGAGTGAAAAA-CAAATACTTTCATGCTTGTTGT-----AGAAATATTTAGATTG -s Anc1.Anc1refChr2 88062 107 + 144309 CTCCATGTGCTGGGATAACAATATTTTTGAAAAACATTAGGTAGTATGTGGCGGTACAAGAGTGAAAAA-CAAATACTTTCATGCTTGTTGT-----AGAAATATTTAGATTG -s Anc2.Anc2refChr2 25639 107 + 27695 CTCCATGTGCTGGGTTAAGAATATGGTTGAAAAACATTAAGTACTTTGTGGCAGTACAAGAATGAAAAA-AAAATACTTTTATGCTTGTTGT-----AGAAATATTTAGATTG -s mr.mrrefChr0 111249 112 + 130230 CATCATGTGTAAAAATAACAATATTTTTGAAAAACACCAGGGTGTATCTGGTGATCTAAAAGTGAAAAA-CAAATACTTTCATGCTTGTTGTGATGTAGGAATATTTAGAACA -s simCow_chr6.simCow.chr6 120182 105 + 602619 CTCCATGTGTAGGGTTAAGAATATGGTTGAAAAACATTAAGTACTTTGTGGCAGTACAAGAACAGATAA-AAAATACTTTTTTGCTTGTTGT-----TG-AATATCTAAA-CG -s simDog_chr6.simDog.chr6 512377 60 - 593897 -----TGTGCTGGG-----------------------------------------ACAAGAATGAAAAA-AATATCCCT-TATGTGTGTTGT-----AGAAATATTTAGATTG -s simHuman_chr6.simHuman.chr6 111948 107 + 601863 CCCCATGTGCGGGGATAACAACATTTTTGCAAAACATTTGGAAGTATGTGTGGGCACAAGAGTGAAAAA-CAAGTACTTACATACTTGTTGT-----AGAAGTATTTGGATTG -s simRat_chr6.simRat.chr6 108987 112 + 647215 CATCATGTGTAAAAATAACAATATTTTCGAAAAACACCAGGGTGTATCTGGTGATCTATAAGTGAAAAA-CAAAGACTTTCATGCTTGTTATGATGTAGGAATATTTCGAGCA - -a -s simMouse_chr6.simMouse.chr6 116687 79 + 636262 CCCAAAAAGCATAAGGTTGTTGGAGTTCCTCTCTGGTTACAGCAGTATCATTCAGTGTGAGAAGATTCAGACTGACAGT -s Anc0.Anc0refChr1 9910 79 - 62388 CCCAAAGACCAAGAAGTTGTGGGCGTTCCACTTTGGTTACTACAATGTCACTCAGTGTAAGAAGCTTTGTATAATGAAT -s Anc1.Anc1refChr2 88169 79 + 144309 CCCAAAGACCAAGAAGTTGTGGGCGTTCCACTTTGGTTACTACAATGTCACTCAGTGTAAGAAGCTTTGTATAATGAAT -s Anc2.Anc2refChr2 25746 79 + 27695 CCCAAAGACCAAAAAGTGGTGGGCATTCCACTTTGGTTACTACAATGTTCCTCAGTGTAGTAAGCTTTGTATAATGAAT -s mr.mrrefChr0 111361 79 + 130230 CCCAAAAAGCATGAGGTTGTGGGAGTTCCTCTTTGGTTACAGCAGTATCATTCAGTGTGAGAAGATTCGGACTGACAGT -s simCow_chr6.simCow.chr6 120287 78 + 602619 CCCAAAGACCAAAAAGTAGTGGG-ATTCCACATTGGTTAGTACAATGTGCCCCAGTAGAGCAAGACTTGTATGATGGGT -s simDog_chr6.simDog.chr6 512438 79 - 593897 CCCAAAGGCCAAAGAGTGGTGGGCATTCCACTTTGGTTACCACAATGTTCCTAAGTGTAGTAAACTTTATACAATGAAT -s simHuman_chr6.simHuman.chr6 112055 77 + 601863 CCCAGGCACCAAGAAGCTGTGGGCGTACCACCTT--TTACTACGATGTCACTCAGTGTAAGAAGTTTTGTATAATGAAT -s simRat_chr6.simRat.chr6 109099 79 + 647215 CCAGAAAAGCATGAGGTTGTGGGGGTTCCTCTTTGGTTACGGCAGTATCATTCAGTGTGAGAAGATTCGGACTGACAAT - -a -s simMouse_chr6.simMouse.chr6 116766 14 + 636262 TCTTCCTAGCTTTC -s Anc0.Anc0refChr1 9995 11 - 62388 ---CCCTAATTTTC -s Anc1.Anc1refChr2 88254 14 + 144309 TCTCCCTAATTTTC -s Anc2.Anc2refChr2 25831 11 + 27695 ---CCCTAATCTTC -s mr.mrrefChr0 111440 14 + 130230 TCTCCCTAGTTTTC -s simCow_chr6.simCow.chr6 120371 11 + 602619 ---CCCCAATCTTC -s simDog_chr6.simDog.chr6 512523 11 - 593897 ---CCCTAATCTTC -s simHuman_chr6.simHuman.chr6 112139 14 + 601863 TCTCCCTAATTTCT -s simRat_chr6.simRat.chr6 109178 14 + 647215 TCTCCCTAGTTTTC - -a -s simMouse_chr6.simMouse.chr6 116780 7 + 636262 AAGATAT -s Anc0.Anc0refChr1 10006 7 - 62388 AAGGTAT -s Anc1.Anc1refChr2 88268 7 + 144309 AAGGTAT -s Anc2.Anc2refChr2 25842 7 + 27695 ACAGTAT -s mr.mrrefChr0 111454 7 + 130230 AAGGTAT -s simCow_chr6.simCow.chr6 120382 7 + 602619 ACAGCAT -s simDog_chr6.simDog.chr6 512534 7 - 593897 ACAGTAA -s simHuman_chr6.simHuman.chr6 112153 7 + 601863 AAGGTAT -s simRat_chr6.simRat.chr6 109194 7 + 647215 AAGGTAT - -a -s simMouse_chr6.simMouse.chr6 116787 50 + 636262 TTGTGAGGATGTACCACACAATTAACAACACAGAATTGGCAGGGTCAATG -s Anc0.Anc0refChr1 10013 45 - 62388 CTCTGAGGATGTACCACA---TTAACAACA--GAATGGTCAAGATCAATG -s Anc1.Anc1refChr2 88275 45 + 144309 CTCTGAGGATGTACCACA---TTAACAACA--GAATGGTCAAGATCAATG -s Anc2.Anc2refChr2 25849 45 + 27695 CTCTGAGGATGTACCAGA---CTAACAACA--GAATGGTCAAGAGCAATG -s mr.mrrefChr0 111461 45 + 130230 CTGTGAGGATGTACCACA---TTAACAACA--GAATTGTCAAGGTCAATG -s simCow_chr6.simCow.chr6 120389 44 + 602619 CTCTGAGGGTGTACCAGA---CTAAC-ACT--GATTGGTCTAGGGTAACA -s simDog_chr6.simDog.chr6 512541 45 - 593897 CTCTGAGGATGTACCAGA---CTAACAACA--GAATGGTTAAGAGCAATG -s simHuman_chr6.simHuman.chr6 112178 45 + 601863 CTCTGAGGTTGTAGCACA---TTAATGACA--GAATGGTCAAGATCAACT -s simRat_chr6.simRat.chr6 109201 45 + 647215 CTGTGAGGATGTATCATG---TTAACAACA--GAATTGTCAAGGCCAATA - -a -s simMouse_chr6.simMouse.chr6 116837 24 + 636262 TCTCTTGAGAAATCAACATATTAT -s Anc0.Anc0refChr1 10058 24 - 62388 TCACCTGAGGAGTTAACATATTAT -s Anc1.Anc1refChr2 88320 24 + 144309 TCACCTGAGGAGTTAACATATTAT -s Anc2.Anc2refChr2 25898 24 + 27695 TCACCTGAGGAGTTAGCATATTAC -s mr.mrrefChr0 111506 24 + 130230 TCTCCTGAGAAGTCAACATATTAT -s simCow_chr6.simCow.chr6 120437 24 + 602619 TCACATGAGGAGTTAGACTACCAC -s simDog_chr6.simDog.chr6 512593 24 - 593897 CCACCTGAGGAGTCAGCATCTTAC -s simHuman_chr6.simHuman.chr6 112223 24 + 601863 TCACCCGAGGAGCTAACACATTAT -s simRat_chr6.simRat.chr6 109246 24 + 647215 TCTCCTGAGAAGACAACATTTTAT - -a -s simMouse_chr6.simMouse.chr6 116861 42 + 636262 TAACTTCCCAACTTCCACTGGTGGGCTACTGTCCCCAGACCA -s Anc0.Anc0refChr1 10106 38 - 62388 TAACTTCATGGTTTCCACTGACT--CT--TATCCCCATAATG -s Anc1.Anc1refChr2 88368 40 + 144309 TAACTTCATGGTTTCCACTGACT--CTATTATCCCCATAATG -s Anc2.Anc2refChr2 25946 38 + 27695 TAACTTCATGGTATCGCCTGGCT--CT--TATCCCCATAATA -s mr.mrrefChr0 111530 42 + 130230 TAACTTCACGGTTTCCACTGACTGGCTACTATCCCCAGACCG -s simCow_chr6.simCow.chr6 120484 38 + 602619 TAACATTGTGGTATCAGTTGGCT--AT--TATCCCCTTAATA -s simDog_chr6.simDog.chr6 512641 38 - 593897 TAACTTCATGGTATTGCCTGGCT--CT--TATCCCCATAATA -s simHuman_chr6.simHuman.chr6 112271 35 + 601863 TAATTGCATGGTTTCCACTGACT--CTATTATCCCC-----G -s simRat_chr6.simRat.chr6 109270 42 + 647215 TAACTTCACGGTTTCCACTGACTGGCCACTATCCCCAGATTG - -a -s simMouse_chr6.simMouse.chr6 116903 31 + 636262 GATCAGGAAGGAGAAGCATTGTGTTCAACAG -s Anc0.Anc0refChr1 10144 31 - 62388 TCTCAGGAAGGGGTGGTATGGTGTTCTACAA -s Anc1.Anc1refChr2 88408 31 + 144309 TCTCAGGAAGGGGTGGTATGGTGTTCTACAA -s Anc2.Anc2refChr2 25991 31 + 27695 TCTCAGGAAGGAGTGCTATGGTGTTCTACAA -s mr.mrrefChr0 111572 31 + 130230 GATCAGGAAGGGGAAGCATTGTGTTCAACAG -s simCow_chr6.simCow.chr6 120529 31 + 602619 TCTAAGAAAGGAGTGGCATGGTGTTCTGCCA -s simDog_chr6.simDog.chr6 512686 31 - 593897 TCGCTAGAAGGAGCGCTATGGTGTTCCACAG -s simHuman_chr6.simHuman.chr6 112306 27 + 601863 TCTCAGGAAGGGGTGGT----TGTTCTACAA -s simRat_chr6.simRat.chr6 109312 30 + 647215 GATGAGGAAGGGGAAGCATTGTGTTCAACA- - -a -s simMouse_chr6.simMouse.chr6 116934 27 + 636262 GAAGTGTTCAACATCTAAACTGCTGAC -s Anc0.Anc0refChr1 10175 21 - 62388 GAGGTGTTCAACTTCTAATCT------ -s Anc1.Anc1refChr2 88439 27 + 144309 GAGGTGTTCAACTTCTAATCTGCTAAT -s Anc2.Anc2refChr2 26022 21 + 27695 GGGGTGTTCAACTTCTAATCT------ -s mr.mrrefChr0 111603 27 + 130230 GAAGTGTTCAACATCTAATCTGCTAAT -s simCow_chr6.simCow.chr6 120560 21 + 602619 GTGGTGTTCAGCTTCTAATCT------ -s simDog_chr6.simDog.chr6 512717 21 - 593897 GGGGTGTCCAACTTCTCATCT------ -s simHuman_chr6.simHuman.chr6 112341 27 + 601863 TAGGTGTTCAACTGTTAATCTGCTAAT -s simRat_chr6.simRat.chr6 109342 19 + 647215 --------CAACATCTAATCTGCTAAT - -a -s simMouse_chr6.simMouse.chr6 116961 10 + 636262 CCCAATAAGT -s Anc0.Anc0refChr1 10215 10 - 62388 CCCAATATGG -s Anc1.Anc1refChr2 88485 10 + 144309 CCCAATATGG -s Anc2.Anc2refChr2 26062 10 + 27695 CTCAATATGG -s mr.mrrefChr0 111630 10 + 130230 CCCAATAAGT -s simCow_chr6.simCow.chr6 120601 10 + 602619 CTCAATATGG -s simDog_chr6.simDog.chr6 512757 10 - 593897 CTCAATGTGG -s simHuman_chr6.simHuman.chr6 112411 10 + 601863 CCCGATATAG -s simRat_chr6.simRat.chr6 109361 10 + 647215 CACAATAGGT - -a -s simMouse_chr6.simMouse.chr6 116971 6 + 636262 ATTGAG -s Anc0.Anc0refChr1 10225 6 - 62388 ATTGAG -s Anc1.Anc1refChr2 88495 6 + 144309 ATTGAG -s Anc2.Anc2refChr2 26072 6 + 27695 ATTGAC -s mr.mrrefChr0 111640 6 + 130230 ATTGAG -s simCow_chr6.simCow.chr6 120611 6 + 602619 ATTGAC -s simDog_chr6.simDog.chr6 512768 6 - 593897 ATCAGC -s simHuman_chr6.simHuman.chr6 112421 6 + 601863 ATTGAG -s simRat_chr6.simRat.chr6 109371 6 + 647215 ATTGAG - -a -s simMouse_chr6.simMouse.chr6 116977 39 + 636262 TCAAGAACAACTTCACCTAATGAGGAAACGAAAAATGCC -s Anc0.Anc0refChr1 10237 37 - 62388 TCAAAAGCAACTTCACCTGATCAGCCTAT--ATACTGCC -s Anc1.Anc1refChr2 88507 37 + 144309 TCAAAAGCAACTTCACCTGATCAGCCTAT--ATACTGCC -s Anc2.Anc2refChr2 26084 37 + 27695 TCAAAAGCAACTTCATGTGATCAGCCTAT--ATACTGCC -s mr.mrrefChr0 111646 37 + 130230 TCAAAAACAACTTCACCTGATGAGCCAAC--AAAATGCC -s simCow_chr6.simCow.chr6 120623 37 + 602619 TCAACAACAACTTCATGTGATCAACCAAT--ATAATGCC -s simDog_chr6.simDog.chr6 512780 37 - 593897 TCAAAAGCAGCTTCATGTGATCAGCCTAT--ATACTGCC -s simHuman_chr6.simHuman.chr6 112433 37 + 601863 TCAAAGGCAACTTCACCTGATCAGCCTAT--ATACTGCC -s simRat_chr6.simRat.chr6 109377 37 + 647215 TTAAAAACAACTTCACCTGATGAGCCAAC--AATATCCC - -a -s simMouse_chr6.simMouse.chr6 117016 4 + 636262 TCAA -s Anc0.Anc0refChr1 10274 4 - 62388 TCAA -s Anc1.Anc1refChr2 88544 4 + 144309 TCAA -s Anc2.Anc2refChr2 26121 4 + 27695 TCAA -s mr.mrrefChr0 111683 4 + 130230 TCAA -s simCow_chr6.simCow.chr6 120663 4 + 602619 TCAA -s simDog_chr6.simDog.chr6 512817 4 - 593897 TTAA -s simHuman_chr6.simHuman.chr6 112470 4 + 601863 TCAA -s simRat_chr6.simRat.chr6 109414 4 + 647215 TCAA - -a -s simMouse_chr6.simMouse.chr6 117020 1 + 636262 T -s Anc0.Anc0refChr1 10278 1 - 62388 A -s Anc1.Anc1refChr2 88548 1 + 144309 A -s Anc2.Anc2refChr2 26126 1 + 27695 A -s mr.mrrefChr0 111687 1 + 130230 T -s simCow_chr6.simCow.chr6 120668 1 + 602619 A -s simDog_chr6.simDog.chr6 512822 1 - 593897 A -s simHuman_chr6.simHuman.chr6 112474 1 + 601863 A -s simRat_chr6.simRat.chr6 109418 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 117021 5 + 636262 AATTA -s Anc0.Anc0refChr1 10282 5 - 62388 AATTA -s Anc1.Anc1refChr2 88552 5 + 144309 AATTA -s Anc2.Anc2refChr2 26130 5 + 27695 AATTA -s mr.mrrefChr0 111688 5 + 130230 AATTA -s simCow_chr6.simCow.chr6 120672 5 + 602619 AAATA -s simDog_chr6.simDog.chr6 512826 5 - 593897 AATTA -s simHuman_chr6.simHuman.chr6 112478 5 + 601863 AATTA -s simRat_chr6.simRat.chr6 109419 5 + 647215 AATGA - -a -s simMouse_chr6.simMouse.chr6 117026 3 + 636262 TGA -s Anc0.Anc0refChr1 10287 3 - 62388 GGG -s Anc1.Anc1refChr2 88557 3 + 144309 GGG -s Anc2.Anc2refChr2 26135 3 + 27695 GGG -s mr.mrrefChr0 111693 3 + 130230 GGA -s simCow_chr6.simCow.chr6 120677 3 + 602619 GTG -s simDog_chr6.simDog.chr6 512831 3 - 593897 GGG -s simHuman_chr6.simHuman.chr6 112483 3 + 601863 GAG -s simRat_chr6.simRat.chr6 109424 3 + 647215 GGA -s simRat_chr6.simRat.chr6 109899 3 + 647215 GGA - -a -s simMouse_chr6.simMouse.chr6 117029 8 + 636262 ATTACTCA -s Anc0.Anc0refChr1 10295 8 - 62388 ATAACTCA -s Anc1.Anc1refChr2 88565 8 + 144309 ATAACTCA -s Anc2.Anc2refChr2 26143 8 + 27695 ATAGCTCA -s mr.mrrefChr0 111696 8 + 130230 ATTACTCA -s simCow_chr6.simCow.chr6 120685 8 + 602619 ATAGCTCA -s simDog_chr6.simDog.chr6 512839 8 - 593897 TAAGCTTG -s simHuman_chr6.simHuman.chr6 112491 8 + 601863 ATAACTCA -s simRat_chr6.simRat.chr6 109427 8 + 647215 ATCACTCA -s simRat_chr6.simRat.chr6 109902 8 + 647215 ATTACTCA - -a -s simMouse_chr6.simMouse.chr6 117037 1 + 636262 G -s Anc0.Anc0refChr1 10305 1 - 62388 G -s Anc1.Anc1refChr2 88575 1 + 144309 G -s Anc2.Anc2refChr2 26153 1 + 27695 C -s mr.mrrefChr0 111704 1 + 130230 G -s simCow_chr6.simCow.chr6 120695 1 + 602619 T -s simDog_chr6.simDog.chr6 512849 1 - 593897 C -s simHuman_chr6.simHuman.chr6 112501 1 + 601863 G -s simRat_chr6.simRat.chr6 109435 1 + 647215 T -s simRat_chr6.simRat.chr6 109910 1 + 647215 G - -a -s simMouse_chr6.simMouse.chr6 117038 20 + 636262 TAGGCGCTTGGTCATACTCA -s Anc0.Anc0refChr1 10310 20 - 62388 TGACTAGTTGTTCATGCTCA -s Anc1.Anc1refChr2 88580 20 + 144309 TGACTAGTTGTTCATGCTCA -s Anc2.Anc2refChr2 26158 20 + 27695 TGACTAGGTGTTCATGCTCA -s mr.mrrefChr0 111709 20 + 130230 TGGCTGTTTGGTCATACTCA -s simCow_chr6.simCow.chr6 120700 20 + 602619 TGACAAGGTGTGCATGCTCA -s simDog_chr6.simDog.chr6 512854 20 - 593897 TGACTAGGTGTTACTGCTCA -s simHuman_chr6.simHuman.chr6 112506 20 + 601863 AGACTAGTTGTTCATGCACA -s simRat_chr6.simRat.chr6 109440 20 + 647215 TGGCTGTTTGGTCATACTCA -s simRat_chr6.simRat.chr6 109915 20 + 647215 TGACTATATGGTCATACTCA - -a -s simMouse_chr6.simMouse.chr6 117058 55 + 636262 AATAATGGTTCCCAAAGTGAAGGGTAGTAGGGAGTTCCACTGGAGGTGTCCACAT -s Anc0.Anc0refChr1 10330 55 - 62388 AATACCAGTACCTCAAGGGAGGGGCAGTATGGTGTCCCTCTGGAGGTGTCCACTT -s Anc1.Anc1refChr2 88600 55 + 144309 AATACCAGTACCTCAAGGGAGGGGCAGTATGGTGTCCCTCTGGAGGTGTCCACTT -s Anc2.Anc2refChr2 26178 55 + 27695 AATACCAGTATCTCAAGGGAGGGGCAATATGGTGTCCCACTGGTGGTGTCCACTT -s mr.mrrefChr0 111729 55 + 130230 AATAATGGTACCCAAAGTGAAGGGTAGTAGGGAGTTCCTCTGGAGGTGTCCACTT -s simCow_chr6.simCow.chr6 120720 51 + 602619 AAAACAAGTCTCCAAGGGGAGGGGCAATATGGTCTTCAACTGGTGGTGTCC---- -s simDog_chr6.simDog.chr6 512923 55 - 593897 AGTACCAGTATCTCAAGGGAAGGGCAATATGCTGTCTCACCAGTGGTGTTCACTT -s simHuman_chr6.simHuman.chr6 112526 55 + 601863 AATACCAGTACCTCAAGGGAGGGGCAGTATGGTGTCCCTCTGGAGGTGTCCTCTT -s simRat_chr6.simRat.chr6 109460 55 + 647215 AATGATGGTACCCAAAGTGAACGGTAGTAGGGAGTTCCTCTGGAGGTGTCCACTT -s simRat_chr6.simRat.chr6 109935 55 + 647215 AATAATGGTACCCAAATTGAAGGGTGGTAGGGAGATCCTCTGGAGGTGTCCACTT - -a -s simMouse_chr6.simMouse.chr6 117113 11 + 636262 CTCATAAGACA -s Anc0.Anc0refChr1 10386 11 - 62388 CTGATGGGTAA -s Anc1.Anc1refChr2 88656 11 + 144309 CTGATGGGTAA -s Anc2.Anc2refChr2 26234 11 + 27695 CTGATGGGTAA -s mr.mrrefChr0 111784 11 + 130230 CTTATAAGGAA -s simCow_chr6.simCow.chr6 120771 11 + 602619 CTGATGGGTAA -s simDog_chr6.simDog.chr6 512979 11 - 593897 CCGACGGGTAA -s simHuman_chr6.simHuman.chr6 112582 11 + 601863 CTGATGGGTAA -s simRat_chr6.simRat.chr6 109515 11 + 647215 CTTATAAGGGA -s simRat_chr6.simRat.chr6 109990 11 + 647215 CTTATAAGGAA - -a -s simMouse_chr6.simMouse.chr6 117124 1 + 636262 T -s Anc0.Anc0refChr1 10397 1 - 62388 A -s Anc1.Anc1refChr2 88667 1 + 144309 A -s Anc2.Anc2refChr2 26245 1 + 27695 A -s mr.mrrefChr0 111795 1 + 130230 T -s simCow_chr6.simCow.chr6 120785 1 + 602619 T -s simDog_chr6.simDog.chr6 512990 1 - 593897 A -s simHuman_chr6.simHuman.chr6 112593 1 + 601863 C -s simRat_chr6.simRat.chr6 109526 1 + 647215 T -s simRat_chr6.simRat.chr6 110001 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 117125 170 + 636262 TAGTAGTCTCAATAGGTAAATAAAACCTTGCTAACTTAATAAGGAACAGTAAAGACCAATCTGCTGACTCACAGGCCAAGAAAAATGTTATGTCTGTCTGGGAATGAGTATGTTTAATGATGGTGCAGTATAAAGCCTATAGCCCTACTAGATTATCTCTCGTGTACATA -s Anc0.Anc0refChr1 10399 170 - 62388 AATTAGCCTCAATAAGTATATAAAAACTAGTCAACTTAGTGAAGAGCAGTAAAGAACAATTTCCTGACTCAAGGACCAAGAAAAAGGTGACATTTGACTTTGAATGAGTGTGGTTAATGATGACACATTACAAGGTCAACCACACGGCAAGATTATGTCTTGTGAATGTA -s Anc1.Anc1refChr2 88669 170 + 144309 AATTAGCCTCAATAAGTATATAAAAACTAGTCAACTTAGTGAAGAGCAGTAAAGAACAATTTCCTGACTCAAGGACCAAGAAAAAGGTGACATTTGACTTTGAATGAGTGTGGTTAATGATGACACATTACAAGGTCAACCACACGGCAAGATTATGTCTTGTGAATGTA -s Anc2.Anc2refChr2 26247 170 + 27695 AATTAGCCTCAATAAGTATATAAAAACTAGTCAACTTAGTGAAGAGCAATAAAGAACAATTTCCTGACTCAAGGACTAAGAAAAAGGTGACATTTGACTTTGAATGGGTGTGGTTAATGATGACACATTACAAGGTCAACCACACGGCAAGATTATGCCTTATGAATGTA -s mr.mrrefChr0 111797 170 + 130230 TAGTAGTCTCAATAGGTATATAAAACTTTGCTAACTTAATAAAGAACAGTAAAGACCAATCTGCTGACTCAAAGGCCAAGAAAAATGTTATGTCTGTCTGTTAATGAGTATGTTTAATGATGGTGCAGTATAAAGCCTATAGCTCTACTAGATTATCTCTTGTGAACATA -s simCow_chr6.simCow.chr6 120787 169 + 602619 TATTAGCCTCAATAAGTATATAAAAACTAGTCAACTTAGTGAAGGGCAACATAAACAAATTTCCTAACTCAAGCACAAAGCAAAAGGTGACATTTGACATTGAATAGGTATGGTTAATGAGGTCAGATT-CAAGGTCAACCACACTGCAAGACGATGCCTCATGAATGTA -s simDog_chr6.simDog.chr6 512992 167 - 593897 ATATAGTCTCAATAGGTATATAAAAACTAGTCAACTTAGTGAAGAACAATCAAGAACACTTGCCTGACTCAAGGCCT---AAAAAGGTGACATTTGGCTTAGAATGGGTGTGGTTGATGATGACGCATTACACAGTCAACCACATGGCAAGATTATGCCTTATGAATATA -s simHuman_chr6.simHuman.chr6 112595 170 + 601863 CATTATCCTCAAAAAGTTTATAAAAACTAGTCAACTTAGTGAAGAGAAGTAAAGAACAATTTCCTGACTCAAGGAACAAGAAAAAGGTGACATTTGACTTTGAATCAGTGTGGTTAGTGATGACACATTACAAGGTCAACCACACCTCAAAATTATGTCTAGCGAATGCA -s simRat_chr6.simRat.chr6 109528 170 + 647215 TAGTGGTCTCAATAGGTATATAAAACTTTGCTAACCTAATAAAGAACAGTAAAGACCAATCTGCTGACTCAAAGACCAAGAAAAATGTTATGTCTGTCTGTTAATGAGTATGTTTATTGATCGTGCAGTACAAAGTCTATAGCTCTACTAGATTATCTCATGTCAACATA -s simRat_chr6.simRat.chr6 110003 170 + 647215 TCGTAGTCTCAATAGGTATATAAAACTTTGCCAGTTTAATAAAGAACAGTAGAGACCAATCTGCTGACTCAAAGGCCAAGAAAAATGCTATGTCTGTTTGTTAATGAATATGTTTAATGATGGTGTAGTATTAAGCCTATAGTTGTACTAGATTATCTCTTGTGAACATA - -a -s simMouse_chr6.simMouse.chr6 117295 18 + 636262 TTCATTCCAGCTAGCGAA -s Anc0.Anc0refChr1 10569 18 - 62388 TCTACTACGGCTAGTAAA -s Anc1.Anc1refChr2 88839 18 + 144309 TCTACTACGGCTAGTAAA -s Anc2.Anc2refChr2 26417 18 + 27695 TCTACCACGGCTAGTAAA -s mr.mrrefChr0 111967 18 + 130230 TTCACTCCAGCTAGCGAA -s simCow_chr6.simCow.chr6 120958 18 + 602619 TCTACCATGGCTCATAAA -s simDog_chr6.simDog.chr6 513159 18 - 593897 TCTACCACCACTAGTAAA -s simHuman_chr6.simHuman.chr6 112765 18 + 601863 TCTGCTACGGCCATTAAA -s simRat_chr6.simRat.chr6 109698 18 + 647215 TTCACTCCAGCTAGCGAA -s simRat_chr6.simRat.chr6 110173 18 + 647215 TTCACTCCAGCTAGCGAA - -a -s simMouse_chr6.simMouse.chr6 117313 40 + 636262 CAGTAACACAATGCACCATTATGCTTCCTGTGTTAGTTTA -s Anc0.Anc0refChr1 10593 39 - 62388 CAACAAGACATTGGACCATTATGCTTCTTGTCTCAG-TTA -s Anc1.Anc1refChr2 88863 39 + 144309 CAACAAGACATTGGACCATTATGCTTCTTGTCTCAG-TTA -s Anc2.Anc2refChr2 26441 39 + 27695 AAACAAGACATTGGACCATTATACTTCTTGTCGCAG-TTA -s mr.mrrefChr0 111985 39 + 130230 CAGTAAAACAATGGACCATTATGCCTCCTGTGTTAG-TTA -s simCow_chr6.simCow.chr6 120982 39 + 602619 AAACAGGACATTGGACTATTATACTTCTTGTCATAG-TTA -s simDog_chr6.simDog.chr6 513183 39 - 593897 AAACAAGATATTGGACCATTATACTTCTTGTTGCAG-TTG -s simHuman_chr6.simHuman.chr6 112789 39 + 601863 CAAGAAGACATTGGCCCATTATGCTTCTTGGCTCAG-TTA -s simRat_chr6.simRat.chr6 109716 39 + 647215 CAGTAAAACAATGGACCATTATGCCTTGTGTGCTAG-TTA -s simRat_chr6.simRat.chr6 110191 39 + 647215 CAGTAAAACTATGGACCATTATGCCTCCAGTGTTAG-TCA - -a -s simMouse_chr6.simMouse.chr6 117353 3 + 636262 CAA -s Anc0.Anc0refChr1 10632 3 - 62388 CAA -s Anc1.Anc1refChr2 88902 3 + 144309 CAA -s Anc2.Anc2refChr2 26480 3 + 27695 CAA -s mr.mrrefChr0 112024 3 + 130230 CAA -s simCow_chr6.simCow.chr6 121021 3 + 602619 CAA -s simDog_chr6.simDog.chr6 513222 3 - 593897 CAA -s simHuman_chr6.simHuman.chr6 112828 3 + 601863 TAT -s simRat_chr6.simRat.chr6 110230 3 + 647215 CAC - -a -s simMouse_chr6.simMouse.chr6 117356 3 + 636262 ACA -s Anc0.Anc0refChr1 10635 3 - 62388 ACA -s Anc1.Anc1refChr2 88905 3 + 144309 ACA -s Anc2.Anc2refChr2 26483 3 + 27695 ACA -s mr.mrrefChr0 112027 3 + 130230 ACA -s simCow_chr6.simCow.chr6 121024 3 + 602619 ACA -s simDog_chr6.simDog.chr6 513225 3 - 593897 GCA -s simHuman_chr6.simHuman.chr6 112831 3 + 601863 ACA -s simRat_chr6.simRat.chr6 109755 3 + 647215 ACA -s simRat_chr6.simRat.chr6 110233 3 + 647215 ACA - -a -s simMouse_chr6.simMouse.chr6 117359 3 + 636262 CTC -s Anc0.Anc0refChr1 10638 3 - 62388 CGC -s Anc1.Anc1refChr2 88908 3 + 144309 CGC -s Anc2.Anc2refChr2 26486 3 + 27695 CGC -s mr.mrrefChr0 112030 3 + 130230 CCC -s simCow_chr6.simCow.chr6 121027 3 + 602619 TGC -s simDog_chr6.simDog.chr6 513231 3 - 593897 CGC -s simHuman_chr6.simHuman.chr6 112834 3 + 601863 CAC -s simRat_chr6.simRat.chr6 109758 3 + 647215 CCT -s simRat_chr6.simRat.chr6 110236 3 + 647215 CCC - -a -s simMouse_chr6.simMouse.chr6 117362 30 + 636262 TGAGGTGAGAACATTATTAACGGCCATCAG -s Anc0.Anc0refChr1 10642 30 - 62388 TAAGGTGTGAAAACATTTGACGCCCATCAT -s Anc1.Anc1refChr2 88912 30 + 144309 TAAGGTGTGAAAACATTTGACGCCCATCAT -s Anc2.Anc2refChr2 26490 30 + 27695 TAAGGTGTGAAAGTATTTGACGCCCATCAT -s mr.mrrefChr0 112033 30 + 130230 TGAGGTGAGAAAACTTTTGATGGCCATCAT -s simCow_chr6.simCow.chr6 121031 30 + 602619 TAAGCTGTGAAAGTATTTGGTGCCCATCAT -s simDog_chr6.simDog.chr6 513235 30 - 593897 TATGGTGTAAAAGTTTTTGACGCCCATCAT -s simHuman_chr6.simHuman.chr6 112838 30 + 601863 TAAGGTGTGAAAACATTTGAAGACAATCAT -s simRat_chr6.simRat.chr6 109761 30 + 647215 AGAGGTGAGAAAACTTTTGATGGCCATCAT -s simRat_chr6.simRat.chr6 110239 23 + 647215 TGAGGTGA-------TGTGATGGCCATCAT - -a -s simMouse_chr6.simMouse.chr6 117392 8 + 636262 ATTGTTTT -s Anc0.Anc0refChr1 10672 8 - 62388 AAACCCTT -s Anc1.Anc1refChr2 88942 8 + 144309 AAACCCTT -s Anc2.Anc2refChr2 26520 8 + 27695 AAACCCTT -s mr.mrrefChr0 112063 8 + 130230 ATAGTTTT -s simCow_chr6.simCow.chr6 121067 8 + 602619 AAGTTTGT -s simDog_chr6.simDog.chr6 513265 8 - 593897 ATACCCTA -s simHuman_chr6.simHuman.chr6 112868 8 + 601863 AAACCCTT -s simRat_chr6.simRat.chr6 109791 8 + 647215 ATAGTTTT -s simRat_chr6.simRat.chr6 110262 8 + 647215 ATAGTTTT - -a -s simMouse_chr6.simMouse.chr6 117400 1 + 636262 G -s Anc0.Anc0refChr1 10681 1 - 62388 G -s Anc1.Anc1refChr2 88951 1 + 144309 G -s Anc2.Anc2refChr2 26529 1 + 27695 G -s mr.mrrefChr0 112072 1 + 130230 G -s simCow_chr6.simCow.chr6 121076 1 + 602619 G -s simDog_chr6.simDog.chr6 513274 1 - 593897 A -s simHuman_chr6.simHuman.chr6 112877 1 + 601863 G -s simRat_chr6.simRat.chr6 109800 1 + 647215 G -s simRat_chr6.simRat.chr6 110271 1 + 647215 G - -a -s simMouse_chr6.simMouse.chr6 117401 81 + 636262 AATACCTAGGGTCTACCCCCTCAGCAACTCTAATGTCACAACAACTGACCGTGCCATGGCAGTCACTGAGCATGCCTTTGA -s Anc0.Anc0refChr1 10686 59 - 62388 ATTATATAAGATTTTCCCCCTCAGTAACTCTATTGCCAAAATAGCAGCCCATGGCATTG---------------------- -s Anc1.Anc1refChr2 88956 81 + 144309 ATTATATAAGATTTTCCCCCTCAGTAACTCTATTGCCAAAATAGCAGCCCATGGCATTGTAATTGCCCAGCAAGCATTTGA -s Anc2.Anc2refChr2 26534 59 + 27695 ATTATATAAGATTTTCCCCCTAAGTGACTCTATTGCCAAAATAGCAGCCCATGGCATTG---------------------- -s mr.mrrefChr0 112073 81 + 130230 AATACCTAGGGTCTACCCCCTCAGCAACTCTAATGTCAAAACAACTGACCATGCCATGGTAGTCACTGAGCATGCCTTTGA -s simCow_chr6.simCow.chr6 121200 59 + 602619 ATTATATACAATTTACCCCCTAAGTCACCCTATTGCCAATATTGCAGGCCATAACATTG---------------------- -s simDog_chr6.simDog.chr6 513279 59 - 593897 AAAATTTAAGGTCTTTCCCCTAAGTGACTCTATTGCCAAATTAGCAGCACATGGCATCG---------------------- -s simHuman_chr6.simHuman.chr6 112882 80 + 601863 ATTATATAAGATTTTCTCCCTCAATAACTCTATCGCCAAAATG-CAGCCCATGGCATTGTAATTGCCCAGCAAGCATTTGA -s simRat_chr6.simRat.chr6 109801 76 + 647215 AATACCCAGGGTCTGC----TCAGCAACTCTAATGTCAAGACAACTGGCCATGCCATGGTAGACATTGAGCATGCC-TGGA -s simRat_chr6.simRat.chr6 110272 8 + 647215 GATACCTA------------------------------------------------------------------------- - -a -s simMouse_chr6.simMouse.chr6 117482 58 + 636262 TAACCGTGTGGCCAGGTCAGTTAAGCTATGTAATCAGACTGACATGGAACACCACCCC -s Anc1.Anc1refChr2 89037 58 + 144309 TAACCAAGTAGCCAAATAAGTAAAGATATGTGGGTACACAGACTTGGCCTGCCACTCC -s mr.mrrefChr0 112154 58 + 130230 TAACCATGTGGCCAAATAAGTAAAGCTATGTAATCAGACTGACATGGAACACCACCCC -s simHuman_chr6.simHuman.chr6 112964 58 + 601863 TAACCAAGTAGCCAAATAAGTAAAGATATGTGGGTACACAGACTTGGCCTGCCACTCC -s simRat_chr6.simRat.chr6 109877 22 + 647215 TAACAATATGTCTCAATAACTA------------------------------------ - -a -s simMouse_chr6.simMouse.chr6 117540 39 + 636262 TGTGTGCAGTACCAAAGAGCATAAGACCACAAACCTCTT -s Anc0.Anc0refChr1 10745 3 - 62388 ------------------------------------CTT -s Anc1.Anc1refChr2 89095 39 + 144309 TATGTGCAGTGCCAGGGAGCATAAAGCCACAAAAGTCTT -s Anc2.Anc2refChr2 26593 3 + 27695 ------------------------------------CTC -s mr.mrrefChr0 112212 39 + 130230 TGTGTGCAGTACCAAAGAGCATAAGACCACAAAAGTCTT -s simCow_chr6.simCow.chr6 121259 3 + 602619 ------------------------------------CTC -s simDog_chr6.simDog.chr6 513338 3 - 593897 ------------------------------------CTC -s simHuman_chr6.simHuman.chr6 113022 39 + 601863 TATGTGCAGTGCCAGGGAGCATAAAGCCACAAAAGTCCT -s simRat_chr6.simRat.chr6 110280 39 + 647215 TGTGTGCAGTACCAAAGGGCATAAGACCACAAAAGTGTT - -a -s simMouse_chr6.simMouse.chr6 117579 4 + 636262 GGGA -s Anc0.Anc0refChr1 10748 4 - 62388 AGGA -s Anc1.Anc1refChr2 89134 4 + 144309 AGGA -s Anc2.Anc2refChr2 26596 4 + 27695 AGGG -s mr.mrrefChr0 112251 4 + 130230 GGGA -s simCow_chr6.simCow.chr6 121264 4 + 602619 AGGG -s simDog_chr6.simDog.chr6 513341 4 - 593897 AGGG -s simHuman_chr6.simHuman.chr6 113061 4 + 601863 AGGA -s simRat_chr6.simRat.chr6 110319 4 + 647215 GCAA - -a -s simMouse_chr6.simMouse.chr6 117583 15 + 636262 GTCCAGAAAGTCAGC -s Anc0.Anc0refChr1 10753 15 - 62388 GTCCAGAAAGCCAGT -s Anc1.Anc1refChr2 89139 15 + 144309 GTCCAGAAAGCCAGT -s Anc2.Anc2refChr2 26601 15 + 27695 GTCCAGAAAGCCAGT -s mr.mrrefChr0 112255 15 + 130230 GTCCAGAAAGTCAGC -s simCow_chr6.simCow.chr6 121269 15 + 602619 GGCGGGAAAGCCTGT -s simDog_chr6.simDog.chr6 513346 15 - 593897 GTCCATAAAGCCAGT -s simHuman_chr6.simHuman.chr6 113066 15 + 601863 GTCCCGAAAGCCAGT -s simRat_chr6.simRat.chr6 110323 15 + 647215 GTCCAGAAAGTCAGC - -a -s simMouse_chr6.simMouse.chr6 117598 46 + 636262 CAGCATAAAGTGGTGGGCTGGAGTCAGTCTGCATTAAATGGCTGGC -s Anc0.Anc0refChr1 10769 22 - 62388 CAGCTTGAAGTGGCTGATTGGA------------------------ -s Anc1.Anc1refChr2 89155 22 + 144309 CAGCTTGAAGTGGCTGATTGGA------------------------ -s Anc2.Anc2refChr2 26617 22 + 27695 CAGCTTGAACAGGCTGATTGGA------------------------ -s mr.mrrefChr0 112270 46 + 130230 CAGCATAAAGTGGCTGACTGGAGTCAGTCTGCATTAAATGGCTGGC -s simCow_chr6.simCow.chr6 121285 22 + 602619 TTGTTTTAACAGGCAGATTGGG------------------------ -s simDog_chr6.simDog.chr6 513362 22 - 593897 CAGCTTGAACAGGCTGATCAGA------------------------ -s simHuman_chr6.simHuman.chr6 113082 22 + 601863 CAGCTTGAAGTGGCTGATTGGA------------------------ -s simRat_chr6.simRat.chr6 110338 46 + 647215 CAACATAAAGTGGCTTACTTGTGTCAGTCTGCATAAAATGGCTGGC - -a -s simMouse_chr6.simMouse.chr6 117644 36 + 636262 TGGAAAAGAAGAGAAAAAGTAAGAACACACTGTACT -s Anc0.Anc0refChr1 10791 30 - 62388 TGGCAGGGAT------AAGAAAGAAGACCCAGTATA -s Anc1.Anc1refChr2 89177 30 + 144309 TGGCAGGGAT------AAGAAAGAAGACCCAGTATA -s Anc2.Anc2refChr2 26641 30 + 27695 TGGCAGGGAT------GAGAATGAAAACCCAGTATA -s mr.mrrefChr0 112316 34 + 130230 TGGAAAAGAAGA--AAAAGTAAGAAGACACTGTACT -s simCow_chr6.simCow.chr6 121309 11 + 602619 TGACAGGGAT------G------------------- -s simDog_chr6.simDog.chr6 513386 30 - 593897 TGGCAGTGAT------GAGAATGAAAACCCAGTATA -s simHuman_chr6.simHuman.chr6 113104 28 + 601863 TGCCAGGGAC------AAGAAAGAAGATCCAGTA-- -s simRat_chr6.simRat.chr6 110384 34 + 647215 TGGAAAAGAAGA--CAAAGTATGAAGACACTGTACT - -a -s simMouse_chr6.simMouse.chr6 117680 7 + 636262 CACTATT -s Anc0.Anc0refChr1 10821 7 - 62388 CATTAAT -s Anc1.Anc1refChr2 89207 7 + 144309 CATTAAT -s Anc2.Anc2refChr2 26671 7 + 27695 CATAAAT -s mr.mrrefChr0 112350 7 + 130230 CACTATT -s simCow_chr6.simCow.chr6 121320 7 + 602619 CATTCAT -s simDog_chr6.simDog.chr6 513440 7 - 593897 CATAAAT -s simHuman_chr6.simHuman.chr6 113132 4 + 601863 ---TAGT -s simRat_chr6.simRat.chr6 110418 7 + 647215 CACTACT - -a -s simMouse_chr6.simMouse.chr6 117687 13 + 636262 ATTCTATGTTTGT -s Anc0.Anc0refChr1 10828 4 - 62388 ATTC--------- -s Anc1.Anc1refChr2 89214 4 + 144309 ATTC--------- -s Anc2.Anc2refChr2 26678 4 + 27695 ATTC--------- -s mr.mrrefChr0 112357 13 + 130230 ATTCTATGTTTGT -s simCow_chr6.simCow.chr6 121330 4 + 602619 ATTC--------- -s simDog_chr6.simDog.chr6 513447 4 - 593897 ATTC--------- -s simHuman_chr6.simHuman.chr6 113136 3 + 601863 ATT---------- -s simRat_chr6.simRat.chr6 110425 13 + 647215 ATTCCATGTTTGT - -a -s simMouse_chr6.simMouse.chr6 117700 84 + 636262 ACAATGCAACTACATCCATGCTCTTCCCAATTTTGTAAGCTAGTTCATCTCTAATATGTTGATTACTTATTGACTGTCTCCTGT -s Anc0.Anc0refChr1 10832 79 - 62388 -----ACAAGTACAGACGTGCTCTTTCCACTTTTCTCAGCCTGCTCACTTATTATATGTTGATTATCTATTGACTGTTTCCTGT -s Anc1.Anc1refChr2 89218 79 + 144309 -----ACAAGTACAGACGTGCTCTTTCCACTTTTCTCAGCCTGCTCACTTATTATATGTTGATTATCTATTGACTGTTTCCTGT -s Anc2.Anc2refChr2 26682 79 + 27695 -----ACAAGTACAGACGTGCTCTTTCCACTTTTCTCAGCCTGCTCACTTATTATATGTTGATTATCTATTGACTGTTTCCTGT -s mr.mrrefChr0 112370 84 + 130230 ACAATGCAACTACATCCATGCTCTTCCCAATTTTGTAAGCTAGTTCATCTCTAATATGTTGATTATTTATTGACTGTCTCCTGT -s simCow_chr6.simCow.chr6 121334 79 + 602619 -----ACAAATACAGGCATGCTCTTCCCATTTTTCTCAGCCAGCTCATAGATTATATGGTGATTATTTATTGACTGTTTCCAGT -s simDog_chr6.simDog.chr6 513451 79 - 593897 -----ACAAGTACAGACGTGCTCTTTCCACTTTTCTCAGCCTGCTCACTTATTGTATGTTGGTTGTCTATGGACTGTCTCCTGT -s simHuman_chr6.simHuman.chr6 113139 31 + 601863 -----------------------------------------------------ATATGTTGAATATGTATTGACTGTTTTCTGT -s simRat_chr6.simRat.chr6 110442 84 + 647215 ACACTGCAACTACAGCCATGCTCTTCTCAGTTTTTTAACCTAGTTCACCTATAATATGTTGGTTATTTATTGACTGTCTCCTGT - -a -s simMouse_chr6.simMouse.chr6 117784 14 + 636262 CTAAACTGCGAGGA -s Anc0.Anc0refChr1 10920 14 - 62388 CTGAAATGCTAGGG -s Anc1.Anc1refChr2 89306 14 + 144309 CTGAAATGCTAGGG -s Anc2.Anc2refChr2 26770 14 + 27695 CTGAAATGCTAGGG -s mr.mrrefChr0 112454 14 + 130230 CTAAACTGCGAGGA -s simCow_chr6.simCow.chr6 121422 14 + 602619 CTGAAATTCTAGAG -s simDog_chr6.simDog.chr6 513539 14 - 593897 CTGAAGTGCTAGGG -s simHuman_chr6.simHuman.chr6 113179 14 + 601863 CTGAAATGCTAGGG -s simRat_chr6.simRat.chr6 110526 14 + 647215 CTAAACTGCCAGGA - -a -s simMouse_chr6.simMouse.chr6 117798 25 + 636262 CCACGGTGATGGCTGTATCTGTGAA -s Anc0.Anc0refChr1 10947 25 - 62388 CTACAGTTGCAGCTGCATCTATAAA -s Anc1.Anc1refChr2 89333 25 + 144309 CTACAGTTGCAGCTGCATCTATAAA -s Anc2.Anc2refChr2 26797 25 + 27695 CTTCAGCTGCAGCTGCATCCATAAA -s mr.mrrefChr0 112468 25 + 130230 CTACAGTGATGGCTGCATCTGTGAA -s simCow_chr6.simCow.chr6 121451 24 + 602619 CTTCAGCTGCAGCTTCATCCATAA- -s simDog_chr6.simDog.chr6 513566 25 - 593897 CTTCAGCTGCAGCTGTATCCATAAA -s simHuman_chr6.simHuman.chr6 113206 25 + 601863 CTACAGTCCCAGCGGCATCTATAAA -s simRat_chr6.simRat.chr6 110540 25 + 647215 CTACAGTGATGGCTGCATCTGTGCA - -a -s simMouse_chr6.simMouse.chr6 117823 11 + 636262 TTGCGGACCTT -s Anc0.Anc0refChr1 10972 11 - 62388 TTGCAGAACTT -s Anc1.Anc1refChr2 89358 11 + 144309 TTGCAGAACTT -s Anc2.Anc2refChr2 26823 11 + 27695 TTGCAGAACCT -s mr.mrrefChr0 112493 11 + 130230 TTGCAGACCTT -s simCow_chr6.simCow.chr6 121476 11 + 602619 TTGCAGAACCT -s simDog_chr6.simDog.chr6 513593 11 - 593897 TTGCAGAACCT -s simHuman_chr6.simHuman.chr6 113231 10 + 601863 T-GCAGATCTT -s simRat_chr6.simRat.chr6 110565 11 + 647215 TTACAGACTTG - -a -s simMouse_chr6.simMouse.chr6 117834 9 + 636262 GTCTGATTC -s Anc0.Anc0refChr1 10984 9 - 62388 GTCTAAATC -s Anc1.Anc1refChr2 89370 9 + 144309 GTCTAAATC -s Anc2.Anc2refChr2 26835 9 + 27695 ATCTAAATC -s mr.mrrefChr0 112504 9 + 130230 GTCTAATTC -s simCow_chr6.simCow.chr6 121488 9 + 602619 ACCTGAATC -s simDog_chr6.simDog.chr6 513605 9 - 593897 ATCCAAATC -s simHuman_chr6.simHuman.chr6 113242 9 + 601863 GTCTAAATC -s simRat_chr6.simRat.chr6 110576 9 + 647215 GTCTAATTC - -a -s simMouse_chr6.simMouse.chr6 117843 50 + 636262 AGTGAGGGCATTTAACTCAAATTGGATATTCTATTAGACTGCTGGCAATT -s Anc0.Anc0refChr1 11005 50 - 62388 AGTCAGTAGGTTCTACTCAAACTGGATACTCTATTAGACCATTGCCAAAT -s Anc1.Anc1refChr2 89391 50 + 144309 AGTCAGTAGGTTCTACTCAAACTGGATACTCTATTAGACCATTGCCAAAT -s Anc2.Anc2refChr2 26856 50 + 27695 AGTCAGTAGGTTCTACTCAAACTGGATACTCTATTAGACCATTGCCAAAT -s mr.mrrefChr0 112513 50 + 130230 AGTGAGGGCATTCAACTCAAACTGGATATTCTATTAGACTGCTGCCAATT -s simCow_chr6.simCow.chr6 121509 50 + 602619 GGTTAGTAGGTAAAACTCCAACTGGATACTCAAGTGGACCATTGCCAAAT -s simDog_chr6.simDog.chr6 513626 50 - 593897 AGTCAGTAAGTTCTCCTCAAACTGGATACTTTATTAGACCACTGCCAAAT -s simHuman_chr6.simHuman.chr6 113263 50 + 601863 AGTCAGAAGCTTCTACTCAAACTGGATACTCTACCAGACCATTGCCAAAT -s simRat_chr6.simRat.chr6 110585 50 + 647215 AGTGAGGGCATTCCACTCGAACTGGATATTCTATTGGACTGCTGCCAATT - -a -s simMouse_chr6.simMouse.chr6 117893 43 + 636262 TGTCCTAGTTGATTCTCCCCATTCTTAATGGTGTAGAGGTCAA -s Anc0.Anc0refChr1 11064 43 - 62388 TGTCCTAATTGCTTTCTTCCATTTTTACCAACAGATAGGTGAA -s Anc1.Anc1refChr2 89450 43 + 144309 TGTCCTAATTGCTTTCTTCCATTTTTACCAACAGATAGGTGAA -s Anc2.Anc2refChr2 26915 43 + 27695 TGTCCTAATTGCTTTCTTCCAATTTTACCAACAGATAGGTGAA -s mr.mrrefChr0 112563 43 + 130230 TGTCCTAGTTGATTTTTCCCATTCTTAATGGTGTATAGGTGAA -s simCow_chr6.simCow.chr6 121568 43 + 602619 TGTCCTAATTGCTTTCTTTCAATTTTACCAACAGATAGGTAAA -s simDog_chr6.simDog.chr6 513685 43 - 593897 TGTCCTTATCACTTTCTCCCAATATTACAAACAGATAGGTGAA -s simHuman_chr6.simHuman.chr6 113322 43 + 601863 TGTCCTAATTGCCTTCTTCCATTTTTACCAACAAATAGGTGAA -s simRat_chr6.simRat.chr6 110635 43 + 647215 TGTCCTAGTTGATTTTTCCCATTCTTCATGGTGTATAGGTGAA - -a -s simMouse_chr6.simMouse.chr6 117936 32 + 636262 GGTTTTATTACCTGTATTTTGCAGCTCAAAGT -s Anc0.Anc0refChr1 11107 32 - 62388 GGTTTTGTTTCTAGTATTTTGCAGCTCAAAGC -s Anc1.Anc1refChr2 89493 32 + 144309 GGTTTTGTTTCTAGTATTTTGCAGCTCAAAGC -s Anc2.Anc2refChr2 26958 32 + 27695 GGTTTTGTTTCTAGCATCCTGCAGCTCAAAGC -s mr.mrrefChr0 112606 32 + 130230 GGTTTTGTTACCTGTATTTTGCAGCTCAAAGT -s simCow_chr6.simCow.chr6 121611 29 + 602619 GGTATTGTTACTGGAATCCTGCAG---AAAGA -s simDog_chr6.simDog.chr6 513741 32 - 593897 GGTTTCATTTCCAGCATCCCACAGCTCAAGTC -s simHuman_chr6.simHuman.chr6 113365 32 + 601863 GGTTCTGTTGCTAGTACTTTGCACCTTGAAGC -s simRat_chr6.simRat.chr6 110678 32 + 647215 GGTTTTGTTACCTGTATTTTGCAGCTCAAGGT - -a -s simMouse_chr6.simMouse.chr6 117968 5 + 636262 GCCAG -s Anc0.Anc0refChr1 11168 5 - 62388 GCCAG -s Anc1.Anc1refChr2 89554 5 + 144309 GCCAG -s Anc2.Anc2refChr2 27019 5 + 27695 GCCAG -s mr.mrrefChr0 112644 5 + 130230 GCCAG -s simCow_chr6.simCow.chr6 121667 5 + 602619 CCCCG -s simDog_chr6.simDog.chr6 513802 5 - 593897 GTCAG -s simHuman_chr6.simHuman.chr6 113426 5 + 601863 GCCAG -s simRat_chr6.simRat.chr6 110716 5 + 647215 GCCAG - -a -s simMouse_chr6.simMouse.chr6 117973 5 + 636262 AGCAG -s Anc0.Anc0refChr1 11173 5 - 62388 ACCAG -s Anc1.Anc1refChr2 89559 5 + 144309 ACCAG -s Anc2.Anc2refChr2 27025 5 + 27695 ACCAG -s mr.mrrefChr0 112649 5 + 130230 AGCAG -s simCow_chr6.simCow.chr6 121673 5 + 602619 ACCAA -s simDog_chr6.simDog.chr6 513808 5 - 593897 ACCAG -s simHuman_chr6.simHuman.chr6 113431 5 + 601863 ACCAG -s simRat_chr6.simRat.chr6 110721 5 + 647215 ATTAG - -a -s simMouse_chr6.simMouse.chr6 117978 11 + 636262 GTTTGGGAGAG -s Anc0.Anc0refChr1 11178 11 - 62388 GTTTAGATGTG -s Anc1.Anc1refChr2 89564 11 + 144309 GTTTAGATGTG -s Anc2.Anc2refChr2 27030 11 + 27695 GTTTAGATGTG -s mr.mrrefChr0 112654 11 + 130230 GTTTAGGAGAG -s simCow_chr6.simCow.chr6 121688 11 + 602619 GTTTAGCTGTG -s simDog_chr6.simDog.chr6 513813 11 - 593897 GTTCAAATGAG -s simHuman_chr6.simHuman.chr6 113436 11 + 601863 GTTTAGTTGTG -s simRat_chr6.simRat.chr6 110726 11 + 647215 CTTTAGGAAAG - -a -s simMouse_chr6.simMouse.chr6 117989 11 + 636262 TAGCCGTGTTT -s Anc0.Anc0refChr1 11191 11 - 62388 TAACTGTATTC -s Anc1.Anc1refChr2 89577 11 + 144309 TAACTGTATTC -s Anc2.Anc2refChr2 27043 11 + 27695 TAACTGTATTA -s mr.mrrefChr0 112665 11 + 130230 TAGCTGTGTTC -s simCow_chr6.simCow.chr6 121701 11 + 602619 AAATGTTGTTA -s simDog_chr6.simDog.chr6 513826 11 - 593897 TGGCTGTATTA -s simHuman_chr6.simHuman.chr6 113449 11 + 601863 TAACTGCACTC -s simRat_chr6.simRat.chr6 110737 11 + 647215 TTGCTGTGTTC - -a -s simMouse_chr6.simMouse.chr6 118000 9 + 636262 TCAGTTCTT -s Anc0.Anc0refChr1 11207 9 - 62388 TCAGTACTT -s Anc1.Anc1refChr2 89593 9 + 144309 TCAGTACTT -s Anc2.Anc2refChr2 27059 9 + 27695 TCAGTACTT -s mr.mrrefChr0 112681 9 + 130230 TCAGTTCTT -s simCow_chr6.simCow.chr6 121717 9 + 602619 TCAGTACAC -s simDog_chr6.simDog.chr6 513842 9 - 593897 TCAGCACTT -s simHuman_chr6.simHuman.chr6 113465 9 + 601863 TCGGTACTT -s simRat_chr6.simRat.chr6 110753 9 + 647215 TCCATTCTT - -a -s simMouse_chr6.simMouse.chr6 118009 19 + 636262 CAGCGATTCATCTGCCTAG -s Anc0.Anc0refChr1 11217 19 - 62388 CAGTTACTCATGTGCCCAG -s Anc1.Anc1refChr2 89603 19 + 144309 CAGTTACTCATGTGCCCAG -s Anc2.Anc2refChr2 27069 19 + 27695 CAGTTACCTATGTGCCCAG -s mr.mrrefChr0 112690 19 + 130230 CAGCTACTCATCTGCCTAG -s simCow_chr6.simCow.chr6 121727 19 + 602619 CGGTTGCCTATGTGCCCAG -s simDog_chr6.simDog.chr6 513852 19 - 593897 CAGTTACCTATGTTCCCAG -s simHuman_chr6.simHuman.chr6 113475 19 + 601863 CACTTACTCATGTGCCCAG -s simRat_chr6.simRat.chr6 110762 19 + 647215 CAGCTACTCATCTGCCTAG - -a -s simMouse_chr6.simMouse.chr6 118028 5 + 636262 ATTTT -s Anc0.Anc0refChr1 11236 2 - 62388 AT--- -s Anc1.Anc1refChr2 89622 2 + 144309 AT--- -s Anc2.Anc2refChr2 27105 2 + 27695 AT--- -s mr.mrrefChr0 112709 5 + 130230 ATTTT -s simCow_chr6.simCow.chr6 121763 2 + 602619 AT--- -s simDog_chr6.simDog.chr6 513888 2 - 593897 GT--- -s simHuman_chr6.simHuman.chr6 113494 2 + 601863 AT--- -s simRat_chr6.simRat.chr6 110781 5 + 647215 ATTTT - -a -s simMouse_chr6.simMouse.chr6 118033 6 + 636262 ACACCA -s Anc0.Anc0refChr1 11245 6 - 62388 ACCCAA -s Anc1.Anc1refChr2 89631 6 + 144309 ACCCAA -s Anc2.Anc2refChr2 27114 6 + 27695 ATCCAA -s mr.mrrefChr0 112721 6 + 130230 ACACCA -s simCow_chr6.simCow.chr6 121772 6 + 602619 ATCCAA -s simDog_chr6.simDog.chr6 513897 6 - 593897 ATCCCA -s simHuman_chr6.simHuman.chr6 113503 6 + 601863 ACCCAA -s simRat_chr6.simRat.chr6 110795 6 + 647215 ACACCA - -a -s simMouse_chr6.simMouse.chr6 118039 22 + 636262 ACTAATCAAAAGTATTCACATC -s Anc0.Anc0refChr1 11251 22 - 62388 ACTATACCAAAGTATATACATT -s Anc1.Anc1refChr2 89637 22 + 144309 ACTATACCAAAGTATATACATT -s Anc2.Anc2refChr2 27120 22 + 27695 ACTATACCACAGTATATACATT -s mr.mrrefChr0 112727 22 + 130230 ACTAATCAAAAGTATTCACATC -s simCow_chr6.simCow.chr6 121787 22 + 602619 AGTATACCACAGTATATATATT -s simDog_chr6.simDog.chr6 513903 22 - 593897 ACCAAATCACAGTATATACTTT -s simHuman_chr6.simHuman.chr6 113509 19 + 601863 ACTGTACTAAAGTA---ACATT -s simRat_chr6.simRat.chr6 110801 21 + 647215 ACTAAT-AAAAGTAGCTACATC - -a -s simMouse_chr6.simMouse.chr6 118061 18 + 636262 TTTACGGATTCGTTCACT -s Anc0.Anc0refChr1 11273 17 - 62388 TCTTTTGAT-ACTTTTCT -s Anc1.Anc1refChr2 89659 17 + 144309 TCTTTTGAT-ACTTTTCT -s Anc2.Anc2refChr2 27142 17 + 27695 TCTTTTAAG-ACTTTTCT -s mr.mrrefChr0 112749 17 + 130230 TCTACTGAT-AGTTCACT -s simCow_chr6.simCow.chr6 121809 17 + 602619 TCTTTTAAA-ACTTTACT -s simDog_chr6.simDog.chr6 514096 17 - 593897 TCTTTTAAG-ACTTTTCT -s simHuman_chr6.simHuman.chr6 113528 17 + 601863 TCCTTTGAT-ACTTTTCT -s simRat_chr6.simRat.chr6 110822 17 + 647215 TCTGCTGAG-AGTTGACT - -a -s simMouse_chr6.simMouse.chr6 118079 46 + 636262 AATACATACATGTTACAGGCTATTACAGTTAAGGCCTGCTCATGTG -s Anc0.Anc0refChr1 11298 46 - 62388 CAAACATACATGTTAAAGGCTATTATAGTCATTGCCCACTCAGGTG -s Anc1.Anc1refChr2 89684 46 + 144309 CAAACATACATGTTAAAGGCTATTATAGTCATTGCCCACTCAGGTG -s Anc2.Anc2refChr2 27167 46 + 27695 CAAACATTAATGTTAAAGGCTATTATAGTCATTCCCCACTCAGGTG -s mr.mrrefChr0 112766 46 + 130230 AAAACATACATGTTACAGGCTATTACAGTTAAGGCCTACTCATGTG -s simCow_chr6.simCow.chr6 121834 43 + 602619 CAAACATTAATGTTAAAGGCTATTAGAGGCA---CCCACTAAGGTG -s simDog_chr6.simDog.chr6 514119 46 - 593897 CACACATTAGTGTTAAAGGCTATTATAGTCATTCCCAACTCAGGTG -s simHuman_chr6.simHuman.chr6 113553 38 + 601863 CAAACATACATATCAAGGGCCATT--------TGCCCACTCAGGTG -s simRat_chr6.simRat.chr6 110839 44 + 647215 AAAACATATCTGTTACAGGCTATTATGGTTTTGGC--ACTCATGTG - -a -s simMouse_chr6.simMouse.chr6 118125 78 + 636262 GGACCCTTGATCCTGGTGTACTGCGTAATAGCATTGTGTATGTTGAGAATTGTACTGCACTGTTAGATCTGCCCTCAC -s Anc0.Anc0refChr1 11345 71 - 62388 GATTCCTGGATCCTGGCCTA-------ACACCATTCTGGATGTTGAGAATAACAAAGCACTGACAACTCTGCCCTCAC -s Anc1.Anc1refChr2 89731 71 + 144309 GATTCCTGGATCCTGGCCTA-------ACACCATTCTGGATGTTGAGAATAACAAAGCACTGACAACTCTGCCCTCAC -s Anc2.Anc2refChr2 27214 71 + 27695 GACTCCTGGACCCTAGCCTA-------ACACCATTCTGGATGTTGAGAATAACCAAGCACTGACAACTCTGCCCTCAC -s mr.mrrefChr0 112812 78 + 130230 GATCCCTTGATCCTGGCGTACTGCGTAATAGCATTGTGTATGTTGAGAATTGTACAGCACTGTTAGATCTGCCCTCAC -s simCow_chr6.simCow.chr6 121878 69 + 602619 AACTCCTTGAACCTAGCCTA-------ATACCATTCTGGATGTTGAGAATAACTAAGCATTGACA--TCTGCTGTCAC -s simDog_chr6.simDog.chr6 514166 71 - 593897 GACTCCTGGACCCTAGCCTA-------ACACCATTTTGGTTGTTAAGAATAACCCAGCACTGGCAACTCTGCCCTCAC -s simHuman_chr6.simHuman.chr6 113592 71 + 601863 GATTCCTAGATCTTGACCTA-------ACACCATTCTACATGTTGAGAATAACAAAGCACTGACAACTCGGCCCTCAC -s simRat_chr6.simRat.chr6 110883 78 + 647215 CATCTCTTGATCCCAGCGTAATGCATAATAACTTTATGTATGGTGAGTATTGTACAGCACTGTTAGATCTGCCCTCAC - -a -s simMouse_chr6.simMouse.chr6 118203 7 + 636262 CAACCGA -s Anc0.Anc0refChr1 11418 7 - 62388 CAACCTA -s Anc1.Anc1refChr2 89804 7 + 144309 CAACCTA -s Anc2.Anc2refChr2 27287 7 + 27695 CAATCTG -s mr.mrrefChr0 112892 7 + 130230 CAACCGA -s simCow_chr6.simCow.chr6 121949 7 + 602619 CAAACTC -s simDog_chr6.simDog.chr6 514239 7 - 593897 CAATCTG -s simHuman_chr6.simHuman.chr6 113665 7 + 601863 CAACCCA -s simRat_chr6.simRat.chr6 110963 7 + 647215 CAACCAA - -a -s simMouse_chr6.simMouse.chr6 118210 31 + 636262 GTTGCATACACCAAAGTGGGATTAGATCAGA -s Anc0.Anc0refChr1 11426 31 - 62388 GTTGTATATACCAAAGTGGGATTAGATCAAA -s Anc1.Anc1refChr2 89812 31 + 144309 GTTGTATATACCAAAGTGGGATTAGATCAAA -s Anc2.Anc2refChr2 27295 31 + 27695 GTTGTATATACCAAAGTGGGATTAGATCAGA -s mr.mrrefChr0 112899 31 + 130230 GTTGCATACACCAAAGTGGGATTAGATCAAA -s simCow_chr6.simCow.chr6 121957 31 + 602619 GTTGTATACAGAAAAGTGAGGTTAGATTAGA -s simDog_chr6.simDog.chr6 514247 31 - 593897 GTCGTTTATACCAAAGTGGGATTTGATCAGA -s simHuman_chr6.simHuman.chr6 113673 31 + 601863 GTTGTATATACCAGAGTGGGATTAGACCCAA -s simRat_chr6.simRat.chr6 110970 31 + 647215 TTTGCATACACCAAAATGGGATTAGATTGAA - -a -s simMouse_chr6.simMouse.chr6 118241 25 + 636262 ACTCATCATTAGCTTTAAGAAAACC -s Anc0.Anc0refChr1 11457 24 - 62388 TCTCA-CCTTGTCTTGAAGATGTCT -s Anc1.Anc1refChr2 89843 24 + 144309 TCTCA-CCTTGTCTTGAAGATGTCT -s Anc2.Anc2refChr2 27326 24 + 27695 TCTCA-CCTTGTCTTGAAGATGTCT -s mr.mrrefChr0 112930 25 + 130230 ACTCATCCTTGGCTTTAAGAAAACC -s simCow_chr6.simCow.chr6 121988 15 + 602619 ACTCT-CCTAGTCTTG--------- -s simDog_chr6.simDog.chr6 514278 24 - 593897 TATCA-CCTTGTCTTGAAGATGTCT -s simHuman_chr6.simHuman.chr6 113704 24 + 601863 TCTCA-ACTTGTCTTGAAGATGTCT -s simRat_chr6.simRat.chr6 111004 25 + 647215 ACTCATCCTTGGCGTTAAGAAAACC - -a -s simMouse_chr6.simMouse.chr6 118266 10 + 636262 AACCATGATG -s Anc0.Anc0refChr1 11482 10 - 62388 AACCTTGATT -s Anc1.Anc1refChr2 89868 10 + 144309 AACCTTGATT -s Anc2.Anc2refChr2 27351 10 + 27695 AACCTTGATT -s mr.mrrefChr0 112955 10 + 130230 AACCATGATT -s simCow_chr6.simCow.chr6 122003 10 + 602619 GACCTTGATT -s simDog_chr6.simDog.chr6 514303 10 - 593897 AGTCTTGATT -s simHuman_chr6.simHuman.chr6 113729 10 + 601863 AACCCTGATT -s simRat_chr6.simRat.chr6 111029 10 + 647215 CACCATGATT - -a -s simMouse_chr6.simMouse.chr6 118276 14 + 636262 ACGACCCACATTCA -s Anc0.Anc0refChr1 11493 14 - 62388 ACGATCCACTATCC -s Anc1.Anc1refChr2 89879 14 + 144309 ACGATCCACTATCC -s Anc2.Anc2refChr2 27362 14 + 27695 ATGATCCACTATCC -s mr.mrrefChr0 112966 14 + 130230 ACGACCCACAATCA -s simCow_chr6.simCow.chr6 122014 14 + 602619 GTGATCCACTATCA -s simDog_chr6.simDog.chr6 514314 14 - 593897 ATGATCCACTGTCC -s simHuman_chr6.simHuman.chr6 113740 14 + 601863 ACAATCCACTATCC -s simRat_chr6.simRat.chr6 111040 14 + 647215 ATGCCCCAAAATCA - -a -s simMouse_chr6.simMouse.chr6 118290 16 + 636262 TAAAAAACTCTCAGTT -s Anc0.Anc0refChr1 11507 16 - 62388 TCAGAAACTCTCAGTT -s Anc1.Anc1refChr2 89893 16 + 144309 TCAGAAACTCTCAGTT -s Anc2.Anc2refChr2 27376 16 + 27695 GCAGAAACTCTCAGTT -s mr.mrrefChr0 112980 16 + 130230 TCAAAAACTCTCAGTT -s simCow_chr6.simCow.chr6 122028 16 + 602619 GCAGAAAATCTCCCGT -s simDog_chr6.simDog.chr6 514329 16 - 593897 GCAGAAACTCCTAGTT -s simHuman_chr6.simHuman.chr6 113754 16 + 601863 TCTGGAACTCTCAGTT -s simRat_chr6.simRat.chr6 111054 16 + 647215 TCAAAAACTCTCAGTC - -a -s simMouse_chr6.simMouse.chr6 118306 24 + 636262 GAATGCTTGTCTTTTGATGCCAAA -s Anc0.Anc0refChr1 11523 23 - 62388 ATATGCTTGTCTGTCA-TGCTAGT -s Anc1.Anc1refChr2 89909 23 + 144309 ATATGCTTGTCTGTCA-TGCTAGT -s Anc2.Anc2refChr2 27392 23 + 27695 ATATGCTTGTCTGTCA-TGCTAGT -s mr.mrrefChr0 112996 24 + 130230 ATATGCTTGTCTTTCAATGCTAAA -s simCow_chr6.simCow.chr6 122063 23 + 602619 ATATGCTGGTCTGTCT-TACTAAT -s simDog_chr6.simDog.chr6 514345 23 - 593897 ATAGGCTTGTCTGTCA-TGTTAGG -s simHuman_chr6.simHuman.chr6 113770 22 + 601863 ATATGCTTGTCTGTCA-TGCTAT- -s simRat_chr6.simRat.chr6 111070 24 + 647215 ATATGCTTATCTCTCAGTGCTAAA - -a -s simMouse_chr6.simMouse.chr6 118330 39 + 636262 CATTTCATCCGGTAAACTACGCACCTGTGATTAGAACAA -s Anc0.Anc0refChr1 11560 39 - 62388 CATTTCATAAGACAAACCATGCAATTATGGTTATGACAA -s Anc1.Anc1refChr2 89946 39 + 144309 CATTTCATAAGACAAACCATGCAATTATGGTTATGACAA -s Anc2.Anc2refChr2 27429 39 + 27695 CAATTCATAAGACAAACCATGCCATTATGGTTATGACAA -s mr.mrrefChr0 113034 39 + 130230 CATTTCATCAGGTAAACTATGCACCTGTGATTAGAACAA -s simCow_chr6.simCow.chr6 122100 38 + 602619 TAACTCATGATAGAAACCATGCCATTGAGATTATGTC-A -s simDog_chr6.simDog.chr6 514382 39 - 593897 CAATGCATAGGGCAAACTATGCCATTATAGTTATGACAA -s simHuman_chr6.simHuman.chr6 113806 39 + 601863 CATTTCATAAAACAAACCATCCAGTTAGGGTTATGACAA -s simRat_chr6.simRat.chr6 111108 39 + 647215 CATTTCATCAGGTAAATTATGCACCTGTGACTAGAACAA - -a -s simMouse_chr6.simMouse.chr6 118369 14 + 636262 TATGGCCAATCATG -s Anc0.Anc0refChr1 11599 14 - 62388 TAAGGCAAATCGTG -s Anc1.Anc1refChr2 89985 14 + 144309 TAAGGCAAATCGTG -s Anc2.Anc2refChr2 27469 14 + 27695 TAAGACAAATCGTG -s mr.mrrefChr0 113073 14 + 130230 TATGGCCAATCATG -s simCow_chr6.simCow.chr6 122139 14 + 602619 TAAGACAAATCATG -s simDog_chr6.simDog.chr6 514422 14 - 593897 TAAGACAAACTGTG -s simHuman_chr6.simHuman.chr6 113845 12 + 601863 T--TGCAAGTCGTC -s simRat_chr6.simRat.chr6 111147 14 + 647215 TAAGGCTAATCATG - -a -s simMouse_chr6.simMouse.chr6 118383 1 + 636262 C -s Anc0.Anc0refChr1 11613 1 - 62388 C -s Anc1.Anc1refChr2 89999 1 + 144309 C -s Anc2.Anc2refChr2 27483 1 + 27695 C -s mr.mrrefChr0 113087 1 + 130230 C -s simCow_chr6.simCow.chr6 122153 1 + 602619 C -s simDog_chr6.simDog.chr6 514436 1 - 593897 C -s simHuman_chr6.simHuman.chr6 113857 1 + 601863 C -s simRat_chr6.simRat.chr6 111164 1 + 647215 C - -a -s simMouse_chr6.simMouse.chr6 118384 24 + 636262 ACTCATTATTATAACAGCAACAAT -s Anc0.Anc0refChr1 11614 24 - 62388 ATTCATAATTATAACAGCAATAAT -s Anc1.Anc1refChr2 90000 24 + 144309 ATTCATAATTATAACAGCAATAAT -s Anc2.Anc2refChr2 27484 24 + 27695 ATTTATAATTGTAACAGCAATAGC -s mr.mrrefChr0 113088 24 + 130230 ACTCATTATTATAACAGCAACAAT -s simCow_chr6.simCow.chr6 122154 24 + 602619 AATTATAATTGTGGCAGCATTACC -s simDog_chr6.simDog.chr6 514444 24 - 593897 ATTTATAATTGTAACAGCAATAGC -s simHuman_chr6.simHuman.chr6 113858 24 + 601863 GTTCATAATTATAACAGCAATAAT -s simRat_chr6.simRat.chr6 111165 24 + 647215 ACTTGTTATTGTAACAGCAACAAT - -a -s simMouse_chr6.simMouse.chr6 118408 78 + 636262 CGGGGTCCCTAGTGCTGTACCTAGTACATATCCTTGTCCACTAGCAGTTCATATATTGTCCACTAGCTGGTTAAACAA -s Anc0.Anc0refChr1 11639 32 - 62388 TGGAGTCCCTAG-GTTGTACTTGGTACA---------------------------------------------GACAA -s Anc1.Anc1refChr2 90025 32 + 144309 TGGAGTCCCTAG-GTTGTACTTGGTACA---------------------------------------------GACAA -s Anc2.Anc2refChr2 27509 32 + 27695 TGGAGTCCCTAT-GTTGAACTTGGTACA---------------------------------------------GACAG -s mr.mrrefChr0 113113 78 + 130230 CGGGGTCCCTAGTGCTGTACCTAGTACATATCCTTGTCCACTAGCAGTTCATATATTGTCCACTAGCTGGTTAAACAA -s simCow_chr6.simCow.chr6 122179 32 + 602619 CAAAGTACATAT-GTTAAACTAGGTACA---------------------------------------------GCCAC -s simDog_chr6.simDog.chr6 514469 32 - 593897 TGGTGTCCCTAT-GTTGAACTTGGTACA---------------------------------------------GACTG -s simHuman_chr6.simHuman.chr6 113883 32 + 601863 TGGAGTCCCTAG-GTTGTACTTCGCACA---------------------------------------------GACAA -s simRat_chr6.simRat.chr6 111190 78 + 647215 CGGGGTCCTTAGTGCTGCACCTAGTACATATCCATGTCCACTAGCAGTACATATATTGTCCACTAGCTCGTTATACAA - -a -s simMouse_chr6.simMouse.chr6 118486 28 + 636262 CAACTACTCCCCTACTGACAATAAACAA -s Anc0.Anc0refChr1 11671 28 - 62388 TACTCACTCCTCTAGCATCAAAAAACAA -s Anc1.Anc1refChr2 90057 28 + 144309 TACTCACTCCTCTAGCATCAAAAAACAA -s Anc2.Anc2refChr2 27541 28 + 27695 CACTCACTCCTTTAGCATCAACAAACAA -s mr.mrrefChr0 113191 28 + 130230 TACCTACTCCCCTAGTGTCAAAAAACAA -s simCow_chr6.simCow.chr6 122211 28 + 602619 CGCTCTCCTGCTTAGCACGAAGAAACAA -s simDog_chr6.simDog.chr6 514676 28 - 593897 CACTCACTCCTTTAGCATCAACAAACAA -s simHuman_chr6.simHuman.chr6 113915 28 + 601863 TACTCATTCCTCTAGCATCAAAAAGCAA -s simRat_chr6.simRat.chr6 111268 28 + 647215 TACCTACTCCCCTAGTGTCAAAAAACAA - -a -s simMouse_chr6.simMouse.chr6 118514 2 + 636262 TT -s Anc0.Anc0refChr1 11701 2 - 62388 TT -s Anc1.Anc1refChr2 90087 2 + 144309 TT -s Anc2.Anc2refChr2 27571 2 + 27695 TT -s mr.mrrefChr0 113221 2 + 130230 TT -s simCow_chr6.simCow.chr6 122241 2 + 602619 TT -s simDog_chr6.simDog.chr6 514706 2 - 593897 CT -s simHuman_chr6.simHuman.chr6 113945 2 + 601863 TT -s simRat_chr6.simRat.chr6 111298 2 + 647215 TT - -a -s simMouse_chr6.simMouse.chr6 118516 7 + 636262 CATCAGA -s Anc0.Anc0refChr1 11703 7 - 62388 CATCAGA -s Anc1.Anc1refChr2 90089 7 + 144309 CATCAGA -s Anc2.Anc2refChr2 27573 7 + 27695 AATCAGA -s mr.mrrefChr0 113223 7 + 130230 CATCAGA -s simCow_chr6.simCow.chr6 122243 7 + 602619 CATCAGA -s simDog_chr6.simDog.chr6 514708 7 - 593897 AATCAGA -s simHuman_chr6.simHuman.chr6 113949 7 + 601863 CACCAGA -s simRat_chr6.simRat.chr6 111300 7 + 647215 CATCAGA - -a -s simMouse_chr6.simMouse.chr6 118523 145 + 636262 CATGGTATATAATAAAGTACTTGATTATATTACGTCCATTCTTATTGAAGTTTATCCATCCCAGCATAGTGTGAGAGTCATCTATAGGTAAAACTCCAGTCAGTAGCAAGTGGTGTGTATTAAATGAGGTATGTACTGTGATCAC -s Anc0.Anc0refChr1 11711 91 - 62388 CATGCTTCACCATAAGGCACTTGATTATATTATGTCCAACTTTGTTGAAATCTATCCATCCAAGCAGAATGTGTGATT------------------------------------------------------GTATTGTAAATAA -s Anc1.Anc1refChr2 90097 91 + 144309 CATGCTTCACCATAAGGCACTTGATTATATTATGTCCAACTTTGTTGAAATCTATCCATCCAAGCAGAATGTGTGATT------------------------------------------------------GTATTGTAAATAA -s Anc2.Anc2refChr2 27581 91 + 27695 CATGCTTCACCATCAGGCAGTTGATTATATTATGTCCAACTTCATTGAAATCTATCCATCCAAGCAGAATGTGTGATT------------------------------------------------------TTATTGTAAATAA -s mr.mrrefChr0 113230 145 + 130230 CATGGTACATAATAAGGTACTTGATTATATTACGTCCATTCTTGTTGAAGTTTATCCATCCCAGCAGAGTGTGAGAGTCATCTATAGGTAAAACTCCAGTCAGTAGCAAGTGGTGTGTATTAAATGAGGTATGTATTGTGATCAC -s simCow_chr6.simCow.chr6 122251 90 + 602619 CATACTTCACCATCAAGCAGTAGCTTATACTATTCCCAACTTCATTGAAATCTGTCCATCCAGCCACAATTGGTG-TT------------------------------------------------------TTAATGTAAATAC -s simDog_chr6.simDog.chr6 514716 91 - 593897 CATGCTTTACCAACAGGAAGTTGATTATATTATGTCCAACTTCATCTAAATCTATCCATCCAAGTAGAATGTGTGATG------------------------------------------------------TTTTTGTAAATAA -s simHuman_chr6.simHuman.chr6 113957 91 + 601863 CAAGCTTCACCATAAGGCACTTGACTATATTTTGGCCCACTTTGCTGGAATATTTCTATCCATACAGAATGTGTGATT------------------------------------------------------GTATTGTAAATAA -s simRat_chr6.simRat.chr6 111307 145 + 647215 CATGGTACAGAATTAGGTACTTGATTATATTACATCCATTCTTGTTGAAGTTTATCCATCCCAGCAGAGTGTGAGAGTCATCTATGGGTAAAACTCCAGTTACTAGCAGGTGGCGTGTATTAATTGAGGTATGTATTGTGATCAT - -a -s simMouse_chr6.simMouse.chr6 118668 13 + 636262 GAGGAGAATATGT -s Anc0.Anc0refChr1 11802 13 - 62388 CTAGAGAATATAG -s Anc1.Anc1refChr2 90188 13 + 144309 CTAGAGAATATAG -s Anc2.Anc2refChr2 27672 13 + 27695 CTAGAGAGTATAG -s mr.mrrefChr0 113375 13 + 130230 GAGGAGAATATGT -s simCow_chr6.simCow.chr6 122341 13 + 602619 CTAGAGTGTATGG -s simDog_chr6.simDog.chr6 514810 13 - 593897 CTAGAGAGTACAG -s simHuman_chr6.simHuman.chr6 114048 13 + 601863 CGAGAGAACATAG -s simRat_chr6.simRat.chr6 111452 13 + 647215 GTGAAGAGTATGT - -a -s simMouse_chr6.simMouse.chr6 118681 8 + 636262 GGGTCCAC -s Anc0.Anc0refChr1 11817 8 - 62388 GCAGCCAC -s Anc1.Anc1refChr2 90203 8 + 144309 GCAGCCAC -s Anc2.Anc2refChr2 27687 8 + 27695 GCAGCCAC -s mr.mrrefChr0 113388 8 + 130230 GGATCCAC -s simCow_chr6.simCow.chr6 122356 8 + 602619 GCAGCCAG -s simDog_chr6.simDog.chr6 514825 8 - 593897 GCGGCCAC -s simHuman_chr6.simHuman.chr6 114063 8 + 601863 GCAGCGAC -s simRat_chr6.simRat.chr6 111465 8 + 647215 GGATTCAC - -a -s simMouse_chr6.simMouse.chr6 118689 53 + 636262 AACTTCCATTAAGGGGGAGTTCACCCTGATATCAGGGGAATTAGCTGATGCAA -s Anc0.Anc0refChr1 11825 32 - 62388 ATCTTCCATTAAGAGAAAATTCACC---------------TTAGCT------A -s Anc1.Anc1refChr2 90211 32 + 144309 ATCTTCCATTAAGAGAAAATTCACC---------------TTAGCT------A -s Anc2.Anc2refChr3 0 32 + 53186 ATCTTCCATTAAGAGAATATTCACC---------------TTAGTA------G -s mr.mrrefChr0 113396 53 + 130230 AACTTCCATTAAGGGGGAGTTCACCCTGATATCAGGGGAATTAGCTGATGCAA -s simCow_chr6.simCow.chr6 122364 32 + 602619 AATTTCCATTAAGAGAGTGTTCACC---------------TTAGTA------G -s simDog_chr6.simDog.chr6 410660 32 - 593897 GTCAGCCGTTAAGGGAATATTCACC---------------ATGTTA------G -s simHuman_chr6.simHuman.chr6 114071 32 + 601863 AGCTTCCATTAAGAGAAAATTCACC---------------TTAGCT------A -s simRat_chr6.simRat.chr6 111473 53 + 647215 AACTCCCATTCAGGGGTTGTTCAGCCTGGTACCAGGAGAGTTAGCTGACATAA - -a -s simMouse_chr6.simMouse.chr6 118742 32 + 636262 AGCACACAACAGCTGATGTAAAGTACACAAAA -s Anc0.Anc0refChr1 11857 10 - 62388 AGTGCACAA----------------------A -s Anc1.Anc1refChr2 90243 10 + 144309 AGTGCACAA----------------------A -s Anc2.Anc2refChr3 32 10 + 53186 GGTACACAA----------------------A -s mr.mrrefChr0 113449 10 + 130230 AGTGCACAA----------------------A -s simCow_chr6.simCow.chr6 122397 10 + 602619 GTTACACAA----------------------A -s simDog_chr6.simDog.chr6 410692 10 - 593897 GGTACACAA----------------------A -s simHuman_chr6.simHuman.chr6 114103 10 + 601863 AGTGCACAA----------------------A -s simRat_chr6.simRat.chr6 111526 10 + 647215 AGTGCACAA----------------------A - -a -s simMouse_chr6.simMouse.chr6 118774 2 + 636262 AG -s Anc0.Anc0refChr1 11868 2 - 62388 AG -s Anc1.Anc1refChr2 90254 2 + 144309 AG -s Anc2.Anc2refChr3 43 2 + 53186 AG -s mr.mrrefChr0 113459 2 + 130230 AG -s simCow_chr6.simCow.chr6 122408 2 + 602619 AG -s simDog_chr6.simDog.chr6 410703 2 - 593897 GG -s simHuman_chr6.simHuman.chr6 114114 2 + 601863 AG -s simRat_chr6.simRat.chr6 111536 2 + 647215 AG - -a -s simMouse_chr6.simMouse.chr6 118776 24 + 636262 GTTGAATTCTGAAGCAATTGTTGA -s Anc0.Anc0refChr1 11870 24 - 62388 GTTGAATCCTGAAGCAATTGTTGA -s Anc1.Anc1refChr2 90256 24 + 144309 GTTGAATCCTGAAGCAATTGTTGA -s Anc2.Anc2refChr3 45 24 + 53186 GTTGAATCCTGAAGCAATTATTGA -s mr.mrrefChr0 113461 24 + 130230 GTTGAATTCTGAAGCAATTGTTGA -s simCow_chr6.simCow.chr6 122414 24 + 602619 GTTTAGGCCCGAGGCAATTATTGG -s simDog_chr6.simDog.chr6 410705 24 - 593897 GTAGAATATTGAAGCACTCATTGA -s simHuman_chr6.simHuman.chr6 114116 24 + 601863 TTTGAATCCTGAAGCAATTGTTGA -s simRat_chr6.simRat.chr6 111538 24 + 647215 GTTGAATTCAGAAGCAATTGTTGA - -a -s simMouse_chr6.simMouse.chr6 118800 21 + 636262 CTGAATGGACGCTCCTTGTAG -s Anc0.Anc0refChr1 11895 21 - 62388 CTGAATAAGCTCTCCATATAG -s Anc1.Anc1refChr2 90281 21 + 144309 CTGAATAAGCTCTCCATATAG -s Anc2.Anc2refChr3 70 21 + 53186 CTGAATAAGCTATCCATATAG -s mr.mrrefChr0 113485 21 + 130230 CTGAATGGGCTCTCCTTGTAG -s simCow_chr6.simCow.chr6 122439 21 + 602619 CTCAATAAGCTATCCATATTG -s simDog_chr6.simDog.chr6 410730 21 - 593897 CAGAATGAGCTATCCAAATAG -s simHuman_chr6.simHuman.chr6 114141 21 + 601863 CTGAATAAGCTCTCCATACCG -s simRat_chr6.simRat.chr6 111562 21 + 647215 CTGAATGGGCTCTCTGTCTAG - -a -s simMouse_chr6.simMouse.chr6 118821 5 + 636262 CACAT -s Anc0.Anc0refChr1 11916 5 - 62388 CCATT -s Anc1.Anc1refChr2 90302 5 + 144309 CCATT -s Anc2.Anc2refChr3 91 5 + 53186 CCATT -s mr.mrrefChr0 113506 5 + 130230 CACAT -s simCow_chr6.simCow.chr6 122460 5 + 602619 ACATT -s simDog_chr6.simDog.chr6 410752 5 - 593897 CCATT -s simHuman_chr6.simHuman.chr6 114162 5 + 601863 CCATT -s simRat_chr6.simRat.chr6 111583 5 + 647215 GACAT - -a -s simMouse_chr6.simMouse.chr6 118826 22 + 636262 CTCCATGTGCTCTAGCACAACA -s Anc0.Anc0refChr1 11921 3 - 62388 CTC------------------- -s Anc1.Anc1refChr2 90307 3 + 144309 CTC------------------- -s Anc2.Anc2refChr3 96 3 + 53186 CTC------------------- -s mr.mrrefChr0 113511 21 + 130230 CTCCATGTGCT-TAGCACAACA -s simCow_chr6.simCow.chr6 122465 3 + 602619 CTC------------------- -s simDog_chr6.simDog.chr6 410757 3 - 593897 CTT------------------- -s simHuman_chr6.simHuman.chr6 114167 3 + 601863 CTC------------------- -s simRat_chr6.simRat.chr6 111594 21 + 647215 CTCCATGTGCT-GACCATAACT - -a -s simMouse_chr6.simMouse.chr6 118848 64 + 636262 TATCCTCCATGTGCTCATCATAATTCCTATGTTTACCACCACAGATAAGTTTGTATCCTGCGGC -s Anc0.Anc0refChr1 11924 59 - 62388 --TCCCCCATGCCCTCACTATAATTTGTATGT---CTACCACAAACAAGTTGATATTCTGCAGT -s Anc1.Anc1refChr2 90310 59 + 144309 --TCCCCCATGCCCTCACTATAATTTGTATGT---CTACCACAAACAAGTTGATATTCTGCAGT -s Anc2.Anc2refChr3 99 59 + 53186 --TCCCCCATGCCCTCACTATAATTTGTATGT---CTACCAGAAACAAGTTGACATTCTGCAGT -s mr.mrrefChr0 113532 64 + 130230 TATCCTCCATGCGCTCACCATAATTCCTATGTTTACCACCACAGATAAGTTTGTATCCTGCAGC -s simCow_chr6.simCow.chr6 122468 59 + 602619 --TCCCCCATGCCCTGGCTATAATTTGTATGT---CTACTGTGAAGAAATTGAAATTCTGCTGT -s simDog_chr6.simDog.chr6 410760 58 - 593897 --TCCCCCA-GCCCTCACTATAATTTGTATTT---TTACCAGAACCAAGTTGACATTCCGCATT -s simHuman_chr6.simHuman.chr6 114170 59 + 601863 --TCCCCCATGCCCTCACTATAATTTGTATGT---CTACCACAAACGAGTTGATATTCTGCAGT -s simRat_chr6.simRat.chr6 111623 64 + 647215 TATCCTCCATGCACTGACCATAATTCATATGTTTGTAACCACAGATAAGTCAGTATCCTGCAGC - -a -s simMouse_chr6.simMouse.chr6 118912 15 + 636262 TCACTATCCTATGAT -s Anc0.Anc0refChr1 11983 7 - 62388 ACACCAT-------- -s Anc1.Anc1refChr2 90369 7 + 144309 ACACCAT-------- -s Anc2.Anc2refChr3 158 7 + 53186 ACACCAT-------- -s mr.mrrefChr0 113596 15 + 130230 TCACTATCCTATGAT -s simCow_chr6.simCow.chr6 122527 7 + 602619 ACACCAT-------- -s simDog_chr6.simDog.chr6 410818 7 - 593897 ACACCAG-------- -s simHuman_chr6.simHuman.chr6 114229 7 + 601863 ACACCAT-------- -s simRat_chr6.simRat.chr6 111689 15 + 647215 TCTATATCCTATGTT - -a -s simMouse_chr6.simMouse.chr6 118927 4 + 636262 GGCC -s Anc0.Anc0refChr1 11990 4 - 62388 AGGC -s Anc1.Anc1refChr2 90376 4 + 144309 AGGC -s Anc2.Anc2refChr3 165 4 + 53186 AGGC -s mr.mrrefChr0 113611 4 + 130230 GGCC -s simCow_chr6.simCow.chr6 122534 4 + 602619 AGGA -s simDog_chr6.simDog.chr6 410828 4 - 593897 AGGC -s simHuman_chr6.simHuman.chr6 114236 4 + 601863 AGGC -s simRat_chr6.simRat.chr6 111704 4 + 647215 TGCC - -a -s simMouse_chr6.simMouse.chr6 118931 39 + 636262 ACCACAAATAGGTTCCTATCCTGCAGCACACTATGGAGG -s Anc0.Anc0refChr1 11994 30 - 62388 GGCACAGAGTGA-CTGTGTCC--------ACTCAGTGGT -s Anc1.Anc1refChr2 90380 32 + 144309 GGCACAGAGTGA-CTGTGTCCT------CACTCAGTGGT -s Anc2.Anc2refChr3 169 30 + 53186 GGCACAGAGTGA-CTATGGCG--------GCTCAGTGGT -s mr.mrrefChr0 113615 39 + 130230 ACCACAGATAGGTCCGTATCCTGCAGCACACTATGGAGG -s simCow_chr6.simCow.chr6 122538 30 + 602619 GACACAGAGGGA-CTATAGCT--------GCTCCTTGGC -s simDog_chr6.simDog.chr6 410838 28 - 593897 GGCTCGGAGTGT-CTATGGCG--------GCTCAGT--T -s simHuman_chr6.simHuman.chr6 114240 32 + 601863 GGCACAGAGTGA-CTGTGTCCT------CACTCAGTGGT -s simRat_chr6.simRat.chr6 111708 39 + 647215 ACCACAGATGAGTCGGTATTCTGCAGCACACTAGGGACG - -a -s simMouse_chr6.simMouse.chr6 118970 4 + 636262 GCAC -s Anc0.Anc0refChr1 12024 4 - 62388 TTAT -s Anc1.Anc1refChr2 90412 4 + 144309 TTAT -s Anc2.Anc2refChr3 199 4 + 53186 TTAT -s mr.mrrefChr0 113654 4 + 130230 GCAC -s simCow_chr6.simCow.chr6 122570 4 + 602619 TTAT -s simDog_chr6.simDog.chr6 410866 4 - 593897 CTAA -s simHuman_chr6.simHuman.chr6 114272 4 + 601863 TTAT -s simRat_chr6.simRat.chr6 111747 4 + 647215 GCAC - -a -s simMouse_chr6.simMouse.chr6 118974 18 + 636262 AGCCGCCCAACTTTTTTG -s Anc0.Anc0refChr1 12028 10 - 62388 AACCTCGCA--------T -s Anc1.Anc1refChr2 90416 10 + 144309 AACCTCGCA--------T -s Anc2.Anc2refChr3 203 10 + 53186 AACCTTGCA--------T -s mr.mrrefChr0 113658 18 + 130230 AGCCGCCCAACTTTTTTG -s simCow_chr6.simCow.chr6 122575 10 + 602619 AACCTAGTG--------T -s simDog_chr6.simDog.chr6 410870 10 - 593897 AATTTTGCA--------T -s simHuman_chr6.simHuman.chr6 114276 10 + 601863 AACCTCACA--------T -s simRat_chr6.simRat.chr6 111751 18 + 647215 AGGTCCCCAACTTTTTTG - -a -s simMouse_chr6.simMouse.chr6 118992 1 + 636262 T -s Anc0.Anc0refChr1 12038 1 - 62388 T -s Anc1.Anc1refChr2 90426 1 + 144309 T -s Anc2.Anc2refChr3 213 1 + 53186 T -s mr.mrrefChr0 113676 1 + 130230 T -s simCow_chr6.simCow.chr6 122588 1 + 602619 T -s simDog_chr6.simDog.chr6 410880 1 - 593897 C -s simHuman_chr6.simHuman.chr6 114286 1 + 601863 T -s simRat_chr6.simRat.chr6 111783 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 118993 37 + 636262 ATGTGACCACCCCTCTGGACACAATAGCAGCACTCTC -s Anc0.Anc0refChr1 12039 36 - 62388 TTGCGACTGCCT-TCTGGACACAATAGTAATGCTCTT -s Anc1.Anc1refChr2 90427 36 + 144309 TTGCGACTGCCT-TCTGGACACAATAGTAATGCTCTT -s Anc2.Anc2refChr3 214 36 + 53186 TTGCCACTGTCT-TCTGGATACAATAGTAATGCTCTT -s mr.mrrefChr0 113677 36 + 130230 ATGTGACCACCC-TCTGGACACAATAGTAGCACTCTT -s simCow_chr6.simCow.chr6 122589 36 + 602619 TTGCCACTGTCT-TCTGGATATAATAGTAACACTCTT -s simDog_chr6.simDog.chr6 411077 36 - 593897 TTGCCACTGTCT-TCTTAATACAATAGTAATGATCTT -s simHuman_chr6.simHuman.chr6 114287 36 + 601863 TCGCGACTGCCT-TCTGGACACAATAGTAATGCTCTT -s simRat_chr6.simRat.chr6 111784 36 + 647215 ATGTGACCACCC-TCTGGGGAGAATAGTAGCACTCTT - -a -s simMouse_chr6.simMouse.chr6 119030 25 + 636262 TGTGCCAGTATATGCCTGAGCATGA -s Anc0.Anc0refChr1 12075 17 - 62388 TTTGCCACCATAGAG--------GC -s Anc1.Anc1refChr2 90463 17 + 144309 TTTGCCACCATAGAG--------GC -s Anc2.Anc2refChr3 250 17 + 53186 TTTGCCACCATAGAG--------GC -s mr.mrrefChr0 113713 25 + 130230 TTTGCCAGTATATGGCTGAGCATGA -s simCow_chr6.simCow.chr6 122625 17 + 602619 TTTGCCACCATAGAG--------AA -s simDog_chr6.simDog.chr6 411113 14 - 593897 TT---CACTATGGAG--------GC -s simHuman_chr6.simHuman.chr6 114324 17 + 601863 TTTGCCACCATAGAG--------GT -s simRat_chr6.simRat.chr6 111820 25 + 647215 TTTGCCAGTATATGGCTGAGCATGA - -a -s simMouse_chr6.simMouse.chr6 119055 14 + 636262 GTTACTTTTACTAA -s Anc0.Anc0refChr1 12092 12 - 62388 CTTAGTCTTA--AA -s Anc1.Anc1refChr2 90480 12 + 144309 CTTAGTCTTA--AA -s Anc2.Anc2refChr3 267 12 + 53186 CTTAGTTTCA--AA -s mr.mrrefChr0 113738 14 + 130230 GTTACTCTTACTAA -s simCow_chr6.simCow.chr6 122671 12 + 602619 CTTGGTTTCA--AA -s simDog_chr6.simDog.chr6 411127 12 - 593897 CTTAGCTTCA--AA -s simHuman_chr6.simHuman.chr6 114341 12 + 601863 CTTAGTCTTA--AA -s simRat_chr6.simRat.chr6 111845 14 + 647215 GTTACTCTTACTAA - -a -s simMouse_chr6.simMouse.chr6 119069 13 + 636262 TTGGATCACACCA -s Anc0.Anc0refChr1 12104 13 - 62388 CTGAACCATGGGC -s Anc1.Anc1refChr2 90492 13 + 144309 CTGAACCATGGGC -s Anc2.Anc2refChr3 280 13 + 53186 CTGAACCATGGGC -s mr.mrrefChr0 113752 13 + 130230 TTGGATCATGCGA -s simCow_chr6.simCow.chr6 122684 13 + 602619 CTGAACCATGGGC -s simDog_chr6.simDog.chr6 411140 13 - 593897 TTGCGGCATGGGC -s simHuman_chr6.simHuman.chr6 114353 13 + 601863 CTGAACCATGAGC -s simRat_chr6.simRat.chr6 111859 13 + 647215 TTGGATCATGCGA - -a -s simMouse_chr6.simMouse.chr6 119082 9 + 636262 TCTAAATTA -s Anc0.Anc0refChr1 12124 9 - 62388 TCTCAAGTA -s Anc1.Anc1refChr2 90512 9 + 144309 TCTCAAGTA -s Anc2.Anc2refChr3 300 9 + 53186 ACTCAAGTA -s mr.mrrefChr0 113765 9 + 130230 TCTAAATTA -s simCow_chr6.simCow.chr6 122704 9 + 602619 CATCATTTA -s simDog_chr6.simDog.chr6 411160 8 - 593897 ACTCAAGC- -s simHuman_chr6.simHuman.chr6 114373 9 + 601863 TCTCAAGTA -s simRat_chr6.simRat.chr6 111872 9 + 647215 CCTAAATCA - -a -s simMouse_chr6.simMouse.chr6 119091 4 + 636262 GAAC -s Anc0.Anc0refChr1 12133 4 - 62388 CAGA -s Anc1.Anc1refChr2 90521 4 + 144309 CAGA -s Anc2.Anc2refChr3 309 4 + 53186 CAGA -s mr.mrrefChr0 113774 4 + 130230 GAAA -s simCow_chr6.simCow.chr6 122714 4 + 602619 CAGA -s simHuman_chr6.simHuman.chr6 114382 4 + 601863 CAGA -s simRat_chr6.simRat.chr6 111881 4 + 647215 GAAA - -a -s simMouse_chr6.simMouse.chr6 119095 12 + 636262 AACTTTATGGGG -s Anc0.Anc0refChr1 12146 12 - 62388 CACTCTAAGAGG -s Anc1.Anc1refChr2 90534 12 + 144309 CACTCTAAGAGG -s Anc2.Anc2refChr3 322 12 + 53186 CATTCTAAAAGA -s mr.mrrefChr0 113778 12 + 130230 CACTTTATGGGG -s simCow_chr6.simCow.chr6 122727 12 + 602619 CATTCAAAAAGT -s simDog_chr6.simDog.chr6 411170 12 - 593897 CTTAGTACAATA -s simHuman_chr6.simHuman.chr6 114395 12 + 601863 CACTCTAAGAGG -s simRat_chr6.simRat.chr6 111885 12 + 647215 CACTTTATGGGG - -a -s simMouse_chr6.simMouse.chr6 119107 11 + 636262 TGGAGATGGCC -s Anc0.Anc0refChr1 12159 11 - 62388 TGGGGATCTTA -s Anc1.Anc1refChr2 90547 11 + 144309 TGGGGATCTTA -s Anc2.Anc2refChr3 335 11 + 53186 TGGGGATCTTA -s mr.mrrefChr0 113790 11 + 130230 TGGAGATGGCC -s simCow_chr6.simCow.chr6 122740 11 + 602619 TGGGGGTCTTG -s simDog_chr6.simDog.chr6 411183 11 - 593897 TAATGATCTTA -s simHuman_chr6.simHuman.chr6 114408 11 + 601863 TGGGGATCTTA -s simRat_chr6.simRat.chr6 111897 11 + 647215 TGGAGATGGCC - -a -s simMouse_chr6.simMouse.chr6 119118 4 + 636262 CCTC -s Anc0.Anc0refChr1 12170 4 - 62388 CCTG -s Anc1.Anc1refChr2 90558 4 + 144309 CCTG -s Anc2.Anc2refChr3 346 4 + 53186 CCTG -s mr.mrrefChr0 113801 4 + 130230 CCTG -s simCow_chr6.simCow.chr6 122751 4 + 602619 CCTG -s simDog_chr6.simDog.chr6 411284 4 - 593897 CCTG -s simHuman_chr6.simHuman.chr6 114419 4 + 601863 CCTG -s simRat_chr6.simRat.chr6 111908 4 + 647215 CCTG - -a -s simMouse_chr6.simMouse.chr6 119122 26 + 636262 CTAAGCATGTACTGCCAAATAAATGC -s Anc0.Anc0refChr1 12174 18 - 62388 CTAGTCCTGTACTGCTAA-------- -s Anc1.Anc1refChr2 90562 26 + 144309 CTAGTCCTGTACTGCTAATAAGATGC -s Anc2.Anc2refChr3 350 18 + 53186 CTAATCCTGTAGTGCTAA-------- -s mr.mrrefChr0 113805 26 + 130230 CTAGTCATGTACTGCTAAATAAATGC -s simCow_chr6.simCow.chr6 122755 18 + 602619 CCGCTTATGTATTGCCAA-------- -s simDog_chr6.simDog.chr6 411288 18 - 593897 CTAATCCTGTAGTGCTCA-------- -s simHuman_chr6.simHuman.chr6 114435 26 + 601863 CTAGTCCTGTACTGCTAATAAGATGC -s simRat_chr6.simRat.chr6 111912 26 + 647215 CTAGTCATGTACTGCTAAATAAATGC - -a -s simMouse_chr6.simMouse.chr6 119148 18 + 636262 ATTGAATACATAGTCCTG -s Anc0.Anc0refChr1 12231 18 - 62388 ATTAAATACATAAACCTG -s Anc1.Anc1refChr2 90627 18 + 144309 ATTAAATACATAAACCTG -s Anc2.Anc2refChr3 407 18 + 53186 ATTAAATACATCAACCAG -s mr.mrrefChr0 113831 18 + 130230 ATTGAATACATAGTCCTG -s simCow_chr6.simCow.chr6 122813 18 + 602619 ATTAAATACATCAACCAG -s simDog_chr6.simDog.chr6 411345 18 - 593897 CAAAAATGTGCCAACCAG -s simHuman_chr6.simHuman.chr6 114589 18 + 601863 ATTATGTACATAAAGCTG -s simRat_chr6.simRat.chr6 111938 18 + 647215 ACTGAATACATAGTCCTG - -a -s simMouse_chr6.simMouse.chr6 119166 24 + 636262 TTAACATCTGACACAGCTGGCTTT -s Anc0.Anc0refChr1 12261 24 - 62388 TTAACATGAGACAAAGCTACTTGG -s Anc1.Anc1refChr2 90657 24 + 144309 TTAACATGAGACAAAGCTACTTGG -s Anc2.Anc2refChr3 437 24 + 53186 TTAACATGAGACAAAGCTACTTGG -s mr.mrrefChr0 113849 24 + 130230 TTAACATCTGACACAGCTGGCTTT -s simCow_chr6.simCow.chr6 122843 24 + 602619 TTAACATGAGACAAAGCCGCTTGT -s simDog_chr6.simDog.chr6 411375 24 - 593897 TTAACATGAGCTAAAGCTACTTGG -s simHuman_chr6.simHuman.chr6 114619 24 + 601863 TTTACATAAGACAAAAAAACTTGA -s simRat_chr6.simRat.chr6 111956 24 + 647215 TTAATAGCTGACGAAGCTCGCTGT - -a -s simMouse_chr6.simMouse.chr6 119190 36 + 636262 TCGAGCTGGCTGTGCTCAACCTTATCATGTACTATG -s Anc0.Anc0refChr1 12285 24 - 62388 TC------------CACAATTTCTTCAAATACTATA -s Anc1.Anc1refChr2 90681 24 + 144309 TC------------CACAATTTCTTCAAATACTATA -s Anc2.Anc2refChr3 461 24 + 53186 TC------------CACAATTTCTTCAAATACTATA -s mr.mrrefChr0 113873 36 + 130230 TCGAGCTGGCTGTGCTCAACCTTATCATGTACTATG -s simCow_chr6.simCow.chr6 122867 24 + 602619 TC------------TACAATTTTTTCACATACCGTT -s simDog_chr6.simDog.chr6 411407 24 - 593897 TC------------CATAATTTCTTTAAATACTATA -s simHuman_chr6.simHuman.chr6 114643 24 + 601863 TC------------CACAATTTCTTCCAACCTTACC -s simRat_chr6.simRat.chr6 111980 36 + 647215 TTGAGCTGGCTGTGCTCAATATTATCACGTGCTATG - -a -s simMouse_chr6.simMouse.chr6 119226 1 + 636262 A -s Anc0.Anc0refChr1 12309 1 - 62388 A -s Anc1.Anc1refChr2 90705 1 + 144309 A -s Anc2.Anc2refChr3 502 1 + 53186 A -s mr.mrrefChr0 113909 1 + 130230 A -s simCow_chr6.simCow.chr6 122908 1 + 602619 A -s simDog_chr6.simDog.chr6 411448 1 - 593897 A -s simHuman_chr6.simHuman.chr6 114667 1 + 601863 A -s simRat_chr6.simRat.chr6 112016 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 119227 6 + 636262 TAAAGC -s Anc0.Anc0refChr1 12310 6 - 62388 TAGAGC -s Anc1.Anc1refChr2 90706 6 + 144309 TAGAGC -s Anc2.Anc2refChr3 503 6 + 53186 TAGAGG -s mr.mrrefChr0 113910 6 + 130230 TAAAGC -s simCow_chr6.simCow.chr6 122909 6 + 602619 TAGAGG -s simDog_chr6.simDog.chr6 411449 6 - 593897 TAGAGG -s simHuman_chr6.simHuman.chr6 114737 6 + 601863 TACAGC -s simRat_chr6.simRat.chr6 112017 6 + 647215 TAAAGA - -a -s simMouse_chr6.simMouse.chr6 119233 28 + 636262 TCACCAATGTTGGATACACTGAGATCTC -s Anc0.Anc0refChr1 12316 28 - 62388 TCAACAATGTTGGATACACTGTAGTTTT -s Anc1.Anc1refChr2 90712 28 + 144309 TCAACAATGTTGGATACACTGTAGTTTT -s Anc2.Anc2refChr3 509 28 + 53186 TCAACAATGTAGGATAAACTGTAGTTTT -s mr.mrrefChr0 113916 28 + 130230 TCACCAATGTTGGATACACTGAGATCTC -s simCow_chr6.simCow.chr6 122915 28 + 602619 TCATCAATGTAAGATATACTGTAGTTTT -s simDog_chr6.simDog.chr6 411455 28 - 593897 TCAACAATGTAGGATAAACTTTGGTTTT -s simHuman_chr6.simHuman.chr6 114744 28 + 601863 CCAACAATGTTGAATCCACTGTAGTTTT -s simRat_chr6.simRat.chr6 112023 28 + 647215 TCACCAATGTCGGATACACTGAGATCTG - -a -s simMouse_chr6.simMouse.chr6 119261 10 + 636262 TGCTTTTTAT -s Anc0.Anc0refChr1 12344 10 - 62388 TATAAGTTAT -s Anc1.Anc1refChr2 90740 10 + 144309 TATAAGTTAT -s Anc2.Anc2refChr3 537 10 + 53186 TATAAGTTAT -s mr.mrrefChr0 113944 10 + 130230 TGCTTTTTAT -s simCow_chr6.simCow.chr6 122943 9 + 602619 -ACAAGGTAC -s simDog_chr6.simDog.chr6 411495 10 - 593897 TATGAGTTAT -s simHuman_chr6.simHuman.chr6 114772 10 + 601863 TATAAGTTAT -s simRat_chr6.simRat.chr6 112051 10 + 647215 CGCTTTTTAT - -a -s simMouse_chr6.simMouse.chr6 119271 18 + 636262 GAATTACTGGGAAATACA -s Anc0.Anc0refChr1 12356 17 - 62388 GTATTACCGAGAAATA-A -s Anc1.Anc1refChr2 90752 17 + 144309 GTATTACCGAGAAATA-A -s Anc2.Anc2refChr3 549 17 + 53186 GTATTACCGAGAAATA-A -s mr.mrrefChr0 113954 17 + 130230 GAATTACTGGGAAATA-A -s simCow_chr6.simCow.chr6 122954 17 + 602619 GTACTACCAAAAAATA-A -s simDog_chr6.simDog.chr6 411507 17 - 593897 GTATTACAGAGAAATG-A -s simHuman_chr6.simHuman.chr6 114784 17 + 601863 GTAGTACCGAGAAATA-A -s simRat_chr6.simRat.chr6 112061 17 + 647215 GGACTACTGGGAAGTA-A - -a -s simMouse_chr6.simMouse.chr6 119289 13 + 636262 GAGATTTACTGTT -s Anc0.Anc0refChr1 12408 13 - 62388 GATATTTGCACTT -s Anc1.Anc1refChr2 90804 13 + 144309 GATATTTGCACTT -s Anc2.Anc2refChr3 601 13 + 53186 GATAGTTGCACTT -s mr.mrrefChr0 113971 13 + 130230 GAGATTTACTGTT -s simCow_chr6.simCow.chr6 122993 13 + 602619 GATACTTGCATTT -s simDog_chr6.simDog.chr6 411565 13 - 593897 GATGGTTGCACTT -s simHuman_chr6.simHuman.chr6 114837 13 + 601863 GACATTTGTACTT -s simRat_chr6.simRat.chr6 112078 13 + 647215 GGAAGTTACTGTT - -a -s simMouse_chr6.simMouse.chr6 119302 3 + 636262 TGA -s Anc0.Anc0refChr1 12422 3 - 62388 TGA -s Anc1.Anc1refChr2 90818 3 + 144309 TGA -s Anc2.Anc2refChr3 615 3 + 53186 CGA -s mr.mrrefChr0 113984 3 + 130230 TGA -s simCow_chr6.simCow.chr6 123007 3 + 602619 GGA -s simDog_chr6.simDog.chr6 411579 3 - 593897 CAA -s simHuman_chr6.simHuman.chr6 114851 3 + 601863 TGA -s simRat_chr6.simRat.chr6 112091 3 + 647215 TGC - -a -s simMouse_chr6.simMouse.chr6 119305 8 + 636262 CAGCCCTT -s Anc0.Anc0refChr1 12425 8 - 62388 CAGTCCTT -s Anc1.Anc1refChr2 90821 8 + 144309 CAGTCCTT -s Anc2.Anc2refChr3 618 8 + 53186 CAGTCCTT -s mr.mrrefChr0 113987 8 + 130230 CAGCCCTT -s simCow_chr6.simCow.chr6 123010 8 + 602619 CACTCCAA -s simDog_chr6.simDog.chr6 411582 8 - 593897 CAGGCATT -s simHuman_chr6.simHuman.chr6 114854 8 + 601863 CAGTCCTT -s simRat_chr6.simRat.chr6 112105 8 + 647215 TAGCCCTT - -a -s simMouse_chr6.simMouse.chr6 119313 3 + 636262 TAA -s Anc0.Anc0refChr1 12433 3 - 62388 TAA -s Anc1.Anc1refChr2 90829 3 + 144309 TAA -s Anc2.Anc2refChr3 626 3 + 53186 TTA -s mr.mrrefChr0 113995 3 + 130230 TAA -s simCow_chr6.simCow.chr6 123018 3 + 602619 TTA -s simDog_chr6.simDog.chr6 411590 1 - 593897 T-- -s simHuman_chr6.simHuman.chr6 114862 3 + 601863 TAA -s simRat_chr6.simRat.chr6 112131 3 + 647215 TAA - -a -s simMouse_chr6.simMouse.chr6 119316 26 + 636262 GCTTTTCTATATTTAGCGTTGAAGAG -s Anc0.Anc0refChr1 12438 20 - 62388 GCTTTTCAAAATTTTGAGTT------ -s Anc1.Anc1refChr2 90834 20 + 144309 GCTTTTCAAAATTTTGAGTT------ -s Anc2.Anc2refChr3 631 20 + 53186 GCTTTTCAAAATTTTGAATT------ -s mr.mrrefChr0 113998 26 + 130230 GCTTTTCTATATTTAGCGTTGAAGAG -s simCow_chr6.simCow.chr6 123023 19 + 602619 GCTTTT-AGTATGTTGGATT------ -s simDog_chr6.simDog.chr6 411591 17 - 593897 ---TTTCAAAATTTTGAATT------ -s simHuman_chr6.simHuman.chr6 114867 20 + 601863 GCTTTTCAAAATTTGGAGTT------ -s simRat_chr6.simRat.chr6 112134 26 + 647215 GCTTTTCTATATTTTGAGTTGGAGTA - -a -s simMouse_chr6.simMouse.chr6 119342 9 + 636262 CTAGCCAGT -s Anc0.Anc0refChr1 12458 9 - 62388 CAGACCATT -s Anc1.Anc1refChr2 90854 9 + 144309 CAGACCATT -s Anc2.Anc2refChr3 652 9 + 53186 CAGACCATT -s mr.mrrefChr0 114024 9 + 130230 CTAGCCAGT -s simCow_chr6.simCow.chr6 123043 9 + 602619 CAGACCAAT -s simDog_chr6.simDog.chr6 411609 9 - 593897 CAGACCGTT -s simHuman_chr6.simHuman.chr6 114887 9 + 601863 CAGACTATT -s simRat_chr6.simRat.chr6 112160 9 + 647215 CTAGCCAGT - -a -s simMouse_chr6.simMouse.chr6 119351 10 + 636262 TTTAATGAGC -s Anc0.Anc0refChr1 12467 10 - 62388 TTTAATGAAC -s Anc1.Anc1refChr2 90863 10 + 144309 TTTAATGAAC -s Anc2.Anc2refChr3 661 10 + 53186 TTTAATGAAC -s mr.mrrefChr0 114033 10 + 130230 TTTAATGAGC -s simCow_chr6.simCow.chr6 123052 10 + 602619 TCTGATGAGC -s simDog_chr6.simDog.chr6 411625 10 - 593897 TTTAACGAAG -s simHuman_chr6.simHuman.chr6 114896 10 + 601863 TTTAATGAAC -s simRat_chr6.simRat.chr6 112169 10 + 647215 TTTAATGAGC - -a -s simMouse_chr6.simMouse.chr6 119361 33 + 636262 AAAGGACATATAGACCCAATTAGACTTCAAGTG -s Anc0.Anc0refChr1 12477 33 - 62388 AATTGACATACAGCCCTAATCAGACTTCAAGTG -s Anc1.Anc1refChr2 90873 33 + 144309 AATTGACATACAGCCCTAATCAGACTTCAAGTG -s Anc2.Anc2refChr3 671 33 + 53186 AATTGACATACAGCCCTAATCAGACTTCAAGTC -s mr.mrrefChr0 114043 33 + 130230 AAAGGACATATAGACCCAATTAGACTTCAAGTG -s simCow_chr6.simCow.chr6 123062 32 + 602619 AATTGATGTGCAGGTCTCATCACACTTCAAGT- -s simDog_chr6.simDog.chr6 411635 33 - 593897 AGTCGACATACAGCCCTAAACAGACTTCAAGTC -s simHuman_chr6.simHuman.chr6 114906 33 + 601863 AATTGCCATAAAGCCCTAATCAGACTTTAAGTG -s simRat_chr6.simRat.chr6 112180 33 + 647215 AAAGGACCTGTTGACCTAATTAAATCTCAAGTG - -a -s simMouse_chr6.simMouse.chr6 119394 115 + 636262 ACTAGTCTTCTGACATCCTGCGCTGGCAGTGCACAGCATGTATTGATTCTATAGCAGCATTAGAACACTCTAAGACTCTATGCCAGTCAAAATTAGTGGTTCTGTATCGGGAACC -s Anc0.Anc0refChr1 12517 7 - 62388 GGTAGTC------------------------------------------------------------------------------------------------------------ -s Anc1.Anc1refChr2 90913 7 + 144309 GGTAGTC------------------------------------------------------------------------------------------------------------ -s Anc2.Anc2refChr3 711 7 + 53186 GGTGCTC------------------------------------------------------------------------------------------------------------ -s mr.mrrefChr0 114076 73 + 130230 ACTAGTCTTCTGACATCCTGCGCTGGCAGT-CACAGCAT-----------------------------------------TGCCAGTCAAAATTAGTGGTTCTGTATCGGGAACC -s simCow_chr6.simCow.chr6 123100 7 + 602619 AGTGCTC------------------------------------------------------------------------------------------------------------ -s simDog_chr6.simDog.chr6 411740 5 - 593897 GTT--TC------------------------------------------------------------------------------------------------------------ -s simHuman_chr6.simHuman.chr6 114946 7 + 601863 GGTAGTC------------------------------------------------------------------------------------------------------------ -s simRat_chr6.simRat.chr6 112231 73 + 647215 ACTAGTCTTCTGTCATCTTTCCCTGGCAGT-TACATCAT-----------------------------------------TCCATGTTAAAATCAGTGGTTCTGTAGCTAGAATT - -a -s simMouse_chr6.simMouse.chr6 119509 31 + 636262 GACTTTCTTATCTTCTTCTATCCTATCCACA -s Anc0.Anc0refChr1 12524 17 - 62388 ---------ATCTTCTTCTATCC-----ACA -s Anc1.Anc1refChr2 90920 17 + 144309 ---------ATCTTCTTCTATCC-----ACA -s Anc2.Anc2refChr3 718 17 + 53186 ---------ATCTTTTTCTATCC-----ACA -s mr.mrrefChr0 114149 26 + 130230 GACTTTCTTATCTTCATCTATCC-----ACA -s simCow_chr6.simCow.chr6 123107 17 + 602619 ---------ATCTTTCTACATTC-----GCA -s simDog_chr6.simDog.chr6 411745 17 - 593897 ---------ATCTTTTTCTATCC-----ACA -s simHuman_chr6.simHuman.chr6 114953 17 + 601863 ---------ATCTTCTTCTGTCC-----ACA -s simRat_chr6.simRat.chr6 112305 26 + 647215 GAATTTCTTATCTTCATCTATCC-----ACA - -a -s simMouse_chr6.simMouse.chr6 119540 9 + 636262 GAACACCAG -s Anc0.Anc0refChr1 12542 8 - 62388 AAACAC-AG -s Anc1.Anc1refChr2 90938 8 + 144309 AAACAC-AG -s Anc2.Anc2refChr3 736 8 + 53186 AAACAC-AG -s mr.mrrefChr0 114176 8 + 130230 GAACAC-AG -s simCow_chr6.simCow.chr6 123125 5 + 602619 AGATA---- -s simDog_chr6.simDog.chr6 411763 8 - 593897 AAGCAC-AG -s simHuman_chr6.simHuman.chr6 114971 8 + 601863 AAACAT-AA -s simRat_chr6.simRat.chr6 112332 8 + 647215 GAACAC-AG - -a -s simMouse_chr6.simMouse.chr6 119549 128 + 636262 CCATCATTCACAAAAAGAAAAGAGGGTGACTGCACGGCCAGCATTGTCGGGTGAAACTACTCTTCTACCGATCAGAACTGTTTGTTATTAGTGCTTTAATTCATTTAGTACCCCTAATCTATAGATGT -s Anc0.Anc0refChr1 12551 45 - 62388 CCATCT-----------------------------------------------------------------------------------AGTGTTTACAGGCATTTTGAACCCCTAATCTTTAAACAC -s Anc1.Anc1refChr2 90947 45 + 144309 CCATCT-----------------------------------------------------------------------------------AGTGTTTACAGGCATTTTGAACCCCTAATCTTTAAACAC -s Anc2.Anc2refChr3 745 45 + 53186 CCATCT-----------------------------------------------------------------------------------AGTGTTCACAGGCATTTTGAACCCCTAATCTTTAAACAC -s mr.mrrefChr0 114184 45 + 130230 CTATCA-----------------------------------------------------------------------------------GGTGCTTTAATTCATTTAGAACCCCTAATCTATAAATGC -s simCow_chr6.simCow.chr6 123130 32 + 602619 ------------------------------------------------------------------------------------------------AAAGGCATTTTGAACCCCTAATTTTTCAACAC -s simDog_chr6.simDog.chr6 411772 45 - 593897 CCATCT-----------------------------------------------------------------------------------AGTGTTCACAGGCATTTTAGACCCCTAATCTTTAAACAC -s simHuman_chr6.simHuman.chr6 114980 45 + 601863 CCATTG-----------------------------------------------------------------------------------TGCGTTTACAGGCATGTTGAACCACTATTCATTGAACAC -s simRat_chr6.simRat.chr6 112340 45 + 647215 CTGTCA-----------------------------------------------------------------------------------GGTGCTTTAATTCATTTAGAATGTCTAATCCATAAATGC - -a -s simMouse_chr6.simMouse.chr6 119677 23 + 636262 GCGATTGCAATGTATGTATAAAT -s Anc0.Anc0refChr1 12597 23 - 62388 GTGTTTGCAATTTATGCATAAAT -s Anc1.Anc1refChr2 90993 23 + 144309 GTGTTTGCAATTTATGCATAAAT -s Anc2.Anc2refChr3 791 23 + 53186 GTGTTTGCAATTTATGCATAAAT -s mr.mrrefChr0 114230 23 + 130230 GCGATTGCAATGTATGTATAAAT -s simCow_chr6.simCow.chr6 123163 23 + 602619 ATGTTTGCATTTTATGCATAAAT -s simDog_chr6.simDog.chr6 411818 23 - 593897 GAGTTTGCAATTTGTGCAGGAAT -s simHuman_chr6.simHuman.chr6 115026 23 + 601863 TTGTTTGCAAATTATCCATAAAC -s simRat_chr6.simRat.chr6 112386 23 + 647215 GAGGTTGCAATGTATATATAAAT - -a -s simMouse_chr6.simMouse.chr6 119700 55 + 636262 TAGCTAGGTCCTGGACCCATGGGTATTGATCTTTGAAGATGTCTGTTTGTATTTT -s Anc0.Anc0refChr1 12620 54 - 62388 GGGCTAAGTCTTGGCTACATGGGTATTCGCCCTGGAAG-CATCAGTATGTACTTT -s Anc1.Anc1refChr2 91016 54 + 144309 GGGCTAAGTCTTGGCTACATGGGTATTCGCCCTGGAAG-CATCAGTATGTACTTT -s Anc2.Anc2refChr3 814 54 + 53186 GGGCTAAGTCTTGGCTACATGGGTATTCGCCCTGGCAG-CATCAGTATGTACTTT -s mr.mrrefChr0 114253 55 + 130230 TAACTAGGTCCTGGCCACATGGGTATTGATCTTTGAAGACATCTGTTTGTATCTT -s simCow_chr6.simCow.chr6 123186 54 + 602619 ATACTAAGTCTTCACTACATGGGTATACGCACTGGCAC-CATCAGTATGTATCTT -s simDog_chr6.simDog.chr6 411841 53 - 593897 GGGCTAAGTAT-GGTCATGTGGGTATTTGCCCTGGCAG-CATCGTTTTATACTTT -s simHuman_chr6.simHuman.chr6 115050 50 + 601863 GGGCTAAGTCTTGGCTACATTGGTATTCTCTCTAGAG-----CAGCATGTAGTTT -s simRat_chr6.simRat.chr6 112409 51 + 647215 TAACTAGG----GGCCACATGGGTATTGATCTTTGAAGACATCTATTTGTATCTT - -a -s simMouse_chr6.simMouse.chr6 119755 58 + 636262 AAGAAATGATTTGGTGGCTGAGTATGAGTGCGCATGGGCAAATAGTGTGTTCAACCTA -s Anc0.Anc0refChr1 12675 57 - 62388 AAGGAATGGTCTTGTGGTTGAGTGGTAATGTGCACGATCAATTAGTGGGTGCAAT-TA -s Anc1.Anc1refChr2 91071 57 + 144309 AAGGAATGGTCTTGTGGTTGAGTGGTAATGTGCACGATCAATTAGTGGGTGCAAT-TA -s Anc2.Anc2refChr3 869 57 + 53186 GAGGAATGGTCTTCTGGTTGAGTGGTAATGTGCACGATCAGTTAGTGGGTGCAAT-TA -s mr.mrrefChr0 114309 57 + 130230 AAGAAATGATTTTGTGGCTGAGTATTAGTGTGCACGAGCAAATAGTGGGTTCAAC-TA -s simCow_chr6.simCow.chr6 123241 57 + 602619 GAGGAATGATGTTCTGGTTGCATGGTAATGTGCACGATCAGCTAGTGGGCTCAAT-CA -s simDog_chr6.simDog.chr6 411895 46 - 593897 GAGGAATGGTCTTCTGTTTGAGTGGTAGTG-----------TTAGTGGGTGTAAT-TA -s simHuman_chr6.simHuman.chr6 115101 47 + 601863 AAA----------GTGGTTGAGTCAAAATAAGCATGAACAATTAGTGCGTGCAAT-GA -s simRat_chr6.simRat.chr6 112461 57 + 647215 AAGTAGTGATCTTGTGGCTGAGTACTAGTGTGCACGAGCAAATAGTGGGTACAAC-TA - -a -s simMouse_chr6.simMouse.chr6 119813 25 + 636262 ACTATGTCTGTCCAGAAGGGCTTAA -s Anc0.Anc0refChr1 12733 25 - 62388 GTTATGACATTCAAAAAGGGCTTGT -s Anc1.Anc1refChr2 91129 25 + 144309 GTTATGACATTCAAAAAGGGCTTGT -s Anc2.Anc2refChr3 927 25 + 53186 GTTCTGACATTCAAAAAGGGCTTGT -s mr.mrrefChr0 114366 25 + 130230 ACTATGTCTGTCCAAAAGGGCTTAA -s simCow_chr6.simCow.chr6 123299 24 + 602619 GTTCTGACAT-CAAAAAATGCTTGT -s simDog_chr6.simDog.chr6 411942 25 - 593897 GTTCTGACAGTCAAAAAGGGCTCGT -s simHuman_chr6.simHuman.chr6 115149 25 + 601863 GTTATGACATTCAAGAAGAGCTTTT -s simRat_chr6.simRat.chr6 112518 25 + 647215 ACTATGTCTGCTGAAAAGGGCTTAA - -a -s simMouse_chr6.simMouse.chr6 119838 4 + 636262 ATTA -s Anc0.Anc0refChr1 12758 4 - 62388 ATTA -s Anc1.Anc1refChr2 91154 4 + 144309 ATTA -s Anc2.Anc2refChr3 957 4 + 53186 ATCA -s mr.mrrefChr0 114391 4 + 130230 ATTA -s simCow_chr6.simCow.chr6 123328 4 + 602619 ATCG -s simDog_chr6.simDog.chr6 411972 4 - 593897 ATCA -s simHuman_chr6.simHuman.chr6 115174 4 + 601863 ATTA -s simRat_chr6.simRat.chr6 112543 4 + 647215 ATTA - -a -s simMouse_chr6.simMouse.chr6 119842 25 + 636262 AAGGATGAGCTGCACTCTTGGTATA -s Anc0.Anc0refChr1 12763 25 - 62388 AAGGATGAACTGCCCACTCGGTTTT -s Anc1.Anc1refChr2 91159 25 + 144309 AAGGATGAACTGCCCACTCGGTTTT -s Anc2.Anc2refChr3 962 25 + 53186 AAGGATGAACTGCCCATTCGGTTTT -s mr.mrrefChr0 114395 25 + 130230 AAGGATGAACTGCACTCTTGGTTTA -s simCow_chr6.simCow.chr6 123333 25 + 602619 AATGATGAATTGCCAAATTGATTTT -s simDog_chr6.simDog.chr6 411977 25 - 593897 AAGGATGAACTGTCCGTTCGGTTTT -s simHuman_chr6.simHuman.chr6 115179 25 + 601863 AAGGATGCACTCCCCACTAGGTATC -s simRat_chr6.simRat.chr6 112547 25 + 647215 AAGAATGAACTGCACTCTTGGTTTA - -a -s simMouse_chr6.simMouse.chr6 119867 10 + 636262 TAATTTCCTA -s Anc0.Anc0refChr1 12788 10 - 62388 TAACTTACAA -s Anc1.Anc1refChr2 91184 10 + 144309 TAACTTACAA -s Anc2.Anc2refChr3 987 10 + 53186 TAACTTACAA -s mr.mrrefChr0 114420 10 + 130230 TAATTTCCAA -s simCow_chr6.simCow.chr6 123358 10 + 602619 CAATTTCCAA -s simDog_chr6.simDog.chr6 412002 10 - 593897 TAACTTACAA -s simHuman_chr6.simHuman.chr6 115204 3 + 601863 TTT------- -s simRat_chr6.simRat.chr6 112575 10 + 647215 GAATGTCCAA - -a -s simMouse_chr6.simMouse.chr6 119877 14 + 636262 GTTTAGGATGACCT -s Anc0.Anc0refChr1 12798 10 - 62388 ATT----ATTACCT -s Anc1.Anc1refChr2 91194 10 + 144309 ATT----ATTACCT -s Anc2.Anc2refChr3 997 10 + 53186 ATT----ATTACTC -s mr.mrrefChr0 114430 14 + 130230 GTTTAGGATGACCT -s simCow_chr6.simCow.chr6 123385 10 + 602619 ATT----ATTACTT -s simDog_chr6.simDog.chr6 412012 10 - 593897 ATT----ATTACTC -s simHuman_chr6.simHuman.chr6 115207 2 + 601863 ------------CT -s simRat_chr6.simRat.chr6 112585 14 + 647215 GTTTAACATGATCT - -a -s simMouse_chr6.simMouse.chr6 119891 7 + 636262 AACCCTA -s Anc0.Anc0refChr1 12808 5 - 62388 A--CATA -s Anc1.Anc1refChr2 91204 7 + 144309 AGCCATA -s Anc2.Anc2refChr3 1007 5 + 53186 A--CATA -s mr.mrrefChr0 114444 7 + 130230 AACCCCA -s simCow_chr6.simCow.chr6 123396 5 + 602619 G--CATA -s simDog_chr6.simDog.chr6 412022 5 - 593897 A--CATA -s simHuman_chr6.simHuman.chr6 115209 7 + 601863 AGCTGTA -s simRat_chr6.simRat.chr6 112599 7 + 647215 AATCCCA - -a -s simMouse_chr6.simMouse.chr6 119898 62 + 636262 GCCTAGCTTTAAGCTTGTTGTCTACATTACATGTTAAAGAGACACAGAGAATGAGTAGTTAG -s Anc0.Anc0refChr1 12813 62 - 62388 GAGTGACCTTGATCTTACTGTCCACATGATATTTGAAAGGGAAACAAAAATTAAGTAGTCAG -s Anc1.Anc1refChr2 91211 62 + 144309 GAGTGACCTTGATCTTACTGTCCACATGATATTTGAAAGGGAAACAAAAATTAAGTAGTCAG -s Anc2.Anc2refChr3 1012 62 + 53186 GAGTGACCTTGATCTTACTGTGCACATGATATTTGAAAGGAAAACAAAAATTATGTAGTCAG -s mr.mrrefChr0 114451 62 + 130230 GCCTAGCCTTGAGCTTGTTGTCCACATGACATGTTAAAGGGACACAGAGAATGAGTAGTCAG -s simCow_chr6.simCow.chr6 123406 62 + 602619 GAGTGACCTTGATCGAGTTGTGCACATGATATTTGAAAGGAAAACAAAAATTAGGTAGTCAG -s simDog_chr6.simDog.chr6 412027 62 - 593897 GAATGACCTTGATCTTACTGTGCACATCATATTTGAGAGGAAAACAAAAATTTTGTAGTCAG -s simHuman_chr6.simHuman.chr6 115216 57 + 601863 GAGTGACCTTGATCTTACTTTCCCCGTGATATTTGAAAGGGAATCAAAAATTAAG-----AG -s simRat_chr6.simRat.chr6 112606 62 + 647215 GCCTAGCCTTGAACTTGTTGTCCACATGGCATGTAACAGGGATACAGAGAATGAGTAGTCAG - -a -s simMouse_chr6.simMouse.chr6 119960 1 + 636262 G -s Anc0.Anc0refChr1 12875 1 - 62388 T -s Anc1.Anc1refChr2 91273 1 + 144309 T -s Anc2.Anc2refChr3 1112 1 + 53186 T -s mr.mrrefChr0 114513 1 + 130230 G -s simCow_chr6.simCow.chr6 123507 1 + 602619 T -s simDog_chr6.simDog.chr6 412127 1 - 593897 G -s simHuman_chr6.simHuman.chr6 115273 1 + 601863 T -s simRat_chr6.simRat.chr6 112668 1 + 647215 G - -a -s simMouse_chr6.simMouse.chr6 119961 11 + 636262 CTTAACAAAAT -s Anc0.Anc0refChr1 12876 11 - 62388 TTTAACTACAT -s Anc1.Anc1refChr2 91274 11 + 144309 TTTAACTACAT -s Anc2.Anc2refChr3 1113 11 + 53186 TTTAGCTACAT -s mr.mrrefChr0 114514 11 + 130230 CTTAACAAAAT -s simCow_chr6.simCow.chr6 123509 11 + 602619 TTTAGCTAAAC -s simDog_chr6.simDog.chr6 412128 11 - 593897 CCTAGCTACGT -s simHuman_chr6.simHuman.chr6 115274 11 + 601863 TTTAACTACAT -s simRat_chr6.simRat.chr6 112669 11 + 647215 CTTAACAAAAT - -a -s simMouse_chr6.simMouse.chr6 119972 78 + 636262 GGTACACCAGTGCTAGCATCTTAGTCCCACACATTGTTTAACAGGGGGTTCAGGTAACAAGGGTGTAATCTAATGTCC -s mr.mrrefChr0 114527 78 + 130230 GGTACACCAGTGCTAGCATCTTAGTCCCACACATTGTTTAACAGGGGGTTCAGGTAACAAGGGTGTAATCTAATGTCC -s simRat_chr6.simRat.chr6 112682 78 + 647215 GGTACACTAGTGCTAGCATCTTAGTCCTACACATTGCTTAATGGGGGGTTCAGATAACAAGGGTGGAATCTAATTTCC - -a -s simMouse_chr6.simMouse.chr6 120050 179 + 636262 AAGATTGATATCTGTCCCCAAGATTGATAGCCCACTCAGACATGTACCTGCATATAATTGTCAATAACAGAACTGCATGACAAAAAGAGAATATCAGAGTGTGAATCTGCTTCTACCGCCTTGGGAGGCCTGCATACTTAAACCTACATCTTAGGCTCTGTGTCCTACATCCAGATGGA -s Anc0.Anc0refChr1 12888 98 - 62388 -----------------------------------------------------ATCATTGTTAACAATAGAGCTGTACAATAAAAAGAG----------------------------GCCTTGGAAGACATGCATCATTAAAGATACATCTCCTGCTCTATGTCCTACTTCCAGCTTAA -s Anc1.Anc1refChr2 91286 98 + 144309 -----------------------------------------------------ATCATTGTTAACAATAGAGCTGTACAATAAAAAGAG----------------------------GCCTTGGAAGACATGCATCATTAAAGATACATCTCCTGCTCTATGTCCTACTTCCAGCTTAA -s Anc2.Anc2refChr3 1125 98 + 53186 -----------------------------------------------------ATCATTGTTAACAATAGAGTTGTACAATAAACAGGG----------------------------GCCTTGGAAGACATCCATCATTAATGATACATCTCCTGCTCCATATCCTATTTCCAGCTTAA -s mr.mrrefChr0 114605 174 + 130230 AAGATTGATATCTGTCCCCAAGATTG-TAGCCCACTCA----TGTACCTGCATATAATTGTCAATAACAGAACTGCATGACAAAAAGAGAATATCAGAGTGTGAATCTGCTTCTACCGCCTTGGGAGGCCTGCATACTTAAACCTACATCTTAGGCTCTGTGTCCTACATCCAGATGGA -s simCow_chr6.simCow.chr6 123521 75 + 602619 -----------------------------------------------------CTCACTATTGACAGTAGCGGTGTACAATAAAGAGGG----------------------------ACCTAGGAAGATATCCATCATTAATG------------CTACATATC-----------TTAA -s simDog_chr6.simDog.chr6 412140 98 - 593897 -----------------------------------------------------ATCATTGTTAGCAATAAAGTGGTACAACAGACAGGG----------------------------GTTATGCAAGACATCCATTGTTAATCATACATCTCCTGCTCCATATCCTATTTCCAGCAGAA -s simHuman_chr6.simHuman.chr6 115286 94 + 601863 -----------------------------------------------------ATCTTTGTAAACGATAGAGCTGTACAATTAAAAGAG----------------------------GCCTTGGACAACATGCATCATTAAAGGTACATCAGCTACCCTCCGTCCTACCTACAGC---- -s simRat_chr6.simRat.chr6 112761 174 + 647215 AAGATTGATATCGATCCCCAAGATTG-CAGCTAACTCA----TATACCTGTGTACCATTGTTAATTACTGAACCGCATGACAAAAAGAGAATAGCAGAGTGTGAATCTGGTTCTATAGCCTTGAAAGGTTTGCATACTGATACATACATCTTTGGTTCCACGTCCTACATCCAGGTGGA - -a -s simMouse_chr6.simMouse.chr6 120229 1 + 636262 T -s Anc0.Anc0refChr1 12986 1 - 62388 T -s Anc1.Anc1refChr2 91384 1 + 144309 T -s Anc2.Anc2refChr3 1223 1 + 53186 T -s mr.mrrefChr0 114779 1 + 130230 T -s simCow_chr6.simCow.chr6 123596 1 + 602619 T -s simDog_chr6.simDog.chr6 412238 1 - 593897 T -s simHuman_chr6.simHuman.chr6 115521 1 + 601863 T -s simRat_chr6.simRat.chr6 112935 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 120230 23 + 636262 ATAGAGCTAATAACAGAACTTGG -s Anc0.Anc0refChr1 12987 23 - 62388 ATATGGCTAATAACCAAACTAGA -s Anc1.Anc1refChr2 91385 23 + 144309 ATATGGCTAATAACCAAACTAGA -s Anc2.Anc2refChr3 1224 23 + 53186 ATATGGCTAATAACCAAACAAGA -s mr.mrrefChr0 114780 23 + 130230 ATAGAGCTAATAACAGAACTTGG -s simCow_chr6.simCow.chr6 123597 23 + 602619 ATGGGGCAAATAGTCAAACAAGA -s simDog_chr6.simDog.chr6 412239 23 - 593897 ATATGACTAATAACCTAACAAGA -s simHuman_chr6.simHuman.chr6 115523 23 + 601863 ATAAGGCTATTAACCATACTGGA -s simRat_chr6.simRat.chr6 112936 23 + 647215 AAAAAGCTAATAACAGAACTTGA - -a -s simMouse_chr6.simMouse.chr6 120253 1 + 636262 A -s Anc0.Anc0refChr1 13010 1 - 62388 A -s Anc1.Anc1refChr2 91408 1 + 144309 A -s Anc2.Anc2refChr3 1247 1 + 53186 A -s mr.mrrefChr0 114803 1 + 130230 A -s simCow_chr6.simCow.chr6 123620 1 + 602619 A -s simDog_chr6.simDog.chr6 412262 1 - 593897 A -s simHuman_chr6.simHuman.chr6 115546 1 + 601863 A -s simRat_chr6.simRat.chr6 112975 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 120254 25 + 636262 CACATAGTACTGTAACCCTTTGAGC -s Anc0.Anc0refChr1 13011 25 - 62388 CGCAAAGTACTGGGACCCCTTAAGC -s Anc1.Anc1refChr2 91409 25 + 144309 CGCAAAGTACTGGGACCCCTTAAGC -s Anc2.Anc2refChr3 1248 25 + 53186 CGCAAAGTACTGGGACTCCTTAAGC -s mr.mrrefChr0 114804 25 + 130230 CACATAGTACTGTAACCCTTTGAGC -s simCow_chr6.simCow.chr6 123621 25 + 602619 CACAAAGTACTGGGACTCCTCAAGC -s simDog_chr6.simDog.chr6 412280 25 - 593897 CGCAAAGTATCCAGACTCCTTGAAC -s simHuman_chr6.simHuman.chr6 115547 25 + 601863 CGCAAAGTACTGGGTCCTCTTAAGC -s simRat_chr6.simRat.chr6 112976 25 + 647215 CACATAGTGCTGTAACCCTTTGAGC - -a -s simMouse_chr6.simMouse.chr6 120279 58 + 636262 CATATTGAATGTGGCATCGCTGCAATTGCAGTGTTTGCCATGTCATGACCAATCCAGC -s Anc0.Anc0refChr1 13036 5 - 62388 CATAT----------------------------------------------------- -s Anc1.Anc1refChr2 91434 5 + 144309 CATAT----------------------------------------------------- -s Anc2.Anc2refChr3 1273 5 + 53186 CATAT----------------------------------------------------- -s mr.mrrefChr0 114829 58 + 130230 CATATTGAATGTGGCATCGCTGCAATTGCAGTGTTTGCCATGTCATGACCAATCCAGC -s simCow_chr6.simCow.chr6 123806 5 + 602619 CATCC----------------------------------------------------- -s simDog_chr6.simDog.chr6 412305 5 - 593897 TATAT----------------------------------------------------- -s simHuman_chr6.simHuman.chr6 115572 5 + 601863 CATAT----------------------------------------------------- -s simRat_chr6.simRat.chr6 113001 58 + 647215 CATATCAAATGTGGCATTCGTGCAATTGCAGTGTATGCCATGTTTTGATCAATTGAAC - -a -s simMouse_chr6.simMouse.chr6 120337 144 + 636262 TAAAACTGTTCTAAAAGACAAGTCAATAAGCACTATTACAACATAAACATATCCAGACTCTGTTACCAAGAACAGCTAATGATGTTGTGCCTCAGTTGATTCCAGCCTATTAATTGGCAGAACACACAGGCCTGTGGGAGACTG -s Anc0.Anc0refChr1 13041 41 - 62388 -------------------------------------------------------------------------------------------------------AACCTATCAATTAGCAGAACACACAAGCCTGAGGCAGACTA -s Anc1.Anc1refChr2 91439 41 + 144309 -------------------------------------------------------------------------------------------------------AACCTATCAATTAGCAGAACACACAAGCCTGAGGCAGACTA -s Anc2.Anc2refChr3 1278 41 + 53186 -------------------------------------------------------------------------------------------------------TACCTATCAATTAGCAGACCACACAAGCCTGAGGCAGGCTA -s mr.mrrefChr0 114887 144 + 130230 TAAAACTGTTCTAAAAGACAAGTCAATAAGCACTATTACAACATAAACATATCCAGACTCTGTTACCAAGAACAGCTAATGATGTTGTGCCTCAGTTGATTCCAGCCTATCAATTAGCAGAACACACAAGCCTGTGGCAGACTA -s simCow_chr6.simCow.chr6 123811 41 + 602619 -------------------------------------------------------------------------------------------------------TACCTATTAATTAGCAAACCACACATGCCTGAGGCAGGCTA -s simDog_chr6.simDog.chr6 412345 41 - 593897 -------------------------------------------------------------------------------------------------------TACCTATCAATTGACAGACAATTAAAGCTTGGGGCAGGCTA -s simHuman_chr6.simHuman.chr6 115577 41 + 601863 -------------------------------------------------------------------------------------------------------AACCATTCAATTAGTGGAACACACAACCCTGACACAGACTA -s simRat_chr6.simRat.chr6 113061 144 + 647215 TAAAACTGTTCTAAAAGGCAAGTGAGTAAGTACTATTACTACATAATTGCATCCAAACTCTGTTACCAAGAAAAGCTAATGATGTTGTCCCTCAGTTGATTCCACCCCATCAATTAGCAAAACACACGAGCCTATGGCACACTA - -a -s simMouse_chr6.simMouse.chr6 120481 37 + 636262 CATTAACCTTTTGTATTATACACCTTGTATTATACAC -s Anc0.Anc0refChr1 13092 37 - 62388 TATCACATTGTTTCTACTTACTGCTTGTATTATGCAT -s Anc1.Anc1refChr2 91490 37 + 144309 TATCACATTGTTTCTACTTACTGCTTGTATTATGCAT -s Anc2.Anc2refChr3 1329 37 + 53186 TATCACATTGTCTCTACTAACTGCTTGTATTATGTAT -s mr.mrrefChr0 115031 37 + 130230 CATTAACTTTTTTTATTATACACCTTGTATTATACAC -s simCow_chr6.simCow.chr6 123862 37 + 602619 TATAGCATTTTCTCTACTAACTGAGTGGATTATAGCT -s simDog_chr6.simDog.chr6 412396 36 - 593897 TATCATGTTGGCTTTATAAACTGCT-GTATTATGTAT -s simHuman_chr6.simHuman.chr6 115628 37 + 601863 TATCACATTGTTTCTGCTTACTGCTTGTATTATGCAT -s simRat_chr6.simRat.chr6 113205 23 + 647215 CATTAACTTTCTTTA--------------TCATACAC - -a -s simMouse_chr6.simMouse.chr6 120518 51 + 636262 CCCCACACCAAAAAGTTCAAAATCAAAAAAAACTATAGCATATCTACTAGA -s Anc0.Anc0refChr1 13129 44 - 62388 TCCAACACCAAACAGGTC-------AAAAGAACTATAGCACATCTATTAAA -s Anc1.Anc1refChr2 91527 44 + 144309 TCCAACACCAAACAGGTC-------AAAAGAACTATAGCACATCTATTAAA -s Anc2.Anc2refChr3 1366 44 + 53186 TACAACACCAAACAGGTC-------AAAAGAACTATAGCACACCTATTAAA -s mr.mrrefChr0 115068 51 + 130230 CCCCACACCAAAAAGTTCAAAATCAAAAAAAACTATAGCACATCTACTAGA -s simCow_chr6.simCow.chr6 123899 44 + 602619 CTCCGCACCAAACAGGTC-------AACGGACCTATAGCACACCTATTAAA -s simDog_chr6.simDog.chr6 412433 42 - 593897 TACAAC--CAAATAGGTC-------AAAAGGACAATAGCACACCTATCATA -s simHuman_chr6.simHuman.chr6 115665 44 + 601863 TCCAACACCAAACAGGTC-------AAAAGAGCTATGGCACATCTATTAAA -s simRat_chr6.simRat.chr6 113228 51 + 647215 CCCCACACCAAAAAGTTCAAGGTCAAAAAAGACTATAGCACATCTACCAGG - -a -s simMouse_chr6.simMouse.chr6 120569 5 + 636262 TTGAT -s Anc0.Anc0refChr1 13177 5 - 62388 TTAAG -s Anc1.Anc1refChr2 91575 5 + 144309 TTAAG -s Anc2.Anc2refChr3 1414 5 + 53186 TTAAG -s mr.mrrefChr0 115119 5 + 130230 TTGAT -s simCow_chr6.simCow.chr6 123947 5 + 602619 TTAAG -s simDog_chr6.simDog.chr6 412479 5 - 593897 CTAAG -s simHuman_chr6.simHuman.chr6 115713 5 + 601863 TTAAC -s simRat_chr6.simRat.chr6 113279 4 + 647215 CCGA- - -a -s simMouse_chr6.simMouse.chr6 120574 26 + 636262 GAACGTAGGGCCTTCCGGGCCTGATA -s Anc0.Anc0refChr1 13184 26 - 62388 AAATGTAGGGCTTTCCAAGGCTGAGA -s Anc1.Anc1refChr2 91582 26 + 144309 AAATGTAGGGCTTTCCAAGGCTGAGA -s Anc2.Anc2refChr3 1421 26 + 53186 AAATGTAGGGCTTTCCAAGGCTGAGA -s mr.mrrefChr0 115124 26 + 130230 GAACGTAGGGCCTTCCGGGCCTGATA -s simCow_chr6.simCow.chr6 123954 25 + 602619 ATATGTGAGTCTTTCCAAA-CTGAGA -s simDog_chr6.simDog.chr6 412486 26 - 593897 GAATGCAGGGCTTTCCATGGTTGAGA -s simHuman_chr6.simHuman.chr6 115720 26 + 601863 AAATGTAGGGCTTTCCAAGGCTGCAA - -a -s simMouse_chr6.simMouse.chr6 120600 62 + 636262 GGTAAAGGTATAATTGAGTGCATCTGTGAGAGATGCATTAAGTAGAGGGAGTTCTATGGCTA -s Anc0.Anc0refChr1 13210 62 - 62388 GGTTAAGGTATGATTGAATGCATCTGTCAAGGATGCATTAAGTAGAGGGAGTTATTGGGCTA -s Anc1.Anc1refChr2 91608 62 + 144309 GGTTAAGGTATGATTGAATGCATCTGTCAAGGATGCATTAAGTAGAGGGAGTTATTGGGCTA -s Anc2.Anc2refChr3 1447 62 + 53186 GGTTAAGGTATGATTGAATGCATCTGTCAAGGATACATTAAATAGAGTGAGTTATTGGGCCA -s mr.mrrefChr0 115150 62 + 130230 GGTAAAGGTATAATTGAGTGCATCTGTGAGAGATGCATTAAGTAGAGGGAGTTCTATGGCTA -s simCow_chr6.simCow.chr6 124012 62 + 602619 GGTTAAGGTATGATTGAATGCATGTGTGTAAGATACATTAAATAGCCAGAGTTTTTGGACCA -s simDog_chr6.simDog.chr6 412512 61 - 593897 GGTAAAAGTATGATTGAATGCATCTGTCAAGGATACATTGAATAGAGTGAGTCATTGGGCC- -s simHuman_chr6.simHuman.chr6 115746 62 + 601863 GGTTAAGGTATGAATGATTGCATCTTTAAATAATGCATTACGTAGAGGGAGTTATTAATCTA - -a -s simMouse_chr6.simMouse.chr6 120662 9 + 636262 TCTCTCCAG -s Anc0.Anc0refChr1 13280 9 - 62388 TCTCCCAAG -s Anc1.Anc1refChr2 91678 9 + 144309 TCTCCCAAG -s Anc2.Anc2refChr3 1517 9 + 53186 ACTCCCAAG -s mr.mrrefChr0 115212 9 + 130230 TCTCTCCAG -s simCow_chr6.simCow.chr6 124083 9 + 602619 ACTCCCAAG -s simDog_chr6.simDog.chr6 412573 4 - 593897 -----TAAG -s simHuman_chr6.simHuman.chr6 115816 9 + 601863 TCTCCCAAG - -a -s simMouse_chr6.simMouse.chr6 120671 12 + 636262 ATAAACCTTACC -s Anc0.Anc0refChr1 13292 12 - 62388 ATGAATCTCACC -s Anc1.Anc1refChr2 91690 12 + 144309 ATGAATCTCACC -s Anc2.Anc2refChr3 1529 12 + 53186 ATGAATCTCACC -s mr.mrrefChr0 115221 12 + 130230 ATAAACCTTACC -s simCow_chr6.simCow.chr6 124095 12 + 602619 ATAAATCTCACT -s simDog_chr6.simDog.chr6 412580 12 - 593897 ATGAATCTTACC -s simHuman_chr6.simHuman.chr6 115828 12 + 601863 ATGAATCTCACC - -a -s simMouse_chr6.simMouse.chr6 120683 9 + 636262 ACTGCGGGG -s Anc0.Anc0refChr1 13321 9 - 62388 ACTGGAAGG -s Anc1.Anc1refChr2 91719 9 + 144309 ACTGGAAGG -s Anc2.Anc2refChr3 1558 9 + 53186 ACTGGAAGC -s mr.mrrefChr0 115233 9 + 130230 ACTGCGGGG -s simCow_chr6.simCow.chr6 124123 9 + 602619 ACTGGGAGT -s simDog_chr6.simDog.chr6 412618 9 - 593897 CTGGGATGC -s simHuman_chr6.simHuman.chr6 115857 9 + 601863 ACTGGAAGG - -a -s simMouse_chr6.simMouse.chr6 120692 21 + 636262 CTGGGCTGAGGCTCCCCCTAG -s Anc0.Anc0refChr1 13330 11 - 62388 CTGGGGT----------CTAG -s Anc1.Anc1refChr2 91728 11 + 144309 CTGGGGT----------CTAG -s Anc2.Anc2refChr3 1567 11 + 53186 CCCCTGT----------CTAG -s mr.mrrefChr0 115242 11 + 130230 CTGGGCT----------CTAG -s simCow_chr6.simCow.chr6 124145 11 + 602619 CCCCTGT----------CTAA -s simDog_chr6.simDog.chr6 412627 11 - 593897 CCCCTGT----------CTAG -s simHuman_chr6.simHuman.chr6 115866 11 + 601863 CTGGGAT----------CTAG - -a -s simMouse_chr6.simMouse.chr6 120713 16 + 636262 GTTTAGCTACAGTGAA -s Anc0.Anc0refChr1 13342 16 - 62388 GTTTAGGTACATTGAA -s Anc1.Anc1refChr2 91740 16 + 144309 GTTTAGGTACATTGAA -s Anc2.Anc2refChr3 1579 16 + 53186 GTTTAGGTACATTGAA -s mr.mrrefChr0 115253 16 + 130230 GTTTAGCTACAGTGAA -s simCow_chr6.simCow.chr6 124157 16 + 602619 GTTTAGGCACTTTGGA -s simDog_chr6.simDog.chr6 412639 16 - 593897 GATTGGGTACACAGAA -s simHuman_chr6.simHuman.chr6 115878 16 + 601863 GTTTAGGTACATTGAA - -a -s simMouse_chr6.simMouse.chr6 120729 33 + 636262 CGTTGAAGAATGAGAAGGTTGAACAGGTCAGTT -s Anc0.Anc0refChr1 13361 32 - 62388 TATGGTAGAATTGCAAGTTTTAGCATGTAAGT- -s Anc1.Anc1refChr2 91759 32 + 144309 TATGGTAGAATTGCAAGTTTTAGCATGTAAGT- -s Anc2.Anc2refChr3 1598 32 + 53186 TATGATAGAATTGCAAATTTTAGCATGTAAGT- -s mr.mrrefChr0 115269 32 + 130230 CGTTGAAGAATGAGAAGGTTGAACAGGTCAGT- -s simCow_chr6.simCow.chr6 124176 31 + 602619 TATGATAGAATTGCAAATTT-AGCGTGTAATT- -s simDog_chr6.simDog.chr6 412658 28 - 593897 TATGACAGA----CAAATTTTAGCATGCGAGT- -s simHuman_chr6.simHuman.chr6 115897 32 + 601863 TATCGTGGAATTGCAAGCTTTAGCATGTAAGC- - -a -s simMouse_chr6.simMouse.chr6 120762 26 + 636262 GACTAGAAACTGACATTTCTTTCCAC -s Anc0.Anc0refChr1 13393 26 - 62388 GACCAGGAACTAATACTGCTTGCCAC -s Anc1.Anc1refChr2 91791 26 + 144309 GACCAGGAACTAATACTGCTTGCCAC -s Anc2.Anc2refChr3 1632 26 + 53186 GACCAGGAACTAATACTGCTTGCCCC -s mr.mrrefChr0 115301 26 + 130230 GACTAGAAACTGACATTTCTTTCCAC -s simCow_chr6.simCow.chr6 124209 26 + 602619 GACTAGGAACCAACACTGCTTGCCTC -s simDog_chr6.simDog.chr6 412688 26 - 593897 GATCAGGAACTAATACTGTTTGCCCC -s simHuman_chr6.simHuman.chr6 115929 26 + 601863 GCCAAAGAATTAATACTACTTGTCAC - -a -s simMouse_chr6.simMouse.chr6 120788 4 + 636262 TAAA -s Anc0.Anc0refChr1 13419 4 - 62388 TTTA -s Anc1.Anc1refChr2 91817 4 + 144309 TTTA -s Anc2.Anc2refChr3 1658 4 + 53186 TTTG -s mr.mrrefChr0 115327 4 + 130230 TAAA -s simCow_chr6.simCow.chr6 124235 4 + 602619 TTTG -s simDog_chr6.simDog.chr6 412716 4 - 593897 TTTG -s simHuman_chr6.simHuman.chr6 115955 4 + 601863 TTTA - -a -s simMouse_chr6.simMouse.chr6 120792 2 + 636262 GA -s Anc0.Anc0refChr1 13437 2 - 62388 GA -s Anc1.Anc1refChr2 91835 2 + 144309 GA -s Anc2.Anc2refChr3 1676 2 + 53186 GC -s mr.mrrefChr0 115331 2 + 130230 GA -s simCow_chr6.simCow.chr6 124253 2 + 602619 TC -s simDog_chr6.simDog.chr6 412734 2 - 593897 GC -s simHuman_chr6.simHuman.chr6 115973 2 + 601863 GA - -a -s simMouse_chr6.simMouse.chr6 120794 12 + 636262 GGGAGGGACAGG -s Anc0.Anc0refChr1 13439 12 - 62388 AGCAAGGACAGG -s Anc1.Anc1refChr2 91837 12 + 144309 AGCAAGGACAGG -s Anc2.Anc2refChr3 1745 12 + 53186 AGCAAGGACAGG -s mr.mrrefChr0 115333 12 + 130230 GGGAGGGACAGG -s simCow_chr6.simCow.chr6 124323 12 + 602619 AGCAAGGACAGG -s simDog_chr6.simDog.chr6 412818 12 - 593897 AACAAGGACATG -s simHuman_chr6.simHuman.chr6 115975 12 + 601863 AGCAAGGACAGG - -a -s simMouse_chr6.simMouse.chr6 120806 2 + 636262 AT -s Anc0.Anc0refChr1 13452 2 - 62388 AT -s Anc1.Anc1refChr2 91850 2 + 144309 AT -s Anc2.Anc2refChr3 1758 2 + 53186 AT -s mr.mrrefChr0 115345 2 + 130230 AT -s simCow_chr6.simCow.chr6 124336 2 + 602619 AT -s simDog_chr6.simDog.chr6 412831 2 - 593897 AT -s simHuman_chr6.simHuman.chr6 115988 2 + 601863 AT - -a -s simMouse_chr6.simMouse.chr6 120808 94 + 636262 GGTTCTAACATACTGGCCATAGCTGAGTTGTTTAGGAAGCAATTGTTTAGGAAGCAAAATGGTGGGTGAGTGATGATTTATACGTAAACACCTG -s Anc0.Anc0refChr1 13454 51 - 62388 GGTTTTAACAAACTGTCCATAGATGT--------------------------------------AATGAAT--TGTTCCAGA---AAATACCTG -s Anc1.Anc1refChr2 91852 73 + 144309 GGTTTTAACAAACTGTCCATAGATGTGTT----------------TTCAGGATAGAGAATAGTGAATGAAT--TGTTCCAGA---AAATACCTG -s Anc2.Anc2refChr3 1760 51 + 53186 GATTTCAACAAATTGTCCATAGATGT--------------------------------------AATGAAT--TGTTCCAGA---AAATACTTG -s mr.mrrefChr0 115347 79 + 130230 GGTTCTAACATACTGGCCATAGCTGAGTT------------ATTGTTTAGGAAGCAAAATGGTGAGTGAGTGATGTTTTAGA---AAATACCTG -s simCow_chr6.simCow.chr6 124532 51 + 602619 GACTTCAACAAATTTTCCTTAGCTGT--------------------------------------AAAGAAT--TGCACCAGA---GAATCCTCC -s simDog_chr6.simDog.chr6 412833 51 - 593897 GATCCCAACAAATTGTCCATACATGT--------------------------------------AATGAAT--TGTTCCAAA---ACATACTTG -s simHuman_chr6.simHuman.chr6 115990 73 + 601863 GGTTTTAATGAACTGTCCATAGATGTGTT----------------TTCAGGATAGAGAATAGTGAATAAAT--TGTTCCAGA---AAATTCCTG -s simRat_chr6.simRat.chr6 113283 50 + 647215 -----------------------------------------ATTGTCTAGGAATCAAAATGGAGAGTGAGTGATGTTTTAGA---AAATACCTG - -a -s simMouse_chr6.simMouse.chr6 120902 1 + 636262 C -s Anc0.Anc0refChr1 13505 1 - 62388 C -s Anc1.Anc1refChr2 91925 1 + 144309 C -s Anc2.Anc2refChr3 1811 1 + 53186 C -s mr.mrrefChr0 115426 1 + 130230 C -s simCow_chr6.simCow.chr6 124583 1 + 602619 C -s simDog_chr6.simDog.chr6 412887 1 - 593897 C -s simHuman_chr6.simHuman.chr6 116063 1 + 601863 C -s simRat_chr6.simRat.chr6 113333 1 + 647215 G - -a -s simMouse_chr6.simMouse.chr6 120903 5 + 636262 CCCAA -s Anc0.Anc0refChr1 13508 5 - 62388 TCTAT -s Anc1.Anc1refChr2 91928 5 + 144309 TCTAT -s Anc2.Anc2refChr3 1814 5 + 53186 TCTAT -s mr.mrrefChr0 115427 5 + 130230 CCCAA -s simCow_chr6.simCow.chr6 124590 5 + 602619 TCTAT -s simDog_chr6.simDog.chr6 412890 5 - 593897 TCTAT -s simHuman_chr6.simHuman.chr6 116066 5 + 601863 TCTAT -s simRat_chr6.simRat.chr6 113334 5 + 647215 CCAGC - -a -s simMouse_chr6.simMouse.chr6 120908 17 + 636262 AAAATGGTATTAACCCT -s Anc0.Anc0refChr1 13513 17 - 62388 ACAATGTCATTGACTTT -s Anc1.Anc1refChr2 91933 17 + 144309 ACAATGTCATTGACTTT -s Anc2.Anc2refChr3 1819 17 + 53186 ACAATGTCATTGACTTT -s mr.mrrefChr0 115432 17 + 130230 ACAATGGTATTAACCCT -s simCow_chr6.simCow.chr6 124595 17 + 602619 GCAATGTCAGTGGCATT -s simDog_chr6.simDog.chr6 412895 17 - 593897 ATAATCTCATTGACTTT -s simHuman_chr6.simHuman.chr6 116071 17 + 601863 ACAATGCCATTGACTTC -s simRat_chr6.simRat.chr6 113344 17 + 647215 ACAATCTTACTAACCCT - -a -s simMouse_chr6.simMouse.chr6 120925 37 + 636262 GACACAATTTTACTTGTATGCAGCAGGTCCAGCAAAG -s Anc0.Anc0refChr1 13544 37 - 62388 GCCAGAGTTTTTTTGGTATGTAACAGGTCCAGCAAAG -s Anc1.Anc1refChr2 91964 37 + 144309 GCCAGAGTTTTTTTGGTATGTAACAGGTCCAGCAAAG -s Anc2.Anc2refChr3 1850 37 + 53186 GCCAGAGTTTTTTTGGTATGTAACAGGTCCAACAAAG -s mr.mrrefChr0 115456 37 + 130230 GACACAATTTTATTTGTATGCAGCAGGTCCAGCAAAG -s simCow_chr6.simCow.chr6 124625 37 + 602619 GCCCGGATTTTTTGGGTATGTAACAGGCCGAACAGGG -s simDog_chr6.simDog.chr6 412926 37 - 593897 GCCAAAGTTTTTTTGGTATGCAACAGTTCCAACAAAG -s simHuman_chr6.simHuman.chr6 116102 37 + 601863 GCTAGAGTTTTTTTGGTACGTAATAGGTCTAGCAAAG -s simRat_chr6.simRat.chr6 113368 37 + 647215 GGCACAATTTTATTTGTATGCAGCAGGTCCAGCAAAG - -a -s simMouse_chr6.simMouse.chr6 120962 8 + 636262 GCCTACAA -s Anc0.Anc0refChr1 13581 4 - 62388 ACC----A -s Anc1.Anc1refChr2 92001 4 + 144309 ACC----A -s Anc2.Anc2refChr3 1887 4 + 53186 ATC----A -s mr.mrrefChr0 115493 8 + 130230 GCCTACAA -s simCow_chr6.simCow.chr6 124665 4 + 602619 GTT----G -s simDog_chr6.simDog.chr6 412964 4 - 593897 ATC----A -s simHuman_chr6.simHuman.chr6 116139 4 + 601863 ACC----A -s simRat_chr6.simRat.chr6 113405 8 + 647215 GCTTATAA - -a -s simMouse_chr6.simMouse.chr6 120970 61 + 636262 CAGTACTTTTATTGGTTTTAGCTCATATCTGTGGGTGGCAACCACATTGTAAAGGCGATGT -s Anc0.Anc0refChr1 13585 43 - 62388 CAGCTCTTT------------------TCTGCAGGTGAGGACCCCAATGTAAAGGTAATGT -s Anc1.Anc1refChr2 92005 43 + 144309 CAGCTCTTT------------------TCTGCAGGTGAGGACCCCAATGTAAAGGTAATGT -s Anc2.Anc2refChr3 1891 43 + 53186 CAGCTCTTG------------------TCAGCAGGTGAGGACACCAATATAAAGGTAACAT -s mr.mrrefChr0 115501 61 + 130230 CAGTACTTTTATTGGTTTTAGCTCATATCTGTGGGTGGCAACCCCATTGTAAAGGCAATGT -s simCow_chr6.simCow.chr6 124669 43 + 602619 AAGCTCTTA------------------TCAGCAGGGGCTCACACCAGTATAAAGGTAACAT -s simDog_chr6.simDog.chr6 412985 41 - 593897 CAGCTCTTG------------------TCAGCACGTGAGGACATCCAT--AAAGGTGACAT -s simHuman_chr6.simHuman.chr6 116143 43 + 601863 CAGCTCTTT------------------TCTGCAGGTGAGGCCCCCAATGTAAAGGTAATGT -s simRat_chr6.simRat.chr6 113413 60 + 647215 CAATACTTTCATTGGTTTTGGCTAATATGTGTGGGTG-CAGACCCATAGTAAAGGCAGTGT - -a -s simMouse_chr6.simMouse.chr6 121031 34 + 636262 GTGGATCCTCTACTTACACTGCACCTGACCATGG -s Anc0.Anc0refChr1 13628 34 - 62388 GTGGATCCTCTAGTCACACCAGCCCTGTTCACAG -s Anc1.Anc1refChr2 92048 34 + 144309 GTGGATCCTCTAGTCACACCAGCCCTGTTCACAG -s Anc2.Anc2refChr3 1934 34 + 53186 GAGGATCCTCTAGTCACACCAGCCCTGTTCACAG -s mr.mrrefChr0 115562 34 + 130230 GTGGATCCTCTACTTACACTGCACCTGACCATGG -s simCow_chr6.simCow.chr6 124723 34 + 602619 AAGGATCCTCTAATTGCATCAGCACTGTCCATAG -s simDog_chr6.simDog.chr6 413026 34 - 593897 GAGGATCCCCTAGTCACACTGGCCCGGTTCACAT -s simHuman_chr6.simHuman.chr6 116186 34 + 601863 GTGGATCCTCTATTCACACCATGCCTGGGCACAG -s simRat_chr6.simRat.chr6 113473 34 + 647215 GTGAATCCTCTACTTATACTGCACCTGACTATGG - -a -s simMouse_chr6.simMouse.chr6 121065 9 + 636262 GAGAGAAAA -s Anc0.Anc0refChr1 13662 9 - 62388 AAGAGAGGA -s Anc1.Anc1refChr2 92082 9 + 144309 AAGAGAGGA -s Anc2.Anc2refChr3 1968 9 + 53186 AAAAGAGGA -s mr.mrrefChr0 115596 9 + 130230 GAGAGAAAA -s simCow_chr6.simCow.chr6 124757 9 + 602619 AGAAGAGGA -s simDog_chr6.simDog.chr6 413060 9 - 593897 AAAGGAGCA -s simHuman_chr6.simHuman.chr6 116220 9 + 601863 AAGAGAGGA -s simRat_chr6.simRat.chr6 113510 9 + 647215 GAGAGAAAG - -a -s simMouse_chr6.simMouse.chr6 121074 1 + 636262 A -s Anc0.Anc0refChr1 13671 1 - 62388 A -s Anc1.Anc1refChr2 92091 1 + 144309 A -s Anc2.Anc2refChr3 1979 1 + 53186 A -s mr.mrrefChr0 115605 1 + 130230 A -s simCow_chr6.simCow.chr6 124768 1 + 602619 A -s simDog_chr6.simDog.chr6 413071 1 - 593897 A -s simHuman_chr6.simHuman.chr6 116229 1 + 601863 A -s simRat_chr6.simRat.chr6 113519 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 121075 44 + 636262 TATTTGTGTCTGGGAATTCTTAATTAAGATGTAGCTCTTGCTTA -s Anc0.Anc0refChr1 13672 41 - 62388 TGTTAGTGTGTGGGATTCTTTAGGC---ATGTAGTTCTTGTTTA -s Anc1.Anc1refChr2 92092 43 + 144309 TGTTAGTGTGTGGGATTCTTTAGGC-GTATGTAGTTCTTGTTTA -s Anc2.Anc2refChr3 1980 41 + 53186 TGTTAGTGTGTGGGATTCTTTAGGC---ATGTAGTTCTGGTTTA -s mr.mrrefChr0 115606 44 + 130230 TATTAGTGTCTGGGAATTCTTAAGTAAGATGTAGCTCTTGCTTA -s simCow_chr6.simCow.chr6 124785 37 + 602619 TGTTCATGTAGAG----GTTTAGGG---ATGTAGTCGTGGTTTA -s simDog_chr6.simDog.chr6 413072 41 - 593897 TGTTAGTGTGTGGGATTCTTTAGCC---ATGTAGTTCTGGTTTA -s simHuman_chr6.simHuman.chr6 116230 42 + 601863 TGTTAGTGTGTGTTATTCTTTAGG--GTGTGTAGTTCTTGTTTA -s simRat_chr6.simRat.chr6 113520 44 + 647215 TATTAGTGTCTGGGAAGTCTTAAGAAAGATGTAGCTCCTGCTTA - -a -s simMouse_chr6.simMouse.chr6 121119 13 + 636262 TCTCTTTAGGACA -s Anc0.Anc0refChr1 13713 13 - 62388 TTCCTTGAGTTAT -s Anc1.Anc1refChr2 92135 13 + 144309 TTCCTTGAGTTAT -s Anc2.Anc2refChr3 2021 13 + 53186 TTCCTTGAGTTAT -s mr.mrrefChr0 115650 13 + 130230 TTCCTTTAGGACA -s simCow_chr6.simCow.chr6 124822 13 + 602619 CTCCTTAAGTTAT -s simDog_chr6.simDog.chr6 413117 13 - 593897 TTCCTTGAGTCAA -s simHuman_chr6.simHuman.chr6 116272 13 + 601863 TTCCTTGAGATAT -s simRat_chr6.simRat.chr6 113564 13 + 647215 TTCCTTTAGGACA - -a -s simMouse_chr6.simMouse.chr6 121132 2 + 636262 CG -s Anc0.Anc0refChr1 13726 2 - 62388 CA -s Anc1.Anc1refChr2 92148 2 + 144309 CA -s Anc2.Anc2refChr3 2038 2 + 53186 CA -s mr.mrrefChr0 115663 2 + 130230 CG -s simCow_chr6.simCow.chr6 124839 2 + 602619 CA -s simDog_chr6.simDog.chr6 413134 2 - 593897 CA -s simHuman_chr6.simHuman.chr6 116285 2 + 601863 CC -s simRat_chr6.simRat.chr6 113577 2 + 647215 CG - -a -s simMouse_chr6.simMouse.chr6 121134 55 + 636262 ATTAATGGGTGATACCATAGTTTTAATCTTTCTGCATGATATGAAGAATGCCAAG -s Anc0.Anc0refChr1 13730 44 - 62388 ACTAATGGGTGAGATCATAGAATTAATATACCTGGATAA-----------CCAAT -s Anc1.Anc1refChr2 92152 55 + 144309 ACTAATGGGTGAGATCATAGAATTAATATACCTGGATAAAATGGTGAACACCAAT -s Anc2.Anc2refChr3 2042 44 + 53186 ACTAATGCGTGAGATTGTATAATTAATATACCTGGATAA-----------CCAAT -s mr.mrrefChr0 115667 55 + 130230 ACTAATGGGTGAGACCATAGTATTAATCTTTCTGCATGATATGAAGAATGCCAAG -s simCow_chr6.simCow.chr6 124843 23 + 602619 ATGAA-------------------AATATACCTGTACAA-----------C--AT -s simDog_chr6.simDog.chr6 413138 44 - 593897 ACTAATGCGTGAGATTGTATAATTAATGTACCTGGATAA-----------CCAAT -s simHuman_chr6.simHuman.chr6 116289 54 + 601863 ACTAATGGGTGAGAGCATAGGACTTATA-CCCTGGATTAAATGGTGAACACCAAT -s simRat_chr6.simRat.chr6 113581 55 + 647215 ACTAATGGGTGAGACCATAGTATTAATCTATTTGCATAATATGAGGAATGCCAAG - -a -s simMouse_chr6.simMouse.chr6 121189 43 + 636262 ATTTGTTATTTTTCTTATAACTTAAGAAATCCTCCTATAGATG -s Anc0.Anc0refChr1 13781 39 - 62388 A----TAATTTTTTTTAAAACTTAAGAGTAGCTCTTACAAATG -s Anc1.Anc1refChr2 92214 43 + 144309 ACTCATAATTTTTTTTAAAACTTAAGAGTAGCTCTTACAAATG -s Anc2.Anc2refChr3 2093 39 + 53186 A----TAACTTTTTTTAAAACTTAAGAGTAGCTCTTACAAATG -s mr.mrrefChr0 115722 43 + 130230 ACTTGTTATTTTTCTTAAAACTTAAGAAATCCTCCTACAGATG -s simCow_chr6.simCow.chr6 124873 38 + 602619 C----TTACTTTTTTC-AAACTTAAGAGAAGCTCCTACAAATA -s simDog_chr6.simDog.chr6 413189 39 - 593897 A----CAACTTTTTTTAGAACTTAAGAGTAGCTCTTACAAATG -s simHuman_chr6.simHuman.chr6 116351 43 + 601863 ACTCATAATTTTTTTTAAAACCTAAGAGCAGCTTGTACAAACG -s simRat_chr6.simRat.chr6 113636 43 + 647215 ACTTGTTATTTTTCCTAAAACTTAAGAAACCCTCCTACAGGTG - -a -s simMouse_chr6.simMouse.chr6 121232 6 + 636262 TGGGGT -s Anc0.Anc0refChr1 13821 6 - 62388 TGATGT -s Anc1.Anc1refChr2 92258 6 + 144309 TGATGT -s Anc2.Anc2refChr3 2133 6 + 53186 TGGTGT -s mr.mrrefChr0 115765 6 + 130230 TGAGGT -s simCow_chr6.simCow.chr6 124912 6 + 602619 TGGTGT -s simDog_chr6.simDog.chr6 413229 6 - 593897 TGGAGT -s simHuman_chr6.simHuman.chr6 116395 6 + 601863 TAATGA -s simRat_chr6.simRat.chr6 113679 6 + 647215 TGAGGT - -a -s simMouse_chr6.simMouse.chr6 121238 5 + 636262 ATGTC -s Anc0.Anc0refChr1 13827 5 - 62388 TGGTC -s Anc1.Anc1refChr2 92264 5 + 144309 TGGTC -s Anc2.Anc2refChr3 2149 5 + 53186 TGGCT -s mr.mrrefChr0 115771 5 + 130230 TTGTC -s simCow_chr6.simCow.chr6 124928 5 + 602619 TGGCT -s simDog_chr6.simDog.chr6 413245 5 - 593897 TGGCT -s simHuman_chr6.simHuman.chr6 116401 5 + 601863 TGGTC -s simRat_chr6.simRat.chr6 113685 5 + 647215 TCGTC - -a -s simMouse_chr6.simMouse.chr6 121243 15 + 636262 AAACATAGCTAGGCA -s Anc0.Anc0refChr1 13834 15 - 62388 AAAAATATCCGAGCA -s Anc1.Anc1refChr2 92271 15 + 144309 AAAAATATCCGAGCA -s Anc2.Anc2refChr3 2156 15 + 53186 AAAAATATCCGAGAA -s mr.mrrefChr0 115776 15 + 130230 AAACATAGCTAGGCA -s simCow_chr6.simCow.chr6 124935 15 + 602619 GAAAATATCTAAGAA -s simDog_chr6.simDog.chr6 413252 15 - 593897 AAAAATGTCCGAGAA -s simHuman_chr6.simHuman.chr6 116408 11 + 601863 ----ATATCCCAGCA -s simRat_chr6.simRat.chr6 113690 15 + 647215 AAACATAGCTGGGCA - -a -s simMouse_chr6.simMouse.chr6 121258 20 + 636262 ACATCAAAACATCAAAAAGT -s Anc0.Anc0refChr1 13854 20 - 62388 GTACCATAGCATTCTAAACT -s Anc1.Anc1refChr2 92291 20 + 144309 GTACCATAGCATTCTAAACT -s Anc2.Anc2refChr3 2176 20 + 53186 GTACCATAGCATTCTAAACC -s mr.mrrefChr0 115791 20 + 130230 GTATCAAAACATCAAAAACT -s simCow_chr6.simCow.chr6 124955 20 + 602619 GCACCATAGCATTCAAAAAC -s simDog_chr6.simDog.chr6 413272 20 - 593897 GTACCATAGCACTCTAAACC -s simHuman_chr6.simHuman.chr6 116424 20 + 601863 GTACCATACCATTCTAAACT -s simRat_chr6.simRat.chr6 113705 13 + 647215 GTATCAAAA-------AACT - -a -s simMouse_chr6.simMouse.chr6 121278 19 + 636262 TCCATGTACCATTCTTAAT -s Anc0.Anc0refChr1 13882 17 - 62388 TCCATGTGT--TCCTTATT -s Anc1.Anc1refChr2 92319 19 + 144309 TCCATGTGTGGTCCTTATT -s Anc2.Anc2refChr3 2204 17 + 53186 GCAGTGTGT--TCCTTATT -s mr.mrrefChr0 115811 19 + 130230 TCCATGTACCATTCTTAAT -s simCow_chr6.simCow.chr6 124983 17 + 602619 CCAGTTTGT--TCCTTATT -s simDog_chr6.simDog.chr6 413300 17 - 593897 GCAGTGTGT--TCCTTACT -s simHuman_chr6.simHuman.chr6 116452 19 + 601863 TCCAGGGCGGGTCCTTATT -s simRat_chr6.simRat.chr6 113718 19 + 647215 CATGTATACCATTCTTAAT - -a -s simMouse_chr6.simMouse.chr6 121297 29 + 636262 CCTTAATCATGTCAGCGCGGTTCCCTACT -s Anc0.Anc0refChr1 13906 29 - 62388 CCTTATTGAAGAAACCCCAGTGCTCCACT -s Anc1.Anc1refChr2 92345 29 + 144309 CCTTATTGAAGAAACCCCAGTGCTCCACT -s Anc2.Anc2refChr3 2228 29 + 53186 CTTTATTGAAGAAACCCCAGTGCTACCAT -s mr.mrrefChr0 115830 29 + 130230 CCTTAATCATGTCAGCGCAGTTCCCTACT -s simCow_chr6.simCow.chr6 125007 29 + 602619 CTTTATTGAACAAACCCCAGGGCTACCAT -s simDog_chr6.simDog.chr6 413324 29 - 593897 CTTTACTGAAGCAACACCTGTGCTACCAT -s simHuman_chr6.simHuman.chr6 116484 29 + 601863 CCTTGTTTAAGAAACCCCAGTGCTCCACT -s simRat_chr6.simRat.chr6 113737 29 + 647215 CCTTAATCACGTCAGCGCAGTTTCCTACT - -a -s simMouse_chr6.simMouse.chr6 121326 6 + 636262 TTCCAC -s Anc0.Anc0refChr1 13935 2 - 62388 ----AC -s Anc1.Anc1refChr2 92374 6 + 144309 CTGCAC -s Anc2.Anc2refChr3 2257 2 + 53186 ----AC -s mr.mrrefChr0 115859 6 + 130230 TTTCAC -s simCow_chr6.simCow.chr6 125036 2 + 602619 ----CC -s simDog_chr6.simDog.chr6 413353 2 - 593897 ----AC -s simHuman_chr6.simHuman.chr6 116517 6 + 601863 CTGCAC -s simRat_chr6.simRat.chr6 113766 6 + 647215 TTTCAC - -a -s simMouse_chr6.simMouse.chr6 121332 2 + 636262 AG -s Anc0.Anc0refChr1 13937 2 - 62388 AA -s Anc1.Anc1refChr2 92380 2 + 144309 AA -s Anc2.Anc2refChr3 2259 2 + 53186 AA -s mr.mrrefChr0 115865 2 + 130230 AG -s simCow_chr6.simCow.chr6 125039 2 + 602619 AA -s simDog_chr6.simDog.chr6 413355 2 - 593897 AA -s simHuman_chr6.simHuman.chr6 116523 2 + 601863 AA -s simRat_chr6.simRat.chr6 113772 2 + 647215 AG - -a -s simMouse_chr6.simMouse.chr6 121334 41 + 636262 GTGATCTTCACAATACAGTATAGGTGTTTGGATCTTTTGAG -s Anc0.Anc0refChr1 13954 32 - 62388 ATGATCTCCACTATTCCTTGTAAGTGCTTGG---------C -s Anc1.Anc1refChr2 92397 32 + 144309 ATGATCTCCACTATTCCTTGTAAGTGCTTGG---------C -s Anc2.Anc2refChr3 2276 32 + 53186 ATATTCTCCACTATTCCTTGTAAGTGCTTGG---------C -s mr.mrrefChr0 115882 41 + 130230 GTGATCTTCACAATACATTATAAGTGTTTGGATCTTTTGAG -s simCow_chr6.simCow.chr6 125056 32 + 602619 ACATTCCCCACTATGCCCTGTGGATGCTTTG---------C -s simDog_chr6.simDog.chr6 413372 30 - 593897 ATA--TTCCACTACTCCTTGCAAGTGCTTGG---------C -s simHuman_chr6.simHuman.chr6 116540 32 + 601863 ATGATCTCCACTATCGGTTGTAAGTTCTTGG---------T -s simRat_chr6.simRat.chr6 113789 41 + 647215 GTGGTCCTCACAACTCATTATAAGTATTTGGATCTTTTGAG - -a -s simMouse_chr6.simMouse.chr6 121375 20 + 636262 TCTTGATATGATGAGTTACC -s Anc0.Anc0refChr1 13986 20 - 62388 TCTTGGTATGATGCTTTACC -s Anc1.Anc1refChr2 92429 20 + 144309 TCTTGGTATGATGCTTTACC -s Anc2.Anc2refChr3 2308 20 + 53186 TCTTAGTATGATGCTTTACC -s mr.mrrefChr0 115923 20 + 130230 TCTTGATATGATGAGTTACC -s simCow_chr6.simCow.chr6 125088 20 + 602619 TCTTACTATGAAGCTGTACC -s simDog_chr6.simDog.chr6 413404 20 - 593897 TTTTAGTATGATGCTTTACC -s simHuman_chr6.simHuman.chr6 116572 20 + 601863 TCTTGGTATGATGCTTTACC -s simRat_chr6.simRat.chr6 113830 20 + 647215 TCCTGATATGATGAATTACT - -a -s simMouse_chr6.simMouse.chr6 121395 8 + 636262 ACCTTGAA -s Anc0.Anc0refChr1 14024 8 - 62388 ACCATCAA -s Anc1.Anc1refChr2 92467 8 + 144309 ACCATCAA -s Anc2.Anc2refChr3 2346 8 + 53186 ACCATCAG -s mr.mrrefChr0 115943 8 + 130230 ACCTTGAA -s simCow_chr6.simCow.chr6 125126 8 + 602619 ACCAACAC -s simDog_chr6.simDog.chr6 413442 8 - 593897 ACCATCAG -s simHuman_chr6.simHuman.chr6 116610 8 + 601863 ACCATCAA -s simRat_chr6.simRat.chr6 113850 8 + 647215 GTCTTGAA - -a -s simMouse_chr6.simMouse.chr6 121403 11 + 636262 TCCAGGAGGAA -s Anc0.Anc0refChr1 14034 11 - 62388 TCCAGGAGAAG -s Anc1.Anc1refChr2 92477 11 + 144309 TCCAGGAGAAG -s Anc2.Anc2refChr3 2356 11 + 53186 TAGAGGAGAAG -s mr.mrrefChr0 115951 11 + 130230 TCCAGGAGGAA -s simCow_chr6.simCow.chr6 125136 11 + 602619 TAGAGGAGAGG -s simDog_chr6.simDog.chr6 413452 11 - 593897 TAGACAAGAAG -s simHuman_chr6.simHuman.chr6 116620 11 + 601863 TCCAGGAGAAG -s simRat_chr6.simRat.chr6 113859 11 + 647215 TCTATGAGGGA - -a -s simMouse_chr6.simMouse.chr6 121414 23 + 636262 TCCCTTGCAGCATAGTGACAACT -s Anc0.Anc0refChr1 14045 23 - 62388 TCCCTCCAAGTACAGCAACAATT -s Anc1.Anc1refChr2 92488 23 + 144309 TCCCTCCAAGTACAGCAACAATT -s Anc2.Anc2refChr3 2367 23 + 53186 TCCTTCCAAGTACAGCAACAATT -s mr.mrrefChr0 115962 23 + 130230 TCCCTCGAAGTACAGTGACAACT -s simCow_chr6.simCow.chr6 125147 23 + 602619 CCCTGCCAAGTACAGCAATAGTT -s simDog_chr6.simDog.chr6 413464 23 - 593897 TCCTTCAAAGTAAGGCAACAATT -s simHuman_chr6.simHuman.chr6 116631 23 + 601863 TCCCTCCAAGTACAGCAACAATT -s simRat_chr6.simRat.chr6 113870 23 + 647215 TCCCTCAAGGTGCAGTGACAACT - -a -s simMouse_chr6.simMouse.chr6 121437 10 + 636262 TCTCAACATG -s Anc0.Anc0refChr1 14069 10 - 62388 TCCCAACGGG -s Anc1.Anc1refChr2 92512 10 + 144309 TCCCAACGGG -s Anc2.Anc2refChr3 2391 10 + 53186 TCCCAACGGG -s mr.mrrefChr0 115985 10 + 130230 TCTCAACAGG -s simCow_chr6.simCow.chr6 125171 10 + 602619 CCCTAATGGG -s simDog_chr6.simDog.chr6 413488 10 - 593897 TCCCAACAGG -s simHuman_chr6.simHuman.chr6 116655 10 + 601863 TCCCAACGGG -s simRat_chr6.simRat.chr6 113893 10 + 647215 TCTCAACAGG - -a -s simMouse_chr6.simMouse.chr6 121447 20 + 636262 ATGTGTACAGCCAGCATAGC -s Anc0.Anc0refChr1 14085 15 - 62388 AAGTGTAA-----GTCCAGC -s Anc1.Anc1refChr2 92528 15 + 144309 AAGTGTAA-----GTCCAGC -s Anc2.Anc2refChr3 2407 15 + 53186 AATTATAA-----ATCCACC -s mr.mrrefChr0 115995 20 + 130230 ATGTGTACAGCCAGCATAGC -s simCow_chr6.simCow.chr6 125187 15 + 602619 AATTATAC-----ATCCACC -s simDog_chr6.simDog.chr6 413504 15 - 593897 AATTATAA-----ATCCACC -s simHuman_chr6.simHuman.chr6 116671 15 + 601863 AGGTGTAT-----GTCCTGC -s simRat_chr6.simRat.chr6 113903 20 + 647215 GTGGGTACAGCCATCATAGA - -a -s simMouse_chr6.simMouse.chr6 121467 38 + 636262 ATATAAAAGCTTGATATGAAAACATGGCTTAATTATAT -s Anc0.Anc0refChr1 14100 9 - 62388 ATATAAAAG----------------------------- -s Anc1.Anc1refChr2 92543 9 + 144309 ATATAAAAG----------------------------- -s Anc2.Anc2refChr3 2422 9 + 53186 ATATAAAAG----------------------------- -s mr.mrrefChr0 116015 35 + 130230 ATATAAAAGCTTGATAT---AACATGGCTTAATTATAT -s simCow_chr6.simCow.chr6 125202 9 + 602619 ACATAAAGG----------------------------- -s simDog_chr6.simDog.chr6 413525 9 - 593897 ATATAAAAG----------------------------- -s simHuman_chr6.simHuman.chr6 116686 9 + 601863 ATATAAAAG----------------------------- -s simRat_chr6.simRat.chr6 113923 35 + 647215 GTATAAAACCTTGATAT---CACATGGCTTAGTTATAT - -a -s simMouse_chr6.simMouse.chr6 121505 148 + 636262 TTATTACCACAGCACTTCATCCATTTAATGACCTGGAGCTACCTTTGGCGTTCCAACCCTGAATAGCACATTTTCATATTATTTCCTGTATTAGGTCTTATCAAGCTGTGCTAGGTCTTATCATCCGTTAACACAGACAGTTGTATTG -s mr.mrrefChr0 116050 126 + 130230 TTATTACCACAGCACTTCATCCATTTAATGACCTGGAGCTACCTTTGGCGTTCCAACCCTGAATAGCACA--TTCATATTATTTCCTGTA--------------------CTAGGTCTTATCATCCGTTAACACAGACAGTTGTATTG -s simRat_chr6.simRat.chr6 113961 126 + 647215 TTATGAACATGGCGCTTCATCGATCTAATAACCTGGAGGTAGCTTTGGTGTTTCAACCCTGAATAGCACG--TTCATCTTATTTCTTGTC--------------------CTAGGTCTTGTCATCAGTTAAGACAGGGAGTTGTATGG - -a -s simMouse_chr6.simMouse.chr6 121653 60 + 636262 TGAGCCTCCAGGAGATCTGCAGTATTTACGCATAACAATGTATAGACATGCTGCTATTGA -s mr.mrrefChr0 116176 60 + 130230 TGAGCCTCCAGGAGATCTGCAGTATTTACGCATAACAATGTATAGACATGCTGCTATTGA -s simRat_chr6.simRat.chr6 114093 60 + 647215 GGAGCCTCCAGGAGACCTGCAGTATTTTCACATAGCAATGTGTAGACATGCTGCTATTGA - -a -s simMouse_chr6.simMouse.chr6 121713 21 + 636262 CTGTCTGGCTCAGGTATGATG -s mr.mrrefChr0 116236 21 + 130230 CTGTCTGGCTCAGGTATGATG -s simRat_chr6.simRat.chr6 114154 21 + 647215 CTGTCTGGCTCAGGTATGGTG - -a -s simMouse_chr6.simMouse.chr6 121734 364 + 636262 GTTTCTAAGATTCATACTTGGTTCGGGCCTATTAGTTATTTGTGCACTTTGGCATGCTGCTCTGTGTGTTGACTATATCATAAGACATTATACCAACCAAAAAGGATAGCCTCTGTTGTGCTTCTTTGTCACTATCTCATCCTAACTGTGTGAAAGTAATTGTTAGAGATCACCTAGGCATACATATAAGTCTTCGCACCTGTTTCATTCTCTTGGTGATCCCAATGAGCAAAGGTTGAGGCTACAAAGTGCCACTCTACATATTGATAAGAGACTCCATTAATTCTTCCTGAGGTTTCCATTGATGACAAGGATGATTGTTTTTCTCTTTTATTTTTGACTTGATCATTGGGAACAATAATGG -s Anc0.Anc0refChr1 14109 2 - 62388 --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GG -s Anc1.Anc1refChr2 92552 2 + 144309 --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GG -s Anc2.Anc2refChr3 2431 2 + 53186 --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GG -s mr.mrrefChr0 116257 357 + 130230 GTTTCTAAGATTCATACTTGGTTCGGGCCTATTAGTTATTTGTGCACTTTGGCATGCTGCTCTGTGTGTTGACTATATCATAAGACATTAT----ACCAAAAAGGATAGCCTCTGTTGTGCTTCTTTGTCACTATCTCATCCTAACTGTGTGAAAGTAATTGTTAGAGATCACCTAGGCATACATATAAGTCTTCGCACCTGTTTCATTCTCTTGGTGATCCCAATGAGCAAAGGTT---GCTACAAAGTGCCACTCTACATATTGATAAGAGACTCCATTAATTCTTCCTGAGGTTTCCATTGATGACAAGGATGATTGTTTTTCTCTTTTATTTTTGACTTGATCATTGGGAACAATAATGG -s simCow_chr6.simCow.chr6 125211 2 + 602619 --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GA -s simDog_chr6.simDog.chr6 413534 2 - 593897 --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AG -s simHuman_chr6.simHuman.chr6 116695 2 + 601863 --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GG -s simRat_chr6.simRat.chr6 114178 357 + 647215 GTTTTTAAGATTCATACTTGGTTTGAGCCTATTAGTTATTAGTGCACTTGGGCAGGCTGCTCTGTGTGTTGACTACATGATTAGTGATTAT----GCCAAAAAAAATAGCCTCTTTTGTGCTTTGTTGGCATTATTTCATCCTGACTGTGCAAGAGTAGTACTTAGAAATCATGTAGACATACATATAAGTCTTCTGAACTGTTTCACCCTCTTGGTGACCCCGATGAGCAAAGGTT---GCAACTAAGTGCCACTCTGCAGATTGATAACAGACCCCATTAAACCTTCCTGAGGTTTCCATTGATGTCAAGAGTGATTTTTTTCCTCTTTTATATTTGATGTCTTTAGCTTAGTTGTCCTTGG - -a -s simMouse_chr6.simMouse.chr6 122098 10 + 636262 CCTTATTTAG -s Anc0.Anc0refChr1 14466 9 - 62388 CCTTATTTA- -s Anc1.Anc1refChr2 92909 10 + 144309 CCTTATTTAG -s Anc2.Anc2refChr3 2800 9 + 53186 CCATAATTA- -s mr.mrrefChr0 116614 10 + 130230 CCTTATTTAG -s simCow_chr6.simCow.chr6 125588 9 + 602619 CCATAATTA- -s simHuman_chr6.simHuman.chr6 117106 10 + 601863 CCTTTTCCAG -s simRat_chr6.simRat.chr6 114535 10 + 647215 GCTTAGTTAC - -a -s simMouse_chr6.simMouse.chr6 122108 1 + 636262 A -s Anc0.Anc0refChr1 14475 1 - 62388 A -s Anc1.Anc1refChr2 92919 1 + 144309 A -s Anc2.Anc2refChr3 2809 1 + 53186 A -s mr.mrrefChr0 116624 1 + 130230 A -s simCow_chr6.simCow.chr6 125597 1 + 602619 A -s simHuman_chr6.simHuman.chr6 117116 1 + 601863 A -s simRat_chr6.simRat.chr6 114550 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 122109 32 + 636262 CTTGATCATTGGGAACAATAATGGCCTTATTT -s Anc0.Anc0refChr1 14476 32 - 62388 CCTAGTCCTTGGGAACAACAATGACCATACTT -s Anc1.Anc1refChr2 92920 32 + 144309 CCTAGTCCTTGGGAACAACAATGACCATACTT -s Anc2.Anc2refChr3 2810 32 + 53186 CCTAGTTCTTGGGAACAACAACGAACATACTT -s mr.mrrefChr0 116625 32 + 130230 CCTGGTCATTGGGAACAATAATGGCCTTACTT -s simCow_chr6.simCow.chr6 125598 32 + 602619 CCTAGTTCTTGGGAACAACAACGAGCATGCTT -s simDog_chr6.simDog.chr6 413899 9 - 593897 -----------------------AACTTACTT -s simHuman_chr6.simHuman.chr6 117122 32 + 601863 CCTAGTCCTTGGGAACAGCAATGACCATACTT -s simRat_chr6.simRat.chr6 114551 32 + 647215 CCTGGTCATTGGGAACAATAATGGCCTGACTT - -a -s simMouse_chr6.simMouse.chr6 122141 67 + 636262 AAAAATATTTCAGGGGCTATCAAGTTCTACAAATTGACCCATATTAGCCCAATATGCTGCACATCAT -s Anc0.Anc0refChr1 14509 67 - 62388 AAAAATATTTAGAGGGCCATCAAGTTCTGCAAGTTGAGCCATATCAACCCAGTATATTGCACATCGC -s Anc1.Anc1refChr2 92953 67 + 144309 AAAAATATTTAGAGGGCCATCAAGTTCTGCAAGTTGAGCCATATCAACCCAGTATATTGCACATCGC -s Anc2.Anc2refChr3 2843 67 + 53186 AAAAATATTTTGAGGGCCATTAGGTTCTGGAAGTTGAGCCGTATCAACCCAGCATATTGCACATTGC -s mr.mrrefChr0 116658 67 + 130230 AAAAATATTTAAGGGGCTATCAAGTTCTACAAGTTGACCCATATCAGCCCAATATGCTGCACATCGC -s simCow_chr6.simCow.chr6 125631 67 + 602619 AAAAATATTTTGCAAGCTGTTATGTTCTGCATGTTGAGCCGTATCATCACAGCACATTCCACCCAGC -s simDog_chr6.simDog.chr6 413909 67 - 593897 AAAAATGTTTTGAGGGCCATTGGGTCCTGGAAGTCGAACCGTTTCAACCTAGCATATTGCACATTGC -s simHuman_chr6.simHuman.chr6 117155 64 + 601863 AAGAATATTTA--GGGCCATCAAGTTCTGC-AGTTGAGCCATATCAACCCAGTGTATTGCACATCGC -s simRat_chr6.simRat.chr6 114584 67 + 647215 AAAAACACTTAAGGGGCTGTCAAATTCTACAAGTTGACCCATATCAGCCCAATATGCTTCAACTTGC - -a -s simMouse_chr6.simMouse.chr6 122208 41 + 636262 GTAAGTTATTTCCAGTAGGCGATTATGTTGCCAATAGGCAG -s Anc0.Anc0refChr1 14576 40 - 62388 AT-ATTCATTTACTGTGTGTGGTTGTCTTGCCAATATGCAG -s Anc1.Anc1refChr2 93020 40 + 144309 AT-ATTCATTTACTGTGTGTGGTTGTCTTGCCAATATGCAG -s Anc2.Anc2refChr3 2910 40 + 53186 AT-ATTCATTTGCTGTGTGTGGTTGTCTTACAAATATGCAG -s mr.mrrefChr0 116725 41 + 130230 ATAAGTTATTTACAGTATGTGATTATCTTGCCAATAGGCAG -s simCow_chr6.simCow.chr6 125698 40 + 602619 AT-ATCCATTTGCTGTGTGTGGCTAAGTTCCTAATATGCAG -s simDog_chr6.simDog.chr6 413980 40 - 593897 AT-ATTAATTTGTTGTGTGTGGTTGTCTTACAAATATGCAC -s simHuman_chr6.simHuman.chr6 117219 40 + 601863 AT-GTTCATTTACTGTGTATGGTTGCCGTGCCAATATGCAG -s simRat_chr6.simRat.chr6 114651 41 + 647215 ATAAGTTATTTACAGTATGTGATTATCTCTCCAGTAGGCAG - -a -s simMouse_chr6.simMouse.chr6 122249 32 + 636262 CAAAATCACCGGGTTCTTTGGTTTAGACACAT -s Anc0.Anc0refChr1 14616 32 - 62388 TAGCATCCCAGGGCTCTTTGGTTTGGACTTAT -s Anc1.Anc1refChr2 93060 32 + 144309 TAGCATCCCAGGGCTCTTTGGTTTGGACTTAT -s Anc2.Anc2refChr3 2950 32 + 53186 TGGCATCCCAGGACTCTTTGGTTTGGACTTAT -s mr.mrrefChr0 116766 32 + 130230 CAAAATCCCCGGGTTCTTTGGTTTAGACACAT -s simCow_chr6.simCow.chr6 125738 32 + 602619 TGGCATCCCAGGTCTCTTTGGTTTAGACAAAT -s simDog_chr6.simDog.chr6 414020 32 - 593897 TGGCATCCCAGTACTTTTTGGTTTGGACTTAT -s simHuman_chr6.simHuman.chr6 117273 32 + 601863 TAGGATCCCATGGCTCTTTGGTATGGACGTAT -s simRat_chr6.simRat.chr6 114692 32 + 647215 CTAAACCCCCAGGTTCTTTTGTTTAGACACAT - -a -s simMouse_chr6.simMouse.chr6 122281 26 + 636262 TGGGATGAGGTTGAACATCAGCCGTA -s Anc0.Anc0refChr1 14656 25 - 62388 AGTAGTGAGGTAAAACATGAG-TATA -s Anc1.Anc1refChr2 93100 25 + 144309 AGTAGTGAGGTAAAACATGAG-TATA -s Anc2.Anc2refChr3 2990 25 + 53186 AGTAGTGAGATAAAACATGAG-TATA -s mr.mrrefChr0 116806 26 + 130230 TGGGATGAGGTTGAACATGAGCTGTA -s simCow_chr6.simCow.chr6 125778 25 + 602619 AGCAGTGAGATGAATAATGAG-TATA -s simDog_chr6.simDog.chr6 414058 25 - 593897 AGTAGTCTGATAAGACATGTG-TATA -s simHuman_chr6.simHuman.chr6 117313 25 + 601863 AGTAGTGAGGTAAAACCTGAG-TATA -s simRat_chr6.simRat.chr6 114732 26 + 647215 TGGGATGAAGTTGAACATGAGCTGTG - -a -s simMouse_chr6.simMouse.chr6 122307 13 + 636262 AAGGAAGTGAGCT -s Anc0.Anc0refChr1 14687 13 - 62388 AAGGAAGTGTAAT -s Anc1.Anc1refChr2 93131 13 + 144309 AAGGAAGTGTAAT -s Anc2.Anc2refChr3 3021 13 + 53186 AAGGAAGTGTAAT -s mr.mrrefChr0 116832 13 + 130230 AAGGAAGTGAGAT -s simCow_chr6.simCow.chr6 125809 13 + 602619 ATGGAAGTGTAAT -s simDog_chr6.simDog.chr6 414088 13 - 593897 CAGAAAGTGTAAT -s simHuman_chr6.simHuman.chr6 117344 13 + 601863 AGGGGAGTGTAAT -s simRat_chr6.simRat.chr6 114758 13 + 647215 CAGGAAGTGAGAT - -a -s simMouse_chr6.simMouse.chr6 122320 45 + 636262 ACTTGGCCCATCGAAGAATTGTGCTTTTAATGCACAATAAAGCAT -s Anc0.Anc0refChr1 14700 45 - 62388 TCCTGGCCCATGGGTAATTCGCACTTTTAATGCACTCTTAGGCAT -s Anc1.Anc1refChr2 93144 45 + 144309 TCCTGGCCCATGGGTAATTCGCACTTTTAATGCACTCTTAGGCAT -s Anc2.Anc2refChr3 3034 45 + 53186 TCCTGGCCCATGGGTAATTCTCACTACCAATGCACTCTTGGGCAT -s mr.mrrefChr0 116845 45 + 130230 ACTTGGCCCATCGAAGATTTGTGCTTTTAATGCACAATAAAGCAT -s simCow_chr6.simCow.chr6 125825 45 + 602619 TCTTGTCCCATGAGTAATTCTCACTACCAATGGACTCTTGGGCAT -s simDog_chr6.simDog.chr6 414101 38 - 593897 TCCTGGCCCATGGGTATATCTCACT-------CACTCTTGGGCAT -s simHuman_chr6.simHuman.chr6 117357 45 + 601863 CCCTAGCCCATGGGTAATCCGCACTTTTAATGCACGCTCAGTCAT -s simRat_chr6.simRat.chr6 114771 45 + 647215 ACTTGGCCCATTGAATATTTGTGCTTTTAATGCACAATAAAGCAT - -a -s simMouse_chr6.simMouse.chr6 122365 36 + 636262 GCTCCAAGTAGTTCAAGAATGGCTATTTTATCCTAT -s Anc0.Anc0refChr1 14746 33 - 62388 TCACCAAGTAGTT---GAATTGATATCTGAACTTTT -s Anc1.Anc1refChr2 93190 33 + 144309 TCACCAAGTAGTT---GAATTGATATCTGAACTTTT -s Anc2.Anc2refChr3 3080 33 + 53186 TCACCAAGTAGTT---GAAATGATATCTGAATTTTT -s mr.mrrefChr0 116891 36 + 130230 GCTCCAAGTAGTTCAAGAATGGCTATTTTATCCTAT -s simCow_chr6.simCow.chr6 125871 33 + 602619 TCACCAAGTAGGT---GAAATGATATCTAAATTTTT -s simDog_chr6.simDog.chr6 414140 33 - 593897 TCACCAAGTAGTA---GAAATGATATCTGAATTTTT -s simHuman_chr6.simHuman.chr6 117403 33 + 601863 TCACTAAGTAGTT---GAATTGATGTCTCCCCTTTT -s simRat_chr6.simRat.chr6 114817 36 + 647215 GGTCCAAGTAGTTCAGTAATGGCTATTTTTTCCTAT - -a -s simMouse_chr6.simMouse.chr6 122401 46 + 636262 AGATTTTATTGGAGCTCCTGCATTAAGCTTAACAAAACCAGATGTG -s Anc0.Anc0refChr1 14781 46 - 62388 AAGTTTTATTTCAACTATAGCATAAAAGTTAAAGAGATCGGATGTG -s Anc1.Anc1refChr2 93225 46 + 144309 AAGTTTTATTTCAACTATAGCATAAAAGTTAAAGAGATCGGATGTG -s Anc2.Anc2refChr3 3115 46 + 53186 AAGTTTTATTTCAACTATAGCATAAAAGTTAAAGAGATCGGATGTG -s mr.mrrefChr0 116927 46 + 130230 AGATTTTATTGGAACTCCTGCATTAAACTTAACGAAACCAGATGTG -s simCow_chr6.simCow.chr6 125906 46 + 602619 GAGTTTAACATCAACTATAGCATCAAAGTTAAAGAGATGGGAAGGG -s simDog_chr6.simDog.chr6 414175 46 - 593897 AAGTCTTTTTTCAACTATAGCGTAGTAGGTAGAGAGATCAGATGTG -s simHuman_chr6.simHuman.chr6 117439 46 + 601863 AAGTTTTATTCCAACTATAGCATAAAATTTAAAGTGAGTGGACATG -s simRat_chr6.simRat.chr6 114853 46 + 647215 AGATTTTATTTGAACTCCTGCATTACACTTTATGAAACCAGATGTG - -a -s simMouse_chr6.simMouse.chr6 122447 39 + 636262 CCAACCATGATAATGATATGTAAGGTTGGTGGGTACCGT -s Anc0.Anc0refChr1 14827 39 - 62388 CTAACTATGATAATGATATATAAGCTTGGTGGTCTTGGC -s Anc1.Anc1refChr2 93271 39 + 144309 CTAACTATGATAATGATATATAAGCTTGGTGGTCTTGGC -s Anc2.Anc2refChr3 3165 39 + 53186 CTAACTATGATAATGATATATAAGCTTGGTGGTCTTGGC -s mr.mrrefChr0 116973 39 + 130230 CTAACCATGATAATGATATGTAAGGTTGGTGGGTTCCGT -s simCow_chr6.simCow.chr6 125956 39 + 602619 TTGACTATGATAAAAATATGTAAGTCCGGTGGTCTTGGC -s simDog_chr6.simDog.chr6 414225 39 - 593897 CAAACCATGATAATGATATATAAGCTTGGCAGTCTTGCC -s simHuman_chr6.simHuman.chr6 117485 39 + 601863 CTAACTATAATAATGTTATATAAGCTTGCTGGACTTGGC -s simRat_chr6.simRat.chr6 114899 39 + 647215 CTAACCAGGATAATGATATGTAAGATTGGTAGGTTCTGT - -a -s simMouse_chr6.simMouse.chr6 122486 60 + 636262 ACTGTAAGTGCGTATCAAACACTGATGGCTTTTGCAAAGATTAGGATTCGCAATCTGTCA -s Anc0.Anc0refChr1 14870 56 - 62388 GCTGTGAGCC--CATCAAA--GTGATGGCTCTTGCAAAGATTAGGATATGCTATGTGGGA -s Anc1.Anc1refChr2 93314 60 + 144309 GCTGTGAGCCAGCATCAAACAGTGATGGCTCTTGCAAAGATTAGGATATGCTATGTGGGA -s Anc2.Anc2refChr3 3208 56 + 53186 GCTGTGAGCC--CATCAGG--GTGATGGCTCTTGCAAAGATTATGATATGCTCTGTGGGA -s mr.mrrefChr0 117016 60 + 130230 ACTGTAAGTGCGTATCAAACACTGATGGCTTTTGCAAAGATTAGGATTCGCAATCTGTCA -s simCow_chr6.simCow.chr6 125999 56 + 602619 GTTGTAAGCC--CATAATA--GTGAAGGCTCTTGTAAAGATTATGATATGCTCTGTGGCA -s simDog_chr6.simDog.chr6 414268 56 - 593897 GCTGTGAGCC--CATCAGG--GTGATGGCTCTAACAAAGATTATGATATGCTCTGTGGGA -s simHuman_chr6.simHuman.chr6 117528 60 + 601863 GCTGTGAGCCAGGAACAAACAGTGGCGGCACTTGCAAAAAGTAGGATATGCGAGGTTATA -s simRat_chr6.simRat.chr6 114942 60 + 647215 ACTGTAAGTGTATATCAAACACTGATGGCTTATGCAAAGATTAGGATTCGCAATCTGTCA - -a -s simMouse_chr6.simMouse.chr6 122546 31 + 636262 TCCTGGAACCTAGGAAAGTGGCACACCCTGC -s Anc0.Anc0refChr1 14926 31 - 62388 TCTTGGACCCTGGTAGAATGGAACACCATGC -s Anc1.Anc1refChr2 93374 31 + 144309 TCTTGGACCCTGGTAGAATGGAACACCATGC -s Anc2.Anc2refChr3 3264 31 + 53186 TCTTGGACCATGGTAGAATAGAACACCATGC -s mr.mrrefChr0 117076 31 + 130230 TCCTGGAACCTAGGAAAGTGGCACACCCTGC -s simCow_chr6.simCow.chr6 126055 31 + 602619 TATTGGGCCTGGGTAGAATAGTACATCATGA -s simDog_chr6.simDog.chr6 414324 31 - 593897 TCTTGGATCATGGCAGAATAGATTACCATGC -s simHuman_chr6.simHuman.chr6 117588 31 + 601863 TCTTGAACCCTGCTAGAATGGAACACCATGC -s simRat_chr6.simRat.chr6 115006 30 + 647215 TCCTGGAAC-TAGGAAAGTGGGACACCCTGC - -a -s simMouse_chr6.simMouse.chr6 122577 29 + 636262 TAAACTATTGTGTTGTGCCTTTTACCATG -s Anc0.Anc0refChr1 14957 21 - 62388 TGAACTACAGTG-TGCACCC-------AG -s Anc1.Anc1refChr2 93405 28 + 144309 TGAACTACAGTG-TGCACCCTGCACCCAG -s Anc2.Anc2refChr3 3296 21 + 53186 TGAACTTCAGTG-TGCACCC-------AG -s mr.mrrefChr0 117107 29 + 130230 TAAACTATTGTGTTGTGCCTTTTACCATG -s simCow_chr6.simCow.chr6 126087 21 + 602619 TGAACTGAAGTA-TGCCCCC-------CG -s simDog_chr6.simDog.chr6 414356 21 - 593897 TCAATTTCAGTG-TGCACTC-------AG -s simHuman_chr6.simHuman.chr6 117619 28 + 601863 TGAACTACAGTG-TGCACCCTGCACCCAG -s simRat_chr6.simRat.chr6 115036 29 + 647215 TAAACTATTGTGTTGTGCCTTTTACCACG - -a -s simMouse_chr6.simMouse.chr6 122606 4 + 636262 ACCA -s Anc0.Anc0refChr1 14990 4 - 62388 AACA -s Anc1.Anc1refChr2 93445 4 + 144309 AACA -s Anc2.Anc2refChr3 3329 4 + 53186 AACA -s mr.mrrefChr0 117136 4 + 130230 AACA -s simCow_chr6.simCow.chr6 126120 2 + 602619 AA-- -s simDog_chr6.simDog.chr6 414389 4 - 593897 AACA -s simHuman_chr6.simHuman.chr6 117659 4 + 601863 AACA -s simRat_chr6.simRat.chr6 115065 4 + 647215 AACA - -a -s simMouse_chr6.simMouse.chr6 122610 15 + 636262 TATAGATAGTAAAAT -s Anc0.Anc0refChr1 14994 15 - 62388 TATACATGGCAAAAA -s Anc1.Anc1refChr2 93449 15 + 144309 TATACATGGCAAAAA -s Anc2.Anc2refChr3 3337 15 + 53186 CACACATGGCAAAGA -s mr.mrrefChr0 117140 15 + 130230 TATAGATAGCAAAAA -s simCow_chr6.simCow.chr6 126122 14 + 602619 -ACACATGGCTATGG -s simDog_chr6.simDog.chr6 414397 15 - 593897 CACACATAGTAGAGA -s simHuman_chr6.simHuman.chr6 117663 15 + 601863 TGTACATGGCAAAAA -s simRat_chr6.simRat.chr6 115069 15 + 647215 TATATATAGCAAAAA - -a -s simMouse_chr6.simMouse.chr6 122625 21 + 636262 CGAACCCCCTTCTTGAAAACC -s Anc0.Anc0refChr1 15010 21 - 62388 TGTGCCCCCTTCTTTCGAACA -s Anc1.Anc1refChr2 93465 21 + 144309 TGTGCCCCCTTCTTTCGAACA -s Anc2.Anc2refChr3 3353 21 + 53186 TGTGCTCCCTTCTTTCGAAGA -s mr.mrrefChr0 117155 21 + 130230 TGAGCCCCCTTCTTGAAAACC -s simCow_chr6.simCow.chr6 126137 21 + 602619 TGTGCTCCCTTCTTTCAAAGA -s simDog_chr6.simDog.chr6 414413 21 - 593897 CATGCTCCCTTCTTTCGAAGA -s simHuman_chr6.simHuman.chr6 117679 21 + 601863 TGTGCCCCCCTCTTTTGAGCT -s simRat_chr6.simRat.chr6 115084 21 + 647215 TGAGCCCCCTTCTTGGAAACC - -a -s simMouse_chr6.simMouse.chr6 122646 3 + 636262 CCA -s Anc0.Anc0refChr1 15032 3 - 62388 CCT -s Anc1.Anc1refChr2 93487 3 + 144309 CCT -s Anc2.Anc2refChr3 3375 3 + 53186 CCT -s mr.mrrefChr0 117176 3 + 130230 CCA -s simCow_chr6.simCow.chr6 126159 3 + 602619 CCT -s simDog_chr6.simDog.chr6 414435 3 - 593897 CCT -s simHuman_chr6.simHuman.chr6 117701 3 + 601863 CCC -s simRat_chr6.simRat.chr6 115105 3 + 647215 CCA - -a -s simMouse_chr6.simMouse.chr6 122649 23 + 636262 TAAGCCAACTGGCATTCATTAGA -s Anc0.Anc0refChr1 15035 23 - 62388 TAAGCCAAGGGGTATGCATTAGG -s Anc1.Anc1refChr2 93490 23 + 144309 TAAGCCAAGGGGTATGCATTAGG -s Anc2.Anc2refChr3 3378 23 + 53186 TAAGCCAAGGGGTATGCATAAGG -s mr.mrrefChr0 117179 23 + 130230 TAAGCCAACTGGCATTCATTAGA -s simCow_chr6.simCow.chr6 126162 23 + 602619 TAAGCCAAGTGGTATACATAGGG -s simDog_chr6.simDog.chr6 414516 23 - 593897 TAAGCCAAAGGGTGTGTGTAAGC -s simHuman_chr6.simHuman.chr6 117704 23 + 601863 TAAGCTGAGCGGTATGCATTAGG -s simRat_chr6.simRat.chr6 115108 23 + 647215 TAAGGCAACTGGCATTCATTGGA - -a -s simMouse_chr6.simMouse.chr6 122672 12 + 636262 CGACCATCTTAT -s Anc0.Anc0refChr1 15060 12 - 62388 CCAACATCTTGT -s Anc1.Anc1refChr2 93515 12 + 144309 CCAACATCTTGT -s Anc2.Anc2refChr3 3403 12 + 53186 CCAATGTCTTGT -s mr.mrrefChr0 117202 12 + 130230 CGACCATCTTAT -s simCow_chr6.simCow.chr6 475857 12 - 602619 CCTCTCTCTTGT -s simDog_chr6.simDog.chr6 414541 12 - 593897 CCAATGTCTTGT -s simHuman_chr6.simHuman.chr6 117729 12 + 601863 CCAACATCTTCT -s simRat_chr6.simRat.chr6 115131 12 + 647215 CAACCATCTTGT - -a -s simMouse_chr6.simMouse.chr6 122684 9 + 636262 CTTATAGGT -s Anc0.Anc0refChr1 15072 9 - 62388 TTCATAGCA -s Anc1.Anc1refChr2 93527 9 + 144309 TTCATAGCA -s Anc2.Anc2refChr3 3415 9 + 53186 TTCACAGCA -s mr.mrrefChr0 117214 9 + 130230 CTTATAGGT -s simCow_chr6.simCow.chr6 475871 9 - 602619 TTCAGAGCA -s simDog_chr6.simDog.chr6 414553 9 - 593897 CTCCCAGCA -s simHuman_chr6.simHuman.chr6 117741 9 + 601863 TTCATAGCA -s simRat_chr6.simRat.chr6 115143 9 + 647215 CTTACAGGT - -a -s simMouse_chr6.simMouse.chr6 122693 15 + 636262 TGGGCCTTTTGTGTC -s Anc0.Anc0refChr1 15081 15 - 62388 TGGTCCTTTGTGATT -s Anc1.Anc1refChr2 93536 15 + 144309 TGGTCCTTTGTGATT -s Anc2.Anc2refChr3 3424 15 + 53186 TGGTCCTTTGTGATT -s mr.mrrefChr0 117223 15 + 130230 TGGGCCTTTTGTGTT -s simCow_chr6.simCow.chr6 475881 15 - 602619 TGATTCCTTGTGGCT -s simDog_chr6.simDog.chr6 414562 15 - 593897 TGGCCCTTTGTGATT -s simHuman_chr6.simHuman.chr6 117750 15 + 601863 TGGTCCTATGCAATT -s simRat_chr6.simRat.chr6 115152 15 + 647215 TGGGCCTTTTGTGTT - -a -s simMouse_chr6.simMouse.chr6 122708 47 + 636262 GTGGGACATAAGCTTCAGACTCCTCCTATGCTTGTATTATAAAGAGA -s Anc0.Anc0refChr1 15097 44 - 62388 CTGGGACACAAGCTTGAAATTTCTGCTGTGCTTG---GATGAAGATT -s Anc1.Anc1refChr2 93552 47 + 144309 CTGGGACACAAGCTTGAAATTTCTGCTGTGCTTGTATGATGAAGATT -s Anc2.Anc2refChr3 3440 44 + 53186 CCAAGATGCAAGCTTGAAGTTTCTGCTGTGCTTG---GATGAAGATT -s mr.mrrefChr0 117239 47 + 130230 CTGGGACATAAGCTTCAGACTCCTGCTATGCTTGTATTATAAAGAGA -s simCow_chr6.simCow.chr6 475897 40 - 602619 ----GGTGCAAGCTTGAAGTTTCTGCTGTGCTGG---TACAAAGATT -s simDog_chr6.simDog.chr6 414578 44 - 593897 CCAAGATGCGAGCTAGGAGTTTCTGCTGTGCTTG---GATGTAGCTT -s simHuman_chr6.simHuman.chr6 117766 47 + 601863 CTGGGACACAGCCTTGAAATTTCTGCTGTGCTTGTATGGTGAAGACT -s simRat_chr6.simRat.chr6 115168 47 + 647215 CTTGGATGTAAGCTTCAGTCTGCTGCTATTCTTGTGTTATAAAGAGA - -a -s simMouse_chr6.simMouse.chr6 122755 3 + 636262 TCT -s Anc0.Anc0refChr1 15141 3 - 62388 TCT -s Anc1.Anc1refChr2 93599 3 + 144309 TCT -s Anc2.Anc2refChr3 3484 3 + 53186 TCT -s mr.mrrefChr0 117286 3 + 130230 TCT -s simCow_chr6.simCow.chr6 475937 3 - 602619 TCT -s simDog_chr6.simDog.chr6 414622 3 - 593897 TCT -s simHuman_chr6.simHuman.chr6 117813 3 + 601863 TCC -s simRat_chr6.simRat.chr6 115251 3 + 647215 TCT - -a -s simMouse_chr6.simMouse.chr6 122758 10 + 636262 TCTTTTCAGC -s Anc0.Anc0refChr1 15177 10 - 62388 TCTCTTCAGC -s Anc1.Anc1refChr2 93635 10 + 144309 TCTCTTCAGC -s Anc2.Anc2refChr3 3528 10 + 53186 TTTCTCCAGC -s mr.mrrefChr0 117289 10 + 130230 TCTTTTCAGC -s simCow_chr6.simCow.chr6 475987 10 - 602619 TTTCTCAAGC -s simDog_chr6.simDog.chr6 414666 10 - 593897 TTTCTCCAGA -s simHuman_chr6.simHuman.chr6 117849 10 + 601863 TCTCGTCAGC -s simRat_chr6.simRat.chr6 115254 10 + 647215 TCCTTTCAGC - -a -s simMouse_chr6.simMouse.chr6 122768 56 + 636262 ATTTAGAGGTAAAACATTGTGCTAACAAAGGCAATACCATTGATGAATGTTTTAGT -s Anc0.Anc0refChr1 15187 56 - 62388 AATTAGTGGTAAAATATAGGGTGCACAAAAGCTGTGCCATTGACAAATGATTTACT -s Anc1.Anc1refChr2 93645 56 + 144309 AATTAGTGGTAAAATATAGGGTGCACAAAAGCTGTGCCATTGACAAATGATTTACT -s Anc2.Anc2refChr3 3538 56 + 53186 AATTAGTGGTAAAATATAGGGTGCACAAAAGCAGTGCTATTTACAAATGTTTTACT -s mr.mrrefChr0 117299 56 + 130230 ATTTAGAGGTAAAACATTGTGCTCACAAAGGCTATACCATTGATGAATGATTTAGT -s simCow_chr6.simCow.chr6 475998 56 - 602619 ATTTAGTGCTGAAATATAGGCTGCACAAAAGCAGGGCTGTTTACAAATGTTTTACT -s simDog_chr6.simDog.chr6 414676 56 - 593897 CATAAGTGGTAAAATATAGTGTGCATAAAAGCAGTTCTATTTACAACTGTTTTACT -s simHuman_chr6.simHuman.chr6 117859 56 + 601863 ACTTGGCAGTAAAATATAAGATGCACAGAATCTGTGCCATTGACAAATGATTTACT -s simRat_chr6.simRat.chr6 115264 55 + 647215 ATTTAGTGGTAAA-CATTGTGCCCACGAAGGCTATATCATTGATGAACGATTTAGT - -a -s simMouse_chr6.simMouse.chr6 122824 8 + 636262 CCCCTGTA -s Anc0.Anc0refChr1 15243 8 - 62388 GTTACTTA -s Anc1.Anc1refChr2 93701 8 + 144309 GTTACTTA -s Anc2.Anc2refChr3 3594 8 + 53186 GTTACTTT -s mr.mrrefChr0 117355 8 + 130230 CCCACGTA -s simCow_chr6.simCow.chr6 476054 8 - 602619 GTTACTTG -s simDog_chr6.simDog.chr6 414733 8 - 593897 ATGACTTT -s simHuman_chr6.simHuman.chr6 117915 8 + 601863 GTTACTTA -s simRat_chr6.simRat.chr6 115319 8 + 647215 CCCACGTA - -a -s simMouse_chr6.simMouse.chr6 122832 4 + 636262 GATA -s Anc0.Anc0refChr1 15277 4 - 62388 TAGG -s Anc1.Anc1refChr2 93735 4 + 144309 TAGG -s Anc2.Anc2refChr3 3628 4 + 53186 TAGG -s mr.mrrefChr0 117363 4 + 130230 GAGG -s simCow_chr6.simCow.chr6 476089 4 - 602619 TAGG -s simDog_chr6.simDog.chr6 414764 4 - 593897 CAGT -s simHuman_chr6.simHuman.chr6 117950 4 + 601863 TAGG -s simRat_chr6.simRat.chr6 115327 4 + 647215 GAGG - -a -s simMouse_chr6.simMouse.chr6 122836 5 + 636262 CAACC -s Anc0.Anc0refChr1 15281 1 - 62388 C---- -s Anc1.Anc1refChr2 93739 1 + 144309 C---- -s Anc2.Anc2refChr3 3632 1 + 53186 C---- -s mr.mrrefChr0 117367 1 + 130230 C---- -s simCow_chr6.simCow.chr6 476101 1 - 602619 T---- -s simDog_chr6.simDog.chr6 414768 1 - 593897 C---- -s simHuman_chr6.simHuman.chr6 117954 1 + 601863 C---- -s simRat_chr6.simRat.chr6 115331 1 + 647215 C---- - -a -s simMouse_chr6.simMouse.chr6 122841 53 + 636262 TACACAATTGTGGTGTCCTTATTGAAAGTTTGATCAAGGAAAATTTTGATCAA -s Anc0.Anc0refChr1 15282 47 - 62388 TTCTCAATGGTGGCCTCCATATTGAGATTGTCATCAAG-AA-----TGAAAAA -s Anc1.Anc1refChr2 93740 47 + 144309 TTCTCAATGGTGGCCTCCATATTGAGATTGTCATCAAG-AA-----TGAAAAA -s Anc2.Anc2refChr3 3637 47 + 53186 TTCTCCAAGGTGGGCTCCATATTGAGGTTGTCATCAAG-AA-----TGAAAAC -s mr.mrrefChr0 117368 52 + 130230 TACACAATTGTGGCGTCCTTATTGAGAGTTTGATCAAG-AAAATTTTGATCAA -s simCow_chr6.simCow.chr6 476106 46 - 602619 TTC-CTAACGTGGTCTCCATATTGAGCTCCTCATCAAG-AA-----TGAGCAC -s simDog_chr6.simDog.chr6 414773 47 - 593897 TTCTCCAAGGTGGGTTTCATATTGAGGTTGTCATCAAG-AA-----TGAAAAC -s simHuman_chr6.simHuman.chr6 117955 47 + 601863 TGTGCACTCATGGCCTCCATATTCAGATTGTAATGAGG-AA-----TGAAAAA -s simRat_chr6.simRat.chr6 115332 52 + 647215 TACACAATTGTGGCATCCTGATTGAGAGTTTGATCAAG-AAAATTTTGATCAA - -a -s simMouse_chr6.simMouse.chr6 122894 27 + 636262 GATGTGAGTGCAAAGCACTCACTATGG -s Anc0.Anc0refChr1 15333 27 - 62388 GATTTGAGCACAAAGCCTTCACTATAA -s Anc1.Anc1refChr2 93791 27 + 144309 GATTTGAGCACAAAGCCTTCACTATAA -s Anc2.Anc2refChr3 3688 27 + 53186 GAATTGAGCACAAGGCCTTCACTATAA -s mr.mrrefChr0 117420 27 + 130230 GATGTGAGTGCAAAGCACTCACTATGA -s simCow_chr6.simCow.chr6 476156 27 - 602619 GCCTTGAACACAGGGACTGCACTATAA -s simDog_chr6.simDog.chr6 414824 27 - 593897 GAACTGAGCACAAGGCCTTCACTATAA -s simHuman_chr6.simHuman.chr6 118006 27 + 601863 GGTTTAAGCACAAAGTGATCACTATAA -s simRat_chr6.simRat.chr6 115384 26 + 647215 GATGTGAGTGTAAATCATT-GCTATGA - -a -s simMouse_chr6.simMouse.chr6 122921 15 + 636262 GTTTTTAACTGACGC -s Anc0.Anc0refChr1 15360 15 - 62388 AATTTTAACTGACAC -s Anc1.Anc1refChr2 93818 15 + 144309 AATTTTAACTGACAC -s Anc2.Anc2refChr3 3715 15 + 53186 AATTTTAACTGACAC -s mr.mrrefChr0 117447 15 + 130230 GTTTTTAACTGACAC -s simCow_chr6.simCow.chr6 476183 13 - 602619 AATTTTAACTG--AC -s simDog_chr6.simDog.chr6 414852 15 - 593897 GATCTTAACTGACAT -s simHuman_chr6.simHuman.chr6 118033 15 + 601863 AATTTTAACTGATAC -s simRat_chr6.simRat.chr6 115410 15 + 647215 GTTCTTAACTGACAC - -a -s simMouse_chr6.simMouse.chr6 122936 80 + 636262 AACTTGGGTTGAGCTATTAAATACTACTCAAAAGATTTTAACTCTAACTCATGTGTTCCTTTGCACCAGGTGGAACTGTT -s Anc0.Anc0refChr1 15376 51 - 62388 GACTTTGGTGAA---TTTGAAC------------ATGCTGGCTTAAGCCCAGG--------------AGGTGGCTGTAGC -s Anc1.Anc1refChr2 93834 53 + 144309 GACTTTGGTGAA---TTTGAAC------------ATGCTGGCTTAAGCCCAGGGA------------AGGTGGCTGTAGC -s Anc2.Anc2refChr3 3731 51 + 53186 GACTTTGGTGAA---ATTGAAC------------ATGCTGGCTTAAGCCCAGG--------------ATGTGGCTGTAGC -s mr.mrrefChr0 117462 80 + 130230 AACTTGGGTGGAGCTTTTAAATACTACTCAAAAGATTTTAACTCTAACTCATGTGTTCCTTTGCACCAGGTGGAACTATT -s simCow_chr6.simCow.chr6 476197 51 - 602619 AATTTTGGTGAA---ATTGAAC------------ATGCTTGCTTAAGTCCAGG--------------ATGTAGCTGCAGC -s simDog_chr6.simDog.chr6 414868 51 - 593897 GACTTTAGTAAA---ATTGAAC------------ATGCTGGCTTTGGCACAGG--------------ATGTGGCTGTGGT -s simHuman_chr6.simHuman.chr6 118049 53 + 601863 GACCTTGGTGAA---TTTGAAC------------ATGCTCGCTTAAGCCCAGGGA------------AGGGGGCTGTAGC -s simRat_chr6.simRat.chr6 115425 80 + 647215 AACTCGGGTGGAGCTTTCCAATACTAATTAAAGGATTTTAACTCTAACTCATTTGTTCCTTTGCACCAGGTGGAACTATT - -a -s simMouse_chr6.simMouse.chr6 123016 18 + 636262 GAATACTAACTATAAGCT -s Anc0.Anc0refChr1 15427 18 - 62388 AACTAAAAAGTACTAGCT -s Anc1.Anc1refChr2 93887 18 + 144309 AACTAAAAAGTACTAGCT -s Anc2.Anc2refChr3 3805 18 + 53186 AACTAAAAAGTACTAGCT -s mr.mrrefChr0 117542 18 + 130230 GAATACTAACTATAAGCT -s simCow_chr6.simCow.chr6 476271 18 - 602619 CATTAAACAATCCTACAT -s simDog_chr6.simDog.chr6 414942 18 - 593897 AACTAAAAAGTACTAGCT -s simHuman_chr6.simHuman.chr6 118102 10 + 601863 CAGTA-----CGCTA--- -s simRat_chr6.simRat.chr6 115505 18 + 647215 GAATACCAATTAAAAGCT - -a -s simMouse_chr6.simMouse.chr6 123034 22 + 636262 TTAACTAATTTGTTCCTTTGAG -s Anc0.Anc0refChr1 15445 22 - 62388 CTACTCACCTTATTCCTTCAAA -s Anc1.Anc1refChr2 93905 22 + 144309 CTACTCACCTTATTCCTTCAAA -s Anc2.Anc2refChr3 3823 22 + 53186 CTACTCACCTTATTCCTTCAAA -s mr.mrrefChr0 117560 22 + 130230 CTAACTCATTTGTTCCTTTGAG -s simCow_chr6.simCow.chr6 476290 22 - 602619 CCACTCACCTTACTCCTTCAAA -s simDog_chr6.simDog.chr6 414960 22 - 593897 CTACTCACATTATTCCTTCAAA -s simHuman_chr6.simHuman.chr6 118112 20 + 601863 --ACTCACCTCATTCCTCCAAA -s simRat_chr6.simRat.chr6 115523 22 + 647215 CTAACTCATATGTTCTTTTTAG - -a -s simMouse_chr6.simMouse.chr6 123056 29 + 636262 CCTTTCAGCTTTTGTTAGAGTTTCACAGT -s Anc0.Anc0refChr1 15467 26 - 62388 CCTTCCA---TCAGTTGGAGTTTTGTAAT -s Anc1.Anc1refChr2 93927 26 + 144309 CCTTCCA---TCAGTTGGAGTTTTGTAAT -s Anc2.Anc2refChr3 3845 26 + 53186 CCTTCCT---TCAGTTGGAGTTTTGTAAC -s mr.mrrefChr0 117582 29 + 130230 CCTTTCAGCTTTAGTTAGAGTTTCACAGT -s simCow_chr6.simCow.chr6 476312 15 - 602619 CCTTACT---TTAGTTGG----------- -s simDog_chr6.simDog.chr6 414992 26 - 593897 CCTCCCT---TCAGTTCGAGTTTTGTAAC -s simHuman_chr6.simHuman.chr6 118132 26 + 601863 CCCTCCA---TCAATTGGAATTCTGTAAT -s simRat_chr6.simRat.chr6 115545 29 + 647215 TCTTTCAGCTTTAGTTAGAGTTTCACAGT - -a -s simMouse_chr6.simMouse.chr6 123085 3 + 636262 TTG -s Anc0.Anc0refChr1 15494 3 - 62388 TTC -s Anc1.Anc1refChr2 93954 3 + 144309 TTC -s Anc2.Anc2refChr3 3872 3 + 53186 TTC -s mr.mrrefChr0 117611 3 + 130230 TTG -s simDog_chr6.simDog.chr6 415019 3 - 593897 TTC -s simHuman_chr6.simHuman.chr6 118159 3 + 601863 CTA -s simRat_chr6.simRat.chr6 115574 3 + 647215 TTG - -a -s simMouse_chr6.simMouse.chr6 123088 7 + 636262 TGAATAG -s Anc0.Anc0refChr1 15497 7 - 62388 TGAAGTG -s Anc1.Anc1refChr2 93957 7 + 144309 TGAAGTG -s Anc2.Anc2refChr3 3875 7 + 53186 TGGAGTT -s mr.mrrefChr0 117614 7 + 130230 TGAATAG -s simCow_chr6.simCow.chr6 476327 4 - 602619 ---AGTT -s simDog_chr6.simDog.chr6 415039 7 - 593897 TGGAGTT -s simHuman_chr6.simHuman.chr6 118162 7 + 601863 TGAAGTG -s simRat_chr6.simRat.chr6 115577 7 + 647215 TGAATAG - -a -s simMouse_chr6.simMouse.chr6 123095 12 + 636262 AGCCTGAATGAT -s Anc0.Anc0refChr1 15507 10 - 62388 CTCC--CATAAT -s Anc1.Anc1refChr2 93967 10 + 144309 CTCC--CATAAT -s Anc2.Anc2refChr3 3885 10 + 53186 CTCC--CACAGT -s mr.mrrefChr0 117621 10 + 130230 CTCC--AATAAT -s simCow_chr6.simCow.chr6 476334 10 - 602619 CTGA--CACAGT -s simDog_chr6.simDog.chr6 415049 10 - 593897 CCCC--CGCAGT -s simHuman_chr6.simHuman.chr6 118172 10 + 601863 CTCT--GATAAT -s simRat_chr6.simRat.chr6 115584 10 + 647215 CTCC--AATAAC - -a -s simMouse_chr6.simMouse.chr6 123107 92 + 636262 TAGCAGTCATTATTTGCTCGTATTGCTATGATAAGCAACCATAGTTGAGCTATGACTGTGTTGCTGTGAAGTACTAGATAAAGGACTCTGCT -s Anc0.Anc0refChr1 15517 92 - 62388 TAGCAGCTGTTATTTGCTTGTATTGCTATAATCAGTAACCATAGCTGAGCTAAGACTGTGTTGCTGTGAAGTAGAAGTGAAAGGACTTTGCT -s Anc1.Anc1refChr2 93977 92 + 144309 TAGCAGCTGTTATTTGCTTGTATTGCTATAATCAGTAACCATAGCTGAGCTAAGACTGTGTTGCTGTGAAGTAGAAGTGAAAGGACTTTGCT -s Anc2.Anc2refChr3 3903 92 + 53186 TAGCAGCTGTTATTTGCTTGTATTGCTATAATCAGTAATCATAGCTGAGCTAAGACTGTGTTGCTGGAAAATAGAAGTGCAAGGACTTTACT -s mr.mrrefChr0 117631 92 + 130230 TAGCAGTCATTATTTGCTTGTATTGCTATGATAAGCAACCATAGCTGAGCTATGACTGTGTTGCTGTGAAGTACTAGATAAAGGACTCTGCT -s simCow_chr6.simCow.chr6 476352 79 - 602619 TAGCAGCCCTTATTTACTTGTTTTGCTATCATCAGTAATCACAGCTGAGCTAAGACTGCATAGTGGGAAAAAAGAATTG------------- -s simDog_chr6.simDog.chr6 415067 86 - 593897 TAGCTGCTGTTATTGGAATGTATGGTTATAATGTGTAATCGTAGCTGAGCTCAGACTGTGTTGCT------TAGAAGTACAAGGACTTTACT -s simHuman_chr6.simHuman.chr6 118182 92 + 601863 TAGCAACTGTCATTTGCTTGTATTGCTATAATCAGTAACCATAGCAGTGCTAAGACTGTGTTGCTGTGAAGTAAAAGTGAAAGAATTTGGCT -s simRat_chr6.simRat.chr6 115594 92 + 647215 TAGCAGTCATTATTTTCTTGTATCGCGATGATAAGCAACCATAGCTGAGCTATGACTGTGTTGCTGCGAAGTACTAGATAAAGGTCTCTGCT - -a -s simMouse_chr6.simMouse.chr6 123199 69 + 636262 TATTAGCATGGTCCAGGTTGCTATCCGACTTCAAGTGGCCCCAATGTCCTTAGCTCATATGACCAACAG -s Anc0.Anc0refChr1 15609 69 - 62388 CATTAGCATGGTCTAGGTTACTACCCCATTTGAAGTGCCCCCAATTTCCCTAACTGATATGACTAACAT -s Anc1.Anc1refChr2 94069 69 + 144309 CATTAGCATGGTCTAGGTTACTACCCCATTTGAAGTGCCCCCAATTTCCCTAACTGATATGACTAACAT -s Anc2.Anc2refChr3 3995 69 + 53186 CACTAGCATGGTCTAGATTGGTACCCCATTTGAAGTGCCCCCAATTTCCCTAAATGATATGACTAAAGT -s mr.mrrefChr0 117723 69 + 130230 TATTAGCATGGTCCAGGTTACTATCCGACTTCAAGTGCCCCCAATGTCCTTAGCTCATATGACCAACAG -s simCow_chr6.simCow.chr6 126770 69 + 602619 CACTAGCATGGTCTGGATTGTTACCCCATTTTAACTGCCCCCAAATTTCTTAGGTGGAATGAATAATTT -s simDog_chr6.simDog.chr6 415153 69 - 593897 CACTAGCCTGGTCTAGATTGGTACCCCATTTGAAGTGCCCCTAATTTCCCTAAATGATATGACTAAAGT -s simHuman_chr6.simHuman.chr6 118274 69 + 601863 CATTAGCATGGTTTTGGTTACTACCCCAATTGAAGTCCCCCCAATTTCCATGACTGATGTGACTAACAT -s simRat_chr6.simRat.chr6 115686 69 + 647215 TACTAGCATCGTCCAAGCTATTATCTGACTTCAAGTGCTCCCAATGTCCCCAGCTCATATAACCAACAG - -a -s simMouse_chr6.simMouse.chr6 123268 9 + 636262 ATCCTAAGA -s Anc0.Anc0refChr1 15690 8 - 62388 ATC-TGAGA -s Anc1.Anc1refChr2 94150 8 + 144309 ATC-TGAGA -s Anc2.Anc2refChr3 4076 8 + 53186 GTG-TGAGA -s mr.mrrefChr0 117792 8 + 130230 ATC-TAAGA -s simCow_chr6.simCow.chr6 126851 8 + 602619 GTG-TGAGA -s simDog_chr6.simDog.chr6 415234 8 - 593897 GTG-TGAGA -s simHuman_chr6.simHuman.chr6 118355 8 + 601863 ATC-TGAGA -s simRat_chr6.simRat.chr6 115755 8 + 647215 ATC-TAAGA - -a -s simMouse_chr6.simMouse.chr6 123277 36 + 636262 TACATCATTCTAGGTAGCTCAGATTTGGTCAGCTGG -s Anc0.Anc0refChr1 15698 36 - 62388 GACATCACACTAGGCAGATTAGATCTTGTCAGCTAG -s Anc1.Anc1refChr2 94158 36 + 144309 GACATCACACTAGGCAGATTAGATCTTGTCAGCTAG -s Anc2.Anc2refChr3 4084 36 + 53186 GGCATCACACTAGGCAGATTAGATCTTATCAGCTAG -s mr.mrrefChr0 117800 36 + 130230 TACATCATTCTAGGTAGATTAGATTTGGTCAGCTGG -s simCow_chr6.simCow.chr6 126860 36 + 602619 GGCATCACACCTGGCACATCAGATCTTATCTGCTAC -s simDog_chr6.simDog.chr6 415242 36 - 593897 GGCATCACACTAGGCAGATTAGATCTTATCAGCTGG -s simHuman_chr6.simHuman.chr6 118363 30 + 601863 GACACCACACTGAGCAGATTA------GTCAGTTAG -s simRat_chr6.simRat.chr6 115763 36 + 647215 TACATCATTCTAGGTAGATTAGATTTAGTCAGCTGG - -a -s simMouse_chr6.simMouse.chr6 123313 3 + 636262 TAT -s Anc0.Anc0refChr1 15734 3 - 62388 CAG -s Anc1.Anc1refChr2 94194 3 + 144309 CAG -s Anc2.Anc2refChr3 4134 3 + 53186 CAG -s mr.mrrefChr0 117836 3 + 130230 TAT -s simCow_chr6.simCow.chr6 126910 3 + 602619 CAT -s simDog_chr6.simDog.chr6 415292 3 - 593897 CAG -s simHuman_chr6.simHuman.chr6 118393 3 + 601863 CAG -s simRat_chr6.simRat.chr6 115799 3 + 647215 TAT - -a -s simMouse_chr6.simMouse.chr6 123316 18 + 636262 GGCACTATATTATTTATA -s Anc0.Anc0refChr1 15737 18 - 62388 ATCACAACAGGATTAATA -s Anc1.Anc1refChr2 94197 18 + 144309 ATCACAACAGGATTAATA -s Anc2.Anc2refChr3 4148 18 + 53186 ATCACAACAGGATTAATA -s mr.mrrefChr0 117839 18 + 130230 AGCACTACATGATTTATA -s simCow_chr6.simCow.chr6 126931 18 + 602619 ATCACAACAGGATTAATA -s simDog_chr6.simDog.chr6 415306 18 - 593897 ATCACAACAGGATTAATA -s simHuman_chr6.simHuman.chr6 118396 18 + 601863 ATCACAACAGGATTAATA -s simRat_chr6.simRat.chr6 115802 18 + 647215 AGCACTACATGATTCATA - -a -s simMouse_chr6.simMouse.chr6 123334 3 + 636262 AAT -s Anc0.Anc0refChr1 15756 3 - 62388 AAT -s Anc1.Anc1refChr2 94216 3 + 144309 AAT -s Anc2.Anc2refChr3 4167 3 + 53186 AAT -s mr.mrrefChr0 117857 3 + 130230 AAT -s simCow_chr6.simCow.chr6 126950 3 + 602619 AAT -s simDog_chr6.simDog.chr6 415325 2 - 593897 A-C -s simHuman_chr6.simHuman.chr6 118415 3 + 601863 AAT -s simRat_chr6.simRat.chr6 115820 3 + 647215 AGT - -a -s simMouse_chr6.simMouse.chr6 123337 34 + 636262 TTGGCAACAATTATAAATTTAGGCACAATAGTGT -s Anc0.Anc0refChr1 15759 34 - 62388 TTGGCAATGATTATATATTGTAATGCAATAGTGT -s Anc1.Anc1refChr2 94219 34 + 144309 TTGGCAATGATTATATATTGTAATGCAATAGTGT -s Anc2.Anc2refChr3 4170 34 + 53186 TTGGCAGTGTTTATATATTGTAATGCAATAGTGT -s mr.mrrefChr0 117860 34 + 130230 TTGGCAACAATTATAAATTTAGGCACAATAGTGT -s simCow_chr6.simCow.chr6 126957 33 + 602619 TTGGCAGGGTTTCTATATTGTAATCCAAT-GTGT -s simDog_chr6.simDog.chr6 415327 34 - 593897 CTGGCAGTGTTTATATACTGTAATGCAATAGTGT -s simHuman_chr6.simHuman.chr6 118418 34 + 601863 TTGGCAATGATTATTTATTGTAATGCAATAGTGT -s simRat_chr6.simRat.chr6 115823 34 + 647215 TGGGCAGCAATTGTAAATTTAGGCACAATAGTGT - -a -s simMouse_chr6.simMouse.chr6 123371 3 + 636262 TGA -s Anc0.Anc0refChr1 15798 3 - 62388 GGA -s Anc1.Anc1refChr2 94258 3 + 144309 GGA -s Anc2.Anc2refChr3 4209 3 + 53186 GGA -s mr.mrrefChr0 117894 3 + 130230 GGA -s simCow_chr6.simCow.chr6 126995 3 + 602619 GGA -s simDog_chr6.simDog.chr6 415366 3 - 593897 GGA -s simHuman_chr6.simHuman.chr6 118457 3 + 601863 GAA -s simRat_chr6.simRat.chr6 115857 3 + 647215 GGA - -a -s simMouse_chr6.simMouse.chr6 123374 46 + 636262 GGTTATCAGGACTTTGGTATTTCTAAATAAAGAGACTAGCCCTAAT -s Anc0.Anc0refChr1 15801 46 - 62388 GGATGTTGTGAATTTGGTATTTTTAAATAAATAAAATGGGCTTAAT -s Anc1.Anc1refChr2 94261 46 + 144309 GGATGTTGTGAATTTGGTATTTTTAAATAAATAAAATGGGCTTAAT -s Anc2.Anc2refChr3 4212 46 + 53186 GGATGTTGTGAATTTGGTATTTTTAAATAAATAAAATGGGCTTAAT -s mr.mrrefChr0 117897 46 + 130230 GGTTATCATGACTTTGGTATTTCTAAATAAAGAGACTAGGCCTAAT -s simCow_chr6.simCow.chr6 126998 46 + 602619 GGATGTTGTGAATTTGGTATTCCTAAATATATTAAATGGGCTTAAT -s simDog_chr6.simDog.chr6 415455 46 - 593897 GGGTGCTGTGAATTTGGTATTTTTAAATAATTAGAATGGGCTTAAT -s simHuman_chr6.simHuman.chr6 118460 46 + 601863 GGATGTGGTGAAATTAGTATTTTTAAATAAATGAAATGGGCTTAAT -s simRat_chr6.simRat.chr6 115860 46 + 647215 GGTTATCATGACTCTGGTATTTCTAGGTAAAGAGACTAGGGCCAAT - -a -s simMouse_chr6.simMouse.chr6 123420 9 + 636262 TTTTTAATT -s Anc0.Anc0refChr1 15847 9 - 62388 TTATTTATT -s Anc1.Anc1refChr2 94307 9 + 144309 TTATTTATT -s Anc2.Anc2refChr3 4258 9 + 53186 TTATTTATT -s mr.mrrefChr0 117943 9 + 130230 TTTTTAAAT -s simCow_chr6.simCow.chr6 127044 9 + 602619 TTAGTGATT -s simDog_chr6.simDog.chr6 415501 9 - 593897 TTATTTACT -s simHuman_chr6.simHuman.chr6 118507 9 + 601863 TTATTTATT -s simRat_chr6.simRat.chr6 115906 9 + 647215 TTTTTGAAT - -a -s simMouse_chr6.simMouse.chr6 123429 58 + 636262 GCATGCAACTACACAGCTTCAGTCTCTCTCCACCTTCCACACATGGCCACAGGGTAAT -s Anc0.Anc0refChr1 15861 55 - 62388 GCGGACAACTGCTCAACTTCAG--TCTTCTCACCTTACACACATCTAAACA-GGTAAT -s Anc1.Anc1refChr2 94321 55 + 144309 GCGGACAACTGCTCAACTTCAG--TCTTCTCACCTTACACACATCTAAACA-GGTAAT -s Anc2.Anc2refChr3 4272 55 + 53186 GCGGACAAATGCTCAACTTCAG--TCTTCTCACCTTACACACATCTAGACA-GGTAAG -s mr.mrrefChr0 117952 58 + 130230 GCATGCAACTGCACAGCTTCAGTCTCTCTCCACCTTCCACACATGTAAACAGGGTAAT -s simCow_chr6.simCow.chr6 127058 54 + 602619 GCTGACAAATACTCAACTG-AG--ACTATTCACCCCCCACATAACCAGACA-GCTAAG -s simDog_chr6.simDog.chr6 415515 55 - 593897 GCGGACAAATGCTCAACCTCAG--TCCTCTCACCTTACACACATGTAGACA-GGTAAG -s simHuman_chr6.simHuman.chr6 118521 55 + 601863 GTGGACAACTGCTCAACTCCAG--TCTTCTCACCTTACACACATCTAAACA-GGTAAT -s simRat_chr6.simRat.chr6 115915 58 + 647215 CCACGCAACTGCACAGCTTCAGTCTCTCTGCACCTTCCACACATGTAAGCAGGGTAAT - -a -s simMouse_chr6.simMouse.chr6 123487 1 + 636262 T -s Anc0.Anc0refChr1 15916 1 - 62388 T -s Anc1.Anc1refChr2 94376 1 + 144309 T -s Anc2.Anc2refChr3 4341 1 + 53186 T -s mr.mrrefChr0 118010 1 + 130230 T -s simCow_chr6.simCow.chr6 127126 1 + 602619 G -s simDog_chr6.simDog.chr6 415584 1 - 593897 T -s simHuman_chr6.simHuman.chr6 118576 1 + 601863 T -s simRat_chr6.simRat.chr6 115973 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 123488 4 + 636262 CAGC -s Anc0.Anc0refChr1 15954 4 - 62388 CGGT -s Anc1.Anc1refChr2 94414 4 + 144309 CGGT -s Anc2.Anc2refChr3 4379 4 + 53186 CGGT -s mr.mrrefChr0 118011 4 + 130230 CAGC -s simCow_chr6.simCow.chr6 127164 4 + 602619 CAGT -s simDog_chr6.simDog.chr6 415617 3 - 593897 -GAT -s simHuman_chr6.simHuman.chr6 118614 4 + 601863 TGGT -s simRat_chr6.simRat.chr6 115974 4 + 647215 CAGC - -a -s simMouse_chr6.simMouse.chr6 123492 9 + 636262 ACATTTTTA -s Anc0.Anc0refChr1 15958 9 - 62388 ATGTTTCTG -s Anc1.Anc1refChr2 94418 9 + 144309 ATGTTTCTG -s Anc2.Anc2refChr3 4383 9 + 53186 GTGTTTCTG -s mr.mrrefChr0 118015 9 + 130230 ATATTTTTG -s simCow_chr6.simCow.chr6 127169 9 + 602619 GTGTATCTG -s simDog_chr6.simDog.chr6 415620 9 - 593897 GTGTTTCTG -s simHuman_chr6.simHuman.chr6 118618 9 + 601863 ATGTTTCTG -s simRat_chr6.simRat.chr6 115978 9 + 647215 ATATTTTCG - -a -s simMouse_chr6.simMouse.chr6 123501 66 + 636262 CCACTGCAAAAACAGACTCTCATGCTTGAACTATTCTGAGTGAGCAATCAGACTATGATCTTAATG -s Anc0.Anc0refChr1 15999 34 - 62388 GCACTGTAAGAACAAGTTCTCATGTTT-------------------ACCAGAC------------- -s Anc1.Anc1refChr2 94459 43 + 144309 GCACTGTAAGAACAAGTTCTCATGTTT-------------------ACCAGACCGTGAGTTC---- -s Anc2.Anc2refChr3 4424 34 + 53186 GCAATGTAAGAAGAAGTCCTCATGTTT-------------------ACCAGGC------------- -s mr.mrrefChr0 118049 47 + 130230 CCACTGTAAAAACAAACTCTCATGCTT-------------------ACCAGACTATGATTTTAATG -s simCow_chr6.simCow.chr6 127210 34 + 602619 GCATTGTAATGAGAAGTCTACATCTCA-------------------GCCCAGT------------- -s simDog_chr6.simDog.chr6 415643 34 - 593897 GCAATGGAAGAAGAAGTCCTCATGTTT-------------------ACTAGGC------------- -s simHuman_chr6.simHuman.chr6 118659 43 + 601863 ACACTGTAAGAACAAGTTCTCATGTTT-------------------ACCTGACCGTGAGTTC---- -s simRat_chr6.simRat.chr6 116012 47 + 647215 CCACTGTAAAAACAAACTCTCATCCTT-------------------ACCAAACAATGATTTTAATT - -a -s simMouse_chr6.simMouse.chr6 123567 45 + 636262 AATGCAACATCAAAAATACAATTGACATCAAAAGACATATATTTT -s Anc0.Anc0refChr1 16033 9 - 62388 ------------------------------------ACCTAGATT -s Anc1.Anc1refChr2 94502 21 + 144309 -ATGCAAGATT-----------------------ACACCTAGATT -s Anc2.Anc2refChr3 4458 9 + 53186 ------------------------------------ACCTAGATT -s mr.mrrefChr0 118096 43 + 130230 AATGCAACATCAAAAATACAATT--CATCAAAAGACATATATATT -s simCow_chr6.simCow.chr6 127244 9 + 602619 ------------------------------------GCAAAGACT -s simDog_chr6.simDog.chr6 415677 9 - 593897 ------------------------------------ACCTAGCTT -s simHuman_chr6.simHuman.chr6 118702 21 + 601863 -ATGCAAGATT-----------------------ATACCTAGATT -s simRat_chr6.simRat.chr6 116060 43 + 647215 AATGCAACATCAAATATACAATT--CACCAAAAAACATATATATT - -a -s simMouse_chr6.simMouse.chr6 123612 7 + 636262 GATGTCT -s Anc0.Anc0refChr1 16042 7 - 62388 GATGTTC -s Anc1.Anc1refChr2 94523 7 + 144309 GATGTTC -s Anc2.Anc2refChr3 4467 7 + 53186 GATGTTC -s mr.mrrefChr0 118139 7 + 130230 GATGTTT -s simCow_chr6.simCow.chr6 127257 7 + 602619 GATGTTC -s simDog_chr6.simDog.chr6 415686 7 - 593897 GATGTCT -s simHuman_chr6.simHuman.chr6 118723 7 + 601863 GACGTTC -s simRat_chr6.simRat.chr6 116103 7 + 647215 GATGTTT - -a -s simMouse_chr6.simMouse.chr6 123619 16 + 636262 TAACCTCCCATAAGCT -s Anc0.Anc0refChr1 16049 16 - 62388 CAACCTGCCACATCCT -s Anc1.Anc1refChr2 94530 16 + 144309 CAACCTGCCACATCCT -s Anc2.Anc2refChr3 4474 16 + 53186 CAACATGCCACATCCC -s mr.mrrefChr0 118146 16 + 130230 CAACCTCCCATAAGCT -s simCow_chr6.simCow.chr6 127276 16 + 602619 CAGCGTGCCTGATCAC -s simDog_chr6.simDog.chr6 415693 16 - 593897 CGACATGCCACATCCC -s simHuman_chr6.simHuman.chr6 118730 16 + 601863 CAACCCTCCGCATCCT -s simRat_chr6.simRat.chr6 116110 16 + 647215 CAACCTCCCATAAGCT - -a -s simMouse_chr6.simMouse.chr6 123635 9 + 636262 CATAAGTGT -s Anc0.Anc0refChr1 16065 9 - 62388 CATGTATTT -s Anc1.Anc1refChr2 94546 9 + 144309 CATGTATTT -s Anc2.Anc2refChr3 4490 9 + 53186 CATGTATTT -s mr.mrrefChr0 118162 9 + 130230 CATATGTGT -s simCow_chr6.simCow.chr6 127418 9 + 602619 CATGCGTAT -s simDog_chr6.simDog.chr6 415709 9 - 593897 CATATATTT -s simHuman_chr6.simHuman.chr6 118746 9 + 601863 TATGTATTT -s simRat_chr6.simRat.chr6 116126 9 + 647215 CATATGTGT - -a -s simMouse_chr6.simMouse.chr6 123644 21 + 636262 TCCTACTGGATTTAAGGACAT -s Anc0.Anc0refChr1 16074 14 - 62388 GCAATC-TGAGTCAA------ -s Anc1.Anc1refChr2 94555 21 + 144309 GCAATCCTGAGTCAATAACAT -s Anc2.Anc2refChr3 4500 14 + 53186 GCAATC-TGAGTCAA------ -s mr.mrrefChr0 118171 21 + 130230 TCATACTGGATTCAAGAACAT -s simCow_chr6.simCow.chr6 127428 14 + 602619 GCAATC-AGAATGCA------ -s simDog_chr6.simDog.chr6 415719 14 - 593897 GCAATT-TGAGTCAA------ -s simHuman_chr6.simHuman.chr6 118755 21 + 601863 GCAATCATGCAACAATAACAT -s simRat_chr6.simRat.chr6 116135 21 + 647215 TTATACTGGATTCAAGAACAT - -a -s simMouse_chr6.simMouse.chr6 123665 7 + 636262 GACAAGA -s Anc0.Anc0refChr1 16094 7 - 62388 AACATGC -s Anc1.Anc1refChr2 94584 7 + 144309 AACATGC -s Anc2.Anc2refChr3 4520 7 + 53186 AACATGC -s mr.mrrefChr0 118192 7 + 130230 GACAAGA -s simCow_chr6.simCow.chr6 127448 7 + 602619 AACATGC -s simDog_chr6.simDog.chr6 415739 7 - 593897 AACATGT -s simHuman_chr6.simHuman.chr6 118784 7 + 601863 AGTACGC -s simRat_chr6.simRat.chr6 116156 7 + 647215 GACATGA - -a -s simMouse_chr6.simMouse.chr6 123672 19 + 636262 CAGATTTTTATGCAGTTTT -s Anc0.Anc0refChr1 16101 19 - 62388 CAGATTTCTATGCAGTTTT -s Anc1.Anc1refChr2 94591 19 + 144309 CAGATTTCTATGCAGTTTT -s Anc2.Anc2refChr3 4527 19 + 53186 CAGATTTCTATGCAGTTTT -s mr.mrrefChr0 118199 19 + 130230 CAGATTTTTATGCAGTTTT -s simCow_chr6.simCow.chr6 127455 19 + 602619 CAGATTTCTATGCAGTTTT -s simDog_chr6.simDog.chr6 415748 19 - 593897 CAGATTTCCACGCAGTTTT -s simHuman_chr6.simHuman.chr6 118791 19 + 601863 TAGATTCCTATGCAGTATT -s simRat_chr6.simRat.chr6 116163 19 + 647215 CAGGTTTTTATGTAGTTTT - -a -s simMouse_chr6.simMouse.chr6 123691 2 + 636262 CA -s Anc0.Anc0refChr1 16120 2 - 62388 CA -s Anc1.Anc1refChr2 94610 2 + 144309 CA -s Anc2.Anc2refChr3 4546 2 + 53186 CA -s mr.mrrefChr0 118218 2 + 130230 CA -s simCow_chr6.simCow.chr6 127474 2 + 602619 CA -s simDog_chr6.simDog.chr6 415768 2 - 593897 CA -s simHuman_chr6.simHuman.chr6 118810 2 + 601863 CA -s simRat_chr6.simRat.chr6 116182 2 + 647215 CA - -a -s simMouse_chr6.simMouse.chr6 123693 4 + 636262 AAGG -s Anc0.Anc0refChr1 16123 4 - 62388 AAGG -s Anc1.Anc1refChr2 94613 4 + 144309 AAGG -s Anc2.Anc2refChr3 4549 4 + 53186 AAGG -s mr.mrrefChr0 118220 4 + 130230 AAGG -s simCow_chr6.simCow.chr6 127477 4 + 602619 AAGG -s simDog_chr6.simDog.chr6 415771 4 - 593897 AGTG -s simHuman_chr6.simHuman.chr6 118813 4 + 601863 AAGG -s simRat_chr6.simRat.chr6 116184 4 + 647215 AAGG - -a -s simMouse_chr6.simMouse.chr6 123697 72 + 636262 TGATTAATCCAATTTTCTATTTCACATGAAATTTGCTTTGTAATTGTTAATATGAATTTTATACTCTATTCT -s Anc0.Anc0refChr1 16127 52 - 62388 TGCTTAATCCAATACTCT-TTTCACATGGGAATTTCTT-----------------AA--TGGTCTTTATGTG -s Anc1.Anc1refChr2 94617 54 + 144309 TGCTTAATCCAATACTCT-TTTCACATGGGAATTTCTT-----------------AACTTGGTCTTTATGTG -s Anc2.Anc2refChr3 4553 52 + 53186 TGCTTAATCCAATACTCT-TTTCATATGGGAATTTCTT-----------------CA--TGGTCTTTATGTG -s mr.mrrefChr0 118224 71 + 130230 TGATTAATCCAATTCTCT-TTTCACATGAAATTTGCTTTGTAATTGTTAATATGAATTTTATACTCTATTCT -s simCow_chr6.simCow.chr6 127483 52 + 602619 TGCTTGATCCAGTACTCC-TTTCATATGGGAATTTCTT-----------------TA--TAGTCTTTAAGTG -s simDog_chr6.simDog.chr6 415775 52 - 593897 TGCTTATTCCGATACTCT-CTTCATATGTCAACTTTTT-----------------CA--TGGTCCTTATGCG -s simHuman_chr6.simHuman.chr6 118817 54 + 601863 TCCTTAATTCAATACTGT-TTTCACATGGGAATTTCTT-----------------AACTTGCTCTTTACGTG -s simRat_chr6.simRat.chr6 116188 71 + 647215 TGATTGACCCAATTCTCT-CTCCACATGAAATTTGCTTTGTAATCATTAATGTGATCTTTATACTCTATTAC - -a -s simMouse_chr6.simMouse.chr6 123769 6 + 636262 ATGACA -s Anc0.Anc0refChr1 16179 6 - 62388 ATGACA -s Anc1.Anc1refChr2 94671 6 + 144309 ATGACA -s Anc2.Anc2refChr3 4610 6 + 53186 CTGGCA -s mr.mrrefChr0 118295 6 + 130230 ATGACA -s simDog_chr6.simDog.chr6 415827 6 - 593897 CTGGCA -s simHuman_chr6.simHuman.chr6 118871 6 + 601863 ATAAGG -s simRat_chr6.simRat.chr6 116259 6 + 647215 ATGACA - -a -s simMouse_chr6.simMouse.chr6 123775 10 + 636262 TGCTTTCACA -s Anc0.Anc0refChr1 16185 10 - 62388 TTCTTCCACT -s Anc1.Anc1refChr2 94677 10 + 144309 TTCTTCCACT -s Anc2.Anc2refChr3 4616 10 + 53186 TTCTTCCAAT -s mr.mrrefChr0 118301 10 + 130230 TGCTTTCACA -s simCow_chr6.simCow.chr6 127540 10 + 602619 TTCCCCCCAC -s simDog_chr6.simDog.chr6 415923 10 - 593897 TTCTTCCAAT -s simHuman_chr6.simHuman.chr6 118877 10 + 601863 CCCCCCCCCT -s simRat_chr6.simRat.chr6 116265 6 + 647215 GGCTTT---- - -a -s simMouse_chr6.simMouse.chr6 123785 1 + 636262 C -s Anc0.Anc0refChr1 16195 1 - 62388 C -s Anc1.Anc1refChr2 94687 1 + 144309 C -s Anc2.Anc2refChr3 4627 1 + 53186 C -s mr.mrrefChr0 118311 1 + 130230 C -s simCow_chr6.simCow.chr6 127551 1 + 602619 C -s simDog_chr6.simDog.chr6 415934 1 - 593897 C -s simHuman_chr6.simHuman.chr6 118887 1 + 601863 C - -a -s simMouse_chr6.simMouse.chr6 123786 3 + 636262 GTC -s Anc0.Anc0refChr1 16197 3 - 62388 GTC -s Anc1.Anc1refChr2 94689 3 + 144309 GTC -s Anc2.Anc2refChr3 4629 3 + 53186 GTC -s mr.mrrefChr0 118312 3 + 130230 GTC -s simCow_chr6.simCow.chr6 127553 3 + 602619 GTC -s simDog_chr6.simDog.chr6 415936 3 - 593897 GTC -s simHuman_chr6.simHuman.chr6 118889 3 + 601863 GTC - -a -s simMouse_chr6.simMouse.chr6 123789 15 + 636262 AGGGATTGCTGTAAA -s Anc0.Anc0refChr1 16200 15 - 62388 ATGGATTGCCCTGAC -s Anc1.Anc1refChr2 94692 15 + 144309 ATGGATTGCCCTGAC -s Anc2.Anc2refChr3 4632 15 + 53186 ATAGATTGCCCTGAC -s mr.mrrefChr0 118315 15 + 130230 AGGGATTGCTGTAAA -s simCow_chr6.simCow.chr6 127556 15 + 602619 ATAGATTGCCCTGAC -s simDog_chr6.simDog.chr6 415953 15 - 593897 ATAGATTGCCCTGAC -s simHuman_chr6.simHuman.chr6 118892 15 + 601863 AAGGACTGCCTTGAC - -a -s simMouse_chr6.simMouse.chr6 123804 12 + 636262 CTGCTGTTCACA -s Anc0.Anc0refChr1 16215 7 - 62388 TT-----TCACA -s Anc1.Anc1refChr2 94707 12 + 144309 TTGGTTTTCACA -s Anc2.Anc2refChr3 4647 7 + 53186 TT-----TCGCA -s mr.mrrefChr0 118330 12 + 130230 CTGCTGTTCACA -s simCow_chr6.simCow.chr6 127576 7 + 602619 TT-----TCAGA -s simDog_chr6.simDog.chr6 415968 7 - 593897 TT-----TCGCA -s simHuman_chr6.simHuman.chr6 118907 12 + 601863 TTGGTTTTCACA - -a -s simMouse_chr6.simMouse.chr6 123816 18 + 636262 TGGGGTAAGCTATTGTCT -s Anc0.Anc0refChr1 16222 18 - 62388 CAGGGCAGGCTGTGGTCT -s Anc1.Anc1refChr2 94719 18 + 144309 CAGGGCAGGCTGTGGTCT -s Anc2.Anc2refChr3 4655 18 + 53186 CAGGGCAGGCTGTGGTAT -s mr.mrrefChr0 118342 18 + 130230 TGGGGTAAGCTATTGTCT -s simCow_chr6.simCow.chr6 127584 18 + 602619 CAGGTTAGACTGTGGTGC -s simDog_chr6.simDog.chr6 415976 18 - 593897 CAGGGCAGGCTGTGGTAT -s simHuman_chr6.simHuman.chr6 118919 18 + 601863 CAGAGCAGGTTGAGGTCT - -a -s simMouse_chr6.simMouse.chr6 123834 8 + 636262 GATGTCTT -s Anc0.Anc0refChr1 16241 8 - 62388 GTTGACCT -s Anc1.Anc1refChr2 94738 8 + 144309 GTTGACCT -s Anc2.Anc2refChr3 4674 8 + 53186 GTTTACCT -s mr.mrrefChr0 118360 8 + 130230 GATGTCTT -s simCow_chr6.simCow.chr6 127603 8 + 602619 GTTTACCT -s simDog_chr6.simDog.chr6 415995 8 - 593897 GTTTACCT -s simHuman_chr6.simHuman.chr6 118938 8 + 601863 GCTGACCT - -a -s simMouse_chr6.simMouse.chr6 123842 3 + 636262 GAT -s Anc0.Anc0refChr1 16249 3 - 62388 GAT -s Anc1.Anc1refChr2 94746 3 + 144309 GAT -s Anc2.Anc2refChr3 4682 3 + 53186 TAC -s mr.mrrefChr0 118368 3 + 130230 GAT -s simCow_chr6.simCow.chr6 127615 3 + 602619 TAC -s simDog_chr6.simDog.chr6 416003 3 - 593897 TAC -s simHuman_chr6.simHuman.chr6 118946 3 + 601863 GAT - -a -s simMouse_chr6.simMouse.chr6 123845 26 + 636262 GGCAGTATGAAATATGATTAAAAAAT -s Anc0.Anc0refChr1 16252 26 - 62388 GGCAATATGAAATATAATTAGAAGTT -s Anc1.Anc1refChr2 94749 26 + 144309 GGCAATATGAAATATAATTAGAAGTT -s Anc2.Anc2refChr3 4685 26 + 53186 GGCAACATTGAATAGAATCAGGTGTT -s mr.mrrefChr0 118371 26 + 130230 GGCAGTATGAAATATGATTAAAAAAT -s simCow_chr6.simCow.chr6 127660 26 + 602619 GACTATATGAAACAGAATTAATAGTC -s simDog_chr6.simDog.chr6 416006 26 - 593897 GGCAACATTGAATAGAATCAGGTGTT -s simHuman_chr6.simHuman.chr6 118949 26 + 601863 GGCAATATGAAATATAATTATAAGTT - -a -s simMouse_chr6.simMouse.chr6 123871 36 + 636262 TTGGCTTCAAGCACAAGCTAAGTTTCCATAACATTA -s Anc0.Anc0refChr1 16278 7 - 62388 TGGATT-----------------------------A -s Anc1.Anc1refChr2 94775 7 + 144309 TGGATT-----------------------------A -s Anc2.Anc2refChr3 4711 7 + 53186 GGCATG-----------------------------C -s mr.mrrefChr0 118397 7 + 130230 TTGGCT-----------------------------A -s simCow_chr6.simCow.chr6 127686 7 + 602619 GACATT-----------------------------C -s simDog_chr6.simDog.chr6 416038 7 - 593897 GGCATG-----------------------------C -s simHuman_chr6.simHuman.chr6 118975 7 + 601863 TGGAAT-----------------------------A -s simRat_chr6.simRat.chr6 116271 1 + 647215 -----------------------------------G - -a -s simMouse_chr6.simMouse.chr6 123907 12 + 636262 ACAAACATAACT -s Anc0.Anc0refChr1 16285 7 - 62388 AC-----TGACT -s Anc1.Anc1refChr2 94782 7 + 144309 AC-----TGACT -s Anc2.Anc2refChr3 4718 7 + 53186 AC-----TGGGT -s mr.mrrefChr0 118404 12 + 130230 ACAAACATAACT -s simCow_chr6.simCow.chr6 127696 7 + 602619 AC-----TGGGT -s simDog_chr6.simDog.chr6 416045 7 - 593897 AC-----TGGGT -s simHuman_chr6.simHuman.chr6 118982 7 + 601863 AC-----TGACT -s simRat_chr6.simRat.chr6 116272 12 + 647215 TCAGACTTAGCT - -a -s simMouse_chr6.simMouse.chr6 123919 36 + 636262 GCTTAACTTGCAACAAATGAGGATGCATGGCTTGTT -s Anc0.Anc0refChr1 16292 36 - 62388 GTTAAACCATCAATAAGTATGACTGCTTGACTGGCG -s Anc1.Anc1refChr2 94789 36 + 144309 GTTAAACCATCAATAAGTATGACTGCTTGACTGGCG -s Anc2.Anc2refChr3 4730 36 + 53186 GTCACACCATCAATAAGTATGACTGCTTGACTGGCG -s mr.mrrefChr0 118416 36 + 130230 GCTTAACTTGCAACAAATGAGGATGCATGGCTTGTT -s simCow_chr6.simCow.chr6 127708 36 + 602619 ACCACAACATTAACAGATGTAGTTGTTTGGCTGGCT -s simDog_chr6.simDog.chr6 416057 36 - 593897 GTCACACCATCAATAAGTATGACTGCTTGACTGGCG -s simHuman_chr6.simHuman.chr6 118989 7 + 601863 GTTAAAT----------------------------- -s simRat_chr6.simRat.chr6 116284 36 + 647215 GCTTAACTTGTGACAGATGTGGATGCTTGGCTCGTT - -a -s simMouse_chr6.simMouse.chr6 123955 8 + 636262 TCTGTATT -s Anc0.Anc0refChr1 16328 7 - 62388 T-TGTATT -s Anc1.Anc1refChr2 94825 7 + 144309 T-TGTATT -s Anc2.Anc2refChr3 4766 7 + 53186 T-TGTATT -s mr.mrrefChr0 118452 8 + 130230 TCTGTATT -s simCow_chr6.simCow.chr6 127745 7 + 602619 C-TGTATT -s simDog_chr6.simDog.chr6 416093 7 - 593897 T-TGTATT -s simRat_chr6.simRat.chr6 116320 8 + 647215 TCTGTATC - -a -s simMouse_chr6.simMouse.chr6 123963 13 + 636262 TGAGGGTTATACT -s Anc0.Anc0refChr1 16335 13 - 62388 TAATGGCTACACT -s Anc1.Anc1refChr2 94832 13 + 144309 TAATGGCTACACT -s Anc2.Anc2refChr3 4774 13 + 53186 TAATGGCTACACT -s mr.mrrefChr0 118460 13 + 130230 TGAGGGTTATACT -s simCow_chr6.simCow.chr6 127753 13 + 602619 TAATGATTAAACT -s simDog_chr6.simDog.chr6 416101 13 - 593897 TAATGGCTACACT -s simRat_chr6.simRat.chr6 116328 13 + 647215 AGAGGGCTAGGCT - -a -s simMouse_chr6.simMouse.chr6 123976 19 + 636262 GAGCCGAGTACACTCACCT -s Anc0.Anc0refChr1 16348 19 - 62388 GGGCTAAGTACACTCACCT -s Anc1.Anc1refChr2 94845 19 + 144309 GGGCTAAGTACACTCACCT -s Anc2.Anc2refChr3 4789 19 + 53186 GGGCTAAGTACACTCACCT -s mr.mrrefChr0 118473 19 + 130230 GAGCCGAGTACACTCACCT -s simCow_chr6.simCow.chr6 127768 19 + 602619 GAGGTAAGTGCACTCACCT -s simDog_chr6.simDog.chr6 416116 19 - 593897 GGGCTAAGTACACTCACCT -s simRat_chr6.simRat.chr6 116341 19 + 647215 GAGCCGAGTACACTCACCT - -a -s simMouse_chr6.simMouse.chr6 123995 3 + 636262 GAC -s Anc0.Anc0refChr1 16367 3 - 62388 AAT -s Anc1.Anc1refChr2 94864 3 + 144309 AAT -s Anc2.Anc2refChr3 4814 3 + 53186 AAT -s mr.mrrefChr0 118492 3 + 130230 GAC -s simCow_chr6.simCow.chr6 127793 3 + 602619 AAT -s simDog_chr6.simDog.chr6 416144 3 - 593897 AAT -s simHuman_chr6.simHuman.chr6 118996 2 + 601863 -AT -s simRat_chr6.simRat.chr6 116360 3 + 647215 GAC - -a -s simMouse_chr6.simMouse.chr6 123998 21 + 636262 TCGATTGTCCCTGCCCTAACC -s Anc0.Anc0refChr1 16370 21 - 62388 TCAGTAGTTCCTACCCCAACC -s Anc1.Anc1refChr2 94867 21 + 144309 TCAGTAGTTCCTACCCCAACC -s Anc2.Anc2refChr3 4817 21 + 53186 TCAGTAGTTCCCACTCCAACT -s mr.mrrefChr0 118495 21 + 130230 TCAATAGTCCCTGCCCTAACC -s simCow_chr6.simCow.chr6 127796 21 + 602619 TCAATAGTTCCCACTCTAACT -s simDog_chr6.simDog.chr6 416147 21 - 593897 TTAGTTGTTCCCACTCCAACT -s simHuman_chr6.simHuman.chr6 118998 21 + 601863 TCAGTAGTTCCTATCCAAGCC -s simRat_chr6.simRat.chr6 116365 21 + 647215 TCAATAGTCCCTGCCCTAACT - -a -s simMouse_chr6.simMouse.chr6 124019 12 + 636262 CACTCATTTATT -s Anc0.Anc0refChr1 16393 12 - 62388 CATTCATTTATC -s Anc1.Anc1refChr2 94890 12 + 144309 CATTCATTTATC -s Anc2.Anc2refChr3 4840 12 + 53186 GATTTGTCTATT -s mr.mrrefChr0 118516 12 + 130230 CACTCATTTATC -s simCow_chr6.simCow.chr6 127819 12 + 602619 AATTTTTCTGTT -s simDog_chr6.simDog.chr6 416170 12 - 593897 GACTTGTCTATT -s simHuman_chr6.simHuman.chr6 119021 12 + 601863 CATTCATTTATC -s simRat_chr6.simRat.chr6 116386 12 + 647215 TTCTCACTTATC - -a -s simMouse_chr6.simMouse.chr6 124031 23 + 636262 GTTATATTTTTTTTCACATTTGT -s Anc0.Anc0refChr1 16411 23 - 62388 GTTATATTTTTTCTCACACCTGT -s Anc1.Anc1refChr2 94908 23 + 144309 GTTATATTTTTTCTCACACCTGT -s Anc2.Anc2refChr3 4858 23 + 53186 GTTATATTATTTCTCACACCTGT -s mr.mrrefChr0 118528 23 + 130230 GTTATATTTTTTTTCACATTTGT -s simCow_chr6.simCow.chr6 127837 23 + 602619 GTCATATATTTTATCACACCTGT -s simDog_chr6.simDog.chr6 416188 23 - 593897 GTTATATTATTCCTCACACCTGT -s simHuman_chr6.simHuman.chr6 119039 22 + 601863 ATTATA-TTTTTCTCACACCTAT -s simRat_chr6.simRat.chr6 116398 23 + 647215 GTTATTTTTTTTTTCACATTTGT - -a -s simMouse_chr6.simMouse.chr6 124054 17 + 636262 TGCTTCCAGTCACACAG -s Anc0.Anc0refChr1 16435 17 - 62388 TGCACTCAGATGAGCAG -s Anc1.Anc1refChr2 94932 17 + 144309 TGCACTCAGATGAGCAG -s Anc2.Anc2refChr3 4882 17 + 53186 TGCACTCAGATGAGAAG -s mr.mrrefChr0 118553 17 + 130230 TGCTCCCAGTCACACAG -s simCow_chr6.simCow.chr6 127861 17 + 602619 TGCACCCAGATGAGAAG -s simDog_chr6.simDog.chr6 416212 17 - 593897 TGCACTCACATAAGAAA -s simHuman_chr6.simHuman.chr6 119062 17 + 601863 TGCACGCAGATGAGCAG -s simRat_chr6.simRat.chr6 116423 17 + 647215 TGCTCCCAGTCACACAG - -a -s simMouse_chr6.simMouse.chr6 124071 59 + 636262 GGGGCATCTTTCAAACTAAAGTCTATGTCTGTGTTATTCGGTTAGGATGCGTTGTTGAC -s Anc0.Anc0refChr1 16455 57 - 62388 GAGGCATCTGTCAGCTTGAAAGCCATGTCCCTACTAGATGTCTA--ACGTACCCTTGAC -s Anc1.Anc1refChr2 94952 57 + 144309 GAGGCATCTGTCAGCTTGAAAGCCATGTCCCTACTAGATGTCTA--ACGTACCCTTGAC -s Anc2.Anc2refChr3 4902 57 + 53186 GAGGCATCTGTCAGCTTGAAAGACATGTCCCTACTAGATGTCTA--ATGTATCCTTGAC -s mr.mrrefChr0 118570 59 + 130230 GGGGCATCTTTCAAACTAAAGTCTATGTCTGTGCTATTTGGCTAGGACGCGCCGTTGAC -s simCow_chr6.simCow.chr6 127881 57 + 602619 GAGGCATCTGCCAGCTTGAAAGACACGTCACTACTAGATGTATA--ATGTATCCTTGAC -s simDog_chr6.simDog.chr6 416232 57 - 593897 GAGGCGTCTGTCAGCTTGAAAGACATGGCCCTAATACATGTCTG--GTGTATTCTTGAC -s simHuman_chr6.simHuman.chr6 119082 56 + 601863 GAGGCATCTGTCAC-TTGACAGCCATGTCCCTACTAGATGTCTA--ACGTCCCCTTGAC -s simRat_chr6.simRat.chr6 116440 59 + 647215 GTGGCATCTTTCAAACTAAAGTCTACGTTTGTGCTATTTGGCTCGTACGCACCATTGGC - -a -s simMouse_chr6.simMouse.chr6 124130 42 + 636262 TTCCACATAAACCTCAACTGCAAGCTGACACATAACGGATTT -s Anc0.Anc0refChr1 16515 42 - 62388 TCTCATCAACACCTCATCTGCAGGCTGACACAAAATGGATTT -s Anc1.Anc1refChr2 95012 42 + 144309 TCTCATCAACACCTCATCTGCAGGCTGACACAAAATGGATTT -s Anc2.Anc2refChr3 4962 42 + 53186 CCTCATCAACACCTCATCTGCAGGCTGACACAAAATGGACTT -s mr.mrrefChr0 118629 42 + 130230 TTCCACATAAACCTCAACTGCAAGCTGACACATAACGGATTT -s simCow_chr6.simCow.chr6 127941 41 + 602619 CATAGTCAACAC-TCATCTGTACGCTGGCACAAAATGGACTT -s simDog_chr6.simDog.chr6 416292 36 - 593897 CCTCA------CCTCATCTGCAGGTTGATCCAAAATGGACAT -s simHuman_chr6.simHuman.chr6 119141 42 + 601863 TCTCATGGACACCTCATCTGCAGGCTGACACAGGAGGGATTG -s simRat_chr6.simRat.chr6 116499 22 + 647215 CTCCACATAAA--------------------ACAATGGATTT - -a -s simMouse_chr6.simMouse.chr6 124172 13 + 636262 CACTTTGGGCTTT -s Anc0.Anc0refChr1 16558 10 - 62388 CATTT---GCTTT -s Anc1.Anc1refChr2 95055 10 + 144309 CATTT---GCTTT -s Anc2.Anc2refChr3 5005 10 + 53186 TATTT---GCTCT -s mr.mrrefChr0 118672 13 + 130230 CACTTTGGGCTTT -s simCow_chr6.simCow.chr6 127983 10 + 602619 TTCTA---GCTGA -s simDog_chr6.simDog.chr6 416329 10 - 593897 TATTT---GCTCT -s simHuman_chr6.simHuman.chr6 119184 10 + 601863 CATTT---GCTTT -s simRat_chr6.simRat.chr6 116522 13 + 647215 CACTTTGGGCTTT - -a -s simMouse_chr6.simMouse.chr6 124185 18 + 636262 AGAAAATACAGCAACTCA -s Anc0.Anc0refChr1 16568 13 - 62388 AGAAAAT-----AACTCA -s Anc1.Anc1refChr2 95065 13 + 144309 AGAAAAT-----AACTCA -s Anc2.Anc2refChr3 5019 13 + 53186 AGAAAAT-----ATAGCA -s mr.mrrefChr0 118685 18 + 130230 AGAAAATACAGCAACTCA -s simCow_chr6.simCow.chr6 127997 13 + 602619 AGAAAGT-----ATAGCA -s simDog_chr6.simDog.chr6 416343 13 - 593897 AGAAAAA-----ATAGCA -s simHuman_chr6.simHuman.chr6 119194 13 + 601863 AGAAAAT-----AACTCA -s simRat_chr6.simRat.chr6 116535 18 + 647215 GGAAAATACAGCAACTCA - -a -s simMouse_chr6.simMouse.chr6 124203 10 + 636262 GTTCCCATAG -s Anc0.Anc0refChr1 16581 10 - 62388 GTTGCAGCAA -s Anc1.Anc1refChr2 95078 10 + 144309 GTTGCAGCAA -s Anc2.Anc2refChr3 5032 10 + 53186 GGTGCAGCAA -s mr.mrrefChr0 118703 10 + 130230 GTTCCAATAA -s simCow_chr6.simCow.chr6 128015 10 + 602619 GGTGCAGCAA -s simDog_chr6.simDog.chr6 416356 8 - 593897 A--GCATCAA -s simHuman_chr6.simHuman.chr6 119207 10 + 601863 GTTGCAGCAA -s simRat_chr6.simRat.chr6 116553 10 + 647215 GTTACAATAA - -a -s simMouse_chr6.simMouse.chr6 124213 126 + 636262 CTCTGTACCTCAAGTTAATTTCAATGAGGGCCTTTTGGGTGGTAGTAGGGTAAAATAGACATTTAGCTAAAGCTTCTTTTAAGGTACAACAGCATAAAATATTGTCATTATATGTAAAAGCTCATT -s Anc0.Anc0refChr1 16591 123 - 62388 CTCTGTAACTTAAGGTAAACTCAATGAGGGCTTTTTGGGTAGCACTAGGGTAGAAGAGACATTTAGTCGAGGTTTCTTCTAAGGT---ATAGGGTAATAAATTGTCACTATGGCCAAATGCTCACT -s Anc1.Anc1refChr2 95088 123 + 144309 CTCTGTAACTTAAGGTAAACTCAATGAGGGCTTTTTGGGTAGCACTAGGGTAGAAGAGACATTTAGTCGAGGTTTCTTCTAAGGT---ATAGGGTAATAAATTGTCACTATGGCCAAATGCTCACT -s Anc2.Anc2refChr3 5042 123 + 53186 CTCTGTAACTTAAGGTATACTCAATGAGGGTTTCTTGGGTAGCACCAGGGTAGAGGTGACATTTAGTCGAGGTTTTTTCTAGGGT---ATAGGGTAATAAATAACCACTATGGCCAAATGCTAACT -s mr.mrrefChr0 118713 126 + 130230 CTCTGTACCTCAAGTTAATTTCAATGAGGGCCTTTTGGGTGGTAGTAGGGTAAAATAGACATTTAGCTAAAGCTTCTTTTAAGGTACAACAGCATAATATATTGTCATTATATGTAAAAGCTCATT -s simCow_chr6.simCow.chr6 128025 92 + 602619 CTCTGTAACTTGAGGTACACTCAATGATGGTTTCTTGGATGGTACCAGGGTGGAAGAGACGTTTAGTTGCAGTTTTTTCTAGGGT---ATAGGGT------------------------------- -s simDog_chr6.simDog.chr6 416365 121 - 593897 CTCTGTGATTTAAAGTATACTCAATGAGGGTTCCTTGGGTAGCGCCAGGGTAGAGGTGACATTGAGTCAAGTCTTTTCTTA--GT---ATAGGGTAATAAATAACCACTATGGCCAAATGCTAACT -s simHuman_chr6.simHuman.chr6 119217 118 + 601863 CTCTGTATCTAAAGGGAAACTCAATGAGGGCTTTTTGACTTCCACTAG-----AACAGACATTTAGTAGAGGTTTCTTCTAAGGT---ATAGGGTAATAGACTGTCACTATGCTCAGATGCTCACT -s simRat_chr6.simRat.chr6 116563 126 + 647215 CTCCGTACCTTAAGTTAATTCCAATGAGGGCCTTTTGGTTGGTAGTAGGGAACAATAGATATTTAGCTAAAGCTTCTTTTAGGGTACAACAGCATAATAAATTGCCATTATATGTAAAAGCTCATT - -a -s simMouse_chr6.simMouse.chr6 124339 12 + 636262 GGAAAATGGTGA -s Anc0.Anc0refChr1 16722 12 - 62388 GGCAAACATTGT -s Anc1.Anc1refChr2 95219 12 + 144309 GGCAAACATTGT -s Anc2.Anc2refChr3 5173 12 + 53186 GGCAAACATTGT -s mr.mrrefChr0 118847 12 + 130230 GGAAAATGGTGA -s simCow_chr6.simCow.chr6 128122 12 + 602619 GGTACACATTTT -s simDog_chr6.simDog.chr6 416494 12 - 593897 GGCAAATACTGT -s simHuman_chr6.simHuman.chr6 119343 12 + 601863 GGCAGACATCAT -s simRat_chr6.simRat.chr6 116697 12 + 647215 GGAAAGTGGTGA - -a -s simMouse_chr6.simMouse.chr6 124351 26 + 636262 ACAAGCAGGTAAGTGCTCAGTCAGGT -s Anc0.Anc0refChr1 16734 26 - 62388 CCAAGTAGGAGAGTGTTGTGCAAGAA -s Anc1.Anc1refChr2 95231 26 + 144309 CCAAGTAGGAGAGTGTTGTGCAAGAA -s Anc2.Anc2refChr3 5185 26 + 53186 CCAAGTGGGAGAGTGTTGTGCAAGAA -s mr.mrrefChr0 118859 26 + 130230 ACAAGCAGGTAAGTGCTCAGCAAGGT -s simCow_chr6.simCow.chr6 128134 26 + 602619 CCAAGTGGGAGAGTATTGTGCAAAAA -s simDog_chr6.simDog.chr6 416507 26 - 593897 CCAAGTGGGTGAGTGCTATGTAAGCA -s simHuman_chr6.simHuman.chr6 119355 26 + 601863 CTAAGTAGGAGAGTGTTGTGCAAGAG -s simRat_chr6.simRat.chr6 116709 26 + 647215 ACAAGCTGGTAAGTGCCAGGCAGGGT - -a -s simMouse_chr6.simMouse.chr6 124377 5 + 636262 GGCAC -s Anc0.Anc0refChr1 16760 4 - 62388 GT-AC -s Anc1.Anc1refChr2 95257 5 + 144309 GTCAC -s Anc2.Anc2refChr3 5211 4 + 53186 GT-AG -s mr.mrrefChr0 118885 5 + 130230 GGCAC -s simCow_chr6.simCow.chr6 128162 4 + 602619 GT-AG -s simDog_chr6.simDog.chr6 416533 4 - 593897 GT-AG -s simHuman_chr6.simHuman.chr6 119381 5 + 601863 GTCAC -s simRat_chr6.simRat.chr6 116735 5 + 647215 GGTAC - -a -s simMouse_chr6.simMouse.chr6 124382 42 + 636262 AATCACATTCTGACTTAACCTATTTATTTGACTTGTGTTCAT -s Anc0.Anc0refChr1 16767 42 - 62388 AATCACATTCTGATTTAACCCACTTATTTCACTTACATTCAC -s Anc1.Anc1refChr2 95265 42 + 144309 AATCACATTCTGATTTAACCCACTTATTTCACTTACATTCAC -s Anc2.Anc2refChr3 5218 42 + 53186 AATCGCATTCTGATTTAACCCACTTATTTCACTTACATTCAC -s mr.mrrefChr0 118890 42 + 130230 AATCACATTCTGACTTAACCTACTTATTTGACTTGCATTCAC -s simCow_chr6.simCow.chr6 128169 42 + 602619 AATCTCATTCTGATTCAAGCCACTTATTTCATTTGTGTTCAC -s simDog_chr6.simDog.chr6 416540 42 - 593897 AATCGCATTCTGATCTAACCTACTTATCTCACTTACATTTAC -s simHuman_chr6.simHuman.chr6 119389 42 + 601863 AACCACCTTCTGATTTAACCCACTTATTTCACTTACATTCAC -s simRat_chr6.simRat.chr6 116740 42 + 647215 ATGCACATTCTGACTAAACCTACTTATTTGACATGCATGCAC - -a -s simMouse_chr6.simMouse.chr6 124424 9 + 636262 TGTGGTAGG -s Anc0.Anc0refChr1 16816 2 - 62388 TG------- -s Anc1.Anc1refChr2 95314 9 + 144309 TGTGGCAGG -s Anc2.Anc2refChr3 5267 2 + 53186 TG------- -s mr.mrrefChr0 118932 9 + 130230 TGTGGCAGG -s simCow_chr6.simCow.chr6 128218 2 + 602619 CG------- -s simDog_chr6.simDog.chr6 416589 2 - 593897 TG------- -s simHuman_chr6.simHuman.chr6 119438 8 + 601863 TGTGGCAG- -s simRat_chr6.simRat.chr6 116782 9 + 647215 TATGGCAGG - -a -s simMouse_chr6.simMouse.chr6 124433 35 + 636262 ATCAATTCTGGTAAATTGTCAGTGATGGCTATAAA -s Anc0.Anc0refChr1 16818 31 - 62388 AATGACTATGGGAAAATATCATTGCT----ATAAA -s Anc1.Anc1refChr2 95323 35 + 144309 AATGACTATGGGAAAATATCATTGCTTGCTATAAA -s Anc2.Anc2refChr3 5269 31 + 53186 AATGACTATAGGAAGATATCATTGCT----ATAAA -s mr.mrrefChr0 118941 35 + 130230 ATCAATTCTGGTAAATTGTCAGTGATGGCTATAAA -s simCow_chr6.simCow.chr6 128221 31 + 602619 AATGACTATAGGAAAACACCAATGCT----TTAGA -s simDog_chr6.simDog.chr6 416591 31 - 593897 AATGGTTATAGGAAGATATCATTGCT----ATAAA -s simHuman_chr6.simHuman.chr6 119446 32 + 601863 ACTGACTATGT---AATATCATTGCTTGCTATAAA -s simRat_chr6.simRat.chr6 116791 35 + 647215 AGTGGTTCTGGTAAATTGTCGATGATGGCTATAAA - -a -s simMouse_chr6.simMouse.chr6 124468 21 + 636262 CTTCAAATGAGGATTGTCACT -s Anc0.Anc0refChr1 16869 21 - 62388 CTTCAAATTGAGATTGCCTAT -s Anc1.Anc1refChr2 95378 21 + 144309 CTTCAAATTGAGATTGCCTAT -s Anc2.Anc2refChr3 5320 21 + 53186 CTTCAAAGTGAGATTGCTTAC -s mr.mrrefChr0 118976 21 + 130230 CTTCAAATTAGGATTGTCACT -s simCow_chr6.simCow.chr6 128275 21 + 602619 ATTCAAGGTAAAACTGCTTAC -s simDog_chr6.simDog.chr6 416642 20 - 593897 CTTCAAAGTGAGGTTGCT-AC -s simHuman_chr6.simHuman.chr6 119498 21 + 601863 CTTCGAATTGAGAATGCCGAT -s simRat_chr6.simRat.chr6 116826 21 + 647215 CTTCAAATTAGGATTGTCACT - -a -s simMouse_chr6.simMouse.chr6 124489 40 + 636262 GGGATCTTTATCCAATGATGCTGAGTGTGACAGCACAATC -s Anc0.Anc0refChr1 16890 37 - 62388 GGGATCATTTTTCAATGA---CAAGTGTTACAGTACAGTC -s Anc1.Anc1refChr2 95399 37 + 144309 GGGATCATTTTTCAATGA---CAAGTGTTACAGTACAGTC -s Anc2.Anc2refChr3 5341 37 + 53186 AGGATCATTTTTCAATGC---CAAGTGTTATAGTACAGTC -s mr.mrrefChr0 118997 39 + 130230 GGGATCTTTATTCAATGAT-CTGAGTGTGACAGCACAATC -s simCow_chr6.simCow.chr6 128296 33 + 602619 TGGATCATTTTTCTGTGC---CAATTGT----GTACAATC -s simDog_chr6.simDog.chr6 416662 37 - 593897 AGAATCATTTTTCAATTC---CAAGTGTTATAGTACAGTT -s simHuman_chr6.simHuman.chr6 119519 37 + 601863 GGGATCATTTTTCAACGA---CAAGTGTAACAGTATAGTC -s simRat_chr6.simRat.chr6 116848 39 + 647215 GGGATCTTTATTCAGTGAT-CTGAATGTGACAGCACAAGA - -a -s simMouse_chr6.simMouse.chr6 124529 5 + 636262 CACAC -s Anc0.Anc0refChr1 16928 5 - 62388 CAAAG -s Anc1.Anc1refChr2 95437 5 + 144309 CAAAG -s Anc2.Anc2refChr3 5379 5 + 53186 CAAAG -s mr.mrrefChr0 119036 5 + 130230 CACAC -s simCow_chr6.simCow.chr6 128330 5 + 602619 CAAAG -s simDog_chr6.simDog.chr6 416700 5 - 593897 CGAAG -s simHuman_chr6.simHuman.chr6 119557 5 + 601863 CAAAT -s simRat_chr6.simRat.chr6 116887 5 + 647215 CACAT - -a -s simMouse_chr6.simMouse.chr6 124534 28 + 636262 AATGCTAGCTAAATGTGCATGACAGCTC -s Anc0.Anc0refChr1 16937 27 - 62388 AATGCTTGCAAAATGCTTA-GACAGTCT -s Anc1.Anc1refChr2 95446 27 + 144309 AATGCTTGCAAAATGCTTA-GACAGTCT -s Anc2.Anc2refChr3 5388 27 + 53186 AATGCTTCCAAAATGCTTA-GATAGTCT -s mr.mrrefChr0 119041 28 + 130230 AATGCTAGCTAAATGCGCATGACAGCTT -s simCow_chr6.simCow.chr6 128339 22 + 602619 AATGCT-----AACACTTT-GATAGTAT -s simDog_chr6.simDog.chr6 416709 27 - 593897 AATGCTTCCAAAATGCTTA-GGTAGTCT -s simHuman_chr6.simHuman.chr6 119566 27 + 601863 AATGCTTGCGAAATGCTTA-GACAGTCT -s simRat_chr6.simRat.chr6 116892 28 + 647215 AATGCTAGATAAATGCACATGACACCTT - -a -s simMouse_chr6.simMouse.chr6 124562 18 + 636262 AATCTTGGTTGTTCAAGT -s Anc0.Anc0refChr1 16964 15 - 62388 GATCTCTATTGTTTA--- -s Anc1.Anc1refChr2 95473 15 + 144309 GATCTCTATTGTTTA--- -s Anc2.Anc2refChr3 5415 15 + 53186 GATCTCTATTGTTTA--- -s mr.mrrefChr0 119069 18 + 130230 GATCTCGGTTGTTCAAGT -s simCow_chr6.simCow.chr6 128363 15 + 602619 GACCTCTATTGTTTA--- -s simDog_chr6.simDog.chr6 416736 4 - 593897 GATC-------------- -s simHuman_chr6.simHuman.chr6 119593 15 + 601863 GATCTCTATTGTTTA--- -s simRat_chr6.simRat.chr6 116920 18 + 647215 GATGTCGGTTGTCacact - -a -s simMouse_chr6.simMouse.chr6 124580 53 + 636262 CAGGAATCATGGACCAGAGGGTGTAGCTTGTTCTGCAGATAAAGGAACAATCA -s Anc0.Anc0refChr1 16979 5 - 62388 ------------------------------------------------AATCA -s Anc1.Anc1refChr2 95488 5 + 144309 ------------------------------------------------AATCA -s Anc2.Anc2refChr3 5430 5 + 53186 ------------------------------------------------AATCA -s mr.mrrefChr0 119518 53 + 130230 CAGGAATCATGGACCAGGGGGTGTAACTTGTTCTGCAGATAAAAGAACAATCA -s simCow_chr6.simCow.chr6 128378 5 + 602619 ------------------------------------------------GATTA -s simDog_chr6.simDog.chr6 416740 5 - 593897 ------------------------------------------------AAGCT -s simHuman_chr6.simHuman.chr6 119608 5 + 601863 ------------------------------------------------AATCA -s simRat_chr6.simRat.chr6 123093 53 + 647215 caggaatcattgaCCAGGGAGAGTTACTTGTTTTGCAGATGAAAGAACAATAT - -a -s simMouse_chr6.simMouse.chr6 124633 8 + 636262 TGCAGTGG -s Anc0.Anc0refChr1 16984 7 - 62388 TG-AATGG -s Anc1.Anc1refChr2 95493 7 + 144309 TG-AATGG -s Anc2.Anc2refChr3 5435 7 + 53186 TG-AATGG -s mr.mrrefChr0 119571 7 + 130230 TG-AGTGG -s simCow_chr6.simCow.chr6 128403 7 + 602619 TG-AATGA -s simDog_chr6.simDog.chr6 416745 7 - 593897 TG-GATGG -s simHuman_chr6.simHuman.chr6 119613 7 + 601863 TG-AATAG -s simRat_chr6.simRat.chr6 123146 7 + 647215 TG-GGCGG - -a -s simMouse_chr6.simMouse.chr6 124641 10 + 636262 AGGAATTAAC -s Anc0.Anc0refChr1 16991 5 - 62388 -----TTAAG -s Anc1.Anc1refChr2 95500 10 + 144309 AGGCATTAAG -s Anc2.Anc2refChr3 5442 5 + 53186 -----TTAAG -s mr.mrrefChr0 119578 10 + 130230 AGGAATTAAC -s simCow_chr6.simCow.chr6 128410 5 + 602619 -----TTAAG -s simDog_chr6.simDog.chr6 416752 5 - 593897 -----TTAAG -s simHuman_chr6.simHuman.chr6 119626 10 + 601863 AGGCACTAAA -s simRat_chr6.simRat.chr6 123153 10 + 647215 AGGAATGAAC - -a -s simMouse_chr6.simMouse.chr6 124651 16 + 636262 AGAATTGAATCCAAAC -s Anc0.Anc0refChr1 16996 9 - 62388 ACAGA-------AAAC -s Anc1.Anc1refChr2 95510 9 + 144309 ACAGA-------AAAC -s Anc2.Anc2refChr3 5447 9 + 53186 ACAGA-------AAAC -s mr.mrrefChr0 119588 9 + 130230 AGAAT-------AAAC -s simCow_chr6.simCow.chr6 128415 9 + 602619 ACAGA-------CAAC -s simDog_chr6.simDog.chr6 416757 9 - 593897 AGAAA-------AAAC -s simHuman_chr6.simHuman.chr6 119644 9 + 601863 ACAGA-------AAAC -s simRat_chr6.simRat.chr6 123163 9 + 647215 AGAAT-------AAAC - -a -s simMouse_chr6.simMouse.chr6 124667 25 + 636262 AAGACCCAAAATAACACCTAAGCAG -s Anc0.Anc0refChr1 17012 25 - 62388 AATCCCTAAAAGAACTGCTGACTAG -s Anc1.Anc1refChr2 95526 25 + 144309 AATCCCTAAAAGAACTGCTGACTAG -s Anc2.Anc2refChr3 5466 25 + 53186 AATCCCTAAAAGAACTGCTGCCTAT -s mr.mrrefChr0 119597 25 + 130230 AAGCCCCAAAATAACACCTGAGCAG -s simCow_chr6.simCow.chr6 128434 24 + 602619 AATCGCT-AAAGAACTGCTGCCTAT -s simDog_chr6.simDog.chr6 416776 25 - 593897 AACCCTCAAAAGAACTACTGCCTAT -s simHuman_chr6.simHuman.chr6 119660 25 + 601863 AATCCCTAAAAGAACTGCTGACTAG -s simRat_chr6.simRat.chr6 123172 25 + 647215 GAGCCCCAAAATAACGACTGAGCAG - -a -s simMouse_chr6.simMouse.chr6 124692 19 + 636262 CTATTGTGAGACCCATGTC -s Anc0.Anc0refChr1 17037 17 - 62388 CTTTTGT--GACCTATGTC -s Anc1.Anc1refChr2 95551 17 + 144309 CTTTTGT--GACCTATGTC -s Anc2.Anc2refChr3 5491 17 + 53186 CTTTTGT--AACTTATGTC -s mr.mrrefChr0 119622 19 + 130230 CTATTGTGAGACCTATGTC -s simCow_chr6.simCow.chr6 128458 17 + 602619 CTTTTGT--TACTTATGCC -s simDog_chr6.simDog.chr6 416801 17 - 593897 ATTTTGT--AACTAATGTC -s simHuman_chr6.simHuman.chr6 119686 17 + 601863 CTGTTGT--GACCTATGTC -s simRat_chr6.simRat.chr6 123197 19 + 647215 CTATTGTGAGACCTGTGTC - -a -s simMouse_chr6.simMouse.chr6 124711 42 + 636262 AGATTTTGACTGATGCAATGTTTGATCAGCAGAACAATAGCA -s Anc0.Anc0refChr1 17054 42 - 62388 AAATTGATACTAATGCAATGATTGATCAGCAAAAGAATAGGA -s Anc1.Anc1refChr2 95568 42 + 144309 AAATTGATACTAATGCAATGATTGATCAGCAAAAGAATAGGA -s Anc2.Anc2refChr3 5508 42 + 53186 AAATCGATACTAATGCAATGATTGATCAACAAAAGAATAGGA -s mr.mrrefChr0 119641 42 + 130230 AGATTGTGACTGATGCAATGTTTGATCAGCAGAACAATAGCA -s simCow_chr6.simCow.chr6 128475 42 + 602619 AACTAGATAGTAATGCGATGAGTGATCTACAAAAAAAAAAGA -s simDog_chr6.simDog.chr6 416818 42 - 593897 AAATCAACACTCATGCAATGATTGATCAACGAAAGTATTGGA -s simHuman_chr6.simHuman.chr6 119704 42 + 601863 AAATTGATACTAATGCAGTTATTAGTCAGCAAGAGAATAGGA -s simRat_chr6.simRat.chr6 123216 42 + 647215 AGATTGTGACTGATGCAATGTTTGATCAGCAGAACAATAGCG - -a -s simMouse_chr6.simMouse.chr6 124753 81 + 636262 GGGAGCTGAGAAGTGTATGAATGCAGGGTGATGAGCCCGAATTGTTCTGGGTTTTCAGTATAGCACCATTGCCCTGCTCAA -s Anc0.Anc0refChr1 17096 72 - 62388 GGGAGCCGACAAAAGTA-----G----ATGATGAGCCCCTAGTGTTCTGGATTATCAGCATAGCACCATTGATCCACTCAA -s Anc1.Anc1refChr2 95610 76 + 144309 GGGAGCCGACAAAAGTA-----GTATTATGATGAGCCCCTAGTGTTCTGGATTATCAGCATAGCACCATTGATCCACTCAA -s Anc2.Anc2refChr3 5553 72 + 53186 GGGAGCATGCAAAAGTA-----G----ATGATGAGTACCTAGTGTTCTGGATTATCAGCATAGCACCATGGATCCACTTAA -s mr.mrrefChr0 119683 81 + 130230 GGGAGCCGAGAAGTGTATGAATGTATGGTGATGAGCCCGAAGTGTTCTGGGTTTTCAGTATAGCACCATTGCCCTGCTCAA -s simCow_chr6.simCow.chr6 128520 42 + 602619 --------------------------------------CTAGTATTCTGAATTATCAATATAGCACCATGGATCTGCTTG- -s simDog_chr6.simDog.chr6 416867 72 - 593897 GGGAGCATGCAAAAGTA-----G----ATGATGAGTACCTAGTGTTTTGGATTATTAGCATTGCACCGTGGATTCACATAA -s simHuman_chr6.simHuman.chr6 119746 76 + 601863 GGGAGCCGACAATAAGA-----GTATTATGATGAGCCCCTAGTGTTCTGGATTATCAGCGTAACACCATTGATCCACTCAA -s simRat_chr6.simRat.chr6 123258 76 + 647215 -----CCGAGAAATTTATGAATGTATGGTCATGAGCCTGAAGTGTTCCGGGTTTTCAGTATAGCACCACTGCCCTGCTCAA - -a -s simMouse_chr6.simMouse.chr6 124834 26 + 636262 GAGGGTTTAGTATTGTTGCCCAATGT -s Anc0.Anc0refChr1 17169 26 - 62388 GGGGGTTCAGAATTCTTGCCCTATGT -s Anc1.Anc1refChr2 95687 26 + 144309 GGGGGTTCAGAATTCTTGCCCTATGT -s Anc2.Anc2refChr3 5626 26 + 53186 AGGGATTAAGAATTCTTGCCCTATGT -s mr.mrrefChr0 119764 26 + 130230 GAGGGTTCAGTATTGTTGCCCAATGT -s simCow_chr6.simCow.chr6 128562 17 + 602619 ---------GAATTCTTGCCCTATGC -s simDog_chr6.simDog.chr6 416940 26 - 593897 AGGGATTAAGAATTCTTGCCCTATGT -s simHuman_chr6.simHuman.chr6 119823 26 + 601863 GGGGGTTCAGAATTCTTGCCCTCTGT -s simRat_chr6.simRat.chr6 123334 26 + 647215 GAGGGTTCAGTATTGTTGCCCAATGT - -a -s simMouse_chr6.simMouse.chr6 124860 22 + 636262 TGTGGTGTGATCCTCTTAGAAG -s Anc0.Anc0refChr1 17195 22 - 62388 GACGATGTGACACTCTTAGAAG -s Anc1.Anc1refChr2 95713 22 + 144309 GACGATGTGACACTCTTAGAAG -s Anc2.Anc2refChr3 5652 22 + 53186 GATGATGTGACACTCTTTGAAG -s mr.mrrefChr0 119790 22 + 130230 TGCGATGTGATCCTCTTAGAAG -s simCow_chr6.simCow.chr6 128579 22 + 602619 GGTGATGCAAAACTCTTTCAAG -s simDog_chr6.simDog.chr6 416973 22 - 593897 GATGATGTGACACTTTTTGAAG -s simHuman_chr6.simHuman.chr6 119849 22 + 601863 GACAATGTGGCACTCTTAGAAG -s simRat_chr6.simRat.chr6 123360 22 + 647215 TGCGATGTGAGCCTCTTAGAAG - -a -s simMouse_chr6.simMouse.chr6 124882 19 + 636262 GAAAAGCAAATAGCCGGTA -s Anc0.Anc0refChr1 17217 19 - 62388 AGAATGTAACCAGCTGGTA -s Anc1.Anc1refChr2 95735 19 + 144309 AGAATGTAACCAGCTGGTA -s Anc2.Anc2refChr3 5674 19 + 53186 AGAATGTAACCAGCTGGTA -s mr.mrrefChr0 119812 19 + 130230 GAAATGCAAATAGCTGGTA -s simCow_chr6.simCow.chr6 128601 19 + 602619 AGAATGCAACCAGTTGCTA -s simDog_chr6.simDog.chr6 416996 19 - 593897 AGAATGTAACCAGCTGGAA -s simHuman_chr6.simHuman.chr6 119871 19 + 601863 AGAATGTAACCAGCTCGTA -s simRat_chr6.simRat.chr6 123382 19 + 647215 GAAATGCAAATAGCTGGTA - -a -s simMouse_chr6.simMouse.chr6 124901 21 + 636262 GACATTATCAGTTGTCGCAAT -s Anc0.Anc0refChr1 17236 20 - 62388 AACATCAGCAGT-GTGGTGAT -s Anc1.Anc1refChr2 95754 20 + 144309 AACATCAGCAGT-GTGGTGAT -s Anc2.Anc2refChr3 5693 20 + 53186 AAAATCAGCAGT-GTGTTGAA -s mr.mrrefChr0 119831 20 + 130230 GACATCAGCAGT-GTGGCAAT -s simCow_chr6.simCow.chr6 128620 17 + 602619 AA---CAGCTGT-ATATTGAA -s simDog_chr6.simDog.chr6 417015 20 - 593897 AAAATTGGCAGT-GTGTTGAA -s simHuman_chr6.simHuman.chr6 119893 20 + 601863 TACATCAGCAGT-GTGGTGAT -s simRat_chr6.simRat.chr6 123401 20 + 647215 ACCATCAGCGGT-GTGGCAAT - -a -s simMouse_chr6.simMouse.chr6 124922 30 + 636262 AGTGAGGATGAGCCTCATATACGATGTTTA -s Anc0.Anc0refChr1 17256 30 - 62388 AATGACATGTGTCCTGATCTATGATGGTAG -s Anc1.Anc1refChr2 95774 30 + 144309 AATGACATGTGTCCTGATCTATGATGGTAG -s Anc2.Anc2refChr3 5713 30 + 53186 GATGACATGTATCCAGATCTGTGATGGTAG -s mr.mrrefChr0 119851 30 + 130230 AGTGAGGATGGTCCTCATATACGATGTTTG -s simCow_chr6.simCow.chr6 128637 1 + 602619 G----------------------------- -s simDog_chr6.simDog.chr6 417035 30 - 593897 GATGACATGTATCCAGATCTGTGATGGTAG -s simHuman_chr6.simHuman.chr6 119914 30 + 601863 AATGACATGTGTCCTAATCTATGATGGCAG -s simRat_chr6.simRat.chr6 123421 30 + 647215 TGTGAGGATGGTCCTCATATAGGATGTTTG - -a -s simMouse_chr6.simMouse.chr6 124952 1 + 636262 C -s Anc0.Anc0refChr1 17286 1 - 62388 C -s Anc1.Anc1refChr2 95804 1 + 144309 C -s Anc2.Anc2refChr3 5743 1 + 53186 C -s mr.mrrefChr0 119881 1 + 130230 C -s simDog_chr6.simDog.chr6 417065 1 - 593897 C -s simHuman_chr6.simHuman.chr6 119954 1 + 601863 C -s simRat_chr6.simRat.chr6 123451 1 + 647215 C - -a -s simMouse_chr6.simMouse.chr6 124953 6 + 636262 TACAAA -s Anc0.Anc0refChr1 17287 6 - 62388 TACAAC -s Anc1.Anc1refChr2 95805 6 + 144309 TACAAC -s Anc2.Anc2refChr3 5748 6 + 53186 TATAAC -s mr.mrrefChr0 119882 6 + 130230 TACAAA -s simCow_chr6.simCow.chr6 128638 6 + 602619 TGTAAC -s simDog_chr6.simDog.chr6 417070 6 - 593897 TATAAC -s simHuman_chr6.simHuman.chr6 119955 6 + 601863 TACAAC -s simRat_chr6.simRat.chr6 123452 6 + 647215 TACACG - -a -s simMouse_chr6.simMouse.chr6 124959 12 + 636262 CTTACCATACTG -s Anc0.Anc0refChr1 17293 12 - 62388 TTCAGCATCCTG -s Anc1.Anc1refChr2 95811 12 + 144309 TTCAGCATCCTG -s Anc2.Anc2refChr3 5754 12 + 53186 TCCAGCATCCTG -s mr.mrrefChr0 119888 12 + 130230 CTTAGCATCCTG -s simCow_chr6.simCow.chr6 128648 12 + 602619 TCCCGCATCCTG -s simDog_chr6.simDog.chr6 417076 12 - 593897 TCCAGCATTATG -s simHuman_chr6.simHuman.chr6 119961 12 + 601863 TTCAGTATCCTG -s simRat_chr6.simRat.chr6 123458 12 + 647215 CTTAGCTTCCTG - -a -s simMouse_chr6.simMouse.chr6 124971 12 + 636262 GGATGCTGATGG -s Anc0.Anc0refChr1 17306 12 - 62388 GGATTTTGATTC -s Anc1.Anc1refChr2 95824 12 + 144309 GGATTTTGATTC -s Anc2.Anc2refChr3 5767 12 + 53186 GGGTTTTGATTC -s mr.mrrefChr0 119900 12 + 130230 GGATGTTGATTC -s simCow_chr6.simCow.chr6 128660 12 + 602619 AGGTGTTGGTTT -s simDog_chr6.simDog.chr6 417089 12 - 593897 GGGTTTTGATTC -s simHuman_chr6.simHuman.chr6 119974 12 + 601863 GGATATTGTTTC -s simRat_chr6.simRat.chr6 123470 12 + 647215 GGATGTTGGTTC - -a -s simMouse_chr6.simMouse.chr6 124983 9 + 636262 GGAAGTTCC -s Anc0.Anc0refChr1 17321 9 - 62388 GGTTAGCCC -s Anc1.Anc1refChr2 95839 9 + 144309 GGTTAGCCC -s Anc2.Anc2refChr3 5782 9 + 53186 GGTTAGCCC -s mr.mrrefChr0 119915 9 + 130230 GGAAGGTCC -s simCow_chr6.simCow.chr6 128675 9 + 602619 GGTTAGCCC -s simDog_chr6.simDog.chr6 417104 9 - 593897 GGTTAGCCC -s simHuman_chr6.simHuman.chr6 119989 9 + 601863 GGTTAGCCC -s simRat_chr6.simRat.chr6 123485 9 + 647215 GGGAGGTCC - -a -s simMouse_chr6.simMouse.chr6 124992 11 + 636262 AGACAGGGATG -s Anc0.Anc0refChr1 17330 11 - 62388 AGAAAGGGATA -s Anc1.Anc1refChr2 95848 11 + 144309 AGAAAGGGATA -s Anc2.Anc2refChr3 5791 11 + 53186 AGAAAGGGATA -s mr.mrrefChr0 119924 11 + 130230 AGACAGGGATG -s simCow_chr6.simCow.chr6 128684 11 + 602619 AGAAAAGGATA -s simDog_chr6.simDog.chr6 417115 11 - 593897 AAATAGAGATA -s simHuman_chr6.simHuman.chr6 119998 11 + 601863 AGAAAGGGATA -s simRat_chr6.simRat.chr6 123494 11 + 647215 ACACAGGGATG - -a -s simMouse_chr6.simMouse.chr6 125003 10 + 636262 CCACCCCATA -s Anc0.Anc0refChr1 17344 9 - 62388 TAGCCC-AGA -s Anc1.Anc1refChr2 95862 10 + 144309 TAGCCCCAGA -s Anc2.Anc2refChr3 5805 9 + 53186 TAGCCC-AGA -s mr.mrrefChr0 119935 10 + 130230 CCACCCCATA -s simCow_chr6.simCow.chr6 128698 9 + 602619 TAGCCC-AGA -s simDog_chr6.simDog.chr6 417129 6 - 593897 TAGACC---- -s simHuman_chr6.simHuman.chr6 120012 10 + 601863 TAGCCCTAGA -s simRat_chr6.simRat.chr6 123505 10 + 647215 CCACCCCATA - -a -s simMouse_chr6.simMouse.chr6 125013 5 + 636262 TGAAG -s Anc0.Anc0refChr1 17360 5 - 62388 AGAAG -s Anc1.Anc1refChr2 95879 5 + 144309 AGAAG -s Anc2.Anc2refChr3 5821 5 + 53186 AGAAG -s mr.mrrefChr0 119945 5 + 130230 AGAAG -s simCow_chr6.simCow.chr6 128714 5 + 602619 AGGAG -s simDog_chr6.simDog.chr6 417140 5 - 593897 AGACA -s simHuman_chr6.simHuman.chr6 120029 5 + 601863 AGAAG -s simRat_chr6.simRat.chr6 123515 5 + 647215 AGAAG - -a -s simMouse_chr6.simMouse.chr6 125018 8 + 636262 TATGCTTT -s Anc0.Anc0refChr1 17365 8 - 62388 CATGCTTT -s Anc1.Anc1refChr2 95884 8 + 144309 CATGCTTT -s Anc2.Anc2refChr3 5826 8 + 53186 CATGCTTT -s mr.mrrefChr0 119950 8 + 130230 CATGCTTT -s simCow_chr6.simCow.chr6 128721 8 + 602619 CATGCTTT -s simDog_chr6.simDog.chr6 417145 8 - 593897 CATGCTTT -s simHuman_chr6.simHuman.chr6 120034 8 + 601863 CGTGCTTT -s simRat_chr6.simRat.chr6 123520 7 + 647215 CAT-CTTT - -a -s simMouse_chr6.simMouse.chr6 125026 52 + 636262 ATATCCTGCCTTACTAAGGTGTGACTTAATGCAAAGTCTAAGTTTGTACTAA -s Anc0.Anc0refChr1 17377 52 - 62388 ACATCAAATCTGGCTGAGATATAACTAAATGCCAAACGTGAGTTCATAGTGA -s Anc1.Anc1refChr2 95896 52 + 144309 ACATCAAATCTGGCTGAGATATAACTAAATGCCAAACGTGAGTTCATAGTGA -s Anc2.Anc2refChr3 5838 52 + 53186 ACATAAAATCTGGCTGAGATATAACTAAATGGCAAACGTATGTTCATAGTGA -s mr.mrrefChr0 119958 52 + 130230 ATATCATATCTTACTGAGATGTAACTTAATGCAAAGTGTGAGTTTGTACTGA -s simCow_chr6.simCow.chr6 128733 52 + 602619 ACATGAAATCTGGCTGAGATATAGCTAGATGGCAAGTGTACATGCATATTGA -s simDog_chr6.simDog.chr6 417157 52 - 593897 ACATAAAATCTGGCAGGGATATAAGTAAATGGCAAACATATGTTCATAGTGA -s simHuman_chr6.simHuman.chr6 120046 52 + 601863 ACATCAAATCTAGCTGAGAAATACCTAAATGCCAACCGTGAGTCCATAGTGT -s simRat_chr6.simRat.chr6 123527 52 + 647215 ATGTCACATCTCACTGAGATGTAACTTAATCCAAAGTGTGAGTTTGTACTGA - -a -s simMouse_chr6.simMouse.chr6 125078 7 + 636262 TCTACTC -s Anc0.Anc0refChr1 17429 6 - 62388 GCTG-TA -s Anc1.Anc1refChr2 95948 6 + 144309 GCTG-TA -s Anc2.Anc2refChr3 5890 6 + 53186 GCTG-TA -s mr.mrrefChr0 120010 7 + 130230 TCTACTC -s simCow_chr6.simCow.chr6 128785 6 + 602619 TCTG-AG -s simDog_chr6.simDog.chr6 417209 6 - 593897 GCTG-TA -s simHuman_chr6.simHuman.chr6 120099 6 + 601863 GCTG-TA -s simRat_chr6.simRat.chr6 123579 7 + 647215 TCTATCC - -a -s simMouse_chr6.simMouse.chr6 125085 1 + 636262 A -s Anc0.Anc0refChr1 17435 1 - 62388 A -s Anc1.Anc1refChr2 95954 1 + 144309 A -s Anc2.Anc2refChr3 5898 1 + 53186 A -s mr.mrrefChr0 120017 1 + 130230 A -s simCow_chr6.simCow.chr6 128793 1 + 602619 A -s simDog_chr6.simDog.chr6 417217 1 - 593897 A -s simHuman_chr6.simHuman.chr6 120105 1 + 601863 A -s simRat_chr6.simRat.chr6 123586 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 125086 28 + 636262 ACGAGAGGGCTCGTAAATATCATGACCA -s Anc0.Anc0refChr1 17436 28 - 62388 ACAAGAATACTCCTTAATAATATGACTA -s Anc1.Anc1refChr2 95955 28 + 144309 ACAAGAATACTCCTTAATAATATGACTA -s Anc2.Anc2refChr3 5899 28 + 53186 ACAAGAATACTCCTTAATAATAGGACTA -s mr.mrrefChr0 120018 28 + 130230 ACGAGAAGGCTCGTAAATATCATGACCA -s simCow_chr6.simCow.chr6 128794 28 + 602619 ACAAAAATAATCCTTCATACTAGGACTA -s simDog_chr6.simDog.chr6 417218 28 - 593897 ACAAGAATACTCCTTAGTAACAGGACTA -s simHuman_chr6.simHuman.chr6 120106 28 + 601863 ACATGAATACTCCTTAATAGTATGACTT -s simRat_chr6.simRat.chr6 123588 28 + 647215 ACGAGGAGCCTCATAAATATCATGACCA - -a -s simMouse_chr6.simMouse.chr6 125114 7 + 636262 GAATTGG -s Anc0.Anc0refChr1 17464 7 - 62388 GAATTTG -s Anc1.Anc1refChr2 95983 7 + 144309 GAATTTG -s Anc2.Anc2refChr3 5932 7 + 53186 GAAGTTG -s mr.mrrefChr0 120046 7 + 130230 GAATTGG -s simCow_chr6.simCow.chr6 128827 3 + 602619 GAA---- -s simDog_chr6.simDog.chr6 417251 7 - 593897 GAAGTTG -s simHuman_chr6.simHuman.chr6 120134 7 + 601863 GAATTTG -s simRat_chr6.simRat.chr6 123616 7 + 647215 GAATTGG - -a -s simMouse_chr6.simMouse.chr6 125121 8 + 636262 ATGTGTTC -s Anc0.Anc0refChr1 17518 8 - 62388 GTGTGGTC -s Anc1.Anc1refChr2 96037 8 + 144309 GTGTGGTC -s Anc2.Anc2refChr3 5986 8 + 53186 GTGTGGTC -s mr.mrrefChr0 120053 8 + 130230 ATGTGTTC -s simCow_chr6.simCow.chr6 128879 8 + 602619 GTTTAGTC -s simDog_chr6.simDog.chr6 417305 8 - 593897 GTGTGGTC -s simHuman_chr6.simHuman.chr6 120188 8 + 601863 GTGAGGTC -s simRat_chr6.simRat.chr6 123623 8 + 647215 ATTTGTTC - -a -s simMouse_chr6.simMouse.chr6 125129 28 + 636262 ATTAAGGCCAGCGCAAACCTGTTCAAGT -s Anc0.Anc0refChr1 17527 28 - 62388 ATTAAGGCCAGCACACAGAAGTTTGTAT -s Anc1.Anc1refChr2 96046 28 + 144309 ATTAAGGCCAGCACACAGAAGTTTGTAT -s Anc2.Anc2refChr3 5995 28 + 53186 ATTGGGGTCAGCACACAGAAGTTTGTAT -s mr.mrrefChr0 120061 28 + 130230 ATTAAGGCCAGCGCAAAGCAGTTCAAGT -s simCow_chr6.simCow.chr6 128888 28 + 602619 ATTGGGGGCTGCACACAGAAGTTTGTAT -s simDog_chr6.simDog.chr6 417314 28 - 593897 GTTGGGGTCAGCGCACAGAAGTTTGTAT -s simHuman_chr6.simHuman.chr6 120197 28 + 601863 ATTAAGGCCAGCACTCAGAAGTTTGTAG -s simRat_chr6.simRat.chr6 123631 28 + 647215 GTTGAGGTCAGTGCAAAGCAGTCCCAGT - -a -s simMouse_chr6.simMouse.chr6 125157 40 + 636262 GAATAAAGCCACCCTACCCTTTACCTCTCTAAAGCACCTA -s Anc0.Anc0refChr1 17555 38 - 62388 GACTAAAGCTACTCAACCCTCAAC--TTCATAAACACCTA -s Anc1.Anc1refChr2 96074 38 + 144309 GACTAAAGCTACTCAACCCTCAAC--TTCATAAACACCTA -s Anc2.Anc2refChr3 6032 38 + 53186 GACTAAAGCTACTCAACCCTCAAC--TTCATAAATACTTA -s mr.mrrefChr0 120089 40 + 130230 GAATAAAGCCACCCTACCCTTAACCTCTCATAAGCACCTA -s simCow_chr6.simCow.chr6 128925 38 + 602619 GATTAAAGCTACTCAAGCCTCAAC--TTCATAAATGCTGA -s simDog_chr6.simDog.chr6 417351 38 - 593897 GACTAACACTACTCAACGCTTAAC--TTCATAAATACTTA -s simHuman_chr6.simHuman.chr6 120225 38 + 601863 GACTAAAGCTACTCAACCCTCAAC--TTGATAAACACCTA -s simRat_chr6.simRat.chr6 123659 40 + 647215 GCATAAAGCCGCCCTACCCATAACCACTCATAAGCACCTA - -a -s simMouse_chr6.simMouse.chr6 125197 20 + 636262 ACCTATGATGGGAGGCTGAT -s Anc0.Anc0refChr1 17595 20 - 62388 ACCTTTGGTAATAAGATGAA -s Anc1.Anc1refChr2 96114 20 + 144309 ACCTTTGGTAATAAGATGAA -s Anc2.Anc2refChr3 6072 20 + 53186 ACCTTTGATAATAAGATGAA -s mr.mrrefChr0 120129 20 + 130230 ACCTATGGTGGGAGGCTGAT -s simCow_chr6.simCow.chr6 128965 12 + 602619 ACCTTAGTTAAT-------- -s simDog_chr6.simDog.chr6 417391 20 - 593897 ACCTTTGATGGAAAGATGAA -s simHuman_chr6.simHuman.chr6 120265 20 + 601863 ACTTTTGGTAATAAGATGAA -s simRat_chr6.simRat.chr6 123699 20 + 647215 ACCTATGGTGGAAGGCTGAT - -a -s simMouse_chr6.simMouse.chr6 125217 6 + 636262 GGACTC -s Anc0.Anc0refChr1 17616 6 - 62388 GGCCTG -s Anc1.Anc1refChr2 96135 6 + 144309 GGCCTG -s Anc2.Anc2refChr3 6093 6 + 53186 GGCCTG -s mr.mrrefChr0 120150 6 + 130230 GGACTC -s simCow_chr6.simCow.chr6 128977 6 + 602619 GGCCTG -s simDog_chr6.simDog.chr6 417412 6 - 593897 TGCCTG -s simHuman_chr6.simHuman.chr6 120286 6 + 601863 GGCCTG -s simRat_chr6.simRat.chr6 123720 6 + 647215 GGACTC - -a -s simMouse_chr6.simMouse.chr6 125223 10 + 636262 CACTAACTGT -s Anc0.Anc0refChr1 17622 10 - 62388 CACTAACTGC -s Anc1.Anc1refChr2 96141 10 + 144309 CACTAACTGC -s Anc2.Anc2refChr3 6099 10 + 53186 CACTAAATGC -s mr.mrrefChr0 120156 10 + 130230 CACTAACTGT -s simCow_chr6.simCow.chr6 128984 10 + 602619 CACTAAATGC -s simDog_chr6.simDog.chr6 417418 10 - 593897 CACTAAATGT -s simHuman_chr6.simHuman.chr6 120292 10 + 601863 TGCTAACTGC -s simRat_chr6.simRat.chr6 123726 5 + 647215 CACTA----- - -a -s simMouse_chr6.simMouse.chr6 125233 57 + 636262 AGGATGCACAGTTCTACGGTAACTGTTCTCTTCTTTCAACACTATTTTATGTCTAGA -s Anc0.Anc0refChr1 17639 57 - 62388 GAGATGGGCAGTTCCATTGGAGCTGTTCTCTTTTTTCAACAACACTTTAGGTTTAGA -s Anc1.Anc1refChr2 96158 57 + 144309 GAGATGGGCAGTTCCATTGGAGCTGTTCTCTTTTTTCAACAACACTTTAGGTTTAGA -s Anc2.Anc2refChr3 6116 57 + 53186 GAGATGGGCAGTGCCATTGGCGCTGTTCTCTTTTTTCAACAGCACTTTAGGTTTAGA -s mr.mrrefChr0 120166 57 + 130230 AGGATGCACAGTTCTATGGTAACTGTTCTCTTTTTTCAACAACATTTTATGTCTAGA -s simCow_chr6.simCow.chr6 128999 53 + 602619 GAGATAGGCAGTACCATTGTCGCTGTTCTCTT----CAATAGCACTTTAGGTCAAGA -s simDog_chr6.simDog.chr6 417435 54 - 593897 GAGATGGGCAGTGCCAGTGGCACCGTTCT---TTTTCAACAGCACTTTATGTTTGGA -s simHuman_chr6.simHuman.chr6 120309 57 + 601863 GAGGTGGGCAGTTCCATTGGAGCTGTTCTCTTTTTTCAAAAACAATTTAGGTTTAGA -s simRat_chr6.simRat.chr6 123731 49 + 647215 --------CAGTTCTATGATAATCGTTCTTTTTTTTCAACAACTTTTTATGTCTAGA - -a -s simMouse_chr6.simMouse.chr6 125290 17 + 636262 CTAGGGCCTAGCAAGCT -s Anc0.Anc0refChr1 17699 16 - 62388 CTA-GGTCTAGCATGCT -s Anc1.Anc1refChr2 96218 16 + 144309 CTA-GGTCTAGCATGCT -s Anc2.Anc2refChr3 6176 16 + 53186 CTA-GATCTACCATGCT -s mr.mrrefChr0 120226 17 + 130230 CTAGGGCCTAGCAAGCT -s simCow_chr6.simCow.chr6 129055 16 + 602619 CTG-GATTTACCATGCC -s simDog_chr6.simDog.chr6 417492 16 - 593897 CTA-GATCTACCATGCT -s simHuman_chr6.simHuman.chr6 120379 16 + 601863 CTA-GGTCTAGCATGCT -s simRat_chr6.simRat.chr6 123783 17 + 647215 CTAGGGCCTAGTAAGTT - -a -s simMouse_chr6.simMouse.chr6 125307 7 + 636262 AAGTAAC -s Anc0.Anc0refChr1 17718 7 - 62388 AGGTAAC -s Anc1.Anc1refChr2 96237 7 + 144309 AGGTAAC -s Anc2.Anc2refChr3 6195 7 + 53186 AGGTAAC -s mr.mrrefChr0 120243 7 + 130230 AAGTAGC -s simCow_chr6.simCow.chr6 129074 7 + 602619 TGGTAAC -s simDog_chr6.simDog.chr6 417511 7 - 593897 AAGTAAT -s simHuman_chr6.simHuman.chr6 120398 7 + 601863 AGGTAAC -s simRat_chr6.simRat.chr6 123800 7 + 647215 AAGTAGC - -a -s simMouse_chr6.simMouse.chr6 125314 3 + 636262 AAT -s Anc0.Anc0refChr1 17731 3 - 62388 GAG -s Anc1.Anc1refChr2 96250 3 + 144309 GAG -s Anc2.Anc2refChr3 6208 3 + 53186 GAG -s mr.mrrefChr0 120250 3 + 130230 AAT -s simCow_chr6.simCow.chr6 129087 3 + 602619 GAG -s simDog_chr6.simDog.chr6 417524 3 - 593897 GGG -s simHuman_chr6.simHuman.chr6 120411 3 + 601863 GAG -s simRat_chr6.simRat.chr6 123807 3 + 647215 AAT - -a -s simMouse_chr6.simMouse.chr6 125317 45 + 636262 TACCACCACTTCAGCCCTCAACTGATGCTAACATATCATGTGATG -s Anc0.Anc0refChr1 17734 43 - 62388 CATTAACAGTTTGACTATGGACTA-T-TTAATTTACTCTGTGATA -s Anc1.Anc1refChr2 96253 44 + 144309 CATTAACAGTTTGACTATGGACTAAT-TTAATTTACTCTGTGATA -s Anc2.Anc2refChr3 6211 43 + 53186 CATTAACAGTTTGACTATGGGCTA-T-TTCATTTACTCTGTGATA -s mr.mrrefChr0 120253 45 + 130230 TACCACCACTTCAGCCCTCAACTGATGCTAACATATCATGTGATG -s simCow_chr6.simCow.chr6 129090 35 + 602619 CATCAACAGGTTGACTATGGGTTA-T-TTTGTTTAGT-------- -s simDog_chr6.simDog.chr6 417527 43 - 593897 CATTAACAGTTTGACTATGGGCTA-T-TTCATATGCTCTGTGATA -s simHuman_chr6.simHuman.chr6 120414 44 + 601863 CATTAACAGATTGATTATGGACTAGT-TTAATTCACTCTATGTTA -s simRat_chr6.simRat.chr6 123812 45 + 647215 TACCACCACTTCAGCCCTTAACCAACGCCAACATATCATGTGATG - -a -s simMouse_chr6.simMouse.chr6 125362 9 + 636262 GATTACTCT -s Anc0.Anc0refChr1 17780 9 - 62388 GACTATTCT -s Anc1.Anc1refChr2 96300 9 + 144309 GACTATTCT -s Anc2.Anc2refChr3 6257 9 + 53186 GACTATTCT -s mr.mrrefChr0 120298 9 + 130230 GATTACTCT -s simCow_chr6.simCow.chr6 133730 8 + 602619 -AGTATTCT -s simDog_chr6.simDog.chr6 417573 9 - 593897 GACTATTCT -s simHuman_chr6.simHuman.chr6 120461 9 + 601863 GACTGATCT -s simRat_chr6.simRat.chr6 123857 9 + 647215 GATTACTCT - -a -s simMouse_chr6.simMouse.chr6 125371 9 + 636262 GGGACTTCA -s Anc0.Anc0refChr1 17790 9 - 62388 ACCACTTCA -s Anc1.Anc1refChr2 96310 9 + 144309 ACCACTTCA -s Anc2.Anc2refChr3 6267 9 + 53186 ACCACTTCA -s mr.mrrefChr0 120307 9 + 130230 GGGACTTCA -s simCow_chr6.simCow.chr6 133739 9 + 602619 ACCGCTTCA -s simDog_chr6.simDog.chr6 417583 9 - 593897 ACCACCTCA -s simHuman_chr6.simHuman.chr6 120471 9 + 601863 ACCACTTCA -s simRat_chr6.simRat.chr6 123866 9 + 647215 TCAACTTCA - -a -s simMouse_chr6.simMouse.chr6 125380 41 + 636262 ACTTATTGTGTTATTGGGCAATGCTATGTGTGGTTTACCTT -s Anc0.Anc0refChr1 17799 30 - 62388 A--------GATATAGAGCAGGAC---AGGAGCCCTAcctT -s Anc1.Anc1refChr2 96319 30 + 144309 A--------GATATAGAGCAGGAC---AGGAGCCCTACCTT -s Anc2.Anc2refChr3 6290 30 + 53186 A--------GATGTAGAGCAGGAC---AGGAGCCCTAcagT -s mr.mrrefChr0 120316 41 + 130230 ACTTATTGTGTTATTGGGCAATGCTATGTGTGGTTTACCTT -s simCow_chr6.simCow.chr6 133762 21 + 602619 A--------GATGTA-AGCAGGAC---TGATG--------A -s simDog_chr6.simDog.chr6 417608 30 - 593897 A--------GATGTAGAGCAGGAC---AGGAGCCCTACAGT -s simHuman_chr6.simHuman.chr6 120480 25 + 601863 A--------GACATAGAGCAGGAC---AGGAG-----CCTT -s simRat_chr6.simRat.chr6 123875 41 + 647215 ACTTTTTACATCATTGGGCAAGGCTATGTGCGGTTTACCTT - -a -s simMouse_chr6.simMouse.chr6 125421 36 + 636262 TACCAACCGCTTGAGCACCCCTCAAACACCACTAGT -s Anc0.Anc0refChr1 17829 25 - 62388 TA--AACTGCTCCAGGACA--TCAA-------CATT -s Anc1.Anc1refChr2 96349 27 + 144309 TACCAACTGCTCCAGGACA--TCAA-------CATT -s Anc2.Anc2refChr3 6320 25 + 53186 TG--GACTGGTCCAGGACA--TCAA-------CATT -s mr.mrrefChr0 120357 34 + 130230 TACCAACCGCTTGAGCATC--TCAAACACCCCTATT -s simCow_chr6.simCow.chr6 133783 25 + 602619 TG--GACGCCTCCAGGACA--TTAA-------CATT -s simDog_chr6.simDog.chr6 417638 25 - 593897 TG--GACTGGTCCAGGACA--TCAA-------TATT -s simHuman_chr6.simHuman.chr6 120581 26 + 601863 CACCAA-TACTCCAGGACA--TCAA-------CATT -s simRat_chr6.simRat.chr6 123916 34 + 647215 TACCAACCACTCGCTCATT--TCAAACACCCCTATT - -a -s simMouse_chr6.simMouse.chr6 125457 65 + 636262 ACTACTTAATAGCATTAGGAATTATAACTGACACTGATAAATTATTAATCCCCAATCAAACTACT -s Anc0.Anc0refChr1 17854 45 - 62388 ACTGTCTTGT----------ACAATGCC--------CTGCATGATTTACCTCT-ACC-AACCCCT -s Anc1.Anc1refChr2 96376 45 + 144309 ACTGTCTTGT----------ACAATGCC--------CTGCATGATTTACCTCT-ACC-AACCCCT -s Anc2.Anc2refChr3 6347 45 + 53186 ACTGTCTTGT----------ACAATGCC--------CTGCATGATTTACCTCT-ACA-AATGCCT -s mr.mrrefChr0 120391 57 + 130230 ACTACTTAATAGCATTAGGAATTATAAC--------ATAAATTATTAATCCCCAATCAAACCACT -s simCow_chr6.simCow.chr6 133810 32 + 602619 ACTGTCTCGT----------ATAATGCC--------C-----AATCTACCTCT-AA--------- -s simDog_chr6.simDog.chr6 417665 45 - 593897 ACTTTCTTGT----------ACAATGGC--------CTGCATGATTTGCCTTC-ACA-AATGCCT -s simHuman_chr6.simHuman.chr6 120607 45 + 601863 GCTGTATTGT----------ACAAGGCC--------CTGGGTGATATACCTCT-GCC-AACCCCT -s simRat_chr6.simRat.chr6 123950 54 + 647215 ACTACTTAGTAGCATTAGGAATTATAAC--------ATAAATTATTAATCCCCAATCGAACC--- - -a -s simMouse_chr6.simMouse.chr6 125522 29 + 636262 CCCTCACTTCTCAAACACCCCAATTACTG -s Anc0.Anc0refChr1 17899 21 - 62388 CCCTCCCTTCCCAAAGA--------ATTG -s Anc1.Anc1refChr2 96421 29 + 144309 CCCTCCCTTCCCAAAGACCCCTATTATTG -s Anc2.Anc2refChr3 6392 21 + 53186 GCCCTCGTTCCCAAAGA--------ATTG -s mr.mrrefChr0 120448 29 + 130230 CCCTCACTTCTCAAACACCCCAATTATTG -s simCow_chr6.simCow.chr6 133842 1 + 602619 ----------------------------G -s simDog_chr6.simDog.chr6 417710 21 - 593897 GCCCTCGTTCCCAAAGA--------ATTG -s simHuman_chr6.simHuman.chr6 120653 29 + 601863 CCCTCCCCTACCAAAGACCCCTATTACTA -s simRat_chr6.simRat.chr6 124004 20 + 647215 ---------CTAAAACACCCCTATCATTA - -a -s simMouse_chr6.simMouse.chr6 125551 54 + 636262 CATATAAGCATAAGGAATTATAACTGACACTGATGAATTATTAATTGACAATTA -s Anc0.Anc0refChr1 17920 44 - 62388 ----------TAGGGAATTACAACTAACAGTGATAAATTATTAATTCACTGTTC -s Anc1.Anc1refChr2 96453 54 + 144309 AAGACAAGCTTAGGGAATTACAACTAACAGTGATAAATTATTAATTCACTGTTC -s Anc2.Anc2refChr3 6413 44 + 53186 ----------TAGGGAATTACAAGTAACAGTGATAAATTATTAATTCACTGTTC -s mr.mrrefChr0 120480 54 + 130230 AATATAGGCATAAGGAATTATAACTGACACTGATGAATTATTAATTGACAATTG -s simCow_chr6.simCow.chr6 133843 44 + 602619 ----------TAGGGCATTACAAGTAACAGCGACAAATTATTAGTTCACTGTTC -s simDog_chr6.simDog.chr6 417731 44 - 593897 ----------TACGGATTTACAAGTGAGAGTGATAAATTATTAATTCACCGTTG -s simHuman_chr6.simHuman.chr6 120685 54 + 601863 AAGACAAGCTTAGGGAATCGCAACTAACAGTGATAAATTATCATTTCACTGATC -s simRat_chr6.simRat.chr6 124027 54 + 647215 AATATAGGCATAAGGAGCTATAACAGACCCTGATGAATTATTAATTGACAATTG - -a -s simMouse_chr6.simMouse.chr6 125605 8 + 636262 AATCAGTG -s Anc0.Anc0refChr1 17965 8 - 62388 AACCACTG -s Anc1.Anc1refChr2 96508 8 + 144309 AACCACTG -s Anc2.Anc2refChr3 6458 8 + 53186 AACAACTG -s mr.mrrefChr0 120534 8 + 130230 AATCAGTG -s simCow_chr6.simCow.chr6 133888 8 + 602619 AACAATTG -s simDog_chr6.simDog.chr6 417776 8 - 593897 AACAACTG -s simHuman_chr6.simHuman.chr6 120740 8 + 601863 AACCACTG -s simRat_chr6.simRat.chr6 124081 8 + 647215 AATCACTG - -a -s simMouse_chr6.simMouse.chr6 125613 49 + 636262 AACCTTTTTCATACATTCAGCATTTTTTCTTTTATAAAACCTGCGCCTT -s Anc0.Anc0refChr1 17983 45 - 62388 AAT-TTTTTCATACATTT--CATGTTTCTTTTTGTAGAACCTGC-CCTT -s Anc1.Anc1refChr2 96526 45 + 144309 AAT-TTTTTCATACATTT--CATGTTTCTTTTTGTAGAACCTGC-CCTT -s Anc2.Anc2refChr3 6476 45 + 53186 AAT-TTTTTGATATATTT--CATGTTGCTTTTTGTAGAACCTGC-CCTT -s mr.mrrefChr0 120542 48 + 130230 AAC-TTTTCCATACATTCAGCATTTTTTCTTTTGTAAAACCTGCGCCTT -s simCow_chr6.simCow.chr6 133906 24 + 602619 AAG-GTTATTATATACTT--CATGT----------------------TC -s simDog_chr6.simDog.chr6 417807 45 - 593897 AAT-TTCTTGATATATAT--CATGTTGCTTTTTGTAGAACCTGC-CCTT -s simHuman_chr6.simHuman.chr6 120758 45 + 601863 AAT-TTTTTCATACATTT--CATGTCTCTATTCATATTACCTGC-CCTT -s simRat_chr6.simRat.chr6 124089 48 + 647215 AAC-TTTTCCATACATTCAGCATTTTTTCTTTTGTAACACCTGCGCCTT - -a -s simMouse_chr6.simMouse.chr6 125662 18 + 636262 TGGATCATATTCTAAGTA -s Anc0.Anc0refChr1 18028 18 - 62388 TATGTCATATTCTAAATG -s Anc1.Anc1refChr2 96571 18 + 144309 TATGTCATATTCTAAATG -s Anc2.Anc2refChr3 6522 18 + 53186 TATGTCATACTCTAAATG -s mr.mrrefChr0 120590 18 + 130230 TAGATCATATTCTAAGTA -s simCow_chr6.simCow.chr6 133931 15 + 602619 TATGTAGTACTCT---TT -s simDog_chr6.simDog.chr6 417853 18 - 593897 TATGTCATACTCTAAATG -s simHuman_chr6.simHuman.chr6 120803 18 + 601863 AGTGTCATATTCTAAATG -s simRat_chr6.simRat.chr6 124137 18 + 647215 TAGATCATATTCTAAGTA - -a -s simMouse_chr6.simMouse.chr6 125680 10 + 636262 AGGGTAAGAA -s Anc0.Anc0refChr1 18046 10 - 62388 AGGGTAGGAA -s Anc1.Anc1refChr2 96589 10 + 144309 AGGGTAGGAA -s Anc2.Anc2refChr3 6540 10 + 53186 AGGGTAGGAG -s mr.mrrefChr0 120608 10 + 130230 AGGGTAAGAA -s simCow_chr6.simCow.chr6 133946 10 + 602619 GGGGTCTGAG -s simDog_chr6.simDog.chr6 417879 10 - 593897 AGGGTAGGAG -s simHuman_chr6.simHuman.chr6 120821 10 + 601863 AAGGTAGGAA -s simRat_chr6.simRat.chr6 124155 10 + 647215 AGGGTATTAA - -a -s simMouse_chr6.simMouse.chr6 125690 30 + 636262 TAGATTCACTTCCTTGTGGCATTCTGCAGC -s Anc0.Anc0refChr1 18058 28 - 62388 CAAAGCCACCTCCTTGTGG--TTCTGCAAC -s Anc1.Anc1refChr2 96601 30 + 144309 CAAAGCCACCTCCTTGTGGGATTCTGCAAC -s Anc2.Anc2refChr3 6552 28 + 53186 CAAAGCCACCTCCTTGTGG--TTCTGCAAC -s mr.mrrefChr0 120618 30 + 130230 TAGATTCACTTCCTTGTGGCATTCTGCAGC -s simCow_chr6.simCow.chr6 133958 28 + 602619 CAAAGTTGCATCCTTGTGG--TTCTGCAAG -s simDog_chr6.simDog.chr6 417891 28 - 593897 CAAAGCCACCTCTTTGTGG--TCCAGCAAC -s simHuman_chr6.simHuman.chr6 120833 30 + 601863 CAAAGCCACCTTCTTGTGGGATTCTGCGAC -s simRat_chr6.simRat.chr6 124165 29 + 647215 TGGACTCACTTCCTT-TCACATTCTGCAGT - -a -s simMouse_chr6.simMouse.chr6 125720 116 + 636262 AGTATACACTATTGTCTGTCTCAGATAACAATCAAATAGTTAGCAGCCAGTTAAAGACAAATGACGTATCTTAAGAAGAAGGTGCTCTCCAAACTGACAGGCAAATATACCTCAAA -s Anc0.Anc0refChr1 18086 108 - 62388 AGTATACACTATGGTCTGCCTCAGATATCAGTCTAACAGTTA----TCAGTCAAAGGCAAATGACATGTTCAAGGAAGAAGGTACCCCCCAAACTGACTGGAAGATACACC----A -s Anc1.Anc1refChr2 96631 108 + 144309 AGTATACACTATGGTCTGCCTCAGATATCAGTCTAACAGTTA----TCAGTCAAAGGCAAATGACATGTTCAAGGAAGAAGGTACCCCCCAAACTGACTGGAAGATACACC----A -s Anc2.Anc2refChr3 6580 108 + 53186 AGTATACACTATGGTCTGCCTCAGATATCAGTCTAACAGATA----TCAGTCAAAGGTAAATGACATGTTCAAGGAAGAAGGTACCCCCCAAACTGACTGGAAGATACACC----A -s mr.mrrefChr0 120648 116 + 130230 AGTATACACTATTGTCTGTCTCAGATAACAATCAAATAGTTAGCAGCCAGTTAAAGACAAATGACATATCTTAAGAAGAAGGTACTCTCCAAACTGACTGGCAAATATACCTCAAA -s simCow_chr6.simCow.chr6 133987 107 + 602619 ACCAACCCTCATGGTCTGCCTCGGATATCAATCTAGCAGATA----TCAGTCAAAGGTAAATGATATGTTC-AGGAAGAAGGTACCCCACAAACTGGCTGGAAGCTACATG----A -s simDog_chr6.simDog.chr6 417919 107 - 593897 AGTCTACACTATGGTCTGCCTCAGATATCAGTCTAACAG-AG----TCAGTTAAACATTAGTGACATGTGCAAGGAAGAACATACTCCCCAAGCTGACTGAAAGATGCACC----A -s simHuman_chr6.simHuman.chr6 120863 102 + 601863 AGTATACACTATGGGCTACCTC---TATCAGTCTAACAGTTA----TTAGTCAAAGGCAGATGACAAGTTCCAGACAGAAGGTACCCCGCAAACTGACTGGAAGACACA------- -s simRat_chr6.simRat.chr6 124194 115 + 647215 GGTAGACACTATTGTCTGTCTCAGATA-TAATCAAATAGCAAGCAGCCAGTCAAAGACAAATGACATATCTTAAGAAGAAGGTACTCTCCAAACTTACTGGCAAATATCCCTCAAA - -a -s simMouse_chr6.simMouse.chr6 125836 27 + 636262 CTACTCACTAACCTAAAATATGGAAGT -s Anc0.Anc0refChr1 18194 27 - 62388 CAACTTCCTGAACTAAAATATGCATGC -s Anc1.Anc1refChr2 96739 27 + 144309 CAACTTCCTGAACTAAAATATGCATGC -s Anc2.Anc2refChr3 6688 27 + 53186 CAACTTCCTGAACTAAAATATGCATGC -s mr.mrrefChr0 120764 27 + 130230 CTACTCACTAACCTAAAATATGCAAGT -s simCow_chr6.simCow.chr6 134094 27 + 602619 CAACTTCCTGAACTAAAATACACATGC -s simDog_chr6.simDog.chr6 418030 27 - 593897 CAACCTCCTAAACTAAAATATGCATGC -s simHuman_chr6.simHuman.chr6 120965 25 + 601863 --AGTTCCTGAACTCAAATATGCATGC -s simRat_chr6.simRat.chr6 124309 27 + 647215 CTACTCACTAACCTAAAATGTGCAAGT - -a -s simMouse_chr6.simMouse.chr6 125863 2 + 636262 TC -s Anc0.Anc0refChr1 18221 2 - 62388 TA -s Anc1.Anc1refChr2 96766 2 + 144309 TA -s Anc2.Anc2refChr3 6715 2 + 53186 TA -s mr.mrrefChr0 120791 2 + 130230 TC -s simCow_chr6.simCow.chr6 134122 2 + 602619 TA -s simDog_chr6.simDog.chr6 418057 2 - 593897 TA -s simHuman_chr6.simHuman.chr6 120990 2 + 601863 TA -s simRat_chr6.simRat.chr6 124336 2 + 647215 TC - -a -s simMouse_chr6.simMouse.chr6 125865 4 + 636262 CCCA -s Anc0.Anc0refChr1 18226 4 - 62388 CCCA -s Anc1.Anc1refChr2 96771 4 + 144309 CCCA -s Anc2.Anc2refChr3 6720 4 + 53186 CCCA -s mr.mrrefChr0 120793 4 + 130230 CCCA -s simCow_chr6.simCow.chr6 134127 4 + 602619 TCCA -s simDog_chr6.simDog.chr6 418062 4 - 593897 CCCA -s simHuman_chr6.simHuman.chr6 120995 4 + 601863 CCAA -s simRat_chr6.simRat.chr6 124338 4 + 647215 CCCA - -a -s simMouse_chr6.simMouse.chr6 125869 12 + 636262 TGGGCTGACCAC -s Anc0.Anc0refChr1 18231 12 - 62388 TGGGCTGCTCAC -s Anc1.Anc1refChr2 96776 12 + 144309 TGGGCTGCTCAC -s Anc2.Anc2refChr3 6725 12 + 53186 TGGGCTGCTCAC -s mr.mrrefChr0 120798 12 + 130230 TGGGCTGACCAC -s simCow_chr6.simCow.chr6 134132 12 + 602619 TGTGCTGCTCAC -s simDog_chr6.simDog.chr6 418067 12 - 593897 TGGGCTGCTCAC -s simHuman_chr6.simHuman.chr6 121000 12 + 601863 TGAGTTGCTCAC -s simRat_chr6.simRat.chr6 124343 12 + 647215 TGGGCTGACCAC - -a -s simMouse_chr6.simMouse.chr6 125881 3 + 636262 GAA -s Anc0.Anc0refChr1 18243 3 - 62388 GGA -s Anc1.Anc1refChr2 96788 3 + 144309 GGA -s Anc2.Anc2refChr3 6737 3 + 53186 TGT -s mr.mrrefChr0 120810 3 + 130230 GAA -s simCow_chr6.simCow.chr6 134144 3 + 602619 TGT -s simDog_chr6.simDog.chr6 418079 3 - 593897 TGT -s simHuman_chr6.simHuman.chr6 121036 3 + 601863 GCA -s simRat_chr6.simRat.chr6 124355 3 + 647215 AAA - -a -s simMouse_chr6.simMouse.chr6 125884 24 + 636262 TTGACGATAGCAAACAGATGTTAC -s Anc0.Anc0refChr1 18246 24 - 62388 ATGAAGTTAACTAATTGATGTTAC -s Anc1.Anc1refChr2 96791 24 + 144309 ATGAAGTTAACTAATTGATGTTAC -s Anc2.Anc2refChr3 6740 24 + 53186 ATGAAGTTAACTACTTGATTTTAC -s mr.mrrefChr0 120813 24 + 130230 TTGAAGTTAACTAACAGATGTTAC -s simCow_chr6.simCow.chr6 134148 11 + 602619 ATGAAGTTAAC------------- -s simDog_chr6.simDog.chr6 418082 24 - 593897 ATGAAGTTAACTACTTGATTTTAC -s simHuman_chr6.simHuman.chr6 121039 24 + 601863 ATGATGTTAACTAATTGAAGTTAC -s simRat_chr6.simRat.chr6 124358 24 + 647215 TTGAAGTTAACTAGCAGATGTTCC - -a -s simMouse_chr6.simMouse.chr6 125908 9 + 636262 TCATTTTTT -s Anc0.Anc0refChr1 18270 9 - 62388 CATTTTGTT -s Anc1.Anc1refChr2 96815 9 + 144309 CATTTTGTT -s Anc2.Anc2refChr3 6764 9 + 53186 CATTTTGCT -s mr.mrrefChr0 120837 9 + 130230 TCATTTTTT -s simCow_chr6.simCow.chr6 134159 5 + 602619 ----TTGCT -s simDog_chr6.simDog.chr6 418107 9 - 593897 CATTTTTCT -s simHuman_chr6.simHuman.chr6 121063 9 + 601863 CATCTTGTT -s simRat_chr6.simRat.chr6 124382 9 + 647215 TCATTTTTT - -a -s simMouse_chr6.simMouse.chr6 125917 66 + 636262 ATCATTCAACTCTCACAAGGGTCATGTGCATTTAAATTCTCACAAGGGTCATGTTCTAAATACAGA -s Anc0.Anc0refChr1 18279 42 - 62388 ATCATTCAACTCTCACAGGGGTCATGTACAT------------------------ATAAATACAGA -s Anc1.Anc1refChr2 96824 42 + 144309 ATCATTCAACTCTCACAGGGGTCATGTACAT------------------------ATAAATACAGA -s Anc2.Anc2refChr3 6775 42 + 53186 ATCATTCAACTCTCACAGGGGTTATGTATAT------------------------ATAAATACAGG -s mr.mrrefChr0 120846 42 + 130230 ATCATTCAACTCTCACAAGGGTCATGTGCAT------------------------CTAAATACAGA -s simCow_chr6.simCow.chr6 134166 42 + 602619 TTCATTCAACTCTCACAGGGGTTATGTATAT------------------------GTAAATACAGG -s simDog_chr6.simDog.chr6 418118 42 - 593897 ATCATACAACTCTCACAGGGGTTATGCATAT------------------------ATAAAGACAGG -s simHuman_chr6.simHuman.chr6 121072 41 + 601863 A-CATTCAACTCTCACAGGGATCACATACGT------------------------ATGGATACAGA -s simRat_chr6.simRat.chr6 124391 39 + 647215 ATCATTCAACTCTCATAAGGGT---GTGCAT------------------------CTAAATACAGA - -a -s simMouse_chr6.simMouse.chr6 125983 12 + 636262 TACCTTAATTTC -s Anc0.Anc0refChr1 18321 12 - 62388 TACCATAGCTTC -s Anc1.Anc1refChr2 96866 12 + 144309 TACCATAGCTTC -s Anc2.Anc2refChr3 6817 12 + 53186 TACCATAGCTTC -s mr.mrrefChr0 120888 12 + 130230 TACCTTAATTTC -s simCow_chr6.simCow.chr6 134237 12 + 602619 TACCATAGTTTC -s simDog_chr6.simDog.chr6 418160 12 - 593897 TACCATAGCTTC -s simHuman_chr6.simHuman.chr6 121113 12 + 601863 TACTGTAGCTTA -s simRat_chr6.simRat.chr6 124430 12 + 647215 TACCTTAATTTC - -a -s simMouse_chr6.simMouse.chr6 125995 20 + 636262 TTCCAATGAAAAAAAGTAAA -s Anc0.Anc0refChr1 18333 20 - 62388 TTCCAGTGAAACAAAGTGAA -s Anc1.Anc1refChr2 96878 20 + 144309 TTCCAGTGAAACAAAGTGAA -s Anc2.Anc2refChr3 6829 20 + 53186 TTCCAGTGAATCAAAATGAA -s mr.mrrefChr0 120900 20 + 130230 TTCCAATGAAAAAAAGTGAA -s simCow_chr6.simCow.chr6 134250 20 + 602619 TTTCAGTGACTCAAAATGAA -s simDog_chr6.simDog.chr6 418172 20 - 593897 TTCCAATGAATCAAGATGAA -s simHuman_chr6.simHuman.chr6 121125 20 + 601863 CTCCAGTGGAACAAAGTGGA -s simRat_chr6.simRat.chr6 124442 20 + 647215 CTCCAATGGAAAAAAGTGAA - -a -s simMouse_chr6.simMouse.chr6 126015 66 + 636262 AAAAGACACCACCCTATGTGGTGTCACTGCTCCTCTGGTGTACACCATATCTGACAGGTCCAGCTA -s Anc0.Anc0refChr1 18355 10 - 62388 AGAAAACACC-------------------------------------------------------- -s Anc1.Anc1refChr2 96900 10 + 144309 AGAAAACACC-------------------------------------------------------- -s Anc2.Anc2refChr3 6852 10 + 53186 AGAAAGCACC-------------------------------------------------------- -s mr.mrrefChr0 120920 61 + 130230 AAAAGACACCACCCTATGTGGTGTCACTGCTCCTCTGGTGTACA-----TCTGACAGGTCCAGCTA -s simCow_chr6.simCow.chr6 134273 10 + 602619 ACAAGGCACC-------------------------------------------------------- -s simDog_chr6.simDog.chr6 418195 10 - 593897 AGAGAGCACC-------------------------------------------------------- -s simHuman_chr6.simHuman.chr6 121147 10 + 601863 AGAAAACACC-------------------------------------------------------- -s simRat_chr6.simRat.chr6 124462 61 + 647215 AAAAGACACCGCGCTACGTGGTGTCACTGCTCCTGTGGTGTACT-----TCTGATAAATCCAGCTA - -a -s simMouse_chr6.simMouse.chr6 126081 168 + 636262 CCGTTTTAACCGACAAGTATGTCAGTAGAGGCGGATTAGGGTTTTGTAGTAACTCACGGATCATGCGAGGAATGATAGTATGCAACACACTATAGGAGTCACACAAATAGGAGTCACACAATTACCATCCCAGCATGGGATTCGCAGGAGACATTTATTAATAGGTAA -s Anc0.Anc0refChr1 18365 26 - 62388 ----------------------------------------------------------------------------------------------------------------------------------------------CGAAGGAAACAGTTATCAGTAAGTAA -s Anc1.Anc1refChr2 96910 26 + 144309 ----------------------------------------------------------------------------------------------------------------------------------------------CGAAGGAAACAGTTATCAGTAAGTAA -s Anc2.Anc2refChr3 6862 26 + 53186 ----------------------------------------------------------------------------------------------------------------------------------------------CCAAGGAAACAGTTATCAGTAAGTAA -s mr.mrrefChr0 120981 148 + 130230 CCGTTTTAACCGACAAGTATGTCAGTAGAGGCGGATTAGGGTTTTGTA---ACTCACGGATCATGCGAGGAATGATAGTATGCAACACACTATAGGAGTCACACAA---------------TTACCATCCCAGCA--GGATTCGCAGGAAACATTTATTAATAGGTAA -s simCow_chr6.simCow.chr6 134283 26 + 602619 ----------------------------------------------------------------------------------------------------------------------------------------------CGAAGGAAACAGTTATCATTAGATAA -s simDog_chr6.simDog.chr6 418205 26 - 593897 ----------------------------------------------------------------------------------------------------------------------------------------------CCAAGGAAACAGTTAGAAGTAAGCAA -s simHuman_chr6.simHuman.chr6 121157 25 + 601863 ----------------------------------------------------------------------------------------------------------------------------------------------CG-AGGAAACAGTCATCGGTAAGTAA -s simRat_chr6.simRat.chr6 124526 148 + 647215 CTGTCTTAGCGGACTAGGATGTCAGCAGGGGTGACTTAGGGTATTGTA---CCTCACATGTCTTGCCAGGAATGATAATATGCCACACACTACAGGAGTCACACAA---------------TCACAATCCCAGCA--GGATTCGCAGGAAACATTTATTTATAGGTAA - -a -s simMouse_chr6.simMouse.chr6 126249 30 + 636262 CAGGCCATATACTTGTCTCTTGGTGACATT -s Anc0.Anc0refChr1 18392 30 - 62388 AAGGTCAGATATATGTCTCTTGCTGACATT -s Anc1.Anc1refChr2 96937 30 + 144309 AAGGTCAGATATATGTCTCTTGCTGACATT -s Anc2.Anc2refChr3 6889 30 + 53186 AAGTTCAGAAATATGTCTATTGCTGATATC -s mr.mrrefChr0 121129 30 + 130230 CAGGCCAGATACTTGTCTCTTGGTGACATT -s simCow_chr6.simCow.chr6 134310 27 + 602619 AAGTGCAGAAATATGCCTATTGCTGAT--- -s simDog_chr6.simDog.chr6 418232 30 - 593897 AAGTTCAAAAATATGTCTATTGCTGATATC -s simHuman_chr6.simHuman.chr6 121183 30 + 601863 GAGGTAAGATATATGTTGCCTGCTAACATT -s simRat_chr6.simRat.chr6 124674 30 + 647215 CAGGCCAGATACTTGTCTCGTGGTGATATT - -a -s simMouse_chr6.simMouse.chr6 126279 37 + 636262 GTCTCTTAGTAATAACAATGTACTAACTCTCCAGCCG -s Anc0.Anc0refChr1 18422 26 - 62388 TG-TACTAATACCACAAAT----------TACAGCCA -s Anc1.Anc1refChr2 96967 27 + 144309 TGCTACTAATACCACAAAT----------TACAGCCA -s Anc2.Anc2refChr3 6919 26 + 53186 TG-TACTAACCCCGCAAAT----------TACAGCCA -s mr.mrrefChr0 121159 37 + 130230 GTCTCTTAGTAATAACAATGTACTAACTCTCCAGCCA -s simCow_chr6.simCow.chr6 134337 12 + 602619 ---------------GAAT----------TACAGCCA -s simDog_chr6.simDog.chr6 418265 26 - 593897 TG-TACTAACCCCGCAAAT----------TACAGCCA -s simHuman_chr6.simHuman.chr6 121213 27 + 601863 TGCTACTAATACCAGAAGT----------TACAGCCA -s simRat_chr6.simRat.chr6 124704 37 + 647215 GTCTCTTAGTTATAACAAAGTACTTATTCTCCAGCCA - -a -s simMouse_chr6.simMouse.chr6 126316 50 + 636262 TTCTTGAACACACCTGTAGAGAAAGTGATATGAATTAGTATATGTAAGAG -s Anc0.Anc0refChr1 18448 50 - 62388 TTCTTAAATATACATGTAGAAAAAAACACATGAATGGTGATATGTAGGAA -s Anc1.Anc1refChr2 96994 50 + 144309 TTCTTAAATATACATGTAGAAAAAAACACATGAATGGTGATATGTAGGAA -s Anc2.Anc2refChr3 6945 50 + 53186 TTCTTAAATATACATGTAGAAATAACCACATGAATGGTGATATGTAGGAA -s mr.mrrefChr0 121196 50 + 130230 TTCTTAAATACACCTGTAGAGAAAGAGATATGAATTAGTATATGTAAGAA -s simCow_chr6.simCow.chr6 134349 50 + 602619 TCCTTAAATATACATGTAGGAACAACCACATGAATGGTGATATACAGGAA -s simDog_chr6.simDog.chr6 418292 48 - 593897 TTCCTAAATATATATGTGGAAATAACCACATGAAT--TGATATGTAGAAA -s simHuman_chr6.simHuman.chr6 121240 50 + 601863 TTCTTAATTAAACATGTAGAAAAAAACGCATGAATAGTGATATTTAGGAA -s simRat_chr6.simRat.chr6 124741 43 + 647215 TTCTTAAATTCACCTGTAGGGAAAGAGATC-------GTATATATAAGAA - -a -s simMouse_chr6.simMouse.chr6 126366 10 + 636262 TCACAACCAA -s Anc0.Anc0refChr1 18498 10 - 62388 TCATAGACAA -s Anc1.Anc1refChr2 97044 10 + 144309 TCATAGACAA -s Anc2.Anc2refChr3 6995 10 + 53186 TCATAGACAA -s mr.mrrefChr0 121246 10 + 130230 TCACAACCAA -s simCow_chr6.simCow.chr6 134399 10 + 602619 TCATACACAA -s simDog_chr6.simDog.chr6 418340 10 - 593897 CCATAGACAA -s simHuman_chr6.simHuman.chr6 121329 10 + 601863 TCATAGACAA -s simRat_chr6.simRat.chr6 124784 10 + 647215 TCACAATCAG - -a -s simMouse_chr6.simMouse.chr6 126376 5 + 636262 GGTCA -s Anc0.Anc0refChr1 18508 5 - 62388 GTTCA -s Anc1.Anc1refChr2 97054 5 + 144309 GTTCA -s Anc2.Anc2refChr3 7005 5 + 53186 GTTCA -s mr.mrrefChr0 121256 5 + 130230 GGTCA -s simCow_chr6.simCow.chr6 134409 5 + 602619 GTTCA -s simDog_chr6.simDog.chr6 418350 5 - 593897 GTTCA -s simHuman_chr6.simHuman.chr6 121339 5 + 601863 GATCA -s simRat_chr6.simRat.chr6 124795 5 + 647215 AGAGT - -a -s simMouse_chr6.simMouse.chr6 126381 6 + 636262 TCCCCT -s Anc0.Anc0refChr1 18516 6 - 62388 TTCTCT -s Anc1.Anc1refChr2 97062 6 + 144309 TTCTCT -s Anc2.Anc2refChr3 7013 6 + 53186 TTCTCT -s mr.mrrefChr0 121261 6 + 130230 TCCCCT -s simCow_chr6.simCow.chr6 134417 6 + 602619 TCATCT -s simDog_chr6.simDog.chr6 418358 6 - 593897 TTCTTT -s simHuman_chr6.simHuman.chr6 121347 6 + 601863 TTCTCT -s simRat_chr6.simRat.chr6 124800 6 + 647215 TCCCCT - -a -s simMouse_chr6.simMouse.chr6 126387 25 + 636262 TGTTATAACTTCTGTCTGGGACTAT -s Anc0.Anc0refChr1 18522 25 - 62388 TATTTTGACTTCTGTCTTGGACTAT -s Anc1.Anc1refChr2 97068 25 + 144309 TATTTTGACTTCTGTCTTGGACTAT -s Anc2.Anc2refChr3 7019 25 + 53186 TTTTTTGACTTCTGTCTTGGACTAT -s mr.mrrefChr0 121267 25 + 130230 TATTATAACTTCTGTCTGGGACTAT -s simCow_chr6.simCow.chr6 134428 25 + 602619 TTTTTTAACTCCTCTCTTGGGCTAT -s simDog_chr6.simDog.chr6 418364 25 - 593897 TTTTTTGACTTCTGTCTTGGACTAT -s simHuman_chr6.simHuman.chr6 121353 25 + 601863 AATCTTGACTTTTGTCTTGGACTAT -s simRat_chr6.simRat.chr6 124806 25 + 647215 TATTATAACTTCTGTTTGGGACCAT - -a -s simMouse_chr6.simMouse.chr6 126412 23 + 636262 ACTTCCGGTTGGGACTATATAGG -s Anc0.Anc0refChr1 18547 5 - 62388 A------------------AAGG -s Anc1.Anc1refChr2 97093 23 + 144309 ACTTCTGTCCTGGACTATAAAGG -s Anc2.Anc2refChr3 7044 5 + 53186 A------------------AAGG -s mr.mrrefChr0 121292 23 + 130230 ACTTCTGGTTGGGACTATATAGG -s simCow_chr6.simCow.chr6 134453 5 + 602619 A------------------AAGG -s simDog_chr6.simDog.chr6 418389 5 - 593897 A------------------AAGG -s simHuman_chr6.simHuman.chr6 121411 23 + 601863 ACTTCTGTCCTGGACAATAAAGG -s simRat_chr6.simRat.chr6 124831 23 + 647215 ACTCCTGGTTGGGACTATATAGG - -a -s simMouse_chr6.simMouse.chr6 126435 24 + 636262 GCAGCTGACTCAGGGTTGCTCAGT -s Anc0.Anc0refChr1 18553 24 - 62388 ACAACTGTCTAGGACTCTCCCATT -s Anc1.Anc1refChr2 97117 24 + 144309 ACAACTGTCTAGGACTCTCCCATT -s Anc2.Anc2refChr3 7050 24 + 53186 ACAACTATCTAGGACTCTCCCATT -s mr.mrrefChr0 121315 24 + 130230 GCAGCTGTCTCAGGGTTGCTCATT -s simCow_chr6.simCow.chr6 134459 24 + 602619 ACAACTATCTAGGACTCTCCTATT -s simDog_chr6.simDog.chr6 418394 24 - 593897 GCAACTATCTAGGACTCTCCCATT -s simHuman_chr6.simHuman.chr6 121435 24 + 601863 ACAACTGTCTAGGTCTCTCCCATT -s simRat_chr6.simRat.chr6 124854 24 + 647215 GCGGATGTTTCAGGGTTGCTCATT - -a -s simMouse_chr6.simMouse.chr6 126459 49 + 636262 ACAAACTAACATGACATATTATGACATGAATGATATAAAGGCATGCAAA -s Anc0.Anc0refChr1 18582 43 - 62388 ACAAAGTCACATCGCATATTGGCATATAGATGGCA-GGAGG-----GAA -s Anc1.Anc1refChr2 97146 44 + 144309 ACAAAGTCACATCGCATATTGGCATATAGATGGCATGGAGG-----GAA -s Anc2.Anc2refChr3 7079 43 + 53186 ATAAAGTCACATCGCATATTGGCATATAGCTGGCA-GGAGG-----GCA -s mr.mrrefChr0 121339 49 + 130230 ACAAACTAACATGACATATTATGACATGAATGATATGAAGGCATGCAAA -s simCow_chr6.simCow.chr6 134488 43 + 602619 ATAAAATCACATAGCATATTAGCAGATAGCTGGCA-GGAGG-----GCA -s simDog_chr6.simDog.chr6 418423 25 - 593897 ATAAAGTCACATCCCACATTGGCAT------------------------ -s simHuman_chr6.simHuman.chr6 121464 44 + 601863 ACGAAGTCACGTTGCATATTTGCATGTACATGGCATGGAGT-----GAA -s simRat_chr6.simRat.chr6 124878 49 + 647215 ACAATCTAACATAACATATTATGGCATGAATGATATGAAGGCGTGCAAA - -a -s simMouse_chr6.simMouse.chr6 126508 12 + 636262 GACATATTTTTC -s Anc0.Anc0refChr1 18625 12 - 62388 GATGTTTTTTTC -s Anc1.Anc1refChr2 97190 12 + 144309 GATGTTTTTTTC -s Anc2.Anc2refChr3 7122 12 + 53186 GATGCTTTCTTC -s mr.mrrefChr0 121388 12 + 130230 GACATTTTTTTC -s simCow_chr6.simCow.chr6 134533 12 + 602619 GATGCTTTCTTC -s simHuman_chr6.simHuman.chr6 121508 12 + 601863 GATGTTTTTTTT -s simRat_chr6.simRat.chr6 124927 12 + 647215 GAGATTTTGTTC - -a -s simMouse_chr6.simMouse.chr6 126520 15 + 636262 TTCTGTGCTCACCTT -s Anc0.Anc0refChr1 18641 15 - 62388 ACCTGTTACTACACA -s Anc1.Anc1refChr2 97206 15 + 144309 ACCTGTTACTACACA -s Anc2.Anc2refChr3 7138 15 + 53186 ACCTCCTACTACACA -s mr.mrrefChr0 121400 15 + 130230 TTCTGTGCTCACCTA -s simCow_chr6.simCow.chr6 134549 15 + 602619 ACCTCCTACTACATA -s simDog_chr6.simDog.chr6 418448 3 - 593897 ------------ACA -s simHuman_chr6.simHuman.chr6 121524 15 + 601863 ACCTGTTACTGTACA -s simRat_chr6.simRat.chr6 124939 15 + 647215 TTCTGTGCTCACCTA - -a -s simMouse_chr6.simMouse.chr6 126535 23 + 636262 ACTCTACCGAATCAGTGACAGCC -s Anc0.Anc0refChr1 18656 22 - 62388 ACTCTACTGAATTAGTG-TAGCC -s Anc1.Anc1refChr2 97221 22 + 144309 ACTCTACTGAATTAGTG-TAGCC -s Anc2.Anc2refChr3 7153 22 + 53186 ACTCTACTGAAGTAGTG-TGGCC -s mr.mrrefChr0 121415 23 + 130230 ACTCTACCGAATCAGTGACAGCC -s simCow_chr6.simCow.chr6 134568 22 + 602619 GCTCTACTGAAGTAGTG-TGGCT -s simDog_chr6.simDog.chr6 418451 22 - 593897 AATATACTGAAGTAATG-TGGCC -s simHuman_chr6.simHuman.chr6 121539 22 + 601863 ACTCTACTGGATTAGTG-TAGCC -s simRat_chr6.simRat.chr6 124954 23 + 647215 ACTCTACCAAATCACTGGCAGCT - -a -s simMouse_chr6.simMouse.chr6 126558 1 + 636262 T -s Anc0.Anc0refChr1 18734 1 - 62388 T -s Anc1.Anc1refChr2 97299 1 + 144309 T -s Anc2.Anc2refChr3 7231 1 + 53186 T -s mr.mrrefChr0 121438 1 + 130230 T -s simCow_chr6.simCow.chr6 134646 1 + 602619 T -s simDog_chr6.simDog.chr6 418529 1 - 593897 T -s simHuman_chr6.simHuman.chr6 121617 1 + 601863 T -s simRat_chr6.simRat.chr6 124977 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 126559 22 + 636262 TTACCCACCTCCCATTTTGATT -s Anc0.Anc0refChr1 18749 22 - 62388 TTTTTCACCCCTCAATTTGAAC -s Anc1.Anc1refChr2 97314 22 + 144309 TTTTTCACCCCTCAATTTGAAC -s Anc2.Anc2refChr3 7246 22 + 53186 TTTTTCACCCCTCAATTTGAAC -s mr.mrrefChr0 121453 22 + 130230 TTACTCACCTCCCAATTTGATC -s simCow_chr6.simCow.chr6 134661 21 + 602619 TTTTTC-CCCCTCAATTTGAAC -s simDog_chr6.simDog.chr6 418565 22 - 593897 TTTTTAATCCCTCAATTTGAAC -s simHuman_chr6.simHuman.chr6 121632 22 + 601863 TCTTTCACCGCTCAATTTGAAC -s simRat_chr6.simRat.chr6 124992 22 + 647215 TTCCTCTCCTCCCAATTTGATC - -a -s simMouse_chr6.simMouse.chr6 126581 3 + 636262 GTC -s Anc0.Anc0refChr1 18776 3 - 62388 GTT -s Anc1.Anc1refChr2 97341 3 + 144309 GTT -s Anc2.Anc2refChr3 7273 3 + 53186 GTT -s mr.mrrefChr0 121475 3 + 130230 GTC -s simCow_chr6.simCow.chr6 134687 3 + 602619 GTT -s simDog_chr6.simDog.chr6 418592 3 - 593897 GCT -s simHuman_chr6.simHuman.chr6 121659 3 + 601863 GTT -s simRat_chr6.simRat.chr6 125014 3 + 647215 GTC - -a -s simMouse_chr6.simMouse.chr6 126584 29 + 636262 CTAAGAATGGTACCCGGGTGTGACTAGCT -s Anc0.Anc0refChr1 18779 26 - 62388 CTAAGGATGCTACCTGGGCATGAC---CT -s Anc1.Anc1refChr2 97344 26 + 144309 CTAAGGATGCTACCTGGGCATGAC---CT -s Anc2.Anc2refChr3 7278 26 + 53186 CTAAGGATGTTACCTGGGCATGGG---CT -s mr.mrrefChr0 121478 29 + 130230 CTAAGAATGCTACCCGGGTGTGACTAGCT -s simCow_chr6.simCow.chr6 134692 26 + 602619 CTAAGGATGTTACTTGGGCATGGG---CT -s simDog_chr6.simDog.chr6 418597 26 - 593897 CTAAGAATGTTATCTGGGCATGGG---CT -s simHuman_chr6.simHuman.chr6 121662 26 + 601863 CTAGGGATACAACCTGGGCATGAC---CT -s simRat_chr6.simRat.chr6 125017 29 + 647215 CTAAGAATGCTACCAGGGTGTGACTAGCT - -a -s simMouse_chr6.simMouse.chr6 126613 20 + 636262 GAGCCACTCTGTGCAATGAA -s Anc0.Anc0refChr1 18805 20 - 62388 GAGGCACTTTATTCAATGAC -s Anc1.Anc1refChr2 97370 20 + 144309 GAGGCACTTTATTCAATGAC -s Anc2.Anc2refChr3 7304 20 + 53186 GAGGCACTTCATTCAATGAC -s mr.mrrefChr0 121507 20 + 130230 GAGCCACTCTGTGCAATGAC -s simCow_chr6.simCow.chr6 134772 20 + 602619 GAGGCACTTCATTCAATGAC -s simDog_chr6.simDog.chr6 418623 20 - 593897 GACGCACTTCGTTCAGTAAC -s simHuman_chr6.simHuman.chr6 121688 20 + 601863 GAGACACTTTATTCAATGAC -s simRat_chr6.simRat.chr6 125046 20 + 647215 GAGCCACTGTGTGCAATGAC - -a -s simMouse_chr6.simMouse.chr6 126633 46 + 636262 CTGGTCAAACACTTAATGAAATATTCTATCTCAAAGCTCAACTTAA -s Anc0.Anc0refChr1 18828 45 - 62388 CTTGTCAGACAGTTAATAAAATATTCTA-CCCCAAGCCCAATTAAT -s Anc1.Anc1refChr2 97393 46 + 144309 CTTGTCAGACAGTTAATAAAATATTCTAGCCCCAAGCCCAATTAAT -s Anc2.Anc2refChr3 7327 45 + 53186 TTTGCCAGGCACTTAATAAAATATTCTA-CCCCAAGCCCAATTAGT -s mr.mrrefChr0 121527 46 + 130230 CTGGTCAAACAGTTAATGAAATATTCTAGCTCAAAGCTCAACTTAA -s simCow_chr6.simCow.chr6 134795 44 + 602619 TCTGCCAGGCACTTGAC-AAATATTCCA-GCACAAAACCAATTAGT -s simDog_chr6.simDog.chr6 418646 41 - 593897 TTTGC----CACTTAATAAAATATCCTG-CCCCAAGCCCAATTAGT -s simHuman_chr6.simHuman.chr6 121711 42 + 601863 CTTGTAAGACAGTTAATAAAATATTCTAG----AAGCCCAATTAAC -s simRat_chr6.simRat.chr6 125066 46 + 647215 CTGGTCAAACAGTTAATGAAATATTCTAGCTCAAAGCTCAACTTGT - -a -s simMouse_chr6.simMouse.chr6 126679 55 + 636262 TGGGAAATACACCTACACAGGTGCAATATGTAGTGGCATTGCCTGCAAGTAGGTG -s Anc0.Anc0refChr1 18876 51 - 62388 GGGGCAATATACAGACACAGGTG-AATATGTAGTGGGGCCCCCTGCACCTAG--- -s Anc1.Anc1refChr2 97442 54 + 144309 GGGGCAATATACAGACACAGGTG-AATATGTAGTGGGGCCCCCTGCACCTAGGTG -s Anc2.Anc2refChr3 7375 51 + 53186 GGGCCAATATACAGATATGGGTG-AATATGTAGTGGGGCCCTCTGCGCCTAG--- -s mr.mrrefChr0 121576 54 + 130230 GGGGAAATATACCTACACAGGTG-AATATGTAGTGGCATTGCCTGCAAGTAGGTG -s simCow_chr6.simCow.chr6 134842 48 + 602619 GGG-CAATATACAGAGATGGCTA-AATATGTAGTGGGGCCCAAT--GTCCAA--- -s simDog_chr6.simDog.chr6 418690 50 - 593897 GGGCCAGTATTC-GATATGGGTG-AGTATGTAGTGGGGCCCTCTGCGCCTGG--- -s simHuman_chr6.simHuman.chr6 121756 54 + 601863 GGGGCAATATACTGACACAGGTG-AATAAGTAGTGGAGCACCTGGCAGATAGGTG -s simRat_chr6.simRat.chr6 125118 50 + 647215 GGGGAAATATATCCATACAGGAG-AATATGTAGTGACATTGCCTGCCTGCA---- - -a -s simMouse_chr6.simMouse.chr6 126734 75 + 636262 CAAATTAATACCTTCTCCAGTGCACCAGCTGTATAGAAGGACCTCACACACTTGCAGACTTGCACTAGAATCAAT -s Anc0.Anc0refChr1 18927 70 - 62388 CAAATTAATGCCCTCCTCA-TGCATCAGCTGTATAGGAGAACCTCAGACACTTGCTGAGTCACACTAGAAC---- -s Anc1.Anc1refChr2 97496 70 + 144309 CAAATTAATGCCCTCCTCA-TGCATCAGCTGTATAGGAGAACCTCAGACACTTGCTGAGTCACACTAGAAC---- -s Anc2.Anc2refChr3 7426 70 + 53186 TAAATTAATGCCCTCCTTG-TGCATCAGCTGTATAGGATAACCTCAGACACTTGCTGAGTCACATGAGAAC---- -s mr.mrrefChr0 121630 71 + 130230 CAAATTAATACCTTCTTCAGTGCACCAGCTGTATAGGAGGACCTCACACACTTGCAGACTCGCACTAGAAC---- -s simCow_chr6.simCow.chr6 134890 70 + 602619 TAAGTGAATGTCCTCCTTG-TGCATCAGCTGTATAGGATAACTTCAGACACTTGTTGAATCATATGAGAAC---- -s simDog_chr6.simDog.chr6 418740 68 - 593897 TAAATTAATGCCCTCCTTG-TGCATCAGCCATATGGGATAAACTT--ACACTTGCTGAGATACATGAGAGC---- -s simHuman_chr6.simHuman.chr6 121816 70 + 601863 CAGATTAATGCCCTTCTCA-TGCATCAGCTGTATAGGAGAACCTCAGACACTTGCTGAGTCACACTAGAAC---- -s simRat_chr6.simRat.chr6 125168 60 + 647215 -------ATACCTTCTTCAGTGTACCAGCTGCATAGGAGGACCTCACATAC----AGATGCTTACTAGAAC---- - -a -s simMouse_chr6.simMouse.chr6 126809 11 + 636262 AATTTATTTGT -s Anc0.Anc0refChr1 19011 11 - 62388 AGTTTGTCTGT -s Anc1.Anc1refChr2 97580 11 + 144309 AGTTTGTCTGT -s Anc2.Anc2refChr3 7510 11 + 53186 AGTTTGTCTGT -s mr.mrrefChr0 121701 11 + 130230 AATTTATTTGT -s simCow_chr6.simCow.chr6 134975 11 + 602619 AGTTTGCCTCT -s simDog_chr6.simDog.chr6 418822 11 - 593897 AGTTTGTCTGT -s simHuman_chr6.simHuman.chr6 121900 11 + 601863 AGTTTGTCTGT -s simRat_chr6.simRat.chr6 125228 11 + 647215 AATTATTTTGC - -a -s simMouse_chr6.simMouse.chr6 126820 15 + 636262 GATATCCCATAGCAG -s Anc0.Anc0refChr1 19031 15 - 62388 GTTCTCCCATATCAA -s Anc1.Anc1refChr2 97601 15 + 144309 GTTCTCCCATATCAA -s Anc2.Anc2refChr3 7530 15 + 53186 GTTCTCTTGTATCAA -s mr.mrrefChr0 121712 15 + 130230 GATATCCCATAGCAG -s simCow_chr6.simCow.chr6 134995 15 + 602619 GTTCTCTTGTATCAA -s simDog_chr6.simDog.chr6 418842 15 - 593897 GTTCTCTTGTATCCA -s simHuman_chr6.simHuman.chr6 121921 15 + 601863 GTTCTTCCATATCAA -s simRat_chr6.simRat.chr6 125239 15 + 647215 AATATCCCGTAGCAG - -a -s simMouse_chr6.simMouse.chr6 126835 20 + 636262 ATGTACCAGAGGATGCACAA -s Anc0.Anc0refChr1 19047 20 - 62388 ATGTACCAGAGGATTCTCAA -s Anc1.Anc1refChr2 97617 20 + 144309 ATGTACCAGAGGATTCTCAA -s Anc2.Anc2refChr3 7546 20 + 53186 ATGTACCAGAGTATTCTCAA -s mr.mrrefChr0 121727 20 + 130230 ATGTACCAGAGGATGCACAA -s simCow_chr6.simCow.chr6 135011 20 + 602619 GTTTACCAGAGTATTCTCAA -s simDog_chr6.simDog.chr6 418858 20 - 593897 ATGTACCAGAGTATTCCCAA -s simHuman_chr6.simHuman.chr6 121937 20 + 601863 ATGTATCAGTGGATTCTTGA -s simRat_chr6.simRat.chr6 125254 20 + 647215 ATGTACCAGGGGATCCCCAA - -a -s simMouse_chr6.simMouse.chr6 126855 3 + 636262 GAC -s Anc0.Anc0refChr1 19067 3 - 62388 AAC -s Anc1.Anc1refChr2 97637 3 + 144309 AAC -s Anc2.Anc2refChr3 7566 3 + 53186 AAC -s mr.mrrefChr0 121747 3 + 130230 GAC -s simCow_chr6.simCow.chr6 135031 3 + 602619 AGC -s simDog_chr6.simDog.chr6 418878 3 - 593897 AAC -s simHuman_chr6.simHuman.chr6 121957 3 + 601863 AGC -s simRat_chr6.simRat.chr6 125275 3 + 647215 GAC - -a -s simMouse_chr6.simMouse.chr6 126858 4 + 636262 AACT -s Anc0.Anc0refChr1 19070 4 - 62388 CCCC -s Anc1.Anc1refChr2 97640 4 + 144309 CCCC -s Anc2.Anc2refChr3 7572 4 + 53186 CCAC -s mr.mrrefChr0 121750 4 + 130230 CACT -s simCow_chr6.simCow.chr6 135037 4 + 602619 TCAC -s simDog_chr6.simDog.chr6 418884 4 - 593897 CCAC -s simHuman_chr6.simHuman.chr6 121960 4 + 601863 CCCG -s simRat_chr6.simRat.chr6 125278 4 + 647215 CAAT - -a -s simMouse_chr6.simMouse.chr6 126862 62 + 636262 TTGAGTTATAATCTAACACTAATGCTGAGAAAATAAAATAAGCACAGCTTCAAATCACCACA -s Anc0.Anc0refChr1 19074 52 - 62388 TTGAGTGACAATCAAACACTAAT----------CAAAATGAGTACAGGTCCAAGTCACCACA -s Anc1.Anc1refChr2 97644 62 + 144309 TTGAGTGACAATCAAACACTAATGCCATGAGAACAAAATGAGTACAGGTCCAAGTCACCACA -s Anc2.Anc2refChr3 7576 52 + 53186 TTGTGTGACAATCAAGTACTAAT----------CAACATGAGTACAGGCTCAAGTCACCACA -s mr.mrrefChr0 121754 62 + 130230 TTGAGTTACAATCTAACACTAATGCTGAGAAAATAAAATAAGCACAGCTCCAAATCACCACA -s simCow_chr6.simCow.chr6 135042 51 + 602619 TTGTTTGACAATCAAGTATTAAT----------CCACCTGAGGA-AGGCTCAAATTACCACA -s simDog_chr6.simDog.chr6 418888 52 - 593897 TTGTGTGAGAATCAAGTACTAAT----------CAACATAAATACAGGCTCAAGTCACCGCA -s simHuman_chr6.simHuman.chr6 121964 62 + 601863 TTGAGTGGCCATTCAACACTAAGGCCATGAGAACAAAATGAGTACGGGTCCAAGCCACCACA -s simRat_chr6.simRat.chr6 125282 62 + 647215 TTGAGTTACAATCTAACACTAATGCTGGGAAAATAAAATAGGCACAGCTCCAAATCACCACA - -a -s simMouse_chr6.simMouse.chr6 126924 6 + 636262 GTTCAT -s Anc0.Anc0refChr1 19128 4 - 62388 GTGG-- -s Anc1.Anc1refChr2 97708 6 + 144309 GTGGAT -s Anc2.Anc2refChr3 7630 4 + 53186 GTGA-- -s mr.mrrefChr0 121816 6 + 130230 GTTGAT -s simCow_chr6.simCow.chr6 135095 4 + 602619 GTGA-- -s simDog_chr6.simDog.chr6 418942 4 - 593897 CTGA-- -s simHuman_chr6.simHuman.chr6 122028 6 + 601863 GTGGAT -s simRat_chr6.simRat.chr6 125344 6 + 647215 GTTGAT - -a -s simMouse_chr6.simMouse.chr6 126930 7 + 636262 TGATACA -s Anc0.Anc0refChr1 19138 7 - 62388 TGCCACA -s Anc1.Anc1refChr2 97720 7 + 144309 TGCCACA -s Anc2.Anc2refChr3 7640 7 + 53186 TTCCACA -s mr.mrrefChr0 121822 7 + 130230 TGATACA -s simCow_chr6.simCow.chr6 135105 7 + 602619 CTTCACA -s simDog_chr6.simDog.chr6 418952 7 - 593897 TTCCAAA -s simHuman_chr6.simHuman.chr6 122041 7 + 601863 TGCGACA -s simRat_chr6.simRat.chr6 125350 7 + 647215 TGTTACA - -a -s simMouse_chr6.simMouse.chr6 126937 9 + 636262 GCAATACTG -s Anc0.Anc0refChr1 19146 9 - 62388 ACAAAAATA -s Anc1.Anc1refChr2 97728 9 + 144309 ACAAAAATA -s Anc2.Anc2refChr3 7648 9 + 53186 ACAGCAATA -s mr.mrrefChr0 121830 9 + 130230 GCAAAACTA -s simCow_chr6.simCow.chr6 135113 9 + 602619 ACAGCAGTA -s simDog_chr6.simDog.chr6 418960 9 - 593897 ACAGCAATG -s simHuman_chr6.simHuman.chr6 122049 9 + 601863 ACAAAAATA -s simRat_chr6.simRat.chr6 125358 9 + 647215 GCAAAAGTA - -a -s simMouse_chr6.simMouse.chr6 126946 52 + 636262 ACACTGCTCTGTGTCTTCTGGTACTCATCAGAAACACCATAAGTTGTATTAA -s Anc0.Anc0refChr1 19156 43 - 62388 ATGCAGTACTGAAGATCCTGATGCTTGACAGAAA---------TTACATCAA -s Anc1.Anc1refChr2 97738 43 + 144309 ATGCAGTACTGAAGATCCTGATGCTTGACAGAAA---------TTACATCAA -s Anc2.Anc2refChr3 7658 43 + 53186 ATGCAGTACTGAAGATCCTGATGCTTGACAGAAA---------TTACATCAT -s mr.mrrefChr0 121839 52 + 130230 ACACTGCTCTGTGTCTTCTGGTACTCATCAGAAACACCATAAGTTGTATTAA -s simCow_chr6.simCow.chr6 135123 42 + 602619 ATGCAGTACT-AAGATCCTGGTGCTTGACAGAAA---------TGACATGAC -s simDog_chr6.simDog.chr6 418970 43 - 593897 ATGCAGTACTGAAGATCCAGATGCTTCACAGAAA---------TTACATCAT -s simHuman_chr6.simHuman.chr6 122059 43 + 601863 ATGCAGTACTGAAGACCCTGATGCCTGATAGGAA---------TTACATCAA -s simRat_chr6.simRat.chr6 125367 50 + 647215 ACACTGCTCTACGTC--CTGGTACTCATCAGAAGCATCAGAAGTTGAATTAA - -a -s simMouse_chr6.simMouse.chr6 126998 10 + 636262 CATCCATTCT -s Anc0.Anc0refChr1 19199 10 - 62388 CACCAACACT -s Anc1.Anc1refChr2 97781 10 + 144309 CACCAACACT -s Anc2.Anc2refChr3 7701 10 + 53186 CACCAACACT -s mr.mrrefChr0 121891 10 + 130230 CATCCATTCT -s simCow_chr6.simCow.chr6 135165 5 + 602619 CATCA----- -s simDog_chr6.simDog.chr6 419016 10 - 593897 CACCAACACT -s simHuman_chr6.simHuman.chr6 122102 10 + 601863 CACCAAAGCT -s simRat_chr6.simRat.chr6 125417 10 + 647215 CATCCATTTT - -a -s simMouse_chr6.simMouse.chr6 127008 47 + 636262 GGGGCCAAGCCATGAGGGATCACTTATGGCATTCAAGGCTTTGGAGA -s Anc0.Anc0refChr1 19213 43 - 62388 AGTGC----CCATGAAGAAGCAGCTATAGGATTCAAGGCTTTGTAGA -s Anc1.Anc1refChr2 97795 43 + 144309 AGTGC----CCATGAAGAAGCAGCTATAGGATTCAAGGCTTTGTAGA -s Anc2.Anc2refChr3 7715 43 + 53186 AGTGC----CCATGAAGAAGCAGCTATAGCATTCAAGACTTTGTAGA -s mr.mrrefChr0 121901 47 + 130230 GGGGCCAAGCCATGAGGGATCACTTATGGGATTCAAGGCTTTGGAGA -s simCow_chr6.simCow.chr6 135170 39 + 602619 ----C----CCATGAAGATGCAGCTATAGTATTCAAGACTTTGGAAA -s simDog_chr6.simDog.chr6 419030 40 - 593897 AGTGC----TC-TGACGAAGCTGCCATGGCATTCAC--CTTTATAGA -s simHuman_chr6.simHuman.chr6 122117 43 + 601863 AGAGC----CCATGAAGAAGCAGCTCCAGGATCCAAGGCTTTGTAGA -s simRat_chr6.simRat.chr6 125427 47 + 647215 GGGGCCAAGCCATGAGGGATCACTTATGGGATTCGGGGCTTTGGAGA - -a -s simMouse_chr6.simMouse.chr6 127055 110 + 636262 CAGGTAACTTCATTACCTCCTCTAGAATAGCCATGACCATTCAGTGTTCTTATGTCCAAACTACACTTACTGTATCTCATAACACAAACTGGATGAATCAATGATGTCAT -s Anc0.Anc0refChr1 19256 43 - 62388 GATGCAAC-------------------------------------------------------------------CTTGTAAGAGGAACTGTATGGACCAATATTGTTAT -s Anc1.Anc1refChr2 97838 43 + 144309 GATGCAAC-------------------------------------------------------------------CTTGTAAGAGGAACTGTATGGACCAATATTGTTAT -s Anc2.Anc2refChr3 7765 43 + 53186 GATGCAAC-------------------------------------------------------------------GTTGTAAGAGGAACTGTATGGACCAATATTGTTAT -s mr.mrrefChr0 121948 110 + 130230 GAGGTAACTTCATTACCTCCTCTAGAATAGCCATGACCATTCAGTGTTCTTATGTCCAAACTACACTTACTGTATCTCATAACACAAACTGGATGAATCAATGATGTCAT -s simCow_chr6.simCow.chr6 135216 32 + 602619 GATGCAAC-------------------------------------------------------------------TTTG-----------GTATGAATCGATATTGTTAT -s simDog_chr6.simDog.chr6 419077 43 - 593897 GATGCAAC-------------------------------------------------------------------GTTGTAAGAGGAACTGTATGGACCAATATTGTTAT -s simHuman_chr6.simHuman.chr6 122160 40 + 601863 GATGCAAC-------------------------------------------------------------------CTTGCAGGAAGAACTGCATGG---AATATTGTGAT -s simRat_chr6.simRat.chr6 125474 110 + 647215 GAGGTATCTTTGTTACCTCCTCTAGAGAAGCCATGCTCATTCAGTGTTCTTATGTCCAAACTACACTTTCTGTATCTCATAACAGAAACTGTATAAATCAATGATGACAT - -a -s simMouse_chr6.simMouse.chr6 127165 4 + 636262 CCTG -s Anc0.Anc0refChr1 19299 4 - 62388 TCTG -s Anc1.Anc1refChr2 97881 4 + 144309 TCTG -s Anc2.Anc2refChr3 7849 4 + 53186 TCTG -s mr.mrrefChr0 122058 4 + 130230 CCTG -s simCow_chr6.simCow.chr6 135289 1 + 602619 ---G -s simDog_chr6.simDog.chr6 419316 4 - 593897 TCTG -s simHuman_chr6.simHuman.chr6 122200 4 + 601863 TCTG -s simRat_chr6.simRat.chr6 125584 4 + 647215 TCTG - -a -s simMouse_chr6.simMouse.chr6 127169 6 + 636262 TGTATA -s Anc0.Anc0refChr1 19303 6 - 62388 AGTATA -s Anc1.Anc1refChr2 97885 6 + 144309 AGTATA -s Anc2.Anc2refChr3 7853 6 + 53186 AGTATA -s mr.mrrefChr0 122062 6 + 130230 TGTATA -s simCow_chr6.simCow.chr6 135290 6 + 602619 AGTATA -s simDog_chr6.simDog.chr6 419322 6 - 593897 ACTATA -s simHuman_chr6.simHuman.chr6 122204 6 + 601863 AGTATA -s simRat_chr6.simRat.chr6 125588 6 + 647215 TGTAGA - -a -s simMouse_chr6.simMouse.chr6 127175 2 + 636262 GG -s Anc0.Anc0refChr1 19309 2 - 62388 GG -s Anc1.Anc1refChr2 97891 2 + 144309 GG -s Anc2.Anc2refChr3 7859 2 + 53186 GG -s mr.mrrefChr0 122068 2 + 130230 GG -s simCow_chr6.simCow.chr6 135296 2 + 602619 GC -s simDog_chr6.simDog.chr6 419328 2 - 593897 GG -s simHuman_chr6.simHuman.chr6 122210 2 + 601863 GG -s simRat_chr6.simRat.chr6 125597 2 + 647215 GG - -a -s simMouse_chr6.simMouse.chr6 127177 6 + 636262 TGCAAC -s Anc0.Anc0refChr1 19315 6 - 62388 TGCAAC -s Anc1.Anc1refChr2 97897 6 + 144309 TGCAAC -s Anc2.Anc2refChr3 7865 6 + 53186 TGCAAC -s mr.mrrefChr0 122070 6 + 130230 TGCAAC -s simCow_chr6.simCow.chr6 135302 6 + 602619 TGCAAC -s simDog_chr6.simDog.chr6 419334 6 - 593897 TGCAAC -s simHuman_chr6.simHuman.chr6 122216 6 + 601863 TACAAC -s simRat_chr6.simRat.chr6 125599 6 + 647215 TGCAAC - -a -s simMouse_chr6.simMouse.chr6 127183 126 + 636262 TCAATGCTGTGAAGAGAATAGTTTGTCTTATAAACTAGCATATATTGTCCTGTTGCTTGGGGAATAGATGAAGATTCGCACCTTGCACCAACCTGGATTCCTGCTAGGATATCTCATCACCTCACC -s Anc0.Anc0refChr1 19321 18 - 62388 TCAATGCT------------------------------------------------------------------------------------------------------------TCACCCCACA -s Anc1.Anc1refChr2 97903 18 + 144309 TCAATGCT------------------------------------------------------------------------------------------------------------TCACCCCACA -s Anc2.Anc2refChr3 7871 18 + 53186 TAAATGCT------------------------------------------------------------------------------------------------------------TCACCCCACA -s mr.mrrefChr0 122076 126 + 130230 TCAATGCTGTGAAGAGAATAGTTTGTCTTATAAACTAGCATATATTGTCCTGTTGCTTGGGGAATAGATGAAGATTCGCACCTTGCACCAACCTGGATTCCTGCTAGGATATCTCATCACCTCACC -s simCow_chr6.simCow.chr6 135308 18 + 602619 TAAATGCT------------------------------------------------------------------------------------------------------------TCAACCCTCA -s simDog_chr6.simDog.chr6 419340 18 - 593897 TAAATGCT------------------------------------------------------------------------------------------------------------CCACCCCACA -s simHuman_chr6.simHuman.chr6 122223 18 + 601863 TCAATGCT------------------------------------------------------------------------------------------------------------TCTTCCCACA -s simRat_chr6.simRat.chr6 125605 126 + 647215 TCAATGTCATGAAATGAACAGACTTTCTTATAATCTGACATATATTGTCCTGTTGCTTGGGGAATGGATGAATATTTGCACCTTGCATCAACCTGGATTCACGTTAGGATATCTCATCACCTCACC - -a -s simMouse_chr6.simMouse.chr6 127309 25 + 636262 AGCATGAGATCTCAGATCAATAGCT -s Anc0.Anc0refChr1 19339 24 - 62388 GGCATGTGATTTC-AATCAATAGCT -s Anc1.Anc1refChr2 97921 24 + 144309 GGCATGTGATTTC-AATCAATAGCT -s Anc2.Anc2refChr3 7889 24 + 53186 GGCATGTGACTTC-AATCAATAGCT -s mr.mrrefChr0 122202 25 + 130230 AGCATGAGATCTCAAATCAATAGCT -s simCow_chr6.simCow.chr6 135329 10 + 602619 TGCATGGGAC--------------- -s simDog_chr6.simDog.chr6 419358 24 - 593897 GACGTTTGACTTC-AATCAATAGCT -s simHuman_chr6.simHuman.chr6 122241 24 + 601863 GGCATGCGATTTC-AATCAATAGCT -s simRat_chr6.simRat.chr6 125731 25 + 647215 AGCATGAGATCTCAAATCAATAGCT - -a -s simMouse_chr6.simMouse.chr6 127334 33 + 636262 CTAACAATCTGTCAGAAAAGAAATTTTACCAGC -s Anc0.Anc0refChr1 19363 28 - 62388 CATAGTTTTATTCAAA-----AATTTTATAAGA -s Anc1.Anc1refChr2 97945 33 + 144309 CATAGTTTTATTCAAAGTAAAAATTTTATAAGA -s Anc2.Anc2refChr3 7913 28 + 53186 TATAGTTTTATTCAAA-----AATTTTATAAGA -s mr.mrrefChr0 122227 33 + 130230 CTAACAATCTGTCAGAAAAGAAATTTTACCAGC -s simCow_chr6.simCow.chr6 135339 13 + 602619 ---------------A-----AGTTTTACATGA -s simDog_chr6.simDog.chr6 419383 28 - 593897 TATAGTTTTATTCAAA-----AATTTCATGAGA -s simHuman_chr6.simHuman.chr6 122265 33 + 601863 CATAGTTCTATTCAAAGTAAAAATTTTATAAGA -s simRat_chr6.simRat.chr6 125756 33 + 647215 CCAATGATCTGTCACAAAATTAACTTTACCAGC - -a -s simMouse_chr6.simMouse.chr6 127367 9 + 636262 GCTAACCAA -s Anc0.Anc0refChr1 19391 9 - 62388 CCTATCCCC -s Anc1.Anc1refChr2 97978 9 + 144309 CCTATCCCC -s Anc2.Anc2refChr3 7941 9 + 53186 CCTATCCCC -s mr.mrrefChr0 122260 9 + 130230 GCTAACCCA -s simCow_chr6.simCow.chr6 135352 9 + 602619 GTGATCCCC -s simDog_chr6.simDog.chr6 419411 9 - 593897 CCTATCCCC -s simHuman_chr6.simHuman.chr6 122298 9 + 601863 CCTATCCCT -s simRat_chr6.simRat.chr6 125791 9 + 647215 GGTAACCCA - -a -s simMouse_chr6.simMouse.chr6 127376 12 + 636262 GACATTTTAAGT -s Anc0.Anc0refChr1 19400 12 - 62388 GATATTTTAAGT -s Anc1.Anc1refChr2 97987 12 + 144309 GATATTTTAAGT -s Anc2.Anc2refChr3 7950 12 + 53186 GATATTTTAAGT -s mr.mrrefChr0 122269 12 + 130230 GACATTTTAAGT -s simCow_chr6.simCow.chr6 135361 12 + 602619 GATATTTTAAGT -s simDog_chr6.simDog.chr6 419422 12 - 593897 AATATTTTATCT -s simHuman_chr6.simHuman.chr6 122307 12 + 601863 GATATTCTAAGT -s simRat_chr6.simRat.chr6 125800 12 + 647215 GACATTTTAAGT - -a -s simMouse_chr6.simMouse.chr6 127388 80 + 636262 ACCCAGTTCCCTTTCCGGCAGACATCTAAGCAACATTAGGTCGTCTGCAAAAGCCATGTTATATTCTACACCTGAGAGGT -s Anc0.Anc0refChr1 19412 63 - 62388 ATCCAGTTCCATTTCCGGCAGACTTATC-------------TGT-TGC---AGCCTGGTTAAGAGTTAGAGCTGCGAGGT -s Anc1.Anc1refChr2 97999 64 + 144309 ATCCAGTTCCATTTCCGGCAGACTTATC-------------TGTCTGC---AGCCTGGTTAAGAGTTAGAGCTGCGAGGT -s Anc2.Anc2refChr3 7962 63 + 53186 ATCCAGTTCCATTCCCAGCAGACTTAGC-------------TGT-TGC---AGCCTGGTCAAGAGTTAGAGTTGCAAGGT -s mr.mrrefChr0 122281 80 + 130230 ATCCAGTTCCCTTTCCGGCAGACATCTCAGCAACATTAGGTTGTCTGCAAAAGCCAGGTTATGTTCTACACCTGAGAGGT -s simCow_chr6.simCow.chr6 135388 63 + 602619 ATCCAGTTTCATTCCCAGCAGACTTAGC-------------TGT-TGT---AGCCTGGTCAAGAGTTAGAGTTGCAAGAA -s simDog_chr6.simDog.chr6 419434 63 - 593897 ATCCCATTCCATTCCCAGCAGACTTAGC-------------AGT-TGC---AGCCTGGTCGAGTGTTAGAATTGCATAGT -s simHuman_chr6.simHuman.chr6 122319 58 + 601863 ATTCAGTTCCATTTCCGGCAGACTTATC-------------TGTCTG---------GGTTAAGAGTTAGAGCTGTGAGGT -s simRat_chr6.simRat.chr6 125812 80 + 647215 ATCCAATTCCCTTTGCGGCAGAGATCTCAGCAATGTTAAGTTGTCTGCAAAAGCCAGGTTATGTTCTACATATGAAAGGT - -a -s simMouse_chr6.simMouse.chr6 127468 38 + 636262 ACTCCTGATGCACTGAGCCTTTACCACCCTCTAAGGCT -s Anc0.Anc0refChr1 19477 38 - 62388 ACCCTTGACTCAGTGTGACTTTAACTCCCTCTGTAGTT -s Anc1.Anc1refChr2 98065 38 + 144309 ACCCTTGACTCAGTGTGACTTTAACTCCCTCTGTAGTT -s Anc2.Anc2refChr3 8027 38 + 53186 ACCTTTGACTCAGTGTGACTTTAATTCCCTCTGTAGTT -s mr.mrrefChr0 122361 38 + 130230 ACTCTTGATGCACTGAGCCTTTACCACCCTCTAAAGTT -s simCow_chr6.simCow.chr6 135453 27 + 602619 ACTTCTGACTC---------TTAA--CTCCCTATGGTG -s simDog_chr6.simDog.chr6 419499 38 - 593897 GCCTTTGAATCAGTGTGACTTTAATTCCCTCTGTAGTT -s simHuman_chr6.simHuman.chr6 122379 38 + 601863 ACCCTTGGCTCATTGTAACTTTTTCTCCCTCTGTAGTT -s simRat_chr6.simRat.chr6 125892 38 + 647215 ACTCTTGATGCACTGAGTTTTTACAACCCTCTAAAGTT - -a -s simMouse_chr6.simMouse.chr6 127506 21 + 636262 CAGACTTTATAGAATAGGTAG -s Anc0.Anc0refChr1 19516 21 - 62388 TGAGCTTTCTAGAATGGGTAG -s Anc1.Anc1refChr2 98104 21 + 144309 TGAGCTTTCTAGAATGGGTAG -s Anc2.Anc2refChr3 8066 21 + 53186 TGAGCTTTCTAGAATGGGTAG -s mr.mrrefChr0 122400 21 + 130230 CAAGCTTTATAGAATAGGTAG -s simCow_chr6.simCow.chr6 135481 21 + 602619 TGGGCTTTCTAGAATGGGCAA -s simDog_chr6.simDog.chr6 419538 21 - 593897 TTAGCTTTCTAGAATGGGTAG -s simHuman_chr6.simHuman.chr6 122418 21 + 601863 TGAGCATACTAGAATGGGTAG -s simRat_chr6.simRat.chr6 125931 21 + 647215 CAAGCTTTATTGAATAGGTAG - -a -s simMouse_chr6.simMouse.chr6 127527 27 + 636262 AATTAGAAATGAACGGTACACACCATG -s Anc0.Anc0refChr1 19539 27 - 62388 AATTATAAATGAACACTACACACTATG -s Anc1.Anc1refChr2 98127 27 + 144309 AATTATAAATGAACACTACACACTATG -s Anc2.Anc2refChr3 8089 27 + 53186 GATTATAAACTAATACTACGCACTATG -s mr.mrrefChr0 122421 27 + 130230 AATTAGAAATGAACGGTACACACCATG -s simCow_chr6.simCow.chr6 135504 22 + 602619 GGTTGTAAACAAATGCTACTCA----- -s simDog_chr6.simDog.chr6 419561 26 - 593897 GATTATAAACTAATA-CATGCCCTATG -s simHuman_chr6.simHuman.chr6 122441 27 + 601863 AATTATAAATGACCATTACACACTATG -s simRat_chr6.simRat.chr6 125952 27 + 647215 AATTAGAAATGAATGGTACACACCATG - -a -s simMouse_chr6.simMouse.chr6 127554 20 + 636262 CACATGAGAGGCTAAACTCT -s Anc0.Anc0refChr1 19567 19 - 62388 GAC-TGAGGGGCTAAATTCC -s Anc1.Anc1refChr2 98155 20 + 144309 GACATGAGGGGCTAAATTCC -s Anc2.Anc2refChr3 8117 19 + 53186 GAC-TGAGGGACTAAATTCC -s mr.mrrefChr0 122448 20 + 130230 GACATGAGGGGCTAAATTCT -s simCow_chr6.simCow.chr6 135526 3 + 602619 -----------------TCG -s simDog_chr6.simDog.chr6 419588 19 - 593897 GAC-TGAGGGACTAAATTCC -s simHuman_chr6.simHuman.chr6 122469 20 + 601863 GTCATGAGGGGTTAAATTCC -s simRat_chr6.simRat.chr6 125979 20 + 647215 GACTTGAGGGGCTGAATTCT - -a -s simMouse_chr6.simMouse.chr6 127574 46 + 636262 GCAGAGTGAAAGGCTGCTCCAACCAAATGCCTTTTAATGTCTTTTA -s Anc0.Anc0refChr1 19587 36 - 62388 GCTGAGTAAAAGCCAGATCCAACCA----------AGTGTCTTTGA -s Anc1.Anc1refChr2 98176 36 + 144309 GCTGAGTAAAAGCCAGATCCAACCA----------AGTGTCTTTGA -s Anc2.Anc2refChr3 8137 36 + 53186 GCTGAGTAAAAGCCAGTTCCAACCA----------AGTATCCTTGG -s mr.mrrefChr0 122468 46 + 130230 GCAGAGTGAAAGGCTGATCCAACCAAATGCCTTTTAATGTCTTTTA -s simCow_chr6.simCow.chr6 135530 36 + 602619 GCTGAGTGGATGTCAGTTCCACCCA----------AGCATACTTGG -s simDog_chr6.simDog.chr6 419608 35 - 593897 GCTAAGTAAAAACCAGTGGCAACCA----------AGTATCCTTG- -s simHuman_chr6.simHuman.chr6 122490 36 + 601863 ACTGATTAAGGGCTGGATCCAGCCA----------AGTGTCTTTGA -s simRat_chr6.simRat.chr6 125999 45 + 647215 GCAGAGTGAAAGGCCAATCCAACCAAATGCCTCTCAATGACCTTA- - -a -s simMouse_chr6.simMouse.chr6 127620 18 + 636262 TTTGTAGATGCCCTGACT -s Anc0.Anc0refChr1 19623 18 - 62388 TTTGCACATGCCCTCACT -s Anc1.Anc1refChr2 98212 18 + 144309 TTTGCACATGCCCTCACT -s Anc2.Anc2refChr3 8173 18 + 53186 TTTGCACACACCATCACT -s mr.mrrefChr0 122514 18 + 130230 TTTGTAGATGCCCTGACT -s simCow_chr6.simCow.chr6 135567 18 + 602619 TTTGCACACACCATCACT -s simHuman_chr6.simHuman.chr6 122526 18 + 601863 TTTGCAAATGCCCTCTTT -s simRat_chr6.simRat.chr6 126044 15 + 647215 ---GTAGGTGCCCTAACT - -a -s simMouse_chr6.simMouse.chr6 127638 78 + 636262 CCTGTATGTTTCACAGCAATCTATGTGTATATCAGCGGCTTACTTGTTATTGGATGGTTCTGAAGTGCAAAGTTATCC -s Anc0.Anc0refChr1 19642 77 - 62388 CTTGTATGTTGCATAGGAATCTATCTGTTTATCAGCAGCCTACTTGTTTTTGAATGG-TCTGAAGTGCAAGGTTATCC -s Anc1.Anc1refChr2 98231 77 + 144309 CTTGTATGTTGCATAGGAATCTATCTGTTTATCAGCAGCCTACTTGTTTTTGAATGG-TCTGAAGTGCAAGGTTATCC -s Anc2.Anc2refChr3 8192 77 + 53186 CTAGTACATTGTATAGGATTCTATCTGTTTATCAGCAGCCTACTTGTTTTAGAATGG-TTTGAAATGCAAGGTCATCC -s mr.mrrefChr0 122532 78 + 130230 CCTGTATGTTTCATAGCAATCTATGTGTATATCAGCGGCCTACTTGTTATTGAATGGTTCTGAAGTGCAAAGTTATCC -s simCow_chr6.simCow.chr6 135586 77 + 602619 CTAGTACATTGTATAGGATTCTATCTGCTTATCAGCAGCCTACTTGTTTTAGGATGG-TTTGAGATGCAAGGTCATCC -s simDog_chr6.simDog.chr6 419643 50 - 593897 ---------------------------TTTATCAGCAGACTACTCGTTTTAGAATGG-TTTGCAATGCCAGGTCGTGC -s simHuman_chr6.simHuman.chr6 122545 77 + 601863 CTTGTATGTAGCATAGGAATCTATTTATTTATCACCAGCCTACTTGTTTTTGAATGG-TCTGAAGTGCAATGTTATCC -s simRat_chr6.simRat.chr6 126059 78 + 647215 CATGTATACTTTATAGCAATCTATGTGTATATCCGTGGCCTCCTTGTTATTGAATGGCTCTGAAATGCAAGGCTGTCC - -a -s simMouse_chr6.simMouse.chr6 127716 43 + 636262 TTTAAGTAAAAAGCGTATAACCAAACAAAACTTGGCCGTGGTG -s Anc0.Anc0refChr1 19719 43 - 62388 CTCGTGTAAAAATGATATATCAAAACAAAGCTTGGCTATTGCG -s Anc1.Anc1refChr2 98308 43 + 144309 CTCGTGTAAAAATGATATATCAAAACAAAGCTTGGCTATTGCG -s Anc2.Anc2refChr3 8269 43 + 53186 CTTGTGTAGAAATGATATATCAAAACAATGCTTGGCTATTGCT -s mr.mrrefChr0 122610 43 + 130230 TTCAAGTAAAAAGCATATAACCAAACAAAACTTGGCCGTGGTG -s simCow_chr6.simCow.chr6 135663 43 + 602619 CTTGTGTAGTAATCATGTCCCAAAACAATGGTTGGCTATTGTT -s simDog_chr6.simDog.chr6 419725 43 - 593897 CTTGTGCAGAAATGATATATAAAAACAATGCTTGGCTATTGCT -s simHuman_chr6.simHuman.chr6 122622 43 + 601863 CTCGTTTAAAAATGATATATCTAAGCAAAGCTTGGCTATTGCG -s simRat_chr6.simRat.chr6 126137 43 + 647215 TTCAAGTAAAAAGTATAAAACCAAACAAAACTTGGCCGTGGTG - -a -s simMouse_chr6.simMouse.chr6 127759 28 + 636262 AATCAACACAAAGTTCTTAGATAGTGAT -s Anc0.Anc0refChr1 19762 28 - 62388 ATTAGCCAGAAAATTCTCAAATGGTAAT -s Anc1.Anc1refChr2 98351 28 + 144309 ATTAGCCAGAAAATTCTCAAATGGTAAT -s Anc2.Anc2refChr3 8312 28 + 53186 ATTAGCCAGAAAATTCTCAAATGGTAAT -s mr.mrrefChr0 122653 28 + 130230 AATCAACACAAAATTCTTAGATAGTGAT -s simCow_chr6.simCow.chr6 135735 28 + 602619 ATTAGCCAGAAAATTCTCAGATGGTAAT -s simDog_chr6.simDog.chr6 419768 18 - 593897 ATTGGATA----------CATTGTTAGT -s simHuman_chr6.simHuman.chr6 122665 28 + 601863 GTTAGCCAAAAAAGTCTCAAATGGTAAT -s simRat_chr6.simRat.chr6 126180 28 + 647215 AATCAACATAAAATTCTTACATAGTGAT - -a -s simMouse_chr6.simMouse.chr6 127787 3 + 636262 TCA -s Anc0.Anc0refChr1 19790 3 - 62388 TCA -s Anc1.Anc1refChr2 98379 3 + 144309 TCA -s Anc2.Anc2refChr3 8340 3 + 53186 GCA -s mr.mrrefChr0 122681 3 + 130230 TCA -s simDog_chr6.simDog.chr6 419786 3 - 593897 GCA -s simHuman_chr6.simHuman.chr6 122693 3 + 601863 TTA -s simRat_chr6.simRat.chr6 126217 3 + 647215 TCA - -a -s simMouse_chr6.simMouse.chr6 127790 50 + 636262 AAGCCTTGTTACCTACTACACATAATCTTGTCTTCCTAACATTATGGAAT -s Anc0.Anc0refChr1 19794 50 - 62388 AAGTTTTCTTACCTACTGCACATAGACTTGTGTTCCTAGCATAAAATCCT -s Anc1.Anc1refChr2 98383 50 + 144309 AAGTTTTCTTACCTACTGCACATAGACTTGTGTTCCTAGCATAAAATCCT -s Anc2.Anc2refChr3 8344 50 + 53186 GAGTTTTCTTACCTAGTGCACATAGACTTGTGTTGCTAGCAGAAAATTCT -s mr.mrrefChr0 122684 50 + 130230 AAGCCTTGTTACCTACTACACATAATCTTGTGTTCCTAACATTATGGCAT -s simCow_chr6.simCow.chr6 135763 39 + 602619 ---TTTTGTTACCTATGGCCCATAAGCTTCTGTTGCTAACA--------T -s simDog_chr6.simDog.chr6 419793 45 - 593897 GAGTGATCCTCCTTAGTGCATCTAGAGTGGT-----TAGCAGAAAATTCT -s simHuman_chr6.simHuman.chr6 122697 50 + 601863 AAGTTTCATTACCTACTGCACATAGACTTGTGCTCCTGGCATAACTCCCT -s simRat_chr6.simRat.chr6 126220 50 + 647215 AAGCCTTGTTACCTGCTAGACATAATCTTGTGTTCCTAACATTATGGCAT - -a -s simMouse_chr6.simMouse.chr6 127840 38 + 636262 GTCACTAGACCCTAGCAGGCCTCATTACCTCCAACAGG -s Anc0.Anc0refChr1 19845 36 - 62388 TTCATTAG--CTTAACAAGTCTCATTACCTACAACTTA -s Anc1.Anc1refChr2 98434 38 + 144309 TTCATTAGACCTTAACAAGTCTCATTACCTACAACTTA -s Anc2.Anc2refChr3 8395 36 + 53186 TGCATTAA--CTTAACAAATCTTAGTACCTACTACTTA -s mr.mrrefChr0 122734 38 + 130230 GTCACTAGACCCTAGCAGGTCTCATTACCTCCAACAGG -s simCow_chr6.simCow.chr6 135803 33 + 602619 TGCAT-----CCTAGTGATTCTTACTACCTATGACGGC -s simDog_chr6.simDog.chr6 419839 35 - 593897 AGATGTAA---TTTACAAATCTTGGTACCTACTGCTTA -s simHuman_chr6.simHuman.chr6 122748 38 + 601863 TTCATTAGACCTTAACAAGTCTCATTAGCAACAACCAA -s simRat_chr6.simRat.chr6 126270 38 + 647215 GTCACTAGATCCTAGCAGGTCCCATTACCTTCAACAGG - -a -s simMouse_chr6.simMouse.chr6 127878 20 + 636262 TGCCTTGTGTCAGCAACATT -s Anc0.Anc0refChr1 19882 20 - 62388 AGGCTtgTGTCACTAACATA -s Anc1.Anc1refChr2 98473 20 + 144309 AGGCTtgTGTCACTAACATA -s Anc2.Anc2refChr3 8432 20 + 53186 AGGCTtgTGTCGCTAACATA -s mr.mrrefChr0 122773 20 + 130230 TGCCTTGTGTCACCAACATT -s simCow_chr6.simCow.chr6 135837 20 + 602619 AGGCTCGTGTCCCTAATATA -s simDog_chr6.simDog.chr6 419875 20 - 593897 AAGCTtgtgtggctaacatt -s simHuman_chr6.simHuman.chr6 122787 18 + 601863 AGTCT--TGTCACGAGCATA -s simRat_chr6.simRat.chr6 126309 20 + 647215 TGTCTTGTGTCACCAACATT - -a -s simMouse_chr6.simMouse.chr6 127898 33 + 636262 GCTCACTCTTTGGTGCATCAAAGCATCTGAAAA -s Anc0.Anc0refChr1 19902 33 - 62388 ACTCACTCTTCGTTGCAGCTTAGTATCTGAAAA -s Anc1.Anc1refChr2 98493 33 + 144309 ACTCACTCTTCGTTGCAGCTTAGTATCTGAAAA -s Anc2.Anc2refChr3 8452 33 + 53186 ACTCACTCTTCATTGCAGCTTAGTATCTGGAAA -s mr.mrrefChr0 122793 33 + 130230 GCTCACTCTTTGGTGCATCAAAGCATCTGAAAA -s simCow_chr6.simCow.chr6 135857 33 + 602619 ACTCACTCTTCATTGCATCCTGGTATCCAGGAA -s simDog_chr6.simDog.chr6 419961 33 - 593897 gctcactctccattgcaGTTTAGTATATGGAAA -s simHuman_chr6.simHuman.chr6 122805 33 + 601863 ACTCACTCTTCGTTGCACCTTAGTATCTGAAAA -s simRat_chr6.simRat.chr6 126329 33 + 647215 GCCCACTCTTTGGTGCATCAAAGCATCTGAGAG - -a -s simMouse_chr6.simMouse.chr6 127931 15 + 636262 AATATGACATAAAAT -s Anc0.Anc0refChr1 19949 15 - 62388 AATATGACATCCAAT -s Anc1.Anc1refChr2 98540 15 + 144309 AATATGACATCCAAT -s Anc2.Anc2refChr3 8502 15 + 53186 AATATGACATCCAAT -s mr.mrrefChr0 122826 15 + 130230 AATATGACATACAAT -s simCow_chr6.simCow.chr6 135907 15 + 602619 AATATGACATCCAGT -s simDog_chr6.simDog.chr6 420011 15 - 593897 GATATGATACCTAAC -s simHuman_chr6.simHuman.chr6 122852 15 + 601863 AATATGACATGCAAT -s simRat_chr6.simRat.chr6 126362 15 + 647215 AATATAACATACAAT - -a -s simMouse_chr6.simMouse.chr6 127946 26 + 636262 ATTCTTTGAAAGGGGCTCAACGGATC -s Anc0.Anc0refChr1 20039 23 - 62388 ATCCACTG---GGGGGCCAGTGAACC -s Anc1.Anc1refChr2 98630 23 + 144309 ATCCACTG---GGGGGCCAGTGAACC -s Anc2.Anc2refChr3 8592 23 + 53186 ATCCACAT---GGGGGCCAGTGAACC -s mr.mrrefChr0 122841 26 + 130230 ATTCTTTGAAAGGGGCTCAACGGATC -s simCow_chr6.simCow.chr6 465598 23 - 602619 ATCCACAT---GGAGCCCATTGAACC -s simDog_chr6.simDog.chr6 420072 23 - 593897 ATCTGCAT---AGGGGCCAGTGATCC -s simHuman_chr6.simHuman.chr6 123030 23 + 601863 ATCCACTG---GGGAGCCTGTGAACC -s simRat_chr6.simRat.chr6 126377 24 + 647215 ATTCTTTGAAAGGAGGTCAACGG--C - -a -s simMouse_chr6.simMouse.chr6 127972 34 + 636262 TGGACCAAGTCCACCTTTGTCCCTTGACACTTAA -s Anc0.Anc0refChr1 20084 27 - 62388 T-AACAAAGTCCAG------TCCTTGACACTTCA -s Anc1.Anc1refChr2 98675 28 + 144309 TGAACAAAGTCCAG------TCCTTGACACTTCA -s Anc2.Anc2refChr3 8637 27 + 53186 T-AACAAAGTCCAG------TCCTTGTCACTTCA -s mr.mrrefChr0 122867 34 + 130230 TGAACAAAGTCCAGCTTTGTCCCTTGACACTTAA -s simCow_chr6.simCow.chr6 465638 16 - 602619 ---------TCCAG------TTGTTGTCATT--- -s simDog_chr6.simDog.chr6 420117 27 - 593897 T-AACAAAGTCCAG------CCCTTGTCACTTCA -s simHuman_chr6.simHuman.chr6 123075 28 + 601863 TGAACAAAGTTCTG------TCCTAGACACTTCA -s simRat_chr6.simRat.chr6 126401 34 + 647215 TGAACAGAGCCCAGCCTTGTCCTTTGACACTTAA - -a -s simMouse_chr6.simMouse.chr6 128006 33 + 636262 AAAGGATGATGTGAAGTCCCTGAGAAATACATA -s Anc0.Anc0refChr1 20116 30 - 62388 AAAGAACAGAGAGA---CTCTGAGAAATGCATA -s Anc1.Anc1refChr2 98708 30 + 144309 AAAGAACAGAGAGA---CTCTGAGAAATGCATA -s Anc2.Anc2refChr3 8669 30 + 53186 AAAGAACAGAAAGT---CTCTGAGTAATGCATA -s mr.mrrefChr0 122901 30 + 130230 AAAGGATGGTGTGA---CCCTGAGAAATACATA -s simCow_chr6.simCow.chr6 465656 29 - 602619 AAAGAAGTGAAGAT---CCCTGAG-AATGCACA -s simDog_chr6.simDog.chr6 420149 30 - 593897 AAAAAACAGAAAGT---CTGTGAGTAATGCATA -s simHuman_chr6.simHuman.chr6 123108 30 + 601863 AATGAACAGAGAGA---CTCTGAGAAATGCATA -s simRat_chr6.simRat.chr6 126435 27 + 647215 AAAGGATGGTG------CCCTGAGAAATACATA - -a -s simMouse_chr6.simMouse.chr6 128039 100 + 636262 ATGTTTGACAGGCCTCCACTGGGAATGCCACCTTTAGGTAGAAGATTATAACAATACATTGCTTAACCAATACATTGCTCTTGAGGAGAAGATGCGAAAA -s Anc0.Anc0refChr1 20149 77 - 62388 GGGTTTGGTGGGGTTCCACTGGGAATGCTGCCCT----TAGAGGATGATACCAAGACATTGCTTA--CAGTA-------T----------GAAGTAAAAA -s Anc1.Anc1refChr2 98741 83 + 144309 GGGTTTGGTGGGGTTCCACTGGGAATGCTGCCCT----TAGAGGATGATACCAAGACATTGCTTA--CAGTA-ATTGCTT----------GAAGTAAAAA -s Anc2.Anc2refChr3 8702 77 + 53186 GGGTTTAGTGGGGTTCCACTGGGAATGCTGCCCT----TAGAGTATGATACCAAGACATTGCTTA--CAGTA-------T----------GAAGTAAGAA -s mr.mrrefChr0 122934 100 + 130230 AGGTTTGATAGGCATCCACTGGGAATGCCACCTTTAGGTAGAAGATTATAACAATACATTGCTTAACCAATACATTGCTCTTGAGGAGAAGATGCGAAAA -s simCow_chr6.simCow.chr6 465688 77 - 602619 GGGTGTAGTGGGCTTCTACTGTGCATTCTGCCTT----TGGAGTATGATACCTGGGCGTTGCTTA--TAGTA-------G----------GAAGTAAGAA -s simDog_chr6.simDog.chr6 420182 77 - 593897 AGGTTTAGTCGGGTTCCACTGGGAATGCTGCCCT----TAGAGTACGAGACCAAGACATTGCTTA--CAGTA-------T----------GAAGTAAGAA -s simHuman_chr6.simHuman.chr6 123141 44 + 601863 GGGTTTGGT----------------------------------GGTGATACCAAGACATTG------------ATTGCTT----------GAAGTAAAAA -s simRat_chr6.simRat.chr6 126465 100 + 647215 AGGTTTGATAGGCATCCATTGGGAATGTTACCTTTTTGTTGAATATTGTACCAATACATTGCTTAACCAATACATTGCTTACTAGGAGAAGATGCAAAAA - -a -s simMouse_chr6.simMouse.chr6 128139 85 + 636262 TACTTATCTGTTCATATAGTCTGAGTCTGTATGTAAATGTAGATATGTGTGGAAATGTGGCTGTGTGTTGTGATTCAAGCTCCCT -s Anc0.Anc0refChr1 20226 67 - 62388 TACCAACCTGTCCATTTAGTCTAAATCTATA------------------TGGAAGTGTAGCTGTGTGTTGCAATTTAAGCACCCT -s Anc1.Anc1refChr2 98824 67 + 144309 TACCAACCTGTCCATTTAGTCTAAATCTATA------------------TGGAAGTGTAGCTGTGTGTTGCAATTTAAGCACCCT -s Anc2.Anc2refChr3 8783 67 + 53186 TACCAACCTATCCATTTAGTCTAAATCTATA------------------TGGAAGTGTAGCTGTGTGTTGCAATTTAAGCACCCT -s mr.mrrefChr0 123034 85 + 130230 TACTTATCTGTTCATATAGTCTGAGTCTGTATGTAAATGTAGATATGTGTGGAAATGTAGCTGTGTGTTGCAATTCAAGCTCCCT -s simCow_chr6.simCow.chr6 465769 66 - 602619 TAGCAACATATCTATTTAGTCTAAACCTATA------------------TGGAAGTG-AGTGGTGTGTTGCAATCTATGCACCCT -s simDog_chr6.simDog.chr6 420263 64 - 593897 TACCAACCTATCCATTTAGTCTGAATCTGTA------------------GG--AGTGTGACTGTGTGTTGC-ATTTAAGTGCCCT -s simHuman_chr6.simHuman.chr6 123185 67 + 601863 TACGAACTTGTCCATTTAGTCTAAATCCATA------------------TGGAAGTATAGCTATGTGTTGCAATTTAAGCACCCT -s simRat_chr6.simRat.chr6 126565 85 + 647215 TACTTATCTGTTCATACACCCTGACTCTGTATGTAAATCTAGCTATGTACAGAAATGTATCTGTGTGTTGCAATTCAAGCTCCCT - -a -s simMouse_chr6.simMouse.chr6 128224 86 + 636262 CTGGATCATCAGATGTTATACTCTTCATTTATGGACAGGTATACCAGAGCACCAATGGAACTTTTAATCAGTGACAGTGTCAGATA -s Anc0.Anc0refChr1 20294 86 - 62388 CCAAATCATCATATGGTATACTCTTCATGTATAGGTAGCCATATCAGAGCACCAATGGTACTTTCATTCAGTGACAGTGTCAGAGA -s Anc1.Anc1refChr2 98892 86 + 144309 CCAAATCATCATATGGTATACTCTTCATGTATAGGTAGCCATATCAGAGCACCAATGGTACTTTCATTCAGTGACAGTGTCAGAGA -s Anc2.Anc2refChr3 8851 86 + 53186 CCAACTCATCATATGGTATGCTCTTCATGTATGGTTAGCCATATCAGAGCACCAATGGTACTTTCATTCAGTGCCAGTGTCAGTGG -s mr.mrrefChr0 123119 86 + 130230 CTGGATCATCATATGTTATACTCTTCATGTATAGGTAGGTATACCAGAGCACCAATGGAACTTTTAATCAGTGACAGTGTCAGAGA -s simCow_chr6.simCow.chr6 465836 83 - 602619 CCAACTCATCATATAGTATTCTCTTCAAGTCTGGTTAGCCATACCAGAGCAGTAATGGTACTTTCATTAAGTGGCAGTGTCA---G -s simDog_chr6.simDog.chr6 420327 86 - 593897 CCAACTCATCATATGGTATGCTCTTCATGTATGGTTAGCCACATCACAGCACCAATGGTTATTTCATTCATTGCCAGTGTCAGTGG -s simHuman_chr6.simHuman.chr6 123253 86 + 601863 CAAAATCAGCATATGGCATACTTCTCATGTACAGGTAGCCATATCAGAGCACCAATGGTACTTTCATTTAGTGACAGTGTCAGAGA -s simRat_chr6.simRat.chr6 126650 86 + 647215 CTGTATCATCGTATGTTATGCCCTCCATGTATAGGTAGGTATACCAGAGCACCAATGGAGATTTTAATCAGTGACAATGTCAGAGA - -a -s simMouse_chr6.simMouse.chr6 128310 22 + 636262 ATTAGTCATTCTGAATGCACAA -s Anc0.Anc0refChr1 20380 22 - 62388 ATTAATAATTCTAATTGCACGA -s Anc1.Anc1refChr2 98978 22 + 144309 ATTAATAATTCTAATTGCACGA -s Anc2.Anc2refChr3 8954 22 + 53186 GTTAATAATTCTAATTGCATGA -s mr.mrrefChr0 123205 22 + 130230 ATTAGTCATTCTGAATGCACAA -s simCow_chr6.simCow.chr6 465937 22 - 602619 GTTACTCATCCTAGAAGCATGA -s simDog_chr6.simDog.chr6 420430 22 - 593897 GTTGAGAATTCTAATTGCATGA -s simHuman_chr6.simHuman.chr6 123339 22 + 601863 ATTAATTATTCTAACTGAACGA -s simRat_chr6.simRat.chr6 126736 20 + 647215 ATTA--CATCCTGGATGCATAA - -a -s simMouse_chr6.simMouse.chr6 128332 8 + 636262 AATTCTGG -s Anc0.Anc0refChr1 20402 8 - 62388 AATTTTGG -s Anc1.Anc1refChr2 99000 8 + 144309 AATTTTGG -s Anc2.Anc2refChr3 8976 8 + 53186 AATTTTGG -s mr.mrrefChr0 123227 8 + 130230 AATTCTGG -s simCow_chr6.simCow.chr6 465974 8 - 602619 AATTTCGG -s simDog_chr6.simDog.chr6 420452 8 - 593897 AATTTTGG -s simHuman_chr6.simHuman.chr6 123361 7 + 601863 AATT-TGG -s simRat_chr6.simRat.chr6 126756 8 + 647215 AATTCTGG - -a -s simMouse_chr6.simMouse.chr6 128340 53 + 636262 GAACCTTTAGGTCACAATTTGGCCCCAAAAAGTTGCTTGGATTTAATTCCCAC -s Anc0.Anc0refChr1 20410 52 - 62388 GAAACTTTTGATCACAATCTGGCCCAAAAAATTTCCTT-CATTTAATTTACAC -s Anc1.Anc1refChr2 99008 52 + 144309 GAAACTTTTGATCACAATCTGGCCCAAAAAATTTCCTT-CATTTAATTTACAC -s Anc2.Anc2refChr3 8984 52 + 53186 GAAACTTTTGATCACAATCTGGCCTGAAAAATTTCCTT-TCTTTAATTTACAC -s mr.mrrefChr0 123235 53 + 130230 GAAACTTTAGGTCACAATCTGGCCCAAAAAAGTTGCTTGCATTTAATTTCCAC -s simCow_chr6.simCow.chr6 465984 52 - 602619 GAAACTTTTGATCACAATCTGGCCTGAAAAATTTCCTT-TCCTTACTATACAC -s simDog_chr6.simDog.chr6 420460 33 - 593897 GTACCTTTAGATC-------------------TTCCTT-TCTTTTATTTACAC -s simHuman_chr6.simHuman.chr6 123368 52 + 601863 GAAACTTTTGATCACAATCTGGTCCAAGGTGATTCCTT-CATTTAGTTTGCAC -s simRat_chr6.simRat.chr6 126764 51 + 647215 AAAACTTTAGGTCACAATCTGGCCCAAAAA-GTTGCTTGCATT-AATTTCCAC - -a -s simMouse_chr6.simMouse.chr6 128393 29 + 636262 ATTATTCCCATGGATGATTGACAGCCAGA -s Anc0.Anc0refChr1 20462 24 - 62388 ATTAATTCTGTGGATGATTACC-----TC -s Anc1.Anc1refChr2 99060 29 + 144309 ATTAATTCTGTGGATGATTACCAACCATC -s Anc2.Anc2refChr3 9036 24 + 53186 ATTAATTCTGGGAATGATCCCC-----TC -s mr.mrrefChr0 123288 29 + 130230 ATTATTCCCATGGATGATTAACAACCAGA -s simCow_chr6.simCow.chr6 466042 2 - 602619 AT--------------------------- -s simDog_chr6.simDog.chr6 420493 24 - 593897 ATTAATTCTGGGAATGATCCCC-----TC -s simHuman_chr6.simHuman.chr6 123420 29 + 601863 ATTACTACTGTGGATGATTACCAACCACT -s simRat_chr6.simRat.chr6 126815 29 + 647215 ACGATTCCCATGGATGATCATCAACCAAA - -a -s simMouse_chr6.simMouse.chr6 128422 19 + 636262 TTAGCATGAGCTTTGCCAC -s Anc0.Anc0refChr1 20486 19 - 62388 TTAACGCCACATTTGACAT -s Anc1.Anc1refChr2 99089 19 + 144309 TTAACGCCACATTTGACAT -s Anc2.Anc2refChr3 9060 19 + 53186 TTAATGCCACATTTGACAT -s mr.mrrefChr0 123317 19 + 130230 TTAGCACGAGCTTTGCCAC -s simCow_chr6.simCow.chr6 466405 19 - 602619 CTAATGCCACATTTGACAT -s simDog_chr6.simDog.chr6 420517 19 - 593897 TTAATGCCACATTAGCCAC -s simHuman_chr6.simHuman.chr6 123449 19 + 601863 TTAACGCCACATTTGACAT -s simRat_chr6.simRat.chr6 126844 14 + 647215 TTAGCACAAGC-----CAC - -a -s simMouse_chr6.simMouse.chr6 128441 59 + 636262 ATTACCTGCATTTCATTATTTTTTCAAATTAAGGCTGCCACTATTGAAAGTCCATCTGA -s Anc0.Anc0refChr1 20506 59 - 62388 ATTACTTGCACTTTGTTATTTCTACATATTAATGCTGCCACTATAGAAAGTCTGTCTGT -s Anc1.Anc1refChr2 99109 59 + 144309 ATTACTTGCACTTTGTTATTTCTACATATTAATGCTGCCACTATAGAAAGTCTGTCTGT -s Anc2.Anc2refChr3 9080 59 + 53186 ATTACTTGCACTCTGTTATTTCTACATGACAATGCTGCCACTACAGAAAGTCTGTCTGT -s mr.mrrefChr0 123336 59 + 130230 ATTACTTGCATTTCATTATTTTTACAAATTAAGGCTGCCACTATTGAAAGTCCATCTGT -s simCow_chr6.simCow.chr6 466425 59 - 602619 ATTATTAGCACTCTGTTATTTCTACATGACAATGCTGCCACTACAGAAAGTTTGTCTGT -s simDog_chr6.simDog.chr6 420537 59 - 593897 TTTACATCCACTCTGTAATTTCTTCATGACAATGCCGCTACTACAGAAAGTCTGTGAGT -s simHuman_chr6.simHuman.chr6 123469 57 + 601863 ATTGCTTGCACTTTGTTATTTCTAC--ATTATTGCTCCCACTATAGTGAGTCTGTCTGT -s simRat_chr6.simRat.chr6 126858 59 + 647215 ATTACTTGCAGTTCATTATTTTTACAAAGTAAGGCTGCCACTATTGAAAGTCCATCTGT - -a -s simMouse_chr6.simMouse.chr6 128500 21 + 636262 CCATTAGTGAAAATTCTTGAT -s Anc0.Anc0refChr1 20566 21 - 62388 CCATTAGTGAAAATTATCAGT -s Anc1.Anc1refChr2 99169 21 + 144309 CCATTAGTGAAAATTATCAGT -s Anc2.Anc2refChr3 9140 21 + 53186 CTATTAGTAAATATTATCAGT -s mr.mrrefChr0 123396 21 + 130230 CCATTAGTGAAAATTCTTGAT -s simCow_chr6.simCow.chr6 466485 21 - 602619 CTATCAGTACTCATTATTAGT -s simDog_chr6.simDog.chr6 420597 19 - 593897 CTATTAG--AATATTATCGGT -s simHuman_chr6.simHuman.chr6 123527 21 + 601863 CCGTTAGTGAAAATAATCAGT -s simRat_chr6.simRat.chr6 126918 21 + 647215 CCATTAGTGAGAATTCTGGAT - -a -s simMouse_chr6.simMouse.chr6 128521 31 + 636262 TGACAAGATCACTCACAATATAGACTATAAG -s Anc0.Anc0refChr1 20589 17 - 62388 TTAAAGGACAGCCCTC--------------G -s Anc1.Anc1refChr2 99192 17 + 144309 TTAAAGGACAGCCCTC--------------G -s Anc2.Anc2refChr3 9163 17 + 53186 CTTAAGATCAGCCTTC--------------T -s mr.mrrefChr0 123417 31 + 130230 TGAAAAGATCACTCACAATATAGACTATAAG -s simCow_chr6.simCow.chr6 466508 17 - 602619 CTTAAAATCAGCATAC--------------T -s simDog_chr6.simDog.chr6 420618 17 - 593897 CCTAAGATCAGTCTTC--------------T -s simHuman_chr6.simHuman.chr6 123550 17 + 601863 TTAAAGGACAGCCCTC--------------G -s simRat_chr6.simRat.chr6 126939 31 + 647215 CAAAAAGACCAGCCACAATCTAGACTATAAG - -a -s simMouse_chr6.simMouse.chr6 128552 17 + 636262 TGCGCATTGCTCACACG -s Anc0.Anc0refChr1 20606 10 - 62388 TGTAC------CAC-CA -s Anc1.Anc1refChr2 99209 10 + 144309 TGTAC------CAC-CA -s Anc2.Anc2refChr3 9180 10 + 53186 TGTAC------TAG-CA -s mr.mrrefChr0 123448 16 + 130230 TGCGCATTGCTCAC-CA -s simCow_chr6.simCow.chr6 466525 10 - 602619 TGAAC------TAG-CA -s simDog_chr6.simDog.chr6 420635 10 - 593897 TGTAC------TAG-CA -s simHuman_chr6.simHuman.chr6 123567 10 + 601863 TGTAC------CAC-CA -s simRat_chr6.simRat.chr6 126971 16 + 647215 TGCACATTGCTGAC-CA - -a -s simMouse_chr6.simMouse.chr6 128569 9 + 636262 AGCCTTACG -s Anc0.Anc0refChr1 20616 9 - 62388 GTTCTTACG -s Anc1.Anc1refChr2 99219 9 + 144309 GTTCTTACG -s Anc2.Anc2refChr3 9190 9 + 53186 GTTCTTATA -s mr.mrrefChr0 123464 9 + 130230 GGCCTTACG -s simCow_chr6.simCow.chr6 466535 9 - 602619 GTCCTTATA -s simDog_chr6.simDog.chr6 420745 9 - 593897 GTTCTTATA -s simHuman_chr6.simHuman.chr6 123577 9 + 601863 GTTCTTACG -s simRat_chr6.simRat.chr6 126987 9 + 647215 GGCCTTACG - -a -s simMouse_chr6.simMouse.chr6 128578 15 + 636262 AGGCGGCAAACCAGC -s Anc0.Anc0refChr1 20630 7 - 62388 AGATGAC-------- -s Anc1.Anc1refChr2 99233 7 + 144309 AGATGAC-------- -s Anc2.Anc2refChr3 9204 7 + 53186 AAATGAG-------- -s mr.mrrefChr0 123473 15 + 130230 AGGCGGCAAACCAGC -s simCow_chr6.simCow.chr6 466549 7 - 602619 AAGTGAG-------- -s simDog_chr6.simDog.chr6 420759 7 - 593897 AAATCAG-------- -s simHuman_chr6.simHuman.chr6 123591 7 + 601863 AGATGAC-------- -s simRat_chr6.simRat.chr6 126996 15 + 647215 AGGCAGCAAACCAGC - -a -s simMouse_chr6.simMouse.chr6 128593 10 + 636262 AATTAGCAAC -s Anc0.Anc0refChr1 20637 9 - 62388 -ATTAGAAAC -s Anc1.Anc1refChr2 99240 9 + 144309 -ATTAGAAAC -s Anc2.Anc2refChr3 9211 9 + 53186 -ATTAGAAAC -s mr.mrrefChr0 123488 10 + 130230 AATTAGCAAC -s simCow_chr6.simCow.chr6 466556 9 - 602619 -TCTAGATAC -s simDog_chr6.simDog.chr6 420766 9 - 593897 -ATTGGAAAC -s simHuman_chr6.simHuman.chr6 123598 9 + 601863 -ATTAGAAAC -s simRat_chr6.simRat.chr6 127044 10 + 647215 AGTTAGCAAC - -a -s simMouse_chr6.simMouse.chr6 128603 54 + 636262 CAATTGAGCAAACAGGTTATGATGTGCATTTAAAATAACCTGAGAGTAGTTTTT -s Anc0.Anc0refChr1 20655 54 - 62388 CAATTGTACAAGCATGTTCTGCTACATATCTTTAATAACCTGAGAGTAGACTGT -s Anc1.Anc1refChr2 99258 54 + 144309 CAATTGTACAAGCATGTTCTGCTACATATCTTTAATAACCTGAGAGTAGACTGT -s Anc2.Anc2refChr3 9229 54 + 53186 CAACTGTACAAGCATGTTCTGCTACATATCTTTAGTAACCTGAGAGTAGACTGA -s mr.mrrefChr0 123498 54 + 130230 CAATTGAGCAAGCAGGTTATGATGCACATTTAAAATAACCTGAGAGTAGTTTTT -s simCow_chr6.simCow.chr6 466574 31 - 602619 CAACTGTACAGGCATATTCT---AGCTATCTTCG-------------------- -s simDog_chr6.simDog.chr6 420775 44 - 593897 ----------AGCATGTACTGCTACATATCTTTAGTAACCTGAGAGTAGACTGA -s simHuman_chr6.simHuman.chr6 123616 54 + 601863 CAATTGTACAAGCATGTTCTGCTACATATCTTTAATAACCAGAGAGTAGGCTCT -s simRat_chr6.simRat.chr6 127054 54 + 647215 CAATTGAGCAAGCAGGTTATGAAGCACATTTAAAATAACCTTAGAGTTGTTTTT - -a -s simMouse_chr6.simMouse.chr6 128657 46 + 636262 CCATCATCCATGCGGCAAACTAAACTAGCTGCTACCCAAACACCAC -s Anc0.Anc0refChr1 20709 44 - 62388 --TTCATCCATGTGATGAACGAAACTAGCCGCTACCCTTACCCTAG -s Anc1.Anc1refChr2 99312 46 + 144309 CTTTCATCCATGTGATGAACGAAACTAGCCGCTACCCTTACCCTAG -s Anc2.Anc2refChr3 9283 44 + 53186 --TTCATCTATGTGATGAATGAAACCAATTGCTACCCTTTGCCTAG -s mr.mrrefChr0 123552 46 + 130230 CTATCATCCATGTGACGAACTAAACTAGCCGCTACCCTAACACCAC -s simCow_chr6.simCow.chr6 466605 21 - 602619 ---TCATCTATGTGATGAATGAAA---------------------- -s simDog_chr6.simDog.chr6 420819 44 - 593897 --TTCGTCTATGTGATGAATGAAACCAATTGCTACCCTTTGCCTAG -s simHuman_chr6.simHuman.chr6 123672 46 + 601863 CTTTCACCCATGTGAAGAACAAAACTAGCCGCTACCTTTACCCTAT -s simRat_chr6.simRat.chr6 127108 46 + 647215 CTGTCATCCATGTGATGAGCTAAACTAGCCGCAACCCTAACAACAC - -a -s simMouse_chr6.simMouse.chr6 128703 45 + 636262 TTTTGTGTGATGTACATGAGCAAAGGAAAGTGATAATCTACCTAT -s Anc0.Anc0refChr1 20756 7 - 62388 TTTTGTT-------------------------------------- -s Anc1.Anc1refChr2 99361 45 + 144309 TTTTGTTCAATGCTTATGAGCGCAGGAAGGCAAATGTCTATTCAT -s Anc2.Anc2refChr3 9330 7 + 53186 CTTTGTT-------------------------------------- -s mr.mrrefChr0 123598 45 + 130230 TTTTGTGTGATGTACATGAGCAAAGGAAAGCAATAATCTACCTAT -s simDog_chr6.simDog.chr6 420866 7 - 593897 CTTTGTT-------------------------------------- -s simHuman_chr6.simHuman.chr6 123721 45 + 601863 TTTTGGTCAATGCTTATGAGCGCAGGAAGGCAAATGTCTATTCAT -s simRat_chr6.simRat.chr6 127154 43 + 647215 TTTTGTGTGATGTACAGGAGCATATGAAAGCAATAAT--ACCTAT - -a -s simMouse_chr6.simMouse.chr6 128748 13 + 636262 AGCCATGTCATAC -s Anc1.Anc1refChr2 99406 13 + 144309 GGCCATAGTGTCC -s mr.mrrefChr0 123643 13 + 130230 AGCCATGTTGTAC -s simHuman_chr6.simHuman.chr6 123767 13 + 601863 GGCCATAGTGTCC -s simRat_chr6.simRat.chr6 127197 13 + 647215 AATCATGATGTAC - -a -s simMouse_chr6.simMouse.chr6 128761 32 + 636262 CCTTTGTCTTGCTAGTTGACTCCACATTGTAA -s Anc0.Anc0refChr1 20763 28 - 62388 ----TGTTGTGCTACTTTACCTAACATTGTAA -s Anc1.Anc1refChr2 99424 32 + 144309 CCTTTGTTGTGCTACTTTACCTAACATTGTAA -s Anc2.Anc2refChr3 9337 28 + 53186 ----TGACGTGCTGCTGAGGCTAACAATGTAA -s mr.mrrefChr0 123661 32 + 130230 CCTTTGTTTTGCTAGTTTACTCCACATTGTAA -s simCow_chr6.simCow.chr6 137082 10 + 602619 ----------------------GACAGTATAA -s simDog_chr6.simDog.chr6 420873 28 - 593897 ----TGACGTGCTGCTGAGGCTAACGAAGTAA -s simHuman_chr6.simHuman.chr6 123785 32 + 601863 CCTTTGTTGTTCTATTTTACATAACATTGTAA -s simRat_chr6.simRat.chr6 127215 32 + 647215 CCTTAGTTTTGCTAGTTTAGCCCACATTGTAA - -a -s simMouse_chr6.simMouse.chr6 128793 14 + 636262 TACCAGCAGAACAT -s Anc0.Anc0refChr1 20791 14 - 62388 TACTAGCCAACACT -s Anc1.Anc1refChr2 99456 14 + 144309 TACTAGCCAACACT -s Anc2.Anc2refChr3 9365 14 + 53186 TACTGGCCCATACT -s mr.mrrefChr0 123693 14 + 130230 TACCAGCAAACCAT -s simCow_chr6.simCow.chr6 137099 14 + 602619 TATTGGCCCAAACC -s simDog_chr6.simDog.chr6 420901 12 - 593897 CACTGGCT--TCCT -s simHuman_chr6.simHuman.chr6 123817 14 + 601863 TACTAGCCAACACT -s simRat_chr6.simRat.chr6 127247 14 + 647215 CACCAGCAAACTGT - -a -s simMouse_chr6.simMouse.chr6 128807 8 + 636262 TGCTAAAT -s Anc0.Anc0refChr1 20805 8 - 62388 TTCTATAT -s Anc1.Anc1refChr2 99470 8 + 144309 TTCTATAT -s Anc2.Anc2refChr3 9379 8 + 53186 TTATATAT -s mr.mrrefChr0 123707 8 + 130230 TGCTAAAT -s simCow_chr6.simCow.chr6 137129 8 + 602619 TTATGTAT -s simDog_chr6.simDog.chr6 420913 8 - 593897 TTATATAT -s simHuman_chr6.simHuman.chr6 123831 8 + 601863 TTCTATAT -s simRat_chr6.simRat.chr6 127261 8 + 647215 TGTTAAAT - -a -s simMouse_chr6.simMouse.chr6 128815 7 + 636262 ATTATCC -s Anc0.Anc0refChr1 20813 7 - 62388 ATTATTT -s Anc1.Anc1refChr2 99478 7 + 144309 ATTATTT -s Anc2.Anc2refChr3 9387 7 + 53186 ATTGTGT -s mr.mrrefChr0 123715 7 + 130230 ATTATTT -s simCow_chr6.simCow.chr6 137138 7 + 602619 ATCCTGT -s simDog_chr6.simDog.chr6 420921 7 - 593897 ATTGTGT -s simHuman_chr6.simHuman.chr6 123839 7 + 601863 ATTATTT -s simRat_chr6.simRat.chr6 127269 7 + 647215 ATTATTT - -a -s simMouse_chr6.simMouse.chr6 128822 6 + 636262 ATTTCA -s Anc0.Anc0refChr1 20820 6 - 62388 CTATCA -s Anc1.Anc1refChr2 99485 6 + 144309 CTATCA -s Anc2.Anc2refChr3 9394 6 + 53186 CTATCA -s mr.mrrefChr0 123722 6 + 130230 ATTTCA -s simCow_chr6.simCow.chr6 137145 6 + 602619 CTATCT -s simDog_chr6.simDog.chr6 420928 6 - 593897 CAAGCA -s simHuman_chr6.simHuman.chr6 123846 6 + 601863 CTATCA -s simRat_chr6.simRat.chr6 127277 6 + 647215 ACTTCA - -a -s simMouse_chr6.simMouse.chr6 128828 13 + 636262 ATTTAACCAGACT -s Anc0.Anc0refChr1 20826 6 - 62388 AGC-------ACT -s Anc1.Anc1refChr2 99491 6 + 144309 AGC-------ACT -s Anc2.Anc2refChr3 9400 6 + 53186 AGC-------ACT -s mr.mrrefChr0 123728 13 + 130230 ATTTAACCAGACT -s simCow_chr6.simCow.chr6 137151 6 + 602619 ATA-------ACC -s simDog_chr6.simDog.chr6 420935 6 - 593897 AGC-------TCT -s simHuman_chr6.simHuman.chr6 123852 6 + 601863 AGC-------ACT -s simRat_chr6.simRat.chr6 127283 13 + 647215 ATTTAAGCAGACC - -a -s simMouse_chr6.simMouse.chr6 128841 2 + 636262 GT -s Anc0.Anc0refChr1 20832 2 - 62388 GT -s Anc1.Anc1refChr2 99497 2 + 144309 GT -s Anc2.Anc2refChr3 9406 2 + 53186 GT -s mr.mrrefChr0 123741 2 + 130230 GT -s simCow_chr6.simCow.chr6 137157 2 + 602619 AT -s simDog_chr6.simDog.chr6 420941 2 - 593897 GT -s simHuman_chr6.simHuman.chr6 123858 2 + 601863 GT -s simRat_chr6.simRat.chr6 127297 2 + 647215 GT - -a -s simMouse_chr6.simMouse.chr6 128843 8 + 636262 TTACAGTC -s Anc0.Anc0refChr1 20834 6 - 62388 T--GAATC -s Anc1.Anc1refChr2 99499 6 + 144309 T--GAATC -s Anc2.Anc2refChr3 9408 6 + 53186 T--GAAGC -s mr.mrrefChr0 123743 8 + 130230 TTACAATC -s simCow_chr6.simCow.chr6 137161 6 + 602619 T--GAAGC -s simDog_chr6.simDog.chr6 420943 6 - 593897 T--GGAGC -s simHuman_chr6.simHuman.chr6 123860 6 + 601863 T--AAATA -s simRat_chr6.simRat.chr6 127299 8 + 647215 TTACAATC - -a -s simMouse_chr6.simMouse.chr6 128851 15 + 636262 CACTGACCCTCTCAG -s Anc0.Anc0refChr1 20840 15 - 62388 CACAAGCCCTCTTAG -s Anc1.Anc1refChr2 99505 15 + 144309 CACAAGCCCTCTTAG -s Anc2.Anc2refChr3 9415 15 + 53186 CACAAGCTCTCTTAG -s mr.mrrefChr0 123751 15 + 130230 CACTAACCCTCTCAG -s simCow_chr6.simCow.chr6 137167 13 + 602619 --CAGGGTCTCTCTG -s simDog_chr6.simDog.chr6 420950 15 - 593897 CACAAGCTTTCTTAG -s simHuman_chr6.simHuman.chr6 123866 15 + 601863 TACGAGACCTCTTAG -s simRat_chr6.simRat.chr6 127307 12 + 647215 CACTAACT---TCAG - -a -s simMouse_chr6.simMouse.chr6 128866 12 + 636262 ATCACTCAATGT -s Anc0.Anc0refChr1 20855 12 - 62388 ATTGCTCAATGC -s Anc1.Anc1refChr2 99520 12 + 144309 ATTGCTCAATGC -s Anc2.Anc2refChr3 9430 12 + 53186 ATTGCTCAATGC -s mr.mrrefChr0 123766 12 + 130230 ATCACTCAATGT -s simCow_chr6.simCow.chr6 137180 12 + 602619 ATTGCTCAATGC -s simDog_chr6.simDog.chr6 420971 12 - 593897 ATTGGTCAATGC -s simHuman_chr6.simHuman.chr6 123881 12 + 601863 ATTGCTCGATGC -s simRat_chr6.simRat.chr6 127319 12 + 647215 ATCACTCCATGT - -a -s simMouse_chr6.simMouse.chr6 128878 1 + 636262 G -s Anc0.Anc0refChr1 20876 1 - 62388 G -s Anc1.Anc1refChr2 99541 1 + 144309 G -s Anc2.Anc2refChr3 9451 1 + 53186 G -s mr.mrrefChr0 123778 1 + 130230 G -s simCow_chr6.simCow.chr6 137201 1 + 602619 A -s simDog_chr6.simDog.chr6 420993 1 - 593897 G -s simHuman_chr6.simHuman.chr6 123902 1 + 601863 G -s simRat_chr6.simRat.chr6 127331 1 + 647215 G - -a -s simMouse_chr6.simMouse.chr6 128879 7 + 636262 TTGAATC -s Anc0.Anc0refChr1 20877 7 - 62388 TTGACTT -s Anc1.Anc1refChr2 99542 7 + 144309 TTGACTT -s Anc2.Anc2refChr3 9453 7 + 53186 TTAACCT -s mr.mrrefChr0 123779 7 + 130230 TTGAATC -s simCow_chr6.simCow.chr6 137203 7 + 602619 TTAACCT -s simDog_chr6.simDog.chr6 420995 7 - 593897 TTAACCT -s simHuman_chr6.simHuman.chr6 123903 7 + 601863 TTGGCTT -s simRat_chr6.simRat.chr6 127332 7 + 647215 TTGAATC - -a -s simMouse_chr6.simMouse.chr6 128886 37 + 636262 CGCTTGAATATTACATCAGAAGTGAATCCCCAGTATA -s Anc0.Anc0refChr1 20889 30 - 62388 CGGTGAAATGTCTCATTAG-------TCCTCAGTATA -s Anc1.Anc1refChr2 99554 30 + 144309 CGGTGAAATGTCTCATTAG-------TCCTCAGTATA -s Anc2.Anc2refChr3 9473 30 + 53186 CAGTGAAATGACTTATTGA-------TCCTCAGTATT -s mr.mrrefChr0 123786 37 + 130230 CGCTGGAATATTACATCAGAAGTGAATCCCCAGTATA -s simCow_chr6.simCow.chr6 137222 3 + 602619 CAG---------------------------------- -s simDog_chr6.simDog.chr6 421016 30 - 593897 CAGTGAAATGACTTATTGA-------TCCTCAGTATT -s simHuman_chr6.simHuman.chr6 123915 30 + 601863 CGGTGAAATCTCTCATAAG-------TCCTTAGTATA -s simRat_chr6.simRat.chr6 127339 37 + 647215 CACAGGAATATTACAGCAGAAGTGATTCCCCAGTATA - -a -s simMouse_chr6.simMouse.chr6 128923 68 + 636262 TAGTTATTTGTAAGTGTTGACATCTGAATGTTAATATTTCGAGATGCAAGGTGTCACATGAGGTTTCT -s Anc0.Anc0refChr1 20919 66 - 62388 TAGGTATTTGTGAG-GTTGACATCTGATTGTTAATTTTGCAGGATGCAAGGGCA-ACATGCAGGTTTG -s Anc1.Anc1refChr2 99584 68 + 144309 TAGGTATTTGTGAGTGTTGACATCTGATTGTTAATTTTGCAGGATGCAAGGGCATACATGCAGGTTTG -s Anc2.Anc2refChr3 9503 66 + 53186 CATTTATTTGTGAG-ACTGACATCTGATTGTTGATTTTGCAGGATGCAAGGGCA-ACACACAGGTTTG -s mr.mrrefChr0 123823 68 + 130230 TAGGTATTTGTAAGTGTTGACATCTGAATGTTAATATTTCGAGATGCAAGGTGTCACATGAGGTTTCT -s simDog_chr6.simDog.chr6 421046 66 - 593897 CATTTATTTGTGAG-ACTGACATCTGATTGTTGATTTTGCAGGATGCAAGGGCA-ACACACAGGTTTG -s simHuman_chr6.simHuman.chr6 123977 68 + 601863 TCGGTATTTGTGCATGTTGACATCTGGTTGCTATTTTTGCAGGATGCAAGGACATACATGCAGCTTTG -s simRat_chr6.simRat.chr6 127376 7 + 647215 CAAGTGT------------------------------------------------------------- - -a -s simMouse_chr6.simMouse.chr6 128991 22 + 636262 CGCCAGTCACAGGAGGTTAGGT -s Anc0.Anc0refChr1 20985 22 - 62388 CCTAGGTCCCAGGTGGTCAGGT -s Anc1.Anc1refChr2 99652 22 + 144309 CCTAGGTCCCAGGTGGTCAGGT -s Anc2.Anc2refChr3 9569 22 + 53186 CCTAGGGTCCAGGTGATCAGGT -s mr.mrrefChr0 123891 22 + 130230 CGCCAGTCCCAGGAGGTTAGGT -s simDog_chr6.simDog.chr6 421112 22 - 593897 CCTAGGGTCCAGGTGATCAGGT -s simHuman_chr6.simHuman.chr6 124046 22 + 601863 ACTAGGTCCCAGGGGGTGAGGT -s simRat_chr6.simRat.chr6 127383 16 + 647215 --CCAGTCCCATGAAGTT---- - -a -s simMouse_chr6.simMouse.chr6 129013 58 + 636262 TTCTCACCAGCATCACATGATGAGGTGTATGAGGTGCACCTTCCTTCATATAACATGG -s Anc0.Anc0refChr1 21007 19 - 62388 T-------AACA--------------------------------TTCATATAATACAG -s Anc1.Anc1refChr2 99674 19 + 144309 T-------AACA--------------------------------TTCATATAATACAG -s Anc2.Anc2refChr3 9591 19 + 53186 C-------CCCC--------------------------------TTCATATATTACAA -s mr.mrrefChr0 123913 52 + 130230 TTCTCACCAACATCACATGATGAGGTGTATGAGGTGC------CTTCATATAACATGG -s simDog_chr6.simDog.chr6 421135 19 - 593897 C-------CCCC--------------------------------TTCATATATTACAA -s simHuman_chr6.simHuman.chr6 124068 19 + 601863 T-------AACA--------------------------------TTCATGTAATGCAG -s simRat_chr6.simRat.chr6 127399 51 + 647215 -TCTTGCCAACATCACGTGATGAGGTGCATGAGGTGT------CTTTACAAAACATGG - -a -s simMouse_chr6.simMouse.chr6 129071 49 + 636262 TCCACAAAAGTTCTGTTTCCAGGGGCACTGGTGTCTTGCCTAAGCAATA -s Anc0.Anc0refChr1 21027 49 - 62388 TCTAAAAAAATCCTGTGTCCAGGGGCATCCGGGCCTTGCTCATGCAGTA -s Anc1.Anc1refChr2 99694 49 + 144309 TCTAAAAAAATCCTGTGTCCAGGGGCATCCGGGCCTTGCTCATGCAGTA -s Anc2.Anc2refChr3 9611 49 + 53186 CCTAAGAAAATCCTGTGACCAGGAGCATCCGGACCTTGCTCCTGCAGTA -s mr.mrrefChr0 123966 49 + 130230 TCCACAAAAGTTCTGTGTCCAGGGGCACTGGGGTCTTGCCTAAGCAATA -s simDog_chr6.simDog.chr6 421155 49 - 593897 CCTAAGAAAATCCTGTGACCAGGAGCATCCGGACCTTGCTCCTGCAGTA -s simHuman_chr6.simHuman.chr6 124088 49 + 601863 TCTAGAGAAATCCTGTGTCCAGGGGCATCAGGGCCTTGCTCATGCAGTA -s simRat_chr6.simRat.chr6 127451 47 + 647215 TTCACAAAAGTTCTGGGTCCAGGGGCACTGGGGTCTTGTCTAAGCAA-- - -a -s simMouse_chr6.simMouse.chr6 129120 75 + 636262 GAGAATGTACAGTATCTTATGACTTATAATGTGAGGACTTAACTTTGGTACTGATTTTGACCTACTTATGTGGCT -s Anc0.Anc0refChr1 21085 75 - 62388 CAAAATGTATAGTATCTTTTGACTAACTATGCTAGGACAAGACTTGCGTACTGACCTTGTACTAATCATGTAGCC -s Anc1.Anc1refChr2 99752 75 + 144309 CAAAATGTATAGTATCTTTTGACTAACTATGCTAGGACAAGACTTGCGTACTGACCTTGTACTAATCATGTAGCC -s Anc2.Anc2refChr3 9669 75 + 53186 CAAAATGTTTAGTATCTTTTGACTAACTGTGCTAGGACAAGACTTGCGTATAGACCTTGTACTCATCATGTAGCC -s mr.mrrefChr0 124015 75 + 130230 GAGAATGTACAGTATCTTATGACTTATAATGTGAGGACTTGACTTTGGTACTGACTTTGACCTACTTATGTGGCT -s simDog_chr6.simDog.chr6 421213 75 - 593897 CAAAATGTTTAGTATCTTTTGACTAACTGTGCTAGGACAAGACTTGCGTATAGACCTTGTACTCATCATGTAGCC -s simHuman_chr6.simHuman.chr6 124146 75 + 601863 CAAAATGTAAGGTATCCTTTGACTAAAGATGACAAGAAGCGACTTGAGTACTTACCTTGTACTAATCATGTAGCC -s simRat_chr6.simRat.chr6 127498 62 + 647215 --GAATGTACAGTATCTTATGACTTACAATGTGAGGACTTGAATTTGGTACTGACTTTGACCTA----------- - -a -s simMouse_chr6.simMouse.chr6 129195 21 + 636262 CTAGAAGTGCTGACAACTCTT -s Anc0.Anc0refChr1 21160 21 - 62388 CTAGATGGGATGACAACTCTT -s Anc1.Anc1refChr2 99827 21 + 144309 CTAGATGGGATGACAACTCTT -s Anc2.Anc2refChr3 9744 21 + 53186 CTAGATAGGATGAGAACTCTT -s mr.mrrefChr0 124090 21 + 130230 CTAGAAGTGCTGACAACTCTT -s simCow_chr6.simCow.chr6 137225 9 + 602619 ------------AGAAATCAC -s simDog_chr6.simDog.chr6 421293 21 - 593897 CTAGATAGGATGAGAACTCTT -s simHuman_chr6.simHuman.chr6 124221 21 + 601863 CTAGATGGGGTGACAACTCTT - -a -s simMouse_chr6.simMouse.chr6 129216 23 + 636262 ATATGGTAGATGTTACTGAGATC -s Anc0.Anc0refChr1 21188 21 - 62388 ATATGGTAGATTTT--TGAGATC -s Anc1.Anc1refChr2 99855 23 + 144309 ATATGGTAGATTTTCCTGAGATC -s Anc2.Anc2refChr3 9772 21 + 53186 ATATGGTAGATTGT--TGATATC -s mr.mrrefChr0 124111 23 + 130230 ATATGGTAGATGTTACTGAGATC -s simCow_chr6.simCow.chr6 137249 21 + 602619 ATATGTTTGAGTGG--TGATGTC -s simDog_chr6.simDog.chr6 421321 21 - 593897 ATAGGGTAGATTGT--TGATATC -s simHuman_chr6.simHuman.chr6 124249 23 + 601863 ATATGGTATATTTTCCTGAGATC - -a -s simMouse_chr6.simMouse.chr6 129239 27 + 636262 ACTATATAAAATTGTGAGAGGTATATT -s Anc0.Anc0refChr1 21209 15 - 62388 CCTATATAAAA------------TGTG -s Anc1.Anc1refChr2 99878 15 + 144309 CCTATATAAAA------------TGTG -s Anc2.Anc2refChr3 9793 15 + 53186 CCTATATAAAA------------TGTG -s mr.mrrefChr0 124134 15 + 130230 ACTATATAAAA------------TATT -s simCow_chr6.simCow.chr6 137277 15 + 602619 CTTGTATACAA------------TGTA -s simDog_chr6.simDog.chr6 421342 15 - 593897 CCTATATAAAA------------TGTG -s simHuman_chr6.simHuman.chr6 124272 11 + 601863 CCTATGTAAAC---------------- -s simRat_chr6.simRat.chr6 127560 4 + 647215 -----------------------TATT - -a -s simMouse_chr6.simMouse.chr6 129266 24 + 636262 ATGACAGTCCTTTGTGACTATAGG -s Anc0.Anc0refChr1 21224 24 - 62388 ATCACAGTCCTTCGTGCTTTTAGG -s Anc1.Anc1refChr2 99893 24 + 144309 ATCACAGTCCTTCGTGCTTTTAGG -s Anc2.Anc2refChr3 9821 24 + 53186 ATCACAGTCCTTCGTGCTTTTAGG -s mr.mrrefChr0 124149 24 + 130230 ATGACAGTCCTTTGTGATTATAGG -s simCow_chr6.simCow.chr6 137305 24 + 602619 ATCACATTCCTTGGTGTTTTTAGG -s simDog_chr6.simDog.chr6 421370 24 - 593897 ATCACAGGCCTTCATGCTTTTAGG -s simHuman_chr6.simHuman.chr6 124283 21 + 601863 ---GCAGTCCTTCGTGCTTTTAGG -s simRat_chr6.simRat.chr6 127564 24 + 647215 ATGACAGTCCATTGTGATTATAAG - -a -s simMouse_chr6.simMouse.chr6 129290 23 + 636262 AAATCTTTAAAAACTCTTTGATC -s Anc0.Anc0refChr1 21250 23 - 62388 AAAACTTTAAAAACTCTTTGATC -s Anc1.Anc1refChr2 99919 23 + 144309 AAAACTTTAAAAACTCTTTGATC -s Anc2.Anc2refChr3 9847 23 + 53186 AAGACTTTAAGAACTCTTTGATC -s mr.mrrefChr0 124173 23 + 130230 AAAACTTTAAAAACTCTTTGATC -s simCow_chr6.simCow.chr6 137331 23 + 602619 AAGACTTTAGCTACTATTTGTTC -s simDog_chr6.simDog.chr6 421396 23 - 593897 AAGACTCTCAGAATTCCTTGACC -s simHuman_chr6.simHuman.chr6 124306 23 + 601863 AAAACATTAAAAACTCTTTGATC -s simRat_chr6.simRat.chr6 127588 23 + 647215 AAAACTTTCGAAACTATTTGATC - -a -s simMouse_chr6.simMouse.chr6 129313 32 + 636262 TATCATGCAGAACATGGTCTCAAGTCGATGAA -s Anc0.Anc0refChr1 21273 8 - 62388 TATGATGC------------------------ -s Anc1.Anc1refChr2 99942 8 + 144309 TATGATGC------------------------ -s Anc2.Anc2refChr3 9870 8 + 53186 TATGTTGC------------------------ -s mr.mrrefChr0 124196 32 + 130230 TATCATGCAGAACATGGTCTCAAGTCGATGAA -s simCow_chr6.simCow.chr6 137357 8 + 602619 TATAGTGC------------------------ -s simDog_chr6.simDog.chr6 421419 8 - 593897 TATGTGGC------------------------ -s simHuman_chr6.simHuman.chr6 124329 8 + 601863 TATGATGC------------------------ -s simRat_chr6.simRat.chr6 127611 32 + 647215 TATCATGCAGAACATGGTCTCAAGTTGATGAG - -a -s simMouse_chr6.simMouse.chr6 129345 1 + 636262 A -s Anc0.Anc0refChr1 21281 1 - 62388 A -s Anc1.Anc1refChr2 99950 1 + 144309 A -s Anc2.Anc2refChr3 9878 1 + 53186 A -s mr.mrrefChr0 124228 1 + 130230 A -s simCow_chr6.simCow.chr6 137368 1 + 602619 A -s simDog_chr6.simDog.chr6 421427 1 - 593897 A -s simHuman_chr6.simHuman.chr6 124337 1 + 601863 A -s simRat_chr6.simRat.chr6 127643 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 129346 4 + 636262 TTGT -s Anc0.Anc0refChr1 21282 4 - 62388 TTAT -s Anc1.Anc1refChr2 99951 4 + 144309 TTAT -s Anc2.Anc2refChr3 9879 4 + 53186 TTAT -s mr.mrrefChr0 124229 4 + 130230 TTGT -s simCow_chr6.simCow.chr6 137369 4 + 602619 TTGT -s simDog_chr6.simDog.chr6 421462 4 - 593897 TTAT -s simHuman_chr6.simHuman.chr6 124338 4 + 601863 TTCT -s simRat_chr6.simRat.chr6 127644 4 + 647215 TGGT - -a -s simMouse_chr6.simMouse.chr6 129350 2 + 636262 AT -s Anc0.Anc0refChr1 21286 2 - 62388 AT -s Anc1.Anc1refChr2 99955 2 + 144309 AT -s Anc2.Anc2refChr3 9883 2 + 53186 AT -s mr.mrrefChr0 124233 2 + 130230 AT -s simCow_chr6.simCow.chr6 137373 2 + 602619 AT -s simDog_chr6.simDog.chr6 421466 2 - 593897 AT -s simHuman_chr6.simHuman.chr6 124342 2 + 601863 AT -s simRat_chr6.simRat.chr6 127653 2 + 647215 AT - -a -s simMouse_chr6.simMouse.chr6 129352 75 + 636262 AATTGTAACCAATTATATTGCATAGGTGTTATTCAACAAGAAAGCAGTAACATTTCTCAAGTATACCTAAGTTAC -s Anc0.Anc0refChr1 21288 75 - 62388 AGGAGCAATCATTTATATTGTATATATGTTATCCAACATGAAGGCAGTAACATTTTTCCAAAACACTCAGGTTGC -s Anc1.Anc1refChr2 99957 75 + 144309 AGGAGCAATCATTTATATTGTATATATGTTATCCAACATGAAGGCAGTAACATTTTTCCAAAACACTCAGGTTGC -s Anc2.Anc2refChr3 9885 75 + 53186 AAGAGCAATGATTTATACTGTGTAAATCTCATCCAACATGAAGGCAGCAACATTTTCCCAAAACACTCAGGTTGC -s mr.mrrefChr0 124235 75 + 130230 AGTTGTAACCAATTATATTGCATATGTGTTATTCAACAAGAAAGCAGTAACATTTTTCAAGTATACCCAAGTTAC -s simCow_chr6.simCow.chr6 137375 68 + 602619 AAGAGCAATTATTT-------GTAAATCTCATCCAGTGTGAAAGCAGAAACAGTTTCCCAAGATACTCAGGTTCC -s simDog_chr6.simDog.chr6 421468 75 - 593897 AAAAGCACTGATTTATACTGTGTAAACCCCATCTGACATGAAGGCAGCAACATTTTCCCAAAACACTCAGGTTGC -s simHuman_chr6.simHuman.chr6 124344 73 + 601863 AGGGGCAATCATTTATATCGTATATATGTTATCCAACATGAGGGCAGTAGCATTTTT--AACACACTCAGGTTGC -s simRat_chr6.simRat.chr6 127657 74 + 647215 AGTTGTAACCAATTAGATTTCATATGTGTTATTCAACAAGAAA-CAGTAACACTTTTCCAGTATACCCAAGTTAC - -a -s simMouse_chr6.simMouse.chr6 129427 40 + 636262 TATGAAGGTCAATTGCTACAAGTCTGATGGTTGTTTGCTC -s Anc0.Anc0refChr1 21381 40 - 62388 TATGTAGCTCAATTGTGACAAGTATGATGGCCTTTTTCTC -s Anc1.Anc1refChr2 100050 40 + 144309 TATGTAGCTCAATTGTGACAAGTATGATGGCCTTTTTCTC -s Anc2.Anc2refChr3 9978 40 + 53186 TATGTGGCTCAATTGTGAGAGGTATGATTGCCTTTTTCTC -s mr.mrrefChr0 124310 40 + 130230 TATGAAGGTCAATTGCTACAAGTCTGATGGTTGTTTGCTC -s simCow_chr6.simCow.chr6 137461 31 + 602619 TATGT----CAATTGTGATGAGTATGATTGCC-----CCC -s simDog_chr6.simDog.chr6 421561 40 - 593897 TATGTGGCTCAATTGTCAGAGGTATGGTTGTCTTTTTCTC -s simHuman_chr6.simHuman.chr6 124435 37 + 601863 TATGTAGCTCAATTG---CGAGTATGACGGCCTTGTTTTC -s simRat_chr6.simRat.chr6 127731 40 + 647215 TATGAAGGTCAATTACTATAAGTCTGATGGTTGTTTACTT - -a -s simMouse_chr6.simMouse.chr6 129467 9 + 636262 ACAAGAGGG -s Anc0.Anc0refChr1 21421 9 - 62388 ATAACTTGG -s Anc1.Anc1refChr2 100090 9 + 144309 ATAACTTGG -s Anc2.Anc2refChr3 10018 9 + 53186 ATAACTTGG -s mr.mrrefChr0 124350 9 + 130230 ACAAGAGGG -s simCow_chr6.simCow.chr6 137492 9 + 602619 ATAACTTGG -s simDog_chr6.simDog.chr6 421603 9 - 593897 ATAACTTGG -s simHuman_chr6.simHuman.chr6 124472 9 + 601863 ATAACTTGG -s simRat_chr6.simRat.chr6 127771 9 + 647215 GCAAGAGAG - -a -s simMouse_chr6.simMouse.chr6 129476 22 + 636262 TCCAATGATTAATGTCATCGTT -s Anc0.Anc0refChr1 21432 22 - 62388 TCCAATGGTGAATGTTATCACT -s Anc1.Anc1refChr2 100101 22 + 144309 TCCAATGGTGAATGTTATCACT -s Anc2.Anc2refChr3 10029 22 + 53186 TCCAATGGTGAATGTTATCACT -s mr.mrrefChr0 124359 22 + 130230 TCCAATGATTAATGTTATCATT -s simCow_chr6.simCow.chr6 137503 22 + 602619 TCCAATGGTGGATGTTATCACT -s simDog_chr6.simDog.chr6 421614 22 - 593897 GCTAATGGTAAATGTTATCACT -s simHuman_chr6.simHuman.chr6 124483 22 + 601863 TCCAATGGTGAATGTTATCACT -s simRat_chr6.simRat.chr6 127780 22 + 647215 TCCAATGATTAATGTTATCATT - -a -s simMouse_chr6.simMouse.chr6 129498 22 + 636262 CATATGTTTGGACTTGAGATGG -s Anc0.Anc0refChr1 21454 22 - 62388 CATATGTTATAACTCAAAATAA -s Anc1.Anc1refChr2 100123 22 + 144309 CATATGTTATAACTCAAAATAA -s Anc2.Anc2refChr3 10051 22 + 53186 CATATGTTATAACTCAAAATAA -s mr.mrrefChr0 124381 22 + 130230 CATATGTTTGAACTTGAGATAG -s simCow_chr6.simCow.chr6 137525 22 + 602619 CATACGTTATAACTCAGAAGAA -s simDog_chr6.simDog.chr6 421647 22 - 593897 CATATGTTATAGTGCAAAATAA -s simHuman_chr6.simHuman.chr6 124505 22 + 601863 CATATGTTATAACTCAAAGTAA -s simRat_chr6.simRat.chr6 127802 22 + 647215 CATATGTTTGAATGTGAGATAG - -a -s simMouse_chr6.simMouse.chr6 129520 47 + 636262 GTTGCATTCCACACCCAGCGGCTATTACAATGTTCCTCAATTGAGTT -s Anc0.Anc0refChr1 21476 47 - 62388 AATGCATTGCACACACATAGGCTATTACAATGTTCATCAATTTAGTT -s Anc1.Anc1refChr2 100145 47 + 144309 AATGCATTGCACACACATAGGCTATTACAATGTTCATCAATTTAGTT -s Anc2.Anc2refChr3 10073 47 + 53186 AATGCATTGCACACACAGAGGCTATTACAATGTTCATATATTTAGTT -s mr.mrrefChr0 124403 47 + 130230 GTTGCATTGCACACCCATAGGCTATTACAATGTTCCTCAATTGAGTT -s simCow_chr6.simCow.chr6 137547 37 + 602619 GATGAATCACACACACAGAGGCTATGACAATGTTCAT---------- -s simDog_chr6.simDog.chr6 421670 47 - 593897 AATGCGTTGTACACACAGAGACTATTACAATCTTCTTATATTTAGTT -s simHuman_chr6.simHuman.chr6 124527 47 + 601863 AATCCATTGCACACACGTAGGCTATTACAATGTTCATCAAATTAATT -s simRat_chr6.simRat.chr6 127824 47 + 647215 GTTGCATTGCACACCCATAGGCTCTCACAATGTTCCTCAATTGAGTT - -a -s simMouse_chr6.simMouse.chr6 129567 8 + 636262 TTTCTATC -s Anc0.Anc0refChr1 21526 8 - 62388 ATTCTATC -s Anc1.Anc1refChr2 100195 8 + 144309 ATTCTATC -s Anc2.Anc2refChr3 10123 8 + 53186 ATTCTATC -s mr.mrrefChr0 124450 8 + 130230 TTTCTATC -s simDog_chr6.simDog.chr6 421720 8 - 593897 ATTCTATC -s simHuman_chr6.simHuman.chr6 124577 8 + 601863 ATTCTATC -s simRat_chr6.simRat.chr6 127871 8 + 647215 TTTCTATC - -a -s simMouse_chr6.simMouse.chr6 129575 27 + 636262 TAGTATCTTTCCATATCAATTAATATT -s Anc0.Anc0refChr1 21534 26 - 62388 TA-TAACTTACCATCTCAATCAATAAT -s Anc1.Anc1refChr2 100203 26 + 144309 TA-TAACTTACCATCTCAATCAATAAT -s Anc2.Anc2refChr3 10131 26 + 53186 TA-TAACTCACCATCTCTATCGATAAT -s mr.mrrefChr0 124458 27 + 130230 TAGTATCTTTCCATATCAATTAATATT -s simDog_chr6.simDog.chr6 421729 26 - 593897 TA-TAACTCACCATCTCTATCGATAAT -s simHuman_chr6.simHuman.chr6 124585 26 + 601863 TA-TAGCCTGCCATCTCAATCAACAGT -s simRat_chr6.simRat.chr6 127879 27 + 647215 CAGCAATTTACCATTTCAATTAATATT - -a -s simMouse_chr6.simMouse.chr6 129602 10 + 636262 CTTTCTCCAA -s Anc0.Anc0refChr1 21562 4 - 62388 CTTT------ -s Anc1.Anc1refChr2 100231 10 + 144309 CTTTGTCAAA -s Anc2.Anc2refChr3 10159 4 + 53186 CTTT------ -s mr.mrrefChr0 124485 10 + 130230 CTTTGTCAAA -s simDog_chr6.simDog.chr6 421757 4 - 593897 CTTT------ -s simHuman_chr6.simHuman.chr6 124613 10 + 601863 CTTGGTCAAA -s simRat_chr6.simRat.chr6 127906 10 + 647215 CTTTGTCAAA - -a -s simMouse_chr6.simMouse.chr6 129612 36 + 636262 AGTCCTTACAGATATCAAGTCATTCCATGTTCAGAT -s Anc0.Anc0refChr1 21589 35 - 62388 ATTCTTTATGGATATC-AGTGATTCTGCACCCGGAC -s Anc1.Anc1refChr2 100264 35 + 144309 ATTCTTTATGGATATC-AGTGATTCTGCACCCGGAC -s Anc2.Anc2refChr3 10186 35 + 53186 ATTCTTTATGGATATC-TGTGTTTCTGCACCCGAAC -s mr.mrrefChr0 124495 36 + 130230 AGTCTTTATGGATATCAAGTCATTCCATGTTCGGAT -s simCow_chr6.simCow.chr6 137592 32 + 602619 GTTCTTTATCAATACC-TGTGTTTCTAGGC---AGC -s simDog_chr6.simDog.chr6 421785 35 - 593897 ATTCTTTATGGATATA-TTTGTTTCTGCACCCGAAC -s simHuman_chr6.simHuman.chr6 124649 35 + 601863 ATTCTTTATGGACATC-AGTGATTCAGCACCTGGAC -s simRat_chr6.simRat.chr6 127916 36 + 647215 AGTCTTTATGGATATCTAGTCATTCCATGTTCGGAT - -a -s simMouse_chr6.simMouse.chr6 129648 27 + 636262 TAGCCATCAGTAATTAACCCAACCGCT -s Anc0.Anc0refChr1 21624 27 - 62388 TACTAAGAAGCAGTTATACCAAACACT -s Anc1.Anc1refChr2 100299 27 + 144309 TACTAAGAAGCAGTTATACCAAACACT -s Anc2.Anc2refChr3 10221 27 + 53186 TGCTAAGAAGCAGTTATACCAAACACT -s mr.mrrefChr0 124531 27 + 130230 TAGCAATCAGTAATTAACCCAAACGCT -s simCow_chr6.simCow.chr6 137624 27 + 602619 TGTTAAGAAGCAGTTAAACCAAACACC -s simDog_chr6.simDog.chr6 421822 27 - 593897 TGCTGAGAAGCAGTTATATTGAACACT -s simHuman_chr6.simHuman.chr6 124684 27 + 601863 TACTAAGAAGCAGTTATACCAGAGACT -s simRat_chr6.simRat.chr6 127952 26 + 647215 TAGCAATTAGAAATTAATCCAAAC-CT - -a -s simMouse_chr6.simMouse.chr6 129675 30 + 636262 TGAGTTCCAGTATGTATTTGCCCAATCTGT -s Anc0.Anc0refChr1 21652 30 - 62388 GGGGGTCCAGTATATATTCACCCAATCTAT -s Anc1.Anc1refChr2 100327 30 + 144309 GGGGGTCCAGTATATATTCACCCAATCTAT -s Anc2.Anc2refChr3 10249 30 + 53186 GGGGGTCCAGTATATATTCACCCAATCCAT -s mr.mrrefChr0 124558 30 + 130230 GGAGTTCCAGTATATATTTGCCCAATCTGT -s simCow_chr6.simCow.chr6 137652 30 + 602619 GGGGATCCAGTATATATTGACCCAATCCAT -s simDog_chr6.simDog.chr6 421850 30 - 593897 GGGGGTCCAGCATATATTCACCGAATCCAT -s simHuman_chr6.simHuman.chr6 124712 30 + 601863 GGGGGTCCAGTATATATCCACTCAATCTAT -s simRat_chr6.simRat.chr6 127978 30 + 647215 GGAGTTCCAGTATATATTTGCCTAAACTGT - -a -s simMouse_chr6.simMouse.chr6 129705 2 + 636262 TC -s Anc0.Anc0refChr1 21687 2 - 62388 AC -s Anc1.Anc1refChr2 100362 2 + 144309 AC -s Anc2.Anc2refChr3 10284 2 + 53186 AC -s mr.mrrefChr0 124588 2 + 130230 TC -s simCow_chr6.simCow.chr6 137687 2 + 602619 AT -s simDog_chr6.simDog.chr6 421885 2 - 593897 AC -s simHuman_chr6.simHuman.chr6 124747 2 + 601863 AC -s simRat_chr6.simRat.chr6 128008 2 + 647215 TC - -a -s simMouse_chr6.simMouse.chr6 129707 5 + 636262 TAACT -s Anc0.Anc0refChr1 21689 5 - 62388 TAACT -s Anc1.Anc1refChr2 100364 5 + 144309 TAACT -s Anc2.Anc2refChr3 10286 5 + 53186 TAACT -s mr.mrrefChr0 124590 5 + 130230 TAACT -s simCow_chr6.simCow.chr6 137689 5 + 602619 TGACA -s simDog_chr6.simDog.chr6 421887 5 - 593897 TAACT -s simHuman_chr6.simHuman.chr6 124749 5 + 601863 TAACT -s simRat_chr6.simRat.chr6 128011 5 + 647215 CAACT - -a -s simMouse_chr6.simMouse.chr6 129712 24 + 636262 CCTGTGATTAGTAATACAGGGGGC -s Anc0.Anc0refChr1 21704 23 - 62388 AATGTGAACAGTCATACA-TGGGC -s Anc1.Anc1refChr2 100379 24 + 144309 AATGTGAACAGTCATACAATGGGC -s Anc2.Anc2refChr3 10301 23 + 53186 AATGTGATCAGTCAAACA-TGGGC -s mr.mrrefChr0 124595 24 + 130230 ACTGTGAACAGTAATACAGGGGGC -s simCow_chr6.simCow.chr6 137704 23 + 602619 AATGTCAGCAGTCAAACA-TGGAC -s simDog_chr6.simDog.chr6 421901 23 - 593897 AATATGATCAGTCAAGCA-TGGGC -s simHuman_chr6.simHuman.chr6 124764 22 + 601863 ATGGTGAACAGT--TGCAATGAGC -s simRat_chr6.simRat.chr6 128016 24 + 647215 ACTGTGAACAGTGAAATAGGGGGC - -a -s simMouse_chr6.simMouse.chr6 129736 21 + 636262 CTACTGCCACACAGCACCTAC -s Anc0.Anc0refChr1 21731 4 - 62388 CTAC----------------- -s Anc1.Anc1refChr2 100407 4 + 144309 CTAC----------------- -s Anc2.Anc2refChr3 10328 4 + 53186 CTAC----------------- -s mr.mrrefChr0 124619 4 + 130230 CTAC----------------- -s simCow_chr6.simCow.chr6 137731 4 + 602619 CTAG----------------- -s simDog_chr6.simDog.chr6 421928 4 - 593897 CTAC----------------- -s simHuman_chr6.simHuman.chr6 124790 4 + 601863 CTAC----------------- -s simRat_chr6.simRat.chr6 128040 4 + 647215 CTAC----------------- - -a -s simMouse_chr6.simMouse.chr6 129757 80 + 636262 TGCCACACAGCACCCACAAAAGTGTGAGAACTACTTTGGCCAGATCTTGTCCATTTCAATAATCATGTGCACCCATCATG -s Anc0.Anc0refChr1 21736 76 - 62388 TGCAATATAGAACCTCC----GAAACAGAACTACTTTGGCTGAATCTTGGCCACTACAATAATCATATGCACACACCACA -s Anc1.Anc1refChr2 100412 76 + 144309 TGCAATATAGAACCTCC----GAAACAGAACTACTTTGGCTGAATCTTGGCCACTACAATAATCATATGCACACACCACA -s Anc2.Anc2refChr3 10333 76 + 53186 TGCAATATAGAACCTCC----CAAACAGAACTACTTTGGCTGAATCTTGGCCACTACAATAATGGTAAGCACACACCACA -s mr.mrrefChr0 124623 80 + 130230 TGCAACACAGCACCCACAAAAGAGTGAGAACTACTTTGGCCAGATCTTGTCCATTTCAATAATCATGTGCACCCATCATG -s simCow_chr6.simCow.chr6 137736 76 + 602619 TGCAATGCAGCACCTCC----CAAACAGAACAACTTTGCCTGAACCTTGGCCACTGCAATATTGGTAAGCTCACAACATA -s simDog_chr6.simDog.chr6 421933 76 - 593897 TGTGATATAGAATCTCC----CAAACAGAACTACTTTGGCTGAATCCTGGCCACTACAATAATGGTAAACACACACCACA -s simHuman_chr6.simHuman.chr6 124795 76 + 601863 TACAATATGGGACCTCT----GAACTAGAACTACTTCGGCTGAATATTGGCCACCACAAGAACCATATGCACACACTGCA -s simRat_chr6.simRat.chr6 128044 80 + 647215 TGTAACACAGCATCCACAAAAGAGGGAGAACTACTTTGGCCAGATCTTGCCCATTTCAGTAATGATGTGCACCCATCATG - -a -s simMouse_chr6.simMouse.chr6 129837 38 + 636262 CCCCCATCACTGACATCTAAGGCCTTGGATCTATTTAT -s Anc0.Anc0refChr1 21812 28 - 62388 CC----------ATGTCTAAGCACATGGATGTGTTAAT -s Anc1.Anc1refChr2 100488 28 + 144309 CC----------ATGTCTAAGCACATGGATGTGTTAAT -s Anc2.Anc2refChr3 10409 28 + 53186 CC----------ATGTGTAAGCACATGGATGTGTTAAC -s mr.mrrefChr0 124703 38 + 130230 CCCCCATCACTGACATCTAAGGCCTTGGATGTATTAAT -s simCow_chr6.simCow.chr6 137815 28 + 602619 CT----------ATGTGTAAGCACATGGATGTGTTTAC -s simDog_chr6.simDog.chr6 422009 28 - 593897 CC----------ATCTGTAGTTACATGGATGTGATAAC -s simHuman_chr6.simHuman.chr6 124871 27 + 601863 -C----------ATGTCTAAGCACACGGATGTGTTAAT -s simRat_chr6.simRat.chr6 128124 38 + 647215 CCCCCATCACTGACATCTAAGGCCTTGGATGTATTAAT - -a -s simMouse_chr6.simMouse.chr6 129875 1 + 636262 T -s Anc0.Anc0refChr1 21841 1 - 62388 A -s Anc1.Anc1refChr2 100517 1 + 144309 A -s Anc2.Anc2refChr3 10438 1 + 53186 C -s mr.mrrefChr0 124741 1 + 130230 A -s simCow_chr6.simCow.chr6 137844 1 + 602619 T -s simDog_chr6.simDog.chr6 422038 1 - 593897 C -s simHuman_chr6.simHuman.chr6 124899 1 + 601863 A -s simRat_chr6.simRat.chr6 128162 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 129876 11 + 636262 TGGCAAGAGGC -s Anc0.Anc0refChr1 21842 11 - 62388 TAATTAGGGGC -s Anc1.Anc1refChr2 100518 11 + 144309 TAATTAGGGGC -s Anc2.Anc2refChr3 10439 11 + 53186 TAATTAGGGGG -s mr.mrrefChr0 124742 11 + 130230 TGGCAAGAGGC -s simCow_chr6.simCow.chr6 137845 11 + 602619 TAATTTGGGGT -s simDog_chr6.simDog.chr6 422041 11 - 593897 AAATTAGGGGG -s simHuman_chr6.simHuman.chr6 124900 11 + 601863 TAATTAGGGCC -s simRat_chr6.simRat.chr6 128163 11 + 647215 TGGCAAGAAGC - -a -s simMouse_chr6.simMouse.chr6 129887 103 + 636262 CTGTATATAGCAGTGCTGACGGGTTGAGACGTGGATTCCGGGGTTAGGACCGTGCTGTCAGCAGGTTCCATAGGAATTGTGCTACCTCCCAATTTCACTCAAA -s Anc0.Anc0refChr1 21855 3 - 62388 CTA---------------------------------------------------------------------------------------------------- -s Anc1.Anc1refChr2 100531 3 + 144309 CTA---------------------------------------------------------------------------------------------------- -s Anc2.Anc2refChr3 10452 3 + 53186 CTA---------------------------------------------------------------------------------------------------- -s mr.mrrefChr0 124753 3 + 130230 CTG---------------------------------------------------------------------------------------------------- -s simCow_chr6.simCow.chr6 137858 2 + 602619 CT----------------------------------------------------------------------------------------------------- -s simDog_chr6.simDog.chr6 422054 3 - 593897 CTA---------------------------------------------------------------------------------------------------- -s simHuman_chr6.simHuman.chr6 124913 3 + 601863 CTA---------------------------------------------------------------------------------------------------- -s simRat_chr6.simRat.chr6 128174 3 + 647215 CTG---------------------------------------------------------------------------------------------------- - -a -s simMouse_chr6.simMouse.chr6 129990 63 + 636262 AATGCTTACGGAGCGGTCCCCAGTAACTACTAGTTTATGTACACACTAATTGTTTAAAAATGG -s Anc0.Anc0refChr1 21858 42 - 62388 CATCTTTACTCATCTGT-----GTGGGC----------------CCAAAACTTTTAAAATTCG -s Anc1.Anc1refChr2 100534 58 + 144309 CATCTTTACTCATCTGT-----GTGGGCACAAAACTATTAAAATCCAAAACTTTTAAAATTCG -s Anc2.Anc2refChr3 10455 42 + 53186 CATCTTCACTCATCTGT-----GTGGGC----------------CCAAAACTTTTGGAATTCG -s mr.mrrefChr0 124756 63 + 130230 AATGCTTACGGAGCGGTCCCCAGTAATTACTAGTTTATGTACACACTAATTGTTTAAAAATGG -s simCow_chr6.simCow.chr6 137860 21 + 602619 -------------CTG-----------------------------CAAAACATTTGGAATTTG -s simDog_chr6.simDog.chr6 422057 42 - 593897 CATCTTCACTCATTGGT-----GTGGGC----------------CTAAAACTTTTGGACTTCG -s simHuman_chr6.simHuman.chr6 124916 58 + 601863 CATCTTTACTTGACTGT-----ATGGGCACAAAACTATTAAAATTCGAAACTTTTAAAATTCA -s simMouse_chr6.simMouse.chr6 130311 63 + 636262 AATGCTTACGGAGCGGTCCCCAGTAATTACTAGTTTATGTACACACTAATTGTTTAAAAATGG -s simRat_chr6.simRat.chr6 128177 43 + 647215 --------------------CAGTAATTACTAGTTTATGTACACACTAATTGTTTAAAAATGG - -a -s simMouse_chr6.simMouse.chr6 130053 32 + 636262 CTTATTAAAAATCTAAGCTTGGGCTAACCCCT -s Anc0.Anc0refChr1 21901 32 - 62388 TTTATATAATATCTAAGTTAGGGCAAACCTTG -s Anc1.Anc1refChr2 100593 32 + 144309 TTTATATAATATCTAAGTTAGGGCAAACCTTG -s Anc2.Anc2refChr3 10498 32 + 53186 TTTATATAATATTTAGGTTAGGGCAAACCTTG -s mr.mrrefChr0 124820 32 + 130230 CTTATTAAAAATCTAAGCTTGGGCTAACCCCT -s simCow_chr6.simCow.chr6 137882 32 + 602619 TATATATAATATTTAGGTCAGGGCAAACTTTG -s simDog_chr6.simDog.chr6 422100 32 - 593897 CTTATATAATATTTAGGTTACGGCAGACCTTG -s simHuman_chr6.simHuman.chr6 124975 32 + 601863 TTTTTATAATATCAAATTTGGGGCCAACCTTG -s simMouse_chr6.simMouse.chr6 130374 32 + 636262 CTTATTAAAAATCTAAGCTTGGGCTAACCCCT -s simRat_chr6.simRat.chr6 128221 32 + 647215 CTTATTAAAAATCTAAGCTTGGGCTGACCCCT - -a -s simMouse_chr6.simMouse.chr6 130085 40 + 636262 CCTTAGTTGGAATTGAAATCGAACAATATTATCTTAAGGA -s Anc0.Anc0refChr1 21934 40 - 62388 CCTTGTATGGCATTGACATTCAACAACATCATCTTAATAA -s Anc1.Anc1refChr2 100626 40 + 144309 CCTTGTATGGCATTGACATTCAACAACATCATCTTAATAA -s Anc2.Anc2refChr3 10531 40 + 53186 CCTTGTATGGCATTGACATTCAACAACATCATCTTAATAA -s mr.mrrefChr0 124852 40 + 130230 CCTTAGTTGGAATTGAAATCGAACAATATTATCTTAAGGA -s simCow_chr6.simCow.chr6 137915 40 + 602619 TCTCACATGGCAGTGAAATTCAATGACATCATCTAAATAA -s simDog_chr6.simDog.chr6 422133 40 - 593897 CCTTGTGTGGTATTGACATTCAACATCATCATCTTAACAA -s simHuman_chr6.simHuman.chr6 125008 40 + 601863 CCTTGTATGGCATTGATACTCAACAACATCATGTTAATAA -s simMouse_chr6.simMouse.chr6 130406 40 + 636262 CCTTAGTTGGAATTGAAATCGAACAATATTATCTTAAGGA -s simRat_chr6.simRat.chr6 128253 36 + 647215 CCTTCGTTGG----AACATCCAACAATATTATCTTAACAA - -a -s simMouse_chr6.simMouse.chr6 130125 19 + 636262 ACAATGTGGCAATCAGTAG -s Anc0.Anc0refChr1 21986 11 - 62388 --------GCAATCACTAG -s Anc1.Anc1refChr2 100680 11 + 144309 --------GCAATCACTAG -s Anc2.Anc2refChr3 10583 11 + 53186 --------TGAATCACTGG -s mr.mrrefChr0 124906 19 + 130230 ACAATGTGGCAATCAGTAG -s simCow_chr6.simCow.chr6 137962 9 + 602619 ----------AACCATTGG -s simDog_chr6.simDog.chr6 422185 11 - 593897 --------TGAATCACTGG -s simHuman_chr6.simHuman.chr6 125062 11 + 601863 --------GCAATCACTAC -s simMouse_chr6.simMouse.chr6 130446 19 + 636262 ACAATGTGGCAATCAGTAG -s simRat_chr6.simRat.chr6 128303 19 + 647215 ACAATCAGCCAATCAGCAG - -a -s simMouse_chr6.simMouse.chr6 130144 11 + 636262 CGGTTGCTTTG -s Anc0.Anc0refChr1 21997 9 - 62388 AAGCT--TTTG -s Anc1.Anc1refChr2 100691 9 + 144309 AAGCT--TTTG -s Anc2.Anc2refChr3 10594 9 + 53186 AAGCT--TCTG -s mr.mrrefChr0 124925 11 + 130230 CGGTTGCTTTG -s simCow_chr6.simCow.chr6 137977 9 + 602619 AAGCT--TCTG -s simDog_chr6.simDog.chr6 422196 9 - 593897 AAGCT--TCTA -s simHuman_chr6.simHuman.chr6 125073 9 + 601863 AAGCT--TTCG -s simMouse_chr6.simMouse.chr6 130465 11 + 636262 CGGTTGCTTTG -s simRat_chr6.simRat.chr6 128322 11 + 647215 GGGTTTCTTTG - -a -s simMouse_chr6.simMouse.chr6 130155 94 + 636262 TTATTCTTTTGGTAATCTACAAGAATGTGTGCCGTTAACAGGCTGGAACGGGGACTCATGTAATACAGCTCCTTGTTTGGTGGATTACAGCTTA -s Anc0.Anc0refChr1 22007 38 - 62388 TTACTGTTTTTGTATTAATCAAGAATGTGTGACGTTAG-------------------------------------------------------- -s Anc1.Anc1refChr2 100701 38 + 144309 TTACTGTTTTTGTATTAATCAAGAATGTGTGACGTTAG-------------------------------------------------------- -s Anc2.Anc2refChr3 10604 38 + 53186 TTACTGTTTTTGTATTAATCAAGAATGTGAGAGGTTGG-------------------------------------------------------- -s mr.mrrefChr0 124936 94 + 130230 TTATTCTTTTGGTAATCTACAAGAATGTGTGCCGTTAACAGGCTGGAACGGGGACTCATGTAATACAGCTCCTTGTTTGGTGGATTACAGCTTA -s simCow_chr6.simCow.chr6 137987 38 + 602619 TTACTGTTCTTCAATTAAAGGAGAATGTGCGAGGTTGG-------------------------------------------------------- -s simDog_chr6.simDog.chr6 422206 38 - 593897 TTGCTGTTTTTGTATTAATCAAGGATGTGAGAGGTTGG-------------------------------------------------------- -s simHuman_chr6.simHuman.chr6 125083 36 + 601863 TTACTTTTTCTTTATTAGTC--GAATGTGTAACATTAG-------------------------------------------------------- -s simMouse_chr6.simMouse.chr6 130476 94 + 636262 TTATTCTTTTGGTAATCTACAAGAATGTGTGCCGTTAACAGGCTGGAACGGGGACTCATGTAATACAGCTCCTTGTTTGGTGGATTACAGCTTA -s simRat_chr6.simRat.chr6 128333 91 + 647215 CTATTCTTTTGATTATC---AAGAATGTGTGCTGTTAACAGGTTGGAAGGGAGACTTATGTAATGCAGCTCCTTGGTCGGTGGATTACAGCTTA - -a -s simMouse_chr6.simMouse.chr6 130249 62 + 636262 CCCTCTTGTTTAATTAATGAGGGGGCTTGAACCTCTTGCAGCTCCTTGTTTAGTGGTTCTTA -s mr.mrrefChr0 125030 62 + 130230 CCCTCTTGTTTAATTAATGAGGGGGCTTGAACCTCTTGCAGCTCCTTGTTTAGTGGTTCTTA -s simMouse_chr6.simMouse.chr6 130570 62 + 636262 CCCTCTTGTTTAATTAGTGAGGGGGCTTGAACCTCTTGCAGCTCCTTGTTTAGTGGTTCTTA -s simRat_chr6.simRat.chr6 128441 61 + 647215 CCCTCTTGTATAATTAATGAAAGGCCAAGGGTCCCATGCAGCTCCTTGTGTGGTGATTC-TA - -a -s simMouse_chr6.simMouse.chr6 130632 52 + 636262 CCCTTTCAGTCCGATTGATGAGGGTGTGACCCTAATGTCTCTCAGACCGATA -s mr.mrrefChr0 125092 52 + 130230 CCCCTTCAGTCCGATTGATGAGGGTGTGACCCTAATGTCTCTCAGACCGATA -s simRat_chr6.simRat.chr6 128502 52 + 647215 CCCCTTCCATCCGGTTGATGAGGGTGTGACCCTAAAGTCCCTCAGTCTGATA - -a -s simMouse_chr6.simMouse.chr6 130684 71 + 636262 CCACCCAAAACACATTACAAAATAGAGTTGAGTGCTACAGTATCAAGATTTTATGTAGACTTGAATATGTG -s Anc0.Anc0refChr1 22045 5 - 62388 ------------------------------------------------------------------ATGTG -s Anc1.Anc1refChr2 100739 5 + 144309 ------------------------------------------------------------------ATGTG -s Anc2.Anc2refChr3 10642 5 + 53186 ------------------------------------------------------------------ATGTG -s mr.mrrefChr0 125144 49 + 130230 CCACCCAAAACACATTACAAAATAGA----------------------TTTTATGTAGACTTGAATATGTG -s simCow_chr6.simCow.chr6 138025 5 + 602619 ------------------------------------------------------------------ATGTG -s simDog_chr6.simDog.chr6 422244 5 - 593897 ------------------------------------------------------------------ATGTC -s simHuman_chr6.simHuman.chr6 125119 5 + 601863 ------------------------------------------------------------------ATGTG -s simRat_chr6.simRat.chr6 128556 49 + 647215 CTACCCAAAATACATCACAAAATAGA----------------------TTTCATGTAGACTTGGATATGTG - -a -s simMouse_chr6.simMouse.chr6 130755 44 + 636262 ACGAGGCTAGACCACCTGTCTATCATGCCGTACCCCAAGCAAAT -s Anc0.Anc0refChr1 22050 44 - 62388 ACCAGGTTTTACCACCTGTTTTTCACACGGTACCCTAAGCAAAT -s Anc1.Anc1refChr2 100744 44 + 144309 ACCAGGTTTTACCACCTGTTTTTCACACGGTACCCTAAGCAAAT -s Anc2.Anc2refChr3 10653 44 + 53186 ACCAGGTTTTACCACCTGTTTTTTACACGGTACCCTAAGCAAAT -s mr.mrrefChr0 125193 44 + 130230 ACCAGGCTATACTACCTGTTTATCATTCTGTACCCCAAGCAAAT -s simCow_chr6.simCow.chr6 138036 42 + 602619 ACCAGGTTTTACCACCTGTCTT--ACACGGTACCCTAAGCAAAT -s simDog_chr6.simDog.chr6 422255 44 - 593897 ACCAGGTTTTGCTACCTGTTTATTACTCTATACCCTAAGCAAAT -s simHuman_chr6.simHuman.chr6 125124 44 + 601863 TATGAGTTTTACCACCTATTTTTCACACGGTACTCTAAACAAAT -s simRat_chr6.simRat.chr6 128605 44 + 647215 ACCAGGCTATACTACCTGTTTATCATTCTGTACTCAAAGCAAAT - -a -s simMouse_chr6.simMouse.chr6 130799 3 + 636262 GAA -s Anc0.Anc0refChr1 22102 3 - 62388 GAA -s Anc1.Anc1refChr2 100796 3 + 144309 GAA -s Anc2.Anc2refChr3 10705 3 + 53186 GAA -s mr.mrrefChr0 125245 3 + 130230 GAA -s simCow_chr6.simCow.chr6 138086 3 + 602619 GAA -s simDog_chr6.simDog.chr6 422307 3 - 593897 GAA -s simHuman_chr6.simHuman.chr6 125176 3 + 601863 AAA -s simRat_chr6.simRat.chr6 128657 3 + 647215 GAG - -a -s simMouse_chr6.simMouse.chr6 130802 3 + 636262 AGT -s Anc0.Anc0refChr1 22106 3 - 62388 AGT -s Anc1.Anc1refChr2 100800 3 + 144309 AGT -s Anc2.Anc2refChr3 10709 3 + 53186 AGT -s mr.mrrefChr0 125248 3 + 130230 ATT -s simCow_chr6.simCow.chr6 138090 3 + 602619 AGT -s simDog_chr6.simDog.chr6 422311 3 - 593897 AGT -s simHuman_chr6.simHuman.chr6 125180 3 + 601863 AAT -s simRat_chr6.simRat.chr6 128660 3 + 647215 ATT - -a -s simMouse_chr6.simMouse.chr6 130805 26 + 636262 GAAATGATTCCCCCTGTGACCCATTA -s Anc0.Anc0refChr1 22109 26 - 62388 GCAAAGTCTCCCCCTGTGACCCATTA -s Anc1.Anc1refChr2 100803 26 + 144309 GCAAAGTCTCCCCCTGTGACCCATTA -s Anc2.Anc2refChr3 10712 26 + 53186 GCAAAGTCTCCCCCTGTGACCCATTA -s mr.mrrefChr0 125251 26 + 130230 GAAATGATTCCCCCTGTGACCCATTA -s simCow_chr6.simCow.chr6 138093 26 + 602619 ACTAAGTTTCCCCTTGTGACCAATTG -s simDog_chr6.simDog.chr6 422315 26 - 593897 GCACAGTCTCCCCCTTTGACCCATTA -s simHuman_chr6.simHuman.chr6 125183 26 + 601863 GCAAATTCTCCCCCTGTGTCCTAATA -s simRat_chr6.simRat.chr6 128663 26 + 647215 GAAATGATTCCCCCTGTGACCTATTA - -a -s simMouse_chr6.simMouse.chr6 130831 23 + 636262 CAATGGTTGGCCTTCATCCATTC -s Anc0.Anc0refChr1 22136 19 - 62388 GAATCGTAGGCCTTTAAC----T -s Anc1.Anc1refChr2 100830 19 + 144309 GAATCGTAGGCCTTTAAC----T -s Anc2.Anc2refChr3 10739 19 + 53186 GGATCGTAGGCCTTTAAC----T -s mr.mrrefChr0 125278 23 + 130230 CAATGGTTGGCCTTCATCCATTC -s simCow_chr6.simCow.chr6 138120 19 + 602619 CGATGGTAGGCCATCAAC----T -s simDog_chr6.simDog.chr6 422342 19 - 593897 GGTTCACCGTCATCTGAT----T -s simHuman_chr6.simHuman.chr6 125210 16 + 601863 AAACAGTAGGCCTTTA------- -s simRat_chr6.simRat.chr6 128690 23 + 647215 CAATGTTTGGCCTTCATCCATTA - -a -s simMouse_chr6.simMouse.chr6 130854 52 + 636262 TTTGGGAATGCCCTGAGACCTACAGCCTGGGCTGTACGAGGTTTTGAAAAGG -s Anc0.Anc0refChr1 22155 52 - 62388 CTTGTGAGTGCAGTGAGACCTACAGTCTTGTCTGTATGTGGGTTGGAACAGG -s Anc1.Anc1refChr2 100849 52 + 144309 CTTGTGAGTGCAGTGAGACCTACAGTCTTGTCTGTATGTGGGTTGGAACAGG -s Anc2.Anc2refChr3 10758 52 + 53186 CTTGTGAGTGCAGTGAGGTCTACACTCTTGTCTGTATGTGGGCTGGAGCAGG -s mr.mrrefChr0 125301 52 + 130230 CTTGGGAATGCCCTGAGACCTACAGTCTGGGCTGTATGAGGTTTTGAAAAGG -s simCow_chr6.simCow.chr6 138143 52 + 602619 TTTGTGAATGCAGTGAGACTTGTTCTCTTGCCAGTATGTGGGCAGGAGCAGG -s simDog_chr6.simDog.chr6 422361 52 - 593897 CTTGTGAGTGCAGTGAGGTCTACACTCTTGTCTGCATGTGGGCTGGAGCAGG -s simHuman_chr6.simHuman.chr6 125226 35 + 601863 -----------------ACCCACAGACTTGTCTGTATGTGGGTTGGAACAGG -s simRat_chr6.simRat.chr6 128713 52 + 647215 CTTGGGAATGCCCTGAGACCCACAGTCCGGGCTGTATGAGGTTTAGAAAAGG - -a -s simMouse_chr6.simMouse.chr6 130906 3 + 636262 CAA -s Anc0.Anc0refChr1 22209 3 - 62388 GAA -s Anc1.Anc1refChr2 100903 3 + 144309 GAA -s Anc2.Anc2refChr3 10812 3 + 53186 GAA -s mr.mrrefChr0 125353 3 + 130230 CAA -s simCow_chr6.simCow.chr6 138197 3 + 602619 AAA -s simDog_chr6.simDog.chr6 422415 3 - 593897 GAA -s simHuman_chr6.simHuman.chr6 125263 3 + 601863 GAA -s simRat_chr6.simRat.chr6 128765 3 + 647215 TAA - -a -s simMouse_chr6.simMouse.chr6 130909 4 + 636262 TTAG -s Anc0.Anc0refChr1 22212 3 - 62388 CTA- -s Anc1.Anc1refChr2 100906 3 + 144309 CTA- -s Anc2.Anc2refChr3 10817 3 + 53186 CAA- -s mr.mrrefChr0 125356 4 + 130230 TTAG -s simCow_chr6.simCow.chr6 138202 3 + 602619 CAA- -s simDog_chr6.simDog.chr6 422420 3 - 593897 CAT- -s simHuman_chr6.simHuman.chr6 125266 3 + 601863 CTA- -s simRat_chr6.simRat.chr6 128768 4 + 647215 TTAG - -a -s simMouse_chr6.simMouse.chr6 130913 19 + 636262 TGTTATTGGAACGATACAC -s Anc0.Anc0refChr1 22216 19 - 62388 TGATACTGGGTCAATACGC -s Anc1.Anc1refChr2 100910 19 + 144309 TGATACTGGGTCAATACGC -s Anc2.Anc2refChr3 10821 19 + 53186 AGATACTGTGTCAATACGA -s mr.mrrefChr0 125361 19 + 130230 TGTTATTGGAACAATACGC -s simCow_chr6.simCow.chr6 138206 19 + 602619 AAACATTGCATCAATACAC -s simDog_chr6.simDog.chr6 422424 19 - 593897 AGATACTGTGCCAATACGA -s simHuman_chr6.simHuman.chr6 125270 19 + 601863 TGATGCTGGGTCAATAGTC -s simRat_chr6.simRat.chr6 128773 19 + 647215 TATTATTGGAATAATACGC - -a -s simMouse_chr6.simMouse.chr6 130932 26 + 636262 CAGGTGCGAGCACCAGCTGCTAGGAA -s Anc0.Anc0refChr1 22235 26 - 62388 TAGTTAAGAGCATCAGTTGGGGGGCC -s Anc1.Anc1refChr2 100929 26 + 144309 TAGTTAAGAGCATCAGTTGGGGGGCC -s Anc2.Anc2refChr3 10840 26 + 53186 TAGTTAAGAACATCAGTTGGGGAGCC -s mr.mrrefChr0 125380 26 + 130230 CAGGTGCGAGCACCAGCTGGTGGGAA -s simCow_chr6.simCow.chr6 138225 26 + 602619 TGGTTAGGAACATCTGTTGGGGAGCT -s simDog_chr6.simDog.chr6 422443 26 - 593897 TAGTTGAGAACACCATTTGGGGGGCC -s simHuman_chr6.simHuman.chr6 125297 25 + 601863 TAGTCAAGAGCATCAGTTGG-GGATG -s simRat_chr6.simRat.chr6 128792 26 + 647215 CAGATGTGACCACCAGCTGGAGGGGA - -a -s simMouse_chr6.simMouse.chr6 130958 21 + 636262 CACGACCGTAGCCATTCTCAC -s Anc0.Anc0refChr1 22263 21 - 62388 CACTCCTGAACCCTTTCTTAC -s Anc1.Anc1refChr2 100957 21 + 144309 CACTCCTGAACCCTTTCTTAC -s Anc2.Anc2refChr3 10868 21 + 53186 CACTCCTGAACCCTTTATTAT -s mr.mrrefChr0 125408 21 + 130230 CACTCCTGTAGCCATTCTTAC -s simCow_chr6.simCow.chr6 138253 21 + 602619 CACACCTGAACCCTTTTTTAT -s simDog_chr6.simDog.chr6 422471 21 - 593897 TACTCCTGAACCCTTTATTAT -s simHuman_chr6.simHuman.chr6 125324 21 + 601863 CACTCCCAGACCCCTTCTTAC -s simRat_chr6.simRat.chr6 128820 21 + 647215 CACTCGTGTAGCCGTTCTTAC - -a -s simMouse_chr6.simMouse.chr6 130979 2 + 636262 TG -s Anc0.Anc0refChr1 22284 2 - 62388 CT -s Anc1.Anc1refChr2 100978 2 + 144309 CT -s Anc2.Anc2refChr3 10889 2 + 53186 CT -s mr.mrrefChr0 125429 2 + 130230 TG -s simCow_chr6.simCow.chr6 138274 2 + 602619 GT -s simDog_chr6.simDog.chr6 422506 2 - 593897 CT -s simHuman_chr6.simHuman.chr6 125345 2 + 601863 CT -s simRat_chr6.simRat.chr6 128841 2 + 647215 TA - -a -s simMouse_chr6.simMouse.chr6 130981 6 + 636262 GTCGAG -s Anc0.Anc0refChr1 22286 6 - 62388 GGAGAG -s Anc1.Anc1refChr2 100980 6 + 144309 GGAGAG -s Anc2.Anc2refChr3 10891 6 + 53186 GGAGAG -s mr.mrrefChr0 125431 6 + 130230 GACGAG -s simCow_chr6.simCow.chr6 138280 6 + 602619 AGAGAG -s simDog_chr6.simDog.chr6 422508 6 - 593897 GGAGAG -s simHuman_chr6.simHuman.chr6 125347 6 + 601863 GGAGGG -s simRat_chr6.simRat.chr6 128843 6 + 647215 GATGAG - -a -s simMouse_chr6.simMouse.chr6 130987 7 + 636262 TTGGTCA -s Anc0.Anc0refChr1 22370 7 - 62388 TTGGTTA -s Anc1.Anc1refChr2 101064 7 + 144309 TTGGTTA -s Anc2.Anc2refChr3 11010 7 + 53186 TTGATTA -s mr.mrrefChr0 125497 7 + 130230 TTGGTCA -s simCow_chr6.simCow.chr6 138359 7 + 602619 CTGATTA -s simDog_chr6.simDog.chr6 422649 7 - 593897 TTGATTA -s simHuman_chr6.simHuman.chr6 125431 7 + 601863 TTGGTTA -s simRat_chr6.simRat.chr6 128909 7 + 647215 TTGGTCA - -a -s simMouse_chr6.simMouse.chr6 130994 6 + 636262 GAGTTA -s Anc0.Anc0refChr1 22380 6 - 62388 GTTTTA -s Anc1.Anc1refChr2 101074 6 + 144309 GTTTTA -s Anc2.Anc2refChr3 11020 6 + 53186 GTTTTA -s mr.mrrefChr0 125504 6 + 130230 GAGTTA -s simCow_chr6.simCow.chr6 138369 6 + 602619 GTTTTA -s simDog_chr6.simDog.chr6 422659 6 - 593897 GTTTTA -s simHuman_chr6.simHuman.chr6 125441 6 + 601863 GTTTTA -s simRat_chr6.simRat.chr6 128916 6 + 647215 GGGTTA - -a -s simMouse_chr6.simMouse.chr6 131000 46 + 636262 TATACTAGTATCTCTGAAAGATTTCTAGCACCACCTGTCTGGGGTG -s Anc0.Anc0refChr1 22386 42 - 62388 ----CTAGTATCTTTGAGAAATTTCTAGCACCACCTGTCAGAGGTG -s Anc1.Anc1refChr2 101080 46 + 144309 TATACTAGTATCTTTGAGAAATTTCTAGCACCACCTGTCAGAGGTG -s Anc2.Anc2refChr3 11026 42 + 53186 ----CTACTATCTTTGAGAAATTTCTAGCACCACCTGTCAGAGGTG -s mr.mrrefChr0 125510 46 + 130230 TATACTAGTATCTTTGAAAGATTTCTAGCACCACCTGTCTGGGGTG -s simCow_chr6.simCow.chr6 138375 42 + 602619 ----CTACTGTCTTTGACAAATTTCTAGCACCAGCTGTCAGAGGTG -s simDog_chr6.simDog.chr6 422665 42 - 593897 ----CTACTATCTTTGAGAAATTTCTAGCACCACCTGTCAGAGGTG -s simHuman_chr6.simHuman.chr6 125456 46 + 601863 TATAGTTGGATCTTTGATAAATTTCTAGCGCCACCTGTCGGAGATG -s simRat_chr6.simRat.chr6 128922 46 + 647215 TAGACTAGTATCTTTGAAAGATTTCTAGCACTATCTGTTTGGGGTG - -a -s simMouse_chr6.simMouse.chr6 131046 15 + 636262 GTCATCGAATACAAC -s Anc0.Anc0refChr1 22428 15 - 62388 GTTAATTATGGCCAC -s Anc1.Anc1refChr2 101126 15 + 144309 GTTAATTATGGCCAC -s Anc2.Anc2refChr3 11068 15 + 53186 GTTAATTATGGCCAC -s mr.mrrefChr0 125556 15 + 130230 GTCATCGAATACAAC -s simCow_chr6.simCow.chr6 138423 15 + 602619 GTCAATTATGGCCAT -s simDog_chr6.simDog.chr6 422707 15 - 593897 GTTAATTATGGCCAC -s simHuman_chr6.simHuman.chr6 125502 15 + 601863 ATTAGTTATAGCCAC -s simRat_chr6.simRat.chr6 128968 15 + 647215 GTCATCCAATACTGC - -a -s simMouse_chr6.simMouse.chr6 131061 10 + 636262 TGTTTCCTGG -s Anc0.Anc0refChr1 22444 10 - 62388 GGTTACCTGG -s Anc1.Anc1refChr2 101142 10 + 144309 GGTTACCTGG -s Anc2.Anc2refChr3 11084 10 + 53186 GCTTACCTGG -s mr.mrrefChr0 125571 10 + 130230 TGTTTCCTGG -s simCow_chr6.simCow.chr6 138439 10 + 602619 GTTTACCTGG -s simDog_chr6.simDog.chr6 422723 10 - 593897 GCTTACCTGG -s simHuman_chr6.simHuman.chr6 125518 10 + 601863 GGTTACCTGG -s simRat_chr6.simRat.chr6 128983 10 + 647215 TGTTTGCTGG - -a -s simMouse_chr6.simMouse.chr6 131071 13 + 636262 TAGTTGGGCAGTT -s Anc0.Anc0refChr1 22454 13 - 62388 TAGTTGAGTAGCC -s Anc1.Anc1refChr2 101152 13 + 144309 TAGTTGAGTAGCC -s Anc2.Anc2refChr3 11094 13 + 53186 TAGTTGAGTCGCC -s mr.mrrefChr0 125581 13 + 130230 TAGTTGGGCAGTT -s simCow_chr6.simCow.chr6 138450 13 + 602619 TAGCTGAGTCACC -s simDog_chr6.simDog.chr6 422733 11 - 593897 TAGTTGAG--GCT -s simHuman_chr6.simHuman.chr6 125528 13 + 601863 TAGATTAGTAGAC -s simRat_chr6.simRat.chr6 128993 13 + 647215 TAGTTGAGTAGTT - -a -s simMouse_chr6.simMouse.chr6 131084 11 + 636262 GATATCCAAGA -s Anc0.Anc0refChr1 39131 11 + 62388 GAACACCAAAA -s Anc1.Anc1refChr2 42305 11 - 144309 GAACACCAAAA -s Anc2.Anc2refChr3 41278 11 - 53186 AAACAACAAAA -s mr.mrrefChr0 125594 11 + 130230 GATATCCAAGA -s simCow_chr6.simCow.chr6 463412 11 - 602619 AAATGACAAGA -s simDog_chr6.simDog.chr6 170263 11 + 593897 AAACAACAGAA -s simHuman_chr6.simHuman.chr6 475430 11 - 601863 GAACACCAAAA -s simRat_chr6.simRat.chr6 129006 11 + 647215 AATACCCAGGA - -a -s simMouse_chr6.simMouse.chr6 131095 9 + 636262 ACACCCAAT -s Anc0.Anc0refChr1 39149 9 + 62388 ACACTCAAT -s Anc1.Anc1refChr2 42323 9 - 144309 ACACTCAAT -s Anc2.Anc2refChr3 41296 9 - 53186 ACACTCACG -s mr.mrrefChr0 125605 9 + 130230 ACACCCAAT -s simDog_chr6.simDog.chr6 170281 9 + 593897 ACACTCACG -s simHuman_chr6.simHuman.chr6 475448 9 - 601863 ACACTCAAT -s simRat_chr6.simRat.chr6 129017 9 + 647215 ACACCTAAT - -a -s simMouse_chr6.simMouse.chr6 131104 1 + 636262 G -s Anc0.Anc0refChr1 39158 1 + 62388 G -s Anc1.Anc1refChr2 42332 1 - 144309 G -s Anc2.Anc2refChr3 41305 1 - 53186 G -s mr.mrrefChr0 125614 1 + 130230 G -s simDog_chr6.simDog.chr6 170290 1 + 593897 G -s simHuman_chr6.simHuman.chr6 475457 1 - 601863 G -s simRat_chr6.simRat.chr6 129039 1 + 647215 G - -a -s simMouse_chr6.simMouse.chr6 131105 4 + 636262 TCAA -s Anc0.Anc0refChr1 39161 4 + 62388 TCAA -s Anc1.Anc1refChr2 42335 4 - 144309 TCAA -s Anc2.Anc2refChr3 41308 4 - 53186 CCAA -s mr.mrrefChr0 125615 4 + 130230 TCAA -s simDog_chr6.simDog.chr6 170293 4 + 593897 CCAA -s simHuman_chr6.simHuman.chr6 475460 4 - 601863 TCAA -s simRat_chr6.simRat.chr6 129040 4 + 647215 TCAA - -a -s simMouse_chr6.simMouse.chr6 131109 15 + 636262 AATTACCTCACATTT -s Anc0.Anc0refChr1 39173 14 + 62388 AATTACCTC-AATTT -s Anc1.Anc1refChr2 42347 14 - 144309 AATTACCTC-AATTT -s Anc2.Anc2refChr3 41320 14 - 53186 GATTACATC-AATTT -s mr.mrrefChr0 125619 14 + 130230 AATTACCTC-CATTT -s simDog_chr6.simDog.chr6 170305 14 + 593897 GATTACATC-AATTT -s simHuman_chr6.simHuman.chr6 475475 14 - 601863 AATCAGCTC-AATTT -s simRat_chr6.simRat.chr6 129044 14 + 647215 AATTACCTC-CCTTT - -a -s simMouse_chr6.simMouse.chr6 131124 18 + 636262 GTTTGAGCCATTTAGCCA -s Anc0.Anc0refChr1 39188 18 + 62388 GTTTGAGCCGTTTAACAA -s Anc1.Anc1refChr2 42362 18 - 144309 GTTTGAGCCGTTTAACAA -s Anc2.Anc2refChr3 41335 18 - 53186 GTTTGAGCTGTTGCAGAA -s mr.mrrefChr0 125633 18 + 130230 GTTTGAGCCATTTAGCCA -s simCow_chr6.simCow.chr6 463430 6 - 602619 ------------GCAGAA -s simDog_chr6.simDog.chr6 170320 18 + 593897 GTTTGAGCTGTTGCAGAA -s simHuman_chr6.simHuman.chr6 475490 18 - 601863 GCTCGAGCCGCTTATCTA -s simRat_chr6.simRat.chr6 129058 18 + 647215 GTTTGAGCCATTTAGCTA - -a -s simMouse_chr6.simMouse.chr6 131142 39 + 636262 GCATAACAGAACAATCCTCAAGTACGTTTAGGTGGATCA -s Anc0.Anc0refChr1 39206 1 + 62388 G-------------------------------------- -s Anc1.Anc1refChr2 42380 32 - 144309 G-----TGCAATGATTATCAATAATGTCTA--TGAACCA -s Anc2.Anc2refChr3 41353 1 - 53186 G-------------------------------------- -s mr.mrrefChr0 125651 39 + 130230 GCATAACAGAACAATCCTCAAGTACGTTTAGGTGGATCA -s simCow_chr6.simCow.chr6 463437 1 - 602619 G-------------------------------------- -s simDog_chr6.simDog.chr6 170338 1 + 593897 G-------------------------------------- -s simHuman_chr6.simHuman.chr6 475508 31 - 601863 ------TGCAATGATTATCAATAATGTCTA--TGAACCA -s simRat_chr6.simRat.chr6 129077 39 + 647215 GTGGAACAAAACAATCCTCAAGCATGTTGAGGTGGATCA - -a -s simMouse_chr6.simMouse.chr6 131181 16 + 636262 TTGGTGGCCACTTATG -s Anc0.Anc0refChr1 39267 4 + 62388 TTG------------T -s Anc1.Anc1refChr2 42472 4 - 144309 TTG------------T -s Anc2.Anc2refChr3 41422 4 - 53186 GTG------------T -s mr.mrrefChr0 125690 4 + 130230 TTG------------G -s simCow_chr6.simCow.chr6 463506 4 - 602619 GTG------------T -s simDog_chr6.simDog.chr6 170407 4 + 593897 GTG------------T -s simHuman_chr6.simHuman.chr6 475653 4 - 601863 TTG------------T -s simRat_chr6.simRat.chr6 129116 4 + 647215 GTG------------G - -a -s simMouse_chr6.simMouse.chr6 131197 25 + 636262 TACCCATAGAAAGGAGGAATCCTGG -s Anc0.Anc0refChr1 39271 25 + 62388 GACCCATAGAAAGAGGTAATATTGG -s Anc1.Anc1refChr2 42476 25 - 144309 GACCCATAGAAAGAGGTAATATTGG -s Anc2.Anc2refChr3 41426 25 - 53186 GACCCATGGAAAGAGGTAATATTCG -s mr.mrrefChr0 125694 25 + 130230 TACCCATAGAAAGGAGGAATCCTGG -s simCow_chr6.simCow.chr6 463510 25 - 602619 GATCCATGGAAAGGGGTACTCTTAG -s simDog_chr6.simDog.chr6 170412 25 + 593897 GACCCATGGTAAAAGGTAATATACG -s simHuman_chr6.simHuman.chr6 475657 25 - 601863 GACCCATAGAAAGCGGTAATTTTGG -s simRat_chr6.simRat.chr6 129120 25 + 647215 TACCCATAGAAAGGAGGGATCCTCA - -a -s simMouse_chr6.simMouse.chr6 131222 18 + 636262 GCTTACTACACTGGGAAC -s Anc0.Anc0refChr1 39308 18 + 62388 GGCTACTACACTGGGTAC -s Anc1.Anc1refChr2 42513 18 - 144309 GGCTACTACACTGGGTAC -s Anc2.Anc2refChr3 41463 18 - 53186 GGCTACTACACTGGATAC -s mr.mrrefChr0 125719 18 + 130230 GCTTACTACACTGGGAAC -s simCow_chr6.simCow.chr6 463547 18 - 602619 GGCTACTTCACTGGCTAC -s simDog_chr6.simDog.chr6 170449 18 + 593897 GGCTGATACATCTGATTC -s simHuman_chr6.simHuman.chr6 475694 18 - 601863 GGCTACCATACTGGGTAC -s simRat_chr6.simRat.chr6 129145 18 + 647215 GCTTACTACAGTGGGAAG - -a -s simMouse_chr6.simMouse.chr6 131240 60 + 636262 ACAGGGGTTAAAAAAAAAACCACACTTAGTTTACTTGTACTGCGCATAGGGTAACTGTGG -s Anc1.Anc1refChr2 42536 9 - 144309 AGAAGGGCT--------------------------------------------------- -s mr.mrrefChr0 125737 60 + 130230 ACAGGGGTTAAAAAAAAAACCACACTTAGTTTACTTGTACTGCGCATAGGGTAACTGTGG -s simHuman_chr6.simHuman.chr6 475717 9 - 601863 AGAAGGGCT--------------------------------------------------- -s simRat_chr6.simRat.chr6 129163 60 + 647215 ACAGGGGTTAAAAAAAACACCGCACTTGGTTGACATGTACTGTGCATAGGGTAACTGTGA - -a -s simMouse_chr6.simMouse.chr6 131300 35 + 636262 CTTAGGAGACCTATTGTATAGAAAAACTCTACTGG -s Anc0.Anc0refChr1 39331 16 + 62388 -----------------ATG--AGAACTCTACTGG -s Anc1.Anc1refChr2 42545 23 - 144309 ----------CTACTGGATG--AGAACTCTACTGG -s Anc2.Anc2refChr3 41486 16 - 53186 -----------------ATG--AGAACTCTACTGG -s mr.mrrefChr0 125797 35 + 130230 CTTAGGAGACCTATTGTATAGAAAAACTCTACTGG -s simCow_chr6.simCow.chr6 463570 16 - 602619 -----------------ATG--AGAACTCTACTGG -s simDog_chr6.simDog.chr6 170472 16 + 593897 -----------------ATG--GGAACTCTACTGG -s simHuman_chr6.simHuman.chr6 475726 23 - 601863 ----------CTACTGGATG--AGAACTCTACTGG -s simRat_chr6.simRat.chr6 129232 35 + 647215 CTTATGAGAACTATTGTATAGAATAACACTACTGG - -a -s simMouse_chr6.simMouse.chr6 131335 43 + 636262 AATTCGAGCAAGTACAAGGAAAAACATCGTATTGAAATTGCTA -s Anc0.Anc0refChr1 39347 42 + 62388 ACTTTCAGATA-TAGAGGAACACACATAGTATTGAGTTTGGTA -s Anc1.Anc1refChr2 42568 43 - 144309 ACTTTCAGATAGTAGAGGAACACACATAGTATTGAGTTTGGTA -s Anc2.Anc2refChr3 41502 42 - 53186 ACTTTCAGATA-CAGAGGAACACACATAGTATTGAGTTTGGTA -s mr.mrrefChr0 125832 43 + 130230 AATTTGAGCAAGTACAAGAAAAAACATAGTATTGAGATTGCTA -s simCow_chr6.simCow.chr6 463586 42 - 602619 ACTTTCAGATA-CACAAAAACAAACCAGGTACTGAGTTTGATA -s simDog_chr6.simDog.chr6 170489 42 + 593897 ACTTTCAGATA-CAGAGGAACACACATAGTATCGAGTTTGGTA -s simHuman_chr6.simHuman.chr6 475749 31 - 601863 GCTTTTAGATAGT------------AGAATAATTAGCATGGTA -s simRat_chr6.simRat.chr6 129267 43 + 647215 CCTTTGAGCTAGTACAAGAAAAAACATAGTATTGAGGTTGCCA - -a -s simMouse_chr6.simMouse.chr6 131378 9 + 636262 AGTAGAAGT -s Anc0.Anc0refChr1 39389 9 + 62388 GGTAGAGGT -s Anc1.Anc1refChr2 42611 9 - 144309 GGTAGAGGT -s Anc2.Anc2refChr3 41544 9 - 53186 GGTAGAGGT -s mr.mrrefChr0 125875 9 + 130230 AGTAGAAGT -s simCow_chr6.simCow.chr6 463644 9 - 602619 GGTAGATGT -s simDog_chr6.simDog.chr6 170531 9 + 593897 AGTAGAGGT -s simHuman_chr6.simHuman.chr6 475780 9 - 601863 GTGAAAGGT -s simRat_chr6.simRat.chr6 129310 9 + 647215 AGTAGAATT - -a -s simMouse_chr6.simMouse.chr6 131387 17 + 636262 TGTCCTGTTAGTCTTGT -s Anc0.Anc0refChr1 39398 13 + 62388 GGTCC---TGGT-TTGT -s Anc1.Anc1refChr2 42620 13 - 144309 GGTCC---TGGT-TTGT -s Anc2.Anc2refChr3 41556 13 - 53186 GGTCT---TGGT-TTTT -s mr.mrrefChr0 125884 17 + 130230 TGTCCTGTTAGTCTTGT -s simCow_chr6.simCow.chr6 463656 13 - 602619 GGTGT---TGGT-TTTT -s simDog_chr6.simDog.chr6 170543 13 + 593897 GGTCT---TGGT-CTTT -s simHuman_chr6.simHuman.chr6 475789 13 - 601863 GGTAC---ACAT-TTGT -s simRat_chr6.simRat.chr6 129319 17 + 647215 TGCACCACTAGGTTTGT - -a -s simMouse_chr6.simMouse.chr6 131404 41 + 636262 TAGTAAAATGTCTAATGAATCTCTCTGCCCCTGTTTGTGAA -s Anc0.Anc0refChr1 39415 41 + 62388 TGATAGGATGTCTAAAGAATCCCTTAGCTTCTGTTAGTCGA -s Anc1.Anc1refChr2 42637 41 - 144309 TGATAGGATGTCTAAAGAATCCCTTAGCTTCTGTTAGTCGA -s Anc2.Anc2refChr3 41573 41 - 53186 TGATAGGATGTCTAAAAAATCCATTAGCTTCTGCTAGTCGA -s mr.mrrefChr0 125901 41 + 130230 TAATAAAATGTCTAAAGAATCCCTCAGCCCCTGTTTGTGAA -s simCow_chr6.simCow.chr6 463679 41 - 602619 TGATGGAATGTCTAAAAAATCCATCAACTCCTGCTAGGGGT -s simDog_chr6.simDog.chr6 170560 41 + 593897 TGATAGGATGTCTAAAAAATCCATTAGCTTCTGCTAGTCAA -s simHuman_chr6.simHuman.chr6 475806 37 - 601863 TGTCAGGCTTT----GGAAACCCTGAGCGTTGATAAGTAGA -s simRat_chr6.simRat.chr6 129336 39 + 647215 CAATAAAATGTCCAAAGAGTCCGTAAGCACCT--TTGTGAA - -a -s simMouse_chr6.simMouse.chr6 131445 11 + 636262 TTGAAGGCTAT -s Anc0.Anc0refChr1 39456 11 + 62388 TTGTTGAATAT -s Anc1.Anc1refChr2 42678 11 - 144309 TTGTTGAATAT -s Anc2.Anc2refChr3 41614 11 - 53186 TTGTTGAATAT -s mr.mrrefChr0 125942 11 + 130230 TTGAAGGCTAT -s simCow_chr6.simCow.chr6 463720 11 - 602619 TTCTTAGATAT -s simDog_chr6.simDog.chr6 170601 11 + 593897 TTGTTGAATAT -s simHuman_chr6.simHuman.chr6 475850 11 - 601863 CTGTTGTTTTT -s simRat_chr6.simRat.chr6 129375 11 + 647215 TTGAAGGCAAT - -a -s simMouse_chr6.simMouse.chr6 131456 126 + 636262 GAACAGCGGTCTCAGCAAGGCATGTCATAATGATCTTAACTACAATTTGAACACTATCCAGTATCTCATCATGATATGATACTAACACGTGATGCTATGCATAGAGCGCTTACGGAGTGGTCCCTC -s Anc0.Anc0refChr1 39467 96 + 62388 GACCAATGGTCTCAGCAATGAATGGCAAAATGATATTTGCTATGATTTTTACACTATTCATTATTTGAGCCC-------------CACATGATGCTAGTTATAGGGC-----------------TC -s Anc1.Anc1refChr2 42689 96 - 144309 GACCAATGGTCTCAGCAATGAATGGCAAAATGATATTTGCTATGATTTTTACACTATTCATTATTTGAGCCC-------------CACATGATGCTAGTTATAGGGC-----------------TC -s Anc2.Anc2refChr3 41625 96 - 53186 GACCAATGGTCTCAGCAATGAATGGCAAAATGATATTTGCTATGATTTTTACACTATTCATTATTTGTGCCC-------------CACATGATACTTGTTGTAGGGC-----------------TC -s mr.mrrefChr0 125953 109 + 130230 GAACAGTGGTCTCAGCAAGGCATGTCATAATGATATTAACTACAATTTTTACACTATTCAGTATCTCATCATGATATGATACTAACACATGATGCTATGTATAGAGC-----------------TC -s simCow_chr6.simCow.chr6 463731 79 - 602619 AACCAGTGGTCCCAGCCATGAGTGGCAAAATGATATTCACTATGATCTATACACTAGTCATTATTTGCACC------------------------------TATGGC-----------------TT -s simDog_chr6.simDog.chr6 170612 96 + 593897 GGCCAATGGCCTGGGCAAGGAATGGCAAAATGATACTTGCGATGATTCTTACACTATTCATTATTTATGCTC-------------CACATGATACTTGTTGTAGGGC-----------------TC -s simHuman_chr6.simHuman.chr6 475866 92 - 601863 GACCATTGGTCTCAGCAATGAATGGGA----GATATTTGCTATGATTTGTACACTAATCACTATTTGAGCCC-------------CATATGATGCTAGCTAAAGGGC-----------------TC -s simRat_chr6.simRat.chr6 129386 105 + 647215 GA----TGGTCTCAGCAAGGCATGTCATAATGATATTAACTACAATTTTTACTCTAATCAGTATCTGGTCATGATGTGAAACTAACACATGATGCTATATATAGAGC-----------------TA - -a -s simMouse_chr6.simMouse.chr6 131582 13 + 636262 AATATAATGCAAG -s Anc0.Anc0refChr1 39566 13 + 62388 AAGATAGTGAGAG -s Anc1.Anc1refChr2 42788 13 - 144309 AAGATAGTGAGAG -s Anc2.Anc2refChr3 41724 13 - 53186 AAGATAGTGAGAG -s mr.mrrefChr0 126062 13 + 130230 AAGATAATGCAAG -s simCow_chr6.simCow.chr6 463813 13 - 602619 AAGATAGTGGGAG -s simDog_chr6.simDog.chr6 170711 13 + 593897 AAGATAGTGAGAG -s simHuman_chr6.simHuman.chr6 475961 13 - 601863 AAGATAGTGAGAG -s simRat_chr6.simRat.chr6 129491 13 + 647215 AAGATAATGCAAG - -a -s simMouse_chr6.simMouse.chr6 131595 14 + 636262 CCTGCTTGGGACAA -s Anc0.Anc0refChr1 39579 14 + 62388 CCTGCTCAGGATAA -s Anc1.Anc1refChr2 42801 14 - 144309 CCTGCTCAGGATAA -s Anc2.Anc2refChr3 41737 14 - 53186 CTTGCTCAAGATAA -s mr.mrrefChr0 126075 14 + 130230 CCTGCTTGGGACAA -s simCow_chr6.simCow.chr6 463830 14 - 602619 CTTGCTCGAGATAA -s simDog_chr6.simDog.chr6 170724 14 + 593897 CTTGCTCAAGATAA -s simHuman_chr6.simHuman.chr6 475974 14 - 601863 CCTGCTCAGCTTAA -s simRat_chr6.simRat.chr6 129504 14 + 647215 CCTGCTTGGGACAG - -a -s simMouse_chr6.simMouse.chr6 131609 88 + 636262 TTCTAGCCTCTATATGTGGTGCTCTTTCTCAATGCACTTATGCTAAAAACTTGGGACAATTCTAGCCTCCATATGTGGTGCTCTTTCT -s Anc0.Anc0refChr1 39593 21 + 62388 TTCTAGCCCCCATCTGTGG-------------------------------------------------------------------CT -s Anc1.Anc1refChr2 42815 21 - 144309 TTCTAGCCCCCATCTGTGG-------------------------------------------------------------------CT -s Anc2.Anc2refChr3 41751 21 - 53186 ATCTAGCCCCCATCTGTGG-------------------------------------------------------------------CT -s mr.mrrefChr0 126089 21 + 130230 TTCTAGCCTCTATATGTGG-------------------------------------------------------------------CT -s simCow_chr6.simCow.chr6 463844 17 - 602619 GTCTAG----TATCTAGGG-------------------------------------------------------------------TT -s simDog_chr6.simDog.chr6 170738 21 + 593897 ATCTAGCCCCCATCTGTGG-------------------------------------------------------------------CT -s simHuman_chr6.simHuman.chr6 475994 21 - 601863 TTCTAGCCCCCATCTGTGG-------------------------------------------------------------------CT -s simRat_chr6.simRat.chr6 129518 1 + 647215 T--------------------------------------------------------------------------------------- - -a -s simMouse_chr6.simMouse.chr6 131697 10 + 636262 CAATGCACTT -s Anc0.Anc0refChr1 39625 10 + 62388 CAAAGGATCT -s Anc1.Anc1refChr2 42847 10 - 144309 CAAAGGATCT -s Anc2.Anc2refChr3 41783 10 - 53186 CAAAGGATCT -s mr.mrrefChr0 126110 10 + 130230 CAATGCACTT -s simCow_chr6.simCow.chr6 463872 10 - 602619 CAGAGCATCG -s simDog_chr6.simDog.chr6 170762 10 + 593897 TAAAGGACCT -s simHuman_chr6.simHuman.chr6 476026 10 - 601863 CATGGTATCT -s simRat_chr6.simRat.chr6 129519 6 + 647215 ----GCACTT - -a -s simMouse_chr6.simMouse.chr6 131707 4 + 636262 ATGC -s Anc0.Anc0refChr1 39635 4 + 62388 ATGC -s Anc1.Anc1refChr2 42857 4 - 144309 ATGC -s Anc2.Anc2refChr3 41793 4 - 53186 ATGC -s mr.mrrefChr0 126120 4 + 130230 ATGC -s simCow_chr6.simCow.chr6 463882 4 - 602619 ATGC -s simDog_chr6.simDog.chr6 170772 4 + 593897 ATGC -s simHuman_chr6.simHuman.chr6 476036 4 - 601863 ATGC -s simRat_chr6.simRat.chr6 129526 4 + 647215 ATGC - -a -s simMouse_chr6.simMouse.chr6 131711 8 + 636262 TAAAAACT -s Anc0.Anc0refChr1 39639 8 + 62388 AATAAACT -s Anc1.Anc1refChr2 42861 8 - 144309 AATAAACT -s Anc2.Anc2refChr3 41797 8 - 53186 AATAAACT -s mr.mrrefChr0 126124 8 + 130230 AAAAAACT -s simCow_chr6.simCow.chr6 463886 8 - 602619 CATAAACG -s simDog_chr6.simDog.chr6 170782 8 + 593897 AATAAATT -s simHuman_chr6.simHuman.chr6 476040 8 - 601863 AATAAACT -s simRat_chr6.simRat.chr6 129530 8 + 647215 AAAAAACT - -a -s simMouse_chr6.simMouse.chr6 131719 6 + 636262 GACACT -s Anc0.Anc0refChr1 39648 6 + 62388 AACCTT -s Anc1.Anc1refChr2 42870 6 - 144309 AACCTT -s Anc2.Anc2refChr3 41806 6 - 53186 AACCTT -s mr.mrrefChr0 126132 6 + 130230 AACACT -s simCow_chr6.simCow.chr6 463895 6 - 602619 CACCTT -s simDog_chr6.simDog.chr6 170791 6 + 593897 AACCTT -s simHuman_chr6.simHuman.chr6 476049 6 - 601863 AACCTT -s simRat_chr6.simRat.chr6 129538 6 + 647215 AACACT - -a -s simMouse_chr6.simMouse.chr6 131725 10 + 636262 GACACATAAC -s Anc0.Anc0refChr1 39654 10 + 62388 GCTTCTTCTC -s Anc1.Anc1refChr2 42876 10 - 144309 GCTTCTTCTC -s Anc2.Anc2refChr3 41812 10 - 53186 GCTTCTTCTC -s mr.mrrefChr0 126138 10 + 130230 GATACATCAC -s simCow_chr6.simCow.chr6 463901 10 - 602619 GCATAGTCTC -s simDog_chr6.simDog.chr6 170797 10 + 593897 GCTTCTTCTC -s simHuman_chr6.simHuman.chr6 476055 10 - 601863 GCTTCTTCTT -s simRat_chr6.simRat.chr6 129579 10 + 647215 GTTGCGTCAC - -a -s simMouse_chr6.simMouse.chr6 131735 102 + 636262 ACTTCGCTTCATGACCGTCCCAGGTTATAATTTTTGTCTGAGAACAGCCAGTTATTTACTAGCACATTTATCATGCAAGCTGGAGCTCCATTCATTGCTGCA -s Anc0.Anc0refChr1 39667 100 + 62388 GCATTGCTGCACAACTGTCCCAGGTTATAATTTTTGTCTAAGAACAACTGGTATTTTTTCAGGGCATCTATCCTAGAAGCTGAACCTCAATT--GTTCTCCA -s Anc1.Anc1refChr2 42889 100 - 144309 GCATTGCTGCACAACTGTCCCAGGTTATAATTTTTGTCTAAGAACAACTGGTATTTTTTCAGGGCATCTATCCTAGAAGCTGAACCTCAATT--GTTCTCCA -s Anc2.Anc2refChr3 41825 100 - 53186 GCATTGCTGCACAACTGTCCCAGGTTATAATTCCTGTCTAAAAACAACTGGTATTTTTTCAGGGCACCTATGCTAGAAGCTGAACCTCAATT--GTTCTCCA -s mr.mrrefChr0 126148 102 + 130230 ACTTTGCTTCATGACCGTCCCAGGTTATAATTTTTGTCTGAGAACAACTGGTTATTTACCAGCACATTTATCCTGCAAGCTGGAGCTTCATTCATTGCTGCA -s simCow_chr6.simCow.chr6 463914 100 - 602619 GTGTGGCTGCACAACTGTCCCAGGTGCTAATTCCTGTCAAAAAGAAACTGGTAATTTATCAGGGCAGCTATGCTAGAAGCTAACCATCAATT--GTTTTCCA -s simDog_chr6.simDog.chr6 170810 100 + 593897 GCATTTCTGCAGAACTCTCCCAGGTTATAATTCCTTTCTACAAACAACTGGTATTTCTTCAGGACACCTATGCTAAAATCTGAACCTTAATC--ATTCGCTG -s simHuman_chr6.simHuman.chr6 476068 99 - 601863 GCATCGCTGCACAACTGTCCCAGGTCATAA-TTTTGTCCAAGAACAACTGGCATTTTCACAGGGCATCTATCTTAGATGGAGAGCCTCAAGT--GTTCTCCA -s simRat_chr6.simRat.chr6 129589 101 + 647215 AGTTTGCTTCATGACCGTCCCAGATTATAATTTTTGTCTGAGAACAACTGGTTGTTTACCAG-ATGTTTATCCTGCAAGCTGGAGCGTCATTCATTTCCCCA - -a -s simMouse_chr6.simMouse.chr6 131837 18 + 636262 ACACCAACATGATCCAAT -s Anc0.Anc0refChr1 39768 17 + 62388 GCA-CAACAAAATCTAAT -s Anc1.Anc1refChr2 42990 18 - 144309 GCATCAACAAAATCTAAT -s Anc2.Anc2refChr3 41926 17 - 53186 GCA-CAACAAAATCTAAT -s mr.mrrefChr0 126250 18 + 130230 ACACCAACATGATCCAAT -s simCow_chr6.simCow.chr6 464015 17 - 602619 GCA-CAACTAGATCTGGT -s simDog_chr6.simDog.chr6 170911 17 + 593897 GCA-CAACATAATCTAAT -s simHuman_chr6.simHuman.chr6 476168 18 - 601863 GCATCAGCAAAATCTAAT -s simRat_chr6.simRat.chr6 129690 18 + 647215 ACATCAAGAAGATCCAAC - -a -s simMouse_chr6.simMouse.chr6 131855 9 + 636262 ATACCTTGT -s Anc0.Anc0refChr1 39785 9 + 62388 ATGACCTAT -s Anc1.Anc1refChr2 43008 9 - 144309 ATGACCTAT -s Anc2.Anc2refChr3 41943 9 - 53186 ATGACCTAT -s mr.mrrefChr0 126268 9 + 130230 ATACCTTGT -s simCow_chr6.simCow.chr6 464032 9 - 602619 ATGACATAT -s simDog_chr6.simDog.chr6 171001 9 + 593897 ATGTCCGAT -s simHuman_chr6.simHuman.chr6 476186 9 - 601863 GTGACCTAT -s simRat_chr6.simRat.chr6 129708 9 + 647215 ATGTCTTGT - -a -s simMouse_chr6.simMouse.chr6 131864 26 + 636262 TGGGTGTTGAAGGAGCCTTTAGTGTT -s Anc0.Anc0refChr1 39796 26 + 62388 TAAGTGTTGACGGAACCTTGAGTGTC -s Anc1.Anc1refChr2 43019 26 - 144309 TAAGTGTTGACGGAACCTTGAGTGTC -s Anc2.Anc2refChr3 41954 26 - 53186 AAAGTGTTGACAGAACCTTGAGTGTC -s mr.mrrefChr0 126277 26 + 130230 TGGGTGTTGAAGGAGCCTTTAGTGTT -s simCow_chr6.simCow.chr6 464043 26 - 602619 GAAGTGGTGGCAAAACCTTGAGTGTC -s simDog_chr6.simDog.chr6 171012 26 + 593897 AGAGTGTTGACAGGGCCTCGAGTGTC -s simHuman_chr6.simHuman.chr6 476197 26 - 601863 TAAGTGTTGAGGGAACCTTGAGTGTC -s simRat_chr6.simRat.chr6 129717 26 + 647215 TGACTGTTGAAGGAACCCTTAGGGTT - -a -s simMouse_chr6.simMouse.chr6 131890 57 + 636262 CAAGGATTTAAGTAGGATTAGACTGATATAAGCAGGGCTCAATCTGTGTGACAATGT -s Anc0.Anc0refChr1 39822 57 + 62388 TGAGGAATTGAATGGGATGAATCTGATATAAGTGGGGGCCTAAATATGCAACAGTGT -s Anc1.Anc1refChr2 43045 57 - 144309 TGAGGAATTGAATGGGATGAATCTGATATAAGTGGGGGCCTAAATATGCAACAGTGT -s Anc2.Anc2refChr3 41980 57 - 53186 TGAGTAATTGAATGGGATGAATCTGATATAAATGGGGGCCTAAATATGCAACAGTGT -s mr.mrrefChr0 126303 57 + 130230 CAAGGATTTAAGTAGGATTAGACTGATATAAGCAGGGCTCAATCTGTGTGACAATGT -s simCow_chr6.simCow.chr6 464069 45 - 602619 CGA-----------GGATGAAGCTGATATAAATGGTAGCCAAAATATGC-ACAGTGT -s simDog_chr6.simDog.chr6 171055 57 + 593897 TGAGTAATTGAATGGGATGAATCTGATAGAAATGGGGGCCTGAATATGCAACAGTGT -s simHuman_chr6.simHuman.chr6 476223 57 - 601863 TGGGGAATTGAATGGGATGAATTTGATATAAGTTGGGGCCTAAATATCCAACTGCGC -s simRat_chr6.simRat.chr6 129743 57 + 647215 TGAGGATTTACATAGAATGAGATTGATATAAGCAGGGTACAGTCTATGCAACAGTGT - -a -s simMouse_chr6.simMouse.chr6 131947 6 + 636262 CTTGGA -s Anc0.Anc0refChr1 39889 6 + 62388 CTGGGA -s Anc1.Anc1refChr2 43112 6 - 144309 CTGGGA -s Anc2.Anc2refChr3 42047 6 - 53186 CTGTGA -s mr.mrrefChr0 126360 6 + 130230 CTTGGA -s simCow_chr6.simCow.chr6 464124 6 - 602619 CAGCGA -s simDog_chr6.simDog.chr6 171122 6 + 593897 CTGTGA -s simHuman_chr6.simHuman.chr6 476290 6 - 601863 CTGGGA -s simRat_chr6.simRat.chr6 129800 6 + 647215 CTTGGA - -a -s simMouse_chr6.simMouse.chr6 131953 18 + 636262 TTTATCAAATGATTAGTT -s Anc0.Anc0refChr1 39898 18 + 62388 TCTGGTACATGCTAAAGT -s Anc1.Anc1refChr2 43121 18 - 144309 TCTGGTACATGCTAAAGT -s Anc2.Anc2refChr3 42056 18 - 53186 TCTGGTACATGCCAAAGC -s mr.mrrefChr0 126366 18 + 130230 TTTATCAAATGATTAGTT -s simCow_chr6.simCow.chr6 464133 18 - 602619 TCTAGTACATGCCAAAGC -s simDog_chr6.simDog.chr6 171131 17 + 593897 TCTGGTACATGC-AGAGC -s simHuman_chr6.simHuman.chr6 476299 18 - 601863 TCTGGTACATGCTAAAGT -s simRat_chr6.simRat.chr6 129806 18 + 647215 TTCAGCAAATCATTTGTT - -a -s simMouse_chr6.simMouse.chr6 131971 2 + 636262 TC -s Anc0.Anc0refChr1 39916 2 + 62388 TC -s Anc1.Anc1refChr2 43139 2 - 144309 TC -s Anc2.Anc2refChr3 42074 2 - 53186 TC -s mr.mrrefChr0 126384 2 + 130230 TC -s simCow_chr6.simCow.chr6 464151 2 - 602619 TC -s simDog_chr6.simDog.chr6 171148 2 + 593897 TC -s simHuman_chr6.simHuman.chr6 476317 2 - 601863 GC -s simRat_chr6.simRat.chr6 129829 2 + 647215 TC - -a -s simMouse_chr6.simMouse.chr6 131973 37 + 636262 ACTTTTACTGTACACACATAACCCTGTAATGTCTAAT -s Anc0.Anc0refChr1 23261 37 - 62388 ACTTTAATAGCACACAACTAACACTGTTTGATTTAAT -s Anc1.Anc1refChr2 102008 37 + 144309 ACTTTAATAGCACACAACTAACACTGTTTGATTTAAT -s Anc2.Anc2refChr3 11912 37 + 53186 ACTTTAGTAGCACACAACCAACACTGTTTGATTTAAT -s mr.mrrefChr0 126386 37 + 130230 ACTTTTACTGTACACACATAACCCTGTAATGTCTAAT -s simCow_chr6.simCow.chr6 139211 37 + 602619 ACTTAAGTAGCACACAACCAACAGCATATGATTTGAT -s simDog_chr6.simDog.chr6 423638 35 - 593897 ACTTTAGTAGCACATAAC--ACACTGTTTGATTTAAT -s simHuman_chr6.simHuman.chr6 126437 37 + 601863 ACTTTAATGGCACACAACTAACACTGAGTGTTTTAAT -s simRat_chr6.simRat.chr6 129831 37 + 647215 ACTTTTAATGCACACAAATAACACTATAAGGTCTAAT - -a -s simMouse_chr6.simMouse.chr6 132010 6 + 636262 CTGATG -s Anc0.Anc0refChr1 23303 6 - 62388 CTGATG -s Anc1.Anc1refChr2 102050 6 + 144309 CTGATG -s Anc2.Anc2refChr3 11954 6 + 53186 CTGATG -s mr.mrrefChr0 126423 6 + 130230 CTGATG -s simCow_chr6.simCow.chr6 139253 6 + 602619 CTGATG -s simDog_chr6.simDog.chr6 423678 6 - 593897 CTGATG -s simHuman_chr6.simHuman.chr6 126479 6 + 601863 CTGATG -s simRat_chr6.simRat.chr6 129868 6 + 647215 CTGATG - -a -s simMouse_chr6.simMouse.chr6 132016 39 + 636262 CTTATTATATCAGATTGTCCTGACCTAGGTATGTAGCCA -s Anc0.Anc0refChr1 23310 39 - 62388 CCTCCTATCTTAGATTGTCCATACCTAGGTACATAATCA -s Anc1.Anc1refChr2 102057 39 + 144309 CCTCCTATCTTAGATTGTCCATACCTAGGTACATAATCA -s Anc2.Anc2refChr3 11961 39 + 53186 CCTCCTAACTTAGATTGTCCATACCTAGGTACATAATCA -s mr.mrrefChr0 126429 39 + 130230 CTTATTATATCAGATTGTCCTGACCTAGGTATGTAGCCA -s simCow_chr6.simCow.chr6 139260 30 + 602619 CCTCCTAAATTAGATCATCTATACTTAGGT--------- -s simDog_chr6.simDog.chr6 423685 39 - 593897 CCCCCAAACTTAGGTTGTCCGCACCTAGGTACATAATCA -s simHuman_chr6.simHuman.chr6 126486 39 + 601863 CCTCCTATCCTAGATTGTCCATACCTTGGGACATAATCA -s simRat_chr6.simRat.chr6 129874 39 + 647215 ATTACTTCAACAGATTGCCCTTACCTAGGTATGTAATCA - -a -s simMouse_chr6.simMouse.chr6 132055 4 + 636262 TCCA -s Anc0.Anc0refChr1 23349 4 - 62388 TCCA -s Anc1.Anc1refChr2 102096 4 + 144309 TCCA -s Anc2.Anc2refChr3 12000 4 + 53186 TCCA -s mr.mrrefChr0 126468 4 + 130230 TCCA -s simDog_chr6.simDog.chr6 423724 4 - 593897 TCCA -s simHuman_chr6.simHuman.chr6 126525 4 + 601863 TCCA -s simRat_chr6.simRat.chr6 129915 4 + 647215 TCCA - -a -s simMouse_chr6.simMouse.chr6 132059 17 + 636262 GCTCTAGTATTTGTTTT -s Anc0.Anc0refChr1 23353 3 - 62388 G---T-----------T -s Anc1.Anc1refChr2 102100 7 + 144309 G---TAGG-T------T -s Anc2.Anc2refChr3 12004 3 + 53186 G---T-----------T -s mr.mrrefChr0 126472 11 + 130230 GCTCTAGTAT------T -s simDog_chr6.simDog.chr6 423733 3 - 593897 G---T-----------T -s simHuman_chr6.simHuman.chr6 126529 5 + 601863 G---TAGG--------- -s simRat_chr6.simRat.chr6 129919 11 + 647215 GCTCTAGTGT------T - -a -s simMouse_chr6.simMouse.chr6 132076 101 + 636262 TGTTCTAGTTAACATATTGCATTATCTTACCCATAAGGCCAACCGCCTGAGTGTCACAAAACTTGTTTTCCACCAAGCAAGAAGAATGCGTCTCAGTTATG -s Anc0.Anc0refChr1 23356 46 - 62388 TACTCTAGTTAGCATATTGCACTAAATTACTAATAGATCAAATTGC------------------------------------------------------- -s Anc1.Anc1refChr2 102107 46 + 144309 TACTCTAGTTAGCATATTGCACTAAATTACTAATAGATCAAATTGC------------------------------------------------------- -s Anc2.Anc2refChr3 12007 46 + 53186 TACTCTAGTTAGCATATTGCACTAAATTACTAATAGATCAAATTGC------------------------------------------------------- -s mr.mrrefChr0 126483 46 + 130230 TGTTCTAGTTAACATATTGCATTATCTTACCCATAAGGCCAACCGC------------------------------------------------------- -s simCow_chr6.simCow.chr6 139290 46 + 602619 TAGTCTAGTTAGCATATTGTATTAGTTTACTCATAGACCTAGCCAC------------------------------------------------------- -s simDog_chr6.simDog.chr6 423739 46 - 593897 TACTCTAGTTAGCATATTGCACTAAATTACTAATAGATCAAATTGC------------------------------------------------------- -s simRat_chr6.simRat.chr6 129930 46 + 647215 TGCTCTAGTTGACATATTGCATTATCTTACCCACAAGTCCAACCAC------------------------------------------------------- - -a -s simMouse_chr6.simMouse.chr6 132177 19 + 636262 AATACTGTCTCAATTATTT -s Anc0.Anc0refChr1 23402 19 - 62388 AATGCTGTTAATATTGGTT -s Anc1.Anc1refChr2 102153 19 + 144309 AATGCTGTTAATATTGGTT -s Anc2.Anc2refChr3 12056 19 + 53186 AATGCTGTTAATATTGGTT -s mr.mrrefChr0 126529 19 + 130230 AATACTGTCTCAATTATTT -s simCow_chr6.simCow.chr6 139339 19 + 602619 AATGTTGTTGATATGGGTC -s simDog_chr6.simDog.chr6 423788 19 - 593897 AATGCTGTTAATATTGGTT -s simRat_chr6.simRat.chr6 129976 19 + 647215 AATGTGGCCTCAAATATTT - -a -s simMouse_chr6.simMouse.chr6 132196 12 + 636262 GCAAATAATTAC -s Anc0.Anc0refChr1 23421 12 - 62388 GCCGATATTGAC -s Anc1.Anc1refChr2 102172 12 + 144309 GCCGATATTGAC -s Anc2.Anc2refChr3 12078 12 + 53186 GCCGATATTGAC -s mr.mrrefChr0 126548 12 + 130230 GCAAATAATTAC -s simCow_chr6.simCow.chr6 139361 12 + 602619 ATTAATATTAAT -s simDog_chr6.simDog.chr6 423810 12 - 593897 GCCGATATTGAC -s simRat_chr6.simRat.chr6 129995 12 + 647215 GCAAACAATTAC - -a -s simMouse_chr6.simMouse.chr6 132208 24 + 636262 AATGTTGTATTGGTTCACTCACAA -s Anc0.Anc0refChr1 23433 24 - 62388 AATGTCTTCTTAATCTACTGATAG -s Anc1.Anc1refChr2 102184 24 + 144309 AATGTCTTCTTAATCTACTGATAG -s Anc2.Anc2refChr3 12091 24 + 53186 AATGTCTTCTTAATCTACTGATAG -s mr.mrrefChr0 126560 24 + 130230 AATGTTGTATTGGTTCACTCACAA -s simCow_chr6.simCow.chr6 139374 24 + 602619 AACAACTTTTTAATCTGATAATAG -s simDog_chr6.simDog.chr6 423823 24 - 593897 AATGTCTTCTTAATCTACTGATAG -s simRat_chr6.simRat.chr6 130007 24 + 647215 TATGTTGTATTGGCTTGCTCGCAA - -a -s simMouse_chr6.simMouse.chr6 132232 41 + 636262 GCACATTCTCATCTCCCTGTCAACGATGGAGTTAATGCTGG -s Anc0.Anc0refChr1 23457 16 - 62388 CTCACTTTTCATTTAA------------------------- -s Anc1.Anc1refChr2 102208 16 + 144309 CTCACTTTTCATTTAA------------------------- -s Anc2.Anc2refChr3 12115 16 + 53186 CTCACTTTTCATTTAA------------------------- -s mr.mrrefChr0 126584 16 + 130230 GCACATTCTCATCTCC------------------------- -s simCow_chr6.simCow.chr6 139408 16 + 602619 CTCATCTTTCATTTAA------------------------- -s simDog_chr6.simDog.chr6 423847 16 - 593897 CTCACTTTTCATTTAA------------------------- -s simRat_chr6.simRat.chr6 130031 16 + 647215 ATACATTTTTATCTCC------------------------- - -a -s simMouse_chr6.simMouse.chr6 132273 11 + 636262 AAGCAGAGAGA -s Anc0.Anc0refChr1 23473 11 - 62388 AAGCATAGAGG -s Anc1.Anc1refChr2 102224 11 + 144309 AAGCATAGAGG -s Anc2.Anc2refChr3 12199 11 + 53186 AAGCATAGAGG -s mr.mrrefChr0 126600 11 + 130230 AAGCAGAGAGA -s simCow_chr6.simCow.chr6 139492 10 + 602619 TTGCA-AAATA -s simDog_chr6.simDog.chr6 423960 11 - 593897 AACCGTAGAGG -s simHuman_chr6.simHuman.chr6 126534 11 + 601863 AAGCACAGAGG -s simRat_chr6.simRat.chr6 130047 11 + 647215 AAGCAAAGAGA - -a -s simMouse_chr6.simMouse.chr6 132284 15 + 636262 GGAGTTCAGAATTTT -s Anc0.Anc0refChr1 23486 15 - 62388 GATTTTTGGAATTTT -s Anc1.Anc1refChr2 102237 15 + 144309 GATTTTTGGAATTTT -s Anc2.Anc2refChr3 12212 15 + 53186 GATTTTTGGAATTTT -s mr.mrrefChr0 126611 15 + 130230 GGAGTTCAGAATTTT -s simCow_chr6.simCow.chr6 139504 15 + 602619 GCTTTTTGGTATTTT -s simDog_chr6.simDog.chr6 423973 15 - 593897 AATTTATGTACTTTT -s simHuman_chr6.simHuman.chr6 126547 15 + 601863 GATTTTTGGAATTTT -s simRat_chr6.simRat.chr6 130058 15 + 647215 GGAGTTCAGAATTTT - -a -s simMouse_chr6.simMouse.chr6 132299 58 + 636262 CCCTGCTGCTCTGGAAGTTGAAATAGAAGCAGGTACTTAGTTGGGTAGGACATGTTTA -s Anc0.Anc0refChr1 23505 56 - 62388 CCTGGGCACCCAGGAAGATGAAAAAGATCTTAGGACTTAGGTGAGTAGG--TTGTTTA -s Anc1.Anc1refChr2 102256 56 + 144309 CCTGGGCACCCAGGAAGATGAAAAAGATCTTAGGACTTAGGTGAGTAGG--TTGTTTA -s Anc2.Anc2refChr3 12231 56 + 53186 CCTGGGCAACCAGGAAGATGAAAAAGATCTTAGGACTTAGGTGAGTAGG--TACATTA -s mr.mrrefChr0 126626 58 + 130230 CCCTGCCACTCAGGAAGTTGAAATAGATGCAGGTACTTAGTTGGGTAGGACTTGTTTA -s simCow_chr6.simCow.chr6 139523 49 + 602619 CTGGGCCAACCAGAAAGATGAAAAAGATCTTAGG-------TGAGTGAA--TACCTCA -s simDog_chr6.simDog.chr6 423992 56 - 593897 CCTGCGCAATCAGGAAGATGAAAGAGTTCTTAGTACTTAGGTGAGTAGG--TACACTG -s simHuman_chr6.simHuman.chr6 126566 56 + 601863 CCTAGGCACCCAAGAAAATGAAAAAGATCTTAGGACTAGGGTGAGTAGG--TTGTTAA -s simRat_chr6.simRat.chr6 130073 57 + 647215 CCTTGCCACCCAGGAAGTTGAAATAGATGCATGTACTT-GTTGGGTAGGACTTGTTTA - -a -s simMouse_chr6.simMouse.chr6 132357 65 + 636262 TCAGTATGCAATGGGCCCTTAGTAACAGCCAACTAACACATGCATCTAGTGTTCAATCAATAGTT -s Anc0.Anc0refChr1 23566 65 - 62388 TCAATATACAATGTGTCCTTAGTAACAGCCAGCTAAAGGGTGCATCTACAGTTTAATTTATATTT -s Anc1.Anc1refChr2 102317 65 + 144309 TCAATATACAATGTGTCCTTAGTAACAGCCAGCTAAAGGGTGCATCTACAGTTTAATTTATATTT -s Anc2.Anc2refChr3 12292 65 + 53186 TCAATATACTATGTGTCCTTGCTAACAGCCAGTAAAAGGGTGCATCTACAGTTTAATTTATATGT -s mr.mrrefChr0 126684 65 + 130230 TCAGTATGCAATGTGCCCTTAGTAACAGCCAGCTAACACATGCATCTAGTGTTCAATTAATAGTT -s simCow_chr6.simCow.chr6 139577 65 + 602619 TCAACAAGCTATGTGTCCTTTCTAACAACCAGTGGAAGGGTGCATCTACAGTTCAATTTATTTCT -s simDog_chr6.simDog.chr6 424053 65 - 593897 TCAATATACTATGTGTCCTAGCCAGTAGCCAGTAAAAGGGTGCATCTGGAGTTTAATTAATATGT -s simHuman_chr6.simHuman.chr6 126627 65 + 601863 TCAATATTCAATGTGTTCTTAGTAACAGACAGCTAAAGGGTGCATCTACAGTTTAACCTCACTTT -s simRat_chr6.simRat.chr6 130130 65 + 647215 TCAGTATGGAATGTGCCCTTAGTAACAGCCAGCTAACACATGCATCTAGTGTTCAATTTATAGTT - -a -s simMouse_chr6.simMouse.chr6 132422 8 + 636262 CTCCTATG -s Anc0.Anc0refChr1 23631 8 - 62388 CTCCTATG -s Anc1.Anc1refChr2 102382 8 + 144309 CTCCTATG -s Anc2.Anc2refChr3 12357 8 + 53186 ATCCTATG -s mr.mrrefChr0 126749 8 + 130230 CTCCTATG -s simCow_chr6.simCow.chr6 139642 8 + 602619 GTCCTATg -s simDog_chr6.simDog.chr6 424118 8 - 593897 ATCCTATG -s simHuman_chr6.simHuman.chr6 126694 8 + 601863 CTTCCATG -s simRat_chr6.simRat.chr6 130195 8 + 647215 CTCCTATG - -a -s simMouse_chr6.simMouse.chr6 132430 5 + 636262 CTCAC -s Anc0.Anc0refChr1 23639 5 - 62388 CTGAC -s Anc1.Anc1refChr2 102390 5 + 144309 CTGAC -s Anc2.Anc2refChr3 12369 5 + 53186 CTGAC -s mr.mrrefChr0 126757 5 + 130230 CTCAC -s simDog_chr6.simDog.chr6 424131 5 - 593897 CTGAC -s simHuman_chr6.simHuman.chr6 126702 5 + 601863 CTAAC -s simRat_chr6.simRat.chr6 130203 5 + 647215 TTCAC - -a -s simMouse_chr6.simMouse.chr6 132435 11 + 636262 TTCCCTCCCTA -s Anc0.Anc0refChr1 23644 8 - 62388 ttttcttc--- -s Anc1.Anc1refChr2 102395 11 + 144309 TTTTCTTCCTA -s Anc2.Anc2refChr3 12374 8 + 53186 tttttttt--- -s mr.mrrefChr0 126762 11 + 130230 TTCCCTCCCTA -s simCow_chr6.simCow.chr6 139650 8 + 602619 cctttgtt--- -s simDog_chr6.simDog.chr6 424140 8 - 593897 TTTTTTTT--- -s simHuman_chr6.simHuman.chr6 126707 11 + 601863 TGTACCACCTA -s simRat_chr6.simRat.chr6 130208 11 + 647215 GTTACCCCCTA - -a -s simMouse_chr6.simMouse.chr6 132446 23 + 636262 CATGGAATGGTGGAGGGCCCTTA -s Anc0.Anc0refChr1 23652 8 - 62388 ---------------gaccttta -s Anc1.Anc1refChr2 102406 23 + 144309 TGTGGAATGGTGAAGGACCTTTA -s Anc2.Anc2refChr3 12382 8 + 53186 ---------------gatcttca -s mr.mrrefChr0 126773 23 + 130230 CATGGAATGGTGGAGGGCCTTTA -s simCow_chr6.simCow.chr6 139658 8 + 602619 ---------------gatcttca -s simDog_chr6.simDog.chr6 424148 8 - 593897 ---------------GATCTTCA -s simHuman_chr6.simHuman.chr6 126719 23 + 601863 TGTGGAATGGTGAAGGACACTTG -s simRat_chr6.simRat.chr6 130219 23 + 647215 TATGGAATGGTGTAGGACCTTTG - -a -s simMouse_chr6.simMouse.chr6 132469 2 + 636262 TC -s Anc0.Anc0refChr1 23660 2 - 62388 tc -s Anc1.Anc1refChr2 102429 2 + 144309 TC -s Anc2.Anc2refChr3 12390 2 + 53186 tc -s mr.mrrefChr0 126796 2 + 130230 TC -s simCow_chr6.simCow.chr6 139666 2 + 602619 tc -s simDog_chr6.simDog.chr6 424160 2 - 593897 TC -s simHuman_chr6.simHuman.chr6 126742 2 + 601863 GC -s simRat_chr6.simRat.chr6 130242 2 + 647215 TC - -a -s simMouse_chr6.simMouse.chr6 132471 1 + 636262 T -s Anc0.Anc0refChr1 23664 1 - 62388 t -s Anc1.Anc1refChr2 102433 1 + 144309 T -s Anc2.Anc2refChr3 12394 1 + 53186 t -s mr.mrrefChr0 126798 1 + 130230 T -s simCow_chr6.simCow.chr6 139670 1 + 602619 t -s simDog_chr6.simDog.chr6 424164 1 - 593897 T -s simHuman_chr6.simHuman.chr6 126746 1 + 601863 T -s simRat_chr6.simRat.chr6 130244 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 132472 34 + 636262 GGTGTGTACCAGTTCTCCGGTGAACGGACCAGTC -s Anc0.Anc0refChr1 23665 26 - 62388 ggtgtgtaccaggtgt--------tgtaccagtc -s Anc1.Anc1refChr2 102434 26 + 144309 GGTGTGTACCAGGTGT--------TGTACCAGTC -s Anc2.Anc2refChr3 12399 26 + 53186 agtgcgttccaagtgc--------tataactgac -s mr.mrrefChr0 126799 34 + 130230 GGTGTGTACCAGTTCTCCGGTGTGCGGACCAGTC -s simCow_chr6.simCow.chr6 139682 26 + 602619 agagtgttctaggtgt--------tacaataagc -s simDog_chr6.simDog.chr6 424169 26 - 593897 AGTGCGTTCCAAGTGC--------TATAACTGAC -s simHuman_chr6.simHuman.chr6 126747 26 + 601863 GCTATGGACTGGCTTT--------TGCACTAGTG -s simRat_chr6.simRat.chr6 130245 34 + 647215 GTTGTGGACCAGTTCTCTGGGGTGCAGACCAGTT - -a -s simMouse_chr6.simMouse.chr6 132506 6 + 636262 TTGGTC -s Anc1.Anc1refChr2 102479 6 + 144309 AAGTTC -s mr.mrrefChr0 126846 6 + 130230 TTGCTC -s simHuman_chr6.simHuman.chr6 126792 6 + 601863 AAGTTC -s simRat_chr6.simRat.chr6 130292 6 + 647215 TTGCTC - -a -s simMouse_chr6.simMouse.chr6 132512 16 + 636262 TTCCTGTCCAACGGAT -s Anc0.Anc0refChr1 23707 11 - 62388 --gaagtccagcg--- -s Anc1.Anc1refChr2 102485 16 + 144309 TTGAAGTCCAGCGAGT -s Anc2.Anc2refChr3 12441 11 + 53186 --gaagtacagtg--- -s mr.mrrefChr0 126852 16 + 130230 TTCCTGTCCAACGGAT -s simCow_chr6.simCow.chr6 139728 11 + 602619 --gctgtatggta--- -s simDog_chr6.simDog.chr6 424211 11 - 593897 --GAAGTACAGTG--- -s simHuman_chr6.simHuman.chr6 126800 16 + 601863 TTGAAGTCTTCCGAGT -s simRat_chr6.simRat.chr6 130298 16 + 647215 TTCCTGCCCAACGGAT - -a -s simMouse_chr6.simMouse.chr6 132528 10 + 636262 TCTGCAGATC -s Anc0.Anc0refChr1 23718 6 - 62388 --tg--aatt -s Anc1.Anc1refChr2 102501 8 + 144309 TCTG--AATT -s Anc2.Anc2refChr3 12452 6 + 53186 --tg--agtt -s mr.mrrefChr0 126868 10 + 130230 TCTGCAGATT -s simCow_chr6.simCow.chr6 139739 6 + 602619 --ta--tatt -s simDog_chr6.simDog.chr6 424222 6 - 593897 --TG--AGTT -s simHuman_chr6.simHuman.chr6 392561 8 + 601863 TCTG--AATT -s simRat_chr6.simRat.chr6 130314 10 + 647215 TCTACATATT - -a -s simMouse_chr6.simMouse.chr6 132538 52 + 636262 GGATTGGCCCCTGTGATTCCAGCTTATTGGTAGGTTAGCCTCCCCCAACTCA -s Anc0.Anc0refChr1 23724 52 - 62388 ccattAGCCCCTGTGCTTCCAACTTATTGGTTGGTTAGCCTCCTCCAAATCA -s Anc1.Anc1refChr2 102509 52 + 144309 CCATTAGCCCCTGTGCTTCCAACTTATTGGTTGGTTAGCCTCCTCCAAATCA -s Anc2.Anc2refChr3 12458 52 + 53186 ctcatAACCCCTGTGCTTTCAACTTATCGGTTGATTAGCCTCCTCCAAGTCA -s mr.mrrefChr0 126878 52 + 130230 GCATTGGCCCCTGTGATTCCAACTTATTGGTAGGTTAGCCTCCCCCAAATCA -s simCow_chr6.simCow.chr6 139745 52 + 602619 cacataccccctgggccttcaacttatcggttgataagcctcctcccagctg -s simDog_chr6.simDog.chr6 424228 52 - 593897 CTCATAACCCCTGTGCTTTCAACTAATCTGTTGATTAACCTCCTCCAAGTCA -s simHuman_chr6.simHuman.chr6 392576 52 + 601863 ACATTAGCCCCTGTGCTTCCTACTTATTGGTTGGTAAGCCTCCTCCAAATCA -s simRat_chr6.simRat.chr6 130324 52 + 647215 GCATTGGCCCCTGTGATTCCAACCTATTGGTAAGTCAGCCTCCCCCTAATCA - -a -s simMouse_chr6.simMouse.chr6 132590 71 + 636262 TGATATTCACCCCCATACCCCTTGATGAACAGGCCCACCCTTGTGAAAATACAGTTAGCGCAATACTGAAT -s Anc0.Anc0refChr1 23776 71 - 62388 TGTTATGTATCCCCATAGCCTGTGGTGAACACCCCCACCCTTGTGAAAATACAGTTAGCCCAATGCTAAAT -s Anc1.Anc1refChr2 102561 71 + 144309 TGTTATGTATCCCCATAGCCTGTGGTGAACACCCCCACCCTTGTGAAAATACAGTTAGCCCAATGCTAAAT -s Anc2.Anc2refChr3 12510 71 + 53186 TGTTATGTATCCCCATAGCCTGTGGTGAACACCCCCACCCTTGTGAAAATACAGTTAGCCCAATGCTAAAT -s mr.mrrefChr0 126930 71 + 130230 TGATATGCACCCCCATACCCCTTGATGAACAGGCCCACCCTTGTGAAAATACAGTTAGCCCAATGCTAAAT -s simCow_chr6.simCow.chr6 139797 71 + 602619 tggtaggtgttcccatagcctctggtgaacactcccacccttATGCAAATACAGTTAGCCCAACGCTAAAC -s simDog_chr6.simDog.chr6 424280 71 - 593897 TGTTATGTATCCCCATAGCCTGTGGTAAACACCCACATTTTTGTGAAAATACAGTTAGCCCATTGCTAAAT -s simHuman_chr6.simHuman.chr6 392628 39 + 601863 T--------------------------------CCAACCTTTGTGAGAATACAATTTGCCCAATGCTAAAT -s simRat_chr6.simRat.chr6 130377 71 + 647215 TGGTATGCGCCCCCAGACCCCTTGATGAACAGGCCCACTCTTGTGAAAATACAGTTAGCCCAATGGTAAAT - -a -s simMouse_chr6.simMouse.chr6 132661 2 + 636262 GA -s Anc0.Anc0refChr1 23855 2 - 62388 AC -s Anc1.Anc1refChr2 102640 2 + 144309 AC -s Anc2.Anc2refChr3 12589 2 + 53186 AT -s mr.mrrefChr0 127001 2 + 130230 GA -s simCow_chr6.simCow.chr6 139876 2 + 602619 AT -s simDog_chr6.simDog.chr6 424359 2 - 593897 AT -s simHuman_chr6.simHuman.chr6 126819 2 + 601863 AC -s simRat_chr6.simRat.chr6 130448 2 + 647215 GA - -a -s simMouse_chr6.simMouse.chr6 132663 21 + 636262 AGGCTGTTGCTAGACAAGAGC -s Anc0.Anc0refChr1 23857 21 - 62388 AGCCCAATGCTAAATGAGAGC -s Anc1.Anc1refChr2 102642 21 + 144309 AGCCCAATGCTAAATGAGAGC -s Anc2.Anc2refChr3 12592 21 + 53186 AGCCCAATGCTAAATGGGAAC -s mr.mrrefChr0 127003 21 + 130230 AGGCTATTGCTAGACAAGAGC -s simCow_chr6.simCow.chr6 139879 21 + 602619 AGCCCAATACTAAATGGGATC -s simDog_chr6.simDog.chr6 424362 21 - 593897 AGCTTAATGTTAAATGGGTAT -s simHuman_chr6.simHuman.chr6 126821 21 + 601863 AGCCCAGTGCTCAATGAGAGC -s simRat_chr6.simRat.chr6 130450 21 + 647215 AGGCCAGTGCTAGACAAGAGC - -a -s simMouse_chr6.simMouse.chr6 132684 61 + 636262 GAAAAATGGAATCAAAATCAAGTGCTAGGGTCGGTACATAAAGAAGATCAGTGAGGCCAAA -s Anc0.Anc0refChr1 23895 35 - 62388 ACAAAATGGACTCAAAATTGAGGG------------------------ATGAGA--CGGAA -s Anc1.Anc1refChr2 102680 35 + 144309 ACAAAATGGACTCAAAATTGAGGG------------------------ATGAGA--CGGAA -s Anc2.Anc2refChr3 12630 35 + 53186 ACAAAATGGACTCAAAATTGAGGG------------------------ATAAAA--AGGCA -s mr.mrrefChr0 127041 37 + 130230 GAAAAATGGAATCAAAATCAAGTG------------------------CAGTGAGGCCAAA -s simCow_chr6.simCow.chr6 139917 35 + 602619 ACAAAATAGACTCAAAACTGAGGG------------------------ATAAAT--AAGAA -s simDog_chr6.simDog.chr6 424400 35 - 593897 ACAGAATGGACTCAAAGTTGAGGG------------------------ATAAAA--AGGCA -s simHuman_chr6.simHuman.chr6 126859 35 + 601863 ACAAAATGGACTCAAAATTGAGGG------------------------GTGGGG--CTGAA -s simRat_chr6.simRat.chr6 130488 37 + 647215 GAAAAATGGGATCAAAATCCAGCG------------------------CAGTGAGGCCAAA - -a -s simMouse_chr6.simMouse.chr6 132745 31 + 636262 GAAAGAGGATCTAAGTCCTGGGGGAGTGTGC -s Anc0.Anc0refChr1 23946 31 - 62388 GATAGTGGATTTAAACCCCTGGGAAGTGTAC -s Anc1.Anc1refChr2 102731 31 + 144309 GATAGTGGATTTAAACCCCTGGGAAGTGTAC -s Anc2.Anc2refChr3 12681 31 + 53186 GATAGTGGATTTATACCCCTGGGAAGTGTAC -s mr.mrrefChr0 127078 31 + 130230 GAAAGTGGATCTAAATCCTGGGGAAGTGTGC -s simCow_chr6.simCow.chr6 139968 31 + 602619 AATAGTGAGTTTATACCCCTGGGATGTGTAC -s simDog_chr6.simDog.chr6 424451 31 - 593897 GATGGTGGAATTATACCCCTAGGAAGTGTAC -s simHuman_chr6.simHuman.chr6 126937 31 + 601863 GATAGTGGATTTAAACCTGTGGGAAATGTAC -s simRat_chr6.simRat.chr6 130525 31 + 647215 GAAAGTAGATCTAAATCCTGGGGAAGTGTGC - -a -s simMouse_chr6.simMouse.chr6 132776 20 + 636262 CAATGGGTGTGGTCCCTCTT -s Anc0.Anc0refChr1 23989 19 - 62388 AAAGGG-TGTGGTCCCTCTT -s Anc1.Anc1refChr2 102774 20 + 144309 AAAGGGGTGTGGTCCCTCTT -s Anc2.Anc2refChr3 12724 19 + 53186 AAAGGG-TGTGGTCCATCTT -s mr.mrrefChr0 127109 20 + 130230 AAATGGGTGTGGTCCCTCTT -s simCow_chr6.simCow.chr6 140011 19 + 602619 AAGGGG-TGTGATCCATCTT -s simDog_chr6.simDog.chr6 424494 19 - 593897 AAAGGA-TGTAGTCCATCTT -s simHuman_chr6.simHuman.chr6 126980 20 + 601863 AAAGGTGTGTGGTCCCACTT -s simRat_chr6.simRat.chr6 130556 20 + 647215 AAATGGGTGTGTTCCCTCTT - -a -s simMouse_chr6.simMouse.chr6 132796 78 + 636262 TCAACTCTAACGAACTTGGGTGCATACCTTGGTACACTGTCTGCCTACTTGCTGACCTTGTTATTTATAAGAAGTTTG -s Anc0.Anc0refChr1 24021 58 - 62388 TCAACTCTAATGAAGCAGGGTGAATACACTG-------GTCTGCTGACTTGCTGACTTCATTATT------------- -s Anc1.Anc1refChr2 102807 58 + 144309 TCAACTCTAATGAAGCAGGGTGAATACACTG-------GTCTGCTGACTTGCTGACTTCATTATT------------- -s Anc2.Anc2refChr3 12757 58 + 53186 TCAGATCCACTGAAGCAGGGTGAATACACTG-------GTCTACTGACTTGCTGACTTCATTATT------------- -s mr.mrrefChr0 127142 71 + 130230 TCAACTCTAATGAACTAGGATGCATACCTTG-------GTCTGCTTACTTGCTGACTTTGTTATTTATAAGAAGTTTG -s simCow_chr6.simCow.chr6 140044 58 + 602619 TCAGATCCACTGAAGCAGAGAGAATTCACTG-------GTCTACTGACTCACTAACATCATTATT------------- -s simDog_chr6.simDog.chr6 424527 48 - 593897 TC----------AAGCAGGATGGATACACTG-------GTCTACTTACTTGCTGATTTTATTATT------------- -s simHuman_chr6.simHuman.chr6 127069 58 + 601863 TCTACTCTAATGAAAAACGGTGAATACACTA-------GATTGCTGACTTGCTGACTTCATTTTT------------- -s simRat_chr6.simRat.chr6 130595 65 + 647215 TCAACTCTAATAAACTAGGATGATGAC-------------CTGCTGACCTGCAGACTTTGTTACTAATAAGAGGTTTG - -a -s simMouse_chr6.simMouse.chr6 132874 77 + 636262 ACTGGCCAGCTTTTCATTATCAGTTCCATTGTCCGAGAGAGATATTTGTGATGGGATATGAATAGTGCAGTGGATGT -s Anc0.Anc0refChr1 24079 37 - 62388 ---------------------------------------AGAT-TTGTGGCTGGGATATGATTAATGCAATTGATAT -s Anc1.Anc1refChr2 102865 37 + 144309 ---------------------------------------AGAT-TTGTGGCTGGGATATGATTAATGCAATTGATAT -s Anc2.Anc2refChr3 12815 37 + 53186 ---------------------------------------AGAG-TTGTGGCTGGGATATGATTAATGCAATTGATAT -s mr.mrrefChr0 127213 77 + 130230 ACTGGCCAGCTTTTCATTATCAGTTCCATTGTCCGAGAGAGATATTTTGGCTGGGATATGAATAGTGCAGTGGATGT -s simCow_chr6.simCow.chr6 140102 36 + 602619 ---------------------------------------AGA--TTGCAGCCAGGATGTGAATAATGAAATCGATTT -s simDog_chr6.simDog.chr6 424575 37 - 593897 ---------------------------------------AGAG-TTGTGGCTGGGATATGATTCATGCAGTTGATAT -s simHuman_chr6.simHuman.chr6 127127 37 + 601863 ---------------------------------------AGAT-TTGTGGCTGGGAAATGTTTAATGCAATTGATAA -s simRat_chr6.simRat.chr6 130661 77 + 647215 ATTGGCCAGCTTTTCATTATCAGATCTATTGTCCAAGAGAGATATTTTGACTGGGATATGAATAGTGCAGTGGATGT - -a -s simMouse_chr6.simMouse.chr6 132951 44 + 636262 TTAGGTATAAGAAGACTCTTGTTGGCCCACTGGCAAGTCGTCAA -s Anc0.Anc0refChr1 24117 44 - 62388 TTAGGTGTACCATAAATCCAGTTGTTCCATTTACAATTCGTCTA -s Anc1.Anc1refChr2 102903 44 + 144309 TTAGGTGTACCATAAATCCAGTTGTTCCATTTACAATTCGTCTA -s Anc2.Anc2refChr3 12853 44 + 53186 TTAGGCGTACCATAAATCCAGTTGTTCCATTTACAATACGTCTA -s mr.mrrefChr0 127291 44 + 130230 TTAGGTATAAGAAGACTTTTATTGGCCCACTGGCAAGTCGTCAA -s simCow_chr6.simCow.chr6 140139 44 + 602619 TTAGGCGTACCATAAGTAGAGTTGGTCCATTTACAATATGTCTA -s simDog_chr6.simDog.chr6 424613 44 - 593897 TTAGGCATACCATAGACCCAATTGTTTCATTTAAAATACGTCTA -s simHuman_chr6.simHuman.chr6 127165 44 + 601863 TTAGATGCACCATAAATCCAGTTGATCCATTTACAACTCATCTA -s simRat_chr6.simRat.chr6 130739 44 + 647215 TTAGATATAAGAAGACTTTTATTGGCCCCCTGGCAAGTCATCAA - -a -s simMouse_chr6.simMouse.chr6 132995 20 + 636262 AGTGTATAAATTATCTTGAT -s Anc0.Anc0refChr1 24197 20 - 62388 AGTGTATAAGCTATCTCTAT -s Anc1.Anc1refChr2 102983 20 + 144309 AGTGTATAAGCTATCTCTAT -s Anc2.Anc2refChr3 12933 20 + 53186 AGTGTAAAGGCTATCTCTAT -s mr.mrrefChr0 127349 20 + 130230 AGTGTATAAACTATCTTGAT -s simCow_chr6.simCow.chr6 140219 20 + 602619 AGTGTAAAGGCTATCTATAT -s simDog_chr6.simDog.chr6 424693 20 - 593897 AGTGTAAAGGCTACCTCTAT -s simHuman_chr6.simHuman.chr6 127251 19 + 601863 ATCGAAT-AGCTATCTGTAT -s simRat_chr6.simRat.chr6 130797 20 + 647215 AGTGTACAAACTATCTTGAT - -a -s simMouse_chr6.simMouse.chr6 133015 51 + 636262 ACCTTATAATGGGCTTATTTGGCAGTTACAAGTCTTTCTAAATTTCACCTC -s Anc0.Anc0refChr1 24218 50 - 62388 ATCTTATGCTGGGCTTATGGCGCAGTTGTGAGCCTTTCTGACTTTC-CTTC -s Anc1.Anc1refChr2 103004 51 + 144309 ATCTTATGCTGGGCTTATGGCGCAGTTGTGAGCCTTTCTGACTTTCACTTC -s Anc2.Anc2refChr3 12954 50 + 53186 ATCTTATGCTGGGCTTATGGCGCAGTTGTGAGCCTTTCTGACTGTC-CTTC -s mr.mrrefChr0 127370 51 + 130230 ACCTTATAATGGGCTTATTTGGCAGTTACAAGTCTTTCTAAATTTCACCCC -s simCow_chr6.simCow.chr6 140240 49 + 602619 ATCTCATGCTGGGCCTATGGC-CAGTTGCAAGCCTTTCTGCCTGTC-CCTC -s simDog_chr6.simDog.chr6 424714 45 - 593897 GTCTT-TGGTGAGCTAATGGCGTAGTTGTGAGCCTTTCTGACT-----TTC -s simHuman_chr6.simHuman.chr6 127271 42 + 601863 ATCTTGTGCTGGGCTTATGGTGCGG---------TTTCTGACTTTCACTTC -s simRat_chr6.simRat.chr6 130818 51 + 647215 ACCTTATATTGGACTTATTTGGCAGCTACAAGTCTTTCTAAATTTCACCCT - -a -s simMouse_chr6.simMouse.chr6 133066 1 + 636262 A -s Anc0.Anc0refChr1 24269 1 - 62388 C -s Anc1.Anc1refChr2 103056 1 + 144309 C -s Anc2.Anc2refChr3 13005 1 + 53186 C -s mr.mrrefChr0 127421 1 + 130230 A -s simCow_chr6.simCow.chr6 140290 1 + 602619 C -s simDog_chr6.simDog.chr6 424760 1 - 593897 C -s simHuman_chr6.simHuman.chr6 127314 1 + 601863 C -s simRat_chr6.simRat.chr6 130869 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 133067 25 + 636262 TCTCTAACTCTCATTTGTCTAGCAG -s Anc0.Anc0refChr1 24270 25 - 62388 TCCCTAACTTTCCTTTTTAGATCAC -s Anc1.Anc1refChr2 103057 25 + 144309 TCCCTAACTTTCCTTTTTAGATCAC -s Anc2.Anc2refChr3 13006 25 + 53186 TCCCTAACCTTCCTTTTTAGATCAC -s mr.mrrefChr0 127422 25 + 130230 TCTCTAACTTTCATTTTTATAGCAG -s simCow_chr6.simCow.chr6 140291 25 + 602619 ACCCTAACCTTCCTTTTTAGATCAC -s simDog_chr6.simDog.chr6 424761 25 - 593897 TCCATAACCTTCGTTTTTAGATCAC -s simHuman_chr6.simHuman.chr6 127315 25 + 601863 TCCCTAACTTTCCTTTTTAGATCAC -s simRat_chr6.simRat.chr6 130871 25 + 647215 TCTCTAACTTTCCTTTTTATAACAG - -a -s simMouse_chr6.simMouse.chr6 133092 7 + 636262 TATATCA -s Anc0.Anc0refChr1 24295 7 - 62388 TATGTCA -s Anc1.Anc1refChr2 103082 7 + 144309 TATGTCA -s Anc2.Anc2refChr3 13031 7 + 53186 TATGTCA -s mr.mrrefChr0 127447 7 + 130230 TATATCA -s simCow_chr6.simCow.chr6 140317 7 + 602619 TAGGTCA -s simDog_chr6.simDog.chr6 424786 7 - 593897 TATGTCA -s simHuman_chr6.simHuman.chr6 127340 7 + 601863 TATGTCA -s simRat_chr6.simRat.chr6 130896 7 + 647215 TATATCA - -a -s simMouse_chr6.simMouse.chr6 133099 4 + 636262 AAGG -s Anc0.Anc0refChr1 24304 4 - 62388 AAAG -s Anc1.Anc1refChr2 103091 4 + 144309 AAAG -s Anc2.Anc2refChr3 13040 4 + 53186 AAAG -s mr.mrrefChr0 127454 4 + 130230 AAGG -s simCow_chr6.simCow.chr6 140326 4 + 602619 AAAG -s simDog_chr6.simDog.chr6 424795 4 - 593897 TAAG -s simHuman_chr6.simHuman.chr6 127349 4 + 601863 AAAA -s simRat_chr6.simRat.chr6 130903 4 + 647215 AAGG - -a -s simMouse_chr6.simMouse.chr6 133103 4 + 636262 TATA -s Anc0.Anc0refChr1 24308 4 - 62388 TATA -s Anc1.Anc1refChr2 103095 4 + 144309 TATA -s Anc2.Anc2refChr3 13047 4 + 53186 TCTC -s mr.mrrefChr0 127458 4 + 130230 TATA -s simCow_chr6.simCow.chr6 140333 4 + 602619 ATTC -s simDog_chr6.simDog.chr6 424802 4 - 593897 TCTC -s simHuman_chr6.simHuman.chr6 127353 4 + 601863 TATA -s simRat_chr6.simRat.chr6 130907 4 + 647215 TATA - -a -s simMouse_chr6.simMouse.chr6 133107 22 + 636262 CTTCCACTGTACAACTCCTTCA -s Anc0.Anc0refChr1 24312 22 - 62388 CTCCCACTATACACCTCCTTCA -s Anc1.Anc1refChr2 103099 22 + 144309 CTCCCACTATACACCTCCTTCA -s Anc2.Anc2refChr3 13051 22 + 53186 CTCCCACTATACACCACCTTCC -s mr.mrrefChr0 127462 22 + 130230 CTTCCACTGTACACCTCCTTCA -s simCow_chr6.simCow.chr6 140340 22 + 602619 TTCCCACTATACACCACCTTCC -s simDog_chr6.simDog.chr6 424806 22 - 593897 CTCCCATTAGATACCACCTTTC -s simHuman_chr6.simHuman.chr6 127357 22 + 601863 CTCCCACTATACACCTTTCTCA -s simRat_chr6.simRat.chr6 130911 22 + 647215 CATCCACTGTACACCTCCTTCA - -a -s simMouse_chr6.simMouse.chr6 133129 156 + 636262 TCAACAACAGGACACTTTGAATACTTCTCTTACTTTCCTTTTTATAACAGTGAATCAAAGGCATACTTCCACTGTACACCTCCACCTCCTTCACCAATAAGAGGACACTATGAATACTTCTCTTGGCCCTAGCTAACCAGGCTAATATACTCTGGG -s Anc0.Anc0refChr1 24336 33 - 62388 TAAACAAT---------------------------------------------------------------------------------------------GGGAC------------------------------CCATGATGACACATCTTGGG -s Anc1.Anc1refChr2 103123 33 + 144309 TAAACAAT---------------------------------------------------------------------------------------------GGGAC------------------------------CCATGATGACACATCTTGGG -s Anc2.Anc2refChr3 13075 33 + 53186 TAAACAAT---------------------------------------------------------------------------------------------GGGAT------------------------------CCATCATGACACATCTTGTG -s mr.mrrefChr0 127484 63 + 130230 TCAACAAC---------------------------------------------------------------------------------------------AAGACACTATGAATACTTCTCTTGGTCCTAACTAACCAGGCTAATATACTCTGGG -s simCow_chr6.simCow.chr6 140364 31 + 602619 TAAACA-----------------------------------------------------------------------------------------------GGGAT------------------------------CTATCAGGACACATCTCATG -s simDog_chr6.simDog.chr6 424830 28 - 593897 T-AACAAT---------------------------------------------------------------------------------------------GG----------------------------------CATCATAACAAATCTTGTG -s simHuman_chr6.simHuman.chr6 127381 30 + 601863 TAAAAAAT---------------------------------------------------------------------------------------------GGGAC------------------------------CCACGATGACACA---TCGA -s simRat_chr6.simRat.chr6 130933 63 + 647215 TCAACAGC---------------------------------------------------------------------------------------------AAGACGCTATGAATACTTCTCTTGGTCCTAACTGACCAGGCTAATATACTCTGGG - -a -s simMouse_chr6.simMouse.chr6 133285 19 + 636262 TCCTAACCAGCCAGGCTCT -s Anc0.Anc0refChr1 24369 19 - 62388 TTCTAACTGGATAGGCTCT -s Anc1.Anc1refChr2 103156 19 + 144309 TTCTAACTGGATAGGCTCT -s Anc2.Anc2refChr3 13111 19 + 53186 TTCTAACTGGATAGGCTCT -s mr.mrrefChr0 127547 19 + 130230 TCCTAACCAGCCAGGCTCT -s simCow_chr6.simCow.chr6 140398 19 + 602619 CTCTAGCTGGGTTGGCGTT -s simDog_chr6.simDog.chr6 424861 19 - 593897 TTCTAACTCGACAGGTTGT -s simHuman_chr6.simHuman.chr6 127411 19 + 601863 TTCTAACTGGTTAGACCCT -s simRat_chr6.simRat.chr6 130996 19 + 647215 TCCTAACCAGCTCAGCTCT - -a -s simMouse_chr6.simMouse.chr6 133304 12 + 636262 ATCTTTGAGTGT -s Anc0.Anc0refChr1 24389 12 - 62388 ATCTCTGAGTGT -s Anc1.Anc1refChr2 103176 12 + 144309 ATCTCTGAGTGT -s Anc2.Anc2refChr3 13131 12 + 53186 ATCTCTGAGTGT -s mr.mrrefChr0 127566 12 + 130230 ATCTTTGAGTGT -s simCow_chr6.simCow.chr6 140418 12 + 602619 TTCTCTGATTGT -s simDog_chr6.simDog.chr6 424881 12 - 593897 ATCTCAGAGTGT -s simHuman_chr6.simHuman.chr6 127431 12 + 601863 ATCTCTAAGTGT -s simRat_chr6.simRat.chr6 131015 12 + 647215 ATTCTTGAGTGT - -a -s simMouse_chr6.simMouse.chr6 133316 105 + 636262 CATGGGCATGAGATTTCCCTTAATTCAAAGATTGCTTAACAGAGTATCAGAATATGCTCATGACTCCATACAATTTTAATCTTAGTCAAGGCAATGCCTTAGTAA -s Anc0.Anc0refChr1 24401 105 - 62388 CATGGTGGCTAGGATTCCCTTACTTGAAAGAATGTTTAGCAGAGTATCAAAATGGTTTCATAACTATATATAATTTCAGTCTTAATCAAGGCCATGCCTTAGTAA -s Anc1.Anc1refChr2 103188 105 + 144309 CATGGTGGCTAGGATTCCCTTACTTGAAAGAATGTTTAGCAGAGTATCAAAATGGTTTCATAACTATATATAATTTCAGTCTTAATCAAGGCCATGCCTTAGTAA -s Anc2.Anc2refChr3 13143 105 + 53186 CATGGTGGCTAGGATTTCCTTACTTGAAAGAATGTTTAGCAGAGTATCTAAATGGTTTCATAACTATATATGATTTCAGTCTTAATCAAGGCCATGCCTTAGTAA -s mr.mrrefChr0 127578 105 + 130230 CATGGGCATGAGGTTTCCCTTAATTGAAAGATTGATTAACAGAGTATCAGAATAGGTTCATGACTCCATACAATTTTAATCTTAGTCAAGGCCATGCCTTAGTAA -s simCow_chr6.simCow.chr6 140430 104 + 602619 TGTGGTG-CTAGGATTTCTTTGCCTTAATGAATGTTTAGCAGAGTTTCTAAATGGTTTCACAACTATATGTGATTTCAGGCTTATTCAAGCCCATGCCTTAGTGA -s simDog_chr6.simDog.chr6 424893 105 - 593897 CATGGTGGCTAGGATCTCCTGACTTGAAAGAATGATTAACAGAGTATCTGAATGGTTTCATAACTTTATACGATTTCAGTCTTAATCAAGGCCAAGCCTTAGTAA -s simHuman_chr6.simHuman.chr6 127446 52 + 601863 CAAGG-----------CCCT----------AGTATTTAGTATATCCCTAAAATTGTTGCAACCCCAAGTATAA-------------------------------- -s simRat_chr6.simRat.chr6 131027 105 + 647215 CATGGGCATGTGGTTTCCCTTAATTGAAAGATTGATTAACAGAGTGTCGGAATAGGTTCATGACTCCATACAACTCTAATCTTAGTTAAGGCCATGTCTTAGTAA - -a -s simMouse_chr6.simMouse.chr6 133421 18 + 636262 TGTTAACCTACTTATCAA -s Anc0.Anc0refChr1 24527 18 - 62388 TGGTACCCTGCCTAGCAG -s Anc1.Anc1refChr2 103314 18 + 144309 TGGTACCCTGCCTAGCAG -s Anc2.Anc2refChr3 13269 18 + 53186 TGGTACCCTGCCTAGCAG -s mr.mrrefChr0 127704 18 + 130230 TGTTAACCTACCTAGCAG -s simCow_chr6.simCow.chr6 140563 18 + 602619 GTGCTCCCTGCCCAGTAG -s simDog_chr6.simDog.chr6 425019 18 - 593897 TGGTACCCTGCCTAGCAG -s simHuman_chr6.simHuman.chr6 127498 7 + 601863 -----------CTCCTAG -s simRat_chr6.simRat.chr6 131153 18 + 647215 TGTTGAGCTACCTAGTAG - -a -s simMouse_chr6.simMouse.chr6 133439 8 + 636262 TACTTAGG -s Anc0.Anc0refChr1 24545 8 - 62388 TACTTCTG -s Anc1.Anc1refChr2 103332 8 + 144309 TACTTCTG -s Anc2.Anc2refChr3 13289 8 + 53186 TACCTCTG -s mr.mrrefChr0 127722 8 + 130230 TACTTAGG -s simCow_chr6.simCow.chr6 140583 8 + 602619 TAATTCTT -s simDog_chr6.simDog.chr6 425039 8 - 593897 TACCTCTG -s simHuman_chr6.simHuman.chr6 127505 8 + 601863 TGATTCTG -s simRat_chr6.simRat.chr6 131171 8 + 647215 TACTTAGG - -a -s simMouse_chr6.simMouse.chr6 133447 9 + 636262 AACGGGAAG -s Anc0.Anc0refChr1 24553 9 - 62388 AATGGGAAA -s Anc1.Anc1refChr2 103340 9 + 144309 AATGGGAAA -s Anc2.Anc2refChr3 13298 9 + 53186 GATTGGAAA -s mr.mrrefChr0 127730 9 + 130230 AATGGGAAA -s simCow_chr6.simCow.chr6 140592 9 + 602619 GATCGGGGC -s simDog_chr6.simDog.chr6 425048 9 - 593897 GATTAGAAA -s simHuman_chr6.simHuman.chr6 127513 9 + 601863 AGTGGAAAA -s simRat_chr6.simRat.chr6 131179 9 + 647215 AATGGGAAA - -a -s simMouse_chr6.simMouse.chr6 133456 8 + 636262 AACCTTAA -s Anc0.Anc0refChr1 24563 8 - 62388 AATGTTTA -s Anc1.Anc1refChr2 103350 8 + 144309 AATGTTTA -s Anc2.Anc2refChr3 13308 8 + 53186 ACTGTTTA -s mr.mrrefChr0 127739 8 + 130230 AACCTTAA -s simCow_chr6.simCow.chr6 140602 8 + 602619 GCTGTTGA -s simDog_chr6.simDog.chr6 425058 8 - 593897 ACTGTTTA -s simHuman_chr6.simHuman.chr6 127523 8 + 601863 AATGTTTC -s simRat_chr6.simRat.chr6 131188 8 + 647215 AATGATAA - -a -s simMouse_chr6.simMouse.chr6 133464 11 + 636262 AGAACTCCTAG -s Anc0.Anc0refChr1 24571 11 - 62388 GGAACTCTCAG -s Anc1.Anc1refChr2 103358 11 + 144309 GGAACTCTCAG -s Anc2.Anc2refChr3 13316 11 + 53186 GGAACTCTCAG -s mr.mrrefChr0 127747 11 + 130230 GGAACTCTCAG -s simCow_chr6.simCow.chr6 140610 11 + 602619 GAGACTCTCAG -s simDog_chr6.simDog.chr6 425066 11 - 593897 GGAGCCATCAG -s simHuman_chr6.simHuman.chr6 127531 11 + 601863 GGAACTCTCAG -s simRat_chr6.simRat.chr6 131199 11 + 647215 GTAATTCTCGG - -a -s simMouse_chr6.simMouse.chr6 133475 68 + 636262 TGATTATTGGTAATCCTCAAACTGTACATTTTGGATCCACTTGGGATAAATTATTCATGTCACCAGAT -s Anc0.Anc0refChr1 24582 44 - 62388 TGATTATTGGTAATTGCCGAACTGTACATTTTACAACCACCT-A-----------------------T -s Anc1.Anc1refChr2 103369 67 + 144309 TGATTATTGGTAATTGCCGAACTGTACATTTTACAACCACCT-AGATAAATTCTCAGCATCACCAGAT -s Anc2.Anc2refChr3 13327 44 + 53186 TGACTATGGGTAATTGCCGAACTGTACATTTTACAACCACAT-A-----------------------T -s mr.mrrefChr0 127758 68 + 130230 TGATAATTGGTAATTCTCAAACTGTACATTTTAGATCCACTTGGGATAAATTATTCATGTCACCAGAT -s simCow_chr6.simCow.chr6 140621 43 + 602619 TGACTATGGGTAATTGC-GAACTGTACATTTTGTACTGCCAG-A-----------------------T -s simDog_chr6.simDog.chr6 425077 44 - 593897 TGACAATGGGTGATTGACGAACTATACATTTAACCACCATAT-A-----------------------T -s simHuman_chr6.simHuman.chr6 127542 67 + 601863 TGATTATTGGTAACTGCAGAACTGTACATTTTAAAACTACCT-AGATAAATTCTCAGCATCACCCGAT -s simRat_chr6.simRat.chr6 131216 67 + 647215 TGATAATTTGTAATTCTCAGACTGTACATTTTAAATACACTCTGGACAAATTCTTCATGG-ATCAGAT - -a -s simMouse_chr6.simMouse.chr6 133543 34 + 636262 TAGTAATGTTTTTTTGGTCTGGCACTCAGGACAT -s Anc0.Anc0refChr1 24627 34 - 62388 TGGTAATGTCTCTTTGGTCTGGCCCTGAGGACAA -s Anc1.Anc1refChr2 103437 34 + 144309 TGGTAATGTCTCTTTGGTCTGGCCCTGAGGACAA -s Anc2.Anc2refChr3 13372 34 + 53186 TGGTAATGTCGCTTTGGTCTGGCCCTGAGGGCAA -s mr.mrrefChr0 127826 34 + 130230 TAGTAATGTTTTTTTGGTCTGGCACTCAGGACAT -s simCow_chr6.simCow.chr6 140665 32 + 602619 TGGTAATGTCATTCTGGT--GGCCCTCAGGGCAA -s simDog_chr6.simDog.chr6 425122 33 - 593897 TGGTAATGTTGCCTTAGTCTAGCCCTGAGGGCA- -s simHuman_chr6.simHuman.chr6 127610 34 + 601863 TGGCAATGTCTATTTGGTCTGGCCATTAGGACAA -s simRat_chr6.simRat.chr6 131283 34 + 647215 TAGTGATGTTTTTTTGGTCTGGCACTCAGGACAC - -a -s simMouse_chr6.simMouse.chr6 133577 12 + 636262 GTCAGGCATAAT -s Anc0.Anc0refChr1 24661 4 - 62388 CA--------AT -s Anc1.Anc1refChr2 103471 12 + 144309 CACAGCCATAAT -s Anc2.Anc2refChr3 13406 4 + 53186 CA--------AG -s mr.mrrefChr0 127860 12 + 130230 GTCAGGCATAAT -s simCow_chr6.simCow.chr6 140705 4 + 602619 CA--------AC -s simDog_chr6.simDog.chr6 425155 4 - 593897 CA--------AG -s simHuman_chr6.simHuman.chr6 127644 12 + 601863 CACAGCCATAAT -s simRat_chr6.simRat.chr6 131317 12 + 647215 TTCAGGTATAAT - -a -s simMouse_chr6.simMouse.chr6 133589 34 + 636262 ATCTGGAGTCTTAGCTGGAGTCTGGATATGCATA -s Anc0.Anc0refChr1 24665 22 - 62388 ATCTTAAGTCTT------------GATATGCCTC -s Anc1.Anc1refChr2 103483 22 + 144309 ATCTTAAGTCTT------------GATATGCCTC -s Anc2.Anc2refChr3 13410 22 + 53186 ATCTTAAGTCTT------------GATATGCCTC -s mr.mrrefChr0 127872 22 + 130230 ATCTGGAGTCTT------------GATATGCATA -s simCow_chr6.simCow.chr6 140709 22 + 602619 AGCTTAAGTCTT------------GATATGCCTT -s simDog_chr6.simDog.chr6 425159 22 - 593897 ATCCTGAATCTT------------AATATACTTC -s simHuman_chr6.simHuman.chr6 127665 22 + 601863 ATCTTAAGTCTG------------GATATGCCTC -s simRat_chr6.simRat.chr6 131329 22 + 647215 ATCTGGAGCCTT------------GATATGCATT - -a -s simMouse_chr6.simMouse.chr6 133623 30 + 636262 AGAGTAGCCAGCATCGGAGTACTAAGTGGG -s Anc0.Anc0refChr1 24687 29 - 62388 AGAGGTACCATCATC-TAATATTAAGTGGA -s Anc1.Anc1refChr2 103505 29 + 144309 AGAGGTACCATCATC-TAATATTAAGTGGA -s Anc2.Anc2refChr3 13432 29 + 53186 AGAGGTACCATCATC-TAATATTAAGTGGA -s mr.mrrefChr0 127894 30 + 130230 AGAGTAACCAGCATCGGAGTACTAAGTGGG -s simCow_chr6.simCow.chr6 140731 29 + 602619 AGAGATACCATCATC-TACTGTTAAGTAGA -s simDog_chr6.simDog.chr6 425181 29 - 593897 AGAGGTACCATCAGC-CAATATTAAGTGGA -s simHuman_chr6.simHuman.chr6 127688 28 + 601863 AGGGACACTATCATC-TAATA-TAAGGGCA -s simRat_chr6.simRat.chr6 131351 28 + 647215 TGAGAAATC--CGTTGGAGTACCAAGTTGG - -a -s simMouse_chr6.simMouse.chr6 133653 4 + 636262 TTTT -s Anc0.Anc0refChr1 37354 4 + 62388 TGAA -s Anc1.Anc1refChr2 40457 4 - 144309 TGAA -s Anc2.Anc2refChr3 39407 4 - 53186 TGAA -s mr.mrrefChr0 127924 4 + 130230 TTTT -s simCow_chr6.simCow.chr6 461535 4 - 602619 TGAA -s simDog_chr6.simDog.chr6 168375 4 + 593897 TGAA -s simHuman_chr6.simHuman.chr6 473836 4 - 601863 TAGG -s simRat_chr6.simRat.chr6 131379 4 + 647215 ATTT - -a -s simMouse_chr6.simMouse.chr6 133657 30 + 636262 TTAGGAGACACTATACATGGTCAAGAGATA -s Anc0.Anc0refChr1 37359 30 + 62388 GTAGAAGCCACTATCCAAAGTCAAGGGAGC -s Anc1.Anc1refChr2 40462 30 - 144309 GTAGAAGCCACTATCCAAAGTCAAGGGAGC -s Anc2.Anc2refChr3 39412 30 - 53186 GTAGAAGCCACTATCCAAAGTCAAGGGAGC -s mr.mrrefChr0 127928 30 + 130230 TTAGGAGACACTATACATGGTCAAGAGAGA -s simCow_chr6.simCow.chr6 461540 30 - 602619 GTAGAAGTCACTATCCAAAGTCAAGGGAGC -s simDog_chr6.simDog.chr6 168380 30 + 593897 GTAGAAGCCACTATCCAAAGTCAAGGGAGC -s simHuman_chr6.simHuman.chr6 473841 30 - 601863 CCAGAAGCCACTATCCAAAGTGAAGGGAGC -s simRat_chr6.simRat.chr6 131383 30 + 647215 TTAGGAGACACTATACAGGGTCAAGAGAGA - -a -s simMouse_chr6.simMouse.chr6 133687 104 + 636262 TATTATAGACTGTAGCTTTACATGAACCTGTCAACAGCTTAACTATCAATTAGTTACTACCAGTGCTCACAACTGTCAAATTCTTACTGGATAATGGCCATCAT -s Anc0.Anc0refChr1 37393 104 + 62388 TATTACATATTATGGCTTTGCATAAACCTAACAATAGCATAACTATCAATCAATCCCTGTCAGAGTTCAGAGCTGTCATGTTCTTAATGGATCACTGCCATCTT -s Anc1.Anc1refChr2 40496 104 - 144309 TATTACATATTATGGCTTTGCATAAACCTAACAATAGCATAACTATCAATCAATCCCTGTCAGAGTTCAGAGCTGTCATGTTCTTAATGGATCACTGCCATCTT -s Anc2.Anc2refChr3 39446 104 - 53186 TATTACATATTATGGCTTTGCATAAACCTAACAATAGCATAACAATCAATCAATCCCTGTCAGAGTTCAGGGCGTTCATGTTCTTAATAGATCACTGTGATCTT -s mr.mrrefChr0 127962 104 + 130230 TATTACAGACTGTGGCTTTGCATGAACCTGTCAACAGCTTAACTATCAATCAGTTCCTACCAGTGCTCACAACTGTCAAATTCTTACTGGATAATGGCCATCAT -s simCow_chr6.simCow.chr6 461574 104 - 602619 TGTTACTTATCATGGCTTTGCATAAACCTAAAAATAGCATAAAAATCAATCAATCCCTGTCAGTGTTCAGAGCCTTCATTCCCTTGATAGATCACTGTTACCTC -s simDog_chr6.simDog.chr6 168414 104 + 593897 TATTACATATTTAGTATTAGCATGAACCTAACAATAGCCTCACAATTAATCAATCCCTGTCAGAGTTCAGGGCGTTCATGTTCTTAATAGATGACTGTGATCTT -s simHuman_chr6.simHuman.chr6 473875 97 - 601863 TATTACGTATTATGGCTTTGTGTAAACCTTACAATAGCATAATTATCGATCAATGCCCGTCAG-------AGCTGTCATGTACTTAATGGTTCGCAGCCATCTT -s simRat_chr6.simRat.chr6 131417 104 + 647215 TATTTCAGACTGTGGCTTTGCATGAACCTGTCAACAGCTTAACAATCAATCAGTTCCTACCAGTGCTCACAACTGTCAAATTCTTACTGGATAATGGCCATCAT - -a -s simMouse_chr6.simMouse.chr6 133791 14 + 636262 ATGAGAGAGCATAT -s Anc0.Anc0refChr1 37498 14 + 62388 ATAAGAGAGAAAAT -s Anc1.Anc1refChr2 40601 14 - 144309 ATAAGAGAGAAAAT -s Anc2.Anc2refChr3 39551 14 - 53186 TTAAGAGGGAAAAT -s mr.mrrefChr0 128066 14 + 130230 ATAAGAGAGCATAT -s simCow_chr6.simCow.chr6 461679 4 - 602619 TTAA---------- -s simDog_chr6.simDog.chr6 168519 14 + 593897 TCAGGAGGGAAAAT -s simHuman_chr6.simHuman.chr6 473973 14 - 601863 ATAAGAGAGAAGAT -s simRat_chr6.simRat.chr6 131521 14 + 647215 ATAAGAGTGCATGT - -a -s simMouse_chr6.simMouse.chr6 133805 51 + 636262 AGCCAAAATGTTTTAAAACTTTCTTATTCACACCATGGACCTTGGACATTA -s Anc0.Anc0refChr1 37512 51 + 62388 CTCCCAAGTTTTTTAAAATTTTCATTTTTGCACCACTGAGATTGAACATTA -s Anc1.Anc1refChr2 40615 51 - 144309 CTCCCAAGTTTTTTAAAATTTTCATTTTTGCACCACTGAGATTGAACATTA -s Anc2.Anc2refChr3 39565 51 - 53186 CTCCCAAGTTCTTTAGAATTTTCATTTTTGCACCACTGAGATTGAACATCA -s mr.mrrefChr0 128080 51 + 130230 AGCCCAAATGTTTTAAAACTTTCTTATTCACACCATGGACATTGAACATTA -s simCow_chr6.simCow.chr6 461683 50 - 602619 -CCCCAATTTCTTTATAATTTTCATTTTTACATCACTAACATTTAACATCA -s simDog_chr6.simDog.chr6 168534 50 + 593897 CTTCCAAGTTCTTTAGAACTTTCATTATCG-ACCACTGAGATTGAATATCA -s simHuman_chr6.simHuman.chr6 473987 51 - 601863 CACCCAAGTCTTTTAAAATTTTCATCTTTGCACCAATGATATTGAACATTA -s simRat_chr6.simRat.chr6 131535 51 + 647215 AGCCCAAATGTTTTAAAACTTTCCCATTCACACCATGGCCATTGAACATTA - -a -s simMouse_chr6.simMouse.chr6 133856 31 + 636262 GATGATAAATGGGTATACAATCTTGTATAAT -s Anc0.Anc0refChr1 37563 31 + 62388 GATGATAAACGGAAATACAATCTTGTGTACT -s Anc1.Anc1refChr2 40666 31 - 144309 GATGATAAACGGAAATACAATCTTGTGTACT -s Anc2.Anc2refChr3 39616 31 - 53186 GATGACAAACGTAAATACAATCTAGTGTACT -s mr.mrrefChr0 128131 31 + 130230 GATGATAAATGGGAATACAATCTTGTATACT -s simCow_chr6.simCow.chr6 461743 31 - 602619 GATGACAAATGTAGATACAATCTGGCGTTCC -s simDog_chr6.simDog.chr6 168584 31 + 593897 GATGACATTCGTAAATACATTCTAGTGTACT -s simHuman_chr6.simHuman.chr6 474038 31 - 601863 GATGATAAAAGGAAATACAATCTTGTTGACT -s simRat_chr6.simRat.chr6 131586 31 + 647215 GATGATAAATGGGAATACAATCTTGTGTACT - -a -s simMouse_chr6.simMouse.chr6 133887 23 + 636262 TCAGCAACTAGATATGAATCTCT -s Anc0.Anc0refChr1 37597 23 + 62388 TCAGCAACCTGATACAGATCTGT -s Anc1.Anc1refChr2 40700 23 - 144309 TCAGCAACCTGATACAGATCTGT -s Anc2.Anc2refChr3 39650 23 - 53186 TCAGCAACCTGATACAGATCTGT -s mr.mrrefChr0 128162 23 + 130230 TCAGCAACCAGATATAAATCTCT -s simCow_chr6.simCow.chr6 461777 23 - 602619 TCAGCAACCTGATACAGATCTGT -s simDog_chr6.simDog.chr6 168618 17 + 593897 TAAGC------ATACAGATCTGG -s simHuman_chr6.simHuman.chr6 474072 23 - 601863 TCAGCAACCGTATCCAGATCTGT -s simRat_chr6.simRat.chr6 131617 23 + 647215 TCAGCAACCAGAAATAAATCTCT - -a -s simMouse_chr6.simMouse.chr6 133910 6 + 636262 GCCCAA -s Anc0.Anc0refChr1 37620 6 + 62388 GACCAA -s Anc1.Anc1refChr2 40723 6 - 144309 GACCAA -s Anc2.Anc2refChr3 39673 6 - 53186 GACCAA -s mr.mrrefChr0 128185 6 + 130230 GCCCAA -s simCow_chr6.simCow.chr6 461809 6 - 602619 GACCAA -s simDog_chr6.simDog.chr6 168635 6 + 593897 GACCAA -s simHuman_chr6.simHuman.chr6 474095 6 - 601863 GACCAA -s simRat_chr6.simRat.chr6 131640 6 + 647215 GCCTGA - -a -s simMouse_chr6.simMouse.chr6 133916 31 + 636262 TACATCAAGCTAAATTTAGCACTGCAAACTT -s Anc0.Anc0refChr1 37627 31 + 62388 TAAATCATGCTAAACCAAGGACTATAAGGGT -s Anc1.Anc1refChr2 40730 31 - 144309 TAAATCATGCTAAACCAAGGACTATAAGGGT -s Anc2.Anc2refChr3 39680 31 - 53186 TAAATCATGCTAAACCAAGGACTATAAGGGT -s mr.mrrefChr0 128191 31 + 130230 TACATCATGCTAAATTAAGCACTGCAAACTT -s simCow_chr6.simCow.chr6 461816 29 - 602619 TGTATCATGCTAAATCAAG--CCATAAAGGT -s simDog_chr6.simDog.chr6 168642 31 + 593897 TAAAACATGCTAAACTAAGGACTAGAAGGAT -s simHuman_chr6.simHuman.chr6 474102 31 - 601863 TAAATCATGCTAAACCAAGGATTATAAGGGT -s simRat_chr6.simRat.chr6 131646 31 + 647215 TACGTCATGCTAAATTAAGCAAAGCAAACTT - -a -s simMouse_chr6.simMouse.chr6 133947 2 + 636262 TT -s Anc0.Anc0refChr1 37658 2 + 62388 GG -s Anc1.Anc1refChr2 40761 2 - 144309 GG -s Anc2.Anc2refChr3 39711 2 - 53186 GG -s mr.mrrefChr0 128222 2 + 130230 TT -s simCow_chr6.simCow.chr6 461845 2 - 602619 GG -s simDog_chr6.simDog.chr6 168673 2 + 593897 GG -s simHuman_chr6.simHuman.chr6 474133 2 - 601863 GG -s simRat_chr6.simRat.chr6 131682 2 + 647215 TT - -a -s simMouse_chr6.simMouse.chr6 133949 1 + 636262 A -s Anc0.Anc0refChr1 37671 1 + 62388 A -s Anc1.Anc1refChr2 40774 1 - 144309 A -s Anc2.Anc2refChr3 39724 1 - 53186 G -s mr.mrrefChr0 128224 1 + 130230 A -s simCow_chr6.simCow.chr6 461858 1 - 602619 G -s simDog_chr6.simDog.chr6 168686 1 + 593897 G -s simHuman_chr6.simHuman.chr6 474146 1 - 601863 A -s simRat_chr6.simRat.chr6 131684 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 133950 38 + 636262 TTTTAGGCAGCTCTGTACCGAGGAAAGAGGATAGTCCC -s Anc0.Anc0refChr1 25034 38 - 62388 TGTTAGGCAGCATTGCACACAGAAAAGAGGATAATTCT -s Anc1.Anc1refChr2 103852 38 + 144309 TGTTAGGCAGCATTGCACACAGAAAAGAGGATAATTCT -s Anc2.Anc2refChr3 13779 38 + 53186 TGTCAAGCAGCATTGCACACAGAAAAGAGGATGATTAT -s mr.mrrefChr0 128225 38 + 130230 TTTTAGGCAGCACTGTACCGAGGAAAGAGGATAGTCCT -s simCow_chr6.simCow.chr6 141084 37 + 602619 TGTCAAGCAGCATTGCACACA-AAGAGAGGATGATTAT -s simDog_chr6.simDog.chr6 425522 30 - 593897 TGTCAAGCAGCAATACACACGGAAAAGAGG-------- -s simHuman_chr6.simHuman.chr6 128027 38 + 601863 TGTTAGGCAGCATAGCACACAGAAAAGAGGATAATTCT -s simRat_chr6.simRat.chr6 131685 38 + 647215 TTTTAGGCAGCACTGTACCGCGGAGAGAGGATTGGCCT - -a -s simMouse_chr6.simMouse.chr6 133988 45 + 636262 TGCTCACAGGTGATGCTTGGGGAAGCATAACAATGTACAACATTG -s Anc0.Anc0refChr1 25072 40 - 62388 TGCTTGCAAGTGATTCTGGGGGGACCATAATAGTGCACAG----- -s Anc1.Anc1refChr2 103890 40 + 144309 TGCTTGCAAGTGATTCTGGGGGGACCATAATAGTGCACAG----- -s Anc2.Anc2refChr3 13817 40 + 53186 TTCTTGCAAGTTATTCTGGGAGGACTTCAATAGAACACAG----- -s mr.mrrefChr0 128263 45 + 130230 TGCTCACAGGTGATGCTTGGGGAAGCATAACAATGCACAACATTG -s simCow_chr6.simCow.chr6 141127 40 + 602619 TTCTTGCAAGTTATTCTGGGAGGACTGCAATAGCACACAG----- -s simDog_chr6.simDog.chr6 425552 17 - 593897 -----------------------AGTTCCATAAAACTCAG----- -s simHuman_chr6.simHuman.chr6 128065 40 + 601863 TGCTTGCAAGTGATTCTGGGGACACCATAATAGTGCACAT----- -s simRat_chr6.simRat.chr6 131723 36 + 647215 TGGTCACACATGATGCTT---------CACCACTGCACAACATTG - -a -s simMouse_chr6.simMouse.chr6 134033 37 + 636262 AAAAGCATCCACCCATAGCATAGACACATTAACATTA -s Anc0.Anc0refChr1 25112 28 - 62388 GCATGCATC---------AAGAGATGCATTAACATTA -s Anc1.Anc1refChr2 103930 28 + 144309 GCATGCATC---------AAGAGATGCATTAACATTA -s Anc2.Anc2refChr3 13857 28 + 53186 GCATGAATC---------AAGAGATGCATTAACATTA -s mr.mrrefChr0 128308 37 + 130230 AAAAGCATCCACCCATAGCATAGACGCATTAACATTA -s simCow_chr6.simCow.chr6 141176 28 + 602619 GCATGAATC---------GAAACATGCTTTAACATTA -s simDog_chr6.simDog.chr6 425569 22 - 593897 T------TT---------AAGAGATCCATTAGCATTA -s simHuman_chr6.simHuman.chr6 128105 28 + 601863 GCAGGCATC---------AAGAGATGCATTAATATTA -s simRat_chr6.simRat.chr6 131759 36 + 647215 AAAAGCGTCCACCCACAGCATAGAAGCATTAAC-TTA - -a -s simMouse_chr6.simMouse.chr6 134070 7 + 636262 TGCTAAT -s Anc0.Anc0refChr1 25143 7 - 62388 AGCCAAC -s Anc1.Anc1refChr2 103961 7 + 144309 AGCCAAC -s Anc2.Anc2refChr3 13888 7 + 53186 AGCCAAC -s mr.mrrefChr0 128345 7 + 130230 TGCTAAC -s simCow_chr6.simCow.chr6 141207 7 + 602619 ATCCAAC -s simDog_chr6.simDog.chr6 425594 7 - 593897 AGCCAAC -s simHuman_chr6.simHuman.chr6 128136 7 + 601863 CGCCAAC -s simRat_chr6.simRat.chr6 131795 7 + 647215 TGCTAAC - -a -s simMouse_chr6.simMouse.chr6 134077 10 + 636262 GCCAACAATT -s Anc0.Anc0refChr1 25151 10 - 62388 GTCAACAGGT -s Anc1.Anc1refChr2 103969 10 + 144309 GTCAACAGGT -s Anc2.Anc2refChr3 13896 10 + 53186 GTCAGCAGGT -s mr.mrrefChr0 128352 10 + 130230 GCCAACAATT -s simCow_chr6.simCow.chr6 141215 10 + 602619 GTCAGCAGGT -s simDog_chr6.simDog.chr6 425602 10 - 593897 GTCAGCAGGT -s simHuman_chr6.simHuman.chr6 128144 10 + 601863 GTCAACATGT -s simRat_chr6.simRat.chr6 131802 10 + 647215 GCCAACAATT - -a -s simMouse_chr6.simMouse.chr6 134087 4 + 636262 ATGG -s Anc0.Anc0refChr1 25170 4 - 62388 GAGA -s Anc1.Anc1refChr2 103988 4 + 144309 GAGA -s Anc2.Anc2refChr3 13915 4 + 53186 GAGA -s mr.mrrefChr0 128362 4 + 130230 GTGG -s simCow_chr6.simCow.chr6 141234 4 + 602619 GAGT -s simDog_chr6.simDog.chr6 425621 4 - 593897 GTAA -s simHuman_chr6.simHuman.chr6 128163 4 + 601863 GAGA -s simRat_chr6.simRat.chr6 131812 4 + 647215 GTGG - -a -s simMouse_chr6.simMouse.chr6 134091 4 + 636262 GAAC -s Anc0.Anc0refChr1 25174 4 - 62388 GAAC -s Anc1.Anc1refChr2 103992 4 + 144309 GAAC -s Anc2.Anc2refChr3 13919 4 + 53186 GAAC -s mr.mrrefChr0 128366 4 + 130230 GAAC -s simCow_chr6.simCow.chr6 141245 4 + 602619 GAAC -s simDog_chr6.simDog.chr6 425625 4 - 593897 GAGT -s simHuman_chr6.simHuman.chr6 128167 4 + 601863 GAAC -s simRat_chr6.simRat.chr6 131816 4 + 647215 GAGC - -a -s simMouse_chr6.simMouse.chr6 134095 10 + 636262 AAGACCCTCT -s Anc0.Anc0refChr1 25178 10 - 62388 AAGACCCCAT -s Anc1.Anc1refChr2 103996 10 + 144309 AAGACCCCAT -s Anc2.Anc2refChr3 13923 10 + 53186 AAGACCCCAT -s mr.mrrefChr0 128370 10 + 130230 AAGACCCCCT -s simCow_chr6.simCow.chr6 141249 10 + 602619 AAGACCTCAT -s simDog_chr6.simDog.chr6 425641 10 - 593897 AAGACCCCAT -s simHuman_chr6.simHuman.chr6 128171 10 + 601863 AAGACCCCAT -s simRat_chr6.simRat.chr6 131820 10 + 647215 AAGACCCCCT - -a -s simMouse_chr6.simMouse.chr6 134105 13 + 636262 AGGGAGTCACTCT -s Anc0.Anc0refChr1 25189 13 - 62388 AGGGTCTCAGTCT -s Anc1.Anc1refChr2 104007 13 + 144309 AGGGTCTCAGTCT -s Anc2.Anc2refChr3 13934 13 + 53186 AGGGTCTCAGTCA -s mr.mrrefChr0 128380 13 + 130230 AGGGAGTCACTCT -s simCow_chr6.simCow.chr6 141260 13 + 602619 GAGGTCCCAGTCA -s simDog_chr6.simDog.chr6 425652 13 - 593897 AGGGTCTCAATCA -s simHuman_chr6.simHuman.chr6 128182 13 + 601863 AGGGTCTCAGTCT -s simRat_chr6.simRat.chr6 131830 13 + 647215 AGGGAGTCAATCT - -a -s simMouse_chr6.simMouse.chr6 134118 33 + 636262 TCAATCATGAGGAGTCTACGTTCCGTGTCTTTT -s Anc0.Anc0refChr1 25203 31 - 62388 TCAATTACTGGGCCACT--GTTCCATGTTTTTT -s Anc1.Anc1refChr2 104021 31 + 144309 TCAATTACTGGGCCACT--GTTCCATGTTTTTT -s Anc2.Anc2refChr3 13948 31 + 53186 TCAATTACTGGGCCAAT--GTTCCATTTTTTTT -s mr.mrrefChr0 128393 33 + 130230 TCAATTACGAGGAGTCTACGTTCCGTGTCTTTT -s simCow_chr6.simCow.chr6 141274 31 + 602619 TCACTTACTGGCCCAAT--GTTCCATATGTTCT -s simDog_chr6.simDog.chr6 425666 31 - 593897 TCAATTAGTGGGCCAAA--GTTCCATTTTTTTT -s simHuman_chr6.simHuman.chr6 128196 31 + 601863 TCAGTTACTGGGTTGCT--GTTCCTCGTTTTTT -s simRat_chr6.simRat.chr6 131843 33 + 647215 TTAATTACCAGGAGTCCATATTCCATGTCTTTT - -a -s simMouse_chr6.simMouse.chr6 134151 56 + 636262 CCAATGGACTGCACATGTGTAGGCATCCTTGGGGTTGGTGCACACCAAGGACTTCA -s Anc0.Anc0refChr1 25235 52 - 62388 CCAATTGATTGCACATGTGTTAGCACTCTTGGGGCTGGT----ACCAAGGGCATCA -s Anc1.Anc1refChr2 104053 52 + 144309 CCAATTGATTGCACATGTGTTAGCACTCTTGGGGCTGGT----ACCAAGGGCATCA -s Anc2.Anc2refChr3 13980 52 + 53186 CCAATTGATTGCACAAGTGCTAGCACTTTTGGGGCTGGT----ACCAAGGGCATCA -s mr.mrrefChr0 128426 56 + 130230 CCAATGGACTGCACATGTGTAGGCATCCTTGGGGTTGGTGCACACCAAGGACTTCA -s simCow_chr6.simCow.chr6 141306 52 + 602619 CCAATTGACTACACGAGTGCTAGCACTTTTGGGGCTAGT----ACCAAGGAGATCA -s simDog_chr6.simDog.chr6 425698 50 - 593897 CCAATTGATTGCACAAGTGCAAGCACTTTTA--GCAGGT----ACCAAGAGCATCC -s simHuman_chr6.simHuman.chr6 128228 51 + 601863 CCATTTGATTGCATAT-TGTTAGCACTCATGAGGCTCGT----ACCAAAGGCATCA -s simRat_chr6.simRat.chr6 131876 56 + 647215 CCAATGGCCTGCACATGTGTAGGCATCCTTGGGGTTTATGCACACCAAGGACTTTA - -a -s simMouse_chr6.simMouse.chr6 134207 60 + 636262 TGAAACCCTTAATACCTGGTTCTAAAAAGTGGATTAATGGTGAACAGAAACAAATGTGCT -s Anc0.Anc0refChr1 25287 59 - 62388 TGTAACCCTGAATGGCT-GTTCTAAATGGTAGATAAATGATAAGTTATAACACACGTTTT -s Anc1.Anc1refChr2 104105 59 + 144309 TGTAACCCTGAATGGCT-GTTCTAAATGGTAGATAAATGATAAGTTATAACACACGTTTT -s Anc2.Anc2refChr3 14032 59 + 53186 TGTAATCCTGAATGGCT-GTTTTAAATGATAGATAAATGATAAGTTATAACACACGTTTT -s mr.mrrefChr0 128482 60 + 130230 TGAAACCCTTAATACCTGGTTCTAAAAAGTGGATTAATGGTGAGTAGAAACAAATGTTCT -s simCow_chr6.simCow.chr6 141358 41 + 602619 TGTAATCC-------------------GATAAATAAATGGTAAGGTCTAACACACATTCT -s simDog_chr6.simDog.chr6 425748 59 - 593897 TGTAATCCTGAATGGCT-GTTTTAAATGATAGATACATGATAAGTTATAACACACGTTTT -s simHuman_chr6.simHuman.chr6 128285 56 + 601863 TGTAACTCTGAATGACT-GTTCTAAATGGTAGATAAATGTTAAGT---AATAGACACTAT -s simRat_chr6.simRat.chr6 131932 60 + 647215 TGAAACCCTAAATACCTGGTTTTAAACAGTGGATTAATGGTGAGTAGAAACAAATGTTCT - -a -s simMouse_chr6.simMouse.chr6 134267 75 + 636262 TGTCTGTTGGCCATAACACATGGTGCAAGTTTCTATGTCCAAAAATGATGCCTAACAGTAAATGTGCCCTTATCA -s Anc0.Anc0refChr1 25346 74 - 62388 TGTCGGTTAACCATAATACATGGTGCAGAGCTGTATGT-TAAAAATAATGCCTAACAGGAAATTTGGCTTTGTAA -s Anc1.Anc1refChr2 104164 75 + 144309 TGTCGGTTAACCATAATACATGGTGCAGAGCTGTATGTCTAAAAATAATGCCTAACAGGAAATTTGGCTTTGTAA -s Anc2.Anc2refChr3 14091 74 + 53186 TGTCGGTTAACCATAATACATGGTGCAGAGATGTATGT-TAAAAATAATGCCTAACAGGAAATTTGGCTTTGTAA -s mr.mrrefChr0 128542 75 + 130230 TGTCTGTTGGCCATAATACATGGTGCAAGTCTCTATGTCCAAAAATGATGCCTAACAGTAAATGTGCCTTTATCA -s simCow_chr6.simCow.chr6 141399 65 + 602619 -GTCAGTTAACCATG------GGTGCAGATATGTATGT-TAAGAATAGTGCCTAACGGGAAATCTGGCTGTGT-- -s simDog_chr6.simDog.chr6 425809 72 - 593897 TGTCGGTTAACCATAATACATGGTGCAGAGATGTATGT---AAGATGATACCTAGCAGGAAATTGGGCTTCATAA -s simHuman_chr6.simHuman.chr6 128341 72 + 601863 TGTC---TCACTATAATATATGGTGCAGACCTGTATGTCTAAAAACAATGCCTAATAGGAAATATGACTTTGTTA -s simRat_chr6.simRat.chr6 131992 75 + 647215 TGTCTGGTGGCCATAATACATGGTGCAACTCTCTATGTCCTAAAATGATGCTTAACAGTAAATGTGCCTTTCTCA - -a -s simMouse_chr6.simMouse.chr6 134342 1 + 636262 C -s Anc0.Anc0refChr1 25420 1 - 62388 C -s Anc1.Anc1refChr2 104239 1 + 144309 C -s Anc2.Anc2refChr3 14165 1 + 53186 C -s mr.mrrefChr0 128617 1 + 130230 C -s simCow_chr6.simCow.chr6 141464 1 + 602619 C -s simDog_chr6.simDog.chr6 425882 1 - 593897 C -s simHuman_chr6.simHuman.chr6 128413 1 + 601863 T -s simRat_chr6.simRat.chr6 132067 1 + 647215 C - -a -s simMouse_chr6.simMouse.chr6 134343 48 + 636262 GTGGTTATTTACAACCTGGTTATTACCAGATTGTATTACAAGGTATAT -s Anc0.Anc0refChr1 25421 20 - 62388 GT-----------------TTGGGTACAGATGT-----------ATAT -s Anc1.Anc1refChr2 104240 30 + 144309 GT-----------------TTGGGTACAGATGTT-TTGAAAAGTATAT -s Anc2.Anc2refChr3 14167 20 + 53186 GG-----------------TTGGGTATGGATTT-----------ATCT -s mr.mrrefChr0 128618 48 + 130230 GTGGTTATTTACAACCTGGTTATTTACAGATGTTATTACAAAGTATAT -s simCow_chr6.simCow.chr6 141466 20 + 602619 GG-----------------TTGGGTATGGATTT-----------GTGG -s simDog_chr6.simDog.chr6 425884 20 - 593897 GG-----------------TTGTATATGGATTT-----------ATCT -s simHuman_chr6.simHuman.chr6 128414 30 + 601863 GT-----------------TTGGGTACAGGTGTT-TTGAAAAGTATAT -s simRat_chr6.simRat.chr6 132068 48 + 647215 ATCGTTACTTACAACCTAGCTATTTACAAATGTTATTCCAAAGTATAT - -a -s simMouse_chr6.simMouse.chr6 134391 2 + 636262 AT -s Anc0.Anc0refChr1 25441 2 - 62388 CT -s Anc1.Anc1refChr2 104270 2 + 144309 CT -s Anc2.Anc2refChr3 14187 2 + 53186 CT -s mr.mrrefChr0 128666 2 + 130230 AT -s simCow_chr6.simCow.chr6 141486 2 + 602619 CT -s simDog_chr6.simDog.chr6 425904 2 - 593897 CT -s simHuman_chr6.simHuman.chr6 128444 2 + 601863 CT -s simRat_chr6.simRat.chr6 513089 2 - 647215 AG - -a -s simMouse_chr6.simMouse.chr6 134393 4 + 636262 TTTA -s Anc0.Anc0refChr1 25443 4 - 62388 TTTG -s Anc1.Anc1refChr2 104272 4 + 144309 TTTG -s Anc2.Anc2refChr3 14189 4 + 53186 TTTG -s mr.mrrefChr0 128668 4 + 130230 TTTA -s simCow_chr6.simCow.chr6 141497 4 + 602619 TTTG -s simDog_chr6.simDog.chr6 425906 4 - 593897 TTTG -s simHuman_chr6.simHuman.chr6 128446 4 + 601863 TTTG -s simRat_chr6.simRat.chr6 513091 4 - 647215 ACTA - -a -s simMouse_chr6.simMouse.chr6 134397 13 + 636262 CTATGGATGATAA -s Anc0.Anc0refChr1 25447 13 - 62388 CTTTGGATGATAA -s Anc1.Anc1refChr2 104276 13 + 144309 CTTTGGATGATAA -s Anc2.Anc2refChr3 14193 13 + 53186 CTTTGTATCATAA -s mr.mrrefChr0 128672 13 + 130230 CTATGGATGATAA -s simCow_chr6.simCow.chr6 141501 13 + 602619 CTTTGTGTTATAA -s simDog_chr6.simDog.chr6 425910 13 - 593897 CTTTGTATCATAA -s simHuman_chr6.simHuman.chr6 128450 13 + 601863 CTTTTGATGATAA -s simRat_chr6.simRat.chr6 513099 13 - 647215 TTAAGGATGATAA - -a -s simMouse_chr6.simMouse.chr6 134410 36 + 636262 AATAGCTTTGTAGGACTTTTTCTGGTCCACATGAAA -s Anc0.Anc0refChr1 25460 36 - 62388 TATAGCTTTGTAGGACTTTCTTTGGTTCACATGAGA -s Anc1.Anc1refChr2 104289 36 + 144309 TATAGCTTTGTAGGACTTTCTTTGGTTCACATGAGA -s Anc2.Anc2refChr3 14206 36 + 53186 TACAGCTTTATAGGACTTTCTTTGGTTCACATGAGA -s mr.mrrefChr0 128685 36 + 130230 AATAGCTTTGTAGGACTTTTTTTGGTCCACATGAAA -s simCow_chr6.simCow.chr6 141514 36 + 602619 TTCAGCTTTATAGATGTGTCTTTGGCTCACATGAGA -s simDog_chr6.simDog.chr6 425924 36 - 593897 TACGGTTTTATAGGACTTTCTCTGGTTCACACGAGA -s simHuman_chr6.simHuman.chr6 128463 35 + 601863 CGTAGCCTTGCAGGACTCTCTTTGAT-TACATGAGA -s simRat_chr6.simRat.chr6 513112 36 - 647215 AACGGCTTTGTAGGACTTTTTTTAGTCCACATGAAA - -a -s simMouse_chr6.simMouse.chr6 134446 1 + 636262 A -s Anc0.Anc0refChr1 25496 1 - 62388 A -s Anc1.Anc1refChr2 104325 1 + 144309 A -s Anc2.Anc2refChr3 14243 1 + 53186 A -s mr.mrrefChr0 128721 1 + 130230 A -s simCow_chr6.simCow.chr6 141551 1 + 602619 A -s simDog_chr6.simDog.chr6 425961 1 - 593897 A -s simHuman_chr6.simHuman.chr6 128498 1 + 601863 A -s simRat_chr6.simRat.chr6 513148 1 - 647215 A - -a -s simMouse_chr6.simMouse.chr6 134447 8 + 636262 GGGTCATA -s Anc0.Anc0refChr1 25501 8 - 62388 GGTTCATA -s Anc1.Anc1refChr2 104330 8 + 144309 GGTTCATA -s Anc2.Anc2refChr3 14248 8 + 53186 GGTCCATA -s mr.mrrefChr0 128722 8 + 130230 GGGTCATA -s simCow_chr6.simCow.chr6 141556 8 + 602619 GGTCCATA -s simDog_chr6.simDog.chr6 425966 8 - 593897 GGTCCATA -s simHuman_chr6.simHuman.chr6 128503 8 + 601863 GGCTCATA -s simRat_chr6.simRat.chr6 513149 8 - 647215 GGGTCATA - -a -s simMouse_chr6.simMouse.chr6 134455 9 + 636262 ATCTGGTCA -s Anc0.Anc0refChr1 25512 9 - 62388 ATCCAATTA -s Anc1.Anc1refChr2 104341 9 + 144309 ATCCAATTA -s Anc2.Anc2refChr3 14259 9 + 53186 ATCCAATTA -s mr.mrrefChr0 128730 9 + 130230 ATCTGGTCA -s simCow_chr6.simCow.chr6 141567 9 + 602619 ATCCAATTA -s simDog_chr6.simDog.chr6 425977 9 - 593897 GTCCAATTA -s simHuman_chr6.simHuman.chr6 128514 9 + 601863 ATTCAATTA -s simRat_chr6.simRat.chr6 513157 9 - 647215 ATCTGGTCA - -a -s simMouse_chr6.simMouse.chr6 134464 8 + 636262 TCCATCTA -s Anc0.Anc0refChr1 25522 8 - 62388 TCCCACCA -s Anc1.Anc1refChr2 104351 8 + 144309 TCCCACCA -s Anc2.Anc2refChr3 14269 8 + 53186 TCCCACCA -s mr.mrrefChr0 128739 8 + 130230 TCCATCCA -s simCow_chr6.simCow.chr6 141577 8 + 602619 CCCCACCA -s simDog_chr6.simDog.chr6 425987 8 - 593897 TCCCACCA -s simHuman_chr6.simHuman.chr6 128524 8 + 601863 TCCCACCA -s simRat_chr6.simRat.chr6 513166 8 - 647215 TCCATCCA - -a -s simMouse_chr6.simMouse.chr6 134472 18 + 636262 TATCCTTTACAGAATACA -s Anc0.Anc0refChr1 25548 18 - 62388 TATCAATAAAGAGATACA -s Anc1.Anc1refChr2 104377 18 + 144309 TATCAATAAAGAGATACA -s Anc2.Anc2refChr3 14295 18 + 53186 TATCAATAAAGAGATACA -s mr.mrrefChr0 128747 18 + 130230 TATCCATTACAGAATACA -s simCow_chr6.simCow.chr6 141602 18 + 602619 TATCAATAAAGAGAGACA -s simDog_chr6.simDog.chr6 426013 18 - 593897 AATCGATAAAGAGATAGA -s simHuman_chr6.simHuman.chr6 128550 18 + 601863 TATCAATAATGACACCCA -s simRat_chr6.simRat.chr6 513174 18 - 647215 TATCCACTACAGAATACA - -a -s simMouse_chr6.simMouse.chr6 134490 3 + 636262 GGA -s Anc0.Anc0refChr1 25566 3 - 62388 GGA -s Anc1.Anc1refChr2 104395 3 + 144309 GGA -s Anc2.Anc2refChr3 14313 3 + 53186 GGA -s mr.mrrefChr0 128765 3 + 130230 GGA -s simCow_chr6.simCow.chr6 141636 3 + 602619 GGA -s simDog_chr6.simDog.chr6 426031 3 - 593897 GTA -s simHuman_chr6.simHuman.chr6 128568 3 + 601863 GGA -s simRat_chr6.simRat.chr6 513192 3 - 647215 GGA - -a -s simMouse_chr6.simMouse.chr6 134493 32 + 636262 TACTCTATCTCATGTAGTCCTATTTACTGAAA -s Anc0.Anc0refChr1 25571 32 - 62388 TATCATATTTCTTATAGTCCTATTTACTATAA -s Anc1.Anc1refChr2 104400 32 + 144309 TATCATATTTCTTATAGTCCTATTTACTATAA -s Anc2.Anc2refChr3 14318 32 + 53186 TGTCATATTTCTCATAGTCCTATTTACTATAC -s mr.mrrefChr0 128768 32 + 130230 TATTCTATCTCTTGTAGTCCTATTTACTGAAA -s simCow_chr6.simCow.chr6 141641 32 + 602619 TGTCATATTTCTCATAATCCTATTTACCATTG -s simDog_chr6.simDog.chr6 426036 32 - 593897 TGTATCACTTCTCATAGTCCTGTTTATTATAC -s simHuman_chr6.simHuman.chr6 128573 32 + 601863 TATCATATTGCTTATAGTCTTATTTACTATAA -s simRat_chr6.simRat.chr6 513195 32 - 647215 TATTCTATCTTTTGTAGTCCTATTTACTGAAA - -a -s simMouse_chr6.simMouse.chr6 134525 102 + 636262 ATACCACTTAGACAAAAGAGTATACAAATAGACTGAATACATGGTATACCAATGTGGGGGATGCACATGTGTTCATATGCATGGATTCTGGTCAATGTACTT -s Anc0.Anc0refChr1 25604 96 - 62388 GTACCACTTAGACAGAATATTGTACAAATGAAGTGAAT------TTTACCAACATGAGAGATCTGCATCTGGTCATCTGCAGAAAGCCTGGCTAATGTACTC -s Anc1.Anc1refChr2 104433 102 + 144309 GTACCACTTAGACAGAATATTGTACAAATGAAGTGAATACATACTTTACCAACATGAGAGATCTGCATCTGGTCATCTGCAGAAAGCCTGGCTAATGTACTC -s Anc2.Anc2refChr3 14351 96 + 53186 GTACCACTTAGACAGAATATTGTACAAATGAGGTGAAT------TTTACCAACATGAGAGCTCTGCATCTAGTCATCTGCGGAAAGCCTGCCTGATGTATAC -s mr.mrrefChr0 128801 102 + 130230 ATACCACTTAGACAAAATAGTGTACAAATGGAGTGAATACATGGTATACCAATGTGAGGGATGTACATGTGTTCATATGCATGGATTCTGGCTAATGTACTT -s simCow_chr6.simCow.chr6 141674 96 + 602619 GTACCACTTAGCCAAAATATTGTGCAAATGCTGTGAAT------TCGACCAATGCCAGAGCTCTGCATCTAGCGATCTGCCAAAAGCCTGCCTGATGTGTGA -s simDog_chr6.simDog.chr6 426069 92 - 593897 TTACCCCCTAGACAGAATATGGTATACATGAGGTGAAG------TTTACCAACATGA----TCTGCATCTAGTCATTTGCGGAATACCTACCAGATGTATAC -s simHuman_chr6.simHuman.chr6 128606 102 + 601863 GTACCACTTAGTCAGCATATTGCACAAATGAAGTGAATACATACTTTACCAACATGAGAGATCTGCACCTGATCATCTTCAGCAAGCCCGGCTAACGTACTC -s simRat_chr6.simRat.chr6 513228 102 - 647215 ATACCTCTTAGAAAAAATAGCGTACAAATGGAGTGAATACATGGTATACCAATGTGATGGAGGTACATGTGGACATATGCATGGATTCTGGCTAATGTACTT - -a -s simMouse_chr6.simMouse.chr6 134627 45 + 636262 CCAAAAAGTATAAAAATTGATTACACCAATTTAACCATAGTCATA -s Anc0.Anc0refChr1 25710 32 - 62388 CAGAAAAGTATAAAAATCAATTA-------------ATGCTCATA -s Anc1.Anc1refChr2 104545 32 + 144309 CAGAAAAGTATAAAAATCAATTA-------------ATGCTCATA -s Anc2.Anc2refChr3 14459 32 + 53186 CAGAAAAGTATAAAAACCAATTA-------------ATGCTCATA -s mr.mrrefChr0 128903 45 + 130230 CCAAAAAGTATAAAAATTAATTACACCAATTTAACCATGGTCATA -s simCow_chr6.simCow.chr6 141782 31 + 602619 CTGAAAAGCATAAAAAGCAATCA--------------TGCTCATT -s simDog_chr6.simDog.chr6 426173 30 - 593897 CAGAGAACTATAAAAGC--ATTT-------------ATGTTCATA -s simHuman_chr6.simHuman.chr6 128718 32 + 601863 CAGAAAAGTATAAAAATCAATTA-------------ATGCTTATA -s simRat_chr6.simRat.chr6 513330 44 - 647215 CCAAAAGGTATAAAAAGTAATT-TGCTAATTTAATCATGGTCGCT - -a -s simMouse_chr6.simMouse.chr6 134672 21 + 636262 CAGTTCATATAGTTATAGACC -s Anc0.Anc0refChr1 25743 17 - 62388 CAAGTAGTGTATTTTGA---- -s Anc1.Anc1refChr2 104578 17 + 144309 CAAGTAGTGTATTTTGA---- -s Anc2.Anc2refChr3 14492 17 + 53186 CAAGTAGTGTATTTTGA---- -s mr.mrrefChr0 128948 21 + 130230 CAGTTCATATAGTTATAGACC -s simCow_chr6.simCow.chr6 141814 17 + 602619 CAAGTAGTGTATTTTGA---- -s simDog_chr6.simDog.chr6 426204 7 - 593897 CAAGTGG-------------- -s simHuman_chr6.simHuman.chr6 128751 17 + 601863 CAAGTAGAGTATTTTGA---- -s simRat_chr6.simRat.chr6 513374 21 - 647215 CAGGTTATATGGCTATAGACC - -a -s simMouse_chr6.simMouse.chr6 134693 16 + 636262 AAGTCTAAGGACGCTC -s Anc0.Anc0refChr1 25760 14 - 62388 AGCCCAGAGGA--CTC -s Anc1.Anc1refChr2 104595 14 + 144309 AGCCCAGAGGA--CTC -s Anc2.Anc2refChr3 14509 14 + 53186 AGCCCAGAGGA--CTC -s mr.mrrefChr0 128969 16 + 130230 AAGTCTGAGGACGCTC -s simCow_chr6.simCow.chr6 141832 14 + 602619 AGCCCAGGGGA--ATC -s simDog_chr6.simDog.chr6 426211 8 - 593897 ------GAGGA--CTC -s simHuman_chr6.simHuman.chr6 128768 14 + 601863 AGAACAGAGGA--CTG -s simRat_chr6.simRat.chr6 513395 16 - 647215 AAGTCTGAGCAGGATC - -a -s simMouse_chr6.simMouse.chr6 134709 4 + 636262 GTTG -s Anc0.Anc0refChr1 25776 4 - 62388 GTTG -s Anc1.Anc1refChr2 104611 4 + 144309 GTTG -s Anc2.Anc2refChr3 14525 4 + 53186 GTTG -s mr.mrrefChr0 128987 4 + 130230 GTTG -s simCow_chr6.simCow.chr6 141848 4 + 602619 GTTA -s simDog_chr6.simDog.chr6 426221 4 - 593897 GTTG -s simHuman_chr6.simHuman.chr6 128784 4 + 601863 GTTG -s simRat_chr6.simRat.chr6 513413 4 - 647215 GTTG - -a -s simMouse_chr6.simMouse.chr6 134713 12 + 636262 TACGAATTCCAG -s Anc0.Anc0refChr1 25781 12 - 62388 CGCTGATTCCAG -s Anc1.Anc1refChr2 104616 12 + 144309 CGCTGATTCCAG -s Anc2.Anc2refChr3 14530 12 + 53186 CGCTGATTCCAG -s mr.mrrefChr0 128991 12 + 130230 TACGAATTCCAG -s simCow_chr6.simCow.chr6 141853 12 + 602619 TGCTGACTCCAG -s simDog_chr6.simDog.chr6 426226 12 - 593897 CGCTGATTCCTG -s simHuman_chr6.simHuman.chr6 128789 12 + 601863 CTCTGAGTCCAG -s simRat_chr6.simRat.chr6 513417 12 - 647215 TACCGATTCCAC - -a -s simMouse_chr6.simMouse.chr6 134725 54 + 636262 TATGACTTCCCCTTGACAAACCAAAATTGTCTGCACTTCCAAAGTGGGGTGGAA -s Anc0.Anc0refChr1 25796 52 - 62388 CATGATTTCTCTTCCACAAACCAAAA--GTCAAGATTTCCAAAGTGGGGTGGAA -s Anc1.Anc1refChr2 104631 54 + 144309 CATGATTTCTCTTCCACAAACCAAAACTGTCAAGATTTCCAAAGTGGGGTGGAA -s Anc2.Anc2refChr3 14545 52 + 53186 CATGATTTCTCTTTCACAAACCAACA--GTCAAGATTTCCACAGTGGGGTGGAA -s mr.mrrefChr0 129003 54 + 130230 TATGATTTCCCCTCGACAAACCAAAACTGTCTGCACTTCCAAAGTGGGGTGGAA -s simCow_chr6.simCow.chr6 141868 52 + 602619 CATGATTTCTCCTACGCAAACCAACA--GTCAAGGTTTCCACAGTGAGGTGGAA -s simDog_chr6.simDog.chr6 426241 52 - 593897 CATTGTTTATATTTCATGGACCAACA--GTCAAGATTTCCACAGTGGGGTGAAA -s simHuman_chr6.simHuman.chr6 128804 54 + 601863 CATGATGTCTCTACTACAAACCAAAACTGTCACAATTGACAAAGTGGGGTGGAA -s simRat_chr6.simRat.chr6 513429 53 - 647215 TTTGATTTCCCCTCCACAAAC-AAAACAGTCTGGAATTCCACAGTGGGGTGGAC - -a -s simMouse_chr6.simMouse.chr6 134779 6 + 636262 CTAGGA -s Anc0.Anc0refChr1 25849 6 - 62388 CAGGAA -s Anc1.Anc1refChr2 104686 6 + 144309 CAGGAA -s Anc2.Anc2refChr3 14598 6 + 53186 CAGGAA -s mr.mrrefChr0 129057 6 + 130230 CAAGAA -s simCow_chr6.simCow.chr6 141921 6 + 602619 CAAGGA -s simDog_chr6.simDog.chr6 426294 6 - 593897 CAGGAA -s simHuman_chr6.simHuman.chr6 128859 6 + 601863 CATGAA -s simRat_chr6.simRat.chr6 513482 6 - 647215 CAAGAA - -a -s simMouse_chr6.simMouse.chr6 134785 5 + 636262 GGTGT -s Anc0.Anc0refChr1 25858 5 - 62388 GGTGT -s Anc1.Anc1refChr2 104695 5 + 144309 GGTGT -s Anc2.Anc2refChr3 14607 5 + 53186 GGTGT -s mr.mrrefChr0 129066 5 + 130230 GGTGT -s simCow_chr6.simCow.chr6 141930 5 + 602619 GGTGA -s simDog_chr6.simDog.chr6 426303 5 - 593897 GGTGT -s simHuman_chr6.simHuman.chr6 128868 5 + 601863 GGTGT -s simRat_chr6.simRat.chr6 513491 5 - 647215 GGTGT - -a -s simMouse_chr6.simMouse.chr6 134790 18 + 636262 TCCATCTCTACATCAGCA -s Anc0.Anc0refChr1 25872 12 - 62388 TTTACAGCA------CCA -s Anc1.Anc1refChr2 104709 18 + 144309 TTTACAGCACCAGCACCA -s Anc2.Anc2refChr3 14621 12 + 53186 TTTACAGCA------CCA -s mr.mrrefChr0 129071 18 + 130230 TCTATCTCTACATCACCA -s simCow_chr6.simCow.chr6 141944 12 + 602619 TTTACAGCA------CCA -s simDog_chr6.simDog.chr6 426317 12 - 593897 TTTACAGCA------CCA -s simHuman_chr6.simHuman.chr6 128882 18 + 601863 TTTACAGCACCAGCACCA -s simRat_chr6.simRat.chr6 513496 18 - 647215 TCTATCTCTACATCACCA - -a -s simMouse_chr6.simMouse.chr6 134808 20 + 636262 CATATCCAAGCTTATGTCAG -s Anc0.Anc0refChr1 25884 18 - 62388 AATATCCAGACCTA--TCAG -s Anc1.Anc1refChr2 104727 18 + 144309 AATATCCAGACCTA--TCAG -s Anc2.Anc2refChr3 14633 18 + 53186 AATATCTAGACCTA--TCAG -s mr.mrrefChr0 129089 20 + 130230 CATATCCAAGCTTATGTCAG -s simCow_chr6.simCow.chr6 141962 18 + 602619 AATATCTAGACTTA--TCAG -s simDog_chr6.simDog.chr6 426329 18 - 593897 AATATCTAAGCCTA--TCAG -s simHuman_chr6.simHuman.chr6 128900 18 + 601863 TACATCCGGATCTA--TTAG -s simRat_chr6.simRat.chr6 513514 20 - 647215 CATCTCCAAGCTTATGACAG - -a -s simMouse_chr6.simMouse.chr6 134828 15 + 636262 TCTAACTAAATCATA -s Anc0.Anc0refChr1 25902 15 - 62388 TCTAACTAAATCATG -s Anc1.Anc1refChr2 104745 15 + 144309 TCTAACTAAATCATG -s Anc2.Anc2refChr3 14655 15 + 53186 TCTAACTAAATCATG -s mr.mrrefChr0 129109 15 + 130230 TCTAACTAAATCATG -s simCow_chr6.simCow.chr6 141984 15 + 602619 TCTAACTAAATCATG -s simDog_chr6.simDog.chr6 426351 15 - 593897 TCCAAATAAATCATG -s simHuman_chr6.simHuman.chr6 128918 15 + 601863 TCTACCTAAATCATG -s simRat_chr6.simRat.chr6 513534 15 - 647215 TCTAACTATATCATG - -a -s simMouse_chr6.simMouse.chr6 134843 24 + 636262 ATTCTCTGCTATTATCTCCCTTCT -s Anc0.Anc0refChr1 25924 24 - 62388 TTTATCTGCTTTTGTCACACTTTG -s Anc1.Anc1refChr2 104767 24 + 144309 TTTATCTGCTTTTGTCACACTTTG -s Anc2.Anc2refChr3 14677 24 + 53186 TTTATCAGCTTTTGTCACACTTTG -s mr.mrrefChr0 129124 24 + 130230 TTTCTCTGCTATTGTCTCCCTTCT -s simCow_chr6.simCow.chr6 142006 24 + 602619 TTTCCCAATTTCTGTCACACTTTT -s simDog_chr6.simDog.chr6 426373 24 - 593897 TTTATAAGCTTTTGTCACACTTTG -s simHuman_chr6.simHuman.chr6 128941 24 + 601863 TTCAGCTGCTTTTGTCACACTTTG -s simRat_chr6.simRat.chr6 513549 15 - 647215 TTT---------TGTCCCTCTCCT - -a -s simMouse_chr6.simMouse.chr6 134867 1 + 636262 A -s Anc0.Anc0refChr1 25949 1 - 62388 A -s Anc1.Anc1refChr2 104792 1 + 144309 A -s Anc2.Anc2refChr3 14702 1 + 53186 A -s mr.mrrefChr0 129148 1 + 130230 A -s simCow_chr6.simCow.chr6 142031 1 + 602619 A -s simHuman_chr6.simHuman.chr6 128966 1 + 601863 A -s simRat_chr6.simRat.chr6 513564 1 - 647215 A - -a -s simMouse_chr6.simMouse.chr6 134868 14 + 636262 ATAACATGACACAC -s Anc0.Anc0refChr1 25950 14 - 62388 AGGCCCTGACATGC -s Anc1.Anc1refChr2 104793 14 + 144309 AGGCCCTGACATGC -s Anc2.Anc2refChr3 14703 14 + 53186 AGGCCCCAACATAC -s mr.mrrefChr0 129149 14 + 130230 ATAGCCTGACACGC -s simCow_chr6.simCow.chr6 142033 14 + 602619 AGGCCTAAACATAC -s simDog_chr6.simDog.chr6 426398 10 - 593897 ----CCCAACATAC -s simHuman_chr6.simHuman.chr6 128967 13 + 601863 GGGCCCTGACAGG- -s simRat_chr6.simRat.chr6 513565 14 - 647215 ACAGCCTGACAAGC - -a -s simMouse_chr6.simMouse.chr6 134882 4 + 636262 TTTA -s Anc0.Anc0refChr1 25964 4 - 62388 GTTG -s Anc1.Anc1refChr2 104807 4 + 144309 GTTG -s Anc2.Anc2refChr3 14728 4 + 53186 GTTG -s mr.mrrefChr0 129163 4 + 130230 TTTA -s simCow_chr6.simCow.chr6 142058 4 + 602619 ATTG -s simDog_chr6.simDog.chr6 426419 4 - 593897 GTTG -s simRat_chr6.simRat.chr6 513579 4 - 647215 TTTA - -a -s simMouse_chr6.simMouse.chr6 134886 2 + 636262 AT -s Anc0.Anc0refChr1 25968 2 - 62388 GT -s Anc1.Anc1refChr2 104811 2 + 144309 GT -s Anc2.Anc2refChr3 14732 2 + 53186 GT -s mr.mrrefChr0 129167 2 + 130230 AT -s simDog_chr6.simDog.chr6 426509 2 - 593897 GT -s simRat_chr6.simRat.chr6 513583 2 - 647215 AT - -a -s simMouse_chr6.simMouse.chr6 134888 7 + 636262 TGAGGGC -s Anc0.Anc0refChr1 26018 7 - 62388 TGTGGAT -s Anc1.Anc1refChr2 104861 7 + 144309 TGTGGAT -s Anc2.Anc2refChr3 14782 7 + 53186 TATGGAT -s mr.mrrefChr0 129217 7 + 130230 TGAGGGC -s simCow_chr6.simCow.chr6 142104 7 + 602619 GATGAAT -s simDog_chr6.simDog.chr6 426559 7 - 593897 TATGGAC -s simHuman_chr6.simHuman.chr6 129028 7 + 601863 TGTGGAT -s simRat_chr6.simRat.chr6 513643 7 - 647215 TAAGGGC - -a -s simMouse_chr6.simMouse.chr6 134895 1 + 636262 T -s Anc0.Anc0refChr1 26026 1 - 62388 T -s Anc1.Anc1refChr2 104869 1 + 144309 T -s Anc2.Anc2refChr3 14790 1 + 53186 T -s mr.mrrefChr0 129224 1 + 130230 T -s simCow_chr6.simCow.chr6 142112 1 + 602619 T -s simDog_chr6.simDog.chr6 426567 1 - 593897 T -s simHuman_chr6.simHuman.chr6 129036 1 + 601863 C -s simRat_chr6.simRat.chr6 513650 1 - 647215 T - -a -s simMouse_chr6.simMouse.chr6 134896 32 + 636262 AGGATATTTGGGGACTGAACAATTGAACCCCT -s Anc0.Anc0refChr1 26027 24 - 62388 AGGATC--------CTAAAAAACTGATCTCTT -s Anc1.Anc1refChr2 104870 24 + 144309 AGGATC--------CTAAAAAACTGATCTCTT -s Anc2.Anc2refChr3 14792 24 + 53186 AGAAAC--------TTAAAAAACTGATCTCTT -s mr.mrrefChr0 129225 30 + 130230 AGGATCTTTGGG--CTGAACAATTGATCTCCT -s simCow_chr6.simCow.chr6 142114 24 + 602619 AGGAAC--------GTAAAAAGCTGATCTATT -s simDog_chr6.simDog.chr6 426569 20 - 593897 AGAAAC--------TTGAAAGA----TCTCTT -s simHuman_chr6.simHuman.chr6 129037 24 + 601863 AAGATC--------CCAAAAAAATCATCTTTT -s simRat_chr6.simRat.chr6 513651 30 - 647215 AGGAGCTTTGGG--CTGAACAGTTGATCTCCT - -a -s simMouse_chr6.simMouse.chr6 134928 16 + 636262 ATAGTACATCCTAAAC -s Anc0.Anc0refChr1 26053 15 - 62388 ATAATCCATCCTAGA- -s Anc1.Anc1refChr2 104896 15 + 144309 ATAATCCATCCTAGA- -s Anc2.Anc2refChr3 14818 15 + 53186 ATAATCCATCCTAGA- -s mr.mrrefChr0 129255 16 + 130230 ATAGTACATCCTAAAC -s simCow_chr6.simCow.chr6 142140 15 + 602619 ATAACCCATCCTAGA- -s simDog_chr6.simDog.chr6 426591 15 - 593897 ACAATTCATCCTAAA- -s simHuman_chr6.simHuman.chr6 129063 15 + 601863 ATAATCCATACTAGA- -s simRat_chr6.simRat.chr6 513681 16 - 647215 ATAGTACCTCCTAAGC - -a -s simMouse_chr6.simMouse.chr6 134944 19 + 636262 TCACTCCTAGGCATAGTCA -s Anc0.Anc0refChr1 26068 19 - 62388 TCAAACCCAGTCATAGTAA -s Anc1.Anc1refChr2 104911 19 + 144309 TCAAACCCAGTCATAGTAA -s Anc2.Anc2refChr3 14833 19 + 53186 TCAAACCCAGTCATAGTAA -s mr.mrrefChr0 129271 19 + 130230 TCACTCCCAGGCATAGTAA -s simCow_chr6.simCow.chr6 142156 19 + 602619 TCAAACCCATGCCGAGAAG -s simDog_chr6.simDog.chr6 426606 18 - 593897 -CAGACCCAGTCATGGTAA -s simHuman_chr6.simHuman.chr6 129078 19 + 601863 TCAAACCCAAACATAGTAA -s simRat_chr6.simRat.chr6 513697 19 - 647215 TTACTCCCAGGCATAGTAA - -a -s simMouse_chr6.simMouse.chr6 134963 28 + 636262 GCAACTATATCTGGCAAAGCCTTCTGCC -s Anc0.Anc0refChr1 26087 28 - 62388 GAGACTTTATATGGCAAGGCCTTCTACT -s Anc1.Anc1refChr2 104930 28 + 144309 GAGACTTTATATGGCAAGGCCTTCTACT -s Anc2.Anc2refChr3 14853 28 + 53186 GAGACTTTATATGGCAAGGCCTTCTACT -s mr.mrrefChr0 129290 28 + 130230 GCAACTATATCTGGCAAGGCCTTCTGCC -s simCow_chr6.simCow.chr6 142176 28 + 602619 GACACATTATAAGGCAAGGCCTTCTACT -s simDog_chr6.simDog.chr6 426625 28 - 593897 GAGACTTTATATGGCAAAGCCTTTTACA -s simHuman_chr6.simHuman.chr6 129097 23 + 601863 A-----GTATATAGCAAGGCCTTCTACT -s simRat_chr6.simRat.chr6 513716 28 - 647215 GCAACTATATCTGGCTAGCCCTTCCGCC - -a -s simMouse_chr6.simMouse.chr6 134991 12 + 636262 ATTTTCTACTGT -s Anc0.Anc0refChr1 26115 12 - 62388 AGTCTCTTCTGA -s Anc1.Anc1refChr2 104958 12 + 144309 AGTCTCTTCTGA -s Anc2.Anc2refChr3 14881 12 + 53186 AGCCTTTTCCTA -s mr.mrrefChr0 129318 12 + 130230 ATTTTCTACTGT -s simCow_chr6.simCow.chr6 142204 6 + 602619 A------TCCTA -s simDog_chr6.simDog.chr6 426656 12 - 593897 AGCCTTTTACTA -s simHuman_chr6.simHuman.chr6 129120 12 + 601863 AGTGTCTTCTGA -s simRat_chr6.simRat.chr6 513744 12 - 647215 ATGATCTAATGT - -a -s simMouse_chr6.simMouse.chr6 135003 10 + 636262 GTTCTCTAAT -s Anc0.Anc0refChr1 26127 7 - 62388 TTTTTTT--- -s Anc1.Anc1refChr2 104970 10 + 144309 TTTTTTTAAG -s Anc2.Anc2refChr3 14893 7 + 53186 TATTTTT--- -s mr.mrrefChr0 129330 10 + 130230 GTTCTTTAAT -s simCow_chr6.simCow.chr6 142210 7 + 602619 TATTTCT--- -s simDog_chr6.simDog.chr6 426674 7 - 593897 TATATTT--- -s simHuman_chr6.simHuman.chr6 129132 10 + 601863 TTTTTTTAAG -s simRat_chr6.simRat.chr6 513756 10 - 647215 GTTCTTTTAA - -a -s simMouse_chr6.simMouse.chr6 135013 10 + 636262 TAGACCTGAA -s Anc0.Anc0refChr1 26143 10 - 62388 TAGATCTGAA -s Anc1.Anc1refChr2 104991 10 + 144309 TAGATCTGAA -s Anc2.Anc2refChr3 14909 10 + 53186 TAGATCTAGA -s mr.mrrefChr0 129340 10 + 130230 TAGACCTGAA -s simCow_chr6.simCow.chr6 142226 9 + 602619 AAGATCTA-A -s simDog_chr6.simDog.chr6 426690 10 - 593897 TAGGTCTAGA -s simHuman_chr6.simHuman.chr6 129161 10 + 601863 TAGATCTGAA -s simRat_chr6.simRat.chr6 513766 10 - 647215 TAGACCTGAA - -a -s simMouse_chr6.simMouse.chr6 135023 4 + 636262 GTTT -s Anc0.Anc0refChr1 26163 4 - 62388 GTTT -s Anc1.Anc1refChr2 105011 4 + 144309 GTTT -s Anc2.Anc2refChr3 14929 4 + 53186 TTTT -s mr.mrrefChr0 129350 4 + 130230 GTTT -s simCow_chr6.simCow.chr6 142245 4 + 602619 TTTC -s simDog_chr6.simDog.chr6 426710 4 - 593897 TTTT -s simHuman_chr6.simHuman.chr6 129181 4 + 601863 GTTT -s simRat_chr6.simRat.chr6 513776 4 - 647215 GTGT - -a -s simMouse_chr6.simMouse.chr6 135027 2 + 636262 TC -s Anc0.Anc0refChr1 26167 2 - 62388 CC -s Anc1.Anc1refChr2 105015 2 + 144309 CC -s Anc2.Anc2refChr3 14940 2 + 53186 CC -s mr.mrrefChr0 129354 2 + 130230 TC -s simCow_chr6.simCow.chr6 142256 2 + 602619 CC -s simDog_chr6.simDog.chr6 426721 2 - 593897 CT -s simHuman_chr6.simHuman.chr6 129185 2 + 601863 CC -s simRat_chr6.simRat.chr6 513780 2 - 647215 TC - -a -s simMouse_chr6.simMouse.chr6 135029 28 + 636262 TGAGGATCTGTCACATTTGGCTTGGCTG -s Anc0.Anc0refChr1 26177 28 - 62388 GGAGGATTTGTCACACTAGAGTTGGCTG -s Anc1.Anc1refChr2 105025 28 + 144309 GGAGGATTTGTCACACTAGAGTTGGCTG -s Anc2.Anc2refChr3 14950 28 + 53186 GGAGGATTTGTCACACTAGAGTTGGCTG -s mr.mrrefChr0 129356 28 + 130230 TGAGGATCTGTCACATTTGGCTTGGCTG -s simCow_chr6.simCow.chr6 142266 27 + 602619 AG-GGGTCTGTCACACTAGAGCAGGCTG -s simDog_chr6.simDog.chr6 426731 28 - 593897 GGAGGATTTGTTACACTAGAGTTGGCTG -s simHuman_chr6.simHuman.chr6 129195 15 + 601863 GGAGTATTCATCACA------------- -s simRat_chr6.simRat.chr6 513782 28 - 647215 TGAGGATCTGTCATGTTTGGCTTGGCTG - -a -s simMouse_chr6.simMouse.chr6 135057 17 + 636262 AATTCTCAGGTTCTCAA -s Anc0.Anc0refChr1 26205 17 - 62388 AGCTTCTGGTTTCTCAA -s Anc1.Anc1refChr2 105053 17 + 144309 AGCTTCTGGTTTCTCAA -s Anc2.Anc2refChr3 14990 17 + 53186 AGCTTCTGGTTTCTCAA -s mr.mrrefChr0 129384 17 + 130230 AATTCTCAGGTTCTCAA -s simCow_chr6.simCow.chr6 142305 17 + 602619 AGTTTTTGGTTTCTTAA -s simDog_chr6.simDog.chr6 426771 17 - 593897 AGCTTCTGGTTTCTCAA -s simHuman_chr6.simHuman.chr6 129210 3 + 601863 --------------CAA -s simRat_chr6.simRat.chr6 513810 17 - 647215 AATTGTTAGTTTCTCAG - -a -s simMouse_chr6.simMouse.chr6 135074 17 + 636262 GTTGAAATTGTTCTGAT -s Anc0.Anc0refChr1 26223 6 - 62388 GTT-----------GAT -s Anc1.Anc1refChr2 105071 17 + 144309 GTTAATTTTGTTCTGAT -s Anc2.Anc2refChr3 15008 6 + 53186 GTT-----------GAG -s mr.mrrefChr0 129401 17 + 130230 GTTGAAATTGTTCTGAT -s simCow_chr6.simCow.chr6 142323 6 + 602619 GTT-----------GAG -s simDog_chr6.simDog.chr6 426789 6 - 593897 GTT-----------GAG -s simHuman_chr6.simHuman.chr6 129214 17 + 601863 GTTAATTTTGTTCTGGT -s simRat_chr6.simRat.chr6 513827 17 - 647215 GTTGAGATTGTTCTGAC - -a -s simMouse_chr6.simMouse.chr6 135091 11 + 636262 GAATTTTTACT -s Anc0.Anc0refChr1 26229 11 - 62388 TAGCTTTCGCT -s Anc1.Anc1refChr2 105088 11 + 144309 TAGCTTTCGCT -s Anc2.Anc2refChr3 15014 11 + 53186 TAGCTTTTGCT -s mr.mrrefChr0 129418 11 + 130230 TAATTTTCACT -s simCow_chr6.simCow.chr6 142340 11 + 602619 TAGCTTTTGCC -s simDog_chr6.simDog.chr6 426795 11 - 593897 TAGCTCTTGCT -s simHuman_chr6.simHuman.chr6 129231 11 + 601863 TAGCCTTCGCT -s simRat_chr6.simRat.chr6 513844 11 - 647215 TAATTCTCACC - -a -s simMouse_chr6.simMouse.chr6 135102 2 + 636262 CT -s Anc0.Anc0refChr1 26240 2 - 62388 CT -s Anc1.Anc1refChr2 105099 2 + 144309 CT -s Anc2.Anc2refChr3 15026 2 + 53186 CT -s mr.mrrefChr0 129429 2 + 130230 CT -s simCow_chr6.simCow.chr6 142352 2 + 602619 CT -s simDog_chr6.simDog.chr6 426807 2 - 593897 CT -s simHuman_chr6.simHuman.chr6 129242 2 + 601863 CT -s simRat_chr6.simRat.chr6 513855 2 - 647215 CC - -a -s simMouse_chr6.simMouse.chr6 135104 3 + 636262 TAT -s Anc0.Anc0refChr1 26249 3 - 62388 TCT -s Anc1.Anc1refChr2 105108 3 + 144309 TCT -s Anc2.Anc2refChr3 15036 3 + 53186 CCT -s mr.mrrefChr0 129431 3 + 130230 TCT -s simCow_chr6.simCow.chr6 142362 3 + 602619 CCT -s simDog_chr6.simDog.chr6 426817 3 - 593897 CCT -s simHuman_chr6.simHuman.chr6 129251 3 + 601863 TCT -s simRat_chr6.simRat.chr6 513857 3 - 647215 TCT - -a -s simMouse_chr6.simMouse.chr6 135107 68 + 636262 TATGGTAACCCTCAATGCATTCTGCTTGATTGCTCTTTCTCCATACATGCATGGGTGGAGGTCTACCT -s Anc0.Anc0refChr1 26262 67 - 62388 TATGATAACCCTAGATATATTCTGGTTTATATCTTTTTTTACATACCTG-GAAGCTGGGGATCTACCT -s Anc1.Anc1refChr2 105121 67 + 144309 TATGATAACCCTAGATATATTCTGGTTTATATCTTTTTTTACATACCTG-GAAGCTGGGGATCTACCT -s Anc2.Anc2refChr3 15049 67 + 53186 TATGATAACCCTAGATATATTCTGGTTTATATCCTTTTTTACACACCTA-GAAGCTGGGGATCTACCT -s mr.mrrefChr0 129434 68 + 130230 TATGGTAACCCTCAATACATTCTGCTTGATTGCTCTTTCTACATACATGCATGGCTGGGGGTCTACCT -s simCow_chr6.simCow.chr6 142375 62 + 602619 TATGGTAGCCCTAGTGATGTTCTGGTCTATTTCCTTTTTTACACACC------ACTGGGGATTCACCT -s simDog_chr6.simDog.chr6 426830 67 - 593897 TATGACAACCCTAGATATATCCTGGTTTATATCCTTTTCTACACACCTA-GAAGCTGGGGATCTACCT -s simHuman_chr6.simHuman.chr6 129264 67 + 601863 TAAGATAACCCTAGATAGATTCTGGTTTATATCTTTTTTTACATACCTG-GGAGCTGGGGATCTACCT -s simRat_chr6.simRat.chr6 513860 68 - 647215 TATGGTAACCCTCAGCACATTCTGCTTGATTGCTCTTTCTACATACATGCATGGCTGAGGGTCTGCTT - -a -s simMouse_chr6.simMouse.chr6 135175 23 + 636262 CTATGCTTCACACTGAGTGGGCT -s Anc0.Anc0refChr1 26329 23 - 62388 TTGTGTATCACACTGGCCCTGTT -s Anc1.Anc1refChr2 105188 23 + 144309 TTGTGTATCACACTGGCCCTGTT -s Anc2.Anc2refChr3 15120 23 + 53186 TTGTGTATCATGCTGGCCCTGTT -s mr.mrrefChr0 129502 23 + 130230 TTATGCATCACACTGGGTGGGCT -s simCow_chr6.simCow.chr6 142441 23 + 602619 TTATGTATCATCCTAGCCATGCT -s simDog_chr6.simDog.chr6 426901 23 - 593897 TTGTGTATCATGCTGGCCCAGTT -s simHuman_chr6.simHuman.chr6 129331 17 + 601863 TTGTGTATCACACTGGT------ -s simRat_chr6.simRat.chr6 513928 23 - 647215 TTATGCATCACACTGGATGAGCT - -a -s simMouse_chr6.simMouse.chr6 135198 133 + 636262 GATTGGGTTTTGCTGTAGAAGGGGCCCAGGATAGTTGGGAATGTTATGAGCACTTTGTCCTTGTTAGAAAGTTGTCTCCGTCTCAGGCTCTAACAATCAGGCATAACACAGCTAGTTAATCAATCCTTGATGT -s Anc0.Anc0refChr1 26352 119 - 62388 GGTTGCCTTTTGCTACGGAAGT------GGATAGATGATGATCTTACAATCTTTTCAGCCTTGTTAA--AG------GCTTCCTAAGCTCTGGTAGTCAGGGATAACTCAGCTAGGTAATTACTCCTTGTTCT -s Anc1.Anc1refChr2 105211 119 + 144309 GGTTGCCTTTTGCTACGGAAGT------GGATAGATGATGATCTTACAATCTTTTCAGCCTTGTTAA--AG------GCTTCCTAAGCTCTGGTAGTCAGGGATAACTCAGCTAGGTAATTACTCCTTGTTCT -s Anc2.Anc2refChr3 15143 119 + 53186 GGTTGCCTTTTGCTACGGAAGT------GGATAGATGATGTACTTACAATCTTTTCAGCCCTGTTAA--AG------GCTTCCTAAGCTCTGGTAGTCAGGGATTACTCAGCTAGGTAATTACTCCTTGTTCT -s mr.mrrefChr0 129525 127 + 130230 GATTGGGTTTTGCTGTAGAAGGGGCCCAGGATAGTTGGGAATGTTATGATCACTTTGTCCTTGTTAGAAAG------CCTTCTCAGGCTCTGACAATCAGGCATAACACAGCTAGTTAATCAATCCTTGATGT -s simCow_chr6.simCow.chr6 142468 116 + 602619 GGTTGCTTTTTGCTGCCGAAGC------AGATATAAGTCATACGTACAATCTATTAAGCCGTGTTAA--AG------GCTTCCTAAGCT---GTAGGCGGGCATTACTTAGCTAGGTCATTACTATTTGTTCT -s simDog_chr6.simDog.chr6 426924 119 - 593897 GGTTGCCTTTTGCTACGGAAGT------GGATAGATGATGTACTTAGAATCTTTTCATCTCTGTTTA--AG------GCTTCTTAAACTCTGGCACTCAGGGAATAATCAGCTAGGTACTTACTCCTTGTTGT -s simHuman_chr6.simHuman.chr6 129348 88 + 601863 -------------------------------------ACTATCTTCCAATCTTTTCAGCCTTATTAT--AG------GCTTCCTGAGCTCGGGTGGTCAGGAATAACGCAGCAGTGTAACTATTCCTTGTCCT -s simRat_chr6.simRat.chr6 513951 127 - 647215 AATTGGCTTTTGCTGTAGAAGTGACCCAGGATAGTTGGGAAAATAATCATCACTTTGTCTCTGTTACAAAG------ACTTCTCAGTCTCTGACACTTGGGCATAACTCAGCTAGTTAATCAATCCTTGATAT - -a -s simMouse_chr6.simMouse.chr6 135331 34 + 636262 GCTCAGGCGTGAACGGGAGTGGGATCTTGAGGGA -s Anc0.Anc0refChr1 26476 31 - 62388 GCCCTACTTTGAATA---ATAGGATCTTGCAGGA -s Anc1.Anc1refChr2 105335 34 + 144309 GCCCTACTTTGAATAGGAATAGGATCTTGCAGGA -s Anc2.Anc2refChr3 15267 31 + 53186 GCCCTATTTTGAATA---ATAGGATCTTGCAGGA -s mr.mrrefChr0 129652 34 + 130230 GCTCAGCTGTGAATGGGAGTGGGATCTTGAAGGA -s simCow_chr6.simCow.chr6 142589 31 + 602619 TCTCTATTTTGAGTG---TCAGGGTCTTGCAGAA -s simDog_chr6.simDog.chr6 427048 31 - 593897 GCCTTCTGTTGAATA---ATAGGAACTTGTAGGA -s simHuman_chr6.simHuman.chr6 129441 34 + 601863 GCCCCACTTTGGATAGGATTAGGTTCTTGCAGGA -s simRat_chr6.simRat.chr6 514078 34 - 647215 GCTCTGCTGTTAATGGGAGGGGGATCTTGAAGGA - -a -s simMouse_chr6.simMouse.chr6 135365 34 + 636262 AGTTGGTTAATAGAAAGTATGTCAACTCAGTTAA -s Anc0.Anc0refChr1 26510 34 - 62388 GGTTGTGCACTAAAAAGTTCATCTACTTAATTAA -s Anc1.Anc1refChr2 105372 34 + 144309 GGTTGTGCACTAAAAAGTTCATCTACTTAATTAA -s Anc2.Anc2refChr3 15301 34 + 53186 GGATGTGCACTAAAAAGTTCATCTACTTACTCAA -s mr.mrrefChr0 129686 34 + 130230 AGTTGGTTAATAAAAAGTATATCAACTCAATTAA -s simCow_chr6.simCow.chr6 142623 32 + 602619 GGATGT--AGTAAGAAGTGCATCAGCTCACTCAA -s simDog_chr6.simDog.chr6 427082 32 - 593897 GGATGTGCACCAAACAGCTCATCTA--TACTCAA -s simHuman_chr6.simHuman.chr6 129478 34 + 601863 GGTTGCGCACTGAAAAATCCACCTACTTAACTAA -s simRat_chr6.simRat.chr6 514112 34 - 647215 AGTTAGTTAATAAAGAGTAAATCAACTGAATTAA - -a -s simMouse_chr6.simMouse.chr6 135399 2 + 636262 TG -s Anc0.Anc0refChr1 26553 2 - 62388 CA -s Anc1.Anc1refChr2 105415 2 + 144309 CA -s Anc2.Anc2refChr3 15344 2 + 53186 CA -s mr.mrrefChr0 129720 2 + 130230 TG -s simCow_chr6.simCow.chr6 142664 2 + 602619 TA -s simDog_chr6.simDog.chr6 427123 2 - 593897 CG -s simHuman_chr6.simHuman.chr6 129521 2 + 601863 CA -s simRat_chr6.simRat.chr6 514146 2 - 647215 TG - -a -s simMouse_chr6.simMouse.chr6 135401 8 + 636262 TGCCAAAA -s Anc0.Anc0refChr1 26555 8 - 62388 TGCCAACA -s Anc1.Anc1refChr2 105417 8 + 144309 TGCCAACA -s Anc2.Anc2refChr3 15346 8 + 53186 TTTTAACA -s mr.mrrefChr0 129722 8 + 130230 TGCCAAAA -s simCow_chr6.simCow.chr6 142666 8 + 602619 CTATATCA -s simDog_chr6.simDog.chr6 427125 8 - 593897 TTTTAACA -s simHuman_chr6.simHuman.chr6 129523 8 + 601863 TGCCTACA -s simRat_chr6.simRat.chr6 514151 8 - 647215 TACCAAGA - -a -s simMouse_chr6.simMouse.chr6 135409 1 + 636262 T -s Anc0.Anc0refChr1 26563 1 - 62388 T -s Anc1.Anc1refChr2 105425 1 + 144309 T -s Anc2.Anc2refChr3 15354 1 + 53186 T -s mr.mrrefChr0 129730 1 + 130230 T -s simCow_chr6.simCow.chr6 142674 1 + 602619 T -s simDog_chr6.simDog.chr6 427135 1 - 593897 T -s simHuman_chr6.simHuman.chr6 129531 1 + 601863 G -s simRat_chr6.simRat.chr6 514159 1 - 647215 T - -a -s simMouse_chr6.simMouse.chr6 135410 6 + 636262 AATGTT -s Anc0.Anc0refChr1 26564 6 - 62388 ATTATT -s Anc1.Anc1refChr2 105426 6 + 144309 ATTATT -s Anc2.Anc2refChr3 15370 6 + 53186 ATTATT -s mr.mrrefChr0 129731 6 + 130230 AATGTT -s simCow_chr6.simCow.chr6 142690 6 + 602619 ATTATT -s simDog_chr6.simDog.chr6 427151 6 - 593897 ATTATT -s simHuman_chr6.simHuman.chr6 129532 6 + 601863 ATTATT -s simRat_chr6.simRat.chr6 514160 6 - 647215 AATGTT - -a -s simMouse_chr6.simMouse.chr6 135416 23 + 636262 TGCTTGTCTATAGCACAAATACA -s Anc0.Anc0refChr1 26579 22 - 62388 TAGCAGTAT-TTGTTCAAGAACA -s Anc1.Anc1refChr2 105441 23 + 144309 TAGCAGTATATTGTTCAAGAACA -s Anc2.Anc2refChr3 15385 22 + 53186 TAGCAATAT-TTGTTCAAGAACA -s mr.mrrefChr0 129737 23 + 130230 TGCTTGTCTATAGCACAAATACA -s simCow_chr6.simCow.chr6 142711 19 + 602619 TAGTCATAT-TT---CAATAATA -s simDog_chr6.simDog.chr6 427166 22 - 593897 TAGCAATTT-TTGTTCAAGAACA -s simHuman_chr6.simHuman.chr6 129547 23 + 601863 TAGCGGTATATCAATCCAGAACA -s simRat_chr6.simRat.chr6 514166 23 - 647215 CCCTTGTTTGTAGCATGAATACA - -a -s simMouse_chr6.simMouse.chr6 135439 19 + 636262 ATGGAAAAGTGACAGAATG -s Anc0.Anc0refChr1 26601 19 - 62388 TCATAGAAGCAACTGAATG -s Anc1.Anc1refChr2 105464 19 + 144309 TCATAGAAGCAACTGAATG -s Anc2.Anc2refChr3 15409 19 + 53186 TCATAGAAGCGACTAAATT -s mr.mrrefChr0 129760 19 + 130230 ACGGAAAAGTAACAGAATG -s simCow_chr6.simCow.chr6 142732 19 + 602619 TCATAGAAGGTACAAAATT -s simDog_chr6.simDog.chr6 427190 18 - 593897 TCATAGAGGCGACTAAGC- -s simHuman_chr6.simHuman.chr6 129570 19 + 601863 CCATAGAAGCAATGGAATG -s simRat_chr6.simRat.chr6 514189 19 - 647215 TCTGAAAAGTAACAGTATG - -a -s simMouse_chr6.simMouse.chr6 135458 15 + 636262 GATAAAGCACGCTGC -s Anc0.Anc0refChr1 26621 13 - 62388 TGAAAAGCATCCT-- -s Anc1.Anc1refChr2 105484 15 + 144309 TGAAAAGCATCCTGC -s Anc2.Anc2refChr3 15429 13 + 53186 GGAATTGCATCCT-- -s mr.mrrefChr0 129779 15 + 130230 TATAAAGCACCCTGC -s simCow_chr6.simCow.chr6 142752 13 + 602619 GGAATTGCATCCC-- -s simDog_chr6.simDog.chr6 427209 13 - 593897 GAAATTGCATCCT-- -s simHuman_chr6.simHuman.chr6 129590 15 + 601863 TGCAAAGCATCTTGC -s simRat_chr6.simRat.chr6 514208 15 - 647215 TATAAATCACCCTGT - -a -s simMouse_chr6.simMouse.chr6 135473 14 + 636262 AATCTTTAAAAGTG -s Anc0.Anc0refChr1 26634 13 - 62388 -AGATTTAAAAGGG -s Anc1.Anc1refChr2 105499 14 + 144309 AAGATTTAAAAGGG -s Anc2.Anc2refChr3 15442 13 + 53186 -AGATTTAAACGGG -s mr.mrrefChr0 129794 14 + 130230 AAGATTTAAAAGTG -s simCow_chr6.simCow.chr6 142765 13 + 602619 -ACATTTAAAGGGG -s simDog_chr6.simDog.chr6 427222 13 - 593897 -AGATTTAAACAGG -s simHuman_chr6.simHuman.chr6 129610 14 + 601863 AAGATTTAACAGGG -s simRat_chr6.simRat.chr6 514223 14 - 647215 GAGATTTAAATGCG - -a -s simMouse_chr6.simMouse.chr6 135487 13 + 636262 TGGGTTTTGACAT -s Anc0.Anc0refChr1 26647 13 - 62388 GGGGTATTGACCC -s Anc1.Anc1refChr2 105513 13 + 144309 GGGGTATTGACCC -s Anc2.Anc2refChr3 15455 13 + 53186 GGGGTATTGGCCC -s mr.mrrefChr0 129808 13 + 130230 GGGGTTTTGACAT -s simCow_chr6.simCow.chr6 142778 13 + 602619 GAGGTATTGCCCT -s simDog_chr6.simDog.chr6 427235 12 - 593897 GGGA-ATTGGCTC -s simHuman_chr6.simHuman.chr6 129624 13 + 601863 GGGGTGCTGACCC -s simRat_chr6.simRat.chr6 514253 13 - 647215 GGCGTTTCGAAAT - -a -s simMouse_chr6.simMouse.chr6 135500 18 + 636262 TAGATGTACGCACCTTGC -s Anc0.Anc0refChr1 26660 18 - 62388 TAGATGAGCCCACCCTAT -s Anc1.Anc1refChr2 105526 18 + 144309 TAGATGAGCCCACCCTAT -s Anc2.Anc2refChr3 15468 18 + 53186 TTGATGAGCCCACCCTAT -s mr.mrrefChr0 129821 18 + 130230 TAGATGTACGCACCCTGC -s simCow_chr6.simCow.chr6 142795 18 + 602619 TTAATGAATGCACCCTAT -s simDog_chr6.simDog.chr6 427247 18 - 593897 TTGGTGAGCCCACGCTAT -s simHuman_chr6.simHuman.chr6 129637 18 + 601863 TAGATAAGCACACCCCAT -s simRat_chr6.simRat.chr6 514266 18 - 647215 TAGATGTACGCACCCTGC - -a -s simMouse_chr6.simMouse.chr6 135518 3 + 636262 AAT -s Anc0.Anc0refChr1 26683 3 - 62388 AAG -s Anc1.Anc1refChr2 105549 3 + 144309 AAG -s Anc2.Anc2refChr3 15491 3 + 53186 GAG -s mr.mrrefChr0 129839 3 + 130230 AAT -s simCow_chr6.simCow.chr6 142818 3 + 602619 GAG -s simDog_chr6.simDog.chr6 427270 3 - 593897 GAG -s simHuman_chr6.simHuman.chr6 129660 3 + 601863 AAG -s simRat_chr6.simRat.chr6 514284 3 - 647215 AAT - -a -s simMouse_chr6.simMouse.chr6 135521 46 + 636262 CACCCTGGGGTGTTGTTATATATATGTCCAGGATATCTCAACCTGC -s Anc0.Anc0refChr1 26686 45 - 62388 CACCCTAGGGGGTTGTTATCTGAGCCTC-AGGGAGTCTCCACCAAC -s Anc1.Anc1refChr2 105552 45 + 144309 CACCCTAGGGGGTTGTTATCTGAGCCTC-AGGGAGTCTCCACCAAC -s Anc2.Anc2refChr3 15494 45 + 53186 CACCCTAGGGGGTTGTTCTCTGAGCTTC-AGGGAATCTCCACCAAT -s mr.mrrefChr0 129842 45 + 130230 CACCCTGGGGTGTTGTTATATATATCTC-AGGATGTCTCAACCTGC -s simCow_chr6.simCow.chr6 142837 45 + 602619 CATCCTAGGGGGTTGTTTTCTGAGTTTT-GGGTAAACTCCACGACT -s simDog_chr6.simDog.chr6 427273 45 - 593897 CACCCTAGGGGGTTGTTCTTTGAGCTTC-ACAGAATGTCTACCAAT -s simHuman_chr6.simHuman.chr6 129663 45 + 601863 CACCCTAGGAGGTTGTTATCTGCGCCTC-AGGGAGTCTCCACCACC -s simRat_chr6.simRat.chr6 514287 45 - 647215 CACCCCGGGGTGTTGTTATATATATCTC-AGGATGTCTCAACCTGC - -a -s simMouse_chr6.simMouse.chr6 135567 4 + 636262 TCAC -s Anc0.Anc0refChr1 26731 4 - 62388 CCCC -s Anc1.Anc1refChr2 105597 4 + 144309 CCCC -s Anc2.Anc2refChr3 15545 4 + 53186 CCCC -s mr.mrrefChr0 129887 4 + 130230 TCAC -s simCow_chr6.simCow.chr6 142888 4 + 602619 CCGC -s simDog_chr6.simDog.chr6 427324 4 - 593897 CCCC -s simHuman_chr6.simHuman.chr6 129708 4 + 601863 CTGC -s simRat_chr6.simRat.chr6 514332 4 - 647215 TCAC - -a -s simMouse_chr6.simMouse.chr6 135571 29 + 636262 ATCTCTCAACTTGGGGTCCAAGGGCCCAT -s Anc0.Anc0refChr1 26736 28 - 62388 ATCTCTTGAA-CAGGGTTTAAGGGCCTGT -s Anc1.Anc1refChr2 105602 28 + 144309 ATCTCTTGAA-CAGGGTTTAAGGGCCTGT -s Anc2.Anc2refChr3 15550 28 + 53186 ATCTCTTGAA-CAGGGTTTAAGGGTCTGT -s mr.mrrefChr0 129891 29 + 130230 ATCTCTCAACTTGGGGTCTAAGGGCCTGT -s simCow_chr6.simCow.chr6 142893 28 + 602619 ATCTCTTGAA-CAGGGTCTAGAAGTCTGT -s simDog_chr6.simDog.chr6 427329 28 - 593897 ACCTCTTGAC-CAGGGTTTAAGGGTCTGT -s simHuman_chr6.simHuman.chr6 129713 28 + 601863 ATCTCTTGAA-CAGGGTTTAAGGGCCTGT -s simRat_chr6.simRat.chr6 514336 29 - 647215 ATCTCTCACCTTGGGGTCTAAGGGTCTGT - -a -s simMouse_chr6.simMouse.chr6 135600 2 + 636262 TC -s Anc0.Anc0refChr1 26764 2 - 62388 TC -s Anc1.Anc1refChr2 105630 2 + 144309 TC -s Anc2.Anc2refChr3 15578 2 + 53186 TC -s mr.mrrefChr0 129920 2 + 130230 TC -s simCow_chr6.simCow.chr6 142921 2 + 602619 TC -s simDog_chr6.simDog.chr6 427357 2 - 593897 TC -s simHuman_chr6.simHuman.chr6 129741 2 + 601863 TC -s simRat_chr6.simRat.chr6 514367 2 - 647215 TC - -a -s simMouse_chr6.simMouse.chr6 135602 50 + 636262 ATATAAATAGCTAGGACTACCCAATTTGAATAAACAAAAAACAGACAGAT -s Anc0.Anc0refChr1 26773 43 - 62388 -----ACTGACTATGACAACTTGATTTGACCAAATGAATAACAGACAG-- -s Anc1.Anc1refChr2 105639 50 + 144309 GTGTAACTGACTATGACAACTTGATTTGACCAAATGAATAACAGACAGAA -s Anc2.Anc2refChr3 15587 43 + 53186 -----ACTGACTATGACAACTTGATTTGACCAAATTAATAACAGGCAG-- -s mr.mrrefChr0 129922 50 + 130230 ATATAAATAACTAGGACTACTTAATTTGAACAAATGAAAAACAGACAGAT -s simCow_chr6.simCow.chr6 142930 43 + 602619 -----ACTGACGATGATGACTTGATTCGACCAAACAAATAACAGGCAG-- -s simDog_chr6.simDog.chr6 427366 43 - 593897 -----ACTGACTATGACAACTTGACTTGACCAAATTAATGGCAGGTAG-- -s simHuman_chr6.simHuman.chr6 129760 50 + 601863 GTGTAAGTGATTATGACAACTTCATTTGACCAAATGACTAACAGACAGAA -s simRat_chr6.simRat.chr6 514369 50 - 647215 ATATAAATAACTAGGATTACTTGATTTGAACAAATGAAAAACAGACAGAT - -a -s simMouse_chr6.simMouse.chr6 135652 37 + 636262 GGATAATTTGTTAGAGGGTTACAACCATCTGCCATAT -s Anc0.Anc0refChr1 26816 36 - 62388 GGTTAACTTTCAAGAGGGCAACAACCATCTGCCATA- -s Anc1.Anc1refChr2 105689 37 + 144309 GGTTAACTTTCAAGAGGGCAACAACCATCTGCCATAC -s Anc2.Anc2refChr3 15630 36 + 53186 GGTAAACTTTCAAGAGGGCAACAACCAGCTGCCATA- -s mr.mrrefChr0 129972 37 + 130230 GGATAATTTTCTAGAGGGTAACAACCATCTGCCATAC -s simCow_chr6.simCow.chr6 142973 36 + 602619 GGTAAACTTTCAAGAGGGCAACAACCAGCTACCATA- -s simDog_chr6.simDog.chr6 427409 35 - 593897 GG-AAACTTTCTAAAAGGCAACAACTAGCTGCCATA- -s simHuman_chr6.simHuman.chr6 129810 37 + 601863 GGGTAAGCTTCAGGAGGGCAACAACCATCTGCCATAC -s simRat_chr6.simRat.chr6 514426 37 - 647215 GGATAACTTTCTAGAGGGTAACAACCAACTGCCATAC - -a -s simMouse_chr6.simMouse.chr6 135689 51 + 636262 AATTAGCATTCTCCTAACGTACAAGGGACGGGAAAAAGTGTAGACCTACAG -s Anc0.Anc0refChr1 26852 51 - 62388 AATAAGGGCTATCCTAGCATGGGAGGGATAGGAGAAGTCCTGGGCCCACAG -s Anc1.Anc1refChr2 105726 51 + 144309 AATAAGGGCTATCCTAGCATGGGAGGGATAGGAGAAGTCCTGGGCCCACAG -s Anc2.Anc2refChr3 15666 51 + 53186 GATAAGGGCTATCCTGGCATGGGAGGGATAGGGGAAGTCCTGGGCCCACAG -s mr.mrrefChr0 130009 51 + 130230 AATCAGCATTCTCCTAACGTAGGAGGGACAGGAGAAAGTGTAGGCCTACAG -s simCow_chr6.simCow.chr6 143009 50 + 602619 GATATAAGCTCTCCT-GCATCGGAGGGATAGGGGAATGCCCGGGACCACAG -s simDog_chr6.simDog.chr6 427445 51 - 593897 GATAAGGGTTATTTCGGCATGGTAGGGATAGGGGGAGTCCTGGGCCCACAG -s simHuman_chr6.simHuman.chr6 129847 42 + 601863 AA---------TCCTAGCATGGGAGGGATAGCAGAAGTCCTGGGTCCACAG -s simRat_chr6.simRat.chr6 514463 51 - 647215 AATCAGCACTCTCCTAATGTAGGACAGACAGGGGAGAGTGTAGGCCTACAG - -a -s simMouse_chr6.simMouse.chr6 135740 17 + 636262 ATTTTCAGCACAGGGGG -s Anc0.Anc0refChr1 26903 16 - 62388 GTTTTCA-TACAGAAGT -s Anc1.Anc1refChr2 105777 16 + 144309 GTTTTCA-TACAGAAGT -s Anc2.Anc2refChr3 15717 16 + 53186 GTGTTCA-GACAGAAGT -s mr.mrrefChr0 130060 17 + 130230 ATTTTCAGTACAGGGGG -s simCow_chr6.simCow.chr6 143059 16 + 602619 GTGACCA-GCCAGAAGT -s simDog_chr6.simDog.chr6 427496 16 - 593897 ATGTTCA-GACAGAAGC -s simHuman_chr6.simHuman.chr6 129890 16 + 601863 GTTTTTG-TACAAAAGT -s simRat_chr6.simRat.chr6 514514 17 - 647215 ATTTCCAGTACAGGGGG - -a -s simMouse_chr6.simMouse.chr6 135757 94 + 636262 CATTCTTATCATCCTCCCACTCTTTGGTTTCTCAGGAGTTGCCTCTTGGGCTAGGTTAGGTGAAACCTTTAAGGTCAGCTAGCCTGTTCAGGGC -s Anc0.Anc0refChr1 26923 7 - 62388 ATTTCTT--------------------------------------------------------------------------------------- -s Anc1.Anc1refChr2 105797 7 + 144309 ATTTCTT--------------------------------------------------------------------------------------- -s Anc2.Anc2refChr3 15737 7 + 53186 ATTTCTT--------------------------------------------------------------------------------------- -s mr.mrrefChr0 130081 91 + 130230 CATTCTTATCA---TCCCACTCTTTGGTTTCTCAGGAGTTGCCTCTTGGGCTAGGTTAGGTGAAACCTTTAAGGTCAGCTAGCCTGTTCAGGGC -s simCow_chr6.simCow.chr6 143079 7 + 602619 ATTTTTT--------------------------------------------------------------------------------------- -s simDog_chr6.simDog.chr6 427516 7 - 593897 ATTTCTT--------------------------------------------------------------------------------------- -s simHuman_chr6.simHuman.chr6 129910 7 + 601863 ATTTCTC--------------------------------------------------------------------------------------- -s simRat_chr6.simRat.chr6 514535 91 - 647215 CATTCTTATAA---TCCCACTCTTGGGCGCCTCATGAGTTGCCTCTGGAGCTGGATTTGGTGAGACCTTTTAGGTCACCTAGCGTGTTCAGGGC - -a -s simMouse_chr6.simMouse.chr6 135851 45 + 636262 ATGAGGAGTAGACGAAAGTGCCACTAGTGAAAAGTACCTACATAA -s Anc0.Anc0refChr1 26930 14 - 62388 -------------------------------AAGGAGATACATAA -s Anc1.Anc1refChr2 105804 14 + 144309 -------------------------------AAGGAGATACATAA -s Anc2.Anc2refChr3 15744 14 + 53186 -------------------------------GAGGAGATACCTAA -s mr.mrrefChr0 130172 45 + 130230 ATGAGGAGTAGACGAAAGTGCCACTAGTGAAAAGTACCTACATAA -s simCow_chr6.simCow.chr6 143086 14 + 602619 -------------------------------GAAGTGATACCCAA -s simDog_chr6.simDog.chr6 427523 12 - 593897 -------------------------------GAGGAGATACCT-- -s simHuman_chr6.simHuman.chr6 129917 14 + 601863 -------------------------------AAGGAGATACATAA -s simRat_chr6.simRat.chr6 514627 45 - 647215 ATGAGCAGCAGATGGAAGCGCGACAGGTGAAAAGTATATACATAA - -a -s simMouse_chr6.simMouse.chr6 135896 6 + 636262 TTGTGC -s Anc0.Anc0refChr1 26944 5 - 62388 TTCTG- -s Anc1.Anc1refChr2 105818 5 + 144309 TTCTG- -s Anc2.Anc2refChr3 15758 5 + 53186 TTCTA- -s mr.mrrefChr0 130217 5 + 130230 TTGTG- -s simCow_chr6.simCow.chr6 143101 5 + 602619 TTCCA- -s simDog_chr6.simDog.chr6 427535 5 - 593897 TTCTA- -s simHuman_chr6.simHuman.chr6 129931 5 + 601863 TTCTG- -s simRat_chr6.simRat.chr6 514672 5 - 647215 TTGTG- - -a -s simMouse_chr6.simMouse.chr6 135902 1 + 636262 A -s Anc0.Anc0refChr1 26950 1 - 62388 A -s Anc1.Anc1refChr2 105824 1 + 144309 A -s Anc2.Anc2refChr3 15764 1 + 53186 A -s mr.mrrefChr0 130222 1 + 130230 A -s simCow_chr6.simCow.chr6 143107 1 + 602619 A -s simDog_chr6.simDog.chr6 427541 1 - 593897 A -s simHuman_chr6.simHuman.chr6 129937 1 + 601863 A -s simRat_chr6.simRat.chr6 514677 1 - 647215 G - -a -s simMouse_chr6.simMouse.chr6 135903 7 + 636262 CATCTCA -s Anc0.Anc0refChr1 26951 6 - 62388 TATCTC- -s Anc1.Anc1refChr2 105825 6 + 144309 TATCTC- -s Anc2.Anc2refChr3 15765 6 + 53186 TATCTT- -s mr.mrrefChr0 130223 7 + 130230 CATCTCA -s simCow_chr6.simCow.chr6 143108 6 + 602619 TATATT- -s simDog_chr6.simDog.chr6 427543 6 - 593897 TATCTT- -s simHuman_chr6.simHuman.chr6 129938 6 + 601863 TATCTC- -s simRat_chr6.simRat.chr6 514678 7 - 647215 CATCTCA - -a -s simMouse_chr6.simMouse.chr6 135910 19 + 636262 GGTGCTATTCCAGGAAACC -s Anc0.Anc0refChr1 34845 3 + 62388 ----------------ACA -s Anc1.Anc1refChr2 37883 3 - 144309 ----------------ACA -s Anc2.Anc2refChr3 15783 3 + 53186 ----------------AGG -s mr.mrrefChr4 0 18 - 408 GGTGC-ATTCCAGGACACA -s simCow_chr6.simCow.chr6 143126 3 + 602619 ----------------AGG -s simDog_chr6.simDog.chr6 427561 3 - 593897 ----------------AGG -s simHuman_chr6.simHuman.chr6 471278 3 - 601863 ----------------ACA -s simRat_chr6.simRat.chr6 514685 18 - 647215 GGTGC-GTTCCAGGGCACA - -a -s simMouse_chr6.simMouse.chr6 135929 18 + 636262 CAGATTCCTAGGCTAACC -s Anc0.Anc0refChr1 34848 18 + 62388 CAGGTTCCAGGACTAACC -s Anc1.Anc1refChr2 37886 18 - 144309 CAGGTTCCAGGACTAACC -s Anc2.Anc2refChr3 15789 18 + 53186 CAGGTTCAAGGACTATCC -s mr.mrrefChr4 18 18 - 408 CAGATTCCTAGGCTAACC -s simCow_chr6.simCow.chr6 143134 18 + 602619 AAGATTAAGGGGTTAACC -s simDog_chr6.simDog.chr6 427567 18 - 593897 CAGGTTCAAGGACTATCC -s simHuman_chr6.simHuman.chr6 471281 18 - 601863 CAGGTCACAGGCCTAACC -s simRat_chr6.simRat.chr6 514703 18 - 647215 CAGATTCCTAGGCTAACC - -a -s simMouse_chr6.simMouse.chr6 135947 58 + 636262 TTATCCCTTTACCAATGCCATATGTAAATATTTTTTTATGAGAACATATAGTGGGGTT -s Anc0.Anc0refChr1 34866 53 + 62388 TTA----TTTCCTAATGATATCTTTGAATATTTTTT-ATGAGAACATATGGTGGGGTT -s Anc1.Anc1refChr2 37904 57 - 144309 TTATCTCTTTCCTAATGATATCTTTGAATATTTTTT-ATGAGAACATATGGTGGGGTT -s Anc2.Anc2refChr3 15807 53 + 53186 TTA----TTGCATAATGATACCGTTGAATATTTATC-ATGGGAATATATGGTGGGGTT -s mr.mrrefChr4 36 58 - 408 TTATCCCTTTACCAATGCCATATGTGAATATTTTTTTATGAGAACATATGGTGGGGTT -s simCow_chr6.simCow.chr6 143152 53 + 602619 TTA----TTGCATAATGATACCGTTGAATATTTATC-ATGGGAATATGTGGTGAGGTT -s simDog_chr6.simDog.chr6 427585 31 - 593897 TTA--------------------------ATTTACC-ATAGGAGTGTAGGGCAGGGTT -s simHuman_chr6.simHuman.chr6 471308 57 - 601863 TTTTCTCTTTCCTAATTATTTCTACGAATATTTTTT-ATGAGAACATATGGTGGGATT -s simRat_chr6.simRat.chr6 514722 55 - 647215 TTACCCCTTTATCAATGCCATTTGTGAATGTTTTCTTATGAGAA---ATGGTGGGGTT - -a -s simMouse_chr6.simMouse.chr6 136005 15 + 636262 ATCCACCACAAGTTT -s Anc0.Anc0refChr1 34923 15 + 62388 CTCCACCACAAGTTT -s Anc1.Anc1refChr2 37965 15 - 144309 CTCCACCACAAGTTT -s Anc2.Anc2refChr3 15864 15 + 53186 CTCTACCACAAGTTT -s mr.mrrefChr4 94 15 - 408 CTCCACCACAAGTTT -s simCow_chr6.simCow.chr6 143209 15 + 602619 CTCTACCTCAACTTT -s simDog_chr6.simDog.chr6 427620 15 - 593897 GTCTATTACAAGTTT -s simHuman_chr6.simHuman.chr6 471369 15 - 601863 CTCCTCCACAAGTTT -s simRat_chr6.simRat.chr6 514777 15 - 647215 CTTCGCCACAAGTTT - -a -s simMouse_chr6.simMouse.chr6 136020 10 + 636262 ACCCAGTCCC -s Anc0.Anc0refChr1 34941 10 + 62388 ACCTGGTCCC -s Anc1.Anc1refChr2 37983 10 - 144309 ACCTGGTCCC -s Anc2.Anc2refChr3 15882 10 + 53186 ACCTGGTCCC -s mr.mrrefChr4 109 10 - 408 ACCCAGTCCC -s simCow_chr6.simCow.chr6 143227 10 + 602619 ACCTGGTCCC -s simDog_chr6.simDog.chr6 427638 10 - 593897 ACCTGATCCC -s simHuman_chr6.simHuman.chr6 471387 10 - 601863 GCCTGGTCCC -s simRat_chr6.simRat.chr6 514792 10 - 647215 ACCCAGTCCC - -a -s simMouse_chr6.simMouse.chr6 136030 12 + 636262 ATTTGACATAGA -s Anc0.Anc0refChr1 34961 11 + 62388 -TTTTACATGGA -s Anc1.Anc1refChr2 38005 12 - 144309 ATTTTACATGGA -s Anc2.Anc2refChr3 15902 11 + 53186 -TTTTGCATGGA -s mr.mrrefChr4 119 12 - 408 ATTTGACATAGA -s simCow_chr6.simCow.chr6 143247 10 + 602619 -TT-TTTATGAA -s simDog_chr6.simDog.chr6 427655 9 - 593897 ---TTGCATGGG -s simHuman_chr6.simHuman.chr6 471410 12 - 601863 ATTTTACATGGA -s simRat_chr6.simRat.chr6 514802 12 - 647215 ATTTGACATAGA - -a -s simMouse_chr6.simMouse.chr6 136042 4 + 636262 TAAG -s Anc0.Anc0refChr1 34973 4 + 62388 TAAG -s Anc1.Anc1refChr2 38018 4 - 144309 TAAG -s Anc2.Anc2refChr3 15914 4 + 53186 TAAG -s mr.mrrefChr4 131 4 - 408 TAAG -s simCow_chr6.simCow.chr6 143258 4 + 602619 CAAG -s simDog_chr6.simDog.chr6 427665 4 - 593897 TAAG -s simHuman_chr6.simHuman.chr6 471423 4 - 601863 TAAG -s simRat_chr6.simRat.chr6 514814 4 - 647215 CAAG - -a -s simMouse_chr6.simMouse.chr6 136046 20 + 636262 TGTGAAGACATAAGGCCAGA -s Anc0.Anc0refChr1 34984 20 + 62388 GATGAAGATATAAAGTCAGA -s Anc1.Anc1refChr2 38029 20 - 144309 GATGAAGATATAAAGTCAGA -s Anc2.Anc2refChr3 15925 20 + 53186 GATGAAGATATAAAGTCATA -s mr.mrrefChr4 135 20 - 408 TGTGAAGATATAAGGCCAGA -s simCow_chr6.simCow.chr6 143269 18 + 602619 TTTG--TATATAAAGTCATA -s simDog_chr6.simDog.chr6 427676 20 - 593897 GATGAAGATATGAGGTCATA -s simHuman_chr6.simHuman.chr6 471434 16 - 601863 CATGAAGATGTAA----AGA -s simRat_chr6.simRat.chr6 514818 20 - 647215 TGTGAAGATAAAAGGCCTGA - -a -s simMouse_chr6.simMouse.chr6 136066 33 + 636262 CCTCAAAGGCTTTAGACTACATTCTGTTAATCC -s Anc0.Anc0refChr1 35004 33 + 62388 CCTTGGTAGCTTTAGAGTACATTCTGTTGATCC -s Anc1.Anc1refChr2 38049 33 - 144309 CCTTGGTAGCTTTAGAGTACATTCTGTTGATCC -s Anc2.Anc2refChr3 15945 33 + 53186 CCTTGGTAGCTTTAGAGTGCATTCTTTTGATCC -s mr.mrrefChr4 155 33 - 408 CCTCAATAGCTTTAGACTACATTCTGTTAATCC -s simCow_chr6.simCow.chr6 143287 33 + 602619 TCTTGGTGGTAATAGAGTGCCTTCTGTTGATCC -s simDog_chr6.simDog.chr6 427696 33 - 593897 CCTTTGTAGCTTTAGAGTGCATTTTTTTGACCC -s simHuman_chr6.simHuman.chr6 471502 33 - 601863 CCTTGGTAGCTTTAGAGTACATTCTGTTGATCC -s simRat_chr6.simRat.chr6 514838 33 - 647215 CCTCAATATCTTTAGACTACATTCTGCCAATCC - -a -s simMouse_chr6.simMouse.chr6 136099 14 + 636262 TGACCCTCCTTAAT -s Anc0.Anc0refChr1 35037 14 + 62388 TGCTCCTCTTTGAG -s Anc1.Anc1refChr2 38082 14 - 144309 TGCTCCTCTTTGAG -s Anc2.Anc2refChr3 15980 14 + 53186 TGCTCCTCTTTGAG -s mr.mrrefChr4 188 14 - 408 TGACCCTCCTTAAT -s simCow_chr6.simCow.chr6 143322 14 + 602619 TGCTCGTTTTTGAG -s simDog_chr6.simDog.chr6 427731 14 - 593897 TGCTCCTCTTTGAA -s simHuman_chr6.simHuman.chr6 471535 9 - 601863 -----CTATTTGAG -s simRat_chr6.simRat.chr6 514871 14 - 647215 TCACCCTCCTTAAT - -a -s simMouse_chr6.simMouse.chr6 136113 8 + 636262 AACTTTAT -s Anc0.Anc0refChr1 35051 8 + 62388 AAATTTCT -s Anc1.Anc1refChr2 38096 8 - 144309 AAATTTCT -s Anc2.Anc2refChr3 15994 8 + 53186 AAAGTTCT -s mr.mrrefChr4 202 8 - 408 AACTTTAT -s simCow_chr6.simCow.chr6 143342 8 + 602619 AAAGTTTT -s simDog_chr6.simDog.chr6 427745 8 - 593897 CAAGTTCT -s simHuman_chr6.simHuman.chr6 471544 8 - 601863 AAATCTGC -s simRat_chr6.simRat.chr6 514885 8 - 647215 AAGTTTAT - -a -s simMouse_chr6.simMouse.chr6 136121 7 + 636262 TGCTTGA -s Anc0.Anc0refChr1 35059 7 + 62388 AGTTTAA -s Anc1.Anc1refChr2 38104 7 - 144309 AGTTTAA -s Anc2.Anc2refChr3 16002 7 + 53186 ATTTTAA -s mr.mrrefChr4 210 7 - 408 AGCTTGA -s simCow_chr6.simCow.chr6 143355 7 + 602619 ATTTTAC -s simDog_chr6.simDog.chr6 427753 7 - 593897 ATTTTCA -s simHuman_chr6.simHuman.chr6 471552 7 - 601863 AGTTTAA -s simRat_chr6.simRat.chr6 514893 7 - 647215 AGCTTGG - -a -s simMouse_chr6.simMouse.chr6 136128 35 + 636262 TAGTAAGCAGAACTCTCTGTCCTACAGATTGTATT -s Anc0.Anc0refChr1 35067 35 + 62388 TAGTTAGCAAACCTCCCTGTCCTGCAGATTGTATT -s Anc1.Anc1refChr2 38112 35 - 144309 TAGTTAGCAAACCTCCCTGTCCTGCAGATTGTATT -s Anc2.Anc2refChr3 16010 35 + 53186 TAGTTAGCAAACCTCCCTGTCCTGTAGATTGTATT -s mr.mrrefChr4 218 35 - 408 TAGTAAGCAGAACTCTCTGTCCTGCAGATTGTATT -s simCow_chr6.simCow.chr6 143363 35 + 602619 GAGTAAGCAAACCTCCCTGTGCTGTGGTTTGTATT -s simDog_chr6.simDog.chr6 427761 35 - 593897 TAGTTAACGAACCTCCCTGTCCTGTAGATTGTACT -s simHuman_chr6.simHuman.chr6 471560 35 - 601863 TACTTAGCAAGCCTCCCTGTACTGCAGATTGGATT -s simRat_chr6.simRat.chr6 514901 35 - 647215 TAGTCAGCAGAACTCTCTGTTCTGCAGATTGTATT - -a -s simMouse_chr6.simMouse.chr6 136163 80 + 636262 GCCCCATAAAAATATGTAAGCAGATCTTTAAGATCCTGCAATATTGTATTTCAACTTCCTGAGTAGATCCATCCTGGTTG -s Anc0.Anc0refChr1 35102 74 + 62388 ACTGCAT--CAAGTTGTAAGCGGATCTTTAAGATCCTGCAACGTTGTTTTCCAATTTACTAAGTAGACTCAT----GCTG -s Anc1.Anc1refChr2 38147 76 - 144309 ACTGCATAACAAGTTGTAAGCGGATCTTTAAGATCCTGCAACGTTGTTTTCCAATTTACTAAGTAGACTCAT----GCTG -s Anc2.Anc2refChr3 16045 74 + 53186 ACTGCAC--CAAGTTGTTAGTGGATCTTTAAGATCCTGCAACGTTGTTTTCCAATTTACTAAGTAGACTCAT----CCTG -s mr.mrrefChr4 253 80 - 408 GCTCCATAAAAAGATGTAAGCAGATCTTTAAGATCCTGCAATATTGTATTTCAACTTCCTGAGTAGATCCATCCTGGTTG -s simCow_chr6.simCow.chr6 143398 57 + 602619 CCTGCA------------------TCTTTCAGATGCTGCAATGCTGTTTTACAATT-ACTAAGTAGACGCAT----CCTG -s simDog_chr6.simDog.chr6 427799 72 - 593897 ACTGCAC--CAAGTTGTTAGTGGATATTTAAGACCTTCTAACATTGTTTTCCAATTTGCTCAGTAGACT--T----CCTG -s simHuman_chr6.simHuman.chr6 471595 76 - 601863 ACTGCATAACGAGTTGTAAGCTGATCTTTAAGGTCCTGCAAGGTTGTTTTCCAATGCAATAAGAAGACTCAT----GCTG -s simRat_chr6.simRat.chr6 514936 80 - 647215 GTTCCATAATAAGATGTAAGCAGATCTTTAAGATCCTCCAATATAGTATTTTGACTTTCTGAGTGGATCCATCCTGGTTG - -a -s simMouse_chr6.simMouse.chr6 136243 82 + 636262 ATTGGTTAAGGCGAATTTCCCAAAAAAACGAGAGATTCTTCCCCGACCATCCTTGCAAAGTGCTGACCTTATTTTACTGGTA -s Anc0.Anc0refChr1 35176 46 + 62388 AATGATCA------------------------------------GTTAGTCATTGCAAAGTGCTGGTCTTACTTTGCTGATA -s Anc1.Anc1refChr2 38223 46 - 144309 AATGATCA------------------------------------GTTAGTCATTGCAAAGTGCTGGTCTTACTTTGCTGATA -s Anc2.Anc2refChr3 16119 46 + 53186 GATGATCA------------------------------------GTTAGTAATTGCAAAGTGCTGGTCTTACTTTGCTGATA -s mr.mrrefChr4 333 46 - 408 ATTGATCA------------------------------------GTTAATCCTTGCAAAGTGCTGACCTTATTTTACTGGTA -s simCow_chr6.simCow.chr6 143455 46 + 602619 GATGATCG------------------------------------GCTATTAATTGCAAGGTGCTAGTCTCACCTTGCTGATA -s simDog_chr6.simDog.chr6 427871 46 - 593897 GATGATCA------------------------------------GTTAGTAATTGCAAAGCGCTGGTCTTTCTTTGCTGATG -s simHuman_chr6.simHuman.chr6 471671 40 - 601863 AATGATCA------------------------------------GTTAGTCATTGAAAAGTGC-GGTCTTACT-----CATA -s simRat_chr6.simRat.chr6 515019 46 - 647215 ATTGATCA------------------------------------GTTAATCCTTGCAAAGTGCTGGCCTTACTTTGCTGGTA - -a -s simMouse_chr6.simMouse.chr6 136325 13 + 636262 ATTACAATATGTC -s Anc0.Anc0refChr1 35222 13 + 62388 AAGTCTTTATGTC -s Anc1.Anc1refChr2 38269 13 - 144309 AAGTCTTTATGTC -s Anc2.Anc2refChr3 16165 13 + 53186 AAGTCTTTATGCC -s mr.mrrefChr4 379 13 - 408 ATTACAATATGTC -s simCow_chr6.simCow.chr6 143523 13 + 602619 AAGTCTTTATGCC -s simDog_chr6.simDog.chr6 427917 13 - 593897 AAGTCCTTATGCC -s simHuman_chr6.simHuman.chr6 471711 13 - 601863 GAAGCTCTATGTC -s simRat_chr6.simRat.chr6 515065 13 - 647215 ATTACGGTATGTC - -a -s simMouse_chr6.simMouse.chr6 136338 1 + 636262 A -s Anc0.Anc0refChr1 35235 1 + 62388 A -s Anc1.Anc1refChr2 38282 1 - 144309 A -s Anc2.Anc2refChr3 16179 1 + 53186 A -s mr.mrrefChr4 392 1 - 408 A -s simCow_chr6.simCow.chr6 143537 1 + 602619 A -s simDog_chr6.simDog.chr6 427931 1 - 593897 A -s simHuman_chr6.simHuman.chr6 471724 1 - 601863 A -s simRat_chr6.simRat.chr6 515078 1 - 647215 G - -a -s simMouse_chr6.simMouse.chr6 136339 14 + 636262 ATCTAATTTATAGC -s Anc0.Anc0refChr1 35239 10 + 62388 ATGTGATCGT---- -s Anc1.Anc1refChr2 38286 10 - 144309 ATGTGATCGT---- -s Anc2.Anc2refChr3 16183 10 + 53186 GTGTGATCGT---- -s mr.mrrefChr4 393 10 - 408 ATCTAATTTA---- -s simCow_chr6.simCow.chr6 143541 10 + 602619 GTGTGATTGT---- -s simDog_chr6.simDog.chr6 427935 10 - 593897 GTGTGATCGT---- -s simHuman_chr6.simHuman.chr6 471728 10 - 601863 ATATGATAGT---- -s simRat_chr6.simRat.chr6 515079 10 - 647215 ATCTAATTTA---- - -a -s simMouse_chr6.simMouse.chr6 136353 47 + 636262 TAATTTCTAGTCCTAACTGATCTTTTCAAGAAGGTGCGAGTTGTTTT -s Anc0.Anc0refChr1 35254 32 + 62388 ---------------ACTGATCTTTTCAAGAAAGTGTGTATTATTTT -s Anc1.Anc1refChr2 38301 32 - 144309 ---------------ACTGATCTTTTCAAGAAAGTGTGTATTATTTT -s Anc2.Anc2refChr3 16198 32 + 53186 ---------------ACTGATCCTTTCAAGAAAGTGTGTATTATTTT -s mr.mrrefChr5 0 37 + 294540 T----------CCTGACTGATCTTTTCAAGAAGGTGTGAATTGTTTT -s simCow_chr6.simCow.chr6 143556 32 + 602619 ---------------ACTGACCCTTTCAAAAAAGTGTGTGTTATTTT -s simDog_chr6.simDog.chr6 427950 32 - 593897 ---------------ACTGATCCTTGCAAGAAAGTGCATATCATTTT -s simHuman_chr6.simHuman.chr6 471743 32 - 601863 ---------------ACTGATTTTTTCAAGAAAATGTGCATTATGTT -s simRat_chr6.simRat.chr6 134126 34 + 647215 -------------TGACTGATCTTTTCTAGAAGGTGTGAATTGTTTT - -a -s simMouse_chr6.simMouse.chr6 136400 6 + 636262 CACTTT -s Anc0.Anc0refChr1 35290 6 + 62388 CACTTT -s Anc1.Anc1refChr2 38337 6 - 144309 CACTTT -s Anc2.Anc2refChr3 16234 6 + 53186 CACTTC -s mr.mrrefChr5 37 6 + 294540 CACTTT -s simCow_chr6.simCow.chr6 143592 6 + 602619 CACTTC -s simDog_chr6.simDog.chr6 427986 6 - 593897 CACTTC -s simHuman_chr6.simHuman.chr6 471779 6 - 601863 CACTTT -s simRat_chr6.simRat.chr6 134160 6 + 647215 CACTTT - -a -s simMouse_chr6.simMouse.chr6 136406 5 + 636262 GACAA -s Anc0.Anc0refChr1 35296 4 + 62388 GG-AG -s Anc1.Anc1refChr2 38343 4 - 144309 GG-AG -s Anc2.Anc2refChr3 16241 4 + 53186 GG-GG -s mr.mrrefChr5 43 5 + 294540 GACAA -s simCow_chr6.simCow.chr6 143599 4 + 602619 GG-GG -s simDog_chr6.simDog.chr6 427993 4 - 593897 GG-GG -s simHuman_chr6.simHuman.chr6 471785 4 - 601863 GG-AT -s simRat_chr6.simRat.chr6 134166 5 + 647215 GATGA - -a -s simMouse_chr6.simMouse.chr6 136411 45 + 636262 CTAAAGTAAAATGCTCTGCCCACACCAAGCTCCAAGCCCATGCAA -s Anc0.Anc0refChr1 35300 45 + 62388 CCAAAGTAAGATGCTCTGCTCACACCAAGCTCAAAACTAATGCAA -s Anc1.Anc1refChr2 38347 45 - 144309 CCAAAGTAAGATGCTCTGCTCACACCAAGCTCAAAACTAATGCAA -s Anc2.Anc2refChr3 16245 45 + 53186 CCAAAGTGAGATGCTCTGCTCACACCAAGCTCAGAACTAATGGAA -s mr.mrrefChr5 48 45 + 294540 CTAAAGTAAAATGCTCTGCCCACACCAAGCTCCAAGCCCATGCAA -s simCow_chr6.simCow.chr6 143604 44 + 602619 CCAAAGTGAGGTGCTCTGCT-ACACAGAGCTCAGGACTAATGGAA -s simDog_chr6.simDog.chr6 427997 45 - 593897 CCAAAGTGAGAGGCTCTGCCCACACCAGGCTCAGAATTAAAGGAA -s simHuman_chr6.simHuman.chr6 471789 44 - 601863 CCAGAGTAAGATGGTTTGCTCACACCAAGCTC-AAACTAATGCAA -s simRat_chr6.simRat.chr6 134171 45 + 647215 CTAAAGTAAAATGCTCTGCCCACACCAAGCTCCAAGCCCATGCAA - -a -s simMouse_chr6.simMouse.chr6 136456 14 + 636262 GAACAAGCACCTCA -s Anc0.Anc0refChr1 35345 14 + 62388 GAACAAACACCTTG -s Anc1.Anc1refChr2 38392 14 - 144309 GAACAAACACCTTG -s Anc2.Anc2refChr3 16290 14 + 53186 GAACAAACACCTTG -s mr.mrrefChr5 93 14 + 294540 GAACAAACACCTTA -s simCow_chr6.simCow.chr6 143648 14 + 602619 GAACAAACACCTTG -s simDog_chr6.simDog.chr6 428042 14 - 593897 GAACAAACACCCTG -s simHuman_chr6.simHuman.chr6 471833 14 - 601863 GAACAAACACATTG -s simRat_chr6.simRat.chr6 134217 14 + 647215 GAACAAACATCTTT - -a -s simMouse_chr6.simMouse.chr6 136470 11 + 636262 AGCAGAGACTT -s Anc0.Anc0refChr1 35365 11 + 62388 AGCAGAGACTT -s Anc1.Anc1refChr2 38412 11 - 144309 AGCAGAGACTT -s Anc2.Anc2refChr3 16310 11 + 53186 AGCAGAGATTT -s mr.mrrefChr5 107 11 + 294540 AGCAGAGACTT -s simCow_chr6.simCow.chr6 143668 11 + 602619 ATCAGAGATTT -s simDog_chr6.simDog.chr6 428062 7 - 593897 AGCAG----TT -s simHuman_chr6.simHuman.chr6 471853 11 - 601863 AGCAGAGACTT -s simRat_chr6.simRat.chr6 134231 11 + 647215 AGCAGTGATTT - -a -s simMouse_chr6.simMouse.chr6 136481 39 + 636262 AATTGAACAGTTCATAGGTATGGGGCTTTCCCCCTCCCT -s Anc0.Anc0refChr1 35381 39 + 62388 AATTTAGCATTTAAGAAGTATGGGACTTTCCCCCTCCAT -s Anc1.Anc1refChr2 38428 39 - 144309 AATTTAGCATTTAAGAAGTATGGGACTTTCCCCCTCCAT -s Anc2.Anc2refChr3 16326 39 + 53186 AATTTAGCATCTAAGAAGTATGGGACTTTCCCCCTCTAT -s mr.mrrefChr5 118 39 + 294540 AATTGAACAGTTCATAAGTATGGGGCTTTCCCCCTCCCT -s simCow_chr6.simCow.chr6 143684 39 + 602619 AATTTGGCATGTAAGGAGTATGGGACCCTCCCCCTCTGT -s simDog_chr6.simDog.chr6 428074 39 - 593897 ACTTTAGCATCTAAGAAGTATGGGACTTTTGTCCTTTAT -s simHuman_chr6.simHuman.chr6 471869 39 - 601863 AATTCAGCATTAAGGAAGCACAGGACTTTCCCCCTCCTG -s simRat_chr6.simRat.chr6 134242 39 + 647215 AATTGGACAGTTCAAAAGTATGGGGCTTTCCCCCTCCCT - -a -s simMouse_chr6.simMouse.chr6 136520 2 + 636262 GT -s Anc0.Anc0refChr1 27543 2 - 62388 GT -s Anc1.Anc1refChr2 106426 2 + 144309 GT -s Anc2.Anc2refChr3 37403 2 - 53186 GG -s mr.mrrefChr5 157 2 + 294540 GT -s simCow_chr6.simCow.chr6 459493 2 - 602619 GG -s simDog_chr6.simDog.chr6 166336 2 + 593897 GG -s simHuman_chr6.simHuman.chr6 130585 2 + 601863 GT -s simRat_chr6.simRat.chr6 134281 2 + 647215 GT - -a -s simMouse_chr6.simMouse.chr6 136522 31 + 636262 CTCCATCTAGTTTTTTTGACATCAACGTAAA -s Anc0.Anc0refChr1 27545 8 - 62388 CTCTATTT----------------------- -s Anc1.Anc1refChr2 106428 8 + 144309 CTCTATTT----------------------- -s Anc2.Anc2refChr3 16367 8 + 53186 CTCCATTT----------------------- -s mr.mrrefChr5 159 31 + 294540 CTCTATCTAGTTTTTTTGGCATCAACTTAAA -s simCow_chr6.simCow.chr6 143725 8 + 602619 CTTGTTTT----------------------- -s simDog_chr6.simDog.chr6 428115 8 - 593897 CTCCATTT----------------------- -s simHuman_chr6.simHuman.chr6 130587 8 + 601863 CCATGTTT----------------------- -s simRat_chr6.simRat.chr6 134283 31 + 647215 CTGTATCTAGTTTTTTTGGCATCAACTCAAA - -a -s simMouse_chr6.simMouse.chr6 136553 25 + 636262 CCTGGGCCATAACTGGCCTCTCATG -s Anc0.Anc0refChr1 27553 19 - 62388 ------CCATGGCTTTCACCAAATG -s Anc1.Anc1refChr2 106436 19 + 144309 ------CCATGGCTTTCACCAAATG -s Anc2.Anc2refChr3 16375 19 + 53186 ------GGCTGGCTTTCACCAAATA -s mr.mrrefChr5 190 25 + 294540 CCTGGGCCATAGCTGGCCTCTCATG -s simCow_chr6.simCow.chr6 143733 19 + 602619 ------GGCTAGCTTTCACCAAGTA -s simDog_chr6.simDog.chr6 428123 19 - 593897 ------GGCTGGCTTACACCAAAAA -s simHuman_chr6.simHuman.chr6 130595 19 + 601863 ------CCATGGCTATCACCATATG -s simRat_chr6.simRat.chr6 134322 25 + 647215 CCCAGGCCATAGCTGGCCTCTCATG - -a -s simMouse_chr6.simMouse.chr6 136578 43 + 636262 ATCAATAAATAAACACAATAAGGCTTTAATTGCTAGCTAAGTT -s Anc0.Anc0refChr1 27577 42 - 62388 GTCAATAAATAAAAATAA-AGAACTTCAATTGCTATCTAAGTG -s Anc1.Anc1refChr2 106460 42 + 144309 GTCAATAAATAAAAATAA-AGAACTTCAATTGCTATCTAAGTG -s Anc2.Anc2refChr3 16399 42 + 53186 GTCAATAAATAAAAGTAA-AGAACTTCAATTGCTATCTAAGTG -s mr.mrrefChr5 215 43 + 294540 ATCAATAAATAAACATAATAAAACTTTAATTGCTAGCTAAGTT -s simCow_chr6.simCow.chr6 143757 42 + 602619 GTCAATAAATAGAAGTAA-AGAACTGCAATTGCTGTCTAATTG -s simDog_chr6.simDog.chr6 428147 42 - 593897 GTCAATGGATAAAAGTAA-AGATCTTCAATGGCTACCTAAGAG -s simHuman_chr6.simHuman.chr6 130620 42 + 601863 GTCAATAAAAGTAGATAA-AGAACATCAATTGCTATCTAAGTA -s simRat_chr6.simRat.chr6 134347 43 + 647215 ATCAATAAACAAACGTAACAAAATTTTATTTGCTAGCTAAGTC - -a -s simMouse_chr6.simMouse.chr6 136621 72 + 636262 ATCCTGGTGGCCAAGCAATGTTGTTCTCACAGTGTAACTCAAAAGTGCTTATGGAGCAGTCCCCCTCACCAG -s Anc0.Anc0refChr1 27619 45 - 62388 ATCCTGGAAGCAGAGGAGTCTATTGTTCACCATATA---------------------------CCTCACCAG -s Anc1.Anc1refChr2 106502 45 + 144309 ATCCTGGAAGCAGAGGAGTCTATTGTTCACCATATA---------------------------CCTCACCAG -s Anc2.Anc2refChr3 16441 45 + 53186 ATCCTGGAAGCAGAGGAGTCTATTGTTCACCATATA---------------------------CCTCACCAG -s mr.mrrefChr5 258 45 + 294540 ATCCTGGTGGCCAAGCAGTGTAGTTCTCACAGTGTA---------------------------CCTCACCAG -s simCow_chr6.simCow.chr6 143799 45 + 602619 ATCCTAGTAGCGGAGCAGTCTATTTCTCACAGTATA---------------------------CTTCTCCAT -s simDog_chr6.simDog.chr6 428191 45 - 593897 ATCTTGGAGGCAGAGGAAACTATTGTTCACCATATA---------------------------CCTCACCAG -s simHuman_chr6.simHuman.chr6 130662 24 + 601863 ATCCTGGCAGTAGAGTAGTCTATT------------------------------------------------ -s simRat_chr6.simRat.chr6 134390 45 + 647215 ACCCTGGTGGCCAAGCAGTGTAGTTCTCACACTGTA---------------------------CCTCACCAG - -a -s simMouse_chr6.simMouse.chr6 136693 10 + 636262 GGGCATGGTC -s Anc0.Anc0refChr1 27664 10 - 62388 GAGCCTGGGC -s Anc1.Anc1refChr2 106547 10 + 144309 GAGCCTGGGC -s Anc2.Anc2refChr3 16486 10 + 53186 GAGCCTGGGC -s mr.mrrefChr5 303 10 + 294540 GGGCATGGGC -s simCow_chr6.simCow.chr6 143863 10 + 602619 GAGCCTGGGC -s simDog_chr6.simDog.chr6 428236 10 - 593897 GGGCCTGGGC -s simHuman_chr6.simHuman.chr6 130686 10 + 601863 GAACCTGGGC -s simRat_chr6.simRat.chr6 134435 10 + 647215 GAGGATGGGC - -a -s simMouse_chr6.simMouse.chr6 136703 42 + 636262 TGTACAGCTTCTGTCTTTGCCCTGTATGATCACCATGCCTTT -s Anc0.Anc0refChr1 27676 42 - 62388 TGTACAGCTTTTGTCTTTGTCCTGTATGATTTGATCACCTTT -s Anc1.Anc1refChr2 106559 42 + 144309 TGTACAGCTTTTGTCTTTGTCCTGTATGATTTGATCACCTTT -s Anc2.Anc2refChr3 16498 42 + 53186 TGTACAGCTTTTGTCTTTGTCCTGTATGATTTGATCACCTTG -s mr.mrrefChr5 315 42 + 294540 TGTACAGCTTCTGTCTTTGCCCTGTATGATCACCTTGCCTTT -s simCow_chr6.simCow.chr6 143875 41 + 602619 TGTACAGCTGTTGTACTTGTCCTGTAGGACTTGAT-ACCTTG -s simDog_chr6.simDog.chr6 428248 42 - 593897 TGTACAGCTTGTGTCTTTGTCCTGTATGTTTTGATCACCTTG -s simHuman_chr6.simHuman.chr6 130698 42 + 601863 TGTACAGCTCTTGTCTTTGTCCTTTCTGATTTGATCACCTTT -s simRat_chr6.simRat.chr6 134447 42 + 647215 TGTACAGCTTCTCTCTTTGCCCTGTAAGATCACTTTGCCTTT - -a -s simMouse_chr6.simMouse.chr6 136745 19 + 636262 AAAAACTCCCAATCCTAAT -s Anc0.Anc0refChr1 27719 19 - 62388 AGAAACTCCCAATCCTAGT -s Anc1.Anc1refChr2 106602 19 + 144309 AGAAACTCCCAATCCTAGT -s Anc2.Anc2refChr3 16541 19 + 53186 AGAAACTCCCAATCCTAGT -s mr.mrrefChr5 357 19 + 294540 AAAAACTCCCAATCCTAAT -s simCow_chr6.simCow.chr6 143917 13 + 602619 AGAAACTCCAAAT------ -s simDog_chr6.simDog.chr6 428291 19 - 593897 AAAAACTCCCAGTCCTAGT -s simHuman_chr6.simHuman.chr6 130741 19 + 601863 AGAAACTCTCAATCCTAGT -s simRat_chr6.simRat.chr6 134489 19 + 647215 AAAAACTCCCAATCCTAAT - -a -s simMouse_chr6.simMouse.chr6 136764 21 + 636262 ACATCATATGGCTGTCCCCCC -s Anc0.Anc0refChr1 27754 15 - 62388 ACAACAGTTGATT------CC -s Anc1.Anc1refChr2 106637 15 + 144309 ACAACAGTTGATT------CC -s Anc2.Anc2refChr3 16594 15 + 53186 ACAATAGTTGATT------CC -s mr.mrrefChr5 376 15 + 294540 ACATCATATGGCT------CC -s simCow_chr6.simCow.chr6 143962 15 + 602619 ACAATAGTTGGTT------CC -s simDog_chr6.simDog.chr6 428344 15 - 593897 TTAATGGCTGATT------CC -s simHuman_chr6.simHuman.chr6 130776 15 + 601863 ACAACAGTTAATT------CC -s simRat_chr6.simRat.chr6 134508 12 + 647215 A---CATGTGGCT------CC - -a -s simMouse_chr6.simMouse.chr6 136785 5 + 636262 CAATG -s Anc0.Anc0refChr1 27776 5 - 62388 CAATG -s Anc1.Anc1refChr2 106659 5 + 144309 CAATG -s Anc2.Anc2refChr3 16616 5 + 53186 GAAAG -s mr.mrrefChr5 391 5 + 294540 CAATG -s simCow_chr6.simCow.chr6 143984 5 + 602619 AGGAG -s simDog_chr6.simDog.chr6 428366 5 - 593897 GAAAG -s simHuman_chr6.simHuman.chr6 130798 5 + 601863 CAATG -s simRat_chr6.simRat.chr6 134520 5 + 647215 CAATG - -a -s simMouse_chr6.simMouse.chr6 136790 5 + 636262 TGGTA -s Anc0.Anc0refChr1 27783 5 - 62388 GGGAA -s Anc1.Anc1refChr2 106666 5 + 144309 GGGAA -s Anc2.Anc2refChr3 16623 5 + 53186 AGGAA -s mr.mrrefChr5 396 5 + 294540 GGGTA -s simCow_chr6.simCow.chr6 143991 5 + 602619 AGGAT -s simDog_chr6.simDog.chr6 428373 5 - 593897 AGGAA -s simHuman_chr6.simHuman.chr6 130805 5 + 601863 GGGAA -s simRat_chr6.simRat.chr6 134525 5 + 647215 GGTTG - -a -s simMouse_chr6.simMouse.chr6 136795 10 + 636262 GTTCCTATTT -s Anc0.Anc0refChr1 27788 10 - 62388 GTTTTTTTTT -s Anc1.Anc1refChr2 106671 10 + 144309 GTTTTTTTTT -s Anc2.Anc2refChr3 16628 10 + 53186 TTTTTTTTTT -s mr.mrrefChr5 401 10 + 294540 GTTCTTATTT -s simCow_chr6.simCow.chr6 144019 10 + 602619 attttttttt -s simDog_chr6.simDog.chr6 428378 10 - 593897 TATTTTTTTT -s simHuman_chr6.simHuman.chr6 130810 10 + 601863 GTTTTTTTTT -s simRat_chr6.simRat.chr6 134530 10 + 647215 ATTCTTATTC - -a -s simMouse_chr6.simMouse.chr6 136805 26 + 636262 TATACACTTGAACTTGCTCAGTGTAT -s Anc0.Anc0refChr1 27800 12 - 62388 TATTCACT--------CTCA------ -s Anc1.Anc1refChr2 106683 18 + 144309 TATTCACT--------CTCAGTTTAT -s Anc2.Anc2refChr3 16640 12 + 53186 TATTCACT--------CTCA------ -s mr.mrrefChr5 411 26 + 294540 TATACACTTGAACTTACTCAGTGTAT -s simCow_chr6.simCow.chr6 144031 12 + 602619 tattaaCT--------CTCA------ -s simDog_chr6.simDog.chr6 428390 12 - 593897 TATTCACT--------ATCA------ -s simHuman_chr6.simHuman.chr6 130822 18 + 601863 TATTCTCT--------CTCAGTTTAT -s simRat_chr6.simRat.chr6 134540 23 + 647215 TATACACTTATCCTTAC---ATGTAT - -a -s simMouse_chr6.simMouse.chr6 136831 13 + 636262 CACCAGCATGAGG -s Anc0.Anc0refChr1 27861 13 - 62388 CGCCTGCATGTGA -s Anc1.Anc1refChr2 106750 13 + 144309 CGCCTGCATGTGA -s Anc2.Anc2refChr3 16701 13 + 53186 TGCCTGCATGTGA -s mr.mrrefChr5 437 13 + 294540 CACCAGCATGAGG -s simCow_chr6.simCow.chr6 144092 13 + 602619 TGCCTGTGTGTGA -s simDog_chr6.simDog.chr6 428991 13 - 593897 TGCCTGGCCATGA -s simDog_chr6.simDog.chr6 428447 13 - 593897 CATCTGCATGTTA -s simHuman_chr6.simHuman.chr6 130898 13 + 601863 CGTCTGCATGTTA -s simRat_chr6.simRat.chr6 134563 13 + 647215 TACCAGCATGAGG - -a -s simMouse_chr6.simMouse.chr6 136844 2 + 636262 TG -s Anc0.Anc0refChr1 27874 2 - 62388 TA -s Anc1.Anc1refChr2 106763 2 + 144309 TA -s Anc2.Anc2refChr3 16714 2 + 53186 TA -s mr.mrrefChr5 450 2 + 294540 TG -s simCow_chr6.simCow.chr6 144105 2 + 602619 TA -s simDog_chr6.simDog.chr6 428460 2 - 593897 TA -s simHuman_chr6.simHuman.chr6 130911 2 + 601863 TA -s simRat_chr6.simRat.chr6 134576 2 + 647215 TG - -a -s simMouse_chr6.simMouse.chr6 136846 14 + 636262 AATAATTCCTCATT -s Anc0.Anc0refChr1 27885 14 - 62388 AATACTCCCCCATT -s Anc1.Anc1refChr2 106774 14 + 144309 AATACTCCCCCATT -s Anc2.Anc2refChr3 16725 14 + 53186 AGTACTCCTCAATT -s mr.mrrefChr5 452 14 + 294540 AATAATTCCTCATT -s simCow_chr6.simCow.chr6 144111 13 + 602619 -GTATTCCACAATT -s simDog_chr6.simDog.chr6 429007 14 - 593897 AATGCCTAGCAATC -s simDog_chr6.simDog.chr6 428471 14 - 593897 GGTACTCCTCCATT -s simHuman_chr6.simHuman.chr6 130922 14 + 601863 AATATTCCCCCATA -s simRat_chr6.simRat.chr6 134578 14 + 647215 AATAATTCCTCATT - -a -s simMouse_chr6.simMouse.chr6 136860 1 + 636262 A -s Anc0.Anc0refChr1 27899 1 - 62388 A -s Anc1.Anc1refChr2 106788 1 + 144309 A -s Anc2.Anc2refChr3 16739 1 + 53186 A -s mr.mrrefChr5 466 1 + 294540 A -s simCow_chr6.simCow.chr6 144124 1 + 602619 A -s simDog_chr6.simDog.chr6 428485 1 - 593897 A -s simHuman_chr6.simHuman.chr6 130936 1 + 601863 A -s simRat_chr6.simRat.chr6 134592 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 136861 34 + 636262 TTTTTTACTGTGGCCTCTGGATGGATCTCTATGA -s Anc0.Anc0refChr1 27900 34 - 62388 TTTGTTGCTGTGACCTCCGGATGCATCTCTATGA -s Anc1.Anc1refChr2 106789 34 + 144309 TTTGTTGCTGTGACCTCCGGATGCATCTCTATGA -s Anc2.Anc2refChr3 16740 34 + 53186 TCTGTTGCTGTGATCTCCAGAAGCATCTCTATGA -s mr.mrrefChr5 467 34 + 294540 TTTTTTGCTGTGGCCTCTGGATGGATCTCTATGA -s simCow_chr6.simCow.chr6 144125 34 + 602619 TCTGTTGCTGTGATCTCCAGATGCATCTCTATGA -s simDog_chr6.simDog.chr6 429021 34 - 593897 TCACTTACTCTGATAGTATGAAGCATAGCTAACA -s simDog_chr6.simDog.chr6 428486 34 - 593897 TTCGTTGCTGAGGCCCCCAGAAGCATTTCTATGA -s simHuman_chr6.simHuman.chr6 130937 34 + 601863 TTTGTTGCCATGACTTCAGGGTGCATCTCTATGA -s simRat_chr6.simRat.chr6 134593 34 + 647215 TTTTTTGCTGTGGCCTCTTGATAGGTTTCTATGA - -a -s simMouse_chr6.simMouse.chr6 136895 4 + 636262 CCAC -s Anc0.Anc0refChr1 27934 4 - 62388 TCAC -s Anc1.Anc1refChr2 106823 4 + 144309 TCAC -s Anc2.Anc2refChr3 16774 4 + 53186 TCAC -s mr.mrrefChr5 501 4 + 294540 CCAC -s simCow_chr6.simCow.chr6 144159 4 + 602619 TCAC -s simDog_chr6.simDog.chr6 428520 3 - 593897 TCA- -s simHuman_chr6.simHuman.chr6 130971 4 + 601863 TCAC -s simRat_chr6.simRat.chr6 134627 4 + 647215 CTAC - -a -s simMouse_chr6.simMouse.chr6 136899 37 + 636262 ATGTAAGAAGAGGCTGGGTCAACGAGATGGGCCCTGC -s Anc0.Anc0refChr1 27938 36 - 62388 ATGCAAGTACAGGCTAGGTCAGTGAGAT-GGCCCTGA -s Anc1.Anc1refChr2 106827 36 + 144309 ATGCAAGTACAGGCTAGGTCAGTGAGAT-GGCCCTGA -s Anc2.Anc2refChr3 16778 36 + 53186 ATGCAAGTACAGATGAGGTCAGTGAGAT-GGGCCTGA -s mr.mrrefChr5 505 37 + 294540 ATGTAAGAAGAGGCTGGGTCAATGAGATGGGCCCTGC -s simCow_chr6.simCow.chr6 144163 36 + 602619 ATCCATGTACAGATGAGGTTAGTGAGAT-GGGCCTGA -s simDog_chr6.simDog.chr6 429055 36 - 593897 ATGACAGGACTGATGGTGTCAGAGGAAT-GGATTTAA -s simDog_chr6.simDog.chr6 428523 29 - 593897 -------TAAAGGTCAAGTCAGTGAGAT-GGGCCTTG -s simHuman_chr6.simHuman.chr6 130975 36 + 601863 ATGCAAGTACAGGCTAGGTAAGTGAAAT-GGCCCTGA -s simRat_chr6.simRat.chr6 134631 37 + 647215 ATGTAAGAAGAGGATGGGTCAATGAGATGGGCCATGC - -a -s simMouse_chr6.simMouse.chr6 136936 14 + 636262 ATCAAATATATGGT -s Anc0.Anc0refChr1 27974 14 - 62388 ATCAAATACATGGT -s Anc1.Anc1refChr2 106863 14 + 144309 ATCAAATACATGGT -s Anc2.Anc2refChr3 16814 14 + 53186 ATCAAATACATGGT -s mr.mrrefChr5 542 14 + 294540 ATCAAATATATGGT -s simCow_chr6.simCow.chr6 144199 14 + 602619 ATCAAATGCATGGT -s simDog_chr6.simDog.chr6 429095 14 - 593897 CCCTCAAAAAGTGC -s simDog_chr6.simDog.chr6 428552 14 - 593897 ATCAAACACATGGT -s simHuman_chr6.simHuman.chr6 131011 14 + 601863 ATCACATACATGGC -s simRat_chr6.simRat.chr6 134668 14 + 647215 ATGAAATAGATGGT - -a -s simMouse_chr6.simMouse.chr6 136950 1 + 636262 C -s Anc0.Anc0refChr1 27988 1 - 62388 C -s Anc1.Anc1refChr2 106877 1 + 144309 C -s Anc2.Anc2refChr3 16828 1 + 53186 C -s mr.mrrefChr5 556 1 + 294540 C -s simCow_chr6.simCow.chr6 144213 1 + 602619 A -s simDog_chr6.simDog.chr6 428566 1 - 593897 C -s simHuman_chr6.simHuman.chr6 131025 1 + 601863 T -s simRat_chr6.simRat.chr6 134682 1 + 647215 C - -a -s simMouse_chr6.simMouse.chr6 136951 7 + 636262 CCTGAGT -s Anc0.Anc0refChr1 27989 7 - 62388 CATGAGA -s Anc1.Anc1refChr2 106878 7 + 144309 CATGAGA -s Anc2.Anc2refChr3 16829 7 + 53186 CATGAGA -s mr.mrrefChr5 557 7 + 294540 CATGAGA -s simCow_chr6.simCow.chr6 144214 7 + 602619 CATGAGA -s simDog_chr6.simDog.chr6 429109 7 - 593897 CAGAAGA -s simDog_chr6.simDog.chr6 428567 7 - 593897 CACGAGA -s simHuman_chr6.simHuman.chr6 131026 7 + 601863 CATGAGA -s simRat_chr6.simRat.chr6 134683 7 + 647215 CATGAGA - -a -s simMouse_chr6.simMouse.chr6 136958 1 + 636262 G -s Anc0.Anc0refChr1 28343 1 - 62388 G -s Anc1.Anc1refChr2 107239 1 + 144309 G -s Anc2.Anc2refChr3 17205 1 + 53186 G -s mr.mrrefChr5 916 1 + 294540 G -s simCow_chr6.simCow.chr6 144586 1 + 602619 G -s simDog_chr6.simDog.chr6 429563 1 - 593897 G -s simHuman_chr6.simHuman.chr6 131391 1 + 601863 G -s simMouse_chr6.simMouse.chr6 137204 1 + 636262 G -s simRat_chr6.simRat.chr6 135077 1 + 647215 G - -a -s simMouse_chr6.simMouse.chr6 136959 4 + 636262 ATAC -s Anc0.Anc0refChr1 28386 4 - 62388 AGAC -s Anc1.Anc1refChr2 107282 4 + 144309 AGAC -s Anc2.Anc2refChr3 17248 4 + 53186 AGAC -s mr.mrrefChr5 929 4 + 294540 ATAC -s simCow_chr6.simCow.chr6 144629 4 + 602619 TGAC -s simDog_chr6.simDog.chr6 429604 4 - 593897 AAAC -s simHuman_chr6.simHuman.chr6 131434 4 + 601863 AGAC -s simMouse_chr6.simMouse.chr6 137217 4 + 636262 ATAC -s simRat_chr6.simRat.chr6 135090 4 + 647215 ATAC - -a -s simMouse_chr6.simMouse.chr6 136963 8 + 636262 ATCTAGAG -s Anc0.Anc0refChr1 28390 8 - 62388 ATCTAGAT -s Anc1.Anc1refChr2 107286 8 + 144309 ATCTAGAT -s Anc2.Anc2refChr3 17252 8 + 53186 ATCTAGAT -s mr.mrrefChr5 933 8 + 294540 ATCTAGAG -s simCow_chr6.simCow.chr6 144633 4 + 602619 ATCT---- -s simDog_chr6.simDog.chr6 429616 8 - 593897 GTCAAGAT -s simHuman_chr6.simHuman.chr6 131438 8 + 601863 ATCTAGAT -s simMouse_chr6.simMouse.chr6 137221 8 + 636262 TTCTCGAA -s simRat_chr6.simRat.chr6 135094 8 + 647215 AACTAGAG - -a -s simMouse_chr6.simMouse.chr6 136971 17 + 636262 CATGCTCTGTGTGCTCC -s Anc0.Anc0refChr1 28398 17 - 62388 CTTAATCTGTTAAATAT -s Anc1.Anc1refChr2 107294 17 + 144309 CTTAATCTGTTAAATAT -s Anc2.Anc2refChr3 17263 17 + 53186 CTTAATCTGTTAAATAT -s mr.mrrefChr5 941 17 + 294540 CATGCTCTGTGTGCTCC -s simCow_chr6.simCow.chr6 144640 15 + 602619 CTTA--CTGTTTAATAT -s simDog_chr6.simDog.chr6 429630 17 - 593897 CTTGATATTTCAAATGT -s simHuman_chr6.simHuman.chr6 131446 17 + 601863 CTTATTCTGTTGAATAT -s simMouse_chr6.simMouse.chr6 137229 17 + 636262 CATGCTCTGTGTACTCC -s simRat_chr6.simRat.chr6 135102 17 + 647215 TGTGCTCTGTATGCTCC - -a -s simMouse_chr6.simMouse.chr6 136988 17 + 636262 TCTTCTAATGGGGTGCA -s Anc0.Anc0refChr1 28415 16 - 62388 CCTTGTAGT-TAGTCCA -s Anc1.Anc1refChr2 107311 16 + 144309 CCTTGTAGT-TAGTCCA -s Anc2.Anc2refChr3 17280 16 + 53186 CCTTGTAGT-TAGTCCA -s mr.mrrefChr5 958 17 + 294540 TCTTCTAATGGAGTGCA -s simCow_chr6.simCow.chr6 144655 16 + 602619 CCTTGCAGC-TAGTCCA -s simDog_chr6.simDog.chr6 429653 16 - 593897 CCCTGTAAT-CTATACA -s simHuman_chr6.simHuman.chr6 131463 16 + 601863 CCTTTTGGT-TAGTCCA -s simMouse_chr6.simMouse.chr6 137246 17 + 636262 TCTTCTAATGGAGTGCA -s simRat_chr6.simRat.chr6 135119 17 + 647215 TGTTCTAATGGAGTGCA - -a -s simMouse_chr6.simMouse.chr6 137005 8 + 636262 GTGCTCCT -s Anc0.Anc0refChr1 28444 8 - 62388 CTACTAGG -s Anc1.Anc1refChr2 107340 8 + 144309 CTACTAGG -s Anc2.Anc2refChr3 17309 8 + 53186 CTACTAGG -s mr.mrrefChr5 988 8 + 294540 GTGCTCCT -s simCow_chr6.simCow.chr6 144700 8 + 602619 CTACTAGG -s simDog_chr6.simDog.chr6 429679 8 - 593897 CTATTAGC -s simHuman_chr6.simHuman.chr6 131492 8 + 601863 CCACTATG -s simMouse_chr6.simMouse.chr6 137263 8 + 636262 CTGCTCCT -s simRat_chr6.simRat.chr6 135149 8 + 647215 ATGCTCCT - -a -s simMouse_chr6.simMouse.chr6 137013 48 + 636262 CTAAGTTGATGCAGCACATTCCTTGTAGATAAGAGGCGACTTTCTAGC -s Anc0.Anc0refChr1 28459 4 - 62388 --------------------------------------------TAAC -s Anc1.Anc1refChr2 107355 4 + 144309 --------------------------------------------TAAC -s Anc2.Anc2refChr3 17324 4 + 53186 --------------------------------------------TAAC -s mr.mrrefChr5 1015 48 + 294540 CTAAGTTGATGCAGCACATTTCTTGTAGATAAGAGGCGACTTTCTAGT -s simCow_chr6.simCow.chr6 144715 4 + 602619 --------------------------------------------TGAC -s simDog_chr6.simDog.chr6 429694 4 - 593897 --------------------------------------------TAAC -s simHuman_chr6.simHuman.chr6 131507 4 + 601863 --------------------------------------------TAAC -s simMouse_chr6.simMouse.chr6 137271 48 + 636262 CTTAGTTGATGCAGCACATTTCTTGTGGATATGCGGCGACTTTCTAGT -s simRat_chr6.simRat.chr6 135179 46 + 647215 CCAAGTTGAAGCAGCACATTTCTTGTAGATAAGAGGCAACTTTC--GG - -a -s simMouse_chr6.simMouse.chr6 137061 4 + 636262 AAGT -s Anc0.Anc0refChr1 28463 4 - 62388 AAGT -s Anc1.Anc1refChr2 107359 4 + 144309 AAGT -s Anc2.Anc2refChr3 17336 4 + 53186 AAGT -s mr.mrrefChr5 1063 4 + 294540 AAGT -s simCow_chr6.simCow.chr6 144728 4 + 602619 ATGT -s simDog_chr6.simDog.chr6 429706 4 - 593897 AACT -s simHuman_chr6.simHuman.chr6 131511 4 + 601863 AAGT -s simMouse_chr6.simMouse.chr6 137319 4 + 636262 AAGT -s simRat_chr6.simRat.chr6 135225 4 + 647215 ATGT - -a -s simMouse_chr6.simMouse.chr6 137065 8 + 636262 ATCAAATG -s Anc0.Anc0refChr1 28468 8 - 62388 GTCAAATG -s Anc1.Anc1refChr2 107364 8 + 144309 GTCAAATG -s Anc2.Anc2refChr3 17341 8 + 53186 GTCAAATG -s mr.mrrefChr5 1068 8 + 294540 ATCAAATG -s simCow_chr6.simCow.chr6 144733 8 + 602619 GTCGAATG -s simDog_chr6.simDog.chr6 429711 8 - 593897 GTCAAATG -s simHuman_chr6.simHuman.chr6 131516 8 + 601863 GTCAAACG -s simMouse_chr6.simMouse.chr6 137323 8 + 636262 ATCAAATG -s simRat_chr6.simRat.chr6 135230 8 + 647215 ATCAAAGG - -a -s simMouse_chr6.simMouse.chr6 137073 29 + 636262 CAAACCAATGAACTCAGTGTTTAGATTGC -s Anc0.Anc0refChr1 28477 28 - 62388 CATGCCAATGAACTCCCTG-TAAGATTGT -s Anc1.Anc1refChr2 107373 28 + 144309 CATGCCAATGAACTCCCTG-TAAGATTGT -s Anc2.Anc2refChr3 17350 28 + 53186 GATGCCAATGAACTCCCTG-TAAGATTGT -s mr.mrrefChr5 1076 28 + 294540 CAAACTAATGAACTCAATG-TTAGATTGT -s simCow_chr6.simCow.chr6 144742 26 + 602619 AATGCCAATGAAATCCCT---AATACTGT -s simDog_chr6.simDog.chr6 429720 26 - 593897 GAT--TGAGGAACTCCCTG-TTAGATCAT -s simHuman_chr6.simHuman.chr6 131525 28 + 601863 CACGCCAATTAACCCCCTG-TAAGATTGT -s simMouse_chr6.simMouse.chr6 137331 28 + 636262 AGAACTAATGAACTCAATG-TTAAATTGT -s simRat_chr6.simRat.chr6 135238 28 + 647215 CAAGTTGATGAACTCAATG-TTAGATTGT - -a -s simMouse_chr6.simMouse.chr6 137102 20 + 636262 TATCTGGATCGAGGCTGCTA -s Anc0.Anc0refChr1 28249 19 - 62388 TTTTTGCATCAGGACTCTT- -s Anc1.Anc1refChr2 107144 20 + 144309 TTTTTGCATCAGGACTCTTA -s Anc2.Anc2refChr3 17111 19 + 53186 TTTTTGCATCAAGACTCTT- -s mr.mrrefChr5 816 20 + 294540 TATCTGGATCGGGGCTGCTA -s simCow_chr6.simCow.chr6 144495 18 + 602619 TTTTTGTATCAAG-CTCTT- -s simDog_chr6.simDog.chr6 429474 19 - 593897 TTTTTACATCAATACTCTT- -s simHuman_chr6.simHuman.chr6 131294 20 + 601863 TTTTTGCATCAGGACTTTTA -s simRat_chr6.simRat.chr6 134977 20 + 647215 TGTCTGGACTGGGGCTGGTA - -a -s simMouse_chr6.simMouse.chr6 137122 76 + 636262 CCACTTGTAGAAAGGAGCTATGAGCCTAAGGCACTAAATGATATGCACTTGCTTGTGCATTTCGATGAGAGCAGAT -s Anc0.Anc0refChr1 28268 67 - 62388 CAACTTGCAGACAG-------GAGCCTGAGCCATCACA--TGATGCACTTGCTTGTGGATTTGTACCAAAGTAGAT -s Anc1.Anc1refChr2 107164 67 + 144309 CAACTTGCAGACAG-------GAGCCTGAGCCATCACA--TGATGCACTTGCTTGTGGATTTGTACCAAAGTAGAT -s Anc2.Anc2refChr3 17130 67 + 53186 CAACTTGCGGACCG-------GAGCCTGAGCCATCACA--TGATGCACTTGCTTGTGGATTTGTACCAAGGTAGAT -s mr.mrrefChr5 836 74 + 294540 CAACTTGTAGACAGGAGCTATGAGCCTAAGGCATTACA--ATATGCACTTGCTTGTGCATTTGGATGAGAGTAGAT -s simCow_chr6.simCow.chr6 144513 65 + 602619 GCAC--GATGATGG-------GTGCCTGAACCATCACA--TGACATACCTCCTTGTGGATTTGTACTGATGTAGAT -s simDog_chr6.simDog.chr6 429493 62 - 593897 CAACTTACGGACCG-------AAGCCTGGGCCAT-------GATGCACTTGTTTGTGGATGGGTACCAAGGTAGAT -s simHuman_chr6.simHuman.chr6 131316 67 + 601863 CAACTTGCAGACAG-------GAGCCTGAGCCATCACA--TGATGCACTTGCTTGTGGATTTGTACCCAAGTAAAT -s simRat_chr6.simRat.chr6 134997 74 + 647215 CAACTTGTAGGCAGGAGCTATGAGCCTAAGGCATTACA--ATACGCACTTGCTTGTGCATTTGGATGAGAGTAGAT - -a -s simMouse_chr6.simMouse.chr6 137198 6 + 636262 GTTGCA -s Anc0.Anc0refChr1 28337 6 - 62388 GTTGAG -s Anc1.Anc1refChr2 107233 6 + 144309 GTTGAG -s Anc2.Anc2refChr3 17199 6 + 53186 GTTGAG -s mr.mrrefChr5 910 6 + 294540 GTTGCA -s simCow_chr6.simCow.chr6 144580 6 + 602619 GTTGAG -s simDog_chr6.simDog.chr6 429557 6 - 593897 TCCAAG -s simHuman_chr6.simHuman.chr6 131385 6 + 601863 GTTGAG -s simRat_chr6.simRat.chr6 135071 6 + 647215 GTTGCA - -a -s simMouse_chr6.simMouse.chr6 137205 4 + 636262 TTTT -s Anc0.Anc0refChr1 28344 4 - 62388 TATT -s Anc1.Anc1refChr2 107240 4 + 144309 TATT -s Anc2.Anc2refChr3 17206 4 + 53186 TATT -s mr.mrrefChr5 917 4 + 294540 TATT -s simCow_chr6.simCow.chr6 144587 4 + 602619 CATT -s simDog_chr6.simDog.chr6 429564 4 - 593897 TATT -s simHuman_chr6.simHuman.chr6 131392 4 + 601863 TATT -s simRat_chr6.simRat.chr6 135078 4 + 647215 TATT - -a -s simMouse_chr6.simMouse.chr6 137209 8 + 636262 ACTGAATG -s Anc0.Anc0refChr1 28378 8 - 62388 ATTCAGTC -s Anc1.Anc1refChr2 107274 8 + 144309 ATTCAGTC -s Anc2.Anc2refChr3 17240 8 + 53186 ATCCAGCC -s mr.mrrefChr5 921 8 + 294540 ACTGAGTG -s simCow_chr6.simCow.chr6 144621 8 + 602619 ATCCAGCC -s simDog_chr6.simDog.chr6 429599 5 - 593897 AT---GCC -s simHuman_chr6.simHuman.chr6 131426 8 + 601863 ATTAAGTC -s simRat_chr6.simRat.chr6 135082 8 + 647215 ATTGAGTG - -a -s simMouse_chr6.simMouse.chr6 137359 19 + 636262 CTGTGCCTCGTGTATATAA -s Anc0.Anc0refChr1 28505 16 - 62388 CTATGCCCCATATAT---G -s Anc1.Anc1refChr2 107401 19 + 144309 CTATGCCCCATATATATCG -s Anc2.Anc2refChr3 17378 16 + 53186 CTATGCCCCATATAT---G -s mr.mrrefChr5 1104 19 + 294540 CTGTGCCCCATGTATATAA -s simCow_chr6.simCow.chr6 144768 16 + 602619 CTATCCCTCATATAT---A -s simDog_chr6.simDog.chr6 429746 16 - 593897 CTACGCCCCATATAT---G -s simHuman_chr6.simHuman.chr6 131553 12 + 601863 CTATGCC-------TATCG -s simRat_chr6.simRat.chr6 135266 19 + 647215 CTGTGCCCTATGTATATAT - -a -s simMouse_chr6.simMouse.chr6 137378 14 + 636262 AGTAGTGCCATGTG -s Anc0.Anc0refChr1 28521 14 - 62388 AGTAGTGCTATGTG -s Anc1.Anc1refChr2 107420 14 + 144309 AGTAGTGCTATGTG -s Anc2.Anc2refChr3 17394 14 + 53186 AGTAGTGCTATGTA -s mr.mrrefChr5 1123 14 + 294540 AGTAGTGCCATGTG -s simCow_chr6.simCow.chr6 144787 14 + 602619 AATAGGGCTAAGTA -s simDog_chr6.simDog.chr6 429762 14 - 593897 AGAAGTTCTATGTA -s simHuman_chr6.simHuman.chr6 131565 14 + 601863 AGTAGTGCTATGTG -s simRat_chr6.simRat.chr6 135285 14 + 647215 AGTAGTGACATATG - -a -s simMouse_chr6.simMouse.chr6 137392 8 + 636262 GCCAACCT -s Anc0.Anc0refChr1 28535 8 - 62388 ACCAGCCT -s Anc1.Anc1refChr2 107434 8 + 144309 ACCAGCCT -s Anc2.Anc2refChr3 17408 8 + 53186 ACCAGCCT -s mr.mrrefChr5 1137 8 + 294540 ACCAGCCT -s simCow_chr6.simCow.chr6 144801 8 + 602619 ACCAGCTT -s simDog_chr6.simDog.chr6 429776 8 - 593897 ATCAGCCT -s simHuman_chr6.simHuman.chr6 131579 8 + 601863 ACCAGCCT -s simRat_chr6.simRat.chr6 135301 8 + 647215 ATAAGAAA - -a -s simMouse_chr6.simMouse.chr6 137400 62 + 636262 CGTGACATATGGAATGAGAAAGACAAGGGTGCTAACACACAACATTTTCCAGGACGCAAGCC -s Anc0.Anc0refChr1 28555 56 - 62388 CATAACATATGGAATGAGAAAGGTATGAGTGTGAACACACCACATTTACCA------AGACC -s Anc1.Anc1refChr2 107454 56 + 144309 CATAACATATGGAATGAGAAAGGTATGAGTGTGAACACACCACATTTACCA------AGACC -s Anc2.Anc2refChr3 17428 56 + 53186 TATAACATATGGAGTCAGAAAGGTGTGAGTGTGAACACACCACATCTACCA------AGACC -s mr.mrrefChr5 1153 56 + 294540 CGTGACATATGGAATGAGAAAGACAAGGGTGCTAACACACAACATTTTCCA------AAGCC -s simCow_chr6.simCow.chr6 144821 56 + 602619 TATAACATATGGAGTCAGAAGGGTGTATGAGTGAACACACCACAGCTACTC------AGACC -s simDog_chr6.simDog.chr6 429796 56 - 593897 TATGACATGTGGGGTCAGAAAGGTGTGAGTGTGAGCACACCATATCTAGCA------AGACC -s simHuman_chr6.simHuman.chr6 131599 56 + 601863 CATAACATAGGGAATGGGAAAGGTATGAGTGTGAACACATCACATTTACCA------ACACT - -a -s simMouse_chr6.simMouse.chr6 137462 10 + 636262 TCAGTTTTAG -s Anc0.Anc0refChr1 28611 10 - 62388 TTAATGTTAG -s Anc1.Anc1refChr2 107510 10 + 144309 TTAATGTTAG -s Anc2.Anc2refChr3 17484 10 + 53186 CTAATGTTAG -s mr.mrrefChr5 1209 10 + 294540 TCAGTTTTAG -s simCow_chr6.simCow.chr6 144878 10 + 602619 CTAACATTAC -s simDog_chr6.simDog.chr6 429852 10 - 593897 CTAGTGCTAG -s simHuman_chr6.simHuman.chr6 131655 10 + 601863 TAAATGTGAG - -a -s simMouse_chr6.simMouse.chr6 137472 142 + 636262 TTTCCTCAGGGCTATAAATATGGCGCGGAAGTAAACCTATAGTCAGGGCAAAGGAGCCTCTAAATCCAGGAGATGGAGGTTCCTTCTGACACAAAGGTCTGTCACTTTTATGGGGTGGCCACACTTATCCACTAACACACCC -s Anc0.Anc0refChr1 28621 138 - 62388 CTTCCGATGGCC-ATAATGATGGCTAAGTAGTACACATATAATTAGGGCTGAGGAGCCTCTAA-TCCGTAGGATTGAG--TGCTTCTGACATAAAACTCTGTCACATTTATGGTGTGACCTCAGTTATTCAGTAACACACCC -s Anc1.Anc1refChr2 107520 138 + 144309 CTTCCGATGGCC-ATAATGATGGCTAAGTAGTACACATATAATTAGGGCTGAGGAGCCTCTAA-TCCGTAGGATTGAG--TGCTTCTGACATAAAACTCTGTCACATTTATGGTGTGACCTCAGTTATTCAGTAACACACCC -s Anc2.Anc2refChr3 17497 138 + 53186 CTTGTGATAGCC-ATAATGATGGCTAAATAATACACATATAATTACAGCTGAGGAGTCTCTAT-TCAGTAGGATTGAG--TGCTTTTGACATAAAACTCTGACACATTAATGGTGTGACCTCAGTTATTCAGTAACATACCC -s mr.mrrefChr5 1219 139 + 294540 TTTCCTCAGGGCTATAAATATGGCGCGGAAGTAAACCTATAGTCAGGGCAAAGGAGCCTCTAA-TCCAGGAGATGGAG--TCCTTCTGACACAAAGGTCTGTCACTTTTATGGGGTGGCCACACTTATCCACTAACACACCC -s simCow_chr6.simCow.chr6 144891 137 + 602619 CCCTTGA-AGCC-ATAATTATGGCTAATTGATACACATATAATCACAGCTGAAGAGTCTCTAC-TTATGGTTAGTGGG--CTGATTTAGCATATAACTCTGTCACTTTAATGGTGTGACCTCAGTTATTCAGTGACATACCC -s simDog_chr6.simDog.chr6 429865 138 - 593897 CTTGTGATAACC-ATAATGATGGCTAAATAATTCCCATAAACTTACAGCTGAGGGATCTCTAT-TCAGTAGGATTGAG--TGCTTTTGACGCAAAACTCTGACACATTAATGGTGTGACCTTAGTCATTCAGCAATATACCC -s simHuman_chr6.simHuman.chr6 131665 117 + 601863 CTTCCAATGGCC--TAATCATTGCTAAGCAGTACACATATAATTAGGGCTGAGGAGCCTCTAA-TCC---------AG--TATTCCAACCA----------TCAGATTTAT-GTGTGACCTCAGTTATGCGGTAACACACCC - -a -s simMouse_chr6.simMouse.chr6 137614 26 + 636262 AGTTTTCCTTCCCTACTTGTACAAGT -s Anc0.Anc0refChr1 28760 26 - 62388 AGTTTTCCATTCCTACTTGTACAAGT -s Anc1.Anc1refChr2 107659 26 + 144309 AGTTTTCCATTCCTACTTGTACAAGT -s Anc2.Anc2refChr3 17636 26 + 53186 AGTTTTCCATTCCTACTTGTACAAGT -s mr.mrrefChr5 1358 26 + 294540 AGTTTTCCTTCCCTACTTGTACAAGT -s simCow_chr6.simCow.chr6 145029 22 + 602619 AGTTTTCTATTCCTA----TACAGGT -s simDog_chr6.simDog.chr6 430004 26 - 593897 AGTTTTCCATTCTTACTTGTAGAAGT -s simHuman_chr6.simHuman.chr6 131783 26 + 601863 AGTTTTCCATTCCTACTTATACAAGT - -a -s simMouse_chr6.simMouse.chr6 137640 11 + 636262 ATATTTGACTT -s Anc0.Anc0refChr1 28786 11 - 62388 ATATTCAACTT -s Anc1.Anc1refChr2 107685 11 + 144309 ATATTCAACTT -s Anc2.Anc2refChr3 17668 11 + 53186 ATATTCAACTT -s mr.mrrefChr5 1384 11 + 294540 ATATTTGACTT -s simCow_chr6.simCow.chr6 145057 11 + 602619 ATGTACAACTT -s simDog_chr6.simDog.chr6 430036 11 - 593897 ACATTCAACTT -s simHuman_chr6.simHuman.chr6 131809 11 + 601863 ATATTCCACTT - -a -s simMouse_chr6.simMouse.chr6 137651 13 + 636262 TCATATTCGGATA -s Anc0.Anc0refChr1 28799 13 - 62388 TCATGGTAGGACA -s Anc1.Anc1refChr2 107698 13 + 144309 TCATGGTAGGACA -s Anc2.Anc2refChr3 17681 13 + 53186 TCATGGTAGGACA -s mr.mrrefChr5 1395 13 + 294540 TCATATTCGGATA -s simCow_chr6.simCow.chr6 145070 13 + 602619 TCATGTCAGGGCA -s simDog_chr6.simDog.chr6 430049 13 - 593897 TAATGGTAGGACA -s simHuman_chr6.simHuman.chr6 131822 13 + 601863 TCATGCTAGGACA - -a -s simMouse_chr6.simMouse.chr6 137664 58 + 636262 GTAACGCTCCCGAATGCAATGTATGGAGTATTCTCTATATATCCTCTGCATCGGGTGT -s Anc0.Anc0refChr1 28812 50 - 62388 G--------CCTAATGCAATGGATGGAACAGTCTCTATACATCCTCTGCACCAGGTGT -s Anc1.Anc1refChr2 107711 50 + 144309 G--------CCTAATGCAATGGATGGAACAGTCTCTATACATCCTCTGCACCAGGTGT -s Anc2.Anc2refChr3 17694 50 + 53186 G--------GCTAATGCAATGGATGGAACAGTCTCTATACATCCTCTGCACCAGGTGT -s mr.mrrefChr5 1408 50 + 294540 G--------CCGAATGCAATGTATGGAGTATTCTCTATATATCCTCTGCATTAGGTGT -s simCow_chr6.simCow.chr6 145086 50 + 602619 G--------GCTATTGCAATGGATGGAACACCACCTACACAGCCCCTTCACCAGGTGT -s simDog_chr6.simDog.chr6 430062 50 - 593897 G--------GCTAATCCAATGGATGGAATGGTCTCTATACATCCTCTGCACCAGGTGT -s simHuman_chr6.simHuman.chr6 131835 41 + 601863 G--------CCTAATGCAATGGATGGAACAGTC---------CCTCTGCACCAGATGT -s simRat_chr6.simRat.chr6 135317 10 + 647215 ------------------------------------------------CACTAGGTGT - -a -s simMouse_chr6.simMouse.chr6 137722 14 + 636262 CAAGGGCATTACAT -s Anc0.Anc0refChr1 28887 14 - 62388 CAGGAGCATTACAT -s Anc1.Anc1refChr2 107786 14 + 144309 CAGGAGCATTACAT -s Anc2.Anc2refChr3 17769 14 + 53186 CAGGAAGATTACAT -s mr.mrrefChr5 1458 14 + 294540 CAGGGGCATTACAT -s simCow_chr6.simCow.chr6 145161 14 + 602619 CAAGAAAATTGCAT -s simDog_chr6.simDog.chr6 430137 14 - 593897 CAGGAAGATTACAT -s simHuman_chr6.simHuman.chr6 131901 14 + 601863 CAGGAGCATTAGAT -s simRat_chr6.simRat.chr6 135327 14 + 647215 CAGGGGCATTACCT - -a -s simMouse_chr6.simMouse.chr6 137736 36 + 636262 GTTTTGGTACTGCCTGTAGTCAGTGTAAATATTCAT -s Anc0.Anc0refChr1 28902 36 - 62388 GTTTTGTTTCTGCCTGTAAGTGGTATAAAGATTTAT -s Anc1.Anc1refChr2 107801 36 + 144309 GTTTTGTTTCTGCCTGTAAGTGGTATAAAGATTTAT -s Anc2.Anc2refChr3 17784 36 + 53186 GTTTTGTTTCTGCCTGTAAGTGGTATAAAGATTTAT -s mr.mrrefChr5 1473 36 + 294540 GTTTTGGTACTGCCTGTAATCAGTGTAAAGATTCAT -s simCow_chr6.simCow.chr6 145176 36 + 602619 GCTTTGTTTCTGCATGTAAGTAATATAGAGGTTTAT -s simDog_chr6.simDog.chr6 430152 36 - 593897 GTTTTATCTCTGCCTGTAAGTGGTATAAAGATTTAT -s simHuman_chr6.simHuman.chr6 131916 36 + 601863 ATTCTGTTTCTGCCTGTAAGTGGTACAAAGATTTAT -s simRat_chr6.simRat.chr6 135342 35 + 647215 GTTTTGGTAATGCCTGTAATCAGC-TAAAGAGTCAC - -a -s simMouse_chr6.simMouse.chr6 137772 12 + 636262 GGGATCAGGAGT -s Anc0.Anc0refChr1 28939 12 - 62388 GGGATCATTAAT -s Anc1.Anc1refChr2 107838 12 + 144309 GGGATCATTAAT -s Anc2.Anc2refChr3 17821 12 + 53186 GGGATCATTAAT -s mr.mrrefChr5 1509 12 + 294540 GGGATCATGAGT -s simCow_chr6.simCow.chr6 145213 12 + 602619 GGTATCATTAAT -s simDog_chr6.simDog.chr6 430189 12 - 593897 GGGATCATTAAT -s simHuman_chr6.simHuman.chr6 131953 12 + 601863 GGGATCACTGAT -s simRat_chr6.simRat.chr6 135377 12 + 647215 AGGCTCATGAGT - -a -s simMouse_chr6.simMouse.chr6 137784 41 + 636262 AGCACACAGTAGTATTTGATACAAACAAAGGTTCACCCCAG -s Anc0.Anc0refChr1 28952 41 - 62388 AGTACATCACAGGATTTAATACTGACAGTAGCTGACCTTTG -s Anc1.Anc1refChr2 107851 41 + 144309 AGTACATCACAGGATTTAATACTGACAGTAGCTGACCTTTG -s Anc2.Anc2refChr3 17834 41 + 53186 AGCACATCACAGGACTTAATACTTACAGTAGTTGGCCTTTG -s mr.mrrefChr5 1522 41 + 294540 AGTACACAGTAGTATTTGATACAGACAAAGGCTCACCCCTG -s simCow_chr6.simCow.chr6 145226 41 + 602619 AGCACGTAATGGGACTAAATACCTACAGTAGTTGGCCTTTG -s simDog_chr6.simDog.chr6 430202 40 - 593897 AGCATATCACAGGACTTAATACT-ACAGTATTTGGCCTTTG -s simHuman_chr6.simHuman.chr6 131966 41 + 601863 AGTACATTACAGGATTTAATACTGACAGTAGCTGACCTTTG -s simRat_chr6.simRat.chr6 135390 41 + 647215 AGTGCACAGTAGTATTTGATACAGACAAAGGCTCACCCCTG - -a -s simMouse_chr6.simMouse.chr6 137825 26 + 636262 ATGGAAGTAGAAGATGAAACAATTGA -s Anc0.Anc0refChr1 28993 26 - 62388 ATAAAAGTAAAAGACAGGGTAATTCT -s Anc1.Anc1refChr2 107892 26 + 144309 ATAAAAGTAAAAGACAGGGTAATTCT -s Anc2.Anc2refChr3 17875 26 + 53186 ATAAAAGTAAAAGACAGGGTAACTCT -s mr.mrrefChr5 1563 26 + 294540 ATGGAAGTAGAAGATGGGACAATTCT -s simCow_chr6.simCow.chr6 145271 26 + 602619 ATGAAAGTAAAGGATGGGGTAACTCT -s simDog_chr6.simDog.chr6 430242 26 - 593897 ATAATAGTTAAAGACAGGGGAACTTT -s simHuman_chr6.simHuman.chr6 132007 26 + 601863 CCAAAAGCAAAAGACAGGGTAATGCT -s simRat_chr6.simRat.chr6 135431 26 + 647215 ATGGAAGTAGAAGATTGGACAACTCT - -a -s simMouse_chr6.simMouse.chr6 137851 3 + 636262 CTA -s Anc0.Anc0refChr1 29019 3 - 62388 CTA -s Anc1.Anc1refChr2 107918 3 + 144309 CTA -s Anc2.Anc2refChr3 17902 3 + 53186 TTA -s mr.mrrefChr5 1589 3 + 294540 CTA -s simCow_chr6.simCow.chr6 145298 3 + 602619 CTA -s simDog_chr6.simDog.chr6 430269 3 - 593897 TTA -s simHuman_chr6.simHuman.chr6 132033 3 + 601863 CTG -s simRat_chr6.simRat.chr6 135457 3 + 647215 CGA - -a -s simMouse_chr6.simMouse.chr6 137854 31 + 636262 TGATAGTTCAGTGAATGTTTGAGCTACTCAG -s Anc0.Anc0refChr1 29022 31 - 62388 TGATGGGCCAGTATATATTTGGTGCACTCAG -s Anc1.Anc1refChr2 107921 31 + 144309 TGATGGGCCAGTATATATTTGGTGCACTCAG -s Anc2.Anc2refChr3 17905 31 + 53186 TGATGGGCCACTATATATTTGGTGCACTCAG -s mr.mrrefChr5 1592 31 + 294540 TGATAGTTCAGTGAATATTTGAGCTACTCAG -s simCow_chr6.simCow.chr6 145301 31 + 602619 TGATGTGTCACTATATATTCGGTGCACTCAG -s simDog_chr6.simDog.chr6 430272 31 - 593897 TGATGGGCCACTATTTGTTTGGTGCTCTCAG -s simHuman_chr6.simHuman.chr6 132042 31 + 601863 TGATGGCCCAGTATACATTTGGTGCACTCAG -s simRat_chr6.simRat.chr6 135460 31 + 647215 TGATAGTTCAGTGAATATTTCAGCTACTCGG - -a -s simMouse_chr6.simMouse.chr6 137885 27 + 636262 TCTTAACATTCCTTACTTTAGTATATG -s Anc0.Anc0refChr1 29133 26 - 62388 TCTAAG-GTTCCTTACTTTAGTCTACA -s Anc1.Anc1refChr2 108032 26 + 144309 TCTAAG-GTTCCTTACTTTAGTCTACA -s Anc2.Anc2refChr3 18020 26 + 53186 TGTAAG-GTTCCTTACTTTAGTCTACA -s mr.mrrefChr5 1623 27 + 294540 TCTTAGCGTTCCTTACTTTAGTATACA -s simCow_chr6.simCow.chr6 145408 22 + 602619 ----AG-GTTCCTTACTTTAGTCCACA -s simDog_chr6.simDog.chr6 430366 26 - 593897 TGTAAG-GCATCTTACTTTCGTGTACA -s simHuman_chr6.simHuman.chr6 132159 26 + 601863 TCTCAG-GTTCCTAACTTTAGTCTACA -s simRat_chr6.simRat.chr6 135491 27 + 647215 TCTTAGTGTTCCTTACTTTAGTATACA - -a -s simMouse_chr6.simMouse.chr6 137912 90 + 636262 GTAAACTTAGAGTATGAACCTAGCAAAACCCAAAAGAATCTAGATGTAACAGACATGCTACTTGGGTATCACACTGTGTACAGCTCTATC -s Anc0.Anc0refChr1 29159 84 - 62388 GTAGACTTAAAGTATGAACCAAGCAGAACCCAAAAGAAA------GCCACAGGCATGTTGGTTGGGTACCAAACCATGTATATTTTTACC -s Anc1.Anc1refChr2 108058 84 + 144309 GTAGACTTAAAGTATGAACCAAGCAGAACCCAAAAGAAA------GCCACAGGCATGTTGGTTGGGTACCAAACCATGTATATTTTTACC -s Anc2.Anc2refChr3 18046 84 + 53186 GTAGACGTAAAGTATGAACCAAGCAGAACTCAAAAGAAA------CCCACAGGCATGTAGGTTGGGTACTAAATCATGTATATTTTTACC -s mr.mrrefChr5 1650 90 + 294540 GTAAACTTAGAGTATGAACCTAGCAAAACCCAAAAGAAACTAGATGTAACAGACATGTTACTTGGGTATCAAACTGTGTACATCTCTATC -s simCow_chr6.simCow.chr6 145430 84 + 602619 GCAGACATCAAATATGAACTAAGCAGAGCTCAAAAGAAA------CCCACAGACATGTGGGTTGGGTACAAAGTCATACACATTTTACCC -s simDog_chr6.simDog.chr6 430392 84 - 593897 GTGGAAGTAACGTATGAACCGAGCAGAACTCAGAAGAAG------CACACAGGCATGTAGGTTGAGTACTAAATTATGTATATTTTTACT -s simHuman_chr6.simHuman.chr6 132186 82 + 601863 GTAGACTTAAAGTATGAACCAAGT--AACCCAAAAGAAA------GCCACAGGCACATTGGTTGGGTAGCAAACCACGTATGTTTTTACC -s simRat_chr6.simRat.chr6 135518 90 + 647215 GTACAATTAGAGTATGAACTTAGCCAAACCCAAAAGAAACTAGATGTAACAGACATGTTACTTGGGTATCAAGCTGTGTACATCTCCATC - -a -s simMouse_chr6.simMouse.chr6 138002 66 + 636262 TAACTGCCCTCCAGATCCATGCCTTCTCAACACTACCTTACAACCAGCTGTACTTTAGTCTTGTTA -s Anc0.Anc0refChr1 29249 66 - 62388 TGGCTGCTCTCTGGGGCCATGCCTACTCAGCACTACTTTGACCCCAGCCATACTTTAGCCTTGTTG -s Anc1.Anc1refChr2 108148 66 + 144309 TGGCTGCTCTCTGGGGCCATGCCTACTCAGCACTACTTTGACCCCAGCCATACTTTAGCCTTGTTG -s Anc2.Anc2refChr3 18136 66 + 53186 TGGCTACTCTCTAGGGCCATGTCTACTCAGCAGCACTTTAACCCTACCCATACTTTAGCCTTGTTG -s mr.mrrefChr5 1740 66 + 294540 TAACTGCCCTCCGGATCCATGCCTTCTCAACACTACTTTGCACCCAGCTGTACTTTAGCCTTGTTA -s simCow_chr6.simCow.chr6 145520 51 + 602619 TGGCT---CTCTAGAGCCATGGCTTCTCAGCA------------TGTCCATACTTTAGCCTTGTTG -s simDog_chr6.simDog.chr6 430479 64 - 593897 --GCTACTCTCCAGGGCCATGTCTATTCAGCAGCACTTTAACCCTACCCATTCTTTAGCCTTTTTG -s simHuman_chr6.simHuman.chr6 132274 65 + 601863 TGGCTGCTCTCTGGGGCCATGCCTCCTCATCACTGCTTTGACCCCAGCCATAC-TTAGCCTTGTTG -s simRat_chr6.simRat.chr6 135608 58 + 647215 T--------TGCGGATCCATGCCTTCTCAGCACCACTTTGCACCTAGCTGTATTTTAGCCTTGTTA - -a -s simMouse_chr6.simMouse.chr6 138068 4 + 636262 AGAG -s Anc0.Anc0refChr1 29315 4 - 62388 ATAG -s Anc1.Anc1refChr2 108214 4 + 144309 ATAG -s Anc2.Anc2refChr3 18202 4 + 53186 ATAG -s mr.mrrefChr5 1806 4 + 294540 AGAG -s simCow_chr6.simCow.chr6 145571 4 + 602619 ATGG -s simDog_chr6.simDog.chr6 430552 4 - 593897 ATAG -s simHuman_chr6.simHuman.chr6 132339 4 + 601863 ATTG -s simRat_chr6.simRat.chr6 135666 4 + 647215 AGGG - -a -s simMouse_chr6.simMouse.chr6 138072 5 + 636262 GCCAA -s Anc0.Anc0refChr1 29320 5 - 62388 TCTAA -s Anc1.Anc1refChr2 108219 5 + 144309 TCTAA -s Anc2.Anc2refChr3 18207 5 + 53186 TCTAA -s mr.mrrefChr5 1810 5 + 294540 TCCAA -s simCow_chr6.simCow.chr6 145576 5 + 602619 TCGAA -s simDog_chr6.simDog.chr6 430557 5 - 593897 TCTAA -s simHuman_chr6.simHuman.chr6 132344 5 + 601863 TCTAG -s simRat_chr6.simRat.chr6 135670 5 + 647215 TCCAC - -a -s simMouse_chr6.simMouse.chr6 138077 41 + 636262 CTGCAGCATGTCCACAGCTGTTATCACCCATATAGGTCCCA -s Anc0.Anc0refChr1 29325 41 - 62388 CCATAGCATGTCCAAAGCTGTTGACACCTATATAGGTCCAG -s Anc1.Anc1refChr2 108224 41 + 144309 CCATAGCATGTCCAAAGCTGTTGACACCTATATAGGTCCAG -s Anc2.Anc2refChr3 18212 41 + 53186 CCATAGCATGTCCAAAGCTGTTGACACCTATATAAGTCCAG -s mr.mrrefChr5 1815 41 + 294540 CTGCAGCATGTCCACAGCTGTTATCACCCATATAGGTCCCA -s simCow_chr6.simCow.chr6 145582 41 + 602619 CTGTAGTATGTCTAAAGTTTTTGAAACCCATATAAGTTCAG -s simDog_chr6.simDog.chr6 430562 41 - 593897 CCATGGCATATCCAAAGCTGTTAACAACTTTATAAGACCAG -s simHuman_chr6.simHuman.chr6 132349 41 + 601863 TCATAGCATGCCCAAAGCTGTTGACACCTATGTAGGTCCAG -s simRat_chr6.simRat.chr6 135675 41 + 647215 CTGCAGCATGTCCAGAGCTATTAGCACCCATATAGATCCCA - -a -s simMouse_chr6.simMouse.chr6 138118 13 + 636262 CAATGATATGGAT -s Anc0.Anc0refChr1 29366 13 - 62388 TAGGGATATGGAT -s Anc1.Anc1refChr2 108265 13 + 144309 TAGGGATATGGAT -s Anc2.Anc2refChr3 18253 13 + 53186 TAGGGATATGGAT -s mr.mrrefChr5 1856 13 + 294540 CAATGATATGGAT -s simCow_chr6.simCow.chr6 145624 13 + 602619 TAGGGATATGGAT -s simDog_chr6.simDog.chr6 430603 13 - 593897 TAGGGATATGGAT -s simHuman_chr6.simHuman.chr6 132390 13 + 601863 TAGGGATATGGAT -s simRat_chr6.simRat.chr6 135716 13 + 647215 CAATGATATGGCT - -a -s simMouse_chr6.simMouse.chr6 138131 13 + 636262 TTTTGGGTGGAAT -s Anc0.Anc0refChr1 29389 13 - 62388 TTTTGACAGAAAT -s Anc1.Anc1refChr2 108288 13 + 144309 TTTTGACAGAAAT -s Anc2.Anc2refChr3 18276 13 + 53186 TTTTGACAGAAAT -s mr.mrrefChr5 1869 13 + 294540 TTTTGGGTGAAAT -s simCow_chr6.simCow.chr6 145647 13 + 602619 TTTTGACAAAAAT -s simDog_chr6.simDog.chr6 430626 13 - 593897 TTTTGACAGAAAT -s simHuman_chr6.simHuman.chr6 132413 13 + 601863 TTTTGACAGAAAT -s simRat_chr6.simRat.chr6 135729 13 + 647215 TTTTGGGTGAAAT - -a -s simMouse_chr6.simMouse.chr6 138144 5 + 636262 GCTTA -s Anc0.Anc0refChr1 29402 5 - 62388 GCCTA -s Anc1.Anc1refChr2 108301 5 + 144309 GCCTA -s Anc2.Anc2refChr3 18289 5 + 53186 GCCTT -s mr.mrrefChr5 1882 5 + 294540 GCCTA -s simCow_chr6.simCow.chr6 145660 5 + 602619 GCCTC -s simDog_chr6.simDog.chr6 430639 5 - 593897 GGCTT -s simHuman_chr6.simHuman.chr6 132433 5 + 601863 GCCTA -s simRat_chr6.simRat.chr6 135742 5 + 647215 CCCTA - -a -s simMouse_chr6.simMouse.chr6 138149 11 + 636262 ATATTCTTCTT -s Anc0.Anc0refChr1 29409 11 - 62388 ATGGCATTGTT -s Anc1.Anc1refChr2 108308 11 + 144309 ATGGCATTGTT -s Anc2.Anc2refChr3 18296 11 + 53186 ATGGCATTGTT -s mr.mrrefChr5 1887 11 + 294540 ATAGTCTTCTT -s simCow_chr6.simCow.chr6 145667 11 + 602619 ATGGTATTATT -s simDog_chr6.simDog.chr6 430646 9 - 593897 ATGGCACTG-- -s simHuman_chr6.simHuman.chr6 132440 11 + 601863 ATGGCATTGTT -s simRat_chr6.simRat.chr6 135747 11 + 647215 ATAGTCTTCGT - -a -s simMouse_chr6.simMouse.chr6 138160 27 + 636262 TGTCCTCAAAACGCCCACAGGGACCAA -s Anc0.Anc0refChr1 29421 23 - 62388 TGTCAAAAAAA----CACAGGGAGGAA -s Anc1.Anc1refChr2 108320 23 + 144309 TGTCAAAAAAA----CACAGGGAGGAA -s Anc2.Anc2refChr3 18308 23 + 53186 TGGCAAAAAAA----CACAAGGAGGGA -s mr.mrrefChr5 1898 27 + 294540 TGTCCTCAAAACGCCCACAGGGACCAA -s simCow_chr6.simCow.chr6 145679 23 + 602619 TGGCAAAAAAA----CACAAGGAGGGA -s simHuman_chr6.simHuman.chr6 132452 23 + 601863 TGTCACGAGGA----CACAGGGAGGAA -s simRat_chr6.simRat.chr6 135758 27 + 647215 TGTTCTCAAAACGACCACAGGGACAAA - -a -s simMouse_chr6.simMouse.chr6 138187 24 + 636262 CCATCATGATTTGACTGTCCCTCA -s Anc0.Anc0refChr1 29444 24 - 62388 CTGTGATGATTAAATAGTCCCTTA -s Anc1.Anc1refChr2 108343 24 + 144309 CTGTGATGATTAAATAGTCCCTTA -s Anc2.Anc2refChr3 18331 24 + 53186 CTGTGATGACTAAATACTCCCATG -s mr.mrrefChr5 1925 24 + 294540 CCATCATGATTTGACTGTCCCTCA -s simCow_chr6.simCow.chr6 145703 24 + 602619 CTGTGATGACTAAATACTCCCATG -s simHuman_chr6.simHuman.chr6 132475 24 + 601863 TTGTTGTGATTAAATAGTCCCTTA -s simRat_chr6.simRat.chr6 135785 24 + 647215 ACATCATGATTTGACTGCCCCTCC - -a -s simMouse_chr6.simMouse.chr6 138211 8 + 636262 TAAAAGCA -s Anc0.Anc0refChr1 29468 8 - 62388 TAAAAGTA -s Anc1.Anc1refChr2 108367 8 + 144309 TAAAAGTA -s Anc2.Anc2refChr3 18355 8 + 53186 CAACAGTA -s mr.mrrefChr5 1949 8 + 294540 TAAAAGTA -s simCow_chr6.simCow.chr6 145746 8 + 602619 CAACAGTA -s simDog_chr6.simDog.chr6 430655 6 - 593897 --ACAGTA -s simHuman_chr6.simHuman.chr6 132499 8 + 601863 TAAAAGTA -s simRat_chr6.simRat.chr6 135809 8 + 647215 TAAAAGTA - -a -s simMouse_chr6.simMouse.chr6 138219 6 + 636262 CCTATA -s Anc0.Anc0refChr1 29476 6 - 62388 CCCATA -s Anc1.Anc1refChr2 108375 6 + 144309 CCCATA -s Anc2.Anc2refChr3 18363 6 + 53186 CCCATA -s mr.mrrefChr5 1957 6 + 294540 CCTATA -s simCow_chr6.simCow.chr6 145764 6 + 602619 TCCATA -s simDog_chr6.simDog.chr6 430661 6 - 593897 CCCATT -s simHuman_chr6.simHuman.chr6 132507 6 + 601863 CTCATA -s simRat_chr6.simRat.chr6 135817 6 + 647215 CCTATA - -a -s simMouse_chr6.simMouse.chr6 138225 31 + 636262 GACATTAACTCATGCAATTTAAGAATTCCAC -s Anc0.Anc0refChr1 29483 31 - 62388 GACAGTGACTGATACAAATCCAGAATTCTAC -s Anc1.Anc1refChr2 108382 31 + 144309 GACAGTGACTGATACAAATCCAGAATTCTAC -s Anc2.Anc2refChr3 18370 31 + 53186 GACAGTGAATTATACAAATCCAGGATTCTAC -s mr.mrrefChr5 1963 31 + 294540 GACATTAACTGATGCAATTCAAGAATTCCAC -s simCow_chr6.simCow.chr6 145771 19 + 602619 GACAG----------AAATCCAGTATTCT-- -s simDog_chr6.simDog.chr6 430668 31 - 593897 GACAGTGAATTATACAAATGCAGGATTCCAC -s simHuman_chr6.simHuman.chr6 132514 31 + 601863 GACAGTGACTGATACAAAACCTGACTTCTAC -s simRat_chr6.simRat.chr6 135823 31 + 647215 GACATTAACTGATGCAACTCAAGAATTCCAC - -a -s simMouse_chr6.simMouse.chr6 138256 14 + 636262 AGCATGGCGAGGAT -s Anc0.Anc0refChr1 29514 14 - 62388 TACAGGAGGAGGGT -s Anc1.Anc1refChr2 108413 14 + 144309 TACAGGAGGAGGAT -s Anc2.Anc2refChr3 18401 14 + 53186 TACAGGGGGAGGGT -s Anc2.Anc2refChr3 34451 14 - 53186 TTCAAGACGAGGGT -s mr.mrrefChr5 1994 14 + 294540 AGCAGGGCGAGGAT -s simCow_chr6.simCow.chr6 456649 14 - 602619 TTCAAGACGAGGGT -s simDog_chr6.simDog.chr6 430699 14 - 593897 TACAGGGGGAGGGT -s simHuman_chr6.simHuman.chr6 132545 14 + 601863 TACAGGAGGAGGAT -s simRat_chr6.simRat.chr6 135854 14 + 647215 AGCAGGGCAAGGAT - -a -s simMouse_chr6.simMouse.chr6 138270 10 + 636262 AAGCAGGTGG -s Anc0.Anc0refChr1 29528 10 - 62388 GAGCAGGTGG -s Anc1.Anc1refChr2 108427 10 + 144309 GAGCAGGTGG -s Anc2.Anc2refChr3 18415 10 + 53186 TAGCAGTCGG -s Anc2.Anc2refChr3 34465 6 - 53186 GGGCAG---- -s mr.mrrefChr5 2008 10 + 294540 AAGCAGGTGG -s simCow_chr6.simCow.chr6 456663 6 - 602619 GGGCAG---- -s simDog_chr6.simDog.chr6 430713 10 - 593897 TAGCAGTCGG -s simHuman_chr6.simHuman.chr6 132575 10 + 601863 GAGCAGGTGG -s simRat_chr6.simRat.chr6 135868 10 + 647215 AAGCAGGTGG - -a -s simMouse_chr6.simMouse.chr6 138280 33 + 636262 GGTACCAAACAAATATATTGTAGACAGTATGTT -s Anc0.Anc0refChr1 29538 31 - 62388 GTTAC--ACCCAAGGTATAGTAGACAGTATTTT -s Anc1.Anc1refChr2 108437 31 + 144309 GTTAC--ACCCAAAGTATAGTAGACAGTATTTT -s Anc2.Anc2refChr3 18425 31 + 53186 GTTAC--ACCCAAGATACACCAGACAGTATTTT -s Anc2.Anc2refChr3 34471 31 - 53186 GTTAC--ACCCAGGGTATAGTAGACAGTACGTT -s mr.mrrefChr5 2018 33 + 294540 GGTACCAAACAAAAGTATAGTAGACAGTATGTT -s simCow_chr6.simCow.chr6 456670 31 - 602619 GTTAC--ACCCAGGGTATAGTAGACAGTACGTT -s simDog_chr6.simDog.chr6 430723 31 - 593897 GTTAC--ACCCAAGATACACCAGACAGTATTTT -s simHuman_chr6.simHuman.chr6 132585 31 + 601863 GTTAC--ACACAAAGTATAGTAGACAATATTTT -s simRat_chr6.simRat.chr6 135878 33 + 647215 CATAACAGACAAAAGTATAGTAGACAGTATGTT - -a -s simMouse_chr6.simMouse.chr6 138313 1 + 636262 T -s Anc0.Anc0refChr1 29569 1 - 62388 T -s Anc1.Anc1refChr2 108468 1 + 144309 T -s Anc2.Anc2refChr3 18456 1 + 53186 T -s Anc2.Anc2refChr3 34502 1 - 53186 A -s mr.mrrefChr5 2051 1 + 294540 T -s simCow_chr6.simCow.chr6 456701 1 - 602619 A -s simDog_chr6.simDog.chr6 430759 1 - 593897 T -s simHuman_chr6.simHuman.chr6 132616 1 + 601863 T -s simRat_chr6.simRat.chr6 135911 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 138314 2 + 636262 GA -s Anc0.Anc0refChr1 29570 2 - 62388 CA -s Anc1.Anc1refChr2 108469 2 + 144309 CA -s Anc2.Anc2refChr3 18457 2 + 53186 CC -s Anc2.Anc2refChr3 34508 2 - 53186 CT -s mr.mrrefChr5 2052 2 + 294540 GA -s simCow_chr6.simCow.chr6 456707 2 - 602619 CT -s simDog_chr6.simDog.chr6 430760 2 - 593897 CC -s simHuman_chr6.simHuman.chr6 132617 2 + 601863 CA -s simRat_chr6.simRat.chr6 135912 2 + 647215 GA - -a -s simMouse_chr6.simMouse.chr6 138316 13 + 636262 TGACTAAGATCTC -s Anc0.Anc0refChr1 29573 7 - 62388 GGACCC------C -s Anc1.Anc1refChr2 108472 13 + 144309 GGACCCATACCCC -s Anc2.Anc2refChr3 18460 7 + 53186 GGACCC------C -s Anc2.Anc2refChr3 34511 7 - 53186 AGACCC------C -s mr.mrrefChr5 2054 13 + 294540 TGACCAAGATCTC -s simCow_chr6.simCow.chr6 456710 7 - 602619 AGACCC------C -s simDog_chr6.simDog.chr6 430763 7 - 593897 GGACCC------C -s simHuman_chr6.simHuman.chr6 132620 13 + 601863 GGCCCCATAACAC -s simRat_chr6.simRat.chr6 135914 13 + 647215 TGACCAAGATCCC - -a -s simMouse_chr6.simMouse.chr6 138329 9 + 636262 AAAGGTATA -s Anc0.Anc0refChr1 29580 9 - 62388 ATAGGTGTG -s Anc1.Anc1refChr2 108485 9 + 144309 ATAGGTGTG -s Anc2.Anc2refChr3 34518 9 - 53186 ATAGATGTG -s mr.mrrefChr5 2067 9 + 294540 AAAGGTGTA -s simCow_chr6.simCow.chr6 456717 9 - 602619 ATAGATGTG -s simHuman_chr6.simHuman.chr6 132633 9 + 601863 ACAAGTGCT -s simRat_chr6.simRat.chr6 135927 9 + 647215 ATAGGTGTA - -a -s simMouse_chr6.simMouse.chr6 138338 29 + 636262 GATACTTGATCACCACAACTAGCGATCAA -s Anc0.Anc0refChr1 29589 29 - 62388 GATGCTTAGTCACCACAGTTTATCATCAA -s Anc1.Anc1refChr2 108494 29 + 144309 GATGCTTGGTCACCACAGTTTATCATCAA -s Anc2.Anc2refChr3 18467 29 + 53186 TATGCCTAGTCACCACAGTTTACCATCAA -s Anc2.Anc2refChr3 34527 29 - 53186 GAGGCTTAGTCACCACAGTTTATTATCAA -s mr.mrrefChr5 2076 29 + 294540 GATACTTGATCACCACAATTAGCGATCAA -s simCow_chr6.simCow.chr6 456726 29 - 602619 GAGGCTTAGTCACCACAGTTTATTATCAA -s simDog_chr6.simDog.chr6 430770 29 - 593897 TATGCCTAGTCACCACAGTTTACCATCAA -s simHuman_chr6.simHuman.chr6 132642 29 + 601863 GATGCTTGGTTATGACAGTTTATCATCAA -s simRat_chr6.simRat.chr6 135936 29 + 647215 GATACTTGATCACCACAATTAGCAATCAA - -a -s simMouse_chr6.simMouse.chr6 138367 17 + 636262 CACCAACTCAGAAGAGT -s Anc0.Anc0refChr1 29618 11 - 62388 GA------CAATTGAGT -s Anc1.Anc1refChr2 108523 11 + 144309 GA------CAATTGAGT -s Anc2.Anc2refChr3 18496 11 + 53186 GA------CAATTGACT -s Anc2.Anc2refChr3 34556 7 - 53186 GG------A----GGGT -s mr.mrrefChr5 2105 17 + 294540 CACCAACTCAGTAGAGT -s simCow_chr6.simCow.chr6 456755 7 - 602619 GG------A----GGGT -s simDog_chr6.simDog.chr6 430805 11 - 593897 GA------CAATTGACT -s simHuman_chr6.simHuman.chr6 132671 11 + 601863 AA------TGATTGAAT -s simRat_chr6.simRat.chr6 135965 17 + 647215 CACCAACCCAGTAGAGT - -a -s simMouse_chr6.simMouse.chr6 138384 25 + 636262 AATGGGAAGTAGTGAGCTCTTTTTA -s Anc0.Anc0refChr1 29629 25 - 62388 AATGAGAAGTAGTGAGATTTTTTTA -s Anc1.Anc1refChr2 108534 25 + 144309 AATGGGAAGTAGTGAGATTTTTTTA -s Anc2.Anc2refChr3 18507 25 + 53186 AATGAGAGGTAGTGAGATTTTTTTA -s Anc2.Anc2refChr3 34563 25 - 53186 AATAATGAGAAGTGAGATTTTTTTA -s mr.mrrefChr5 2122 25 + 294540 AATGGGAAGTAGTGAGATCTTTTTA -s simCow_chr6.simCow.chr6 456764 25 - 602619 AATAATGAGAAGTGAGATTTTTTTA -s simDog_chr6.simDog.chr6 430816 25 - 593897 AATGAGAGGTAGTGAGATTTTTTTA -s simHuman_chr6.simHuman.chr6 132682 25 + 601863 AGTGGGAAGTAGTGGGATTTTTCTA -s simRat_chr6.simRat.chr6 135982 25 + 647215 AATAGGAAGTAGTGAGAGCTTTTTA - -a -s simMouse_chr6.simMouse.chr6 138409 1 + 636262 G -s Anc0.Anc0refChr1 29654 1 - 62388 G -s Anc1.Anc1refChr2 108559 1 + 144309 G -s Anc2.Anc2refChr3 18532 1 + 53186 G -s Anc2.Anc2refChr3 34588 1 - 53186 G -s mr.mrrefChr5 2147 1 + 294540 G -s simCow_chr6.simCow.chr6 456789 1 - 602619 G -s simDog_chr6.simDog.chr6 430843 1 - 593897 G -s simHuman_chr6.simHuman.chr6 132707 1 + 601863 G -s simRat_chr6.simRat.chr6 136007 1 + 647215 G - -a -s simMouse_chr6.simMouse.chr6 138410 27 + 636262 GGTGATTAATAACAGTGTCCAGAACCT -s Anc0.Anc0refChr1 29657 27 - 62388 AATTATTATTAACTCAGTCCAGAATGA -s Anc1.Anc1refChr2 108562 27 + 144309 AATTATTATTAACACAGTCCAGAATGA -s Anc2.Anc2refChr3 18535 27 + 53186 AACTATTATAAACTCAGTACAGCATGA -s Anc2.Anc2refChr3 34589 18 - 53186 AATTATTATTAACTCAGT--------- -s mr.mrrefChr5 2148 27 + 294540 GGTGATTAATAACAGTGTCCAGAATCT -s simCow_chr6.simCow.chr6 456794 18 - 602619 AATTATTATTAACTCAGT--------- -s simDog_chr6.simDog.chr6 430846 27 - 593897 AACTATTATAAACTCAGTACAGCATGA -s simHuman_chr6.simHuman.chr6 132710 27 + 601863 CATTATTACTAACACAATCCAGAATGA -s simRat_chr6.simRat.chr6 136008 27 + 647215 GGTGATTAATAAGATTGTCCAGAATCT - -a -s simMouse_chr6.simMouse.chr6 138437 17 + 636262 AACACCAAATGCGCTAG -s Anc0.Anc0refChr1 29684 17 - 62388 AACACCAGATAAACTAG -s Anc1.Anc1refChr2 108589 17 + 144309 AACACCAGATAAACTAG -s Anc2.Anc2refChr3 18562 17 + 53186 AACACCATATAATCTGA -s mr.mrrefChr5 2175 17 + 294540 AACACCAAATGAACTAG -s simCow_chr6.simCow.chr6 145790 17 + 602619 TACACTGTACAATCTGA -s simDog_chr6.simDog.chr6 430873 12 - 593897 AGTTCCATATAG----- -s simHuman_chr6.simHuman.chr6 132737 17 + 601863 AACACCAGATAAACTAC -s simRat_chr6.simRat.chr6 136035 17 + 647215 AGCACCAAAGGAACTAG - -a -s simMouse_chr6.simMouse.chr6 138454 9 + 636262 AATCCTTTT -s Anc0.Anc0refChr1 29701 9 - 62388 AATTCTTTC -s Anc1.Anc1refChr2 108606 9 + 144309 AATTCTTTC -s Anc2.Anc2refChr3 18742 9 + 53186 AATTCTTTT -s mr.mrrefChr5 2192 9 + 294540 AATCCTTTC -s simCow_chr6.simCow.chr6 145977 9 + 602619 AATTCTTTT -s simDog_chr6.simDog.chr6 430890 5 - 593897 AATGG---- -s simHuman_chr6.simHuman.chr6 132754 9 + 601863 AATTCTTTC -s simRat_chr6.simRat.chr6 136052 9 + 647215 AATCCGTTC - -a -s simMouse_chr6.simMouse.chr6 138463 60 + 636262 GTGCTCCTGTTTCTTAGCGCATCAGTTCTAGCAAAGTCGCTAATTAGATTAGACTGAAGA -s Anc0.Anc0refChr1 29717 51 - 62388 GAGCTGTCTATTTCCAG---------TCTAGTCTATTAGCTAGTTAGCTAGAACTGGTGA -s Anc1.Anc1refChr2 108622 51 + 144309 GAGCTGTCTATTTCCAG---------TCTAGTCTATTAGCTAGTTAGCTAGAACTGGTGA -s Anc2.Anc2refChr3 18758 51 + 53186 GAGCTGTCTATTTCCTG---------TCAAGTCTATTAGCTAGTTAACGAGAACTGATGA -s mr.mrrefChr5 2201 60 + 294540 GTGCTCCTGTTTCTTAGCGCATCAGTTCTAGCAAAGTAGCTAATTAGATTAGACTGGAGA -s simCow_chr6.simCow.chr6 145993 50 + 602619 GAGCCATCTTTCGTCT----------TCAAGACTATTAGTTAGTTGATGAAAATCGAGCC -s simDog_chr6.simDog.chr6 430900 51 - 593897 GAGTTGTCTACTTCCTG---------TCAAGTCTATAAGCTAGTTAACGAGAGCTGATGA -s simHuman_chr6.simHuman.chr6 132770 51 + 601863 GAGCTGTCAATTTCCAG---------TCTAATCTGTTAGCCACTTAGCTAGAAGTGGTGA -s simRat_chr6.simRat.chr6 136061 59 + 647215 GTGCTCCTGTTTCTGTGTGCATCAGCTCTGGCAAAGTAGCTGAT-AGACTAGATTGGAAG - -a -s simMouse_chr6.simMouse.chr6 138523 54 + 636262 TAAACGGCTCCTTTTTACCATTCCTTTTAACATGACCTATACTGTGACAAGGAC -s Anc0.Anc0refChr1 29773 50 - 62388 CAAACTCACC----CCACCATCCCTTTAAACACAAGCTAGAGTGTGAGATGTAG -s Anc1.Anc1refChr2 108678 50 + 144309 CAAACTCACC----CCACCATCCCTTTAAACACAAGCTAGAGTGTGAGATGTAG -s Anc2.Anc2refChr3 18814 50 + 53186 CAAACTCACC----CCACCATCCCTTTAAACACAAGCTGGAGTGTGAGATGTAG -s mr.mrrefChr5 2261 54 + 294540 TAAACAGCCCCTTTTTACCATTCCTTTTAACATGACCTATACTGTGAGAAGGAC -s simCow_chr6.simCow.chr6 146048 50 + 602619 CAAACTCATC----CCACCATCCCTTGAGAAACAAGATGGTCAGTGAGATGTAG -s simDog_chr6.simDog.chr6 430956 41 - 593897 CAAACTCACC----CCA---------TAAACACAAGCTGGAGTGCGAGGTGTAG -s simHuman_chr6.simHuman.chr6 132826 50 + 601863 CAAACTAACC----CCACCATCTGTTTCAACACAAGCTACAATGTGTGACACAG -s simRat_chr6.simRat.chr6 136120 54 + 647215 TAAACAGCCCCTTTTTACCATTCCTTTTAACATGACCTATACTGTGAGAAGGGC - -a -s simMouse_chr6.simMouse.chr6 138577 50 + 636262 TCAGTCGACTTACCTGATAGCCATTCCCTCATTCTTTGAATACCACCTTT -s Anc0.Anc0refChr1 29823 43 - 62388 ATAGTGGGCTTACCATTTTG-------CTCATTCTTTGCATATAGGTTCC -s Anc1.Anc1refChr2 108728 43 + 144309 ATAGTGGGCTTACCATTTTG-------CTCATTCTTTGCATATAGGTTCC -s Anc2.Anc2refChr3 18864 43 + 53186 ATAGTGGGCTTACCATTTTA-------CTCATTCTTTGCATTTAGGTTCC -s mr.mrrefChr5 2315 43 + 294540 TCAGTCGACTTACCTTATAG-------CTCATTCTTTGAATATAACCTTT -s simCow_chr6.simCow.chr6 146100 43 + 602619 ATAGTAGGCCTACCTTTTTA-------CTCATTATTTGCATTTAGGTTCC -s simDog_chr6.simDog.chr6 430997 43 - 593897 ATAGAGGACTTGCAACCTTA-------CTCTTTCGTTGCATTTAGGTTCC -s simHuman_chr6.simHuman.chr6 132876 41 + 601863 ATAGTGGGC--ACCATTTTG-------CTCATTCTTTGCATATAGGTTCC -s simRat_chr6.simRat.chr6 136174 42 + 647215 TCAGTAGACTTACCTTCTAG-------CTCATTC-TTGAATATAACCTAT - -a -s simMouse_chr6.simMouse.chr6 138627 1 + 636262 T -s Anc0.Anc0refChr1 29866 1 - 62388 A -s Anc1.Anc1refChr2 108771 1 + 144309 A -s Anc2.Anc2refChr3 18907 1 + 53186 A -s mr.mrrefChr5 2358 1 + 294540 A -s simCow_chr6.simCow.chr6 146143 1 + 602619 A -s simDog_chr6.simDog.chr6 431040 1 - 593897 T -s simHuman_chr6.simHuman.chr6 132917 1 + 601863 A -s simRat_chr6.simRat.chr6 136219 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 138628 7 + 636262 CAATTGG -s Anc0.Anc0refChr1 29867 7 - 62388 CAATTGT -s Anc1.Anc1refChr2 108772 7 + 144309 CAATTGT -s Anc2.Anc2refChr3 18908 7 + 53186 CAAACGT -s mr.mrrefChr5 2359 7 + 294540 CAATTGG -s simCow_chr6.simCow.chr6 146167 7 + 602619 CAGGCAT -s simDog_chr6.simDog.chr6 431041 7 - 593897 TGAACGT -s simHuman_chr6.simHuman.chr6 132918 7 + 601863 CAATTGT -s simRat_chr6.simRat.chr6 136220 7 + 647215 CAATTGG - -a -s simMouse_chr6.simMouse.chr6 138635 6 + 636262 TATTTG -s Anc0.Anc0refChr1 29874 6 - 62388 AGGTTG -s Anc1.Anc1refChr2 108779 6 + 144309 AGGTTG -s Anc2.Anc2refChr3 18915 6 + 53186 AGGTTG -s mr.mrrefChr5 2366 6 + 294540 TAGTTG -s simCow_chr6.simCow.chr6 146174 6 + 602619 AGGTTG -s simDog_chr6.simDog.chr6 431054 6 - 593897 AGGTTG -s simHuman_chr6.simHuman.chr6 132925 6 + 601863 AGGTTG -s simRat_chr6.simRat.chr6 136227 6 + 647215 TAGTTG - -a -s simMouse_chr6.simMouse.chr6 138641 19 + 636262 GACAACACTTCTACCAATA -s Anc0.Anc0refChr1 29881 15 - 62388 AACTGCAC-TCTAC---TA -s Anc1.Anc1refChr2 108786 15 + 144309 AACTGCAC-TCTAC---TA -s Anc2.Anc2refChr3 18922 15 + 53186 AACTGTAC-ACTAC---TA -s mr.mrrefChr5 2372 18 + 294540 GACAGCAC-TCTACCAATA -s simCow_chr6.simCow.chr6 146181 15 + 602619 AACTGTAC-ACTAT---TA -s simDog_chr6.simDog.chr6 431061 11 - 593897 AA----AC-ACTAC---TA -s simHuman_chr6.simHuman.chr6 132932 15 + 601863 AATTGCAC-TCTAC---TA -s simRat_chr6.simRat.chr6 136233 18 + 647215 GACAGCAA-TCTCCCAATA - -a -s simMouse_chr6.simMouse.chr6 138660 30 + 636262 CTAGAGAGGCAATTAGGACACAGTGAAAGT -s Anc0.Anc0refChr1 29898 21 - 62388 CTACAG-AGCAAGTAGGAC--------AGT -s Anc1.Anc1refChr2 108803 21 + 144309 CTACAG-AGCAAGTAGGAC--------AGT -s Anc2.Anc2refChr3 18939 21 + 53186 CTACAG-AGCAAGTAAGAC--------AGT -s mr.mrrefChr5 2392 29 + 294540 CTAGAG-GGCAATTAGGACACAGTGAAAGT -s simCow_chr6.simCow.chr6 146198 21 + 602619 CTATGG-AGAATAAGACAC--------AGT -s simDog_chr6.simDog.chr6 431074 21 - 593897 CTACAG-GGCAAGTAAGAC--------ACA -s simHuman_chr6.simHuman.chr6 132949 21 + 601863 CTACAG-AGTAGGGAGGAC--------AGT -s simRat_chr6.simRat.chr6 136253 29 + 647215 CTAGAG-GGAAACTAGGACATGGGCAAAGT - -a -s simMouse_chr6.simMouse.chr6 138690 99 + 636262 ACAAGCGATATTTTATGTTCTATCTGCAATTGATGCCAAGCTTGACTTGGTGACCCTTCTCTTGTTTAGTTAATCCTGGAGCCACCTTGGATAGCTGTC -s Anc0.Anc0refChr1 29919 98 - 62388 ACGACTCATATTTTATGTTCAATTTGCATTTTGAGCCAACCTTAACTTGGTGACCCTTTTCTTGTTTGGTT-GTCTAGGAGGCAACTTAGATAGTTGTC -s Anc1.Anc1refChr2 108824 98 + 144309 ACGACTCATATTTTATGTTCAATTTGCATTTTGAGCCAACCTTAACTTGGTGACCCTTTTCTTGTTTGGTT-GTCTAGGAGGCAACTTAGATAGTTGTC -s Anc2.Anc2refChr3 18960 98 + 53186 ACGACTCATATGTTCTGTTCAATTTGCATTTTGAGCTGACCTTAACTTGGTGACCCTTTTCTTGTTTGGTT-GTATAGAAGGCAACATAGATAGTTGTG -s mr.mrrefChr5 2421 99 + 294540 ACAAGCGATATTTTATGTTCTATCTGCAATTGGTGCCAAGCTTGACTTGGTGACCCTTCTCTTGTTTAGTTAATCCTGGAGCCACCTTGGATAGCTGTC -s simCow_chr6.simCow.chr6 146226 98 + 602619 ACAAGTCACATGTTCTGTTCGATTTGCGTTTTGAGCTGACCTTAACCGGAGGACCCTCTTCTTGTTTGGCT-GTATAGAAGGCAACATCGATAGTCATA -s simDog_chr6.simDog.chr6 431095 79 - 593897 ATG-CTGGTAT--------AAGTTAACATGTTATGT----------TTGGTGAGCCTTTTCTTGTTTGGTT-GTATTGAAGGTAAGATAGATACTTGTG -s simHuman_chr6.simHuman.chr6 132970 98 + 601863 ACGACTCATATTTTATGTTCAATTTGCATTTTGAGCCAATCTTCACTTGGTGACCCTTTACTTGTTTGGTT-GTCTACGAGGCAACTCAGATAGATGCC -s simRat_chr6.simRat.chr6 136282 91 + 647215 ACAAGCAATATTTTATGTTCTATC------TGGTGCCAACCTTGACTTGGTGACCCTTGTCTTGTTTAGCTAATC--AGAGCCACCTTGGATAGCCATC - -a -s simMouse_chr6.simMouse.chr6 138789 66 + 636262 ATAATAATACAATACAGTTAGACATGTAAGGATACTGTTATTCATCAGAGAGCTTGTTTACTTTCA -s Anc0.Anc0refChr1 30017 42 - 62388 GTAATAATACAATACAGTT---------------------ATTATCTGAGAAC---TTTGCCTTTG -s Anc1.Anc1refChr2 108922 42 + 144309 GTAATAATACAATACAGTT---------------------ATTATCTGAGAAC---TTTGCCTTTG -s Anc2.Anc2refChr3 19058 42 + 53186 GTAATAATACAATACAGTT---------------------ATTATCTGAGAAC---TTTGGCTTTG -s mr.mrrefChr5 2520 66 + 294540 ATAATAATACAATACAGTTAGACATGTAAGGATACTGTTAATCATCTGAGAACTTGTTTACCTTCA -s simCow_chr6.simCow.chr6 146324 42 + 602619 ATAGTAATACAATACAGTT---------------------ATCATCTGAGAAT---TCTGTCTTTG -s simDog_chr6.simDog.chr6 431174 42 - 593897 GTAATAGTACAATACAGTT---------------------ATTATCTGAAAAC---TTTGGCTTTG -s simHuman_chr6.simHuman.chr6 133068 42 + 601863 GTAATAATACAATACGGTT---------------------ATTATCTAAGAAC---TTTGCCTCTG -s simRat_chr6.simRat.chr6 136699 66 + 647215 AAAATGATACAATACAGTTAGAGATGCAAGAATACTGTTAATCATCTGAGAACTTGTTTACCTTCA - -a -s simMouse_chr6.simMouse.chr6 138855 17 + 636262 TGGGGTCGGCATACCAG -s Anc0.Anc0refChr1 30063 17 - 62388 TGCTGTTGGCaTACCAG -s Anc1.Anc1refChr2 108968 17 + 144309 TGCTGTTGGCaTACCAG -s Anc2.Anc2refChr3 19104 17 + 53186 TCCTGTTGGCaTACCAG -s mr.mrrefChr5 2590 17 + 294540 TGGGGTTGGCATACCAG -s simCow_chr6.simCow.chr6 146370 16 + 602619 TCCTGTTAGC-TACCAG -s simDog_chr6.simDog.chr6 431220 17 - 593897 TCTGGTTGGCATACCGG -s simHuman_chr6.simHuman.chr6 133114 17 + 601863 TGCTGTTGAcataccag -s simRat_chr6.simRat.chr6 136769 17 + 647215 TGGGGTTGGTATACCAG - -a -s simMouse_chr6.simMouse.chr6 138872 24 + 636262 ATGATAATAAATAGATATGAGCTA -s Anc0.Anc0refChr1 30080 24 - 62388 ATGATAATAAGTAGATCCGATTTG -s Anc1.Anc1refChr2 108985 24 + 144309 ATGATAATAAGTAGATCCGATTTG -s Anc2.Anc2refChr3 19121 24 + 53186 TTGATAATAAGTAAATCCGATTTG -s mr.mrrefChr5 2607 24 + 294540 ATGATAATAAATAGATATGAGCTA -s simCow_chr6.simCow.chr6 146386 24 + 602619 ATGATAATAAGTAAATCCAACTTG -s simDog_chr6.simDog.chr6 431237 24 - 593897 TTGATAAGAGGTAAATCTGATTTG -s simHuman_chr6.simHuman.chr6 133177 24 + 601863 ATGATCATAAGTAGATCCGAATTG -s simRat_chr6.simRat.chr6 136786 24 + 647215 GTGATAAGAAATAAATATGAGCTA - -a -s simMouse_chr6.simMouse.chr6 138896 82 + 636262 AACTGTGATTAAGACTGTTGTCTTGCTCTGTTGTTTGGATTGAGCCCACAATGTTAATTACTAGCTAAACTGTGATTAAGAC -s Anc0.Anc0refChr1 30109 14 - 62388 AACTGAGACTAAGA-------------------------------------------------------------------- -s Anc1.Anc1refChr2 109014 14 + 144309 AACTGAGACTAAGA-------------------------------------------------------------------- -s Anc2.Anc2refChr3 19150 14 + 53186 GACTAAGCCTAAGA-------------------------------------------------------------------- -s mr.mrrefChr5 2631 18 + 294540 AACTGTGATTAAGACT----------------------------------------------------------------AC -s simCow_chr6.simCow.chr6 146415 7 + 602619 CG-------TAAGA-------------------------------------------------------------------- -s simDog_chr6.simDog.chr6 431266 14 - 593897 GACTAAGCCTATGG-------------------------------------------------------------------- -s simHuman_chr6.simHuman.chr6 133206 14 + 601863 AACTGAGACTAAGA-------------------------------------------------------------------- -s simRat_chr6.simRat.chr6 136810 18 + 647215 AACTGTGATTAAGATT----------------------------------------------------------------AT - -a -s simMouse_chr6.simMouse.chr6 138978 10 + 636262 TGTTGTCCTT -s Anc0.Anc0refChr1 30123 10 - 62388 TTTTGTCTTT -s Anc1.Anc1refChr2 109028 10 + 144309 TTTTGTCTTT -s Anc2.Anc2refChr3 19165 10 + 53186 CTTTATCTTT -s mr.mrrefChr5 2649 10 + 294540 TTTTGTCCTT -s simCow_chr6.simCow.chr6 146423 9 + 602619 ATATATCTT- -s simDog_chr6.simDog.chr6 431281 10 - 593897 CTTCATCTTT -s simHuman_chr6.simHuman.chr6 133220 10 + 601863 TTTTGTCTTG -s simRat_chr6.simRat.chr6 136828 10 + 647215 TTTTGTCATT - -a -s simMouse_chr6.simMouse.chr6 138988 59 + 636262 TGCTCTGTTGTTTGGATTGAGCCCACAATGTTAATAACTGCTTGTAGCCAAACATAAAT -s Anc0.Anc0refChr1 30133 59 - 62388 TCCTCTGTTGTTTTGAGTAAATCCATGCTGTAGATTACTGCATGTGACTAAACATGAAC -s Anc1.Anc1refChr2 109038 59 + 144309 TCCTCTGTTGTTTTGAGTAAATCCATGCTGTAGATTACTGCATGTGACTAAACATGAAC -s Anc2.Anc2refChr3 19175 59 + 53186 TCCTCTGTTGTTTTGAGTAAATCCATGCTGGAGGTTACTGCATGTGACTAAACATGAAC -s mr.mrrefChr5 2659 59 + 294540 TGCTCTGTTGTTTGGATTGAGTCCACGATGTTAATTACTGCTTGTGGCTAAACATAAAT -s simCow_chr6.simCow.chr6 146432 59 + 602619 TTCTCTGGTGTTTTGAGTACACCCATGATCGGGGTTACCACCTGTGAATAAACATGAAC -s simDog_chr6.simDog.chr6 431293 59 - 593897 CCCTCTGTTGTTTTGAAAAACTCTGTGCTGGAGGTTATTGCATGTGACTAAACATGAAC -s simHuman_chr6.simHuman.chr6 133230 59 + 601863 TCCTCTGTTGTTTTGAGTAAATCCATGGTGTAGATTACTGCATGTGACTAAACATGAAC -s simRat_chr6.simRat.chr6 136838 56 + 647215 TGCTCTGTTGTATGGATTGAGT---CGATGTTAATTACTGCTTGTGGCTAAACATAAAT - -a -s simMouse_chr6.simMouse.chr6 139047 46 + 636262 TTCCCATCTGAACACAAAATCAACTTTGTGTTCTTTCACTAACACC -s Anc0.Anc0refChr1 30192 45 - 62388 TTCCCATGTGAATACAAAATCAGCTTTGT-CTATTACAATAACACC -s Anc1.Anc1refChr2 109097 45 + 144309 TTCCCATGTGAATACAAAATCAGCTTTGT-CTATTACAATAACACC -s Anc2.Anc2refChr3 19234 45 + 53186 TTCCCATGTGAATACAAAATCAGCCTTGT-CTATTACAATACCACC -s mr.mrrefChr5 2718 46 + 294540 TTCCCATCTGAATACAAAATCAACTTTGTGTTCTTTCACTAACACC -s simCow_chr6.simCow.chr6 146491 45 + 602619 TCCCAATGTGAGCACAAAATCAGCCTTCT-CTCTTACAATACCACC -s simDog_chr6.simDog.chr6 431355 45 - 593897 TTCCCATGTGAATATAAAATCAGCCTTGT-CTATTACAAAACCGTT -s simHuman_chr6.simHuman.chr6 133289 45 + 601863 TTCCCATGTGGATACAAAACCAGCTTTGT-CTATTACAATGAGACC -s simRat_chr6.simRat.chr6 136894 46 + 647215 TTCCCATCTGAATACAAAATCAACTTTCTGTTCTTTCTCTAACACC - -a -s simMouse_chr6.simMouse.chr6 139093 14 + 636262 TCAATACAAAGTAA -s Anc0.Anc0refChr1 30238 14 - 62388 TCAATGCGAAGCAA -s Anc1.Anc1refChr2 109143 14 + 144309 TCAATGCGAAGCAA -s Anc2.Anc2refChr3 19280 14 + 53186 TCAAAGCGAAGCAA -s mr.mrrefChr5 2764 14 + 294540 TCAATACAAAGTAA -s simCow_chr6.simCow.chr6 146537 14 + 602619 TCAAAGCAAAACAA -s simDog_chr6.simDog.chr6 431401 14 - 593897 TCAAAGCGAAGCAA -s simHuman_chr6.simHuman.chr6 133335 5 + 601863 TCAAT--------- -s simRat_chr6.simRat.chr6 136940 14 + 647215 TCAATAGAAAGTAA - -a -s simMouse_chr6.simMouse.chr6 139107 6 + 636262 TTACCC -s Anc0.Anc0refChr1 30252 6 - 62388 TTATCT -s Anc1.Anc1refChr2 109157 6 + 144309 TTATCT -s Anc2.Anc2refChr3 19295 6 + 53186 TTATCT -s mr.mrrefChr5 2778 6 + 294540 TTACCC -s simCow_chr6.simCow.chr6 146553 6 + 602619 CAATCT -s simDog_chr6.simDog.chr6 431416 6 - 593897 TTATCT -s simRat_chr6.simRat.chr6 136954 6 + 647215 TTACCC - -a -s simMouse_chr6.simMouse.chr6 139113 1 + 636262 A -s Anc0.Anc0refChr1 30258 1 - 62388 G -s Anc1.Anc1refChr2 109163 1 + 144309 G -s Anc2.Anc2refChr3 19301 1 + 53186 G -s mr.mrrefChr5 2784 1 + 294540 A -s simCow_chr6.simCow.chr6 146559 1 + 602619 C -s simDog_chr6.simDog.chr6 431422 1 - 593897 G -s simRat_chr6.simRat.chr6 136963 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 139114 27 + 636262 GACTCTTTTTAATCCCAAAGGAACCTG -s Anc0.Anc0refChr1 30259 27 - 62388 GACTCTTTTGGATCCCACAAGATCCTG -s Anc1.Anc1refChr2 109164 27 + 144309 GACTCTTTTGGATCCCACAAGATCCTG -s Anc2.Anc2refChr3 19308 27 + 53186 GACTCTTTTGGATCCCACAAGATCCTG -s mr.mrrefChr5 2785 27 + 294540 GACTCTTTTTGATCCCAAAGGAACCTG -s simCow_chr6.simCow.chr6 146566 27 + 602619 TACTCTTTAGGATCCCACAAGATCCTG -s simDog_chr6.simDog.chr6 431429 27 - 593897 GACTCTCTTGGATCCTACATGATCCCA -s simHuman_chr6.simHuman.chr6 133340 27 + 601863 GACTCTTTCAGATCCCACGAAATCCTG -s simRat_chr6.simRat.chr6 136964 27 + 647215 GACTCTCTTTGATCCCAAAGGAGCCTG - -a -s simMouse_chr6.simMouse.chr6 139141 47 + 636262 GTTCAAGGTTTTTTCCAACACAACAGGGGAGATGGTTGAGAAGGAGA -s Anc0.Anc0refChr1 30290 27 - 62388 GTCCTGGGTTGTTTCCAACA--------------------AAGGATA -s Anc1.Anc1refChr2 109195 27 + 144309 GTCCTGGGTTGTTTCCAACA--------------------AAGGATA -s Anc2.Anc2refChr3 19339 27 + 53186 GTCCTGGGTTGTCTCCAACA--------------------AAGGATA -s mr.mrrefChr5 2816 47 + 294540 GTTCAAGGTTTTTTCCAACACAACAGAGGAGATGGTTGAGAAGGAGA -s simCow_chr6.simCow.chr6 146597 27 + 602619 GTCCTTGGTTGACTCGAGAA--------------------AAGGATA -s simDog_chr6.simDog.chr6 431460 27 - 593897 GGCCTGGGTTGTCCTCAACC--------------------AAGGACA -s simHuman_chr6.simHuman.chr6 133371 27 + 601863 GTCTGGGGGTGTTTCCAACA--------------------AAGGATA -s simRat_chr6.simRat.chr6 136995 47 + 647215 GTTCAAGGTTAATTCCAACACAACAGATAAGACAGTTAAGAAAGAGA - -a -s simMouse_chr6.simMouse.chr6 139188 32 + 636262 CAGTTAAGATATTTGTAGTATATCCGGACACC -s Anc0.Anc0refChr1 30318 32 - 62388 CAGATAAGATATTTGTAGTATAACCAGCCCTC -s Anc1.Anc1refChr2 109223 32 + 144309 CAGATAAGATATTTGTAGTATAACCAGCCCTC -s Anc2.Anc2refChr3 19367 32 + 53186 CAGATGAGATAATTGTAGTATGACCAACCCTT -s mr.mrrefChr5 2863 32 + 294540 CAGTTAAGATATTTGTAGTATATCCAGACCCC -s simCow_chr6.simCow.chr6 146625 24 + 602619 --------ATGATTGTAGTATGCCTATATCTT -s simDog_chr6.simDog.chr6 431488 30 - 593897 CAGATGAGATAATTGTAGTATGACCAACCC-- -s simHuman_chr6.simHuman.chr6 133399 32 + 601863 CAGATAAGAAATTTGTAGTATAGCCAGGCCAC -s simRat_chr6.simRat.chr6 137042 32 + 647215 TGGTTAAGATATTTGTAGTATATCTAGACCCC - -a -s simMouse_chr6.simMouse.chr6 139220 6 + 636262 CTATAG -s Anc0.Anc0refChr1 30354 6 - 62388 TTGTGG -s Anc1.Anc1refChr2 109259 6 + 144309 TTGTGG -s Anc2.Anc2refChr3 19403 6 + 53186 TTGTGG -s mr.mrrefChr5 2895 6 + 294540 CTATAG -s simCow_chr6.simCow.chr6 146653 6 + 602619 TTGTGG -s simHuman_chr6.simHuman.chr6 133435 6 + 601863 TTTTGG -s simRat_chr6.simRat.chr6 137074 6 + 647215 CTATGG - -a -s simMouse_chr6.simMouse.chr6 139226 4 + 636262 GCAC -s Anc0.Anc0refChr1 30360 4 - 62388 CAAA -s Anc1.Anc1refChr2 109265 4 + 144309 CAAA -s Anc2.Anc2refChr3 19409 4 + 53186 CAAA -s mr.mrrefChr5 2901 4 + 294540 GCAC -s simCow_chr6.simCow.chr6 146675 4 + 602619 CAAA -s simHuman_chr6.simHuman.chr6 133441 4 + 601863 CAAA -s simRat_chr6.simRat.chr6 137080 4 + 647215 GCAC - -a -s simMouse_chr6.simMouse.chr6 139230 12 + 636262 TTCGGCGTGCAT -s Anc0.Anc0refChr1 30371 10 - 62388 T--GACATACAT -s Anc1.Anc1refChr2 109276 10 + 144309 T--GACATACAT -s Anc2.Anc2refChr3 19420 10 + 53186 T--AATAGATAT -s mr.mrrefChr5 2907 12 + 294540 TTCGGCGTGCAT -s simCow_chr6.simCow.chr6 146687 10 + 602619 T--AATAGATAT -s simHuman_chr6.simHuman.chr6 133452 10 + 601863 T--GACATACAT -s simRat_chr6.simRat.chr6 137086 12 + 647215 TGGGGTGTGTAT - -a -s simMouse_chr6.simMouse.chr6 139242 67 + 636262 GGAGAGCTTATTTCTTTAGATTGACCTTTTATGTATGATTCAAGACACTTTGCGGTCATCATTCAAA -s Anc0.Anc0refChr1 30381 67 - 62388 TCAGAGCCTGCACCTTTAGATTTACCTTTTATGCACCATTCAAGACAGTCTATTGCCATCATTTATA -s Anc1.Anc1refChr2 109286 67 + 144309 TCAGAGCCTGCACCTTTAGATTTACCTTTTATGCACCATTCAAGACAGTCTATTGCCATCATTTATA -s Anc2.Anc2refChr3 19430 67 + 53186 TCTGGGCCTGCACCTCTAGGTTTGCTCTTTATGCACCACTAAGGACAGTCCATTGCCATTATTTACG -s mr.mrrefChr5 2919 67 + 294540 GGAGAGCTTGTTTCTTTAGATTGACCTTTTATGCACGATTCAAGACAGTTTGCTGTCATCATTCATA -s simCow_chr6.simCow.chr6 146700 67 + 602619 TCTGGGCCTGCACCTCTAGGTTTGCTCTTTATGCACCACTAAGGACAGTCCATTGCCATTATTTACG -s simHuman_chr6.simHuman.chr6 133462 67 + 601863 TCAGAGCCTGCACCCTTGGACTTACCTTTTATGCACCATGCAAGACAGTCTATTGCCAACATTTATA -s simRat_chr6.simRat.chr6 137098 67 + 647215 GGCGAGCTCGTTTCTCTAGGTTGATCTTCTATGCACAATTCAAGAAAGTTTGCTTTCATCATTCATA - -a -s simMouse_chr6.simMouse.chr6 139309 6 + 636262 TATAAC -s Anc0.Anc0refChr1 30448 6 - 62388 TATAAC -s Anc1.Anc1refChr2 109353 6 + 144309 TATAAC -s Anc2.Anc2refChr3 19497 6 + 53186 TATGAC -s mr.mrrefChr5 2986 6 + 294540 TATAAC -s simCow_chr6.simCow.chr6 146770 6 + 602619 TATGAC -s simHuman_chr6.simHuman.chr6 133529 6 + 601863 TATAAC -s simRat_chr6.simRat.chr6 137165 6 + 647215 TACAAC - -a -s simMouse_chr6.simMouse.chr6 139315 36 + 636262 AGCTCCCCCCTACAAAGGGAAGAGGACCTTCAATCT -s Anc0.Anc0refChr1 30454 19 - 62388 AGCTCC-----ACAAAAGA-----------CAGTC- -s Anc1.Anc1refChr2 109359 36 + 144309 AGCTCCCCCTCACAAAAGAATGAGGAACTTCAGTCT -s Anc2.Anc2refChr3 19503 19 + 53186 GGCTCC-----ACTAAAGA-----------CAGTC- -s mr.mrrefChr5 2992 36 + 294540 AGCTCCCCCCCACAAAAGGAAGAGGACCTTCAATCT -s simCow_chr6.simCow.chr6 146779 19 + 602619 GGCTCC-----ACTAAAGA-----------CAGTC- -s simHuman_chr6.simHuman.chr6 133535 36 + 601863 AGCTCCCCCTCACAAAACAATGAGGAACTTGAGTGT -s simRat_chr6.simRat.chr6 137171 34 + 647215 AGCTCCCCCCCACAAAAGGAGGAGGACCTTCA--CT - -a -s simMouse_chr6.simMouse.chr6 139351 13 + 636262 AGCTGACTGCGCT -s Anc0.Anc0refChr1 30473 4 - 62388 ---------CACC -s Anc1.Anc1refChr2 109395 13 + 144309 CGCTAACTGCACC -s Anc2.Anc2refChr3 19522 4 + 53186 ---------CATT -s mr.mrrefChr5 3028 13 + 294540 AGCTGACTGCGCC -s simCow_chr6.simCow.chr6 146798 4 + 602619 ---------CATT -s simHuman_chr6.simHuman.chr6 133583 13 + 601863 CGCTAACTGCACC -s simRat_chr6.simRat.chr6 137205 13 + 647215 AGTTGACTGTGCC - -a -s simMouse_chr6.simMouse.chr6 139364 8 + 636262 ACCATCTT -s Anc0.Anc0refChr1 30477 8 - 62388 ACCATGTT -s Anc1.Anc1refChr2 109408 8 + 144309 ACCATGTT -s Anc2.Anc2refChr3 19526 8 + 53186 GCCATGAT -s mr.mrrefChr5 3041 8 + 294540 ACCATCTT -s simCow_chr6.simCow.chr6 146802 8 + 602619 GCCATGAT -s simHuman_chr6.simHuman.chr6 133597 8 + 601863 ACCACTTT -s simRat_chr6.simRat.chr6 137218 8 + 647215 ACCATCTA - -a -s simMouse_chr6.simMouse.chr6 139372 29 + 636262 TCAACATAATGTCACAATACTACCACATG -s Anc0.Anc0refChr1 30485 4 - 62388 ACCA------------------------- -s Anc1.Anc1refChr2 109416 29 + 144309 ACCACATAAGGTCACCTTATCGCATCATG -s Anc2.Anc2refChr3 19534 4 + 53186 ACAA------------------------- -s mr.mrrefChr5 3049 29 + 294540 TCAACATAATGTCACAATATTACCACATG -s simCow_chr6.simCow.chr6 146812 4 + 602619 ACAA------------------------- -s simHuman_chr6.simHuman.chr6 133605 29 + 601863 ACCACATTACAACACCTTATCGCATCATG -s simRat_chr6.simRat.chr6 137226 27 + 647215 TCAACGTCATGT--CAACATTACCACATG - -a -s simMouse_chr6.simMouse.chr6 139401 9 + 636262 GGTGGTGGG -s Anc0.Anc0refChr1 30489 3 - 62388 ------GGT -s Anc1.Anc1refChr2 109445 9 + 144309 AAGCATGGT -s Anc2.Anc2refChr3 19538 3 + 53186 ------GGT -s mr.mrrefChr5 3078 9 + 294540 GGTGGTGGG -s simCow_chr6.simCow.chr6 146816 3 + 602619 ------GGT -s simHuman_chr6.simHuman.chr6 133634 9 + 601863 AAGCATGGT -s simRat_chr6.simRat.chr6 137257 9 + 647215 GGTGGAGGG - -a -s simMouse_chr6.simMouse.chr6 139410 7 + 636262 TCCGACT -s Anc0.Anc0refChr1 30492 7 - 62388 TCTGACT -s Anc1.Anc1refChr2 109454 7 + 144309 TCTGACT -s Anc2.Anc2refChr3 19541 7 + 53186 CCTGGCT -s mr.mrrefChr5 3087 7 + 294540 TCCGACT -s simCow_chr6.simCow.chr6 146820 7 + 602619 CCTGGCT -s simHuman_chr6.simHuman.chr6 133643 7 + 601863 TCAGACT -s simRat_chr6.simRat.chr6 137266 7 + 647215 TCCAGCT - -a -s simMouse_chr6.simMouse.chr6 139417 11 + 636262 GTTATCCAATT -s Anc0.Anc0refChr1 30512 11 - 62388 GACCTCCAACT -s Anc1.Anc1refChr2 109474 11 + 144309 GACCTCCAACT -s Anc2.Anc2refChr3 19561 11 + 53186 GACCCCCAACT -s mr.mrrefChr5 3094 11 + 294540 GTTATCCAATT -s simCow_chr6.simCow.chr6 146840 11 + 602619 GACCCCCAACT -s simHuman_chr6.simHuman.chr6 133663 11 + 601863 GACCTCCAACT -s simRat_chr6.simRat.chr6 137273 11 + 647215 GTTATCCAATT - -a -s simMouse_chr6.simMouse.chr6 139428 4 + 636262 GGCC -s Anc0.Anc0refChr1 30533 4 - 62388 GTTG -s Anc1.Anc1refChr2 109495 4 + 144309 GTTG -s Anc2.Anc2refChr3 19582 4 + 53186 ATTG -s mr.mrrefChr5 3105 4 + 294540 GGCC -s simCow_chr6.simCow.chr6 146870 4 + 602619 ATTG -s simHuman_chr6.simHuman.chr6 133684 4 + 601863 GTTT -s simRat_chr6.simRat.chr6 137284 4 + 647215 GGCC - -a -s simMouse_chr6.simMouse.chr6 139432 29 + 636262 TATGACAATTGGTGCCAAGGCTAAAGCTA -s Anc0.Anc0refChr1 30537 29 - 62388 TATGACAATTGCTGGCAAGGCTGAACCTA -s Anc1.Anc1refChr2 109499 29 + 144309 TATGACAATTGCTGGCAAGGCTGAACCTA -s Anc2.Anc2refChr3 19586 29 + 53186 CACAACAATTGCCGGCAAGGCTGAACCTA -s mr.mrrefChr5 3109 29 + 294540 TATGACAATTGCTGCCAAGGCTAAAGCTA -s simCow_chr6.simCow.chr6 146877 29 + 602619 CACAACAATTGCCGGCAAGGCTGAACCTA -s simHuman_chr6.simHuman.chr6 133688 29 + 601863 TATGACAATTCCTGTCAAAGCTGAATCTA -s simRat_chr6.simRat.chr6 137288 29 + 647215 TATGGCAAACGCTACCAAGGCTACAGGTA - -a -s simMouse_chr6.simMouse.chr6 139461 11 + 636262 TTAGAAAGAGT -s Anc0.Anc0refChr1 30566 11 - 62388 TTAGAAAGAGT -s Anc1.Anc1refChr2 109528 11 + 144309 TTAGAAAGAGT -s Anc2.Anc2refChr3 19615 11 + 53186 TTGGAAAAAGT -s mr.mrrefChr5 3138 11 + 294540 TTAGAAAGAGT -s simCow_chr6.simCow.chr6 146906 11 + 602619 TTGGAAAAAGT -s simHuman_chr6.simHuman.chr6 133718 11 + 601863 TTAGAATGAGT -s simRat_chr6.simRat.chr6 137317 11 + 647215 TCTGAAAGAGT - -a -s simMouse_chr6.simMouse.chr6 139472 14 + 636262 GTTAAAATGTTGGC -s Anc0.Anc0refChr1 30581 11 - 62388 GTTGTGAGGAG--- -s Anc1.Anc1refChr2 109543 14 + 144309 GTTGTGAGGAGAGG -s Anc2.Anc2refChr3 19630 11 + 53186 GTTGTGAGAAG--- -s mr.mrrefChr5 3149 14 + 294540 GTTAAGATGTTGGC -s simCow_chr6.simCow.chr6 146925 11 + 602619 GTTGTGAGAAG--- -s simHuman_chr6.simHuman.chr6 133733 14 + 601863 ATTGTGAGGAGAGG -s simRat_chr6.simRat.chr6 137328 14 + 647215 GTTAAGATGTTGGC - -a -s simMouse_chr6.simMouse.chr6 139486 37 + 636262 CATGTGTAACCGGAATACTTAAGCGAGTAACAAGCTG -s Anc0.Anc0refChr1 30594 26 - 62388 CATGTGTATCAAGTA-----------GTAACAAGCTG -s Anc1.Anc1refChr2 109559 37 + 144309 CATGTGTATCAAGTATACGTCAGATAGTAACAAGCTG -s Anc2.Anc2refChr3 19643 26 + 53186 CATGTGTATCAGGTA-----------GTAACAAGCTG -s mr.mrrefChr5 3163 37 + 294540 CATGTGTAACCAGGATACTTAAGAGAGTAACAAGCTG -s simCow_chr6.simCow.chr6 146938 26 + 602619 CATGTGTATCAGGTA-----------GTAACAAGCTG -s simHuman_chr6.simHuman.chr6 133749 36 + 601863 TATGT-TATCAAGTATACGTCAGACAGTAACGAGGCG -s simRat_chr6.simRat.chr6 137342 37 + 647215 CATGTGGAACCAGGATACTTAAGATAATAACAAACTG - -a -s simMouse_chr6.simMouse.chr6 139523 18 + 636262 CACCAAGTCAAAACATGC -s Anc0.Anc0refChr1 30621 18 - 62388 TACAGACTCAGAACATGC -s Anc1.Anc1refChr2 109597 18 + 144309 TACAGACTCAGAACATGC -s Anc2.Anc2refChr3 19670 18 + 53186 TCCAGACACAGGACATGT -s mr.mrrefChr5 3200 18 + 294540 CACCGAGTCAAAACATGC -s simCow_chr6.simCow.chr6 146965 18 + 602619 TCCAGACACAGGACATGT -s simHuman_chr6.simHuman.chr6 133788 18 + 601863 TACAGACTCAGAACATGC -s simRat_chr6.simRat.chr6 137379 15 + 647215 CACCGAGTC---ACATGT - -a -s simMouse_chr6.simMouse.chr6 139541 24 + 636262 AGGACAATAGAGAGTCAACAAAAG -s Anc0.Anc0refChr1 30639 13 - 62388 A-----------AGTTAACAACAG -s Anc1.Anc1refChr2 109615 13 + 144309 A-----------AGTTAACAACAG -s Anc2.Anc2refChr3 19688 13 + 53186 A-----------AGTTGACAACAA -s mr.mrrefChr5 3218 23 + 294540 AGGACAAT-GAGAGTCAACAAAAG -s simCow_chr6.simCow.chr6 146994 13 + 602619 A-----------AGTTGACAACAA -s simHuman_chr6.simHuman.chr6 133806 13 + 601863 A-----------AGTTAACAATAG -s simRat_chr6.simRat.chr6 137394 23 + 647215 GGGACAAT-GAGAGTCAACAAAAG - -a -s simMouse_chr6.simMouse.chr6 139565 7 + 636262 CAAAAAT -s Anc0.Anc0refChr1 30652 3 - 62388 ----GAT -s Anc1.Anc1refChr2 109628 3 + 144309 ----GAT -s Anc2.Anc2refChr3 19701 3 + 53186 ----GGT -s mr.mrrefChr5 3241 7 + 294540 CAAAAAT -s simCow_chr6.simCow.chr6 147007 3 + 602619 ----GGT -s simHuman_chr6.simHuman.chr6 133819 3 + 601863 ----GAT -s simRat_chr6.simRat.chr6 137418 7 + 647215 CAAAAAT - -a -s simMouse_chr6.simMouse.chr6 139572 12 + 636262 TATTTTATTTAA -s Anc0.Anc0refChr1 30655 8 - 62388 TATGTAAG---- -s Anc1.Anc1refChr2 109631 8 + 144309 TATGTAAG---- -s Anc2.Anc2refChr3 19704 8 + 53186 TATGTAAG---- -s mr.mrrefChr5 3248 12 + 294540 TATGTTATTTAA -s simCow_chr6.simCow.chr6 147056 8 + 602619 TATGTAAG---- -s simHuman_chr6.simHuman.chr6 133822 8 + 601863 TATGTAAC---- -s simRat_chr6.simRat.chr6 137425 12 + 647215 TGTGTTATTTAA - -a -s simMouse_chr6.simMouse.chr6 139584 55 + 636262 AAGGTAACTTCACATATTAATGTAGAATGAAATTACAGGAACACTGGACATCTGG -s Anc0.Anc0refChr1 30663 8 - 62388 AAGATAAC----------------------------------------------- -s Anc1.Anc1refChr2 109639 8 + 144309 AAGATAAC----------------------------------------------- -s Anc2.Anc2refChr3 19712 8 + 53186 AAGATAGC----------------------------------------------- -s mr.mrrefChr5 3260 8 + 294540 AAGGTAAC----------------------------------------------- -s simCow_chr6.simCow.chr6 147065 8 + 602619 AAGATAGC----------------------------------------------- -s simHuman_chr6.simHuman.chr6 133830 8 + 601863 AAGATAAC----------------------------------------------- -s simRat_chr6.simRat.chr6 137437 8 + 647215 AAGGCAAC----------------------------------------------- - -a -s simMouse_chr6.simMouse.chr6 139639 3 + 636262 TAA -s Anc0.Anc0refChr1 30673 3 - 62388 TAA -s Anc1.Anc1refChr2 109649 3 + 144309 TAA -s Anc2.Anc2refChr3 19722 3 + 53186 TAA -s mr.mrrefChr5 3268 3 + 294540 TAA -s simCow_chr6.simCow.chr6 147075 3 + 602619 TAA -s simHuman_chr6.simHuman.chr6 133840 3 + 601863 TAA -s simRat_chr6.simRat.chr6 137445 3 + 647215 TAA - -a -s simMouse_chr6.simMouse.chr6 139642 1 + 636262 A -s Anc0.Anc0refChr1 30681 1 - 62388 A -s Anc1.Anc1refChr2 109657 1 + 144309 A -s Anc2.Anc2refChr3 19730 1 + 53186 A -s mr.mrrefChr5 3271 1 + 294540 A -s simCow_chr6.simCow.chr6 147083 1 + 602619 A -s simHuman_chr6.simHuman.chr6 133848 1 + 601863 A -s simRat_chr6.simRat.chr6 137448 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 139643 6 + 636262 GTCAAT -s Anc0.Anc0refChr1 30682 6 - 62388 GTTGAG -s Anc1.Anc1refChr2 109658 6 + 144309 GTTGAG -s Anc2.Anc2refChr3 19731 6 + 53186 GTTGGG -s mr.mrrefChr5 3272 6 + 294540 GTCAAT -s simCow_chr6.simCow.chr6 147091 6 + 602619 GTTGGG -s simHuman_chr6.simHuman.chr6 133849 6 + 601863 GTTGAG -s simRat_chr6.simRat.chr6 137449 6 + 647215 GTCAAT - -a -s simMouse_chr6.simMouse.chr6 139649 1 + 636262 C -s Anc0.Anc0refChr1 30690 1 - 62388 C -s Anc1.Anc1refChr2 109666 1 + 144309 C -s Anc2.Anc2refChr3 19739 1 + 53186 T -s mr.mrrefChr5 3280 1 + 294540 C -s simCow_chr6.simCow.chr6 147099 1 + 602619 T -s simHuman_chr6.simHuman.chr6 133857 1 + 601863 C -s simRat_chr6.simRat.chr6 137457 1 + 647215 C - -a -s simMouse_chr6.simMouse.chr6 139650 30 + 636262 ACCAAGTAACAAGCCATGTGAGCCTTAAGA -s Anc0.Anc0refChr1 30691 29 - 62388 ATTCAGTAACAAACCAC-TGAACCGTAAGA -s Anc1.Anc1refChr2 109667 29 + 144309 ATTCAGTAACAAACCAC-TGAACCGTAAGA -s Anc2.Anc2refChr3 19740 29 + 53186 ATCCAACAATACCCCAC-TTAACCGTAAGA -s mr.mrrefChr5 3281 30 + 294540 ATTAAGTAACAAACCATGTGAGCCTTAAGA -s simCow_chr6.simCow.chr6 147103 29 + 602619 ATCCAACAATACCCCAC-TTAACCGTAAGA -s simHuman_chr6.simHuman.chr6 133858 29 + 601863 ATTGAGTAACCAACCAC-TGAACTCTGAGA -s simRat_chr6.simRat.chr6 137458 30 + 647215 ATTAAGTAACAAACCATGCGAGTGTTAAGA - -a -s simMouse_chr6.simMouse.chr6 139680 14 + 636262 TCCAAAGTAGTTTC -s Anc0.Anc0refChr1 30720 14 - 62388 TGCAGAAGAAATTC -s Anc1.Anc1refChr2 109696 14 + 144309 TGCAGAAGAAATTC -s Anc2.Anc2refChr3 19769 14 + 53186 TGCAGTAGAAATTC -s mr.mrrefChr5 3311 14 + 294540 TCCAAAGTAGATTC -s simCow_chr6.simCow.chr6 147333 14 + 602619 TGCAGTAGAAATTC -s simHuman_chr6.simHuman.chr6 133887 14 + 601863 TGCACATGAAATCC -s simRat_chr6.simRat.chr6 137488 14 + 647215 TCCAAAGTAGATGC - -a -s simMouse_chr6.simMouse.chr6 139694 27 + 636262 CTGAGACTCTATAATTAGGAAATAGAG -s Anc0.Anc0refChr1 30734 27 - 62388 TTTACATTCTATAGTTAGGCAATAGAG -s Anc1.Anc1refChr2 109710 27 + 144309 TTTACATTCTATAGTTAGGCAATAGAG -s Anc2.Anc2refChr3 19783 27 + 53186 TTTACATTTTATAGTTTAGCAATAGAG -s mr.mrrefChr5 3325 27 + 294540 CTGAGACTCTATAATTAGGAAATAGAG -s simCow_chr6.simCow.chr6 147347 27 + 602619 TTTACATTTGGTAATTTAGTAATAGAG -s simDog_chr6.simDog.chr6 431518 23 - 593897 TTTACATTTTATAG----GCGATAGAG -s simHuman_chr6.simHuman.chr6 133901 27 + 601863 TTCACATTCTATAGTTAGGGAATAGAG -s simRat_chr6.simRat.chr6 137502 27 + 647215 CTGAGACTCTTTAATTAGGAAAGAGAG - -a -s simMouse_chr6.simMouse.chr6 139721 6 + 636262 TCACAG -s Anc0.Anc0refChr1 30762 6 - 62388 TCACAG -s Anc1.Anc1refChr2 109738 6 + 144309 TCACAG -s Anc2.Anc2refChr3 19811 6 + 53186 TCACAG -s mr.mrrefChr5 3353 6 + 294540 TCACAG -s simCow_chr6.simCow.chr6 147375 6 + 602619 TCACAG -s simDog_chr6.simDog.chr6 431542 6 - 593897 TAACAG -s simHuman_chr6.simHuman.chr6 133929 6 + 601863 TCACAG -s simRat_chr6.simRat.chr6 137530 6 + 647215 TCACAG - -a -s simMouse_chr6.simMouse.chr6 139727 48 + 636262 CTGTGCCCTGCTCTTTAGGCCTATGAATGTCTACCACATAGTTGCGGC -s Anc0.Anc0refChr1 30781 43 - 62388 CTACACCCTTCTCTTTAGGCTTATGAATGTT-----CACACCAGAGGC -s Anc1.Anc1refChr2 109757 47 + 144309 CTACACCCTTCTCTTTAGGCTTATGAATGTTTA-CACACACCAGAGGC -s Anc2.Anc2refChr3 19830 43 + 53186 CTACAACCATCTCTTCAGGCTTATGAATGTT-----CACACCAGAGCC -s mr.mrrefChr5 3359 48 + 294540 CTGCGCCCTGCTCTTTAGGCCTATGAATGTCTACCACATAGTTGAGGC -s simCow_chr6.simCow.chr6 147394 43 + 602619 CTACGAGCGTCTCCTCCAGCTTATGAATATT-----TAAACCAGAGTC -s simDog_chr6.simDog.chr6 431561 42 - 593897 CTACAACCATTAATTCAG-CTTATGGATGTT-----CCCACCGAGTCT -s simHuman_chr6.simHuman.chr6 133948 47 + 601863 CTACACCCTTCTCTTTAGGCTTATGAATGTTTA-CACACACCAGAGGC -s simRat_chr6.simRat.chr6 137536 47 + 647215 CTGCGCCCTACTCTTT-GGCCTATAAATGTCTACCACATAGTTGAGGC - -a -s simMouse_chr6.simMouse.chr6 139775 55 + 636262 ACAGTTGCCACAGACCCAAACATGGCCTCGGTGATGGAGTAGAAGCCACCCTGAT -s Anc0.Anc0refChr1 30828 54 - 62388 ACAGATGTCACAGACCCAAACAAGGCCTGGGTGATGGAGTGGAAGGCT-TCCAAT -s Anc1.Anc1refChr2 109808 54 + 144309 ACAGATGTCACAGACCCAAACAAGGCCTGGGTGATGGAGTGGAAGGCT-TCCAAT -s Anc2.Anc2refChr3 19877 54 + 53186 ACAGATGTCAAAGCCCACATTAAGTCTTGGGTGATGGAGTGGAAGGCT-TCCATT -s mr.mrrefChr5 3407 54 + 294540 ACAGTTGCCACAGACCCAAACATGGCCTCGGTGATGGAGTAGAAGCCA-TCTGAT -s simCow_chr6.simCow.chr6 147667 54 + 602619 AGAGATGCCAAAGTGTATCTGAAGTCCTAGGTGGTGAAGTGGAATGTT-ACTATT -s simDog_chr6.simDog.chr6 431607 54 - 593897 ACAGATGTTAAAGCCCACATTAAGGCTTGGGTGATGGCATGGAGGCCT-TCCATC -s simHuman_chr6.simHuman.chr6 133999 52 + 601863 ACAGATG--GCAGACTCAAACCAAGTCTGGGTGCTGGAGTGGAAGGAT-TCCAAT -s simRat_chr6.simRat.chr6 137583 54 + 647215 ACAGTTGCCACAGGCCTAAACATGGCCTAAGTGGTGGAGTAGAAGCCA-TCTGAT - -a -s simMouse_chr6.simMouse.chr6 139830 10 + 636262 GGCAACCCTG -s Anc0.Anc0refChr1 30882 10 - 62388 GACAACCCAG -s Anc1.Anc1refChr2 109862 10 + 144309 GACAACCCAG -s Anc2.Anc2refChr3 19931 10 + 53186 GACAACCCAG -s mr.mrrefChr5 3461 10 + 294540 GACAACCCTG -s simCow_chr6.simCow.chr6 147721 10 + 602619 GATGACCCGG -s simDog_chr6.simDog.chr6 431661 10 - 593897 AACAACCCAG -s simHuman_chr6.simHuman.chr6 134051 7 + 601863 GACTACC--- -s simRat_chr6.simRat.chr6 137690 10 + 647215 GACAACCCTG - -a -s simMouse_chr6.simMouse.chr6 139840 11 + 636262 CGTGCCTAGGT -s Anc0.Anc0refChr1 30930 11 - 62388 TGTTACCAGGA -s Anc1.Anc1refChr2 109910 11 + 144309 TGTTACCAGGA -s Anc2.Anc2refChr3 19980 11 + 53186 TATTACCAGGA -s mr.mrrefChr5 3509 11 + 294540 CGTTACTAGGT -s simCow_chr6.simCow.chr6 147770 11 + 602619 AATTATCAGGA -s simDog_chr6.simDog.chr6 431709 11 - 593897 TATTACCAGGA -s simHuman_chr6.simHuman.chr6 134096 11 + 601863 TGTTACCAGGA -s simRat_chr6.simRat.chr6 137739 11 + 647215 CGTTACTAGAT - -a -s simMouse_chr6.simMouse.chr6 139851 23 + 636262 AGTCGACAGAAAGCTGGAGACGA -s Anc0.Anc0refChr1 30941 20 - 62388 AGTGGACACCAGGCTGGAGG--- -s Anc1.Anc1refChr2 109921 23 + 144309 AGTGGACACCAGGCTGGAGGTGA -s Anc2.Anc2refChr3 19991 20 + 53186 AGTGGACACCAGTCTTTAGG--- -s mr.mrrefChr5 3520 23 + 294540 AGTCGACACAAAGCTGGAGATGA -s simCow_chr6.simCow.chr6 147781 20 + 602619 AGTGGGCAACAGTCTATAGG--- -s simDog_chr6.simDog.chr6 431721 20 - 593897 AGTGGACACCAGTCTTTAGG--- -s simHuman_chr6.simHuman.chr6 134107 23 + 601863 AGTGTACACCAGGCTGGAGGTGA -s simRat_chr6.simRat.chr6 137750 23 + 647215 AGTACACACAAAGCTGCAGATGA - -a -s simMouse_chr6.simMouse.chr6 139874 16 + 636262 AGTTTACTTCTTATCT -s Anc0.Anc0refChr1 30963 16 - 62388 AGTGTATTTCCTGTAT -s Anc1.Anc1refChr2 109946 16 + 144309 AGTGTATTTCCTGTAT -s Anc2.Anc2refChr3 20013 16 + 53186 TGTGTATTTCCTGTAT -s mr.mrrefChr5 3543 16 + 294540 AGTTTACTTCTTATCT -s simCow_chr6.simCow.chr6 147803 16 + 602619 CGTGTATTTTTTGCAT -s simDog_chr6.simDog.chr6 431743 16 - 593897 TGTGCATCCCCTATAT -s simHuman_chr6.simHuman.chr6 134132 16 + 601863 AGTGTATTTCATGTAT -s simRat_chr6.simRat.chr6 137773 16 + 647215 ACTTTACTTCTGATCT - -a -s simMouse_chr6.simMouse.chr6 139890 10 + 636262 GCATCCTCCT -s Anc0.Anc0refChr1 30982 10 - 62388 ACATCCTCTT -s Anc1.Anc1refChr2 109965 10 + 144309 ACATCCTCTT -s Anc2.Anc2refChr3 20032 10 + 53186 ACATCCTCTT -s mr.mrrefChr5 3559 10 + 294540 ACATCCTCCT -s simCow_chr6.simCow.chr6 147822 10 + 602619 ACATCCCCTT -s simDog_chr6.simDog.chr6 431762 8 - 593897 ACATTCTC-- -s simHuman_chr6.simHuman.chr6 134151 10 + 601863 ACATCCTCTT -s simRat_chr6.simRat.chr6 137789 10 + 647215 Acatcctcct - -a -s simMouse_chr6.simMouse.chr6 139900 4 + 636262 AATA -s Anc0.Anc0refChr1 30992 4 - 62388 AATT -s Anc1.Anc1refChr2 109975 4 + 144309 AATT -s Anc2.Anc2refChr3 20042 4 + 53186 AAAT -s mr.mrrefChr5 3569 4 + 294540 AATT -s simCow_chr6.simCow.chr6 147832 3 + 602619 A-GT -s simDog_chr6.simDog.chr6 431770 3 - 593897 -AAT -s simHuman_chr6.simHuman.chr6 134167 4 + 601863 AATT -s simRat_chr6.simRat.chr6 137799 4 + 647215 aatt - -a -s simMouse_chr6.simMouse.chr6 139904 14 + 636262 TGTACTGATCCAAT -s Anc0.Anc0refChr1 30996 14 - 62388 TGTACTGAgccAAT -s Anc1.Anc1refChr2 109979 14 + 144309 TGTACTGAgccAAT -s Anc2.Anc2refChr3 20047 14 + 53186 TGTACTGTGCCAAT -s mr.mrrefChr5 3573 14 + 294540 TGTACTGAtccAAT -s simCow_chr6.simCow.chr6 147836 14 + 602619 TGTACTGTGCCCAT -s simDog_chr6.simDog.chr6 431774 14 - 593897 TGTACTGTGCCAGT -s simHuman_chr6.simHuman.chr6 134171 11 + 601863 TGTACTGA---AAT -s simRat_chr6.simRat.chr6 137803 14 + 647215 tgtactgatccaat - -a -s simMouse_chr6.simMouse.chr6 139918 17 + 636262 GTTCAATATCAAATTTG -s Anc0.Anc0refChr1 31011 17 - 62388 GCTCAATATCAAATTTG -s Anc1.Anc1refChr2 109994 17 + 144309 GCTCAATATCAAATTTG -s Anc2.Anc2refChr3 20062 17 + 53186 CCTCAATATCAAATTTG -s mr.mrrefChr5 3587 17 + 294540 GCTCAATATCAAATTTG -s simCow_chr6.simCow.chr6 147851 17 + 602619 CCTCAATATCAAATCCA -s simDog_chr6.simDog.chr6 431789 17 - 593897 CCTACATATCAAATTTG -s simHuman_chr6.simHuman.chr6 134183 17 + 601863 GCTCAATAGCAAATTTG -s simRat_chr6.simRat.chr6 137817 17 + 647215 gctcaatatcaaatttg - -a -s simMouse_chr6.simMouse.chr6 139935 24 + 636262 GATATATTGATGAGAGGGGGCTGG -s Anc0.Anc0refChr1 31028 24 - 62388 GATGTAACACTGAGTGGGGGCTGG -s Anc1.Anc1refChr2 110011 24 + 144309 GATGTAACACTGAGTGGGGGCTGG -s Anc2.Anc2refChr3 20079 24 + 53186 GATGTAACACTGAGAGGGGGCTGG -s mr.mrrefChr5 3604 24 + 294540 GATATATTGATGAGTGGGGGCTGG -s simCow_chr6.simCow.chr6 147869 24 + 602619 GATGTAAAACTGAGAGGGGACTGG -s simDog_chr6.simDog.chr6 431806 24 - 593897 GATGTAACACTGAGAGGGGGGTGG -s simHuman_chr6.simHuman.chr6 134200 14 + 601863 GAT----------GTGGGGGCCGG -s simRat_chr6.simRat.chr6 137834 19 + 647215 gagTTAATGATGAGTGGGA----- - -a -s simMouse_chr6.simMouse.chr6 139959 57 + 636262 TGGCTGGCATCTCACCCTGGCATTATTCACTTGAGAAGTCACTCAAACAAAGTGGAC -s Anc0.Anc0refChr1 31052 1 - 62388 C-------------------------------------------------------- -s Anc1.Anc1refChr2 110035 1 + 144309 C-------------------------------------------------------- -s Anc2.Anc2refChr3 20103 1 + 53186 C-------------------------------------------------------- -s mr.mrrefChr5 3628 54 + 294540 TGGCTGGCATCTCACCCTGG---TATTCACTTGAGAAGTCACTCAAACAAAGTGGAC -s simCow_chr6.simCow.chr6 147913 1 + 602619 C-------------------------------------------------------- -s simDog_chr6.simDog.chr6 431830 1 - 593897 C-------------------------------------------------------- -s simHuman_chr6.simHuman.chr6 134214 1 + 601863 C-------------------------------------------------------- -s simRat_chr6.simRat.chr6 137853 53 + 647215 -GACTGGCATCCCAGGCTGG---TGCTCACTTGAGAAATCACTCAAACATAATGGAA - -a -s simMouse_chr6.simMouse.chr6 140016 31 + 636262 ACTTACACTCATGTCAGAAGTGGCTTGAACA -s Anc0.Anc0refChr1 31053 28 - 62388 -CTTACTTACATG--GGAAGTGGCTTGAGCA -s Anc1.Anc1refChr2 110036 28 + 144309 -CTTACTTACATG--GGAAGTGGCTTGAGCA -s Anc2.Anc2refChr3 20104 28 + 53186 -ATAACTTATATG--GGAAGTGGTCTGAGCA -s mr.mrrefChr5 3682 31 + 294540 ACTTACACTCATGTCAGAAGTGGCTTGAACA -s simCow_chr6.simCow.chr6 147914 19 + 602619 -ATGACTTATATG--AGATGT---------A -s simDog_chr6.simDog.chr6 431831 28 - 593897 -ATAACCTATATG--GGAAGTGGTCTGAGCA -s simHuman_chr6.simHuman.chr6 134215 28 + 601863 -CTTACTTGCATG--TAAAGTGGCTCACGCA -s simRat_chr6.simRat.chr6 137907 31 + 647215 ACTTACACTCTTATCAGAAGTGGTTAGAACA - -a -s simMouse_chr6.simMouse.chr6 140047 82 + 636262 CCAATGAACACCTTACCAGCAACAAAGTAGGGAATGTAAATATTGAGTATAAAATCTATCAAGTAGCCAGGAGGTAGTATGG -s Anc0.Anc0refChr1 31081 64 - 62388 CAATTGAAGA-CTTGCAAGGATCTGGGTAGG---------------GTATAAAATCTTTGCACTAGCCACTAGGTAGT--GT -s Anc1.Anc1refChr2 110064 81 + 144309 CAATTGAAGA-CTTGCAAGGATCTGGGTAGGAAACATATTTACTGAGTATAAAATCTTTGCACTAGCCACTAGGTAGTATGT -s Anc2.Anc2refChr3 20132 64 + 53186 CAAGTGAAGA-CTTGCAAGGATCTGGGTAGG---------------GTATAAAATCTTTGCACTAGCCACTAGGTAGT--GT -s mr.mrrefChr5 3713 82 + 294540 CCATTGAACACCTTACAAGCAACAAAGTAGGAAATGTAATTATTGAGTATAAAATCTATCAAGTAGCCAGTAGGTAGTATGG -s simCow_chr6.simCow.chr6 147933 53 + 602619 CAAGTGAAGA-CTTGCAAGG--------------------------GTATAAAATCTTTGCACTAGCCATTAGGTAGT--GT -s simDog_chr6.simDog.chr6 431860 64 - 593897 CAAGTGAAGA-TATGTAAGCATCTGGGTAGG---------------GTATAAAATCTCTGCACTAGCCACTCAGCAGT--GT -s simHuman_chr6.simHuman.chr6 134243 80 + 601863 CAATTAAAGA-CTTGCAAGGAGCTGGGTAGGAAACATATTTACTGAGTAT-GAATCTTTGTACTAGCCACTAGGTAATATGT -s simRat_chr6.simRat.chr6 137938 80 + 647215 CCATTGAACACCTTACAAGCGACAAAGTAGGAAATGTGATCATTGA--ATAAACTCTATCAAGTAGCCAATAGGTAGTATGG - -a -s simMouse_chr6.simMouse.chr6 140129 32 + 636262 CTGAAGACTGCTTAAATAGTGTCTGTCGAATG -s Anc0.Anc0refChr1 31145 15 - 62388 TGGAAGGTTGAGTAA----------------- -s Anc1.Anc1refChr2 110145 32 + 144309 TGGAAGGTTGAGTAAATAGCCAATGCCAAATG -s Anc2.Anc2refChr3 20196 15 + 53186 TGGAAGGTTGAGTGA----------------- -s mr.mrrefChr5 3795 32 + 294540 TTGAAGACTGCGTAAATAGTGTCTGTCAAATG -s simCow_chr6.simCow.chr6 147988 15 + 602619 TGGGAGCTGGAGTGA----------------- -s simDog_chr6.simDog.chr6 431924 15 - 593897 TGGAAAGTTGGGTGA----------------- -s simHuman_chr6.simHuman.chr6 134323 32 + 601863 TGGAAGGTTGAGTATATAGCCAATGCCAAATG -s simRat_chr6.simRat.chr6 138018 32 + 647215 TTGATGACTGCGTAAATAGTGCCTGTCAAATG - -a -s simMouse_chr6.simMouse.chr6 140161 56 + 636262 TACATAATTATGAGGGGCTTTAATATAATCTACAGGTTATGCTTATGATACGTTAC -s Anc0.Anc0refChr1 31244 55 - 62388 TATGTAA-TATGACAGAATTTGATATACTCTATCAGTTATGTTTAAGATACATTAC -s Anc1.Anc1refChr2 110261 55 + 144309 TATGTAA-TATGACAGAATTTGATATACTCTATCAGTTATGTTTAAGATACATTAC -s Anc2.Anc2refChr3 20298 55 + 53186 ACTGTAA-TATGACAGAATTTGATTTACTCTATCAGTTATGTTTAAGATACATTAC -s mr.mrrefChr5 3827 55 + 294540 TACATAA-TATGAGGGGCTTTAATATACTCTACAGGTTATGCTTATGATACATTAC -s simCow_chr6.simCow.chr6 148088 54 + 602619 ACTGTA--TATGACAGAATCTGATTCACTCTATCACTTATGTTTATGATACATTAT -s simDog_chr6.simDog.chr6 432025 55 - 593897 ACTGTCA-TATGACAGAATTTGATTTACTATACCAGTTATGTTTAAGATACATTAC -s simHuman_chr6.simHuman.chr6 134569 55 + 601863 TATGTAA-TATGACAGAATTTCATATACTCTGTCAATTATGTTTAAGGTACATTAA -s simRat_chr6.simRat.chr6 138050 55 + 647215 TACACAA-TATGAGGAGCTTTGATATACTCTACAGGTTATGCTTATCATAAATTAC - -a -s simMouse_chr6.simMouse.chr6 140217 57 + 636262 TTAAGACTGGTCTTCTTGCTTGAAGACCACCCTCAAATCTGCCTAATCAAAGACTGA -s Anc0.Anc0refChr1 31316 57 - 62388 TTAAGCTCACTCTCCTCCCTAGAAGAACACCCTGGAAGATGCAACATCAAAAATTCA -s Anc1.Anc1refChr2 110333 57 + 144309 TTAAGCTCACTCTCCTCCCTAGAAGAACACCCTGGAAGATGCAACATCAAAAATTCA -s Anc2.Anc2refChr3 20370 57 + 53186 TTAAGCTCACTCTCCCCCCTAGAAGAACACCCTGGAAGATGGAACATCAAAAATTCA -s mr.mrrefChr5 3882 57 + 294540 TTAAGACTGGTCTTCTTGCTTGAAGAACACCCTCAAATCTGCATAATCAAAGACTGA -s simCow_chr6.simCow.chr6 148161 51 + 602619 TTAAGCTCACTCTCTCCCCTAGAAGAGCACCCTGGTAG------CCTCAAGAGTAAA -s simDog_chr6.simDog.chr6 432097 57 - 593897 TTAGGCTCACTCTCCCCCCTAGAAGAACACCCTGGAGGATGGAACAACAAAAATTCA -s simHuman_chr6.simHuman.chr6 134641 49 + 601863 TTAAGCTCAACCTCCTCCCTAGAAGAACACCCTGGGAGATGCACCATC--------A -s simRat_chr6.simRat.chr6 138105 57 + 647215 TTAAGACTGGTCTTCTTGCTTGAAGAACACCCTCCAAACTGCAATATCAAAGACAGA - -a -s simMouse_chr6.simMouse.chr6 140274 33 + 636262 GAGATTATTATGTACGGGATCCTACAGGTGTAT -s Anc0.Anc0refChr1 31387 33 - 62388 TAGATTATTATGCATGATATCCTACAGATGCAT -s Anc1.Anc1refChr2 110404 33 + 144309 TAGATTATTATGCATGATATCCTACAGATGCAT -s Anc2.Anc2refChr3 20450 33 + 53186 TAGATTATTATGCATGATATCCTACAGACACAT -s mr.mrrefChr5 3953 33 + 294540 GAGATTATTATGTATGGTATCCTACAGATGTAT -s simCow_chr6.simCow.chr6 148233 27 + 602619 ----TTATTAAACATGCTATCTTAC--AAACAC -s simDog_chr6.simDog.chr6 432177 33 - 593897 TAGATTATTATGCATGATATTCTTTAGACACAT -s simHuman_chr6.simHuman.chr6 134704 33 + 601863 TAGATTATTATGCATGATATCCTACAGATGCAT -s simRat_chr6.simRat.chr6 138182 33 + 647215 GAGATTATTATCTATGGTATCCTACAGATGTAT - -a -s simMouse_chr6.simMouse.chr6 140307 7 + 636262 GAGTAGC -s Anc0.Anc0refChr1 31420 7 - 62388 GAGTAAC -s Anc1.Anc1refChr2 110437 7 + 144309 GAGTAAC -s Anc2.Anc2refChr3 20486 7 + 53186 GGTTACT -s mr.mrrefChr5 3986 7 + 294540 GAGTAAC -s simCow_chr6.simCow.chr6 148263 7 + 602619 TGTAACT -s simDog_chr6.simDog.chr6 432213 7 - 593897 GGTTACT -s simHuman_chr6.simHuman.chr6 134737 7 + 601863 GAGAAAC -s simRat_chr6.simRat.chr6 138215 7 + 647215 GAGCAAC - -a -s simMouse_chr6.simMouse.chr6 140314 9 + 636262 ATTGTACTA -s Anc0.Anc0refChr1 31427 8 - 62388 ATTGT-CAA -s Anc1.Anc1refChr2 110444 8 + 144309 ATTGT-CAA -s Anc2.Anc2refChr3 20493 8 + 53186 ATTGT-CAA -s mr.mrrefChr5 3993 9 + 294540 ATTGCACTA -s simCow_chr6.simCow.chr6 148270 8 + 602619 ATTGT-CTA -s simDog_chr6.simDog.chr6 432220 8 - 593897 ATTGT-CAA -s simHuman_chr6.simHuman.chr6 134745 8 + 601863 ATTGT-CAA -s simRat_chr6.simRat.chr6 138222 9 + 647215 ATTGCACTA - -a -s simMouse_chr6.simMouse.chr6 140323 11 + 636262 ATGTATGTCCG -s Anc0.Anc0refChr1 31435 10 - 62388 ATGTAT-TCCC -s Anc1.Anc1refChr2 110452 10 + 144309 ATGTAT-TCCC -s Anc2.Anc2refChr3 20501 10 + 53186 AGAAAT-TGTG -s mr.mrrefChr5 4002 10 + 294540 ATGTAT-TCCC -s simCow_chr6.simCow.chr6 148278 10 + 602619 AAATAT-CACC -s simDog_chr6.simDog.chr6 432228 10 - 593897 AGAAAT-TGTG -s simHuman_chr6.simHuman.chr6 134755 10 + 601863 ATGTGT-CCCC -s simRat_chr6.simRat.chr6 138231 10 + 647215 ATGTAT-TCCC - -a -s simMouse_chr6.simMouse.chr6 140334 20 + 636262 TTGTAGCTTTTGGTAAAGGG -s Anc0.Anc0refChr1 31445 20 - 62388 TTGAGGCTTGTGGTCAAGGA -s Anc1.Anc1refChr2 110462 20 + 144309 TTGAGGCTTGTGGTCAAGGA -s Anc2.Anc2refChr3 20512 20 + 53186 TTGAGCCTCGTGGTCAAGAA -s mr.mrrefChr5 4012 20 + 294540 TTGAAGCTTTTGGTCAAGGA -s simCow_chr6.simCow.chr6 148289 14 + 602619 TTGAAACTCATGCT------ -s simDog_chr6.simDog.chr6 432239 20 - 593897 TTGAGCCTCGTGGTCAAGAA -s simHuman_chr6.simHuman.chr6 134765 20 + 601863 TTGAGGCTTGTGGACAAGGA -s simRat_chr6.simRat.chr6 138241 20 + 647215 TTGAAGCCTTTGGTCAAGGA - -a -s simMouse_chr6.simMouse.chr6 140354 12 + 636262 CCAGAAATTTTT -s Anc0.Anc0refChr1 31465 12 - 62388 CCGGAAATTTTT -s Anc1.Anc1refChr2 110482 12 + 144309 CCGGAAATTTTT -s Anc2.Anc2refChr3 20532 12 + 53186 CTGGAAATGCTT -s mr.mrrefChr5 4032 12 + 294540 CCAGAAATTTTT -s simCow_chr6.simCow.chr6 18856 12 + 602619 CTAGAAATGCTT -s simDog_chr6.simDog.chr6 432259 12 - 593897 CTGGAGATGCTT -s simHuman_chr6.simHuman.chr6 134785 12 + 601863 CCGCCAATTTTT -s simRat_chr6.simRat.chr6 138261 12 + 647215 CCAGAAATTTTT - -a -s simMouse_chr6.simMouse.chr6 140366 22 + 636262 TTGCCTGTGAACACACTTAGGC -s Anc0.Anc0refChr1 31487 22 - 62388 ATTCCTGTGCGAACACTTAGGC -s Anc1.Anc1refChr2 110504 22 + 144309 ATTCCTGTGCGAACACTTAGGC -s Anc2.Anc2refChr3 20554 22 + 53186 ATTCCTGTGCGAACACTTAGGC -s mr.mrrefChr5 4044 22 + 294540 TTGCCTGTGAGCACACTTAGGC -s simCow_chr6.simCow.chr6 18878 22 + 602619 CTTTCTGTGTGAACACTTAGGC -s simDog_chr6.simDog.chr6 432281 22 - 593897 ACTCCTGTGCAAACACTTTGGC -s simHuman_chr6.simHuman.chr6 134807 22 + 601863 ATTCCTGTGCGAGCACTTAGGC -s simRat_chr6.simRat.chr6 138273 22 + 647215 TTGGCTATGAGGACACTTAGGC - -a -s simMouse_chr6.simMouse.chr6 140388 63 + 636262 AACCGAATGCATTTAGGCTACAAGCAATTGGCATTTAGGCTACAAGCAATTGGCATAAGATTG -s Anc0.Anc0refChr1 31519 32 - 62388 AACTGCA---------------------------TT----TATAAGAAATAGGTGTAAGATTG -s Anc1.Anc1refChr2 110536 36 + 144309 AACTGCA---------------------------TTAGGTTATAAGAAATAGGTGTAAGATTG -s Anc2.Anc2refChr3 20586 32 + 53186 AACTTCA---------------------------TT----TATAAGAAATAGGTGTAAGATTG -s mr.mrrefChr5 4066 36 + 294540 AACCGAA---------------------------TTAGGTTACAAGCAATTGGCATAAGATTG -s simCow_chr6.simCow.chr6 18910 32 + 602619 AACTTCC---------------------------TA----TATAAGTACTAGGTGTAAGATAG -s simDog_chr6.simDog.chr6 432313 32 - 593897 AACTTCA---------------------------TT----TATAAGATATAGGTGTCAGATTG -s simHuman_chr6.simHuman.chr6 134839 36 + 601863 AACTGCA---------------------------TTAGGTTATAAGAAATAGGTGTAAGATTG -s simRat_chr6.simRat.chr6 138295 36 + 647215 AACAGAG---------------------------TTGGGTTACAGACAAATGGCATAAGATTG - -a -s simMouse_chr6.simMouse.chr6 140451 2 + 636262 GT -s Anc0.Anc0refChr1 31553 2 - 62388 GT -s Anc1.Anc1refChr2 110574 2 + 144309 GT -s Anc2.Anc2refChr3 20620 2 + 53186 GT -s mr.mrrefChr5 4102 2 + 294540 GT -s simCow_chr6.simCow.chr6 18944 2 + 602619 GT -s simDog_chr6.simDog.chr6 432347 2 - 593897 GT -s simHuman_chr6.simHuman.chr6 134877 2 + 601863 GT -s simRat_chr6.simRat.chr6 138331 2 + 647215 AT - -a -s simMouse_chr6.simMouse.chr6 140453 30 + 636262 CAGAGGCCGTTACTAGGATCCCTAGGCAGA -s Anc0.Anc0refChr1 31555 26 - 62388 CAGAGGCCGTTATTGGGATCCCTATG---- -s Anc1.Anc1refChr2 110576 30 + 144309 CAGAGGCCGTTATTGGGATCCCTATGCCAA -s Anc2.Anc2refChr3 20623 26 + 53186 CAGAGGCCATTATTGGGATCCCTATG---- -s mr.mrrefChr5 4104 30 + 294540 CAGAGGCCGTTACTAGGATCCCTAGGCAAA -s simCow_chr6.simCow.chr6 18947 24 + 602619 CTGAGACCATGATTGGGATCCTTG------ -s simDog_chr6.simDog.chr6 432350 26 - 593897 CAGAGGCCAATATTGGAATCCCCATG---- -s simHuman_chr6.simHuman.chr6 134879 30 + 601863 TGGAGGCTGTTATTGGGATCCATATGCCAA -s simRat_chr6.simRat.chr6 138333 30 + 647215 CAGAGGCCATTCCTAGGATACCTAAGCAAA - -a -s simMouse_chr6.simMouse.chr6 140483 18 + 636262 TGCTGGAGCTCACCATAG -s Anc0.Anc0refChr1 31581 17 - 62388 TGC-GGAGCTTAGCATAA -s Anc1.Anc1refChr2 110606 18 + 144309 TGCAGGAGCTTAGCATAA -s Anc2.Anc2refChr3 20649 17 + 53186 TGC-GGAGCTTAGCATAA -s mr.mrrefChr5 4134 18 + 294540 TGCTGGAGCTCACCATAG -s simCow_chr6.simCow.chr6 18971 17 + 602619 TGC-TGAACTTATCATAG -s simDog_chr6.simDog.chr6 432382 17 - 593897 TGC-GGAGCTTAGCATAA -s simHuman_chr6.simHuman.chr6 134909 6 + 601863 TGTAAG------------ -s simRat_chr6.simRat.chr6 138363 18 + 647215 TGCTGGAGCTTATGATAG - -a -s simMouse_chr6.simMouse.chr6 140501 1 + 636262 A -s Anc0.Anc0refChr1 31598 1 - 62388 A -s Anc1.Anc1refChr2 110624 1 + 144309 A -s Anc2.Anc2refChr3 20667 1 + 53186 A -s mr.mrrefChr5 4152 1 + 294540 A -s simCow_chr6.simCow.chr6 18989 1 + 602619 A -s simDog_chr6.simDog.chr6 432400 1 - 593897 A -s simRat_chr6.simRat.chr6 138381 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 140502 30 + 636262 CATCTGTTCACAGGAATGTGATGGTGGTAC -s Anc0.Anc0refChr1 31599 28 - 62388 TATTATTA--CAGGTAAGTAGTGCTGGTAC -s Anc1.Anc1refChr2 110625 28 + 144309 TATTATTA--CAGGTAAGTAGTGCTGGTAC -s Anc2.Anc2refChr3 20668 28 + 53186 TATTATTA--CAGGTAAGAAGTGCTGGTAC -s mr.mrrefChr5 4153 28 + 294540 CATCTGTT--CAGGAATGTGATGGTGGTAC -s simCow_chr6.simCow.chr6 18991 28 + 602619 TTTTATTT--AAGGTAAGAAGTGTTGGTAC -s simDog_chr6.simDog.chr6 432401 28 - 593897 TATTATTA--CAGGACAGAAGTCCTGATAC -s simHuman_chr6.simHuman.chr6 134915 19 + 601863 -----------AGTTAAGTAGTGATGGTAC -s simRat_chr6.simRat.chr6 138382 28 + 647215 TATCTGTC--CAGGAATGTGATGGTAGTAC - -a -s simMouse_chr6.simMouse.chr6 140532 31 + 636262 CAACTAACACTTCGGTGGCTGAATGATTTAG -s Anc0.Anc0refChr1 31627 31 - 62388 CCATTGATACATGAATGACCAAATGACTTAG -s Anc1.Anc1refChr2 110653 31 + 144309 CCATTGATACATGAATGACCAAATGACTTAG -s Anc2.Anc2refChr3 20696 31 + 53186 CCATTGATGCATGAATGATCAAATGACTTAG -s mr.mrrefChr5 4181 31 + 294540 CAATTAACACTTCGATGGCTGAATGATTTAG -s simCow_chr6.simCow.chr6 19019 26 + 602619 CCATTGGCGCATCAATGATCAAATGC----- -s simDog_chr6.simDog.chr6 432430 31 - 593897 CCATTGATGCATGAATGATGAGATGACTTAG -s simHuman_chr6.simHuman.chr6 134934 31 + 601863 CCATTTATACAGGAATCACCTAATGACTCAG -s simRat_chr6.simRat.chr6 138410 31 + 647215 CAATTAACACTTAGATGGCTGAATGATTTAG - -a -s simMouse_chr6.simMouse.chr6 140563 18 + 636262 GCTGAGCTCACTATTGCA -s Anc0.Anc0refChr1 31658 18 - 62388 GCTGGATTCATCATTGCA -s Anc1.Anc1refChr2 110684 18 + 144309 GCTGGATTCATCATTGCA -s Anc2.Anc2refChr3 20727 18 + 53186 GCTGGATTCATCACTGCA -s mr.mrrefChr5 4212 18 + 294540 GCTGGGCTCATTATTGCA -s simCow_chr6.simCow.chr6 148303 18 + 602619 GCTGGATTCTTCACTGCA -s simDog_chr6.simDog.chr6 432461 18 - 593897 GCTGGATTCATTACTGCT -s simHuman_chr6.simHuman.chr6 134965 18 + 601863 CACGGATTCCTCCTCACA -s simRat_chr6.simRat.chr6 138441 18 + 647215 GCTGGGCTCATTATTGCA - -a -s simMouse_chr6.simMouse.chr6 140581 22 + 636262 ACTGAATGACAATCTTATATTT -s Anc0.Anc0refChr1 31678 22 - 62388 ACAGAATGATAACCTTGTGTTT -s Anc1.Anc1refChr2 110704 22 + 144309 ACAGAATGATAACCTTGTGTTT -s Anc2.Anc2refChr3 20747 22 + 53186 ACAGAATGATCACCTTGTGTTT -s mr.mrrefChr5 4230 22 + 294540 ACTGAATGACAATCTTATATTT -s simCow_chr6.simCow.chr6 148323 22 + 602619 ACAGAATGGTCACCTTGTAGTC -s simDog_chr6.simDog.chr6 432481 22 - 593897 ACAGAAAGATCACCTTGTGTCT -s simHuman_chr6.simHuman.chr6 134985 21 + 601863 ACAGGATAATAG-CGTGCGTTT -s simRat_chr6.simRat.chr6 138459 22 + 647215 GCTAAATGACAATCTTATATTT - -a -s simMouse_chr6.simMouse.chr6 140603 74 + 636262 GGTCTGTTGCTAGACTTAGCTATAAAAATGATACAGCTGTCACAAAGAAGAATGGTTAAAGATGGAATTTTGTC -s Anc0.Anc0refChr1 31700 56 - 62388 AGGATGGAACTAGTCTTAACTGTA-----------------ACAA-GAAGGGTGGCTGAAGATGAAATTTTGTT -s Anc1.Anc1refChr2 110726 57 + 144309 AGGATGGAACTAGTCTTAACTGTA-----------------ACAAAGAAGGGTGGCTGAAGATGAAATTTTGTT -s Anc2.Anc2refChr3 20769 56 + 53186 AGGATGGAACTAGTCTTAACTGTA-----------------ACAA-GAAGGGTGGCAGAAGATGAAATTTTGTT -s mr.mrrefChr5 4252 74 + 294540 GGTCTGTAGCTAGACTTAGCTATAAAAATGATACAGCTGTCACAAAGAAGAATGGTTAAAGATGGAATTTTGTC -s simCow_chr6.simCow.chr6 148345 56 + 602619 AGAATAGAACTATTCCCATTGATG-----------------ACAA-GAACGGAGCCAAAAGATGAAATTTTGCT -s simDog_chr6.simDog.chr6 432503 56 - 593897 GGGATGGAACTAGTCTTAACTGTA-----------------ACAA-GAAGGGTAGTAGAAGATGAAATTTTGTG -s simHuman_chr6.simHuman.chr6 135006 57 + 601863 AGGATCGAACTAGTCTTAACCGCA-----------------ACAAAGAAAGGTGGCTGAGGATGAAAGTTTGTT -s simRat_chr6.simRat.chr6 138485 74 + 647215 GGCCTGTAGCTAGACTTAGCTATAATAATGATATAGCTATCACAAAGAAGAATGGTTAAAGATGGAATTTTGTC - -a -s simMouse_chr6.simMouse.chr6 140677 105 + 636262 ATTGGCCAAGGTGGTCACATAACAAAGAGTGAGTAAGTTAAATTAAACATGATGTAGGAACAACTTGCCATTTGAGCAAAGACATGCATAGTTAAAGGAGACTGA -s Anc0.Anc0refChr1 31777 101 - 62388 TGGGGCCAAGGGGGTCACATAACAAAAAGTGGGTAAGTCAGATGACACATGATGGAGG--CTACATAACACTTGAGCAGAGA--TCCATAGTTACATGAAACTGC -s Anc1.Anc1refChr2 110804 105 + 144309 TGGGGCCAAGGGGGTCACATAACAAAAAGTGGGTAAGTCAGATGACACATGATGGAGGAGCTACATAACACTTGAGCAGAGACATCCATAGTTACATGAAACTGC -s Anc2.Anc2refChr3 20846 101 + 53186 CAGGGCTAAGTGGGTCATGCGAAAGAGAGTGGGTGAGTCAGATGACACATGATGGAGG--CTACATTACACTTGAGCAGAGA--TCCATAGTCACATGAAACTGC -s mr.mrrefChr5 4326 105 + 294540 TGTGGCCAAGGTGGTCACATAACAAAAAGTGAGTAAGTCAGATTAAACATGATGTAGGAACTACATACCATTTGAGCAAAGACATGCATAGTTACAGGAGACTGA -s simCow_chr6.simCow.chr6 148422 96 + 602619 CAGAGCTAAGCGGGTCA-----AAGAGGGTAGATGAGTCAGATGACAGGTGTTGTGAG--CTACATGACACATGGACAGAGA--CCCATAGTCTCGAGAACTTTC -s simDog_chr6.simDog.chr6 432580 97 - 593897 CAGGGCTAAGTGCGTCATGCGAAAGAGAGAGAGTGAG---GATGGCACATAATCGAGG--CTAGGTTAC-CTTGAGCAGAGA--TCCATAGCCACATGAAACTGC -s simHuman_chr6.simHuman.chr6 135084 105 + 601863 TGGGGCCAAGGAGGTCACATAACAAAAAGTGGGTAAGTCGGATGACACATGATGCAGGAGCTACATAACACTTGAGCAGGGACATTCATAGTTACATGAAACTGT -s simRat_chr6.simRat.chr6 138559 104 + 647215 TGAAGCCAAAGT-GTCACATAACAAAAATTGAGTAAGTCAGATTAAACATGATGTAGGTACTACAGACCATTTGAGCAAAGACATGCATGGTTACAGGAGACTGA - -a -s simMouse_chr6.simMouse.chr6 140782 2 + 636262 AT -s Anc0.Anc0refChr1 31879 2 - 62388 AT -s Anc1.Anc1refChr2 110910 2 + 144309 AT -s Anc2.Anc2refChr3 20948 2 + 53186 AT -s mr.mrrefChr5 4432 2 + 294540 AT -s simDog_chr6.simDog.chr6 432678 2 - 593897 AT -s simHuman_chr6.simHuman.chr6 135190 2 + 601863 AT -s simRat_chr6.simRat.chr6 138664 2 + 647215 AT - -a -s simMouse_chr6.simMouse.chr6 140784 112 + 636262 ATCCCTGTGTGTGTGGACAGTACCTGCACCTGGTGTGTATGGTTCTGAAGGCATAAAGTCGGGATTTTGACCCTCCACACAAAGTACTGTGTTTTTGGCCACGAAACTGTCA -s Anc0.Anc0refChr1 31881 41 - 62388 A------------------------------GATGTGTATAATGATGA-------------------------------------ACTGCGTCTTAGACCAAGCAGCT---- -s Anc1.Anc1refChr2 110912 41 + 144309 A------------------------------GATGTGTATAATGATGA-------------------------------------ACTGCGTCTTAGACCAAGCAGCT---- -s Anc2.Anc2refChr3 20950 41 + 53186 A------------------------------TATGTGTATAATGATGA-------------------------------------ACTGCATCTTAGACCAAGCAGCT---- -s mr.mrrefChr5 4434 107 + 294540 ATCCCTGTGTGTGTGGACAGTACCTACACCTGGTGTGTATGGTTCTGAAGGCATAGAGTCGGGATTTTG-----CCACACAAAGTACTGTGTTTTTGGCCACGAAACTGTCA -s simCow_chr6.simCow.chr6 148518 41 + 602619 A------------------------------TATGTGTATAATGATAA-------------------------------------ACGGCATCTTAGACCAAGAAGCT---- -s simDog_chr6.simDog.chr6 432694 41 - 593897 A------------------------------TATGTGCATAATGACGA-------------------------------------ACTGCACCTTAGACCAAGCAGCT---- -s simHuman_chr6.simHuman.chr6 135192 37 + 601863 A------------------------------GTTGTGTACAATGATGA-------------------------------------ACTACGTCTTAGACCAAGG-------- -s simRat_chr6.simRat.chr6 138666 99 + 647215 ATACCTGTGTGTCTGGACGGTACCTACCCCTGGTGTCTATGGTTCTGGTATCATGGAGCCAG-------------CACACCAGGTACTGTGCTCTTGACCACAAAGCTGTCA - -a -s simMouse_chr6.simMouse.chr6 140896 16 + 636262 TTTGCCAAATCCCACC -s Anc0.Anc0refChr1 31922 16 - 62388 TTTGCAAAGTCCTAAT -s Anc1.Anc1refChr2 110953 16 + 144309 TTTGCAAAGTCCTAAT -s Anc2.Anc2refChr3 20991 16 + 53186 TTTGCAAAGTCCTAAT -s mr.mrrefChr5 4541 16 + 294540 TTTGCTAAATCCCACC -s simCow_chr6.simCow.chr6 148563 16 + 602619 TTTGCAAAGCCCTAAT -s simDog_chr6.simDog.chr6 432735 16 - 593897 TTTGCCAAATCCTAAT -s simHuman_chr6.simHuman.chr6 135229 14 + 601863 --TGCAGAGTCCTAAT -s simRat_chr6.simRat.chr6 138765 16 + 647215 TTTGCTAAGTCCCACC - -a -s simMouse_chr6.simMouse.chr6 140912 13 + 636262 TGGCAACAAAGTT -s Anc0.Anc0refChr1 31939 13 - 62388 TTGCAACAGAGTT -s Anc1.Anc1refChr2 110970 13 + 144309 TTGCAACAGAGTT -s Anc2.Anc2refChr3 21014 13 + 53186 TTGCAACAGAGTT -s mr.mrrefChr5 4557 13 + 294540 TGGCAACAAAGTT -s simCow_chr6.simCow.chr6 148586 12 + 602619 TTGCAACAGAGT- -s simDog_chr6.simDog.chr6 432758 13 - 593897 TTGCAACAGAGCT -s simHuman_chr6.simHuman.chr6 135244 13 + 601863 TTGCAACATAGTT -s simRat_chr6.simRat.chr6 138781 13 + 647215 TGGCAACAAAGTT - -a -s simMouse_chr6.simMouse.chr6 140925 8 + 636262 TTTCCCTC -s Anc0.Anc0refChr1 31958 8 - 62388 TTGTGCAC -s Anc1.Anc1refChr2 110989 8 + 144309 TTGTGCAC -s Anc2.Anc2refChr3 21033 8 + 53186 TTGTGCAC -s mr.mrrefChr5 4570 8 + 294540 TTTCCCTC -s simCow_chr6.simCow.chr6 148601 8 + 602619 TTGTGTAC -s simDog_chr6.simDog.chr6 432777 8 - 593897 TTGTGCAC -s simHuman_chr6.simHuman.chr6 135263 8 + 601863 TTGTGCAC -s simRat_chr6.simRat.chr6 138794 8 + 647215 TTTCCCTC - -a -s simMouse_chr6.simMouse.chr6 140933 5 + 636262 CTGCA -s Anc0.Anc0refChr1 31968 5 - 62388 CTACA -s Anc1.Anc1refChr2 110999 5 + 144309 CTACA -s Anc2.Anc2refChr3 21043 5 + 53186 CTACA -s mr.mrrefChr5 4580 5 + 294540 CTGCA -s simCow_chr6.simCow.chr6 148611 5 + 602619 CTACA -s simDog_chr6.simDog.chr6 432787 5 - 593897 CTACG -s simHuman_chr6.simHuman.chr6 135273 5 + 601863 CTAAA -s simRat_chr6.simRat.chr6 138804 5 + 647215 ATGGA - -a -s simMouse_chr6.simMouse.chr6 140938 31 + 636262 CACCTTATAGCTGAAAAATCGCTCCATATAT -s Anc0.Anc0refChr1 31991 30 - 62388 GACATTACAGCTGAGGAATCATTTTACA-AT -s Anc1.Anc1refChr2 111022 30 + 144309 GACATTACAGCTGAGGAATCATTTTACA-AT -s Anc2.Anc2refChr3 21066 30 + 53186 GGCATCACGGTTGAGGAATCATTTCACA-TT -s mr.mrrefChr5 4585 31 + 294540 CACCTTATAGCTGAAAAATCGTTCTACATAT -s simCow_chr6.simCow.chr6 148634 30 + 602619 GGCATCTCGGAGAAGGAATCATTTCACA-TT -s simDog_chr6.simDog.chr6 432810 30 - 593897 GGCATCATGGTTGAGGAGTCATTGCATA-TG -s simHuman_chr6.simHuman.chr6 135296 30 + 601863 TACACTGCAGCTGAGGAATCCTTTTACA-AT -s simRat_chr6.simRat.chr6 138809 31 + 647215 CACCTTATAGCTGAAAAATCATTCTACATAT - -a -s simMouse_chr6.simMouse.chr6 140969 2 + 636262 CA -s Anc0.Anc0refChr1 32021 2 - 62388 CA -s Anc1.Anc1refChr2 111052 2 + 144309 CA -s Anc2.Anc2refChr3 21096 2 + 53186 CA -s mr.mrrefChr5 4616 2 + 294540 CA -s simCow_chr6.simCow.chr6 148665 2 + 602619 CA -s simDog_chr6.simDog.chr6 432840 2 - 593897 CA -s simHuman_chr6.simHuman.chr6 135326 2 + 601863 CA -s simRat_chr6.simRat.chr6 138840 2 + 647215 CA - -a -s simMouse_chr6.simMouse.chr6 140971 10 + 636262 GCAGTTTTAG -s Anc0.Anc0refChr1 32023 10 - 62388 GTAGTTTCAG -s Anc1.Anc1refChr2 111054 10 + 144309 GTAGTTTCAG -s Anc2.Anc2refChr3 21098 10 + 53186 GTAGTTTCCA -s mr.mrrefChr5 4618 10 + 294540 GTAGTTTCAG -s simCow_chr6.simCow.chr6 148667 10 + 602619 GTAGTTTCCA -s simDog_chr6.simDog.chr6 432843 7 - 593897 GTAGTTT--- -s simHuman_chr6.simHuman.chr6 135328 10 + 601863 GTAGTTTCAG -s simRat_chr6.simRat.chr6 138842 10 + 647215 GTAGTTTCAG - -a -s simMouse_chr6.simMouse.chr6 140981 25 + 636262 CTGTTAAGTAATTACTGTACCAACA -s Anc0.Anc0refChr1 32040 25 - 62388 CTGTGAAGTACTTACTGTACCAACC -s Anc1.Anc1refChr2 111071 25 + 144309 CTGTGAAGTACTTACTGTACCAACC -s Anc2.Anc2refChr3 21115 25 + 53186 CTGTGAAGTGCTTACTGTACCAACC -s mr.mrrefChr5 4635 25 + 294540 CTGTGAAGTAATTACTGTACCAACA -s simCow_chr6.simCow.chr6 148684 25 + 602619 TTATTAAGTGCTTACTGAACCAAAC -s simDog_chr6.simDog.chr6 432853 25 - 593897 CTGTGAAGTGTTTACTGTATCCACC -s simHuman_chr6.simHuman.chr6 135345 25 + 601863 CTGTGAAGTACTTACTGTACCAATG -s simRat_chr6.simRat.chr6 138859 25 + 647215 CTATGGAGTGATTACTTTAACAACT - -a -s simMouse_chr6.simMouse.chr6 141006 11 + 636262 GGGAAGTAAAG -s Anc0.Anc0refChr1 32067 11 - 62388 GAAGTACATGG -s Anc1.Anc1refChr2 111098 11 + 144309 GAAGTACATGG -s Anc2.Anc2refChr3 21142 11 + 53186 GAAGTACATGG -s mr.mrrefChr5 4662 11 + 294540 GGGAAGCAAAG -s simCow_chr6.simCow.chr6 148711 11 + 602619 GGAGCACATGG -s simDog_chr6.simDog.chr6 432880 11 - 593897 GAAGTACATGG -s simHuman_chr6.simHuman.chr6 135372 11 + 601863 GAAGTACATTG -s simRat_chr6.simRat.chr6 138886 11 + 647215 GGGAAGCAAAG - -a -s simMouse_chr6.simMouse.chr6 141017 30 + 636262 TGTGTTCAAAATGTCTCCCTCTAACAGGGG -s Anc0.Anc0refChr1 32081 30 - 62388 TGTATTTACAATGTATTCCTCTGACGGGGG -s Anc1.Anc1refChr2 111112 30 + 144309 TGTATTTACAATGTATTCCTCTGACGGGGG -s Anc2.Anc2refChr3 21156 30 + 53186 TGTATTTACAATGTATTCCCCTGACGGTGG -s mr.mrrefChr5 4676 30 + 294540 TGTATTCAAAATGTCTTCCTCTAACAGGGG -s simCow_chr6.simCow.chr6 148725 30 + 602619 TGTATTCACAATGTACTCCCCTGACAGTGG -s simDog_chr6.simDog.chr6 432894 27 - 593897 TGTATTTATGACATATCCCCCTAAGGG--- -s simHuman_chr6.simHuman.chr6 135386 30 + 601863 CATATTTACAATGTGTTCCTCTGACGGGGG -s simRat_chr6.simRat.chr6 138983 30 + 647215 TGTATTCAAAATGTCCTGATCAAACAGGGG - -a -s simMouse_chr6.simMouse.chr6 141047 1 + 636262 C -s Anc0.Anc0refChr1 32111 1 - 62388 C -s Anc1.Anc1refChr2 111142 1 + 144309 C -s Anc2.Anc2refChr3 21186 1 + 53186 C -s mr.mrrefChr5 4706 1 + 294540 C -s simCow_chr6.simCow.chr6 148755 1 + 602619 C -s simHuman_chr6.simHuman.chr6 135420 1 + 601863 C -s simRat_chr6.simRat.chr6 139013 1 + 647215 C - -a -s simMouse_chr6.simMouse.chr6 141048 29 + 636262 AATGGTGCTTTAGTACTATTAGATCATTA -s Anc0.Anc0refChr1 32112 29 - 62388 AAATGTGTTTTTGTGTTAATAGATCATTA -s Anc1.Anc1refChr2 111143 29 + 144309 AAATGTGTTTTTGTGTTAATAGATCATTA -s Anc2.Anc2refChr3 21188 29 + 53186 AAATGTGTTTTTGTGTAAATAGACCATTA -s mr.mrrefChr5 4707 29 + 294540 AATGGTGCTTTTGTATTATTAGATCATTA -s simCow_chr6.simCow.chr6 148756 29 + 602619 AAATATCTTTATGTGTGAGTAGACCATTA -s simDog_chr6.simDog.chr6 432922 29 - 593897 AAATGTGTTTTTGTATAAATAGACCCATA -s simHuman_chr6.simHuman.chr6 135421 29 + 601863 AAACCTGTTTTTGTGTTAATCGTTCATTA -s simRat_chr6.simRat.chr6 139014 29 + 647215 AATGGTGCTTTTGCATTACTAAGTCATTA - -a -s simMouse_chr6.simMouse.chr6 141077 43 + 636262 TAGCCAATATCTTACACATATATTTGATTTGATGTGCTTGCAT -s Anc0.Anc0refChr1 32141 36 - 62388 TACTCTATACCTTACATGTATGTTTGAT-----GC--TTTCTT -s Anc1.Anc1refChr2 111172 36 + 144309 TACTCTATACCTTACATGTATGTTTGAT-----GC--TTTCTT -s Anc2.Anc2refChr3 21217 36 + 53186 TACTCTATACCTTACCTGTATGTTTGAT-----GC--TTTCTT -s mr.mrrefChr5 4736 38 + 294540 TAGTCAATATCTTACACATATATTTGAT-----GCGCTTTCAT -s simCow_chr6.simCow.chr6 148785 36 + 602619 CACTCTTTATCTTACCTGTATGTTTGAT-----GC--TCTCTT -s simDog_chr6.simDog.chr6 432951 36 - 593897 TGCTCGATACCTTACCTGTAGGTTTGAT-----GT--CTTCTT -s simHuman_chr6.simHuman.chr6 135451 36 + 601863 TATTCTATAGCTTACATGTATGTTTGAT-----GC--TGTCTT -s simRat_chr6.simRat.chr6 139043 38 + 647215 GAGTTGATATCTTACACATATATTTGAT-----GCACTTTCAT - -a -s simMouse_chr6.simMouse.chr6 141120 8 + 636262 ACATGGCT -s Anc0.Anc0refChr1 32177 8 - 62388 GCAAGGCT -s Anc1.Anc1refChr2 111208 8 + 144309 GCAAGGCT -s Anc2.Anc2refChr3 21255 8 + 53186 GCAAGGTT -s mr.mrrefChr5 4774 8 + 294540 ACATGACT -s simCow_chr6.simCow.chr6 148823 8 + 602619 ACAAGATT -s simDog_chr6.simDog.chr6 432991 8 - 593897 GCAATGTT -s simHuman_chr6.simHuman.chr6 135487 7 + 601863 GCCAGCC- -s simRat_chr6.simRat.chr6 139081 8 + 647215 GTATGACT - -a -s simMouse_chr6.simMouse.chr6 141128 22 + 636262 CAGTTTGTGGTCATGATGCACA -s Anc0.Anc0refChr1 32185 21 - 62388 GGTGTAGTGGTA-TAGTGCACA -s Anc1.Anc1refChr2 111216 21 + 144309 GGTGTAGTGGTA-TAGTGCACA -s Anc2.Anc2refChr3 21263 21 + 53186 GGTGTAGTGGTA-TAGTGCCCA -s mr.mrrefChr5 4782 22 + 294540 CAGTTTGTGGTAATGATGCACA -s simCow_chr6.simCow.chr6 148831 21 + 602619 GGCGTAGTGGTA-TGGTGCCCA -s simDog_chr6.simDog.chr6 432999 21 - 593897 GGTGTGGTGGTA-TAGTACCCA -s simHuman_chr6.simHuman.chr6 465483 21 - 601863 GGTGGAGTGGTA-CAGTGCACA -s simRat_chr6.simRat.chr6 139089 22 + 647215 TAGCTTGTGGTAATGATACACA - -a -s simMouse_chr6.simMouse.chr6 141150 27 + 636262 AATCAACAGATAATTGAGTACAAGCCT -s Anc0.Anc0refChr1 32206 27 - 62388 CATCTACAGACAATTAGGTACAGGTCT -s Anc1.Anc1refChr2 111237 27 + 144309 CATCTACAGACAATTAGGTACAGGTCT -s Anc2.Anc2refChr3 21284 27 + 53186 CATCTACACAAAATTAGGTACAGGTCT -s mr.mrrefChr5 4804 27 + 294540 AATCAACAGACAATTGAGTACAGGCCT -s simCow_chr6.simCow.chr6 148853 27 + 602619 CATCTACACAACATCAGGTACAGGTCT -s simDog_chr6.simDog.chr6 433020 27 - 593897 CGTCTACACAAAATTAGGTACAGGTCT -s simHuman_chr6.simHuman.chr6 465504 27 - 601863 CATCTACAGACAATTAGGTACAGGTCT -s simRat_chr6.simRat.chr6 139111 27 + 647215 AATCCACAGACAATTGAGTGCAGGCCT - -a -s simMouse_chr6.simMouse.chr6 141177 1 + 636262 T -s Anc0.Anc0refChr1 32234 1 - 62388 G -s Anc1.Anc1refChr2 111265 1 + 144309 G -s Anc2.Anc2refChr3 21312 1 + 53186 G -s mr.mrrefChr5 4831 1 + 294540 T -s simCow_chr6.simCow.chr6 148881 1 + 602619 G -s simDog_chr6.simDog.chr6 433048 1 - 593897 G -s simHuman_chr6.simHuman.chr6 465532 1 - 601863 G -s simRat_chr6.simRat.chr6 139138 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 141178 7 + 636262 TTTACCA -s Anc0.Anc0refChr1 32235 7 - 62388 TTTACCA -s Anc1.Anc1refChr2 111266 7 + 144309 TTTACCA -s Anc2.Anc2refChr3 21313 7 + 53186 TGTGCCA -s mr.mrrefChr5 4832 7 + 294540 TTTACCA -s simCow_chr6.simCow.chr6 148882 7 + 602619 TGTGCCA -s simDog_chr6.simDog.chr6 433049 7 - 593897 TGTGCCA -s simHuman_chr6.simHuman.chr6 465622 7 - 601863 TTTACCA -s simRat_chr6.simRat.chr6 139139 6 + 647215 TT-GCCA - -a -s simMouse_chr6.simMouse.chr6 141185 2 + 636262 TG -s Anc0.Anc0refChr1 32245 2 - 62388 TG -s Anc1.Anc1refChr2 111276 2 + 144309 TG -s Anc2.Anc2refChr3 21323 2 + 53186 TG -s mr.mrrefChr5 4839 2 + 294540 TG -s simCow_chr6.simCow.chr6 148892 2 + 602619 TG -s simDog_chr6.simDog.chr6 433059 2 - 593897 TG -s simHuman_chr6.simHuman.chr6 465632 2 - 601863 TG -s simRat_chr6.simRat.chr6 139145 2 + 647215 TG - -a -s simMouse_chr6.simMouse.chr6 141187 26 + 636262 TCTTTATTTCATCGGCCAGCTATTCA -s Anc0.Anc0refChr1 32250 26 - 62388 TTTTTATTTCATTGGCCAGCTGGTCA -s Anc1.Anc1refChr2 111281 26 + 144309 TTTTTATTTCATTGGCCAGCTGGTCA -s Anc2.Anc2refChr3 21328 26 + 53186 CTTTTATTTCATTGACCAGCTGGTCA -s mr.mrrefChr5 4844 26 + 294540 TTTTTATTTCATTGGCCAGCTATTCA -s simCow_chr6.simCow.chr6 148897 26 + 602619 CCTTTATCTCATTGTCCAGCTGGTCA -s simDog_chr6.simDog.chr6 433064 15 - 593897 CTTTTATTTCATTGA----------- -s simHuman_chr6.simHuman.chr6 465637 26 - 601863 TTTTTATTTCATTGGCCAGCTGGTTA -s simRat_chr6.simRat.chr6 139150 26 + 647215 TTTTTATTTCATTGGCCAACTATTCA - -a -s simMouse_chr6.simMouse.chr6 141213 19 + 636262 CATCACTTTCCCCCATTAA -s Anc0.Anc0refChr1 32279 19 - 62388 TTTCACCTGGCCTCATTAA -s Anc1.Anc1refChr2 111310 19 + 144309 TTTCACCTGGCCTCATTAA -s Anc2.Anc2refChr3 21357 19 + 53186 TTTAAACCGGCCTCATTAA -s mr.mrrefChr5 4874 19 + 294540 CATCACCTTCCCTCATTAA -s simCow_chr6.simCow.chr6 148926 19 + 602619 TTTAAACCAGCCTCATTTA -s simDog_chr6.simDog.chr6 433079 11 - 593897 --------GGCCTCATTAA -s simHuman_chr6.simHuman.chr6 465666 19 - 601863 TTTCACCTGTCGTTATTAA -s simRat_chr6.simRat.chr6 139180 19 + 647215 CATCACCTTCCCTCACTAA - -a -s simMouse_chr6.simMouse.chr6 141232 24 + 636262 GGGTCAACAGATGAGTACCAGTCT -s Anc0.Anc0refChr1 32303 24 - 62388 GGGTTGACAGCTGAGTACTAGTCT -s Anc1.Anc1refChr2 111334 24 + 144309 GGGTTGACAGCTGAGTACTAGTCT -s Anc2.Anc2refChr3 21381 24 + 53186 GGGTTGACAGCTGAGTACTAATCT -s mr.mrrefChr5 4893 24 + 294540 GGGTCAACAGATGAGTACCAGTCT -s simCow_chr6.simCow.chr6 148950 24 + 602619 GGGTTGACAACTGAGTACTAATCT -s simDog_chr6.simDog.chr6 433095 24 - 593897 GGGTTGAAAGCTGCGTGCCAATCT -s simHuman_chr6.simHuman.chr6 465690 24 - 601863 GGGTTGACAGCAGAGTACTAGTCT -s simRat_chr6.simRat.chr6 139199 24 + 647215 GGGTCAACAGATACGTACCAGTCT - -a -s simMouse_chr6.simMouse.chr6 141256 157 + 636262 ATCATTTGGGCTTCTTTCATAGAGATAAATCAAATCCCATGTGTTAATTAAGTACTTCAGTACTCAAGCCATTATTTAGGACCCATCATGCCGTTAGTCTGCATAAGTTTGTGATTGGGCCACCTTGTATCATTATGTGTTATTGTACAGGACCTCC -s Anc0.Anc0refChr1 32327 128 - 62388 ATGATTTGAGCTCCTTTCCTAAGGATAAATCA-----TGGGTGTGAATTAAGTGCTTTAAAGCTGGAGACTTCATTTTAGACCCATCATGCCGTTATTCTGCGTG-GTTCTTG-----------------------GTGATGTTGTACAGGACCTCC -s Anc1.Anc1refChr2 111358 128 + 144309 ATGATTTGAGCTCCTTTCCTAAGGATAAATCA-----TGGGTGTGAATTAAGTGCTTTAAAGCTGGAGACTTCATTTTAGACCCATCATGCCGTTATTCTGCGTG-GTTCTTG-----------------------GTGATGTTGTACAGGACCTCC -s Anc2.Anc2refChr3 21405 128 + 53186 ATGATTTGAGCTCCTTTCCTAAGGATAAATCC-----TGGGTGTGAATCAAGTGCTTTAAAGCTGGAGACTCCATTTTAGACCCATCATGCTGTCATTCTGCGTG-GTTCTAA-----------------------GTGATGTTGTACAGGACCTCC -s mr.mrrefChr5 4917 156 + 294540 ATGATTTGAGCTCCTTTCCTAAAGATAAATCAAATCCTGTGTGTTAATTAAGTGCTTCAATGCTCAAGCCTTTATTTAAGACCAATCATGCCGTTAGTCTGCATAGGTTTTTGATTGG-CCACCTTGTATCATTATGTGTTGTTGTACAGGACCTCC -s simCow_chr6.simCow.chr6 148974 128 + 602619 ATGATTTGCGACCCTTTCCTAGGGATAAATTC-----TGGGTATGAATCAAGTGCAGTAAAGTTGGAGACTTGATTTAAGTCCAATCAGGCTGTCATTCGGTGCA-GTTCTAA-----------------------GTGGTATTCTATGGAACCTCC -s simDog_chr6.simDog.chr6 433142 120 - 593897 ATGATTTGAGCTCCTTTCCTAAGGATACATCC-----TGGCTGTGTATCAAGTGCTTTTAACCTGAAGACTCCATTTTAGACCCATCATGGT------CTGCATG-ATTCTAA-----------------------GTGATGTTGCACAGGACTT-- -s simHuman_chr6.simHuman.chr6 465714 121 - 601863 ATGATGTGAGCTCCT----TGAGAATAAATCA-----TGGGTGTGAATTGAGTGCCTTAAAGCTGGAG-TTTCATTC--GACCGATCATGCCGTTACCCTACGTG-GTTCTTG-----------------------ATAAGGTTGTACAGCACCTCT -s simRat_chr6.simRat.chr6 139223 152 + 647215 ATGATTTGAGCTCCTTTCCTAAAGATAAATCAAATCCTGCTTGGTAATTAAGTGCTTCAATGCTTAACCCTTTATTTAA----AATCATACTGTTAGTCTGCATAGGTTTTTGGCTGG-CTACCCCGTATCATCACCTGTTGTTGTGCAGGGTCTCC - -a -s simMouse_chr6.simMouse.chr6 141413 58 + 636262 ATGCTCCCGATGTCAATACTCAGTTGTTCAACCAATGATTAGGTTGAGCTTTGCCATA -s Anc0.Anc0refChr1 32455 58 - 62388 ATGCTTACAATACATATACTCAGATGTTCAACTAGGAATTAGGTGGGGCTTTCACATG -s Anc1.Anc1refChr2 111486 58 + 144309 ATGCTTACAATACATATACTCAGATGTTCAACTAGGAATTAGGTGGGGCTTTCACATG -s Anc2.Anc2refChr3 21533 58 + 53186 ATGCTTACAATACATATACTCAGCTGTTCAACTAGGAATTAGGTGGGGATTTCACATG -s mr.mrrefChr5 5073 58 + 294540 ATGCTTCCGATATAAATACTCAGATGTTCAACCAATGATTAGGTTGAGCTTTCCCATG -s simCow_chr6.simCow.chr6 149104 50 + 602619 ATGCTTACAATACATATACTCAGCTGTTATCCT--------GGTGGGGGGTTCAGATG -s simDog_chr6.simDog.chr6 433262 56 - 593897 --GCTTACAATACATATGCTCAGCTGTCCAACTAGGAATTAGGTGCTGATTTCACATG -s simHuman_chr6.simHuman.chr6 465835 58 - 601863 ATGCTTACAATACATATACTCAGATGTTCAACTTCCAATAAGGTGGGGCTTTCACACC -s simRat_chr6.simRat.chr6 139375 56 + 647215 ATG-TTCCCATATA-ACACTCAGATGTTCAAACAATGATTAGGTTGCCCTTCCCCATG - -a -s simMouse_chr6.simMouse.chr6 141471 3 + 636262 AAG -s Anc0.Anc0refChr1 32525 3 - 62388 AGG -s Anc1.Anc1refChr2 111556 3 + 144309 AGG -s Anc2.Anc2refChr3 21603 3 + 53186 AGG -s mr.mrrefChr5 5143 3 + 294540 AAG -s simCow_chr6.simCow.chr6 149166 3 + 602619 AGG -s simDog_chr6.simDog.chr6 433330 3 - 593897 AGG -s simHuman_chr6.simHuman.chr6 465905 3 - 601863 AGG -s simRat_chr6.simRat.chr6 139443 3 + 647215 AAG - -a -s simMouse_chr6.simMouse.chr6 141474 15 + 636262 AACTTAGTCTACAAG -s Anc0.Anc0refChr1 32528 15 - 62388 AACTTAATCTACAAG -s Anc1.Anc1refChr2 111559 15 + 144309 AACTTAATCTACAAG -s Anc2.Anc2refChr3 21606 15 + 53186 AACTGAAACTACAAG -s mr.mrrefChr5 5146 15 + 294540 AACTTAGTCTACAAG -s simCow_chr6.simCow.chr6 149169 15 + 602619 AACTGAAAATCCAAA -s simDog_chr6.simDog.chr6 433333 13 - 593897 A--TGAAACTACAAG -s simHuman_chr6.simHuman.chr6 465908 15 - 601863 AACTTAATCTAAAAG -s simRat_chr6.simRat.chr6 139448 15 + 647215 GACTTAGTCTACAAA - -a -s simMouse_chr6.simMouse.chr6 141489 8 + 636262 GTGCTGCA -s Anc0.Anc0refChr1 32551 8 - 62388 GTAGCACG -s Anc1.Anc1refChr2 111582 8 + 144309 GTAGCACG -s Anc2.Anc2refChr3 21629 8 + 53186 ACAGCAAG -s mr.mrrefChr5 5161 8 + 294540 GTGCTACT -s simCow_chr6.simCow.chr6 149192 8 + 602619 ACAGCATT -s simDog_chr6.simDog.chr6 433354 8 - 593897 ACAGCAAG -s simHuman_chr6.simHuman.chr6 465931 8 - 601863 GTAGCACG -s simRat_chr6.simRat.chr6 139463 8 + 647215 GTGCTATT - -a -s simMouse_chr6.simMouse.chr6 141497 35 + 636262 GACTTTTTTCTATGTAAAATTCTTATGTTGGTCTA -s Anc0.Anc0refChr1 32559 34 - 62388 TACAA-AACCTTTGTAATATTTTTGTACTGCTCTA -s Anc1.Anc1refChr2 111590 34 + 144309 TACAA-AACCTTTGTAATATTTTTGTACTGCTCTA -s Anc2.Anc2refChr3 21637 34 + 53186 TACAA-AACCTTTGGAATATTTTTGTACTGCTCTA -s mr.mrrefChr5 5169 35 + 294540 GACTATTTTCTATGTAAAATTCTTATGTTGGTCTA -s simCow_chr6.simCow.chr6 149200 34 + 602619 GACAA-AACCTTAGAAATATTTTTGTACTGCTCTA -s simDog_chr6.simDog.chr6 433368 23 - 593897 TACAA-AACCTTTAGAATTTTT-----------TG -s simHuman_chr6.simHuman.chr6 465939 34 - 601863 TATGG-AGCTCTTGTGAGATTTTTGTTCTGTTCTA -s simRat_chr6.simRat.chr6 139471 35 + 647215 GACTATTTCCTATGTAAAATTCTTAAGTTGGTCTA - -a -s simMouse_chr6.simMouse.chr6 141532 76 + 636262 GAAATTGTTATCTTGATCTAGACAGACCCCATTATGCCAGGATGTCCATATTGCCAGAGAAAAGAAAGATTATGCA -s Anc0.Anc0refChr1 32596 70 - 62388 GATATTTTTGTCTTGTTCTAGACAAATCCCATT-TGACAGGAGGTCTATATCACCAGAAAAA-----GGTTATTTA -s Anc1.Anc1refChr2 111627 70 + 144309 GATATTTTTGTCTTGTTCTAGACAAATCCCATT-TGACAGGAGGTCTATATCACCAGAAAAA-----GGTTATTTA -s Anc2.Anc2refChr3 21674 70 + 53186 GATATTTTTGTGTTGTCCTAGACAAATCCCATC-TGACAGGAGGTCTATATCACCAAGAAAA-----GGTTATTTA -s mr.mrrefChr5 5204 71 + 294540 GAAATTCTTATCTTGATCTAGACAAACCCCATTATGACAGGATGTCCATATTACCAGAGAAA-----GATTATGTA -s simCow_chr6.simCow.chr6 149237 68 + 602619 GATGTTCTTGTGTTGTCCTCATCAAACCCCACC-TGACA--AGGTCTATATCACCAAGCAAA-----GGTTCTTTG -s simDog_chr6.simDog.chr6 433394 70 - 593897 GATATTTTTGTGCTGCTCTAGACAAATGCCATC-TGACAGGAGGTTTAAATCATCAAGAAAA-----GGTTATTTA -s simHuman_chr6.simHuman.chr6 465976 69 - 601863 TATATTTTTGCCTTT-TCCAGACAAAACTCATT-TGACAGGACATCTATATCACCAGAAAAA-----GGTTTTATA -s simRat_chr6.simRat.chr6 139506 71 + 647215 GAATTCCATATGTTGAACTAGACAAACCCCATTATGAAGGGATGTGCATATTACCAGAGAAA-----GATTATGTA - -a -s simMouse_chr6.simMouse.chr6 141608 41 + 636262 AACCCCTAATCCCTCTTCAGTACAATTTTGTTCCTTACCCT -s Anc0.Anc0refChr1 32666 38 - 62388 AACCCCTACTCCCTCTCCATTACAAATCTGG---TGACCCC -s Anc1.Anc1refChr2 111697 38 + 144309 AACCCCTACTCCCTCTCCATTACAAATCTGG---TGACCCC -s Anc2.Anc2refChr3 21744 38 + 53186 TACTCCTACTCCCTCTCCATTACAAATCTGG---TGACCCC -s mr.mrrefChr5 5275 41 + 294540 AACCCCTACTCCCTCTTCAGTACAATTTTGTTCCTTACCCC -s simCow_chr6.simCow.chr6 149305 38 + 602619 TACTCCTACTCCCTCACAGTTACAAATTTGT---TTACCCC -s simDog_chr6.simDog.chr6 433464 38 - 593897 TACTCCTACTCCCTTTCCATTACAAATCTGG---TGATTCC -s simHuman_chr6.simHuman.chr6 466046 33 - 601863 ATTCCCTACTCCCTCTCCATTACAAAACT--------CCCC -s simRat_chr6.simRat.chr6 139577 41 + 647215 AACCCCTACGCCCTCTTCAATCCAAGTTCGTTCCTTAGCCC - -a -s simMouse_chr6.simMouse.chr6 141649 16 + 636262 TTGTAGAAGGCTATTT -s Anc0.Anc0refChr1 32713 16 - 62388 AGGTAGTAGGCTATTG -s Anc1.Anc1refChr2 111744 16 + 144309 AGGTAGTAGGCTATTG -s Anc2.Anc2refChr3 21791 16 + 53186 AGGTAGTAGGCCATTG -s mr.mrrefChr5 5325 16 + 294540 TTGTAGAAGGCTATTT -s simCow_chr6.simCow.chr6 149352 16 + 602619 ATGTAGTGGGCCATGC -s simDog_chr6.simDog.chr6 433511 16 - 593897 AGGTAGAAGGCCATTG -s simHuman_chr6.simHuman.chr6 466088 16 - 601863 ACGTAGTAGACTATTG -s simRat_chr6.simRat.chr6 139627 16 + 647215 TTGTAGAAGGCTATTT - -a -s simMouse_chr6.simMouse.chr6 141665 7 + 636262 GCTACTA -s Anc0.Anc0refChr1 32730 7 - 62388 GGTAATA -s Anc1.Anc1refChr2 111761 7 + 144309 GGTAATA -s Anc2.Anc2refChr3 21808 7 + 53186 GGTAATA -s mr.mrrefChr5 5342 7 + 294540 GCTACTA -s simCow_chr6.simCow.chr6 149369 7 + 602619 GGCAATA -s simDog_chr6.simDog.chr6 433528 7 - 593897 GATAGTA -s simHuman_chr6.simHuman.chr6 466105 7 - 601863 GGTAATA -s simRat_chr6.simRat.chr6 139644 7 + 647215 GCTACTA - -a -s simMouse_chr6.simMouse.chr6 141672 87 + 636262 TTCAATCGTCCCTTCCTCATGACCTTACAGATTCCACTGTCGTTATGATTACATTGCTGGTCATAAAACTCTCGTTACTCATTCGCC -s Anc0.Anc0refChr1 32738 20 - 62388 TCCACTTGTCCCTTC-------------------------------------------------------------------TTGGT -s Anc1.Anc1refChr2 111769 20 + 144309 TCCACTTGTCCCTTC-------------------------------------------------------------------TTGGT -s Anc2.Anc2refChr3 21816 20 + 53186 TCCACTTGTCCCTTC-------------------------------------------------------------------TTGGT -s mr.mrrefChr5 5349 87 + 294540 TTCAATTGTCCCTTCCTCATGACCTTATGGATTCCACTGTAGTTATGATTACATTGCAGGTCATAAAGCTCTCGTTCCTTATTCGCC -s simCow_chr6.simCow.chr6 149377 20 + 602619 TCCACTTGTCCCTTC-------------------------------------------------------------------TTGGT -s simDog_chr6.simDog.chr6 433536 20 - 593897 TCCACTTGTCCCTTC-------------------------------------------------------------------TTGGT -s simHuman_chr6.simHuman.chr6 466113 20 - 601863 TCCACTTGTCCCTTC-------------------------------------------------------------------TTGGT -s simRat_chr6.simRat.chr6 139651 87 + 647215 TTCGATTGTCCCTTCCACTTGACCTCATGGATTCCACTGCAGCTAAGATTATCCCACAGGTCACAAAGCTACCGTTCATTGTTCACC - -a -s simMouse_chr6.simMouse.chr6 141759 9 + 636262 GCATCACCA -s Anc0.Anc0refChr1 32759 3 - 62388 GC------G -s Anc1.Anc1refChr2 111790 9 + 144309 GCATCACAG -s Anc2.Anc2refChr3 21837 3 + 53186 GT------G -s mr.mrrefChr5 5437 9 + 294540 GCATCACAG -s simCow_chr6.simCow.chr6 149398 3 + 602619 AT------G -s simDog_chr6.simDog.chr6 433557 3 - 593897 GT------G -s simHuman_chr6.simHuman.chr6 466134 9 - 601863 GCATCACAG -s simRat_chr6.simRat.chr6 139739 9 + 647215 GCGTCACAG - -a -s simMouse_chr6.simMouse.chr6 141768 72 + 636262 CACTTGGTTGATGCTGCATGTTGGTGTATGCCCAGCTTGGCGTATAATGTCTATGTGTACTGGTACATGGTG -s Anc0.Anc0refChr1 32762 72 - 62388 GACTTTCTTGATGCTGCGTGATGCTGCATGCCCAGCTTGGTGTATAGTTTCTATGTGTTGTGATACATGTTG -s Anc1.Anc1refChr2 111799 72 + 144309 GACTTTCTTGATGCTGCGTGATGCTGCATGCCCAGCTTGGTGTATAGTTTCTATGTGTTGTGATACATGTTG -s Anc2.Anc2refChr3 21840 72 + 53186 GACTTTCTTGATGCTGCGTGATGCTGCATGCCCAGCTTGTCTTATAGTTTCTATGTGTTGTGATACATGTGG -s mr.mrrefChr5 5446 72 + 294540 CACTTTGTTGATGCTGCATGTTGGTGTATGCCCAGCTTGGTGTATAATGTCTATGTGTACTGGTACATGGTG -s simCow_chr6.simCow.chr6 149458 72 + 602619 GACTTGCTTGATGCTGCATGATGCCACATGTCTGACTTGTCCTATAGTTGCTATGTGAGGTGACAGAAGTGG -s simDog_chr6.simDog.chr6 433560 72 - 593897 GACTTTCTTGATGCTGCGTGGTGCTGCAAGCTCAGCTAGTCTTGTAGTTTCTATGTGTTGTGGTACATTTGG -s simHuman_chr6.simHuman.chr6 466143 71 - 601863 GACTTTTTTAATGCTGCGTGATGCTGCCTGCCCAGCTTGGTGTATAGTTTCTGTGTACTGGTATATGTG-TG -s simRat_chr6.simRat.chr6 139748 69 + 647215 CACTTTGTTGATGCTGCATGTTGT---ATGCTCAGCTTGGTTTAGAATGTCTATGTGTACTAGTACTTGGAC - -a -s simMouse_chr6.simMouse.chr6 141840 19 + 636262 AAATGATGAGAAAAATATG -s Anc0.Anc0refChr1 32834 19 - 62388 AGATGATAAGAAAAATATG -s Anc1.Anc1refChr2 111871 19 + 144309 AGATGATAAGAAAAATATG -s Anc2.Anc2refChr3 21912 19 + 53186 ACATGATAGGAGAAATATG -s mr.mrrefChr5 5518 19 + 294540 AGATGATGAGAAAAATATG -s simCow_chr6.simCow.chr6 149530 19 + 602619 ACATGATAGGAGAAATATG -s simDog_chr6.simDog.chr6 433632 19 - 593897 GCATGGTAGGAGAAATCTG -s simHuman_chr6.simHuman.chr6 466228 19 - 601863 AGATGATAAGGAGAATATG -s simRat_chr6.simRat.chr6 139817 19 + 647215 AGATGCTGAGAGAAATATG - -a -s simMouse_chr6.simMouse.chr6 141859 14 + 636262 TACAAATGTGAGCA -s Anc0.Anc0refChr1 32856 14 - 62388 AAGAATTGTCAGTG -s Anc1.Anc1refChr2 111893 14 + 144309 AAGAATTGTCAGTG -s Anc2.Anc2refChr3 21934 14 + 53186 AAGAATTGTCAGGG -s mr.mrrefChr5 5537 14 + 294540 GACAAATGTGAGTG -s simCow_chr6.simCow.chr6 149552 14 + 602619 AAGACATGTAAGGG -s simDog_chr6.simDog.chr6 433654 14 - 593897 AAGAATTGTCAGGG -s simHuman_chr6.simHuman.chr6 466250 14 - 601863 AAGAACTCTCAGTG -s simRat_chr6.simRat.chr6 139836 14 + 647215 GACACATGTGAATG - -a -s simMouse_chr6.simMouse.chr6 141873 23 + 636262 CATACTATGAAAGTCCGATAGGC -s Anc0.Anc0refChr1 32870 23 - 62388 CACAGTGTGAGAGTCCTGTAGGC -s Anc1.Anc1refChr2 111907 23 + 144309 CACAGTGTGAGAGTCCTGTAGGC -s Anc2.Anc2refChr3 21966 23 + 53186 CACAGTGTGAGAGTCTTGTAGGC -s mr.mrrefChr5 5551 23 + 294540 CATACTGTGAAAGTCCGATAGGC -s simCow_chr6.simCow.chr6 149584 23 + 602619 CACAGTGCAAGAGACTTGTGGGC -s simDog_chr6.simDog.chr6 433710 23 - 593897 CACAGTGTGAGAGTCTTATATGC -s simHuman_chr6.simHuman.chr6 466264 23 - 601863 CACAGTGTGAGAGTCCTGTAGGC -s simRat_chr6.simRat.chr6 139850 23 + 647215 CAAACTGTGGAAGTCCAATAGGC - -a -s simMouse_chr6.simMouse.chr6 141896 10 + 636262 CAGTTCTTAA -s Anc0.Anc0refChr1 32893 2 - 62388 TG-------- -s Anc1.Anc1refChr2 111930 10 + 144309 TGGTTCTTGA -s Anc2.Anc2refChr3 21989 2 + 53186 TG-------- -s mr.mrrefChr5 5574 10 + 294540 CGGTTCTTAA -s simCow_chr6.simCow.chr6 149607 2 + 602619 TG-------- -s simDog_chr6.simDog.chr6 433733 2 - 593897 TG-------- -s simHuman_chr6.simHuman.chr6 466289 10 - 601863 TGGTTCTTGA -s simRat_chr6.simRat.chr6 139873 10 + 647215 CGGTTCTTAA - -a -s simMouse_chr6.simMouse.chr6 141906 67 + 636262 GATCCCCATTCACCACCCTATGACCTGAGGCTCCATAGGCAGACAGCTGCATCATCCTGCTCTAATA -s Anc0.Anc0refChr1 32895 11 - 62388 --------------------------------------------------------TGGCTCTCATA -s Anc1.Anc1refChr2 111940 27 + 144309 GACTCCTTTTAGCCTT----------------------------------------TGGCTCTCATA -s Anc2.Anc2refChr3 21991 11 + 53186 --------------------------------------------------------TGGCTCTCATA -s mr.mrrefChr5 5584 67 + 294540 GATCCCCATTCGCCACCCTATGACCTGAGGGTCCATAGACAGACAGCTGCATCAGCCTGCTCCAATA -s simCow_chr6.simCow.chr6 149609 11 + 602619 --------------------------------------------------------AGGATCTAATA -s simDog_chr6.simDog.chr6 433735 11 - 593897 --------------------------------------------------------TGGCTCTCATA -s simHuman_chr6.simHuman.chr6 466300 16 - 601863 GACTCCTTTTAGCCTT--------------------------------------------------- -s simRat_chr6.simRat.chr6 139883 67 + 647215 TATCTCCATTTGCCACCCTATCTCCTGAGTGTCCATAGACAGACAGCTGAATCAGCCTGCTCCAATA - -a -s simMouse_chr6.simMouse.chr6 141973 3 + 636262 CCC -s Anc0.Anc0refChr1 32906 3 - 62388 TCC -s Anc1.Anc1refChr2 111967 3 + 144309 TCC -s Anc2.Anc2refChr3 22004 3 + 53186 TCC -s mr.mrrefChr5 5651 3 + 294540 CCC -s simCow_chr6.simCow.chr6 149622 3 + 602619 TCC -s simDog_chr6.simDog.chr6 433748 3 - 593897 TCC -s simRat_chr6.simRat.chr6 139950 3 + 647215 CCC - -a -s simMouse_chr6.simMouse.chr6 141976 21 + 636262 TTATTACAACAATCTAGGGTG -s Anc0.Anc0refChr1 32909 15 - 62388 TTA---GAGC---CTTGGATG -s Anc1.Anc1refChr2 111970 15 + 144309 TTA---GAGC---CTTGGATG -s Anc2.Anc2refChr3 22007 15 + 53186 TTA---GAGC---CTTGCAAG -s mr.mrrefChr5 5654 18 + 294540 TTA---CAACAATCTAGGGTT -s simCow_chr6.simCow.chr6 149625 10 + 602619 TAA---CAGC---CTT----- -s simDog_chr6.simDog.chr6 433756 15 - 593897 TTA---GAGC---CTGGCAAG -s simHuman_chr6.simHuman.chr6 136408 8 + 601863 -------------CTGGGATA -s simRat_chr6.simRat.chr6 139953 18 + 647215 TTA---CAACAATCTAGGGTT - -a -s simMouse_chr6.simMouse.chr6 141997 5 + 636262 GGGTT -s Anc0.Anc0refChr1 32924 5 - 62388 GGGTT -s Anc1.Anc1refChr2 111985 5 + 144309 GGGTT -s Anc2.Anc2refChr3 22022 5 + 53186 GGGTT -s mr.mrrefChr5 5672 5 + 294540 GGGTT -s simCow_chr6.simCow.chr6 149934 5 + 602619 GGATT -s simDog_chr6.simDog.chr6 433771 5 - 593897 GGGTT -s simHuman_chr6.simHuman.chr6 136416 5 + 601863 GGGTT -s simRat_chr6.simRat.chr6 139971 5 + 647215 GGGTT - -a -s simMouse_chr6.simMouse.chr6 142002 350 + 636262 CTGCTCCACAGACCAATTGGAAGACTAGTATTCCGGTATCCTATCTCGTCACTTATAGTAAATAAAGAAGTTAATCTACTCTGGAATTTATGATTCCTGAATGGTTCGAACTCTCAATGCAAGACTATATAGTAATGTTGACGGTTCTAGACGTGGATTCCGGGGGTAGGGTTAAATGGTTTGAACTCTCATCATGAGACTATATAGTAGTGTTATTCTGGGGTTAGGGTTAGCAGGACCATGCAGTCGAAGGGTTCCATAGGAAATGTGCTACCTCCCAATTTCACTATTGCTCTAAACTCAATAACGTATGGAGCGGTCCCTACCCTTGTGCTTACATCATATGCTCA -s Anc0.Anc0refChr1 32930 56 - 62388 ATTTTTAATAAACCAATTGGAAGATTAGCATG----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ACCCTTGTGTCTATGTCATA--CTCT -s Anc1.Anc1refChr2 111991 56 + 144309 ATTTTTAATAAACCAATTGGAAGATTAGCATG----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ACCCTTGTGTCTATGTCATA--CTCT -s Anc2.Anc2refChr3 22028 56 + 53186 ATTTTTAATAAACCAATTGGAAGATTAGCATG----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ACCCTTGTGTCTATGTCATA--CTCT -s mr.mrrefChr5 5677 58 + 294540 CTGCTCCACAGACCAATTGGAAGATTAGCATT----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ACCCTTGTGTTTACGTCATATGCTCA -s simCow_chr6.simCow.chr6 149940 56 + 602619 ATTTTTAACAAACCAATTGGAAGATTAGCATT----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GCTCTTGTGTTTATGTCGTA--CTCT -s simDog_chr6.simDog.chr6 433777 56 - 593897 ATTCTCAATAAACCAATTGGGAGATTAGCTTG----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ACCCTTGCGTCTTTGGCATA--CTCT -s simHuman_chr6.simHuman.chr6 136422 56 + 601863 GTTTCTAAGACACCAATAGTAGGATTAGCATG----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ACCCTTCTGGCTATGTCATA--CTCT -s simRat_chr6.simRat.chr6 139976 58 + 647215 CTGCTCCACAGACCAATTGGACGATTAGCATT----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ACCCTTATGTTCACGTCATATGCTCA - -a -s simMouse_chr6.simMouse.chr6 142352 14 + 636262 ATTTTTTTATGTTG -s Anc0.Anc0refChr1 32986 13 - 62388 ATTTTATTCTGTT- -s Anc1.Anc1refChr2 112047 13 + 144309 ATTTTATTCTGTT- -s Anc2.Anc2refChr3 22084 13 + 53186 ATTTTATTCTGTT- -s mr.mrrefChr5 5735 14 + 294540 ATTTTTTTATGTTG -s simCow_chr6.simCow.chr6 149998 13 + 602619 AGTTTCTACTGTT- -s simDog_chr6.simDog.chr6 433846 13 - 593897 ATTTTATTATGTT- -s simHuman_chr6.simHuman.chr6 136478 13 + 601863 ATCTCATTCTGTT- -s simRat_chr6.simRat.chr6 140034 14 + 647215 ATTTATTTATGTTG - -a -s simMouse_chr6.simMouse.chr6 142366 2 + 636262 TG -s Anc0.Anc0refChr1 32999 2 - 62388 TG -s Anc1.Anc1refChr2 112060 2 + 144309 TG -s Anc2.Anc2refChr3 22097 2 + 53186 TG -s mr.mrrefChr5 5749 2 + 294540 TG -s simCow_chr6.simCow.chr6 150012 2 + 602619 TA -s simDog_chr6.simDog.chr6 433859 2 - 593897 TG -s simHuman_chr6.simHuman.chr6 136491 2 + 601863 TG -s simRat_chr6.simRat.chr6 140048 2 + 647215 TG - -a -s simMouse_chr6.simMouse.chr6 142368 13 + 636262 CTTGGTAGATGTG -s Anc0.Anc0refChr1 33001 12 - 62388 C-TACTAAAAATG -s Anc1.Anc1refChr2 112062 12 + 144309 C-TACTAAAAATG -s Anc2.Anc2refChr3 22099 12 + 53186 C-TACCCAAAATG -s mr.mrrefChr5 5751 13 + 294540 CTTGGTAGATGTG -s simCow_chr6.simCow.chr6 150014 12 + 602619 C-TTGCCAAAAGG -s simDog_chr6.simDog.chr6 433900 12 - 593897 C-CACCCAAAATG -s simHuman_chr6.simHuman.chr6 136493 12 + 601863 C-TACTAAAAATG -s simRat_chr6.simRat.chr6 140050 13 + 647215 CTTGGTAGATGTG - -a -s simMouse_chr6.simMouse.chr6 142381 8 + 636262 ACATGCCC -s Anc0.Anc0refChr1 33013 8 - 62388 ACATTTCC -s Anc1.Anc1refChr2 112074 8 + 144309 ACATTTCC -s Anc2.Anc2refChr3 22111 8 + 53186 ACATTTCC -s mr.mrrefChr5 5764 8 + 294540 ACATGCCC -s simCow_chr6.simCow.chr6 150027 8 + 602619 ACATTTCC -s simDog_chr6.simDog.chr6 433912 5 - 593897 ACATT--- -s simHuman_chr6.simHuman.chr6 136505 8 + 601863 ACATTTCC -s simRat_chr6.simRat.chr6 140063 8 + 647215 ACATGTAC - -a -s simMouse_chr6.simMouse.chr6 142389 3 + 636262 TAG -s Anc0.Anc0refChr1 33086 2 - 62388 -AG -s Anc1.Anc1refChr2 112147 3 + 144309 TAG -s Anc2.Anc2refChr3 22184 2 + 53186 -AA -s mr.mrrefChr5 5772 3 + 294540 TAG -s simCow_chr6.simCow.chr6 150104 2 + 602619 -AA -s simDog_chr6.simDog.chr6 433970 2 - 593897 -AA -s simHuman_chr6.simHuman.chr6 136590 3 + 601863 TAG -s simRat_chr6.simRat.chr6 140071 3 + 647215 CAG - -a -s simMouse_chr6.simMouse.chr6 142392 129 + 636262 CGGGTGTCAAAGTTAGATCCCGGTGGTGCCTGGGTGGTTCCTGGTTTCTAGATAAGGGTCTGTTTTATTGTTATTGTATAAGTGCTTAGGGATTAGTGGTATCTCTGTCTGTCTTTTCCTGTCAGCTAT -s Anc0.Anc0refChr1 33091 106 - 62388 CAGGTGTCAGTGTTGGTTACCAGTGAGGCCTGAAAGGT----------TAGATAA----CTGTCACACT-TTATTACAC-AGTGCTTAGG-------GGTATCTCTATCAGTGTGCCCCAATCAGCTAT -s Anc1.Anc1refChr2 112153 113 + 144309 CAGGTGTCAGTGTTGGTTACCAGTGAGGCCTGAAAGGT----------TAGATAA----CTGTCACACT-TTATTACAC-AGTGCTTAGGCATTAGTGGTATCTCTATCAGTGTGCCCCAATCAGCTAT -s Anc2.Anc2refChr3 22189 106 + 53186 CAGGTGGTAGTGTTGGTTACCAGTGAGGCCTGAAAAAT----------TGAATAA----GTGTCACACT-TTATTACAC-AGTGCTTAGG-------GGTAACCCTACCTGTGTGCCCCAATCAGCTAT -s mr.mrrefChr5 5775 117 + 294540 CGGGTGTCAAAGTTAGATCCCGGTGGTGCCTGGGTGGT----------TAGATAA--GTCTGTTTTATTGTTATTGTATAAGTGCTTAGGGATTAGTGGTATCTCTGTCAGTCTTTCCCAGTCAGCTAT -s simCow_chr6.simCow.chr6 150108 106 + 602619 CAGGTGGTAGTGCTGATTACCAATGAAGCCTGAAAAAT----------TGAATAA----GTGTCACACT-TTATCACCC-AGTGCTTAGG-------GGCAACACCACCTGTGTGCCCCAATCAGCTAT -s simDog_chr6.simDog.chr6 433975 100 - 593897 CAGGTAGTGGCGTCGGTTGCCAGTGAGGCTGGAAA----------------ATAA----GTGTTGCACT-TAATTGCAG-AGTGCTTAGG-------GGTAACCCTACCTGTATGCCCCAATCAGCTAT -s simHuman_chr6.simHuman.chr6 136596 113 + 601863 CAGGTGTCAGTGTTGGTTACCAGTGAGGCCTATAAGGT----------TAGATAA----CTGTCACACT-TTCTTACAC-AGTGCATAGTCATTAGTGGTATCTCTATCAGTGTACCCCAATCAGCTAT -s simRat_chr6.simRat.chr6 140074 99 + 647215 CAGGTATCAAAGCAAGATCCTGGTGGT------------------------------CTCTGTTTTATTGTTATTGTGTAAGTGCTTAGGGACCATTGGTATCTCTGTCAGGCTTTCCCAGTAAGCTGT - -a -s simMouse_chr6.simMouse.chr6 142521 43 + 636262 AATCATGATCCACAACTGGATGGACTGACATGTCTACTTTTCT -s Anc0.Anc0refChr1 33197 41 - 62388 TATCA--ATCCAAAACTAGATGGAAAGACATATTATCTTTTCT -s Anc1.Anc1refChr2 112266 43 + 144309 TATCATGATCCAAAACTAGATGGAAAGACATATTATCTTTTCT -s Anc2.Anc2refChr3 22295 41 + 53186 TATCA--ATCCAGAACTACATGGAAAGACATACTATCTTTTCT -s mr.mrrefChr5 5892 43 + 294540 AATCATGATCCAAAACTGGATGGACTGACATGTCTTCTTTTCT -s simCow_chr6.simCow.chr6 150214 28 + 602619 TATCC---------------TAGAAAGACTTGCTTTCCATTCT -s simDog_chr6.simDog.chr6 434078 41 - 593897 TACCA--ATCCAGAACTACATGGAAAGACATACTAGCTTTTCT -s simHuman_chr6.simHuman.chr6 136709 43 + 601863 TATCATGATCCAAAACTAGATGGAGAGACATATTCTCTTCCTT -s simRat_chr6.simRat.chr6 140173 43 + 647215 AACCATGATCCAAAACCGGATGGACTGACATGTCATCTTTACT - -a -s simMouse_chr6.simMouse.chr6 142564 12 + 636262 TCCAGCAGAAAC -s Anc0.Anc0refChr1 33238 12 - 62388 TACAACAGGTTC -s Anc1.Anc1refChr2 112309 12 + 144309 TACAACAGGTTC -s Anc2.Anc2refChr3 22336 12 + 53186 TACGACAGGTTC -s mr.mrrefChr5 5935 12 + 294540 TCCAGCAGAAAC -s simCow_chr6.simCow.chr6 150242 12 + 602619 TACTACAAATAC -s simDog_chr6.simDog.chr6 434121 12 - 593897 TGTGCGAGGTTG -s simHuman_chr6.simHuman.chr6 136752 12 + 601863 TACAACAGGCTC -s simRat_chr6.simRat.chr6 140216 12 + 647215 TTCAGCGGAAAC - -a -s simMouse_chr6.simMouse.chr6 142576 19 + 636262 TAATTGTAGGAGCACCAAC -s Anc0.Anc0refChr1 33250 19 - 62388 CATCTGTAGGAGCACGAAC -s Anc1.Anc1refChr2 112321 19 + 144309 CATCTGTAGGAGCACGAAC -s Anc2.Anc2refChr3 22348 19 + 53186 CATCTCTAGGAGCACGAAC -s mr.mrrefChr5 5947 19 + 294540 TAATTGTAGGAGCACCAAC -s simCow_chr6.simCow.chr6 150254 19 + 602619 TATCCATAGGAGCACGAGC -s simDog_chr6.simDog.chr6 434153 19 - 593897 CATCTCTAGAAGCACCAAC -s simHuman_chr6.simHuman.chr6 136764 19 + 601863 CATGTGTAGGAGCAAGAAC -s simRat_chr6.simRat.chr6 140228 19 + 647215 TAATTGTGGGAGCACCAAC - -a -s simMouse_chr6.simMouse.chr6 142595 36 + 636262 AAAACACCCAGCGTAAATACGGCCACTATCATGACC -s Anc0.Anc0refChr1 33269 36 - 62388 ACAACATCCAGCCCAAATCAAGCCACTGTCAGGACC -s Anc1.Anc1refChr2 112340 36 + 144309 ACAACATCCAGCCCAAATCAAGCCACTGTCAGGACC -s Anc2.Anc2refChr3 22367 36 + 53186 ACCACATCCAGCCCAAATCAAGCAACTGTCAGGACC -s mr.mrrefChr5 5966 36 + 294540 ACAACACCCAGCGTAAATACGGCCACTATCATGACC -s simCow_chr6.simCow.chr6 150273 36 + 602619 ACGACAACCAGTCCAAATCGAGCCACTGTCAGGACC -s simDog_chr6.simDog.chr6 434172 36 - 593897 CCCATGTCCAGCTCAAATCAAGCAACTGTCAGGACC -s simHuman_chr6.simHuman.chr6 136783 31 + 601863 ACAACATCCCGCCCAAAT-----CACTGTCACGACA -s simRat_chr6.simRat.chr6 140251 32 + 647215 ACATCACCCAGCTTAGATAAGGCCACTA----GATC - -a -s simMouse_chr6.simMouse.chr6 142631 25 + 636262 TAAGTAAGATCCTTATTTAGTTTAT -s Anc0.Anc0refChr1 33305 19 - 62388 T--TTCCAATCC----TTAGATACT -s Anc1.Anc1refChr2 112376 19 + 144309 T--TTCCAATCC----TTAGATACT -s Anc2.Anc2refChr3 22410 19 + 53186 T--TTCCAATAC----TTAGATACT -s mr.mrrefChr5 6002 25 + 294540 TAAGTCAGATCCTTATTTAGTTTAT -s simCow_chr6.simCow.chr6 150316 15 + 602619 A--TTCCAATAA----TCAGA---- -s simDog_chr6.simDog.chr6 434215 19 - 593897 T--TTCCAATAC----TTTGATACT -s simHuman_chr6.simHuman.chr6 136814 19 + 601863 T--TTCCAATCC----TTAGATCCC -s simRat_chr6.simRat.chr6 140283 25 + 647215 TAAGACAGATCCTTTTTTATGTTAT - -a -s simMouse_chr6.simMouse.chr6 142656 10 + 636262 GATTGACCAA -s Anc0.Anc0refChr1 33324 6 - 62388 AATCCC---- -s Anc1.Anc1refChr2 112395 10 + 144309 AATCCCCCCA -s Anc2.Anc2refChr3 22429 6 + 53186 AATCCC---- -s mr.mrrefChr5 6027 10 + 294540 GATTGACCCA -s simCow_chr6.simCow.chr6 150331 3 + 602619 ---CCC---- -s simDog_chr6.simDog.chr6 434236 6 - 593897 AATCCC---- -s simHuman_chr6.simHuman.chr6 136833 10 + 601863 AATCCCCCCA -s simRat_chr6.simRat.chr6 140308 10 + 647215 GATTGACCCA - -a -s simMouse_chr6.simMouse.chr6 142666 22 + 636262 GTGGGCACTAGCATTCAGGGGC -s Anc0.Anc0refChr1 33346 22 - 62388 ATGGGCATTAGCATTCAGGGTC -s Anc1.Anc1refChr2 112421 22 + 144309 ATGGGCATTAGCATTCAGGGTC -s Anc2.Anc2refChr3 22451 22 + 53186 ATGGGCATAAGCATTTAGGGTC -s mr.mrrefChr5 6037 22 + 294540 GTGGGCACTAGCATTCAGGGGC -s simCow_chr6.simCow.chr6 150350 22 + 602619 ATGGGCATAATCATTTGGGGAC -s simDog_chr6.simDog.chr6 434258 22 - 593897 ATGGACATAAGCACTTACGATC -s simHuman_chr6.simHuman.chr6 136875 22 + 601863 ATGGGCATTAACATTCAGGGTC -s simRat_chr6.simRat.chr6 140318 22 + 647215 GTGGGCACTAGCATCCAGGGGC - -a -s simMouse_chr6.simMouse.chr6 142688 8 + 636262 AGTCTAAA -s Anc0.Anc0refChr1 33368 8 - 62388 AGGCGCAA -s Anc1.Anc1refChr2 112443 8 + 144309 AGGCGCAA -s Anc2.Anc2refChr3 22473 8 + 53186 ATGGGCAA -s mr.mrrefChr5 6059 8 + 294540 AGTCTAAA -s simCow_chr6.simCow.chr6 150372 8 + 602619 ATGGACAA -s simDog_chr6.simDog.chr6 434280 8 - 593897 ATGGGTGA -s simHuman_chr6.simHuman.chr6 136975 8 + 601863 AGACGCAG -s simRat_chr6.simRat.chr6 140340 8 + 647215 AGGTCAAA - -a -s simMouse_chr6.simMouse.chr6 142696 6 + 636262 CAATAT -s Anc0.Anc0refChr1 33376 6 - 62388 CGATAT -s Anc1.Anc1refChr2 112451 6 + 144309 CGATAT -s Anc2.Anc2refChr3 22482 6 + 53186 CGATGC -s mr.mrrefChr5 6067 6 + 294540 CAATAT -s simCow_chr6.simCow.chr6 150381 6 + 602619 CGATGC -s simDog_chr6.simDog.chr6 434289 6 - 593897 CAACGC -s simHuman_chr6.simHuman.chr6 136983 6 + 601863 CCATAT -s simRat_chr6.simRat.chr6 140348 6 + 647215 CAATAT - -a -s simMouse_chr6.simMouse.chr6 142702 63 + 636262 TGCCTTACCTGGTACGGGTAAACTATGCAGGTGGAGCACTAAAACTTTGGTTCTATGAGACTA -s Anc0.Anc0refChr1 33382 62 - 62388 TGCCTAG-GTGGGTTGGGCAAGCAATTCAGGTGGAGCATTGACACTCTGCCACTATGTGATAG -s Anc1.Anc1refChr2 112457 62 + 144309 TGCCTAG-GTGGGTTGGGCAAGCAATTCAGGTGGAGCATTGACACTCTGCCACTATGTGATAG -s Anc2.Anc2refChr3 22488 62 + 53186 TGCCTAA-GTGGGTTGGGCAAGCAGTTCAGGTGGAGTATTGACACTCTGCCACTATGTGATAG -s mr.mrrefChr5 6073 63 + 294540 TGCCTTGCGTGGTTCGGGCAAACTATGCAGGTGGAGCATTAAAACTCTGCTTCTATGTGACTA -s simCow_chr6.simCow.chr6 150387 62 + 602619 TGCATAA-GTGGGTTGGGCGGGTAGTTCAGGTGGAGTATTGATCCTCTACCACTACCTGATAG -s simDog_chr6.simDog.chr6 434295 62 - 593897 TGTCAAA-GTAGATCAGTCAAACAGTTTAGGTGGAGTACTTACACTCTGCCACTATGCAATAG -s simHuman_chr6.simHuman.chr6 136993 62 + 601863 TGCCTGG-GTGGGTTGGGCAAGCAACCCAGGTGGAGCATTGACACTCTGCAGCTATGTGATAG -s simRat_chr6.simRat.chr6 140354 63 + 647215 TGCCTTGTGTGGTTCGGGCAAACTATTCAGGTGGAGCATGAAAACTCTCCTTCTATGTGACTA - -a -s simMouse_chr6.simMouse.chr6 142765 63 + 636262 CTTGCTTAACAAAGTCGTAAGTATTAAAGCTTCTAAATTGAAATGTTGCACACATGAGGCAGG -s Anc0.Anc0refChr1 33454 63 - 62388 CTTACTTAACAAGGTTGCAAGGATGGAATGTTGCTCATCTAGATGCTGCATAGACTCTGCGGT -s Anc1.Anc1refChr2 112529 63 + 144309 CTTACTTAACAAGGTTGCAAGGATGGAATGTTGCTCATCTAGATGCTGCATAGACTCTGCGGT -s Anc2.Anc2refChr3 22560 63 + 53186 CTTACTTAACAAGGTTGCAAGGATGGATTGTTGCTCATCTAGATGCTGTGCAGACTCTGCGGT -s mr.mrrefChr5 6143 63 + 294540 CTTGCTTAACAAAGTCGTAAGTATTAAAGCTTCTAAATTGAAATGCTGCATACATGAGGCAGG -s simCow_chr6.simCow.chr6 150459 63 + 602619 CTGACTTAACAAGGCTGGGAGAATGGGTTCCTGCTCATCTAGAAGCTGTGCAGACTCTGCTGT -s simDog_chr6.simDog.chr6 434367 63 - 593897 CTTACTTGACAAGGTTGCAAGGATGGATTGTTTCTCATCTAAATGCTGTGCAGACTCTACGGT -s simHuman_chr6.simHuman.chr6 137065 63 + 601863 CTTACTTAACAAGGTGGCAAGGATAGAATTTTGCTCATCTAGATACTGCATAGGCTCTGTGGT -s simRat_chr6.simRat.chr6 140424 63 + 647215 CTTGCTTAACAAAGTCAAAAGTATTAAAGCTTCTGAATTGAAATCCTGTATACATGAGGCAGG - -a -s simMouse_chr6.simMouse.chr6 142828 54 + 636262 ACCATGGGTGCAGTGAGAGGGGCAAACCATATAGCACAAACTTACTGGATTATT -s Anc0.Anc0refChr1 33517 54 - 62388 AACATGAATCCAGTAGGATGGGCAAACCATATGTCACACACTTACTGAAGTATT -s Anc1.Anc1refChr2 112592 54 + 144309 AACATGAATCCAGTAGGATGGGCAAACCATATGTCACACACTTACTGAAGTATT -s Anc2.Anc2refChr3 22623 54 + 53186 AACATGAATCCAGTAGGATGAACAAACCATATGTCACACAATTACTGAAGTATG -s mr.mrrefChr5 6206 54 + 294540 ACCATGAGTGCAGTGAGAGGGGCAAACCATATGGCACAAACTTACTGAATTATT -s simCow_chr6.simCow.chr6 150525 52 + 602619 AACATGAATATAGTAGAGGAAACACACTATATGCCACACA--CACGGATGTCCA -s simDog_chr6.simDog.chr6 434430 54 - 593897 GACATGAATCCAATAGGATGAACAAACCATATGTCACACAATTACTGGAGTATG -s simHuman_chr6.simHuman.chr6 137128 49 + 601863 ATCATGA----AGTAGCATGGGCGATCCATATGTTACTCACTTACTGAA-TATT -s simRat_chr6.simRat.chr6 140487 54 + 647215 GCCATAATTGCAATGAGAGGGGCAAACCATATGGCACAAACCTACTGAATTATT - -a -s simMouse_chr6.simMouse.chr6 142882 11 + 636262 GAATTGTCTCA -s Anc0.Anc0refChr1 33571 11 - 62388 GAATGGTTTCA -s Anc1.Anc1refChr2 112646 11 + 144309 GAATGGTTTCA -s Anc2.Anc2refChr3 22677 11 + 53186 GAATGGTTTCA -s mr.mrrefChr5 6260 11 + 294540 GAATTGTCTCA -s simCow_chr6.simCow.chr6 150578 11 + 602619 GGATGGCTTCA -s simDog_chr6.simDog.chr6 434484 11 - 593897 AAATGGTTTCA -s simHuman_chr6.simHuman.chr6 137177 11 + 601863 GAATGGATTTA -s simRat_chr6.simRat.chr6 140541 11 + 647215 GAATTGTATCA - -a -s simMouse_chr6.simMouse.chr6 142893 13 + 636262 GTATGTATCCACA -s Anc0.Anc0refChr1 33582 13 - 62388 GTATGTCTCCACC -s Anc1.Anc1refChr2 112657 13 + 144309 GTATGTCTCCACC -s Anc2.Anc2refChr3 22688 13 + 53186 GCATGTCTTCGCC -s mr.mrrefChr5 6271 13 + 294540 GTATGTCTCCACC -s simCow_chr6.simCow.chr6 150648 9 + 602619 GGATGTC----CA -s simDog_chr6.simDog.chr6 434495 13 - 593897 GCATGTCTTCGCC -s simHuman_chr6.simHuman.chr6 137188 13 + 601863 GTATGTCTCCACC -s simRat_chr6.simRat.chr6 140552 13 + 647215 GTATGTCTCTGCC - -a -s simMouse_chr6.simMouse.chr6 142906 7 + 636262 CTTCATG -s Anc0.Anc0refChr1 33601 7 - 62388 CTTCATG -s Anc1.Anc1refChr2 112676 7 + 144309 CTTCATG -s Anc2.Anc2refChr3 22708 7 + 53186 CTTCATG -s mr.mrrefChr5 6290 7 + 294540 CTTCATG -s simCow_chr6.simCow.chr6 150664 7 + 602619 CTTCATG -s simDog_chr6.simDog.chr6 434515 7 - 593897 CTTCATG -s simHuman_chr6.simHuman.chr6 137207 4 + 601863 ---CATG -s simRat_chr6.simRat.chr6 140572 7 + 647215 CTTCATG - -a -s simMouse_chr6.simMouse.chr6 142913 41 + 636262 TCAGGGTACACTGGTAGTGATCAGCACTTTACCTGTCAACT -s Anc0.Anc0refChr1 33608 35 - 62388 GCAGAGTACATTGGCAGTGATCAGCACTTTC------ATGT -s Anc1.Anc1refChr2 112683 35 + 144309 GCAGAGTACATTGGCAGTGATCAGCACTTTC------ATGT -s Anc2.Anc2refChr3 22719 35 + 53186 GCAGAGTACATTGGCAGTGATCAGCACTTTC------TTGC -s mr.mrrefChr5 6297 41 + 294540 TCAGGGTACACTGGTAGTGATCAGCACTTTACCTGTCAACT -s simCow_chr6.simCow.chr6 150675 34 + 602619 GCAGAGTACAATGGCAGTGCT-AGTACATCC------TTGC -s simDog_chr6.simDog.chr6 434526 35 - 593897 ACAGAGTACATTGGTAATGATCGGCATTTTC------TTGC -s simHuman_chr6.simHuman.chr6 137211 35 + 601863 GCAGAGTACATTGGCAGCAATCAGCACTTTG------ATGT -s simRat_chr6.simRat.chr6 140579 41 + 647215 TCTGGGTACACTGGTAGTGATCAGCACTTTTCCTGTCAATT - -a -s simMouse_chr6.simMouse.chr6 142954 108 + 636262 CAACCTATTTTCGCTGAATAAACATCTGTATAACTACAAATGGTGGGGGATTAAGTTATTCTCTAATGGGAGTAAACACCAAGTGCCATCTCATGGAAAGCAAAATGT -s Anc0.Anc0refChr1 33643 107 - 62388 CAACCTATTTTTACTGAATAAACATCCAGTTAACTAAAAATCTTGGGGGCTACAGTCATCCCTTCATA-GAGAAAACACCAAGCATCAAGTCATGGAAAGCAAAATGT -s Anc1.Anc1refChr2 112718 107 + 144309 CAACCTATTTTTACTGAATAAACATCCAGTTAACTAAAAATCTTGGGGGCTACAGTCATCCCTTCATA-GAGAAAACACCAAGCATCAAGTCATGGAAAGCAAAATGT -s Anc2.Anc2refChr3 22754 107 + 53186 CAACCTATTTTTACTGAATAAACATCCAGTTCACTAAACATCTTGGGGGCTACAGTCATCCCTTCATA-GAGAAAATACTAAGCATCAAGTTATGTAAAGCAATATGT -s mr.mrrefChr5 6338 108 + 294540 CAACCTATTTTTGCTGAATAAACATCTGTATAACTAAAAATGTTGGGGGATTAAGTTATTCTCTAATAGGAGAAAACACCAAGTGCCATCTCATGGAAAGCAAAATGT -s simCow_chr6.simCow.chr6 150709 107 + 602619 CAGCCTATTTTTACTGAATAAATATGCACTGTACTAACCAACTTGGGGTCTACAGTCATACGTTCATA-GAGAAAATGCTAAGCATCTAGTTAAGTGAAGCAGCATGT -s simDog_chr6.simDog.chr6 434566 104 - 593897 CAACCTATTGTTACTGACTAAACATCCAGTTCACTAAACATGTTGGGGGCTACAGTTATCCCTTTATA-GAGAGAGTACTAAGCATCAAGTTGTATAGAGCAATA--- -s simHuman_chr6.simHuman.chr6 137246 96 + 601863 CAACCTATTTTTATTGAATAAAGATCCAACTAATTGAAAATCTTG-----------CAACCCTCCATA-AAGAAAACACCACTCATCAATTCATGGAAAGCAAAATGT -s simRat_chr6.simRat.chr6 140620 98 + 647215 CAACCTATCTTTGCTGAATAAACATCTGCATAACTAAGAATGTCGGGGGATCAAGTTATTCTCTTATAGTAGAACACACCAAGTGCCATCCCATGGAA---------- - -a -s simMouse_chr6.simMouse.chr6 143062 2 + 636262 GT -s Anc0.Anc0refChr1 33751 2 - 62388 GT -s Anc1.Anc1refChr2 112826 2 + 144309 GT -s Anc2.Anc2refChr3 22862 2 + 53186 GT -s mr.mrrefChr5 6446 2 + 294540 GT -s simCow_chr6.simCow.chr6 150830 2 + 602619 GT -s simHuman_chr6.simHuman.chr6 137343 2 + 601863 GT - -a -s simMouse_chr6.simMouse.chr6 143064 17 + 636262 AGAAATAAAAGAATCCA -s Anc0.Anc0refChr1 33753 17 - 62388 AAAAATAAGGGAGTCCA -s Anc1.Anc1refChr2 112828 17 + 144309 AAAAATAAGGGAGTCCA -s Anc2.Anc2refChr3 22864 17 + 53186 AAAAACAAGGGAGTGCA -s mr.mrrefChr5 6448 17 + 294540 AAAAATAAAAGAATCCA -s simCow_chr6.simCow.chr6 150835 17 + 602619 AAAAACAAGGGAGTGCA -s simDog_chr6.simDog.chr6 434670 13 - 593897 ----ACAATGGAGTGCA -s simHuman_chr6.simHuman.chr6 137345 17 + 601863 AAATATAGGGGAGTCCA -s simRat_chr6.simRat.chr6 140718 17 + 647215 AAAAATAAAAGAATCCA - -a -s simMouse_chr6.simMouse.chr6 143081 139 + 636262 TCTTTAGGAGTTATATGGCATCATGTTGACATTTAGGATCTAATATATAACACAGACTATACCTGAAATAAGATGCACCTTCATCATACATCCCTTAATTAAGTTTCATGCCATGGATTTGAATAGCCATTTTATCTAA -s Anc0.Anc0refChr1 33771 124 - 62388 TCCTTTGGAGATAAAGCACATCATGTAGAGAAATTGAATC-----TATATCAGAGACTATACC----------GGCCCTTTCATCATACATTCCTTACTCAAGTTTCATGCCATGGTCTTGAATAGCTAGTTTATACAA -s Anc1.Anc1refChr2 112846 137 + 144309 TCCTTTGGAGATAAAGCACATCATGTAGAGAAATTGAATCCCTGATATATCAGAGACTATACCT--AATCAGAGGCCCTTTCATCATACATTCCTTACTCAAGTTTCATGCCATGGTCTTGAATAGCTAGTTTATACAA -s Anc2.Anc2refChr3 22882 124 + 53186 TCCTTTGGGGATAAAGCACATCATTTGAAGAAATTGAATC-----TATATCAGAGACTCCACT----------GGTCATTTCATCATACATTCCTTACTCAAGTCTCATGCCAAGGTCTTGAATAGCTAGTTTATACAA -s mr.mrrefChr5 6465 139 + 294540 TCTTTAGGAGTTATATGGCATCATGTAGACATTTAGGATCTAAGATATAACACAGACTATACCTGAAATAAGATGCCCCTTCATCATACATCCCTTAATCAAGTTTCATGCCATGGATTTGAATAGCCAGTTTATCCAA -s simCow_chr6.simCow.chr6 150853 124 + 602619 TACTTTTGGGAAAAAGTGCATCATTTGAAGAAATTGAATC-----TATATCATAGACTCCACT----------GGTCATCCCATCATACATTCCTTACTCAAGTCTCATGCCACGGTCTTAAATAGCTAGCTTAGACAT -s simDog_chr6.simDog.chr6 434684 110 - 593897 TCTTTTGGGGATAAAGCACATCAT----ACAGATTACACC-----TA-ATCAGAG-CTCC------------------TTTCATCATAGGTTCTTTGCTTAGGTCTCTTGCCAAGATCCTGAATAGCTAGTTTATACAA -s simHuman_chr6.simHuman.chr6 137363 137 + 601863 TCCATTGGAGATAAAGCATATCATGTAGAGAAATTGAATCCCTGATATATCAGAGACTATACCT--AATCAGAGGCCCTTTCATCATACATTCCTTACTCAAGTTCCATGCCATGGTCTTCAATAGCTAGTTGGTACAC -s simRat_chr6.simRat.chr6 140735 136 + 647215 TCTTTAGAAGTTATATGGCATCATGTAGAAGTGTAGGATCTAAGATATA--ACAGAATATACCTGAAATTAGAT-CCTCTTCATCATACATCCCTTATTCAAATTTCATGCCATGGATTTAAATAGTCAGTTTATCCAA - -a -s simMouse_chr6.simMouse.chr6 143220 47 + 636262 ATGTAATAAACTGTAATAACAGTTAAAAGCTCCTTCTGAATAACCAA -s Anc0.Anc0refChr1 33895 46 - 62388 ATGCAATAGGCTGTAACACCAATC-AAAGCTTCTAGTGTGTAGCTAA -s Anc1.Anc1refChr2 112983 46 + 144309 ATGCAATAGGCTGTAACACCAATC-AAAGCTTCTAGTGTGTAGCTAA -s Anc2.Anc2refChr3 23006 46 + 53186 ATGCAATAGGCTGTAACACCATTC-AAAGCTTCTAGTGTGTAGCTGA -s mr.mrrefChr5 6604 46 + 294540 ATGTAATAAACTGTAATAACAATT-AAAGCTCCTTCTGAATAACCAA -s simCow_chr6.simCow.chr6 150977 40 + 602619 ATGTAATAGGCTGTAACAAAATT-----GCTTCTGCTGTGTAGCT-- -s simDog_chr6.simDog.chr6 434794 46 - 593897 ATGCAATAGCCTGTAGCACCGTTC-AAAGCTCCCAGTGTGCAGCTGA -s simHuman_chr6.simHuman.chr6 137500 46 + 601863 ATGCAATAGGTAGTAACAGCAATC-AAGCCTTCTAATGTGTACCTAA -s simRat_chr6.simRat.chr6 140879 46 + 647215 ATGTCATAAACCACAATAACAATT-AAAGCTCCTTCTGGATAACCAA - -a -s simMouse_chr6.simMouse.chr6 143267 22 + 636262 GCAAGCTTAAAGGACACCATAA -s Anc0.Anc0refChr1 33941 20 - 62388 GCTAACATAAGGGAGACA--AA -s Anc1.Anc1refChr2 113029 20 + 144309 GCTAACATAAGGGAGACA--AA -s Anc2.Anc2refChr3 23052 20 + 53186 GTTAACATAAGGGAGACA--AA -s mr.mrrefChr5 6650 22 + 294540 GCAAGCTTAAAGGACACAATAA -s simCow_chr6.simCow.chr6 151017 18 + 602619 --TAACAAAAGGGAGACA--AA -s simDog_chr6.simDog.chr6 434841 20 - 593897 GTTAACCTCAGGGAGATA--AA -s simHuman_chr6.simHuman.chr6 137546 20 + 601863 GCTAACATAAGGGAAACA--AA -s simRat_chr6.simRat.chr6 140925 22 + 647215 GCAAGTTTAAAGGACACAACCA - -a -s simMouse_chr6.simMouse.chr6 143289 55 + 636262 TTGTTAATCCCCTTAAACAAGATTGAAAACTTGATTTTAATTTGGTGTACATTTG -s Anc0.Anc0refChr1 33961 33 - 62388 TTTGAAATCTT-----ATAAGTTAGAAAAC-----T------------AAATTTG -s Anc1.Anc1refChr2 113049 42 + 144309 TTTGAAATCTT-----ATAAGTTAGAAAAC-----TTTAATT---GGTAAATTTG -s Anc2.Anc2refChr3 23072 33 + 53186 TTTGAGGTCTT-----ATCAGTTAGAAAAC-----T------------AATTTTC -s mr.mrrefChr5 6672 55 + 294540 TTGTTAATCCCCTTAAACAAGATTGAAAACTTGATTTTAATTTGGTGTACATTTG -s simCow_chr6.simCow.chr6 151035 21 + 602619 TT-----------------AGCTAGAAAAC-----T------------GATTTTC -s simDog_chr6.simDog.chr6 434866 33 - 593897 TTTGAGGTCTT-----ATCAGTCAGAATAC-----T------------AATTTTC -s simHuman_chr6.simHuman.chr6 137566 42 + 601863 TTTGCAATCTT-----ATAGGTTGGAAAAC-----TTTAATT---GGTAGATCCG -s simRat_chr6.simRat.chr6 140947 55 + 647215 TTGTTAGTCCCCCTGAACAAGATTTAAAAGTTGATGATAATTTGGTGTACATTTG - -a -s simMouse_chr6.simMouse.chr6 143344 81 + 636262 AATGTCCATCTTCAATAAAGGGGATAGGGTTAAATATCGCATTTAGTATTAGCTCTGACCATTTAGAATTTAATTGATGAC -s Anc0.Anc0refChr1 33994 73 - 62388 GATCTCCATCTTC-ATAAAGGGTATAGGGTGAAATTATGCCTTATGTCTTGTCC-------TTTACAATTTAATTAACAAA -s Anc1.Anc1refChr2 113091 74 + 144309 GATCTCCATCTTC-ATAAAGGGTATAGGGTGAAATTATGCCTTATGTCTTGTCCC------TTTACAATTTAATTAACAAA -s Anc2.Anc2refChr3 23105 73 + 53186 GATCTCCATCTTC-ATAAAGGGTATAGGGTGAAATTATACCTTATTTCTTGTCC-------TTTACAATTTAATTAACAAA -s mr.mrrefChr5 6727 81 + 294540 AATGTCCATCTTCAATAAAGGGTATAGGGTTAAATATCGCATTTAGTATTATCTCTGACCATTTAGAATTTAATTGATGAC -s simCow_chr6.simCow.chr6 151073 73 + 602619 GATCTCCATCTTC-ATAAAGGGTATAAGGTGAAATTAGACCTGAGCTCTTGTCC-------TTTACAATTGGATTAACAAA -s simDog_chr6.simDog.chr6 434899 72 - 593897 GATCTCCATCTTC-ATAAAGGGTAT-GGGTAAAATTATACCTTATTTCTTGTCC-------TTAACAATTTAATTAACATA -s simHuman_chr6.simHuman.chr6 137608 73 + 601863 GATCT-CATCTTC-ATAAAGGGTAAAGGGTGAGATTATGCCTTGTGTCTTGTTCC------TTTACAATTTAATTAACAAT -s simRat_chr6.simRat.chr6 141002 81 + 647215 AATGTCCGTCTTCAATAAAGGGTATAATGGTAAATGTAGCATTTAGCGTTATCTCTTACCATTTAGAGTTTACTTGATGAC - -a -s simMouse_chr6.simMouse.chr6 143425 69 + 636262 AACTTCTTGCAGTGCATGGCAGGTTCTGGGTCTGATTGAACTCCTCTCCTGGTACCTTCAGAGCCTGAT -s Anc0.Anc0refChr1 34069 35 - 62388 AACTTCTTGTGTTTCATGTCAGTTTCTGGATCTGA---------------------------------- -s Anc1.Anc1refChr2 113167 35 + 144309 AACTTCTTGTGTTTCATGTCAGTTTCTGGATCTGA---------------------------------- -s Anc2.Anc2refChr3 23180 35 + 53186 AATTTCTTGTGTTTTATGTCAGTTTCTGGATCTGA---------------------------------- -s mr.mrrefChr5 6808 68 + 294540 AACTTCTTGCAGTGCATGGCAGTTTCTGGGTCTGATTGAACTCCTCT-CTGGTACCTTCAGAGCCTGAT -s simCow_chr6.simCow.chr6 151148 35 + 602619 CATTTCTTGTGTTGTATATCAGTTTCTGGGTCTGA---------------------------------- -s simDog_chr6.simDog.chr6 434973 31 - 593897 AATTTCTGGTATTTTAAGTCAGTTTCCAGAT-------------------------------------- -s simHuman_chr6.simHuman.chr6 137683 35 + 601863 GACTTCTTGTGTTACATGTCAGTTTCTGGATCTGA---------------------------------- -s simRat_chr6.simRat.chr6 141083 68 + 647215 AACTTCTTGCAGTGCATGGCAGTTTCTGGGTCTGATTGAACTCCTCT-CTGGTACCTTCAGAGTATGGC - -a -s simMouse_chr6.simMouse.chr6 143494 15 + 636262 TGGACTCCACTCTGG -s Anc0.Anc0refChr1 34104 15 - 62388 TGGATTCCTCTATGG -s Anc1.Anc1refChr2 113202 15 + 144309 TGGATTCCTCTATGG -s Anc2.Anc2refChr3 23215 15 + 53186 TGTATTCCTCTATGG -s mr.mrrefChr5 6876 15 + 294540 TGGACTCCTCTCTGG -s simCow_chr6.simCow.chr6 151185 15 + 602619 TGTCTTCTTCCCCAG -s simDog_chr6.simDog.chr6 435004 15 - 593897 TGTATCACTCTATGG -s simHuman_chr6.simHuman.chr6 137718 15 + 601863 TAGATTCCTTTATGG -s simRat_chr6.simRat.chr6 141151 15 + 647215 TGAACTCCTCTCTGG - -a -s simMouse_chr6.simMouse.chr6 143509 13 + 636262 CTGATTTGTGTGA -s Anc0.Anc0refChr1 34131 13 - 62388 CTGATTTGTGCAA -s Anc1.Anc1refChr2 113229 13 + 144309 CTGATTTGTGCAA -s Anc2.Anc2refChr3 23245 13 + 53186 CTGATTTGTGCAA -s mr.mrrefChr5 6903 13 + 294540 CTGATTTGTGTGA -s simCow_chr6.simCow.chr6 151215 13 + 602619 CTAATTTGTGCAG -s simDog_chr6.simDog.chr6 435034 13 - 593897 TCGATTAGTGTTA -s simHuman_chr6.simHuman.chr6 137745 13 + 601863 CTGATTTGTACAA -s simRat_chr6.simRat.chr6 141181 13 + 647215 CTGATTTGTGTGA - -a -s simMouse_chr6.simMouse.chr6 143522 28 + 636262 GATGGACAGCCTCTTGGACAGTCACCCT -s Anc0.Anc0refChr1 34145 28 - 62388 GATGGACAGCCTCCTGGACAGACTCCCC -s Anc1.Anc1refChr2 113243 28 + 144309 GATGGACAGCCTCCTGGACAGACTCCCC -s Anc2.Anc2refChr3 23259 28 + 53186 GATGGACAGCCTCCTGGACAGAATCCCC -s mr.mrrefChr5 6916 28 + 294540 GATGGACAGCCTCCTGGACAGTCACCCC -s simCow_chr6.simCow.chr6 151229 28 + 602619 GTTAGATAGCCTCTTGGATAGAATCCCC -s simDog_chr6.simDog.chr6 435048 19 - 593897 GATGGACAGCTTCCTGAAC--------- -s simHuman_chr6.simHuman.chr6 137759 28 + 601863 GATGGAAAGCCTTCTGGACAGCCTCCCC -s simRat_chr6.simRat.chr6 141194 28 + 647215 GATGGACTGCCTCCTGAACAGTCACCCC - -a -s simMouse_chr6.simMouse.chr6 143550 27 + 636262 TTCAATTTGGTACAATAATTGGAGTAG -s Anc0.Anc0refChr1 34176 21 - 62388 TTCAGTTTGGTGCAATAATTG------ -s Anc1.Anc1refChr2 113274 21 + 144309 TTCAGTTTGGTGCAATAATTG------ -s Anc2.Anc2refChr3 23290 21 + 53186 TTCAGTTTGGTGGAGTCATTG------ -s mr.mrrefChr5 6944 27 + 294540 TTCAATTTGGTGCAATAATTGGAGTAG -s simCow_chr6.simCow.chr6 151260 12 + 602619 TTCAGATCGATG--------------- -s simDog_chr6.simDog.chr6 435069 21 - 593897 TTCAGTTTGGTGGAGTCATTG------ -s simHuman_chr6.simHuman.chr6 137790 21 + 601863 TTCAGTTTGGTGCAATAATTA------ -s simRat_chr6.simRat.chr6 141222 27 + 647215 TTCAATTTGGTGCAATAATTGGAGTAG - -a -s simMouse_chr6.simMouse.chr6 143577 3 + 636262 CTT -s mr.mrrefChr5 6971 3 + 294540 CTT -s simRat_chr6.simRat.chr6 141253 3 + 647215 CTT - -a -s simMouse_chr6.simMouse.chr6 143580 44 + 636262 GTAGTGTCAGATTTTTTGGTACAATAAGTGGAGGTATGGCACTT -s Anc0.Anc0refChr1 34197 15 - 62388 -----------------------------GGTGTTAGGGCATTT -s Anc1.Anc1refChr2 113295 15 + 144309 -----------------------------GGTGTTAGGGCATTT -s Anc2.Anc2refChr3 23311 15 + 53186 -----------------------------GCTGTTAGAGCATCT -s mr.mrrefChr5 6974 39 + 294540 GTAGTGTCAGATTTTT-----CAATAAGTGGAGGTAGGGCACTT -s simCow_chr6.simCow.chr6 151272 12 + 602619 --------------------------------GGTAGAGCACCT -s simDog_chr6.simDog.chr6 435092 15 - 593897 -----------------------------GCTGTTTGAACATCT -s simHuman_chr6.simHuman.chr6 137811 15 + 601863 -----------------------------GGTGATAGGGCATTT -s simRat_chr6.simRat.chr6 141262 39 + 647215 GTAGTGTTAGATTTTT-----CAATAATTGGATGTTGGGCACTT - -a -s simMouse_chr6.simMouse.chr6 143624 7 + 636262 GCAGTGT -s Anc0.Anc0refChr1 34212 7 - 62388 GAGGTGT -s Anc1.Anc1refChr2 113310 7 + 144309 GAGGTGT -s Anc2.Anc2refChr3 23335 7 + 53186 GAGGTGT -s mr.mrrefChr5 7013 7 + 294540 GCAGTGT -s simCow_chr6.simCow.chr6 151296 7 + 602619 TAGGTGT -s simDog_chr6.simDog.chr6 435116 7 - 593897 GAGGGGT -s simHuman_chr6.simHuman.chr6 137826 7 + 601863 GTGGTGT -s simRat_chr6.simRat.chr6 141301 7 + 647215 GCAGTGT - -a -s simMouse_chr6.simMouse.chr6 143631 24 + 636262 TAGGGGACCTTCTGTGGTGCATGG -s Anc0.Anc0refChr1 34219 24 - 62388 TGGAGGATCTTCTATGAAGTATGG -s Anc1.Anc1refChr2 113317 24 + 144309 TGGAGGATCTTCTATGAAGTATGG -s Anc2.Anc2refChr3 23342 24 + 53186 TGGAGGATCTGCCATGAGGTATGG -s mr.mrrefChr5 7020 24 + 294540 TAGGGGACCTTCTGTGGAGCATGG -s simCow_chr6.simCow.chr6 151303 24 + 602619 TGGAGGATCTACCATGAGGTATGG -s simDog_chr6.simDog.chr6 435123 21 - 593897 ACCAAGAGTTGCCAT---TTATGG -s simHuman_chr6.simHuman.chr6 137834 24 + 601863 TGGAGGATCCTCTACGAAGTGTGG -s simRat_chr6.simRat.chr6 141308 24 + 647215 TAGTGGACCTTCTGTGGAGCATGG - -a -s simMouse_chr6.simMouse.chr6 143655 3 + 636262 TGG -s Anc0.Anc0refChr1 34243 3 - 62388 TAG -s Anc1.Anc1refChr2 113341 3 + 144309 TAG -s Anc2.Anc2refChr3 23366 3 + 53186 TAG -s mr.mrrefChr5 7044 3 + 294540 TAG -s simCow_chr6.simCow.chr6 151327 3 + 602619 CAG -s simDog_chr6.simDog.chr6 435147 3 - 593897 TTG -s simHuman_chr6.simHuman.chr6 137858 3 + 601863 TAG -s simRat_chr6.simRat.chr6 141332 3 + 647215 TAG - -a -s simMouse_chr6.simMouse.chr6 143658 37 + 636262 CACAAAATCCTAATATATGCTTAAGTGTGGGTAAGTT -s Anc0.Anc0refChr1 34247 37 - 62388 AACAAAATCTTAATAAAGGCTTAATTGAGGGGAGGTC -s Anc1.Anc1refChr2 113345 37 + 144309 AACAAAATCTTAATAAAGGCTTAATTGAGGGGAGGTC -s Anc2.Anc2refChr3 23370 37 + 53186 AACAAAATATTAATAAAGGTATAATTGAGGGGAGGTC -s mr.mrrefChr5 7047 37 + 294540 CACAAAATCCTAATAAAGGCTTAAGTGTGGGTAGGTT -s simCow_chr6.simCow.chr6 151331 35 + 602619 --CAAAATGTCAATAAAGGTATAATTGAGGGGGAGTC -s simDog_chr6.simDog.chr6 435151 37 - 593897 AACAAAATATTCATAAAGGTATAATTGAGCTGAGATC -s simHuman_chr6.simHuman.chr6 137862 37 + 601863 AACAAGATCTTAATAAAGGCTAAATTGCGGGGAGGTC -s simRat_chr6.simRat.chr6 141335 37 + 647215 CACTAAATCCTAATAAAGACCTAAGTGTAGGTAGGTT - -a -s simMouse_chr6.simMouse.chr6 143695 10 + 636262 TAAAGTTAGT -s Anc0.Anc0refChr1 34285 5 - 62388 TAAG-----T -s Anc1.Anc1refChr2 113383 5 + 144309 TAAG-----T -s Anc2.Anc2refChr3 23408 5 + 53186 GAAG-----T -s mr.mrrefChr5 7084 5 + 294540 TAAA-----T -s simDog_chr6.simDog.chr6 435189 5 - 593897 GAAG-----T -s simHuman_chr6.simHuman.chr6 137900 5 + 601863 TAAG-----T -s simRat_chr6.simRat.chr6 141372 5 + 647215 TAAA-----T - -a -s simMouse_chr6.simMouse.chr6 143705 49 + 636262 TGGGAGGGCCTTGATTCAGATCATTCAAACTAAGGGCTGGGAGAGAGTT -s Anc0.Anc0refChr1 34290 49 - 62388 TGGCAGGCCCATGATTCGGGTCATTCAAACTGAGGAGTGAGAGGGAGCT -s Anc1.Anc1refChr2 113388 49 + 144309 TGGCAGGCCCATGATTCGGGTCATTCAAACTGAGGAGTGAGAGGGAGCT -s Anc2.Anc2refChr3 23413 49 + 53186 TGGCAGGCCCATGATTTGGGTCATTCAAACTGAGGAGTGAGAGGGAGCT -s mr.mrrefChr5 7089 49 + 294540 TGGGAGGGCCTTGATTCAGATCATTCAAACTGAGGGCTGGGAGAGAGCT -s simCow_chr6.simCow.chr6 151367 40 + 602619 ---------CATAATTTGGGTCATTCAAACTGAGGGGTAAGAGGGAGCT -s simDog_chr6.simDog.chr6 435198 49 - 593897 TGGCAGGCCCATGATTTGGGTCATTCAAAGTGAGGACTGAGAGGGAGCT -s simHuman_chr6.simHuman.chr6 137905 49 + 601863 TGGCAAGACCATGATTCGGGTCAGTCAAACTGAGGAGTGAGAGGGAGCT -s simRat_chr6.simRat.chr6 141377 49 + 647215 TGGGAGGGCCTTGAATCAGATCATTCAAACTGAGGGCTGGGAAAGAGCT - -a -s simMouse_chr6.simMouse.chr6 143754 13 + 636262 CCAAGGATCGGAA -s Anc0.Anc0refChr1 34339 13 - 62388 CCAGGGGTAGGAA -s Anc1.Anc1refChr2 113437 13 + 144309 CCAGGGGTAGGAA -s Anc2.Anc2refChr3 23462 13 + 53186 CCAGGGGTAGGAA -s mr.mrrefChr5 7138 13 + 294540 CCAGGGATCGGAA -s simCow_chr6.simCow.chr6 151408 13 + 602619 CCAGGGGTAGGAA -s simDog_chr6.simDog.chr6 435247 13 - 593897 CCAGGGGTGGGAC -s simHuman_chr6.simHuman.chr6 137954 13 + 601863 CCAGGGGTAGGAA -s simRat_chr6.simRat.chr6 141426 13 + 647215 CCCGGGTTTGGAG - -a -s simMouse_chr6.simMouse.chr6 143767 12 + 636262 GGATTGATACCC -s Anc0.Anc0refChr1 34388 12 - 62388 AAGTTGGTATTC -s Anc1.Anc1refChr2 113486 12 + 144309 AAGTTGGTATTC -s Anc2.Anc2refChr3 23517 12 + 53186 AAGTTGGTGTTC -s mr.mrrefChr5 7151 12 + 294540 GGATTGGTACCC -s simCow_chr6.simCow.chr6 151449 12 + 602619 AAGTTGGTCCCC -s simDog_chr6.simDog.chr6 435303 12 - 593897 AAGTTGGTGTTC -s simHuman_chr6.simHuman.chr6 138003 12 + 601863 AAGTTGGTATAC -s simRat_chr6.simRat.chr6 141439 11 + 647215 GGATCGGTA-CC - -a -s simMouse_chr6.simMouse.chr6 143779 18 + 636262 CATGCTGTACATTCAAGA -s Anc0.Anc0refChr1 34400 18 - 62388 CATGCTACACATTGGAGG -s Anc1.Anc1refChr2 113498 18 + 144309 CATGCTACACATTGGAGG -s Anc2.Anc2refChr3 23529 18 + 53186 CATGCTACACATTGGAGG -s mr.mrrefChr5 7163 18 + 294540 CATGCTGTACATTCAAGA -s simCow_chr6.simCow.chr6 151462 18 + 602619 CATGCCACACATTGGATG -s simDog_chr6.simDog.chr6 435315 18 - 593897 CATGTTACACCTTGGAGG -s simHuman_chr6.simHuman.chr6 138015 18 + 601863 CATGCTACACATTGGAGG -s simRat_chr6.simRat.chr6 141450 18 + 647215 CATGCTGTACATTCAAGA - -a -s simMouse_chr6.simMouse.chr6 143797 6 + 636262 TATTTT -s Anc0.Anc0refChr1 34418 6 - 62388 AAGTTT -s Anc1.Anc1refChr2 113516 6 + 144309 AAGTTT -s Anc2.Anc2refChr3 23547 6 + 53186 AAGTTC -s mr.mrrefChr5 7181 6 + 294540 TATTTT -s simCow_chr6.simCow.chr6 151480 6 + 602619 TACTCC -s simDog_chr6.simDog.chr6 435333 6 - 593897 AAGTTC -s simHuman_chr6.simHuman.chr6 138069 6 + 601863 GAGTTT -s simRat_chr6.simRat.chr6 141468 6 + 647215 TATTTT - -a -s simMouse_chr6.simMouse.chr6 143803 15 + 636262 TATAAAAAGTTAAAA -s Anc0.Anc0refChr1 34424 15 - 62388 TATAAAAAGTTAAAG -s Anc1.Anc1refChr2 113522 15 + 144309 TATAAAAAGTTAAAG -s Anc2.Anc2refChr3 23554 15 + 53186 TATAAAAAGTTAAAG -s mr.mrrefChr5 7187 15 + 294540 TATAAAAAGTTAAAA -s simCow_chr6.simCow.chr6 151487 15 + 602619 CATAAAAAGTTAGAG -s simDog_chr6.simDog.chr6 435340 15 - 593897 TATAAAAAGATAAAG -s simHuman_chr6.simHuman.chr6 138075 15 + 601863 TTTAAAAAGTTAAAG -s simRat_chr6.simRat.chr6 141474 15 + 647215 CACAAAAAGTTGAAA - -a -s simMouse_chr6.simMouse.chr6 143818 73 + 636262 CAATAGACAAAAATATACACAGTAGAGTGGGGGACCCGCCCTCAGATAAGATCTTGTTGGGTAGAGTCAATAG -s Anc0.Anc0refChr1 34450 72 - 62388 CATTAGGAAAAAACATACACAGTAGAGTGGGGGACCTGCTTTCAGATAAGACCAT-TGGGGTAGAGTCAATAG -s Anc1.Anc1refChr2 113548 73 + 144309 CATTAGGAAAAAACATACACAGTAGAGTGGGGGACCTGCTTTCAGATAAGACCATATGGGGTAGAGTCAATAG -s Anc2.Anc2refChr3 23580 72 + 53186 CATTAGGAAAAAACATACACAGTAGAGTGGGGACCCTGGTTTCAGATAAGACAAT-TGGGGTAGAGTCAATAG -s mr.mrrefChr5 7202 73 + 294540 CAATAGAAAAAAATATACACAGTAGAGTGGGGGACCTGCCCTCAGATAAGATCTTGTTGGGTAGAGTCAATAG -s simCow_chr6.simCow.chr6 151513 72 + 602619 CATTAGGAAAAAACATGCATAGTAAAGTGGGGACCCTGGTTTCAGATAAGGCAGT-TAGGGTCAAGTCAATAG -s simDog_chr6.simDog.chr6 435366 72 - 593897 CATTAGGAAACAACATACACAGTAGGGTGGGGACTCTGGTTTCAAGTAAGACAAT-AGGGGTAGAGACAATGG -s simHuman_chr6.simHuman.chr6 138101 69 + 601863 CATTAGGAAAAAACATACACAGTAGAATGGACGACCTGCATTCAGATA----CATATGGAGTAGAGTCACTAG -s simRat_chr6.simRat.chr6 141489 73 + 647215 CAATAGAAATAAAGATACACAGTAGAGTGGGGGACCTGCCCTGAGATGAGACCTTCTTGGGTAGAGTCAATAG - -a -s simMouse_chr6.simMouse.chr6 143891 113 + 636262 AAGCAAGTGGGCAAGAATTTTTAATAGTTCCTGGGTCACTACTGTACTTACACATTTTAAGCATAACTGTGCATTCACAGGACAATCTAATTCCACCTCTAATTATCGTAGTA -s Anc0.Anc0refChr1 34525 111 - 62388 AAGAAGTTGAGGTGAAATATTTAATAGTGCTTGGGTCACTAATGTGCATACACATTTTAAGCATAACTGCACTC--ACCAGACTGTCAAGTTCCATCTCTAACTATCATAGTA -s Anc1.Anc1refChr2 113624 113 + 144309 AAGAAGTTGAGGTGAAATATTTAATAGTGCTTGGGTCACTAATGTGCATACACATTTTAAGCATAACTGCACTCTCACCAGACTGTCAAGTTCCATCTCTAACTATCATAGTA -s Anc2.Anc2refChr3 23655 111 + 53186 AAGAAGTTGAGGTGAAATATTTAATAGTGCTTGGGTCACTAATGTGCATACACATTTTAAGCCTAACTGCACTC--ACCAGACTATCCAGTTTCATCTCTAACTATTACAGTA -s mr.mrrefChr5 7275 113 + 294540 AAGCAGGTGGGCAAGAATTTTTAATAGTTCCTGGGTCACTAATGTGCTTACACATTTTAAGCATAACTGTGCATTCACAGGACAGTCAAATTCCACCTCTAACTATCATAGTA -s simCow_chr6.simCow.chr6 151588 111 + 602619 AAGAAGTTGAGGTGGGATATTTAATAGTGCTTGGGTCCCTCATGTGCCTACACAGTTTAAGCGTAAGTGCACTC--GCCAGACTACTGAGGATCATCTCTAACTGTTACAGTG -s simDog_chr6.simDog.chr6 435440 110 - 593897 AAGAAGTCAAGGTGAAATATTTAATAGTGCTTGGGTCACTAATGTGTATACACATTCTAAGTCTAACTGCACT---ACTGGACCATCCAGTTTCAGCTTGAAATATTTCAGTA -s simHuman_chr6.simHuman.chr6 138173 113 + 601863 AAGAAGTTGAGGTGAAATGTCTAATTATGCTTGGGTCACTAATGTGCATACACATTTTAAGCATAACTGCACTCTGACCAGACTGTCAATTTCCATCACTAACTATCATAGTA -s simRat_chr6.simRat.chr6 141562 113 + 647215 AACCCGGTGGGCCAGAATTTATAATAGTTCCTGAGTCACTAATGTGCTTACACATTTTAAGCATAACTGTGCATTCATAGGATGGTCAAGCTCGAACTCTAACTATCATAGTC - -a -s simMouse_chr6.simMouse.chr6 144004 32 + 636262 GTGTAAAAGTGGATAATGTGTGCTTAGTCTAA -s Anc0.Anc0refChr1 34636 30 - 62388 GTCTAAAA--GGAGAATCTACACTGAGTCTAA -s Anc1.Anc1refChr2 113737 30 + 144309 GTCTAAAA--GGAGAATCTACACTGAGTCTAA -s Anc2.Anc2refChr3 23766 30 + 53186 GTCTAAAA--GTAGAATCTACACTGAGTCTAA -s mr.mrrefChr5 7388 32 + 294540 GTGTAAAAGTGGAGAATGTGCACTTAGTCTAA -s simCow_chr6.simCow.chr6 151699 28 + 602619 GTC--AAA--GTAGATTCTACACTGAGTCCAA -s simDog_chr6.simDog.chr6 435551 26 - 593897 GTCTAAAA--GTAGGACCTACAT----TCTAA -s simHuman_chr6.simHuman.chr6 138286 30 + 601863 GTCTAAAA--GGAGAATCTACACCCTGTCTAA -s simRat_chr6.simRat.chr6 141675 32 + 647215 ATATAAAAGTGGAGAATGTGCATTTAGCCTAA - -a -s simMouse_chr6.simMouse.chr6 144036 27 + 636262 TTATAAAGAAATCGAATTCCATCCTTT -s Anc0.Anc0refChr1 34666 27 - 62388 AAATAAAGAAATAGTATTCCACCCTTT -s Anc1.Anc1refChr2 113767 27 + 144309 AAATAAAGAAATAGTATTCCACCCTTT -s Anc2.Anc2refChr3 23796 27 + 53186 AAATAAGGAAATAGTATCCCACCCTTT -s mr.mrrefChr5 7420 27 + 294540 TTATAAAGAAATCGAATTCCACCCTTT -s simCow_chr6.simCow.chr6 151727 27 + 602619 AAATAAGGAAATAGTAGCCCACCCTCT -s simDog_chr6.simDog.chr6 435577 27 - 593897 AAATAAGGAAATAGTATCCCACCCTTT -s simHuman_chr6.simHuman.chr6 138316 27 + 601863 AAATAAAGAAATAGTATTTCACCCTTT -s simRat_chr6.simRat.chr6 141708 27 + 647215 TTATAAAGAAATCGAATCCCACCCTTT - -a -s simMouse_chr6.simMouse.chr6 144063 64 + 636262 CTTAGCTTTCTGGCTTGGATCTTTTACAAATCCACCTATCAGTACACTTGCAGCAGTAATTAAA -s Anc0.Anc0refChr1 34693 11 - 62388 CTCAA-A----------------------------------------------------TCAAG -s Anc1.Anc1refChr2 113794 12 + 144309 CTCAACA----------------------------------------------------TCAAG -s Anc2.Anc2refChr3 23823 11 + 53186 CTCAA-A----------------------------------------------------TCAAG -s mr.mrrefChr5 7447 12 + 294540 CTTAGCT----------------------------------------------------TTAAA -s simCow_chr6.simCow.chr6 151789 11 + 602619 CTCAA-A----------------------------------------------------TTAAG -s simDog_chr6.simDog.chr6 435604 11 - 593897 CTCAA-A----------------------------------------------------TCAAG -s simHuman_chr6.simHuman.chr6 138343 12 + 601863 CTCGACA----------------------------------------------------TCAAG -s simRat_chr6.simRat.chr6 141735 12 + 647215 CTTAGCT----------------------------------------------------TTAAC - -a -s simMouse_chr6.simMouse.chr6 144127 2 + 636262 GG -s Anc0.Anc0refChr1 34704 2 - 62388 GC -s Anc1.Anc1refChr2 113806 2 + 144309 GC -s Anc2.Anc2refChr3 23834 2 + 53186 GC -s mr.mrrefChr5 7459 2 + 294540 GG -s simCow_chr6.simCow.chr6 151800 2 + 602619 GT -s simDog_chr6.simDog.chr6 435676 2 - 593897 GC -s simHuman_chr6.simHuman.chr6 138355 2 + 601863 GC -s simRat_chr6.simRat.chr6 141747 2 + 647215 GG - -a -s simMouse_chr6.simMouse.chr6 144129 86 + 636262 ATTCTATGTTGTGGCCCCAAGTCACTTTTGTGTTATACCATCTCAATATACAGGTTAGATGATCTATTAATGCAAAGATCTGCGCT -s Anc0.Anc0refChr1 34707 37 - 62388 GTTTCATGTTGT-ACCCCAAGGCAGTTTCATGTTGTAC------------------------------------------------ -s Anc1.Anc1refChr2 113809 69 + 144309 GTTTCATGTTGT-ACCCCAAGGCAGTTTCATGTTGTACCATCTCAACATACAGATAAGA----CTACTA----CAAGA-------- -s Anc2.Anc2refChr3 23837 37 + 53186 GTTTCATGTTGT-ACCCCAAGGAAGTTTCATGTTGTAC------------------------------------------------ -s mr.mrrefChr5 7462 85 + 294540 ATTCCATGTTGT-GCCCCAAGTCACTTTTGTGTTATACCATCTCAATATACAGGTTAGATGATCTACTAATGCAAAGATCTGCGCT -s simCow_chr6.simCow.chr6 151803 37 + 602619 GTTTCATGTTGT-CTCCCAAGGAACTTTTATGTTGTGC------------------------------------------------ -s simDog_chr6.simDog.chr6 435679 37 - 593897 ATTTCTTGTTAT-ACCCCAAGGAAGTTTCATGTTGTAC------------------------------------------------ -s simHuman_chr6.simHuman.chr6 138358 69 + 601863 GTTTCATTTTGT-ACCCCGAGGCAGTTTCATGTCGTACCATCTCAACATACAGATAAGA----CTACTA----CAAGA-------- -s simRat_chr6.simRat.chr6 141750 85 + 647215 ATTCCATGTTGT-GCCCCAGGTCATTTTTGTGTTATACCTTCTCAATATACAGGCTAGATGATCTACTGATGCAAAGATCTGCACT - -a -s simMouse_chr6.simMouse.chr6 144215 39 + 636262 TAAAACTGCTTTAATCCAAAAGTTTGGGGCGAGTGCTAA -s Anc0.Anc0refChr1 34744 30 - 62388 ---------TTTAATCTAAATGACTGTGGGGAGTGCTAA -s Anc1.Anc1refChr2 113878 38 + 144309 -AATTCCCCTTTAATCTAAATGACTGTGGGGAGTGCTAA -s Anc2.Anc2refChr3 23874 30 + 53186 ---------TTTAATCTAAATGACTGTGGGAAGTGCTAA -s mr.mrrefChr5 7547 39 + 294540 TAAAACTGCTTTAATCTAAAAGTTTGGGGCGAGTGCTAA -s simCow_chr6.simCow.chr6 151840 29 + 602619 ---------TTTAATCTAAATGTCTGTTGGAA-GGCTCA -s simDog_chr6.simDog.chr6 435716 30 - 593897 ---------TCTAATTTAAATGACTGTGGGAAGTGCTAG -s simHuman_chr6.simHuman.chr6 138427 38 + 601863 -AATTCCCCTTTGATCTCAATGACTGTGGGGGATGGTAA -s simRat_chr6.simRat.chr6 141839 39 + 647215 TAAAACTGCTTTAATCTAAAAGGTTGGGGTGAGAGCTAA - -a -s simMouse_chr6.simMouse.chr6 144254 5 + 636262 TTGTA -s Anc0.Anc0refChr1 34775 5 - 62388 TTATA -s Anc1.Anc1refChr2 113917 5 + 144309 TTATA -s Anc2.Anc2refChr3 23905 5 + 53186 TTATA -s mr.mrrefChr5 7587 5 + 294540 TTGTA -s simCow_chr6.simCow.chr6 151870 5 + 602619 TTATG -s simDog_chr6.simDog.chr6 435747 5 - 593897 ATATA -s simHuman_chr6.simHuman.chr6 138466 5 + 601863 TTATA -s simRat_chr6.simRat.chr6 141879 5 + 647215 TTGTA - -a -s simMouse_chr6.simMouse.chr6 144259 42 + 636262 AGGTCCCTCATGCCTCATCCATAGGATGCTAGACTTGTTGGA -s Anc0.Anc0refChr1 34790 42 - 62388 AGGCCCCTCATGTTTCATCCATGGGATGCTAGATTTGTTGAA -s Anc1.Anc1refChr2 113932 42 + 144309 AGGCCCCTCATGTTTCATCCATGGGATGCTAGATTTGTTGAA -s Anc2.Anc2refChr3 23920 42 + 53186 AGGCCCCTCATGTTTCATCCATGGGATGCTAGACTTGTTAAA -s mr.mrrefChr5 7592 42 + 294540 AGGTCCCTCATGCCTCATCCATAGGATGCTAGATTTGTTGGA -s simCow_chr6.simCow.chr6 151885 40 + 602619 AGGCGCCATATATGTCATCCATGGGATGCTAAACTTGT--AA -s simDog_chr6.simDog.chr6 435762 42 - 593897 AGGCCCCTCATGTTTCATCCATGGGATGCTAGACTTGTTAAA -s simHuman_chr6.simHuman.chr6 138481 42 + 601863 AGGCCCCTAATGTTTCTTCCATGGGACGCTAGGTTCGTTGAA -s simRat_chr6.simRat.chr6 141884 42 + 647215 AGGTCCCTCATGCCTCATCTGTAGGATGCTAGATTTGTTGGA - -a -s simMouse_chr6.simMouse.chr6 144301 5 + 636262 CTTCC -s Anc0.Anc0refChr1 34832 5 - 62388 CTCCC -s Anc1.Anc1refChr2 113974 5 + 144309 CTCCC -s Anc2.Anc2refChr3 23962 5 + 53186 CTCTC -s mr.mrrefChr5 7634 5 + 294540 CTTCC -s simCow_chr6.simCow.chr6 151925 5 + 602619 CTCTC -s simDog_chr6.simDog.chr6 435804 5 - 593897 CTGTC -s simHuman_chr6.simHuman.chr6 138523 5 + 601863 CCCCC -s simRat_chr6.simRat.chr6 141961 5 + 647215 CTTCC - -a -s simMouse_chr6.simMouse.chr6 144306 11 + 636262 CCTATGTTACA -s Anc0.Anc0refChr1 34842 11 - 62388 CCTATGTTACA -s Anc1.Anc1refChr2 113984 11 + 144309 CCTATGTTACA -s Anc2.Anc2refChr3 23972 11 + 53186 CCTATGTTACA -s mr.mrrefChr5 7639 11 + 294540 CCTATGTTACA -s simCow_chr6.simCow.chr6 151935 11 + 602619 CCTATGTTCCA -s simDog_chr6.simDog.chr6 435814 11 - 593897 CCTATGTTACA -s simHuman_chr6.simHuman.chr6 138533 11 + 601863 CCTATGTTACA -s simRat_chr6.simRat.chr6 141966 11 + 647215 CCTATGTTACA - -a -s simMouse_chr6.simMouse.chr6 144317 4 + 636262 GTTA -s Anc0.Anc0refChr1 34853 4 - 62388 ATCA -s Anc1.Anc1refChr2 113995 4 + 144309 ATCA -s Anc2.Anc2refChr3 23983 4 + 53186 ATCA -s mr.mrrefChr5 7650 4 + 294540 ATCA -s simCow_chr6.simCow.chr6 151957 4 + 602619 ATTA -s simDog_chr6.simDog.chr6 435825 4 - 593897 ATCA -s simHuman_chr6.simHuman.chr6 138544 4 + 601863 ATCA -s simRat_chr6.simRat.chr6 141977 4 + 647215 ATCA - -a -s simMouse_chr6.simMouse.chr6 144321 17 + 636262 GTGAATTGTTGCCAGCA -s Anc0.Anc0refChr1 34861 17 - 62388 CTGTATTGTTATTAGCA -s Anc1.Anc1refChr2 114003 17 + 144309 CTGTATTGTTATTAGCA -s Anc2.Anc2refChr3 23991 17 + 53186 CTTTATTGTTATTAGCA -s mr.mrrefChr5 7654 17 + 294540 GTGAATTGTTGTCAGCA -s simCow_chr6.simCow.chr6 151965 17 + 602619 CAACTTTGTTATTTGTA -s simDog_chr6.simDog.chr6 435833 17 - 593897 CTTTATTGTTATTAGCA -s simHuman_chr6.simHuman.chr6 138552 17 + 601863 TTGTGCTGTTATGAGCA -s simRat_chr6.simRat.chr6 141981 17 + 647215 ATGAATTGTCGTTAGCA - -a -s simMouse_chr6.simMouse.chr6 144338 41 + 636262 GATTTGTACACAGTCAATGGCAAGTCGTTTTATAAAGTGTG -s Anc0.Anc0refChr1 34878 39 - 62388 GG-TTGTGTACAGTCACCGACTAGTTTTTTTATGAACTGT- -s Anc1.Anc1refChr2 114020 40 + 144309 GG-TTGTGTACAGTCACCGACTAGTTTTTTTATGAACTGTT -s Anc2.Anc2refChr3 24008 39 + 53186 GG-TTGTGTACAGTCACCTACTAGTTTTTATATGAAGTGT- -s mr.mrrefChr5 7671 41 + 294540 GGTTTGTACACAGTCAATGGCAAGTCGTTTTATGAACTGTG -s simCow_chr6.simCow.chr6 151982 25 + 602619 GG-TAATGTACTATCT--------------GATGAAGTGT- -s simDog_chr6.simDog.chr6 435850 39 - 593897 GG-TTGTGTGCAGTCACCTACTAGTTTTTATATGAAGTGT- -s simHuman_chr6.simHuman.chr6 138569 40 + 601863 GG-TTGTGTACAGTGATCGCTCAGTTAGCTTATGGACTGTT -s simRat_chr6.simRat.chr6 141999 41 + 647215 GGTGTGTACACAGTCAATCACAAGTCGTTTTATGAACTGTG - -a -s simMouse_chr6.simMouse.chr6 144379 20 + 636262 ACCCTCATTAGAGGGTAGGC -s Anc0.Anc0refChr1 34922 19 - 62388 ACCATTA-TGGAGGATAGAC -s Anc1.Anc1refChr2 114065 19 + 144309 ACCATTA-TGGAGGATAGAC -s Anc2.Anc2refChr3 24052 19 + 53186 ACCATTA-TGGAGGATAGAG -s mr.mrrefChr5 7712 20 + 294540 ACCATCATTAGAGGGTAGGC -s simCow_chr6.simCow.chr6 152011 18 + 602619 ACCA-TA-TGGAGGATAGGG -s simDog_chr6.simDog.chr6 435894 19 - 593897 TCCATTG-TAGATGATAGAA -s simHuman_chr6.simHuman.chr6 138614 19 + 601863 ACCACTA-TGGAGGATAGCC -s simRat_chr6.simRat.chr6 142040 20 + 647215 ACCACCATTAGAGGGTAGGC - -a -s simMouse_chr6.simMouse.chr6 144399 16 + 636262 TATCTATAGTTCCACA -s Anc0.Anc0refChr1 34941 16 - 62388 GATCTATAATCACATT -s Anc1.Anc1refChr2 114084 16 + 144309 GATCTATAATCACATT -s Anc2.Anc2refChr3 24071 16 + 53186 GTTCCATAATCACATT -s mr.mrrefChr5 7732 16 + 294540 TATCTATAGTTCCACA -s simCow_chr6.simCow.chr6 152029 16 + 602619 ATTCCACAGTCACATT -s simDog_chr6.simDog.chr6 435913 16 - 593897 GTTCCATAATCGCATT -s simHuman_chr6.simHuman.chr6 138641 16 + 601863 GAGCTATGATCACATT -s simRat_chr6.simRat.chr6 142060 16 + 647215 TATCTATAGTTACACA - -a -s simMouse_chr6.simMouse.chr6 144415 3 + 636262 GAA -s Anc0.Anc0refChr1 34957 3 - 62388 GAG -s Anc1.Anc1refChr2 114100 3 + 144309 GAG -s Anc2.Anc2refChr3 24087 3 + 53186 GAG -s mr.mrrefChr5 7748 3 + 294540 GAA -s simCow_chr6.simCow.chr6 152045 3 + 602619 GAG -s simDog_chr6.simDog.chr6 435929 3 - 593897 GAG -s simHuman_chr6.simHuman.chr6 138657 3 + 601863 GAG -s simRat_chr6.simRat.chr6 142079 3 + 647215 GAA - -a -s simMouse_chr6.simMouse.chr6 144418 18 + 636262 GGCTATAGCCAGACTGTA -s Anc0.Anc0refChr1 34960 18 - 62388 ATCGATGGCCACATTGAC -s Anc1.Anc1refChr2 114103 18 + 144309 ATCGATGGCCACATTGAC -s Anc2.Anc2refChr3 24091 18 + 53186 ATCGATGGCCACATTGAC -s mr.mrrefChr5 7751 18 + 294540 GGCTATAGCCACACTGTA -s simCow_chr6.simCow.chr6 152049 18 + 602619 AGCTATGGCCACATTGAA -s simDog_chr6.simDog.chr6 435933 18 - 593897 ATCGATGGCCACATTAAC -s simHuman_chr6.simHuman.chr6 138660 8 + 601863 ----------ACATTGAG -s simRat_chr6.simRat.chr6 142082 18 + 647215 GGCTACAGCCACTCTGTA - -a -s simMouse_chr6.simMouse.chr6 144436 4 + 636262 AAGG -s Anc0.Anc0refChr1 34978 4 - 62388 GAGG -s Anc1.Anc1refChr2 114121 4 + 144309 GAGG -s Anc2.Anc2refChr3 24109 4 + 53186 GAGG -s mr.mrrefChr5 7769 4 + 294540 AAGG -s simCow_chr6.simCow.chr6 152067 4 + 602619 TAGG -s simDog_chr6.simDog.chr6 435951 4 - 593897 GAGG -s simHuman_chr6.simHuman.chr6 138668 4 + 601863 CAGG -s simRat_chr6.simRat.chr6 142101 4 + 647215 AAGT - -a -s simMouse_chr6.simMouse.chr6 144440 18 + 636262 TTCACATTCAACTATCTG -s Anc0.Anc0refChr1 34983 18 - 62388 TTCACATTCAACTGTCTA -s Anc1.Anc1refChr2 114126 18 + 144309 TTCACATTCAACTGTCTA -s Anc2.Anc2refChr3 24114 18 + 53186 TTCACATTCAACTGTCTA -s mr.mrrefChr5 7773 18 + 294540 TTCACATTCAACTATCTG -s simCow_chr6.simCow.chr6 152072 18 + 602619 TTCACCTTCAATTGTCTA -s simDog_chr6.simDog.chr6 435956 18 - 593897 TTCACATTCGACTGTCTA -s simHuman_chr6.simHuman.chr6 138673 18 + 601863 TTCACGTTCAACTGTGTA -s simRat_chr6.simRat.chr6 142105 18 + 647215 TTCATATTCAACTATCTG - -a -s simMouse_chr6.simMouse.chr6 144458 24 + 636262 CTCAAGCTGCCTTGCCATTATGTT -s Anc0.Anc0refChr1 35001 11 - 62388 CTCAGACTG-CT------------ -s Anc1.Anc1refChr2 114144 23 + 144309 CTCAGACTG-CTTGCAGAAATGTT -s Anc2.Anc2refChr3 24132 11 + 53186 CCCAGACTG-CT------------ -s mr.mrrefChr5 7791 24 + 294540 CTCAGGCTGCCTTGCCATTATGTT -s simCow_chr6.simCow.chr6 152090 11 + 602619 CCCAAACTG-CT------------ -s simDog_chr6.simDog.chr6 435974 11 - 593897 CCCTGACTA-CT------------ -s simHuman_chr6.simHuman.chr6 138691 23 + 601863 CTCAGCCTG-CTTGCAGAAATGTT -s simRat_chr6.simRat.chr6 142125 24 + 647215 CTCAGGCTGCCTCACCATTATGTT - -a -s simMouse_chr6.simMouse.chr6 144482 6 + 636262 CACCTT -s Anc1.Anc1refChr2 114167 6 + 144309 TAACTT -s mr.mrrefChr5 7815 6 + 294540 TACCTT -s simHuman_chr6.simHuman.chr6 138716 6 + 601863 TAACTT -s simRat_chr6.simRat.chr6 142149 6 + 647215 TACTGT - -a -s simMouse_chr6.simMouse.chr6 144488 11 + 636262 GTCCTATGACT -s Anc1.Anc1refChr2 114173 11 + 144309 GGCATATGTCC -s mr.mrrefChr5 7821 11 + 294540 GTCCTATGACT -s simHuman_chr6.simHuman.chr6 138729 11 + 601863 GGCATATGTCC -s simRat_chr6.simRat.chr6 142155 11 + 647215 GTCCTGCGAGT - -a -s simMouse_chr6.simMouse.chr6 144499 25 + 636262 CATTGTTGTGTCTGCAATGTCCCGT -s Anc0.Anc0refChr1 35013 25 - 62388 CACTATTGTGTGTGCCATGTCCTCT -s Anc1.Anc1refChr2 114186 25 + 144309 CACTATTGTGTGTGCCATGTCCTCT -s Anc2.Anc2refChr3 24144 25 + 53186 CACTATTGTGCTCACCATGTCCCCT -s mr.mrrefChr5 7832 25 + 294540 CATTGTTGTGTGTGCAATGTCCTGT -s simCow_chr6.simCow.chr6 152102 25 + 602619 CACTCTGGTGCTCACCATGTCCCCT -s simDog_chr6.simDog.chr6 435986 11 - 593897 CACTATTGTGC-------------- -s simHuman_chr6.simHuman.chr6 138750 25 + 601863 CACTAGTGTGTGTGCCATGTCTTCT -s simRat_chr6.simRat.chr6 142166 25 + 647215 CATTGTTGTGTGTGCAACGTTCTGT - -a -s simMouse_chr6.simMouse.chr6 144524 96 + 636262 GACTGGTGTGCAAGGCAAGCCATAACACTGCTCAAATCCCATCATATGTCACATGCCATCATAGCTCATTCTTTCAAACTTCTGCTTTGGATGAAT -s Anc0.Anc0refChr1 35043 79 - 62388 AACTAGTGTGCAAGGGAAGCCATATCACCTCTCAAATCCTGTCATATCTAATA----------------TCTTTGGAATTTCT-CTTTGAATTGAT -s Anc1.Anc1refChr2 114216 79 + 144309 AACTAGTGTGCAAGGGAAGCCATATCACCTCTCAAATCCTGTCATATCTAATA----------------TCTTTGGAATTTCT-CTTTGAATTGAT -s Anc2.Anc2refChr3 24174 79 + 53186 ACCTAGTGTGCAAGGGAAGCCATGTCACCTCTCAAATCCTGTCATAACCAATC----------------TCTTTGGGATGTCT-CTCTGAATTGAC -s mr.mrrefChr5 7857 96 + 294540 GACTGGTGTGCAAGGGAAGCCATAACACCTCTCAAATCCCATCATATGTCACATGCCATCATAGCTCATTCTTTCAAACTTCTGCTTTGGATGAAT -s simCow_chr6.simCow.chr6 152132 66 + 602619 A-CTAATGTGCAAGGGAAGCCATGTAACCTCTCAAATC-TGTCATAC---------------------------AGGATATCC-CTCTGACGTAAC -s simDog_chr6.simDog.chr6 436002 70 - 593897 ACCTAGTCTAC---------CATGTCACCTCTCAAATCCTGTCATAACCAATC----------------TCTTTGGGATGGCT-CTCTGAATCGAC -s simHuman_chr6.simHuman.chr6 138780 79 + 601863 AACTAGTGTGCAAGGGAAGTCATATCACCTCTCAAATCAGGTCATATCTGAAA----------------CCTTTGGAATTTCT-CTTCGAATTGGT -s simRat_chr6.simRat.chr6 142191 96 + 647215 GACTTGTGTGCAAGGGAAGCCGTAACACCTCTCAAATCCAATCATACATCATATACCATCATACCTCATTTTTTCAGACTTTTACTTTGGATGAAT - -a -s simMouse_chr6.simMouse.chr6 144620 31 + 636262 GTAGTGGTCCTTTGGAGCAAACAAATGCAAT -s Anc0.Anc0refChr1 35126 27 - 62388 GTTGTTAGCCCATGGAA----AAACTGCCAG -s Anc1.Anc1refChr2 114299 31 + 144309 GTTGTTAGCCCATGGAACCAGAAACTGCCAG -s Anc2.Anc2refChr3 24257 27 + 53186 ATTGTTAGTCCATGGAA----AAACTGCCAA -s mr.mrrefChr5 7953 31 + 294540 GTAGTTGTCCTTTGGAGCAAACAAATGCAAG -s simCow_chr6.simCow.chr6 152202 27 + 602619 CTTGTTAGTCAATGGAT----AAACTCCGAA -s simDog_chr6.simDog.chr6 436076 27 - 593897 ATTGTTAATCCATGGAA----AAACTGCCAA -s simHuman_chr6.simHuman.chr6 138863 31 + 601863 GTTGTTAGCCCATGGAACCAGAAACTGCCAG -s simRat_chr6.simRat.chr6 142287 31 + 647215 CTAGTTGTTATTTGGAGTAAACAAATGCACG - -a -s simMouse_chr6.simMouse.chr6 144651 1 + 636262 G -s Anc0.Anc0refChr1 35153 1 - 62388 G -s Anc1.Anc1refChr2 114330 1 + 144309 G -s Anc2.Anc2refChr3 24286 1 + 53186 G -s mr.mrrefChr5 7984 1 + 294540 G -s simCow_chr6.simCow.chr6 152231 1 + 602619 G -s simDog_chr6.simDog.chr6 436105 1 - 593897 G -s simHuman_chr6.simHuman.chr6 138894 1 + 601863 G -s simRat_chr6.simRat.chr6 142318 1 + 647215 G - -a -s simMouse_chr6.simMouse.chr6 144652 19 + 636262 CAGGTGTCCTGTGATCAAT -s Anc0.Anc0refChr1 35154 19 - 62388 CAGATATCCTGCAATTAGT -s Anc1.Anc1refChr2 114331 19 + 144309 CAGATATCCTGCAATTAGT -s Anc2.Anc2refChr3 24287 19 + 53186 CAGATATCCTGCAATTAGT -s mr.mrrefChr5 7985 19 + 294540 CAGGTATCCTGTGATCAAT -s simCow_chr6.simCow.chr6 152236 19 + 602619 CAGATGTCCTGCAATTAGC -s simDog_chr6.simDog.chr6 436106 19 - 593897 TAAATATCCTGCGGTTAGT -s simHuman_chr6.simHuman.chr6 138895 19 + 601863 CAGATATCCTGCAATTATT -s simRat_chr6.simRat.chr6 142319 19 + 647215 CAGGTATCTTGTGATCAGT - -a -s simMouse_chr6.simMouse.chr6 144671 12 + 636262 AGTGGTCTCCCA -s Anc0.Anc0refChr1 35181 12 - 62388 AGTGGTCATCTG -s Anc1.Anc1refChr2 114358 12 + 144309 AGTGGTCATCTG -s Anc2.Anc2refChr3 24314 12 + 53186 AGTGGTCATCTG -s mr.mrrefChr5 8012 12 + 294540 AGTGGTCTCCCA -s simCow_chr6.simCow.chr6 152263 12 + 602619 AGTGGTCATTTG -s simDog_chr6.simDog.chr6 436133 12 - 593897 AGTGGCCATCTG -s simHuman_chr6.simHuman.chr6 138922 12 + 601863 AGTGTTAGTCTG -s simRat_chr6.simRat.chr6 142346 12 + 647215 AGTGGTTTCCCA - -a -s simMouse_chr6.simMouse.chr6 144683 15 + 636262 CTCATTAGCAGTGAA -s Anc0.Anc0refChr1 35197 11 - 62388 ATCGATAGC----AA -s Anc1.Anc1refChr2 114374 11 + 144309 ATCGATAGC----AA -s Anc2.Anc2refChr3 24330 11 + 53186 ATCGATAGC----AA -s mr.mrrefChr5 8024 15 + 294540 CTCATTAGCAGTGAA -s simCow_chr6.simCow.chr6 152279 11 + 602619 ATTGATTGC----AA -s simDog_chr6.simDog.chr6 436149 11 - 593897 ATCAATAAC----AG -s simHuman_chr6.simHuman.chr6 138938 11 + 601863 ATCGATCGT----AA -s simRat_chr6.simRat.chr6 142358 15 + 647215 ATCATTAGCAGTGAA - -a -s simMouse_chr6.simMouse.chr6 144698 31 + 636262 TTCAGCTCCCTTGGACATCCTTTGGTCATCA -s Anc0.Anc0refChr1 35208 28 - 62388 TTGATCTC---TTGTCAGAGTAGGGTTGTTA -s Anc1.Anc1refChr2 114385 28 + 144309 TTGATCTC---TTGTCAGAGTAGGGTTGTTA -s Anc2.Anc2refChr3 24341 28 + 53186 TTGATCTC---TTGTCAGAGTAGGGGTGTTA -s mr.mrrefChr5 8039 31 + 294540 TTCAGCTCCCTTGGACATCCTTTGGTCATCA -s simCow_chr6.simCow.chr6 152290 25 + 602619 ---ATCAC---TTGTCAAAGTAGAAGTGTTA -s simDog_chr6.simDog.chr6 436163 28 - 593897 TTGGTCTT---TTGTCGGAGTAGGGGCATTA -s simHuman_chr6.simHuman.chr6 138949 28 + 601863 TTGATCTC---TTGTCAGAGTAAGGTTGTTA -s simRat_chr6.simRat.chr6 142373 31 + 647215 TTCAGCCCCCTTGGACATGCCTTGGTCATCA - -a -s simMouse_chr6.simMouse.chr6 144729 6 + 636262 TTTTTC -s Anc0.Anc0refChr1 35236 6 - 62388 TTTTTC -s Anc1.Anc1refChr2 114413 6 + 144309 TTTTTC -s Anc2.Anc2refChr3 24369 6 + 53186 CTTTTG -s mr.mrrefChr5 8070 6 + 294540 TTTTTC -s simCow_chr6.simCow.chr6 152315 6 + 602619 CATTTG -s simDog_chr6.simDog.chr6 436191 6 - 593897 CTTTTG -s simHuman_chr6.simHuman.chr6 138985 6 + 601863 TTTCTC -s simRat_chr6.simRat.chr6 142404 6 + 647215 TTTTTC - -a -s simMouse_chr6.simMouse.chr6 144735 17 + 636262 CTATAAAATGCTTTTTA -s Anc0.Anc0refChr1 35242 17 - 62388 CTAGAAAATGTTTTTTA -s Anc1.Anc1refChr2 114419 17 + 144309 CTAGAAAATGTTTTTTA -s Anc2.Anc2refChr3 24376 17 + 53186 CTAGAAAATATTTTTTA -s mr.mrrefChr5 8076 17 + 294540 CTATAAAATGCTTTTTA -s simCow_chr6.simCow.chr6 152322 17 + 602619 CTAGAAAACATTTCTTA -s simDog_chr6.simDog.chr6 436198 16 - 593897 C-AGAAAATATTCTTTA -s simHuman_chr6.simHuman.chr6 138991 17 + 601863 ATAGAAAATGTTTTTTA -s simRat_chr6.simRat.chr6 142410 17 + 647215 CTAAAAAATGGTTTTTA - -a -s simMouse_chr6.simMouse.chr6 144752 20 + 636262 CTTTTGACAGGAAACACTAA -s Anc0.Anc0refChr1 35259 20 - 62388 ATTATGATAGCTATCACCAA -s Anc1.Anc1refChr2 114436 20 + 144309 ATTATGATAGCTATCACCAA -s Anc2.Anc2refChr3 24393 20 + 53186 TTTATGATAGCTATCACCAA -s mr.mrrefChr5 8093 20 + 294540 ATTTTGACAGGAAACACTAA -s simCow_chr6.simCow.chr6 152340 20 + 602619 CTTATGATAGCTATCACTAG -s simDog_chr6.simDog.chr6 436214 20 - 593897 TTTATGGTAGCTATCACCAA -s simHuman_chr6.simHuman.chr6 139008 20 + 601863 ATTATGATAGCTATAACCAA -s simRat_chr6.simRat.chr6 142427 20 + 647215 ACTTTGACAGTAAACACTAA - -a -s simMouse_chr6.simMouse.chr6 144772 66 + 636262 TGCCCTTATGTAGATTTGCTCTATTTGTAGGTATTGCGCACAGTACCCCAGTGAGAGTGTTAACGA -s Anc0.Anc0refChr1 35279 65 - 62388 TGCCCTTATATAGATTTGTTTTTTTTGTAGGTATTGTGTATGCTA-CACAGTGAGAGTACTAGCCA -s Anc1.Anc1refChr2 114456 65 + 144309 TGCCCTTATATAGATTTGTTTTTTTTGTAGGTATTGTGTATGCTA-CACAGTGAGAGTACTAGCCA -s Anc2.Anc2refChr3 24413 65 + 53186 TGACCCTACATAGATTTGTTTCTTTTGTGGGTATTGTGTATGCTA-CACAGTGAGAGTACTAACCA -s mr.mrrefChr5 8113 66 + 294540 TGCCCTTATGTAGATTTGCTCTATTTGTAGGTATTGCGCACAGTACCCCAGTGAGAGTATTAGCCA -s simCow_chr6.simCow.chr6 152360 63 + 602619 TGACCCTACTTAGACCTGCTTCTTTTGTGGATATTGTGTATGCTA-CGCAG--AGAGTACTGACTC -s simDog_chr6.simDog.chr6 436234 58 - 593897 TGACCCTACATAAATTTGTGTC-------GGCATCATGTATGCTA-CACAGTGTGAGTACCAACCA -s simHuman_chr6.simHuman.chr6 139030 65 + 601863 TGCTCTTATATAGGTTTGTTTTTTTTGAAGGTACTGTGTATGCTG-CACAGTGAGAGTACTTGCCA -s simRat_chr6.simRat.chr6 142447 57 + 647215 TGCCCT----TAGATTTCCTCTATTTGTAGG-----CACGCAGTACCTTAGTGAGAGCATTAGCCA - -a -s simMouse_chr6.simMouse.chr6 144838 3 + 636262 ACA -s Anc0.Anc0refChr1 35344 3 - 62388 ACA -s Anc1.Anc1refChr2 114521 3 + 144309 ACA -s Anc2.Anc2refChr3 24478 3 + 53186 CTG -s mr.mrrefChr5 8179 3 + 294540 ACA -s simCow_chr6.simCow.chr6 152423 3 + 602619 ATG -s simDog_chr6.simDog.chr6 436292 3 - 593897 CTG -s simHuman_chr6.simHuman.chr6 139096 3 + 601863 ACA -s simRat_chr6.simRat.chr6 142504 3 + 647215 ACA - -a -s simMouse_chr6.simMouse.chr6 144841 9 + 636262 GACACTATG -s Anc0.Anc0refChr1 35347 9 - 62388 GACATTGTG -s Anc1.Anc1refChr2 114524 9 + 144309 GACATTGTG -s Anc2.Anc2refChr3 24481 9 + 53186 GACATTGTG -s mr.mrrefChr5 8182 9 + 294540 GACATTGTG -s simCow_chr6.simCow.chr6 152426 7 + 602619 GTCATTG-- -s simDog_chr6.simDog.chr6 436295 9 - 593897 GACATTGTG -s simHuman_chr6.simHuman.chr6 139181 9 + 601863 GACATTGTG -s simRat_chr6.simRat.chr6 142507 8 + 647215 G-CATTGTG - -a -s simMouse_chr6.simMouse.chr6 144850 15 + 636262 CTTGGTGGGTAGTAC -s Anc0.Anc0refChr1 35356 12 - 62388 C---GTGATTGGTAT -s Anc1.Anc1refChr2 114533 15 + 144309 CTTGGTGATTGGTAT -s Anc2.Anc2refChr3 24490 12 + 53186 C---GTGATTGGTAT -s mr.mrrefChr5 8191 15 + 294540 CTTGGTGAGTAGTAC -s simCow_chr6.simCow.chr6 152433 11 + 602619 ----GTGGTCGGTAC -s simDog_chr6.simDog.chr6 436304 9 - 593897 C------ATTGGTAT -s simHuman_chr6.simHuman.chr6 139191 15 + 601863 CTTGGTGATTGGTAT -s simRat_chr6.simRat.chr6 142515 15 + 647215 CTTAGTGAGTAGTAC - -a -s simMouse_chr6.simMouse.chr6 144865 41 + 636262 AGTTGAGGGGATTCATAACAATATATGGTGACTTCGTCCTT -s Anc0.Anc0refChr1 35368 41 - 62388 GGTCTTGGGGATTCATAATGATCTATGGATGCTCCATTCTC -s Anc1.Anc1refChr2 114548 41 + 144309 GGTCTTGGGGATTCATAATGATCTATGGATGCTCCATTCTC -s Anc2.Anc2refChr3 24502 41 + 53186 GGTCTTGGGTATTCATAATGATCTATGGATGCTCCTCTCTC -s mr.mrrefChr5 8206 41 + 294540 AGTTGAGGGGATTCATAACAATATATGGAGACTTCATCCTT -s simCow_chr6.simCow.chr6 152444 41 + 602619 AGCTTTGGGCATTCATAATGATATATGGATACTCCGCTGTC -s simDog_chr6.simDog.chr6 436315 41 - 593897 GGTCTTGGGTATTAATAAGAACCTATGGATGCTCCTCTCTC -s simHuman_chr6.simHuman.chr6 139206 41 + 601863 GGTCTTGGGGATTCCCAATGATGTATGGATGCTCCATTCTC -s simRat_chr6.simRat.chr6 142530 41 + 647215 AGTTGAAGGGATTCATATCAATATATGGACACTTCATCCTT - -a -s simMouse_chr6.simMouse.chr6 144906 48 + 636262 TGCCCTGCAATTATAATACCCAGCTAGCCTATCTCTACTTCAGGTGTG -s Anc0.Anc0refChr1 35410 42 - 62388 TACCCTGA----ATACTGTACAGCTAGTCTACCCCT--TTAAAGGGTG -s Anc1.Anc1refChr2 114590 44 + 144309 TACCCTGA----ATACTGTACAGCTAGTCTACCCCTATTTAAAGGGTG -s Anc2.Anc2refChr3 24544 42 + 53186 CGTCCTGA----ATACTGTACAGCTAGTCTACCCCT--TTAAAGGGTG -s mr.mrrefChr5 8247 48 + 294540 TACCCTGCAATTATAATACCCAGCTAGCCTATCCCTATTTCAGGGGTG -s simCow_chr6.simCow.chr6 152486 40 + 602619 TATCCTGC----ATGATATACAGCTAGCCTACCCCC----AAATGCAG -s simDog_chr6.simDog.chr6 436357 42 - 593897 CGTCCTGA----ATACTGTACAGCTAGTAGACCCCT--TTAAAGGGTG -s simHuman_chr6.simHuman.chr6 139248 35 + 601863 TACCCT-------------ACAGCTAGTCTACCCCTATTTAAAGGGTG -s simRat_chr6.simRat.chr6 142571 48 + 647215 CACCCTGCAATTATAATAACCAGCTAGCCTATCCCTATTTGAGGGGTA - -a -s simMouse_chr6.simMouse.chr6 144954 14 + 636262 CTGTGCAAGAGGTC -s Anc0.Anc0refChr1 35452 13 - 62388 CGGTGCAA-AAGTC -s Anc1.Anc1refChr2 114634 13 + 144309 CGGTGCAA-AAGTC -s Anc2.Anc2refChr3 24586 13 + 53186 TGGTGCAA-AAGTC -s mr.mrrefChr5 8295 14 + 294540 CTGTGCAAGAGGTC -s simCow_chr6.simCow.chr6 152563 13 + 602619 TGGTGCAT-GAGTC -s simDog_chr6.simDog.chr6 436399 13 - 593897 TGGGACAA-AAGTC -s simHuman_chr6.simHuman.chr6 139283 13 + 601863 CAGTGCAA-AAGTC -s simRat_chr6.simRat.chr6 142619 13 + 647215 ATGTGCAAGTGGT- - -a -s simMouse_chr6.simMouse.chr6 144968 108 + 636262 ATGCATATAGGTAAAAAGCAGTAAAAGCAGTAAAGTGGCCTCACCCTACAGTTAGCTCGAGCAGAAATCTGTCTATGTGTGTCCTTCCAACTGTTCTGGCTGGTACAA -s Anc0.Anc0refChr1 35465 31 - 62388 ATGCATCTAGGTAAAAAGCAGCAAAA---------TGGAT-------------------------------------------------------------------- -s Anc1.Anc1refChr2 114647 31 + 144309 ATGCATCTAGGTAAAAAGCAGCAAAA---------TGGAT-------------------------------------------------------------------- -s Anc2.Anc2refChr3 24599 31 + 53186 ATGCATCTAGGCAAAAAGCAGCAAAA---------TGGAC-------------------------------------------------------------------- -s mr.mrrefChr5 8309 99 + 294540 ATGCATATAGGTAAAAAGCAGTAAAA---------TGGCTTCACCCTACAGTTAGCTCGAGCAGAAATCTGTCTATGTGTGTCCTTCCAACTGTTCTGGCTGGTACAA -s simCow_chr6.simCow.chr6 152576 31 + 602619 ATGCATATAGGAAAAAAGCAGCAAAA---------TCGAC-------------------------------------------------------------------- -s simDog_chr6.simDog.chr6 436456 30 - 593897 ATACATCTGG-CAGAAAGCAGCAAAA---------TGTAC-------------------------------------------------------------------- -s simHuman_chr6.simHuman.chr6 139296 31 + 601863 ATGCACTTAGATAAAAAGCACAAGAA---------TGGAT-------------------------------------------------------------------- -s simRat_chr6.simRat.chr6 142632 94 + 647215 -----TATAGGTAAAAAGCAGTAAAA---------CGGCTTCACCCTACAGTTAAGTCAAGCAGAAATTTGTCTATATGTGTCCTTCCACCTGTGCTGGCTATTACAA - -a -s simMouse_chr6.simMouse.chr6 145076 41 + 636262 ATGAAGGTGAAACATCCTGCCAATCAGATATCATGCCTCGC -s mr.mrrefChr5 8408 41 + 294540 ATGAAGGTGAAACATCCTGCCAATCAGATATCATGCCTCGC -s simRat_chr6.simRat.chr6 142735 41 + 647215 ATGAAGATGAATCATCCGGCCAACCCAATTTCATGCCTCAC - -a -s simMouse_chr6.simMouse.chr6 145117 246 + 636262 CTCAACGGCACAGTAGGCATTTATTCATATGGAAAACTGGAATCTTGGGTTATCAACAAATATCTCCATGTCTTATCAAATATCTCCATGTCTTATCGTGTAAATGCCTGTAACTATCTGCATGTTGAATTTAAAGAAAGATGACTATAGTATTGAGATGCCAGTTGTGAACCCATACTGATTCTGAAGGGATAGATATACATTTCTGATCTCTTGACAGTGTGAGCTATCAATCTCATATATTAT -s mr.mrrefChr5 8449 224 + 294540 CTCAACGGCACAGTAGGCATTTATTCATATGGAAAACTGGAATCTTGGGTTATCAA--------------------CAAATATCTCCATGTCTTATCGTGTAAATGCCTGTAACTATCTGCATGTTGAATTTAAAG-AAGATGACTATAGTATTGAGATG-CAGTTGTGAACCCATACTGATTCTGAAGGGATAGATATACATTTCTGATCTCTTGACAGTGTGAGCTATCAATCTCATATATTAT -s simRat_chr6.simRat.chr6 142780 224 + 647215 CTCAATGGTATGGTAGGCATTTATTGACATGGAAAACTGGAACCTTGAGTTATCAA--------------------CAAATATCTCCACGCCTGATTGCGCCAATACCTGTAACTATCTGCATGTTCAATTCAAAG-AAGATGGCTATTATATTGAGATG-CAGTTGTGAACCCATACCGCTTCTGAAGGGATACATATACGTTTAAGAGTTCTTGACATTGTGCACTGTCAGCCTCATATACTAT - -a -s simMouse_chr6.simMouse.chr6 145363 177 + 636262 TCTTAGGGATCCAGGTCCATTTGCCACACAGCTAAGCAGCTATCCTGGAAGATGGTTTGGTGTGTCTGTGCCCATTCTAAGTCTGTCGCTGCTGTACAAATAGTCCACTTAAAGCAGGTCACCTATACAATCTGCATGCTTTGATTAATGTGGGAATAATTCTTCAATGAGTACTAA -s mr.mrrefChr5 8673 175 + 294540 TCTTAGGGATCCAGGTCCATTTGCCACACAGCTAAGCAGCTATCCT-GAAGATGGTTTGGTGTGTCTGTGCCCATTCTAAGTCTGTCGCTGCTGTACAAATAGTCCACTTAAAGCAGGTCACCTATACAATCTGCATGCTTTGA-TAATGTGGGAATAATTCTTCAATGAGTACTAA -s simRat_chr6.simRat.chr6 143005 175 + 647215 TGTTAGGGATCCAGGTCAAGTTACCACACTGTTAACCAGCTATCCT-GAAGAGTGTTTGGTGTGTCTGTGCCCATTCTGAGTCTGTCACTGCTGTATGAACAGTCCACTTGAGGTAGGTCACCTATACAATCTGCATGCTTTAA-TAATGTTGGAATAATTCTACAATGAGGACCAA - -a -s simMouse_chr6.simMouse.chr6 145540 293 + 636262 GTTATATCTTGGTTGATACAGACTGGCTTGACTAATTTACTTAGCTACCTGCCCAAATCTAAAACTTTACTGCTGGAGACCTAATTGTCCAAATCATAGCTCTATATGTCCCCTAACAGCAGGTCAAACACCTGAAAGACTGAATCAAAGTCATTCACAATATAGGGCCCTTCTGGTGCCCACAGATTGAAGTCCATAATGATAATTATGGAAGACCACATGCCTGATTTACGTGTGGCTCTTGAGGGATTCCAGCCTGAAGTATATTATTGAAAGTCAGGTCCCATAAACAG -s Anc0.Anc0refChr1 35496 32 - 62388 ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GTAAATGACAAAAGGTCATATCCCATAAATAG -s Anc1.Anc1refChr2 114678 32 + 144309 ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GTAAATGACAAAAGGTCATATCCCATAAATAG -s Anc2.Anc2refChr3 24640 32 + 53186 ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GTAAATGACAAAAGGTCATATCCTATAAATAC -s mr.mrrefChr5 8848 170 + 294540 GTTATATC-TGGTTGATACAG-------------------------------------------------------------------------------------------------------------------AGACTGAATCAAAGTCATTCACAATATAGGGCCCTTCTGGTGCCCACAGATTGAAGTCCATAATGATAATTATGGAAGACCACATGCCTGATTT-------GCTCTTGAGGGATTCCAGCCTGAAGTATATTATTAAAGGTCAGGTCCCATAAACAG -s simCow_chr6.simCow.chr6 152617 32 + 602619 ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GTAAATTACAAAAGGCTGTACACTGTAAATAC -s simDog_chr6.simDog.chr6 436496 30 - 593897 ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GTAAATGGCAAAAGATCATATC--ATTCATAC -s simHuman_chr6.simHuman.chr6 139327 32 + 601863 ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GTAGACCACAAAGGGTCATATCCCATAAATAG -s simRat_chr6.simRat.chr6 143208 170 + 647215 GTTATATC-TGGTCAGTACGG-------------------------------------------------------------------------------------------------------------------AGACTGAATCAGAATTATTTATAATATAGGGCCCTTCTGGTGCCCACAGATTGAAGTCCATAGTGATAATTACGAAAGACCACATGCCTGATCT-------TCTTTCAAGGGATCCAAGCCTGAAGTATATTATCAAAGGTCAGTTCCCATAAACAG - -a -s simMouse_chr6.simMouse.chr6 145833 10 + 636262 TGTAGTTGTA -s Anc0.Anc0refChr1 35528 10 - 62388 TGCAATTTTA -s Anc1.Anc1refChr2 114710 10 + 144309 TGCAATTTTA -s Anc2.Anc2refChr3 24672 10 + 53186 AGCAATTTCA -s mr.mrrefChr5 9018 10 + 294540 TGTAGTTGTA -s simCow_chr6.simCow.chr6 152659 10 + 602619 AGCAACTACA -s simDog_chr6.simDog.chr6 436526 8 - 593897 AGC--TGTCA -s simHuman_chr6.simHuman.chr6 139359 10 + 601863 TGCAATTTTG -s simRat_chr6.simRat.chr6 143378 10 + 647215 TGTAGTTGTA - -a -s simMouse_chr6.simMouse.chr6 145843 29 + 636262 GGGGGAATACAATAGTGTTCCATCATCAT -s Anc0.Anc0refChr1 35538 29 - 62388 GAGGGAATACAAAAATGTTCCACCATCAT -s Anc1.Anc1refChr2 114720 29 + 144309 GAGGGAATACAAAAATGTTCCACCATCAT -s Anc2.Anc2refChr3 24682 29 + 53186 GAGGGACTACAAAAATGTTCCACCATCAT -s mr.mrrefChr5 9028 29 + 294540 GAGGGAATACAAAAGTGTTCCATCATCAT -s simCow_chr6.simCow.chr6 152684 29 + 602619 GAACGACTACAAAAGTGCTCAAATGTCAT -s simDog_chr6.simDog.chr6 436534 29 - 593897 GAGGGACTACAAACATTTTCCACCATCAT -s simHuman_chr6.simHuman.chr6 139369 29 + 601863 GAGGGAATACAAAAATGTTCCACCATCAT -s simRat_chr6.simRat.chr6 143388 29 + 647215 GAGGGAATACCAAAGTGTTCCATCATCAT - -a -s simMouse_chr6.simMouse.chr6 145872 4 + 636262 GCCA -s Anc0.Anc0refChr1 35568 4 - 62388 GCCA -s Anc1.Anc1refChr2 114750 4 + 144309 GCCA -s Anc2.Anc2refChr3 24712 4 + 53186 GCCA -s mr.mrrefChr5 9057 4 + 294540 GCCA -s simCow_chr6.simCow.chr6 152714 4 + 602619 GCCA -s simHuman_chr6.simHuman.chr6 139399 4 + 601863 CCCA -s simRat_chr6.simRat.chr6 143417 4 + 647215 GCCA - -a -s simMouse_chr6.simMouse.chr6 145876 2 + 636262 TG -s Anc0.Anc0refChr1 35593 2 - 62388 CA -s Anc1.Anc1refChr2 114775 2 + 144309 CA -s Anc2.Anc2refChr3 24737 2 + 53186 CA -s mr.mrrefChr5 9081 2 + 294540 TG -s simCow_chr6.simCow.chr6 152739 2 + 602619 CA -s simHuman_chr6.simHuman.chr6 139424 2 + 601863 CA -s simRat_chr6.simRat.chr6 143441 2 + 647215 TG - -a -s simMouse_chr6.simMouse.chr6 145878 12 + 636262 TACCTTGCCAGC -s Anc0.Anc0refChr1 35595 12 - 62388 TACCTGGACGGC -s Anc1.Anc1refChr2 114777 12 + 144309 TACCTGGACGGC -s Anc2.Anc2refChr3 24739 12 + 53186 TACCTGGACGGG -s mr.mrrefChr5 9083 12 + 294540 TACCTTGCCAGC -s simCow_chr6.simCow.chr6 152742 12 + 602619 TACCTGGACGGG -s simHuman_chr6.simHuman.chr6 139426 12 + 601863 TAGCTCATCTGC -s simRat_chr6.simRat.chr6 143443 12 + 647215 TACCCTGCCAGC - -a -s simMouse_chr6.simMouse.chr6 145890 8 + 636262 GCAGAGTG -s Anc0.Anc0refChr1 35608 8 - 62388 GCAGAGTA -s Anc1.Anc1refChr2 114790 8 + 144309 GCAGAGTA -s Anc2.Anc2refChr3 24752 8 + 53186 ATAGAGTA -s mr.mrrefChr5 9096 8 + 294540 GCAGAGTG -s simCow_chr6.simCow.chr6 152755 8 + 602619 ATAGAGTG -s simDog_chr6.simDog.chr6 436563 4 - 593897 ----GGTA -s simHuman_chr6.simHuman.chr6 139439 8 + 601863 GCACAGTA -s simRat_chr6.simRat.chr6 143456 8 + 647215 GCAGAGTG - -a -s simMouse_chr6.simMouse.chr6 145898 13 + 636262 CTATACCACAACT -s Anc0.Anc0refChr1 35616 13 - 62388 GTGTATCACATCA -s Anc1.Anc1refChr2 114798 13 + 144309 GTGTATCACATCA -s Anc2.Anc2refChr3 24760 13 + 53186 GTGTATCACATCA -s mr.mrrefChr5 9104 13 + 294540 CTATACCACAACT -s simCow_chr6.simCow.chr6 152763 13 + 602619 GTATATCACATAA -s simDog_chr6.simDog.chr6 436568 13 - 593897 GTGAATCATATCA -s simHuman_chr6.simHuman.chr6 139447 13 + 601863 GTGTATCACATCA -s simRat_chr6.simRat.chr6 143464 13 + 647215 CTATACCACAACT - -a -s simMouse_chr6.simMouse.chr6 145911 9 + 636262 TCTTCCTTC -s Anc0.Anc0refChr1 35630 2 - 62388 TC------- -s Anc1.Anc1refChr2 114812 9 + 144309 TCTTCCTTC -s Anc2.Anc2refChr3 24774 2 + 53186 TC------- -s mr.mrrefChr5 9118 9 + 294540 TCTTCCTTC -s simCow_chr6.simCow.chr6 152777 2 + 602619 TC------- -s simDog_chr6.simDog.chr6 436582 2 - 593897 TC------- -s simHuman_chr6.simHuman.chr6 139461 9 + 601863 TCTTCCATC -s simRat_chr6.simRat.chr6 143478 9 + 647215 TCCTCTTTC - -a -s simMouse_chr6.simMouse.chr6 145920 18 + 636262 ACACTAAAGTCCAACTTC -s Anc0.Anc0refChr1 35632 18 - 62388 ACAATAAAACCAGAGTTC -s Anc1.Anc1refChr2 114821 18 + 144309 ACAATAAAACCAGAGTTC -s Anc2.Anc2refChr3 24776 18 + 53186 ACAATAAAACCAGAGTTC -s mr.mrrefChr5 9127 18 + 294540 ACATTAAAGTCCAACTTC -s simCow_chr6.simCow.chr6 152786 18 + 602619 ACAAGAGAGTCTAAACTC -s simDog_chr6.simDog.chr6 436584 18 - 593897 ACAATAAAACCAGAGTTC -s simHuman_chr6.simHuman.chr6 139470 1 + 601863 A----------------- -s simRat_chr6.simRat.chr6 143487 18 + 647215 ACATTAAGGTCCAACTTC - -a -s simMouse_chr6.simMouse.chr6 145938 29 + 636262 CTTCTTGTGACCGAGTTTCAACCTTGTGA -s Anc0.Anc0refChr1 35650 26 - 62388 CT--TTGTGTCTAAGTTTTAACATT-TTA -s Anc1.Anc1refChr2 114839 26 + 144309 CT--TTGTGTCTAAGTTTTAACATT-TTA -s Anc2.Anc2refChr3 24796 26 + 53186 CT--TTGTGTCTAAGTTTTAACATT-TTA -s mr.mrrefChr5 9145 26 + 294540 CT--TTGTGACCAAGTTTCAACATT-TGA -s simCow_chr6.simCow.chr6 152806 26 + 602619 TT--TTGTCTTCAAGTTTTAACATT-TTA -s simDog_chr6.simDog.chr6 436604 26 - 593897 CT--TTGTGTCTAAATTTAAAAATT-TTA -s simHuman_chr6.simHuman.chr6 139471 15 + 601863 -------------GGTTGTAACATT-TTA -s simRat_chr6.simRat.chr6 143505 26 + 647215 CT--TTGTGACCAAGTTTTAACATC-TGA - -a -s simMouse_chr6.simMouse.chr6 145967 1 + 636262 G -s Anc0.Anc0refChr1 35681 1 - 62388 G -s Anc1.Anc1refChr2 114870 1 + 144309 G -s Anc2.Anc2refChr3 24828 1 + 53186 A -s mr.mrrefChr5 9171 1 + 294540 G -s simCow_chr6.simCow.chr6 152838 1 + 602619 A -s simDog_chr6.simDog.chr6 436636 1 - 593897 A -s simHuman_chr6.simHuman.chr6 139491 1 + 601863 G -s simRat_chr6.simRat.chr6 143531 1 + 647215 G - -a -s simMouse_chr6.simMouse.chr6 145968 9 + 636262 TACTCAGTG -s Anc0.Anc0refChr1 35682 9 - 62388 TTTGCAGTG -s Anc1.Anc1refChr2 114871 9 + 144309 TTTGCAGTG -s Anc2.Anc2refChr3 24829 9 + 53186 TTTGCAGTG -s mr.mrrefChr5 9172 9 + 294540 TACTCAGTG -s simCow_chr6.simCow.chr6 152839 9 + 602619 TTTTCAGTG -s simDog_chr6.simDog.chr6 436638 9 - 593897 TTTGCAGCG -s simHuman_chr6.simHuman.chr6 139492 9 + 601863 TTTGCAGTA -s simRat_chr6.simRat.chr6 143532 9 + 647215 TATTCAGTG - -a -s simMouse_chr6.simMouse.chr6 145977 40 + 636262 AAACTTCTTGCTTCTCAGTAAATTCTAATATTTGAGGCTT -s Anc0.Anc0refChr1 35704 39 - 62388 AAACTGT-CATTTGTCAGTACTTACTAAAATCTAAAGCTT -s Anc1.Anc1refChr2 114893 39 + 144309 AAACTGT-CATTTGTCAGTACTTACTAAAATCTAAAGCTT -s Anc2.Anc2refChr3 24851 39 + 53186 ATATGGT-CATTTGTCAGTACTCACTAAAATCTAGAGCTT -s mr.mrrefChr5 9181 39 + 294540 AAACTTC-TACTTCTCAGTAAATTCTAATATTTGAGGCTT -s simCow_chr6.simCow.chr6 152861 39 + 602619 ATATGGT-CATGTGGCAGTACTCACTAAAATCTAGAGCTT -s simDog_chr6.simDog.chr6 436660 38 - 593897 ATATGGT-TATTTGTCAGTACTCCCTAAAATCTAGAGCT- -s simHuman_chr6.simHuman.chr6 139514 39 + 601863 AAACTGT-CATTTGTCAGTGGTTAAAAAAATCTAAAGCTT -s simRat_chr6.simRat.chr6 143541 39 + 647215 AAACTTA-TACTTCTTAGTAAAATCGAATACTTTAGGCTT - -a -s simMouse_chr6.simMouse.chr6 146017 3 + 636262 GCA -s Anc0.Anc0refChr1 35743 3 - 62388 CAA -s Anc1.Anc1refChr2 114932 3 + 144309 CAA -s Anc2.Anc2refChr3 24890 3 + 53186 CAG -s mr.mrrefChr5 9220 3 + 294540 CAA -s simCow_chr6.simCow.chr6 152911 3 + 602619 CAG -s simHuman_chr6.simHuman.chr6 139553 3 + 601863 CAA -s simRat_chr6.simRat.chr6 143580 3 + 647215 CAA - -a -s simMouse_chr6.simMouse.chr6 146020 45 + 636262 TATTGGTAGGTAGTGGGCGGACGTCAGATCTGTGGGACTTGCAGG -s Anc0.Anc0refChr1 35752 45 - 62388 TAAATGTGACCAGTGGGCGGACATCGGATCTATGGGACTTGCAGG -s Anc1.Anc1refChr2 114941 45 + 144309 TAAATGTGACCAGTGGGCGGACATCGGATCTATGGGACTTGCAGG -s Anc2.Anc2refChr3 24899 45 + 53186 TAAATGTGACCAGTGGGCGGACATCGAATCTATGGGACTTGCAGG -s mr.mrrefChr5 9223 45 + 294540 TATTGGTAGGCAGTGGGCGGACATCAGATCTGTGGGACTTGCAGG -s simCow_chr6.simCow.chr6 152920 45 + 602619 TAAATGTGACCAGTGGACGGACATTGAATCTATGGGATTTGTAGT -s simDog_chr6.simDog.chr6 436698 34 - 593897 -----------AGTGGGCGGACATCGAATTTATAGGACTTGCCAG -s simHuman_chr6.simHuman.chr6 139562 45 + 601863 TAGGTGTGACCAGTGGGCGGACATCGGCTCCATGGGACTTGCAGG -s simRat_chr6.simRat.chr6 143583 44 + 647215 TATTGGTAGGCAG-GGGCGGACATCAAATCTGTGGGACTTGCAGG - -a -s simMouse_chr6.simMouse.chr6 146065 5 + 636262 TAAGG -s Anc0.Anc0refChr1 35808 5 - 62388 TAGGG -s Anc1.Anc1refChr2 114997 5 + 144309 TAGGG -s Anc2.Anc2refChr3 24956 5 + 53186 CTGGG -s mr.mrrefChr5 9268 5 + 294540 TAAGG -s simCow_chr6.simCow.chr6 152977 5 + 602619 CCGGG -s simDog_chr6.simDog.chr6 436744 5 - 593897 CTGGA -s simHuman_chr6.simHuman.chr6 139618 5 + 601863 TAGGG -s simRat_chr6.simRat.chr6 143627 5 + 647215 TAAGG - -a -s simMouse_chr6.simMouse.chr6 146070 20 + 636262 TTAGGATATAGTAAGAATTG -s Anc0.Anc0refChr1 35813 20 - 62388 TTACAGTATAGTAAGAATTG -s Anc1.Anc1refChr2 115002 20 + 144309 TTACAGTATAGTAAGAATTG -s Anc2.Anc2refChr3 24961 20 + 53186 TTACAATATAGTAAGAATTG -s mr.mrrefChr5 9273 20 + 294540 TTAGGGTATAGTAAGAATTG -s simCow_chr6.simCow.chr6 152992 20 + 602619 TTGCAATATAATAAGAATTC -s simDog_chr6.simDog.chr6 436749 20 - 593897 TTATGATATAGTAAGAATAG -s simHuman_chr6.simHuman.chr6 139623 20 + 601863 TTACAGTATAGTAAGAATTG -s simRat_chr6.simRat.chr6 143632 20 + 647215 TTAGGGTATAGTAAGAATTG - -a -s simMouse_chr6.simMouse.chr6 146090 13 + 636262 GAACTGTAGTTAC -s Anc0.Anc0refChr1 35835 13 - 62388 GAATTGTTGCCAC -s Anc1.Anc1refChr2 115024 13 + 144309 GAATTGTTGCCAC -s Anc2.Anc2refChr3 24983 13 + 53186 GAATTGTTGCCAC -s mr.mrrefChr5 9295 13 + 294540 GAACTGTAGTTAC -s simCow_chr6.simCow.chr6 153014 13 + 602619 GAATTGTAGCCAC -s simDog_chr6.simDog.chr6 436769 8 - 593897 -----GTTGCCAC -s simHuman_chr6.simHuman.chr6 139645 13 + 601863 GAATTGTGGCCAC -s simRat_chr6.simRat.chr6 143654 13 + 647215 GAACTGTAGTTGC - -a -s simMouse_chr6.simMouse.chr6 146103 36 + 636262 AGGAAATGATTTTGGTACAGTTTTGATCAGCTGGTT -s Anc0.Anc0refChr1 35848 36 - 62388 AGGAAACCATTTTGGTACAGTGTGGACAAGCTGGTT -s Anc1.Anc1refChr2 115037 36 + 144309 AGGAAACCATTTTGGTACAGTGTGGACAAGCTGGTT -s Anc2.Anc2refChr3 24996 36 + 53186 AGGACACCATTTTGGTACAGTGTGGACAAGCTGGTT -s mr.mrrefChr5 9308 36 + 294540 AGGAAATGATTTTGGTACAGTTTTGATCAGCTGGTT -s simCow_chr6.simCow.chr6 153027 28 + 602619 AGGGTACCATTTTGGTACA-TATGAAC-------TT -s simDog_chr6.simDog.chr6 436778 36 - 593897 AGGACACTATTTTGGAACAGTGTGGACAAGCTGGTA -s simHuman_chr6.simHuman.chr6 139658 36 + 601863 AGGAAACCATTTTGGTACAGTGTGGACAAGCTGGTT -s simRat_chr6.simRat.chr6 143667 35 + 647215 AGGAAATGATTTTGGT-CAGTTTTGATCAACTGGTC - -a -s simMouse_chr6.simMouse.chr6 146139 10 + 636262 TTAATATTAT -s Anc0.Anc0refChr1 35887 10 - 62388 TCAAGATTGT -s Anc1.Anc1refChr2 115076 10 + 144309 TCAAGATTGT -s Anc2.Anc2refChr3 25035 10 + 53186 TCAAGATTGT -s mr.mrrefChr5 9344 10 + 294540 TTAATATTAT -s simCow_chr6.simCow.chr6 153058 10 + 602619 TCAAGATTGC -s simDog_chr6.simDog.chr6 436817 10 - 593897 TCAAGATTGT -s simHuman_chr6.simHuman.chr6 139697 10 + 601863 TCAAGATTGT -s simRat_chr6.simRat.chr6 143702 10 + 647215 TTAATATTAT - -a -s simMouse_chr6.simMouse.chr6 146149 108 + 636262 TTTCATAGTGGTGTTTAGGCTACAACTGGTCATTCGTTTTTGCACACACTGGCAGGGAAGTCTGCTACTCTCTGCTGACACTGAGTAGTGCCTATGATCTCAATATAT -s Anc0.Anc0refChr1 35919 106 - 62388 TTTCAC--CTCTGTTAGGACTGCATCTGATCATTTGTTTCAACTCACATAAGCAGGTAATTTGGCCACTCTCCCTTGACGCCAAGTGATCCCTATAGTCTCCATATAC -s Anc1.Anc1refChr2 115108 108 + 144309 TTTCACGTCTCTGTTAGGACTGCATCTGATCATTTGTTTCAACTCACATAAGCAGGTAATTTGGCCACTCTCCCTTGACGCCAAGTGATCCCTATAGTCTCCATATAC -s Anc2.Anc2refChr3 25067 106 + 53186 TTTCAC--CTCTGTTAGGACTGCATCTAATCATTTCTTTCAACTCACATAAGCAGGTGATTTGGCCACTCTCCCTTGATGACAAGTGATCCCTATAGTCTCCATATAT -s mr.mrrefChr5 9354 108 + 294540 TTTCATAGTGGTGTTTAGGCTACAACTGGTCATTTGTTTTTGCACACACTGGCAGGGAAGTTTGCTACTCTCTGTTGACACTGAGTAATGCCTATGATCTCCATATAC -s simCow_chr6.simCow.chr6 153090 90 + 602619 TTGCAT--CTCTGTTAGGACTGAAACCAATCATTTCCTTCAACTCACATCAGCAG-TGATTTGGCCAC---------------AGTGATCCTTATAGTTGCCATCTAT -s simDog_chr6.simDog.chr6 436849 105 - 593897 CTTCAC--CTTTGTTAGGACTGCATCTAATCATTTCTTGC-ACTCACATATGCAGGGGATTTGGCCACTCTCCCTTGATGACAAGCGATCCCTATAGTCTCCATATGT -s simHuman_chr6.simHuman.chr6 139729 107 + 601863 TTTCTCGTCACTGTTAGGACTGCA-ATGACCATTTGTTTGAACCCAAATGAGCAGGTAATTTGGTCGCTCTTCTTCGACCCCTAGTCACCACTTTAGTCTCCAGATAC -s simRat_chr6.simRat.chr6 143712 108 + 647215 TCGCATAGTGGTGTTTAGGGTACAACTGGTCATTTGTTTCTGCACACACTGGCAGGGAGATTTGCTACTCTCTGTTGACATTGAGTAATGCCTGTGATCTTCATATAC - -a -s simMouse_chr6.simMouse.chr6 146257 10 + 636262 TTGGAGGTTG -s Anc0.Anc0refChr1 36027 9 - 62388 -TGGAGGTTC -s Anc1.Anc1refChr2 115218 9 + 144309 -TGGAGGTTC -s Anc2.Anc2refChr3 25175 9 + 53186 -TGGAGGTTC -s mr.mrrefChr5 9464 10 + 294540 TTGGAGGTTG -s simCow_chr6.simCow.chr6 153182 9 + 602619 -TTGAGGTTC -s simDog_chr6.simDog.chr6 436956 9 - 593897 -TGATGATGC -s simHuman_chr6.simHuman.chr6 139838 9 + 601863 -TGGAGGTTC -s simRat_chr6.simRat.chr6 143823 10 + 647215 TTTGGGGTTG - -a -s simMouse_chr6.simMouse.chr6 146267 52 + 636262 TTAAACCCCATTACAGTTAACTGTCTCTTCATGCAACATAGCTATTTTCTTT -s Anc0.Anc0refChr1 36036 52 - 62388 TTAAACCCCATTACAGTTAACTGTCTGTACGTGCAACATAGCTATTTTCAGT -s Anc1.Anc1refChr2 115227 52 + 144309 TTAAACCCCATTACAGTTAACTGTCTGTACGTGCAACATAGCTATTTTCAGT -s Anc2.Anc2refChr3 25184 52 + 53186 TTAAGCCCCATTACAGTTAACTGTCTGTACGTGCAACATAGCTATTTTCAGT -s mr.mrrefChr5 9474 52 + 294540 TTAAACCCCATTACAGTTAACTGTCTCTTCATGCAACATAGCTATTTTCTGT -s simCow_chr6.simCow.chr6 153191 52 + 602619 TCAAGCCCTATTACAGTTAACTGTCTGTATGTGCAACTTAGCTATTTTCAGT -s simDog_chr6.simDog.chr6 436969 52 - 593897 TTAAGCCCCATTACAGATAACTGTCTGTACATCCAACATAGCTATTTTCAGT -s simHuman_chr6.simHuman.chr6 139847 52 + 601863 TTAAACCCCATTACAGTTAACTGTCTGCACGTGCAACATATCTATTTTCGGT -s simRat_chr6.simRat.chr6 143833 52 + 647215 TTAAACCCCATTACAGTTAACCGTCTCTTCATGCAACATAGCTATTTTCTGT - -a -s simMouse_chr6.simMouse.chr6 146319 48 + 636262 ACATCTTCCAAACTACCAGCTGATTTTCCAACTTCTTCCATCTAAAAT -s Anc0.Anc0refChr1 36088 48 - 62388 ATATCTTCCTAACTACCAACTGATTTCACAGCTTCTTCCATGTGAGAT -s Anc1.Anc1refChr2 115279 48 + 144309 ATATCTTCCTAACTACCAACTGATTTCACAGCTTCTTCCATGTGAGAT -s Anc2.Anc2refChr3 25242 48 + 53186 ATATCTGCCTAACTACTAACTGATCTCACAGCTTCTTCCATGTGAGAT -s mr.mrrefChr5 9526 48 + 294540 ATATCTTCCAAACTACCAGCTGATTTTCCAACTTCTTCCATCTAAAAT -s simCow_chr6.simCow.chr6 153249 45 + 602619 ATATC---ATAACTATCAACTGGTCTCACAGCTTGTTCCCTGAAAGAT -s simDog_chr6.simDog.chr6 437027 47 - 593897 ATCTCTGCCAAACTACTAACTGATCTCAGTGCTTCTTCGAT-TGAGAT -s simHuman_chr6.simHuman.chr6 139899 47 + 601863 ATATCTTCCTAACTA-CAACTGATTTCACAGTTCCTTCCATGTGAGAT -s simRat_chr6.simRat.chr6 143885 36 + 647215 ATGTCTTCCAAACTACCAGCAAAATGTGCA------------CGAAAT - -a -s simMouse_chr6.simMouse.chr6 146367 9 + 636262 GTGCATAAA -s Anc0.Anc0refChr1 36147 9 - 62388 CCTCCTCAA -s Anc1.Anc1refChr2 115338 9 + 144309 CCTCCTCAA -s Anc2.Anc2refChr3 25301 9 + 53186 CCTCCTCAA -s mr.mrrefChr5 9574 9 + 294540 GCTCATAAA -s simCow_chr6.simCow.chr6 153305 9 + 602619 CTGCCTCAG -s simDog_chr6.simDog.chr6 437085 9 - 593897 CCTCCTCAA -s simHuman_chr6.simHuman.chr6 139957 9 + 601863 CCTCCTCGA -s simRat_chr6.simRat.chr6 143921 9 + 647215 GCTCATTAA - -a -s simMouse_chr6.simMouse.chr6 146376 23 + 636262 GTAACTCAGAAGTGTACACATCC -s Anc0.Anc0refChr1 36162 23 - 62388 TCAAGTCAGGAGTGTACATAAAT -s Anc1.Anc1refChr2 115353 23 + 144309 TCAAGTCAGGAGTGTACATAAAT -s Anc2.Anc2refChr3 25316 23 + 53186 TGAAGTACAGAATGTACATAAAT -s mr.mrrefChr5 9588 23 + 294540 GCAACTCAGAAGTGTACATAACC -s simCow_chr6.simCow.chr6 153320 23 + 602619 TGAAGTACAGAATGTATGCAAAT -s simDog_chr6.simDog.chr6 437094 7 - 593897 ----------------CATAAAT -s simHuman_chr6.simHuman.chr6 139972 23 + 601863 TCAAATCAGGAGTGTGCATAAAT -s simRat_chr6.simRat.chr6 143935 23 + 647215 ACAATTCAGAAGTGTACATAACC - -a -s simMouse_chr6.simMouse.chr6 146399 38 + 636262 AGAGAAGGCACAGATTCCCTCATCATCCAAGCTAATGC -s Anc0.Anc0refChr1 36198 38 - 62388 AGAGAAGGCACATATCCCCGAGTCAATTAAGAGAAGAG -s Anc1.Anc1refChr2 115389 38 + 144309 AGAGAAGGCACATATCCCCGAGTCAATTAAGAGAAGAG -s Anc2.Anc2refChr3 25352 38 + 53186 AAGGTAGGTATATATCCCTGAGTCAATTGAGAGAAGAG -s mr.mrrefChr5 9611 38 + 294540 AGAGAAGGCACAGATCCCCTCATCATCTAAGCTAATGC -s simCow_chr6.simCow.chr6 153356 38 + 602619 AAGATAGGTATATGTCCCTGATTCAATTGAGAGAAGGT -s simDog_chr6.simDog.chr6 437112 34 - 593897 ---GTAGGTA-ATATCCCTGAGTTAAATGAGAGAATAG -s simHuman_chr6.simHuman.chr6 140009 38 + 601863 AGAGAAGGCACATAGCCCCAAGTCAATTAAGAGATGAG -s simRat_chr6.simRat.chr6 143958 38 + 647215 AGAGAAGGCACTGATCCCCTCCACATCTAAGCTAATGC - -a -s simMouse_chr6.simMouse.chr6 146437 5 + 636262 CTAAC -s Anc0.Anc0refChr1 36236 5 - 62388 ATGCC -s Anc1.Anc1refChr2 115427 5 + 144309 ATGCC -s Anc2.Anc2refChr3 25390 5 + 53186 ATGCC -s mr.mrrefChr5 9649 5 + 294540 ATACC -s simCow_chr6.simCow.chr6 153394 5 + 602619 ACGCC -s simDog_chr6.simDog.chr6 437148 5 - 593897 ATACC -s simHuman_chr6.simHuman.chr6 140047 5 + 601863 ATGCC -s simRat_chr6.simRat.chr6 143996 5 + 647215 ACACC - -a -s simMouse_chr6.simMouse.chr6 146442 34 + 636262 CATATACTTCCCATGAATGTGCTGAAGACCATAG -s Anc0.Anc0refChr1 36253 27 - 62388 TCTCTTCCTTACATGAATG-GCTGAT------AG -s Anc1.Anc1refChr2 115444 27 + 144309 TCTCTTCCTTACATGAATG-GCTGAT------AG -s Anc2.Anc2refChr3 25407 27 + 53186 TCTCTTTCTTACATGAATG-TCTTAT------AG -s mr.mrrefChr5 9654 34 + 294540 CCTATACTTCCCATGAATGTGCTGAAGACCATAG -s simCow_chr6.simCow.chr6 153411 27 + 602619 CCTATTATTTACATGAATA-TCTTAT------AG -s simDog_chr6.simDog.chr6 437165 27 - 593897 TCTCTTTCTTACATGAACG-TCTTAT------AG -s simHuman_chr6.simHuman.chr6 140064 27 + 601863 TCTGTTCCTTTCATGAATG-GCTGAG------AG -s simRat_chr6.simRat.chr6 144001 34 + 647215 CCTAAACTTCGCACAAATGTCCTGTAGACCATAG - -a -s simMouse_chr6.simMouse.chr6 146476 51 + 636262 TAAAAGTCATAATGATGTTCCTGTCTTATTTTTGTTGTCTCTCCTAGAAGG -s Anc0.Anc0refChr1 36280 33 - 62388 TATC--T----------------TCACATTTTTGTGCCCTTTCCTAGAAGG -s Anc1.Anc1refChr2 115471 35 + 144309 TATCAGT----------------TCACATTTTTGTGCCCTTTCCTAGAAGG -s Anc2.Anc2refChr3 25434 33 + 53186 TATC--T----------------TCACATTTTTGTGCCCTTTCCTAGAAGG -s mr.mrrefChr5 9688 51 + 294540 TAAAAGTCATAATGATGTTCCTGTCATATTTTTGTTGCCTCTCCTAGAAGG -s simCow_chr6.simCow.chr6 153449 33 + 602619 TGTC--T----------------CCATACTTTTGTCCCATTTCCTAGAAGG -s simDog_chr6.simDog.chr6 437192 33 - 593897 GATC--T----------------TCACATTTTTGTGCCCTTTCCTAGGACA -s simHuman_chr6.simHuman.chr6 140091 35 + 601863 TACCAGT----------------TCACATTTTTGTGCCCTTTCCTAGAAGG -s simRat_chr6.simRat.chr6 144035 51 + 647215 TATAAATCATAACTATGTTCCTGTCAGATTTTTGTTGCCTCTCCTAGAAGA - -a -s simMouse_chr6.simMouse.chr6 146527 155 + 636262 TCTGTCTTTTTGCCATGGATTTATTTCATCCTAATAATATAGACCTGTCCCTGTCATATTTTTGTTTCCCCTCCAAGAAGTTTTATCTTTTTGCCGTGAATTCTTTTCATCCTAATAATGTAGACTCTTAGAGAAAAAAGATGATGCTAGTCCCT -s Anc0.Anc0refChr1 36317 63 - 62388 TTAGTCTTTTTACTGTGAATTTATTTCATC---ATATTATAAACC---------------------------------------------------------------------------------------GTAAAAAGATGATCCTAAT--CT -s Anc1.Anc1refChr2 115510 63 + 144309 TTAGTCTTTTTACTGTGAATTTATTTCATC---ATATTATAAACC---------------------------------------------------------------------------------------GTAAAAAGATGATCCTAAT--CT -s Anc2.Anc2refChr3 25471 63 + 53186 TTAGTCTTTTTACTGTGAATTTATTTCAAC---TCATTATGAACC---------------------------------------------------------------------------------------CTAAATAAATGATCCTCAG--CT -s mr.mrrefChr5 9739 112 + 294540 TTTGTCTTTTTGCCATGAATTTATTTCATCCTAATAATATAGACCTGTCCCTGTCATATTTTTGTTTCCCCTCCAAGAAGTTTTATCTT-------------------------------------------GAAAAAAGATGATCCTAGTCCCT -s simCow_chr6.simCow.chr6 153486 63 + 602619 TTAGTCTTTTTACCGCTAAGGTCTTTCAAC---TCATTATGGACC---------------------------------------------------------------------------------------TCAAATAAATTATCCATAC--CT -s simDog_chr6.simDog.chr6 437229 63 - 593897 ATAGTCTTTTTACTATGAATTTATTTTAAC---TCATTATGAGCC---------------------------------------------------------------------------------------CTGATTAAATGATCCTCAG--CT -s simHuman_chr6.simHuman.chr6 140130 63 + 601863 TTGGCCTTTTTTCTGTGAATTTGTTTCATC---ATAGTCTAAACC---------------------------------------------------------------------------------------GTAAAAAGATGAACCTAAT--CT -s simRat_chr6.simRat.chr6 144086 107 + 647215 TTTGTTTTTTTGGCATAAATTTATTTCATCCTAATAACATAGACATATTCTCATTATATTTTAATTGCCCCTCCAAGAAGATTTATCTT------------------------------------------------AAGATGATCCTAGTCTTT - -a -s simMouse_chr6.simMouse.chr6 146682 20 + 636262 AGGAACAGGAAGAAAAGTTT -s Anc0.Anc0refChr1 36380 20 - 62388 AGGAATCTGAAGCAAAACAT -s Anc1.Anc1refChr2 115573 20 + 144309 AGGAATCTGAAGCAAAACAT -s Anc2.Anc2refChr3 25535 20 + 53186 AGGAGTCTGAAGCAAAACAT -s mr.mrrefChr5 9851 20 + 294540 AGGAACAGGAAGAAAAGTTT -s simCow_chr6.simCow.chr6 153550 20 + 602619 AGGAGTTCAAAGCAAAACAC -s simDog_chr6.simDog.chr6 437293 20 - 593897 AGGGGTCTGAAGCAAAATAT -s simHuman_chr6.simHuman.chr6 140193 20 + 601863 GAGAATGTGAAGCAAAACAT -s simRat_chr6.simRat.chr6 144193 20 + 647215 AGAAGCAGGAAGAAAAGTTT - -a -s simMouse_chr6.simMouse.chr6 146702 26 + 636262 CACTAATACAGTTGCTCGTCTTGCCA -s Anc0.Anc0refChr1 36401 21 - 62388 TGCCAGTACATATGCTTATCT----- -s Anc1.Anc1refChr2 115594 21 + 144309 TGCCAGTACATATGCTTATCT----- -s Anc2.Anc2refChr3 25556 21 + 53186 TGCCAGTACATATGCTTATCT----- -s mr.mrrefChr5 9872 21 + 294540 CACTAGTACAGTTGCTTGTCT----- -s simCow_chr6.simCow.chr6 153571 20 + 602619 TGCCAGTA-ATATGCTCATTT----- -s simDog_chr6.simDog.chr6 437314 21 - 593897 TGCCAGTACATATGCATATCT----- -s simHuman_chr6.simHuman.chr6 140214 19 + 601863 TGCCAGTACA--TGCTTATCT----- -s simRat_chr6.simRat.chr6 144214 21 + 647215 CACGAGTACAGTTGCTTGTCT----- - -a -s simMouse_chr6.simMouse.chr6 146728 131 + 636262 CTGACACTCTTTAAGCTTTGACGCCTATGTGGTTTCAAAACCACCACAGAGCCTTGATCATGATCTACCCTAGATCTACGTGCTCTAATCTTAAACTTCCCCAATCTAAATGTCATCAAGACTACAGACAG -s Anc0.Anc0refChr1 36429 114 - 62388 CTGACACTCTTTTGGACTC-----------------AAAACCTACACAGAGGCTTTATTCTAATCTACCCTAGTTTTACTTGCTATACTCACGTACGTCCCCAATATGAATACTGCTAGGCCTATAAACAG -s Anc1.Anc1refChr2 115622 131 + 144309 CTGACACTCTTTTGGACTCTTAACCTACATGGTCTCAAAACCTACACAGAGGCTTTATTCTAATCTACCCTAGTTTTACTTGCTATACTCACGTACGTCCCCAATATGAATACTGCTAGGCCTATAAACAG -s Anc2.Anc2refChr3 25584 114 + 53186 CTGACACTCTTTTGGACTC-----------------AAAACCTACACAGAGGCTTTATTCTAATCTACCTTCGTTTTATTTGCTATACTCACGTACGTCCCCAATATGAATACTGCTAGGCCCATAAACAG -s mr.mrrefChr5 9893 131 + 294540 CTGACACTCTTTAAGCTTTGAAGCCTATGTGGTTTCAAAACCACCACAGAGCCTTGATTATGATCTACCCTAGATTTACGTGCTCTAATCATGAACTTCCCCAATCTAAATGCTGCCAAGACTACAAACAG -s simCow_chr6.simCow.chr6 153598 114 + 602619 CTAATGCCCTGTTCGACTC-----------------AAAACCCACACAGAGGCTTTATTCTAATCTACCTGGGTTTCATCTGCTATTCTTAAGGATGTCCCCAATATGAATACTGCCAGGCCCATTAACAA -s simDog_chr6.simDog.chr6 437342 108 - 593897 CTGACACTCTTTTGGACCC-----------------AAAACCTACACAGAGGCTTTAAACTCATTTACTTTCGTTTTATTTACTATACTCTCGTACATCCCCAATAGGAATACTGCT------ATAAAGAG -s simHuman_chr6.simHuman.chr6 140240 131 + 601863 CTGTCACTCTTTTGGTCTCTTAACCTACATGGTCTCTAAACCTACACAGAGGCTTTATTCTAATCTACCCTAGTTTTACTTGCTTTAGTCAGGTACGTCCCCAATGTGAATACTGCTGGGTATATAAACAG -s simRat_chr6.simRat.chr6 144235 131 + 647215 CTGACACCCTTTAAGCTTTGAAGCCTATGTGGTTTCAAAACCACCACTGAGCCTTGATTACGATCTACCCTAGATTTATGTGCTCTAATCATGAAAATCCCCAACCTAAATGCTGCCAAGACTACAAACAG - -a -s simMouse_chr6.simMouse.chr6 146859 4 + 636262 ACTT -s Anc0.Anc0refChr1 36543 4 - 62388 ACAC -s Anc1.Anc1refChr2 115753 4 + 144309 ACAC -s Anc2.Anc2refChr3 25699 4 + 53186 ACAC -s mr.mrrefChr5 10024 4 + 294540 ACTT -s simCow_chr6.simCow.chr6 153713 4 + 602619 ACAC -s simDog_chr6.simDog.chr6 437451 4 - 593897 ACAC -s simHuman_chr6.simHuman.chr6 140371 4 + 601863 ATCA -s simRat_chr6.simRat.chr6 144366 4 + 647215 ACTT - -a -s simMouse_chr6.simMouse.chr6 146863 43 + 636262 TACTATGGATATGGGGATTTATCTAAAAATCTCTGAGCCATTA -s Anc0.Anc0refChr1 36547 41 - 62388 TAGTGTGG--ATGGGGATTTATATACAATTATGCTAGCAATGA -s Anc1.Anc1refChr2 115757 41 + 144309 TAGTGTGG--ATGGGGATTTATATACAATTATGCTAGCAATGA -s Anc2.Anc2refChr3 25703 41 + 53186 TAGTGTGG--ATGAGGATTTATATACAATTATGCTAGCAATGA -s mr.mrrefChr5 10028 43 + 294540 TACTATGGATATGGGGATTTATCTAAAAATCTCTGAGCCATTA -s simCow_chr6.simCow.chr6 153733 41 + 602619 TAGTATGG--ATGAGGGTTTATATATGATTAAACTAGCTATCA -s simDog_chr6.simDog.chr6 437455 41 - 593897 TATAGCAT--ATGAGGATTTATATACAATCATGCTATCAAGGA -s simHuman_chr6.simHuman.chr6 140375 41 + 601863 TAGTGTGG--ATGGAGATTGATTAGCAATTATGCTAGCAATGA -s simRat_chr6.simRat.chr6 144370 43 + 647215 TCCTATGGATATGAGGATTTATCTAAAAGTCTCAGAGCCTTTA - -a -s simMouse_chr6.simMouse.chr6 146906 14 + 636262 AGATGATTTTCTAC -s Anc0.Anc0refChr1 36588 14 - 62388 AAATGTTGATTTAT -s Anc1.Anc1refChr2 115798 14 + 144309 AAATGTTGATTTAT -s Anc2.Anc2refChr3 25744 14 + 53186 TAATGTTGATTTAT -s mr.mrrefChr5 10071 14 + 294540 AGATGATTTTTTAC -s simCow_chr6.simCow.chr6 153774 14 + 602619 GAATGTTGATCTAT -s simDog_chr6.simDog.chr6 437519 14 - 593897 TAATGTTGATTTAT -s simHuman_chr6.simHuman.chr6 140416 14 + 601863 AAATGTTGATTTAT -s simRat_chr6.simRat.chr6 144413 14 + 647215 AGTCAATTTTTTAC - -a -s simMouse_chr6.simMouse.chr6 146920 55 + 636262 TTTTATTGCTATACACAGCCATGTTCTGGATGATCATATTAATAACACAGACATA -s Anc0.Anc0refChr1 36603 55 - 62388 CTTTATTGTTACACCCAACCATGTTCTGGACAATCACACTAGCAACACAGCCGTA -s Anc1.Anc1refChr2 115813 55 + 144309 CTTTATTGTTACACCCAACCATGTTCTGGACAATCACACTAGCAACACAGCCGTA -s Anc2.Anc2refChr3 25759 55 + 53186 CATTATTGTTACACCTGCCCATGTCCTAGACAGTCACACTAGCAACACAACTGTA -s mr.mrrefChr5 10085 55 + 294540 TTTTATTGCTATACACAACCATGTTCTGGATGATCATATTAGTAACACAGACATA -s simCow_chr6.simCow.chr6 153789 51 + 602619 CACTATTGTTACACCTGC----GTCCTTGACAGTCATACTAGCAACACAGACGTG -s simDog_chr6.simDog.chr6 437534 55 - 593897 CATTATTGCTGCACCTGCCCATGTCCTAGACAGTCACACTATCAACACAACTGTA -s simHuman_chr6.simHuman.chr6 140431 55 + 601863 CTTTATTGTCACACCCAACCATGTTCTGGTCAATCAAACAAGCAACACAGTCTTa -s simRat_chr6.simRat.chr6 144427 55 + 647215 TTTTATTGCTATACACAACCATGTTCTGGATGATCATGTTAGTAAAACAGGCATA - -a -s simMouse_chr6.simMouse.chr6 146975 3 + 636262 CTA -s Anc0.Anc0refChr1 36658 3 - 62388 CTA -s Anc1.Anc1refChr2 115868 3 + 144309 CTA -s Anc2.Anc2refChr3 25814 3 + 53186 CTA -s mr.mrrefChr5 10140 3 + 294540 CTA -s simCow_chr6.simCow.chr6 153840 3 + 602619 TTA -s simDog_chr6.simDog.chr6 437589 3 - 593897 CTA -s simHuman_chr6.simHuman.chr6 140579 3 + 601863 ctA -s simRat_chr6.simRat.chr6 144482 3 + 647215 CTA - -a -s simMouse_chr6.simMouse.chr6 146978 13 + 636262 ATAATTTTTACCT -s Anc0.Anc0refChr1 36683 13 - 62388 ATGATTTTTACCT -s Anc1.Anc1refChr2 115893 13 + 144309 ATGATTTTTACCT -s Anc2.Anc2refChr3 25844 13 + 53186 GTGTTTTTTACCT -s mr.mrrefChr5 10143 13 + 294540 ATAATTTTTACCT -s simCow_chr6.simCow.chr6 153870 11 + 602619 --GCTTTTTACCT -s simDog_chr6.simDog.chr6 437619 13 - 593897 GTGTTTTTTACCA -s simHuman_chr6.simHuman.chr6 140604 13 + 601863 AGGATTTTTACCT -s simRat_chr6.simRat.chr6 144485 13 + 647215 ATAATTTTTACTC - -a -s simMouse_chr6.simMouse.chr6 146991 34 + 636262 CTTATATAACTAAGATTTTTCTATCTAACATACG -s Anc0.Anc0refChr1 36706 28 - 62388 CTAGTGTGAGTGAGATTTTTCT------CATATG -s Anc1.Anc1refChr2 115916 34 + 144309 CTAGTGTGAGTGAGATTTTTCTATATCACATATG -s Anc2.Anc2refChr3 25867 28 + 53186 CTAGTGTGAGTGAGGTTTTTCT------CACATG -s mr.mrrefChr5 10156 34 + 294540 CTTATATAACTAAGATTTTTCTATCTAACATACG -s simCow_chr6.simCow.chr6 153891 25 + 602619 CTGTTGTAAG---GGTCTGTCT------CCCTGG -s simDog_chr6.simDog.chr6 437642 28 - 593897 CCAGTGTGAGTGAGGTTTTTCT------CACATG -s simHuman_chr6.simHuman.chr6 140627 34 + 601863 CTAGTGTGAGTGAGATTTTTCTATATCACATGAA -s simRat_chr6.simRat.chr6 144498 34 + 647215 ATTATATAACTAAGATTTTTCTATCTAACATGAG - -a -s simMouse_chr6.simMouse.chr6 147025 11 + 636262 TTATTCTGTAA -s Anc0.Anc0refChr1 36734 11 - 62388 TCATTCTGTAA -s Anc1.Anc1refChr2 115950 11 + 144309 TCATTCTGTAA -s Anc2.Anc2refChr3 25895 11 + 53186 TCATTTTGTAG -s mr.mrrefChr5 10190 11 + 294540 TTATTCTGTAA -s simCow_chr6.simCow.chr6 153916 11 + 602619 TCATTTTGTAG -s simDog_chr6.simDog.chr6 437681 11 - 593897 TCATTTTGTAG -s simHuman_chr6.simHuman.chr6 140661 11 + 601863 GCATTCAGAAA -s simRat_chr6.simRat.chr6 144532 11 + 647215 TCATTCAGTAA - -a -s simMouse_chr6.simMouse.chr6 147036 17 + 636262 GGCACTTAGTCCTTAAA -s Anc0.Anc0refChr1 36745 17 - 62388 GGGTCTTTGTCCTTACA -s Anc1.Anc1refChr2 115961 17 + 144309 GGGTCTTTGTCCTTACA -s Anc2.Anc2refChr3 25906 17 + 53186 GGGTCTTTGTCCTTACA -s mr.mrrefChr5 10201 17 + 294540 GGCACTTAGTCCTTAAA -s simCow_chr6.simCow.chr6 153927 17 + 602619 GGGACTGTCTCCCTGCA -s simDog_chr6.simDog.chr6 437692 17 - 593897 GGGTCTTTGTCCTTACA -s simHuman_chr6.simHuman.chr6 140732 17 + 601863 GGGGCTATGTTCTTACA -s simRat_chr6.simRat.chr6 144543 17 + 647215 GACACTGAGTCCTTATA - -a -s simMouse_chr6.simMouse.chr6 147053 10 + 636262 TTTTATGTTC -s Anc0.Anc0refChr1 36762 10 - 62388 CTCTAACACT -s Anc1.Anc1refChr2 115978 10 + 144309 CTCTAACACT -s Anc2.Anc2refChr3 25923 10 + 53186 CTTTAACACT -s mr.mrrefChr5 10218 10 + 294540 TTCTATGTTC -s simCow_chr6.simCow.chr6 154011 10 + 602619 CAGTAAGACT -s simDog_chr6.simDog.chr6 437709 10 - 593897 TTTTAACATT -s simHuman_chr6.simHuman.chr6 140749 10 + 601863 CTCTAAAACT -s simRat_chr6.simRat.chr6 144560 10 + 647215 TTCTATGTTC - -a -s simMouse_chr6.simMouse.chr6 147063 8 + 636262 ATCATTAC -s Anc0.Anc0refChr1 36772 8 - 62388 ATTCTTAC -s Anc1.Anc1refChr2 115988 8 + 144309 ATTCTTAC -s Anc2.Anc2refChr3 25933 8 + 53186 CTTCCTAC -s mr.mrrefChr5 10228 8 + 294540 ATCATTAC -s simCow_chr6.simCow.chr6 154038 8 + 602619 CTACCCAG -s simDog_chr6.simDog.chr6 437719 8 - 593897 CTTCCTAC -s simHuman_chr6.simHuman.chr6 140759 8 + 601863 ATTGTTAC -s simRat_chr6.simRat.chr6 144570 8 + 647215 ACCATTAC - -a -s simMouse_chr6.simMouse.chr6 147071 26 + 636262 TAGGATCATGATGTAATACTCTTATT -s Anc0.Anc0refChr1 36780 24 - 62388 CAGGATCATGATGTAAT--TCTTATT -s Anc1.Anc1refChr2 115996 24 + 144309 CAGGATCATGATGTAAT--TCTTATT -s Anc2.Anc2refChr3 25941 24 + 53186 CAGAAGCATGATCTAAT--TCTTATT -s mr.mrrefChr5 10236 26 + 294540 CAGGATCATGATGTAATACTCTTATT -s simCow_chr6.simCow.chr6 154051 24 + 602619 CAAATGTATAACTTAAT--TCTAATT -s simDog_chr6.simDog.chr6 437727 24 - 593897 AAGAAGCATGATCTAAT--TCTTATT -s simHuman_chr6.simHuman.chr6 140767 24 + 601863 CAGGATGATGATGCAAT--TCTTACT -s simRat_chr6.simRat.chr6 144578 20 + 647215 CAGGATCAT------ACACTCTTATT - -a -s simMouse_chr6.simMouse.chr6 147097 27 + 636262 TACCATGTACTAGACTTGAATACCACA -s Anc0.Anc0refChr1 36804 27 - 62388 CTCCATGCACTGGCCATCAAAACCACA -s Anc1.Anc1refChr2 116020 27 + 144309 CTCCATGCACTGGCCATCAAAACCACA -s Anc2.Anc2refChr3 25966 27 + 53186 CTCCATGCACTGGCCATCAAAACCACA -s mr.mrrefChr5 10262 27 + 294540 TACCATGTACTAGACATCAATACCACA -s simCow_chr6.simCow.chr6 154076 27 + 602619 CCCCCTGCACTAGCCATCAAGACCAAA -s simDog_chr6.simDog.chr6 437752 27 - 593897 CTCCATGCACTGGTCATCTAAATCACA -s simHuman_chr6.simHuman.chr6 140791 27 + 601863 CTCCTTGCACTCACCATCAAAACCATA -s simRat_chr6.simRat.chr6 144598 27 + 647215 TACCATGTACTAGACATCAATACCACA - -a -s simMouse_chr6.simMouse.chr6 147124 2 + 636262 AA -s Anc0.Anc0refChr1 36831 2 - 62388 AG -s Anc1.Anc1refChr2 116047 2 + 144309 AG -s Anc2.Anc2refChr3 25995 2 + 53186 AG -s mr.mrrefChr5 10289 2 + 294540 AA -s simCow_chr6.simCow.chr6 154105 2 + 602619 AA -s simDog_chr6.simDog.chr6 437781 2 - 593897 AG -s simHuman_chr6.simHuman.chr6 140818 2 + 601863 AG -s simRat_chr6.simRat.chr6 144625 2 + 647215 AC - -a -s simMouse_chr6.simMouse.chr6 147126 19 + 636262 TATAACTATGACTGCCAAC -s Anc0.Anc0refChr1 36844 19 - 62388 TATAGCTATGATTGCCAAC -s Anc1.Anc1refChr2 116060 19 + 144309 TATAGCTATGATTGCCAAC -s Anc2.Anc2refChr3 26015 19 + 53186 TATAGCTATGATTGCACAC -s mr.mrrefChr5 10291 19 + 294540 TATAACTATGACTGCCAAC -s simCow_chr6.simCow.chr6 154125 15 + 602619 TGTCTGTATGATTGC---- -s simDog_chr6.simDog.chr6 437810 19 - 593897 TATAGCTATGACTGCACAC -s simHuman_chr6.simHuman.chr6 140831 18 + 601863 TATAGCTATGA-TGGCAAC -s simRat_chr6.simRat.chr6 144627 19 + 647215 TATAACTATGACTGCCAAC - -a -s simMouse_chr6.simMouse.chr6 147145 10 + 636262 AGGCTAGGAT -s Anc0.Anc0refChr1 36863 10 - 62388 AAACTAAGAT -s Anc1.Anc1refChr2 116079 10 + 144309 AAACTAAGAT -s Anc2.Anc2refChr3 26037 10 + 53186 AAACTAAGAT -s mr.mrrefChr5 10310 10 + 294540 AGGCTAGGAT -s simCow_chr6.simCow.chr6 154142 10 + 602619 AGGCTAAGAC -s simDog_chr6.simDog.chr6 437832 10 - 593897 AAACTAAAAT -s simHuman_chr6.simHuman.chr6 140857 10 + 601863 AAACTTAGAT -s simRat_chr6.simRat.chr6 144646 10 + 647215 AGGCCAGAAC - -a -s simMouse_chr6.simMouse.chr6 147155 69 + 636262 GCATTTTTTTGGCCTCCCATCCCTACAAGGGACATAAAGTAATTGCATCATACATCCCTATTATTTGAG -s Anc0.Anc0refChr1 36877 37 - 62388 GCATTCATTGAACCACCCATCCCCACAGGGGACA--------------------------------GAG -s Anc1.Anc1refChr2 116093 37 + 144309 GCATTCATTGAACCACCCATCCCCACAGGGGACA--------------------------------GAG -s Anc2.Anc2refChr3 26051 37 + 53186 GCATTCATTGAACCACCCATTCCCACAAGGGACA--------------------------------GAG -s mr.mrrefChr5 10320 68 + 294540 GCATTCTTTTGACCTCCCATCCCTACAGGGGACATAAAGTAA-TGCATCATACATCCCTATTATTTGAG -s simCow_chr6.simCow.chr6 154156 37 + 602619 ACGTTCATTGAGCCATCCATTCCCACAAGGTACA--------------------------------GAG -s simDog_chr6.simDog.chr6 437846 37 - 593897 GCAATCATTGAACCGCCTGCTCCCACAAGGGACA--------------------------------GAG -s simHuman_chr6.simHuman.chr6 140876 37 + 601863 GCATTCATTGAACAAACCATCCCAAAAGAAGAAA--------------------------------GAA -s simRat_chr6.simRat.chr6 144656 68 + 647215 GCATTCTTTCGACCTCCCATCCCTACAGGGGGCATAAAGTAA-GGCCTCATACATCCCTATTATTTGAG - -a -s simMouse_chr6.simMouse.chr6 147224 27 + 636262 GTAGCTCATTGTATGCTGAAGGAAAAA -s Anc0.Anc0refChr1 36914 18 - 62388 GTGGTTCATGGAATGC---------AG -s Anc1.Anc1refChr2 116130 18 + 144309 GTGGTTCATGGAATGC---------AG -s Anc2.Anc2refChr3 26094 18 + 53186 GTGGTTCATGGAATGT---------AG -s mr.mrrefChr5 10388 27 + 294540 GTAGCTCATTGTATGCTGAAGGAAAAA -s simCow_chr6.simCow.chr6 154199 18 + 602619 GTGGTTCACAGAATGT---------AT -s simDog_chr6.simDog.chr6 437889 18 - 593897 GTGGGTCATGGAATGT---------AG -s simHuman_chr6.simHuman.chr6 140913 18 + 601863 GTGGTTCATCCATTGC---------AG -s simRat_chr6.simRat.chr6 144724 27 + 647215 GTAGTTCATTGCGTCCTGAGGGAAAAA - -a -s simMouse_chr6.simMouse.chr6 147251 51 + 636262 TTAATTCTTATCTAGCACTTGCCCGATGCTGTGAAGATGTTACTATCAACG -s Anc0.Anc0refChr1 36932 28 - 62388 TGATGTACCAT---ATA---GCCA-----------------ACTATCTACT -s Anc1.Anc1refChr2 116148 31 + 144309 TGATGTACCATCTAATA---GCCA-----------------ACTATCTACT -s Anc2.Anc2refChr3 26112 28 + 53186 TGATGTACCAT---ATA---GTCA-----------------CCCATTTTCT -s mr.mrrefChr5 10415 51 + 294540 TTAATTCTTATCTAGCACTTGCCCGATGCTGTGAAGATGTTACTATCAACT -s simCow_chr6.simCow.chr6 154217 28 + 602619 TGATGTACCTT---ATA---GTCA-----------------CTCATTTTCT -s simDog_chr6.simDog.chr6 437907 28 - 593897 CAACCTACAAT---ATA---GTCA-----------------CCCATTTTCT -s simHuman_chr6.simHuman.chr6 140931 31 + 601863 TGCTGTACCATCTAATA---GCCA-----------------ACTATCCACT -s simRat_chr6.simRat.chr6 144752 51 + 647215 TTAATTCTTATCTAGTACCTGCTCGATGACGTGAAGATGTTACTATCAACT - -a -s simMouse_chr6.simMouse.chr6 147302 25 + 636262 AGTAACCTCTTACAGTATGTGAAGC -s Anc0.Anc0refChr1 36967 24 - 62388 TGTAACCTC-TACAGTGTGTGAAAC -s Anc1.Anc1refChr2 116186 24 + 144309 TGTAACCTC-TACAGTGTGTGAAAC -s Anc2.Anc2refChr3 26147 24 + 53186 TGTAGCCTC-AACAGTGAGTGGAAC -s mr.mrrefChr5 10466 24 + 294540 TGTAACCTC-TACAGTATGTGAAGC -s simCow_chr6.simCow.chr6 154250 4 + 602619 ---------------------GAAG -s simDog_chr6.simDog.chr6 437942 24 - 593897 TGTAGCCTC-AACAGTGAGTGGAAC -s simHuman_chr6.simHuman.chr6 140971 24 + 601863 TGTAACCTC-TACAGTTTATGAAAC -s simRat_chr6.simRat.chr6 144803 23 + 647215 TGT-ACCTC-TACAGTCTGTGAAGT - -a -s simMouse_chr6.simMouse.chr6 147327 19 + 636262 CACCTCCATTTGTAGGTGC -s Anc0.Anc0refChr1 36991 19 - 62388 CACACCCATTTGTAGGTGC -s Anc1.Anc1refChr2 116210 19 + 144309 CACACCCATTTGTAGGTGC -s Anc2.Anc2refChr3 26171 19 + 53186 CACACTCAACTGTGAGTGG -s mr.mrrefChr5 10490 19 + 294540 CACCTCCATTTGTAGGTGC -s simCow_chr6.simCow.chr6 154254 19 + 602619 GTAACTCTACTGGTACCGG -s simDog_chr6.simDog.chr6 437966 19 - 593897 CACACTCAACAGTGAGTGG -s simHuman_chr6.simHuman.chr6 140995 19 + 601863 CACACCCATTTGTAGGTGC -s simRat_chr6.simRat.chr6 144828 19 + 647215 CACCTCCATTTGTAGGTGC - -a -s simMouse_chr6.simMouse.chr6 147346 16 + 636262 CACCACTTACAGTAGC -s Anc0.Anc0refChr1 37010 5 - 62388 CACCC----------- -s Anc1.Anc1refChr2 116229 5 + 144309 CACCC----------- -s Anc2.Anc2refChr3 26211 5 + 53186 CAACC----------- -s mr.mrrefChr5 10509 16 + 294540 CACCACTTACAGTAGC -s simCow_chr6.simCow.chr6 154294 5 + 602619 CCAAT----------- -s simDog_chr6.simDog.chr6 438006 5 - 593897 CAACC----------- -s simHuman_chr6.simHuman.chr6 141014 5 + 601863 CACCC----------- -s simRat_chr6.simRat.chr6 144847 16 + 647215 CATCACTTACCGTAGC - -a -s simMouse_chr6.simMouse.chr6 147362 25 + 636262 CTTGTGCAACTGTAGGTGGTAGGTC -s mr.mrrefChr5 10527 25 + 294540 CTTGTGCAACTGTAGGTGGTAGGTT -s simRat_chr6.simRat.chr6 144865 25 + 647215 CTTATGCAAATGTAGGTGGTAGGTT - -a -s simMouse_chr6.simMouse.chr6 147387 102 + 636262 ACTTAAGCAATTGGCTTGGAATGTGGAGGGATTATTGGTTATCATGAGTGATGCATGACACAAGACTGTTAACAGTAGCAACTTGACTGCAATTATAGATTG -s Anc0.Anc0refChr1 37015 34 - 62388 --------------------------------------------------------------------TTAGCAGTAGCAACTTGATTGCAACTATAGGGAG -s Anc1.Anc1refChr2 116234 34 + 144309 --------------------------------------------------------------------TTAGCAGTAGCAACTTGATTGCAACTATAGGGAG -s Anc2.Anc2refChr3 26216 34 + 53186 --------------------------------------------------------------------TCAGCAGTAGCAACTTGATTGCAACTGTAGGGAG -s mr.mrrefChr5 10552 102 + 294540 ACTTAAGCAATTAGCTTGGAATGTGGAGGCATTATTGGTTATCATGAGTGATGCATGACACAAGACTGTTAACAGTAGCAACTTGACTGCAATTATAGATTG -s simCow_chr6.simCow.chr6 154299 34 + 602619 --------------------------------------------------------------------TCAACAGTAGCAACTTGATTGCAACTGTAGGGAG -s simDog_chr6.simDog.chr6 438011 27 - 593897 --------------------------------------------------------------------ACAGCAGTA-------GATTGCAAGTGTAGGGAG -s simHuman_chr6.simHuman.chr6 141019 34 + 601863 --------------------------------------------------------------------TTAGCAGTGTCAACCTGATTGCAACTATAGGGAG -s simRat_chr6.simRat.chr6 144891 102 + 647215 ACTTAAGCAATTAGCTCGGAATGTAGAGGCATTATTGGTTATCATGAGTGATGCATGATACAAGACTGATAATAGTGGCAACGTGATTGCAATTATAGATTG - -a -s simMouse_chr6.simMouse.chr6 147489 15 + 636262 CCCTACGTGGTACAA -s Anc0.Anc0refChr1 37049 15 - 62388 CCTTAAGTGGTCCGA -s Anc1.Anc1refChr2 116268 15 + 144309 CCTTAAGTGGTCCGA -s Anc2.Anc2refChr3 26250 15 + 53186 ACTTAAGTGGTCTGA -s mr.mrrefChr5 10654 15 + 294540 CCCTACGTGGTACAA -s simCow_chr6.simCow.chr6 154333 15 + 602619 TCTTAAGTGATCTTA -s simDog_chr6.simDog.chr6 438038 15 - 593897 ACATAAGTTGTCTGA -s simHuman_chr6.simHuman.chr6 141098 15 + 601863 CCTCAATTGGTCCCA -s simRat_chr6.simRat.chr6 144993 15 + 647215 CCCTATGTGATATAA - -a -s simMouse_chr6.simMouse.chr6 147504 54 + 636262 GCCCTTCACAGACAAGCCCCTATGACTCTGAAGAAACAAAAATAAGAATAATTA -s Anc0.Anc0refChr1 37065 53 - 62388 GCCATTAGCCAATGAGTAATTATGATCCTGATCCAAC-CAAATAGGAATAATTA -s Anc1.Anc1refChr2 116284 53 + 144309 GCCATTAGCCAATGAGTAATTATGATCCTGATCCAAC-CAAATAGGAATAATTA -s Anc2.Anc2refChr3 26266 53 + 53186 GCCATTAGCCAATGAGTAATTATGATCCTGATCCAAC-CAAATAGGAATAACTA -s mr.mrrefChr5 10669 54 + 294540 GCCCTTCACAGACAAGCCCCTATGACTCTGATGAAACAAAAATAAGAATAATTA -s simCow_chr6.simCow.chr6 154349 53 + 602619 GCCACGAGCCAGTGAGCAATTATGATCCTGATTGAAC-TGAATAGGAACAACTA -s simDog_chr6.simDog.chr6 438054 51 - 593897 GCCATTAGCCAAAGAGTAATTATGATCCTAATCCGAC-CAAATAGGAATAA--A -s simHuman_chr6.simHuman.chr6 141114 53 + 601863 GCCATTAGCTAATGAGAATTTATCATCTTGATCTAAC-CAAATATGAATAATTA -s simRat_chr6.simRat.chr6 145008 54 + 647215 GCCCTTCACGGACAACCTCCTATGGCTCTGATGAAAAAACAATAAGAATCATTA - -a -s simMouse_chr6.simMouse.chr6 147558 45 + 636262 TATCAGTGTATGAAAAGTAACTGCATGAGTTATCCCATTGTATAC -s Anc0.Anc0refChr1 37119 45 - 62388 TATTAGTGTGTGAGCAATGCCTGACTAAGTTATTCCATTGGATTC -s Anc1.Anc1refChr2 116338 45 + 144309 TATTAGTGTGTGAGCAATGCCTGACTAAGTTATTCCATTGGATTC -s Anc2.Anc2refChr3 26320 45 + 53186 TATTAGCGTGCGAGCAATGCCTAACTAAGCTATTCCATTGGATTC -s mr.mrrefChr5 10723 45 + 294540 TATCAGTGTATGAGAAGTACCTGCATGAGTTATCCCATTGTATAC -s simCow_chr6.simCow.chr6 154403 42 + 602619 TCTTTGCATACGAGTAATGCTTAACTAAG---TCCCGTTGGATTC -s simDog_chr6.simDog.chr6 438106 45 - 593897 TATCAGCGTGCAAGCAATGCCTAACTGAACTATTCCAATGAGCTC -s simHuman_chr6.simHuman.chr6 141168 45 + 601863 TAGTGGTGTGTGAGCAATCCCTGACTAAGTCATTCCATTGGATTC -s simRat_chr6.simRat.chr6 145062 45 + 647215 CATCACTGTATGAGAAGTACCTGCAGGAGTTATCCCATTGTATAC - -a -s simMouse_chr6.simMouse.chr6 147603 14 + 636262 CTGCTGAGCTGTTA -s Anc0.Anc0refChr1 37166 14 - 62388 CCATGGAACTGTTA -s Anc1.Anc1refChr2 116385 14 + 144309 CCATGGAACTGTTA -s Anc2.Anc2refChr3 26367 14 + 53186 TTATGATACTGTCA -s mr.mrrefChr5 10768 14 + 294540 CCACTGAACTGTTA -s simCow_chr6.simCow.chr6 154447 14 + 602619 TTATGATACTGTCA -s simHuman_chr6.simHuman.chr6 141215 14 + 601863 CCATGGAACTGTTA -s simRat_chr6.simRat.chr6 145107 14 + 647215 GCACTGAACTGTTG - -a -s simMouse_chr6.simMouse.chr6 147617 59 + 636262 TACCTCCTGGTTCTCTGGTCTTAGTGACTGGAGCATGATCCCCAGGGAAATGCCTATCA -s Anc0.Anc0refChr1 37181 52 - 62388 TATGCTCTGATCATCTGATTCTCTCCACTAGA-CAT-ATCT-----GATGTTCTTTTTA -s Anc1.Anc1refChr2 116400 52 + 144309 TATGCTCTGATCATCTGATTCTCTCCACTAGA-CAT-ATCT-----GATGTTCTTTTTA -s Anc2.Anc2refChr3 26382 52 + 53186 TATGCTCTGATCATCTAACTCTCTCCATCAGG-CAC-ATCT-----GATGTTCTTTATA -s mr.mrrefChr5 10782 52 + 294540 TACCTCCTGGTTCTCTGGTCTTAGTGACTGGA-CAT-ATCC-----GAAATGCCTATCA -s simCow_chr6.simCow.chr6 154469 52 + 602619 TATGCTCTGATCATCTAACTCTCTCCATCAGC-GAC-ATCT-----GATGTTCTTTATT -s simDog_chr6.simDog.chr6 438151 31 - 593897 ---------------------TCGCTATCAGG-CAC-ATCT-----GCGTTTCTTTATA -s simHuman_chr6.simHuman.chr6 141230 52 + 601863 TATGCTCTAATCATCTGATTCACTCCACTAGA-CAT-ATCT-----GATGTTCTTTTTA -s simRat_chr6.simRat.chr6 145121 28 + 647215 AACCTCCTGGTTCTC-------------------------------AAAATGCCTACCA - -a -s simMouse_chr6.simMouse.chr6 147676 10 + 636262 ACAGGTGAGC -s Anc0.Anc0refChr1 37235 10 - 62388 ACAGGGAAGA -s Anc1.Anc1refChr2 116454 10 + 144309 ACAGGGAAGA -s Anc2.Anc2refChr3 26436 10 + 53186 ACAGGGAAGA -s mr.mrrefChr5 10834 10 + 294540 ACAGGTGAGC -s simCow_chr6.simCow.chr6 154523 10 + 602619 ACAGGGAAGA -s simDog_chr6.simDog.chr6 438184 10 - 593897 ACAGGGAAGG -s simHuman_chr6.simHuman.chr6 141284 10 + 601863 ACAGGGAAGA -s simRat_chr6.simRat.chr6 145149 10 + 647215 ACAGTTGAGC - -a -s simMouse_chr6.simMouse.chr6 147686 6 + 636262 ACATGG -s Anc0.Anc0refChr1 37245 6 - 62388 ATAGGC -s Anc1.Anc1refChr2 116464 6 + 144309 ATAGGC -s Anc2.Anc2refChr3 26446 6 + 53186 ATAGGC -s mr.mrrefChr5 10844 6 + 294540 ACATGG -s simCow_chr6.simCow.chr6 154533 6 + 602619 ATAGGC -s simDog_chr6.simDog.chr6 438194 6 - 593897 ATATGC -s simHuman_chr6.simHuman.chr6 141294 6 + 601863 ATAGGC -s simRat_chr6.simRat.chr6 145161 6 + 647215 ACATGG - -a -s simMouse_chr6.simMouse.chr6 147692 9 + 636262 TACAGAATA -s Anc0.Anc0refChr1 37251 9 - 62388 TGATCAATT -s Anc1.Anc1refChr2 116470 9 + 144309 TGATCAATT -s Anc2.Anc2refChr3 26452 9 + 53186 TGATCGATT -s mr.mrrefChr5 10850 9 + 294540 TACACAATA -s simCow_chr6.simCow.chr6 154541 9 + 602619 TCATCCACT -s simDog_chr6.simDog.chr6 438200 9 - 593897 TGATCGATT -s simHuman_chr6.simHuman.chr6 141300 9 + 601863 TGATCAATT -s simRat_chr6.simRat.chr6 145167 9 + 647215 TACACAATA - -a -s simMouse_chr6.simMouse.chr6 147701 107 + 636262 GCTTTAATGATATGGTTCTGCATTGAGTGCATCTAAGGGTCTGCTTGATACGGGCTAAGGTGGTATAACATTAGTTAAAGTATGAGCCCAAAAGCCCAAACTTGTGA -s Anc0.Anc0refChr1 37260 78 - 62388 GCTT-----------------ACTGACAGCACACAAGAATTT------------CTAGAGCAGTATAGCGCTAGTCAAAGTATAAATCCAAACTCATTACCTAATGA -s Anc1.Anc1refChr2 116479 78 + 144309 GCTT-----------------ACTGACAGCACACAAGAATTT------------CTAGAGCAGTATAGCGCTAGTCAAAGTATAAATCCAAACTCATTACCTAATGA -s Anc2.Anc2refChr3 26461 78 + 53186 GCTT-----------------ACTGACACCACACAAGAATTT------------CTAGAACAATATAGTGCTAGTCAAAGTATAAATCCTAACTCATTACTTAATGT -s mr.mrrefChr5 10859 107 + 294540 GCTTTAATGATATGGTTCTGCATTGAGTGCATCTAAGGGTCTGCTTGATACGGGCTAAGGTGGTATAACATTAGTCAAAGTATGAGCCCAAAAGCCCAAACTTGTGA -s simCow_chr6.simCow.chr6 154550 60 + 602619 ACTT-----------------ACTTACACTACAC------------------------------ATAGTGCTGCACAAGGTATAAATCCTAACTTGCTACATAATAC -s simDog_chr6.simDog.chr6 438209 78 - 593897 GCTT-----------------ACTGACACCACACAAGAATTT------------CTAGAACAATATAGTGCTAGTCAAAGTAGAGACCCTAGCCCATTGCTTAATGT -s simHuman_chr6.simHuman.chr6 141309 76 + 601863 GCTT-----------------ACTGACAGCACACTACAATTT------------CGAGAGCAGTATACC--TAGTCAGAGTATAAATCCAAACTCATGACCCAATGA -s simRat_chr6.simRat.chr6 145177 83 + 647215 GCTTTAACTATATGGTTTTGCATTGTGCGCATCTAAGGGTCTGCTTGGCACAGGCTAAGGTGGTATAACATTCGTCAAAGTAT------------------------ - -a -s simMouse_chr6.simMouse.chr6 147808 3 + 636262 AGC -s Anc0.Anc0refChr1 37339 3 - 62388 AGA -s Anc1.Anc1refChr2 116558 3 + 144309 AGA -s Anc2.Anc2refChr3 26540 3 + 53186 AGA -s mr.mrrefChr5 10966 3 + 294540 AGC -s simCow_chr6.simCow.chr6 154611 3 + 602619 AGA -s simDog_chr6.simDog.chr6 438288 3 - 593897 AAA -s simHuman_chr6.simHuman.chr6 141386 3 + 601863 AGA -s simRat_chr6.simRat.chr6 145260 1 + 647215 --T - -a -s simMouse_chr6.simMouse.chr6 147811 37 + 636262 GATCTATACTCTGTAGATGATTCATAAGGTACACAAC -s Anc0.Anc0refChr1 37342 13 - 62388 GGGCTATTCGCAG------------------------ -s Anc1.Anc1refChr2 116561 13 + 144309 GGGCTATTCGCAG------------------------ -s Anc2.Anc2refChr3 26543 13 + 53186 GGGCTGTTTGCAG------------------------ -s mr.mrrefChr5 10969 37 + 294540 GATCTATACTCTGTAGATGATTCATAAGGTACACAAC -s simCow_chr6.simCow.chr6 154615 13 + 602619 GGGCTGTTTGCAG------------------------ -s simDog_chr6.simDog.chr6 438291 2 - 593897 GC----------------------------------- -s simHuman_chr6.simHuman.chr6 141389 13 + 601863 GGGCCATCCACAG------------------------ -s simRat_chr6.simRat.chr6 145261 37 + 647215 GACCTATACTATGTAGAATATTCATAAGGTACACAAC - -a -s simMouse_chr6.simMouse.chr6 147848 110 + 636262 TGGCTGAGTACCCTTTGGAGGACCCATAATGTATACAACAAATAGCTGCGTCCTTTTCTTAGTGGCATTGCTGTGCGCATAGTGTACACTAGCAAGGTGCCAGCTCATTC -s Anc0.Anc0refChr1 37355 70 - 62388 ---------GTTATGTAGAAGATCCATAAAGTGTACAACAAGTAGCTGAGTAATCTTCTT-------------------------------GTAGAGCACCAGCCACTCT -s Anc1.Anc1refChr2 116574 70 + 144309 ---------GTTATGTAGAAGATCCATAAAGTGTACAACAAGTAGCTGAGTAATCTTCTT-------------------------------GTAGAGCACCAGCCACTCT -s Anc2.Anc2refChr3 26556 70 + 53186 ---------GTTATGTAGAAGATCCATAGACTGCACAACAAGTAGCTGAGTAATCTTCTT-------------------------------GTAGAGCACCAGCCACTCT -s mr.mrrefChr5 11006 109 + 294540 TGGCTGAGTACCCTTTGGAGGACCCATAAAGTATACAACAAATAGCTGCGTCCTCTTCTTAGTGGCATTGCTGTGCGC-TAGTGTACACTAGTAGGGTGCCAGCTCCTCC -s simCow_chr6.simCow.chr6 154628 70 + 602619 ---------GTTATGTGGGAGGGCCATAGGCTGCACAACAAGTAGCTGAGCAGTTTTCTT-------------------------------GTAGAGAACCAACCACTCT -s simDog_chr6.simDog.chr6 438293 67 - 593897 ----------TTAAGTAGAAGATCCATAGACTGCACAACAA--AGCTGAGTAACCTTCTT-------------------------------ATTGAACACCAGGCACTCT -s simHuman_chr6.simHuman.chr6 141402 70 + 601863 ---------GTGATGTAGTAGATCCATAAAGTGTGTAACTACTAACTGAGTAATCTTCTT-------------------------------GTAGAGCACCATCCACTCT -s simRat_chr6.simRat.chr6 145301 108 + 647215 TGGCTGAGCACCCCTTGGGGGACCTATAAAGAATACAACAAATGGCTGTGTCC-CTTCCTAGTGGCATTGCTGTGCTC-TAGTGTATGCTAGTAGGGTGCCAGCTCCTCC - -a -s simMouse_chr6.simMouse.chr6 147958 8 + 636262 CAGGTAGC -s Anc0.Anc0refChr1 37425 8 - 62388 TAAGCAAC -s Anc1.Anc1refChr2 116644 8 + 144309 TAAGCAAC -s Anc2.Anc2refChr3 26626 8 + 53186 TGAGCAAC -s mr.mrrefChr5 11115 8 + 294540 TAGGTAGC -s simCow_chr6.simCow.chr6 154698 8 + 602619 TTGGCAAC -s simDog_chr6.simDog.chr6 438378 8 - 593897 TGAACACC -s simHuman_chr6.simHuman.chr6 141472 8 + 601863 TAAGCAAC -s simRat_chr6.simRat.chr6 145409 8 + 647215 TAGGTAGC - -a -s simMouse_chr6.simMouse.chr6 147966 1 + 636262 T -s Anc0.Anc0refChr1 37434 1 - 62388 T -s Anc1.Anc1refChr2 116653 1 + 144309 T -s Anc2.Anc2refChr3 26635 1 + 53186 G -s mr.mrrefChr5 11123 1 + 294540 T -s simCow_chr6.simCow.chr6 154707 1 + 602619 G -s simDog_chr6.simDog.chr6 438387 1 - 593897 G -s simHuman_chr6.simHuman.chr6 141481 1 + 601863 T -s simRat_chr6.simRat.chr6 145417 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 147967 10 + 636262 GCTATCTGGG -s Anc0.Anc0refChr1 37435 10 - 62388 ATTATGTGGG -s Anc1.Anc1refChr2 116654 10 + 144309 ATTATGTGGG -s Anc2.Anc2refChr3 26636 10 + 53186 ATTATGTAGG -s mr.mrrefChr5 11124 10 + 294540 GCTATCTGGG -s simCow_chr6.simCow.chr6 154708 10 + 602619 ATTATGTAGG -s simDog_chr6.simDog.chr6 438399 10 - 593897 ATAATGTATA -s simHuman_chr6.simHuman.chr6 141482 10 + 601863 AGTATGTGGG -s simRat_chr6.simRat.chr6 145418 10 + 647215 GCTACCTGGC - -a -s simMouse_chr6.simMouse.chr6 147977 16 + 636262 AAAGCTGGGTAGGTTG -s Anc0.Anc0refChr1 37445 13 - 62388 AAACCTGGTTA---TG -s Anc1.Anc1refChr2 116664 13 + 144309 AAACCTGGTTA---TG -s Anc2.Anc2refChr3 26647 13 + 53186 AAACCTGGGTA---TG -s mr.mrrefChr5 11134 13 + 294540 AAAGCTGGTTA---TG -s simCow_chr6.simCow.chr6 154719 8 + 602619 -----TGGGTA---TG -s simDog_chr6.simDog.chr6 438415 13 - 593897 AAACCTGGGTA---TG -s simHuman_chr6.simHuman.chr6 141492 13 + 601863 AAACCTGGTTA---TG -s simRat_chr6.simRat.chr6 145428 13 + 647215 AAAGCTGATTA---TG - -a -s simMouse_chr6.simMouse.chr6 147993 6 + 636262 GTTAGG -s Anc0.Anc0refChr1 37463 6 - 62388 GGTAGG -s Anc1.Anc1refChr2 116682 6 + 144309 GGTAGG -s Anc2.Anc2refChr3 26665 6 + 53186 GGTGGG -s mr.mrrefChr5 11147 6 + 294540 GGTAGG -s simCow_chr6.simCow.chr6 154730 6 + 602619 GGTGGG -s simDog_chr6.simDog.chr6 438433 6 - 593897 GGTGGT -s simHuman_chr6.simHuman.chr6 141510 6 + 601863 GGGAGG -s simRat_chr6.simRat.chr6 145441 6 + 647215 GGTAGG - -a -s simMouse_chr6.simMouse.chr6 147999 16 + 636262 TACCAGGTGACTGTAA -s Anc0.Anc0refChr1 37471 16 - 62388 TACCAGATGACCATAA -s Anc1.Anc1refChr2 116690 16 + 144309 TACCAGATGACCATAA -s Anc2.Anc2refChr3 26673 16 + 53186 CAACAGATGACCATAA -s mr.mrrefChr5 11153 16 + 294540 TACCAGGTGACTGTAA -s simCow_chr6.simCow.chr6 154738 11 + 602619 CAGTAGATGAC----- -s simDog_chr6.simDog.chr6 438441 15 - 593897 C-ACAGATGACCATAA -s simHuman_chr6.simHuman.chr6 141518 16 + 601863 TACCAGATAACCATAA -s simRat_chr6.simRat.chr6 145447 16 + 647215 TACCAGGTGACTGTGA - -a -s simMouse_chr6.simMouse.chr6 148015 72 + 636262 AACATTACGAAATGTATGTAGAGACAGGGCCTGCTTTTGTTCACTCTATAGCCTAGGGCTGTTAGTGCAGTC -s Anc0.Anc0refChr1 37488 66 - 62388 AACAT------ATGTATGTAAAGACAGGGCCTGACTTTCTTTGTTCTAGAGCCTAGGGCTGTTAATGCAGTC -s Anc1.Anc1refChr2 116707 66 + 144309 AACAT------ATGTATGTAAAGACAGGGCCTGACTTTCTTTGTTCTAGAGCCTAGGGCTGTTAATGCAGTC -s Anc2.Anc2refChr3 26690 66 + 53186 CATGT------AGGTATGTAAAGACAGGGTCTGACTTTCTCTGTTCTAGAGCCTAGGGCTGTTAATGCAGTC -s mr.mrrefChr5 11169 72 + 294540 AACATTACGAAATGTATGTAGAGACAGGGCCTGCTTTTGTTTGCTCTAGAGCCTAGGGCTGTTAATGCAGTC -s simCow_chr6.simCow.chr6 154749 44 + 602619 ---------------------------AGTCTGACCTTCTGTGCTCTGGAGCCTAGGGCTGTTAG-GCAGTC -s simDog_chr6.simDog.chr6 438462 66 - 593897 CATGT------AGGTATGTAAAGACAGGGTTTGACTTGCTCTATTCTAGAGCCTAGGGCTGCTAATGCAGTC -s simHuman_chr6.simHuman.chr6 141535 66 + 601863 AACAT------ATGTATGTGAGGATAGGGCCTGGCTTTCTTTGTTCTAGAGCCTAGGGCTGTTAATGCAGTC -s simRat_chr6.simRat.chr6 145463 64 + 647215 AACATTACGAAATGT--------TCAGGGCCTGCTTTTGTTTGCTCTAGAGCCTAGGGCTGTGAATGCAGTC - -a -s simMouse_chr6.simMouse.chr6 148087 54 + 636262 CCTGGTCGAGACCTCCCACAGAGCAAATGATGTTCTTATCATATACACCTACAA -s Anc0.Anc0refChr1 37568 52 - 62388 CTTGGTTAAGGCCTCTCACAGAACAAATGATGCTCTCTTCA--GATAGCCTCTA -s Anc1.Anc1refChr2 116787 54 + 144309 CTTGGTTAAGGCCTCTCACAGAACAAATGATGCTCTCTTCATAGATAGCCTCTA -s Anc2.Anc2refChr3 26771 52 + 53186 TTTGGTTATGGCCTCTCACAGAACAAATGATGCTCTCTTCA--GATAGCCTCTA -s mr.mrrefChr5 11241 54 + 294540 CCTGGTTGAGACCTCTCACAGAGCAAATGATGTTCTTTTCATATATACCTACAA -s simCow_chr6.simCow.chr6 154808 52 + 602619 TTTGGTTATAGCCCCTCACAGAACAAATGATGCTCTCTTCA--TATAGCCTATA -s simDog_chr6.simDog.chr6 438543 51 - 593897 TTTGGTTATGGCCTTTAAAGGAATAAATGATGCTAACTTCA--GATAG-CTCAA -s simHuman_chr6.simHuman.chr6 141616 54 + 601863 CTTTGGTAAGTCCTCTCACAGAACAACTGCTGCTCTCTTCATAGATAGTCTGTA -s simRat_chr6.simRat.chr6 145527 53 + 647215 CATGGTTGGGACCTCTCACAGAGGAAATGATGTTCTATTCATATTT-CCTACAA - -a -s simMouse_chr6.simMouse.chr6 148141 23 + 636262 CTAACATTAGTTCTGCCCTACAC -s Anc0.Anc0refChr1 37620 23 - 62388 TTAACACTAATTTTATCCTACAC -s Anc1.Anc1refChr2 116841 23 + 144309 TTAACACTAATTTTATCCTACAC -s Anc2.Anc2refChr3 26823 23 + 53186 TTAACACTAATTTTATCGTACAC -s mr.mrrefChr5 11295 23 + 294540 TTAACATTAGTTTTGCCCTACAC -s simCow_chr6.simCow.chr6 154861 23 + 602619 GTATAACTGATTTTAACTTACAC -s simDog_chr6.simDog.chr6 438594 23 - 593897 TTAACACCAATTTCATTGTACAC -s simHuman_chr6.simHuman.chr6 141670 23 + 601863 TTCACAGTATATTTATCCTACAC -s simRat_chr6.simRat.chr6 145580 23 + 647215 TTAACACTAGCTTTGGCCTACAC - -a -s simMouse_chr6.simMouse.chr6 148164 32 + 636262 TACTTGCAAAATATGGTGGGCTTCTAAGAAAT -s Anc0.Anc0refChr1 37653 32 - 62388 TACCTACAGAGCATGGTGGGTTGCTCAGAAAT -s Anc1.Anc1refChr2 116874 32 + 144309 TACCTACAGAGCATGGTGGGTTGCTCAGAAAT -s Anc2.Anc2refChr3 26858 32 + 53186 GACCTACAGAGCATGGTGAGTTGCTCAGAAAT -s mr.mrrefChr5 11318 32 + 294540 TACTTGCAGAATATGGTGGGCTTCTAAGAAAT -s simCow_chr6.simCow.chr6 154896 32 + 602619 CACCTACAAACCATGGTGTGTTGCTCAGAAAT -s simDog_chr6.simDog.chr6 438629 32 - 593897 GACCTACAGAGCATGGTGAGTTGCTCAGAAAT -s simHuman_chr6.simHuman.chr6 141703 32 + 601863 TACCTACTGAGCATGGTGGTTTGCTCAGAAAC -s simRat_chr6.simRat.chr6 145603 32 + 647215 TACTTGCAGTATATGGTGGGCTTCTTAGGAAT - -a -s simMouse_chr6.simMouse.chr6 148196 37 + 636262 TCCACACCACAATGCTTTATATCAACGATGGGATCTG -s Anc0.Anc0refChr1 37687 34 - 62388 TCCGCACCACAAAGCTTTGCATCCACTAAGGG---TG -s Anc1.Anc1refChr2 116908 34 + 144309 TCCGCACCACAAAGCTTTGCATCCACTAAGGG---TG -s Anc2.Anc2refChr3 26892 34 + 53186 TCCGCACCACACAGCTTTGCATCCACTAAGGG---TG -s mr.mrrefChr5 11350 37 + 294540 TCCGCACCACAATGCTTTATATCAACGAAGGGATCTG -s simCow_chr6.simCow.chr6 154936 34 + 602619 TATGCACCACAGAGCTTTGGGTCCACTCAGGG---TG -s simDog_chr6.simDog.chr6 438663 34 - 593897 TCCATACTGCACAGCTTTACATCCACTAAGTG---TG -s simHuman_chr6.simHuman.chr6 141737 34 + 601863 TTCGCACCACGAAGCTTTGAATCTGCCAGGGG---TG -s simRat_chr6.simRat.chr6 145635 37 + 647215 TCCGCACCACAACACTTTATATCAACGAAGGAATCCG - -a -s simMouse_chr6.simMouse.chr6 148233 4 + 636262 GTGT -s Anc0.Anc0refChr1 37721 4 - 62388 GTGT -s Anc1.Anc1refChr2 116942 4 + 144309 GTGT -s Anc2.Anc2refChr3 26928 4 + 53186 GTGT -s mr.mrrefChr5 11387 4 + 294540 GTGT -s simCow_chr6.simCow.chr6 154972 4 + 602619 GTGT -s simDog_chr6.simDog.chr6 438699 4 - 593897 GTGT -s simHuman_chr6.simHuman.chr6 141771 4 + 601863 AAGT -s simRat_chr6.simRat.chr6 145672 4 + 647215 GTGT - -a -s simMouse_chr6.simMouse.chr6 148237 15 + 636262 TCAAGCAGAGTGAGA -s Anc0.Anc0refChr1 37725 15 - 62388 TTAAGCAGAGTGAGA -s Anc1.Anc1refChr2 116946 15 + 144309 TTAAGCAGAGTGAGA -s Anc2.Anc2refChr3 26932 15 + 53186 TTAAGGGGACTGAGA -s mr.mrrefChr5 11391 15 + 294540 TCAAGCAGAGTGAGA -s simCow_chr6.simCow.chr6 154976 15 + 602619 TGAAGGGGATTGTGA -s simDog_chr6.simDog.chr6 438703 15 - 593897 TTAAGGGGACTGAGA -s simHuman_chr6.simHuman.chr6 141776 15 + 601863 TGAAGCAAAGTGAGC -s simRat_chr6.simRat.chr6 145676 15 + 647215 TCAAGCAGAAAGAGA - -a -s simMouse_chr6.simMouse.chr6 148252 13 + 636262 ATCCCCAAGGTAG -s Anc0.Anc0refChr1 37741 13 - 62388 ATCACCAAGATAA -s Anc1.Anc1refChr2 116962 13 + 144309 ATCACCAAGATAA -s Anc2.Anc2refChr3 26948 13 + 53186 ATCACCAAGATAA -s mr.mrrefChr5 11406 13 + 294540 ATCCCCAAGGTAG -s simCow_chr6.simCow.chr6 154992 11 + 602619 ATCAC--AGATTA -s simDog_chr6.simDog.chr6 438719 13 - 593897 ATTGCCAAAGGAA -s simHuman_chr6.simHuman.chr6 141792 13 + 601863 ATCACGAAGATAA -s simRat_chr6.simRat.chr6 145691 13 + 647215 ATCCCTGAGGTAG - -a -s simMouse_chr6.simMouse.chr6 148265 18 + 636262 CAACATCTTTACCTTATA -s Anc0.Anc0refChr1 37768 18 - 62388 GAACATCTTTACCTTGTA -s Anc1.Anc1refChr2 116989 18 + 144309 GAACATCTTTACCTTGTA -s Anc2.Anc2refChr3 26975 18 + 53186 GTACATCTTTACCTTGTA -s mr.mrrefChr5 11433 18 + 294540 CAACATCTTTACCTTATA -s simCow_chr6.simCow.chr6 155017 18 + 602619 TGACATTTGTACCTTGTA -s simDog_chr6.simDog.chr6 438746 13 - 593897 GTACACCTTTATA----- -s simHuman_chr6.simHuman.chr6 141819 18 + 601863 GAACATCTTTACCTTGTA -s simRat_chr6.simRat.chr6 145718 18 + 647215 CAACATCTTTACCTTATA - -a -s simMouse_chr6.simMouse.chr6 148283 39 + 636262 AGTAGGGGGCATGTGGACCAATTCTTCTGGGTATAAGTA -s Anc0.Anc0refChr1 37786 35 - 62388 GGTTGAT-GTAGATGGAGCAATC---TTAGCTGGAACTA -s Anc1.Anc1refChr2 117007 36 + 144309 GGTTGATAGTAGATGGAGCAATC---TTAGCTGGAACTA -s Anc2.Anc2refChr3 26993 35 + 53186 GGTTGAT-GTAGATAGAGCAATC---CTATCTGGAACTA -s mr.mrrefChr5 11451 39 + 294540 AGTAGGGGGCATGTGGACCAATTCTTTTGGGTATAAGTA -s simCow_chr6.simCow.chr6 155035 35 + 602619 GGTTGAT-GGTGGCTGAGCAATC---CTATCTGGAACTA -s simDog_chr6.simDog.chr6 438759 31 - 593897 ----GAC-GTAGATAGAGCAACC---CTATCTGGAACTA -s simHuman_chr6.simHuman.chr6 141837 36 + 601863 GGCTGATAGTAGATGAAGCAATC---TTAGCTGGAACTG -s simRat_chr6.simRat.chr6 145739 39 + 647215 AGTAGCAGGCCTCTGGATCAATTCTATTGGGAATGAGTA - -a -s simMouse_chr6.simMouse.chr6 148322 16 + 636262 TTGGGTTTCTTGCATA -s Anc0.Anc0refChr1 37821 16 - 62388 ATAACTTCTTTGTGTG -s Anc1.Anc1refChr2 117043 16 + 144309 ATAACTTCTTTGTGTG -s Anc2.Anc2refChr3 27028 16 + 53186 ACAACTTCTTTGTGTG -s mr.mrrefChr5 11490 16 + 294540 TTGGGTTTCTTGCATA -s simCow_chr6.simCow.chr6 155070 16 + 602619 ACACCCCCTTTGTGTG -s simDog_chr6.simDog.chr6 438799 16 - 593897 ACAATTTCATTGTGTG -s simHuman_chr6.simHuman.chr6 141873 16 + 601863 ATAACTTCTTTGTGTG -s simRat_chr6.simRat.chr6 145778 16 + 647215 TATGGTTTCTTGCATA - -a -s simMouse_chr6.simMouse.chr6 148338 28 + 636262 GCTATTTACACCAGTTAACTGTTTTTGT -s Anc0.Anc0refChr1 37840 28 - 62388 GCAATTCATACTAATTAATTGTTTCTGT -s Anc1.Anc1refChr2 117062 28 + 144309 GCAATTCATACTAATTAATTGTTTCTGT -s Anc2.Anc2refChr3 27047 28 + 53186 GCAATTCATACTAATTGATTGTTTCTGA -s mr.mrrefChr5 11509 28 + 294540 GCTATTCACACCAGTTAACTGTTTTTGT -s simCow_chr6.simCow.chr6 155089 26 + 602619 GTCCCTCATACTAGTGG--TGCTTCTGA -s simDog_chr6.simDog.chr6 438818 26 - 593897 GCAAT--ACACTAATTGATTGTTTCTGA -s simHuman_chr6.simHuman.chr6 141892 28 + 601863 GCAGTTCATATTCATTAATTGTTTCTGT -s simRat_chr6.simRat.chr6 145798 28 + 647215 GCTATTCACACCAGTCAACTGTTTTTGT - -a -s simMouse_chr6.simMouse.chr6 148366 81 + 636262 GTTGATCAATTTCTGATAGCTCATCACCGTTAAACTGTAAAAACCTGCAAACCATAAGCATAGGGAGCTAGAGTTTCTGCA -s Anc0.Anc0refChr1 37873 71 - 62388 GTTGATCAAATTCTAATGGCCCATTGCCATT---------AAA-CTGCAAATCATAAGCATAGCAAGATAGAGATTCTACA -s Anc1.Anc1refChr2 117095 71 + 144309 GTTGATCAAATTCTAATGGCCCATTGCCATT---------AAA-CTGCAAATCATAAGCATAGCAAGATAGAGATTCTACA -s Anc2.Anc2refChr3 27080 71 + 53186 GTTGATCAAATTCTAATGGCCCATTGCTATT---------AAA-CTGAAAATCATGATTATAGCAAGATAGAGATTCTACA -s mr.mrrefChr5 11537 80 + 294540 GTTGATCAATTTCTAATAGCTCATTACCGTTAAACTGTAAAAA-CTGCAAACCATAAGCATAGGGAGCTAGAGTTTCTGCA -s simCow_chr6.simCow.chr6 155120 64 + 602619 GTTGATCAAATTCTAATGGGCCATTGCTACT---------AAA-CCGAAAATCAGGATTATGTCAAGATAGGCA------- -s simDog_chr6.simDog.chr6 438849 71 - 593897 GTTGATCAGATTCAAATAGCCCATTACTATT---------AAA-CTGAAAATCATGATTGTAGCAAAATAGAGCTTCTACA -s simHuman_chr6.simHuman.chr6 141925 71 + 601863 GTTAATCAAATTCTAACGGTCCATTGCCCTT---------AAA-CAGCCAATCATAAGCATAGCAGGATAGTGATTCTACA -s simRat_chr6.simRat.chr6 145826 80 + 647215 GTGTATCAATTTCTAATAGCTCGTTACTGTTAAACTGTAAAAA-CTGCAAAGCATAAACATAGGGAGCCAGAGTTCCTGCA - -a -s simMouse_chr6.simMouse.chr6 148447 10 + 636262 TGTAGAAGTT -s Anc0.Anc0refChr1 37944 9 - 62388 CAT-TATGTA -s Anc1.Anc1refChr2 117166 9 + 144309 CAT-TATGTA -s Anc2.Anc2refChr3 27151 9 + 53186 CAT-TATGTA -s mr.mrrefChr5 11617 10 + 294540 TGTATAAGTT -s simDog_chr6.simDog.chr6 438920 9 - 593897 CAT-TATGTA -s simHuman_chr6.simHuman.chr6 142233 9 + 601863 CAC-GATGTA -s simRat_chr6.simRat.chr6 145906 10 + 647215 TGTATAAGCT - -a -s simMouse_chr6.simMouse.chr6 148457 26 + 636262 TAACATGCTGAGATCATGTGGTGATG -s Anc0.Anc0refChr1 37953 26 - 62388 GAACATGCTGAGATCATGTAGTGATG -s Anc1.Anc1refChr2 117175 26 + 144309 GAACATGCTGAGATCATGTAGTGATG -s Anc2.Anc2refChr3 27160 26 + 53186 GAGCGTGCTGAGATCAAGTAGTGATG -s mr.mrrefChr5 11627 26 + 294540 TAACATGCTGAGATCATGTGGTGATG -s simCow_chr6.simCow.chr6 155184 15 + 602619 -----------GATCAATTAGTGACG -s simDog_chr6.simDog.chr6 438929 26 - 593897 GAGCGTGCTGAGATCAAGTAGTGATG -s simHuman_chr6.simHuman.chr6 142249 26 + 601863 GAACATGCTGACTTCATGTAGTAATG -s simRat_chr6.simRat.chr6 145916 26 + 647215 TAACATGCTGAGATCACATGGTGTTG - -a -s simMouse_chr6.simMouse.chr6 148483 8 + 636262 ATGGTTGA -s Anc0.Anc0refChr1 37983 8 - 62388 ATGGTTGT -s Anc1.Anc1refChr2 117205 8 + 144309 ATGGTTGT -s Anc2.Anc2refChr3 27190 8 + 53186 ATGGTTGT -s mr.mrrefChr5 11657 8 + 294540 ATGGTTGT -s simCow_chr6.simCow.chr6 155203 8 + 602619 ATCGTTGT -s simDog_chr6.simDog.chr6 438959 8 - 593897 ATGGTTGT -s simHuman_chr6.simHuman.chr6 142279 8 + 601863 ATGGTTGT -s simRat_chr6.simRat.chr6 145946 8 + 647215 AAGGTCGT - -a -s simMouse_chr6.simMouse.chr6 148491 2 + 636262 AT -s Anc0.Anc0refChr1 37991 2 - 62388 AT -s Anc1.Anc1refChr2 117213 2 + 144309 AT -s Anc2.Anc2refChr3 27198 2 + 53186 AG -s mr.mrrefChr5 11665 2 + 294540 AT -s simCow_chr6.simCow.chr6 155211 2 + 602619 AC -s simDog_chr6.simDog.chr6 438967 2 - 593897 AG -s simHuman_chr6.simHuman.chr6 142287 2 + 601863 AT -s simRat_chr6.simRat.chr6 145955 2 + 647215 AT - -a -s simMouse_chr6.simMouse.chr6 148493 13 + 636262 CCTGTGGGAAAGG -s Anc0.Anc0refChr1 37994 12 - 62388 CCTGTAAGA-GAG -s Anc1.Anc1refChr2 117216 12 + 144309 CCTGTAAGA-GAG -s Anc2.Anc2refChr3 27201 12 + 53186 CCTGTAATA-GAG -s mr.mrrefChr5 11667 13 + 294540 CCTGTGGGAAAAG -s simCow_chr6.simCow.chr6 155214 12 + 602619 CCTGTAATA-AAG -s simDog_chr6.simDog.chr6 438970 12 - 593897 CCTGTAATA-GAT -s simHuman_chr6.simHuman.chr6 142290 12 + 601863 CTGGTAAGA-GAG -s simRat_chr6.simRat.chr6 145957 13 + 647215 CCTGTGGGAAAAG - -a -s simMouse_chr6.simMouse.chr6 148506 16 + 636262 TTGTAAGCTTGGTGGG -s Anc0.Anc0refChr1 38006 16 - 62388 ATGTAAGCTTTTTGAG -s Anc1.Anc1refChr2 117228 16 + 144309 ATGTAAGCTTTTTGAG -s Anc2.Anc2refChr3 27213 16 + 53186 ATTTAAGCTTTTTGAG -s mr.mrrefChr5 11680 16 + 294540 TTGTAAGCTTGGTGGG -s simCow_chr6.simCow.chr6 155226 15 + 602619 ATTCAAGCTTTT-GAG -s simDog_chr6.simDog.chr6 438989 16 - 593897 ATTTAAGTTTATTGAG -s simHuman_chr6.simHuman.chr6 142302 16 + 601863 ATGTAGGCTTTTTGAG -s simRat_chr6.simRat.chr6 145970 16 + 647215 TTGTAAGCTTGGTGGG - -a -s simMouse_chr6.simMouse.chr6 148522 28 + 636262 TTCATACCTAAGGGACAAGATTTATCAC -s Anc0.Anc0refChr1 38043 28 - 62388 CTCATACCTGGAGGTCAAGATTTACCAT -s Anc1.Anc1refChr2 117265 28 + 144309 CTCATACCTGGAGGTCAAGATTTACCAT -s Anc2.Anc2refChr3 27250 28 + 53186 CTCATGCCTGGAGGTCAAGATTTACCAT -s mr.mrrefChr5 11717 28 + 294540 TTCATACCTAAAGGACAAGATTTATCAC -s simCow_chr6.simCow.chr6 155258 26 + 602619 --CATGCCTGGAGGTCAAGGTTTGCCAC -s simDog_chr6.simDog.chr6 439026 28 - 593897 CTCATGCCTGGGGGTCAATATTTACCAT -s simHuman_chr6.simHuman.chr6 142339 28 + 601863 CTCATACCTGGAGGTCAAGACTTCCCAG -s simRat_chr6.simRat.chr6 146007 28 + 647215 TTCATACCTAAAGGACAAGATTTGTCAT - -a -s simMouse_chr6.simMouse.chr6 148550 15 + 636262 CAGTACACTCAATTT -s Anc0.Anc0refChr1 38071 15 - 62388 CAACAAAATCAGTTG -s Anc1.Anc1refChr2 117293 15 + 144309 CAACAAAATCAGTTG -s Anc2.Anc2refChr3 27278 15 + 53186 CAACAACATCAGTTG -s mr.mrrefChr5 11745 15 + 294540 CAGCACACTCAATTT -s simCow_chr6.simCow.chr6 155284 15 + 602619 AAACAAGATCAGTTG -s simDog_chr6.simDog.chr6 439054 12 - 593897 CAACAACATCAG--- -s simHuman_chr6.simHuman.chr6 142367 15 + 601863 CAACAAAGTTAGCTG -s simRat_chr6.simRat.chr6 146038 15 + 647215 GAGCATACTCAATTC - -a -s simMouse_chr6.simMouse.chr6 148565 17 + 636262 TACTAAGTTATACAGTC -s Anc0.Anc0refChr1 38086 17 - 62388 TAGTCAGTTGAATAGGT -s Anc1.Anc1refChr2 117308 17 + 144309 TAGTCAGTTGAATAGGT -s Anc2.Anc2refChr3 27293 17 + 53186 TAGGCAGTTGAATAGGT -s mr.mrrefChr5 11760 17 + 294540 TACTAAGTTATACAGTC -s simCow_chr6.simCow.chr6 155301 17 + 602619 TAGGCAGTTGAATAGGT -s simDog_chr6.simDog.chr6 439066 10 - 593897 -------TTGAATAGGT -s simHuman_chr6.simHuman.chr6 142382 17 + 601863 TATTCAGTTGAATAGGT -s simRat_chr6.simRat.chr6 146053 17 + 647215 TACTAAGTTATACAGTG - -a -s simMouse_chr6.simMouse.chr6 148582 6 + 636262 CATTAG -s Anc0.Anc0refChr1 38103 6 - 62388 CATTTA -s Anc1.Anc1refChr2 117325 6 + 144309 CATTTA -s Anc2.Anc2refChr3 27310 6 + 53186 CATTTA -s mr.mrrefChr5 11777 6 + 294540 CATTAA -s simCow_chr6.simCow.chr6 155327 6 + 602619 CATTAA -s simDog_chr6.simDog.chr6 439076 6 - 593897 CATTTA -s simHuman_chr6.simHuman.chr6 142399 6 + 601863 CATCTA -s simRat_chr6.simRat.chr6 146070 6 + 647215 TATGAA - -a -s simMouse_chr6.simMouse.chr6 148588 14 + 636262 CTCAAGAAGGATTG -s Anc0.Anc0refChr1 38109 14 - 62388 CTCCAGAAGGATTA -s Anc1.Anc1refChr2 117331 14 + 144309 CTCCAGAAGGATTA -s Anc2.Anc2refChr3 27316 14 + 53186 CTCCAGAAGGATTA -s mr.mrrefChr5 11783 14 + 294540 CTCAAGAAGGATTG -s simCow_chr6.simCow.chr6 155348 14 + 602619 CTCCAGCAGGATTG -s simDog_chr6.simDog.chr6 439082 14 - 593897 TTCCAGAAGGATTA -s simHuman_chr6.simHuman.chr6 142405 14 + 601863 CTCCAGAAGGATTA -s simRat_chr6.simRat.chr6 146076 14 + 647215 CTTAAGAATAATTG - -a -s simMouse_chr6.simMouse.chr6 148602 57 + 636262 CATTAACTTGGGCCCAAGATTTACGGAGGATAACAATTGTGGTACAGAGCCTAGTGG -s Anc0.Anc0refChr1 38123 57 - 62388 CATGATTTTGGGGTCAAGATTAAATGAAGAGAGCAATTGTGGTGCAGACCCTAGGGG -s Anc1.Anc1refChr2 117345 57 + 144309 CATGATTTTGGGGTCAAGATTAAATGAAGAGAGCAATTGTGGTGCAGACCCTAGGGG -s Anc2.Anc2refChr3 27331 57 + 53186 CAAGATTCTGGGGTCAAGATTAAATGAAGAGAGCAATTGTGGAGAAGACAATTGGGG -s mr.mrrefChr5 11797 57 + 294540 CATTAACTTGGGCCCAAGATTTACGGAGGATAGCAATTGTGGTACAGAGCCTAGTGG -s simCow_chr6.simCow.chr6 155363 57 + 602619 CAGGATCCTAGTCTTGAAATTAAAGAAAGAGACCAATTGTGGAGAGAACAATCGTGG -s simDog_chr6.simDog.chr6 439097 57 - 593897 CAAGAATCTGGGGTCAAGATTAAATGAAGAGAGCAATTGTAGAGAAGGCAATTGGGG -s simHuman_chr6.simHuman.chr6 142419 57 + 601863 CATGTTGTTGGGGTCAAGATTAAATGAAGAGAGCACTTGTGGTGCAGACCCTAGAGG -s simRat_chr6.simRat.chr6 146090 55 + 647215 GATTAATTTGGGCCCAAGATTGAGGGAGGATAGCAATTTTGGTACAGAGCCTA--GG - -a -s simMouse_chr6.simMouse.chr6 148659 9 + 636262 GCATAATTA -s Anc0.Anc0refChr1 38180 9 - 62388 ACACCATTA -s Anc1.Anc1refChr2 117402 9 + 144309 ACACCATTA -s Anc2.Anc2refChr3 27388 9 + 53186 AAACCATCA -s mr.mrrefChr5 11854 9 + 294540 GCATAATTA -s simCow_chr6.simCow.chr6 155432 9 + 602619 AAACCATCA -s simHuman_chr6.simHuman.chr6 142476 9 + 601863 ACACCATTA -s simRat_chr6.simRat.chr6 146145 9 + 647215 GCATAATTA - -a -s simMouse_chr6.simMouse.chr6 148668 71 + 636262 GTCATAAATTTGGAAGCCTAATAAACACAAGGGAAACACAGAACATGACAATACACAGAACATGACAATCA -s Anc0.Anc0refChr1 38190 54 - 62388 GTGCAAAACTTGGAATCCTGGTAAACACAAAATAAA-----------------CACAAAATATGACTACAA -s Anc1.Anc1refChr2 117412 54 + 144309 GTGCAAAACTTGGAATCCTGGTAAACACAAAATAAA-----------------CACAAAATATGACTACAA -s Anc2.Anc2refChr3 27398 54 + 53186 GTGCAAAGCTTGGAATCCTGGTAAACGCAAAATAAA-----------------CACAAAATATGACTACAG -s mr.mrrefChr5 11863 54 + 294540 GTCATAAATTTGGAAGCCTAGTAAACACAAGGGAAA-----------------CACAGAACATGACAATCA -s simCow_chr6.simCow.chr6 155442 53 + 602619 GTGGTAAGCTTGGAATCCTGGTAAACCCAAAATAAA------------------ACAGAATACGACAACAG -s simDog_chr6.simDog.chr6 439155 43 - 593897 GTGCAGAGCCTAGAA-----------GCATAATAAC-----------------CACAAAATATGACTACAG -s simHuman_chr6.simHuman.chr6 142486 54 + 601863 GTGCCAAACTTGGAATCCTGGTAAACACAAAACAAA-----------------CGCAAAATATGACGAAAA -s simRat_chr6.simRat.chr6 146154 53 + 647215 GTCAT-GATTTGGAAGCCTAGTAAACACAAGGGAAA-----------------CATGGAACACGACAATCA - -a -s simMouse_chr6.simMouse.chr6 148739 8 + 636262 TAACTATG -s Anc0.Anc0refChr1 38246 8 - 62388 TAACTATT -s Anc1.Anc1refChr2 117468 8 + 144309 TAACTATT -s Anc2.Anc2refChr3 27454 8 + 53186 TAACTATT -s mr.mrrefChr5 11917 8 + 294540 TAACTATG -s simCow_chr6.simCow.chr6 155497 8 + 602619 TAACTATT -s simDog_chr6.simDog.chr6 439200 7 - 593897 -AACTATT -s simHuman_chr6.simHuman.chr6 142542 8 + 601863 TAACTATT -s simRat_chr6.simRat.chr6 146207 8 + 647215 TAACTATG - -a -s simMouse_chr6.simMouse.chr6 148747 12 + 636262 AAACCATGGGCT -s Anc0.Anc0refChr1 38254 12 - 62388 ACACCATGAGCT -s Anc1.Anc1refChr2 117476 12 + 144309 ACACCATGAGCT -s Anc2.Anc2refChr3 27465 12 + 53186 CCACCATGAGTT -s mr.mrrefChr5 11925 12 + 294540 AAACCATGGGCT -s simCow_chr6.simCow.chr6 155508 12 + 602619 CAACCATGAGTC -s simDog_chr6.simDog.chr6 439210 12 - 593897 CCGCCATGAGTT -s simHuman_chr6.simHuman.chr6 142550 12 + 601863 ACACCATGAGCT -s simRat_chr6.simRat.chr6 146215 12 + 647215 AAACCATGGGCT - -a -s simMouse_chr6.simMouse.chr6 148759 12 + 636262 AGTTACAAGGGC -s Anc0.Anc0refChr1 38266 12 - 62388 AGTAGCAAGGGC -s Anc1.Anc1refChr2 117488 12 + 144309 AGTAGCAAGGGC -s Anc2.Anc2refChr3 27478 12 + 53186 AGTAGCAAGAGC -s mr.mrrefChr5 11937 12 + 294540 AGTTACAAGGGC -s simCow_chr6.simCow.chr6 155521 12 + 602619 AGTAGTACGAAT -s simDog_chr6.simDog.chr6 439223 12 - 593897 AGTAGCAAGAGC -s simHuman_chr6.simHuman.chr6 142562 12 + 601863 AGTAGCAAAGGC -s simRat_chr6.simRat.chr6 146227 11 + 647215 AGTCATAA-GGC - -a -s simMouse_chr6.simMouse.chr6 148771 11 + 636262 AATTGTCAGAA -s Anc0.Anc0refChr1 38278 10 - 62388 AAATATT-GGA -s Anc1.Anc1refChr2 117500 11 + 144309 AAATATTAGGA -s Anc2.Anc2refChr3 27490 10 + 53186 AAATATT-GGA -s mr.mrrefChr5 11949 11 + 294540 AATTGTCAGAA -s simCow_chr6.simCow.chr6 155535 10 + 602619 GAATACT-GGA -s simDog_chr6.simDog.chr6 439235 10 - 593897 AAATGTT-GGA -s simHuman_chr6.simHuman.chr6 142574 11 + 601863 AAATATTAAGT -s simRat_chr6.simRat.chr6 146238 11 + 647215 CATTGTCAGAA - -a -s simMouse_chr6.simMouse.chr6 148782 26 + 636262 ACCCTGGAGTCCTATAATCAGACTTG -s Anc0.Anc0refChr1 38288 23 - 62388 GCCT---ACTGTTATAATTACAGTTG -s Anc1.Anc1refChr2 117511 23 + 144309 GCCT---ACTGTTATAATTACAGTTG -s Anc2.Anc2refChr3 27500 23 + 53186 GCCT---GCAGTTATAATTGCAGTTG -s mr.mrrefChr5 11960 26 + 294540 ACCCTGGAGTCCTATAATCACACTTG -s simCow_chr6.simCow.chr6 155547 23 + 602619 GCCT---GCAGTTATAATTGCAGTCG -s simDog_chr6.simDog.chr6 439245 23 - 593897 GCCT---GCAGTTATAATTGCAGTTG -s simHuman_chr6.simHuman.chr6 142585 23 + 601863 TGCT---ACTGTTGTAATGACAGTTG -s simRat_chr6.simRat.chr6 146249 26 + 647215 ACCCTGGAGTCCTATAATCACACTTG - -a -s simMouse_chr6.simMouse.chr6 148808 19 + 636262 TATATGTACACAATCCCTA -s Anc0.Anc0refChr1 38311 18 - 62388 TAAATGTATTCAATC-CTG -s Anc1.Anc1refChr2 117534 18 + 144309 TAAATGTATTCAATC-CTG -s Anc2.Anc2refChr3 27523 18 + 53186 AAAATGTATTCAATC-CTG -s mr.mrrefChr5 11986 18 + 294540 TATATGTACACAATC-CTA -s simCow_chr6.simCow.chr6 155571 18 + 602619 AAGATGTACTCAACC-CTG -s simDog_chr6.simDog.chr6 439268 18 - 593897 AAAATATATACAATC-CTA -s simHuman_chr6.simHuman.chr6 142608 18 + 601863 TCAATGTAATCAATT-CTG -s simRat_chr6.simRat.chr6 146275 18 + 647215 TACATGTATACAATC-CTA - -a -s simMouse_chr6.simMouse.chr6 148827 7 + 636262 AACAGAA -s Anc0.Anc0refChr1 38329 7 - 62388 AATAGGG -s Anc1.Anc1refChr2 117552 7 + 144309 AATAGGG -s Anc2.Anc2refChr3 27542 7 + 53186 AATATGG -s mr.mrrefChr5 12004 7 + 294540 AATAGAG -s simCow_chr6.simCow.chr6 155590 7 + 602619 GATATGG -s simDog_chr6.simDog.chr6 439287 7 - 593897 AATATGG -s simHuman_chr6.simHuman.chr6 142626 7 + 601863 AATAGGG -s simRat_chr6.simRat.chr6 146293 7 + 647215 AATAGAG - -a -s simMouse_chr6.simMouse.chr6 148834 32 + 636262 ACCGTGGCAGCCATAGGACCTCAACTTTGCTG -s Anc0.Anc0refChr1 38342 32 - 62388 ACTGTGGTAGTCCCGGGCCCTCCATCTTGCTA -s Anc1.Anc1refChr2 117565 32 + 144309 ACTGTGGTAGTCCCGGGCCCTCCATCTTGCTA -s Anc2.Anc2refChr3 27555 32 + 53186 ACTGTGGTAGTCCCGGGCCCTCCATCTTGCTA -s mr.mrrefChr5 12011 32 + 294540 ACCGTGGCAGCCATAGGACCTCAACTTTGCTA -s simCow_chr6.simCow.chr6 155603 32 + 602619 ACTGTTGTAGTCATGGGCCCTCCATCTTGCTA -s simDog_chr6.simDog.chr6 439300 32 - 593897 ACTGTGGCAGCCCCGGGCCCTCCATCTTGCTA -s simHuman_chr6.simHuman.chr6 142639 25 + 601863 ACTGCGGTAGT-------CCTCCATCTTGCTA -s simRat_chr6.simRat.chr6 146300 32 + 647215 ACCATGTCAGCCATGTGCCCTCAACTCTGCTA - -a -s simMouse_chr6.simMouse.chr6 148866 5 + 636262 TCCGT -s Anc0.Anc0refChr1 38374 5 - 62388 TCCCT -s Anc1.Anc1refChr2 117597 5 + 144309 TCCCT -s Anc2.Anc2refChr3 27587 5 + 53186 ACCCT -s mr.mrrefChr5 12043 5 + 294540 TCCCT -s simCow_chr6.simCow.chr6 155635 4 + 602619 ACTC- -s simDog_chr6.simDog.chr6 439332 5 - 593897 ACCCT -s simHuman_chr6.simHuman.chr6 142728 5 + 601863 TACCT -s simRat_chr6.simRat.chr6 146332 5 + 647215 TCCCC - -a -s simMouse_chr6.simMouse.chr6 148871 32 + 636262 GAGACATAGGAATGCGTTGGCCCTATCTTCCA -s Anc0.Anc0refChr1 38379 32 - 62388 GAGACACAGGGATACCTTGGACTTATCTTTCA -s Anc1.Anc1refChr2 117602 32 + 144309 GAGACACAGGGATACCTTGGACTTATCTTTCA -s Anc2.Anc2refChr3 27593 32 + 53186 GAGACACAGGGATACCTTGGACTTATTTCTAA -s mr.mrrefChr5 12048 32 + 294540 GAGACATAGGAATACGTTGGCCCTATCTTCCA -s simCow_chr6.simCow.chr6 155640 32 + 602619 GAGACACAGGGATGCATTGGACTTATTCCCTA -s simDog_chr6.simDog.chr6 439338 32 - 593897 AGGACACACAAATACCTTGGAATTATTTCTAA -s simHuman_chr6.simHuman.chr6 142733 32 + 601863 CAGACACAGGGACACCTTGGACTTATCTTTCA -s simRat_chr6.simRat.chr6 146337 32 + 647215 AAGACATAGGAATACATTGGGCCTATCTTCCA - -a -s simMouse_chr6.simMouse.chr6 148903 2 + 636262 AC -s Anc0.Anc0refChr1 38412 2 - 62388 AT -s Anc1.Anc1refChr2 117635 2 + 144309 AT -s Anc2.Anc2refChr3 27626 2 + 53186 AT -s mr.mrrefChr5 12080 2 + 294540 AC -s simCow_chr6.simCow.chr6 155673 2 + 602619 AT -s simDog_chr6.simDog.chr6 439371 2 - 593897 TT -s simHuman_chr6.simHuman.chr6 142766 2 + 601863 AT -s simRat_chr6.simRat.chr6 146369 2 + 647215 AC - -a -s simMouse_chr6.simMouse.chr6 148905 43 + 636262 CATACGAATAATTATTTCCATACAATTTGAGACAGTCAAATTT -s Anc0.Anc0refChr1 38448 43 - 62388 CATAATCATAATTATTTCCATGCATCTTGACATAGTCAAATTT -s Anc1.Anc1refChr2 117671 43 + 144309 CATAATCATAATTATTTCCATGCATCTTGACATAGTCAAATTT -s Anc2.Anc2refChr3 27662 43 + 53186 CACAATCATAATTATTTCCATGCATCTTGACATAGTCAAATTT -s mr.mrrefChr5 12116 43 + 294540 CATACGCATAATTATTTCCATACAATTTGACACAGTCAAATTT -s simCow_chr6.simCow.chr6 155714 43 + 602619 CACTTTCATAATTATTTCCATGCATGCAGGGATAGTTAAAATT -s simDog_chr6.simDog.chr6 439407 43 - 593897 CACAATCATATTTATTTCCATGCATCTTGACATGGTCAAATTT -s simHuman_chr6.simHuman.chr6 142801 39 + 601863 GATGATCATAATTATTTCCATCC----TGACATAGTCAAACTT -s simRat_chr6.simRat.chr6 146405 43 + 647215 CATACACATAATTATTTCCATGCAATTTGACACAGTCAAATTT - -a -s simMouse_chr6.simMouse.chr6 148948 15 + 636262 CTTGACTATTTGACT -s Anc0.Anc0refChr1 38492 15 - 62388 CTCCACTAGTCATCT -s Anc1.Anc1refChr2 117715 15 + 144309 CTCCACTAGTCATCT -s Anc2.Anc2refChr3 27706 15 + 53186 CTCCACTAGTCATCT -s mr.mrrefChr5 12159 15 + 294540 CTTGACTATTTGACT -s simCow_chr6.simCow.chr6 155758 15 + 602619 CTCCACTAGTCATCT -s simDog_chr6.simDog.chr6 439451 8 - 593897 TTCCACTG------- -s simHuman_chr6.simHuman.chr6 142841 15 + 601863 CCCCACTAGACATAT -s simRat_chr6.simRat.chr6 146448 15 + 647215 GTTGACTATTTGACT - -a -s simMouse_chr6.simMouse.chr6 148963 15 + 636262 TCATGGGGAAAAAGG -s Anc0.Anc0refChr1 38507 4 - 62388 TCA--A--------- -s Anc1.Anc1refChr2 117730 13 + 144309 TCA--AGCAGAAAGG -s Anc2.Anc2refChr3 27721 4 + 53186 TCA--A--------- -s mr.mrrefChr5 12174 15 + 294540 TCATGGGCAAAAAGG -s simCow_chr6.simCow.chr6 155845 4 + 602619 TCA--A--------- -s simDog_chr6.simDog.chr6 439459 4 - 593897 TCA--A--------- -s simHuman_chr6.simHuman.chr6 142856 13 + 601863 TCA--AGCAGAAAGG -s simRat_chr6.simRat.chr6 146463 15 + 647215 TTATGTGCAAAAAGG - -a -s simMouse_chr6.simMouse.chr6 148978 22 + 636262 GTAGATTACTCTAAGCAATTAC -s Anc0.Anc0refChr1 38511 18 - 62388 ----ATTACTCTCAACTATTAC -s Anc1.Anc1refChr2 117747 22 + 144309 GCTGATTACTCTCAACTATTAC -s Anc2.Anc2refChr3 27725 18 + 53186 ----ATTATTCTCTAATGTTAC -s mr.mrrefChr5 12193 22 + 294540 GTAGATTACTCTCAGCAATTAC -s simCow_chr6.simCow.chr6 155849 18 + 602619 ----ATTATTTTCTAATGTTAC -s simDog_chr6.simDog.chr6 439463 18 - 593897 ----ATCATTCTTTAATGTTAC -s simHuman_chr6.simHuman.chr6 142873 22 + 601863 GCTGATTACTCCCAACTATCAC -s simRat_chr6.simRat.chr6 146482 22 + 647215 GTAGATTACCCTCAGCAATTAC - -a -s simMouse_chr6.simMouse.chr6 149000 7 + 636262 CTGGGCA -s Anc0.Anc0refChr1 38529 7 - 62388 CTGTGCA -s Anc1.Anc1refChr2 117769 7 + 144309 CTGTGCA -s Anc2.Anc2refChr3 27744 7 + 53186 TTGTGCT -s mr.mrrefChr5 12215 7 + 294540 CTGGGCA -s simCow_chr6.simCow.chr6 155868 7 + 602619 TTGCGCT -s simDog_chr6.simDog.chr6 439482 7 - 593897 TTGTGCT -s simHuman_chr6.simHuman.chr6 142895 5 + 601863 CTAA--A -s simRat_chr6.simRat.chr6 146504 7 + 647215 CGGGGTA - -a -s simMouse_chr6.simMouse.chr6 149007 42 + 636262 AAGAGGCACTGGACCTTGCTGGCCTGGATAAAAACTGTCAAA -s Anc0.Anc0refChr1 38536 42 - 62388 AGGAAGTATTGAACTTAGCTGGCATGATTAAAGACTGTCAGA -s Anc1.Anc1refChr2 117776 42 + 144309 AGGAAGTATTGAACTTAGCTGGCATGATTAAAGACTGTCAGA -s Anc2.Anc2refChr3 27764 42 + 53186 AGCAAATATTGAACTTAGCTGGTATGATTAAAGACTGTCAGA -s mr.mrrefChr5 12222 42 + 294540 AAGAGGCACTGGACCTTGCTGGCCTGAATAAAAACTGTCAGA -s simCow_chr6.simCow.chr6 155889 42 + 602619 AGTGCATATTGAGCTTGGCTGCTATGATCAAAGACTGCTAGA -s simDog_chr6.simDog.chr6 439502 42 - 593897 AGCAAATATTGAACCTAGCTGGTCTGATTAAAGACTGTCAGA -s simHuman_chr6.simHuman.chr6 142900 42 + 601863 AGGAAGTATTGTACTTAGCTGGCATGATTAAATATTATGAGA -s simRat_chr6.simRat.chr6 146511 39 + 647215 AAGACGCACTAGACCTTGCTGGC---ACTAAAGACTGTTAGA - -a -s simMouse_chr6.simMouse.chr6 149049 128 + 636262 CAAATAACTTGGCTAAAGCTGATGCGTGGTAATTTTTATTGCATGAATGAATCATTCTCCACTCGGTTTAGCTGGAGCAAACTCTTTAATACACCCAATAAGCATTTTTGTCATGTTTACTATCTTCT -s Anc0.Anc0refChr1 38578 127 - 62388 CAATTAAC-TGGCCAGAGCTGGTATGTGGGAATTTCCATTGCACAGATGAATCATTCTTCTCTCGGTTTCTCTGGGCCAAGTTATTTGATGTGTCCAACAGGCATTTTTGTCCTATTTCCTTTCCTAT -s Anc1.Anc1refChr2 117818 127 + 144309 CAATTAAC-TGGCCAGAGCTGGTATGTGGGAATTTCCATTGCACAGATGAATCATTCTTCTCTCGGTTTCTCTGGGCCAAGTTATTTGATGTGTCCAACAGGCATTTTTGTCCTATTTCCTTTCCTAT -s Anc2.Anc2refChr3 27806 127 + 53186 CAAAAAAC-TGGCCAGAGCTGGTATGAGGGAACTTCCATTGCACAGATGAGTCATTCTTCTCTCAGTTTCTCTGGGCCAAGTTATTAGATGTGTCCAACAGGCATTTTTGTCCTATTTCCTTTCCTAT -s mr.mrrefChr5 12264 127 + 294540 CAATTAAC-TGGCCAGAGCTGATGTGTGGTAATTTTTATTGCACGGATGAATCATTCTCCACTCGGTTTAGCTGGGGCAAATTCTTTGATATACCCAATAAGCATTTTTGTCATATTTACTATCCTCT -s simCow_chr6.simCow.chr6 155932 127 + 602619 CAAGAAAA-TGGCCAGAGCTGGCGTGAGGGAAATTCCATTGCACAGATGATTCAGTCTTCTTTCAGTTTATCTGGGCCAACTCATTAGATATGTCCAACAGGCATTTTTGTCCTATTTCCTCTCATAT -s simDog_chr6.simDog.chr6 439592 127 - 593897 CAAAAAAC-TGGCCAAGGCTGGTATGAGGGAACTTTTATTGCACGGGTGAGTCATTCTTCTCTCAGTTTCGCTGGGCCAAGTTATTACGTGTGTCCAACAGGCATTTTTATTCTATTTCCCTCCCAAT -s simHuman_chr6.simHuman.chr6 142942 127 + 601863 CAATTAAC-TGCCCAGAGCTGGTATGTAAGAATTTCCATTGCACAGATGAATCATTCTACCCTCGGTTTCTCTGGGCAAAGTTTTTTGATGTTTCCAACAGGCATTTGTGTCCTATTTCCTTTCCTAT -s simRat_chr6.simRat.chr6 146550 127 + 647215 CAATTAAC-TGGCCAGAGCTGATGTGTGTCAATTTTTATTGCACGGATGAACCATTCTCCACCCAGTTTAGCCTAGGCAAATTCTTTGATATGCCCAATAAGCATTTTTGTCATACTTACTATCCTCT - -a -s simMouse_chr6.simMouse.chr6 149177 8 + 636262 TGCTATGA -s Anc0.Anc0refChr1 38705 8 - 62388 TGGTATGA -s Anc1.Anc1refChr2 117945 8 + 144309 TGGTATGA -s Anc2.Anc2refChr3 27933 8 + 53186 CAGCATGA -s mr.mrrefChr5 12391 8 + 294540 TGCTATGA -s simCow_chr6.simCow.chr6 156059 8 + 602619 CAGCATGA -s simDog_chr6.simDog.chr6 439719 8 - 593897 CAGCATGA -s simHuman_chr6.simHuman.chr6 143069 8 + 601863 TGTTATGA -s simRat_chr6.simRat.chr6 146680 8 + 647215 TGCTATGA - -a -s simMouse_chr6.simMouse.chr6 149185 95 + 636262 CATTGTAGAAATGTGACAACTGGGGACTGGGGGCTCGTTGAGGGCCAATGCACTGACAGTTGCTGGAGACACCATATTGAATCAAGGCAGTACCT -s Anc0.Anc0refChr1 38722 94 - 62388 CATTGTAGAGACAGAACAAGGGCTGTTTGGGGGGCTGCTGAGGGTCCATACATTGACAGCTGCTGGATTGGCTACAATGAATGAA-GCAGTATTA -s Anc1.Anc1refChr2 117962 94 + 144309 CATTGTAGAGACAGAACAAGGGCTGTTTGGGGGGCTGCTGAGGGTCCATACATTGACAGCTGCTGGATTGGCTACAATGAATGAA-GCAGTATTA -s Anc2.Anc2refChr3 27950 94 + 53186 CATTGGAGAGACAGAACAAGGGCTGTTTGGGGGGCTGATGAGGGTCCATACATTGACAGCTGCTGTATTGGCTACAATGAATGAA-GCAGTATCA -s mr.mrrefChr5 12399 94 + 294540 CATTGTAGAAATGTGACAACTGGGGACTGGGGGCCTGCTGAGGGCCAATACACTGACAGCTGCTGGATACACCATATTGAATCAA-GCAGTACTA -s simCow_chr6.simCow.chr6 156074 86 + 602619 -ATTGAAAAGACAGAAGAAGGTTTGTTTTGGGGGCTGTTGAGGGTCCATACATTGATGGCTGCTG-------TTCAATGAATTAA-GCAGTATCA -s simDog_chr6.simDog.chr6 439736 93 - 593897 CATTGGAGAGAGAGATCAAGGGCAGTTTGGGGG-CTGATTAGGGCCCATAGATCGTCAGCTGCAGTATTGGCTATAATGAATGAA-GCAACATCA -s simHuman_chr6.simHuman.chr6 143086 94 + 601863 CATTGTAGTGACACAACAAGGGCTGTTTGGGGGGCTGCTGGGGGTCCATACATTGACACCTGCTAGATTGTTTACAATGAATGAA-GCAGTATTA -s simRat_chr6.simRat.chr6 146688 94 + 647215 CAATGTAGAAATGTGAGAGCTGGGGCCTGGGGGCCTGCTGAGGGGCAATACACTGACAGCTACTGGATACACCATATCAAATCAC-ACAGTACTA - -a -s simMouse_chr6.simMouse.chr6 149280 9 + 636262 TTACTATTC -s Anc0.Anc0refChr1 38822 9 - 62388 CTATTATGC -s Anc1.Anc1refChr2 118062 9 + 144309 CTATTATGC -s Anc2.Anc2refChr3 28050 9 + 53186 CCATTATGC -s mr.mrrefChr5 12493 9 + 294540 TTACTATTC -s simCow_chr6.simCow.chr6 156166 9 + 602619 CCATTATGC -s simDog_chr6.simDog.chr6 439835 9 - 593897 CCATTATGC -s simHuman_chr6.simHuman.chr6 143186 9 + 601863 CTATTGTGC -s simRat_chr6.simRat.chr6 146782 9 + 647215 TTACTATTC - -a -s simMouse_chr6.simMouse.chr6 149289 9 + 636262 TTCTCAGAT -s Anc0.Anc0refChr1 38831 9 - 62388 TTTGCAGAA -s Anc1.Anc1refChr2 118071 9 + 144309 TTTGCAGAA -s Anc2.Anc2refChr3 28059 9 + 53186 CTTGCAGAA -s mr.mrrefChr5 12502 9 + 294540 TTTTCAGAT -s simCow_chr6.simCow.chr6 156177 9 + 602619 CTAGCAGAA -s simDog_chr6.simDog.chr6 439844 9 - 593897 CTTGCAGAA -s simHuman_chr6.simHuman.chr6 143195 9 + 601863 TTTGCAGAA -s simRat_chr6.simRat.chr6 146791 8 + 647215 TCT-CAGAT - -a -s simMouse_chr6.simMouse.chr6 149298 17 + 636262 TATTGAGCAGAATGTTA -s Anc0.Anc0refChr1 38840 17 - 62388 TAGTGAGCAGACTGTAA -s Anc1.Anc1refChr2 118080 17 + 144309 TAGTGAGCAGACTGTAA -s Anc2.Anc2refChr3 28068 17 + 53186 TAGTGAGCAAACTGTAA -s mr.mrrefChr5 12511 17 + 294540 TAGTGAGCAGAATGTTA -s simCow_chr6.simCow.chr6 156188 17 + 602619 TAGGGATCAAACAGTAG -s simDog_chr6.simDog.chr6 439853 17 - 593897 TAGTGAGCAAACTGTGA -s simHuman_chr6.simHuman.chr6 143204 17 + 601863 TAGTGAGCAGACTGCAA -s simRat_chr6.simRat.chr6 146799 17 + 647215 TAGGGAGCAGAGTGTGG - -a -s simMouse_chr6.simMouse.chr6 149315 13 + 636262 CTACAGCCAAGGG -s Anc0.Anc0refChr1 38857 13 - 62388 CAAGAGCCAAGGG -s Anc1.Anc1refChr2 118097 13 + 144309 CAAGAGCCAAGGG -s Anc2.Anc2refChr3 28085 13 + 53186 CAAGAGCCAAGGG -s mr.mrrefChr5 12528 13 + 294540 CTACAGCCAAGGG -s simCow_chr6.simCow.chr6 156208 13 + 602619 CAACCGTAAAGGG -s simDog_chr6.simDog.chr6 439870 13 - 593897 CAAGAGCCAGGCG -s simHuman_chr6.simHuman.chr6 143221 13 + 601863 CAATAGCCAAGGG -s simRat_chr6.simRat.chr6 146816 13 + 647215 CTACAGGCAAGGG - -a -s simMouse_chr6.simMouse.chr6 149328 14 + 636262 TCTCCATCATAATT -s Anc0.Anc0refChr1 38880 14 - 62388 TGTTTATTATGATT -s Anc1.Anc1refChr2 118120 14 + 144309 TGTTTATTATGATT -s Anc2.Anc2refChr3 28108 14 + 53186 AGTTTATTATGACT -s mr.mrrefChr5 12541 14 + 294540 TGTCCATCATAATT -s simCow_chr6.simCow.chr6 156226 10 + 602619 ----TATTATGACT -s simDog_chr6.simDog.chr6 439893 8 - 593897 AGTTTGTT------ -s simHuman_chr6.simHuman.chr6 143244 14 + 601863 TGTTTATTATGCTT -s simRat_chr6.simRat.chr6 146829 14 + 647215 TGTCCATCATAATT - -a -s simMouse_chr6.simMouse.chr6 149342 2 + 636262 TA -s Anc0.Anc0refChr1 38895 2 - 62388 TA -s Anc1.Anc1refChr2 118135 2 + 144309 TA -s Anc2.Anc2refChr3 28123 2 + 53186 TA -s mr.mrrefChr5 12556 2 + 294540 TA -s simCow_chr6.simCow.chr6 156237 2 + 602619 TA -s simHuman_chr6.simHuman.chr6 143259 2 + 601863 TA -s simRat_chr6.simRat.chr6 146844 2 + 647215 TA - -a -s simMouse_chr6.simMouse.chr6 149344 26 + 636262 TATGGTTCAAGCCTTGTAAAATGCAG -s Anc0.Anc0refChr1 38902 16 - 62388 TATGCTTCTATTCTT----------T -s Anc1.Anc1refChr2 118142 16 + 144309 TATGCTTCTATTCTT----------T -s Anc2.Anc2refChr3 28130 16 + 53186 TATGCCTCTATTCTT----------T -s mr.mrrefChr5 12558 26 + 294540 TATGGTTCAATCCTTGTAAAATGCAT -s simCow_chr6.simCow.chr6 156257 16 + 602619 TATGACTCTATTCTT----------T -s simDog_chr6.simDog.chr6 439901 16 - 593897 TATACCTCTATTCTT----------T -s simHuman_chr6.simHuman.chr6 143266 16 + 601863 TATGCTTCTATTCTT----------T -s simRat_chr6.simRat.chr6 146846 26 + 647215 TATGGTTCAGTCCTTGTAAAATGCGT - -a -s simMouse_chr6.simMouse.chr6 149370 37 + 636262 CATCTGAATTTAAACAAACACATACTTTAGTATGTGT -s Anc0.Anc0refChr1 38922 33 - 62388 CATCTAAACT---ACAAAATCAGGATTCC-CATGCAT -s Anc1.Anc1refChr2 118162 33 + 144309 CATCTAAACT---ACAAAATCAGGATTCC-CATGCAT -s Anc2.Anc2refChr3 28150 33 + 53186 TATCTATACT---ACATAATCAGGATTCC-CATGCAT -s mr.mrrefChr5 12588 37 + 294540 CATCTGAATTTAAACAAATACATGCTTTAGTATGTGT -s simCow_chr6.simCow.chr6 156277 33 + 602619 TACCTATACT---ACATAACCATGATTTC-CATGCAT -s simDog_chr6.simDog.chr6 439921 33 - 593897 TCTCTATCCT---ATATAATCAGGATTCT-CATTCAT -s simHuman_chr6.simHuman.chr6 143286 33 + 601863 CATCTAAACT---ACGAGATAACGATTCC-CATGCAA -s simRat_chr6.simRat.chr6 146876 37 + 647215 CATCTGGATTTAAACAAATACACGATATAGTATGTGT - -a -s simMouse_chr6.simMouse.chr6 149407 3 + 636262 TAT -s Anc0.Anc0refChr1 38955 3 - 62388 TTT -s Anc1.Anc1refChr2 118195 3 + 144309 TTT -s Anc2.Anc2refChr3 28183 3 + 53186 TTT -s mr.mrrefChr5 12625 3 + 294540 TAT -s simCow_chr6.simCow.chr6 156310 3 + 602619 TTT -s simDog_chr6.simDog.chr6 439954 2 - 593897 TT- -s simHuman_chr6.simHuman.chr6 143319 3 + 601863 TCT -s simRat_chr6.simRat.chr6 146994 3 + 647215 TAT - -a -s simMouse_chr6.simMouse.chr6 149410 41 + 636262 GCCTGGGTCAAAATTCATGGTAATAGTTATTTCTCAGATAG -s Anc0.Anc0refChr1 38959 32 - 62388 ACCTGGGCTTCAATACT-------A--TACATGCTATATTG -s Anc1.Anc1refChr2 118199 32 + 144309 ACCTGGGCTTCAATACT-------A--TACATGCTATATTG -s Anc2.Anc2refChr3 28187 32 + 53186 ACCTGGGCTTCAATACT-------A--GACATGCTATATTG -s mr.mrrefChr5 12628 34 + 294540 GCCTGGGTCAAAATTCA-------AGTTACATCTCAGATAG -s simCow_chr6.simCow.chr6 156314 32 + 602619 ACCTGGGCTTCAATACT-------A--GACATGCTATATTG -s simDog_chr6.simDog.chr6 439956 27 - 593897 -----GGCCTCAATACT-------G--GACATGCTATATTG -s simHuman_chr6.simHuman.chr6 143323 32 + 601863 ACCCAGGCTTGGATACT-------A--TACATGCTGTATTG -s simRat_chr6.simRat.chr6 146997 34 + 647215 GCCTGGGTCAAAATTCA-------ATTCCCATCCCAAAAAT - -a -s simMouse_chr6.simMouse.chr6 149451 8 + 636262 AGGGGGCA -s Anc0.Anc0refChr1 39002 8 - 62388 ATGCCGCA -s Anc1.Anc1refChr2 118242 8 + 144309 ATGCCGCA -s Anc2.Anc2refChr3 28230 8 + 53186 ATGCCGCA -s mr.mrrefChr5 12662 8 + 294540 AGGGGGCA -s simCow_chr6.simCow.chr6 156357 8 + 602619 ACGCTGCT -s simDog_chr6.simDog.chr6 439994 8 - 593897 ATGCCGGA -s simHuman_chr6.simHuman.chr6 143366 8 + 601863 ATGCCGCA -s simRat_chr6.simRat.chr6 147031 8 + 647215 AGGGGGCA - -a -s simMouse_chr6.simMouse.chr6 149459 32 + 636262 TCTAACTTGACTTGTGTATGATGTCATAGAAA -s Anc0.Anc0refChr1 39016 30 - 62388 TCTAATTTGACTTGTAGATTATGCCA--GAGA -s Anc1.Anc1refChr2 118256 32 + 144309 TCTAATTTGACTTGTAGATTATGCCACAGAGA -s Anc2.Anc2refChr3 28244 30 + 53186 TCTACTTTGACTCCTAGATTGTGCTA--AAGA -s mr.mrrefChr5 12670 32 + 294540 TCTAATTTGACTTGTGTATGATGCCATAGAAA -s simCow_chr6.simCow.chr6 156365 26 + 602619 ----CTTTGACTCCTAGATTGTGCTA--AAGA -s simDog_chr6.simDog.chr6 440008 10 - 593897 TCTACTT----------------------AGG -s simHuman_chr6.simHuman.chr6 143380 32 + 601863 TCTAATTTGACTTGTAAATTATACCACAGAGA -s simRat_chr6.simRat.chr6 147039 32 + 647215 TCTAATTTGACTTGTGTATGTTGCTATAGAAA - -a -s simMouse_chr6.simMouse.chr6 149491 16 + 636262 GATGTCTTATGGATAG -s Anc0.Anc0refChr1 39050 16 - 62388 CAAGTCTTGTGAATAA -s Anc1.Anc1refChr2 118292 16 + 144309 CAAGTCTTGTGAATAA -s Anc2.Anc2refChr3 28278 16 + 53186 CAAGTCTTGTGAAGAA -s mr.mrrefChr5 12702 16 + 294540 GATGTCTTATGGATAG -s simCow_chr6.simCow.chr6 156395 16 + 602619 CAAGTCTTATGCAGAG -s simDog_chr6.simDog.chr6 440022 16 - 593897 CAAGTCCTGTGAAGAA -s simHuman_chr6.simHuman.chr6 143416 16 + 601863 CAAATCTTGTGAATAA -s simRat_chr6.simRat.chr6 147071 16 + 647215 GATGTCTTATAGAAAG - -a -s simMouse_chr6.simMouse.chr6 149507 84 + 636262 TGCAGTCTCATGGACACCACCTAGAGACATCCCAGTTTTCCCTGACTTGAAGCACCTCAGATAATGCCCCTGAGAAAAGACTGG -s Anc0.Anc0refChr1 39067 84 - 62388 TGCCATTTTATGAATACCCTCTGGAGACATTCCAGTTTTCACAGGCTCGAAACACCTCAGATGATGTCCCTGAGATTAGACTCG -s Anc1.Anc1refChr2 118309 84 + 144309 TGCCATTTTATGAATACCCTCTGGAGACATTCCAGTTTTCACAGGCTCGAAACACCTCAGATGATGTCCCTGAGATTAGACTCG -s Anc2.Anc2refChr3 28295 84 + 53186 ATCCATTTTATGAATACCCTATGGAGACATTCCAGTTTTCACAAGCTCAAAACACCTCAGATGATGTCCCTGAGATTAGACTCG -s mr.mrrefChr5 12718 84 + 294540 TGCAATCTTATGAACACCACCTGGAGACATCCCAGTTTTCCCTGACTTGAAGCACCTCAGATAATGCCCCTGAGAAAAGACTGG -s simCow_chr6.simCow.chr6 156412 81 + 602619 ATGCATTTTATGAATACCCT---AGGACACTTTCGTTTTCACAAACTCTAAACAGCCCAGATGATGTCCCTGAGATTAGACTGG -s simDog_chr6.simDog.chr6 440040 83 - 593897 ATCCATCTTATGAATACCCCATGGAGACATTCCAGTTATCTCAAGCTCAGAA-ACCTAAGATAATGTCCCTGAGATAAGATTCG -s simHuman_chr6.simHuman.chr6 143433 84 + 601863 TGCTATTTTATGAATTCCCTCTGGTTACATGCCAGTTTTCACAGCCTCGAAACACCTCAGATGATGTCCTTGAGATTAGGCTAG -s simRat_chr6.simRat.chr6 147087 84 + 647215 TGCAATCTTATGAACACCGCCTGCAGACATCCCAATTTTCCCTGGCTTGAAGTACCTCAGATAATGCCCCTGGGAAAAGTCTGG - -a -s simMouse_chr6.simMouse.chr6 149591 21 + 636262 TTAACACATGAGACCTGAATG -s Anc0.Anc0refChr1 39160 21 - 62388 TTGCAAAACTAGCTCTGTATC -s Anc1.Anc1refChr2 118405 21 + 144309 TTGCAAAACTAGCTCTGTATC -s Anc2.Anc2refChr3 28388 21 + 53186 TTGCAAAACTAGCTCTGTGTC -s mr.mrrefChr5 12808 21 + 294540 CTAACACATGAGACCTGAATG -s simCow_chr6.simCow.chr6 156502 21 + 602619 TTGTGAAACTAGCTCTTTGTC -s simDog_chr6.simDog.chr6 440132 21 - 593897 CTGCAAGATTAGCCCTGTGTC -s simHuman_chr6.simHuman.chr6 143532 21 + 601863 TTGCAAAACTAGCTCTGTATC -s simRat_chr6.simRat.chr6 147177 21 + 647215 CTAACACATGAGGCCTGAGTT - -a -s simMouse_chr6.simMouse.chr6 149612 10 + 636262 TTGCTCTCTG -s Anc0.Anc0refChr1 39187 10 - 62388 TTGCTCTCTA -s Anc1.Anc1refChr2 118432 10 + 144309 TTGCTCTCTA -s Anc2.Anc2refChr3 28415 10 + 53186 TTGCTCTAAA -s mr.mrrefChr5 12829 10 + 294540 TTGCTCTCTG -s simCow_chr6.simCow.chr6 156529 10 + 602619 TTGCTCTGCA -s simDog_chr6.simDog.chr6 440154 9 - 593897 -TGCGCTAAC -s simHuman_chr6.simHuman.chr6 143559 10 + 601863 TTGCTCTCTA -s simRat_chr6.simRat.chr6 147198 10 + 647215 TTGCTTGCTG - -a -s simMouse_chr6.simMouse.chr6 149622 32 + 636262 TGATATGGTTCAGCATGCTCTAATATCCAAGT -s Anc0.Anc0refChr1 39198 32 - 62388 TGTCAAGGATCAGCATCTCCTATTATATAAGT -s Anc1.Anc1refChr2 118443 32 + 144309 TGTCAAGGATCAGCATCTCCTATTATATAAGT -s Anc2.Anc2refChr3 28426 32 + 53186 TGTCGAGGATCAGCATCTCCTATCATATAAGT -s mr.mrrefChr5 12839 32 + 294540 TGTCATGGTTCAGCATGTTCTATTATCCAAGT -s simCow_chr6.simCow.chr6 156540 31 + 602619 TGTCGAGGATCAGCATCTC-TATCCTATAATT -s simDog_chr6.simDog.chr6 440164 32 - 593897 TGCTGGGGATCAGTGTTCCCCATCACATAAGT -s simHuman_chr6.simHuman.chr6 143570 32 + 601863 TGTCAAGGAACAGCATCTCCTATTATATAAGT -s simRat_chr6.simRat.chr6 147208 32 + 647215 TGTCATGGGCTAGCATATGCTATCATCCGAGT - -a -s simMouse_chr6.simMouse.chr6 149654 1 + 636262 G -s Anc0.Anc0refChr1 39259 1 - 62388 G -s Anc1.Anc1refChr2 118504 1 + 144309 G -s Anc2.Anc2refChr3 28493 1 + 53186 C -s mr.mrrefChr5 12871 1 + 294540 G -s simCow_chr6.simCow.chr6 156606 1 + 602619 C -s simDog_chr6.simDog.chr6 440231 1 - 593897 C -s simHuman_chr6.simHuman.chr6 143634 1 + 601863 G -s simRat_chr6.simRat.chr6 147240 1 + 647215 G - -a -s simMouse_chr6.simMouse.chr6 149655 31 + 636262 GTGTCAGTTAGGGAGTTTGGGTTGTAAGCGG -s Anc0.Anc0refChr1 39260 31 - 62388 CCTTCAGTTAGGTACTTTGGGATGGATGCGG -s Anc1.Anc1refChr2 118505 31 + 144309 CCTTCAGTTAGGTACTTTGGGATGGATGCGG -s Anc2.Anc2refChr3 28494 31 + 53186 CCTTCAGTTAGGTACATTGGGATGGTTACGG -s mr.mrrefChr5 12872 31 + 294540 GTGTCAGTTAGGGAGTTTGGGTTGTAAGCGG -s simCow_chr6.simCow.chr6 156654 31 + 602619 CTTTCAGTTAGGTACATTGGGATGGTTACGG -s simDog_chr6.simDog.chr6 440232 31 - 593897 CCTTCAGTTAGGTACATTGGGATGGTTACGT -s simHuman_chr6.simHuman.chr6 143635 31 + 601863 CCCTCAGTTAGCTATTTTGGGATGGATGCGG -s simRat_chr6.simRat.chr6 147241 31 + 647215 TTGTCAGTTAGGGAGTGTGGGTTGTGAGCGG - -a -s simMouse_chr6.simMouse.chr6 149686 11 + 636262 GTTTGATGGCA -s Anc0.Anc0refChr1 39291 7 - 62388 G----ATGGCC -s Anc1.Anc1refChr2 118536 11 + 144309 GCTAGATGGCC -s Anc2.Anc2refChr3 28525 7 + 53186 G----ATGGCC -s mr.mrrefChr5 12903 11 + 294540 GTTTGATGGCA -s simCow_chr6.simCow.chr6 156685 7 + 602619 G----ATGGCC -s simDog_chr6.simDog.chr6 440263 7 - 593897 G----ATGTCT -s simHuman_chr6.simHuman.chr6 143669 11 + 601863 GCTAGAGGGCC -s simRat_chr6.simRat.chr6 147272 11 + 647215 GTTTGATGACA - -a -s simMouse_chr6.simMouse.chr6 149697 128 + 636262 AGGGACAGAATCCTTGGCTTTATAGCAAGGGACAGGCTCCCATATGCACATCATGTTATTAAAATCTATCCCTCGGAGCTCAATTCATTACTGAGGCAATAAATCATCCCTCCTGTGTGTAGAAGACC -s Anc0.Anc0refChr1 39298 14 - 62388 AGGGACAGAATCCT------------------------------------------------------------------------------------------------------------------ -s Anc1.Anc1refChr2 118547 33 + 144309 AGGGACAGAATCCTGGG-------------------------------------------------------------------------------------------TATCCTGGGTCTC----ACT -s Anc2.Anc2refChr3 28532 14 + 53186 AGAGACAGAATTCT------------------------------------------------------------------------------------------------------------------ -s mr.mrrefChr5 12914 128 + 294540 AGGGACAGAATCCTGGGCTTGATAGCAAGGGACAGGCTCCCATATGCACATCATGTTATTAAAATCTATCCCTCGGAGCTCAATTCATTACTGAGGCAATAAATCATCCCTCCTGTGTGTAGAAGACC -s simCow_chr6.simCow.chr6 156692 14 + 602619 AGAGGCTGAATTGG------------------------------------------------------------------------------------------------------------------ -s simDog_chr6.simDog.chr6 440270 14 - 593897 AGAGACAGAATTCT------------------------------------------------------------------------------------------------------------------ -s simHuman_chr6.simHuman.chr6 143680 33 + 601863 AGGGACAGAATCCTGGG-------------------------------------------------------------------------------------------TATCCTGGGTCTC----ACT -s simRat_chr6.simRat.chr6 147289 128 + 647215 AGGGATAGTATCCTGGGCTTGATGGCATGGGACAGACTCCCATATATGCAACATGTTACTTAACTCTATCCCTTGGAGCTCAATTCATTACTGAGGCATTAAATCATATCTTCTGAGTGTACATGATC - -a -s simMouse_chr6.simMouse.chr6 149825 34 + 636262 TGCCACAGTTCACAAATGCTCAAAATTCAATGGG -s Anc0.Anc0refChr1 39312 11 - 62388 -----------ACACATGCTCA------------ -s Anc1.Anc1refChr2 118580 22 + 144309 TGTTGTATGTAACACATGCTCA------------ -s Anc2.Anc2refChr3 28546 11 + 53186 -----------AAACATGCTCA------------ -s mr.mrrefChr5 13042 34 + 294540 TGCCACAGTTCACAAATGCTCAAAATTCAATGGG -s simCow_chr6.simCow.chr6 156706 11 + 602619 -----------TAATAGGCACA------------ -s simDog_chr6.simDog.chr6 440284 11 - 593897 -----------AAACATGCTCA------------ -s simHuman_chr6.simHuman.chr6 143713 22 + 601863 TGTTGTATGTAACGGATGCTCA------------ -s simRat_chr6.simRat.chr6 147423 34 + 647215 TTCCACAGCTTACAAATGCTGAAAATTCCATGGG - -a -s simMouse_chr6.simMouse.chr6 149859 4 + 636262 AAAG -s Anc0.Anc0refChr5 72043 4 - 87904 GAAG -s Anc1.Anc1refChr8 28404 4 - 57822 GAAG -s Anc2.Anc2refChr15 77135 4 - 86568 GAAG -s mr.mrrefChr5 13098 4 + 294540 AAAG -s simCow_chr6.simCow.chr6 410054 4 - 602619 GAAG -s simDog_chr6.simDog.chr6 473874 4 - 593897 GAAG -s simHuman_chr6.simHuman.chr6 405358 4 - 601863 GGGG -s simRat_chr6.simRat.chr6 147479 4 + 647215 AAAG - -a -s simMouse_chr6.simMouse.chr6 149863 7 + 636262 TGATTTC -s Anc0.Anc0refChr5 72047 7 - 87904 TGAGTTC -s Anc1.Anc1refChr8 28408 7 - 57822 TGAGTTC -s Anc2.Anc2refChr15 77139 7 - 86568 TGAGTGT -s mr.mrrefChr5 13102 7 + 294540 TGATTTC -s simCow_chr6.simCow.chr6 410058 7 - 602619 TGACTGT -s simDog_chr6.simDog.chr6 473883 7 - 593897 TGGGTGT -s simHuman_chr6.simHuman.chr6 405362 7 - 601863 TGAGTTC -s simRat_chr6.simRat.chr6 147483 7 + 647215 TGATTTC - -a -s simMouse_chr6.simMouse.chr6 149870 25 + 636262 ATGCTATACCTTTGGGCATGACTGG -s Anc0.Anc0refChr5 72054 19 - 87904 CACC--T---TCTGG-CATGACTGG -s Anc1.Anc1refChr8 28415 21 - 57822 CACCTTT---TCTGG-CATGACTGG -s Anc2.Anc2refChr15 77146 19 - 86568 CACC--T---TCTGG-CATCACTGG -s mr.mrrefChr5 13109 24 + 294540 ATGCTATACCTTTGG-CATGACTGG -s simCow_chr6.simCow.chr6 410076 19 - 602619 CACC--T---TGTGG-CATCACTGG -s simDog_chr6.simDog.chr6 473890 19 - 593897 CACC--T---CCCGG-CATCACTGG -s simHuman_chr6.simHuman.chr6 405369 21 - 601863 CCTCTTT---TCTGG-CATGACTGG -s simRat_chr6.simRat.chr6 147490 24 + 647215 ATGCTCTACGCTCGG-CATGACTGG - -a -s simMouse_chr6.simMouse.chr6 149895 148 + 636262 GAATGGGATAAGAAAAGCTATGATGTGCTACTAGGTATGAGAGACTGGTCTAATGATAGCCAGAATGTCCTTGCCAGCGGGTGAATACGATTATTTGGCCGTTTGCACAATCATTTGGCTGCTGTTGTTCAGATTATAACTTACCAAC -s Anc0.Anc0refChr5 72074 25 - 87904 AACTGGGATGAGAGATACTAAATTG--------------------------------------------------------------------------------------------------------------------------- -s Anc1.Anc1refChr8 28437 25 - 57822 AACTGGGATGAGAGATACTAAATTG--------------------------------------------------------------------------------------------------------------------------- -s Anc2.Anc2refChr15 77166 25 - 86568 AACTGGGATGACAGATACTAAATTG--------------------------------------------------------------------------------------------------------------------------- -s mr.mrrefChr5 13133 25 + 294540 AACTGGGATGAGAAATGCTATGATG--------------------------------------------------------------------------------------------------------------------------- -s simCow_chr6.simCow.chr6 410096 25 - 602619 AACTGGGGTGAAAGACACTAAATTC--------------------------------------------------------------------------------------------------------------------------- -s simDog_chr6.simDog.chr6 473910 25 - 593897 AACAGGGATAACAGATGCTAAATTG--------------------------------------------------------------------------------------------------------------------------- -s simHuman_chr6.simHuman.chr6 405391 25 - 601863 AACTGAAATGAGAGATACTAAATTG--------------------------------------------------------------------------------------------------------------------------- -s simRat_chr6.simRat.chr6 147514 25 + 647215 AACTGTGATGAGAAATGATGTTATG--------------------------------------------------------------------------------------------------------------------------- - -a -s simMouse_chr6.simMouse.chr6 150043 46 + 636262 AATTGGGTTGGCATGTCAGACCTCGATAGTTATGTTGACTAGACTG -s Anc0.Anc0refChr5 72118 46 - 87904 AGTTGGGATGGCACCTCAGGCCCCAACAGTTGGGTTGGCTAGACTG -s Anc1.Anc1refChr8 28481 46 - 57822 AGTTGGGATGGCACCTCAGGCCCCAACAGTTGGGTTGGCTAGACTG -s Anc2.Anc2refChr15 77210 46 - 86568 AGTTGGGATGGCACCTCAGGCCCCAACAGTTGGGTTGGCTAGACTG -s mr.mrrefChr5 13158 46 + 294540 AGTTGGGTTGGCATGTCAGACCCCAACAGTTATGTTGACTAGACTG -s simCow_chr6.simCow.chr6 410143 46 - 602619 AGTTGAGTTGGCACGTCAGGCCCCAACAGATGGGTTGGCCAGACTA -s simDog_chr6.simDog.chr6 473948 46 - 593897 AGTTGGGATGGCACCTCAGGCCCCAACAGTTGGGGTGGCTAGACTG -s simHuman_chr6.simHuman.chr6 405435 46 - 601863 AGGCGGGCTGGCACCTCAGCCCCCAACAGTTGGGTTGGCTAGGCTG -s simRat_chr6.simRat.chr6 147539 38 + 647215 AG--------GCGTGTCAGACACCAACAGTTATGTTGACTAGAATG - -a -s simMouse_chr6.simMouse.chr6 150089 16 + 636262 GGTATGGGCTTAAGAG -s Anc0.Anc0refChr5 72164 9 - 87904 GGTTTATG-------A -s Anc1.Anc1refChr8 28527 9 - 57822 GGTTTATG-------A -s Anc2.Anc2refChr15 77256 9 - 86568 GGTTGATG-------A -s mr.mrrefChr5 13204 16 + 294540 GGTATGGGCTTAAGAG -s simCow_chr6.simCow.chr6 410194 9 - 602619 GGTTGATT-------A -s simDog_chr6.simDog.chr6 473994 9 - 593897 TACTGATG-------G -s simHuman_chr6.simHuman.chr6 405481 9 - 601863 GGTTTATG-------A -s simRat_chr6.simRat.chr6 147577 16 + 647215 GGTATGGGCCTAAGAG - -a -s simMouse_chr6.simMouse.chr6 150105 10 + 636262 GGGCAGCATT -s Anc0.Anc0refChr5 72173 10 - 87904 CGGCCGCAGC -s Anc1.Anc1refChr8 28536 10 - 57822 CGGCCGCAGC -s Anc2.Anc2refChr15 77265 10 - 86568 CGGCCGCAGC -s mr.mrrefChr5 13220 10 + 294540 GGGCAGCATT -s simCow_chr6.simCow.chr6 410214 10 - 602619 CCACAGCAGC -s simDog_chr6.simDog.chr6 474003 10 - 593897 TGGCCACAGC -s simHuman_chr6.simHuman.chr6 405490 10 - 601863 CAGCTGCAGC -s simRat_chr6.simRat.chr6 147593 10 + 647215 GGCCAGCATT - -a -s simMouse_chr6.simMouse.chr6 150115 10 + 636262 AGCCACATGA -s Anc0.Anc0refChr5 72184 9 - 87904 CAAT-TATGC -s Anc1.Anc1refChr8 28547 10 - 57822 CAATATATGC -s Anc2.Anc2refChr15 77276 9 - 86568 CAAT-TATGC -s mr.mrrefChr5 13230 10 + 294540 AGCCACATGA -s simCow_chr6.simCow.chr6 410225 9 - 602619 AGTT-TATCC -s simDog_chr6.simDog.chr6 474014 9 - 593897 CAAT-TTCGC -s simHuman_chr6.simHuman.chr6 405501 10 - 601863 CAATATATGC -s simRat_chr6.simRat.chr6 147603 10 + 647215 GGGGGCATAA - -a -s simMouse_chr6.simMouse.chr6 150125 64 + 636262 GGGGGCAGGTAAGTAACTGAAGCACTAACTACCATCATTCAATGTCCCTAAATTATTTAGATAT -s Anc0.Anc0refChr5 72193 22 - 87904 TG------------------------------------------TGCCCAAATCATTCAGACAT -s Anc1.Anc1refChr8 28557 22 - 57822 TG------------------------------------------TGCCCAAATCATTCAGACAT -s Anc2.Anc2refChr15 77285 22 - 86568 TG------------------------------------------TGGTCAAACCATTCAAAGAC -s mr.mrrefChr5 13240 22 + 294540 TG------------------------------------------TCCCCAAATTATTTAGACAT -s simCow_chr6.simCow.chr6 410234 22 - 602619 TG------------------------------------------TGGTCGCACCATTTTCAGAC -s simDog_chr6.simDog.chr6 474023 22 - 593897 TG------------------------------------------TGGTCAAACCATTCAAAGAT -s simHuman_chr6.simHuman.chr6 405511 22 - 601863 TA------------------------------------------TGCCCAAATGATTCAGACAT -s simRat_chr6.simRat.chr6 147644 22 + 647215 TG------------------------------------------TCTCCAAATTATTTAGACAT - -a -s simMouse_chr6.simMouse.chr6 150189 2 + 636262 AA -s Anc0.Anc0refChr5 72215 2 - 87904 CA -s Anc1.Anc1refChr8 28579 2 - 57822 CA -s Anc2.Anc2refChr15 77307 2 - 86568 CT -s mr.mrrefChr5 13262 2 + 294540 AA -s simCow_chr6.simCow.chr6 410256 2 - 602619 TT -s simDog_chr6.simDog.chr6 474045 2 - 593897 CA -s simHuman_chr6.simHuman.chr6 405533 2 - 601863 CA -s simRat_chr6.simRat.chr6 147772 2 + 647215 AG - -a -s simMouse_chr6.simMouse.chr6 150191 12 + 636262 CATAAATTCAGT -s Anc0.Anc0refChr5 72229 12 - 87904 CAGACCTTCAAG -s Anc1.Anc1refChr8 28593 12 - 57822 CAGACCTTCAAG -s Anc2.Anc2refChr15 77321 12 - 86568 CAGACCTTCAAG -s mr.mrrefChr5 13264 12 + 294540 CATAAATTCAGT -s simCow_chr6.simCow.chr6 410270 12 - 602619 GAGACATTCAAG -s simDog_chr6.simDog.chr6 474058 12 - 593897 CAGACCTTTCAC -s simHuman_chr6.simHuman.chr6 405547 12 - 601863 CAGAGCTTCAAG -s simRat_chr6.simRat.chr6 147774 12 + 647215 CATAAATCCAAT - -a -s simMouse_chr6.simMouse.chr6 150203 27 + 636262 AGATAATTGAGATCTCAGGTCGGAGTT -s Anc0.Anc0refChr5 72267 27 - 87904 ACATAATCCGTATCTTAGCTCGGAGTT -s Anc1.Anc1refChr8 28631 27 - 57822 ACATAATCCGTATCTTAGCTCGGAGTT -s Anc2.Anc2refChr15 77359 27 - 86568 ACATAATCCGTATCTTAGCTAGGAGTC -s mr.mrrefChr5 13276 27 + 294540 AGATAATTGAGATCTCAAGTCGGAGTT -s simCow_chr6.simCow.chr6 410308 27 - 602619 ACATAATTCATATCTTAGCTAGTAGTC -s simDog_chr6.simDog.chr6 474096 27 - 593897 ACATAATCTGTATCTTAGCTAGGAGTC -s simHuman_chr6.simHuman.chr6 405585 20 - 601863 ACATAAGCCGTA-------TCAGAGAT -s simRat_chr6.simRat.chr6 147786 27 + 647215 ATATAATTGAGATCTTAAGTAGGAGTT - -a -s simMouse_chr6.simMouse.chr6 150230 14 + 636262 CATAAGGTCAGCCA -s Anc0.Anc0refChr5 72294 14 - 87904 CATAGGATCAGCCC -s Anc1.Anc1refChr8 28658 14 - 57822 CATAGGATCAGCCC -s Anc2.Anc2refChr15 77386 14 - 86568 CATAGGATCAGCCC -s mr.mrrefChr5 13303 14 + 294540 CATAAGGTCAGCCC -s simCow_chr6.simCow.chr6 410335 14 - 602619 CATAGAACCAGCCC -s simDog_chr6.simDog.chr6 474125 14 - 593897 CATAGGATCAACGC -s simHuman_chr6.simHuman.chr6 405605 14 - 601863 CTTAGGAGTAGCCC -s simRat_chr6.simRat.chr6 147813 14 + 647215 CATAAGGTCAGCCC - -a -s simMouse_chr6.simMouse.chr6 150244 19 + 636262 TTATAGACACCTGACATAC -s Anc0.Anc0refChr5 72360 14 - 87904 TTTTAGACATCTG-----T -s Anc1.Anc1refChr8 28724 14 - 57822 TTTTAGACATCTG-----T -s Anc2.Anc2refChr15 77452 14 - 86568 TTTTGGACATGTG-----T -s mr.mrrefChr5 13317 19 + 294540 TTATAGACACCTGACATAT -s simCow_chr6.simCow.chr6 410392 14 - 602619 TTTTTGACATGTG-----T -s simDog_chr6.simDog.chr6 474198 14 - 593897 ATTTGGACATGTG-----T -s simHuman_chr6.simHuman.chr6 405672 14 - 601863 TTTCAGACATCTG-----T -s simRat_chr6.simRat.chr6 147827 19 + 647215 TTATAGATACTTGACACAT - -a -s simMouse_chr6.simMouse.chr6 150263 4 + 636262 TGTG -s Anc0.Anc0refChr5 72374 4 - 87904 CCTT -s Anc1.Anc1refChr8 28738 4 - 57822 CCTT -s Anc2.Anc2refChr15 77468 4 - 86568 CCAT -s mr.mrrefChr5 13336 4 + 294540 TGTG -s simCow_chr6.simCow.chr6 410408 4 - 602619 CACT -s simDog_chr6.simDog.chr6 474214 4 - 593897 CCAT -s simHuman_chr6.simHuman.chr6 405686 4 - 601863 CTTT -s simRat_chr6.simRat.chr6 147846 4 + 647215 TGTG - -a -s simMouse_chr6.simMouse.chr6 150267 25 + 636262 TTTTAGCAGTCACATGCCACATCAT -s Anc0.Anc0refChr5 72378 25 - 87904 TTTTACTAGCCAGATAACACATCAT -s Anc1.Anc1refChr8 28742 25 - 57822 TTTTACTAGCCAGATAACACATCAT -s Anc2.Anc2refChr15 77472 25 - 86568 TTTTACTAGCCAGATAACACATCAT -s mr.mrrefChr5 13340 25 + 294540 TTTTAGTAGCCACATGCCACATCAT -s simCow_chr6.simCow.chr6 410415 25 - 602619 TTTTGGTGACCGTATAACACCTCAC -s simDog_chr6.simDog.chr6 474218 25 - 593897 GTTTACTAGCCAGATAACACATCAT -s simHuman_chr6.simHuman.chr6 405690 25 - 601863 TTTTATTAGCAAGATCTCACATCAT -s simRat_chr6.simRat.chr6 147850 25 + 647215 TTTTAGTAGCCTCATGCCACATCAT - -a -s simMouse_chr6.simMouse.chr6 150292 6 + 636262 TGTGAA -s Anc0.Anc0refChr5 72403 6 - 87904 CTTTAA -s Anc1.Anc1refChr8 28767 6 - 57822 CTTTAA -s Anc2.Anc2refChr15 77497 6 - 86568 CTTTAA -s mr.mrrefChr5 13365 6 + 294540 TGTGAA -s simCow_chr6.simCow.chr6 410440 6 - 602619 CTTAAA -s simDog_chr6.simDog.chr6 474246 4 - 593897 CTTT-- -s simHuman_chr6.simHuman.chr6 405715 6 - 601863 CTTTAA -s simRat_chr6.simRat.chr6 147875 6 + 647215 TGTGAA - -a -s simMouse_chr6.simMouse.chr6 150298 29 + 636262 CCTGTTTTCAAGTCCAAGCTATGGATATT -s Anc0.Anc0refChr5 72410 25 - 87904 --TATTCTCAGACCCATGCTATGTATG-- -s Anc1.Anc1refChr8 28774 29 - 57822 TCTATTCTCAGACCCATGCTATGTATGTT -s Anc2.Anc2refChr15 77504 25 - 86568 --TATTCTTAGACCCATGCTGTGTATG-- -s mr.mrrefChr5 13371 29 + 294540 CCTGTTTTCAAACCCAAGCTATGGATATT -s simCow_chr6.simCow.chr6 410447 25 - 602619 --TATTCTTAGACCCATGCTGTGTATG-- -s simHuman_chr6.simHuman.chr6 405722 29 - 601863 TCTATTCTCAGACCAATGCTATGTAGGTT -s simRat_chr6.simRat.chr6 147881 29 + 647215 CCTGTCTCCATACCCAAGCTGTGGATATT - -a -s simMouse_chr6.simMouse.chr6 150327 34 + 636262 TCAGATGCGCCATGCCTGCTAATCCATTAGCTGC -s Anc0.Anc0refChr5 72435 28 - 87904 TTTGATGCTCCAAGCTTGCTAGCCTGTT------ -s Anc1.Anc1refChr8 28803 28 - 57822 TTTGATGCTCCAAGCTTGCTAGCCTGTT------ -s Anc2.Anc2refChr15 77529 28 - 86568 TTTGATGTTTCAAGCTTGCTAGCCTGTT------ -s mr.mrrefChr5 13400 34 + 294540 TTAGATGCGCCATGCCTGCTAGTCCATTAGCTGC -s simCow_chr6.simCow.chr6 410472 28 - 602619 TTTGATGTTTCAAGCTTGCTAGCCTGTT------ -s simHuman_chr6.simHuman.chr6 405752 28 - 601863 TTTAATGCCCCAAGCTTGCTAGCCAGTT------ -s simRat_chr6.simRat.chr6 147910 34 + 647215 TTAGATTCACCATGCCTGCTAGTCCATGAGCGGC - -a -s simMouse_chr6.simMouse.chr6 150361 27 + 636262 ATTGTGTTTACAGGGACATACAAGAAT -s Anc0.Anc0refChr5 72463 27 - 87904 ATTGTGTTTGTAATGACCAAAAAAAAT -s Anc1.Anc1refChr8 28831 27 - 57822 ATTGTGTTTGTAATGACCAAAAAAAAT -s Anc2.Anc2refChr15 77557 27 - 86568 ATTGTGTTTGTAATGTCCAAAACAACT -s mr.mrrefChr5 13434 27 + 294540 ATTGTGTTTGCAGGGACCAACAAGAAT -s simCow_chr6.simCow.chr6 410506 27 - 602619 ATTGTGTTTGTAATGTCCAAAACAACT -s simHuman_chr6.simHuman.chr6 405780 27 - 601863 ATGGTGTTTGTAAAGACCAATGAAAAT -s simRat_chr6.simRat.chr6 147944 27 + 647215 ATTGTCTTTGCAGGGACCAAAAAGAAA - -a -s simMouse_chr6.simMouse.chr6 150388 37 + 636262 GCTACTCATTATAGACATAGGGTTTGAGACCCCTGTA -s Anc0.Anc0refChr5 72490 37 - 87904 GCTACTCCCTGTGGATGTATGGTTTGAGACCCATGCA -s Anc1.Anc1refChr8 28858 37 - 57822 GCTACTCCCTGTGGATGTATGGTTTGAGACCCATGCA -s Anc2.Anc2refChr15 77584 37 - 86568 GCTACTCCCTGAGGCTGTATAGTTTGAGACCCATGCA -s mr.mrrefChr5 13461 37 + 294540 GCTACTCATTATAGACATATGGTTTGAGACCCCTGTA -s simCow_chr6.simCow.chr6 410535 26 - 602619 GTTGCACCCCAAGGCTG-----------ACCCATGCA -s simDog_chr6.simDog.chr6 474250 36 - 593897 -CCACTCCCTGAGGCAGTATAGTTTGAGACCCATGCA -s simHuman_chr6.simHuman.chr6 405807 37 - 601863 GCTCCCCCATCTGGATGTGTGGTTTGAGACCCATGCA -s simRat_chr6.simRat.chr6 147971 37 + 647215 GCTACTCACTATAGACATATGGTTTAAGACCCCCGTA - -a -s simMouse_chr6.simMouse.chr6 150425 7 + 636262 AATCTAA -s Anc0.Anc0refChr5 72527 7 - 87904 ACTAAGG -s Anc1.Anc1refChr8 28895 7 - 57822 ACTAAGG -s Anc2.Anc2refChr15 77624 7 - 86568 ACTAAGA -s mr.mrrefChr5 13498 7 + 294540 AATCTAG -s simCow_chr6.simCow.chr6 410564 7 - 602619 GTTAAGA -s simDog_chr6.simDog.chr6 474289 7 - 593897 ACTAAGA -s simHuman_chr6.simHuman.chr6 405844 7 - 601863 ACTAAGG -s simRat_chr6.simRat.chr6 148008 7 + 647215 AATCTAG - -a -s simMouse_chr6.simMouse.chr6 150432 84 + 636262 TAGAGTGAAAAGTAGTAGGCTTCTCTTTTCTAATGTGATTGCTTCTCTACTGTCAGCTCTCTAACTCGATTGCTTCTCTACTGT -s Anc0.Anc0refChr5 72534 52 - 87904 TAGAGTCAT-AGTAGCAGGCTTCCCTCTTCTAAGTT-------------------------------GATTGCTTTTCTGCTGT -s Anc1.Anc1refChr8 28902 52 - 57822 TAGAGTCAT-AGTAGCAGGCTTCCCTCTTCTAAGTT-------------------------------GATTGCTTTTCTGCTGT -s Anc2.Anc2refChr15 77631 52 - 86568 TAGAGTCAT-AGTAGCAGGCTTCCCTCTTCTAAGTT-------------------------------GATTGCTTTTCTGCTGT -s mr.mrrefChr5 13505 84 + 294540 TAGAGTGATAAGTAGTAGGCTTCCCTTTTCTAATGTGATTGCTTCTCTACTGTCAGCTCTCTAACTCGATTGCTTCTCTACTGT -s simCow_chr6.simCow.chr6 410571 52 - 602619 TAAAATCGT-AGTCACAAGCTTCCCTCATCTGAGTT-------------------------------GGTTGCTTTTCTCCTGT -s simDog_chr6.simDog.chr6 474296 52 - 593897 TAGAGTCAC-AGTAGCAGACTTCCCACTTCTAAGTT-------------------------------GACTGCTTCTTTGCTGT -s simHuman_chr6.simHuman.chr6 405865 52 - 601863 TAGAGCCAT-GGTACCAGGCTTCCCTCTTCTAAGAT-------------------------------CATTGCTCTTCCGCTGT -s simRat_chr6.simRat.chr6 148015 84 + 647215 TAGAGTAATAAGTAGTAGGCTTCCCCTTTCTAACGTAATTGCTTCTCTACTGTCTACTCTCTAACTTGATTGCTTCTCTACTGT - -a -s simMouse_chr6.simMouse.chr6 150516 46 + 636262 CAACCCTATCATCTATTGACCAGACGGAGGAAATATCATTTGCCAT -s Anc0.Anc0refChr5 72586 45 - 87904 CAACTCTGTCATCTCTTG-ACAGTTGGAGGAAATATCATTTACCAT -s Anc1.Anc1refChr8 28954 45 - 57822 CAACTCTGTCATCTCTTG-ACAGTTGGAGGAAATATCATTTACCAT -s Anc2.Anc2refChr15 77683 45 - 86568 CAACTATGTCATCTCTTG-ATGGTTGGAGACAATATCATTTATCAT -s mr.mrrefChr5 13589 46 + 294540 CAACTCTATCATCTATTGACCAGATGGAGGAAATATCATTTACCAT -s simCow_chr6.simCow.chr6 410631 45 - 602619 CACCTATATCATCACTGG-ATGGTTGGTGACAATATTATTTATCAT -s simDog_chr6.simDog.chr6 474348 45 - 593897 TAACTATGTCATCTCTTG-ATGGTTGGAGACAACCTCATTTATCAT -s simHuman_chr6.simHuman.chr6 405917 45 - 601863 CAACTCTGTTATTTCTTG-TCAGTTGGAGGAAATATCAGTTACCAT -s simRat_chr6.simRat.chr6 148099 46 + 647215 CAACTCTATCATCTATTGACCAGATGGAAAAAATATCATTTACCAT - -a -s simMouse_chr6.simMouse.chr6 150562 6 + 636262 TCCTGA -s Anc0.Anc0refChr5 72632 6 - 87904 TCTTGA -s Anc1.Anc1refChr8 29000 6 - 57822 TCTTGA -s Anc2.Anc2refChr15 77729 6 - 86568 TCTTGA -s mr.mrrefChr5 13635 6 + 294540 TCCTGA -s simCow_chr6.simCow.chr6 410677 6 - 602619 GCTTGA -s simDog_chr6.simDog.chr6 474394 1 - 593897 T----- -s simHuman_chr6.simHuman.chr6 405963 6 - 601863 TCTCGA -s simRat_chr6.simRat.chr6 148145 6 + 647215 TCCTGA - -a -s simMouse_chr6.simMouse.chr6 150568 6 + 636262 ACAGGT -s Anc0.Anc0refChr5 72638 6 - 87904 ACAGTT -s Anc1.Anc1refChr8 29006 6 - 57822 ACAGTT -s Anc2.Anc2refChr15 77735 6 - 86568 ACAGTC -s mr.mrrefChr5 13641 6 + 294540 ACAGGT -s simCow_chr6.simCow.chr6 410683 6 - 602619 ACATTC -s simDog_chr6.simDog.chr6 120338 6 + 593897 CAAGAC -s simHuman_chr6.simHuman.chr6 405969 6 - 601863 ACAGTT -s simRat_chr6.simRat.chr6 148151 6 + 647215 ACAGAT - -a -s simMouse_chr6.simMouse.chr6 150574 1 + 636262 T -s Anc0.Anc0refChr5 72644 1 - 87904 T -s Anc1.Anc1refChr8 29012 1 - 57822 T -s Anc2.Anc2refChr15 77741 1 - 86568 T -s mr.mrrefChr5 13647 1 + 294540 T -s simCow_chr6.simCow.chr6 410690 1 - 602619 G -s simDog_chr6.simDog.chr6 120344 1 + 593897 T -s simHuman_chr6.simHuman.chr6 405975 1 - 601863 T -s simRat_chr6.simRat.chr6 148157 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 150575 27 + 636262 AGTCATCCAGTTGGGAAAGTTACAAAT -s Anc0.Anc0refChr5 72647 27 - 87904 AGATATTCAGTTGGAGAGGTCACAACT -s Anc1.Anc1refChr8 29015 27 - 57822 AGATATTCAGTTGGAGAGGTCACAACT -s Anc2.Anc2refChr15 77744 27 - 86568 AGATATTCAGCTGCAGAGGTCACAACT -s mr.mrrefChr5 13648 27 + 294540 AGTCATCCAGTTGGGGAAGTCACAAAT -s simCow_chr6.simCow.chr6 410693 27 - 602619 AGATATTCAGCTGCAGAGGTCACAACT -s simDog_chr6.simDog.chr6 120347 25 + 593897 --ATATTCAGCTGCTCAAGTCACAACC -s simHuman_chr6.simHuman.chr6 405978 27 - 601863 AGATATTCAGTTGGAGAGGTCACAACT -s simRat_chr6.simRat.chr6 148158 27 + 647215 AGTGATCCAGTTGGGGAAGTCACGAGT - -a -s simMouse_chr6.simMouse.chr6 150602 64 + 636262 CATCTGATGATATAAGCACACAACTCATTAGTCAACCTTGTATTATTATTCCGAATCACCCATG -s Anc0.Anc0refChr5 72685 55 - 87904 CATATGA--------GAGTACAACTCATTAGTC-ACTTGGCAGTATTGCTCCAAATCACACAGG -s Anc1.Anc1refChr8 29053 56 - 57822 CATATGA--------GAGTACAACTCATTAGTCAACTTGGCAGTATTGCTCCAAATCACACAGG -s Anc2.Anc2refChr15 77783 55 - 86568 CATACAA--------CAGTACAACTAATTGGTC-ACTTGGCAGCATTGCTCCAAATCACACGGG -s mr.mrrefChr5 13686 64 + 294540 CATATGATGATATAAGCATACAACTCATTAGTCAACTTTGCATTATTGTTCCAAATCACACATG -s simCow_chr6.simCow.chr6 410732 55 - 602619 TATACAA--------TGGTACACTTTATTGGAC-ACCTGGTTGCATCACTTCAAATCACACGAG -s simDog_chr6.simDog.chr6 120384 55 + 593897 CACACAG--------CAGTACAACTAATTGGTC-ACTTGTCAGCATTGCCCCCAATCACACGGG -s simHuman_chr6.simHuman.chr6 406016 56 - 601863 CATATGA--------GTGTATAACACATTAGCCAAATTGGCCCTATTGCTCCAAACCACACAGG -s simRat_chr6.simRat.chr6 148196 64 + 647215 CATATGAGAATATAAACATACAACTCACTAGTGAACTTTGCATTATTGTTTCAAATTACACATG - -a -s simMouse_chr6.simMouse.chr6 150666 1 + 636262 C -s Anc0.Anc0refChr5 72740 1 - 87904 C -s Anc1.Anc1refChr8 29109 1 - 57822 C -s Anc2.Anc2refChr15 77839 1 - 86568 C -s mr.mrrefChr5 13750 1 + 294540 C -s simCow_chr6.simCow.chr6 410788 1 - 602619 C -s simDog_chr6.simDog.chr6 120440 1 + 593897 C -s simHuman_chr6.simHuman.chr6 406079 1 - 601863 C -s simRat_chr6.simRat.chr6 148260 1 + 647215 C - -a -s simMouse_chr6.simMouse.chr6 150667 31 + 636262 ACTGGTTCTTCTCTAGTGATGATTAAGATCA -s Anc0.Anc0refChr5 72741 31 - 87904 ACTGGCCATTCTCTGTTGAGGATTGTGAGTA -s Anc1.Anc1refChr8 29110 31 - 57822 ACTGGCCATTCTCTGTTGAGGATTGTGAGTA -s Anc2.Anc2refChr15 77840 31 - 86568 ACTGGCCATTCTCTGTTGAGGATTGTGAGTA -s mr.mrrefChr5 13751 31 + 294540 ACTGGCTCTTCTCTAGTGATGATTGAGATCA -s simCow_chr6.simCow.chr6 410789 31 - 602619 AGTGGCCTTTCACTGTTGAGGATTGTGAGTA -s simDog_chr6.simDog.chr6 120441 18 + 593897 ACTGGCCATTCTCT----AGGA--------- -s simHuman_chr6.simHuman.chr6 406080 31 - 601863 ACTGGCCATCCTCTGTTGAGGATTGTGGGTG -s simRat_chr6.simRat.chr6 148262 31 + 647215 ACTGGCTCTTCTCTAGTGATGACTGAGATCA - -a -s simMouse_chr6.simMouse.chr6 150698 18 + 636262 GGGGTTCAAGCTTCTGTG -s Anc0.Anc0refChr5 72772 18 - 87904 GAGGTTTAGGCTTGTGTG -s Anc1.Anc1refChr8 29141 18 - 57822 GAGGTTTAGGCTTGTGTG -s Anc2.Anc2refChr15 77871 18 - 86568 GAGGTTTAGGCTTGTGTG -s mr.mrrefChr5 13782 18 + 294540 GGGGTTCAAGCTTCTGTG -s simCow_chr6.simCow.chr6 410821 16 - 602619 GAGGTTT--GTTTTTGTG -s simDog_chr6.simDog.chr6 120459 12 + 593897 ------CAGGCTTGTGCG -s simHuman_chr6.simHuman.chr6 406111 18 - 601863 GAGATTTAGGCTTGTGTG -s simRat_chr6.simRat.chr6 148293 18 + 647215 GGGGTTCCAGCTTCTGTG - -a -s simMouse_chr6.simMouse.chr6 150716 14 + 636262 TTGTCCTGACGTAT -s Anc0.Anc0refChr5 72791 14 - 87904 TTGTCCTTAATTAT -s Anc1.Anc1refChr8 29160 14 - 57822 TTGTCCTTAATTAT -s Anc2.Anc2refChr15 77890 14 - 86568 GTGTCCTTAATTAT -s mr.mrrefChr5 13801 14 + 294540 TTGTCCTGAAGTAT -s simCow_chr6.simCow.chr6 410838 14 - 602619 GTGTCCTTAATTAT -s simDog_chr6.simDog.chr6 120472 14 + 593897 GTGTCCTTAACTAT -s simHuman_chr6.simHuman.chr6 406130 14 - 601863 TTGTGATTAATTTC -s simRat_chr6.simRat.chr6 148312 14 + 647215 TTGTCCTGAAGTAT - -a -s simMouse_chr6.simMouse.chr6 150730 76 + 636262 ACTTGGCAACCACACAGATGAGGAGTGGTATGGTATTCTAGTGGTATTCTTGTGCTGATTCTATAAAGGCCATCCT -s Anc0.Anc0refChr5 72809 69 - 87904 ACTAGGCAGCCACAAGGATGA-GAGTGGAATGGTTTTTTT------TTCTTGTCTTGATTTTACAAAAGCCTTAGG -s Anc1.Anc1refChr8 29178 70 - 57822 ACTAGGCAGCCACAAGGATGAGGAGTGGAATGGTTTTTTT------TTCTTGTCTTGATTTTACAAAAGCCTTAGG -s Anc2.Anc2refChr15 77908 69 - 86568 ACTAGGCAGCCACAAGGATGA-GAGTGGAATGGTTTTTTT------TTCCTGCCTTGTTTTTACAAAAGCCTTAGG -s mr.mrrefChr5 13815 76 + 294540 ACTTGGCAACCACACAGATGAGGAGTGGAATGGTATTCTTGTGGTATTCTTGTGCTGATTCTATAAAGGCCATCCT -s simCow_chr6.simCow.chr6 410856 69 - 602619 ACTAGGCATCCACAAGGATGA-GAGCAGCATGATTTTTTT------TTCCTGCCTTATTTTTACAAAACCCTTAGG -s simDog_chr6.simDog.chr6 120499 59 + 593897 ACTAGGCAGCCACAAAGATGA-GAGTGGAGTGGTATTT----------------TTGTTTTTACAGAGGGCATAGG -s simHuman_chr6.simHuman.chr6 406148 69 - 601863 ACTAGGTAGCTACAAGGATGCGGAATGG-AGGGGTATTTT------TTCTAGTATTGATTTTACAAAAGCCTTAGG -s simRat_chr6.simRat.chr6 148326 76 + 647215 ACTTGGCAACCACACAGACGAGGAGTGGAATGGTTTTCTTGTGGTATTCTTGTGCTGATTCTATAAAGGCCGTCCT - -a -s simMouse_chr6.simMouse.chr6 150806 19 + 636262 ATTCTTGTATTTAATTGTA -s Anc0.Anc0refChr5 72878 13 - 87904 ATGCTTGAGTC------CA -s Anc1.Anc1refChr8 29248 13 - 57822 ATGCTTGAGTC------CA -s Anc2.Anc2refChr15 77977 13 - 86568 ATGCTTGAGTC------CA -s mr.mrrefChr5 13891 19 + 294540 ATTCTTGTATTTAATTGTA -s simCow_chr6.simCow.chr6 410925 13 - 602619 ATGTTTGAGTC------CA -s simDog_chr6.simDog.chr6 120558 13 + 593897 ATGCTTAAGTC------CA -s simHuman_chr6.simHuman.chr6 406217 13 - 601863 ATGGTTGGGTC------CA -s simRat_chr6.simRat.chr6 148403 19 + 647215 ATTCATATATTTAATTTAA - -a -s simMouse_chr6.simMouse.chr6 150825 7 + 636262 ACACTCA -s Anc0.Anc0refChr5 72891 7 - 87904 AGGCTTA -s Anc1.Anc1refChr8 29261 7 - 57822 AGGCTTA -s Anc2.Anc2refChr15 77990 7 - 86568 AAGCTTA -s mr.mrrefChr5 13910 7 + 294540 AGACTTA -s simCow_chr6.simCow.chr6 410939 7 - 602619 AAGCTGA -s simDog_chr6.simDog.chr6 120571 7 + 593897 AAGCTTA -s simHuman_chr6.simHuman.chr6 406230 7 - 601863 AGGATTT -s simRat_chr6.simRat.chr6 148422 7 + 647215 AGATTTC - -a -s simMouse_chr6.simMouse.chr6 150832 114 + 636262 TGTTGCAACTGAGTGAACTGAAAAATGTGGATTATGAACACAGATTAATTGAGGGGAACACAGACTAATTGAGGGTGAAGCAAGACAATTATGGTGAGGACTAGTTGGTCACTG -s Anc0.Anc0refChr5 72906 93 - 87904 TG-TGTAATTGAATGACCAGAATAATGTGGATTATGAATGCAAGTTAATTAAGGGG--------------------TAACCAAAACGCTTGAGGAGAGGACTAATTGAGCACTG -s Anc1.Anc1refChr8 29276 93 - 57822 TG-TGTAATTGAATGACCAGAATAATGTGGATTATGAATGCAAGTTAATTAAGGGG--------------------TAACCAAAACGCTTGAGGAGAGGACTAATTGAGCACTG -s Anc2.Anc2refChr15 78005 93 - 86568 TT-GGTAATTGAATGACCAGAATAATGTGGATTATGAATGTAAGTTAATTAAGGGG--------------------TGACCAAAATGCTTGAGGAGAGGACTGATTGAGCACCT -s mr.mrrefChr5 13925 114 + 294540 TGTTGCAACTGAGTGAACTGAATAATGTGGATTATGAACACAGATTAATTGAGGGGAACACAGACTAATTGAGGGTGAAGCAAGACAATTGAGGTGAGGACTAGTTGGTCACTG -s simCow_chr6.simCow.chr6 410954 90 - 602619 TA-GGTAATTCACTGACTAGATTAATGTGGATTGTGAATGAAGGT---TTAAGGAG--------------------TGACCAAAATGCTTGAGGAAAGGACTGATTGATCGCCT -s simDog_chr6.simDog.chr6 120586 93 + 593897 TT-GGTAATTGAATGACCAGGATAATATAGTTTATGAACTTCAGTTAATTAAAGGG--------------------TGAGCAAACTACTTGAGGAGAGAAGTGATAGAGCACCT -s simHuman_chr6.simHuman.chr6 406245 93 - 601863 TG-TGTAATTGGATGACCAGAATGATGTGGATTATAAATGCAAGTTAATTAAGGGG--------------------TAACCAAAACGCTTGAGGAGAGGACTAATTGACCATTG -s simRat_chr6.simRat.chr6 148437 114 + 647215 TATTGCAACTGAGCGAACTGAATAATGTGGTTTGTGAACACAGATTAACTGAGGGGAACACAGACTAATTGAGGGTGAATCAAGACAATTGAGCTGAAGGCTAGTTGGTCACTG - -a -s simMouse_chr6.simMouse.chr6 150946 5 + 636262 TTAGA -s Anc0.Anc0refChr5 72999 5 - 87904 TATGA -s Anc1.Anc1refChr8 29369 5 - 57822 TATGA -s Anc2.Anc2refChr15 78103 5 - 86568 TATGA -s mr.mrrefChr5 14039 5 + 294540 TTAGA -s simCow_chr6.simCow.chr6 411049 5 - 602619 TATGA -s simDog_chr6.simDog.chr6 120684 5 + 593897 TAGGA -s simHuman_chr6.simHuman.chr6 406338 5 - 601863 TGTGA -s simRat_chr6.simRat.chr6 148551 5 + 647215 TTAGT - -a -s simMouse_chr6.simMouse.chr6 150951 5 + 636262 AGGTA -s Anc0.Anc0refChr5 73006 5 - 87904 AGGCA -s Anc1.Anc1refChr8 29376 5 - 57822 AGGCA -s Anc2.Anc2refChr15 78110 5 - 86568 AGGCA -s mr.mrrefChr5 14044 5 + 294540 AGGTA -s simCow_chr6.simCow.chr6 411056 5 - 602619 AGGCA -s simDog_chr6.simDog.chr6 120691 5 + 593897 AAGTA -s simHuman_chr6.simHuman.chr6 406345 5 - 601863 GGGCA -s simRat_chr6.simRat.chr6 148556 5 + 647215 AGGTA - -a -s simMouse_chr6.simMouse.chr6 150956 20 + 636262 TAATCTGTGAATACATGCAA -s Anc0.Anc0refChr5 73012 17 - 87904 TTGTCTATGAATGGATG--- -s Anc1.Anc1refChr8 29382 17 - 57822 TTGTCTATGAATGGATG--- -s Anc2.Anc2refChr15 78116 17 - 86568 TTGTCTATGAATGGATG--- -s mr.mrrefChr5 14050 20 + 294540 TAATCTATGAATACATGCAA -s simCow_chr6.simCow.chr6 411062 17 - 602619 TTGTCTATAAATAGATG--- -s simDog_chr6.simDog.chr6 120697 17 + 593897 TTGTCTATGAGTGAATC--- -s simHuman_chr6.simHuman.chr6 406351 17 - 601863 TTGTGTATGAAATGATG--- -s simRat_chr6.simRat.chr6 148562 20 + 647215 TAATCTATGAAGACACACAA - -a -s simMouse_chr6.simMouse.chr6 150976 4 + 636262 TCTT -s mr.mrrefChr5 14070 4 + 294540 TCTT -s simRat_chr6.simRat.chr6 148583 4 + 647215 TCTT - -a -s simMouse_chr6.simMouse.chr6 150980 2 + 636262 TC -s Anc0.Anc0refChr5 73030 2 - 87904 CA -s Anc1.Anc1refChr8 29400 2 - 57822 CA -s Anc2.Anc2refChr15 78134 2 - 86568 CA -s mr.mrrefChr5 14075 2 + 294540 TA -s simCow_chr6.simCow.chr6 411080 2 - 602619 CA -s simDog_chr6.simDog.chr6 120715 2 + 593897 CA -s simHuman_chr6.simHuman.chr6 406369 2 - 601863 CA -s simRat_chr6.simRat.chr6 148588 2 + 647215 TA - -a -s simMouse_chr6.simMouse.chr6 150982 7 + 636262 ACTCATT -s Anc0.Anc0refChr5 73032 7 - 87904 ACTGGTT -s Anc1.Anc1refChr8 29402 7 - 57822 ACTGGTT -s Anc2.Anc2refChr15 78144 7 - 86568 ACTGGTT -s mr.mrrefChr5 14077 7 + 294540 ACTCATT -s simCow_chr6.simCow.chr6 411090 7 - 602619 ACTCGTT -s simDog_chr6.simDog.chr6 120725 7 + 593897 ACTGGTT -s simHuman_chr6.simHuman.chr6 406371 7 - 601863 ACTGGTT -s simRat_chr6.simRat.chr6 148590 7 + 647215 ACTCATT - -a -s simMouse_chr6.simMouse.chr6 150989 32 + 636262 GTTCAAAGCTAATTACTATTGGTAGGCTTTGT -s Anc0.Anc0refChr5 73042 32 - 87904 GTTCAAAGCTTATCTGTATTAATAAGCTATGT -s Anc1.Anc1refChr8 29412 32 - 57822 GTTCAAAGCTTATCTGTATTAATAAGCTATGT -s Anc2.Anc2refChr15 78154 32 - 86568 GTTCCAAGCTTATCTGTATTGATAAGCCATGT -s mr.mrrefChr5 14084 32 + 294540 GTTCAAAGCTAATTTGTATTAGTAGGCTTTGT -s simCow_chr6.simCow.chr6 411100 32 - 602619 GCTCCAAGCTAATCTGTATTTATAAGCCATGT -s simDog_chr6.simDog.chr6 120735 32 + 593897 GTCCCAAGCTTATCTGTATTGATAAGCCATGT -s simHuman_chr6.simHuman.chr6 406381 32 - 601863 GTTCAGAGCTTGTCTGCATTAATAAGCTGTGT -s simRat_chr6.simRat.chr6 148597 32 + 647215 GTGCAAAACTAATTTGTATTAGTATGCTATGT - -a -s simMouse_chr6.simMouse.chr6 151021 36 + 636262 CATAACTGCCAGCATTTATGGTACCTAGCCCTTGGA -s Anc0.Anc0refChr5 73077 36 - 87904 CATAATTGCAAACATTTAAGGCAACTAACACTGGAA -s Anc1.Anc1refChr8 29447 36 - 57822 CATAATTGCAAACATTTAAGGCAACTAACACTGGAA -s Anc2.Anc2refChr15 78189 36 - 86568 CATAATCACAAACATTTAAGGCAACTAACACTGGAA -s mr.mrrefChr5 14119 36 + 294540 CATAACTGCCAGCATTTATGGTAACTAGCCCTTGAA -s simCow_chr6.simCow.chr6 411135 36 - 602619 CATAATCACCATCATTTAAGGCAACTAAGATTGGAA -s simDog_chr6.simDog.chr6 120770 33 + 593897 CACAATCACAAACAATTAAGGCAACTAACACTG--- -s simHuman_chr6.simHuman.chr6 406416 36 - 601863 CATATGTGCAGACATTTAAGGAAACTAACACTGGAA -s simRat_chr6.simRat.chr6 148632 36 + 647215 TATAACTGCCAGCCCTTATGGTAACTAGCCCTTGAA - -a -s simMouse_chr6.simMouse.chr6 151057 14 + 636262 GATCTGTCCAATTA -s Anc0.Anc0refChr5 73142 9 - 87904 -----GCCCAATTC -s Anc1.Anc1refChr8 29512 14 - 57822 TATCTGCCCAATTC -s Anc2.Anc2refChr15 78254 9 - 86568 -----GCCTAATTC -s mr.mrrefChr5 14155 14 + 294540 TATCTGTCCAATTA -s simCow_chr6.simCow.chr6 411177 9 - 602619 -----GCTGAATTC -s simDog_chr6.simDog.chr6 120876 9 + 593897 -----GCCTAATTC -s simHuman_chr6.simHuman.chr6 406488 14 - 601863 TATCTGCCCAATCC -s simRat_chr6.simRat.chr6 148668 13 + 647215 TATC-GTCCAATTA - -a -s simMouse_chr6.simMouse.chr6 151071 8 + 636262 TGAACTGG -s Anc0.Anc0refChr5 73151 8 - 87904 TGAGCTGG -s Anc1.Anc1refChr8 29526 8 - 57822 TGAGCTGG -s Anc2.Anc2refChr15 78263 8 - 86568 TGAGCTGG -s mr.mrrefChr5 14169 8 + 294540 TGAACTGG -s simCow_chr6.simCow.chr6 411187 8 - 602619 TTAGCTGG -s simDog_chr6.simDog.chr6 120885 8 + 593897 TGAGCTGG -s simHuman_chr6.simHuman.chr6 406502 8 - 601863 TGAGCTGA -s simRat_chr6.simRat.chr6 148681 8 + 647215 TGAACTGG - -a -s simMouse_chr6.simMouse.chr6 151079 66 + 636262 GGTAGGAGATATAAGAACTATGTAAGCCATCGTCACCTTGTACCCCCATATATACAAAGACATTTT -s Anc0.Anc0refChr5 73159 66 - 87904 GATAGGAATTATAAAGATTATGTATCCTCTCATCACCTTGTACCCCCATATGTATGGGGGCATTTT -s Anc1.Anc1refChr8 29534 66 - 57822 GATAGGAATTATAAAGATTATGTATCCTCTCATCACCTTGTACCCCCATATGTATGGGGGCATTTT -s Anc2.Anc2refChr15 78274 66 - 86568 GATAGGAATTATAAAGATAATGTATCCTCTTATCACCTTATACCCTTATATGTATGGGGGCATTTT -s mr.mrrefChr5 14177 66 + 294540 GATAGGAATTATAAAAACTATGTAAGCCATCGTCACCTTGTACCCCCATATATATAGAGACATTTT -s simCow_chr6.simCow.chr6 411198 66 - 602619 AGGAGGGATGCTAAAGATAATGAATGCCCTTATCTCCCTTTTCCCTTGTATGCATGGGGGCATTTG -s simDog_chr6.simDog.chr6 120896 62 + 593897 GATGGGAATTATAAAG---AAGTATCCT-TTGTCACCTTATACCCTTATCTGTCTGGGGGCATTTT -s simHuman_chr6.simHuman.chr6 406510 66 - 601863 GATAGGAATAATAAAGATTATGTATACTGTCATCACCGTGTACCCCCATATGTATGGGGGCATTTT -s simRat_chr6.simRat.chr6 148689 63 + 647215 AATAGGAATTATAAAAACTACGCAAGCCATCGTCACCTTGTACCCCTGTATATATAGAGAC---CT - -a -s simMouse_chr6.simMouse.chr6 151145 9 + 636262 AATATATGT -s Anc0.Anc0refChr5 73235 9 - 87904 AATGGACGA -s Anc1.Anc1refChr8 29610 9 - 57822 AATGGACGA -s Anc2.Anc2refChr15 78350 9 - 86568 AATGGGCTA -s mr.mrrefChr5 14243 9 + 294540 AATATATGT -s simCow_chr6.simCow.chr6 411274 9 - 602619 AATGGGCAT -s simDog_chr6.simDog.chr6 120968 9 + 593897 AATGGGTTA -s simHuman_chr6.simHuman.chr6 406586 9 - 601863 AATGGACGC -s simRat_chr6.simRat.chr6 148752 9 + 647215 AATCTATGT - -a -s simMouse_chr6.simMouse.chr6 151154 41 + 636262 AAGCTGTTATCCAGCCTCTATTCCCCGTATTCCAATGGCAT -s Anc0.Anc0refChr5 73244 41 - 87904 AAGTTGTTGTCCAGCCTCTACTTCCTATGTTCACATGGCAC -s Anc1.Anc1refChr8 29619 41 - 57822 AAGTTGTTGTCCAGCCTCTACTTCCTATGTTCACATGGCAC -s Anc2.Anc2refChr15 78359 41 - 86568 AAGTTGCTGCCCAGCCTCTGCTTCCTATGTTCACATGGCAC -s mr.mrrefChr5 14252 41 + 294540 AAGTTGTTGTCCAGCCTCTATTCCCCATGTTCACATGGCAT -s simCow_chr6.simCow.chr6 411283 41 - 602619 AAGTTGCTGCCCAGCCTCTCGCTCCTCTGTTTACATAGCAT -s simDog_chr6.simDog.chr6 120977 34 + 593897 AAGTTGC-------CCTCTGCTTCCTATGCTCACACGGCAC -s simHuman_chr6.simHuman.chr6 406595 41 - 601863 AAGTTGTTGTCCGGCCTCTACTTCCTATGTCCACATGGCAC -s simRat_chr6.simRat.chr6 148765 41 + 647215 GAGTTGTCGTCCAGCCTCCATTCCCCATGTTCACATGTCAT - -a -s simMouse_chr6.simMouse.chr6 151195 14 + 636262 ACACTATCAGTTTT -s Anc0.Anc0refChr5 73297 14 - 87904 ATATCATGAGTTTT -s Anc1.Anc1refChr8 29672 14 - 57822 ATATCATGAGTTTT -s Anc2.Anc2refChr15 78412 14 - 86568 ATATCATGAGTTTT -s mr.mrrefChr5 14293 14 + 294540 ACACTATCAGTTTT -s simCow_chr6.simCow.chr6 411335 14 - 602619 ATACCATGAGTTTT -s simDog_chr6.simDog.chr6 121023 14 + 593897 ATATCATGAGTTAT -s simHuman_chr6.simHuman.chr6 406648 14 - 601863 ATAACAGGAGTTTT -s simRat_chr6.simRat.chr6 148806 14 + 647215 GCTCTATGAGTTTT - -a -s simMouse_chr6.simMouse.chr6 151209 23 + 636262 ACCAGATCTTAGTATTCTAAACC -s Anc0.Anc0refChr5 73336 23 - 87904 ATCAGATTTTAGTATCCTGAACC -s Anc1.Anc1refChr8 29711 23 - 57822 ATCAGATTTTAGTATCCTGAACC -s Anc2.Anc2refChr15 78452 23 - 86568 ATCAGATTTTAGTATCCTGAACC -s mr.mrrefChr5 14307 23 + 294540 ACCAGATTTTAGTATTCTAAACC -s simCow_chr6.simCow.chr6 411375 23 - 602619 ATCAGATATTAGTATCCTAAACC -s simDog_chr6.simDog.chr6 121063 23 + 593897 ACTAGCTTTTAGCATCCTGAGGC -s simHuman_chr6.simHuman.chr6 406687 22 - 601863 ATCAGATTTTAGTA-CCTGAACC -s simRat_chr6.simRat.chr6 148820 23 + 647215 ACCAGATTTCAATATTCTAAGCC - -a -s simMouse_chr6.simMouse.chr6 151232 9 + 636262 CCCTATATG -s Anc0.Anc0refChr5 73359 9 - 87904 CTCTGTATG -s Anc1.Anc1refChr8 29734 9 - 57822 CTCTGTATG -s Anc2.Anc2refChr15 78475 9 - 86568 CTCTGTATG -s mr.mrrefChr5 14330 9 + 294540 CTCTATATG -s simCow_chr6.simCow.chr6 411400 7 - 602619 CTCTGTA-- -s simDog_chr6.simDog.chr6 121086 9 + 593897 CTCTGTATG -s simHuman_chr6.simHuman.chr6 406709 9 - 601863 CTCTGTATG -s simRat_chr6.simRat.chr6 148843 9 + 647215 CTCCATATG - -a -s simMouse_chr6.simMouse.chr6 151241 63 + 636262 GGGTCTACCTGTGAGTGTAATTTATTAGTGGGCTGAATATTGGATGAGAACTGCCCATAGAGG -s Anc0.Anc0refChr5 73368 46 - 87904 GGATCTACTTG---------TTTACCAG--------AGATTGTATGGAAACTGCCCATAGCTG -s Anc1.Anc1refChr8 29743 46 - 57822 GGATCTACTTG---------TTTACCAG--------AGATTGTATGGAAACTGCCCATAGCTG -s Anc2.Anc2refChr15 78484 46 - 86568 GGATTTACTTG---------TATGCCAG--------GGATCGTATGGAAACTGCCCATATCTG -s mr.mrrefChr5 14339 63 + 294540 GGATCTACCTGTGAGTGTAATTTACTAGTGGGCTGAATATTGGATGGGAACTGCCCATAGAGG -s simCow_chr6.simCow.chr6 411407 46 - 602619 GGATTCACCTG---------TAAGCCAG--------GGATGGGGTGGAAACTGTCCATATCTG -s simDog_chr6.simDog.chr6 121095 46 + 593897 GGCTTTACTTG---------CATGCTAG--------GGGCCATATGGAAACTGCCCATCTCTG -s simHuman_chr6.simHuman.chr6 406723 46 - 601863 GGATCTACATG---------TTTACCAT--------AGATTGCATGGAAGCTGGCCATAGGAG -s simRat_chr6.simRat.chr6 148852 63 + 647215 GGATCTACCTGTGAGTGTAATTTACTAGTGGGCTGAATATTGGATGGGAACTGCCTATAGAGG - -a -s simMouse_chr6.simMouse.chr6 151304 5 + 636262 ACTGA -s Anc0.Anc0refChr5 73414 5 - 87904 AATGA -s Anc1.Anc1refChr8 29789 5 - 57822 AATGA -s Anc2.Anc2refChr15 78531 5 - 86568 AATGA -s mr.mrrefChr5 14402 5 + 294540 ACTGA -s simCow_chr6.simCow.chr6 411454 5 - 602619 AATGA -s simDog_chr6.simDog.chr6 121142 5 + 593897 AATAT -s simHuman_chr6.simHuman.chr6 406769 5 - 601863 AGTGA -s simRat_chr6.simRat.chr6 148916 5 + 647215 ATTGA - -a -s simMouse_chr6.simMouse.chr6 151309 14 + 636262 CTGGACACTAACCA -s Anc0.Anc0refChr5 73419 14 - 87904 CTAGAGACTAACCA -s Anc1.Anc1refChr8 29794 14 - 57822 CTAGAGACTAACCA -s Anc2.Anc2refChr15 78536 14 - 86568 CTAGAGGCTAACCA -s mr.mrrefChr5 14407 14 + 294540 CTGGACACTAACCA -s simCow_chr6.simCow.chr6 411459 13 - 602619 CTAGAGGCGAA-CA -s simDog_chr6.simDog.chr6 121147 14 + 593897 CTAGAGGCTAACCA -s simHuman_chr6.simHuman.chr6 406774 14 - 601863 TGAGAGACTAACCA -s simRat_chr6.simRat.chr6 148959 14 + 647215 CTGAGCACTAACCA - -a -s simMouse_chr6.simMouse.chr6 151323 49 + 636262 ATTCCTAATCCATAGATCATTTGTTGAGACCTGACACTTGGGCCTACCA -s Anc0.Anc0refChr5 73433 48 - 87904 ATTCCTTAACCATGGATTCTTGCTTGAGGCCT-ACACTGGGGCCTACCA -s Anc1.Anc1refChr8 29808 48 - 57822 ATTCCTTAACCATGGATTCTTGCTTGAGGCCT-ACACTGGGGCCTACCA -s Anc2.Anc2refChr15 78550 48 - 86568 AATCCCTAACCGTGGATTCTTGCTTGAGGCCT-ACACTGGGGCCTACCA -s mr.mrrefChr5 14421 48 + 294540 ATTCCTAATCCATAGATCATTTGTTGAGACCT-ACACTTGGGCCTACCA -s simCow_chr6.simCow.chr6 411472 48 - 602619 AATGCCTACTCCTGGATTCTTGCTTGAGGCCT-ACACTGGGGCTTACCA -s simDog_chr6.simDog.chr6 121166 48 + 593897 AATCCCTAACTGTGGATTCTCGCTTGAGTCTT-ACACTGGGGCCTGCCA -s simHuman_chr6.simHuman.chr6 406788 48 - 601863 ATCCCTTGAACATGGGTTTTTGATTGGGGCCT-ACACTGATGCCTACCA -s simRat_chr6.simRat.chr6 149034 47 + 647215 ATTCCTAATC-ATAGATCATTTGTTGAGACAT-ACAGTTGGGCCTGCCA - -a -s simMouse_chr6.simMouse.chr6 151372 8 + 636262 TTTGGGCC -s Anc0.Anc0refChr5 73481 8 - 87904 TGTGGGCC -s Anc1.Anc1refChr8 29856 8 - 57822 TGTGGGCC -s Anc2.Anc2refChr15 78652 8 - 86568 TGTAGGCC -s mr.mrrefChr5 14469 8 + 294540 TTTGGGCC -s simCow_chr6.simCow.chr6 411585 8 - 602619 TGTACGCT -s simDog_chr6.simDog.chr6 121271 8 + 593897 TGTAGACC -s simHuman_chr6.simHuman.chr6 406836 8 - 601863 TGTGGGCC -s simRat_chr6.simRat.chr6 149081 8 + 647215 TTTGGGCC - -a -s simMouse_chr6.simMouse.chr6 151380 26 + 636262 AGATAAGATTTAGTGGTCAATAGATA -s Anc0.Anc0refChr5 73489 23 - 87904 ACATAGGAAGAGAGGGTTT-TAA--A -s Anc1.Anc1refChr8 29864 25 - 57822 ACATAGGAAGAGAGGGTTT-TAAGCA -s Anc2.Anc2refChr15 78660 23 - 86568 ACTTTGGAAGAGAGGGTTT-TAA--A -s mr.mrrefChr5 14477 25 + 294540 AGATAGGATTAAGTGGTCA-TAAATA -s simCow_chr6.simCow.chr6 411595 23 - 602619 ATTCTTAAAGAGAGGGTTT-TAG--A -s simDog_chr6.simDog.chr6 121279 23 + 593897 ACTTTGGAAAAGAGGGTTT-TAA--A -s simHuman_chr6.simHuman.chr6 406844 25 - 601863 ACATAGGCGGAGAGGGTTT-TAAGCA -s simRat_chr6.simRat.chr6 149089 25 + 647215 AGATAGGATTAAGTGGCCA-TAAATA - -a -s simMouse_chr6.simMouse.chr6 151406 14 + 636262 GTTGCAGATCAGGT -s Anc0.Anc0refChr5 73534 14 - 87904 GACATAGATCAGGT -s Anc1.Anc1refChr8 29914 14 - 57822 GACATAGATCAGGT -s Anc2.Anc2refChr15 78706 14 - 86568 GACATAGATCAGGT -s mr.mrrefChr5 14528 14 + 294540 GTTGTAGATCAGGT -s simCow_chr6.simCow.chr6 411641 14 - 602619 GTCATACATAAGGT -s simDog_chr6.simDog.chr6 121325 14 + 593897 GACATAGATCAGGT -s simHuman_chr6.simHuman.chr6 406894 14 - 601863 GACATAGATTAGGT -s simRat_chr6.simRat.chr6 149145 14 + 647215 GTTGTTAACCAAGC - -a -s simMouse_chr6.simMouse.chr6 151420 19 + 636262 GGTAAAAATGAAGTGTTTT -s Anc0.Anc0refChr5 73548 18 - 87904 AGTAAAAT-AAACAATTTG -s Anc1.Anc1refChr8 29928 19 - 57822 AGTAAAATAAAACAATTTG -s Anc2.Anc2refChr15 78720 18 - 86568 AGTAAAAT-AAACAATCTG -s mr.mrrefChr5 14542 19 + 294540 AGTAAAAATGAAGTGTTTT -s simCow_chr6.simCow.chr6 411655 18 - 602619 AGTAAAAC-ATACAATCTA -s simDog_chr6.simDog.chr6 121339 18 + 593897 AGTGAAAT-AAACAATCTG -s simHuman_chr6.simHuman.chr6 406908 19 - 601863 AGTAAAATAAAACACTTGG -s simRat_chr6.simRat.chr6 149165 19 + 647215 AGTGACAGTGCAGTGATTT - -a -s simMouse_chr6.simMouse.chr6 151439 70 + 636262 GACCAGTAAATTAAGTCGCTGTCTCTTAGATAACATGTGTCCAAGATCTATAACTTGCTAAGTTTCGTTA -s Anc0.Anc0refChr5 73566 45 - 87904 GAGAGGTAAATTAAGTT-------------------------AGGGTGTGTAACTTGCTGAATTTCATTA -s Anc1.Anc1refChr8 29947 45 - 57822 GAGAGGTAAATTAAGTT-------------------------AGGGTGTGTAACTTGCTGAATTTCATTA -s Anc2.Anc2refChr15 78738 45 - 86568 GAGAGGTAAATTAAGTT-------------------------AGGGTGTGTATCTTGCTGTATCTCATTA -s mr.mrrefChr5 14561 70 + 294540 GACCAGTAAATTAAGTTGCTGTCTCTTAGATAACATGTGTCCAAGATGTGTAACTTGCTAAGTTTCGTTA -s simCow_chr6.simCow.chr6 411673 45 - 602619 GAGAGGTAGATTACATT-------------------------AAGGTGTGTAGCTTGTTGTTTCTCATTA -s simDog_chr6.simDog.chr6 121357 42 + 593897 GAGAGGGAATTTAAGTT-------------------------AGGGTGTGTATCTTGCTGTATC---TTA -s simHuman_chr6.simHuman.chr6 406927 45 - 601863 GAGTGGTACATTAAGTT-------------------------AGGGTGAGTAACTTGCTGAATTTCATTA -s simRat_chr6.simRat.chr6 149242 70 + 647215 GACCAGTAAATTAAGTTGCTGTCTCTTAGGTAACATGAGTCCAAAAGGTGTAACTGGCTAGGTCTCGTTA - -a -s simMouse_chr6.simMouse.chr6 151509 15 + 636262 AAATAACTCAAATTT -s Anc0.Anc0refChr5 73611 15 - 87904 GAATACTTTCAATTT -s Anc1.Anc1refChr8 29992 15 - 57822 GAATACTTTCAATTT -s Anc2.Anc2refChr15 78783 15 - 86568 GAATGCTTCCAATTT -s mr.mrrefChr5 14631 15 + 294540 AAATAACTTAAATTT -s simCow_chr6.simCow.chr6 411719 15 - 602619 GAATGCTTCCAATCT -s simDog_chr6.simDog.chr6 121399 14 + 593897 GAGTGCTCC-AACTT -s simHuman_chr6.simHuman.chr6 406972 15 - 601863 GAACATTTTGAATTT -s simRat_chr6.simRat.chr6 149312 15 + 647215 AAATTCCTTAAATTT - -a -s simMouse_chr6.simMouse.chr6 151524 19 + 636262 AAGGAAGTACCTATCATAA -s Anc0.Anc0refChr5 73627 19 - 87904 CAGGATGTCCGTGCTCTAA -s Anc1.Anc1refChr8 30008 19 - 57822 CAGGATGTCCGTGCTCTAA -s Anc2.Anc2refChr15 78799 19 - 86568 CAGGATGTCCGTGCTCTAA -s mr.mrrefChr5 14646 19 + 294540 AAGGAAGTACCTGTCCTAA -s simCow_chr6.simCow.chr6 411735 19 - 602619 GAGGATGTCCCTGTGCTAA -s simDog_chr6.simDog.chr6 121414 19 + 593897 CAGGATATCCGTGCTCTAA -s simHuman_chr6.simHuman.chr6 406988 19 - 601863 CAGGATGTCCTTGCTCAAA -s simRat_chr6.simRat.chr6 149327 19 + 647215 AAGGAAGCACCTGTCCTAA - -a -s simMouse_chr6.simMouse.chr6 151543 30 + 636262 CTAAAGTTATCATTAGCCATATGTTACCCA -s Anc0.Anc0refChr5 73646 30 - 87904 CCCAAATTATCATTAGCCAAATGCAACTCA -s Anc1.Anc1refChr8 30027 30 - 57822 CCCAAATTATCATTAGCCAAATGCAACTCA -s Anc2.Anc2refChr15 78818 30 - 86568 CCCAAATCATCATTAGCCAAATGCAAGTTA -s mr.mrrefChr5 14665 30 + 294540 CTCAAGTTATCATTAGCCATATGTTACCCA -s simCow_chr6.simCow.chr6 411754 30 - 602619 CTCAAATCATCATTATCCAAATGCAATCTG -s simDog_chr6.simDog.chr6 121433 30 + 593897 CCCAATTCATCATCAGCCAAATGCAAGTTA -s simHuman_chr6.simHuman.chr6 407007 30 - 601863 CCCCAATTATCATTAGCCAAATGCAACACA -s simRat_chr6.simRat.chr6 149347 30 + 647215 CTCAAGTTATGATTAACAATATGTTGCCCA - -a -s simMouse_chr6.simMouse.chr6 151573 63 + 636262 AATCTGTGCAACTTAAGAACCTGGAATGGTTATGTGTATATGTTAATCAGATATCAGATGAGG -s Anc0.Anc0refChr5 73676 48 - 87904 AATCCATGTGCCT--AGAACCTGAAAGGGTGACTTGT-------------TAATCTGATTAGG -s Anc1.Anc1refChr8 30057 50 - 57822 AATCCATGTGCCTTAAGAACCTGAAAGGGTGACTTGT-------------TAATCTGATTAGG -s Anc2.Anc2refChr15 78848 48 - 86568 AATCAATGTGCCT--AGAACCTGTAAGGGTGACTTGA-------------TAATCTAATTAGG -s mr.mrrefChr5 14695 63 + 294540 AATCCATGCAACTTAAGAACCTGAAATGGTTATGTGTATATGTTAATCAGATATCAGATGAGG -s simCow_chr6.simCow.chr6 411784 48 - 602619 AATTGATGTGCCT--AGAACCTGTAAGGGTGACTTGA-------------TAATCTAATTAGG -s simDog_chr6.simDog.chr6 121464 6 + 593897 GACCAT--------------------------------------------------------- -s simHuman_chr6.simHuman.chr6 407037 50 - 601863 AATCCATGTGTATTAAGAACACGAAAGGGTGAAATGT-------------TCATCTGATTAGG -s simRat_chr6.simRat.chr6 149377 63 + 647215 AAGCCATGCACCTGAAGAGCCTTAAATAGTAATGTGTATATGTTAATCAGATATCAGGTAAAG - -a -s simMouse_chr6.simMouse.chr6 151636 11 + 636262 GTAGGCTCCTT -s Anc0.Anc0refChr5 73724 11 - 87904 ACACCCTGCTT -s Anc1.Anc1refChr8 30107 11 - 57822 ACACCCTGCTT -s Anc2.Anc2refChr15 78896 11 - 86568 ACACCCTGCTT -s mr.mrrefChr5 14758 11 + 294540 GCAGGCTCCTT -s simCow_chr6.simCow.chr6 411833 11 - 602619 ACACCCTGCTT -s simDog_chr6.simDog.chr6 121470 7 + 593897 ----CCTGCTT -s simHuman_chr6.simHuman.chr6 407087 11 - 601863 ACATCCTACTG -s simRat_chr6.simRat.chr6 149440 11 + 647215 GCAGGCTCCTT - -a -s simMouse_chr6.simMouse.chr6 151647 55 + 636262 GGATAAGTCCCATTACCATGGCGTGGGGGCACACTGGACTGAGTCTAACTCTCAC -s Anc0.Anc0refChr5 73735 55 - 87904 GGATAAGTCTCAACACTATGGCCTGGGGACTCACTGGACTGTGTTTAGCTCTATC -s Anc1.Anc1refChr8 30118 55 - 57822 GGATAAGTCTCAACACTATGGCCTGGGGACTCACTGGACTGTGTTTAGCTCTATC -s Anc2.Anc2refChr15 78907 55 - 86568 AGATAAGTCTTAATGCTATGGCCTGAGGACTCACTGGACTGTGTTTAGCTCTATC -s mr.mrrefChr5 14769 55 + 294540 GGATAAGTCCCAACACCATGGCGTGGGGGCTCACTGGACTGAGTCTAACTCTCAC -s simCow_chr6.simCow.chr6 411845 33 - 602619 AGATAAG----------------------CTCACAGGACTGTGTTTAGCTTTATG -s simDog_chr6.simDog.chr6 121477 55 + 593897 AGATAAGTCTTAATGCTATGGCCTGAGGATTCACTGGACTGTGTCCTGCTCTCTC -s simHuman_chr6.simHuman.chr6 407098 55 - 601863 GGATAAGACTCGACACTATGGCCTGGGGACTCACTAGACTGTGTTTAGCTCTATC -s simRat_chr6.simRat.chr6 149451 55 + 647215 GGATCTGTCACAACATCATGGTGTGGGGTCTCACTGGACTGAGTCTACCTATGCC - -a -s simMouse_chr6.simMouse.chr6 151702 9 + 636262 AGTTGGGAG -s Anc0.Anc0refChr5 73790 9 - 87904 CAGTGGGAG -s Anc1.Anc1refChr8 30173 9 - 57822 CAGTGGGAG -s Anc2.Anc2refChr15 78971 9 - 86568 CAGTGGGAA -s mr.mrrefChr5 14824 9 + 294540 AGTTGGGAG -s simCow_chr6.simCow.chr6 411887 9 - 602619 TAGTAGGAA -s simDog_chr6.simDog.chr6 121541 9 + 593897 CAGTGGGAA -s simHuman_chr6.simHuman.chr6 407153 9 - 601863 CAGTGTGAG -s simRat_chr6.simRat.chr6 149506 9 + 647215 AGTTGGAAG - -a -s simMouse_chr6.simMouse.chr6 151711 7 + 636262 TATCAAT -s Anc0.Anc0refChr5 73801 7 - 87904 TTTTAAT -s Anc1.Anc1refChr8 30184 7 - 57822 TTTTAAT -s Anc2.Anc2refChr15 78982 7 - 86568 TTTTAAC -s mr.mrrefChr5 14833 7 + 294540 TATCAAT -s simCow_chr6.simCow.chr6 411898 7 - 602619 TTTCAAC -s simDog_chr6.simDog.chr6 121552 7 + 593897 TTTTGAC -s simHuman_chr6.simHuman.chr6 407164 7 - 601863 TTTTAAT -s simRat_chr6.simRat.chr6 149515 7 + 647215 TGTCAAA - -a -s simMouse_chr6.simMouse.chr6 151718 6 + 636262 TTGTGA -s Anc0.Anc0refChr5 73808 6 - 87904 TTCTGG -s Anc1.Anc1refChr8 30191 6 - 57822 TTCTGG -s Anc2.Anc2refChr15 78989 6 - 86568 TGCTGG -s mr.mrrefChr5 14840 6 + 294540 TTCTGA -s simCow_chr6.simCow.chr6 411939 6 - 602619 AGCCGG -s simDog_chr6.simDog.chr6 121559 6 + 593897 TGCTGG -s simHuman_chr6.simHuman.chr6 407171 6 - 601863 TTCTGG -s simRat_chr6.simRat.chr6 149522 6 + 647215 TTCTGA - -a -s simMouse_chr6.simMouse.chr6 151724 29 + 636262 GAGTCCTTTTTAGCACAATAAGGTTACCT -s Anc0.Anc0refChr5 73818 29 - 87904 TAACCCTCTTTGGCTAAATAAGATTTCCT -s Anc1.Anc1refChr8 30201 29 - 57822 TAACCCTCTTTGGCTAAATAAGATTTCCT -s Anc2.Anc2refChr15 78999 29 - 86568 TAACCCTCTTTGGCTAAATAAGATTTCCT -s mr.mrrefChr5 14850 29 + 294540 GAGCCCTTTTTAGCACAATAAGGTTACCT -s simCow_chr6.simCow.chr6 411949 29 - 602619 TAACCCTCTTTGGCTAAATAAGGTTTCCT -s simDog_chr6.simDog.chr6 121569 29 + 593897 TAACCCTTTTTGGCTTAACAAGATTTCCT -s simHuman_chr6.simHuman.chr6 407181 29 - 601863 TAACCCTCTCTGGCCAAATGCAATTTCCT -s simRat_chr6.simRat.chr6 149532 29 + 647215 AAGCCCTTTTTAGCGCAATAAGGTTTACT - -a -s simMouse_chr6.simMouse.chr6 151753 5 + 636262 TACTA -s Anc0.Anc0refChr5 73847 5 - 87904 TACTA -s Anc1.Anc1refChr8 30230 5 - 57822 TACTA -s Anc2.Anc2refChr15 79028 5 - 86568 TACTA -s mr.mrrefChr5 14879 5 + 294540 TACTA -s simCow_chr6.simCow.chr6 411978 5 - 602619 TACTA -s simDog_chr6.simDog.chr6 121598 5 + 593897 TACTA -s simHuman_chr6.simHuman.chr6 407395 5 - 601863 TACTA -s simRat_chr6.simRat.chr6 149561 5 + 647215 TACTA - -a -s simMouse_chr6.simMouse.chr6 151758 38 + 636262 CACTCATTAGCAACATACCATAGGGCTCATGGCACGCT -s Anc0.Anc0refChr5 73857 38 - 87904 CAGGCATTAACATTATACCATAGGGCTTATGGCATGCT -s Anc1.Anc1refChr8 30240 38 - 57822 CAGGCATTAACATTATACCATAGGGCTTATGGCATGCT -s Anc2.Anc2refChr15 79038 38 - 86568 CAGGCATTAACATTATATCATAGGGCTTATGGCATGCT -s mr.mrrefChr5 14884 38 + 294540 CAGTCATTAGCAATATACCATAGGGCTCATGGCACGCT -s simCow_chr6.simCow.chr6 411988 38 - 602619 CAGGCATTAACCTTATATCATGGGTCTTATGGCATGCT -s simDog_chr6.simDog.chr6 121608 36 + 593897 CAAGCATTAACATTATATCACAGGGCTTATGTTGTG-- -s simHuman_chr6.simHuman.chr6 407405 38 - 601863 CAGGCAGGAACATTATACCATAGGGTTTGTAGCATGCT -s simRat_chr6.simRat.chr6 149566 38 + 647215 CAGACATTAGCAATATAGCATAGGGATCATGGCACACT - -a -s simMouse_chr6.simMouse.chr6 151796 20 + 636262 ACCACAGTAGGCATGTAAAT -s Anc0.Anc0refChr5 73895 20 - 87904 AATACAGTAAGCACGTAAGT -s Anc1.Anc1refChr8 30278 20 - 57822 AATACAGTAAGCACGTAAGT -s Anc2.Anc2refChr15 79076 20 - 86568 AATGAAGTAAGCACGTAAGT -s mr.mrrefChr5 14922 20 + 294540 ACTACAGTAAGCATGTAAGT -s simCow_chr6.simCow.chr6 412035 20 - 602619 AATGAAATAAGCAAGTAAGT -s simDog_chr6.simDog.chr6 121644 14 + 593897 ------GTAAGCACGTAAAT -s simHuman_chr6.simHuman.chr6 407443 20 - 601863 AATACAGCAATCAGGTAAGT -s simRat_chr6.simRat.chr6 149604 20 + 647215 GCTACAGGAAGTATGTAAGT - -a -s simMouse_chr6.simMouse.chr6 151816 26 + 636262 GAACAACTGCAAGGATGTAAGAGATC -s Anc0.Anc0refChr5 73915 26 - 87904 GAACAACCTTCAGGACCTGAAAGACA -s Anc1.Anc1refChr8 30298 26 - 57822 GAACAACCTTCAGGACCTGAAAGACA -s Anc2.Anc2refChr15 79101 26 - 86568 GAACAACCTTCAGGACCTGAAAGACA -s mr.mrrefChr5 14942 26 + 294540 GAACAACTGCAAGGATGTAAGAGATC -s simCow_chr6.simCow.chr6 412060 26 - 602619 GAACAACTTTCAGGACCTGAAAAATA -s simDog_chr6.simDog.chr6 121663 26 + 593897 GAACTACCTACAGGACTTGCAAGACG -s simHuman_chr6.simHuman.chr6 407463 26 - 601863 GAACATCCATCAGGACCAGAAGGACA -s simRat_chr6.simRat.chr6 149624 26 + 647215 AGACAATTGCAAGGATGTAAGAGATC - -a -s simMouse_chr6.simMouse.chr6 151842 38 + 636262 GTGATATGTGGGCTACCTGAGATAGAATTAATTTAATC -s Anc0.Anc0refChr5 73941 38 - 87904 AGGATGTGTGGACTACCTGAGTTAGGGTTAATTTAGTC -s Anc1.Anc1refChr8 30324 38 - 57822 AGGATGTGTGGACTACCTGAGTTAGGGTTAATTTAGTC -s Anc2.Anc2refChr15 79127 38 - 86568 AGGATGTGTGGACTACCTGTGTTAGGGTTAATTTAGTC -s mr.mrrefChr5 14968 38 + 294540 ATGATATGTGGGCTACCTGAGATAGAATTAATTTAATC -s simCow_chr6.simCow.chr6 412095 38 - 602619 AGGAGGTGTGAATTAACTAGGTTAGGGTTAATTTAGTC -s simDog_chr6.simDog.chr6 121689 38 + 593897 AGTATGTGTGGACTACTTGTGTTAGGTATAATTTAGTC -s simHuman_chr6.simHuman.chr6 407489 38 - 601863 AGGATGTGTGGACTACCTGAGGTAGGGTTAGTGGAGTC -s simRat_chr6.simRat.chr6 149650 38 + 647215 ATGATATGTGGGTTACCTGACATAAAATCAATTTAATC - -a -s simMouse_chr6.simMouse.chr6 151880 9 + 636262 CAATCCTAA -s Anc0.Anc0refChr5 73979 4 - 87904 C-----CAA -s Anc1.Anc1refChr8 30362 4 - 57822 C-----CAA -s Anc2.Anc2refChr15 79165 4 - 86568 C-----CAA -s mr.mrrefChr5 15006 4 + 294540 C-----TAA -s simCow_chr6.simCow.chr6 412133 4 - 602619 C-----TAA -s simDog_chr6.simDog.chr6 121734 4 + 593897 C-----CTA -s simHuman_chr6.simHuman.chr6 407527 4 - 601863 C-----CAA -s simRat_chr6.simRat.chr6 149688 4 + 647215 C-----TAA - -a -s simMouse_chr6.simMouse.chr6 151889 28 + 636262 GCCTACCAAAAATCCATTCTTCCCAGTT -s Anc0.Anc0refChr5 73983 28 - 87904 GCCTTCCAAAAATCTATCCCTCCCAGCT -s Anc1.Anc1refChr8 30366 28 - 57822 GCCTTCCAAAAATCTATCCCTCCCAGCT -s Anc2.Anc2refChr15 79169 28 - 86568 GCCCTCCAAAAATCTATCCCTCCTAGCT -s mr.mrrefChr5 15010 28 + 294540 GCCTACCAAAAATCCATTCTTCCCAGCT -s simCow_chr6.simCow.chr6 412137 28 - 602619 GTCCTCCAAAAATCTATTCCTCGTGGCT -s simDog_chr6.simDog.chr6 121740 28 + 593897 GCCCTCCAGAAATCTATCCCTCCTAGCT -s simHuman_chr6.simHuman.chr6 407531 17 - 601863 GCCTGCCAAA-----------CCCAGCT -s simRat_chr6.simRat.chr6 149692 28 + 647215 GCCTACCAAAGATTGATTCCTCTCAGCT - -a -s simMouse_chr6.simMouse.chr6 151917 54 + 636262 AACAAATCAGGTATGACCACTGATACTGGGTGGTGTGGAGTGAATGTCACTAGA -s Anc0.Anc0refChr5 74012 44 - 87904 AACAAGTCAGGTATTACTACTGA-------TGGTGTAGAGTGAATGCCACT--- -s Anc1.Anc1refChr8 30395 44 - 57822 AACAAGTCAGGTATTACTACTGA-------TGGTGTAGAGTGAATGCCACT--- -s Anc2.Anc2refChr15 79198 44 - 86568 AACATGTCAGGTATTACTACTGA-------TGGTGTAGAGTGAATGCCACC--- -s mr.mrrefChr5 15038 54 + 294540 AACAAGTCAGGTATGACTACTGATACTGGGTGGTGTGGAGTGAATGCCACTAAA -s simCow_chr6.simCow.chr6 412166 44 - 602619 AACAGGTCAAGTATAACCACTTA-------TGGTGTAGAGTAAGTGTTAAA--- -s simDog_chr6.simDog.chr6 121769 44 + 593897 AACATGTCAGGTATTACTACCGA-------TAGCGTAGAATGAATGCCACC--- -s simHuman_chr6.simHuman.chr6 407549 44 - 601863 AACAAGTCAGGTATTGCTGCTGA-------TGGTGCACAGTGAATGCCTCT--- -s simRat_chr6.simRat.chr6 149720 54 + 647215 AACAAGTCAGGTATAAGTACTGATAGCGGGTGGTGTGGAGTGCATGCCACTAAA - -a -s simMouse_chr6.simMouse.chr6 151971 28 + 636262 AACAATTGGTCTTGTTAGCAAAGTGGGG -s Anc0.Anc0refChr5 74056 25 - 87904 CACAATTGGTCTTGTTGGCA---TGGAG -s Anc1.Anc1refChr8 30439 25 - 57822 CACAATTGGTCTTGTTGGCA---TGGAG -s Anc2.Anc2refChr15 79242 25 - 86568 CACAATTGGTCTTGTTGGCA---AGGAG -s mr.mrrefChr5 15092 28 + 294540 AACAATTGGTCTTGTTGGCAAAGTGGGG -s simCow_chr6.simCow.chr6 412210 25 - 602619 CACACTTGGTCTTGTTAGCA---AGGAG -s simDog_chr6.simDog.chr6 121817 25 + 593897 CACAATTGGTCTTGTTGGCA---AGGAG -s simHuman_chr6.simHuman.chr6 407593 25 - 601863 GACATTTGGTCTTGTTGTCA---TGAAG -s simRat_chr6.simRat.chr6 149774 28 + 647215 AACAGTTGGTCTTGTTGGCAAAGTGGGG - -a -s simMouse_chr6.simMouse.chr6 151999 18 + 636262 CAAGCTTAATAGGAGGCA -s Anc0.Anc0refChr5 74083 18 - 87904 CAAGCTTAGTAGAAGGTA -s Anc1.Anc1refChr8 30466 18 - 57822 CAAGCTTAGTAGAAGGTA -s Anc2.Anc2refChr15 79269 18 - 86568 CAAGCTTAGTAGGAGGTA -s mr.mrrefChr5 15122 18 + 294540 CAAGCTTAATAGAAGGCA -s simCow_chr6.simCow.chr6 412237 18 - 602619 CAAGCTTAGTAGGAGGTT -s simDog_chr6.simDog.chr6 121844 18 + 593897 CAACCTTATTAGGAGGTA -s simHuman_chr6.simHuman.chr6 407620 16 - 601863 TAAGCTTAGTAGAAGG-- -s simRat_chr6.simRat.chr6 149804 18 + 647215 GAAGCTGAATAGAAGGCA - -a -s simMouse_chr6.simMouse.chr6 152017 32 + 636262 GTTTTATTCTGGTGTGTGCATCATTTAATTTG -s Anc0.Anc0refChr5 74105 32 - 87904 GTTTTGTGCAGGTGTACACATTCTTTACTTTA -s Anc1.Anc1refChr8 30488 32 - 57822 GTTTTGTGCAGGTGTACACATTCTTTACTTTA -s Anc2.Anc2refChr15 79293 32 - 86568 GTTTTGTGCAGGTGTACACATTCTTTGCTTTA -s mr.mrrefChr5 15140 32 + 294540 GTTTTATTCTGGTGTGTGCATCATTTACTTTG -s simCow_chr6.simCow.chr6 412261 32 - 602619 GTTTTGTTCAGTTGCACAGAACCTTTGCTTTG -s simDog_chr6.simDog.chr6 121868 32 + 593897 GTTTTGTGCAGGTATACACATTCCTTGCTTTA -s simHuman_chr6.simHuman.chr6 407640 29 - 601863 ATTTTGTCCAGGTGTACACAGTTTTGACT--- -s simRat_chr6.simRat.chr6 149822 31 + 647215 GTTCTATTCTGGTGT-TGCATCAGTTGCTCTG - -a -s simMouse_chr6.simMouse.chr6 152049 17 + 636262 ACTAATATAGGGAAAGG -s Anc0.Anc0refChr5 74137 17 - 87904 ACTAATATAAGGAAAGG -s Anc1.Anc1refChr8 30520 17 - 57822 ACTAATATAAGGAAAGG -s Anc2.Anc2refChr15 79325 17 - 86568 ACTAATATAAGAAAAGG -s mr.mrrefChr5 15172 17 + 294540 ACTAATATAGGGAAAGG -s simCow_chr6.simCow.chr6 412296 17 - 602619 ACTAATAAACAATAAGG -s simDog_chr6.simDog.chr6 121900 17 + 593897 AATAATATAAGAAGAGA -s simHuman_chr6.simHuman.chr6 407669 17 - 601863 ACTAACAGAAGGAAAGG -s simRat_chr6.simRat.chr6 149853 17 + 647215 ACTAATATAGGGAAAGG - -a -s simMouse_chr6.simMouse.chr6 152066 42 + 636262 TATGACAAGTTGCACTTGGTTAAAGAAGTTGCACCAGGTCAT -s Anc0.Anc0refChr5 74155 42 - 87904 AACAACAAGTTGCACTGGGTTAAACAAGTTGCACTGGGTTAT -s Anc1.Anc1refChr8 30538 42 - 57822 AACAACAAGTTGCACTGGGTTAAACAAGTTGCACTGGGTTAT -s Anc2.Anc2refChr15 79343 42 - 86568 AACAACAAGTTGTGTTTGGTTAAACAAGTTGCACTGGGTTGT -s mr.mrrefChr5 15189 42 + 294540 AATGACAAGTTGCACTGGGTTAAAGAAGTTGCACTGGGTCAT -s simCow_chr6.simCow.chr6 412314 42 - 602619 GACAACACATTCTGGCAGGTTGAACAAATTGCACTAGATTGT -s simDog_chr6.simDog.chr6 121918 42 + 593897 AACTGCAAGTTGTGTTTGTTTAAACAAGTTACACTGGGTTGT -s simHuman_chr6.simHuman.chr6 407687 42 - 601863 AACAACAAGTTGCACTGGGTTAAACAAGCTGCACTGGGTTAT -s simRat_chr6.simRat.chr6 149870 42 + 647215 AATGACAAGTTGCACTGGGTTAAAGAAGTTGCACTGGGTCAT - -a -s simMouse_chr6.simMouse.chr6 152108 24 + 636262 GAAATGACGAATACTAGATAGTCC -s Anc0.Anc0refChr5 74197 21 - 87904 GAAACA---AACACTATCTAGTCC -s Anc1.Anc1refChr8 30580 21 - 57822 GAAACA---AACACTATCTAGTCC -s Anc2.Anc2refChr15 79385 21 - 86568 GAAACA---AACACTATCTAATCC -s mr.mrrefChr5 15231 24 + 294540 GAAACAACGAATACTAGATAGTCC -s simCow_chr6.simCow.chr6 412356 19 - 602619 GAAACA---AACATTAT--AAACC -s simDog_chr6.simDog.chr6 122022 21 + 593897 GAAACA---AACACCACCTGATCC -s simHuman_chr6.simHuman.chr6 407729 21 - 601863 GAAACA---AACACTGTCCAGTCC -s simRat_chr6.simRat.chr6 149912 24 + 647215 GAAACAACGAATACTAGATTGTCC - -a -s simMouse_chr6.simMouse.chr6 152132 4 + 636262 TTCA -s Anc0.Anc0refChr5 74218 4 - 87904 ATCT -s Anc1.Anc1refChr8 30601 4 - 57822 ATCT -s Anc2.Anc2refChr15 79406 4 - 86568 ATCT -s mr.mrrefChr5 15255 4 + 294540 TTCA -s simCow_chr6.simCow.chr6 412375 4 - 602619 ATCT -s simDog_chr6.simDog.chr6 122043 4 + 593897 AGCT -s simHuman_chr6.simHuman.chr6 407752 4 - 601863 CTCT -s simRat_chr6.simRat.chr6 149936 4 + 647215 TTCA - -a -s simMouse_chr6.simMouse.chr6 152136 9 + 636262 CTAAATGTA -s Anc0.Anc0refChr5 74225 8 - 87904 CTA-ATGTA -s Anc1.Anc1refChr8 30608 9 - 57822 CTACATGTA -s Anc2.Anc2refChr15 79413 8 - 86568 CTA-ATGTA -s mr.mrrefChr5 15262 9 + 294540 CTAAATGTA -s simCow_chr6.simCow.chr6 412382 8 - 602619 CTA-GTGTA -s simDog_chr6.simDog.chr6 122050 8 + 593897 CTA-ATGTA -s simHuman_chr6.simHuman.chr6 407759 9 - 601863 CTACATGTA -s simRat_chr6.simRat.chr6 149943 9 + 647215 CTAAATGTA - -a -s simMouse_chr6.simMouse.chr6 152145 14 + 636262 CAGGTTCAATCAGT -s Anc0.Anc0refChr5 74233 14 - 87904 CAAGTTCAAGCACT -s Anc1.Anc1refChr8 30617 14 - 57822 CAAGTTCAAGCACT -s Anc2.Anc2refChr15 79421 14 - 86568 CCAGTTCAAGGACT -s mr.mrrefChr5 15271 14 + 294540 CAGGTTCAATCAGT -s simCow_chr6.simCow.chr6 412420 14 - 602619 CCAGTCAACAGACC -s simDog_chr6.simDog.chr6 122058 14 + 593897 CCAGTTCAAGGACT -s simHuman_chr6.simHuman.chr6 407768 14 - 601863 CAAGTTCAAGCAAT -s simRat_chr6.simRat.chr6 149952 14 + 647215 CAGGTTCACTAAGT - -a -s simMouse_chr6.simMouse.chr6 152159 13 + 636262 AACCCCATCTAGG -s Anc0.Anc0refChr5 74247 13 - 87904 AACCCCACCATGG -s Anc1.Anc1refChr8 30631 13 - 57822 AACCCCACCATGG -s Anc2.Anc2refChr15 79435 13 - 86568 AACCCCACCATGG -s mr.mrrefChr5 15285 13 + 294540 AACCCCACCTAGG -s simCow_chr6.simCow.chr6 412439 13 - 602619 GACCTGACCATGG -s simDog_chr6.simDog.chr6 122072 13 + 593897 AACCCCACCATGG -s simHuman_chr6.simHuman.chr6 407782 13 - 601863 AACCCCACCAGGG -s simRat_chr6.simRat.chr6 149966 13 + 647215 AGCCCCACCCAGG - -a -s simMouse_chr6.simMouse.chr6 152172 3 + 636262 TTA -s Anc0.Anc0refChr5 74261 3 - 87904 TTA -s Anc1.Anc1refChr8 30645 3 - 57822 TTA -s Anc2.Anc2refChr15 79449 3 - 86568 TTA -s mr.mrrefChr5 15298 3 + 294540 TTA -s simCow_chr6.simCow.chr6 412453 3 - 602619 TTG -s simDog_chr6.simDog.chr6 122086 3 + 593897 CTA -s simHuman_chr6.simHuman.chr6 407796 3 - 601863 TTA -s simRat_chr6.simRat.chr6 149979 3 + 647215 TTA - -a -s simMouse_chr6.simMouse.chr6 152175 1 + 636262 C -s Anc0.Anc0refChr5 74264 1 - 87904 C -s Anc1.Anc1refChr8 30648 1 - 57822 C -s Anc2.Anc2refChr15 79486 1 - 86568 T -s mr.mrrefChr5 15301 1 + 294540 C -s simCow_chr6.simCow.chr6 412497 1 - 602619 T -s simDog_chr6.simDog.chr6 122135 1 + 593897 T -s simHuman_chr6.simHuman.chr6 407799 1 - 601863 C -s simRat_chr6.simRat.chr6 149982 1 + 647215 C - -a -s simMouse_chr6.simMouse.chr6 152176 30 + 636262 CAGTCAGCAGTGCTGGTAAAAGGTCCCTAA -s Anc0.Anc0refChr5 74265 30 - 87904 CAGTCAACTGTGCTGGTATAAGATCTCTAG -s Anc1.Anc1refChr8 30649 30 - 57822 CAGTCAACTGTGCTGGTATAAGATCTCTAG -s Anc2.Anc2refChr15 79487 30 - 86568 CAGACAACTGTACTGGTGTAAGACCTCTAG -s mr.mrrefChr5 15302 30 + 294540 CAGTCAGCAGTGCTGGTAAAAGATCCCTAG -s simCow_chr6.simCow.chr6 412513 30 - 602619 CAGACAATTGTCATTGTGTAAGACCTCTAG -s simDog_chr6.simDog.chr6 122136 30 + 593897 CAGACAACTGTACTGGTGTAAGACCTCTAG -s simHuman_chr6.simHuman.chr6 407800 30 - 601863 CAGTCAACTGTGCTGGCATAGGATCTCTAG -s simRat_chr6.simRat.chr6 149983 30 + 647215 CACTCAGAATTGCTGATAAAAGATCCCTAG - -a -s simMouse_chr6.simMouse.chr6 152206 78 + 636262 TTGGAGTTGATATAGGCTGGGTTCCACTGGGCTCCATGTCACTCTTTGAGTACGAGTTAACACTTAATGACACTATCA -s Anc0.Anc0refChr5 74299 68 - 87904 CTATGGTTGTTATAGGTTGGATTCCATTG----------CACTCTTCTAGTGCTAGTTAACACTTTGAGACACTATCA -s Anc1.Anc1refChr8 30683 68 - 57822 CTATGGTTGTTATAGGTTGGATTCCATTG----------CACTCTTCTAGTGCTAGTTAACACTTTGAGACACTATCA -s Anc2.Anc2refChr15 79521 68 - 86568 CTTTGGTTGTTATAAGTTAGATTTTATAC----------CACTCTTCTAGTGCTTGTTAACACTTTGAGACACTACCT -s mr.mrrefChr5 15332 78 + 294540 TTAGAGTTGATATAGGCTGGGTTCCACTGGGCTCCATGTCACTCTTTGAGTGCGAGTTAACACTTAATGACACTATCA -s simCow_chr6.simCow.chr6 412547 66 - 602619 CTTTGGTTGTTATAAGCTTGACTGTAT------------CACTCTTCTAGTGCTTGTTAACACTTTGAGACACTATCT -s simDog_chr6.simDog.chr6 122170 68 + 593897 CTTTGGTTGTTATAAGTTAGATTTTATAC----------TACTCTTCTAATGCTTGTTAACACTTCAAGACACTACCC -s simHuman_chr6.simHuman.chr6 407834 68 - 601863 CTATGGTTGTTATAGGTTGGATTCCATTG----------CACTCTTGTAGTGCCAGTTAACACTGTGAAAGACTATTA -s simRat_chr6.simRat.chr6 150013 78 + 647215 TTACAATTGAAATAGGCTGGGTTCCACTGGGCTTCATGTCACTCTTTGAGTGGGAGTTAAGACTTAATGACACTATCA - -a -s simMouse_chr6.simMouse.chr6 152284 17 + 636262 CTACTTCACATTGGACA -s Anc0.Anc0refChr5 74367 17 - 87904 TTACTTCACACCCAACA -s Anc1.Anc1refChr8 30751 17 - 57822 TTACTTCACACCCAACA -s Anc2.Anc2refChr15 79589 17 - 86568 TTACTTCACACCCAACA -s mr.mrrefChr5 15410 17 + 294540 CTACTTCACATTGGACA -s simCow_chr6.simCow.chr6 412613 17 - 602619 ATACTTCACACCGAACA -s simDog_chr6.simDog.chr6 122238 17 + 593897 TTACTTCACACCCAACA -s simHuman_chr6.simHuman.chr6 407905 10 - 601863 TTAATTCG-------CA -s simRat_chr6.simRat.chr6 150091 17 + 647215 CTACTTCACATTGAACA - -a -s simMouse_chr6.simMouse.chr6 152301 3 + 636262 CCA -s Anc0.Anc0refChr5 74384 3 - 87904 CCT -s Anc1.Anc1refChr8 30768 3 - 57822 CCT -s Anc2.Anc2refChr15 79607 3 - 86568 CCT -s mr.mrrefChr5 15427 3 + 294540 CCA -s simCow_chr6.simCow.chr6 412631 3 - 602619 CCT -s simDog_chr6.simDog.chr6 122256 3 + 593897 CCT -s simHuman_chr6.simHuman.chr6 407915 3 - 601863 CCC -s simRat_chr6.simRat.chr6 150108 3 + 647215 CCA - -a -s simMouse_chr6.simMouse.chr6 152304 55 + 636262 TATCGACTAGCTAGCTCTTTAAATCTTGCAGCGTATAACTGGGTTTCGAGGCAGA -s Anc0.Anc0refChr5 74387 55 - 87904 TATTGATGTGCCAATTCTTTAATTCTTGTAGTGGATAATTGAGTTTCCAGGCAGG -s Anc1.Anc1refChr8 30771 55 - 57822 TATTGATGTGCCAATTCTTTAATTCTTGTAGTGGATAATTGAGTTTCCAGGCAGG -s Anc2.Anc2refChr15 79610 55 - 86568 TGTTGATGTGCTGATTCTTTAATTCTTGTAGTGGATAATTGAATTTCCAGGCAGG -s mr.mrrefChr5 15430 55 + 294540 TATTGACTTGCCAATTCTTTAAATCTTGCAGCGTATAACTGGGTTTCCAGGCAGA -s simCow_chr6.simCow.chr6 412634 55 - 602619 TGCTTATGTGATGAGTCTTTCATTCTTGTACCAAATAATTGAATTTCCAGGAAGG -s simDog_chr6.simDog.chr6 122260 55 + 593897 TGTTGATGTGCTGATTCTTTAACTCTTGTAGTGGATAATTGAATTTCCAGGCAGG -s simHuman_chr6.simHuman.chr6 407918 49 - 601863 TATTG---TGCCAATTCTTTAATCCTTGTGGT---TAATTGAGTTTCCAGGCAGG -s simRat_chr6.simRat.chr6 150111 55 + 647215 TATTGACTTGCCAATCCTTTAAATCATGCAGCGTATAACTGGGTCTCCAGGCAAA - -a -s simMouse_chr6.simMouse.chr6 152359 16 + 636262 ATTCGTTAGGCTAAAT -s Anc0.Anc0refChr5 74445 16 - 87904 TTCCTTCAGGCTGAAT -s Anc1.Anc1refChr8 30829 16 - 57822 TTCCTTCAGGCTGAAT -s Anc2.Anc2refChr15 79668 16 - 86568 TGCATTCAGGCTGAAT -s mr.mrrefChr5 15485 16 + 294540 ATTCGTTAGGCTAAAT -s simCow_chr6.simCow.chr6 412692 16 - 602619 AGCATTCAGGCTGCAT -s simDog_chr6.simDog.chr6 122318 16 + 593897 TGCATTCAGGCCGAGT -s simHuman_chr6.simHuman.chr6 407970 16 - 601863 TTCCTTCAGGCTGAAT -s simRat_chr6.simRat.chr6 150166 16 + 647215 ATTCCTTAGGCTAAAT - -a -s simMouse_chr6.simMouse.chr6 152375 8 + 636262 CCAATACT -s Anc0.Anc0refChr5 74466 8 - 87904 CCTATCAT -s Anc1.Anc1refChr8 30850 8 - 57822 CCTATCAT -s Anc2.Anc2refChr15 79711 8 - 86568 CCTATCAT -s mr.mrrefChr5 15501 8 + 294540 CCAATAAT -s simCow_chr6.simCow.chr6 412735 5 - 602619 CCTAT--- -s simDog_chr6.simDog.chr6 122361 8 + 593897 CCTACCAT -s simHuman_chr6.simHuman.chr6 407991 8 - 601863 CCCATCAT -s simRat_chr6.simRat.chr6 150182 8 + 647215 CCAATAAT - -a -s simMouse_chr6.simMouse.chr6 152383 45 + 636262 GACAACCCTTTCCATTTCATGATGTCTGATTGGGAAGAATAGGAA -s Anc0.Anc0refChr5 74490 43 - 87904 GACTACT-CTGCTCTACCAT-ATGTTTTATTGGGAAGAATAATAA -s Anc1.Anc1refChr8 30874 44 - 57822 GACTACTCCTGCTCTACCAT-ATGTTTTATTGGGAAGAATAATAA -s Anc2.Anc2refChr15 79735 43 - 86568 AACTACT-CTGTTCCATCAT-ATGTTTTATTGTGAAGAATGATTA -s mr.mrrefChr5 15509 45 + 294540 GACAACTCTTTCCATACCATGATGTCTGATTGGGAAGAATAGGAA -s simDog_chr6.simDog.chr6 122385 43 + 593897 AACTACT-CTGTTCCATCAT-ATGTTTTATTGTGAAGAATGATTA -s simHuman_chr6.simHuman.chr6 408015 44 - 601863 GACTACTCCTGCAGTACCTT-GTGTTTCATTAGGAAGAACAATAA -s simRat_chr6.simRat.chr6 150190 45 + 647215 GGCGATTCTTTCCATACCATCATGTCAGATTGGGAAGTAGAGGAA - -a -s simMouse_chr6.simMouse.chr6 152428 16 + 636262 CAAGAAAGAATCTTTA -s Anc0.Anc0refChr5 74544 16 - 87904 CTAGAGTGAATCTGTA -s Anc1.Anc1refChr8 30929 16 - 57822 CTAGAGTGAATCTGTA -s Anc2.Anc2refChr15 79789 16 - 86568 CTAGAGTGAACCTGTA -s mr.mrrefChr5 15554 16 + 294540 CAAGAAAGAATCTTTA -s simCow_chr6.simCow.chr6 412742 16 - 602619 CTAGAGTGAACCTGTA -s simDog_chr6.simDog.chr6 122439 16 + 593897 TTAGAGTGAACTTGTA -s simHuman_chr6.simHuman.chr6 408070 16 - 601863 CTAGAGTGAATCTGTA -s simRat_chr6.simRat.chr6 150235 16 + 647215 CAAAAAAGAAACTTTA - -a -s simMouse_chr6.simMouse.chr6 152444 4 + 636262 GACA -s Anc0.Anc0refChr5 74560 4 - 87904 TATA -s Anc1.Anc1refChr8 30945 4 - 57822 TATA -s Anc2.Anc2refChr15 79806 4 - 86568 TATA -s mr.mrrefChr5 15570 4 + 294540 GACA -s simCow_chr6.simCow.chr6 412759 4 - 602619 TATA -s simDog_chr6.simDog.chr6 122456 4 + 593897 TACA -s simHuman_chr6.simHuman.chr6 408086 4 - 601863 TATA -s simRat_chr6.simRat.chr6 150251 4 + 647215 GACA - -a -s simMouse_chr6.simMouse.chr6 152448 23 + 636262 ATAGGATTTTAAACGCAAAAATA -s Anc0.Anc0refChr5 74573 23 - 87904 ATATGTGTTGACCTACAAAGACA -s Anc1.Anc1refChr8 30958 23 - 57822 ATATGTGTTGACCTACAAAGACA -s Anc2.Anc2refChr15 79819 23 - 86568 ATATGTGTTGACCTACAAAGACA -s mr.mrrefChr5 15574 23 + 294540 ATAGGATTTTAAACACAAAAATA -s simCow_chr6.simCow.chr6 412772 23 - 602619 ATATGGGTTGACCTACAAAGACT -s simDog_chr6.simDog.chr6 122469 11 + 593897 ATATGT------------AGACA -s simHuman_chr6.simHuman.chr6 408099 23 - 601863 ATATATGTTGATCTACAAAGACA -s simRat_chr6.simRat.chr6 150255 22 + 647215 ATA-GATTTTAAACACAAAAATA - -a -s simMouse_chr6.simMouse.chr6 152471 27 + 636262 GTTAATTATGTGTTCTATGGAAGTAAA -s Anc0.Anc0refChr5 74596 23 - 87904 GCTAATCTTGTGATCC----AAGAAAG -s Anc1.Anc1refChr8 30981 27 - 57822 GCTAATCTTGTGATCCAAATAAGAAAG -s Anc2.Anc2refChr15 79842 23 - 86568 GCTAATCTTGTGATCC----AAGAAAG -s mr.mrrefChr5 15597 27 + 294540 GTTAATTATGTGTTCCATGGAAGAAAG -s simCow_chr6.simCow.chr6 412795 23 - 602619 TCTAATCTTGTGACCC----AAGAGAG -s simDog_chr6.simDog.chr6 122480 23 + 593897 GCTAATCTTGTCATGC----AAGAAAG -s simHuman_chr6.simHuman.chr6 408134 24 - 601863 GCTAACCTTGTGATCCAAATAAGA--- -s simRat_chr6.simRat.chr6 150277 27 + 647215 TTTAGTTATGTGTTCCATGGAAGAAAG - -a -s simMouse_chr6.simMouse.chr6 152498 3 + 636262 GTA -s Anc0.Anc0refChr5 74619 3 - 87904 ATA -s Anc1.Anc1refChr8 31008 3 - 57822 ATA -s Anc2.Anc2refChr15 79865 3 - 86568 ATA -s mr.mrrefChr5 15624 3 + 294540 GTA -s simCow_chr6.simCow.chr6 412824 2 - 602619 AT- -s simDog_chr6.simDog.chr6 122503 3 + 593897 ATA -s simRat_chr6.simRat.chr6 150304 3 + 647215 GTG - -a -s simMouse_chr6.simMouse.chr6 152501 17 + 636262 ATTGTTGCATGTCCAAG -s Anc0.Anc0refChr5 74622 17 - 87904 ATTGTTCTGTGTCAAAG -s Anc1.Anc1refChr8 31011 17 - 57822 ATTGTTCTGTGTCAAAG -s Anc2.Anc2refChr15 79868 17 - 86568 ATTGTTCTGTGTCAAAG -s mr.mrrefChr5 15627 17 + 294540 ATTGTTGCATGTCCAAG -s simCow_chr6.simCow.chr6 412827 17 - 602619 GTTGTTATGTGTCAAAG -s simDog_chr6.simDog.chr6 122506 17 + 593897 ATTGTTCTGTTTCAATG -s simHuman_chr6.simHuman.chr6 408158 1 - 601863 ----T------------ -s simRat_chr6.simRat.chr6 150307 17 + 647215 ATTGTTTCATGTCCAAG - -a -s simMouse_chr6.simMouse.chr6 152518 44 + 636262 AGTGGCCTCGGTTTTACACTTGAGGGGATAAAGGTGCTAAGGAG -s Anc0.Anc0refChr5 74639 40 - 87904 AGTAGCTTGTATTTTACACGTAAGGGGGAAAAAGGG----GGAG -s Anc1.Anc1refChr8 31028 40 - 57822 AGTAGCTTGTATTTTACACGTAAGGGGGAAAAAGGG----GGAG -s Anc2.Anc2refChr15 79896 40 - 86568 AGTAGCTTGTATTTTACATGTAAGGGGGAAAAAAGG----GGAG -s mr.mrrefChr5 15644 40 + 294540 AGTGGCCTTGGTTTTACACTTGAGGGGGTAAAGGTG----GGAG -s simCow_chr6.simCow.chr6 412855 40 - 602619 ATGAGCTTATATTTTACATGTAAGGGGGAAGAAAGG----GGGG -s simDog_chr6.simDog.chr6 122533 40 + 593897 CGTAGCTTGTATTTTACATGTAAGGGGGAAAAAAGG----GGAG -s simHuman_chr6.simHuman.chr6 408866 34 - 601863 ------TTGTAGATTACACATAAGGGAGAAAAAGGG----GGAG -s simRat_chr6.simRat.chr6 150324 36 + 647215 AGTGGTCTTGGTTTTACACTTGAGGGGGTAAAGGTA-------- - -a -s simMouse_chr6.simMouse.chr6 152562 10 + 636262 AATTAGCTCC -s Anc0.Anc0refChr5 74680 10 - 87904 GGTCAGCTCC -s Anc1.Anc1refChr8 31069 10 - 57822 GGTCAGCTCC -s Anc2.Anc2refChr15 79937 10 - 86568 GGGCTGCTTC -s mr.mrrefChr5 15684 10 + 294540 AATTAGCTCC -s simCow_chr6.simCow.chr6 412896 10 - 602619 GGGTTGGTTC -s simDog_chr6.simDog.chr6 122574 10 + 593897 GGGCTGCTTC -s simHuman_chr6.simHuman.chr6 408901 10 - 601863 GGTCAGCTCC -s simRat_chr6.simRat.chr6 150360 10 + 647215 AACTAGCTTT - -a -s simMouse_chr6.simMouse.chr6 152572 42 + 636262 TAATCACCTTGAGTCAGTGTGACACTCAAGACTTAGTCAAAA -s Anc0.Anc0refChr5 74690 42 - 87904 TGAAAACCCTGAACCACTATGACATTGAAGAGATAGACAAGA -s Anc1.Anc1refChr8 31079 42 - 57822 TGAAAACCCTGAACCACTATGACATTGAAGAGATAGACAAGA -s Anc2.Anc2refChr15 79947 42 - 86568 TGAAAACCCTGAACCACTATGACATTGAAAAGATATACAAGA -s mr.mrrefChr5 15694 42 + 294540 TAATCACCTTGAGCCAGTGTGACACTCAAGACATAGTCAAAA -s simCow_chr6.simCow.chr6 412906 35 - 602619 TGAAAA-----AAC--CTATGACATTGAAAAGATATCCAAGA -s simDog_chr6.simDog.chr6 122594 42 + 593897 TGAAAACCCTGAACCATTACGACATTGAAAAGATATACATGA -s simHuman_chr6.simHuman.chr6 408911 42 - 601863 TGAAAACCCTGAACCACTATGACATTGAAGAGATAGACAAGA -s simRat_chr6.simRat.chr6 150370 42 + 647215 TAATCACCTTGGGCAAATGTGACACCCAAGATATAGGCACAT - -a -s simMouse_chr6.simMouse.chr6 152614 54 + 636262 TGAAATCAATCACCGAGATTGCACCTATTAGAGGACATAACAATAAGCTATTCA -s Anc0.Anc0refChr5 74732 54 - 87904 TGAAATCAATTACTGAGATTGCACCTAATAGGAGACACAACAACAAGCTTTTCA -s Anc1.Anc1refChr8 31121 54 - 57822 TGAAATCAATTACTGAGATTGCACCTAATAGGAGACACAACAACAAGCTTTTCA -s Anc2.Anc2refChr15 79989 54 - 86568 TGAAATCAATTACTAAGGTTGCACCCAATAGGAGACACAACAACAAGCTTTTAA -s mr.mrrefChr5 15736 54 + 294540 TGAAATCAATCACTGAGATTGCACCTATTAGAGGACACAACAACAAGCTATTCA -s simCow_chr6.simCow.chr6 412941 53 - 602619 TGAAATCAATTACT-AGCTTGTACCCAATAGGAAACATAAAAACAAGCTTCTAA -s simDog_chr6.simDog.chr6 122636 54 + 593897 TGAAATCAATGAACAAGGTTGCACCCAATAGAAGACACAACAACAAGCATTTAA -s simHuman_chr6.simHuman.chr6 408961 54 - 601863 TGAAATCAATTACTGAAATTGCACCTAATAGGAGACACAACAACATGCTTTTCA -s simRat_chr6.simRat.chr6 150412 53 + 647215 TGAAATCAATCACTGAGATTGCAC-TATTAGAGGGCACAATAACAAGCTATTTA - -a -s simMouse_chr6.simMouse.chr6 152668 39 + 636262 CCAATATTACTTGAATACAATGATTATGTCATAGGATGT -s Anc0.Anc0refChr5 74792 25 - 87904 AAT---------AAATACA--GGTTATGTTATAA---GT -s Anc1.Anc1refChr8 31181 36 - 57822 AATATTTTA---AAATACAATGGTTATGTTATAAGATGT -s Anc2.Anc2refChr15 80049 25 - 86568 AAT---------CAATACA--GGTTATGTTATCA---GT -s mr.mrrefChr5 15796 39 + 294540 CCAATATTACTTGAATACAATGATTATGTCATAAGATGT -s simCow_chr6.simCow.chr6 413000 25 - 602619 AAA---------CAATGCA--AGTTATGTTATCA---GG -s simDog_chr6.simDog.chr6 122696 25 + 593897 AAT---------CAATACA--GATTATGTTATCA---GT -s simHuman_chr6.simHuman.chr6 409021 35 - 601863 ATTATTTTA---AAATACAATGGTTATGGTA-AAGATGT -s simRat_chr6.simRat.chr6 150473 39 + 647215 CCAATCTTACTTGTATACAATGATTATGTGATAAGATGT - -a -s simMouse_chr6.simMouse.chr6 152707 13 + 636262 CACTCGCGTCTGA -s Anc0.Anc0refChr5 74817 13 - 87904 CACCAATGTCTGG -s Anc1.Anc1refChr8 31217 13 - 57822 CACCAATGTCTGG -s Anc2.Anc2refChr15 80074 13 - 86568 CACCAATGTCTGG -s mr.mrrefChr5 15835 13 + 294540 CACTCATGTCTGA -s simCow_chr6.simCow.chr6 413028 13 - 602619 CACCAACATCTGG -s simDog_chr6.simDog.chr6 122721 13 + 593897 CACCTATGTCTAG -s simHuman_chr6.simHuman.chr6 409056 13 - 601863 CATCAATGTCTGG -s simRat_chr6.simRat.chr6 150512 13 + 647215 CACTTATGTCTGA - -a -s simMouse_chr6.simMouse.chr6 152720 1 + 636262 T -s Anc0.Anc0refChr5 74830 1 - 87904 C -s Anc1.Anc1refChr8 31230 1 - 57822 C -s Anc2.Anc2refChr15 80088 1 - 86568 C -s mr.mrrefChr5 15848 1 + 294540 T -s simCow_chr6.simCow.chr6 413042 1 - 602619 T -s simDog_chr6.simDog.chr6 122735 1 + 593897 C -s simHuman_chr6.simHuman.chr6 409069 1 - 601863 C -s simRat_chr6.simRat.chr6 150525 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 152721 18 + 636262 AACATGACTACGATTATG -s Anc0.Anc0refChr5 74831 18 - 87904 AAAATGTCCGTGGTTATG -s Anc1.Anc1refChr8 31231 18 - 57822 AAAATGTCCGTGGTTATG -s Anc2.Anc2refChr15 80089 18 - 86568 AAAGTGTTCGTGGTTGTC -s mr.mrrefChr5 15849 18 + 294540 AACATGACTATGATTATG -s simCow_chr6.simCow.chr6 413043 18 - 602619 CAAGTATTCATTGTTGTC -s simDog_chr6.simDog.chr6 122736 17 + 593897 AAAGTGTTTGTGCTTGT- -s simHuman_chr6.simHuman.chr6 409095 18 - 601863 AATATGTCCGTGGTTATG -s simRat_chr6.simRat.chr6 150526 18 + 647215 AACATGGCTATGATTATA - -a -s simMouse_chr6.simMouse.chr6 152739 22 + 636262 CCCTTACTGTTGCGTGCCCGAA -s Anc0.Anc0refChr5 74849 22 - 87904 CTCTTCCCACTGCGTGCCCAAA -s Anc1.Anc1refChr8 31249 22 - 57822 CTCTTCCCACTGCGTGCCCAAA -s Anc2.Anc2refChr15 80107 22 - 86568 CTCTTCCCACAGCATGCTCAAA -s mr.mrrefChr5 15867 22 + 294540 CTCTTACTGTTGCGTGCCCGAA -s simCow_chr6.simCow.chr6 413061 22 - 602619 CTCTTCCCACAGCATGCACAAA -s simDog_chr6.simDog.chr6 122753 6 + 593897 ----------------CTTCAA -s simHuman_chr6.simHuman.chr6 409114 22 - 601863 CTTTTCCCAGTGCGTGCCCAAA -s simRat_chr6.simRat.chr6 150544 21 + 647215 CTCT-ACTGTTGCATGCCCTGA - -a -s simMouse_chr6.simMouse.chr6 152761 3 + 636262 AAA -s Anc0.Anc0refChr5 74877 3 - 87904 TTA -s Anc1.Anc1refChr8 31277 3 - 57822 TTA -s Anc2.Anc2refChr15 80135 3 - 86568 TTA -s mr.mrrefChr5 15895 3 + 294540 ATA -s simCow_chr6.simCow.chr6 413089 3 - 602619 TTA -s simDog_chr6.simDog.chr6 122765 3 + 593897 CTA -s simHuman_chr6.simHuman.chr6 409142 3 - 601863 TTA -s simRat_chr6.simRat.chr6 150571 3 + 647215 ATA - -a -s simMouse_chr6.simMouse.chr6 152764 3 + 636262 GAA -s Anc0.Anc0refChr5 74880 3 - 87904 CAA -s Anc1.Anc1refChr8 31280 3 - 57822 CAA -s Anc2.Anc2refChr15 80138 3 - 86568 CGG -s mr.mrrefChr5 15898 3 + 294540 GAA -s simCow_chr6.simCow.chr6 413095 3 - 602619 CGG -s simDog_chr6.simDog.chr6 122768 3 + 593897 CGG -s simHuman_chr6.simHuman.chr6 409145 3 - 601863 CAA -s simRat_chr6.simRat.chr6 150574 3 + 647215 GAA - -a -s simMouse_chr6.simMouse.chr6 152767 48 + 636262 TCTCAAAAAGCTCGTTCACTTTAACCTAAAGTTTTAACATTGTTCATT -s Anc0.Anc0refChr5 74883 46 - 87904 TGTCGAATAGGT--TTCATTTTAACCTAGAGTTCTATCGTTCTTCTTG -s Anc1.Anc1refChr8 31283 48 - 57822 TGTCGAATAGGTTGTTCATTTTAACCTAGAGTTCTATCGTTCTTCTTG -s Anc2.Anc2refChr15 80141 46 - 86568 TGTAGAATCAGT--TTCATTTTAACCTGGAATTCTATCGTTCTTCTTG -s mr.mrrefChr5 15901 48 + 294540 TCTCAAAAAGCTTGTTCACTTTAACCTAAAGTTTTAACGTTGTTCATT -s simCow_chr6.simCow.chr6 413098 46 - 602619 TGTAGAATCAGT--TTCATTTTGACTTGTCATTCTACCATTCTACTTG -s simDog_chr6.simDog.chr6 122773 39 + 593897 TGT-------TC--TTCATTTTAGGCTGGAATTATATCGCTCTTCTTG -s simHuman_chr6.simHuman.chr6 409148 48 - 601863 TGCCGAAGAGGTTGTTTATTTTAACCTAGAGTACCATCGTTCTTATTG -s simRat_chr6.simRat.chr6 150577 48 + 647215 TTTAAAAAAGCTTGTTCACTTTAACCTAAAGTTATGACGTTGTTCATT - -a -s simMouse_chr6.simMouse.chr6 152815 3 + 636262 GTC -s Anc0.Anc0refChr5 74935 3 - 87904 GTC -s Anc1.Anc1refChr8 31337 3 - 57822 GTC -s Anc2.Anc2refChr15 80193 3 - 86568 GTG -s mr.mrrefChr5 15949 3 + 294540 GTC -s simCow_chr6.simCow.chr6 413150 3 - 602619 GTG -s simDog_chr6.simDog.chr6 122818 3 + 593897 GTG -s simHuman_chr6.simHuman.chr6 409202 3 - 601863 GCC -s simRat_chr6.simRat.chr6 150625 3 + 647215 GTC - -a -s simMouse_chr6.simMouse.chr6 152818 21 + 636262 TTTGTATCTATCAATTAAATG -s Anc0.Anc0refChr5 74938 19 - 87904 TT-ACATCTATCAATGAC-CA -s Anc1.Anc1refChr8 31340 20 - 57822 TTCACATCTATCAATGAC-CA -s Anc2.Anc2refChr15 80196 19 - 86568 TT-ACATCTATGAATGAC-CA -s mr.mrrefChr5 15952 21 + 294540 TTTGTATCTATCAATGAAATG -s simCow_chr6.simCow.chr6 413154 19 - 602619 TG-ACATCCATGAAGAAC-CA -s simDog_chr6.simDog.chr6 122821 19 + 593897 TT-ACATCTATGAATGAT-GA -s simHuman_chr6.simHuman.chr6 409205 20 - 601863 TTCACATTTATCAATGAC-CA -s simRat_chr6.simRat.chr6 150628 21 + 647215 TTTGTATCTATCAATGAATTG - -a -s simMouse_chr6.simMouse.chr6 152839 13 + 636262 TTTCCTCCTAGAG -s Anc0.Anc0refChr5 74957 12 - 87904 TTT-CCCCTAGAG -s Anc1.Anc1refChr8 31360 13 - 57822 TTTCCCCCTAGAG -s Anc2.Anc2refChr15 80215 12 - 86568 TTT-CCCCTAGAG -s mr.mrrefChr5 15973 13 + 294540 TTTCCTCCTAGAG -s simCow_chr6.simCow.chr6 413173 2 - 602619 TT----------- -s simDog_chr6.simDog.chr6 122840 12 + 593897 GTT-CCCCTAGAG -s simHuman_chr6.simHuman.chr6 409225 13 - 601863 TTTCCCCCTAGAA -s simRat_chr6.simRat.chr6 150685 13 + 647215 TTTTCTCCTAGAG - -a -s simMouse_chr6.simMouse.chr6 152852 13 + 636262 ATTGCTCCCTTCT -s Anc0.Anc0refChr5 74980 13 - 87904 ATTGCTTTCTTAT -s Anc1.Anc1refChr8 31384 13 - 57822 ATTGCTTTCTTAT -s Anc2.Anc2refChr15 80238 13 - 86568 ACTGCTTTCTTAT -s mr.mrrefChr5 15986 13 + 294540 ATTGCTCTCTTCT -s simCow_chr6.simCow.chr6 413179 13 - 602619 ACTGCTTTCATTT -s simDog_chr6.simDog.chr6 122863 10 + 593897 ACTA---TCTTAT -s simHuman_chr6.simHuman.chr6 409249 13 - 601863 ATTGCCTTCTTAC -s simRat_chr6.simRat.chr6 150698 13 + 647215 ATTGCTCTCTTCT - -a -s simMouse_chr6.simMouse.chr6 152865 5 + 636262 TTCTT -s Anc0.Anc0refChr5 74999 5 - 87904 TTCTT -s Anc1.Anc1refChr8 31403 5 - 57822 TTCTT -s Anc2.Anc2refChr15 80257 5 - 86568 TTCTT -s mr.mrrefChr5 16005 5 + 294540 TTCTT -s simCow_chr6.simCow.chr6 413198 5 - 602619 CTCTT -s simDog_chr6.simDog.chr6 122879 5 + 593897 TTCTG -s simHuman_chr6.simHuman.chr6 409268 5 - 601863 TCCTT -s simRat_chr6.simRat.chr6 150717 5 + 647215 TTCTT - -a -s simMouse_chr6.simMouse.chr6 152870 34 + 636262 ACTCATGCTTCTTACTGGACCAGTTATTGGATCA -s Anc0.Anc0refChr5 75009 30 - 87904 A---ATGGTCCTTAG-ACATGTGTTATCGGAACA -s Anc1.Anc1refChr8 31413 30 - 57822 A---ATGGTCCTTAG-ACATGTGTTATCGGAACA -s Anc2.Anc2refChr15 80267 30 - 86568 G---ATGGACCTGAG-ACCTGTATAACCGGAACA -s mr.mrrefChr5 16015 33 + 294540 ACTCATGCTTCTTAC-GGACCAGTTATTGGATCA -s simCow_chr6.simCow.chr6 413208 29 - 602619 G---ATGGTTGTGAG-ACCTGTATAACCAGGAC- -s simDog_chr6.simDog.chr6 122889 27 + 593897 G---ATAGACCTGAG-ACCTATAAA---GGAACA -s simHuman_chr6.simHuman.chr6 409278 29 - 601863 A---ATGGTACTTAG--CATGTGTTATAGGAACA -s simRat_chr6.simRat.chr6 150727 15 + 647215 ACTCATGCTTCTTAT------------------- - -a -s simMouse_chr6.simMouse.chr6 152904 8 + 636262 TATTGATA -s Anc0.Anc0refChr5 75137 8 - 87904 TTTTCATA -s Anc1.Anc1refChr8 31541 8 - 57822 TTTTCATA -s Anc2.Anc2refChr15 80395 8 - 86568 TTTTCCTA -s mr.mrrefChr5 16048 8 + 294540 TATTGATA -s simCow_chr6.simCow.chr6 413328 8 - 602619 TCTTCTTC -s simDog_chr6.simDog.chr6 123013 8 + 593897 TTCTCCTA -s simHuman_chr6.simHuman.chr6 409406 8 - 601863 TTTTCATA - -a -s simMouse_chr6.simMouse.chr6 152912 34 + 636262 TGATAGGATGTGGAGCGTATTCAAGTCTCTTCCA -s Anc0.Anc0refChr5 75146 34 - 87904 TAATAGGATGCTGAGTGTATTTAAGTCTCTTCTA -s Anc1.Anc1refChr8 31550 34 - 57822 TAATAGGATGCTGAGTGTATTTAAGTCTCTTCTA -s Anc2.Anc2refChr15 80404 34 - 86568 TAATAGGATGCTGAGTGTATTTAAGTCTCTTCTA -s mr.mrrefChr5 16056 34 + 294540 TGATAGGATGTGGAGCGTATTCAAGTCTCTTCCA -s simCow_chr6.simCow.chr6 413337 34 - 602619 AAATAGGATGCTGAGTGGATCTAAGTCTCTTCTA -s simDog_chr6.simDog.chr6 123022 33 + 593897 TGATAGGATAGTAAGTGTATTTA-GTCTCTGCTA -s simHuman_chr6.simHuman.chr6 409417 34 - 601863 CAATCAGATGCTGAGTGTATTTACCTCTCTTCTA - -a -s simMouse_chr6.simMouse.chr6 152946 6 + 636262 GCCTTG -s Anc0.Anc0refChr5 75180 6 - 87904 GTTTTG -s Anc1.Anc1refChr8 31584 6 - 57822 GTTTTG -s Anc2.Anc2refChr15 80442 6 - 86568 GTTTTG -s mr.mrrefChr5 16090 6 + 294540 GCCTTG -s simCow_chr6.simCow.chr6 413375 6 - 602619 GGCTTG -s simDog_chr6.simDog.chr6 123059 6 + 593897 GTTTTG -s simHuman_chr6.simHuman.chr6 409451 6 - 601863 GTTTTG - -a -s simMouse_chr6.simMouse.chr6 152952 4 + 636262 TCTC -s Anc0.Anc0refChr5 75187 4 - 87904 TCTC -s Anc1.Anc1refChr8 31591 4 - 57822 TCTC -s Anc2.Anc2refChr15 80449 4 - 86568 TCTC -s mr.mrrefChr5 16096 4 + 294540 TCTC -s simCow_chr6.simCow.chr6 413382 4 - 602619 TTTC -s simDog_chr6.simDog.chr6 123066 4 + 593897 TCCC -s simHuman_chr6.simHuman.chr6 409458 4 - 601863 TCTA - -a -s simMouse_chr6.simMouse.chr6 152956 38 + 636262 GGCACCCTATATAGCCTCGCAACTGCAAGATAATATCT -s Anc0.Anc0refChr5 75212 32 - 87904 GGCACCCTGTGTAGCC------CTATGAGATAGTATCT -s Anc1.Anc1refChr8 31616 32 - 57822 GGCACCCTGTGTAGCC------CTATGAGATAGTATCT -s Anc2.Anc2refChr15 80474 32 - 86568 GGCACCCTGTGTAGCC------CCATGAAAGGGTAACT -s mr.mrrefChr5 16100 32 + 294540 GGCACCCTATATAGCC------CTGCAAGATAATATCT -s simCow_chr6.simCow.chr6 413401 24 - 602619 ----CCCTGTGTAGCC------CCATGACACGG----T -s simDog_chr6.simDog.chr6 123082 32 + 593897 GGCACCCTATGTAGCC------CCATGAAAGGGTAACT -s simHuman_chr6.simHuman.chr6 409487 32 - 601863 GGGACCCTGTGTAGCT------CTATGAGTTAGTATCT -s simRat_chr6.simRat.chr6 150742 5 + 647215 ---------------------------------TATCT - -a -s simMouse_chr6.simMouse.chr6 152994 12 + 636262 TACTCTGCAACT -s Anc0.Anc0refChr5 75246 12 - 87904 TACTGTGAATTT -s Anc1.Anc1refChr8 31650 12 - 57822 TACTGTGAATTT -s Anc2.Anc2refChr15 80508 12 - 86568 TACTGTGAATTT -s mr.mrrefChr5 16132 12 + 294540 TACTCTGCAACT -s simCow_chr6.simCow.chr6 413427 12 - 602619 TACTGTCAATTT -s simDog_chr6.simDog.chr6 123116 12 + 593897 GACTGTGAATTT -s simHuman_chr6.simHuman.chr6 409521 12 - 601863 TACTTCTAATTT -s simRat_chr6.simRat.chr6 150747 12 + 647215 TTCTCTGTGAAT - -a -s simMouse_chr6.simMouse.chr6 153006 13 + 636262 GGTGTCTATCTTG -s Anc0.Anc0refChr5 75258 13 - 87904 GGTGTTAATGTTG -s Anc1.Anc1refChr8 31662 13 - 57822 GGTGTTAATGTTG -s Anc2.Anc2refChr15 80520 13 - 86568 GGTGCTAATGTTG -s mr.mrrefChr5 16144 13 + 294540 GGTGTCTATCTTG -s simCow_chr6.simCow.chr6 413439 13 - 602619 GGTGCTAATTTTG -s simDog_chr6.simDog.chr6 123128 7 + 593897 G------ATGTTG -s simHuman_chr6.simHuman.chr6 409533 13 - 601863 GGTGTGCATGTTG -s simRat_chr6.simRat.chr6 150761 13 + 647215 GGTGTGTATCTTG - -a -s simMouse_chr6.simMouse.chr6 153019 13 + 636262 GTGTTTAATCCAT -s Anc0.Anc0refChr5 75271 11 - 87904 CTGAT--ATCCAT -s Anc1.Anc1refChr8 31675 11 - 57822 CTGAT--ATCCAT -s Anc2.Anc2refChr15 80533 11 - 86568 CTGAT--TTCCAT -s mr.mrrefChr5 16157 13 + 294540 GTGTTTAATCCAT -s simCow_chr6.simCow.chr6 413454 11 - 602619 CTGAT--TTTCAT -s simDog_chr6.simDog.chr6 123135 11 + 593897 CTACT--TCCTAT -s simHuman_chr6.simHuman.chr6 409546 11 - 601863 CTGAT--ATACAT -s simRat_chr6.simRat.chr6 150774 13 + 647215 GTGTTTACATCAT - -a -s simMouse_chr6.simMouse.chr6 153032 33 + 636262 AATAGGGGAAGCAGGCATGTTAGCATCCCTGGT -s Anc0.Anc0refChr5 75285 33 - 87904 GATAGGGGCAACAGGCAAGTTACCATTCCTGGT -s Anc1.Anc1refChr8 31689 33 - 57822 GATAGGGGCAACAGGCAAGTTACCATTCCTGGT -s Anc2.Anc2refChr15 80547 33 - 86568 GATAGGGGCAACAGCCAAGTTACCATTCCTGGC -s mr.mrrefChr5 16170 33 + 294540 AATAGGGGAAGCAGGCATGTTAGCATCCCTGGT -s simCow_chr6.simCow.chr6 413468 33 - 602619 GATGGGGGCAACAATCATGTTATCACTTCTGGC -s simDog_chr6.simDog.chr6 123149 33 + 593897 GATAGTGGCAACAGCCAAGTTACTATTCCTGGC -s simHuman_chr6.simHuman.chr6 409560 33 - 601863 GATTTGGACAACAGGTAGGTTACCATTCCTGGT -s simRat_chr6.simRat.chr6 150787 33 + 647215 GGTAGGGGCAACAGGCGAGTTAGCATCCCTGGT - -a -s simMouse_chr6.simMouse.chr6 153065 8 + 636262 TTTAATAA -s Anc0.Anc0refChr5 75318 8 - 87904 TGTAATTA -s Anc1.Anc1refChr8 31722 8 - 57822 TGTAATTA -s Anc2.Anc2refChr15 80580 8 - 86568 TGTAATTA -s mr.mrrefChr5 16203 8 + 294540 TTTAATAA -s simCow_chr6.simCow.chr6 413501 8 - 602619 TGTGATTA -s simDog_chr6.simDog.chr6 123182 8 + 593897 TGTAATTA -s simHuman_chr6.simHuman.chr6 409598 8 - 601863 TGTAACTA -s simRat_chr6.simRat.chr6 150820 8 + 647215 TATAAGAA - -a -s simMouse_chr6.simMouse.chr6 153073 11 + 636262 GGAAAATGAGA -s Anc1.Anc1refChr8 31765 11 - 57822 GGAAGACGAGA -s mr.mrrefChr5 16211 11 + 294540 GGAAAATGAGA -s simHuman_chr6.simHuman.chr6 409682 11 - 601863 GGAAGACGAGA -s simRat_chr6.simRat.chr6 150828 11 + 647215 AGAAAGAGATA - -a -s simMouse_chr6.simMouse.chr6 153084 13 + 636262 CTCAGGCTATTAC -s Anc1.Anc1refChr8 31776 13 - 57822 CTCAGTTTCTTGC -s mr.mrrefChr5 16222 13 + 294540 CTCAGGCTATTAC -s simHuman_chr6.simHuman.chr6 409697 13 - 601863 CTCAGTTTCTTGC -s simRat_chr6.simRat.chr6 150839 13 + 647215 CTCAGACAGTTAC - -a -s simMouse_chr6.simMouse.chr6 153097 34 + 636262 AAGTACAAGCTCCAAGTAAGTGGAACCATAGTTC -s Anc1.Anc1refChr8 31789 11 - 57822 AAGTTCAAGCT----------------------- -s mr.mrrefChr5 16235 34 + 294540 AAGTACAAGCTCCAAGTAAGTGGAACCATAGTTC -s simHuman_chr6.simHuman.chr6 409711 11 - 601863 AAGTTCAAGCT----------------------- -s simRat_chr6.simRat.chr6 150853 34 + 647215 AAGTACAAGCTCCAAGTAAGTGGAGCCATAGTTC - -a -s simMouse_chr6.simMouse.chr6 153131 102 + 636262 TGAGTAGCACAGGCACCACATAAATGATCACAAACACACTTGTTTAGTAAATGGTATAATTGTTTGATCATGATAGATAAAACTTTGACTCAAACATCTCTA -s Anc0.Anc0refChr5 75361 7 - 87904 -----------------------------------------------------------------------------------------------ATCTCTA -s Anc1.Anc1refChr8 31800 22 - 57822 --------------------------------------------------------------------------------GAGCGTGATTCAGACATCTCTA -s Anc2.Anc2refChr15 80623 7 - 86568 -----------------------------------------------------------------------------------------------CTCTCTA -s mr.mrrefChr5 16269 102 + 294540 TGAGTAGCACAGGCACCACATAAATGATCACAAACACACTTGTTTAGTAAATGGTATAATTGTTTGATCATGATAGATAAAACTTTGACTCAAACATCTCTA -s simCow_chr6.simCow.chr6 413537 7 - 602619 -----------------------------------------------------------------------------------------------CTCTCTA -s simDog_chr6.simDog.chr6 123245 7 + 593897 -----------------------------------------------------------------------------------------------CTCTCTA -s simHuman_chr6.simHuman.chr6 409722 22 - 601863 --------------------------------------------------------------------------------GAGCGTGATTCAGACATCTCTG -s simRat_chr6.simRat.chr6 150901 102 + 647215 TGTGTAGTACAGACCCCACATAAATGATCAAAAACACACTTGTTTAGTAAATAGTATAAGTGTTTGATCATGATAGATAAAACTTTGACTCAAAGATCTCTA - -a -s simMouse_chr6.simMouse.chr6 153233 14 + 636262 TCGCCTGGGTTTAT -s Anc0.Anc0refChr5 75368 14 - 87904 TCGCCTGGCTCTAT -s Anc1.Anc1refChr8 31822 14 - 57822 TCGCCTGGCTCTAT -s Anc2.Anc2refChr15 80630 14 - 86568 TCACATGGCTCTCT -s mr.mrrefChr5 16371 14 + 294540 TCGCCTGGGTTTAT -s simCow_chr6.simCow.chr6 413546 14 - 602619 TCATGTGGCCCTCT -s simDog_chr6.simDog.chr6 123252 14 + 593897 TCACATGGCTCTCT -s simHuman_chr6.simHuman.chr6 409744 14 - 601863 TGGCCTGACTCTAT -s simRat_chr6.simRat.chr6 151003 14 + 647215 TTGCCTGGGTTTAA - -a -s simMouse_chr6.simMouse.chr6 153247 3 + 636262 CAC -s Anc0.Anc0refChr5 75386 2 - 87904 CA- -s Anc1.Anc1refChr8 31840 3 - 57822 CAC -s Anc2.Anc2refChr15 80648 2 - 86568 CA- -s mr.mrrefChr5 16385 3 + 294540 CAC -s simCow_chr6.simCow.chr6 413564 2 - 602619 CA- -s simDog_chr6.simDog.chr6 123270 2 + 593897 CA- -s simHuman_chr6.simHuman.chr6 409762 3 - 601863 CAC -s simRat_chr6.simRat.chr6 151017 3 + 647215 TGC - -a -s simMouse_chr6.simMouse.chr6 153250 4 + 636262 ATTG -s Anc0.Anc0refChr5 75388 4 - 87904 TGGG -s Anc1.Anc1refChr8 31843 4 - 57822 TGGG -s Anc2.Anc2refChr15 80650 4 - 86568 TGGG -s mr.mrrefChr5 16388 4 + 294540 ATTG -s simCow_chr6.simCow.chr6 413566 4 - 602619 TGGG -s simDog_chr6.simDog.chr6 123276 4 + 593897 TGGG -s simHuman_chr6.simHuman.chr6 409765 4 - 601863 TGGG -s simRat_chr6.simRat.chr6 151020 4 + 647215 ACTG - -a -s simMouse_chr6.simMouse.chr6 153254 4 + 636262 CTCT -s Anc0.Anc0refChr5 75392 4 - 87904 CTCT -s Anc1.Anc1refChr8 31847 4 - 57822 CTCT -s Anc2.Anc2refChr15 80654 4 - 86568 CTCT -s mr.mrrefChr5 16392 4 + 294540 CTCT -s simCow_chr6.simCow.chr6 413570 4 - 602619 CTCT -s simDog_chr6.simDog.chr6 123280 4 + 593897 CTCT -s simHuman_chr6.simHuman.chr6 409769 4 - 601863 CTCT -s simRat_chr6.simRat.chr6 151026 4 + 647215 CTCT - -a -s simMouse_chr6.simMouse.chr6 153258 7 + 636262 AGAGGTC -s Anc0.Anc0refChr5 75396 7 - 87904 AGTCGTC -s Anc1.Anc1refChr8 31851 7 - 57822 AGTCGTC -s Anc2.Anc2refChr15 80658 7 - 86568 ATTCCTC -s mr.mrrefChr5 16396 7 + 294540 AGAGGTC -s simDog_chr6.simDog.chr6 123302 7 + 593897 ATTCCTC -s simHuman_chr6.simHuman.chr6 409773 7 - 601863 GGGCGTC -s simRat_chr6.simRat.chr6 151030 7 + 647215 ACAGGTC - -a -s simMouse_chr6.simMouse.chr6 153265 98 + 636262 ACAAGTTACAAGAACAACAACACATGCCCAAATCGATTTAATGAGGCATTAATTGAGCAAGGTCACATCGCCAATACCTCAAGGCCTTTCTGTGTCCA -s Anc0.Anc0refChr5 75403 18 - 87904 ACA--TTGCAAGAACAA------------CAA------------------------------------------------------------------ -s Anc1.Anc1refChr8 31858 18 - 57822 ACA--TTGCAAGAACAA------------CAA------------------------------------------------------------------ -s Anc2.Anc2refChr15 80674 18 - 86568 ACA--TTGCAGGAACAA------------CAA------------------------------------------------------------------ -s mr.mrrefChr5 16403 67 + 294540 ACA--TTACAAGAACAA------------AAATCGATTTAATGAGGCATTAATTGAGCAAGG-----------------CAAGGCCTTTCTGTGTCCA -s simCow_chr6.simCow.chr6 413574 18 - 602619 ACA--TTCCAAGAGCAA------------CAG------------------------------------------------------------------ -s simDog_chr6.simDog.chr6 123318 18 + 593897 ACA--TTGCAGAAACAA------------CAA------------------------------------------------------------------ -s simHuman_chr6.simHuman.chr6 409780 18 - 601863 ACA--TTGCCAGTATAA------------CAG------------------------------------------------------------------ -s simRat_chr6.simRat.chr6 151037 67 + 647215 ACA--TTACAACAACAA------------AGATCAATTTAATGAGGCATTAATTGAGCTGGG-----------------CAAGACCTTTCTGTGTTCA - -a -s simMouse_chr6.simMouse.chr6 153363 58 + 636262 GACATAATGCCAATACTTGAGACAAGTGTATGTGACAGTGACAACTAAGGATGACCTT -s Anc0.Anc0refChr5 75421 13 - 87904 ------------------------------------------AACTTACGCAGA---T -s Anc1.Anc1refChr8 31876 13 - 57822 ------------------------------------------AACTTACGCAGA---T -s Anc2.Anc2refChr15 80692 13 - 86568 ------------------------------------------AAGTTACTCAGA---T -s mr.mrrefChr5 16470 58 + 294540 GACATAATGCCAATACTTGAGACAAGTGTATGTGACAGTGACAACTAAGGATGACCTT -s simCow_chr6.simCow.chr6 413592 13 - 602619 ------------------------------------------AAGTTACTCAAA---T -s simDog_chr6.simDog.chr6 123336 13 + 593897 ------------------------------------------AAGTTACTCAGA---T -s simHuman_chr6.simHuman.chr6 409798 13 - 601863 ------------------------------------------AACTTATGCAAG---T -s simRat_chr6.simRat.chr6 151110 58 + 647215 GACACAATGCCTATACCTGAAACAAGTGGATGTGACATGGACACCTAAGGATGACCTC - -a -s simMouse_chr6.simMouse.chr6 153421 3 + 636262 TAT -s Anc0.Anc0refChr5 75434 3 - 87904 GAA -s Anc1.Anc1refChr8 31889 3 - 57822 GAA -s Anc2.Anc2refChr15 80705 3 - 86568 GAA -s mr.mrrefChr5 16528 3 + 294540 TAT -s simCow_chr6.simCow.chr6 413605 3 - 602619 GGA -s simDog_chr6.simDog.chr6 123349 3 + 593897 GAA -s simHuman_chr6.simHuman.chr6 409811 3 - 601863 GAA -s simRat_chr6.simRat.chr6 151172 3 + 647215 TAC - -a -s simMouse_chr6.simMouse.chr6 153424 39 + 636262 CTTGTATGGGAGTGGGACCCTATGTCCTCCCCACTATCC -s Anc0.Anc0refChr5 75437 33 - 87904 CTCACATGGGACTAAGACTTCAT-TCATCCT-----TCC -s Anc1.Anc1refChr8 31892 33 - 57822 CTCACATGGGACTAAGACTTCAT-TCATCCT-----TCC -s Anc2.Anc2refChr15 80818 33 - 86568 CTCACATGGGACTAAGACTTCAT-TCATCCT-----TCC -s mr.mrrefChr5 16531 34 + 294540 CTTGTATGGGAGTGGGACCCTATGTCCTCCC-----TCC -s simCow_chr6.simCow.chr6 413729 33 - 602619 TTTGCATGTGACTCAGACTTCAT-TTAATCT-----TTC -s simDog_chr6.simDog.chr6 123455 33 + 593897 CTCATATGGAACTAAGACTTCAT-TCTTCCT-----TCC -s simHuman_chr6.simHuman.chr6 409814 33 - 601863 CTCTCATGGGGTCAAGACTTCAT-TCAGCCT-----TCT -s simRat_chr6.simRat.chr6 151175 34 + 647215 TTTGTGTGGAAGTGGGACCCTGTGTCCTCCC-----TCC - -a -s simMouse_chr6.simMouse.chr6 153463 4 + 636262 TCAA -s Anc0.Anc0refChr5 75470 4 - 87904 ACTA -s Anc1.Anc1refChr8 31925 4 - 57822 ACTA -s Anc2.Anc2refChr15 80851 4 - 86568 ACTA -s mr.mrrefChr5 16565 4 + 294540 TCAA -s simCow_chr6.simCow.chr6 413767 4 - 602619 TCTA -s simDog_chr6.simDog.chr6 123488 4 + 593897 ACTA -s simHuman_chr6.simHuman.chr6 409847 2 - 601863 --TA -s simRat_chr6.simRat.chr6 151209 4 + 647215 TCAA - -a -s simMouse_chr6.simMouse.chr6 153467 23 + 636262 GCGGCCCCTTTACCTGGTTAGAA -s Anc0.Anc0refChr5 75480 23 - 87904 ACCTCCCCTTTATCTGCTTAGGA -s Anc1.Anc1refChr8 31935 23 - 57822 ACCTCCCCTTTATCTGCTTAGGA -s Anc2.Anc2refChr15 80861 23 - 86568 ACCTCCACTTTATCTGCTCAGGA -s mr.mrrefChr5 16569 23 + 294540 GCGGCCCCTTTACCTGCTTAGAA -s simCow_chr6.simCow.chr6 413777 23 - 602619 ACCTCCTCTTCATCTGCTCAGGA -s simDog_chr6.simDog.chr6 123498 23 + 593897 ACCTCCACTTTTTCTGTCCAGCA -s simHuman_chr6.simHuman.chr6 409855 23 - 601863 ACTACCCCTTTATCTGCTTAGGA -s simRat_chr6.simRat.chr6 151213 22 + 647215 GCG-CCCCTTTACCTGCTTAGCA - -a -s simMouse_chr6.simMouse.chr6 153490 92 + 636262 TTCTGCTGGTTTCTGGAGAGGGAAGGAAGAGACCACTAACCCCCATGTGGCAAGTAGTAGTAATAGGGTCAGGCTTTTGCACATGATCACAC -s Anc0.Anc0refChr5 75503 10 - 87904 T----------------------------------------------------------------------------------TCCGCTGGT -s Anc1.Anc1refChr8 31958 10 - 57822 T----------------------------------------------------------------------------------TCCGCTGGT -s Anc2.Anc2refChr15 80884 10 - 86568 T----------------------------------------------------------------------------------TCTGCTGGT -s mr.mrrefChr5 16592 10 + 294540 T----------------------------------------------------------------------------------TGCTCACGC -s simCow_chr6.simCow.chr6 413801 10 - 602619 T----------------------------------------------------------------------------------TCTGCTGGT -s simDog_chr6.simDog.chr6 123521 10 + 593897 T----------------------------------------------------------------------------------CTTGATGGT -s simHuman_chr6.simHuman.chr6 409878 10 - 601863 T----------------------------------------------------------------------------------TCCCCTGGT -s simRat_chr6.simRat.chr6 151235 10 + 647215 T----------------------------------------------------------------------------------TGCTCACGC - -a -s simMouse_chr6.simMouse.chr6 153582 4 + 636262 GAAG -s Anc0.Anc0refChr5 75516 4 - 87904 GGAG -s Anc1.Anc1refChr8 31971 4 - 57822 GGAG -s Anc2.Anc2refChr15 80897 4 - 86568 GGAG -s mr.mrrefChr5 16602 4 + 294540 GGAG -s simCow_chr6.simCow.chr6 413814 4 - 602619 ATAC -s simDog_chr6.simDog.chr6 123534 4 + 593897 GGAG -s simHuman_chr6.simHuman.chr6 409891 4 - 601863 GGAG -s simRat_chr6.simRat.chr6 151245 4 + 647215 CGAG - -a -s simMouse_chr6.simMouse.chr6 153586 13 + 636262 AGAGGTGCTGTTT -s Anc0.Anc0refChr5 75522 13 - 87904 AGAAGCAATGTCT -s Anc1.Anc1refChr8 31977 13 - 57822 AGAAGCAATGTCT -s Anc2.Anc2refChr15 80903 13 - 86568 AGAAGCAATGTCT -s mr.mrrefChr5 16608 13 + 294540 AGAAGTGCTGTTT -s simCow_chr6.simCow.chr6 413820 13 - 602619 AGAAGCAATGTCT -s simDog_chr6.simDog.chr6 123540 7 + 593897 AGAAGCA------ -s simHuman_chr6.simHuman.chr6 409897 13 - 601863 AGAAGCAACGCCT -s simRat_chr6.simRat.chr6 151251 13 + 647215 AGAAGTGCTTTTT - -a -s simMouse_chr6.simMouse.chr6 153599 9 + 636262 TGCAGATAT -s Anc0.Anc0refChr5 75536 9 - 87904 TGCAGATAC -s Anc1.Anc1refChr8 31991 9 - 57822 TGCAGATAC -s Anc2.Anc2refChr15 80917 9 - 86568 TGCAGATAC -s mr.mrrefChr5 16621 9 + 294540 TGCAGATAC -s simCow_chr6.simCow.chr6 413834 9 - 602619 TGCAGATCC -s simDog_chr6.simDog.chr6 123647 7 + 593897 --CATATAC -s simHuman_chr6.simHuman.chr6 409911 9 - 601863 TGCAGATAC -s simRat_chr6.simRat.chr6 151264 9 + 647215 TGCAGATAC - -a -s simMouse_chr6.simMouse.chr6 153608 10 + 636262 TTTTTATGAA -s Anc0.Anc0refChr5 75548 10 - 87904 TTTTTATTAA -s Anc1.Anc1refChr8 32003 10 - 57822 TTTTTATTAA -s Anc2.Anc2refChr15 80929 10 - 86568 CTTTTATTAT -s mr.mrrefChr5 16630 10 + 294540 TTTTTATGAA -s simCow_chr6.simCow.chr6 413846 10 - 602619 CTTTCGTTAG -s simDog_chr6.simDog.chr6 123657 8 + 593897 --TTTACTAT -s simHuman_chr6.simHuman.chr6 409923 10 - 601863 TTTTTATTAA -s simRat_chr6.simRat.chr6 151273 10 + 647215 TTTTTATGAA - -a -s simMouse_chr6.simMouse.chr6 153618 66 + 636262 TTCAACTTTTATTAGAGTTGTTCTTGTGTTAAGTATCTCTGCTGACCTTGATGTTACTCTTGCTCA -s Anc0.Anc0refChr5 75568 65 - 87904 TTCAACGCTTAGATGATTTG-TTTTGTGCGACGCATCTCTAGTGATCATGATGTCATCCATGACCA -s Anc1.Anc1refChr8 32023 65 - 57822 TTCAACGCTTAGATGATTTG-TTTTGTGCGACGCATCTCTAGTGATCATGATGTCATCCATGACCA -s Anc2.Anc2refChr15 80949 65 - 86568 TTTAATGCCTAGATGATTTG-TTTTGTGCGACGCATCTCTAGTGATCATGATACCATCCATGACCA -s mr.mrrefChr5 16650 65 + 294540 TTCAACTTTTATTAGAGTTG-TCTTGTGTTAAGTATCTCTGCTGACCTTGATGTTACTCATGCTCA -s simCow_chr6.simCow.chr6 413863 46 - 602619 --------------GATCTG-TTTCGAGCGAGGC-TTTCTAGT----ATGATACCATCCATGACCA -s simDog_chr6.simDog.chr6 123675 59 + 593897 TTTAATGCCTAGATGA-TGG-CTTTGTGC-ACACATCTCTAGTGATCATGACA----CCATGCCCA -s simHuman_chr6.simHuman.chr6 409943 65 - 601863 TTCTACACTTACATGATTTG-TTTTGTGAGATGCATCTCTTGTGATCATGATGTAATCCATGACCA -s simRat_chr6.simRat.chr6 151293 65 + 647215 TTCAATTTTTAATAGAGTTG-TCTAGTGGTAGGTATCTCTGCTGACCTTGATGCTACTCATGTTCA - -a -s simMouse_chr6.simMouse.chr6 153684 90 + 636262 GTTCCCCTAGCGTACTGCAACTCTTTACTTTCATTTGCTGATCTCTTGGAGGCATGGGCATGGCGGCTACAATAATGACTATTCCTGAGA -s Anc0.Anc0refChr5 75633 89 - 87904 CTTTCCCTAGAGTATTGCCAATCATTGCTTTCTTATGTCGAATTCTTGGAAGCATGGTTCTGGCATCTGTGATAA-GAATAACACCTTAA -s Anc1.Anc1refChr8 32088 89 - 57822 CTTTCCCTAGAGTATTGCCAATCATTGCTTTCTTATGTCGAATTCTTGGAAGCATGGTTCTGGCATCTGTGATAA-GAATAACACCTTAA -s Anc2.Anc2refChr15 81014 89 - 86568 CTTTCCCTAGAGTATTGCCAATCATTGCTTTCTTATGTCGAATTCTTAGAAGCATGGTTCTGGCATCTGTGATAA-GAACAACACCTTAA -s mr.mrrefChr5 16715 90 + 294540 GTTCCCCTAGCGTACTGCAACTCTTTACTTTCTTATGCTGATCTCTTGGAGGCATGGGCATGGCAGCTATGATAATGACTATCACTGAGA -s simCow_chr6.simCow.chr6 413909 88 - 602619 CTTTCCCTAGATTATTGCCAACCATTGCTTTCTTATGTC-AGTTCTTAGAAGCATGGTTCTGGTATCTGTGATAG-GAACAACATCTTAA -s simDog_chr6.simDog.chr6 123734 76 + 593897 CTTTCCATAGTGTATTGTCAGTCA-------CTCATGTTGAATTTTTAGA---ACGGTTCTGGCATTTATGATAA-GAACAACACCT--- -s simHuman_chr6.simHuman.chr6 410011 89 - 601863 TTTTCCCTAGAGCATTGCCAATTGTGGCTTTCTTATGTCGACTTCTTGGATGCATGGCTCTGGCACCTGTGATAA-GAATGCCACCTTAA -s simRat_chr6.simRat.chr6 151358 90 + 647215 GTTCCCCTAGTGTACTGCAGCCCTTTACTTTCTTATGCTGATCTTTTGGAGGCATGGACGTGGCATCTATGGTAATGACTATCACTGAGA - -a -s simMouse_chr6.simMouse.chr6 153774 40 + 636262 CTCTTATTATTTACCCTTCAATCGTGCTATGATTATAAAT -s Anc0.Anc0refChr5 75726 40 - 87904 TTTTTATTCATCATCCTTCAATCTTATTATGATTAAAAAT -s Anc1.Anc1refChr8 32181 40 - 57822 TTTTTATTCATCATCCTTCAATCTTATTATGATTAAAAAT -s Anc2.Anc2refChr15 81107 40 - 86568 CTTTTATTCATCATCCTTTAATCTTATTATGATTAAAAAT -s mr.mrrefChr5 16805 40 + 294540 TTCTTATTAATTACCCTTCAATCTTATTATGATTATAAAT -s simCow_chr6.simCow.chr6 414001 40 - 602619 CTTTTATTCATCATGTTTTTATCTTATTAAAATTAAAAGT -s simDog_chr6.simDog.chr6 123813 40 + 593897 CTTTTATTCATCATCCTTTAATCTTATCATGATTAAAAAT -s simHuman_chr6.simHuman.chr6 410104 40 - 601863 TTTTTATTCATCATCATACAGTCTTATTATGATTAGAAAT -s simRat_chr6.simRat.chr6 151448 40 + 647215 TTCTTATTAATTACCCTTCAATCTTATTATGATTATAGAT - -a -s simMouse_chr6.simMouse.chr6 153814 37 + 636262 TGTACGCTTGTGACAGAGGGTTTCTTTTTATCACTAC -s Anc0.Anc0refChr5 75768 37 - 87904 TGTGCACTTGTATTGGAGGGTTTCTTTTTATCACTTC -s Anc1.Anc1refChr8 32223 37 - 57822 TGTGCACTTGTATTGGAGGGTTTCTTTTTATCACTTC -s Anc2.Anc2refChr15 81149 37 - 86568 TGTGCACTTGTATTGGAGGACTTCTTTTTATCACTTG -s mr.mrrefChr5 16845 37 + 294540 TGTGCGCTTGTGACAGAGGGTTTCTTTTTATCACTAC -s simCow_chr6.simCow.chr6 414043 37 - 602619 CGAGCACTTGCACTGCAGGCCTACTTTTTATTGCTGA -s simDog_chr6.simDog.chr6 123855 37 + 593897 TGTCCACTTGTATTGGTGGACTTCTTTTTATCATGTG -s simHuman_chr6.simHuman.chr6 410146 37 - 601863 TATGCACTTGTATTGGAGGGTCTCTTTTTATCACTTC -s simRat_chr6.simRat.chr6 151488 34 + 647215 TGTGCG---GCGACAGAAGGTTACTTTTTATCACTAC - -a -s simMouse_chr6.simMouse.chr6 153851 22 + 636262 AACCACTTGTTTTTTCTGACAG -s Anc0.Anc0refChr5 75806 22 - 87904 GAGCACCTTTTCTTATTGATAG -s Anc1.Anc1refChr8 32261 22 - 57822 GAGCACCTTTTCTTATTGATAG -s Anc2.Anc2refChr15 81187 22 - 86568 GAGCCCCTTTTCTTATTGATAG -s mr.mrrefChr5 16882 22 + 294540 AACCACTTTTTTTTTCTGATAG -s simCow_chr6.simCow.chr6 414081 22 - 602619 GAGCTCCTTTTCTTGTTGACAG -s simDog_chr6.simDog.chr6 123893 22 + 593897 GAGCCCCTTTTTTTATTGATAG -s simHuman_chr6.simHuman.chr6 410184 22 - 601863 GAGCACCTTTTCTTATTGATTG -s simRat_chr6.simRat.chr6 151522 22 + 647215 AACCACTTTTTTTTTCTGATAG - -a -s simMouse_chr6.simMouse.chr6 153873 10 + 636262 CTAAAAGTAA -s Anc0.Anc0refChr5 75840 10 - 87904 TCTAGTATGT -s Anc1.Anc1refChr8 32295 10 - 57822 TCTAGTATGT -s Anc2.Anc2refChr15 81230 10 - 86568 TCTAGTATGT -s mr.mrrefChr5 16904 10 + 294540 CCAAAAGTGA -s simCow_chr6.simCow.chr6 414124 10 - 602619 TCTAGTATGT -s simDog_chr6.simDog.chr6 123939 10 + 593897 TCTAGTACGT -s simHuman_chr6.simHuman.chr6 410218 10 - 601863 TCTAGTATGG -s simRat_chr6.simRat.chr6 151544 10 + 647215 CCACAAGTGA - -a -s simMouse_chr6.simMouse.chr6 153883 12 + 636262 CATGACAGTCCA -s Anc0.Anc0refChr5 75850 12 - 87904 GGTGACAGTATG -s Anc1.Anc1refChr8 32305 12 - 57822 GGTGACAGTATG -s Anc2.Anc2refChr15 81251 12 - 86568 GGTGGCAGTATG -s mr.mrrefChr5 16914 12 + 294540 GATGACAGTCCA -s simCow_chr6.simCow.chr6 414145 12 - 602619 GATGGCAGTATG -s simDog_chr6.simDog.chr6 123960 12 + 593897 AGGGGCAGTATG -s simHuman_chr6.simHuman.chr6 410228 12 - 601863 GGTGACAGTATG -s simRat_chr6.simRat.chr6 151554 12 + 647215 GATGACAGTCCA - -a -s simMouse_chr6.simMouse.chr6 153895 13 + 636262 GGGGTGTCCCTCA -s Anc0.Anc0refChr5 75871 13 - 87904 GTGGCCTCACCCA -s Anc1.Anc1refChr8 32326 13 - 57822 GTGGCCTCACCCA -s Anc2.Anc2refChr15 81272 13 - 86568 GTGGCCTCACCCA -s mr.mrrefChr5 16926 13 + 294540 GGGGCGTCCCTCA -s simCow_chr6.simCow.chr6 414166 13 - 602619 GTGGCCTCACCCA -s simDog_chr6.simDog.chr6 123981 13 + 593897 GTTGCCCCATCCA -s simHuman_chr6.simHuman.chr6 410249 13 - 601863 GTGGCCTCACCTA -s simRat_chr6.simRat.chr6 151566 11 + 647215 -GGGCATCCCTC- - -a -s simMouse_chr6.simMouse.chr6 153908 10 + 636262 GAATGCTTCA -s Anc0.Anc0refChr5 75884 10 - 87904 GAGTGATTTG -s Anc1.Anc1refChr8 32339 10 - 57822 GAGTGATTTG -s Anc2.Anc2refChr15 81285 10 - 86568 GAGTGACTTG -s mr.mrrefChr5 16939 10 + 294540 GAATGCTTTG -s simCow_chr6.simCow.chr6 414183 10 - 602619 GAGTGAGTTG -s simDog_chr6.simDog.chr6 123994 10 + 593897 GAGTGACTTG -s simHuman_chr6.simHuman.chr6 410262 10 - 601863 GAGTGATTTG -s simRat_chr6.simRat.chr6 151577 10 + 647215 GAATGCTTTG - -a -s simMouse_chr6.simMouse.chr6 153918 41 + 636262 GGTTGTACCTTCCCACAGTGATGAGAGTGATATACACAGAA -s Anc0.Anc0refChr5 75943 41 - 87904 AGTTGCACATTTCCATTGTGATGAGGGTAATAGGCAAATAA -s Anc1.Anc1refChr8 32398 41 - 57822 AGTTGCACATTTCCATTGTGATGAGGGTAATAGGCAAATAA -s Anc2.Anc2refChr15 81350 41 - 86568 AGTTGCACATTTCCATTGTGATGAGGGCAATAGGCAAATAA -s mr.mrrefChr5 16949 41 + 294540 AGTTGTACCTTCCCATAGTGATGAGAGTGATATACACAGAA -s simCow_chr6.simCow.chr6 414248 35 - 602619 AATTTTACATTTCCATTGTGTTGAGTG---TAGGCCAA--- -s simDog_chr6.simDog.chr6 124059 41 + 593897 AGGTGCATATTTCCTTTGTGATGATGGCAATAGGCACGTAA -s simHuman_chr6.simHuman.chr6 410322 41 - 601863 AGTTGAACATTTCCATTGTGATGAGGGTAATAGGCAAAAAA -s simRat_chr6.simRat.chr6 151587 41 + 647215 AGTTGTACCTTCACATGGTGATGAGAGTGACATACACAGAA - -a -s simMouse_chr6.simMouse.chr6 153959 24 + 636262 AATCACTGTGTATAATAGAATTGT -s Anc0.Anc0refChr5 75985 16 - 87904 AATCCCTGGCTCAA--------GT -s Anc1.Anc1refChr8 32440 24 - 57822 AATCCCTGGCTCAAATTAAAATGT -s Anc2.Anc2refChr15 81392 16 - 86568 AATCCCTGGCTCAA--------GT -s mr.mrrefChr5 16990 24 + 294540 AATCACTGTGTCTAATAGAATTGT -s simDog_chr6.simDog.chr6 124101 16 + 593897 AATCCCTGGCTCAA--------GT -s simHuman_chr6.simHuman.chr6 410364 24 - 601863 AATTCCTAGCTCCAATTAAAATGT -s simRat_chr6.simRat.chr6 151628 24 + 647215 AACCACTGTGTCTAATAGAATTGT - -a -s simMouse_chr6.simMouse.chr6 153983 20 + 636262 TATACAATGTCCTTCAGTCT -s Anc0.Anc0refChr5 76002 20 - 87904 TACACCATGTCCTTCAGTTT -s Anc1.Anc1refChr8 32465 20 - 57822 TACACCATGTCCTTCAGTTT -s Anc2.Anc2refChr15 81409 20 - 86568 TACACCATGCCCATCAGTTT -s mr.mrrefChr5 17014 20 + 294540 TATACAATGTCCTTCAGTCT -s simCow_chr6.simCow.chr6 414283 10 - 602619 ----------CCCTTCGTTT -s simDog_chr6.simDog.chr6 124118 20 + 593897 TACACCATGCCCATCATTTT -s simHuman_chr6.simHuman.chr6 410389 20 - 601863 TACACCATGTCCTCCAGTTT -s simRat_chr6.simRat.chr6 151652 20 + 647215 TATACAAAGTCCTTCAGTCT - -a -s simMouse_chr6.simMouse.chr6 154003 22 + 636262 TACTGAGAGGACATACCTGGGG -s Anc0.Anc0refChr5 76022 20 - 87904 CACTAGGAGCACATACCTTG-- -s Anc1.Anc1refChr8 32485 22 - 57822 CACTAGGAGCACATACCTTGTG -s Anc2.Anc2refChr15 81429 20 - 86568 CACCAGGGGCACATACCTTA-- -s mr.mrrefChr5 17034 22 + 294540 TACTAAGAGCACATACCTTGGG -s simCow_chr6.simCow.chr6 414293 20 - 602619 GACCAGGGGCACATACTTCA-- -s simDog_chr6.simDog.chr6 124140 20 + 593897 CCCCACGGGCACATGACTTA-- -s simHuman_chr6.simHuman.chr6 410409 22 - 601863 CACTAGGAGCATATACCTTGTG -s simRat_chr6.simRat.chr6 151672 22 + 647215 TACCAAGAGCACATACCTTGGG - -a -s simMouse_chr6.simMouse.chr6 154025 50 + 636262 ATATGTTACGTAAGTTATACTGTTGATTGGAAAAGGGGAAATCAGTCTCT -s Anc0.Anc0refChr5 76042 34 - 87904 ------TATGTAAGTTATATTGTTGGTAGGAAAAGGGAAA---------- -s Anc1.Anc1refChr8 32508 40 - 57822 GTGTGTTATGTAAGTTATATTGTTGGTAGGAAAAGGGAAA---------- -s Anc2.Anc2refChr15 81449 34 - 86568 ------TATGTAAGTTATATTGTTGGTAAGAAAAGGGAAA---------- -s mr.mrrefChr5 17057 50 + 294540 ATATGTTACGTAAGTTATACTGTTGATTGGAAAAGGGAAAATCAGTCTCT -s simCow_chr6.simCow.chr6 414313 33 - 602619 ------TATA-AAATTCTATTGTTGGTATGAAAGGGAAAA---------- -s simDog_chr6.simDog.chr6 124160 34 + 593897 ------TATGTAAGTCATATTGTTGGTCAGAAAAGGGAAG---------- -s simHuman_chr6.simHuman.chr6 410432 40 - 601863 GTGTGTTATGTAAGTTATGTTGCGGGAAGGAAAAGGGAAA---------- -s simRat_chr6.simRat.chr6 151695 50 + 647215 ATATGTTACGTAAGTTATACTGTTGATTGGAAAAGGGAAAATCAGACTCT - -a -s simMouse_chr6.simMouse.chr6 154075 22 + 636262 TTCGCATTCAAATTTCACTGTC -s Anc1.Anc1refChr6 172054 22 + 197743 TTGTGATTCAAACATCATTGTG -s mr.mrrefChr5 17107 22 + 294540 TTCGCATTCAAATTTCACTGTC -s simHuman_chr6.simHuman.chr6 503895 22 + 601863 TTGTGATTCAAACATCATGGTG -s simRat_chr6.simRat.chr6 151745 22 + 647215 TCTGCATTTAAATTTTACCGGC - -a -s simMouse_chr6.simMouse.chr6 154097 38 + 636262 CTGGCTGTGACCTGGCAGTCTAGCGGACTTGGCTTTGG -s Anc1.Anc1refChr6 172077 28 + 197743 CCCG----------GCTCTCTAGCACACCTGGCTTTGG -s mr.mrrefChr5 17129 28 + 294540 CTGG----------GCAGTCTAGCGGACTTGGCTTTGG -s simHuman_chr6.simHuman.chr6 503918 28 + 601863 CCCG----------GCTCTCTAGCACACCTGGCTTTGG -s simRat_chr6.simRat.chr6 151767 28 + 647215 CTGG----------GCAGTCTAGCAGACTTGGCTTTGG - -a -s simMouse_chr6.simMouse.chr6 154135 11 + 636262 CATTACTTCTA -s Anc1.Anc1refChr6 172109 11 + 197743 CATTGCAAGAA -s mr.mrrefChr5 17157 11 + 294540 CATTACTTCTA -s simHuman_chr6.simHuman.chr6 503950 11 + 601863 CCTTGCAAGAG -s simRat_chr6.simRat.chr6 151795 11 + 647215 CATCACTTCTA - -a -s simMouse_chr6.simMouse.chr6 154146 79 + 636262 CATAAAATGTTCACTCATATGAATTTAGTGCTTCGGTGTAGTATTAATTAAGCTGGGCATGGCACATGTTTTCTATCAT -s Anc1.Anc1refChr6 172120 71 + 197743 CAGCAAAAGTTTACTCGTATGGATTTAGTGC--------AGTCTTAATTAAGCTGGGCAGGGCATATCTTTTTTATCAT -s mr.mrrefChr5 17168 79 + 294540 CATAAAATGTTCACTCATATGAATTTAGTGCTTCGGTGTAGTATTAATTAAGCTGGGCATGGCACATGTTTTCTATCAT -s simHuman_chr6.simHuman.chr6 503961 71 + 601863 CAGGAACCATGTACTCTTATGGATTTTGTGC--------AGTCTTAATTAAACTAAGCAGGGCATACTTTTTTTATCAT -s simRat_chr6.simRat.chr6 151809 79 + 647215 CTCAAAATGGGCACTCATATGGGTTGAGTGATTAGGTGTAGTAATAATTAAGCAGGGCAAGGCACATGTTTTTTATTAT - -a -s simMouse_chr6.simMouse.chr6 154225 1 + 636262 T -s Anc0.Anc0refChr3 137005 1 + 222631 T -s Anc1.Anc1refChr6 172197 1 + 197743 T -s Anc2.Anc2refChr1 50325 1 + 142988 T -s mr.mrrefChr5 17247 1 + 294540 T -s simCow_chr6.simCow.chr6 507421 1 + 602619 T -s simDog_chr6.simDog.chr6 496713 1 + 593897 T -s simHuman_chr6.simHuman.chr6 504038 1 + 601863 T -s simRat_chr6.simRat.chr6 151888 1 + 647215 C - -a -s simMouse_chr6.simMouse.chr6 154226 4 + 636262 ACCT -s Anc0.Anc0refChr3 137006 3 + 222631 ACT- -s Anc1.Anc1refChr6 172198 3 + 197743 ACT- -s Anc2.Anc2refChr1 50326 3 + 142988 ACT- -s mr.mrrefChr5 17248 4 + 294540 ACCT -s simCow_chr6.simCow.chr6 507425 3 + 602619 ACT- -s simDog_chr6.simDog.chr6 496714 3 + 593897 ACT- -s simHuman_chr6.simHuman.chr6 504039 3 + 601863 ACT- -s simRat_chr6.simRat.chr6 151889 4 + 647215 ATTC - -a -s simMouse_chr6.simMouse.chr6 154230 25 + 636262 CTTATGGGACAGAACTAGCTTGTCT -s Anc0.Anc0refChr5 76094 25 - 87904 CTCATGGGACAGAACTAGCTTATTT -s Anc1.Anc1refChr8 32566 25 - 57822 CTCATGGGACAGAACTAGCTTATTT -s Anc2.Anc2refChr15 81661 25 - 86568 CTCAGGGGACAGAACTTGCTTATTT -s mr.mrrefChr5 17252 25 + 294540 CTTATGGGACAGAACTAGCTTGTCT -s simCow_chr6.simCow.chr6 414523 25 - 602619 CTTTTGGGACAGAACTTGTTTATTT -s simDog_chr6.simDog.chr6 124372 25 + 593897 CTCAGGGGACAGAACTTGCTTCTTG -s simHuman_chr6.simHuman.chr6 410490 25 - 601863 CTCATGGGACAGGACTAACTTATTT -s simRat_chr6.simRat.chr6 151893 25 + 647215 TTTATGGGACAGAACTAGCTTGTCT - -a -s simMouse_chr6.simMouse.chr6 154255 5 + 636262 TAGGA -s Anc0.Anc0refChr5 76119 5 - 87904 TAGGA -s Anc1.Anc1refChr8 32591 5 - 57822 TAGGA -s Anc2.Anc2refChr15 81691 5 - 86568 TAGAA -s mr.mrrefChr5 17277 5 + 294540 TAGGA -s simCow_chr6.simCow.chr6 414553 5 - 602619 TAGAA -s simDog_chr6.simDog.chr6 124402 5 + 593897 TAGAA -s simHuman_chr6.simHuman.chr6 410515 3 - 601863 T--GC -s simRat_chr6.simRat.chr6 151918 5 + 647215 TACGA - -a -s simMouse_chr6.simMouse.chr6 154260 88 + 636262 AGTCTCAGTGTTCATTTCTTCAACCTCTCATTTTCCCACCTACTTCCCTCTGTCTGCACCAGTACTTCGTAGGACTTTGTTGATTGTG -s Anc0.Anc0refChr5 76124 75 - 87904 AATCTCAGCATTCATTCATTCTTCCTCCTATCTATCCACTTCCTCCCCTCTATTTGC-TCAG----------GATTCTGCTGA--GTG -s Anc1.Anc1refChr8 32596 75 - 57822 AATCTCAGCATTCATTCATTCTTCCTCCTATCTATCCACTTCCTCCCCTCTATTTGC-TCAG----------GATTCTGCTGA--GTG -s Anc2.Anc2refChr15 81696 75 - 86568 GATCTCAGCATTCATTCATTCTTCCTCCTATCTATCCACTTCCCCCCCTCTATTTGC-TCAG----------GATTCAGCTGG--TTG -s mr.mrrefChr5 17282 76 + 294540 AGTCTCAGTGTTCATTTCTTCAACCTCTCATTTTCCCACCTACTTCCCTCTGTCTGCACCAG----------GACTTTGTTGA--GTG -s simCow_chr6.simCow.chr6 414558 70 - 602619 GATCCCAGCATTCATTCATTCTTTCTCCCATCCATCCACTTCCCCC-CTCTAGTTGC-TCAG----------GATTCAGCCA------ -s simDog_chr6.simDog.chr6 124408 75 + 593897 GATTTCAGCATTCATTAATTCTCCCTCCTGTCTATCCACTGCCCCTCTTGCATCTGC-TCAG----------GGTTCAGGTGG--TTG -s simHuman_chr6.simHuman.chr6 410518 75 - 601863 AAGCTCAGCATTCACTCATTCTTCCTCATATCTATCCACTTTGTCCTCTCTATTTGC-TCAG----------GATTCTGCTGA--GTG -s simRat_chr6.simRat.chr6 151923 76 + 647215 AGTCTCAGTGTTCACTTAATCAAACTCTCATTTTCCCACCTATTTCCCTCTGTCTGCACCAG----------GACTTTGCTGA--GTG - -a -s simMouse_chr6.simMouse.chr6 154348 2 + 636262 GA -s Anc0.Anc0refChr5 76200 2 - 87904 GC -s Anc1.Anc1refChr8 32672 2 - 57822 GC -s Anc2.Anc2refChr15 81772 2 - 86568 GC -s mr.mrrefChr5 17358 2 + 294540 GA -s simCow_chr6.simCow.chr6 414628 2 - 602619 GC -s simDog_chr6.simDog.chr6 124484 2 + 593897 GC -s simHuman_chr6.simHuman.chr6 410594 2 - 601863 GG -s simRat_chr6.simRat.chr6 151999 2 + 647215 GA - -a -s simMouse_chr6.simMouse.chr6 154350 16 + 636262 CTGCAGGCACAACTCC -s Anc0.Anc0refChr5 76202 16 - 87904 CGCCAGGGACAAAGTC -s Anc1.Anc1refChr8 32674 16 - 57822 CGCCAGGGACAAAGTC -s Anc2.Anc2refChr15 81774 16 - 86568 CGCCAGGGACAAAGTC -s mr.mrrefChr5 17360 16 + 294540 CTGCAGGCACAACTCC -s simCow_chr6.simCow.chr6 414630 16 - 602619 TGCCTGGGACAAAGTC -s simDog_chr6.simDog.chr6 124486 15 + 593897 CGACAGG-ACAAAGTC -s simHuman_chr6.simHuman.chr6 410596 16 - 601863 AGCCAGGGACAATGTC -s simRat_chr6.simRat.chr6 152017 16 + 647215 CTACAGGCATAATACC - -a -s simMouse_chr6.simMouse.chr6 154366 7 + 636262 ATAGTTG -s Anc0.Anc0refChr5 76218 7 - 87904 ATAGTTG -s Anc1.Anc1refChr8 32690 7 - 57822 ATAGTTG -s Anc2.Anc2refChr15 81790 7 - 86568 TCAGTGA -s mr.mrrefChr5 17376 7 + 294540 ATAGTTG -s simCow_chr6.simCow.chr6 414646 7 - 602619 ACAGCAA -s simDog_chr6.simDog.chr6 124501 7 + 593897 TAAGTGA -s simHuman_chr6.simHuman.chr6 410794 7 - 601863 ATACTTG -s simRat_chr6.simRat.chr6 152033 7 + 647215 ATAGTTG - -a -s simMouse_chr6.simMouse.chr6 154373 17 + 636262 AATTGTTTCACCTTCAT -s Anc0.Anc0refChr5 76228 6 - 87904 -----------CTTCAT -s Anc1.Anc1refChr8 32700 17 - 57822 ATCTCGTTCATCTTCAT -s Anc2.Anc2refChr15 81800 6 - 86568 -----------CTTAAT -s mr.mrrefChr5 17383 17 + 294540 AATTGTTTCACCTTCAT -s simDog_chr6.simDog.chr6 124511 6 + 593897 -----------CTTAAT -s simHuman_chr6.simHuman.chr6 410804 17 - 601863 ATCTCGTTCATTTTCAT -s simRat_chr6.simRat.chr6 152040 17 + 647215 AATTGTTTCACCTTCAC - -a -s simMouse_chr6.simMouse.chr6 154390 1 + 636262 C -s Anc0.Anc0refChr5 76234 1 - 87904 C -s Anc1.Anc1refChr8 32717 1 - 57822 C -s Anc2.Anc2refChr15 81806 1 - 86568 T -s mr.mrrefChr5 17400 1 + 294540 C -s simDog_chr6.simDog.chr6 124517 1 + 593897 T -s simHuman_chr6.simHuman.chr6 410821 1 - 601863 C -s simRat_chr6.simRat.chr6 152057 1 + 647215 C -s simRat_chr6.simRat.chr6 52307 1 - 647215 C - -a -s simMouse_chr6.simMouse.chr6 154391 3 + 636262 ACA -s Anc0.Anc0refChr5 76235 3 - 87904 ACT -s Anc1.Anc1refChr8 32718 3 - 57822 ACT -s Anc2.Anc2refChr15 81807 3 - 86568 ATT -s mr.mrrefChr5 17401 3 + 294540 ACA -s simDog_chr6.simDog.chr6 124521 3 + 593897 ATT -s simHuman_chr6.simHuman.chr6 410822 3 - 601863 ACC -s simRat_chr6.simRat.chr6 152058 3 + 647215 ACA -s simRat_chr6.simRat.chr6 52308 3 - 647215 ATA - -a -s simMouse_chr6.simMouse.chr6 154394 11 + 636262 TAAATGATCTC -s Anc0.Anc0refChr5 76238 11 - 87904 TTCATGATCTC -s Anc1.Anc1refChr8 32721 11 - 57822 TTCATGATCTC -s Anc2.Anc2refChr15 81810 11 - 86568 TTCATGATCTC -s mr.mrrefChr5 17404 11 + 294540 TAAATGATCTC -s simCow_chr6.simCow.chr6 414654 7 - 602619 ----TGTTCTT -s simDog_chr6.simDog.chr6 124524 11 + 593897 TTCATGATCTC -s simHuman_chr6.simHuman.chr6 410825 11 - 601863 TGCATGATTTC -s simRat_chr6.simRat.chr6 152061 11 + 647215 TAAATGATGTC -s simRat_chr6.simRat.chr6 52312 11 - 647215 TAGATGATCTC - -a -s simMouse_chr6.simMouse.chr6 154405 16 + 636262 TTTAAAGTGCGTGCTC -s Anc0.Anc0refChr5 76249 13 - 87904 TT--ATGTG-GTGCAC -s Anc1.Anc1refChr8 32732 15 - 57822 TTTAATGTG-GTGCAC -s Anc2.Anc2refChr15 81821 13 - 86568 TT--ATGTG-GTGTAC -s mr.mrrefChr5 17415 15 + 294540 TTTAAAGTA-GTGCTC -s simCow_chr6.simCow.chr6 414661 13 - 602619 CT--TAGTG-AATTAC -s simDog_chr6.simDog.chr6 124535 13 + 593897 TT--ATGTG-GTGTAC -s simHuman_chr6.simHuman.chr6 410837 15 - 601863 TTTAGTGTG-GTGCAC -s simRat_chr6.simRat.chr6 152072 15 + 647215 TTTAAAGTA-GTTCTC -s simRat_chr6.simRat.chr6 52323 15 - 647215 TTTAAAGTA-GTGCTC - -a -s simMouse_chr6.simMouse.chr6 154421 2 + 636262 AT -s Anc0.Anc0refChr5 76262 2 - 87904 CT -s Anc1.Anc1refChr8 32747 2 - 57822 CT -s Anc2.Anc2refChr15 81834 2 - 86568 TT -s mr.mrrefChr5 17430 2 + 294540 CT -s simCow_chr6.simCow.chr6 414674 2 - 602619 TT -s simDog_chr6.simDog.chr6 124548 2 + 593897 TT -s simHuman_chr6.simHuman.chr6 410852 2 - 601863 CT -s simRat_chr6.simRat.chr6 152097 2 + 647215 CT -s simRat_chr6.simRat.chr6 52338 2 - 647215 CT - -a -s simMouse_chr6.simMouse.chr6 154423 12 + 636262 ATAATGAACACA -s Anc0.Anc0refChr5 76264 7 - 87904 ATAATGA----- -s Anc1.Anc1refChr8 32749 7 - 57822 ATAATGA----- -s Anc2.Anc2refChr15 81836 7 - 86568 ATAATGA----- -s mr.mrrefChr5 17432 12 + 294540 ATAATGAAGACA -s simCow_chr6.simCow.chr6 414677 7 - 602619 ATCTTTG----- -s simDog_chr6.simDog.chr6 124550 7 + 593897 ATAATGA----- -s simHuman_chr6.simHuman.chr6 410854 7 - 601863 ATAATGA----- -s simRat_chr6.simRat.chr6 152099 12 + 647215 ATAATGAAGACA -s simRat_chr6.simRat.chr6 52340 12 - 647215 ATAATGAAGACA - -a -s simMouse_chr6.simMouse.chr6 154435 39 + 636262 CCAATAGTAAGCAAAGTAAGCTTTATTAAATTTGTATCC -s Anc0.Anc0refChr5 76273 39 - 87904 ATGATGTGAAGAAAAGTGAGCTTTGTTAAAATTATTGCC -s Anc1.Anc1refChr8 32758 39 - 57822 ATGATGTGAAGAAAAGTGAGCTTTGTTAAAATTATTGCC -s Anc2.Anc2refChr15 81845 39 - 86568 ATGATGTGAAGAAAAGTGAGCTTTGTTAAAATTATTACC -s mr.mrrefChr5 17447 39 + 294540 ATGATAGGAAGGAAAGTAAGCTTTATTGAATTTGTTGCC -s simCow_chr6.simCow.chr6 414688 39 - 602619 CTGATGTGAAGGCAAGTGAGCCATGTTAAAATCATTATT -s simDog_chr6.simDog.chr6 124559 39 + 593897 ATGATGTGATGAAAAGAACGCTTTGTGAAATATATTACC -s simHuman_chr6.simHuman.chr6 410863 39 - 601863 GTGATGCAAAGCAAAGTGAGCTTTGTTAAAATGATTGCC -s simRat_chr6.simRat.chr6 152111 39 + 647215 ATGATAGGAAGGAAAGCAAGCTTTATTGGATTTGTTGTC -s simRat_chr6.simRat.chr6 52355 39 - 647215 ATGATAGGAAGGAAAGTAAACTTTATCGAATTTGTTGCC - -a -s simMouse_chr6.simMouse.chr6 154474 25 + 636262 AACACGCAAGAACTGAACCATAATA -s Anc0.Anc0refChr5 76321 25 - 87904 AACACTCAAGAAGTGAACCATTATT -s Anc1.Anc1refChr8 32806 25 - 57822 AACACTCAAGAAGTGAACCATTATT -s Anc2.Anc2refChr15 81893 25 - 86568 AACACTCAAGAAGTGAACCAGTATT -s mr.mrrefChr5 17495 25 + 294540 AACACTCAAGAACTGAACCATAATA -s simCow_chr6.simCow.chr6 414736 25 - 602619 ACCACTTATGAAGTGAACTAATATG -s simDog_chr6.simDog.chr6 124607 24 + 593897 AACACCCAAGAC-TGAACCAGTATT -s simHuman_chr6.simHuman.chr6 410911 25 - 601863 AACGATCAAGAAATGGAACATTGTT -s simRat_chr6.simRat.chr6 152159 25 + 647215 AACATTCAAGAACTGAACCATAATA -s simRat_chr6.simRat.chr6 52403 15 - 647215 ----------AACCGAACCATAATA - -a -s simMouse_chr6.simMouse.chr6 154499 21 + 636262 GCCTGGTGTGATGGTGGAGAG -s Anc0.Anc0refChr5 76346 21 - 87904 GGCTGCTATGGCCATTAACAG -s Anc1.Anc1refChr8 32831 21 - 57822 GGCTGCTATGGCCATTAACAG -s Anc2.Anc2refChr15 81918 21 - 86568 GGCTGCTACAGCCATTAACAG -s mr.mrrefChr5 17520 21 + 294540 GCCTGGTGTGATGATGGAGAG -s simCow_chr6.simCow.chr6 414761 21 - 602619 GACTGCTGCACCCATTCACAG -s simDog_chr6.simDog.chr6 124631 21 + 593897 GGCCTCCACAGCCATTAACAG -s simHuman_chr6.simHuman.chr6 410936 21 - 601863 GGCTGCTATGGCCATTTACAG -s simRat_chr6.simRat.chr6 152184 21 + 647215 GTATGGTCTGATGATGGAGAG -s simRat_chr6.simRat.chr6 52419 21 - 647215 GCGTAGTGTGATGACGGAGAG - -a -s simMouse_chr6.simMouse.chr6 154520 3 + 636262 GGA -s Anc0.Anc0refChr5 76368 3 - 87904 GGA -s Anc1.Anc1refChr8 32853 3 - 57822 GGA -s Anc2.Anc2refChr15 81940 3 - 86568 GGA -s mr.mrrefChr5 17541 3 + 294540 GGA -s simCow_chr6.simCow.chr6 414783 3 - 602619 AGA -s simDog_chr6.simDog.chr6 124653 3 + 593897 GGC -s simHuman_chr6.simHuman.chr6 410958 3 - 601863 GGA -s simRat_chr6.simRat.chr6 152205 3 + 647215 GGC -s simRat_chr6.simRat.chr6 52440 3 - 647215 GAA - -a -s simMouse_chr6.simMouse.chr6 154523 25 + 636262 AGCATTAGCAATGTCTACTCCTGGT -s Anc0.Anc0refChr5 76372 24 - 87904 -GCACTAGCTATCTCTATTCCTGGT -s Anc1.Anc1refChr8 32857 24 - 57822 -GCACTAGCTATCTCTATTCCTGGT -s Anc2.Anc2refChr15 81944 24 - 86568 -GCACTAGCTATCTCTATTCCTGGT -s mr.mrrefChr5 17557 25 + 294540 AGCATTAGCTATGTCTACTCCTGGT -s simCow_chr6.simCow.chr6 414787 24 - 602619 -GCAATAGGAATCACTCTTCCTGGT -s simDog_chr6.simDog.chr6 124657 24 + 593897 -GCCCTAGCTATCTGTATTCTTGGT -s simHuman_chr6.simHuman.chr6 410962 24 - 601863 -GCACTAGTTATTTCTATTCCTGAC -s simRat_chr6.simRat.chr6 152221 25 + 647215 AGCATTAGCTATCTCTACTCCTGGT -s simRat_chr6.simRat.chr6 52456 6 - 647215 ATCATT------------------- - -a -s simMouse_chr6.simMouse.chr6 154548 71 + 636262 TATTATACTACATGAGACTTGCCCCCTGATATCAGAACACATGTCAGTTGAAGCCATATGAGCAGGTGGAA -s Anc0.Anc0refChr5 76396 34 - 87904 TATTATACTACCTGAGAC-------------------------------------ATATGAAGAGCTGCAA -s Anc1.Anc1refChr8 32881 34 - 57822 TATTATACTACCTGAGAC-------------------------------------ATATGAAGAGCTGCAA -s Anc2.Anc2refChr15 81971 34 - 86568 TATTATATTACCTGAAGC-------------------------------------ATATGAAGAGCTGCAA -s mr.mrrefChr5 17582 71 + 294540 TATTATACTACATGAGACTTGCCCCCTGATATCAGAACACATGTCAGTTGAAGCCATATGAGGAGGTGGAA -s simCow_chr6.simCow.chr6 414814 34 - 602619 TATGATAGTACCTGGAGC-------------------------------------ATATGAAGAGCTTCAT -s simDog_chr6.simDog.chr6 124684 34 + 593897 TATTATATTACCTGAAGC-------------------------------------ATGCAAAGAGCTGCAA -s simHuman_chr6.simHuman.chr6 410986 34 - 601863 TATTATACTACCTGAGAC-------------------------------------ATATGAAGAGCTGCAA -s simRat_chr6.simRat.chr6 152246 71 + 647215 CATTATACTACATAAAACTTGCCACCTAACATCTCAACACATGTCAGTTGAAGTTATACAAGGAAGTGGAA - -a -s simMouse_chr6.simMouse.chr6 154619 11 + 636262 ATGTCAATACT -s Anc0.Anc0refChr5 76430 11 - 87904 AGGTCAACACC -s Anc1.Anc1refChr8 32915 11 - 57822 AGGTCAACACC -s Anc2.Anc2refChr15 82005 11 - 86568 AGGTCAACACC -s mr.mrrefChr5 17653 11 + 294540 ATGTCAATACT -s simCow_chr6.simCow.chr6 414848 11 - 602619 AGGACAACACC -s simDog_chr6.simDog.chr6 124718 11 + 593897 GGCTCAATACC -s simHuman_chr6.simHuman.chr6 411020 11 - 601863 AAGTCAACACC -s simRat_chr6.simRat.chr6 152319 11 + 647215 ATGTCAATACT - -a -s simMouse_chr6.simMouse.chr6 154630 60 + 636262 AAGCCCTTAATGATATCTAATGTCTTACTACCACATTGGATAGAAGGTTCATGGACTAAG -s Anc0.Anc0refChr5 76442 57 - 87904 AAGCCCTTAATGATGTTCAA---CTTGTTACCTCATTGGTTAGAAAATACATGTACTAAA -s Anc1.Anc1refChr8 32927 57 - 57822 AAGCCCTTAATGATGTTCAA---CTTGTTACCTCATTGGTTAGAAAATACATGTACTAAA -s Anc2.Anc2refChr15 82017 57 - 86568 AAGCCCTTGATGATGTTCAA---CTTGTTACCTCATTGGTTAGAAAATACATGTACTAAA -s mr.mrrefChr5 17664 60 + 294540 AAGCCCTTAATGATATCTAATGTCTTATTACCACATTGGATAGAAGGTTCATGGACTAAG -s simCow_chr6.simCow.chr6 414860 57 - 602619 AAGTTCTTGATGATGTTCAG---TTTGTTACCTCATTAGTTAGAGGGTACATGTACTAAA -s simDog_chr6.simDog.chr6 124730 57 + 593897 AAGCCCTTGAAGATGTTGAA---CTTGTTACCTCATTGGCAAAAAAATACATGTACTAAC -s simHuman_chr6.simHuman.chr6 411032 57 - 601863 AAGCCCTCAATGATGTTCAA---CTTGTTACCTTATTGGTTAGGACACACATGTACTAAA -s simRat_chr6.simRat.chr6 152330 59 + 647215 GAGCCCTTAATGATATCTGTTGTC-TATTACCACATTGGATGGAAGGTCCATGGACTAAG - -a -s simMouse_chr6.simMouse.chr6 154690 37 + 636262 ACATTCAGAGTTGAGTGGAAAAGTTAGCCATAATCCA -s Anc0.Anc0refChr5 76500 37 - 87904 AGGTACAGAGTTGAGAGGAAAGGTTAGTCATAAGTTA -s Anc1.Anc1refChr8 32985 37 - 57822 AGGTACAGAGTTGAGAGGAAAGGTTAGTCATAAGTTA -s Anc2.Anc2refChr15 82075 37 - 86568 AGGTACAGCATTGAGAGGAAAGGTCAATCATAAGTTA -s mr.mrrefChr5 17724 37 + 294540 ACATTCAGAGTTGAGTGGAAAAGTTAGCCATAATCCA -s simCow_chr6.simCow.chr6 414918 37 - 602619 AGCTACAGGATTGAGAGGAAAGGCCAATCGTAAGTCA -s simDog_chr6.simDog.chr6 124788 37 + 593897 AGGTACAGCATTGTAGGGAAGGGTCAACTACAAGTTA -s simHuman_chr6.simHuman.chr6 411090 37 - 601863 AGGTGAATAGTTGAGAGGACAGGTTAGTCATTAGTTA -s simRat_chr6.simRat.chr6 152389 15 + 647215 ACATTCAGAG----------------------ATCCA - -a -s simMouse_chr6.simMouse.chr6 154727 7 + 636262 ACCATAA -s Anc0.Anc0refChr5 76537 7 - 87904 CCTGATT -s Anc1.Anc1refChr8 33022 7 - 57822 CCTGATT -s Anc2.Anc2refChr15 82112 7 - 86568 CCTGATT -s mr.mrrefChr5 17761 7 + 294540 ACCAAAA -s simCow_chr6.simCow.chr6 414955 7 - 602619 CCTGATT -s simDog_chr6.simDog.chr6 124835 7 + 593897 CTTGCTT -s simHuman_chr6.simHuman.chr6 411127 7 - 601863 CCTGATT -s simRat_chr6.simRat.chr6 152404 7 + 647215 ACAAAAA - -a -s simMouse_chr6.simMouse.chr6 154734 5 + 636262 TAGAG -s Anc0.Anc0refChr5 76544 5 - 87904 TAAAG -s Anc1.Anc1refChr8 33029 5 - 57822 TAAAG -s Anc2.Anc2refChr15 82129 5 - 86568 TAATA -s mr.mrrefChr5 17768 5 + 294540 TAGAG -s simCow_chr6.simCow.chr6 414972 5 - 602619 TAAAA -s simDog_chr6.simDog.chr6 124918 5 + 593897 TAATA -s simHuman_chr6.simHuman.chr6 411134 5 - 601863 CCAAG -s simRat_chr6.simRat.chr6 152411 5 + 647215 TAGAG - -a -s simMouse_chr6.simMouse.chr6 154739 30 + 636262 AAATTTTGTTAAATTAATACATAGAAGCCC -s Anc0.Anc0refChr5 76549 25 - 87904 AAGTATT-----ATTAGTACATAGAAGGCC -s Anc1.Anc1refChr8 33034 25 - 57822 AAGTATT-----ATTAGTACATAGAAGGCC -s Anc2.Anc2refChr15 82134 25 - 86568 ATGCATT-----ATTAGTAAGTAGAAGGCC -s mr.mrrefChr5 17773 30 + 294540 AAATTTTGTTAAATTAATACATAGAAGCCC -s simCow_chr6.simCow.chr6 414977 25 - 602619 ATTTCTT-----ATTGATGAGTAGAAGGTC -s simDog_chr6.simDog.chr6 124931 25 + 593897 ATGCATT-----ATTAGTAAGTAGAAGGCC -s simHuman_chr6.simHuman.chr6 411139 20 - 601863 CAGTATC----------CGCATAGCACACC -s simRat_chr6.simRat.chr6 152416 30 + 647215 AAATCTTGTTAAATTAGTACATGGAAACCC - -a -s simMouse_chr6.simMouse.chr6 154769 11 + 636262 ATGTGTCATAT -s Anc0.Anc0refChr5 76574 11 - 87904 ACATGCCATAT -s Anc1.Anc1refChr8 33059 11 - 57822 ACATGCCATAT -s Anc2.Anc2refChr15 82164 11 - 86568 ACATGCCATAT -s mr.mrrefChr5 17803 11 + 294540 ATGTGTCATAT -s simCow_chr6.simCow.chr6 415006 11 - 602619 ACATGCCCTAT -s simDog_chr6.simDog.chr6 124961 11 + 593897 ACATGCCATAT -s simHuman_chr6.simHuman.chr6 411159 3 - 601863 A--------AT -s simRat_chr6.simRat.chr6 152446 11 + 647215 ATGTGTCGTAT - -a -s simMouse_chr6.simMouse.chr6 154780 37 + 636262 TAATAGCAATGCAGGACATTTCAACTATCCAATGAAT -s Anc0.Anc0refChr5 76585 37 - 87904 GAATATCAATGAGGCACATTACAACTATCTGATCAAG -s Anc1.Anc1refChr8 33070 37 - 57822 GAATATCAATGAGGCACATTACAACTATCTGATCAAG -s Anc2.Anc2refChr15 82175 37 - 86568 GAAGATCAATGAGGCACATTACAACTATCTGATCAAG -s mr.mrrefChr5 17814 37 + 294540 TAATAGCAATGCAGGACATTTCAACTATCCAATGAAT -s simCow_chr6.simCow.chr6 415018 37 - 602619 AAAGATTCATGAGGTACATTAAAACTAACATACCAAG -s simDog_chr6.simDog.chr6 124972 36 + 593897 GAAGATCAATGAGGCATATTTCAACGAT-TGATCAAG -s simHuman_chr6.simHuman.chr6 411162 37 - 601863 GAATATGAATTAGGCACATTACAACTATCTGATTAAG -s simRat_chr6.simRat.chr6 152457 37 + 647215 TAATGGCAATGTAGGATATTTCAACTATCAAATGGAT - -a -s simMouse_chr6.simMouse.chr6 154817 85 + 636262 ATATCATATAAATATATCTCAAGGACCAGCATAATATGACTTTCAGATCACCACTTGAGTGTCTTAAAATGAATAACAGTGGCCA -s Anc0.Anc0refChr5 76624 82 - 87904 AAATCTGCTA--CATGTCTTAAGGACCAGTATAATATGACTTTTGAATTACCACATGAGTGTCTTAAAA-GAATAATAGTGGTCA -s Anc1.Anc1refChr8 33109 82 - 57822 AAATCTGCTA--CATGTCTTAAGGACCAGTATAATATGACTTTTGAATTACCACATGAGTGTCTTAAAA-GAATAATAGTGGTCA -s Anc2.Anc2refChr15 82214 82 - 86568 AAAGCTGCTA--CATGTTTTAAGGACCAGTATAATATGACTTTTGAATTACTACATGAGTGTCATAAAA-GAATAATAGTGGTCA -s mr.mrrefChr5 17851 85 + 294540 ATATCAGATAAATATGTCTCAAGGACCAGCATAATATGACTTTCAGATCACCACTTGAGTGTCTTAAAATGAATAATAGTGGTCA -s simCow_chr6.simCow.chr6 415057 79 - 602619 AAAGCTGCTG--CAT---TCAGGAACCAGTATAATGGAACTATTCAATATCTACATGAGTGTCATACAA-AAATAATAGTTGTAA -s simDog_chr6.simDog.chr6 125010 82 + 593897 AAAGTTGCTA--CATGTTGTAAGGACCAGTATAATATGGTTTTTGGGTTACTACATGAGTGTCATAAAA-GAATAACAGGGGTCA -s simHuman_chr6.simHuman.chr6 411201 82 - 601863 AGATCTGCTA--CATGTCTTAAGGACCAGTATCATATGACTTGTGAATGACCACATGAGTGGCTTAAAA-GAATAATAGTGGTCA -s simRat_chr6.simRat.chr6 152494 85 + 647215 ATATCAGATGAAAATGTCTCAAGGACCAACATAATATGACTCTCAGATAACCACTTGAGTGTCTTGAAGTGAATAATAGTGGTGT - -a -s simMouse_chr6.simMouse.chr6 154902 78 + 636262 TCAGCTAAGCCAGAAGGATTGTGTAAGTTGTTGTGCCAGGTCAGTATCACTTGGTAAAGTTACATTTTCTATTGGGCA -s Anc0.Anc0refChr5 76706 55 - 87904 TCAGCTAAG----------------------TATGTCAGGTTAGTATCACTC-ATAATGTTACATTTTCTTTGGTCCA -s Anc1.Anc1refChr8 33191 71 - 57822 TCAGCTAAG------AGATAGTATAAGTTCCTATGTCAGGTTAGTATCACTC-ATAATGTTACATTTTCTTTGGTCCA -s Anc2.Anc2refChr15 82297 55 - 86568 TCAGCTAAG----------------------TATGTCACGTCAGTATCACTC-ATATTGTTACATTTTCTTTGGTCTA -s mr.mrrefChr5 17936 78 + 294540 TCAGCTAAGCCAGAAAGATTGTGTAAGTTGTTATGCCAGGTTAGTATCACTCGATAAAGTTACATTTTCTTTTGGGCA -s simCow_chr6.simCow.chr6 415137 55 - 602619 TCAGCTAAA----------------------TATGTCATGTCAGTATCACTC-ATACTCTTACATTTTCTTTGGCCTA -s simDog_chr6.simDog.chr6 125093 55 + 593897 TCAGCTAAG----------------------TATGTCACATCATTACTACTC-GTATTGTAACATTTTCTTTAGTCTA -s simHuman_chr6.simHuman.chr6 411283 71 - 601863 GTCACGAAG------AGATAGTATAAGTTCCTATGTCAGGTTAGTATCACGC-ATAATGTTACATTTTCTTTGGTACA -s simRat_chr6.simRat.chr6 152579 72 + 647215 TCAGCTCAGCCAGAAA------GTAAATTGTTATGCTAGGTTAGTATCGCCCAATAGAGTTACATTTTCTTTTGGGCA - -a -s simMouse_chr6.simMouse.chr6 154980 20 + 636262 GTGTACAGTATTTTTGGACC -s Anc0.Anc0refChr5 76762 20 - 87904 CTGTGAAGTTTTTATGGACT -s Anc1.Anc1refChr8 33263 20 - 57822 CTGTGAAGTTTTTATGGACT -s Anc2.Anc2refChr15 82353 20 - 86568 CTGTGAAGTTTTTATGGACT -s mr.mrrefChr5 18014 20 + 294540 CTGTACAGTATTTTTGGACT -s simCow_chr6.simCow.chr6 415193 20 - 602619 CTCTGAGGTTTTTTTGGACT -s simDog_chr6.simDog.chr6 125149 20 + 593897 CTGTGAAGTTTTTATGGATT -s simHuman_chr6.simHuman.chr6 411355 20 - 601863 CTGTCAAATTCTTATGGACT -s simRat_chr6.simRat.chr6 152651 20 + 647215 CTGTACAGTATTTTTGTGTT - -a -s simMouse_chr6.simMouse.chr6 155000 4 + 636262 TTTA -s Anc0.Anc0refChr5 76782 4 - 87904 TCTG -s Anc1.Anc1refChr8 33283 4 - 57822 TCTG -s Anc2.Anc2refChr15 82373 4 - 86568 TCTG -s mr.mrrefChr5 18034 4 + 294540 TTTA -s simCow_chr6.simCow.chr6 415221 4 - 602619 TCTG -s simDog_chr6.simDog.chr6 125169 4 + 593897 TCTA -s simHuman_chr6.simHuman.chr6 411375 4 - 601863 TATG -s simRat_chr6.simRat.chr6 152671 4 + 647215 TTTA - -a -s simMouse_chr6.simMouse.chr6 155004 31 + 636262 ATAGTACAAGTATAAAATAAATCTATGCAGT -s Anc0.Anc0refChr5 76786 31 - 87904 TTGGCACATGTAAAGAGCAGAGCTTTGCAGT -s Anc1.Anc1refChr8 33287 31 - 57822 TTGGCACATGTAAAGAGCAGAGCTTTGCAGT -s Anc2.Anc2refChr15 82377 31 - 86568 TTGCCAGATGTAAAGAGCAGAGCTTTGCAGT -s mr.mrrefChr5 18038 31 + 294540 TTAGTACAAGTATAAAATAAATCTATGCAGT -s simCow_chr6.simCow.chr6 415230 30 - 602619 TTTCCGGACTTATAGTGCGAAGCTTAGTGG- -s simDog_chr6.simDog.chr6 125173 30 + 593897 TTG-TAGATGTAACAAGCAGAGCTTTGCAAT -s simHuman_chr6.simHuman.chr6 411379 31 - 601863 TTGGCACATGTACAGAGCAGTGTTTTGCAGT -s simRat_chr6.simRat.chr6 152675 31 + 647215 TGAGGACGAGTATAAAATAAATCTATGCAGT - -a -s simMouse_chr6.simMouse.chr6 155035 14 + 636262 TAGGGGCCTCAATG -s Anc0.Anc0refChr5 76823 14 - 87904 TATGGCCCTTAACA -s Anc1.Anc1refChr8 33324 14 - 57822 TATGGCCCTTAACA -s Anc2.Anc2refChr15 82414 14 - 86568 TATGGCCCTTAACA -s mr.mrrefChr5 18074 14 + 294540 TAGGGCCCTCAATG -s simCow_chr6.simCow.chr6 415265 14 - 602619 TATGGCCCTCAACA -s simDog_chr6.simDog.chr6 125209 14 + 593897 TATGACCCTTGACA -s simHuman_chr6.simHuman.chr6 411416 14 - 601863 TATGGCCCTGAACA -s simRat_chr6.simRat.chr6 152711 14 + 647215 TAGGGCCCTCAATC - -a -s simMouse_chr6.simMouse.chr6 155049 5 + 636262 TTGTC -s Anc0.Anc0refChr5 76843 5 - 87904 TTGTT -s Anc1.Anc1refChr8 33344 5 - 57822 TTGTT -s Anc2.Anc2refChr15 82444 5 - 86568 TTGTT -s mr.mrrefChr5 18088 5 + 294540 TTGTT -s simCow_chr6.simCow.chr6 415295 5 - 602619 TGGTT -s simDog_chr6.simDog.chr6 125241 5 + 593897 TTGTT -s simHuman_chr6.simHuman.chr6 411436 5 - 601863 TTGTT -s simRat_chr6.simRat.chr6 152725 5 + 647215 TTGTT - -a -s simMouse_chr6.simMouse.chr6 155054 64 + 636262 TTGATAAGTTCAACATACTCTAAGATAGCTATTTCACAAGATAGCTATTTCACATTATCCACTA -s Anc0.Anc0refChr5 76854 48 - 87904 TTGATGAGTCCAACATACTCTAGCATAGCTATCTCACAT----------------AATGCATTA -s Anc1.Anc1refChr8 33355 48 - 57822 TTGATGAGTCCAACATACTCTAGCATAGCTATCTCACAT----------------AATGCATTA -s Anc2.Anc2refChr15 82455 48 - 86568 TTGATGAGTCCAACATACTCTAGCATAGCTAGCTCACAT----------------AATGCATTA -s mr.mrrefChr5 18099 48 + 294540 TTGATAAGTTCAACATACTCTAAGATAGCTATTTCACAA----------------TATCCACTA -s simCow_chr6.simCow.chr6 415306 48 - 602619 TTGATGAGTCCAAAATTCTCTAGCATAGCTAGCTCACAT----------------AATACATTA -s simDog_chr6.simDog.chr6 125252 39 + 593897 TTGACAAGACCAACATACTCTAGCATAAATAGC-------------------------GCACTA -s simHuman_chr6.simHuman.chr6 411447 48 - 601863 TTGATGAGTCCGACATACTCTAGCATAGCAATCTTGCAT----------------AATGCATTA -s simRat_chr6.simRat.chr6 152736 48 + 647215 TTGATAAGTTTAACATTCTCTACAATAGCTATTACACAA----------------TATCTACTA - -a -s simMouse_chr6.simMouse.chr6 155118 14 + 636262 TGACTCCATAAGCT -s Anc0.Anc0refChr5 76906 14 - 87904 TAACTCCATAAACT -s Anc1.Anc1refChr8 33407 14 - 57822 TAACTCCATAAACT -s Anc2.Anc2refChr15 82507 14 - 86568 TAACTCCATAAACT -s mr.mrrefChr5 18147 14 + 294540 TAACTCCATAAGCT -s simCow_chr6.simCow.chr6 415358 14 - 602619 TAATTCCAGAAACT -s simDog_chr6.simDog.chr6 125295 12 + 593897 --ACTCCATAAAGT -s simHuman_chr6.simHuman.chr6 411499 14 - 601863 TAACTCCTTAAACT -s simRat_chr6.simRat.chr6 152784 14 + 647215 TAACTCCGTGAGCT - -a -s simMouse_chr6.simMouse.chr6 155132 10 + 636262 TGTCTCGAGT -s Anc0.Anc0refChr5 76921 10 - 87904 TGTCCCCATT -s Anc1.Anc1refChr8 33422 10 - 57822 TGTCCCCATT -s Anc2.Anc2refChr15 82522 10 - 86568 TCTCCCCATT -s mr.mrrefChr5 18161 10 + 294540 TGTCTCCAGT -s simCow_chr6.simCow.chr6 415373 10 - 602619 TCTCTCCATT -s simDog_chr6.simDog.chr6 125308 10 + 593897 TCTCCGCATT -s simHuman_chr6.simHuman.chr6 411514 10 - 601863 TGTCCCCATT -s simRat_chr6.simRat.chr6 152798 10 + 647215 TGTCTCCAGT - -a -s simMouse_chr6.simMouse.chr6 155142 75 + 636262 GGAACATTTCAAACAGGATGTAGTCAATTTAAAAACAGTTTTCACGTACGTAGATTCCTTTGAAAAATTAAAACT -s Anc0.Anc0refChr5 76931 70 - 87904 GGAATGTATCACACAGTATGCAGTCAATTTCTCAACAGTTTTC----ACTTAAAGGCCCTTGAATAATGAAAA-T -s Anc1.Anc1refChr8 33432 70 - 57822 GGAATGTATCACACAGTATGCAGTCAATTTCTCAACAGTTTTC----ACTTAAAGGCCCTTGAATAATGAAAA-T -s Anc2.Anc2refChr15 82532 70 - 86568 GAGATGTATCACACAGTATGCAGTCAATTGCTCAATAGTCTTC----ACTTAAAGGCCCTTGAATAATGGAAA-T -s mr.mrrefChr5 18171 71 + 294540 GGAACATATCAAACAGTATGTAGTCAATTTAACAACAGTTTTC----ACGTAGAGGCCTTTGAATAATGAAAACT -s simCow_chr6.simCow.chr6 415383 63 - 602619 GTGATGTATCATGCAGTATGCAGTCAACAGCTCAATAGTC-----------AAAGGCCCTTGACTAATGGAAG-T -s simDog_chr6.simDog.chr6 125322 62 + 593897 GAGACATCTCACACAGAATACAGTCAATT--------ATCTTC----ACTTAAAGGCCCTTGAACACTGGAAA-T -s simHuman_chr6.simHuman.chr6 411524 70 - 601863 GGAATGTATTACACATTATGCAGTCAATTTCTCAACGGTTGTC----ACATCAAGGCCCTTGAGTAATGAAAA-T -s simRat_chr6.simRat.chr6 152808 71 + 647215 GGGTCATATCAAACAGTATGTAGTCAATTTAACCACAGTTTTC----ATGTAGAGGCCTTTGAATAATGAACACT - -a -s simMouse_chr6.simMouse.chr6 155217 16 + 636262 ATGAAAATGAATGATG -s Anc0.Anc0refChr5 77001 16 - 87904 ATGGGAACGGAATATG -s Anc1.Anc1refChr8 33502 16 - 57822 ATGGGAACGGAATATG -s Anc2.Anc2refChr15 82602 16 - 86568 ATGGGAATGGAATATG -s mr.mrrefChr5 18242 16 + 294540 ATGAGAACGAATGATG -s simCow_chr6.simCow.chr6 415446 14 - 602619 ATGGGA--GGAATATG -s simDog_chr6.simDog.chr6 125384 16 + 593897 ATGGGAATAGAATGTG -s simHuman_chr6.simHuman.chr6 411594 15 - 601863 ATG-GATCGGAATATG -s simRat_chr6.simRat.chr6 152934 16 + 647215 ATGAGAACGAACGATG - -a -s simMouse_chr6.simMouse.chr6 155233 73 + 636262 TGGGACGCTACTGACTAATTGAAAGGATTGACGTATAGTATCCTCACTATTTTGACCCAGGAGTACAAATCTT -s Anc0.Anc0refChr5 77022 59 - 87904 TGCAATGCTCCCAATTGATGGTATT---TA----AAAGTATCCCCAGTCTTCTGAACAAGG-------ATTTT -s Anc1.Anc1refChr8 33523 66 - 57822 TGCAATGCTCCCAATTGATGGTATT---TA----AAAGTATCCCCAGTCTTCTGAACAAGGAGTACTAATTTT -s Anc2.Anc2refChr15 82623 59 - 86568 TGCAATGCTCCCAATTGATGGTATT---TA----AAAGTATCCCCAGTCTTCTGAACAAGG-------ATTTT -s mr.mrrefChr5 18258 69 + 294540 TGGGATGCTACTAACTGATTGTAATGATTG----ATAGTATCCTCACTATTTTGACCCAGGAGTACAAATCTT -s simCow_chr6.simCow.chr6 415465 59 - 602619 TGCAATGCTCCTAATTGATGGTATT---GA----AAAGCATCCCCAGTCTCCTGAACAAGG-------ATTTT -s simDog_chr6.simDog.chr6 125405 59 + 593897 TGAGATGCTCCCAATTGATTGTACT---TA----AAAGTATCCCCGGTCTTTTGAACTAAC-------ATTTT -s simHuman_chr6.simHuman.chr6 411614 66 - 601863 TGCAATGTTTCCAATTGATGGTATT---TA----AAAGTATCACCAGTCTTCTGAACAAGGAGTACTAATTTT -s simRat_chr6.simRat.chr6 152950 55 + 647215 TGGGATGCTACTAACAGATCATGATGATTG--------------TGCTATTTTGACCCAGGAGT----ATCTT - -a -s simMouse_chr6.simMouse.chr6 155306 28 + 636262 GATGAGACAGTAGCATCTTTTCCAACTG -s Anc0.Anc0refChr5 77081 28 - 87904 AATGCAAAAATAGAATCTTTTTACACTA -s Anc1.Anc1refChr8 33589 28 - 57822 AATGCAAAAATAGAATCTTTTTACACTA -s Anc2.Anc2refChr15 82682 28 - 86568 AATGCAAAAATAGAATCTTTTTATTTTA -s mr.mrrefChr5 18327 28 + 294540 AATGAAAAAGTAGCATCTTTTTACACTG -s simCow_chr6.simCow.chr6 415524 28 - 602619 AATGCAAAAATAAAATCTTTTTATGATA -s simDog_chr6.simDog.chr6 125464 28 + 593897 AATGCAAAAATAGAATCTTTTTATTTTT -s simHuman_chr6.simHuman.chr6 411681 28 - 601863 AATGCAAAAATAGAATCTCTTTACACTA -s simRat_chr6.simRat.chr6 153005 28 + 647215 AATGAAAAAGTAACATCTTTTTACACTG - -a -s simMouse_chr6.simMouse.chr6 155334 53 + 636262 CTTCTCATCTAGATAGCTCAGGATCACCCCATGCAATAAGTGTCCTTGACCTG -s Anc0.Anc0refChr5 77109 33 - 87904 CTTCCTATCTAGGTGGCTCAAGACAGACCCATG-------------------- -s Anc1.Anc1refChr8 33617 33 - 57822 CTTCCTATCTAGGTGGCTCAAGACAGACCCATG-------------------- -s Anc2.Anc2refChr15 82710 33 - 86568 CTTCCTATCTAGGTGGCTCGAGACAGACCCATG-------------------- -s mr.mrrefChr5 18355 51 + 294540 CTTCTCATCTAGATAGCTCAGGATCGACCCATGCAATAAGTGTCCTTGA--TG -s simCow_chr6.simCow.chr6 415552 33 - 602619 CTTCCTGTTTAGGTGCGTCTAGACAGGCCCATA-------------------- -s simDog_chr6.simDog.chr6 125500 33 + 593897 TTTTCCATCTAGGTGGCTGGGGACAGACCTGTG-------------------- -s simHuman_chr6.simHuman.chr6 411709 33 - 601863 CTTCCTATCTGGGTGGCTCAAGACAGACTCATG-------------------- -s simRat_chr6.simRat.chr6 153033 42 + 647215 ---------TAGATAGCTCAGGATTGACCCATGCAATAAGTGTCCTTGG--TG - -a -s simMouse_chr6.simMouse.chr6 155387 22 + 636262 GGAGAAGTGGTCTTGACTTTGT -s Anc0.Anc0refChr5 77142 22 - 87904 GGACAAGCAGTTTTGACTCAAC -s Anc1.Anc1refChr8 33650 22 - 57822 GGACAAGCAGTTTTGACTCAAC -s Anc2.Anc2refChr15 82743 22 - 86568 GGACAAGCAGTTTCAACTCAAC -s mr.mrrefChr5 18406 22 + 294540 GGAGAAGTGGTCTTGACTTAGT -s simCow_chr6.simCow.chr6 415601 22 - 602619 ACACAAACAGTTAACACTCAAC -s simDog_chr6.simDog.chr6 125533 22 + 593897 GGATCAGCAGTCTCAATTGAAA -s simHuman_chr6.simHuman.chr6 411742 22 - 601863 GGACAAGCAGTTTTGACTCAAC -s simRat_chr6.simRat.chr6 153075 22 + 647215 TGATAAGTGGTCTTGACTTAGT - -a -s simMouse_chr6.simMouse.chr6 155409 32 + 636262 CTAAAGAATGTGATTGGTAATAACTAGCTTTG -s Anc0.Anc0refChr5 77164 31 - 87904 TTAGAGGATATAAAT-TTAACAACTAGTCTTG -s Anc1.Anc1refChr8 33672 31 - 57822 TTAGAGGATATAAAT-TTAACAACTAGTCTTG -s Anc2.Anc2refChr15 82765 31 - 86568 TTAGAGGATATAAAT-TTAACACTTAGTCTTG -s mr.mrrefChr5 18428 31 + 294540 CTAGAGAATATGATT-GTAATAACTAGCTTTG -s simCow_chr6.simCow.chr6 415623 31 - 602619 TTAGGAGACATAGTC-TTGGTCCATAGTCCTG -s simDog_chr6.simDog.chr6 125555 31 + 593897 TTAGAGTATATAAAT-TTAACACTTAGTCTAG -s simHuman_chr6.simHuman.chr6 411766 27 - 601863 TTAGAGGATATT-----TAACAACTAGTCTTG -s simRat_chr6.simRat.chr6 153097 31 + 647215 CTAGAGAATATGATT-GTAATAACTAGCTTTG - -a -s simMouse_chr6.simMouse.chr6 155441 92 + 636262 ATCTAGGAGCAGATAAGGTGAACAAAGGTATACCTTGAGGTCTAAAGAATATGATTGTAATAACTAGCTTTGATCTAGGAGCAGATAAGGTG -s Anc0.Anc0refChr5 77195 21 - 87904 ATC---------TGTGAAAG--------------------------------------------------------------GGGTGGGATG -s Anc1.Anc1refChr8 33703 30 - 57822 ATCTAAGGGCTGTGTGAAAG--------------------------------------------------------------GGGTGGGATG -s Anc2.Anc2refChr15 82796 21 - 86568 GTC---------TGTGAAAG--------------------------------------------------------------GAGTGGGATG -s mr.mrrefChr5 18459 30 + 294540 ATCTAGGAGCAGATAGGATG--------------------------------------------------------------AGATAGGATG -s simCow_chr6.simCow.chr6 415654 18 - 602619 GTC---------TGTAAAGG--------------------------------------------------------------G---GGGGTG -s simDog_chr6.simDog.chr6 125586 21 + 593897 GTC---------TGTGAAAG--------------------------------------------------------------GAGTGGGATG -s simHuman_chr6.simHuman.chr6 411813 30 - 601863 ATGAAAGGGCTGTGTGAAAG--------------------------------------------------------------GGGTGGGATG -s simRat_chr6.simRat.chr6 153128 30 + 647215 ATCTAGGAGCAGATAGCATG--------------------------------------------------------------AGATAGCATG - -a -s simMouse_chr6.simMouse.chr6 155533 8 + 636262 AACAAAGG -s Anc0.Anc0refChr5 77216 8 - 87904 AATGAAAG -s Anc1.Anc1refChr8 33733 8 - 57822 AATGAAAG -s Anc2.Anc2refChr15 82817 8 - 86568 AATGAAAG -s mr.mrrefChr5 18489 8 + 294540 AACGAAGG -s simCow_chr6.simCow.chr6 415672 8 - 602619 AACGAAAG -s simDog_chr6.simDog.chr6 125607 8 + 593897 AATGGAAG -s simHuman_chr6.simHuman.chr6 411843 8 - 601863 AATGAAAG -s simRat_chr6.simRat.chr6 153163 8 + 647215 AACGAAGG - -a -s simMouse_chr6.simMouse.chr6 155541 163 + 636262 TATACCTTGAAGGTCCAACAGTCTATACTCAAGGTACTACATCATTGTTTTGGAACTATTTACACTCTAGATATTGGAAGCCCTCACCTCGTCATGCTGCATAATGCATAGTTTTTAGCATTTCATCTGAATTTAAATGCGTGGTACCTCGTTGCCACATGAA -s Anc0.Anc0refChr5 77227 82 - 87904 TAAACTTTTAAAATCCCACAGTAAATACCCCAGGTATCACATAGTTTTTTTGAAACTCTTTACACTCTAGACATTGGC---------------------------------------------------------------------------------TGGG -s Anc1.Anc1refChr8 33744 82 - 57822 TAAACTTTTAAAATCCCACAGTAAATACCCCAGGTATCACATAGTTTTTTTGAAACTCTTTACACTCTAGACATTGGC---------------------------------------------------------------------------------TGGG -s Anc2.Anc2refChr15 82828 82 - 86568 TAAATTTTTAAAATCCCACACTAAACACCCCATGTATCATATAGTTTTTTTGAAACTCTTCACACTCTAGACATTGGC---------------------------------------------------------------------------------AGGG -s mr.mrrefChr5 18497 163 + 294540 TATACCTTGAAGGTCCAACAGTCTATACCCAAGGTACTACATAATTTTTTTGGAACTCTTTACACTCTAGACATTGGAAGCCCTCACCTCGTCATGCTGCATAATGCATAGTTTTTAGCATTTCATCTGAATTTAAATGCGTGGTACCTCGTTGCCACATGAA -s simCow_chr6.simCow.chr6 415683 82 - 602619 TAAATTTTTAGGATCCCACACTGAAGGCCCCAAGTATTATATAGGTTTTTTGAAACTCTTCACACTCTAGAAGTTGAT---------------------------------------------------------------------------------ATGG -s simDog_chr6.simDog.chr6 125618 82 + 593897 TAAATTTTTAAAATCCCACACTAAACACCCCATGTATCATGTGGTTTTTTTGAGATTCCTCACACTCTAGACATAGGC---------------------------------------------------------------------------------AGTT -s simHuman_chr6.simHuman.chr6 411854 76 - 601863 TTGACTTTTAA------ACAGTAAATACCCCAGGTATGACATAGTTTGTTGGAAACTCTTTGCACTCTAGACATTGGC---------------------------------------------------------------------------------TGGG -s simRat_chr6.simRat.chr6 153171 163 + 647215 CATAATTTGAAGGTCCAACAGTCTATACCCAATGTACTACGTAATTTTGTTGGAACTCTTTACACTCTAGACACTGGCAGCCCTCACCTTGTCATACTGCATAATGCATAGTTTTTAGCATTTCATGCTAATTTAAATGACTAGTACCTCATTGCCACCTGAA - -a -s simMouse_chr6.simMouse.chr6 155704 12 + 636262 AGCACCCAATGC -s Anc0.Anc0refChr5 77309 12 - 87904 GGCACCCACTGC -s Anc1.Anc1refChr8 33826 12 - 57822 GGCACCCACTGC -s Anc2.Anc2refChr15 82910 12 - 86568 GGTACCCACTGC -s mr.mrrefChr5 18660 12 + 294540 GGCACCCAATGC -s simCow_chr6.simCow.chr6 415766 12 - 602619 ACTACCCACTGC -s simDog_chr6.simDog.chr6 125700 12 + 593897 GGTGGCCAGTGC -s simHuman_chr6.simHuman.chr6 411930 12 - 601863 GGCACCCACTGT -s simRat_chr6.simRat.chr6 153334 12 + 647215 GACATCCAATGC - -a -s simMouse_chr6.simMouse.chr6 155716 71 + 636262 CATGTTGAAAGCTCACATTTGCATCAGTACAGGAATAGGAAGCAAACATGGGAGACCCACAATATCTTTTC -s Anc0.Anc0refChr5 77321 68 - 87904 CAGGTTTAATATTCAGATCAGTATCAGTACAGGAT--GGGCATGAAAATGGTAAATCCAGGAAGTTCTTT- -s Anc1.Anc1refChr8 33838 69 - 57822 CAGGTTTAATATTCAGATCAGTATCAGTACAGGAT--GGGCATGAAAATGGTAAATCCAGGAAGTTCTTTC -s Anc2.Anc2refChr15 82922 68 - 86568 CAGGTTTAATATTCAGATCAGTATCAGTACAGGAT--GGGCATGAAAATGGTAAATCCAGGAAGTTCTTT- -s mr.mrrefChr5 18672 71 + 294540 CATGTTTAAAACTCACATTTGTATCAGTACAGGAATAGGAAGCGAACATGGGAGACCCACAATATCTTTTC -s simCow_chr6.simCow.chr6 415780 68 - 602619 CAGGTTAAATCTTCAGATCACTAACAGTACAGGAT--GGGCATGAAAATGGTAAATCCAAGAAGTCCTTT- -s simDog_chr6.simDog.chr6 125712 68 + 593897 CAGGTTTAATATTTAGTTCAGTATCAGTACAGCAT--GGGCGCGAAATTGGTGAATCCAGGAAGTTCTTT- -s simHuman_chr6.simHuman.chr6 411942 68 - 601863 CAGGTT-AATATACAAATCAGTATCAGTACAGGAT--GGTCATGAAAATGGTAAATCGAGGACGCTGTTTC -s simRat_chr6.simRat.chr6 153346 63 + 647215 CATGTTTAAAACTCACATTTGTATCAGTATGGGAATAGGAAGCGAACATAGGAGACCCACAAT-------- - -a -s simMouse_chr6.simMouse.chr6 155787 14 + 636262 CCACAACATCTTCT -s Anc0.Anc0refChr5 77389 7 - 87904 ---TGAACTC---- -s Anc1.Anc1refChr8 33907 14 - 57822 CTATGAACTCTCCT -s Anc2.Anc2refChr15 82990 7 - 86568 ---TGAACTC---- -s mr.mrrefChr5 18743 14 + 294540 CCACAACATCTTCT -s simCow_chr6.simCow.chr6 415848 7 - 602619 ---AGATCTC---- -s simDog_chr6.simDog.chr6 125780 7 + 593897 ---TGCACTC---- -s simHuman_chr6.simHuman.chr6 412022 14 - 601863 CTATGAACTATCCT -s simRat_chr6.simRat.chr6 153409 7 + 647215 -------ATCTTCT - -a -s simMouse_chr6.simMouse.chr6 155801 31 + 636262 CACTCTTAGGAGTAATCTGCCATCCAAGTGC -s Anc0.Anc0refChr5 77396 28 - 87904 --TACTTAGGATTAATCTATCAATCAAGTG- -s Anc1.Anc1refChr8 33921 31 - 57822 CTTACTTAGGATTAATCTATCAATCAAGTGC -s Anc2.Anc2refChr15 82997 28 - 86568 --TACTTAGAATTAGTCTATCATTCAGGTG- -s mr.mrrefChr5 18757 31 + 294540 CTCTCTTAGGAGTAATCTGCCAATCAAGTGC -s simCow_chr6.simCow.chr6 415855 27 - 602619 ---AATAAGAACTAGTTTCCCATTCATGTG- -s simDog_chr6.simDog.chr6 125787 28 + 593897 --TACTTAAAATTAGTCTATCATTCAGTTG- -s simHuman_chr6.simHuman.chr6 412037 31 - 601863 CTTACTTAGGATTAATCCTTCAATCAAATGA -s simRat_chr6.simRat.chr6 153416 31 + 647215 CTATCTTAGGGGTAATCTGCCAATCAAGTGC - -a -s simMouse_chr6.simMouse.chr6 155832 6 + 636262 CCCCAG -s Anc0.Anc0refChr5 77424 6 - 87904 CCTTCG -s Anc1.Anc1refChr8 33952 6 - 57822 CCTTCG -s Anc2.Anc2refChr15 83025 6 - 86568 CCTTCG -s mr.mrrefChr5 18788 6 + 294540 CCCCAG -s simCow_chr6.simCow.chr6 415882 6 - 602619 CTTTCA -s simDog_chr6.simDog.chr6 125815 6 + 593897 CCTTCG -s simHuman_chr6.simHuman.chr6 412071 6 - 601863 CCTTGG -s simRat_chr6.simRat.chr6 153447 6 + 647215 CCCCTG - -a -s simMouse_chr6.simMouse.chr6 155838 52 + 636262 CTGGGGTAACAACCCGAATTCTGTACATATAATTTACCCAATCCCAAACACT -s Anc0.Anc0refChr5 77430 52 - 87904 TTGGGGCAAGGACCAGAAATCTGTCTGCATAATCTAGCCAATCCCAAACACC -s Anc1.Anc1refChr8 33958 52 - 57822 TTGGGGCAAGGACCAGAAATCTGTCTGCATAATCTAGCCAATCCCAAACACC -s Anc2.Anc2refChr15 83031 52 - 86568 TTGGGGCTCGGACCAGAAATCTGTCTGCATAATCTAGCCAATCCCAAACACC -s mr.mrrefChr5 18794 52 + 294540 TTGGGGTAACAACCAGAATTCTGTACATATAATTTACCCAATCCCAAACACT -s simCow_chr6.simCow.chr6 415888 45 - 602619 GCGGGG----GACTGGAAATCTGCCTGCATAACCTAGCCA---CTAAGCACC -s simDog_chr6.simDog.chr6 125822 49 + 593897 TTGGGGCTCGGACCAGAAAGCTGTATGTATAATCT---CAATCCCCAACACC -s simHuman_chr6.simHuman.chr6 412077 52 - 601863 TTGGGGCAAGGACCAGCACTCCATCTGCATAATCTATCCAATCCCAAACACC -s simRat_chr6.simRat.chr6 153453 52 + 647215 TTGGGGTAACAACCAGAATTCTGTACATGTAATTTACGCAATCCCAAACACT - -a -s simMouse_chr6.simMouse.chr6 155890 51 + 636262 GTCAGGGGAGGACTGACGTGATGTGTTCATTTGACCAAACCTGTGGCATTA -s Anc0.Anc0refChr5 77485 29 - 87904 GTGGGAGGAGGACTGACTCA----------------------GTGGCATTA -s Anc1.Anc1refChr8 34013 29 - 57822 GTGGGAGGAGGACTGACTCA----------------------GTGGCATTA -s Anc2.Anc2refChr15 83086 29 - 86568 GTGGGAGGAGGATTCACACA----------------------CTAGATTGA -s mr.mrrefChr5 18846 51 + 294540 GTCAGAGGAGGACTGACTTGATGTGTTCATTTGACCAAACCTGTGGCATTA -s simCow_chr6.simCow.chr6 415936 29 - 602619 GTGGGAGGAGGATTAACGCA----------------------CTAGATTGA -s simDog_chr6.simDog.chr6 125874 29 + 593897 GTGGAAGGAGGATACGCACA----------------------CTAGATTGA -s simHuman_chr6.simHuman.chr6 412132 29 - 601863 GTAGGAGGAGGACTGACTGT----------------------GTGGCATTA -s simRat_chr6.simRat.chr6 153505 51 + 647215 GTCAGAGGAGGACTGACTTCATGGGATCATTTGACCAAACCTGTGGCAGTA - -a -s simMouse_chr6.simMouse.chr6 155941 40 + 636262 TTGATACAATTGTACTTATGGCTGCACACATCTGTGCAAA -s Anc0.Anc0refChr5 77514 39 - 87904 TTG-TATATTTGCACTTTTGGCTATCCTCATATGAACAGA -s Anc1.Anc1refChr8 34042 39 - 57822 TTG-TATATTTGCACTTTTGGCTATCCTCATATGAACAGA -s Anc2.Anc2refChr15 83115 39 - 86568 TTG-GATATTTGCACTTTTGACTATCCTTATATGAACAGA -s mr.mrrefChr5 18897 40 + 294540 TTGATACAATTGTACTTATGGCTGTACACATCTGTGCAAA -s simCow_chr6.simCow.chr6 416005 39 - 602619 TTA-GATATTTGTACTTCTAACTGCCCTGACCTGAACACA -s simDog_chr6.simDog.chr6 125903 38 + 593897 TTG-GATTGTGGCACTATTGAC-ATATTTGTATGAACAGA -s simHuman_chr6.simHuman.chr6 412161 39 - 601863 CTT-TATATTTGCACTTTTGGCTCTCCTCATGTGAATGGA -s simRat_chr6.simRat.chr6 153556 40 + 647215 TTGAGACAATTGTATTTATCACTGTACACATTTGTGCAAA - -a -s simMouse_chr6.simMouse.chr6 155981 18 + 636262 ACATTCAACCAAGCCTAT -s Anc0.Anc0refChr5 77554 18 - 87904 ATCTTCAAAAAACCCTAT -s Anc1.Anc1refChr8 34082 18 - 57822 ATCTTCAAAAAACCCTAT -s Anc2.Anc2refChr15 83155 18 - 86568 ATCTTTAGAAAACCTTAT -s mr.mrrefChr5 18937 18 + 294540 ACATTCAACCAAGCCTAT -s simCow_chr6.simCow.chr6 416045 18 - 602619 CTGTTTAGAAAACCTTAT -s simDog_chr6.simDog.chr6 125942 3 + 593897 ATC--------------- -s simHuman_chr6.simHuman.chr6 412201 18 - 601863 ATCTTCCAGAAACCCTTA -s simRat_chr6.simRat.chr6 153596 18 + 647215 ACATTCAACCAAGCTTGT - -a -s simMouse_chr6.simMouse.chr6 155999 15 + 636262 CAAATAGGCCAACCA -s Anc0.Anc0refChr5 77579 15 - 87904 CAAATAGGAATAATG -s Anc1.Anc1refChr8 34107 15 - 57822 CAAATAGGAATAATG -s Anc2.Anc2refChr15 83180 15 - 86568 CAAATAGGAATAATG -s mr.mrrefChr5 18962 15 + 294540 CAAATAGGCCAACCA -s simCow_chr6.simCow.chr6 416070 14 - 602619 CAAATAG-AATAATG -s simDog_chr6.simDog.chr6 125949 15 + 593897 CAGGCAGGAATAATG -s simHuman_chr6.simHuman.chr6 412226 15 - 601863 CAAATAGGAATTATG -s simRat_chr6.simRat.chr6 153621 15 + 647215 TAAATAGGCCCACCA - -a -s simMouse_chr6.simMouse.chr6 156014 33 + 636262 ATGAGTCATGAAAGGTCAGGCCACAAAAACAGG -s Anc0.Anc0refChr5 77614 19 - 87904 AT--------------CAGGCTACAAAGATGAG -s Anc1.Anc1refChr8 34153 19 - 57822 AT--------------CAGGCTACAAAGATGAG -s Anc2.Anc2refChr15 83215 19 - 86568 AT--------------CAGGCTACAAAGATGAG -s mr.mrrefChr5 19008 33 + 294540 ATGAGTCATGAAAGGTCAGGCCACAAAAACAGG -s simCow_chr6.simCow.chr6 416104 19 - 602619 GT--------------CAGGCCACAAAGACAAG -s simDog_chr6.simDog.chr6 125984 19 + 593897 AT--------------CAGGCTACACAGATGAG -s simHuman_chr6.simHuman.chr6 412272 17 - 601863 AT--------------CAAGCTACAAAGA--AG -s simRat_chr6.simRat.chr6 153668 33 + 647215 ATGAGTCATGAAAGGTCAGGCCACAAAAACAGG - -a -s simMouse_chr6.simMouse.chr6 156047 76 + 636262 GCTGAAAGCCTAGGTTCAGATTTAGGATACGTCATTATGTGTAATCTCTCCAATTTCCAGGGAAATAAAGATAGGA -s Anc0.Anc0refChr5 77633 76 - 87904 ACTGAAAGCCTAAGTTCAGACTTAGGGCAGCACATTATGTGCAATCTCATTAATTTTTGGGGTAATCAAGATGATT -s Anc1.Anc1refChr8 34172 76 - 57822 ACTGAAAGCCTAAGTTCAGACTTAGGGCAGCACATTATGTGCAATCTCATTAATTTTTGGGGTAATCAAGATGATT -s Anc2.Anc2refChr15 83234 76 - 86568 ACAGAAAGCCCAAGTTCAGACTCAGGGCAGCACAGTATGTGCAATCTTATTAATTTTTGGGGTAATCAAGATGAGT -s mr.mrrefChr5 19041 76 + 294540 ACTGAAAGCCTAGGTTCAGACTTAGGATACCTCATTATGTGTAATCTCTCCAATTTCCAGGGAAATAAAGATAGTT -s simCow_chr6.simCow.chr6 416123 75 - 602619 ACAGAAAGCACACGTTCAAACTCAG-GCAAAACAGAACGTGCAATCTTATTAGTCTTTGGGGAAATCAAGATGAAT -s simDog_chr6.simDog.chr6 126004 75 + 593897 ACAGAAAGCCCAAGTTCAG-CTCAGGGCAGCACAGTATGTGCGATTTTATTAATTTTCGGGGTAATCAAGATGAGT -s simHuman_chr6.simHuman.chr6 412289 75 - 601863 ACTCAAAGACTAAGTTCAGACTTTGAGCAGCATATTATGTGCAATCTC-ATAATTTTTGGGGTAATCAAGATGATT -s simRat_chr6.simRat.chr6 153701 76 + 647215 ACTGAAAGCCTAGGTTCAGACTTAGGCTACCTCATTATGTGTAACCTCTCCAATTTCAAGGGAAATGAGGATAGTT - -a -s simMouse_chr6.simMouse.chr6 156123 24 + 636262 GTGGTAAGCTGATCTGGGATGTTT -s Anc0.Anc0refChr5 77709 24 - 87904 AGAGTAAGCTGATATGGGGTGTTT -s Anc1.Anc1refChr8 34248 24 - 57822 AGAGTAAGCTGATATGGGGTGTTT -s Anc2.Anc2refChr15 83312 24 - 86568 AGAGTAAGCTGATATGGGGTTTTC -s mr.mrrefChr5 19117 24 + 294540 GTGGTAAGCTGATCTGGGATGTTT -s simCow_chr6.simCow.chr6 416200 24 - 602619 GCAGTAGGCTGATATGGGGTTTTC -s simDog_chr6.simDog.chr6 126081 16 + 593897 AGAGTAAGCTGATATG-------- -s simHuman_chr6.simHuman.chr6 412364 24 - 601863 AGAGTTAGCCCATATGAGGTGTTT -s simRat_chr6.simRat.chr6 153777 23 + 647215 GTGATAAGTTAAACT-GGATGTTT - -a -s simMouse_chr6.simMouse.chr6 156147 12 + 636262 CTATGATTCTTG -s Anc0.Anc0refChr5 77733 12 - 87904 TTGTGCTTCTTG -s Anc1.Anc1refChr8 34272 12 - 57822 TTGTGCTTCTTG -s Anc2.Anc2refChr15 83336 12 - 86568 TTGTGCTCCTTG -s mr.mrrefChr5 19141 12 + 294540 CTATGATTCTTG -s simCow_chr6.simCow.chr6 416227 12 - 602619 TTGTGCTCCTTG -s simHuman_chr6.simHuman.chr6 412388 12 - 601863 TTGTGCTTCTTG -s simRat_chr6.simRat.chr6 153800 12 + 647215 CTACAATTCTTG - -a -s simMouse_chr6.simMouse.chr6 156159 50 + 636262 GCTTTCCAGACCAAGGTGCAATCATGGGATGAGTCTAGGATGATATTAGC -s Anc0.Anc0refChr5 77772 50 - 87904 TCTTTTCACACCAAGGTACAGTGCTAAAATGAATCCTGGATGACACTAGC -s Anc1.Anc1refChr8 34311 50 - 57822 TCTTTTCACACCAAGGTACAGTGCTAAAATGAATCCTGGATGACACTAGC -s Anc2.Anc2refChr15 83375 50 - 86568 TCTTTTCACACTGAGGTACAGTGCTAAAATGAACCCTGGATGACACTAGC -s mr.mrrefChr5 19153 50 + 294540 TCTTTCCAGACCAAGGTGCAATCATGGGATGAGTCTAGGATGATATTAGC -s simCow_chr6.simCow.chr6 416274 50 - 602619 CCTTTTCACACTGAGGCACAATGCTAAAGTGTAGCTGGGATAACACTAGT -s simDog_chr6.simDog.chr6 126104 50 + 593897 TCTTTTCACACTGGGGTGCAGTGCTAAAATGAACCCTGGATGACATTAGC -s simHuman_chr6.simHuman.chr6 412427 47 - 601863 TCTTTTCACACCAAGGTACAGTGCTAAAATGAATT---GATGACACTCGC -s simRat_chr6.simRat.chr6 153812 50 + 647215 TCCTCCCAGACCAACATGCAATCATGGGATGAGTCCAGGATGATATTAGC - -a -s simMouse_chr6.simMouse.chr6 156209 40 + 636262 AAAGAACAGGATTACTAATTCTCACACCTATACCTAGGTT -s Anc0.Anc0refChr5 77822 40 - 87904 AAGGAACAGGGTCACAACTTTACACACCTATGACTAGGTT -s Anc1.Anc1refChr8 34361 40 - 57822 AAGGAACAGGGTCACAACTTTACACACCTATGACTAGGTT -s Anc2.Anc2refChr15 83425 40 - 86568 AAGAAACAGGGTCACAACTTTACACACCTATGACTAGGTT -s mr.mrrefChr5 19203 40 + 294540 AAAGAACAGGATTACTAATTCTCACACCTATACCTAGGTT -s simCow_chr6.simCow.chr6 416327 40 - 602619 AAGAAACAGGGTCACTAATTTACACACATCTGGCTAGGTT -s simDog_chr6.simDog.chr6 126154 38 + 593897 AAGAACCAGCGTCACAACTTTACACACCTATGACAGTG-- -s simHuman_chr6.simHuman.chr6 412474 28 - 601863 AATGAACAGG------------CACACCTAGGACTAGGTT -s simRat_chr6.simRat.chr6 153862 40 + 647215 AAAGAAATGGATTACTAGTTGACACACCTATACCTAGGTT - -a -s simMouse_chr6.simMouse.chr6 156249 9 + 636262 ACACTTATT -s Anc0.Anc0refChr5 77862 9 - 87904 ACTTATACT -s Anc1.Anc1refChr8 34401 9 - 57822 ACTTATACT -s Anc2.Anc2refChr15 83465 9 - 86568 ACTTATACT -s mr.mrrefChr5 19243 9 + 294540 ACACTTATT -s simCow_chr6.simCow.chr6 416371 9 - 602619 ACTTATACT -s simDog_chr6.simDog.chr6 126192 3 + 593897 ------ATT -s simHuman_chr6.simHuman.chr6 412502 9 - 601863 ACTGGTACT -s simRat_chr6.simRat.chr6 153902 9 + 647215 ACACTTATT - -a -s simMouse_chr6.simMouse.chr6 156258 26 + 636262 AATTTTTGACCATATCAGCTATTCAC -s Anc0.Anc0refChr5 77871 26 - 87904 AACATATAGCCACACCATATATGCAC -s Anc1.Anc1refChr8 34410 26 - 57822 AACATATAGCCACACCATATATGCAC -s Anc2.Anc2refChr15 83474 26 - 86568 AACATATAGCCACACCATCTATGCAC -s mr.mrrefChr5 19252 26 + 294540 AATTTTTGACCATATCATATATTCAC -s simCow_chr6.simCow.chr6 416384 26 - 602619 AACATGCAACCATACCATGTATTCAC -s simDog_chr6.simDog.chr6 126195 26 + 593897 AACACATAGCTACATCATCTGTGCAC -s simHuman_chr6.simHuman.chr6 412511 26 - 601863 AACATATATCCACACCATATATGCAC -s simRat_chr6.simRat.chr6 153911 26 + 647215 AATTTTTGACCATGTCATATATTCTC - -a -s simMouse_chr6.simMouse.chr6 156284 34 + 636262 TGTTTCTCCCGGTCTCACATGTCTAGCTGTACAC -s Anc0.Anc0refChr5 77897 34 - 87904 TGTGTCTCTGAGTCTTACATGTCTGGCTTCACAT -s Anc1.Anc1refChr8 34436 34 - 57822 TGTGTCTCTGAGTCTTACATGTCTGGCTTCACAT -s Anc2.Anc2refChr15 83503 34 - 86568 TGTGGCTCTGAGTCTTACATATCTGTCTTCACAT -s mr.mrrefChr5 19278 34 + 294540 TGTGTCTCCCGGTCTTACATGTCTAGCTGTACAT -s simCow_chr6.simCow.chr6 416413 34 - 602619 CATGGCTCTGAGTCTTACATCTCTGTCTTCACAT -s simDog_chr6.simDog.chr6 126224 34 + 593897 TGTGGCTCCGAGTCTAACATATCTGTCTTCACAT -s simHuman_chr6.simHuman.chr6 412537 34 - 601863 TGTGTTTCTGAGCTGTGCATGTCTGGCTTGACAT -s simRat_chr6.simRat.chr6 153937 34 + 647215 TGTGTCTCCAGGTCATCCAGGTCTAGCTGCACAT - -a -s simMouse_chr6.simMouse.chr6 156318 12 + 636262 TTATAGCTCCTA -s Anc0.Anc0refChr5 77932 3 - 87904 TTG--------- -s Anc1.Anc1refChr8 34471 12 - 57822 TTGTAACTCCTA -s Anc2.Anc2refChr15 83538 3 - 86568 TTG--------- -s mr.mrrefChr5 19312 12 + 294540 TTATAACTCCTA -s simCow_chr6.simCow.chr6 416448 3 - 602619 TTC--------- -s simDog_chr6.simDog.chr6 126259 3 + 593897 TTG--------- -s simHuman_chr6.simHuman.chr6 412572 12 - 601863 TTTTAACTCCTA -s simRat_chr6.simRat.chr6 153971 12 + 647215 TTACAACTCATA - -a -s simMouse_chr6.simMouse.chr6 156330 14 + 636262 CAAAACAAGGGAAG -s Anc1.Anc1refChr8 34483 7 - 57822 CAGAACA------- -s mr.mrrefChr5 19324 7 + 294540 CAAAACA------- -s simHuman_chr6.simHuman.chr6 412586 7 - 601863 CAGAACA------- -s simRat_chr6.simRat.chr6 153983 7 + 647215 CAAAACA------- - -a -s simMouse_chr6.simMouse.chr6 156344 3 + 636262 ACA -s Anc0.Anc0refChr5 77935 2 - 87904 -AG -s Anc1.Anc1refChr8 34490 3 - 57822 AAG -s Anc2.Anc2refChr15 83541 2 - 86568 -AG -s mr.mrrefChr5 19331 3 + 294540 ACA -s simCow_chr6.simCow.chr6 416451 2 - 602619 -AG -s simDog_chr6.simDog.chr6 126262 2 + 593897 -AA -s simHuman_chr6.simHuman.chr6 412594 3 - 601863 AAG -s simRat_chr6.simRat.chr6 153990 3 + 647215 ACA - -a -s simMouse_chr6.simMouse.chr6 156347 69 + 636262 GAAGAAGGTAGGTGTTTACCCACACTTAAGTGGCTAAGTTTTTGTCTAATTGTCTACAGTGCTGTGACA -s Anc0.Anc0refChr5 77937 56 - 87904 GAAGAAGCTGAGAGTTGACTCACACACATGTGGCTAGGTTTTATTTTA---------GGCACTGT---- -s Anc1.Anc1refChr8 34493 56 - 57822 GAAGAAGCTGAGAGTTGACTCACACACATGTGGCTAGGTTTTATTTTA---------GGCACTGT---- -s Anc2.Anc2refChr15 83543 56 - 86568 GAAGAAGCTGAGAGTTGACTCACACACATGTGGCTAGGTTTTATTTTA---------GGCACTGT---- -s mr.mrrefChr5 19334 56 + 294540 GAAGAAGGTGGGTGTTTACCCACACTTAAGTGGCTAAGTTTTTGTCTA---------AGTGCTGT---- -s simCow_chr6.simCow.chr6 416495 56 - 602619 GAAAAAGGTGAAAGTTGATTCGTACACATGTGACTAGGTTTTAATTTA---------GGCAGTGT---- -s simDog_chr6.simDog.chr6 126264 56 + 593897 GAAGAAGCCTAGATTTGACTTACACACACGTGGCTAGGTTTTATCTCA---------AGCACTTT---- -s simHuman_chr6.simHuman.chr6 412597 56 - 601863 GAAGAAGATGAGGGTCAACTCACACCCTTACGGGTGTATTTTCTTTTA---------GGCACTGT---- -s simRat_chr6.simRat.chr6 153993 14 + 647215 TTGGGTGGTGGGTG------------------------------------------------------- - -a -s simMouse_chr6.simMouse.chr6 156416 5 + 636262 TAGTG -s Anc0.Anc0refChr5 77993 5 - 87904 TAACA -s Anc1.Anc1refChr8 34549 5 - 57822 TAACA -s Anc2.Anc2refChr15 83599 5 - 86568 ACACA -s mr.mrrefChr5 19390 5 + 294540 TAGTG -s simCow_chr6.simCow.chr6 416553 5 - 602619 GCACA -s simDog_chr6.simDog.chr6 126320 5 + 593897 ACACA -s simHuman_chr6.simHuman.chr6 412653 5 - 601863 TAACA - -a -s simMouse_chr6.simMouse.chr6 156421 48 + 636262 TGTCCCATGACACTCTCGAGCAGAATTTAAGCATTGATGGGTAAGGGC -s Anc0.Anc0refChr5 77998 47 - 87904 CATTCCCTGAAACTTTCAAGCAGAACGCTAACGCAGATGGGTAGAGG- -s Anc1.Anc1refChr8 34554 47 - 57822 CATTCCCTGAAACTTTCAAGCAGAACGCTAACGCAGATGGGTAGAGG- -s Anc2.Anc2refChr15 83609 47 - 86568 CATTCCCTGGAACTTTTAAGCTGAGTGCTAACGCAGATGGGTAGAGG- -s mr.mrrefChr5 19395 47 + 294540 TGTCCCATGACACTTTCAAGCAGAACTTAAGCATTGATGGGTAGGGG- -s simCow_chr6.simCow.chr6 416563 47 - 602619 TGTTCCCTGGAACTTTTAAGCTGAGTGCTAACACAGATGGGCAGTGG- -s simDog_chr6.simDog.chr6 126330 47 + 593897 CATTCCCTGGTGCTCTTAAGCTAAGTGCTAACGCAGATGGGTAGAGA- -s simHuman_chr6.simHuman.chr6 412658 47 - 601863 CATTCCCTGAAACTTTCAAGCAGAACACTAACCCAGATGGGTAGAGG- -s simRat_chr6.simRat.chr6 154007 39 + 647215 --------GCCACTTCCAAGCAGAACTTAGGCATGGATGGGTAGGGG- - -a -s simMouse_chr6.simMouse.chr6 156469 31 + 636262 TAATCAAGATTGCCTTAACAGCAGTTACAGG -s Anc0.Anc0refChr5 78055 31 - 87904 TAGTCATAAATGCCTTTACATCTGTTATATA -s Anc1.Anc1refChr8 34611 31 - 57822 TAGTCATAAATGCCTTTACATCTGTTATATA -s Anc2.Anc2refChr15 83666 31 - 86568 TAGTCATAAATGCCTATATATCTGTTATATA -s mr.mrrefChr5 19442 31 + 294540 TAATCAAAATTGCCTTAACAGCAGTTATAGA -s simCow_chr6.simCow.chr6 416619 31 - 602619 TAGTCATAAATGGCTATATAACTGTAATAGA -s simDog_chr6.simDog.chr6 126387 31 + 593897 TAGTCATAAATGCCTATATATCTACTATATA -s simHuman_chr6.simHuman.chr6 412715 31 - 601863 TAGTCATAACTGCCTTTACACCTGTTATACA -s simRat_chr6.simRat.chr6 154046 31 + 647215 TAATCAAAATAACCCTAACAGCAGTTATAGA - -a -s simMouse_chr6.simMouse.chr6 156500 80 + 636262 GCTGTTTCTTGTTAGCCTCACTGGAGTTGTACTCATAGGCCAAACACACCCTATCTTGTCCAAAGTGAGGAGAGGTTTAG -s Anc0.Anc0refChr5 78086 71 - 87904 GCTGCTTCTTGCTAGCCTCATTAGAGTTATATTTATAGGGCCAACACA-AATATGT--------GTGATCAGATAATTGG -s Anc1.Anc1refChr8 34642 71 - 57822 GCTGCTTCTTGCTAGCCTCATTAGAGTTATATTTATAGGGCCAACACA-AATATGT--------GTGATCAGATAATTGG -s Anc2.Anc2refChr15 83697 71 - 86568 GCTGCTTCTTGCTAGCCTCATTAGAGCTATATTTATAGGGCCAACACA-AATATGT--------GTGGTCAGATAATAGA -s mr.mrrefChr5 19473 79 + 294540 GCTGTTTCTTGTTAGCCTCATTGGAGTTGTACTTATAGGCCAAACACA-CATATCTTGTCCAAAGTGAGGAGAGGTTTAG -s simCow_chr6.simCow.chr6 416650 53 - 602619 GCTGCTTCTCATTACTCTCA------------------GGCCAACACA-GATGTGT--------GTAGCCAGATAATAGA -s simDog_chr6.simDog.chr6 126425 68 + 593897 GCTGCTTCTTGCAAGCCTCATTAGAGCTATATTTATAGGGCCAACGCA-AA-ATGT--------GTGGT--GATAATAGA -s simHuman_chr6.simHuman.chr6 412746 71 - 601863 GCTGCTTCTTGCTAGCCTCGTTAGAGTTATAGTTATAGGGCCAACACA-AACATGT--------GTGATCAAATAATTGG -s simRat_chr6.simRat.chr6 154077 71 + 647215 GCTGTTTCTTGTTAGCCTCAT--------TAATTATTGGCCAAACATA-CATATCTTGTACAAAGTGAAGTGAGGTTTAG - -a -s simMouse_chr6.simMouse.chr6 156580 23 + 636262 CACTAATCTATTAGTACTAGTGT -s Anc0.Anc0refChr5 78160 23 - 87904 CCCTGCATCTTTAGTACTAGGGT -s Anc1.Anc1refChr8 34716 23 - 57822 CCCTGCATCTTTAGTACTAGGGT -s Anc2.Anc2refChr15 83771 23 - 86568 CCCTGCATCTTCAGTACTAGGGT -s mr.mrrefChr5 19552 23 + 294540 CACTAATCTTTTAGTACTAGTGT -s simCow_chr6.simCow.chr6 416706 23 - 602619 CCATGCTTTTTCAGTACTAGGAT -s simDog_chr6.simDog.chr6 126496 23 + 593897 TCCTGCATCTTCAGTACTAGGGT -s simHuman_chr6.simHuman.chr6 412820 23 - 601863 CCCTGCGTCTTTGATACTAGGGT -s simRat_chr6.simRat.chr6 154148 23 + 647215 CACTCATCTTTCAGTACTAGAGT - -a -s simMouse_chr6.simMouse.chr6 156603 66 + 636262 CTTACACCAGCTGGGCAGTCTATTGCATCCGCGATCTAAATATTATTACTCAGTTAAACTACTAAG -s Anc0.Anc0refChr5 78184 65 - 87904 CCTACACCAGCTAGGCAGCCTACTGCATTCACTAACTTGATGCTATTATTCAATTAATCT-TTTAC -s Anc1.Anc1refChr8 34740 65 - 57822 CCTACACCAGCTAGGCAGCCTACTGCATTCACTAACTTGATGCTATTATTCAATTAATCT-TTTAC -s Anc2.Anc2refChr15 83795 65 - 86568 CCTACACCCGCTAGCCAGCCTGGTGCATTCACAAAATTGACTCTATTATTCAATCAATAT-TCTGC -s mr.mrrefChr5 19575 65 + 294540 CTTACACCAGCTGGGCAGTCTACTGCATCCGCTATCTTGATGCTATTATTCAGTTAAACT-CTAAG -s simCow_chr6.simCow.chr6 416730 56 - 602619 CCTACACCCGATAGCCATCCTGATGCATTCACA---------CCATTATTCAATCAAAAC-ACTGC -s simDog_chr6.simDog.chr6 126520 63 + 593897 CCTCCAT--GCTGGCCAGCCTGGTGCACTCACAAAATTGACTCTATTACTCAGCCAATAT-TCTGC -s simHuman_chr6.simHuman.chr6 412844 65 - 601863 CCTACACCAGGTAGGCAGCCCACTGCATTCACTAACTTGATGCTATTGTTCAATTAAGCT-TTGAC -s simRat_chr6.simRat.chr6 154171 65 + 647215 CTTACACCAGCTGAGTACTCTGCTGCATCCTCTATCTTGATGCTATTATTCAGTTATACT-CTAAT - -a -s simMouse_chr6.simMouse.chr6 156669 41 + 636262 TCTGGGGATTCACCTGTCTTCCACTATCAATATGAAATAGA -s Anc0.Anc0refChr5 78263 39 - 87904 TCTGGGGGTTTGCGTGTCTGCCAGTATCAGTATGAGATA-- -s Anc1.Anc1refChr8 34819 41 - 57822 TCTGGGGGTTTGCGTGTCTGCCAGTATCAGTATGAGATATG -s Anc2.Anc2refChr15 83874 39 - 86568 TCTGGGGGTTTGCGTGTCTGCCAGTATCAGTATGAGACA-- -s mr.mrrefChr5 19640 41 + 294540 TCTGGGGATTCACCTGTCTTCCACTATCAATATGAAATAGA -s simCow_chr6.simCow.chr6 416800 39 - 602619 GCTGGGGGCCCGTGTGTCTGCCAGGGTCAGTGTGAGACA-- -s simDog_chr6.simDog.chr6 126597 39 + 593897 TCTGGGGGTTTACGTATTTGCCAGTATCTATATGAGACA-- -s simHuman_chr6.simHuman.chr6 412923 41 - 601863 TCTGGTAGTTTGCTTGTCTGCCAGTATCAGTATGGGATATG -s simRat_chr6.simRat.chr6 154236 41 + 647215 TCTGGGGATTCACCTGTTTTCCACTATCAATATGAAATAGA - -a -s simMouse_chr6.simMouse.chr6 156710 55 + 636262 CAATTATATTCTGCACATATGCCAGTTTTGAATAGGATTCAAATCCCGCACACAT -s Anc0.Anc0refChr5 78304 44 - 87904 CAATTACA----------ACTCC-GTTTTGGGTAGGATTCAAAACCTGCACACAT -s Anc1.Anc1refChr8 34867 55 - 57822 CAATTACACTCTGCAGACACTCCAGTTTTGGGTAGGATTCAAAACCTGCACACAT -s Anc2.Anc2refChr15 83915 44 - 86568 TAATTTCA----------ACTCC-GTTTTGGGTAGGATTAAAAACCTTCACACAA -s mr.mrrefChr5 19688 55 + 294540 CAATTATATTCTGCACATATGCCAGTTTTGGATAGGATTCAAATCCTGCACACAT -s simCow_chr6.simCow.chr6 416840 44 - 602619 TAATTTCA----------ACTCC-GTTTTGGGTAGGATTAAAAACCTTCACACAA -s simHuman_chr6.simHuman.chr6 412971 55 - 601863 CAATCAGGCTCTGCAGACACTCCAGATTTGGGTAGGATTCAAAACCTGCACACAT -s simRat_chr6.simRat.chr6 154284 55 + 647215 TGACTACATTCTGCACATATCCCAGTTTTGGATAGGATTCAAGTCCTGCACACAC - -a -s simMouse_chr6.simMouse.chr6 156765 16 + 636262 TGCAGTTCTTGTGTGG -s Anc0.Anc0refChr5 78348 15 - 87904 TGCCGTT-TTGTGTAG -s Anc1.Anc1refChr8 34922 15 - 57822 TGCCGTT-TTGTGTAG -s Anc2.Anc2refChr15 83959 15 - 86568 TGCCATT-TTGTGTAG -s mr.mrrefChr5 19743 16 + 294540 TGCAGTTCTTGTGTGG -s simCow_chr6.simCow.chr6 416917 15 - 602619 TGCCATT-TTGTGTAG -s simHuman_chr6.simHuman.chr6 413026 15 - 601863 TGCTGTT-TTGTGTAG -s simRat_chr6.simRat.chr6 154339 16 + 647215 TGCAGTTCTTGTGTGG - -a -s simMouse_chr6.simMouse.chr6 156781 3 + 636262 GGG -s Anc0.Anc0refChr5 78373 3 - 87904 GGG -s Anc1.Anc1refChr8 34947 3 - 57822 GGG -s Anc2.Anc2refChr15 83984 3 - 86568 AGG -s mr.mrrefChr5 19769 3 + 294540 GGG -s simCow_chr6.simCow.chr6 416943 3 - 602619 AGG -s simHuman_chr6.simHuman.chr6 413051 3 - 601863 GGG -s simRat_chr6.simRat.chr6 154366 3 + 647215 GGG - -a -s simMouse_chr6.simMouse.chr6 156784 78 + 636262 GATTGATTGTGTAAGTATTTCTACATAAGTTATCATTGTTGGTTCAGCACCACTAAAGACTCCTCTGTATTAAACTCA -s Anc0.Anc0refChr5 78377 63 - 87904 GATT-AT-----------TTCTAATTTACATATTATT---GTTTCAGCCACAATAAAGACACCTCCAGATGAATATCA -s Anc1.Anc1refChr8 34951 73 - 57822 GATT-ATTGTGTAA-TAGTTCTAATTTACATATTATT---GTTTCAGCCACAATAAAGACACCTCCAGATGAATATCA -s Anc2.Anc2refChr15 83988 63 - 86568 GATT-AT-----------TTATAATTTACTTATTGTC---ATCTCAGCCACAAAAGAGACACCTTCAGATGTGTATCA -s mr.mrrefChr5 19772 78 + 294540 GATTGATTGTGTAAGTATTTCTACATAACATATTATTGTTGGTTCAGCACCAATAAAGACTCCTCCATATGAAACTCA -s simCow_chr6.simCow.chr6 416947 63 - 602619 GATT-AT-----------TTATAATTTACTTATTGTC---ATCTCAGCCACAAAATAGACACCTTCACATGTGAATGA -s simDog_chr6.simDog.chr6 126637 24 + 593897 ------------------------------------------------------AGAGACATCTTCAGATGTGTATCA -s simHuman_chr6.simHuman.chr6 413055 70 - 601863 AATT-ATTGTGTAA-TAGTCCCAAGTTACATATTATT---GTTTCAGGCTCAATAAAGA-ACCTCCAAATGAA--TCA -s simRat_chr6.simRat.chr6 154369 78 + 647215 GATTGATTGTGTATGTATATCTACATAACATATTATTGTTGGTTCAGCACTAATAAAGACTCCTCCATATGAAACTGA - -a -s simMouse_chr6.simMouse.chr6 156862 22 + 636262 TACATAATGTAGTTTTTAACAT -s Anc0.Anc0refChr5 78441 21 - 87904 TCCATGATA-AGTTTTGGGCCT -s Anc1.Anc1refChr8 35025 21 - 57822 TCCATGATA-AGTTTTGGGCCT -s Anc2.Anc2refChr15 84052 21 - 86568 TCCATGATA-AGTTTTGGGCCT -s mr.mrrefChr5 19850 22 + 294540 TACATAATATAGTTTTTAACAT -s simCow_chr6.simCow.chr6 417011 15 - 602619 TCCATGATG-AGTTTC------ -s simDog_chr6.simDog.chr6 126662 21 + 593897 TCCATGATA-CATTTTGGGCCT -s simHuman_chr6.simHuman.chr6 413126 21 - 601863 TCCATGATA-AGTTTTGGGCCT -s simRat_chr6.simRat.chr6 154447 22 + 647215 TATGTAACATGGTTTTTCACAT - -a -s simMouse_chr6.simMouse.chr6 156884 26 + 636262 AGATGTCTTTGTGACAAAGATGTCAT -s Anc0.Anc0refChr5 78462 20 - 87904 ATCTGAAACT------AATATGTCAC -s Anc1.Anc1refChr8 35046 24 - 57822 ATCTGAAACTA--ACCAATATGTCAC -s Anc2.Anc2refChr15 84073 20 - 86568 ATCTGAAACT------AATACATAAC -s mr.mrrefChr5 19872 26 + 294540 AGATGTCTTTGTCACAAAGATGTCAT -s simCow_chr6.simCow.chr6 417026 13 - 602619 -------ACT------AATAGATAAC -s simDog_chr6.simDog.chr6 126684 20 + 593897 ATCTGAAACT------AATACATAAC -s simHuman_chr6.simHuman.chr6 413147 24 - 601863 GCCTGAAACCA--ACCAATATGTCAC -s simRat_chr6.simRat.chr6 154469 26 + 647215 AGATGTTTTTTTCATATAGGTGTCAT - -a -s simMouse_chr6.simMouse.chr6 156910 2 + 636262 CT -s Anc0.Anc0refChr5 78482 2 - 87904 AT -s Anc1.Anc1refChr8 35070 2 - 57822 AT -s Anc2.Anc2refChr15 84093 2 - 86568 AT -s mr.mrrefChr5 19898 2 + 294540 CT -s simCow_chr6.simCow.chr6 417039 2 - 602619 TT -s simDog_chr6.simDog.chr6 126705 2 + 593897 AA -s simHuman_chr6.simHuman.chr6 413171 2 - 601863 AT -s simRat_chr6.simRat.chr6 154495 2 + 647215 CT - -a -s simMouse_chr6.simMouse.chr6 156912 6 + 636262 TTTTCA -s Anc0.Anc0refChr5 78486 6 - 87904 TTTCTT -s Anc1.Anc1refChr8 35074 6 - 57822 TTTCTT -s Anc2.Anc2refChr15 84097 6 - 86568 TTTCTT -s mr.mrrefChr5 19900 6 + 294540 TTTCCA -s simCow_chr6.simCow.chr6 417043 6 - 602619 GTTCTT -s simDog_chr6.simDog.chr6 126709 6 + 593897 TTCTTT -s simHuman_chr6.simHuman.chr6 413175 6 - 601863 TTTCAT -s simRat_chr6.simRat.chr6 154497 6 + 647215 TTTCCA - -a -s simMouse_chr6.simMouse.chr6 156918 69 + 636262 CATAGATGTCTCATACAGATTCAATTCCTGTGATTGGGCTCTTTGTAAAGTAATTAAACATTGAATTTT -s Anc0.Anc0refChr5 78492 69 - 87904 CATGGATGTCTCATGCAGAATCAACCCCTGTGATTGGGCTGTGTGTAAAGTAATAAAAAATTGCATTTT -s Anc1.Anc1refChr8 35080 69 - 57822 CATGGATGTCTCATGCAGAATCAACCCCTGTGATTGGGCTGTGTGTAAAGTAATAAAAAATTGCATTTT -s Anc2.Anc2refChr15 84103 69 - 86568 CAGGGATGTCTCATGCAGAATCAACCCCTGTTATTATGATGGGTGTAAAGTAATAAAAAATTGCATTTA -s mr.mrrefChr5 19906 69 + 294540 CATAGATGTCTCATACAGATTCAATTCCTGTGATTGGGCTCTTTGTAAAGTAATTAAACATTGAATTTT -s simCow_chr6.simCow.chr6 417050 46 - 602619 CAGGGATGTCTCTTGCAGACTCAACCC-----------------------TAACTAAACATTGCATTTG -s simDog_chr6.simDog.chr6 126715 69 + 593897 CAGAGGCATCTCATGCAGAACCAACGCCTGTTATTATGATGGGTGTAAAGTGATAAAAAATTGCATTTA -s simHuman_chr6.simHuman.chr6 413181 69 - 601863 AATGGATGTCTCATGCAGAGTCAACCCCTGTGATTGGGCTTTATGTAGAGTAATCAAAGACCGTATTTT -s simRat_chr6.simRat.chr6 154503 69 + 647215 CATAGATGTCTCATACAGATGCAATTCCTGTGATTGAGCTCTTTATAAAGTAACTAAGCATTGAATTTA - -a -s simMouse_chr6.simMouse.chr6 156987 27 + 636262 TGCTAAAAGTTCTAATTATGACATTCT -s Anc0.Anc0refChr5 78562 27 - 87904 TGCCAAAAGCTTTAATTACAACATTAC -s Anc1.Anc1refChr8 35150 27 - 57822 TGCCAAAAGCTTTAATTACAACATTAC -s Anc2.Anc2refChr15 84173 27 - 86568 TACCAAAAGCTCTAATTACAACATTAC -s mr.mrrefChr5 19975 27 + 294540 TGCCAAAAGTTTTAATTATGACATTAT -s simCow_chr6.simCow.chr6 417097 27 - 602619 TTCCAAAAATTCTGATCACAACATTAC -s simDog_chr6.simDog.chr6 126785 27 + 593897 TACCAAATGCCCTAAATACAACATTAC -s simHuman_chr6.simHuman.chr6 413251 27 - 601863 TGCCAAGAGCTTTAATTACTACATTAC -s simRat_chr6.simRat.chr6 154572 27 + 647215 TGCCAAAAGTTTTAATTATGACATTAT - -a -s simMouse_chr6.simMouse.chr6 157014 12 + 636262 CTAGGTGGGTGA -s Anc0.Anc0refChr5 78590 12 - 87904 CTAAACTGGTGA -s Anc1.Anc1refChr8 35178 12 - 57822 CTAAACTGGTGA -s Anc2.Anc2refChr15 84201 12 - 86568 CCAAACTGGTAA -s mr.mrrefChr5 20002 12 + 294540 CTAGACGGGTGA -s simCow_chr6.simCow.chr6 417125 12 - 602619 CCCCACTTGTTG -s simDog_chr6.simDog.chr6 126813 12 + 593897 GCAAACAGGTAA -s simHuman_chr6.simHuman.chr6 413279 12 - 601863 CTATACTCGTGC -s simRat_chr6.simRat.chr6 154607 12 + 647215 CTAGACGGGTGA - -a -s simMouse_chr6.simMouse.chr6 157026 12 + 636262 CTCTAATCTGTT -s Anc0.Anc0refChr5 78602 12 - 87904 TGTGAATCTGTT -s Anc1.Anc1refChr8 35190 12 - 57822 TGTGAATCTGTT -s Anc2.Anc2refChr15 84213 12 - 86568 TGTGAATCTGTT -s mr.mrrefChr5 20014 12 + 294540 CTCTAATCTGTT -s simCow_chr6.simCow.chr6 417137 12 - 602619 ATTGAATCTGTT -s simDog_chr6.simDog.chr6 126832 12 + 593897 TGTGAATCTGTC -s simHuman_chr6.simHuman.chr6 413291 12 - 601863 TAGGGATCTGTT -s simRat_chr6.simRat.chr6 154619 12 + 647215 CTCTAATTTGTT - -a -s simMouse_chr6.simMouse.chr6 157038 31 + 636262 TCCAAATTACCCATTGCGATTAAAGACTGAG -s Anc0.Anc0refChr5 78614 31 - 87904 ACTCAGGTACCCATGATGATTAAGGGCTGAG -s Anc1.Anc1refChr8 35202 31 - 57822 ACTCAGGTACCCATGATGATTAAGGGCTGAG -s Anc2.Anc2refChr15 84225 31 - 86568 AGTCAGGTACCCATGATGATAAAGGGCTGAG -s mr.mrrefChr5 20026 31 + 294540 TCCAAATTACCCATTGTGATTAAAGACTGAG -s simCow_chr6.simCow.chr6 418301 31 - 602619 GGTGAGGTACCTCTGCTGACAAAGCGCTGAG -s simCow_chr6.simCow.chr6 417149 31 - 602619 AGCCAGGTACCTCTGCTTACAAAGGAATGAG -s simDog_chr6.simDog.chr6 126844 31 + 593897 ATGCAGGTACTCATGATGATCAAGGGCTGAG -s simHuman_chr6.simHuman.chr6 413303 31 - 601863 ACTTGGGTACCCATGATGATTAAGGGCTTAG -s simRat_chr6.simRat.chr6 154631 31 + 647215 TCGAAATTACCCGTTGTGACTAAAGACTGAG - -a -s simMouse_chr6.simMouse.chr6 157069 48 + 636262 GAACTGCATTCATGGATAGAGTCATGTTTTATCTGAGCAGTGCCTATA -s Anc0.Anc0refChr5 78645 48 - 87904 GAACTGCATGCATTGATAGCATCGTGTTTAATCTGAACAGTGACTGTA -s Anc1.Anc1refChr8 35233 48 - 57822 GAACTGCATGCATTGATAGCATCGTGTTTAATCTGAACAGTGACTGTA -s Anc2.Anc2refChr15 84257 48 - 86568 GAACTGCATGCATTGATAGCATCGTGTTCAATCTGAATAGTAAATGCA -s mr.mrrefChr5 20057 48 + 294540 GAACTGCATTCATTGATAGAGTCATGTTTTATCTGAACAGTGACTGTA -s simCow_chr6.simCow.chr6 418333 45 - 602619 GAACTGCATGCATTGTTAGCATCATGTTCAATCTGA---ATACATCCC -s simCow_chr6.simCow.chr6 417181 45 - 602619 GAACTGCATGCATTGATAGCATCATGTTCAATCTGA---GTAATTGCC -s simDog_chr6.simDog.chr6 126876 48 + 593897 GAATTGCATGCATTGGGAGAATTGTGGACAATCTGAATAGTAAATGCA -s simHuman_chr6.simHuman.chr6 413334 48 - 601863 AGACTGCATGCATTTATAGCATCGTGTTTAATCTGAACAGTGACTGTA -s simRat_chr6.simRat.chr6 154662 48 + 647215 GAACTGCATTCATTGATAGAGTCATGTCTCATCTGAACAGTGACTGTA - -a -s simMouse_chr6.simMouse.chr6 157117 4 + 636262 AGTC -s Anc0.Anc0refChr5 78694 4 - 87904 AGGC -s Anc1.Anc1refChr8 35282 4 - 57822 AGGC -s Anc2.Anc2refChr15 84306 4 - 86568 AAGC -s mr.mrrefChr5 20105 4 + 294540 AGTC -s simCow_chr6.simCow.chr6 418379 4 - 602619 AAGC -s simCow_chr6.simCow.chr6 417227 4 - 602619 AAGC -s simDog_chr6.simDog.chr6 126925 4 + 593897 AAGC -s simHuman_chr6.simHuman.chr6 413383 4 - 601863 AGGC -s simRat_chr6.simRat.chr6 154710 4 + 647215 AGTC - -a -s simMouse_chr6.simMouse.chr6 157121 4 + 636262 CTGA -s Anc0.Anc0refChr5 78704 4 - 87904 CTGA -s Anc1.Anc1refChr8 35292 4 - 57822 CTGA -s Anc2.Anc2refChr15 84316 4 - 86568 CTGA -s mr.mrrefChr5 20115 4 + 294540 CTGA -s simCow_chr6.simCow.chr6 418389 4 - 602619 CTGA -s simCow_chr6.simCow.chr6 417237 4 - 602619 CTGA -s simDog_chr6.simDog.chr6 126935 4 + 593897 CTGA -s simHuman_chr6.simHuman.chr6 413393 4 - 601863 CTGA -s simRat_chr6.simRat.chr6 154720 4 + 647215 CTGA - -a -s simMouse_chr6.simMouse.chr6 157125 61 + 636262 AACATATTGGATACTTCATTTTTAAAAACTGTCTTCTCCAGAATTCCAAACTCCAGCATTA -s Anc0.Anc0refChr5 78715 59 - 87904 AACATATAGCATGCTTCATTATCAAAAACTGTTTTTTCCAGCA-CCCAAACTC-AGCATTA -s Anc1.Anc1refChr8 35303 60 - 57822 AACATATAGCATGCTTCATTATCAAAAACTGTTTTTTCCAGCATCCCAAACTC-AGCATTA -s Anc2.Anc2refChr15 84327 59 - 86568 AACATGTAGCATGCTTCATCATCAAAAACTGTTTTTTCCAGCA-CCCTAACTC-AGCATTA -s mr.mrrefChr5 20126 61 + 294540 AACATATTGGATGCTTCATTTTCAAAAACTGTCTTCTCCAGAATTCCAAACTCCAGCATTA -s simCow_chr6.simCow.chr6 418400 59 - 602619 CACATATAGCATGCTTCAGCATCAGAAACCATTTCTTCGAGCA-CCCTAACTC-AGCATTA -s simCow_chr6.simCow.chr6 417248 59 - 602619 AACATGTAGCATGCTTCAGCATCAAATACTGTATTTTCCAGCA-CCCTAACTC-AGCATTA -s simDog_chr6.simDog.chr6 126946 59 + 593897 GACATGTAGCATGCTTCATCATCTAAAACTGTTTTCTCCAACA-CTTTACTTC-TAGATTA -s simHuman_chr6.simHuman.chr6 413404 59 - 601863 AGCATATAGCATGCGTCATTGTCAAAAACTATTTT-TCCAGCATCCCAAACTC-AGTATTG -s simRat_chr6.simRat.chr6 154731 61 + 647215 AACATATTGGATGCTTCATTTTCAAAAACTGTCTTCTCCAGAATTCCGAACTGCAGCATTA - -a -s simMouse_chr6.simMouse.chr6 157186 20 + 636262 CTGGAAGGGCCTTCCCCGAA -s Anc0.Anc0refChr5 78776 19 - 87904 CT-GGAAGGGTCCCCCAGAG -s Anc1.Anc1refChr8 35365 19 - 57822 CT-GGAAGGGTCCCCCAGAG -s Anc2.Anc2refChr15 84388 19 - 86568 CT-GGAAGGGTCCCCCAGAG -s mr.mrrefChr5 20187 19 + 294540 CT-GAAAGGCCCTCCCAGAA -s simCow_chr6.simCow.chr6 418461 19 - 602619 TT-GGAAGGGTCCCCCAGAG -s simCow_chr6.simCow.chr6 417309 2 - 602619 TT------------------ -s simDog_chr6.simDog.chr6 127007 19 + 593897 CT-GGAAGGGTCCACCAAAG -s simHuman_chr6.simHuman.chr6 413465 19 - 601863 CT-GGAAGGGTCCCCCAGAG -s simRat_chr6.simRat.chr6 154792 19 + 647215 CT-GAAAGGCCCTCCCAGAA - -a -s simMouse_chr6.simMouse.chr6 157206 43 + 636262 ATACTGTGATACAATAGGAAATAAAATTAATACTTGGTCACAT -s Anc0.Anc0refChr5 78795 28 - 87904 C-------ACATGAGGGGTTAT--------TACTTGGTCACAT -s Anc1.Anc1refChr8 35384 28 - 57822 C-------ACATGAGGGGTTAT--------TACTTGGTCACAT -s Anc2.Anc2refChr15 84413 28 - 86568 C-------ACATGAGGGGTTAT--------TACTCTGTCACAT -s mr.mrrefChr5 20206 41 + 294540 ATACTGTGATATAATAGGTAATAAA--TAATACTTGGTCACAT -s simCow_chr6.simCow.chr6 418486 28 - 602619 C-------ACATGAGGTGTTAT--------TACTCTGTTACAT -s simDog_chr6.simDog.chr6 127032 28 + 593897 C-------ATATGAGCGGATAT--------TATTCTGTCACAT -s simHuman_chr6.simHuman.chr6 413484 27 - 601863 C-------ACATGAGGGGTTAT--------CACTTG-TCACAT -s simRat_chr6.simRat.chr6 154811 41 + 647215 ATACTATGATATAATAGGTAATGAA--TGATACTTGGTCACGT - -a -s simMouse_chr6.simMouse.chr6 157249 4 + 636262 CCAA -s Anc0.Anc0refChr5 78823 4 - 87904 CCTG -s Anc1.Anc1refChr8 35412 4 - 57822 CCTG -s Anc2.Anc2refChr15 84441 4 - 86568 CATG -s mr.mrrefChr5 20247 4 + 294540 CCAA -s simCow_chr6.simCow.chr6 418514 4 - 602619 CATG -s simDog_chr6.simDog.chr6 127062 4 + 593897 CATG -s simHuman_chr6.simHuman.chr6 413511 4 - 601863 TCTG -s simRat_chr6.simRat.chr6 154852 4 + 647215 CCAA - -a -s simMouse_chr6.simMouse.chr6 157253 52 + 636262 CTGACAATGTATCCACCATATTGAGAAAACTAGCAATAGGTGTGCTCCAGAA -s Anc0.Anc0refChr5 78827 13 - 87904 CTGACAATGTG--CA------------------------------------- -s Anc1.Anc1refChr8 35416 15 - 57822 CTGACAATGTGCACA------------------------------------- -s Anc2.Anc2refChr15 84445 13 - 86568 CTGTCAATGTG--CA------------------------------------- -s mr.mrrefChr5 20251 52 + 294540 CTGACAATGTACACACCATATTGAGAAAACTAGCAATAGGTGTGCTCCAGAA -s simCow_chr6.simCow.chr6 418530 13 - 602619 CTGCCAATGTG--CA------------------------------------- -s simCow_chr6.simCow.chr6 417311 2 - 602619 -------------CA------------------------------------- -s simDog_chr6.simDog.chr6 127066 13 + 593897 CACTCAATGTG--CA------------------------------------- -s simHuman_chr6.simHuman.chr6 413515 15 - 601863 CTGATAATCTGCACA------------------------------------- -s simRat_chr6.simRat.chr6 154856 52 + 647215 CTGACATTGTACACATCAAATCAACAGAACTAGCAATAGTGGTGCTCCAGAA - -a -s simMouse_chr6.simMouse.chr6 157305 45 + 636262 CAGATAAAGTGCAAACTATACCTGCGTCAAAACAAATAATGTGGG -s Anc0.Anc0refChr5 78840 30 - 87904 -------------GACCATACCAGTGTCGAAAATGGCAAGA--GA -s Anc1.Anc1refChr8 35431 30 - 57822 -------------GACCATACCAGTGTCGAAAATGGCAAGA--GA -s Anc2.Anc2refChr15 84458 30 - 86568 -------------GACCATACTAGTGTCGAAAATGGCAAGA--GA -s mr.mrrefChr5 20303 45 + 294540 CAGATAAAGTGCAAACCATACCTGCGTCAAAACAAATAAGGTGGG -s simCow_chr6.simCow.chr6 418543 30 - 602619 -------------GATCATGCTAGTCTTGAAAATGGCAAGA--GA -s simCow_chr6.simCow.chr6 417313 30 - 602619 -------------GATCATGCTAGTCTTGAAAATGGCAAGA--GA -s simDog_chr6.simDog.chr6 127079 30 + 593897 -------------GACAATACTCGTGTCAAAAATGGCAAGT--GA -s simHuman_chr6.simHuman.chr6 413530 30 - 601863 -------------GACCATACCAGTGTCGAAAATGGCAAGA--GT -s simMouse_chr6.simMouse.chr6 157460 45 + 636262 CAGATAAAGTGCAAACCATACCTGCGTCAAAACAAATAAGGTGGG -s simRat_chr6.simRat.chr6 154908 45 + 647215 CAGATAAAGTGCAGACCATACCTGCTTCAGGACTAACAAGGGGGG - -a -s simMouse_chr6.simMouse.chr6 157350 52 + 636262 CTAACTCTGGAATAGATATCTCACTAACCCTTATTATAAGAGGATGTAGTGT -s Anc0.Anc0refChr5 78870 39 - 87904 CTAACT----------TATCTCACTAACCCTTAT---ACAAAGATGCAGACT -s Anc1.Anc1refChr8 35461 49 - 57822 CTAACTCTCGAACAAATATCTCACTAACCCTTAT---ACAAAGATGCAGACT -s Anc2.Anc2refChr15 84494 39 - 86568 CTAACT----------TATCTCACTAACCCTTAT---ACAGAGATGCAGACT -s mr.mrrefChr5 20348 52 + 294540 CTAACTCTGGAATAGATATCTCACTAACCCTTATTATAAGAGGATGTAGTGT -s simCow_chr6.simCow.chr6 418579 39 - 602619 CTAACT----------TATTTCACTAGCTGTTAT---ACAGGGATGCAGAAT -s simCow_chr6.simCow.chr6 417349 39 - 602619 CTAACT----------TATCTTACTAGCTCTTAA---ACAGAGATGCAGACT -s simDog_chr6.simDog.chr6 127115 39 + 593897 CTAACT----------TATCTCACTAAGCCTTAT---ACATAGATGCAGACT -s simHuman_chr6.simHuman.chr6 413560 49 - 601863 CCCCCACTCGAACAAATATCTCACTAACCCTCAT---ACAAAGATGCAGGCT -s simMouse_chr6.simMouse.chr6 157505 52 + 636262 CTAACTCTGGAATAGATATCTCACTAACCCTTATTATAAGAGGATGTAGTGT -s simRat_chr6.simRat.chr6 154953 52 + 647215 CTAACTTTGGAATAGATATTTCACTAACCCTTATTATATGAAGGTGTAGTGT - -a -s simMouse_chr6.simMouse.chr6 157402 37 + 636262 TTTCTTTTAATACCAGATGAGTTCTGTATCTGCCTAG -s Anc0.Anc0refChr5 78909 37 - 87904 TTCCATCTAGGACCAGTTGAATTCTGTGAATGCCCAT -s Anc1.Anc1refChr8 35510 37 - 57822 TTCCATCTAGGACCAGTTGAATTCTGTGAATGCCCAT -s Anc2.Anc2refChr15 84533 37 - 86568 CTCCATCTAGGACCAGTCAAATTCTGTGAATGCCCAT -s mr.mrrefChr5 20400 37 + 294540 TTTCTTTTAATACCAGATGAGTTCTGTATCTGCCTAG -s simCow_chr6.simCow.chr6 418618 37 - 602619 CTCCATCAAGGCCCAGTCAAATTCAGTGAATGTATAT -s simCow_chr6.simCow.chr6 417388 37 - 602619 CTCCATCAAAGACCAGTCAAATTCTGTGAATGACCAT -s simDog_chr6.simDog.chr6 127154 37 + 593897 CTTCATCTAGGACCAGCCAAATTGTGTGAATGCCCAT -s simHuman_chr6.simHuman.chr6 413629 37 - 601863 TTCCCTCTAGGACCAGTTGGATTTAGTTAATGCCCAC -s simMouse_chr6.simMouse.chr6 157557 37 + 636262 TTTCTTTTAATACCAGATGAGTTCTGTATCTGCCTAG -s simRat_chr6.simRat.chr6 155005 37 + 647215 TTTCTTTCAAAACCAGATGAGTTCTGTGTCTGCCTAC - -a -s simMouse_chr6.simMouse.chr6 157439 14 + 636262 TCCCTTTCCTTTCT -s Anc0.Anc0refChr5 78947 14 - 87904 TTTTTTTGCTTTCT -s Anc1.Anc1refChr8 35548 14 - 57822 TTTTTTTGCTTTCT -s Anc2.Anc2refChr15 84571 14 - 86568 TTTTTTTGCTTTCT -s mr.mrrefChr5 20437 14 + 294540 TCCCTTTCCTTTCT -s simCow_chr6.simCow.chr6 418656 14 - 602619 TTTTTTTGCTTTGT -s simCow_chr6.simCow.chr6 417426 14 - 602619 TTTTTTTGCTTTGT -s simDog_chr6.simDog.chr6 127192 14 + 593897 TTCTTTTGCTTTCT -s simHuman_chr6.simHuman.chr6 413667 14 - 601863 TTTATTTGCTACCT -s simMouse_chr6.simMouse.chr6 157594 11 + 636262 TCCCTT---TTTCT -s simRat_chr6.simRat.chr6 155042 10 + 647215 -CCTTT---TTTCT - -a -s simMouse_chr6.simMouse.chr6 157453 7 + 636262 GCCCAAA -s Anc0.Anc0refChr5 78961 7 - 87904 GCCCCCA -s Anc1.Anc1refChr8 35562 7 - 57822 GCCCCCA -s Anc2.Anc2refChr15 84585 7 - 86568 AGACCCA -s mr.mrrefChr5 20451 7 + 294540 GCCCACA -s simCow_chr6.simCow.chr6 418670 5 - 602619 C--CACA -s simCow_chr6.simCow.chr6 417440 5 - 602619 A--CACA -s simDog_chr6.simDog.chr6 127206 7 + 593897 AGACCCA -s simHuman_chr6.simHuman.chr6 413681 7 - 601863 GCCCCCA -s simMouse_chr6.simMouse.chr6 157605 7 + 636262 GCCCTCA -s simRat_chr6.simRat.chr6 155056 7 + 647215 ACCCATG - -a -s simMouse_chr6.simMouse.chr6 157612 15 + 636262 GGGCCCTCACCCATT -s Anc0.Anc0refChr5 78968 15 - 87904 TGGCCCCCAGCTATT -s Anc1.Anc1refChr8 35569 15 - 57822 TGGCCCCCAGCTATT -s Anc2.Anc2refChr15 84592 15 - 86568 TGGCTCCCAGCTGTT -s mr.mrrefChr5 20458 15 + 294540 GGGCCCCCAGCTATT -s simCow_chr6.simCow.chr6 418675 15 - 602619 TGGCTCCCAGTTGAT -s simCow_chr6.simCow.chr6 417445 15 - 602619 TCACTCCCAGTTGAT -s simDog_chr6.simDog.chr6 127213 15 + 593897 TTGCTCCTAGCTGTT -s simHuman_chr6.simHuman.chr6 413688 15 - 601863 TGGTCTCCAGCTATT -s simRat_chr6.simRat.chr6 155063 15 + 647215 GGGCCACCTGCTGTT - -a -s simMouse_chr6.simMouse.chr6 157627 14 + 636262 AGACACCCAACACC -s Anc0.Anc0refChr5 78983 9 - 87904 ATATACCTG----- -s Anc1.Anc1refChr8 35584 9 - 57822 ATATACCTG----- -s Anc2.Anc2refChr15 84607 9 - 86568 ATATACCTG----- -s mr.mrrefChr5 20473 9 + 294540 AGATACCCG----- -s simCow_chr6.simCow.chr6 418711 9 - 602619 ATATGCCTG----- -s simCow_chr6.simCow.chr6 417460 9 - 602619 ATATGCCTG----- -s simDog_chr6.simDog.chr6 127228 9 + 593897 ACATACCTG----- -s simHuman_chr6.simHuman.chr6 413703 7 - 601863 ATACAC--G----- -s simRat_chr6.simRat.chr6 155078 9 + 647215 GTATGCCCG----- - -a -s simMouse_chr6.simMouse.chr6 157641 43 + 636262 AAAACTACTTGGTAGCAGTAGGTAGGGATTGCGAGTACCACTA -s Anc0.Anc0refChr1 4630 43 + 62388 AGAATTACTTAGTGGTGGTAAGTGGAGATTGTGAATATCATGG -s Anc1.Anc1refChr2 5068 43 - 144309 AGAATTACTTAGTGGTGGTAAGTGGAGATTGTGAATATCATGG -s Anc2.Anc2refChr3 5122 43 - 53186 AGAATTACTTAGGGGTGGTAAGTGGAGATTGTGAATATCATGG -s mr.mrrefChr5 20569 43 + 294540 AAAACTACTTAGTGGTAGTAGGTAGGGATTGTGAGTACCATGA -s simCow_chr6.simCow.chr6 425850 39 - 602619 G----TACTTACAGGTGGTAAGGGGAGATTGTGAGCACCATGG -s simDog_chr6.simDog.chr6 133787 37 + 593897 AGAAT-----AGGGGTGGTAGGTGGAGAT-GTCAATATCATGG -s simHuman_chr6.simHuman.chr6 427393 43 - 601863 TGAATTACTTAGTGGTGGTAAGTGGAGATTGTGAATATCATGG -s simRat_chr6.simRat.chr6 155174 43 + 647215 AAAACTACTTAGTGGTAGTATGTAGGGATTGTGAGTACCATGA - -a -s simMouse_chr6.simMouse.chr6 157684 16 + 636262 TCCACCCACAAAACCA -s Anc0.Anc0refChr1 4673 15 + 62388 CCA-CCCACAAAACAG -s Anc1.Anc1refChr2 5111 15 - 144309 CCA-CCCACAAAACAG -s Anc2.Anc2refChr3 5165 15 - 53186 CCA-TCCACAAAACAG -s mr.mrrefChr5 20612 15 + 294540 TCC-CCCACAAAACCA -s simCow_chr6.simCow.chr6 425890 15 - 602619 CCC-TCCACAAGACAG -s simDog_chr6.simDog.chr6 133824 15 + 593897 TCA-TCCACAAAACAG -s simHuman_chr6.simHuman.chr6 427436 12 - 601863 ----CCCACAAAACAG -s simRat_chr6.simRat.chr6 155217 15 + 647215 TTC-CCCACAAAACCA - -a -s simMouse_chr6.simMouse.chr6 157700 65 + 636262 ACCATTGTGGATATAATTGTGGATATAATTTGGGAATTGATAAGCTTGGTGGTCTGGGGTTGTGA -s Anc0.Anc0refChr1 4693 48 + 62388 CT-----------------TGAAGATAATTTTGGAATTGATAAGCTTGGTGTTTTGGGATTTTGA -s Anc1.Anc1refChr2 5131 48 - 144309 CT-----------------TGAAGATAATTTTGGAATTGATAAGCTTGGTGTTTTGGGATTTTGA -s Anc2.Anc2refChr3 5185 48 - 53186 CT-----------------TGAAGATAATTTTGGAATTAATAACCTTGGTGTTTTGAGATCTTGC -s mr.mrrefChr5 20627 48 + 294540 CT-----------------TGGAGATAATTTTGGAATTGATAAGCTTGGTGGTCTGGGGTTGTGA -s simCow_chr6.simCow.chr6 425908 48 - 602619 CT-----------------TGTAGATAATGTTGGAATTAATAACCTTGGAGTTTTCACAGCTTGT -s simDog_chr6.simDog.chr6 133844 48 + 593897 CT-----------------TGAAGATAATTTTGGAATTAATAACCTTAGTATTTTGAGATCTTGC -s simHuman_chr6.simHuman.chr6 427453 48 - 601863 CT-----------------TGAAGATCATTTTGGAATTGATAAGCTTGGTGTTTTGGGATTATGA -s simRat_chr6.simRat.chr6 155232 48 + 647215 CT-----------------TGGAGATGGTTTTGGGATAGCTAAGTTTAGTGGTCTGGTGTTGCGA - -a -s simMouse_chr6.simMouse.chr6 157765 3 + 636262 GAT -s Anc0.Anc0refChr1 4742 3 + 62388 GGT -s Anc1.Anc1refChr2 5180 3 - 144309 GGT -s Anc2.Anc2refChr3 5234 3 - 53186 GGT -s mr.mrrefChr5 20675 3 + 294540 GAT -s simCow_chr6.simCow.chr6 425957 3 - 602619 GGT -s simDog_chr6.simDog.chr6 133893 3 + 593897 GGT -s simHuman_chr6.simHuman.chr6 427502 3 - 601863 GGT -s simRat_chr6.simRat.chr6 155280 3 + 647215 GAT - -a -s simMouse_chr6.simMouse.chr6 157768 19 + 636262 CTACTAAAGAGGAATTACT -s Anc0.Anc0refChr1 4751 17 + 62388 CTATTAGAGA--AATCACT -s Anc1.Anc1refChr2 5189 19 - 144309 CTATTAGAGAGAAATCACT -s Anc2.Anc2refChr3 5243 17 - 53186 CTATTAGAGA--AACCACT -s mr.mrrefChr5 20678 19 + 294540 CTACTAAAGAGGAATTACT -s simCow_chr6.simCow.chr6 425966 17 - 602619 CTATTAGGAA--AACCACT -s simDog_chr6.simDog.chr6 133902 17 + 593897 CTATTAAAGA--AACCGCT -s simHuman_chr6.simHuman.chr6 427511 19 - 601863 CTATTAGAGAGAACTCACT -s simRat_chr6.simRat.chr6 155283 19 + 647215 CTACTAAGGATGAATTACT - -a -s simMouse_chr6.simMouse.chr6 157787 5 + 636262 CCTGT -s Anc0.Anc0refChr1 4771 5 + 62388 TTTGT -s Anc1.Anc1refChr2 5211 5 - 144309 TTTGT -s Anc2.Anc2refChr3 5263 5 - 53186 TTTGT -s mr.mrrefChr5 20700 5 + 294540 CCTGT -s simCow_chr6.simCow.chr6 425986 5 - 602619 ATTGT -s simDog_chr6.simDog.chr6 133922 5 + 593897 TTTGT -s simHuman_chr6.simHuman.chr6 427533 5 - 601863 TTTGT -s simRat_chr6.simRat.chr6 155305 5 + 647215 CCTTT - -a -s simMouse_chr6.simMouse.chr6 157792 23 + 636262 AGAGAAAGCCCTAGTAATCCTGA -s Anc0.Anc0refChr1 4776 17 + 62388 AGAGAAAG------TAATCCTGG -s Anc1.Anc1refChr2 5216 17 - 144309 AGAGAAAG------TAATCCTGG -s Anc2.Anc2refChr3 5268 17 - 53186 AGAGAAAG------TAATCCTGG -s mr.mrrefChr5 20705 23 + 294540 AGAGAAAGCCCTAGTAATCCTGG -s simCow_chr6.simCow.chr6 425991 16 - 602619 AGAGAAAG------AAA-CTTGG -s simDog_chr6.simDog.chr6 133930 17 + 593897 AGAGTAAG------TAATCCTGG -s simHuman_chr6.simHuman.chr6 427538 17 - 601863 AGAGAAAG------TAGTCCTGG -s simRat_chr6.simRat.chr6 155310 23 + 647215 AGAGAAAGCCCTAGTTATCCTGG - -a -s simMouse_chr6.simMouse.chr6 157815 50 + 636262 ATTGTTTTCTGGGGCTTGGAGAAGTACTTCTCTCTGCCATGTCCTTACTC -s Anc0.Anc0refChr1 4794 50 + 62388 ATTGTTTTCTGGGGCTTGGAGGGGTACTTCTCTCTGCCATGTTCTTACTA -s Anc1.Anc1refChr2 5234 50 - 144309 ATTGTTTTCTGGGGCTTGGAGGGGTACTTCTCTCTGCCATGTTCTTACTA -s Anc2.Anc2refChr3 5286 50 - 53186 ATTGTTTTCAGGGGCTTGGGGGGGTACTTCTCTTTGCCATATTCTTACTA -s mr.mrrefChr5 20728 50 + 294540 ATTGTTTTCTGGGGCTTGGAGAGGTACTTCTCTCTGCCATGTCCTTACTC -s simCow_chr6.simCow.chr6 426008 50 - 602619 ATTGTTTTGGGGGGCTTGTGGGGGTACTCGTCTATGCCATATTCTGATTA -s simDog_chr6.simDog.chr6 133948 50 + 593897 GTTGTTTTCAGGGGCATGGGGGGGTACTTCTCTTTGCCACATTCTTGCTA -s simHuman_chr6.simHuman.chr6 427556 50 - 601863 ACTGTTTTCTGGGGCTTGGAGCGGTTCTGCTCTCTGCCATGTTCTTAATA -s simRat_chr6.simRat.chr6 155333 50 + 647215 ATTGTTTTCTGGGGCTTGGGGAGGCATTTCTCTCTGCCATGTCCTTATTC - -a -s simMouse_chr6.simMouse.chr6 157865 43 + 636262 TAGAGCTTGATGGACAGTTTGTGACACCAGGTTGTGATAAGCT -s Anc0.Anc0refChr1 4844 43 + 62388 TAGAACTTGATAGACAATTTGTAACACCAGATTGAAATAAGCC -s Anc1.Anc1refChr2 5284 43 - 144309 TAGAACTTGATAGACAATTTGTAACACCAGATTGAAATAAGCC -s Anc2.Anc2refChr3 5336 43 - 53186 TAGAACTTGATAGACAATTTGTAACACCAAATTGAAATAAGCC -s mr.mrrefChr5 20778 43 + 294540 TAGAGCTTGATGGACAATTTGTGACACCAGGTTGTGATAAGCC -s simCow_chr6.simCow.chr6 426058 43 - 602619 TAGAACTTGATAGAAAATTAGTAACACCAAATTGAAATAAGTC -s simDog_chr6.simDog.chr6 133998 43 + 593897 TAGAATTTAACAGACAATTTCTGATACCAAATTGAAGTAAGCT -s simHuman_chr6.simHuman.chr6 427606 42 - 601863 TAGACCTTGATAGACGATTTGTAACACCAG-CTGGAATAAGCC -s simRat_chr6.simRat.chr6 155393 41 + 647215 TAGAGCTTGATGGA--ATTTGTGGCACTGGGTTGAGATAAGCC - -a -s simMouse_chr6.simMouse.chr6 157908 37 + 636262 TTTGGGAATTTGCAATGCAATCTACACCTTGCATGTG -s Anc0.Anc0refChr1 4893 27 + 62388 CTTGGGAATTT----------CTGCCCTATGTGAGTG -s Anc1.Anc1refChr2 5333 27 - 144309 CTTGGGAATTT----------CTGCCCTATGTGAGTG -s Anc2.Anc2refChr3 5387 27 - 53186 CTTGGGAATTT----------GTGCCCTATGTGAGAG -s mr.mrrefChr5 20827 37 + 294540 TTTGGGAATTTGCAATGCAATCTACACCTTGTATGTG -s simCow_chr6.simCow.chr6 426109 27 - 602619 CTTGGGAATTT----------GTGCCCTCTGTGCGAA -s simDog_chr6.simDog.chr6 134049 26 + 593897 TTTGGGAAGTT----------GTGCCC-ATGTGAGAG -s simHuman_chr6.simHuman.chr6 427654 27 - 601863 CTTGTGAATTT----------CTGCCTTATGTGGGTT -s simRat_chr6.simRat.chr6 155442 37 + 647215 TTTGGGAATTTGCAACACAATTATCGCCTTGTATGTG - -a -s simMouse_chr6.simMouse.chr6 157945 12 + 636262 AATCCAGAAGCT -s Anc0.Anc0refChr1 4920 9 + 62388 AGTTG---AAGT -s Anc1.Anc1refChr2 5360 12 - 144309 AGTTGATAAAGT -s Anc2.Anc2refChr3 5414 9 - 53186 TGCTG---AAGC -s mr.mrrefChr5 20864 12 + 294540 AATCCAGAAGCT -s simCow_chr6.simCow.chr6 426138 9 - 602619 TGTTG---GAGC -s simDog_chr6.simDog.chr6 134075 9 + 593897 TGCTG---AAGC -s simHuman_chr6.simHuman.chr6 427681 12 - 601863 ATTTGACAAAAT -s simRat_chr6.simRat.chr6 155479 12 + 647215 AAACCAGAAGCT - -a -s simMouse_chr6.simMouse.chr6 157957 35 + 636262 TAAGGGCTTCAGGATACCACATTAAGCTATATAGA -s Anc0.Anc0refChr1 4929 34 + 62388 TAAGGACCTCAGGGGCTCCCCTT-AGCCACAGAGA -s Anc1.Anc1refChr2 5372 35 - 144309 TAAGGACCTCAGGGGCTCCCCTTTAGCCACAGAGA -s Anc2.Anc2refChr3 5423 34 - 53186 ATAGAACCTTAGGGGCTCCCCTT-AGCCACAAGGG -s mr.mrrefChr5 20876 35 + 294540 TAAGGGCTTCAGGATACCACATTTAGCTATAGAGA -s simCow_chr6.simCow.chr6 426147 32 - 602619 A--GAACCTTAGTGGCTCCCCTT-TGCCCCCAGAG -s simDog_chr6.simDog.chr6 134084 25 + 593897 ATA-------AGGGGTT--CTTT-AGCTACAAGGG -s simHuman_chr6.simHuman.chr6 427694 35 - 601863 TATGGACAGCAGGGGCTCCCCTTTAGCCACAGAGA -s simRat_chr6.simRat.chr6 155491 35 + 647215 TAAGGGCTTCAGGATACCACATTTAGCGATAGAGA - -a -s simMouse_chr6.simMouse.chr6 157992 16 + 636262 ATTATTGATTGTTATT -s Anc0.Anc0refChr1 4963 16 + 62388 GTTGTTGAATGTTCCT -s Anc1.Anc1refChr2 5407 16 - 144309 GTTGTTGAATGTTCCT -s Anc2.Anc2refChr3 5457 16 - 53186 GTTGTTGAATCTTCCT -s mr.mrrefChr5 20911 16 + 294540 ATTATTGATTGTTATT -s simCow_chr6.simCow.chr6 426180 16 - 602619 GTTGTTGAATTTTCCT -s simDog_chr6.simDog.chr6 134109 16 + 593897 CTTGTTGAATCTTCAC -s simHuman_chr6.simHuman.chr6 427729 16 - 601863 GTTGTTAAATGTTCCT -s simRat_chr6.simRat.chr6 155526 16 + 647215 ATCATTGATTGTCATT - -a -s simMouse_chr6.simMouse.chr6 158008 15 + 636262 CTTGTTTTGGTTCCT -s Anc0.Anc0refChr1 4983 14 + 62388 -TTGCTTCGGTTCCT -s Anc1.Anc1refChr2 5427 15 - 144309 CTTGCTTCGGTTCCT -s Anc2.Anc2refChr3 5477 14 - 53186 -GTGCTTCAGTTCGT -s mr.mrrefChr5 20927 15 + 294540 CTTGTTTTGGTTCCT -s simCow_chr6.simCow.chr6 426217 14 - 602619 -GTGCTTCAGTTTGT -s simDog_chr6.simDog.chr6 134129 14 + 593897 -GTGCTTCAGTTCGT -s simHuman_chr6.simHuman.chr6 427749 15 - 601863 CTTGCTACGGTTCCT -s simRat_chr6.simRat.chr6 155542 15 + 647215 CTTGTTTTGGTTCCT - -a -s simMouse_chr6.simMouse.chr6 158023 3 + 636262 ATG -s Anc0.Anc0refChr1 5100 3 + 62388 ATG -s Anc1.Anc1refChr2 5545 3 - 144309 ATG -s Anc2.Anc2refChr3 5604 3 - 53186 ATG -s mr.mrrefChr5 20942 3 + 294540 ATG -s simCow_chr6.simCow.chr6 426343 3 - 602619 ACA -s simDog_chr6.simDog.chr6 134256 3 + 593897 ATG -s simHuman_chr6.simHuman.chr6 427869 3 - 601863 ATG -s simRat_chr6.simRat.chr6 155557 3 + 647215 ATG - -a -s simMouse_chr6.simMouse.chr6 158026 21 + 636262 AACTGTGAGTCTCATAGCTGA -s Anc0.Anc0refChr1 5105 21 + 62388 AGCCCTGGAATTCATAACTAA -s Anc1.Anc1refChr2 5550 21 - 144309 AGCCCTGGAATTCATAACTAA -s Anc2.Anc2refChr3 5609 21 - 53186 AGCCCTGGAATTCATGACCAA -s mr.mrrefChr5 20945 21 + 294540 AACCGTGAGTCTCATAGCTGA -s simCow_chr6.simCow.chr6 426348 21 - 602619 AGCCCTGGAATTCATGCCCAA -s simDog_chr6.simDog.chr6 134260 21 + 593897 AGCTCTGGAATACAAGACCAA -s simHuman_chr6.simHuman.chr6 427875 21 - 601863 AGCCCTGGAATTCATAAATAG -s simRat_chr6.simRat.chr6 155560 21 + 647215 AACCGTGAGTCTCATAGTTGA - -a -s simMouse_chr6.simMouse.chr6 158047 75 + 636262 CAAAAGTATCGTCACTACTCAGAGGAAAAATCAAATCTCCATTGCACCCAACTTGCCAAATCATGTGTATGATTC -s Anc0.Anc0refChr1 5128 75 + 62388 CAAAAGTATCACCACTATTCACAAGACTAATCAAAATTCCATGACACCCAACTTGCCCAATGATGTGTATGAATA -s Anc1.Anc1refChr2 5573 75 - 144309 CAAAAGTATCACCACTATTCACAAGACTAATCAAAATTCCATGACACCCAACTTGCCCAATGATGTGTATGAATA -s Anc2.Anc2refChr3 5632 75 - 53186 CAAAAGTATCACTGCTATTCACAAGACTAACCAAAATATCATGACACCCAACTGGCCCAATGGTGTTTATGAATA -s mr.mrrefChr5 20968 75 + 294540 CAAAAGTATCGTCACTATTCAGAGGAAAAATCAAAACTCCATTGCACCCAACTTGCCCAATCATGTGTATGAATC -s simCow_chr6.simCow.chr6 426371 69 - 602619 CAAAAGTATCACTGCTAATCACAAGACTAACCAAACTATTAT------CAACTGGGCCAACGTTGTTTATGAATA -s simDog_chr6.simDog.chr6 134283 64 + 593897 CAAAA----CACTGCTATTCACAAGACTAACTAGAATATCATGACACCCAACTGACCCAATGGTGT-------TA -s simHuman_chr6.simHuman.chr6 427898 75 - 601863 CAAAAGTATCACCACTATTCACAAGATTAATCAAAATTCCTTGACACCATACTTGCCCAATGATGTGTCTGAATA -s simRat_chr6.simRat.chr6 155583 75 + 647215 CAAAAGCATTGTCACTGTTCAGAGGACAAATCAAAACTCCATTGCACGCAATGTGGCCAATCATGTGTATGAATC - -a -s simMouse_chr6.simMouse.chr6 158122 8 + 636262 CCCACTTA -s Anc0.Anc0refChr1 5203 8 + 62388 CCCACTTG -s Anc1.Anc1refChr2 5648 8 - 144309 CCCACTTG -s Anc2.Anc2refChr3 5707 8 - 53186 CCCACTTG -s mr.mrrefChr5 21043 8 + 294540 CCCACTTG -s simCow_chr6.simCow.chr6 426440 8 - 602619 CCAACTTG -s simDog_chr6.simDog.chr6 134348 8 + 593897 CCCACTTG -s simHuman_chr6.simHuman.chr6 427973 8 - 601863 CCCACTTG -s simRat_chr6.simRat.chr6 155658 8 + 647215 CCCACTTG - -a -s simMouse_chr6.simMouse.chr6 158130 31 + 636262 GGTTCAAGTTCCAGTAAGTTGTATTATGAGA -s Anc0.Anc0refChr1 5211 27 + 62388 GGTTAAAGTA----TGGGTTGCATAATGAGA -s Anc1.Anc1refChr2 5656 27 - 144309 GGTTAAAGTA----TGGGTTGCATAATGAGA -s Anc2.Anc2refChr3 5716 27 - 53186 GGTTAAAGTA----TGGGTTGCATAATGAGA -s mr.mrrefChr5 21051 31 + 294540 GGTTCAAGTACCAGTAAGTTGCATTATGAGA -s simCow_chr6.simCow.chr6 426449 26 - 602619 GGTCAAGGTA----TGGGTTGCA-ATTGAGA -s simDog_chr6.simDog.chr6 134357 27 + 593897 GGCTAAAGTA----CGGGTTGCATAATGAGA -s simHuman_chr6.simHuman.chr6 427981 27 - 601863 GGTTAAAGTA----TGGGTTGCATAGTGAGA -s simRat_chr6.simRat.chr6 155666 31 + 647215 GGTTTATGTAACAGTAAGTTGCATGAAGAGA - -a -s simMouse_chr6.simMouse.chr6 158161 5 + 636262 CCAGG -s Anc0.Anc0refChr1 5246 5 + 62388 CCTGG -s Anc1.Anc1refChr2 5691 5 - 144309 CCTGG -s Anc2.Anc2refChr3 5751 5 - 53186 CCTGG -s mr.mrrefChr5 21082 5 + 294540 CCAGG -s simCow_chr6.simCow.chr6 426490 5 - 602619 CCTGG -s simDog_chr6.simDog.chr6 134391 5 + 593897 CCCAG -s simHuman_chr6.simHuman.chr6 428016 5 - 601863 CCTGG -s simRat_chr6.simRat.chr6 155697 5 + 647215 CCAGG - -a -s simMouse_chr6.simMouse.chr6 158166 10 + 636262 TGCCCCATCT -s Anc0.Anc0refChr1 5251 10 + 62388 TTCTATAGTT -s Anc1.Anc1refChr2 5696 10 - 144309 TTCTATAGTT -s Anc2.Anc2refChr3 5756 10 - 53186 TTCTATAGTT -s mr.mrrefChr5 21087 10 + 294540 TGCCCCATCT -s simCow_chr6.simCow.chr6 426496 10 - 602619 TTCTATAGTT -s simDog_chr6.simDog.chr6 134396 10 + 593897 GTAAATAGTT -s simHuman_chr6.simHuman.chr6 428021 10 - 601863 TACTATGGTT -s simRat_chr6.simRat.chr6 155702 10 + 647215 TGCGCCATCT - -a -s simMouse_chr6.simMouse.chr6 158176 8 + 636262 GGGTCTAT -s Anc0.Anc0refChr1 5261 8 + 62388 GTGACTGT -s Anc1.Anc1refChr2 5706 8 - 144309 GTGACTGT -s Anc2.Anc2refChr3 5766 8 - 53186 GTAACAGT -s mr.mrrefChr5 21097 8 + 294540 GGGTCTAT -s simCow_chr6.simCow.chr6 426506 8 - 602619 GTAACAAT -s simDog_chr6.simDog.chr6 134406 8 + 593897 ATAACAGT -s simHuman_chr6.simHuman.chr6 428031 8 - 601863 GTGACTGT -s simRat_chr6.simRat.chr6 155714 8 + 647215 GGGTCTAT - -a -s simMouse_chr6.simMouse.chr6 158184 16 + 636262 CTAACCATGTATGATG -s Anc0.Anc0refChr1 5280 16 + 62388 CCAAGCTTTTATGATA -s Anc1.Anc1refChr2 5725 16 - 144309 CCAAGCTTTTATGATA -s Anc2.Anc2refChr3 5785 16 - 53186 CCAAGCTATTACGATA -s mr.mrrefChr5 21105 16 + 294540 CTAACCATGTATGATG -s simCow_chr6.simCow.chr6 426525 16 - 602619 CCAAGGTATTAGGATA -s simDog_chr6.simDog.chr6 134425 16 + 593897 CCATGCTATTGCGATA -s simHuman_chr6.simHuman.chr6 428050 16 - 601863 CCAAGCTTTTATTATA -s simRat_chr6.simRat.chr6 155722 16 + 647215 CTAGCCATGTACAATG - -a -s simMouse_chr6.simMouse.chr6 158200 6 + 636262 TCTGAA -s Anc0.Anc0refChr1 5297 6 + 62388 TCTGAA -s Anc1.Anc1refChr2 5742 6 - 144309 TCTGAA -s Anc2.Anc2refChr3 5802 6 - 53186 TCAGGA -s mr.mrrefChr5 21121 6 + 294540 TCTGAA -s simCow_chr6.simCow.chr6 426542 6 - 602619 TGAGGG -s simDog_chr6.simDog.chr6 134442 6 + 593897 TCAGGA -s simHuman_chr6.simHuman.chr6 428067 6 - 601863 TCTAAA -s simRat_chr6.simRat.chr6 155738 6 + 647215 TCTGAA - -a -s simMouse_chr6.simMouse.chr6 158206 11 + 636262 TTCAGACAGAA -s Anc0.Anc0refChr1 5303 9 + 62388 CTCA--TAGAA -s Anc1.Anc1refChr2 5748 9 - 144309 CTCA--TAGAA -s Anc2.Anc2refChr3 5809 9 - 53186 CTCC--CAGAA -s mr.mrrefChr5 21127 11 + 294540 TTCAGATAGAA -s simCow_chr6.simCow.chr6 426549 9 - 602619 CTCC--CAGAA -s simDog_chr6.simDog.chr6 134449 9 + 593897 CTCC--CAGAG -s simHuman_chr6.simHuman.chr6 428073 9 - 601863 CTCA--TGGAA -s simRat_chr6.simRat.chr6 155744 11 + 647215 TTCAGATAGAA - -a -s simMouse_chr6.simMouse.chr6 158217 8 + 636262 CAGCATTT -s Anc0.Anc0refChr1 5329 8 + 62388 CACCGTCA -s Anc1.Anc1refChr2 5774 8 - 144309 CACCGTCA -s Anc2.Anc2refChr3 5838 8 - 53186 CACCGTCA -s mr.mrrefChr5 21138 8 + 294540 CAGCATTT -s simCow_chr6.simCow.chr6 426578 8 - 602619 CTCCATCA -s simDog_chr6.simDog.chr6 134478 8 + 593897 CACTGTTG -s simHuman_chr6.simHuman.chr6 428099 8 - 601863 TACCGTCA -s simRat_chr6.simRat.chr6 155755 8 + 647215 TAACATTT - -a -s simMouse_chr6.simMouse.chr6 158225 39 + 636262 GGAACCCTGGAAGGTGTTCTGCTGAGGCTACTAAAAATG -s Anc0.Anc0refChr1 5337 39 + 62388 GCAACTCTGGAGGGTGTTCTGCTGAGGCTACTAAAAAGG -s Anc1.Anc1refChr2 5782 39 - 144309 GCAACTCTGGAGGGTGTTCTGCTGAGGCTACTAAAAAGG -s Anc2.Anc2refChr3 5846 39 - 53186 GCAACTCTACAGATTATTCTGCTAAGGCTACTAAAGAGG -s mr.mrrefChr5 21146 39 + 294540 GCAACCCTGGAAGGTGTTCTGCTGAGGCTACTAAAAATG -s simCow_chr6.simCow.chr6 426587 39 - 602619 GCAACTCTACTGATTAGTCTGCTAGGGCCGCTAAAGAGG -s simDog_chr6.simDog.chr6 134486 39 + 593897 GAAACTCTACAGATTATTCTGCTAAGGCTACTAAAGAGG -s simHuman_chr6.simHuman.chr6 428107 39 - 601863 GCAACTCTGGAGGGTGTTCAGCTGAGGCTACTAAAAAGG -s simRat_chr6.simRat.chr6 155763 39 + 647215 GCAACCCTGGAAGGAGTTCTGCTGAGGCTACTAAAAATG - -a -s simMouse_chr6.simMouse.chr6 158264 39 + 636262 GTCCCCAAATGTGGAACAACCCAGTACCACTCAGGTCAT -s Anc0.Anc0refChr1 5376 39 + 62388 GTTTCTTAATGTGGAAGGACCCAATAGTGCTCGGGATAC -s Anc1.Anc1refChr2 5821 39 - 144309 GTTTCTTAATGTGGAAGGACCCAATAGTGCTCGGGATAC -s Anc2.Anc2refChr3 5885 39 - 53186 GTTTCTTAATGTGGAAGGACCCAATAGTGCTCAGGATAC -s mr.mrrefChr5 21185 39 + 294540 GTCCCCAAATGTGGAACAACCCAGTACCACTCGGGTCAT -s simCow_chr6.simCow.chr6 426626 32 - 602619 GATCATTAATGTGGAAGCATTCAATAGCGCTC------- -s simDog_chr6.simDog.chr6 134527 39 + 593897 GTTTCTTAATGTGGAAGGACCCAAGAGTGCTCAGGATAC -s simHuman_chr6.simHuman.chr6 428146 39 - 601863 GTTTCTCAAAGCAGAGAGACCCAATAGTGCTCGGGAGAA -s simRat_chr6.simRat.chr6 155802 39 + 647215 GTCCCCAAATGTGGATCAATCCAGTACCACTCGGGTCAT - -a -s simMouse_chr6.simMouse.chr6 158303 21 + 636262 GTAACTATTGCTTAAGGAGGG -s Anc0.Anc0refChr1 5420 21 + 62388 ATAAGTATTACTTAAGGAGGA -s Anc1.Anc1refChr2 5865 21 - 144309 ATAAGTATTACTTAAGGAGGA -s Anc2.Anc2refChr3 5935 21 - 53186 ATAAGTATTACTTAAGGAGGA -s mr.mrrefChr5 21224 21 + 294540 GTAACTATTGCTTAAGGAGGG -s simCow_chr6.simCow.chr6 426665 21 - 602619 GTAACAATCACTTAAAGAGGA -s simDog_chr6.simDog.chr6 134584 21 + 593897 ATAAGTATTACTTAAGGAGGA -s simHuman_chr6.simHuman.chr6 428190 9 - 601863 ------------TAAGGAGGA -s simRat_chr6.simRat.chr6 155841 21 + 647215 GCAACTATTGCTTAAGGAGGG - -a -s simMouse_chr6.simMouse.chr6 158324 24 + 636262 TAAAGGTGTTGTGGATAACAGATT -s Anc0.Anc0refChr1 5441 24 + 62388 TGTAGGTATTGTGGGTATCAAATT -s Anc1.Anc1refChr2 5886 24 - 144309 TGTAGGTATTGTGGGTATCAAATT -s Anc2.Anc2refChr3 5961 24 - 53186 TGTAGGTATTGCAGATATCAACTT -s mr.mrrefChr5 21245 24 + 294540 TAAAGGTGTTGTGGGTATCAGATT -s simCow_chr6.simCow.chr6 426691 24 - 602619 TGAAAGTATCACAGAGATCAGCTT -s simDog_chr6.simDog.chr6 134610 22 + 593897 TGTAGGT--TGCAGATATCAACTG -s simHuman_chr6.simHuman.chr6 428199 24 - 601863 TGTAGGTCTTGTGGGTATCAAATT -s simRat_chr6.simRat.chr6 155862 23 + 647215 TAAAGGTGTTGCAGGGATCG-ATT - -a -s simMouse_chr6.simMouse.chr6 158348 8 + 636262 CTAATGGG -s Anc0.Anc0refChr1 5465 8 + 62388 CTGTTGGA -s Anc1.Anc1refChr2 5910 8 - 144309 CTGTTGGA -s Anc2.Anc2refChr3 5985 8 - 53186 CTGTTGGA -s mr.mrrefChr5 21269 8 + 294540 CTGATGGG -s simCow_chr6.simCow.chr6 426722 8 - 602619 CTGTTGGA -s simDog_chr6.simDog.chr6 134632 8 + 593897 CTGTTGGG -s simHuman_chr6.simHuman.chr6 428223 8 - 601863 TTGTAGGA -s simRat_chr6.simRat.chr6 155885 8 + 647215 CTGATGGG - -a -s simMouse_chr6.simMouse.chr6 158356 12 + 636262 TGATGAGATTCT -s Anc0.Anc0refChr1 5480 12 + 62388 GGATGAGATTGT -s Anc1.Anc1refChr2 5925 12 - 144309 GGATGAGATTGT -s Anc2.Anc2refChr3 6000 12 - 53186 GGATGAGTTTGT -s mr.mrrefChr5 21277 12 + 294540 TGATGAGATTCT -s simCow_chr6.simCow.chr6 426735 12 - 602619 GGATCAGTGTGT -s simDog_chr6.simDog.chr6 134647 12 + 593897 GGTTGAGTTTGT -s simHuman_chr6.simHuman.chr6 428238 12 - 601863 GGATGAAATTGT -s simRat_chr6.simRat.chr6 155893 12 + 647215 TGATGAGATACT - -a -s simMouse_chr6.simMouse.chr6 158368 16 + 636262 CAAAGCTGCTCTCTAG -s Anc0.Anc0refChr1 5493 16 + 62388 CATAGCTACTTTCGAG -s Anc1.Anc1refChr2 5938 16 - 144309 CATAGCTACTTTCGAG -s Anc2.Anc2refChr3 6013 16 - 53186 CATAGCTACTTTTGAG -s mr.mrrefChr5 21289 16 + 294540 CAAAGCTGCTCTCTAG -s simCow_chr6.simCow.chr6 426748 16 - 602619 CATAGCTGATTTTTAC -s simDog_chr6.simDog.chr6 134660 16 + 593897 CATACCTACTTTTGAG -s simHuman_chr6.simHuman.chr6 428251 16 - 601863 CATAGTTTCTTTCGAG -s simRat_chr6.simRat.chr6 155905 16 + 647215 CAAAGCTGTTCTCATG - -a -s simMouse_chr6.simMouse.chr6 158384 12 + 636262 TACAGCATCTCT -s Anc0.Anc0refChr1 5509 11 + 62388 TACTGCTTC-TC -s Anc1.Anc1refChr2 5954 12 - 144309 TACTGCTTCCTC -s Anc2.Anc2refChr3 6031 11 - 53186 TACTGCTTT-TC -s mr.mrrefChr5 21305 12 + 294540 TACAGCATCCCT -s simCow_chr6.simCow.chr6 426764 11 - 602619 TACTGGTTC-TC -s simDog_chr6.simDog.chr6 134678 11 + 593897 TACTGCTTT-TC -s simHuman_chr6.simHuman.chr6 428267 10 - 601863 CAC--CTTCCTC -s simRat_chr6.simRat.chr6 155921 12 + 647215 TACAGCATCCCT - -a -s simMouse_chr6.simMouse.chr6 158396 45 + 636262 ACTTCCCCCATCAGGGATCTGGTCTTATGCTGACTAAAGATTGCC -s Anc0.Anc0refChr1 5520 45 + 62388 ATCTCTCCCATTAGGGACCTGGTATTGTATTGGCCAATGATTGCC -s Anc1.Anc1refChr2 5966 45 - 144309 ATCTCTCCCATTAGGGACCTGGTATTGTATTGGCCAATGATTGCC -s Anc2.Anc2refChr3 6042 45 - 53186 ATCTCTCCCATTAGGGACCTGGTATTGTATTGGCCATTGATTGGC -s mr.mrrefChr5 21317 45 + 294540 ACTTCTCCCATCAGGGATCTGGTCTTATACTGACTAAAGATTGCC -s simCow_chr6.simCow.chr6 426776 44 - 602619 ACCTTTCCCATTAGGGATC-AGTGTTGTATTGGACATTGATTGGC -s simDog_chr6.simDog.chr6 134689 45 + 593897 TTCTCTCCTATTAGGGACATGGTATCGTATTAGCCCTTGATTGGC -s simHuman_chr6.simHuman.chr6 428277 45 - 601863 ATGTCTCCCGTTAGGGACCTGGGACTGCATTGGCAAATGGTTGCT -s simRat_chr6.simRat.chr6 155933 45 + 647215 ACTTCTCCCATCAAGGATCTGGTGTTATACTGACTAAGGATTGGA - -a -s simMouse_chr6.simMouse.chr6 158441 26 + 636262 ACAGCATGAGCCTCTCTTTAACTGAA -s Anc0.Anc0refChr1 5565 26 + 62388 ATTGTACAAGCCTATCTTTGATTGAA -s Anc1.Anc1refChr2 6011 26 - 144309 ATTGTACAAGCCTATCTTTGATTGAA -s Anc2.Anc2refChr3 6087 26 - 53186 ATTGCACAGGCCTATCTTTGATTCAA -s mr.mrrefChr5 21362 26 + 294540 ACAGTATAAGCCTCTCTTTAACTGAA -s simCow_chr6.simCow.chr6 426820 26 - 602619 ATTGCACAGGCCTATCCTTGAGGCAA -s simDog_chr6.simDog.chr6 134734 26 + 593897 ACGGCATAGGCCTATCTTTGTTTCAA -s simHuman_chr6.simHuman.chr6 428328 26 - 601863 ATTGTACAAGCCTATCTTTGATTGAG -s simRat_chr6.simRat.chr6 155978 26 + 647215 TCAGTATAAGCCTCTCTTTAACTGAA - -a -s simMouse_chr6.simMouse.chr6 158467 12 + 636262 AAGTCTGACTCG -s Anc0.Anc0refChr1 5591 12 + 62388 AAGTCCAACTCC -s Anc1.Anc1refChr2 6037 12 - 144309 AAGTCCAACTCC -s Anc2.Anc2refChr3 6113 12 - 53186 AAGTGCAACTCC -s mr.mrrefChr5 21388 12 + 294540 AAGTCTGACTCG -s simCow_chr6.simCow.chr6 426846 12 - 602619 AGGTGCAACTCT -s simDog_chr6.simDog.chr6 134760 12 + 593897 AAGAGCGTCTAC -s simHuman_chr6.simHuman.chr6 428355 12 - 601863 AAGTCAAACTCC -s simRat_chr6.simRat.chr6 156004 12 + 647215 AAGTCTGACTTG - -a -s simMouse_chr6.simMouse.chr6 158479 22 + 636262 TTAGCCCCTTTATTAGGTGGCT -s Anc0.Anc0refChr1 5604 20 + 62388 TTGGTCCCTTTAAA--GAGGCT -s Anc1.Anc1refChr2 6050 22 - 144309 TTGGTCCCTTTAAAAAGAGGCT -s Anc2.Anc2refChr3 6126 20 - 53186 TTGGTCCCTTTAAA--GAGTCT -s mr.mrrefChr5 21400 22 + 294540 TTAGCCCCTTTATTAGGAGGCT -s simCow_chr6.simCow.chr6 426859 15 - 602619 TTGGTCCCTC-------AGACT -s simDog_chr6.simDog.chr6 134773 20 + 593897 TTGGTCCCTTTAAA--GAGTCT -s simHuman_chr6.simHuman.chr6 428368 22 - 601863 TTGGTCCCTTTAAAAAGAGGCT -s simRat_chr6.simRat.chr6 156016 20 + 647215 TTAGCC--TTTACTAGGAGGCT - -a -s simMouse_chr6.simMouse.chr6 158501 72 + 636262 CCCATCGTCTTGCTTGGCCAGAAGGCAGTCACCAGATTGTCACACCACACAGAAGGGTTGCTGTAGAGCTTT -s Anc0.Anc0refChr1 5624 72 + 62388 CTCTTGGTCTCACACAGCCAGAAGGTGGTCTCATGATTGCCATACCACACAGGAGGGTTGTTACAGAGGTTT -s Anc1.Anc1refChr2 6072 72 - 144309 CTCTTGGTCTCACACAGCCAGAAGGTGGTCTCATGATTGCCATACCACACAGGAGGGTTGTTACAGAGGTTT -s Anc2.Anc2refChr3 6146 72 - 53186 CTCTTGGTCTCATACAGCCAGAAGGTGGTCTCATGATTGCCATACCACACAGGAGGGTTGTTACAAAGGTTT -s mr.mrrefChr5 21422 72 + 294540 CCCTTCGTCTTGCATGGCCAGAAGGCAGTCACATGATTGCCATACCACACAGAAGGGTTGCTGCAGAGCTTT -s simCow_chr6.simCow.chr6 426875 69 - 602619 ATAGTGGTCTCAT---TCCAGAAGGTAGTCCAATGAGTGCCGTAACAAACAGGAGGGCTTTTACAATGGTCC -s simDog_chr6.simDog.chr6 134793 70 + 593897 CTCTTC--TTCATACAGCCGGAAGTTGGTCTCATGATTGCTAGACCACATAGGGGGGTTGTTACAAAGGTTT -s simHuman_chr6.simHuman.chr6 428390 72 - 601863 CTCTTGGGCTCACACAGCCAGAAGGTGGTCTCATAATTACCATACCACACAGGAGGGTTGTTACCGAGGTTT -s simRat_chr6.simRat.chr6 156036 66 + 647215 CCCTTTGTCTTGCATTGCCAGAAGGCAGT-ACATGATTGCCATACCACA-----GGGTTGCTTCAGAGCTTT - -a -s simMouse_chr6.simMouse.chr6 158573 21 + 636262 GGACTGCTACAACAATCTTAG -s Anc0.Anc0refChr1 5700 18 + 62388 GAGCTGCTACAAAGGTTT--- -s Anc1.Anc1refChr2 6148 21 - 144309 GAGCTGCTACAAAGGTTTCAG -s Anc2.Anc2refChr3 6222 18 - 53186 GAGCTACTACAAAGGTTT--- -s mr.mrrefChr5 21494 21 + 294540 GGGCTGCTACAACAATCTTAG -s simCow_chr6.simCow.chr6 426948 18 - 602619 GAGCTACTGCAAAGGTTT--- -s simDog_chr6.simDog.chr6 134867 18 + 593897 GAGCTACTACAAACGTTT--- -s simHuman_chr6.simHuman.chr6 428466 21 - 601863 GAGCTGCTACAAAGGTTTCAG -s simRat_chr6.simRat.chr6 156102 21 + 647215 GGGCTGCTACAACAATGTTAG - -a -s simMouse_chr6.simMouse.chr6 158594 11 + 636262 CATGTCCTGAG -s Anc0.Anc0refChr1 58183 11 - 62388 catgtcttaag -s Anc1.Anc1refChr2 139666 11 + 144309 catgtcttaag -s Anc2.Anc2refChr3 48498 11 + 53186 catgtcttaag -s mr.mrrefChr5 21515 11 + 294540 CATGTCCTGAG -s simCow_chr6.simCow.chr6 177174 11 + 602619 catgtcttgag -s simDog_chr6.simDog.chr6 460558 11 - 593897 CAAGCTTTAAG -s simHuman_chr6.simHuman.chr6 174882 11 + 601863 catgtcttcag -s simRat_chr6.simRat.chr6 156123 11 + 647215 CATGTCCTGAG - -a -s simMouse_chr6.simMouse.chr6 158605 11 + 636262 TGCCACCGATA -s Anc0.Anc0refChr1 58194 9 - 62388 t--caCTGATA -s Anc1.Anc1refChr2 139677 9 + 144309 t--caCTGATA -s Anc2.Anc2refChr3 48509 9 + 53186 t--caCTGACA -s mr.mrrefChr5 21526 11 + 294540 TGCCACCGATA -s simCow_chr6.simCow.chr6 177185 9 + 602619 t--caCTCACA -s simCow_chr6.simCow.chr6 177527 9 + 602619 T--CGGCCATG -s simDog_chr6.simDog.chr6 460569 9 - 593897 T--CATTGACA -s simHuman_chr6.simHuman.chr6 174893 9 + 601863 t--caCTGATG -s simRat_chr6.simRat.chr6 156134 11 + 647215 TGCCACCAATG - -a -s simMouse_chr6.simMouse.chr6 158616 3 + 636262 TAT -s Anc0.Anc0refChr1 58203 3 - 62388 TAT -s Anc1.Anc1refChr2 139686 3 + 144309 TAT -s Anc2.Anc2refChr3 48518 3 + 53186 TAT -s mr.mrrefChr5 21537 3 + 294540 TAT -s simCow_chr6.simCow.chr6 177536 3 + 602619 TAT -s simHuman_chr6.simHuman.chr6 174902 3 + 601863 TAT -s simRat_chr6.simRat.chr6 156145 3 + 647215 TAT - -a -s simMouse_chr6.simMouse.chr6 158619 164 + 636262 CCTCTGTAAACATAATGTGTTATTTTACTTGGCTGCTGATAGTATACCACTGTCAAGCAAGTATTTAGGTAAGATTCTTGTGAGTGGTGGGAAAGTACTTGACTTGTCTGCTGTCTACCTGCCATAACACATCTGCACATTTTTTTCAACCACTGAACTTTCAA -s Anc0.Anc0refChr1 58206 5 - 62388 CCTAT--------------------------------------------------------------------------------------------------------------------------------------------------------------- -s Anc1.Anc1refChr2 139689 5 + 144309 CCTAT--------------------------------------------------------------------------------------------------------------------------------------------------------------- -s Anc2.Anc2refChr3 48521 5 + 53186 CCTAT--------------------------------------------------------------------------------------------------------------------------------------------------------------- -s mr.mrrefChr5 21540 164 + 294540 CCTCTGTAAACATAATGTGTTATTTTACTTGGCTGCTGATAGTATACCACTGTCAAGCAAGTATTTAGGTAAGATTCTTGTGAGTGGTGGGAAAGTACTTGACTTGTCTGCTGTCTACCTGCCATAACACATCTGCACATTTTTTTCAACCACTGAACTTTCAA -s simCow_chr6.simCow.chr6 177194 5 + 602619 ACTAT--------------------------------------------------------------------------------------------------------------------------------------------------------------- -s simCow_chr6.simCow.chr6 177539 5 + 602619 CCTAT--------------------------------------------------------------------------------------------------------------------------------------------------------------- -s simDog_chr6.simDog.chr6 460578 5 - 593897 GATAT--------------------------------------------------------------------------------------------------------------------------------------------------------------- -s simHuman_chr6.simHuman.chr6 174905 5 + 601863 CCTAT--------------------------------------------------------------------------------------------------------------------------------------------------------------- -s simRat_chr6.simRat.chr6 156148 164 + 647215 CCTCTGTAGTCATAATATGTTATTTTATGTGGCTGTTGATAGTATAGTACTGTACTGCAAGTATTAGGGTAGGATTCTTATGAGTGGTGTCAAAGTACTTGACTTGTCTGCTGTCTACTTGCCATAACATACCTGCACATTTTTTTCAACTACTGACCTTTCAA - -a -s simMouse_chr6.simMouse.chr6 158783 3 + 636262 ATG -s Anc0.Anc0refChr1 58211 3 - 62388 ATG -s Anc1.Anc1refChr2 139694 3 + 144309 ATG -s Anc2.Anc2refChr3 48526 3 + 53186 ATG -s mr.mrrefChr5 21704 3 + 294540 ATG -s simCow_chr6.simCow.chr6 177199 3 + 602619 GTG -s simCow_chr6.simCow.chr6 177544 3 + 602619 GTG -s simDog_chr6.simDog.chr6 460583 3 - 593897 ATC -s simHuman_chr6.simHuman.chr6 174910 3 + 601863 ATG -s simRat_chr6.simRat.chr6 156314 3 + 647215 ATG - -a -s simMouse_chr6.simMouse.chr6 158786 5 + 636262 TTTTG -s Anc0.Anc0refChr1 58216 5 - 62388 TTTTT -s Anc1.Anc1refChr2 139699 5 + 144309 TTTTT -s Anc2.Anc2refChr3 48538 5 + 53186 TATTT -s mr.mrrefChr5 21707 5 + 294540 TTTTG -s simCow_chr6.simCow.chr6 177211 5 + 602619 TATTT -s simCow_chr6.simCow.chr6 177556 5 + 602619 TATTA -s simDog_chr6.simDog.chr6 460594 5 - 593897 TATTT -s simHuman_chr6.simHuman.chr6 174915 5 + 601863 TTTTC -s simRat_chr6.simRat.chr6 156317 5 + 647215 TTTAG - -a -s simMouse_chr6.simMouse.chr6 158791 5 + 636262 ACTGG -s Anc0.Anc0refChr1 58221 5 - 62388 ATTGG -s Anc1.Anc1refChr2 139704 5 + 144309 ATTGG -s Anc2.Anc2refChr3 48543 5 + 53186 GTTGG -s mr.mrrefChr5 21712 5 + 294540 ACTGG -s simCow_chr6.simCow.chr6 177216 5 + 602619 GCTCT -s simCow_chr6.simCow.chr6 177561 5 + 602619 GCTCT -s simDog_chr6.simDog.chr6 460734 5 - 593897 GTTGG -s simHuman_chr6.simHuman.chr6 174920 5 + 601863 ATTGG -s simRat_chr6.simRat.chr6 156322 5 + 647215 ACTGG - -a -s simMouse_chr6.simMouse.chr6 158796 10 + 636262 GTGCCTGCCA -s Anc0.Anc0refChr1 58226 10 - 62388 TAACATCCCA -s Anc1.Anc1refChr2 139709 10 + 144309 TAACATCCCA -s Anc2.Anc2refChr3 48548 10 + 53186 TAACATCCCA -s mr.mrrefChr5 21717 10 + 294540 GTGCCTGCCA -s simCow_chr6.simCow.chr6 177221 10 + 602619 TGACAGTTCT -s simCow_chr6.simCow.chr6 177573 10 + 602619 TGACAGTTCT -s simDog_chr6.simDog.chr6 460739 10 - 593897 GAACCTCCCA -s simHuman_chr6.simHuman.chr6 174925 10 + 601863 TAACGTCCCA -s simRat_chr6.simRat.chr6 156327 10 + 647215 GCACCTGCCA - -a -s simMouse_chr6.simMouse.chr6 158806 7 + 636262 CCCATTC -s Anc0.Anc0refChr1 58236 7 - 62388 ACTTTCC -s Anc1.Anc1refChr2 139719 7 + 144309 ACTTTCC -s Anc2.Anc2refChr3 48558 7 + 53186 ACTTTCC -s mr.mrrefChr5 21727 7 + 294540 CCCATTC -s simCow_chr6.simCow.chr6 177231 7 + 602619 GTTTTGC -s simCow_chr6.simCow.chr6 177583 7 + 602619 GTTTGGC -s simDog_chr6.simDog.chr6 460749 7 - 593897 ACCTTCC -s simHuman_chr6.simHuman.chr6 174935 7 + 601863 ACTTTCC -s simRat_chr6.simRat.chr6 156343 7 + 647215 CCCATTC - -a -s simMouse_chr6.simMouse.chr6 158813 20 + 636262 TCTTGAGCTCACATAGTGTG -s Anc0.Anc0refChr1 58251 20 - 62388 TTTTAAGCTCACACAGAATG -s Anc1.Anc1refChr2 139734 20 + 144309 TTTTAAGCTCACACAGAATG -s Anc2.Anc2refChr3 48573 20 + 53186 TTTTAAGCTCACACAGAAGG -s mr.mrrefChr5 21734 20 + 294540 TCTTGAGCTCACATAGTGTG -s simDog_chr6.simDog.chr6 460764 20 - 593897 TTTTAAGCTCACACAGAAGG -s simHuman_chr6.simHuman.chr6 174950 20 + 601863 TTTTAAGCTCATGCAGAATG -s simRat_chr6.simRat.chr6 156350 20 + 647215 TCTTGAACTCACACAGTGTG - -a -s simMouse_chr6.simMouse.chr6 158833 2 + 636262 CT -s Anc0.Anc0refChr1 58271 2 - 62388 CT -s Anc1.Anc1refChr2 139754 2 + 144309 CT -s Anc2.Anc2refChr3 48593 2 + 53186 CT -s mr.mrrefChr5 21754 2 + 294540 CT -s simDog_chr6.simDog.chr6 460784 2 - 593897 CT -s simHuman_chr6.simHuman.chr6 174970 2 + 601863 TT -s simRat_chr6.simRat.chr6 156395 2 + 647215 CT - -a -s simMouse_chr6.simMouse.chr6 158835 29 + 636262 CGAACAATGACAGTGTAGTGAACCCAAAT -s Anc0.Anc0refChr1 58275 19 - 62388 CGAATGA-GACTGTGTATTG--------- -s Anc1.Anc1refChr2 139758 29 + 144309 CGAATGATGACTGTGTATTGTCCCCAGAT -s Anc2.Anc2refChr3 48597 19 + 53186 CGAATGA-GACTGTGTATTG--------- -s mr.mrrefChr5 21756 29 + 294540 CGAACAATGACAGTGTAGTGAACCCAAAT -s simDog_chr6.simDog.chr6 460788 19 - 593897 CGAATGA-GACTGTGTATTG--------- -s simHuman_chr6.simHuman.chr6 174974 29 + 601863 TGAGTGATGACTGTGCATTGTCCCCAGAT -s simRat_chr6.simRat.chr6 156397 29 + 647215 TGGATGATGACAGTATAGTGAACCCAGAT - -a -s simMouse_chr6.simMouse.chr6 158864 2 + 636262 AA -s Anc1.Anc1refChr2 139787 2 + 144309 AA -s mr.mrrefChr5 21785 2 + 294540 AA -s simHuman_chr6.simHuman.chr6 175003 2 + 601863 AA -s simRat_chr6.simRat.chr6 156427 2 + 647215 AA - -a -s simMouse_chr6.simMouse.chr6 158866 27 + 636262 TGTCATTTCATGTGTGTCCTTCATTAA -s Anc0.Anc0refChr1 58320 27 - 62388 CATCATCTTGTGTGTGTCTTTCATTAA -s Anc1.Anc1refChr2 139815 27 + 144309 CATCATCTTGTGTGTGTCTTTCATTAA -s Anc2.Anc2refChr3 48642 27 + 53186 CATCATCCTGTGTGTGTCTTTCATTAA -s mr.mrrefChr5 21787 27 + 294540 TGTCATTTCATGTGTGTCCTTCATTAA -s simCow_chr6.simCow.chr6 177269 27 + 602619 CATTATTCTAGGTATGGCTTTCATTAA -s simCow_chr6.simCow.chr6 177620 27 + 602619 CACCATTTTGTGTATGTCTTTCATTGA -s simDog_chr6.simDog.chr6 460812 27 - 593897 CATCATCCAGTGTGTGTCTTTCATTAG -s simHuman_chr6.simHuman.chr6 175063 27 + 601863 CATCATCTTGTGTGTGTCTTTCATTAA -s simRat_chr6.simRat.chr6 156429 27 + 647215 TGTCATTCAATGCATGTCTCTCATAAA - -a -s simMouse_chr6.simMouse.chr6 158893 9 + 636262 TAGGCTCAT -s Anc0.Anc0refChr1 58347 9 - 62388 TAACTTGAT -s Anc1.Anc1refChr2 139842 9 + 144309 TAACTTGAT -s Anc2.Anc2refChr3 48684 9 + 53186 TAACTTGAT -s mr.mrrefChr5 21814 9 + 294540 TAGGCTCAT -s simCow_chr6.simCow.chr6 177311 9 + 602619 TAACTTGAC -s simCow_chr6.simCow.chr6 177650 9 + 602619 TAACTTGAT -s simDog_chr6.simDog.chr6 460862 9 - 593897 TGGCTTGAT -s simHuman_chr6.simHuman.chr6 175090 9 + 601863 TAACTTAAC -s simRat_chr6.simRat.chr6 156456 9 + 647215 TAAGCTCAT - -a -s simMouse_chr6.simMouse.chr6 158902 2 + 636262 AA -s Anc0.Anc0refChr1 58419 2 - 62388 AA -s Anc1.Anc1refChr2 139914 2 + 144309 AA -s Anc2.Anc2refChr3 48759 2 + 53186 AA -s mr.mrrefChr5 21823 2 + 294540 AA -s simCow_chr6.simCow.chr6 177386 2 + 602619 AA -s simCow_chr6.simCow.chr6 177721 2 + 602619 AA -s simDog_chr6.simDog.chr6 460937 2 - 593897 AA -s simHuman_chr6.simHuman.chr6 175162 2 + 601863 AA -s simRat_chr6.simRat.chr6 156465 1 + 647215 A- - -a -s simMouse_chr6.simMouse.chr6 158904 11 + 636262 AGAGTCTCAAC -s Anc0.Anc0refChr1 58421 11 - 62388 GGAATCTCATA -s Anc1.Anc1refChr2 139916 11 + 144309 GGAATCTCATA -s Anc2.Anc2refChr3 48761 11 + 53186 GGAATCTGGTA -s mr.mrrefChr5 21825 11 + 294540 AGAGTCTCATC -s simCow_chr6.simCow.chr6 177388 11 + 602619 GGCATCTGATA -s simCow_chr6.simCow.chr6 177723 11 + 602619 GGAATCTAGTA -s simDog_chr6.simDog.chr6 460939 11 - 593897 GGAATCTGGGA -s simHuman_chr6.simHuman.chr6 175164 11 + 601863 GGAACCTCATA -s simRat_chr6.simRat.chr6 156651 11 + 647215 AAATTCTCATT - -a -s simMouse_chr6.simMouse.chr6 158915 40 + 636262 TCGTTGACCTGGCCGCAGACGCAGCTGTCAGGTAACCTCT -s Anc0.Anc0refChr1 58433 34 - 62388 TTGATGCTAT------GGATGCAGCAGTCAAGTAGCCTTT -s Anc1.Anc1refChr2 139928 40 + 144309 TTGATGCTATGGTTGCGGATGCAGCAGTCAAGTAGCCTTT -s Anc2.Anc2refChr3 48773 34 + 53186 CTGATGCTAT------GGATGCAGCAGTCAAGTAGCCTTT -s mr.mrrefChr5 21836 40 + 294540 TCGTTGACCTGGCCGCAGATGCAGCAGTCAGGTAACCTCT -s simCow_chr6.simCow.chr6 177400 34 + 602619 CTGATGCTAT------TGACGTAGCGGTCAAGTAGCCTCT -s simCow_chr6.simCow.chr6 177735 26 + 602619 CTGATGCTAT------GGATGCAGCAGTCAA--------T -s simDog_chr6.simDog.chr6 460951 34 - 593897 CTTATGCTGC------AGATACAGCAATCAAGTAGACCTT -s simHuman_chr6.simHuman.chr6 175176 40 + 601863 TTGGTGCTATGGTTGCGGATGTAGCAGTTAAGTAGCCTTT -s simRat_chr6.simRat.chr6 156662 31 + 647215 TAGT---------CACAGATGCAGTAGTCGGGTGACCTCT - -a -s simMouse_chr6.simMouse.chr6 158955 5 + 636262 ATTCC -s Anc0.Anc0refChr1 58467 5 - 62388 ATTTC -s Anc1.Anc1refChr2 139968 5 + 144309 ATTTC -s Anc2.Anc2refChr3 48807 5 + 53186 ATTTC -s mr.mrrefChr5 21876 5 + 294540 ATTCC -s simCow_chr6.simCow.chr6 177437 5 + 602619 ATCAC -s simCow_chr6.simCow.chr6 177761 5 + 602619 ATTTC -s simDog_chr6.simDog.chr6 460985 5 - 593897 ATTTT -s simHuman_chr6.simHuman.chr6 175216 5 + 601863 ATTTC -s simRat_chr6.simRat.chr6 156693 5 + 647215 CTTCC - -a -s simMouse_chr6.simMouse.chr6 158960 28 + 636262 AGCAAACGCAAAATCTCACACATCTTAC -s Anc0.Anc0refChr1 58472 25 - 62388 TGTAAATG-AGAATCTAACAA--CTTTC -s Anc1.Anc1refChr2 139973 25 + 144309 TGTAAATG-AGAATCTAACAA--CTTTC -s Anc2.Anc2refChr3 48812 25 + 53186 TGTAAATG-AGAATCTAACAA--CTTTC -s mr.mrrefChr5 21881 28 + 294540 AGCAAATGCAAAATCTCACACATCTTAC -s simCow_chr6.simCow.chr6 177766 25 + 602619 TGTAAAAA-AAAATCTAACAA--CTTTC -s simDog_chr6.simDog.chr6 460990 25 - 593897 CGCAAATG-AGAATCTCACAA--TTTTC -s simHuman_chr6.simHuman.chr6 175221 25 + 601863 TGTAAATG-AGAATCTAACAA--CTTTC -s simRat_chr6.simRat.chr6 156698 28 + 647215 AGAAGATGCAAAATCTCGCACATCTTAC - -a -s simMouse_chr6.simMouse.chr6 158988 12 + 636262 TTTAGTTGGGGC -s Anc0.Anc0refChr1 58497 11 - 62388 TTTAGTTGGGG- -s Anc1.Anc1refChr2 139998 11 + 144309 TTTAGTTGGGG- -s Anc2.Anc2refChr3 48837 11 + 53186 TTTAGTTGGAG- -s mr.mrrefChr5 21909 11 + 294540 TTTAGTTGGGG- -s simCow_chr6.simCow.chr6 177796 11 + 602619 TTTAATTGGAG- -s simDog_chr6.simDog.chr6 461015 11 - 593897 TTTAGTTGGAG- -s simHuman_chr6.simHuman.chr6 175246 11 + 601863 TTTAAGTAGGA- -s simRat_chr6.simRat.chr6 156726 11 + 647215 TTTAGTTGGAG- - -a -s simMouse_chr6.simMouse.chr6 159000 14 + 636262 AGGGTTGCCAATCC -s Anc0.Anc0refChr1 58508 1 - 62388 A------------- -s Anc1.Anc1refChr2 140009 14 + 144309 ATGGTTGTAGACAC -s Anc2.Anc2refChr3 48848 1 + 53186 A------------- -s mr.mrrefChr5 21920 14 + 294540 AGGGTTGCCAATCC -s simCow_chr6.simCow.chr6 177807 1 + 602619 A------------- -s simDog_chr6.simDog.chr6 461026 1 - 593897 A------------- -s simHuman_chr6.simHuman.chr6 175261 14 + 601863 ATGGTTGTAGACAC -s simRat_chr6.simRat.chr6 156737 14 + 647215 GGGGTTGCCAATCC - -a -s simMouse_chr6.simMouse.chr6 159014 39 + 636262 TATATTTCAATGAATGAAATCTCACAAACCCCCTAAGTT -s Anc1.Anc1refChr2 140023 36 + 144309 TATTTTTC-ATAAATGAAA-CTC-CAACTTTCTTTAGTT -s mr.mrrefChr5 21934 37 + 294540 TATATTTCAATGAATGAAA-CTC-CAAACCCCTTAAGTT -s simHuman_chr6.simHuman.chr6 175292 36 + 601863 TATTTTTC-ATAAATGAAA-CTC-CAACTTTCTTTAGTT -s simRat_chr6.simRat.chr6 156751 28 + 647215 TATATTTCAATGA-----------CAAACCGATGAAGTT - -a -s simMouse_chr6.simMouse.chr6 159053 57 + 636262 GGGTACCAACCATCTACTCTGTAATGCTTCGTACCATATCAAAGTGGGTGAGATTCT -s Anc0.Anc0refChr1 58509 44 - 62388 ----ATCAACCATCTGCTCC---------TGTAACTCATGGAAGGGGGTGAGATTCT -s Anc1.Anc1refChr2 140059 48 + 144309 GTGTATCAACCATCTGCTCC---------TGTAACTCATGGAAGGGGGTGAGATTCT -s Anc2.Anc2refChr3 48849 44 + 53186 ----ATCAACCATCTGCTCC---------TGTAACTCATGGAAAGGGGCAAGATTCT -s mr.mrrefChr5 21971 57 + 294540 GTGTACCAACCATCTACTCCGTAATGCTTCGTACCATATGAAAGTGGGTGAGATTCT -s simCow_chr6.simCow.chr6 177808 43 + 602619 ----ATCAACCATCTGCTCC---------TGTAACTCATGGAAAGGGG-AGGACTCT -s simDog_chr6.simDog.chr6 461027 44 - 593897 ----ATCAACCATCTGCTCC---------TGTAACTCATGGACATGGGCAAGATTCT -s simHuman_chr6.simHuman.chr6 175329 48 + 601863 GTGTATCAATCATCTGCTCC---------TGTAACTCACGGAAGGGTGTGAGATTCT -s simRat_chr6.simRat.chr6 156779 52 + 647215 GTGTACCAGCCATCTACTCCGTAATGCTTCATACTATATGAAAATGGGGTA-----T - -a -s simMouse_chr6.simMouse.chr6 159110 57 + 636262 TTGCTAGCCATAAGGTGTGTGCTCAGTATTTTTGGCATAGACACATTCTTGAAGGAG -s Anc0.Anc0refChr1 58558 46 - 62388 CT-------ATGAGTTGTATGTTCAGTAATTTTGGAATAGACTCATTCT----GGAA -s Anc1.Anc1refChr2 140112 53 + 144309 CTGCCAGCCATGAGTTGTATGTTCAGTAATTTTGGAATAGACTCATTCT----GGAA -s Anc2.Anc2refChr3 48898 46 + 53186 CT-------ATGAGCTGTATGTTCAGTAATCTTGGAATAGACTCATTCT----GGAA -s mr.mrrefChr5 22028 57 + 294540 CTGCTAGCCATAAGTTGTATGTTCAGTATTTTTGGAATAGACACATTCTTGAAGGAG -s simCow_chr6.simCow.chr6 177856 46 + 602619 TT-------CAGAGCTATGAGCTCAGCACTCTTGGAAAAGTCTCTTTCT----GGAA -s simDog_chr6.simDog.chr6 461076 46 - 593897 CT-------ATGACCTGTATGTTCAGTGATCTTGGAATAGACTCATTCT----GGAA -s simHuman_chr6.simHuman.chr6 175382 52 + 601863 CTGCCAGCCATGAGTTGTATCTTCAGTAACTTTGGAATAGACTAATTCT-----GAA -s simRat_chr6.simRat.chr6 156831 57 + 647215 CTGCTAGCTACAAGTGGTATGTTCAGTATTTTTGGAATAGGCACATTCTTGAAGGAC - -a -s simMouse_chr6.simMouse.chr6 159167 16 + 636262 GAACAGCTCAATTGCA -s Anc0.Anc0refChr1 58604 16 - 62388 CACCTGCTAAATTGCA -s Anc1.Anc1refChr2 140165 16 + 144309 CACCTGCTAAATTGCA -s Anc2.Anc2refChr3 48944 16 + 53186 CACCTGCTAAATTGCA -s mr.mrrefChr5 22085 16 + 294540 GACCAGCTCAATTGCA -s simCow_chr6.simCow.chr6 177903 16 + 602619 CACTACCAAAAATGCA -s simDog_chr6.simDog.chr6 461122 16 - 593897 CACCTGCTAAATTGCA -s simHuman_chr6.simHuman.chr6 175434 16 + 601863 CACCCACTAAATTGCA -s simRat_chr6.simRat.chr6 156888 16 + 647215 GACTGGCTCAATTGCA - -a -s simMouse_chr6.simMouse.chr6 159183 15 + 636262 TATGACTTGACAGGA -s Anc0.Anc0refChr1 58621 15 - 62388 TATGAGGTGACAAGA -s Anc1.Anc1refChr2 140182 15 + 144309 TATGAGGTGACAAGA -s Anc2.Anc2refChr3 48961 15 + 53186 TATGAGGTGGCAAGA -s mr.mrrefChr5 22102 15 + 294540 TATGACTTGACAGGA -s simCow_chr6.simCow.chr6 177920 15 + 602619 TATGAGGTGCGGACA -s simDog_chr6.simDog.chr6 461139 15 - 593897 TATGTGGTGGCAAGA -s simHuman_chr6.simHuman.chr6 175451 15 + 601863 TATAAGGTGATGAGA -s simRat_chr6.simRat.chr6 156905 15 + 647215 TATGACTTGACAGGA - -a -s simMouse_chr6.simMouse.chr6 159198 13 + 636262 ATGATAGTCAGTA -s Anc0.Anc0refChr1 58636 13 - 62388 GTGAAGGTAAGTA -s Anc1.Anc1refChr2 140197 13 + 144309 GTGAAGGTAAGTA -s Anc2.Anc2refChr3 48979 13 + 53186 GGGGAGGTAAATA -s mr.mrrefChr5 22117 13 + 294540 ATGATAGTCAGTA -s simCow_chr6.simCow.chr6 177938 12 + 602619 GGGGAGGTAAAT- -s simDog_chr6.simDog.chr6 461157 13 - 593897 AGAGAAGTAAATA -s simHuman_chr6.simHuman.chr6 175466 13 + 601863 GTGAAGGTAAGTA -s simRat_chr6.simRat.chr6 156920 13 + 647215 ATGATAGTGAGTA - -a -s simMouse_chr6.simMouse.chr6 159211 27 + 636262 GTTCCAGTAACTTCCATCAAACTCTTT -s Anc0.Anc0refChr1 58650 23 - 62388 ATTCTATGTACCTCCACTATACC---- -s Anc1.Anc1refChr2 140211 23 + 144309 ATTCTATGTACCTCCACTATACC---- -s Anc2.Anc2refChr3 48993 23 + 53186 ATTCTATGTACCTCCACTATACC---- -s mr.mrrefChr5 22131 23 + 294540 GTTCTAGTAACTTCCATTATACT---- -s simCow_chr6.simCow.chr6 177951 23 + 602619 ATTCCATGTACTTCTACTGTACC---- -s simDog_chr6.simDog.chr6 461171 23 - 593897 ATTCTATGCACCTCCTCCACCAT---- -s simHuman_chr6.simHuman.chr6 175480 23 + 601863 ATTCTATGTACCTCCACTATACC---- -s simRat_chr6.simRat.chr6 156934 23 + 647215 GTTCTAGTAACTGCCATTATGCT---- - -a -s simMouse_chr6.simMouse.chr6 159238 27 + 636262 GCTCACTGCTTAGTTAACATGCTCAAC -s Anc0.Anc0refChr1 58681 27 - 62388 GCTCAGTGCTTAGTTCCCATGCTCAAT -s Anc1.Anc1refChr2 140242 27 + 144309 GCTCAGTGCTTAGTTCCCATGCTCAAT -s Anc2.Anc2refChr3 49024 27 + 53186 GCTGAGTGCTTAGTTCCCATGCTCCAT -s mr.mrrefChr5 22154 27 + 294540 GCTCACTGCTTAGTTCACATGCTCAAT -s simCow_chr6.simCow.chr6 177982 27 + 602619 GCTATGTTCGTAGTTCCCATGCTCTAT -s simDog_chr6.simDog.chr6 461202 27 - 593897 GCAGAGTGCTTAGTTCCCATGCTCCAC -s simHuman_chr6.simHuman.chr6 175511 27 + 601863 GCTCAGTGCTCAGTTCCCATCCTCAAT -s simRat_chr6.simRat.chr6 156957 27 + 647215 GTCCACTGCTTAGTACACATGCTCAAT - -a -s simMouse_chr6.simMouse.chr6 159265 53 + 636262 ACTCGGTTTAGTTATCAACAGAACCTTGGGCAATACGGCGTGCGATTGAATAT -s Anc0.Anc0refChr1 58708 19 - 62388 GCTTAGTTCA-TTATCAA---------------------------------AT -s Anc1.Anc1refChr2 140269 19 + 144309 GCTTAGTTCA-TTATCAA---------------------------------AT -s Anc2.Anc2refChr3 49051 19 + 53186 GCTTATTTCA-CTATCAA---------------------------------AT -s mr.mrrefChr5 22181 53 + 294540 GCTCAGTTCAGTTATCAACAGAACCTTGGGCAATACGGCGTGCGATTGAATAT -s simCow_chr6.simCow.chr6 178009 19 + 602619 GCTTAATTCA-CTATCAA---------------------------------AT -s simDog_chr6.simDog.chr6 461242 19 - 593897 GCTTATTTCA-CTATCAT---------------------------------AT -s simHuman_chr6.simHuman.chr6 175538 19 + 601863 GCTTAGTTCA-TTACCAA---------------------------------AT -s simRat_chr6.simRat.chr6 156984 53 + 647215 GTGCAGTTCAGTTATTGTCAGAACCTCGGGCAATACAACGTGAGATCGCATAT - -a -s simMouse_chr6.simMouse.chr6 159318 9 + 636262 CAAACTACC -s Anc0.Anc0refChr1 58727 9 - 62388 CCAACCATC -s Anc1.Anc1refChr2 140288 9 + 144309 CCAACCATC -s Anc2.Anc2refChr3 49070 9 + 53186 CCAACCATC -s mr.mrrefChr5 22234 9 + 294540 CAAACCACC -s simCow_chr6.simCow.chr6 178028 9 + 602619 CAAACCATC -s simDog_chr6.simDog.chr6 461262 9 - 593897 CCAACCACC -s simHuman_chr6.simHuman.chr6 175557 9 + 601863 CCAACCTTC -s simRat_chr6.simRat.chr6 157037 9 + 647215 CAAACCACC - -a -s simMouse_chr6.simMouse.chr6 159327 12 + 636262 AACACTACAACA -s Anc0.Anc0refChr1 58736 12 - 62388 AACACTGCAACT -s Anc1.Anc1refChr2 140297 12 + 144309 AACACTGCAACT -s Anc2.Anc2refChr3 49079 12 + 53186 AACACTACAACT -s mr.mrrefChr5 22243 12 + 294540 AACACTGCAACA -s simCow_chr6.simCow.chr6 178050 12 + 602619 AACATTAACACT -s simDog_chr6.simDog.chr6 461271 12 - 593897 AGCACTACAACT -s simHuman_chr6.simHuman.chr6 175566 12 + 601863 AACACTGCACCC -s simRat_chr6.simRat.chr6 157046 12 + 647215 AACACTGCAACA - -a -s simMouse_chr6.simMouse.chr6 159339 59 + 636262 TGAAAATAGATACCAAATGTTGCTGTTTGCATATGTTCAGTCCTTAAACTGCCAACTGG -s Anc0.Anc0refChr1 58748 55 - 62388 TGAA---AGATAAC-AATGTTGTTTTGCCCATATGTTCAATCTTAAAATTTGTACATAT -s Anc1.Anc1refChr2 140309 57 + 144309 TGAA-ACAGATAAC-AATGTTGTTTTGCCCATATGTTCAATCTTAAAATTTGTACATAT -s Anc2.Anc2refChr3 49091 55 + 53186 TGAA---AGATAAC-AGTGTTGTTTTGCCCATATGTTCAATCTTAATATTTGTACATAT -s mr.mrrefChr5 22255 59 + 294540 TGAAAATAGATAACAAATGTTGCTGTGTGCATATGTTCAATCTTTAAACTGCCAACTGG -s simCow_chr6.simCow.chr6 178066 55 + 602619 TGAA---AGATAAC-AGAGTTGTTGTGCTCATATGTTCAATCTTAATATATTTATAGAT -s simDog_chr6.simDog.chr6 461283 55 - 593897 TGAA---AGGTCAC-AGTATTGTTTTGCCCATATGTTGAATCTTAATATTTGTACATAT -s simHuman_chr6.simHuman.chr6 175578 55 + 601863 CT---ACATATAAC-AATGTTGTTATGCCCATGTGTTCAATCTTAGAATTTATACATCT -s simRat_chr6.simRat.chr6 157058 59 + 647215 TCAAAATAGACAACAAATGTTGCTGTGTGCATATGTTCAATCTTTAAACTGCAAACTGC - -a -s simMouse_chr6.simMouse.chr6 159398 2 + 636262 AA -s Anc0.Anc0refChr1 58803 2 - 62388 TA -s Anc1.Anc1refChr2 140366 2 + 144309 TA -s Anc2.Anc2refChr3 49146 2 + 53186 TA -s mr.mrrefChr5 22314 2 + 294540 AA -s simCow_chr6.simCow.chr6 178121 2 + 602619 TA -s simDog_chr6.simDog.chr6 461343 2 - 593897 TA -s simHuman_chr6.simHuman.chr6 175633 2 + 601863 TA -s simRat_chr6.simRat.chr6 157117 2 + 647215 AA - -a -s simMouse_chr6.simMouse.chr6 159400 34 + 636262 ACCATTCACACAGTTTGGAAATAAACCATAGATC -s Anc0.Anc0refChr1 58805 34 - 62388 ATCATTCTCACCGTTTGAAAGTAAACCCCAAATT -s Anc1.Anc1refChr2 140368 34 + 144309 ATCATTCTCACCGTTTGAAAGTAAACCCCAAATT -s Anc2.Anc2refChr3 49148 34 + 53186 ATCATTCTCACAGTTTGAAAGTAAACCCCAGATG -s mr.mrrefChr5 22316 34 + 294540 ACCATTCACACCGTTTGGAAGTAAACCCTAAATT -s simCow_chr6.simCow.chr6 178125 34 + 602619 ATCATTCTCATAGTTTGAAAGTAAACCCCCGATC -s simDog_chr6.simDog.chr6 461345 34 - 593897 ATGATTCTCACAGTTTGAAAGTAAACCCCAGATG -s simHuman_chr6.simHuman.chr6 175635 34 + 601863 AGCATTCTCACCGTTTGAAAGTGAACCCCAAAAT -s simRat_chr6.simRat.chr6 157119 34 + 647215 ACCATTCACACCGTGTGGCAGTAAACCCTAAACT - -a -s simMouse_chr6.simMouse.chr6 159434 32 + 636262 ATTGCTACTAGAATTTTTGGCGTGCATCCAAT -s Anc0.Anc0refChr1 58844 32 - 62388 ATTGTTACTAGAACTTTTGGCGTGCATTCAGT -s Anc1.Anc1refChr2 140407 32 + 144309 ATTGTTACTAGAACTTTTGGCGTGCATTCAGT -s Anc2.Anc2refChr3 49187 32 + 53186 ATTGTTACTAGAACTTTTGGCATGCATTCCGT -s mr.mrrefChr5 22350 32 + 294540 ATTGCTACTAGAACTTTTGGCGTGCATTCAGT -s simCow_chr6.simCow.chr6 178164 32 + 602619 ACTGTTACTAGAACTTTTGGCATGATCACTGT -s simDog_chr6.simDog.chr6 461384 32 - 593897 ATAGTCACTAGAGCTTTTGGCATGCATTCCGT -s simHuman_chr6.simHuman.chr6 175674 32 + 601863 ATTGTTACTAGAACTTTTGGCGTGCAATCAGT -s simRat_chr6.simRat.chr6 157153 32 + 647215 ATTGCTACTAGATCTTTTGGGATGCATTCAGT - -a -s simMouse_chr6.simMouse.chr6 159466 16 + 636262 AAAAGATAGCATGTTA -s Anc0.Anc0refChr1 58876 16 - 62388 AGGAGATAGCATACTA -s Anc1.Anc1refChr2 140439 16 + 144309 AGGAGATAGCATACTA -s Anc2.Anc2refChr3 49219 16 + 53186 AGGAGATAGCATACTA -s mr.mrrefChr5 22382 16 + 294540 AAAAGATAGCATATTA -s simCow_chr6.simCow.chr6 178196 16 + 602619 AAGAGATAACATACTA -s simDog_chr6.simDog.chr6 461416 16 - 593897 AGGAAATAGTTTATTA -s simHuman_chr6.simHuman.chr6 175707 15 + 601863 AGGGGATAGCATACT- -s simRat_chr6.simRat.chr6 157185 16 + 647215 AAAAGATAGCACATTA - -a -s simMouse_chr6.simMouse.chr6 159482 15 + 636262 CTCTTAAAGACCCTA -s Anc0.Anc0refChr1 58892 15 - 62388 TTCACCTAGAGCTTC -s Anc1.Anc1refChr2 140455 15 + 144309 TTCACCTAGAGCTTC -s Anc2.Anc2refChr3 49235 15 + 53186 TTCACCTAGAGCTTC -s mr.mrrefChr5 22398 15 + 294540 CTCTTAAAGACCCTA -s simCow_chr6.simCow.chr6 178212 15 + 602619 TTCATCTAGAGCTTC -s simDog_chr6.simDog.chr6 461444 15 - 593897 TTCACCTAGAGCTTC -s simHuman_chr6.simHuman.chr6 175722 7 + 601863 --------GAGCTTC -s simRat_chr6.simRat.chr6 157201 15 + 647215 CACTTAAAGACCCTA - -a -s simMouse_chr6.simMouse.chr6 159497 3 + 636262 ACT -s Anc0.Anc0refChr1 58907 3 - 62388 ACT -s Anc1.Anc1refChr2 140470 3 + 144309 ACT -s Anc1.Anc1refChr2 140636 3 + 144309 ACT -s Anc2.Anc2refChr3 49250 3 + 53186 ACT -s Anc2.Anc2refChr3 49419 3 + 53186 ACT -s mr.mrrefChr5 22413 3 + 294540 ACT -s mr.mrrefChr5 22582 3 + 294540 ACA -s simCow_chr6.simCow.chr6 178386 3 + 602619 ACT -s simCow_chr6.simCow.chr6 178227 3 + 602619 ACC -s simDog_chr6.simDog.chr6 461698 3 - 593897 ACT -s simDog_chr6.simDog.chr6 461459 3 - 593897 ACT -s simHuman_chr6.simHuman.chr6 175895 3 + 601863 ACT -s simHuman_chr6.simHuman.chr6 175729 3 + 601863 ACT -s simMouse_chr6.simMouse.chr6 159666 3 + 636262 GCA -s simRat_chr6.simRat.chr6 157385 3 + 647215 ACA -s simRat_chr6.simRat.chr6 157216 3 + 647215 ATC - -a -s simMouse_chr6.simMouse.chr6 159500 1 + 636262 T -s Anc0.Anc0refChr1 58910 1 - 62388 T -s Anc1.Anc1refChr2 140473 1 + 144309 T -s Anc1.Anc1refChr2 140639 1 + 144309 T -s Anc2.Anc2refChr3 49253 1 + 53186 T -s Anc2.Anc2refChr3 49422 1 + 53186 T -s mr.mrrefChr5 22416 1 + 294540 T -s mr.mrrefChr5 22585 1 + 294540 T -s simCow_chr6.simCow.chr6 178230 1 + 602619 T -s simDog_chr6.simDog.chr6 461701 1 - 593897 T -s simDog_chr6.simDog.chr6 461462 1 - 593897 T -s simHuman_chr6.simHuman.chr6 175898 1 + 601863 T -s simHuman_chr6.simHuman.chr6 175732 1 + 601863 T -s simMouse_chr6.simMouse.chr6 159669 1 + 636262 T -s simRat_chr6.simRat.chr6 157388 1 + 647215 T -s simRat_chr6.simRat.chr6 157219 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 159501 2 + 636262 GA -s Anc0.Anc0refChr1 58911 2 - 62388 GA -s Anc1.Anc1refChr2 140474 2 + 144309 GA -s Anc2.Anc2refChr3 49254 2 + 53186 GA -s Anc2.Anc2refChr3 49423 2 + 53186 CA -s mr.mrrefChr5 22417 2 + 294540 GA -s simCow_chr6.simCow.chr6 178231 2 + 602619 GA -s simDog_chr6.simDog.chr6 461702 2 - 593897 CA -s simDog_chr6.simDog.chr6 461463 2 - 593897 GA -s simHuman_chr6.simHuman.chr6 175733 2 + 601863 GA -s simRat_chr6.simRat.chr6 157220 2 + 647215 GA - -a -s simMouse_chr6.simMouse.chr6 159503 1 + 636262 T -s Anc0.Anc0refChr1 58913 1 - 62388 T -s Anc1.Anc1refChr2 140476 1 + 144309 T -s Anc2.Anc2refChr3 49256 1 + 53186 T -s Anc2.Anc2refChr3 49425 1 + 53186 T -s mr.mrrefChr5 22419 1 + 294540 T -s simCow_chr6.simCow.chr6 178389 1 + 602619 T -s simCow_chr6.simCow.chr6 178233 1 + 602619 T -s simDog_chr6.simDog.chr6 461706 1 - 593897 T -s simDog_chr6.simDog.chr6 461465 1 - 593897 C -s simHuman_chr6.simHuman.chr6 175735 1 + 601863 T -s simRat_chr6.simRat.chr6 157222 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 159504 1 + 636262 G -s Anc0.Anc0refChr1 58914 1 - 62388 A -s Anc1.Anc1refChr2 140477 1 + 144309 A -s Anc2.Anc2refChr3 49257 1 + 53186 A -s Anc2.Anc2refChr3 49431 1 + 53186 A -s mr.mrrefChr5 22420 1 + 294540 G -s simCow_chr6.simCow.chr6 178395 1 + 602619 A -s simCow_chr6.simCow.chr6 178234 1 + 602619 A -s simDog_chr6.simDog.chr6 461712 1 - 593897 A -s simDog_chr6.simDog.chr6 461466 1 - 593897 A -s simHuman_chr6.simHuman.chr6 175736 1 + 601863 A -s simRat_chr6.simRat.chr6 157223 1 + 647215 G - -a -s simMouse_chr6.simMouse.chr6 159505 2 + 636262 GA -s Anc0.Anc0refChr1 58917 2 - 62388 GA -s Anc1.Anc1refChr2 140478 2 + 144309 GA -s Anc2.Anc2refChr3 49260 2 + 53186 GC -s Anc2.Anc2refChr3 49434 2 + 53186 GA -s mr.mrrefChr5 22421 2 + 294540 GA -s simCow_chr6.simCow.chr6 178398 2 + 602619 CA -s simCow_chr6.simCow.chr6 178237 2 + 602619 GA -s simDog_chr6.simDog.chr6 461724 2 - 593897 GA -s simDog_chr6.simDog.chr6 461469 2 - 593897 GC -s simHuman_chr6.simHuman.chr6 175737 2 + 601863 GA -s simRat_chr6.simRat.chr6 157224 2 + 647215 GC - -a -s simMouse_chr6.simMouse.chr6 159507 2 + 636262 GT -s Anc0.Anc0refChr1 58920 2 - 62388 GT -s Anc1.Anc1refChr2 140481 2 + 144309 GT -s Anc2.Anc2refChr3 49263 2 + 53186 GC -s Anc2.Anc2refChr3 49437 2 + 53186 GT -s mr.mrrefChr5 22424 2 + 294540 GT -s simCow_chr6.simCow.chr6 178401 2 + 602619 GT -s simCow_chr6.simCow.chr6 178240 2 + 602619 AC -s simDog_chr6.simDog.chr6 461727 2 - 593897 GT -s simDog_chr6.simDog.chr6 461472 2 - 593897 GC -s simHuman_chr6.simHuman.chr6 175740 2 + 601863 GT -s simRat_chr6.simRat.chr6 157227 2 + 647215 GT - -a -s simMouse_chr6.simMouse.chr6 159509 4 + 636262 TCTG -s Anc0.Anc0refChr1 58922 4 - 62388 TCCA -s Anc1.Anc1refChr2 140483 4 + 144309 TCCA -s Anc2.Anc2refChr3 49265 4 + 53186 TCCA -s Anc2.Anc2refChr3 49439 4 + 53186 CCCA -s mr.mrrefChr5 22426 4 + 294540 TCCA -s simCow_chr6.simCow.chr6 178403 4 + 602619 TCAA -s simCow_chr6.simCow.chr6 178256 4 + 602619 ACCA -s simDog_chr6.simDog.chr6 461729 4 - 593897 CCCA -s simDog_chr6.simDog.chr6 461474 4 - 593897 TCCA -s simHuman_chr6.simHuman.chr6 175742 4 + 601863 TCCA -s simRat_chr6.simRat.chr6 157229 4 + 647215 TCCA - -a -s simMouse_chr6.simMouse.chr6 159513 8 + 636262 AAGATTTT -s Anc0.Anc0refChr1 58926 8 - 62388 AAAATTTC -s Anc1.Anc1refChr2 140487 8 + 144309 AAAATTTC -s Anc2.Anc2refChr3 49269 8 + 53186 AAAATTTC -s Anc2.Anc2refChr3 49443 8 + 53186 AACATTTT -s mr.mrrefChr5 22430 8 + 294540 AAGATTTT -s simCow_chr6.simCow.chr6 178407 8 + 602619 GACATCTT -s simCow_chr6.simCow.chr6 178260 8 + 602619 AGAATTTC -s simDog_chr6.simDog.chr6 461733 8 - 593897 AACATTTT -s simDog_chr6.simDog.chr6 461538 8 - 593897 AAAGTCTC -s simHuman_chr6.simHuman.chr6 175746 8 + 601863 AATATTTC -s simRat_chr6.simRat.chr6 157233 8 + 647215 AAGATTTT - -a -s simMouse_chr6.simMouse.chr6 159521 29 + 636262 GGGATGTCAAAATAGATGTTGGCCCACTG -s Anc0.Anc0refChr1 58934 23 - 62388 GGGGGGT--GAACCAATGA-GATCCA--- -s Anc1.Anc1refChr2 140495 23 + 144309 GGGGGGT--GAACCAATGA-GATCCA--- -s Anc2.Anc2refChr3 49277 23 + 53186 GGGGGGT--GAACCAATGA-CATCCA--- -s Anc2.Anc2refChr3 49451 23 + 53186 GGGGTGA--GAATCAATGA-GATACT--- -s mr.mrrefChr5 22438 29 + 294540 GGGATGTCAAAACAAATGATGGCCCACTG -s simCow_chr6.simCow.chr6 178415 23 + 602619 GGGGGGT--TAACTTATTA-CATGCC--- -s simCow_chr6.simCow.chr6 178268 23 + 602619 AGGGGGT--GAACCAATGA-CATCCA--- -s simDog_chr6.simDog.chr6 461741 23 - 593897 GGGGTGA--GAATCAATGA-GATACT--- -s simDog_chr6.simDog.chr6 461550 23 - 593897 GGGGGGT--GAACCTATGA-CATCCA--- -s simHuman_chr6.simHuman.chr6 175754 23 + 601863 GGGGGGT--GAACCAATGA-GATCCA--- -s simRat_chr6.simRat.chr6 157241 29 + 647215 GAGATGTCAAAACTAATGACGGCCGGCTT - -a -s simMouse_chr6.simMouse.chr6 159550 6 + 636262 CTGCAT -s Anc0.Anc0refChr1 58962 6 - 62388 CCACAA -s Anc1.Anc1refChr2 140523 6 + 144309 CCACAA -s Anc2.Anc2refChr3 49305 6 + 53186 CCACAA -s Anc2.Anc2refChr3 49479 6 + 53186 CCACAA -s mr.mrrefChr5 22472 6 + 294540 CCACAT -s simCow_chr6.simCow.chr6 178443 6 + 602619 CCATAA -s simCow_chr6.simCow.chr6 178296 6 + 602619 CCATAA -s simDog_chr6.simDog.chr6 461769 6 - 593897 CCACAA -s simDog_chr6.simDog.chr6 461578 6 - 593897 CTACAA -s simHuman_chr6.simHuman.chr6 175782 6 + 601863 CCACAG -s simRat_chr6.simRat.chr6 157275 6 + 647215 CCACAT - -a -s simMouse_chr6.simMouse.chr6 159556 1 + 636262 C -s Anc0.Anc0refChr1 58968 1 - 62388 A -s Anc1.Anc1refChr2 140529 1 + 144309 A -s Anc1.Anc1refChr2 140640 1 + 144309 C -s Anc2.Anc2refChr3 49311 1 + 53186 A -s Anc2.Anc2refChr3 49485 1 + 53186 T -s mr.mrrefChr5 22478 1 + 294540 C -s mr.mrrefChr5 22586 1 + 294540 A -s simCow_chr6.simCow.chr6 178449 1 + 602619 C -s simCow_chr6.simCow.chr6 178302 1 + 602619 A -s simDog_chr6.simDog.chr6 461775 1 - 593897 T -s simDog_chr6.simDog.chr6 461584 1 - 593897 A -s simHuman_chr6.simHuman.chr6 175899 1 + 601863 G -s simHuman_chr6.simHuman.chr6 175788 1 + 601863 T -s simMouse_chr6.simMouse.chr6 159670 1 + 636262 A -s simRat_chr6.simRat.chr6 157389 1 + 647215 A -s simRat_chr6.simRat.chr6 157281 1 + 647215 C - -a -s simMouse_chr6.simMouse.chr6 159557 4 + 636262 TGAG -s Anc0.Anc0refChr1 58969 4 - 62388 TAAC -s Anc1.Anc1refChr2 140530 4 + 144309 TAAC -s Anc1.Anc1refChr2 140641 4 + 144309 TAGC -s Anc2.Anc2refChr3 49312 4 + 53186 TAAC -s Anc2.Anc2refChr3 49486 4 + 53186 TAGC -s mr.mrrefChr5 22479 4 + 294540 TGAG -s mr.mrrefChr5 22587 4 + 294540 TAGC -s simCow_chr6.simCow.chr6 178450 4 + 602619 TAGG -s simCow_chr6.simCow.chr6 178303 4 + 602619 TAGC -s simDog_chr6.simDog.chr6 461776 4 - 593897 TAGC -s simDog_chr6.simDog.chr6 461585 4 - 593897 TAAC -s simHuman_chr6.simHuman.chr6 175789 4 + 601863 TAAC -s simMouse_chr6.simMouse.chr6 159671 4 + 636262 TAGC -s simRat_chr6.simRat.chr6 157390 4 + 647215 TAGC -s simRat_chr6.simRat.chr6 157282 4 + 647215 TCAG - -a -s simMouse_chr6.simMouse.chr6 159561 1 + 636262 C -s Anc0.Anc0refChr1 58973 1 - 62388 C -s Anc1.Anc1refChr2 140534 1 + 144309 C -s Anc1.Anc1refChr2 140645 1 + 144309 C -s Anc2.Anc2refChr3 49316 1 + 53186 C -s Anc2.Anc2refChr3 49490 1 + 53186 C -s mr.mrrefChr5 22483 1 + 294540 C -s mr.mrrefChr5 22591 1 + 294540 T -s simCow_chr6.simCow.chr6 178454 1 + 602619 C -s simCow_chr6.simCow.chr6 178307 1 + 602619 C -s simDog_chr6.simDog.chr6 461780 1 - 593897 C -s simDog_chr6.simDog.chr6 461589 1 - 593897 C -s simHuman_chr6.simHuman.chr6 175900 1 + 601863 A -s simHuman_chr6.simHuman.chr6 175793 1 + 601863 C -s simMouse_chr6.simMouse.chr6 159675 1 + 636262 T -s simRat_chr6.simRat.chr6 157394 1 + 647215 T -s simRat_chr6.simRat.chr6 157286 1 + 647215 C - -a -s simMouse_chr6.simMouse.chr6 159562 5 + 636262 TTACA -s Anc0.Anc0refChr1 58974 5 - 62388 TGGCT -s Anc1.Anc1refChr2 140535 5 + 144309 TGGCT -s Anc1.Anc1refChr2 140646 5 + 144309 TGGCT -s Anc2.Anc2refChr3 49317 5 + 53186 TGGCT -s Anc2.Anc2refChr3 49491 5 + 53186 TGGCT -s mr.mrrefChr5 22484 5 + 294540 TTGCA -s mr.mrrefChr5 22592 5 + 294540 TGGCT -s simCow_chr6.simCow.chr6 178465 5 + 602619 TTGCT -s simCow_chr6.simCow.chr6 178308 5 + 602619 TATCT -s simDog_chr6.simDog.chr6 461781 5 - 593897 TGGCT -s simDog_chr6.simDog.chr6 461590 5 - 593897 TGGCT -s simHuman_chr6.simHuman.chr6 175901 5 + 601863 TAGAT -s simHuman_chr6.simHuman.chr6 175794 5 + 601863 TGGCT -s simMouse_chr6.simMouse.chr6 159676 5 + 636262 TGGCT -s simRat_chr6.simRat.chr6 157395 5 + 647215 TGGCT -s simRat_chr6.simRat.chr6 157287 5 + 647215 TTGCA - -a -s simMouse_chr6.simMouse.chr6 159567 2 + 636262 TG -s Anc0.Anc0refChr1 58979 2 - 62388 AA -s Anc1.Anc1refChr2 140540 2 + 144309 AA -s Anc1.Anc1refChr2 140651 2 + 144309 AA -s Anc2.Anc2refChr3 49322 2 + 53186 AA -s Anc2.Anc2refChr3 49496 2 + 53186 AA -s mr.mrrefChr5 22489 2 + 294540 TG -s mr.mrrefChr5 22597 2 + 294540 AA -s simCow_chr6.simCow.chr6 178313 2 + 602619 AA -s simDog_chr6.simDog.chr6 461786 2 - 593897 AA -s simDog_chr6.simDog.chr6 461595 2 - 593897 GA -s simHuman_chr6.simHuman.chr6 175906 2 + 601863 AA -s simHuman_chr6.simHuman.chr6 175799 2 + 601863 AA -s simMouse_chr6.simMouse.chr6 159681 2 + 636262 AA -s simRat_chr6.simRat.chr6 157400 2 + 647215 GA -s simRat_chr6.simRat.chr6 157292 2 + 647215 CT - -a -s simMouse_chr6.simMouse.chr6 159569 14 + 636262 CTCCTTGTCACACA -s Anc0.Anc0refChr1 58981 8 - 62388 ACTCT------AAG -s Anc1.Anc1refChr2 140542 8 + 144309 ATTCT------ACA -s Anc1.Anc1refChr2 140653 8 + 144309 ACACT------CAG -s Anc2.Anc2refChr3 49324 8 + 53186 ATTCT------AAA -s Anc2.Anc2refChr3 49498 8 + 53186 ACACT------CAG -s mr.mrrefChr5 22491 8 + 294540 CTCCT------ACA -s mr.mrrefChr5 22599 8 + 294540 ACACT------AAT -s simCow_chr6.simCow.chr6 178470 8 + 602619 ACACT------TAG -s simCow_chr6.simCow.chr6 178315 8 + 602619 AAGCT------AAA -s simDog_chr6.simDog.chr6 461788 8 - 593897 ACACT------CAG -s simDog_chr6.simDog.chr6 461597 8 - 593897 ATTTT------AAA -s simHuman_chr6.simHuman.chr6 175908 8 + 601863 ACACT------CAG -s simHuman_chr6.simHuman.chr6 175801 8 + 601863 ATACT------ACA -s simMouse_chr6.simMouse.chr6 159683 8 + 636262 TCACT------AAT -s simRat_chr6.simRat.chr6 157402 8 + 647215 ACACG------AAT -s simRat_chr6.simRat.chr6 157294 8 + 647215 CTTCT------ACA - -a -s simMouse_chr6.simMouse.chr6 159583 9 + 636262 CCCATGGGG -s mr.mrrefChr5 22499 9 + 294540 CCCATGGGG -s simRat_chr6.simRat.chr6 157302 9 + 647215 TTGATGGGT - -a -s simMouse_chr6.simMouse.chr6 159592 3 + 636262 CGG -s Anc0.Anc0refChr1 58989 3 - 62388 CAT -s Anc1.Anc1refChr2 140550 3 + 144309 CAT -s Anc1.Anc1refChr2 140661 3 + 144309 CAT -s Anc2.Anc2refChr3 49332 3 + 53186 CAT -s Anc2.Anc2refChr3 49506 3 + 53186 CAT -s mr.mrrefChr5 22508 3 + 294540 CAG -s mr.mrrefChr5 22607 3 + 294540 CAT -s simCow_chr6.simCow.chr6 178478 3 + 602619 CAT -s simCow_chr6.simCow.chr6 178323 3 + 602619 CAT -s simDog_chr6.simDog.chr6 461796 3 - 593897 CAT -s simDog_chr6.simDog.chr6 461605 3 - 593897 CAT -s simHuman_chr6.simHuman.chr6 175916 3 + 601863 CAT -s simHuman_chr6.simHuman.chr6 175809 3 + 601863 CAT -s simMouse_chr6.simMouse.chr6 159691 3 + 636262 CGT -s simRat_chr6.simRat.chr6 157410 3 + 647215 CAT -s simRat_chr6.simRat.chr6 157311 3 + 647215 CAG - -a -s simMouse_chr6.simMouse.chr6 159595 7 + 636262 CTATTAA -s Anc0.Anc0refChr1 58993 7 - 62388 CCTTAAT -s Anc1.Anc1refChr2 140553 7 + 144309 CCTTAAT -s Anc1.Anc1refChr2 140665 7 + 144309 CCTTAAT -s Anc2.Anc2refChr3 49336 7 + 53186 CCTTAAT -s Anc2.Anc2refChr3 49510 7 + 53186 CCTTAAT -s mr.mrrefChr5 22511 7 + 294540 CTATTAA -s mr.mrrefChr5 22611 7 + 294540 CCTTAAT -s simCow_chr6.simCow.chr6 178482 7 + 602619 CCTTAAT -s simCow_chr6.simCow.chr6 178327 7 + 602619 CGTTAAT -s simDog_chr6.simDog.chr6 461800 7 - 593897 CCTTAAT -s simDog_chr6.simDog.chr6 461609 7 - 593897 CCCTAAT -s simHuman_chr6.simHuman.chr6 175920 7 + 601863 CATTAAT -s simHuman_chr6.simHuman.chr6 175812 7 + 601863 CCTTAAT -s simMouse_chr6.simMouse.chr6 159695 7 + 636262 CCTTAAT -s simRat_chr6.simRat.chr6 157414 7 + 647215 CCTTAAT -s simRat_chr6.simRat.chr6 157314 7 + 647215 CAATTAA - -a -s simMouse_chr6.simMouse.chr6 159602 18 + 636262 AGACATACCGATTACATG -s Anc0.Anc0refChr10 0 18 - 76 AGATGTTCCAATAACATG -s Anc1.Anc1refChr2 140560 18 + 144309 AGATGTTCCAATAACATG -s Anc2.Anc2refChr3 49343 18 + 53186 AGATGTTCCAAGGGAGTG -s mr.mrrefChr5 22518 18 + 294540 AGACATACCAATAACATG -s simCow_chr6.simCow.chr6 178334 12 + 602619 AGAAGTTCCAAG------ -s simDog_chr6.simDog.chr6 461616 18 - 593897 ACATGTTCCAAGGGAGTG -s simHuman_chr6.simHuman.chr6 175819 18 + 601863 AGATTTTCCAATAACATG -s simRat_chr6.simRat.chr6 157321 18 + 647215 GGGCATACCAATACCATG - -a -s simMouse_chr6.simMouse.chr6 159620 2 + 636262 AC -s Anc0.Anc0refChr10 26 2 - 76 AC -s Anc1.Anc1refChr2 140586 2 + 144309 AC -s Anc2.Anc2refChr3 49369 2 + 53186 GG -s mr.mrrefChr5 22536 2 + 294540 AC -s simDog_chr6.simDog.chr6 461642 2 - 593897 GG -s simHuman_chr6.simHuman.chr6 175845 2 + 601863 AC -s simRat_chr6.simRat.chr6 157339 2 + 647215 AG - -a -s simMouse_chr6.simMouse.chr6 159622 8 + 636262 CATTGTGC -s Anc0.Anc0refChr10 29 8 - 76 TATTGGTA -s Anc1.Anc1refChr2 140589 8 + 144309 TATTGGTA -s Anc2.Anc2refChr3 49372 8 + 53186 TAATGGTA -s mr.mrrefChr5 22538 8 + 294540 CATTGTGC -s simCow_chr6.simCow.chr6 178346 8 + 602619 TTATGGTA -s simDog_chr6.simDog.chr6 461645 8 - 593897 TAATGGTG -s simHuman_chr6.simHuman.chr6 175848 8 + 601863 TATTGGTA -s simRat_chr6.simRat.chr6 157341 8 + 647215 CATTGTGC - -a -s simMouse_chr6.simMouse.chr6 159630 19 + 636262 TTGATAAGGCGTCGGCCCA -s Anc0.Anc0refChr10 37 15 - 76 TTAAT----CTAAAAACCA -s Anc1.Anc1refChr2 140597 15 + 144309 TTAAT----CTAAAAACCA -s Anc2.Anc2refChr3 49380 15 + 53186 TTAAA----GTAAAAACCA -s mr.mrrefChr5 22546 19 + 294540 TTAATAAGGCGTAAGACCA -s simCow_chr6.simCow.chr6 178354 10 + 602619 TTAAC----ATGAG----- -s simDog_chr6.simDog.chr6 461659 15 - 593897 TTAAA----GTAGAAACCA -s simHuman_chr6.simHuman.chr6 175856 15 + 601863 CTAAT----CTAAAAACCA -s simRat_chr6.simRat.chr6 157349 19 + 647215 TTAATAGGGCATAAGAAAA - -a -s simMouse_chr6.simMouse.chr6 159649 17 + 636262 ATGGTATCCATGGATCC -s Anc0.Anc0refChr10 59 17 - 76 ATGGCATACAGAGCTTC -s Anc1.Anc1refChr2 140619 17 + 144309 ATGGCATACAGAGCTTC -s Anc2.Anc2refChr3 49402 17 + 53186 AAGGCATACAGTGCTTC -s mr.mrrefChr5 22565 17 + 294540 ATGGTATCCAGAGATCC -s simCow_chr6.simCow.chr6 178369 17 + 602619 AAGGCATGCAGGGGTTC -s simDog_chr6.simDog.chr6 461681 17 - 593897 AAGGCATATAGTGCCTC -s simHuman_chr6.simHuman.chr6 175878 17 + 601863 ATGGAATACAGAGTTAG -s simRat_chr6.simRat.chr6 157368 17 + 647215 ATGGTTTCCAGAGATCC - -a -s simMouse_chr6.simMouse.chr6 159694 1 + 636262 C -s Anc0.Anc0refChr1 58992 1 - 62388 C -s Anc1.Anc1refChr2 140664 1 + 144309 C -s Anc2.Anc2refChr3 49335 1 + 53186 C -s Anc2.Anc2refChr3 49509 1 + 53186 C -s mr.mrrefChr5 22610 1 + 294540 C -s simCow_chr6.simCow.chr6 178481 1 + 602619 C -s simCow_chr6.simCow.chr6 178326 1 + 602619 C -s simDog_chr6.simDog.chr6 461799 1 - 593897 T -s simDog_chr6.simDog.chr6 461608 1 - 593897 C -s simHuman_chr6.simHuman.chr6 175919 1 + 601863 C -s simRat_chr6.simRat.chr6 157413 1 + 647215 C - -a -s simMouse_chr6.simMouse.chr6 159702 5 + 636262 AGATG -s Anc0.Anc0refChr1 59000 5 - 62388 AGATG -s Anc1.Anc1refChr2 140672 5 + 144309 AGATG -s Anc2.Anc2refChr3 49517 5 + 53186 AGATG -s mr.mrrefChr5 22618 5 + 294540 AGATG -s simCow_chr6.simCow.chr6 178489 5 + 602619 GGACA -s simDog_chr6.simDog.chr6 461807 5 - 593897 AGATG -s simHuman_chr6.simHuman.chr6 175927 5 + 601863 AGATG -s simRat_chr6.simRat.chr6 157421 5 + 647215 AGATG - -a -s simMouse_chr6.simMouse.chr6 159707 14 + 636262 GCAAATCAAATACT -s Anc0.Anc0refChr1 59011 14 - 62388 GGAAATGCAATACT -s Anc1.Anc1refChr2 140683 14 + 144309 GGAAATGCAATACT -s Anc2.Anc2refChr3 49528 14 + 53186 AGAAATGCAATACT -s mr.mrrefChr5 22623 14 + 294540 GCAAATCAAATACT -s simCow_chr6.simCow.chr6 178500 14 + 602619 CGAGATGCAATACT -s simDog_chr6.simDog.chr6 461818 14 - 593897 AGTAATGCAAAACT -s simHuman_chr6.simHuman.chr6 175938 14 + 601863 GGAAATGCAATCTT -s simRat_chr6.simRat.chr6 157426 14 + 647215 GCAAATCAAATACT - -a -s simMouse_chr6.simMouse.chr6 159721 39 + 636262 TAATAGCACAAATATGAAAAATAGCATTTAAAAGATCAT -s Anc0.Anc0refChr1 59028 38 - 62388 TAATGGTGCTAATGTAAAAATCAGCATTC-AAAAATCAT -s Anc1.Anc1refChr2 140700 39 + 144309 TAATGGTGCTAATGTAAAAATCAGCATTCAAAAAATCAT -s Anc2.Anc2refChr3 49545 38 + 53186 TAATGGTGCTAATGTAAAAATCAACATTC-AAAAATCAT -s mr.mrrefChr5 22637 39 + 294540 TAATAGCACAAATATAAAAATCAGCATTTAAAAGATCAT -s simCow_chr6.simCow.chr6 178518 38 + 602619 TAATGGTGCTAATATAAAAATCAACATTC-AATAGCCGT -s simDog_chr6.simDog.chr6 461834 29 - 593897 ----GATGCTAATGTAAAAA-----ATTT-AAACATCAT -s simHuman_chr6.simHuman.chr6 175955 39 + 601863 TAATGGTGCTAACGTAAAAATCAGCATTCAAAGAATAAT -s simRat_chr6.simRat.chr6 157440 39 + 647215 TAATAGCACAAATATAAAGATCAGGATTTAAATGATCAT - -a -s simMouse_chr6.simMouse.chr6 159760 25 + 636262 GGACAGACACCACACTCAACAGAGA -s Anc0.Anc0refChr1 59067 25 - 62388 GGACAGGCACCACACTCAACAGGGG -s Anc1.Anc1refChr2 140740 25 + 144309 GGACAGGCACCACACTCAACAGGGG -s Anc2.Anc2refChr3 49584 25 + 53186 GGACAGACACCCCCCTCAACTGGGG -s mr.mrrefChr5 22676 25 + 294540 GGACAGGCACCACACTCAACAGAGA -s simCow_chr6.simCow.chr6 178557 25 + 602619 GGACATCCACCTCCCTCAACTGGGG -s simDog_chr6.simDog.chr6 461864 25 - 593897 GGACAGACACCCCCCCCAACTGGGG -s simHuman_chr6.simHuman.chr6 175995 25 + 601863 GGACAGGTGCCACACTCAACAGGGG -s simRat_chr6.simRat.chr6 157479 25 + 647215 GGACATGCACCACACTCAAAAGAGA - -a -s simMouse_chr6.simMouse.chr6 159785 50 + 636262 AGCCTGCTACTAGTGTGTACCCTATTTTTAAATTCTATGACATTTTGCTT -s Anc0.Anc0refChr1 59093 34 - 62388 AGCCTGAAGCCAGCATA---CCT--------ATGGTAAGCAAGTC----- -s Anc1.Anc1refChr2 140766 42 + 144309 AGCCTGAAGCCAGCATA---CCTG-----GAATGGTAAGCAAGTCCACTG -s Anc2.Anc2refChr3 49610 34 + 53186 AGTCTGAAGCCAACATA---CCC--------ATGGCAAGCAAGCC----- -s mr.mrrefChr5 22701 50 + 294540 AGCCTGCTACTAGTGTATACCCTGTTTTTAAATTCTATGACATTTTGCTT -s simCow_chr6.simCow.chr6 178583 34 + 602619 AGTCTGAAGCCAACATA---CCC--------ATGGCAAGCAAGCC----- -s simDog_chr6.simDog.chr6 461890 4 - 593897 TGTC---------------------------------------------- -s simHuman_chr6.simHuman.chr6 176021 42 + 601863 AGCGTGGGGCCAGAATA---CCTG-----GAATGGTGAACTACTCCACTG -s simRat_chr6.simRat.chr6 157504 50 + 647215 AGCCTGCTACTAGTGTATACCCTGTTTTTCAATTCTTTGACATTTTTCCC - -a -s simMouse_chr6.simMouse.chr6 159835 19 + 636262 GTGGCCTGAGGCCACTATA -s Anc0.Anc0refChr1 59127 18 - 62388 -TAGCCTGAGGACAACCTA -s Anc1.Anc1refChr2 140808 19 + 144309 GTAGCCTGAGGACAACCTA -s Anc2.Anc2refChr3 49644 18 + 53186 -TAGTCTGAGGACAACCTA -s mr.mrrefChr5 22751 19 + 294540 GTGGCCTGAGGCCACTATA -s simCow_chr6.simCow.chr6 178617 18 + 602619 -TAGTCTGAGGCCAACTTA -s simDog_chr6.simDog.chr6 461894 13 - 593897 ------TGAAGACAACCTA -s simHuman_chr6.simHuman.chr6 176067 19 + 601863 GCAGCCTGAGGGCAGCGTA -s simRat_chr6.simRat.chr6 157554 19 + 647215 GTGGCCTGGGGCCACTACA - -a -s simMouse_chr6.simMouse.chr6 159854 16 + 636262 CCAAAATGATAAACTG -s Anc0.Anc0refChr1 59146 16 - 62388 CCAGAATGGTGAACTA -s Anc1.Anc1refChr2 140828 16 + 144309 CCAGAATGGTGAACTA -s Anc2.Anc2refChr3 49663 16 + 53186 CCAGCATGGTGAGCTA -s mr.mrrefChr5 22771 16 + 294540 CCAAAATGATAAACTA -s simCow_chr6.simCow.chr6 178636 15 + 602619 CCA-CATGGTGAGCAG -s simDog_chr6.simDog.chr6 461908 16 - 593897 CCAGCATGGCAAGCTA -s simHuman_chr6.simHuman.chr6 176087 16 + 601863 TCAGAATGGTGAACTA -s simRat_chr6.simRat.chr6 157574 16 + 647215 CCAAACTGATAAACTA - -a -s simMouse_chr6.simMouse.chr6 159870 47 + 636262 GATGCATGGAGAACATTTAGATTCTGGCCATTTGCCTTTATGTGTTA -s Anc0.Anc0refChr1 59173 45 - 62388 A--GCTTGGGGAAGTTACAGTTGCTGACCATTTGTCTTTTTGAGTTG -s Anc1.Anc1refChr2 140856 45 + 144309 A--GCTTGGGGAAGTTACAGTTGCTGACCATTTGTCTTTTTGAGTTG -s Anc2.Anc2refChr3 49690 45 + 53186 A--GCTTGAGGAAGTTACAGTTGCTGACCATTTGTCTTTTTGAGTTG -s mr.mrrefChr5 22799 47 + 294540 AATGCATGGAGAACATTTAGATTCTGGCCATTTGCCTTTATGTGTTA -s simCow_chr6.simCow.chr6 178662 45 + 602619 A--GCATTAGGAGGTTACAGTTGCTGCCCAGTTACCTTTCTGAGTTG -s simDog_chr6.simDog.chr6 461935 42 - 593897 A--GCTTGAGGAACT---AGTTGCTAACCATTTGTCTTTTCGAGTTG -s simHuman_chr6.simHuman.chr6 176115 42 + 601863 A--GCTTAGGAAAGTTACAGTTGCTGACCATTAGTATTTTTGAG--- -s simRat_chr6.simRat.chr6 157602 46 + 647215 AATGCGCGGAGAAAACTTAGGT-CTGGCCATTTGCCTTTATGTGTTA - -a -s simMouse_chr6.simMouse.chr6 159917 10 + 636262 GGTTATCACC -s Anc0.Anc0refChr1 59218 10 - 62388 GGTTATCACC -s Anc1.Anc1refChr2 140901 10 + 144309 GGTTATCACC -s Anc2.Anc2refChr3 49736 10 + 53186 GGTTATCACC -s mr.mrrefChr5 22846 10 + 294540 GGTTATCACC -s simCow_chr6.simCow.chr6 178708 10 + 602619 GGTTATCACC -s simDog_chr6.simDog.chr6 461978 10 - 593897 GATTTTCACC -s simHuman_chr6.simHuman.chr6 176157 10 + 601863 GGTTATCACC -s simRat_chr6.simRat.chr6 157648 10 + 647215 GGTTATCACC - -a -s simMouse_chr6.simMouse.chr6 159927 43 + 636262 TTATGTAATGCCCTTCAAAGTTTTACTCACCAAGTGCAATTTT -s Anc0.Anc0refChr1 59228 43 - 62388 TTATGTAAAGCCCAGCAAGTTTTGCCCTGTCAAGAGCAATTTC -s Anc1.Anc1refChr2 140911 43 + 144309 TTATGTAAAGCCCAGCAAGTTTTGCCCTGTCAAGAGCAATTTC -s Anc2.Anc2refChr3 49746 43 + 53186 TTATGTAAAGCCCAGCACGTTTTGCCCTGTCAAGAGCAATTTC -s mr.mrrefChr5 22856 43 + 294540 TTATGTAATGCCCTGCAAAGTTTTACTCATCAAGTGCAATTTT -s simCow_chr6.simCow.chr6 178718 43 + 602619 TTACATAAAGCCCAGCAGGTTTTACCCTATCAAGAGCAATTTC -s simDog_chr6.simDog.chr6 461988 43 - 593897 TTATGTAAAGCCCAGCACGCTTTGACCTGTGGAGAGCAGTTTC -s simHuman_chr6.simHuman.chr6 176199 43 + 601863 TCATGTAAAGCCCAGAAAGTTTTGCCCGTTCAAGAGCAATTTC -s simRat_chr6.simRat.chr6 157658 40 + 647215 TTATGTAAGGGCCTGCAAAGTT--ACTCATCCAG-ACAATTCT - -a -s simMouse_chr6.simMouse.chr6 159970 8 + 636262 CGTAAATG -s Anc0.Anc0refChr1 59271 8 - 62388 CATAAATG -s Anc1.Anc1refChr2 140954 8 + 144309 CATAAATG -s Anc2.Anc2refChr3 49790 8 + 53186 CATAAATG -s mr.mrrefChr5 22899 8 + 294540 CGTAAATG -s simCow_chr6.simCow.chr6 178763 8 + 602619 TATACATG -s simDog_chr6.simDog.chr6 462032 8 - 593897 CAGAAATG -s simHuman_chr6.simHuman.chr6 176242 8 + 601863 CATAGATG -s simRat_chr6.simRat.chr6 157698 8 + 647215 GCTAAATG - -a -s simMouse_chr6.simMouse.chr6 159978 18 + 636262 TTCCAGGGTTTAGCGCTT -s Anc0.Anc0refChr1 59279 18 - 62388 TTCCAGGATTTAACACCT -s Anc1.Anc1refChr2 140962 18 + 144309 TTCCAGGATTTAACACCT -s Anc2.Anc2refChr3 49798 18 + 53186 TTCCAGGATTTGACACCT -s mr.mrrefChr5 22907 18 + 294540 TTCAAGGGTTTAGCACCT -s simCow_chr6.simCow.chr6 178771 18 + 602619 TTCCGGGATGTGACAACT -s simDog_chr6.simDog.chr6 462040 18 - 593897 TTCCAGGAGTTGACACCT -s simHuman_chr6.simHuman.chr6 176260 18 + 601863 TTCTAAGATTTAACACCT -s simRat_chr6.simRat.chr6 157706 18 + 647215 TTCAACAGTTTGGCACCT - -a -s simMouse_chr6.simMouse.chr6 159996 5 + 636262 CTGAT -s Anc0.Anc0refChr1 59299 5 - 62388 ATGGT -s Anc1.Anc1refChr2 140982 5 + 144309 ATGGT -s Anc2.Anc2refChr3 49818 5 + 53186 ATGGT -s mr.mrrefChr5 22927 5 + 294540 CTGAT -s simCow_chr6.simCow.chr6 178791 5 + 602619 ATGGT -s simDog_chr6.simDog.chr6 462060 5 - 593897 ATGGT -s simHuman_chr6.simHuman.chr6 176280 5 + 601863 ATGGT -s simRat_chr6.simRat.chr6 157726 5 + 647215 CTGAT - -a -s simMouse_chr6.simMouse.chr6 160001 20 + 636262 CTGGCACTGGAAGTTCAATT -s Anc0.Anc0refChr1 59304 15 - 62388 TTGACACTGGA-----AAAT -s Anc1.Anc1refChr2 140987 15 + 144309 TTGACACTGGA-----AAAT -s Anc2.Anc2refChr3 49823 15 + 53186 TTGACAATGGA-----AAAT -s mr.mrrefChr5 22932 20 + 294540 CTGACACTGGAAGTTCAATT -s simCow_chr6.simCow.chr6 178796 14 + 602619 CTGACAATGGA-----TA-T -s simDog_chr6.simDog.chr6 462081 15 - 593897 TTGACAATGGG-----AAAT -s simHuman_chr6.simHuman.chr6 176285 15 + 601863 TTGACACTGGA-----AAGT -s simRat_chr6.simRat.chr6 157731 20 + 647215 CTGACACTGGAAGTTCAATT - -a -s simMouse_chr6.simMouse.chr6 160021 16 + 636262 CTGACCTTACAATAGC -s Anc0.Anc0refChr1 59319 15 - 62388 CTG-CCTCCCAATGAC -s Anc1.Anc1refChr2 141002 15 + 144309 CTG-CCTCCCAATGAC -s Anc2.Anc2refChr3 49846 15 + 53186 CTG-CCCCCCAATGAC -s mr.mrrefChr5 22952 16 + 294540 CTGACCTTACAATAGC -s simCow_chr6.simCow.chr6 178819 15 + 602619 CTG-CTGCCCAATGAC -s simDog_chr6.simDog.chr6 462104 15 - 593897 CTC-CCCCCCAGTGAC -s simHuman_chr6.simHuman.chr6 176300 15 + 601863 CTG-CCTCCCAATGAC -s simRat_chr6.simRat.chr6 157751 16 + 647215 GTAGTCTTACAATAGT - -a -s simMouse_chr6.simMouse.chr6 160037 1 + 636262 T -s Anc0.Anc0refChr1 59334 1 - 62388 T -s Anc1.Anc1refChr2 141017 1 + 144309 T -s Anc2.Anc2refChr3 49861 1 + 53186 T -s mr.mrrefChr5 22968 1 + 294540 T -s simCow_chr6.simCow.chr6 178834 1 + 602619 T -s simDog_chr6.simDog.chr6 462119 1 - 593897 T -s simHuman_chr6.simHuman.chr6 176315 1 + 601863 T -s simRat_chr6.simRat.chr6 157770 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 160038 44 + 636262 TGGTTATGGTTCCCTTAATTGGGCCTCACCATCTTGAGTGTGTG -s Anc0.Anc0refChr1 59335 40 - 62388 TGGCTATACTTCC----ATCAGGCCCCACCATGTTGAGTATGCC -s Anc1.Anc1refChr2 141018 40 + 144309 TGGCTATACTTCC----ATCAGGCCCCACCATGTTGAGTATGCC -s Anc2.Anc2refChr3 49865 40 + 53186 TGGCTACACTTCC----CTCAGGCCCCACCATGTTGATTATGCC -s mr.mrrefChr5 22969 44 + 294540 TGGTTATGGTTCCCTTAATTGGGCCTCACCATCTTGAGTGTGCG -s simCow_chr6.simCow.chr6 178838 40 + 602619 TGGTTACACTTCC----CTCGAGCTTCACCATGTTGATTACGCC -s simDog_chr6.simDog.chr6 462123 40 - 593897 TGGCCACACTTCC----CTTAGGCCCCACCATGTTGATTATGCC -s simHuman_chr6.simHuman.chr6 176316 35 + 601863 ---ATATACTTCC----ATCACGCCCCACCATATT--GTCTGCC -s simRat_chr6.simRat.chr6 157771 44 + 647215 TGGTTATGGTCCCCTTAATTGGGCCTTACCATCTTGAGTGTGCT - -a -s simMouse_chr6.simMouse.chr6 160082 7 + 636262 CTGCCAG -s Anc0.Anc0refChr1 59375 7 - 62388 ATACTGG -s Anc1.Anc1refChr2 141058 7 + 144309 ATACTGG -s Anc2.Anc2refChr3 49905 7 + 53186 ATACTGG -s mr.mrrefChr5 23013 7 + 294540 ATGCCAG -s simCow_chr6.simCow.chr6 178878 7 + 602619 ACACTGG -s simDog_chr6.simDog.chr6 462201 7 - 593897 ATGCTGC -s simHuman_chr6.simHuman.chr6 176351 7 + 601863 ATACTGG -s simRat_chr6.simRat.chr6 157815 7 + 647215 ATGCCAG - -a -s simMouse_chr6.simMouse.chr6 160089 34 + 636262 ATGACATCACATTAATCCATAATTATTTGCTTTA -s Anc0.Anc0refChr1 59384 34 - 62388 ATGAAGTGTAATTAGTCCATAATTATTTGCAATT -s Anc1.Anc1refChr2 141067 34 + 144309 ATGAAGTGTAATTAGTCCATAATTATTTGCAATT -s Anc2.Anc2refChr3 49914 34 + 53186 ATGAAGTGTAATTAGTCTATAATTATTTGCAATT -s mr.mrrefChr5 23020 34 + 294540 ATGACATCACATTAATCCATAATTATTTGCTTTA -s simCow_chr6.simCow.chr6 178887 34 + 602619 ATGAATTGTAGTTGTTCTATAATTATTTGCAATC -s simDog_chr6.simDog.chr6 462210 34 - 593897 TTGGTGTGTAATTAGTCTATAATTATTAGCAATT -s simHuman_chr6.simHuman.chr6 176360 34 + 601863 AGGAAGTGCATTTAGTCCATAATTATCTGCAATT -s simRat_chr6.simRat.chr6 157822 34 + 647215 ATGCCATCACATTAATCCATGATTATTTGCTTTA - -a -s simMouse_chr6.simMouse.chr6 160123 99 + 636262 TTAAAGAAGCTACCAAAGTTTGCAACCCTCCACAGACCCTGTCTGAAAATGTACTGTTCAGAGTGCAGTCAAGTGTGTTAATACCAAGATTTCCATTGT -s Anc0.Anc0refChr1 59423 99 - 62388 TTACCAAAACTACCCAACTTCGCAAACCTCCACAGACCCTGTCTGAACATGTTCTGTTCAGAAAGCAGTCAAGTGGAATTATACCAAGGTTTCCATTGT -s Anc1.Anc1refChr2 141106 99 + 144309 TTACCAAAACTACCCAACTTCGCAAACCTCCACAGACCCTGTCTGAACATGTTCTGTTCAGAAAGCAGTCAAGTGGAATTATACCAAGGTTTCCATTGT -s Anc2.Anc2refChr3 49953 99 + 53186 TTACCAAAACTACCCAACTTCCCATACCTCCACACACCCTGTCTGAACATATTCTGTTTAGGAAGCCATCAAGGAGAATTATACCAAGGCATCCATTGT -s mr.mrrefChr5 23059 99 + 294540 TTAAAGAAGCTACCCAAGTTTGCAACCCTCCACAGACCCTGTCTGAAAATGTACTGTTCAGAATGCAGTCAAGTGTATTAATACCAAGATTTCCATTGT -s simCow_chr6.simCow.chr6 178926 95 + 602619 TTACCAAAACTACCTAGCTTCCCAAACCGCCACACCCCCTGTCTGAACATCTACTGTTTAAGAAG----CAAGAGGAATTATACCACGGCATCCATTGT -s simDog_chr6.simDog.chr6 462249 99 - 593897 TTATAACAAGTATTCAACCCCCCATACCTCCACACACCCTGTCTTAACACAGTCTGTTTAGGAAGCCATCAAGGAGATCTATACCAAGGCATCTATTGT -s simHuman_chr6.simHuman.chr6 176399 97 + 601863 TTACCAAAACTACCCAACTTCGC-ATACTCCACAGACCCTGTCAGAACATGTCCTGTTCAGAAAGTAGTCAAGTG-AATTATACCAAGGTTTCCATTGT -s simRat_chr6.simRat.chr6 157861 98 + 647215 TTAAAGAAGCTCCCCAATTT-GCGACCCTCCACAGACCCTGGCTGAAAATGTACTGTTCAGAATGCAGTCAAGTGGATTAATACCGAGATTTCAATTGT - -a -s simMouse_chr6.simMouse.chr6 160222 60 + 636262 TATCTCTGACAATCTCCACTTTAACCTGAACTCTCAGAAGAGACAGTAATCAGTAACCTT -s Anc0.Anc0refChr1 59522 59 - 62388 TATCTTTGACACCCTCCACTATAACCAGGATTTCCTGAAGAAACAGTAACC-AAATGGTT -s Anc1.Anc1refChr2 141205 60 + 144309 TATCTTTGACACCCTCCACTATAACCAGGATTTCCTGAAGAAACAGTAACCAAAATGGTT -s Anc2.Anc2refChr3 50052 59 + 53186 TATCTTTGACACCCTCCACTATAACCAGGATTTCCTGAAGAAACAGTAACC-AAATGGTT -s mr.mrrefChr5 23158 60 + 294540 TATCTCTGACAATCTCCACTTTAACCTGAACTCTCAGAAGAGACAGTAATCAGTAACCTT -s simCow_chr6.simCow.chr6 179029 59 + 602619 TCTCCTTTGCGCTATATGCTATAGCCAGGATTTGCCGAAGGAACAGTAACC-AAATGATT -s simDog_chr6.simDog.chr6 462348 59 - 593897 TATCTCTGACACCCTCCAATACAATCAGAATTGCCTGAAGAAACAGTAACC-AAATGGTT -s simHuman_chr6.simHuman.chr6 176496 60 + 601863 TACTTTCGACACCTTCCACCATAACCAGGATTTCCTGAAAAAACAGTGACCAAAAGGGTT -s simRat_chr6.simRat.chr6 157959 10 + 647215 GATCTCTGAC-------------------------------------------------- - -a -s simMouse_chr6.simMouse.chr6 160282 30 + 636262 ACGGCAGCAGTTCACTCAGGGCAGCAGACT -s Anc0.Anc0refChr1 59586 24 - 62388 ACAGTAGCATT------AGGGGAGCAGCCC -s Anc1.Anc1refChr2 141270 24 + 144309 ACAGTAGCATT------AGGGGAGCAGCCC -s Anc2.Anc2refChr3 50116 24 + 53186 TCAGTAGCATT------AGGGGAGCAGCCC -s mr.mrrefChr5 23218 24 + 294540 ACGGCAGCAGT------AGGGCAGCAGACT -s simCow_chr6.simCow.chr6 179093 24 + 602619 TCAGTAGCATT------GGAGGACCTGCTC -s simDog_chr6.simDog.chr6 462412 24 - 593897 TTAGTGGCGTT------AGGGGAGCAGCCT -s simHuman_chr6.simHuman.chr6 176561 24 + 601863 ACAGAAGCACT------AGGGAAGCAGCCC - -a -s simMouse_chr6.simMouse.chr6 160312 50 + 636262 GGGGTTGGCATTGAAAGATATTCTGTGATGCCTCTATTACACTACATGTA -s Anc0.Anc0refChr1 59610 48 - 62388 GAGGCTGGCATCAAAATATATCTTACCATACCTCTATTACACT--ATAGA -s Anc1.Anc1refChr2 141294 50 + 144309 GAGGCTGGCATCAAAATATATCTTACCATACCTCTATTACACTACATAGA -s Anc2.Anc2refChr3 50140 48 + 53186 GAGGCCGGCATCAAAATATGTCTTACCATACCTCTATTACACT--ATACA -s mr.mrrefChr5 23242 50 + 294540 GGGGTTGGCATTGAAAGATATTCTGTGATGCCTCTATTACACTACATAGA -s simCow_chr6.simCow.chr6 179118 46 + 602619 AAGGCAGCCATC--AATAGGTCTTGCCATACCTCTATCACTGT--ATACA -s simDog_chr6.simDog.chr6 462436 47 - 593897 GAGGCCGGCATCAAAAGATGCCTTACCAT-CCTCTTTTACACT--ATACA -s simHuman_chr6.simHuman.chr6 176585 50 + 601863 TATGCTGGCAACCAAATATATCTTTCCATACCTCTAGTACACTACATAGA -s simRat_chr6.simRat.chr6 157969 16 + 647215 --------------------------------TCTATTAGAC--CTTAGA - -a -s simMouse_chr6.simMouse.chr6 160362 94 + 636262 CCCCCCATGAGTAAACCCATTAACCTGGCAGCTACATTTATAGCCCTCTCTCAGGACGTCAAAATTGTTCTATCAACCGCTGGCATAGGACTGG -s Anc0.Anc0refChr1 59660 87 - 62388 CCCCGAAAAGCTAAACCTATCAACCTGACTGTCACATTTATAACCCTC-ATCAGGCCGCCAAAACTGTCCTATCAATTGTTGGCATAG------ -s Anc1.Anc1refChr2 141346 93 + 144309 CCCCGAAAAGCTAAACCTATCAACCTGACTGTCACATTTATAACCCTC-ATCAGGCCGCCAAAACTGTCCTATCAATTGTTGGCATAGGACTGC -s Anc2.Anc2refChr3 50190 87 + 53186 CCCCGAAAAGCTAAGCCTATCAACCTGACTGTCACATTTATAACCCTC-ATCAGGCCGCCAAAACTGTCCTATCAATTGTTGGCATTG------ -s mr.mrrefChr5 23292 93 + 294540 CCCCCCATGAGTCAACCTATTAACCTGGCAGCTACATTTATAGCCCTC-CTCAGGACGTCAAAATTGTTCTATCAACTGCTGGCATAGGACTGG -s simCow_chr6.simCow.chr6 179166 86 + 602619 CCCCCAAAGGCTAAGCCTATCAAGCTAACTGCCACGTCTA-AACCCTC-ATCAGGCCGCCAAAACTGTCCTATCAATCGTTGATATTG------ -s simDog_chr6.simDog.chr6 462485 87 - 593897 CCCGGGAAAGCTAAGCCTATCAACCTGACTGTCACATTTGTAACCCTC-ATTAGTTCGCCAAGACTGTACTATCAATTGTTGGCAATG------ -s simHuman_chr6.simHuman.chr6 176637 93 + 601863 CCCCTAAAAGTCACACCTATCAAACCGAATGACACCTTTATAACCCTC-ATCAAGCCGCCAAAACTGTCCTATCAAATATTGGCATAGAACTGC -s simRat_chr6.simRat.chr6 157985 86 + 647215 CCCCTTATGAGCCAACCTATTAACCTGG----TCCATTTATAGACCTT----GGGACGTCAAACTTGTTCTATCAATTGGTGACTTAGGCCTGG - -a -s simMouse_chr6.simMouse.chr6 160456 30 + 636262 ATTTGTACAATTTAAGCAACACCTTGTGAT -s Anc0.Anc0refChr1 59747 29 - 62388 -GTTGTACAATTGAACCAACATCTTGTGAT -s Anc1.Anc1refChr2 141439 30 + 144309 AGTTGTACAATTGAACCAACATCTTGTGAT -s Anc2.Anc2refChr3 50277 29 + 53186 -GTTGTACAATTGAACCAACATCTTGTAAT -s mr.mrrefChr5 23385 30 + 294540 ATTTGTACAATTTAAGCAACACCTTGTGAT -s simCow_chr6.simCow.chr6 179252 29 + 602619 -GTTGTACAATTTAAGCAACATCTTGTATG -s simDog_chr6.simDog.chr6 462572 29 - 593897 -GTTGTCCAAGTGAACCCACATCTTGTAAT -s simHuman_chr6.simHuman.chr6 176730 30 + 601863 AGTTGTACAATTCAACCAACATCTTGTGAT -s simRat_chr6.simRat.chr6 158072 30 + 647215 GTTGGGACAATTTAAGTGACACATCGTGAT - -a -s simMouse_chr6.simMouse.chr6 160486 21 + 636262 AAGACTTTCCCTGCAATTCCA -s Anc0.Anc0refChr1 59777 21 - 62388 AGCAATTGCCATGGGATCTAA -s Anc1.Anc1refChr2 141470 21 + 144309 AGCAATTGCCATGGGATCTAA -s Anc2.Anc2refChr3 50307 21 + 53186 AGCAATTGCCGTGGGATCTAA -s mr.mrrefChr5 23416 21 + 294540 AAGACTTTCCATGCAATTCCA -s simCow_chr6.simCow.chr6 179282 21 + 602619 AGCAATCACCGTGGGATCTAA -s simDog_chr6.simDog.chr6 462602 21 - 593897 AGCATTTGCTGTGGGACCTAG -s simHuman_chr6.simHuman.chr6 176761 21 + 601863 AGCAATTGCCATGGTATCTAA -s simRat_chr6.simRat.chr6 158103 21 + 647215 AAGACTTTCCATGTGATTGCA - -a -s simMouse_chr6.simMouse.chr6 160507 12 + 636262 CATGCAATACAT -s Anc0.Anc0refChr1 59798 12 - 62388 TAAGCAAGACAT -s Anc1.Anc1refChr2 141491 12 + 144309 TAAGCAAGACAT -s Anc2.Anc2refChr3 50328 12 + 53186 TAAGCTAGACTT -s mr.mrrefChr5 23437 12 + 294540 CATGCAATACAT -s simCow_chr6.simCow.chr6 179303 3 + 602619 CAA--------- -s simDog_chr6.simDog.chr6 462624 12 - 593897 TAAGCTAGACTT -s simHuman_chr6.simHuman.chr6 176782 12 + 601863 TAAGCAAGACAT -s simRat_chr6.simRat.chr6 158124 12 + 647215 CATGAGATACAT - -a -s simMouse_chr6.simMouse.chr6 160519 40 + 636262 TTCTCTCAATGATACATACAGTTGTGTTTGCAGGGAAACT -s Anc0.Anc0refChr1 59810 39 - 62388 TTCTCTCTATGACTCATACAATTGCGTTTGC-AGGAAGCT -s Anc1.Anc1refChr2 141503 39 + 144309 TTCTCTCTATGACTCATACAATTGCGTTTGC-AGGAAGCT -s Anc2.Anc2refChr3 50340 39 + 53186 CTCTCTCTATGACTTATACAATTGCATTTGC-AGGAAGAT -s mr.mrrefChr5 23449 40 + 294540 TTCTCTCAATGATACATACAGTTGTGTTTGCAGGGAAGCT -s simCow_chr6.simCow.chr6 179306 9 + 602619 ------------------------------C-AGGTAGTT -s simDog_chr6.simDog.chr6 462636 39 - 593897 CTCTCTCTATGACTTATACAATTGCATTTGC-AGGAAGAT -s simHuman_chr6.simHuman.chr6 176795 39 + 601863 TTCTCTGTATGACTCTTATAATTGGGTATGC-TGGAAGCT -s simRat_chr6.simRat.chr6 158136 40 + 647215 TTCTCTCAATGATACATACTGTTATGTTTGCAGGGAAGCT - -a -s simMouse_chr6.simMouse.chr6 160559 26 + 636262 ATAAATGAAGTATGGGCAAAAGGAGA -s Anc0.Anc0refChr1 59849 26 - 62388 GTAAATGAAGAATGGGCAAAGGAAGA -s Anc1.Anc1refChr2 141542 26 + 144309 GTAAATGAAGAATGGGCAAAGGAAGA -s Anc2.Anc2refChr3 50379 26 + 53186 GTAAATGAAGAATGGACAGAGGAAGA -s mr.mrrefChr5 23489 26 + 294540 GTAAATGAAGTATGGGCAAAAGGAGA -s simCow_chr6.simCow.chr6 179315 14 + 602619 GTAAATACAGAAT------------A -s simDog_chr6.simDog.chr6 462675 26 - 593897 GTAAATGAAGAATGGACAGAGGAAGA -s simHuman_chr6.simHuman.chr6 176838 26 + 601863 GTAAGTGGAGAATGGGCAAACGAAGA -s simRat_chr6.simRat.chr6 158176 25 + 647215 GTAAATGAAGTATGGGCAAAAGGAG- - -a -s simMouse_chr6.simMouse.chr6 160585 35 + 636262 AAAGTGTAAGGACAAACTACCAACATAAGAATTGA -s Anc0.Anc0refChr1 59875 35 - 62388 AAATTGCAAGGACATACTCCCAACGTAACAATTGA -s Anc1.Anc1refChr2 141568 35 + 144309 AAATTGCAAGGACATACTCCCAACGTAACAATTGA -s Anc2.Anc2refChr3 50405 35 + 53186 AAATTGCAAGGACATACTCCCAACACAACCATTGA -s mr.mrrefChr5 23515 35 + 294540 AAAGTGTAAGGACAAACTACCAACGTAAGAATTGA -s simCow_chr6.simCow.chr6 179329 35 + 602619 AGATTGCAAAGACATACTTCCAACACAACTCTTGG -s simDog_chr6.simDog.chr6 462706 35 - 593897 AAATTGCAAGGAGACACTCCCGATACAACCATTTA -s simHuman_chr6.simHuman.chr6 176864 35 + 601863 AAATTGGAAGGACATACTCCCAACGTAACAATTGA -s simRat_chr6.simRat.chr6 158201 26 + 647215 ---------GGACACACTACCAATGTAAGAATTGA - -a -s simMouse_chr6.simMouse.chr6 160620 35 + 636262 TGTAACTTGCTATAATTTTCTTATATTAAACCTTT -s Anc0.Anc0refChr1 59911 33 - 62388 TGTAAGTTGATATAAA--ATTTATATTAATCCTTT -s Anc1.Anc1refChr2 141604 33 + 144309 TGTAAGTTGATATAAA--ATTTATATTAATCCTTT -s Anc2.Anc2refChr3 50441 33 + 53186 TGTAAGTTGATATAAA--ATTTATATTAATCCTTT -s mr.mrrefChr5 23551 35 + 294540 TGTAACTTGATATAAATTTTTTATATTAAACCTTT -s simCow_chr6.simCow.chr6 179365 33 + 602619 TTTAACTTGATAGAAA--ATTTATCTTAACCGCTT -s simDog_chr6.simDog.chr6 462742 33 - 593897 CGTAAGTTGCTATAAA--ACCTGTATTAATTCTTT -s simHuman_chr6.simHuman.chr6 176900 33 + 601863 TGTCATTCGATATAAA--ATTTATATTACTCCTTT -s simRat_chr6.simRat.chr6 158228 35 + 647215 TGTAACTTGATATAAATCTTTTATATTAAACCTTT - -a -s simMouse_chr6.simMouse.chr6 160655 3 + 636262 TTA -s Anc0.Anc0refChr1 59947 3 - 62388 TTA -s Anc1.Anc1refChr2 141640 3 + 144309 TTA -s Anc2.Anc2refChr3 50477 3 + 53186 TTA -s mr.mrrefChr5 23586 3 + 294540 TTA -s simCow_chr6.simCow.chr6 179401 3 + 602619 GTA -s simDog_chr6.simDog.chr6 462778 3 - 593897 TTA -s simHuman_chr6.simHuman.chr6 176936 3 + 601863 TTA -s simRat_chr6.simRat.chr6 158263 3 + 647215 ATA - -a -s simMouse_chr6.simMouse.chr6 160658 2 + 636262 AG -s Anc0.Anc0refChr1 59950 2 - 62388 AG -s Anc1.Anc1refChr2 141643 2 + 144309 AG -s Anc2.Anc2refChr3 50480 2 + 53186 AG -s mr.mrrefChr5 23589 2 + 294540 AG -s simCow_chr6.simCow.chr6 179404 2 + 602619 AG -s simDog_chr6.simDog.chr6 462788 2 - 593897 AG -s simHuman_chr6.simHuman.chr6 176939 2 + 601863 AG -s simRat_chr6.simRat.chr6 158266 2 + 647215 AG - -a -s simMouse_chr6.simMouse.chr6 160660 30 + 636262 CACATCACCTTGTCCAAATAGTAAGGATGG -s Anc0.Anc0refChr1 59953 30 - 62388 CACATCACCTTTTATACATAGAAACAATGG -s Anc1.Anc1refChr2 141646 30 + 144309 CACATCACCTTTTATACATAGAAACAATGG -s Anc2.Anc2refChr3 50483 30 + 53186 CACATCACCTTTTATACATTGAAACAATGG -s mr.mrrefChr5 23591 30 + 294540 CACATCACCTTGTACAAATAGTAAGGATGG -s simCow_chr6.simCow.chr6 179407 30 + 602619 CATATCTCCTTTCATACATTGAAACAATGG -s simDog_chr6.simDog.chr6 462791 30 - 593897 CACATCACCTTTTGTACATTGAAGCAATAG -s simHuman_chr6.simHuman.chr6 176942 30 + 601863 CACATCACCCTTTATACTTAGAAACAATGG -s simRat_chr6.simRat.chr6 158268 30 + 647215 CACATCAGCTTGTACAAGTAGTAAAGGTGG - -a -s simMouse_chr6.simMouse.chr6 160690 32 + 636262 ATCTGAATATTGAATTAGTTGAGATTTACTAA -s Anc0.Anc0refChr1 59984 32 - 62388 ATCCAAACATGGGATTAGCTGAGATTTACCTA -s Anc1.Anc1refChr2 141677 32 + 144309 ATCCAAACATGGGATTAGCTGAGATTTACCTA -s Anc2.Anc2refChr3 50514 32 + 53186 ATCCAAACATGGGATTAGCTGAGATTTACCTG -s mr.mrrefChr5 23621 32 + 294540 ATCTGAATATTGAATTAGTTGAGATTTACTAA -s simCow_chr6.simCow.chr6 179438 31 + 602619 ATCCAAACATGGGATTGGCTCA-ACTTACCTG -s simDog_chr6.simDog.chr6 462822 32 - 593897 ATCGAAATATGGGATTAGCCGAGATTTACCTG -s simHuman_chr6.simHuman.chr6 176973 32 + 601863 ATCCAAACATGGGATTATCTGAGATTCACCTA -s simRat_chr6.simRat.chr6 158298 32 + 647215 ATCTGAATACTGAATTAGTGGAGATTTACTAA - -a -s simMouse_chr6.simMouse.chr6 160722 64 + 636262 CTGTTTCCCTTTTCATAGCAATGCCTTACTCTTCAGTTATAACCACTTGTCTATAAACAAGATT -s Anc0.Anc0refChr1 60020 55 - 62388 -TGTTTCTCATTCCACAACAATCACATACTGTTCT-T--TAACCATTTGACCATAAACC----- -s Anc1.Anc1refChr2 141713 57 + 144309 GTGTTTCTCATTCCACAACAATCACATACTGTTCTGT--TAACCATTTGACCATAAACC----- -s Anc2.Anc2refChr3 50550 55 + 53186 -TGTTTCTCATTTCACAACAATCACATACTGTTCT-T--TAACCATTTGACCATAAAGC----- -s mr.mrrefChr5 23653 64 + 294540 GTGTTTCTCATTCCATAGCAATGACTTACTCTTCTGTTATAACCATTTGTCTATAAACAAGATT -s simCow_chr6.simCow.chr6 179473 55 + 602619 -TGTTTCTCAATTTTTAACAATCAGATACTGATGT-C--TAACAATTTGACTGTAAATC----- -s simDog_chr6.simDog.chr6 462858 55 - 593897 -TGTTTCTCCTTTCACAACAATCACATACTGTTCT-T--TAACCATCTGACCATAAAGC----- -s simHuman_chr6.simHuman.chr6 177010 57 + 601863 GTTTCACTCATTCCACAACAGTCACATACCATGCTGT--TAACCATTTGACCACAAACC----- -s simRat_chr6.simRat.chr6 158330 64 + 647215 GTGTTTCTCATTCCATAGCAATGACTTACACTTCTGTTATAACTATTTGTCTATAAACAAGTAT - -a -s simMouse_chr6.simMouse.chr6 160786 39 + 636262 AGTCCTTAACAGAGTATCCAAAATCTCCAGCTAACATGC -s Anc0.Anc0refChr1 60080 39 - 62388 ATTACCTTACTGAGTATCCTAAATGTCCAGCAAACATAC -s Anc1.Anc1refChr2 141775 39 + 144309 ATTACCTTACTGAGTATCCTAAATGTCCAGCAAACATAC -s Anc2.Anc2refChr3 50610 39 + 53186 ATAACTTTACTGAGTATCCTTAATGTCCAGCAAACATAC -s mr.mrrefChr5 269184 39 - 294540 AGTCCCTAACAGAGTATCCAAAATCTCCAGCAAACATGC -s simCow_chr6.simCow.chr6 179533 39 + 602619 ACAATTTGCCTGAGTATTCTTAAAGTTCAGCATACATAC -s simDog_chr6.simDog.chr6 462917 39 - 593897 ATAGCTTTACTGAATATCCATTATGTCCAGCAAACATAC -s simHuman_chr6.simHuman.chr6 177072 39 + 601863 ATTACCTCACTGAGTATCCTAAATGTCCATCAATCATAC -s simRat_chr6.simRat.chr6 487092 39 - 647215 AGTCCCTAACAGAGTATCCAACATATCCAGCAAACATGT - -a -s simMouse_chr6.simMouse.chr6 160825 65 + 636262 AGTATATGCTTTCTTAATATGTCAACACAACAAACACAATAGCAATTTTCTGATCCCTGTGCTGC -s Anc0.Anc0refChr1 60119 56 - 62388 AACATATGCTTTCTTCACATGTGCACACAA---------CAGTAATTTTTTAATCTATGTGCTGC -s Anc1.Anc1refChr2 141814 56 + 144309 AACATATGCTTTCTTCACATGTGCACACAA---------CAGTAATTTTTTAATCTATGTGCTGC -s Anc2.Anc2refChr3 50649 56 + 53186 AACATGTGCTTACTTCACATGTGCACACAA---------TAGTAATTTTTTAATCTATGTGTTGC -s mr.mrrefChr5 269223 56 - 294540 AGTATATGCTTTCTTAATATGTCAACACAA---------CAGCAATTTTCTGATCCATGTGCTGC -s simCow_chr6.simCow.chr6 179572 56 + 602619 AACAAGAGCTTCCTTCACATGTGCACATAA---------TAATGATTTTGTAATCTACGTGTTGC -s simDog_chr6.simDog.chr6 462957 56 - 593897 AACCTGTGCTTACTTCATAAGTGCACACGA---------TAGAAATCTTTTAACTAATGTGTTGC -s simHuman_chr6.simHuman.chr6 177111 56 + 601863 AACATATGATTTCTTCACATGAGCACACAA---------CAGTAATTTTATAATCTATGTGCTGC -s simRat_chr6.simRat.chr6 487131 56 - 647215 AGTATATGCTTTCTTAGTATGTAAACACAA---------CAGCAATTTCCTGATCCATGTGTTGC - -a -s simMouse_chr6.simMouse.chr6 160890 4 + 636262 ACAT -s Anc0.Anc0refChr1 60175 4 - 62388 ACAT -s Anc1.Anc1refChr2 141870 4 + 144309 ACAT -s Anc2.Anc2refChr3 50705 4 + 53186 ACAT -s mr.mrrefChr5 269279 4 - 294540 ACAT -s simCow_chr6.simCow.chr6 179628 4 + 602619 ACAT -s simDog_chr6.simDog.chr6 463013 4 - 593897 ACAT -s simHuman_chr6.simHuman.chr6 177167 4 + 601863 ACAT -s simRat_chr6.simRat.chr6 487197 4 - 647215 ACAT - -a -s simMouse_chr6.simMouse.chr6 160894 1 + 636262 A -s Anc0.Anc0refChr1 60179 1 - 62388 A -s Anc1.Anc1refChr2 141874 1 + 144309 A -s Anc2.Anc2refChr3 50709 1 + 53186 A -s mr.mrrefChr5 269283 1 - 294540 A -s simCow_chr6.simCow.chr6 179632 1 + 602619 A -s simDog_chr6.simDog.chr6 463028 1 - 593897 A -s simHuman_chr6.simHuman.chr6 177171 1 + 601863 A -s simRat_chr6.simRat.chr6 487201 1 - 647215 A - -a -s simMouse_chr6.simMouse.chr6 160895 11 + 636262 TATTATATAGA -s Anc0.Anc0refChr1 60186 11 - 62388 TACAATACAGA -s Anc1.Anc1refChr2 141881 11 + 144309 TACAATACAGA -s Anc2.Anc2refChr3 50716 11 + 53186 TACAATACAGA -s mr.mrrefChr5 269284 11 - 294540 TATTATATAGA -s simCow_chr6.simCow.chr6 179639 11 + 602619 TACAGCACAGA -s simDog_chr6.simDog.chr6 463035 6 - 593897 CACAAT----- -s simHuman_chr6.simHuman.chr6 177178 11 + 601863 TACAATACAGA -s simRat_chr6.simRat.chr6 487202 11 - 647215 TATTATATAGA - -a -s simMouse_chr6.simMouse.chr6 160906 21 + 636262 TGATCCCTATATTATACCCTC -s Anc0.Anc0refChr1 60197 13 - 62388 TGATCCCTAT--------CTC -s Anc1.Anc1refChr2 141892 14 + 144309 TGATCCCTATA-------CTC -s Anc2.Anc2refChr3 50727 13 + 53186 GGATTCCCAT--------CTC -s mr.mrrefChr5 269295 21 - 294540 TGATCCCTATATTATATCCTC -s simCow_chr6.simCow.chr6 179651 13 + 602619 GGATTCCCAT--------CTC -s simHuman_chr6.simHuman.chr6 177189 11 + 601863 TGATCCCTGTA---------- -s simRat_chr6.simRat.chr6 487213 21 - 647215 TGATCCCTATGTTATATCCTC - -a -s simMouse_chr6.simMouse.chr6 160927 35 + 636262 AAAAAGAATGGCGCACATCCCATGGTTACACAGCT -s Anc0.Anc0refChr1 60210 34 - 62388 GAGCAAAAC-ACCTGCCTACCTTTGTCATGCTGAT -s Anc1.Anc1refChr2 141906 34 + 144309 GAGCAAAAC-ACCTGCCTACCTTTGTCATGCTGAT -s Anc2.Anc2refChr3 50740 34 + 53186 GAGCAAAAC-ACCTGCCTACCTTTGTCATGCTGAT -s mr.mrrefChr5 269316 35 - 294540 AAAAAGAATGGCGCACATCCCATGGTTATACAGCT -s simCow_chr6.simCow.chr6 179701 34 + 602619 GAGCAGAAT-ATGTGCCCACCTTGATCGTACAGAT -s simDog_chr6.simDog.chr6 463041 34 - 593897 GAGCAAAAC-ACCTGCCTACCTTTGTCATGCTGAT -s simRat_chr6.simRat.chr6 487234 35 - 647215 ACAAAGAACAGCACACATCCCATGGTTATACAGCT - -a -s simMouse_chr6.simMouse.chr6 160962 39 + 636262 CAGAGTTTGATTTGATTGTGGTACCTAACTCTTGCCTTG -s Anc0.Anc0refChr1 60244 38 - 62388 GAT-GTTTGACCTATTGGCAGTACCTGATTCAAGCCCTG -s Anc1.Anc1refChr2 141940 38 + 144309 GAT-GTTTGACCTATTGGCAGTACCTGATTCAAGCCCTG -s Anc2.Anc2refChr3 50774 38 + 53186 GAT-GTTTGACCTATTGGCAGTACCTGATTCAAGCCCTG -s mr.mrrefChr5 269351 39 - 294540 CAGAGTTTGATTTGTTTGTGGTACCTAACTCTTGCCTTG -s simCow_chr6.simCow.chr6 179736 38 + 602619 AAT-ATTTGACCTACTAATGGTCCATAATTCATACCCTG -s simDog_chr6.simDog.chr6 463075 38 - 593897 GAT-GTTTGACCTATTGGCAGTACCTGATTCAAGCCCTG -s simRat_chr6.simRat.chr6 487269 35 - 647215 CAGG----AATTTGTTTGTGGTACCTAACTCTTGCCTTG - -a -s simMouse_chr6.simMouse.chr6 161001 68 + 636262 TGCTGCGTTTGCAGTTACATACCCAACTTCTTAAAAAAGAACTTCATTCTCAGAAGGATTAAGATATA -s Anc0.Anc0refChr1 60282 67 - 62388 T-CAGGGTATTCGGCCCCATACTTAACTTCTTAAATGGGACCTCCATTCTCAGAAGAGTTAAGGTCTA -s Anc1.Anc1refChr2 141978 67 + 144309 T-CAGGGTATTCGGCCCCATACTTAACTTCTTAAATGGGACCTCCATTCTCAGAAGAGTTAAGGTCTA -s Anc2.Anc2refChr3 50812 67 + 53186 T-CAGGGTATTCGGCCCCATACTTAACTTCTTAAATGGGACCTCCATTCTGAGAAGAGTCAAGGTCTA -s mr.mrrefChr5 269390 68 - 294540 TGCTGCGTTTGCAGTTCCATACCCAACTTCTTAAAAGAGAACTTCATTCTCAGAAGGGTTAAGATATA -s simCow_chr6.simCow.chr6 179774 66 + 602619 T-CAGTGTATTTGGTGCCGTACTTA-CTTCTTAAATGGGCCCCCCATTCTTAGAAGAGTCGGGGTATG -s simDog_chr6.simDog.chr6 463114 67 - 593897 T-CAGGGTATTCGGCCCCATACTTAACTTCTTAAATGGGACTTATGTTCTGAGAAGAGTCAAGGTCTA -s simHuman_chr6.simHuman.chr6 177200 48 + 601863 --------------------GCTTAACTTCTTATATGGGACCTCCATTCTCAAAAAAATTAAGGTGTA -s simRat_chr6.simRat.chr6 487304 67 - 647215 TGCTGTGTTTCCAGTTCCATACCCAACTTCTTAAAAGAGAACTTCATTCTCAGAAGGGTTAAGATAT- - -a -s simMouse_chr6.simMouse.chr6 161069 3 + 636262 TAG -s Anc0.Anc0refChr1 60349 3 - 62388 TAG -s Anc1.Anc1refChr2 142045 3 + 144309 TAG -s Anc2.Anc2refChr3 50879 3 + 53186 TAG -s mr.mrrefChr5 269458 3 - 294540 TAG -s simCow_chr6.simCow.chr6 179840 3 + 602619 TAG -s simDog_chr6.simDog.chr6 463187 3 - 593897 TAG -s simHuman_chr6.simHuman.chr6 177248 3 + 601863 CAG -s simRat_chr6.simRat.chr6 487371 3 - 647215 TAG - -a -s simMouse_chr6.simMouse.chr6 161072 1 + 636262 T -s Anc0.Anc0refChr1 60356 1 - 62388 T -s Anc1.Anc1refChr2 142052 1 + 144309 T -s Anc2.Anc2refChr3 50886 1 + 53186 T -s mr.mrrefChr5 269461 1 - 294540 T -s simCow_chr6.simCow.chr6 179847 1 + 602619 G -s simDog_chr6.simDog.chr6 463195 1 - 593897 T -s simHuman_chr6.simHuman.chr6 177255 1 + 601863 C -s simRat_chr6.simRat.chr6 487374 1 - 647215 T - -a -s simMouse_chr6.simMouse.chr6 161073 43 + 636262 TCAAGCCCACTTATGGCAATGGGCTGTGGGTGGGTACTGATTA -s Anc0.Anc0refChr1 60357 43 - 62388 CCTAGAAGACACATAGTAAGTGTCTGTGGGTGGGTGGTAATTA -s Anc1.Anc1refChr2 142053 43 + 144309 CCTAGAAGACACATAGTAAGTGTCTGTGGGTGGGTGGTAATTA -s Anc2.Anc2refChr3 50887 43 + 53186 CCTAGAAGACACATAGTAAGTGTCTGTGGGTGGGTGGTAATTA -s mr.mrrefChr5 269462 43 - 294540 TCTAGCCCACTTATAGTAATGGGCTGTGGGTGGGTACTGATTA -s simCow_chr6.simCow.chr6 179848 43 + 602619 CCTTGAAGACACATAGTACATGTCTCTTTGTGGATGGTAATTA -s simDog_chr6.simDog.chr6 463196 43 - 593897 CTTAGAAGAGACACAGTAAGCATCTGTGGGAGGGTGGTAAATA -s simHuman_chr6.simHuman.chr6 177256 43 + 601863 CCTAGAAGACACATAGTAAGTGTCTGTGGGTGGGTGGTCATTA -s simRat_chr6.simRat.chr6 487379 43 - 647215 TCTCGACCACTTGTAGTGATGGGCTGTGGGTGGGTACTGATTA - -a -s simMouse_chr6.simMouse.chr6 161116 52 + 636262 AGCAACATCATGAATATTATCTCCCCCTAGAAGCAGCATCATGAATATTATC -s Anc0.Anc0refChr1 60410 38 - 62388 AGCAAAATCATG-ATATGTTCT---------ATTGACGTAATGA----TATT -s Anc1.Anc1refChr2 142106 38 + 144309 AGCAAAATCATG-ATATGTTCT---------ATTGACGTAATGA----TATT -s Anc2.Anc2refChr3 50940 38 + 53186 AGCAAAATCATG-ATGTGTTCT---------ATTGACGTAATGG----TATT -s mr.mrrefChr5 269505 38 - 294540 AGCAACATCATG-ATATTATCT---------AGCAGCATCATGA----TATC -s simCow_chr6.simCow.chr6 179901 38 + 602619 AACAACCTTGTG-GTGTGTTTT---------ATGGGCGTAGTGG----TATT -s simDog_chr6.simDog.chr6 463249 38 - 593897 AGTGAAATCATG-ATGTGTTCT---------ATTGACATGATGG----CATT -s simHuman_chr6.simHuman.chr6 177319 38 + 601863 AGCAATATCATG-ATATGTTCT---------ATTGATGCAATAA----TATT -s simRat_chr6.simRat.chr6 487422 7 - 647215 CCCAACA--------------------------------------------- - -a -s simMouse_chr6.simMouse.chr6 161168 7 + 636262 TCCCCCT -s Anc0.Anc0refChr1 60448 7 - 62388 TCCCGCA -s Anc1.Anc1refChr2 142144 7 + 144309 TCCCCCT -s Anc1.Anc1refChr2 142263 7 + 144309 TCTTACA -s Anc2.Anc2refChr3 50978 7 + 53186 TCCCGCT -s Anc2.Anc2refChr3 51093 7 + 53186 TCTTGCA -s mr.mrrefChr5 269543 7 - 294540 TCCCCCT -s mr.mrrefChr5 269600 7 - 294540 CATCACA -s simCow_chr6.simCow.chr6 179939 7 + 602619 TCCCTCT -s simDog_chr6.simDog.chr6 463402 7 - 593897 TCTTGCA -s simDog_chr6.simDog.chr6 463287 7 - 593897 TCCTGCT -s simHuman_chr6.simHuman.chr6 177476 7 + 601863 ACTGACT -s simHuman_chr6.simHuman.chr6 177357 7 + 601863 TCCCCCT -s simMouse_chr6.simMouse.chr6 161225 7 + 636262 CATCACA -s simRat_chr6.simRat.chr6 487492 7 - 647215 CATCACA - -a -s simMouse_chr6.simMouse.chr6 161175 11 + 636262 AGCACAGTGTT -s Anc0.Anc0refChr1 60455 11 - 62388 GTCACAATTTC -s Anc1.Anc1refChr2 142151 11 + 144309 AGCACAGTGTC -s Anc1.Anc1refChr2 142270 11 + 144309 GTCACAATTTC -s Anc2.Anc2refChr3 50985 11 + 53186 GGCACAATGTC -s Anc2.Anc2refChr3 51100 11 + 53186 GTCACAATTTC -s mr.mrrefChr5 269550 11 - 294540 AGCACAGTGTT -s mr.mrrefChr5 269607 11 - 294540 ATAAAAATTTC -s simCow_chr6.simCow.chr6 179946 11 + 602619 GGTACTCTGCC -s simDog_chr6.simDog.chr6 463409 11 - 593897 GTCACAATTTC -s simDog_chr6.simDog.chr6 463294 11 - 593897 GGCACAATGTC -s simHuman_chr6.simHuman.chr6 177483 11 + 601863 GTCCCAATGTA -s simHuman_chr6.simHuman.chr6 177364 11 + 601863 AGCACAGTGTC -s simMouse_chr6.simMouse.chr6 161232 11 + 636262 ATAAAAATGCT -s simRat_chr6.simRat.chr6 487499 11 - 647215 ATATAAATTTC -s simRat_chr6.simRat.chr6 487429 11 - 647215 AGTACAGTTTT - -a -s simMouse_chr6.simMouse.chr6 161186 5 + 636262 CTCTG -s Anc0.Anc0refChr1 60466 5 - 62388 CTATG -s Anc1.Anc1refChr2 142162 5 + 144309 CTATG -s Anc1.Anc1refChr2 142281 5 + 144309 CTTTG -s Anc2.Anc2refChr3 50996 5 + 53186 CCATG -s Anc2.Anc2refChr3 51111 5 + 53186 CTTTG -s mr.mrrefChr5 269561 5 - 294540 CTCTG -s mr.mrrefChr5 269618 5 - 294540 CTTAG -s simCow_chr6.simCow.chr6 180043 5 + 602619 CTTCA -s simCow_chr6.simCow.chr6 179957 5 + 602619 CCCTG -s simDog_chr6.simDog.chr6 463420 5 - 593897 CTTTG -s simDog_chr6.simDog.chr6 463305 5 - 593897 CCATG -s simHuman_chr6.simHuman.chr6 177494 5 + 601863 CTCGG -s simHuman_chr6.simHuman.chr6 177375 5 + 601863 ATAAG -s simMouse_chr6.simMouse.chr6 161243 5 + 636262 CTTAG -s simRat_chr6.simRat.chr6 487510 5 - 647215 CTTGG -s simRat_chr6.simRat.chr6 487440 1 - 647215 C---- - -a -s simMouse_chr6.simMouse.chr6 161191 5 + 636262 TTATT -s Anc0.Anc0refChr1 60472 5 - 62388 CAATC -s Anc1.Anc1refChr2 142168 5 + 144309 CTATT -s Anc1.Anc1refChr2 142287 5 + 144309 CAATC -s Anc2.Anc2refChr3 51002 5 + 53186 CTATT -s Anc2.Anc2refChr3 51117 5 + 53186 CAATC -s mr.mrrefChr5 269566 5 - 294540 TTATT -s mr.mrrefChr5 269624 5 - 294540 CAATT -s simCow_chr6.simCow.chr6 180049 5 + 602619 TGATT -s simCow_chr6.simCow.chr6 179963 3 + 602619 C--TT -s simDog_chr6.simDog.chr6 463426 5 - 593897 CAATC -s simDog_chr6.simDog.chr6 463311 5 - 593897 CTATT -s simHuman_chr6.simHuman.chr6 177500 5 + 601863 GAGTC -s simHuman_chr6.simHuman.chr6 177381 5 + 601863 CTATT -s simMouse_chr6.simMouse.chr6 161249 5 + 636262 CAGTT -s simRat_chr6.simRat.chr6 487516 5 - 647215 CAATT -s simRat_chr6.simRat.chr6 487441 2 - 647215 ---TG - -a -s simMouse_chr6.simMouse.chr6 161196 4 + 636262 CACT -s Anc0.Anc0refChr1 60478 4 - 62388 AACT -s Anc1.Anc1refChr2 142173 4 + 144309 AACT -s Anc1.Anc1refChr2 142293 4 + 144309 AACT -s Anc2.Anc2refChr3 51007 4 + 53186 AACT -s Anc2.Anc2refChr3 51123 4 + 53186 AACT -s mr.mrrefChr5 269571 4 - 294540 CACT -s mr.mrrefChr5 269629 4 - 294540 AATT -s simCow_chr6.simCow.chr6 180054 4 + 602619 GACT -s simCow_chr6.simCow.chr6 179966 4 + 602619 AACT -s simDog_chr6.simDog.chr6 463438 4 - 593897 AACT -s simDog_chr6.simDog.chr6 463316 4 - 593897 AACT -s simHuman_chr6.simHuman.chr6 177506 4 + 601863 AACT -s simHuman_chr6.simHuman.chr6 177386 4 + 601863 AACT -s simMouse_chr6.simMouse.chr6 161254 4 + 636262 AATT -s simRat_chr6.simRat.chr6 487521 4 - 647215 AATT -s simRat_chr6.simRat.chr6 487443 4 - 647215 CACC - -a -s simMouse_chr6.simMouse.chr6 161200 1 + 636262 A -s Anc0.Anc0refChr1 60482 1 - 62388 T -s Anc1.Anc1refChr2 142177 1 + 144309 T -s Anc1.Anc1refChr2 142297 1 + 144309 T -s Anc2.Anc2refChr3 51127 1 + 53186 T -s mr.mrrefChr5 269575 1 - 294540 A -s mr.mrrefChr5 269633 1 - 294540 T -s simCow_chr6.simCow.chr6 180058 1 + 602619 T -s simDog_chr6.simDog.chr6 463442 1 - 593897 T -s simHuman_chr6.simHuman.chr6 177510 1 + 601863 T -s simHuman_chr6.simHuman.chr6 177390 1 + 601863 T -s simMouse_chr6.simMouse.chr6 161258 1 + 636262 T -s simRat_chr6.simRat.chr6 487525 1 - 647215 T -s simRat_chr6.simRat.chr6 487447 1 - 647215 G - -a -s simMouse_chr6.simMouse.chr6 161201 3 + 636262 TAA -s Anc0.Anc0refChr1 60483 3 - 62388 TAC -s Anc1.Anc1refChr2 142178 3 + 144309 TAA -s Anc1.Anc1refChr2 142298 3 + 144309 TAC -s Anc2.Anc2refChr3 51128 3 + 53186 TTC -s mr.mrrefChr5 269576 3 - 294540 TAA -s mr.mrrefChr5 269634 3 - 294540 TAC -s simCow_chr6.simCow.chr6 180059 3 + 602619 TGC -s simDog_chr6.simDog.chr6 463451 3 - 593897 CTC -s simHuman_chr6.simHuman.chr6 177511 3 + 601863 TAC -s simHuman_chr6.simHuman.chr6 177391 3 + 601863 TAA -s simMouse_chr6.simMouse.chr6 161259 3 + 636262 TAC -s simRat_chr6.simRat.chr6 487526 3 - 647215 TAC -s simRat_chr6.simRat.chr6 487448 3 - 647215 TAA - -a -s simMouse_chr6.simMouse.chr6 161204 4 + 636262 AACA -s Anc0.Anc0refChr11 38 4 - 77 AAAA -s Anc1.Anc1refChr2 142224 4 + 144309 AAAA -s Anc2.Anc2refChr3 51054 4 + 53186 AAAA -s mr.mrrefChr5 269579 4 - 294540 AACA -s simCow_chr6.simCow.chr6 180008 4 + 602619 AAAA -s simDog_chr6.simDog.chr6 463362 4 - 593897 AAAA -s simHuman_chr6.simHuman.chr6 177437 4 + 601863 AAAA -s simRat_chr6.simRat.chr6 487451 4 - 647215 AACA - -a -s simMouse_chr6.simMouse.chr6 161208 11 + 636262 TATCTGACATC -s Anc0.Anc0refChr11 42 11 - 77 TCACTGGTGTC -s Anc1.Anc1refChr2 142228 11 + 144309 TCACTGGTGTC -s Anc2.Anc2refChr3 51058 11 + 53186 TCACTGGTGTC -s mr.mrrefChr5 269583 11 - 294540 TAACTGACATC -s simCow_chr6.simCow.chr6 180012 11 + 602619 TCACCAGTGTC -s simDog_chr6.simDog.chr6 463366 11 - 593897 TCAGTGGTGTT -s simHuman_chr6.simHuman.chr6 177441 11 + 601863 TCACTGGTGTC -s simRat_chr6.simRat.chr6 487475 11 - 647215 TAACTGACATC - -a -s simMouse_chr6.simMouse.chr6 161219 3 + 636262 TTG -s Anc0.Anc0refChr11 71 3 - 77 TTT -s Anc1.Anc1refChr2 142257 3 + 144309 TTT -s Anc2.Anc2refChr3 51087 3 + 53186 TTT -s mr.mrrefChr5 269594 3 - 294540 TTG -s simCow_chr6.simCow.chr6 180041 2 + 602619 TT- -s simDog_chr6.simDog.chr6 463395 3 - 593897 TTT -s simHuman_chr6.simHuman.chr6 177470 3 + 601863 TTT -s simRat_chr6.simRat.chr6 487486 3 - 647215 CTG - -a -s simMouse_chr6.simMouse.chr6 161222 3 + 636262 TGT -s Anc0.Anc0refChr11 74 3 - 77 TGT -s Anc1.Anc1refChr2 142260 3 + 144309 TGT -s Anc2.Anc2refChr3 51090 3 + 53186 TGT -s mr.mrrefChr5 269597 3 - 294540 TGT -s simDog_chr6.simDog.chr6 463399 3 - 593897 TGT -s simHuman_chr6.simHuman.chr6 177473 3 + 601863 TGT -s simRat_chr6.simRat.chr6 487489 3 - 647215 TGT - -a -s simMouse_chr6.simMouse.chr6 161248 1 + 636262 A -s Anc0.Anc0refChr1 60471 1 - 62388 C -s Anc1.Anc1refChr2 142286 1 + 144309 A -s Anc1.Anc1refChr2 142167 1 + 144309 C -s Anc2.Anc2refChr3 51001 1 + 53186 C -s Anc2.Anc2refChr3 51116 1 + 53186 A -s mr.mrrefChr5 269623 1 - 294540 A -s simCow_chr6.simCow.chr6 180048 1 + 602619 C -s simCow_chr6.simCow.chr6 179962 1 + 602619 C -s simDog_chr6.simDog.chr6 463425 1 - 593897 A -s simDog_chr6.simDog.chr6 463310 1 - 593897 C -s simHuman_chr6.simHuman.chr6 177380 1 + 601863 A -s simHuman_chr6.simHuman.chr6 177499 1 + 601863 A -s simRat_chr6.simRat.chr6 487515 1 - 647215 G - -a -s simMouse_chr6.simMouse.chr6 161262 5 + 636262 AAAAT -s Anc0.Anc0refChr1 60486 5 - 62388 AAAAC -s Anc1.Anc1refChr2 142301 5 + 144309 AAAAC -s Anc1.Anc1refChr2 142181 5 + 144309 AACAC -s Anc2.Anc2refChr3 51011 5 + 53186 AACAC -s Anc2.Anc2refChr3 51131 5 + 53186 AAAAC -s mr.mrrefChr5 269637 5 - 294540 AAAAC -s simCow_chr6.simCow.chr6 180062 5 + 602619 AAAAC -s simDog_chr6.simDog.chr6 463454 5 - 593897 AGAAC -s simDog_chr6.simDog.chr6 463320 5 - 593897 AACAC -s simHuman_chr6.simHuman.chr6 177394 5 + 601863 AACGA -s simHuman_chr6.simHuman.chr6 177514 5 + 601863 AAAAC -s simRat_chr6.simRat.chr6 487529 5 - 647215 AAAAC - -a -s simMouse_chr6.simMouse.chr6 161267 15 + 636262 TTGCAATACTGACCA -s Anc0.Anc0refChr1 60491 15 - 62388 TTGTGATACTGACCC -s Anc1.Anc1refChr2 142306 15 + 144309 TTGTGATACTGACCC -s Anc2.Anc2refChr3 51136 15 + 53186 TTATGATACTGACCC -s mr.mrrefChr5 269642 15 - 294540 TTGCAATACTGACCC -s simCow_chr6.simCow.chr6 180067 14 + 602619 TTA-GATACCGACCC -s simDog_chr6.simDog.chr6 463459 15 - 593897 TTATGAGACTAACCC -s simHuman_chr6.simHuman.chr6 177519 15 + 601863 TTGTGATACTGACAC -s simRat_chr6.simRat.chr6 487534 15 - 647215 TGGCAATACTGGCCC - -a -s simMouse_chr6.simMouse.chr6 161282 29 + 636262 ACCTTAACTAACCAGGTTTGGAATGCCAC -s Anc0.Anc0refChr1 60508 29 - 62388 ACTACATTCAACCATGTTTGGAATGTCAC -s Anc1.Anc1refChr2 142323 29 + 144309 ACTACATTCAACCATGTTTGGAATGTCAC -s Anc2.Anc2refChr3 51153 29 + 53186 GCTACATTCAACCATGTTTGGAATATCAC -s mr.mrrefChr5 269657 29 - 294540 ACCTTAACTAACCAGGTTTGGAATGTCAC -s simCow_chr6.simCow.chr6 180083 29 + 602619 GCTACAGTTGACCATCTTAGGAACATCAC -s simDog_chr6.simDog.chr6 463476 29 - 593897 GCTACATTCAACCATGTTTGGAATATCAC -s simHuman_chr6.simHuman.chr6 177536 29 + 601863 ACTACATGCAACCATGTTCGGATTGTTAC -s simRat_chr6.simRat.chr6 487549 29 - 647215 ACCTAAACTAACTAAGTTTGGAATGTCAC - -a -s simMouse_chr6.simMouse.chr6 161311 8 + 636262 ATGTGCTA -s Anc0.Anc0refChr1 60541 8 - 62388 ATCCTCCA -s Anc1.Anc1refChr2 142356 8 + 144309 ATCCTCCA -s Anc2.Anc2refChr3 51186 8 + 53186 GTCCTCCA -s mr.mrrefChr5 269686 8 - 294540 ATGTGCTA -s simCow_chr6.simCow.chr6 180116 8 + 602619 GTCCTTCG -s simDog_chr6.simDog.chr6 463509 8 - 593897 GTCCTCCA -s simHuman_chr6.simHuman.chr6 177569 8 + 601863 ATCCTCCA -s simRat_chr6.simRat.chr6 487578 8 - 647215 ATGTGCTA - -a -s simMouse_chr6.simMouse.chr6 161319 25 + 636262 TATCTGCTAGCGTATCTATAGTATT -s Anc0.Anc0refChr1 60549 25 - 62388 TACCTGCTACCATACCTATGGTATT -s Anc1.Anc1refChr2 142364 25 + 144309 TACCTGCTACCATACCTATGGTATT -s Anc2.Anc2refChr3 51194 25 + 53186 TACCTCCTACCATACCTATGGTAAT -s mr.mrrefChr5 269694 25 - 294540 TATCTGCTACCGTACCTATGGTATT -s simCow_chr6.simCow.chr6 180124 25 + 602619 CATATCCTATCATACCTATGGTAAT -s simDog_chr6.simDog.chr6 463520 21 - 593897 TCCCTCTGGCAGTAC--ATGACA-- -s simHuman_chr6.simHuman.chr6 177577 25 + 601863 TACCTGCTACCATACCAATGGTATT -s simRat_chr6.simRat.chr6 487586 25 - 647215 TATCTCATACCATACCTAGGGTATT - -a -s simMouse_chr6.simMouse.chr6 161344 5 + 636262 TAAAT -s Anc0.Anc0refChr1 60574 5 - 62388 TAAAT -s Anc1.Anc1refChr2 142389 5 + 144309 TAAAT -s Anc2.Anc2refChr3 51219 5 + 53186 TAAAT -s mr.mrrefChr5 269719 5 - 294540 TAAAT -s simCow_chr6.simCow.chr6 180158 5 + 602619 TAAAT -s simDog_chr6.simDog.chr6 463541 5 - 593897 TAAAT -s simHuman_chr6.simHuman.chr6 177602 5 + 601863 TGAAT -s simRat_chr6.simRat.chr6 487611 5 - 647215 TAGCT - -a -s simMouse_chr6.simMouse.chr6 161349 28 + 636262 TTCATAGTTTTGGAGGTAATTGGTCTAA -s Anc0.Anc0refChr1 60579 19 - 62388 TTG---------GAGATAGTGGGTCTAG -s Anc1.Anc1refChr2 142394 19 + 144309 TTG---------GAGATAGTGGGTCTAG -s Anc2.Anc2refChr3 51224 19 + 53186 TTG---------GAGATAGTGGGTCTAG -s mr.mrrefChr5 269724 28 - 294540 TTCATAATTTTGGAGGTAGTGGGTCTAA -s simCow_chr6.simCow.chr6 180163 19 + 602619 TTG---------CAGATAGTAGGTCTAG -s simDog_chr6.simDog.chr6 463546 19 - 593897 TTG---------GAGGTAGTGGGTCAGG -s simHuman_chr6.simHuman.chr6 177607 19 + 601863 CTT---------GAGATAGTGGGTCTAG -s simRat_chr6.simRat.chr6 487617 28 - 647215 TTCATAATTTTGGAGGTAGTGGGTCTAA - -a -s simMouse_chr6.simMouse.chr6 161377 31 + 636262 ATGTTTGATGTATAATAGTTCCGGGTAGACT -s Anc0.Anc0refChr1 60598 28 - 62388 ATTTTTGATAT---ATGGTTTCTTGTAGACT -s Anc1.Anc1refChr2 142413 28 + 144309 ATTTTTGATAT---ATGGTTTCTTGTAGACT -s Anc2.Anc2refChr3 51243 28 + 53186 ATTTTTGATAT---ATGGTTTCTTATAGACT -s mr.mrrefChr5 269752 31 - 294540 ATGTTTGATATATAATAGTTCCGGGTAGACT -s simCow_chr6.simCow.chr6 180182 28 + 602619 CTGTTTGATAT---ATGTTTTCTGTTAGATT -s simDog_chr6.simDog.chr6 463569 28 - 593897 ATTTTTGATAT---ATGGTTTCTTATAGACC -s simHuman_chr6.simHuman.chr6 177626 26 + 601863 GTTTTTGATAT---TTGGTTACTTGC--GCT -s simRat_chr6.simRat.chr6 487645 31 - 647215 ATGTTTGATATATAATAATTCCAGGTAGACT - -a -s simMouse_chr6.simMouse.chr6 161408 36 + 636262 TACTGAGAGTCTCTGGGGTGATGGATACCCATCTTG -s Anc0.Anc0refChr1 60626 15 - 62388 TAACTAGAG------------------CCCAAC--- -s Anc1.Anc1refChr2 142441 36 + 144309 TAACTAGAGTCTCAGGTGTGACGAAATCCCAACTTG -s Anc2.Anc2refChr3 51271 15 + 53186 TCACTAGAG------------------CCCAAC--- -s mr.mrrefChr5 269783 36 - 294540 TACCGAGGGTCTCTGGGGTGATGGATACCCATCTTG -s simCow_chr6.simCow.chr6 180210 15 + 602619 TCACTAGAA------------------CGCAGC--- -s simDog_chr6.simDog.chr6 463597 15 - 593897 TCACTAGGG------------------CCCAAC--- -s simHuman_chr6.simHuman.chr6 177652 36 + 601863 TAACCAGAGTCTCAGGTGTGACGAAATGCCAGATTG -s simRat_chr6.simRat.chr6 487678 36 - 647215 TACCGAGGGTCTCTGGGGCAATGAAGAACCATCTTG - -a -s simMouse_chr6.simMouse.chr6 161444 37 + 636262 GAACTTTTTGCGGCGTAAATCACAAAATTTCCTGTCT -s Anc0.Anc0refChr1 60641 37 - 62388 GAACCCTTTACGGCATAAGTTAGAAAAATTCCTGTCT -s Anc1.Anc1refChr2 142477 37 + 144309 GAACCCTTTACGGCATAAGTTAGAAAAATTCCTGTCT -s Anc2.Anc2refChr3 51286 37 + 53186 GAACCCTTTACAGCATAAGTTAGAAGAATTCCTGTCT -s mr.mrrefChr5 269819 37 - 294540 GAACCTTTTGCGGCATAAATCACAAAATTTCCTGTCT -s simCow_chr6.simCow.chr6 180228 37 + 602619 GAACTCTTTACAGCATAAGTTAGAAGAATCACTGTCT -s simDog_chr6.simDog.chr6 463612 37 - 593897 GAACCTTTTACAGCATAAGCTAGGAGAATTCCTGTCT -s simHuman_chr6.simHuman.chr6 177688 37 + 601863 GAATCCCTTTTGGGGTAAGTTATATAAATTCCTGCCT -s simRat_chr6.simRat.chr6 487714 37 - 647215 GATCCTTTTGCGGCATAAATCATAAAATTTCGTGTCT - -a -s simMouse_chr6.simMouse.chr6 161481 188 + 636262 CCATTTTGTGTTGATAGCCTTAACGTTGTTGAGAAAAAACCTTGGATACTCCCTTCGCTCATTCGGTCCCTTCCTACAGCACCTCGTCTACAACAACAAGCAATCACAGGCACCTGTGAAAGGATCCTACCCGCCTCGTGCAGTGTCAAGTGATCGCAGGCCCCTGTAGAAGGATCCAACACGCTTCA -s Anc0.Anc0refChr1 60678 20 - 62388 CCATCTTCCATTGATAAAAT------------------------------------------------------------------------------------------------------------------------------------------------------------------------ -s Anc1.Anc1refChr2 142514 20 + 144309 CCATCTTCCATTGATAAAAT------------------------------------------------------------------------------------------------------------------------------------------------------------------------ -s Anc2.Anc2refChr3 51323 20 + 53186 TCATCTTCCATTGATAAAAT------------------------------------------------------------------------------------------------------------------------------------------------------------------------ -s mr.mrrefChr5 269856 151 - 294540 CCATTTTGTGTTGATAGCCTTAACGTTGTTGAGA-----------------------------------CTTCCTACAG--CCTCGTCTACAACAACAAGCAATCACAGGCACCTGTGAAAGGATCCTACCCGCCTCGTGCAGTGTCAAGTGATCGCAGGCCCCTGTAGAAGGATCCAACACGCTTCA -s simCow_chr6.simCow.chr6 180266 20 + 602619 TCATCTTTCAATGGTAAAGT------------------------------------------------------------------------------------------------------------------------------------------------------------------------ -s simDog_chr6.simDog.chr6 463649 20 - 593897 TCATCTTCCATTGATAGAAT------------------------------------------------------------------------------------------------------------------------------------------------------------------------ -s simHuman_chr6.simHuman.chr6 177725 20 + 601863 CCATCCTACATTGTTAAAAT------------------------------------------------------------------------------------------------------------------------------------------------------------------------ -s simRat_chr6.simRat.chr6 487751 140 - 647215 CC-----------ATAGCCTTAACGTTGATGAGA-----------------------------------TTTCATACAG--CCTTGTGCACAACAACAAGCAATCACACGCACCTGTAGAAGGATCATACATGCCTCATACAGTGTCAAGTGATCACAGGCCCCTGTAGAAGGACCCAACACCCTTTA - -a -s simMouse_chr6.simMouse.chr6 161669 32 + 636262 CCCTGATGAGTGAGATGCTATCTTATTTATAT -s Anc0.Anc0refChr1 60698 23 - 62388 ---------GTGACATGATACATGATACATAT -s Anc1.Anc1refChr2 142534 23 + 144309 ---------GTGACATGATACATGATACATAT -s Anc2.Anc2refChr3 51343 23 + 53186 ---------GTGACATGATACATGATACATAT -s mr.mrrefChr5 270007 32 - 294540 CCCTGATGAGTGAGATGCTATCTTATTTATAT -s simCow_chr6.simCow.chr6 180286 23 + 602619 ---------GTGATATGATACATAATACATAG -s simDog_chr6.simDog.chr6 463669 23 - 593897 ---------GTGACATGATGCATGATACATAT -s simHuman_chr6.simHuman.chr6 177745 23 + 601863 ---------GTGACCTGATACGTGATACATAT -s simRat_chr6.simRat.chr6 487892 32 - 647215 CCCTTAAGAGTGAGATGCTATCTTATACATAT - -a -s simMouse_chr6.simMouse.chr6 161701 13 + 636262 CTATGTTCTAGAT -s Anc0.Anc0refChr1 60721 13 - 62388 CTATGTCCCCAAA -s Anc1.Anc1refChr2 142557 13 + 144309 CTATGTCCCCAAA -s Anc2.Anc2refChr3 51366 13 + 53186 CTATGTCCCCAAA -s mr.mrrefChr5 270039 13 - 294540 CTATGTTCTAGAT -s simCow_chr6.simCow.chr6 180309 13 + 602619 CTATGTCCCCAAA -s simDog_chr6.simDog.chr6 463692 13 - 593897 CTATGTCCCCAAA -s simHuman_chr6.simHuman.chr6 177768 13 + 601863 CTCTGTCCCCAAC -s simRat_chr6.simRat.chr6 487930 13 - 647215 CTATGTCCTAAAT - -a -s simMouse_chr6.simMouse.chr6 161714 26 + 636262 ATAGCTAGATGTGGCTGAGCTAGGCC -s Anc0.Anc0refChr1 60735 20 - 62388 ACAGCTAGATGTGACTGAGT------ -s Anc1.Anc1refChr2 142571 20 + 144309 ACAGCTAGATGTGACTGAGT------ -s Anc2.Anc2refChr3 51380 20 + 53186 ACTGCGAGATGTGACTGAAT------ -s mr.mrrefChr5 270052 26 - 294540 ATAGCTAGATGTGGCTGAGCTAGGCC -s simCow_chr6.simCow.chr6 180323 20 + 602619 AGTGCCAGATGGGACTGAAT------ -s simDog_chr6.simDog.chr6 463706 18 - 593897 ACTGCGAGATGTGATT--AT------ -s simHuman_chr6.simHuman.chr6 177782 20 + 601863 ACAGTTATATGTGACTGAGT------ -s simRat_chr6.simRat.chr6 487943 26 - 647215 ACAGCTAGATGTGGCTGAGCTATGCC - -a -s simMouse_chr6.simMouse.chr6 161740 33 + 636262 ATGGGGTGACATGACCACATGAGCTGTTACAGG -s Anc0.Anc0refChr1 60755 4 - 62388 -----------------------------CATG -s Anc1.Anc1refChr2 142591 4 + 144309 -----------------------------CATG -s Anc2.Anc2refChr3 51400 4 + 53186 -----------------------------CATG -s mr.mrrefChr5 270078 33 - 294540 ATGGGGTGACATGACCACATGAGCTGTTACAGG -s simCow_chr6.simCow.chr6 180343 4 + 602619 -----------------------------CATG -s simDog_chr6.simDog.chr6 463724 4 - 593897 -----------------------------CATG -s simHuman_chr6.simHuman.chr6 177802 4 + 601863 -----------------------------CATT -s simRat_chr6.simRat.chr6 487978 33 - 647215 ATGGTGTGACATGACCACATGAGCTGAGACAGG - -a -s simMouse_chr6.simMouse.chr6 161773 49 + 636262 CTACAGAAATCTGGGGCCATCTAATTTACTGTGGACCACTTGGGTTCCT -s Anc0.Anc0refChr1 60759 49 - 62388 CTTCTGAAAACTGGGTTCATCCAATTTAACCTAAACCACCTGGTTTCCT -s Anc1.Anc1refChr2 142595 49 + 144309 CTTCTGAAAACTGGGTTCATCCAATTTAACCTAAACCACCTGGTTTCCT -s Anc2.Anc2refChr3 51404 49 + 53186 CCTCTGAAAACTGGGTTCATCCAATTTAACCTAAACTACCTGGTTTCCT -s mr.mrrefChr5 270111 49 - 294540 CTACAGAAATCTGGGGCCATCTAATTTACTGTGGACCACTTGGGTTCCT -s simCow_chr6.simCow.chr6 180352 49 + 602619 CCTCTGAAGACTGGGTTCATCCAATTTGACCTAAAGTACTTGGTATCTT -s simDog_chr6.simDog.chr6 463728 49 - 593897 CCTCTGAAAACTGGGTTCACTTAATTTAACCCAAACTGCCTGGTTTCCT -s simHuman_chr6.simHuman.chr6 177806 49 + 601863 CTTCTGAAAACTGGGTTCATCCAACTTCACCTAAACCACCTGGCTTCCC -s simRat_chr6.simRat.chr6 488011 49 - 647215 CCACAGAAATCTGGGGCCACCTAATTTAATGTCAGCCACTTAGTTTCCT - -a -s simMouse_chr6.simMouse.chr6 161822 10 + 636262 TTCCAAGTTC -s Anc0.Anc0refChr1 60808 10 - 62388 TTTCAAGCTC -s Anc1.Anc1refChr2 142644 10 + 144309 TTTCAAGCTC -s Anc2.Anc2refChr3 51453 10 + 53186 TTTCAAGCTC -s mr.mrrefChr5 270160 10 - 294540 TTCCAAGTTC -s simCow_chr6.simCow.chr6 180401 10 + 602619 TTTAAAGCTC -s simDog_chr6.simDog.chr6 463777 10 - 593897 TTCCAAGTTC -s simHuman_chr6.simHuman.chr6 177855 10 + 601863 TTTCAAGCTC -s simRat_chr6.simRat.chr6 488094 10 - 647215 TTCCAAGTTC - -a -s simMouse_chr6.simMouse.chr6 161832 5 + 636262 CTTTT -s Anc0.Anc0refChr1 60818 5 - 62388 CTTTT -s Anc1.Anc1refChr2 142654 5 + 144309 CTTTT -s Anc2.Anc2refChr3 51463 5 + 53186 TTTTT -s mr.mrrefChr5 270170 5 - 294540 CTTTT -s simCow_chr6.simCow.chr6 180516 5 + 602619 ATTTT -s simDog_chr6.simDog.chr6 463787 5 - 593897 TTTTT -s simHuman_chr6.simHuman.chr6 177865 5 + 601863 CTTTT -s simRat_chr6.simRat.chr6 488104 5 - 647215 CTTTT - -a -s simMouse_chr6.simMouse.chr6 161837 10 + 636262 GTCATACATA -s Anc0.Anc0refChr1 60868 9 - 62388 GTCATACAC- -s Anc1.Anc1refChr2 142704 10 + 144309 GTCATACACA -s Anc2.Anc2refChr3 51513 9 + 53186 ATAGAGCGC- -s mr.mrrefChr5 270175 10 - 294540 GTCATACATA -s simCow_chr6.simCow.chr6 180569 9 + 602619 CCTGAGTGC- -s simDog_chr6.simDog.chr6 463838 9 - 593897 ATAGAGCGC- -s simHuman_chr6.simHuman.chr6 177916 10 + 601863 GACATACACA -s simRat_chr6.simRat.chr6 488109 10 - 647215 GCCATACAAA - -a -s simMouse_chr6.simMouse.chr6 161847 6 + 636262 AAACGC -s Anc0.Anc0refChr1 60888 6 - 62388 AAATGC -s Anc1.Anc1refChr2 142725 6 + 144309 AAATGC -s Anc2.Anc2refChr3 51533 6 + 53186 AAGTGC -s mr.mrrefChr5 270185 6 - 294540 AAACGC -s simCow_chr6.simCow.chr6 180589 6 + 602619 TACTGC -s simDog_chr6.simDog.chr6 463858 6 - 593897 AGGTGC -s simHuman_chr6.simHuman.chr6 177938 6 + 601863 AAATGC -s simRat_chr6.simRat.chr6 488119 6 - 647215 AAATGC - -a -s simMouse_chr6.simMouse.chr6 161853 86 + 636262 GCTGGGTACCACTAAGCCCTGAGTGACTAGACGGTCTGACTGACCACACTGTAATGAATGGCTTTACCTCTTGGTGTAATAGATAT -s Anc0.Anc0refChr1 60894 64 - 62388 GCTATGAACCACTAAGCAC-----GACT-----------------ACACTATAGTGTATGGCTTTATATATTGGTATAACAGATAT -s Anc1.Anc1refChr2 142731 69 + 144309 GCTATGAACCACTAAGCACTTAGTGACT-----------------ACACTATAGTGTATGGCTTTATATATTGGTATAACAGATAT -s Anc2.Anc2refChr3 51544 64 + 53186 GTTATGAACCAATATATAC-----GTCT-----------------ACACTATAGTGTCTGGCTTTATAGATTGATATGACAGATAT -s mr.mrrefChr5 270191 86 - 294540 GCTGGGTACCACTAAGCCCTGAGTGACTAGACGGTCTGACTGACCACACTGTAATGAATGGCTTTACCTCTTGGTGTAATAGATAT -s simCow_chr6.simCow.chr6 180600 63 + 602619 GTTAGGTACCAATATATAC-----ACCT-----------------ATACTG-GGTGTCTGGCTCTATACATTAATCTGCCAGTTTC -s simDog_chr6.simDog.chr6 463869 64 - 593897 GTTGTGAACAAATATATAT-----GTTT-----------------ACACTATAGCGTCTGGCTTTATAGCTTGATATGACAGAAAT -s simHuman_chr6.simHuman.chr6 177944 69 + 601863 ACTATGCACCACTAAGCACTTAGTTACT-----------------ACACTATAGTGTATGGCTGCGTATATTGGTATAGCAGATAT -s simRat_chr6.simRat.chr6 488125 86 - 647215 ACTAGGTACCACTAATCCCGGAGTGACTGGACTGTCTGAGTGATCACACTGTAATGTATGGCTTTATAGCTTGATGTAACGGATAT - -a -s simMouse_chr6.simMouse.chr6 161939 11 + 636262 GGACAAACTTA -s Anc0.Anc0refChr1 60958 8 - 62388 GGACAACC--- -s Anc1.Anc1refChr2 142800 8 + 144309 GGACAACC--- -s Anc2.Anc2refChr3 51608 8 + 53186 GAATAACC--- -s mr.mrrefChr5 270277 11 - 294540 GGACAAACTTA -s simCow_chr6.simCow.chr6 180663 8 + 602619 TAAGAACT--- -s simDog_chr6.simDog.chr6 463933 8 - 593897 GAATGAGC--- -s simHuman_chr6.simHuman.chr6 178013 8 + 601863 GGACAACC--- -s simRat_chr6.simRat.chr6 488228 11 - 647215 AAACAACCTTA - -a -s simMouse_chr6.simMouse.chr6 161950 29 + 636262 GTATGCATGCAGGCAATGGGACCCTACGC -s Anc0.Anc0refChr1 60966 14 - 62388 GTATGC---------------CCACACGG -s Anc1.Anc1refChr2 142808 14 + 144309 GTATGC---------------CCACACGG -s Anc2.Anc2refChr3 51616 14 + 53186 GTATGC---------------CCACATGG -s mr.mrrefChr5 270288 29 - 294540 GTATGCATGCAGGCAATGGGACCCTACGC -s simCow_chr6.simCow.chr6 180671 12 + 602619 G--TGC---------------CCTCATGG -s simDog_chr6.simDog.chr6 463945 14 - 593897 TTATGC---------------TCATTTGG -s simHuman_chr6.simHuman.chr6 178021 14 + 601863 GTATGC---------------CCACACGG -s simRat_chr6.simRat.chr6 488239 29 - 647215 GTGTACATGCAGGCTATGGGACCCTACTC - -a -s simMouse_chr6.simMouse.chr6 161979 27 + 636262 TGATTGACCCATCCAAACTTTATTGCA -s Anc0.Anc0refChr1 60980 22 - 62388 TGCCTGATCAAT-----ATGTATTGCA -s Anc1.Anc1refChr2 142822 22 + 144309 TGCCTGATCAAT-----ATGTATTGCA -s Anc2.Anc2refChr3 51644 22 + 53186 TGCCTGATCAAT-----ATGTGTTGCA -s mr.mrrefChr5 270317 27 - 294540 TGATTGACCCATCCAAACTTTATTGCA -s simCow_chr6.simCow.chr6 180701 22 + 602619 TGCCTGGTCAAT-----ATGTGTTGCA -s simDog_chr6.simDog.chr6 463973 22 - 593897 TGCCTGATCAAT-----ATGTGTTGCA -s simHuman_chr6.simHuman.chr6 178035 22 + 601863 TACCTGATCAGT-----TTGCATCACA -s simRat_chr6.simRat.chr6 488268 27 - 647215 TGTTTGGCCCCTCCAATCTTTATTGCA - -a -s simMouse_chr6.simMouse.chr6 162006 51 + 636262 TTTTGCAAAGTATGTATATGGTAACTGACCTTCCAATGAAAATAAGCGGCT -s Anc0.Anc0refChr1 61002 51 - 62388 TTATAGGAAGTATATATACAACAACTAACCTTCCAATGAGACCAACTGGTT -s Anc1.Anc1refChr2 142844 51 + 144309 TTATAGGAAGTATATATACAACAACTAACCTTCCAATGAGACCAACTGGTT -s Anc2.Anc2refChr3 51666 51 + 53186 TTATAGGAAGTATATAGACAACAACTAACCATCCAATGAGACCAACTGGTG -s mr.mrrefChr5 270344 51 - 294540 TTTTGCAAAGTATGTATATGGTAACTGACCTTCCAATGAAAATAAGCGGCT -s simCow_chr6.simCow.chr6 180878 51 + 602619 TGATTGGCAGTATATAAACAACAACTAACCATCCAATCAGATCAACTGGCC -s simDog_chr6.simDog.chr6 463995 51 - 593897 TTATAGGAAGTATCTAGACAACAATTCACCATCCAATGACACCAACTGATG -s simHuman_chr6.simHuman.chr6 178057 51 + 601863 TTATATGTAGCATATATACATCAACTAACCTTCCAGTAAGACCAATTGGTT -s simRat_chr6.simRat.chr6 488295 51 - 647215 TTTTACAAAGTATGTGTATGGTAACTAACCTTCCAATGAAACTAAGTGACT - -a -s simMouse_chr6.simMouse.chr6 162057 19 + 636262 TCAATTCCCAGCCTCAGAA -s Anc0.Anc0refChr1 61070 19 - 62388 TCAATTTCCAGCCTCAGGA -s Anc1.Anc1refChr2 142912 19 + 144309 TCAATTTCCAGCCTCAGGA -s Anc2.Anc2refChr3 51734 19 + 53186 TCAACTTCCAGCCCCAAGA -s mr.mrrefChr5 270395 19 - 294540 TCAATTCCCAGCCTCAGAA -s simCow_chr6.simCow.chr6 180946 19 + 602619 TCCACTTCAAGCCCCAAGA -s simDog_chr6.simDog.chr6 464063 18 - 593897 TCAA-CCCCAGCCCCAAGA -s simHuman_chr6.simHuman.chr6 178125 17 + 601863 TAAATTTCCAGCCT--GGA -s simRat_chr6.simRat.chr6 488346 19 - 647215 TCAATTCCCAGCCTCAGAA - -a -s simMouse_chr6.simMouse.chr6 162076 29 + 636262 GAGGAGGAGTCCAGGCACATGTCACATTA -s Anc0.Anc0refChr1 61089 8 - 62388 GAGGAG---------------------TA -s Anc1.Anc1refChr2 142931 8 + 144309 GAGGAG---------------------TA -s Anc2.Anc2refChr3 51756 8 + 53186 GAGGAG---------------------TA -s mr.mrrefChr5 270414 28 - 294540 GAGGAGGAGTCCAGGCACATGTCAC-TTA -s simCow_chr6.simCow.chr6 180968 8 + 602619 GAGGAT---------------------TA -s simDog_chr6.simDog.chr6 464084 8 - 593897 GAGGAG---------------------TA -s simHuman_chr6.simHuman.chr6 178142 8 + 601863 GAAAAG---------------------TA -s simRat_chr6.simRat.chr6 488365 28 - 647215 GAGGAGGAGTCCAGGGACATGTCAC-TTA - -a -s simMouse_chr6.simMouse.chr6 162105 8 + 636262 TGCGCCAC -s Anc0.Anc0refChr1 61097 8 - 62388 TGTGCCAT -s Anc1.Anc1refChr2 142939 8 + 144309 TGTGCCAT -s Anc2.Anc2refChr3 51768 8 + 53186 TGTGCCAT -s mr.mrrefChr5 270442 8 - 294540 TGCGCCAC -s simCow_chr6.simCow.chr6 180983 8 + 602619 TGTGCAAT -s simDog_chr6.simDog.chr6 464096 8 - 593897 TGTGCCCT -s simHuman_chr6.simHuman.chr6 178150 7 + 601863 TG-GCCAT -s simRat_chr6.simRat.chr6 488393 8 - 647215 TGTACCAC - -a -s simMouse_chr6.simMouse.chr6 162113 16 + 636262 TACCTGAGTGTGATAG -s Anc0.Anc0refChr1 61105 1 - 62388 T--------------- -s Anc1.Anc1refChr2 142947 1 + 144309 T--------------- -s Anc2.Anc2refChr3 51776 1 + 53186 T--------------- -s mr.mrrefChr5 270450 16 - 294540 TACCTGAGTGTGATAG -s simCow_chr6.simCow.chr6 180992 1 + 602619 G--------------- -s simDog_chr6.simDog.chr6 464104 1 - 593897 T--------------- -s simHuman_chr6.simHuman.chr6 178157 1 + 601863 T--------------- -s simRat_chr6.simRat.chr6 488401 16 - 647215 TACCTGAGGGTAATTT - -a -s simMouse_chr6.simMouse.chr6 162129 17 + 636262 GGCTTCTCTATATTTAG -s Anc0.Anc0refChr1 61106 17 - 62388 GGCTTCTCTATATTTAG -s Anc1.Anc1refChr2 142948 17 + 144309 GGCTTCTCTATATTTAG -s Anc2.Anc2refChr3 51777 17 + 53186 GGCTTCTCTATTTTTAG -s mr.mrrefChr5 270466 17 - 294540 GGCTTCTCTATATTTAG -s simCow_chr6.simCow.chr6 180993 17 + 602619 GGCTTATTTATTTCTAG -s simDog_chr6.simDog.chr6 464128 14 - 593897 GGCTCCTCTA---TTAA -s simHuman_chr6.simHuman.chr6 178158 17 + 601863 GGCTTCCCTATATTTAG -s simRat_chr6.simRat.chr6 488417 17 - 647215 AGCTTCTCTACATTTAG - -a -s simMouse_chr6.simMouse.chr6 162146 25 + 636262 TTGGAGTATGATGGGGGAAGAATGA -s Anc0.Anc0refChr1 61125 17 - 62388 -TGGAGTATGATGG-------ATCA -s Anc1.Anc1refChr2 142967 18 + 144309 TTGGAGTATGATGG-------ATCA -s Anc2.Anc2refChr3 51796 17 + 53186 -TGGAGTATGATGG-------AACA -s mr.mrrefChr5 270483 25 - 294540 TTGGAGTATGATGGGGGAAGAATGA -s simCow_chr6.simCow.chr6 181012 16 + 602619 -TGGAATATGATAA-------A-CA -s simDog_chr6.simDog.chr6 464144 17 - 593897 -TGGAGTATACTGG-------AAAA -s simHuman_chr6.simHuman.chr6 178185 18 + 601863 TTGGCATATGATGG-------ATCA -s simRat_chr6.simRat.chr6 488434 25 - 647215 ATGGAGCATGGTGAAGGAAGAATGA - -a -s simMouse_chr6.simMouse.chr6 162171 3 + 636262 TGC -s Anc0.Anc0refChr1 61215 3 - 62388 TGC -s Anc1.Anc1refChr2 143058 3 + 144309 TGC -s Anc2.Anc2refChr3 51886 3 + 53186 TAC -s mr.mrrefChr5 270508 3 - 294540 TGC -s simCow_chr6.simCow.chr6 181102 3 + 602619 TAC -s simDog_chr6.simDog.chr6 464241 3 - 593897 TAC -s simHuman_chr6.simHuman.chr6 178276 3 + 601863 TGC -s simRat_chr6.simRat.chr6 488459 3 - 647215 TGC - -a -s simMouse_chr6.simMouse.chr6 162174 1 + 636262 A -s Anc0.Anc0refChr1 61218 1 - 62388 A -s Anc1.Anc1refChr2 143061 1 + 144309 A -s Anc2.Anc2refChr3 51889 1 + 53186 A -s mr.mrrefChr5 270511 1 - 294540 A -s simCow_chr6.simCow.chr6 181105 1 + 602619 A -s simDog_chr6.simDog.chr6 464244 1 - 593897 A -s simHuman_chr6.simHuman.chr6 178279 1 + 601863 A -s simRat_chr6.simRat.chr6 488478 1 - 647215 A - -a -s simMouse_chr6.simMouse.chr6 162175 2 + 636262 AC -s Anc0.Anc0refChr1 61219 2 - 62388 CC -s Anc1.Anc1refChr2 143062 2 + 144309 CC -s Anc2.Anc2refChr3 51890 2 + 53186 CC -s mr.mrrefChr5 270512 2 - 294540 AC -s simCow_chr6.simCow.chr6 181106 2 + 602619 CT -s simDog_chr6.simDog.chr6 464245 2 - 593897 CC -s simHuman_chr6.simHuman.chr6 178281 2 + 601863 TC -s simRat_chr6.simRat.chr6 488479 2 - 647215 AC - -a -s simMouse_chr6.simMouse.chr6 162177 98 + 636262 TGACAATCAGTTGGGTTTCTCATTTAGTTGACACCAATCACATGCCGAGATGTTTTAACTTTAGATGATACTATATCAGATGTCTCTGTGGCGATAAG -s Anc0.Anc0refChr1 61221 52 - 62388 TGTCAAACCGTTGGGTTTCCCACTCAGTTGATATTG-------GACCAGGTGTTTTAG---------------------------------------G -s Anc1.Anc1refChr2 143064 66 + 144309 TGTCAAACCGTTGGGTTTCCCACTCAGTTGATATTG-------GACCAGGTGTTTTAG-----------------------GTTTC--TTGAGCTTAG -s Anc2.Anc2refChr3 51913 52 + 53186 TGTCAAAGCGTAAGGTTTCCCACTCAGTTGGTATTG-------GATCAGGTGTCTTAG---------------------------------------G -s mr.mrrefChr5 270514 96 - 294540 TGACAATCAGTTGGGTTTCTCATTTAGTTGACACCAATCACATGCCGAGATGTTTTAACTTTAGATGATACTATATCAGATGTCTC--TGGCGATAAG -s simCow_chr6.simCow.chr6 181129 52 + 602619 TGTCAAATCGACAGGTTTCTTGCACACGTGGTATTG-------GATTAAGTGTCTTGG---------------------------------------G -s simDog_chr6.simDog.chr6 464268 50 - 593897 TGTTGAAGGGTAAAGTTTCCCACTCAGTTG--AATG-------GATCAGGTGTCATAG---------------------------------------G -s simHuman_chr6.simHuman.chr6 178283 66 + 601863 TGTCAAACCGCTGGGTTTCGCACTAAGTTGATATTG-------GACCAGGTGTTTTAG-----------------------GTTTC--TTGAGCTTAG -s simRat_chr6.simRat.chr6 488481 96 - 647215 TGACAATCAGTTGGGTCTCTCATTTAGTTGATACTGATGACATGCCCAGGTGTTTTAAGCTTAGCCGTTACTGGCTCAGATGTCTC--TGGTGATAAG - -a -s simMouse_chr6.simMouse.chr6 162275 33 + 636262 TGTGTCCGAGCTTAGATGATACTGGATTGTATG -s Anc0.Anc0refChr1 61273 32 - 62388 TGT-TCCAAGCTTAGTTGATACTGGATCAGGTG -s Anc1.Anc1refChr2 143130 32 + 144309 TGT-TCCAAGCTTAGTTGATACTGGATCAGGTG -s Anc2.Anc2refChr3 51965 32 + 53186 TGT-GTCAAGCTCAGTTGATACTGGATCAGGTG -s mr.mrrefChr5 270610 32 - 294540 TGT-TCCGAGCTTAGATGATACTGGATTGTATG -s simCow_chr6.simCow.chr6 181188 32 + 602619 TGT-GTGAAGTTCAGTTAATACGGCATCAGGTG -s simDog_chr6.simDog.chr6 464318 32 - 593897 TGT-GTCAAGCTCAGTTGATACTGGATCAGGTG -s simHuman_chr6.simHuman.chr6 178350 30 + 601863 TGG-TCC--TCTTAGTTGGTACTGGATCAAGTG -s simRat_chr6.simRat.chr6 488577 32 - 647215 TGT-TGCAAGCTTAGATGATACTGGATCAGATG - -a -s simMouse_chr6.simMouse.chr6 162308 8 + 636262 TGTTCGGT -s Anc0.Anc0refChr1 61305 8 - 62388 TGTTCATG -s Anc1.Anc1refChr2 143162 8 + 144309 TGTTCATG -s Anc2.Anc2refChr3 51998 8 + 53186 TGTTGATG -s mr.mrrefChr5 270642 8 - 294540 TGTTCGGT -s simCow_chr6.simCow.chr6 181221 8 + 602619 TTTTGGTG -s simDog_chr6.simDog.chr6 464351 8 - 593897 TGTTGATG -s simHuman_chr6.simHuman.chr6 178380 7 + 601863 T-CTCATC -s simRat_chr6.simRat.chr6 488609 8 - 647215 TCTTTGGT - -a -s simMouse_chr6.simMouse.chr6 162316 10 + 636262 ACAATAAGCG -s Anc0.Anc0refChr1 61313 9 - 62388 TCAAC-AGTG -s Anc1.Anc1refChr2 143170 10 + 144309 TCAACAAGTG -s Anc2.Anc2refChr3 52006 9 + 53186 TCTAC-AGTG -s mr.mrrefChr5 270650 10 - 294540 ACAATAAGCG -s simCow_chr6.simCow.chr6 181516 9 + 602619 TCTAA-AGTC -s simDog_chr6.simDog.chr6 464359 8 - 593897 TC-GC-GGTG -s simHuman_chr6.simHuman.chr6 178387 10 + 601863 CCAACAGATT -s simRat_chr6.simRat.chr6 488620 10 - 647215 ACAATAAGTG - -a -s simMouse_chr6.simMouse.chr6 162326 8 + 636262 TGTGCAAC -s Anc0.Anc0refChr1 61322 8 - 62388 TCTGCAAC -s Anc1.Anc1refChr2 143180 8 + 144309 TCTGCAAC -s Anc2.Anc2refChr3 52015 8 + 53186 TCTTCAAT -s mr.mrrefChr5 270660 8 - 294540 TGTGCAAC -s simCow_chr6.simCow.chr6 181525 8 + 602619 TTTTCAAA -s simDog_chr6.simDog.chr6 464367 8 - 593897 TCTTCAAT -s simHuman_chr6.simHuman.chr6 178401 8 + 601863 TATGCAGC -s simRat_chr6.simRat.chr6 488630 8 - 647215 TGTGCAGC - -a -s simMouse_chr6.simMouse.chr6 162334 3 + 636262 ATC -s Anc0.Anc0refChr1 61330 3 - 62388 ATC -s Anc1.Anc1refChr2 143188 3 + 144309 ATC -s Anc2.Anc2refChr3 52023 3 + 53186 ACC -s mr.mrrefChr5 270668 3 - 294540 ATC -s simCow_chr6.simCow.chr6 181533 3 + 602619 ATC -s simDog_chr6.simDog.chr6 464375 3 - 593897 ACC -s simHuman_chr6.simHuman.chr6 178413 3 + 601863 ATC -s simRat_chr6.simRat.chr6 488638 3 - 647215 ATC - -a -s simMouse_chr6.simMouse.chr6 162337 5 + 636262 TCATA -s Anc0.Anc0refChr1 61333 5 - 62388 TCATA -s Anc1.Anc1refChr2 143191 5 + 144309 TCATA -s Anc2.Anc2refChr3 52026 5 + 53186 TGTTA -s mr.mrrefChr5 270671 5 - 294540 TCATA -s simCow_chr6.simCow.chr6 181536 5 + 602619 TGACA -s simDog_chr6.simDog.chr6 464378 5 - 593897 TGTTA -s simHuman_chr6.simHuman.chr6 178416 5 + 601863 TCATG -s simRat_chr6.simRat.chr6 488664 5 - 647215 TCATA - -a -s simMouse_chr6.simMouse.chr6 162342 17 + 636262 ATCTTCAACTGATTCAA -s Anc0.Anc0refChr1 61338 17 - 62388 ATGTTAAATTGATTCAA -s Anc1.Anc1refChr2 143196 17 + 144309 ATGTTAAATTGATTCAA -s Anc2.Anc2refChr3 52031 17 + 53186 CTGTTAAATTGATGCAA -s mr.mrrefChr5 270676 17 - 294540 ATCTTCAACTGATTCAA -s simCow_chr6.simCow.chr6 181541 17 + 602619 CTCTTCAAATGATGCAA -s simDog_chr6.simDog.chr6 464383 17 - 593897 CTGTTAAATTGATGCAA -s simHuman_chr6.simHuman.chr6 178423 17 + 601863 ATGTTAAGTTCATTCAA -s simRat_chr6.simRat.chr6 488669 17 - 647215 CCCTTCAGCTGATTCAA - -a -s simMouse_chr6.simMouse.chr6 162359 10 + 636262 CTGATGGTTT -s Anc0.Anc0refChr1 61355 10 - 62388 CTTGTGCTTT -s Anc1.Anc1refChr2 143213 10 + 144309 CTTGTGCTTT -s Anc2.Anc2refChr3 52048 10 + 53186 CTTGTGCTTT -s mr.mrrefChr5 270693 10 - 294540 CTGATGGTTT -s simCow_chr6.simCow.chr6 181558 10 + 602619 CCTACGGTTA -s simDog_chr6.simDog.chr6 464400 10 - 593897 CTTGTGCTTT -s simHuman_chr6.simHuman.chr6 178441 6 + 601863 CTAGTG---- -s simRat_chr6.simRat.chr6 488686 10 - 647215 CTTATGGTTT - -a -s simMouse_chr6.simMouse.chr6 162369 12 + 636262 GGTTGACTGCTG -s Anc0.Anc0refChr1 61365 12 - 62388 GTTTTACTAGTG -s Anc1.Anc1refChr2 143223 12 + 144309 GTTTTACTAGTG -s Anc2.Anc2refChr3 52058 12 + 53186 GTTTTACTAGTG -s mr.mrrefChr5 270703 12 - 294540 GGTTGACTGCTG -s simCow_chr6.simCow.chr6 181568 12 + 602619 GGTTTATGAGTG -s simDog_chr6.simDog.chr6 464410 12 - 593897 GTTTTACTAATG -s simHuman_chr6.simHuman.chr6 178447 2 + 601863 ----------TA -s simRat_chr6.simRat.chr6 488697 12 - 647215 GGTTGACTGGTG - -a -s simMouse_chr6.simMouse.chr6 162381 18 + 636262 AAGGAGTCAAATATTACT -s Anc0.Anc0refChr1 61377 18 - 62388 AAGGAGTTGGATACTCCT -s Anc1.Anc1refChr2 143235 18 + 144309 AAGGAGTTGGATACTCCT -s Anc2.Anc2refChr3 52072 18 + 53186 AAAGAGTTGGATACTCCT -s mr.mrrefChr5 270715 18 - 294540 AAGGAGTCAAATATTACT -s simCow_chr6.simCow.chr6 181582 16 + 602619 AAAGAGTTGGATACGC-- -s simDog_chr6.simDog.chr6 464424 18 - 593897 GAAGAGTTGGGTTCTCCT -s simHuman_chr6.simHuman.chr6 178449 18 + 601863 ACGGAGCTGGATACTGCT -s simRat_chr6.simRat.chr6 488710 18 - 647215 AAAGAGTCAGATGCTACT - -a -s simMouse_chr6.simMouse.chr6 162399 14 + 636262 CCTCTCTTATGTTT -s Anc0.Anc0refChr1 61395 13 - 62388 CCTATCTCAT-TTC -s Anc1.Anc1refChr2 143253 13 + 144309 CCTATCTCAT-TTC -s Anc2.Anc2refChr3 52090 13 + 53186 CCTATCTCAT-TTC -s mr.mrrefChr5 270733 13 - 294540 CCTCTCTTAT-TTT -s simCow_chr6.simCow.chr6 181598 10 + 602619 ---ATCTAGT-TTC -s simDog_chr6.simDog.chr6 464443 13 - 593897 CCTACCTCAT-TTC -s simHuman_chr6.simHuman.chr6 178467 13 + 601863 CCTATCTCAT-GTC -s simRat_chr6.simRat.chr6 488728 13 - 647215 CCTCTCTTAT-TTT - -a -s simMouse_chr6.simMouse.chr6 162413 16 + 636262 TACAGGTGTCTACCTA -s Anc0.Anc0refChr1 61409 14 - 62388 T--ATATGTCTACCAA -s Anc1.Anc1refChr2 143267 16 + 144309 TACATATGTCTACCAA -s Anc2.Anc2refChr3 52104 14 + 53186 T--GTATGTCTACCAG -s mr.mrrefChr5 270746 16 - 294540 TACAGGTGTCTACCTA -s simCow_chr6.simCow.chr6 181609 12 + 602619 ----TATGTTTGTTAG -s simDog_chr6.simDog.chr6 464457 14 - 593897 T--GTGTGTCCACCAG -s simHuman_chr6.simHuman.chr6 178481 16 + 601863 TACATATGTCTACCGA -s simRat_chr6.simRat.chr6 488741 16 - 647215 TGCAGGTGTCTTCCTA - -a -s simMouse_chr6.simMouse.chr6 162429 41 + 636262 CTCTGTTTTGTATATAATCTGTATCATCCATCTTGCATTTA -s Anc0.Anc0refChr1 61427 29 - 62388 CTCTGTTTCATTTGTAAGCTGTATCAAAT------------ -s Anc1.Anc1refChr2 143287 36 + 144309 CTCTGTTTCATTTGTAAGCTGTATCAAATATTTGGC----- -s Anc2.Anc2refChr3 52122 29 + 53186 CTCTGTATCATTTGTAAGCTGTCTCAAAT------------ -s mr.mrrefChr5 270762 41 - 294540 CTCTGTTTTGTATATAATCTGTATCATCCATCTTGCATTTA -s simCow_chr6.simCow.chr6 181625 29 + 602619 CTCTGAATCATTTGTAAGCTGTCTCAATT------------ -s simDog_chr6.simDog.chr6 464475 24 - 593897 -----TATCATTTGAAAGCTGTCTCAAAT------------ -s simHuman_chr6.simHuman.chr6 178501 35 + 601863 CTATGTTTCATTTGTTACCTGTA-CAAATATTTGGC----- -s simRat_chr6.simRat.chr6 488757 41 - 647215 CTCTGTTTTGTTTGCAACCCGTATTATCCACCTTGAATTTA - -a -s simMouse_chr6.simMouse.chr6 162470 20 + 636262 GGAAAGCAGAAGAAGCACTA -s mr.mrrefChr5 270803 20 - 294540 GGAAAGCAGAAGAAGCACTA -s simRat_chr6.simRat.chr6 488799 20 - 647215 GGAAGGCAGAAGAAGCACTA - -a -s simMouse_chr6.simMouse.chr6 162490 5 + 636262 AGATA -s Anc0.Anc0refChr1 2308 4 + 62388 AGTT- -s Anc1.Anc1refChr2 2534 4 - 144309 AGTT- -s Anc2.Anc2refChr3 2576 4 - 53186 AGTC- -s mr.mrrefChr5 25356 5 + 294540 AGATA -s simCow_chr6.simCow.chr6 423086 4 - 602619 AGCC- -s simDog_chr6.simDog.chr6 130980 3 + 593897 G-TC- -s simHuman_chr6.simHuman.chr6 424791 4 - 601863 AATT- - -a -s simMouse_chr6.simMouse.chr6 162495 40 + 636262 ATGCAGTGCAGCTGCTGACTAGGTTCTATTGAATCTTCCA -s Anc0.Anc0refChr1 61463 39 - 62388 GTGTATTGCAGCTGTTAACTAGATTATATCCAG-CTTGCA -s Anc1.Anc1refChr2 143330 39 + 144309 GTGTATTGCAGCTGTTAACTAGATTATATCCAG-CTTGCA -s Anc2.Anc2refChr3 52160 39 + 53186 GTGTGTTGTAGCTGTTAACTAGATTATATCCAG-CCTGCC -s mr.mrrefChr5 25361 40 + 294540 ATGCAGTGCAGCTGCTGACTAGGTTATATTGAATCTTCCA -s simCow_chr6.simCow.chr6 181660 39 + 602619 GTGTGTTGTAGCTGTTACCTAGATTATATCCAG-CCTGCC -s simDog_chr6.simDog.chr6 464509 39 - 593897 GCGTGTTGTAGCTGTTAACTAGGGTCCATCCAG-CCTTCC -s simHuman_chr6.simHuman.chr6 178577 39 + 601863 GTGTATTGCAGAAGTTAACTAGATTATAGCCAG-CTTGCA -s simRat_chr6.simRat.chr6 160131 35 + 647215 -----GTGCAGCTGCTGGCTAGGTTATATAGAATCTTCCA - -a -s simMouse_chr6.simMouse.chr6 162535 12 + 636262 GTGTGAAGCATG -s Anc0.Anc0refChr1 61502 10 - 62388 GAGC--AGCATG -s Anc1.Anc1refChr2 143369 10 + 144309 GAGC--AGCATG -s Anc2.Anc2refChr3 52209 10 + 53186 GAGC--AGCATG -s mr.mrrefChr5 25401 12 + 294540 GTGTGAAGCATG -s simCow_chr6.simCow.chr6 181709 10 + 602619 GAGC--AGCATT -s simDog_chr6.simDog.chr6 464558 10 - 593897 GAGC--AACATG -s simHuman_chr6.simHuman.chr6 178616 10 + 601863 GAGC--AGCATG -s simRat_chr6.simRat.chr6 160166 12 + 647215 GTGTCATGTATG - -a -s simMouse_chr6.simMouse.chr6 162547 10 + 636262 GTCATGGGTC -s Anc0.Anc0refChr1 61514 10 - 62388 GTGATGGGTC -s Anc1.Anc1refChr2 143383 10 + 144309 GTGATGGGTC -s Anc2.Anc2refChr3 52221 10 + 53186 GTGATGGGCT -s mr.mrrefChr5 25413 10 + 294540 GTCATGGGTC -s simCow_chr6.simCow.chr6 181721 10 + 602619 GTGATGGGCT -s simDog_chr6.simDog.chr6 464570 10 - 593897 GTGATGGGCT -s simHuman_chr6.simHuman.chr6 178632 10 + 601863 GTAATGGGTC -s simRat_chr6.simRat.chr6 160178 10 + 647215 GTCAAGGGTC - -a -s simMouse_chr6.simMouse.chr6 162557 39 + 636262 TACGTAGTCAGAAATGTCATGCCATAGGCAGTCCATCCG -s Anc0.Anc0refChr1 61609 36 - 62388 ---GCATTTTGAAATGCCATGTCATAGGTGATTCACTAC -s Anc1.Anc1refChr2 143478 39 + 144309 TATGCATTTTGAAATGCCATGTCATAGGTGATTCACTAC -s Anc2.Anc2refChr3 52316 36 + 53186 ---GCATTTTGAAATACCATGCCATAGGTGATTCACTCC -s mr.mrrefChr5 25423 39 + 294540 TATGCAGTCAGAAATGTCATGTCATAGGCAGTTCATCAG -s simCow_chr6.simCow.chr6 181837 36 + 602619 ---GCATTTATAAATACCATGCCATGGCTAATTCACTCT -s simDog_chr6.simDog.chr6 464665 36 - 593897 ---ACATTTTGAAATACCATGCCATAGGTGATTTACTCC -s simHuman_chr6.simHuman.chr6 178756 39 + 601863 TATGCACTTTGCAATGCCATGTCACAGGTGATTCACTAC -s simRat_chr6.simRat.chr6 160188 39 + 647215 TATGCAGTCAGAAATGTAATGTCATAGGCAGTTCATCAG - -a -s simMouse_chr6.simMouse.chr6 162596 10 + 636262 ATAACATCAC -s Anc0.Anc0refChr1 61645 10 - 62388 ACAACTTCAC -s Anc1.Anc1refChr2 143517 10 + 144309 ACAACTTCAC -s Anc2.Anc2refChr3 52352 10 + 53186 ACAACTTCAC -s mr.mrrefChr5 25462 10 + 294540 ATAACTTCAC -s simCow_chr6.simCow.chr6 181905 10 + 602619 ACAACTTCAC -s simDog_chr6.simDog.chr6 464701 10 - 593897 ACAAAGTCAC -s simHuman_chr6.simHuman.chr6 178795 10 + 601863 ACAACTTCAC -s simRat_chr6.simRat.chr6 160227 10 + 647215 ATAACTTCAT - -a -s simMouse_chr6.simMouse.chr6 162606 51 + 636262 TTTCTACCATCACAATGTTTACCACTACTGGATCCATGCCAACTGCAAGCT -s Anc0.Anc0refChr1 61655 43 - 62388 TTCATAGCTTCACAATATT-AACATTACTGTTTCCACACCAAAT------- -s Anc1.Anc1refChr2 143527 50 + 144309 TTCATAGCTTCACAATATT-AACATTACTGTTTCCACACCAAATGCAAGTT -s Anc2.Anc2refChr3 52362 43 + 53186 TTCATAGCTTCACAATATT-AACATTGCTGTTTCCACACCAAAT------- -s mr.mrrefChr5 25472 50 + 294540 TTTCTAGCATCACAATGTT-ACCACTACTGTATCCACGCCAACTGCAAGCT -s simCow_chr6.simCow.chr6 181915 43 + 602619 ATTATAGCTTCACAATATT-AACATTTCTGTTCCTACACCAAAT------- -s simDog_chr6.simDog.chr6 464712 35 - 593897 TTCATAGCTTCTCAATATT-AACACTGCTTTTTCCA--------------- -s simHuman_chr6.simHuman.chr6 178805 50 + 601863 TTCGTAGATTCACAACATT-AACATTACTGTTTCCACACCAAATGCAAGTT -s simRat_chr6.simRat.chr6 160237 42 + 647215 TTTCTAGCATCACAA---------CTACTGTATCCACGTCAACTGTAAACT - -a -s simMouse_chr6.simMouse.chr6 162657 14 + 636262 ATATAGACAACATC -s Anc0.Anc0refChr1 61698 9 - 62388 -----GACAACATT -s Anc1.Anc1refChr2 143589 14 + 144309 ATATAGACAACATT -s Anc2.Anc2refChr3 52405 9 + 53186 -----GACATTAAT -s mr.mrrefChr5 25534 14 + 294540 ATATAGACAACATC -s simDog_chr6.simDog.chr6 464747 9 - 593897 -----GACATTAAT -s simHuman_chr6.simHuman.chr6 178867 14 + 601863 ATATAGACAACATT -s simRat_chr6.simRat.chr6 160291 14 + 647215 ATATAGACAACATC - -a -s simMouse_chr6.simMouse.chr6 162671 42 + 636262 TTCCCATCATAAAGTGTGCATGCTGCACTGAATCTCAAAACC -s Anc0.Anc0refChr1 61707 26 - 62388 TTCACATTATAG----------------TAATCTTAGAAACT -s Anc1.Anc1refChr2 143603 42 + 144309 TTCACATTATAGAATTTACATGTTGAGCTAATCTTAGAAACT -s Anc2.Anc2refChr3 52414 26 + 53186 TCCATATTATAG----------------TAATCTTAGAACCT -s mr.mrrefChr5 25548 42 + 294540 TTCCCATCATAAAGTTTGCATGCTGCACTGAATCTCAAAACC -s simDog_chr6.simDog.chr6 464756 26 - 593897 TCCATATTATAG----------------TAATCTTAGAACCT -s simHuman_chr6.simHuman.chr6 178881 42 + 601863 TTCACATGATAGAATTTACATGTTGAGCTAGTCTTGGAAACT -s simRat_chr6.simRat.chr6 160306 42 + 647215 TTCCCACCATAAAGTTTGCATGCTGCACTGAATCTCAAAACC - -a -s simMouse_chr6.simMouse.chr6 162713 7 + 636262 TAACAAA -s Anc0.Anc0refChr1 61733 7 - 62388 GGACAAG -s Anc1.Anc1refChr2 143645 7 + 144309 GGACAAG -s Anc2.Anc2refChr3 52440 7 + 53186 GACCAGG -s mr.mrrefChr5 25590 7 + 294540 TGACAAG -s simDog_chr6.simDog.chr6 464850 7 - 593897 GACCAGG -s simHuman_chr6.simHuman.chr6 178923 7 + 601863 GGATAAG -s simRat_chr6.simRat.chr6 160348 7 + 647215 TGTCAAG - -a -s simMouse_chr6.simMouse.chr6 162720 1 + 636262 T -s Anc0.Anc0refChr1 61745 1 - 62388 T -s Anc1.Anc1refChr2 143657 1 + 144309 T -s Anc2.Anc2refChr3 52452 1 + 53186 T -s mr.mrrefChr5 25597 1 + 294540 T -s simDog_chr6.simDog.chr6 464862 1 - 593897 T -s simHuman_chr6.simHuman.chr6 178935 1 + 601863 T -s simRat_chr6.simRat.chr6 160355 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 162721 14 + 636262 ATTGGTTGAATCCC -s Anc0.Anc0refChr1 61746 10 - 62388 GCTGGTAGGT---- -s Anc1.Anc1refChr2 143658 14 + 144309 GCTGGTAGGTTCTA -s Anc2.Anc2refChr3 52453 10 + 53186 GCTGGTAGGT---- -s mr.mrrefChr5 25598 14 + 294540 ATTGGTTGAATCCA -s simDog_chr6.simDog.chr6 464863 10 - 593897 GCTGGTAGGT---- -s simHuman_chr6.simHuman.chr6 178936 14 + 601863 GCTGGTAGGTTCTA -s simRat_chr6.simRat.chr6 160358 14 + 647215 ATTGGTTGCATCCA - -a -s simMouse_chr6.simMouse.chr6 162735 2 + 636262 CC -s Anc1.Anc1refChr2 143672 2 + 144309 CC -s mr.mrrefChr5 25612 2 + 294540 CC -s simHuman_chr6.simHuman.chr6 178950 2 + 601863 CC -s simRat_chr6.simRat.chr6 160373 2 + 647215 CC - -a -s simMouse_chr6.simMouse.chr6 162737 82 + 636262 CCTTGCTCAAACATCAGAAATGAATCAGTGAGAATGAAGCAGCAGAATGAATAGCCAATCTGGAGCAACCCTCCTGAATTTT -s Anc0.Anc0refChr1 61756 64 - 62388 TATTGCTTATCCAGCAG--------CAGGCAGAAGGAATCTAGA----------CCTAACTGGAGGATGCCTCCTGAACTCT -s Anc1.Anc1refChr2 143674 64 + 144309 TATTGCTTATCCAGCAG--------CAGGCAGAAGGAATCTAGA----------CCTAACTGGAGGATGCCTCCTGAACTCT -s Anc2.Anc2refChr3 52463 64 + 53186 TATTTCATATCCTGCAG--------CAGGCACAAGGAATGTAGG----------CCTAATTGGGTGATGCCTCCTCAACTCT -s mr.mrrefChr5 25614 82 + 294540 CCTTGCTTAAACATCAGAAATGAATCAGTGAGAATGAAGCAGCAGAATGAATAGCCTATCTGGAGCAACCCTCCTGAACTTT -s simDog_chr6.simDog.chr6 464873 64 - 593897 TATTTCATATCCTGCAG--------CAGGCACAAGGAATGTAGG----------CCTAATTGGGTGATGCCTCCTCAACTCT -s simHuman_chr6.simHuman.chr6 178958 64 + 601863 TTTTGGTTATCCAGCAG--------CGGGTAGAAGGAGTCTATA----------CCTAACTGGAGTAGACCTCCTGAACTCT -s simRat_chr6.simRat.chr6 160375 82 + 647215 CCTTGCTTAAACATCAGAAATGAATCAGTGAGAATGAAGCAGCAGAATGGATAGCCTATCTGGATCATCCCCCCTGAACCTT - -a -s simMouse_chr6.simMouse.chr6 162819 21 + 636262 GAAACCATTTAAGGGTCCTCT -s Anc0.Anc0refChr1 61820 20 - 62388 AAAA-CATCCAAGGGCCCTCT -s Anc1.Anc1refChr2 143738 20 + 144309 AAAA-CATCCAAGGGCCCTCT -s Anc2.Anc2refChr3 52527 20 + 53186 AAAA-CATCCAAGGGCCCTCT -s mr.mrrefChr5 25696 21 + 294540 GAAACCATTCAAGGGTCCTCT -s simCow_chr6.simCow.chr6 181958 20 + 602619 AAGA-AATCCAGGGGCCCTCT -s simDog_chr6.simDog.chr6 464938 20 - 593897 AAAA-CATCCAAGGCCCCGCT -s simHuman_chr6.simHuman.chr6 179022 14 + 601863 -------TCCAAGGGCCCTCT -s simRat_chr6.simRat.chr6 160457 21 + 647215 AAAACTATTCAAGGGTCCTCT - -a -s simMouse_chr6.simMouse.chr6 162840 7 + 636262 AAAAGTA -s Anc0.Anc0refChr1 61845 7 - 62388 AATAGTA -s Anc1.Anc1refChr2 143763 7 + 144309 AATAGTA -s Anc2.Anc2refChr3 52552 7 + 53186 ACTAGTA -s mr.mrrefChr5 25717 7 + 294540 AAAAGTA -s simCow_chr6.simCow.chr6 181983 7 + 602619 ACTAGTA -s simDog_chr6.simDog.chr6 464963 7 - 593897 ACTAGTA -s simHuman_chr6.simHuman.chr6 179041 7 + 601863 AACAGTA -s simRat_chr6.simRat.chr6 160478 7 + 647215 AAAAGTA - -a -s simMouse_chr6.simMouse.chr6 162847 4 + 636262 GTCG -s Anc0.Anc0refChr1 61852 4 - 62388 GTGT -s Anc1.Anc1refChr2 143770 4 + 144309 GTGT -s Anc2.Anc2refChr3 52559 4 + 53186 GTGT -s mr.mrrefChr5 25724 4 + 294540 GTCT -s simCow_chr6.simCow.chr6 181995 4 + 602619 GTGT -s simDog_chr6.simDog.chr6 464970 4 - 593897 GTGT -s simHuman_chr6.simHuman.chr6 179048 4 + 601863 GAGT -s simRat_chr6.simRat.chr6 160485 4 + 647215 GTCT - -a -s simMouse_chr6.simMouse.chr6 162851 14 + 636262 AAAATTAGAGGAGT -s Anc0.Anc0refChr1 61859 14 - 62388 AAGATTAGAGGAGT -s Anc1.Anc1refChr2 143777 14 + 144309 AAGATTAGAGGAGT -s Anc2.Anc2refChr3 52566 14 + 53186 AGGATTAGAGGCGT -s mr.mrrefChr5 25730 14 + 294540 AAGATTAGAGGAGT -s simCow_chr6.simCow.chr6 182002 14 + 602619 AGGATTAGAGGGAA -s simDog_chr6.simDog.chr6 464977 14 - 593897 AGGACTAGATGCGT -s simHuman_chr6.simHuman.chr6 179055 14 + 601863 TAGATTAGAGGAGT -s simRat_chr6.simRat.chr6 160491 14 + 647215 AAGCTTAGAGTAGT - -a -s simMouse_chr6.simMouse.chr6 162865 33 + 636262 GGTTTTAGCTAGGGTTGGTTAGCCCGCTAACCT -s Anc0.Anc0refChr1 61878 33 - 62388 GGTTATAGCTAAGGCTCTATAGTGCAATTGCTT -s Anc1.Anc1refChr2 143796 33 + 144309 GGTTATAGCTAAGGCTCTATAGTGCAATTGCTT -s Anc2.Anc2refChr3 52585 33 + 53186 GGTCATAGCAAAGGCTCTATAGTGCAATTGCTT -s mr.mrrefChr5 25744 33 + 294540 GGTTTTAGCTAAGGTTGGTTAGCCCGCTTACCT -s simCow_chr6.simCow.chr6 182021 33 + 602619 GGACAGAGCAAAGGCTCTCTAGTGCAATTGCAA -s simDog_chr6.simDog.chr6 464996 33 - 593897 GGTCATACTAAAGGCGCTATATTGCGATTGGTT -s simHuman_chr6.simHuman.chr6 179074 33 + 601863 GGTTGTAGCTAAGGCTCCATAGTGCAATTGCTT -s simRat_chr6.simRat.chr6 160505 31 + 647215 GAGC--ACCTAAGGTTGGGTAGCTTGCTTACCT - -a -s simMouse_chr6.simMouse.chr6 162898 14 + 636262 CTAAAGGTCTCTAT -s Anc0.Anc0refChr1 61911 10 - 62388 ----AGTTTTCTAG -s Anc1.Anc1refChr2 143829 10 + 144309 ----AGTTTTCTAG -s Anc2.Anc2refChr3 52618 10 + 53186 ----ACTTTTTTAG -s mr.mrrefChr5 25777 14 + 294540 CTAAAGGTCTCTAT -s simCow_chr6.simCow.chr6 182054 10 + 602619 ----AATTTGCTAG -s simDog_chr6.simDog.chr6 465029 10 - 593897 ----ACTTTTTTAG -s simHuman_chr6.simHuman.chr6 179107 10 + 601863 ----AGTTTGCTTA -s simRat_chr6.simRat.chr6 160585 14 + 647215 CTAAAGGCCTCAAT - -a -s simMouse_chr6.simMouse.chr6 162912 23 + 636262 TGTGGGAACAGGTGTGCGCGACT -s Anc0.Anc0refChr1 61921 22 - 62388 TGAGGATGCAGACATG-GTTTCC -s Anc1.Anc1refChr2 143839 22 + 144309 TGAGGATGCAGACATG-GTTTCC -s Anc2.Anc2refChr3 52709 22 + 53186 TGAGGATGCAGACATG-CTTTTC -s mr.mrrefChr5 25791 23 + 294540 TGTGGGAGCAGGTGTGCGCGACT -s simCow_chr6.simCow.chr6 182156 22 + 602619 TGATGATGCAGACATG-TTGCTC -s simDog_chr6.simDog.chr6 465120 22 - 593897 TGAGGATGCAGACATG-CTTTTC -s simHuman_chr6.simHuman.chr6 179117 22 + 601863 CGAGGATGCAGACATG-GTTTCC -s simRat_chr6.simRat.chr6 160599 23 + 647215 TGTGGGGGCATGTGTGCGCAACT - -a -s simMouse_chr6.simMouse.chr6 162935 5 + 636262 GTATG -s Anc0.Anc0refChr1 61943 5 - 62388 ATGTT -s Anc1.Anc1refChr2 143861 5 + 144309 ATGTT -s Anc2.Anc2refChr3 52731 5 + 53186 ATGTT -s mr.mrrefChr5 25814 5 + 294540 GTGTG -s simCow_chr6.simCow.chr6 182178 5 + 602619 ATGTT -s simDog_chr6.simDog.chr6 465143 5 - 593897 ATGTT -s simHuman_chr6.simHuman.chr6 179139 5 + 601863 ATGTT -s simRat_chr6.simRat.chr6 160622 5 + 647215 GTGTG - -a -s simMouse_chr6.simMouse.chr6 162940 5 + 636262 GTGGA -s Anc0.Anc0refChr1 61952 5 - 62388 GTGAG -s Anc1.Anc1refChr2 143870 5 + 144309 GTGAG -s Anc2.Anc2refChr3 52740 5 + 53186 GTGAG -s mr.mrrefChr5 25823 5 + 294540 GTGAA -s simCow_chr6.simCow.chr6 182187 5 + 602619 GTCAG -s simDog_chr6.simDog.chr6 465152 5 - 593897 TTGAG -s simHuman_chr6.simHuman.chr6 179148 5 + 601863 GTGAG -s simRat_chr6.simRat.chr6 160631 5 + 647215 GTGAA - -a -s simMouse_chr6.simMouse.chr6 162945 32 + 636262 TGCATTTTATAAAGGAGCTGCTTCAGTGCCAG -s Anc0.Anc0refChr1 61958 30 - 62388 TGC--TTAATCAAGGAGCCACTTCACAACCAG -s Anc1.Anc1refChr2 143876 30 + 144309 TGC--TTAATCAAGGAGCCACTTCACAACCAG -s Anc2.Anc2refChr3 52746 30 + 53186 TGC--TGAATCAAGGAGCCACTCCACAACCAG -s mr.mrrefChr5 25828 32 + 294540 TGCATTTTATAAAGGAGCTGCTTCAGTGCCAG -s simCow_chr6.simCow.chr6 182193 30 + 602619 TGC--TGAATCAAGGAACCGCTCCAAAATCAG -s simDog_chr6.simDog.chr6 465158 25 - 593897 -------AATCAAGGAGTGACTCCACAACCAG -s simHuman_chr6.simHuman.chr6 179154 30 + 601863 TGC--CTAAACAAGGAGCCACTTCACACCCAA -s simRat_chr6.simRat.chr6 160636 32 + 647215 TACATTTTATAAAGGAGCTGCTCCAGGACCAG - -a -s simMouse_chr6.simMouse.chr6 162977 15 + 636262 CATATTCAATTGTTC -s Anc0.Anc0refChr1 61988 15 - 62388 CATATTCAGCTGTTT -s Anc1.Anc1refChr2 143906 15 + 144309 CATATTCAGCTGTTT -s Anc2.Anc2refChr3 52777 15 + 53186 CATATTCAGCTGTTT -s mr.mrrefChr5 25860 15 + 294540 CATATTCAACTGTTC -s simCow_chr6.simCow.chr6 182224 15 + 602619 CATAATCAGCTGTTC -s simDog_chr6.simDog.chr6 465184 15 - 593897 CATATTCAGCTGTTT -s simHuman_chr6.simHuman.chr6 179184 15 + 601863 CATATTCAGCCGTTT -s simRat_chr6.simRat.chr6 160668 15 + 647215 CATATCTAACTGTTC - -a -s simMouse_chr6.simMouse.chr6 162992 26 + 636262 CCTCTCCCCCCCCACATGAGTTTTGG -s Anc0.Anc0refChr1 62004 26 - 62388 CCCCTCCCCCCTCACATGAGCTCAGG -s Anc1.Anc1refChr2 143922 26 + 144309 CCCCTCCCCCCTCACATGAGCTCAGG -s Anc2.Anc2refChr3 52793 26 + 53186 CCCCTCCCCCCTCACATGATCTCAGG -s mr.mrrefChr5 25875 26 + 294540 CCTCTCCCCCCCCACATGAGTTTTGG -s simCow_chr6.simCow.chr6 182240 26 + 602619 CCCCTCCCCCCTCACATGAACTCAGG -s simDog_chr6.simDog.chr6 465200 26 - 593897 CTCCCCCCCCCTCATGTGATCTCAGG -s simHuman_chr6.simHuman.chr6 179200 26 + 601863 CCCCTCCCACCTCACATGAGCTCCAG -s simRat_chr6.simRat.chr6 160683 26 + 647215 CCTCTCCTCCCCCACATGAGTTTTGG - -a -s simMouse_chr6.simMouse.chr6 163018 4 + 636262 ATCA -s Anc0.Anc0refChr1 62030 4 - 62388 CTCA -s Anc1.Anc1refChr2 143948 4 + 144309 CTCA -s Anc2.Anc2refChr3 52819 4 + 53186 CTCA -s mr.mrrefChr5 25901 4 + 294540 ATCA -s simCow_chr6.simCow.chr6 182266 4 + 602619 GTCA -s simDog_chr6.simDog.chr6 465226 4 - 593897 CTCA -s simHuman_chr6.simHuman.chr6 179227 4 + 601863 TTTA -s simRat_chr6.simRat.chr6 160709 4 + 647215 ATCA - -a -s simMouse_chr6.simMouse.chr6 163022 10 + 636262 TCAGGAGTAA -s Anc0.Anc0refChr1 62034 10 - 62388 TCAGGATTAG -s Anc1.Anc1refChr2 143952 10 + 144309 TCAGGATTAG -s Anc2.Anc2refChr3 52823 10 + 53186 CCAGGATTTG -s mr.mrrefChr5 25905 10 + 294540 TCAGGAGTAG -s simCow_chr6.simCow.chr6 182275 10 + 602619 CCAGGATTTG -s simDog_chr6.simDog.chr6 465230 10 - 593897 CCAGGATTTG -s simHuman_chr6.simHuman.chr6 179231 10 + 601863 TCAGGATTAG -s simRat_chr6.simRat.chr6 160713 10 + 647215 TCAGGAGTAG - -a -s simMouse_chr6.simMouse.chr6 163032 6 + 636262 GTTAGA -s Anc0.Anc0refChr1 62044 6 - 62388 GTTAGG -s Anc1.Anc1refChr2 143962 6 + 144309 GTTAGG -s Anc2.Anc2refChr3 52833 6 + 53186 GTTAGG -s mr.mrrefChr5 25915 6 + 294540 GTTAGA -s simCow_chr6.simCow.chr6 182285 6 + 602619 TTTAGT -s simDog_chr6.simDog.chr6 465240 6 - 593897 GTTAGG -s simHuman_chr6.simHuman.chr6 179241 6 + 601863 GTTAGG -s simRat_chr6.simRat.chr6 160726 6 + 647215 GTCAAA - -a -s simMouse_chr6.simMouse.chr6 163038 31 + 636262 AGTACACACAGGCTGTTGGCACTCTCCCAAG -s Anc0.Anc0refChr1 62050 31 - 62388 TGTACCCACAGGCCATTGGCACTCTCCTGAA -s Anc1.Anc1refChr2 143968 31 + 144309 TGTACCCACAGGCCATTGGCACTCTCCTGAA -s Anc2.Anc2refChr3 52839 31 + 53186 TGTACCCATAGGCCATTGGCACTCTTCTGAA -s mr.mrrefChr5 25921 31 + 294540 AGTACACACAGGCCGTTGGCACTCTCCCAAG -s simCow_chr6.simCow.chr6 182291 31 + 602619 GGTGCCCATGGGCCATTGGCACTCCACTGAA -s simDog_chr6.simDog.chr6 465279 31 - 593897 TGTACCCTTAGGCCATTGGCACTCTTCTTAA -s simHuman_chr6.simHuman.chr6 179247 31 + 601863 CGCACCCACAGGCCATTGGCACTCTCCTGAT -s simRat_chr6.simRat.chr6 160732 31 + 647215 AGTAAATACAGACCGTTGGCACTTTCCCAAG - -a -s simMouse_chr6.simMouse.chr6 163069 58 + 636262 AGAACCCACTTACAAGATCACCTTTGACTTCTATCAGTGCAAGTGGGTCAAGCTTCCT -s Anc0.Anc0refChr1 62082 58 - 62388 AGAACCCACTTACAGGGTCACCTCTGACTTCCATCTGTGCAAGTGGGTTAACTTTTGT -s Anc1.Anc1refChr2 144000 58 + 144309 AGAACCCACTTACAGGGTCACCTCTGACTTCCATCTGTGCAAGTGGGTTAACTTTTGT -s Anc2.Anc2refChr3 52871 58 + 53186 AGTACCCACTTACAGGGTCACCTCTGACTTCCGTCTGTGCAAGTGGGGTAGCTTTTGT -s mr.mrrefChr5 25953 58 + 294540 AGAACCCACTTACAAGATCACCTTTGACTTCTATCAGTGCAAGTGGGTCAAGCTTCCT -s simCow_chr6.simCow.chr6 182323 58 + 602619 ATGACCCACTTACAGGGTCACCTCTGCCTTCCGTTTGTGAGAGCAGGGCAGCCTTTGT -s simDog_chr6.simDog.chr6 465311 55 - 593897 AGTAGCCACTCACAGAGTCACCCCTGACCTCTGTCT---CAGGTGGGGTAGCTTTTGC -s simHuman_chr6.simHuman.chr6 179279 57 + 601863 AGAACCCATGTA-AGGGTCACCTCTCACTTCCATCTGTGCAAGTGGATTAACTTTTGT -s simRat_chr6.simRat.chr6 160764 51 + 647215 AGAACCCACTAACAAAATCACCTTTGACTCCT------GCAAGCAGGTCGAG-GTCAT - -a -s simMouse_chr6.simMouse.chr6 163127 6 + 636262 GGCTCT -s Anc0.Anc0refChr1 62153 4 - 62388 --ATCA -s Anc1.Anc1refChr2 144071 6 + 144309 GGATCA -s Anc2.Anc2refChr3 52942 4 + 53186 --ATCA -s mr.mrrefChr5 26011 6 + 294540 GGATCA -s simCow_chr6.simCow.chr6 182394 4 + 602619 --ACCA -s simDog_chr6.simDog.chr6 465379 4 - 593897 --ATCA -s simHuman_chr6.simHuman.chr6 179353 6 + 601863 GGATCA -s simRat_chr6.simRat.chr6 160815 6 + 647215 GGATCA - -a -s simMouse_chr6.simMouse.chr6 163133 1 + 636262 A -s Anc0.Anc0refChr1 62163 1 - 62388 A -s Anc1.Anc1refChr2 144083 1 + 144309 A -s Anc2.Anc2refChr3 52952 1 + 53186 A -s mr.mrrefChr5 26017 1 + 294540 A -s simCow_chr6.simCow.chr6 182404 1 + 602619 A -s simDog_chr6.simDog.chr6 465389 1 - 593897 A -s simHuman_chr6.simHuman.chr6 179365 1 + 601863 A -s simRat_chr6.simRat.chr6 160821 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 163134 16 + 636262 AAAGCCTCTTGCCCAC -s Anc0.Anc0refChr1 62164 16 - 62388 AAAATCTCTTGCCCAA -s Anc1.Anc1refChr2 144084 16 + 144309 AAAATCTCTTGCCCAA -s Anc2.Anc2refChr3 52954 16 + 53186 AAAAGCTCTTGCCCAA -s mr.mrrefChr5 26018 16 + 294540 AAAGTCTCTTGCCCAC -s simCow_chr6.simCow.chr6 182406 16 + 602619 AAAAGCTCTTGCCTAA -s simDog_chr6.simDog.chr6 465391 16 - 593897 AAAAGCTTTCGCCCAA -s simHuman_chr6.simHuman.chr6 179366 16 + 601863 TAAATCTCTTGCACAA -s simRat_chr6.simRat.chr6 160822 16 + 647215 AAAGTCTCTTGCCCAC - -a -s simMouse_chr6.simMouse.chr6 163150 67 + 636262 ATGAGGTCTTGAATTGTGATTCACTAGAACTGCTAGTGCCCTTCCAATAATGTTCACCCCACCAACA -s Anc0.Anc0refChr1 62180 67 - 62388 GTCTGATCATAAGTTGTGATTTTCTAGAACTGCTACTGCTCTTCCTATAATGTACACCCCACCAACA -s Anc1.Anc1refChr2 144100 67 + 144309 GTCTGATCATAAGTTGTGATTTTCTAGAACTGCTACTGCTCTTCCTATAATGTACACCCCACCAACA -s Anc2.Anc2refChr3 52970 67 + 53186 GCCTGAACATAAGTTGTGATTTTCTAGAACTGCTACTGCTCTGCCTATAATGTACACCCCACCAACA -s mr.mrrefChr5 26034 67 + 294540 ATGAGATCTTAAATTGTGATTCACTAGAACTGCTAGTGCCCTTCCAATAATGTTCACCCCACCAACA -s simCow_chr6.simCow.chr6 182422 67 + 602619 GACTGACCATAAGTGGCATTTTTCTAGAACTGTTAGTGCTCTTCCTATTATGTACACCCCACCACCA -s simDog_chr6.simDog.chr6 465408 67 - 593897 GCCTGAACACAAGTTGTGATTTGTTCGAGCTTCTACTCCTCTGCTGATAATTTAGACCCCGCCAATA -s simHuman_chr6.simHuman.chr6 179382 66 + 601863 GTTTGATCATAAGTTGTGACTTTCTAGCACTGCTATTG-TCGTCCTATAATGTACACCCCATTATCA -s simRat_chr6.simRat.chr6 160838 67 + 647215 ATAAGATCTTAAATTGTGATTCACTTGGAATGCTAGTGCCCTTCCAATAATGTTCACCCCACCAACA - -a -s simMouse_chr6.simMouse.chr6 163217 36 + 636262 CTTATTTTTTCTATCTGGGTCTGGAGGCCATATGCT -s Anc0.Anc0refChr1 62249 36 - 62388 TCTCTTTCTTCCATCAGGATCTAGAAGTTATATACT -s Anc1.Anc1refChr2 144169 36 + 144309 TCTCTTTCTTCCATCAGGATCTAGAAGTTATATACT -s Anc2.Anc2refChr3 53039 36 + 53186 TCGCTTTCTTCCATCAGGATCTAGAAGTTATATACT -s mr.mrrefChr5 26101 36 + 294540 CTTATTTCTTCCATCAGGATCTGGAGGCCATATGCT -s simCow_chr6.simCow.chr6 182491 36 + 602619 TCGCTTTCTTCCATCAGGGTCTAGAGGTTATATATT -s simDog_chr6.simDog.chr6 465477 36 - 593897 TCGCTTTCTTCCATCAGGATCAAGAAGTTATATACT -s simHuman_chr6.simHuman.chr6 179450 36 + 601863 TCTCTTTCCTCCACCAGGATCTAGAAGTTATATACC -s simRat_chr6.simRat.chr6 160905 36 + 647215 CTTATTGCTTCCATCAGGATCTGGAGGCCATATGTT - -a -s simMouse_chr6.simMouse.chr6 163253 46 + 636262 CATCTCTACACTCATTTCAGCACTGGGGCCTGGTAATTGGATCTCA -s Anc0.Anc0refChr1 62285 43 - 62388 CATCTGAACATCCAGGTCCAGGTTAG---TCAGTATTTGGGTACCA -s Anc1.Anc1refChr2 144205 43 + 144309 CATCTGAACATCCAGGTCCAGGTTAG---TCAGTATTTGGGTACCA -s Anc2.Anc2refChr3 53075 43 + 53186 CATCTGAACATCCAGGTCCAGGTCAG---TCAGTTTTTGGGTACCA -s mr.mrrefChr5 26137 46 + 294540 CATCTCTACACTCATTTCAACACTAGGGCCTGGTAATTGGATCCCA -s simCow_chr6.simCow.chr6 182530 43 + 602619 CATCTGAGGATCTGGGTCCAGCTCAT---TCAGTTTTTGGGTACCA -s simDog_chr6.simDog.chr6 465513 29 - 593897 CATCCGAACACCCAGGTCCAGGTCAG---TCA-------------- -s simHuman_chr6.simHuman.chr6 179486 43 + 601863 CATCTGGACATCCAGGTCCAATTTAG---TCAGTATGTGGGTACCA -s simRat_chr6.simRat.chr6 160941 46 + 647215 TGTCTCTACACTCATTTCAACACCAGGTCCTGGTAATTGGATCCCA - -a -s simMouse_chr6.simMouse.chr6 163299 7 + 636262 AAATGGT -s Anc0.Anc0refChr1 62328 7 - 62388 AGCTGGT -s Anc1.Anc1refChr2 144248 7 + 144309 AGCTGGT -s Anc2.Anc2refChr3 53118 7 + 53186 GGCTGGT -s mr.mrrefChr5 26183 7 + 294540 AAATGGT -s simCow_chr6.simCow.chr6 182584 7 + 602619 GGCTGGT -s simDog_chr6.simDog.chr6 465542 2 - 593897 -----GT -s simHuman_chr6.simHuman.chr6 179529 7 + 601863 AGGTGGT -s simRat_chr6.simRat.chr6 160987 7 + 647215 AAATGAT - -a -s simMouse_chr6.simMouse.chr6 163306 81 + 636262 GTAATTGAGCATTTTTGAATGTTTCAACCTTTTTGAAAACCTTACTTGATACAGGGCAGTTGGTTCTGAGTCATTTCGAAA -s Anc0.Anc0refChr1 62336 35 - 62388 ATATTTCAGCATTTTTGAATG----------------------------------------------GAGTCATTTAGATA -s Anc1.Anc1refChr2 144256 36 + 144309 ATATTTCAGCATTTTTGAATG---------------------------------------------AGAGTCATTTAGATA -s Anc2.Anc2refChr3 53126 35 + 53186 ATATTTCAGAATTTCTGAATG----------------------------------------------GAGTCAATTAAATA -s mr.mrrefChr5 26190 79 + 294540 GTAATTGAGCATTTTTGAATGTTTCAACCTTTTTGAAAACCTTACTTGATACAGGGCAGTTG--TCTGAGTCATTTAGAAA -s simCow_chr6.simCow.chr6 182592 35 + 602619 ACATTTCATAATTTCTGAATG----------------------------------------------GAACCAATTTTAAA -s simDog_chr6.simDog.chr6 465545 35 - 593897 GTAGTTCAGAGTTTCTGAATG----------------------------------------------GTGTCaaataaata -s simHuman_chr6.simHuman.chr6 179537 36 + 601863 ATATTCCAGCATTTTTGGATG---------------------------------------------AGAGTCATTTAGATA -s simRat_chr6.simRat.chr6 160994 76 + 647215 GTATTTTAACATTTTTGAATGTTTCAACTTTTTTCAAAACCCTACTTGGTACAGGGCAGTAG--TCTA---CTTTTAGAAA - -a -s simMouse_chr6.simMouse.chr6 163387 7 + 636262 CATATTA -s Anc0.Anc0refChr1 62371 7 - 62388 CATATTG -s Anc1.Anc1refChr2 144292 7 + 144309 CATATTG -s Anc2.Anc2refChr3 53161 7 + 53186 TATATCG -s mr.mrrefChr5 26269 7 + 294540 CATATTA -s simCow_chr6.simCow.chr6 182627 7 + 602619 TATATCG -s simDog_chr6.simDog.chr6 465587 7 - 593897 tatatCA -s simHuman_chr6.simHuman.chr6 179573 7 + 601863 CATATTG -s simRat_chr6.simRat.chr6 161070 7 + 647215 TATATTA - -a -s simMouse_chr6.simMouse.chr6 163394 15 + 636262 TAAAGGAATCAGCAT -s Anc0.Anc0refChr1 62379 9 - 62388 TAAAGAAAT------ -s Anc1.Anc1refChr2 144300 9 + 144309 TAAAGAAAT------ -s Anc2.Anc2refChr3 53169 9 + 53186 TAAAGAAAT------ -s mr.mrrefChr5 26276 15 + 294540 TAAAGGAATCAACAT -s simCow_chr6.simCow.chr6 182635 9 + 602619 TAAATAAAT------ -s simDog_chr6.simDog.chr6 465595 9 - 593897 TAAAGACAT------ -s simHuman_chr6.simHuman.chr6 179581 9 + 601863 TAAAGAAAT------ -s simRat_chr6.simRat.chr6 161077 12 + 647215 ---AGGGATCAACAT - -a -s simMouse_chr6.simMouse.chr6 163409 8 + 636262 GCACCAGA -s Anc0.Anc0refChr5 7830 8 + 87904 GCAACAGA -s Anc1.Anc1refChr8 21143 8 + 57822 GCAACAGA -s Anc2.Anc2refChr15 804 8 + 86568 TCAAAACC -s mr.mrrefChr5 26291 8 + 294540 GCACCAGA -s simCow_chr6.simCow.chr6 182659 8 + 602619 TTGAAACT -s simDog_chr6.simDog.chr6 465624 8 - 593897 TCAAAACC -s simHuman_chr6.simHuman.chr6 187061 8 + 601863 GCATCAGA -s simRat_chr6.simRat.chr6 161089 8 + 647215 GCCCCAGA - -a -s simMouse_chr6.simMouse.chr6 163417 17 + 636262 TTTTGAAGCCAATTCTG -s Anc0.Anc0refChr5 7838 17 + 87904 GTTTAAAACCAGTTCAA -s Anc1.Anc1refChr8 21151 17 + 57822 GTTTAAAACCAGTTCAA -s Anc2.Anc2refChr15 812 17 + 86568 GTTTAAAACCAGTTCAA -s mr.mrrefChr5 26299 17 + 294540 TTTTGAAGCCAATTCTG -s simCow_chr6.simCow.chr6 182707 17 + 602619 GTTTGAAACTAATTCTA -s simDog_chr6.simDog.chr6 465632 17 - 593897 GTTTAAAACCAGTCCAA -s simHuman_chr6.simHuman.chr6 187069 17 + 601863 CTTTAAAACCAGTTCAA -s simRat_chr6.simRat.chr6 161097 17 + 647215 TTTAGAAGCCATTTCGG - -a -s simMouse_chr6.simMouse.chr6 163434 52 + 636262 TCAGGCTCAGTACACCCCCCCTGGTTGTACCACCGCTATTCAGGGCATTGGA -s Anc0.Anc0refChr5 7855 15 + 87904 CCTGGCCCAGTACAC------------------------------------- -s Anc1.Anc1refChr8 21168 15 + 57822 CCTGGCCCAGTACAC------------------------------------- -s Anc2.Anc2refChr15 829 15 + 86568 CCTAGGCCAGTACAC------------------------------------- -s mr.mrrefChr5 26316 52 + 294540 TCAGGCCCAGTACACCCCCCCTGGTTGTACCACCGCTATTCAGGGCATTGGA -s simCow_chr6.simCow.chr6 182724 14 + 602619 CC-AGTCCAGTAAAC------------------------------------- -s simDog_chr6.simDog.chr6 465650 15 - 593897 CCTAGGCCAGCACAC------------------------------------- -s simHuman_chr6.simHuman.chr6 187086 15 + 601863 CCTGGCCAAGTACAT------------------------------------- -s simRat_chr6.simRat.chr6 161114 52 + 647215 TCAGGCCTAGTACACCCTCCCTGGCTGTACCACTGCAATTCAGGGCATTGCA - -a -s simMouse_chr6.simMouse.chr6 163486 87 + 636262 TGCACCAGATTGTCTGGTTGTCATGGGGCTGGTGCATGATGACTGCCCATAGATGTTGCCCATACACATGTAGAATGTGGTTCCTAG -s Anc0.Anc0refChr5 7870 81 + 87904 ------AGACTGTCTGGTCATCATGAGGCTGGTGCCTGGTGACTACCCACAGATGCGGCATGTAAAGATGTAGTATGTTGCTCCTAA -s Anc1.Anc1refChr8 21183 81 + 57822 ------AGACTGTCTGGTCATCATGAGGCTGGTGCCTGGTGACTACCCACAGATGCGGCATGTAAAGATGTAGTATGTTGCTCCTAA -s Anc2.Anc2refChr15 844 81 + 86568 ------AGACTGTCTGGTCATCATGAGACAGATGCCTGGTGAACACCCACGGATGTGGCATGTAAAGATGTAGTATGTTGCACCTAA -s mr.mrrefChr5 26368 87 + 294540 TGCACCAGATTGTCTGGTCATCATGGGGCTGGTGCCTGATGACTGCCCATAGATGCGGCCCATACACATGTAGTATGTGGTTCCTAG -s simCow_chr6.simCow.chr6 182738 76 + 602619 ------AGACTGACTGGTCATCATGA---AGCTGCCTGATGA--CCTCACCAATGTGGGATGTACAGATGTAGTATGTTGCACCTAA -s simDog_chr6.simDog.chr6 465677 60 - 593897 ------AGACTGTCTGGTCATAATGAGACAGATGCCTGGTGAACACCCATGGATCTGGCATGTAAA--------------------- -s simHuman_chr6.simHuman.chr6 187101 81 + 601863 ------AGACTGTCTGCCCATCATTAGGCTGGTGTCGTGTGACTACCCACAGGTGCGGCATGTATAGATGTTGTACGTTGCTCCTAA -s simRat_chr6.simRat.chr6 161168 87 + 647215 TGCCCCAGATTGCTCGGTCATCATGGGGATGGTGCCTGATGACTGCCCATAGACGCGGCCCATACACACGTAGTATGTGGTTCCTAG - -a -s simMouse_chr6.simMouse.chr6 163573 1 + 636262 A -s Anc0.Anc0refChr5 7951 1 + 87904 A -s Anc1.Anc1refChr8 21264 1 + 57822 A -s Anc2.Anc2refChr15 925 1 + 86568 A -s mr.mrrefChr5 26455 1 + 294540 A -s simCow_chr6.simCow.chr6 182814 1 + 602619 A -s simHuman_chr6.simHuman.chr6 187182 1 + 601863 A -s simRat_chr6.simRat.chr6 161260 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 163574 17 + 636262 ACCTGTGACTAGCATCA -s Anc0.Anc0refChr5 7952 17 + 87904 ACATGTAATTAGCACAG -s Anc1.Anc1refChr8 21265 17 + 57822 ACATGTAATTAGCACAG -s Anc2.Anc2refChr15 926 17 + 86568 ACATGTAATTAGCACAG -s mr.mrrefChr5 26456 17 + 294540 ACCTGTGACTAGCATCA -s simCow_chr6.simCow.chr6 182898 17 + 602619 ACATGTAGTTAGCACAG -s simDog_chr6.simDog.chr6 465737 17 - 593897 ACATGTAATTAGCCCAA -s simHuman_chr6.simHuman.chr6 187183 17 + 601863 ACATGTAATTAGCACAG -s simRat_chr6.simRat.chr6 161261 15 + 647215 ACCTCTGACTAGCAT-- - -a -s simMouse_chr6.simMouse.chr6 163591 13 + 636262 CAAAGTAACCATC -s Anc0.Anc0refChr5 7969 13 + 87904 CAAAGTTACCCTT -s Anc1.Anc1refChr8 21282 13 + 57822 CAAAGTTACCCTT -s Anc2.Anc2refChr15 944 13 + 86568 CAAAGTTACCCTT -s mr.mrrefChr5 26473 13 + 294540 CAAAGTAACCATC -s simCow_chr6.simCow.chr6 182916 13 + 602619 CAGAGTTACCCTT -s simDog_chr6.simDog.chr6 465755 13 - 593897 CAAAGTTACCCTT -s simHuman_chr6.simHuman.chr6 187200 13 + 601863 CAAAGTTACCCTT -s simRat_chr6.simRat.chr6 161276 8 + 647215 -----TAATGATC - -a -s simMouse_chr6.simMouse.chr6 163604 49 + 636262 TGGGAAGTGGAATAATTAAGGAATAGCAAACAGTTATACCTGTCTGTGT -s Anc0.Anc0refChr5 7982 49 + 87904 TCAGAAATGGAATGAATAAGAAATAGCAAATGTTCAAACATGTCTGTGT -s Anc1.Anc1refChr8 21295 49 + 57822 TCAGAAATGGAATGAATAAGAAATAGCAAATGTTCAAACATGTCTGTGT -s Anc2.Anc2refChr15 957 49 + 86568 TCAGAAATGGAATGAATAAGAAATGGCAAATGTTCAAATATGTCCATGT -s mr.mrrefChr5 26486 49 + 294540 TGGGAAGTGGAATAATTAAGGAATAGCAAACAGTTATACATGTCTGTGT -s simCow_chr6.simCow.chr6 182934 48 + 602619 CCAGAAATGGAAAGAATAAGGGATGGTGAATGTTTAAATAT-TCCATGT -s simDog_chr6.simDog.chr6 465768 47 - 593897 TC--AAGTGGAATGAATTAGAAATGGCAAAAGTTCAAATACGTCCATGT -s simHuman_chr6.simHuman.chr6 187213 49 + 601863 TCAGAAATTCACTTAATAACAAACAGCAAATGTTCAAACATGTCTGTCT -s simRat_chr6.simRat.chr6 161284 49 + 647215 TGTGAAGTGAAGTAATTAAGGAATAGGAAACTGTTGTATATGTCTGCGT - -a -s simMouse_chr6.simMouse.chr6 163653 3 + 636262 ATT -s Anc0.Anc0refChr5 8031 3 + 87904 ATC -s Anc1.Anc1refChr8 21344 3 + 57822 ATC -s Anc2.Anc2refChr15 1006 3 + 86568 ATC -s mr.mrrefChr5 26535 3 + 294540 ATC -s simCow_chr6.simCow.chr6 182994 3 + 602619 ATC -s simDog_chr6.simDog.chr6 465815 3 - 593897 ATC -s simHuman_chr6.simHuman.chr6 187262 3 + 601863 ATC -s simRat_chr6.simRat.chr6 161333 3 + 647215 ATC - -a -s simMouse_chr6.simMouse.chr6 163656 1 + 636262 G -s Anc0.Anc0refChr5 8037 1 + 87904 G -s Anc1.Anc1refChr8 21350 1 + 57822 G -s Anc2.Anc2refChr15 1012 1 + 86568 A -s mr.mrrefChr5 26538 1 + 294540 G -s simCow_chr6.simCow.chr6 183000 1 + 602619 T -s simDog_chr6.simDog.chr6 465821 1 - 593897 A -s simHuman_chr6.simHuman.chr6 187268 1 + 601863 G -s simRat_chr6.simRat.chr6 161336 1 + 647215 G - -a -s simMouse_chr6.simMouse.chr6 163657 27 + 636262 GTGCAGTTATGACAGAAAACTTGCAGG -s Anc0.Anc0refChr5 8038 27 + 87904 GTGCAGTTATGACAGGAAACTTGTTGG -s Anc1.Anc1refChr8 21351 27 + 57822 GTGCAGTTATGACAGGAAACTTGTTGG -s Anc2.Anc2refChr15 1013 27 + 86568 GTACAGTTATGACAGGAAACTTGTTGC -s mr.mrrefChr5 26539 27 + 294540 GTGCAGTTATGACAGAAAACTTGCAGG -s simCow_chr6.simCow.chr6 183001 27 + 602619 GTACAATTATGACAGGAGACTTGTTGC -s simDog_chr6.simDog.chr6 465822 27 - 593897 GCACAGTCTTGACAGGAAGCCTGTTGC -s simHuman_chr6.simHuman.chr6 187269 27 + 601863 GTGCAGTTATGACAGGGAACTTGTTGG -s simRat_chr6.simRat.chr6 161339 27 + 647215 AGGCAGTTATGACTGAAAACTTGCAGG - -a -s simMouse_chr6.simMouse.chr6 163684 24 + 636262 GACTTCTAGGATGGTGTTATAATA -s Anc0.Anc0refChr5 8065 24 + 87904 GACCTGGAGGATGGTGTTATAGTG -s Anc1.Anc1refChr8 21378 24 + 57822 GACCTGGAGGATGGTGTTATAGTG -s Anc2.Anc2refChr15 1040 24 + 86568 AACCTGGAGGATTGTGTTATAGTG -s mr.mrrefChr5 26566 24 + 294540 GACCTGGAGGATGGTGTTATAATA -s simCow_chr6.simCow.chr6 183028 24 + 602619 AACCTGGAGGATTGTGTTATAGTA -s simDog_chr6.simDog.chr6 465849 24 - 593897 AACCTGGAGGGCTGTGTTATAGTG -s simHuman_chr6.simHuman.chr6 187301 24 + 601863 GACCTGGAGGATGGTGTCATAGTC -s simRat_chr6.simRat.chr6 161366 24 + 647215 GACCAGGAGGATGATGTTACAATA - -a -s simMouse_chr6.simMouse.chr6 163708 15 + 636262 GACTTGAAACAGGAC -s Anc0.Anc0refChr5 8089 13 + 87904 GACTTGAACCA--AC -s Anc1.Anc1refChr8 21402 15 + 57822 GACTTGAACCAGGAC -s Anc2.Anc2refChr15 1064 13 + 86568 GACTGGATCCA--AC -s mr.mrrefChr5 26590 15 + 294540 GACTTGAAACAGGAC -s simCow_chr6.simCow.chr6 183053 9 + 602619 GAATG----TG--AC -s simDog_chr6.simDog.chr6 465873 13 - 593897 GACTGGATCCA--AC -s simHuman_chr6.simHuman.chr6 187325 15 + 601863 GACTTGAAGGAGGAC -s simRat_chr6.simRat.chr6 161390 15 + 647215 GACTCGAAATAGGAC - -a -s simMouse_chr6.simMouse.chr6 163723 2 + 636262 TA -s Anc0.Anc0refChr5 8102 1 + 87904 T- -s Anc1.Anc1refChr8 21417 1 + 57822 T- -s Anc2.Anc2refChr15 1077 1 + 86568 T- -s mr.mrrefChr5 26605 2 + 294540 TA -s simCow_chr6.simCow.chr6 183062 1 + 602619 T- -s simCow_chr6.simCow.chr6 184318 1 + 602619 T- -s simDog_chr6.simDog.chr6 465886 1 - 593897 T- -s simHuman_chr6.simHuman.chr6 187340 1 + 601863 T- -s simRat_chr6.simRat.chr6 161405 2 + 647215 TA - -a -s simMouse_chr6.simMouse.chr6 163725 116 + 636262 TGGAGTTAATGATGCAATTCTAGGAAAGTCTGGGGAAAGTCGTTGTGTGTTTCATCTTTTTGTCACTATCAATATGTAGGACATGAGGTCAGCCGACCCAGTACACCTGGTTTAGT -s Anc0.Anc0refChr5 8103 115 + 87904 TGGAGCTAGCGGTGCAATTCTAGGAAAATCCAGAGAAATTTGTTGCCTATGTAGGCTTGTCATCACTATCAATCCCCAGGAGAAGAG-TCAGAAGATACAGTACACTTGGTGTAAT -s Anc1.Anc1refChr8 21418 116 + 57822 TGGAGCTAGCGGTGCAATTCTAGGAAAATCCAGAGAAATTTGTTGCCTATGTAGGCTTGTCATCACTATCAATCCCCAGGAGAAGAGGTCAGAAGATACAGTACACTTGGTGTAAT -s Anc2.Anc2refChr15 1078 115 + 86568 TGGAGCTAGCAGTGCAATTCCAGGAAAATTCAGAGAAATTTGTTGCCTATGTAGGCTTGTCATCACTATCAACCCCCAGGAGAAGAG-TTAGAAGATACAGTACACTTGGTGTAAT -s mr.mrrefChr5 26607 116 + 294540 TGGAGTTAGTGGTGCAATTCTAGGAAAATCTGGGGAAATTTGTTGTGTGTTTCATCTTTTTGTCACTATCAATATGTAGGACAAGAGGTCAGCAGACCCAGTACACTTGGTTTAGT -s simCow_chr6.simCow.chr6 183063 115 + 602619 TGGAGCTCACAGTGCAATTCCAGGAAAATTCAGAGAAATTTATTGGCTGTGTAGGCTCGTCATCACAAAAAACCCCGAGGAGAAAAG-TTAAAAGATACAGTACCCTTGGTGTAAC -s simCow_chr6.simCow.chr6 184319 115 + 602619 TGGATCCCATAGTGCAATTCCAGGAAAATTCAGAGAAGTTTGTTGCCCATGTAGGCTTGTCATTACAAACAACCCCCAGGAAAAGGG-TTACAAGATACAGCACACTTGGTATAAC -s simDog_chr6.simDog.chr6 465887 110 - 593897 TGTAGCTAGCAGTTCAATTTCAGGA-----CTGAGAAATTTGTTGTCTATGTAGGAAGTGCATCACTATTTGCCTTCAGGAGAAGAG-TTAGAAGATACAGTACACTTTGTGTAAT -s simHuman_chr6.simHuman.chr6 187341 116 + 601863 TGGAGCTAGCGGTGTAATTCTAGGAAAATCAAGAGAAATTTGCTGCCTATGTAGCCTTGCCATCACTTTCAATCCCCAGGAGAAGAAGTCAGAAAGTACAGTGACCTTGGTGTAAT -s simRat_chr6.simRat.chr6 161424 114 + 647215 TGGAGTTCGTGGTGCAATTCTAGGAAAATCTGGTGAAATTTGTTGTGTG--TGATCTTTTTCTCACTGTCAATATATAGGTCAAGGGGTCAGGAGTCCCAGTATACTTGGTTTAGT - -a -s simMouse_chr6.simMouse.chr6 163841 1 + 636262 T -s Anc0.Anc0refChr5 8219 1 + 87904 T -s Anc1.Anc1refChr8 21535 1 + 57822 T -s Anc2.Anc2refChr15 1194 1 + 86568 T -s mr.mrrefChr5 26724 1 + 294540 T -s simCow_chr6.simCow.chr6 183179 1 + 602619 T -s simCow_chr6.simCow.chr6 184435 1 + 602619 T -s simDog_chr6.simDog.chr6 465998 1 - 593897 T -s simHuman_chr6.simHuman.chr6 187458 1 + 601863 T -s simRat_chr6.simRat.chr6 161539 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 163842 11 + 636262 AATGACCTCCA -s Anc0.Anc0refChr5 8220 11 + 87904 AATATCCTCCC -s Anc1.Anc1refChr8 21536 11 + 57822 AATATCCTCCC -s Anc2.Anc2refChr15 1195 11 + 86568 AATATCCTCCC -s mr.mrrefChr5 26725 11 + 294540 AATGACCTCCA -s simCow_chr6.simCow.chr6 183182 11 + 602619 AATACCCTCCC -s simCow_chr6.simCow.chr6 184436 11 + 602619 AATCTCCTCCC -s simDog_chr6.simDog.chr6 465999 10 - 593897 TATATCCTCC- -s simHuman_chr6.simHuman.chr6 187459 11 + 601863 ATTATCCTCTG -s simRat_chr6.simRat.chr6 161540 11 + 647215 AGTGACCTCCA - -a -s simMouse_chr6.simMouse.chr6 163853 35 + 636262 TATATAGAGCAATGATATTCTGAATAGATAGGTAG -s Anc0.Anc0refChr5 8231 35 + 87904 TGTATGGGGCAATTATAATCTGACTGAATAGATAG -s Anc1.Anc1refChr8 21547 35 + 57822 TGTATGGGGCAATTATAATCTGACTGAATAGATAG -s Anc2.Anc2refChr15 1209 35 + 86568 TGTATGGGGTAATTATAATCTGACTGAATAGATAA -s mr.mrrefChr5 26736 35 + 294540 TATATGGAGCAATGATAATCTGAATAGATAGATAG -s simCow_chr6.simCow.chr6 183196 35 + 602619 TGTGTGGGGTAATTATAATCTGACTGAATAGGTCA -s simCow_chr6.simCow.chr6 184450 35 + 602619 TGTGTGGGGTAATTGTAATCTGACTGAATAGGTAA -s simDog_chr6.simDog.chr6 466010 20 - 593897 GACATGGGGTAATTAT---------------ATAT -s simHuman_chr6.simHuman.chr6 187470 35 + 601863 TGTATGGGACAATTATAATCTGACTGAAGAGATAG -s simRat_chr6.simRat.chr6 161551 35 + 647215 TATATGGACCAATGATAACCCAAATAGACAGATAC - -a -s simMouse_chr6.simMouse.chr6 163888 16 + 636262 GATATATCTTCTGCAG -s Anc0.Anc0refChr5 8266 16 + 87904 GAAACACCTACTGTGC -s Anc1.Anc1refChr8 21582 16 + 57822 GAAACACCTACTGTGC -s Anc2.Anc2refChr15 1272 16 + 86568 GAAACACCTACTGTGC -s mr.mrrefChr5 26771 16 + 294540 GATATATCTACTGCAG -s simCow_chr6.simCow.chr6 183259 16 + 602619 GAAAAACATGCTGTGC -s simCow_chr6.simCow.chr6 184513 16 + 602619 GAAACACATACTGTGC -s simDog_chr6.simDog.chr6 466030 16 - 593897 AAAACACCGACTTTGC -s simHuman_chr6.simHuman.chr6 187505 16 + 601863 GAAACACCTACTGTGC -s simRat_chr6.simRat.chr6 161586 16 + 647215 GACATGTCTACTGCAA - -a -s simMouse_chr6.simMouse.chr6 163904 9 + 636262 CCGCAGTGA -s Anc0.Anc0refChr5 8282 9 + 87904 AAGTAGTGG -s Anc1.Anc1refChr8 21598 9 + 57822 AAGTAGTGG -s Anc2.Anc2refChr15 1288 9 + 86568 AAATAGAGG -s mr.mrrefChr5 26787 9 + 294540 CCGCAGTGA -s simCow_chr6.simCow.chr6 183275 9 + 602619 AAGCAGAGT -s simCow_chr6.simCow.chr6 184529 9 + 602619 AAATAGAGT -s simDog_chr6.simDog.chr6 466046 9 - 593897 AAAAAGAGG -s simHuman_chr6.simHuman.chr6 187521 9 + 601863 ATGTAGTGG -s simRat_chr6.simRat.chr6 161631 9 + 647215 CCACAATGA - -a -s simMouse_chr6.simMouse.chr6 163913 1 + 636262 G -s Anc0.Anc0refChr5 8293 1 + 87904 G -s Anc1.Anc1refChr8 21609 1 + 57822 G -s Anc2.Anc2refChr15 1299 1 + 86568 G -s mr.mrrefChr5 26796 1 + 294540 G -s simCow_chr6.simCow.chr6 183286 1 + 602619 G -s simCow_chr6.simCow.chr6 184540 1 + 602619 G -s simDog_chr6.simDog.chr6 466057 1 - 593897 G -s simHuman_chr6.simHuman.chr6 187532 1 + 601863 C -s simRat_chr6.simRat.chr6 161640 1 + 647215 G - -a -s simMouse_chr6.simMouse.chr6 163914 17 + 636262 AGATCAGCGGTCTAGAC -s Anc0.Anc0refChr5 8294 17 + 87904 AGATGAGCTAGTGAGAC -s Anc1.Anc1refChr8 21610 17 + 57822 AGATGAGCTAGTGAGAC -s Anc2.Anc2refChr15 1300 17 + 86568 AGATGAGCTAGTGAGAT -s mr.mrrefChr5 26797 17 + 294540 AGATCAGCGGTTTAGAC -s simCow_chr6.simCow.chr6 183287 17 + 602619 AGATGAGCTAGTAAGAC -s simCow_chr6.simCow.chr6 184541 17 + 602619 AGATGAGCCAGAAAGAT -s simDog_chr6.simDog.chr6 466058 17 - 593897 AGATGAGCTGATGAGAT -s simHuman_chr6.simHuman.chr6 187533 17 + 601863 AGATGAGCAAGTGAGAC -s simRat_chr6.simRat.chr6 161644 17 + 647215 AGATTAGTGGTTTAGAC - -a -s simMouse_chr6.simMouse.chr6 163931 9 + 636262 AAACTGTAA -s Anc0.Anc0refChr5 8311 7 + 87904 AAATAGT-- -s Anc1.Anc1refChr8 21627 7 + 57822 AAATAGT-- -s Anc2.Anc2refChr15 1317 7 + 86568 AAATAGT-- -s mr.mrrefChr5 26814 9 + 294540 AAATAGTAA -s simCow_chr6.simCow.chr6 183304 7 + 602619 AAATAAT-- -s simCow_chr6.simCow.chr6 184558 7 + 602619 AAATAGT-- -s simDog_chr6.simDog.chr6 466076 7 - 593897 AAATAGT-- -s simHuman_chr6.simHuman.chr6 187550 7 + 601863 GAATAGT-- -s simRat_chr6.simRat.chr6 161661 9 + 647215 AAATAGTAA - -a -s simMouse_chr6.simMouse.chr6 163940 85 + 636262 CTCCTGGCTGGGCTGGTTATCTATTGTGCATACACTGAGTGAGATGAGCCGGTTGGACAACTGGTGAGTACCAACTAGGTCCCTT -s Anc0.Anc0refChr5 8318 68 + 87904 -----------------TACCTACTGTGCATACAGTGTGTGAGATGAGCCAGTCAGACAACTGGTTGGCAAAAGTTAGGAGCCTT -s Anc1.Anc1refChr8 21634 68 + 57822 -----------------TACCTACTGTGCATACAGTGTGTGAGATGAGCCAGTCAGACAACTGGTTGGCAAAAGTTAGGAGCCTT -s Anc2.Anc2refChr15 1324 68 + 86568 -----------------TACCTACTGTGCATACAGTGTGTGTGATGAGCCAATCAGACAACTGGTTGGTAAAAGTTAGGAGCCTT -s mr.mrrefChr5 26823 85 + 294540 CTCCTGGCTGGGCTGGTTACCTATTGTGCATACACTGTGTGAGATGAGCCAGTTGGACAACTGGTGAGCACCAACTAGGTCCCTT -s simCow_chr6.simCow.chr6 183311 68 + 602619 -----------------TACCTACTGTGCATACAGTGTGTGTGATGAGCTGGTTGGGCAACCGGTTGGTAAAAGATAGGAGCCCT -s simCow_chr6.simCow.chr6 184565 68 + 602619 -----------------TACCTACTGTGCATACAGTGTGTGTGATGAGCTGATTGGACAACTGGTTGGTAAAAGACAAGAGCCTT -s simDog_chr6.simDog.chr6 466083 51 - 593897 -----------------TACC----------------TGTGTAAAGAGCCAATCA-CCAAATGGTTAGTACAAGTTTGGAGCCTT -s simHuman_chr6.simHuman.chr6 187557 68 + 601863 -----------------TACCTACTGTGCATACAGTATGTGAGATGAGACAGTCAGACAACTGGTCGGCAATAGTTAGAAGCCTC -s simRat_chr6.simRat.chr6 161671 81 + 647215 CTCCTGGCTGGGCTGGTTACCTATCGTGTATGCAATGTGTGA----AGCCAGTTGCACCACTGGTAAGCACCAACTAGGTCCCTT - -a -s simMouse_chr6.simMouse.chr6 164025 121 + 636262 GTTTGTGATCATGCTAAGAAAATTAATCCTATTGGCTGGTAATTTTAGCTGGCAAAACTATTCACGTCTTACATTGTGTGGCCTTACGTTGTGTGGCCGGAACTTGTGGATCTGCCAGTGA -s Anc0.Anc0refChr5 8386 26 + 87904 GTTTGTCATAATGCTATAA-----------------------------------------------------------------------------------------------CCAGTAA -s Anc1.Anc1refChr8 21702 26 + 57822 GTTTGTCATAATGCTATAA-----------------------------------------------------------------------------------------------CCAGTAA -s Anc2.Anc2refChr15 1392 26 + 86568 GTTTGTCATAAAGCTATAA-----------------------------------------------------------------------------------------------CTAGTAA -s mr.mrrefChr5 26908 105 + 294540 GTTTGTGATCATGCTAAGAAAATTAATCCTATTGGCTGGTAATTTTAGCTGGCAAAACTATTCACGTCTTAC----------------TTGTGTGGCCGGAACTTGTGGATCTGCCAGTGA -s simCow_chr6.simCow.chr6 183380 26 + 602619 GTTTGTCATAAAGCTATAA-----------------------------------------------------------------------------------------------CTATTAA -s simCow_chr6.simCow.chr6 184633 26 + 602619 GTTTGTCATAAAGCTATAA-----------------------------------------------------------------------------------------------CTAGTAA -s simDog_chr6.simDog.chr6 466134 25 - 593897 GTTTGTC-TAACACTATAA-----------------------------------------------------------------------------------------------CTAGTAA -s simHuman_chr6.simHuman.chr6 187625 26 + 601863 GTTTGTCATAATGCTAGAA-----------------------------------------------------------------------------------------------CCAGTAA -s simRat_chr6.simRat.chr6 161752 105 + 647215 GTTTGTGATCATGCTAAGAAAATTTACCCTGTCAGCTGATCACTGCAGCTGGTCCAACTATTCACATCTTAC----------------CTGTGGGGCCGGAACTTCTGAGTCGGCCAGTGA - -a -s simMouse_chr6.simMouse.chr6 164146 28 + 636262 GTATGCACTCACGCAAAGAACCTCACAT -s Anc0.Anc0refChr5 8412 28 + 87904 GTATACACCCACTGGAAGAAACTCACAT -s Anc1.Anc1refChr8 21728 28 + 57822 GTATACACCCACTGGAAGAAACTCACAT -s Anc2.Anc2refChr15 1418 28 + 86568 GTATACACCCACTGGAAGAAACTCACAT -s mr.mrrefChr5 27013 28 + 294540 GTATGCACTCACGCAAAGAACCTCACAT -s simCow_chr6.simCow.chr6 183434 28 + 602619 GTATACTTCCACTGGAAGAAGCTTACAC -s simCow_chr6.simCow.chr6 184659 28 + 602619 GTATACTCCCACTGGAAGAAGCTTACAC -s simDog_chr6.simDog.chr6 466159 27 - 593897 GTTTGCACTCACT-GAAGAAACTCACAT -s simHuman_chr6.simHuman.chr6 187651 28 + 601863 GGATACACACATTGGAAGAAACTCACAT -s simRat_chr6.simRat.chr6 161857 28 + 647215 GTATGTACTCACTCGAAGAACCTCACAT - -a -s simMouse_chr6.simMouse.chr6 164174 10 + 636262 AACACAACCA -s Anc0.Anc0refChr5 8605 10 + 87904 AACAGATTCA -s Anc1.Anc1refChr8 21921 10 + 57822 AACAGATTCA -s Anc2.Anc2refChr15 1616 10 + 86568 AACAGATTCA -s mr.mrrefChr5 27041 10 + 294540 AACACAACCA -s simCow_chr6.simCow.chr6 183610 10 + 602619 AGCAGATTCA -s simCow_chr6.simCow.chr6 184830 10 + 602619 AGCAGGTTCA -s simDog_chr6.simDog.chr6 466356 10 - 593897 AACAGATTCA -s simHuman_chr6.simHuman.chr6 187845 10 + 601863 AACAGATTCA -s simRat_chr6.simRat.chr6 161885 10 + 647215 AACACAACCA - -a -s simMouse_chr6.simMouse.chr6 164184 7 + 636262 TTGGGCT -s Anc0.Anc0refChr5 8620 7 + 87904 TGGGGCT -s Anc1.Anc1refChr8 21936 7 + 57822 TGGGGCT -s Anc2.Anc2refChr15 1631 7 + 86568 TGAGGCT -s mr.mrrefChr5 27051 7 + 294540 TTGGGCT -s simCow_chr6.simCow.chr6 183625 7 + 602619 CGAGGCT -s simCow_chr6.simCow.chr6 184845 7 + 602619 TGAGGCT -s simDog_chr6.simDog.chr6 466371 7 - 593897 TGAGGCT -s simHuman_chr6.simHuman.chr6 187860 7 + 601863 TGGGGCC -s simRat_chr6.simRat.chr6 161895 7 + 647215 TTGGGTT - -a -s simMouse_chr6.simMouse.chr6 164191 1 + 636262 G -s Anc0.Anc0refChr5 8627 1 + 87904 A -s Anc1.Anc1refChr8 21943 1 + 57822 A -s Anc2.Anc2refChr15 1638 1 + 86568 A -s mr.mrrefChr5 27058 1 + 294540 G -s simCow_chr6.simCow.chr6 184852 1 + 602619 T -s simDog_chr6.simDog.chr6 466378 1 - 593897 A -s simHuman_chr6.simHuman.chr6 187867 1 + 601863 A -s simRat_chr6.simRat.chr6 161902 1 + 647215 G - -a -s simMouse_chr6.simMouse.chr6 164192 1 + 636262 A -s Anc0.Anc0refChr5 8628 1 + 87904 A -s Anc1.Anc1refChr8 21944 1 + 57822 A -s Anc2.Anc2refChr15 1639 1 + 86568 A -s mr.mrrefChr5 27059 1 + 294540 A -s simCow_chr6.simCow.chr6 183632 1 + 602619 A -s simCow_chr6.simCow.chr6 184853 1 + 602619 A -s simDog_chr6.simDog.chr6 466379 1 - 593897 G -s simHuman_chr6.simHuman.chr6 187868 1 + 601863 A -s simRat_chr6.simRat.chr6 161903 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 164193 34 + 636262 CCCAGAGTCCAAACATACCAACAAACTGCATTGC -s Anc0.Anc0refChr5 8629 34 + 87904 CCCAGAGTCCAAATATATCAAGGAGCTGCATTGC -s Anc1.Anc1refChr8 21945 34 + 57822 CCCAGAGTCCAAATATATCAAGGAGCTGCATTGC -s Anc2.Anc2refChr15 1640 34 + 86568 CCCAGTGTCCAAATATATCAAGGAGCTAGGTTAC -s mr.mrrefChr5 27060 34 + 294540 CCCAGAGTCCAAACATACCAACAAACTGCATTGC -s simCow_chr6.simCow.chr6 183633 34 + 602619 CCCAGTATGCAGATATACCAAGGAGCTAAGTTAC -s simCow_chr6.simCow.chr6 184854 34 + 602619 CCCAGTATACAGATATACCAAGGAGCCAGGTTAT -s simDog_chr6.simDog.chr6 466389 25 - 593897 CTTGATGACAAAACACTTCATTGAT--------- -s simHuman_chr6.simHuman.chr6 187869 34 + 601863 CCCAGAGGCCAAGTAGATCAAGGAGCTGCATTGC -s simRat_chr6.simRat.chr6 161904 25 + 647215 ACTGGAGTCCAAAAATAC---------GCATTGC - -a -s simMouse_chr6.simMouse.chr6 164227 2 + 636262 TT -s Anc0.Anc0refChr5 8663 2 + 87904 TC -s Anc1.Anc1refChr8 21979 2 + 57822 TC -s Anc2.Anc2refChr15 1677 2 + 86568 TC -s mr.mrrefChr5 27094 2 + 294540 TT -s simCow_chr6.simCow.chr6 183670 2 + 602619 CC -s simCow_chr6.simCow.chr6 184891 2 + 602619 TC -s simHuman_chr6.simHuman.chr6 187903 2 + 601863 TC -s simRat_chr6.simRat.chr6 161929 2 + 647215 TT - -a -s simMouse_chr6.simMouse.chr6 164229 27 + 636262 GTAGTGACAACACAGTTTAGTTCAGAT -s Anc0.Anc0refChr5 8665 26 + 87904 GTATTGACAACACAG-ATCATGGAGAT -s Anc1.Anc1refChr8 21981 26 + 57822 GTATTGACAACACAG-ATCATGGAGAT -s Anc2.Anc2refChr15 1679 26 + 86568 TTGATGACAACAAAG-ATCATGGAGAT -s mr.mrrefChr5 27096 26 + 294540 GTATTGACAACACAG-TTAATTGAGAT -s simCow_chr6.simCow.chr6 184893 26 + 602619 TTGATGACAACAAAG-ATCATTGAGGT -s simDog_chr6.simDog.chr6 466414 6 - 593897 ---------------------GGAGAT -s simHuman_chr6.simHuman.chr6 187905 26 + 601863 GTATTGACAACACAG-CTTACCGAGAT -s simRat_chr6.simRat.chr6 161931 26 + 647215 GTATTGACAACACAG-TTAATTGAGAT - -a -s simMouse_chr6.simMouse.chr6 164256 3 + 636262 ATC -s Anc0.Anc0refChr5 8691 3 + 87904 ATC -s Anc1.Anc1refChr8 22007 3 + 57822 ATC -s Anc2.Anc2refChr15 1705 3 + 86568 ATC -s mr.mrrefChr5 27122 3 + 294540 ATC -s simCow_chr6.simCow.chr6 183672 3 + 602619 ACC -s simCow_chr6.simCow.chr6 184919 3 + 602619 ATC -s simDog_chr6.simDog.chr6 466420 3 - 593897 TTC -s simHuman_chr6.simHuman.chr6 187931 3 + 601863 ATC -s simRat_chr6.simRat.chr6 161957 3 + 647215 ATC - -a -s simMouse_chr6.simMouse.chr6 164259 21 + 636262 GCTTCAGCCTCATCTGACTAC -s Anc0.Anc0refChr5 8695 2 + 87904 GC------------------- -s Anc1.Anc1refChr8 22011 2 + 57822 GC------------------- -s Anc2.Anc2refChr15 1709 2 + 86568 AC------------------- -s mr.mrrefChr5 27125 21 + 294540 GCTTCAGCCTCATCTGACTAC -s simCow_chr6.simCow.chr6 183676 2 + 602619 AC------------------- -s simCow_chr6.simCow.chr6 184923 2 + 602619 AC------------------- -s simDog_chr6.simDog.chr6 466424 2 - 593897 AC------------------- -s simHuman_chr6.simHuman.chr6 187935 2 + 601863 GC------------------- -s simRat_chr6.simRat.chr6 161960 21 + 647215 ACTTTGGCTTCATCTGACTAC - -a -s simMouse_chr6.simMouse.chr6 164280 32 + 636262 AGGAAGGGACGTTAAGTACACTCCCTCTCTGG -s Anc0.Anc0refChr5 8697 4 + 87904 ----------------------------CTGG -s Anc1.Anc1refChr8 22013 4 + 57822 ----------------------------CTGG -s Anc2.Anc2refChr15 1711 4 + 86568 ----------------------------CTGG -s mr.mrrefChr5 27146 31 + 294540 AGGAAGGGACGTTAAG-ACACTCCCTCTCTGG -s simCow_chr6.simCow.chr6 183678 4 + 602619 ----------------------------CTGG -s simCow_chr6.simCow.chr6 184925 4 + 602619 ----------------------------CTAG -s simDog_chr6.simDog.chr6 466426 4 - 593897 ----------------------------CTGG -s simHuman_chr6.simHuman.chr6 187937 4 + 601863 ----------------------------CTGG -s simRat_chr6.simRat.chr6 161982 31 + 647215 GGGAAGGGATGTTAAA-AGACTCCCTCTCTGA - -a -s simMouse_chr6.simMouse.chr6 164312 9 + 636262 GTCATGTGT -s Anc0.Anc0refChr5 8701 9 + 87904 GTGTTGAGT -s Anc1.Anc1refChr8 22017 9 + 57822 GTGTTGAGT -s Anc2.Anc2refChr15 1721 9 + 86568 GTGTTGAGT -s mr.mrrefChr5 27177 9 + 294540 GTCATGTGT -s simCow_chr6.simCow.chr6 183687 9 + 602619 CTGTTGGGT -s simCow_chr6.simCow.chr6 184935 9 + 602619 TTGTTGACT -s simDog_chr6.simDog.chr6 466436 9 - 593897 GTGTTGAGT -s simHuman_chr6.simHuman.chr6 187941 9 + 601863 CTGTTGAGT -s simRat_chr6.simRat.chr6 162013 9 + 647215 GTCATGCGT - -a -s simMouse_chr6.simMouse.chr6 164321 1 + 636262 A -s Anc0.Anc0refChr5 8712 1 + 87904 G -s Anc1.Anc1refChr8 22028 1 + 57822 G -s Anc2.Anc2refChr15 1732 1 + 86568 G -s mr.mrrefChr5 27186 1 + 294540 A -s simDog_chr6.simDog.chr6 466447 1 - 593897 G -s simHuman_chr6.simHuman.chr6 187952 1 + 601863 G -s simRat_chr6.simRat.chr6 162022 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 164322 35 + 636262 CTCCTGAGTACCTTTATAGCAAATTGACCGGTGCA -s Anc0.Anc0refChr5 8713 35 + 87904 TTGGTGAATACCTTAATAGCAAAACAACTAGTGTA -s Anc1.Anc1refChr8 22029 35 + 57822 TTGGTGAATACCTTAATAGCAAAACAACTAGTGTA -s Anc2.Anc2refChr15 1737 35 + 86568 TTGGTGAATACCTTAATAACAAAACAACTAGTGTA -s mr.mrrefChr5 27187 35 + 294540 CTCCTGAGTACCTTTATAGCAAATTGACCGGTGCA -s simCow_chr6.simCow.chr6 183698 28 + 602619 -------ATACCTTAATAACAAATTAAGTAGTATA -s simCow_chr6.simCow.chr6 184946 28 + 602619 -------ATACCTTAATAACAAATCAAGTAGTGCA -s simDog_chr6.simDog.chr6 466452 35 - 593897 TTGGTGAGTATCTTAAGAACAAAACAACTAGTGTA -s simHuman_chr6.simHuman.chr6 187953 35 + 601863 TTGATGAATGCCATAACAGCAAAACAACAAATGTA -s simRat_chr6.simRat.chr6 162023 35 + 647215 CTCCTGAATAACTTAATAGCAAACTCACCAGTGTA - -a -s simMouse_chr6.simMouse.chr6 164357 7 + 636262 GCATTTG -s Anc0.Anc0refChr5 8751 7 + 87904 GCATTTG -s Anc1.Anc1refChr8 22067 7 + 57822 GCATTTG -s Anc2.Anc2refChr15 1777 7 + 86568 GCATTTG -s mr.mrrefChr5 27222 7 + 294540 GCATTTG -s simCow_chr6.simCow.chr6 183730 7 + 602619 CCGTTCG -s simCow_chr6.simCow.chr6 184979 7 + 602619 CCATTTG -s simDog_chr6.simDog.chr6 466492 7 - 593897 GCATTGG -s simHuman_chr6.simHuman.chr6 187991 7 + 601863 GCATATG -s simRat_chr6.simRat.chr6 162114 7 + 647215 GCATTTG - -a -s simMouse_chr6.simMouse.chr6 164364 1 + 636262 C -s Anc0.Anc0refChr5 8770 1 + 87904 C -s Anc1.Anc1refChr8 22086 1 + 57822 C -s Anc2.Anc2refChr15 1807 1 + 86568 A -s mr.mrrefChr5 27229 1 + 294540 C -s simCow_chr6.simCow.chr6 185009 1 + 602619 A -s simDog_chr6.simDog.chr6 466523 1 - 593897 A -s simHuman_chr6.simHuman.chr6 188010 1 + 601863 C -s simRat_chr6.simRat.chr6 162121 1 + 647215 C - -a -s simMouse_chr6.simMouse.chr6 164365 8 + 636262 CTTTTATT -s Anc0.Anc0refChr5 8771 8 + 87904 CTTATATT -s Anc1.Anc1refChr8 22087 8 + 57822 CTTATATT -s Anc2.Anc2refChr15 1808 8 + 86568 CTTATATT -s mr.mrrefChr5 27230 8 + 294540 CTTTTATT -s simCow_chr6.simCow.chr6 183760 8 + 602619 TTTATACT -s simCow_chr6.simCow.chr6 185010 8 + 602619 TTTATACT -s simDog_chr6.simDog.chr6 466524 8 - 593897 CTGATATG -s simHuman_chr6.simHuman.chr6 188011 8 + 601863 CTTATATT -s simRat_chr6.simRat.chr6 162122 8 + 647215 CTTTTATT - -a -s simMouse_chr6.simMouse.chr6 164373 6 + 636262 GGAACT -s Anc0.Anc0refChr5 8794 6 + 87904 GGAACT -s Anc1.Anc1refChr8 22110 6 + 57822 GGAACT -s Anc2.Anc2refChr15 1831 6 + 86568 GCAACT -s mr.mrrefChr5 27238 6 + 294540 GGAACT -s simCow_chr6.simCow.chr6 183783 6 + 602619 GCAACA -s simCow_chr6.simCow.chr6 185033 6 + 602619 GCAACT -s simDog_chr6.simDog.chr6 466547 3 - 593897 G---CT -s simHuman_chr6.simHuman.chr6 188034 6 + 601863 GGAACT -s simRat_chr6.simRat.chr6 162130 6 + 647215 GTAGCT - -a -s simMouse_chr6.simMouse.chr6 164379 6 + 636262 TTGTCC -s Anc0.Anc0refChr5 8801 6 + 87904 TTACTA -s Anc1.Anc1refChr8 22117 6 + 57822 TTACTA -s Anc2.Anc2refChr15 1838 6 + 86568 TTACTA -s mr.mrrefChr5 27244 6 + 294540 TTGTCC -s simCow_chr6.simCow.chr6 183790 6 + 602619 TTACTA -s simCow_chr6.simCow.chr6 185040 6 + 602619 TTACTA -s simDog_chr6.simDog.chr6 466551 6 - 593897 TTACTA -s simHuman_chr6.simHuman.chr6 188041 6 + 601863 TTACTG -s simRat_chr6.simRat.chr6 162136 6 + 647215 TTATTC - -a -s simMouse_chr6.simMouse.chr6 164385 4 + 636262 GAGG -s Anc0.Anc0refChr5 8807 4 + 87904 GAGG -s Anc1.Anc1refChr8 22123 4 + 57822 GAGG -s Anc2.Anc2refChr15 1844 4 + 86568 GAGG -s mr.mrrefChr5 27250 4 + 294540 GAGG -s simCow_chr6.simCow.chr6 183796 3 + 602619 GA-C -s simCow_chr6.simCow.chr6 185046 3 + 602619 GA-G -s simDog_chr6.simDog.chr6 466557 4 - 593897 GAGG -s simHuman_chr6.simHuman.chr6 188047 4 + 601863 GAGG -s simRat_chr6.simRat.chr6 162149 4 + 647215 AAGG - -a -s simMouse_chr6.simMouse.chr6 164389 50 + 636262 TACTGTGCAACTTCTAAACAATGTTAAAGTTTCATTCACACTAGTACTGG -s Anc0.Anc0refChr5 8812 35 + 87904 TATCATCCAACATGCTAACA---------------TGATACTATTACTAG -s Anc1.Anc1refChr8 22128 35 + 57822 TATCATCCAACATGCTAACA---------------TGATACTATTACTAG -s Anc2.Anc2refChr15 1849 35 + 86568 CATCATCCAACATGCTAACA---------------TGTTACTATTACTAG -s mr.mrrefChr5 27254 50 + 294540 TACTGTGCAACTTCTAAACAATGTTAAAGTTTCATTCACACTAGTACTGG -s simCow_chr6.simCow.chr6 183800 33 + 602619 CATCCTCCAACATGCTAAGA---------------TGTCACTATTACT-- -s simCow_chr6.simCow.chr6 185050 33 + 602619 CATCATCCAACATGCTAAGA---------------TGTTACTATTACT-- -s simDog_chr6.simDog.chr6 466562 35 - 593897 CATCATCCAACATGCTAACA---------------TGCTACTATTACTAG -s simHuman_chr6.simHuman.chr6 188052 35 + 601863 TGTCCTTCAACATGCTAACA---------------TGATACTACTACTAG -s simRat_chr6.simRat.chr6 162153 50 + 647215 CATTGTGTAAAGTCTAAACAATGTTAGGGTTTCATTCACACTACCAGTGG - -a -s simMouse_chr6.simMouse.chr6 164439 19 + 636262 AGGAAAGCCTGCATTGAAG -s Anc0.Anc0refChr5 8847 19 + 87904 AGGACATCCTGCATTGAAG -s Anc1.Anc1refChr8 22163 19 + 57822 AGGACATCCTGCATTGAAG -s Anc2.Anc2refChr15 1884 19 + 86568 AGGACATCCTACCTGGAAG -s mr.mrrefChr5 27304 19 + 294540 AGGAAATCCTGCATTGAAG -s simCow_chr6.simCow.chr6 183834 17 + 602619 AAGACATCCCCCCGG--AG -s simCow_chr6.simCow.chr6 185083 17 + 602619 AAGACATCCCACCAG--AG -s simDog_chr6.simDog.chr6 466597 19 - 593897 AGGACATCATAGCTGGAAG -s simHuman_chr6.simHuman.chr6 188087 19 + 601863 AGGGCATCCTGCATTGAAG -s simRat_chr6.simRat.chr6 162203 19 + 647215 AGGAAATCCTACATTGAAG - -a -s simMouse_chr6.simMouse.chr6 164458 3 + 636262 TGT -s Anc0.Anc0refChr5 8875 3 + 87904 TGG -s Anc1.Anc1refChr8 22191 3 + 57822 TGG -s Anc2.Anc2refChr15 1912 3 + 86568 TGG -s mr.mrrefChr5 27323 3 + 294540 TGT -s simCow_chr6.simCow.chr6 183860 3 + 602619 TAG -s simCow_chr6.simCow.chr6 185109 3 + 602619 TAG -s simDog_chr6.simDog.chr6 466625 3 - 593897 TGG -s simHuman_chr6.simHuman.chr6 188115 3 + 601863 CGA -s simRat_chr6.simRat.chr6 162222 3 + 647215 TCT - -a -s simMouse_chr6.simMouse.chr6 164461 30 + 636262 CCAATCTAGCCTAATGTAACCCCTTCCTAT -s Anc0.Anc0refChr5 8878 13 + 87904 CTAATTTAGC---AAG-------------- -s Anc1.Anc1refChr8 22194 13 + 57822 CTAATTTAGC---AAG-------------- -s Anc2.Anc2refChr15 1915 13 + 86568 CTAATTTAGC---AAG-------------- -s mr.mrrefChr5 27326 27 + 294540 CTAATCTAGC---ATGTAACCTCTTCCTAT -s simCow_chr6.simCow.chr6 183863 13 + 602619 CTAAGTTAAC---AAG-------------- -s simCow_chr6.simCow.chr6 185112 13 + 602619 CTAGGTTAAC---AAG-------------- -s simDog_chr6.simDog.chr6 466628 13 - 593897 CTAATTTGGG---AAT-------------- -s simHuman_chr6.simHuman.chr6 188118 13 + 601863 CTGATTTAGC---AAG-------------- -s simRat_chr6.simRat.chr6 162294 27 + 647215 CTAATCTAGC---ATGTAACCTCTTCCTAT - -a -s simMouse_chr6.simMouse.chr6 164491 24 + 636262 ATTGACCTTTCCAACTAGACTGTA -s Anc0.Anc0refChr1 58002 14 - 62388 ----------CCAACCAgATTATT -s Anc1.Anc1refChr2 139485 14 + 144309 ----------CCAACCAgATTATT -s Anc2.Anc2refChr3 48314 14 + 53186 ----------CCAACCAgATTATT -s mr.mrrefChr5 27353 24 + 294540 ATTGACCTTTCCAACCAGACTGTA -s simCow_chr6.simCow.chr6 176991 13 + 602619 ----------CTGACCC-ATTATT -s simDog_chr6.simDog.chr6 460374 14 - 593897 ----------CCAACCAGATTGTC -s simHuman_chr6.simHuman.chr6 174719 14 + 601863 ----------ccaataagattatt -s simRat_chr6.simRat.chr6 162329 24 + 647215 ATTGACCTTTCCAACCAGACGGTA - -a -s simMouse_chr6.simMouse.chr6 164515 37 + 636262 AGTGAAACTCGGTCAGtcaattggcatgtcaactctg -s Anc0.Anc0refChr1 58077 37 - 62388 AGCGAAACTTAGTTAGTCAATTGGCCTGTcatcttta -s Anc1.Anc1refChr2 139560 37 + 144309 AGCGAAACTTAGTTAGTCAATTGGCCTGTcatcttta -s Anc2.Anc2refChr3 48392 37 + 53186 TGCGAAACTTAGTTAGTCAATTGACCTTCcatcttta -s mr.mrrefChr5 27438 37 + 294540 AGTGAAACTTGGTCAGTCAATTGGCATGTCAACTCTG -s simCow_chr6.simCow.chr6 177068 37 + 602619 CGTGGAATTTAGTCAGTGAATTGTCCATGcatctcta -s simDog_chr6.simDog.chr6 460452 37 - 593897 TACGAAACTTTGTTAGACAACTGACCTTCCAACTTTA -s simHuman_chr6.simHuman.chr6 174784 37 + 601863 AGCGAAACTTAGTTAGtcaattggcctgtcatcttta -s simRat_chr6.simRat.chr6 162414 37 + 647215 AGTGAAACTTGGTCTGTCAATTGGCATGTCAACTCTG - -a -s simMouse_chr6.simMouse.chr6 164552 4 + 636262 tgag -s Anc0.Anc0refChr1 58119 4 - 62388 caag -s Anc1.Anc1refChr2 139602 4 + 144309 caag -s Anc2.Anc2refChr3 48434 4 + 53186 caag -s mr.mrrefChr5 27475 4 + 294540 TGAG -s simCow_chr6.simCow.chr6 177110 4 + 602619 gaag -s simDog_chr6.simDog.chr6 460494 4 - 593897 CAGG -s simHuman_chr6.simHuman.chr6 174826 4 + 601863 caaa -s simRat_chr6.simRat.chr6 162451 4 + 647215 TGAT - -a -s simMouse_chr6.simMouse.chr6 164556 77 + 636262 atgatttcatggttctttgaatgagagcaggctataggttccatcacatttagaggcttTCAGCTGCAACAGAGGTT -s Anc0.Anc0refChr1 58123 54 - 62388 atggttatgtggttcttttgatttatatggactataggttgtatcttatttatg----------------------- -s Anc1.Anc1refChr2 139606 54 + 144309 atggttatgtggttcttttgatttatatggactataggttgtatcttatttatg----------------------- -s Anc2.Anc2refChr3 48438 54 + 53186 atggttatgtggttcttttgatttatatggactataggttgtatcttatttatg----------------------- -s mr.mrrefChr5 27479 77 + 294540 ATGATTATGTGGTTCTTTTAATGAGAGCAGGCTATAGGTTCCATCACATTTAGAGGCTTTGAGCTGCAACAGAGGTT -s simCow_chr6.simCow.chr6 177114 54 + 602619 gtgattaagtggttcttttgacttatatggacaataggttgcatctcacttatg----------------------- -s simDog_chr6.simDog.chr6 460498 54 - 593897 ATGGTCATGTGGTTCTTTTGATTTGGATGGACTATAGGTTGTATCCTATTTATC----------------------- -s simHuman_chr6.simHuman.chr6 174830 46 + 601863 atagttatatggttattc------atatgaacta--ggttgtatcttatttatg----------------------- -s simRat_chr6.simRat.chr6 162460 77 + 647215 ATGATTATGTGGTTCTTTTAATGAGCGCTGGCTACCCGTTTCATTTCATTTAGAGGCTTTGAGCTGCAGCAGAGCTT - -a -s simMouse_chr6.simMouse.chr6 164633 3 + 636262 CAT -s Anc0.Anc0refChr1 5718 2 + 62388 -AT -s Anc1.Anc1refChr2 6169 3 - 144309 CAT -s Anc2.Anc2refChr3 6240 2 - 53186 -AT -s mr.mrrefChr5 27556 3 + 294540 CAT -s simCow_chr6.simCow.chr6 426966 2 - 602619 -AT -s simDog_chr6.simDog.chr6 134885 2 + 593897 -AT -s simHuman_chr6.simHuman.chr6 428490 3 - 601863 CAT -s simRat_chr6.simRat.chr6 162537 3 + 647215 CAT - -a -s simMouse_chr6.simMouse.chr6 164636 69 + 636262 GGCAGGTAGCTATTGCTCACGTAGTCCTCTTGATAAGTTAAAGACGTGTGTGATATTAAAGCCATGTAA -s Anc0.Anc0refChr1 5720 68 + 62388 AGCAG-CACCTATTTATCATGTAGCCCCCTTGAGAAGTTAAAGATGTGTATGATATCAAAGCCACATAA -s Anc1.Anc1refChr2 6172 68 - 144309 AGCAG-CACCTATTTATCATGTAGCCCCCTTGAGAAGTTAAAGATGTGTATGATATCAAAGCCACATAA -s Anc2.Anc2refChr3 6242 68 - 53186 AGGAG-CACCTATTTATCATGTAGCCCCCTTGACAAGTTAAAGCTGTGTATGATATCAAAGCCACATAA -s mr.mrrefChr5 27559 68 + 294540 GGCAG-TAGCTATTGCTCACGTAGCCCCCTTGAGAAGTTAAAGATGTGTGTGATATTAAAGCCATGTAA -s simCow_chr6.simCow.chr6 426968 67 - 602619 AGGAG-CACCTACTTATCATGTAGTCCCCTTGAAAAGTTAAAGCTGTCCATGTTACTAAAGC-ACCTGA -s simDog_chr6.simDog.chr6 134887 68 + 593897 AGGAG-CACCTATTTATCCTGTAGCCTCCTTGACTAGTCAAAGCTTTGTATGATGTCAAAGTCCTATAA -s simHuman_chr6.simHuman.chr6 428494 68 - 601863 AGCGG-CATCTATTCATCATGTAGCCCCCTTAAGAAGTTAAAGATGTATATGATATCCCAGCTACATAA -s simRat_chr6.simRat.chr6 162540 68 + 647215 GGCAG-TACCTACTGCTCACATAGCCTCCTTGAGAAGTTAAAGATGTGTGTGATATTTAAGCCATGTAA - -a -s simMouse_chr6.simMouse.chr6 164705 2 + 636262 AC -s Anc0.Anc0refChr1 5797 2 + 62388 AC -s Anc1.Anc1refChr2 6249 2 - 144309 AC -s Anc2.Anc2refChr3 6523 2 - 53186 CA -s mr.mrrefChr5 27627 2 + 294540 AC -s simCow_chr6.simCow.chr6 427319 2 - 602619 CA -s simDog_chr6.simDog.chr6 135189 2 + 593897 CA -s simHuman_chr6.simHuman.chr6 428571 2 - 601863 AC -s simRat_chr6.simRat.chr6 162608 2 + 647215 AT - -a -s simMouse_chr6.simMouse.chr6 164707 338 + 636262 TGCTTCAGTACTATCTTTATAGCCATATTTTTAACGCTACTTAGACTTTGCACAGCGCCTCGTGCAAATTTCCAAAAAAACGCGAATGCGGGCATGCACACATGGATAGTGCTTGGCTATGACCCTTCCCTGCGCGGCCATGTACAAACAGTTAGTGCTTGGCTATGCTCGCCCCGCGTGGCCACGTACAAGTGTCAGAGCTTGGCTATGAGCTGTCCAGAACTACACTCTGTCAAGCGATGACAGTCCTCCTGTACATTGTGAATCACAAGACTCAAGGACACTTGGTGTGATTAGACTCTAGGGCTCTTTCTTCTTCATCTGATGAAGCTTGTGTG -s Anc0.Anc0refChr1 5805 21 + 62388 TGCTTACGTACACGCTT-AT----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TG -s Anc1.Anc1refChr2 6257 62 - 144309 TGCTTACGTACACGCTT-ATagaaatatt-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------gagttgagatactc--------ttgctgtgataaagc----------------------------------gggTG -s Anc2.Anc2refChr3 6531 21 - 53186 TGCTCACATACACGCAA-AT----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TG -s mr.mrrefChr5 27635 102 + 294540 TGCTTCAGTACAATCTTTATAGCCATATT-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GAATCACAATACTCAAGGA---TTGGTGTGATAAGGCTCTAGGGCTCTTTCTTCTTCATCTGATGAAGCTTGTGTG -s simCow_chr6.simCow.chr6 427327 21 - 602619 TGCTTAGGTACAGCCAA-AA----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TG -s simDog_chr6.simDog.chr6 135197 21 + 593897 TGCTCACATACACGCAA-AT----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CG -s simHuman_chr6.simHuman.chr6 428575 62 - 601863 TGCATAGGTACACGCTT-acagaaatatt-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------gagttgagatactc--------ttgctgtgataaagc----------------------------------gggtg -s simRat_chr6.simRat.chr6 162616 102 + 647215 TGCTCCAGTACAATCTTTATAGCCATATT-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GAAACACAATACTCACGGG---TTGGTGTGATAAGGCTCCAGGGCTCATGCCTCTTGATCTGATGAGGCTCATGTG - -a -s simMouse_chr6.simMouse.chr6 165045 1 + 636262 G -s Anc0.Anc0refChr1 5826 1 + 62388 G -s Anc1.Anc1refChr2 6319 1 - 144309 G -s Anc2.Anc2refChr3 6552 1 - 53186 G -s mr.mrrefChr5 27737 1 + 294540 G -s simCow_chr6.simCow.chr6 427348 1 - 602619 G -s simDog_chr6.simDog.chr6 135218 1 + 593897 G -s simHuman_chr6.simHuman.chr6 428640 1 - 601863 g -s simRat_chr6.simRat.chr6 162718 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 165046 29 + 636262 GATGAACATAACCGCTACAGGAATCTCAA -s Anc0.Anc0refChr1 5827 28 + 62388 GATGGAC-AAACCACAACAGgaatgtcaa -s Anc1.Anc1refChr2 6320 28 - 144309 GATGGAC-AAACCACAACAGgaatgtcaa -s Anc2.Anc2refChr3 6553 28 - 53186 AATGGAC-AAACCACAGCAGgaatgtcaa -s mr.mrrefChr5 27738 29 + 294540 GATGAACATAACCGCTACAGGAATCTCAA -s simCow_chr6.simCow.chr6 427350 25 - 602619 ACTGGGC-AGACCATACTGGGA---TCAa -s simDog_chr6.simDog.chr6 135219 28 + 593897 AATGGAC-AAACCACAGCAGgaatgttgg -s simHuman_chr6.simHuman.chr6 428641 28 - 601863 ggtggac-caaccacaacagaaatatcaa -s simRat_chr6.simRat.chr6 162719 29 + 647215 GATGAAAATAACTGCCACAGAAATCTGAA - -a -s simMouse_chr6.simMouse.chr6 165075 5 + 636262 TTGCA -s Anc0.Anc0refChr1 5856 5 + 62388 ttgca -s Anc1.Anc1refChr2 6349 5 - 144309 ttgca -s Anc2.Anc2refChr3 6582 5 - 53186 ttgtg -s mr.mrrefChr5 27767 5 + 294540 TTGCA -s simCow_chr6.simCow.chr6 427376 5 - 602619 ttgtg -s simDog_chr6.simDog.chr6 135248 5 + 593897 ttgtg -s simHuman_chr6.simHuman.chr6 428670 5 - 601863 ctgca -s simRat_chr6.simRat.chr6 162748 5 + 647215 TTCCC - -a -s simMouse_chr6.simMouse.chr6 165080 16 + 636262 TGTACCATTCATGCTA -s Anc0.Anc0refChr1 5871 16 + 62388 tataccactaatgctg -s Anc1.Anc1refChr2 6364 16 - 144309 tataccactaatgctg -s Anc2.Anc2refChr3 6597 16 - 53186 catactactaatgctg -s mr.mrrefChr5 27772 16 + 294540 TGTACCATTCATGCTA -s simCow_chr6.simCow.chr6 427391 16 - 602619 catactactaacgttg -s simDog_chr6.simDog.chr6 135263 16 + 593897 cacactactgatgctg -s simHuman_chr6.simHuman.chr6 428685 16 - 601863 tataccaccaatgctg -s simRat_chr6.simRat.chr6 162753 16 + 647215 TGCACCAGCCATGCTA - -a -s simMouse_chr6.simMouse.chr6 165096 49 + 636262 TGGATGCCCCACAGAAATATGAACTGCATGCCCTAGTCACACAATGGAT -s Anc0.Anc0refChr1 5890 35 + 62388 tagatggtacagggagttacgtcatg--------------acaatggac -s Anc1.Anc1refChr2 6383 35 - 144309 tagatggtacagggagttacgtcatg--------------acaatggac -s Anc2.Anc2refChr3 6616 35 - 53186 cagacagtactgggagttacgtcatg--------------acaccagac -s mr.mrrefChr5 27788 49 + 294540 TGGATGCCCCACAGAAATATGAACTGCATGCCCTAGTCACACAATGGAT -s simCow_chr6.simCow.chr6 427408 35 - 602619 caaacagtactgagagttatgttgtg--------------gcaccagac -s simDog_chr6.simDog.chr6 135282 35 + 593897 cagacagtactgggagttacgtcatg--------------acaccaggc -s simHuman_chr6.simHuman.chr6 428704 35 - 601863 tacatggtacagggagttaggtgatg--------------acaatggac -s simRat_chr6.simRat.chr6 162769 49 + 647215 TGGATGCACCACAAAAATATGAATTGCATGCCCCAGCCACACAATTGAT - -a -s simMouse_chr6.simMouse.chr6 165145 16 + 636262 GTTGAGTCCACAGTAC -s Anc0.Anc0refChr1 5937 16 + 62388 TTTGATTCAGGAACAT -s Anc1.Anc1refChr2 6430 16 - 144309 TTTGATTCAGGAACAT -s Anc2.Anc2refChr3 6663 16 - 53186 TGTGATTCAGGAACAT -s mr.mrrefChr5 27837 16 + 294540 GTTGAGTCCACAGTAC -s simCow_chr6.simCow.chr6 427456 16 - 602619 TGTGCTACACAAAGAT -s simDog_chr6.simDog.chr6 135324 13 + 593897 ---GATTCAGGAACAG -s simHuman_chr6.simHuman.chr6 428751 16 - 601863 TTTGACTCAGGAACAT -s simRat_chr6.simRat.chr6 162818 16 + 647215 GCCGAGTCCACAGTAC - -a -s simMouse_chr6.simMouse.chr6 165161 10 + 636262 TGAGATAGGT -s Anc0.Anc0refChr1 5960 9 + 62388 GGAAGT-GGT -s Anc1.Anc1refChr2 6453 10 - 144309 GGAAGTAGGT -s Anc2.Anc2refChr3 6686 9 - 53186 GGAAGT-GGT -s mr.mrrefChr5 27853 10 + 294540 TGAGATAGGT -s simCow_chr6.simCow.chr6 427479 9 - 602619 GGAAGT-GGT -s simDog_chr6.simDog.chr6 135344 9 + 593897 GGAAGT-GGT -s simHuman_chr6.simHuman.chr6 428774 10 - 601863 GGAATTAATT -s simRat_chr6.simRat.chr6 162834 10 + 647215 TGAAATAGGG - -a -s simMouse_chr6.simMouse.chr6 165171 22 + 636262 CATGATACCATACTAATCATGA -s Anc0.Anc0refChr1 5979 22 + 62388 TATAATGACCTAATAATCTTGA -s Anc1.Anc1refChr2 6473 22 - 144309 TATAATGACCTAATAATCTTGA -s Anc2.Anc2refChr3 6705 22 - 53186 TATAATGACCTAATAATCTTGA -s mr.mrrefChr5 27863 22 + 294540 CATGATACCATACTAATCATGA -s simCow_chr6.simCow.chr6 427497 22 - 602619 TATAATGACCTTATAATCTTGA -s simDog_chr6.simDog.chr6 135363 22 + 593897 TATAACAACCTAATAAACTTGA -s simHuman_chr6.simHuman.chr6 428794 22 - 601863 TATAATGACCTAATAATCTCAA -s simRat_chr6.simRat.chr6 162844 22 + 647215 CATGACACCATACTAATCCTGA - -a -s simMouse_chr6.simMouse.chr6 165193 16 + 636262 CACAGTCAGTGTGATC -s Anc0.Anc0refChr1 6002 16 + 62388 CACAGTGGGTGTGTTT -s Anc1.Anc1refChr2 6496 16 - 144309 CACAGTGGGTGTGTTT -s Anc2.Anc2refChr3 6728 16 - 53186 CACAGTGGGTGTGTTT -s mr.mrrefChr5 27885 16 + 294540 CACAGTCAGTGTGATC -s simCow_chr6.simCow.chr6 427520 16 - 602619 CACAGTGGGTGCATTT -s simDog_chr6.simDog.chr6 135386 16 + 593897 TGCAGTGGGTGTGTTT -s simHuman_chr6.simHuman.chr6 428817 16 - 601863 CACAGTGGGTGTGTTT -s simRat_chr6.simRat.chr6 162866 16 + 647215 CACAGTCAGTGTGATA - -a -s simMouse_chr6.simMouse.chr6 165209 14 + 636262 AAGATGGCTCATTT -s Anc0.Anc0refChr1 6019 13 + 62388 AATGTAGC-CAATT -s Anc1.Anc1refChr2 6513 13 - 144309 AATGTAGC-CAATT -s Anc2.Anc2refChr3 6745 13 - 53186 AATGTGGC-CAATT -s mr.mrrefChr5 27901 14 + 294540 AAGATAGCTCATTT -s simCow_chr6.simCow.chr6 427537 13 - 602619 AATGTCGC-CAAAT -s simDog_chr6.simDog.chr6 135403 12 + 593897 AATG-GGC-CAATT -s simHuman_chr6.simHuman.chr6 428834 13 - 601863 AATGTAGC-CAATT -s simRat_chr6.simRat.chr6 162882 14 + 647215 AGGATAGCTTGTTT - -a -s simMouse_chr6.simMouse.chr6 165223 2 + 636262 AG -s Anc0.Anc0refChr1 6032 2 + 62388 GG -s Anc1.Anc1refChr2 6526 2 - 144309 GG -s Anc2.Anc2refChr3 6760 2 - 53186 GG -s mr.mrrefChr5 27915 2 + 294540 AG -s simCow_chr6.simCow.chr6 427552 2 - 602619 GG -s simDog_chr6.simDog.chr6 135417 2 + 593897 GG -s simHuman_chr6.simHuman.chr6 428847 2 - 601863 GG -s simRat_chr6.simRat.chr6 162896 2 + 647215 AG - -a -s simMouse_chr6.simMouse.chr6 165225 14 + 636262 GGCTATATCACTGC -s Anc0.Anc0refChr1 6034 14 + 62388 GACTATATCACCAC -s Anc1.Anc1refChr2 6528 14 - 144309 GACTATATCACCAC -s Anc2.Anc2refChr3 6762 14 - 53186 GAGTATACCAGCAC -s mr.mrrefChr5 27917 14 + 294540 GGCTATATCACTGC -s simCow_chr6.simCow.chr6 427554 13 - 602619 G-TTATACCATTGC -s simDog_chr6.simDog.chr6 135428 14 + 593897 GAGTATACCAGCAC -s simHuman_chr6.simHuman.chr6 428849 12 - 601863 GACTATATCACG-- -s simRat_chr6.simRat.chr6 162898 14 + 647215 GTTTATACCACTGC - -a -s simMouse_chr6.simMouse.chr6 165239 44 + 636262 CTATATTCATCATAAAGTGTATGCACAATCAGAACCATGCATAC -s Anc0.Anc0refChr1 6048 44 + 62388 CTACAATCATTAGAATGTATATGCACCACAAGAAGCATCTATAC -s Anc1.Anc1refChr2 6542 44 - 144309 CTACAATCATTAGAATGTATATGCACCACAAGAAGCATCTATAC -s Anc2.Anc2refChr3 6776 44 - 53186 CTACAATCATTAGAATGTATATGCACCACAAGAAGCATCTATAC -s mr.mrrefChr5 27931 44 + 294540 CTATATTCATCATAAAGTGTATGCACAACAAGAACCATGTATAC -s simCow_chr6.simCow.chr6 427568 44 - 602619 CTGCATATATTAGAATGTACATGCACGACAAGAAGCATCTATAC -s simDog_chr6.simDog.chr6 135442 44 + 593897 CTACAATCAATAGAATGTATATCTACCACAAGGAGCATCTATAC -s simHuman_chr6.simHuman.chr6 428861 40 - 601863 ----AATCATTAGGATTTATATGCACCCCAAGAAGTATCTACAC -s simRat_chr6.simRat.chr6 162912 44 + 647215 CTACACTCATCATAAAGTGTATGCACAACAAAAACCATGTATAA - -a -s simMouse_chr6.simMouse.chr6 165283 2 + 636262 TC -s Anc0.Anc0refChr1 6093 2 + 62388 TC -s Anc1.Anc1refChr2 6587 2 - 144309 TC -s Anc2.Anc2refChr3 6821 2 - 53186 TC -s mr.mrrefChr5 27975 2 + 294540 TC -s simCow_chr6.simCow.chr6 427613 2 - 602619 TC -s simDog_chr6.simDog.chr6 135487 2 + 593897 TT -s simHuman_chr6.simHuman.chr6 428902 2 - 601863 TC - -a -s simMouse_chr6.simMouse.chr6 165285 9 + 636262 CTAAGTTTT -s Anc0.Anc0refChr1 6095 9 + 62388 CTACGCTTT -s Anc1.Anc1refChr2 6589 9 - 144309 CTACGCTTT -s Anc2.Anc2refChr3 6835 9 - 53186 CCACTCTAT -s mr.mrrefChr5 27977 9 + 294540 CTAAGTTTT -s simCow_chr6.simCow.chr6 427647 9 - 602619 CCCCTCTAG -s simDog_chr6.simDog.chr6 135501 9 + 593897 CCACTCTAT -s simHuman_chr6.simHuman.chr6 428904 9 - 601863 ATGGGCATT - -a -s simMouse_chr6.simMouse.chr6 165294 16 + 636262 TCTAGACTGAGTACTA -s Anc0.Anc0refChr1 6108 16 + 62388 TCTAGACTGGGCAGTA -s Anc1.Anc1refChr2 6602 16 - 144309 TCTAGACTGGGCAGTA -s Anc2.Anc2refChr3 6848 16 - 53186 TCTAGAATGGGCAGTG -s mr.mrrefChr5 27986 16 + 294540 TCTAGACTGAGTACTA -s simCow_chr6.simCow.chr6 427660 16 - 602619 TCTAGAATTGGGAAGG -s simDog_chr6.simDog.chr6 135514 16 + 593897 TCTAGAATGGGCAGTG -s simHuman_chr6.simHuman.chr6 428917 16 - 601863 TCCAGACTGGGCAGCA - -a -s simMouse_chr6.simMouse.chr6 165310 33 + 636262 CACTGGTGTGGTGACACTGTGCCATGTAGTATT -s Anc0.Anc0refChr1 6124 30 + 62388 CACTGTTGATGCAACACTGAGCAGT---GCATT -s Anc1.Anc1refChr2 6618 33 - 144309 CACTGTTGATGCAACACTGAGCAGTAGTGCATT -s Anc2.Anc2refChr3 6864 30 - 53186 CACTGTTGATGCAACACTGAGCAGT---GCATG -s mr.mrrefChr5 28002 33 + 294540 CACTGGTGTGGTGACACTGTGCCATGTAGTATT -s simCow_chr6.simCow.chr6 427676 30 - 602619 CACTGTTGCTGTAGCACTGAGCTGT---GCATG -s simDog_chr6.simDog.chr6 135530 28 + 593897 CCCT--CGATGCAACACCAAGCAGT---GCGTG -s simHuman_chr6.simHuman.chr6 428938 33 - 601863 CACAGTTGGTGGAACACTGAGCAGTAGTGCATT - -a -s simMouse_chr6.simMouse.chr6 165343 3 + 636262 GGT -s Anc0.Anc0refChr1 6154 3 + 62388 GCT -s Anc1.Anc1refChr2 6651 3 - 144309 GCT -s Anc2.Anc2refChr3 6894 3 - 53186 TCG -s mr.mrrefChr5 28035 3 + 294540 GGT -s simCow_chr6.simCow.chr6 427706 3 - 602619 TCA -s simDog_chr6.simDog.chr6 135601 3 + 593897 TTG -s simHuman_chr6.simHuman.chr6 428971 3 - 601863 GCT - -a -s simMouse_chr6.simMouse.chr6 165346 14 + 636262 TGCAACCATTGCAG -s Anc0.Anc0refChr1 6158 7 + 62388 TGTAACC------- -s Anc1.Anc1refChr2 6655 7 - 144309 TGTAACC------- -s Anc2.Anc2refChr3 6898 7 - 53186 TGTAACC------- -s mr.mrrefChr5 28038 7 + 294540 TGCAACC------- -s simCow_chr6.simCow.chr6 427710 7 - 602619 TGTAACC------- -s simDog_chr6.simDog.chr6 135605 7 + 593897 CATGACC------- -s simHuman_chr6.simHuman.chr6 428975 7 - 601863 TGTAACC------- - -a -s simMouse_chr6.simMouse.chr6 165360 13 + 636262 CAGGTAGAATGTA -s Anc0.Anc0refChr1 6165 13 + 62388 CAGATTGACTGCA -s Anc1.Anc1refChr2 6662 13 - 144309 CAGATTGACTGCA -s Anc2.Anc2refChr3 6912 13 - 53186 CAGATTGACTGCA -s mr.mrrefChr5 28045 13 + 294540 CAGGTAGAATGTA -s simCow_chr6.simCow.chr6 427724 13 - 602619 CAGATAGACTGCA -s simDog_chr6.simDog.chr6 135619 13 + 593897 CAACTTGACTACA -s simHuman_chr6.simHuman.chr6 428982 13 - 601863 CAGATTGACTGCA - -a -s simMouse_chr6.simMouse.chr6 165373 9 + 636262 GCTTCATCT -s Anc0.Anc0refChr1 6178 9 + 62388 GCTTTACCC -s Anc1.Anc1refChr2 6675 9 - 144309 GCTTTACCC -s Anc2.Anc2refChr3 6925 9 - 53186 GCTTTACCC -s mr.mrrefChr5 28058 9 + 294540 GCTTCATCT -s simCow_chr6.simCow.chr6 427737 7 - 602619 GATCTAC-- -s simDog_chr6.simDog.chr6 135632 9 + 593897 GCTTTACCC -s simHuman_chr6.simHuman.chr6 428996 9 - 601863 ACTTTACCC - -a -s simMouse_chr6.simMouse.chr6 165382 9 + 636262 AATATTGGC -s Anc0.Anc0refChr1 6187 9 + 62388 AATATAGGA -s Anc1.Anc1refChr2 6684 9 - 144309 AATATAGGA -s Anc2.Anc2refChr3 6934 9 - 53186 AATATAGGA -s mr.mrrefChr5 28067 9 + 294540 AATATTGGC -s simDog_chr6.simDog.chr6 135641 9 + 593897 AATATAGGA -s simHuman_chr6.simHuman.chr6 429006 9 - 601863 AATACAGGG - -a -s simMouse_chr6.simMouse.chr6 165391 6 + 636262 TAATTA -s Anc0.Anc0refChr1 6196 6 + 62388 CAATTA -s Anc1.Anc1refChr2 6693 6 - 144309 CAATTA -s Anc2.Anc2refChr3 6943 6 - 53186 CAATTA -s mr.mrrefChr5 28076 6 + 294540 TAATTA -s simCow_chr6.simCow.chr6 427744 1 - 602619 -----A -s simDog_chr6.simDog.chr6 135714 6 + 593897 CAATTG -s simHuman_chr6.simHuman.chr6 429015 6 - 601863 CAATTA - -a -s simMouse_chr6.simMouse.chr6 165397 68 + 636262 ACGACTCAGTACGGAATTTCCAGATGTTGGATCTGTTTAGAGAAAGTATGCATGAGAATTTCAGTGCC -s Anc0.Anc0refChr1 6204 68 + 62388 AAGACACAGTAGAGAATTCCCAGCTGTGGAACCTGTTTAGAGGAAATATGCACAAGAATTTCAGGGCC -s Anc1.Anc1refChr2 6701 68 - 144309 AAGACACAGTAGAGAATTCCCAGCTGTGGAACCTGTTTAGAGGAAATATGCACAAGAATTTCAGGGCC -s Anc2.Anc2refChr3 6951 68 - 53186 AAGACACAGTAGAGAATTCCCAGCTGTGGAACCTGTTTAGAGAAAATATGCACAAGAGTTTCAGGGCC -s mr.mrrefChr5 28082 68 + 294540 ACGACTCAGTACGGAATTTCCAGATGTTGGATCTGTTTAGAGGAAATATGCACGAGAATTTCAGTGCC -s simCow_chr6.simCow.chr6 427747 68 - 602619 AAGACACAGTAGGGAATTCCAAGGTGTGGAACCTGTTTAGAGAGGATATGTACAAGGGTTTATGGGCC -s simDog_chr6.simDog.chr6 135722 68 + 593897 AAAACACAGTAGAGAATTCCCAGCTGTAGAACCTGTTTAGAGAAAGTATGCACGAGAGTTTCAGGACT -s simHuman_chr6.simHuman.chr6 429023 68 - 601863 AGGACACACTAGAAAATTCGCAGCTATGGAACCTGTTTAGAGGAAATATGCACAAGAATCTCAGGGCC -s simRat_chr6.simRat.chr6 162956 66 + 647215 --GACCCAGTACGGAATTTCCAGATGTTGGATCTGTTTAGAGGAAATATGCACCACAATTTTAGTTCG - -a -s simMouse_chr6.simMouse.chr6 165465 31 + 636262 AAGCGATGATTCCAGTACTTGACTGATAAAA -s Anc0.Anc0refChr1 6272 31 + 62388 AAGTGTGGGTTTCAGTACTTGGCTCATAAGG -s Anc1.Anc1refChr2 6769 31 - 144309 AAGTGTGGGTTTCAGTACTTGGCTCATAAGG -s Anc2.Anc2refChr3 7020 31 - 53186 CAGTGTGGGGTTCAGTACTTGGCTCATAAGG -s mr.mrrefChr5 28150 31 + 294540 AAGCGATGATTTCAGTACTTGACTGATAAAG -s simCow_chr6.simCow.chr6 427816 30 - 602619 CAGTGTGAGCTTCAATACCTGGCTC-TAAGG -s simDog_chr6.simDog.chr6 135791 30 + 593897 CAGTGTGGGGTTCAGT-CTTGGTTCATGAGG -s simHuman_chr6.simHuman.chr6 429091 31 - 601863 AAATGTGGGTTTCAGTACTTGGCTCATAAGG -s simRat_chr6.simRat.chr6 163022 31 + 647215 GAGCGATAATTTCAGTATTTGACTGATAAAG - -a -s simMouse_chr6.simMouse.chr6 165496 3 + 636262 CAG -s Anc0.Anc0refChr1 6303 3 + 62388 CAT -s Anc1.Anc1refChr2 6800 3 - 144309 CAT -s Anc2.Anc2refChr3 7051 3 - 53186 CAT -s mr.mrrefChr5 28181 3 + 294540 CAG -s simCow_chr6.simCow.chr6 427846 3 - 602619 CAT -s simDog_chr6.simDog.chr6 135821 3 + 593897 CAT -s simHuman_chr6.simHuman.chr6 429141 3 - 601863 CAA -s simRat_chr6.simRat.chr6 163053 3 + 647215 CAG - -a -s simMouse_chr6.simMouse.chr6 165499 21 + 636262 TTGTACTGGATTGTTCTATCT -s Anc0.Anc0refChr1 6306 15 + 62388 TT-AACTGGATTGTT-----T -s Anc1.Anc1refChr2 6803 21 - 144309 TTGAACTGGATTGTTCTACCT -s Anc2.Anc2refChr3 7054 15 - 53186 TT-AACTGGATTGTG-----T -s mr.mrrefChr5 28184 21 + 294540 TTGAACTGGATTGTTCTATCT -s simCow_chr6.simCow.chr6 427853 15 - 602619 TC-AACTGGATTGTG-----T -s simDog_chr6.simDog.chr6 135824 8 + 593897 TT-AACTAG------------ -s simHuman_chr6.simHuman.chr6 429144 21 - 601863 CTGAACTGGATTGTTCTACCT -s simRat_chr6.simRat.chr6 163056 20 + 647215 T-GAACTAAATTGTTCTATCT - -a -s simMouse_chr6.simMouse.chr6 165520 45 + 636262 AATGTAGGAGAGGTGGATAGGTGGAAGATGAGCATGAGCACTCTA -s Anc0.Anc0refChr1 6321 39 + 62388 AATGTAAAAGAGAGTGATCAATGTAAGCCAAGCA------CTCAA -s Anc1.Anc1refChr2 6824 39 - 144309 AATGTAAAAGAGAGTGATCAATGTAAGCCAAGCA------CTCAA -s Anc2.Anc2refChr3 7069 39 - 53186 AATGTAAAAGAGAGTGATCAATGTAAGCCAAGCA------CTCAA -s mr.mrrefChr5 28205 39 + 294540 AATGTAGGAGAGGTGGATAGATGGAAGATGAGCA------CTCTA -s simCow_chr6.simCow.chr6 427868 38 - 602619 GTTGTAATAGAGCCTGATCTATGTAAGC-AATCA------CTCGA -s simDog_chr6.simDog.chr6 457652 39 - 593897 AATGTAAAAGGGAGTGATCAATGCAAAACAAGGC------CTCAA -s simHuman_chr6.simHuman.chr6 429165 39 - 601863 AATGTAAAAGAGTGTGATCAATGTGAGCCTAGCA------CTCAC -s simRat_chr6.simRat.chr6 163076 39 + 647215 GATGTAGGGGAGGTGGATAGATGCAAGGTGAGCA------CTCTA - -a -s simMouse_chr6.simMouse.chr6 165565 71 + 636262 GGGCTAAGTTCAAATTATACCTAGTTAGGTCAAAAGCCCAATTCTCACACTGTTGGAGTGACCACTCCCGT -s Anc0.Anc0refChr1 6363 32 + 62388 GGACAAATTTCAGATTAGCCCGAGCTATGTCA--------------------------------------- -s Anc1.Anc1refChr2 6866 32 - 144309 GGACAAATTTCAGATTAGCCCGAGCTATGTCA--------------------------------------- -s Anc2.Anc2refChr3 7111 32 - 53186 GAACAGATTTCAGATTAGTCCGAGCTATGTCA--------------------------------------- -s mr.mrrefChr5 28247 71 + 294540 GGGCTAAGTTCAAATTATCCCTAGTTATGTCAAAAGCCCAATTCTCACACTGTTGGAGTGACCACTCCCGT -s simCow_chr6.simCow.chr6 427909 30 - 602619 --ACAGATTTCAGATTATGCCTAGCTATGTCA--------------------------------------- -s simDog_chr6.simDog.chr6 457694 32 - 593897 GAATGGATTTCAGATTAGTCTGAGTTATGTTA--------------------------------------- -s simHuman_chr6.simHuman.chr6 429207 32 - 601863 GGACAAATTTCAGATTGGCCCCAGCTATGTCA--------------------------------------- -s simRat_chr6.simRat.chr6 163118 71 + 647215 GGGCTAGGTGCCAATTATCGCTAGTTATGTCAAAAGCCCAATTCTCACACCGTTCGAGTGACCACTCCTGT - -a -s simMouse_chr6.simMouse.chr6 165636 108 + 636262 GGATTGGTATGTTGAATCAGCCAAGGTGAAATCAAAGTGCTTGAACTTAGTTCCTTGCGGTTTCTAAGGGCCGCGCATAAGTTGGTCCCACCTCAATCAATGATAGTG -s mr.mrrefChr5 28318 107 + 294540 GGATTGGTATGTTGAATCAGCCAAGGTGAAATCAAAGTGCTTGAACTTAGTTCCTTGCGGTTT-TAAGGGCCGCGCATAAGTTGGTCCCACCTCAATCAATGATAGTG -s simRat_chr6.simRat.chr6 163190 107 + 647215 GGATTGGTATGTTGAATCAGCCAATGTGTGATCAGAGTGCTTGAACTTAGTTCCTTGCAGCTT-TAAGAGTAGCCCATGAGATGGTCCCACCTCAAGCAAGTAAAGGG - -a -s simMouse_chr6.simMouse.chr6 165744 72 + 636262 CTATTGTGGTCGCGATTGAGGTGGCCACACACAGATGAGCTCAGTTGTGTACCTTTACCCCATGCTAGATGT -s Anc0.Anc0refChr1 6395 5 + 62388 -------------------------------------------------------------------GATGT -s Anc1.Anc1refChr2 6898 5 - 144309 -------------------------------------------------------------------GATGT -s Anc2.Anc2refChr3 7143 5 - 53186 -------------------------------------------------------------------GATAT -s mr.mrrefChr5 28425 62 + 294540 CTATTGTGGTCGCGATTGAGGTG----------GATGAGCTCAGTTGTGTACCTTTACCCCATGCTAGATGT -s simCow_chr6.simCow.chr6 427939 5 - 602619 -------------------------------------------------------------------GATAT -s simDog_chr6.simDog.chr6 457726 5 - 593897 -------------------------------------------------------------------CATAT -s simHuman_chr6.simHuman.chr6 429239 5 - 601863 -------------------------------------------------------------------GATGT -s simRat_chr6.simRat.chr6 163299 62 + 647215 CTATTGTGGTTGCAATTGGGGTG----------AATGAGCTCAGTTGTGTACTTTGTCCTCATGGTAGATAT - -a -s simMouse_chr6.simMouse.chr6 165816 13 + 636262 GGTCAGCAGACAC -s Anc0.Anc0refChr1 6401 13 + 62388 GGTCAGCAGTTGC -s Anc1.Anc1refChr2 6904 13 - 144309 GGTCAGCAGTTGC -s Anc2.Anc2refChr3 7149 13 - 53186 GGTCAGCAGTTGC -s mr.mrrefChr5 28487 13 + 294540 GGTCAGCAGTTAC -s simCow_chr6.simCow.chr6 427945 13 - 602619 GGTCAGCAGTTGC -s simDog_chr6.simDog.chr6 457732 13 - 593897 GGTCACCAGTTGC -s simHuman_chr6.simHuman.chr6 429245 13 - 601863 GGTTAGCAGTTGC -s simRat_chr6.simRat.chr6 163361 13 + 647215 AGTCAGCAGTTAC - -a -s simMouse_chr6.simMouse.chr6 165829 1 + 636262 A -s Anc0.Anc0refChr1 6416 1 + 62388 G -s Anc1.Anc1refChr2 6919 1 - 144309 G -s Anc2.Anc2refChr3 7164 1 - 53186 G -s mr.mrrefChr5 28502 1 + 294540 G -s simCow_chr6.simCow.chr6 428015 1 - 602619 G -s simDog_chr6.simDog.chr6 457747 1 - 593897 G -s simHuman_chr6.simHuman.chr6 429260 1 - 601863 G -s simRat_chr6.simRat.chr6 163376 1 + 647215 G - -a -s simMouse_chr6.simMouse.chr6 165830 64 + 636262 CCCTTATAAGTCTGCCTAACAGTGCACAAGCGTGGGCTCATAGGATTTGAACAGCTCATAGGAT -s Anc0.Anc0refChr1 6417 46 + 62388 CTCTTGCCAGCTC-TCCAACCGTGTACAAGTGCTA-----------------AACTCATAGGAT -s Anc1.Anc1refChr2 6920 46 - 144309 CTCTTGCCAGCTC-TCCAACCGTGTACAAGTGCTA-----------------AACTCATAGGAT -s Anc2.Anc2refChr3 7165 46 - 53186 CTCTTGCCAGCTG-TCCAACCGTGTACAGGTGTTA-----------------AACTCATAGGAG -s mr.mrrefChr5 28503 47 + 294540 CCCTTGCAAGTCCGCCCAACAGTGCACAAGTGCTG-----------------AGCTCATAGGAT -s simCow_chr6.simCow.chr6 428016 45 - 602619 CTCTTGCCGGCTG-TCCAAC-ATGTACAGGTATTG-----------------AACTCATGGGAC -s simDog_chr6.simDog.chr6 457751 46 - 593897 CTTTTGCCAGCTG-TCCAACCGTGTACAGGTGTTA-----------------AACTTGGAGAAG -s simHuman_chr6.simHuman.chr6 429261 46 - 601863 CTCTTGCCAGCTC-TCCCACTGTGTACAAGTGCTA-----------------AACTCATAGGAT -s simRat_chr6.simRat.chr6 163377 47 + 647215 CCCTTGCTAGTCCCCCCAACAGTGGACAAGTGCTG-----------------AGCATATAGGAT - -a -s simMouse_chr6.simMouse.chr6 165894 8 + 636262 TTGAATAG -s Anc0.Anc0refChr1 6476 8 + 62388 TAGAATAG -s Anc1.Anc1refChr2 6979 8 - 144309 TAGAATAG -s Anc2.Anc2refChr3 7224 8 - 53186 TAGAACAG -s mr.mrrefChr5 28550 8 + 294540 TAGAATAG -s simCow_chr6.simCow.chr6 428074 8 - 602619 TAGAAGAT -s simDog_chr6.simDog.chr6 457808 8 - 593897 TAAAACAG -s simHuman_chr6.simHuman.chr6 429320 8 - 601863 TAGAATAC -s simRat_chr6.simRat.chr6 163424 8 + 647215 TACAACAG - -a -s simMouse_chr6.simMouse.chr6 165902 23 + 636262 GCATGGCCTGATATGATTGTATT -s Anc0.Anc0refChr1 6496 16 + 62388 TGGTGGATTGAC--GATT----- -s Anc1.Anc1refChr2 6999 18 - 144309 TGGTGGATTGACTTGATT----- -s Anc2.Anc2refChr3 7244 16 - 53186 TGGGGGATTGAC--AAAC----- -s mr.mrrefChr5 28558 23 + 294540 TGGTGGCCTGATATGATTGTATT -s simCow_chr6.simCow.chr6 428106 12 - 602619 TGTGAGCTTGAT----------- -s simDog_chr6.simDog.chr6 457887 16 - 593897 TGGGGCATTGAC--AAAC----- -s simHuman_chr6.simHuman.chr6 429340 18 - 601863 TGGTGGATTGACTTGATT----- -s simRat_chr6.simRat.chr6 163432 23 + 647215 TGGTTGCCTGATCTGATTGTATT - -a -s simMouse_chr6.simMouse.chr6 165925 15 + 636262 CTGAACACGTTCCTG -s Anc0.Anc0refChr1 6512 9 + 62388 ------CTGTTCTTG -s Anc1.Anc1refChr2 7017 9 - 144309 ------CTGTTCTTG -s Anc2.Anc2refChr3 7260 9 - 53186 ------CTGTTCTTG -s mr.mrrefChr5 28582 15 + 294540 CTGAACTCGTTCCTG -s simCow_chr6.simCow.chr6 428118 6 - 602619 ---------TTCTTG -s simDog_chr6.simDog.chr6 457903 7 - 593897 ------CTGTTCT-- -s simHuman_chr6.simHuman.chr6 429358 9 - 601863 ------CTATTCTTG -s simRat_chr6.simRat.chr6 163456 15 + 647215 CTGAACTTGTTCCTG - -a -s simMouse_chr6.simMouse.chr6 165940 16 + 636262 TGGCTGCTAAAATGTC -s Anc0.Anc0refChr1 6526 15 + 62388 TGGCTGATAAAATGT- -s Anc1.Anc1refChr2 7031 16 - 144309 TGGCTGATAAAATGTT -s Anc2.Anc2refChr3 7274 15 - 53186 TGGCTGATAGGATGT- -s mr.mrrefChr5 28597 16 + 294540 TGGCTGCTAAAATGTC -s simCow_chr6.simCow.chr6 428127 9 - 602619 ------AGAAGATGT- -s simDog_chr6.simDog.chr6 457912 15 - 593897 TGGCTGATAGGATTT- -s simHuman_chr6.simHuman.chr6 429375 16 - 601863 TGGCTGGTCAAATGTT -s simRat_chr6.simRat.chr6 163471 16 + 647215 TGGCTGCTAAAAAGTC - -a -s simMouse_chr6.simMouse.chr6 165956 46 + 636262 CCGACCTCTACTAGAACAATTTCTCCCAGTAATTGCTGGTAACAAG -s Anc0.Anc0refChr1 6543 45 + 62388 CAA-CCTCTACCAGAACATTTTCTTCTAGAATTTACTGTTAACAAG -s Anc1.Anc1refChr2 7049 45 - 144309 CAA-CCTCTACCAGAACATTTTCTTCTAGAATTTACTGTTAACAAG -s Anc2.Anc2refChr3 7291 45 - 53186 CAA-CCTCTACCACAACAATTTGTTCTAGAATTTACTGTTAACAAG -s mr.mrrefChr5 28613 45 + 294540 CCG-CCTCTACTAGAACATTTTCTCCCAGAAATTGCTGGTAACAAG -s simCow_chr6.simCow.chr6 428138 45 - 602619 CAA-CCTCTACCAAAACAATTTGTTCTAGAATTTACTGTTAACAAG -s simDog_chr6.simDog.chr6 457929 45 - 593897 TGA-CCTCTGTCACAACAATTTGTTCTAGAGTTTATTGTTAACAAG -s simHuman_chr6.simHuman.chr6 429395 43 - 601863 CAA-CCTCTACCAGGACATTGTC--CTAGAATCTACTGTTACCAGG -s simRat_chr6.simRat.chr6 163487 45 + 647215 CTG-CCTCTATTAGAACATTTTTTCCCAGAAAGTGCTGGTAATAAG - -a -s simMouse_chr6.simMouse.chr6 166002 48 + 636262 CCCTGAGAGATGGGCTAGTTTCTGAAAGCCCAAAGTTCACACTAATCA -s Anc0.Anc0refChr1 6593 48 + 62388 CCTGGAGTGATAAGCTAGTTTCTGGAAGCCTGCAGTTCACTCTAACCA -s Anc1.Anc1refChr2 7099 48 - 144309 CCTGGAGTGATAAGCTAGTTTCTGGAAGCCTGCAGTTCACTCTAACCA -s Anc2.Anc2refChr3 7341 48 - 53186 CCTGGAGTGATAGGCTAGTTTCTGGAAGCCTGCATTTCACTCTAACTA -s mr.mrrefChr5 28663 48 + 294540 CCTTGAGAGATAAGCTAGTTTCTGAAAGCCCAAAGTTCACACTAATCA -s simCow_chr6.simCow.chr6 428188 48 - 602619 CCTGGAGTGATGTGCTAGTCTCTGGCAGCCTGCAATTCAACCTAACTG -s simDog_chr6.simDog.chr6 457979 47 - 593897 TATGGAGTGATAGACTAGTT-CTGGAAGCCTGCATTTCACTCTAACTA -s simHuman_chr6.simHuman.chr6 429443 43 - 601863 CCTGGAGTGATAAGCTAGTTTCTGGAA-----CAGCTCACTCTAACCA -s simRat_chr6.simRat.chr6 163537 47 + 647215 CCTAT-GAAATAAGCTAGTTTCTGAAAACCCAAAGTTCACACGAATCA - -a -s simMouse_chr6.simMouse.chr6 166050 10 + 636262 ATTGTGAAGC -s Anc0.Anc0refChr1 6641 10 + 62388 TGTGAGACTT -s Anc1.Anc1refChr2 7147 10 - 144309 TGTGAGACTT -s Anc2.Anc2refChr3 7391 10 - 53186 TGTGGGGCTT -s mr.mrrefChr5 28711 10 + 294540 ATTGAGACGT -s simCow_chr6.simCow.chr6 428238 10 - 602619 TTTGGGGTTT -s simDog_chr6.simDog.chr6 458028 10 - 593897 CGTGGGGCTT -s simHuman_chr6.simHuman.chr6 429486 10 - 601863 TATGAGACTT -s simRat_chr6.simRat.chr6 163584 10 + 647215 ATTAACGCCT - -a -s simMouse_chr6.simMouse.chr6 166060 19 + 636262 TTTCAAACTTGATGATTGT -s Anc0.Anc0refChr1 6651 19 + 62388 ACTCAAGCTTGATAATTGT -s Anc1.Anc1refChr2 7157 19 - 144309 ACTCAAGCTTGATAATTGT -s Anc2.Anc2refChr3 7401 19 - 53186 TCTCAGGCTTGATAATTGT -s mr.mrrefChr5 28721 19 + 294540 ATTCAAACTTGATAATTGT -s simCow_chr6.simCow.chr6 428248 19 - 602619 TCTCAGAATTGATAATTGT -s simDog_chr6.simDog.chr6 458038 19 - 593897 TCTCAGGCTTGATAAAAGG -s simHuman_chr6.simHuman.chr6 429500 19 - 601863 AATGAAGCTTGATAATTGT -s simRat_chr6.simRat.chr6 163594 19 + 647215 AGGTAGACTTGATAATTGT - -a -s simMouse_chr6.simMouse.chr6 166079 12 + 636262 AGTCACCAGGAT -s Anc0.Anc0refChr1 6670 8 + 62388 AGTAGC----AT -s Anc1.Anc1refChr2 7176 8 - 144309 AGTAGC----AT -s Anc2.Anc2refChr3 7420 8 - 53186 AGAAAA----AT -s mr.mrrefChr5 28740 12 + 294540 AGTCGCCAGGAT -s simCow_chr6.simCow.chr6 428271 8 - 602619 ACCAAT----AT -s simDog_chr6.simDog.chr6 458057 8 - 593897 AGAAAA----AT -s simHuman_chr6.simHuman.chr6 429519 8 - 601863 AGTTGC----AT -s simRat_chr6.simRat.chr6 163613 12 + 647215 AGTCGCGACGAT - -a -s simMouse_chr6.simMouse.chr6 166091 43 + 636262 TAGAATGACTCACATGTGAAGCTACAAGTAGATTTACAGGCTC -s Anc0.Anc0refChr1 6678 43 + 62388 TAGAATGACTCAAGTGTGAATCAACTTGTATATTTATAGGTTC -s Anc1.Anc1refChr2 7184 43 - 144309 TAGAATGACTCAAGTGTGAATCAACTTGTATATTTATAGGTTC -s Anc2.Anc2refChr3 7428 43 - 53186 TAGAATGACTCAAGTGTGAATCAACTTGTATATTTATAGGTTC -s mr.mrrefChr5 28752 43 + 294540 TAGAATGACTCACATGTGAAGCAACATGTAGATTTACAGGCTC -s simCow_chr6.simCow.chr6 428279 43 - 602619 TAGAATGCCTCAAGCGTGAAGCAGCCAGTATATTTATAGGTTC -s simDog_chr6.simDog.chr6 136260 41 + 593897 TAGAATGACTCAGGTG--AATCAACTTGTCTATTTATAGGTTC -s simHuman_chr6.simHuman.chr6 429527 43 - 601863 TAGAATGACTCAAGTGCGAATCAACTTGTATGTTTATAGGTTC -s simRat_chr6.simRat.chr6 163625 43 + 647215 TAGGTTGACTCACATATGAAGCAACATGTGGATTTACAGGCTC - -a -s simMouse_chr6.simMouse.chr6 166134 7 + 636262 TTCTATG -s Anc0.Anc0refChr1 6726 7 + 62388 TTTTATA -s Anc1.Anc1refChr2 7232 7 - 144309 TTTTATA -s Anc2.Anc2refChr3 7476 7 - 53186 TTTTATA -s mr.mrrefChr5 28795 7 + 294540 TTTTATG -s simCow_chr6.simCow.chr6 428327 7 - 602619 TTTTATA -s simDog_chr6.simDog.chr6 136306 7 + 593897 TTTTAAC -s simHuman_chr6.simHuman.chr6 429575 7 - 601863 TTTTATA -s simRat_chr6.simRat.chr6 163668 7 + 647215 TTTTATG - -a -s simMouse_chr6.simMouse.chr6 166141 20 + 636262 GAGGGTTATTCAGAGATTAA -s Anc0.Anc0refChr1 6763 20 + 62388 GAGAGTAATTCAGAGATTAA -s Anc1.Anc1refChr2 7269 20 - 144309 GAGAGTAATTCAGAGATTAA -s Anc2.Anc2refChr3 7513 20 - 53186 AAGAGTAATTCAGAGGTCAA -s mr.mrrefChr5 28802 20 + 294540 GAGGGTAATTCAGAGATTAA -s simCow_chr6.simCow.chr6 428364 19 - 602619 AAGATCAATTCAGAGGT-AA -s simDog_chr6.simDog.chr6 136343 20 + 593897 AACAGTAATTCAGAGGTCAA -s simHuman_chr6.simHuman.chr6 429612 20 - 601863 GGGAGTAATTCAGAGATTGA -s simRat_chr6.simRat.chr6 163675 20 + 647215 AAGGGTAATTAAGAGATTAA - -a -s simMouse_chr6.simMouse.chr6 166161 41 + 636262 TACTGCTTCCTACGTAAACCACTTGCCCCATAGAGAAACCA -s Anc0.Anc0refChr1 6783 41 + 62388 TACTGGTTGTTATGTAGACCACTTGCTCCATAAAGTAACCA -s Anc1.Anc1refChr2 7289 41 - 144309 TACTGGTTGTTATGTAGACCACTTGCTCCATAAAGTAACCA -s Anc2.Anc2refChr3 7533 41 - 53186 CAGTGGTTGTTATGTAGACCACTTCCTTCACCAAGTCACCA -s mr.mrrefChr5 28822 41 + 294540 TACTGCTTCTTACGTAAACCACTTGCCCCATAGAGAAACCA -s simCow_chr6.simCow.chr6 428383 40 - 602619 CAGTGGTTGTTATGTATACCACTTTCTTTACGAAGTCACC- -s simDog_chr6.simDog.chr6 136363 41 + 593897 CAGTCGTTGTTAAATAGACCATTTCCTTCACCAAGTCACCA -s simHuman_chr6.simHuman.chr6 429644 41 - 601863 TACTGTTTATTATGTAGACTTCTTGCACCATATAATAACCA -s simRat_chr6.simRat.chr6 163695 40 + 647215 TACTGCTACTTACGTAAACCACTTGC-CTATAGAGAAACTA - -a -s simMouse_chr6.simMouse.chr6 166202 80 + 636262 CTGAACACCATGTGTAAAGTCAGCATGCACCTCAAGTAAACAACACAGGGTAGGATTCGCTTTTTTTTTATCATATAAGA -s Anc0.Anc0refChr1 6825 77 + 62388 CTGAACACCTCTGGTAAAGTCAGTATTCACCTCCAGTAACCA---CTAACAGGGATGTGCTTTTGCTTTCTCAGATAAAA -s Anc1.Anc1refChr2 7331 77 - 144309 CTGAACACCTCTGGTAAAGTCAGTATTCACCTCCAGTAACCA---CTAACAGGGATGTGCTTTTGCTTTCTCAGATAAAA -s Anc2.Anc2refChr3 7575 77 - 53186 CTGTAGACCTCTGGTAAAGTCAGTCTTCACCTCCAGTAACTA---CTAACAGGTATGTGCTCTTGCTTTCTCGGATATAA -s mr.mrrefChr5 28864 77 + 294540 CTGAACACCATGTGTAAAGTCAGTATTCACCTCAAGTAAACA---CAAGGTAGGATTTGCTTTTTCTTTATCATATAAGA -s simCow_chr6.simCow.chr6 428423 68 - 602619 TTGTAGGCCTCTGGTAAAGTCAATTTTGACCTCCAGTAACTA---CTGACAAGTATGTCCTCTTGCTTT---------GA -s simDog_chr6.simDog.chr6 136405 77 + 593897 CTGTAGACCTCTGGTAAAGTCAGTCTTCAACTACAGTAACTA---CTAACTGGTACTTGCCCTTTCTTTCTCGGATATAA -s simHuman_chr6.simHuman.chr6 429686 77 - 601863 CTGAACACCTCTGGTAAAGTCAGTATCCACCTCCAATAACCA---CCAACAGGGATGTGATTTTGCTTTCTCAGATAAAA -s simRat_chr6.simRat.chr6 163736 77 + 647215 TTGAACACCATGTGTAAAGTCTGTATTCATCTCAAGTAGACA---CAAGGTAGGATTTGCTTTTTCTTTATCATATAAGA - -a -s simMouse_chr6.simMouse.chr6 166282 12 + 636262 TTAATGTTTGGT -s Anc0.Anc0refChr1 6902 12 + 62388 TTAATGTTTGGT -s Anc1.Anc1refChr2 7408 12 - 144309 TTAATGTTTGGT -s Anc2.Anc2refChr3 7652 12 - 53186 TTAATGTTGGGT -s mr.mrrefChr5 28941 12 + 294540 TTAATGTTTGGT -s simCow_chr6.simCow.chr6 428491 12 - 602619 TTAATGTTGAAT -s simDog_chr6.simDog.chr6 136482 12 + 593897 TTGATGTTGGGT -s simHuman_chr6.simHuman.chr6 429765 12 - 601863 TTAATGTTTGGT -s simRat_chr6.simRat.chr6 163813 12 + 647215 TTAATGTTTGGT - -a -s simMouse_chr6.simMouse.chr6 166294 1 + 636262 C -s Anc0.Anc0refChr1 6914 1 + 62388 C -s Anc1.Anc1refChr2 7420 1 - 144309 C -s Anc2.Anc2refChr3 7664 1 - 53186 C -s mr.mrrefChr5 28953 1 + 294540 C -s simCow_chr6.simCow.chr6 428504 1 - 602619 C -s simDog_chr6.simDog.chr6 136494 1 + 593897 C -s simHuman_chr6.simHuman.chr6 429777 1 - 601863 C -s simRat_chr6.simRat.chr6 163825 1 + 647215 C - -a -s simMouse_chr6.simMouse.chr6 166295 6 + 636262 CCAGAG -s Anc0.Anc0refChr1 6918 6 + 62388 CCAAAG -s Anc1.Anc1refChr2 7424 6 - 144309 CCAAAG -s Anc2.Anc2refChr3 7668 6 - 53186 CCAAAG -s mr.mrrefChr5 28957 6 + 294540 CCAGAG -s simCow_chr6.simCow.chr6 428508 6 - 602619 CCACAG -s simDog_chr6.simDog.chr6 136498 6 + 593897 CATAAG -s simHuman_chr6.simHuman.chr6 429781 6 - 601863 CCAATG -s simRat_chr6.simRat.chr6 163829 6 + 647215 GCAGAT - -a -s simMouse_chr6.simMouse.chr6 166301 47 + 636262 GACCACCAATCATTTCCACAAACTTTTACAATTTGGAATTGCCTGGA -s Anc0.Anc0refChr1 6928 47 + 62388 GACCCCTACTCATTTCCACAGACTTTTATCATTTAGCTTTGCCTGAA -s Anc1.Anc1refChr2 7434 47 - 144309 GACCCCTACTCATTTCCACAGACTTTTATCATTTAGCTTTGCCTGAA -s Anc2.Anc2refChr3 7678 47 - 53186 TACCCCTCCTCATTTCCACAGACTTTTATCATTTAGCTTTGCCTGAA -s mr.mrrefChr5 28963 47 + 294540 GACCACCAATCATTTCCACAAACTTTTACAATTTGGAATTGCCTGGA -s simCow_chr6.simCow.chr6 428518 47 - 602619 TATCCCCCCTCATTTCCACAGTTTTTTATCGTTTAGCCTTGACTGAA -s simDog_chr6.simDog.chr6 136508 44 + 593897 TTCCCCTCGTCACTTCCACAGACTTTTATCA---AACTTTGCCTGAA -s simHuman_chr6.simHuman.chr6 429791 47 - 601863 GACCCCTACTCATTTCCAAAGAATTTTATCACTTAGTTCAGTCTGAC -s simRat_chr6.simRat.chr6 163835 47 + 647215 GACAACCAAGCATTTCCACCAACTTTTACAATTTGGGATGGCTTGGA - -a -s simMouse_chr6.simMouse.chr6 166348 18 + 636262 CAATTTATGGTTGGTTTT -s Anc0.Anc0refChr1 6979 17 + 62388 -AATTTGTGCTCAGTCTC -s Anc1.Anc1refChr2 7486 18 - 144309 CAATTTGTGCTCAGTCTC -s Anc2.Anc2refChr3 7729 17 - 53186 -AATTTGTGCTCACTCCC -s mr.mrrefChr5 29015 18 + 294540 CAATTTATGGTTAGTCTC -s simCow_chr6.simCow.chr6 428569 17 - 602619 -ACTTTGTGTGCACTCCT -s simDog_chr6.simDog.chr6 136556 17 + 593897 -AATTTGTGCTTACTCCC -s simHuman_chr6.simHuman.chr6 429843 18 - 601863 CAGCTAGTGATCAGTCTC -s simRat_chr6.simRat.chr6 163887 18 + 647215 CAATTTATGGCTAATCTC - -a -s simMouse_chr6.simMouse.chr6 166366 1 + 636262 G -s Anc0.Anc0refChr1 6996 1 + 62388 A -s Anc1.Anc1refChr2 7504 1 - 144309 A -s Anc2.Anc2refChr3 7746 1 - 53186 A -s mr.mrrefChr5 29033 1 + 294540 T -s simCow_chr6.simCow.chr6 428586 1 - 602619 A -s simDog_chr6.simDog.chr6 136576 1 + 593897 A -s simHuman_chr6.simHuman.chr6 429861 1 - 601863 A -s simRat_chr6.simRat.chr6 163905 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 166367 9 + 636262 ACCTGATGT -s Anc0.Anc0refChr1 6997 9 + 62388 CCCTGATTT -s Anc1.Anc1refChr2 7505 9 - 144309 CCCTGATTT -s Anc2.Anc2refChr3 7747 9 - 53186 CCCTGATTT -s mr.mrrefChr5 29034 9 + 294540 CCCTGATTT -s simCow_chr6.simCow.chr6 428618 9 - 602619 CTCTGATTT -s simDog_chr6.simDog.chr6 136577 9 + 593897 CCCTGATTT -s simHuman_chr6.simHuman.chr6 429862 9 - 601863 CCCTGATTT -s simRat_chr6.simRat.chr6 163906 9 + 647215 CCCTGATTT - -a -s simMouse_chr6.simMouse.chr6 166376 6 + 636262 TCCCCA -s Anc0.Anc0refChr1 7006 2 + 62388 TC---- -s Anc1.Anc1refChr2 7514 2 - 144309 TC---- -s Anc2.Anc2refChr3 7756 2 - 53186 TC---- -s mr.mrrefChr5 29043 6 + 294540 TCTCCA -s simCow_chr6.simCow.chr6 428627 2 - 602619 TC---- -s simDog_chr6.simDog.chr6 136587 2 + 593897 TC---- -s simHuman_chr6.simHuman.chr6 429871 2 - 601863 TC---- -s simRat_chr6.simRat.chr6 163915 6 + 647215 TCTCCT - -a -s simMouse_chr6.simMouse.chr6 166382 6 + 636262 AGAGTA -s Anc0.Anc0refChr1 7008 6 + 62388 AGAATA -s Anc1.Anc1refChr2 7516 6 - 144309 AGAATA -s Anc2.Anc2refChr3 7758 6 - 53186 AGAATA -s mr.mrrefChr5 29049 6 + 294540 AGAGTA -s simCow_chr6.simCow.chr6 428633 6 - 602619 AGAATA -s simDog_chr6.simDog.chr6 136589 6 + 593897 AATATC -s simHuman_chr6.simHuman.chr6 429873 6 - 601863 AGAATA -s simRat_chr6.simRat.chr6 163921 6 + 647215 AGAGTA - -a -s simMouse_chr6.simMouse.chr6 166388 27 + 636262 TCTATAAATAAGACATGTTTATTGAGC -s Anc0.Anc0refChr1 7014 20 + 62388 TCTGG-------ACATGATTATCTAGC -s Anc1.Anc1refChr2 7522 23 - 144309 TCTGGTG----GACATGATTATCTAGC -s Anc2.Anc2refChr3 7764 20 - 53186 GCTGG-------ACACAATTATTTAGC -s mr.mrrefChr5 29055 27 + 294540 TCTATAAATAAGACATGATTATCGAGC -s simCow_chr6.simCow.chr6 428639 20 - 602619 GCAGG-------GCACTATTATTCAGC -s simDog_chr6.simDog.chr6 136596 20 + 593897 GTTGG-------ACACAATTATTTAGC -s simHuman_chr6.simHuman.chr6 429879 23 - 601863 TCTGGTG----GACATGATTAGCTGTC -s simRat_chr6.simRat.chr6 163927 27 + 647215 TCTATAAATAAGACATAATTATCAAGC - -a -s simMouse_chr6.simMouse.chr6 166415 39 + 636262 CATTGTAGTCTGGCGGTACATCATCCTTGAGGTTTTTGA -s Anc0.Anc0refChr1 7044 28 + 62388 AATTGAGATTAGGC-----CCAATCTTTGAG------AG -s Anc1.Anc1refChr2 7555 29 - 144309 AATTGAGATTAGGC-----CCAATCTTTGAG-----CAG -s Anc2.Anc2refChr3 7795 28 - 53186 AATTGAGATTAGGC-----CCAATCTTTGAG------AG -s mr.mrrefChr5 29092 39 + 294540 CATTGTAGTCTGGCGGTACATCATCTTTGAGGTTTTCAG -s simCow_chr6.simCow.chr6 428670 28 - 602619 AATTTAAATCTGAT-----TTCTTCTTTGTG------GT -s simDog_chr6.simDog.chr6 136627 28 + 593897 AATTGAGATTAGGC-----CCAATCTTTGAG------AG -s simHuman_chr6.simHuman.chr6 429906 3 - 601863 ------------------------------------CAG -s simRat_chr6.simRat.chr6 163964 39 + 647215 CATTGTAGTTTGGGGGTACATCATGTTTGAGGTGTTCAG - -a -s simMouse_chr6.simMouse.chr6 166454 22 + 636262 TGTAACAGCGGTGTCTGTTTGT -s Anc0.Anc0refChr1 7077 22 + 62388 TGAATCAGCAGTGTGTGTTTGT -s Anc1.Anc1refChr2 7589 22 - 144309 TGAATCAGCAGTGTGTGTTTGT -s Anc2.Anc2refChr3 7828 22 - 53186 TGAATCAGCAGTGTGTATTTGT -s mr.mrrefChr5 29131 22 + 294540 TGTAACAGCAGTGTCTGTTTGT -s simCow_chr6.simCow.chr6 428704 22 - 602619 TGTATCATCAGCGTGTTTTTGT -s simDog_chr6.simDog.chr6 136660 22 + 593897 TGAATCAGCTGTGTGTATTTGT -s simHuman_chr6.simHuman.chr6 429914 22 - 601863 TGCATGAACAGTGTGTGTTTCT -s simRat_chr6.simRat.chr6 164003 22 + 647215 TGTAGCAGCAGTGTCTGTTTGT - -a -s simMouse_chr6.simMouse.chr6 166476 15 + 636262 CTACCACATCAAATT -s Anc0.Anc0refChr1 7099 15 + 62388 CTTACCTATCAAACC -s Anc1.Anc1refChr2 7611 15 - 144309 CTTACCTATCAAACC -s Anc2.Anc2refChr3 7883 15 - 53186 CTTACCTATCAAACC -s mr.mrrefChr5 29153 15 + 294540 CTACCACATCAAATT -s simCow_chr6.simCow.chr6 428767 10 - 602619 -----CTATCAAACC -s simDog_chr6.simDog.chr6 136752 15 + 593897 CTTACGTATCAAACC -s simHuman_chr6.simHuman.chr6 429936 15 - 601863 CTCTCCTATCAAACC -s simRat_chr6.simRat.chr6 164025 15 + 647215 CTACTGCAACAAATG - -a -s simMouse_chr6.simMouse.chr6 166491 16 + 636262 CCATTATAGAAGCCAA -s Anc0.Anc0refChr1 7117 16 + 62388 CACTTACAGCAGCCAA -s Anc1.Anc1refChr2 7629 16 - 144309 CACTTACAGCAGCCAA -s Anc2.Anc2refChr3 7901 16 - 53186 CACTTACAGCAGTCAA -s mr.mrrefChr5 29168 16 + 294540 CAATTATAGAAGCCAA -s simCow_chr6.simCow.chr6 428780 16 - 602619 CACTTACAGTAGACAA -s simDog_chr6.simDog.chr6 136770 16 + 593897 CACATACTGCTGTCAA -s simHuman_chr6.simHuman.chr6 429954 16 - 601863 CACTTACAGCAGCCAA -s simRat_chr6.simRat.chr6 164040 16 + 647215 CAATTATAGGAGCCAA - -a -s simMouse_chr6.simMouse.chr6 166507 42 + 636262 TAGTCACAACAATTCATACTTTTAATACATTCATTAATCACC -s Anc0.Anc0refChr1 7133 39 + 62388 CAGTCACCA---CCTATCCCTTTAATATATGCGTTACTCCCC -s Anc1.Anc1refChr2 7645 39 - 144309 CAGTCACCA---CCTATCCCTTTAATATATGCGTTACTCCCC -s Anc2.Anc2refChr3 7918 39 - 53186 CAGTCACCA---CCTATCCCTTTAATATATGCGTCACTCCCC -s mr.mrrefChr5 29184 39 + 294540 TAGTCACAA---TTCATACCTTTAATATATTCATTAATCACC -s simCow_chr6.simCow.chr6 428797 39 - 602619 CAGTCTCCA---CCTAGCCCTTTGATATATGCATGAACCGCC -s simDog_chr6.simDog.chr6 136787 39 + 593897 CAGTCACCA---CTGATCCCAGTAATTTATGTGTCCCTTCCC -s simHuman_chr6.simHuman.chr6 429970 39 - 601863 CAGTCACCA---CCTATCCCTTTAATATATGCTTTAGTCCCT -s simRat_chr6.simRat.chr6 164056 39 + 647215 TAGTCACAA---TTCATACCTTTAATTTATTCATTAATCACC - -a -s simMouse_chr6.simMouse.chr6 166549 41 + 636262 CTTAAGCCACTATAGTAGCAAGAAGTAATTTCTGCTGCTCA -s Anc0.Anc0refChr1 7172 31 + 62388 TATAGGC-CCTATAATAG---------ATTTCTGATGTTTA -s Anc1.Anc1refChr2 7684 31 - 144309 TATAGGC-CCTATAATAG---------ATTTCTGATGTTTA -s Anc2.Anc2refChr3 7957 31 - 53186 TATAGGT-CCAGGAAAAA---------ATTTCTGATGTTTA -s mr.mrrefChr5 29223 41 + 294540 TTTAAGCCACTATAGTAGCAAGAAATAATTTCTGCTGCTCA -s simCow_chr6.simCow.chr6 428836 23 - 602619 AATGGG---------ATA---------ACTTCTGATGTTTA -s simDog_chr6.simDog.chr6 136828 31 + 593897 TATAATT-CCAGGAAAAA---------ATTTCTGCTTTTTA -s simHuman_chr6.simHuman.chr6 430009 31 - 601863 TATAGGC-GCTATAATAG---------CTTTCTGATGTTTA -s simRat_chr6.simRat.chr6 164095 41 + 647215 TTTAAGCCACTATAGCAGCAGGAAATAATTTCTGCTGCTCA - -a -s simMouse_chr6.simMouse.chr6 166590 108 + 636262 GGTCTATGTCCCCCCATGGGACTGGGTCCAGGGTATAGCACCCACCATTGTCTCGAGGGACTAACCATATATAATGACATGGATAATTCATTTGTATGTCACAACAAT -s Anc0.Anc0refChr1 7205 106 + 62388 GGACTGTGTTCCCCCAAGAGACTGTGCCTGGGACATATCATCCATCATTTTCTTAAG--ACTAACCATATATAATGCCATAGATGATGGGATTGTACATCACAACATT -s Anc1.Anc1refChr2 7717 106 - 144309 GGACTGTGTTCCCCCAAGAGACTGTGCCTGGGACATATCATCCATCATTTTCTTAAG--ACTAACCATATATAATGCCATAGATGATGGGATTGTACATCACAACATT -s Anc2.Anc2refChr3 7990 106 - 53186 GGACTGCACTCCCCCAAGAGACTGTGCCTGGGACATATAATCCATCATTTTTTTAAA--GCTAACCAGATCAAATGCCATAGATGATGGGATTGTACATCACAACATT -s mr.mrrefChr5 29266 108 + 294540 GGTCTATGTCCCCCCATGGGACTGGGTCCAGGGCATATCACCCACCATTGTCTTGAGGGACTAACCATATATAATGACATGGATAATTCAATTGTATGTCACAACAAT -s simCow_chr6.simCow.chr6 428861 97 - 602619 GGAATGAA-TCACCCATAAGGCTGTGCCTGGGACAAATAAGCCATCATTTTTTTAAA--G--AATCAGAC------CCACAGATGAGGGAAGTGTACATCACAACATT -s simDog_chr6.simDog.chr6 136861 92 + 593897 GGACTGCACTCCCTCAAGAGACTGTGTCTGGGACATATAATTCA----------------CTAACTAGATCAAATGCCATAGACGCTGGGATTGTCCATCACATCAGT -s simHuman_chr6.simHuman.chr6 430042 106 - 601863 GGATTGTGTTACCCCAAGAGACTGTGCCTGGGACATATCATCCATAGTTTTCTGAAG--ACTAACCATGTATAATGCCATCAATGAAGGGATTGTACATCACAACATT -s simRat_chr6.simRat.chr6 164138 108 + 647215 GGTCTATTTCCCCCCAGGGGACTGGGTCCAGTGCATATCACCCGCCATTGTCTTGAGGGATTAACCTTATATAACGTCATGGTTAATTCAATTGTGTGTCACAACAAT - -a -s simMouse_chr6.simMouse.chr6 166698 19 + 636262 TTAAAGTGTCCTGCATACA -s Anc0.Anc0refChr1 7311 17 + 62388 TCATATTGTCCTG--TACA -s Anc1.Anc1refChr2 7823 17 - 144309 TCATATTGTCCTG--TACA -s Anc2.Anc2refChr3 8096 17 - 53186 TCATATTGTCCTT--TACA -s mr.mrrefChr5 29374 17 + 294540 TTAAATTGTCCTG--TACA -s simCow_chr6.simCow.chr6 428958 17 - 602619 CCTTATTGTCCAG--TACA -s simDog_chr6.simDog.chr6 136953 17 + 593897 TCATATTGCCCTT--TACA -s simHuman_chr6.simHuman.chr6 430148 16 - 601863 TCATATGGTCCTG--GAC- -s simRat_chr6.simRat.chr6 164248 12 + 647215 TTACATTG-ACTG------ - -a -s simMouse_chr6.simMouse.chr6 166717 2 + 636262 CT -s Anc0.Anc0refChr1 7328 2 + 62388 CA -s Anc1.Anc1refChr2 7840 2 - 144309 CA -s Anc2.Anc2refChr3 8115 2 - 53186 CA -s mr.mrrefChr5 29391 2 + 294540 CT -s simCow_chr6.simCow.chr6 428977 2 - 602619 CA -s simDog_chr6.simDog.chr6 136972 2 + 593897 CA - -a -s simMouse_chr6.simMouse.chr6 166719 28 + 636262 GAATGACATAGAATGTTGCAACATGAAG -s Anc0.Anc0refChr1 7330 27 + 62388 AGATGTCATAGAATGCT-GAACAAGAAG -s Anc1.Anc1refChr2 7842 27 - 144309 AGATGTCATAGAATGCT-GAACAAGAAG -s Anc2.Anc2refChr3 8117 27 - 53186 AGATGTCATAGAATGCT-GAACAAGTAG -s mr.mrrefChr5 29393 27 + 294540 GAATGACATAGAATGTT-CAACATGAAG -s simCow_chr6.simCow.chr6 428979 25 - 602619 --ATGTCATAGAATGCT-GAGCGAGTAG -s simDog_chr6.simDog.chr6 136976 23 + 593897 AGATGTTATAAAATACT-GAACAA---- -s simHuman_chr6.simHuman.chr6 430164 23 - 601863 ----GTCATGGAATGCT-GTACAAGAAA -s simRat_chr6.simRat.chr6 164260 26 + 647215 -AATGACATAGTATGTT-CAACATGAAG - -a -s simMouse_chr6.simMouse.chr6 166747 62 + 636262 TTTCTCCAATGTACGAAGATGTAATTATGTGGGGTATAGGCACGATGTAAAACCATCAAGGA -s Anc0.Anc0refChr1 7357 62 + 62388 ATTCTGCTATGTAGGCAGATCTAGCTATTTGGAGTATAGGCACAATCCAGAACTATCAAGGA -s Anc1.Anc1refChr2 7869 62 - 144309 ATTCTGCTATGTAGGCAGATCTAGCTATTTGGAGTATAGGCACAATCCAGAACTATCAAGGA -s Anc2.Anc2refChr3 8144 62 - 53186 ATTCTGCTATGTAAGCAGATCTAGCTATTAGGAGTATAGGCCCAATCCGGAACTATCAAGGA -s mr.mrrefChr5 29420 62 + 294540 TTTCTCCAATGTAGGAAGATGTAATTATGTGGGGTATAGGCACGATGTAAAACAATCAAGGA -s simCow_chr6.simCow.chr6 429004 57 - 602619 ACTCTGCTATGTAACCAGATCTAGCTATTAGGAGTATGGGCCCA-----GAACAATCAAGGA -s simDog_chr6.simDog.chr6 136999 61 + 593897 -TTCTGCTATGTAAGCAGATCTAGCTATTAGGAGTATAGGCCCAATCCGGAGCTGTCAAGGA -s simHuman_chr6.simHuman.chr6 430192 58 - 601863 CTTCTGCTATGTAGGCAGAT-CAGCTAGTTGAAG---AGGCACAATCAAGGACTATCAAGGA -s simRat_chr6.simRat.chr6 164286 62 + 647215 TTTCTCCAATGTTGGAAGATGTAATTATGTGGGGTATAGGTATGATGTAAAACAATCAAGGA - -a -s simMouse_chr6.simMouse.chr6 166809 12 + 636262 TAAAACTCGGCT -s Anc0.Anc0refChr1 7420 12 + 62388 TAAAACTTAGCC -s Anc1.Anc1refChr2 7932 12 - 144309 TAAAACTTAGCC -s Anc2.Anc2refChr3 8207 12 - 53186 TAAAACTTAGCC -s mr.mrrefChr5 29483 12 + 294540 TAAAACTCGGCC -s simCow_chr6.simCow.chr6 429062 12 - 602619 TAAAACTTAACC -s simDog_chr6.simDog.chr6 137061 12 + 593897 TAAAACTTAGTC -s simHuman_chr6.simHuman.chr6 430251 12 - 601863 TAAACTTTAGCC -s simRat_chr6.simRat.chr6 164349 12 + 647215 TGAAACTAGGCC - -a -s simMouse_chr6.simMouse.chr6 166821 3 + 636262 GTG -s Anc0.Anc0refChr1 7432 3 + 62388 ATG -s Anc1.Anc1refChr2 7944 3 - 144309 ATG -s Anc2.Anc2refChr3 8219 3 - 53186 ATG -s mr.mrrefChr5 29495 3 + 294540 ATG -s simCow_chr6.simCow.chr6 429076 3 - 602619 ATG -s simDog_chr6.simDog.chr6 137073 3 + 593897 ATG -s simHuman_chr6.simHuman.chr6 430263 3 - 601863 ATG -s simRat_chr6.simRat.chr6 164361 3 + 647215 ATG - -a -s simMouse_chr6.simMouse.chr6 166824 7 + 636262 TGCATGG -s Anc0.Anc0refChr1 7435 7 + 62388 TGGATGA -s Anc1.Anc1refChr2 7947 7 - 144309 TGGATGA -s Anc2.Anc2refChr3 8222 7 - 53186 TAGATAA -s mr.mrrefChr5 29498 7 + 294540 TGGATGG -s simCow_chr6.simCow.chr6 429079 7 - 602619 TAGATAG -s simDog_chr6.simDog.chr6 137119 7 + 593897 TAGATAA -s simHuman_chr6.simHuman.chr6 430266 7 - 601863 TGGATGA -s simRat_chr6.simRat.chr6 164364 7 + 647215 TGGATGG - -a -s simMouse_chr6.simMouse.chr6 166831 1 + 636262 G -s Anc0.Anc0refChr1 7449 1 + 62388 G -s Anc1.Anc1refChr2 7961 1 - 144309 G -s Anc2.Anc2refChr3 8236 1 - 53186 A -s mr.mrrefChr5 29505 1 + 294540 G -s simCow_chr6.simCow.chr6 429095 1 - 602619 A -s simDog_chr6.simDog.chr6 137133 1 + 593897 A -s simHuman_chr6.simHuman.chr6 430280 1 - 601863 G -s simRat_chr6.simRat.chr6 164371 1 + 647215 G - -a -s simMouse_chr6.simMouse.chr6 166832 36 + 636262 ATATAAGGAGGGTATCTCTGATTGCAGACATAGCCT -s Anc0.Anc0refChr1 7450 36 + 62388 GAACAAGGAAGGTAACTCTACTACCAAACTTAGCTG -s Anc1.Anc1refChr2 7962 36 - 144309 GAACAAGGAAGGTAACTCTACTACCAAACTTAGCTG -s Anc2.Anc2refChr3 8237 36 - 53186 GAACAAGGAAGGTAAGTCCACTACCAAGCTTATCTG -s mr.mrrefChr5 29506 36 + 294540 AAATAAGGAGGGTATCTCTGATAGCAGACATAGCCT -s simCow_chr6.simCow.chr6 429109 36 - 602619 GAACAGGGTGGATAATTCCACTACCCATCTCATCTG -s simDog_chr6.simDog.chr6 137134 36 + 593897 GAGTGAGGAAGGTAAGCCCACTACTATGCTTATCTG -s simHuman_chr6.simHuman.chr6 430281 36 - 601863 GAACATGTAAGGTAACTCTACTATCAAACTTAGCTG -s simRat_chr6.simRat.chr6 164372 36 + 647215 AATTAAGGAGGGTATTTTTGATAGCAGACATAGCCT - -a -s simMouse_chr6.simMouse.chr6 166868 6 + 636262 ATTCTG -s Anc0.Anc0refChr1 7491 6 + 62388 ATTCTG -s Anc1.Anc1refChr2 8003 6 - 144309 ATTCTG -s Anc2.Anc2refChr3 8278 6 - 53186 GTTCTG -s mr.mrrefChr5 29542 6 + 294540 ATTCTG -s simCow_chr6.simCow.chr6 429150 6 - 602619 GTTCTG -s simDog_chr6.simDog.chr6 137175 6 + 593897 GTTCTG -s simHuman_chr6.simHuman.chr6 430322 6 - 601863 ATTATG -s simRat_chr6.simRat.chr6 164408 6 + 647215 ATTCTG - -a -s simMouse_chr6.simMouse.chr6 166874 26 + 636262 CCATTCAGCACATAAAGAGGATAAAT -s Anc0.Anc0refChr1 7497 2 + 62388 CT------------------------ -s Anc1.Anc1refChr2 8009 22 - 144309 CT-TTAAGAACA---AAGAGATAAAT -s Anc2.Anc2refChr3 8284 2 - 53186 CT------------------------ -s mr.mrrefChr5 29548 26 + 294540 TCATTCAGCACATAAAGGGGATAAAT -s simCow_chr6.simCow.chr6 429167 2 - 602619 CT------------------------ -s simDog_chr6.simDog.chr6 137181 2 + 593897 CT------------------------ -s simHuman_chr6.simHuman.chr6 430328 22 - 601863 CA-TTAAGAACA---AAGAGATAAAT -s simRat_chr6.simRat.chr6 164414 26 + 647215 TCCTTCAGCACATAAAGGGGATAAAT - -a -s simMouse_chr6.simMouse.chr6 166900 54 + 636262 CCCCCTGCTAGTTTTAGGACATGTTGGAAACTTGCCGGACCCCTACAGACCCAC -s Anc1.Anc1refChr2 8031 47 - 144309 TCC-------ACTTGAAACAATGTTGAATGCCCACGACACCACTACAGACCCAC -s mr.mrrefChr5 29574 54 + 294540 CCCCCTGCTAATTTTAGGACATGTTGGATACTTGCCAGACCCCTACAGACCCAC -s simHuman_chr6.simHuman.chr6 430350 47 - 601863 TCC-------ACTTGAAACAATGTTGAATGCCCACGACACCACTACAGACCCAC -s simRat_chr6.simRat.chr6 164442 54 + 647215 CCCCCTGCCAATTTTAGGACATATTGGATACTTGCAAGACCCCTACAGACCTAA - -a -s simMouse_chr6.simMouse.chr6 166954 8 + 636262 TGGTCCCC -s Anc1.Anc1refChr2 8078 8 - 144309 TGGTTCCT -s mr.mrrefChr5 29628 8 + 294540 TGGTCCCC -s simHuman_chr6.simHuman.chr6 430545 8 - 601863 TGGTTCCT -s simRat_chr6.simRat.chr6 164496 8 + 647215 TGGTCCTC - -a -s simMouse_chr6.simMouse.chr6 166962 16 + 636262 TGTGTACACTTTTGTC -s Anc1.Anc1refChr2 8086 16 - 144309 TGTATACACTTTTACT -s mr.mrrefChr5 29636 16 + 294540 TGTGTACACTTTTGCT -s simHuman_chr6.simHuman.chr6 430555 16 - 601863 TGTATACACTTTTACT -s simRat_chr6.simRat.chr6 164504 16 + 647215 TGTGTACACTCTTGCT - -a -s simMouse_chr6.simMouse.chr6 166978 77 + 636262 ATCTAACATGCAGTCTTAATGAGGACGTGAAAGCTAAAGCATACCTCACATGACAGTGTACTTGGTCTGATTGAACA -s Anc0.Anc0refChr1 7499 44 + 62388 ---------------------------------CTAAAGCACATTTTTACTGATGTTGCACTTGGTATGGTTGAACA -s Anc1.Anc1refChr2 8102 77 - 144309 ATTAAGTATGCAGTCTTAATTGGGATCTGAAATCTAAAGCACATTTTTACTGATGTTGCACTTGGTATGGTTGAACA -s Anc2.Anc2refChr3 8286 44 - 53186 ---------------------------------CTAAAACACATTTTTACTGATGTCACACTTGGTACAGTTGAACA -s mr.mrrefChr5 29652 77 + 294540 ATCTAACATGCAGTCTTAATGAGGACGTGAAAGCTAAAGCATATCTCACATGACAGTGTACTTGGTCTGGTTGAACA -s simCow_chr6.simCow.chr6 429169 43 - 602619 ---------------------------------CTAATACACATTCCTATTGACATCACACTTGGTACAGTT-AACA -s simDog_chr6.simDog.chr6 137183 44 + 593897 ---------------------------------TTAAAAGACACTTTCACTGGTGTCATACTTGGTACAGCTGAATA -s simHuman_chr6.simHuman.chr6 430572 77 - 601863 ATTAAGTATGCAGTCTTAATTGGGATCTGAAATCTAAAGCACATTTTTACTGAAGTTGCACCTGGCATGGTTGAACA -s simRat_chr6.simRat.chr6 164520 77 + 647215 ATCTAACCCGCAGGCTTAAACAGGACATGAAAGCTAAGGCATATCCCACATGATAGTGTACTTGGTTTGGCTGAACA - -a -s simMouse_chr6.simMouse.chr6 167055 32 + 636262 AATTGACCAGTTGTGCGTCATTGGAGTTCACC -s Anc0.Anc0refChr1 7543 20 + 62388 AACTGCTCAGTTG------------GTTCACC -s Anc1.Anc1refChr2 8179 20 - 144309 AACTGCTCAGTTG------------GTTCACC -s Anc2.Anc2refChr3 8330 20 - 53186 AACTGCTCAGCTG------------GTTCACC -s mr.mrrefChr5 29729 32 + 294540 AATTGACCAGTTGTGCGCCATTGGAGTTCACC -s simCow_chr6.simCow.chr6 429212 20 - 602619 AACTGTTCAACTG------------GTTTACC -s simDog_chr6.simDog.chr6 137257 20 + 593897 AACTGCTCAGCTA------------GTTCATC -s simHuman_chr6.simHuman.chr6 430649 20 - 601863 AACTACTCGGTTG------------GTTCACC -s simRat_chr6.simRat.chr6 164597 27 + 647215 GATTG-----TCGTACCCCATTGGTGTTCACC - -a -s simMouse_chr6.simMouse.chr6 167087 16 + 636262 TACATGATAGACCCTT -s Anc0.Anc0refChr1 7636 15 + 62388 TCCAAAGTCTACCCA- -s Anc1.Anc1refChr2 8272 15 - 144309 TCCAAAGTCTACCCA- -s Anc2.Anc2refChr3 8425 15 - 53186 TCCAAAGTCTACCCA- -s mr.mrrefChr5 29764 16 + 294540 TACAAGATATACCCTT -s simCow_chr6.simCow.chr6 429306 15 - 602619 TCCGAAGTCTACCCA- -s simDog_chr6.simDog.chr6 137356 15 + 593897 TCCAAACTCCTCCCA- -s simHuman_chr6.simHuman.chr6 430746 15 - 601863 TCCAAAGTCTACCCA- -s simRat_chr6.simRat.chr6 164627 16 + 647215 TACAAGATATACCCCT - -a -s simMouse_chr6.simMouse.chr6 167103 17 + 636262 TCACCATATCTTTTGTT -s Anc0.Anc0refChr1 7651 8 + 62388 ---------ACTTTGTT -s Anc1.Anc1refChr2 8287 8 - 144309 ---------ACTTTGTT -s Anc2.Anc2refChr3 8440 8 - 53186 ---------ACTTTGTT -s mr.mrrefChr5 29780 17 + 294540 TCACCATATCTTTTGTT -s simCow_chr6.simCow.chr6 429321 8 - 602619 ---------ACTTTGTT -s simDog_chr6.simDog.chr6 137371 8 + 593897 ---------ACTTTGTT -s simHuman_chr6.simHuman.chr6 430761 8 - 601863 ---------ACTTTGTT -s simRat_chr6.simRat.chr6 164644 17 + 647215 TCATCATATCTTTTGTT - -a -s simMouse_chr6.simMouse.chr6 167120 30 + 636262 TAACTATCAATTCTGAATACAGCCGGGTGC -s Anc0.Anc0refChr1 7659 30 + 62388 TAAGTAACAATTAGGTATACATCCTGGCAC -s Anc1.Anc1refChr2 8295 30 - 144309 TAAGTAACAATTAGGTATACATCCTGGCAC -s Anc2.Anc2refChr3 8448 30 - 53186 TAAGTAACAATCAGGTAAACATCCTAGCAC -s mr.mrrefChr5 29797 30 + 294540 TAACTATCAATTCTGAATACATCCGGGTGC -s simCow_chr6.simCow.chr6 429329 11 - 602619 TAAAGAACGA-------------------C -s simDog_chr6.simDog.chr6 137379 30 + 593897 TAAGTAATAGTCAGGTAAACATCCTAGCAC -s simHuman_chr6.simHuman.chr6 430769 30 - 601863 TAAGCAACAATTTGGTATACATCCTGGCAC -s simRat_chr6.simRat.chr6 164664 30 + 647215 TAACTATCAATTCCAAATACATCCAAGTGC - -a -s simMouse_chr6.simMouse.chr6 167150 22 + 636262 ATAACAAATATGATTCTACAAC -s Anc0.Anc0refChr1 7689 22 + 62388 AAAACAAATAAGATTCTGCATC -s Anc1.Anc1refChr2 8325 22 - 144309 AAAACAAATAAGATTCTGCATC -s Anc2.Anc2refChr3 8478 22 - 53186 AAAACAAATAAGGTTATGCATG -s mr.mrrefChr5 29827 22 + 294540 ATAACAAATATGATTCTACAAC -s simCow_chr6.simCow.chr6 429340 22 - 602619 AAAACAGATAAGGTTATGCTCA -s simDog_chr6.simDog.chr6 137409 22 + 593897 AAAACAAATAAGGTTATGCATG -s simHuman_chr6.simHuman.chr6 430799 22 - 601863 AAAACAAATAAGATTCTGCATC -s simRat_chr6.simRat.chr6 164709 22 + 647215 ATAACAAATATGATTCTATAAC - -a -s simMouse_chr6.simMouse.chr6 167172 17 + 636262 CTCGACATCCAAGAACA -s Anc0.Anc0refChr1 7712 17 + 62388 CTTGATATCCAAGAACA -s Anc1.Anc1refChr2 8348 17 - 144309 CTTGATATCCAAGAACA -s Anc2.Anc2refChr3 8501 17 - 53186 ATTGATATCTCTTAATA -s mr.mrrefChr5 29849 17 + 294540 CTCGACATCCAAGAACA -s simCow_chr6.simCow.chr6 429363 17 - 602619 TCTTGCATCACTTAATA -s simDog_chr6.simDog.chr6 137432 17 + 593897 ATTGATATCTCTTGATA -s simHuman_chr6.simHuman.chr6 430822 17 - 601863 CTTAATATCCAAGAACA -s simRat_chr6.simRat.chr6 164731 17 + 647215 CTCGACATCCAAGAACA - -a -s simMouse_chr6.simMouse.chr6 167189 2 + 636262 AC -s Anc0.Anc0refChr1 7729 2 + 62388 TC -s Anc1.Anc1refChr2 8365 2 - 144309 TC -s Anc2.Anc2refChr3 8518 2 - 53186 TA -s mr.mrrefChr5 29866 2 + 294540 AC -s simCow_chr6.simCow.chr6 429380 2 - 602619 CA -s simDog_chr6.simDog.chr6 137449 2 + 593897 TA -s simHuman_chr6.simHuman.chr6 430839 2 - 601863 TC -s simRat_chr6.simRat.chr6 164750 2 + 647215 AC - -a -s simMouse_chr6.simMouse.chr6 167191 1 + 636262 A -s Anc0.Anc0refChr1 7731 1 + 62388 A -s Anc1.Anc1refChr2 8367 1 - 144309 A -s Anc2.Anc2refChr3 8523 1 - 53186 A -s mr.mrrefChr5 29868 1 + 294540 A -s simCow_chr6.simCow.chr6 429385 1 - 602619 A -s simDog_chr6.simDog.chr6 137454 1 + 593897 A -s simHuman_chr6.simHuman.chr6 430841 1 - 601863 A -s simRat_chr6.simRat.chr6 164752 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 167192 4 + 636262 CCAA -s Anc0.Anc0refChr1 7732 4 + 62388 CCAA -s Anc1.Anc1refChr2 8368 4 - 144309 CCAA -s Anc2.Anc2refChr3 8524 4 - 53186 CCAA -s mr.mrrefChr5 29869 4 + 294540 CCAA -s simCow_chr6.simCow.chr6 429393 4 - 602619 CCAG -s simDog_chr6.simDog.chr6 137455 4 + 593897 CAAA -s simHuman_chr6.simHuman.chr6 430842 4 - 601863 CCAA -s simRat_chr6.simRat.chr6 164753 4 + 647215 CCAA - -a -s simMouse_chr6.simMouse.chr6 167196 7 + 636262 CATCTTA -s Anc0.Anc0refChr1 7742 7 + 62388 TATGATA -s Anc1.Anc1refChr2 8378 7 - 144309 TATGATA -s Anc2.Anc2refChr3 8534 7 - 53186 TATGTTA -s mr.mrrefChr5 29873 7 + 294540 CATCATA -s simCow_chr6.simCow.chr6 429403 7 - 602619 TATGTTA -s simDog_chr6.simDog.chr6 137465 7 + 593897 TACGTTA -s simHuman_chr6.simHuman.chr6 430852 7 - 601863 TATGATA -s simRat_chr6.simRat.chr6 164757 7 + 647215 CAGCATA - -a -s simMouse_chr6.simMouse.chr6 167203 3 + 636262 ATT -s Anc0.Anc0refChr1 7749 3 + 62388 TTT -s Anc1.Anc1refChr2 8385 3 - 144309 TTT -s Anc2.Anc2refChr3 8542 3 - 53186 TTT -s mr.mrrefChr5 29880 3 + 294540 ATT -s simCow_chr6.simCow.chr6 429411 3 - 602619 TCT -s simDog_chr6.simDog.chr6 137473 3 + 593897 TTT -s simHuman_chr6.simHuman.chr6 430859 3 - 601863 TTT -s simRat_chr6.simRat.chr6 164764 3 + 647215 AAT - -a -s simMouse_chr6.simMouse.chr6 167206 25 + 636262 CTTGAAGTGAACTCACATTCTCCAA -s Anc0.Anc0refChr1 7753 25 + 62388 CCTGATGTGAACTCAAGTTCTGTAG -s Anc1.Anc1refChr2 8389 25 - 144309 CCTGATGTGAACTCAAGTTCTGTAG -s Anc2.Anc2refChr3 8546 25 - 53186 CCTGATGTGAACTCAAGATCTGTGG -s mr.mrrefChr5 29883 25 + 294540 CCTGAAGTGAACTCACATTCTCCAG -s simCow_chr6.simCow.chr6 429415 25 - 602619 CCTGACGTGAACTCAAGATCCGTGG -s simDog_chr6.simDog.chr6 137477 25 + 593897 CCTGATGTCAACTCAAGATCTGTGG -s simHuman_chr6.simHuman.chr6 430863 23 - 601863 CCTGGTGTGAACTCAAGTTCT--AG -s simRat_chr6.simRat.chr6 164767 25 + 647215 CCTGAAGTGAACTCACACTCTCCAG - -a -s simMouse_chr6.simMouse.chr6 167231 12 + 636262 GTGAACTCAGTC -s Anc0.Anc0refChr1 7778 12 + 62388 GTGGACCTAGTC -s Anc1.Anc1refChr2 8414 12 - 144309 GTGGACCTAGTC -s Anc2.Anc2refChr3 8571 12 - 53186 ATGGACCTAGTA -s mr.mrrefChr5 29908 12 + 294540 GTGAACTCAGTC -s simCow_chr6.simCow.chr6 429441 12 - 602619 ATGGACTTAGTA -s simDog_chr6.simDog.chr6 137502 12 + 593897 ATGGACCTAGTA -s simHuman_chr6.simHuman.chr6 430886 12 - 601863 GTGGACCTGGTC -s simRat_chr6.simRat.chr6 164792 12 + 647215 TTAAACTCAGTC - -a -s simMouse_chr6.simMouse.chr6 167243 9 + 636262 CATTGCCAT -s Anc0.Anc0refChr1 7801 9 + 62388 TATGGCCAT -s Anc1.Anc1refChr2 8437 9 - 144309 TATGGCCAT -s Anc2.Anc2refChr3 8594 9 - 53186 TATGGCCAT -s mr.mrrefChr5 29920 9 + 294540 CATTGCCAT -s simDog_chr6.simDog.chr6 137525 9 + 593897 TATGGCCAT -s simHuman_chr6.simHuman.chr6 430909 9 - 601863 TATAACATT -s simRat_chr6.simRat.chr6 164804 9 + 647215 CATTGCCAT - -a -s simMouse_chr6.simMouse.chr6 167252 32 + 636262 ATAAATGAATGTCAGGTGGAGATAGGATGACT -s Anc0.Anc0refChr1 7810 30 + 62388 ATA--TCAGGCTCTGCTGAAGCCAAGAGAGCA -s Anc1.Anc1refChr2 8446 30 - 144309 ATA--TCAGGCTCTGCTGAAGCCAAGAGAGCA -s Anc2.Anc2refChr3 8620 30 - 53186 ATA--TCAGGCTCTGCTGAAGCCAAGAGAGAA -s mr.mrrefChr5 29929 32 + 294540 ATAAATGAATGTCAGGTGAAGATAGGATGGCA -s simCow_chr6.simCow.chr6 429473 30 - 602619 ATA--TAAGGCTCCACTGAAGCCAAGAGAGAA -s simDog_chr6.simDog.chr6 137551 29 + 593897 ATA--TCAAGCCCTGTTGAAGCCAAGCAAG-A -s simHuman_chr6.simHuman.chr6 430918 30 - 601863 ATA--TCAGGCTCTGCTGAAGCCAAGAGAGCA -s simRat_chr6.simRat.chr6 164813 30 + 647215 ATAGATGAATGTTA--TGAAGGTAGTAAGGCA - -a -s simMouse_chr6.simMouse.chr6 167284 4 + 636262 CCAA -s Anc0.Anc0refChr1 7843 4 + 62388 CTAA -s Anc1.Anc1refChr2 8479 4 - 144309 CTAA -s Anc2.Anc2refChr3 8657 4 - 53186 CTAA -s mr.mrrefChr5 29961 4 + 294540 CCAA -s simCow_chr6.simCow.chr6 429510 4 - 602619 TCAT -s simDog_chr6.simDog.chr6 137587 4 + 593897 CTAA -s simHuman_chr6.simHuman.chr6 430951 4 - 601863 CAGG -s simRat_chr6.simRat.chr6 164843 4 + 647215 CCAA - -a -s simMouse_chr6.simMouse.chr6 167288 7 + 636262 AACTAAT -s Anc0.Anc0refChr1 7847 7 + 62388 AACTAat -s Anc1.Anc1refChr2 8483 7 - 144309 AACTAAT -s Anc2.Anc2refChr3 8661 7 - 53186 GAGTAat -s mr.mrrefChr5 29965 7 + 294540 AACTAAT -s simCow_chr6.simCow.chr6 429514 7 - 602619 GAGCAAT -s simDog_chr6.simDog.chr6 137591 7 + 593897 GAGTAat -s simHuman_chr6.simHuman.chr6 430955 7 - 601863 AGCTAAC -s simRat_chr6.simRat.chr6 164982 7 + 647215 AACTAAT - -a -s simMouse_chr6.simMouse.chr6 167295 10 + 636262 ATTTACACAG -s Anc0.Anc0refChr1 7854 10 + 62388 ATTTGCACAG -s Anc1.Anc1refChr2 8490 10 - 144309 ATTTGCACAG -s Anc2.Anc2refChr3 8710 10 - 53186 ACTTGGGCAG -s mr.mrrefChr5 29972 10 + 294540 ATTTACACAG -s simCow_chr6.simCow.chr6 429591 9 - 602619 ACTTGA-CAA -s simDog_chr6.simDog.chr6 137644 10 + 593897 ACTTGGGCAG -s simHuman_chr6.simHuman.chr6 430962 10 - 601863 ATTTGCACTT -s simRat_chr6.simRat.chr6 164989 10 + 647215 ATTTATACAG - -a -s simMouse_chr6.simMouse.chr6 167305 8 + 636262 GTTGTTCC -s Anc0.Anc0refChr1 7864 8 + 62388 GCTGAGCC -s Anc1.Anc1refChr2 8500 8 - 144309 GCTGAGCC -s Anc2.Anc2refChr3 8722 8 - 53186 GTTGAGCC -s mr.mrrefChr5 29982 8 + 294540 GCTGTTCC -s simCow_chr6.simCow.chr6 429602 8 - 602619 GTTGAGCC -s simDog_chr6.simDog.chr6 137656 8 + 593897 GTTGAGCT -s simHuman_chr6.simHuman.chr6 430972 8 - 601863 GCTGAGCC -s simRat_chr6.simRat.chr6 164999 8 + 647215 GCTGGTCC - -a -s simMouse_chr6.simMouse.chr6 167313 57 + 636262 CTTCCCCTATACAACCATGGGGTAACACCATGAAACACTTACCCACGGAACTCACAG -s Anc0.Anc0refChr1 7872 57 + 62388 TTAGCCCAACACAACCATGGACTAACAACATGAGACAAGTACCAAAGAAACACACAA -s Anc1.Anc1refChr2 8508 57 - 144309 TTAGCCCAACACAACCATGGACTAACAACATGAGACAAGTACCAAAGAAACACACAA -s Anc2.Anc2refChr3 8730 57 - 53186 TTAGCCCACTACAACTATGGACTAACAACATGAGACAAGAACCAAAGAACCACACAA -s mr.mrrefChr5 29990 57 + 294540 CTTCCCCTACACAACCATGGGGTAACAACATGAAACACTTACCAACGGAACTCACAG -s simCow_chr6.simCow.chr6 429610 39 - 602619 CTAG------------------TTACAATCTGAAATGAGGACCAAAGAAGCACACAA -s simDog_chr6.simDog.chr6 137664 57 + 593897 TTAGCCCACTACAACTATGGACTAACAACATATGACAAGAACCAAAGAACCACACAA -s simHuman_chr6.simHuman.chr6 430980 57 - 601863 TTATTCCCACACAACCATGGAACAACAACATGAGAGAAATACCAAAGAAATACACAA -s simRat_chr6.simRat.chr6 165012 57 + 647215 CTTCCTCTACACAACCATGGGGTGACAACATGAAACACTTACCAATGGAACTCACAC - -a -s simMouse_chr6.simMouse.chr6 167370 16 + 636262 GCATTGAACTCTATCA -s Anc0.Anc0refChr1 7929 16 + 62388 GAGTTGAAATTTCACC -s Anc1.Anc1refChr2 8565 16 - 144309 GAGTTGAAATTTCACC -s Anc2.Anc2refChr3 8792 16 - 53186 GGGTTGAAATTCCACC -s mr.mrrefChr5 30047 16 + 294540 GAGTTGAACTCTATCA -s simDog_chr6.simDog.chr6 137727 16 + 593897 GGGTTGAAATTCCACC -s simHuman_chr6.simHuman.chr6 431037 16 - 601863 GAGTTGAAATTTGCCT -s simRat_chr6.simRat.chr6 165069 16 + 647215 GAGTTGAACTCTATCA - -a -s simMouse_chr6.simMouse.chr6 167386 60 + 636262 AAGTGCACCTAAAAACACCTAAGAACGGGTCTGGTCTAGCTGCATAAGTGGGTTACCGAA -s Anc0.Anc0refChr1 7945 45 + 62388 GAGTGCACTTAAAAACA---------------GGTCTGACTGCATCAATGGGTTACGAAA -s Anc1.Anc1refChr2 8581 45 - 144309 GAGTGCACTTAAAAACA---------------GGTCTGACTGCATCAATGGGTTACGAAA -s Anc2.Anc2refChr3 8808 45 - 53186 GAGTGTACTTAAAAACA---------------GGTCTGACTGCATCAATGGGTTACGAAA -s mr.mrrefChr5 30063 60 + 294540 AAGTGCACCTAAAAACACCTAAGAACAGGTCTGGTCTAGCTGCATAAGTGGGTTACAGAA -s simCow_chr6.simCow.chr6 429654 44 - 602619 GAGTGTA-TTACAAACA---------------TGTATCACTGCATTATTGGGTTACAAAA -s simDog_chr6.simDog.chr6 137752 45 + 593897 GAGTGTACTTAAAAACA---------------GGTCTGACTGCATCAATGGGTTACGAAG -s simHuman_chr6.simHuman.chr6 431053 45 - 601863 GAGTGCTCTTAAAAACA---------------GGTCTGACCGCATCAATGGGTTAATAAA -s simRat_chr6.simRat.chr6 165085 60 + 647215 AAGTGCACCTCAAAACACCTAAGAACAGGTCTGTACTAGCTGCATAAGTGGGATACAGAG - -a -s simMouse_chr6.simMouse.chr6 167446 33 + 636262 GCCAACGTGGTAGCTTGCTTCTGTATGTTTCTG -s Anc0.Anc0refChr1 7991 33 + 62388 ACCAACGTGGCGGCCTGCTTCTGTATATCACTG -s Anc1.Anc1refChr2 8627 33 - 144309 ACCAACGTGGCGGCCTGCTTCTGTATATCACTG -s Anc2.Anc2refChr3 8854 33 - 53186 ACCAACGCGGCGGCCTGCATCTGTATATCACTG -s mr.mrrefChr5 30123 33 + 294540 GCCAACGTGGCGGCTTGCTTCTGTATGTTTCTG -s simCow_chr6.simCow.chr6 429699 33 - 602619 ACCAACGGGGCAGCCCGCATCTGTAGATCACTG -s simDog_chr6.simDog.chr6 137798 33 + 593897 CCCGACGCGGCGGCATGCATCTGTATACCATTG -s simHuman_chr6.simHuman.chr6 431099 30 - 601863 ACCAACGTGACGGC---CTTCTGCATATCCCTG -s simRat_chr6.simRat.chr6 165145 33 + 647215 GCCAACGTGGCGGCATGCCTCTGTACGTTTCTG - -a -s simMouse_chr6.simMouse.chr6 167479 17 + 636262 GACCAAGAGTGCAGCAG -s Anc0.Anc0refChr1 8024 17 + 62388 GCCGGGGAGTGCAGCAG -s Anc1.Anc1refChr2 8660 17 - 144309 GCCGGGGAGTGCAGCAG -s Anc2.Anc2refChr3 8887 17 - 53186 GCCGGGGAGTGCAGCAG -s mr.mrrefChr5 30156 17 + 294540 GACCAAGAGTGCAGCAG -s simCow_chr6.simCow.chr6 429732 17 - 602619 GACGGGGAGTGCAGCAG -s simDog_chr6.simDog.chr6 137831 17 + 593897 GCCGGGGAGTGCAGCCG -s simHuman_chr6.simHuman.chr6 431129 17 - 601863 GGCGGGGAGTGCAGCAC -s simRat_chr6.simRat.chr6 165185 17 + 647215 GACTAAGAGTGTAGCAG - -a -s simMouse_chr6.simMouse.chr6 167496 18 + 636262 TCACATCACCACATGTGT -s Anc0.Anc0refChr1 8041 18 + 62388 CTACTTCGCCGCTCATGT -s Anc1.Anc1refChr2 8677 18 - 144309 CTACTTCGCCGCTCATGT -s Anc2.Anc2refChr3 8904 18 - 53186 CTACTTCGCCGCTCATGT -s mr.mrrefChr5 30173 18 + 294540 TCACATCGCCACATGTGT -s simCow_chr6.simCow.chr6 429749 18 - 602619 CTACATCGTCGCTCATGT -s simDog_chr6.simDog.chr6 137849 18 + 593897 CTCGTTCGCCGCTTATGT -s simHuman_chr6.simHuman.chr6 431146 18 - 601863 CTACGTCGCCGCTCATGT -s simRat_chr6.simRat.chr6 165202 18 + 647215 TCACATCGCCACATGTGT - -a -s simMouse_chr6.simMouse.chr6 167514 13 + 636262 TTATTTAAATCTA -s Anc0.Anc0refChr1 8121 13 + 62388 TTATTTAAATCCC -s Anc1.Anc1refChr2 8757 13 - 144309 TTATTTAAATCCC -s Anc2.Anc2refChr3 8984 13 - 53186 TTATTTAAATCCC -s mr.mrrefChr5 30191 13 + 294540 TTATTTAAATCTA -s simCow_chr6.simCow.chr6 429829 13 - 602619 ATATTTAAATCAC -s simDog_chr6.simDog.chr6 137930 13 + 593897 TAAGTTAAATCCG -s simHuman_chr6.simHuman.chr6 431226 13 - 601863 TTATTTAAATCCC -s simRat_chr6.simRat.chr6 165220 13 + 647215 TTATTTAAATCTA - -a -s simMouse_chr6.simMouse.chr6 167527 11 + 636262 CATACGGTGTA -s Anc0.Anc0refChr1 8135 11 + 62388 CGCACGACGTA -s Anc1.Anc1refChr2 8771 11 - 144309 CGCACGACGTA -s Anc2.Anc2refChr3 8998 11 - 53186 TGCATGACGTA -s mr.mrrefChr5 30204 11 + 294540 CATACGGTGTA -s simCow_chr6.simCow.chr6 429843 11 - 602619 TGTATGACGTA -s simDog_chr6.simDog.chr6 137944 11 + 593897 TGCATGACGTG -s simHuman_chr6.simHuman.chr6 431240 11 - 601863 CGCACGAAGTA -s simRat_chr6.simRat.chr6 165233 11 + 647215 CATATGGCGTA - -a -s simMouse_chr6.simMouse.chr6 167538 21 + 636262 GCCTCAAGTAAGTATGCCCTA -s Anc0.Anc0refChr1 8147 17 + 62388 GT----GGCAACTATGCCCTA -s Anc1.Anc1refChr2 8783 17 - 144309 GT----GGCAACTATGCCCTA -s Anc2.Anc2refChr3 9010 17 - 53186 GT----GGCAACTATGCCCTA -s mr.mrrefChr5 30215 17 + 294540 GC----GGCAAGTATGCCCTA -s simCow_chr6.simCow.chr6 429855 17 - 602619 GT----CGTAACTATGCCCTA -s simDog_chr6.simDog.chr6 137956 17 + 593897 GT----GCCAACTATGCCCTA -s simHuman_chr6.simHuman.chr6 431252 17 - 601863 GT----GGCAACTATGTCCTA -s simRat_chr6.simRat.chr6 165244 17 + 647215 GC----GGCAAGTATGCCCTA - -a -s simMouse_chr6.simMouse.chr6 167559 22 + 636262 GACATGGTTTGGATCGCATGAT -s Anc0.Anc0refChr1 8164 22 + 62388 GACGTGGGTTAGATCGCAAGAT -s Anc1.Anc1refChr2 8800 22 - 144309 GACGTGGGTTAGATCGCAAGAT -s Anc2.Anc2refChr3 9027 22 - 53186 GACGTGGGTTAGATTGCAAGAT -s mr.mrrefChr5 30232 22 + 294540 GACATGGTTTGGATCGCATGAT -s simCow_chr6.simCow.chr6 429872 22 - 602619 GACGTGGGTTAGATGGCAAGAT -s simDog_chr6.simDog.chr6 137976 22 + 593897 GACGTGGATTAGCTTGCATGAT -s simHuman_chr6.simHuman.chr6 431269 22 - 601863 GACGTGGGTTAGATCGCAAGAT -s simRat_chr6.simRat.chr6 165261 22 + 647215 GACATATTTTGGATCGCACGAT - -a -s simMouse_chr6.simMouse.chr6 167581 119 + 636262 GTACATTTTTATTCTTTATACACGGCGTTTATACACAGCGTACGGTCATCCGAGTCACACGCCAGATAAAGGACGTTCTCTCAGTGGCATTTATATGTTTGACAACATATGGAACATAA -s Anc0.Anc0refChr1 8189 105 + 62388 TTACATTTTTGTTTTTTATACTCGGTG------GACGG-GTA---TCGCG--AGTCACACGTCAGATAACAGACGTTCTCTGGGTGGCATCAAGATGTCTAACAACAT--GGAAGATAA -s Anc1.Anc1refChr2 8825 107 - 144309 TTACATTTTTGTTTTTTATACTCGGTG------GACGG-GTA---TCGCGCGAGTCACACGTCAGATAACAGACGTTCTCTGGGTGGCATCAAGATGTCTAACAACAT--GGAAGATAA -s Anc2.Anc2refChr3 9052 105 - 53186 TTACATTTTTGTTTTTTAAAGTCGATG------GACGG-TTT---TCGCG--AGCCACACGTCAGATAACAGACGTTCTCGGGGTGGCATCAAGATGCCTAACAACAT--GGAAGATAA -s mr.mrrefChr5 30254 119 + 294540 GTACATTTTTATTCTTTATACACGGCGTTTATACACAGCGTACGGTCATCCGAGTCACACGCCAGATAAAGGACGTTCTCTCGGTGGCATTTAGATGTTTGACAACATATGGAACATAA -s simCow_chr6.simCow.chr6 429897 105 - 602619 CACCATCTTTGTCTTTTAGAGTCGATG------GACGG-CTT---TCGCG--AACCACACGTCAGATAACAAACTTTCTCAGGTTGGCATTTAAATGCCTAACAGCAT--GGGGGATAA -s simDog_chr6.simDog.chr6 138001 105 + 593897 TTACATTTTTGTTTTGTAAAGTCGATG------GACTG-TTT---TCGTG--AGCCACACGCCAGATAACAGACGTTCTCGGGGTGGCATCAAGATGCCTTACAATAT--AGAAGATAA -s simHuman_chr6.simHuman.chr6 431294 105 - 601863 TTACATTTTTGTGTCTTATACTCGGTG------GACGG-GTA---TCGCGCGATTCACACGTCAGATATCAGACGTTCTCTGGGTGGCAT--GGATGTCTAACAACAT--GGAAGATAA -s simRat_chr6.simRat.chr6 165283 119 + 647215 GTACAGTTTTATTCTTTATACACGGCGTGTATACACGGCGTACGGTCATCCCAGTCACACGCCAGATAAAGGACGTTCTCTCGGTCGTATTTAGATGTTTGACAACATATGGAACATGA - -a -s simMouse_chr6.simMouse.chr6 167700 2 + 636262 GG -s Anc0.Anc0refChr1 8294 2 + 62388 GG -s Anc1.Anc1refChr2 8932 2 - 144309 GG -s Anc2.Anc2refChr3 9157 2 - 53186 GG -s mr.mrrefChr5 30373 2 + 294540 GG -s simCow_chr6.simCow.chr6 430002 2 - 602619 GG -s simDog_chr6.simDog.chr6 138106 2 + 593897 GG -s simHuman_chr6.simHuman.chr6 431405 2 - 601863 GG -s simRat_chr6.simRat.chr6 165402 2 + 647215 GG - -a -s simMouse_chr6.simMouse.chr6 167702 7 + 636262 CTGGCTG -s Anc0.Anc0refChr1 8296 7 + 62388 CTGGCTC -s Anc1.Anc1refChr2 8934 7 - 144309 CTGGCTC -s Anc2.Anc2refChr3 9159 7 - 53186 TTGGCTC -s mr.mrrefChr5 30375 7 + 294540 CTGGCTG -s simCow_chr6.simCow.chr6 430004 7 - 602619 TTGGCTC -s simDog_chr6.simDog.chr6 138108 7 + 593897 TTGGCTC -s simHuman_chr6.simHuman.chr6 431407 7 - 601863 CTGGCTC -s simRat_chr6.simRat.chr6 165405 7 + 647215 ATGACTG - -a -s simMouse_chr6.simMouse.chr6 167709 3 + 636262 CTA -s Anc0.Anc0refChr1 8303 3 + 62388 ACA -s Anc1.Anc1refChr2 8941 3 - 144309 ACA -s Anc2.Anc2refChr3 9169 3 - 53186 ACA -s mr.mrrefChr5 30382 3 + 294540 CTA -s simCow_chr6.simCow.chr6 430014 3 - 602619 ACC -s simDog_chr6.simDog.chr6 138118 3 + 593897 GCA -s simHuman_chr6.simHuman.chr6 431414 3 - 601863 ACA -s simRat_chr6.simRat.chr6 165412 3 + 647215 TTA - -a -s simMouse_chr6.simMouse.chr6 167712 7 + 636262 AGGCATT -s Anc0.Anc0refChr1 8306 7 + 62388 TGGCCTT -s Anc1.Anc1refChr2 8944 7 - 144309 TGGCCTT -s Anc2.Anc2refChr3 9172 7 - 53186 TGGCCTT -s mr.mrrefChr5 30385 7 + 294540 TGGCATT -s simCow_chr6.simCow.chr6 430017 7 - 602619 TGCCTCT -s simDog_chr6.simDog.chr6 138121 7 + 593897 TGGCCTT -s simHuman_chr6.simHuman.chr6 431417 7 - 601863 TGGCCTT -s simRat_chr6.simRat.chr6 165418 7 + 647215 TGGCATT - -a -s simMouse_chr6.simMouse.chr6 167719 4 + 636262 TTCT -s Anc0.Anc0refChr1 8314 4 + 62388 TTCT -s Anc1.Anc1refChr2 8952 4 - 144309 TTCT -s Anc2.Anc2refChr3 9180 4 - 53186 TTCT -s mr.mrrefChr5 30392 4 + 294540 TTCT -s simCow_chr6.simCow.chr6 430025 4 - 602619 TTCT -s simDog_chr6.simDog.chr6 138129 4 + 593897 TTCT -s simHuman_chr6.simHuman.chr6 431425 4 - 601863 TTCT -s simRat_chr6.simRat.chr6 165425 4 + 647215 TTCT - -a -s simMouse_chr6.simMouse.chr6 167723 30 + 636262 CTGTGGAAAGTACAACATAATGATGTGGGC -s Anc0.Anc0refChr1 8318 29 + 62388 CACTGGAGAATACCCCGAAATCATGTGGG- -s Anc1.Anc1refChr2 8956 29 - 144309 CACTGGAGAATACCCCGAAATCATGTGGG- -s Anc2.Anc2refChr3 9184 29 - 53186 CACTGAAGAATACCCCGAAACCATGTGGG- -s mr.mrrefChr5 30396 30 + 294540 CTGTGGAAAGTACAACATAATGATGTGGGC -s simCow_chr6.simCow.chr6 430038 29 - 602619 CTCTGAAGAATACCTGGTATCCATGTGAG- -s simDog_chr6.simDog.chr6 138133 24 + 593897 CAC-----AACACCCCAAAACCATCTGGG- -s simHuman_chr6.simHuman.chr6 431429 29 - 601863 CCCTGGCGAATAGCCCGGGATAATGAGGG- -s simRat_chr6.simRat.chr6 165429 30 + 647215 CTGTGGAAATTACAACATAATGATGTGGGC - -a -s simMouse_chr6.simMouse.chr6 167753 21 + 636262 AGGAGTGTGTCGCTTCGTTCT -s Anc0.Anc0refChr1 8347 21 + 62388 AGGATTGCCGCGCTTCATTCT -s Anc1.Anc1refChr2 8985 21 - 144309 AGGATTGCCGCGCTTCATTCT -s Anc2.Anc2refChr3 9222 21 - 53186 AGGATTGCCGCGCTTCATTCT -s mr.mrrefChr5 30426 21 + 294540 AGGAGTGCGTCGCTTCATTCT -s simCow_chr6.simCow.chr6 430076 21 - 602619 AGGATTGCCCCGCATCATTCC -s simDog_chr6.simDog.chr6 138166 21 + 593897 AGGATTGCCGTGGTTCATTCT -s simHuman_chr6.simHuman.chr6 431458 21 - 601863 AGTGTTGCCACGCTTCATTCT -s simRat_chr6.simRat.chr6 165459 21 + 647215 AGGAGTGCATCGCTTCATTCT - -a -s simMouse_chr6.simMouse.chr6 167774 11 + 636262 TTTTCCTTTCA -s Anc0.Anc0refChr1 8368 11 + 62388 TTCTGCTTTCA -s Anc1.Anc1refChr2 9006 11 - 144309 TTCTGCTTTCA -s Anc2.Anc2refChr3 9249 11 - 53186 TTCTGCCTGCA -s mr.mrrefChr5 30447 11 + 294540 TTTTCCTTTCA -s simCow_chr6.simCow.chr6 430097 7 - 602619 ----ACCTGCA -s simDog_chr6.simDog.chr6 138193 11 + 593897 TTCTGCCTGCA -s simHuman_chr6.simHuman.chr6 431479 11 - 601863 TTCTACTTTTG -s simRat_chr6.simRat.chr6 165480 11 + 647215 TTTTCCTTTCA - -a -s simMouse_chr6.simMouse.chr6 167785 16 + 636262 CTTTCACACACTGCTT -s Anc0.Anc0refChr1 8379 10 + 62388 C------GCACTGCCG -s Anc1.Anc1refChr2 9017 10 - 144309 C------GCACTGCCG -s Anc2.Anc2refChr3 9260 10 - 53186 T------GCACTGCCG -s mr.mrrefChr5 30458 10 + 294540 C------ACACTGCCT -s simCow_chr6.simCow.chr6 430104 9 - 602619 T------GCACTTCC- -s simDog_chr6.simDog.chr6 138204 10 + 593897 T------ACACTGCCG -s simHuman_chr6.simHuman.chr6 431495 10 - 601863 C------GCACTGCCC -s simRat_chr6.simRat.chr6 165491 10 + 647215 C------ACACTGCCT - -a -s simMouse_chr6.simMouse.chr6 167801 9 + 636262 CACTAGCCC -s Anc0.Anc0refChr1 8389 9 + 62388 CACTAGAGA -s Anc1.Anc1refChr2 9027 9 - 144309 CACTAGAGA -s Anc2.Anc2refChr3 9270 9 - 53186 CACTGGAGA -s mr.mrrefChr5 30468 9 + 294540 CACTAGCCC -s simDog_chr6.simDog.chr6 138214 9 + 593897 CACTGGAGA -s simHuman_chr6.simHuman.chr6 431509 9 - 601863 CACTAGTAA -s simRat_chr6.simRat.chr6 165501 9 + 647215 CACTACCCC - -a -s simMouse_chr6.simMouse.chr6 167810 15 + 636262 TGGTAAAATTGTGTA -s Anc0.Anc0refChr1 8400 15 + 62388 TTGTCAAAATGAGTA -s Anc1.Anc1refChr2 9038 15 - 144309 TTGTCAAAATGAGTA -s Anc2.Anc2refChr3 9281 15 - 53186 TTGTCAAAATGAGTA -s mr.mrrefChr5 30477 15 + 294540 TGGTAAAATTGTGTA -s simCow_chr6.simCow.chr6 430115 15 - 602619 TTGTCCAATTGTGTA -s simDog_chr6.simDog.chr6 138225 15 + 593897 TTGTCAAAACAAGTA -s simHuman_chr6.simHuman.chr6 431520 15 - 601863 TTGTCAAAATGCGTA -s simRat_chr6.simRat.chr6 165510 15 + 647215 TTGTCAAATTGTGTA - -a -s simMouse_chr6.simMouse.chr6 167825 17 + 636262 ACACTTAGATTATACTC -s Anc0.Anc0refChr1 8431 17 + 62388 GAATACCATTTAGGCTT -s Anc1.Anc1refChr2 9069 17 - 144309 GAATACCATTTAGGCTT -s Anc2.Anc2refChr3 9312 17 - 53186 GAATACCATTTAGGCTT -s mr.mrrefChr5 30492 17 + 294540 AAACTTAAATTATACTC -s simCow_chr6.simCow.chr6 430146 7 - 602619 GGATTCC---------- -s simDog_chr6.simDog.chr6 138256 17 + 593897 GAATACCATTTAGGCTT -s simHuman_chr6.simHuman.chr6 431551 17 - 601863 GAATCCCATTTAGGCTT -s simRat_chr6.simRat.chr6 165525 17 + 647215 AACCTTAAATTATACTC - -a -s simMouse_chr6.simMouse.chr6 167842 21 + 636262 ACTCCGAAAGTGTAAAAGTTG -s Anc0.Anc0refChr1 8448 21 + 62388 ACTCCAGAAATGACAAAGTTG -s Anc1.Anc1refChr2 9086 21 - 144309 ACTCCAGAAATGACAAAGTTG -s Anc2.Anc2refChr3 9329 21 - 53186 ACTCCAGAAATGAGAAAGCTG -s mr.mrrefChr5 30509 21 + 294540 ACTCCAAAAATGTCAAAGTTG -s simCow_chr6.simCow.chr6 430153 19 - 602619 --TTCAGACATGTGAAAGCTG -s simDog_chr6.simDog.chr6 138274 21 + 593897 ACTCCAGAAACGAGAAAGCTG -s simHuman_chr6.simHuman.chr6 431568 21 - 601863 ACTCCAGAAATGCCTACGTTG -s simRat_chr6.simRat.chr6 165542 21 + 647215 ACTCCAAAAATGTCAAAGTTG - -a -s simMouse_chr6.simMouse.chr6 167863 68 + 636262 TCAAGCTAGGGGTTCTAACATTCCAAAGGCATCCTCGCACGGCAAGTTATATGTAAACTAGATAAGGC -s Anc0.Anc0refChr1 8469 68 + 62388 TCAAACTAGGGGTTCTAAGACCCCAAAAGCATCATCCCATGGCAATTTGTATGTAAACATGATGTGTC -s Anc1.Anc1refChr2 9107 68 - 144309 TCAAACTAGGGGTTCTAAGACCCCAAAAGCATCATCCCATGGCAATTTGTATGTAAACATGATGTGTC -s Anc2.Anc2refChr3 9350 68 - 53186 TCAAACCAGGGGTTCTATGACCCCAAAAGCATCATCCCATGGCAATTTGTATGTAAACATGAGGTGTC -s mr.mrrefChr5 30530 68 + 294540 TCAAGCTAGGGGTTCTAACATTCCAAAGGCATCCTCCCATGGCAAGTTGTATGTAAACTAGATAAGGC -s simCow_chr6.simCow.chr6 430178 68 - 602619 ACAAGCAAGGGGTTCTATGACACCAAATGCAACATGTCACCGCAATTTGTATGTAAACTTGAGGTGTC -s simDog_chr6.simDog.chr6 138295 67 + 593897 TCAAACCAGGGGTTCTATTAACCCCAAAGCATCATCCCATGGCCAATTGTATGTAA-CACCAGGTCTT -s simHuman_chr6.simHuman.chr6 431589 68 - 601863 GCAATCTAGGGGTTCTAAGACCCCAAAAGCATCATCCTGTGGAAATTTGTATGTAAGCGTGATGTGTC -s simRat_chr6.simRat.chr6 165563 64 + 647215 TTAAGCTAGGGGTTCTAACATGCCAAA----TCCTCCCATGGCAAGTTGTATGTAAACTAGATTGGGC - -a -s simMouse_chr6.simMouse.chr6 167931 4 + 636262 AGCA -s Anc0.Anc0refChr1 8537 4 + 62388 AGCA -s Anc1.Anc1refChr2 9175 4 - 144309 AGCA -s Anc2.Anc2refChr3 9418 4 - 53186 AGCA -s mr.mrrefChr5 30598 4 + 294540 AGCA -s simCow_chr6.simCow.chr6 430246 4 - 602619 AGCA -s simDog_chr6.simDog.chr6 138369 4 + 593897 AGCA -s simHuman_chr6.simHuman.chr6 431657 4 - 601863 AGCA -s simRat_chr6.simRat.chr6 165627 4 + 647215 AGTG - -a -s simMouse_chr6.simMouse.chr6 167935 40 + 636262 TTTTAAAAACTATTCCTACCTTAAATTTTCATTTAAAGAC -s Anc0.Anc0refChr1 8541 28 + 62388 TCTTGAAA-TTAAGCCTACCATA--------TTCATA--- -s Anc1.Anc1refChr2 9179 39 - 144309 TCTTGAAA-TTAAGCCTACCATAGATGCCCATTCATAGAC -s Anc2.Anc2refChr3 9422 28 - 53186 TCTTGAAA-TTGAGCCTACCATA--------TTAATA--- -s mr.mrrefChr5 30602 40 + 294540 TTTTAAAAACTATTCCTACCTTAAATTTTCATTCAAAGAC -s simCow_chr6.simCow.chr6 430250 28 - 602619 CTTTGAAG-TTGAGACTACCATA--------TAAACA--- -s simDog_chr6.simDog.chr6 138375 28 + 593897 TCTTGAGA-ATGAGCCTACCATA--------TTAATA--- -s simHuman_chr6.simHuman.chr6 431661 39 - 601863 TCTTGAAA-TTAAGCCTACCATAGATGCCCATTCATAGAC -s simRat_chr6.simRat.chr6 165631 40 + 647215 TTTTAAAAACCATACCTACCTTAAATTTACATCCAAAGAC - -a -s simMouse_chr6.simMouse.chr6 167975 22 + 636262 CTATTTGTCCTCCCCTTTCCTT -s Anc0.Anc0refChr1 8573 22 + 62388 CCTCTCTTCCATTCCTCTACAT -s Anc1.Anc1refChr2 9222 22 - 144309 CCTCTCTTCCATTCCTCTACAT -s Anc2.Anc2refChr3 9454 22 - 53186 CCTCTCTTCCATTCCTCTACAT -s mr.mrrefChr5 30642 22 + 294540 CTACTCGTCCTCCCCTTTCCTT -s simCow_chr6.simCow.chr6 430282 22 - 602619 CTTCTCTCCCATTCCTTTACAG -s simDog_chr6.simDog.chr6 138407 22 + 593897 CCTCTCTTCCATTCCTCTACAT -s simHuman_chr6.simHuman.chr6 431705 22 - 601863 CCTCCCTTACCTTTCCCTACAT -s simRat_chr6.simRat.chr6 165671 21 + 647215 CTACACGTCCTCCCCTTTC-TT - -a -s simMouse_chr6.simMouse.chr6 167997 10 + 636262 TTGGGGGCAG -s Anc0.Anc0refChr1 8606 10 + 62388 TTTGGGGCAG -s Anc1.Anc1refChr2 9255 10 - 144309 TTTGGGGCAG -s Anc2.Anc2refChr3 9487 10 - 53186 TTTGGGGCAG -s mr.mrrefChr5 30664 10 + 294540 TTGGGGGCAG -s simCow_chr6.simCow.chr6 430315 5 - 602619 TTTGG----- -s simDog_chr6.simDog.chr6 138440 10 + 593897 TTTGGGGCAG -s simHuman_chr6.simHuman.chr6 431738 10 - 601863 TCTGGGGCAG -s simRat_chr6.simRat.chr6 165692 10 + 647215 TTGGGGGCAG - -a -s simMouse_chr6.simMouse.chr6 168007 32 + 636262 TAATTGTACAGCCAGTTTCAGGAAAAGTTGTG -s Anc0.Anc0refChr1 8616 32 + 62388 TGATTGTATAGCCAATTTCAAGCCAAGTTCTG -s Anc1.Anc1refChr2 9265 32 - 144309 TGATTGTATAGCCAATTTCAAGCCAAGTTCTG -s Anc2.Anc2refChr3 9497 32 - 53186 TGGTTGTATAGCCAATTTCAAGCCAAGTTCTG -s mr.mrrefChr5 30674 32 + 294540 TAATTGTACAGCCAGTTTCAGGAAAAGTTGTG -s simCow_chr6.simCow.chr6 430320 29 - 602619 ---TTGTATACTCAAGTTTTAGCCAAGTTCTG -s simDog_chr6.simDog.chr6 138528 32 + 593897 TGGCTGTACGGCCAATTTCATGCCAAGTTCTG -s simHuman_chr6.simHuman.chr6 431748 32 - 601863 TGATTGCATAGCCAATTTCAAGTCAACTTCTG -s simRat_chr6.simRat.chr6 165702 32 + 647215 TAATTGTACAGCCAGTTTCAGGAAAAGTTGTA - -a -s simMouse_chr6.simMouse.chr6 168039 8 + 636262 AGCCTATG -s Anc0.Anc0refChr1 8648 8 + 62388 AGCCTGTG -s Anc1.Anc1refChr2 9297 8 - 144309 AGCCTGTG -s Anc2.Anc2refChr3 9529 8 - 53186 GGCCTGTG -s mr.mrrefChr5 30706 8 + 294540 AGCCTGTG -s simCow_chr6.simCow.chr6 430352 8 - 602619 GGCCTGTG -s simDog_chr6.simDog.chr6 138560 8 + 593897 GGCCTGTG -s simHuman_chr6.simHuman.chr6 431780 8 - 601863 AGCCTGTG -s simRat_chr6.simRat.chr6 165734 8 + 647215 AGCCTGTG - -a -s simMouse_chr6.simMouse.chr6 168047 4 + 636262 TCCT -s Anc0.Anc0refChr1 8656 4 + 62388 ATCT -s Anc1.Anc1refChr2 9305 4 - 144309 ATCT -s Anc2.Anc2refChr3 9537 4 - 53186 ATCT -s mr.mrrefChr5 30714 4 + 294540 TCCT -s simCow_chr6.simCow.chr6 430360 4 - 602619 ATCT -s simDog_chr6.simDog.chr6 138568 4 + 593897 GTCT -s simHuman_chr6.simHuman.chr6 431788 4 - 601863 AACT -s simRat_chr6.simRat.chr6 165743 4 + 647215 TCCT - -a -s simMouse_chr6.simMouse.chr6 168051 73 + 636262 AGGGCAAGATGTATTATGAGTACTAAGTACTGACAGGATATAGGGAATAAGGAACACACATTGTTAATTACTA -s Anc0.Anc0refChr1 8660 12 + 62388 AAGGGAAAATGT------------------------------------------------------------- -s Anc1.Anc1refChr2 9309 12 - 144309 AAGGGAAAATGT------------------------------------------------------------- -s Anc2.Anc2refChr3 9541 12 - 53186 AAGGGAAAATGT------------------------------------------------------------- -s mr.mrrefChr5 30718 72 + 294540 AGGGCAAGATGTATTATGAGTACTAAGTACTGACAGGATATAGGGAATAAGGAACACAC-TTGTTAATTACTA -s simCow_chr6.simCow.chr6 430370 12 - 602619 AGGGGGAAATGT------------------------------------------------------------- -s simDog_chr6.simDog.chr6 138572 12 + 593897 AAGGGAAAATGT------------------------------------------------------------- -s simHuman_chr6.simHuman.chr6 431792 12 - 601863 ATGGGAAAATGT------------------------------------------------------------- -s simRat_chr6.simRat.chr6 165747 72 + 647215 AGGGCAATATGTATTATGGGTACTGAGCACTGATAGGATATTGTGTATAAAGAACATAC-TTGTTAATTAATA - -a -s simMouse_chr6.simMouse.chr6 168124 18 + 636262 CCTGCCAACTCATCATTA -s mr.mrrefChr5 30790 18 + 294540 CCTGCCAACTCATCATTA -s simRat_chr6.simRat.chr6 165822 18 + 647215 CCTGTCAACTCACCATTA - -a -s simMouse_chr6.simMouse.chr6 168142 75 + 636262 TGTTATTGTATGTAATGTACCAAACGATAGGCTATCTATTCAAAGCAACCTAGCATAAAGTTGAGGGTGGACCGA -s mr.mrrefChr5 30808 75 + 294540 TGTTATTGTATGTAATGTACCAAACGATAGGCTATCTATTCAAAGCAACCTAGCATAAAGTTGAGGGTGGACCGA -s simRat_chr6.simRat.chr6 165909 75 + 647215 CGTAATTGTATGTATTGTACCAAATGATGGGCTATCTGTTCCAAGCAACCTAATATAAAGTTAAGGGCAAACCTA - -a -s simMouse_chr6.simMouse.chr6 168217 118 + 636262 AAACTTCCAGTCTAGCTATGCTGCACTGGCACATAAGCCACCTCTGCTGTACTGGATTACATCCCCTTACATGTCCTGGAAATACCTGATTTTCCTTTTAAACTCAAGAAGTTTGGTG -s Anc0.Anc0refChr1 8672 2 + 62388 --------------------------------------------------------------------------------------------------------------------TG -s Anc1.Anc1refChr2 9321 2 - 144309 --------------------------------------------------------------------------------------------------------------------TG -s Anc2.Anc2refChr3 9553 2 - 53186 --------------------------------------------------------------------------------------------------------------------AT -s mr.mrrefChr5 30883 117 + 294540 AAACTTCCAGTCTAGCTATGCTGCACTGGCACATAAGCCACCTCTGCTGTACTGGATTACATCCCCTTACATGTCCTGGAAA-ACCTGATTTTCCTTTTAAACTCAAGAAGTTTGGTG -s simCow_chr6.simCow.chr6 430382 2 - 602619 --------------------------------------------------------------------------------------------------------------------AT -s simDog_chr6.simDog.chr6 138584 2 + 593897 --------------------------------------------------------------------------------------------------------------------AT -s simHuman_chr6.simHuman.chr6 431804 2 - 601863 --------------------------------------------------------------------------------------------------------------------TG -s simRat_chr6.simRat.chr6 165985 117 + 647215 AAACTTCCAGTCTAGCTGCACTGCACTGGCATGTAAGCTAACTACGCTGTGCTGCTTAACATCCCCTTACATGTTTTGAAAA-ACCTGGTTTTCCTTTTAAACTCAAGGAGTTTGGTG - -a -s simMouse_chr6.simMouse.chr6 168335 19 + 636262 CAACAGCTTGCTACAGAGC -s Anc0.Anc0refChr1 8674 17 + 62388 TTA-AG-TTGCTACGAAGC -s Anc1.Anc1refChr2 9323 17 - 144309 TTA-AG-TTGCTACGAAGC -s Anc2.Anc2refChr3 9800 17 - 53186 TTA-AA-TTGCTATGAAGC -s mr.mrrefChr5 31000 18 + 294540 CAA-AGCTTGCTACAGAGC -s simCow_chr6.simCow.chr6 430634 17 - 602619 TGA-AA-TTGCTATGAAAT -s simDog_chr6.simDog.chr6 138863 17 + 593897 TTA-AA-TTGCTATGAAGC -s simHuman_chr6.simHuman.chr6 431806 17 - 601863 TTA-AG-TTGCTACGAAGC -s simRat_chr6.simRat.chr6 166102 3 + 647215 CCA---------------- - -a -s simMouse_chr6.simMouse.chr6 168354 38 + 636262 GCACCACATGGAGACTTATGAGAATATTTACAGCTTGC -s Anc0.Anc0refChr1 8694 38 + 62388 TCACCATATGGAGAATTATGAGAACATTCCCAGCTTAA -s Anc1.Anc1refChr2 9343 38 - 144309 TCACCATATGGAGAATTATGAGAACATTCCCAGCTTAA -s Anc2.Anc2refChr3 9820 38 - 53186 TCAACATATGGCAAATCATGAGCACATTCCCAACCTAA -s mr.mrrefChr5 31018 38 + 294540 GCACCACATGGAGACTTATGAGAATATTTACAGCTTGA -s simCow_chr6.simCow.chr6 430654 31 - 602619 ACAATATATGGCAAGCCATGAGTTCATT-------TAG -s simDog_chr6.simDog.chr6 138883 38 + 593897 TTTACATATGGCAAATCATGAGCACAACCCCAACCTAA -s simHuman_chr6.simHuman.chr6 431826 38 - 601863 TCACCATATGAAGAATTATGAGAACATTCCAAGCTTAA -s simRat_chr6.simRat.chr6 166105 11 + 647215 ---------------------------TTACAACTTGA - -a -s simMouse_chr6.simMouse.chr6 168392 13 + 636262 ACTGATATTAAAT -s Anc0.Anc0refChr1 8733 13 + 62388 GAATAAACAAAAT -s Anc1.Anc1refChr2 9382 13 - 144309 GAATAAACAAAAT -s Anc2.Anc2refChr3 9859 13 - 53186 AAGTAAACAAAAT -s mr.mrrefChr5 31056 13 + 294540 GCAGATATTAAAT -s simCow_chr6.simCow.chr6 430686 13 - 602619 AGGTAAACTAAAT -s simDog_chr6.simDog.chr6 138922 13 + 593897 AAGTAAACAAAAA -s simHuman_chr6.simHuman.chr6 431865 13 - 601863 GAATAAACGAAAT -s simRat_chr6.simRat.chr6 166116 13 + 647215 GCAGACATTAAAT - -a -s simMouse_chr6.simMouse.chr6 168405 32 + 636262 AGTGGCCTCTGGTACCATTGCCAGTATTGGAT -s Anc0.Anc0refChr1 8746 32 + 62388 AGTAACCTGCAGTATCATTACCAGTAATGGAA -s Anc1.Anc1refChr2 9395 32 - 144309 AGTAACCTGCAGTATCATTACCAGTAATGGAA -s Anc2.Anc2refChr3 9872 32 - 53186 GGTAATCTGCAGTATCATTACCAGTAATGGGA -s mr.mrrefChr5 31069 32 + 294540 AGTAGCCTCTGGTATCATTGCCAGTATTGGAT -s simCow_chr6.simCow.chr6 430699 32 - 602619 GGTAATCTGCAGTATCAATACCAGTAATGGGG -s simDog_chr6.simDog.chr6 138935 32 + 593897 GGTAATCTGTGGTATCATTGCCAGTAATGGGA -s simHuman_chr6.simHuman.chr6 431879 32 - 601863 AGTAACCTGCAGTATCATTATCAGTACTAGAA -s simRat_chr6.simRat.chr6 166129 32 + 647215 AATAGCCTCTGGTATCATTGCCAGTATTGGAT - -a -s simMouse_chr6.simMouse.chr6 168437 2 + 636262 AA -s Anc0.Anc0refChr1 8778 2 + 62388 AA -s Anc1.Anc1refChr2 9427 2 - 144309 AA -s Anc2.Anc2refChr3 9904 2 - 53186 AA -s mr.mrrefChr5 31101 2 + 294540 AA -s simCow_chr6.simCow.chr6 430731 2 - 602619 AA -s simDog_chr6.simDog.chr6 138968 2 + 593897 GA -s simHuman_chr6.simHuman.chr6 431911 2 - 601863 AA -s simRat_chr6.simRat.chr6 166161 2 + 647215 TA - -a -s simMouse_chr6.simMouse.chr6 168439 3 + 636262 TGA -s Anc0.Anc0refChr1 8785 3 + 62388 TGA -s Anc1.Anc1refChr2 9434 3 - 144309 TGA -s Anc2.Anc2refChr3 9911 3 - 53186 TGA -s mr.mrrefChr5 31103 3 + 294540 TGA -s simCow_chr6.simCow.chr6 430738 3 - 602619 TGA -s simDog_chr6.simDog.chr6 138975 3 + 593897 TGA -s simHuman_chr6.simHuman.chr6 431918 3 - 601863 TGA -s simRat_chr6.simRat.chr6 166163 3 + 647215 TGA - -a -s simMouse_chr6.simMouse.chr6 168442 34 + 636262 CTCTGTCACACAGAATGATGACTCCAGGTTAAAA -s Anc0.Anc0refChr1 8811 34 + 62388 CCTTGTACCACAATATGGTGACCCCAGATTAAAA -s Anc1.Anc1refChr2 9460 34 - 144309 CCTTGTACCACAATATGGTGACCCCAGATTAAAA -s Anc2.Anc2refChr3 9937 34 - 53186 CCTTTTACCACAATATAGTGACCCTGGATTAAAA -s mr.mrrefChr5 31106 34 + 294540 CTCTGTCACACAAAATGATGACTCCAGATTAAAA -s simCow_chr6.simCow.chr6 430764 34 - 602619 CCTCTGACCACAGTATAGACACCCTGCATTAAGA -s simDog_chr6.simDog.chr6 139001 34 + 593897 CCATTTACCATGATATAGTGATCCTGGATTAAAA -s simHuman_chr6.simHuman.chr6 431944 34 - 601863 CCTTGTATGACAATATGGTAACCCCAGATTAAAA -s simRat_chr6.simRat.chr6 166166 34 + 647215 CTCTGTTACACAAAATGATGACTCCAGAGTAGAA - -a -s simMouse_chr6.simMouse.chr6 168476 80 + 636262 TTGTAGCCCAAGAGACAGATGTTGCCTTGAAACACTACAAAAGCCAGAGTCATTCCTTCTATTGGATTGGGGAAGATTGA -s Anc0.Anc0refChr1 8845 59 + 62388 GTGTAATGCAAGAGTTGTAGTGTAGCTTGGAAAATTACAAAAGTCAGACTCATTTCTTC--------------------- -s Anc1.Anc1refChr2 9494 59 - 144309 GTGTAATGCAAGAGTTGTAGTGTAGCTTGGAAAATTACAAAAGTCAGACTCATTTCTTC--------------------- -s Anc2.Anc2refChr3 9971 59 - 53186 GTGTAATGCAGCAGTTGTAGTGTAGCTTGGAAAATTCCAAAGGTCCGTCCCACTTCTTC--------------------- -s mr.mrrefChr5 31140 80 + 294540 GTGTAGCCCAAGAGACAGATGTTGCCTTGGAACACTACAAAAGCCAGAGTCATTCCTTCTATTGGATTGGGGAAGATTGA -s simCow_chr6.simCow.chr6 430798 57 - 602619 GTGTAATGCAGTTGTTGCGGTGTACATTGTAAAGTT-CAAAGGTCTGTCGCACTCCAG---------------------- -s simDog_chr6.simDog.chr6 139035 59 + 593897 GTGTAATGCAGCAGTTTTAATGTAGCTTGGAAAATCCTAAAGGTCCGTCCCACTTCTTC--------------------- -s simHuman_chr6.simHuman.chr6 431978 58 - 601863 GTGTAATGTGAGAGTTGAAGTATAGCTTGGAAAATTACAAAAGTCAGA-TCATTTCTTT--------------------- -s simRat_chr6.simRat.chr6 166202 80 + 647215 GGGTTGCACAGGGGCCAGATGTTGTGTAGGCGGTCTATGAAGGGCAGAGTCACTCCTTCTATTGGATTGAGGAAGATCAA - -a -s simMouse_chr6.simMouse.chr6 168556 17 + 636262 GGAATCTTAGGAGTACC -s Anc0.Anc0refChr1 8904 17 + 62388 AGAATCCTTGGAAAACT -s Anc1.Anc1refChr2 9553 17 - 144309 AGAATCCTTGGAAAACT -s Anc2.Anc2refChr3 10030 17 - 53186 AGAACCCTTGGAAAACT -s mr.mrrefChr5 31220 17 + 294540 GGAATCTTAGGAGTACC -s simCow_chr6.simCow.chr6 430855 17 - 602619 AGCACCCCTGGAAAACT -s simDog_chr6.simDog.chr6 139103 17 + 593897 AGAACCTTTTGAGAGCT -s simHuman_chr6.simHuman.chr6 432036 17 - 601863 AGTATCCTTGGAAAACT -s simRat_chr6.simRat.chr6 166282 17 + 647215 GGATTCTTAGGAGTACG - -a -s simMouse_chr6.simMouse.chr6 168573 7 + 636262 AAGGGCT -s Anc0.Anc0refChr1 8921 7 + 62388 AGGGGCC -s Anc1.Anc1refChr2 9570 7 - 144309 AGGGGCC -s Anc2.Anc2refChr3 10047 7 - 53186 AGGGAAC -s mr.mrrefChr5 31237 7 + 294540 AAGGGCT -s simCow_chr6.simCow.chr6 430872 4 - 602619 GGGG--- -s simDog_chr6.simDog.chr6 139127 7 + 593897 AGAGAAC -s simHuman_chr6.simHuman.chr6 432053 7 - 601863 ATGGGCC -s simRat_chr6.simRat.chr6 166299 7 + 647215 AATGGCT - -a -s simMouse_chr6.simMouse.chr6 168580 61 + 636262 AGGCATACAAATTCATCTGGAAAAGAGAGTTAGGTGGTGTGGGTAAAGTCCGGTGAAATGC -s Anc0.Anc0refChr1 8934 45 + 62388 GAGCATACATATTCACATGGAAGAGAAACT----------------AATTAGGTGGAATGC -s Anc1.Anc1refChr2 9583 60 - 144309 GAGCATACATATTCACATGGAAGAGAAACTGAGGGGAAAGG-CCAGAATTAGGTGGAATGC -s Anc2.Anc2refChr3 10060 45 - 53186 AAGCATACATGTTCACATGGAAGAAAAGCT----------------AATTGGGTGGAATGC -s mr.mrrefChr5 31244 60 + 294540 GAGCATACATATTCATCTGGAAAAGAAAGTTAGGTGGTATG-GTAAAGTCAGGTGAAATGC -s simCow_chr6.simCow.chr6 430877 42 - 602619 AAGCATACATGTTCACATGTAAGAGAA-------------------AATTGGGTGGAATGC -s simDog_chr6.simDog.chr6 139140 36 + 593897 AAGCATACGTGTTCATGTGGAAGAAAAGCT-------------------------GAATGC -s simHuman_chr6.simHuman.chr6 432067 54 - 601863 GAATACACACATCAACA------AGAAAATGAGGGGAAAGG-CCAGAATTAGGTGGAATGC -s simRat_chr6.simRat.chr6 166306 60 + 647215 GATCATACATATTCATCTGCAAAAGAAAGTTAGGTGGTATG-GTGAAGCCAGGTGAAAAGC - -a -s simMouse_chr6.simMouse.chr6 168641 45 + 636262 CAATAGATCCCTTCAGTGTGGTGCTCTTGCTCTACCAACTGGCCA -s Anc0.Anc0refChr1 8980 45 + 62388 TGATATCTCCCTTCAGTCTCGTGCTCTTTTTCTCCTAACTGACAA -s Anc1.Anc1refChr2 9644 45 - 144309 TGATATCTCCCTTCAGTCTCGTGCTCTTTTTCTCCTAACTGACAA -s Anc2.Anc2refChr3 10106 45 - 53186 TGATATCTCCCTTCAGTCACAGGCTATTTTTCTCCTAACTGAGAC -s mr.mrrefChr5 31304 45 + 294540 TGATAGATCCCTTCAGTGTGGTGCTCTTGTTCTACTAACTGACAA -s simCow_chr6.simCow.chr6 430920 45 - 602619 TGATCTCTCCCCTCAGTCACAGGCTATTTTTCTCCTAACTGAAGC -s simDog_chr6.simDog.chr6 139177 32 + 593897 TGATATATTCCTTCA-------------GTTCTCCCAACTGAGAC -s simHuman_chr6.simHuman.chr6 432122 43 - 601863 TGATA--TCTCTTGCATCTAGTGCTCTTTTTCTCCTAAATGACAA -s simRat_chr6.simRat.chr6 166366 43 + 647215 TGATAGATCCCTTCGGATT--TGCTCTTGTGCTAGTAACTGAGAA - -a -s simMouse_chr6.simMouse.chr6 168686 3 + 636262 TGT -s Anc0.Anc0refChr1 9025 3 + 62388 TGT -s Anc1.Anc1refChr2 9689 3 - 144309 TGT -s Anc2.Anc2refChr3 10151 3 - 53186 TGT -s mr.mrrefChr5 31349 3 + 294540 TGT -s simCow_chr6.simCow.chr6 430967 3 - 602619 TTC -s simDog_chr6.simDog.chr6 139209 3 + 593897 TGT -s simHuman_chr6.simHuman.chr6 432165 3 - 601863 TGT -s simRat_chr6.simRat.chr6 166409 3 + 647215 TGT - -a -s simMouse_chr6.simMouse.chr6 168689 5 + 636262 AGCTC -s Anc0.Anc0refChr1 9028 5 + 62388 AACCA -s Anc1.Anc1refChr2 9692 5 - 144309 AACCA -s Anc2.Anc2refChr3 10154 5 - 53186 AACCA -s mr.mrrefChr5 31352 5 + 294540 AGCTC -s simCow_chr6.simCow.chr6 430974 5 - 602619 AACTG -s simDog_chr6.simDog.chr6 139212 5 + 593897 AACCA -s simHuman_chr6.simHuman.chr6 432168 5 - 601863 AACCA -s simRat_chr6.simRat.chr6 166412 5 + 647215 AGCTG - -a -s simMouse_chr6.simMouse.chr6 168694 39 + 636262 CAAGGGTAACTGAGACGGGGTTAGCCAATAGGGGAAGCC -s Anc0.Anc0refChr1 9037 37 + 62388 CAAGGGAAGCACAAAAGTGGCCATCCGAAAGGG--AGCA -s Anc1.Anc1refChr2 9701 37 - 144309 CAAGGGAAGCACAAAAGTGGCCATCCGAAAGGG--AGCA -s Anc2.Anc2refChr3 10163 37 - 53186 AAAAGGAAGCACAAAAGTGGCCATCTGAAAGGG--AGCA -s mr.mrrefChr5 31357 39 + 294540 CAAGGGTAACTGAGACGGGGTTAGCCAATAGGGGAAGCC -s simCow_chr6.simCow.chr6 430983 29 - 602619 AAAAG--------AATGTGGCCATCTGCAAGGG--CGCA -s simDog_chr6.simDog.chr6 139221 37 + 593897 AAAAGGAAGCACAAAAGGGGCCGTCTGACAGGG--AGCA -s simHuman_chr6.simHuman.chr6 432177 37 - 601863 CAAGGGGACCACACAAGTAGCCATCCCAAAGGG--AGCA -s simRat_chr6.simRat.chr6 166417 12 + 647215 C---------------------------TAGGGGAAGCC - -a -s simMouse_chr6.simMouse.chr6 168733 11 + 636262 CACAAGTGGCC -s Anc0.Anc0refChr1 9074 11 + 62388 CAAAAATGAGC -s Anc1.Anc1refChr2 9738 11 - 144309 CAAAAATGAGC -s Anc2.Anc2refChr3 10200 11 - 53186 CAAAAATGAGC -s mr.mrrefChr5 31396 11 + 294540 CACAAGTGGCC -s simCow_chr6.simCow.chr6 431021 11 - 602619 CAAAAATGGGC -s simDog_chr6.simDog.chr6 139258 11 + 593897 CTAAAATAAGC -s simHuman_chr6.simHuman.chr6 432214 11 - 601863 CAAAGTTGAGC -s simRat_chr6.simRat.chr6 166429 11 + 647215 CTCAAATGGCT - -a -s simMouse_chr6.simMouse.chr6 168744 86 + 636262 CTCACAGACAAATATCCTCTGTTGAGGTCTAGAACTTCAGGTGGAGGTCTAGAACTTCAGCAGGCACCGGCCCATCATTAAGTGTC -s Anc0.Anc0refChr1 9094 63 + 62388 CTCCCAGGCGTATATCTTCTAA--------------------GGAGATCTAGGACATCAATATGCGCCAGCACAT---TTAATGTC -s Anc1.Anc1refChr2 9758 63 - 144309 CTCCCAGGCGTATATCTTCTAA--------------------GGAGATCTAGGACATCAATATGCGCCAGCACAT---TTAATGTC -s Anc2.Anc2refChr3 10220 63 - 53186 CTCCCAGGCGTATGTCTTCTAA--------------------GGAGATCTAGGGCATCAATATGCGCCAGCACAT---TTAATATT -s mr.mrrefChr5 31407 63 + 294540 CTCACAGACAAATATCCTCTGG--------------------GGAGGTCTAGAACTTCAGCAGGCACCGGCCCAT---TAAGTGTC -s simCow_chr6.simCow.chr6 431041 63 - 602619 CTCCCAGGTGTGGCTCTCCTAA--------------------CGATATCATGGCACTCAGTATGCACCAGCACAT---CTAGCATT -s simDog_chr6.simDog.chr6 139278 60 + 593897 CTCCCAGGCATATGTCTTCTAA--------------------GGAGATCTAGGGCACCAATAGGTGCCAGCATTT---TTAAT--- -s simHuman_chr6.simHuman.chr6 432234 63 - 601863 CTCTCAGGCGTAAATCATCTAA--------------------GTAGATCTGGGACATGAATATGCGCCAGCACAT---TTAATGTC -s simRat_chr6.simRat.chr6 166440 63 + 647215 CTCACAGGAAAACATCCTCTGG--------------------GGAGGTCTAGAATTTTAGCAGGCACTGGCCCAT---TAAGTACC - -a -s simMouse_chr6.simMouse.chr6 168830 123 + 636262 AAGCTTATTAGCTAGTTTTGACCAACTCGGCAATTAGTTTTGATTATCTTGGTAATTATCTCAAGCTAATTAGATAACAGGATTTAAAATCAGTTCAATGTTATAGTGGTGAACTGGAGGCCA -s Anc0.Anc0refChr1 9157 77 + 62388 AAGCTTATTGGCTAATTTTCACCATCTTGATTATTA--------TCT--------------------------------------AAAGTCAGTTAAATGTTATGCTGGTGAGCTGGAGGTCA -s Anc1.Anc1refChr2 9821 105 - 144309 AAGCTTATTGGCTAATTTTCACCATCTTGATTATTA--------TCTCAGTTTAATTATTCGTCACTA------TAACA----TTAAAGTCAGTTAAATGTTATGCTGGTGAGCTGGAGGTCA -s Anc2.Anc2refChr3 10283 77 - 53186 AGGGTTACTGGCTAATTTCCACCATCTTTATTATTA--------CCT--------------------------------------AAAGACAGTTAAGTGTTTTACTGATGAGCGGGAGGTTA -s mr.mrrefChr5 31470 115 + 294540 AAGCTTATTAGCTAGTTTTGACCAACTTGATAATTA--------TATCTTGGTAATTATCTCAAGCTAATTAGATAACAGGATTTAAAATCAGTTCAATGTTATGGTGGTGAACTGGAGGCCA -s simCow_chr6.simCow.chr6 431122 74 - 602619 AGGGTTACTGGCTAATTGCCACCATCCTAATTTTTA--------CCT--------------------------------------AT---CAGTTAAGTGTTATACTGTTGAGTGGGAGGTTA -s simDog_chr6.simDog.chr6 139338 61 + 593897 ----------------TTCCACCATGTTTATGATTA--------CCT--------------------------------------AAAGACAGTTAAGTGTTTTAGTGATGAGCGGGAAGTTA -s simHuman_chr6.simHuman.chr6 432297 105 - 601863 AAGCTTGTTGGCTAATTTTCACCACCTTGATTATTA--------TTTCAGTTTAATTATTCGTCACTA------TAACA----TTTAACTGATTTTAAGTTCAAGCTGGTAAGCTGGAGGTCA -s simRat_chr6.simRat.chr6 166503 115 + 647215 AAGCCTATTAGTTAGTTTTGATCAACTTGATAATTA--------TAACTTGGTAATTATCTCAAGCTAATTAAATACCAGCATTTAAATTCAGTTCAGCGTTATGGTGGTGAACTGGAGGCCA - -a -s simMouse_chr6.simMouse.chr6 168953 31 + 636262 CCATTCAAGGTTCTTAAATTCATACTTGTTT -s Anc0.Anc0refChr1 9236 23 + 62388 CTGCCCAAAGTCCTGAACTT--T------TT -s Anc1.Anc1refChr2 9928 25 - 144309 CTGCCCAAAGTCCTGAACTTAAT------TT -s Anc2.Anc2refChr3 10362 23 - 53186 CTGCCCAAAGTCCTGAACTT--T------TT -s mr.mrrefChr5 31585 31 + 294540 CCATTCAAGGTTCTTAAATTCATACTTGTTT -s simCow_chr6.simCow.chr6 431198 23 - 602619 CTGCTCAAGGCCTTGAATCT--T------TT -s simDog_chr6.simDog.chr6 139401 23 + 593897 CTGCCCAAAGTCCTGAACTT--T------TC -s simHuman_chr6.simHuman.chr6 432404 25 - 601863 CTGCCCAAAGTCCTGAACTTAAT------TT -s simRat_chr6.simRat.chr6 166618 28 + 647215 CCTTTCTAGGTTCTTA---TCATATTTGTTT - -a -s simMouse_chr6.simMouse.chr6 168984 120 + 636262 TATTACTTCTTGTGGCAGCTCACATATTGCCTCAAAGATATTCTTTCACATAAAAATTAGAACTTCATCATTCTGACAGCCCCGAGTAGAAATATGAACAATGAGTGGCGATGCACCAGA -s Anc0.Anc0refChr1 9259 120 + 62388 TATTTCTTTTTGTGGCAGCTCACCTAATACCTCAAAGACATTCTCTCACATGAGTAGTAGAACTGCATCATCCTGTGCCCCCTGAGCCAAGTTATTTAGAATAAATGGCGATGCACAAAA -s Anc1.Anc1refChr2 9953 120 - 144309 TATTTCTTTTTGTGGCAGCTCACCTAATACCTCAAAGACATTCTCTCACATGAGTAGTAGAACTGCATCATCCTGTGCCCCCTGAGCCAAGTTATTTAGAATAAATGGCGATGCACAAAA -s Anc2.Anc2refChr3 10385 120 - 53186 TATTTCTTTTTATGGCAACTCACCTAACATTTCAAAGACATTCTCTCGCATGAGTAGTAGAACTGCATCATCCTCTGCCCCCTGAGCCAAGTTACTTAGAATAAATGGCAATGCACAACA -s mr.mrrefChr5 31616 120 + 294540 TATTACTTCTTGTGGCAGCTCACATATTGCCTCAAAGACATTCTTTCACATAAAAATTAGAACTTCATCATCCTGTCCCCCCCGAGTAGAGATATGTACAATAAGTGGCGATGCACCAAA -s simCow_chr6.simCow.chr6 431229 120 - 602619 TCTTTCTTTTTATGGCAACTCACCTAACATTTCAAAGACATTCTCTCGCATGAGTAGTAGAACTGCACCATCTTCTGCCCCCTGCGCCAAGTTCCTTGAAATAATTGGCAGTGCATAGGA -s simDog_chr6.simDog.chr6 139424 57 + 593897 TAT---------------------------------------------------------------ATCATCCTCTACCTCCTGAGCAAAGTTACGTAGAATAAATGGTAATGCACAACA -s simHuman_chr6.simHuman.chr6 432429 120 - 601863 TATGTCTTTTTGTGGCAGCTCACCTACTACCTCGAAGGCATTCCCTCACATGGGCAATAGAAATCCATCATCCTGTGCCCCCGGAGCCAAGTTATTTATGATAACTGGCGATGCACAAAA -s simRat_chr6.simRat.chr6 166646 120 + 647215 TATTACTTCTTATGGTATATCACATATTGTCTCAAAGACATTCTTTCATATAAAGATTAGAACTTCATCATCCTGTCCCCTCCGAGTGGAGGTCCGTACAATAAGTGGAGATGCACCAAA - -a -s simMouse_chr6.simMouse.chr6 169104 11 + 636262 GATTTCCAGGT -s Anc0.Anc0refChr1 9379 11 + 62388 GATCTCCAGGC -s Anc1.Anc1refChr2 10073 11 - 144309 GATCTCCAGGC -s Anc2.Anc2refChr3 10505 11 - 53186 GGTCTCCAGGC -s mr.mrrefChr5 31736 11 + 294540 GATTTCCAGGT -s simCow_chr6.simCow.chr6 431349 11 - 602619 GGTCTTCAGAC -s simDog_chr6.simDog.chr6 139481 11 + 593897 TGTCTCTAGGC -s simHuman_chr6.simHuman.chr6 432549 11 - 601863 GATCTCCAGGC -s simRat_chr6.simRat.chr6 166767 11 + 647215 GATTTCCAGGT - -a -s simMouse_chr6.simMouse.chr6 169115 77 + 636262 GGACTAAGTTACAATATTCCTGTTGACCCATTACTAACCCCCAAAAGTGCTTCCAGTCATTGCAATTTCCATTCTTT -s Anc0.Anc0refChr1 9390 56 + 62388 GGACTA-TTTTTGATATGCCTGTTGACCTATTACTAACCCCCAAGAGTG------------GATATGTC-------- -s Anc1.Anc1refChr2 10084 72 - 144309 GGACTA-TTTTTGATATGCCTGTTGACCTATTACTAACCCCCAAGAGTGCCGT--GTGA--GATATGTCCATTCCTC -s Anc2.Anc2refChr3 10517 56 - 53186 GGACTA-TTTTTGATATGCCTGTTGACATATTACTAACCCCCAAGAGTG------------GATATGGC-------- -s mr.mrrefChr5 31747 76 + 294540 GGACTA-GTTACAATATTCCTGTTGACCCATTACTAACCCCCAAGAGTGCTGCCAGTCATTGAAATTTCCATTCTTT -s simCow_chr6.simCow.chr6 431361 55 - 602619 GTACTA-TTTCTGATATGTCAGTTGACTCATTACTAACCCCCAAGAGTG-------------ACGTAGA-------- -s simDog_chr6.simDog.chr6 139493 56 + 593897 GGACTG-GTTTTGATATGCCTGTTGACATACTACTAATCCCCAAGAGTG------------GTTATGGC-------- -s simHuman_chr6.simHuman.chr6 432560 72 - 601863 TGGACA-TTTTTGATATGCCTGTTGACCTATTATGATCCCCAAAGAGTGCCGT--GTGA--GATATGTCCATTCCTC -s simRat_chr6.simRat.chr6 166778 76 + 647215 GGACTA-GTTACAATATTCCTGTTGGCCCATTGCTAACCCCCAAGAGTTTTGCCAGTCATTGAGATTTCCATTCTTT - -a -s simMouse_chr6.simMouse.chr6 169192 15 + 636262 TCATTGACATATGTG -s Anc0.Anc0refChr1 9446 15 + 62388 TCACTGACATATGTG -s Anc1.Anc1refChr2 10156 15 - 144309 TCACTGACATATGTG -s Anc2.Anc2refChr3 10573 15 - 53186 TCACTGACATATGTC -s mr.mrrefChr5 31823 15 + 294540 TCATTGACATATGTG -s simCow_chr6.simCow.chr6 431416 15 - 602619 TCACTGACATATGTC -s simDog_chr6.simDog.chr6 139549 15 + 593897 TCACTGACAGATTTC -s simHuman_chr6.simHuman.chr6 432634 15 - 601863 TCACTGATATATGTG -s simRat_chr6.simRat.chr6 166854 15 + 647215 TCATTGACATATATG - -a -s simMouse_chr6.simMouse.chr6 169207 100 + 636262 CAATTGTCACCACTTCCCTGATCCTTTTAAGTCTGCAGTTTAAGAGAGACTAGGTGCAAAGATGCTACTTATCACAGGTAATGCTGAGTTAGTGGTGAGT -s Anc0.Anc0refChr1 9461 94 + 62388 CATTCCTCCCCACTTGCTTGATTCTTTTATGTCTACAAGTTAAGAGAAACTA------AAAAAGCAACTTATTATCGGTAGTGCTTAGTTAGTGATTGGT -s Anc1.Anc1refChr2 10171 94 - 144309 CATTCCTCCCCACTTGCTTGATTCTTTTATGTCTACAAGTTAAGAGAAACTA------AAAAAGCAACTTATTATCGGTAGTGCTTAGTTAGTGATTGGT -s Anc2.Anc2refChr3 10588 94 - 53186 CATTCCTCCCCACTTGCTTGATTCTTTTATATCTACAAGTTAAGAGGAATCA------AAAAAGCAACTTATTATCGGTAGTGTTTAGTTATTGATTGGT -s mr.mrrefChr5 31838 100 + 294540 CAATTGTCACCACTTCCTTGATCCTTTTAAGTCTGCAGTTTAAGAGAGACTAGGTGCAAAGATGCTACTTATTATAGGTAATGCTGAGTTAGTGGTGAGT -s simCow_chr6.simCow.chr6 431435 94 - 602619 CGTTCCTCCCTACCTGCTCGATTCTTGTATATTTACAAGTGAAGAGGAATCA------AAAGAGCAACTTATTACAGGTAGTAATTGGTTATTGATTAAT -s simDog_chr6.simDog.chr6 139564 94 + 593897 CATTCCTTCCCACTTGCTTGCTACTTTTATATCTAGAGGTTAAGAGGAATCA------AGAAGACAATTTATTGTCGGTGGTGTTTAGTTATTTATTGGT -s simHuman_chr6.simHuman.chr6 432649 94 - 601863 CATTCCTCCCCACTTGCTTGATTCTTTTATGTCCACAAGTTAAGAGAAACTA------AAAAAGCAACTTAGTATGAGTAGCGCTTAGCTTGTGATAGGT -s simRat_chr6.simRat.chr6 166869 100 + 647215 CAAATGTAGCCACTTCCTTGATCCTTTTAAGACTGCAGTTTAATGGAGACTAGGAGAAAAGCTGCTACTTATTATAGGTAATGCCAAGTTATTCGTGAGT - -a -s simMouse_chr6.simMouse.chr6 169307 10 + 636262 TCATTTGATA -s Anc0.Anc0refChr1 9559 9 + 62388 TC-TTAGATA -s Anc1.Anc1refChr2 10269 9 - 144309 TC-TTAGATA -s Anc2.Anc2refChr3 10686 9 - 53186 TC-CTAAATA -s mr.mrrefChr5 31938 10 + 294540 TCATTTGATA -s simCow_chr6.simCow.chr6 431533 9 - 602619 TC-CTAAATA -s simDog_chr6.simDog.chr6 139662 9 + 593897 TC-CAAAAAA -s simHuman_chr6.simHuman.chr6 432747 9 - 601863 TC-TTAGATA -s simRat_chr6.simRat.chr6 166969 10 + 647215 TCATCTTATA - -a -s simMouse_chr6.simMouse.chr6 169317 4 + 636262 GTGG -s Anc0.Anc0refChr1 9573 4 + 62388 ATGG -s Anc1.Anc1refChr2 10283 4 - 144309 ATGG -s Anc2.Anc2refChr3 10700 4 - 53186 ATGG -s mr.mrrefChr5 31948 4 + 294540 GTGG -s simCow_chr6.simCow.chr6 431547 4 - 602619 GTGT -s simDog_chr6.simDog.chr6 139676 4 + 593897 ATGG -s simHuman_chr6.simHuman.chr6 432761 4 - 601863 ATGG -s simRat_chr6.simRat.chr6 166979 4 + 647215 GTGG - -a -s simMouse_chr6.simMouse.chr6 169321 23 + 636262 CTATCTTGACAAAGCAATATTAA -s Anc0.Anc0refChr1 9577 23 + 62388 GTATCTTGACAAGGCAGTCTAAA -s Anc1.Anc1refChr2 10287 23 - 144309 GTATCTTGACAAGGCAGTCTAAA -s Anc2.Anc2refChr3 10709 23 - 53186 GTATCTTGACAAGGCAGTCTAAA -s mr.mrrefChr5 31952 23 + 294540 CTATCTTGACAAAGCAATATTAA -s simCow_chr6.simCow.chr6 431556 23 - 602619 GTATCTTAACAAGGCACTTTAAA -s simDog_chr6.simDog.chr6 139685 23 + 593897 GTATCTTGACAAGGCAGTCTAGA -s simHuman_chr6.simHuman.chr6 432765 23 - 601863 GTATCTTGGCAAGGCAGACTCAA -s simRat_chr6.simRat.chr6 166983 23 + 647215 ATATCTCAACAAAGCAATACTTA - -a -s simMouse_chr6.simMouse.chr6 169344 6 + 636262 TCCTTC -s Anc0.Anc0refChr1 9600 6 + 62388 TCATTC -s Anc1.Anc1refChr2 10310 6 - 144309 TCATTC -s Anc2.Anc2refChr3 10732 6 - 53186 TCATTC -s mr.mrrefChr5 31975 6 + 294540 TCATTC -s simCow_chr6.simCow.chr6 431579 6 - 602619 TTATTC -s simDog_chr6.simDog.chr6 139712 6 + 593897 TCATTC -s simHuman_chr6.simHuman.chr6 432788 6 - 601863 TCATTC -s simRat_chr6.simRat.chr6 167006 5 + 647215 TCATT- - -a -s simMouse_chr6.simMouse.chr6 169350 2 + 636262 TT -s Anc0.Anc0refChr1 9606 1 + 62388 C- -s Anc1.Anc1refChr2 10316 2 - 144309 CT -s Anc2.Anc2refChr3 10738 1 - 53186 C- -s mr.mrrefChr5 31981 2 + 294540 TT -s simCow_chr6.simCow.chr6 431588 1 - 602619 C- -s simDog_chr6.simDog.chr6 139718 1 + 593897 C- -s simHuman_chr6.simHuman.chr6 432794 2 - 601863 CT -s simRat_chr6.simRat.chr6 167011 2 + 647215 TT - -a -s simMouse_chr6.simMouse.chr6 169352 9 + 636262 TGTAACTAG -s Anc0.Anc0refChr1 9607 6 + 62388 ---AACTAG -s Anc1.Anc1refChr2 10318 9 - 144309 TGTAACTAG -s Anc2.Anc2refChr3 10739 6 - 53186 ---AACTGG -s mr.mrrefChr5 31983 9 + 294540 TGTAACTAG -s simCow_chr6.simCow.chr6 431589 6 - 602619 ---AACTAG -s simDog_chr6.simDog.chr6 139719 6 + 593897 ---AACTGG -s simHuman_chr6.simHuman.chr6 432799 9 - 601863 TGTACCTAG -s simRat_chr6.simRat.chr6 167013 9 + 647215 TGCAACTAG - -a -s simMouse_chr6.simMouse.chr6 169361 3 + 636262 GTT -s Anc0.Anc0refChr1 9613 3 + 62388 GTG -s Anc1.Anc1refChr2 10327 3 - 144309 GTG -s Anc2.Anc2refChr3 10745 3 - 53186 ATG -s mr.mrrefChr5 31992 3 + 294540 GTG -s simCow_chr6.simCow.chr6 431595 3 - 602619 ATG -s simDog_chr6.simDog.chr6 139725 3 + 593897 ATG -s simHuman_chr6.simHuman.chr6 432818 3 - 601863 GTG -s simRat_chr6.simRat.chr6 167022 3 + 647215 GTG - -a -s simMouse_chr6.simMouse.chr6 169364 14 + 636262 GCCATGCTAAATAA -s Anc0.Anc0refChr1 9617 14 + 62388 GCTGTGCTATACTA -s Anc1.Anc1refChr2 10331 14 - 144309 GCTGTGCTATACTA -s Anc2.Anc2refChr3 10749 14 - 53186 TCTGTGCTATACTA -s mr.mrrefChr5 31995 14 + 294540 GCTATGCTAAATAA -s simCow_chr6.simCow.chr6 431599 14 - 602619 ATCGTGCTATACTA -s simDog_chr6.simDog.chr6 139729 14 + 593897 TCTGTTCTAAATGA -s simHuman_chr6.simHuman.chr6 432822 14 - 601863 GCTGAGTTATTCTG -s simRat_chr6.simRat.chr6 167025 14 + 647215 GATATGCTAAATAA - -a -s simMouse_chr6.simMouse.chr6 169378 22 + 636262 TTCTCATTATATTATTATAGAT -s Anc0.Anc0refChr1 9631 16 + 62388 CC-TCATTGT-----CATAGGT -s Anc1.Anc1refChr2 10345 16 - 144309 CC-TCATTGT-----CATAGGT -s Anc2.Anc2refChr3 10763 16 - 53186 CC-TCAATGT-----CATAGGT -s mr.mrrefChr5 32009 22 + 294540 TCCTCATTATATTATTATAGGT -s simCow_chr6.simCow.chr6 431614 16 - 602619 CC-TCAAGGG-----TGTAGGT -s simDog_chr6.simDog.chr6 139743 16 + 593897 CC-TTGATGT-----CATAGAT -s simHuman_chr6.simHuman.chr6 432836 16 - 601863 CC-TCATTGT-----CCTATGT -s simRat_chr6.simRat.chr6 167039 22 + 647215 TCCTCATCATATTATTATAGGT - -a -s simMouse_chr6.simMouse.chr6 169400 25 + 636262 TGAGTTACCCTTTTGAGCAGTCTCC -s Anc0.Anc0refChr1 9652 25 + 62388 AAGGTTACCCTTTTGAGCATTCTCA -s Anc1.Anc1refChr2 10366 25 - 144309 AAGGTTACCCTTTTGAGCATTCTCA -s Anc2.Anc2refChr3 10784 25 - 53186 AAGGATACCATTATAAGCATTCTCT -s mr.mrrefChr5 32031 25 + 294540 TGAGTTACCCTTTTGAGCAGTCTCA -s simCow_chr6.simCow.chr6 431635 13 - 602619 AGGGATACTGTCA------------ -s simDog_chr6.simDog.chr6 139764 25 + 593897 AAGAATGCCATTATAAGCATTCTCT -s simHuman_chr6.simHuman.chr6 432857 25 - 601863 ACGGTTACCCTTTTGAGCAACCTCA -s simRat_chr6.simRat.chr6 167061 25 + 647215 TGAGTTACCCTTTTGAGCATTCTCA - -a -s simMouse_chr6.simMouse.chr6 169425 7 + 636262 CAAGCTT -s Anc0.Anc0refChr1 9687 7 + 62388 CAAGCTT -s Anc1.Anc1refChr2 10401 7 - 144309 CAAGCTT -s Anc2.Anc2refChr3 10819 7 - 53186 CAAGCTT -s mr.mrrefChr5 32056 7 + 294540 CAAGCTT -s simCow_chr6.simCow.chr6 431656 7 - 602619 CCAGCTT -s simDog_chr6.simDog.chr6 139799 7 + 593897 CAAGTTT -s simHuman_chr6.simHuman.chr6 432892 7 - 601863 CAAGCCT -s simRat_chr6.simRat.chr6 167086 7 + 647215 CAAGCTT - -a -s simMouse_chr6.simMouse.chr6 169432 40 + 636262 ATATATATGGCCTATTAACAAATGTTAATAGTGTATCATA -s Anc0.Anc0refChr1 9694 38 + 62388 ATAT--ATGGTCATCTAAGCAATCTTAATAGCATAGCATA -s Anc1.Anc1refChr2 10408 38 - 144309 ATAT--ATGGTCATCTAAGCAATCTTAATAGCATAGCATA -s Anc2.Anc2refChr3 10826 38 - 53186 ATAT--ATGGTCATCTAAGCAATCTTAATAGCATAGCATA -s mr.mrrefChr5 32063 40 + 294540 ATATATATGGCCTATTAACCAATGTTAATAGTGTATCATA -s simCow_chr6.simCow.chr6 431663 38 - 602619 ATAC--ATGGTGAACAAAGCAATCTTAATAGCTTAGCATA -s simDog_chr6.simDog.chr6 139806 38 + 593897 ACAT--ATGGTCATCTAAGTGATCTTATTGACATAGCATA -s simHuman_chr6.simHuman.chr6 432899 38 - 601863 ATAT--ATGGTCATCTAGGCAATCTTAATAGCATAACATA -s simRat_chr6.simRat.chr6 167100 40 + 647215 ATATATATGACCTAGTAACCAATGTTGGTAATGTATCATA - -a -s simMouse_chr6.simMouse.chr6 169472 32 + 636262 GTATATATTATGAGGTTATTTCTATAAATCTA -s Anc0.Anc0refChr1 9736 20 + 62388 ------ACTATG------CTCAAATAAAGCTG -s Anc1.Anc1refChr2 10450 25 - 144309 ------ACTATGAGGG-ACTCAAATAAAGCTG -s Anc2.Anc2refChr3 10868 20 - 53186 ------ACTATG------CTCAAATAAAGCTG -s mr.mrrefChr5 32107 32 + 294540 GTATATATTATGAGGTTATTTCTATAAATCTA -s simCow_chr6.simCow.chr6 431704 17 - 602619 ---------GCG------CCCGAATAGAGCTG -s simDog_chr6.simDog.chr6 139848 20 + 593897 ------ACTATG------CTCAAATAAAGTTG -s simHuman_chr6.simHuman.chr6 432941 25 - 601863 ------ACTATGAGGG-ACTCACATAAAGCTG -s simRat_chr6.simRat.chr6 167144 32 + 647215 GTACATATTATGAGTTTTTGTCTATAAATCAA - -a -s simMouse_chr6.simMouse.chr6 169504 38 + 636262 TAGGTACAACTAGAAAACTACCTACAAAGTCAATACTT -s Anc0.Anc0refChr1 9756 38 + 62388 TAGGTACAACAAGAGAACTACCAACAAGGTCAGTCCTC -s Anc1.Anc1refChr2 10475 38 - 144309 TAGGTACAACAAGAGAACTACCAACAAGGTCAGTCCTC -s Anc2.Anc2refChr3 10888 38 - 53186 AAGGTACAACAAGAGAACTAGCAAAAAGGTCAGTCACC -s mr.mrrefChr5 32139 38 + 294540 TAGGTACAACTAGAGAACTACCTACAAAGTCAGTACTC -s simCow_chr6.simCow.chr6 431728 38 - 602619 AAGGTACAACAACAGAACTAGCTAAAGGGTTGGTTTCC -s simDog_chr6.simDog.chr6 139868 38 + 593897 AAGGCAGAACAGGGGAACTAGCAAAAAGGTCAGTCACC -s simHuman_chr6.simHuman.chr6 432966 38 - 601863 TAGGTACAACAATAGAACTACCAACAATGTCAGTCCTC -s simRat_chr6.simRat.chr6 167176 37 + 647215 T-GGTACAACTACAGAACTACCCACAAAGTCAGTACTC - -a -s simMouse_chr6.simMouse.chr6 169542 12 + 636262 AAATGTTGTGCC -s Anc0.Anc0refChr1 9795 12 + 62388 GGATATCGTGTC -s Anc1.Anc1refChr2 10514 12 - 144309 GGATATCGTGTC -s Anc2.Anc2refChr3 10927 12 - 53186 GGATATCGTGTC -s mr.mrrefChr5 32177 12 + 294540 AAATATTGTGTC -s simCow_chr6.simCow.chr6 431767 12 - 602619 GGATATTGTGTC -s simDog_chr6.simDog.chr6 139907 12 + 593897 GGATATCGTGTC -s simHuman_chr6.simHuman.chr6 433005 12 - 601863 GGATATCGTGTC -s simRat_chr6.simRat.chr6 167213 12 + 647215 AAATATTGTGTC - -a -s simMouse_chr6.simMouse.chr6 169554 11 + 636262 AAAATAAAGTA -s Anc0.Anc0refChr1 9808 11 + 62388 AAGGTAAAGTA -s Anc1.Anc1refChr2 10527 11 - 144309 AAGGTAAAGTA -s Anc2.Anc2refChr3 10940 11 - 53186 AAGGTAAAGTA -s mr.mrrefChr5 32189 11 + 294540 AAAGTAAAGTA -s simCow_chr6.simCow.chr6 431780 11 - 602619 AAGGTAAAGTG -s simDog_chr6.simDog.chr6 139920 11 + 593897 AAGGTAAAGTA -s simHuman_chr6.simHuman.chr6 433018 11 - 601863 AAGGTAAAGTT -s simRat_chr6.simRat.chr6 167225 11 + 647215 TAAGTAAAGTA - -a -s simMouse_chr6.simMouse.chr6 169565 34 + 636262 CATAGAGCTTTAAATATCAGAAGTACAACATCAG -s Anc0.Anc0refChr1 9819 34 + 62388 CATAGAGCTTTAAATATTAGAGGAACAAAACCAA -s Anc1.Anc1refChr2 10538 34 - 144309 CATAGAGCTTTAAATATTAGAGGAACAAAACCAA -s Anc2.Anc2refChr3 10951 34 - 53186 GATAGAGCTTTAAATATTAGAGGAACAAAACCAA -s mr.mrrefChr5 32200 34 + 294540 CATAGAGCTTTAAATATCAGAAGTACAACATCAG -s simCow_chr6.simCow.chr6 431791 34 - 602619 TCTGGATCTATTAATATTAGAGGAGCAAAACAGA -s simDog_chr6.simDog.chr6 139931 34 + 593897 GATAGAGCTTTAAAAGTTAGGGGAATAAAGCCAG -s simHuman_chr6.simHuman.chr6 433029 34 - 601863 CAGAGAGCTTTGATTATTAGATGATCAAAAACCA -s simRat_chr6.simRat.chr6 167240 34 + 647215 CATAGAGCTTTAAATATCAGAAGTACAACATCAG - -a -s simMouse_chr6.simMouse.chr6 169599 45 + 636262 GCTGGGAGTACTACACTTAGTTGAAAACTAACGGATAAGTCATAC -s Anc0.Anc0refChr1 9854 45 + 62388 GCTAGAAGTAGTAGACTTAGCTGAAAACTGACAGATAAGTCATAC -s Anc1.Anc1refChr2 10573 45 - 144309 GCTAGAAGTAGTAGACTTAGCTGAAAACTGACAGATAAGTCATAC -s Anc2.Anc2refChr3 10986 45 - 53186 GCTATAAGTAGTAGACTTAACTGAAAACTGACAGATAATTCATAC -s mr.mrrefChr5 32234 45 + 294540 GCTAGAAGTACTACACTTAGTTGAAAACTGACAGATAAGTCATAC -s simCow_chr6.simCow.chr6 431826 45 - 602619 GCTACAATTAGTAGATTTATTTGAAAACTGCTAGATAGAGCATAC -s simDog_chr6.simDog.chr6 139966 45 + 593897 GCGATATGCAGTAGTCTTAACTGAAAACTGACAGATGATTCACAC -s simHuman_chr6.simHuman.chr6 433064 45 - 601863 TCTAGAAGTAGTAGACTAGGCTATAAACAGACATATATGTCCTAC -s simRat_chr6.simRat.chr6 167274 45 + 647215 GCTAGAAGTACTACACTTAATTGAAAACTGACAGATAAGTCATAC - -a -s simMouse_chr6.simMouse.chr6 169644 58 + 636262 TGTATGCTGGTATAGTGCATTTTCGGCCATGCCAGGAATTTAGAGGTCATGGCCAGCT -s Anc0.Anc0refChr1 9899 56 + 62388 TGTACACTGGCATAATGCACTATCCACCATGCTGGGAAATTAG--TTTATGGTTGACT -s Anc1.Anc1refChr2 10618 58 - 144309 TGTACACTGGCATAATGCACTATCCACCATGCTGGGAAATTAGGGTTTATGGTTGACT -s Anc2.Anc2refChr3 11031 56 - 53186 TGTACACTGGCATAATGCACTATCCACCATGCTGGGAAACTAG--TTTATAGTTGACT -s mr.mrrefChr5 32279 58 + 294540 TGTATGCTGGTATAGTGCATTTTCGGCCATGCTGGGAAATTAGAGGTCATGGCCAGCT -s simCow_chr6.simCow.chr6 431871 56 - 602619 TGTACACTGGCATATTGCAACATCCACCATGCTGGGGAAGTAG--ATCATCGTTGGCT -s simDog_chr6.simDog.chr6 140013 56 + 593897 TTTACACTGGCATAATGCACTATCCTCCATGCTGGGAAACTAG--TTTACAGTCGACT -s simHuman_chr6.simHuman.chr6 433109 58 - 601863 TGTACACTGGCATAATGCACTATCCACCATGCTGGGAAATTAGGGCTTGTGGTTGACT -s simRat_chr6.simRat.chr6 167319 58 + 647215 TGTATGCTTGTATAGTGCATCGTCTGCCATGCTGGAAAATTGGAGGTCATGGCCCGCT - -a -s simMouse_chr6.simMouse.chr6 169702 12 + 636262 TTTTCTTTTGTG -s Anc0.Anc0refChr1 9955 12 + 62388 CCTCCTTTTGTG -s Anc1.Anc1refChr2 10676 12 - 144309 CCTCCTTTTGTG -s Anc2.Anc2refChr3 11087 12 - 53186 TCTCCTTTTGTG -s mr.mrrefChr5 32337 12 + 294540 CTTTCTTTTGTG -s simCow_chr6.simCow.chr6 431927 11 - 602619 GCTT-TTCTATG -s simDog_chr6.simDog.chr6 140069 12 + 593897 TCTCCTTTTGTG -s simHuman_chr6.simHuman.chr6 433167 12 - 601863 CCTCCTTTTGTG -s simRat_chr6.simRat.chr6 167381 12 + 647215 CTTTCTTTTGTA - -a -s simMouse_chr6.simMouse.chr6 169714 3 + 636262 GCA -s Anc0.Anc0refChr1 9967 3 + 62388 GCA -s Anc1.Anc1refChr2 10688 3 - 144309 GCA -s Anc2.Anc2refChr3 11099 3 - 53186 GCA -s mr.mrrefChr5 32349 3 + 294540 GCA -s simCow_chr6.simCow.chr6 431938 3 - 602619 ACA -s simDog_chr6.simDog.chr6 140081 3 + 593897 GCA -s simHuman_chr6.simHuman.chr6 433406 3 - 601863 GCA -s simRat_chr6.simRat.chr6 167393 3 + 647215 GCA - -a -s simMouse_chr6.simMouse.chr6 169717 7 + 636262 TCTTGGG -s Anc0.Anc0refChr1 9970 7 + 62388 TCTTGGG -s Anc1.Anc1refChr2 10691 7 - 144309 TCTTGGG -s Anc2.Anc2refChr3 11102 7 - 53186 TCTTGGG -s mr.mrrefChr5 32352 7 + 294540 TCTTGGG -s simCow_chr6.simCow.chr6 431941 7 - 602619 TCCTGGG -s simDog_chr6.simDog.chr6 140084 7 + 593897 TCTTGGG -s simHuman_chr6.simHuman.chr6 433409 7 - 601863 CCTTGGG -s simRat_chr6.simRat.chr6 167398 7 + 647215 TCCTGGG - -a -s simMouse_chr6.simMouse.chr6 169724 60 + 636262 AAAAACAACAACTGCCAAGGGGGGGTAAATTATAAATCCCTTGAGCACCATACATAACCA -s Anc0.Anc0refChr1 9979 57 + 62388 AAACACAAAAGCTACCCTGGGGGGGTCAGTTGTGAATCCCTTGAGTAT---ATATTACCA -s Anc1.Anc1refChr2 10700 57 - 144309 AAACACAAAAGCTACCCTGGGGGGGTCAGTTGTGAATCCCTTGAGTAT---ATATTACCA -s Anc2.Anc2refChr3 11111 57 - 53186 AAACACAAAAGCTACCCTGGGGGGGTCAGTTGTGAGTCCCTTGAGTAT---ATATTACCA -s mr.mrrefChr5 32359 60 + 294540 AAAAACAACAACTGCCAAGGGGGGGTAAATTATGAATCCCTTGAGCATCATACATAACCA -s simCow_chr6.simCow.chr6 431951 57 - 602619 AATCACAAAAGCTGCCCTGGGGTCGTCAGTCATGAGTCCCTTGGATAT---ATGTTATCA -s simDog_chr6.simDog.chr6 140093 50 + 593897 AAACACTAAAGCTACCCTGGGGGGGTCAGTTGT-------TTGAGTAT---ATATTACCA -s simHuman_chr6.simHuman.chr6 433418 52 - 601863 AAGCACAA-----ACCCTGAAGGGGTCAGTTGTGAATGCACTGAGTAT---ATATTACCA -s simRat_chr6.simRat.chr6 167405 60 + 647215 AAGAACAACAACTGCCAAGGGGGGCTGGATTATGAATCCCTTGAGCATCATAAATGACCA - -a -s simMouse_chr6.simMouse.chr6 169784 29 + 636262 TCCCACCATTCCGGCTATTAGATATCAAC -s Anc0.Anc0refChr1 10037 18 + 62388 TCCAACTATT--AATTATT---------C -s Anc1.Anc1refChr2 10758 27 - 144309 TCCAACTATT--AATTATTAGGTATCAAC -s Anc2.Anc2refChr3 11169 18 - 53186 CCCAACTATT--AATTATT---------C -s mr.mrrefChr5 32419 29 + 294540 TCCAACCATTCCAGTTATTAGGTATCAAC -s simCow_chr6.simCow.chr6 432009 17 - 602619 CCCAACTATT--CATTAT----------C -s simDog_chr6.simDog.chr6 140144 18 + 593897 CCCAACTATT--AGGCATT---------C -s simHuman_chr6.simHuman.chr6 433471 27 - 601863 TCTAATTATT--AATTATTAGGTATCAAC -s simRat_chr6.simRat.chr6 167465 29 + 647215 TCCAAGCATTCCAGTGATTAGGTATCAAC - -a -s simMouse_chr6.simMouse.chr6 169813 24 + 636262 TTTGCCTTTTCTCATCTTGTATTC -s Anc0.Anc0refChr1 10064 23 + 62388 TTTACCTGTGCTCATCT-GTATTT -s Anc1.Anc1refChr2 10794 23 - 144309 TTTACCTGTGCTCATCT-GTATTT -s Anc2.Anc2refChr3 11196 23 - 53186 TTTACCTGTGCCCATCG-GTATTT -s mr.mrrefChr5 32448 24 + 294540 TTTGCCTTTGCTCATCTTGTATTC -s simCow_chr6.simCow.chr6 432035 23 - 602619 TTTGCCCATGCCCATCC-GTATTT -s simDog_chr6.simDog.chr6 140171 23 + 593897 TTTACCTGATCCCATTG-GTATTC -s simHuman_chr6.simHuman.chr6 433507 23 - 601863 CTGACCTGTGCTCAACT-GAACTT -s simRat_chr6.simRat.chr6 167494 24 + 647215 ATTGTGCTCGCTCTTCTTGTATTC - -a -s simMouse_chr6.simMouse.chr6 169837 12 + 636262 CTCTTGAACACT -s Anc0.Anc0refChr1 10087 12 + 62388 CTCTTGAACACT -s Anc1.Anc1refChr2 10817 12 - 144309 CTCTTGAACACT -s Anc2.Anc2refChr3 11219 12 - 53186 CTCTTGAACCCT -s mr.mrrefChr5 32472 12 + 294540 CTCTTGAACACT -s simCow_chr6.simCow.chr6 432059 12 - 602619 CTCGTGAACCCA -s simDog_chr6.simDog.chr6 140194 12 + 593897 CTCTCGAACCCT -s simHuman_chr6.simHuman.chr6 433530 12 - 601863 CTCTTGAACACT -s simRat_chr6.simRat.chr6 167518 12 + 647215 ATCCTGAACACT - -a -s simMouse_chr6.simMouse.chr6 169849 57 + 636262 TTTACACCATCCTGACAGCCTTTGAATTTAACAGACAGGCATTCTAGACAGCCTTTC -s Anc0.Anc0refChr1 10099 22 + 62388 TGCAGGCAATCTGGAC-----------------------------------CCTTTT -s Anc1.Anc1refChr2 10829 57 - 144309 TGCAGGCAATCTGGACGGCCTTCCAATCAGACTTGCAAGCAATCTTGACAGCCTTTT -s Anc2.Anc2refChr3 11231 22 - 53186 TGCAGGCAGTCTGGAC-----------------------------------CTTTTG -s mr.mrrefChr5 32484 57 + 294540 TTTACACCATCCTGACAGCCTTTGAATTTAACAGACAGGCAATCTAGACAGCCTTTT -s simCow_chr6.simCow.chr6 432072 22 - 602619 TGCAGGCAGTCTGGTC-----------------------------------GGTTTA -s simDog_chr6.simDog.chr6 140206 22 + 593897 TGCAGGCAGACTGTAC-----------------------------------CTTTTG -s simHuman_chr6.simHuman.chr6 433542 57 - 601863 TGCAGGCAATCTGGACGGCCTTCCAATCAGACTTGCAAGCAATCTTGACAGCCTTAT -s simRat_chr6.simRat.chr6 167530 56 + 647215 TTTACACCATCCTGATCACCTTTGAATTGAA-AGACAGCCAATCTGGACAGACTCTT - -a -s simMouse_chr6.simMouse.chr6 169906 13 + 636262 GATCAGAATGGAA -s Anc0.Anc0refChr1 10121 13 + 62388 AGCCAAAATGGAA -s Anc1.Anc1refChr2 10886 13 - 144309 AGCCAAAATGGAA -s Anc2.Anc2refChr3 11253 13 - 53186 AGCCAAAATGGAA -s mr.mrrefChr5 32541 13 + 294540 AACCAGAATGGAA -s simCow_chr6.simCow.chr6 432097 13 - 602619 AGCCGAAATAGAA -s simDog_chr6.simDog.chr6 140228 13 + 593897 AGCCAAAATGGAA -s simHuman_chr6.simHuman.chr6 433599 11 - 601863 --CAAAAATGGAA -s simRat_chr6.simRat.chr6 167586 13 + 647215 AACCAGGATGGAA - -a -s simMouse_chr6.simMouse.chr6 169919 5 + 636262 ACAAT -s Anc0.Anc0refChr1 10134 5 + 62388 AGAAT -s Anc1.Anc1refChr2 10899 5 - 144309 AGAAT -s Anc2.Anc2refChr3 11266 5 - 53186 AGATT -s mr.mrrefChr5 32554 5 + 294540 ACAAT -s simCow_chr6.simCow.chr6 432110 5 - 602619 AAATA -s simDog_chr6.simDog.chr6 140241 5 + 593897 AGATT -s simHuman_chr6.simHuman.chr6 433610 5 - 601863 AGAAT -s simRat_chr6.simRat.chr6 167607 5 + 647215 ACAAC - -a -s simMouse_chr6.simMouse.chr6 169924 12 + 636262 TTAAAGCAAGTA -s Anc0.Anc0refChr1 10139 12 + 62388 ACAAAGCAAGTA -s Anc1.Anc1refChr2 10904 12 - 144309 ACAAAGCAAGTA -s Anc2.Anc2refChr3 11272 12 - 53186 ACAAAGCAAGTA -s mr.mrrefChr5 32559 12 + 294540 TTAAAGCAAGTA -s simCow_chr6.simCow.chr6 432116 12 - 602619 ACAAAACAAGTC -s simDog_chr6.simDog.chr6 140247 12 + 593897 GCAAAGCAAGTA -s simHuman_chr6.simHuman.chr6 433615 12 - 601863 ACAAATTGCGTA -s simRat_chr6.simRat.chr6 167612 12 + 647215 TTAAAGCAAATA - -a -s simMouse_chr6.simMouse.chr6 169936 54 + 636262 GATGGTTTGCTGTTGAGAGCTTTGACACCACAGAGCAAGAGGAAATTAAGCTGT -s Anc0.Anc0refChr1 10151 14 + 62388 GAGAGTTT----------------------------------------AGCTGT -s Anc1.Anc1refChr2 10916 14 - 144309 GAGAGTTT----------------------------------------AGCTGT -s Anc2.Anc2refChr3 11284 14 - 53186 CAGATTTT----------------------------------------AGCTGT -s mr.mrrefChr5 32571 54 + 294540 GATAGTTTGCTGTTGAGAGCTTTGACACCACAGAGCAAGAGGAAATTAAGCTGT -s simCow_chr6.simCow.chr6 432128 6 - 602619 TAGGTT------------------------------------------------ -s simDog_chr6.simDog.chr6 140259 14 + 593897 CAGATTTT----------------------------------------AGCTGT -s simHuman_chr6.simHuman.chr6 433627 14 - 601863 GAGAGTTT----------------------------------------AGCTGT -s simRat_chr6.simRat.chr6 167628 54 + 647215 GATAGTTTTCTGTTGAAAGCTTTAACATCAGAAAGCAAGACAAAATTAAGCTGT - -a -s simMouse_chr6.simMouse.chr6 169990 26 + 636262 TTAGAACTTTAACCATTAGGGCAAGC -s Anc0.Anc0refChr1 10165 26 + 62388 TGAGAACTTTAGCTGTTAGGGCAAGC -s Anc1.Anc1refChr2 10930 26 - 144309 TGAGAACTTTAGCTGTTAGGGCAAGC -s Anc2.Anc2refChr3 11298 26 - 53186 TGAGAAATTTAGCTGTGAGGGCAAGC -s mr.mrrefChr5 32625 26 + 294540 TTAGAACTTTAGCCATTAGGGCAAGC -s simCow_chr6.simCow.chr6 432134 21 - 602619 -----AGCTTAACTGTAAGGGCAAGC -s simDog_chr6.simDog.chr6 140275 26 + 593897 TGAGAAATTTAGCTGTGAGAGCAAGC -s simHuman_chr6.simHuman.chr6 433641 26 - 601863 TGAGAACTTTAGCTGATAGGGCAACC -s simRat_chr6.simRat.chr6 167682 13 + 647215 TTAGAACTTTAGC------------- - -a -s simMouse_chr6.simMouse.chr6 170016 61 + 636262 TTAAAATTAAGGCAAGCTTAAAGGAATAGAGGCTCAAGAATGCAGTTAGTAAGTTGAGTCA -s Anc0.Anc0refChr1 10191 44 + 62388 TTAAAA----G-------------AATAGGGGCCCAAGAACACAGTTAGTAAGTTAAGTAA -s Anc1.Anc1refChr2 10956 44 - 144309 TTAAAA----G-------------AATAGGGGCCCAAGAACACAGTTAGTAAGTTAAGTAA -s Anc2.Anc2refChr3 11324 44 - 53186 TTAAAA----G-------------AATAGGGGCCCAAGAACAAAGTTCGTAAGCTAAGTTT -s mr.mrrefChr5 32651 57 + 294540 TTAAAA----GGCAAGCTTAAAGGAATAGAGGCCCAAGAATGCAGTTAGTAAGTTGAGTAA -s simCow_chr6.simCow.chr6 432156 43 - 602619 ATAAGT----G-------------GACAGGGGCC-AAGGACAGATTCGGTAAGCTAAGTTT -s simDog_chr6.simDog.chr6 140301 36 + 593897 TTAAAA----G-------------AATAGGGGCCCAAGAACAATGTTCGTATG-------- -s simHuman_chr6.simHuman.chr6 433667 44 - 601863 CTAAAA----G-------------AATAGGGGCCCAAGAGCACAGTTAGTAAGTTCAGTAA -s simRat_chr6.simRat.chr6 167695 51 + 647215 ----------ACCAAGCTTAAAGCAATAGAGGTCCAAGAATGCAGTTAGTAAGTTGAGTAA - -a -s simMouse_chr6.simMouse.chr6 170077 47 + 636262 AGCACGGAAACAAGATATAGGTCCAAATGAAAATTTATCTATCGAAT -s Anc0.Anc0refChr1 10235 38 + 62388 AGAAAGGAAGCAGGATATAGGTCCAAGTAAAAGTCAAT--------- -s Anc1.Anc1refChr2 11000 38 - 144309 AGAAAGGAAGCAGGATATAGGTCCAAGTAAAAGTCAAT--------- -s Anc2.Anc2refChr3 11368 38 - 53186 AGAAAGGATTTGGGATATAGGCCCAAGTAGGAGTCAAT--------- -s mr.mrrefChr5 32708 47 + 294540 AGCAAGGAAGCAAGATATAGGTCCAAGTGAAAATTTATCTATCGAAT -s simCow_chr6.simCow.chr6 432199 38 - 602619 AGAAAGGATTTGGGAAATAGGCCCAAGTAGGAGTCAAT--------- -s simDog_chr6.simDog.chr6 140337 26 + 593897 ------------GAGTATAGGCCCAAGTAGGAGCCAAT--------- -s simHuman_chr6.simHuman.chr6 433717 38 - 601863 AGAAAGGAAGCAGGATATGGGTCCAAGTAAAAGTCAAT--------- -s simRat_chr6.simRat.chr6 167746 47 + 647215 AGGAAGGAAGCAAAATTTAGGTCCAAGTGAAAATTTATCTAGTGAGT - -a -s simMouse_chr6.simMouse.chr6 170124 23 + 636262 GATTACTAACCAGGGGAGATGTG -s Anc0.Anc0refChr1 10273 18 + 62388 -ATTGCTGCCT----GAGTGGTA -s Anc1.Anc1refChr2 11038 18 - 144309 -ATTGCTGCCT----GAGTGGTA -s Anc2.Anc2refChr3 11406 18 - 53186 -ATAGCTGCCT----GAGTGGTA -s mr.mrrefChr5 32755 23 + 294540 GATTACTAACCAGGGGAGATGTG -s simCow_chr6.simCow.chr6 432237 11 - 602619 -ATAGCTGCCT----G------- -s simDog_chr6.simDog.chr6 140363 18 + 593897 -ATAGCTGTCT----GAGTGGTA -s simHuman_chr6.simHuman.chr6 433755 18 - 601863 -ATTGCTGCCT----GAGTGGCA -s simRat_chr6.simRat.chr6 167794 21 + 647215 GA--ACCAACCAGGGGAGATGTG - -a -s simMouse_chr6.simMouse.chr6 170147 7 + 636262 AGCATAG -s Anc0.Anc0refChr1 10291 7 + 62388 ACAACCA -s Anc1.Anc1refChr2 11056 7 - 144309 ACAACCA -s Anc2.Anc2refChr3 11424 7 - 53186 ACAACCA -s mr.mrrefChr5 32778 7 + 294540 AGAATCA -s simCow_chr6.simCow.chr6 432433 3 - 602619 ----TGA -s simDog_chr6.simDog.chr6 140387 7 + 593897 ACAACCA -s simHuman_chr6.simHuman.chr6 433773 7 - 601863 ACAACCA -s simRat_chr6.simRat.chr6 167815 7 + 647215 AGAATCA - -a -s simMouse_chr6.simMouse.chr6 170154 1 + 636262 C -s Anc0.Anc0refChr1 10299 1 + 62388 C -s Anc1.Anc1refChr2 11064 1 - 144309 C -s Anc2.Anc2refChr3 11432 1 - 53186 C -s mr.mrrefChr5 32785 1 + 294540 C -s simCow_chr6.simCow.chr6 432437 1 - 602619 G -s simDog_chr6.simDog.chr6 140395 1 + 593897 C -s simHuman_chr6.simHuman.chr6 433781 1 - 601863 C -s simRat_chr6.simRat.chr6 167822 1 + 647215 C - -a -s simMouse_chr6.simMouse.chr6 170155 30 + 636262 TTCATATCATAGGACAACCCAACCGGGTTA -s Anc0.Anc0refChr1 10300 26 + 62388 TTTTTATTACTGGGCAACTT----TGTATA -s Anc1.Anc1refChr2 11065 26 - 144309 TTTTTATTACTGGGCAACTT----TGTATA -s Anc2.Anc2refChr3 11456 26 - 53186 TTTTTATGACTGGGCATCTT----TATATG -s mr.mrrefChr5 32786 26 + 294540 TTCATATTATTGGACAACTT----GGGTTA -s simCow_chr6.simCow.chr6 432461 21 - 602619 TTTTCATCACTGGGC---------TAGATG -s simDog_chr6.simDog.chr6 140430 26 + 593897 TGTTTATGATTGGACATCTT----CATATG -s simHuman_chr6.simHuman.chr6 433782 26 - 601863 TTTCTATTACTGGGCAACTT----TGTATA -s simRat_chr6.simRat.chr6 167823 26 + 647215 TTGGCATTATTGGACAGCTT----GAGTTA - -a -s simMouse_chr6.simMouse.chr6 170185 3 + 636262 CCA -s Anc0.Anc0refChr1 10326 3 + 62388 GTA -s Anc1.Anc1refChr2 11091 3 - 144309 GTA -s Anc2.Anc2refChr3 11482 3 - 53186 GTA -s mr.mrrefChr5 32812 3 + 294540 CCA -s simCow_chr6.simCow.chr6 432482 3 - 602619 GTA -s simDog_chr6.simDog.chr6 140456 3 + 593897 GTA -s simHuman_chr6.simHuman.chr6 433808 3 - 601863 GTA -s simRat_chr6.simRat.chr6 167854 3 + 647215 CCA - -a -s simMouse_chr6.simMouse.chr6 170188 44 + 636262 CTTCATATTATGTGTCTGTATCTTTGATTTGCAAGAATAGTGTT -s Anc0.Anc0refChr1 10329 42 + 62388 TCTC-TAGTTTGTAGCTTTAACATAG-TTTGCAAGAATGGTAGC -s Anc1.Anc1refChr2 11094 42 - 144309 TCTC-TAGTTTGTAGCTTTAACATAG-TTTGCAAGAATGGTAGC -s Anc2.Anc2refChr3 11486 42 - 53186 TCTC-TAGTTTGTAGCTTTGAGATAG-TTTACAAGAATGGTAGC -s mr.mrrefChr5 32815 44 + 294540 CTTCATATTATGTGTCTGTATCTTTGATTTGCAAGAATAGTGTT -s simCow_chr6.simCow.chr6 432486 40 - 602619 TCCT---GTTTGTAGCCTTGAGATAG-TTCACAAGGATGGTAGC -s simDog_chr6.simDog.chr6 140460 42 + 593897 TTTC-TAGTTGGTAGCTTTGAGATAG-TTTACAAGAATGGTAGG -s simHuman_chr6.simHuman.chr6 433811 42 - 601863 TCTC-TAGCTTGTAGCTTTAACATAG-TTTGTAAGAATGGTAGC -s simRat_chr6.simRat.chr6 167857 44 + 647215 CTACATATTATGTGTCTGTACCTTTGATTTGCAAGAATAGCGTT - -a -s simMouse_chr6.simMouse.chr6 170232 99 + 636262 TCCTAAGAGTGGCTGCCTTCTAAGAGCCCTCCTCAAATGGATGTTATCCAGCAAGAGCGAACGAATTGAGAACATTGTGCATCCTGAAGAGAAACAGAA -s Anc0.Anc0refChr1 10373 97 + 62388 TCCTAAGAGTGGTAGCTTCCTGGAGGTCCTCCTCAAATAAATGTTGTACAGCAAGAGTGCATGTGTTTAAAAAAATGTGCATCCTGTAAAGGAAAT-A- -s Anc1.Anc1refChr2 11138 98 - 144309 TCCTAAGAGTGGTAGCTTCCTGGAGGTCCTCCTCAAATAAATGTTGTACAGCAAGAGTGCATGTGTTTAAAAAAATGTGCATCCTGTAAAGGAAATTA- -s Anc2.Anc2refChr3 11530 97 - 53186 TCCCAAGAGTGGTAGCTTCCTGGAGGTCCTCCTCAAGTAAATGTTGTACAGAAAGAGTGAATGTGTTTGAAAAAAAGTGTACCCTGTAAGAGAAAT-A- -s mr.mrrefChr5 32859 99 + 294540 TCCTAAGAGTGGCTGCCTTCTGAGAGCCCTCCTCAAATGGATGTTATACAGCAAGAGTGCATGAGTTGAAAACATTGTGCATCCTGAAGAGAAAAAGAA -s simCow_chr6.simCow.chr6 432527 92 - 602619 TCCAAAGAGTGTTGGCTTCCTGGAGGTCCTTCTCAATAAATTGTTGAACAGAAAGAGTGAATCTATTTGAAAACAC-----CCCCATAAGAGAAAT-A- -s simDog_chr6.simDog.chr6 140504 97 + 593897 CCCCAAAAGTGGTAGCTTTCTGGAGGTCCTCTTCAAGTAAATGTTGTACAGAAAGAGTGAATGTGTTTGAAACACAGTGTACCATGTAAGAGAAAT-A- -s simHuman_chr6.simHuman.chr6 433855 96 - 601863 TCCTATGAGTGGGACCTTCCTGGAGGTCCCCCTTAAATAAGTGTGGTACAGCAAGAGTGCATGTGTTAAAAA--ATGTGCATCCTGTAAAGGAAATTA- -s simRat_chr6.simRat.chr6 167901 99 + 647215 TTCTAAGAATGGTTGCCTTCTGAGAGCCCTCCTGAAATGGATGTTATACAGAAAGACTGCATGAGTCGAAAACATTGTGCATCCCGAGTAGAAAAGGAA - -a -s simMouse_chr6.simMouse.chr6 170331 55 + 636262 GATTATGGAAATTAAACTGTCAAATAGCAGTGTAGACACAGAAACTACTGCTAAT -s Anc0.Anc0refChr1 10473 55 + 62388 GATTATTGAAATCAAACTGTGGAATTGCAGGGTAAGAATACAAACTACCACATGT -s Anc1.Anc1refChr2 11239 55 - 144309 GATTATTGAAATCAAACTGTGGAATTGCAGGGTAAGAATACAAACTACCACATGT -s Anc2.Anc2refChr3 11630 55 - 53186 GATTATTGAAATCAAACTGTGGAATTGCAAGGTAAGAATACAAACTACCACATGT -s mr.mrrefChr5 32961 55 + 294540 GATTATGGAAATTAAACTGTCAAATTGCAGTGTAGACATAGAAACTACTGCAAAT -s simCow_chr6.simCow.chr6 432626 55 - 602619 GATTATTGAAATCAATCTGTAGATTTGCAAGGTAAGAATACTAACTAGCATATAC -s simDog_chr6.simDog.chr6 140604 54 + 593897 GGTTACTGAAATTAAACTGTGGAAT-GTAAGGTAAGAACACAAACTACCACATGT -s simHuman_chr6.simHuman.chr6 433954 55 - 601863 GATTATTGAAATCAAACTGTGGAATTGCAGGGCAAGAATATGAATTACCACATGT -s simRat_chr6.simRat.chr6 168003 55 + 647215 GATTATGGAAATTAAACAATCAAATTGTAGTGTAGACATAGAAACTGCTGCAAAC - -a -s simMouse_chr6.simMouse.chr6 170386 8 + 636262 CTTCAGAT -s Anc0.Anc0refChr1 10528 8 + 62388 CTTTGGAT -s Anc1.Anc1refChr2 11294 8 - 144309 CTTTGGAT -s Anc2.Anc2refChr3 11685 8 - 53186 CTTTGGAT -s mr.mrrefChr5 33016 8 + 294540 CTTCAGAT -s simCow_chr6.simCow.chr6 432681 8 - 602619 CTTTGGAT -s simDog_chr6.simDog.chr6 140663 8 + 593897 CTTCAAAT -s simHuman_chr6.simHuman.chr6 434009 8 - 601863 CTTTGGAT -s simRat_chr6.simRat.chr6 168058 8 + 647215 CTTCAGAT - -a -s simMouse_chr6.simMouse.chr6 170394 97 + 636262 CTGATGTGGTCCACTAATCAATACACCTACAATCTACTTCTCTAACTAATCCGGCCCCTTGCAGTGCACAAATACAAATTACTGCAATCTTAGATGA -s Anc0.Anc0refChr1 10536 2 + 62388 C-----------------------------------------------------------------------------------------------A -s Anc1.Anc1refChr2 11302 2 - 144309 C-----------------------------------------------------------------------------------------------A -s Anc2.Anc2refChr3 11693 2 - 53186 A-----------------------------------------------------------------------------------------------A -s mr.mrrefChr5 33024 97 + 294540 CTGATGTGGTCCACTAATCAATACACCTACAATCTACTTCTCTAACTAATCCGGCCCCTTGCAGTGCACAAATACAAATTACTGCAATCTTAGATGA -s simCow_chr6.simCow.chr6 432689 2 - 602619 G-----------------------------------------------------------------------------------------------A -s simDog_chr6.simDog.chr6 140671 2 + 593897 A-----------------------------------------------------------------------------------------------A -s simHuman_chr6.simHuman.chr6 434017 2 - 601863 C-----------------------------------------------------------------------------------------------A -s simRat_chr6.simRat.chr6 168072 97 + 647215 CTGATGTTTTCCACTAATCGATACACCTACAACCAATTTCTCTAATTAATCTGGCCCCTTGCAGTACACAAATACAAACTACTGCAATTTCAGATGA - -a -s simMouse_chr6.simMouse.chr6 170491 12 + 636262 ACCACTGGCTAC -s Anc0.Anc0refChr1 10538 12 + 62388 GCCATTAACTGT -s Anc1.Anc1refChr2 11304 12 - 144309 GCCATTAACTGT -s Anc2.Anc2refChr3 11695 12 - 53186 GCCATTAACTGT -s mr.mrrefChr5 33121 12 + 294540 ACCACTGGCTGT -s simCow_chr6.simCow.chr6 432691 12 - 602619 ACTGTTAACTGT -s simDog_chr6.simDog.chr6 140684 12 + 593897 GGCATTAACGAT -s simHuman_chr6.simHuman.chr6 434019 12 - 601863 GCCATTAACTGT -s simRat_chr6.simRat.chr6 168169 12 + 647215 ACCACTGGCTGT - -a -s simMouse_chr6.simMouse.chr6 170503 6 + 636262 AGTCCA -s Anc0.Anc0refChr1 10550 6 + 62388 TGGCTG -s Anc1.Anc1refChr2 11316 6 - 144309 TGGCTG -s Anc2.Anc2refChr3 11707 6 - 53186 TGGCTG -s mr.mrrefChr5 33133 6 + 294540 AGTCCA -s simCow_chr6.simCow.chr6 432703 6 - 602619 TGGCTG -s simDog_chr6.simDog.chr6 140702 6 + 593897 TGGATG -s simHuman_chr6.simHuman.chr6 434031 6 - 601863 TGGCTG -s simRat_chr6.simRat.chr6 168181 6 + 647215 AGTCCA - -a -s simMouse_chr6.simMouse.chr6 170509 10 + 636262 CTGATTAATG -s Anc0.Anc0refChr1 10556 10 + 62388 CTAATCAATA -s Anc1.Anc1refChr2 11322 10 - 144309 CTAATCAATA -s Anc2.Anc2refChr3 11713 10 - 53186 CTAATCAATA -s mr.mrrefChr5 33139 10 + 294540 CTAATTAATG -s simCow_chr6.simCow.chr6 432709 9 - 602619 C-AATCAATA -s simDog_chr6.simDog.chr6 140719 10 + 593897 CTAATCAATA -s simHuman_chr6.simHuman.chr6 434037 10 - 601863 CTAATCAATA -s simRat_chr6.simRat.chr6 168187 10 + 647215 CTAATTAATG - -a -s simMouse_chr6.simMouse.chr6 170519 21 + 636262 TGTCTACAACCTAATTCTCTA -s Anc0.Anc0refChr1 10566 16 + 62388 TGTC-AAGA----GTCCACTA -s Anc1.Anc1refChr2 11332 16 - 144309 TGTC-AAGA----GTCCACTA -s Anc2.Anc2refChr3 11723 16 - 53186 TGTC-AAGA----ATCCACTA -s mr.mrrefChr5 33149 17 + 294540 TGTCTACGA----GTTCTCTA -s simCow_chr6.simCow.chr6 432718 16 - 602619 TGCC-AATA----ATCCACTT -s simDog_chr6.simDog.chr6 140729 16 + 593897 TGTC-AGGA----AACCACTA -s simHuman_chr6.simHuman.chr6 434047 16 - 601863 TGTC-AAGA----GTCCACGT -s simRat_chr6.simRat.chr6 168198 17 + 647215 TATCTACGT----GTTTCCTA - -a -s simMouse_chr6.simMouse.chr6 170540 23 + 636262 ATTGATCCTGCTTTAAAGAAGAA -s Anc0.Anc0refChr1 10582 23 + 62388 ATTGATCCTGCCTTAGAGTAGAG -s Anc1.Anc1refChr2 11348 23 - 144309 ATTGATCCTGCCTTAGAGTAGAG -s Anc2.Anc2refChr3 11744 23 - 53186 ATTGATTCTGCCTTAGAGTAGAG -s mr.mrrefChr5 33166 23 + 294540 ATTGATCCTGCCTTAAAGAAGAA -s simCow_chr6.simCow.chr6 432739 22 - 602619 ACTGATTCTGTCTTTGAGT-GAG -s simDog_chr6.simDog.chr6 140750 22 + 593897 ATTGGT-CTGCCTTAGAGTAGAG -s simHuman_chr6.simHuman.chr6 434063 23 - 601863 CTTGATCCTACCTTAGTGTAGAG -s simRat_chr6.simRat.chr6 168215 23 + 647215 ATTGATCCTGCCTTAAAGAAGAA - -a -s simMouse_chr6.simMouse.chr6 170563 11 + 636262 AAAGCACGGCT -s Anc0.Anc0refChr1 10643 11 + 62388 AAAGCAAATCA -s Anc1.Anc1refChr2 11409 11 - 144309 AAAGCAAATCA -s Anc2.Anc2refChr3 11805 11 - 53186 AAAGCAAATCA -s mr.mrrefChr5 33189 11 + 294540 AAAGCACAGCC -s simCow_chr6.simCow.chr6 432811 11 - 602619 AAAACAAATCA -s simDog_chr6.simDog.chr6 140811 11 + 593897 AAAGCAAATCA -s simHuman_chr6.simHuman.chr6 434124 11 - 601863 AAAGCAAATTA -s simRat_chr6.simRat.chr6 168238 11 + 647215 AAAGAACAGCC - -a -s simMouse_chr6.simMouse.chr6 170574 20 + 636262 AATAGTAACATCTCCTAGTG -s Anc0.Anc0refChr1 10660 20 + 62388 AATAGTAATGACCCCTACTG -s Anc1.Anc1refChr2 11426 20 - 144309 AATAGTAATGACCCCTACTG -s Anc2.Anc2refChr3 11822 20 - 53186 AATAGCAATGACCCCTACTG -s mr.mrrefChr5 33200 20 + 294540 AATAGTAACAACCCCTAGTG -s simCow_chr6.simCow.chr6 432827 20 - 602619 AATAGCAATAACCCCTGCCG -s simDog_chr6.simDog.chr6 140828 20 + 593897 ACCAGCAATGGCCCATACTG -s simHuman_chr6.simHuman.chr6 434141 20 - 601863 AATGGTAATGATCCCTACTG -s simRat_chr6.simRat.chr6 168249 20 + 647215 AATAGTAACAACCCCTAGTG - -a -s simMouse_chr6.simMouse.chr6 170594 14 + 636262 AGAACCACCACAAA -s Anc0.Anc0refChr1 10680 14 + 62388 ATCACCATCACTAA -s Anc1.Anc1refChr2 11446 14 - 144309 ATCACCATCACTAA -s Anc2.Anc2refChr3 11842 14 - 53186 ATCACCATCACTAA -s mr.mrrefChr5 33220 14 + 294540 ATAACCATCACAAA -s simCow_chr6.simCow.chr6 432848 14 - 602619 ATCACCATCACTAA -s simDog_chr6.simDog.chr6 140848 14 + 593897 AGGACCATCACTAA -s simHuman_chr6.simHuman.chr6 434161 14 - 601863 ATCACCATCACTAA -s simRat_chr6.simRat.chr6 168269 14 + 647215 ATAACCATCACAAA - -a -s simMouse_chr6.simMouse.chr6 170608 22 + 636262 GTTTGGGGATTGAGTGCCCCCT -s Anc0.Anc0refChr1 10694 22 + 62388 AATTGGAGATGGAGTGCCATCT -s Anc1.Anc1refChr2 11460 22 - 144309 AATTGGAGATGGAGTGCCATCT -s Anc2.Anc2refChr3 11856 22 - 53186 AATTGTAGATGCAGGGCCATCT -s mr.mrrefChr5 33234 22 + 294540 ATTTGGAGATGGAGTGCCCCCT -s simCow_chr6.simCow.chr6 432862 22 - 602619 AATTGTAGAGGCAGGACCATCT -s simDog_chr6.simDog.chr6 140863 22 + 593897 AATTGTAGATGCAGGGCCATCT -s simHuman_chr6.simHuman.chr6 434175 16 - 601863 AATTGGAGCAGGCCTG------ -s simRat_chr6.simRat.chr6 168283 22 + 647215 ATTTGGAGATGGTGTGCCCCCT - -a -s simMouse_chr6.simMouse.chr6 170630 18 + 636262 TCTTGCATGAGAGCCCCC -s Anc0.Anc0refChr1 10716 12 + 62388 TCCTGCAAA------TCC -s Anc1.Anc1refChr2 11482 12 - 144309 TCCTGCAAA------TCC -s Anc2.Anc2refChr3 11880 12 - 53186 TCCTGCAAA------TCC -s mr.mrrefChr5 33256 17 + 294540 TCTTGCATGAGA-CCCCC -s simCow_chr6.simCow.chr6 432886 1 - 602619 T----------------- -s simDog_chr6.simDog.chr6 140887 12 + 593897 TCCTGCAAA------TCC -s simRat_chr6.simRat.chr6 168305 17 + 647215 TCTTGGATGGTA-CCCCC - -a -s simMouse_chr6.simMouse.chr6 170648 18 + 636262 TTCTTGCATGTAAGCACT -s Anc0.Anc0refChr1 10728 14 + 62388 TTGTAG-ATGCAGG---G -s Anc1.Anc1refChr2 11494 14 - 144309 TTGTAG-ATGCAGG---G -s Anc2.Anc2refChr3 11892 14 - 53186 TTGTAG-ATGCAGG---G -s mr.mrrefChr5 33273 18 + 294540 TTCTTGCATGTAAGCACT -s simCow_chr6.simCow.chr6 432887 14 - 602619 TTGTAG-AGGCGGG---G -s simDog_chr6.simDog.chr6 140905 14 + 593897 TTGTAG-ATGCAGG---G -s simRat_chr6.simRat.chr6 168322 18 + 647215 TCCTTGCATGTAAGCACT - -a -s simMouse_chr6.simMouse.chr6 170666 21 + 636262 ACATCTAGTTATGCGGGCCCC -s Anc0.Anc0refChr1 10742 21 + 62388 CCATCTAGTCATGCAAATCCA -s Anc1.Anc1refChr2 11508 21 - 144309 CCATCTAGTCATGCAAATCCA -s Anc2.Anc2refChr3 11906 21 - 53186 CCATCTAGTCCTGCAAATCCA -s mr.mrrefChr5 33291 21 + 294540 ACATCTAGTCATGCGGGCCCC -s simCow_chr6.simCow.chr6 432902 21 - 602619 CTATCTTATCCTGCAAATTCA -s simDog_chr6.simDog.chr6 140919 21 + 593897 CCATCTAGTCCTGCAAATCCA -s simHuman_chr6.simHuman.chr6 434191 18 - 601863 ---TCTAGTCATGCAAATCCA -s simRat_chr6.simRat.chr6 168340 21 + 647215 ACATCTAGTCCTGCTGGCCCT - -a -s simMouse_chr6.simMouse.chr6 170687 41 + 636262 ATCAGTTTGGGATGTGTCATGTCCAGCCATAGGCGATAAGG -s Anc0.Anc0refChr1 10763 39 + 62388 GTCAGTTTGGGATGT--TATGTTCAGCAGTAGGCTAACAGG -s Anc1.Anc1refChr2 11529 39 - 144309 GTCAGTTTGGGATGT--TATGTTCAGCAGTAGGCTAACAGG -s Anc2.Anc2refChr3 11937 39 - 53186 GTCAGTTTTGGATGT--TATGTTCAGCAGTGGGCTAACAGG -s mr.mrrefChr5 33312 41 + 294540 GTCAGTTTGGGATGTGTCATGTCCAGCCATAGGCGATAAGG -s simCow_chr6.simCow.chr6 432933 38 - 602619 TCCATTATAAGATGT--TATATTCAATCATGGGC-AAGAGA -s simDog_chr6.simDog.chr6 140950 39 + 593897 GTCAGTTTTGGCTGG--TATGTTCAGCAGTGGGCTAACGGG -s simHuman_chr6.simHuman.chr6 434209 39 - 601863 GTCAGTTTGTGATGT--TATGTTCTGGAGTAGACTAATAGT -s simRat_chr6.simRat.chr6 168361 41 + 647215 GTCAGTTTGGGGTGTGTCATGTCCAGCCATAGGTGATAAGG - -a -s simMouse_chr6.simMouse.chr6 170728 10 + 636262 CCAAGTCTAC -s Anc0.Anc0refChr1 10802 9 + 62388 CCTAGGTTA- -s Anc1.Anc1refChr2 11568 9 - 144309 CCTAGGTTA- -s Anc2.Anc2refChr3 11976 9 - 53186 CCTAAGTTA- -s mr.mrrefChr5 33353 10 + 294540 CCAAGTCTAT -s simCow_chr6.simCow.chr6 432971 9 - 602619 GATAAGGTA- -s simDog_chr6.simDog.chr6 140990 9 + 593897 CCTAAGTTA- -s simHuman_chr6.simHuman.chr6 434248 9 - 601863 CTTAGGTTA- -s simRat_chr6.simRat.chr6 168402 10 + 647215 CCAAGTCCAT - -a -s simMouse_chr6.simMouse.chr6 170738 13 + 636262 AGAGCTGAGTTTG -s Anc0.Anc0refChr1 10811 13 + 62388 ACAGCAAAGTTTG -s Anc1.Anc1refChr2 11577 13 - 144309 ACAGCAAAGTTTG -s Anc2.Anc2refChr3 11985 13 - 53186 ACAGCAAAGTTTG -s mr.mrrefChr5 33363 13 + 294540 AGAGCTGAGTTTG -s simCow_chr6.simCow.chr6 432980 13 - 602619 TCAGCAAAGTCCG -s simDog_chr6.simDog.chr6 141024 13 + 593897 ACAGCAAAGTTTG -s simHuman_chr6.simHuman.chr6 434257 13 - 601863 ATAGCAAAGTTTG -s simRat_chr6.simRat.chr6 168412 13 + 647215 AGAACTGAGTTTG - -a -s simMouse_chr6.simMouse.chr6 170751 35 + 636262 ATGACTTGGCTGCTTGGTTCACTATTACAAGTGTA -s Anc0.Anc0refChr1 10824 26 + 62388 ATGACTAGGCTGCTT---------TCATGAGTGTA -s Anc1.Anc1refChr2 11590 26 - 144309 ATGACTAGGCTGCTT---------TCATGAGTGTA -s Anc2.Anc2refChr3 11998 26 - 53186 ATGACTAGCCTGCTT---------TCATGAGTGGA -s mr.mrrefChr5 33376 34 + 294540 ATGACTTGGCTGCTTGGTT-ACTATCATGAGTGTA -s simCow_chr6.simCow.chr6 432993 26 - 602619 ATGACTAACCTGCTT---------TCATGAGTGAA -s simDog_chr6.simDog.chr6 141132 26 + 593897 ATGACTTGCATGCTT---------TCGCGAGTGGA -s simHuman_chr6.simHuman.chr6 434270 26 - 601863 ATGACTAGGCTGCTT---------TCATGAGCATA -s simRat_chr6.simRat.chr6 168425 34 + 647215 ATGACTTGGCTGCTTGGTT-GCTATCATGGGTGTA - -a -s simMouse_chr6.simMouse.chr6 170786 22 + 636262 CTGATGGGCTTAGACAATTTGC -s Anc0.Anc0refChr1 10850 22 + 62388 CTGACAGGTCAAGACAGTTTGC -s Anc1.Anc1refChr2 11616 22 - 144309 CTGACAGGTCAAGACAGTTTGC -s Anc2.Anc2refChr3 12024 22 - 53186 CTGACAGGTCAAGACAGTTTGC -s mr.mrrefChr5 33410 22 + 294540 CTGATGGGTCTAGACAATTTGC -s simCow_chr6.simCow.chr6 433021 16 - 602619 CTGATAGGCCAAG------TGA -s simDog_chr6.simDog.chr6 141158 22 + 593897 CGGACAGATCAAGACAGTTTGC -s simHuman_chr6.simHuman.chr6 434296 22 - 601863 CTGACAGGTCAAGACAGTTTGC -s simRat_chr6.simRat.chr6 168459 22 + 647215 CCGATGGGTCTCGACAATTGGC - -a -s simMouse_chr6.simMouse.chr6 170808 40 + 636262 GTGTCTCATAATGGATTGCTTACACCTAAATGTTGAATTT -s Anc0.Anc0refChr1 10887 40 + 62388 ATGTCTTATAATGGACTATCTACATCTAAATGTGGTATTT -s Anc1.Anc1refChr2 11653 40 - 144309 ATGTCTTATAATGGACTATCTACATCTAAATGTGGTATTT -s Anc2.Anc2refChr3 12061 40 - 53186 ACATCTTGTAATGGACTATCTACATCTAAGTGTGGTATTT -s mr.mrrefChr5 33432 40 + 294540 ATGTCTCATAATGGATTGCTTACACCTAAATGTTGAATTT -s simCow_chr6.simCow.chr6 433052 40 - 602619 ACATCTTGTAATGTACTAACTACATCTAAGTGTGGTATTC -s simDog_chr6.simDog.chr6 141195 38 + 593897 ACATCTTGTAATGGACTATCTACAT--AAGTATGGCATTT -s simHuman_chr6.simHuman.chr6 434333 40 - 601863 ATGTCTTATGACGGACCATCTACATCTAAATGTGGTATTT -s simRat_chr6.simRat.chr6 168481 33 + 647215 ATGTCTCATAATG-------TACACCTAAATGTTGAATTC - -a -s simMouse_chr6.simMouse.chr6 170848 21 + 636262 GACAGAGATGCAATACGCTAG -s Anc0.Anc0refChr1 10927 20 + 62388 GACAAAGATGTGATAC-TTAA -s Anc1.Anc1refChr2 11693 20 - 144309 GACAAAGATGTGATAC-TTAA -s Anc2.Anc2refChr3 12101 20 - 53186 GACAAGGATGTGATAC-TTAA -s mr.mrrefChr5 33472 21 + 294540 GACAGAGATGCAATACGCTAG -s simCow_chr6.simCow.chr6 433092 20 - 602619 AACAAAGATGTGATAC-TTTA -s simDog_chr6.simDog.chr6 141233 20 + 593897 GAGAAGGATGTGATAC-TTAA -s simHuman_chr6.simHuman.chr6 434373 19 - 601863 GACA-AGATGTCATAC-TTAA -s simRat_chr6.simRat.chr6 168515 21 + 647215 GACAGAGATGCGATACGCTAG - -a -s simMouse_chr6.simMouse.chr6 170869 1 + 636262 A -s Anc0.Anc0refChr1 10947 1 + 62388 A -s Anc1.Anc1refChr2 11713 1 - 144309 A -s Anc2.Anc2refChr3 12121 1 - 53186 A -s mr.mrrefChr5 33493 1 + 294540 A -s simCow_chr6.simCow.chr6 433112 1 - 602619 A -s simDog_chr6.simDog.chr6 141255 1 + 593897 A -s simHuman_chr6.simHuman.chr6 434392 1 - 601863 A -s simRat_chr6.simRat.chr6 168536 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 170870 2 + 636262 GC -s Anc0.Anc0refChr1 10953 2 + 62388 GG -s Anc1.Anc1refChr2 11719 2 - 144309 GG -s Anc2.Anc2refChr3 12127 2 - 53186 GG -s mr.mrrefChr5 33494 2 + 294540 GC -s simCow_chr6.simCow.chr6 433118 2 - 602619 GG -s simHuman_chr6.simHuman.chr6 434398 2 - 601863 GG -s simRat_chr6.simRat.chr6 168537 2 + 647215 GC - -a -s simMouse_chr6.simMouse.chr6 170872 7 + 636262 AGCAGTA -s Anc0.Anc0refChr1 10955 7 + 62388 AGCAGTA -s Anc1.Anc1refChr2 11721 7 - 144309 AGCAGTA -s Anc2.Anc2refChr3 12129 7 - 53186 AGCGGTA -s mr.mrrefChr5 33496 7 + 294540 AGCAGTA -s simCow_chr6.simCow.chr6 433125 7 - 602619 AGCGGTA -s simHuman_chr6.simHuman.chr6 434400 7 - 601863 GGCAGTA -s simRat_chr6.simRat.chr6 168539 7 + 647215 AGCAGTA - -a -s simMouse_chr6.simMouse.chr6 170879 19 + 636262 AAAAACATATAGTCTTCGA -s Anc0.Anc0refChr1 10963 19 + 62388 GCAAGCATACAGTTCTATA -s Anc1.Anc1refChr2 11729 19 - 144309 GCAAGCATACAGTTCTATA -s Anc2.Anc2refChr3 12137 19 - 53186 GCAAGCATACGTTTCTATA -s mr.mrrefChr5 33503 19 + 294540 AAAAACATACAGTCTTCGA -s simCow_chr6.simCow.chr6 433134 19 - 602619 GCAAGCATACGTTTCTATA -s simHuman_chr6.simHuman.chr6 434408 19 - 601863 GCAAGCATACAGTTCTACA -s simRat_chr6.simRat.chr6 168546 19 + 647215 AAAAATGGACAGTCTTTGA - -a -s simMouse_chr6.simMouse.chr6 170898 38 + 636262 TATCTATGTGACTTCAATCAGTGATATCCCTATCCCAA -s Anc0.Anc0refChr1 10983 37 + 62388 CATT-ATATGGCTTCAACCAGTGATGTCTTTATCCTGA -s Anc1.Anc1refChr2 11749 38 - 144309 CATTTATATGGCTTCAACCAGTGATGTCTTTATCCTGA -s Anc2.Anc2refChr3 12157 37 - 53186 CGTT-ATATGGCTTCTACCTGTGTTGTCTTTATCCTGA -s mr.mrrefChr5 33522 38 + 294540 CATCTATGTGACTTCAACCAGTGATATCCCTATCCCGA -s simCow_chr6.simCow.chr6 433154 35 - 602619 CGTT---CTAGCTTCTAGCGGCATTGTATCTATCCTGA -s simDog_chr6.simDog.chr6 141259 33 + 593897 -----ATATGGCTTATACCTGTGTTGTCTTTATCCTGA -s simHuman_chr6.simHuman.chr6 434428 38 - 601863 CATTGATATGGCCTCAACCAGTGATGTCTTTATCTAGA -s simRat_chr6.simRat.chr6 168565 38 + 647215 CATCTATGTGATTTCAACAAGCAATATCCCTATCCTGA - -a -s simMouse_chr6.simMouse.chr6 170936 44 + 636262 AATCCCATTGGAACTAGGAGGGCTGACTGATTGTTCTTGTTCTA -s Anc0.Anc0refChr1 11020 44 + 62388 GATCCTGTTGAAGGTAGGAGAGCTGATATGTTGTTATTCTTCTA -s Anc1.Anc1refChr2 11787 44 - 144309 GATCCTGTTGAAGGTAGGAGAGCTGATATGTTGTTATTCTTCTA -s Anc2.Anc2refChr3 12194 44 - 53186 GATCCTGTTGAGGGTTAGAGAATTGATATGCTGTTATTCTTCTA -s mr.mrrefChr5 33560 44 + 294540 AATCCCATTGGAACTAGGAGGGCTGACTGATTGTTCTTGTTCTA -s simCow_chr6.simCow.chr6 433193 44 - 602619 GATCCTGTAGAGTGGCAGAGAAGTGTTATGCTGTTACTCTTCCA -s simDog_chr6.simDog.chr6 141292 44 + 593897 GATCCTGTTGAGGGTTAGGAAATTGATATGCTGTTTTTCTTCTA -s simHuman_chr6.simHuman.chr6 434466 42 - 601863 GATCCTGTTGAAGGTAGGAGAGCTGAAATGTTGTTATG--TCTA -s simRat_chr6.simRat.chr6 168603 44 + 647215 AATCCCATTGGAACTGGGAGGACTGATTCATTGTTCTTGTTCTA - -a -s simMouse_chr6.simMouse.chr6 170980 32 + 636262 GAATGCTCTCACTCCACAACTGTAATGAGAGA -s Anc0.Anc0refChr1 11066 32 + 62388 GCACTCCCTCAGCCTACACGTAGAATGATATC -s Anc1.Anc1refChr2 11833 32 - 144309 GCACTCCCTCAGCCTACACGTAGAATGATATC -s Anc2.Anc2refChr3 12240 32 - 53186 GCACTCCCTCAGCCCACACGTAGAATGATATG -s mr.mrrefChr5 33606 32 + 294540 GAATGCTCTCACTCTACAACTGTAATGATAGC -s simCow_chr6.simCow.chr6 433239 32 - 602619 GCACTCCCTCAGCCCACACTTAGATTGATCTG -s simDog_chr6.simDog.chr6 141338 31 + 593897 GCATTCCCTCAGTCCTCA-GTAGAATGATATG -s simHuman_chr6.simHuman.chr6 434510 32 - 601863 TCACTCCCTTAGCCTACACATAAAATGATATC -s simRat_chr6.simRat.chr6 168649 29 + 647215 GA---CTATCCCTCTGCAATTGTAAGGATAAC - -a -s simMouse_chr6.simMouse.chr6 171012 15 + 636262 AAGGTACAGTACTGG -s Anc0.Anc0refChr1 11098 13 + 62388 TAAGTACAGTAC--A -s Anc1.Anc1refChr2 11865 15 - 144309 TAAGTACAGTACTGA -s Anc2.Anc2refChr3 12272 13 - 53186 TAAGTACAGTAC--A -s mr.mrrefChr5 33638 15 + 294540 TAGGTACAGTACTGG -s simCow_chr6.simCow.chr6 433271 12 - 602619 CAAGTACA-TAC--A -s simDog_chr6.simDog.chr6 141369 13 + 593897 TAAGTACAGTTC--A -s simHuman_chr6.simHuman.chr6 434543 15 - 601863 TAAGTACAGTACTGA -s simRat_chr6.simRat.chr6 168678 15 + 647215 TAGGTACAGTACTGG - -a -s simMouse_chr6.simMouse.chr6 171027 7 + 636262 GGTCAGT -s Anc0.Anc0refChr1 11111 7 + 62388 GGTAAGT -s Anc1.Anc1refChr2 11880 7 - 144309 GGTAAGT -s Anc2.Anc2refChr3 12285 7 - 53186 GGTAAGT -s mr.mrrefChr5 33653 7 + 294540 GGTCAGT -s simCow_chr6.simCow.chr6 433283 7 - 602619 GGTCAGT -s simDog_chr6.simDog.chr6 141384 7 + 593897 GGTAAGT -s simHuman_chr6.simHuman.chr6 434558 3 - 601863 GGT---- -s simRat_chr6.simRat.chr6 168693 7 + 647215 GGTCAGT - -a -s simMouse_chr6.simMouse.chr6 171034 20 + 636262 GCTGTGAGAGTGTGAGCGCA -s Anc0.Anc0refChr1 11118 17 + 62388 GTTGAGAAA-TG-GAGAG-A -s Anc1.Anc1refChr2 11887 18 - 144309 GTTGAGAAA-TG-GAGAGCA -s Anc2.Anc2refChr3 12293 17 - 53186 GTTGAGAAA-CT-GAGAG-A -s mr.mrrefChr5 33660 20 + 294540 GCTGTGAGAGTGTGAGCGCA -s simCow_chr6.simCow.chr6 433291 17 - 602619 GTTGGGAAA-CT-AAGAG-A -s simDog_chr6.simDog.chr6 141392 17 + 593897 GTTGAGAAA-TT-GAGAG-A -s simHuman_chr6.simHuman.chr6 434561 15 - 601863 ---GAGACA-TG-GAGAGCA -s simRat_chr6.simRat.chr6 168700 20 + 647215 GCTGTGGGAGTGTATGTGCA - -a -s simMouse_chr6.simMouse.chr6 171054 6 + 636262 CCTTCC -s Anc0.Anc0refChr1 11143 6 + 62388 TGTTCT -s Anc1.Anc1refChr2 11913 6 - 144309 TGTTCT -s Anc2.Anc2refChr3 12318 6 - 53186 TGTTCT -s mr.mrrefChr5 33688 6 + 294540 CCTTCC -s simCow_chr6.simCow.chr6 433326 6 - 602619 TGTTCT -s simDog_chr6.simDog.chr6 141417 6 + 593897 TGTTCT -s simHuman_chr6.simHuman.chr6 434584 6 - 601863 TGTTCT -s simRat_chr6.simRat.chr6 168728 6 + 647215 CATTCC - -a -s simMouse_chr6.simMouse.chr6 171060 18 + 636262 TGTTTCTCACTGAATTAC -s Anc0.Anc0refChr1 11158 18 + 62388 TCTTGCTGACTGTACCAC -s Anc1.Anc1refChr2 11928 18 - 144309 TCTTGCTGACTGTACCAC -s Anc2.Anc2refChr3 12333 18 - 53186 TCTTGTTGACTGTACCAC -s mr.mrrefChr5 33694 18 + 294540 TGTTTCTGACTGAACTAC -s simCow_chr6.simCow.chr6 433341 18 - 602619 TCTTATTGACTATACCAC -s simDog_chr6.simDog.chr6 141432 18 + 593897 TCTGGTTGACTGTACCAT -s simHuman_chr6.simHuman.chr6 434599 18 - 601863 TCTTGCTGACTGTGCCAC -s simRat_chr6.simRat.chr6 168734 18 + 647215 TGTTTCTGACTGAACTAC - -a -s simMouse_chr6.simMouse.chr6 171078 15 + 636262 TTAACCTACAATAAT -s Anc0.Anc0refChr1 11178 15 + 62388 TTCACCTAATGAAAT -s Anc1.Anc1refChr2 11948 15 - 144309 TTCACCTAATGAAAT -s Anc2.Anc2refChr3 12353 15 - 53186 CTCACCTTATGAAAT -s mr.mrrefChr5 33712 15 + 294540 TTAACCTAAAATAAT -s simCow_chr6.simCow.chr6 433361 15 - 602619 CTCACCTTACGAAGT -s simDog_chr6.simDog.chr6 141452 15 + 593897 CCCAACTTATGTAAT -s simHuman_chr6.simHuman.chr6 434619 15 - 601863 TTCACCTAATTAAAT -s simRat_chr6.simRat.chr6 168752 15 + 647215 TTAACCTAAAATAAT - -a -s simMouse_chr6.simMouse.chr6 171093 2 + 636262 GC -s Anc0.Anc0refChr1 11193 2 + 62388 GC -s Anc1.Anc1refChr2 11963 2 - 144309 GC -s Anc2.Anc2refChr3 12368 2 - 53186 GC -s mr.mrrefChr5 33727 2 + 294540 GC -s simCow_chr6.simCow.chr6 433377 2 - 602619 GC -s simDog_chr6.simDog.chr6 141467 2 + 593897 GC -s simHuman_chr6.simHuman.chr6 434634 2 - 601863 GC -s simRat_chr6.simRat.chr6 168767 2 + 647215 GG - -a -s simMouse_chr6.simMouse.chr6 171095 39 + 636262 CACAACTACCTTCGCAAAACAAGTCAGTATCTCAAATAA -s Anc0.Anc0refChr1 11200 39 + 62388 CACCATTGGCCTTTCCAAACATATCAGTATCTCAAATAT -s Anc1.Anc1refChr2 11970 39 - 144309 CACCATTGGCCTTTCCAAACATATCAGTATCTCAAATAT -s Anc2.Anc2refChr3 12375 39 - 53186 CACCATTGGCCTTTCCAAGCATATCAGTATCTTAAATAT -s mr.mrrefChr5 33729 39 + 294540 CACAACTACCTTTGCAAAACAAGTCAGTATCTCAAATAT -s simCow_chr6.simCow.chr6 433384 39 - 602619 TGCCATTGGCCCTTCCAAGCATATGAGTATCTTAAATAT -s simDog_chr6.simDog.chr6 141474 39 + 593897 CACTATTTGCCTTTCCCAGCATGTCAGTATCTTAAATAT -s simHuman_chr6.simHuman.chr6 434641 39 - 601863 CACCATTGGCCTTTCCAAACATACCAGTGTGTCAAATAT -s simRat_chr6.simRat.chr6 168769 33 + 647215 ATG------CTTTGCAAAACACCTCAGTATCTCAAAAAT - -a -s simMouse_chr6.simMouse.chr6 171134 6 + 636262 CCTAAT -s Anc0.Anc0refChr1 11239 6 + 62388 ACTAAT -s Anc1.Anc1refChr2 12009 6 - 144309 ACTAAT -s Anc2.Anc2refChr3 12414 6 - 53186 ATTAAT -s mr.mrrefChr5 33768 6 + 294540 CCTAAT -s simCow_chr6.simCow.chr6 433431 6 - 602619 ATTAAT -s simDog_chr6.simDog.chr6 141513 6 + 593897 ATTAAT -s simHuman_chr6.simHuman.chr6 434680 6 - 601863 ACTAAT -s simRat_chr6.simRat.chr6 168802 6 + 647215 CCTAAT - -a -s simMouse_chr6.simMouse.chr6 171140 3 + 636262 AGA -s Anc0.Anc0refChr1 11245 3 + 62388 AAA -s Anc1.Anc1refChr2 12015 3 - 144309 AAA -s Anc2.Anc2refChr3 12420 3 - 53186 AAA -s mr.mrrefChr5 33774 3 + 294540 AGA -s simCow_chr6.simCow.chr6 433437 3 - 602619 AGA -s simDog_chr6.simDog.chr6 141521 3 + 593897 AAA -s simHuman_chr6.simHuman.chr6 434686 3 - 601863 AAA -s simRat_chr6.simRat.chr6 168808 3 + 647215 AGA - -a -s simMouse_chr6.simMouse.chr6 171143 7 + 636262 CACAAAA -s Anc0.Anc0refChr1 11248 7 + 62388 CACAAGA -s Anc1.Anc1refChr2 12018 7 - 144309 CACAAGA -s Anc2.Anc2refChr3 12423 7 - 53186 CACAAGA -s mr.mrrefChr5 33777 7 + 294540 CACAAAA -s simCow_chr6.simCow.chr6 433443 7 - 602619 CGCAAGA -s simDog_chr6.simDog.chr6 141524 7 + 593897 CACAGGA -s simHuman_chr6.simHuman.chr6 434689 7 - 601863 CACAAGA -s simRat_chr6.simRat.chr6 168811 7 + 647215 CACAAAA - -a -s simMouse_chr6.simMouse.chr6 171150 45 + 636262 GAAACAGCTATTAGCATTCCATATGTCCAACCAGCAATGTGCTCC -s Anc0.Anc0refChr1 11257 45 + 62388 GACACAGCCATCTCATTCTTATATGTGCAAAAAGTAATGTGCTTC -s Anc1.Anc1refChr2 12027 45 - 144309 GACACAGCCATCTCATTCTTATATGTGCAAAAAGTAATGTGCTTC -s Anc2.Anc2refChr3 12432 45 - 53186 GACACACCCATCTCATTCTTATATGTGCACAAAGTAATGTGCTTT -s mr.mrrefChr5 33784 45 + 294540 GAAACAGCCATTAGCATTCCATATGTCCAACCAGCAATGTGCTCC -s simCow_chr6.simCow.chr6 433452 45 - 602619 GGCACACCCATCCCCTTTTTATATATGCTCAAAGTAATGTGCTTA -s simDog_chr6.simDog.chr6 141533 45 + 593897 GACACACCCCTCTCATTCTTATATGTGCACAAACTAATGTCCCTT -s simHuman_chr6.simHuman.chr6 434698 45 - 601863 GACACAGCCATCTTATTCTTATATCTACAAAAAGTATTGAGCTTC -s simRat_chr6.simRat.chr6 168818 43 + 647215 GAAAAAGCCATTACCAGTCCATATGTCCAAGCAGCAGTGTGCT-- - -a -s simMouse_chr6.simMouse.chr6 171195 62 + 636262 ATGAGAGGGAGTTTTTAAACTAAGTCATCTCCTTTACATCCATCCTCTATTTATCTAGTGGA -s Anc0.Anc0refChr1 11303 61 + 62388 ATGAGAGGGTGCTTTTAAACTAATCCATCTCCTTTACATCCAGC-TCCATCTAACTGGTGGA -s Anc1.Anc1refChr2 12073 61 - 144309 ATGAGAGGGTGCTTTTAAACTAATCCATCTCCTTTACATCCAGC-TCCATCTAACTGGTGGA -s Anc2.Anc2refChr3 12478 61 - 53186 ATGAGAGGGTGCTTTTGAACTAATCCATCTCCTTTACATCCAGC-TCCATCTAACTGGTGGA -s mr.mrrefChr5 33829 62 + 294540 ATGAGAGGGAGTTTTTAAACTAAGTCATCTCCTTTACATCCATCCTCTATTTATCTAGTGGA -s simCow_chr6.simCow.chr6 433498 61 - 602619 ATGACAGGGTGCCTTTGAACTAAATCATCTCCTTAACATCCACC-CCTATCTAACTGGTGAA -s simDog_chr6.simDog.chr6 141579 61 + 593897 ATGAGATGGTGCTTTTGAAGTAATCCATCTCCTTTACATCCAGC-TCCATGTAACTGGTGGG -s simHuman_chr6.simHuman.chr6 434744 61 - 601863 ATGAGAGGGTGCTTTTAAACTAATCCATCTCCTCTACATCAAGC-TCCATCTAACTGGTGGA -s simRat_chr6.simRat.chr6 168861 54 + 647215 --------GAGTTTTTGAACGAAGTCATCTCCTTTACATTCATCCTCTATTTATCTAGTGGG - -a -s simMouse_chr6.simMouse.chr6 171257 9 + 636262 ATCCACTAG -s Anc0.Anc0refChr1 11367 9 + 62388 ATACAGTAG -s Anc1.Anc1refChr2 12137 9 - 144309 ATACAGTAG -s Anc2.Anc2refChr3 12542 9 - 53186 ACACAGAAG -s mr.mrrefChr5 33891 9 + 294540 ATCCACTAG -s simCow_chr6.simCow.chr6 433562 9 - 602619 GGCCAGCAG -s simDog_chr6.simDog.chr6 141643 9 + 593897 ACACGAATG -s simHuman_chr6.simHuman.chr6 434808 9 - 601863 ATACAGTAG -s simRat_chr6.simRat.chr6 168915 8 + 647215 ATCCA-GAG - -a -s simMouse_chr6.simMouse.chr6 171266 40 + 636262 TAACTATTCTTCCCTTCAGGAGTAACATTATCTTATGGAT -s Anc0.Anc0refChr1 11376 39 + 62388 -AACTGTTCTTGTCTTCAGCAGTAGCAGTATCTTATGCAC -s Anc1.Anc1refChr2 12146 40 - 144309 TAACTGTTCTTGTCTTCAGCAGTAGCAGTATCTTATGCAC -s Anc2.Anc2refChr3 12551 39 - 53186 -AACTGTTCTTGTCTTCAGCAGTAGCAATATTTTATGCAC -s mr.mrrefChr5 33900 40 + 294540 TAACTATTCTTCCCTTCAGGAGTAACAGTATCTTATGGAT -s simCow_chr6.simCow.chr6 433571 39 - 602619 -AACTGTTCTTGTCTTCAGCAGTAGTAACATATTATGCAC -s simDog_chr6.simDog.chr6 141652 36 + 593897 ----TGTTTTTGTTTTTAGCAGTACCAATATTTTATGCAC -s simHuman_chr6.simHuman.chr6 434818 40 - 601863 TAACTGTTCTCTTCTTCAGCAGTAGCAGTATCTTATGCAC -s simRat_chr6.simRat.chr6 168923 40 + 647215 TAACTATTCTTCCTTTCAGGAGTAACGGTATGGTATGAAT - -a -s simMouse_chr6.simMouse.chr6 171306 14 + 636262 TCAGAGTCATAAAG -s Anc0.Anc0refChr1 11415 14 + 62388 TCACACTCATCGAG -s Anc1.Anc1refChr2 12186 14 - 144309 TCACACTCATCGAG -s Anc2.Anc2refChr3 12590 14 - 53186 TCACACTCATCGAG -s mr.mrrefChr5 33940 14 + 294540 TCAGAGTCATAAAG -s simCow_chr6.simCow.chr6 433610 14 - 602619 TCACACACACCCAG -s simDog_chr6.simDog.chr6 141688 14 + 593897 TCACACTCATCGCG -s simHuman_chr6.simHuman.chr6 434859 14 - 601863 TCACAATCATTGAG -s simRat_chr6.simRat.chr6 168963 14 + 647215 TCAGAGTCATAAAG - -a -s simMouse_chr6.simMouse.chr6 171320 73 + 636262 TTATTTTATATAAGTCACCCCCATTAGTCAGAAATATGTCCGGTTGTTTGTAAGAAAGGTCTGAATAAGATAG -s Anc0.Anc0refChr1 11429 65 + 62388 ATATCCTATATGACTTACCCCCATTAGGCACAAGTATGTT-AGTTATTTGCAGTAAA-------ATAAGAATC -s Anc1.Anc1refChr2 12200 65 - 144309 ATATCCTATATGACTTACCCCCATTAGGCACAAGTATGTT-AGTTATTTGCAGTAAA-------ATAAGAATC -s Anc2.Anc2refChr3 12604 65 - 53186 ATATCCTATATGACTTCCCTCCATTAGGCGCAAGTATGTT-AATTATTTGTAATGAA-------ATAAGAATC -s mr.mrrefChr5 33954 73 + 294540 TTATTTTATATAAGTCACCCCCATTAGGCAGAAATATGTCCAGTTATTTGCAGGAAAGGTCTGAATAAGATAC -s simCow_chr6.simCow.chr6 433633 65 - 602619 ATATCCTATATGACTTCCCACCATTAGGCTTAAGGATGCT-ACCTATTTGTGATGAA-------ATAAGAATC -s simDog_chr6.simDog.chr6 141702 60 + 593897 ATATCCTATATGA-----CTCTGTTAGGTGCAAATATGTT-AATTATTTGTAATGAA-------ATAACAATC -s simHuman_chr6.simHuman.chr6 434873 65 - 601863 ATATCCTATATGGTTTACCCCCATTAGGCACAAGTGTGTT-AGTAATCTGCAGTAAG-------ATAAGAATC -s simRat_chr6.simRat.chr6 168977 73 + 647215 TTATTTTGTATAAGTCACCCCCATTAGGTAGAAATATGTCCAGTTATTCGCAGGAAAAGTCTGAATAAGATAC - -a -s simMouse_chr6.simMouse.chr6 171393 76 + 636262 TAAATCTGCATAAGAAGCAAAACCTACAGTGCCATGTTGCGTAGTTCAAATAAGTCAGGAAAAAGCAGAGTTGTGG -s Anc0.Anc0refChr1 11494 58 + 62388 TAACTGTGC--------------CTGCAGAACCATGTTGTGAAGTTCAATCAAGTCCAGAGGTGGCAGAGTA---- -s Anc1.Anc1refChr2 12265 62 - 144309 TAACTGTGC--------------CTGCAGAACCATGTTGTGAAGTTCAATCAAGTCCAGAGGTGGCAGAGTAGAGG -s Anc2.Anc2refChr3 12670 58 - 53186 TAACTGTGC--------------CTGAAGAACCATGTTGTGAAGATCAATCAAATCCAGAGGTGGCAGAGTA---- -s mr.mrrefChr5 34027 62 + 294540 TAAATGTGC--------------CTACAGTGCCATGTTGCGTAGTTCAAATAAGTCAGGAAAAAGCAGAGTTGTGG -s simCow_chr6.simCow.chr6 433699 55 - 602619 TAACTGTG---------------CTGAGAAGCCATGTTGTGAAGATCAGT--AACCCAGAATTGGCAGAGTA---- -s simDog_chr6.simDog.chr6 141763 51 + 593897 TAACTGTGC--------------TTGAAGAACCACGTTGTAGAGATCAATCAAATCTAGAGGTGG----------- -s simHuman_chr6.simHuman.chr6 434938 62 - 601863 TAATTGTGT--------------CTGCAGGCCCATGTCGTGAAGTTCAATGAAGTCCAGAGGTGGCAGAGTAGAGG -s simRat_chr6.simRat.chr6 169050 8 + 647215 TAAATGTG-------------------------------------------------------------------- - -a -s simMouse_chr6.simMouse.chr6 171469 32 + 636262 TTCCATGCAAACATGGTTATTACAGTGCATTT -s Anc0.Anc0refChr1 11552 32 + 62388 TTAGAAGCAGACATTGGTCTTAAGGTGCATTT -s Anc1.Anc1refChr2 12327 32 - 144309 TTAGAAGCAGACATTGGTCTTAAGGTGCATTT -s Anc2.Anc2refChr3 12728 32 - 53186 TGACAAGCAGACATTGGTCTTAAGGTGCATTC -s mr.mrrefChr5 34089 32 + 294540 TTCGATGCAGACATGGGTATTACGGTGCATTT -s simCow_chr6.simCow.chr6 433754 30 - 602619 --ACAGGTAGACTTTGGTCATAAGGTATATTC -s simDog_chr6.simDog.chr6 141814 32 + 593897 TGACAAGCAGATATTGGTCTTAAGTTGCATTC -s simHuman_chr6.simHuman.chr6 435002 32 - 601863 TTAGAAGCAGACATTAGTCTTAAGGTGCATCT -s simRat_chr6.simRat.chr6 169058 31 + 647215 -TCGTTGCCGATATGGGTATTACGGTGCATTT - -a -s simMouse_chr6.simMouse.chr6 171501 8 + 636262 AATCTTCC -s Anc0.Anc0refChr1 11586 8 + 62388 AATCTTCT -s Anc1.Anc1refChr2 12361 8 - 144309 AATCTTCT -s Anc2.Anc2refChr3 12762 8 - 53186 AATCTTCT -s mr.mrrefChr5 34121 8 + 294540 AATCTTCC -s simCow_chr6.simCow.chr6 433786 8 - 602619 AATCTTCT -s simDog_chr6.simDog.chr6 141848 8 + 593897 GACCTTCA -s simHuman_chr6.simHuman.chr6 435036 8 - 601863 AATCATCT -s simRat_chr6.simRat.chr6 169089 8 + 647215 AATCTTCC - -a -s simMouse_chr6.simMouse.chr6 171509 2 + 636262 GT -s Anc0.Anc0refChr1 11594 2 + 62388 CT -s Anc1.Anc1refChr2 12369 2 - 144309 CT -s Anc2.Anc2refChr3 12770 2 - 53186 CT -s mr.mrrefChr5 34129 2 + 294540 CT -s simCow_chr6.simCow.chr6 433796 2 - 602619 CT -s simDog_chr6.simDog.chr6 141856 2 + 593897 CT -s simHuman_chr6.simHuman.chr6 435044 2 - 601863 CT -s simRat_chr6.simRat.chr6 169097 2 + 647215 CT - -a -s simMouse_chr6.simMouse.chr6 171511 42 + 636262 GAGACTAATAAGGTTAAGAGTGAAAGGTAAACCAGACTAATA -s Anc0.Anc0refChr1 11602 36 + 62388 GAAAATA------TTCTGTATTAAACATAATACTATCAAATT -s Anc1.Anc1refChr2 12377 36 - 144309 GAAAATA------TTCTGTATTAAACATAATACTATCAAATT -s Anc2.Anc2refChr3 12778 36 - 53186 GAAAATA------TTCTGTATTTAACATAATACTATCAAATT -s mr.mrrefChr5 34137 42 + 294540 GAGACTAATAAGGTTAAGAGTGAAAGGTAAACCAGACAAATA -s simCow_chr6.simCow.chr6 433804 35 - 602619 GAAAATA------TTG-GAAACTAACATTATACCATCAAACT -s simDog_chr6.simDog.chr6 141864 36 + 593897 GAAAATA------TTCTGTATTTAACATAATACTATCAAATT -s simHuman_chr6.simHuman.chr6 435052 36 - 601863 GAAAATA------TTCTGTATTAAACATAATACTTTCAAATT -s simRat_chr6.simRat.chr6 169105 42 + 647215 GAGATTAACAAGATTAAGAGTAACAAGTAAATCAGACAAATA - -a -s simMouse_chr6.simMouse.chr6 171553 68 + 636262 ACTCAGAATGGAAGGCAAGTTTACATCCTAGCTCAGCAGTAATACTTAAAAAGTGGAAAGTTTAACGT -s Anc0.Anc0refChr1 11638 47 + 62388 AGTCATAAT-------AAATTTAACT--------------AATACTTACAAAATATAAAGTTTAACGT -s Anc1.Anc1refChr2 12413 61 - 144309 AGTCATAAT-------AAATTTAACTCTTAGCTTAGCCACAATACTTACAAAATATAAAGTTTAACGT -s Anc2.Anc2refChr3 12814 47 - 53186 AGTACTAAC-------AAATTTAACT--------------AATACTTATAAAATATAAAGTTCCCAGA -s mr.mrrefChr5 34179 68 + 294540 ACTCAGAATGGAAGGCAAATTTACATCCTAGCTTAGCCATAATACTTACAAAGTGGAAAGTTTAACGT -s simCow_chr6.simCow.chr6 433841 41 - 602619 ATTACTAAC-------aaatttaata--------------aata------aaatataaaGTTCAAAGG -s simDog_chr6.simDog.chr6 141900 47 + 593897 AGTACTAAC-------AAATTTAACT--------------AATACTTATAGAATACAAAGTTTCCAGA -s simHuman_chr6.simHuman.chr6 435088 61 - 601863 AATCAAATT-------AAAGTTCTCTCTTAGCTTAGCCACAATACTGACAAACTATAAAGCTTAACGT -s simRat_chr6.simRat.chr6 169147 66 + 647215 --TTAGAATGGAAGGCAAATTTACTTCCTAGCTTAGCCATAATACTTACAAAGTGAAAAGTTTAAATG - -a -s simMouse_chr6.simMouse.chr6 171621 23 + 636262 CAAATTATGCATTTGAATGTCGA -s Anc0.Anc0refChr1 11685 23 + 62388 CAAATTATGCATTTGAATGTCGA -s Anc1.Anc1refChr2 12474 23 - 144309 CAAATTATGCATTTGAATGTCGA -s Anc2.Anc2refChr3 12861 23 - 53186 CAAATTATGTATTCCAATGTTGG -s mr.mrrefChr5 34247 23 + 294540 CAAATTATGCATTTGAATGTCGA -s simCow_chr6.simCow.chr6 433882 23 - 602619 CAAATTATGTATTCCAATGTTGG -s simDog_chr6.simDog.chr6 141947 20 + 593897 CAAATTATGTTTTCCAATGT--- -s simHuman_chr6.simHuman.chr6 435179 23 - 601863 CAAATTATGCATTTGAATGTCGA -s simRat_chr6.simRat.chr6 169213 23 + 647215 CAAATTATGCATCTGAATGTTGA - -a -s simMouse_chr6.simMouse.chr6 171644 6 + 636262 CTGAGG -s Anc0.Anc0refChr1 11708 6 + 62388 CTAAGG -s Anc1.Anc1refChr2 12497 6 - 144309 CTAAGG -s Anc2.Anc2refChr3 12884 6 - 53186 CTAACA -s mr.mrrefChr5 34270 6 + 294540 CTGAGG -s simCow_chr6.simCow.chr6 433905 6 - 602619 CTAACA -s simHuman_chr6.simHuman.chr6 435202 6 - 601863 CCAAGG -s simRat_chr6.simRat.chr6 169242 6 + 647215 CTGAGG - -a -s simMouse_chr6.simMouse.chr6 171650 10 + 636262 AGATCTGAGT -s Anc0.Anc0refChr1 11715 10 + 62388 AGATCCCAGT -s Anc1.Anc1refChr2 12504 10 - 144309 AGATCCCAGT -s Anc2.Anc2refChr3 12891 10 - 53186 AGATCCCAGT -s mr.mrrefChr5 34276 10 + 294540 AGATCCGAGT -s simCow_chr6.simCow.chr6 433912 10 - 602619 AGATCCCAGT -s simDog_chr6.simDog.chr6 141967 9 + 593897 -GGTCGGAGT -s simHuman_chr6.simHuman.chr6 435209 10 - 601863 AGATCCCAGT -s simRat_chr6.simRat.chr6 169248 10 + 647215 AGATCCAGGT - -a -s simMouse_chr6.simMouse.chr6 171660 18 + 636262 GGTGAATGGATGTGGAGA -s Anc0.Anc0refChr1 11733 18 + 62388 GCCCAATGTATGTGGAGG -s Anc1.Anc1refChr2 12522 18 - 144309 GCCCAATGTATGTGGAGG -s Anc2.Anc2refChr3 12909 18 - 53186 GCCCAAAATATGTGGAGG -s mr.mrrefChr5 34286 18 + 294540 GGCCAATGGATGTGGAGA -s simCow_chr6.simCow.chr6 433930 18 - 602619 ACTCAAAATATGTGAAAG -s simDog_chr6.simDog.chr6 141984 18 + 593897 GCCCAAAATATGTGGAGG -s simHuman_chr6.simHuman.chr6 435227 18 - 601863 GCCCAATGTATGTGGAGG -s simRat_chr6.simRat.chr6 169258 18 + 647215 GGCCAATGGATGTGGGGA - -a -s simMouse_chr6.simMouse.chr6 171678 10 + 636262 CTGTTTTTTA -s Anc0.Anc0refChr1 11751 9 + 62388 GA-CTTTTTA -s Anc1.Anc1refChr2 12540 9 - 144309 GA-CTTTTTA -s Anc2.Anc2refChr3 12927 9 - 53186 GA-CTTTTTA -s mr.mrrefChr5 34304 10 + 294540 CAGTTTTTTA -s simCow_chr6.simCow.chr6 433949 7 - 602619 GA-CTGTT-- -s simDog_chr6.simDog.chr6 142002 9 + 593897 GA-CTTTTTA -s simHuman_chr6.simHuman.chr6 435245 9 - 601863 GA-CTTTTTA -s simRat_chr6.simRat.chr6 169276 10 + 647215 CAGTTTTTTG - -a -s simMouse_chr6.simMouse.chr6 171688 10 + 636262 GGGCCCACCT -s Anc0.Anc0refChr1 11760 10 + 62388 GTTCCCATCT -s Anc1.Anc1refChr2 12549 10 - 144309 GTTCCCATCT -s Anc2.Anc2refChr3 12936 10 - 53186 GTTCCCATCT -s mr.mrrefChr5 34314 10 + 294540 GTGCCCACCT -s simCow_chr6.simCow.chr6 433956 8 - 602619 --GCCCATCT -s simDog_chr6.simDog.chr6 142012 10 + 593897 GTTCCCATCT -s simHuman_chr6.simHuman.chr6 435254 10 - 601863 GTACCCATCT -s simRat_chr6.simRat.chr6 169286 10 + 647215 GTGCCTACCT - -a -s simMouse_chr6.simMouse.chr6 171698 13 + 636262 GTTTTTATAgtta -s Anc0.Anc0refChr1 11770 13 + 62388 GTTATCATAAGAA -s Anc1.Anc1refChr2 12559 13 - 144309 GTTATCATAAGAA -s Anc2.Anc2refChr3 12946 13 - 53186 GTTATCATAACAA -s mr.mrrefChr5 34324 13 + 294540 GTTTTCATAAGTA -s simCow_chr6.simCow.chr6 433964 13 - 602619 GTTATCATAACAA -s simDog_chr6.simDog.chr6 142024 13 + 593897 ATTATCATAGCAA -s simHuman_chr6.simHuman.chr6 435264 12 - 601863 GTTATC-TAAGGA -s simRat_chr6.simRat.chr6 169296 13 + 647215 GTATTCATAAGAA - -a -s simMouse_chr6.simMouse.chr6 171711 222 + 636262 ctttgactgccgtcagtgttgagagtatcgtggggtagggaccttcccaatgggtatccagcaatggaggatgtgacggaagcgaagctagttaactgataccatattgcctggatgaaataactcttttccttctcgatgcagacaagtcccgaggagtgctttgaggatttgctgaaacttagccagggagataatatctgtaaccaaaattgcagtctc -s mr.mrrefChr5 220894 221 + 294540 ctttgactgccgtcagtgttgagagtatcgtggg-tagggaccttcccaatgggtatccagcaatggaggatgtgacggaagcgaagctagttaactgataccatattgcctggatgaaataactcttttccttctcgatgcagacaagtcccgaggagtgctttgaggatttgctgaaacttagccagggagataatatctgtaaccaaaattgcagtctc -s simRat_chr6.simRat.chr6 366387 221 + 647215 ctctgactactgtcggtgttgagagtaccatggg-tggggactttcccgaggggtaactagcaatggagaatgcgatggaaaagaagcaatttaactagtatcatattggctggatgcaataactgctttccttctcagtgtggacaagtcccgggaagtgctttgagaatttgctgaaacttacccaatgagataatatccgtgaccaaatttgcagtctc - -a -s simMouse_chr6.simMouse.chr6 171933 6 + 636262 tgacaa -s mr.mrrefChr5 221115 6 + 294540 tgacaa -s simRat_chr6.simRat.chr6 366612 6 + 647215 tgccaa - -a -s simMouse_chr6.simMouse.chr6 171939 158 + 636262 agataatatctgtgaccaaattcgcagcctcatggtcgagaatcaaattttgtcttaggaagggctgtctgtacaacatcttgtataggctaagtcccaccttttgcagtgaatttatggtgcatcgaagagcaattggtaacagcaccagccatgct -s mr.mrrefChr5 221121 158 + 294540 agataatatctgtgaccaaattcgcagcctcatggtcgagaatcaaattttgtcttaggaagggctgtctgtacaacatcttgtataggctaagtcccaccttttgcagtgaatttatggtgcatcgaagagcaattggtaacagcaccagccatgct -s simRat_chr6.simRat.chr6 366620 158 + 647215 agataacatctgtgaccaaattcgcagcctcatggtcaagaactgaatcattcactaggaaggtctgtccctacagcatctcatataggttaagtcccacttctttcggtgaatttctggttcatagaagagcaagtggtaacagcaacagccatgct - -a -s simMouse_chr6.simMouse.chr6 172097 19 + 636262 agatgggtctgttgtgtta -s mr.mrrefChr5 221279 19 + 294540 agatgggtctgttgtgtta -s simRat_chr6.simRat.chr6 366779 19 + 647215 atatgaatctgttgtgtta - -a -s simMouse_chr6.simMouse.chr6 172116 230 + 636262 aggtgacacttcagtgtttcattcatcttctcagccttacctgaagattgcggcctccatgtacaatgagagtaatcttgtattctaagtgctcgaaacgcaccatgagtgacagcccccttaagtgcaggtcctggattgctctgaaaaccgtgaggtaaccgaagtgaagtataatgtcatgcacaagtgccttaattacctccttggccttctctatgcgtcaggag -s mr.mrrefChr5 221298 210 + 294540 aggtgacacttcagtgtttcat-----------gccttacctgaagattgcggcctccatgtacaatgagagtaatcttgtattctaagtgctcgaaacgcaccatgagtgacagcccccttaagtgca---------ttgctctgaaaaccgtgaggtaaccgaagtgaagtataatgtcatgcacaagtgccttaattacctccttggccttctctatgcgtcaggag -s simRat_chr6.simRat.chr6 366806 210 + 647215 aggtgacatttcagtgtttcat-----------gtgtttcatgaagattgtggcctccatgcacaatgagagtaatattgtattccaagcgcttgagacacacctgcagtgacagcccccttgagtgca---------tctctctgtaaaccatgaggtaactggaccaaggtataattttgtgcacaagtgcctggattacctcctgggccttctctgtgtgccggagg - -a -s simMouse_chr6.simMouse.chr6 172346 72 + 636262 gcctcagcccaactgataaacatgttgacccaccctaataggtattagaatccttgagacttgggcatatgc -s mr.mrrefChr5 221508 72 + 294540 gcctcagcccaactgataaacatgttgacccaccctaataggtattagaatccttgagacttgggcatatgc -s simRat_chr6.simRat.chr6 367019 72 + 647215 gcctcagctcaagcgataagcatgtcgacccacccttataggtattggcatccttgagactttggcatatgt - -a -s simMouse_chr6.simMouse.chr6 172418 132 + 636262 taaagcctaactcccaatcctccctcaggttatggtcaagcctctgctctcgcaacaatgcctgacactaaggtaacaggtcatttctttgggaacaatccaggtccaataaatagttacttagccatccga -s mr.mrrefChr5 221580 132 + 294540 taaagcctaactcccaatcctccctcaggttatggtcaagcctctgctctcgcaacaatgcctgacactaaggtaacaggtcatttctttgggaacaatccaggtccaataaatagttacttagccatccga -s simRat_chr6.simRat.chr6 367092 132 + 647215 taaagcctaactgccaatcctctctcaggtaatagtcgggcctctgctctttcaacggttcctgacactaaggtaacaggtcatttctttgcgaacaatccaggtccagtaaatagatacttggtcatctga - -a -s simMouse_chr6.simMouse.chr6 172550 155 + 636262 gcctaagtcaaatgtttttggttaagagcctttaccaatttccactggttggctgcaagcaggctgcaagcagcaaaattttcccctcctcagtcgcggaacagttacagggcaagaaactgtgcccataagatttgccccattcaatttcctcc -s mr.mrrefChr5 221712 137 + 294540 gcctaagtcaaatgttt--ggttaagagcctttaccaatttccactggttggctgcaagcag-----------caaaattttcccctcctcagtcgcggaacagttacagggcaagaaactgtgcccataagatttgccc-----aatttcctcc -s simRat_chr6.simRat.chr6 367237 137 + 647215 gcctaagtgaaatgttt--ggtaaagagcctttaacaatttccactggttggatgcacacag-----------ccaaattttcccctcctcagtcactgaccagcctcaggttaagaaactatccccatgagatttgtcc-----aatttcctcc - -a -s simMouse_chr6.simMouse.chr6 172705 50 + 636262 ccaaatattgtggtttcacctctcttaacaggtctccccagaccagtgga -s mr.mrrefChr5 221849 42 + 294540 ccaaatattgtggtttcacctctct--------ctccccagaccagtgga -s simRat_chr6.simRat.chr6 367375 42 + 647215 ccaaatattgtggttatgtctcttc--------ccccccagaccagtaga - -a -s simMouse_chr6.simMouse.chr6 172755 30 + 636262 acaagcctcttgagaggagggtcctgtcaa -s mr.mrrefChr5 221891 30 + 294540 acaagcctcttgagaggagggtcctgtcaa -s simRat_chr6.simRat.chr6 367423 30 + 647215 ataagcatctctagatgagggtcctgtcaa - -a -s simMouse_chr6.simMouse.chr6 172785 24 + 636262 gcagcatgtttggcatcaacatct -s mr.mrrefChr5 221921 24 + 294540 gcagcatgtttggcatcaacatct -s simRat_chr6.simRat.chr6 367455 24 + 647215 gaggcttgttaggcttcaacatct - -a -s simMouse_chr6.simMouse.chr6 172809 19 + 636262 cttgagagttgccttcgat -s mr.mrrefChr5 221945 19 + 294540 cttgagagttgccttcgat -s simRat_chr6.simRat.chr6 367480 19 + 647215 cttgacagtttccttcaat - -a -s simMouse_chr6.simMouse.chr6 172828 76 + 636262 ctcatgctctttctctttctgatgtccccaacagtacaacactgtcatctgttttggcttctggatggctaacaat -s mr.mrrefChr5 221964 62 + 294540 ctcatgctctttct----------tccccaacagt----cactgtcatctgttttggcttctggatggctaacaat -s simRat_chr6.simRat.chr6 367501 62 + 647215 ttcacgctctttcc----------tatacagcagt----tattgttacccatcaagaagccaaaagaggtcacagt - -a -s simMouse_chr6.simMouse.chr6 172904 93 + 636262 aactgccatatagcttcctgaggttttattggtgtaccttaggaggtcagaaactctctctcgtgccagatagccacatgtgcatgtagccag -s mr.mrrefChr5 222026 93 + 294540 aactgccatatagcttcctgaggttttattggtgtaccttaggaggtcagaaactctctctcgtgccagatagccacatgtgcatgtagccag -s simRat_chr6.simRat.chr6 367578 93 + 647215 accagcagtaaggcttcctgatgtcttattggtgtaccttaggaagtcagaaatccttcctcatgccagataggcgcatgtgcatggagcatg - -a -s simMouse_chr6.simMouse.chr6 172997 16 + 636262 tatgtggagtctctgc -s mr.mrrefChr5 222119 16 + 294540 tatgtggagtctctgc -s simRat_chr6.simRat.chr6 367680 16 + 647215 tatttggagtctgcgc - -a -s simMouse_chr6.simMouse.chr6 173013 36 + 636262 ctcgcatagtttgcgtgcctctgtgagtgtgatgaa -s mr.mrrefChr5 222135 36 + 294540 ctcgcatagtttgcgtgcctctgtgagtgtgatgaa -s simRat_chr6.simRat.chr6 367715 36 + 647215 ctcacctagttcaagtgcctgtgtaagtgtggtgaa - -a -s simMouse_chr6.simMouse.chr6 173049 94 + 636262 atgaattcagccagctgagtaccagtgcctggcatcagggggttacttccttgaaaaccattctcgctaataacagcatactttgctttgcgaa -s mr.mrrefChr5 222171 94 + 294540 atgaattcagccagctgagtaccagtgcctggcatcagggggttacttccttgaaaaccattctcgctaataacagcatactttgctttgcgaa -s simRat_chr6.simRat.chr6 367783 94 + 647215 gtgaattcagccagctgaccactagtccccggcataaaggggtttctttctagaatgccattatcactaacaacagcatactctgtcttgcaaa - -a -s simMouse_chr6.simMouse.chr6 173143 15 + 636262 gacccttttctacaa -s mr.mrrefChr5 222265 15 + 294540 gacccttttctacaa -s simRat_chr6.simRat.chr6 367880 15 + 647215 gacccttttctacaa - -a -s simMouse_chr6.simMouse.chr6 173158 68 + 636262 acgagcaaatgtcagcatatacattgaggtcagggtcagtcactggaacctccagtagatcagcgcaa -s mr.mrrefChr5 222280 68 + 294540 acgagcaaatgtcagcatatacattgaggtcagggtcagtcactggaacctccagtagatcagcgcaa -s simRat_chr6.simRat.chr6 367896 68 + 647215 acgagctactgtcagtatataccttgaggtcagggtcagactgtggaacctccagtagatcagcgtga - -a -s simMouse_chr6.simMouse.chr6 173226 5 + 636262 gctgc -s Anc0.Anc0refChr5 259 5 + 87904 GATGC -s Anc1.Anc1refChr6 35139 5 + 197743 GATGC -s Anc2.Anc2refChr14 261 5 + 7748 GATGG -s mr.mrrefChr5 222348 5 + 294540 gctgc -s simCow_chr6.simCow.chr6 346746 5 + 602619 GAAGG -s simDog_chr6.simDog.chr6 249068 5 - 593897 GATGG -s simHuman_chr6.simHuman.chr6 358836 5 + 601863 GGTGC -s simRat_chr6.simRat.chr6 367964 5 + 647215 gctgc - -a -s simMouse_chr6.simMouse.chr6 173231 3 + 636262 atg -s Anc0.Anc0refChr5 264 3 + 87904 ATG -s Anc1.Anc1refChr6 35144 3 + 197743 ATG -s Anc2.Anc2refChr14 266 3 + 7748 ACA -s mr.mrrefChr5 222353 3 + 294540 atg -s simCow_chr6.simCow.chr6 346751 3 + 602619 GCA -s simDog_chr6.simDog.chr6 249079 3 - 593897 ACA -s simHuman_chr6.simHuman.chr6 358841 3 + 601863 ATG -s simRat_chr6.simRat.chr6 367969 3 + 647215 aaa - -a -s simMouse_chr6.simMouse.chr6 173234 7 + 636262 cattcaa -s Anc0.Anc0refChr5 270 7 + 87904 CATTGAA -s Anc1.Anc1refChr6 35150 7 + 197743 CATTGAA -s Anc2.Anc2refChr14 272 7 + 7748 CATTGAA -s mr.mrrefChr5 222356 7 + 294540 cattcaa -s simCow_chr6.simCow.chr6 346757 7 + 602619 CATTGAA -s simDog_chr6.simDog.chr6 249085 7 - 593897 AATTGAA -s simHuman_chr6.simHuman.chr6 358847 7 + 601863 CATTGAA -s simRat_chr6.simRat.chr6 367972 7 + 647215 catttga - -a -s simMouse_chr6.simMouse.chr6 173241 19 + 636262 actctcacTCGTCAGTTCA -s Anc0.Anc0refChr5 277 19 + 87904 TACCCCACCCATGGGTTCA -s Anc1.Anc1refChr6 35157 19 + 197743 TACCCCACCCATGGGTTCA -s Anc2.Anc2refChr14 279 19 + 7748 TACCCCACCCTTGGGCTCA -s mr.mrrefChr5 222363 19 + 294540 ACTCTCACCCATCGGTTCA -s simCow_chr6.simCow.chr6 346764 19 + 602619 TATCCTATCCTTGGGCTCA -s simDog_chr6.simDog.chr6 249092 18 - 593897 TACCCCACCCTCGGGCTA- -s simHuman_chr6.simHuman.chr6 358854 19 + 601863 TACCCCACCCATGGGTTCA -s simRat_chr6.simRat.chr6 368000 19 + 647215 ACTCTCACCGATTGGTTCA - -a -s simMouse_chr6.simMouse.chr6 173260 11 + 636262 ATTACATACCC -s Anc0.Anc0refChr5 304 11 + 87904 ATTACATACCG -s Anc1.Anc1refChr6 35184 11 + 197743 ATTACATACCG -s Anc2.Anc2refChr14 306 11 + 7748 GTTATGTACCG -s mr.mrrefChr5 222382 11 + 294540 ATTACATACCC -s simCow_chr6.simCow.chr6 346791 11 + 602619 GTTATGTACCG -s simHuman_chr6.simHuman.chr6 358881 11 + 601863 ATTGCATACCA -s simRat_chr6.simRat.chr6 368019 11 + 647215 ATTACATACCC - -a -s simMouse_chr6.simMouse.chr6 173271 11 + 636262 CATTATTTTAA -s Anc0.Anc0refChr5 315 9 + 87904 AATTA--TTAA -s Anc1.Anc1refChr6 35195 9 + 197743 AATTA--TTAA -s Anc2.Anc2refChr14 317 9 + 7748 AACTA--TTAA -s mr.mrrefChr5 222393 11 + 294540 CATTATTTTAA -s simCow_chr6.simCow.chr6 346823 9 + 602619 AACTA--TTAA -s simHuman_chr6.simHuman.chr6 358892 9 + 601863 GATTA--TTAA -s simRat_chr6.simRat.chr6 368030 11 + 647215 CATTATTTTAA - -a -s simMouse_chr6.simMouse.chr6 173282 17 + 636262 GTCTATGTCATACCATA -s Anc0.Anc0refChr5 324 15 + 87904 GTCTGTGTCAT-CT-TA -s Anc1.Anc1refChr6 35204 16 + 197743 GTCTGTGTCATACT-TA -s Anc2.Anc2refChr14 326 15 + 7748 GTCTGTGTTAT-CT-TA -s mr.mrrefChr5 222404 17 + 294540 GTCTATGTCATACCATA -s simCow_chr6.simCow.chr6 346833 15 + 602619 GTCTGTGTTAT-CT-TA -s simDog_chr6.simDog.chr6 249110 2 - 593897 ---------------TA -s simHuman_chr6.simHuman.chr6 358901 16 + 601863 GTCTGAGGCATACT-TA -s simRat_chr6.simRat.chr6 368041 17 + 647215 TTCTATGTCATGCCATA - -a -s simMouse_chr6.simMouse.chr6 173299 78 + 636262 GACTCTCTGAACATACTCTGTCAATTTACACAGACAACAACATTCGCCTCATCCCTTTCTTTCCAAGATGTCCATGAT -s Anc0.Anc0refChr5 339 76 + 87904 TACCTT--CAATATACCCAATGGATTTACACAGATAGCCACATTCTCCTTACCCCCTTCTTCACGAGCTCTCCATGAC -s Anc1.Anc1refChr6 35220 76 + 197743 TACCTT--CAATATACCCAATGGATTTACACAGATAGCCACATTCTCCTTACCCCCTTCTTCACGAGCTCTCCATGAC -s Anc2.Anc2refChr14 341 76 + 7748 TACCTT--CAATATACCCAATGGATTTACACAGATAGCCCTATTCTGCTTACCCCACTTTTCAAGGGCTCTCTGTGAC -s mr.mrrefChr5 222421 76 + 294540 GACTCT--GAATATACTCTATCAATTTACACAGACAACAACATTCGCCTCATCCCCTTCTTTCCAAGATGTCCATGAT -s simCow_chr6.simCow.chr6 346850 76 + 602619 TACCTT--CAACATTCCAAGTGGATTTGAACAGATAGCCCTATTCTGCTTACCCCACTTTTCAAGGGCTCTCTGTGAC -s simDog_chr6.simDog.chr6 249112 35 - 593897 TACTTT--CAATATACCCAATGGATTTACACAGAGAT----------------------------------------- -s simHuman_chr6.simHuman.chr6 358917 76 + 601863 TATCTT--CAATATACCCAATGGATTTACACAGATGGGCACATTCCCCTTACCCCCTTCTTCACCAGCTATCCATGGA -s simRat_chr6.simRat.chr6 368058 61 + 647215 GAGTCT--GAATATCCTCTATCAATTTACACAGACA---------------TCCCCTTCTTTGCGAGGTGTCCATGAT - -a -s simMouse_chr6.simMouse.chr6 173377 7 + 636262 ACATCTG -s Anc0.Anc0refChr5 417 7 + 87904 ACCTCAA -s Anc1.Anc1refChr6 35298 7 + 197743 ACCTCAA -s Anc2.Anc2refChr14 419 7 + 7748 ACCTGAA -s mr.mrrefChr5 222497 7 + 294540 ACATCAG -s simCow_chr6.simCow.chr6 346928 7 + 602619 ACCTGAA -s simHuman_chr6.simHuman.chr6 358995 7 + 601863 ACCTCAA -s simRat_chr6.simRat.chr6 368119 7 + 647215 GCAACAG - -a -s simMouse_chr6.simMouse.chr6 173384 15 + 636262 GGTAATAGATCCCCA -s Anc0.Anc0refChr5 424 15 + 87904 GGTAATAGACCCCCA -s Anc1.Anc1refChr6 35305 15 + 197743 GGTAATAGACCCCCA -s Anc2.Anc2refChr14 426 15 + 7748 AGTAATAGACACCCA -s mr.mrrefChr5 222504 15 + 294540 GGTAATAGATCCCCA -s simCow_chr6.simCow.chr6 346936 15 + 602619 AGTAATAGACTGCCA -s simDog_chr6.simDog.chr6 249147 8 - 593897 -------GACACCTA -s simHuman_chr6.simHuman.chr6 359002 15 + 601863 GGTAATAGACCCCCA -s simRat_chr6.simRat.chr6 368126 15 + 647215 GGTAATGGATCCCCA - -a -s simMouse_chr6.simMouse.chr6 173399 12 + 636262 GAGTGGTTTCCT -s Anc0.Anc0refChr5 439 11 + 87904 AAATGG-TTTTC -s Anc1.Anc1refChr6 35320 12 + 197743 AAATGGTTTTTC -s Anc2.Anc2refChr14 441 11 + 7748 AAATGG-TTTCC -s mr.mrrefChr5 222519 12 + 294540 GAGTGGTTTTTT -s simCow_chr6.simCow.chr6 346951 11 + 602619 GAATGG-TTTCC -s simDog_chr6.simDog.chr6 249156 11 - 593897 AGATGG-TTTCC -s simHuman_chr6.simHuman.chr6 359017 12 + 601863 AAATGGTTTTTG -s simRat_chr6.simRat.chr6 368141 12 + 647215 GAGTGGTTTTTT - -a -s simMouse_chr6.simMouse.chr6 173411 17 + 636262 AGTTGCCATCACTGTTT -s Anc0.Anc0refChr5 450 17 + 87904 AATTCTCATCACTGCTG -s Anc1.Anc1refChr6 35332 17 + 197743 AATTCTCATCACTGCTG -s Anc2.Anc2refChr14 452 17 + 7748 AATTCCCATGACTGCTG -s mr.mrrefChr5 222531 17 + 294540 AGTTGTCATCACTGTTG -s simCow_chr6.simCow.chr6 346963 14 + 602619 AAGTCCTATTGCTG--- -s simDog_chr6.simDog.chr6 249167 17 - 593897 AATTCCCATGACTGCTG -s simHuman_chr6.simHuman.chr6 359029 17 + 601863 AATTCTGATCACTGCTG -s simRat_chr6.simRat.chr6 368153 17 + 647215 AGTTGTCATCACTGTTG - -a -s simMouse_chr6.simMouse.chr6 173428 77 + 636262 GTGGTTAGTTTCGTAATTTAGTAGCAGTGCCAGTTTGATAGCATGGAGTTTATCTGTAATCCAGCTGAGCTTAGCAG -s Anc0.Anc0refChr5 469 76 + 87904 ATGCTTAGTGGTAATATTTAGTAGCATGGCCATTTTGAAAGCTCTTAA-ATGAATGTGAACCAGCTGAGGTTAGCAA -s Anc1.Anc1refChr6 35351 77 + 197743 ATGCTTAGTGGTAATATTTAGTAGCATGGCCATTTTGAAAGCTCTTAATATGAATGTGAACCAGCTGAGGTTAGCAA -s Anc2.Anc2refChr14 471 76 + 7748 ATGCTTAGTGGTAATATTTAATAGCATGGCCTTTTTGAAAGCTCTTAA-ATGAATGTGAACTAGCTGAGGTTAGCAA -s mr.mrrefChr5 222548 77 + 294540 GTGGTTAGTTTCGTAATTTAGTAGCAGTGCCAGTTTGATAGCATGGAGTTTATCTGTGATCCAGCTGAGCTTAGCAG -s simCow_chr6.simCow.chr6 346977 13 + 602619 ----------------------------------------------------------------CTTAAGTTAGCAA -s simDog_chr6.simDog.chr6 249186 76 - 593897 ATGCTTAGTGGTAATATTTAATAGCATGGCCTTTTTGAAAGCTCTTAA-ATGAATGTGAACTAGCTGAGGTTAGTAA -s simHuman_chr6.simHuman.chr6 359048 77 + 601863 ACGTTTAGTAGTAATATTTAGTAGCACGGCCAATTTGACAGCTCTTAATGTGAATGTGAACCAGCTGAGGTTAGCAA -s simRat_chr6.simRat.chr6 368170 76 + 647215 GTGGTTAGTTTAGTATTTTAATAGCAGTGCCAGTTTGATAGCATGGAGTTTATCTGTGATCCAGCTAAGCTTTGCA- - -a -s simMouse_chr6.simMouse.chr6 173505 36 + 636262 TTAGGCATAAGGATTTAAAATGGTCTCGGTGCACTA -s Anc0.Anc0refChr5 551 36 + 87904 TTAGAGCTGTTGGTACAGGCTGTGCTGGGTGAACTA -s Anc1.Anc1refChr6 35434 36 + 197743 TTAGAGCTGTTGGTACAGGCTGTGCTGGGTGAACTA -s Anc2.Anc2refChr14 553 36 + 7748 TTAGAGCAGTTGGTACAGGCTGTGCTGGGTGAACTA -s mr.mrrefChr5 222625 36 + 294540 TTAGGCATAAGGATTTAAGCTGGTCTCGGTGAACTA -s simCow_chr6.simCow.chr6 346996 36 + 602619 TTAGAGAGGTTGGTACAGGCTGCGATGGGTGAACTA -s simDog_chr6.simDog.chr6 249268 36 - 593897 CAAGAGCAGTTGATATGGGCTGTGCTAGGTGAACTA -s simHuman_chr6.simHuman.chr6 359131 36 + 601863 TTAGAGGTGTTGGTACAGGCTGTGCTGGGTGAACTA -s simRat_chr6.simRat.chr6 368246 36 + 647215 TTAGGCCTAGGGATTTAAGCTGGTCTTGGTGATCTA - -a -s simMouse_chr6.simMouse.chr6 173541 8 + 636262 TAACAAGC -s Anc0.Anc0refChr5 588 8 + 87904 TTACAAGC -s Anc1.Anc1refChr6 35471 8 + 197743 TTACAAGC -s Anc2.Anc2refChr14 590 8 + 7748 TTACAAGC -s mr.mrrefChr5 222661 8 + 294540 TAACAAGC -s simCow_chr6.simCow.chr6 347033 8 + 602619 TTATAAGT -s simDog_chr6.simDog.chr6 249305 8 - 593897 GTACGAGC -s simHuman_chr6.simHuman.chr6 359168 8 + 601863 TCACAAGC -s simRat_chr6.simRat.chr6 368282 8 + 647215 TAATAAAG - -a -s simMouse_chr6.simMouse.chr6 173549 19 + 636262 CCAAAAAGTATAAAAAAAC -s Anc0.Anc0refChr5 596 19 + 87904 ACAAAAAGTAGAAACAAAC -s Anc1.Anc1refChr6 35479 19 + 197743 ACAAAAAGTAGAAACAAAC -s Anc2.Anc2refChr14 598 19 + 7748 ACAAAAAGTAGAAACAAAC -s mr.mrrefChr5 222669 19 + 294540 ACAAAAAGTATAAAAAAAC -s simCow_chr6.simCow.chr6 347085 19 + 602619 ACAAAAGGTAGAAACAAAT -s simDog_chr6.simDog.chr6 249313 19 - 593897 ATACGAAGTAGAAATAAAC -s simHuman_chr6.simHuman.chr6 359176 19 + 601863 ACAAAAAGTAGACACAAAC -s simRat_chr6.simRat.chr6 368290 19 + 647215 ACAGAAAGTAAAAAAAAAC - -a -s simMouse_chr6.simMouse.chr6 173568 2 + 636262 CA -s Anc0.Anc0refChr5 615 2 + 87904 CA -s Anc1.Anc1refChr6 35498 2 + 197743 CA -s Anc2.Anc2refChr14 617 2 + 7748 CA -s mr.mrrefChr5 222688 2 + 294540 CA -s simCow_chr6.simCow.chr6 347104 2 + 602619 CA -s simDog_chr6.simDog.chr6 249332 2 - 593897 CA -s simHuman_chr6.simHuman.chr6 359195 2 + 601863 CA -s simRat_chr6.simRat.chr6 368313 2 + 647215 CA - -a -s simMouse_chr6.simMouse.chr6 173570 22 + 636262 TTTGACATTGCGGGATCAGTCA -s Anc0.Anc0refChr5 620 21 + 87904 GTTGAAATAGTGGGATCAGTC- -s Anc1.Anc1refChr6 35503 21 + 197743 GTTGAAATAGTGGGATCAGTC- -s Anc2.Anc2refChr14 622 21 + 7748 GTTGAACTAGTGGGATCAATC- -s mr.mrrefChr5 222690 22 + 294540 TTTGACATTGCGGGATCAGTCA -s simCow_chr6.simCow.chr6 347109 21 + 602619 ATTAAACTAGTGGGATCAATC- -s simDog_chr6.simDog.chr6 249337 18 - 593897 GTTGAGCTAACTCAATCA---- -s simHuman_chr6.simHuman.chr6 359200 21 + 601863 GTTGAAATAGTGGGATCAGTC- -s simRat_chr6.simRat.chr6 368315 20 + 647215 CTGGA--TTGCAGGATCAGTCA - -a -s simMouse_chr6.simMouse.chr6 173592 47 + 636262 CAGAGGGTAAACTTCAGTATTTGCCATTTGTGGGGTACATTGTTTGC -s Anc0.Anc0refChr5 641 46 + 87904 CAAAGGGTAACCTGCAACTTTTGCCATTTGTGGGG-ATGTGGTTTGC -s Anc1.Anc1refChr6 35524 46 + 197743 CAAAGGGTAACCTGCAACTTTTGCCATTTGTGGGG-ATGTGGTTTGC -s Anc2.Anc2refChr14 643 46 + 7748 CAAAGGGTAACCTGCAACTTTTGTCAATTGTGGGG-GTGTGGTCTGC -s mr.mrrefChr5 222712 47 + 294540 CAGAGGGTAAACTTCAGTATTTGCCATTTGTGGGGTACATTGTTTGC -s simCow_chr6.simCow.chr6 347131 42 + 602619 CAAAGGTTAACCTA----TGCTGTCACTTGTGGGG-GTGTGGTCTGC -s simDog_chr6.simDog.chr6 249355 40 - 593897 CAAAGGGTAACCTGCAACTTTTGTGAATCGCGGGG-GTGTG------ -s simHuman_chr6.simHuman.chr6 359221 46 + 601863 TAAAGGGTAACTTGCAACTATTGCCATTTGTGAGA-ATGTGGTTTGC -s simRat_chr6.simRat.chr6 368335 47 + 647215 CAGAGGGCAGACTTTGGTGTTTGCCATTTGTGGGGTACATTGTTTGC - -a -s simMouse_chr6.simMouse.chr6 173639 2 + 636262 AC -s Anc0.Anc0refChr5 687 2 + 87904 AC -s Anc1.Anc1refChr6 35570 2 + 197743 AC -s Anc2.Anc2refChr14 689 2 + 7748 AT -s mr.mrrefChr5 222759 2 + 294540 AC -s simCow_chr6.simCow.chr6 347173 2 + 602619 AT -s simHuman_chr6.simHuman.chr6 359267 2 + 601863 AC -s simRat_chr6.simRat.chr6 368383 2 + 647215 AT - -a -s simMouse_chr6.simMouse.chr6 173641 91 + 636262 AAGTTAATTACAAGTCTCATGAATCCTACTAGAGTATACCTTGCATGTCCCCTTACTCTTTGAAAAACCCCAACCTAGCTCATACTTCCAA -s Anc0.Anc0refChr5 697 91 + 87904 GTGTTACTTAGAAGTCTCATGAATCATACTAGAGCATACCTGGCATATCCTTTTACGCTTTGCAAAACCATAACCTTGGTCCAGCTTCCAA -s Anc1.Anc1refChr6 35580 91 + 197743 GTGTTACTTAGAAGTCTCATGAATCATACTAGAGCATACCTGGCATATCCTTTTACGCTTTGCAAAACCATAACCTTGGTCCAGCTTCCAA -s Anc2.Anc2refChr14 699 91 + 7748 GTGTCACTTAGAAATGTCCTGAATCATACTAGAGCATACCTGGCATACCCTTTTACGTCTTGCAAAACCATAACCTTGGTCCACCTTCCAG -s mr.mrrefChr5 222761 91 + 294540 GTGTTAATTACAAGTCTCATGAATCCTACTAGAGTATACCTTGCATGTCCCTTTACTCTTTGAAAAACCCTAACCTAGCTCATGCTTCCAA -s simCow_chr6.simCow.chr6 347183 91 + 602619 TTGCCACTCATAAAGTGCCTTAATCATACTGGGAGATACCTGGCATACCCTTTTATGTCTTTTAAAACCATCCCCTTGGTCCAACTTGCAG -s simDog_chr6.simDog.chr6 249402 75 - 593897 GTGTCACTTGGAAATGTCCTGAGTCATACTAGAGCAT----------------TGCGTCTTGCAAAACCATAACCTTGGTCCACCTTCCAG -s simHuman_chr6.simHuman.chr6 359277 91 + 601863 GTGGTACTTAGTAGTCTCATGAATCATACTAGAGCATACCTAGTATATCTTTCTAGGCTTTGCAAAACCATATCCTTGGTCCAGTTTCCAA -s simRat_chr6.simRat.chr6 368385 90 + 647215 GTGTTAATGACAAATCTCATGAGTCCTACTAGAGTATACCTTGCGTGTCCCTTTTTTCTTTGGAACACCCTA-CCTAGCTCATGCTTCATA - -a -s simMouse_chr6.simMouse.chr6 173732 18 + 636262 CTTTAGCTGTATACTTTG -s Anc0.Anc0refChr5 793 18 + 87904 TCTTTGTTGAATAAGCTG -s Anc1.Anc1refChr6 35676 18 + 197743 TCTTTGTTGAATAAGCTG -s Anc2.Anc2refChr14 795 18 + 7748 TCTTTGTTGAATAAGCTG -s mr.mrrefChr5 222857 18 + 294540 CTTTAGCTGTATACTTTG -s simCow_chr6.simCow.chr6 347279 18 + 602619 TCTTTGTCAAATAAGTTG -s simDog_chr6.simDog.chr6 249482 18 - 593897 CCTTTGTTGGATAATCTG -s simHuman_chr6.simHuman.chr6 359373 18 + 601863 TCTTCGTTGAATAAGCTG -s simRat_chr6.simRat.chr6 368480 18 + 647215 CTTTGGCTGGATACTTTG - -a -s simMouse_chr6.simMouse.chr6 173750 4 + 636262 TGTG -s Anc0.Anc0refChr5 811 4 + 87904 TCGA -s Anc1.Anc1refChr6 35694 4 + 197743 TCGA -s Anc2.Anc2refChr14 813 4 + 7748 TCGA -s mr.mrrefChr5 222875 4 + 294540 TGTG -s simCow_chr6.simCow.chr6 347297 4 + 602619 TCTG -s simDog_chr6.simDog.chr6 336919 4 + 593897 TTGA -s simHuman_chr6.simHuman.chr6 359391 4 + 601863 CCCA -s simRat_chr6.simRat.chr6 368498 4 + 647215 TGTG - -a -s simMouse_chr6.simMouse.chr6 173754 1 + 636262 G -s Anc0.Anc0refChr5 815 1 + 87904 G -s Anc1.Anc1refChr6 35698 1 + 197743 G -s Anc2.Anc2refChr14 817 1 + 7748 G -s mr.mrrefChr5 222879 1 + 294540 G -s simCow_chr6.simCow.chr6 347301 1 + 602619 G -s simDog_chr6.simDog.chr6 336924 1 + 593897 A -s simHuman_chr6.simHuman.chr6 359395 1 + 601863 G -s simRat_chr6.simRat.chr6 368502 1 + 647215 G - -a -s simMouse_chr6.simMouse.chr6 173755 11 + 636262 GAAAGATAGAA -s Anc0.Anc0refChr5 818 11 + 87904 GTTATATAGAA -s Anc1.Anc1refChr6 35701 11 + 197743 GTTATATAGAA -s Anc2.Anc2refChr14 820 11 + 7748 GTTATATAGAA -s mr.mrrefChr5 222880 11 + 294540 GAAAGATAGAA -s simCow_chr6.simCow.chr6 347302 11 + 602619 ATTATATTGAT -s simDog_chr6.simDog.chr6 336927 11 + 593897 GTTTAATAGCA -s simHuman_chr6.simHuman.chr6 359398 11 + 601863 GTTATATAGAA -s simRat_chr6.simRat.chr6 368503 11 + 647215 GCAAGATATAA - -a -s simMouse_chr6.simMouse.chr6 173766 68 + 636262 TATGGACTTAGCTTGAATAGGATGTGCTGGAAACCTTTCACCCTGCTCCACAAAGGTTGTTCATAGGT -s Anc0.Anc0refChr5 829 54 + 87904 TAAAGATTTACCTTGAATAGGATGCATTG---------CTCCTG-----GTAAAGGTTGGTCACAGAG -s Anc1.Anc1refChr6 35712 54 + 197743 TAAAGATTTACCTTGAATAGGATGCATTG---------CTCCTG-----GTAAAGGTTGGTCACAGAG -s Anc2.Anc2refChr14 831 54 + 7748 TAAAGATTTACTTTAAATAGGATGCATTT---------CTCCTG-----GTAAAGGTTGGTAACAGAG -s mr.mrrefChr5 222891 63 + 294540 TATAGACTTAGCTTGAATAGGATGCACTGGAAACCTTTCACCCT-----ACAAAGGTTGGTCATAGGT -s simCow_chr6.simCow.chr6 347313 40 + 602619 TAGA--------------AGGATGTGTTT---------CTCCCG-----GTAAAGGTTGGTTACAGGG -s simDog_chr6.simDog.chr6 336948 54 + 593897 CAAAGATTTACTTTAAATAGGATGCATTT---------CTCCTG-----GTAAAGGTTGGTAACACAG -s simHuman_chr6.simHuman.chr6 359409 54 + 601863 TAAAGATTTACCTTGAATAGGATGCATTG---------CCCCTG-----GTAAAGGTTGGTCACAGAG -s simRat_chr6.simRat.chr6 368514 63 + 647215 TATAGACTTAGCTTGGATAGAATGCACTGGACGAATTTCACCCT-----ACAAAGGTTGGTCATGGGT - -a -s simMouse_chr6.simMouse.chr6 173834 15 + 636262 AAAGGCCAATTGGTT -s Anc0.Anc0refChr5 884 15 + 87904 AAAGGGCACATGGTC -s Anc1.Anc1refChr6 35767 15 + 197743 AAAGGGCACATGGTC -s Anc2.Anc2refChr14 886 15 + 7748 AAAGGGCACATGGTC -s mr.mrrefChr5 222955 15 + 294540 AAAGGCCAATTGGTT -s simCow_chr6.simCow.chr6 347355 15 + 602619 AAAGGGCACATAGTC -s simDog_chr6.simDog.chr6 337003 15 + 593897 AAAGGGCACGTGGTC -s simHuman_chr6.simHuman.chr6 359464 15 + 601863 AAAGGGCACATGGTC -s simRat_chr6.simRat.chr6 368578 15 + 647215 AAAGGCCGACGGGTT - -a -s simMouse_chr6.simMouse.chr6 173849 28 + 636262 TCCACCTTCATATCATCACTGGGAATCA -s Anc0.Anc0refChr5 905 28 + 87904 TCCATCTTCATATAATTGCTGGGATTCA -s Anc1.Anc1refChr6 35788 28 + 197743 TCCATCTTCATATAATTGCTGGGATTCA -s Anc2.Anc2refChr14 907 28 + 7748 TCCATCTTTGTATACTTGCTGGGATTCA -s mr.mrrefChr5 222976 28 + 294540 TCCACCTTCATATCATCACTGGGAATCA -s simCow_chr6.simCow.chr6 347377 28 + 602619 TCCATATTTGTACAGTTGCTCAGGTTCA -s simDog_chr6.simDog.chr6 337024 28 + 593897 ACCACCTTTGTATACTGGCTGGGATTCA -s simHuman_chr6.simHuman.chr6 359485 28 + 601863 TCCATCTTCATATAAGTGCTAGGATTCA -s simRat_chr6.simRat.chr6 368599 28 + 647215 TCCACCTTCATATCATCACTGGGAATCA - -a -s simMouse_chr6.simMouse.chr6 173877 26 + 636262 TCATTTCCTCCCAGAGTCACTTCACT -s Anc0.Anc0refChr5 934 21 + 87904 TTGTCTCCTCCAAGAGTCACT----- -s Anc1.Anc1refChr6 35817 21 + 197743 TTGTCTCCTCCAAGAGTCACT----- -s Anc2.Anc2refChr14 936 21 + 7748 TTGTCTCCTCCAAGAGTCACT----- -s mr.mrrefChr5 223005 21 + 294540 TCATCTCCTCCAAGAGTCACT----- -s simCow_chr6.simCow.chr6 347406 21 + 602619 TTGTATCCTCCAAAAGTTACT----- -s simDog_chr6.simDog.chr6 337053 21 + 593897 TTGTCCCCTCCAAGGGTCACC----- -s simHuman_chr6.simHuman.chr6 359514 21 + 601863 TTGTCTCCTTCAAGAGTCACT----- -s simRat_chr6.simRat.chr6 368628 21 + 647215 TCATCTCCTCCAAGAGTCACT----- - -a -s simMouse_chr6.simMouse.chr6 173903 11 + 636262 TCTGAGCTTTG -s Anc0.Anc0refChr5 955 8 + 87904 TCTGAGGT--- -s Anc1.Anc1refChr6 35838 8 + 197743 TCTGAGGT--- -s Anc2.Anc2refChr14 957 8 + 7748 TCTGAGGT--- -s mr.mrrefChr5 223026 11 + 294540 TCTGAGCTTTG -s simCow_chr6.simCow.chr6 347427 8 + 602619 CCTGAGGT--- -s simDog_chr6.simDog.chr6 337077 4 + 593897 TCTG------- -s simHuman_chr6.simHuman.chr6 359535 8 + 601863 TCTGAGGT--- -s simRat_chr6.simRat.chr6 368649 11 + 647215 TCTGAACTTTG - -a -s simMouse_chr6.simMouse.chr6 173914 32 + 636262 GAAGTCCTTCCGTCTCAAGGTACAACACTTGA -s Anc0.Anc0refChr5 963 32 + 87904 GGAGTATTCCCATCATTGGGCACAACACTTGG -s Anc1.Anc1refChr6 35846 32 + 197743 GGAGTATTCCCATCATTGGGCACAACACTTGG -s Anc2.Anc2refChr14 965 32 + 7748 GGAATATTCCCATCTTTGGGTGCAATACTTGG -s mr.mrrefChr5 223037 32 + 294540 GAAGTATTTCCATCACTAGGCACAACACTTGG -s simCow_chr6.simCow.chr6 347441 28 + 602619 GGAATAT-CCCATCTTTAGGTGAAATACT--- -s simDog_chr6.simDog.chr6 337081 25 + 593897 -------TCCCATCTTAGGGTGCAATACTTGG -s simHuman_chr6.simHuman.chr6 359543 32 + 601863 GCAGTATTCCAATCATTGGGCACAACACTTGG -s simRat_chr6.simRat.chr6 368660 32 + 647215 GAAGTATGTCCATGAGTAAGCACAACACTTGG - -a -s simMouse_chr6.simMouse.chr6 173946 14 + 636262 TCATATTACTGGGG -s Anc0.Anc0refChr5 1119 14 + 87904 TCACATAACTGGGG -s Anc1.Anc1refChr6 36002 14 + 197743 TCACATAACTGGGG -s Anc2.Anc2refChr14 1121 14 + 7748 TCACACAACTAGGG -s mr.mrrefChr5 223069 14 + 294540 TCATATTACTGGGG -s simCow_chr6.simCow.chr6 347585 14 + 602619 TCACAAAACCAGGG -s simDog_chr6.simDog.chr6 337228 14 + 593897 TCACACATCTAGGG -s simHuman_chr6.simHuman.chr6 359730 14 + 601863 TCACATAACTGGAG -s simRat_chr6.simRat.chr6 368692 14 + 647215 TCATATTACTGGGG - -a -s simMouse_chr6.simMouse.chr6 173960 6 + 636262 GAATGG -s Anc0.Anc0refChr5 1136 6 + 87904 GAATGG -s Anc1.Anc1refChr6 36019 6 + 197743 GAATGG -s Anc2.Anc2refChr14 1138 6 + 7748 GAATGG -s mr.mrrefChr5 223083 6 + 294540 GAATGG -s simCow_chr6.simCow.chr6 347602 6 + 602619 GAATTG -s simDog_chr6.simDog.chr6 337245 6 + 593897 GAATGG -s simHuman_chr6.simHuman.chr6 359747 6 + 601863 GAACGG -s simRat_chr6.simRat.chr6 368706 5 + 647215 GAA-GG - -a -s simMouse_chr6.simMouse.chr6 173966 30 + 636262 GAGTCGAAGATGGGGATGAATGAAAATGGA -s Anc0.Anc0refChr5 1142 29 + 87904 AAGTGGGCCAC-GGGTTGAATGGAAGTGGG -s Anc1.Anc1refChr6 36025 29 + 197743 AAGTGGGCCAC-GGGTTGAATGGAAGTGGG -s Anc2.Anc2refChr14 1144 29 + 7748 AAGTGGGCCAC-TGGTTGAATGGAAGTGGG -s mr.mrrefChr5 223089 30 + 294540 GAGTGGAACATGGGGTTGAATGAAAGTGGG -s simCow_chr6.simCow.chr6 347609 29 + 602619 AAGTGGGCTAC-TGATTGAACGGAAGTCGG -s simDog_chr6.simDog.chr6 337251 29 + 593897 AAGTGGGTCAC-TAGTTGAATGGAGGTGGG -s simHuman_chr6.simHuman.chr6 359753 29 + 601863 AAGTGGGCCAC-GGGTTGAATGGAAGTGGG -s simRat_chr6.simRat.chr6 368711 30 + 647215 GAGTGGAACATGGGGTTGAATGAAAGTGGG - -a -s simMouse_chr6.simMouse.chr6 173996 18 + 636262 GCTACCAGGCTTCACATA -s Anc0.Anc0refChr5 1173 13 + 87904 ACCATCAGG-----AACA -s Anc1.Anc1refChr6 36056 13 + 197743 ACCATCAGG-----AACA -s Anc2.Anc2refChr14 1175 13 + 7748 ACCATGAGC-----AACA -s mr.mrrefChr5 223119 18 + 294540 GCTACCAGGCTTCACATA -s simCow_chr6.simCow.chr6 347640 13 + 602619 ATCATGAGC-----AACG -s simDog_chr6.simDog.chr6 337282 13 + 593897 ACCATGGGC-----AACA -s simHuman_chr6.simHuman.chr6 359784 13 + 601863 ACCATCAGG-----AACA -s simRat_chr6.simRat.chr6 368741 18 + 647215 GCTAATGGGCTTGACATA - -a -s simMouse_chr6.simMouse.chr6 174014 7 + 636262 TAAAGAT -s Anc0.Anc0refChr5 1186 7 + 87904 TAAAGAT -s Anc1.Anc1refChr6 36069 7 + 197743 TAAAGAT -s Anc2.Anc2refChr14 1190 7 + 7748 TAAAGAT -s mr.mrrefChr5 223137 7 + 294540 TAAAGAT -s simCow_chr6.simCow.chr6 347655 7 + 602619 TACAGAT -s simDog_chr6.simDog.chr6 337297 7 + 593897 TAAAGAC -s simHuman_chr6.simHuman.chr6 359797 7 + 601863 CAAAGAT -s simRat_chr6.simRat.chr6 368759 7 + 647215 TGAAGAT - -a -s simMouse_chr6.simMouse.chr6 174021 24 + 636262 GCTTGAAATCAACGACACTCCTCC -s Anc0.Anc0refChr5 1217 17 + 87904 ------A-CAAGCAATGCCACTCT -s Anc1.Anc1refChr6 36100 17 + 197743 ------A-CAAGCAATGCCACTCT -s Anc2.Anc2refChr14 1221 17 + 7748 ------C-AAAGCAATGTCACCCT -s mr.mrrefChr5 223168 23 + 294540 GCTTGAA-CCAACAACACCCCTCC -s simCow_chr6.simCow.chr6 347663 4 + 602619 --------------------TCCT -s simDog_chr6.simDog.chr6 337338 14 + 593897 ------C-AAAGCAATGTCAC--- -s simHuman_chr6.simHuman.chr6 359828 17 + 601863 ------A-CAAGCAATGCCGCTCT -s simRat_chr6.simRat.chr6 368807 23 + 647215 GCTTGAA-CCAACAACACCCCTCC - -a -s simMouse_chr6.simMouse.chr6 174045 1 + 636262 C -s Anc0.Anc0refChr5 1235 1 + 87904 C -s Anc1.Anc1refChr6 36118 1 + 197743 C -s Anc2.Anc2refChr14 1239 1 + 7748 C -s mr.mrrefChr5 223191 1 + 294540 C -s simCow_chr6.simCow.chr6 347668 1 + 602619 C -s simHuman_chr6.simHuman.chr6 359846 1 + 601863 C -s simRat_chr6.simRat.chr6 368830 1 + 647215 C - -a -s simMouse_chr6.simMouse.chr6 174046 9 + 636262 TTCTGCTGT -s Anc0.Anc0refChr5 1236 8 + 87904 TTCTGCTG- -s Anc1.Anc1refChr6 36119 9 + 197743 TTCTGCTGC -s Anc2.Anc2refChr14 1240 8 + 7748 TTCTGCCG- -s mr.mrrefChr5 223192 9 + 294540 TTCTGCTGT -s simCow_chr6.simCow.chr6 347670 8 + 602619 TTCTGCCG- -s simHuman_chr6.simHuman.chr6 359847 9 + 601863 TTCTGCTGC -s simRat_chr6.simRat.chr6 368831 9 + 647215 TTTTGCTGT - -a -s simMouse_chr6.simMouse.chr6 174055 217 + 636262 ACTGTAGGCATTTAGTGAGGGTCTAGAACCAAAAGTGATTTCAGCTGTCTCTCAAATGAAAGTCATCATACTTGTCTTATAATCAGAACAGAGCACCACACACATTGGAATTTGCTGGTTGTTTTGCTGGACACCAAGCGAAATATTGACGCTTCCACCTAGATTATACCCAAACCTACAACTATACAAACTGACAAACCCTAAAACAGAGACCTGC -s Anc0.Anc0refChr5 1249 72 + 87904 A------------------------------------------------------------------------------------------------------------------------------------------GAAACAGTGACA-----ACCTCAATTTTTCCCAAACCTTCATTAATTCAAACTAACAAATCCTAAGAAAAAAGC--AC -s Anc1.Anc1refChr6 36133 79 + 197743 A------------------------------------------------------------------------------------------------------------------------------------------GAAACAGTGACACTACCACCTCAATTTTTCCCAAACCTTCATTAATTCAAACTAACAAATCCTAAGAAAAAAGCCTAC -s Anc2.Anc2refChr14 1253 72 + 7748 A------------------------------------------------------------------------------------------------------------------------------------------GAAACAGTGACA-----ACCTCAATTTGTTCCAAACCTTCATTAACTCAAACTAACAAATGCTAAGAAAAAAGC--AC -s mr.mrrefChr5 223201 79 + 294540 A------------------------------------------------------------------------------------------------------------------------------------------GAAATATTGACGCTTCCACCTAGATTATACCCAAACCTACAACTATACAAACTGACAAACCCTAAAACAGAGACCTGC -s simCow_chr6.simCow.chr6 347683 72 + 602619 A------------------------------------------------------------------------------------------------------------------------------------------GAAACAGTGACA-----ACCTCAATTTGTTCCAAACCTTCAACAACATAAACTAACAAACTCTAAGACACCAGG--AA -s simDog_chr6.simDog.chr6 337352 42 + 593897 -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------TCCTTCTTTAACTCAGACCAACAAATGCTAAGAAAAAAGC--AC -s simHuman_chr6.simHuman.chr6 359861 79 + 601863 A------------------------------------------------------------------------------------------------------------------------------------------GAAACAGTGACACTACCACCTTTATTCTTCCCCAACCTTTAGTGATTCGAATTAACAAATCCAAAGATAAAAGCCTTT -s simRat_chr6.simRat.chr6 368840 55 + 647215 A------------------------------------------------------------------------------------------------------------------------------------------GCAATAATGACGCTTCCACCTAGCTGAGGCAAACACCTACC----TGCAAAATGGCAA-------------------- - -a -s simMouse_chr6.simMouse.chr6 174272 36 + 636262 CTGTACACTGGCTCTCCACTCTGTAACCTACAAAAT -s Anc0.Anc0refChr5 1321 36 + 87904 CTGTACACTGCCCCCCCATTCTGTAGCCTAAAATAT -s Anc1.Anc1refChr6 36212 36 + 197743 CTGTACACTGCCCCCCCATTCTGTAGCCTAAAATAT -s Anc2.Anc2refChr14 1325 36 + 7748 CTGTACACTGCCCCCCCACTTTGTAGCCGAAAGTAT -s mr.mrrefChr5 223280 36 + 294540 CTGTACACTGGCTCTCCATTCTGTAACCTAAAAAAT -s simCow_chr6.simCow.chr6 347755 36 + 602619 AAGTACACCAACCCCCCACTTTGCAGCCCTAAGCAT -s simDog_chr6.simDog.chr6 337394 36 + 593897 CTGTACACTGCCATCCCACTTTGTAGCCGAAAGTAT -s simHuman_chr6.simHuman.chr6 359945 36 + 601863 CTGTACACTGCCCCCCAATTCTGTAGCCTGAAATAT -s simRat_chr6.simRat.chr6 368895 28 + 647215 --------TGGCTCTCCATTCTGCAACCTAAAAAAT - -a -s simMouse_chr6.simMouse.chr6 174308 21 + 636262 GACTGAGATAGTTTGTAACGA -s Anc0.Anc0refChr5 1394 21 + 87904 GACTGGGATAGTTTTTGCTTA -s Anc1.Anc1refChr6 36285 21 + 197743 GACTGGGATAGTTTTTGCTTA -s Anc2.Anc2refChr14 1398 21 + 7748 TACTGGGATAGTTTTAGCTTA -s mr.mrrefChr5 223316 21 + 294540 GACTGAGATAGTTTGTACTGA -s simCow_chr6.simCow.chr6 347824 21 + 602619 TGCTTGGATAGTCCTCACTTA -s simDog_chr6.simDog.chr6 337466 21 + 593897 TACTGGGATAGTTTTAGGTTT -s simHuman_chr6.simHuman.chr6 360018 21 + 601863 GACTGGCATAGTTTTTGCTTA -s simRat_chr6.simRat.chr6 368923 21 + 647215 GACTGTGATAGTTTGCACTGA - -a -s simMouse_chr6.simMouse.chr6 174329 25 + 636262 GGAATGGCCAATTCCCTTTGTCTAT -s Anc0.Anc0refChr5 1415 25 + 87904 GGAATGGCCAATTGTCTTTCTCAAT -s Anc1.Anc1refChr6 36306 25 + 197743 GGAATGGCCAATTGTCTTTCTCAAT -s Anc2.Anc2refChr14 1419 25 + 7748 GGAATGGCCAATTGTCTTTCTCCAT -s mr.mrrefChr5 223337 25 + 294540 GGAATGGCCAATTCTCTTTCTCAAT -s simCow_chr6.simCow.chr6 347850 25 + 602619 AGAATGGCCAATTGTCTTTCTCAGT -s simDog_chr6.simDog.chr6 337487 24 + 593897 GAAAT-GCCGGTTGCCTTTCTCCAT -s simHuman_chr6.simHuman.chr6 360039 25 + 601863 GGAATGGCCAATTGTCTATCTCACT -s simRat_chr6.simRat.chr6 368944 25 + 647215 GAGGTGTCCACTGCTCTTTCTAAAT - -a -s simMouse_chr6.simMouse.chr6 174354 55 + 636262 AAAGGGGATAGGCCAGATGCATCTCCTGGAGGCATGTAATAAGCCTGCATCTACG -s Anc0.Anc0refChr5 1440 54 + 87904 AAATTGGATAGGCCACATGCATCTGCAGAAAG-TTGTGATAAGCCTGCATCTATG -s Anc1.Anc1refChr6 36331 54 + 197743 AAATTGGATAGGCCACATGCATCTGCAGAAAG-TTGTGATAAGCCTGCATCTATG -s Anc2.Anc2refChr14 1445 54 + 7748 AAATTGGATGGGCCACATGCATCTACAGAAAG-CTGTGATAAGCCTGCACCAATG -s mr.mrrefChr5 223362 55 + 294540 AAAGGGGATAGGCCAGATGCATCTGCTGGAGGCTTGTAATAAGCCTGCATCTACG -s simCow_chr6.simCow.chr6 347876 54 + 602619 AAAGGGGATGGGCCACATGCATTGATGGAAAG-CTATGATAATCCTGTGCCAATG -s simDog_chr6.simDog.chr6 337512 54 + 593897 AAATTGGATGGGCCACATGCATCTACAGGATG-CTGTGGTAAGCCTGCACCAATA -s simHuman_chr6.simHuman.chr6 360064 49 + 601863 -----GGACAGGCTGCATGAGTCTGCAGAAAA-TTGTGATAAGCCTGAATCTATG -s simRat_chr6.simRat.chr6 368969 55 + 647215 AAAGGGGATAGGCCAGATGCATTTGCTGGAGGCTTGTACTAAGCCTGCGTTTACG - -a -s simMouse_chr6.simMouse.chr6 174409 13 + 636262 GCAGCATAACTTG -s Anc0.Anc0refChr5 1495 13 + 87904 CCAGCAGATCAAG -s Anc1.Anc1refChr6 36386 13 + 197743 CCAGCAGATCAAG -s Anc2.Anc2refChr14 1500 13 + 7748 CCAGCAGCTCAAG -s mr.mrrefChr5 223417 13 + 294540 GCAGCATAACTAG -s simCow_chr6.simCow.chr6 347931 13 + 602619 GCAGCAGGTGAGG -s simDog_chr6.simDog.chr6 337567 13 + 593897 CCAGTAGCTCAAG -s simHuman_chr6.simHuman.chr6 360114 13 + 601863 ACAGCAGATCAAG -s simRat_chr6.simRat.chr6 369024 13 + 647215 GCAACATAACTAG - -a -s simMouse_chr6.simMouse.chr6 174422 46 + 636262 CAAGTGATAACAAAAAATATGGTCACACAGCAGACCAGGAAAGCCC -s Anc0.Anc0refChr5 1508 46 + 87904 TAAGCGATAACAAAAAATATCATCACACATCAGACCAGGAAAGCCC -s Anc1.Anc1refChr6 36399 46 + 197743 TAAGCGATAACAAAAAATATCATCACACATCAGACCAGGAAAGCCC -s Anc2.Anc2refChr14 1513 46 + 7748 TAAGCGATAATAAAAACTATCATCACATATCAGACCAGGAAAGCCC -s mr.mrrefChr5 223430 46 + 294540 TAAGTGATAACAAAAAATATGGTCACACAGCAGACCAGGAAAGCCC -s simCow_chr6.simCow.chr6 347944 46 + 602619 TAAGTGATAATACAAACTATCATCAGATGTCATATCCGGAAAGTCT -s simDog_chr6.simDog.chr6 337597 46 + 593897 TAAGCGATATTAAAGCCTATCATCACATATCAGACCATGAAAGCCC -s simHuman_chr6.simHuman.chr6 360127 46 + 601863 TAAGCGATCACAAAAAATATCACCACACATCAGACCAGGTAAGCTC -s simRat_chr6.simRat.chr6 369037 46 + 647215 TAAATGATAACAAAAAACATGGTCGTGTGGTAGACCAGCAAATCCC - -a -s simMouse_chr6.simMouse.chr6 174468 12 + 636262 ACACTAATATAT -s Anc0.Anc0refChr5 1557 12 + 87904 ACACTAAGAGAT -s Anc1.Anc1refChr6 36448 12 + 197743 ACACTAAGAGAT -s Anc2.Anc2refChr14 1562 12 + 7748 ACACTAGGAGAC -s mr.mrrefChr5 223476 12 + 294540 ACACTAATATAT -s simCow_chr6.simCow.chr6 347993 12 + 602619 ACACTATGGGCC -s simDog_chr6.simDog.chr6 337646 12 + 593897 ACACTAGGAGAC -s simHuman_chr6.simHuman.chr6 360176 12 + 601863 ACACTAAGAGAT -s simRat_chr6.simRat.chr6 369084 12 + 647215 GCACTAGTATAC - -a -s simMouse_chr6.simMouse.chr6 174480 11 + 636262 ATCAGGTAATA -s Anc0.Anc0refChr5 1569 11 + 87904 GTCAGGTATTA -s Anc1.Anc1refChr6 36460 11 + 197743 GTCAGGTATTA -s Anc2.Anc2refChr14 1578 11 + 7748 GTCAAGTATTA -s mr.mrrefChr5 223488 11 + 294540 ATCAGGTAATA -s simCow_chr6.simCow.chr6 348010 11 + 602619 GCCAAGTATTA -s simDog_chr6.simDog.chr6 337662 11 + 593897 GTCAAGTATTA -s simHuman_chr6.simHuman.chr6 360188 7 + 601863 ----GGCTTTA -s simRat_chr6.simRat.chr6 369096 11 + 647215 ATCAAGTAATA - -a -s simMouse_chr6.simMouse.chr6 174491 9 + 636262 ACACATCCA -s Anc0.Anc0refChr5 1580 9 + 87904 ACACATCCA -s Anc1.Anc1refChr6 36471 9 + 197743 ACACATCCA -s Anc2.Anc2refChr14 1592 9 + 7748 CTCCATCCA -s mr.mrrefChr5 223499 9 + 294540 ACACATCCA -s simCow_chr6.simCow.chr6 348025 9 + 602619 CTCCATCAA -s simDog_chr6.simDog.chr6 337676 9 + 593897 CTCCATCCA -s simHuman_chr6.simHuman.chr6 360195 9 + 601863 ACACACCCA -s simRat_chr6.simRat.chr6 369107 9 + 647215 GCAAATCCA - -a -s simMouse_chr6.simMouse.chr6 174500 34 + 636262 GGCTGTATGTACATATGGTCTTTATGGGAGGTCA -s Anc0.Anc0refChr5 1589 34 + 87904 GGCAGTTCAAATACATGGTCTTTATGGGTGGTCA -s Anc1.Anc1refChr6 36480 34 + 197743 GGCAGTTCAAATACATGGTCTTTATGGGTGGTCA -s Anc2.Anc2refChr14 1601 34 + 7748 GGCAGTTCAAATACATGGTCTTTATGGGTGGTCC -s mr.mrrefChr5 223508 34 + 294540 GGCTGTATGTATATATGGTCTTTATGGGTGGTCA -s simCow_chr6.simCow.chr6 348035 34 + 602619 GGGAGTTCAAATAAATGGGCTTTATGAGTGGACC -s simDog_chr6.simDog.chr6 337685 34 + 593897 GGCACTTCAAATACAAGGTCATTATGGGTGGTCC -s simHuman_chr6.simHuman.chr6 360204 33 + 601863 AACAGTTCAAATACATGGTCTGTATGGGT-GTCA -s simRat_chr6.simRat.chr6 369116 33 + 647215 GGCTGTATTTATATATGGTCTT-ATCAGTGGTCA - -a -s simMouse_chr6.simMouse.chr6 174534 7 + 636262 TAAGCTT -s Anc0.Anc0refChr5 1626 7 + 87904 TGAGCTT -s Anc1.Anc1refChr6 36517 7 + 197743 TGAGCTT -s Anc2.Anc2refChr14 1638 7 + 7748 TGAGCTT -s mr.mrrefChr5 223542 7 + 294540 TAAGCTT -s simCow_chr6.simCow.chr6 348072 7 + 602619 TGAGCTT -s simDog_chr6.simDog.chr6 337722 7 + 593897 TGAGCAT -s simHuman_chr6.simHuman.chr6 360240 7 + 601863 TGAGCTT -s simRat_chr6.simRat.chr6 369149 7 + 647215 TAAGCTC - -a -s simMouse_chr6.simMouse.chr6 174541 63 + 636262 CTTCATTGTCTTCTTGATAGAACTGGATGCAGTCTGCCGGTCTCTTTAGTGTTAGAATGGTTA -s Anc0.Anc0refChr5 1643 63 + 87904 CTTCAGCATTCTCTTAGTAGTGCTGGATGTGGTCTACTGTTCTCTTTACAGTTAGAATGATTC -s Anc1.Anc1refChr6 36534 63 + 197743 CTTCAGCATTCTCTTAGTAGTGCTGGATGTGGTCTACTGTTCTCTTTACAGTTAGAATGATTC -s Anc2.Anc2refChr14 1655 63 + 7748 CTTCAGCATTCCCTTAGTAGTGCTGGATGTGGTCTACTGTTCTCTTTACAGTTATAACAATTC -s mr.mrrefChr5 223549 63 + 294540 CTTCAGTGTCCTCTTGATAGAGCTGGATGCAGTCTGCTGGTCTCTTTAGAGTTAGAATGGTTA -s simCow_chr6.simCow.chr6 348089 63 + 602619 CTTTAACATTCCCTTGGTAGTGCTGAATGTGGTCTACTGCTTTCTTTACAGTTATAACAATGA -s simDog_chr6.simDog.chr6 337739 62 + 593897 CTTCAGCATTCCCT-ATTAGTGCTGGGTGTGGTCTACCGTTCTCTTTACACTAATAACAATTC -s simHuman_chr6.simHuman.chr6 360257 63 + 601863 CTGCAGCATTCTCTTAGTACTGCTGGATTTGGTCTACTGTTCTCCTTACAGTTAGATTGATTG -s simRat_chr6.simRat.chr6 369156 63 + 647215 CTTCAGTGTCCTCCTGATAGAGCTGGATGCAGTCTGCTGGTCTCTTTAGAGTCAGAACGGTTA - -a -s simMouse_chr6.simMouse.chr6 174604 2 + 636262 AA -s Anc0.Anc0refChr5 1706 2 + 87904 AT -s Anc1.Anc1refChr6 36597 2 + 197743 AT -s Anc2.Anc2refChr14 1718 2 + 7748 AT -s mr.mrrefChr5 223612 2 + 294540 AA -s simCow_chr6.simCow.chr6 348152 2 + 602619 AA -s simDog_chr6.simDog.chr6 337802 2 + 593897 AT -s simHuman_chr6.simHuman.chr6 360320 2 + 601863 AT -s simRat_chr6.simRat.chr6 369219 2 + 647215 AA - -a -s simMouse_chr6.simMouse.chr6 174606 1 + 636262 T -s Anc0.Anc0refChr5 1708 1 + 87904 T -s Anc1.Anc1refChr6 36599 1 + 197743 T -s Anc2.Anc2refChr14 1721 1 + 7748 C -s mr.mrrefChr5 223614 1 + 294540 T -s simCow_chr6.simCow.chr6 348155 1 + 602619 C -s simDog_chr6.simDog.chr6 337805 1 + 593897 C -s simHuman_chr6.simHuman.chr6 360322 1 + 601863 T -s simRat_chr6.simRat.chr6 369221 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 174607 49 + 636262 GCACATGCTCTTTCTTAATGTCTGTTTTAATAATTTGTCTTATGAGTAG -s Anc0.Anc0refChr5 1709 48 + 87904 GCATATTCATTTTCTTAATGTGTGTTTAAGTAATTCAAC-TAAGAGCAG -s Anc1.Anc1refChr6 36600 48 + 197743 GCATATTCATTTTCTTAATGTGTGTTTAAGTAATTCAAC-TAAGAGCAG -s Anc2.Anc2refChr14 1722 48 + 7748 ACATATTCATTTTCTTAATGTGTGTTTAATTACCTCAAC-TAAGAGCAG -s mr.mrrefChr5 223615 49 + 294540 GCACATGCTTTTTCTTAATGTCTGTTTTAGTAATTTGTCTTATGAGTAG -s simCow_chr6.simCow.chr6 348156 48 + 602619 ACATATTCATTTTCTTAATGCGTGTTTAACTAGCTTTCT-TTAGAGAAG -s simDog_chr6.simDog.chr6 337806 48 + 593897 ACATATTTATTTTCTTAATGTGTGGATAATTACCTCAAC-TAAGAGCCA -s simHuman_chr6.simHuman.chr6 360329 41 + 601863 GCGTACTCATTTTCTTAATGTGTGTTTAAGTAAT--------AGGGCAG -s simRat_chr6.simRat.chr6 369222 49 + 647215 GCAGATGTCTTTTCTTAATGTCTGTTCTAGTTACTTGTCTTATGAGTAG - -a -s simMouse_chr6.simMouse.chr6 174656 44 + 636262 GCAGCTTTGTAGAATTTACCTCAGGTCATAGCACTAGCACTCCA -s Anc0.Anc0refChr5 1757 44 + 87904 GCAGCTTTGTAGACCTTTCCACGGCTCATGGCACTGTCACCACA -s Anc1.Anc1refChr6 36648 44 + 197743 GCAGCTTTGTAGACCTTTCCACGGCTCATGGCACTGTCACCACA -s Anc2.Anc2refChr14 1770 44 + 7748 GCAGCTTTATGGACCTTTCCATGGCTTGTGGAACTGTCACCACA -s mr.mrrefChr5 223664 44 + 294540 GCAGCTTTGTAGAACTTACCTCAGGTCATGGCACTGGCACTACA -s simCow_chr6.simCow.chr6 348210 41 + 602619 GTAACATTACGCACCATTCCAG---TTGTATGGGTGTCACCACA -s simDog_chr6.simDog.chr6 337854 37 + 593897 GCAGCTTTATGGACCTTTCCATGGCCTGTGGAACTGT------- -s simHuman_chr6.simHuman.chr6 360370 44 + 601863 GCAGCTTTGTAGACCTTTCTGCGGTTCAAGGCACTGTCACAACA -s simRat_chr6.simRat.chr6 369271 44 + 647215 GCAACTTTGTAGTACTTACCTCAGGTCATGGCACTGGTACTACA - -a -s simMouse_chr6.simMouse.chr6 174700 19 + 636262 GTAGGTAAGGCTTACCGGT -s Anc0.Anc0refChr5 1801 19 + 87904 GCAGGAGAGGCTCACCATT -s Anc1.Anc1refChr6 36692 19 + 197743 GCAGGAGAGGCTCACCATT -s Anc2.Anc2refChr14 1814 19 + 7748 ACACGAGAGGCTCACTGTT -s mr.mrrefChr5 223708 19 + 294540 GCAGGTAAGGCTTACCAGT -s simCow_chr6.simCow.chr6 348305 19 + 602619 ACACGAGAGGCTTACTTTT -s simDog_chr6.simDog.chr6 337891 15 + 593897 ----AAGAGGATCACTGGT -s simHuman_chr6.simHuman.chr6 360414 19 + 601863 GCAGGAGAGGCTCACCATT -s simRat_chr6.simRat.chr6 369315 19 + 647215 GCAGGTAAGGCTTACCAGT - -a -s simMouse_chr6.simMouse.chr6 174719 2 + 636262 AA -s Anc1.Anc1refChr6 36715 2 + 197743 AG -s mr.mrrefChr5 223727 2 + 294540 AA -s simHuman_chr6.simHuman.chr6 360437 2 + 601863 AG -s simRat_chr6.simRat.chr6 369334 2 + 647215 AA - -a -s simMouse_chr6.simMouse.chr6 174721 11 + 636262 GCTATCATATG -s Anc0.Anc0refChr3 4098 11 + 222631 GCTGACATATG -s Anc1.Anc1refChr6 36717 11 + 197743 GCTGACATATG -s Anc2.Anc2refChr13 6528 11 + 96486 GCTGATATAAG -s mr.mrrefChr5 223729 11 + 294540 GCTGTCATATG -s simCow_chr6.simCow.chr6 361868 10 + 602619 GTTGG-ATACG -s simDog_chr6.simDog.chr6 352811 11 + 593897 GCTAATATTAG -s simHuman_chr6.simHuman.chr6 360439 11 + 601863 GCTGACATATG -s simRat_chr6.simRat.chr6 369336 11 + 647215 GTTGTTGTATG - -a -s simMouse_chr6.simMouse.chr6 174732 12 + 636262 ATAACAGTAACA -s Anc0.Anc0refChr3 4109 12 + 222631 ACATTAGTAGCA -s Anc1.Anc1refChr6 36728 12 + 197743 ACATTAGTAGCA -s Anc2.Anc2refChr13 6539 12 + 96486 ACATTAGGGGTA -s mr.mrrefChr5 223740 12 + 294540 ATATCAGTAACA -s simCow_chr6.simCow.chr6 361878 12 + 602619 ACATTAGGGATG -s simDog_chr6.simDog.chr6 352835 12 + 593897 ACATTGGGGGTA -s simHuman_chr6.simHuman.chr6 360450 12 + 601863 ACATTAGTAGCA -s simRat_chr6.simRat.chr6 369347 12 + 647215 ATATCCGAAACA - -a -s simMouse_chr6.simMouse.chr6 174744 11 + 636262 AGATGAGAAGT -s Anc0.Anc0refChr3 4122 11 + 222631 ATAGGAGAGGC -s Anc1.Anc1refChr6 36741 11 + 197743 ATAGGAGAGGC -s Anc2.Anc2refChr13 6552 11 + 96486 ATAGGAGAGGC -s mr.mrrefChr5 223752 11 + 294540 AGATGAGAGGT -s simCow_chr6.simCow.chr6 361891 11 + 602619 ATAGGAGAGGT -s simDog_chr6.simDog.chr6 352848 11 + 593897 ATAGGAGGGGC -s simHuman_chr6.simHuman.chr6 360463 11 + 601863 ATAGGAGAGGA -s simRat_chr6.simRat.chr6 369359 11 + 647215 AGATGAGAGGT - -a -s simMouse_chr6.simMouse.chr6 174755 14 + 636262 GTCAGTTGTTCATG -s Anc0.Anc0refChr3 4133 12 + 222631 AGCAGGTA--CATC -s Anc1.Anc1refChr6 36752 12 + 197743 AGCAGGTA--CATC -s Anc2.Anc2refChr13 6563 12 + 96486 AGCAGGTA--CTTC -s mr.mrrefChr5 223763 14 + 294540 GTCAGTTGTTCATG -s simCow_chr6.simCow.chr6 361905 12 + 602619 AGTTGGTT--CTTT -s simDog_chr6.simDog.chr6 352859 12 + 593897 ACCAGTCA--CTTC -s simHuman_chr6.simHuman.chr6 360474 12 + 601863 AGCAGGTA--CATC -s simRat_chr6.simRat.chr6 369370 14 + 647215 GACAGTCATTCATT - -a -s simMouse_chr6.simMouse.chr6 174769 1 + 636262 G -s Anc0.Anc0refChr3 4145 1 + 222631 A -s Anc1.Anc1refChr6 36764 1 + 197743 A -s Anc2.Anc2refChr13 6587 1 + 96486 A -s mr.mrrefChr5 223777 1 + 294540 G -s simCow_chr6.simCow.chr6 361929 1 + 602619 A -s simDog_chr6.simDog.chr6 352883 1 + 593897 A -s simHuman_chr6.simHuman.chr6 360486 1 + 601863 A -s simRat_chr6.simRat.chr6 369384 1 + 647215 G - -a -s simMouse_chr6.simMouse.chr6 174770 197 + 636262 TTCAGAGCTGTGCAAAGAAAAAGATCATTATGGTTCTCCCAGTAGCCATGAAAGCTGGGAATAATTGAATGGGGCCAGAGTTCATTATGGTTTTCCCAGTAGCCATGACAGTTGGGAATAATTGAATGGGGCCAAAGCAGCTACAACCAATTAGCTCCCACATTTTGTTCACTCAAAAGTGGTAGGTGTAAAACACT -s Anc0.Anc0refChr3 4146 139 + 222631 TACAAAGATGTGCAAGGCAAAAGACCATTCTGGATCTCCAAGGAGCCATGACGGCTCAGA----------------------------------------------------------TAAATGAAAGGGATCATAGCAGCCACAACCAACTAGCTCCCACATATTGTTCACTCTAAGATGGTAGTAGTACAACACA -s Anc1.Anc1refChr6 36765 139 + 197743 TACAAAGATGTGCAAGGCAAAAGACCATTCTGGATCTCCAAGGAGCCATGACGGCTCAGA----------------------------------------------------------TAAATGAAAGGGATCATAGCAGCCACAACCAACTAGCTCCCACATATTGTTCACTCTAAGATGGTAGTAGTACAACACA -s Anc2.Anc2refChr13 6588 139 + 96486 TACAAAGATGTGCAAGGCAAAAGACCATTCTGGATCTCCAAGGAGCCATGACGGTTCAGA----------------------------------------------------------TAAAAGAAAGGGATCATGGCAGCCACAACCAACTAGCTCCCACATATTGTTCACTGTAAGACAGTGGTAGTACAGCATA -s mr.mrrefChr5 223778 197 + 294540 TACAGAGATGTGCAAGGAAAAAGATCATTATGGTTCTCCCAGTAGCCATGAAAGCTGGGAATAATTGAATGGGGCCAGAGTTCATTATGGTTTTCCCAGTAGCCATGACAGTTGGGAATAATTGAATGGGGCCAAAGCAGCTACAACCAATTAGCTCCCACATTTTGTTCACTCAAAAGTGGTAGGTGTAAAACACT -s simCow_chr6.simCow.chr6 361931 117 + 602619 GACATAGATGTGCAAGGCAAAATACCATTATGGTTCTACAAGTAGCCGTGATGGGTCAGA----------------------------------------------------------GGATGGAAAGGGATCATCGCAGCCACAACCAACTTGCTCCCACATATTTTTCATTGT---------------------- -s simDog_chr6.simDog.chr6 352884 139 + 593897 TACAAAGACGTGCAAGGCAAAAGACTATTCTGGATCTCCAAGGAGCCAGGACTGTTCAGA----------------------------------------------------------TAAAAGAAAGGGATTATGGGAGACACAACCAATTAGCTCCCACATATTGTTCACTGTAAGACAGTGGTAGTACAGCATA -s simHuman_chr6.simHuman.chr6 360487 138 + 601863 TACAAAAATGTGCAAGGCAAAAGACCATTGTGCCTCTCCAAGAAGCCATGAGGGCCCAGA----------------------------------------------------------TAAGTGTA-GGGATCACAGCAGCCACAACCAACTAGCTCCCACGTATTATTTCCTCTAAGATGGCAGAAGTATAACACA -s simRat_chr6.simRat.chr6 369385 171 + 647215 TACAGAGATGTGCAGGGAAAAAGATCATTATGATACTCCCAGTAGCCATGATAGTTGGGAATAATTGAATAGGGCCAAAGTTCATTATGGTTTCCCCAGTAGCCATGGTAGTTGGGAACAATTGAATGGGGCCAAAGCAGCTACAACCAATAAGCTCCTAC--------------------------GTAAAACATT - -a -s simMouse_chr6.simMouse.chr6 174967 33 + 636262 GTGATATGCATACCATGGCAGAGCTCAGATTTG -s Anc0.Anc0refChr3 4288 28 + 222631 GTAATATGCTG-----GGTTTAGGGTCGAGCTG -s Anc1.Anc1refChr6 36907 28 + 197743 GTAATATGCTG-----GGTTTAGGGTCGAGCTG -s Anc2.Anc2refChr13 6730 28 + 96486 GTAATACATTG-----GGCTTAGGGTCGAGCTG -s mr.mrrefChr5 223975 33 + 294540 GTGATATGCATACCATGGTTGAGCTTAGATTTG -s simCow_chr6.simCow.chr6 362048 25 + 602619 ---ATACATTT-----GGCTTAGGGTCAAGCTG -s simDog_chr6.simDog.chr6 353026 28 + 593897 GTAATACATTG-----GGCTTAGGGTTGAACTG -s simHuman_chr6.simHuman.chr6 360628 28 + 601863 GTAATATGCTC-----GGTTTAGGGTCGAGCTG -s simRat_chr6.simRat.chr6 369556 33 + 647215 GTGATATGCATACCGTGGTTGAACTTAGATTTG - -a -s simMouse_chr6.simMouse.chr6 175000 24 + 636262 AGAGGCAGAAGGAATAACAATTTA -s Anc0.Anc0refChr3 4316 23 + 222631 AGAGGTAGAGGGCATTACATCT-A -s Anc1.Anc1refChr6 36935 24 + 197743 AGAGGTAGAGGGCATTACATCTCA -s Anc2.Anc2refChr13 6764 23 + 96486 AGAGGTAGAGAGCACTGCATCT-A -s mr.mrrefChr5 224008 24 + 294540 AGAGGCAGAGGGAATAACAATTTA -s simCow_chr6.simCow.chr6 362079 23 + 602619 AGAGGCATAGTGCACTTCGGCC-A -s simDog_chr6.simDog.chr6 353060 23 + 593897 AGAGGTAGAGAGCACTGCATCT-A -s simHuman_chr6.simHuman.chr6 360656 24 + 601863 AGAGATAGAGGGCATTACACCTCA -s simRat_chr6.simRat.chr6 369589 24 + 647215 AGAGGGAGAGGGAATAACAATTTA - -a -s simMouse_chr6.simMouse.chr6 175024 13 + 636262 TGTCATACTAGAT -s Anc0.Anc0refChr3 4347 13 + 222631 TGTCAAATTAGAC -s Anc1.Anc1refChr6 36967 13 + 197743 TGTCAAATTAGAC -s Anc2.Anc2refChr13 6797 13 + 96486 TGTCAAGTTGGAC -s mr.mrrefChr5 224032 13 + 294540 TGTCATACTAGAT -s simCow_chr6.simCow.chr6 362111 13 + 602619 TGCCAAGTTGGAC -s simDog_chr6.simDog.chr6 353093 3 + 593897 TGT---------- -s simHuman_chr6.simHuman.chr6 360688 13 + 601863 TGTCAAAACAAAC -s simRat_chr6.simRat.chr6 369613 13 + 647215 TGTCATACTAGAT - -a -s simMouse_chr6.simMouse.chr6 175037 28 + 636262 CACTTGCTGTTGAGATGGGGCTGAGTTT -s Anc0.Anc0refChr3 4361 23 + 222631 CTCCTGTTGTAGAGATGGTGTTA----- -s Anc1.Anc1refChr6 36981 23 + 197743 CTCCTGTTGTAGAGATGGTGTTA----- -s Anc2.Anc2refChr13 6811 23 + 96486 CTCCTGTTGTAGAGATGGTGTTA----- -s mr.mrrefChr5 224046 23 + 294540 CACCTGCTGTAGAGATGGGGCTA----- -s simCow_chr6.simCow.chr6 362125 23 + 602619 CTCCTCTTGTAGAGATGGTGTTA----- -s simDog_chr6.simDog.chr6 353096 22 + 593897 -TCCTGAGGGAGAGATGGTGGCA----- -s simHuman_chr6.simHuman.chr6 360702 23 + 601863 ATCCTGTTGTAGAGATAGTGTTA----- -s simRat_chr6.simRat.chr6 369627 23 + 647215 CACCTGCTGTAGGGAGGGGGCTA----- - -a -s simMouse_chr6.simMouse.chr6 175065 36 + 636262 TGTATGCATGGTTATAAACCTCTTATGTCTCCTTTA -s Anc0.Anc0refChr3 4384 36 + 222631 AATAGGTATAGTTATAGACCTTTTATGTCTCCTTTA -s Anc1.Anc1refChr6 37004 36 + 197743 AATAGGTATAGTTATAGACCTTTTATGTCTCCTTTA -s Anc2.Anc2refChr13 6834 36 + 96486 AATAGGTGTAGTTATAGATCTTTCAGGTATCCTCTA -s mr.mrrefChr5 224069 36 + 294540 TGTATGCATGGTTATAGACCTCTTATGTCTCCTTTA -s simCow_chr6.simCow.chr6 362150 36 + 602619 AATTTGTGCAGTTATAGGTCGTTAACATTTCCTCTA -s simDog_chr6.simDog.chr6 353118 36 + 593897 AATAGGTGTGGTTATAGATCTTTCAGGTATCCTCTA -s simHuman_chr6.simHuman.chr6 360725 36 + 601863 AATACGTATAGTTATAGACCTTTTATGTCTCCTTAA -s simRat_chr6.simRat.chr6 369650 36 + 647215 TGCATGCATGGGTATAGACCTATTATGTATTCTTTG - -a -s simMouse_chr6.simMouse.chr6 175101 21 + 636262 CAAATTGTTTAAGTGTCTCGC -s Anc0.Anc0refChr3 4420 21 + 222631 CTGATTGTTTACATGTCTGTC -s Anc1.Anc1refChr6 37040 21 + 197743 CTGATTGTTTACATGTCTGTC -s Anc2.Anc2refChr13 6870 21 + 96486 CTGATTGTTTACATGTCTGTT -s mr.mrrefChr5 224105 21 + 294540 CAAATTGTTTAAGTGTCTCGC -s simCow_chr6.simCow.chr6 362186 21 + 602619 CTGATTGTCTACATGTCTGTT -s simDog_chr6.simDog.chr6 353154 21 + 593897 CTGAGTTTTTACATGTCAGTT -s simHuman_chr6.simHuman.chr6 360762 21 + 601863 CTGTTTGTTTACAGGTCTGTC -s simRat_chr6.simRat.chr6 369686 21 + 647215 TGTATTGTTTAAGTGTCTCAC - -a -s simMouse_chr6.simMouse.chr6 175122 5 + 636262 TTAGT -s Anc0.Anc0refChr3 4441 1 + 222631 T---- -s Anc1.Anc1refChr6 37061 1 + 197743 T---- -s Anc2.Anc2refChr13 6891 1 + 96486 T---- -s mr.mrrefChr5 224126 5 + 294540 TTAGT -s simCow_chr6.simCow.chr6 362209 1 + 602619 T---- -s simDog_chr6.simDog.chr6 353175 1 + 593897 T---- -s simHuman_chr6.simHuman.chr6 360783 1 + 601863 T---- -s simRat_chr6.simRat.chr6 369707 5 + 647215 TTAGT - -a -s simMouse_chr6.simMouse.chr6 175127 33 + 636262 GTTGGTATTTATAAGTTTCCATCACAACCACCC -s Anc0.Anc0refChr3 4442 33 + 222631 GCTGGTGTTTATGAGCCTCCATTGCAACCACCT -s Anc1.Anc1refChr6 37062 33 + 197743 GCTGGTGTTTATGAGCCTCCATTGCAACCACCT -s Anc2.Anc2refChr13 6892 33 + 96486 GCTGGTGTTTATGAGCCTACATTGCAACCGCCT -s mr.mrrefChr5 224131 33 + 294540 GTTGGTATTTATAAGTTTCCATTACAACCACCC -s simCow_chr6.simCow.chr6 362210 32 + 602619 GTTGGTGTTTAT-AACTTATGTTACAACGGCCT -s simDog_chr6.simDog.chr6 353210 29 + 593897 GCCAGTGTTTATGAGCCTACATTGTAATC---- -s simHuman_chr6.simHuman.chr6 360784 33 + 601863 ACTGGTGTTTATGAGCCTCCATTGCAACCACCT -s simRat_chr6.simRat.chr6 369712 33 + 647215 GTTGGTATTTATAAGTTCCCATTACAACCACCC - -a -s simMouse_chr6.simMouse.chr6 175160 3 + 636262 GTA -s Anc0.Anc0refChr3 4476 3 + 222631 GTA -s Anc1.Anc1refChr6 37096 3 + 197743 GTA -s Anc2.Anc2refChr13 6926 3 + 96486 GTA -s mr.mrrefChr5 224164 3 + 294540 GTA -s simCow_chr6.simCow.chr6 362243 3 + 602619 GTA -s simDog_chr6.simDog.chr6 353240 3 + 593897 GTA -s simHuman_chr6.simHuman.chr6 360818 3 + 601863 GTA -s simRat_chr6.simRat.chr6 369745 3 + 647215 GTA - -a -s simMouse_chr6.simMouse.chr6 175163 9 + 636262 TATTGTTAT -s Anc0.Anc0refChr3 4479 9 + 222631 TAATATTAC -s Anc1.Anc1refChr6 37099 9 + 197743 TAATATTAC -s Anc2.Anc2refChr13 6929 9 + 96486 TAGTATTAC -s mr.mrrefChr5 224167 9 + 294540 TAATATTAT -s simCow_chr6.simCow.chr6 362253 9 + 602619 TAGTATTAC -s simDog_chr6.simDog.chr6 353243 9 + 593897 TAGTATTAC -s simHuman_chr6.simHuman.chr6 360821 9 + 601863 TTATATTAC -s simRat_chr6.simRat.chr6 369748 9 + 647215 TAATATTAT - -a -s simMouse_chr6.simMouse.chr6 175172 89 + 636262 TCAAATGGAAAAACCAAGCTGTTCTAAGACCAGAACAATATGTTTGTTTCTTGCCTTTATGTCAGAACACTTGTTCACACCCATGTGAA -s Anc0.Anc0refChr3 4488 82 + 222631 CTTAATGGAAAAATAGAACTGTGCCAAGCATGGAATGGTGTGTTA---TCTTGCTTTAATTTCAGAACATTTGTTCGT--CCAGGTT-- -s Anc1.Anc1refChr6 37108 87 + 197743 CTTAATGGAAAAATAGAACTGTGCCAAGCATGGAATGGTGTGTTAAGGTCTTGCTTTAATTTCAGAACATTTGTTCGT--CCAGGTTAA -s Anc2.Anc2refChr13 6958 82 + 96486 CTTAATGGAAATATAGAACTGTGCCTAGCATGGAATGGCGTGTTA---TCTTGCTTCAATTTCAAAACATTTGTTTGT--CCAGGAT-- -s mr.mrrefChr5 224176 87 + 294540 CCTAATGGAAAAACCAAACTGTTCTAAGCACAGAATGATGTGTTTATGTCTTGCCTTAATGTCAGAACATTTGTTCAC--CCATGTGAA -s simCow_chr6.simCow.chr6 362282 75 + 602619 TGTAATGGAACTACAGGACTGTTGCCAGTACGGAATGG----------TCTTGCTTAAATTTCAAACCCTGTCTTTGT--GCAGGCT-- -s simDog_chr6.simDog.chr6 353272 82 + 593897 CTTGATGACAATATAGAACTGTGCCTAGCATGGAATGACGTGTTA---TCTTGCTTCAACTTCAAAACAATAGTTTGA--CTAGGAT-- -s simHuman_chr6.simHuman.chr6 360830 83 + 601863 CTTAATGGAAAAA----ACTGTCCCAAGCATGGAATGGTGCATTAAGGTATTGCTTTAATTTCAGAACATTTATTCGT--CCAGGTTAA -s simRat_chr6.simRat.chr6 369757 87 + 647215 CCTAATGGAAAAACCAAACTGTTCTAAACACAGAATGATGTGTTTAAGTCTTACATTAATGTCAGAACATTTGTTCAC--CCAAGTGAA - -a -s simMouse_chr6.simMouse.chr6 175261 6 + 636262 AAAAGT -s Anc0.Anc0refChr3 4570 6 + 222631 AAAAGT -s Anc1.Anc1refChr6 37195 6 + 197743 AAAAGT -s Anc2.Anc2refChr13 7040 6 + 96486 AAAAGT -s mr.mrrefChr5 224263 6 + 294540 AAAAGT -s simCow_chr6.simCow.chr6 362357 6 + 602619 AAAGGT -s simDog_chr6.simDog.chr6 353354 6 + 593897 AAAAGT -s simHuman_chr6.simHuman.chr6 360917 6 + 601863 AAAAAT -s simRat_chr6.simRat.chr6 369844 6 + 647215 AAGAGT - -a -s simMouse_chr6.simMouse.chr6 175267 71 + 636262 GTTTCTTAGAGGAATGTAATGATGTGGACATAACATGATAGGTGTGTAACTGTGCATTTCTCTTGTGCTTT -s Anc0.Anc0refChr3 4579 71 + 222631 ATTTCTAGGAATAATGTAATGATGTTGACTTACCATGATAGGTGTGTAACTGTGCATTTCTCTCTCATTTT -s Anc1.Anc1refChr6 37204 71 + 197743 ATTTCTAGGAATAATGTAATGATGTTGACTTACCATGATAGGTGTGTAACTGTGCATTTCTCTCTCATTTT -s Anc2.Anc2refChr13 7049 71 + 96486 ATTTTTAGGAATAATGTAATGATGTTGACTTACCATCATAGGTGTGTAGCTGCACATTTCTCTCTCATTTT -s mr.mrrefChr5 224269 71 + 294540 GTTTCTTAGAGGAATGTAATGATGTGGACATAACATGATAGGTGTGTAACTGTGCATTTCTCTTGTGCTTT -s simCow_chr6.simCow.chr6 362366 71 + 602619 ATTGTTAGGAAGGATGGAATGATGCTGACTTACTATCATAGCTGTGTAGCTGCCCATTTCTTTCTCATTTG -s simDog_chr6.simDog.chr6 353363 71 + 593897 ATTTTTGGGAATAATGTAATGATGTTGACTTACCATCATGTGTGTGTAGCTCCACATTTCTCTTCCATTTT -s simHuman_chr6.simHuman.chr6 360926 71 + 601863 ATTACTAGGAAAAATGTAACAGTGTTGACTCACCATGATAGGTGTGTAACCGTGCATTTTTCTCTCATTCT -s simRat_chr6.simRat.chr6 369850 62 + 647215 GTTTCTGAGAGGAACGTAATGATGTGGACAT---------GGTGTGTAACTGTGCATTCCTCTTGTGCTTT - -a -s simMouse_chr6.simMouse.chr6 175338 8 + 636262 TCTAGATA -s Anc0.Anc0refChr3 4651 8 + 222631 TCTAGATA -s Anc1.Anc1refChr6 37276 8 + 197743 TCTAGATA -s Anc2.Anc2refChr13 7121 8 + 96486 TCTCAATA -s mr.mrrefChr5 224341 8 + 294540 TCTAGATA -s simCow_chr6.simCow.chr6 362438 8 + 602619 TCTCAATG -s simDog_chr6.simDog.chr6 353435 3 + 593897 -----ATA -s simHuman_chr6.simHuman.chr6 360998 8 + 601863 TCTAGGAA -s simRat_chr6.simRat.chr6 369913 8 + 647215 TCTAGATA - -a -s simMouse_chr6.simMouse.chr6 175346 7 + 636262 CAATCGC -s Anc0.Anc0refChr3 4659 7 + 222631 CAATGTC -s Anc1.Anc1refChr6 37284 7 + 197743 CAATGTC -s Anc2.Anc2refChr13 7135 7 + 96486 CCTTGTC -s mr.mrrefChr5 224349 7 + 294540 CAATCTC -s simCow_chr6.simCow.chr6 362452 7 + 602619 CATTTTC -s simDog_chr6.simDog.chr6 353444 7 + 593897 CCTTGTC -s simHuman_chr6.simHuman.chr6 361006 7 + 601863 AAATGTC -s simRat_chr6.simRat.chr6 369921 7 + 647215 TAATCTC - -a -s simMouse_chr6.simMouse.chr6 175353 31 + 636262 TAATTTTTGTAAGGATGAAAGACAAAATCCC -s Anc0.Anc0refChr3 4666 31 + 222631 CAGTTTTTATAAGTATGAAAAACAAAATACC -s Anc1.Anc1refChr6 37291 31 + 197743 CAGTTTTTATAAGTATGAAAAACAAAATACC -s Anc2.Anc2refChr13 7142 31 + 96486 CAGTTTTTATAAGTATGAAAAGCAAAATACC -s mr.mrrefChr5 224356 31 + 294540 TAATTTTTGTAAGGATGAAAGACAAAATCCC -s simCow_chr6.simCow.chr6 362484 31 + 602619 CAGTTTTTATAAGTATGAGAAGCAAACTACC -s simDog_chr6.simDog.chr6 353451 31 + 593897 TAGTTTTTGTAAGTATGAAAAGCAAAATACC -s simHuman_chr6.simHuman.chr6 361013 31 + 601863 CACTTTTTATTAGTATCAAAAACAAAATACC -s simRat_chr6.simRat.chr6 369928 31 + 647215 TAATCCTTGCAAGGGTGTCGGACAAAATGCC - -a -s simMouse_chr6.simMouse.chr6 175384 19 + 636262 CCATGGACTCCAGTACCTC -s Anc0.Anc0refChr3 4698 19 + 222631 TCATGGCCTCCAGCACTAC -s Anc1.Anc1refChr6 37323 19 + 197743 TCATGGCCTCCAGCACTAC -s Anc2.Anc2refChr13 7174 19 + 96486 TCATGGCCTCCAGCACTTC -s mr.mrrefChr5 224387 19 + 294540 CCATGGACTCCAGTACTAC -s simCow_chr6.simCow.chr6 362516 19 + 602619 TAACGGCCTCCAGCACTTC -s simDog_chr6.simDog.chr6 353483 19 + 593897 TCATGGCCTCCAGTGGTTC -s simHuman_chr6.simHuman.chr6 361045 19 + 601863 TCATGGCCACCAGCACTAC -s simRat_chr6.simRat.chr6 369959 19 + 647215 CCATGGTCTCCAGTACTAC - -a -s simMouse_chr6.simMouse.chr6 175403 13 + 636262 TCTTGGTGTAAGA -s Anc0.Anc0refChr3 4719 13 + 222631 TCCTGGTGTAAGG -s Anc1.Anc1refChr6 37344 13 + 197743 TCCTGGTGTAAGG -s Anc2.Anc2refChr13 7195 13 + 96486 TCCTAGTGTAAGG -s mr.mrrefChr5 224406 13 + 294540 TCTTGGTGTAAGA -s simCow_chr6.simCow.chr6 362537 13 + 602619 ACGTAGTGTAAGG -s simDog_chr6.simDog.chr6 353504 13 + 593897 TACCAGTGCTAGG -s simHuman_chr6.simHuman.chr6 361066 13 + 601863 CCCTGGTGTAAGG -s simRat_chr6.simRat.chr6 369978 13 + 647215 TCTTGATTTAAGA - -a -s simMouse_chr6.simMouse.chr6 175416 22 + 636262 AATATGGCTTTAGCCCCAGTGC -s Anc0.Anc0refChr3 4746 22 + 222631 GATATGCATTTAATCTGGATGC -s Anc1.Anc1refChr6 37371 22 + 197743 GATATGCATTTAATCTGGATGC -s Anc2.Anc2refChr13 7222 22 + 96486 GATATGCATTTAATCTGGATGC -s mr.mrrefChr5 224419 22 + 294540 AATATGGCTTTAGTCCCAGTGC -s simCow_chr6.simCow.chr6 362565 22 + 602619 GGTATGCATTCAGTCTTGATGC -s simDog_chr6.simDog.chr6 353531 22 + 593897 GATAGGCATTTAATCTGGATGC -s simHuman_chr6.simHuman.chr6 361093 19 + 601863 CATATGCATTTATTCT---TGC -s simRat_chr6.simRat.chr6 369991 22 + 647215 AATATGACTTTAGTCCCAGTGC - -a -s simMouse_chr6.simMouse.chr6 175438 51 + 636262 AGTTGAATTAAATCTTGCTAAAGATAGATATTGTATGTTCTGCTTAACTGG -s Anc0.Anc0refChr3 4769 51 + 222631 AGTAGGATTGAATCCTGCTAAACATAGAAATTGTATATCCTGCCTTACTGG -s Anc1.Anc1refChr6 37394 51 + 197743 AGTAGGATTGAATCCTGCTAAACATAGAAATTGTATATCCTGCCTTACTGG -s Anc2.Anc2refChr13 7245 51 + 96486 AGTAGGATTGAATTCTGCTAGACATAGAAATTGTATATCTTGCCTTACTGG -s mr.mrrefChr5 224442 51 + 294540 AGTTGAATTAAATCTTGCTAAACATAGATATTGTATATTCTGCTTTACTGG -s simCow_chr6.simCow.chr6 362588 48 + 602619 AGTAGGACTGAATTCTGTTAGACATAGA---TATATATCTCACCTTACTGG -s simDog_chr6.simDog.chr6 353554 50 + 593897 AGAAGAATTGGATTCTGCTAGACATAGAAATTGTACCTCTTGCC-TAGTGG -s simHuman_chr6.simHuman.chr6 361113 51 + 601863 AGTATGATTGAATCCTGCTAAACCTAGACATTGTATATCCTGCCTTACCAG -s simRat_chr6.simRat.chr6 370014 51 + 647215 AGTTGAATTAAATCTTGCTAGACATAGATATTGTATATTCTGATCTACTGG - -a -s simMouse_chr6.simMouse.chr6 175489 66 + 636262 GTCTTTCTCTAGCAACTCACCCAAAGGCTCTGCTCCCTTTCGAGTGCTCTTGTAGGTCCATAACTT -s Anc0.Anc0refChr3 4831 66 + 222631 GCCTTGCCCTAGCAATTCTCCCAATAGTACCAACCCATCTCTGATGCTCTCGCAAGACCTTAATGT -s Anc1.Anc1refChr6 37456 66 + 197743 GCCTTGCCCTAGCAATTCTCCCAATAGTACCAACCCATCTCTGATGCTCTCGCAAGACCTTAATGT -s Anc2.Anc2refChr13 7307 66 + 96486 TCCTTGCCCTAGCAATTCTCCCAATAGTACCAACCCATCGGTGATGCTCTCGCAAGACCTCAATGT -s mr.mrrefChr5 224493 66 + 294540 GTCTTTCTCTAGCAACTCACCCAAAGGCTCCGCCCCCTTTCTGATGCTCTTGTAAGTCCATAACTT -s simCow_chr6.simCow.chr6 362647 62 + 602619 TCCTTGCACTAGCAATTCTCCCCATAGTACCAACCCGTCAATAATGCTCTCACAAGATCTCA---- -s simDog_chr6.simDog.chr6 353612 65 + 593897 -CCTTGGCCTAGAATTACTCCGAGCAGTACCAACCCATTGGCGATGCTCTTGCCAGACCTCAATGT -s simHuman_chr6.simHuman.chr6 361175 66 + 601863 GCCTTGCCCTGGCAATTCTCCCAATCGTACCAACCCAACTCTGATGCTTTCGCAAGACCTTGATGT -s simRat_chr6.simRat.chr6 370065 66 + 647215 GTTCTTCTCTAGCAACTCGTCCAGAGGCTCCGCCCTCTTTCTGATACTCTTGTAAGTCCATAACTT - -a -s simMouse_chr6.simMouse.chr6 175555 23 + 636262 ATGATGCCAATAACGAAGCTGAA -s Anc0.Anc0refChr3 4902 23 + 222631 AGGATGACAACAATTAAGCTGAG -s Anc1.Anc1refChr6 37527 23 + 197743 AGGATGACAACAATTAAGCTGAG -s Anc2.Anc2refChr13 7378 23 + 96486 AGGATGACAACAATTATGCTGAG -s mr.mrrefChr5 224559 23 + 294540 ATGATGCCAATAATGAAGCTGAA -s simCow_chr6.simCow.chr6 362713 23 + 602619 AGGATAACAATAATTAGGCTGAG -s simDog_chr6.simDog.chr6 353678 21 + 593897 --GATGACGACAATTGTGCTGAG -s simHuman_chr6.simHuman.chr6 361247 23 + 601863 AGGATGACAACAATCAAGCTGAG -s simRat_chr6.simRat.chr6 370131 23 + 647215 GCGATACCGATAATGTAGGTGAA - -a -s simMouse_chr6.simMouse.chr6 175578 23 + 636262 CTGCCTTTCATGTCATGTTAACT -s Anc0.Anc0refChr3 4925 23 + 222631 CTGCCTTTCAGGGTCAGTCAATT -s Anc1.Anc1refChr6 37550 23 + 197743 CTGCCTTTCAGGGTCAGTCAATT -s Anc2.Anc2refChr13 7401 23 + 96486 CTGCCTTTCAGGGTCAGTCAATT -s mr.mrrefChr5 224582 23 + 294540 CTGCCTTTCATGTCATGTTAACT -s simCow_chr6.simCow.chr6 362740 23 + 602619 CTGCCTTTCGGGTTCAGTTAATT -s simDog_chr6.simDog.chr6 353699 23 + 593897 CTGCATTTTAGGGTCAGTCAACT -s simHuman_chr6.simHuman.chr6 361270 23 + 601863 CCGCCTTCCAGACTCAGTAAATT -s simRat_chr6.simRat.chr6 370154 23 + 647215 CTACCTTTCATGTCACGTTTACT - -a -s simMouse_chr6.simMouse.chr6 175601 9 + 636262 AAGTAACAG -s Anc0.Anc0refChr3 4949 9 + 222631 AACCTACAG -s Anc1.Anc1refChr6 37574 9 + 197743 AACCTACAG -s Anc2.Anc2refChr13 7425 9 + 96486 AACCTACAG -s mr.mrrefChr5 224605 9 + 294540 AAGTAACAG -s simCow_chr6.simCow.chr6 362764 7 + 602619 AAGCAAC-- -s simDog_chr6.simDog.chr6 353723 9 + 593897 AACCTACAG -s simHuman_chr6.simHuman.chr6 361294 9 + 601863 AAACGACAG -s simRat_chr6.simRat.chr6 370177 9 + 647215 AAGTAACAG - -a -s simMouse_chr6.simMouse.chr6 175610 7 + 636262 GTGATGG -s Anc0.Anc0refChr3 4959 7 + 222631 ATGATTG -s Anc1.Anc1refChr6 37584 7 + 197743 ATGATTG -s Anc2.Anc2refChr13 7435 7 + 96486 ATGATTG -s mr.mrrefChr5 224614 7 + 294540 GTGATGG -s simCow_chr6.simCow.chr6 362772 7 + 602619 ATGATTG -s simDog_chr6.simDog.chr6 353733 7 + 593897 AGGATTG -s simHuman_chr6.simHuman.chr6 361304 7 + 601863 ATGATTG -s simRat_chr6.simRat.chr6 370186 7 + 647215 GTGATGG - -a -s simMouse_chr6.simMouse.chr6 175617 20 + 636262 CTGTGGCATCCAAATTACTG -s Anc0.Anc0refChr3 4967 20 + 222631 CTGTGCCATCCTTATTATTG -s Anc1.Anc1refChr6 37592 20 + 197743 CTGTGCCATCCTTATTATTG -s Anc2.Anc2refChr13 7443 20 + 96486 CTGTGCCATCCTTATTGTTG -s mr.mrrefChr5 224622 20 + 294540 CTGTGGCATCCTTATTACTG -s simCow_chr6.simCow.chr6 362780 20 + 602619 CTATGCCATCTGTATGCTTG -s simDog_chr6.simDog.chr6 353741 20 + 593897 TGGAGCCATCCTTATTGTTG -s simHuman_chr6.simHuman.chr6 361312 20 + 601863 CTGTCACATCCTTAGTATTG -s simRat_chr6.simRat.chr6 370194 20 + 647215 CTGTGGGATCCTTATTACTG - -a -s simMouse_chr6.simMouse.chr6 175637 43 + 636262 CTCTAGACAACTAGCACCTTGGGAGTACACACCAGGTTGATGT -s Anc0.Anc0refChr3 4991 43 + 222631 TATTGGGCAACTAGCACATTGGGAATGCGTGACAGGTCGCTGT -s Anc1.Anc1refChr6 37616 43 + 197743 TATTGGGCAACTAGCACATTGGGAATGCGTGACAGGTCGCTGT -s Anc2.Anc2refChr13 7467 43 + 96486 TATTGGGCAAACAGCATATTGGGAAGGCGTGACAGGTCACTGT -s mr.mrrefChr5 224642 43 + 294540 CTCTAGACAACTAGCACCTTGGGAGTGCACACCAGGTTGCTGT -s simCow_chr6.simCow.chr6 362804 43 + 602619 AATTGGGCAAACAGCATATTGGGAAGGCGTGAGAGGTCACTGT -s simDog_chr6.simDog.chr6 353765 43 + 593897 TATTGGGCAAACTGCATATTGGGAAGTCATGACAGGTCAATGT -s simHuman_chr6.simHuman.chr6 361336 43 + 601863 TATTGGGCAACTAGCACATTGGGAATGAGTGACAGGTCGCTGT -s simRat_chr6.simRat.chr6 370214 40 + 647215 CCCCATACAACAAGCACCTTGGGAGTGCACA---GGTTGCTGA - -a -s simMouse_chr6.simMouse.chr6 175680 11 + 636262 GAGCATGTGTC -s Anc0.Anc0refChr3 5034 11 + 222631 GAGCATGTGAC -s Anc1.Anc1refChr6 37659 11 + 197743 GAGCATGTGAC -s Anc2.Anc2refChr13 7510 11 + 96486 GAGCATGTGAC -s mr.mrrefChr5 224685 11 + 294540 GAGCATGTGTC -s simCow_chr6.simCow.chr6 362847 11 + 602619 GGGCAAGGCAC -s simDog_chr6.simDog.chr6 353808 11 + 593897 GAGCATGTGAC -s simHuman_chr6.simHuman.chr6 361406 11 + 601863 GAGTATGTGGC -s simRat_chr6.simRat.chr6 370254 10 + 647215 G-GCATGTGTC - -a -s simMouse_chr6.simMouse.chr6 175691 2 + 636262 AG -s Anc0.Anc0refChr3 5045 2 + 222631 AG -s Anc1.Anc1refChr6 37670 2 + 197743 AG -s Anc2.Anc2refChr13 7525 2 + 96486 GG -s mr.mrrefChr5 224696 2 + 294540 AG -s simCow_chr6.simCow.chr6 362862 2 + 602619 GG -s simDog_chr6.simDog.chr6 353823 2 + 593897 GG -s simHuman_chr6.simHuman.chr6 361417 2 + 601863 AG -s simRat_chr6.simRat.chr6 370264 2 + 647215 AG - -a -s simMouse_chr6.simMouse.chr6 175693 7 + 636262 ACTGTAA -s Anc0.Anc0refChr3 5048 7 + 222631 ACTGTAA -s Anc1.Anc1refChr6 37673 7 + 197743 ACTGTAA -s Anc2.Anc2refChr13 7528 7 + 96486 ACTGTAA -s mr.mrrefChr5 224699 7 + 294540 ACTGTAA -s simCow_chr6.simCow.chr6 362865 7 + 602619 ACTGTAA -s simDog_chr6.simDog.chr6 353826 7 + 593897 ACTGTAA -s simHuman_chr6.simHuman.chr6 361420 7 + 601863 ACTGTAT -s simRat_chr6.simRat.chr6 370267 7 + 647215 ACTATAA - -a -s simMouse_chr6.simMouse.chr6 175700 58 + 636262 AAGTTCCACTGCTCTAGGATACATGGTCTAAAAGTTAGGATTTAACAGTAACGAGGGT -s Anc0.Anc0refChr3 5056 58 + 222631 AAGTTCCACTACACTAGGATAGATAGGCTACAAGTCAGGCTTTAACAGTAGCAAAGGT -s Anc1.Anc1refChr6 37681 58 + 197743 AAGTTCCACTACACTAGGATAGATAGGCTACAAGTCAGGCTTTAACAGTAGCAAAGGT -s Anc2.Anc2refChr13 7536 58 + 96486 AAGTTCCACTACACTAGGATAGATATGCTACAAGTCAGGCTTTAACAGTAGCAAAGGT -s mr.mrrefChr5 224706 58 + 294540 AAGTTCCACTGCACTAGGATACATGGTCTAAAAGTTAGGATTTAACAGTAACAAAGGT -s simCow_chr6.simCow.chr6 362873 55 + 602619 TAGCTCCACTATACTAG--TAGATACGCT-CAAGTCATGCTTTAACAGTGGCAAAGGT -s simDog_chr6.simDog.chr6 353834 58 + 593897 ACATTCCATCACACTAGGATAGGTATGCTACAGGTCAGGCTGTAACAGCAGCAATGGT -s simHuman_chr6.simHuman.chr6 361428 58 + 601863 CAGTCCCACTAAACTAGGGCAGATCGGCTACAAGTCAGGTTTTAACAGTAGCAAAGGT -s simRat_chr6.simRat.chr6 370274 58 + 647215 AAGGTCCACTGCACTAGCATACATAGTCTAGAAGTTAGGATTTAACGGTAACAAAGGT - -a -s simMouse_chr6.simMouse.chr6 175758 36 + 636262 CTGGCGTTCTACCCCCCTCCCAGTGCTAATGTGAAA -s Anc0.Anc0refChr3 5116 32 + 222631 CCAGTGTTCAACC----TCCCAGCGCTCTTGTGAAG -s Anc1.Anc1refChr6 37741 32 + 197743 CCAGTGTTCAACC----TCCCAGCGCTCTTGTGAAG -s Anc2.Anc2refChr13 7596 32 + 96486 CCAGTGTTCATCC----TCCCAGCGCTCTTGCTAAG -s mr.mrrefChr5 224764 36 + 294540 CTGGCGTTCTACCCCCCTCCCAGTGCTAATGTGAAA -s simCow_chr6.simCow.chr6 362930 32 + 602619 CCAGTGTTCATCC----TCTCAGTGCTCTTAGTAGG -s simDog_chr6.simDog.chr6 353894 32 + 593897 CAAGTGTTCATCC----TCCCAGCGCTGTTGCTAAG -s simHuman_chr6.simHuman.chr6 361488 32 + 601863 CCAGTGTTCAACC----GCCCAGCACTCTTGTGAAG -s simRat_chr6.simRat.chr6 370332 36 + 647215 CTGGCGTTCTACCTCCCTCCTAGTGCTAATGTGAAA - -a -s simMouse_chr6.simMouse.chr6 175794 74 + 636262 GATCTCTTTTTCTACTGGAATAGGCTGAACATAAAGACTTAAAGTTGCTGTTACATGCTATGTGCAAAGAGGTG -s Anc0.Anc0refChr3 5150 67 + 222631 ------CTCTTCTACTGGAGTGGGGTGAGTATGCAGACCAACAATTGCTGATACATACAATTTGCAAAGAGGT- -s Anc1.Anc1refChr6 37776 74 + 197743 CTTCTACTCTTCTACTGGAGTGGGGTGAGTATGCAGACCAACAATTGCTGATACATACAATTTGCAAAGAGGTG -s Anc2.Anc2refChr13 7630 67 + 96486 ------CTCTTCTTCTGGAGTGGGGTGAATATGCTGACCAACAATTGCCAATACATACAATTTGCAAAGAGGT- -s mr.mrrefChr5 224800 74 + 294540 CATCTCTTTTTCTACTGGAATAGGCTGAGCATAAAGACTTAAAGTTGCTGTTACATGCTATGTGCAAAGAGGTG -s simCow_chr6.simCow.chr6 362964 67 + 602619 ------CTATTTTTCTGGAGTGGGGTGAATGTGCTGACCAACACTTGCCAATACATACAATTTGCAACGAAGT- -s simDog_chr6.simDog.chr6 353928 67 + 593897 ------CGCACCTTCTGGAGTGGGGTGAATATGCTGACCAGCAATTGCCAACACATACAATTAACAAAGAGGT- -s simHuman_chr6.simHuman.chr6 361524 68 + 601863 CTTCTACTCTTCTACTGGAGTGAGATGGGGATGGA------CAATTGCTGATACATACAATTTGCAAAGAGGTG -s simRat_chr6.simRat.chr6 370368 74 + 647215 CATCTTTTTTTCTACTGAGACAGGCTGAGCATAATGACTTAAATTCCCTGTTACGTGCCAAGTGCAAAGAGGTG - -a -s simMouse_chr6.simMouse.chr6 175868 89 + 636262 GCACTCTAAATGTAAGGCCAACGGATTAACAGAGATGATATGATGAGTTCAGCTCTTCAATTCTGTCCTACACAGGGGAATATGCTTCC -s Anc0.Anc0refChr3 5220 76 + 222631 TCACGATAAATGTAAGACCGACTAATTAGAAGAGATGATATTGTGAGTTCATTTCT-------------ACATAGAGGAATTCAGTTCC -s Anc1.Anc1refChr6 37853 76 + 197743 TCACGATAAATGTAAGACCGACTAATTAGAAGAGATGATATTGTGAGTTCATTTCT-------------ACATAGAGGAATTCAGTTCC -s Anc2.Anc2refChr13 7700 76 + 96486 TCACAATAAATGTAAGACCGACTCATTAGAAGAGATGATATTGTGAGTTCATTTCT-------------GCATAGAGTAATTCAATTCC -s mr.mrrefChr5 224874 89 + 294540 GCACGCTAAATGTAAGGCCAACGAATTAGCAGAGATGATATGATGAGTTCAGTTCTTCAATTCTGTCCTACACAGGGGAATATAGTTCC -s simCow_chr6.simCow.chr6 363034 69 + 602619 GCAGAATAAATGTACGACCAATTGATTAGAAGAGATGGTGTTGTGAGTTCACTTCT-------------GCATAG-------TAATCTC -s simDog_chr6.simDog.chr6 353998 76 + 593897 TCACAATAAGTGTAAGGCCGACTCATTAAAAGAGCTGATATTGTGAGCTCATTTAT-------------GCACAGAGTAATTCAATTCC -s simHuman_chr6.simHuman.chr6 361596 76 + 601863 ACATGACAAATGTAAGACCGACCAATTAGAAGAGATGATATTTTGAGTTAATTTCT-------------ACGTAGACGAATTGAGTTCC -s simRat_chr6.simRat.chr6 370442 89 + 647215 GCACGCTGAATGTAAGGCCAACAAATTAGCAGAGATGATATGATGAGTGCAGTTCTTCAGTCCTGTCCTGCACAGGGGAATATAGCTCC - -a -s simMouse_chr6.simMouse.chr6 175957 4 + 636262 TAAT -s Anc0.Anc0refChr3 5299 4 + 222631 TAAT -s Anc1.Anc1refChr6 37932 4 + 197743 TAAT -s Anc2.Anc2refChr13 7779 4 + 96486 TAAT -s mr.mrrefChr5 224963 4 + 294540 TAAT -s simCow_chr6.simCow.chr6 363106 4 + 602619 TAAT -s simDog_chr6.simDog.chr6 354077 4 + 593897 TAAT -s simHuman_chr6.simHuman.chr6 361675 4 + 601863 CAAT -s simRat_chr6.simRat.chr6 370531 4 + 647215 TAAT - -a -s simMouse_chr6.simMouse.chr6 175961 7 + 636262 AACAGTC -s Anc0.Anc0refChr3 5303 7 + 222631 AAGAGTC -s Anc1.Anc1refChr6 37936 7 + 197743 AAGAGTC -s Anc2.Anc2refChr13 7783 7 + 96486 AAGAGCC -s mr.mrrefChr5 224967 7 + 294540 AACAGTC -s simCow_chr6.simCow.chr6 363110 7 + 602619 AACAGCC -s simDog_chr6.simDog.chr6 354081 7 + 593897 AGGAGCT -s simHuman_chr6.simHuman.chr6 361679 7 + 601863 AATAGTC -s simRat_chr6.simRat.chr6 370537 7 + 647215 AACAGTC - -a -s simMouse_chr6.simMouse.chr6 175968 38 + 636262 CAACTACCCTGCTGTTAAATCCTTCCCTGCTGTTAAAT -s Anc0.Anc0refChr3 5317 20 + 222631 CAATCTCCCATCA------------------GCTAAAG -s Anc1.Anc1refChr6 37950 20 + 197743 CAATCTCCCATCA------------------GCTAAAG -s Anc2.Anc2refChr13 7797 20 + 96486 CAATCTCCCATCA------------------CCTAAAG -s mr.mrrefChr5 224974 20 + 294540 CAATCACCCTGCT------------------GTTAAAT -s simCow_chr6.simCow.chr6 363117 20 + 602619 CTAACTCCTATCT------------------CCTAAAG -s simDog_chr6.simDog.chr6 354128 19 + 593897 CAATCTCCCATCA------------------CCT-AAG -s simHuman_chr6.simHuman.chr6 361693 20 + 601863 CAATCTCCCACCG------------------GCTAAAG -s simRat_chr6.simRat.chr6 370544 20 + 647215 CAATCACCCTGCT------------------GTCAAGT - -a -s simMouse_chr6.simMouse.chr6 176006 7 + 636262 CCTTCCA -s Anc0.Anc0refChr3 5339 7 + 222631 CTTTTCA -s Anc1.Anc1refChr6 37972 7 + 197743 CTTTTCA -s Anc2.Anc2refChr13 7819 7 + 96486 CTGTTCA -s mr.mrrefChr5 224994 7 + 294540 CCTTCCA -s simCow_chr6.simCow.chr6 363139 7 + 602619 CAGTTCA -s simDog_chr6.simDog.chr6 354149 7 + 593897 CTGTCCA -s simHuman_chr6.simHuman.chr6 361715 7 + 601863 CTTTTCA -s simRat_chr6.simRat.chr6 370564 7 + 647215 CCTTCCA - -a -s simMouse_chr6.simMouse.chr6 176013 20 + 636262 CTACATTAATGACAGTGGTT -s Anc0.Anc0refChr3 5360 20 + 222631 CTCCAATGCAGGCAGTGGTT -s Anc1.Anc1refChr6 37993 20 + 197743 CTCCAATGCAGGCAGTGGTT -s Anc2.Anc2refChr13 7840 20 + 96486 CTCCAATGCAGGCAGTGGTT -s mr.mrrefChr5 225001 20 + 294540 CTACATTAATGGCAGTGGTT -s simCow_chr6.simCow.chr6 363160 20 + 602619 CTCCAACACAGTCAGTGGTT -s simDog_chr6.simDog.chr6 354170 20 + 593897 TTCCAATGCTGGGAGTGGTT -s simHuman_chr6.simHuman.chr6 361736 20 + 601863 CTCCAATGCAGGCAGTGGTT -s simRat_chr6.simRat.chr6 370571 20 + 647215 CTACATTAATGGCAGTGGTT - -a -s simMouse_chr6.simMouse.chr6 176033 5 + 636262 CAAGT -s Anc0.Anc0refChr3 5381 5 + 222631 TCAGT -s Anc1.Anc1refChr6 38014 5 + 197743 TCAGT -s Anc2.Anc2refChr13 7861 5 + 96486 TCAGT -s mr.mrrefChr5 225022 5 + 294540 TAAGT -s simCow_chr6.simCow.chr6 363181 5 + 602619 CCAGT -s simDog_chr6.simDog.chr6 354191 4 + 593897 TCAG- -s simHuman_chr6.simHuman.chr6 361757 5 + 601863 TCAGT -s simRat_chr6.simRat.chr6 370592 5 + 647215 TGAGT - -a -s simMouse_chr6.simMouse.chr6 176038 22 + 636262 GAAACAAATGTTTATCAGAATT -s Anc0.Anc0refChr3 5389 22 + 222631 GCAACAAATGTTTCTCAAAGTC -s Anc1.Anc1refChr6 38022 22 + 197743 GCAACAAATGTTTCTCAAAGTC -s Anc2.Anc2refChr13 7869 22 + 96486 GCAACAAATGTTTCTCAAAGTC -s mr.mrrefChr5 225027 22 + 294540 GAAACAAATGTTTATCAGAATT -s simCow_chr6.simCow.chr6 363189 22 + 602619 GCAACAGATGTTTCTCAAAATC -s simDog_chr6.simDog.chr6 354198 22 + 593897 GCAACAAATGCTTCTCAAAGTC -s simHuman_chr6.simHuman.chr6 361765 22 + 601863 GCAACAAATGTATCCCAAGGTC -s simRat_chr6.simRat.chr6 370597 13 + 647215 GAAACAGATATTT--------- - -a -s simMouse_chr6.simMouse.chr6 176060 11 + 636262 AAAGACTACCT -s Anc0.Anc0refChr3 5412 11 + 222631 AAAGATTATAT -s Anc1.Anc1refChr6 38045 11 + 197743 AAAGATTATAT -s Anc2.Anc2refChr13 7892 11 + 96486 AAAGATTATAT -s mr.mrrefChr5 225049 11 + 294540 AAAGACTACCT -s simCow_chr6.simCow.chr6 363212 11 + 602619 AAAGATTACAT -s simDog_chr6.simDog.chr6 354221 11 + 593897 AAAGGTGATAT -s simHuman_chr6.simHuman.chr6 361788 11 + 601863 AAAGATTATAT -s simRat_chr6.simRat.chr6 370610 3 + 647215 --------CCT - -a -s simMouse_chr6.simMouse.chr6 176071 190 + 636262 AAGGTGAATGGCTGTAGTTGGTTAGATGTTAGCTGCcactgtttttgtttaagtggatggtcatataactcttccagttaactttacaaagatgcacccttaagttccccagactagtgctgaggtcccagcaattcctttgatgtacagtaaatataacttgaggactcccagtctaaaaaccttatat -s Anc0.Anc0refChr3 5423 16 + 222631 GAAGTGAATAGTTA------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AT -s Anc1.Anc1refChr6 38056 16 + 197743 GAAGTGAATAGTTA------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AT -s Anc2.Anc2refChr13 7903 16 + 96486 GAGATGAATAATTA------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AT -s mr.mrrefChr5 225060 189 + 294540 AAAGTGAATGGCTGTAGTTGGTTAGATGTTAGCTGCcactgtttttgtttaagtggatggtcatataactcttccagttaactttacaaagatgcacccttaag-tccccagactagtgctgaggtcccagcaattcctttgatgtacagtaaatataacttgaggactcccagtctaaaaaccttatat -s simCow_chr6.simCow.chr6 363224 16 + 602619 GAGATGATTAATTA------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AT -s simDog_chr6.simDog.chr6 354232 16 + 593897 AAGATAGATAATTA------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AT -s simHuman_chr6.simHuman.chr6 361799 16 + 601863 GCAGTGAATAGTTA------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AC -s simRat_chr6.simRat.chr6 370613 189 + 647215 AGAATGAATGGGTGTAGTTGGTTAGATGTTACCTGCCGCTCTTTCTGTTTAAGTGGATGGTCATATAGCTCTTCAAGCTTACTTTACAAGGATGTACCTTCGGG-TCAAAATGCTAGTGCTGAGGTCCCAACAAATCCTTTGATGTATATAGAATATAACTTGAGGACTCCCAACCTACAAACTTTATAT - -a -s simMouse_chr6.simMouse.chr6 176261 19 + 636262 agacgacatCTGGTAGACT -s Anc0.Anc0refChr3 5439 19 + 222631 AGTAGCAATGTGGCAGACT -s Anc1.Anc1refChr6 38072 19 + 197743 AGTAGCAATGTGGCAGACT -s Anc2.Anc2refChr13 7919 19 + 96486 AGTACCAATGTGGCAGACT -s mr.mrrefChr5 225249 19 + 294540 agacgacatCTGGTAGACT -s simCow_chr6.simCow.chr6 363240 19 + 602619 AGTAACAACGTGGCAGACT -s simDog_chr6.simDog.chr6 354248 19 + 593897 AGCACCAATGTCGCAGGCT -s simHuman_chr6.simHuman.chr6 361815 19 + 601863 AGTAGCAATGTGGCAGACT -s simRat_chr6.simRat.chr6 370806 19 + 647215 AGACAGAATGCAGTCGCCT - -a -s simMouse_chr6.simMouse.chr6 176280 45 + 636262 CCACCTAAGAAGCAGCCCTAAGTGCATCCCAATTGATATATGTGT -s Anc0.Anc0refChr3 5458 45 + 222631 CCACTTATGAACTACTTATGGGAACATCTGAAAACATATATGTGT -s Anc1.Anc1refChr6 38091 45 + 197743 CCACTTATGAACTACTTATGGGAACATCTGAAAACATATATGTGT -s Anc2.Anc2refChr13 7938 45 + 96486 CCACTCATGAACTACTTATGGGAACATCTGAAAACATATATGTGT -s mr.mrrefChr5 225268 45 + 294540 CCACCTAAGAAGCAGCCCTAAGTGCATCCCAATTGATATATGTGT -s simCow_chr6.simCow.chr6 363263 45 + 602619 ACACTCATGAACGACCCCTGAGAACTTGTCAATATATATAAGTGT -s simDog_chr6.simDog.chr6 354267 45 + 593897 CTACTCATGAACTACTTATGGGAACATCTGAAAACATATATGTGT -s simHuman_chr6.simHuman.chr6 361834 11 + 601863 CCACTTATGAA---------------------------------- -s simRat_chr6.simRat.chr6 370825 45 + 647215 CCACCCAAGAACCAGCCTTAAGTGCATACAAATATATATATGTTT - -a -s simMouse_chr6.simMouse.chr6 176325 14 + 636262 GTGTACTACCCATT -s Anc0.Anc0refChr3 5503 14 + 222631 ATATATCCCCTTTT -s Anc1.Anc1refChr6 38136 14 + 197743 ATATATCCCCTTTT -s Anc2.Anc2refChr13 7990 14 + 96486 ATATATCCCCTTTT -s mr.mrrefChr5 225313 14 + 294540 GTGTACTACCCATT -s simCow_chr6.simCow.chr6 363318 14 + 602619 ATATATATAAGTGT -s simDog_chr6.simDog.chr6 354319 14 + 593897 ATATATCCCCTTTT -s simHuman_chr6.simHuman.chr6 361845 2 + 601863 ------------CT -s simRat_chr6.simRat.chr6 370870 14 + 647215 GTGTACTACCCGTT - -a -s simMouse_chr6.simMouse.chr6 176339 3 + 636262 TTT -s Anc0.Anc0refChr3 5517 3 + 222631 TAT -s Anc1.Anc1refChr6 38150 3 + 197743 TAT -s Anc2.Anc2refChr13 8004 3 + 96486 TAT -s mr.mrrefChr5 225327 3 + 294540 TTT -s simCow_chr6.simCow.chr6 363342 3 + 602619 TTT -s simDog_chr6.simDog.chr6 354333 3 + 593897 TAT -s simHuman_chr6.simHuman.chr6 361847 3 + 601863 ACT -s simRat_chr6.simRat.chr6 370884 3 + 647215 TTT - -a -s simMouse_chr6.simMouse.chr6 176342 31 + 636262 CAACATTTAAAATAAGACCCAATTTAATTGC -s Anc0.Anc0refChr3 5520 31 + 222631 CCACATTTAAAAGTAGACCACATTTCATGGC -s Anc1.Anc1refChr6 38153 31 + 197743 CCACATTTAAAAGTAGACCACATTTCATGGC -s Anc2.Anc2refChr13 8007 31 + 96486 CCACTTTTAAAAGTAGACCACATTTCATGGC -s mr.mrrefChr5 225330 31 + 294540 CAACATTTAAAATAAGACCCAATTTCATTGC -s simCow_chr6.simCow.chr6 363345 31 + 602619 CCACGTTTAAAAATAGTCCATGGTTCATAGC -s simDog_chr6.simDog.chr6 354336 31 + 593897 CCGCTTTTACAAGTAGACCACATTTTGTGAC -s simHuman_chr6.simHuman.chr6 361850 31 + 601863 CTACATCAAAAACTAGACCACATTTCATGGC -s simRat_chr6.simRat.chr6 370888 31 + 647215 CAACATTTAAGAGAAGACCCAATTTCATTGC - -a -s simMouse_chr6.simMouse.chr6 176373 1 + 636262 A -s Anc0.Anc0refChr3 5552 1 + 222631 A -s Anc1.Anc1refChr6 38185 1 + 197743 A -s Anc2.Anc2refChr13 8039 1 + 96486 A -s mr.mrrefChr5 225361 1 + 294540 A -s simCow_chr6.simCow.chr6 363377 1 + 602619 A -s simDog_chr6.simDog.chr6 354368 1 + 593897 A -s simHuman_chr6.simHuman.chr6 361882 1 + 601863 A -s simRat_chr6.simRat.chr6 370919 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 176374 4 + 636262 GAGG -s Anc0.Anc0refChr3 5553 4 + 222631 GATG -s Anc1.Anc1refChr6 38186 4 + 197743 GATG -s Anc2.Anc2refChr13 8040 4 + 96486 AGTG -s mr.mrrefChr5 225362 4 + 294540 GAGG -s simCow_chr6.simCow.chr6 363379 4 + 602619 AGTG -s simDog_chr6.simDog.chr6 354369 4 + 593897 AGTG -s simHuman_chr6.simHuman.chr6 361883 4 + 601863 GAAG -s simRat_chr6.simRat.chr6 370920 4 + 647215 TAGG - -a -s simMouse_chr6.simMouse.chr6 176378 10 + 636262 AGTCCAATGC -s Anc0.Anc0refChr3 5557 6 + 222631 GGTTC----G -s Anc1.Anc1refChr6 38190 6 + 197743 GGTTC----G -s Anc2.Anc2refChr13 8044 6 + 96486 GGTTC----A -s mr.mrrefChr5 225366 10 + 294540 AGTTCAATGG -s simCow_chr6.simCow.chr6 363383 6 + 602619 AGATT----A -s simDog_chr6.simDog.chr6 354373 6 + 593897 GGTTC----A -s simHuman_chr6.simHuman.chr6 361887 6 + 601863 GGTTC----G -s simRat_chr6.simRat.chr6 370926 10 + 647215 AGTTCAATGG - -a -s simMouse_chr6.simMouse.chr6 176388 3 + 636262 TTC -s Anc0.Anc0refChr3 5563 3 + 222631 AAT -s Anc1.Anc1refChr6 38196 3 + 197743 AAT -s Anc2.Anc2refChr13 8050 3 + 96486 AAT -s mr.mrrefChr5 225376 3 + 294540 TTC -s simCow_chr6.simCow.chr6 363392 3 + 602619 AAT -s simDog_chr6.simDog.chr6 354379 3 + 593897 AAT -s simHuman_chr6.simHuman.chr6 361893 3 + 601863 GAT -s simRat_chr6.simRat.chr6 370936 3 + 647215 TTC - -a -s simMouse_chr6.simMouse.chr6 176391 12 + 636262 TATGACTGAGAC -s Anc0.Anc0refChr3 5566 12 + 222631 TATGAATGGGAC -s Anc1.Anc1refChr6 38199 12 + 197743 TATGAATGGGAC -s Anc2.Anc2refChr13 8053 12 + 96486 TATGAATGGGAC -s mr.mrrefChr5 225379 12 + 294540 TATGACTGAGAC -s simCow_chr6.simCow.chr6 363395 12 + 602619 TATGAATGGGAC -s simDog_chr6.simDog.chr6 354387 12 + 593897 TATGAATGTAAC -s simHuman_chr6.simHuman.chr6 361896 12 + 601863 TACAAGTGGGAC -s simRat_chr6.simRat.chr6 370939 12 + 647215 TATGTCTGAGAC - -a -s simMouse_chr6.simMouse.chr6 176403 16 + 636262 AACAGAAGTGAGGACT -s Anc0.Anc0refChr3 5579 16 + 222631 AGCAGAATTGAGGCCT -s Anc1.Anc1refChr6 38212 16 + 197743 AGCAGAATTGAGGCCT -s Anc2.Anc2refChr13 8066 16 + 96486 AGCAGAACTGAGGCCT -s mr.mrrefChr5 225391 16 + 294540 AGCAGAATTGAGGCCT -s simCow_chr6.simCow.chr6 363408 16 + 602619 ATTGGAAGTGTGGCCT -s simDog_chr6.simDog.chr6 354400 16 + 593897 AGCAGAGCTGAGGCCT -s simHuman_chr6.simHuman.chr6 361909 16 + 601863 AGGAGAATTGAAGCTT -s simRat_chr6.simRat.chr6 370951 16 + 647215 AGCAGAATTGAGGCCT - -a -s simMouse_chr6.simMouse.chr6 176419 48 + 636262 GGGACCCGCATAATTGAGGCCTTGATGGTGATGTTTGAAGTATGAAGC -s Anc0.Anc0refChr3 5598 46 + 222631 CGGCAGGACATGATTGATGTTTGG--GAGACAAAGTTCAATATGGATT -s Anc1.Anc1refChr6 38231 46 + 197743 CGGCAGGACATGATTGATGTTTGG--GAGACAAAGTTCAATATGGATT -s Anc2.Anc2refChr13 8085 46 + 96486 CGGCAGGACATGATTGATGTTTGG--AATACAAAGTTCAATATGGATT -s mr.mrrefChr5 225407 48 + 294540 GGGACGAGCATAATTGAGGCCTTGATGGGGATGATTGCAGTATGAAGC -s simCow_chr6.simCow.chr6 363427 45 + 602619 CGGCAGGACATGATTGTTG-TTAA--AATATGCAGTTCAATAAGGTCT -s simDog_chr6.simDog.chr6 354419 46 + 593897 CTGCAGGACATAATTGATGTTTGG--AATACAAGGTTCAATGTGGATC -s simHuman_chr6.simHuman.chr6 361928 46 + 601863 AGGCAAGACATGATTGATGTTTGG--GAGACAAAGTTCAATATGGAAT -s simRat_chr6.simRat.chr6 370967 48 + 647215 GGTACGAGCATAACTGAGGCCTCCATGGGGATGATTGCAGTACGAAGA - -a -s simMouse_chr6.simMouse.chr6 176467 15 + 636262 ATGAGCAATGGTGGA -s Anc0.Anc0refChr3 5649 15 + 222631 CCCAGCAATGATGAA -s Anc1.Anc1refChr6 38282 15 + 197743 CCCAGCAATGATGAA -s Anc2.Anc2refChr13 8136 15 + 96486 CCCAGCAATGATGAA -s mr.mrrefChr5 225455 15 + 294540 ATGAGCAATGGTGGA -s simCow_chr6.simCow.chr6 363477 15 + 602619 CCCAGCAATGATGAC -s simDog_chr6.simDog.chr6 354470 14 + 593897 CACAACAA-GCTCAA -s simHuman_chr6.simHuman.chr6 361979 15 + 601863 CCCAGTAATGATGAA -s simRat_chr6.simRat.chr6 371015 15 + 647215 ATGGGCAATGGTGGA - -a -s simMouse_chr6.simMouse.chr6 176482 5 + 636262 TCCTG -s Anc0.Anc0refChr3 5664 5 + 222631 GACTG -s Anc1.Anc1refChr6 38297 5 + 197743 GACTG -s Anc2.Anc2refChr13 8151 5 + 96486 GACTG -s mr.mrrefChr5 225470 5 + 294540 TACTG -s simCow_chr6.simCow.chr6 363492 5 + 602619 AACTG -s simDog_chr6.simDog.chr6 354489 5 + 593897 GACTG -s simHuman_chr6.simHuman.chr6 361994 5 + 601863 GACTT -s simRat_chr6.simRat.chr6 371030 5 + 647215 TACTG - -a -s simMouse_chr6.simMouse.chr6 176487 51 + 636262 AATCCAGATCATAACTCACAGGGTTACAATGACCATCCTCAGCTGTCTTTG -s Anc0.Anc0refChr3 5672 51 + 222631 AATCTGGATTAAAACTCATAGGGTTACAATGACCATTCTCATCTGGCATTG -s Anc1.Anc1refChr6 38305 51 + 197743 AATCTGGATTAAAACTCATAGGGTTACAATGACCATTCTCATCTGGCATTG -s Anc2.Anc2refChr13 8159 51 + 96486 AGTCTGGGTTAAAGCTCATAGGGTTTCAATGACCATTCTCATCTGGCATTG -s mr.mrrefChr5 225475 51 + 294540 AATCCAGATTATAACTCACAGGGTTACAATGACCATTCTCAGCTGTCTTTG -s simCow_chr6.simCow.chr6 363500 50 + 602619 AGTCTGGGTTATA-CTCAGAGGGTTTCAATGATCATTTTCACTTGGCATGG -s simDog_chr6.simDog.chr6 354497 51 + 593897 AGTCTGGGTTGAAGCTCATAAGGTTTCAATGACCAATCTCATCTGGAATTG -s simHuman_chr6.simHuman.chr6 362002 51 + 601863 AAACTGGATTACAAGTCATAGGGTTACAATGACCATTCTCATCTGCCATAG -s simRat_chr6.simRat.chr6 371035 51 + 647215 ACTTCAGGGTATATCTCACAGGGTTACAATTACCATTCTCAACTCGCTTTG - -a -s simMouse_chr6.simMouse.chr6 176538 37 + 636262 GAAATGAAACAGAGTTGCCAAGTTGAATGCCCTAGTG -s Anc0.Anc0refChr3 5916 37 + 222631 GACATGAAACAAAATTGCCAAGTTAAATGTCCTAGTT -s Anc1.Anc1refChr6 38551 37 + 197743 GACATGAAACAAAATTGCCAAGTTAAATGTCCTAGTT -s Anc2.Anc2refChr13 8452 37 + 96486 GACATGAAACCAAAGCGCCAAGTTAAATGTCCCAGCT -s mr.mrrefChr5 225702 37 + 294540 GAAATGAAACAGAGTTGCCAAGTTAAATGTCCTAGTG -s simCow_chr6.simCow.chr6 363905 31 + 602619 GACATGAAACGGAACCACCAAGCTAAATGTC------ -s simDog_chr6.simDog.chr6 354799 35 + 593897 G--ATGAGGCCAAAGCGCCATGTTAAATGTCCCAGCT -s simHuman_chr6.simHuman.chr6 362263 37 + 601863 GACATGAAACAAAATTGCCAAGTTAAATGTCCTAGTA -s simRat_chr6.simRat.chr6 371329 34 + 647215 GAAATGAAACAGAGTTGC---GCTAAATGTCCTAGTG - -a -s simMouse_chr6.simMouse.chr6 176575 73 + 636262 GTCTTCACATGATTCATTATGCTCTTTTGAACCCAGCTGGAGCCAGAGTTGTGTAAAGGCTTTCCTACTCAAA -s Anc0.Anc0refChr3 5953 73 + 222631 GTTTTCACAGGAAACCTTGTACCTTTTTGAGCCCAATTGAAGCCAGACTTGGGTAGAGACTTTTGTACTCAAG -s Anc1.Anc1refChr6 38588 73 + 197743 GTTTTCACAGGAAACCTTGTACCTTTTTGAGCCCAATTGAAGCCAGACTTGGGTAGAGACTTTTGTACTCAAG -s Anc2.Anc2refChr13 8489 73 + 96486 GTTTTCACAGGAAACCTTGTACCTTTTTGAGCCCAATTGAAACCAGACTTGGGTAGAGACTTTTGTACTCAAA -s mr.mrrefChr5 225739 73 + 294540 GTTTTCACATGAATCATTATGCTTTTTTGAGCCCAGCTGGAGCCAGAGTTGTGTAAAGGCTTTCCTACTCAAG -s simCow_chr6.simCow.chr6 363936 50 + 602619 ---------------TTTGTAGCTTTTTGAGCCCA--------CAGACTTGGGTAGAGGCTTTTGTACTCAAA -s simDog_chr6.simDog.chr6 354834 71 + 593897 GTTTTCACAGGAAACCATGTACC--CTAAAACCCAATTGAAACCAGACTTGGGTAAAGACTCTTATACTCAAA -s simHuman_chr6.simHuman.chr6 362304 73 + 601863 TTTTTCACAAGAAACCTTGTACCTTTTTGAGCCCACTTGAAGCCATACTTGGGTAGAGTCTTTTGTGCTCAAG -s simRat_chr6.simRat.chr6 371363 73 + 647215 GTTTTCACATGAATCATTATGCATGTTTAAGATCAGCTGGAACAAGAGTTGAGTAAAGGCTTTGCTACTCAAG - -a -s simMouse_chr6.simMouse.chr6 176648 29 + 636262 CTACTGAAAACTCATTCTGGTTCTTGTGC -s Anc0.Anc0refChr3 6027 29 + 222631 CTACTGAAAACTGGTTCTGGTTCTTGTGC -s Anc1.Anc1refChr6 38662 29 + 197743 CTACTGAAAACTGGTTCTGGTTCTTGTGC -s Anc2.Anc2refChr13 8563 29 + 96486 CTACTAAAAACTGGTTCTGGTTGTTGTGC -s mr.mrrefChr5 225812 29 + 294540 CTACTGAAAACTCATTCTGGTTCTTGTGC -s simCow_chr6.simCow.chr6 363987 29 + 602619 CTGTGAAAAACCAATTCTAGTTATACTGC -s simDog_chr6.simDog.chr6 354906 29 + 593897 CTACTAAAAACTGGTTCTGGTTGTTGTGC -s simHuman_chr6.simHuman.chr6 362378 29 + 601863 CTACTGGAAACTGGTTTTGGTTCTTGTTC -s simRat_chr6.simRat.chr6 371436 29 + 647215 CTACTGTAATCTCATTCTGGTTCTTGCAC - -a -s simMouse_chr6.simMouse.chr6 176677 37 + 636262 ATCTGGTAGTGTTATTAGTATTTCTAAGTCACACAAA -s Anc0.Anc0refChr3 6058 37 + 222631 ATCTGGTAATATTTTTATAATCTTTAAGTCACATAAG -s Anc1.Anc1refChr6 38693 37 + 197743 ATCTGGTAATATTTTTATAATCTTTAAGTCACATAAG -s Anc2.Anc2refChr13 8594 37 + 96486 ATCTGGTAATATTTTTATAATCTTTAAGTCACATAAG -s mr.mrrefChr5 225841 37 + 294540 ATCTGGTAATGTTATTATTATCTCTAAGTCACATAAA -s simCow_chr6.simCow.chr6 364018 36 + 602619 ATCTAGTGAT-TTATCATAATCTTTAAGTCCCATAAG -s simDog_chr6.simDog.chr6 354937 37 + 593897 GTCTGGCAATATTTTTATAATCTTAAAATCACATAAG -s simHuman_chr6.simHuman.chr6 362409 36 + 601863 ATCTGGTAACATTTTTGTAATCTTTAAGTCACATAA- -s simRat_chr6.simRat.chr6 371465 37 + 647215 ATCTGGTAATTTTATCATTATCTCTAAGTCACATAAA - -a -s simMouse_chr6.simMouse.chr6 176714 2 + 636262 TA -s Anc0.Anc0refChr3 6095 2 + 222631 TA -s Anc1.Anc1refChr6 38730 2 + 197743 TA -s Anc2.Anc2refChr13 8631 2 + 96486 TA -s mr.mrrefChr5 225878 2 + 294540 TA -s simCow_chr6.simCow.chr6 364055 2 + 602619 TA -s simDog_chr6.simDog.chr6 354974 2 + 593897 TA -s simHuman_chr6.simHuman.chr6 362445 2 + 601863 TA -s simRat_chr6.simRat.chr6 371502 2 + 647215 TA - -a -s simMouse_chr6.simMouse.chr6 176716 55 + 636262 AGAACGCGAGCTACACAAGCAAAATCAGAACATCTGACATCTTTTTGTAGCTCGT -s Anc0.Anc0refChr3 6099 46 + 222631 ATAATCTGAACTGCATAAGAAAAATCAGAACATCTGACAACTTA---------AT -s Anc1.Anc1refChr6 38734 51 + 197743 ATAATCTGAACTGCATAAGAAAAATCAGAACATCTGACAACTTA----AGTTCAT -s Anc2.Anc2refChr13 8635 46 + 96486 ATAATCTGAACTGCATAAAAAAAATCAGAACATCTGACAACCTA---------AT -s mr.mrrefChr5 225882 55 + 294540 AGAACCTGAGCTACACAAGCAAAATCAGAACATCTGACATCTTTTTGTAGCTCAT -s simCow_chr6.simCow.chr6 364059 43 + 602619 ATAATATGAACTGCTTAAAAAAGAT---AACATTGGACAACCCC---------AT -s simDog_chr6.simDog.chr6 354978 46 + 593897 ATAACCTGAGCCTCATAAAAAAAGTCAGAACATCTGACAACCTA---------AT -s simHuman_chr6.simHuman.chr6 362449 51 + 601863 ACAATCTGAACTGTATAAGAACAATTAGAACCTCTGACAAGTTA----AGTTCAT -s simRat_chr6.simRat.chr6 371506 55 + 647215 AGAACCTGAGCTACACAAACAAAATCAGAACATCTGACATCTTTCTGTGGCTCAT - -a -s simMouse_chr6.simMouse.chr6 176771 5 + 636262 AGAGA -s Anc0.Anc0refChr3 6156 5 + 222631 TGAAA -s Anc1.Anc1refChr6 38796 5 + 197743 TGAAA -s Anc2.Anc2refChr13 8692 5 + 96486 TGAAC -s mr.mrrefChr5 225948 5 + 294540 AGAAA -s simCow_chr6.simCow.chr6 364113 5 + 602619 GGAAC -s simDog_chr6.simDog.chr6 355035 5 + 593897 TGAGC -s simHuman_chr6.simHuman.chr6 362511 5 + 601863 TGGAA -s simRat_chr6.simRat.chr6 371573 5 + 647215 AGAAA - -a -s simMouse_chr6.simMouse.chr6 176776 54 + 636262 AAAGCAAGCATGTGAGCAACATGCCTTCTGAGACATTGATCTATAGCCCATGTA -s Anc0.Anc0refChr3 6163 49 + 222631 AAGACAAGGATGGGAGCAGAATACCCTGAGAGACAGCAATT-----CTCATGTA -s Anc1.Anc1refChr6 38803 54 + 197743 AAGACAAGGATGGGAGCAGAATACCCTGAGAGACAGCAATTTATGGCTCATGTA -s Anc2.Anc2refChr13 8699 49 + 96486 AAGACAAGGGTGGGAGCAGAATACCCTGAGAGACAGCAATT-----CTCATGTA -s mr.mrrefChr5 225953 54 + 294540 AAGGCAAGGATGTGAGCAAAATACCTTCTGAGACATTGATCTATAGCCCATGTA -s simCow_chr6.simCow.chr6 364120 49 + 602619 AAGACAAGGGTGGGAGCAGCATACCCTGAGAGACAGCCATT-----CTCATGCA -s simDog_chr6.simDog.chr6 355042 49 + 593897 AAGACAAGGGTGGGAGTAGAATACCCTGAGAGACATCAGTT-----CTCATGTA -s simHuman_chr6.simHuman.chr6 362518 53 + 601863 AAGACAAAGATGGGA-CACAATACCCTGAGAGACAGCTATATATGGCTCATGTA -s simRat_chr6.simRat.chr6 371578 54 + 647215 GAGGCAAGGATGTGAGCAAAAGACCTTCTGAGACACTGATCTATAGCCCATGTA - -a -s simMouse_chr6.simMouse.chr6 176830 17 + 636262 GAAACCTTAATTGCTGT -s Anc0.Anc0refChr3 6213 17 + 222631 CAGACCTTTATTACTGT -s Anc1.Anc1refChr6 38858 17 + 197743 CAGACCTTTATTACTGT -s Anc2.Anc2refChr13 8749 17 + 96486 CAGACCTTTATTACTGT -s mr.mrrefChr5 226008 17 + 294540 GAGACCTTAATTACTGT -s simCow_chr6.simCow.chr6 364170 13 + 602619 CAGACCTTAATTA---- -s simDog_chr6.simDog.chr6 355092 15 + 593897 CAGAC--TTATTACTGT -s simHuman_chr6.simHuman.chr6 362572 17 + 601863 CAGACCTTTATTATTGT -s simRat_chr6.simRat.chr6 371633 17 + 647215 TAGACTTCAATTACTGT - -a -s simMouse_chr6.simMouse.chr6 176847 7 + 636262 ACTGTGT -s Anc0.Anc0refChr3 6231 7 + 222631 GCTGTGT -s Anc1.Anc1refChr6 38876 7 + 197743 GCTGTGT -s Anc2.Anc2refChr13 8767 7 + 96486 GCTGTGT -s mr.mrrefChr5 226025 7 + 294540 ACTGTGT -s simCow_chr6.simCow.chr6 364184 2 + 602619 GC----- -s simDog_chr6.simDog.chr6 355108 7 + 593897 GCTGTGT -s simHuman_chr6.simHuman.chr6 362590 7 + 601863 GATGTGT -s simRat_chr6.simRat.chr6 371650 7 + 647215 ACTGTGG - -a -s simMouse_chr6.simMouse.chr6 176854 60 + 636262 CCATATGCCCAGGTGAACTTGCTTCTACAGAAGGTATCCCCTATAATATAGCTGAATGCG -s Anc0.Anc0refChr3 6239 55 + 222631 CCATAAGATAAGGTGAACTTGCTTCTAC--AG---AACCCCCATAATATAGGTAAATGTA -s Anc1.Anc1refChr6 38884 57 + 197743 CCATAAGATAAGGTGAACTTGCTTCTACAGAG---AACCCCCATAATATAGGTAAATGTA -s Anc2.Anc2refChr13 8775 55 + 96486 TCATAAGATAAGCTGAACTTGCTTCGAC--AG---AACCCCCATAATATGGGTAAATGTA -s mr.mrrefChr5 226032 60 + 294540 CCATATGCCCAGGTGAACTTGCTTCTACAGAAGGTATCCCCTATAATATAGCTGAATGCA -s simCow_chr6.simCow.chr6 364186 49 + 602619 -----AACCAAGTGGAACCTACTGC-AC--AG---AAACCCCATAATAGGGATCAATGTA -s simDog_chr6.simDog.chr6 355116 55 + 593897 TCATAAGATACGCTGAAATTGCTTTGAC--AG---AACCCCCATAATATGGGTAGATGTA -s simHuman_chr6.simHuman.chr6 362598 57 + 601863 CCATAAGGTGAGGTGAACTTGCTTCTACAGAG---AACCCCCATAATATAGGCAACTGTA -s simRat_chr6.simRat.chr6 371657 60 + 647215 CCATAGGCCCAGGTAAACTTGCTTCTACAGAAGTTATCCCCTATAATATAGCTGAATGAA - -a -s simMouse_chr6.simMouse.chr6 176914 4 + 636262 GCAG -s Anc0.Anc0refChr3 6294 4 + 222631 GTTC -s Anc1.Anc1refChr6 38941 4 + 197743 GTTC -s Anc2.Anc2refChr13 8830 4 + 96486 GTTC -s mr.mrrefChr5 226092 4 + 294540 GCAG -s simCow_chr6.simCow.chr6 364242 4 + 602619 GTAC -s simDog_chr6.simDog.chr6 355171 4 + 593897 GCTG -s simHuman_chr6.simHuman.chr6 362655 4 + 601863 GTGC -s simRat_chr6.simRat.chr6 371717 4 + 647215 GCAG - -a -s simMouse_chr6.simMouse.chr6 176918 12 + 636262 TTGGTGCACAAT -s Anc0.Anc0refChr3 6298 12 + 222631 CTAGTGCATGAT -s Anc1.Anc1refChr6 38945 12 + 197743 CTAGTGCATGAT -s Anc2.Anc2refChr13 8834 12 + 96486 CTAGTGCATGAT -s mr.mrrefChr5 226096 12 + 294540 TTGGTGCACAAT -s simCow_chr6.simCow.chr6 364247 12 + 602619 CTAGTGAATACT -s simDog_chr6.simDog.chr6 355175 12 + 593897 CTAGTGCATGAT -s simHuman_chr6.simHuman.chr6 362659 12 + 601863 CTAGTGCATCAT -s simRat_chr6.simRat.chr6 371721 12 + 647215 TTGGTGCACTAT - -a -s simMouse_chr6.simMouse.chr6 176930 2 + 636262 CT -s Anc0.Anc0refChr3 6310 2 + 222631 AC -s Anc1.Anc1refChr6 38957 2 + 197743 AC -s Anc2.Anc2refChr13 8847 2 + 96486 AC -s mr.mrrefChr5 226108 2 + 294540 CT -s simCow_chr6.simCow.chr6 364260 2 + 602619 TC -s simDog_chr6.simDog.chr6 355188 2 + 593897 AC -s simHuman_chr6.simHuman.chr6 362671 2 + 601863 AC -s simRat_chr6.simRat.chr6 371733 2 + 647215 CT - -a -s simMouse_chr6.simMouse.chr6 176932 21 + 636262 AAAATTGAAAGCTTGAGACTC -s Anc0.Anc0refChr3 6312 21 + 222631 AAATTTAAGAGCTTTATACTC -s Anc1.Anc1refChr6 38959 21 + 197743 AAATTTAAGAGCTTTATACTC -s Anc2.Anc2refChr13 8849 21 + 96486 AAATTTAAGAGCTTTGTACTA -s mr.mrrefChr5 226110 21 + 294540 AAAATTAAAAGCTTGAGACTC -s simCow_chr6.simCow.chr6 364337 16 + 602619 AAATTTAAGAGTGTTG----- -s simDog_chr6.simDog.chr6 355190 21 + 593897 AAATTTAAGAGCTATGTACTA -s simHuman_chr6.simHuman.chr6 362673 21 + 601863 AAATTTAAGAGCTTCATGCTC -s simRat_chr6.simRat.chr6 371735 21 + 647215 AAAATTAAAAGCTTACGACTC - -a -s simMouse_chr6.simMouse.chr6 176953 55 + 636262 ATACTCACTTAGAATACACAGCAAATGGTTTGATATTGGCAAGTGATGGTATGGA -s Anc0.Anc0refChr3 6334 30 + 222631 ATACTCACTTAAAACAGATAGCAAATGAC-------------------------T -s Anc1.Anc1refChr6 38981 30 + 197743 ATACTCACTTAAAACAGATAGCAAATGAC-------------------------T -s Anc2.Anc2refChr13 8871 30 + 96486 AGACTCACTTAAAACAGATAGCTAATGAC-------------------------T -s mr.mrrefChr5 226132 30 + 294540 ATACTCACTTAGAATACACAGCAAATGAT-------------------------A -s simCow_chr6.simCow.chr6 364353 26 + 602619 ----TCGCTTTAAAAAGATAGCTAATGAG-------------------------T -s simDog_chr6.simDog.chr6 355212 30 + 593897 AGACTCACTTAAAACAGATAGCTAATGAC-------------------------T -s simHuman_chr6.simHuman.chr6 362695 30 + 601863 CTACTCACCTAAAACAGATAGCAAATGAC-------------------------T -s simRat_chr6.simRat.chr6 371757 29 + 647215 ATACTCACTTTGAATACAC-GCAAATGAT-------------------------A - -a -s simMouse_chr6.simMouse.chr6 177008 19 + 636262 GTAATAGTAATAAAACAGA -s Anc0.Anc0refChr3 6423 19 + 222631 GAAATAGTGATACAAAAGA -s Anc1.Anc1refChr6 39070 19 + 197743 GAAATAGTGATACAAAAGA -s Anc2.Anc2refChr13 8960 19 + 96486 GAAATAGTGATACAAAAGA -s mr.mrrefChr5 226162 19 + 294540 GTAATAGTAATAAAACAGA -s simCow_chr6.simCow.chr6 364442 19 + 602619 GAGATAGTGATAAAAAGGA -s simDog_chr6.simDog.chr6 355309 19 + 593897 GAAATAGTGATACAAAAGA -s simHuman_chr6.simHuman.chr6 362784 8 + 601863 AAAATAGT----------- -s simRat_chr6.simRat.chr6 371786 19 + 647215 GTAATAGCAATAAAACAGA - -a -s simMouse_chr6.simMouse.chr6 177027 38 + 636262 TTCACTTCTTAGGATTGGTGGAATCCTAACCTTTTGAT -s Anc0.Anc0refChr3 6442 38 + 222631 TTGACCTCTTAGGATTTACAGAAATCTAACTTGTTAAT -s Anc1.Anc1refChr6 39089 38 + 197743 TTGACCTCTTAGGATTTACAGAAATCTAACTTGTTAAT -s Anc2.Anc2refChr13 8980 38 + 96486 TTGACCTCTTAGGATTTACAGAAATCTAACTGGTGTAT -s mr.mrrefChr5 226181 38 + 294540 TTCACTTCTTAGGATTGATGGAATCCTAACTTTTTAAT -s simCow_chr6.simCow.chr6 364462 38 + 602619 TTGACGTCACAGAATTCATATAAATCTAACCGTTTGAT -s simDog_chr6.simDog.chr6 355329 38 + 593897 TTGACCTCTTAGGATTTACAGAACTCTAACTGGTGTAT -s simHuman_chr6.simHuman.chr6 362792 14 + 601863 ------------------------TGTGACTTCTTAAG -s simRat_chr6.simRat.chr6 371805 38 + 647215 TTGACTTCTTAGGATTTATGAAATCCTAACTTTTTAAT - -a -s simMouse_chr6.simMouse.chr6 177065 1 + 636262 T -s Anc0.Anc0refChr3 6480 1 + 222631 T -s Anc1.Anc1refChr6 39127 1 + 197743 T -s Anc2.Anc2refChr13 9018 1 + 96486 T -s mr.mrrefChr5 226219 1 + 294540 T -s simCow_chr6.simCow.chr6 364500 1 + 602619 T -s simDog_chr6.simDog.chr6 355367 1 + 593897 T -s simHuman_chr6.simHuman.chr6 362812 1 + 601863 T -s simRat_chr6.simRat.chr6 371843 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 177066 57 + 636262 GTGGGTACTATCTGATCTGACTCTTTCAAGTATAAGGGGCTATGGTACAGTTGCATC -s Anc0.Anc0refChr3 6481 52 + 222631 AAGGGCACTATCTTGTCTTACTCTTACAAGTATAAGGGGATATGGTG-----GTATT -s Anc1.Anc1refChr6 39128 52 + 197743 AAGGGCACTATCTTGTCTTACTCTTACAAGTATAAGGGGATATGGTG-----GTATT -s Anc2.Anc2refChr13 9019 52 + 96486 AGGGGCACTATCTTGTCTTACTCTTACAAGTATAAAGGGATATGGTG-----GTATT -s mr.mrrefChr5 226220 57 + 294540 GAGGGTACTATCTGGTCTGACTCTTTCAAGTATAAGGGGCTATGGTACAGTTGCATC -s simCow_chr6.simCow.chr6 364503 50 + 602619 AGGGGCACCATCTTTTCTTAGTCTTACAAGCATACAGGGATATG--A-----GTATC -s simDog_chr6.simDog.chr6 355368 51 + 593897 AGGGGCACTATCTTGTC-TACTCTTACAAGTATAAAGGGAAGTGGTG-----GTGCT -s simHuman_chr6.simHuman.chr6 362813 52 + 601863 AAGGTCACTATCGTGTCTTACTCTTACCAGTATAAGGGCATATGGTG-----GTATT -s simRat_chr6.simRat.chr6 371844 57 + 647215 GAGGGTACTATCTGGTCTGACTCTTCCAAGTATAAGGTGCTACGGTACGGTTGCATC - -a -s simMouse_chr6.simMouse.chr6 177123 40 + 636262 AGAACCCAGCCAGCTTTATCTCTTCCAATAAATTTAATGC -s Anc0.Anc0refChr3 6533 36 + 222631 GGAGCCCAGG----TTTATAACTTACATCAAGTTTAATGT -s Anc1.Anc1refChr6 39180 36 + 197743 GGAGCCCAGG----TTTATAACTTACATCAAGTTTAATGT -s Anc2.Anc2refChr13 9071 36 + 96486 GGAGCCCAGG----TTTATAACTAACTTTAAGTTTAATGT -s mr.mrrefChr5 226277 40 + 294540 AGAACCCAGCCAGCTTTATATCTTCCAACAAATTTAATGC -s simCow_chr6.simCow.chr6 364553 36 + 602619 GGAGCCCAGC----TTTATAACTAACTTTGAGTTTAATGT -s simDog_chr6.simDog.chr6 355425 25 + 593897 GCAGCTGTCG----CTTA-----------AAGTTTAATGT -s simHuman_chr6.simHuman.chr6 362865 36 + 601863 GGAGCCCAGG----TTTACAACTTTAAGCAAGTTTACTGT -s simRat_chr6.simRat.chr6 371901 40 + 647215 AGAATCCAGCTAGCTTTATATCTTCCAACATATTTAATGC - -a -s simMouse_chr6.simMouse.chr6 177163 21 + 636262 AGTCAGTTTGCTTTTGATCTT -s Anc0.Anc0refChr3 6572 21 + 222631 ATTAAGTTTGCTTTTAATCCT -s Anc1.Anc1refChr6 39219 21 + 197743 ATTAAGTTTGCTTTTAATCCT -s Anc2.Anc2refChr13 9110 21 + 96486 ATTAAGTTTGCTTTTAATCCT -s mr.mrrefChr5 226317 21 + 294540 AGTCAGTTTGCTTTTGATCTT -s simCow_chr6.simCow.chr6 364592 21 + 602619 ATTCAGTTTACTTTTAATCCT -s simDog_chr6.simDog.chr6 355453 21 + 593897 GGTAAGACTGCATTTAATCCT -s simHuman_chr6.simHuman.chr6 362904 21 + 601863 ATTTAATTTGCTTGTAATCCT -s simRat_chr6.simRat.chr6 371941 21 + 647215 AGTCAGTTTGCTTTTGTTCTT - -a -s simMouse_chr6.simMouse.chr6 177184 20 + 636262 CAGTAATTCTCAAACCAAGT -s Anc0.Anc0refChr3 6612 20 + 222631 CAGCAATTCTAGAAGCAAGT -s Anc1.Anc1refChr6 39259 20 + 197743 CAGCAATTCTAGAAGCAAGT -s Anc2.Anc2refChr13 9150 20 + 96486 CAGCAATTCTAGAAGCAAGT -s mr.mrrefChr5 226338 20 + 294540 CAGCAATTCTCAAACCAAGT -s simCow_chr6.simCow.chr6 364632 20 + 602619 CAGCAATTATAGAAGCAAGT -s simDog_chr6.simDog.chr6 355492 20 + 593897 CAGCAATTCTAGAAGTAAGT -s simHuman_chr6.simHuman.chr6 362944 20 + 601863 CAGCAATTCCAGAGGCAAGT -s simRat_chr6.simRat.chr6 371962 20 + 647215 TAGCAATTTTGAAACCAAGT - -a -s simMouse_chr6.simMouse.chr6 177204 12 + 636262 GATTCTAGAACT -s Anc0.Anc0refChr3 6632 12 + 222631 AATTTTAGAACT -s Anc1.Anc1refChr6 39279 12 + 197743 AATTTTAGAACT -s Anc2.Anc2refChr13 9170 12 + 96486 AATTTTAGAACT -s mr.mrrefChr5 226358 12 + 294540 AATTCTAGAACT -s simCow_chr6.simCow.chr6 364657 12 + 602619 AACTTCAGAACT -s simDog_chr6.simDog.chr6 355512 12 + 593897 AATTCTAGATGT -s simHuman_chr6.simHuman.chr6 362964 12 + 601863 AATTTTGGGACT -s simRat_chr6.simRat.chr6 371982 12 + 647215 AATTCTAGAACT - -a -s simMouse_chr6.simMouse.chr6 177216 19 + 636262 ATGGTATCTCATATTATGC -s Anc0.Anc0refChr3 6649 19 + 222631 AATGTATCTCATGCTATAT -s Anc1.Anc1refChr6 39296 19 + 197743 AATGTATCTCATGCTATAT -s Anc2.Anc2refChr13 9187 19 + 96486 AATGTATCTCATGCTATAT -s mr.mrrefChr5 226375 19 + 294540 ATGGTATCTCATATTATAC -s simCow_chr6.simCow.chr6 364674 19 + 602619 AATATGTCTGATGCTTTAT -s simDog_chr6.simDog.chr6 355529 19 + 593897 AATGTATCTCATGCTATAT -s simHuman_chr6.simHuman.chr6 362981 19 + 601863 AATGTATCTCATGCTACAT -s simRat_chr6.simRat.chr6 371999 19 + 647215 ATGGTATCTCATATTATAC - -a -s simMouse_chr6.simMouse.chr6 177235 4 + 636262 ACTT -s Anc0.Anc0refChr3 6717 1 + 222631 ---T -s Anc1.Anc1refChr6 39364 4 + 197743 ATCT -s Anc2.Anc2refChr13 9255 1 + 96486 ---T -s mr.mrrefChr5 226394 4 + 294540 ACTT -s simCow_chr6.simCow.chr6 364749 1 + 602619 ---T -s simDog_chr6.simDog.chr6 355597 1 + 593897 ---T -s simHuman_chr6.simHuman.chr6 363067 4 + 601863 ATCT -s simRat_chr6.simRat.chr6 372018 4 + 647215 ACAT - -a -s simMouse_chr6.simMouse.chr6 177239 32 + 636262 GACTTTGTAAAATATGTGCTGAGAGTTAAGAG -s Anc0.Anc0refChr3 6718 28 + 222631 GACTTTGTATAATATGTGCTG----TTACGGG -s Anc1.Anc1refChr6 39368 28 + 197743 GACTTTGTATAATATGTGCTG----TTACGGG -s Anc2.Anc2refChr13 9256 28 + 96486 GACTGTGTATAATATGTGCAG----TCACGGG -s mr.mrrefChr5 226398 32 + 294540 GACTTTGTAAAATATGTGCTGAGAGTTAAGGG -s simCow_chr6.simCow.chr6 364757 28 + 602619 GACTGTGTATAATATATGCAT----TAAGGGA -s simDog_chr6.simDog.chr6 355598 28 + 593897 TGTTGTGTCTAAGATGTGCAG----TCACGGG -s simHuman_chr6.simHuman.chr6 363071 27 + 601863 GACTTTGCATAATATGTGCTG----CTATGG- -s simRat_chr6.simRat.chr6 372022 32 + 647215 GACTTTGTAAAATATGTGCTGAGAGTCAAGGG - -a -s simMouse_chr6.simMouse.chr6 177271 40 + 636262 CTCCCCAAAACGTTAATAAAGATTTAACGTTTAGATCTTG -s Anc0.Anc0refChr3 6746 31 + 222631 T---CAGAGACATTAATTAAGCCTTGGCATTA------TG -s Anc1.Anc1refChr6 39396 31 + 197743 T---CAGAGACATTAATTAAGCCTTGGCATTA------TG -s Anc2.Anc2refChr13 9284 31 + 96486 T---CAGGGCCATTAATTAAGCATTGGCATTA------TG -s mr.mrrefChr5 226430 40 + 294540 CTCCCCAAAACATTAATAAAGCCTTAACATTTAGATCTTG -s simCow_chr6.simCow.chr6 364787 31 + 602619 T---CCAGCCCATTACCTAAGCATTGGGACCA------CG -s simDog_chr6.simDog.chr6 355626 31 + 593897 T---CAGGGCCACTAATTAGGCACCAGCATTA------TG -s simHuman_chr6.simHuman.chr6 363098 27 + 601863 -------AGACATTAATTAAGCCTTGGCATTA------TG -s simRat_chr6.simRat.chr6 372054 40 + 647215 CTCTCCAAAACATCAACAAAGCCTTAACATTTAGACCTTG - -a -s simMouse_chr6.simMouse.chr6 177311 115 + 636262 TCTGAGTAAAGCTTTGTATGACTTCAATTATAGTTaggcagtatcactgtggcttgtacttcttcactggattcattcagtctatttcctgtctacttggaaagctgaacagcCC -s Anc0.Anc0refChr3 6777 39 + 222631 TGTTGGCAATGCTTTGGAGGCCTTCAAGTATAGCCAGgt---------------------------------------------------------------------------- -s Anc1.Anc1refChr6 39427 111 + 197743 TGTTGGCAATGCTTTGGAGGCCTTCAAGTATAGCCAGgtagtatcacagaggttgattcctcctcactg----cattcagtctacttactgtctacttgaagagttcaactgcac -s Anc2.Anc2refChr13 9316 39 + 96486 TGTTGTCAATGCTTTGGAGGCCTTCAAGTATACCCAGgt---------------------------------------------------------------------------- -s mr.mrrefChr5 226470 115 + 294540 TCTGAGCAAAGCTTTGTATGACTTCAAGTATAGTTaggtagtatcactgaggcttgtacttcttcactggattcattcagtctatttcctgtctacttggaaagttgaacagccc -s simCow_chr6.simCow.chr6 364819 39 + 602619 CCTTGTCAAAATTATGGAGGTCTTCAGGAATACCCAGGT---------------------------------------------------------------------------- -s simDog_chr6.simDog.chr6 355658 31 + 593897 TGTTGTCAATGCTTAGGGGGCCTTCAAGTAT------------------------------------------------------------------------------------ -s simHuman_chr6.simHuman.chr6 363125 111 + 601863 TTTTGGCAATGCTTTGCAGGCCTCTAAGTATAGACAGgttgtgtcacagaggttgattcctcctcactg----cattcagtctacttactgtctacttgaagagttcaactgcac -s simRat_chr6.simRat.chr6 372094 115 + 647215 TCAGAGCAAAGCTTTGTGTGACTTCAAGTATAGTTaggtagtatgactgaggcttgtctgtctacactgaattcattcagtctatttcctgtctactcagaatgtcgaatggccc - -a -s simMouse_chr6.simMouse.chr6 177426 49 + 636262 ATCAGATCATCATAATTGAGCTAAAAGAGTTACATAGCATCAAATGAAA -s Anc1.Anc1refChr6 39538 49 + 197743 atcatgccctcataattgaactagaagatctctatggaatccaccggaa -s mr.mrrefChr5 226585 49 + 294540 atcaGATCCTCATAATTGAACTAAAAGAGTTACATAGCATCCAACGAAA -s simHuman_chr6.simHuman.chr6 363387 49 + 601863 atcatgccctcataattgaactagaagatctctatggaatccaccggaa -s simRat_chr6.simRat.chr6 372209 49 + 647215 atgaGATCCTCATAATCAAACTAAAAGAGTTACATAGCATCCAACAAAA - -a -s simMouse_chr6.simMouse.chr6 177475 4 + 636262 TAGA -s Anc1.Anc1refChr6 39587 4 + 197743 taga -s mr.mrrefChr5 226634 4 + 294540 TAGA -s simHuman_chr6.simHuman.chr6 363437 4 + 601863 taga -s simRat_chr6.simRat.chr6 372258 4 + 647215 TAGA - -a -s simMouse_chr6.simMouse.chr6 177479 30 + 636262 GGATAGGGGAATTATGATGATTGTTGCTAC -s Anc0.Anc0refChr3 6816 28 + 222631 --ATAAGAGCATTGTGATGATCATGGCTAC -s Anc1.Anc1refChr6 39591 30 + 197743 GGATAAGAGCATTGTGATGATCATGGCTAC -s Anc2.Anc2refChr13 9355 28 + 96486 --ATAACACCACTATGATGATCATGGCTAC -s mr.mrrefChr5 226638 30 + 294540 GGATAAGGGAATTGTGATGATTGTTGCTAC -s simCow_chr6.simCow.chr6 364858 28 + 602619 --ATAACACCACTATGAAAATCATGGCTGC -s simDog_chr6.simDog.chr6 355689 14 + 593897 ----------------ATGATCATGGCTAC -s simHuman_chr6.simHuman.chr6 363463 30 + 601863 GGATAAGAGCATCGTGATGATCATGGCTAC -s simRat_chr6.simRat.chr6 372262 30 + 647215 GGATCAGGGAATTGTGATGATTGTTGCTAC - -a -s simMouse_chr6.simMouse.chr6 177509 35 + 636262 ATGTATTGCCTCTCCCTATGCAATTAATGTTCAAA -s Anc0.Anc0refChr3 6844 33 + 222631 AGGTTTCACCTCTCCCTATGCAA--AAGGCTCAAA -s Anc1.Anc1refChr6 39621 33 + 197743 AGGTTTCACCTCTCCCTATGCAA--AAGGCTCAAA -s Anc2.Anc2refChr13 9383 33 + 96486 AGGTTTCAACCCCCCCTATGCAA--AAGGCTCAAA -s mr.mrrefChr5 226668 35 + 294540 ATGTATTGCCTCTCCCTATGCAATTAAGGTTCAAA -s simCow_chr6.simCow.chr6 364888 33 + 602619 ATGTGTCTTCCCCCCCTATGCAA--AAGCCTCAAA -s simDog_chr6.simDog.chr6 355703 33 + 593897 AGGTTTCAACCCCCCCTATGCAA--AAGGCTCAAA -s simHuman_chr6.simHuman.chr6 363493 16 + 601863 ACC-----CCTCTTCCTG--------------AAT -s simRat_chr6.simRat.chr6 372292 30 + 647215 ATGTATTGCCTCTCCC-----AATTGAGGTACAAA - -a -s simMouse_chr6.simMouse.chr6 177544 27 + 636262 GGTCGTTTCATGTGTTCTATTAATATA -s Anc0.Anc0refChr3 6877 27 + 222631 GGTTTTTTCATGTATTTTATTAAAAAA -s Anc1.Anc1refChr6 39654 27 + 197743 GGTTTTTTCATGTATTTTATTAAAAAA -s Anc2.Anc2refChr13 9417 27 + 96486 GATTTTTTCATGTGGTTTATTAAAAAA -s mr.mrrefChr5 226703 27 + 294540 GGTTGTTTCATGTATTTTATTAATATA -s simCow_chr6.simCow.chr6 364922 27 + 602619 GAACTTTTCTTGCCGTTTATTGTAAGG -s simDog_chr6.simDog.chr6 355737 27 + 593897 GATTTTCTCATGTGGTTTATTAAATAA -s simHuman_chr6.simHuman.chr6 363509 27 + 601863 GGTTTCTTCATATATTTTATTTAGACA -s simRat_chr6.simRat.chr6 372322 27 + 647215 GGTTGTTTCATGTATTTTATTAATATA - -a -s simMouse_chr6.simMouse.chr6 177571 165 + 636262 TCTCTTGCCATCTCAAACTCCAGCATCTAAGGCAACAGTCCTTTTGGAGGCGCACCAGTCCTTTTGGAGGCCAAAACATTGCAACATGGCCAAGACACTAGAAGAAAAGACCAGATTTTTAATGAAATGACCAGATTTTTAATGTAGTTCCTACCTTGCAGAAGA -s Anc0.Anc0refChr3 6909 78 + 222631 CCTCTAATTGTCTCAAATTCCAGCATTTAAGGCA--------------------TCAGTCTTTTTGGTGGCCAAAAC----------AGCC---------GAAGAAAGGACCAGA-----------AT------------------------------------- -s Anc1.Anc1refChr6 39686 80 + 197743 CCTCTAATTGTCTCAAATTCCAGCATTTAAGGCA--------------------TCAGTCTTTTTGGTGGCCAAAACA--------TAGCC---------GAAGAAAGGACCAGA-----------AT------------------------------------- -s Anc2.Anc2refChr13 9449 78 + 96486 CCTCTAATTGTCTCAAATTCCAGCATTAAAGCCA--------------------TTAGTCTTTTTGGTGACGAAAAC----------AACA---------GAAGAAAGGATCAGA-----------AT------------------------------------- -s mr.mrrefChr5 226735 133 + 294540 TCTCTTGCCATCTCAAATTCCAGCATCTAAGGCA--------------------CCAGTCTTTTTGGAGGCCAAAACATTGCAACATGGCCAAGACACTAGAAGAAAAGACCAGA-----------ATGACC-GATTTTTAATGTAGTTCCTACCTTGCAGAAGA -s simCow_chr6.simCow.chr6 364954 74 + 602619 CCTCTAATGGTCTCAAATTTTAGCCC----GCCA--------------------CTAGTCTTCTTGGTGACAAAAAC----------AATG---------GAAGAAAGGATCATA-----------AT------------------------------------- -s simDog_chr6.simDog.chr6 355769 78 + 593897 CCTCTAATTGCCTCAAACTCCAGAATTAAAGCCA--------------------TTGATCATTTTGGTCATGTAAAC----------AACA---------GAAAAGAAGATCAGA-----------AT------------------------------------- -s simHuman_chr6.simHuman.chr6 363541 75 + 601863 CCTCTAATTGTCTCAAATCCCGGCATTTAAGGCA--------------------TCAGTCTTTTTGGTGGCCA-------------TAGCC---------TAAGAAAGGACCAGA-----------AT------------------------------------- -s simRat_chr6.simRat.chr6 372354 133 + 647215 TCTCTTGCCATCTCAAATTCCACCATCTAAGGCA--------------------AAAGTCTTTTTGGGGGCCAAAACATTGGAAGATGGTCAAGACACTAGAAGAAAAGACCAGA-----------AAGACT-GATTTTTAATGTAGTTCCTACCTCGCAGAAAA - -a -s simMouse_chr6.simMouse.chr6 177736 28 + 636262 AGATTTTATTTTCAATGTAGTTCCACTG -s Anc0.Anc0refChr3 6987 18 + 222631 ----------TCCAATCTAGATTCTTTG -s Anc1.Anc1refChr6 39766 18 + 197743 ----------TCCAATCTAGATTCTTTG -s Anc2.Anc2refChr13 9527 18 + 96486 ----------TCCAATCTAGATTCTTTG -s mr.mrrefChr5 226868 28 + 294540 AGATTTTATTTTCAATGTAGTTCCTCTG -s simCow_chr6.simCow.chr6 365028 18 + 602619 ----------TTCGATCTAGGTTCTTTG -s simDog_chr6.simDog.chr6 355847 18 + 593897 ----------TCCAATCTAGATTCTTTG -s simHuman_chr6.simHuman.chr6 363616 18 + 601863 ----------TCCAATCTAGCTGCTTTG -s simRat_chr6.simRat.chr6 372491 28 + 647215 AGCTTTCATTTTCAAAGTAGTTCCTCTG - -a -s simMouse_chr6.simMouse.chr6 177764 56 + 636262 AGGGGTGGTTTTTATCTCAAGATTGCACAGACATTATATACGTGTATATGTAGATA -s Anc0.Anc0refChr3 7022 56 + 222631 AGTAGTTATTCTTCTCTCTGAATTACACAGATATTATGGTAGTGTATGTGCAGGTA -s Anc1.Anc1refChr6 39801 56 + 197743 AGTAGTTATTCTTCTCTCTGAATTACACAGATATTATGGTAGTGTATGTGCAGGTA -s Anc2.Anc2refChr13 9562 56 + 96486 AGTAGTTATTCTTCGCTCTGAATTACACAGATATTATGGTAGTGTATGTGCATGTA -s mr.mrrefChr5 226912 56 + 294540 AGGGGTGGTTTTTATCTCAAGATTGCACAGATATTATAGACGTGTATGTGTAGATA -s simCow_chr6.simCow.chr6 365063 54 + 602619 GATCATTAT--TTCACTCTGAATTACACAGGTATTGTGGAAGCATACATGAGTTAA -s simDog_chr6.simDog.chr6 355880 56 + 593897 AGTAGTTATTCTTTGTGCTGAACTGTACAGATATTATGTTAGTGTATGTGCATGTA -s simHuman_chr6.simHuman.chr6 363647 49 + 601863 -------ATTCTTCTCTCTGAATTACATGGATATTATGGGAGTGTGTGCGCAGGTA -s simRat_chr6.simRat.chr6 372535 56 + 647215 ACAGGTGGTTTTTATCTCAAGATTGCACAGATAATATAGATGTCTATGTGTAGATA - -a -s simMouse_chr6.simMouse.chr6 177820 27 + 636262 CTGTTAGGGTCTGGTAATGGCTGGGGG -s Anc0.Anc0refChr3 7078 27 + 222631 CTTTTAGAGGTTGGTCATGGTTGTGGC -s Anc1.Anc1refChr6 39857 27 + 197743 CTTTTAGAGGTTGGTCATGGTTGTGGC -s Anc2.Anc2refChr13 9618 27 + 96486 CCTTTAGAGGTTGGTCATGATTGTGGC -s mr.mrrefChr5 226968 27 + 294540 CTGTTAGAGTCTGGTCATGGCTGTGGA -s simCow_chr6.simCow.chr6 365131 27 + 602619 CATTTAAAGGTTGGTCATGAATGTGGC -s simDog_chr6.simDog.chr6 355936 27 + 593897 ACTTTAGAGTCTGGTAATAATTGTGGC -s simHuman_chr6.simHuman.chr6 363696 27 + 601863 CTTTTAGAGGTTGGTCATGGTTGTGGC -s simRat_chr6.simRat.chr6 372591 27 + 647215 CTGTTAGAGTCTGGTCATAGCTGTGGA - -a -s simMouse_chr6.simMouse.chr6 177847 11 + 636262 CCTGGAGAGTA -s Anc0.Anc0refChr3 7125 11 + 222631 CCTAGAGAGTG -s Anc1.Anc1refChr6 39904 11 + 197743 CCTAGAGAGTG -s Anc2.Anc2refChr13 9665 11 + 96486 CCTAGAGAGTG -s mr.mrrefChr5 226995 11 + 294540 CCTGGAGAGTA -s simCow_chr6.simCow.chr6 365178 11 + 602619 CTTGGGGAGTG -s simDog_chr6.simDog.chr6 355965 8 + 593897 CCTAGAGA--- -s simHuman_chr6.simHuman.chr6 363744 11 + 601863 CCTTCAGAGTG -s simRat_chr6.simRat.chr6 372618 11 + 647215 CCTGGTGAGTT - -a -s simMouse_chr6.simMouse.chr6 177858 16 + 636262 AAACAATAGGTCTTGG -s Anc0.Anc0refChr3 7136 16 + 222631 AAAGGATAGGTTTTGG -s Anc1.Anc1refChr6 39915 16 + 197743 AAAGGATAGGTTTTGG -s Anc2.Anc2refChr13 9676 16 + 96486 AAAGGATAGGTTATGG -s mr.mrrefChr5 227006 16 + 294540 AAACAATAGGTCTTGG -s simCow_chr6.simCow.chr6 365204 16 + 602619 AAGGGACAGGCTATAG -s simDog_chr6.simDog.chr6 355973 16 + 593897 CAAGGATAAGTTATGG -s simHuman_chr6.simHuman.chr6 363755 16 + 601863 AGAGGATAGGTGTCGG -s simRat_chr6.simRat.chr6 372629 16 + 647215 AAACAACAGGTCTTGG - -a -s simMouse_chr6.simMouse.chr6 177874 24 + 636262 TGGGGAAACATAGTGTCTACATCC -s Anc0.Anc0refChr3 7152 24 + 222631 GTGGGTAATATGATGTCTAGGTCC -s Anc1.Anc1refChr6 39931 24 + 197743 GTGGGTAATATGATGTCTAGGTCC -s Anc2.Anc2refChr13 9692 24 + 96486 TTAGGTAATATGATGTCTAGGTCC -s mr.mrrefChr5 227022 24 + 294540 GGGGGAAACATAGTGTCTACATCC -s simCow_chr6.simCow.chr6 365220 24 + 602619 ATAGTAAATATGTTGTCTAGGTCC -s simDog_chr6.simDog.chr6 355989 24 + 593897 TGAGGTAATATGATATCTAGGTCC -s simHuman_chr6.simHuman.chr6 363771 15 + 601863 GTGGGGAATGTGATG--------- -s simRat_chr6.simRat.chr6 372647 24 + 647215 GAGGAAAACATAGTGTCTACAACA - -a -s simMouse_chr6.simMouse.chr6 177898 34 + 636262 TAACGCACTCTTATTTTTTAGTCTCCTATAAGCG -s Anc0.Anc0refChr3 7176 30 + 222631 TGATGTATTCTTATTTTTTAGTCTC----AATTG -s Anc1.Anc1refChr6 39955 30 + 197743 TGATGTATTCTTATTTTTTAGTCTC----AATTG -s Anc2.Anc2refChr13 9716 30 + 96486 TGATGTATTCTTATTTTTTAGCCTC----AGTGA -s mr.mrrefChr5 227046 34 + 294540 TAACGCATTCTTATTTTTTAGTCTCCTATAAGTG -s simCow_chr6.simCow.chr6 365245 30 + 602619 TAATGTGTCCTTATTTTTTAGCCTC----AGTGA -s simDog_chr6.simDog.chr6 356013 30 + 593897 TGATGTATTCTTAATTTTTAGCCCC----AGTGA -s simHuman_chr6.simHuman.chr6 363786 24 + 601863 ------ATTCCTATTTCTTTGTCTC----AATTG -s simRat_chr6.simRat.chr6 372671 34 + 647215 TAACACATTCTTATTTTTTAGCCTCCTATAAGTG - -a -s simMouse_chr6.simMouse.chr6 177932 7 + 636262 GATAATG -s Anc0.Anc0refChr3 7243 7 + 222631 GACAATG -s Anc1.Anc1refChr6 40022 7 + 197743 GACAATG -s Anc2.Anc2refChr13 9783 7 + 96486 GACAATG -s mr.mrrefChr5 227080 7 + 294540 GACAATG -s simCow_chr6.simCow.chr6 365309 7 + 602619 GATAATT -s simDog_chr6.simDog.chr6 356081 7 + 593897 CACAAGG -s simHuman_chr6.simHuman.chr6 363847 7 + 601863 GACAATG -s simRat_chr6.simRat.chr6 372705 7 + 647215 GTCAATG - -a -s simMouse_chr6.simMouse.chr6 177939 13 + 636262 AAGTCAGTTTTAG -s Anc0.Anc0refChr3 7250 13 + 222631 GAACTAGTTATTG -s Anc1.Anc1refChr6 40029 13 + 197743 GAACTAGTTATTG -s Anc2.Anc2refChr13 9793 13 + 96486 GAACTAGTTATTG -s mr.mrrefChr5 227087 13 + 294540 GAGTTAGTTTTAG -s simCow_chr6.simCow.chr6 365319 13 + 602619 CAACTAGTTAACA -s simDog_chr6.simDog.chr6 356091 13 + 593897 GAACTAGTAATTG -s simHuman_chr6.simHuman.chr6 363854 13 + 601863 GACCTAGTTATTG -s simRat_chr6.simRat.chr6 372712 13 + 647215 GAGTTAGTTTTAG - -a -s simMouse_chr6.simMouse.chr6 177952 5 + 636262 CGCCA -s Anc0.Anc0refChr3 7269 5 + 222631 TGCCA -s Anc1.Anc1refChr6 40048 5 + 197743 TGCCA -s Anc2.Anc2refChr13 9812 5 + 96486 TGCCA -s mr.mrrefChr5 227100 5 + 294540 TGCCA -s simCow_chr6.simCow.chr6 365338 5 + 602619 TGCCA -s simDog_chr6.simDog.chr6 356112 5 + 593897 CGCCA -s simHuman_chr6.simHuman.chr6 363873 5 + 601863 TGCCA -s simRat_chr6.simRat.chr6 372725 5 + 647215 TGCCA - -a -s simMouse_chr6.simMouse.chr6 177957 17 + 636262 TACCCTGTAAGATCTAG -s Anc0.Anc0refChr3 7274 17 + 222631 TGCATTGTTGGGTACAG -s Anc1.Anc1refChr6 40053 17 + 197743 TGCATTGTTGGGTACAG -s Anc2.Anc2refChr13 9817 17 + 96486 TGCATCGTTGGGTACAG -s mr.mrrefChr5 227105 17 + 294540 TACCCTGTAAGATCTAG -s simCow_chr6.simCow.chr6 365343 10 + 602619 -------TTAGGTCTAG -s simDog_chr6.simDog.chr6 356136 15 + 593897 TGCATCG--GGAGACAG -s simHuman_chr6.simHuman.chr6 363878 17 + 601863 TGCTTTGTTGGGTTCAG -s simRat_chr6.simRat.chr6 372730 17 + 647215 TACCCTGTAAGATCTAG - -a -s simMouse_chr6.simMouse.chr6 177974 15 + 636262 AGGGAATCATTTACA -s Anc0.Anc0refChr3 7291 15 + 222631 AGGGATTTATTTGCA -s Anc1.Anc1refChr6 40070 15 + 197743 AGGGATTTATTTGCA -s Anc2.Anc2refChr13 9834 15 + 96486 AGGGATTTATTTGCC -s mr.mrrefChr5 227122 15 + 294540 AGGGAATCATTTACA -s simCow_chr6.simCow.chr6 365353 8 + 602619 AAAGGGTT------- -s simDog_chr6.simDog.chr6 356154 15 + 593897 GGGAATTCATTTGCC -s simHuman_chr6.simHuman.chr6 363895 15 + 601863 AGGGATTTGTTTGCA -s simRat_chr6.simRat.chr6 372747 15 + 647215 AGGGGATCATTTACA - -a -s simMouse_chr6.simMouse.chr6 177989 45 + 636262 ATGTTACCTCTATCCCATGTGTCACAGCTTCCTAGGGCTAACACA -s Anc0.Anc0refChr3 7318 45 + 222631 ATATTCCCTCTTTCTCATATTTCTCAGCCTCATAGAGCTGACAGA -s Anc1.Anc1refChr6 40097 45 + 197743 ATATTCCCTCTTTCTCATATTTCTCAGCCTCATAGAGCTGACAGA -s Anc2.Anc2refChr13 9861 45 + 96486 ATATTCCCTCTTTCTCATATTTCTCAGCCTCATAGAGCTGACAGA -s mr.mrrefChr5 227150 45 + 294540 ATATTACCTCTATCCCATGTGTCACAGCTTCCTAGGGCTGACAGA -s simCow_chr6.simCow.chr6 365372 45 + 602619 ATACTCCCTCTTTCTCATATTTCTCAGCCTTCTATAGCTTACTGA -s simDog_chr6.simDog.chr6 356182 45 + 593897 ATATTCCCTTTTTCTTATGTTTGTCAGCCTCATAGAGCAGACAGA -s simHuman_chr6.simHuman.chr6 363922 45 + 601863 CTATTCTCTCCTCCTCATATTTCCTAGCCTCTTAGAGCTGCCAGA -s simRat_chr6.simRat.chr6 372775 45 + 647215 ATATTACCTCTATCCCATGTGTCACAGCTTCCTAGGGCTGACAGT - -a -s simMouse_chr6.simMouse.chr6 178034 2 + 636262 AT -s Anc0.Anc0refChr3 7363 2 + 222631 AT -s Anc1.Anc1refChr6 40142 2 + 197743 AT -s Anc2.Anc2refChr13 9906 2 + 96486 TT -s mr.mrrefChr5 227195 2 + 294540 AT -s simCow_chr6.simCow.chr6 365417 2 + 602619 TT -s simDog_chr6.simDog.chr6 356242 2 + 593897 TT -s simHuman_chr6.simHuman.chr6 363967 2 + 601863 AT -s simRat_chr6.simRat.chr6 372820 2 + 647215 GT - -a -s simMouse_chr6.simMouse.chr6 178036 28 + 636262 GCTTAAAACAGCATCCTATTGTCCTGCC -s Anc0.Anc0refChr3 7365 28 + 222631 ACTTGAAACCCCATTATACTGTCCTGCC -s Anc1.Anc1refChr6 40144 28 + 197743 ACTTGAAACCCCATTATACTGTCCTGCC -s Anc2.Anc2refChr13 9908 28 + 96486 ACTTGAAATCCCATTAGACTGTCCTGCC -s mr.mrrefChr5 227197 28 + 294540 GCTTAAAACAGCATCCTATTGTCCTGCC -s simCow_chr6.simCow.chr6 365420 28 + 602619 ACTTGAAATCCCACCAGATTGTCCTGCC -s simDog_chr6.simDog.chr6 356244 28 + 593897 ACTTGGAATCCCATTGGACTGTTCAGCC -s simHuman_chr6.simHuman.chr6 363969 28 + 601863 ACTTGAAACCCCATAATACTGTCCTGTC -s simRat_chr6.simRat.chr6 372822 28 + 647215 GCTTAAAACAGCATGCTATTGTCCTGCC - -a -s simMouse_chr6.simMouse.chr6 178064 1 + 636262 A -s Anc0.Anc0refChr3 7393 1 + 222631 A -s Anc1.Anc1refChr6 40172 1 + 197743 A -s Anc2.Anc2refChr13 9936 1 + 96486 A -s mr.mrrefChr5 227225 1 + 294540 A -s simCow_chr6.simCow.chr6 365448 1 + 602619 A -s simDog_chr6.simDog.chr6 356273 1 + 593897 A -s simHuman_chr6.simHuman.chr6 363997 1 + 601863 A -s simRat_chr6.simRat.chr6 372850 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 178065 24 + 636262 TCCCTCTAGCCTGTACTCTATATG -s Anc0.Anc0refChr3 7399 24 + 222631 TCCCTCTAGCCTGTACTTGATATC -s Anc1.Anc1refChr6 40178 24 + 197743 TCCCTCTAGCCTGTACTTGATATC -s Anc2.Anc2refChr13 9942 24 + 96486 TCCCCCTAGTCTGTACTTGATACC -s mr.mrrefChr5 227226 24 + 294540 TCCCTCTAGCCTGTACTCTATATG -s simCow_chr6.simCow.chr6 365454 24 + 602619 TCCCCCTATTCTGTACTAGTTGCC -s simDog_chr6.simDog.chr6 356279 24 + 593897 TCCCCCCAGTCTGTACTTGATACC -s simHuman_chr6.simHuman.chr6 364003 24 + 601863 TCCCTCTAACCTGTACCTGATATC -s simRat_chr6.simRat.chr6 372851 24 + 647215 TCCCTCTAGCCTGTACTCCATATG - -a -s simMouse_chr6.simMouse.chr6 178089 31 + 636262 CCACCATTCTATACTACCTAAGTATCCCCCC -s Anc0.Anc0refChr3 7423 31 + 222631 CCATCATACTGTACTGCCTAAGTATCCCCCC -s Anc1.Anc1refChr6 40202 31 + 197743 CCATCATACTGTACTGCCTAAGTATCCCCCC -s Anc2.Anc2refChr13 9966 31 + 96486 CAATCATACTGTACTGCCTCAGTATCCCCCC -s mr.mrrefChr5 227250 31 + 294540 CCACCATTCTGTACTACCTAAGTATCCCCCC -s simCow_chr6.simCow.chr6 365478 31 + 602619 CCACCATGCCATAATACCTTCATCTCCTACC -s simDog_chr6.simDog.chr6 356303 31 + 593897 CAATCATACTGTACTGCCTCAGTATCCCCCT -s simHuman_chr6.simHuman.chr6 364033 31 + 601863 TCATTATAATGTACTGCCCAAGTATCCCCCC -s simRat_chr6.simRat.chr6 372875 31 + 647215 CCACCAGTCTGTACTACCTAAGTGTCCCCCC - -a -s simMouse_chr6.simMouse.chr6 178120 6 + 636262 GATTTG -s Anc0.Anc0refChr3 7454 6 + 222631 AATCTG -s Anc1.Anc1refChr6 40233 6 + 197743 AATCTG -s Anc2.Anc2refChr13 9997 6 + 96486 AATCTG -s mr.mrrefChr5 227290 6 + 294540 AATTTG -s simCow_chr6.simCow.chr6 365509 6 + 602619 AATCTG -s simDog_chr6.simDog.chr6 356334 6 + 593897 AATCTG -s simHuman_chr6.simHuman.chr6 364064 6 + 601863 AGTCTG -s simRat_chr6.simRat.chr6 372916 6 + 647215 AATTTG - -a -s simMouse_chr6.simMouse.chr6 178126 101 + 636262 TAGCAGCTGCAGAGCATACCCGATTCATTTTTTAGCATCACACTACCCTTCTTAGCATCACGTTACCCTATTTAATTACCACTTCGTTTTGCTATCAGTTC -s Anc0.Anc0refChr3 7460 86 + 222631 TAGCAGCTGAACTACATGCCCAATCGACTTCCTAGGATGTTGTCAC-------------ACATCACCCT-TTTGCTTACA-CTTCTCTTTGCCATGATTTC -s Anc1.Anc1refChr6 40239 86 + 197743 TAGCAGCTGAACTACATGCCCAATCGACTTCCTAGGATGTTGTCAC-------------ACATCACCCT-TTTGCTTACA-CTTCTCTTTGCCATGATTTC -s Anc2.Anc2refChr13 10003 86 + 96486 TAGCAGCTGAATTACATGCCCAATCGACTTCCTAGGAGGTTCTCAC-------------ACATCTCCCT-TTTGCTCACA-CTTCTCTTTGCCATGATGTC -s mr.mrrefChr5 227296 100 + 294540 TAGCAGCTGCACAGCATGCCCAATTCACTTCTTAGCATCACGTTACCCTTCTTAGCATCACATTACCCT-TTTAATTACAACTTCGTTTTGCCATCAGTTC -s simCow_chr6.simCow.chr6 365515 86 + 602619 TAGCAGGTGCATTACACGAACTATCGGGTTACTAGGACGTTATCAC-------------ACATTTTCCT-TTTGATCTCA-CCCCTCCTTGCCATGATGTC -s simDog_chr6.simDog.chr6 356354 86 + 593897 TAGCAGCTGAATAACATGCCCAATTAACCTCCAGGGAGATTCTCAC-------------ACATCTCCCT-TTTGCTCACA-CTTCTCTTTGCCATGATGTC -s simHuman_chr6.simHuman.chr6 364070 81 + 601863 TAACAGCTGGACTATGTGCCCAACCGACTTCCTAGGATGGTGTCAC-------------ACATCACCTT-TCTGGCTAC------TCTTTGCCATAATTTA -s simRat_chr6.simRat.chr6 372922 100 + 647215 TAGCATCTGCACAGCTTGCCTAATTCACTTCTTAGCATCACGTTACCCTTTTTAGCATCACATTACCCT-TTTCTTTACAACTGCATTTTCTCATCTGTTC - -a -s simMouse_chr6.simMouse.chr6 178227 10 + 636262 CATGCCATCA -s Anc0.Anc0refChr3 7546 10 + 222631 CATCCCATCA -s Anc1.Anc1refChr6 40325 10 + 197743 CATCCCATCA -s Anc2.Anc2refChr13 10089 10 + 96486 CATCCCACCA -s mr.mrrefChr5 227396 10 + 294540 CATGCCATCA -s simCow_chr6.simCow.chr6 365601 10 + 602619 CATTCCATCA -s simDog_chr6.simDog.chr6 356440 10 + 593897 CATCCCACCA -s simHuman_chr6.simHuman.chr6 364152 10 + 601863 TAGACCATCC -s simRat_chr6.simRat.chr6 373022 10 + 647215 CATGCCATCA - -a -s simMouse_chr6.simMouse.chr6 178237 48 + 636262 TTTGCAGTAACCATTTGACATTTGTGTCAACTTGTTTGTTTTGCTATG -s Anc0.Anc0refChr3 7556 46 + 222631 TTTGCAGTAACTTGTTGACAGTTGTACCA-CTTGGTAGAGG-GCTGCA -s Anc1.Anc1refChr6 40335 46 + 197743 TTTGCAGTAACTTGTTGACAGTTGTACCA-CTTGGTAGAGG-GCTGCA -s Anc2.Anc2refChr13 10100 46 + 96486 TTTGCAGCAACTTGTTGATAGTTGTACCA-CTTGGTAGAGG-GCTGCA -s mr.mrrefChr5 227406 48 + 294540 TTTGCAGTAACTATTTGACATTTGTATCAACTTGTTTGTTGTGCTATG -s simCow_chr6.simCow.chr6 365612 46 + 602619 TTTACAGCAACTTTTTGATAGGTGTACCA-TTTGGGAGAGG-GCTGCA -s simDog_chr6.simDog.chr6 356451 46 + 593897 TTTGTAGCAACTTGTTGATAGTTGTACCA-CTTGGTAGAGG-GCTGTG -s simHuman_chr6.simHuman.chr6 364162 46 + 601863 TATGCAGTGACTTATTGTCAGTAGCACCA-CTTGGTAGAGG-GCTGCA -s simRat_chr6.simRat.chr6 373032 48 + 647215 TTTGCAGTTACTATTTGACATTTGTATCAACTTGTTTGTTGTGCTAGG - -a -s simMouse_chr6.simMouse.chr6 178285 48 + 636262 CCTGCAGACAGGATGACTCATGAAAAGATAAGTAGAATCCCCCACCCT -s Anc0.Anc0refChr3 7602 48 + 222631 CCTGCAGACAGGATAATTCCTGACAGGATAGCTGGAATCCCCCACCCT -s Anc1.Anc1refChr6 40381 48 + 197743 CCTGCAGACAGGATAATTCCTGACAGGATAGCTGGAATCCCCCACCCT -s Anc2.Anc2refChr13 10146 48 + 96486 CCTGCAGACAGGATAATTGCTGACAGGATAGCTGGAATCCCCCACTCT -s mr.mrrefChr5 227454 48 + 294540 CCTGCAGACAGGATAATTCATGAAAAGATAGGTAGAATCCCCCACCCT -s simCow_chr6.simCow.chr6 365658 48 + 602619 CTTGCAGACAGGATAATTGCTGACTGGATAGCTGGAATCCCCCACTCT -s simDog_chr6.simDog.chr6 356498 48 + 593897 CCTGCAGACAGGATAATTGCTGACAGGATAGCTGGAATCCCTCACTCT -s simHuman_chr6.simHuman.chr6 364208 47 + 601863 CCTGCAGACAGGATAATTCCTGACAGGATAG-TGGAATCCCCTGTCCT -s simRat_chr6.simRat.chr6 373080 48 + 647215 CCTGCACACAGGATAATTGATGAAGAGATAGATAGAATTCCTCACCCT - -a -s simMouse_chr6.simMouse.chr6 178333 17 + 636262 GGAGTCAAGAGGGCACT -s Anc0.Anc0refChr3 7650 11 + 222631 GGAGTCA------CAGT -s Anc1.Anc1refChr6 40429 11 + 197743 GGAGTCA------CAGT -s Anc2.Anc2refChr13 10194 11 + 96486 GGAGTCA------CTGT -s mr.mrrefChr5 227502 11 + 294540 GGAGTCA------CAGT -s simCow_chr6.simCow.chr6 365707 11 + 602619 GGAGTCA------CTGT -s simDog_chr6.simDog.chr6 356546 11 + 593897 GGAGCCA------CTGT -s simHuman_chr6.simHuman.chr6 364255 11 + 601863 GGAGTCA------CAGT -s simRat_chr6.simRat.chr6 373128 11 + 647215 TGAGTCA------CAGT - -a -s simMouse_chr6.simMouse.chr6 178350 41 + 636262 AAGTTGCTATAGTTATGGAGATCTTGTCGCTGGATGGAATA -s Anc0.Anc0refChr3 7662 27 + 222631 AAATTGC--------------TCTTGTAGGTGGATGGAATA -s Anc1.Anc1refChr6 40441 40 + 197743 AAATTGCT-CAGTTAAGGTTGTCTTGTAGGTGGATGGAATA -s Anc2.Anc2refChr13 10206 27 + 96486 AAATTAC--------------TCTTGCAGGTGGATGGGATA -s mr.mrrefChr5 227514 41 + 294540 AAGTTGCTATAGTTAAGGAGATCTTGTCGCTGGATGGAATA -s simCow_chr6.simCow.chr6 365719 27 + 602619 AAATTAC--------------TCTTGCAGGTGGATAGGATA -s simDog_chr6.simDog.chr6 356558 27 + 593897 AAATTAC--------------TCTTGCAGGTGGAGGGGATA -s simHuman_chr6.simHuman.chr6 364267 40 + 601863 GCCGTGCT-CAGTTAAGGTTGTCTTGTAGGTGGATGGAATA -s simRat_chr6.simRat.chr6 373140 41 + 647215 AAGTTGCTATAGGTAAGGAGCTCATGTCACTGGATGGAATA - -a -s simMouse_chr6.simMouse.chr6 178391 25 + 636262 TTCCAGTAATCTTGAGGATATCGCA -s Anc0.Anc0refChr3 7689 25 + 222631 CTCCAGTAATATTGAGCATAAAGCA -s Anc1.Anc1refChr6 40481 25 + 197743 CTCCAGTAATATTGAGCATAAAGCA -s Anc2.Anc2refChr13 10233 25 + 96486 CTCCAGTAATATTGAGCATAAAGCC -s mr.mrrefChr5 227555 25 + 294540 TTCCAGTAATATTGAGGATATCGCA -s simCow_chr6.simCow.chr6 365750 25 + 602619 CTCCAGTAGTATTGACCATAAAGCC -s simDog_chr6.simDog.chr6 356585 25 + 593897 CTCCAGTAATATTGAGTATAAATCC -s simHuman_chr6.simHuman.chr6 364307 25 + 601863 CTCCAGTATTACTGAGCATAAAGTA -s simRat_chr6.simRat.chr6 373181 25 + 647215 TTCCAGCAACATTGAGGATATGGCA - -a -s simMouse_chr6.simMouse.chr6 178416 33 + 636262 CAGGGAGGAAATTATATCAATTATGTCATATAG -s Anc0.Anc0refChr3 7721 32 + 222631 CAGGGATGGAATTATACCAA-CGTATTATATAG -s Anc1.Anc1refChr6 40513 32 + 197743 CAGGGATGGAATTATACCAA-CGTATTATATAG -s Anc2.Anc2refChr13 10265 32 + 96486 CAGGGATGGAATTATACAGA-CGTATTACATAG -s mr.mrrefChr5 227587 33 + 294540 CAGGGAGGGAATTATATCAATCATGTTATATAG -s simCow_chr6.simCow.chr6 365782 23 + 602619 CAGGGATGGAAT----------GTACTACATTG -s simDog_chr6.simDog.chr6 356617 32 + 593897 CAGGGGTGGAATTATACAGA-CACATTACATAG -s simHuman_chr6.simHuman.chr6 364339 32 + 601863 TCGGGATGGAGTTATACCAA-CGTATTATATAC -s simRat_chr6.simRat.chr6 373213 33 + 647215 AAGGGAGGGAATTATATCAATCATGTTCTATAG - -a -s simMouse_chr6.simMouse.chr6 178449 61 + 636262 ACACTAAATTGCACCAATGAGCAGCAAAGGAGTCTGATGGTTTCATAAAGCCTTTAGTTTA -s Anc0.Anc0refChr3 7756 42 + 222631 ACACTAAAGTACAC---TAAGCTGTAAAGAGGTCTAATGG----------------TTTTA -s Anc1.Anc1refChr6 40548 42 + 197743 ACACTAAAGTACAC---TAAGCTGTAAAGAGGTCTAATGG----------------TTTTA -s Anc2.Anc2refChr13 10300 42 + 96486 ATACTAGAGTACAC---TGAGATGTAAAGAGGTCTAATGG----------------TGTTA -s mr.mrrefChr5 227623 55 + 294540 ACACTAAATTGCACCAATAAGCAGCAAAGGGGTCTGATGG------AAAGCCTTTAGTTTA -s simCow_chr6.simCow.chr6 365808 42 + 602619 ATACTAGATTACAC---TGAGTTGGAAAGAGGTCTAATAG----------------TGCAT -s simDog_chr6.simDog.chr6 356652 42 + 593897 ATGCTAGAGCACAC---TGAGATGTTAAGAGGTCTGTTGG----------------TGTTA -s simHuman_chr6.simHuman.chr6 364374 42 + 601863 ACACTAAACTACAC---TAAACTGTAGAGAGGTCTAATGG----------------TTTTA -s simRat_chr6.simRat.chr6 373249 55 + 647215 ACACTAAATCGCACCAATAAGCAGCAAAGGGGCCTTATGG------AAAACCTTTAGTTTA - -a -s simMouse_chr6.simMouse.chr6 178510 7 + 636262 AAAACGA -s Anc0.Anc0refChr3 7799 7 + 222631 AAAATCT -s Anc1.Anc1refChr6 40591 7 + 197743 AAAATCT -s Anc2.Anc2refChr13 10343 7 + 96486 AAAATCT -s mr.mrrefChr5 227678 7 + 294540 AAAACCA -s simCow_chr6.simCow.chr6 365851 7 + 602619 AAAATCT -s simDog_chr6.simDog.chr6 356695 7 + 593897 AAAATCT -s simHuman_chr6.simHuman.chr6 364417 7 + 601863 AAAATCC -s simRat_chr6.simRat.chr6 373304 7 + 647215 AGAACCA - -a -s simMouse_chr6.simMouse.chr6 178517 35 + 636262 TTAGTCTATTATGACAAGCAGAGTAAATGCTCGAC -s Anc0.Anc0refChr3 7806 35 + 222631 CTGGTTTACTATGCCAAGCATAGTAAAAGCTCAAC -s Anc1.Anc1refChr6 40598 35 + 197743 CTGGTTTACTATGCCAAGCATAGTAAAAGCTCAAC -s Anc2.Anc2refChr13 10350 35 + 96486 CTGGTTTACTATGCCAAGCATAGTAAAAGCTCAAC -s mr.mrrefChr5 227685 35 + 294540 CTAGTTTACTATGACAAGCAGAGTAAATGCTCAAC -s simCow_chr6.simCow.chr6 365858 35 + 602619 CTGCTTTACTATGCCAGGTATAGTAAAAGCCCAAC -s simDog_chr6.simDog.chr6 356702 35 + 593897 CTGGTTTACTTTGCCAAGCATAGTAACAGCTGAGC -s simHuman_chr6.simHuman.chr6 364425 35 + 601863 CTGGTTTACTATGCCAAGCATCATAAAAGCTCAAC -s simRat_chr6.simRat.chr6 373311 35 + 647215 CTAGTTTACTATAACAAGCAGATTAAAGGCTCAAC - -a -s simMouse_chr6.simMouse.chr6 178552 10 + 636262 AAAGTGGTCA -s Anc0.Anc0refChr3 7841 10 + 222631 AAAGTGGTCA -s Anc1.Anc1refChr6 40633 10 + 197743 AAAGTGGTCA -s Anc2.Anc2refChr13 10385 10 + 96486 AAAGTGGTCA -s mr.mrrefChr5 227720 10 + 294540 AAAGTGGTCA -s simCow_chr6.simCow.chr6 365893 10 + 602619 AAAGTCGTTA -s simDog_chr6.simDog.chr6 356737 10 + 593897 AGAGTGGTCA -s simHuman_chr6.simHuman.chr6 364460 10 + 601863 AAAGCAGTCA -s simRat_chr6.simRat.chr6 373351 10 + 647215 AAAGTGGTGA - -a -s simMouse_chr6.simMouse.chr6 178562 18 + 636262 GTTACTGTGTGGTTGGGA -s Anc0.Anc0refChr3 7852 18 + 222631 GATACCATGTGTGTGGGG -s Anc1.Anc1refChr6 40644 18 + 197743 GATACCATGTGTGTGGGG -s Anc2.Anc2refChr13 10396 18 + 96486 GATACCATGTGTGTGAGG -s mr.mrrefChr5 227730 18 + 294540 GTTACTGTGTGTTTGGGA -s simCow_chr6.simCow.chr6 365904 18 + 602619 GATACCATGTGTGAGAGG -s simDog_chr6.simDog.chr6 356748 17 + 593897 GATATCATGTAGGT-AGG -s simHuman_chr6.simHuman.chr6 364471 18 + 601863 GATACCATGTGTGTGGGG -s simRat_chr6.simRat.chr6 373361 18 + 647215 GTTATTGTGTGTACGGGA - -a -s simMouse_chr6.simMouse.chr6 178580 24 + 636262 CACCTTGCCCTGGCTAGGTTCATG -s Anc0.Anc0refChr3 7870 24 + 222631 CACAATGTCATGGTTTTGGTTCCT -s Anc1.Anc1refChr6 40662 24 + 197743 CACAATGTCATGGTTTTGGTTCCT -s Anc2.Anc2refChr13 10414 24 + 96486 CACAATGTCATGGTTTTGGTTCCT -s mr.mrrefChr5 227748 24 + 294540 CACCTTGCCCTGGCTAGGTTAACG -s simCow_chr6.simCow.chr6 365922 24 + 602619 CACAACGATATGCATTTGGTTCTC -s simDog_chr6.simDog.chr6 356765 24 + 593897 GTCAATGTCATGGTCTCAGTTCCT -s simHuman_chr6.simHuman.chr6 364489 24 + 601863 CACGGTGTCATTGTTGTGGTTCAT -s simMouse_chr6.simMouse.chr6 178753 24 + 636262 AACCTTGCCCTAGCTAGGTTAACA -s simRat_chr6.simRat.chr6 373379 20 + 647215 CACCCTGCCCTGGCTATTTT---- - -a -s simMouse_chr6.simMouse.chr6 178604 31 + 636262 TGGTCTCGTCCCTTCGAGGGAGACTAATAAT -s Anc0.Anc0refChr3 7894 31 + 222631 TGGTCTCCCCCTTTCTGGGGGGACTAATAAT -s Anc1.Anc1refChr6 40686 31 + 197743 TGGTCTCCCCCTTTCTGGGGGGACTAATAAT -s Anc2.Anc2refChr13 10438 31 + 96486 GGTTGTCCCCCTTTCTGGGGGGGCTAATAAT -s mr.mrrefChr5 227772 31 + 294540 TGGTCTTGTCCCTTCGAGGGAAACTAATAAT -s simCow_chr6.simCow.chr6 365946 30 + 602619 AGTTATCCTCCTTTCTGGGGGGGCTAATAA- -s simDog_chr6.simDog.chr6 356789 31 + 593897 GGTTGTCCCTTTTTCGGGGGGGGCTAATTAT -s simHuman_chr6.simHuman.chr6 364514 29 + 601863 TTGTC--CACCTCTCTGGGGGGATTAATAAT -s simMouse_chr6.simMouse.chr6 178777 31 + 636262 TGGTCTTTTCCCTTCGAGGAAAACTAATAAT -s simRat_chr6.simRat.chr6 373399 31 + 647215 CCATCTTGTCCCAGCTAGGGAAACTAATAAT - -a -s simMouse_chr6.simMouse.chr6 178635 1 + 636262 T -s Anc0.Anc0refChr3 7925 1 + 222631 T -s Anc1.Anc1refChr6 40717 1 + 197743 T -s Anc2.Anc2refChr13 10469 1 + 96486 T -s mr.mrrefChr5 227803 1 + 294540 T -s simCow_chr6.simCow.chr6 365976 1 + 602619 C -s simDog_chr6.simDog.chr6 356838 1 + 593897 T -s simHuman_chr6.simHuman.chr6 364543 1 + 601863 T -s simMouse_chr6.simMouse.chr6 178808 1 + 636262 T -s simRat_chr6.simRat.chr6 373430 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 178636 16 + 636262 CTGGTGACTTACTGTG -s Anc0.Anc0refChr3 7936 16 + 222631 CTGGTAATTTGCTGTT -s Anc1.Anc1refChr6 40728 16 + 197743 CTGGTAATTTGCTGTT -s Anc2.Anc2refChr13 10480 16 + 96486 CTGGTAATTTGCTGTT -s mr.mrrefChr5 227814 16 + 294540 CTGGTGACTTACTGTG -s simCow_chr6.simCow.chr6 365987 14 + 602619 CTGGGAA--TGTTGTT -s simDog_chr6.simDog.chr6 356849 16 + 593897 CTGGTAATTTGCCATT -s simHuman_chr6.simHuman.chr6 364554 16 + 601863 CTGATAATCCGCTGTT -s simMouse_chr6.simMouse.chr6 178809 16 + 636262 CTGGTGACTTACTGTG -s simRat_chr6.simRat.chr6 373441 16 + 647215 CTGGTGACTTGCTGCG - -a -s simMouse_chr6.simMouse.chr6 178652 27 + 636262 GTAGGTCTAGGTCCTGGGTAGATACAT -s Anc0.Anc0refChr3 7952 27 + 222631 GTGGGCCTGGTCCCTGGGTGGCTACCG -s Anc1.Anc1refChr6 40744 27 + 197743 GTGGGCCTGGTCCCTGGGTGGCTACCG -s Anc2.Anc2refChr13 10496 27 + 96486 GTGGGCCTGGTCTCTCGGTGGCTACCG -s mr.mrrefChr5 227830 27 + 294540 GTAGGTCTAGGTCCTGGGTAGATACAT -s simCow_chr6.simCow.chr6 366001 26 + 602619 GTGCACCTGGTCTCTAGGTAGCT-CTG -s simDog_chr6.simDog.chr6 356865 27 + 593897 ATGGGCTTGGTCTTGCAGTGGCTACCT -s simHuman_chr6.simHuman.chr6 364570 27 + 601863 GTGAGCCCGGTCCCTGGGTGTCTACCG -s simMouse_chr6.simMouse.chr6 178827 27 + 636262 GTAGGTCTAGGTCCTGGGTAGTTACAT -s simRat_chr6.simRat.chr6 373457 27 + 647215 GTAGGCCTGGGTTTTGGGTAGATACAT - -a -s simMouse_chr6.simMouse.chr6 178679 74 + 636262 GATTTAATTCCATACATTAATGTGAGGCAGCCAAAGGTGTGGCCACACCTCTAAGTCTAGCCTGGCTAGACAGC -s Anc0.Anc0refChr3 7979 38 + 222631 AATTTAGTTCCATACATTAGTATGGGGAAGCCAAAAGT------------------------------------ -s Anc1.Anc1refChr6 40771 38 + 197743 AATTTAGTTCCATACATTAGTATGGGGAAGCCAAAAGT------------------------------------ -s Anc2.Anc2refChr13 10523 38 + 96486 AATTAAGTTCCATACATTAGTATGGGGAAGTGAACAGT------------------------------------ -s mr.mrrefChr5 227857 74 + 294540 AATTTAGTTCCATACATTAATGTGAGGCAGCCAAAGGTGTGGCCACACCTCTAAGGCTAGCCTGGCGAGACAGC -s simCow_chr6.simCow.chr6 366030 31 + 602619 AACTAAGATCCATACATTAGCATGGAG-------CAGG------------------------------------ -s simDog_chr6.simDog.chr6 356892 38 + 593897 GATCAAGTTCCATCCATTAGTATGGGGAAGTGAACAGT------------------------------------ -s simHuman_chr6.simHuman.chr6 364597 38 + 601863 AATTTAGTTTCATACATTTGTATGGGATAGCCAAAAAT------------------------------------ -s simMouse_chr6.simMouse.chr6 178854 68 + 636262 AATTTAGTTCCATACATTAATGTGAG------AAAGGTGTGTCCACACCTCTAAGGCTAGCCTGGCGAGACAGC -s simRat_chr6.simRat.chr6 373484 38 + 647215 AATTTAGTTCCATACATTCGTGTGAGGCAGCCAAAGGT------------------------------------ - -a -s simMouse_chr6.simMouse.chr6 178825 2 + 636262 TG - -a -s simMouse_chr6.simMouse.chr6 178922 95 + 636262 AATCAATTGGGCCTGCTGCCATCATGTTCTTCTGATCCGGCTACTCTTCATTTCGGGTTGGTTAAAAAGGATATAACATGGACCGCCAGGCTCTG -s Anc0.Anc0refChr3 8017 13 + 222631 ----------------------------------------------------------------------------------CCGCTAAGTTCTG -s Anc1.Anc1refChr6 40809 13 + 197743 ----------------------------------------------------------------------------------CCGCTAAGTTCTG -s Anc2.Anc2refChr13 10561 13 + 96486 ----------------------------------------------------------------------------------TTGCTAAGTTCTG -s mr.mrrefChr5 227931 13 + 294540 ----------------------------------------------------------------------------------CCGCCAGGCTCTG -s simCow_chr6.simCow.chr6 366061 13 + 602619 ----------------------------------------------------------------------------------ATGCTAAGTTCTG -s simDog_chr6.simDog.chr6 356930 13 + 593897 ----------------------------------------------------------------------------------TTGCTATGTTCTG -s simHuman_chr6.simHuman.chr6 364635 13 + 601863 ----------------------------------------------------------------------------------CCACTAAGTCCAG -s simRat_chr6.simRat.chr6 373522 13 + 647215 ----------------------------------------------------------------------------------CTGCCAGGCTCTG - -a -s simMouse_chr6.simMouse.chr6 179017 9 + 636262 AGTAGAATA -s Anc0.Anc0refChr3 8030 9 + 222631 ACTGCAATA -s Anc1.Anc1refChr6 40822 9 + 197743 ACTGCAATA -s Anc2.Anc2refChr13 10574 9 + 96486 ACTGCAGAA -s mr.mrrefChr5 227944 9 + 294540 ACTAGAATA -s simCow_chr6.simCow.chr6 366074 9 + 602619 ACTACAGAA -s simDog_chr6.simDog.chr6 356946 9 + 593897 AGTGGTGAA -s simHuman_chr6.simHuman.chr6 364648 9 + 601863 ACTGCAATA -s simRat_chr6.simRat.chr6 373535 9 + 647215 ACTAGAATA - -a -s simMouse_chr6.simMouse.chr6 179026 10 + 636262 GATATGTATG -s Anc0.Anc0refChr3 8039 10 + 222631 GGTCCCTAAG -s Anc1.Anc1refChr6 40831 10 + 197743 GGTCCCTAAG -s Anc2.Anc2refChr13 10583 10 + 96486 GGTCCCTAAG -s mr.mrrefChr5 227953 10 + 294540 GATATGTATG -s simCow_chr6.simCow.chr6 366083 10 + 602619 GGTCCCTAAG -s simDog_chr6.simDog.chr6 356957 10 + 593897 GTTTGCTAAG -s simHuman_chr6.simHuman.chr6 364657 10 + 601863 GGTCCTTAAG -s simRat_chr6.simRat.chr6 373544 10 + 647215 GATGTGTATG - -a -s simMouse_chr6.simMouse.chr6 179036 9 + 636262 TAGTTTTGA -s Anc0.Anc0refChr3 8049 8 + 222631 TC-CTTTGA -s Anc1.Anc1refChr6 40841 8 + 197743 TC-CTTTGA -s Anc2.Anc2refChr13 10593 8 + 96486 TC-CTCTGA -s mr.mrrefChr5 227963 9 + 294540 TAGCTTTGA -s simCow_chr6.simCow.chr6 366094 8 + 602619 AC-CGCTGA -s simDog_chr6.simDog.chr6 356967 4 + 593897 TT-CT---- -s simHuman_chr6.simHuman.chr6 364667 8 + 601863 TC-CTTTGA -s simRat_chr6.simRat.chr6 373554 9 + 647215 TAGCTTTGA - -a -s simMouse_chr6.simMouse.chr6 179045 7 + 636262 CAATTGA -s Anc0.Anc0refChr3 8058 7 + 222631 GACTTGA -s Anc1.Anc1refChr6 40850 7 + 197743 GACTTGA -s Anc2.Anc2refChr13 10602 7 + 96486 GATTTGA -s mr.mrrefChr5 227973 7 + 294540 CACTTGA -s simCow_chr6.simCow.chr6 366115 7 + 602619 GATTTGA -s simHuman_chr6.simHuman.chr6 364676 7 + 601863 TACTTGA -s simRat_chr6.simRat.chr6 373564 7 + 647215 CACTTGA - -a -s simMouse_chr6.simMouse.chr6 179052 3 + 636262 CGA -s Anc0.Anc0refChr3 8068 3 + 222631 TGT -s Anc1.Anc1refChr6 40860 3 + 197743 TGT -s Anc2.Anc2refChr13 10612 3 + 96486 TGT -s mr.mrrefChr5 227980 3 + 294540 TGA -s simCow_chr6.simCow.chr6 366125 3 + 602619 TGT -s simHuman_chr6.simHuman.chr6 364686 3 + 601863 TGT -s simRat_chr6.simRat.chr6 373571 3 + 647215 TGA - -a -s simMouse_chr6.simMouse.chr6 179055 2 + 636262 GA -s Anc0.Anc0refChr3 8071 2 + 222631 GA -s Anc1.Anc1refChr6 40863 2 + 197743 GA -s Anc2.Anc2refChr13 10615 2 + 96486 GA -s mr.mrrefChr5 227983 2 + 294540 GA -s simCow_chr6.simCow.chr6 366136 2 + 602619 GA -s simHuman_chr6.simHuman.chr6 364689 2 + 601863 GA -s simRat_chr6.simRat.chr6 373574 2 + 647215 GA - -a -s simMouse_chr6.simMouse.chr6 179057 2 + 636262 AA -s Anc0.Anc0refChr3 8079 2 + 222631 CT -s Anc1.Anc1refChr6 40871 2 + 197743 CT -s Anc2.Anc2refChr13 10623 2 + 96486 TT -s mr.mrrefChr5 227989 2 + 294540 CC -s simCow_chr6.simCow.chr6 366180 2 + 602619 TT -s simHuman_chr6.simHuman.chr6 364697 2 + 601863 CT -s simRat_chr6.simRat.chr6 373580 2 + 647215 CC - -a -s simMouse_chr6.simMouse.chr6 179059 17 + 636262 GTGTCTTCCCTACTGCA -s Anc0.Anc0refChr1 11784 17 + 62388 ATATCTAGTCTCCTGGA -s Anc1.Anc1refChr2 12573 17 - 144309 ATATCTAGTCTCCTGGA -s Anc2.Anc2refChr3 12960 17 - 53186 ATATCTAGTCTCCTGGA -s mr.mrrefChr5 34338 17 + 294540 ATATCTTCTCTGCTGCA -s simCow_chr6.simCow.chr6 433978 17 - 602619 ATATCTAGCATCCTGCA -s simDog_chr6.simDog.chr6 142038 17 + 593897 ATATCTGGTCTCCTGGA -s simHuman_chr6.simHuman.chr6 435277 17 - 601863 ACATCTAGTTTCCGCAA -s simRat_chr6.simRat.chr6 169310 17 + 647215 ATATCTACTCTGCTGCA - -a -s simMouse_chr6.simMouse.chr6 179076 1 + 636262 G -s Anc0.Anc0refChr1 11801 1 + 62388 G -s Anc1.Anc1refChr2 12590 1 - 144309 G -s Anc2.Anc2refChr3 12977 1 - 53186 G -s mr.mrrefChr5 34355 1 + 294540 G -s simCow_chr6.simCow.chr6 433995 1 - 602619 A -s simDog_chr6.simDog.chr6 142055 1 + 593897 G -s simHuman_chr6.simHuman.chr6 435297 1 - 601863 G -s simRat_chr6.simRat.chr6 169327 1 + 647215 G - -a -s simMouse_chr6.simMouse.chr6 179077 16 + 636262 TAGATCTCCTAAATTA -s Anc0.Anc0refChr1 11802 16 + 62388 TACTACACTTCTGCTA -s Anc1.Anc1refChr2 12591 16 - 144309 TACTACACTTCTGCTA -s Anc2.Anc2refChr3 12984 16 - 53186 TACTACACTTCTGCTA -s mr.mrrefChr5 34356 16 + 294540 TAGATCTCCTAAATTA -s simCow_chr6.simCow.chr6 434002 16 - 602619 TACTACACTTCTGATA -s simDog_chr6.simDog.chr6 142062 16 + 593897 TGCTACATCTCTGCTA -s simHuman_chr6.simHuman.chr6 435298 16 - 601863 TACTACACTTCTGCTA -s simRat_chr6.simRat.chr6 169328 16 + 647215 TAGATCTCCTAAATTA - -a -s simMouse_chr6.simMouse.chr6 179093 3 + 636262 GGG -s Anc0.Anc0refChr1 11819 3 + 62388 GGG -s Anc1.Anc1refChr2 12608 3 - 144309 GGG -s Anc2.Anc2refChr3 13001 3 - 53186 GGG -s mr.mrrefChr5 34372 3 + 294540 GGG -s simCow_chr6.simCow.chr6 434019 3 - 602619 GGG -s simDog_chr6.simDog.chr6 142079 3 + 593897 GGG -s simHuman_chr6.simHuman.chr6 435315 3 - 601863 GGG -s simRat_chr6.simRat.chr6 169344 3 + 647215 GAT - -a -s simMouse_chr6.simMouse.chr6 179096 81 + 636262 ATCACCTCACCCTTTTCAATTACTTGAACCAATAAGTCAGCCAAATAATATCATGAACATCTCAGAATTTACCACTTCGGT -s Anc0.Anc0refChr1 11822 69 + 62388 AATACCTTCTCCTATCCAAATATTTG-----------CAGAAA-ATAACATCACGAATGTCTTGGAATTTACCATTCGGGC -s Anc1.Anc1refChr2 12611 70 - 144309 AATACCTTCTCCTATCCAAATATTTG-----------CAGAAACATAACATCACGAATGTCTTGGAATTTACCATTCGGGC -s Anc2.Anc2refChr3 13004 69 - 53186 AATACCTTCTCCTATCCCAATGTTTG-----------GTGAAA-ATAACATCACAAATGTCTTGGAATTCACCATTCGGGC -s mr.mrrefChr5 34375 70 + 294540 ATTACCTCCCCCTTTTCAATTACTTG-----------CAGCCAAATAATATCATGAACATCTCAGAATTTACCACTTGGGT -s simCow_chr6.simCow.chr6 434022 69 - 602619 AATACCTTCTCTTATCCCATTGTTTG-----------GTGCAA-ATAGCATCACAATCGGCTAGGAACTGACCATTTGGGC -s simDog_chr6.simDog.chr6 142082 69 + 593897 AATTCCTTCCACCATTCCAATGTTTG-----------GTGAAA-ATAACATTACAAATGTCTTGGAATTCACCATTCGGGC -s simHuman_chr6.simHuman.chr6 435318 70 - 601863 AATATTTTCTCCTATCCAACTATTTG-----------CAGAAACATAACATCCCGAATGTTTTGGAATTTTCCATTAGGGC -s simRat_chr6.simRat.chr6 169348 64 + 647215 ACTACCTCCCCGTTTTCAATTACTT-----------------CAATAATATCATAAACATCTCCGAATTTGCCACTTGGGT - -a -s simMouse_chr6.simMouse.chr6 179177 25 + 636262 GCACGTGCTCTACTAGTTCACTAGC -s Anc0.Anc0refChr1 11895 25 + 62388 GCATAGGCTCTCCTGGTTCCTTAGC -s Anc1.Anc1refChr2 12685 25 - 144309 GCATAGGCTCTCCTGGTTCCTTAGC -s Anc2.Anc2refChr3 13077 25 - 53186 GCATAGGCTCTCCTGGTTCCTTAGC -s mr.mrrefChr5 34445 25 + 294540 GCACATGCTCTACTAGTTCACTAGC -s simCow_chr6.simCow.chr6 434096 25 - 602619 GCATAGACTCTCCTGGTTCCTTAGC -s simDog_chr6.simDog.chr6 142155 25 + 593897 GGATTGGCTCTCCTGGTTCCTTAGC -s simHuman_chr6.simHuman.chr6 435392 25 - 601863 GCATAGGCCCTGCTGGTTTCATAGC -s simRat_chr6.simRat.chr6 169412 25 + 647215 GCACATGCTCTACTAGTTCATTAAC - -a -s simMouse_chr6.simMouse.chr6 179202 66 + 636262 TCCTGTGGCAGGTTATAAAAACAGCCAACCCAGGATTTGGGGATATACTGTATACCATTTCTTGCT -s Anc0.Anc0refChr1 11920 59 + 62388 TTTTGTGGGAGGTTGCACAAACAGCTAGTATAGGATTTGGGGATA-------AACCCTTTCTTGCT -s Anc1.Anc1refChr2 12710 59 - 144309 TTTTGTGGGAGGTTGCACAAACAGCTAGTATAGGATTTGGGGATA-------AACCCTTTCTTGCT -s Anc2.Anc2refChr3 13102 59 - 53186 CTTTGTGGGATGTTGCACAAACAGCTATTATAGGATTTGGGAATA-------TATCCTTTCTTGCT -s mr.mrrefChr5 34470 65 + 294540 TCCTGTGGCAGGTTACAAAAACAGCCAGCCCAGGATTTGGGGATATAC-GTAAACCATTTCTTGCT -s simCow_chr6.simCow.chr6 434121 47 - 602619 CTTTGTGTGGTGTTGCACGAATA------------CTTGGGAATA-------TATCCTCTCTTGCT -s simDog_chr6.simDog.chr6 142182 59 + 593897 CTTTGTGGGATGTTGTACAAACAGCTATTATAGGATTTGGGAATA-------TATCCTTTCTTGCT -s simHuman_chr6.simHuman.chr6 435417 51 - 601863 TT--------GGTTGCAGAAACAGCTAGATTAGGGATTGGGGATA-------AACCCTTTCTTTCT -s simRat_chr6.simRat.chr6 169437 65 + 647215 TCCAGTAGAAGGTGACAAAAACAGCCAGCCCAGGATTTGGGGATATAC-ATAAACCATTTCTTACT - -a -s simMouse_chr6.simMouse.chr6 179268 44 + 636262 GCATTTAGGGCAAGACTTTCGACCTCCTCCTGACACCATGATGC -s Anc0.Anc0refChr1 11979 44 + 62388 GCATTTAGGGTAAGACTTTTGTCCTCCTTTTGATACAATGATGC -s Anc1.Anc1refChr2 12769 44 - 144309 GCATTTAGGGTAAGACTTTTGTCCTCCTTTTGATACAATGATGC -s Anc2.Anc2refChr3 13161 44 - 53186 GCACTTAGGTTAAGACTTTTGTCCTCCATTTGATACAATGAGGC -s mr.mrrefChr5 34535 44 + 294540 GCATTTAGGGCAAGACTTTTGACCTCCTCCTGACACCATGATGC -s simCow_chr6.simCow.chr6 434168 43 - 602619 GCCCCTGGGCTAGGACTT-TGTCCTCCATTTGACACAATGAGGC -s simDog_chr6.simDog.chr6 142259 44 + 593897 GCACTTAGGTCAAGAACTTTGTCCTCCATTTGATATATAGAGGC -s simHuman_chr6.simHuman.chr6 435468 44 - 601863 GCATTTAGGGTAAGACTTTTGTCCCCCTGTTGATACAATGATGC -s simRat_chr6.simRat.chr6 169502 43 + 647215 GCATTTAGGGCAAGATTTTTGACCTCCTCCTGACACCAGGAT-C - -a -s simMouse_chr6.simMouse.chr6 179312 43 + 636262 TACTGCAGAGACCTGGTATAATGCTGCATTCTTATGGTCTTGA -s Anc0.Anc0refChr1 12023 36 + 62388 TACTTCAGATA-------TACTGTTATATTCTTATTCTTGTTA -s Anc1.Anc1refChr2 12813 42 - 144309 TACTTCAGATAC-TAGTATACTGTTATATTCTTATTCTTGTTA -s Anc2.Anc2refChr3 13205 36 - 53186 TACTTAAGATA-------TACTGTTATTTTCTTATTCTTGTTA -s mr.mrrefChr5 34579 43 + 294540 TACTGCAGAGACCTGGTATAATGCTACATTCTTATGGTCTTTA -s simCow_chr6.simCow.chr6 434215 36 - 602619 TACTTAATACA-------TACTGTTATTTTCTTATTCTCTTTA -s simDog_chr6.simDog.chr6 142303 31 + 593897 GA-----GATA-------TACTGGTATTTTCTTATTCATGTTA -s simHuman_chr6.simHuman.chr6 435512 41 - 601863 TACTCCAGATAC-TAGTA-GCTGTTATATTCTTATTCTTCTTA -s simRat_chr6.simRat.chr6 169545 43 + 647215 AACTGCAGAGCCCTGATATAATGCTACGTTCTTATGGTCTTTA - -a -s simMouse_chr6.simMouse.chr6 179355 1 + 636262 T -s Anc0.Anc0refChr1 12059 1 + 62388 C -s Anc1.Anc1refChr2 12855 1 - 144309 C -s Anc2.Anc2refChr3 13241 1 - 53186 C -s mr.mrrefChr5 34622 1 + 294540 T -s simCow_chr6.simCow.chr6 434251 1 - 602619 T -s simDog_chr6.simDog.chr6 142334 1 + 593897 C -s simHuman_chr6.simHuman.chr6 435553 1 - 601863 C -s simRat_chr6.simRat.chr6 169601 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 179356 67 + 636262 TCTCTTACTATGTCAGATAACTCTATCAGGTGACTCACACTCCATCTATGAACTCACATATACTACT -s Anc0.Anc0refChr1 12060 65 + 62388 TTTCTCACTATGTGGGGGAATTCTATTATATGACTTGGAGTC-ACTCAGAAGCCCAGTCAC-TTAGT -s Anc1.Anc1refChr2 12856 66 - 144309 TTTCTCACTATGTGGGGGAATTCTATTATATGACTTGGAGTC-ACTCAGAAGCCCAGTCACATTAGT -s Anc2.Anc2refChr3 13242 65 - 53186 TTTCTCACTATGTGGGGGAATTTTGTTATATGACTTGGAGTC-ACTCAGAAGCCCAGTCAC-TTGGT -s mr.mrrefChr5 34623 67 + 294540 TTTCTTACTATGTCAGGTAACTCTATCAGGTGACTCACACTCCATTTATGAACCCACACATACTACT -s simCow_chr6.simCow.chr6 434252 60 - 602619 TTTCTTGCTAGGTGGGAGAATTTTGATATGTGACCTGCAGTT-ACACTAAAGCCTAGTTAC------ -s simDog_chr6.simDog.chr6 142336 65 + 593897 TTTCTCACTATGTGGGGGAATATTGTTATATGACTCCGAGTC-ATTCAGTAGCCCAGTCAC-TTGGT -s simHuman_chr6.simHuman.chr6 435554 66 - 601863 TTTGTCAGTATGTTGAGGAATTCTATTGTTTGACTTGAAGTC-ACTCAGAGCCCCAGTCACATTAGT -s simRat_chr6.simRat.chr6 169602 67 + 647215 TTTCTTAATTTGTCAGGTAGCTCTATCAGGTGACTCACACTCCATTTATGAACCCAACCATACTAAT - -a -s simMouse_chr6.simMouse.chr6 179423 24 + 636262 GAAAAGATACGACAAGCTTATACA -s Anc0.Anc0refChr1 12150 14 + 62388 GATAACATAC----------CACA -s Anc1.Anc1refChr2 12947 14 - 144309 GATAACATAC----------CACA -s Anc2.Anc2refChr3 13332 14 - 53186 GATAACATAC----------CACA -s mr.mrrefChr5 34690 14 + 294540 GAAAAGATAC----------CACA -s simCow_chr6.simCow.chr6 434318 14 - 602619 GATATTATAC----------CATA -s simDog_chr6.simDog.chr6 142475 14 + 593897 GATAACATAC----------TACG -s simHuman_chr6.simHuman.chr6 435645 14 - 601863 GATACCATAT----------CACA -s simRat_chr6.simRat.chr6 169669 14 + 647215 GAAAAGATAC----------CACA - -a -s simMouse_chr6.simMouse.chr6 179447 33 + 636262 AGCTTATACTGCTCTCCTTAGTGTTTTTATGGC -s Anc0.Anc0refChr1 12179 33 + 62388 AGGTGACACTGCTCTCCTTTGTGTTTTTGTGGC -s Anc1.Anc1refChr2 12976 33 - 144309 AGGTGACACTGCTCTCCTTTGTGTTTTTGTGGC -s Anc2.Anc2refChr3 13361 33 - 53186 TGGCGACACTGCTCTCCTCTGTGTTTTTGTGGC -s mr.mrrefChr5 34704 33 + 294540 AGCTTATACTGCTCTCCTTAGTGTTTTTATGGC -s simCow_chr6.simCow.chr6 434347 33 - 602619 TGGAGACACTGCTCTCCTCTGTGTTTTTGTGGC -s simDog_chr6.simDog.chr6 142504 32 + 593897 TGGCAACACGGCTCTCTTCTGTGTTTT-GTGGT -s simHuman_chr6.simHuman.chr6 435674 33 - 601863 AGGTGACACTGCTCTCCTTTGTGTTTTTGTGGC -s simRat_chr6.simRat.chr6 169683 33 + 647215 AACCTATACTGTTCTCCTCAGTGTTTTTATGGC - -a -s simMouse_chr6.simMouse.chr6 179480 43 + 636262 CAGACACAGAACAAACTCTTCATATTGTGCTTAATGTTGGATA -s Anc0.Anc0refChr1 12212 38 + 62388 CAGACAGAGA-----CTCATCATGTCATGCTGAATGTTGGATT -s Anc1.Anc1refChr2 13009 38 - 144309 CAGACAGAGA-----CTCATCATGTCATGCTGAATGTTGGATT -s Anc2.Anc2refChr3 13394 38 - 53186 CAGACAGAAA-----CTCATCATGTCATCCTGGATGTTGGATT -s mr.mrrefChr5 34737 43 + 294540 CAGACACAGAACAAACTCTTCATGTTGTGCTTAATGTTGGATA -s simCow_chr6.simCow.chr6 434384 38 - 602619 CAGACAGAAA-----CTCATCATATCAGCCAGTATGTTGGAAG -s simDog_chr6.simDog.chr6 142536 38 + 593897 CAGACAGAAA-----CTCATCATGTCATCCTGGATGTTGGCTT -s simHuman_chr6.simHuman.chr6 435707 38 - 601863 CAGACAGAGG-----CTCATCATGTCATGCTCAATGTTGGATT -s simRat_chr6.simRat.chr6 169716 43 + 647215 CAGACACAAAACAAACTCTTCATGTTGTGCATAGTGTTGGATA - -a -s simMouse_chr6.simMouse.chr6 179523 28 + 636262 TGCGCATCTGAGCAAGCCTGTTTTTGAG -s Anc0.Anc0refChr1 12253 28 + 62388 TGTGCTGCTGAGCATACCTACTTCGGAG -s Anc1.Anc1refChr2 13050 28 - 144309 TGTGCTGCTGAGCATACCTACTTCGGAG -s Anc2.Anc2refChr3 13435 28 - 53186 TATACAGCTGAGCATACCTACTTCGGAG -s mr.mrrefChr5 34780 28 + 294540 TGTGCTTCTGAGCATGCCTGTTTTTGAG -s simCow_chr6.simCow.chr6 434425 28 - 602619 TATATATCTGAGCATACCTGGTCCTCAG -s simDog_chr6.simDog.chr6 142583 28 + 593897 TATACAGCTGAGTATACCTACTTCGGAG -s simHuman_chr6.simHuman.chr6 435748 28 - 601863 TGTGCTCCTAAGCATACCTACTTAAGTG -s simRat_chr6.simRat.chr6 169759 28 + 647215 TGTGCTTCTGAACATGCCTGTTCTTGAG - -a -s simMouse_chr6.simMouse.chr6 179551 20 + 636262 TAGTTACTCAAGGATGTATT -s Anc0.Anc0refChr1 12281 20 + 62388 TAATTACTCAAGGATATATT -s Anc1.Anc1refChr2 13078 20 - 144309 TAATTACTCAAGGATATATT -s Anc2.Anc2refChr3 13465 20 - 53186 TAATTACTCAAGGATATATT -s mr.mrrefChr5 34808 20 + 294540 TAGTTACTCAAGGATGTATT -s simCow_chr6.simCow.chr6 434455 20 - 602619 TATGTACTCAAGGATACATC -s simDog_chr6.simDog.chr6 142613 20 + 593897 TAATTACACAAGGATATAAT -s simHuman_chr6.simHuman.chr6 435776 20 - 601863 TACCAACTCAAGGACATATT -s simRat_chr6.simRat.chr6 169787 20 + 647215 CATTTACTCAAGGATGTATT - -a -s simMouse_chr6.simMouse.chr6 179571 9 + 636262 TGAGCTTAG -s Anc0.Anc0refChr1 12304 9 + 62388 TGGGCCTGG -s Anc1.Anc1refChr2 13101 9 - 144309 TGGGCCTGG -s Anc2.Anc2refChr3 13488 9 - 53186 TGGGCCTGG -s mr.mrrefChr5 34828 9 + 294540 TTGGCTTAG -s simCow_chr6.simCow.chr6 434478 9 - 602619 TCAGCTTGG -s simDog_chr6.simDog.chr6 142636 9 + 593897 TGGGCCTGA -s simHuman_chr6.simHuman.chr6 435799 9 - 601863 TGGATGTGG -s simRat_chr6.simRat.chr6 169807 9 + 647215 TTGGCCTAG - -a -s simMouse_chr6.simMouse.chr6 179580 57 + 636262 GTAGAGTGGTAATAAGGGTGCATACATACGCTGCCAACATTGTTTGACTTATGCATT -s Anc0.Anc0refChr1 12325 57 + 62388 TTTGTGTAGTCATAAATTTGCGTGCATACACCGCCAAGGATGTTTGAGTTGAGCATC -s Anc1.Anc1refChr2 13122 57 - 144309 TTTGTGTAGTCATAAATTTGCGTGCATACACCGCCAAGGATGTTTGAGTTGAGCATC -s Anc2.Anc2refChr3 13509 57 - 53186 TTTGTGTAGTCATCAATTTGTGTGCATACATCGCCAAGGATGTTTGAGCTGAGCATC -s mr.mrrefChr5 34837 57 + 294540 GTAGAGTGGTAATAAGGTTGCATACATACACTGCCAACATTGTTTGACTTGTGCATT -s simCow_chr6.simCow.chr6 434499 57 - 602619 CTTGTATTGTCATGAATTTGTGTGTATACATTGCCAAGGTTGTTTGAGCTGAGTACC -s simDog_chr6.simDog.chr6 142657 57 + 593897 TTGGTGTAGTCATCAAATTGTGTGCATACATCGCCAGGGATGTTTAAGCTAAGCATC -s simHuman_chr6.simHuman.chr6 435820 57 - 601863 TTTGTGTAGCGATAAATTTGCCTGCATACACGGCCAAGGATGCTAGAGTTGAGAATC -s simRat_chr6.simRat.chr6 169816 57 + 647215 GTGGACTGGTCATAAGGTTGCATACATACACAGCCAACATTGTTTGATTTGCACATT - -a -s simMouse_chr6.simMouse.chr6 179637 12 + 636262 AAGCTGACCACA -s Anc0.Anc0refChr1 12382 12 + 62388 AAGCTGACCACA -s Anc1.Anc1refChr2 13179 12 - 144309 AAGCTGACCACA -s Anc2.Anc2refChr3 13566 12 - 53186 GAGCTGACCACA -s mr.mrrefChr5 34894 12 + 294540 AAGCTGACCACA -s simCow_chr6.simCow.chr6 434557 12 - 602619 GAGCTGACTACA -s simDog_chr6.simDog.chr6 142714 12 + 593897 GAACTGTCCACA -s simHuman_chr6.simHuman.chr6 435877 12 - 601863 AAGCTGAACACA -s simRat_chr6.simRat.chr6 169873 12 + 647215 AAGCTAACCAGA - -a -s simMouse_chr6.simMouse.chr6 179649 24 + 636262 ACTCAAATTTAGCCTGGCTGTCCC -s Anc0.Anc0refChr1 12396 24 + 62388 ACTCCAATTTAACATAACTGTCCC -s Anc1.Anc1refChr2 13193 24 - 144309 ACTCCAATTTAACATAACTGTCCC -s Anc2.Anc2refChr3 13580 24 - 53186 ACTCCAATTTAACATAATTGTCCC -s mr.mrrefChr5 34906 24 + 294540 ACTCAAATTTAACCTGGCTGTCCC -s simCow_chr6.simCow.chr6 434571 8 - 602619 ACTCCAA----------------A -s simDog_chr6.simDog.chr6 142728 24 + 593897 ACTCCCATTTAACATAATTGTCCC -s simHuman_chr6.simHuman.chr6 435891 24 - 601863 ACTCCAATTCAACTTAACTGTCCC -s simRat_chr6.simRat.chr6 169885 24 + 647215 ACTTGAATTTAACCTGGCTGTCCC - -a -s simMouse_chr6.simMouse.chr6 179673 31 + 636262 ATTTACCTGTCTAATCTGCGCTCTCTCATCC -s Anc0.Anc0refChr1 12421 30 + 62388 ATTCCCCTGTC-AATCTATACTCTCTTTTCT -s Anc1.Anc1refChr2 13218 31 - 144309 ATTCCCCTGTCCAATCTATACTCTCTTTTCT -s Anc2.Anc2refChr3 13605 30 - 53186 ATTCCCCTGTC-ATTCCATACTCTCTTTTTT -s mr.mrrefChr5 34930 31 + 294540 ATATACCTGTCCAATCTGCACTCTCTTATCC -s simCow_chr6.simCow.chr6 434580 30 - 602619 ATTCCCCTGTC-CTTCAGCACACTCTCTTTT -s simDog_chr6.simDog.chr6 142753 30 + 593897 ACTCCCCCGTC-ATTCCATACTCTTTTTTTT -s simHuman_chr6.simHuman.chr6 435916 29 - 601863 ATT--CTTGTCCAATCTATAACCTCTTTTCT -s simRat_chr6.simRat.chr6 169909 31 + 647215 GTATACCTGTACAATCTGCACTCTCTTATCC - -a -s simMouse_chr6.simMouse.chr6 179704 7 + 636262 ATTTACA -s Anc0.Anc0refChr1 12451 7 + 62388 GTCTAAA -s Anc1.Anc1refChr2 13249 7 - 144309 GTCTAAA -s Anc2.Anc2refChr3 13635 7 - 53186 GTCTAAA -s mr.mrrefChr5 34961 7 + 294540 ATTTACA -s simCow_chr6.simCow.chr6 434610 7 - 602619 ATCCCAA -s simDog_chr6.simDog.chr6 142785 7 + 593897 GTTTAAA -s simHuman_chr6.simHuman.chr6 435945 7 - 601863 GTCTAAA -s simRat_chr6.simRat.chr6 169940 7 + 647215 ATTTGCA - -a -s simMouse_chr6.simMouse.chr6 179711 27 + 636262 GTTTCTTTCCTGGAGGCCTGAAACCCT -s Anc0.Anc0refChr1 12460 27 + 62388 GTTTTTTTCTTGAAATCTTCAAACTCT -s Anc1.Anc1refChr2 13258 27 - 144309 GTTTTTTTCTTGAAATCTTCAAACTCT -s Anc2.Anc2refChr3 13644 27 - 53186 GTTTTTTTCTTGGAATCTGCAAACTCT -s mr.mrrefChr5 34968 27 + 294540 GTTTCTTTCCTGAAGGCCTGAAACCCT -s simCow_chr6.simCow.chr6 434619 27 - 602619 GTTTTTTTCTTGGAAGCTCCAAGTTCT -s simDog_chr6.simDog.chr6 142794 27 + 593897 GTTTCTTTCATGGAATCTGCAAACTCT -s simHuman_chr6.simHuman.chr6 435954 27 - 601863 GTTTTTTTCTTGATATCTTCAAACTCT -s simRat_chr6.simRat.chr6 169947 27 + 647215 GTTTCTTTCCTGAAGACCTGAAACCCC - -a -s simMouse_chr6.simMouse.chr6 179738 5 + 636262 AACTT -s Anc0.Anc0refChr1 12487 5 + 62388 AGTTT -s Anc1.Anc1refChr2 13285 5 - 144309 AGTTT -s Anc2.Anc2refChr3 13671 5 - 53186 AGTTT -s mr.mrrefChr5 34995 5 + 294540 AACTT -s simCow_chr6.simCow.chr6 434646 5 - 602619 AGTCT -s simDog_chr6.simDog.chr6 142864 5 + 593897 AGTTT -s simHuman_chr6.simHuman.chr6 435981 5 - 601863 AGTTT -s simRat_chr6.simRat.chr6 169974 5 + 647215 ATCTT - -a -s simMouse_chr6.simMouse.chr6 179743 18 + 636262 TCAGGCACACACTTAGAC -s Anc0.Anc0refChr1 12493 18 + 62388 TGTAGAGCACAATTAGAC -s Anc1.Anc1refChr2 13291 18 - 144309 TGTAGAGCACAATTAGAC -s Anc2.Anc2refChr3 13677 18 - 53186 TGTAGAGCACAACTAGGC -s mr.mrrefChr5 35001 18 + 294540 TCAGGCACACACTTAGAC -s simCow_chr6.simCow.chr6 434664 16 - 602619 TGTGGATCGCAAC--GGC -s simDog_chr6.simDog.chr6 142870 18 + 593897 TTTAGAGCACAACTAGGC -s simHuman_chr6.simHuman.chr6 435987 18 - 601863 TGTAGAGCACAGTTAGAC -s simRat_chr6.simRat.chr6 169980 18 + 647215 TCAGGCACACACTTAGAC - -a -s simMouse_chr6.simMouse.chr6 179761 3 + 636262 TGG -s Anc0.Anc0refChr1 12511 3 + 62388 CAG -s Anc1.Anc1refChr2 13309 3 - 144309 CAG -s Anc2.Anc2refChr3 13696 3 - 53186 CTG -s mr.mrrefChr5 35019 3 + 294540 CAG -s simCow_chr6.simCow.chr6 434681 3 - 602619 CTG -s simDog_chr6.simDog.chr6 142889 3 + 593897 TTG -s simHuman_chr6.simHuman.chr6 436005 3 - 601863 CAG -s simRat_chr6.simRat.chr6 169998 3 + 647215 CAG - -a -s simMouse_chr6.simMouse.chr6 179764 27 + 636262 CTGACTCTCCATGCACTATTCTGCTTA -s Anc0.Anc0refChr1 12514 25 + 62388 TTGACACTCCACTCACT--TCTGTTCA -s Anc1.Anc1refChr2 13312 25 - 144309 TTGACACTCCACTCACT--TCTGTTCA -s Anc2.Anc2refChr3 13699 25 - 53186 TTGACACTCCACTCACT--TCTGTTCT -s mr.mrrefChr5 35022 27 + 294540 CTGACTCTCCATGCACTATTCTGCTTA -s simCow_chr6.simCow.chr6 434684 25 - 602619 CTGACTCTCCACTCACT--TCTGTTCT -s simDog_chr6.simDog.chr6 142892 25 + 593897 TTGACACTTCAATCACT--TCCGTTCT -s simHuman_chr6.simHuman.chr6 436008 25 - 601863 GTGGACTTCCACTTACT--TCTGTTAA -s simRat_chr6.simRat.chr6 170002 27 + 647215 CTGACTCTCCATGCACTCTTCTGCTCA - -a -s simMouse_chr6.simMouse.chr6 179791 35 + 636262 CTTCTAGCTCAAAAAGCAGGGGCATTGTCATAAAC -s Anc0.Anc0refChr1 12539 35 + 62388 CTTCTAGCTGAGAAGGGTAGGGTAATGTCAAACAC -s Anc1.Anc1refChr2 13337 35 - 144309 CTTCTAGCTGAGAAGGGTAGGGTAATGTCAAACAC -s Anc2.Anc2refChr3 13724 35 - 53186 CTTCTAGCTGAGGAGGGTAGGGTAATGTCAAACAC -s mr.mrrefChr5 35049 35 + 294540 CTTCTAGCTCAAAAAGCAGGGGCATTGTCATAAAC -s simCow_chr6.simCow.chr6 434714 35 - 602619 CTTCTAGCTCAGGAGGTTACGGTAATGTCAAAAAC -s simDog_chr6.simDog.chr6 142917 35 + 593897 TGTCTAACTGAGGAGGGTAGGGTAATGTCAAACAC -s simHuman_chr6.simHuman.chr6 436033 35 - 601863 CTGCTAGCTGAGAATAGTAGGGTAATGTCAGACAC -s simRat_chr6.simRat.chr6 170029 35 + 647215 TGTTTAGCTCAATAAGCAGGGGCATTGTCAAAGAC - -a -s simMouse_chr6.simMouse.chr6 179826 19 + 636262 TGCTAGATCATTCAACTAG -s Anc0.Anc0refChr1 12576 15 + 62388 TGCC----CATGCACCTTG -s Anc1.Anc1refChr2 13374 15 - 144309 TGCC----CATGCACCTTG -s Anc2.Anc2refChr3 13761 15 - 53186 CCAC----CATGCACCTTG -s mr.mrrefChr5 35084 19 + 294540 TGCCAGATCATGCAACTAG -s simCow_chr6.simCow.chr6 434751 15 - 602619 CCAC----CATACACCTTG -s simDog_chr6.simDog.chr6 142954 15 + 593897 CCAC----CATGCACCATG -s simHuman_chr6.simHuman.chr6 436070 15 - 601863 TGCC----CATGCACCTTG -s simRat_chr6.simRat.chr6 170064 19 + 647215 TGCCAGATCATGCAACTAG - -a -s simMouse_chr6.simMouse.chr6 179845 4 + 636262 CCAG -s Anc0.Anc0refChr1 12594 4 + 62388 CCTG -s Anc1.Anc1refChr2 13392 4 - 144309 CCTG -s Anc2.Anc2refChr3 13779 4 - 53186 CCTC -s mr.mrrefChr5 35103 4 + 294540 CCAG -s simCow_chr6.simCow.chr6 434769 4 - 602619 CCTT -s simDog_chr6.simDog.chr6 142972 4 + 593897 CCTC -s simHuman_chr6.simHuman.chr6 436088 4 - 601863 CCTG -s simRat_chr6.simRat.chr6 170083 4 + 647215 CCAG - -a -s simMouse_chr6.simMouse.chr6 179849 13 + 636262 ACCCTACAATCAT -s Anc0.Anc0refChr1 12602 13 + 62388 ACACTACCATCCT -s Anc1.Anc1refChr2 13400 13 - 144309 ACACTACCATCCT -s Anc2.Anc2refChr3 13787 13 - 53186 ACACTACCACCCT -s mr.mrrefChr5 35107 13 + 294540 ACCCTACAATCAT -s simCow_chr6.simCow.chr6 434777 12 - 602619 ACACTACCACA-G -s simDog_chr6.simDog.chr6 142980 13 + 593897 ACAATACCACCCT -s simHuman_chr6.simHuman.chr6 436096 13 - 601863 ACACTCCCATCCT -s simRat_chr6.simRat.chr6 170087 13 + 647215 ACCCTACAATCAC - -a -s simMouse_chr6.simMouse.chr6 179862 116 + 636262 GGAACAAGGCTAGATCATGCAACTTGTTAAACCCTACAACCATGGAACAAGGCTAATCTTAGTGCCATTCTAATCTTGGATTAGGACGCTTTTACTTATCCATACTGGTATTGCTT -s Anc0.Anc0refChr1 12615 87 + 62388 GCACCA------------GCTATATG-----CACTACTACTC----ACAAGACT-------GGGCCATTCTAGT-TTGGATTAACATGCTTTTACTTATCCATACTGGTATCAGTT -s Anc1.Anc1refChr2 13413 95 - 144309 GCACCA------------GCTATATG-----CACTACTACTC----ACAAGACTCATCTTAGGGCCATTCTAGTCTTGGATTAACATGCTTTTACTTATCCATACTGGTATCAGTT -s Anc2.Anc2refChr3 13801 87 - 53186 GCACCA------------GTTATATG-----CACTACTACTC----ACAAGATT-------GGGACATCCTAGT-TTGGATTAACATGCTTTTACTCATCAATACTGGTATCAGTT -s mr.mrrefChr5 35120 116 + 294540 GGAACAAGGCTAGATCATGCAATTTGTTAAACCCTACAACCATGGAACAAGGCTAATCTTAGTGCCATTCTAATCTTGGATTAACATGCTTTTACTTATCCATACTGGTATTGCTT -s simCow_chr6.simCow.chr6 434790 87 - 602619 GCATCA------------GTTATATG-----CACTACTACTC----ACAAGATT-------GGGACATCCTAGT-TTGGATTAACAGACTTTTACTCATCAATACTGGTATCAGTC -s simDog_chr6.simDog.chr6 142994 24 + 593897 GCACC----------------------------------------------------------------------------TCACTTGCT----------------GGTACCTATT -s simHuman_chr6.simHuman.chr6 436109 95 - 601863 GCACCA------------GCTATCTG-----CACTACCACTT----ACAAAACTCATCTTAAGCCCATTCTAGTCTTGGATTAACATGCTTTAACTTATCCATACTGGTATCAGCT -s simRat_chr6.simRat.chr6 170100 96 + 647215 GGAACAAGGCTAGATCGTCCAATGTGTTAAACCCTACAACCATGGAATAAG--------------------AATCTTGGATTAACATACTTTTATTTATCCAAACTGGTATTGCTC - -a -s simMouse_chr6.simMouse.chr6 179978 25 + 636262 GGAATGATGATTACAGTTACTCACT -s Anc0.Anc0refChr1 12702 25 + 62388 AAAATGATGATTAAAGCTATTCCCT -s Anc1.Anc1refChr2 13508 25 - 144309 AAAATGATGATTAAAGCTATTCCCT -s Anc2.Anc2refChr3 13888 25 - 53186 AAAATGATGATTAAAGCTATTCCCT -s mr.mrrefChr5 35236 25 + 294540 AGAATGATGATTACAGTTACTCACT -s simCow_chr6.simCow.chr6 434877 25 - 602619 ATAACTATGATTAAAGCCATCCCCT -s simDog_chr6.simDog.chr6 143020 25 + 593897 AAAATGATGATTAGAGCTATTGCCT -s simHuman_chr6.simHuman.chr6 436204 25 - 601863 AAAATAATGATTAAAGCGATTCTCT -s simRat_chr6.simRat.chr6 170196 25 + 647215 AGAATGATGATTAGAGTTCCTCCCT - -a -s simMouse_chr6.simMouse.chr6 180003 5 + 636262 CTATC -s Anc0.Anc0refChr1 12728 5 + 62388 CTATC -s Anc1.Anc1refChr2 13534 5 - 144309 CTATC -s Anc2.Anc2refChr3 13914 5 - 53186 CTATC -s mr.mrrefChr5 35261 5 + 294540 CTATC -s simCow_chr6.simCow.chr6 434903 5 - 602619 CTATC -s simDog_chr6.simDog.chr6 143046 5 + 593897 CTATC -s simHuman_chr6.simHuman.chr6 436230 5 - 601863 CTATC -s simRat_chr6.simRat.chr6 170221 5 + 647215 TCATC - -a -s simMouse_chr6.simMouse.chr6 180008 61 + 636262 CACTGTTCCTGATCACTTTGTAGGAGAATTTGTGGGATTTAGACTATGTTATTTGCTTTGC -s Anc0.Anc0refChr1 12733 51 + 62388 CACTGTCATTGATTGCTTGGTATAAAAATTTGT----------CCATATGGTTCTCCTCTG -s Anc1.Anc1refChr2 13539 51 - 144309 CACTGTCATTGATTGCTTGGTATAAAAATTTGT----------CCATATGGTTCTCCTCTG -s Anc2.Anc2refChr3 13919 51 - 53186 CACTGTCATTGATTACCTGGTATAAAAATATGT----------CCATATGGTTCTCCTCTG -s mr.mrrefChr5 35266 61 + 294540 CACTGTCCTTGATCGCTTTGTAGGAGAATTTGTGGGATTTAGACTACATATTTTGCTTTTC -s simCow_chr6.simCow.chr6 434908 51 - 602619 CGCTATTCTTGATGATCTGGTATAAAAATATGT----------CCATATGGTTCTCCTGAG -s simDog_chr6.simDog.chr6 143051 51 + 593897 CACTGTCATCGATTACCTGGTATACAAATATGG----------ACCTATGGTTCTCCTCTC -s simHuman_chr6.simHuman.chr6 436235 51 - 601863 CACTCTCTTTGATTGCTTGGTATAAAAATTTGT----------CCATATGATTCTCCTCTG -s simRat_chr6.simRat.chr6 170228 60 + 647215 CACTGTCCTTGAAAGCTT-GTAGGAGAATCTATGTGTTTTAGACTACATATTTTGCTTTTC - -a -s simMouse_chr6.simMouse.chr6 180069 34 + 636262 CATGGTGAGTCACTCTCACCATGTAAAGCACATG -s Anc0.Anc0refChr1 12786 31 + 62388 CTTGGTGAACCACTCACAACAGGTAA-GCA--TA -s Anc1.Anc1refChr2 13592 31 - 144309 CTTGGTGAACCACTCACAACAGGTAA-GCA--TA -s Anc2.Anc2refChr3 13972 31 - 53186 CTTGGTGAACCACTCACAACAGGTAA-GCA--TA -s mr.mrrefChr5 35327 32 + 294540 CATGGTGAGTCACTCTCACCATGTAAAGCA--TG -s simCow_chr6.simCow.chr6 434961 31 - 602619 CTTGGTGAACTGCATGCACCAAGTAA-GTA--TA -s simDog_chr6.simDog.chr6 143104 31 + 593897 TGTAGTGAACCACTCACCACAGGTAA-GCA--TA -s simHuman_chr6.simHuman.chr6 436288 31 - 601863 CTGGGTGAACCACTCCCAAAAGGTAA-GCA--CT -s simRat_chr6.simRat.chr6 170288 18 + 647215 CATG--------------CCCTGTAAGGCA--TG - -a -s simMouse_chr6.simMouse.chr6 180103 2 + 636262 TT -s Anc0.Anc0refChr1 12817 2 + 62388 TC -s Anc1.Anc1refChr2 13623 2 - 144309 TC -s Anc1.Anc1refChr6 27456 2 + 197743 TC -s Anc2.Anc2refChr3 14003 2 - 53186 TC -s Anc2.Anc2refChr17 21306 2 + 28526 TC -s mr.mrrefChr5 35359 2 + 294540 TT -s mr.mrrefChr5 213056 2 + 294540 TC -s simCow_chr6.simCow.chr6 339443 2 + 602619 TC -s simCow_chr6.simCow.chr6 434992 2 - 602619 TC -s simDog_chr6.simDog.chr6 143135 2 + 593897 TG -s simHuman_chr6.simHuman.chr6 351186 2 + 601863 TT -s simHuman_chr6.simHuman.chr6 436319 2 - 601863 TC -s simMouse_chr6.simMouse.chr6 365977 2 + 636262 TC -s simRat_chr6.simRat.chr6 358435 2 + 647215 TC -s simRat_chr6.simRat.chr6 170306 2 + 647215 TT - -a -s simMouse_chr6.simMouse.chr6 180105 1 + 636262 T -s Anc0.Anc0refChr1 12819 1 + 62388 T -s Anc1.Anc1refChr2 13625 1 - 144309 T -s Anc1.Anc1refChr6 27458 1 + 197743 A -s Anc2.Anc2refChr3 14005 1 - 53186 T -s Anc2.Anc2refChr17 21308 1 + 28526 A -s mr.mrrefChr5 35361 1 + 294540 T -s simCow_chr6.simCow.chr6 339445 1 + 602619 A -s simCow_chr6.simCow.chr6 434994 1 - 602619 T -s simDog_chr6.simDog.chr6 329194 1 + 593897 A -s simDog_chr6.simDog.chr6 143137 1 + 593897 T -s simHuman_chr6.simHuman.chr6 351188 1 + 601863 A -s simHuman_chr6.simHuman.chr6 436321 1 - 601863 T -s simRat_chr6.simRat.chr6 170308 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 180106 1 + 636262 T -s Anc0.Anc0refChr1 12820 1 + 62388 T -s Anc1.Anc1refChr2 13626 1 - 144309 T -s Anc1.Anc1refChr6 27459 1 + 197743 T -s Anc2.Anc2refChr3 14006 1 - 53186 T -s Anc2.Anc2refChr17 21309 1 + 28526 T -s mr.mrrefChr5 35362 1 + 294540 T -s mr.mrrefChr5 213058 1 + 294540 T -s simCow_chr6.simCow.chr6 434995 1 - 602619 T -s simDog_chr6.simDog.chr6 329195 1 + 593897 T -s simDog_chr6.simDog.chr6 143138 1 + 593897 T -s simHuman_chr6.simHuman.chr6 351189 1 + 601863 T -s simHuman_chr6.simHuman.chr6 436322 1 - 601863 T -s simMouse_chr6.simMouse.chr6 365979 1 + 636262 T -s simRat_chr6.simRat.chr6 358437 1 + 647215 T -s simRat_chr6.simRat.chr6 170309 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 180107 2 + 636262 CT -s Anc0.Anc0refChr1 12821 2 + 62388 GT -s Anc1.Anc1refChr2 13627 2 - 144309 GT -s Anc1.Anc1refChr6 27460 2 + 197743 GT -s Anc2.Anc2refChr3 14007 2 - 53186 GT -s Anc2.Anc2refChr17 21310 2 + 28526 GC -s mr.mrrefChr5 35363 2 + 294540 CT -s mr.mrrefChr5 213059 2 + 294540 CT -s simCow_chr6.simCow.chr6 339446 2 + 602619 GC -s simCow_chr6.simCow.chr6 434996 2 - 602619 GT -s simDog_chr6.simDog.chr6 329196 2 + 593897 GC -s simDog_chr6.simDog.chr6 143139 2 + 593897 TT -s simHuman_chr6.simHuman.chr6 351190 2 + 601863 GT -s simHuman_chr6.simHuman.chr6 436323 2 - 601863 GT -s simMouse_chr6.simMouse.chr6 365980 2 + 636262 CT -s simRat_chr6.simRat.chr6 358438 2 + 647215 CT -s simRat_chr6.simRat.chr6 170310 2 + 647215 CT - -a -s simMouse_chr6.simMouse.chr6 180109 3 + 636262 TTG -s Anc0.Anc0refChr1 12823 3 + 62388 TTG -s Anc1.Anc1refChr2 13629 3 - 144309 TTG -s Anc1.Anc1refChr6 27462 3 + 197743 TTG -s Anc2.Anc2refChr3 14009 3 - 53186 TTG -s mr.mrrefChr5 35365 3 + 294540 TTG -s mr.mrrefChr5 213061 3 + 294540 TAA -s simCow_chr6.simCow.chr6 434998 3 - 602619 TAG -s simDog_chr6.simDog.chr6 143141 3 + 593897 TTG -s simHuman_chr6.simHuman.chr6 351192 3 + 601863 TTG -s simHuman_chr6.simHuman.chr6 436325 3 - 601863 TTG -s simMouse_chr6.simMouse.chr6 365982 3 + 636262 TAA -s simRat_chr6.simRat.chr6 358440 3 + 647215 TAA -s simRat_chr6.simRat.chr6 170312 3 + 647215 TTG - -a -s simMouse_chr6.simMouse.chr6 180112 1 + 636262 C -s Anc0.Anc0refChr1 12826 1 + 62388 C -s Anc1.Anc1refChr2 13632 1 - 144309 C -s Anc1.Anc1refChr6 27470 1 + 197743 C -s Anc2.Anc2refChr3 14012 1 - 53186 C -s mr.mrrefChr5 35368 1 + 294540 C -s mr.mrrefChr5 213069 1 + 294540 T -s simCow_chr6.simCow.chr6 435001 1 - 602619 C -s simDog_chr6.simDog.chr6 143144 1 + 593897 C -s simHuman_chr6.simHuman.chr6 351200 1 + 601863 C -s simHuman_chr6.simHuman.chr6 436328 1 - 601863 C -s simMouse_chr6.simMouse.chr6 365990 1 + 636262 T -s simRat_chr6.simRat.chr6 358448 1 + 647215 T -s simRat_chr6.simRat.chr6 170315 1 + 647215 C - -a -s simMouse_chr6.simMouse.chr6 180113 9 + 636262 ATGTATATG -s Anc0.Anc0refChr1 12827 9 + 62388 ATCTACATG -s Anc1.Anc1refChr2 13633 9 - 144309 ATCTACATG -s Anc1.Anc1refChr6 27471 9 + 197743 ATCTACATA -s Anc2.Anc2refChr3 14013 9 - 53186 ATCTACATG -s Anc2.Anc2refChr17 21312 9 + 28526 ATCTACATG -s mr.mrrefChr5 35369 9 + 294540 ATGTATATG -s mr.mrrefChr5 213070 9 + 294540 ATTTACATA -s simCow_chr6.simCow.chr6 339448 9 + 602619 ATCTACATG -s simCow_chr6.simCow.chr6 435002 9 - 602619 ATATACATG -s simDog_chr6.simDog.chr6 329198 9 + 593897 ATCCGCATG -s simDog_chr6.simDog.chr6 143145 9 + 593897 ATCTACATG -s simHuman_chr6.simHuman.chr6 351201 9 + 601863 ATCTACATA -s simHuman_chr6.simHuman.chr6 436329 9 - 601863 ATCTACATG -s simMouse_chr6.simMouse.chr6 365991 9 + 636262 ATTTACATA -s simRat_chr6.simRat.chr6 358449 9 + 647215 ATTTGTATA -s simRat_chr6.simRat.chr6 170316 9 + 647215 ATATATATG - -a -s simMouse_chr6.simMouse.chr6 180122 1 + 636262 T -s Anc0.Anc0refChr1 12840 1 + 62388 T -s Anc1.Anc1refChr2 13642 1 - 144309 T -s Anc1.Anc1refChr6 27484 1 + 197743 T -s Anc2.Anc2refChr3 14022 1 - 53186 T -s Anc2.Anc2refChr17 21325 1 + 28526 T -s mr.mrrefChr5 35378 1 + 294540 T -s mr.mrrefChr5 213083 1 + 294540 T -s simCow_chr6.simCow.chr6 339461 1 + 602619 T -s simCow_chr6.simCow.chr6 435011 1 - 602619 T -s simDog_chr6.simDog.chr6 329211 1 + 593897 T -s simDog_chr6.simDog.chr6 143154 1 + 593897 T -s simHuman_chr6.simHuman.chr6 351215 1 + 601863 T -s simHuman_chr6.simHuman.chr6 436338 1 - 601863 T -s simMouse_chr6.simMouse.chr6 366004 1 + 636262 T -s simRat_chr6.simRat.chr6 358462 1 + 647215 T -s simRat_chr6.simRat.chr6 170325 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 180123 5 + 636262 CTACA -s Anc0.Anc0refChr1 12841 5 + 62388 CTAAG -s Anc1.Anc1refChr2 13643 5 - 144309 CTACA -s Anc1.Anc1refChr6 27485 5 + 197743 CTAAG -s Anc2.Anc2refChr3 14023 5 - 53186 CTAAG -s Anc2.Anc2refChr17 21326 5 + 28526 CTAAG -s mr.mrrefChr5 35379 5 + 294540 CTACA -s mr.mrrefChr5 213084 5 + 294540 ATAAG -s simCow_chr6.simCow.chr6 339462 5 + 602619 CTAAG -s simCow_chr6.simCow.chr6 435012 2 - 602619 CT--- -s simDog_chr6.simDog.chr6 329212 5 + 593897 CTAAG -s simDog_chr6.simDog.chr6 143155 5 + 593897 CTAAG -s simHuman_chr6.simHuman.chr6 351216 5 + 601863 CTAAG -s simHuman_chr6.simHuman.chr6 436349 5 - 601863 CTACA -s simMouse_chr6.simMouse.chr6 366005 5 + 636262 ATAAG -s simRat_chr6.simRat.chr6 358463 5 + 647215 ATGAG -s simRat_chr6.simRat.chr6 170326 5 + 647215 CTAAA - -a -s simMouse_chr6.simMouse.chr6 180128 1 + 636262 C -s Anc0.Anc0refChr1 12846 1 + 62388 C -s Anc1.Anc1refChr2 13648 1 - 144309 C -s Anc1.Anc1refChr6 27490 1 + 197743 C -s Anc2.Anc2refChr3 14028 1 - 53186 C -s Anc2.Anc2refChr17 21331 1 + 28526 C -s mr.mrrefChr5 35384 1 + 294540 C -s mr.mrrefChr5 213089 1 + 294540 G -s simCow_chr6.simCow.chr6 339467 1 + 602619 C -s simCow_chr6.simCow.chr6 435014 1 - 602619 C -s simDog_chr6.simDog.chr6 329217 1 + 593897 C -s simDog_chr6.simDog.chr6 143160 1 + 593897 C -s simHuman_chr6.simHuman.chr6 436354 1 - 601863 T -s simMouse_chr6.simMouse.chr6 366010 1 + 636262 G -s simRat_chr6.simRat.chr6 358468 1 + 647215 T -s simRat_chr6.simRat.chr6 170331 1 + 647215 C - -a -s simMouse_chr6.simMouse.chr6 180129 2 + 636262 TC -s Anc0.Anc0refChr1 12849 2 + 62388 TG -s Anc1.Anc1refChr2 13649 2 - 144309 TG -s Anc1.Anc1refChr6 27493 2 + 197743 TG -s Anc2.Anc2refChr3 14031 2 - 53186 TG -s Anc2.Anc2refChr17 21334 2 + 28526 TG -s mr.mrrefChr5 35385 2 + 294540 TC -s mr.mrrefChr5 213092 2 + 294540 TG -s simCow_chr6.simCow.chr6 339470 2 + 602619 TG -s simCow_chr6.simCow.chr6 435017 2 - 602619 AG -s simDog_chr6.simDog.chr6 329220 2 + 593897 TG -s simDog_chr6.simDog.chr6 143163 2 + 593897 TG -s simHuman_chr6.simHuman.chr6 351222 2 + 601863 TC -s simHuman_chr6.simHuman.chr6 436355 2 - 601863 TT -s simMouse_chr6.simMouse.chr6 366013 2 + 636262 TG -s simRat_chr6.simRat.chr6 358471 2 + 647215 TG -s simRat_chr6.simRat.chr6 170332 2 + 647215 TC - -a -s simMouse_chr6.simMouse.chr6 180131 4 + 636262 TATC -s Anc0.Anc0refChr1 12851 2 + 62388 T--C -s Anc1.Anc1refChr2 13651 2 - 144309 T--T -s Anc1.Anc1refChr6 27496 2 + 197743 T--C -s Anc2.Anc2refChr3 14033 2 - 53186 T--T -s Anc2.Anc2refChr17 21336 2 + 28526 T--C -s mr.mrrefChr5 35387 2 + 294540 T--C -s mr.mrrefChr5 213095 2 + 294540 T--C -s simCow_chr6.simCow.chr6 339472 2 + 602619 T--T -s simCow_chr6.simCow.chr6 435020 2 - 602619 T--T -s simDog_chr6.simDog.chr6 329222 2 + 593897 T--C -s simDog_chr6.simDog.chr6 143165 2 + 593897 T--T -s simHuman_chr6.simHuman.chr6 351225 2 + 601863 T--C -s simHuman_chr6.simHuman.chr6 436357 2 - 601863 C--T -s simMouse_chr6.simMouse.chr6 366016 2 + 636262 T--C -s simRat_chr6.simRat.chr6 358474 2 + 647215 T--C -s simRat_chr6.simRat.chr6 170334 2 + 647215 T--C - -a -s simMouse_chr6.simMouse.chr6 180135 1 + 636262 T -s Anc0.Anc0refChr1 12853 1 + 62388 G -s Anc1.Anc1refChr2 13653 1 - 144309 G -s Anc1.Anc1refChr6 27498 1 + 197743 T -s Anc2.Anc2refChr3 14035 1 - 53186 G -s Anc2.Anc2refChr17 21338 1 + 28526 T -s mr.mrrefChr5 35389 1 + 294540 G -s simCow_chr6.simCow.chr6 339474 1 + 602619 T -s simCow_chr6.simCow.chr6 435022 1 - 602619 C -s simDog_chr6.simDog.chr6 329224 1 + 593897 T -s simDog_chr6.simDog.chr6 143167 1 + 593897 G -s simHuman_chr6.simHuman.chr6 351227 1 + 601863 T -s simHuman_chr6.simHuman.chr6 436359 1 - 601863 G -s simRat_chr6.simRat.chr6 170336 1 + 647215 G - -a -s simMouse_chr6.simMouse.chr6 180136 7 + 636262 GATCATC -s Anc0.Anc0refChr1 12854 7 + 62388 GTTCATT -s Anc1.Anc1refChr2 13654 7 - 144309 GTTCATC -s Anc1.Anc1refChr6 27499 7 + 197743 GTTTATT -s Anc2.Anc2refChr3 14036 7 - 53186 GTTCATC -s Anc2.Anc2refChr17 21339 7 + 28526 GTTCATT -s mr.mrrefChr5 35390 7 + 294540 GATCATC -s mr.mrrefChr5 213097 7 + 294540 ACTTGGT -s simCow_chr6.simCow.chr6 339475 7 + 602619 GTTCATA -s simCow_chr6.simCow.chr6 435023 7 - 602619 GTCTGTC -s simDog_chr6.simDog.chr6 329225 7 + 593897 GTTCATT -s simDog_chr6.simDog.chr6 143168 7 + 593897 GCTCATC -s simHuman_chr6.simHuman.chr6 351228 7 + 601863 GTTTATC -s simHuman_chr6.simHuman.chr6 436374 7 - 601863 CTTCATC -s simMouse_chr6.simMouse.chr6 366018 7 + 636262 ACTTGGT -s simRat_chr6.simRat.chr6 358476 7 + 647215 ACTAGGT -s simRat_chr6.simRat.chr6 170337 7 + 647215 GCTCACC - -a -s simMouse_chr6.simMouse.chr6 180143 17 + 636262 AAACACATATTTTGACT -s Anc0.Anc0refChr1 12861 17 + 62388 AAACATATATCTTGGTT -s Anc1.Anc1refChr2 13661 17 - 144309 AAACATATATCTTGGCT -s Anc1.Anc1refChr6 27506 17 + 197743 AAATATATATCTTGGTT -s Anc2.Anc2refChr3 14043 17 - 53186 AAACATATATCTTGGTT -s Anc2.Anc2refChr17 21346 17 + 28526 AAACATATATCTTGGTT -s mr.mrrefChr5 35397 17 + 294540 AAACACATATTTTGACT -s mr.mrrefChr5 213104 17 + 294540 AGATAGATATGTTAGTT -s simCow_chr6.simCow.chr6 339482 17 + 602619 AGACATATATCCTGGCT -s simCow_chr6.simCow.chr6 435030 17 - 602619 AAACATATGACTTGTTT -s simDog_chr6.simDog.chr6 329232 17 + 593897 AAACATATATCTTGGTT -s simDog_chr6.simDog.chr6 143175 17 + 593897 ACACCAATATCATAGTT -s simHuman_chr6.simHuman.chr6 351235 17 + 601863 ACCTCCATATTTTGGTT -s simHuman_chr6.simHuman.chr6 436381 17 - 601863 AAATATATATCTTGGCT -s simMouse_chr6.simMouse.chr6 366027 17 + 636262 AGATAGATATGTTAGTT -s simRat_chr6.simRat.chr6 358483 17 + 647215 AGATAGATACCTCAGTT -s simRat_chr6.simRat.chr6 170344 17 + 647215 AAACACATATTTTGATT - -a -s simMouse_chr6.simMouse.chr6 180160 1 + 636262 C -s Anc0.Anc0refChr1 12884 1 + 62388 A -s Anc1.Anc1refChr2 13684 1 - 144309 A -s Anc1.Anc1refChr6 27529 1 + 197743 A -s Anc2.Anc2refChr3 14066 1 - 53186 A -s Anc2.Anc2refChr17 21369 1 + 28526 A -s mr.mrrefChr5 35414 1 + 294540 C -s mr.mrrefChr5 213127 1 + 294540 A -s simCow_chr6.simCow.chr6 339505 1 + 602619 A -s simCow_chr6.simCow.chr6 435053 1 - 602619 A -s simDog_chr6.simDog.chr6 329255 1 + 593897 A -s simDog_chr6.simDog.chr6 143198 1 + 593897 A -s simHuman_chr6.simHuman.chr6 351257 1 + 601863 A -s simHuman_chr6.simHuman.chr6 436404 1 - 601863 T -s simMouse_chr6.simMouse.chr6 366050 1 + 636262 A -s simRat_chr6.simRat.chr6 358506 1 + 647215 A -s simRat_chr6.simRat.chr6 170361 1 + 647215 C - -a -s simMouse_chr6.simMouse.chr6 180161 2 + 636262 TA -s Anc0.Anc0refChr1 12885 2 + 62388 CA -s Anc1.Anc1refChr2 13685 2 - 144309 CA -s Anc1.Anc1refChr6 27530 2 + 197743 CA -s Anc2.Anc2refChr3 14067 2 - 53186 CA -s Anc2.Anc2refChr17 21370 2 + 28526 CA -s mr.mrrefChr5 35415 2 + 294540 TA -s mr.mrrefChr5 213128 2 + 294540 CA -s simCow_chr6.simCow.chr6 339506 2 + 602619 CA -s simCow_chr6.simCow.chr6 435054 2 - 602619 CA -s simDog_chr6.simDog.chr6 329256 2 + 593897 CA -s simDog_chr6.simDog.chr6 143199 2 + 593897 CT -s simHuman_chr6.simHuman.chr6 351258 2 + 601863 CA -s simHuman_chr6.simHuman.chr6 436405 2 - 601863 CA -s simMouse_chr6.simMouse.chr6 366051 2 + 636262 CA -s simRat_chr6.simRat.chr6 170362 2 + 647215 TA - -a -s simMouse_chr6.simMouse.chr6 180163 10 + 636262 CGCATACAAA -s Anc0.Anc0refChr1 12887 10 + 62388 GATATACAAA -s Anc1.Anc1refChr2 13687 10 - 144309 GATATACAAA -s Anc1.Anc1refChr6 27532 10 + 197743 GATATACAAA -s Anc2.Anc2refChr3 14069 10 - 53186 GATATACAAA -s Anc2.Anc2refChr17 21372 10 + 28526 GATATACTAA -s mr.mrrefChr5 35417 10 + 294540 CGTATACAAA -s mr.mrrefChr5 213130 10 + 294540 GTTATACAAA -s simCow_chr6.simCow.chr6 339508 10 + 602619 GATATACCAA -s simCow_chr6.simCow.chr6 435056 10 - 602619 GATACACAAA -s simDog_chr6.simDog.chr6 329258 10 + 593897 GATATATTAA -s simDog_chr6.simDog.chr6 143201 10 + 593897 TATATACAAC -s simHuman_chr6.simHuman.chr6 351260 10 + 601863 GATATACAAA -s simHuman_chr6.simHuman.chr6 436407 10 - 601863 GCTATACAGA -s simMouse_chr6.simMouse.chr6 366053 10 + 636262 GTTATACAAA -s simRat_chr6.simRat.chr6 358507 10 + 647215 GGTATACAAA -s simRat_chr6.simRat.chr6 170364 10 + 647215 TGTATACAAA - -a -s simMouse_chr6.simMouse.chr6 180173 18 + 636262 GAGAATTTGCAGAGTAAA -s Anc0.Anc0refChr1 12897 18 + 62388 GGGTAGTTAGGGGAGTAG -s Anc1.Anc1refChr2 13697 18 - 144309 GGGTATTTGGGGAAGTAG -s Anc1.Anc1refChr6 27542 18 + 197743 GAGTAGTTAGGGGAGTAG -s Anc2.Anc2refChr3 14079 17 - 53186 GGGTA-TTGGGGGAATAG -s Anc2.Anc2refChr17 21382 18 + 28526 GAGTAGTTAGGGGAGTAG -s mr.mrrefChr5 35427 18 + 294540 GAGAATTTGCAGAGTAAA -s mr.mrrefChr5 213140 18 + 294540 GAGTGGTTAAGGTAGCAG -s simCow_chr6.simCow.chr6 262896 18 - 602619 GATTAGTCAGGGGAATAG -s simCow_chr6.simCow.chr6 435066 16 - 602619 GGGT--TTGGGGGAATAG -s simDog_chr6.simDog.chr6 329268 18 + 593897 GAGTAGTTAGGGGAGTAG -s simDog_chr6.simDog.chr6 143211 5 + 593897 GGGTA------------- -s simHuman_chr6.simHuman.chr6 351270 18 + 601863 GAGTAGTTGGGGCAGGAG -s simHuman_chr6.simHuman.chr6 436417 18 - 601863 GGGTAGTTGAGGGAGCAG -s simMouse_chr6.simMouse.chr6 366063 18 + 636262 GAGTGGTTAAGGTAACAG -s simRat_chr6.simRat.chr6 358517 18 + 647215 GAGTGAGTAAGATGGCAG -s simRat_chr6.simRat.chr6 170374 18 + 647215 GAGAATTTGCAGAGTAGA - -a -s simMouse_chr6.simMouse.chr6 180191 2 + 636262 AA -s Anc0.Anc0refChr1 12916 2 + 62388 AA -s Anc1.Anc1refChr2 13715 2 - 144309 AA -s Anc1.Anc1refChr6 27561 2 + 197743 AA -s Anc2.Anc2refChr3 14096 2 - 53186 AA -s Anc2.Anc2refChr17 21401 2 + 28526 AA -s mr.mrrefChr5 35445 2 + 294540 AA -s mr.mrrefChr5 213159 2 + 294540 AA -s simCow_chr6.simCow.chr6 262915 2 - 602619 AA -s simCow_chr6.simCow.chr6 435082 2 - 602619 AA -s simDog_chr6.simDog.chr6 329287 2 + 593897 AA -s simHuman_chr6.simHuman.chr6 351289 2 + 601863 AA -s simHuman_chr6.simHuman.chr6 436435 2 - 601863 AA -s simMouse_chr6.simMouse.chr6 366082 2 + 636262 AA -s simRat_chr6.simRat.chr6 358536 2 + 647215 AA -s simRat_chr6.simRat.chr6 170392 2 + 647215 AA - -a -s simMouse_chr6.simMouse.chr6 180193 3 + 636262 TCT -s Anc0.Anc0refChr1 12918 3 + 62388 TCT -s Anc1.Anc1refChr2 13717 3 - 144309 TCT -s Anc1.Anc1refChr6 27563 3 + 197743 TCT -s Anc2.Anc2refChr3 14098 3 - 53186 TCT -s Anc2.Anc2refChr17 21403 3 + 28526 TCT -s mr.mrrefChr5 35447 3 + 294540 TCT -s mr.mrrefChr5 213161 3 + 294540 CCT -s simCow_chr6.simCow.chr6 262917 3 - 602619 TCT -s simCow_chr6.simCow.chr6 435085 3 - 602619 TCT -s simDog_chr6.simDog.chr6 329289 3 + 593897 TCT -s simHuman_chr6.simHuman.chr6 351291 3 + 601863 TCT -s simHuman_chr6.simHuman.chr6 436437 3 - 601863 TCT -s simMouse_chr6.simMouse.chr6 366084 3 + 636262 CCT -s simRat_chr6.simRat.chr6 358538 3 + 647215 CCT -s simRat_chr6.simRat.chr6 170394 3 + 647215 TCT - -a -s simMouse_chr6.simMouse.chr6 180196 5 + 636262 ATAAA -s Anc0.Anc0refChr1 12921 5 + 62388 CTGAA -s Anc1.Anc1refChr2 13720 5 - 144309 CTCAA -s Anc1.Anc1refChr6 27566 5 + 197743 CTAAA -s Anc2.Anc2refChr3 14101 5 - 53186 CTGAA -s Anc2.Anc2refChr17 21412 5 + 28526 ATGAA -s mr.mrrefChr5 35450 5 + 294540 CTCAA -s mr.mrrefChr5 213164 5 + 294540 CCAAC -s simCow_chr6.simCow.chr6 262926 5 - 602619 ATCAA -s simCow_chr6.simCow.chr6 435088 5 - 602619 CTAAA -s simDog_chr6.simDog.chr6 329298 5 + 593897 ATGAA -s simDog_chr6.simDog.chr6 143216 4 + 593897 -TGAC -s simHuman_chr6.simHuman.chr6 351294 5 + 601863 CTAAA -s simHuman_chr6.simHuman.chr6 436440 5 - 601863 CTCAA -s simMouse_chr6.simMouse.chr6 366087 5 + 636262 CCAAC -s simRat_chr6.simRat.chr6 358541 5 + 647215 CCAAT -s simRat_chr6.simRat.chr6 170397 5 + 647215 CTCAA - -a -s simMouse_chr6.simMouse.chr6 180201 4 + 636262 CATG -s Anc0.Anc0refChr1 12926 4 + 62388 CATG -s Anc1.Anc1refChr2 13725 4 - 144309 CATG -s Anc1.Anc1refChr6 27571 4 + 197743 CATG -s Anc2.Anc2refChr3 14106 4 - 53186 CATG -s Anc2.Anc2refChr17 21417 4 + 28526 CATG -s mr.mrrefChr5 35455 4 + 294540 CATG -s mr.mrrefChr5 213169 4 + 294540 CATG -s simCow_chr6.simCow.chr6 262950 4 - 602619 CATG -s simCow_chr6.simCow.chr6 435093 4 - 602619 CATT -s simDog_chr6.simDog.chr6 329303 4 + 593897 CATG -s simDog_chr6.simDog.chr6 143220 4 + 593897 CATG -s simHuman_chr6.simHuman.chr6 351299 4 + 601863 TCTG -s simHuman_chr6.simHuman.chr6 436445 4 - 601863 CATG -s simMouse_chr6.simMouse.chr6 366092 4 + 636262 CATG -s simRat_chr6.simRat.chr6 358546 4 + 647215 CATG -s simRat_chr6.simRat.chr6 170402 4 + 647215 CATG - -a -s simMouse_chr6.simMouse.chr6 180205 15 + 636262 AAAGTGGAGCTCCCA -s Anc0.Anc0refChr1 12930 15 + 62388 AAAGCAGAGCTCTCA -s Anc1.Anc1refChr2 13729 15 - 144309 AAAGCAGAGCTCTCA -s Anc1.Anc1refChr6 27575 15 + 197743 AAAGCAGAGCTCTCA -s Anc2.Anc2refChr3 14110 15 - 53186 AAAGCAGAGCTCTCA -s Anc2.Anc2refChr17 21421 15 + 28526 AAAGCAGAGGTCTCA -s mr.mrrefChr5 35459 15 + 294540 AAAGTGGAGCTCCCA -s mr.mrrefChr5 213173 15 + 294540 AAAGCAGTGCTTTCA -s simCow_chr6.simCow.chr6 262954 15 - 602619 GCAGAAGAGCTCTCC -s simCow_chr6.simCow.chr6 435105 15 - 602619 GAAGGGGAGCTCTTA -s simDog_chr6.simDog.chr6 329307 15 + 593897 AAAGCAGAGGTCTCA -s simDog_chr6.simDog.chr6 143224 15 + 593897 AAAGCAGAGCTCTCA -s simHuman_chr6.simHuman.chr6 351303 15 + 601863 AAAGCAGATCTCTCA -s simHuman_chr6.simHuman.chr6 436449 15 - 601863 ACAGCAGTGCTCTCA -s simMouse_chr6.simMouse.chr6 366096 15 + 636262 AAAGCAGTGCTTTCA -s simRat_chr6.simRat.chr6 358550 15 + 647215 AAAGCAGCGCTTTCC -s simRat_chr6.simRat.chr6 170406 15 + 647215 AAAGTGGAGCTCCCA - -a -s simMouse_chr6.simMouse.chr6 180220 1 + 636262 T -s Anc0.Anc0refChr1 12945 1 + 62388 T -s Anc1.Anc1refChr2 13744 1 - 144309 T -s Anc1.Anc1refChr6 27590 1 + 197743 T -s Anc2.Anc2refChr3 14125 1 - 53186 T -s Anc2.Anc2refChr17 21436 1 + 28526 T -s mr.mrrefChr5 35474 1 + 294540 T -s simCow_chr6.simCow.chr6 262969 1 - 602619 T -s simCow_chr6.simCow.chr6 435120 1 - 602619 T -s simDog_chr6.simDog.chr6 329322 1 + 593897 T -s simDog_chr6.simDog.chr6 143239 1 + 593897 C -s simHuman_chr6.simHuman.chr6 351318 1 + 601863 T -s simHuman_chr6.simHuman.chr6 436464 1 - 601863 T -s simRat_chr6.simRat.chr6 170421 1 + 647215 C - -a -s simMouse_chr6.simMouse.chr6 180221 7 + 636262 GTTGTGC -s Anc0.Anc0refChr1 12946 7 + 62388 GCTGTGC -s Anc1.Anc1refChr2 13745 7 - 144309 GCTGGGC -s Anc1.Anc1refChr6 27591 7 + 197743 GCTGTGT -s Anc2.Anc2refChr3 14126 7 - 53186 GCTGGGC -s Anc2.Anc2refChr17 21437 7 + 28526 GCTGTGT -s mr.mrrefChr5 35475 7 + 294540 GTTGTGC -s mr.mrrefChr5 213188 7 + 294540 GATGTGT -s simCow_chr6.simCow.chr6 262970 7 - 602619 GCTGTGT -s simCow_chr6.simCow.chr6 435121 7 - 602619 GTAAGGT -s simDog_chr6.simDog.chr6 329323 7 + 593897 GCTGTGT -s simDog_chr6.simDog.chr6 143240 7 + 593897 GCTGGGC -s simHuman_chr6.simHuman.chr6 351319 7 + 601863 GCTGTGT -s simHuman_chr6.simHuman.chr6 436465 7 - 601863 ACTGGGC -s simMouse_chr6.simMouse.chr6 366111 7 + 636262 GATGTGT -s simRat_chr6.simRat.chr6 358565 7 + 647215 AGTCTGT -s simRat_chr6.simRat.chr6 170422 7 + 647215 GTTGTGT - -a -s simMouse_chr6.simMouse.chr6 180228 6 + 636262 GTGGTG -s Anc0.Anc0refChr1 12954 6 + 62388 ATGGTG -s Anc1.Anc1refChr2 13753 6 - 144309 ATGGTG -s Anc1.Anc1refChr6 27599 6 + 197743 ATGGTG -s Anc2.Anc2refChr3 14134 6 - 53186 ATGGTG -s Anc2.Anc2refChr17 21445 6 + 28526 ATGGTG -s mr.mrrefChr5 35482 6 + 294540 GTGGTG -s mr.mrrefChr5 213196 6 + 294540 ATGGCT -s simCow_chr6.simCow.chr6 262978 6 - 602619 ATGGTT -s simCow_chr6.simCow.chr6 435129 6 - 602619 ATTGTG -s simDog_chr6.simDog.chr6 329331 6 + 593897 ATGGTG -s simDog_chr6.simDog.chr6 143248 6 + 593897 GCGGTG -s simHuman_chr6.simHuman.chr6 351327 6 + 601863 ATGGTG -s simHuman_chr6.simHuman.chr6 436473 6 - 601863 ATAGTG -s simMouse_chr6.simMouse.chr6 366119 6 + 636262 AGGGCT -s simRat_chr6.simRat.chr6 358573 6 + 647215 ATGGCC -s simRat_chr6.simRat.chr6 170429 6 + 647215 GTGGTG - -a -s simMouse_chr6.simMouse.chr6 180234 4 + 636262 CACT -s Anc0.Anc0refChr1 12962 4 + 62388 AACT -s Anc1.Anc1refChr2 13759 4 - 144309 CACT -s Anc1.Anc1refChr6 27607 4 + 197743 AACG -s Anc2.Anc2refChr3 14140 4 - 53186 CACT -s Anc2.Anc2refChr17 21453 4 + 28526 AACC -s mr.mrrefChr5 35488 4 + 294540 CACT -s mr.mrrefChr5 213204 4 + 294540 GAGG -s simCow_chr6.simCow.chr6 262986 4 - 602619 AATG -s simCow_chr6.simCow.chr6 435135 4 - 602619 CACA -s simDog_chr6.simDog.chr6 329339 4 + 593897 AACC -s simDog_chr6.simDog.chr6 143254 4 + 593897 CACT -s simHuman_chr6.simHuman.chr6 351335 4 + 601863 AACG -s simHuman_chr6.simHuman.chr6 436479 4 - 601863 TACT -s simMouse_chr6.simMouse.chr6 366127 4 + 636262 GAGG -s simRat_chr6.simRat.chr6 358581 4 + 647215 GAGG -s simRat_chr6.simRat.chr6 170435 4 + 647215 CACT - -a -s simMouse_chr6.simMouse.chr6 180238 3 + 636262 GTG -s Anc0.Anc0refChr1 12966 3 + 62388 ATG -s Anc1.Anc1refChr2 13763 3 - 144309 ATG -s Anc1.Anc1refChr6 27611 3 + 197743 ATC -s Anc2.Anc2refChr3 14144 3 - 53186 ATG -s Anc2.Anc2refChr17 21457 3 + 28526 ATG -s mr.mrrefChr5 35492 3 + 294540 GTG -s mr.mrrefChr5 213208 3 + 294540 ACC -s simCow_chr6.simCow.chr6 262990 3 - 602619 AGG -s simCow_chr6.simCow.chr6 435139 3 - 602619 ATC -s simDog_chr6.simDog.chr6 329343 3 + 593897 ATG -s simDog_chr6.simDog.chr6 143258 3 + 593897 ATG -s simHuman_chr6.simHuman.chr6 351348 3 + 601863 ATC -s simHuman_chr6.simHuman.chr6 436483 3 - 601863 ATG -s simMouse_chr6.simMouse.chr6 366131 3 + 636262 ACC -s simRat_chr6.simRat.chr6 358585 3 + 647215 ACC -s simRat_chr6.simRat.chr6 170439 3 + 647215 GTG - -a -s simMouse_chr6.simMouse.chr6 180241 3 + 636262 CAT -s Anc0.Anc0refChr1 12969 3 + 62388 AAT -s Anc1.Anc1refChr2 13766 3 - 144309 CAT -s Anc1.Anc1refChr6 27614 3 + 197743 AGT -s Anc2.Anc2refChr3 14147 3 - 53186 AAT -s Anc2.Anc2refChr17 21460 3 + 28526 AGT -s mr.mrrefChr5 35495 3 + 294540 CAT -s mr.mrrefChr5 213211 3 + 294540 ACC -s simCow_chr6.simCow.chr6 262993 3 - 602619 AGT -s simCow_chr6.simCow.chr6 435142 3 - 602619 AAT -s simDog_chr6.simDog.chr6 329346 3 + 593897 AGT -s simDog_chr6.simDog.chr6 143261 3 + 593897 AGT -s simHuman_chr6.simHuman.chr6 351351 3 + 601863 AGT -s simHuman_chr6.simHuman.chr6 436489 3 - 601863 CAT -s simMouse_chr6.simMouse.chr6 366134 3 + 636262 ACC -s simRat_chr6.simRat.chr6 358588 3 + 647215 ACC -s simRat_chr6.simRat.chr6 170442 3 + 647215 CAT - -a -s simMouse_chr6.simMouse.chr6 180244 19 + 636262 GGGCACAATGAACAGCTGC -s Anc0.Anc0refChr1 12972 5 + 62388 GGG--------------GG -s Anc1.Anc1refChr2 13769 19 - 144309 GGGCCTTATGAACGGGCGG -s Anc2.Anc2refChr3 14150 5 - 53186 GGG--------------GG -s mr.mrrefChr5 35498 19 + 294540 GGGCACAATGAACAGCTGC -s simCow_chr6.simCow.chr6 435145 5 - 602619 GGG--------------TG -s simDog_chr6.simDog.chr6 143264 5 + 593897 GGG--------------GG -s simHuman_chr6.simHuman.chr6 436492 19 - 601863 GCGCCTTATGAACGGGCAT -s simRat_chr6.simRat.chr6 170445 18 + 647215 GGACACGATGAACAGCAG- - -a -s simMouse_chr6.simMouse.chr6 180263 8 + 636262 AGCGTAGT -s Anc0.Anc0refChr1 12977 8 + 62388 ACAACTAG -s Anc1.Anc1refChr2 13788 8 - 144309 AAAGTTAT -s Anc1.Anc1refChr6 27617 8 + 197743 CCACCTAG -s Anc2.Anc2refChr3 14155 8 - 53186 AAAACTAA -s Anc2.Anc2refChr17 21463 8 + 28526 CCTACTAG -s mr.mrrefChr5 35517 8 + 294540 AGCGTAGT -s mr.mrrefChr5 213214 8 + 294540 CAACCTAA -s simCow_chr6.simCow.chr6 262996 8 - 602619 CCCACTGG -s simCow_chr6.simCow.chr6 435150 2 - 602619 AA------ -s simDog_chr6.simDog.chr6 329349 8 + 593897 CCTACTAG -s simDog_chr6.simDog.chr6 143269 8 + 593897 AAAACTAA -s simHuman_chr6.simHuman.chr6 351354 8 + 601863 CCACCTAT -s simHuman_chr6.simHuman.chr6 436511 8 - 601863 AAAGTTAT -s simMouse_chr6.simMouse.chr6 366137 8 + 636262 CAACCTAA -s simRat_chr6.simRat.chr6 358591 8 + 647215 CAACCCTA - -a -s simMouse_chr6.simMouse.chr6 180271 4 + 636262 ATCC -s Anc1.Anc1refChr2 13796 4 - 144309 TTCC -s mr.mrrefChr5 35525 4 + 294540 ATCC -s simHuman_chr6.simHuman.chr6 436519 4 - 601863 TTCC - -a -s simMouse_chr6.simMouse.chr6 180275 4 + 636262 CTCT -s Anc0.Anc0refChr1 12985 4 + 62388 CTCT -s Anc1.Anc1refChr2 13800 4 - 144309 CTCT -s Anc1.Anc1refChr6 27625 4 + 197743 CACT -s Anc2.Anc2refChr3 14163 4 - 53186 CTCT -s Anc2.Anc2refChr17 21471 4 + 28526 CAGT -s mr.mrrefChr5 35529 4 + 294540 CTCT -s mr.mrrefChr5 213222 4 + 294540 CTCC -s simCow_chr6.simCow.chr6 263004 4 - 602619 CACT -s simCow_chr6.simCow.chr6 435152 4 - 602619 TTCT -s simDog_chr6.simDog.chr6 329357 4 + 593897 CAGT -s simDog_chr6.simDog.chr6 143277 4 + 593897 CTCT -s simHuman_chr6.simHuman.chr6 351362 4 + 601863 CACT -s simHuman_chr6.simHuman.chr6 436523 4 - 601863 CTTT -s simMouse_chr6.simMouse.chr6 366145 4 + 636262 CTCC -s simRat_chr6.simRat.chr6 358599 4 + 647215 TTCA - -a -s simMouse_chr6.simMouse.chr6 180279 13 + 636262 GACTGTTCACGCC -s Anc0.Anc0refChr1 12989 13 + 62388 AACTGATTAGGAC -s Anc1.Anc1refChr2 13804 13 - 144309 AACTGATTAGGAC -s Anc2.Anc2refChr3 14167 13 - 53186 AACTGATTAGGAC -s mr.mrrefChr5 35533 13 + 294540 GACTGTTTACGAC -s simCow_chr6.simCow.chr6 435156 13 - 602619 GACTGACTAGGAC -s simDog_chr6.simDog.chr6 143281 13 + 593897 AAGTGATTGGAAC -s simHuman_chr6.simHuman.chr6 436527 13 - 601863 AACTGGTTAGGAC -s simRat_chr6.simRat.chr6 170463 8 + 647215 -----TTTATGAC - -a -s simMouse_chr6.simMouse.chr6 180292 3 + 636262 TAC -s Anc0.Anc0refChr1 13006 3 + 62388 TAC -s Anc1.Anc1refChr2 13821 3 - 144309 TAC -s Anc2.Anc2refChr3 14184 3 - 53186 TGC -s mr.mrrefChr5 35546 3 + 294540 TAC -s simCow_chr6.simCow.chr6 435173 2 - 602619 TC- -s simDog_chr6.simDog.chr6 143298 3 + 593897 TGC -s simHuman_chr6.simHuman.chr6 436544 3 - 601863 TAC -s simRat_chr6.simRat.chr6 170471 3 + 647215 TAC - -a -s simMouse_chr6.simMouse.chr6 180295 34 + 636262 AATGGCACATGCTTTGTTTCTAGCTACAAACAAC -s Anc0.Anc0refChr1 13009 34 + 62388 AATGGCACATGTTGTGTTTCTACCTACAAACAAC -s Anc1.Anc1refChr2 13824 34 - 144309 AATGGCACATGTTGTGTTTCTACCTACAAACAAC -s Anc2.Anc2refChr3 14188 34 - 53186 AACAGCACATGTTGTGTTTCTACCTACAAACAAC -s mr.mrrefChr5 35549 34 + 294540 AATGGCACATGCTTTGTTTCTACCTACAAACAAC -s simCow_chr6.simCow.chr6 435175 34 - 602619 AACAGCACATGTGTTGTTTCCACCTACTCAGAAT -s simDog_chr6.simDog.chr6 143302 34 + 593897 AACAGCACATGTTGTGTTTCTACCCACAAACAAC -s simHuman_chr6.simHuman.chr6 436547 34 - 601863 AATGGCACATGTTGTGTTTCTACCTACCAACAAC -s simRat_chr6.simRat.chr6 170474 34 + 647215 AATGGGACATACTTTGATTCTACCTACGAGCAAC - -a -s simMouse_chr6.simMouse.chr6 180329 19 + 636262 ATACAGAAAGTGCACAGTC -s Anc0.Anc0refChr1 13044 19 + 62388 ATATAGCAAATGCATAGTC -s Anc1.Anc1refChr2 13859 19 - 144309 ATATAGCAAATGCATAGTC -s Anc2.Anc2refChr3 14223 19 - 53186 ATATAGCAAATGAATAGTC -s mr.mrrefChr5 35584 19 + 294540 ATACAGCAAGTGCACAGTC -s simCow_chr6.simCow.chr6 435210 19 - 602619 ATATAGCAAATGAGTAGTC -s simDog_chr6.simDog.chr6 143337 19 + 593897 ATATAGCGAATGAATAGTC -s simHuman_chr6.simHuman.chr6 436582 19 - 601863 GCATAGCAAATGCTTCCTC -s simRat_chr6.simRat.chr6 170509 18 + 647215 ATACAGCA-GAGCACAGTC - -a -s simMouse_chr6.simMouse.chr6 180348 54 + 636262 CATTTTTAGAAAGTCAAAATGGCAAAATAGGGTAGGTCTCTAAATGCTCTGCCA -s Anc0.Anc0refChr1 13063 52 + 62388 C--CTTCGAAAAGTCTAGACTGCAAGATAGGGTAGGTCCCTAAATGATATGCCT -s Anc1.Anc1refChr2 13878 53 - 144309 CG-CTTCGAAAAGTCTAGACTGCAAGATAGGGTAGGTCCCTAAATGATATGCCT -s Anc2.Anc2refChr3 14242 52 - 53186 C--CTTCGAAAAGTCTAGACTGTAAGATAGGGTAGGTCCCTAAATGATATGCTT -s mr.mrrefChr5 35603 54 + 294540 CATCTTTAGAAAGTCAAAACTGCAAAATAGGGTAGGTCTCTAAATGCTCTGCCA -s simCow_chr6.simCow.chr6 435229 46 - 602619 -------AAACATTCAATATTGTAAAAT-GTGTAGGTCCCTAAATGTTATGCTT -s simDog_chr6.simDog.chr6 143358 52 + 593897 C--CTTCGACAGGTCTAGACTGTAAGATAAGGTAGGTCCATGAATGATATGCTA -s simHuman_chr6.simHuman.chr6 436601 47 - 601863 CG------AAAAGTTGA-GCTACGATGTAGGGCACATCCCTAAATGACATGCCT -s simRat_chr6.simRat.chr6 170527 54 + 647215 CATCTTTAGAAGGTCAAAACTGCAAACTGGGGTGGTTCTATACATGGTCTGCTA - -a -s simMouse_chr6.simMouse.chr6 180402 9 + 636262 TGTTGAATT -s Anc0.Anc0refChr1 13115 9 + 62388 TTTGTAATT -s Anc1.Anc1refChr2 13931 9 - 144309 TTTGTAATT -s Anc2.Anc2refChr3 14294 9 - 53186 TTTGTAATT -s mr.mrrefChr5 35657 9 + 294540 TGTTGAATT -s simCow_chr6.simCow.chr6 435275 9 - 602619 TCTGTAATT -s simDog_chr6.simDog.chr6 143410 9 + 593897 TTCGTAATT -s simHuman_chr6.simHuman.chr6 436648 9 - 601863 TATGTAATT -s simRat_chr6.simRat.chr6 170642 9 + 647215 TGTTGAGTT - -a -s simMouse_chr6.simMouse.chr6 180411 44 + 636262 GCTACTATATGCAATTATCAATTGCTTCAACAAAGGCGCAGCAT -s Anc0.Anc0refChr1 13183 44 + 62388 GTTACCTTATGCTCCTATCAGTTGCTTCAATAGAGGGATAGTAT -s Anc1.Anc1refChr2 13999 44 - 144309 GTTACCTTATGCTCCTATCAGTTGCTTCAATAGAGGGATAGTAT -s Anc2.Anc2refChr3 14375 44 - 53186 GTTACCTTATGCTCCTATCAGTTGCTGCAATAGAGCGATAGTAT -s mr.mrrefChr5 35666 44 + 294540 GCTACTATATGCAATTATCAATTGCTTCAACAAAGGCGTAGCAT -s simCow_chr6.simCow.chr6 435356 44 - 602619 GTTATATTCTGCTCCTATCAGTTGCTGCAACAGAGCAATAGTAT -s simDog_chr6.simDog.chr6 143492 37 + 593897 GTTACTTTATGCTCCTA------GCTGCAAT-GAGCGATAGTAT -s simHuman_chr6.simHuman.chr6 446289 44 - 601863 CTTATGTTCTGTTCCTATCAGTTGCTTCAATAGCGGGATAGTGT -s simRat_chr6.simRat.chr6 170651 44 + 647215 GCTACTTTATGCAATTATCAATTGCTTCAATAAAGGTGTAGCAT - -a -s simMouse_chr6.simMouse.chr6 180455 7 + 636262 GTCCCCG -s Anc0.Anc0refChr1 13230 7 + 62388 GTGCCTG -s Anc1.Anc1refChr2 14046 7 - 144309 GTGCCTG -s Anc2.Anc2refChr3 14422 7 - 53186 GTGTCTT -s mr.mrrefChr5 35710 7 + 294540 GTCCCCG -s simCow_chr6.simCow.chr6 435403 7 - 602619 GTGTCTT -s simDog_chr6.simDog.chr6 143532 7 + 593897 GTGTCTT -s simHuman_chr6.simHuman.chr6 446336 7 - 601863 GTGCCTG -s simRat_chr6.simRat.chr6 170695 7 + 647215 GTCCTCA - -a -s simMouse_chr6.simMouse.chr6 180462 17 + 636262 GCCTCTGTTTAAAGTCC -s Anc0.Anc0refChr1 13239 17 + 62388 GCCTGGTACCAAAGTCC -s Anc1.Anc1refChr2 14055 17 - 144309 GCCTGGTACCAAAGTCC -s Anc2.Anc2refChr3 14431 17 - 53186 CCCTGGTACCAAAGTCC -s mr.mrrefChr5 35717 17 + 294540 GCCTCTGTTTAAAGTCC -s simCow_chr6.simCow.chr6 435412 17 - 602619 TCCTGGTACCAAAACAC -s simDog_chr6.simDog.chr6 143541 17 + 593897 CCCTGGTACCCAAGTCC -s simHuman_chr6.simHuman.chr6 446345 17 - 601863 GCTTGGCACCAGAGTCC -s simRat_chr6.simRat.chr6 170702 17 + 647215 GCCTCATTATAAAGTCC - -a -s simMouse_chr6.simMouse.chr6 180479 1 + 636262 T -s Anc0.Anc0refChr1 13257 1 + 62388 T -s Anc1.Anc1refChr2 14073 1 - 144309 T -s Anc2.Anc2refChr3 14449 1 - 53186 T -s mr.mrrefChr5 35734 1 + 294540 T -s simCow_chr6.simCow.chr6 435429 1 - 602619 T -s simDog_chr6.simDog.chr6 143559 1 + 593897 C -s simHuman_chr6.simHuman.chr6 446363 1 - 601863 T -s simRat_chr6.simRat.chr6 170719 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 180480 47 + 636262 AGTTGCTTAGAAAAGCACTAGAGTGTGCAAGTAACAGGTGAAATGGG -s Anc0.Anc0refChr1 13258 47 + 62388 GGTTGTTTAGAAAGGCAGTGCAGTGTACAGTTAAGAGCAGAAATGTG -s Anc1.Anc1refChr2 14074 47 - 144309 GGTTGTTTAGAAAGGCAGTGCAGTGTACAGTTAAGAGCAGAAATGTG -s Anc2.Anc2refChr3 14450 47 - 53186 GGTTGTTTAGAAAGGCAGTGCAGTGGACAGTTAAGAGCAGAAATATG -s mr.mrrefChr5 35735 47 + 294540 AGTTGCTTAGAAAAGCACTAGAGTGTGCAAGTAACAGGTGAAATGGG -s simCow_chr6.simCow.chr6 435430 43 - 602619 GGTTGCTTAGAAAGGTAGTGCAGTGGACAGCTAAGAACACAGA---- -s simDog_chr6.simDog.chr6 143577 47 + 593897 GGTTGTATAGAAAAGCAGTGTGGTGGACAGTTAATAGCAGAAATATG -s simHuman_chr6.simHuman.chr6 446364 47 - 601863 GGTTGTTTAGAAAGGACGTGCAGTGTACAGTTAAGAGTAGAAATGAG -s simRat_chr6.simRat.chr6 170720 47 + 647215 AGTTGCTTGGGAAAGCACTAGAGCATGCAAGTAAAAGGTGTAATAGG - -a -s simMouse_chr6.simMouse.chr6 180527 12 + 636262 CAGATTCAACAC -s Anc0.Anc0refChr1 13312 12 + 62388 CATATTCAACAC -s Anc1.Anc1refChr2 14128 12 - 144309 CATATTCAACAC -s Anc2.Anc2refChr3 14504 12 - 53186 GATACTCAACGC -s mr.mrrefChr5 35782 12 + 294540 CAGATTCAACAC -s simCow_chr6.simCow.chr6 435473 8 - 602619 ----CTCAACGC -s simDog_chr6.simDog.chr6 143631 7 + 593897 GATACTT----- -s simHuman_chr6.simHuman.chr6 446418 12 - 601863 CGCATTCAACAC -s simRat_chr6.simRat.chr6 170767 12 + 647215 CAGATTTAACAT - -a -s simMouse_chr6.simMouse.chr6 180539 12 + 636262 TTGCTGGCTTTA -s Anc0.Anc0refChr1 13324 9 + 62388 TCCCTGCCT--- -s Anc1.Anc1refChr2 14140 9 - 144309 TCCCTGCCT--- -s Anc2.Anc2refChr3 14516 9 - 53186 CCCCTGCCT--- -s mr.mrrefChr5 35794 9 + 294540 TTGCTGGCT--- -s simCow_chr6.simCow.chr6 435481 9 - 602619 CCCCTGGCT--- -s simDog_chr6.simDog.chr6 143638 7 + 593897 --CCTCCCG--- -s simHuman_chr6.simHuman.chr6 446431 9 - 601863 TCCCTGCCT--- -s simRat_chr6.simRat.chr6 170779 9 + 647215 TGGGTGGCT--- - -a -s simMouse_chr6.simMouse.chr6 180551 2 + 636262 GT -s Anc0.Anc0refChr1 13336 2 + 62388 GT -s Anc1.Anc1refChr2 14152 2 - 144309 GT -s Anc2.Anc2refChr3 14528 2 - 53186 AT -s mr.mrrefChr5 35803 2 + 294540 GT -s simCow_chr6.simCow.chr6 435493 2 - 602619 TT -s simDog_chr6.simDog.chr6 143648 2 + 593897 AT -s simHuman_chr6.simHuman.chr6 446443 2 - 601863 GT -s simRat_chr6.simRat.chr6 170788 2 + 647215 GT - -a -s simMouse_chr6.simMouse.chr6 180553 2 + 636262 TG -s Anc0.Anc0refChr1 13338 2 + 62388 TG -s Anc1.Anc1refChr2 14154 2 - 144309 TG -s Anc2.Anc2refChr3 14531 2 - 53186 TG -s mr.mrrefChr5 35805 2 + 294540 TG -s simCow_chr6.simCow.chr6 435496 2 - 602619 TG -s simDog_chr6.simDog.chr6 143651 2 + 593897 TG -s simHuman_chr6.simHuman.chr6 446445 2 - 601863 AT -s simRat_chr6.simRat.chr6 170790 2 + 647215 TG - -a -s simMouse_chr6.simMouse.chr6 180555 57 + 636262 TGTTCTATGGTTCCCTATCCCTTAATATGAATTACTCGTCGTGTTCTATGGTTCCCT -s Anc0.Anc0refChr1 13340 15 + 62388 TGTTCTA------------------------------------------TGTTCTTT -s Anc1.Anc1refChr2 14156 15 - 144309 TGTTCTA------------------------------------------TGTTCTTT -s Anc2.Anc2refChr3 14533 15 - 53186 TGTTCTA------------------------------------------TGTTCTTT -s mr.mrrefChr5 35807 15 + 294540 TGTTCTA------------------------------------------GGTTCCCT -s simCow_chr6.simCow.chr6 435498 12 - 602619 ---TGTA------------------------------------------TGTCCTTT -s simDog_chr6.simDog.chr6 143656 15 + 593897 TGTTCTA------------------------------------------TGTTCTTT -s simHuman_chr6.simHuman.chr6 446447 15 - 601863 CGTCTAG------------------------------------------TGTTCTTT -s simRat_chr6.simRat.chr6 170792 15 + 647215 TCTTGTA------------------------------------------GGTTCCCT - -a -s simMouse_chr6.simMouse.chr6 180612 15 + 636262 ATCCCTTAATATGAA -s Anc0.Anc0refChr1 13355 15 + 62388 ATGCATCAATATGAG -s Anc1.Anc1refChr2 14171 15 - 144309 ATGCATCAATATGAG -s Anc2.Anc2refChr3 14548 15 - 53186 ATGCATCAGTATGAG -s mr.mrrefChr5 35822 15 + 294540 ATCCCTTAATATGAA -s simCow_chr6.simCow.chr6 435515 15 - 602619 ATGCGTCAGTATGAG -s simDog_chr6.simDog.chr6 143671 15 + 593897 ATGCATCAGTGTGAG -s simHuman_chr6.simHuman.chr6 446462 15 - 601863 ATGCATCAACATGAG -s simRat_chr6.simRat.chr6 170807 15 + 647215 ATCCCTTAGTATGAA - -a -s simMouse_chr6.simMouse.chr6 180627 6 + 636262 TTACTC -s Anc0.Anc0refChr1 13372 6 + 62388 TGAATT -s Anc1.Anc1refChr2 14188 6 - 144309 TGAATT -s Anc2.Anc2refChr3 14565 6 - 53186 TGAATT -s mr.mrrefChr5 35837 6 + 294540 TTACTC -s simCow_chr6.simCow.chr6 435532 6 - 602619 AGAATT -s simDog_chr6.simDog.chr6 143688 6 + 593897 TGAATT -s simHuman_chr6.simHuman.chr6 446479 6 - 601863 TGTATT -s simRat_chr6.simRat.chr6 170822 6 + 647215 CCACTA - -a -s simMouse_chr6.simMouse.chr6 180633 21 + 636262 GTTACGACAATCTGCCTTGCA -s Anc0.Anc0refChr1 13378 20 + 62388 CATATGA-GGTCTGCCTTGCA -s Anc1.Anc1refChr2 14194 20 - 144309 CATATGA-GGTCTGCCTTGCA -s Anc2.Anc2refChr3 14571 20 - 53186 CATATGA-GGTCTGCCTTACA -s mr.mrrefChr5 35843 21 + 294540 GTTACGACAATCTGCCTTGCA -s simCow_chr6.simCow.chr6 435538 20 - 602619 GAAATGA-GGTGTACTTTAGA -s simDog_chr6.simDog.chr6 143724 20 + 593897 CATATGA-GGTCTGCCTCACA -s simHuman_chr6.simHuman.chr6 446485 20 - 601863 TATATGA-GGTCTGCCTTGCA -s simRat_chr6.simRat.chr6 170828 21 + 647215 GTCACTGCAATCCGCCTTGCA - -a -s simMouse_chr6.simMouse.chr6 180654 1 + 636262 A -s Anc0.Anc0refChr1 13398 1 + 62388 A -s Anc1.Anc1refChr2 14214 1 - 144309 A -s Anc2.Anc2refChr3 14591 1 - 53186 A -s mr.mrrefChr5 35864 1 + 294540 A -s simCow_chr6.simCow.chr6 435558 1 - 602619 G -s simDog_chr6.simDog.chr6 143745 1 + 593897 A -s simHuman_chr6.simHuman.chr6 446505 1 - 601863 A -s simRat_chr6.simRat.chr6 170849 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 180655 3 + 636262 ATA -s Anc0.Anc0refChr1 13399 3 + 62388 AAA -s Anc1.Anc1refChr2 14215 3 - 144309 AAA -s Anc2.Anc2refChr3 14592 3 - 53186 AAA -s mr.mrrefChr5 35865 3 + 294540 ATA -s simCow_chr6.simCow.chr6 435559 3 - 602619 AAA -s simDog_chr6.simDog.chr6 143746 3 + 593897 AAA -s simHuman_chr6.simHuman.chr6 446506 3 - 601863 AAA -s simRat_chr6.simRat.chr6 170851 3 + 647215 AAA - -a -s simMouse_chr6.simMouse.chr6 180658 13 + 636262 TTATTTTGGTCTC -s Anc0.Anc0refChr1 13403 13 + 62388 TTAGCTTAGTCTC -s Anc1.Anc1refChr2 14219 13 - 144309 TTAGCTTAGTCTC -s Anc2.Anc2refChr3 14596 13 - 53186 TTAGCTTAATCTC -s mr.mrrefChr5 35868 13 + 294540 TTATTTTGGTCTC -s simCow_chr6.simCow.chr6 435563 13 - 602619 TTAGGTTAATCCC -s simDog_chr6.simDog.chr6 143750 13 + 593897 TTAGCCTGATCTC -s simHuman_chr6.simHuman.chr6 446510 13 - 601863 TTAGCTTAGTCTC -s simRat_chr6.simRat.chr6 170854 13 + 647215 TTATCTTGGTCTC - -a -s simMouse_chr6.simMouse.chr6 180671 13 + 636262 TCGAGCATAACAC -s Anc0.Anc0refChr1 13417 10 + 62388 TC---CATAACAC -s Anc1.Anc1refChr2 14233 10 - 144309 TC---CATAACAC -s Anc2.Anc2refChr3 14610 10 - 53186 TC---CATAACAC -s mr.mrrefChr5 35881 13 + 294540 TCGAGCATAACAC -s simCow_chr6.simCow.chr6 435577 10 - 602619 TC---CAGAACAC -s simDog_chr6.simDog.chr6 143764 10 + 593897 TT---CATAGCAC -s simHuman_chr6.simHuman.chr6 446524 10 - 601863 TC---CATAACAC -s simRat_chr6.simRat.chr6 170867 13 + 647215 TCATGCATAACAC - -a -s simMouse_chr6.simMouse.chr6 180684 35 + 636262 TCTCCTAATGTATTTGAGTAGCACATTCAAACCTT -s Anc0.Anc0refChr1 13441 35 + 62388 GCTGCTAGTGTATATTAATTGTGTGTTGAGATCTT -s Anc1.Anc1refChr2 14257 35 - 144309 GCTGCTAGTGTATATTAATTGTGTGTTGAGATCTT -s Anc2.Anc2refChr3 14634 35 - 53186 GCTGCTAGTGTATATTAATTGTGTGTTGAGATCTT -s mr.mrrefChr5 35894 35 + 294540 TCTCCTAATGTATTTGAGTAGCACATTCAAACCTT -s simCow_chr6.simCow.chr6 435601 35 - 602619 GCAGCTAGTGTGTATTAGTTGTGTGTTCAAATCTT -s simDog_chr6.simDog.chr6 143788 35 + 593897 TCTATTAGTGTATATTAATTTTGTGTTGAGATCAT -s simHuman_chr6.simHuman.chr6 446548 35 - 601863 GCTGCTACTGTATATTAATTGTGTGGTTGGATCTT -s simRat_chr6.simRat.chr6 170880 35 + 647215 TCCACTAATGTATTTGAGTAGCACATTCAAACCTT - -a -s simMouse_chr6.simMouse.chr6 180719 19 + 636262 TCAAGACCAAATGTGAACT -s Anc0.Anc0refChr1 13476 19 + 62388 TCAAGACCAAATCAGAACT -s Anc1.Anc1refChr2 14292 19 - 144309 TCAAGACCAAATCAGAACT -s Anc2.Anc2refChr3 14669 19 - 53186 GTAAGACCCAATCAGCACT -s mr.mrrefChr5 35929 19 + 294540 TCAAGACCAAATGTGAACT -s simCow_chr6.simCow.chr6 435636 14 - 602619 -----ACACAATCAGCACT -s simDog_chr6.simDog.chr6 143823 19 + 593897 GTAAGACCCAATCAGCACT -s simHuman_chr6.simHuman.chr6 446585 19 - 601863 TCAAGACCAAGTCAGAATT -s simRat_chr6.simRat.chr6 170915 19 + 647215 ACAAGATTGTATGAGAACT - -a -s simMouse_chr6.simMouse.chr6 180738 12 + 636262 ATTTTGGTTCCA -s Anc0.Anc0refChr1 13532 12 + 62388 ATTTTGGCTTCT -s Anc1.Anc1refChr2 14348 12 - 144309 ATTTTGGCTTCT -s Anc2.Anc2refChr3 14725 12 - 53186 ATTTTGGCTTCT -s mr.mrrefChr5 35948 12 + 294540 ATTTTGGTTCCA -s simCow_chr6.simCow.chr6 435687 12 - 602619 ACTTTGGCTTCT -s simDog_chr6.simDog.chr6 143879 12 + 593897 GTTCTGCCTTCC -s simHuman_chr6.simHuman.chr6 446680 12 - 601863 ATTTTTGCTTCT -s simRat_chr6.simRat.chr6 170934 12 + 647215 ATTTTGGCTCCA - -a -s simMouse_chr6.simMouse.chr6 180750 14 + 636262 GGCTAATTTTGGCT -s Anc0.Anc0refChr1 13557 14 + 62388 GTCTAATTTTGGCT -s Anc1.Anc1refChr2 14373 14 - 144309 GTCTAATTTTGGCT -s Anc2.Anc2refChr3 14750 14 - 53186 GTCTAATTTAGGCT -s mr.mrrefChr5 35960 14 + 294540 GGCTAATTTTGGCT -s simCow_chr6.simCow.chr6 435712 14 - 602619 GTTTAATTTAAGTT -s simDog_chr6.simDog.chr6 143904 14 + 593897 GTCTAATCTAGGCT -s simHuman_chr6.simHuman.chr6 446705 14 - 601863 GCCTAATTTTGGCT -s simRat_chr6.simRat.chr6 170946 14 + 647215 GTATAATTTTGGCT - -a -s simMouse_chr6.simMouse.chr6 180764 12 + 636262 CACCTTTCTCAA -s Anc0.Anc0refChr1 13572 12 + 62388 CTCTTTTATCAA -s Anc1.Anc1refChr2 14388 12 - 144309 CTCTTTTATCAA -s Anc2.Anc2refChr3 14765 12 - 53186 CTCTTTTATCAA -s mr.mrrefChr5 35974 12 + 294540 CACCTTTCTCAA -s simCow_chr6.simCow.chr6 435727 12 - 602619 CTCCATTGTCAA -s simDog_chr6.simDog.chr6 143919 12 + 593897 CTTTTTTATTAA -s simHuman_chr6.simHuman.chr6 446720 12 - 601863 CTCTTTTATCAA -s simRat_chr6.simRat.chr6 170960 12 + 647215 CACCTTTGTCAA - -a -s simMouse_chr6.simMouse.chr6 180776 29 + 636262 GGGGGCAAATATGTCCCAACAGCATTGGT -s Anc0.Anc0refChr1 13584 29 + 62388 TGTGTCTAATTCTTTCCAACAGCAGTAGT -s Anc1.Anc1refChr2 14400 29 - 144309 TGTGTCTAATTCTTTCCAACAGCAGTAGT -s Anc2.Anc2refChr3 14777 29 - 53186 TGTGTCTAATTCTTTCCAACAGCAGTAGT -s mr.mrrefChr5 35986 29 + 294540 GGGGGCAAATTCTTTCCAACAGCAGTGGT -s simCow_chr6.simCow.chr6 435741 29 - 602619 TGTGTTTAACCCTTTCCAATAGCAGTAGT -s simDog_chr6.simDog.chr6 143931 28 + 593897 TGTGTCTAATTCTTTCAGAC-GCACTAGT -s simHuman_chr6.simHuman.chr6 446732 29 - 601863 TGCGTCTGATTCTTTCCAACAGCAGTAAT -s simRat_chr6.simRat.chr6 170972 29 + 647215 GGGGGCAAATTCTTTCCAACAGCAGTGGT - -a -s simMouse_chr6.simMouse.chr6 180805 20 + 636262 GCTATAACCGTGTACCAATA -s Anc0.Anc0refChr1 13613 19 + 62388 CGTCTTGCTTTG-ACTAAGA -s Anc1.Anc1refChr2 14429 19 - 144309 CGTCTTGCTTTG-ACTAAGA -s Anc2.Anc2refChr3 14806 19 - 53186 CGTCTTGCTTTG-ACTAAGG -s mr.mrrefChr5 36015 20 + 294540 GCTATTGCCTTGTACCAATA -s simCow_chr6.simCow.chr6 435805 19 - 602619 CCTGTTGCTTTG-ACCAATG -s simDog_chr6.simDog.chr6 143959 19 + 593897 TGTCTTGCTTGG-ACTAAGG -s simHuman_chr6.simHuman.chr6 446761 19 - 601863 CGTTTTGCTTTG-ACTGACA -s simRat_chr6.simRat.chr6 171001 20 + 647215 GCTATTGCCTTGTACCAATA - -a -s simMouse_chr6.simMouse.chr6 180825 13 + 636262 GTCCAATTGGCCA -s Anc0.Anc0refChr1 13633 13 + 62388 CTCCAGTTAACCA -s Anc1.Anc1refChr2 14449 13 - 144309 CTCCAGTTAACCA -s Anc2.Anc2refChr3 14826 13 - 53186 CTCCAGTTAACCA -s mr.mrrefChr5 36036 13 + 294540 GTCCAATTAGCCA -s simCow_chr6.simCow.chr6 435825 13 - 602619 TTCCAGTTGGCCA -s simDog_chr6.simDog.chr6 143979 13 + 593897 CTCCAGTTAACCA -s simHuman_chr6.simHuman.chr6 446781 13 - 601863 CCCCAGCTAACCA -s simRat_chr6.simRat.chr6 171022 13 + 647215 GTCCCATTAGCCA - -a -s simMouse_chr6.simMouse.chr6 180838 61 + 636262 AATTTCCATTCAGAGGTAATTTTTGATGTGGATTATTGATAGGGAGGTGTTGTCCCACAGT -s Anc0.Anc0refChr1 13647 61 + 62388 AATTACCACTCAGGGGTACTTGTTATTGTTGGTTATTGATTGATTGGTGTAGTATCACATT -s Anc1.Anc1refChr2 14463 61 - 144309 AATTACCACTCAGGGGTACTTGTTATTGTTGGTTATTGATTGATTGGTGTAGTATCACATT -s Anc2.Anc2refChr3 14840 61 - 53186 AATTACCACTCAGGGGTACTTGTTATTGTTGGTTATTGATTGATTGGTGTAATATCACATT -s mr.mrrefChr5 36049 61 + 294540 AATTTCCACTCAGGGGTAATTTTTAATGTGGGTTATTGATTGAGAGGTGTTGTCCCACAGT -s simCow_chr6.simCow.chr6 435839 60 - 602619 AAT-CCCGCCCCGGGGTACTTGTTATTGGTGGTTATTGATTGATAAATGTAATACAACATT -s simDog_chr6.simDog.chr6 143995 59 + 593897 GAATACCACTCAGGGGTGTTTGTTATCATCGGTTATTGATTGCTTGGTAT--TATCATATT -s simHuman_chr6.simHuman.chr6 446795 61 - 601863 AATTATCACTCAGGAGTACTTGTTATTGTTGGCTATTGATTGAAGGGTGTAGTGTCACATC -s simRat_chr6.simRat.chr6 171035 61 + 647215 AATTTCCACTTGGGGGTAATTTTTAATGTGGGTTATTGATTGAGAGGCATCATACCACAGT - -a -s simMouse_chr6.simMouse.chr6 180899 31 + 636262 GCACAGGCTGACTGGATGTCCTATGCTGAGG -s Anc0.Anc0refChr1 13718 31 + 62388 GCACATCTTGATGGGATATCCTATGCATAGG -s Anc1.Anc1refChr2 14534 31 - 144309 GCACATCTTGATGGGATATCCTATGCATAGG -s Anc2.Anc2refChr3 14911 31 - 53186 GCACATCTTGATGGGATATCCTATACCTAGG -s mr.mrrefChr5 36110 31 + 294540 GCACAGGCTGACTGGATATCCTATGCAGAGG -s simCow_chr6.simCow.chr6 435909 15 - 602619 GCACATCTT--------CTCCTA-------- -s simDog_chr6.simDog.chr6 144064 31 + 593897 GCACATCTTGATGGGATATCATATACCTAGG -s simHuman_chr6.simHuman.chr6 446870 31 - 601863 GCACATCTTGAAGGGATATCCTATGCATAAG -s simRat_chr6.simRat.chr6 171096 31 + 647215 GCATAGGCTGACTGGATATCCTATGCAGAGG - -a -s simMouse_chr6.simMouse.chr6 180930 56 + 636262 CCAGCTAGACACTCTTGAATCATGTCCTAAATGTCCTATCTGTGGATTGTTATAAC -s Anc0.Anc0refChr1 13755 54 + 62388 CTGGTTAGACATTTTGGCACTATGTCCTATATCTGCATT--GTCATTATTCATTGC -s Anc1.Anc1refChr2 14571 54 - 144309 CTGGTTAGACATTTTGGCACTATGTCCTATATCTGCATT--GTCATTATTCATTGC -s Anc2.Anc2refChr3 14948 54 - 53186 CTGGTTAGACATTTTGACACTATGTCTTATATCTGTATC--AACATTATTCATTGC -s mr.mrrefChr5 36141 54 + 294540 CCAGCTAGACACTTTGGAATCATGTCCTAAATGTCCTAT--GTGGATTGTCATTAC -s simCow_chr6.simCow.chr6 435926 54 - 602619 CTAGTTAGACATGCTGACACTGTGTCATATCTCTGTATC--AGCATTATTTATTGT -s simDog_chr6.simDog.chr6 144102 54 + 593897 CAGGTTACACGTTTTCACAGTATGTCTTACACCTGTGTC--AACATTATTCATTGC -s simHuman_chr6.simHuman.chr6 446907 54 - 601863 CTGGTTAGATAGTTTGGCACTATTATCTATATCTGCACT--GTCATTATTCATTGC -s simRat_chr6.simRat.chr6 171127 54 + 647215 CCAGCTAGCCATTTTGGAATCATGTCCTAAATGTCCTAT--ATGGATTGTCATTAC - -a -s simMouse_chr6.simMouse.chr6 180986 12 + 636262 GTATTAGTCATG -s Anc0.Anc0refChr1 13825 12 + 62388 GCATTTGTCCAG -s Anc1.Anc1refChr2 14641 12 - 144309 GCATTTGTCCAG -s Anc2.Anc2refChr3 15018 12 - 53186 TCATTTGTCCAT -s mr.mrrefChr5 36197 12 + 294540 GTATTAGTCATG -s simCow_chr6.simCow.chr6 435996 12 - 602619 TAATTTGTCCAT -s simDog_chr6.simDog.chr6 144172 10 + 593897 TCAT--ATCCAT -s simHuman_chr6.simHuman.chr6 446977 12 - 601863 GCATTTGTCCAG -s simRat_chr6.simRat.chr6 171183 12 + 647215 GTATTAGTCATG - -a -s simMouse_chr6.simMouse.chr6 180998 20 + 636262 TACTGGTCCCATATTAAGGG -s Anc0.Anc0refChr1 13837 20 + 62388 TTCTGGTTCTATATTATGTG -s Anc1.Anc1refChr2 14653 20 - 144309 TTCTGGTTCTATATTATGTG -s Anc2.Anc2refChr3 15030 20 - 53186 TTCTGGTTCTATATTATGTG -s mr.mrrefChr5 36209 20 + 294540 TACTGGTCCCATATTAAGGG -s simCow_chr6.simCow.chr6 436045 19 - 602619 TTCTGGTTCTACATTATGT- -s simDog_chr6.simDog.chr6 144182 20 + 593897 TTCTGGTTTCATCTTATCTG -s simHuman_chr6.simHuman.chr6 446989 20 - 601863 TTCTGGTTCTGTATTATGTG -s simRat_chr6.simRat.chr6 171195 20 + 647215 TACTGGTCCCATCTTAAGGG - -a -s simMouse_chr6.simMouse.chr6 181018 18 + 636262 CGGCAATTCAATCACAAA -s Anc0.Anc0refChr1 13857 13 + 62388 CATTAAT-----CACAAT -s Anc1.Anc1refChr2 14673 13 - 144309 CATTAAT-----CACAAT -s Anc2.Anc2refChr3 15050 13 - 53186 CAGCAAT-----CACTAT -s mr.mrrefChr5 36229 18 + 294540 CATTAATTCAATCACAAA -s simDog_chr6.simDog.chr6 144251 13 + 593897 CAGCAAT-----CACTAT -s simHuman_chr6.simHuman.chr6 447009 13 - 601863 CATTAAT-----AACAAG -s simRat_chr6.simRat.chr6 171215 18 + 647215 AATTAATTCAATCACAAA - -a -s simMouse_chr6.simMouse.chr6 181036 5 + 636262 ATTTT -s Anc0.Anc0refChr1 13871 5 + 62388 ATTTT -s Anc1.Anc1refChr2 14687 5 - 144309 ATTTT -s Anc2.Anc2refChr3 15064 5 - 53186 ATTTT -s mr.mrrefChr5 36247 5 + 294540 ATTTT -s simCow_chr6.simCow.chr6 436065 5 - 602619 ATTCA -s simDog_chr6.simDog.chr6 144265 5 + 593897 GTTTT -s simHuman_chr6.simHuman.chr6 447023 5 - 601863 ATTTT -s simRat_chr6.simRat.chr6 171233 5 + 647215 ATTTT - -a -s simMouse_chr6.simMouse.chr6 181041 25 + 636262 AATGTGGCCAAACATTTACGTGGAT -s Anc0.Anc0refChr1 13876 25 + 62388 AATGAGGCTGAAAACCTATGTGGGT -s Anc1.Anc1refChr2 14692 25 - 144309 AATGAGGCTGAAAACCTATGTGGGT -s Anc2.Anc2refChr3 15069 25 - 53186 AATGAGGCTGGAAACCTATGTGGGT -s mr.mrrefChr5 36252 25 + 294540 AATGTGGCCAAACACTTACGTGGAT -s simCow_chr6.simCow.chr6 436070 23 - 602619 A--TATGTGGGTATACTCTGTGGAT -s simDog_chr6.simDog.chr6 144276 25 + 593897 AATGAGGCTGGAAACCTAAGTAGGT -s simHuman_chr6.simHuman.chr6 447028 25 - 601863 AATGGGGCTGAAAACCTATGTGGGT -s simRat_chr6.simRat.chr6 171238 25 + 647215 AATGCGGCCAAAGACTTACATAGAT - -a -s simMouse_chr6.simMouse.chr6 181066 7 + 636262 AAACGCT -s Anc0.Anc0refChr1 13901 3 + 62388 ATA---- -s Anc1.Anc1refChr2 14717 7 - 144309 ATACTCT -s Anc2.Anc2refChr3 15094 3 - 53186 ATG---- -s mr.mrrefChr5 36277 7 + 294540 AAACTCT -s simCow_chr6.simCow.chr6 436094 3 - 602619 ATG---- -s simDog_chr6.simDog.chr6 144301 3 + 593897 GTG---- -s simHuman_chr6.simHuman.chr6 447053 7 - 601863 AGACTCT -s simRat_chr6.simRat.chr6 171263 7 + 647215 AAGCTCT - -a -s simMouse_chr6.simMouse.chr6 181073 13 + 636262 GTGTTACTTATAA -s Anc0.Anc0refChr1 13904 5 + 62388 --------GATAG -s Anc1.Anc1refChr2 14724 12 - 144309 GTATT-ATGATAG -s Anc2.Anc2refChr3 15097 5 - 53186 --------GATGG -s mr.mrrefChr5 36284 12 + 294540 GTGTT-CTTATAA -s simCow_chr6.simCow.chr6 436097 5 - 602619 --------AATTG -s simDog_chr6.simDog.chr6 144304 5 + 593897 --------GATGG -s simHuman_chr6.simHuman.chr6 447062 12 - 601863 GTATT-ATGATAG -s simRat_chr6.simRat.chr6 171270 12 + 647215 GTGTT-CTTGTGA - -a -s simMouse_chr6.simMouse.chr6 181086 28 + 636262 ATTATTATCTACTGCACTTATATCTTCC -s Anc0.Anc0refChr1 13909 28 + 62388 GAAAATACCACCTGCACTTAGATGTTCC -s Anc1.Anc1refChr2 14736 28 - 144309 GAAAATACCACCTGCACTTAGATGTTCC -s Anc2.Anc2refChr3 15103 28 - 53186 GTAAATTCCACCTGCATTTAGATGTTCC -s mr.mrrefChr5 36296 28 + 294540 AATATTATCAACTGCACTTATATCTTCC -s simCow_chr6.simCow.chr6 436103 28 - 602619 ATAAATTCCACCTGTATTTCTATGTTCC -s simDog_chr6.simDog.chr6 144310 28 + 593897 GTAAATTCCACACACATTAAGATGTTCT -s simHuman_chr6.simHuman.chr6 447074 28 - 601863 GAAGATACCACCTGCACTTAGATGTTCC -s simRat_chr6.simRat.chr6 171282 28 + 647215 CATATTATCAACTGCACTTATATCTTCC - -a -s simMouse_chr6.simMouse.chr6 181114 53 + 636262 TGCTGTTCATGAGCATAATGACTGCTCCTGCTTAGGCTGAGCTTCTCGCTTGT -s Anc0.Anc0refChr1 13943 45 + 62388 T--CATTCATGAGCATAATGCCTGCTCATGCT------GAGTTTATTTTTTGT -s Anc1.Anc1refChr2 14770 45 - 144309 T--CATTCATGAGCATAATGCCTGCTCATGCT------GAGTTTATTTTTTGT -s Anc2.Anc2refChr3 15137 45 - 53186 T--CATTCATCAGCATAATCCCTGATCATGCA------TAGTGTATTTTTTGT -s mr.mrrefChr5 36329 53 + 294540 TGCTGTTCATGAGCATAATGACTGCTCCTGCTTAGGCTGAGCTTATCGCTTGT -s simCow_chr6.simCow.chr6 436137 38 - 602619 C--CATTCATCAGCATAAT-------CATGCA------TAGTATATTTTTTGT -s simDog_chr6.simDog.chr6 144346 45 + 593897 T--CTTCCATCAGCATGATCCCTGATTTTGGA------TAGTGCATTTTTTGT -s simHuman_chr6.simHuman.chr6 447108 45 - 601863 T--CAGTCATGGGCATAATGCCTGCTCATGCT------GAGTTTATTTTTTGT -s simRat_chr6.simRat.chr6 171315 53 + 647215 TACTGTTCATGAGCATAATGACTGCTCCTGCTTAGGCTGAGCTTATCCCTTGT - -a -s simMouse_chr6.simMouse.chr6 181167 17 + 636262 CATGCGCCATTTACTTA -s Anc0.Anc0refChr1 13989 17 + 62388 CATGTGCCATTTACTAA -s Anc1.Anc1refChr2 14816 17 - 144309 CATGTGCCATTTACTAA -s Anc2.Anc2refChr3 15183 17 - 53186 CATGTGCCATCTACTAA -s mr.mrrefChr5 36382 17 + 294540 CATGTGCCATTTACTTA -s simCow_chr6.simCow.chr6 436176 17 - 602619 CATGGACCATCTATTGA -s simDog_chr6.simDog.chr6 144392 17 + 593897 CATGTGCCATCTACTAA -s simHuman_chr6.simHuman.chr6 447154 17 - 601863 CATGTGCCATTTACCAA -s simRat_chr6.simRat.chr6 171368 17 + 647215 CATGTGCCATTTACTCA - -a -s simMouse_chr6.simMouse.chr6 181184 76 + 636262 GTTGATGTATGATCAACAAACAAATGCAACCACAATCTATCCTAGCTTAAGTATTTATCAATCATACCTCTGTTTT -s Anc0.Anc0refChr1 14008 76 + 62388 GCTGATATACAATCAACATATAATTCAAACCACAATCTATCTTAGCTTAAGTATTTGTCAGCTATCCTTCTACCTT -s Anc1.Anc1refChr2 14835 76 - 144309 GCTGATATACAATCAACATATAATTCAAACCACAATCTATCTTAGCTTAAGTATTTGTCAGCTATCCTTCTACCTT -s Anc2.Anc2refChr3 15202 76 - 53186 GCTGATATACAATCAACATACAATTCAAACCACAATCTATCTTAGCTTAAGTATTTGTCAGCCATCCTTCTACCTT -s mr.mrrefChr5 36401 76 + 294540 GTTGATATATGATCAACATATAAATGCAACCACAATCTATCTTAGCTTAAGTATTTATCAATTATACCTCTATCTT -s simCow_chr6.simCow.chr6 436195 75 - 602619 GCTGAAGAACAAGCAACATACAATTGTAACCACAATCAGTCCTAGTTTAAGTACTTGTCA-CCATATTTCTGCCTT -s simDog_chr6.simDog.chr6 144411 76 + 593897 GCTGATATATAATCAACATGCGATTCAAACCGCAACCTATCTTGGCTAAACACTTTGTAAGTCATCCTCCTACCTT -s simHuman_chr6.simHuman.chr6 447173 76 - 601863 GCTGGTACACAATCAACGTATAATTTAAACCACAATCTATCTTAGCTTAAGTATTTGTCAGCTATTCTTCTACCTT -s simRat_chr6.simRat.chr6 171387 76 + 647215 GTAGAGATATGATTGACATATGAATGCAACCACAACCTATCTTGGCTTAGGTATTTATCAATTACACCTCTATCTT - -a -s simMouse_chr6.simMouse.chr6 181260 60 + 636262 CAACCTTTATCAGTGgtgtgttttgtggctacgactgttttaggctgcctcccaatatta -s Anc0.Anc0refChr1 14084 11 + 62388 GGACCTTTACC------------------------------------------------- -s Anc1.Anc1refChr2 14911 56 - 144309 GGACCTTTACCACtg---tgtcttgtaactggaattattttag-ctgtctaaaaagtata -s Anc2.Anc2refChr3 15278 11 - 53186 GGACCTTTACC------------------------------------------------- -s mr.mrrefChr5 36477 60 + 294540 GAACCTTTATCAGTGgtgtgtcttgtagctacaactgttttaggctgcctcccaatttta -s simCow_chr6.simCow.chr6 436270 11 - 602619 GGACCTTTACC------------------------------------------------- -s simDog_chr6.simDog.chr6 144488 11 + 593897 GGACCTTTACC------------------------------------------------- -s simHuman_chr6.simHuman.chr6 447249 56 - 601863 GGACCTTTACCACtg---tgtcttgtaactggaattattttag-ctgtctaaaaagtata -s simRat_chr6.simRat.chr6 171463 60 + 647215 GAACCTTTATCATTGgtgtgtcttgtagctacaactgtgttaggctgccttccaattttg - -a -s simMouse_chr6.simMouse.chr6 181320 34 + 636262 gcatgtgtgtgcaacaagtgtgtgcctgccctgt -s Anc1.Anc1refChr2 14967 34 - 144309 gtccgtgtgcacaaagagtatgtgcctgccccat -s mr.mrrefChr5 36537 34 + 294540 gcatgtgtgtgcaacaagtgtgtgcctgccctgt -s simHuman_chr6.simHuman.chr6 447308 34 - 601863 gtccgtgtgcacaaagagtatgtgcctgccccat -s simRat_chr6.simRat.chr6 171523 34 + 647215 ccatgtgtgtgcaacaaatgtctgcctgccctgt - -a -s simMouse_chr6.simMouse.chr6 181354 89 + 636262 gaaaaggtgacccttcgtgtaatatggtgtagttagagagtaattaggcagggaaggatgacaccaaatctaaggaccccatggacaag -s Anc1.Anc1refChr2 15002 77 - 144309 gagaagatgacccttgctttcatcttatgtg----------a-tcagatgaggaaaatttgcagtagttctgggg-cgcgatgggcaag -s mr.mrrefChr5 36572 87 + 294540 gaaaaggtgacccttcctgtaatattgtgtagttagagagta-ttaggcggggaagaatggcaccaaatctaggg-ccccatggacaag -s simHuman_chr6.simHuman.chr6 447346 77 - 601863 gagaagatgacccttgctttcatcttatgtg----------a-tcagatgaggaaaatttgcagtagttctgggg-cgcgatgggcaag -s simRat_chr6.simRat.chr6 171558 80 + 647215 gaaaaggtaacccttcctgtaatattgtgtagctagagagta-ttaggcggggcagaatggcatcaagtctag---cactcTAG----- - -a -s simMouse_chr6.simMouse.chr6 181443 26 + 636262 ctttgatgagaacttactacaaagtt -s Anc1.Anc1refChr2 15079 26 - 144309 ctaccacaaccacttaccacaaagtt -s mr.mrrefChr5 36659 26 + 294540 ctttgatgagaacttactacaaagtt -s simHuman_chr6.simHuman.chr6 447425 26 - 601863 ctaccacaaccacttaccacaaagtt -s simRat_chr6.simRat.chr6 171638 26 + 647215 TTCAGATGAGAACTTACTACATAGTT - -a -s simMouse_chr6.simMouse.chr6 181469 21 + 636262 aatatgagctttcctactaca -s Anc1.Anc1refChr2 15105 21 - 144309 aatacaggcctctcctgtaaa -s mr.mrrefChr5 36685 21 + 294540 aatatgagcttccccactaca -s simHuman_chr6.simHuman.chr6 447455 21 - 601863 aatacaggcctctcctgtaaa -s simRat_chr6.simRat.chr6 171664 21 + 647215 AATATGAGCTCCCCCACTATA - -a -s simMouse_chr6.simMouse.chr6 181490 28 + 636262 ctaaggctcaacctgttggacaacccct -s Anc1.Anc1refChr2 15126 28 - 144309 ttgaatctcgaccctatggatgagtcct -s mr.mrrefChr5 36706 28 + 294540 ctaaggctcaacctgatggacaacccct -s simHuman_chr6.simHuman.chr6 447476 28 - 601863 ttgaatctcgaccctatggatgagtcct -s simRat_chr6.simRat.chr6 171763 28 + 647215 CTAAGGCTCAACATGATGGACAACCTCT - -a -s simMouse_chr6.simMouse.chr6 181518 307 + 636262 ctgggttgatttactgcaaaattttgaattgtggttctcttctgtccttccaaattcactgctgcttccttactccaaggcttggactgcataagtggggttttgtaattctgacagcatgagttcttgatccagtaccaaatttttgacactttagactcctgttagacccagagagtttgcacaaaaaacaattccttaaactggagaaggttgtagtacaagcttcctccttgaatacacttcaaagagtcactcaaaatatgatctgctcttctaagttgaaagggtctgttgctactatggc -s Anc1.Anc1refChr2 15154 270 - 144309 ccaggtacactcactggaaagtcttaaaatacaagtctcttctgcaatttgaatttcattaccacctccttactaagacccttgagctgactaggcagaaac-----gttcttagagtgtgagtccttcacccaatgtccaattttagatatcatagactcctgttagacctagagggttt---------aagttctcttagagt-----------ctctaaagg-------tttaagtgctctt---ggagtctct--aaatatgagctgctcctctaaattgaatgggtgtcatgctgttgtggc -s mr.mrrefChr5 36734 307 + 294540 ctgggttgatttactgcaaaattttgaattgtgattctcttctgtccttccaaattcactaccacttccttactccaaggcttggactgactaggtggagttttgtaattctgacagcatgagttcttgatccagtatcaaattttagacattttagactcctgttagacctagagagtttgcacaaaaaacaattccttaaactggagaaggttgcactacaagcttcctctttgaatacacttcaaagagtcactcaaaatatgagctgctcttctaagttgaaagggtctgttgctgctatggc -s simHuman_chr6.simHuman.chr6 447505 270 - 601863 ccaggtacactcactggaaagtcttaaaatacaagtctcttctgcaatttgaatttcattaccacctccttactaagacccttgagctgactaggcagaaac-----gttcttagagtgtgagtccttcacccaatgtccaattttagatatcatagactcctgttagacctagagggttt---------aagttctcttagagt-----------ctctaaagg-------tttaagtgctctt---ggagtctct--aaatatgagctgctcctctaaattgaatgggtgtcatgctgttgtggc -s simRat_chr6.simRat.chr6 171791 294 + 647215 CTGGCTTGATTTGCTACAAAAA--------GTGACTctctcctgtccttccaa-ttcactaccacttccttactccagggcttggactgaccaggtggagttttctaattctgacagcatgagttctggatccagtatcaaattttacacattttatactcctgttagacctagagagggtgcacaaaaaagaattccttaaactggagaaggttgcactacaagcctcctctttgaatacgcttaaaagagtcactaaaaatatgagctgc----ctaagctgaaagggcctgtggctgctatggc - -a -s simMouse_chr6.simMouse.chr6 181825 31 + 636262 aacttaattagaaccctttttcctcattctc -s Anc1.Anc1refChr2 15424 31 - 144309 agtgtagttacaacctttttctctcattttc -s mr.mrrefChr5 37041 31 + 294540 aacttaattagaaccctttttcctcattctc -s simHuman_chr6.simHuman.chr6 447780 31 - 601863 agtgtagttacaacctttttctctcattttc -s simRat_chr6.simRat.chr6 172085 31 + 647215 aacttaattagaaggctttttactcattctc - -a -s simMouse_chr6.simMouse.chr6 181856 37 + 636262 tgtgttgttctctactatgtgtttacttatgtgcaca -s Anc1.Anc1refChr2 15460 31 - 144309 t------tttccgttaaggggtttacatatgtgcgca -s mr.mrrefChr5 37077 37 + 294540 tgtgttgttctcttttatgtgtttacttatgtgcaca -s simHuman_chr6.simHuman.chr6 447816 31 - 601863 t------tttccgttaaggggtttacatatgtgcgca -s simRat_chr6.simRat.chr6 172121 37 + 647215 tgtgttgttctcttttatatgtttacttatgtgcaca - -a -s simMouse_chr6.simMouse.chr6 181893 45 + 636262 tgccatcatgtttgtatccataatggcccctctgtcaggttatgc -s Anc1.Anc1refChr2 15491 43 - 144309 ttcctttatgt--gtttacatacaagcccctcccttagattgagc -s mr.mrrefChr5 37114 43 + 294540 tgccttcatgt--gtttacatactggcccctccctcaggttatgc -s simHuman_chr6.simHuman.chr6 447857 43 - 601863 ttcctttatgt--gtttacatacaagcccctcccttagattgagc -s simRat_chr6.simRat.chr6 172158 43 + 647215 tgccttcatgt--gtttacatactggcccctccctcaggttATGC - -a -s simMouse_chr6.simMouse.chr6 181938 149 + 636262 atgccctgagcacagtaatatgagacagctgtgttaattctccaattaagtcaagttggacaggtgctgcaatcacactgcaccacttatttatggtcctaccccttagactgggagtgatgtgtactatcaagttggctggatttctc -s Anc1.Anc1refChr2 15534 131 - 144309 ggactataagcagaataatagggaa--gctatgctcactcactaattaaaagaaattgagtgggtgtcttgatcacat-----ctcttatttatggtcctccccct--gactgggagtaaa---------taaatcgagtggatgtctt -s mr.mrrefChr5 37157 149 + 294540 gtaccctgagcagaataatatgagacagctgtgttaattctccaattaagtcaagttggacaggtgccgcaatcacactgcaccacttatttatggtcctaccccttagactgggagtaatgtgtactatcaaattggctggatttctc -s simHuman_chr6.simHuman.chr6 447901 131 - 601863 ggactataagcagaataatagggaa--gctatgctcactcactaattaaaagaaattgagtgggtgtcttgatcacat-----ctcttatttatggtcctccccct--gactgggagtaaa---------taaatcgagtggatgtctt -s simRat_chr6.simRat.chr6 172201 149 + 647215 GTACCCTGAGTGGAATAATataagacagctgtgttaattctccaattaagtcaagttgcacaggtgccgcaatcattctgcactacctatttatggtcctaccccttagactgagggtaatatgtaccttcaaagtggctggatttctc - -a -s simMouse_chr6.simMouse.chr6 182087 22 + 636262 aagtatggtcctctcaactgag -s Anc1.Anc1refChr2 15667 22 - 144309 cagtatggtcctcctgtgtagc -s mr.mrrefChr5 37308 22 + 294540 aagtatggtcctcccaactgag -s simHuman_chr6.simHuman.chr6 448034 22 - 601863 cagtatggtcctcctgtgtagc -s simRat_chr6.simRat.chr6 172352 22 + 647215 aagtatggtcctcccaacagag - -a -s simMouse_chr6.simMouse.chr6 182109 17 + 636262 ctccacttgtatatcca -s Anc1.Anc1refChr2 15701 17 - 144309 ctccatttgtattccct -s mr.mrrefChr5 37342 17 + 294540 ctccacttgtatatcca -s simHuman_chr6.simHuman.chr6 448068 17 - 601863 ctccatttgtattccct -s simRat_chr6.simRat.chr6 172386 17 + 647215 ctccacttatatatcta - -a -s simMouse_chr6.simMouse.chr6 182126 57 + 636262 agagcggtccttctcccttaggtatttaaggtgaggttaagcttatcttttaagggg -s Anc1.Anc1refChr2 15718 57 - 144309 actatggtcctcctctcttggatgattaggatgtggcttagcccatctattaggggg -s mr.mrrefChr5 37359 57 + 294540 agtgtggtccttctcccttaggtatttaaggtgaggctaagcttatcttttaagggg -s simHuman_chr6.simHuman.chr6 448086 57 - 601863 actatggtcctcctctcttggatgattaggatgtggcttagcccatctattaggggg -s simRat_chr6.simRat.chr6 172403 55 + 647215 agtgtg--ccttctcctttaggtatttaaggtgaggctaagctgatcttttaagggg - -a -s simMouse_chr6.simMouse.chr6 182183 31 + 636262 gctagttaggtagtgctacaagacagtacac -s Anc1.Anc1refChr2 15775 31 - 144309 gccactcacgaggtgctacaagacaatacac -s mr.mrrefChr5 37416 31 + 294540 gctacttaggtggtgctacaagacagtacac -s simHuman_chr6.simHuman.chr6 448144 31 - 601863 gccactcacgaggtgctacaagacaatacac -s simRat_chr6.simRat.chr6 172458 31 + 647215 gctgcttaggtgttgctacaatacagtacac - -a -s simMouse_chr6.simMouse.chr6 182214 34 + 636262 ttttgtgagtgctttcctgcagtatttctaggtt -s Anc1.Anc1refChr2 15806 34 - 144309 ttttgtgagtgctttcctccactatctctaggtt -s mr.mrrefChr5 37447 34 + 294540 ttttgtgagtgctttcctgcagtatttctaggtt -s simHuman_chr6.simHuman.chr6 448177 34 - 601863 ttttgtgagtgctttcctccactatctctaggtt -s simRat_chr6.simRat.chr6 172489 29 + 647215 ttttgtga-----ttcctgcagtatttctaggtt - -a -s simMouse_chr6.simMouse.chr6 182248 11 + 636262 gcttaaagtga -s Anc1.Anc1refChr2 15840 11 - 144309 gattgagacaa -s mr.mrrefChr5 37481 11 + 294540 gattaaagcaa -s simHuman_chr6.simHuman.chr6 448212 11 - 601863 gattgagacaa -s simRat_chr6.simRat.chr6 172518 11 + 647215 gatcaaagcaa - -a -s simMouse_chr6.simMouse.chr6 182259 56 + 636262 aaaccactagaaggctgataagaaggtaccctttcttatttaattactaccctggc -s Anc1.Anc1refChr2 15851 14 - 144309 aacctactaaaatg------------------------------------------ -s mr.mrrefChr5 37492 56 + 294540 aaaccactagaaggctgataagaaggtaccctttcttatttaattactaccctggc -s simHuman_chr6.simHuman.chr6 448232 14 - 601863 aacctactaaaatg------------------------------------------ -s simRat_chr6.simRat.chr6 172529 56 + 647215 aaaccactataaagataataagaaggtaccttttcctatttaattgccaccttggc - -a -s simMouse_chr6.simMouse.chr6 182315 21 + 636262 cagagacatctgaccatgtaa -s mr.mrrefChr5 37548 21 + 294540 cagagacatctgaccatgtaa -s simRat_chr6.simRat.chr6 172586 21 + 647215 catagaaatctgactatgtag - -a -s simMouse_chr6.simMouse.chr6 182336 214 + 636262 aaggtatccaggtcccttgctcatttattaaatcattcttatcaggtatctgtgaaattttgcctgcatagccagtctctttcagacaaataagtggcagatataacactcagtttgttggtcaggattggtcatggtcttttctttttttgtctttaccttccttcagccaattagggcccctaacttgatattagtgtgcgctctcactcaa -s Anc1.Anc1refChr2 15865 58 - 144309 -------------------------------------------------------------------------------------------------------------------------------------------------------ggcttgctctt--ttgagccacataagttttttacgttgataata--tcccattctcattca- -s mr.mrrefChr5 37569 212 + 294540 aaggtatccaggtcccttgctcatttattaaatcattcttatcaggtatctgtgaaattttgcctgcatagccagtctctttcagacaaataagtggcagatataacactcagtttgttggtcaggattggtcatggtcttttctttttttgtctttaccttccttcagccaattagggcccctaacttgatatta--gtgcgctctcactcaa -s simHuman_chr6.simHuman.chr6 448246 58 - 601863 -------------------------------------------------------------------------------------------------------------------------------------------------------ggcttgctctt--ttgagccacataagttttttacgttgataata--tcccattctcattca- -s simRat_chr6.simRat.chr6 172608 212 + 647215 agggaatccaggtcctttgcccatttattaaaacattcttagcaggtatctgtaaaagtttgcctgcatagctagtctctttcaaatgaataagaggcaaatataacactcagtttgttagccaggtttggtcctggttttttccttttttgtctttacgttctttcagccagttaggaccttaaacctgatatta--gcccactctcactcaa - -a -s simMouse_chr6.simMouse.chr6 182550 13 + 636262 cttgcatccattt -s Anc1.Anc1refChr2 15923 7 - 144309 ------tcgatct -s mr.mrrefChr5 37781 13 + 294540 cttgcatccattt -s simHuman_chr6.simHuman.chr6 448304 7 - 601863 ------tcgatct -s simRat_chr6.simRat.chr6 172824 13 + 647215 tttggctccattt - -a -s simMouse_chr6.simMouse.chr6 182563 18 + 636262 taggccccttgagcaata -s Anc1.Anc1refChr2 15930 17 - 144309 cgggtgtcttgagt-ata -s mr.mrrefChr5 37794 17 + 294540 taggccccttgagc-ata -s simHuman_chr6.simHuman.chr6 448312 17 - 601863 cgggtgtcttgagt-ata -s simRat_chr6.simRat.chr6 172837 17 + 647215 tgggcaccttaagc-ata - -a -s simMouse_chr6.simMouse.chr6 182581 14 + 636262 ggtcccttcactgc -s Anc1.Anc1refChr2 15947 7 - 144309 ggtcac-------c -s mr.mrrefChr5 37811 7 + 294540 ggtccc-------c -s simHuman_chr6.simHuman.chr6 448331 7 - 601863 ggtcac-------c -s simRat_chr6.simRat.chr6 172854 7 + 647215 aatgcc-------c - -a -s simMouse_chr6.simMouse.chr6 182595 43 + 636262 caatatttcaaatcatactgtccaagttgccagaatcttcaaa -s Anc1.Anc1refChr2 15954 40 - 144309 cattatcttgag-cacgttccccagatttctgcagtctt--aa -s mr.mrrefChr5 37818 41 + 294540 caatatttcaaatcatactgtccaagttgccagaatctt--aa -s simHuman_chr6.simHuman.chr6 448345 40 - 601863 cattatcttgag-cacgttccccagatttctgcagtctt--aa -s simRat_chr6.simRat.chr6 172861 41 + 647215 caacatttgaaatcatcctgtccaaattatttgaatctt--aa - -a -s simMouse_chr6.simMouse.chr6 182638 3 + 636262 gct -s Anc1.Anc1refChr2 15994 3 - 144309 gct -s mr.mrrefChr5 37859 3 + 294540 gct -s simHuman_chr6.simHuman.chr6 448386 3 - 601863 gct -s simRat_chr6.simRat.chr6 172902 3 + 647215 gct - -a -s simMouse_chr6.simMouse.chr6 182641 69 + 636262 ttcgcagctaagtttttaaatccccaacgcatcagtgtattgtccacacttcgggataaggagcgagaa -s Anc1.Anc1refChr2 15997 69 - 144309 ttggcggcccagactttagatccccgatcaaccagcctctggtctcacctttggtgtagggtgtgaaaa -s mr.mrrefChr5 37862 69 + 294540 ttcgcagctaagtttttaaatccccaacgcatcagtgtattgtccacacttcgggataaggagcgagaa -s simHuman_chr6.simHuman.chr6 448391 69 - 601863 ttggcggcccagactttagatccccgatcaaccagcctctggtctcacctttggtgtagggtgtgaaaa -s simRat_chr6.simRat.chr6 172905 69 + 647215 tttgcaactaaaacttcaaatccccaacccatcagcgttttgtccacactttggggtaaggagtgagaa - -a -s simMouse_chr6.simMouse.chr6 182710 76 + 636262 ggcagtcaagttccaggtcctggtagatagagtgccaatttcttctgcaatcttttggctgaaccataagtccttc -s Anc1.Anc1refChr2 16066 69 - 144309 gagtgtcaggtcccagcctcaggcacatagagggcc-----ctccagcaccattt--gttgaacaatgaatccttc -s mr.mrrefChr5 37931 76 + 294540 ggcagtcaagttccaggtcctggtagatagagtgccaatttcttctgcaatcttttggctgaaccataagtccttc -s simHuman_chr6.simHuman.chr6 448494 69 - 601863 gagtgtcaggtcccagcctcaggcacatagagggcc-----ctccagcaccattt--gttgaacaatgaatccttc -s simRat_chr6.simRat.chr6 172974 76 + 647215 agcagtcaagttccaggtcctggcggatggactgtgaatttcttcaccaatcttttagctgaaccataagtccttc - -a -s simMouse_chr6.simMouse.chr6 182786 251 + 636262 ttgattgttgtctcatatcaaaactggaatgattagagcactcgagagcaaattattctcttcagcaagtctaactacaatgcatatttggtttatggtaccaattcactcagttgggatgctaatgataggttgctacagaatattggtaacactacttcatcttactgcaatggcccaaggacctgaggttctggtgcaagtagagacgagagtgttattttggttgagacaaaacttataacctggtg -s Anc1.Anc1refChr2 16135 138 - 144309 tcaa---tgatttctcag------------------agctatgaaagatgg---act------------------------------------------------------aattagaaagttaacggccattttcttcaaga-------------aatccactttactaccatggtctatgatttcgatcctcttgtaccagtatag----------cattgtgat---------gcttctgactta--- -s mr.mrrefChr5 38007 227 + 294540 ttga---ttgtctcatat------------------agcactcgagagcaa---attctcttcagcaagtctaactacaatgcatatttggtttatggtaccaattcactcagttgggatgctaatgataggttgctacagaatattggtaacactacttcatcttactgcaatggcccaaggacctgaggttctggtgcaagtagagacgagagtgttattttggttgagacaaaacttataacctggtg -s simHuman_chr6.simHuman.chr6 448565 138 - 601863 tcaa---tgatttctcag------------------agctatgaaagatgg---act------------------------------------------------------aattagaaagttaacggccattttcttcaaga-------------aatccactttactaccatggtctatgatttcgatcctcttgtaccagtatag----------cattgtgat---------gcttctgactta--- -s simRat_chr6.simRat.chr6 173050 227 + 647215 ttga---ttgtctcatat------------------aacactctagaacaa---atactcttcagcaaattcaactacaaggcaagtttggcttatgagaccaatttacttggttgggatgctaatgataggttgctacacaatattggaagcactactttatcctactgctatggcctgaggacctgatgttctggtgcaagcagagactagagtgttcttttggttgagacacaacttacaacctggtg - -a -s simMouse_chr6.simMouse.chr6 183037 93 + 636262 taccaccagcttgatttgtctgacttatgggctgctctctttggtggtcttacacaaacttgacaattgtttttttgcactctgtaaccagag -s Anc1.Anc1refChr2 16273 75 - 144309 -------aaatggattt--------tgggg---gctctctactttggttccatgcaagcttgacagttgtggttttgcactctgtaaacagag -s mr.mrrefChr5 38234 90 + 294540 taccaccagcttgatttgtctgacttatgg---gctctctttggtggtcttacacaaacttgacaattgtttttttgcactctgtaaccagag -s simHuman_chr6.simHuman.chr6 448703 75 - 601863 -------aaatggattt--------tgggg---gctctctactttggttccatgcaagcttgacagttgtggttttgcactctgtaaacagag -s simRat_chr6.simRat.chr6 173280 90 + 647215 taccaccagcttgatttatctgacttgtga---gctctctttggtggttccatgcagacttgacaattgttcttttgcactctctaaacagag - -a -s simMouse_chr6.simMouse.chr6 183130 19 + 636262 gggttttttttacagagat -s Anc1.Anc1refChr2 16348 16 - 144309 gggtttcgattgtagt--- -s mr.mrrefChr5 38324 19 + 294540 gggttttttttacagagat -s simHuman_chr6.simHuman.chr6 448784 16 - 601863 gggtttcgattgtagt--- -s simRat_chr6.simRat.chr6 173377 19 + 647215 gggttttttttacagagag - -a -s simMouse_chr6.simMouse.chr6 183149 60 + 636262 tcatcaaacttattagatctgtacatttaatttgcagaacaatatgttaatgtgtgtagg -s Anc1.Anc1refChr2 16364 30 - 144309 --------cttgttaggcctg------------ggag----------taactagtgtagg -s mr.mrrefChr5 38343 60 + 294540 tcatcaaacttattagatctgtacatttaatttgcagaacaatatgttaatgtgtgtagg -s simHuman_chr6.simHuman.chr6 448800 30 - 601863 --------cttgttaggcctg------------ggag----------taactagtgtagg -s simRat_chr6.simRat.chr6 173406 60 + 647215 taatcaaaggtattagatctgtacattttatttgcagaacaatatgtttatgtgcatggg - -a -s simMouse_chr6.simMouse.chr6 183209 23 + 636262 tttagcatcttcaggttgaaaac -s Anc1.Anc1refChr2 16394 22 - 144309 tatagcatctttgag-tctaagc -s mr.mrrefChr5 38403 22 + 294540 tttagcatcttcagg-tgaaaac -s simHuman_chr6.simHuman.chr6 448832 22 - 601863 tatagcatctttgag-tctaagc -s simRat_chr6.simRat.chr6 173466 22 + 647215 tttaccatcttcagg-tgtaatc - -a -s simMouse_chr6.simMouse.chr6 183232 28 + 636262 attgagcctatagacccatgaacgacta -s Anc1.Anc1refChr2 16416 27 - 144309 attgagcatattgacccatgaac-attt -s mr.mrrefChr5 38425 28 + 294540 attgagcctatagacccatgaacgacta -s simHuman_chr6.simHuman.chr6 448857 27 - 601863 attgagcatattgacccatgaac-attt -s simRat_chr6.simRat.chr6 173488 28 + 647215 attgagcctattgatccatgaactaata - -a -s simMouse_chr6.simMouse.chr6 183260 5 + 636262 aacat -s Anc1.Anc1refChr2 16443 5 - 144309 aacat -s mr.mrrefChr5 38453 5 + 294540 aacat -s simHuman_chr6.simHuman.chr6 448884 5 - 601863 aacat -s simRat_chr6.simRat.chr6 173540 5 + 647215 aacat - -a -s simMouse_chr6.simMouse.chr6 183265 23 + 636262 atataaagtcatatatcttgatc -s Anc1.Anc1refChr2 16448 23 - 144309 atagcagcttatgtatcctgatc -s mr.mrrefChr5 38458 23 + 294540 atataaagtcatatatcttgatc -s simHuman_chr6.simHuman.chr6 448924 23 - 601863 atagcagcttatgtatcctgatc -s simRat_chr6.simRat.chr6 173545 23 + 647215 atataaagttacatatcctgatc - -a -s simMouse_chr6.simMouse.chr6 183288 37 + 636262 gtatgcacttgatgccttgggtaaactggggggttca -s Anc1.Anc1refChr2 16471 36 - 144309 gtaagtccttaatgtcccaagtaagt-agagttccta -s mr.mrrefChr5 38481 36 + 294540 gtatgcacttgatgccttgggtaaac-ggggggttca -s simHuman_chr6.simHuman.chr6 448948 36 - 601863 gtaagtccttaatgtcccaagtaagt-agagttccta -s simRat_chr6.simRat.chr6 173568 36 + 647215 atatgtacttgatgtcttgggtaaac-ggggggttca - -a -s simMouse_chr6.simMouse.chr6 183325 52 + 636262 ttcatctggaatcaatgggaatcaatggtcagaggttactacactAGGCTCT -s Anc0.Anc0refChr1 14095 2 + 62388 --------------------------------------------------at -s Anc1.Anc1refChr2 16507 42 - 144309 ttggttt----------gttgtcaataatcagaggtgactcactcatgctat -s Anc2.Anc2refChr3 15289 2 - 53186 --------------------------------------------------AA -s mr.mrrefChr5 38517 42 + 294540 ttcatct----------ggaatcaatggtcagaggttactacactaggctct -s simCow_chr6.simCow.chr6 436281 2 - 602619 --------------------------------------------------AA -s simDog_chr6.simDog.chr6 144499 2 + 593897 --------------------------------------------------AA -s simHuman_chr6.simHuman.chr6 448989 42 - 601863 ttggttt----------gttgtcaataatcagaggtgactcactcatgctat -s simRat_chr6.simRat.chr6 173604 42 + 647215 ttcatct----------ggaatcttctgtcagaggttactacactaggctcc - -a -s simMouse_chr6.simMouse.chr6 183377 18 + 636262 CGATTGGGCTTGCCTGGG -s Anc0.Anc0refChr1 14098 11 + 62388 cagttag-------CAGG -s Anc1.Anc1refChr2 16550 11 - 144309 cagttag-------CAGG -s Anc2.Anc2refChr3 15292 11 - 53186 CAGCTAG-------CAGG -s mr.mrrefChr5 38559 18 + 294540 cgattgggctTGCCTGGG -s simCow_chr6.simCow.chr6 436284 11 - 602619 AAGCTAT-------CGCA -s simDog_chr6.simDog.chr6 144502 11 + 593897 CAGCTAG-------CAGG -s simHuman_chr6.simHuman.chr6 449033 11 - 601863 cagttag-------cagg -s simRat_chr6.simRat.chr6 173646 18 + 647215 tgattggtctTGCCCATT - -a -s simMouse_chr6.simMouse.chr6 183395 22 + 636262 TGAAAGACTAAAGGAGACCTCA -s Anc0.Anc0refChr1 14109 16 + 62388 TAATA-ACTG-----GCCCTGC -s Anc1.Anc1refChr2 16561 16 - 144309 TAATA-ACTG-----GCCCTGC -s Anc2.Anc2refChr3 15303 16 - 53186 TATTA-ATTG-----GCCCTGC -s mr.mrrefChr5 38577 22 + 294540 TGAAAGACTAAAGGAGACCTCA -s simCow_chr6.simCow.chr6 436295 16 - 602619 AATAC-ATTC-----CTTCTGT -s simDog_chr6.simDog.chr6 144517 16 + 593897 TATTA-GTAG-----GCCCTGC -s simHuman_chr6.simHuman.chr6 449044 16 - 601863 tAAGA-ACTG-----GCCCTGC -s simRat_chr6.simRat.chr6 173664 22 + 647215 TGGAGGACTAAAGGAAATCTCA - -a -s simMouse_chr6.simMouse.chr6 183417 63 + 636262 GAACTTGTGCTTTGACGTTGTACCTGCAGAAGCGGATTGATTAGAGTTCCAAAATCCAAGCAG -s Anc0.Anc0refChr1 14125 50 + 62388 AATATTGAACCTGTA----GGAGTTG-A-------ATT-ATCGAGATTCCAAGGCCCAAGCTG -s Anc1.Anc1refChr2 16577 50 - 144309 AATATTGAACCTGTA----GGAGTTG-A-------ATT-ATCGAGATTCCAAGGCCCAAGCTG -s Anc2.Anc2refChr3 15319 50 - 53186 AATATTCAACCTGTA----GGAGTTA-A-------ATT-ATCGAGATTGCAAGGCCCAAGCTG -s mr.mrrefChr5 38599 52 + 294540 GAACTTGTGCTTTGA----GTACCTGCA-------ATTGATTAGAGTTCCAAAATCCAAGCAG -s simCow_chr6.simCow.chr6 436312 50 - 602619 AATTTTTAACCAGTA----GGAGGTA-A-------ATT-ATCAATATTGTAAGGCTCAAGCTG -s simDog_chr6.simDog.chr6 144533 50 + 593897 AGTATTCACCCTGTA----AGAGTTA-T-------GTT-GTTGAGATTGCAAGGCCCAAGCTG -s simHuman_chr6.simHuman.chr6 449060 50 - 601863 AATATTGAACATGCA----GGAGTTG-A-------ATT-ATCGAGATTCCAAGGCCCAGAAGG -s simRat_chr6.simRat.chr6 173686 52 + 647215 GAACTAGTGCTGTGA----GTACCCGCA-------ATTAATTAGGGTTCCAAGATCCAAGCAG - -a -s simMouse_chr6.simMouse.chr6 183480 32 + 636262 GCATCTGCTTGATTTATCTATAGTTACTGAGT -s Anc0.Anc0refChr1 14178 27 + 62388 --ATTTGCTTGATTTAT---TAGTTACCTAGT -s Anc1.Anc1refChr2 16632 29 - 144309 GCATTTGCTTGATTTAT---TAGTTACCTAGT -s Anc2.Anc2refChr3 15372 27 - 53186 --ATTTACTTGATTCAT---ATAGTAACTGAT -s mr.mrrefChr5 38651 32 + 294540 GCATCTGCTTGATTTATCTATAGTTACTGAGT -s simCow_chr6.simCow.chr6 436363 27 - 602619 --ATTTACTTGATTCAT---ACAGTTACTGAT -s simDog_chr6.simDog.chr6 144586 21 + 593897 --------CTTATCCAT---ATAGTAACTGAT -s simHuman_chr6.simHuman.chr6 449115 29 - 601863 GCATTTGCTTGGTTTAT---TAGTTACCTAGT -s simRat_chr6.simRat.chr6 173738 32 + 647215 GCCTTTGCTTGATTTATCTATAGATACCAAGT - -a -s simMouse_chr6.simMouse.chr6 183512 2 + 636262 AG -s Anc0.Anc0refChr1 14206 2 + 62388 AC -s Anc1.Anc1refChr2 16662 2 - 144309 AC -s Anc2.Anc2refChr3 15400 2 - 53186 AC -s mr.mrrefChr5 38683 2 + 294540 AG -s simCow_chr6.simCow.chr6 436391 2 - 602619 AC -s simDog_chr6.simDog.chr6 144608 2 + 593897 AC -s simHuman_chr6.simHuman.chr6 449145 2 - 601863 AC -s simRat_chr6.simRat.chr6 173770 2 + 647215 AG - -a -s simMouse_chr6.simMouse.chr6 183514 41 + 636262 TGTGCTATGAACACAATTGATCAACTCAAGGGCATGTAATG -s Anc0.Anc0refChr1 14208 7 + 62388 TGT----TGAA------------------------------ -s Anc1.Anc1refChr2 16664 7 - 144309 TGT----TGAA------------------------------ -s Anc2.Anc2refChr3 15402 7 - 53186 TGT----TGAT------------------------------ -s mr.mrrefChr5 38685 41 + 294540 TGTGCTATGAACACAATTGATCAACTCAAGGGCATGTAATG -s simCow_chr6.simCow.chr6 436393 7 - 602619 TAT----TGAT------------------------------ -s simDog_chr6.simDog.chr6 144610 7 + 593897 TGT----TGAT------------------------------ -s simHuman_chr6.simHuman.chr6 449147 7 - 601863 TGT----TGAA------------------------------ -s simRat_chr6.simRat.chr6 173773 41 + 647215 TCCAGAATGAACACAACTAATCAACTCAATGGTATGTAATG - -a -s simMouse_chr6.simMouse.chr6 183555 36 + 636262 TTTGGGGCCCATGTTCAGCATTCTATACGCAGACTG -s Anc0.Anc0refChr1 14215 12 + 62388 ------------------------ATACAAAGATTG -s Anc1.Anc1refChr2 16671 12 - 144309 ------------------------ATACAAAGATTG -s Anc2.Anc2refChr3 15409 12 - 53186 ------------------------ATACAAAGATTG -s mr.mrrefChr5 38726 36 + 294540 TTTGGGGCCCATGTTCAGCATTCTATACGCAGACTG -s simCow_chr6.simCow.chr6 436400 8 - 602619 ------------------------ATACAAAA---- -s simDog_chr6.simDog.chr6 144617 12 + 593897 ------------------------ATACAAAGATTG -s simHuman_chr6.simHuman.chr6 449154 12 - 601863 ------------------------AGACAAAGCTTG -s simRat_chr6.simRat.chr6 173815 36 + 647215 TTTAGGACCCATGTTCAGCAGTCCATACGCAGACTG - -a -s simMouse_chr6.simMouse.chr6 183591 40 + 636262 AACTTCCACTGCTCCAAAATCCATGCTATGATAACTATCT -s Anc0.Anc0refChr1 14227 38 + 62388 GGCTTCCACTG-TACAAGCTTCATGCTTT-ACTAATAGCC -s Anc1.Anc1refChr2 16683 39 - 144309 GGCTTCCACTG-TACAAGCTTCATGCTTTGACTAATAGCC -s Anc2.Anc2refChr3 15421 38 - 53186 GGCTTCCACTG-TATAAGCTTCATGCTTT-CCTGATAGTC -s mr.mrrefChr5 38762 40 + 294540 AACTTCCACTGCTCCAAAATCCATGCTATGATAACTATCT -s simCow_chr6.simCow.chr6 436408 23 - 602619 GGTGTCCACTA-TA-AAACTTCATG--------------- -s simDog_chr6.simDog.chr6 144629 38 + 593897 GGCTTGCACTG-TATGAGATTGATGCTTT-CCTGATAGTC -s simHuman_chr6.simHuman.chr6 449166 39 - 601863 GGCTTCCACTG-TACAAGCTTCATGTTTTGACCAATGCCC -s simRat_chr6.simRat.chr6 173861 40 + 647215 AACTTCCACTGGTCCATGCTCCATGCTTTGATAACTATGT - -a -s simMouse_chr6.simMouse.chr6 183631 12 + 636262 TCTTAGCTTGGA -s Anc0.Anc0refChr1 14267 12 + 62388 TAGTAGCTACGA -s Anc1.Anc1refChr2 16724 12 - 144309 TAGTAGCTACGA -s Anc2.Anc2refChr3 15461 12 - 53186 TAGTAGCTACGA -s mr.mrrefChr5 38802 12 + 294540 TCTTAGCTTGGA -s simDog_chr6.simDog.chr6 144669 12 + 593897 TAGTAGCTACGA -s simHuman_chr6.simHuman.chr6 449207 12 - 601863 TAGTAACTATAA -s simRat_chr6.simRat.chr6 173901 12 + 647215 TCTTGGCTAGGA - -a -s simMouse_chr6.simMouse.chr6 183643 14 + 636262 AAACTACATCAATT -s Anc0.Anc0refChr1 14281 10 + 62388 AAACTTC----ATT -s Anc1.Anc1refChr2 16738 10 - 144309 AAACTTC----ATT -s Anc2.Anc2refChr3 15475 10 - 53186 AACCTTC----ACT -s mr.mrrefChr5 38814 10 + 294540 AAACTAC----ATT -s simDog_chr6.simDog.chr6 144683 10 + 593897 AACCTTC----ACT -s simHuman_chr6.simHuman.chr6 449221 10 - 601863 ATACTGC----ATT -s simRat_chr6.simRat.chr6 173913 10 + 647215 GAACTAC----ATT - -a -s simMouse_chr6.simMouse.chr6 183657 18 + 636262 CAGATATCTAAAGTCAGC -s Anc0.Anc0refChr1 14294 18 + 62388 TAGATGTCTAAAGTCAAT -s Anc1.Anc1refChr2 16751 18 - 144309 TAGATGTCTAAAGTCAAT -s Anc2.Anc2refChr3 15488 18 - 53186 TATACGCCTAAAGTCAAT -s mr.mrrefChr5 38824 18 + 294540 CAGATATCTAAAGTCAGC -s simCow_chr6.simCow.chr6 436431 9 - 602619 ---------AAAGTCAAT -s simDog_chr6.simDog.chr6 144696 18 + 593897 TATACGCCTAAAGTCAAT -s simHuman_chr6.simHuman.chr6 449235 18 - 601863 TAGATGTCCAAAGTCAAA -s simRat_chr6.simRat.chr6 173923 18 + 647215 CAGATATCTAAAGTCAGC - -a -s simMouse_chr6.simMouse.chr6 183675 30 + 636262 ACCTATTGATAATGTACTAACTTCAAGGAT -s Anc0.Anc0refChr1 14312 29 + 62388 CCCTATCAATGATGTACTCACTCCAAG-AT -s Anc1.Anc1refChr2 16769 29 - 144309 CCCTATCAATGATGTACTCACTCCAAG-AT -s Anc2.Anc2refChr3 15506 29 - 53186 CCCTATCAATGGTGTACTCACTCCAAG-AT -s mr.mrrefChr5 38842 29 + 294540 ACCTATTGATAATGTACTAACTTCAAG-AT -s simCow_chr6.simCow.chr6 436442 29 - 602619 CCCTATTGATTGTGTAGTCACTCCAAG-AT -s simDog_chr6.simDog.chr6 144714 29 + 593897 CCCTTCCAATGGTGTACTCACTCCTGG-TT -s simHuman_chr6.simHuman.chr6 449253 24 - 601863 CCCTAT-----ATGTGCTCAGTACAAA-AT -s simRat_chr6.simRat.chr6 173941 29 + 647215 ACTTATTGATCATGCACTAACTTCAAG-AT - -a -s simMouse_chr6.simMouse.chr6 183705 26 + 636262 CATGTACTAACTTCAAAGTATTGAGT -s Anc0.Anc0refChr1 14342 6 + 62388 CATG--------------------GT -s Anc1.Anc1refChr2 16799 6 - 144309 CATG--------------------GT -s Anc2.Anc2refChr3 15536 6 - 53186 CATT--------------------GT -s mr.mrrefChr5 38871 26 + 294540 CATGTACTAACTTCAAAGTACTGAGT -s simCow_chr6.simCow.chr6 436472 6 - 602619 CGTT--------------------GT -s simDog_chr6.simDog.chr6 144744 6 + 593897 CATT--------------------GC -s simHuman_chr6.simHuman.chr6 449278 6 - 601863 TATG--------------------GT -s simRat_chr6.simRat.chr6 173970 26 + 647215 CACATGCTAACTTCGAAGTACTGAGT - -a -s simMouse_chr6.simMouse.chr6 183731 15 + 636262 GGTCCCCAGAAGGGT -s Anc0.Anc0refChr1 14348 14 + 62388 GATCCCTTGAA-GGT -s Anc1.Anc1refChr2 16805 15 - 144309 GATCCCTTGAAGGGT -s Anc2.Anc2refChr3 15542 14 - 53186 GATCCCTTGAA-GGT -s mr.mrrefChr5 38897 15 + 294540 GGTCCCCAGAAGGGT -s simCow_chr6.simCow.chr6 436478 14 - 602619 GAACCTTTGAA-GGT -s simDog_chr6.simDog.chr6 144750 14 + 593897 GGTCCCTTGAA-TGT -s simHuman_chr6.simHuman.chr6 449285 15 - 601863 CATCCCATGAAGGGT -s simRat_chr6.simRat.chr6 173996 15 + 647215 GGTTCCCAGAAGGGT - -a -s simMouse_chr6.simMouse.chr6 183746 84 + 636262 TGTTCCTTCCACTAAGAGCTCTTATAATAAGTAGTGTGCCCATAGTGGTAAGGGAATGTATTACATTTCAGTCCTTGCGGCATA -s Anc0.Anc0refChr1 14365 84 + 62388 TGTTCCTTCTCCTATGAGTTCTTGCAACAAGTAGCACATCCATAGTTGTTGGAGAATGGACTACACTCCACTTCTTCCCGCAGT -s Anc1.Anc1refChr2 16823 84 - 144309 TGTTCCTTCTCCTATGAGTTCTTGCAACAAGTAGCACATCCATAGTTGTTGGAGAATGGACTACACTCCACTTCTTCCCGCAGT -s Anc2.Anc2refChr3 15559 84 - 53186 TGGTCCTTCTCCTATGAGTTCTTGCAACAAGTAGCACATACATAGTTGTTGGATAATGGACTACACCCCACTTCTTCCCGCAGT -s mr.mrrefChr5 38915 84 + 294540 TGTTCCTTCTACTAAGAGCTCTTGTAATAAGTAGTGTATCCATAGTGGTAAGGGAATGTATTACATTCCAGTCCTTCCGGCATT -s simCow_chr6.simCow.chr6 436494 84 - 602619 TGGTCCTTCTCCAATGAGCTCTTGCCACAAGTAGCATATACATAGTGGTGAGCTAACGTACTACACCCCATTTCTTCAGGCACT -s simDog_chr6.simDog.chr6 144767 84 + 593897 TGGTCCTTCTCCTACGAGTTCTTGTAACAGATAGCACATACATAGCTGTTGGATAATGGGCTGCAGCCCACCACTTCCCGCAGT -s simHuman_chr6.simHuman.chr6 449303 79 - 601863 TGTTCCCTCACCTATGAGTTCTTGCAACAAGTAGCACACCCATAGTTAGTGAAGAATGAACTACACTTCACTTCTTCC-----C -s simRat_chr6.simRat.chr6 174014 80 + 647215 TGTTCCCTTTACTAAGA---CTTGTAATAAGTGGTCAATCC-TAGTGGTAAGAGAATGTATTACGTTCCACTCCTCCCAGCATT - -a -s simMouse_chr6.simMouse.chr6 183830 7 + 636262 TTGAAAA -s Anc0.Anc0refChr1 14449 7 + 62388 CTGCAGA -s Anc1.Anc1refChr2 16907 7 - 144309 CTGCAGA -s Anc2.Anc2refChr3 15652 7 - 53186 CTGCAGA -s mr.mrrefChr5 38999 7 + 294540 TTGAAAA -s simCow_chr6.simCow.chr6 436587 7 - 602619 CTGCAAA -s simDog_chr6.simDog.chr6 144860 7 + 593897 TTGCAGG -s simHuman_chr6.simHuman.chr6 449382 7 - 601863 CTGCACA -s simRat_chr6.simRat.chr6 174094 7 + 647215 TTGAAAA - -a -s simMouse_chr6.simMouse.chr6 183837 35 + 636262 CAATTTCAGATGGGTATAACTGCAAGCAAGCCTAT -s Anc0.Anc0refChr1 14456 35 + 62388 TAATTTTGGATGAGAATGACTGCAAGCAATGCTAT -s Anc1.Anc1refChr2 16914 35 - 144309 TAATTTTGGATGAGAATGACTGCAAGCAATGCTAT -s Anc2.Anc2refChr3 15659 35 - 53186 TTATTTTGGATGAGAATGACTACAAGCAATGCTAT -s mr.mrrefChr5 39006 35 + 294540 CAATTTTAGATGGGTATAACTGCAAGCAAACCTAT -s simCow_chr6.simCow.chr6 436594 34 - 602619 TTATTTTGGATGGGACTGTCTACAAGCTAT-CTAT -s simDog_chr6.simDog.chr6 144867 35 + 593897 CTAATTTGGATCAGAATGACCACTAGTAATGCTAT -s simHuman_chr6.simHuman.chr6 449389 35 - 601863 TAATTTTGGATGAGAATGACTGCAAGCAATTCTAT -s simRat_chr6.simRat.chr6 174102 35 + 647215 CAATTTTATATGGGTATAACTGCCAGCAAACCTAT - -a -s simMouse_chr6.simMouse.chr6 183872 187 + 636262 AGCCCCCTAGAAACTATAAACCATTTGATCAGCCATCCACTGGCACTTGAGCTGACTGAACCATAACTTTATTCATTAATCACATACTATTATCTACATATTTATTTAAGTATTATAACCACTCTACTCTCAAAAGCCATCCTCCTTGCTAACAGTGAGGTAGCAACAATCAGGCCACTAGATGGAG -s Anc0.Anc0refChr1 14491 126 + 62388 ATCTCGCTAAAAATTAC---CCAGTTGAACTGCCATCCACAGGCACTTCAGTTGTCTGAATGATAGATTCATTC--------------------------TTTATTTAAGTACTAT---TACTCTGCTCACAA--------CTCC--TCTAA----------------ATTGGCACTCTAG---GAA -s Anc1.Anc1refChr2 16949 127 - 144309 ATCTCGCTAAAAATTACT--CCAGTTGAACTGCCATCCACAGGCACTTCAGTTGTCTGAATGATAGATTCATTC--------------------------TTTATTTAAGTACTAT---TACTCTGCTCACAA--------CTCC--TCTAA----------------ATTGGCACTCTAG---GAA -s Anc2.Anc2refChr3 15694 126 - 53186 ATTTTGCTAAAAATTAC---CTAGTTGAACTGCCATACACAGACAAGTCAGTAGTCTGAATGACAGATTCATTC--------------------------TTTATTTAAGTACTAT---TACTTTGTTCACAA--------CCCC--TTTAA----------------ATTGGCACTCTAG---GAA -s mr.mrrefChr5 39041 187 + 294540 ATCCCCCTAGAAACTATAAACCATTTGATCAGCCATCCACTGGCACTTGAGCTGACTGAACCATAACTTTATTCATTAATCACATACTATTATCTACATATTTATTTAAGTATTATAACCACTCTACTCTCAAAAGCCATCCTCCTTGCTAACAGTGAGGTAGCAACAATCAGGCCACTAGATGGAG -s simCow_chr6.simCow.chr6 436628 100 - 602619 ATTTTGCTAAAAATCTC---C--------------------GACATATCAGTGGTTTCAATGAGAGATTCATTC--------------------------TTTATTTGAGGACTAT---T------TGTACAA--------CCCC--TTAAT----------------ATTCGCACTCTAG---GAA -s simDog_chr6.simDog.chr6 144957 126 + 593897 ATTTTGCTAGAAATTAC---CTAGTTGAACTGCCATACACATACAAGTCAGTAGTCTGAATGACAGCTTCATTC--------------------------TTTATTTAAGTAACAT---TACTTTGTTCACAA--------CCCC--TTTAA----------------AGTGGTACTTTAG---GAA -s simHuman_chr6.simHuman.chr6 449424 127 - 601863 ATCTCTCTAAAAATTACT--CCAGTTGAACTGGTGTCCACAGGCACTCCAGTTGTCTGAATGATGGATTCATTC--------------------------TTTATGTAAGCACTAT---TACTCTCCTCACAA--------CTCC--ACTAG----------------ATTGGCAATCTAG---GAA -s simRat_chr6.simRat.chr6 174137 187 + 647215 ATCACTCTAGAAACTATAAACCAGCTGATCAGCCACCCACTTGCACTTGAGCTGACTGAACCGTTGAGTTATCCAATAATCACAAACTATTGTCTACACATTTATTTAAGTACTATCACCACTCTGTTCTCAAAAGCCGTGATCCTTGCTAACAGTGTGGCAGCAAAAATCAGGTCACTTGAGGGGG - -a -s simMouse_chr6.simMouse.chr6 184059 45 + 636262 TTGTGTTTGTGCTTTTCCCGACTGGACCCCTGAATCTCAGAAGCA -s Anc0.Anc0refChr1 14617 22 + 62388 ATAAGTACTTACTTATCTCAAG----------------------- -s Anc1.Anc1refChr2 17076 22 - 144309 ATAAGTACTTACTTATCTCAAG----------------------- -s Anc2.Anc2refChr3 15820 22 - 53186 ATAAGTACTTACTTATCTCAAG----------------------- -s mr.mrrefChr5 39228 44 + 294540 TTGTGTTTGTGCTTTTCCCGACTGG-CCCCTGAATCTCAGAAGCA -s simCow_chr6.simCow.chr6 436728 21 - 602619 ATAAGTA-TTACTTAACTCGAG----------------------- -s simDog_chr6.simDog.chr6 145083 22 + 593897 ATAAGTACTTATTTATCTGAAG----------------------- -s simHuman_chr6.simHuman.chr6 449551 22 - 601863 GTAAGCACTTACTTATCTCAAG----------------------- -s simRat_chr6.simRat.chr6 174325 44 + 647215 TTATGTTCTTGCTTATCCTGACCAG-CCCATGAACCTCACAGACA - -a -s simMouse_chr6.simMouse.chr6 184104 11 + 636262 ATCTGCCAGGT -s Anc0.Anc0refChr1 14639 5 + 62388 ------TATGC -s Anc1.Anc1refChr2 17098 5 - 144309 ------TATGC -s Anc2.Anc2refChr3 15842 5 - 53186 ------TATGC -s mr.mrrefChr5 39272 11 + 294540 ATCTGCCAGGT -s simCow_chr6.simCow.chr6 436749 5 - 602619 ------TATGC -s simDog_chr6.simDog.chr6 145105 5 + 593897 ------TATTC -s simHuman_chr6.simHuman.chr6 449573 5 - 601863 ------TAAGC -s simRat_chr6.simRat.chr6 174371 11 + 647215 ACCTGCTGGGT - -a -s simMouse_chr6.simMouse.chr6 184115 42 + 636262 TGGCCTGGAACTATCTATTGCATAGGAATAATATAGGTCTTC -s Anc0.Anc0refChr1 47148 42 - 62388 GCAGTTGTAACTATCTGTTGCATAGAAATACTGTAAGGCTTC -s Anc1.Anc1refChr2 126593 42 + 144309 GCAGTTGTAACTATCTGTTGCATAGAAATACTGTAAGGCTTC -s Anc2.Anc2refChr3 36728 42 + 53186 GCAGTTGTAACTACCTGTTACACAGAACTACTGTAAAGCTTC -s mr.mrrefChr5 254668 42 - 294540 TCGCTTGTAACTATCTATTGCATAGGAATAATATAGGTCTTC -s simCow_chr6.simCow.chr6 165146 42 + 602619 GCAGTTGTAACTACCTGTTACACAGAACTACTGTAAAGGATC -s simDog_chr6.simDog.chr6 448361 39 - 593897 GCAATTATAACTACCTGTTAAACAG---TACTGTAAAGCTTC -s simHuman_chr6.simHuman.chr6 151624 42 + 601863 GCAGTTGTAATTTTCTGTTGCATAGAAATCTTGTAAGCCTTC -s simRat_chr6.simRat.chr6 472222 42 - 647215 TCGCTTGTAACTATCTATTGCACAGGGATAATAGAGGTCTTC - -a -s simMouse_chr6.simMouse.chr6 184157 17 + 636262 AACTACCTAGGGTTTTC -s Anc0.Anc0refChr1 47191 17 - 62388 AACTACCTAGGGATATC -s Anc1.Anc1refChr2 126636 17 + 144309 AACTACCTAGGGATATC -s Anc2.Anc2refChr3 36771 17 + 53186 AACTCCCTAGAGATATC -s mr.mrrefChr5 254710 17 - 294540 AACTACCTAGGGTTATC -s simCow_chr6.simCow.chr6 165189 17 + 602619 AACTCCCTAGAGATATT -s simDog_chr6.simDog.chr6 448401 17 - 593897 AGCTCCATAGAGACATC -s simHuman_chr6.simHuman.chr6 151667 17 + 601863 AACTACCTATGGATATC -s simRat_chr6.simRat.chr6 472264 17 - 647215 CCCTGCCTACAGGTATC - -a -s simMouse_chr6.simMouse.chr6 184174 5 + 636262 ATGTG -s Anc0.Anc0refChr1 47208 5 - 62388 ATGTG -s Anc1.Anc1refChr2 126653 5 + 144309 ATGTG -s Anc2.Anc2refChr3 36793 5 + 53186 ATGTG -s mr.mrrefChr5 254727 5 - 294540 ATGTG -s simCow_chr6.simCow.chr6 165211 5 + 602619 ATGTG -s simDog_chr6.simDog.chr6 448423 5 - 593897 ACATG -s simHuman_chr6.simHuman.chr6 151684 5 + 601863 ATGTG -s simRat_chr6.simRat.chr6 472281 5 - 647215 ATGTA - -a -s simMouse_chr6.simMouse.chr6 184179 75 + 636262 AAGGCCAAGCCTTGTCAAATGTTCCGTATTGATGGTACTAACGTACCCGACTGTAGGTTGAGACGATATCACACC -s Anc0.Anc0refChr1 47219 62 - 62388 AGGACCAAGCCTTG-------------ATTGATACCACTAATCTACCTGCCTGGATGTTGAGAGACTGTTACACC -s Anc1.Anc1refChr2 126664 75 + 144309 AGGACCAAGCCTTGTAAGATTCTCCATATTGATACCACTAATCTACCTGCCTGGATGTTGAGAGACTGTTACACC -s Anc2.Anc2refChr3 36804 62 + 53186 AGGACCAAACCTTG-------------ATTGACACCACTAATCTACCTGCCTGGATGTTAAGAGACTGTTACACT -s mr.mrrefChr5 254732 75 - 294540 AAGGCCAAGCCTTGTCAAATGTTCCATATTGATACTACTAACGTACCCGACTGTAGGTTGAGACGATATTACACC -s simCow_chr6.simCow.chr6 165222 62 + 602619 AGGACCAAATTTTG-------------ATTGACACCGCTAATTTTCCTGCCTGGAGGTTGAGAGAGGGTTACCCT -s simDog_chr6.simDog.chr6 448434 62 - 593897 AGAACCAAACCTTG-------------ATTGACACCACTAGTCTACCTGCCTGGATGTTAAGAGACTGTGATAAT -s simHuman_chr6.simHuman.chr6 151695 66 + 601863 AGGACAAAGCCTTGTAAGATTCTCCATATTGATACCACTAAACTGC--------ATGCTGAT-GTTTGTTACACC -s simRat_chr6.simRat.chr6 472286 74 - 647215 AAAGCCAAGCGTTGTCAAATGTTTCATATTGACACTACTTCTGTACCCGACTGTAG-TTGAGACGGTATTACACC - -a -s simMouse_chr6.simMouse.chr6 184254 1 + 636262 T -s Anc0.Anc0refChr1 47289 1 - 62388 T -s Anc1.Anc1refChr2 126747 1 + 144309 T -s Anc2.Anc2refChr3 36874 1 + 53186 T -s mr.mrrefChr5 254807 1 - 294540 T -s simCow_chr6.simCow.chr6 165292 1 + 602619 T -s simDog_chr6.simDog.chr6 448504 1 - 593897 C -s simHuman_chr6.simHuman.chr6 151769 1 + 601863 T -s simRat_chr6.simRat.chr6 472360 1 - 647215 T - -a -s simMouse_chr6.simMouse.chr6 184255 12 + 636262 TAATATGTACCA -s Anc0.Anc0refChr1 47291 12 - 62388 TAATGTCGACCC -s Anc1.Anc1refChr2 126749 12 + 144309 TAATGTCGACCC -s Anc2.Anc2refChr3 36876 12 + 53186 TAATGTCGGCCC -s mr.mrrefChr5 254809 12 - 294540 TAATGTGGACCA -s simCow_chr6.simCow.chr6 165294 12 + 602619 TATGGACCCCCT -s simDog_chr6.simDog.chr6 448506 12 - 593897 TAATGTGGGCAC -s simHuman_chr6.simHuman.chr6 151771 12 + 601863 TAATGTCGACCC -s simRat_chr6.simRat.chr6 472362 12 - 647215 TTATGTGGACCT - -a -s simMouse_chr6.simMouse.chr6 184267 7 + 636262 TTAAACA -s Anc0.Anc0refChr1 47303 6 - 62388 TGAA-CA -s Anc1.Anc1refChr2 126761 6 + 144309 TGAA-CA -s Anc2.Anc2refChr3 36888 6 + 53186 TGAA-CA -s mr.mrrefChr5 254821 6 - 294540 TTAA-CA -s simCow_chr6.simCow.chr6 165306 6 + 602619 TGAA-CA -s simDog_chr6.simDog.chr6 448520 6 - 593897 GAGA-CA -s simHuman_chr6.simHuman.chr6 151783 6 + 601863 TGAA-CA -s simRat_chr6.simRat.chr6 472374 6 - 647215 CTAA-CA - -a -s simMouse_chr6.simMouse.chr6 184274 12 + 636262 CCATATGTCTCA -s Anc0.Anc0refChr1 47313 8 - 62388 CCATATGT---- -s Anc1.Anc1refChr2 126771 12 + 144309 CCATATGTCTCT -s Anc2.Anc2refChr3 36898 8 + 53186 CCATATGT---- -s mr.mrrefChr5 254827 12 - 294540 CCATATGTCTCA -s simCow_chr6.simCow.chr6 165316 8 + 602619 CCAGATGT---- -s simDog_chr6.simDog.chr6 448530 8 - 593897 CAATGTGC---- -s simHuman_chr6.simHuman.chr6 151793 12 + 601863 CCATATGTCTCT -s simRat_chr6.simRat.chr6 472380 12 - 647215 CCATATGTCTCA - -a -s simMouse_chr6.simMouse.chr6 184286 15 + 636262 CCTGACTGATGCCCA -s Anc0.Anc0refChr1 47322 15 - 62388 CCTAACTGGGGTACC -s Anc1.Anc1refChr2 126784 15 + 144309 CCTAACTGGGGTACC -s Anc2.Anc2refChr3 36907 15 + 53186 CAAAACCGGGGTACC -s mr.mrrefChr5 254840 15 - 294540 CCTGACTGATGCACA -s simCow_chr6.simCow.chr6 165325 13 + 602619 C--AACAGGAGTATC -s simDog_chr6.simDog.chr6 448539 15 - 593897 CAAAACCATGGTACC -s simHuman_chr6.simHuman.chr6 151806 15 + 601863 CCTAACTGGGGTACC -s simRat_chr6.simRat.chr6 472393 15 - 647215 CCTGACAGATGCATG - -a -s simMouse_chr6.simMouse.chr6 184301 11 + 636262 TCTCCCCAGCA -s Anc0.Anc0refChr1 47337 11 - 62388 GATACTTGGTG -s Anc1.Anc1refChr2 126799 11 + 144309 GATACTTGGTG -s Anc2.Anc2refChr3 36922 11 + 53186 GATACTTGGTG -s mr.mrrefChr5 254855 11 - 294540 TATCCCCAGCA -s simCow_chr6.simCow.chr6 165338 11 + 602619 TATACTTGGTG -s simDog_chr6.simDog.chr6 448554 11 - 593897 GATATGTGGCG -s simHuman_chr6.simHuman.chr6 151822 11 + 601863 AATACTTGGTG -s simRat_chr6.simRat.chr6 472408 11 - 647215 TATCACGAGCA - -a -s simMouse_chr6.simMouse.chr6 184312 16 + 636262 CCAGAAAATGGGTACT -s Anc0.Anc0refChr1 47348 16 - 62388 CCTGATGGTGGTCACA -s Anc1.Anc1refChr2 126810 16 + 144309 CCTGATGGTGGTCACA -s Anc2.Anc2refChr3 36933 16 + 53186 TCTAATGGCAGTCATA -s mr.mrrefChr5 254866 16 - 294540 CCTGAAAGTGGGTACT -s simCow_chr6.simCow.chr6 165352 16 + 602619 TCTAATGAAAGTCATA -s simDog_chr6.simDog.chr6 448565 11 - 593897 TATAATGGCAT----- -s simHuman_chr6.simHuman.chr6 151833 16 + 601863 CCTGATGGTGGTCACA -s simRat_chr6.simRat.chr6 472419 16 - 647215 CCTGAAAGTGGCTACT - -a -s simMouse_chr6.simMouse.chr6 184328 27 + 636262 GTTGTGAACATGTTCACGTATGCCAAT -s Anc0.Anc0refChr1 47364 27 - 62388 GTTGTGAACATGTTTACTCATGCCAAT -s Anc1.Anc1refChr2 126826 27 + 144309 GTTGTGAACATGTTTACTCATGCCAAT -s Anc2.Anc2refChr3 36949 27 + 53186 GTTGTGAACATGTTTACTCATGCCAAG -s mr.mrrefChr5 254882 27 - 294540 GTTGTGAACATGTTCACGTATGCCAAT -s simCow_chr6.simCow.chr6 165370 27 + 602619 ATTGTGAACATGTTTATTCATGCCAAG -s simDog_chr6.simDog.chr6 448576 27 - 593897 GTTGTGAACATGTTTACTCATACCAAG -s simHuman_chr6.simHuman.chr6 151849 27 + 601863 GGTGTGGATAGGTCTGCTCATGCCGAT -s simRat_chr6.simRat.chr6 472435 27 - 647215 GTCGTGAACATGCTCATGTATGCCAAT - -a -s simMouse_chr6.simMouse.chr6 184355 9 + 636262 TTACTGAGG -s Anc0.Anc0refChr1 47397 9 - 62388 TTACTAATG -s Anc1.Anc1refChr2 126859 9 + 144309 TTACTAATG -s Anc2.Anc2refChr3 36982 9 + 53186 TTACTAATG -s mr.mrrefChr5 254909 9 - 294540 TTACTGAGG -s simCow_chr6.simCow.chr6 165485 9 + 602619 TTGCTAATT -s simDog_chr6.simDog.chr6 448609 9 - 593897 TTACCATTG -s simHuman_chr6.simHuman.chr6 151882 9 + 601863 CTAGTAATG -s simRat_chr6.simRat.chr6 472462 9 - 647215 TTGCTGAGG - -a -s simMouse_chr6.simMouse.chr6 184364 3 + 636262 CAC -s Anc0.Anc0refChr1 47406 3 - 62388 CAC -s Anc1.Anc1refChr2 126868 3 + 144309 CAC -s Anc2.Anc2refChr3 36991 3 + 53186 CAT -s mr.mrrefChr5 254918 3 - 294540 CAC -s simCow_chr6.simCow.chr6 165494 3 + 602619 CAT -s simDog_chr6.simDog.chr6 448618 3 - 593897 CAT -s simHuman_chr6.simHuman.chr6 151891 3 + 601863 CAC -s simRat_chr6.simRat.chr6 472472 3 - 647215 CAC - -a -s simMouse_chr6.simMouse.chr6 184367 40 + 636262 CAGACAGACAAGTCCTGTGATAATTATGTTTTGCCACAGA -s Anc0.Anc0refChr1 47416 18 - 62388 CAGACAGAGAAGTCCTAG---------------------- -s Anc1.Anc1refChr2 126878 18 + 144309 CAGACAGAGAAGTCCTAG---------------------- -s Anc2.Anc2refChr3 37001 18 + 53186 CAGATGGAGAAGTCCTAG---------------------- -s mr.mrrefChr5 254921 39 - 294540 CAGACAGACAAGTCCTGTGATAAT-ATGTTTTGCCACAGA -s simCow_chr6.simCow.chr6 165504 18 + 602619 CAGATGGAGAAGTCCTAG---------------------- -s simHuman_chr6.simHuman.chr6 151902 18 + 601863 CAGACAGGGAAGTTCTAG---------------------- -s simRat_chr6.simRat.chr6 472475 39 - 647215 AACACAGACAAGTCCTGTGCTAAT-ATGTTTTGCAATAGA - -a -s simMouse_chr6.simMouse.chr6 184407 26 + 636262 TTCTGGTTAAGATAGGTGTCACAGCA -s Anc0.Anc0refChr1 47434 2 - 62388 ------------------------GA -s Anc1.Anc1refChr2 126896 2 + 144309 ------------------------GA -s Anc2.Anc2refChr3 37019 2 + 53186 ------------------------GA -s mr.mrrefChr5 254960 26 - 294540 TTCTGGTTAAGATAGGTGTCACAGCA -s simCow_chr6.simCow.chr6 165522 2 + 602619 ------------------------GA -s simHuman_chr6.simHuman.chr6 151920 2 + 601863 ------------------------TA -s simRat_chr6.simRat.chr6 472515 26 - 647215 TTCTGTCTAAGATAGGTGTCACAGCA - -a -s simMouse_chr6.simMouse.chr6 184433 4 + 636262 ATCA -s Anc0.Anc0refChr1 47436 4 - 62388 ATAA -s Anc1.Anc1refChr2 126898 4 + 144309 ATAA -s Anc2.Anc2refChr3 37021 4 + 53186 ATAG -s mr.mrrefChr5 254986 4 - 294540 ATCA -s simCow_chr6.simCow.chr6 165525 4 + 602619 ATAG -s simHuman_chr6.simHuman.chr6 151922 4 + 601863 ATAA -s simRat_chr6.simRat.chr6 472541 4 - 647215 ATGA - -a -s simMouse_chr6.simMouse.chr6 184437 34 + 636262 AGGGGTAGTGTAATAGTTCTGGGCCAAGTTTCTC -s Anc0.Anc0refChr1 47440 31 - 62388 GGGGGTGGTG---TAATTCTAGGCAAAATTTGTC -s Anc1.Anc1refChr2 126902 31 + 144309 GGGGGTGGTG---TAATTCTAGGCAAAATTTGTC -s Anc2.Anc2refChr3 37025 31 + 53186 GGGGATGTTT---TAATTTTAAGCAAAATTTGTC -s mr.mrrefChr5 254990 34 - 294540 AGGGGTAGTGTAATAGTTCTAGGCAAAGTTTCTC -s simCow_chr6.simCow.chr6 165537 31 + 602619 GGGGATGTTT---TAATTTTAAGCAAAATTTGTC -s simHuman_chr6.simHuman.chr6 151926 31 + 601863 GGGGGTTGTG---TATCTCTAGGCAAAATTTGTT -s simRat_chr6.simRat.chr6 472545 34 - 647215 TGGGGAGGTGTAGTAGTTCTAGGCAACGTTTCTC - -a -s simMouse_chr6.simMouse.chr6 184471 8 + 636262 CCCTTCAG -s Anc0.Anc0refChr1 47471 8 - 62388 GTCTTCAG -s Anc1.Anc1refChr2 126933 8 + 144309 GTCTTCAG -s Anc2.Anc2refChr3 37056 8 + 53186 GTCTTTAG -s mr.mrrefChr5 255024 8 - 294540 CCCTTCAG -s simCow_chr6.simCow.chr6 165568 8 + 602619 GTCTTTAG -s simHuman_chr6.simHuman.chr6 151957 8 + 601863 TTCTTCAG -s simRat_chr6.simRat.chr6 472580 8 - 647215 CCCTTCAG - -a -s simMouse_chr6.simMouse.chr6 184479 53 + 636262 CAGCTTCAGCTAGATGGCAATATACATCAGTTCACCTGATTAAATGCGCTGTT -s Anc0.Anc0refChr1 47479 19 - 62388 CTATCTCACGTAGATGGC----------------------------------T -s Anc1.Anc1refChr2 126941 19 + 144309 CTATCTCACGTAGATGGC----------------------------------T -s Anc2.Anc2refChr3 37064 19 + 53186 CTATCTCATGTAGATAGC----------------------------------C -s mr.mrrefChr5 255032 19 - 294540 CAGCTTCACCTAGATGGC----------------------------------T -s simCow_chr6.simCow.chr6 165582 19 + 602619 CTATCTCATGTAGATAGC----------------------------------C -s simHuman_chr6.simHuman.chr6 151965 19 + 601863 CCATCTCACATAGATGGC----------------------------------T -s simRat_chr6.simRat.chr6 472588 19 - 647215 TGGGTCCGCCTAGATGGC----------------------------------T - -a -s simMouse_chr6.simMouse.chr6 184532 3 + 636262 TTG -s Anc0.Anc0refChr1 47568 3 - 62388 CTG -s Anc1.Anc1refChr2 127030 3 + 144309 CTG -s Anc2.Anc2refChr3 37153 3 + 53186 CCG -s mr.mrrefChr5 255051 3 - 294540 TTG -s simCow_chr6.simCow.chr6 165671 3 + 602619 CCG -s simHuman_chr6.simHuman.chr6 152088 3 + 601863 CTT -s simRat_chr6.simRat.chr6 472607 3 - 647215 TTG - -a -s simMouse_chr6.simMouse.chr6 184535 11 + 636262 AACAATGAACT -s Anc0.Anc0refChr1 47571 11 - 62388 AATAACAAGTT -s Anc1.Anc1refChr2 127033 11 + 144309 AATAACAAGTT -s Anc2.Anc2refChr3 37156 11 + 53186 AATAGCAAGTT -s mr.mrrefChr5 255054 11 - 294540 AACAATGAACT -s simCow_chr6.simCow.chr6 165680 11 + 602619 AATAGCAAGTT -s simHuman_chr6.simHuman.chr6 152091 11 + 601863 AATAACAGGTT -s simRat_chr6.simRat.chr6 472610 11 - 647215 AACAATGAAAT - -a -s simMouse_chr6.simMouse.chr6 184546 6 + 636262 CTTATC -s Anc0.Anc0refChr1 47582 6 - 62388 CTTTTC -s Anc1.Anc1refChr2 127044 6 + 144309 CTTTTC -s Anc2.Anc2refChr3 37167 6 + 53186 CTTTTC -s mr.mrrefChr5 255065 6 - 294540 CTTATC -s simCow_chr6.simCow.chr6 165691 6 + 602619 CTTTTC -s simHuman_chr6.simHuman.chr6 152123 6 + 601863 CTATTC -s simRat_chr6.simRat.chr6 472621 6 - 647215 CTCATC - -a -s simMouse_chr6.simMouse.chr6 184552 80 + 636262 ATTCACCATATTGGACGGCAAATCCAGCCAGATCCAAAGCGATAAAGCCATTCTTCTGTATTGCTCACGCCTTGGGCCTA -s Anc0.Anc0refChr1 47592 76 - 62388 ATTCACCATATCAGATGGCAAATCCAGC-AGGTCCACAATGATAAAACAA---GTAGGTATTGCTCATTCCTTGGACCTA -s Anc1.Anc1refChr2 127054 76 + 144309 ATTCACCATATCAGATGGCAAATCCAGC-AGGTCCACAATGATAAAACAA---GTAGGTATTGCTCATTCCTTGGACCTA -s Anc2.Anc2refChr3 37177 76 + 53186 ATTCACCGTATCAGATGGCAAATCCAGC-AAGTCCACAATGATAAAACAA---GTAGGTATTGCTCATTCCTTGGACGTA -s mr.mrrefChr5 255075 79 - 294540 ATTCACCATATCGGATGGCAAATCCAGC-AGGTCCAAAGTGATAAAACAATTCTTCTGTATTGCTCATGCCTTGGGCCTA -s simCow_chr6.simCow.chr6 165701 75 + 602619 ATTCACT-TATCAGATGGCAGATCCACT-AAGTCCAGAATGATAAATCAT---GTAGGTATTGCTCATTCTATAGACTAA -s simDog_chr6.simDog.chr6 448627 74 - 593897 ATTCACCGTATCAGATGGC-AATCCAGC-CAGTCCACAATGACAAAACAA---GTATGT-TTGCTCATTCCTTGGATGTA -s simHuman_chr6.simHuman.chr6 152133 76 + 601863 TTTCATCATAACAGATGGCAAATTCAGC-AGGTCCACAATTATAAAACAA---GTAGGTATTGCCCATCCCTAGGACCTA -s simRat_chr6.simRat.chr6 472631 79 - 647215 ATTTACCATATCGGATGGCAAATCCAGC-AGGTCCAAAGTGATAAAACAATTCATCTGTACTGCTCATTCCTGGGGCATA - -a -s simMouse_chr6.simMouse.chr6 184632 3 + 636262 AGT -s Anc0.Anc0refChr1 47668 3 - 62388 AAT -s Anc1.Anc1refChr2 127130 3 + 144309 AAT -s Anc2.Anc2refChr3 37253 3 + 53186 AAT -s mr.mrrefChr5 255154 3 - 294540 AGT -s simCow_chr6.simCow.chr6 165776 3 + 602619 AAC -s simDog_chr6.simDog.chr6 448701 3 - 593897 AAT -s simHuman_chr6.simHuman.chr6 152209 3 + 601863 AAT -s simRat_chr6.simRat.chr6 472712 3 - 647215 AGT - -a -s simMouse_chr6.simMouse.chr6 184635 3 + 636262 CAT -s Anc0.Anc0refChr1 47671 3 - 62388 CAT -s Anc1.Anc1refChr2 127133 3 + 144309 CAT -s Anc2.Anc2refChr3 37257 3 + 53186 CAT -s mr.mrrefChr5 255157 3 - 294540 CAT -s simCow_chr6.simCow.chr6 165780 3 + 602619 CAT -s simDog_chr6.simDog.chr6 448705 3 - 593897 CAT -s simHuman_chr6.simHuman.chr6 152212 3 + 601863 CGT -s simRat_chr6.simRat.chr6 472715 2 - 647215 -AT - -a -s simMouse_chr6.simMouse.chr6 184638 14 + 636262 ACACCAGTATATAT -s Anc0.Anc0refChr1 47678 7 - 62388 ACTGCAA------- -s Anc1.Anc1refChr2 127140 7 + 144309 ACTGCAA------- -s Anc2.Anc2refChr3 37273 7 + 53186 ATTGCTA------- -s mr.mrrefChr5 255160 14 - 294540 ACACCAATATATAT -s simCow_chr6.simCow.chr6 165799 7 + 602619 ATTGCTC------- -s simDog_chr6.simDog.chr6 448721 7 - 593897 ATTGCTA------- -s simHuman_chr6.simHuman.chr6 152219 7 + 601863 ACTGCAA------- -s simRat_chr6.simRat.chr6 472717 13 - 647215 A-GCCAATAGATAT - -a -s simMouse_chr6.simMouse.chr6 184652 7 + 636262 TTAAGCT -s Anc0.Anc0refChr1 47685 5 - 62388 --ACCCC -s Anc1.Anc1refChr2 127147 5 + 144309 --ACCCC -s Anc2.Anc2refChr3 37280 5 + 53186 --ACCCC -s mr.mrrefChr5 255174 7 - 294540 TTAAGCT -s simCow_chr6.simCow.chr6 165806 5 + 602619 --ACCCT -s simDog_chr6.simDog.chr6 448728 5 - 593897 --ACCCC -s simHuman_chr6.simHuman.chr6 152226 5 + 601863 --ACTCC -s simRat_chr6.simRat.chr6 472732 7 - 647215 TTAAGCC - -a -s simMouse_chr6.simMouse.chr6 184659 93 + 636262 GTGGACCATTACAGGGAGTCCTGCAGGCAGGAAGCCTGTTGGTGAGCCAACACTCTTGTGTCATTGAGATACACAGACAAAAGCGACAAATAA -s Anc0.Anc0refChr1 47690 54 - 62388 GTGGACCTAGACATGGAG-----------------CTGCTGATTGGTTAAC-----TGTCTCAATGATAGACATAA----------------- -s Anc1.Anc1refChr2 127152 54 + 144309 GTGGACCTAGACATGGAG-----------------CTGCTGATTGGTTAAC-----TGTCTCAATGATAGACATAA----------------- -s Anc2.Anc2refChr3 37285 54 + 53186 TTGGAACTAGACATGGAC-----------------CTGCTGATTGGTTAAC-----TGTCTCAATGATAGACATGA----------------- -s mr.mrrefChr5 255181 76 - 294540 GTGGACCATTACAGGGAGTCCTGCAGGCAGGAAGCCTGTTGGTGAGCCAACACTCTTGTGTCATTGAGATACACAG----------------- -s simCow_chr6.simCow.chr6 165811 54 + 602619 TTGAAACCAGACATGGAA-----------------TTGCTGGTTGGTTAAC-----TGTCTCAGTGATAGACCTGA----------------- -s simDog_chr6.simDog.chr6 448733 54 - 593897 TTGGAACTAGACATGGAC-----------------CTGCTGATTGGTTAAC-----TGTTTCAATGACAGACATGA----------------- -s simHuman_chr6.simHuman.chr6 152231 54 + 601863 GCGGGCCTAGACATGGAG-----------------CTGCTGATTGGTTAAC-----TGTCTCAATGGTAGACATAA----------------- -s simRat_chr6.simRat.chr6 472740 76 - 647215 GTGGACCCTTACAGAGAGTCCTGCAGGCAAGAAGCCTATTGGTGAGCCAACACCCTTGTGTTATTGAGGTAGACAG----------------- - -a -s simMouse_chr6.simMouse.chr6 184752 24 + 636262 AGAGAGCTGCCATCTTGTCAAGTC -s Anc0.Anc0refChr1 15240 20 + 62388 AGAGAGGCGTAATCTTACT----T -s Anc1.Anc1refChr2 17716 24 - 144309 AGAGAGGCGTAATCTTACTATCAT -s Anc2.Anc2refChr3 16458 20 - 53186 AGAGAGGCATAATCTTACT----T -s mr.mrrefChr5 39872 24 + 294540 AGAGAGCTGCAATCTTGTCAAGTT -s simCow_chr6.simCow.chr6 437473 20 - 602619 AGAGGGCCATAATCTTACC----T -s simDog_chr6.simDog.chr6 145536 20 + 593897 AGAGAGGCATAATCTTCTT----T -s simHuman_chr6.simHuman.chr6 450239 24 - 601863 AGAGAGTCGTAATCTTACTATCAT -s simRat_chr6.simRat.chr6 174993 24 + 647215 AGAGAGCTGCAATCTTGTCAAATT - -a -s simMouse_chr6.simMouse.chr6 184776 10 + 636262 CCTCTCCTCC -s Anc0.Anc0refChr1 15261 10 + 62388 GCTCCCCTCC -s Anc1.Anc1refChr2 17741 10 - 144309 GCTCCCCTCC -s Anc2.Anc2refChr3 16479 10 - 53186 GCTCCCCTCC -s mr.mrrefChr5 39897 10 + 294540 CCTCTCCTCC -s simCow_chr6.simCow.chr6 437498 10 - 602619 GCCCTCCTCC -s simDog_chr6.simDog.chr6 145557 10 + 593897 GCTTCCCTCC -s simHuman_chr6.simHuman.chr6 450264 10 - 601863 GCTCCCCTCC -s simRat_chr6.simRat.chr6 175018 10 + 647215 CCTCTCCTCC - -a -s simMouse_chr6.simMouse.chr6 184786 70 + 636262 TTCTGTAGCCTTAGAGGTTTGGGACCTCCGTGTTTGACATCTGCTTCTTGAGGCATTTATAAGATAAGGA -s Anc0.Anc0refChr1 15271 49 + 62388 CTCTGTAGTCATAGAGGTA---------------------AGCATCTTAACTGCAATTTTAAAATGAGGA -s Anc1.Anc1refChr2 17751 49 - 144309 CTCTGTAGTCATAGAGGTA---------------------AGCATCTTAACTGCAATTTTAAAATGAGGA -s Anc2.Anc2refChr3 16489 49 - 53186 CTCTCTAGTCATAGAGGTC---------------------AGCATCTTAACTGCAATTTTAAAATGAGGA -s mr.mrrefChr5 39907 49 + 294540 TTCTGTAGTCTTAGAGGTA---------------------CTGCTTCTTGAGGCATTTATAAAATGAGGA -s simCow_chr6.simCow.chr6 437508 49 - 602619 ATCTCTAGTCATAGAGGCC---------------------AGGATCTTAACTGCAATTTTAAAATGTGGA -s simDog_chr6.simDog.chr6 145569 49 + 593897 CTCTCTAGTCATAGAGGTC---------------------GACATCTTAACTGCAATTATAAAATCAGGA -s simHuman_chr6.simHuman.chr6 450274 49 - 601863 CTCTGTAGTCATAGAGGTA---------------------AGAATCTTAACTGCAATTTTAAAACGAGGG -s simRat_chr6.simRat.chr6 175028 49 + 647215 TTCTGTAGTTTTAGAGGTA---------------------CTGCTTCTTGAGGCATTTATAAAATGAGGA - -a -s simMouse_chr6.simMouse.chr6 184856 20 + 636262 GCAGGTCAACTCCAAATGTT -s Anc0.Anc0refChr1 15329 20 + 62388 ACACATCTACTCCCAATAAT -s Anc1.Anc1refChr2 17809 20 - 144309 ACACATCTACTCCCAATAAT -s Anc2.Anc2refChr3 16547 20 - 53186 ACACATCTACTCCCAATAAT -s mr.mrrefChr5 39956 20 + 294540 GCAGGTCTACTCCAAATAAT -s simCow_chr6.simCow.chr6 437566 20 - 602619 ACAGCTCTACTCCTAATAAT -s simDog_chr6.simDog.chr6 145648 20 + 593897 AAACATTGACGCCCATGAAT -s simHuman_chr6.simHuman.chr6 450332 20 - 601863 ACACATCTACTCCCAATAAT -s simRat_chr6.simRat.chr6 175077 20 + 647215 GCAGGTCTACTCCAAATAAT - -a -s simMouse_chr6.simMouse.chr6 184876 17 + 636262 GTATGATGGTAATAATG -s Anc0.Anc0refChr1 15350 17 + 62388 GTGTTATGTCAATGATG -s Anc1.Anc1refChr2 17830 17 - 144309 GTGTTATGTCAATGATG -s Anc2.Anc2refChr3 16568 17 - 53186 ATGTTATGTCAAGAATG -s mr.mrrefChr5 39977 17 + 294540 GTATTATGGTAATGATG -s simCow_chr6.simCow.chr6 437587 17 - 602619 CTGTTATGTCAACAGTG -s simDog_chr6.simDog.chr6 145669 17 + 593897 ATGCTATGTCTGGAATG -s simHuman_chr6.simHuman.chr6 450353 17 - 601863 GTGTTGTGTCAATGATG -s simRat_chr6.simRat.chr6 175098 17 + 647215 GTATTATGGTAATGATG - -a -s simMouse_chr6.simMouse.chr6 184893 157 + 636262 ACTGTTGACATGGGAATGATGGTTGATATGGGAATAGCTAAAATTATGGTACACATATTCCTGAAGAATATATGGATTTATAAATCTAACCGCGCAACACCCAAAGCATATTATATCCCTAGGTTCTACACTCTATGATCTCTTTAGGAGTCTACAA -s Anc0.Anc0refChr1 15367 137 + 62388 ACTGTTG------------------ATATGGGAAAAGGTAAAATTAAGGTGCAAGCCTTCCCAAAGGAAATGTAGATTTATAAATCTAACCCAGCATTGGCCACAGCATATTATATCCCTATATCACTCCC--TATGATCTCTTCATGAGTCTACAA -s Anc1.Anc1refChr2 17847 139 - 144309 ACTGTTG------------------ATATGGGAAAAGGTAAAATTAAGGTGCAAGCCTTCCCAAAGGAAATGTAGATTTATAAATCTAACCCAGCATTGGCCACAGCATATTATATCCCTATATCACTCCCTTTATGATCTCTTCATGAGTCTACAA -s Anc2.Anc2refChr3 16585 137 - 53186 ACTGTTG------------------ATATGGGAGAAGGTAAAATTAAGGTGCAAGCCGTCCCAAAGGAAATGTAGATTTATAGATCTAACCCAGCATTGGCCACAGCATAGTATATCCCTGTATCACTCCA--TATGATCCCTTCATGAGTCTACAA -s mr.mrrefChr5 39994 139 + 294540 ACTGTTG------------------ATATGGGAATAGGTAAAATTATGGTACACATATTCCTGAAGAATATATGGATTTATAAATCTAACCGAGCATTGGCCAAAGCATATTATATCCCTATGTTCTACACTCTATGATCTCTTCAGGAGTCTACAA -s simCow_chr6.simCow.chr6 437604 136 - 602619 GCTGTTG------------------ATGTGGGAGAAGGTAAAAGTCAGGTGTATGCCCTCCCAAAGGACACGTGGATCTATACATCTAACCAAACATTGGACAGAGCACAGTATATCCCTGTATCCCTTCA--TATGA-AACTTTATGAGTCTGTAA -s simDog_chr6.simDog.chr6 145686 136 + 593897 ACTACTA------------------ATATAGGAGAAAGTAAAATTAAGGAGCAAGCTGTCCCAA-GGTAATGTAGATTTAAAGATCTAACCCAGTATTTGCCACAGCATAGTATATCCCTGTATCACTCCA--TATGGTCCCTTCTTGAGTCCACAA -s simHuman_chr6.simHuman.chr6 450371 139 - 601863 ACCGTTG------------------ATATGGGAACAGGTAAAATTAAGGTGCAGGCCTTCCCAAAGGAAAAGTAGGTATTTGAATCTAACCCAGCATTGGCCACAGCATATTATATCCCTATATATATCCCTTTATCATCTTTTCATGTGTCTACAA -s simRat_chr6.simRat.chr6 175115 135 + 647215 ACTGTTG------------------TTATGGGAATAGGTAAAATTATGGTACACCAATTCCTGAAGA-TATATGGTTTAATAGAGCTAACCAAGCATTGGCCAAAACATATTATATCCATATGTC--CCACTCCATGATTT-TTCAGGACTCTACAA - -a -s simMouse_chr6.simMouse.chr6 185050 10 + 636262 GCAGAAAGTT -s Anc0.Anc0refChr1 15504 10 + 62388 GAAGAGAGTT -s Anc1.Anc1refChr2 17986 10 - 144309 GAAGAGAGTT -s Anc2.Anc2refChr3 16722 10 - 53186 GAAGAGAGTT -s mr.mrrefChr5 40133 10 + 294540 GAAGAAAGTT -s simCow_chr6.simCow.chr6 437740 10 - 602619 GAGGAGAGTT -s simDog_chr6.simDog.chr6 145825 10 + 593897 GAAGAGGGTG -s simHuman_chr6.simHuman.chr6 450510 10 - 601863 GAAGAGAGTT -s simRat_chr6.simRat.chr6 175250 10 + 647215 AAAGGAAGTG - -a -s simMouse_chr6.simMouse.chr6 185060 96 + 636262 GTCTTTGCAGATTGACACACAAGAGAAAAAATGTCCACAGGTGAACTGCCAACACATTCTTATCTAATCTCAGAACCTCATAGCCACTCACACTGC -s Anc0.Anc0refChr1 15517 90 + 62388 GTCT------ATTGACACATAAAAGAAAAAGTGTCCACAAGTGAAATGCTATCATATTCCTACCTACTCCTAGAACACCAACATCAATCACATTGC -s Anc1.Anc1refChr2 17999 90 - 144309 GTCT------ATTGACACATAAAAGAAAAAGTGTCCACAAGTGAAATGCTATCATATTCCTACCTACTCCTAGAACACCAACATCAATCACATTGC -s Anc2.Anc2refChr3 16735 90 - 53186 GTCG------ATTGACACACAAAAGAAAAAGTGTCAACAAGTGAAATGCTCTTATATTCCTACCTACTCCTAGAACACCAACATCAGTCACATTGC -s mr.mrrefChr5 40143 96 + 294540 GTCTTTGCAGATTGACACATAAGAGAAAAAATGTCCACAGGTGAACTGCCAACATATTCTTATCTACTCTCAGAACCTCAAAACCAATCACACTGC -s simCow_chr6.simCow.chr6 437753 84 - 602619 AT-G------ATTGACACACAAAAGAAAAAGTGAC--CACATGAAATGCTCTTGTATTCTTAGCTACCCTTAGAACACCAAGATTA---ACATTGC -s simDog_chr6.simDog.chr6 145838 73 + 593897 GCC-----------------------AATGGTGTCAACAAGTGAAGTACTCCTATGTTCCTACCTCCTACTAGAACACCAACATCAGTCCCAGTGC -s simHuman_chr6.simHuman.chr6 450523 90 - 601863 GTCT------GTTAACATGTAAAAGAAAAAGTGGCCGCGAGTACAATGCTATCATATTCCTGCCTACTCCTGGAACACCAACATCAATCACATTGC -s simRat_chr6.simRat.chr6 175260 96 + 647215 GTCTTTGCAAATTGACACATTGGATAAAAACTGTCCTCAGGTGAACTGCCAACATATTCTTATCTACTCTCAGAACTTCAAGACCAATCACACTGC - -a -s simMouse_chr6.simMouse.chr6 185156 27 + 636262 TATTCATAGGTTTTGAATACATTTTAG -s Anc0.Anc0refChr1 15623 26 + 62388 CATCCATAGAA-TTGAATACTTTTTAG -s Anc1.Anc1refChr2 18105 27 - 144309 CATCCATAGAATTTGAATACTTTTTAG -s Anc2.Anc2refChr3 16841 26 - 53186 CATCCATAGAA-TTGGGTACTTTTTAG -s mr.mrrefChr5 40239 27 + 294540 TATCCATAGGATTTGAATACATTTTAG -s simCow_chr6.simCow.chr6 437853 24 - 602619 CATCCATAGAA-TTGGGTCCATTTT-- -s simDog_chr6.simDog.chr6 145927 26 + 593897 CATCTATAGAG-TTGGGAACTTTCTAG -s simHuman_chr6.simHuman.chr6 450632 27 - 601863 CATCCATAGAATTTTAATACCTTTTAG -s simRat_chr6.simRat.chr6 175356 27 + 647215 TAACCATTGGATTTGAACACATTTTAG - -a -s simMouse_chr6.simMouse.chr6 185183 190 + 636262 GGATGCAACACAAGGGCAGTGGAGATACTCTTCCCTTGTGTGGGGGGCAGGCTCCTTCTACAGGTGCCTGTAAATGGCTTGACATTGCGTCAAGTGGGACTGGCTCACAGCCAAGCACCAATCATGTGTACATAGCTGCTTTTGCTTTTTATTGGAGCTGCACGAGGTACTGTGGGAAATCTAAACAATG -s Anc0.Anc0refChr1 15649 30 + 62388 G-------------------------------------------------------------------------------------------------------------------------------------------------------------TGGTTGGGGCCCTATCTAGGGT---GATAATG -s Anc1.Anc1refChr2 18132 33 - 144309 G-------------------------------------------------------------------------------------------------------------------------------------------------------------TGGTTGGGGCCCTATCTAGGGTCTAGATAATG -s Anc2.Anc2refChr3 16867 30 - 53186 G-------------------------------------------------------------------------------------------------------------------------------------------------------------TGGTTGGGGCCCTATCTACGGT---GGTAATG -s mr.mrrefChr5 40266 190 + 294540 GGATGCAACACAAGGGCAGTGGAGATACTCTTCCCTTGTGTGGGGGGCAGGCTCCTTCTACAGGTGCCTGTAAATGGCTTGACATTGCGTCAAGTGGGACTGGCTCACAGCCAAGCACCAATCATGTGTACATAGCTGCTTTTGCTTTTTATTGGAGCTGCACGAGGCACTGTGTGGAATCTAAACAATG -s simCow_chr6.simCow.chr6 437877 30 - 602619 G-------------------------------------------------------------------------------------------------------------------------------------------------------------TGGTTGGGACCCTATCCACGGT---GGTAATG -s simDog_chr6.simDog.chr6 145955 18 + 593897 G-------------------------------------------------------------------------------------------------------------------------------------------------------------TGGTTGGGGCTGTGTAT--------------- -s simHuman_chr6.simHuman.chr6 450659 33 - 601863 G-------------------------------------------------------------------------------------------------------------------------------------------------------------TAGTTGGGGCCCTATCTAGGGTCTAGATAATG -s simRat_chr6.simRat.chr6 175383 190 + 647215 GGATGCAACACAGGGGCAGTGGAGGTACTTTCCCCTTGTGTGGGGGGCGGGCTCCTTCTACAGGTGCCTGTAAATTGCTTTACATTGTGTCAAGCAGGACAGGCTTATAGCTAAGCACTAATCATGTGTGCGTGGCCATGTTTGCTTTTTATTGGAGCCGCAAAAGGCACTGTGTGGAATCTAAACAATG - -a -s simMouse_chr6.simMouse.chr6 185373 14 + 636262 CAAGGCAGGCCCCA -s Anc0.Anc0refChr1 15693 9 + 62388 CG----AGGACTC- -s Anc1.Anc1refChr2 18179 10 - 144309 CG----AGGACTCA -s Anc2.Anc2refChr3 16911 9 - 53186 TG----AGGACTC- -s mr.mrrefChr5 40456 10 + 294540 CG----AGGCCCCA -s simCow_chr6.simCow.chr6 437921 9 - 602619 TG----AGGACAC- -s simDog_chr6.simDog.chr6 145973 8 + 593897 -G----AGGACTC- -s simHuman_chr6.simHuman.chr6 450706 10 - 601863 CG----CGGACTCA -s simRat_chr6.simRat.chr6 175573 10 + 647215 TG----AAGCCCCA - -a -s simMouse_chr6.simMouse.chr6 185387 1 + 636262 T -s Anc0.Anc0refChr1 15715 1 + 62388 T -s Anc1.Anc1refChr2 18202 1 - 144309 T -s Anc2.Anc2refChr3 16933 1 - 53186 T -s mr.mrrefChr5 40466 1 + 294540 T -s simCow_chr6.simCow.chr6 437943 1 - 602619 C -s simDog_chr6.simDog.chr6 145994 1 + 593897 T -s simHuman_chr6.simHuman.chr6 450729 1 - 601863 T -s simRat_chr6.simRat.chr6 175583 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 185388 11 + 636262 TTTGGTTTAGA -s Anc0.Anc0refChr1 15716 11 + 62388 TGTGGTTTTGA -s Anc1.Anc1refChr2 18203 11 - 144309 TGTGGTTTTGA -s Anc2.Anc2refChr3 16947 11 - 53186 TGTGGTTTTGA -s mr.mrrefChr5 40467 11 + 294540 TTTGGTTTAGA -s simCow_chr6.simCow.chr6 437957 11 - 602619 TGTGGCTTTGA -s simDog_chr6.simDog.chr6 146008 11 + 593897 TGTAGTTTTGA -s simHuman_chr6.simHuman.chr6 450730 11 - 601863 TGCGGTTTTGA -s simRat_chr6.simRat.chr6 175584 11 + 647215 TTTGATTTAGA - -a -s simMouse_chr6.simMouse.chr6 185399 3 + 636262 AGT -s Anc0.Anc0refChr1 15728 3 + 62388 AGT -s Anc1.Anc1refChr2 18215 3 - 144309 AGT -s Anc2.Anc2refChr3 16959 3 - 53186 AGT -s mr.mrrefChr5 40478 3 + 294540 AGT -s simCow_chr6.simCow.chr6 437969 3 - 602619 AGT -s simDog_chr6.simDog.chr6 146020 3 + 593897 ACT -s simHuman_chr6.simHuman.chr6 450742 3 - 601863 AGT -s simRat_chr6.simRat.chr6 175595 3 + 647215 AGT - -a -s simMouse_chr6.simMouse.chr6 185402 27 + 636262 GGATATTCTGTTGCTTCTTCTCACCAA -s Anc0.Anc0refChr1 15731 27 + 62388 GGATATTGTGCTGTTTCTTTAAACTAG -s Anc1.Anc1refChr2 18218 27 - 144309 GGATATTGTGCTGTTTCTTTAAACTAG -s Anc2.Anc2refChr3 16962 27 - 53186 GGACATTGTGCTGTTTCTTTAAACTTG -s mr.mrrefChr5 40481 27 + 294540 GGATATTGTGCTGCTTCTTCTCACCAA -s simCow_chr6.simCow.chr6 437972 27 - 602619 GGACATTGTCCTGTTTTTTTGAACTGG -s simDog_chr6.simDog.chr6 146027 27 + 593897 AGACATTGTGCTGTTTCTTTAAACTTG -s simHuman_chr6.simHuman.chr6 450745 27 - 601863 GGATATTGTGCCATTTCTTTAGATTAG -s simRat_chr6.simRat.chr6 175598 27 + 647215 GGATATTGTGCTGCTTCTTATCACCAA - -a -s simMouse_chr6.simMouse.chr6 185429 6 + 636262 TCCCTC -s Anc0.Anc0refChr1 44413 5 - 62388 T-CTTT -s Anc1.Anc1refChr2 123811 5 + 144309 T-CTTT -s Anc2.Anc2refChr3 33798 5 + 53186 T-CTTT -s mr.mrrefChr5 40508 5 + 294540 T-CCTC -s simCow_chr6.simCow.chr6 162136 5 + 602619 T-CTTT -s simDog_chr6.simDog.chr6 445390 5 - 593897 C-CTTT -s simHuman_chr6.simHuman.chr6 148815 5 + 601863 T-CTTT -s simRat_chr6.simRat.chr6 175625 5 + 647215 T-CCTC - -a -s simMouse_chr6.simMouse.chr6 185435 16 + 636262 TGGATCCTGGCTGATT -s Anc0.Anc0refChr1 44418 16 - 62388 GTGACCTTAGGGAAAT -s Anc1.Anc1refChr2 123816 16 + 144309 GTGACCTTAGGGAAAT -s Anc2.Anc2refChr3 33803 16 + 53186 GTGACCTTAGGGAAAT -s mr.mrrefChr5 40513 16 + 294540 CGGATCTTGGTTGATT -s simCow_chr6.simCow.chr6 162146 16 + 602619 GTAACTTTTGTGGAAT -s simDog_chr6.simDog.chr6 445395 16 - 593897 GTGGCCTCAGGAAAAT -s simHuman_chr6.simHuman.chr6 148820 16 + 601863 ATGACCTTAGGGAAAT -s simRat_chr6.simRat.chr6 175630 16 + 647215 CGGACCTTGATTTATT - -a -s simMouse_chr6.simMouse.chr6 185451 14 + 636262 TATTTCCCTCTTTT -s Anc0.Anc0refChr1 44434 14 - 62388 CGCTTCCCTTTTGT -s Anc1.Anc1refChr2 123832 14 + 144309 CGCTTCCCTTTTGT -s Anc2.Anc2refChr3 33819 14 + 53186 TGCTTCCCTTTTGT -s mr.mrrefChr5 40529 14 + 294540 CATTTCCCTCTTGT -s simCow_chr6.simCow.chr6 162162 14 + 602619 CGCTTCTGTTCTCT -s simDog_chr6.simDog.chr6 445411 14 - 593897 TGTTTCCCTTTTGT -s simHuman_chr6.simHuman.chr6 148838 14 + 601863 CTCTTGCCTTTTAT -s simRat_chr6.simRat.chr6 175646 14 + 647215 CATTTCCCTCTTGT - -a -s simMouse_chr6.simMouse.chr6 185465 34 + 636262 GCAATGTAGCTCTCTCACAATCACCACCAGTCAC -s Anc0.Anc0refChr1 44453 32 - 62388 GCAAAGATGG--TCTCACAATCACTGCCAGTGCC -s Anc1.Anc1refChr2 123851 32 + 144309 GCAAAGATGG--TCTCACAATCACTGCCAGTGCC -s Anc2.Anc2refChr3 33838 32 + 53186 GCAGAGATGG--TCTCACAATTGCTGCCAGTGCC -s mr.mrrefChr5 40543 34 + 294540 GCAATGTAGGTCTCTCACAATCACCGCCAGTCCC -s simCow_chr6.simCow.chr6 162181 32 + 602619 GCAGAGATGG--TCTCACAATTGCTGCCAGTGCC -s simDog_chr6.simDog.chr6 445430 26 - 593897 GCAGTGATGG--TCTTTC------TGCAAGTGCC -s simHuman_chr6.simHuman.chr6 148857 32 + 601863 GCAAAGATGG--TCTCACAACCACTGTCAGTGCC -s simRat_chr6.simRat.chr6 175660 34 + 647215 GCAATGTAGGTCTCTTACAATCACCGCCAGTCCC - -a -s simMouse_chr6.simMouse.chr6 185499 57 + 636262 GTTTGTTTAGGCTCTTCTAGGACAGCAAGTTCTCCTGTCAGTGTGCTTGCATACCCA -s Anc0.Anc0refChr1 44485 56 - 62388 TTTTGTTATATTAGATCTAAGATGGCAAATTCT-CTGTCAGTGTTTTTGCTTACTCA -s Anc1.Anc1refChr2 123883 56 + 144309 TTTTGTTATATTAGATCTAAGATGGCAAATTCT-CTGTCAGTGTTTTTGCTTACTCA -s Anc2.Anc2refChr3 33870 56 + 53186 TTTTGTTATATTAGATCTAAGATGGCAAATTCT-CTGTCAGTGTTTTTACTTATTAG -s mr.mrrefChr5 40577 57 + 294540 GTTTGTTTAGTTTCTTCTAAGACAGCAAGTTCTCCTGTCAGTGTGCTTGCATACCCA -s simCow_chr6.simCow.chr6 162213 56 + 602619 TTTTGTTCTATTAGATCTAAGACGGCAAATTCT-CTGTCAATATGCTTACTTATTAG -s simDog_chr6.simDog.chr6 445456 49 - 593897 TTGTGTTATTTTAGATCTAAGATGG-------T-GTGTCCGTGTTTCCACTTATTAG -s simHuman_chr6.simHuman.chr6 148889 56 + 601863 TTTTGTTATATTAGATCTAAGATGGCAAAATCT-CTGCCAGTGTTTTTGTTTACTCA -s simRat_chr6.simRat.chr6 175806 48 + 647215 GTTTATTTAGTTCCTTC-AAGAAAGCAATCTCTCCTGTCAGTG--------TACCCA - -a -s simMouse_chr6.simMouse.chr6 185556 1 + 636262 G -s Anc0.Anc0refChr1 44541 1 - 62388 T -s Anc1.Anc1refChr2 123939 1 + 144309 T -s Anc2.Anc2refChr3 33927 1 + 53186 T -s mr.mrrefChr5 40634 1 + 294540 G -s simCow_chr6.simCow.chr6 162270 1 + 602619 T -s simDog_chr6.simDog.chr6 445506 1 - 593897 T -s simHuman_chr6.simHuman.chr6 148945 1 + 601863 T -s simRat_chr6.simRat.chr6 175854 1 + 647215 G - -a -s simMouse_chr6.simMouse.chr6 185557 15 + 636262 TTGAGTGAATAAGAA -s Anc0.Anc0refChr1 44578 15 - 62388 CCAAGAGATTTAGTA -s Anc1.Anc1refChr2 123976 15 + 144309 CCAAGAGATTTAGTA -s Anc2.Anc2refChr3 33964 15 + 53186 CCAGAAAATTTAGTA -s mr.mrrefChr5 40635 15 + 294540 TTGAGTGAATAAGAA -s simCow_chr6.simCow.chr6 162307 10 + 602619 CCACAAAGCT----- -s simDog_chr6.simDog.chr6 445543 15 - 593897 CCAGAAAATTTAGTA -s simHuman_chr6.simHuman.chr6 148985 15 + 601863 CCAAGAGATTCAGCA -s simRat_chr6.simRat.chr6 175855 15 + 647215 TTGAGTGACTAAGAG - -a -s simMouse_chr6.simMouse.chr6 185572 1 + 636262 G -s Anc0.Anc0refChr1 44593 1 - 62388 G -s Anc1.Anc1refChr2 123991 1 + 144309 G -s Anc2.Anc2refChr3 33979 1 + 53186 A -s mr.mrrefChr5 40650 1 + 294540 G -s simCow_chr6.simCow.chr6 162317 1 + 602619 G -s simDog_chr6.simDog.chr6 445559 1 - 593897 A -s simHuman_chr6.simHuman.chr6 149000 1 + 601863 G -s simRat_chr6.simRat.chr6 175870 1 + 647215 G - -a -s simMouse_chr6.simMouse.chr6 185573 83 + 636262 CAAGGTCCTCCTTGAAGGGGAATCTTACATCCAGGGCCTCCAAGGTGCAAAGTGAAGGATTATGATAAAGAATTGTTAAATCT -s Anc0.Anc0refChr1 44599 76 - 62388 TAAGTCCATCCTTGGAGGGGTAACTTATATCCAGGGT-------GTGCATTCTGAAGGATCACCATAAGAGATCCTTTTGTCT -s Anc1.Anc1refChr2 123997 76 + 144309 TAAGTCCATCCTTGGAGGGGTAACTTATATCCAGGGT-------GTGCATTCTGAAGGATCACCATAAGAGATCCTTTTGTCT -s Anc2.Anc2refChr3 33988 76 + 53186 TAAGTCCATCCTTGGAGGGGTGACTTATATCCAGGGT-------GTGGATTCTGACGGATCATCATAAGAGATCCTTTTGTCT -s mr.mrrefChr5 40651 83 + 294540 TAAGGTCCTCCTTGAAGGGGAATCTTACATCCAGGGCCTCCAAGGTGCAAAGTGAAGGATTACGATAAAGAATCGTTAAATCT -s simCow_chr6.simCow.chr6 162326 76 + 602619 TTAGTCCATCTTTGGGGGGGTGACTCATATCCAGGGT-------GCAAATTCTGAGGGATCATCATAAGAGATCCTTCTATCT -s simDog_chr6.simDog.chr6 445568 64 - 593897 TAAGTCGATCCTTGGAGGGGTGATTT-------------------TGGATTCTGACGGATTGTCATAAAAGACCCTTTAGTCT -s simHuman_chr6.simHuman.chr6 149006 76 + 601863 TAAGTCCATCCTTGGAGGTGTAACTTCTATCTGGGGT-------GTGCATTCTGAAGGATCACCATAAGACGTCCCTTTGTCT -s simRat_chr6.simRat.chr6 175871 83 + 647215 TAAACTCCTTCTTGAAGGGGAACCTTACATCCAGGGCCTCCAGGGTGTAAAATGAAGGATTGCTATAAAGAATCGTTAAATCT - -a -s simMouse_chr6.simMouse.chr6 185656 34 + 636262 GTTAAGACAGACCTCATGACCTCTCCGCATGTGT -s Anc0.Anc0refChr1 44675 34 - 62388 GATGAGACAGACTTCACAACCTCTCCACATCTGT -s Anc1.Anc1refChr2 124073 34 + 144309 GATGAGACAGACTTCACAACCTCTCCACATCTGT -s Anc2.Anc2refChr3 34064 34 + 53186 GATGGGACAGACTTCACAACCTCTCCACATCCAT -s mr.mrrefChr5 40734 34 + 294540 GTTGAGACAGACCTCATGACCTCTCCACATGTGT -s simCow_chr6.simCow.chr6 162402 34 + 602619 GAATGGAAACACTTCACAACATCTCCACATCCAT -s simDog_chr6.simDog.chr6 445632 34 - 593897 GATGGGACGGACTTCACAACCTCTCCACACCCAT -s simHuman_chr6.simHuman.chr6 149082 34 + 601863 GGTGAGACAGACTTCTCAACCTCTCCACATATGC -s simRat_chr6.simRat.chr6 175958 34 + 647215 ATTGAGGCTGACCTCATGACCTCTCCACGTCCGA - -a -s simMouse_chr6.simMouse.chr6 185690 3 + 636262 GAA -s Anc0.Anc0refChr1 44709 3 - 62388 GAA -s Anc1.Anc1refChr2 124107 3 + 144309 GAA -s Anc2.Anc2refChr3 34098 3 + 53186 GAG -s mr.mrrefChr5 40768 3 + 294540 GAA -s simCow_chr6.simCow.chr6 162438 3 + 602619 GGG -s simDog_chr6.simDog.chr6 445666 3 - 593897 GAG -s simHuman_chr6.simHuman.chr6 149116 3 + 601863 GAA -s simRat_chr6.simRat.chr6 175992 3 + 647215 GAA - -a -s simMouse_chr6.simMouse.chr6 185693 9 + 636262 CTGTTGTAA -s Anc0.Anc0refChr1 44713 9 - 62388 CTAATGTGC -s Anc1.Anc1refChr2 124111 9 + 144309 CTAATGTGC -s Anc2.Anc2refChr3 34102 9 + 53186 CCAATGTGC -s mr.mrrefChr5 40771 9 + 294540 CTGATGTAA -s simCow_chr6.simCow.chr6 162442 9 + 602619 CCAATGTGC -s simDog_chr6.simDog.chr6 445670 9 - 593897 CCTATAGGC -s simHuman_chr6.simHuman.chr6 149120 9 + 601863 CTAAAGTGC -s simRat_chr6.simRat.chr6 175995 9 + 647215 CCGATGTAA - -a -s simMouse_chr6.simMouse.chr6 185702 6 + 636262 TCATTG -s Anc0.Anc0refChr1 44723 6 - 62388 TCTTTG -s Anc1.Anc1refChr2 124121 6 + 144309 TCTTTG -s Anc2.Anc2refChr3 34112 6 + 53186 CATTTA -s mr.mrrefChr5 40780 6 + 294540 TCATTG -s simCow_chr6.simCow.chr6 162452 6 + 602619 CATTTA -s simDog_chr6.simDog.chr6 445680 6 - 593897 CATTTA -s simHuman_chr6.simHuman.chr6 149130 6 + 601863 TCTTTG -s simRat_chr6.simRat.chr6 176004 6 + 647215 TCAATA - -a -s simMouse_chr6.simMouse.chr6 185708 6 + 636262 TCAAGT -s Anc0.Anc0refChr1 44736 6 - 62388 TCAGGG -s Anc1.Anc1refChr2 124134 6 + 144309 TCAGGG -s Anc2.Anc2refChr3 34125 6 + 53186 GCAGGG -s mr.mrrefChr5 40786 6 + 294540 TCAAGT -s simCow_chr6.simCow.chr6 162465 6 + 602619 CCAGGG -s simDog_chr6.simDog.chr6 445693 6 - 593897 GCAAGG -s simHuman_chr6.simHuman.chr6 149143 6 + 601863 TCAGAG -s simRat_chr6.simRat.chr6 176010 6 + 647215 TCAAGT - -a -s simMouse_chr6.simMouse.chr6 185714 16 + 636262 ACATTGCTATTGGTGC -s Anc0.Anc0refChr1 44742 15 - 62388 ACA-TGTTACTGGTGC -s Anc1.Anc1refChr2 124140 15 + 144309 ACA-TGTTACTGGTGC -s Anc2.Anc2refChr3 34132 15 + 53186 ACA-TGTTACTGGTCC -s mr.mrrefChr5 40792 15 + 294540 ACA-TGCTATTGGTGC -s simCow_chr6.simCow.chr6 162472 15 + 602619 AGT-TGTTACTGGTCC -s simDog_chr6.simDog.chr6 445700 15 - 593897 ACA-TGTTACTGGTCC -s simHuman_chr6.simHuman.chr6 149149 15 + 601863 ACA-TATTGCTGATGC -s simRat_chr6.simRat.chr6 176016 15 + 647215 ACA-GGCTATTGGTGC - -a -s simMouse_chr6.simMouse.chr6 185730 63 + 636262 CGGAGAGGAACAATGAAGTCAAGCTGCAAAGGGTCTACTGATTTGATGTACATTGATGTAAAT -s Anc0.Anc0refChr1 44757 52 - 62388 CTGAGTGGAACAATAAAGT-AAGCTGCACAGGTTCTACTTATTTG----------ATGTAAAT -s Anc1.Anc1refChr2 124155 53 + 144309 CTGAGTGGAACAATAAAGTCAAGCTGCACAGGTTCTACTTATTTG----------ATGTAAAT -s Anc2.Anc2refChr3 34147 52 + 53186 CTGAGTGGAGCAATAAGGT-AAGCTGCACAGGTTCTACTTATTCG----------ATATAAAT -s mr.mrrefChr5 40807 63 + 294540 CTGAGAGGAACAATGAAGTCAAGCTGCAAAGGGTCTACTGATTTGATGTACATTGATGTAAAT -s simCow_chr6.simCow.chr6 162487 49 + 602619 CTGAGTGTAGCCAAATGGT-A-GCTGCACAGGCTCTAGTTA--CG----------ATAAAAAT -s simDog_chr6.simDog.chr6 445715 52 - 593897 TTGAGTGGAGCAATAAGGT-AAGCTGCACAGGTTCTACTGATTCG----------TCATAAAT -s simHuman_chr6.simHuman.chr6 149164 53 + 601863 CTGAGTGGAACTATCGAATCAAGCTGCACAGGTTCTATTTATTTA----------ATGTAAAT -s simRat_chr6.simRat.chr6 176036 63 + 647215 CTAAGAGGAACAATGAAGTCAAGTTGTAAAGGGTCTACTGATTTGATGTACATTGATGTAAAT - -a -s simMouse_chr6.simMouse.chr6 185793 8 + 636262 ATTTTCTT -s Anc0.Anc0refChr1 44809 8 - 62388 ATTTCTTG -s Anc1.Anc1refChr2 124208 8 + 144309 ATTTCTTG -s Anc2.Anc2refChr3 34199 8 + 53186 ATTTCTTG -s mr.mrrefChr5 40870 8 + 294540 ATTTCTTG -s simCow_chr6.simCow.chr6 162536 8 + 602619 ATATTTTG -s simDog_chr6.simDog.chr6 445768 8 - 593897 ATTTCCTG -s simHuman_chr6.simHuman.chr6 149217 8 + 601863 ATTTCTTG -s simRat_chr6.simRat.chr6 176099 8 + 647215 ATTTCTTG - -a -s simMouse_chr6.simMouse.chr6 185801 59 + 636262 CATCATGACCTTCTCTTCTAGGGTGAAATTGTATACCACCCTTGATATTGGTTTCTCTA -s Anc0.Anc0refChr1 44827 38 - 62388 CATCATGGC-----CTTCCATGGTGAAATTATAT----------------GTTTCTCTA -s Anc1.Anc1refChr2 124226 38 + 144309 CATCATGGC-----CTTCCATGGTGAAATTATAT----------------GTTTCTCTA -s Anc2.Anc2refChr3 34217 38 + 53186 CATCATGGC-----CTTCCATGGTGAAATTATAT----------------GTTTCGCTA -s mr.mrrefChr5 40878 59 + 294540 CATCATGACCTTCTCTTCTATGGTGAAATTATATACCACCCTTGATATTGGTTTCTCTA -s simCow_chr6.simCow.chr6 162554 38 + 602619 CATCATAGA-----CTTCCGTGGTAGACTTTTAC----------------ATTTCCCTA -s simDog_chr6.simDog.chr6 445786 38 - 593897 CATCATGGC-----CGTCCATGCTGAAATGACAT----------------GGTTCGCAA -s simHuman_chr6.simHuman.chr6 149235 38 + 601863 CATCATGGC-----CTTCCATGGTGCAATTATAT----------------GTTTCTTTA -s simRat_chr6.simRat.chr6 176107 59 + 647215 CATCATGACCTTCTCTTCTATGGTCAAATTATATAGCACCCTCGATAGTGGTTTCTCTA - -a -s simMouse_chr6.simMouse.chr6 185860 25 + 636262 CTTATTTAAGGCAATAGTAGGCCTG -s Anc0.Anc0refChr1 44866 21 - 62388 CTTATTTAAGTCAATCATA----TG -s Anc1.Anc1refChr2 124265 21 + 144309 CTTATTTAAGTCAATCATA----TG -s Anc2.Anc2refChr3 34256 21 + 53186 CTTATTTAAGTCAATCATA----TG -s mr.mrrefChr5 40937 25 + 294540 CTTATTTAAGGCAATAATAGGCCTG -s simCow_chr6.simCow.chr6 162593 21 + 602619 CTTACTTTAGTCATTCATA----TG -s simDog_chr6.simDog.chr6 445825 20 - 593897 CTCCTTTAGGTCAATCAT-----TG -s simHuman_chr6.simHuman.chr6 149274 21 + 601863 CTTATTTAAGTCAATCATA----TG -s simRat_chr6.simRat.chr6 176166 25 + 647215 CTTATTTAAGGCAATAATAGGCCTG - -a -s simMouse_chr6.simMouse.chr6 185885 2 + 636262 AA -s Anc0.Anc0refChr1 44887 2 - 62388 GA -s Anc1.Anc1refChr2 124286 2 + 144309 GA -s Anc2.Anc2refChr3 34282 2 + 53186 GA -s mr.mrrefChr5 40962 2 + 294540 AA -s simCow_chr6.simCow.chr6 162619 2 + 602619 CA -s simDog_chr6.simDog.chr6 445850 2 - 593897 GC -s simHuman_chr6.simHuman.chr6 149295 2 + 601863 GA -s simRat_chr6.simRat.chr6 176191 2 + 647215 AA - -a -s simMouse_chr6.simMouse.chr6 185887 14 + 636262 CTTCTTCTGTGCAA -s Anc0.Anc0refChr1 44889 14 - 62388 CTTCTTCTGTGCAG -s Anc1.Anc1refChr2 124288 14 + 144309 CTTCTTCTGTGCAG -s Anc2.Anc2refChr3 34284 14 + 53186 CTTCTTCTGTGCAG -s mr.mrrefChr5 40964 14 + 294540 CTTCTTCTGTGCAA -s simCow_chr6.simCow.chr6 162622 14 + 602619 CTTCTTCTGTCCAG -s simDog_chr6.simDog.chr6 445852 14 - 593897 CTTCTTCTGTGCAG -s simHuman_chr6.simHuman.chr6 149297 10 + 601863 CTTCTTCTGT---- -s simRat_chr6.simRat.chr6 176193 14 + 647215 CTTCTTATGTGCAG - -a -s simMouse_chr6.simMouse.chr6 185901 84 + 636262 TAGCAAGCCAAGTTGAATCAGTCCTTTTTGACTCTTAACAGTGTAGTGGCTAGTCACCAGAAATAACTAATGGCATTTCTACCC -s Anc0.Anc0refChr1 44903 83 - 62388 TAGCAAGCCAAG-TGAGTCAACCCTTTTTAACTCTTCCTAGAGTAGTTGCTAGTCACCTGAAATAACTAATGGCATTTCCACCC -s Anc1.Anc1refChr2 124302 83 + 144309 TAGCAAGCCAAG-TGAGTCAACCCTTTTTAACTCTTCCTAGAGTAGTTGCTAGTCACCTGAAATAACTAATGGCATTTCCACCC -s Anc2.Anc2refChr3 34299 83 + 53186 TAGTAAGCCAAG-TGAGTCAACCCTTTTTAACTCTTCCTAGAGTAGTTGCTAGTCACCTGAAATAACTAATGGCATTTCCACCC -s mr.mrrefChr5 40978 84 + 294540 TAGCAAGCCAAGTTGAATCAGTCCTTTTTGACTCTTCACAGTGTAGTGGCTAGTCACCAGAAATAACTAATGGCATTTCTACCC -s simCow_chr6.simCow.chr6 162637 75 + 602619 TAGTAAGCCAAT-TGAGTTGACGCTTTTTAATTCTTCTG--------TGCTAAACATCTGAAATAAGTTATGGCATTTCTGCCC -s simDog_chr6.simDog.chr6 445867 83 - 593897 TAGTAAGCCAAG-TGAGTCAGCCCACTTTGGCTCTTCCTAGAGTAGTTACTAGTCACCTGAAATAACTAATGGCATTTTCACCC -s simHuman_chr6.simHuman.chr6 149307 81 + 601863 --ACAAGCCAAG-CGAGTCAACCCTTTTTAACTCTTCCTAAAGTAGCTGCTAGTCGCCTGAGTTAATTAATGGCATTTCCACCC -s simRat_chr6.simRat.chr6 176207 84 + 647215 CATCAAGCCAAGTTGAATCAGTCTTTTTTGAATCTTCACAGGGTAGAGGCTAGTCACCAGAAGTAACTAATGACATTTCTACCC - -a -s simMouse_chr6.simMouse.chr6 185985 17 + 636262 TGAGGGCCAATTTGGAA -s Anc0.Anc0refChr1 44986 17 - 62388 AAAGAGACGATTTGAAA -s Anc1.Anc1refChr2 124385 17 + 144309 AAAGAGACGATTTGAAA -s Anc2.Anc2refChr3 34382 17 + 53186 AAAGAGACGATTTGAAA -s mr.mrrefChr5 41062 17 + 294540 TGAGAGCCAATTTGAAA -s simCow_chr6.simCow.chr6 162712 17 + 602619 AAAAAGACAACTTGAAA -s simDog_chr6.simDog.chr6 445950 17 - 593897 AAAGAGACGATTTGAAG -s simHuman_chr6.simHuman.chr6 149388 17 + 601863 CAAGAGACCATTTGAAA -s simRat_chr6.simRat.chr6 176294 17 + 647215 TGAGAGCCAATTTGACA - -a -s simMouse_chr6.simMouse.chr6 186002 46 + 636262 CTCACAAGGCTGCATTATGCACATCTGACCATACACTTATTAAGAA -s Anc0.Anc0refChr1 45003 19 - 62388 CCTGTA-GA-------------------------ACTTATTAA-AA -s Anc1.Anc1refChr2 124402 20 + 144309 CCTGTAAGA-------------------------ACTTATTAA-AA -s Anc2.Anc2refChr3 34399 19 + 53186 CCTGTA-GA-------------------------CCTTATTAA-TA -s mr.mrrefChr5 41079 45 + 294540 CTTACAAGACTGCATTATGCACATCTGACCATACACTTATTAA-AA -s simCow_chr6.simCow.chr6 162732 19 + 602619 CTTCTA-GA-------------------------TGTTACTAA-GA -s simDog_chr6.simDog.chr6 445967 19 - 593897 CCTGCA-GA-------------------------CCTTATTAA-TA -s simHuman_chr6.simHuman.chr6 149405 20 + 601863 CCTGTAGGA-------------------------ACTTATTAA-AA -s simRat_chr6.simRat.chr6 176311 45 + 647215 CTTACAAGACTGCCTGATGTACATTTGACCGTAGTCTTATTAA-AA - -a -s simMouse_chr6.simMouse.chr6 186048 11 + 636262 CCTAACAGGGG -s Anc0.Anc0refChr1 45022 11 - 62388 CCTCACAAGTG -s Anc1.Anc1refChr2 124422 11 + 144309 CCTCACAAGTG -s Anc2.Anc2refChr3 34418 11 + 53186 CCTCACAAGTG -s mr.mrrefChr5 41124 11 + 294540 CCTAACAGGGG -s simCow_chr6.simCow.chr6 162751 11 + 602619 CTTCATAAGTG -s simDog_chr6.simDog.chr6 446021 11 - 593897 TCTCACAAGTG -s simHuman_chr6.simHuman.chr6 149425 11 + 601863 CCACACACGTA -s simRat_chr6.simRat.chr6 176356 11 + 647215 CCTAACAAGGG - -a -s simMouse_chr6.simMouse.chr6 186059 33 + 636262 CAATGGTGTGTATGACCAGCTTTCACTCCACAG -s Anc0.Anc0refChr1 45033 33 - 62388 CAATTGTGTGTACAACCAGCTTTCACTACCCAG -s Anc1.Anc1refChr2 124433 33 + 144309 CAATTGTGTGTACAACCAGCTTTCACTACCCAG -s Anc2.Anc2refChr3 34429 33 + 53186 CAGTTGTGTGAACAACCAGCTTTCACTACCCAG -s mr.mrrefChr5 41135 33 + 294540 CAATGGTGTGTACGACCAGCTTTCACTCCACAG -s simCow_chr6.simCow.chr6 162762 33 + 602619 CAGTTCTATGCACAACTGGTTTTCACTACCCAT -s simDog_chr6.simDog.chr6 446039 33 - 593897 CAGTTGTGTGAAGAACCAGCTTTCACTACCCAG -s simHuman_chr6.simHuman.chr6 149436 33 + 601863 CAATTACGTGTACAACCAGCTTTCACTACCCTC -s simRat_chr6.simRat.chr6 176367 33 + 647215 CAATGGTGTGTACTACCAGCTTTCACTCCATGG - -a -s simMouse_chr6.simMouse.chr6 186092 8 + 636262 CTTCCCTC -s Anc0.Anc0refChr1 45066 8 - 62388 CTTCTTTT -s Anc1.Anc1refChr2 124466 8 + 144309 CTTCTTTT -s Anc2.Anc2refChr3 34468 8 + 53186 CTACTTTA -s mr.mrrefChr5 41168 8 + 294540 CTTCCCTT -s simCow_chr6.simCow.chr6 162801 8 + 602619 CTGCTCTG -s simDog_chr6.simDog.chr6 446078 8 - 593897 CTACTTCA -s simHuman_chr6.simHuman.chr6 149469 8 + 601863 CTTCATTT -s simRat_chr6.simRat.chr6 176400 8 + 647215 CTTCCCTT - -a -s simMouse_chr6.simMouse.chr6 186100 15 + 636262 GTAAAATTGCAGCCA -s Anc0.Anc0refChr1 45075 15 - 62388 TTAGAATTCCAGGCA -s Anc1.Anc1refChr2 124475 15 + 144309 TTAGAATTCCAGGCA -s Anc2.Anc2refChr3 34477 15 + 53186 CTAGAATTCCAGGCA -s mr.mrrefChr5 41176 15 + 294540 TTAGAATTGCAGCCA -s simCow_chr6.simCow.chr6 162810 15 + 602619 CTATAATTCCAGGCA -s simDog_chr6.simDog.chr6 446087 15 - 593897 CCAGAATTCCAGGCG -s simHuman_chr6.simHuman.chr6 149478 15 + 601863 TTAGAATTCCAGACA -s simRat_chr6.simRat.chr6 176408 15 + 647215 TTAGAAGTGCAGTCA - -a -s simMouse_chr6.simMouse.chr6 186115 1 + 636262 C -s Anc0.Anc0refChr1 45090 1 - 62388 T -s Anc1.Anc1refChr2 124490 1 + 144309 T -s Anc2.Anc2refChr3 34492 1 + 53186 T -s mr.mrrefChr5 41191 1 + 294540 T -s simCow_chr6.simCow.chr6 162826 1 + 602619 T -s simDog_chr6.simDog.chr6 446102 1 - 593897 C -s simHuman_chr6.simHuman.chr6 149493 1 + 601863 T -s simRat_chr6.simRat.chr6 176423 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 186116 38 + 636262 GAGGATGGGCGGCAGCTCTGCCCATTCCAGCAAATGAA -s Anc0.Anc0refChr1 45091 36 - 62388 TAGGGT--CCTGCAGATCAGCCCATCCAACCAGACAGA -s Anc1.Anc1refChr2 124491 36 + 144309 TAGGGT--CCTGCAGATCAGCCCATCCAACCAGACAGA -s Anc2.Anc2refChr3 34493 36 + 53186 TAGGGT--CCAGCAGATCAGCCCATCCAACCAGACAGA -s mr.mrrefChr5 41192 38 + 294540 TAGGATGGCCTGCAGCTCTGCCCATTCCAGCAAATGAA -s simCow_chr6.simCow.chr6 162827 36 + 602619 TACGGT--CCAGCAGATCAGACCATCTAACCAGACAGA -s simDog_chr6.simDog.chr6 446105 36 - 593897 TAGGGT--CCAGTAGATCAGCCCATACAACCAGACAGA -s simHuman_chr6.simHuman.chr6 149494 36 + 601863 TAGGGT--CCTGCAGATCAGCCTGTCCACCCAGACAGA -s simRat_chr6.simRat.chr6 176424 30 + 647215 TAAGTTGGCCTGCTGTTCTGCCAAT--------ATGAA - -a -s simMouse_chr6.simMouse.chr6 186154 34 + 636262 ATACTCACAGTGTCTGGTTAATGCAAGGAGGGTC -s Anc0.Anc0refChr1 45135 34 - 62388 ATACCATCCGCGTCTGATTGATGTGGGGATGTTT -s Anc1.Anc1refChr2 124535 34 + 144309 ATACCATCCGCGTCTGATTGATGTGGGGATGTTT -s Anc2.Anc2refChr3 34537 34 + 53186 ATACCATCCACATCTTATTGATGTGGGGATGTTT -s mr.mrrefChr5 41230 34 + 294540 ATACTCACAGTGTCTGATTAATGCAAGGAGGGTC -s simCow_chr6.simCow.chr6 162871 33 + 602619 ATGCCTACCACATCTTATTGATGTGGGGA-GTGT -s simDog_chr6.simDog.chr6 446149 20 - 593897 ACACCATAC--------------TGGAGATGTTT -s simHuman_chr6.simHuman.chr6 149538 34 + 601863 ATACCATCTGGGTTTGATGGACGTGGGGAATTTA -s simRat_chr6.simRat.chr6 176454 34 + 647215 ATACTCACAGTGTCTGACTAATACAAGGAGGGTC - -a -s simMouse_chr6.simMouse.chr6 186188 9 + 636262 AAGGTGTGT -s Anc0.Anc0refChr1 45169 9 - 62388 AGGGAGTGT -s Anc1.Anc1refChr2 124569 9 + 144309 AGGGAGTGT -s Anc2.Anc2refChr3 34571 9 + 53186 AGGGAGTGT -s mr.mrrefChr5 41264 9 + 294540 AAGGTGTGT -s simCow_chr6.simCow.chr6 162905 9 + 602619 AGTGAGTGT -s simDog_chr6.simDog.chr6 446169 9 - 593897 AAGTGGTGT -s simHuman_chr6.simHuman.chr6 149572 9 + 601863 AGGGAGTGT -s simRat_chr6.simRat.chr6 176488 9 + 647215 AAGGTGTGT - -a -s simMouse_chr6.simMouse.chr6 186197 7 + 636262 AGCCAGA -s Anc0.Anc0refChr1 45178 7 - 62388 GGGGAGA -s Anc1.Anc1refChr2 124578 7 + 144309 GGGGAGA -s Anc2.Anc2refChr3 34580 7 + 53186 GGGGGGA -s mr.mrrefChr5 41273 7 + 294540 AGCCAGA -s simCow_chr6.simCow.chr6 162914 7 + 602619 AGGGCGA -s simDog_chr6.simDog.chr6 446178 7 - 593897 GGGAGGC -s simHuman_chr6.simHuman.chr6 149581 7 + 601863 GGGGAGA -s simRat_chr6.simRat.chr6 176498 7 + 647215 AACACGA - -a -s simMouse_chr6.simMouse.chr6 186204 11 + 636262 GGATAATCTAC -s Anc0.Anc0refChr1 45185 11 - 62388 GAACAATACAT -s Anc1.Anc1refChr2 124585 11 + 144309 GAACAATACAT -s Anc2.Anc2refChr3 34587 11 + 53186 GAACAAAACAT -s mr.mrrefChr5 41280 11 + 294540 GGATAATCTAC -s simCow_chr6.simCow.chr6 162921 11 + 602619 GAGAAAAACAT -s simDog_chr6.simDog.chr6 446188 11 - 593897 GGACAAAACAC -s simHuman_chr6.simHuman.chr6 149588 11 + 601863 GAACAGTAGAT -s simRat_chr6.simRat.chr6 176505 11 + 647215 GGATAATCTAC - -a -s simMouse_chr6.simMouse.chr6 186215 60 + 636262 AAGCTGAGCACAAACAAAAACAGAATTCAAGATGGTACATTTTCCAGTAAAAGGCTTAGA -s Anc0.Anc0refChr1 45198 55 - 62388 GAGCTGAGCA-----ATAAACAGAACACAAGACATTAAAATTTTCAGTAAAAAGATAAAA -s Anc1.Anc1refChr2 124598 55 + 144309 GAGCTGAGCA-----ATAAACAGAACACAAGACATTAAAATTTTCAGTAAAAAGATAAAA -s Anc2.Anc2refChr3 34600 55 + 53186 GAACTGAACA-----ATAAACAGAACACAGGGCATTCAAATTTTCAGTAAAAAGATAAAA -s mr.mrrefChr5 41291 60 + 294540 AAGCTGAGCAAAAACAAAAACAGAATTCAAGATAGTACATTTTCCAGTAAAAGGCTTAGA -s simCow_chr6.simCow.chr6 162934 55 + 602619 GAACTGATTA-----ATAAACAGCACACAGGGCATTAACATTCTTAGTAAAAAGATTAAA -s simDog_chr6.simDog.chr6 446201 54 - 593897 GA-CTTAACA-----GAAATCAGAATACAGGGCATTCAAATTTTCAGGAAAAGGTAAACA -s simHuman_chr6.simHuman.chr6 149601 54 + 601863 GAGCTGAGCA-----ATAAACAGAACACAAGAAATTA-AATTTTCAGTAAAAAGATAAAA -s simRat_chr6.simRat.chr6 176516 60 + 647215 AAGCTGAGCAAGAAAAAAAACAGAATTCAACACAGTTCACTTTCCAGTAAAAGGCTTCGA - -a -s simMouse_chr6.simMouse.chr6 186275 54 + 636262 TGGACTAACAGGCTCATTTAGATATAATCTTCAAGAGTGTGCATCCTGAATCAC -s Anc0.Anc0refChr1 45253 53 - 62388 CAAACTGACAGGCCCAA-TAGATAAAAGCTTTAAGTATGTACATCTTAAATCAC -s Anc1.Anc1refChr2 124653 53 + 144309 CAAACTGACAGGCCCAA-TAGATAAAAGCTTTAAGTATGTACATCTTAAATCAC -s Anc2.Anc2refChr3 34655 53 + 53186 CAAACTGACAGGCCCAA-TTGATCAAAGCTCTAGGTATATAAATCTCAAATCAC -s mr.mrrefChr5 41351 54 + 294540 TGGACTGACAGGCTCAATTAGATATAATCTTCAAGAGTGTGCATCCTGAATCAC -s simCow_chr6.simCow.chr6 162989 52 + 602619 CAAATTGCTGGGCCCAA-TGGATCAAAGC-CTAGGTGTATAGATTTCAGATCAC -s simDog_chr6.simDog.chr6 446267 53 - 593897 TAAACTGACAGGTTTAA-TTGACCAAAGTTCTAGGAATATAAAACTCAAATCAC -s simHuman_chr6.simHuman.chr6 149655 53 + 601863 CAAACTGACAGGCCCAA-TAGATAAAACCTTAAAGTATGTACATCTTAAACCAC -s simRat_chr6.simRat.chr6 176576 54 + 647215 TTGACTGACAGGCACAATTAGATATAATCTTTAGGAGTGTGCTTCCCGAATCGC - -a -s simMouse_chr6.simMouse.chr6 186329 3 + 636262 TAA -s Anc0.Anc0refChr1 45307 3 - 62388 TAA -s Anc1.Anc1refChr2 124707 3 + 144309 TAA -s Anc2.Anc2refChr3 34709 3 + 53186 TAA -s mr.mrrefChr5 41405 3 + 294540 TAA -s simCow_chr6.simCow.chr6 163042 3 + 602619 TAA -s simDog_chr6.simDog.chr6 446321 3 - 593897 TAA -s simHuman_chr6.simHuman.chr6 149709 3 + 601863 TAA -s simRat_chr6.simRat.chr6 176630 3 + 647215 TAA - -a -s simMouse_chr6.simMouse.chr6 186332 11 + 636262 GATCTATAAGG -s Anc0.Anc0refChr1 45310 11 - 62388 GATTTATAAGG -s Anc1.Anc1refChr2 124710 11 + 144309 GATTTATAAGG -s Anc2.Anc2refChr3 34712 11 + 53186 GATCTAAAAGG -s mr.mrrefChr5 41408 11 + 294540 GATTTATAAGG -s simCow_chr6.simCow.chr6 163049 11 + 602619 AATCTGAAATG -s simDog_chr6.simDog.chr6 446324 11 - 593897 GATCAAAAAGG -s simHuman_chr6.simHuman.chr6 149712 11 + 601863 GATTTTTAAGG -s simRat_chr6.simRat.chr6 176633 11 + 647215 GACTTATATGG - -a -s simMouse_chr6.simMouse.chr6 186343 4 + 636262 AGAA -s Anc0.Anc0refChr1 45322 4 - 62388 AGAG -s Anc1.Anc1refChr2 124722 4 + 144309 AGAG -s Anc2.Anc2refChr3 34724 4 + 53186 ACAG -s mr.mrrefChr5 41419 4 + 294540 AGAA -s simCow_chr6.simCow.chr6 163061 4 + 602619 GTAG -s simDog_chr6.simDog.chr6 446336 3 - 593897 ACA- -s simHuman_chr6.simHuman.chr6 149724 4 + 601863 AGAT -s simRat_chr6.simRat.chr6 176644 4 + 647215 AGAA - -a -s simMouse_chr6.simMouse.chr6 186347 19 + 636262 TACAGGTAGCAACTCACAG -s Anc0.Anc0refChr1 45326 19 - 62388 TATAAGAAAAAACTCACTG -s Anc1.Anc1refChr2 124726 19 + 144309 TATAAGAAAAAACTCACTG -s Anc2.Anc2refChr3 34798 19 + 53186 CATCATTAGTGAGCCATCA -s mr.mrrefChr5 41423 19 + 294540 TATAGGTAACAACTCACAG -s simCow_chr6.simCow.chr6 163135 19 + 602619 CATCATTAGTGAGCCATCA -s simHuman_chr6.simHuman.chr6 149728 19 + 601863 TATAAGAAAAGACATGCTG -s simRat_chr6.simRat.chr6 176648 19 + 647215 TATAGGTAAGAACTCACAG - -a -s simMouse_chr6.simMouse.chr6 186366 18 + 636262 GTACATGGTTAGCCTTAC -s Anc0.Anc0refChr1 45345 18 - 62388 GTACATGGTTAGCCTCAC -s Anc1.Anc1refChr2 124745 18 + 144309 GTACATGGTTAGCCTCAC -s Anc2.Anc2refChr3 34817 18 + 53186 GTATAAGAAAAAACTCAC -s mr.mrrefChr5 41442 18 + 294540 GTACATGGTTAGCCTTAC -s simCow_chr6.simCow.chr6 163204 17 + 602619 ATATAGGAATAAACTCA- -s simDog_chr6.simDog.chr6 446339 18 - 593897 GTATAATGAAAAACTCAC -s simHuman_chr6.simHuman.chr6 149747 18 + 601863 CTACATGGTTAGCCTCAC -s simRat_chr6.simRat.chr6 176667 17 + 647215 GTA-ATGATTAGCCTTGC - -a -s simMouse_chr6.simMouse.chr6 186384 4 + 636262 CTGT -s Anc0.Anc0refChr1 45363 4 - 62388 ACAT -s Anc1.Anc1refChr2 124763 4 + 144309 ACAT -s Anc2.Anc2refChr3 34855 4 + 53186 ATAT -s mr.mrrefChr5 41460 4 + 294540 ACGT -s simCow_chr6.simCow.chr6 163240 4 + 602619 ATAT -s simDog_chr6.simDog.chr6 446377 4 - 593897 ATAT -s simHuman_chr6.simHuman.chr6 149765 4 + 601863 ACAT -s simRat_chr6.simRat.chr6 176684 4 + 647215 ACGT - -a -s simMouse_chr6.simMouse.chr6 186388 28 + 636262 GGTTAACAATTTAATGATGTTGATACTG -s Anc0.Anc0refChr1 45367 28 - 62388 GGTTAACAATGTGGTGATGTTGGTAGTG -s Anc1.Anc1refChr2 124767 28 + 144309 GGTTAACAATGTGGTGATGTTGGTAGTG -s Anc2.Anc2refChr3 34859 28 + 53186 GGTTAACAATGTGATGATGTTGGTAGTG -s mr.mrrefChr5 41464 28 + 294540 GGTTAACAATTTAGTGATGTTGATACTG -s simCow_chr6.simCow.chr6 163244 28 + 602619 GATTAACAATGTGACGATGTTGGTAGTA -s simDog_chr6.simDog.chr6 446381 28 - 593897 AGCTAACAATGTGATGATGTTGGTAGTG -s simHuman_chr6.simHuman.chr6 149771 28 + 601863 GGTTAACAATGTGGTGATGTTGGTATGG -s simRat_chr6.simRat.chr6 176688 28 + 647215 GGGTAACAATTTAGTGATGTTGATAACG - -a -s simMouse_chr6.simMouse.chr6 186416 21 + 636262 TTGATGTGACCAACAGGATAA -s Anc0.Anc0refChr1 45395 21 - 62388 TTGACAAGACCAACAAGATAA -s Anc1.Anc1refChr2 124795 21 + 144309 TTGACAAGACCAACAAGATAA -s Anc2.Anc2refChr3 34887 21 + 53186 TTGACAAGACCAACAAGATAA -s mr.mrrefChr5 41492 21 + 294540 TTGATGTGACCAACAGGATAA -s simCow_chr6.simCow.chr6 163272 21 + 602619 TTAAATAGACCAACAGGATAA -s simDog_chr6.simDog.chr6 446409 21 - 593897 TTGACAAGATCAACCAAATAA -s simHuman_chr6.simHuman.chr6 149815 21 + 601863 CTGACAAGGCCAACATGGTGA -s simRat_chr6.simRat.chr6 176716 21 + 647215 TCAATGCAACAAGCAGAATAA - -a -s simMouse_chr6.simMouse.chr6 186437 41 + 636262 GATTACTTGTATAGGGAGGTGTACAAGAGGCCCTTGATAGG -s Anc0.Anc0refChr1 45416 40 - 62388 GTTCACTTGTATAGAAAGCTGAAAAA-AGGCATTTTATATG -s Anc1.Anc1refChr2 124816 40 + 144309 GTTCACTTGTATAGAAAGCTGAAAAA-AGGCATTTTATATG -s Anc2.Anc2refChr3 34908 40 + 53186 GTTCACTTGTATAGAAAGCTGAACAA-AGGCATAATATATG -s mr.mrrefChr5 41513 41 + 294540 GTTTACTTGTATAGGGAGGTGTAAAAGAGGCCTTTTATAGG -s simCow_chr6.simCow.chr6 163293 39 + 602619 GCGCACTTGTATCGAAAGTTGAACAA-GGGCATGGTATAC- -s simDog_chr6.simDog.chr6 446431 35 - 593897 GTTCACTAGTATAGACAGC-----AA-AGGCATAATATATG -s simHuman_chr6.simHuman.chr6 149836 40 + 601863 GTTCACTTGTGTAGAAAGCTACAAAA-AGATGTTTTATATG -s simRat_chr6.simRat.chr6 176737 41 + 647215 GTTTACCTGTAGAGGGAGATTTAAAAGAGGCCTTTTATAGG - -a -s simMouse_chr6.simMouse.chr6 186478 5 + 636262 AAACA -s Anc0.Anc0refChr1 45456 5 - 62388 AAAAA -s Anc1.Anc1refChr2 124856 5 + 144309 AAAAA -s Anc2.Anc2refChr3 34948 5 + 53186 AAAAA -s mr.mrrefChr5 41554 5 + 294540 AAACA -s simCow_chr6.simCow.chr6 163332 5 + 602619 AAAAG -s simDog_chr6.simDog.chr6 446467 5 - 593897 AAAAA -s simHuman_chr6.simHuman.chr6 149876 5 + 601863 AAAAA -s simRat_chr6.simRat.chr6 176778 5 + 647215 AAACC - -a -s simMouse_chr6.simMouse.chr6 186483 9 + 636262 ACTATGCAA -s Anc0.Anc0refChr1 45461 9 - 62388 AAGAGGCAA -s Anc1.Anc1refChr2 124861 9 + 144309 AAGAGGCAA -s Anc2.Anc2refChr3 34955 9 + 53186 AAGAGGCAA -s mr.mrrefChr5 41559 9 + 294540 ACTATGCAA -s simCow_chr6.simCow.chr6 163339 9 + 602619 AGGAGGCAA -s simDog_chr6.simDog.chr6 446474 9 - 593897 AAGAGTCAG -s simHuman_chr6.simHuman.chr6 149881 9 + 601863 AAGAGGCAA -s simRat_chr6.simRat.chr6 176783 9 + 647215 ATAACGCAA - -a -s simMouse_chr6.simMouse.chr6 186492 7 + 636262 ATCATGA -s Anc0.Anc0refChr1 45472 7 - 62388 ACCATGG -s Anc1.Anc1refChr2 124872 7 + 144309 ACCATGG -s Anc2.Anc2refChr3 34966 7 + 53186 ACCATGG -s mr.mrrefChr5 41568 7 + 294540 ACCATGA -s simCow_chr6.simCow.chr6 163350 7 + 602619 ATTATTG -s simDog_chr6.simDog.chr6 446485 7 - 593897 ACCATGG -s simHuman_chr6.simHuman.chr6 149892 7 + 601863 ACCATGG -s simRat_chr6.simRat.chr6 176792 7 + 647215 ACCATGA - -a -s simMouse_chr6.simMouse.chr6 186499 6 + 636262 TGACTA -s Anc0.Anc0refChr1 45486 6 - 62388 CAACTA -s Anc1.Anc1refChr2 124886 6 + 144309 CAACTA -s Anc2.Anc2refChr3 34980 6 + 53186 CAAATA -s mr.mrrefChr5 41582 6 + 294540 TGACTA -s simCow_chr6.simCow.chr6 163364 6 + 602619 CAAATA -s simDog_chr6.simDog.chr6 446499 6 - 593897 CAAACA -s simHuman_chr6.simHuman.chr6 149906 6 + 601863 CAACTA -s simRat_chr6.simRat.chr6 176806 6 + 647215 AGACTA - -a -s simMouse_chr6.simMouse.chr6 186505 12 + 636262 TGTTAATAGTGA -s Anc0.Anc0refChr1 45492 10 - 62388 TGTTGTTA--AA -s Anc1.Anc1refChr2 124892 10 + 144309 TGTTGTTA--AA -s Anc2.Anc2refChr3 34986 10 + 53186 TCTTGTTA--AA -s mr.mrrefChr5 41588 12 + 294540 TGTTAATAGTGA -s simCow_chr6.simCow.chr6 163370 10 + 602619 TTTTGTCA--AA -s simDog_chr6.simDog.chr6 446505 9 - 593897 TCTTGTTA--A- -s simHuman_chr6.simHuman.chr6 149914 10 + 601863 TGTTGTTA--AA -s simRat_chr6.simRat.chr6 176812 12 + 647215 TGTTAATAGTGA - -a -s simMouse_chr6.simMouse.chr6 186517 8 + 636262 CAACCAAA -s Anc0.Anc0refChr1 45502 8 - 62388 CAATCATA -s Anc1.Anc1refChr2 124902 8 + 144309 CAATCATA -s Anc2.Anc2refChr3 34996 8 + 53186 CTATCATA -s mr.mrrefChr5 41600 8 + 294540 CAACCAAA -s simCow_chr6.simCow.chr6 163387 8 + 602619 CTATCATA -s simDog_chr6.simDog.chr6 446514 4 - 593897 ----CATA -s simHuman_chr6.simHuman.chr6 149924 8 + 601863 CAATCATA -s simRat_chr6.simRat.chr6 176824 8 + 647215 CAGCCAAA - -a -s simMouse_chr6.simMouse.chr6 186525 3 + 636262 ATG -s Anc0.Anc0refChr1 45510 3 - 62388 AGG -s Anc1.Anc1refChr2 124910 3 + 144309 AGG -s Anc2.Anc2refChr3 35004 3 + 53186 AGG -s mr.mrrefChr5 41608 3 + 294540 ATG -s simCow_chr6.simCow.chr6 163395 3 + 602619 AGG -s simDog_chr6.simDog.chr6 446589 3 - 593897 AGG -s simHuman_chr6.simHuman.chr6 149932 3 + 601863 AGG -s simRat_chr6.simRat.chr6 176832 3 + 647215 ATG - -a -s simMouse_chr6.simMouse.chr6 186528 4 + 636262 ATAA -s Anc0.Anc0refChr1 45515 4 - 62388 ATAA -s Anc1.Anc1refChr2 124915 4 + 144309 ATAA -s Anc2.Anc2refChr3 35009 4 + 53186 AGAA -s mr.mrrefChr5 41611 4 + 294540 ATAA -s simCow_chr6.simCow.chr6 163400 4 + 602619 ACAA -s simDog_chr6.simDog.chr6 446594 4 - 593897 AGAA -s simHuman_chr6.simHuman.chr6 149937 4 + 601863 ATAA -s simRat_chr6.simRat.chr6 176835 4 + 647215 ATAA - -a -s simMouse_chr6.simMouse.chr6 186532 2 + 636262 AG -s Anc0.Anc0refChr1 45525 2 - 62388 AG -s Anc1.Anc1refChr2 124925 2 + 144309 AG -s Anc2.Anc2refChr3 35019 2 + 53186 TG -s mr.mrrefChr5 41615 2 + 294540 AG -s simCow_chr6.simCow.chr6 163410 2 + 602619 TG -s simDog_chr6.simDog.chr6 446604 2 - 593897 TA -s simHuman_chr6.simHuman.chr6 149947 2 + 601863 AG -s simRat_chr6.simRat.chr6 176839 2 + 647215 AG - -a -s simMouse_chr6.simMouse.chr6 186534 39 + 636262 GAGACCCGGAGTGCAAAATCAGGGCCGAATAAAAGATTT -s Anc0.Anc0refChr1 45527 39 - 62388 AAGACCTGGTGTAAAAAGTCAGGGCCTAGTAAAAAATTT -s Anc1.Anc1refChr2 124927 39 + 144309 AAGACCTGGTGTAAAAAGTCAGGGCCTAGTAAAAAATTT -s Anc2.Anc2refChr3 35021 39 + 53186 AAGACCTGGTGTAAGAAGTCGGGGCCTAGTAAAGAATAT -s mr.mrrefChr5 41617 39 + 294540 GAGACCTGGAGTACAAAATCAGGGCCGAATAAAAGATTT -s simCow_chr6.simCow.chr6 163412 37 + 602619 ACAAACTGTTGTAAG--GTTGGGCCCTAGGAATGACTTT -s simDog_chr6.simDog.chr6 446606 39 - 593897 AAGACCTAGTTGAAGAAGTCGAGGTCTAGTAAAGAATAT -s simHuman_chr6.simHuman.chr6 149949 39 + 601863 AAGATCTGGTGTAAAAAGTCAGGGCCTAGTAAAAAATTT -s simRat_chr6.simRat.chr6 176846 39 + 647215 GAGTCTTGCAGCACAAAATCAGGGCTGAATAAAAGATTT - -a -s simMouse_chr6.simMouse.chr6 186573 47 + 636262 TGAGATTCAAAACATTCTGGATTTTTCAAAGAGTGAGTTCTCCTTCA -s Anc0.Anc0refChr1 45566 30 - 62388 TGA----------------GATTTGTCACAGAGTCAG-TCCTCCTCT -s Anc1.Anc1refChr2 124966 31 + 144309 TGA----------------GATTTGTCACAGAGTCAGGTCCTCCTCT -s Anc2.Anc2refChr3 35060 30 + 53186 TGA----------------GATTTGTAACAGAGTCAG-TCCTACTCT -s mr.mrrefChr5 41656 47 + 294540 TGAGATTCAAAACATTCTGGATTTTTCAAAGAGTCAGTTCTCCTTCA -s simCow_chr6.simCow.chr6 163449 27 + 602619 TGA----------------GATTTGTTACAGAGTCAG-TCATAC--- -s simDog_chr6.simDog.chr6 446645 30 - 593897 TGA----------------GAATTGTAAGAGAGTCAG-TCCTACTCT -s simHuman_chr6.simHuman.chr6 149990 31 + 601863 TGA----------------GATTTGTCACAGAGTCAAGTCCTCCTCT -s simRat_chr6.simRat.chr6 176885 47 + 647215 TGAGGTGCATAACATTTTGGATTTTTCAAAGAGTCAGTTCTCCTTTA - -a -s simMouse_chr6.simMouse.chr6 186620 116 + 636262 TATTGGTAAAGCTTGACTGAGTTTCCTGGTTTTTGTTCCACATACCAGTGAGATACTATATTATAGCTGCATTGCTCCATTGCTTCTAGATCTAACTTACGTAGAGAGTTGAGAGT -s Anc0.Anc0refChr1 45596 107 - 62388 TATTGGTACTGCTTGACCGAGTTTGCTGACTTTCGTTCTATGTATCAGTGAGATACTATAATCTATCTATATTGC---------TCTAGTTCTAACCTTGCTAGAGAGCTGAGGGT -s Anc1.Anc1refChr2 124997 107 + 144309 TATTGGTACTGCTTGACCGAGTTTGCTGACTTTCGTTCTATGTATCAGTGAGATACTATAATCTATCTATATTGC---------TCTAGTTCTAACCTTGCTAGAGAGCTGAGGGT -s Anc2.Anc2refChr3 35090 107 + 53186 TATTGGTACTACTTGACCGAGTTTGCTGACTTTCATTCTATGTATCAGTGAGATACTATAATCTATCTATATTGC---------TCTAGTTGTAACCTTGCTAGAGAGCTGAGGGT -s mr.mrrefChr5 41703 107 + 294540 TATTGGTAATGCTTGACCGAGTTTCCTGGTTTTTGTTCTACATACCAGTGAGATACTATATTATAGCTGCATTGC---------TCTAGATCTAACTTACGTAGAGAGTTGAGGGT -s simCow_chr6.simCow.chr6 163476 100 + 602619 -ATTGATACCACTTGACTGAGTTTGCTGACTGTCGTTTTATGTACCAGTGAG----TATGGTCTATCCACATTGC---------TCGAATTGTAACCTTACC--AGAGCTGAGGGC -s simDog_chr6.simDog.chr6 446676 107 - 593897 TACTGGTACTACTTGACCGACTTTACTGACTTTCATTCTAGTTATCAGAGAGATACTATAATCTATCTTTGTTAG---------TCTAGTTGTAACCTTGCTAGAGAGCTGAAGGT -s simHuman_chr6.simHuman.chr6 150021 106 + 601863 TATTTGTACTGCTTGACCGAGTTTGCTGAC-TTGGATCTATGTAACAGTGAGGTACTATAATCTATCTATATTGC---------TCTAGCTCTAACCTTGCTATAGAGCCGAGGGT -s simRat_chr6.simRat.chr6 176932 107 + 647215 TGTTGGTAGTGTTTGATCGAGTTTCATGGTTTTTGTTCTACATGCCAGTGAGATACTATGTTATAGCTGCATTGC---------TCTAGATCTAACATGTGTGGAGAGTTGAGGGT - -a -s simMouse_chr6.simMouse.chr6 186736 8 + 636262 AGATTAAG -s Anc0.Anc0refChr1 45704 8 - 62388 AGATTTAG -s Anc1.Anc1refChr2 125105 8 + 144309 AGATTTAG -s Anc2.Anc2refChr3 35198 8 + 53186 AGATCAAG -s mr.mrrefChr5 41811 8 + 294540 AGATTTAG -s simCow_chr6.simCow.chr6 163577 8 + 602619 AGATCAAG -s simDog_chr6.simDog.chr6 446784 8 - 593897 ACATCAAG -s simHuman_chr6.simHuman.chr6 150128 8 + 601863 AGGTTTAG -s simRat_chr6.simRat.chr6 177040 8 + 647215 AGATTTAG - -a -s simMouse_chr6.simMouse.chr6 186744 8 + 636262 ATTCATGT -s Anc0.Anc0refChr1 45713 8 - 62388 ATTCATTT -s Anc1.Anc1refChr2 125114 8 + 144309 ATTCATTT -s Anc2.Anc2refChr3 35207 8 + 53186 ATTCATTT -s mr.mrrefChr5 41819 8 + 294540 ATTCATGT -s simCow_chr6.simCow.chr6 163586 8 + 602619 ATTCATTT -s simDog_chr6.simDog.chr6 446793 8 - 593897 ATTCATTT -s simHuman_chr6.simHuman.chr6 150137 8 + 601863 ATTCATTT -s simRat_chr6.simRat.chr6 177048 8 + 647215 ATTCATGT - -a -s simMouse_chr6.simMouse.chr6 186752 8 + 636262 TTTAGAAA -s Anc0.Anc0refChr1 45721 8 - 62388 GCTAGGAA -s Anc1.Anc1refChr2 125122 8 + 144309 GCTAGGAA -s Anc2.Anc2refChr3 35215 8 + 53186 GCTAGGAA -s mr.mrrefChr5 41827 8 + 294540 TCTAGAAA -s simCow_chr6.simCow.chr6 163612 8 + 602619 GCTAAGAA -s simDog_chr6.simDog.chr6 446801 8 - 593897 GCTAGGAG -s simHuman_chr6.simHuman.chr6 150145 8 + 601863 GCTAGGAA -s simRat_chr6.simRat.chr6 177056 8 + 647215 TCTAGAAA - -a -s simMouse_chr6.simMouse.chr6 186760 10 + 636262 GAATTGAAAA -s Anc0.Anc0refChr1 45734 10 - 62388 GAATGGAAGA -s Anc1.Anc1refChr2 125135 10 + 144309 GAATGGAAGA -s Anc2.Anc2refChr3 35228 10 + 53186 GAATGGAAGA -s mr.mrrefChr5 41835 10 + 294540 GAATTGAAAA -s simCow_chr6.simCow.chr6 163625 10 + 602619 GAATGGGGGA -s simDog_chr6.simDog.chr6 446814 10 - 593897 GAATGGAAGA -s simHuman_chr6.simHuman.chr6 150158 10 + 601863 GAATGGAAGA -s simRat_chr6.simRat.chr6 177064 10 + 647215 GAATTGAAAA - -a -s simMouse_chr6.simMouse.chr6 186770 16 + 636262 GTTGGTTGGCTAGGAA -s Anc0.Anc0refChr1 45744 9 - 62388 GTTCGTT-G------A -s Anc1.Anc1refChr2 125145 15 + 144309 GTTCGTT-GCTAGGAA -s Anc2.Anc2refChr3 35238 9 + 53186 GTTCGTT-G------A -s mr.mrrefChr5 41845 16 + 294540 GTTGGTTGGCTAGGAA -s simCow_chr6.simCow.chr6 163646 9 + 602619 GTCCGTT-G------A -s simDog_chr6.simDog.chr6 446824 9 - 593897 GTTCGTT-G------G -s simHuman_chr6.simHuman.chr6 150168 15 + 601863 ATTCATT-GCTAGGAA -s simRat_chr6.simRat.chr6 177074 16 + 647215 GTTTGTTGGCTAGGAA - -a -s simMouse_chr6.simMouse.chr6 186786 4 + 636262 TACA -s Anc0.Anc0refChr1 45770 4 - 62388 TATC -s Anc1.Anc1refChr2 125177 4 + 144309 TATC -s Anc2.Anc2refChr3 35264 4 + 53186 CCTC -s mr.mrrefChr5 41861 4 + 294540 TACA -s simCow_chr6.simCow.chr6 163681 4 + 602619 GGTC -s simDog_chr6.simDog.chr6 446849 4 - 593897 CCAA -s simHuman_chr6.simHuman.chr6 150200 4 + 601863 TATC -s simRat_chr6.simRat.chr6 177090 4 + 647215 TACA - -a -s simMouse_chr6.simMouse.chr6 186790 32 + 636262 CTGTGAGCTATAGGCCCATACAAGAGATGGGC -s Anc0.Anc0refChr1 45774 32 - 62388 CTGTGAGCCATATACCTATATTAGAGGTGGGC -s Anc1.Anc1refChr2 125181 32 + 144309 CTGTGAGCCATATACCTATATTAGAGGTGGGC -s Anc2.Anc2refChr3 35268 32 + 53186 CTTTAAGCCATATACCTATATTAGAGGTGAAC -s mr.mrrefChr5 41865 32 + 294540 CTGTGAGCTATAGGCCTATATAAGAGATGGGC -s simCow_chr6.simCow.chr6 163692 31 + 602619 ATTTTAGCCATACACCTATA-TACGTGTGAAC -s simDog_chr6.simDog.chr6 446853 29 - 593897 CTTTAAACCATATGCCTATGTTAGAGGTG--- -s simHuman_chr6.simHuman.chr6 150204 32 + 601863 CTGTGAGCCATAAACCTATATTAAAGGTTGGC -s simRat_chr6.simRat.chr6 177094 32 + 647215 CTGTGAGCTATAGGACTATATGAGAGATGGGC - -a -s simMouse_chr6.simMouse.chr6 186822 25 + 636262 CCACTATCACATAAGGGAACAAAAG -s Anc0.Anc0refChr1 45806 24 - 62388 CCACCAGCTCATATAGTAA-ACATG -s Anc1.Anc1refChr2 125213 24 + 144309 CCACCAGCTCATATAGTAA-ACATG -s Anc2.Anc2refChr3 35300 24 + 53186 TCACCAGTTCATATAATAA-ACATG -s mr.mrrefChr5 41897 24 + 294540 CCACTATCACATAAGGGAA-AAAAG -s simCow_chr6.simCow.chr6 163723 24 + 602619 TCACCAGTTCATAACATAA-ACATG -s simDog_chr6.simDog.chr6 446882 21 - 593897 ---CCCCTTCATGTAATAA-ATTTG -s simHuman_chr6.simHuman.chr6 150236 24 + 601863 CTACCAGCTTGTATAGTAA-ACATG -s simRat_chr6.simRat.chr6 177132 24 + 647215 CCACAATTACATAAGGGAA-AAAAT - -a -s simMouse_chr6.simMouse.chr6 186847 12 + 636262 TTGCAAAGGAAT -s Anc0.Anc0refChr1 45838 12 - 62388 TTGCAAAGGGAT -s Anc1.Anc1refChr2 125245 12 + 144309 TTGCAAAGGGAT -s Anc2.Anc2refChr3 35332 12 + 53186 TTGCAAAGGGAT -s mr.mrrefChr5 41921 12 + 294540 TTGCAAAGGAAT -s simCow_chr6.simCow.chr6 163755 12 + 602619 TTGCAAAGGGAT -s simDog_chr6.simDog.chr6 446904 12 - 593897 ATCAAAAGGGAT -s simHuman_chr6.simHuman.chr6 150268 12 + 601863 TTGCAAATGGAT -s simRat_chr6.simRat.chr6 177156 12 + 647215 TTGGAAAGCAAT - -a -s simMouse_chr6.simMouse.chr6 186859 25 + 636262 CCGGCCAGACTCAGAATGAGGGTTG -s Anc0.Anc0refChr1 45860 22 - 62388 CAGTTCAGACTCAGAGTTAG---TG -s Anc1.Anc1refChr2 125267 22 + 144309 CAGTTCAGACTCAGAGTTAG---TG -s Anc2.Anc2refChr3 35354 22 + 53186 CAGTTCAGACCCAGAGTTGG---GG -s mr.mrrefChr5 41933 25 + 294540 CAGGCCAGACTCAGAATGAGGGTTG -s simDog_chr6.simDog.chr6 446918 22 - 593897 CAGTTCAGACCCAGAGTTGG---GG -s simHuman_chr6.simHuman.chr6 150290 22 + 601863 CAGTTCAGATTCGGAGTCAG---TG -s simRat_chr6.simRat.chr6 177168 25 + 647215 CAGGCCAGACTCAGAATGGGGGTTG - -a -s simMouse_chr6.simMouse.chr6 186884 3 + 636262 AGT -s Anc0.Anc0refChr1 45882 3 - 62388 AGC -s Anc1.Anc1refChr2 125289 3 + 144309 AGC -s Anc2.Anc2refChr3 35376 3 + 53186 AGT -s mr.mrrefChr5 41958 3 + 294540 AGC -s simDog_chr6.simDog.chr6 446942 3 - 593897 AGT -s simHuman_chr6.simHuman.chr6 150312 3 + 601863 AGC -s simRat_chr6.simRat.chr6 177193 3 + 647215 AGC - -a -s simMouse_chr6.simMouse.chr6 186887 12 + 636262 GAAGTTTAAGAC -s Anc0.Anc0refChr1 45900 12 - 62388 GCGGTATAAGAC -s Anc1.Anc1refChr2 125307 12 + 144309 GCGGTATAAGAC -s Anc2.Anc2refChr3 35394 12 + 53186 GCGGTATAAGAC -s mr.mrrefChr5 41976 12 + 294540 GAAGTATAAGAC -s simCow_chr6.simCow.chr6 163781 12 + 602619 GAGGTATAAGAC -s simDog_chr6.simDog.chr6 446960 12 - 593897 GCGGTATAAAGA -s simHuman_chr6.simHuman.chr6 150332 12 + 601863 GTGGTATAAGAC -s simRat_chr6.simRat.chr6 177211 12 + 647215 GAAGCATAGAAC - -a -s simMouse_chr6.simMouse.chr6 186899 13 + 636262 TACAGCTTGCCTG -s Anc0.Anc0refChr1 45913 13 - 62388 TATATCTTGCCTG -s Anc1.Anc1refChr2 125320 13 + 144309 TATATCTTGCCTG -s Anc2.Anc2refChr3 35407 13 + 53186 TATATCTTGCCTG -s mr.mrrefChr5 41988 13 + 294540 TATATCTTGCCTG -s simCow_chr6.simCow.chr6 163794 13 + 602619 TATGTCTTGCCTG -s simDog_chr6.simDog.chr6 446973 13 - 593897 TATATCTCGTCAG -s simHuman_chr6.simHuman.chr6 150345 13 + 601863 TATATTGTACCTG -s simRat_chr6.simRat.chr6 177223 13 + 647215 TATATCTTGCCTG - -a -s simMouse_chr6.simMouse.chr6 186912 1 + 636262 A -s Anc0.Anc0refChr1 45929 1 - 62388 A -s Anc1.Anc1refChr2 125336 1 + 144309 A -s Anc2.Anc2refChr3 35423 1 + 53186 A -s mr.mrrefChr5 42001 1 + 294540 A -s simDog_chr6.simDog.chr6 446989 1 - 593897 A -s simHuman_chr6.simHuman.chr6 150361 1 + 601863 A -s simRat_chr6.simRat.chr6 177236 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 186913 2 + 636262 GT -s Anc0.Anc0refChr1 45930 2 - 62388 GG -s Anc1.Anc1refChr2 125337 2 + 144309 GG -s Anc2.Anc2refChr3 35424 2 + 53186 GG -s mr.mrrefChr5 42002 2 + 294540 GT -s simCow_chr6.simCow.chr6 163808 2 + 602619 GG -s simDog_chr6.simDog.chr6 446991 2 - 593897 GG -s simHuman_chr6.simHuman.chr6 150362 2 + 601863 GG -s simRat_chr6.simRat.chr6 177237 2 + 647215 AT - -a -s simMouse_chr6.simMouse.chr6 186915 45 + 636262 GTAGCTTTAACTGGTGCTAAAAATGGTTACAGTATAAGCTAGCTG -s Anc0.Anc0refChr1 45932 45 - 62388 AGAGCTTTAACTGCTGCTGAAAATGGTTAAATTGTAAGCTATTCA -s Anc1.Anc1refChr2 125339 45 + 144309 AGAGCTTTAACTGCTGCTGAAAATGGTTAAATTGTAAGCTATTCA -s Anc2.Anc2refChr3 35426 45 + 53186 AGGGCCTTAACTGCTGCTGAAAATGGTTAAATTGTGAGCTATTCA -s mr.mrrefChr5 42004 45 + 294540 GTAGCTTTAACTGGTGCTAAAAATGGTTACAGTATAAGCTAGCTG -s simCow_chr6.simCow.chr6 163810 45 + 602619 AAGGCCTTAACTGCTGCTGAAAAAGGTTAACTTGTGAGCTATTTG -s simDog_chr6.simDog.chr6 446993 40 - 593897 AGGGC-----CTGCTGCTCAAAATGGTAAAATTGTGAGCTATTCA -s simHuman_chr6.simHuman.chr6 150364 45 + 601863 AGAGCTTTGACTGCTGCTGAAAATGGTTAAATTGTAAGCTATTCA -s simRat_chr6.simRat.chr6 177240 45 + 647215 GTAGCTTTAAATGGTGCTAAAGATGGTTACAGTATAAGCTAGCTG - -a -s simMouse_chr6.simMouse.chr6 186960 17 + 636262 CCAACCTTGTATTCACC -s Anc0.Anc0refChr1 45978 17 - 62388 CAAACATTGTATTCATT -s Anc1.Anc1refChr2 125385 17 + 144309 CAAACATTGTATTCATT -s Anc2.Anc2refChr3 35472 17 + 53186 CAAACACTGTCTTGATT -s mr.mrrefChr5 42050 17 + 294540 CCAACCTTGTATTCACC -s simCow_chr6.simCow.chr6 163856 4 + 602619 CACA------------- -s simDog_chr6.simDog.chr6 447034 17 - 593897 TAAACACTGTCTTGATT -s simHuman_chr6.simHuman.chr6 150410 17 + 601863 CAAACATTGCATTCATT -s simRat_chr6.simRat.chr6 177286 17 + 647215 CCAACCTTGTATTCACC - -a -s simMouse_chr6.simMouse.chr6 186977 15 + 636262 TACATTTCCAGATAC -s Anc0.Anc0refChr1 46001 12 - 62388 TACAGTTCCACA--- -s Anc1.Anc1refChr2 125408 15 + 144309 TACAGTTCCACATAC -s Anc2.Anc2refChr3 35495 12 + 53186 TACAGTTCCACA--- -s mr.mrrefChr5 42067 15 + 294540 TACATTTCCAGATAC -s simCow_chr6.simCow.chr6 163860 6 + 602619 ------TCCACA--- -s simDog_chr6.simDog.chr6 447057 12 - 593897 TACAGTTCCACA--- -s simHuman_chr6.simHuman.chr6 150433 15 + 601863 TGCAGTTCTACATAC -s simRat_chr6.simRat.chr6 177303 15 + 647215 TACATTTCCAGATCC - -a -s simMouse_chr6.simMouse.chr6 186992 9 + 636262 AATTGCACA -s Anc0.Anc0refChr1 46013 1 - 62388 --------A -s Anc1.Anc1refChr2 125423 9 + 144309 AGTTCCAAA -s Anc2.Anc2refChr3 35507 1 + 53186 --------A -s mr.mrrefChr5 42082 9 + 294540 AATTGCACA -s simCow_chr6.simCow.chr6 163866 1 + 602619 --------A -s simDog_chr6.simDog.chr6 447069 1 - 593897 --------A -s simHuman_chr6.simHuman.chr6 150448 9 + 601863 AGTTCCAAA -s simRat_chr6.simRat.chr6 177345 9 + 647215 AATTTCACA - -a -s simMouse_chr6.simMouse.chr6 187001 5 + 636262 ACAGC -s Anc0.Anc0refChr1 46014 5 - 62388 AAAAT -s Anc1.Anc1refChr2 125432 5 + 144309 AAAAT -s Anc2.Anc2refChr3 35508 5 + 53186 AAAAT -s mr.mrrefChr5 42091 5 + 294540 ACAGC -s simCow_chr6.simCow.chr6 163868 5 + 602619 AAATT -s simDog_chr6.simDog.chr6 447070 5 - 593897 CGAAT -s simHuman_chr6.simHuman.chr6 150457 5 + 601863 AAAAT -s simRat_chr6.simRat.chr6 177354 5 + 647215 ACAGG - -a -s simMouse_chr6.simMouse.chr6 187006 5 + 636262 ACTCT -s Anc0.Anc0refChr1 46019 5 - 62388 ACTCC -s Anc1.Anc1refChr2 125437 5 + 144309 ACTCC -s Anc2.Anc2refChr3 35513 5 + 53186 ACTCC -s mr.mrrefChr5 42096 5 + 294540 ACTCT -s simCow_chr6.simCow.chr6 163873 5 + 602619 ACTCC -s simDog_chr6.simDog.chr6 447075 5 - 593897 ACTGT -s simHuman_chr6.simHuman.chr6 150462 5 + 601863 AGTCC -s simRat_chr6.simRat.chr6 177360 5 + 647215 GCTCT - -a -s simMouse_chr6.simMouse.chr6 187011 7 + 636262 CCAAATT -s Anc0.Anc0refChr1 46024 7 - 62388 CCAGATT -s Anc1.Anc1refChr2 125442 7 + 144309 CCAGATT -s Anc2.Anc2refChr3 35518 7 + 53186 CCAGATT -s mr.mrrefChr5 42101 7 + 294540 CCAAATT -s simCow_chr6.simCow.chr6 163886 7 + 602619 CCAGATT -s simDog_chr6.simDog.chr6 447080 7 - 593897 CCAGATT -s simHuman_chr6.simHuman.chr6 150467 7 + 601863 CCAGATT -s simRat_chr6.simRat.chr6 177365 6 + 647215 CCAAA-T - -a -s simMouse_chr6.simMouse.chr6 187018 81 + 636262 TATCAAATTCTATGTGGGGAACGAGGTAACTTTGAATTGTAAATTTTTGGTAGCGAGTCTCTTGATTGGTACAACTTCCCT -s Anc0.Anc0refChr1 46031 67 - 62388 TTGCAAATGCAACATATGGGGCAAGGTAAATTTG--------------GGTAGCAAGTTTCTTTGTCAGGAATCCTTTTCT -s Anc1.Anc1refChr2 125449 67 + 144309 TTGCAAATGCAACATATGGGGCAAGGTAAATTTG--------------GGTAGCAAGTTTCTTTGTCAGGAATCCTTTTCT -s Anc2.Anc2refChr3 35525 67 + 53186 TTGTAAATGCAACACATGGGGCAAGGTAAATTTG--------------GGTAGTAATTTTCTTTGTCAGGAATCCTTTTCT -s mr.mrrefChr5 42108 81 + 294540 TTTCAAATGCTATGTGTGGAACGAGGTAAATTTGAATTGTAAATTTTTGGTAGCAAGTCTCTTGATTGGTACAACTTCCCT -s simCow_chr6.simCow.chr6 163893 67 + 602619 TTTTAAATGGAACACATGGGGCAAAGTAAGTTTG--------------GATAGTAATTTTCTTTGACAGGAATCTTTGTCT -s simDog_chr6.simDog.chr6 447091 67 - 593897 TTGTAAATGCAACACATGGGGCATGGTAAACTAG--------------GGTGGTAATTTTCTTTGTCAGGAATCCTTTTCT -s simHuman_chr6.simHuman.chr6 150474 67 + 601863 TTCCAAATGCAACATATGGGGTTAGGTAAATTTG--------------GGTAGCAAGTTTCTTTGTCAGGAAGCCTTTTCT -s simRat_chr6.simRat.chr6 177371 81 + 647215 TTTCAAATGCTATGTGTGGAACAAGGTAAATTTGAATTGTAAATATACAATGGAAAGTCTTTTGTTTGGTACAACTTCCCT - -a -s simMouse_chr6.simMouse.chr6 187099 49 + 636262 GTTCATGTGATGCGGCAGAAAATAAATGGGGCCAGCACAATCTTTCAGT -s Anc0.Anc0refChr1 46098 49 - 62388 GTCCATATCATGGGGCAGAAAATAAATGAGCCAAGCAGAATCTTTCAGT -s Anc1.Anc1refChr2 125516 49 + 144309 GTCCATATCATGGGGCAGAAAATAAATGAGCCAAGCAGAATCTTTCAGT -s Anc2.Anc2refChr3 35592 49 + 53186 GTCCATATCATGGAGCAGAAAGTAAATGAGCCAATCAGAATCTTTCAGT -s mr.mrrefChr5 42189 49 + 294540 GTTCATGTGATGCGGCAGAAAATAAATGGGGCCAGCACAATCTTTCAGT -s simCow_chr6.simCow.chr6 163960 49 + 602619 GCCTGTATCTTGGAGCAGAAGGTAAATGGGCCAATCAGAGTCCTTCAGT -s simDog_chr6.simDog.chr6 447184 49 - 593897 GTCCACATTATCGAGCAGAAAGTAGATGAGCCAATCTGAACTTTTCAGT -s simHuman_chr6.simHuman.chr6 150541 49 + 601863 GTCCATATCAGGGGGCAGTAAATAAATGAGCCAAGCAGAATCTTTCAGT -s simRat_chr6.simRat.chr6 177452 47 + 647215 GTTCATGTGATGCGTCAGAAAGTAAGTGGGGTCAGCACAATCTTTCA-- - -a -s simMouse_chr6.simMouse.chr6 187148 8 + 636262 GTTTATGT -s Anc0.Anc0refChr1 46147 3 - 62388 TTT----- -s Anc1.Anc1refChr2 125565 8 + 144309 TTTCTTGT -s Anc2.Anc2refChr3 35641 3 + 53186 TCT----- -s mr.mrrefChr5 42238 8 + 294540 GTTTATGT -s simCow_chr6.simCow.chr6 164011 3 + 602619 TGT----- -s simDog_chr6.simDog.chr6 447233 3 - 593897 TCT----- -s simHuman_chr6.simHuman.chr6 150590 8 + 601863 TTTCTTGT -s simRat_chr6.simRat.chr6 177499 8 + 647215 GTTTATGT - -a -s simMouse_chr6.simMouse.chr6 187156 52 + 636262 AACATACCATTTCCATGGTCTAATAGCTTATATTCAATGATTCAGACCCCCA -s Anc0.Anc0refChr1 46150 35 - 62388 -----------------TGCTAATAGCTTATATATGGGAGTTCAGACCCCCA -s Anc1.Anc1refChr2 125573 45 + 144309 GATATATCAT-------TGCTAATAGCTTATATATGGGAGTTCAGACCCCCA -s Anc2.Anc2refChr3 35644 35 + 53186 -----------------TGCTAATAGCTTATATATGGGGGTTCAAACCCCTA -s mr.mrrefChr5 42246 52 + 294540 AACATACCATTTCCATGTTCTAATAGCTTATATTCAGTAATTCAGACCCCCA -s simCow_chr6.simCow.chr6 164014 35 + 602619 -----------------TTCGAATAACTTGTATATGGGGGTTCAAAACTCTA -s simDog_chr6.simDog.chr6 447236 35 - 593897 -----------------TGCTCATAGCTTATGTATGGGGGTTCAAACCCCTA -s simHuman_chr6.simHuman.chr6 150599 45 + 601863 GATATATCAT-------TGCTAATAGCCTATATAAGGGAGCTCAGACCCCCA -s simRat_chr6.simRat.chr6 177507 52 + 647215 AACATACTGTTTTCAAGTTCTAATAGCTTATAATCAGTAATTCAGACCCCCA - -a -s simMouse_chr6.simMouse.chr6 187208 28 + 636262 ATGATTACCAGCAGTAAGAAAGCCAGAA -s Anc0.Anc0refChr1 46185 20 - 62388 ACACTTACCAGCTGTT--------GGAA -s Anc1.Anc1refChr2 125618 20 + 144309 ACACTTACCAGCTGTT--------GGAA -s Anc2.Anc2refChr3 35679 20 + 53186 TCACTTAGCAGCTGTT--------GGAA -s mr.mrrefChr5 42298 20 + 294540 ATAATTACCAGCAGTA--------AGAA -s simCow_chr6.simCow.chr6 164049 20 + 602619 TCACTTGTCAGCTGTT--------AGAA -s simDog_chr6.simDog.chr6 447271 20 - 593897 TCACTTAGCAGCTGTT--------GGGA -s simHuman_chr6.simHuman.chr6 150644 20 + 601863 ACACTTACCAGCTGCT--------GGAA -s simRat_chr6.simRat.chr6 177565 20 + 647215 ATAATTACCAGCAGTA--------AGAA - -a -s simMouse_chr6.simMouse.chr6 187236 22 + 636262 AGCCAGGCATCGTGGTTAGTCA -s Anc0.Anc0refChr1 46205 22 - 62388 AGCCAGGTGAAGTGGCCAATCA -s Anc1.Anc1refChr2 125638 22 + 144309 AGCCAGGTGAAGTGGCCAATCA -s Anc2.Anc2refChr3 35699 22 + 53186 AGCCAAATGAAATGGCCAACCA -s mr.mrrefChr5 42318 22 + 294540 AGCCAGGCATCGTGGTTAGTCA -s simCow_chr6.simCow.chr6 164069 21 + 602619 AGCTAATTGAAATGGCCAACC- -s simDog_chr6.simDog.chr6 447292 10 - 593897 AGCCGAATG------------A -s simHuman_chr6.simHuman.chr6 150664 22 + 601863 AGTCAGGTGAAGTGGGCAATCA -s simRat_chr6.simRat.chr6 177585 22 + 647215 AGCCAGGCATCTCGGCGAGCCA - -a -s simMouse_chr6.simMouse.chr6 187258 2 + 636262 TC -s Anc0.Anc0refChr1 46241 2 - 62388 GA -s Anc1.Anc1refChr2 125674 2 + 144309 GA -s Anc2.Anc2refChr3 35735 2 + 53186 GA -s mr.mrrefChr5 42340 2 + 294540 TC -s simCow_chr6.simCow.chr6 164103 2 + 602619 GA -s simDog_chr6.simDog.chr6 447316 2 - 593897 GA -s simHuman_chr6.simHuman.chr6 150700 2 + 601863 GA -s simRat_chr6.simRat.chr6 177607 2 + 647215 TC - -a -s simMouse_chr6.simMouse.chr6 187260 13 + 636262 AAACCAACACAGG -s Anc0.Anc0refChr1 46243 13 - 62388 AGATCAACACAGT -s Anc1.Anc1refChr2 125676 13 + 144309 AGATCAACACAGT -s Anc2.Anc2refChr3 35739 13 + 53186 AGATCAACACAGT -s mr.mrrefChr5 42342 13 + 294540 AAACCAACACAGG -s simCow_chr6.simCow.chr6 164107 13 + 602619 AGATCACAACAGT -s simDog_chr6.simDog.chr6 447320 13 - 593897 AGATCAACTCAGT -s simHuman_chr6.simHuman.chr6 150702 13 + 601863 AGATCAACACAGT -s simRat_chr6.simRat.chr6 177609 13 + 647215 AAACCAACACAGG - -a -s simMouse_chr6.simMouse.chr6 187273 32 + 636262 TCAGTGGGGAAGTTGGCAGTGTTACATGTTAC -s Anc0.Anc0refChr1 46258 25 - 62388 TCAGTGTGGAGGCTGGCAGC-------ATTAC -s Anc1.Anc1refChr2 125691 25 + 144309 TCAGTGTGGAGGCTGGCAGC-------ATTAC -s Anc2.Anc2refChr3 35754 25 + 53186 TCAGTGTGGAGGCCAGCTGC-------ACTAC -s mr.mrrefChr5 42355 25 + 294540 TCAGTGGGGAAGTTGGCAGC-------GTTAC -s simCow_chr6.simCow.chr6 164122 25 + 602619 TCAGTGTGGAGAGCAGCTGC-------ACCAC -s simDog_chr6.simDog.chr6 447335 25 - 593897 TCAGTGTGGAAGCCAACTGC-------ACTGC -s simHuman_chr6.simHuman.chr6 150717 25 + 601863 TCAGTGAGAGGGATGGCAGC-------ATTAC -s simRat_chr6.simRat.chr6 177622 25 + 647215 TCAGTGGGGAAGTTGGCAGC-------GTTAC - -a -s simMouse_chr6.simMouse.chr6 187305 52 + 636262 ATGTAATGGTACCATATCTTGCCATTTACCTTGTGATTTATTGTGAGAACCC -s Anc0.Anc0refChr1 46283 52 - 62388 ATGTAATAGGAGCATAACTTACCAGTTTCCCTGATATTCACTATGAGAACTA -s Anc1.Anc1refChr2 125716 52 + 144309 ATGTAATAGGAGCATAACTTACCAGTTTCCCTGATATTCACTATGAGAACTA -s Anc2.Anc2refChr3 35779 52 + 53186 ATGTAATAAGAGCATAACTTACCAGTTTCCCTGATATTCACTATAAGCATCA -s mr.mrrefChr5 42380 52 + 294540 ATGTAATGGTACCATAACTTGCCATTTACCCTGTGATTTATTGTGAGAACTC -s simCow_chr6.simCow.chr6 164201 52 + 602619 ATGTAATGAGAGGATAATGTGCCAGTTTCCTTGATATTCACTACAAGTATCA -s simDog_chr6.simDog.chr6 447360 48 - 593897 ATATAAGAAGAGCAACACTCACTAGTTTTCCTAATATTCACTGTAAGC---- -s simHuman_chr6.simHuman.chr6 150742 52 + 601863 ATGTGATAGGAGCATAACTTACCGGTTTCCCTGATATTCACTATGAGAACTG -s simRat_chr6.simRat.chr6 177647 52 + 647215 ATGTAATGATACCATAATTTGCCATTTACCCTGTCATTTATTGTGAGAATTT - -a -s simMouse_chr6.simMouse.chr6 187357 35 + 636262 TACTTCTAAAGAAAGCCAGGTACTATCAAATTGGT -s Anc0.Anc0refChr1 46336 35 - 62388 TGCTTCTAAAGAAAGCCACGTACAGTGAAACTTGT -s Anc1.Anc1refChr2 125769 35 + 144309 TGCTTCTAAAGAAAGCCACGTACAGTGAAACTTGT -s Anc2.Anc2refChr3 35832 35 + 53186 TGCTTCTAAAGAAAGCCACATACAGTGACACTTGT -s mr.mrrefChr5 42433 35 + 294540 TGCTTCTAAAGAAAGCCAGGTACTATCAAATTGGT -s simCow_chr6.simCow.chr6 164254 35 + 602619 TGCATCCAAAGAAAGACACATATAGTGATACCTGT -s simDog_chr6.simDog.chr6 447408 33 - 593897 --CTTCTAAAAAAAGCCACATACAGTGACACTTGT -s simHuman_chr6.simHuman.chr6 150795 35 + 601863 TGCCAGTAAAGAAAGCCATGTCCAGTGAAACTCAT -s simRat_chr6.simRat.chr6 177700 35 + 647215 TGCTTCTAAAGAAAATCAGGTACTATCAAATCGGT - -a -s simMouse_chr6.simMouse.chr6 187392 2 + 636262 CA -s Anc0.Anc0refChr1 46371 2 - 62388 CT -s Anc1.Anc1refChr2 125804 2 + 144309 CT -s Anc2.Anc2refChr3 35867 2 + 53186 CT -s mr.mrrefChr5 42468 2 + 294540 CA -s simCow_chr6.simCow.chr6 164289 2 + 602619 CA -s simDog_chr6.simDog.chr6 447441 2 - 593897 CT -s simHuman_chr6.simHuman.chr6 150831 2 + 601863 CT -s simRat_chr6.simRat.chr6 177735 2 + 647215 CA - -a -s simMouse_chr6.simMouse.chr6 187394 14 + 636262 CCTGATATAGAGCT -s Anc0.Anc0refChr1 46373 13 - 62388 ACTGATATCAA-CT -s Anc1.Anc1refChr2 125806 14 + 144309 ACTGATATCAAACT -s Anc2.Anc2refChr3 35871 13 + 53186 ACTGATATCAA-CT -s mr.mrrefChr5 42470 14 + 294540 CCTGATATAGAGCT -s simCow_chr6.simCow.chr6 164293 13 + 602619 ACTGATATAAA-CT -s simDog_chr6.simDog.chr6 447445 13 - 593897 ACTGATATCAA-CT -s simHuman_chr6.simHuman.chr6 150833 14 + 601863 ACTGATATTAAATT -s simRat_chr6.simRat.chr6 177737 14 + 647215 CCTGATAGAGATCT - -a -s simMouse_chr6.simMouse.chr6 187408 4 + 636262 TTAC -s Anc0.Anc0refChr1 46388 4 - 62388 GGAC -s Anc1.Anc1refChr2 125822 4 + 144309 GGAC -s Anc2.Anc2refChr3 35886 4 + 53186 GGAC -s mr.mrrefChr5 42484 4 + 294540 GTAC -s simCow_chr6.simCow.chr6 164308 4 + 602619 TGAC -s simDog_chr6.simDog.chr6 447460 4 - 593897 GGAC -s simHuman_chr6.simHuman.chr6 150849 4 + 601863 GGAC -s simRat_chr6.simRat.chr6 177751 4 + 647215 GTAC - -a -s simMouse_chr6.simMouse.chr6 187412 18 + 636262 AACATTCTGAACGTCATG -s Anc0.Anc0refChr1 46392 18 - 62388 AACATTTTGGTTGTTATG -s Anc1.Anc1refChr2 125826 18 + 144309 AACATTTTGGTTGTTATG -s Anc2.Anc2refChr3 35890 18 + 53186 AACATTTTGGTTGTTATG -s mr.mrrefChr5 42488 18 + 294540 AACATTTTGAACGTCATG -s simCow_chr6.simCow.chr6 164326 18 + 602619 AATATTTTGATTGTTATG -s simDog_chr6.simDog.chr6 447464 18 - 593897 AACATTCTTGTTGTTAGG -s simHuman_chr6.simHuman.chr6 150853 18 + 601863 AACAGATTGGTTGTTATG -s simRat_chr6.simRat.chr6 177755 18 + 647215 AACATTTCGAACATCATG - -a -s simMouse_chr6.simMouse.chr6 187430 25 + 636262 ATAAGTAGGTTAGTTTGCTACATCT -s Anc0.Anc0refChr1 46410 25 - 62388 ATGAGAATGTTAGTATACTACATCC -s Anc1.Anc1refChr2 125844 25 + 144309 ATGAGAATGTTAGTATACTACATCC -s Anc2.Anc2refChr3 35908 25 + 53186 ATGAAAATGTCAGTATACTACATCC -s mr.mrrefChr5 42506 25 + 294540 ATAAGTATGTTAGTTTACTACATCT -s simCow_chr6.simCow.chr6 164344 15 + 602619 ATGAAAATGT--GTCTA-------- -s simDog_chr6.simDog.chr6 447482 25 - 593897 ATGCAAATGTCAATATGCTACATCC -s simHuman_chr6.simHuman.chr6 150871 25 + 601863 ATGAGAGTGTTAGTATACTACCTCC -s simRat_chr6.simRat.chr6 177775 25 + 647215 ATAAGTATATTAATTTACTACATAT - -a -s simMouse_chr6.simMouse.chr6 187455 30 + 636262 GGATAATGACGCTAAGGGTGAGACTTAATG -s Anc0.Anc0refChr1 46435 30 - 62388 AAATAAGGATGCTAAGTATGAGGCTTAATA -s Anc1.Anc1refChr2 125869 30 + 144309 AAATAAGGATGCTAAGTATGAGGCTTAATA -s Anc2.Anc2refChr3 35933 30 + 53186 AAATGAGGATGCTAAGTATGAGGATTAATA -s mr.mrrefChr5 42531 30 + 294540 GGATAATGACGCTAAGGGTGAGACTTAATG -s simCow_chr6.simCow.chr6 164359 22 + 602619 --------ATGCTAAGTATAAGGGTAAATG -s simDog_chr6.simDog.chr6 447534 30 - 593897 AAATGAGGATGCTAGGTATGCAGATTAATA -s simHuman_chr6.simHuman.chr6 150896 30 + 601863 AAATAAAGATGCTAAGCATGAGGCTTAATA -s simRat_chr6.simRat.chr6 177800 30 + 647215 GGATAATAACTCCAAGGGTGAGACTTAATG - -a -s simMouse_chr6.simMouse.chr6 187485 7 + 636262 TTTGAAA -s Anc0.Anc0refChr1 46466 7 - 62388 ATTGAAA -s Anc1.Anc1refChr2 125900 7 + 144309 ATTGAAA -s Anc2.Anc2refChr3 35964 7 + 53186 ATTGAAA -s mr.mrrefChr5 42561 7 + 294540 ATTGAAA -s simCow_chr6.simCow.chr6 164382 7 + 602619 ATCAAAC -s simDog_chr6.simDog.chr6 447565 7 - 593897 ATTGAAA -s simHuman_chr6.simHuman.chr6 150927 7 + 601863 ATTGAAA -s simRat_chr6.simRat.chr6 177830 5 + 647215 ACTGA-- - -a -s simMouse_chr6.simMouse.chr6 187492 27 + 636262 TGCAATTTTAGAGTCAACTAGATGGGA -s Anc0.Anc0refChr1 46473 27 - 62388 TGAGATTTTAGAATCAACTAGTGGGAA -s Anc1.Anc1refChr2 125907 27 + 144309 TGAGATTTTAGAATCAACTAGTGGGAA -s Anc2.Anc2refChr3 35971 27 + 53186 TGAGATTTTAAAATCAACTAGTGGGAA -s mr.mrrefChr5 42568 27 + 294540 TGCAATTTTAGAGTCAACTAGATGGGA -s simCow_chr6.simCow.chr6 164389 27 + 602619 TAAGATTTTACAATCATCTAGTGGGAA -s simDog_chr6.simDog.chr6 447588 23 - 593897 TGAGATTTTAAAATCCATTA----GAA -s simHuman_chr6.simHuman.chr6 150934 27 + 601863 TGAGATTTTAGAATCAACTAGTAGGAA -s simRat_chr6.simRat.chr6 177835 14 + 647215 -------------TCCACTAGATGGGA - -a -s simMouse_chr6.simMouse.chr6 187519 5 + 636262 AATAA -s Anc0.Anc0refChr1 46500 5 - 62388 AATTA -s Anc1.Anc1refChr2 125934 5 + 144309 AATTA -s Anc2.Anc2refChr3 35998 5 + 53186 AAATA -s mr.mrrefChr5 42595 5 + 294540 AATAA -s simCow_chr6.simCow.chr6 164418 5 + 602619 AAATA -s simDog_chr6.simDog.chr6 447611 5 - 593897 AAATA -s simHuman_chr6.simHuman.chr6 150961 5 + 601863 AATTA -s simRat_chr6.simRat.chr6 177849 4 + 647215 AATA- - -a -s simMouse_chr6.simMouse.chr6 187524 34 + 636262 CCCATGACCCCTAATCATAAAGAGTTTGTGCTTT -s Anc0.Anc0refChr1 46507 31 - 62388 CCCATGG-GGCTAATC--AAAAAGTCTGTGCTTT -s Anc1.Anc1refChr2 125941 31 + 144309 CCCATGG-GGCTAATC--AAAAAGTCTGTGCTTT -s Anc2.Anc2refChr3 36005 31 + 53186 TCCATGG-GGCTAATC--AAACAGCCGGTGCTTT -s mr.mrrefChr5 42600 33 + 294540 CCCATGG-CCCTAATCATAAAAAGTTTGTGCTTT -s simCow_chr6.simCow.chr6 164425 29 + 602619 GGAATGG-GGCTA--C--AAACAGCCCGTGCTTT -s simDog_chr6.simDog.chr6 447618 31 - 593897 TCCATGG-GGCTAATC--ACACACCTGGTGCTTT -s simHuman_chr6.simHuman.chr6 150968 31 + 601863 CCCATGG-GGATGACC--AAAAAGTCTGTGCTTT -s simRat_chr6.simRat.chr6 177853 31 + 647215 --CATGG-CACTAATCATAAAAAGTTTGGGCTTT - -a -s simMouse_chr6.simMouse.chr6 187558 17 + 636262 ATAAATGATTTGCAACA -s Anc0.Anc0refChr1 46540 17 - 62388 TGAAAAGGGCCCCCACA -s Anc1.Anc1refChr2 125974 17 + 144309 TGAAAAGGGCCCCCACA -s Anc2.Anc2refChr3 36038 17 + 53186 TGAAAAGGGCCCCCACA -s mr.mrrefChr5 42633 17 + 294540 ATAAATGATTTGCAACA -s simCow_chr6.simCow.chr6 164456 17 + 602619 TGAGGAGGGCACCCCCC -s simDog_chr6.simDog.chr6 447651 17 - 593897 TAAAATGGGCCCCCACA -s simHuman_chr6.simHuman.chr6 151001 17 + 601863 GGAAAAGGGCCCCCACG -s simRat_chr6.simRat.chr6 177884 17 + 647215 ATACACGATCTGAAACA - -a -s simMouse_chr6.simMouse.chr6 187575 23 + 636262 CACAATAGTTGTAAGGCTGTAAA -s Anc0.Anc0refChr1 46565 19 - 62388 CACAATACATGAAA--TTGTC-- -s Anc1.Anc1refChr2 125999 19 + 144309 CACAATACATGAAA--TTGTC-- -s Anc2.Anc2refChr3 36063 19 + 53186 CAGGATACATGAAA--TCATC-- -s mr.mrrefChr5 42650 23 + 294540 CACAATAGTTGTAAGGCTGTAAA -s simCow_chr6.simCow.chr6 164481 19 + 602619 CAGTGTACATGAAA--TCATT-- -s simDog_chr6.simDog.chr6 447676 18 - 593897 CA-GAGACATGAAA--TCATC-- -s simHuman_chr6.simHuman.chr6 151026 19 + 601863 CACAATACATGAAA--TTGTC-- -s simRat_chr6.simRat.chr6 177901 23 + 647215 CACAATAATTGTAAGGCTGTAAA - -a -s simMouse_chr6.simMouse.chr6 187598 24 + 636262 GAATTCCCCTGGTAGAATCAAGGC -s Anc0.Anc0refChr1 18003 23 + 62388 GACATATTC-GGAAGAACTCAAAC -s Anc1.Anc1refChr2 20526 24 - 144309 GACATATTCTGGAAGAACTCAAAC -s Anc2.Anc2refChr3 19416 23 - 53186 GACAGATTC-GGAAGAACTCAAAC -s mr.mrrefChr5 42673 24 + 294540 GAATTACCCTGGTAGAATCAAGGC -s simCow_chr6.simCow.chr6 440512 23 - 602619 GAAAGTTTC-CCAACAACTCAAAC -s simDog_chr6.simDog.chr6 148536 17 + 593897 GACAGACTC-GGATGAAC------ -s simHuman_chr6.simHuman.chr6 453076 24 - 601863 GAGATATTCTGAAAGAACTGATAC -s simRat_chr6.simRat.chr6 177924 24 + 647215 AAACTACCCTGGTAGAATCAAGGC - -a -s simMouse_chr6.simMouse.chr6 187622 3 + 636262 TGG -s Anc0.Anc0refChr1 18027 3 + 62388 TGG -s Anc1.Anc1refChr2 20551 3 - 144309 TGG -s Anc2.Anc2refChr3 19440 3 - 53186 TGG -s mr.mrrefChr5 42697 3 + 294540 TGG -s simCow_chr6.simCow.chr6 440536 3 - 602619 TGG -s simHuman_chr6.simHuman.chr6 453101 3 - 601863 TGG -s simRat_chr6.simRat.chr6 177981 3 + 647215 TGG - -a -s simMouse_chr6.simMouse.chr6 187625 52 + 636262 GACAAAGTGCAACTTAGCACAGACCTTCACTGCTGTCTATAGTGAGGAGAAG -s Anc0.Anc0refChr1 18030 50 + 62388 AATGAAGTGGA--TTAGCATAGACCTGCCCTGCTGTTTATAGTGAGGAAAAA -s Anc1.Anc1refChr2 20554 50 - 144309 AATGAAGTGGA--TTAGCATAGACCTGCCCTGCTGTTTATAGTGAGGAAAAA -s Anc2.Anc2refChr3 19443 50 - 53186 AGTGTAGTAGG--TTAGCATGGACCTGACCTGCTGTTTATAGTGAGTAAAAA -s mr.mrrefChr5 42700 52 + 294540 GACAAAGTGCAACTTAGCACAGACCTTCACTGCTGTTTATAGTGAGGAGAAG -s simCow_chr6.simCow.chr6 440542 50 - 602619 AGGGTAGCTAT--TTAGTATGGGCCCGACCTGTTTTTTATTGTGGGTAAACA -s simDog_chr6.simDog.chr6 148553 50 + 593897 AGTGTAGTAGG--TTATCATGGACCTGACTTGCTGTTTATAGTGAGTAATAA -s simHuman_chr6.simHuman.chr6 453104 49 - 601863 AATGATGTGGA--TTAGCA-AGATATGCCCTGCTGTTCATAATGATGAAAAA -s simRat_chr6.simRat.chr6 177984 52 + 647215 GGCACAGTGCAATTCAGTGCAGACCTCCACTGGTGTTTATAGCGAGGAGAAG - -a -s simMouse_chr6.simMouse.chr6 187677 14 + 636262 ATAGTAATATGCTA -s Anc0.Anc0refChr1 18080 14 + 62388 ATAGTAATATACTA -s Anc1.Anc1refChr2 20604 14 - 144309 ATAGTAATATACTA -s Anc2.Anc2refChr3 19493 14 - 53186 TTCGTGACATACAA -s mr.mrrefChr5 42752 14 + 294540 ATAGTAATATACTA -s simCow_chr6.simCow.chr6 440592 14 - 602619 TTTGTGACATACAG -s simDog_chr6.simDog.chr6 148603 14 + 593897 TCCGTGACATACAA -s simHuman_chr6.simHuman.chr6 453157 14 - 601863 ATAGCAATATACTA -s simRat_chr6.simRat.chr6 178036 14 + 647215 ATAGTAATATACTA - -a -s simMouse_chr6.simMouse.chr6 187691 3 + 636262 GAG -s Anc0.Anc0refChr1 18097 1 + 62388 --G -s Anc1.Anc1refChr2 20622 3 - 144309 AAG -s Anc2.Anc2refChr3 19510 1 - 53186 --G -s mr.mrrefChr5 42766 3 + 294540 AAG -s simCow_chr6.simCow.chr6 440609 1 - 602619 --C -s simDog_chr6.simDog.chr6 148620 1 + 593897 --G -s simHuman_chr6.simHuman.chr6 453175 3 - 601863 AAG -s simRat_chr6.simRat.chr6 178050 3 + 647215 AAA - -a -s simMouse_chr6.simMouse.chr6 187694 3 + 636262 TTA -s Anc0.Anc0refChr1 18098 3 + 62388 TTA -s Anc1.Anc1refChr2 20625 3 - 144309 TTA -s Anc2.Anc2refChr3 19511 3 - 53186 TTT -s mr.mrrefChr5 42769 3 + 294540 TTA -s simCow_chr6.simCow.chr6 440610 3 - 602619 TTT -s simDog_chr6.simDog.chr6 148621 3 + 593897 TTT -s simHuman_chr6.simHuman.chr6 453178 3 - 601863 TTA -s simRat_chr6.simRat.chr6 178057 3 + 647215 TTA - -a -s simMouse_chr6.simMouse.chr6 187697 7 + 636262 ATGTTGA -s Anc0.Anc0refChr1 18103 7 + 62388 ATGTTGA -s Anc1.Anc1refChr2 20630 7 - 144309 ATGTTGA -s Anc2.Anc2refChr3 19516 7 - 53186 ATGTTGA -s mr.mrrefChr5 42772 7 + 294540 ATGTTGA -s simCow_chr6.simCow.chr6 440615 7 - 602619 ATGTTGA -s simDog_chr6.simDog.chr6 148626 7 + 593897 ATGTCGA -s simHuman_chr6.simHuman.chr6 453183 7 - 601863 ATGTTGA -s simRat_chr6.simRat.chr6 178060 7 + 647215 ATGTTGA - -a -s simMouse_chr6.simMouse.chr6 187704 2 + 636262 GT -s Anc0.Anc0refChr1 18114 2 + 62388 GT -s Anc1.Anc1refChr2 20641 2 - 144309 GT -s Anc2.Anc2refChr3 19527 2 - 53186 GT -s mr.mrrefChr5 42779 2 + 294540 GT -s simCow_chr6.simCow.chr6 440626 2 - 602619 GT -s simDog_chr6.simDog.chr6 148637 2 + 593897 GC -s simHuman_chr6.simHuman.chr6 453194 2 - 601863 GT -s simRat_chr6.simRat.chr6 178067 2 + 647215 GT - -a -s simMouse_chr6.simMouse.chr6 187706 20 + 636262 CTGTGTGTAAATGTTTTAGT -s Anc0.Anc0refChr1 18117 19 + 62388 CACTGTAT-AAGCCTGTAGT -s Anc1.Anc1refChr2 20644 20 - 144309 CACTGTATAAAGCCTGTAGT -s Anc2.Anc2refChr3 19530 19 - 53186 CACTGTAT-AAGCCTGTGGT -s mr.mrrefChr5 42782 20 + 294540 CAGTGTATAAATCTTTTAGT -s simCow_chr6.simCow.chr6 440629 17 - 602619 CACTGTAT-AAGTC--TGGT -s simDog_chr6.simDog.chr6 148640 19 + 593897 TACTGTAT-AAGCCTGTGGT -s simHuman_chr6.simHuman.chr6 453197 20 - 601863 CATTGTATAAAGCCTGTAAT -s simRat_chr6.simRat.chr6 178070 20 + 647215 CAGTGTATAAATCTTCCAGC - -a -s simMouse_chr6.simMouse.chr6 187726 53 + 636262 GTGTGAACTTATGACAACAGTTGTAACTAATGAATGTTAGTACTAATATTAGT -s Anc0.Anc0refChr1 18136 37 + 62388 GTGTGAACTTACGATTGCAGGTAT----------------CACTGATTTTAGT -s Anc1.Anc1refChr2 20664 37 - 144309 GTGTGAACTTACGATTGCAGGTAT----------------CACTGATTTTAGT -s Anc2.Anc2refChr3 19550 37 - 53186 GTGTGATTTGGCAATTGCAGGTAA----------------CACTGATTTTAGT -s mr.mrrefChr5 42802 53 + 294540 GTGTGAACTTATGACAACAGTTGTAACTAATGAATGTTAGTACTAATATTAGT -s simCow_chr6.simCow.chr6 440647 28 - 602619 GTGT---------ACTACAGGTAC----------------TCCCCCTGTTAGT -s simDog_chr6.simDog.chr6 148660 37 + 593897 GTGTGATTTGGCAATTGTGGGTAA----------------CACTGATTGTGCT -s simHuman_chr6.simHuman.chr6 453217 37 - 601863 GTGTCAACTTACGATTGCAGGTAT----------------CACTGATTTTAGT -s simRat_chr6.simRat.chr6 178090 53 + 647215 TTGTGAACTTATGACAACGGTTGTAACAAATGAATGTTAGTACTAATGTTAAT - -a -s simMouse_chr6.simMouse.chr6 187779 7 + 636262 AGCAGAG -s Anc0.Anc0refChr1 18173 7 + 62388 AGCTGAG -s Anc1.Anc1refChr2 20701 7 - 144309 AGCTGAG -s Anc2.Anc2refChr3 19587 7 - 53186 AGCTGAG -s mr.mrrefChr5 42855 7 + 294540 AGCAGAG -s simCow_chr6.simCow.chr6 440675 7 - 602619 AGCCGAC -s simDog_chr6.simDog.chr6 148697 7 + 593897 AGCTGAG -s simHuman_chr6.simHuman.chr6 453254 7 - 601863 AGCTGAG -s simRat_chr6.simRat.chr6 178179 7 + 647215 AGATGAG - -a -s simMouse_chr6.simMouse.chr6 187786 67 + 636262 CTTCAGAGGACAGGGAAAAAGCCATTGCAGGTGGCACAATCAATCAACCTACAGGTCTTTCTATATG -s Anc0.Anc0refChr1 18182 67 + 62388 TTTCAGGTAACTGGGGAGATGCAATTGCAGGTAGTCCAGTCAATTTACCTAGAGGACTTTCTATGTA -s Anc1.Anc1refChr2 20710 67 - 144309 TTTCAGGTAACTGGGGAGATGCAATTGCAGGTAGTCCAGTCAATTTACCTAGAGGACTTTCTATGTA -s Anc2.Anc2refChr3 19596 67 - 53186 TAACAGGTAACTGGGGAGATGCAATTGCAGGTAGTCCAGCCAATTTACCTAGAGGACTTTCTTTGTA -s mr.mrrefChr5 42862 67 + 294540 CTTCAGGGGACAGGGGAAAAGCCATTGCAGGTGGCACAGTCAATCTACCTACAGGTCTTTCTATATG -s simCow_chr6.simCow.chr6 440684 62 - 602619 -AACAGGTAACTGGCATGATGCAATTGCAGATAATCCTACCAATTTACCCAGAGCACGTGCTT---- -s simDog_chr6.simDog.chr6 148706 67 + 593897 TAACAGGGAACTGGGGAGAAGCAATTGCAGGTCGTGCAGCCAATATATCTAGAGGAGTTTCTTTGTA -s simHuman_chr6.simHuman.chr6 453263 67 - 601863 TTTCAGGTCACTGGGGAGATGCAATTGCAGGTAGTCCAGTGAGTTTACCTAGAGGGCTTTTCAGGTA -s simRat_chr6.simRat.chr6 178186 48 + 647215 CTTCAGGGAGCAGGAGAAAAGCCATTGCAGGTGGCACAGTCAATATAC------------------- - -a -s simMouse_chr6.simMouse.chr6 187853 39 + 636262 TTTACCCTGATAATTCAACTCTATGATAATCTCTCTATA -s Anc0.Anc0refChr1 18250 39 + 62388 TCTGTCCTGATAATTCAACTCAATAATAATCTCTCTATA -s Anc1.Anc1refChr2 20778 39 - 144309 TCTGTCCTGATAATTCAACTCAATAATAATCTCTCTATA -s Anc2.Anc2refChr3 19664 39 - 53186 TCTGTCCTGGCAATTCAACTCAATAATGATCCCTCTATA -s mr.mrrefChr5 42929 39 + 294540 TTTACCCTGATAATTCAACTCAATGATAATCTCTCTATA -s simCow_chr6.simCow.chr6 440746 32 - 602619 --AGCCCGA-----TCAACTCAATGTTGATCCCACTAGA -s simDog_chr6.simDog.chr6 148774 39 + 593897 TCTGTCCTGGCAATTTAACCTAATAATGATCCCTTTATA -s simHuman_chr6.simHuman.chr6 453331 39 - 601863 TCTGTCCTGATTATTCAACTCAATAATAATTTCCCTATA -s simRat_chr6.simRat.chr6 178234 35 + 647215 --TACCCTGATAATTCAACTCAATGATACTCTCTCTA-- - -a -s simMouse_chr6.simMouse.chr6 187892 56 + 636262 TTCTTGTTTGTTCATGTTTGAAAATCATACTGGGCATTAAACCTCTTCATCTGATT -s Anc0.Anc0refChr1 18289 49 + 62388 TGCCCGTCTGT----GTGTGAGCATAAAACTGA-TATTAGACC--TTCATCTGAGC -s Anc1.Anc1refChr2 20817 49 - 144309 TGCCCGTCTGT----GTGTGAGCATAAAACTGA-TATTAGACC--TTCATCTGAGC -s Anc2.Anc2refChr3 19707 49 - 53186 TGCCCGTCTGT----GTGTGAGCATAAAACTGA-TACTAGACC--TTCATCTGAGC -s mr.mrrefChr5 42968 52 + 294540 TTCTTGTTTGT----GTTTGAAAATCATACTGGGCATTAAACCCCTTCATCTGATT -s simCow_chr6.simCow.chr6 440782 39 - 602619 TGCCCATCTGT----GTCTGAGCTTGAGCTAAA-TA------------GCCTGAGC -s simDog_chr6.simDog.chr6 148817 49 + 593897 TGCCTGGCTGT----GTGTGAACATAAAACTGA-TACTAGACC--TTCATCTGAGC -s simHuman_chr6.simHuman.chr6 453370 49 - 601863 TGCCCGTCTGT----GTGTGAGCATTAAACCTA-TATTAGGCC--TTCATCTGAGC -s simRat_chr6.simRat.chr6 178269 37 + 647215 -------------------GAAAATTAAACCGGGCATTAAACCCCTTAATCTGATT - -a -s simMouse_chr6.simMouse.chr6 187948 2 + 636262 TG -s Anc0.Anc0refChr1 18341 2 + 62388 TA -s Anc1.Anc1refChr2 20869 2 - 144309 TA -s Anc2.Anc2refChr3 19759 2 - 53186 CA -s mr.mrrefChr5 43020 2 + 294540 TG -s simCow_chr6.simCow.chr6 440824 2 - 602619 AA -s simDog_chr6.simDog.chr6 148869 2 + 593897 CA -s simHuman_chr6.simHuman.chr6 453422 2 - 601863 TT -s simRat_chr6.simRat.chr6 178306 2 + 647215 TG - -a -s simMouse_chr6.simMouse.chr6 187950 6 + 636262 TTAACA -s Anc0.Anc0refChr1 18344 6 + 62388 ACAAAA -s Anc1.Anc1refChr2 20872 6 - 144309 ACAAAA -s Anc2.Anc2refChr3 19762 6 - 53186 ACAAAA -s mr.mrrefChr5 43023 6 + 294540 TTAACA -s simCow_chr6.simCow.chr6 440827 6 - 602619 ACAAAG -s simDog_chr6.simDog.chr6 148872 6 + 593897 AAAAAA -s simHuman_chr6.simHuman.chr6 453425 6 - 601863 ACAAAA -s simRat_chr6.simRat.chr6 178309 6 + 647215 TTAACC - -a -s simMouse_chr6.simMouse.chr6 187956 16 + 636262 ATCACCAATCTCAAAC -s Anc0.Anc0refChr1 18354 15 + 62388 ATTGCTG-TCTCTAAC -s Anc1.Anc1refChr2 20882 15 - 144309 ATTGCTG-TCTCTAAC -s Anc2.Anc2refChr3 19772 15 - 53186 ATTGCTG-TCTCTAAT -s mr.mrrefChr5 43029 16 + 294540 ATCACCAATCTCAAAC -s simCow_chr6.simCow.chr6 440837 15 - 602619 ATTGCTG-TCTCTAAT -s simHuman_chr6.simHuman.chr6 453435 15 - 601863 ATTGCTG-TCCCTAAC -s simRat_chr6.simRat.chr6 178315 16 + 647215 ATCACCAATCTCAAAC - -a -s simMouse_chr6.simMouse.chr6 187972 32 + 636262 AGTTTTGCCTGTTGCACAGATAAATTCCAAGC -s Anc0.Anc0refChr1 18370 32 + 62388 CACTTTGCCTGTTGAACAGATAAATTCCAAGA -s Anc1.Anc1refChr2 20898 32 - 144309 CACTTTGCCTGTTGAACAGATAAATTCCAAGA -s Anc2.Anc2refChr3 19788 32 - 53186 CACTTTGCCTGTTGAACAGGTAAATTCAAAGA -s mr.mrrefChr5 43045 32 + 294540 AACTTTGCCTGTTGAACAGATAAATTCCAAGC -s simCow_chr6.simCow.chr6 440853 32 - 602619 CACTTTGCCTATTGATCAGGTAAATTGAAAGA -s simDog_chr6.simDog.chr6 148879 24 + 593897 --------TTGGTGAACAGGTAAGTTCAAAGA -s simHuman_chr6.simHuman.chr6 453451 32 - 601863 CACCTTGCCTGTTGAACAGATAAACTCCAAGA -s simRat_chr6.simRat.chr6 178331 32 + 647215 AACTTTGCCTGTTGAACAGGTATATTCCAAAC - -a -s simMouse_chr6.simMouse.chr6 188004 25 + 636262 AAAAATCTGGAGGTGATCATTAGAT -s Anc0.Anc0refChr1 18405 25 + 62388 AAAAAACTGAGGATGATAATTAAGT -s Anc1.Anc1refChr2 20933 25 - 144309 AAAAAACTGAGGATGATAATTAAGT -s Anc2.Anc2refChr3 19823 25 - 53186 AAAAAACTGAGAATGATAATTAAGT -s mr.mrrefChr5 43077 25 + 294540 AAAAATCTGAGGGTGATCATTAAAT -s simCow_chr6.simCow.chr6 440888 25 - 602619 AAAAAACAGAGAATGACCATTAATT -s simDog_chr6.simDog.chr6 148906 25 + 593897 CAATAACTGGGAATGATAAGTAGGT -s simHuman_chr6.simHuman.chr6 453486 25 - 601863 AAAAAACTGAGGATGATTATTAAGT -s simRat_chr6.simRat.chr6 178363 25 + 647215 AAAAATCTGAGGGTGATCATTAAAT - -a -s simMouse_chr6.simMouse.chr6 188029 109 + 636262 GATCTTACTTAGCATGCTAACTCTCATGGGACTGCACTCTTTCAGGATTAACTAGTCCCTATATTATGAAAAAATCTGGCTTATAACTGATTTTTATCCACTCAGAAGC -s Anc0.Anc0refChr1 18431 93 + 62388 GATCTTACTTAGTATGCTTAATCTCATGGGGCTATACTCTT---------------CCCTATATCAAAGC-GAATCTGGGTTTTAATTGATTTTTATTTACTCAGAAGC -s Anc1.Anc1refChr2 20959 94 - 144309 GATCTTACTTAGTATGCTTAATCTCATGGGGCTATACTCTT---------------CCCTATATCAAAGCGGAATCTGGGTTTTAATTGATTTTTATTTACTCAGAAGC -s Anc2.Anc2refChr3 19849 93 - 53186 GATCTTGCTCAGTATGCTTTATCTCTTGGGGCTATACTCTT---------------CCATATATCAAAGC-GAATCTTGGTTTTAATTGATTTTTATTTACTCAGAAGC -s mr.mrrefChr5 43102 109 + 294540 GATCTTACTTAGTATGCTAACTCTCATGGGACTGCACTCTTTCAGGATTAACTAGTCCCTATATTATGAAAAAATCTGGCTTATAACTGATTTTTATCCACTCAGAAGC -s simCow_chr6.simCow.chr6 440914 93 - 602619 GATGTTGCTCAGTACGCTTTATCTCTTGGGAGTGTACTCTT---------------CCTTGTATCATATA-AAATCTTTGTTTTAATTGATTTTTTTTTACTCAGTAGC -s simDog_chr6.simDog.chr6 148932 93 + 593897 GATCTCGTCCAATATGCTTTATCTCTTGGGGCAATACTCAC---------------CCATATATCAAAGC-GAATCTTGGTTTTAATTGATTTTTATTTACTCAGAAGC -s simHuman_chr6.simHuman.chr6 453512 91 - 601863 GGTCTTACTTAGTATGCCTAATCTCATGGGGCTAAACTCTT---------------CCCCATATCACAGTGGAATCTGGGTTTTAATAGATTTTTAT---CTCGGAAGC -s simRat_chr6.simRat.chr6 178388 109 + 647215 GATCTTACTTAGTATGCTCATTCTCATTGGACTGCATTCTCTTCGGATTAACTTGTCCCTATATTATGACAAAATCTGGCTTATAACTGATGTTTATCCAGTCAGAAGC - -a -s simMouse_chr6.simMouse.chr6 188138 4 + 636262 AGAG -s Anc0.Anc0refChr1 18524 4 + 62388 TGAG -s Anc1.Anc1refChr2 21053 4 - 144309 TGAG -s Anc2.Anc2refChr3 19943 4 - 53186 TCAG -s mr.mrrefChr5 43211 4 + 294540 AGAG -s simCow_chr6.simCow.chr6 441016 4 - 602619 TCTG -s simDog_chr6.simDog.chr6 149026 4 + 593897 TCAG -s simHuman_chr6.simHuman.chr6 453603 4 - 601863 TGAG -s simRat_chr6.simRat.chr6 178497 4 + 647215 CAAG - -a -s simMouse_chr6.simMouse.chr6 188142 4 + 636262 GGTT -s Anc0.Anc0refChr1 18530 4 + 62388 GGTT -s Anc1.Anc1refChr2 21059 4 - 144309 GGTT -s Anc2.Anc2refChr3 19949 4 - 53186 GGTT -s mr.mrrefChr5 43215 4 + 294540 GGTT -s simCow_chr6.simCow.chr6 441022 4 - 602619 TGTT -s simDog_chr6.simDog.chr6 149032 4 + 593897 GGTT -s simHuman_chr6.simHuman.chr6 453609 4 - 601863 GGCT -s simRat_chr6.simRat.chr6 178501 4 + 647215 TGTT - -a -s simMouse_chr6.simMouse.chr6 188146 6 + 636262 GTAACC -s Anc0.Anc0refChr1 18534 6 + 62388 ATAGCC -s Anc1.Anc1refChr2 21063 6 - 144309 ATAGCC -s Anc2.Anc2refChr3 19953 6 - 53186 ATTGCC -s mr.mrrefChr5 43219 6 + 294540 GTAACC -s simCow_chr6.simCow.chr6 441026 6 - 602619 ACAGTC -s simDog_chr6.simDog.chr6 149036 6 + 593897 ATTGCC -s simHuman_chr6.simHuman.chr6 453613 6 - 601863 ATAGCT -s simRat_chr6.simRat.chr6 178507 6 + 647215 GTCACC - -a -s simMouse_chr6.simMouse.chr6 188152 40 + 636262 TAGTAACATTGACATTGTCATTGTTGACATACCAGAAATT -s Anc0.Anc0refChr1 18540 34 + 62388 TAGTAAGATAGA------CATTGCTGACATAACCAAAGTG -s Anc1.Anc1refChr2 21069 35 - 144309 TAGTAAGATAGAC-----CATTGCTGACATAACCAAAGTG -s Anc2.Anc2refChr3 19959 34 - 53186 TAGTAAGATAGA------CGCTGCTGACATAACCAAAGTG -s mr.mrrefChr5 43225 40 + 294540 TAGTAAGATTGACATTGTCATTGTTGACATACCAGAAATT -s simCow_chr6.simCow.chr6 441032 32 - 602619 TAGGATGATAGA------CAGTGCTGACATAACCAAAT-- -s simDog_chr6.simDog.chr6 149042 34 + 593897 TGGTAAGATAGA------TGCTGCAGACATTACTAAAGTG -s simHuman_chr6.simHuman.chr6 453625 35 - 601863 GACTAAGATAGAC-----CATCGCTGACATATCCAAAGTG -s simRat_chr6.simRat.chr6 178513 40 + 647215 TAGTAAGATTGGCGTTGTCGTTGTTGACATACCAGAAATT - -a -s simMouse_chr6.simMouse.chr6 188192 11 + 636262 AGTGACAACTT -s Anc0.Anc0refChr1 18574 9 + 62388 ATGGGTA--AT -s Anc1.Anc1refChr2 21104 11 - 144309 ATGGGTAAGAT -s Anc2.Anc2refChr3 19993 9 - 53186 ATTGTTA--AT -s mr.mrrefChr5 43265 11 + 294540 AGGGGCAACTT -s simDog_chr6.simDog.chr6 149079 9 + 593897 ATTGTTA--AT -s simHuman_chr6.simHuman.chr6 453660 11 - 601863 ATGGGTAAGAT -s simRat_chr6.simRat.chr6 178553 11 + 647215 AGGGGCAATTT - -a -s simMouse_chr6.simMouse.chr6 188203 146 + 636262 GCAAAGTACATGGGTGCACATGGCTGCGTTTGCCTTTTTTTGGAGCTCTCCATGAGGCACTGTGCAAAATCTAAACAGTGCTAAGACCATGGGCCCTAAAAATTCTGGTGGAAATGTACTTTCATTTCTCCTCTTGCTGGGGGGTC -s Anc0.Anc0refChr1 18583 62 + 62388 GCACAGGTCCTGGA-----------------------------------------------------------------------------GGCACTAACAATTTGGGAGAC-----TCTGTCATTTCTTCTTTT--TGTGTGGTC -s Anc1.Anc1refChr2 21115 68 - 144309 GCACAGGTCCTGGA----------------------------------------------------------------------------GGGCACTAACAATTTGGGAGACAACAATCTGTCATTTCTTCTTTT--TGTGTGGTC -s Anc2.Anc2refChr3 20002 62 - 53186 GCACATGTCCATGA-----------------------------------------------------------------------------GGTACTGACAATTTGGGAAGC-----TTTGCCATTTCCTCTTTT--TGTGTGGTC -s mr.mrrefChr5 43276 146 + 294540 GCAAAGTACATGGGTGCACATGGCTGCGTTTGCCTTTTTTTGGAGCTCTCCATGAGGCACTGTGCAAAATCTAAACAGTGCTAAGACCATGGGCCCTAAAAATTCTGGAGAAAATGAACTGTCATTTCTCCTCTTGCTGGGGGGTC -s simCow_chr6.simCow.chr6 441064 32 - 602619 -----------------------------------------------------------------------------------------------CTGGCAATTTGGG-----------------TTCCTCTGTT--TGTGTGGTC -s simDog_chr6.simDog.chr6 149088 62 + 593897 GCACATGTCCATGA-----------------------------------------------------------------------------GGTACTGACAATTTGGGAAGC-----TTTGCCATTTCCTCTTTT--TGTACCATC -s simHuman_chr6.simHuman.chr6 453671 68 - 601863 AGATTGGGCCTGGA----------------------------------------------------------------------------GGGCACCAACAATTTGGGAGACAACAATCTGTCATTTCTTCTTTT--TCTGTGGTC -s simRat_chr6.simRat.chr6 178566 146 + 647215 GCAAAGTACATGGGTGAATGTGGCCGCATTTGCCTTTTATTGTAGCTTTGCATGAGGCACTGTGCAAAATCTAGTCAATGCTATGACCACGGTCCCTGAAAATTCTGGAGAAAATGAACTGTCATTTCTACTCTTGCTGAGGGGTC - -a -s simMouse_chr6.simMouse.chr6 188349 7 + 636262 CATTAGG -s Anc0.Anc0refChr1 18645 4 + 62388 TAAT--- -s Anc1.Anc1refChr2 21183 4 - 144309 TAAT--- -s Anc2.Anc2refChr3 20064 4 - 53186 TAAT--- -s mr.mrrefChr5 43422 7 + 294540 CATTAGG -s simCow_chr6.simCow.chr6 441098 4 - 602619 TAAA--- -s simDog_chr6.simDog.chr6 149150 4 + 593897 TAAT--- -s simHuman_chr6.simHuman.chr6 453739 4 - 601863 TACT--- -s simRat_chr6.simRat.chr6 178712 7 + 647215 CATTAGG - -a -s simMouse_chr6.simMouse.chr6 188356 30 + 636262 GCTGCTTGATGTCTGTCAATAACCTTTTTG -s Anc0.Anc0refChr1 18649 30 + 62388 GCTGCTTAACGTATGTTAATAAATCTTTTG -s Anc1.Anc1refChr2 21187 30 - 144309 GCTGCTTAACGTATGTTAATAAATCTTTTG -s Anc2.Anc2refChr3 20068 30 - 53186 ATTTCTTAAGATCTGTTAAGAAATCTTTTG -s mr.mrrefChr5 43430 30 + 294540 GCTGCTTGACGTATGTCAATAAATTTTTTG -s simCow_chr6.simCow.chr6 441102 30 - 602619 ATGCCTTAAGATCTGTTAACAAAACTTCTG -s simDog_chr6.simDog.chr6 149154 21 + 593897 ATTT---------GGTTAAGGAATCTTTTG -s simHuman_chr6.simHuman.chr6 453743 30 - 601863 GCTGCTTAACGTATGTTAATAAATCTTTTG -s simRat_chr6.simRat.chr6 178720 30 + 647215 GTTGCTTGACGTATGTCAAGGAATTTTTTG - -a -s simMouse_chr6.simMouse.chr6 188386 11 + 636262 GTTCCTCACAG -s Anc0.Anc0refChr1 18680 11 + 62388 GTCAGTCACAA -s Anc1.Anc1refChr2 21218 11 - 144309 GTCAGTCACAA -s Anc2.Anc2refChr3 20099 11 - 53186 GCCAGTTACAA -s mr.mrrefChr5 43460 11 + 294540 GTTACTCACAA -s simCow_chr6.simCow.chr6 441133 11 - 602619 GACACTGACAA -s simDog_chr6.simDog.chr6 149176 11 + 593897 GCCAGTTGCAA -s simHuman_chr6.simHuman.chr6 453774 11 - 601863 GTCAATCACAA -s simRat_chr6.simRat.chr6 178750 11 + 647215 GTTACTCACAA - -a -s simMouse_chr6.simMouse.chr6 188397 36 + 636262 AGTCCATTTTTAAATTGCACTTCATCATCTTCCATA -s Anc0.Anc0refChr1 18693 36 + 62388 TGTGCATTTTTGAGCTCCACTCCATCCTCTTCCACA -s Anc1.Anc1refChr2 21231 36 - 144309 TGTGCATTTTTGAGCTCCACTCCATCCTCTTCCACA -s Anc2.Anc2refChr3 20112 36 - 53186 TGTGCAATTTTGTGCTCCACACCATCCTCCTCCACA -s mr.mrrefChr5 43471 36 + 294540 TGTCCATTTTTAAGTTGCACTTCATCATCTTCCATA -s simCow_chr6.simCow.chr6 441154 36 - 602619 TGTGCAACCTTGTATTTCACACCATCCTCCTTCACA -s simDog_chr6.simDog.chr6 149187 36 + 593897 TGTGCAATTTAGTGCTCCACAGCATCCAACCCCACA -s simHuman_chr6.simHuman.chr6 453787 36 - 601863 TGTGGATTTTTGAGCTCCCCTCTGTCCTCTTCAACA -s simRat_chr6.simRat.chr6 178761 36 + 647215 TGTCCATTTTTAAGTTGCACTTCATCATTTTCCATA - -a -s simMouse_chr6.simMouse.chr6 188433 5 + 636262 TAACC -s Anc0.Anc0refChr1 18730 5 + 62388 CAACC -s Anc1.Anc1refChr2 21268 5 - 144309 CAACC -s Anc2.Anc2refChr3 20149 5 - 53186 CAACC -s mr.mrrefChr5 43508 5 + 294540 CAACC -s simCow_chr6.simCow.chr6 441191 5 - 602619 CAACC -s simDog_chr6.simDog.chr6 149224 4 + 593897 -ATCC -s simHuman_chr6.simHuman.chr6 453824 5 - 601863 CGACT -s simRat_chr6.simRat.chr6 178798 5 + 647215 CAACC - -a -s simMouse_chr6.simMouse.chr6 188438 11 + 636262 AACACCAGCGT -s Anc0.Anc0refChr1 18743 11 + 62388 AATGTCAGTGC -s Anc1.Anc1refChr2 21281 11 - 144309 AATGTCAGTGC -s Anc2.Anc2refChr3 20162 11 - 53186 GATGTCAGTGC -s mr.mrrefChr5 43513 11 + 294540 AACACCAGTGT -s simCow_chr6.simCow.chr6 441204 11 - 602619 TATGTCAGTGC -s simDog_chr6.simDog.chr6 149236 11 + 593897 GATGTTAGTGT -s simHuman_chr6.simHuman.chr6 453837 11 - 601863 AATGTCAGTGC -s simRat_chr6.simRat.chr6 178803 11 + 647215 AACAGCAGTTA - -a -s simMouse_chr6.simMouse.chr6 188449 3 + 636262 TAC -s Anc0.Anc0refChr1 18754 3 + 62388 TGC -s Anc1.Anc1refChr2 21292 3 - 144309 TGC -s Anc2.Anc2refChr3 20173 3 - 53186 TGC -s mr.mrrefChr5 43524 3 + 294540 TAC -s simCow_chr6.simCow.chr6 441224 3 - 602619 TGC -s simDog_chr6.simDog.chr6 149247 3 + 593897 TGC -s simHuman_chr6.simHuman.chr6 453848 3 - 601863 TGC -s simRat_chr6.simRat.chr6 178814 3 + 647215 TAC - -a -s simMouse_chr6.simMouse.chr6 188452 24 + 636262 TGGTCAGTTCGCCTGGGAGCTTAG -s Anc0.Anc0refChr1 18758 24 + 62388 TGATAAGTTTGCGTGGAAGCTTAG -s Anc1.Anc1refChr2 21296 24 - 144309 TGATAAGTTTGCGTGGAAGCTTAG -s Anc2.Anc2refChr3 20177 24 - 53186 TGATAAGTTCATGTGAAAGCTTAG -s mr.mrrefChr5 43527 24 + 294540 TGATCAGTTTGCCTGGGAGCTTAG -s simCow_chr6.simCow.chr6 441228 24 - 602619 TGACAAGTTCAGCTGAAAGCTTAG -s simDog_chr6.simDog.chr6 149251 24 + 593897 GGGTGAACCCATGGTAAAGCTTAG -s simHuman_chr6.simHuman.chr6 453852 24 - 601863 TGATAAGTTTGCATGGAAACTTAG -s simRat_chr6.simRat.chr6 178817 24 + 647215 TGACCAGTTTACCCAGGAGCTTAG - -a -s simMouse_chr6.simMouse.chr6 188476 58 + 636262 TCCACCCTCTAGCCTTGCGTTTATTATAATCGCTTGTCATAGTGTGCCATGAAGGAAC -s Anc0.Anc0refChr1 18784 12 + 62388 TCCAC----------------------------------------------AAGAGAC -s Anc1.Anc1refChr2 21322 12 - 144309 TCCAC----------------------------------------------AAGAGAC -s Anc2.Anc2refChr3 20203 12 - 53186 TCCAC----------------------------------------------AAGAGAC -s mr.mrrefChr5 43551 12 + 294540 TCCAC----------------------------------------------AAGGAAC -s simCow_chr6.simCow.chr6 441254 12 - 602619 TCCAC----------------------------------------------CACAGAC -s simDog_chr6.simDog.chr6 149277 12 + 593897 TCCAC----------------------------------------------AAGAGAC -s simHuman_chr6.simHuman.chr6 453878 12 - 601863 TCCAC----------------------------------------------AAGAGAC -s simRat_chr6.simRat.chr6 178841 12 + 647215 TCCAC----------------------------------------------AAGGACC - -a -s simMouse_chr6.simMouse.chr6 188534 10 + 636262 TCCTTTCCTT -s Anc0.Anc0refChr1 18812 10 + 62388 TCTCTTTCCT -s Anc1.Anc1refChr2 21350 10 - 144309 TCTCTTTCCT -s Anc2.Anc2refChr3 20231 10 - 53186 TCTCTTTCCT -s mr.mrrefChr5 43563 10 + 294540 TCCTTTCCCT -s simCow_chr6.simCow.chr6 441282 10 - 602619 CCTCTTTCCT -s simDog_chr6.simDog.chr6 149305 10 + 593897 TCTCCTTTCT -s simHuman_chr6.simHuman.chr6 453906 10 - 601863 TCTGTTACCT -s simRat_chr6.simRat.chr6 178853 10 + 647215 TCCTTCCCCT - -a -s simMouse_chr6.simMouse.chr6 188544 9 + 636262 CACACAAGT -s Anc0.Anc0refChr1 18823 9 + 62388 CACCTGAAT -s Anc1.Anc1refChr2 21361 9 - 144309 CACCTGAAT -s Anc2.Anc2refChr3 20242 9 - 53186 CACCTGAAT -s mr.mrrefChr5 43574 9 + 294540 CACCTAAGT -s simCow_chr6.simCow.chr6 441293 9 - 602619 CACCTGAAC -s simDog_chr6.simDog.chr6 149316 9 + 593897 TACCTGAAT -s simHuman_chr6.simHuman.chr6 453917 9 - 601863 CACCTGAAT -s simRat_chr6.simRat.chr6 178864 9 + 647215 CACCTAGGT - -a -s simMouse_chr6.simMouse.chr6 188553 27 + 636262 GACCCTTAAGTGCAACTACAAATTAAC -s Anc0.Anc0refChr1 18832 27 + 62388 GATCCTTAAGTCTAACTACAAATTAAC -s Anc1.Anc1refChr2 21370 27 - 144309 GATCCTTAAGTCTAACTACAAATTAAC -s Anc2.Anc2refChr3 20251 27 - 53186 GACCCTCAAGCCTAACTACAGATTAAC -s mr.mrrefChr5 43583 27 + 294540 GATCCTTAAGTGCAACTACAAATTAAC -s simCow_chr6.simCow.chr6 441302 20 - 602619 AACCCTA-------ACTACAGATTAAC -s simDog_chr6.simDog.chr6 149325 20 + 593897 GACCCTCAAGCCTAACTA-------CC -s simHuman_chr6.simHuman.chr6 453927 27 - 601863 GATCCTTCAGTTTAACTACAAATTGAC -s simRat_chr6.simRat.chr6 178873 27 + 647215 GATCCTCAAATGCGGCTACAAATTAAC - -a -s simMouse_chr6.simMouse.chr6 188580 8 + 636262 TGTTCTTA -s Anc0.Anc0refChr1 18861 8 + 62388 TATTATTT -s Anc1.Anc1refChr2 21399 8 - 144309 TATTATTT -s Anc2.Anc2refChr3 20280 8 - 53186 TATTATTT -s mr.mrrefChr5 43610 8 + 294540 TGTTCTTA -s simCow_chr6.simCow.chr6 441324 8 - 602619 TAATATCA -s simDog_chr6.simDog.chr6 149345 8 + 593897 TATTATTT -s simHuman_chr6.simHuman.chr6 453956 8 - 601863 TATTATTG -s simRat_chr6.simRat.chr6 178900 8 + 647215 TGTTCTTA - -a -s simMouse_chr6.simMouse.chr6 188588 10 + 636262 AAGTGGTGAG -s Anc0.Anc0refChr1 18869 10 + 62388 AAGCCCTAAG -s Anc1.Anc1refChr2 21407 10 - 144309 AAGCCCTAAG -s Anc2.Anc2refChr3 20288 10 - 53186 AAGCCCTAGA -s mr.mrrefChr5 43618 10 + 294540 AAGTGCTGAG -s simCow_chr6.simCow.chr6 441332 10 - 602619 AAGCCCTGGA -s simDog_chr6.simDog.chr6 149354 10 + 593897 AAGCCCTAGA -s simHuman_chr6.simHuman.chr6 453964 10 - 601863 AAGCACTAAG -s simRat_chr6.simRat.chr6 178908 10 + 647215 AAATCCTGAG - -a -s simMouse_chr6.simMouse.chr6 188598 21 + 636262 ACTACACACTAGTGCAGTGCA -s Anc0.Anc0refChr1 18880 14 + 62388 ACCACACACTAGG-------A -s Anc1.Anc1refChr2 21418 14 - 144309 ACCACACACTAGG-------A -s Anc2.Anc2refChr3 20299 14 - 53186 ATCACACACCTTG-------A -s mr.mrrefChr5 43628 21 + 294540 ACTACACACTAGTGCAGTGCA -s simCow_chr6.simCow.chr6 441343 12 - 602619 ATCACACACCCT--------- -s simDog_chr6.simDog.chr6 149365 14 + 593897 ATCACACACCTTG-------A -s simHuman_chr6.simHuman.chr6 453975 14 - 601863 ACCACACACTAGG-------A -s simRat_chr6.simRat.chr6 178918 21 + 647215 ACTACACACCAGTGCATTGCA - -a -s simMouse_chr6.simMouse.chr6 188619 10 + 636262 CTGCATGGTT -s Anc0.Anc0refChr1 18894 10 + 62388 TTGCTTGGTT -s Anc1.Anc1refChr2 21432 10 - 144309 TTGCTTGGTT -s Anc2.Anc2refChr3 20313 10 - 53186 TTGCTTGGTT -s mr.mrrefChr5 43649 10 + 294540 CTGCATGGTT -s simCow_chr6.simCow.chr6 441355 10 - 602619 TGACTTGGTT -s simDog_chr6.simDog.chr6 149381 10 + 593897 TTGCTTGGTT -s simHuman_chr6.simHuman.chr6 453989 10 - 601863 TTGTTTTATG -s simRat_chr6.simRat.chr6 178939 10 + 647215 CTGCATGCTT - -a -s simMouse_chr6.simMouse.chr6 188629 35 + 636262 TAGTTAGTGGCTACACTGATAACAATTAACTTCAA -s Anc0.Anc0refChr1 18904 35 + 62388 TTGATTATTGCTATGCTGATAATGCTTATCTTCCC -s Anc1.Anc1refChr2 21442 35 - 144309 TTGATTATTGCTATGCTGATAATGCTTATCTTCCC -s Anc2.Anc2refChr3 20327 35 - 53186 TTAATTATTGCTATGCTGATAATGCTTATCTTCCC -s mr.mrrefChr5 43659 35 + 294540 TAGTTAGTGGCTACACTGATAACAATTAACTTCAA -s simCow_chr6.simCow.chr6 441369 35 - 602619 TTAATTATTGCCATGCTGGTAATAAGTATCTTTTC -s simDog_chr6.simDog.chr6 149395 35 + 593897 TTAATCATTGCTATGCTGATAATGCTTCTCTTCCC -s simHuman_chr6.simHuman.chr6 453999 35 - 601863 TTGATTATTGCTATGCTGATAATGGTAATCTTCCC -s simRat_chr6.simRat.chr6 178949 35 + 647215 TAATTAGTGGCTCCACTGGTAACAATTAACTTCAA - -a -s simMouse_chr6.simMouse.chr6 188664 2 + 636262 TA -s Anc0.Anc0refChr1 18941 2 + 62388 TG -s Anc1.Anc1refChr2 21479 2 - 144309 TG -s Anc2.Anc2refChr3 20364 2 - 53186 TG -s mr.mrrefChr5 43694 2 + 294540 TA -s simCow_chr6.simCow.chr6 441406 2 - 602619 TG -s simDog_chr6.simDog.chr6 149432 2 + 593897 TG -s simHuman_chr6.simHuman.chr6 454036 2 - 601863 TG -s simRat_chr6.simRat.chr6 178984 2 + 647215 TA - -a -s simMouse_chr6.simMouse.chr6 188666 44 + 636262 AAAATTATGTTCTCACTCACAGTCTACTTTCCCTGATGCCTCCA -s Anc0.Anc0refChr1 18943 28 + 62388 GCAATTACCTTCTC----------------CCTTAATCCCTCGA -s Anc1.Anc1refChr2 21481 28 - 144309 GCAATTACCTTCTC----------------CCTTAATCCCTCGA -s Anc2.Anc2refChr3 20366 28 - 53186 GCAGTTTCATTCTG----------------CCTTAATCCCTTGA -s mr.mrrefChr5 43696 44 + 294540 AAAATTACCTTCTCACTCACAGTCTACTTTCCCTGATGCCTCCA -s simCow_chr6.simCow.chr6 441408 28 - 602619 GCGCTTTCATTCTG----------------CCTTAATCCCTTAA -s simDog_chr6.simDog.chr6 149435 28 + 593897 CCAGTTTCATTTTG----------------CCAGACTCCCTTGA -s simHuman_chr6.simHuman.chr6 454038 28 - 601863 GCAATTACCTTCCC----------------CCTTAATCCCTCTA -s simRat_chr6.simRat.chr6 178986 44 + 647215 AAAATTACCTCCTCACTCACAGTCTACTTTCCCTGATGTATCCA - -a -s simMouse_chr6.simMouse.chr6 188710 8 + 636262 AGATACTT -s Anc0.Anc0refChr1 18971 8 + 62388 AGACTCAT -s Anc1.Anc1refChr2 21509 8 - 144309 AGACTCAT -s Anc2.Anc2refChr3 20394 8 - 53186 AGACTCAT -s mr.mrrefChr5 43740 8 + 294540 AGATACTT -s simCow_chr6.simCow.chr6 441442 8 - 602619 AATCTAGC -s simDog_chr6.simDog.chr6 149463 8 + 593897 AGACACAT -s simHuman_chr6.simHuman.chr6 454066 8 - 601863 AGACTCAT -s simRat_chr6.simRat.chr6 179030 8 + 647215 AGATACTT - -a -s simMouse_chr6.simMouse.chr6 188718 11 + 636262 CTTCACTCACA -s Anc0.Anc0refChr1 18979 11 + 62388 TTTCACCAATA -s Anc1.Anc1refChr2 21517 11 - 144309 TTTCACCAATA -s Anc2.Anc2refChr3 20402 11 - 53186 TCTCACCAATA -s mr.mrrefChr5 43748 11 + 294540 CTTCACTCACA -s simCow_chr6.simCow.chr6 441450 11 - 602619 CCTCTACAACA -s simDog_chr6.simDog.chr6 149471 11 + 593897 TCTTACGAATA -s simHuman_chr6.simHuman.chr6 454074 11 - 601863 ATTCACCAATA -s simRat_chr6.simRat.chr6 179039 11 + 647215 CTTAACTCACA - -a -s simMouse_chr6.simMouse.chr6 188729 23 + 636262 TCCTTAACATCCTTATCTGGACC -s Anc0.Anc0refChr1 18990 10 + 62388 T-------------GTTAGGACA -s Anc1.Anc1refChr2 21528 10 - 144309 T-------------GTTAGGACA -s Anc2.Anc2refChr3 20413 10 - 53186 T-------------GTTAAGACA -s mr.mrrefChr5 43759 23 + 294540 TCCTTAACATCCTTATCTGGACC -s simCow_chr6.simCow.chr6 441461 10 - 602619 T-------------ATTTCCACA -s simDog_chr6.simDog.chr6 149486 10 + 593897 T-------------GTCAAGACA -s simHuman_chr6.simHuman.chr6 454085 10 - 601863 T-------------GTTGGGACA -s simRat_chr6.simRat.chr6 179050 23 + 647215 TCCTTAGCATCCTTATCTGAACC - -a -s simMouse_chr6.simMouse.chr6 188752 35 + 636262 ATGGTCCACGTCTTTCAATGGATTTTGAGCATCAT -s Anc0.Anc0refChr1 19000 34 + 62388 AGCGGGCATATCTTTCAAT-GATTTTGACCATCAT -s Anc1.Anc1refChr2 21538 35 - 144309 AGCGGGCATATCTTTCAATGGATTTTGACCATCAT -s Anc2.Anc2refChr3 20423 34 - 53186 AGCTGGGATATTTTTTGAC-AATTTTGACCATCAT -s mr.mrrefChr5 43782 35 + 294540 ATGGTCCACGTCTTTCAATGGATTTTGAGCATCAT -s simCow_chr6.simCow.chr6 441477 34 - 602619 AGCTGGGATATTTGTTGAC-AATTTCGACCATTAC -s simDog_chr6.simDog.chr6 149496 22 + 593897 ------------CTTTGAC-AATATTGTCCATCAT -s simHuman_chr6.simHuman.chr6 454095 35 - 601863 AGCGGACATATCTTTCAATGGATTTTGACCATCAT -s simRat_chr6.simRat.chr6 179073 35 + 647215 ATAGACCACGACTTTCAATGGATTTTGAGCATCAT - -a -s simMouse_chr6.simMouse.chr6 188787 55 + 636262 ATTTACCATTCTTCTTCTAGCTGGAATTTTCATGGATTGTTGGGATGAAGTCTAG -s Anc0.Anc0refChr1 19034 55 + 62388 ATCAACTAGCATTCTGCTAGCTGCAATTATCATGAATTGTTGAGGTGATGACTAA -s Anc1.Anc1refChr2 21573 55 - 144309 ATCAACTAGCATTCTGCTAGCTGCAATTATCATGAATTGTTGAGGTGATGACTAA -s Anc2.Anc2refChr3 20457 55 - 53186 ATCAACTAGCATTCTGCTAGCTGCAATTATCATGAATTGTTGAGGTGATGACTAA -s mr.mrrefChr5 43817 55 + 294540 ATTTACTATCCTTCTTCTAGCTGCAATTTTCATGGATTGTTGGGATGAAGTCTAA -s simCow_chr6.simCow.chr6 441511 55 - 602619 AACAACTACCATTCAGCTAGCTGCAATTATCATAAATTGTTGAGCTCATAACTAA -s simDog_chr6.simDog.chr6 149524 54 + 593897 ATAATTTAGCATTCTGCTAGCTGCAATTATCATGAATTGTTGAAGGGGTGA-TAA -s simHuman_chr6.simHuman.chr6 454130 55 - 601863 ATCAACTAGCATTCTGCTAGCTGCAATTATCACGATTTGTTGAGGTGATGACTAA -s simRat_chr6.simRat.chr6 179108 55 + 647215 AATCACTATCGTTCTTCTAGCTGCAATTTTCATGGATTGTTGGGATGAAGTCTAA - -a -s simMouse_chr6.simMouse.chr6 188842 29 + 636262 GGCCAAAATAGTGCAAGTCTGGGTCTAGC -s Anc0.Anc0refChr1 19089 29 + 62388 AGCCAAGATAGTTCAAGTGTGGGTCTTGC -s Anc1.Anc1refChr2 21628 29 - 144309 AGCCAAGATAGTTCAAGTGTGGGTCTTGC -s Anc2.Anc2refChr3 20512 29 - 53186 AGCCAAGGTAATTCAAGTGTGGGACCTGC -s mr.mrrefChr5 43872 29 + 294540 GGCCAAAATAGTGCAAGTCTGGGTCTAGC -s simCow_chr6.simCow.chr6 441572 27 - 602619 AGACAAGCTAACTCAA-TGTGGG-CCTGC -s simDog_chr6.simDog.chr6 149578 29 + 593897 AGCCAAGGTTATTCAAGTGTGGGACCTCT -s simHuman_chr6.simHuman.chr6 454185 29 - 601863 AGTCTACATAGACCAAGTGTAGGTCTTGC -s simRat_chr6.simRat.chr6 179163 29 + 647215 CGCCAAAATAGTGCAAGACTGGGTATGGC - -a -s simMouse_chr6.simMouse.chr6 188871 2 + 636262 AA -s Anc0.Anc0refChr1 19120 2 + 62388 AG -s Anc1.Anc1refChr2 21659 2 - 144309 AG -s Anc2.Anc2refChr3 20543 2 - 53186 AG -s mr.mrrefChr5 43901 2 + 294540 AA -s simCow_chr6.simCow.chr6 441601 2 - 602619 AG -s simDog_chr6.simDog.chr6 149609 2 + 593897 AG -s simHuman_chr6.simHuman.chr6 454216 2 - 601863 AG -s simRat_chr6.simRat.chr6 179192 2 + 647215 AA - -a -s simMouse_chr6.simMouse.chr6 188873 10 + 636262 GACTCTCATA -s Anc0.Anc0refChr1 19122 10 + 62388 GACTCTCATA -s Anc1.Anc1refChr2 21661 10 - 144309 GACTCTCATA -s Anc2.Anc2refChr3 20571 10 - 53186 TACCCTCATA -s mr.mrrefChr5 43903 10 + 294540 GACTCTCATA -s simCow_chr6.simCow.chr6 441605 7 - 602619 ---CCTCATG -s simDog_chr6.simDog.chr6 149637 10 + 593897 TACCCTCATA -s simHuman_chr6.simHuman.chr6 454218 10 - 601863 GCCTTTCAGA -s simRat_chr6.simRat.chr6 179194 10 + 647215 GACTCACATA - -a -s simMouse_chr6.simMouse.chr6 188883 28 + 636262 TAGCATGGGAGTTGTACATCTTTTACAC -s Anc0.Anc0refChr1 19132 26 + 62388 TAGTATGGGAGTAGTA--TCTTTACCAC -s Anc1.Anc1refChr2 21671 26 - 144309 TAGTATGGGAGTAGTA--TCTTTACCAC -s Anc2.Anc2refChr3 20584 26 - 53186 AAGTATGGGAGTAGTA--TCTTTTCCAC -s mr.mrrefChr5 43913 28 + 294540 TAGCATGGGAGTTGTACATCTTTAACAC -s simCow_chr6.simCow.chr6 441615 26 - 602619 GAATATGGGAGTAGTA--TCTTTTACAC -s simDog_chr6.simDog.chr6 149650 26 + 593897 AAGTATGGGAGTAGTA--TCTTTTCCAC -s simHuman_chr6.simHuman.chr6 454228 7 - 601863 TA-----------------CTCTA---- -s simRat_chr6.simRat.chr6 179204 28 + 647215 TAGCATGGGAGTTATACATCTTTAACAC - -a -s simMouse_chr6.simMouse.chr6 188911 23 + 636262 ACATATGGGCATCACCTTCTGAA -s Anc0.Anc0refChr1 19158 22 + 62388 CC-TACCTTCATCCCCTTATAAA -s Anc1.Anc1refChr2 21697 23 - 144309 CCGTACCTTCATCCCCTTATAAA -s Anc2.Anc2refChr3 20610 22 - 53186 CC-TACCTTCATTCACTTATTAA -s mr.mrrefChr5 43941 23 + 294540 ACATATGGGCATCACCTTCTAAA -s simCow_chr6.simCow.chr6 441642 22 - 602619 CT-TACCCTCACTCACATATGAA -s simDog_chr6.simDog.chr6 149676 22 + 593897 CC-TACCTTCATTCACTTATTAA -s simHuman_chr6.simHuman.chr6 454235 22 - 601863 -TGTAGAAACATCTCGTTACAAA -s simRat_chr6.simRat.chr6 179232 23 + 647215 ACATATGGGCACCCCCCCCTAAA - -a -s simMouse_chr6.simMouse.chr6 188934 74 + 636262 GAAGCCCTCATTAACCCAGATCTCCAGTTCCTATGTGGGACAAATTAGTCTGTGTTTCCCAGTTTGACAGGTGA -s Anc0.Anc0refChr1 19180 69 + 62388 GAAGCCCTCATTAACCCTGATTTCCAGCCCCTATGAGGGACAAATATGCCTGTGTTTCTCAGGCTG-----TAA -s Anc1.Anc1refChr2 21720 69 - 144309 GAAGCCCTCATTAACCCTGATTTCCAGCCCCTATGAGGGACAAATATGCCTGTGTTTCTCAGGCTG-----TAA -s Anc2.Anc2refChr3 20632 69 - 53186 GAAGCCCTCATAAACCCTGATTGCCAGCCCCCATGAGAGACAAACATCCCTGTGTTTCTCAGGCTG-----AAA -s mr.mrrefChr5 43964 74 + 294540 GAAGCCCTCATTAACCCAGATTTCCAGTCCCTATGTGGGACAAATTAGTCTGTGTTTCCCAGGTTGACAGGTGA -s simCow_chr6.simCow.chr6 441664 69 - 602619 GAAGCCATCATAAACCCTGATTGCCAGGCCCCATGCGAGACAAACATCCTAGTGTTTCTCAGGCTG-----AAA -s simDog_chr6.simDog.chr6 149698 67 + 593897 GAAACCCTGATAGATCCTGATTGCCAGCCCCCATAAGAGACAAACATCCCTATGTTTCTCAGG--G-----AAA -s simHuman_chr6.simHuman.chr6 454261 69 - 601863 ACAGCTTTCATTAACCCTGATTTCCAGCCCCTATGAGGGACAAATATGCCTGTGTTTCTTAGGCTG-----TAA -s simRat_chr6.simRat.chr6 179255 74 + 647215 GGAGACCTCATAAACCGGGACTTCCAGTCCTTATGTGAGACAAATTAGTCTGTGTTTCCCAGGTTGACATGTGC - -a -s simMouse_chr6.simMouse.chr6 189008 57 + 636262 CATCTATTCATGACGACTAAACTTTCTGGGTGGACCACTTGGGTGTGGATGAGTCAA -s Anc0.Anc0refChr1 19249 42 + 62388 C---------------CTAAACTCTCAGGGTGGACCACATGGGTGTGAATGTTTGAA -s Anc1.Anc1refChr2 21789 42 - 144309 C---------------CTAAACTCTCAGGGTGGACCACATGGGTGTGAATGTTTGAA -s Anc2.Anc2refChr3 20701 42 - 53186 C---------------CTAAACTCTCAGGGCGGACCACATGGGTGTGAATGTTTGAG -s mr.mrrefChr5 44038 57 + 294540 CATCTATTCATGACGACTAAACTTTCTGGGTGGACCACATGGGTGTGGATGAGTCAA -s simCow_chr6.simCow.chr6 441733 42 - 602619 C---------------CTAAACTTTCAAGGCAGACCACATAGGTGTGAATGTTTGAG -s simDog_chr6.simDog.chr6 149773 35 + 593897 T---------------CTAAACTCTCAGGCCGGACCACATGGGCATGAAC------- -s simHuman_chr6.simHuman.chr6 454330 42 - 601863 C---------------CTAAACTCTCAGGGTGGATCACATGGCTGTGAATGTTTGGA -s simRat_chr6.simRat.chr6 179329 57 + 647215 CATCTGATCACAATGACTAAACTTTCTAGGTGGACCACATGGGAGTGGATGCGTCAA - -a -s simMouse_chr6.simMouse.chr6 189065 6 + 636262 CAGGAC -s Anc0.Anc0refChr1 19291 6 + 62388 CATAAC -s Anc1.Anc1refChr2 21831 6 - 144309 CATAAC -s Anc2.Anc2refChr3 20743 6 - 53186 CCTAAC -s mr.mrrefChr5 44095 6 + 294540 CAGAAC -s simCow_chr6.simCow.chr6 441779 6 - 602619 CCTAAC -s simHuman_chr6.simHuman.chr6 454372 6 - 601863 CAAAAC -s simRat_chr6.simRat.chr6 179386 6 + 647215 CAGAAG - -a -s simMouse_chr6.simMouse.chr6 189071 17 + 636262 CATGAAGAATACCGTGT -s Anc0.Anc0refChr1 19297 17 + 62388 TATAAAAAGGGCTATGT -s Anc1.Anc1refChr2 21837 17 - 144309 TATAAAAAGGGCTATGT -s Anc2.Anc2refChr3 20749 17 - 53186 TGTAAAAAGGGCTATGT -s mr.mrrefChr5 44101 17 + 294540 TATGAAGAATACTATGT -s simCow_chr6.simCow.chr6 441793 17 - 602619 TGTAAAAAGAGCTATGT -s simDog_chr6.simDog.chr6 149808 13 + 593897 ----AAATAGAGTACAT -s simHuman_chr6.simHuman.chr6 454378 17 - 601863 TATAAAAAGGGCTATGT -s simRat_chr6.simRat.chr6 179392 17 + 647215 TATGAAGATTACTATAT - -a -s simMouse_chr6.simMouse.chr6 189088 6 + 636262 AACATT -s Anc0.Anc0refChr1 19314 5 + 62388 A-CATC -s Anc1.Anc1refChr2 21854 5 - 144309 A-CATC -s Anc2.Anc2refChr3 20767 5 - 53186 A-CATC -s mr.mrrefChr5 44118 5 + 294540 A-CATC -s simCow_chr6.simCow.chr6 441811 5 - 602619 A-CATC -s simDog_chr6.simDog.chr6 149822 5 + 593897 A-CATT -s simHuman_chr6.simHuman.chr6 454395 5 - 601863 A-CATC -s simRat_chr6.simRat.chr6 179409 5 + 647215 A-CATC - -a -s simMouse_chr6.simMouse.chr6 189094 3 + 636262 TTC -s Anc0.Anc0refChr1 19322 3 + 62388 CTT -s Anc1.Anc1refChr2 21862 3 - 144309 CTT -s Anc2.Anc2refChr3 20775 3 - 53186 CTT -s mr.mrrefChr5 44123 3 + 294540 TTT -s simCow_chr6.simCow.chr6 441819 3 - 602619 GTT -s simDog_chr6.simDog.chr6 149830 3 + 593897 CTT -s simHuman_chr6.simHuman.chr6 454403 3 - 601863 CTT -s simRat_chr6.simRat.chr6 179414 3 + 647215 TTT - -a -s simMouse_chr6.simMouse.chr6 189097 6 + 636262 ACTATA -s Anc0.Anc0refChr1 19328 6 + 62388 ACTATA -s Anc1.Anc1refChr2 21868 6 - 144309 ACTATA -s Anc2.Anc2refChr3 20781 6 - 53186 ACTATA -s mr.mrrefChr5 44126 6 + 294540 ACTATA -s simCow_chr6.simCow.chr6 441825 6 - 602619 ACTATA -s simDog_chr6.simDog.chr6 149836 6 + 593897 CTTATA -s simHuman_chr6.simHuman.chr6 454409 6 - 601863 ACTATA -s simRat_chr6.simRat.chr6 179417 6 + 647215 ACTATA - -a -s simMouse_chr6.simMouse.chr6 189103 4 + 636262 CTAT -s Anc0.Anc0refChr1 19334 4 + 62388 CCAT -s Anc1.Anc1refChr2 21874 4 - 144309 CCAT -s Anc2.Anc2refChr3 20787 4 - 53186 CCAT -s mr.mrrefChr5 44132 4 + 294540 CTAT -s simCow_chr6.simCow.chr6 441843 4 - 602619 CCAT -s simDog_chr6.simDog.chr6 149842 4 + 593897 CCAT -s simHuman_chr6.simHuman.chr6 454415 4 - 601863 CCAT -s simRat_chr6.simRat.chr6 179423 4 + 647215 CTAT - -a -s simMouse_chr6.simMouse.chr6 189107 5 + 636262 GCATA -s Anc0.Anc0refChr1 19342 5 + 62388 GGATT -s Anc1.Anc1refChr2 21882 5 - 144309 GGATT -s Anc2.Anc2refChr3 20795 5 - 53186 GGACT -s mr.mrrefChr5 44136 5 + 294540 GCATA -s simCow_chr6.simCow.chr6 441851 5 - 602619 GAACT -s simDog_chr6.simDog.chr6 149850 5 + 593897 GGACT -s simHuman_chr6.simHuman.chr6 454423 5 - 601863 GGATT -s simRat_chr6.simRat.chr6 179427 5 + 647215 GCATA - -a -s simMouse_chr6.simMouse.chr6 189112 2 + 636262 TT -s Anc0.Anc0refChr1 19347 2 + 62388 TC -s Anc1.Anc1refChr2 21887 2 - 144309 TC -s Anc2.Anc2refChr3 20800 2 - 53186 TC -s mr.mrrefChr5 44141 2 + 294540 TC -s simCow_chr6.simCow.chr6 441857 2 - 602619 TC -s simDog_chr6.simDog.chr6 149855 2 + 593897 TC -s simHuman_chr6.simHuman.chr6 454428 2 - 601863 CC -s simRat_chr6.simRat.chr6 179432 2 + 647215 TC - -a -s simMouse_chr6.simMouse.chr6 189114 46 + 636262 GCAAATGACCAATCACAGTGTTGAACCATGATTCACTGTGTTAATC -s Anc0.Anc0refChr1 19358 32 + 62388 GTTAGTGGCCCATCACAGTG--------------ATTGTATTAGAG -s Anc1.Anc1refChr2 21898 46 - 144309 GTTAGTGGCCCATCACAGTGTTGACCTAAGACTTATTGTATTAGAG -s Anc2.Anc2refChr3 20811 32 - 53186 GTTGGTGGCCCAGCACAGTG--------------ATTGTATTGGAG -s mr.mrrefChr5 44143 46 + 294540 GCAAATGACCAATCACAGTGTTGAACCAAGATTTATTGTGTTAAAC -s simCow_chr6.simCow.chr6 441863 18 - 602619 -------------CACA-TA--------------TTCCTTTAGGAT -s simDog_chr6.simDog.chr6 149866 32 + 593897 GTTGGTGGCCCAGCACAGTG--------------ATTGTATTGGAG -s simHuman_chr6.simHuman.chr6 454439 46 - 601863 GTTAGTGGCCCATCACAGTGTTGACCTAAGACTTATTATATTAGAA -s simRat_chr6.simRat.chr6 179434 46 + 647215 GAAAATGACCAATCACAGTGTCAAACCAAGATTTATTGTGTTAAAC - -a -s simMouse_chr6.simMouse.chr6 189160 44 + 636262 AAGTCAGTAACAATTAGCTTTGCACATAAGTCCTCTATGTACTT -s Anc0.Anc0refChr1 19393 43 + 62388 -AGTCTATCACAGGTAGCTTTGTACATAAATCCCCTAAGTACTT -s Anc1.Anc1refChr2 21948 44 - 144309 GAGTCTATCACAGGTAGCTTTGTACATAAATCCCCTAAGTACTT -s Anc2.Anc2refChr3 20846 43 - 53186 -AGTCTATCAGAAGTACCTCTGTACATAAATCCCCTAAGTACTT -s mr.mrrefChr5 44189 44 + 294540 GAGTCAGTAACAGTTAGCTTTGCACATAAATCCTCTATGTACTT -s simCow_chr6.simCow.chr6 441884 43 - 602619 -AGGCTACCAGGATTACTTCTTTACATAAGTCACCTAGGTACTT -s simDog_chr6.simDog.chr6 149901 43 + 593897 -AGTCTGTCAGAAGTACCTCTGTACATATATCCCCTAAGTACTT -s simHuman_chr6.simHuman.chr6 454489 44 - 601863 GAGTCTATCACAGGTAGCTTTGTACACAAATCCCCTAAGTACCT -s simRat_chr6.simRat.chr6 179480 44 + 647215 GAGTCAGTAACAGTTAGCTTTGCACATAAATCCTCTACGTAATT - -a -s simMouse_chr6.simMouse.chr6 189204 18 + 636262 TTAGACATGTTACTAAGT -s Anc0.Anc0refChr1 19439 18 + 62388 TTAGGCATCTCAACTGAT -s Anc1.Anc1refChr2 21995 18 - 144309 TTAGGCATCTCAACTGAT -s Anc2.Anc2refChr3 20892 18 - 53186 TTAGGTATCTCAAGTGAT -s mr.mrrefChr5 44233 18 + 294540 TTAGACATGTTACCAAGT -s simCow_chr6.simCow.chr6 441930 18 - 602619 TTAGGTATCTCAAGTGAT -s simDog_chr6.simDog.chr6 149947 18 + 593897 CCATGTATCCCGAGTGAT -s simHuman_chr6.simHuman.chr6 454536 18 - 601863 TTAGGCATCTCAACTGAT -s simRat_chr6.simRat.chr6 179524 18 + 647215 TTAGACATGTTACCAAGT - -a -s simMouse_chr6.simMouse.chr6 189222 42 + 636262 CTCCTTCATATCATAACCTTGTATAGGTATACTATTGTCTTG -s Anc0.Anc0refChr1 19477 37 + 62388 CCCTTTCATG-----ATCTTGATTTGGTACACTATTATTGTG -s Anc1.Anc1refChr2 22033 37 - 144309 CCCTTTCATG-----ATCTTGATTTGGTACACTATTATTGTG -s Anc2.Anc2refChr3 20930 37 - 53186 CCCTGTCATG-----ATCTTGATTTGGTACACTATTATTGTG -s mr.mrrefChr5 44251 37 + 294540 CCCCTTCATA-----ACCTTGTATAGGTATACTATTGTCTTG -s simCow_chr6.simCow.chr6 441969 35 - 602619 CCTCATTTTG-----ATCTTGATATGGTACACCATTCT--TA -s simDog_chr6.simDog.chr6 149991 37 + 593897 TCCTGTCATG-----ACCCTGGTTTGGTACACTATTATTGTG -s simHuman_chr6.simHuman.chr6 454574 37 - 601863 CCCTTTCATG-----ATCTTGATTTGCAACACTATTATTGTG -s simRat_chr6.simRat.chr6 179542 37 + 647215 CCCCTTCATA-----ACCTTGTATAGGTATACTATTGTCTTG - -a -s simMouse_chr6.simMouse.chr6 189264 16 + 636262 TCTCTCGTTCCGTTGT -s Anc0.Anc0refChr1 19525 13 + 62388 C---CCATTCCCTTCT -s Anc1.Anc1refChr2 22081 16 - 144309 CCATCCATTCCCTTCT -s Anc2.Anc2refChr3 20978 13 - 53186 C---CCATTCCCTACT -s mr.mrrefChr5 44288 16 + 294540 TCTCTCGTTCCCTTGT -s simCow_chr6.simCow.chr6 442015 7 - 602619 C---CCATTC------ -s simDog_chr6.simDog.chr6 150039 13 + 593897 C---CCATTCCCTACT -s simHuman_chr6.simHuman.chr6 454622 16 - 601863 CCATCCATTCCCTTAT -s simRat_chr6.simRat.chr6 179579 16 + 647215 TCTCTTGTTCCCCTGT - -a -s simMouse_chr6.simMouse.chr6 189280 23 + 636262 TGAAATGCATTACTCATCACATG -s Anc0.Anc0refChr1 19539 23 + 62388 TGAAACACATTATCTGTCACATG -s Anc1.Anc1refChr2 22098 23 - 144309 TGAAACACATTATCTGTCACATG -s Anc2.Anc2refChr3 20992 23 - 53186 TGAAACACATTATCTGTCATATG -s mr.mrrefChr5 44304 23 + 294540 TGAAATGCATTACTCATCACATG -s simCow_chr6.simCow.chr6 442022 18 - 602619 -----TGCACTATCTGTCATGTG -s simDog_chr6.simDog.chr6 150053 23 + 593897 TGAAACACATTAACTGTCGTATG -s simHuman_chr6.simHuman.chr6 454639 23 - 601863 TGAATCATATTATCTGTCACATG -s simRat_chr6.simRat.chr6 179595 23 + 647215 TGAAATGCATTACTCATCACATG - -a -s simMouse_chr6.simMouse.chr6 189303 8 + 636262 AAGAAGCT -s Anc0.Anc0refChr1 19562 8 + 62388 AAGAGGCC -s Anc1.Anc1refChr2 22121 8 - 144309 AAGAGGCC -s Anc2.Anc2refChr3 21016 8 - 53186 AAGTAGCC -s mr.mrrefChr5 44327 8 + 294540 AAGAGGCT -s simCow_chr6.simCow.chr6 442041 8 - 602619 AGGTAACC -s simDog_chr6.simDog.chr6 150077 8 + 593897 AAGTAGTC -s simHuman_chr6.simHuman.chr6 454662 7 - 601863 CTTAG-CC -s simRat_chr6.simRat.chr6 179618 8 + 647215 AAAAGACT - -a -s simMouse_chr6.simMouse.chr6 189311 20 + 636262 TAGGCACTGTGAACAGCCTA -s Anc0.Anc0refChr1 19570 20 + 62388 TAAGCACTGTAAATAACCTA -s Anc1.Anc1refChr2 22129 20 - 144309 TAAGCACTGTAAATAACCTA -s Anc2.Anc2refChr3 21024 20 - 53186 TAAGTACTGTAAATAACCTA -s mr.mrrefChr5 44335 20 + 294540 TAGGCACTGTGAACAGCCTA -s simCow_chr6.simCow.chr6 442050 20 - 602619 TAAGTATGGTAAACAACCTA -s simDog_chr6.simDog.chr6 150085 20 + 593897 TAAGTACTGTAAATGACCTC -s simHuman_chr6.simHuman.chr6 454669 20 - 601863 TAAGCACTCTAAATAAACTA -s simRat_chr6.simRat.chr6 179626 20 + 647215 TAGGCACTATGAACAGCCTA - -a -s simMouse_chr6.simMouse.chr6 189331 6 + 636262 CATTGT -s Anc0.Anc0refChr1 19592 4 + 62388 CATT-- -s Anc1.Anc1refChr2 22151 4 - 144309 CATT-- -s Anc2.Anc2refChr3 21046 4 - 53186 CATA-- -s mr.mrrefChr5 44355 6 + 294540 CATTGT -s simCow_chr6.simCow.chr6 442072 4 - 602619 CACA-- -s simDog_chr6.simDog.chr6 150107 4 + 593897 CATA-- -s simHuman_chr6.simHuman.chr6 454691 4 - 601863 CATT-- -s simRat_chr6.simRat.chr6 179646 6 + 647215 CATTGT - -a -s simMouse_chr6.simMouse.chr6 189337 26 + 636262 TGCAAAATCATATGCCAGTTCTCTGC -s Anc0.Anc0refChr1 19596 19 + 62388 ----AATTCATAGGACAGTCCA---G -s Anc1.Anc1refChr2 22155 22 - 144309 ----AATTCATAGGACAGTCCACTGG -s Anc2.Anc2refChr3 21050 19 - 53186 ----AATTCATAGGACAGTCCA---G -s mr.mrrefChr5 44361 26 + 294540 TGCAAAATCATATGCCAGTCCTCTGC -s simCow_chr6.simCow.chr6 442076 16 - 602619 ----AATTCGTAGGACA---CA---G -s simDog_chr6.simDog.chr6 150111 19 + 593897 ----AATTCATAGGACTGTCCA---G -s simHuman_chr6.simHuman.chr6 454695 22 - 601863 ----AATCTATAGGACAATCCACTGA -s simRat_chr6.simRat.chr6 179669 26 + 647215 TGCAAAATCATATGGCAGTCCTCTGC - -a -s simMouse_chr6.simMouse.chr6 189363 19 + 636262 CTTTTCCATATGTTTTCTT -s Anc0.Anc0refChr1 19615 18 + 62388 GGTTTACACATGTTATG-T -s Anc1.Anc1refChr2 22177 19 - 144309 GGTTTACACATGTTATGTT -s Anc2.Anc2refChr3 21069 18 - 53186 GGTTTACACATGTTATG-T -s mr.mrrefChr5 44387 19 + 294540 CTTTTCCATATGTTTTCTT -s simCow_chr6.simCow.chr6 442094 18 - 602619 GGTTTACACACATTGTG-T -s simDog_chr6.simDog.chr6 150130 18 + 593897 GGTTTACACATGTTATG-T -s simHuman_chr6.simHuman.chr6 454717 19 - 601863 AGTCTACAAATGTTATGTT -s simRat_chr6.simRat.chr6 179695 19 + 647215 TTTTTCCACAAATTTTCTT - -a -s simMouse_chr6.simMouse.chr6 189382 32 + 636262 TCATCTTATCAAGGGTTTTGTGTCCACATGAC -s Anc0.Anc0refChr1 19633 32 + 62388 TCATCTCAACCAGGGTTGTGCAACCACATGAT -s Anc1.Anc1refChr2 22196 32 - 144309 TCATCTCAACCAGGGTTGTGCAACCACATGAT -s Anc2.Anc2refChr3 21087 32 - 53186 TCATCTCAACCAGAGTTGTGCAACCACATGAT -s mr.mrrefChr5 44406 32 + 294540 TCATCTTAACAAGGGTTTTGCATCCACATGAT -s simCow_chr6.simCow.chr6 442112 32 - 602619 TCATACCACCCAGAGTTGTGCAATCACATGAT -s simDog_chr6.simDog.chr6 150148 32 + 593897 TCAACTCAACCAGAGTTGTGCCACCACATGAT -s simHuman_chr6.simHuman.chr6 454750 32 - 601863 TCATCTCAACCAGGGTTGTGCAACCACATGAT -s simRat_chr6.simRat.chr6 179714 32 + 647215 TCATCTTAACAAGGGTTTTGCATACACATGAT - -a -s simMouse_chr6.simMouse.chr6 189414 53 + 636262 GGACCATTATACCATTTTTGTGATTGTTAGACTCTTTCATCCTACTTGGGTGT -s Anc0.Anc0refChr1 19665 53 + 62388 TGACCATTATACCATTTTTGTGATTAATATAGTATTTTATCCTATTTAGATGT -s Anc1.Anc1refChr2 22228 53 - 144309 TGACCATTATACCATTTTTGTGATTAATATAGTATTTTATCCTATTTAGATGT -s Anc2.Anc2refChr3 21119 53 - 53186 TGACCATTATTCCATTTTTGTGATTAATATAGAATTTTATCCTATTTAGATGT -s mr.mrrefChr5 44438 53 + 294540 GGACCATTATACCATTTTTGTGATTGTTAGACTCTTTCATCCTATTTGGGTGT -s simCow_chr6.simCow.chr6 442144 53 - 602619 TGACCCTTATTCCATTTTTATCTTTAATGTGGACTTTTATCCTATATAGATGT -s simDog_chr6.simDog.chr6 150180 53 + 593897 TGACCATTACTCCCTTTTTGTGATTAATAGAAAATTTCATCCTATTTAGATGT -s simHuman_chr6.simHuman.chr6 454782 53 - 601863 TGACCATTATACCATTTTTGTGATTAATTTAGTTTTTTATCCTTTTCAGATGT -s simRat_chr6.simRat.chr6 179747 53 + 647215 GGACTATTGTACCACTATTGTGATTGTTGGATACTTTCAACCTATTTGTGTGG - -a -s simMouse_chr6.simMouse.chr6 189467 17 + 636262 ACCTGACTTGTTAGAGG -s Anc0.Anc0refChr1 19725 16 + 62388 -AGTGAATAATTGGAGG -s Anc1.Anc1refChr2 22288 17 - 144309 AAGTGAATAATTGGAGG -s Anc2.Anc2refChr3 21179 16 - 53186 -AGCGAATAATTGGAGG -s mr.mrrefChr5 44491 17 + 294540 ACCTGACTTGTTAGAGG -s simCow_chr6.simCow.chr6 442204 16 - 602619 -CACAAATACTTGGAGG -s simDog_chr6.simDog.chr6 150240 16 + 593897 -AGCGTATAATTGGGGG -s simHuman_chr6.simHuman.chr6 454848 17 - 601863 AAGTCAATAATTGTAGG -s simRat_chr6.simRat.chr6 179800 17 + 647215 ACCTGACTTGTTAGAGG - -a -s simMouse_chr6.simMouse.chr6 189484 8 + 636262 TCATTTCT -s Anc0.Anc0refChr1 19741 8 + 62388 TCATTTCT -s Anc1.Anc1refChr2 22305 8 - 144309 TCATTTCT -s Anc2.Anc2refChr3 21198 8 - 53186 TCATTTCT -s mr.mrrefChr5 44508 8 + 294540 TCATTTCT -s simCow_chr6.simCow.chr6 442223 8 - 602619 TCATTTTT -s simDog_chr6.simDog.chr6 150259 8 + 593897 TCATTTCT -s simHuman_chr6.simHuman.chr6 454865 8 - 601863 TCATGTCT -s simRat_chr6.simRat.chr6 179817 8 + 647215 TTATTTCT - -a -s simMouse_chr6.simMouse.chr6 189492 34 + 636262 TAAGTTGTCTCAGGTTTTAATAGGTATGCCTAGA -s Anc0.Anc0refChr1 19805 34 + 62388 TACACCCTCATGGATATTAACAGGTATGGCTAGA -s Anc1.Anc1refChr2 22369 34 - 144309 TACACCCTCATGGATATTAACAGGTATGGCTAGA -s Anc2.Anc2refChr3 21274 34 - 53186 TACACCCTCATGGATAGTGTCAGGTATGGCTAGA -s mr.mrrefChr5 44516 34 + 294540 TAAGTTCTCTCAGGTTTTAATAGGTATGCCTAGA -s simCow_chr6.simCow.chr6 442304 34 - 602619 TACACCCTCATGGATAGTGTCAGGTACAGCTAGA -s simDog_chr6.simDog.chr6 150332 10 + 593897 -----------------------GTGTG-CTAGA -s simHuman_chr6.simHuman.chr6 454938 34 - 601863 TACACCCTCATGGATCTTAACAGGTATGTCTATA -s simRat_chr6.simRat.chr6 179825 34 + 647215 TAAGTTCTCTCAGGTTTTAATAGGTGTGCCTAGA - -a -s simMouse_chr6.simMouse.chr6 189526 15 + 636262 GTGATGGCTAGGATC -s Anc0.Anc0refChr1 19839 15 + 62388 GTGATGGCTAGGGTG -s Anc1.Anc1refChr2 22403 15 - 144309 GTGATGGCTAGGGTG -s Anc2.Anc2refChr3 21308 15 - 53186 GTGATGGCTAGAGTG -s mr.mrrefChr5 44550 15 + 294540 GTGATGGCTAGGATG -s simCow_chr6.simCow.chr6 442369 15 - 602619 GTGATGGCTAGAGTG -s simDog_chr6.simDog.chr6 150342 15 + 593897 GTGATGGCTAGAGTG -s simHuman_chr6.simHuman.chr6 454972 15 - 601863 GTGATGGCTAGGTTG -s simRat_chr6.simRat.chr6 179859 15 + 647215 GTGATGGCTAGAATG - -a -s simMouse_chr6.simMouse.chr6 189541 11 + 636262 CCAACCAGCTT -s Anc0.Anc0refChr1 19858 7 + 62388 CT----AGCAT -s Anc1.Anc1refChr2 22422 9 - 144309 CT--CCAGCAT -s Anc2.Anc2refChr3 21327 7 - 53186 CT----AGCAA -s mr.mrrefChr5 44565 9 + 294540 CC--CCAGCAT -s simCow_chr6.simCow.chr6 442388 7 - 602619 CT----AGTAA -s simDog_chr6.simDog.chr6 150361 7 + 593897 CT----AGCAA -s simHuman_chr6.simHuman.chr6 454991 9 - 601863 CT--CCAGAAT -s simRat_chr6.simRat.chr6 179874 9 + 647215 CC--CTGTTAT - -a -s simMouse_chr6.simMouse.chr6 189552 15 + 636262 TAGGTTGCTTAAAAT -s Anc0.Anc0refChr1 19865 15 + 62388 TGGGATGCTTTAAAT -s Anc1.Anc1refChr2 22431 15 - 144309 TGGGATGCTTTAAAT -s Anc2.Anc2refChr3 21334 15 - 53186 TGGGATGCTTCAAAA -s mr.mrrefChr5 44574 15 + 294540 TAGGATGCTTTAAAT -s simCow_chr6.simCow.chr6 442395 15 - 602619 TACGATGTTTCAAAG -s simDog_chr6.simDog.chr6 150368 15 + 593897 TGGGGGGCCTCAAAA -s simHuman_chr6.simHuman.chr6 455010 15 - 601863 TGGTATGCTTTAAAT -s simRat_chr6.simRat.chr6 179883 15 + 647215 TAGGATGCTGTAAAT - -a -s simMouse_chr6.simMouse.chr6 189567 36 + 636262 TGCTATCAGTAGGCTCCACTATATAACCTAACAGGC -s Anc0.Anc0refChr1 19881 36 + 62388 GGCTATCTGTAGGTGCCAGTGTACTACCTGATAGGT -s Anc1.Anc1refChr2 22447 36 - 144309 GGCTATCTGTAGGTGCCAGTGTACTACCTGATAGGT -s Anc2.Anc2refChr3 21350 36 - 53186 GGCTATCTGTAGAGGCCAGTGTACTACCTGATAGGT -s mr.mrrefChr5 44589 36 + 294540 TGCTATCTGTAGGTTCCACTGTATAACCTGACAGGC -s simCow_chr6.simCow.chr6 442411 36 - 602619 GACTATCTGTGGAGGCCAGTCCACTACCTGATAGGT -s simDog_chr6.simDog.chr6 150384 27 + 593897 GGATATCTGTAGAGGTTGGAGTACTAC--------- -s simHuman_chr6.simHuman.chr6 455026 36 - 601863 GGCTACTTGTAGGTGCCAGTGTTGTGCCTGATTGGT -s simRat_chr6.simRat.chr6 179898 36 + 647215 TGCTATCTGTAGGTTCCACTGTATAACCTGACAGGC - -a -s simMouse_chr6.simMouse.chr6 189603 28 + 636262 AAATTGACTTTTTAATTCTCGTAACTGT -s Anc0.Anc0refChr1 19917 21 + 62388 AAACT-------TCATTCTCTCAACAGG -s Anc1.Anc1refChr2 22483 21 - 144309 AAACT-------TCATTCTCTCAACAGG -s Anc2.Anc2refChr3 21386 21 - 53186 AAACA-------TCATTCTCTCAACAGG -s mr.mrrefChr5 44625 28 + 294540 AAACTGACTTTTTAATTCTCTTAACTGT -s simCow_chr6.simCow.chr6 442447 21 - 602619 AAACC-------TCATCCCCTTAGCAGG -s simDog_chr6.simDog.chr6 150411 18 + 593897 ---CA-------TCATTTTCTCGACAGG -s simHuman_chr6.simHuman.chr6 455062 21 - 601863 AAACT-------TCACTCTCTCAACAGG -s simRat_chr6.simRat.chr6 179938 28 + 647215 AAACTGACTGTCTAATTTTCTTAACTAT - -a -s simMouse_chr6.simMouse.chr6 189631 67 + 636262 GGATGCACAGAAGAGGACAACAATATTTTGCAAATCTACTTAGTTACCACTGATTAACCTTGTAGAG -s Anc0.Anc0refChr1 19942 65 + 62388 GGACTCACAGAAAAGTACAATGAAATCC-ACAAGTCTAATTACCCACTACTCAT-AAGCTtGTACTG -s Anc1.Anc1refChr2 22508 65 - 144309 GGACTCACAGAAAAGTACAATGAAATCC-ACAAGTCTAATTACCCACTACTCAT-AAGCTTGTACTG -s Anc2.Anc2refChr3 21411 65 - 53186 GGACACACAGTAAAGTACAATGAAATCC-ACAAGTCTCATTACCCACTACTCAT-AAGCTtGTACTA -s mr.mrrefChr5 44653 66 + 294540 GGACTCACAGAAGAGGACAACAATATTCTGCAAGTCTACTTAGTTATCACTCAT-AACCTTGTAGAG -s simCow_chr6.simCow.chr6 442472 65 - 602619 GGACGCAGAGTAAAGTACAAGGTAACCC-ACAAGACTCATTACCCAGTACTCAT-AAGCTtgtattg -s simDog_chr6.simDog.chr6 150433 62 + 593897 GGACACACAGTTAAGT---ATGAGATCC-ACAAGTTTCATTACCCACTACTCAT-GAGCTTATGCTA -s simHuman_chr6.simHuman.chr6 455087 54 - 601863 GGGCTCACACAAAAGTATAATGGAATCC-AAAAGTCTAGT-----------CAT-AAGGAAGTACTG -s simRat_chr6.simRat.chr6 179966 65 + 647215 GGACTCACAGAAGAGGACAACA-TATTCTTCAAGTCTACTTAGTTATCACTCAT-AACCTTGTATTG - -a -s simMouse_chr6.simMouse.chr6 189698 8 + 636262 GCAATTAT -s Anc0.Anc0refChr1 20007 4 + 62388 G----TAT -s Anc1.Anc1refChr2 22573 4 - 144309 G----TAT -s Anc2.Anc2refChr3 21479 4 - 53186 A----TAT -s mr.mrrefChr5 44719 8 + 294540 GCAATTAT -s simCow_chr6.simCow.chr6 442540 4 - 602619 a----tac -s simDog_chr6.simDog.chr6 150498 4 + 593897 A----TAT -s simHuman_chr6.simHuman.chr6 455141 4 - 601863 G----TGT -s simRat_chr6.simRat.chr6 180031 8 + 647215 GCAATAAT - -a -s simMouse_chr6.simMouse.chr6 189706 20 + 636262 TACTCTCTCTTCATTGCTCT -s Anc0.Anc0refChr1 20011 20 + 62388 TACTCTCTCTCCATTGCGTC -s Anc1.Anc1refChr2 22577 20 - 144309 TACTCTCTCTCCATTGCGTC -s Anc2.Anc2refChr3 21483 20 - 53186 TACTCCCTCTCCATTGTGTC -s mr.mrrefChr5 44727 20 + 294540 TACTCTCTCTTCATTGCTCT -s simCow_chr6.simCow.chr6 442544 20 - 602619 tactaccactccattgtgct -s simDog_chr6.simDog.chr6 150503 20 + 593897 TACTCCCTCTCTATTGTGTC -s simHuman_chr6.simHuman.chr6 455145 20 - 601863 TACTCTCTCTCCATTGCGTC -s simRat_chr6.simRat.chr6 180039 20 + 647215 TACTCTCTGTCCATTGATCT - -a -s simMouse_chr6.simMouse.chr6 189726 91 + 636262 TAAGAGTCTTATCAACTACCACTCATAAGGTTCGTTTCACTAACACTACTCTATCTTCATTACATCCTAACACCTGTACTAGTAGGTAGGC -s Anc0.Anc0refChr1 20031 86 + 62388 TACAAGTCTTATCACCTACCACTCATAAGCTT-GTGTTGCTAACAtTACTCTCTCTTCATTGCATCCTAATATCTGTACTAATAGG----C -s Anc1.Anc1refChr2 22597 86 - 144309 TACAAGTCTTATCACCTACCACTCATAAGCTT-GTGTTGCTAACATTACTCTCTCTTCATTGCATCCTAATATCTGTACTAATAGG----C -s Anc2.Anc2refChr3 21505 86 - 53186 GACAAGTCTTATCACCTACCACTCATAAGCTT-GTGTTGCTAACAtGACTCTCTCTTCATTGCAACTTAATTTTTGTACTAAAAGG----C -s mr.mrrefChr5 44747 87 + 294540 TAAGAGTCTTATCAACTACCACTCATAAGGTCCGTGTCACTAACACTACTCTATCTTCATTACATCCTAACACCTGTACTAGTAGG----C -s simCow_chr6.simCow.chr6 442566 86 - 602619 agcaaggctcattgcctagcactcataagctt-gtattcctaacatgattccctcttcactgcaACTTGATTTTTGTACTGAAAGG----C -s simDog_chr6.simDog.chr6 150525 85 + 593897 GACTAGTCTTATCACCTACCACCCCTAAGCTA-ATGTTGCTAAGA-GACTCTCTCTACATTGCAATTTAATTTTTGTACTAAAAGA----C -s simHuman_chr6.simHuman.chr6 455165 86 - 601863 TACAAGTCATGTCACCTATCACTCATAAGCTT-GTGGTGCTATCATTACTCTCTCTTCATTGTGTCCTAATAACTGTACTAATAGG----C -s simRat_chr6.simRat.chr6 180059 87 + 647215 TAACAGTCTTATCAACTACCACTCATAGGGGCGGTGTCACTAACATCACTCTGTCTTCATCACATCCTAACACCTGTACTAATAGG----C - -a -s simMouse_chr6.simMouse.chr6 189817 1 + 636262 A -s Anc0.Anc0refChr1 20117 1 + 62388 A -s Anc1.Anc1refChr2 22683 1 - 144309 A -s Anc2.Anc2refChr3 21591 1 - 53186 A -s mr.mrrefChr5 44834 1 + 294540 A -s simCow_chr6.simCow.chr6 442652 1 - 602619 A -s simDog_chr6.simDog.chr6 150610 1 + 593897 A -s simHuman_chr6.simHuman.chr6 455379 1 - 601863 A -s simRat_chr6.simRat.chr6 180146 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 189818 27 + 636262 AAAACATAGGACTGCCTGTGCTTGGCC -s Anc0.Anc0refChr1 20118 27 + 62388 AAAAACTGAGATTCCTTGAGCTAGATT -s Anc1.Anc1refChr2 22684 27 - 144309 AAAAACTGAGATTCCTTGAGCTAGATT -s Anc2.Anc2refChr3 21592 27 - 53186 AAAAACTGAGATTCCTTGAGCCAGATT -s mr.mrrefChr5 44835 27 + 294540 AAAACATGGGACTGCCTGTGCTTGGCC -s simCow_chr6.simCow.chr6 442654 27 - 602619 AAGAACTCAGTCTCCTTTAGCCAGATT -s simDog_chr6.simDog.chr6 150611 27 + 593897 AAACACTGAGATTCCTTGAACCTGATT -s simHuman_chr6.simHuman.chr6 455380 27 - 601863 ATAAACTGAGAATCCTTGAGGTAGATT -s simRat_chr6.simRat.chr6 180147 27 + 647215 AAAAGTTGGGACTGCCTGTGCTGGGCC - -a -s simMouse_chr6.simMouse.chr6 189845 14 + 636262 ACATACTAATTGAC -s Anc0.Anc0refChr1 20145 10 + 62388 ACATACT----GAC -s Anc1.Anc1refChr2 22711 10 - 144309 ACATACT----GAC -s Anc2.Anc2refChr3 21619 10 - 53186 ACAAATA----GAC -s mr.mrrefChr5 44862 14 + 294540 ACATACTAATTGAC -s simCow_chr6.simCow.chr6 442681 10 - 602619 ACAAATA----GAC -s simDog_chr6.simDog.chr6 150642 10 + 593897 ACCAATA----GAC -s simHuman_chr6.simHuman.chr6 455407 10 - 601863 GCATACT----GAC -s simRat_chr6.simRat.chr6 180174 14 + 647215 ACATACTAGTTGAC - -a -s simMouse_chr6.simMouse.chr6 189859 17 + 636262 GATCTGAACATCCTATA -s Anc0.Anc0refChr1 20155 16 + 62388 AACTTAAGCATCCTA-A -s Anc1.Anc1refChr2 22721 16 - 144309 AACTTAAGCATCCTA-A -s Anc2.Anc2refChr3 21629 16 - 53186 AACTTAAGTATCCTA-A -s mr.mrrefChr5 44876 17 + 294540 AATTTGAACATCCTATA -s simCow_chr6.simCow.chr6 442693 16 - 602619 ATCTTGAAAATCCTA-A -s simDog_chr6.simDog.chr6 150652 16 + 593897 AACCTAAGTATCCTA-A -s simHuman_chr6.simHuman.chr6 455417 16 - 601863 AACTTCAGCATCTTA-A -s simRat_chr6.simRat.chr6 180188 17 + 647215 AATTTGAACATCCTATA - -a -s simMouse_chr6.simMouse.chr6 189876 11 + 636262 GACAAATTCCA -s Anc0.Anc0refChr1 20173 11 + 62388 GACAAACTTAA -s Anc1.Anc1refChr2 22739 11 - 144309 GACAAACTTAA -s Anc2.Anc2refChr3 21647 11 - 53186 GACAAACTTAA -s mr.mrrefChr5 44895 11 + 294540 GACAAATTCCA -s simCow_chr6.simCow.chr6 442711 11 - 602619 GACAATCTTAA -s simDog_chr6.simDog.chr6 150670 11 + 593897 GACAAACTTAA -s simHuman_chr6.simHuman.chr6 455435 11 - 601863 GAGAAACTAAA -s simRat_chr6.simRat.chr6 180207 11 + 647215 GACAAATTCCA - -a -s simMouse_chr6.simMouse.chr6 189887 21 + 636262 GACAATGTACTGGGACTCCTC -s Anc0.Anc0refChr1 20185 21 + 62388 GGCAATGTACTGGGACTCCTC -s Anc1.Anc1refChr2 22751 21 - 144309 GGCAATGTACTGGGACTCCTC -s Anc2.Anc2refChr3 21659 21 - 53186 GGCAGTGTACTGGGACTCCTC -s mr.mrrefChr5 44906 21 + 294540 GACAATGTACTGGGACTCCTC -s simCow_chr6.simCow.chr6 442853 21 - 602619 GGCAATGTGCTGGGACTCATT -s simCow_chr6.simCow.chr6 442723 18 - 602619 AGCAGTGTACTGGGACTC--- -s simDog_chr6.simDog.chr6 150682 21 + 593897 GGCAGTGTACTGGGACTCCTC -s simHuman_chr6.simHuman.chr6 455447 21 - 601863 GGAAATGTACTGGGACTCCTC -s simRat_chr6.simRat.chr6 180218 21 + 647215 GACGATGAACTGGTACTCCTC - -a -s simMouse_chr6.simMouse.chr6 189908 36 + 636262 TGTCAGAGAGCAAAAGCCTGGGAGGGGTTGAGTATT -s Anc0.Anc0refChr1 20228 35 + 62388 CATTGAAGATCAACTGCCTAACAGGG-CTCTGTATT -s Anc1.Anc1refChr2 22794 35 - 144309 CATTGAAGATCAACTGCCTAACAGGG-CTCTGTATT -s Anc2.Anc2refChr3 21705 35 - 53186 CATTGAAGATCAACTGCCTAACAGGG-CCCTGTATT -s mr.mrrefChr5 44927 35 + 294540 TGTTAGAGAGCAACAGCCTGACAGGG-TTGAGTATT -s simCow_chr6.simCow.chr6 442899 35 - 602619 AATTCAGGATCAACTACCCAACAGGG-CCCTGTATG -s simCow_chr6.simCow.chr6 442751 35 - 602619 GATTGAAGACCAACTGCCTAACAGGG-CCCCATATT -s simDog_chr6.simDog.chr6 150728 35 + 593897 CATCAAATATCACCTGTCTAACAGGG-CCCTGTATA -s simHuman_chr6.simHuman.chr6 455490 35 - 601863 CATTGTAGACCAACTTCCTCACAGGG-CTCTGCATT -s simRat_chr6.simRat.chr6 180239 35 + 647215 TGTTAGAGAGCTACAGCATAACAGGG-TTGCGTATT - -a -s simMouse_chr6.simMouse.chr6 189944 21 + 636262 CAAAATCCATCAAGGCTTCCT -s Anc0.Anc0refChr1 20289 21 + 62388 CTATATACGACAAGGCTTTGC -s Anc1.Anc1refChr2 22855 21 - 144309 CTATATACGACAAGGCTTTGC -s Anc2.Anc2refChr3 21766 21 - 53186 CTATATATGATAAGGCTTTGC -s mr.mrrefChr5 44962 21 + 294540 CAAAATACATCAAGGCTTCCT -s simCow_chr6.simCow.chr6 442960 21 - 602619 CTATGTATAGTAAGGCTTTGC -s simCow_chr6.simCow.chr6 442812 21 - 602619 CTATCTATGATAAGGCTTTGC -s simDog_chr6.simDog.chr6 150789 19 + 593897 ATATATATGATAAGACTT--C -s simHuman_chr6.simHuman.chr6 455551 21 - 601863 CTATATACGCCAAGGCTGGGC -s simRat_chr6.simRat.chr6 180274 21 + 647215 GAAAATACATCAAGGCTTCCT - -a -s simMouse_chr6.simMouse.chr6 189965 3 + 636262 GCT -s Anc0.Anc0refChr1 20310 3 + 62388 GCT -s Anc1.Anc1refChr2 22876 3 - 144309 GCT -s Anc2.Anc2refChr3 21803 3 - 53186 ACT -s mr.mrrefChr5 44983 3 + 294540 GCT -s simCow_chr6.simCow.chr6 442997 3 - 602619 ACT -s simCow_chr6.simCow.chr6 442849 3 - 602619 ACT -s simHuman_chr6.simHuman.chr6 455572 3 - 601863 GCT -s simRat_chr6.simRat.chr6 180295 3 + 647215 ACT - -a -s simMouse_chr6.simMouse.chr6 189968 15 + 636262 TCATTGGAATTCATT -s Anc0.Anc0refChr1 20313 15 + 62388 TTACTGAGATTTAGT -s Anc1.Anc1refChr2 22879 15 - 144309 TTACTGAGATTTAGT -s Anc2.Anc2refChr3 21806 15 - 53186 TTACTGAGATTTAGT -s mr.mrrefChr5 44986 15 + 294540 TCATTGGAATTCATT -s simCow_chr6.simCow.chr6 443007 15 - 602619 TTACTGAGATATATT -s simDog_chr6.simDog.chr6 150811 15 + 593897 TTATTGGGATTTAGT -s simHuman_chr6.simHuman.chr6 455575 15 - 601863 GGACTGAGATGTAAT -s simRat_chr6.simRat.chr6 180298 15 + 647215 ACATTGGAATTCATT - -a -s simMouse_chr6.simMouse.chr6 189983 38 + 636262 CCAGGCACTAATAGTTAGGCCAGCCAGATGATCAGTTG -s Anc0.Anc0refChr1 20328 37 + 62388 CCAGGCATTCAAAATTATAACA-TCAGATGATCAGTTC -s Anc1.Anc1refChr2 22894 37 - 144309 CCAGGCATTCAAAATTATAACA-TCAGATGATCAGTTC -s Anc2.Anc2refChr3 21821 37 - 53186 CCAGGCATACAAGACTGTAACA-TCACATTATCAGATC -s mr.mrrefChr5 45001 37 + 294540 CCAGGCACTAATAGTTATGCCA-TCAGATGATCAGTTG -s simCow_chr6.simCow.chr6 443022 37 - 602619 TCAGGCATCCAAGACTGTAACA-TCACATTATCAGATC -s simDog_chr6.simDog.chr6 150846 10 + 593897 CCAGGTACAC---------------------------- -s simHuman_chr6.simHuman.chr6 455590 37 - 601863 CCAGGCATTCAGAATTATAACA-TCAGATGCTCAGTTC -s simRat_chr6.simRat.chr6 180313 37 + 647215 CCAGGCACTAATAGTTATGCCA-TCAGCTGATTAGTTG - -a -s simMouse_chr6.simMouse.chr6 190021 24 + 636262 ATTCCTCTGAGTGCCCTGAACTCA -s Anc0.Anc0refChr1 20365 21 + 62388 AT-CCTCTGA--TCCCTGATCTCA -s Anc1.Anc1refChr2 22931 23 - 144309 AT-CCTCTGACTTCCCTGATCTCA -s Anc2.Anc2refChr3 21858 21 - 53186 AG-CCTTTAA--TCCCTGATCTTA -s mr.mrrefChr5 45038 24 + 294540 ATTCCTCTGAGTGCCCTGATCTCA -s simCow_chr6.simCow.chr6 443060 21 - 602619 AG-CCTTTAA--TCCCTGATCTTA -s simHuman_chr6.simHuman.chr6 455627 23 - 601863 AT-CCTCTGACTTCCCTGATCTCA -s simRat_chr6.simRat.chr6 180350 24 + 647215 ATTCCTCTGAGTGCCCTGATTTCA - -a -s simMouse_chr6.simMouse.chr6 190045 6 + 636262 ACTTTT -s Anc0.Anc0refChr1 20386 6 + 62388 ACTTTC -s Anc1.Anc1refChr2 22954 6 - 144309 ACTTTC -s Anc2.Anc2refChr3 21879 6 - 53186 ACCTTC -s mr.mrrefChr5 45062 6 + 294540 ACTTTT -s simCow_chr6.simCow.chr6 443102 6 - 602619 ACCTTC -s simDog_chr6.simDog.chr6 150856 3 + 593897 ---CTC -s simHuman_chr6.simHuman.chr6 455650 6 - 601863 ACTTTC -s simRat_chr6.simRat.chr6 180374 6 + 647215 ACTTGT - -a -s simMouse_chr6.simMouse.chr6 190051 12 + 636262 GTTTGGAAGGCC -s Anc0.Anc0refChr1 20392 7 + 62388 GA-----AGGGG -s Anc1.Anc1refChr2 22960 7 - 144309 GA-----AGGGG -s Anc2.Anc2refChr3 21885 7 - 53186 GA-----TGTGG -s mr.mrrefChr5 45068 12 + 294540 GTTTGGAAGGCC -s simCow_chr6.simCow.chr6 443113 7 - 602619 GA-----TGTAA -s simDog_chr6.simDog.chr6 150859 7 + 593897 TA-----TGTGG -s simHuman_chr6.simHuman.chr6 455656 7 - 601863 GA-----AGGGG -s simRat_chr6.simRat.chr6 180380 12 + 647215 ATTTAGAAGGCC - -a -s simMouse_chr6.simMouse.chr6 190063 4 + 636262 CAGA -s Anc0.Anc0refChr1 20399 4 + 62388 CAGG -s Anc1.Anc1refChr2 22967 4 - 144309 CAGG -s Anc2.Anc2refChr3 21892 4 - 53186 CAGG -s mr.mrrefChr5 45080 4 + 294540 CAGA -s simCow_chr6.simCow.chr6 443120 4 - 602619 CAGG -s simDog_chr6.simDog.chr6 150866 4 + 593897 GCAG -s simHuman_chr6.simHuman.chr6 455663 4 - 601863 CAGG -s simRat_chr6.simRat.chr6 180393 4 + 647215 CAGA - -a -s simMouse_chr6.simMouse.chr6 190067 54 + 636262 CACAGCTCCATGTGGATGGGACATACCTCTACGGACGGTTTTTTGAGCAATGTA -s Anc0.Anc0refChr1 20403 26 + 62388 CACAGC-------AGGTGGG--------------------TTC-AGTCCAGGTA -s Anc1.Anc1refChr2 22971 26 - 144309 CACAGC-------AGGTGGG--------------------TTC-AGTCCAGGTA -s Anc2.Anc2refChr3 21896 26 - 53186 CACAGC-------AGGTTGG--------------------TTC-AGTCCAGGTA -s mr.mrrefChr5 45084 53 + 294540 CACAGCTCCATGTAGATGGGACATACCTCTACGGACGGTTTTT-GAGCAATGTA -s simCow_chr6.simCow.chr6 443128 26 - 602619 CACAGC-------AGGTTGG--------------------TGC-AGTCCAAGCA -s simDog_chr6.simDog.chr6 150870 24 + 593897 CACAGT-------AGGTTGA--------------------TTC-AGT-TAGGT- -s simHuman_chr6.simHuman.chr6 455667 26 - 601863 CATAGC-------AGGTGGG--------------------TTC-AGTCCAGGTA -s simRat_chr6.simRat.chr6 180397 53 + 647215 TACAGCTCCATGCAGATGGGACATACCTCCACAGACAGGGTTT-GAACAATGCA - -a -s simMouse_chr6.simMouse.chr6 190121 10 + 636262 ACAAATATTA -s Anc0.Anc0refChr1 20429 10 + 62388 ATGACTATTG -s Anc1.Anc1refChr2 22997 10 - 144309 ATGACTATTG -s Anc2.Anc2refChr3 21922 10 - 53186 ATGACTATTA -s mr.mrrefChr5 45137 10 + 294540 ACGAATATTG -s simCow_chr6.simCow.chr6 443160 10 - 602619 ATGACTATTA -s simHuman_chr6.simHuman.chr6 455693 10 - 601863 ATGAGCATTG -s simRat_chr6.simRat.chr6 180450 10 + 647215 ACGAAAATTG - -a -s simMouse_chr6.simMouse.chr6 190131 15 + 636262 CACGTGATGATTTTC -s Anc0.Anc0refChr1 20440 11 + 62388 TGC-TGATGA---TC -s Anc1.Anc1refChr2 23008 12 - 144309 TGCTTGATGA---TC -s Anc2.Anc2refChr3 21933 11 - 53186 TGC-TGATGC---TC -s mr.mrrefChr5 45147 15 + 294540 CGCGTGATGATCTTC -s simCow_chr6.simCow.chr6 443171 11 - 602619 TGC-TGATGC---TC -s simHuman_chr6.simHuman.chr6 455704 12 - 601863 TGCTTGATGA---TC -s simRat_chr6.simRat.chr6 180460 15 + 647215 CGCCCGATGATCTTC - -a -s simMouse_chr6.simMouse.chr6 190146 24 + 636262 CCCTATATCTTAACTGACAGTGCC -s Anc0.Anc0refChr1 20451 23 + 62388 TTCCACTTCT-AACTGATGTTGCC -s Anc1.Anc1refChr2 23020 23 - 144309 TTCCACTTCT-AACTGATGTTGCC -s Anc2.Anc2refChr3 21944 23 - 53186 TTCCACTATC-AACTGATGTTGTC -s mr.mrrefChr5 45162 23 + 294540 CCCTACTTCT-AACTGACAGTGCC -s simCow_chr6.simCow.chr6 443187 23 - 602619 TTCCACTATC-AACTGATGTTGTC -s simHuman_chr6.simHuman.chr6 455716 23 - 601863 TTCCACTTCT-AACTGATGTAGCC -s simRat_chr6.simRat.chr6 180475 23 + 647215 CCCTACTTCT-AACTGACAGTGCC - -a -s simMouse_chr6.simMouse.chr6 190170 29 + 636262 ATCATATAGAATATAATCTGTTACAACAG -s Anc0.Anc0refChr1 20475 29 + 62388 AGCCTATAGAACATAACTTGTGACAACAA -s Anc1.Anc1refChr2 23044 29 - 144309 AGCCTATAGAACATAACTTGTGACAACAA -s Anc2.Anc2refChr3 21968 29 - 53186 AGCCTATAGGACATAACTTAGGAGGACAA -s mr.mrrefChr5 45185 29 + 294540 ATCATATAGAATATAATCTGTTACAACAG -s simCow_chr6.simCow.chr6 443211 29 - 602619 AGCCTATAGGACATAACTTAGGAGGACAA -s simHuman_chr6.simHuman.chr6 455740 29 - 601863 AGCCAATAGAACATAACTCGTGACAACAA -s simRat_chr6.simRat.chr6 180498 29 + 647215 ATCATATGGAATATAATCTGTTACAACAG - -a -s simMouse_chr6.simMouse.chr6 190199 45 + 636262 TTGAATCTTGTTGTTTCATTGCTCTGCATGTTAGGTAGGTGCAGC -s Anc0.Anc0refChr1 20506 11 + 62388 TAAAATCTT----------------------------------AG -s Anc1.Anc1refChr2 23075 45 - 144309 TAAAATCTTGTTGGGTCATTGCTCCATATATTGGGTAGAGAGAAG -s Anc2.Anc2refChr3 21999 11 - 53186 TAAAATCTT----------------------------------AG -s mr.mrrefChr5 45214 45 + 294540 TTGAATCTTGTTGTTTCATTGCTCTGTATATTAGGTAGGTGCAAG -s simCow_chr6.simCow.chr6 443242 9 - 602619 TAAAATCTT------------------------------------ -s simDog_chr6.simDog.chr6 150894 2 + 593897 -------------------------------------------AG -s simHuman_chr6.simHuman.chr6 455771 45 - 601863 TCTAATCTGGTTGGGTCATTGCTCCATATATTGGGTAGAGAGAAG -s simRat_chr6.simRat.chr6 180527 45 + 647215 TTGAATCTTGTTGTATCATTGCTCTGTATATTAGGTAGGTGCCAG - -a -s simMouse_chr6.simMouse.chr6 190244 5 + 636262 AACTT -s Anc0.Anc0refChr1 20535 5 + 62388 GATCA -s Anc1.Anc1refChr2 23138 5 - 144309 GATCA -s Anc2.Anc2refChr3 22028 5 - 53186 TGTCA -s mr.mrrefChr5 45259 5 + 294540 GATTT -s simDog_chr6.simDog.chr6 150914 5 + 593897 TGTCA -s simHuman_chr6.simHuman.chr6 455834 5 - 601863 GATCA -s simRat_chr6.simRat.chr6 180572 5 + 647215 GATTT - -a -s simMouse_chr6.simMouse.chr6 190249 41 + 636262 CTTTTATGGTTAGGATACGATGACTAAGAGGTGCAAGAAAA -s Anc0.Anc0refChr1 20548 41 + 62388 CTCTTATGTTTTGGTTGAGATGAGTATGAGGTGTAAGAAGT -s Anc1.Anc1refChr2 23151 41 - 144309 CTCTTATGTTTTGGTTGAGATGAGTATGAGGTGTAAGAAGT -s Anc2.Anc2refChr3 22041 41 - 53186 CTCTCATGTTCTGGTTGAGAAGAGTATGAGGTGTAAGAAAT -s mr.mrrefChr5 45264 41 + 294540 CTTTTATGGTTTGGATGAGATGAGTAAGAGGTGCAAGAAGA -s simCow_chr6.simCow.chr6 443251 19 - 602619 ----------------------AGTATGAGATGTAATGAAT -s simDog_chr6.simDog.chr6 150927 40 + 593897 CTCTCATGTTCTGGTTGAGAAGAGTACGAGGTGTAGGAA-T -s simHuman_chr6.simHuman.chr6 455847 41 - 601863 CTCTTATGCTTTGCTTGAGATAAGTATGAGGTGTAAGAAGT -s simRat_chr6.simRat.chr6 180577 41 + 647215 CTTTTATGATTTGGACGAGATGAGTAAGAGGTGCAAGAAGA - -a -s simMouse_chr6.simMouse.chr6 190290 9 + 636262 GGGTGTCCA -s Anc0.Anc0refChr1 20589 9 + 62388 GGGGGTCCA -s Anc1.Anc1refChr2 23192 9 - 144309 GGGGGTCCA -s Anc2.Anc2refChr3 22082 9 - 53186 GGGGGTCCA -s mr.mrrefChr5 45305 9 + 294540 GGGGGTCCA -s simCow_chr6.simCow.chr6 443270 9 - 602619 GGGAGTCTG -s simDog_chr6.simDog.chr6 150967 9 + 593897 GGGGGTACA -s simHuman_chr6.simHuman.chr6 455888 9 - 601863 GGGGGTCCA -s simRat_chr6.simRat.chr6 180621 9 + 647215 GGGGCTCCA - -a -s simMouse_chr6.simMouse.chr6 190299 41 + 636262 CAGTTTCAAGGTCCCTTGAATAAGCTACCAGAACTGCTTGA -s Anc0.Anc0refChr1 20598 41 + 62388 CAATTCATAGATCCACTGAATAAGCTACCTGAACTGTTTGC -s Anc1.Anc1refChr2 23201 41 - 144309 CAATTCATAGATCCACTGAATAAGCTACCTGAACTGTTTGC -s Anc2.Anc2refChr3 22092 41 - 53186 CAATTCATAGATCCACTGAATGAGCTACCTGAACTGTTTGC -s mr.mrrefChr5 45314 41 + 294540 CAATTTCAAGGTCCATTGAATAAGCTACCTGAACTGCTTGC -s simCow_chr6.simCow.chr6 443280 40 - 602619 CAATCCATAGATCCAAGGAAT-AGCTACCTAAAGTGCTTGC -s simDog_chr6.simDog.chr6 150977 41 + 593897 CAATTCACACATCCACTGAATGAGCTACCTGAACTGTTTGC -s simHuman_chr6.simHuman.chr6 455934 31 - 601863 CAATTCATAGATCCGCTGAGTAAGCTACCTG---------- -s simRat_chr6.simRat.chr6 180630 41 + 647215 CAATTTCAAGGTCCAATCAATGAGCCACCTGAACTGCTTGC - -a -s simMouse_chr6.simMouse.chr6 190340 3 + 636262 TGA -s Anc0.Anc0refChr1 20639 3 + 62388 TGG -s Anc1.Anc1refChr2 23242 3 - 144309 TGG -s Anc2.Anc2refChr3 22134 3 - 53186 TGG -s mr.mrrefChr5 45355 3 + 294540 TGA -s simCow_chr6.simCow.chr6 443321 3 - 602619 CGA -s simDog_chr6.simDog.chr6 151019 3 + 593897 TGG -s simRat_chr6.simRat.chr6 180671 3 + 647215 TGA - -a -s simMouse_chr6.simMouse.chr6 190343 24 + 636262 GCCACTAGAGGCAGTGTTCATTGC -s Anc0.Anc0refChr1 20642 24 + 62388 CCCACTTGACGCAGTGTTGATTGC -s Anc1.Anc1refChr2 23245 24 - 144309 CCCACTTGACGCAGTGTTGATTGC -s Anc2.Anc2refChr3 22137 24 - 53186 CCCACTTGACGCAGTGCTGATTGC -s mr.mrrefChr5 45358 24 + 294540 CCCACTAGAGGCAGTGTTGATTGC -s simCow_chr6.simCow.chr6 443325 24 - 602619 CCCACTCGATGCAGTGCTGCTTGC -s simDog_chr6.simDog.chr6 151022 24 + 593897 CCCACTTGACGCGGTGCTGATTGC -s simHuman_chr6.simHuman.chr6 455965 22 - 601863 --CACTTGAAGCACTGTTGATTGC -s simRat_chr6.simRat.chr6 180674 24 + 647215 CCTACTAGAGGCAGCGTTGATTGC - -a -s simMouse_chr6.simMouse.chr6 190367 15 + 636262 AAGATCATGAATGTT -s Anc0.Anc0refChr1 20668 15 + 62388 ATGACCCTGAACATT -s Anc1.Anc1refChr2 23271 15 - 144309 ATGACCCTGAACATT -s Anc2.Anc2refChr3 22163 15 - 53186 ATGACCCTGAACATT -s mr.mrrefChr5 45382 15 + 294540 AAGATCATGAATGTT -s simCow_chr6.simCow.chr6 443351 15 - 602619 ATGACCTTGAACATT -s simDog_chr6.simDog.chr6 151048 15 + 593897 ATGACCCTGAACATG -s simHuman_chr6.simHuman.chr6 455989 15 - 601863 ATGGCCCTGAGCATT -s simRat_chr6.simRat.chr6 180698 15 + 647215 AAGATCATAAATGTT - -a -s simMouse_chr6.simMouse.chr6 190382 8 + 636262 TCACCCAT -s Anc0.Anc0refChr1 20684 8 + 62388 GTGCCCAT -s Anc1.Anc1refChr2 23287 8 - 144309 GTGCCCAT -s Anc2.Anc2refChr3 22179 8 - 53186 GTGCCCAT -s mr.mrrefChr5 45397 8 + 294540 GCACCCAT -s simCow_chr6.simCow.chr6 443367 8 - 602619 GTGTCAAT -s simDog_chr6.simDog.chr6 151064 8 + 593897 GTGCCCAT -s simHuman_chr6.simHuman.chr6 456005 8 - 601863 GTGCCCAT -s simRat_chr6.simRat.chr6 180713 8 + 647215 GCACCCAT - -a -s simMouse_chr6.simMouse.chr6 190390 39 + 636262 AAGTCACAGTAGAATTGGGGTAGGAAATTGGGGTAAGAA -s Anc0.Anc0refChr1 20692 33 + 62388 GAATCCCAGGGGAATTGGGATC------TAAATATTGGA -s Anc1.Anc1refChr2 23295 33 - 144309 GAATCCCAGGGGAATTGGGATC------TAAATATTGGA -s Anc2.Anc2refChr3 22187 33 - 53186 GAATCCCAGGGGAATTGGGATC------TAAGTATTGGA -s mr.mrrefChr5 45405 33 + 294540 AAATCACAGGGGAATTGGGGTA------TGGAGTATGAA -s simCow_chr6.simCow.chr6 443408 26 - 602619 GGATGCCAG----ATTTAGAT---------AGTATTGGA -s simDog_chr6.simDog.chr6 151072 33 + 593897 AAATCCCAGGGGAGTTGGGATC------TAAGTATTGGA -s simHuman_chr6.simHuman.chr6 456013 33 - 601863 GATTCTCAGGGGTATTGGGATC------TAAAAATTGGA -s simRat_chr6.simRat.chr6 180721 33 + 647215 AAATCACAGGGGAATTTGAGTA------TGGAGTATGAA - -a -s simMouse_chr6.simMouse.chr6 190429 19 + 636262 TAGTCTAGATGATGGCTTG -s Anc0.Anc0refChr1 20733 19 + 62388 TGGTCCTGACAATGGCTTG -s Anc1.Anc1refChr2 23336 19 - 144309 TGGTCCTGACAATGGCTTG -s Anc2.Anc2refChr3 22228 19 - 53186 TGGTCCTGACAATGACTTG -s mr.mrrefChr5 45438 19 + 294540 TAGTCTAGACGATGGCTTG -s simCow_chr6.simCow.chr6 443442 19 - 602619 TGGCTCTGACAACAACTTG -s simDog_chr6.simDog.chr6 151168 19 + 593897 TGGTCCTGACTGTGACTTG -s simHuman_chr6.simHuman.chr6 456054 19 - 601863 TGGTCCTGAGAATGGCTTG -s simRat_chr6.simRat.chr6 180754 19 + 647215 TAGTCTAGACCATGGCTTG - -a -s simMouse_chr6.simMouse.chr6 190448 9 + 636262 CTGTATAGT -s Anc0.Anc0refChr1 20759 9 + 62388 CTGCATGTC -s Anc1.Anc1refChr2 23362 9 - 144309 CTGCATGTC -s Anc2.Anc2refChr3 22254 9 - 53186 CTGTATGTC -s mr.mrrefChr5 45464 9 + 294540 CTGCATAGT -s simCow_chr6.simCow.chr6 443468 9 - 602619 CTGTATGTC -s simDog_chr6.simDog.chr6 151193 5 + 593897 ----ATGTC -s simHuman_chr6.simHuman.chr6 456080 9 - 601863 CTGCATGTC -s simRat_chr6.simRat.chr6 180780 9 + 647215 CGGCATAGT - -a -s simMouse_chr6.simMouse.chr6 190457 15 + 636262 GTCCCTAAAAATACT -s Anc0.Anc0refChr1 20777 14 + 62388 CT-CCTACAGATAGT -s Anc1.Anc1refChr2 23380 15 - 144309 CTCCCTACAGATAGT -s Anc2.Anc2refChr3 22272 14 - 53186 CT-CATACAGATAGT -s mr.mrrefChr5 45473 15 + 294540 CTCCCTAAAAATACT -s simCow_chr6.simCow.chr6 443486 14 - 602619 CT-CTTACAGGTAAC -s simDog_chr6.simDog.chr6 151207 14 + 593897 CT-CATACAGATGGT -s simHuman_chr6.simHuman.chr6 456098 15 - 601863 CTCCCTACAGATAGT -s simRat_chr6.simRat.chr6 180789 15 + 647215 CTCCCTAAAAATACT - -a -s simMouse_chr6.simMouse.chr6 190472 28 + 636262 CCCTGACAAAAAATGATAATTTATCTTT -s Anc0.Anc0refChr1 20793 23 + 62388 CCATGGCAAGAAAAGATAATATG----- -s Anc1.Anc1refChr2 23397 23 - 144309 CCATGGCAAGAAAAGATAATATG----- -s Anc2.Anc2refChr3 22288 23 - 53186 CTATAGCAAGGAAAAACAGTATG----- -s mr.mrrefChr5 45490 28 + 294540 CCCTGACAAAAAAAGATAATTTATCTTT -s simCow_chr6.simCow.chr6 443502 23 - 602619 AAATAGCAAGAAAACACAGTATG----- -s simDog_chr6.simDog.chr6 151223 23 + 593897 CTATAGCAAGGAAAAACAGTATG----- -s simHuman_chr6.simHuman.chr6 456115 22 - 601863 CCATGGCCAGAAA-GATAATATG----- -s simRat_chr6.simRat.chr6 180806 28 + 647215 CCCTGACAGACAGAGATAATTTATATTT - -a -s simMouse_chr6.simMouse.chr6 190500 7 + 636262 CTGGTTT -s Anc0.Anc0refChr1 20816 7 + 62388 CTAGTTT -s Anc1.Anc1refChr2 23420 7 - 144309 CTAGTTT -s Anc2.Anc2refChr3 22320 7 - 53186 CTAGTCT -s mr.mrrefChr5 45518 7 + 294540 CTAGTTT -s simCow_chr6.simCow.chr6 443534 7 - 602619 CTGGTCT -s simDog_chr6.simDog.chr6 151255 7 + 593897 CCAGTCT -s simHuman_chr6.simHuman.chr6 456137 7 - 601863 CTAGTTT -s simRat_chr6.simRat.chr6 180834 7 + 647215 CCAGCTA - -a -s simMouse_chr6.simMouse.chr6 190507 50 + 636262 GAGAAGATAGCTCATCATGCCATCCCCCACACAATAGAATTGAGTTTGGT -s Anc0.Anc0refChr1 20829 50 + 62388 AGGATAATAGCTTGTCAAGTCTTCCCCCAGATAACAGTTTTGAGTTTGGC -s Anc1.Anc1refChr2 23433 50 - 144309 AGGATAATAGCTTGTCAAGTCTTCCCCCAGATAACAGTTTTGAGTTTGGC -s Anc2.Anc2refChr3 22333 50 - 53186 AGGATAATAGCCTGTCAAGTCTTCCCCCAGATAACAGTTTTGAGTTTGGC -s mr.mrrefChr5 45531 50 + 294540 AAGAAAATAGCTCATCATGCCATCCCCCACACAATAGATTTGAGTTTGGT -s simCow_chr6.simCow.chr6 443547 50 - 602619 AGTATAATAGCCTGTCTAGTCATCCCCCAGGTAACGCTTTTGAGTTAGGC -s simDog_chr6.simDog.chr6 151268 50 + 593897 AGGATAGCAGCCTGTTAAGTCTTCTCCTGGATAACAGTTTTGAATTTGGC -s simHuman_chr6.simHuman.chr6 456150 50 - 601863 AGCATAATAGCTTGTCACGTTGTACTCCAGATAACAACTTTGAGTCTGGA -s simRat_chr6.simRat.chr6 180847 50 + 647215 AAGAAAATAGCTCATCAGGCCATCCCCCACACAATAGATTTGAACTTGGT - -a -s simMouse_chr6.simMouse.chr6 190557 25 + 636262 GAGTATTTGAGGTAATAAATCCATG -s Anc0.Anc0refChr1 20893 24 + 62388 AAGTATTTGAGGCAACAAATCTAT- -s Anc1.Anc1refChr2 23497 24 - 144309 AAGTATTTGAGGCAACAAATCTAT- -s Anc2.Anc2refChr3 22397 24 - 53186 AAGTATTTGAGACAACAAAGGTCT- -s mr.mrrefChr5 45595 24 + 294540 GAGTATTTGAGGTAATAAATCTAT- -s simCow_chr6.simCow.chr6 443611 24 - 602619 AAGTACTTGAGACAACAAGGGTCT- -s simDog_chr6.simDog.chr6 151332 24 + 593897 AATTATTTGGGACCTCAAAGGTCT- -s simHuman_chr6.simHuman.chr6 456214 24 - 601863 AAGTTTTTGAGGCAACAAATCTAT- -s simRat_chr6.simRat.chr6 180911 24 + 647215 GAGTATTTGAGGTAATAAATCTAT- - -a -s simMouse_chr6.simMouse.chr6 190582 1 + 636262 C -s Anc0.Anc0refChr1 20917 1 + 62388 T -s Anc1.Anc1refChr2 23521 1 - 144309 T -s Anc2.Anc2refChr3 22422 1 - 53186 T -s mr.mrrefChr5 45619 1 + 294540 T -s simCow_chr6.simCow.chr6 443636 1 - 602619 T -s simDog_chr6.simDog.chr6 151357 1 + 593897 T -s simHuman_chr6.simHuman.chr6 456238 1 - 601863 T -s simRat_chr6.simRat.chr6 180935 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 190583 16 + 636262 AGGACTAGACATAATA -s Anc0.Anc0refChr1 20925 16 + 62388 AGAAATAGACATAATA -s Anc1.Anc1refChr2 23529 16 - 144309 AGAAATAGACATAATA -s Anc2.Anc2refChr3 22430 16 - 53186 AGAAATAGACATAATA -s mr.mrrefChr5 45620 16 + 294540 AGAACTAGACATAATA -s simCow_chr6.simCow.chr6 443644 16 - 602619 AGAGATAGACATAATA -s simDog_chr6.simDog.chr6 151365 16 + 593897 TAAAATAGACATGATA -s simHuman_chr6.simHuman.chr6 456246 16 - 601863 AGAAGTGGATATAATA -s simRat_chr6.simRat.chr6 180936 15 + 647215 AAAACTAGACACAAC- - -a -s simMouse_chr6.simMouse.chr6 190599 23 + 636262 TGAGCGTGGTGCTGGTATTAAGC -s Anc0.Anc0refChr1 20955 23 + 62388 TTGGCCTGGTGCTGGAATTTAGC -s Anc1.Anc1refChr2 23559 23 - 144309 TTGGCCTGGTGCTGGAATTTAGC -s Anc2.Anc2refChr3 22460 23 - 53186 TTGGCCTGGTGGTGGAATTTAGC -s mr.mrrefChr5 45636 23 + 294540 TGAGCGTGGTGCTGGTAGTAGGC -s simCow_chr6.simCow.chr6 443674 23 - 602619 CTTGCATGGTAGTGAAATCTAGC -s simDog_chr6.simDog.chr6 151395 23 + 593897 TTGGCCTGGTGGTGGAATTTAGC -s simHuman_chr6.simHuman.chr6 456276 23 - 601863 TAGGCCTAGTGCAAGCCTGGATC -s simRat_chr6.simRat.chr6 180951 18 + 647215 -----GTGGTGCTGGTAGTAGGC - -a -s simMouse_chr6.simMouse.chr6 190622 16 + 636262 AGCAAGACAGGAGAAT -s Anc0.Anc0refChr1 20979 16 + 62388 GGTGACACAGGATAAT -s Anc1.Anc1refChr2 23583 16 - 144309 GGTGACACAGGATAAT -s Anc2.Anc2refChr3 22484 16 - 53186 GGTGACACAGGATAAA -s mr.mrrefChr5 45660 16 + 294540 GGTAAGACAGGAGAAT -s simCow_chr6.simCow.chr6 443698 15 - 602619 GGTGACACAGGATAA- -s simDog_chr6.simDog.chr6 151419 16 + 593897 GGTGACACAGGAAACA -s simHuman_chr6.simHuman.chr6 456300 16 - 601863 GGTGACACAGGATAAT -s simRat_chr6.simRat.chr6 180970 16 + 647215 GGTAAGACAGAAGAAT - -a -s simMouse_chr6.simMouse.chr6 190638 117 + 636262 GAGGAGACTCATGTGGAGTATAAAGATCTCAGAGTATGAAGTCTTGTTCATTACCCCAGTTTGCCAAGTTAAGGAGAGTTTCAGACTAAGGAGGCTGTCCAATGGGGCCTAACAAAT -s Anc0.Anc0refChr1 20996 96 + 62388 AATTACAACA---TGGAATATAAAG-TCTCACTTTATGTTGTC---------ACTCCAGT---CTAGGTTGTGGAGAGTTGAAGAATGAG-AGACTGTCTAGGGGTGTTTA----TT -s Anc1.Anc1refChr2 23600 99 - 144309 AATTACAACAGTGTGGAATATAAAG-TCTCACTTTATGTTGTC---------ACTCCAGT---CTAGGTTGTGGAGAGTTGAAGAATGAG-AGACTGTCTAGGGGTGTTTA----TT -s Anc2.Anc2refChr3 22501 96 - 53186 AATTACAACA---TGGAATATAAAG-TCTCACTTTATGTTGTT---------ACTCCAGT---CTAGATTGTGGAGAGTTGAAGCATGAG-AGATTGTCTAGGGGTGTTTA----TT -s mr.mrrefChr5 45676 116 + 294540 AAGGAGACCAGTGTGGAGTATAAAGATCTCAGAGTATGAAGTCTCGTTCGTTACTCCAGTTTGCCAAGTTAAGGAGAGTTTCAGACTAAG-AGACTGTCCAATGGGGCCTAACAAAT -s simCow_chr6.simCow.chr6 443714 96 - 602619 GATAACAGCA---TGGAACATAAAG-TCTCACTGTATGTTGTT---------ACTGCAGT---CGATATTGTGGAGAATTGAAAGGTGAG-AGAATCGCTAGGGATGCTTA----TC -s simDog_chr6.simDog.chr6 151436 96 + 593897 AAATACAACA---TGGCATATAAAG-TCTCACTTTACGTTGTT---------ACTCTAGT---CTAGATGGTGGAGAGTTGAAGCATGAG-AGATTGTCTATGGGTTTTTG----TT -s simHuman_chr6.simHuman.chr6 456317 96 - 601863 AATCACAACAGTGTGGAATATAAAG-TCTCCCTCCATGCTGTC---------ACTCCAGT---CAACGTTGTGAAGAGTT---GAATGAG-AGACTGTCTTGGGCTGGTTA----TT -s simRat_chr6.simRat.chr6 180986 115 + 647215 AAGGAGACCAGTGTAGTGCATAAAGATCTTACAGTATGAAGTCTCGTTCGTTACTACAGTTTGCCAAGTTCAGTAGGGCTTCAGGCTAAG-AGACTATCCAGTAGTCC-TAACAAAT - -a -s simMouse_chr6.simMouse.chr6 190755 23 + 636262 CAAGCAAATATGCATGGCTCCCT -s Anc0.Anc0refChr1 21092 13 + 62388 GAATAAAATGTGC---------- -s Anc1.Anc1refChr2 23699 23 - 144309 GAATAAAATGTGCATGGCACCCT -s Anc2.Anc2refChr3 22597 13 - 53186 GAATAAAATGTAC---------- -s mr.mrrefChr5 45792 23 + 294540 CAATCAAATATGCATGGCTCCCT -s simCow_chr6.simCow.chr6 443810 8 - 602619 AAATTGAA--------------- -s simDog_chr6.simDog.chr6 151532 13 + 593897 GAAAAAGATGTAC---------- -s simHuman_chr6.simHuman.chr6 456413 23 - 601863 GAATGAAATGTGCATGGCACCCT -s simRat_chr6.simRat.chr6 181103 23 + 647215 AAATCAAATATGCATGGCTCCCT - -a -s simMouse_chr6.simMouse.chr6 190778 17 + 636262 AGCTTGACCTCATGTGA -s Anc0.Anc0refChr1 21127 13 + 62388 AGCTTGA---CATGTG- -s Anc1.Anc1refChr2 23744 13 - 144309 AGCTTGA---CATGTG- -s Anc2.Anc2refChr3 22632 13 - 53186 AGCTTAA---CATGTG- -s mr.mrrefChr5 45815 17 + 294540 AGCTTGAGCACTTGTGA -s simCow_chr6.simCow.chr6 443823 6 - 602619 ----------CATGTG- -s simDog_chr6.simDog.chr6 151567 13 + 593897 AGCTTAA---TATCTG- -s simHuman_chr6.simHuman.chr6 456463 13 - 601863 AGGTTGA---CATGTG- -s simRat_chr6.simRat.chr6 181126 17 + 647215 AGCTTGAGCACTTGTGA - -a -s simMouse_chr6.simMouse.chr6 190795 6 + 636262 GGTTTC -s Anc0.Anc0refChr1 21152 1 + 62388 G----- -s Anc1.Anc1refChr2 23769 6 - 144309 GGTCTC -s Anc2.Anc2refChr3 22657 1 - 53186 G----- -s mr.mrrefChr5 45840 6 + 294540 GGTTTC -s simCow_chr6.simCow.chr6 443841 1 - 602619 G----- -s simDog_chr6.simDog.chr6 151592 1 + 593897 G----- -s simHuman_chr6.simHuman.chr6 456489 6 - 601863 GGTCTC -s simRat_chr6.simRat.chr6 181151 6 + 647215 GGTTTC - -a -s simMouse_chr6.simMouse.chr6 190801 10 + 636262 CTTTCAGCTA -s Anc0.Anc0refChr1 21155 10 + 62388 CTTCCTTGCT -s Anc1.Anc1refChr2 23777 10 - 144309 CTTCCTTGCT -s Anc2.Anc2refChr3 22660 10 - 53186 ATGCCTTGGT -s mr.mrrefChr5 45846 10 + 294540 CTTTCATGCT -s simCow_chr6.simCow.chr6 443844 10 - 602619 TTGCTTTGAT -s simDog_chr6.simDog.chr6 151595 10 + 593897 ATGCCTTGGT -s simHuman_chr6.simHuman.chr6 456497 10 - 601863 CTTCCTTGCT -s simRat_chr6.simRat.chr6 181157 10 + 647215 TTTTCATGCT - -a -s simMouse_chr6.simMouse.chr6 190811 49 + 636262 ACAGCTAATACCTAAACACTTCTTGTTGGACTCAGCCATAGCACAGTAT -s Anc0.Anc0refChr1 21170 42 + 62388 ACTCCTAT-ACACTTAATCTT------GGATCCAGGGGCAGCACAGTCC -s Anc1.Anc1refChr2 23792 42 - 144309 ACTCCTAT-ACACTTAATCTT------GGATCCAGGGGCAGCACAGTCC -s Anc2.Anc2refChr3 22675 42 - 53186 ACTCCTAT-ACACTTAATCTT------GGATCCGGGGGCAGTACAGTCC -s mr.mrrefChr5 45856 48 + 294540 ACTCCTAA-ACACTAACACTTCTTGTTGGACTCAGCCATAGCACAGTAT -s simCow_chr6.simCow.chr6 443859 40 - 602619 GTTCC--T-ACACTTAATTTT------GGATCCTGGTGCAGTACAGTCC -s simDog_chr6.simDog.chr6 151610 42 + 593897 ACTCCTAC-CCACACAATCTC------GGATCAGGGGACAGTACAGCCC -s simHuman_chr6.simHuman.chr6 456512 42 - 601863 ACTCCGAT-ACACTTAACCTT------GGATCCAGGGGCTGCACAGTTG -s simRat_chr6.simRat.chr6 181167 48 + 647215 ATTCCTAA-ACACTAACACTTCATGTCAGACTCAGTCATAGCACAGTAT - -a -s simMouse_chr6.simMouse.chr6 190860 13 + 636262 CTATCACAATATG -s Anc0.Anc0refChr1 21214 13 + 62388 CAATCACAGTATG -s Anc1.Anc1refChr2 23836 13 - 144309 CAATCACAGTATG -s Anc2.Anc2refChr3 22719 13 - 53186 TAATCACAGTATG -s mr.mrrefChr5 45906 13 + 294540 CTATCACAATATG -s simCow_chr6.simCow.chr6 443901 13 - 602619 TATTCACAGTATG -s simDog_chr6.simDog.chr6 151654 13 + 593897 TAATCACCGCATG -s simHuman_chr6.simHuman.chr6 456556 13 - 601863 CAATTACACTCTG -s simRat_chr6.simRat.chr6 181217 13 + 647215 CTATCACAATAAG - -a -s simMouse_chr6.simMouse.chr6 190873 98 + 636262 GCATATTTATTTTGTGTGATTAATCACAAGTACTAGCTCATCGGGAGACCAAGTTTGTCTAGTAAGAAAAGTTTGGGGTGTATCACAGTAGCCTCAAG -s Anc0.Anc0refChr1 21227 91 + 62388 ACATATTT----TGTGTGAGTAATCAC---TAAGAGATGATTGGAAGATCAGATTTGCTGGCTGGGAAAAGTTGGGGGGGTGTCAGAGCAGGCTCGAC -s Anc1.Anc1refChr2 23849 91 - 144309 ACATATTT----TGTGTGAGTAATCAC---TAAGAGATGATTGGAAGATCAGATTTGCTGGCTGGGAAAAGTTGGGGGGGTGTCAGAGCAGGCTCGAC -s Anc2.Anc2refChr3 22732 91 - 53186 ACATATTC----AGTGCAAGTAATCAT---TAAGAGACAATTGGGAGATCAGATTTGCTGGCTGGTAAAAGTTGGGGGGGTGTCAGAGCAGGCTTGAC -s mr.mrrefChr5 45919 94 + 294540 GCATATTT----TGTGTGAGTAATCACAAGTACTAGATGATTGGAAGACCAAGTTTGTCTACTGGGAAAAGTTTGGGGTGTATCACAGTAGCCTCAAG -s simCow_chr6.simCow.chr6 443919 91 - 602619 ACATATCC----AGTGCTAGTAATTGT---TAAGAGACAGTTGGGAGAACAGATTTGTCGACTGGCAGACTTTGGTTGGATGCCGGAGCAGGATTGGC -s simDog_chr6.simDog.chr6 151667 90 + 593897 -CATATTC----AGTGCAAGTAGTCAT---GGAGAGACAATTGGGAGATCAGATTTGCTGGTTGGTAAAAGTTGGGGGGGCATCACAGCAGGCCTGAT -s simHuman_chr6.simHuman.chr6 456569 91 - 601863 ACATATTT----TGTGTGAGTAATCAC---TAAGAGATGACTGGAAGGTCAGCTTTGCTGGCTGGGAAAAAATGGGGGGGTGTCAGAGGAGGCTCGAC -s simRat_chr6.simRat.chr6 181230 94 + 647215 GTATATTT----TGTGTGAGTAATCACAAGTACTAAATGATTGGAAGAGTAAGTTTGTCTACTGGGCAAAGTCTGGGGCGTTTCACAGTAGACTCAAG - -a -s simMouse_chr6.simMouse.chr6 190971 25 + 636262 AGGTGCCAAGCTCTGATATGCACTC -s Anc0.Anc0refChr1 21318 25 + 62388 AGATGACAAGCTCTGGTATGCCCTC -s Anc1.Anc1refChr2 23940 25 - 144309 AGATGACAAGCTCTGGTATGCCCTC -s Anc2.Anc2refChr3 22823 25 - 53186 AGATGACAAGCTCTGGTATGCCCTT -s mr.mrrefChr5 46013 25 + 294540 AGGTGCCAAGCTCTGGTATGCACTC -s simCow_chr6.simCow.chr6 444010 23 - 602619 AGCTGACAAGTTCTGTTA--CCCTT -s simDog_chr6.simDog.chr6 151759 25 + 593897 AGATGGCAAGCTCTGGTATGTCCTT -s simHuman_chr6.simHuman.chr6 456660 25 - 601863 AGATGACGGTCTGTGGTATGCCCTC -s simRat_chr6.simRat.chr6 181324 25 + 647215 AGGTACCAAGGTCTGGTATGCACTC - -a -s simMouse_chr6.simMouse.chr6 190996 10 + 636262 CCTCAATGCG -s Anc0.Anc0refChr1 21343 10 + 62388 CCTTAATGAG -s Anc1.Anc1refChr2 23965 10 - 144309 CCTTAATGAG -s Anc2.Anc2refChr3 22848 10 - 53186 CCTTAATGAG -s mr.mrrefChr5 46038 10 + 294540 CCTCAATGAG -s simCow_chr6.simCow.chr6 444033 10 - 602619 CCTTAATCAC -s simDog_chr6.simDog.chr6 151784 10 + 593897 CCTTAATGAG -s simHuman_chr6.simHuman.chr6 456687 10 - 601863 CCTTAATAAT -s simRat_chr6.simRat.chr6 181349 10 + 647215 CCTCAATGAG - -a -s simMouse_chr6.simMouse.chr6 191006 5 + 636262 CGAGA -s Anc0.Anc0refChr1 21353 5 + 62388 ACAGG -s Anc1.Anc1refChr2 23975 5 - 144309 ACAGG -s Anc2.Anc2refChr3 22858 5 - 53186 ACAGG -s mr.mrrefChr5 46048 5 + 294540 CGAGA -s simCow_chr6.simCow.chr6 444043 5 - 602619 ACAGG -s simDog_chr6.simDog.chr6 151824 5 + 593897 ACAGG -s simHuman_chr6.simHuman.chr6 456697 5 - 601863 ACAGG -s simRat_chr6.simRat.chr6 181359 5 + 647215 CGAGA - -a -s simMouse_chr6.simMouse.chr6 191011 15 + 636262 CTACTGAATTAGGAC -s Anc0.Anc0refChr1 21358 15 + 62388 TTACTGAACTAGGAC -s Anc1.Anc1refChr2 23980 15 - 144309 TTACTGAACTAGGAC -s Anc2.Anc2refChr3 22864 15 - 53186 TTACTAAACTAGGAC -s mr.mrrefChr5 46053 15 + 294540 TTACTGAATTAGGAC -s simCow_chr6.simCow.chr6 444049 15 - 602619 TTACTAAACTAGGAA -s simDog_chr6.simDog.chr6 151830 15 + 593897 TTACTAAACCAGGAC -s simHuman_chr6.simHuman.chr6 456702 15 - 601863 ATACTGAACTAGGAC -s simRat_chr6.simRat.chr6 181364 15 + 647215 TTACTGGATTAGGAC - -a -s simMouse_chr6.simMouse.chr6 191026 16 + 636262 ACATGGGAGCCTTCAA -s Anc0.Anc0refChr1 21373 16 + 62388 ACATAGAAGGCTTCAA -s Anc1.Anc1refChr2 23995 16 - 144309 ACATAGAAGGCTTCAA -s Anc2.Anc2refChr3 22880 16 - 53186 ACATAGAAGGCTTCAG -s mr.mrrefChr5 46068 16 + 294540 ACATGGGAGCCTTCAA -s simCow_chr6.simCow.chr6 444065 16 - 602619 AAATAGAAGGCTTCAG -s simDog_chr6.simDog.chr6 151846 15 + 593897 ACATAGAAGGAGTCA- -s simHuman_chr6.simHuman.chr6 456717 16 - 601863 ACATAGAAGGCTTCAA -s simRat_chr6.simRat.chr6 181379 16 + 647215 ACATTGGAGCCTACAA - -a -s simMouse_chr6.simMouse.chr6 191042 14 + 636262 TGAAACAAGTACCG -s Anc0.Anc0refChr1 21431 14 + 62388 TTATACAAGTACCT -s Anc1.Anc1refChr2 24053 14 - 144309 TTATACAAGTACCT -s Anc2.Anc2refChr3 22938 14 - 53186 TTATACAAGTACCT -s mr.mrrefChr5 46116 14 + 294540 TGATACAAGTACCG -s simCow_chr6.simCow.chr6 444126 14 - 602619 TTGTACAGGTACGT -s simDog_chr6.simDog.chr6 151897 14 + 593897 TTATACAAGCAACT -s simHuman_chr6.simHuman.chr6 456779 14 - 601863 TTATACAATTACTT -s simRat_chr6.simRat.chr6 181427 14 + 647215 TGATTCAAGTACAG - -a -s simMouse_chr6.simMouse.chr6 191056 62 + 636262 ATTTGTGATGCTATAGATTTTAGAATATGAATCCGTGGGATTTTCATGGGTTAATTTATGGC -s Anc0.Anc0refChr1 21445 60 + 62388 ATTTGTGATGCCATAGATTA--GAATATGAATTGCTAGGATTTCCATAGTTTAATTTCTGGC -s Anc1.Anc1refChr2 24067 60 - 144309 ATTTGTGATGCCATAGATTA--GAATATGAATTGCTAGGATTTCCATAGTTTAATTTCTGGC -s Anc2.Anc2refChr3 22952 60 - 53186 ATGTGTTACACCATAGATTA--GAATATGAGTTGCTAGGACTTCCATAGTTTAATTTCTGGC -s mr.mrrefChr5 46130 62 + 294540 ATTTGTGATGCTATAGATTATAGAATATGAATTCGTGGGATTTCCATGGGTTAATTTATGGC -s simCow_chr6.simCow.chr6 444140 60 - 602619 AAGTGTTACTCCATAGATTA--GAATATGAGGTGGCAGGACTGTCATAGTATAAGTTCTGGC -s simDog_chr6.simDog.chr6 151927 55 + 593897 ATGTGTTACACCATAGACTA--GAATATGAGTTACTAGTACTTCCATGGTTTAATTT----- -s simHuman_chr6.simHuman.chr6 456793 60 - 601863 ATTTGTGATGCCATAGATTG--GAATATGAATTGCTAGGATTTCCACAGTTTAATTTCCTGC -s simRat_chr6.simRat.chr6 181441 62 + 647215 ATTTGTGAAGCTATAGATTATATAATCTGAATTTGTCAGACTTCCATGGGTTGATTTATGGC - -a -s simMouse_chr6.simMouse.chr6 191118 54 + 636262 CTTACCAATGACTGCGTGTCCATTAACGTTTTAAATGCCACAAAGACATGAGAC -s Anc0.Anc0refChr1 21507 50 + 62388 CTTACCAATGACTTCAT-TCCATT---GCTCCAAATGCTAGAGAGATGCAAGAC -s Anc1.Anc1refChr2 24129 50 - 144309 CTTACCAATGACTTCAT-TCCATT---GCTCCAAATGCTAGAGAGATGCAAGAC -s Anc2.Anc2refChr3 23014 50 - 53186 CTTACCAGTGGCTTCAT-TACACT---GCTCCAAATGCTAGAGAGATGCAAGAC -s mr.mrrefChr5 46194 50 + 294540 CTTACCAATGACTTCGT-TCCATT---GCTTCAAATGCCACAAAGACATGAGAC -s simCow_chr6.simCow.chr6 444202 46 - 602619 CCTACCAGTGGCTTCAT-----AT---GCTCCTAATGCTAGAGAGATGCAAGAC -s simDog_chr6.simDog.chr6 151982 44 + 593897 CTGACC------TACAT-TACACT---GTTTCAAAAACTAGAGAGATGCAAGAC -s simHuman_chr6.simHuman.chr6 456855 50 - 601863 CTTACCAATGATTTCAT-TCCATT---GCTCAAAATGCTAAAGGGATGCAAGAC -s simRat_chr6.simRat.chr6 181505 50 + 647215 CTTACCAATGACATCTT-TCAATT---GCTTCAACTGGCACAAAGACATGAGAC - -a -s simMouse_chr6.simMouse.chr6 191172 2 + 636262 AC -s Anc0.Anc0refChr1 21567 2 + 62388 AC -s Anc1.Anc1refChr2 24189 2 - 144309 AC -s Anc2.Anc2refChr3 23075 2 - 53186 AC -s mr.mrrefChr5 46254 2 + 294540 AC -s simCow_chr6.simCow.chr6 444259 2 - 602619 AC -s simDog_chr6.simDog.chr6 152037 2 + 593897 AC -s simHuman_chr6.simHuman.chr6 456917 2 - 601863 AC -s simRat_chr6.simRat.chr6 181565 2 + 647215 GC - -a -s simMouse_chr6.simMouse.chr6 191174 19 + 636262 TCATGTGCTTTCCTCAACC -s Anc0.Anc0refChr1 21570 19 + 62388 TCATGTGCTGTACTCAACT -s Anc1.Anc1refChr2 24192 19 - 144309 TCATGTGCTGTACTCAACT -s Anc2.Anc2refChr3 23078 19 - 53186 TCATGTGCTGTACTAGGCT -s mr.mrrefChr5 46256 19 + 294540 TCATGTGCTTTCCTCAACC -s simCow_chr6.simCow.chr6 444262 15 - 602619 TCATATGCTGTACC----C -s simDog_chr6.simDog.chr6 152040 19 + 593897 TAATGTGCTGTACTAGGCT -s simHuman_chr6.simHuman.chr6 456920 19 - 601863 TCATGTCCCGTACTCAACT -s simRat_chr6.simRat.chr6 181567 19 + 647215 TCATGTACTTACCTCGACC - -a -s simMouse_chr6.simMouse.chr6 191193 7 + 636262 AGGAATA -s Anc0.Anc0refChr1 21590 7 + 62388 AGGAACA -s Anc1.Anc1refChr2 24212 7 - 144309 AGGAACA -s Anc2.Anc2refChr3 23098 7 - 53186 ATGAACA -s mr.mrrefChr5 46275 7 + 294540 AGGAATA -s simCow_chr6.simCow.chr6 444278 7 - 602619 ATGAAAA -s simDog_chr6.simDog.chr6 152060 7 + 593897 ATGAACA -s simHuman_chr6.simHuman.chr6 456940 7 - 601863 AGGAACA -s simRat_chr6.simRat.chr6 181586 7 + 647215 ATGAATA - -a -s simMouse_chr6.simMouse.chr6 191200 3 + 636262 GAA -s Anc0.Anc0refChr1 21597 3 + 62388 GAA -s Anc1.Anc1refChr2 24219 3 - 144309 GAA -s Anc2.Anc2refChr3 23105 3 - 53186 GCA -s mr.mrrefChr5 46282 3 + 294540 GAA -s simCow_chr6.simCow.chr6 444287 3 - 602619 GCA -s simDog_chr6.simDog.chr6 152067 3 + 593897 TCA -s simHuman_chr6.simHuman.chr6 456947 3 - 601863 GAA -s simRat_chr6.simRat.chr6 181593 3 + 647215 GCA - -a -s simMouse_chr6.simMouse.chr6 191203 50 + 636262 TCTCCTTCATGACATACGAGCCTACACCTGTAACCCACCAAATGATGAAA -s Anc0.Anc0refChr1 21608 50 + 62388 TCACCTTTATGACACATGAGCCTACCCCCATTACCCTCTAAAGGCACAAA -s Anc1.Anc1refChr2 24230 50 - 144309 TCACCTTTATGACACATGAGCCTACCCCCATTACCCTCTAAAGGCACAAA -s Anc2.Anc2refChr3 23116 50 - 53186 TCACCTTTATGACACATAAGCCTACCTCCATTACCCTCTAAAGGCACAAA -s mr.mrrefChr5 46285 50 + 294540 TCTCCTTCATGACATATGAGCCTACACCTGTAACCCACTAAATGATCAAA -s simCow_chr6.simCow.chr6 444298 46 - 602619 TCACCTTTATGACACATAATCCTA----CATGACCCTCCAAAAGTACAAT -s simDog_chr6.simDog.chr6 152078 50 + 593897 TCACCTTCATGACACATAAGCTTACCTCCATTACCCTCTAAAGGCGCAAA -s simHuman_chr6.simHuman.chr6 456958 48 - 601863 TCACCTTTATGATACATGAGCCTACTCCCATTACCCTCTAATCA--CAAA -s simRat_chr6.simRat.chr6 181596 50 + 647215 TCTCCTTCATGTCATATGAGCCTATACCTGTAACCTAATAAGTGATCAAA - -a -s simMouse_chr6.simMouse.chr6 191253 46 + 636262 CCCTGTAATATTTTCTGTAACTTACTTGAAGCAGAGAAAGGGGCAT -s Anc0.Anc0refChr1 21664 34 + 62388 CTCTGTAA-C-----------CTACTTAAAACTGACAAAAGGGCAT -s Anc1.Anc1refChr2 24286 35 - 144309 CTCTGTAACC-----------CTACTTAAAACTGACAAAAGGGCAT -s Anc2.Anc2refChr3 23172 34 - 53186 CCCTGTGA-C-----------CTACTTAAAACTGACAAAAGGGCGT -s mr.mrrefChr5 46341 46 + 294540 CTCTGTAACCTTTTCTGTAACCTACTTGAAGCTGAGAAAGGGGCAT -s simCow_chr6.simCow.chr6 444350 31 - 602619 CCCTGTGA-C-----------CTACTTAAAACTGACAAAAGGG--- -s simDog_chr6.simDog.chr6 152134 29 + 593897 CCCTGT-----------------ACTTAAAACTGACAAAAGGGCGT -s simHuman_chr6.simHuman.chr6 457012 35 - 601863 CTCTATAACC-----------CCACTTAAAACTGACAAAAGGGCAT -s simRat_chr6.simRat.chr6 181652 46 + 647215 TTCCGTAACCTTCTCTATAACCTAATTGAAGCTGGGAAAGGGGCAT - -a -s simMouse_chr6.simMouse.chr6 191299 12 + 636262 GTTCCCCATACC -s Anc0.Anc0refChr1 21698 12 + 62388 GCTCCCTATACC -s Anc1.Anc1refChr2 24321 12 - 144309 GCTCCCTATACC -s Anc2.Anc2refChr3 23206 12 - 53186 GCTCCCTATACC -s mr.mrrefChr5 46387 12 + 294540 GTTCCCCATACC -s simCow_chr6.simCow.chr6 444381 4 - 602619 ---CCCT----- -s simDog_chr6.simDog.chr6 152166 12 + 593897 GCTTCCTATACC -s simHuman_chr6.simHuman.chr6 457047 12 - 601863 GCCCCCTATACT -s simRat_chr6.simRat.chr6 181698 12 + 647215 GTTCCCCATACC - -a -s simMouse_chr6.simMouse.chr6 191311 14 + 636262 TATGGAAGTTGGAG -s Anc0.Anc0refChr1 21732 14 + 62388 TATGGAAGATTGAT -s Anc1.Anc1refChr2 24355 14 - 144309 TATGGAAGATTGAT -s Anc2.Anc2refChr3 23240 14 - 53186 TATGAAAGATTGGG -s mr.mrrefChr5 46399 14 + 294540 TATGGAAGTTGGAT -s simCow_chr6.simCow.chr6 444385 7 - 602619 -------GATTGGG -s simDog_chr6.simDog.chr6 152206 14 + 593897 TATGAAAGATTTGG -s simHuman_chr6.simHuman.chr6 457081 14 - 601863 TATGGATCATTGAT -s simRat_chr6.simRat.chr6 181710 14 + 647215 TATGGACGTGAGCT - -a -s simMouse_chr6.simMouse.chr6 191325 4 + 636262 CTTT -s Anc0.Anc0refChr1 21746 4 + 62388 CTTT -s Anc1.Anc1refChr2 24369 4 - 144309 CTTT -s Anc2.Anc2refChr3 23254 4 - 53186 CTTT -s mr.mrrefChr5 46413 4 + 294540 CTTT -s simCow_chr6.simCow.chr6 444393 4 - 602619 CTTT -s simDog_chr6.simDog.chr6 152220 4 + 593897 CTTT -s simHuman_chr6.simHuman.chr6 457095 4 - 601863 CTTT -s simRat_chr6.simRat.chr6 181724 4 + 647215 CTTC - -a -s simMouse_chr6.simMouse.chr6 191329 35 + 636262 ATGAATAATGAGAAATGAAAGTATTTTGCAGATCT -s Anc0.Anc0refChr1 21750 30 + 62388 AT-AATAATGA----TTAAACTATTTTGCAGATCA -s Anc1.Anc1refChr2 24373 30 - 144309 AT-AATAATGA----TTAAACTATTTTGCAGATCA -s Anc2.Anc2refChr3 23258 30 - 53186 AC-AATAATAA----ATTATCTATTTTGCAGATCA -s mr.mrrefChr5 46417 30 + 294540 AT-AATAATGA----TGAAAGTATTTTGCAGATCT -s simCow_chr6.simCow.chr6 444397 30 - 602619 AC-AATAATAA----ATTATCTTCTTTGCAGATTA -s simDog_chr6.simDog.chr6 152224 30 + 593897 AC-AATAATAA----ATTATCCATTGTGCAGATCA -s simHuman_chr6.simHuman.chr6 457099 30 - 601863 AT-AATAATGA----TCAAACTATTTTGTAGATCA -s simRat_chr6.simRat.chr6 181730 18 + 647215 AT-AATAAT----------------TTGCAGATCT - -a -s simMouse_chr6.simMouse.chr6 191364 12 + 636262 GTAAACAGCCTT -s Anc0.Anc0refChr1 21782 12 + 62388 GAAGAAGGTCTG -s Anc1.Anc1refChr2 24405 12 - 144309 GAAGAAGGTCTG -s Anc2.Anc2refChr3 23290 12 - 53186 GAAGAAGGTCTG -s mr.mrrefChr5 46450 12 + 294540 GTAAACAGCCTT -s simCow_chr6.simCow.chr6 444429 12 - 602619 GCAGAAGGTTGG -s simDog_chr6.simDog.chr6 152256 12 + 593897 GAAGAAGGTCTG -s simHuman_chr6.simHuman.chr6 457131 12 - 601863 GAAGAAGGTCTG -s simRat_chr6.simRat.chr6 181751 12 + 647215 GTAAACAGCCTA - -a -s simMouse_chr6.simMouse.chr6 191376 34 + 636262 AGCTATATATCTGCTTCGTTGCCAATCTGTTTAC -s Anc0.Anc0refChr1 21794 27 + 62388 AGTTAAGTACCTGCTTCATTGCTGACT------- -s Anc1.Anc1refChr2 24417 34 - 144309 AGTTAAGTACCTGCTTCATTGCTGACTTGATTGC -s Anc2.Anc2refChr3 23302 27 - 53186 AGTTAAGTACCTGCTTCATGGCTGACT------- -s mr.mrrefChr5 46462 34 + 294540 AGTTAAGTATCTGCTTCGTTGCCAATCTGTTTAC -s simCow_chr6.simCow.chr6 444441 25 - 602619 AGTTAAGTACCTGCTTCATGG--GACT------- -s simDog_chr6.simDog.chr6 152268 27 + 593897 AGTAAAGTACCCGCATCATGGCTGATT------- -s simHuman_chr6.simHuman.chr6 457148 34 - 601863 AGTTAACTACATGCTTAACTACATGCTTCATTGC -s simRat_chr6.simRat.chr6 181763 34 + 647215 AGTTAAGTCTCTGCTTCGTTGCCAATCTGTTTAC - -a -s simMouse_chr6.simMouse.chr6 191410 11 + 636262 AGTTTCGTATG -s Anc0.Anc0refChr1 21821 11 + 62388 TGATTTGTATG -s Anc1.Anc1refChr2 24451 11 - 144309 TGATTTGTATG -s Anc2.Anc2refChr3 23329 11 - 53186 TGATTTGTAGG -s mr.mrrefChr5 46496 11 + 294540 AGATTCGTATG -s simCow_chr6.simCow.chr6 444541 11 - 602619 TGATTTGTTGG -s simDog_chr6.simDog.chr6 152295 11 + 593897 TGATTTGTAGG -s simHuman_chr6.simHuman.chr6 457182 10 - 601863 TGACTTG-ATG -s simRat_chr6.simRat.chr6 181797 11 + 647215 AGAGTCGTATG - -a -s simMouse_chr6.simMouse.chr6 191421 12 + 636262 ACTCTCCCAAAA -s Anc0.Anc0refChr1 21832 7 + 62388 AATC-----AAG -s Anc1.Anc1refChr2 24462 7 - 144309 AATC-----AAG -s Anc2.Anc2refChr3 23342 7 - 53186 AAAC-----AAG -s mr.mrrefChr5 46507 10 + 294540 ACTCTC--AAAA -s simDog_chr6.simDog.chr6 152310 7 + 593897 AAAC-----AAG -s simHuman_chr6.simHuman.chr6 457192 7 - 601863 AATC-----AAG -s simRat_chr6.simRat.chr6 181808 10 + 647215 ATTCTC--AAAA - -a -s simMouse_chr6.simMouse.chr6 191433 104 + 636262 GTGCCTCCTCTGCACCCGCAGAACTAATGTATTATGGCTAATTCCACACCTGCTGCCTGCCTCTGTCTAGCCTGTCTAGGCTATGGAAAACTGCCCCCTTTGCG -s Anc0.Anc0refChr1 21839 42 + 62388 GGGTGATTCTCCCATATACAGTA--------------------------------------------------------------GAATACTGCCCCCTCTGTG -s Anc1.Anc1refChr2 24469 42 - 144309 GGGTGATTCTCCCATATACAGTA--------------------------------------------------------------GAATACTGCCCCCTCTGTG -s Anc2.Anc2refChr3 23349 42 - 53186 TGATGATTCTCCCATATATAGTA--------------------------------------------------------------GAATACTGCCCCCTCTGTG -s mr.mrrefChr5 46517 100 + 294540 GTGCCTTTTCTGCATCTACAGAACTAATGTATTATGGCTAATTCCACACCTGCTGCCT----CTGTCTAGCCTGTCTAGGCTATGGAAAACTGCCCCCTCTGCG -s simCow_chr6.simCow.chr6 444553 39 - 602619 ---TGATTCTCCCATATATAGTT--------------------------------------------------------------GAATACTGCCCCCTCTGTG -s simDog_chr6.simDog.chr6 152331 42 + 593897 TGACAATTGTCCTATATATAGTA--------------------------------------------------------------GAATGATGCCCCCTCTGTG -s simHuman_chr6.simHuman.chr6 457199 42 - 601863 GGGTGATTCTCCCATATACAGCA--------------------------------------------------------------GAATACTGCCCTCACTGTG -s simRat_chr6.simRat.chr6 181818 100 + 647215 GTACCTTTTCTGCATCTACAGAACTAATGTATTATGGCTAACTCCATCCCTGCCTCGT----CTGTCTAGCTTGTTTAGGCTATGGAAAACTGCCCCCTCTGCA - -a -s simMouse_chr6.simMouse.chr6 191537 3 + 636262 CCT -s Anc0.Anc0refChr1 21881 2 + 62388 A-T -s Anc1.Anc1refChr2 24511 3 - 144309 ACT -s Anc2.Anc2refChr3 23391 2 - 53186 A-T -s mr.mrrefChr5 46617 3 + 294540 ACT -s simCow_chr6.simCow.chr6 444595 2 - 602619 A-C -s simDog_chr6.simDog.chr6 152373 2 + 593897 A-T -s simHuman_chr6.simHuman.chr6 457241 3 - 601863 ACT -s simRat_chr6.simRat.chr6 181918 3 + 647215 ACT - -a -s simMouse_chr6.simMouse.chr6 191540 13 + 636262 CATCCTCATTATA -s Anc0.Anc0refChr1 21887 7 + 62388 CCC------TATA -s Anc1.Anc1refChr2 24518 7 - 144309 CCC------TATA -s Anc2.Anc2refChr3 23397 7 - 53186 ACC------TATA -s mr.mrrefChr5 46620 7 + 294540 CAT------TATA -s simCow_chr6.simCow.chr6 444601 7 - 602619 ACC------TATA -s simDog_chr6.simDog.chr6 152379 7 + 593897 ACC------TAGA -s simHuman_chr6.simHuman.chr6 457248 7 - 601863 CCC------TATA -s simRat_chr6.simRat.chr6 181921 7 + 647215 CGT------TATA - -a -s simMouse_chr6.simMouse.chr6 191553 22 + 636262 GTGCATTTCACCCTTGCCCCTT -s Anc0.Anc0refChr1 21900 22 + 62388 GTTTATTTCACCCCCGCCCCCT -s Anc1.Anc1refChr2 24531 22 - 144309 GTTTATTTCACCCCCGCCCCCT -s Anc2.Anc2refChr3 23411 22 - 53186 GTTTATTTCACTCCCGCCCCCT -s mr.mrrefChr5 46627 22 + 294540 GTGCATTTCACCCTTGCCCCTT -s simCow_chr6.simCow.chr6 444615 20 - 602619 GTTGGTTTCCCT--CACCCCTC -s simDog_chr6.simDog.chr6 152393 22 + 593897 GCTTAAATCACTCCAGCCCCCT -s simHuman_chr6.simHuman.chr6 457261 22 - 601863 GTTTATTTCACCTCCGCCCCCT -s simRat_chr6.simRat.chr6 181928 22 + 647215 GTGCATTTTGCCCTTGCCCATT - -a -s simMouse_chr6.simMouse.chr6 191575 53 + 636262 TGTCTAGTAGTATCACATTGCATCTTGACACCCATGAGATCTCCTGCATAAGT -s Anc0.Anc0refChr1 21927 53 + 62388 TGTCTTCTAGTATCACATTGGGTCTTAATTCTTATGAGATTTCCACCATAAGC -s Anc1.Anc1refChr2 24558 53 - 144309 TGTCTTCTAGTATCACATTGGGTCTTAATTCTTATGAGATTTCCACCATAAGC -s Anc2.Anc2refChr3 23438 53 - 53186 TGTCCTCTAGTATAACATTGGGTCTTAATTCCTATGAGATTTCCACCACAAGC -s mr.mrrefChr5 46649 53 + 294540 TGTCTAGTAGTATCACATTGCATCTTGACACTCATGAGATCTCCTGCATAAGT -s simCow_chr6.simCow.chr6 444640 53 - 602619 TCTCCTTTAGTATAACATTGTGTCTTAATCCCTGTGAGATTCCCACCGCAAGC -s simDog_chr6.simDog.chr6 152420 53 + 593897 TGTCCTCTAGTATAACATTGGGTCTCAATTCCTATGAGATTTCCCCCACAAGC -s simHuman_chr6.simHuman.chr6 457288 52 - 601863 TGTCTTCTAATATCACAATGGGTCTTAATTCTTA-GAGATTTCCACGATAAAA -s simRat_chr6.simRat.chr6 181950 53 + 647215 TGTATGGTAGTATCACCTTGCATCTTGACACTCATGAGATCTCCTGCACAAGT - -a -s simMouse_chr6.simMouse.chr6 191628 2 + 636262 TG -s Anc0.Anc0refChr1 21980 2 + 62388 TG -s Anc1.Anc1refChr2 24611 2 - 144309 TG -s Anc2.Anc2refChr3 23528 2 - 53186 TG -s mr.mrrefChr5 46702 2 + 294540 TG -s simCow_chr6.simCow.chr6 444730 2 - 602619 TG -s simDog_chr6.simDog.chr6 152510 2 + 593897 TG -s simHuman_chr6.simHuman.chr6 457340 2 - 601863 TG -s simRat_chr6.simRat.chr6 182003 2 + 647215 TG - -a -s simMouse_chr6.simMouse.chr6 191630 14 + 636262 CCTTGGCAAGCATG -s Anc0.Anc0refChr1 21987 8 + 62388 CC------AGCATG -s Anc1.Anc1refChr2 24618 8 - 144309 CC------AGCATG -s Anc2.Anc2refChr3 23535 8 - 53186 CT------AGCATA -s mr.mrrefChr5 46704 14 + 294540 CCTTGGCAAGCATG -s simCow_chr6.simCow.chr6 444737 8 - 602619 CT------AGCACA -s simDog_chr6.simDog.chr6 152517 6 + 593897 CT--------CATA -s simHuman_chr6.simHuman.chr6 457347 8 - 601863 CC------AGCATG -s simRat_chr6.simRat.chr6 182005 14 + 647215 CCTTGGCAAGCTTG - -a -s simMouse_chr6.simMouse.chr6 191644 43 + 636262 CTCGGATCCTTTGACATTCAGATTAGATTGTCGAACAATGAAA -s Anc0.Anc0refChr1 22033 43 + 62388 CTCAGCTTCTTTGATATTTGGATTAGATGGTGGCACAATGAAA -s Anc1.Anc1refChr2 24664 43 - 144309 CTCAGCTTCTTTGATATTTGGATTAGATGGTGGCACAATGAAA -s Anc2.Anc2refChr3 23581 43 - 53186 TTCTGCTTCTATGATAGTTGGATTAGATGGTGGCATAATGAAC -s mr.mrrefChr5 46718 43 + 294540 CTCAGATCCTTTGACATTTAGATTAGATTGTCGAACAATGAAA -s simCow_chr6.simCow.chr6 444783 43 - 602619 GTCCGCTTCTATGACAGATGGATTAGCCAGTCGCATAATGAAC -s simDog_chr6.simDog.chr6 152558 43 + 593897 TTCTGCTTCTATGGTAGTAGTACTAAATGGTGGCATAACACAC -s simHuman_chr6.simHuman.chr6 457393 43 - 601863 CTCAGGTTCTTTGATGTTTGGATTAGATGGTTGCACAATGATA -s simRat_chr6.simRat.chr6 182019 43 + 647215 CTCAGATCCTTTGACATTTCGATTAGATTGTCTAATAATGAAA - -a -s simMouse_chr6.simMouse.chr6 191687 12 + 636262 AGTACGATTTGC -s Anc0.Anc0refChr1 22079 12 + 62388 AGTATGATTAGG -s Anc1.Anc1refChr2 24710 12 - 144309 AGTATGATTAGG -s Anc2.Anc2refChr3 23627 12 - 53186 AGTTTGATTAGG -s mr.mrrefChr5 46761 12 + 294540 AGTATGATTTGC -s simCow_chr6.simCow.chr6 444829 12 - 602619 AGTGTGGTTAGC -s simDog_chr6.simDog.chr6 152604 12 + 593897 AGTTTGATTAAG -s simHuman_chr6.simHuman.chr6 457439 12 - 601863 AGTATGATCAGG -s simRat_chr6.simRat.chr6 182062 12 + 647215 GGTATGATACGC - -a -s simMouse_chr6.simMouse.chr6 191699 45 + 636262 TCTCGATTGTTCAACCCTACCAATGTACCAAGAGCTGAGTGATGT -s Anc0.Anc0refChr1 22091 43 + 62388 TGTTCATTGCTCCACCCTACCAATGTCCCAAAGGCTGGGTGA--T -s Anc1.Anc1refChr2 24722 45 - 144309 TGTTCATTGCTCCACCCTACCAATGTCCCAAAGGCTGGGTGATGT -s Anc2.Anc2refChr3 23639 43 - 53186 TGTTCATTGCTCCACCCTATCAACATCCCAAAGGCTGGGTGA--T -s mr.mrrefChr5 46773 45 + 294540 TCTTCATTGCTCAACCCTACCAATGTACCAAGAGCTGAGTGATGT -s simCow_chr6.simCow.chr6 444841 43 - 602619 TGTGCATTGCTCCACCCTATCAACATCACTAATGCTGGGTGA--T -s simDog_chr6.simDog.chr6 152617 43 + 593897 TATTTATGGCTCCACCCGATCAACATCCCAAAGGCTGGGTGA--T -s simHuman_chr6.simHuman.chr6 457451 40 - 601863 TGTTCATTGCTCCACCCTACCAATGTCCCAAAGGCTT-----TGT -s simRat_chr6.simRat.chr6 182074 45 + 647215 TCTTCATTGCTCAACCCTACCAATGTACCAAGAGCTGAGTGATGT - -a -s simMouse_chr6.simMouse.chr6 191744 4 + 636262 GGAG -s Anc0.Anc0refChr1 22134 4 + 62388 GGAG -s Anc1.Anc1refChr2 24767 4 - 144309 GGAG -s Anc2.Anc2refChr3 23682 4 - 53186 AGAG -s mr.mrrefChr5 46818 4 + 294540 GGAG -s simCow_chr6.simCow.chr6 444898 4 - 602619 AGAG -s simDog_chr6.simDog.chr6 152660 4 + 593897 AGAT -s simHuman_chr6.simHuman.chr6 457491 4 - 601863 GGGG -s simRat_chr6.simRat.chr6 182119 4 + 647215 GGCG - -a -s simMouse_chr6.simMouse.chr6 191748 272 + 636262 CATATAGCTCTGCGCTGGTTTGGGACCGCTCCATAAGCATTTTTGAGTTTAGAGCAATAGTGAAATTGGGAGGTAGCACAATTCCTATGGACCCCGTCGACAACATGGTCCTAACCCTGGAATCCATGTCTAAACCCGTCAGCACTACTATATAGTCTTGCGATGAGAATTCGAACCATTTAACCCTACCTTGTCTCTTGCTACAAGACAAGCAGCATCTCTTGTATTTTTTATAGCAAAGATCACCGTCATCTCAATGTGTTGAAACCATG -s Anc0.Anc0refChr1 22138 100 + 62388 TGTACAGCT--GCCCTGGTTT-------------------------------------------------------------------------------------------------------------------------------------------------------------------------TTCTCAGTTCTTTCAACATAAGCAGCATTTCTTGTATTTTGTCTTGTAAAGATTGCT-TGATCTTAATATGTTGAGACCATA -s Anc1.Anc1refChr2 24771 100 - 144309 TGTACAGCT--GCCCTGGTTT-------------------------------------------------------------------------------------------------------------------------------------------------------------------------TTCTCAGTTCTTTCAACATAAGCAGCATTTCTTGTATTTTGTCTTGTAAAGATTGCT-TGATCTTAATATGTTGAGACCATA -s Anc2.Anc2refChr3 23686 100 - 53186 TGTACAGCT--GCCCTAGTTT-------------------------------------------------------------------------------------------------------------------------------------------------------------------------TTCTCAGTTCTTTCAACATAAGCAGCATTTCTTGTACTTTGTCTTGTAGGGATTGCT-TGATCTTAATATGTTGAGACCATA -s mr.mrrefChr5 46822 102 + 294540 CATACAGCTC-GCGCTGGTTT-------------------------------------------------------------------------------------------------------------------------------------------------------------------------TTGTCTCTTTCTACAAGACAAGCAGCATCTCTTGTATTTTTTATAGTAAAGATTGCTGTCATCTCAATGTGTTGAGACCATG -s simCow_chr6.simCow.chr6 444902 100 - 602619 CATACTACT--GCCCTAGTTT-------------------------------------------------------------------------------------------------------------------------------------------------------------------------TTTTCAGTTGCTTCAACACAAGCAGTTTTTCTTGTGGTTTGTCTTGGAGGTCTTGCT-TCATCATAATATATTGACACCAGG -s simDog_chr6.simDog.chr6 152664 99 + 593897 TGTACAGCT--TCCCTAGTTT-------------------------------------------------------------------------------------------------------------------------------------------------------------------------TTCCCGATTCTTTCAACATAAGCAGCATTTTTTGTACTTCATCTTGTAGGGATTAGT--GTCATTAATATGTTGAGACCATA -s simHuman_chr6.simHuman.chr6 457495 98 - 601863 TGTACAGCT--GCCCTGGCTT-------------------------------------------------------------------------------------------------------------------------------------------------------------------------TTCTCAGTC--ATCAACAAAAGTGGCATTTCTTTTATGTTGTCTTGTAAAGATTGCT-CGATCGTGATATGTTGAGATGATA -s simRat_chr6.simRat.chr6 182132 102 + 647215 TATACAGCTC-ACGCTGGTTT-------------------------------------------------------------------------------------------------------------------------------------------------------------------------TTGTCTGTATCTACAAGACAATCAGCATCTCTTGTATTTTTTATAGTAAGGATTGCTGTCATCTCAATGTGTTGAGACTATG - -a -s simMouse_chr6.simMouse.chr6 192020 7 + 636262 GGTCTTG -s Anc0.Anc0refChr1 22239 6 + 62388 GGTC-TG -s Anc1.Anc1refChr2 24872 6 - 144309 GGTC-TG -s Anc2.Anc2refChr3 23787 6 - 53186 GGTC-TC -s mr.mrrefChr5 46924 6 + 294540 GGTC-TG -s simCow_chr6.simCow.chr6 445003 6 - 602619 GGTC-TC -s simDog_chr6.simDog.chr6 152764 5 + 593897 GGTC-T- -s simHuman_chr6.simHuman.chr6 457594 6 - 601863 GGTC-TG -s simRat_chr6.simRat.chr6 182234 6 + 647215 GGTC-TG - -a -s simMouse_chr6.simMouse.chr6 192027 13 + 636262 GAATATAACAAAT -s Anc0.Anc0refChr1 22247 13 + 62388 GAATAGTAAAAAT -s Anc1.Anc1refChr2 24880 13 - 144309 GAATAGTAAAAAT -s Anc2.Anc2refChr3 23795 13 - 53186 GAATAGTAAAAAT -s mr.mrrefChr5 46932 13 + 294540 GAATATAACAAAT -s simCow_chr6.simCow.chr6 445011 13 - 602619 GAATAGTTGAAAT -s simDog_chr6.simDog.chr6 152771 13 + 593897 GAACAGTAAAAAT -s simHuman_chr6.simHuman.chr6 457602 13 - 601863 GAATAATAAAAAT -s simRat_chr6.simRat.chr6 182242 13 + 647215 GGATATAACAAAT - -a -s simMouse_chr6.simMouse.chr6 192040 6 + 636262 GTACCT -s Anc0.Anc0refChr1 22261 6 + 62388 TTATCC -s Anc1.Anc1refChr2 24894 6 - 144309 TTATCC -s Anc2.Anc2refChr3 23809 6 - 53186 TTATCC -s mr.mrrefChr5 46945 6 + 294540 GTATCT -s simCow_chr6.simCow.chr6 445025 6 - 602619 TAGTCC -s simDog_chr6.simDog.chr6 152785 6 + 593897 TTATCT -s simHuman_chr6.simHuman.chr6 457616 6 - 601863 TTATCC -s simRat_chr6.simRat.chr6 182255 6 + 647215 GTATCT - -a -s simMouse_chr6.simMouse.chr6 192046 28 + 636262 GAAGTCAAAGCTTGCTAGTTTAACAGGA -s Anc0.Anc0refChr1 22268 28 + 62388 AAAGTGAAAGCTAGCTAATTTAACAGAA -s Anc1.Anc1refChr2 24901 28 - 144309 AAAGTGAAAGCTAGCTAATTTAACAGAA -s Anc2.Anc2refChr3 23816 28 - 53186 AAAGTGAAAGCTAGCTAATTTAACAGAA -s mr.mrrefChr5 46952 28 + 294540 GAAGTCAAAGCTAGCTAGTTTAACAGGA -s simCow_chr6.simCow.chr6 445032 27 - 602619 AAAGTGAAAGCTCGCTAATTTAGCAG-A -s simDog_chr6.simDog.chr6 152792 28 + 593897 AAAGTGAGAGCTAGCTAATTTAACCAAA -s simHuman_chr6.simHuman.chr6 457623 27 - 601863 AAAATGTAGGC-AGCTAATTTAACAGAA -s simRat_chr6.simRat.chr6 182262 28 + 647215 GAAGTCAAAGCTAGCTGGTGTAACAGGA - -a -s simMouse_chr6.simMouse.chr6 192074 10 + 636262 TCTGCCATGT -s Anc0.Anc0refChr1 22297 10 + 62388 TTTGCCATGT -s Anc1.Anc1refChr2 24930 10 - 144309 TTTGCCATGT -s Anc2.Anc2refChr3 23845 10 - 53186 TTTGCCATGT -s mr.mrrefChr5 46980 10 + 294540 TCTGCCATGT -s simCow_chr6.simCow.chr6 445060 10 - 602619 TTTGCAATGT -s simDog_chr6.simDog.chr6 152821 10 + 593897 TTTGTCATGT -s simHuman_chr6.simHuman.chr6 457651 10 - 601863 TATGCCGCGT -s simRat_chr6.simRat.chr6 182290 10 + 647215 TCTGCCATGT - -a -s simMouse_chr6.simMouse.chr6 192084 23 + 636262 TAGACTCTGGGCTACTAGTGGGT -s Anc0.Anc0refChr1 22318 23 + 62388 TAGACTTTGGGCTACTAGTGAAC -s Anc1.Anc1refChr2 24951 23 - 144309 TAGACTTTGGGCTACTAGTGAAC -s Anc2.Anc2refChr3 23866 23 - 53186 TAGATTTTGTGCTACTAGTAAAC -s mr.mrrefChr5 46990 23 + 294540 TAGACTCTGGGCTACTAGTGAAT -s simCow_chr6.simCow.chr6 445081 19 - 602619 TAAA----GTGCTACTAGTAACC -s simDog_chr6.simDog.chr6 152842 23 + 593897 TGGATTTTGTGCTACTAGTAAAC -s simHuman_chr6.simHuman.chr6 457672 23 - 601863 TAGACTTCGGGCTATTAGTGAAC -s simRat_chr6.simRat.chr6 182300 17 + 647215 TAGACTCGGGGCT------GAAT - -a -s simMouse_chr6.simMouse.chr6 192107 34 + 636262 GATTATTTCTGGCTAAATAATGTGCACATTTGTA -s Anc0.Anc0refChr1 22341 29 + 62388 AATT-----TGGCAAAAGAATGTGCATATTTGTA -s Anc1.Anc1refChr2 24974 29 - 144309 AATT-----TGGCAAAAGAATGTGCATATTTGTA -s Anc2.Anc2refChr3 23891 29 - 53186 AATA-----AGGCAAAAGAATGTGCATATTTGTA -s mr.mrrefChr5 47013 34 + 294540 GATTATTTCTGGCTAAATAATGTGCATATTTGTA -s simCow_chr6.simCow.chr6 445102 28 - 602619 ACTA-----GAAC-AAAGAATGTGCATATCTGTA -s simDog_chr6.simDog.chr6 152867 28 + 593897 AATA-----AGGCAAAGGGATGAGCTTA-TTGTA -s simHuman_chr6.simHuman.chr6 457695 29 - 601863 AATT-----TAACAAAAGAATGTGCATGTTTGTA -s simRat_chr6.simRat.chr6 182317 34 + 647215 CCTTATTTCTGCTTAAATAATGTGCATATTTGTA - -a -s simMouse_chr6.simMouse.chr6 192141 83 + 636262 AGCCAAAAGAGGTGCTTCAGTCTGACACAGCATGCAACAAAAAAAAAAATTGAATCCAACTGGTTTCAATATGATAGATGCTA -s Anc0.Anc0refChr1 22370 30 + 62388 AATTGAAAGAGGTACTTCAAT-----------------------------------------------------TGGATGCTA -s Anc1.Anc1refChr2 25003 30 - 144309 AATTGAAAGAGGTACTTCAAT-----------------------------------------------------TGGATGCTA -s Anc2.Anc2refChr3 23923 30 - 53186 AATTGAAAGAGGTACTTCAAT-----------------------------------------------------TGGATGTTA -s mr.mrrefChr5 47047 80 + 294540 AGCCAAAAGAGGTGCTTCAGTCTGACACAGCATGCAACAAAAAAAA---TTGAATCCAACTGGTTTCAATATGATAGATGCTA -s simCow_chr6.simCow.chr6 445133 30 - 602619 AATTGAAAGCAGTACATCAAT-----------------------------------------------------TGGATCTTA -s simDog_chr6.simDog.chr6 152898 30 + 593897 AATTGAAAGAGGTACTTCAAT-----------------------------------------------------TGAATGTTA -s simHuman_chr6.simHuman.chr6 457724 30 - 601863 AATTCAAAGAGGTACTTCAAC-----------------------------------------------------TGGCTGCTA -s simRat_chr6.simRat.chr6 182351 80 + 647215 AGCCAAAAGAGGTGCTTTGGTCTGACACAGCACGAGACACAAAAAA---TTGTATCCAACGAGTTTCAACATGATAGATGCTA - -a -s simMouse_chr6.simMouse.chr6 192224 2 + 636262 CC -s Anc0.Anc0refChr1 22400 1 + 62388 C- -s Anc1.Anc1refChr2 25033 1 - 144309 C- -s Anc2.Anc2refChr3 23953 1 - 53186 C- -s mr.mrrefChr5 47127 2 + 294540 CC -s simCow_chr6.simCow.chr6 445164 1 - 602619 C- -s simDog_chr6.simDog.chr6 152928 1 + 593897 T- -s simHuman_chr6.simHuman.chr6 457754 1 - 601863 C- -s simRat_chr6.simRat.chr6 182431 2 + 647215 CC - -a -s simMouse_chr6.simMouse.chr6 192226 65 + 636262 AACTTAGGATTAAGCCGAACACCATCATAACACTATACACTTACCTTAGTTATTCACATCATTTA -s Anc0.Anc0refChr1 22401 40 + 62388 AACTTTGCAT------------------AAGGATGTA----TCTC--AGTAACTCA-ACCAGATG -s Anc1.Anc1refChr2 25034 43 - 144309 AACTTTGCAT------------------AAGGATGTA----TCTCTTAGTAACTCATACCAGATG -s Anc2.Anc2refChr3 23954 40 - 53186 AACCTTGCAT------------------AAGGATGTA----TCTC--AGTAGCTCA-ACCAGATG -s mr.mrrefChr5 47129 47 + 294540 AACTTAGGAT------------------AACACTATACACTTACCTTAGTTATTCACATCATTTA -s simCow_chr6.simCow.chr6 445165 40 - 602619 AACCTTGCAT------------------AAGAATGCA----TCTT--AGTTGCTCC-ACAAGATG -s simDog_chr6.simDog.chr6 152931 30 + 593897 AAC----------------------------GACGTA----ACTC--AGTAGCTCA-ACCAGATG -s simHuman_chr6.simHuman.chr6 457755 43 - 601863 AACTTCGCAT------------------AGGGATGTA----TCTCTTAGTCACTCATACCAGATG -s simRat_chr6.simRat.chr6 182433 45 + 647215 AACTTAGGAT------------------AACACAATAAACTTACCTTAGTTATTCACA--ACTCA - -a -s simMouse_chr6.simMouse.chr6 192291 16 + 636262 ACCAGTTACAGTCACA -s Anc0.Anc0refChr1 22449 16 + 62388 AGCACTCACAGGTACA -s Anc1.Anc1refChr2 25085 16 - 144309 AGCACTCACAGGTACA -s Anc2.Anc2refChr3 24002 16 - 53186 AGCACTCCCAGGTACA -s mr.mrrefChr5 47176 16 + 294540 ACCAGTCACAGTCACA -s simCow_chr6.simCow.chr6 445213 16 - 602619 AGCACTCCCAGGTACA -s simDog_chr6.simDog.chr6 152969 16 + 593897 AGCACTCCCAAGTACA -s simHuman_chr6.simHuman.chr6 457806 16 - 601863 AGCACTCACAGGTGTA -s simRat_chr6.simRat.chr6 182478 16 + 647215 AACAGTCACAGTCACA - -a -s simMouse_chr6.simMouse.chr6 192307 3 + 636262 TGG -s Anc0.Anc0refChr1 22465 3 + 62388 TGA -s Anc1.Anc1refChr2 25101 3 - 144309 TGA -s Anc2.Anc2refChr3 24018 3 - 53186 TGA -s mr.mrrefChr5 47192 3 + 294540 TGG -s simCow_chr6.simCow.chr6 445254 3 - 602619 TGA -s simDog_chr6.simDog.chr6 152985 3 + 593897 TGA -s simHuman_chr6.simHuman.chr6 457822 3 - 601863 TGC -s simRat_chr6.simRat.chr6 182494 3 + 647215 TGG - -a -s simMouse_chr6.simMouse.chr6 192310 83 + 636262 CCCTGTGGCTCCCTGTCAACATGAGATTGATCCTTTAAGACAGCATGCCCTGTTAACCTGATGTTGGTCCATTAAGACAGCAC -s Anc0.Anc0refChr1 22469 48 + 62388 CCCTGTGAGGCC-TGTCAA--T--------------------------------AACATGAGGTTATTCCTTTAAGACAGCAC -s Anc1.Anc1refChr2 25105 48 - 144309 CCCTGTGAGGCC-TGTCAA--T--------------------------------AACATGAGGTTATTCCTTTAAGACAGCAC -s Anc2.Anc2refChr3 24022 48 - 53186 CCCTGTGAGGCC-TGTCAA--G--------------------------------CACCTGAGGTTATTACTTTAAGACAGCAC -s mr.mrrefChr5 47196 81 + 294540 CCCTGTGGGGCCCTGTCAA--TGAGATTGATCCTTTAAGACAGCATGCCCTGTTAACATGATGTTGGTCCTTTAAGACAGCAC -s simCow_chr6.simCow.chr6 445258 48 - 602619 CCCTGAGAGGCC-TGTCAA--G--------------------------------CATGTGAGGCTATGACTTTAGGCAAGCAC -s simDog_chr6.simDog.chr6 152989 48 + 593897 CCTTCTGAGGCT-TGTCAA--G--------------------------------CACCTGAGGTTATTACCTTGAGACGGCAC -s simHuman_chr6.simHuman.chr6 457826 48 - 601863 CCCTGTCAGGCC-TGTCAA--T--------------------------------AACATGAACTTAATCCTTTAAAGCATTGC -s simRat_chr6.simRat.chr6 182498 79 + 647215 CCCTCTGGGGCCCCGTC----TGAGGTTGATCCTTTAAGATAGCAGGCCCTGTCAACATGATGTTGGTCCTTTAAGACAGCAC - -a -s simMouse_chr6.simMouse.chr6 192393 1 + 636262 A -s Anc0.Anc0refChr1 22521 1 + 62388 G -s Anc1.Anc1refChr2 25157 1 - 144309 G -s Anc2.Anc2refChr3 24074 1 - 53186 G -s mr.mrrefChr5 47277 1 + 294540 G -s simCow_chr6.simCow.chr6 445310 1 - 602619 G -s simDog_chr6.simDog.chr6 153041 1 + 593897 G -s simHuman_chr6.simHuman.chr6 457878 1 - 601863 G -s simRat_chr6.simRat.chr6 182577 1 + 647215 G - -a -s simMouse_chr6.simMouse.chr6 192394 13 + 636262 TATAATGAACTCA -s Anc0.Anc0refChr1 22522 13 + 62388 TGTAATGACCTTA -s Anc1.Anc1refChr2 25158 13 - 144309 TGTAATGACCTTA -s Anc2.Anc2refChr3 24078 13 - 53186 TGTAGTGACCTTA -s mr.mrrefChr5 47278 13 + 294540 TATAATGAACTCA -s simCow_chr6.simCow.chr6 445314 13 - 602619 TGTAGGAACCTTA -s simDog_chr6.simDog.chr6 153047 13 + 593897 TGTAGTGACCTTA -s simHuman_chr6.simHuman.chr6 457879 12 - 601863 TGTAATGTCCT-G -s simRat_chr6.simRat.chr6 182578 13 + 647215 TATAACGAACTCA - -a -s simMouse_chr6.simMouse.chr6 192407 51 + 636262 GCACTTTATATCTCGTGGACCGCTTACCGGATGTTATTGGCTAATCCAAGC -s Anc0.Anc0refChr1 22535 49 + 62388 GCACTTTGAATATCATGG-CTGCCCACTGGATATTATTGGCCAAGCC-AAT -s Anc1.Anc1refChr2 25171 51 - 144309 GCACTTTGAATATCATGGACTGCCCACTGGATATTATTGGCCAAGCCAAAT -s Anc2.Anc2refChr3 24091 49 - 53186 GCACTCTGAATATCATGG-TTGCCCACTGGATATCATTGACCAAGCT-AAT -s mr.mrrefChr5 47291 51 + 294540 GCACTTTATATCTCATGGACTGCTCACCGGATGTTATTGGCTAATCCAAAT -s simCow_chr6.simCow.chr6 445330 40 - 602619 GCACTGACAACA----------CTCACTGTATATCATTGACCAAGCT-AAT -s simDog_chr6.simDog.chr6 153060 49 + 593897 GCACTCTGCATCTCATGG-TTGCCCACTGGATATCAATGACCAGGCT-AAT -s simHuman_chr6.simHuman.chr6 457891 51 - 601863 GCACTTTGAATATCATGGACTGCCCACTAAATATTATTGGCCAAGCCAAAT -s simRat_chr6.simRat.chr6 182591 51 + 647215 ATACTTTATGTCTCATAGACTGTTCACCGGATGTTATTGGCTAGTCCAAAT - -a -s simMouse_chr6.simMouse.chr6 192458 22 + 636262 ATACATGCAAAGCTTTGCCAGG -s Anc0.Anc0refChr1 22584 22 + 62388 ATACATGCTAAGCTTTGTCAGG -s Anc1.Anc1refChr2 25222 22 - 144309 ATACATGCTAAGCTTTGTCAGG -s Anc2.Anc2refChr3 24140 22 - 53186 ATACATGCTAAGCTTTATAAGG -s mr.mrrefChr5 47342 22 + 294540 ATACATGCAAAGCTTTGCCAGG -s simCow_chr6.simCow.chr6 445370 22 - 602619 ATACATGCTAAGCTTTATAAGG -s simDog_chr6.simDog.chr6 153109 22 + 593897 ATACATGACAAGCTCTATAAGG -s simHuman_chr6.simHuman.chr6 457943 22 - 601863 ATACATGCTAAGCCTTGTCAGG -s simRat_chr6.simRat.chr6 182642 22 + 647215 ATACATGCAAAGCTTTGCTAGG - -a -s simMouse_chr6.simMouse.chr6 192480 16 + 636262 CCCTTGAGCAGAAAAG -s Anc0.Anc0refChr1 22606 16 + 62388 CCCATGAGCAGAAAAG -s Anc1.Anc1refChr2 25244 16 - 144309 CCCATGAGCAGAAAAG -s Anc2.Anc2refChr3 24162 16 - 53186 CCCATGAGCAGAAAAG -s mr.mrrefChr5 47364 16 + 294540 CCCTTGAGCAGAAAAG -s simCow_chr6.simCow.chr6 445392 16 - 602619 CCCATGAGCAGAAAAG -s simDog_chr6.simDog.chr6 153136 16 + 593897 CTCATAATCAGAAAGG -s simHuman_chr6.simHuman.chr6 457965 16 - 601863 CCCCTGAGCAGAAAAG -s simRat_chr6.simRat.chr6 182664 16 + 647215 CCCTGGAGCAGCAAAG - -a -s simMouse_chr6.simMouse.chr6 192496 108 + 636262 AATGTGTTGCTGCATCCGTTGTGGGAGCAGATTTAAGCTGATGACCGCTCCTGTTATATACCAATTACGGTTACCCAGATTCAGGCACAGTCTGACCCTTTCAAGACT -s Anc0.Anc0refChr1 22622 55 + 62388 AATGAGTTGTTCCA-----------------------------------------------CAAATGCAGTTACTCAGA------CACAGTCTGTGTCTTACAAGACT -s Anc1.Anc1refChr2 25260 55 - 144309 AATGAGTTGTTCCA-----------------------------------------------CAAATGCAGTTACTCAGA------CACAGTCTGTGTCTTACAAGACT -s Anc2.Anc2refChr3 24178 55 - 53186 AATGAGTTGTTCCA-----------------------------------------------TAAATGCAGTTACTCAGA------CACAGCCTGTGTCTTACAAGACT -s mr.mrrefChr5 47380 108 + 294540 AATGTGTTGCTGCATCCGTTGTGGGAGCAGATTTAAGCTGATGACCGCTCCTGTTATATACCAATTACAGTTACTCAGATTCAGGCACAGTCTGACTCTTTCAAGACT -s simCow_chr6.simCow.chr6 445413 55 - 602619 AATAAATTGCTCCA-----------------------------------------------TAAACGTAGTTACTCAGA------CACAGCCTGTGCCTTACAAGACT -s simDog_chr6.simDog.chr6 153152 55 + 593897 AATGAGTTGTTCCA-----------------------------------------------TAAATGCAGTTACTCTAA------CACAGCCTGAGTCTTACAAGACT -s simHuman_chr6.simHuman.chr6 457981 55 - 601863 AATGATATGTTACA-----------------------------------------------CAAAAGCAGTTACTCAGA------CCCAGTCTGTGTCATACACAACT -s simRat_chr6.simRat.chr6 182680 108 + 647215 AATGTGTTGCTGCATCTGTCCTGTGAGCAAATTTTAGCTGATGGCCACTCCTGTTATAAACCAATTAAAGTTACTCGGACTCAGGCACAGACTGACTCTTTCAAGACT - -a -s simMouse_chr6.simMouse.chr6 192604 30 + 636262 TCTTCTAGACAACATACCTCTCCTAAAGTC -s Anc0.Anc0refChr1 22677 28 + 62388 GCTTCTATACAACATATCCCAACTAAGG-- -s Anc1.Anc1refChr2 25315 30 - 144309 GCTTCTATACAACATATCCCAACTAAGGTC -s Anc2.Anc2refChr3 24233 28 - 53186 GCTTCTATACAACATTTCCCAACTAAGG-- -s mr.mrrefChr5 47488 30 + 294540 GCTTCTAGACAACATACCTCTCCTAAAGTC -s simCow_chr6.simCow.chr6 445499 28 - 602619 GCTTCTATTCAACATTTCCCAACTAAGG-- -s simDog_chr6.simDog.chr6 153207 28 + 593897 GCTTTTGTACAGCATTTCCCAACTAAGG-- -s simHuman_chr6.simHuman.chr6 458036 30 - 601863 GTTTCTATACAACGGATCCCAATTAAGGTC -s simRat_chr6.simRat.chr6 182788 30 + 647215 GCTTCTAAAGAACATACATCTCCTAAAATC - -a -s simMouse_chr6.simMouse.chr6 192634 24 + 636262 CTAAGATGGGTGTATGATGAAAGG -s Anc0.Anc0refChr1 22706 24 + 62388 CTAGGATGGGTGTTTGAGGAGAGG -s Anc1.Anc1refChr2 25347 24 - 144309 CTAGGATGGGTGTTTGAGGAGAGG -s Anc2.Anc2refChr3 24262 24 - 53186 CTAGGATGGGTGTTTGAGGAGAGG -s mr.mrrefChr5 47535 24 + 294540 CTAAGATGGGTGTATGATGAAAGG -s simCow_chr6.simCow.chr6 445528 24 - 602619 ATAGGATGGGTGTTTGAGGCCAGG -s simDog_chr6.simDog.chr6 153236 24 + 593897 CTAGGATGAGTATTTGAGGAGCAT -s simRat_chr6.simRat.chr6 182835 24 + 647215 TTAAGATGGGTGTACGAAGAAAGG - -a -s simMouse_chr6.simMouse.chr6 192658 129 + 636262 ACACAGAAGTATAGCCCTGCCATAGCACATTAGGTGCAATCAGGTGTAGGGAGATTGTTGGTAAGTGTCCTGGGGCACCACTGTAGCCCGTAATGACTTGCCCAGTTGGCTGGCACACAGTGGATATTG -s Anc0.Anc0refChr1 22730 109 + 62388 GTAAAAAAGCATAGACCTGCCGTAGCTCATTAGCTGCTATGGTGGTTAGTGGGACTGTTGGCAAGTAGTCTGAT-TACCACTGTAGGCCGTAATGAAC-------------------CAGTGAATATTC -s Anc1.Anc1refChr2 25371 109 - 144309 GTAAAAAAGCATAGACCTGCCGTAGCTCATTAGCTGCTATGGTGGTTAGTGGGACTGTTGGCAAGTAGTCTGAT-TACCACTGTAGGCCGTAATGAAC-------------------CAGTGAATATTC -s Anc2.Anc2refChr3 24286 109 - 53186 GTAAAAAAGCATAGACCTGCCGTAGCTCATTAGCTGCTATGGTGGTTAGTGGGACTGTTGGCAAGTAGTCTGAT-TACCACTGTAGGCCGTAATGAAC-------------------CAGTGAATATTC -s mr.mrrefChr5 47559 129 + 294540 ACACAAAAGTATAGCCCTGCTGTAGCACATTAGGTGCAATCATGTGTAGGGAGATTGTTGGTAAGTGTCCTGGGGTACCACTGTAGCCCATAATGACTTGCCCAGTTGGCTGGCACACAGTGGATATTG -s simCow_chr6.simCow.chr6 445554 107 - 602619 GTAAAAAAGCACAA--CTACCGTAACTCATTAGCGGCTATAGTGATCTGTGGAACCATTGACAAGTAGTTTGAC-AACCATTGTAGGCCGTAATGAAC-------------------CAATCAATAATG -s simDog_chr6.simDog.chr6 153260 109 + 593897 GTGAAAGAACATGGACCGGCTGTAGCTCATTAACTGCTATGGTAGTTAGTGGGACTGTTGGCAAGCAGTCTGAT-TACCGCTGTAGGCCATAATGAAC-------------------CAGTGAATATTC -s simRat_chr6.simRat.chr6 182859 121 + 647215 ACACAAAAGTA--------CTGTACCACATTAGGTACAATCATGTGTAGGGAGATTATTGGTGAGTGTCCTGGGCTACCACTGTAGCCCATAATGACTTGCCCAGCTGGCTGACACACAGTGGATATTG - -a -s simMouse_chr6.simMouse.chr6 192787 21 + 636262 GTTAATTTAAGCGCGCGACGG -s Anc0.Anc0refChr1 22844 13 + 62388 GGGAA--------CACAATGG -s Anc1.Anc1refChr2 25485 13 - 144309 GGGAA--------CACAATGG -s Anc2.Anc2refChr3 24400 13 - 53186 GGGAA--------CACAATGG -s mr.mrrefChr5 47693 21 + 294540 GTGAATTTAAGCGCGCGATGG -s simCow_chr6.simCow.chr6 445666 13 - 602619 TGGAA--------CACAAATG -s simDog_chr6.simDog.chr6 153374 13 + 593897 GGGAA--------CACAATGG -s simRat_chr6.simRat.chr6 182985 20 + 647215 GTGAACATAAATGTTCTATG- - -a -s simMouse_chr6.simMouse.chr6 192808 14 + 636262 ACTAATGAAGGGTT -s Anc0.Anc0refChr1 22857 14 + 62388 CCTGGACAATAATT -s Anc1.Anc1refChr2 25498 14 - 144309 CCTGGACAATAATT -s Anc2.Anc2refChr3 24421 14 - 53186 CCTGGACAATAATT -s mr.mrrefChr5 47714 14 + 294540 ACTGATCAATAATT -s simCow_chr6.simCow.chr6 445687 14 - 602619 CCTGGACAATTATT -s simDog_chr6.simDog.chr6 153395 14 + 593897 CCTGGTCAATAATT -s simRat_chr6.simRat.chr6 183005 13 + 647215 -CTGATCAATAATC - -a -s simMouse_chr6.simMouse.chr6 192822 13 + 636262 AGATGTGAACATA -s Anc0.Anc0refChr1 22871 2 + 62388 A--C--------- -s Anc1.Anc1refChr2 25512 2 - 144309 A--C--------- -s Anc2.Anc2refChr3 24435 2 - 53186 A--C--------- -s mr.mrrefChr5 47728 11 + 294540 A--TGTGAACATA -s simCow_chr6.simCow.chr6 445713 2 - 602619 A--C--------- -s simDog_chr6.simDog.chr6 153409 2 + 593897 A--C--------- -s simRat_chr6.simRat.chr6 183018 11 + 647215 A--TCCAGACACC - -a -s simMouse_chr6.simMouse.chr6 192835 77 + 636262 AATGCAATCTAACCTACCAATCTACATATCCCAAGAGGAGTGCTGCCCAGAAAGTCTCCAAAAAACAATAGGAAAAA -s Anc0.Anc0refChr1 22873 70 + 62388 -------TTCAACCTACCAATCTACATATCCCAAAGGGAGTGTTGCCCAATAAGTTTCCAGAAAACCATTAAAGAAA -s Anc1.Anc1refChr2 25514 70 - 144309 -------TTCAACCTACCAATCTACATATCCCAAAGGGAGTGTTGCCCAATAAGTTTCCAGAAAACCATTAAAGAAA -s Anc2.Anc2refChr3 24437 70 - 53186 -------TTCAACCTACCAATCTACATATCCCAAAGGGAGTGTTGCCCAATAAGTTTCCAGAAAACCATTAAAGAAA -s mr.mrrefChr5 47739 77 + 294540 AATGCAATCCAACCTACCAATCTACATATCCCAAGAGGAGTGCTGCCCAGTAAGTCTCCAGAAAACAATAGGAAAAA -s simCow_chr6.simCow.chr6 445715 63 - 602619 -------TTCATCCTACCAAGCTACGTTTCTCAA-------GTCACCCAATAAGTTCCCAGAAAACTATTAAAGAAA -s simDog_chr6.simDog.chr6 153411 70 + 593897 -------TTCAACCTACCAATCTAAATATCCCAAAGGGAGTGTTGCCCAATAAGTTTCTAGAAAAGCATTAAGGAAA -s simRat_chr6.simRat.chr6 183030 73 + 647215 AGTGCAATCCAATCTACAAATCTACATAT----AGAGGAGTGCTTCCGAGTAAGTCTCCAGAAAACAATAGGAAAAA - -a -s simMouse_chr6.simMouse.chr6 192912 16 + 636262 TTCACGTATTGTTCTG -s Anc0.Anc0refChr1 22943 16 + 62388 TCCATGCATTATTCTG -s Anc1.Anc1refChr2 25584 16 - 144309 TCCATGCATTATTCTG -s Anc2.Anc2refChr3 24507 16 - 53186 TCCATGCATTATTCTG -s mr.mrrefChr5 47816 16 + 294540 TCCATGTATTATTCTG -s simCow_chr6.simCow.chr6 445779 16 - 602619 TCCATGCATTACTGAA -s simDog_chr6.simDog.chr6 153481 16 + 593897 TCCATGCATTATGCTG -s simRat_chr6.simRat.chr6 183103 16 + 647215 TCCGTATATTATTGCA - -a -s simMouse_chr6.simMouse.chr6 192928 45 + 636262 TTTGTTTGGTCTGTCACACATAAGTGGCTCAAAATACTAGTTTAA -s Anc0.Anc0refChr1 22959 44 + 62388 TTTGTATGATTATTCACATAAAGGTAGCTATAATTACTAGTA-AA -s Anc1.Anc1refChr2 25600 44 - 144309 TTTGTATGATTATTCACATAAAGGTAGCTATAATTACTAGTA-AA -s Anc2.Anc2refChr3 24523 44 - 53186 TTTGTATGATTATTCACATAAAGGTAGCTATAATTACTAGTA-AA -s mr.mrrefChr5 47832 45 + 294540 TTTATTTGGTTTCTCACACATAGGTGGCCCAAAATACTAGTTTAA -s simCow_chr6.simCow.chr6 445795 44 - 602619 CTCATCTGATTATACACATACAGGTAGTTAGAAGTACTAGTG-AA -s simDog_chr6.simDog.chr6 153498 38 + 593897 TGTGTAC------TCACCTAAAGGTAGCCATAATTAGTAGTA-AA -s simRat_chr6.simRat.chr6 183119 45 + 647215 ATTATTTGGTTTCCCATACATGGGTGGCCTAAAATACTAGTTTAA - -a -s simMouse_chr6.simMouse.chr6 192973 19 + 636262 GGGGACACCGGCTCTGGTG -s Anc0.Anc0refChr1 23003 19 + 62388 GGGGACGCCTGCTTAGGGG -s Anc1.Anc1refChr2 25644 19 - 144309 GGGGACGCCTGCTTAGGGG -s Anc2.Anc2refChr3 24567 19 - 53186 GGGGATGCCTGCTTAGGGG -s mr.mrrefChr5 47877 19 + 294540 GGGGACACCTGCTCAGGTG -s simCow_chr6.simCow.chr6 445842 19 - 602619 GGGGATGTCTACTTGGGGG -s simDog_chr6.simDog.chr6 153536 19 + 593897 GGGGATGCCTGCTTAGGGG -s simHuman_chr6.simHuman.chr6 458067 17 - 601863 --GGTCGCCTGCTTAGAAG -s simRat_chr6.simRat.chr6 183164 19 + 647215 GGGGACACCTGCACAAGTG - -a -s simMouse_chr6.simMouse.chr6 192992 30 + 636262 CTCTTCAGGGATAGAAATATTCCCAGTCCC -s Anc0.Anc0refChr1 23022 26 + 62388 A-TCTTGGGTATAGAAATGTTCCCAGT--- -s Anc1.Anc1refChr2 25663 27 - 144309 ATTCTTGGGTATAGAAATGTTCCCAGT--- -s Anc2.Anc2refChr3 24586 26 - 53186 A-TCTTGGGTATAGACATGTTCCCAAT--- -s mr.mrrefChr5 47896 30 + 294540 CTCTTCAGGGATAGAAATATTCCCAGTCCC -s simCow_chr6.simCow.chr6 445863 25 - 602619 A-TCTTGAATAACGGGTTGTTCCCA-T--- -s simDog_chr6.simDog.chr6 153555 26 + 593897 A-TCTTGGGTATAGACATGTTCCCAAC--- -s simHuman_chr6.simHuman.chr6 458084 27 - 601863 TTTCTTGGGTATAGAAATGTTCCAAGT--- -s simRat_chr6.simRat.chr6 183183 30 + 647215 GCCTTCAGGAACAGAGATATTTCCGGTCCC - -a -s simMouse_chr6.simMouse.chr6 193022 4 + 636262 AGCT -s Anc0.Anc0refChr5 15885 4 + 87904 AACT -s Anc1.Anc1refChr8 29442 4 + 57822 AACT -s Anc2.Anc2refChr15 9459 4 + 86568 AACT -s mr.mrrefChr5 47926 4 + 294540 AGCT -s simCow_chr6.simCow.chr6 192591 4 + 602619 AACT -s simDog_chr6.simDog.chr6 120049 4 + 593897 AACT -s simHuman_chr6.simHuman.chr6 196529 4 + 601863 ACCT -s simRat_chr6.simRat.chr6 183213 4 + 647215 AGCT - -a -s simMouse_chr6.simMouse.chr6 193026 4 + 636262 TTTG -s Anc0.Anc0refChr5 15889 4 + 87904 ACTG -s Anc1.Anc1refChr8 29446 4 + 57822 ACTG -s Anc2.Anc2refChr15 9463 4 + 86568 ACTG -s mr.mrrefChr5 47930 4 + 294540 TTTG -s simCow_chr6.simCow.chr6 192598 4 + 602619 GTTG -s simDog_chr6.simDog.chr6 120053 4 + 593897 ACTG -s simHuman_chr6.simHuman.chr6 196533 4 + 601863 ACTG -s simRat_chr6.simRat.chr6 183217 4 + 647215 TTTG - -a -s simMouse_chr6.simMouse.chr6 193030 11 + 636262 AAAAACAGTGA -s Anc0.Anc0refChr5 15893 11 + 87904 GAACTCAGTGA -s Anc1.Anc1refChr8 29450 11 + 57822 GAACTCAGTGA -s Anc2.Anc2refChr15 9467 11 + 86568 GAACTGAGCGA -s mr.mrrefChr5 47934 11 + 294540 AAAAACAGTGA -s simCow_chr6.simCow.chr6 192602 11 + 602619 GGACCGAGCGA -s simDog_chr6.simDog.chr6 120061 11 + 593897 AAACTGAACAA -s simHuman_chr6.simHuman.chr6 196537 11 + 601863 GAACTCAGTGG -s simRat_chr6.simRat.chr6 183221 11 + 647215 AAAAACAGTTA - -a -s simMouse_chr6.simMouse.chr6 193041 23 + 636262 TATCTCAGAGGCTGTATCAATGC -s Anc0.Anc0refChr5 15909 23 + 87904 TATCATAGAGGCTGTATCAATGC -s Anc1.Anc1refChr8 29466 23 + 57822 TATCATAGAGGCTGTATCAATGC -s Anc2.Anc2refChr15 9483 23 + 86568 TATCATAGAGGTTGTATCAATGC -s mr.mrrefChr5 47945 23 + 294540 TATCTCAGAGGCTGTATCAATGC -s simCow_chr6.simCow.chr6 192618 23 + 602619 TATCATATAGGTTGTATTAATGC -s simDog_chr6.simDog.chr6 120077 23 + 593897 CATCAGAGATGTTGAATCAATAC -s simHuman_chr6.simHuman.chr6 196553 23 + 601863 TATTATAGAGGCTATGTCAATGC -s simRat_chr6.simRat.chr6 183232 23 + 647215 TATCTTAGAGGCTGTATCAATGC - -a -s simMouse_chr6.simMouse.chr6 193064 20 + 636262 TGGCATTCACGGCTATGACT -s Anc0.Anc0refChr5 15937 14 + 87904 T-----TCACAG-TATGACT -s Anc1.Anc1refChr8 29494 15 + 57822 T-----TCACAGCTATGACT -s Anc2.Anc2refChr15 9511 14 + 86568 T-----TCACAG-TATGACT -s mr.mrrefChr5 47968 15 + 294540 T-----TCACGGCTATGACT -s simCow_chr6.simCow.chr6 192646 9 + 602619 T-----TCACAG------CT -s simDog_chr6.simDog.chr6 120105 14 + 593897 T-----CCACAG-TATGACT -s simHuman_chr6.simHuman.chr6 196581 15 + 601863 T-----TCATAGCTATGACC -s simRat_chr6.simRat.chr6 183255 15 + 647215 T-----TCATGTCTATGACT - -a -s simMouse_chr6.simMouse.chr6 193084 3 + 636262 GTG -s Anc0.Anc0refChr5 15951 3 + 87904 GTG -s Anc1.Anc1refChr8 29509 3 + 57822 GTG -s Anc2.Anc2refChr15 9525 3 + 86568 ATG -s mr.mrrefChr5 47983 3 + 294540 GTG -s simCow_chr6.simCow.chr6 192655 3 + 602619 ATG -s simDog_chr6.simDog.chr6 120119 3 + 593897 ATG -s simHuman_chr6.simHuman.chr6 196597 3 + 601863 GTG -s simRat_chr6.simRat.chr6 183270 3 + 647215 ATA - -a -s simMouse_chr6.simMouse.chr6 193087 5 + 636262 GGTTT -s Anc0.Anc0refChr5 15960 5 + 87904 GGTTT -s Anc1.Anc1refChr8 29518 5 + 57822 GGTTT -s Anc2.Anc2refChr15 9534 5 + 86568 GGTTT -s mr.mrrefChr5 47986 5 + 294540 GGTTT -s simCow_chr6.simCow.chr6 192664 5 + 602619 GGTCT -s simDog_chr6.simDog.chr6 120128 5 + 593897 GATTT -s simHuman_chr6.simHuman.chr6 196606 5 + 601863 GGTTT -s simRat_chr6.simRat.chr6 183273 5 + 647215 GGTTC - -a -s simMouse_chr6.simMouse.chr6 193092 1 + 636262 G -s Anc0.Anc0refChr5 15976 1 + 87904 A -s Anc1.Anc1refChr8 29534 1 + 57822 A -s Anc2.Anc2refChr15 9550 1 + 86568 A -s mr.mrrefChr5 47991 1 + 294540 G -s simCow_chr6.simCow.chr6 192680 1 + 602619 G -s simDog_chr6.simDog.chr6 120144 1 + 593897 A -s simHuman_chr6.simHuman.chr6 196622 1 + 601863 A -s simRat_chr6.simRat.chr6 183278 1 + 647215 G - -a -s simMouse_chr6.simMouse.chr6 193093 27 + 636262 GGAAAGTCTTACCTCTCAAAAATTTGG -s Anc0.Anc0refChr5 15977 24 + 87904 AGAAAGTCT---CTCTCCAGAGATTGG -s Anc1.Anc1refChr8 29535 24 + 57822 AGAAAGTCT---CTCTCCAGAGATTGG -s Anc2.Anc2refChr15 9551 24 + 86568 AGAACGTCT---TCCTTCAGAGATTGG -s mr.mrrefChr5 47992 27 + 294540 GGAAAGTCTTACCTCTCAAAAATTTGG -s simCow_chr6.simCow.chr6 192681 24 + 602619 AGAATGTCT---AACTTCAAAGATGGG -s simDog_chr6.simDog.chr6 120145 24 + 593897 AGAACATCC---TCCTTGAGACATTGG -s simHuman_chr6.simHuman.chr6 196623 24 + 601863 AGAAAGTTT---CTCCCCAGAGATTTG -s simRat_chr6.simRat.chr6 183290 27 + 647215 GGACAGTCTTACCTCTCAAAAATTTGG - -a -s simMouse_chr6.simMouse.chr6 193120 12 + 636262 GTAAGCATAAGG -s Anc0.Anc0refChr5 16001 12 + 87904 GCCAGAATGAGG -s Anc1.Anc1refChr8 29559 12 + 57822 GCCAGAATGAGG -s Anc2.Anc2refChr15 9576 12 + 86568 GCCAGAATGAGG -s mr.mrrefChr5 48019 12 + 294540 GTAAGCATAAGG -s simCow_chr6.simCow.chr6 192706 12 + 602619 GCCAGAATGAGG -s simDog_chr6.simDog.chr6 120170 11 + 593897 GCCAGAATGA-G -s simHuman_chr6.simHuman.chr6 196647 12 + 601863 GCCAGTATGAGG -s simRat_chr6.simRat.chr6 183317 12 + 647215 GTCAGCATGAAG - -a -s simMouse_chr6.simMouse.chr6 193132 19 + 636262 ACTCTATGAGAATGATTGC -s Anc0.Anc0refChr5 16013 18 + 87904 AC-CTATGAAAAAGACTGT -s Anc1.Anc1refChr8 29571 18 + 57822 AC-CTATGAAAAAGACTGT -s Anc2.Anc2refChr15 9588 18 + 86568 AC-CTATGAAAAAGACTGT -s mr.mrrefChr5 48031 19 + 294540 ACTCTATGAGAATGATTGC -s simCow_chr6.simCow.chr6 192719 18 + 602619 AC-CTATCACAAAGACTGT -s simDog_chr6.simDog.chr6 120181 18 + 593897 AC-CTATGAAAAATGCTGT -s simHuman_chr6.simHuman.chr6 196659 18 + 601863 AC-CTAAGAAAAAGACTGT -s simRat_chr6.simRat.chr6 183329 19 + 647215 AAACTATGAGAATGACTTC - -a -s simMouse_chr6.simMouse.chr6 193151 67 + 636262 TTTTCTGATGTAGGAGTGGGGCCACCTCCCTACTAAGTCTGGAATGCAGCACATACATCCTCATCTA -s Anc0.Anc0refChr5 16033 57 + 87904 TTCTCTGATGTAGTACT--------T-CCCACATAAGT-TGGCATGCAGCTCTCACATCCTTACCTA -s Anc1.Anc1refChr8 29591 59 + 57822 TTCTCTGATGTAGTACT--------TTCCCACATAAGTCTGGCATGCAGCTCTCACATCCTTACCTA -s Anc2.Anc2refChr15 9608 57 + 86568 CTCTCTGATGTAGTACT--------T-CCCACATTAGT-TGGCATGCAGCTCTCACATCCTTACCTA -s mr.mrrefChr5 48050 67 + 294540 TTTTCTGATGTAGGAGTGGGGCCACCTCCCTACTAAGTCTGGAATGCAGCACATACATCCTCATCTA -s simCow_chr6.simCow.chr6 192739 56 + 602619 -TCTCTAATGTAGGACC--------T-CCCACATTAGT-TGGCATGCAACTCTTGCATCCTTACCTA -s simDog_chr6.simDog.chr6 120201 36 + 593897 CTCTCTGATGTAGTGCT-------------------------------GCCCCCATAAGCCTGCTTA -s simHuman_chr6.simHuman.chr6 196679 59 + 601863 TTCTCTGAGGTGGTACT--------TTGCCCCATAGGTCTAGTATGTGGCTCTCACATCCTTACCTA -s simRat_chr6.simRat.chr6 183348 67 + 647215 TTTTCAGATGTAGGAGTGGAGCCATCTCCCTTGTAAGTTTGGTACGCAGCACTTATGTCCTCCTCTA - -a -s simMouse_chr6.simMouse.chr6 193218 10 + 636262 TTAGGCATAA -s Anc0.Anc0refChr5 16090 10 + 87904 TTAGGAATGA -s Anc1.Anc1refChr8 29650 10 + 57822 TTAGGAATGA -s Anc2.Anc2refChr15 9665 10 + 86568 TTAGGACTGA -s mr.mrrefChr5 48117 10 + 294540 TTAGGCATAA -s simCow_chr6.simCow.chr6 192797 10 + 602619 TTAGGATCAA -s simDog_chr6.simDog.chr6 120237 10 + 593897 TTAGCACTGA -s simHuman_chr6.simHuman.chr6 196738 10 + 601863 TCAGGTATGA -s simRat_chr6.simRat.chr6 183415 10 + 647215 TTAGGTATAA - -a -s simMouse_chr6.simMouse.chr6 193228 10 + 636262 AAAGGGGGTG -s Anc0.Anc0refChr5 16101 10 + 87904 AAATGGTGTG -s Anc1.Anc1refChr8 29661 10 + 57822 AAATGGTGTG -s Anc2.Anc2refChr15 9676 10 + 86568 AAATGGTGTA -s mr.mrrefChr5 48127 10 + 294540 AAAGGGGGTG -s simCow_chr6.simCow.chr6 192808 10 + 602619 CAATTGTGTA -s simDog_chr6.simDog.chr6 120248 10 + 593897 AATTGGAGTA -s simHuman_chr6.simHuman.chr6 196749 10 + 601863 AAATGGTGTG -s simRat_chr6.simRat.chr6 183426 10 + 647215 AAAGGGGGTC - -a -s simMouse_chr6.simMouse.chr6 193238 11 + 636262 GTTCTGCATGA -s Anc0.Anc0refChr5 16111 9 + 87904 TTT--GACTGG -s Anc1.Anc1refChr8 29671 9 + 57822 TTT--GACTGG -s Anc2.Anc2refChr15 9686 9 + 86568 TGT--GACAGG -s mr.mrrefChr5 48137 11 + 294540 GTTCTGCATGA -s simCow_chr6.simCow.chr6 192820 9 + 602619 TGT--AAAAGA -s simDog_chr6.simDog.chr6 120258 9 + 593897 TGT--GACAGG -s simHuman_chr6.simHuman.chr6 196759 9 + 601863 ATT--GATTGG -s simRat_chr6.simRat.chr6 183436 11 + 647215 TCTCTGCATGA - -a -s simMouse_chr6.simMouse.chr6 193249 42 + 636262 CTAAGGGCAAATACTTCTAGCTCTTTATATTTGGTGAAGTAG -s Anc0.Anc0refChr5 16120 42 + 87904 CCAAGGGCAAATATCTCTACTACTTTATGTGTGGAGAAGTAG -s Anc1.Anc1refChr8 29680 42 + 57822 CCAAGGGCAAATATCTCTACTACTTTATGTGTGGAGAAGTAG -s Anc2.Anc2refChr15 9700 42 + 86568 CCTAGGGCAAATATCTCTACTAAGTTATGTGTGGAGAAGTAG -s mr.mrrefChr5 48148 42 + 294540 CTAAGGGCAAATACTTCTAGCTCTTTATATTTGGTGAAGTAG -s simCow_chr6.simCow.chr6 192834 42 + 602619 GTTAGGGCAGATACCTCTACCGACTTATGTGTGGAGAACTAG -s simDog_chr6.simDog.chr6 120272 41 + 593897 CCAAAAGCAAATATCTCTACTA-GTTATGTGTGGAGTGGTGG -s simHuman_chr6.simHuman.chr6 196768 31 + 601863 CCAA-----------TCTATTACTTTATGTGTGGAGAAGTAG -s simRat_chr6.simRat.chr6 183447 42 + 647215 CTCAGGGCAGATACTTCTACCTCTTTATATTTGGTGAAGCAG - -a -s simMouse_chr6.simMouse.chr6 193291 100 + 636262 AGACCTCTGTTTTATTTTATCAATCTACATTTGGTCTAAGCCTCAGCAGCCCTAATAACCCTTTGGGCTGGGGACATGGAACCATTATGTCATGGCTTCA -s Anc0.Anc0refChr5 16162 43 + 87904 ACACCTCAGTTTTATTTTA--------------------------------------------------------ATGGTGTA-TTATGTCAGGGGTTCA -s Anc1.Anc1refChr8 29722 43 + 57822 ACACCTCAGTTTTATTTTA--------------------------------------------------------ATGGTGTA-TTATGTCAGGGGTTCA -s Anc2.Anc2refChr15 9742 43 + 86568 ACACCTCAGTTTTATTTTA--------------------------------------------------------TTGGTGTA-TTATGCCAGGGGTTCA -s mr.mrrefChr5 48190 99 + 294540 AGACCTCTGTTTTATTTTATCAATCTACATTTGGTCTAAGCCTCAGCAGCCCTAATAACCCTTTGGGCTGGGGACATGGAACC-TTATGTCATGGCTTCA -s simCow_chr6.simCow.chr6 192876 43 + 602619 ACACCTCAGTTTTATTTTA--------------------------------------------------------TTGGTGTA-TTACCCCAGGGGTTCA -s simDog_chr6.simDog.chr6 120313 25 + 593897 ACACCTCAGTTTTA----------------------------------------------------------------GTACA-TCATGC---------- -s simHuman_chr6.simHuman.chr6 196799 43 + 601863 GCACCTGAGCTTTATTTTA--------------------------------------------------------ATGGTGTA-TTATGTCAAGAATGCA -s simRat_chr6.simRat.chr6 183492 99 + 647215 AGACCTCTTTTTTATTTTGTCAATCCACATTTGGTTAACGCCTCAGCAACCCCAATAACCCTTCAAGCTGGGGACATGGAACC-TTATGTCATGGCCTCA - -a -s simMouse_chr6.simMouse.chr6 193391 30 + 636262 CGCAGGTACGAACCTTTCAGGCTACGAATG -s Anc0.Anc0refChr5 16241 12 + 87904 CTCA------------------TAAGAATG -s Anc1.Anc1refChr8 29801 12 + 57822 CTCA------------------TAAGAATG -s Anc2.Anc2refChr15 9821 12 + 86568 CTCA------------------CAAGAATA -s mr.mrrefChr5 48289 12 + 294540 CGCA------------------TACGAATG -s simCow_chr6.simCow.chr6 192955 12 + 602619 CTCA------------------CAAGAATA -s simDog_chr6.simDog.chr6 474418 12 - 593897 CGCA------------------CCAGAATA -s simHuman_chr6.simHuman.chr6 196878 12 + 601863 CTCA------------------TAAGAATG -s simRat_chr6.simRat.chr6 183591 12 + 647215 TGCA------------------CATGTATG - -a -s simMouse_chr6.simMouse.chr6 193421 11 + 636262 AACCTTTCAGG -s Anc0.Anc0refChr5 16259 11 + 87904 AAACCCTTGGG -s Anc1.Anc1refChr8 29819 11 + 57822 AAACCCTTGGG -s Anc2.Anc2refChr15 9839 11 + 86568 AAACCCTTGGA -s mr.mrrefChr5 48301 11 + 294540 AACCTTTCAGG -s simCow_chr6.simCow.chr6 192973 11 + 602619 GTACACTTGGA -s simDog_chr6.simDog.chr6 474436 7 - 593897 AAGCCCT---- -s simHuman_chr6.simHuman.chr6 196896 11 + 601863 AAACCCCTGGG -s simRat_chr6.simRat.chr6 183603 11 + 647215 AACCTTTCAGG - -a -s simMouse_chr6.simMouse.chr6 193432 30 + 636262 TTAATGAAGTGGGAGTACAACTGCTTTACC -s Anc0.Anc0refChr5 16270 30 + 87904 TTTAAGAGGTGGGGGAAGAACTGCTCGGCC -s Anc1.Anc1refChr8 29830 30 + 57822 TTTAAGAGGTGGGGGAAGAACTGCTCGGCC -s Anc2.Anc2refChr15 9850 30 + 86568 TTTCAGAGGTGGGGGAAGAGCTGCTCGGCC -s mr.mrrefChr5 48312 30 + 294540 TTAATGAAGTGGGAGTACAACTGCTTTACC -s simCow_chr6.simCow.chr6 192985 30 + 602619 TTTCAGAGGGTGCAGAAGAGCTGCATGGCC -s simDog_chr6.simDog.chr6 474443 25 - 593897 -----GAGATGGGGGAAGAGTTGCTCGGCC -s simHuman_chr6.simHuman.chr6 196907 30 + 601863 CCGAAGAGGTAGGGGAAGAACTGCTCGGCC -s simRat_chr6.simRat.chr6 183614 30 + 647215 CTTACGAGGTGGGACCACAACTGCTTTACC - -a -s simMouse_chr6.simMouse.chr6 193462 13 + 636262 ATTGTAGGCTTCT -s Anc0.Anc0refChr5 16303 13 + 87904 ATTGTGGGCCTCA -s Anc1.Anc1refChr8 29863 13 + 57822 ATTGTGGGCCTCA -s Anc2.Anc2refChr15 9883 13 + 86568 ATTGTGGGCCTCA -s mr.mrrefChr5 48342 13 + 294540 ATTGTAGGCTTCT -s simCow_chr6.simCow.chr6 193018 13 + 602619 ACTGTTGGCTTCA -s simDog_chr6.simDog.chr6 474471 13 - 593897 ATAATGGGCCTCA -s simHuman_chr6.simHuman.chr6 196940 13 + 601863 ATTGAGGGCACCC -s simRat_chr6.simRat.chr6 183644 13 + 647215 ATTGTAGGCTTCT - -a -s simMouse_chr6.simMouse.chr6 193475 180 + 636262 GTTATTACGGGGTGGAATCTCAAGGGTTTCAAAAACCCCAGGCATTACTCGATCAACTTATATTGTGGGCTTCATCTACTTCAGTCATGACTTTAGCAGGTGTACAAATGCTTTAGGCTCGAGAAGTGGGAGAATAAACTGCTTGGTCTAAACAAGAGGCTTTCAGTTATCATGGGATCA -s Anc0.Anc0refChr5 16316 6 + 87904 TTTATT------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ -s Anc1.Anc1refChr8 29876 6 + 57822 TTTATT------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ -s Anc2.Anc2refChr15 9896 6 + 86568 TTTATT------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ -s mr.mrrefChr5 48355 173 + 294540 GTTATTACGGGGTGGAATCTCAAGGGTTTCAAAAACCCCAGGCATTACTCGATCAACTTATATTGTGGGCTTCATCTACTTCAGTCATGACTTTAGCAGGTGTACAAATGCTTTAGGCTCGAGAAGTGGGAGAATAAACTGCT------AAACAAGAGGCTTTCAGT-ATCATGGGATCA -s simCow_chr6.simCow.chr6 193031 6 + 602619 TTTATT------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ -s simDog_chr6.simDog.chr6 474485 6 - 593897 TTTATT------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ -s simHuman_chr6.simHuman.chr6 196953 6 + 601863 TTAATT------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ -s simRat_chr6.simRat.chr6 183657 173 + 647215 GCTATTATGGGGTGGAATCTCAAAGGTTTGAAAAGCCCCAAGAATTACTTGATCAACTCATATTGTGGGCTTCATTTACTTCAGTCATGACTCCAGCAGGTGTACGAACTCTTTAGGCTAGAGAAGTGGGAGAGAAAACTGCT------AAATAATAGGCTTTCAGT-ATTATGGGATCA - -a -s simMouse_chr6.simMouse.chr6 193655 21 + 636262 ATCTCAAAAGCTGCAGGAATT -s mr.mrrefChr5 48528 21 + 294540 ATCTCAAAAGCTGCAGGAATT -s simRat_chr6.simRat.chr6 183835 21 + 647215 ATCTCAAAAGCTGCAGGTATT - -a -s simMouse_chr6.simMouse.chr6 193676 36 + 636262 CTCGCTTGGCTACCTATATTGTGTGTTGGCTTTTCG -s Anc0.Anc0refChr5 16322 2 + 87904 ----------------------------------TT -s Anc1.Anc1refChr8 29882 2 + 57822 ----------------------------------TT -s Anc2.Anc2refChr15 9902 2 + 86568 ----------------------------------TT -s mr.mrrefChr5 48549 27 + 294540 CTCGCTTGGCTAC---------GTGTTGGCTTTTCG -s simCow_chr6.simCow.chr6 193037 2 + 602619 ----------------------------------TT -s simDog_chr6.simDog.chr6 474491 2 - 593897 ----------------------------------TT -s simHuman_chr6.simHuman.chr6 196959 2 + 601863 ----------------------------------TA -s simRat_chr6.simRat.chr6 183857 27 + 647215 CTTGCTTGGCTAA---------GAGTGGGCTTTTCA - -a -s simMouse_chr6.simMouse.chr6 193712 16 + 636262 GGGTGCTATCTGAAAG -s Anc0.Anc0refChr5 16324 16 + 87904 GGGTGGTATCTCAAAG -s Anc1.Anc1refChr8 29884 16 + 57822 GGGTGGTATCTCAAAG -s Anc2.Anc2refChr15 9905 16 + 86568 GGGTGGGATCTCAAAG -s mr.mrrefChr5 48576 16 + 294540 GGGTGCTATCTGAAAG -s simCow_chr6.simCow.chr6 193040 16 + 602619 AGGTGGGATCTCAAAG -s simDog_chr6.simDog.chr6 474494 16 - 593897 GGGTCGGATTTCAAAG -s simHuman_chr6.simHuman.chr6 196961 16 + 601863 GTGTGGTATCTCAAAG -s simRat_chr6.simRat.chr6 183884 16 + 647215 GGGTGCTATCTGAAAG - -a -s simMouse_chr6.simMouse.chr6 193728 19 + 636262 CTTGCAGCATCAGGAATTG -s Anc0.Anc0refChr5 16342 18 + 87904 CTCAAAGCCTCAGGA-ATG -s Anc1.Anc1refChr8 29902 18 + 57822 CTCAAAGCCTCAGGA-ATG -s Anc2.Anc2refChr15 9923 18 + 86568 CTCAAAGCCTCAGGA-ATG -s mr.mrrefChr5 48592 18 + 294540 CTTGCAGCATCAGGA-TTG -s simCow_chr6.simCow.chr6 193058 18 + 602619 CTCAAAGACATAAGA-ATC -s simDog_chr6.simDog.chr6 474512 18 - 593897 CACAAAGCCTCAGGG-ATG -s simHuman_chr6.simHuman.chr6 196979 18 + 601863 CTCAAAGCCTCGGAA-ATG -s simRat_chr6.simRat.chr6 183900 18 + 647215 GTTGCAGCATCATGA-TTG - -a -s simMouse_chr6.simMouse.chr6 193747 27 + 636262 ATGATGTCTTCCATGTGAATCAACATA -s Anc0.Anc0refChr5 16361 27 + 87904 ATGAGGTGTTCCATGTGAATCAAGATA -s Anc1.Anc1refChr8 29921 27 + 57822 ATGAGGTGTTCCATGTGAATCAAGATA -s Anc2.Anc2refChr15 9942 27 + 86568 ATGAGATGTTCCCTGTAAATCAAGATA -s mr.mrrefChr5 48610 27 + 294540 ATGATGTCTTCCATGTGAATCAACATA -s simCow_chr6.simCow.chr6 193077 26 + 602619 ATGCAA-GTTCCCTGTTAAACCAGATA -s simDog_chr6.simDog.chr6 474531 22 - 593897 ATGAGATTT-----GTAAATAAAGATA -s simHuman_chr6.simHuman.chr6 196998 27 + 601863 ATGAGGTGTTCCATATGAATCAAGACA -s simRat_chr6.simRat.chr6 183918 27 + 647215 ATAAGGTCTTCCATGTGAATCAACATG - -a -s simMouse_chr6.simMouse.chr6 193774 8 + 636262 TTATGAAC -s Anc0.Anc0refChr5 16414 6 + 87904 --ATGTAG -s Anc1.Anc1refChr8 29974 8 + 57822 TCATGTAG -s Anc2.Anc2refChr15 9995 6 + 86568 --ATATGG -s mr.mrrefChr5 48637 8 + 294540 TTATGAAC -s simCow_chr6.simCow.chr6 193122 6 + 602619 --ATATGG -s simHuman_chr6.simHuman.chr6 197055 8 + 601863 TCATGTAG -s simRat_chr6.simRat.chr6 183945 8 + 647215 TTATGCAG - -a -s simMouse_chr6.simMouse.chr6 193782 22 + 636262 ACTTTTGAAACTTGAGGTGAAT -s Anc0.Anc0refChr5 16420 22 + 87904 ATTTTAGAGACCCGAAGTGAAC -s Anc1.Anc1refChr8 29982 22 + 57822 ATTTTAGAGACCCGAAGTGAAC -s Anc2.Anc2refChr15 10001 22 + 86568 ATCTCAGAGCCCCGAAGTGAAC -s mr.mrrefChr5 48645 22 + 294540 ACTTTTGAAACTTGAGGTGAAT -s simCow_chr6.simCow.chr6 193129 22 + 602619 ATCTCAGATGCCCAATGTGAAC -s simDog_chr6.simDog.chr6 474565 14 - 593897 --------GCACTGAAGTAGAC -s simHuman_chr6.simHuman.chr6 197063 22 + 601863 ATTTTAGAGACCCGAAGTGAAC -s simRat_chr6.simRat.chr6 183953 22 + 647215 ACTTTTCAAATATAATGTGGAC - -a -s simMouse_chr6.simMouse.chr6 193804 7 + 636262 ATGCACA -s Anc0.Anc0refChr5 16442 7 + 87904 ATGCACA -s Anc1.Anc1refChr8 30004 7 + 57822 ATGCACA -s Anc2.Anc2refChr15 10023 7 + 86568 ATGCACA -s mr.mrrefChr5 48667 7 + 294540 ATGCACA -s simCow_chr6.simCow.chr6 193166 7 + 602619 ATGCACA -s simDog_chr6.simDog.chr6 474579 7 - 593897 ATGTACA -s simHuman_chr6.simHuman.chr6 197085 7 + 601863 ATGCACA -s simRat_chr6.simRat.chr6 183975 7 + 647215 ATGCACA - -a -s simMouse_chr6.simMouse.chr6 193811 9 + 636262 CACCATTAC -s Anc0.Anc0refChr5 16449 9 + 87904 ACTGAAGGC -s Anc1.Anc1refChr8 30011 9 + 57822 ACTGAAGGC -s Anc2.Anc2refChr15 10030 9 + 86568 ACTGAAGGC -s mr.mrrefChr5 48674 9 + 294540 CACCATTAC -s simCow_chr6.simCow.chr6 193175 9 + 602619 GCTCAACGC -s simDog_chr6.simDog.chr6 474594 9 - 593897 ACTGCAGGC -s simHuman_chr6.simHuman.chr6 197092 5 + 601863 ACTGA---- -s simRat_chr6.simRat.chr6 183982 9 + 647215 CACCATTAC - -a -s simMouse_chr6.simMouse.chr6 193820 14 + 636262 GAAGGTTCTCCTTA -s Anc0.Anc0refChr5 16458 14 + 87904 TAATGTTCTCCTTA -s Anc1.Anc1refChr8 30020 14 + 57822 TAATGTTCTCCTTA -s Anc2.Anc2refChr15 10039 14 + 86568 TAATGTTTTAATTA -s mr.mrrefChr5 48683 14 + 294540 GAAGGTTCTCCTTA -s simCow_chr6.simCow.chr6 193184 14 + 602619 AAATGTTTTTTTTA -s simDog_chr6.simDog.chr6 474603 14 - 593897 TGAGGTTTTAATTA -s simHuman_chr6.simHuman.chr6 197097 13 + 601863 -AATGTTCTCCTCA -s simRat_chr6.simRat.chr6 183993 14 + 647215 GAAGGTTCTTCTTA - -a -s simMouse_chr6.simMouse.chr6 193834 5 + 636262 CCTGG -s Anc0.Anc0refChr5 16472 5 + 87904 CCTGG -s Anc1.Anc1refChr8 30034 5 + 57822 CCTGG -s Anc2.Anc2refChr15 10053 5 + 86568 CCTGG -s mr.mrrefChr5 48697 5 + 294540 CCTGG -s simCow_chr6.simCow.chr6 193198 5 + 602619 CCTGG -s simDog_chr6.simDog.chr6 474625 5 - 593897 CCTGG -s simHuman_chr6.simHuman.chr6 197110 5 + 601863 CCTGG -s simRat_chr6.simRat.chr6 184007 5 + 647215 CCTGG - -a -s simMouse_chr6.simMouse.chr6 193839 3 + 636262 GAG -s Anc0.Anc0refChr5 16477 3 + 87904 GTG -s Anc1.Anc1refChr8 30039 3 + 57822 GTG -s Anc2.Anc2refChr15 10058 3 + 86568 GTG -s mr.mrrefChr5 48702 3 + 294540 GAG -s simCow_chr6.simCow.chr6 193203 3 + 602619 GTG -s simDog_chr6.simDog.chr6 474646 3 - 593897 GTG -s simHuman_chr6.simHuman.chr6 197115 3 + 601863 GTG -s simRat_chr6.simRat.chr6 184012 3 + 647215 GAG - -a -s simMouse_chr6.simMouse.chr6 193842 7 + 636262 AACAAGG -s Anc0.Anc0refChr5 16482 7 + 87904 CACAGGT -s Anc1.Anc1refChr8 30044 7 + 57822 CACAGGT -s Anc2.Anc2refChr15 10063 7 + 86568 CCCAGGT -s mr.mrrefChr5 48705 7 + 294540 AACAAGG -s simCow_chr6.simCow.chr6 193208 7 + 602619 CCTGGGT -s simDog_chr6.simDog.chr6 474651 7 - 593897 CCCAGGT -s simHuman_chr6.simHuman.chr6 197120 7 + 601863 CACAGGT -s simRat_chr6.simRat.chr6 184015 7 + 647215 CACAAGG - -a -s simMouse_chr6.simMouse.chr6 193849 1 + 636262 T -s Anc0.Anc0refChr5 16489 1 + 87904 T -s Anc1.Anc1refChr8 30051 1 + 57822 T -s Anc2.Anc2refChr15 10070 1 + 86568 T -s mr.mrrefChr5 48712 1 + 294540 T -s simCow_chr6.simCow.chr6 193215 1 + 602619 T -s simDog_chr6.simDog.chr6 474682 1 - 593897 T -s simHuman_chr6.simHuman.chr6 197127 1 + 601863 T -s simRat_chr6.simRat.chr6 184022 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 193850 4 + 636262 ATCT -s Anc0.Anc0refChr5 16490 4 + 87904 GTCC -s Anc1.Anc1refChr8 30052 4 + 57822 GTCC -s Anc2.Anc2refChr15 10071 4 + 86568 GTCC -s mr.mrrefChr5 48713 4 + 294540 ATCT -s simCow_chr6.simCow.chr6 193217 4 + 602619 GTCC -s simDog_chr6.simDog.chr6 474683 4 - 593897 GTGC -s simHuman_chr6.simHuman.chr6 197128 4 + 601863 GCCC -s simRat_chr6.simRat.chr6 184023 4 + 647215 ATCT - -a -s simMouse_chr6.simMouse.chr6 193854 72 + 636262 TAGTTAAAGCAACCTGAGCTGAGCCTATCATTTCATATCTGCATAACACATCATGAATACTCATTTCTATAA -s Anc0.Anc0refChr5 16508 72 + 87904 TCTTTAAAGTACTAAAACCTGAACCTGCAGTTTCATAACTACATAGCAGATCAGGACTGCTTTTTTATGTAA -s Anc1.Anc1refChr8 30070 72 + 57822 TCTTTAAAGTACTAAAACCTGAACCTGCAGTTTCATAACTACATAGCAGATCAGGACTGCTTTTTTATGTAA -s Anc2.Anc2refChr15 10089 72 + 86568 TCTTTGAAGTACTAAAACTTGAACCTGCAGTTTCATAACTACATAGCAGATTAGGACTGCTTTTTTATGTAA -s mr.mrrefChr5 48717 72 + 294540 TAGTTAAAGCAACCTGAGCTGAGCCTATCATTTCATATCTGCATAACACATCATGAATACTCATTTCTATAA -s simCow_chr6.simCow.chr6 193230 71 + 602619 GGTTTCTAATCATAAAACTTGAACCTGCAGTTTCATAACTAAATAGCAGATTAGGACTGCCTTTCCATGCA- -s simDog_chr6.simDog.chr6 474701 55 - 593897 TCGTTGAAGTACTA-----------------TTCACAACTGCATACCAGATTAAGCCTGCTTTTTTATTTAA -s simHuman_chr6.simHuman.chr6 197146 72 + 601863 TTTTTACATTACTACAACCTGAACCTGCAGTTCCATAGCTACACAGCAGATCAGTACTTCTTTTTTACGTAT -s simRat_chr6.simRat.chr6 184027 72 + 647215 CTGTTAATGCAATGTGAGCTTAACCTGTCATTTCATGTCTGCATAACATGTCAGGAATACTCATTTATACAA - -a -s simMouse_chr6.simMouse.chr6 193926 3 + 636262 ACC -s Anc0.Anc0refChr5 16580 3 + 87904 TTT -s Anc1.Anc1refChr8 30142 3 + 57822 TTT -s Anc2.Anc2refChr15 10161 3 + 86568 TTT -s mr.mrrefChr5 48789 3 + 294540 ACC -s simDog_chr6.simDog.chr6 474770 3 - 593897 TTT -s simHuman_chr6.simHuman.chr6 197218 3 + 601863 TAT -s simRat_chr6.simRat.chr6 184099 3 + 647215 ACC - -a -s simMouse_chr6.simMouse.chr6 193929 46 + 636262 TATTCTCTGCATGCAATGAACTTTCATACCCCTACCCTTGATGTGT -s Anc0.Anc0refChr5 16592 43 + 87904 TATGCT---AATGCGATCAACTTTCATACCCCTATTATGGCTGTGG -s Anc1.Anc1refChr8 30154 43 + 57822 TATGCT---AATGCGATCAACTTTCATACCCCTATTATGGCTGTGG -s Anc2.Anc2refChr15 10173 43 + 86568 TATGCT---AATGCGATCAACTTTCATACCCCTATTATGACTGTGG -s mr.mrrefChr5 48792 46 + 294540 TATTCTCTGCATGCAATGAACTTTCATACCCCTACCCTTGATGTGT -s simCow_chr6.simCow.chr6 193309 43 + 602619 TATGCT---AATGCGATGAACTTTCATACCCCTGTTATGACTATGG -s simDog_chr6.simDog.chr6 474782 43 - 593897 TAAGCT---AGTGCGATCAACTTTTATACCCATAGTATCACTGTGG -s simHuman_chr6.simHuman.chr6 197230 43 + 601863 TATGCT---GATGCGATCAACATTCATACCCCTTTTATGGCTCTGG -s simRat_chr6.simRat.chr6 184102 46 + 647215 TATTCTTCTCATGCAATCAACTTTCATACCCCTACTCTTGATATGT - -a -s simMouse_chr6.simMouse.chr6 193975 38 + 636262 CCAGCAAAGGGCTCACTCGTAGTCAAGTCCACCAAGGG -s Anc0.Anc0refChr5 16635 34 + 87904 ACAAGAAGGGGCTCGCTCATAGCCAAGTCT----AGAA -s Anc1.Anc1refChr8 30197 34 + 57822 ACAAGAAGGGGCTCGCTCATAGCCAAGTCT----AGAA -s Anc2.Anc2refChr15 10216 34 + 86568 ACAAGAAGGGGCTCGCTCATAGCCAAATCT----AGAA -s mr.mrrefChr5 48838 38 + 294540 CCAGCAAAGGGCTCACTCGTAGTCAAGTCCACCAAGGG -s simCow_chr6.simCow.chr6 193352 34 + 602619 ACAAGAAGGGGCTCGTTCACAGGCACATCT----AAAA -s simDog_chr6.simDog.chr6 474825 34 - 593897 ACAATCAGGGGCTCACTCATAGCCAAACTT----AGAA -s simHuman_chr6.simHuman.chr6 197282 34 + 601863 ACAAGAAGGGACCTGCTCATAGACAAGTCT----AGAA -s simRat_chr6.simRat.chr6 184148 38 + 647215 CCAGCAAAGGGCTCACTTCTAGTCAAGTTTAGCAAGGG - -a -s simMouse_chr6.simMouse.chr6 194013 198 + 636262 TTCACTCATAGTCAAGTCTAGAAGCATTTAGAATCAAGGTAAAAACTAGTGGACTGTTCAGTCAGGTGTCTCAAATATATCGCTCCCTAATATTGCAGCAGTCTTCTTGACTATAGCAAGAAACTGAAGTTAACTTCAGCTAAAGTAACCAAGGAAGTGAAAACACTACATTGAGCTGGACCTCTAAGGTCAAGCCAG -s Anc0.Anc0refChr5 16669 24 + 87904 AACATTTGTAGTCA------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GTCCAGCCAG -s Anc1.Anc1refChr8 30231 24 + 57822 AACATTTGTAGTCA------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GTCCAGCCAG -s Anc2.Anc2refChr15 10250 24 + 86568 AACATTTGAAATCG------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GTCCAGCCAG -s mr.mrrefChr5 48876 198 + 294540 TTCACTCATAGTCAAGTCTAGAAGCATTTAGAATCAAGGTAAAAACTAGTGGACTGTTCAGTCAGGTGTCTCAAATATATCGCTCCCTAATATTGCAGCAGTCTTCTTGACTATAGCAAGAAACTGAAGTTAACTTCAGCTAAAGTAACCAAGGAAGTGAAAACACTACATTGAGCTGGACCTCTAAGGTCAAGCCAG -s simCow_chr6.simCow.chr6 193386 24 + 602619 AACGTTTGGAATTG------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ATTTAGCTAG -s simDog_chr6.simDog.chr6 474859 24 - 593897 AACATTTAAGATCG------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GTCCAGCCAG -s simHuman_chr6.simHuman.chr6 197316 24 + 601863 CATATTTGTAGTCA------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GTCCGTCCAG -s simRat_chr6.simRat.chr6 184187 198 + 647215 CTCACTCATAATCAAGTCTAAAAGCATTTTGAATCAAGGTAAAAACCAGTGAACTGTTTAATCAGGTTTTTCAAAAATATTACTTCCTTATATTGCTGCAGTCTTCCTGACTATAATAAGTAGCTAAAGTTAACTGCAGCTAACGGACCCAAAGAAGTGAGAACACTACATTGAACTGGATCTCTATGGTCAAACCAG - -a -s simMouse_chr6.simMouse.chr6 194211 9 + 636262 CAACCTATA -s Anc0.Anc0refChr5 16694 9 + 87904 CAACTTATA -s Anc1.Anc1refChr8 30256 9 + 57822 CAACTTATA -s Anc2.Anc2refChr15 10275 9 + 86568 CAACTTATA -s mr.mrrefChr5 49074 9 + 294540 CAACCTATA -s simCow_chr6.simCow.chr6 193411 9 + 602619 CGACCTATA -s simDog_chr6.simDog.chr6 474884 8 - 593897 -AACTTATG -s simHuman_chr6.simHuman.chr6 197341 9 + 601863 CAAGTTGTA -s simRat_chr6.simRat.chr6 184385 9 + 647215 CAACGTATA - -a -s simMouse_chr6.simMouse.chr6 194220 4 + 636262 ATCG -s Anc0.Anc0refChr5 16703 4 + 87904 ATGT -s Anc1.Anc1refChr8 30265 4 + 57822 ATGT -s Anc2.Anc2refChr15 10284 4 + 86568 ATGT -s mr.mrrefChr5 49083 4 + 294540 ATCT -s simCow_chr6.simCow.chr6 193420 4 + 602619 ACAT -s simDog_chr6.simDog.chr6 474892 4 - 593897 ATGT -s simHuman_chr6.simHuman.chr6 197350 4 + 601863 ATGT -s simRat_chr6.simRat.chr6 184398 4 + 647215 ATCT - -a -s simMouse_chr6.simMouse.chr6 194224 113 + 636262 CTTCCCTTGAAACCAAGACCCTGTTGCAACATCTCCTGTTGAATGGGGAATAGCAGATATGCAGACTGATAGTAGAGCGCAGTCTGGAGGTGTAGCTTTGGGCTACCTGTGTC -s Anc0.Anc0refChr5 16707 92 + 87904 CTTCCATAGAACACAACATCCTGTTGGAGTACCTCCTGTTGGATGGGGAATAGCA-ACATGGTGGCTGATA-------CCAGCATGAAGGTATTGCCTAG------------- -s Anc1.Anc1refChr8 30269 92 + 57822 CTTCCATAGAACACAACATCCTGTTGGAGTACCTCCTGTTGGATGGGGAATAGCA-ACATGGTGGCTGATA-------CCAGCATGAAGGTATTGCCTAG------------- -s Anc2.Anc2refChr15 10288 92 + 86568 CTTCCATAGAACACAACATCCTGTTGGAGTACCTCCTGTTGGCAGGGGAATAGCA-ACATGGTGGCAGACA-------CCAGCATGAAGGTATTGCCTAG------------- -s mr.mrrefChr5 49087 100 + 294540 CTTCCCTTGAAACCAAGATCCTGTTGGAACATCTCCTGTTGGATGGGGAATAGCAGATATGCAGACTGATAGTAGAGCGCAGCCTGAAGGTGTAGCTTTG------------- -s simCow_chr6.simCow.chr6 193424 92 + 602619 CTTGAACAGGACACAACATCCTGTTAGAAGACCTCCTGTTAGCAGGGGAATAGCA-ACATGGAGGCCGACA-------CCAACATGAGGGTATTGCCTGG------------- -s simDog_chr6.simDog.chr6 474896 86 - 593897 CTTCCATACAGCACAACATCCTGTTGGTGTACCTCCTGTTGGCAGGGGAATAGCC----TGATAACAGA----------CAGCATTAAGGAATTGCAAAT------------- -s simHuman_chr6.simHuman.chr6 197354 92 + 601863 CTTACATAGCACACAACATCCTGTGGGATTACTTCTTGTGGGATGGAGAATAGCA-ACATGGGGGCTGATA-------ACAGCATGAAGGTATTGTCTAG------------- -s simRat_chr6.simRat.chr6 184405 95 + 647215 CTTCCCTTGAAACCAAGATCCTGTTGGAACATCTCCTGTTGGATGGGGAATAGCAGGTATGCAGACTGATAGTGGAGTGCAGCCTGAAGGTGTAG------------------ - -a -s simMouse_chr6.simMouse.chr6 194337 3 + 636262 ACT -s Anc0.Anc0refChr5 16799 3 + 87904 ATT -s Anc1.Anc1refChr8 30361 3 + 57822 ATT -s Anc2.Anc2refChr15 10388 3 + 86568 ATT -s mr.mrrefChr5 49187 3 + 294540 ACT -s simCow_chr6.simCow.chr6 193528 3 + 602619 AGT -s simDog_chr6.simDog.chr6 474990 3 - 593897 ATT -s simRat_chr6.simRat.chr6 184678 3 + 647215 ACT - -a -s simMouse_chr6.simMouse.chr6 194340 32 + 636262 GTTGTAAAGGAGCAAATCACATCGAGCAATCT -s Anc0.Anc0refChr5 16802 30 + 87904 TTTG--AATGCTCTAAATACAACAAGCAATTT -s Anc1.Anc1refChr8 30364 30 + 57822 TTTG--AATGCTCTAAATACAACAAGCAATTT -s Anc2.Anc2refChr15 10391 30 + 86568 TTTG--AATGCTCTAAATACAACAAGCAATTT -s mr.mrrefChr5 49190 32 + 294540 GTTGTAAAGGAGCAAATCACATCGAGCAATCT -s simCow_chr6.simCow.chr6 193535 30 + 602619 TTCA--AAGGCTCTAAATACAACAAGCAATCT -s simDog_chr6.simDog.chr6 474993 30 - 593897 TTTG--AATGCTCTAAATACAACAAGCAATTT -s simHuman_chr6.simHuman.chr6 197446 1 + 601863 -------------------------------T -s simRat_chr6.simRat.chr6 184681 32 + 647215 GTTATGAATGAGCAAGCCACAACGAGCAATCT - -a -s simMouse_chr6.simMouse.chr6 194372 1 + 636262 T -s Anc0.Anc0refChr5 16832 1 + 87904 T -s Anc1.Anc1refChr8 30394 1 + 57822 T -s Anc2.Anc2refChr15 10421 1 + 86568 T -s mr.mrrefChr5 49222 1 + 294540 T -s simDog_chr6.simDog.chr6 475090 1 - 593897 T -s simHuman_chr6.simHuman.chr6 197447 1 + 601863 T -s simRat_chr6.simRat.chr6 184713 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 194373 37 + 636262 AATTATACCCCTCCCATCTATTGTTTCCCTCTAGCTG -s Anc0.Anc0refChr5 16833 37 + 87904 AATCATACCCCTCCCGTTTATGGTTTTCCCCCAGCTG -s Anc1.Anc1refChr8 30395 37 + 57822 AATCATACCCCTCCCGTTTATGGTTTTCCCCCAGCTG -s Anc2.Anc2refChr15 10423 37 + 86568 AATCATACCCCTTCCGTTTGTGGTTTTCCCCCAGGTG -s mr.mrrefChr5 49223 37 + 294540 AATTATACCCCTCCCATCTATTGTTTTCCTCTAGCTG -s simCow_chr6.simCow.chr6 193566 37 + 602619 AATTATACCCCTTTCATTTGTGGTTTCCCCTTAGGTG -s simDog_chr6.simDog.chr6 475092 37 - 593897 AATCATATCCCATCTGTTTGTGGTTTTCACCCAGGGG -s simHuman_chr6.simHuman.chr6 197448 37 + 601863 AATAATACCCCTCCCCCTCATGGTTCTCCCCCTGCTG -s simRat_chr6.simRat.chr6 184714 36 + 647215 AAGTAT-CCCCTCCCTTCTATTGTTTTCCTCTAGTTG - -a -s simMouse_chr6.simMouse.chr6 194410 53 + 636262 TTGGCTCGATGCTTTGTGTCTTCTACTTTCTTGATAGGGAGTTTGGACACATT -s Anc0.Anc0refChr5 16872 49 + 87904 TTTACTCCATGCTTTGTG-ATTCTAC---ATTGAGAGGGAGTTTAGACAAATT -s Anc1.Anc1refChr8 30434 50 + 57822 TTTACTCCATGCTTTGTGTATTCTAC---ATTGAGAGGGAGTTTAGACAAATT -s Anc2.Anc2refChr15 10462 49 + 86568 TTTATTCCATGCTTAATG-AGTCTAC---ATTGAGAGAGAATTTAGACAAATT -s mr.mrrefChr5 49260 53 + 294540 TTTGCTCGATGCTTTGTGTCTTCTACTTTCTTGATAGGGAGTTTGGACACATT -s simCow_chr6.simCow.chr6 193605 34 + 602619 TTTAGTCCATGC-----------------ATTGAGAGAGAAT--AGACAAATT -s simDog_chr6.simDog.chr6 475131 49 - 593897 ATTATTCCATGTTTAATG-AGTCTAC---ATTGAGAGAGAATTTAAACTAATT -s simHuman_chr6.simHuman.chr6 197487 50 + 601863 TTTACTCCACGCTTTGTGTATTTTAC---ATGGAGAGGGAGTTTTGGCAAATG -s simRat_chr6.simRat.chr6 184750 53 + 647215 GTTGCTCAATGCTTTGTGTCTTCTACTTTCTTGATAGGGAGTTCAAACATATT - -a -s simMouse_chr6.simMouse.chr6 194463 50 + 636262 TATCAAGCTGTGACCCTGGTCAGCTGTCAGAAACTACTGTAACAGTGCCT -s Anc0.Anc0refChr5 16921 50 + 87904 TATCAACTTGTGACCCTGAGCAACTGTCAGAAACTACTGTAACAGTATCT -s Anc1.Anc1refChr8 30484 50 + 57822 TATCAACTTGTGACCCTGAGCAACTGTCAGAAACTACTGTAACAGTATCT -s Anc2.Anc2refChr15 10511 50 + 86568 TATCAACTTGTGACCCTGAGCAACTGTCAGAAACTACCATAACAGCATCT -s mr.mrrefChr5 49313 50 + 294540 TATCAAGCTGTGACCCTGGGCAACTGTCAGAAACTACTGTAACAGTACCT -s simCow_chr6.simCow.chr6 193661 49 + 602619 TATCAACTTGCAACCCTGAGTAAGTG-CGGAAACTACCCTAACAGCATCT -s simDog_chr6.simDog.chr6 475180 50 - 593897 TATCAACTTGTGACCCTGAACAACTGTCAGAAACAACCACAACAGCATCT -s simHuman_chr6.simHuman.chr6 197537 50 + 601863 TATCAACTGGTGACCCTGAGCAACTGTCAGAAACTATTGTAACAGTATCT -s simRat_chr6.simRat.chr6 184803 50 + 647215 TATCAAGCTCTCACCCTGGGCAACTGTCATAAACTACTGTAACAGTACAT - -a -s simMouse_chr6.simMouse.chr6 194513 34 + 636262 GCCAAACATTACCACTTTTCTGAACCCAAACCTA -s Anc0.Anc0refChr5 16971 31 + 87904 GCAAAGCATTATTTCTTTTCTTG---CAAATTCA -s Anc1.Anc1refChr8 30534 31 + 57822 GCAAAGCATTATTTCTTTTCTTG---CAAATTCA -s Anc2.Anc2refChr15 10561 31 + 86568 GCAGAGGATTATTTCTTTTCTTG---CAAATTCA -s mr.mrrefChr5 49363 34 + 294540 GCCAAACATTACCACTTTTCTGAACCCAAACCCA -s simCow_chr6.simCow.chr6 193710 31 + 602619 GTAGAGGATCATTTCTTTTTTTG---CAACTCCA -s simDog_chr6.simDog.chr6 475232 31 - 593897 ACAGAGGATTATTTCTTATCTCG---CAAATTCA -s simHuman_chr6.simHuman.chr6 197587 31 + 601863 GCAAGGCATTATTCCTATTCTTG---CAAATTCA -s simRat_chr6.simRat.chr6 184853 34 + 647215 GCCAAATATTACCACTTTTCTGAACCCAAAGCCA - -a -s simMouse_chr6.simMouse.chr6 194547 97 + 636262 ATTAATATAATAGAAAATTGAAGGCTTCATACACAGAAAAATAATGGTGGCACCTAACCTGCCAACTTTATGTTCTGTGTCTTTTAATAGACAATGT -s Anc0.Anc0refChr5 17004 46 + 87904 ATGAATATAGTATAAA---GA-TACTTC---------------------------------------------TCTGCATCTT--AGTAGACCACTT -s Anc1.Anc1refChr8 30567 47 + 57822 ATGAATATAGTATAAA---GA-TACTTC---------------------------------------------TCTGCATCTTT-AGTAGACCACTT -s Anc2.Anc2refChr15 10595 46 + 86568 ATGAATATAGTATAAA---GC-TACTAA---------------------------------------------TCTGCATCTG--AGTAAACCACTT -s mr.mrrefChr5 49397 95 + 294540 ATGAATATAATAGAAAATTGA-GACTTCATACACAGAAAAATAATGGTGGCACCTAACCTGCCAACTTTATGTTCTGTGTCTTT-AATAGACAATGT -s simCow_chr6.simCow.chr6 193744 46 + 602619 ATGAATATAGTACCGA---GC-TACTAT---------------------------------------------TCTACATCTA--ATTGAACCACTC -s simDog_chr6.simDog.chr6 475266 46 - 593897 ATGAATATAGTATAAA---GC-TACCAA---------------------------------------------TATGCATGTG--AGTAAGCCACTT -s simHuman_chr6.simHuman.chr6 197620 47 + 601863 ATGAATGTAGTGTAAA---GA-TACTTC---------------------------------------------TCTGCAGCTCT-AGTAGACCACTT -s simRat_chr6.simRat.chr6 184887 95 + 647215 ATGAATATAATAGAAATTTGA-GACTTTACACACAGCATGATAATGGAGGCACATAACCTGCCAACTTTATGATCCATGCCTAT-AATAGACAATGC - -a -s simMouse_chr6.simMouse.chr6 194644 83 + 636262 AGTACACATCATTCAGGTACAGTGTTTATATTTACCAACACATAATGACTCCAGCATACTGCTATCAATGGAAGTTCATTGTG -s Anc0.Anc0refChr5 17054 71 + 87904 GGTTGACT----------ACTAAGTTTATATTTATCAATACATAATGA--TAAGTGTACAGTTACAAATGGGAGCCTGTTGTG -s Anc1.Anc1refChr8 30618 78 + 57822 GGTTGACTTGAC-----TACTAAGTTTATATTTATCAATACATAATGACTTAAGTGTACAGTTACAAATGGGAGCCTGTTGTG -s Anc2.Anc2refChr15 10645 71 + 86568 GGTTGACT----------ACTAAGTTGATATTTATCAATACATAATGA--TAAGTGTACAGTTACAAATGGGGGCCTGTTATG -s mr.mrrefChr5 49492 83 + 294540 AGTAGACTTCATTCAGGTACAGTGTTTATATTTACCAATACATAATGACTCCAGTATACAGCTATAAATGGAAGCTTATTGTG -s simCow_chr6.simCow.chr6 193794 67 + 602619 GGTTGACT----------ACTAAGTTGATAGTTATCAATATGTAATG------GTGCGCAGTTACAAATGGGGGCTTATCATG -s simDog_chr6.simDog.chr6 475316 71 - 593897 GGTTGATT----------ACTAGGTTGATGTTTATTAATACATAATGA--TAAGTGTACAGTTACAAACGGGGGCCTGTTATG -s simHuman_chr6.simHuman.chr6 197671 78 + 601863 GGTTGACTTGAC-----TACCAAGTTTACACCTGGCAATACATATTGACTTAAGTGTACAGTTACAAATGGGAGCCTGTTGTG -s simRat_chr6.simRat.chr6 184982 83 + 647215 AGTAGACTTCATTCAGGTACAGTGTTTATATTTACCAATACATAATGACTCCAGTCTACAGCTATAAATGGAAGCTTATTGTG - -a -s simMouse_chr6.simMouse.chr6 194727 17 + 636262 GGATAGCTAGTCCAAGT -s Anc0.Anc0refChr5 17126 17 + 87904 GGATAGCTAGTGCAAGT -s Anc1.Anc1refChr8 30697 17 + 57822 GGATAGCTAGTGCAAGT -s Anc2.Anc2refChr15 10717 17 + 86568 GGATAGATAGTGCAAGT -s mr.mrrefChr5 49576 17 + 294540 GGATAGCTAGTCCAAGT -s simCow_chr6.simCow.chr6 193862 15 + 602619 GGTTAGGAAGTGCAA-- -s simDog_chr6.simDog.chr6 475388 17 - 593897 GGATAGATAGTTCAAGT -s simHuman_chr6.simHuman.chr6 197750 17 + 601863 GGATAGCTAGTGCAAGT -s simRat_chr6.simRat.chr6 185066 17 + 647215 GGATAGCTAGTCCAAGT - -a -s simMouse_chr6.simMouse.chr6 194744 36 + 636262 GTCTCATCTGAGTTATTCGGCAGTGTTGAGGCTGTT -s Anc0.Anc0refChr5 17165 36 + 87904 GTCCCACTTTTGTTATATGGTAGTGGGCAGGCTGAT -s Anc1.Anc1refChr8 30736 36 + 57822 GTCCCACTTTTGTTATATGGTAGTGGGCAGGCTGAT -s Anc2.Anc2refChr15 10756 36 + 86568 GTCCCACTATTGGCATATGGTAGTGGGCAGGCTGAT -s mr.mrrefChr5 49593 36 + 294540 GTCTCACCTGAGTTATTCGGTAGTGTTCAGGCTGTT -s simCow_chr6.simCow.chr6 193897 35 + 602619 GTCCCACTATTGGCAT-TAGCAGTGGGCAGGCTGAT -s simDog_chr6.simDog.chr6 475428 35 - 593897 GTTCCCTCACTGGCATATGGTGGTGGGC-AGCTGAT -s simHuman_chr6.simHuman.chr6 197789 36 + 601863 GTCCCACTTTTGTTAAAAGGTAGTGGGCTGGCTAAT -s simRat_chr6.simRat.chr6 185083 36 + 647215 CTCTCACCTGAATTATTTGGTGGTGTTCAGTCTGTT - -a -s simMouse_chr6.simMouse.chr6 194780 30 + 636262 GGCTCACTGGGATGCATTGCAACATATGTT -s Anc0.Anc0refChr5 17203 22 + 87904 GGTTC--------GCATTGTAACACATGCT -s Anc1.Anc1refChr8 30774 30 + 57822 GGTTCCATGGGACGCATTGTAACACATGCT -s Anc2.Anc2refChr15 10794 22 + 86568 GGTTC--------GCATTGTAACACATGCT -s mr.mrrefChr5 49629 30 + 294540 GGTTCAATGGGATGCATTGCAACATATGTT -s simCow_chr6.simCow.chr6 193934 22 + 602619 GGTTT--------GCATTGTAACGCATGCT -s simDog_chr6.simDog.chr6 475465 22 - 593897 GGTTC--------GCCTTGTAACACATGCT -s simHuman_chr6.simHuman.chr6 197827 30 + 601863 GGTTCCATGGGACCCACCAAAACACATGCT -s simRat_chr6.simRat.chr6 185119 22 + 647215 GTTTCAAGGGGA--------AACATATGTC - -a -s simMouse_chr6.simMouse.chr6 194810 19 + 636262 ATCTCCTTAAATTTAGTGT -s Anc0.Anc0refChr5 17225 19 + 87904 ATCTCCTTGAATTCAGAGT -s Anc1.Anc1refChr8 30804 19 + 57822 ATCTCCTTGAATTCAGAGT -s Anc2.Anc2refChr15 10816 19 + 86568 ACCTCCTTGAATTCAGAGT -s mr.mrrefChr5 49659 19 + 294540 ATCTCCTTGAATTTAGAGT -s simCow_chr6.simCow.chr6 193956 19 + 602619 ACCTCCTTGAACTTAAAGT -s simDog_chr6.simDog.chr6 475491 19 - 593897 ACCTCCCTGAATTCAGAGT -s simHuman_chr6.simHuman.chr6 197857 17 + 601863 ATCTCCTTGAATT--GAAG -s simRat_chr6.simRat.chr6 185141 19 + 647215 ATCTCCTTGAATTTAGAGT - -a -s simMouse_chr6.simMouse.chr6 194829 10 + 636262 AACATGAAGA -s Anc0.Anc0refChr5 17244 10 + 87904 AACTAGAAGA -s Anc1.Anc1refChr8 30823 10 + 57822 AACTAGAAGA -s Anc2.Anc2refChr15 10854 10 + 86568 AACTAGATGA -s mr.mrrefChr5 49678 10 + 294540 AACATGAAGA -s simCow_chr6.simCow.chr6 193994 10 + 602619 GACTAGATGA -s simDog_chr6.simDog.chr6 475530 10 - 593897 AAATAGATGA -s simHuman_chr6.simHuman.chr6 197874 10 + 601863 ACCTAGAAGA -s simRat_chr6.simRat.chr6 185160 10 + 647215 AACATGAAAA - -a -s simMouse_chr6.simMouse.chr6 194839 9 + 636262 AAAAGCCTG -s Anc0.Anc0refChr5 17255 9 + 87904 ACAAGCCTG -s Anc1.Anc1refChr8 30834 9 + 57822 ACAAGCCTG -s Anc2.Anc2refChr15 10865 9 + 86568 ACAAGTATG -s mr.mrrefChr5 49688 9 + 294540 AAAAGCCTG -s simCow_chr6.simCow.chr6 194005 9 + 602619 ACAAGTGTG -s simDog_chr6.simDog.chr6 475541 9 - 593897 ACAAGTAAG -s simHuman_chr6.simHuman.chr6 197885 9 + 601863 AGAAGCCTG -s simRat_chr6.simRat.chr6 185170 6 + 647215 AAAAGT--- - -a -s simMouse_chr6.simMouse.chr6 194848 11 + 636262 GTTTCTAGTAT -s Anc0.Anc0refChr5 17264 11 + 87904 GTTTCCAGCCT -s Anc1.Anc1refChr8 30843 11 + 57822 GTTTCCAGCCT -s Anc2.Anc2refChr15 10878 11 + 86568 GTTTCCAGCCT -s mr.mrrefChr5 49697 11 + 294540 GTTTCTAGTAT -s simCow_chr6.simCow.chr6 194018 11 + 602619 TATTTCAGTCT -s simDog_chr6.simDog.chr6 475554 11 - 593897 GTTTCCAGCCT -s simHuman_chr6.simHuman.chr6 197894 10 + 601863 G-ATCCAGCCT -s simRat_chr6.simRat.chr6 185176 6 + 647215 -TTTCTA---- - -a -s simMouse_chr6.simMouse.chr6 194859 18 + 636262 GCTTTTGTTATAATATTC -s Anc0.Anc0refChr5 17319 16 + 87904 GCATTTGTGACATT--TT -s Anc1.Anc1refChr8 30898 16 + 57822 GCATTTGTGACATT--TT -s Anc2.Anc2refChr15 10933 16 + 86568 GCATCTGTGGCATT--TT -s mr.mrrefChr5 49708 16 + 294540 GCTTTTGTTATAAT--TC -s simCow_chr6.simCow.chr6 194074 16 + 602619 TCATCTGTGGCATT--TT -s simDog_chr6.simDog.chr6 475609 16 - 593897 GCTTCTGTGGCATC--TT -s simHuman_chr6.simHuman.chr6 197949 16 + 601863 GCATTTGTAACATT--TT - -a -s simMouse_chr6.simMouse.chr6 194877 21 + 636262 ACAGTGACCACGCCTGTTGTA -s Anc0.Anc0refChr5 17335 21 + 87904 ACAGTGACCTCTTCTGTTGTA -s Anc1.Anc1refChr8 30914 21 + 57822 ACAGTGACCTCTTCTGTTGTA -s Anc2.Anc2refChr15 10951 21 + 86568 CCAGTGACCTCTTCTGTTGTA -s mr.mrrefChr5 49724 21 + 294540 ACAGTGACCACTCCTGTTGTA -s simCow_chr6.simCow.chr6 194092 21 + 602619 CCAGTGACCCATACTGTCATA -s simDog_chr6.simDog.chr6 475627 21 - 593897 CCAGTGATCTCTTCTGCTGTA -s simHuman_chr6.simHuman.chr6 197965 21 + 601863 AAAGTGACCTCTTCTGTTGTA -s simRat_chr6.simRat.chr6 185182 12 + 647215 -------CCACTCCTGTTG-- - -a -s simMouse_chr6.simMouse.chr6 194898 8 + 636262 AGTACCTG -s Anc0.Anc0refChr5 17365 8 + 87904 GGTATCAG -s Anc1.Anc1refChr8 30944 8 + 57822 GGTATCAG -s Anc2.Anc2refChr15 10981 8 + 86568 GGTATCAG -s mr.mrrefChr5 49745 8 + 294540 AGTACCTG -s simCow_chr6.simCow.chr6 194122 8 + 602619 GCCATCAG -s simDog_chr6.simDog.chr6 475657 8 - 593897 GGTATCAG -s simHuman_chr6.simHuman.chr6 197995 8 + 601863 GGTATCAG -s simRat_chr6.simRat.chr6 185194 4 + 647215 ----CCTG - -a -s simMouse_chr6.simMouse.chr6 194906 4 + 636262 TTGT -s Anc0.Anc0refChr5 17377 4 + 87904 TCAC -s Anc1.Anc1refChr8 30956 4 + 57822 TCAC -s Anc2.Anc2refChr15 10993 4 + 86568 GCAC -s mr.mrrefChr5 49753 4 + 294540 TTAC -s simCow_chr6.simCow.chr6 194134 4 + 602619 GCAC -s simDog_chr6.simDog.chr6 475669 4 - 593897 GTGC -s simHuman_chr6.simHuman.chr6 198007 4 + 601863 TCAC -s simRat_chr6.simRat.chr6 185198 4 + 647215 TTAC - -a -s simMouse_chr6.simMouse.chr6 194910 34 + 636262 TAGAATTTCAACATATGGTTCACATCCACCCATT -s Anc0.Anc0refChr5 17381 34 + 87904 TAGAATTTCAGCATATGGGTCGCACTCTCTCATT -s Anc1.Anc1refChr8 30960 34 + 57822 TAGAATTTCAGCATATGGGTCGCACTCTCTCATT -s Anc2.Anc2refChr15 10999 34 + 86568 TATAATTTCAGCATATGGGTCGCACTCTCTCATT -s mr.mrrefChr5 49757 34 + 294540 TAGAATTTCAACATATGGTTCACACTCACCCATT -s simCow_chr6.simCow.chr6 194140 34 + 602619 TATAATTTCAGCATATGGGTCACACTCGCTCATC -s simDog_chr6.simDog.chr6 475675 34 - 593897 TGTAATTTCAGTGTATGGGTCGCACTCTCCCATT -s simHuman_chr6.simHuman.chr6 198011 27 + 601863 AAGAATTTCAGCATAGAG-------TCTCTCCTT -s simRat_chr6.simRat.chr6 185202 34 + 647215 TAGAATTTCAAAATGTGGTTCACACTCACCCATT - -a -s simMouse_chr6.simMouse.chr6 194944 15 + 636262 AAACCTTCCATTTCA -s Anc0.Anc0refChr5 17417 15 + 87904 ACACCTCCTATCTCA -s Anc1.Anc1refChr8 30996 15 + 57822 ACACCTCCTATCTCA -s Anc2.Anc2refChr15 11035 15 + 86568 ACACCTCCTATCTCA -s mr.mrrefChr5 49791 15 + 294540 AAACCTTCTATTTCA -s simCow_chr6.simCow.chr6 194176 15 + 602619 ACACCTCCTATCTCA -s simDog_chr6.simDog.chr6 475711 12 - 593897 ATACCTCGTATC--- -s simHuman_chr6.simHuman.chr6 198040 15 + 601863 ACACCCCCTATCTCA -s simRat_chr6.simRat.chr6 185236 15 + 647215 AAACATTCTGTTTCA - -a -s simMouse_chr6.simMouse.chr6 194959 15 + 636262 GTAACTGGAAGGTCC -s Anc0.Anc0refChr5 17432 15 + 87904 GCCACTGTAAACCCC -s Anc1.Anc1refChr8 31011 15 + 57822 GCCACTGTAAACCCC -s Anc2.Anc2refChr15 11050 15 + 86568 ACCACTGTGAACCCC -s mr.mrrefChr5 49806 15 + 294540 GTCACTGGAAAGTCC -s simCow_chr6.simCow.chr6 194193 15 + 602619 ACCACTGTGAACCCC -s simHuman_chr6.simHuman.chr6 198055 15 + 601863 GCCACTGCAAATCCC -s simRat_chr6.simRat.chr6 185251 15 + 647215 CTCACTGGAAAGTCC - -a -s simMouse_chr6.simMouse.chr6 194974 22 + 636262 TAATGTTGCTGTGATATTATAT -s Anc0.Anc0refChr5 17447 22 + 87904 CCATGTTGCTGTGAGATTATAT -s Anc1.Anc1refChr8 31026 22 + 57822 CCATGTTGCTGTGAGATTATAT -s Anc2.Anc2refChr15 11065 22 + 86568 CCATGTTACTATGAGATTATAT -s mr.mrrefChr5 49821 22 + 294540 TAATGTTGCTGTGATATTATAT -s simCow_chr6.simCow.chr6 194211 22 + 602619 CCATGTTACTATGAGATTGCAT -s simDog_chr6.simDog.chr6 475723 12 - 593897 ----------ATGAGATTATAA -s simHuman_chr6.simHuman.chr6 198070 22 + 601863 CCATATTGTTGTGAGATCATAT -s simRat_chr6.simRat.chr6 185266 22 + 647215 TAGTGTTGCCATGAAATTATAT - -a -s simMouse_chr6.simMouse.chr6 194996 25 + 636262 CCATTTCACAGCATACTGAGTCAGT -s Anc0.Anc0refChr5 17470 25 + 87904 CTATTTCACAGTGAACTCACCCACA -s Anc1.Anc1refChr8 31049 25 + 57822 CTATTTCACAGTGAACTCACCCACA -s Anc2.Anc2refChr15 11088 25 + 86568 CTATTTCACAGTGAACTCACCCACA -s mr.mrrefChr5 49844 25 + 294540 CCATTTCACAGCATACTGAGCCAGA -s simCow_chr6.simCow.chr6 194234 25 + 602619 TAATTTCACAGTGAACTCACCCCGA -s simDog_chr6.simDog.chr6 475736 25 - 593897 CTATTTCACACAGAACTGACTCACA -s simHuman_chr6.simHuman.chr6 198093 25 + 601863 ATATTGCAAAGTGGACTCACCCAAA -s simRat_chr6.simRat.chr6 185289 25 + 647215 CCATTTCACAGCATTCTGAGCCAGA - -a -s simMouse_chr6.simMouse.chr6 195021 34 + 636262 TATTGCTTGCAGTACTCACTAAGATCTAAATTAC -s Anc0.Anc0refChr5 17496 24 + 87904 TCTTACTTGCAACACCCACTAA----------AC -s Anc1.Anc1refChr8 31075 34 + 57822 TCTTACTTGCAACACCCACTAAGATCCAAACTAC -s Anc2.Anc2refChr15 11114 24 + 86568 TCTTACTTGCAACACCCACTAA----------AC -s mr.mrrefChr5 49869 34 + 294540 TATTGCTTGCAGTACTCACTAAGATCTAAATTAC -s simCow_chr6.simCow.chr6 194260 24 + 602619 TCTTGCTTGCACTGCCCACTAA----------TC -s simDog_chr6.simDog.chr6 475762 24 - 593897 GCTTACCTGCAACACCTACTAA----------AC -s simHuman_chr6.simHuman.chr6 198119 34 + 601863 TTCTACTTGCAACACCCACTAAGATCCAAACTAC -s simRat_chr6.simRat.chr6 185314 34 + 647215 TATTGCTTGCAGTACTTACTAAGATCTAAATTAC - -a -s simMouse_chr6.simMouse.chr6 195055 10 + 636262 ATAGTAAACC -s Anc0.Anc0refChr5 17521 10 + 87904 ACATTAATCC -s Anc1.Anc1refChr8 31110 10 + 57822 ACATTAATCC -s Anc2.Anc2refChr15 11139 10 + 86568 ACATTAATCC -s mr.mrrefChr5 49904 10 + 294540 ATAGTAAACC -s simCow_chr6.simCow.chr6 194285 10 + 602619 ATTTTAATTC -s simDog_chr6.simDog.chr6 475787 10 - 593897 ACATTAATCC -s simHuman_chr6.simHuman.chr6 198154 10 + 601863 ACATTAAGCC -s simRat_chr6.simRat.chr6 185349 10 + 647215 ATAGTAAACC - -a -s simMouse_chr6.simMouse.chr6 195065 2 + 636262 TG -s Anc0.Anc0refChr5 17531 2 + 87904 TC -s Anc1.Anc1refChr8 31120 2 + 57822 TC -s Anc2.Anc2refChr15 11149 2 + 86568 TC -s mr.mrrefChr5 49914 2 + 294540 TC -s simCow_chr6.simCow.chr6 194300 2 + 602619 TC -s simDog_chr6.simDog.chr6 475797 2 - 593897 CC -s simHuman_chr6.simHuman.chr6 198164 2 + 601863 TC -s simRat_chr6.simRat.chr6 185359 2 + 647215 TC - -a -s simMouse_chr6.simMouse.chr6 195067 48 + 636262 ACCCTTATCTGCATAGGGATATAATGGACTCACTACAAATCAACTCAG -s Anc0.Anc0refChr5 17534 47 + 87904 ACCCTTAACTGTGGATGG-TATAATGGATGCACTTCAAATCAACCCAG -s Anc1.Anc1refChr8 31123 47 + 57822 ACCCTTAACTGTGGATGG-TATAATGGATGCACTTCAAATCAACCCAG -s Anc2.Anc2refChr15 11152 47 + 86568 ACCCCTAACTTTGGATGA-CATAATGGATGCACTTCACATCAACCCAG -s mr.mrrefChr5 49916 48 + 294540 ACCCTTATCTGCATAGGGATATAATGGACTCACTTCAAATCAACCCAG -s simCow_chr6.simCow.chr6 194303 33 + 602619 ACCCCTAACTATGGATGA-CATAGTGGA--------------ACACAG -s simDog_chr6.simDog.chr6 475800 47 - 593897 ACCCCTCAGTTTGTATGA-CATAATGGATGCACTTCACATCAACCCCG -s simHuman_chr6.simHuman.chr6 198167 47 + 601863 ATCCTTACCTGTGGATGG-TGAAATGGAGCCACTTCAAATCAACCCAG -s simRat_chr6.simRat.chr6 185361 48 + 647215 ACCCTTAATTGCATAGGGATATAGTGGACTCACTTCAAATCAACCCAG - -a -s simMouse_chr6.simMouse.chr6 195115 20 + 636262 AAGGGTCCATCTCAATTGTA -s Anc0.Anc0refChr5 17582 20 + 87904 AAGGGTGCACCTCATTTGTA -s Anc1.Anc1refChr8 31171 20 + 57822 AAGGGTGCACCTCATTTGTA -s Anc2.Anc2refChr15 11200 20 + 86568 AGGGGTGCACCTCATTTGTT -s mr.mrrefChr5 49964 20 + 294540 AAGGGTCCATCTCATTTGTA -s simCow_chr6.simCow.chr6 194337 20 + 602619 AGGGGTGCACCTCATTTGTT -s simDog_chr6.simDog.chr6 475848 20 - 593897 AGGGGTGCACCTCATTTGTT -s simHuman_chr6.simHuman.chr6 198215 20 + 601863 AAGGGTGGACCTCATTAGTA -s simRat_chr6.simRat.chr6 185409 12 + 647215 A--------TCTCATTTGTA - -a -s simMouse_chr6.simMouse.chr6 195135 18 + 636262 CAAATTCTCTACCTTAGC -s Anc0.Anc0refChr5 17602 18 + 87904 CAAATTCCCTATCTTAGC -s Anc1.Anc1refChr8 31191 18 + 57822 CAAATTCCCTATCTTAGC -s Anc2.Anc2refChr15 11220 18 + 86568 CAAATTCCCTCTCTTAGC -s mr.mrrefChr5 49984 18 + 294540 CAAATTCTCTACCTTAGC -s simCow_chr6.simCow.chr6 194359 18 + 602619 CAAATTCCCTCTCTTAGC -s simDog_chr6.simDog.chr6 475868 18 - 593897 CAAATTCCCTCTCTTAGC -s simHuman_chr6.simHuman.chr6 198235 18 + 601863 CAAATTCCCTATCTTAGC -s simRat_chr6.simRat.chr6 185421 18 + 647215 CAAATTCTCTACCTTGGC - -a -s simMouse_chr6.simMouse.chr6 195153 59 + 636262 ACATGGAGCAAAATCCATCTGCTAGGCCAGGAAAAATTGCAAGGTCAGTGGTTTTAGCT -s Anc0.Anc0refChr5 17620 41 + 87904 AAAATGAGCAAAAACACTCTGCAAGGTC------------------ATTGATTTAAGGT -s Anc1.Anc1refChr8 31209 41 + 57822 AAAATGAGCAAAAACACTCTGCAAGGTC------------------ATTGATTTAAGGT -s Anc2.Anc2refChr15 11238 41 + 86568 AAAATGAGCAAAAACACTCTGCAAGGTC------------------ATTGATGGAGAGT -s mr.mrrefChr5 50002 59 + 294540 ACAAGGAGCAAAATCCCTCTGCAAGGTCAGGAAAAATTGCAAGGTCAGTGGTTTTAGCT -s simCow_chr6.simCow.chr6 194377 32 + 602619 GAAAAGAGCAAAAACACTCTCCAAGGTG------------------ATTA--------- -s simDog_chr6.simDog.chr6 475911 41 - 593897 AAACTGAGAAAAAACCCTCTGCAAGGTC------------------AGTGATGGAGAGT -s simHuman_chr6.simHuman.chr6 198253 41 + 601863 AGAATGAGCAAAAACACTCTGCAAGGTC------------------ATTGATTTGAGGT -s simRat_chr6.simRat.chr6 185439 59 + 647215 ACAAGGGGGAAAATCCCTCTGCAAGGTCACTAAAAATTGCAAGGTCAGTGGTTTTAGCT - -a -s simMouse_chr6.simMouse.chr6 195212 11 + 636262 AAGCTGGGGGA -s Anc0.Anc0refChr5 17665 11 + 87904 GAGCTGTATAA -s Anc1.Anc1refChr8 31254 11 + 57822 GAGCTGTATAA -s Anc2.Anc2refChr15 11283 11 + 86568 GAGCTATATAA -s mr.mrrefChr5 50061 11 + 294540 GAGCTGGGGGA -s simCow_chr6.simCow.chr6 194411 11 + 602619 GAGCTATATAA -s simDog_chr6.simDog.chr6 475956 11 - 593897 GAGCTATTATA -s simHuman_chr6.simHuman.chr6 198298 11 + 601863 GAGTTGTATAA -s simRat_chr6.simRat.chr6 185498 4 + 647215 GAGC------- - -a -s simMouse_chr6.simMouse.chr6 195223 6 + 636262 AAGAAC -s Anc0.Anc0refChr5 17677 6 + 87904 AAGAGC -s Anc1.Anc1refChr8 31266 6 + 57822 AAGAGC -s Anc2.Anc2refChr15 11295 6 + 86568 AACAGC -s mr.mrrefChr5 50072 6 + 294540 AAGAAC -s simCow_chr6.simCow.chr6 194423 6 + 602619 ACAAGA -s simDog_chr6.simDog.chr6 475968 6 - 593897 AACAGC -s simHuman_chr6.simHuman.chr6 198310 6 + 601863 AAGAGC - -a -s simMouse_chr6.simMouse.chr6 195229 62 + 636262 AATCAATTAATATTGAAAATACCAAATTCATGGAGAAGACTTATATACCCTCATTAAACTGA -s Anc0.Anc0refChr5 17688 62 + 87904 AGTCAACAAATATCATAAATATCAAACTCATTGAGAAGACCTATCTATTTTTTCAACATAAC -s Anc1.Anc1refChr8 31277 62 + 57822 AGTCAACAAATATCATAAATATCAAACTCATTGAGAAGACCTATCTATTTTTTCAACATAAC -s Anc2.Anc2refChr15 11306 62 + 86568 AGTCAACAAATATCATAAATATCAAACTCATTGAGAAGACCTACCTATTTTTTCAACCTAAC -s mr.mrrefChr5 50078 62 + 294540 AATCAATTAATATTGAAAATACCAAATTCATTGAGAAGACTTATATACTCTTATTAAACTGA -s simCow_chr6.simCow.chr6 194434 62 + 602619 AGTCGACAGACATCATAAATATCAAATTTAGTGAAAAGTTCCAGCTATTTTTTAAACCTACC -s simDog_chr6.simDog.chr6 475982 62 - 593897 AGTCAACAAATATCATAAATATCAAACTCATTGGGAAGACCTACCTATTCTTTCAACCTCAC -s simHuman_chr6.simHuman.chr6 198321 62 + 601863 AGTCAACAAATATCAGAAATGTCAAACTCATTGAGAAAACCTATTTATTTTTTCAACATAAC -s simRat_chr6.simRat.chr6 185502 36 + 647215 --------------------------TTCATTGAAAACACTTATGTACTCTTAGTAAACTGA - -a -s simMouse_chr6.simMouse.chr6 195291 25 + 636262 TCTTAGGATACATTAAGCCTCTACA -s Anc0.Anc0refChr5 17750 25 + 87904 TCTTAGGATTTATGCAACCTCTACA -s Anc1.Anc1refChr8 31339 25 + 57822 TCTTAGGATTTATGCAACCTCTACA -s Anc2.Anc2refChr15 11372 25 + 86568 TCTTGGGATTTATGCAACCTCTACA -s mr.mrrefChr5 50140 25 + 294540 TCTTAGGATACATGCAGCCTCTACA -s simCow_chr6.simCow.chr6 194500 25 + 602619 TCTTGGGATTTATGCAGCTTCTACA -s simDog_chr6.simDog.chr6 476048 25 - 593897 TTTTGGGATCAATGCGACCACTACA -s simHuman_chr6.simHuman.chr6 198383 25 + 601863 CCTTAGGATTTATGCAACCTATACA -s simRat_chr6.simRat.chr6 185538 25 + 647215 TCTTAGGATACATGCAGCCTCTGTA - -a -s simMouse_chr6.simMouse.chr6 195316 20 + 636262 ATACTGAAGTGCAGGTTATA -s Anc0.Anc0refChr5 17783 20 + 87904 ATCCTGAAGTAGGGGTTACA -s Anc1.Anc1refChr8 31372 20 + 57822 ATCCTGAAGTAGGGGTTACA -s Anc2.Anc2refChr15 11405 20 + 86568 ATCCTGAAGTAGGGGTTACA -s mr.mrrefChr5 50165 20 + 294540 ATACTGAAGTACAGGTTATA -s simCow_chr6.simCow.chr6 194533 20 + 602619 ACCCTGATGTAGGGGTTACA -s simDog_chr6.simDog.chr6 476081 20 - 593897 GTCCTGAAGTAGGGGTTACA -s simHuman_chr6.simHuman.chr6 198416 20 + 601863 ATCCTGACGTAGGGGTTACA -s simRat_chr6.simRat.chr6 185563 20 + 647215 ATGCTGAAGCACAGACTATA - -a -s simMouse_chr6.simMouse.chr6 195336 2 + 636262 TG -s Anc0.Anc0refChr5 17803 2 + 87904 AG -s Anc1.Anc1refChr8 31392 2 + 57822 AG -s Anc2.Anc2refChr15 11425 2 + 86568 AT -s mr.mrrefChr5 50185 2 + 294540 TG -s simCow_chr6.simCow.chr6 194565 2 + 602619 AT -s simDog_chr6.simDog.chr6 476101 2 - 593897 AT -s simHuman_chr6.simHuman.chr6 198436 2 + 601863 AG -s simRat_chr6.simRat.chr6 185583 2 + 647215 TG - -a -s simMouse_chr6.simMouse.chr6 195338 1 + 636262 T -s Anc0.Anc0refChr5 17805 1 + 87904 T -s Anc1.Anc1refChr8 31394 1 + 57822 T -s Anc2.Anc2refChr15 11442 1 + 86568 T -s mr.mrrefChr5 50187 1 + 294540 T -s simCow_chr6.simCow.chr6 194582 1 + 602619 T -s simDog_chr6.simDog.chr6 476118 1 - 593897 T -s simHuman_chr6.simHuman.chr6 198438 1 + 601863 C -s simRat_chr6.simRat.chr6 185585 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 195339 92 + 636262 GTTTGAAGGCAGGGGAGAAATAAAGAGTTTTCTCATGCAATGATGTACCAGTTAAGTACCCTCATTCACCTGCATCAAAATAATGAGGGAGT -s Anc0.Anc0refChr5 17806 91 + 87904 GTTAGAGAGCAGGGTAGAAATAAAAAACTTTGTCATGCA-TTAAGTACTGACTAAGTACCCTCATTGACATGGATACAATTATTGATGGTAA -s Anc1.Anc1refChr8 31395 92 + 57822 GTTAGAGAGCAGGGTAGAAATAAAAAACTTTGTCATGCAATTAAGTACTGACTAAGTACCCTCATTGACATGGATACAATTATTGATGGTAA -s Anc2.Anc2refChr15 11443 91 + 86568 GTTAAAGAGCAAGGTAGAAATAAGAAACTTTGTCATGCA-TTAAGCACTGACTAAGTACCCTCATTGACATGGATACAATTATTGATGATAA -s mr.mrrefChr5 50188 92 + 294540 GTTTGAAGGCAGGGTAGAAATAAAAAGTTTTCTCATGCAATGATGTACCAGTTAAGTACCCTCATTGACCTGGATCAAAATATTGAGGGTGA -s simCow_chr6.simCow.chr6 194583 79 + 602619 GGCAATGAGTAAG------------GAGTTTGTTATGCA-ATGAGCACTGATTAAGTACACTCATTGAGATTGATACACTTATTGATAATAA -s simDog_chr6.simDog.chr6 476119 89 - 593897 GTTAAAGGTCAAGGTAGAAATAAGAAACTTTGTCACGCA-TGAAG--CTGACAAACAACCCTCATTGACATGGATACAATTATTGGTGATGA -s simHuman_chr6.simHuman.chr6 198442 92 + 601863 GTTGGAGAGCAGAGTAGAAAGAAAAAACTTTGCCATTCAGTTAAGTACTGCATAAGTACCCTAAATGACATGGATACAATTATTCATGGTAA -s simRat_chr6.simRat.chr6 185586 89 + 647215 GTTTGAAGGTAGGGTAAAAATAAAAGTTTTTCTCGT---ATGATGTGCCAATTAAATAACCTCATTGACCTGGATCAAAGTATTAAGGGTGA - -a -s simMouse_chr6.simMouse.chr6 195431 185 + 636262 TAAATCACTCATATTTACTGGTTTAAGTTGCCACGCTGCTTATATAGAGAACATATCAACAACATAGCACTATGGCATGTACCATGTACAGCCACTTGAACCATTTGATCTATTCATTCTGTCCACACAAGATGTCACAGCTAGTGCCCTTTGAGGGACATGATGAGATTGCACCCTTGTTTTTC -s Anc0.Anc0refChr5 17900 32 + 87904 CAATTAAGTCATGTTCACTAGTCTAAGTTGCC--------------------------------------------------------------------------------------------------------------------------------------------------------- -s Anc1.Anc1refChr8 31490 32 + 57822 CAATTAAGTCATGTTCACTAGTCTAAGTTGCC--------------------------------------------------------------------------------------------------------------------------------------------------------- -s Anc2.Anc2refChr15 11537 32 + 86568 CAATAAACTCATGTTCACTAGTCTAAGTTGCC--------------------------------------------------------------------------------------------------------------------------------------------------------- -s mr.mrrefChr5 50280 177 + 294540 CAAATCAGTCATATTTACTGGTTTAAGTTGCCACGCTGCTTATATAGAGAACATATCAACAACATAGCACTATGGCATGTACCA----CAGCCACTTGAACCATTTGATCTAT-CATTCTGTCCACACAAGATGTCACAGCTAGTGCCCTTTGAGGGACATGA---GATTGCACCCTTGTTTTTC -s simCow_chr6.simCow.chr6 194667 32 + 602619 CAATAAATTTATGTTTACTAGTTGCATTTGCC--------------------------------------------------------------------------------------------------------------------------------------------------------- -s simDog_chr6.simDog.chr6 476211 32 - 593897 CAATAAACTCATGTTCACTAGTCTAAGTTGCC--------------------------------------------------------------------------------------------------------------------------------------------------------- -s simHuman_chr6.simHuman.chr6 198537 32 + 601863 CAGTTGAGTCATGTTCACTAGTCTAAATTGCC--------------------------------------------------------------------------------------------------------------------------------------------------------- -s simRat_chr6.simRat.chr6 185675 177 + 647215 CAAATTAGTCATATTTAATGGTTTAAGTTGCCATGCTATGTGTATGGAGAACATATCAACAGCATAGCCCTATGGCATGTACCA----CACCCACTTGAGCCATTCAATCTAT-CGTTCTGTGCACATAAGATGTTGTAGCTAGCACCCTGTAAGGGACATGA---GATTGGACCCATGTTTCTC - -a -s simMouse_chr6.simMouse.chr6 195616 94 + 636262 CTGGTGAAGTTAGGTGGGATCAACTAAACTGGGTACCACAGAGAATCTTTAGGGCCCTCATGAATCAAACTCGGGAGTAAGATGGACTTTACCA -s mr.mrrefChr5 50457 93 + 294540 CTGGTGAAGTTAGGTGGGATCAACTAAACTGGG-ACCACAGAGAATCTTTAGGGCCCTCATGAATCAAACTCGGGAGTAAGATGGACTTTACCA -s simRat_chr6.simRat.chr6 185855 93 + 647215 CTGGTGGAGTTAGATCGAATCACCTAAACCAGG-ACCACAGAGAATCTTTAGGGCCCTCATTGATTAAACTGAGGAGTAAGATAGACTCTACCA - -a -s simMouse_chr6.simMouse.chr6 195710 45 + 636262 CTAGGAGCCATACTGCATAAAAGCCCTTGCCAGACTTGTCATGTA -s Anc0.Anc0refChr5 17932 12 + 87904 ---------------------------------TCTGCCCATGTA -s Anc1.Anc1refChr8 31522 12 + 57822 ---------------------------------TCTGCCCATGTA -s Anc2.Anc2refChr15 11569 12 + 86568 ---------------------------------TCTGCCCATGTT -s mr.mrrefChr5 50550 45 + 294540 CTAGGAGCCATACTGCATAAAAGCCCTTGCCAGACTTGTCATGTA -s simCow_chr6.simCow.chr6 194699 12 + 602619 ---------------------------------CATATCCTTTTT -s simDog_chr6.simDog.chr6 476243 12 - 593897 ---------------------------------TCTGCCCATGTT -s simHuman_chr6.simHuman.chr6 198569 12 + 601863 ---------------------------------TCTGCCCATGTA -s simRat_chr6.simRat.chr6 185949 45 + 647215 CAAGCAGCCATATGGCATAAGAGCCCTCGCCAGACTCATCATGCC - -a -s simMouse_chr6.simMouse.chr6 195755 12 + 636262 GGGTTCATTAGT -s Anc0.Anc0refChr5 17944 9 + 87904 TGGTTTA---GT -s Anc1.Anc1refChr8 31534 12 + 57822 TGGTTTATTAGT -s Anc2.Anc2refChr15 11581 9 + 86568 TGGTTTT---GT -s mr.mrrefChr5 50595 12 + 294540 GGGTTCATTAGT -s simCow_chr6.simCow.chr6 194732 9 + 602619 TGGTTTT---GT -s simDog_chr6.simDog.chr6 476255 9 - 593897 TGGTTTT---GT -s simHuman_chr6.simHuman.chr6 198581 12 + 601863 TGGTTTATTAGT -s simRat_chr6.simRat.chr6 185994 12 + 647215 TGGTTCATTAGT - -a -s simMouse_chr6.simMouse.chr6 195767 4 + 636262 CAGG -s Anc0.Anc0refChr5 17953 3 + 87904 CAA- -s Anc1.Anc1refChr8 31546 3 + 57822 CAA- -s Anc2.Anc2refChr15 11590 3 + 86568 AAA- -s mr.mrrefChr5 50607 3 + 294540 CAG- -s simCow_chr6.simCow.chr6 194744 3 + 602619 AAG- -s simDog_chr6.simDog.chr6 476264 3 - 593897 AAA- -s simHuman_chr6.simHuman.chr6 198593 3 + 601863 CAA- -s simRat_chr6.simRat.chr6 186006 3 + 647215 CAA- - -a -s simMouse_chr6.simMouse.chr6 195771 47 + 636262 AGGTCCCATAAAACACACAATACTGCATAAGGTGCTATTACTGAAAT -s Anc0.Anc0refChr5 17957 47 + 87904 AGGTCCCATTAAACACACAATATTGcataaggtgttattactgaggt -s Anc1.Anc1refChr8 31550 47 + 57822 AGGTCCCATTAAACACACAATATTGCataaggtgttattactgaggt -s Anc2.Anc2refChr15 11594 47 + 86568 AGGTCCCATTAAGCACACAATATTGcataaggtgttattattgaggt -s mr.mrrefChr5 50610 47 + 294540 AGGTCCCATAAAACACACAATACTGCATAAGGTGCTATTACTGAAAT -s simCow_chr6.simCow.chr6 194748 46 + 602619 agttcctcttctgcactctgc-ttgctttctgtctatttaaagagtt -s simDog_chr6.simDog.chr6 476268 47 - 593897 AGGCCCCATGAAGCACACAATATTGcataaggtgttattgttgaggt -s simHuman_chr6.simHuman.chr6 198597 47 + 601863 AGGTCCCATTAAACGCAAAATATTTTataaggatatattactgaggt -s simRat_chr6.simRat.chr6 186009 47 + 647215 AGGTCCTGTAAAACACACAATACTGCATAAGGTGTTCCCCCCAAAAT - -a -s simMouse_chr6.simMouse.chr6 195818 90 + 636262 TAGTCCCACCTCAGCACGGACTAACAGTATTCACTAACCTCCAAGGTTTACAACCTGAACCTCCTTGATGCCTAAACTCCCCTGTAGTGC -s Anc0.Anc0refChr5 18004 55 + 87904 tagtccc--------------------tcttcactgccctct---gtttac---------tttctatctacttaaagagttcaatag--- -s Anc1.Anc1refChr8 31597 58 + 57822 tagtccc--------------------tcttcactgccctct---gtttac---------tttctatctacttaaagagttcaatagtgc -s Anc2.Anc2refChr15 11641 55 + 86568 tagtccc--------------------tcttcactgccctct---gtttgc---------tttctatctacttaaagagttcaatag--- -s mr.mrrefChr5 50657 90 + 294540 TAGTCCCACCTCAGCACGGACTAACAGTATTCACTAACCTCCAAGGTTTACAACCTGAACCTCCTTGATGCCTAAACTCCCCTGTAGTGC -s simCow_chr6.simCow.chr6 194799 55 + 602619 tagtccc--------------------ccttcactgccctct---gcttgc---------tctctgtctacttaaagagtacaatag--- -s simDog_chr6.simDog.chr6 476315 55 - 593897 tggtcct--------------------ttgccactccactct---gtttgc---------tttctatctacttaaggaactcaacag--- -s simHuman_chr6.simHuman.chr6 198644 58 + 601863 tagtccc--------------------tcttcactgccttct---gtctac---------tttctatctacttaaaaagttcaatagtgc -s simRat_chr6.simRat.chr6 186056 90 + 647215 TAGTTCCACCTCAGTGCGGACTAAAAGGATTCACTAGCCTCCAAGGTTTACAACCTGAGCTGACTTGATGGGTAAACTTCCCTATAGTGT - -a -s simMouse_chr6.simMouse.chr6 195908 14 + 636262 TGTCTGAGGTGTCT -s Anc0.Anc0refChr5 18059 5 + 87904 ------catt---t -s Anc1.Anc1refChr8 31655 14 + 57822 tgtgtgcattgcct -s Anc2.Anc2refChr15 11696 5 + 86568 ------catt---t -s mr.mrrefChr5 50747 14 + 294540 TGTCTGAGGTGTCT -s simCow_chr6.simCow.chr6 194854 5 + 602619 ------agct---t -s simDog_chr6.simDog.chr6 476370 5 - 593897 ------catt---t -s simHuman_chr6.simHuman.chr6 198704 14 + 601863 tgtgtgcattgcct -s simRat_chr6.simRat.chr6 186146 14 + 647215 TGTCTGAGGTGTTT - -a -s simMouse_chr6.simMouse.chr6 195922 98 + 636262 TTATCCTTGTTCATATGCAGGATAAAACCAAGGGCTTGCCTGCTGGACGAATCATCAGTAAAGCCAGTATCAGTGTATACGTGGAACTATGAAACAGC -s Anc0.Anc0refChr5 18068 20 + 87904 ttatttga---tacgtgcaga---------------------------------------------------------------------------gc -s Anc1.Anc1refChr8 31673 20 + 57822 ttatttga---tacgtgcaga---------------------------------------------------------------------------gc -s Anc2.Anc2refChr15 11705 20 + 86568 gtatttga---ttcgtgcaca---------------------------------------------------------------------------ga -s mr.mrrefChr5 50761 66 + 294540 TTATCCTT---CATATGCAGGATAAAACCAAGGGCTTGCCTGCTGGA--AATCATC---------------------------GAACTATGAAACAGC -s simCow_chr6.simCow.chr6 194863 20 + 602619 atatttga---ttcgtgcaca---------------------------------------------------------------------------ga -s simDog_chr6.simDog.chr6 476379 20 - 593897 gcacttga---tttgtataca---------------------------------------------------------------------------aa -s simHuman_chr6.simHuman.chr6 198722 20 + 601863 ttatttgc---tacctgcagt---------------------------------------------------------------------------gc -s simRat_chr6.simRat.chr6 186160 66 + 647215 TTTTCCCT---CATGTGCAGGGTAAAACTTAGGTCTTGCCCACTGTA--AATCATC---------------------------GAGCCATAAAACAGC - -a -s simMouse_chr6.simMouse.chr6 196020 4 + 636262 CTCC -s Anc0.Anc0refChr5 18088 4 + 87904 ttcc -s Anc1.Anc1refChr8 31693 4 + 57822 ttcc -s Anc2.Anc2refChr15 11725 4 + 86568 ttcc -s mr.mrrefChr5 50827 4 + 294540 CTCC -s simCow_chr6.simCow.chr6 194884 4 + 602619 ttgc -s simDog_chr6.simDog.chr6 476399 4 - 593897 tccC -s simHuman_chr6.simHuman.chr6 198742 4 + 601863 ttcc -s simRat_chr6.simRat.chr6 186226 4 + 647215 CTTT - -a -s simMouse_chr6.simMouse.chr6 196024 1 + 636262 A -s Anc0.Anc0refChr5 18092 1 + 87904 a -s Anc1.Anc1refChr8 31697 1 + 57822 a -s Anc2.Anc2refChr15 11729 1 + 86568 a -s mr.mrrefChr5 50831 1 + 294540 A -s simCow_chr6.simCow.chr6 194888 1 + 602619 c -s simDog_chr6.simDog.chr6 476409 1 - 593897 A -s simHuman_chr6.simHuman.chr6 198746 1 + 601863 a -s simRat_chr6.simRat.chr6 186230 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 196025 23 + 636262 AAAGGCATACTGCCCCAAATTCA -s Anc0.Anc0refChr5 18098 23 + 87904 aaagtcttgaTGCCTCTACCTCC -s Anc1.Anc1refChr8 31703 23 + 57822 aaagtcttgaTGCCTCTACCTCC -s Anc2.Anc2refChr15 11735 23 + 86568 aaagtcttgaTGCCTATACCTCC -s mr.mrrefChr5 50832 23 + 294540 AAAGGCATACTGCCCCAAATTCA -s simCow_chr6.simCow.chr6 194894 23 + 602619 agagtcttgaTGCCTATACCTCC -s simDog_chr6.simDog.chr6 476415 23 - 593897 AAAGTATTGATGCCTATACCTCC -s simHuman_chr6.simHuman.chr6 198752 23 + 601863 aaagtcttgaTGCCTCTACCTCC -s simRat_chr6.simRat.chr6 186231 23 + 647215 AAAGGCGAACTGCCCTAAATATG - -a -s simMouse_chr6.simMouse.chr6 196048 49 + 636262 GATGATCTAAGCAACCTAATGCTGTCTgaggtgtctttaaccttcatat -s Anc0.Anc0refChr5 18123 38 + 87904 GTAGGACTATG-----CAACTGTGT------TGTCTTTCtccttcatat -s Anc1.Anc1refChr8 31728 38 + 57822 GTAGGACTATG-----CAACTGTGT------TGTCTTTCtccttcatat -s Anc2.Anc2refChr15 11760 38 + 86568 GTAGGACTATG-----CAACTGTGT------TCTCTTTCtccttcatat -s mr.mrrefChr5 50855 44 + 294540 GATGATCTAAG-----TAATGCTGTCTgaggtgtcTTTAaccttcatat -s simCow_chr6.simCow.chr6 194919 38 + 602619 GCAGGACTATC-----CAACTGTGT------TCTCTTTCttcctcatat -s simDog_chr6.simDog.chr6 476440 38 - 593897 GTAGGACTGTG-----TAAGTGTGT------TCTCTTTCtcctttgtat -s simHuman_chr6.simHuman.chr6 198777 38 + 601863 GTAGGACTATT-----CAACTTTGT------CGTCTTTCtccttcatat -s simRat_chr6.simRat.chr6 186254 44 + 647215 GATGGTCTAAA-----TATGGAGGTCTAAGCAACCTCCACCGGACAAAT - -a -s simMouse_chr6.simMouse.chr6 196097 14 + 636262 gcaggataaaacca -s Anc0.Anc0refChr5 18161 14 + 87904 atgaggtagaacca -s Anc1.Anc1refChr8 31766 14 + 57822 atgaggtagaacca -s Anc2.Anc2refChr15 11798 14 + 86568 gtgaggtagagcca -s mr.mrrefChr5 50899 14 + 294540 acaggataaaacca -s simCow_chr6.simCow.chr6 194957 14 + 602619 gtgagccaaagcca -s simDog_chr6.simDog.chr6 476478 14 - 593897 gtgaggtggagcca -s simHuman_chr6.simHuman.chr6 198815 14 + 601863 atgaagtagaacca -s simRat_chr6.simRat.chr6 186299 14 + 647215 ACTTTATAAGGCCA - -a -s simMouse_chr6.simMouse.chr6 196111 5 + 636262 agggc -s Anc0.Anc0refChr5 18175 5 + 87904 aggtc -s Anc1.Anc1refChr8 31780 5 + 57822 aggtc -s Anc2.Anc2refChr15 11812 5 + 86568 aggtc -s mr.mrrefChr5 50913 5 + 294540 agggc -s simCow_chr6.simCow.chr6 194971 5 + 602619 aggtc -s simDog_chr6.simDog.chr6 476492 5 - 593897 aggtc -s simHuman_chr6.simHuman.chr6 198829 5 + 601863 aagtc -s simRat_chr6.simRat.chr6 186314 5 + 647215 AGGGC - -a -s simMouse_chr6.simMouse.chr6 196116 10 + 636262 ttgcctgctg -s Anc0.Anc0refChr5 18180 10 + 87904 ttgtccactt -s Anc1.Anc1refChr8 31785 10 + 57822 ttgtccactt -s Anc2.Anc2refChr15 11817 10 + 86568 ttgtccactt -s mr.mrrefChr5 50918 10 + 294540 ttgcctgctt -s simCow_chr6.simCow.chr6 194976 10 + 602619 ttatccacct -s simDog_chr6.simDog.chr6 476497 10 - 593897 ttgtctgctc -s simHuman_chr6.simHuman.chr6 198834 10 + 601863 ttgtccactt -s simRat_chr6.simRat.chr6 186322 8 + 647215 TCGCCT--TT - -a -s simMouse_chr6.simMouse.chr6 196126 40 + 636262 gaaatcatcagtaagccagtatcattgtatacgtggaacc -s Anc0.Anc0refChr5 18190 40 + 87904 ggagtcatcagtgaacccatatcactgtatatgtgcaacc -s Anc1.Anc1refChr8 31795 40 + 57822 ggagtcatcagtgaacccatatcactgtatatgtgcaacc -s Anc2.Anc2refChr15 11827 40 + 86568 ggagtcatcagtgaacccatatcactgtatatgtgcatgc -s mr.mrrefChr5 50928 40 + 294540 gaaatcatcagtaagccagtatcattgtatatgtggaacc -s simCow_chr6.simCow.chr6 194986 40 + 602619 ggagtcatcagtgaacccatatcactgtgtatgttcatgc -s simDog_chr6.simDog.chr6 476508 40 - 593897 ggagtcatcaatggccccataacattggatatgtgtatgc -s simHuman_chr6.simHuman.chr6 198844 40 + 601863 ggagtcatcagtgaacccatatcacagtatatgtgcaacc -s simRat_chr6.simRat.chr6 186330 38 + 647215 CATAGTGTTGGTATCTGACTATC--TGAATATTTCTAACC - -a -s simMouse_chr6.simMouse.chr6 196166 48 + 636262 atgaaacagccttcaaaaggcaaactgccccaaatacggatgatctaa -s Anc0.Anc0refChr5 18230 46 + 87904 atgaaacagcctccagaaagcaaactacctt--ataaggatggtctaa -s Anc1.Anc1refChr8 31835 46 + 57822 atgaaacagcctccagaaagcaaactacctt--ataaggatggtctaa -s Anc2.Anc2refChr15 11867 46 + 86568 atgaaactgcctccagagggcaaaccacttt--ataaggacagtctaa -s mr.mrrefChr5 50968 48 + 294540 atgaaacagccttcagaaagcaaactgccctaaatacggatggtctaa -s simCow_chr6.simCow.chr6 195026 46 + 602619 atgaatctgcctcgagatggcataccaaagt--ataagaacagtcaaa -s simDog_chr6.simDog.chr6 476548 46 - 593897 attacactacctccagagggcaaaccacttc--acaaggacagcctaa -s simHuman_chr6.simHuman.chr6 198884 45 + 601863 gtgaaacagcctcctgaaagc-aactacctt--ataaggatggtctaa -s simRat_chr6.simRat.chr6 186395 48 + 647215 ATTAAACAGGCTTTAGAAAGCAAACTGCCCTAAATGTGGACGGTCTAA - -a -s simMouse_chr6.simMouse.chr6 196214 13 + 636262 gcaaccttcactg -s Anc0.Anc0refChr5 18278 13 + 87904 acaacctcaattg -s Anc1.Anc1refChr8 31883 13 + 57822 acaacctcaattg -s Anc2.Anc2refChr15 11915 13 + 86568 acaacctcaattg -s mr.mrrefChr5 51016 13 + 294540 gcaacctcaactg -s simCow_chr6.simCow.chr6 195074 13 + 602619 acaacctcaattg -s simDog_chr6.simDog.chr6 476596 13 - 593897 actacctcagttg -s simHuman_chr6.simHuman.chr6 198931 13 + 601863 agaacctcaaatg -s simRat_chr6.simRat.chr6 186443 13 + 647215 GCAACCTCAAGTG - -a -s simMouse_chr6.simMouse.chr6 196227 48 + 636262 gataacctactttataaggccataggccccccctCTGTGGTTTTGGTA -s Anc0.Anc0refChr5 18294 45 + 87904 gacagcttgctttataagggcatagggccct--t-GGTAGAGATGGTG -s Anc1.Anc1refChr8 31899 45 + 57822 gacagcttgctttataagggcatagggccct--t-GGTAGAGATGGTG -s Anc2.Anc2refChr15 11931 45 + 86568 gacaacctgctttataagggcttagggcccT--T-GATAGAGATGGTG -s mr.mrrefChr5 51029 46 + 294540 gacagcttactttataaggccatagggccct--tCTGTAGTGTTGGTA -s simCow_chr6.simCow.chr6 195090 40 + 602619 gactacctgctttataaggg-----GGCCCT--T-AATAGAGTTGGTG -s simDog_chr6.simDog.chr6 476612 45 - 593897 gacaatctgctgtataagggcttagggcccT--G-GATAGAGATGGTG -s simHuman_chr6.simHuman.chr6 198947 45 + 601863 gacggcttgccttataagggcatagggccct--t-ggtatagctggtg -s simRat_chr6.simRat.chr6 186456 46 + 647215 GACAGCTTACTTTATAAGGCCATAGGGCCCT--TCATTAGTGTTGGTA - -a -s simMouse_chr6.simMouse.chr6 196275 23 + 636262 TCTGACTCTCAATATCTGAATAT -s Anc0.Anc0refChr5 18339 17 + 87904 TCTGACt------atatGAATAT -s Anc1.Anc1refChr8 31944 17 + 57822 TCTGACt------atatGAATAT -s Anc2.Anc2refChr15 11976 17 + 86568 TCTAATt------gcacGAATCT -s mr.mrrefChr5 51075 17 + 294540 TCTGACT------ATCTGAATAT -s simCow_chr6.simCow.chr6 195130 12 + 602619 TCTAAT-----------GAATCC -s simDog_chr6.simDog.chr6 476658 17 - 593897 TCTAATT------GCACAAATCT -s simHuman_chr6.simHuman.chr6 198992 17 + 601863 cctggct------atatgaatat -s simRat_chr6.simRat.chr6 186502 17 + 647215 TCTGACT------ATCTGAATAT - -a -s simMouse_chr6.simMouse.chr6 196298 15 + 636262 TTCCGACCTATCTGG -s Anc0.Anc0refChr5 18359 15 + 87904 ttctgagctatgTGG -s Anc1.Anc1refChr8 31964 15 + 57822 ttctgagctatgTGG -s Anc2.Anc2refChr15 11996 15 + 86568 ttctcagctgtgTTG -s mr.mrrefChr5 51092 15 + 294540 TTCTGACCTATGTGG -s simDog_chr6.simDog.chr6 476678 15 - 593897 TTCTCAGCTGTGTTG -s simHuman_chr6.simHuman.chr6 199012 15 + 601863 ttctgagccatgTGG -s simRat_chr6.simRat.chr6 186519 15 + 647215 TTCTAACCTATGTGG - -a -s simMouse_chr6.simMouse.chr6 196313 12 + 636262 TTCTTAGCTGTG -s Anc0.Anc0refChr5 18374 12 + 87904 TATTTGGTACTA -s Anc1.Anc1refChr8 31979 12 + 57822 TATTTGGTACTA -s Anc2.Anc2refChr15 12013 12 + 86568 TAGGTTGTGCCA -s mr.mrrefChr5 51107 12 + 294540 TTCTTAGCTGTG -s simCow_chr6.simCow.chr6 195147 12 + 602619 TAGGTTGTGCCA -s simHuman_chr6.simHuman.chr6 199027 12 + 601863 TATTTGGTATTA -s simRat_chr6.simRat.chr6 186534 12 + 647215 TTCTTAGCTGTG - -a -s simMouse_chr6.simMouse.chr6 196325 21 + 636262 GTTTTTCAATTAGTCACATTA -s Anc0.Anc0refChr5 18386 14 + 87904 GGTTTCCATCC-------TTA -s Anc1.Anc1refChr8 31991 14 + 57822 GGTTTCCATCC-------TTA -s Anc2.Anc2refChr15 12037 14 + 86568 AGTCTCCCTCC-------CTA -s mr.mrrefChr5 51119 21 + 294540 GTTTTCCAATCAGTCACATTA -s simCow_chr6.simCow.chr6 195171 14 + 602619 ATTGCCCCTAC-------TTA -s simDog_chr6.simDog.chr6 476694 14 - 593897 AGCCTCCCTCC-------CTA -s simHuman_chr6.simHuman.chr6 199039 14 + 601863 GGTTTCGATGC-------TGG -s simRat_chr6.simRat.chr6 186546 21 + 647215 GTTTTCCAATCAGTCACATTA - -a -s simMouse_chr6.simMouse.chr6 196346 12 + 636262 ATCACTTCAATT -s Anc0.Anc0refChr5 18400 12 + 87904 ATCCCTTCAATT -s Anc1.Anc1refChr8 32005 12 + 57822 ATCCCTTCAATT -s Anc2.Anc2refChr15 12051 12 + 86568 GTTCTTTTAATT -s mr.mrrefChr5 51140 12 + 294540 ATCACTTCAATT -s simCow_chr6.simCow.chr6 195185 12 + 602619 ATTCTTTTAATT -s simDog_chr6.simDog.chr6 476709 12 - 593897 GTTCTTTTAATT -s simHuman_chr6.simHuman.chr6 199053 12 + 601863 ATCTCCACAATT -s simRat_chr6.simRat.chr6 186567 12 + 647215 CTCATTTGAATT - -a -s simMouse_chr6.simMouse.chr6 196358 8 + 636262 ACACTTGT -s Anc0.Anc0refChr5 18413 8 + 87904 ACAATTGT -s Anc1.Anc1refChr8 32018 8 + 57822 ACAATTGT -s Anc2.Anc2refChr15 12064 8 + 86568 ACAATTAT -s mr.mrrefChr5 51152 8 + 294540 ACACTTGT -s simCow_chr6.simCow.chr6 195198 8 + 602619 ACAATTAT -s simDog_chr6.simDog.chr6 476722 8 - 593897 ACAATTAT -s simHuman_chr6.simHuman.chr6 199066 8 + 601863 ACCAGTGT -s simRat_chr6.simRat.chr6 186579 8 + 647215 ACAATTGT - -a -s simMouse_chr6.simMouse.chr6 196366 64 + 636262 CCCCTCCTCAATAGTGCGTTCAATACGATCACAACATTATCGCCTGCTGTGGATAGCTGTGCTG -s Anc0.Anc0refChr5 18421 7 + 87904 CCTCT---------------------------------------------------------TG -s Anc1.Anc1refChr8 32026 7 + 57822 CCTCT---------------------------------------------------------TG -s Anc2.Anc2refChr15 12072 7 + 86568 CCTCT---------------------------------------------------------TG -s mr.mrrefChr5 51160 63 + 294540 CCCCTCCTCAATAGTGCGT-CAATACGATCACAACATTATCGCCTCCTGTGGATAGCTGTGCTG -s simCow_chr6.simCow.chr6 195206 7 + 602619 CCTCT---------------------------------------------------------TG -s simDog_chr6.simDog.chr6 476730 7 - 593897 CCTCC---------------------------------------------------------TG -s simHuman_chr6.simHuman.chr6 199075 7 + 601863 TTTCT---------------------------------------------------------TG -s simRat_chr6.simRat.chr6 186587 63 + 647215 CCCCTCCTCAATAGTGTGT-CAATACGTTCACAACACTATCGCCTCCTGTGGATAGCTGTGCTG - -a -s simMouse_chr6.simMouse.chr6 196430 62 + 636262 CTCTTTCAGTCCACACACTTGAGGGGTTCTTGCTCACTGCCAATTTTGGTTTTTCTACAAAA -s Anc0.Anc0refChr5 18428 60 + 87904 CTATTCTACTTCACATGTTTGAGGGGTTCTTTCTCAGTGCCAATATGAGTTT--CTACAATG -s Anc1.Anc1refChr8 32033 60 + 57822 CTATTCTACTTCACATGTTTGAGGGGTTCTTTCTCAGTGCCAATATGAGTTT--CTACAATG -s Anc2.Anc2refChr15 12153 60 + 86568 CTATTCTACTTCACATGTTTGAGGGGTTTTTTCTCAGTGCCAGTATGAGTTT--ATCCAGTG -s mr.mrrefChr5 51223 60 + 294540 CTCTTCCAGTCCACATGCTTGAGGGGTTCTTGCTCACTGCCAATTTTAGTTT--CTACAAAA -s simCow_chr6.simCow.chr6 195288 60 + 602619 GTGTTATACTTCAAATGTTTGAGGGGTTCTTTTTCAGTACCATTATGAGTAT--ACGCATTG -s simDog_chr6.simDog.chr6 476812 60 - 593897 CTATTCTACTTCACATGTTTGAGGGGTTTTTTCCTGGTGCCAGTATGAGATT--ATCCAGGA -s simHuman_chr6.simHuman.chr6 199082 60 + 601863 CAATTCACCTTCACTTGATTGAGGGGTCCTTTCTCAGTGCCAATATGAGTTT--CTACAATG -s simRat_chr6.simRat.chr6 186650 60 + 647215 CTCTTCCAGTCCACATGCTTGCAGGGGTATTGCTCACTGGCAGTTTTAGTTT--CTTCAAAG - -a -s simMouse_chr6.simMouse.chr6 196492 50 + 636262 CAAAGAACATTATTGAACTCCTATCTTCATCAGTTTTCCTCTTACCTAAC -s Anc0.Anc0refChr5 18488 42 + 87904 C----ATATTTATACTGCTCCTATTTATACCACCTCACCACTT----GGC -s Anc1.Anc1refChr8 32093 46 + 57822 C----ATATTTATACTGCTCCTATTTATACCACCTCACCACTTATCGGGC -s Anc2.Anc2refChr15 12213 42 + 86568 C----ATATTTATTCTGCTCCTATTTTTACCACCTCACCACTT----GCC -s mr.mrrefChr5 51283 50 + 294540 CAAAGAACATTATAGAGCTCCTATCTATATCAGCTCACCTCTTATCTAAC -s simCow_chr6.simCow.chr6 195348 34 + 602619 C----A--------CTGCCCCTATTCTCATCGCCTCACTGTTT----GCC -s simDog_chr6.simDog.chr6 476873 42 - 593897 C----ATATTTATTTGGCTCTTATTTTTACCACGTCACCACTT----GCC -s simHuman_chr6.simHuman.chr6 199142 46 + 601863 C----ATTTTAATACTGCTCCTATTTATACCACCTCACCACTTATCGGGC -s simRat_chr6.simRat.chr6 186710 50 + 647215 CAAAGAACGTTTTAGAGGTCCTATCTATATCAGCTCACCTCTTATCTAAC - -a -s simMouse_chr6.simMouse.chr6 196542 5 + 636262 CATCC -s Anc0.Anc0refChr5 18530 5 + 87904 CATCC -s Anc1.Anc1refChr8 32139 5 + 57822 CATCC -s Anc2.Anc2refChr15 12255 5 + 86568 CATCC -s mr.mrrefChr5 51333 5 + 294540 CATCC -s simCow_chr6.simCow.chr6 195389 5 + 602619 CATCC -s simDog_chr6.simDog.chr6 476915 5 - 593897 TATAC -s simHuman_chr6.simHuman.chr6 199188 5 + 601863 CATCC -s simRat_chr6.simRat.chr6 186760 5 + 647215 CATCC - -a -s simMouse_chr6.simMouse.chr6 196547 17 + 636262 TGAAACTAGCTCCTTTT -s Anc0.Anc0refChr5 18539 17 + 87904 CAAAACTAGCTCCTTTT -s Anc1.Anc1refChr8 32148 17 + 57822 CAAAACTAGCTCCTTTT -s Anc2.Anc2refChr15 12264 17 + 86568 CAAAACTAGCTCTTTTT -s mr.mrrefChr5 51338 17 + 294540 TGAAACTAGCTCCTTTT -s simCow_chr6.simCow.chr6 195398 17 + 602619 TGCAACTTGCTCGATAG -s simDog_chr6.simDog.chr6 476924 17 - 593897 CAATACCAGCTCTTTTT -s simHuman_chr6.simHuman.chr6 199197 17 + 601863 CAAAACTAGCTCCTTTT -s simRat_chr6.simRat.chr6 186765 17 + 647215 TGAAACTAGCTCCTTTT - -a -s simMouse_chr6.simMouse.chr6 196564 101 + 636262 CCTAACCCCATAGTGATTTCGCCTTATATTCCTCAAATAATCGCAATTGATATAAGCCCAAGTCCATTTTCTGTAACGGAGAGCCATAAGGGAAGTGTAGA -s Anc0.Anc0refChr5 18558 95 + 87904 CCCAGTTACATGGCAAGTTCTTAATCTATTCCTTAAACAATCAAAATTCGTACAA----AGGT--GTTCACTGCAACGACAAAACATAAGGGAAGTGTAGA -s Anc1.Anc1refChr8 32167 95 + 57822 CCCAGTTACATGGCAAGTTCTTAATCTATTCCTTAAACAATCAAAATTCGTACAA----AGGT--GTTCACTGCAACGACAAAACATAAGGGAAGTGTAGA -s Anc2.Anc2refChr15 12283 95 + 86568 CCCAGTTACATGGCAAGTTCTTAATCTATTTCTTAAACAATCAAACTTCGTACAT----AGGT--GTTCATTACAACAACAAAACATAAGGGAAGTGTAGA -s mr.mrrefChr5 51357 101 + 294540 CCCAACCCCATAGTGATTTCGCCTTATATTCCTTAAATAATCACAATTGATACAAGCCCAAGTCCATTTTCTGTAACGGAGAGCCATAAGGGAAGTGTAGA -s simCow_chr6.simCow.chr6 195417 95 + 602619 CATAGCTACATGGCAACTCCTTACTCTATTGCTTAAACAACCAAGGAACGTACAC----AGGT--GTTCGTTTCAACAACAAAACATAAGGGAAGTGTAGA -s simDog_chr6.simDog.chr6 476943 95 - 593897 CCCAGTCACATGGCAAGTTCTCAATCTATTTTTTAAACAATCGAACTTGGTACAT----AGAG--GTTCATTACAACAACAAAACATAAGGGAAGTGTAGA -s simHuman_chr6.simHuman.chr6 199216 95 + 601863 CCCAGTTGCATGACCGGTTCTTGATTTACCCCTTAAACAATCAAAATTCGTACAA----AGGT--GTTCACTGCAATGACACAACATAAGGGAAGTGTAGA -s simRat_chr6.simRat.chr6 186784 88 + 647215 CCCAACCCCATAGTGATTTGCCCTCATATTCCTTAAATAATCACAATTGAAACAAGTCCAAGTCCATGTTCTGTGA-------------GGGAAGTGTAGA - -a -s simMouse_chr6.simMouse.chr6 196665 5 + 636262 TGCCA -s Anc0.Anc0refChr5 18653 5 + 87904 CGCCA -s Anc1.Anc1refChr8 32262 5 + 57822 CGCCA -s Anc2.Anc2refChr15 12378 5 + 86568 CTCCA -s mr.mrrefChr5 51458 5 + 294540 TGCCA -s simCow_chr6.simCow.chr6 195515 5 + 602619 CACCA -s simDog_chr6.simDog.chr6 477038 5 - 593897 TTCCA -s simHuman_chr6.simHuman.chr6 199311 5 + 601863 CGCCA -s simRat_chr6.simRat.chr6 186872 5 + 647215 TGCCA - -a -s simMouse_chr6.simMouse.chr6 196670 4 + 636262 ACAG -s Anc0.Anc0refChr5 18658 4 + 87904 AAAG -s Anc1.Anc1refChr8 32267 4 + 57822 AAAG -s Anc2.Anc2refChr15 12384 4 + 86568 AAAG -s mr.mrrefChr5 51463 4 + 294540 ACAG -s simCow_chr6.simCow.chr6 195521 4 + 602619 AAAG -s simDog_chr6.simDog.chr6 477044 4 - 593897 AAAG -s simHuman_chr6.simHuman.chr6 199316 4 + 601863 GTAG -s simRat_chr6.simRat.chr6 186877 4 + 647215 ACTG - -a -s simMouse_chr6.simMouse.chr6 196674 14 + 636262 CCTATGTGTCCACA -s Anc0.Anc0refChr5 18663 14 + 87904 CCTACTTGTCCTCA -s Anc1.Anc1refChr8 32272 14 + 57822 CCTACTTGTCCTCA -s Anc2.Anc2refChr15 12389 14 + 86568 CCTACTTGTACTCA -s mr.mrrefChr5 51467 14 + 294540 CCTATGTGTCCACA -s simCow_chr6.simCow.chr6 195526 14 + 602619 CTTACTTGTACTCA -s simDog_chr6.simDog.chr6 477049 14 - 593897 CCTACGTGAACTCA -s simHuman_chr6.simHuman.chr6 199321 14 + 601863 CCTACTTGTCCTCA -s simRat_chr6.simRat.chr6 186881 14 + 647215 CCTATGTGTCCGCA - -a -s simMouse_chr6.simMouse.chr6 196688 91 + 636262 GGGTTGCTTTTAAGTGCATCCCAATAAATTAAGTCTAATTTAGAAACTAATTCTGTTCACAATCCTAACTTCTTACTATTTTAAGTTCTGG -s Anc0.Anc0refChr5 18677 89 + 87904 GGGTTGCTCATAAGTGCATCCCAATATATCAAGTATAACTTAGAAACTAATTCGACCCACAATTCTAAC--CTGGTTATTTTAAGTTGTGT -s Anc1.Anc1refChr8 32286 89 + 57822 GGGTTGCTCATAAGTGCATCCCAATATATCAAGTATAACTTAGAAACTAATTCGACCCACAATTCTAAC--CTGGTTATTTTAAGTTGTGT -s Anc2.Anc2refChr15 12413 89 + 86568 AGGTTGCTCATAAGTGCATCCCAATATATCAAGTATAACTTAGAAATTAATTCGACCCACAACTCTAAC--CTAGTTATTTTAAGTTGTGT -s mr.mrrefChr5 51481 91 + 294540 GGGTTGCTTTTAAGTGCATCCCAATAAATTAAGTCTAATTTAGAAACTAATTCTATCCACAATCCTAACTTCTGATTATTTTAAGTTCTGG -s simCow_chr6.simCow.chr6 195550 89 + 602619 AGGTTGCTCAGAAGTGAATCCCCATATATTATGAATACCTTAGAAGTTAATTCGACCCACAACTCTAAC--CTAGTTATTTTAAGTTGTGC -s simDog_chr6.simDog.chr6 477073 83 - 593897 AGGTTGCTCATAAGTGCATCCCAATGTATCAAGTATAACTTAGAAATTAATTAGATCCACAAC---AAC--TC---TCTTTTAAGTCGCGT -s simHuman_chr6.simHuman.chr6 199335 88 + 601863 GAGTTGCTCACAAGTGCATCCCAACATCTCAGGTATAACTTAGAAACT-ATTCGACCCGCAATTCTAAC--CTGGTTATTTTAAGTTGTGT -s simRat_chr6.simRat.chr6 186895 91 + 647215 GGGTTGCTTTTAAGTACATCCCAATAAATTAAGTGTAATTTAGAAACTAATTCTATCCACAATGTTAACTTCTGATAATTTTAAGTTCTGG - -a -s simMouse_chr6.simMouse.chr6 196779 9 + 636262 CAAAAGTGA -s Anc0.Anc0refChr5 18766 9 + 87904 CAGAGGTTA -s Anc1.Anc1refChr8 32375 9 + 57822 CAGAGGTTA -s Anc2.Anc2refChr15 12502 9 + 86568 CAGAGTTTC -s mr.mrrefChr5 51572 9 + 294540 CAAAAGTTA -s simCow_chr6.simCow.chr6 195639 9 + 602619 TGGTATTTC -s simDog_chr6.simDog.chr6 477156 9 - 593897 CAGAGTTTC -s simHuman_chr6.simHuman.chr6 199423 5 + 601863 C----GTTA -s simRat_chr6.simRat.chr6 186987 9 + 647215 CTAAACTTA - -a -s simMouse_chr6.simMouse.chr6 196788 38 + 636262 CATCTAAAAACCCAGTGCCCAGGGGGGGGGGAAGTGGA -s Anc0.Anc0refChr5 18775 33 + 87904 CATCTATAAACCCACTACCCTGGGGTG-----AGGGGA -s Anc1.Anc1refChr8 32384 33 + 57822 CATCTATAAACCCACTACCCTGGGGTG-----AGGGGA -s Anc2.Anc2refChr15 12511 33 + 86568 CATCTATAAACCCACTACCCTGGGGTA-----AGGGGA -s mr.mrrefChr5 51581 33 + 294540 CATCTAAAAACCCAGTGCCCAGGGGGG-----AGTGGA -s simCow_chr6.simCow.chr6 195648 33 + 602619 CATCTGTAAGCCCACTACCCTGGGGTA-----GGGGGG -s simDog_chr6.simDog.chr6 477165 33 - 593897 CATCTATGAACCCACTACCCTGGAGTA-----AGTAGA -s simHuman_chr6.simHuman.chr6 199429 33 + 601863 CATCTATAAACCCAATACTCTAGGGTG-----AGGGGA -s simRat_chr6.simRat.chr6 186996 33 + 647215 CATCTAAAAACCCAGTGCCCACGGGGA-----AGTGGA - -a -s simMouse_chr6.simMouse.chr6 196826 4 + 636262 GTGA -s Anc0.Anc0refChr5 18810 4 + 87904 GGGG -s Anc1.Anc1refChr8 32419 4 + 57822 GGGG -s Anc2.Anc2refChr15 12546 4 + 86568 GGGG -s mr.mrrefChr5 51614 4 + 294540 GTGA -s simCow_chr6.simCow.chr6 195683 4 + 602619 GGGG -s simDog_chr6.simDog.chr6 477200 4 - 593897 GGGG -s simHuman_chr6.simHuman.chr6 199464 4 + 601863 GGGG -s simRat_chr6.simRat.chr6 187029 4 + 647215 GTGA - -a -s simMouse_chr6.simMouse.chr6 196830 27 + 636262 GTGATCAAAGGGAGGACTGCAGCTCTA -s Anc0.Anc0refChr5 18814 27 + 87904 GTGACCCAAGGAAGGATCAGAGCACTA -s Anc1.Anc1refChr8 32423 27 + 57822 GTGACCCAAGGAAGGATCAGAGCACTA -s Anc2.Anc2refChr15 12554 27 + 86568 GTGGCCCAAGGAAGGATCAGAGCACTA -s mr.mrrefChr5 51618 27 + 294540 GTGACCAAAGGGAGGATTAGAGCACTA -s simCow_chr6.simCow.chr6 195691 26 + 602619 -CGGCCCAAGGAAGGATCAGATCACTA -s simDog_chr6.simDog.chr6 477208 27 - 593897 GTGGCTCAAAGATAGATCACAGCACTA -s simHuman_chr6.simHuman.chr6 199468 27 + 601863 GTGACCCAAGGAAGGATAAGAGCACTA -s simRat_chr6.simRat.chr6 187033 27 + 647215 GTGGCCTAAGGGTGGATTAGTGTACTA - -a -s simMouse_chr6.simMouse.chr6 196857 3 + 636262 GTG -s Anc0.Anc0refChr5 18842 3 + 87904 GTC -s Anc1.Anc1refChr8 32451 3 + 57822 GTC -s Anc2.Anc2refChr15 12582 3 + 86568 ATC -s mr.mrrefChr5 51646 3 + 294540 GTG -s simCow_chr6.simCow.chr6 195718 3 + 602619 CTC -s simDog_chr6.simDog.chr6 477236 3 - 593897 ATC -s simHuman_chr6.simHuman.chr6 199496 3 + 601863 GTT -s simRat_chr6.simRat.chr6 187061 3 + 647215 GTG - -a -s simMouse_chr6.simMouse.chr6 196860 11 + 636262 ATCAGTCCAAT -s Anc0.Anc0refChr5 18872 11 + 87904 ATCAGTCAAAA -s Anc1.Anc1refChr8 32481 11 + 57822 ATCAGTCAAAA -s Anc2.Anc2refChr15 12612 11 + 86568 ACCAGTCAAAA -s mr.mrrefChr5 51649 11 + 294540 ATCAGTCCAAA -s simCow_chr6.simCow.chr6 195747 11 + 602619 ACCAGTCAAAA -s simDog_chr6.simDog.chr6 477266 11 - 593897 TCCAGACCAAA -s simHuman_chr6.simHuman.chr6 199527 11 + 601863 ATCAGTCAAAA -s simRat_chr6.simRat.chr6 187064 11 + 647215 ATCAGTCCAAA - -a -s simMouse_chr6.simMouse.chr6 196871 21 + 636262 ACTTGGAACCTGCTTGGGGGC -s Anc0.Anc0refChr5 18884 21 + 87904 ACTTACAACCTGCTAGGGGAC -s Anc1.Anc1refChr8 32493 21 + 57822 ACTTACAACCTGCTAGGGGAC -s Anc2.Anc2refChr15 12624 21 + 86568 ACCCACAACCTGCGAGGATAC -s mr.mrrefChr5 51660 21 + 294540 ACTTGGAACCTGCTTGGGGGC -s simCow_chr6.simCow.chr6 195759 21 + 602619 ACCCACAACCTGGCAAGCTGC -s simDog_chr6.simDog.chr6 477278 21 - 593897 ACCCACAACCTGCGGGGATAC -s simHuman_chr6.simHuman.chr6 199539 21 + 601863 ACTTACAACCTGCTATGGGAC -s simRat_chr6.simRat.chr6 187075 21 + 647215 TCTTGGCACCTGCTCGGGGGC - -a -s simMouse_chr6.simMouse.chr6 196892 17 + 636262 ACACCTCCATGGTTTAG -s Anc0.Anc0refChr5 18906 17 + 87904 ATACTTCCAAGGTTTAG -s Anc1.Anc1refChr8 32515 17 + 57822 ATACTTCCAAGGTTTAG -s Anc2.Anc2refChr15 12646 17 + 86568 GTACTTCCAAGGTTAAG -s mr.mrrefChr5 51681 17 + 294540 ATACCTCCATGGTTTAG -s simCow_chr6.simCow.chr6 195781 17 + 602619 GTACTTCCAAAGTTCAG -s simDog_chr6.simDog.chr6 477300 14 - 593897 GCCC---CAAGGCTAAG -s simHuman_chr6.simHuman.chr6 199561 17 + 601863 ATACTGCCAAGGTTTGG -s simRat_chr6.simRat.chr6 187096 17 + 647215 ATACCTCTATGGTTTAG - -a -s simMouse_chr6.simMouse.chr6 196909 1 + 636262 C -s Anc0.Anc0refChr5 18931 1 + 87904 C -s Anc1.Anc1refChr8 32540 1 + 57822 C -s Anc2.Anc2refChr15 12671 1 + 86568 A -s mr.mrrefChr5 51698 1 + 294540 C -s simCow_chr6.simCow.chr6 195806 1 + 602619 A -s simDog_chr6.simDog.chr6 477322 1 - 593897 A -s simHuman_chr6.simHuman.chr6 199586 1 + 601863 C -s simRat_chr6.simRat.chr6 187113 1 + 647215 C - -a -s simMouse_chr6.simMouse.chr6 196910 87 + 636262 CATTGAGGGGCTCAATGGAGCTAAGACATAAAGGAATGACAGAATTGTCTGTGCCTGCATGAACTCAAGCCCTAATTCACTTGAATA -s Anc0.Anc0refChr5 18932 86 + 87904 CACTTGAGTGCTCCATGGAACT-AGACACAAAGCCCTGACAGGATCGTCTGTTCCAGTGTGGACTAAAGCACTATTTCTATTGAGTC -s Anc1.Anc1refChr8 32541 86 + 57822 CACTTGAGTGCTCCATGGAACT-AGACACAAAGCCCTGACAGGATCGTCTGTTCCAGTGTGGACTAAAGCACTATTTCTATTGAGTC -s Anc2.Anc2refChr15 12675 86 + 86568 CACTTGAGTACTCCATGGAGCC-ACACACAAAGCCCTGATAGGATCATCTTTTCCAGTGTGGACTAAAATACTATTTCTATTGAGTC -s mr.mrrefChr5 51699 87 + 294540 CATTGAGGGGCTCAATGGAACTAAGACATAAAGGAATGACAGAATTGTCTGTGCCTGCATGAACTCAAGCCCTAATTCACTTGAATA -s simCow_chr6.simCow.chr6 195810 86 + 602619 TCCTTGAGTACTCCATGGAGCC-ACACACAAAGCCCTGATAGGATCATCTTTTCCAGTGTGTACTGAGATACTATTTTTCTTGAGGC -s simDog_chr6.simDog.chr6 477326 45 - 593897 CACTTGTCTATTCC------------------------------------------GTGCGGACTAAAATACTACCTCTATCGACTC -s simHuman_chr6.simHuman.chr6 199587 86 + 601863 AGCTTGAGTGCTCCATGAAACT-AGACAAAAAGCCCTGACAGCGTGGTCTGTCCCAGTGTGGACCATAGCACTATTTCTTGTGGGTC -s simRat_chr6.simRat.chr6 187114 87 + 647215 CATCAAGGGGCTCAATGGAACTAAGACATAAAGGAATGACAAAATTATTGGTGCCCGGATGAACTCAATCCCTAATTCACTTGAATA - -a -s simMouse_chr6.simMouse.chr6 196997 29 + 636262 GGGTAAGTTTAGTCAGGAAAACTCTAAAT -s Anc0.Anc0refChr5 19021 29 + 87904 GGGTAAATTTAGACAAGAGAGCCTCAAAT -s Anc1.Anc1refChr8 32630 29 + 57822 GGGTAAATTTAGACAAGAGAGCCTCAAAT -s Anc2.Anc2refChr15 12764 29 + 86568 GGGTAAATTTGGACAAGAAAGCCTCAAAT -s mr.mrrefChr5 51786 29 + 294540 GGGTAAGTTTAGTCAAGAGAACTCCAAAT -s simCow_chr6.simCow.chr6 195899 27 + 602619 GGGTAAATTTGGACAA--ATGCCTTGAAT -s simDog_chr6.simDog.chr6 477374 29 - 593897 GAGCAAATTTGGACAAGAAAGCTTCAGGT -s simHuman_chr6.simHuman.chr6 199676 29 + 601863 GGATAATTTTAGGTGAGAGAGCCTCAAAT -s simRat_chr6.simRat.chr6 187201 29 + 647215 GGGTAAGTTGAGACAAGAGAACTCCAAAT - -a -s simMouse_chr6.simMouse.chr6 197026 49 + 636262 TCAACATAGATCCGAAGATTTAAAAACCCAAAACATGGTTCAGAAGAAT -s Anc0.Anc0refChr5 19050 21 + 87904 TAAACATGGTAC----------------------------CAGAAGAAT -s Anc1.Anc1refChr8 32659 21 + 57822 TAAACATGGTAC----------------------------CAGAAGAAT -s Anc2.Anc2refChr15 12796 21 + 86568 TAAACATGATAC----------------------------CAGAAGGAT -s mr.mrrefChr5 51815 48 + 294540 TAAACATGGAACCGAAGATT-AAAAACCCAAAACATGGTTCAGAAGAAT -s simCow_chr6.simCow.chr6 195929 21 + 602619 GAAGTATGAAAC----------------------------TAGAGGGAT -s simDog_chr6.simDog.chr6 477406 21 - 593897 TAAACATGATAC----------------------------CAGAAGGAT -s simHuman_chr6.simHuman.chr6 199705 21 + 601863 TAAACAAGGCAC----------------------------CAGAAGATT -s simRat_chr6.simRat.chr6 187230 48 + 647215 TAAACATGGGACAAAAGATT-AAAAACCTAAAACATGGTTCGGAAGAAC - -a -s simMouse_chr6.simMouse.chr6 197075 40 + 636262 AAGAAACACATGGCTACAGGGGAGCCCAAGGCTTGCAAAG -s Anc0.Anc0refChr5 19071 34 + 87904 AAGA---ACATGACAACAGGGGAGCCCAAGGCTTGAA--- -s Anc1.Anc1refChr8 32680 37 + 57822 AAGA---ACATGACAACAGGGGAGCCCAAGGCTTGAAGAA -s Anc2.Anc2refChr15 12819 34 + 86568 AAGA---ACATGACAACAGGGGAGACCCAGGCTTGAA--- -s mr.mrrefChr5 51863 40 + 294540 AAGAAACACATGGCTACAGGGGAGCCCAAGGCTTGAAAAG -s simCow_chr6.simCow.chr6 195952 34 + 602619 AAGC---CCATGACAACAGGGGAGACCCAGGCTTGAA--- -s simDog_chr6.simDog.chr6 477429 29 - 593897 AGGA---AAATAACAACGGGGGG-----AGGCTTAAA--- -s simHuman_chr6.simHuman.chr6 199726 37 + 601863 AAGG---ACATGACAATAGGGGAGCTCAAGTCGTGAAGAA -s simRat_chr6.simRat.chr6 187278 40 + 647215 AAGAAGCACATGGCTACAGCGGAGCCCAAGACTTGAAAAG - -a -s simMouse_chr6.simMouse.chr6 197115 13 + 636262 ATTTGTTAGAGTT -s Anc0.Anc0refChr5 19110 13 + 87904 ATTAACTAGGGTT -s Anc1.Anc1refChr8 32722 13 + 57822 ATTAACTAGGGTT -s Anc2.Anc2refChr15 12858 13 + 86568 ATCAACTAGGGTT -s mr.mrrefChr5 51903 13 + 294540 ATTTGTTAGAGTT -s simCow_chr6.simCow.chr6 195991 13 + 602619 ATCAACTAGGGTT -s simDog_chr6.simDog.chr6 477463 13 - 593897 ATCAACTAGGGTT -s simHuman_chr6.simHuman.chr6 199768 13 + 601863 ATTAACTAGGGTT -s simRat_chr6.simRat.chr6 187318 13 + 647215 ATTTGTTAGAGCT - -a -s simMouse_chr6.simMouse.chr6 197128 6 + 636262 AGCATG -s Anc0.Anc0refChr5 19123 6 + 87904 TGCATG -s Anc1.Anc1refChr8 32735 6 + 57822 TGCATG -s Anc2.Anc2refChr15 12871 6 + 86568 TGCATG -s mr.mrrefChr5 51916 6 + 294540 TGCATG -s simCow_chr6.simCow.chr6 196018 6 + 602619 TGCATG -s simDog_chr6.simDog.chr6 477476 2 - 593897 T----G -s simHuman_chr6.simHuman.chr6 199781 6 + 601863 TAGATG -s simRat_chr6.simRat.chr6 187331 6 + 647215 TGCATG - -a -s simMouse_chr6.simMouse.chr6 197134 3 + 636262 AGT -s Anc0.Anc0refChr5 19143 3 + 87904 ACT -s Anc1.Anc1refChr8 32755 3 + 57822 ACT -s Anc2.Anc2refChr15 12891 3 + 86568 ACT -s mr.mrrefChr5 51922 3 + 294540 AGT -s simCow_chr6.simCow.chr6 196038 3 + 602619 ACT -s simDog_chr6.simDog.chr6 477492 3 - 593897 CCC -s simHuman_chr6.simHuman.chr6 199801 3 + 601863 ACT -s simRat_chr6.simRat.chr6 187337 3 + 647215 AGT - -a -s simMouse_chr6.simMouse.chr6 197137 140 + 636262 GCATGAGTCCGGGTCTGTAAGAAGAGAGATGACTAGAAGGCATCTATATATGCTATAGAATGCAGGGACAACTACGGTGGAGTCTATCCGCAATCAGTCTGTTATTGGAAGCAGTTAGTACCATAACTACTTCAAGAGGA -s Anc0.Anc0refChr5 19146 138 + 87904 GGTTGAGGCAGAGTCTGAAAGAAGAAAGATGGCTAGAA-GTGTATATATGCACTATAGAATGCAGGTAGAACTACAGTGGAGTCTATCCTAAATCAGACAGACATTTGAAGCAGT-ATTCTCTTGTCCAATTTAAGAGGA -s Anc1.Anc1refChr8 32758 138 + 57822 GGTTGAGGCAGAGTCTGAAAGAAGAAAGATGGCTAGAA-GTGTATATATGCACTATAGAATGCAGGTAGAACTACAGTGGAGTCTATCCTAAATCAGACAGACATTTGAAGCAGT-ATTCTCTTGTCCAATTTAAGAGGA -s Anc2.Anc2refChr15 12894 138 + 86568 GGTTGAGGCAGAGTCTGAAAGAAGAGGGATGGCTAGAA-ATGTATATAAACACTATAGAATCCAAGTAGAACTACAGTGGAGTCTATCCTAAATCAGATAGACATTTTAAGCAGT-ATACTCTTGTCCAATTTAAGAGGA -s mr.mrrefChr5 51925 139 + 294540 GCATGAGTCAGGGTCTGTAAGAAGAAAGATGACTAGAAGGCATCTATATGTACTATAGAATGCAGGGACAACTACAGTGGAGTCTATCCTCAATCAGTCTGTCATTGGAAGCAGT-AGTCTCTTATCCACTTCAAGAGGA -s simCow_chr6.simCow.chr6 196063 138 + 602619 GGTTGAGACAGAGTTCAGAAGAAGAGGGATGGTTAGAA-TTGTATAGACACACAATAGAACCCAAGTAGAACTACAGTGGAGGGTATCCTAAATCAGCTGGACTTTCTAAGCAGT-ATACTCTTGCCCACTCTGAGAGGA -s simDog_chr6.simDog.chr6 477495 124 - 593897 GGTTGAGGCAGAGCCTGAACGAGGAGGGATGGCTAGAA-ATGTATTTAAACACTATAAAAT-----TAG---------GGAGTCTATCCTAAATCAGATAGACATTTTGAGCAGT-ATACACTTGTCAAATTTAAGAGGA -s simHuman_chr6.simHuman.chr6 199804 136 + 601863 GGTTGAGGCAGAATCTGAAAGAAGAAAGATGGATAGGA-GTGTATATATGCACTATAGAATGCAGGTAGAACTAGAGTGGGGTTTGCCCTATAGAAGACAGACATT-GAAGCAGC-A-TCTTTTGTCCAATTTAAGAGGA -s simRat_chr6.simRat.chr6 187340 139 + 647215 ACATGAGTCATGGTCTGTGTGAAGAAAGATGATTAGAAGGCATCTATATGTACTATAGAATGTAGGAACAACCACAGTGGAGTCTATCCTCAATCAGCCTGTCATTGGAAGCAGT-AGTCTCTTATCCACCTGAAGAGGA - -a -s simMouse_chr6.simMouse.chr6 197277 1 + 636262 C -s Anc0.Anc0refChr5 19285 1 + 87904 C -s Anc1.Anc1refChr8 32897 1 + 57822 C -s Anc2.Anc2refChr15 13033 1 + 86568 C -s mr.mrrefChr5 52065 1 + 294540 C -s simCow_chr6.simCow.chr6 196202 1 + 602619 T -s simDog_chr6.simDog.chr6 477620 1 - 593897 C -s simHuman_chr6.simHuman.chr6 199941 1 + 601863 C -s simRat_chr6.simRat.chr6 187480 1 + 647215 C - -a -s simMouse_chr6.simMouse.chr6 197278 30 + 636262 ATCAGGTCATTGTGAGTTTGATGTGTTGGA -s Anc0.Anc0refChr5 19286 29 + 87904 ATGGATATAGTGTGGGGTTGACGTATTAT- -s Anc1.Anc1refChr8 32898 29 + 57822 ATGGATATAGTGTGGGGTTGACGTATTAT- -s Anc2.Anc2refChr15 13034 29 + 86568 CTGGATATAGTGTGGGGCTGACATATTAT- -s mr.mrrefChr5 52066 30 + 294540 ATGGGGTCATTGTGAGTTTGATGTATTAGA -s simCow_chr6.simCow.chr6 196203 29 + 602619 GTGAATATAGTGTGAGGCTGATATATTAT- -s simDog_chr6.simDog.chr6 477621 22 - 593897 CTGGATATAGTGTGGGACTGAC-------- -s simHuman_chr6.simHuman.chr6 199946 23 + 601863 ATG------GCATGGGGTTAACGTATTAT- -s simRat_chr6.simRat.chr6 187481 27 + 647215 ATGGGGTCATTGTAAGTTTG---TACTAGG - -a -s simMouse_chr6.simMouse.chr6 197308 76 + 636262 CCATACTTCAGATTAACAAATTCAGTTAACAGGTTTTTGCGCCCCTATACCCTTTGGCTTCGGCAACATAGGGATC -s Anc0.Anc0refChr5 19315 71 + 87904 CAATACTTGGGTTTAACTAATTCAGTTAA-----TTTTGTTCCTTTGCACCCTTTGGTGTCAGCAACATTGAGATC -s Anc1.Anc1refChr8 32927 76 + 57822 CAATACTTGGGTTTAACTAATTCAGTTAAAGATTTTTTGTTCCTTTGCACCCTTTGGTGTCAGCAACATTGAGATC -s Anc2.Anc2refChr15 13063 71 + 86568 CAATACTAGGGTTTGATTAATTCAGTTAA-----TTTTGTTCCTTTGCACCCTTTGGTGTCAGTAACACTGAGATT -s mr.mrrefChr5 52096 76 + 294540 CAATACTTCAGATTAACAAATTCAGTTAACGAGTTTTTGTGCCCCTATACCCTTTGGTTTCGGCAACATAGGGATC -s simCow_chr6.simCow.chr6 196233 70 + 602619 CCATACTAGGGTATGATTCGTTCGGCTAA-----TCTTGGTCCTTTGCACCCTCTGGTGTCAGTTACCGAGAGA-T -s simDog_chr6.simDog.chr6 477643 71 - 593897 CATTACTAGGGTTTGATTAATTCAGTTAA-----TTCTGTTCCTTTGCACCCTTCAGTGTCAGTAACACTGGGGTT -s simHuman_chr6.simHuman.chr6 199969 76 + 601863 CAATACTTTGGTTTAACTAATTCAGTAAAAGATTTTTTGTACCTTTGCACCTTTTGGTGTCAGCAACATCGAGATC -s simRat_chr6.simRat.chr6 187508 72 + 647215 CAATACTTCAGATTGACAAATTCAGTTAATGAGTTTTTGTGCCC----ACCCTTTGGTTTTGGCAACATAAGGATC - -a -s simMouse_chr6.simMouse.chr6 197384 8 + 636262 TATGAGCT -s Anc0.Anc0refChr5 19514 8 + 87904 CAGGAACT -s Anc1.Anc1refChr8 33131 8 + 57822 CAGGAACT -s Anc2.Anc2refChr15 13264 8 + 86568 CAGGAACT -s mr.mrrefChr5 52172 8 + 294540 TATGAGCT -s simCow_chr6.simCow.chr6 196433 8 + 602619 CAGGATCG -s simDog_chr6.simDog.chr6 477843 8 - 593897 CAGGAACT -s simHuman_chr6.simHuman.chr6 200173 8 + 601863 CAGGGTCT -s simRat_chr6.simRat.chr6 187580 8 + 647215 TAGGAGCT - -a -s simMouse_chr6.simMouse.chr6 197392 24 + 636262 GACTATGCACTCTTGATGACTGTC -s Anc0.Anc0refChr5 19522 24 + 87904 AACTAAGGACTCTTCATGACTCTC -s Anc1.Anc1refChr8 33139 24 + 57822 AACTAAGGACTCTTCATGACTCTC -s Anc2.Anc2refChr15 13274 24 + 86568 AACTAAGGACTCTCCATGACTCTT -s mr.mrrefChr5 52180 24 + 294540 GACTATGCACTCTTGATGACTGTC -s simCow_chr6.simCow.chr6 196443 24 + 602619 AACTAAAGATACTACATGACCGTT -s simDog_chr6.simDog.chr6 477853 24 - 593897 ATCTAGGGACTCTCCATGACTCTT -s simHuman_chr6.simHuman.chr6 200181 24 + 601863 AACTAAGGACTCTTCAGAACTTTC -s simRat_chr6.simRat.chr6 187588 24 + 647215 GACTACGCACTCTTGATGACTGTC - -a -s simMouse_chr6.simMouse.chr6 197416 36 + 636262 TATTTCTCGTAATGTTATTGATATCCACTACAAGAT -s Anc0.Anc0refChr5 19548 29 + 87904 AATTTC----AATAGTATTGACA---TCTACAACAT -s Anc1.Anc1refChr8 33165 29 + 57822 AATTTC----AATAGTATTGACA---TCTACAACAT -s Anc2.Anc2refChr15 13300 29 + 86568 AATTTC----AATAGTATTGACA---TCCACAACAT -s mr.mrrefChr5 52204 33 + 294540 TATTTCTCGTAATGTTATTGATA---ACTACAAGAT -s simCow_chr6.simCow.chr6 196469 26 + 602619 AATTTC----CATAGTACTGACA---TT---ATTCT -s simDog_chr6.simDog.chr6 477879 29 - 593897 GATTCC----AATGCTATTGACA---TCCACAACAT -s simHuman_chr6.simHuman.chr6 200207 29 + 601863 AACTTC----AATAGTGTTGAGA---TCTACGACAT -s simRat_chr6.simRat.chr6 187612 33 + 647215 TATTTTTAATAATGTTGTTGATA---GCTAAAAGAT - -a -s simMouse_chr6.simMouse.chr6 197452 8 + 636262 GACTTAAT -s Anc0.Anc0refChr5 19578 8 + 87904 AACTTGAT -s Anc1.Anc1refChr8 33195 8 + 57822 AACTTGAT -s Anc2.Anc2refChr15 13330 8 + 86568 AACTTGAT -s mr.mrrefChr5 52237 8 + 294540 GACTTAAT -s simCow_chr6.simCow.chr6 196496 8 + 602619 AACTTGAT -s simDog_chr6.simDog.chr6 477909 8 - 593897 AACTTTAT -s simHuman_chr6.simHuman.chr6 200237 8 + 601863 AACTTGAT -s simRat_chr6.simRat.chr6 187645 8 + 647215 GACTTAAT - -a -s simMouse_chr6.simMouse.chr6 197460 48 + 636262 ACAAGTTTTTGAATTGTGCTGCAGGCTCTAAAGTTTGATGGCCTTTGC -s Anc0.Anc0refChr5 19623 40 + 87904 ACAAATGCTTG--------GGAAGTCAGTAAAGTTTAATGGGCTTTGC -s Anc1.Anc1refChr8 33240 47 + 57822 ACAAATGCTTGTGTAGTG-GGAAGTCAGTAAAGTTTAATGGGCTTTGC -s Anc2.Anc2refChr15 13375 40 + 86568 ACATATGCTTG--------GGAAGTCAGTAAAGTTTAGTTGGCTTTGC -s mr.mrrefChr5 52245 48 + 294540 ACAAGTTTTTGAATTGTGCTGCAGGCTCTAAAGTTTGATGGCCTTTGC -s simCow_chr6.simCow.chr6 196549 38 + 602619 ATAGATGCTTG--------GGCAATTGGTAAAGTTCAGTTTGCCT--C -s simDog_chr6.simDog.chr6 477947 40 - 593897 ACATATGCTCT--------GGAAGTCAGTAAAGTGTAGCTGGCTTTGC -s simHuman_chr6.simHuman.chr6 200283 47 + 601863 ACAAATGCTTGTGTAGTG-GGTAGTCAGTAAAGTTTAATGGGTTTTGC -s simRat_chr6.simRat.chr6 187653 48 + 647215 ACAAGTTTTGGGATTGTGCTGCAGGCATTAAAGTTCGATGGGCTTTGT - -a -s simMouse_chr6.simMouse.chr6 197508 1 + 636262 A -s Anc0.Anc0refChr5 19669 1 + 87904 A -s Anc1.Anc1refChr8 33293 1 + 57822 A -s Anc2.Anc2refChr15 13421 1 + 86568 A -s mr.mrrefChr5 52293 1 + 294540 A -s simCow_chr6.simCow.chr6 196593 1 + 602619 A -s simDog_chr6.simDog.chr6 478072 1 - 593897 A -s simHuman_chr6.simHuman.chr6 200336 1 + 601863 A -s simRat_chr6.simRat.chr6 187701 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 197509 14 + 636262 GGTGGGCAATAGAG -s Anc0.Anc0refChr5 19670 9 + 87904 GTC-----ATAGAG -s Anc1.Anc1refChr8 33294 12 + 57822 GTCGGG--ATAGAG -s Anc2.Anc2refChr15 13422 9 + 86568 GTC-----ACGGAG -s mr.mrrefChr5 52294 14 + 294540 GGTGGGCAATAGAG -s simCow_chr6.simCow.chr6 196594 9 + 602619 ACT-----ACAGAG -s simDog_chr6.simDog.chr6 478073 9 - 593897 GTC-----ACGGAG -s simHuman_chr6.simHuman.chr6 200337 11 + 601863 GTCGGG--ATAGA- -s simRat_chr6.simRat.chr6 187709 14 + 647215 ACTGGGCAATAGAG - -a -s simMouse_chr6.simMouse.chr6 197523 7 + 636262 TGCTGAT -s Anc0.Anc0refChr5 19679 7 + 87904 TCATGAT -s Anc1.Anc1refChr8 33306 7 + 57822 TCATGAT -s Anc2.Anc2refChr15 13431 7 + 86568 TCATGAT -s mr.mrrefChr5 52308 7 + 294540 TGCTGAT -s simCow_chr6.simCow.chr6 196604 7 + 602619 TCAGGCT -s simDog_chr6.simDog.chr6 478082 7 - 593897 TCATGAT -s simHuman_chr6.simHuman.chr6 200348 3 + 601863 ----AAT -s simRat_chr6.simRat.chr6 187723 7 + 647215 TGCATAT - -a -s simMouse_chr6.simMouse.chr6 197530 26 + 636262 GGCTAGACTGCATAGCTGGGTGATAC -s Anc0.Anc0refChr5 19686 26 + 87904 GGCTATGATGAATAGCTGGGTGATAC -s Anc1.Anc1refChr8 33313 26 + 57822 GGCTATGATGAATAGCTGGGTGATAC -s Anc2.Anc2refChr15 13441 26 + 86568 GGCTATGATGAATAGCTGGGTGTGAT -s mr.mrrefChr5 52315 26 + 294540 GGCTAGACTGCATAGCTGGGTGATAC -s simCow_chr6.simCow.chr6 196614 26 + 602619 GGCTACGAAGAATAGCCAGGTGTGAT -s simDog_chr6.simDog.chr6 478092 25 - 593897 GGCTAT-ATGAATAGCTGGGTGTGAT -s simHuman_chr6.simHuman.chr6 200351 22 + 601863 CACGATTTTG----GCCATGTGATAC -s simRat_chr6.simRat.chr6 187730 26 + 647215 GGCTGAGCCGCATAGCTGGGTGCTGC - -a -s simMouse_chr6.simMouse.chr6 197556 4 + 636262 ATGT -s Anc0.Anc0refChr5 19712 4 + 87904 ATAT -s Anc1.Anc1refChr8 33339 4 + 57822 ATAT -s Anc2.Anc2refChr15 13467 4 + 86568 ATAT -s mr.mrrefChr5 52341 4 + 294540 ATGT -s simCow_chr6.simCow.chr6 196640 4 + 602619 ACAT -s simDog_chr6.simDog.chr6 478117 4 - 593897 ATAT -s simHuman_chr6.simHuman.chr6 200377 4 + 601863 ATAT -s simRat_chr6.simRat.chr6 187756 4 + 647215 ATGT - -a -s simMouse_chr6.simMouse.chr6 197560 4 + 636262 GACA -s Anc0.Anc0refChr5 19716 4 + 87904 GACA -s Anc1.Anc1refChr8 33343 4 + 57822 GACA -s Anc2.Anc2refChr15 13471 4 + 86568 AACT -s mr.mrrefChr5 52345 4 + 294540 GACA -s simCow_chr6.simCow.chr6 196647 4 + 602619 AATT -s simDog_chr6.simDog.chr6 478121 4 - 593897 AACT -s simHuman_chr6.simHuman.chr6 200381 4 + 601863 GATA -s simRat_chr6.simRat.chr6 187760 4 + 647215 AACA - -a -s simMouse_chr6.simMouse.chr6 197564 21 + 636262 GACTTTAGTTTACCCTACCTG -s Anc0.Anc0refChr5 19720 21 + 87904 GACTTTAGTTTACCTGAGCTG -s Anc1.Anc1refChr8 33347 21 + 57822 GACTTTAGTTTACCTGAGCTG -s Anc2.Anc2refChr15 13475 21 + 86568 GACTTTAGTTTACCTGAGCTG -s mr.mrrefChr5 52349 21 + 294540 GACTTTAGTTTACCCTACCTG -s simCow_chr6.simCow.chr6 196651 21 + 602619 GACTTTAGTTTACCTGACCTA -s simDog_chr6.simDog.chr6 478125 21 - 593897 GATGTTCATCTACCTGAGTTG -s simHuman_chr6.simHuman.chr6 200386 21 + 601863 GACTTTAGTTTACCTGATCTG -s simRat_chr6.simRat.chr6 187764 21 + 647215 GACTTTAGTTTACCCAACCTG - -a -s simMouse_chr6.simMouse.chr6 197585 20 + 636262 CCTTAGGAAAACCAGGCTCT -s Anc0.Anc0refChr5 19751 20 + 87904 CCTTAGGTAAACCAGGTCCT -s Anc1.Anc1refChr8 33378 20 + 57822 CCTTAGGTAAACCAGGTCCT -s Anc2.Anc2refChr15 13506 20 + 86568 CCTTAGGTAAACCAGGTCCT -s mr.mrrefChr5 52370 20 + 294540 CCTTAGGAAAACCAGGCTCT -s simCow_chr6.simCow.chr6 196682 20 + 602619 CCTTAGGCAAACCAAGCCCT -s simDog_chr6.simDog.chr6 478156 20 - 593897 CCAGAAGTAAACAAGGTCCT -s simHuman_chr6.simHuman.chr6 200417 20 + 601863 CCTTAGATAAAGCAGGTCCA -s simRat_chr6.simRat.chr6 187785 20 + 647215 CCTTAGGAAAACTAGGCTCA - -a -s simMouse_chr6.simMouse.chr6 197605 37 + 636262 TGCATGATTATAGCTCAGCCAACAGACAGTGCCAACA -s Anc0.Anc0refChr5 19771 14 + 87904 CAT----------------------ATGGTGCT-ACA -s Anc1.Anc1refChr8 33398 14 + 57822 CAT----------------------ATGGTGCT-ACA -s Anc2.Anc2refChr15 13526 14 + 86568 CAT----------------------ATGGTGCT-ACC -s mr.mrrefChr5 52390 15 + 294540 TGC----------------------ACAGTGCCAACA -s simCow_chr6.simCow.chr6 196709 14 + 602619 CAT----------------------GCAGTGCC-ACC -s simDog_chr6.simDog.chr6 478176 14 - 593897 CAT----------------------ATGTTGCT-ATC -s simHuman_chr6.simHuman.chr6 200437 14 + 601863 CAT----------------------ATGGTGCT-ACA -s simRat_chr6.simRat.chr6 187805 15 + 647215 CGC----------------------ACAATGATAGCA - -a -s simMouse_chr6.simMouse.chr6 197642 316 + 636262 CAACCtttgatagtactcagttggtgtgcaaatcctaaaaatatttgaaaagtcctaactatttcaaaactccccagagcatgtagcctataagttctgagaccctttgactatattctatgtaagtaaagtcttgaggctgctggggacccTGGGACCCTTTAAGTCTACACTATGCAGGATAAGGTCTTGCAGAAGACATCCTGTGGGTTGGCCGTTGGCTTGCACGACCTTAGTCTACACCCTCATTGATTAAAGCAAAGGAGTGATATCGAGTACATCTAACAAGAAGAGAGAAATAGCTCTCCTAATCAGC -s Anc0.Anc0refChr5 19790 13 + 87904 CA-------ATAGTAC--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CAGC -s Anc1.Anc1refChr8 33417 13 + 57822 CA-------ATAGTAC--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CAGC -s Anc2.Anc2refChr15 13545 13 + 86568 CA-------ATAGTAC--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CGGC -s mr.mrrefChr5 52405 233 + 294540 CA-------atagtactcagttggtgtgcaaatcctaaaaatatttgaaaagt-----------------------gagca--tagcctataa-------------------atattc-------gtaaagtcttgaggctgctggggaccc-----CCCT---AGT-----------------AGGTCTTGCAGAAGACATCCTGTGGGTTGGCCGTTGGCTTGCACGACCTTagtctacaccctcattgattaaagcaaaggagtgatatcgagtacatctaacaagaagagagaaatAGCTCTCCTAATCAGC -s simCow_chr6.simCow.chr6 196728 12 + 602619 CA-------ATAGTGT--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CG-C -s simDog_chr6.simDog.chr6 478195 13 - 593897 CA-------ATAGTAC--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CGGC -s simHuman_chr6.simHuman.chr6 200456 13 + 601863 CA-------ATAGTTC--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CAGC -s simRat_chr6.simRat.chr6 187820 233 + 647215 CA-------TTAACACACAGTGCCAACACAACCtttgatgatacttggttggt-----------------------gtgca--tatcctaaaa-------------------atattc-------gAAAAATCCTAAAACTATTTGAAAACT-----CCCT---AGT-----------------GGGTCTCGAAGCAGACATCCTGTGGGTTTGCCGTTGGTCTGCAGGACTGTaggttacaccctcattgattaaagtggaggagtgatatggaatccatctaacaagaagagccacatACCTCTCCTAATCAGC - -a -s simMouse_chr6.simMouse.chr6 197958 37 + 636262 CTATGATTATGATATGTTTCTCAAGCATAGGGCCACA -s Anc0.Anc0refChr5 19807 37 + 87904 CGATGATTATGACATCTTTCTCAAGTGTAGTGCCACC -s Anc1.Anc1refChr8 33434 37 + 57822 CGATGATTATGACATCTTTCTCAAGTGTAGTGCCACC -s Anc2.Anc2refChr15 13562 37 + 86568 CGATGATTATTACATCTTACTCAAGTGTAGTGCCATC -s mr.mrrefChr5 52638 37 + 294540 CTATGATTATGATATGTTTCTCAAGCATAGGGCCACC -s simCow_chr6.simCow.chr6 196744 36 + 602619 TGATCATTATAACATCTTACTCAAGTGTAGTTCC-TC -s simDog_chr6.simDog.chr6 478212 37 - 593897 CGATGATTACTACATCTTACTCAAGTGTAGTGCCATG -s simHuman_chr6.simHuman.chr6 200473 36 + 601863 CCATGATTATGA-ATCTTTCTCAAGTGTAGTGCTACC -s simRat_chr6.simRat.chr6 188053 37 + 647215 CTCTTATGATGATGTATTTCTCAAGCATAGGGCCACC - -a -s simMouse_chr6.simMouse.chr6 197995 63 + 636262 GTATTAGGGAGTCTGGTTTGAAATCAACATCTTGGATCCACACGGGAATGAAAAAAAATAATT -s Anc0.Anc0refChr5 19853 61 + 87904 GTAATGAGGAGTGTGGTATGAAATGAACATCTTGGATCCACAGAGTAATGAGAGAAAATCA-- -s Anc1.Anc1refChr8 33480 61 + 57822 GTAATGAGGAGTGTGGTATGAAATGAACATCTTGGATCCACAGAGTAATGAGAGAAAATCA-- -s Anc2.Anc2refChr15 13608 61 + 86568 GTAATGAAGAGTGTGGTATGAAATGAACATCTTGGGTCCACTGAGTAATGAGAGAAAATCA-- -s mr.mrrefChr5 52675 63 + 294540 GTATTGGGGAGTGTGGTTTGAAATGAACATCTTGGATCCACACGGCAATGAAAAAAAATAATT -s simCow_chr6.simCow.chr6 196789 58 + 602619 GTAATGAAGAGGGTGGTATGAAACGAACATCTT---TCCACGGAGTAAGGGGAAAAAGTTG-- -s simDog_chr6.simDog.chr6 478258 59 - 593897 GTAATG--GAGTGTAGTATGAAATGAACATTTTGGGTCCACTGAGCGATGAGAGAAAATCA-- -s simHuman_chr6.simHuman.chr6 200518 61 + 601863 GTAATGAGGAGTGTGGTATGAAATAATCATCTAGGATCCACAGAGTAATGAGAGGAAATCA-- -s simRat_chr6.simRat.chr6 188090 63 + 647215 GTACTGGAGACTGTGGTTTGAAATGAGCATCTTGGATCCACAAGGCAATGAAAAAAAACAATT - -a -s simMouse_chr6.simMouse.chr6 198058 163 + 636262 CATTGCATTATTTTACACAAATCTAGAAGAGCCTGTTTTACATTTTCCTTTGCTCACTAGGAGACATGCAGGGTGATCAGATGCAACCATAAGGATTTCTGTGGACAAAGATTCTAGTACAAATGGTTGTAAACTTTCAGTTACTGGTACTCAACTCCTCATA -s Anc0.Anc0refChr5 19914 137 + 87904 AATTGCATTATCTTACACAAATCAAGCAAAGCCATTTTTGTATTATCCTATGGTCATGAGGAGAGATGCAGGATAATTAAATGCAGACATGACAGTACCAGTGGACAA-GATTCTAGTCTGAATTGCTGTAA-------------------------CTCACA -s Anc1.Anc1refChr8 33541 137 + 57822 AATTGCATTATCTTACACAAATCAAGCAAAGCCATTTTTGTATTATCCTATGGTCATGAGGAGAGATGCAGGATAATTAAATGCAGACATGACAGTACCAGTGGACAA-GATTCTAGTCTGAATTGCTGTAA-------------------------CTCACA -s Anc2.Anc2refChr15 13670 137 + 86568 AATTGCATTATCTTACACAAATCAAGCAAAGGCATTTTTGTATTATCCTATGGTCATGAGGAGAGATGCAGGATAGTCAAATGGAGACATGACAGTACCAGTGGACAA-GTTTCTAGTCTGAATTGTTATAA-------------------------CTCACA -s mr.mrrefChr5 52738 137 + 294540 CATTGCATTATTTTACACAAATCAAGAAGAGCCTGTTTTACATTTTCCTTTGCTCATTAGGAGACATGCAGGGTGATTAGATGCAAACATAAGAATTCCAGTGGACAA-GATTCTAGTACAAATGGCTGTAA-------------------------CTCATA -s simCow_chr6.simCow.chr6 196848 135 + 602619 ATTCGCATTATATTATACAAATCAAGCAAAGGC--CTCTGTATTTTCGTAGGGTCACTAGGAGAGATGCAGGATAATCAAATGGAGACATGACAGCAGCAGTGGACAA-GTGTCTATTATGAATTATTATAA-------------------------CTCACA -s simDog_chr6.simDog.chr6 478318 136 - 593897 AATTGCATTATCTTACATCAATCGAGCAAAGGCATTTTTGTATTATCCTATGGTCATGAGGAGAGATGCAGGATAGTCAAATGGTGACATGA-AATACCAGTAGACAA-ATTTCTAGTCTGAATTGTTATAA-------------------------CTCACA -s simHuman_chr6.simHuman.chr6 200579 94 + 601863 AATTGCATTAACTTACACAAATCAAGCAAAGCC------------------------------------------ATTAAATCCAGACATGATAGTACCAGTGGTCAG-GATTC-AGTGTGAATTGCTGTAG-------------------------CTCACA -s simRat_chr6.simRat.chr6 188153 136 + 647215 CATTACATTATTTTACACAAATCAAGTAGAGCCTGTTTAACATTTTCCTTTGCTCATTAGGAGAAATGCAGGGTGGTTAGATGCAAACATAAGAATTCCAGTGGACAA-GATTGTAGTA-AAATGGCTATAA-------------------------CCCGTA - -a -s simMouse_chr6.simMouse.chr6 198221 29 + 636262 CATCATTGAGTTGTGAGAACTGTTGGCAA -s Anc0.Anc0refChr5 20077 29 + 87904 TAGCACTGAGCTGTGAGAATTGATGGCAA -s Anc1.Anc1refChr8 33704 29 + 57822 TAGCACTGAGCTGTGAGAATTGATGGCAA -s Anc2.Anc2refChr15 13833 29 + 86568 TGGCACTGAGCTGTGAGAATTGATGGCAA -s mr.mrrefChr5 52875 29 + 294540 CATCATTGAGTTGTGAGAATTGTTGGCAA -s simCow_chr6.simCow.chr6 197049 29 + 602619 TGACATTGAGCTGTGAGACTTGGTGGCAA -s simDog_chr6.simDog.chr6 478540 29 - 593897 TGGCACTGAGCTGTGAGAATCAATAGCGA -s simHuman_chr6.simHuman.chr6 200699 29 + 601863 TAGCAATGAGCTGTGAGTTATGCTGGCAA -s simRat_chr6.simRat.chr6 188289 29 + 647215 CATCATTGAGTTGTGAGAATTGTTGGCAA - -a -s simMouse_chr6.simMouse.chr6 198250 11 + 636262 GGATAGCGAGC -s Anc0.Anc0refChr5 20107 11 + 87904 GGATAGCCAGC -s Anc1.Anc1refChr8 33734 11 + 57822 GGATAGCCAGC -s Anc2.Anc2refChr15 13863 11 + 86568 GGATAGCCAGT -s mr.mrrefChr5 52904 11 + 294540 GGATAGCGAGC -s simCow_chr6.simCow.chr6 197079 11 + 602619 GGATGGCCAGT -s simDog_chr6.simDog.chr6 478570 11 - 593897 GGATAGCTAGT -s simHuman_chr6.simHuman.chr6 200729 11 + 601863 GGACAGTCAAC -s simRat_chr6.simRat.chr6 188318 11 + 647215 GGATAGCGAGC - -a -s simMouse_chr6.simMouse.chr6 198261 20 + 636262 AACAGCAGTATGATTCTTTT -s Anc0.Anc0refChr5 20119 20 + 87904 AACAGCATTATGTTTCTTTT -s Anc1.Anc1refChr8 33746 20 + 57822 AACAGCATTATGTTTCTTTT -s Anc2.Anc2refChr15 13875 20 + 86568 CACAGCATTATGTTTCTTTT -s mr.mrrefChr5 52916 20 + 294540 AACAGCAGTATGATTCTTTT -s simCow_chr6.simCow.chr6 197091 20 + 602619 GGCAGCATTGTGTTTCCTTT -s simDog_chr6.simDog.chr6 478582 20 - 593897 CACAGCATTATGTTTCTTTC -s simHuman_chr6.simHuman.chr6 200741 20 + 601863 AACAGCATTATGTTTCGTTT -s simRat_chr6.simRat.chr6 188330 20 + 647215 AACAGCAGTATGGTTCTTTT - -a -s simMouse_chr6.simMouse.chr6 198281 64 + 636262 GATCGGATAGATTTAAAACTAGACTTCAATAGATTGATGTTTAGAAAAGCATAACTGCTCTTCA -s Anc0.Anc0refChr5 20139 61 + 87904 GATTGAATAAATTTAAAAGCAGAATACAGGAGT--GGTGTAGAAAAAAACATAACTGCCCT-CA -s Anc1.Anc1refChr8 33766 61 + 57822 GATTGAATAAATTTAAAAGCAGAATACAGGAGT--GGTGTAGAAAAAAACATAACTGCCCT-CA -s Anc2.Anc2refChr15 13895 61 + 86568 GATTGAATAAATTTAAAAGCAGAATACAGGAGT--GGTGTAGAAAAAAACATAAGTGCCCT-CA -s mr.mrrefChr5 52936 61 + 294540 GATCGGATAGATTTAAAAGCAGACTACAATAGA--GATGTATAGAAAAACATAACTGCCCT-CA -s simCow_chr6.simCow.chr6 197112 61 + 602619 GATTGGATATATTTAAGAGCAGAATGCAGGAGT--GGTGTAAAAAAAAACATAATTGCCCT-CA -s simDog_chr6.simDog.chr6 478602 61 - 593897 AATTGAATAAATTTAAAAGCAGGATAAAGGAGA--GGTGTAGAAAAAAATATAAGTGCTCT-CA -s simHuman_chr6.simHuman.chr6 200761 60 + 601863 GATTGCATAAATTTAAAAACGGAATACATGTGT--GGTGTAGAAAAAAAC-TAACTGCCTT-CA -s simRat_chr6.simRat.chr6 188350 53 + 647215 GATCAGATAGATTTAAGGGCAGACTACAA----------TAAAGAAAAACATAACTGCCCT-CA - -a -s simMouse_chr6.simMouse.chr6 198345 34 + 636262 AAATAGCTTGTATGTCTTTATGTGATAGAAGAAT -s Anc0.Anc0refChr5 20203 31 + 87904 AGATCT---GTATGTTATTACTTATTTGAAGAAT -s Anc1.Anc1refChr8 33830 31 + 57822 AGATCT---GTATGTTATTACTTATTTGAAGAAT -s Anc2.Anc2refChr15 13959 31 + 86568 AGACCT---GTACGTTATTACTTATTTGAAGAAT -s mr.mrrefChr5 52997 31 + 294540 ATATAG---GTATGTTTTTATGTAATAGAAGAAT -s simCow_chr6.simCow.chr6 197183 31 + 602619 AGACCT---GAACGTTAGTACTTATTCAAAAAAT -s simDog_chr6.simDog.chr6 478666 29 - 593897 A--CCT---GTACGTTATCACTTATTTGAAGAAT -s simHuman_chr6.simHuman.chr6 200824 31 + 601863 AGATCT---GCATGTTATTACCTATTGGAAGAAT -s simRat_chr6.simRat.chr6 188403 31 + 647215 ATATAG---GTATGTTTTTATGTAATAGAAGAAT - -a -s simMouse_chr6.simMouse.chr6 198379 11 + 636262 TGCATTGTCGT -s Anc0.Anc0refChr5 20235 10 + 87904 CCCATT-TAGC -s Anc1.Anc1refChr8 33862 11 + 57822 CCCATTATAGC -s Anc2.Anc2refChr15 13991 10 + 86568 CCCATT-TAAG -s mr.mrrefChr5 53029 11 + 294540 TCCATTGTCGC -s simCow_chr6.simCow.chr6 197215 10 + 602619 TCCATT-TGAA -s simDog_chr6.simDog.chr6 478696 10 - 593897 CCCATT-GAAG -s simHuman_chr6.simHuman.chr6 200856 11 + 601863 ACCATCATAGC -s simRat_chr6.simRat.chr6 188435 11 + 647215 TCCATTGGTGC - -a -s simMouse_chr6.simMouse.chr6 198390 34 + 636262 TATAGCAGGTCAGTTACAGATATTTGGCCAGTTT -s Anc0.Anc0refChr5 20245 10 + 87904 TATAGCTGGT------------------------ -s Anc1.Anc1refChr8 33873 34 + 57822 TATAGCTGGTCAGTGACAGTTGTCTGAATGGTTT -s Anc2.Anc2refChr15 14001 10 + 86568 TCTCCCAGGT------------------------ -s mr.mrrefChr5 53040 34 + 294540 TATAGCAGGTCAGTTACAGATATTTGGCCAGTTT -s simCow_chr6.simCow.chr6 197225 10 + 602619 ACTCTCAGGT------------------------ -s simDog_chr6.simDog.chr6 478707 10 - 593897 TATACCAGGT------------------------ -s simHuman_chr6.simHuman.chr6 200867 34 + 601863 TATAGCTGGTCAGTGACAGTTGTCTGAATGGTTT -s simRat_chr6.simRat.chr6 188446 34 + 647215 TATGGCAGGTCCGTTACAGATATTTGGCCAGTTT - -a -s simMouse_chr6.simMouse.chr6 198424 154 + 636262 TCATCAGACTTCATTAATGTCTTGTAACCTGTCGTCAGGTACCACAGAAATTCCAGAGTGTTTGAGTCTAAGAGATCACCTCAAATTTTAATTCCAGGGAGTTTGAGCTCAAGAGTCCACCTCAAATTTTGACTTGGCCTAGCCTCTCAACTAT -s Anc1.Anc1refChr8 33907 113 + 57822 TTACCAGACTTCATTAGTGTTTAGCAACTCATTGGCAGACACTTTAGCAATTCCAAAGTCTGGGAATTTAAGAAATT-----------------------------------GAGTCT------AGTTTTGACTTTGCTTACCATCTCAACCAT -s mr.mrrefChr5 53074 154 + 294540 TCATCAGACTTCATTAATGTCTAGTAACCTGTCGTCAGGTACTACAGAAATTCCAGAGTATTTGAGTCTAAGAGATCACCTCAAATTTTAATTCCAGGGAGTTTGAGTTTAAGAGTCCACCTCAAATTTTGACTTGGCTTAGCCTCTCAACTAT -s simHuman_chr6.simHuman.chr6 200902 113 + 601863 TTACCAGACTTCATTAGTGTTTAGCAACTCATTGGCAGACACTTTAGCAATTCCAAAGTCTGGGAATTTAAGAAATT-----------------------------------GAGTCT------AGTTTTGACTTTGCTTACCATCTCAACCAT -s simRat_chr6.simRat.chr6 188480 154 + 647215 TCATCAGACTTCATTAATGTCCAGTAACCTGTCATCAGGTACTACAGTAATTCCAGAGTATTTGGGTCCAAGAGATCACCTCAAATTTTAATTCCAGGGTGTTTGAGTTTAAGAGTCCATCTCAAATTTTGACTTGGCTTAGCCCCTCAACTAT - -a -s simMouse_chr6.simMouse.chr6 198578 24 + 636262 TTACCTGGCCAGACTAATTTTGCA -s Anc1.Anc1refChr8 34020 23 + 57822 TTACCTGGTT-GACTATATTTGCA -s mr.mrrefChr5 53228 24 + 294540 TTACCTGGCCAGACTAATTTTGCA -s simHuman_chr6.simHuman.chr6 201016 23 + 601863 TTACCTGGTT-GACTATATTTGCA -s simRat_chr6.simRat.chr6 188634 24 + 647215 TTACCCGGCAAGACTAATTTTGCA - -a -s simMouse_chr6.simMouse.chr6 198602 18 + 636262 TGCAGGCTAATAGTGGGA -s Anc1.Anc1refChr8 34043 18 + 57822 TGCAGGCCAATAGTGTGT -s mr.mrrefChr5 53252 18 + 294540 TGCAGGCTAATAGTGGGT -s simHuman_chr6.simHuman.chr6 201040 18 + 601863 TGCAGGCCAATAGTGTGT -s simRat_chr6.simRat.chr6 188658 18 + 647215 TGCTGGCTAACAGTGGGT - -a -s simMouse_chr6.simMouse.chr6 198620 16 + 636262 ATCTGCCTTACTGATC -s Anc0.Anc0refChr5 20255 5 + 87904 -----------TAATC -s Anc1.Anc1refChr8 34063 16 + 57822 GTCTCCCTGGTTAATC -s Anc2.Anc2refChr15 14011 5 + 86568 -----------TAATC -s mr.mrrefChr5 53270 16 + 294540 ATCTGCCTTGCTGATC -s simCow_chr6.simCow.chr6 197235 5 + 602619 -----------TGATC -s simDog_chr6.simDog.chr6 478717 5 - 593897 -----------CAGTC -s simHuman_chr6.simHuman.chr6 201060 16 + 601863 GTCTCCCTAGTTTATC -s simRat_chr6.simRat.chr6 188676 16 + 647215 ATCTGCCTTGCTGATC - -a -s simMouse_chr6.simMouse.chr6 198636 29 + 636262 AATGTCGAAGAGCTAGCCTAACTACCCAT -s Anc0.Anc0refChr5 20260 19 + 87904 AGCTATGA----C------CACTATCCAT -s Anc1.Anc1refChr8 34079 24 + 57822 AGCTATGA----CTAGT-CCACTATCCAT -s Anc2.Anc2refChr15 14215 19 + 86568 AGCTATGA----C------CACTATCCAT -s mr.mrrefChr5 53286 28 + 294540 AATGTCGAAGAGCTAGC-TCACTACCCAT -s simCow_chr6.simCow.chr6 197464 19 + 602619 AGATATGA----C------CACAAACCAT -s simDog_chr6.simDog.chr6 478921 19 - 593897 AGCTGTGT----C------CACTGTCCAT -s simHuman_chr6.simHuman.chr6 201076 24 + 601863 AGCTATGA----CTAGT-CCATTAGCCAT -s simRat_chr6.simRat.chr6 188692 28 + 647215 AATGTCGAAGAGCTGGC-TCACTAACCAT - -a -s simMouse_chr6.simMouse.chr6 198665 12 + 636262 GTCCTATTCATA -s Anc0.Anc0refChr5 20280 12 + 87904 TACCTATTTTTA -s Anc1.Anc1refChr8 34104 12 + 57822 TACCTATTTTTA -s Anc2.Anc2refChr15 14235 12 + 86568 TACCTATTTTGA -s mr.mrrefChr5 53314 12 + 294540 GTCCTATTCATA -s simCow_chr6.simCow.chr6 197484 12 + 602619 TGCCCTCCTTAA -s simDog_chr6.simDog.chr6 478941 12 - 593897 TACCTATTTTGA -s simHuman_chr6.simHuman.chr6 201101 12 + 601863 AACCTATTTTTG -s simRat_chr6.simRat.chr6 188720 12 + 647215 GCCCTATTCAGA - -a -s simMouse_chr6.simMouse.chr6 198677 2 + 636262 TG -s Anc0.Anc0refChr5 20292 2 + 87904 TG -s Anc1.Anc1refChr8 34116 2 + 57822 TG -s Anc2.Anc2refChr15 14247 2 + 86568 TG -s mr.mrrefChr5 53326 2 + 294540 TG -s simCow_chr6.simCow.chr6 197505 2 + 602619 GG -s simDog_chr6.simDog.chr6 478953 2 - 593897 TG -s simHuman_chr6.simHuman.chr6 201113 2 + 601863 TG -s simRat_chr6.simRat.chr6 188732 2 + 647215 TG - -a -s simMouse_chr6.simMouse.chr6 198679 35 + 636262 AGTAGTATGTCTCCATAGTGCTATTGAATTGGTTG -s Anc0.Anc0refChr5 20295 35 + 87904 AAAAATATACCTACATAGTGCAAATGAAATTGCTG -s Anc1.Anc1refChr8 34119 35 + 57822 AAAAATATACCTACATAGTGCAAATGAAATTGCTG -s Anc2.Anc2refChr15 14250 35 + 86568 AAAAATATACCTACATAGTGCAAATGAGATTGCCA -s mr.mrrefChr5 53328 35 + 294540 AAAAGTATGTCTCCATAGTGCTATTGAATTGGTTG -s simCow_chr6.simCow.chr6 197508 35 + 602619 AAAAATATACCTACATAGTGTAAATGACATTGTCA -s simDog_chr6.simDog.chr6 478956 35 - 593897 AAATGCATATCTACATGGTGCAAAGTAGATAACCA -s simHuman_chr6.simHuman.chr6 201116 35 + 601863 AAAAATATACATGCATAGTGCAAATGAAATTGCTG -s simRat_chr6.simRat.chr6 188734 35 + 647215 AAAAGTATGTCTACATAGTGATATTGAATTGCTTG - -a -s simMouse_chr6.simMouse.chr6 198714 9 + 636262 AGAGCATGT -s Anc0.Anc0refChr5 20339 9 + 87904 AGACCGTTT -s Anc1.Anc1refChr8 34163 9 + 57822 AGACCGTTT -s Anc2.Anc2refChr15 14294 9 + 86568 AGACCGTTA -s mr.mrrefChr5 53363 9 + 294540 AGAGCACGT -s simCow_chr6.simCow.chr6 197552 9 + 602619 AAATGATTA -s simDog_chr6.simDog.chr6 479000 9 - 593897 AGACCGTTA -s simHuman_chr6.simHuman.chr6 201160 9 + 601863 AGACCCTTT -s simRat_chr6.simRat.chr6 188769 9 + 647215 ACAACACAT - -a -s simMouse_chr6.simMouse.chr6 198723 5 + 636262 GAGGT -s Anc0.Anc0refChr5 20348 5 + 87904 CAGTT -s Anc1.Anc1refChr8 34172 5 + 57822 CAGTT -s Anc2.Anc2refChr15 14303 5 + 86568 CAGTT -s mr.mrrefChr5 53372 5 + 294540 GAGGT -s simCow_chr6.simCow.chr6 197564 5 + 602619 CAGTT -s simDog_chr6.simDog.chr6 479009 5 - 593897 TAGTT -s simHuman_chr6.simHuman.chr6 201169 5 + 601863 CAGTT -s simRat_chr6.simRat.chr6 188778 5 + 647215 GAGGT - -a -s simMouse_chr6.simMouse.chr6 198728 16 + 636262 GGGCAGGCTCTTCCCA -s Anc0.Anc0refChr5 20355 16 + 87904 GAGCAGGCACATATCA -s Anc1.Anc1refChr8 34179 16 + 57822 GAGCAGGCACATATCA -s Anc2.Anc2refChr15 14310 16 + 86568 GAGAAGACACATATCC -s mr.mrrefChr5 53377 16 + 294540 GGGCAGGCTCTTCCCA -s simCow_chr6.simCow.chr6 197571 15 + 602619 AAAGAGACACTCATC- -s simDog_chr6.simDog.chr6 479016 16 - 593897 GAGAAGACACATATCC -s simHuman_chr6.simHuman.chr6 201176 16 + 601863 GAGCAGGCATATATCA -s simRat_chr6.simRat.chr6 188783 16 + 647215 GGACAGGCTATTCCCA - -a -s simMouse_chr6.simMouse.chr6 198744 56 + 636262 CAGGTGCCTGTGACTGCTTGATAGCGCATGAAGCGGGGCAGGTTCATCAGCTGAGT -s Anc0.Anc0refChr5 20371 1 + 87904 C------------------------------------------------------- -s Anc1.Anc1refChr8 34195 1 + 57822 C------------------------------------------------------- -s Anc2.Anc2refChr15 14346 1 + 86568 T------------------------------------------------------- -s mr.mrrefChr5 53393 56 + 294540 CAGGTGCCTGTGACTGCTTGATAGCGCATGAAGCGGGGCAGGTTCATCAGCTGAGT -s simCow_chr6.simCow.chr6 197606 1 + 602619 T------------------------------------------------------- -s simDog_chr6.simDog.chr6 479063 1 - 593897 T------------------------------------------------------- -s simHuman_chr6.simHuman.chr6 201192 1 + 601863 C------------------------------------------------------- -s simRat_chr6.simRat.chr6 188799 56 + 647215 CAAGTGCTTGTGATCACTTGATAGTGCATGAAGCAGGGCAGGTTCATCAGCTGAGT - -a -s simMouse_chr6.simMouse.chr6 198800 177 + 636262 CCTAATGTGTGCGCATGGACATTTACCTCCTAATGGAGCTTTGCACAAAGTACTCTGCAAAGTTTCAATAATGTTAAACTTTGCTGGCTGAAGTAAACCATTATAGCGCAGGGGAACAAGGCAAAGTTGTAAAGTCTATACTTAACTACATTTTCCTACTTCTGATATTGCTCTTTA -s Anc0.Anc0refChr5 20372 34 + 87904 -----------------------------------------------------------------------------------------------------------------------------------------------GACTATATTTTCCTGCTCCTGTTTTTGCTCTATA -s Anc1.Anc1refChr8 34196 34 + 57822 -----------------------------------------------------------------------------------------------------------------------------------------------GACTATATTTTCCTGCTCCTGTTTTTGCTCTATA -s Anc2.Anc2refChr15 14347 34 + 86568 -----------------------------------------------------------------------------------------------------------------------------------------------GACTATATTTTCCTGCTCCTGTTTTTGCTCTATA -s mr.mrrefChr5 53449 175 + 294540 CCTAATGTGTGCGCATGGACATTTACCTCCTAATGGAGCTTTGCACAAAGTACTCTGCAAAGTTTCAATAATGTTAAACTTTGCTGGCTGAAGTAAACCATTATAGCGCAGGGGAACAAGG--AAGTTGTAAAGTCTATACTTAACTACATTTTCCTGCTTCTGATATTGCTCTTTA -s simCow_chr6.simCow.chr6 197607 34 + 602619 -----------------------------------------------------------------------------------------------------------------------------------------------AACTACATTTTCCTGTTTCTGTTTTTGCTCTTTA -s simDog_chr6.simDog.chr6 479064 34 - 593897 -----------------------------------------------------------------------------------------------------------------------------------------------GACTATATTTTCCTGCTCCTGTTTTTGTGCTATA -s simHuman_chr6.simHuman.chr6 201193 34 + 601863 -----------------------------------------------------------------------------------------------------------------------------------------------GACTATATTTTCCTGCTCCTGTTTTTGCTCTGTT -s simRat_chr6.simRat.chr6 188856 175 + 647215 CTTAATGCGTATGCATGGACGCCTGCCTCCTATTGGAGCTTTTCACAAGGTACTCTGCAAAATCTCATTAATGTTAAAGTCTGCTGCCTGAAGGAAACCATTATAGCTCAGGGGAACAAGG--AAGTTGAGAAATCTATCCTTAACCACATTTTCCTGCTTCTGATGTTGCTCTTTA - -a -s simMouse_chr6.simMouse.chr6 198977 3 + 636262 TCC -s Anc0.Anc0refChr5 20406 3 + 87904 TAC -s Anc1.Anc1refChr8 34230 3 + 57822 TAC -s Anc2.Anc2refChr15 14381 3 + 86568 TAC -s mr.mrrefChr5 53624 3 + 294540 TAC -s simCow_chr6.simCow.chr6 197646 3 + 602619 TAC -s simDog_chr6.simDog.chr6 479098 3 - 593897 TAA -s simHuman_chr6.simHuman.chr6 201227 3 + 601863 TAC -s simRat_chr6.simRat.chr6 189031 3 + 647215 TAC - -a -s simMouse_chr6.simMouse.chr6 198980 14 + 636262 TGTATCATTTGTGC -s Anc0.Anc0refChr5 20421 14 + 87904 TGTGATTATTGTGC -s Anc1.Anc1refChr8 34245 14 + 57822 TGTGATTATTGTGC -s Anc2.Anc2refChr15 14396 14 + 86568 TGTGATTATTGTGC -s mr.mrrefChr5 53627 14 + 294540 TGTATCTTTTGTGC -s simCow_chr6.simCow.chr6 197661 14 + 602619 TGTGATTATTGTGC -s simDog_chr6.simDog.chr6 479112 14 - 593897 GGTGATCACCGTGC -s simHuman_chr6.simHuman.chr6 201242 14 + 601863 TGTGATTATTGCAC -s simRat_chr6.simRat.chr6 189034 14 + 647215 TGTATCTTTTGTGC - -a -s simMouse_chr6.simMouse.chr6 198994 20 + 636262 AGTTTTGGGTCTTGCTGCAT -s Anc0.Anc0refChr5 20435 20 + 87904 TGTTGCAGGTCTTGCTGTAG -s Anc1.Anc1refChr8 34259 20 + 57822 TGTTGCAGGTCTTGCTGTAG -s Anc2.Anc2refChr15 14410 20 + 86568 TGTCGCAGGTCTTGATTTGG -s mr.mrrefChr5 53641 20 + 294540 AGTTTTGGGTCTTGCTGCAT -s simCow_chr6.simCow.chr6 197675 20 + 602619 TGTCTCTGGTCTTGATTTGA -s simDog_chr6.simDog.chr6 479126 20 - 593897 AGTTGCAGGTCTTAATTTGG -s simHuman_chr6.simHuman.chr6 201303 20 + 601863 CGTTCACGATCACGCTGTAG -s simRat_chr6.simRat.chr6 189048 20 + 647215 AGTTTTGGGTCTTGTTCACT - -a -s simMouse_chr6.simMouse.chr6 199014 51 + 636262 TGCAACTTATCTTGTAGGCAGTGCAAAGTTAAAAAATATGGGTCAAGTTAA -s Anc0.Anc0refChr5 20458 47 + 87904 G-CAACATATCTCTTCCGCAGTACAGAGTT---AAATATGGGTTGAATTAA -s Anc1.Anc1refChr8 34282 48 + 57822 GGCAACATATCTCTTCCGCAGTACAGAGTT---AAATATGGGTTGAATTAA -s Anc2.Anc2refChr15 14433 47 + 86568 G-CAACATATCCCTTCCACAGTACAGACTT---AAATATGGGTTGAATTAA -s mr.mrrefChr5 53661 51 + 294540 GGCAACTTATCTTTTAGGCAGTGCAAAGTTAAAAAATATGGGTTAAATTAA -s simCow_chr6.simCow.chr6 197698 44 + 602619 A-CAA-GTATAGCTTCCACACTAGAG--TT---AATTATGGGTTGAATAGA -s simDog_chr6.simDog.chr6 479149 47 - 593897 G-TAACATATCCTATCCACAGTACAGACTT---AAACTTGGGTTGAATTAT -s simHuman_chr6.simHuman.chr6 201326 48 + 601863 GGCAGCATATTTCTTGCGCAGCATAGGGCT---AAATATCAGTTGAATTAA -s simRat_chr6.simRat.chr6 189068 51 + 647215 GGCAACTTATCTTTAAGGCATTGCACAGATAAAGAATATTGGTTAAATTGA - -a -s simMouse_chr6.simMouse.chr6 199065 4 + 636262 GTTC -s Anc0.Anc0refChr5 20505 4 + 87904 ATTC -s Anc1.Anc1refChr8 34330 4 + 57822 ATTC -s Anc2.Anc2refChr15 14480 4 + 86568 ATTC -s mr.mrrefChr5 53712 4 + 294540 GTTC -s simCow_chr6.simCow.chr6 197742 4 + 602619 ATCC -s simDog_chr6.simDog.chr6 479196 4 - 593897 ATTC -s simHuman_chr6.simHuman.chr6 201374 4 + 601863 ATTC -s simRat_chr6.simRat.chr6 189136 4 + 647215 GTTC - -a -s simMouse_chr6.simMouse.chr6 199069 18 + 636262 TAAGCCCACAGAAGCCGA -s Anc0.Anc0refChr5 20510 14 + 87904 TAAGCCCACAG----CGG -s Anc1.Anc1refChr8 34335 14 + 57822 TAAGCCCACAG----CGG -s Anc2.Anc2refChr15 14485 14 + 86568 TAAGCCCACAG----AGG -s mr.mrrefChr5 53716 18 + 294540 TAAGCCCACAGAAGCCGA -s simCow_chr6.simCow.chr6 197747 14 + 602619 TAAGTCCACAG----AGG -s simDog_chr6.simDog.chr6 479201 14 - 593897 TACACCCACAG----AGG -s simHuman_chr6.simHuman.chr6 201379 14 + 601863 TAAGGCCACAG----CGG -s simRat_chr6.simRat.chr6 189140 18 + 647215 TAATCACACAGAGGCCAA - -a -s simMouse_chr6.simMouse.chr6 199087 7 + 636262 TTAGCAT -s Anc0.Anc0refChr5 20524 7 + 87904 TGAGAAT -s Anc1.Anc1refChr8 34349 7 + 57822 TGAGAAT -s Anc2.Anc2refChr15 14499 7 + 86568 TGAGAAT -s mr.mrrefChr5 53734 7 + 294540 TTAGAAT -s simCow_chr6.simCow.chr6 197765 7 + 602619 TGGGAAA -s simDog_chr6.simDog.chr6 479215 7 - 593897 TTAGGAT -s simHuman_chr6.simHuman.chr6 201393 7 + 601863 TGAAAAT -s simRat_chr6.simRat.chr6 189158 7 + 647215 TAAGAAT - -a -s simMouse_chr6.simMouse.chr6 199094 14 + 636262 ATAGTAGCTTTTGA -s Anc0.Anc0refChr5 20531 13 + 87904 ATAGTAACTTTTG- -s Anc1.Anc1refChr8 34356 13 + 57822 ATAGTAACTTTTG- -s Anc2.Anc2refChr15 14506 13 + 86568 ATAGTAACTTTTG- -s mr.mrrefChr5 53741 14 + 294540 ATAGTAACTTTTGA -s simCow_chr6.simCow.chr6 197772 13 + 602619 ATGATAATCTTTG- -s simDog_chr6.simDog.chr6 479341 11 - 593897 ATAGTAACTTT--- -s simHuman_chr6.simHuman.chr6 201400 13 + 601863 CTAGAAACATTTG- -s simRat_chr6.simRat.chr6 189165 14 + 647215 ATGGTAACTTTTGA - -a -s simMouse_chr6.simMouse.chr6 199108 49 + 636262 AAAAAACATTCCTGCCCAGGTCCCACCTGTTGCACTCCAACAAAATGCC -s Anc0.Anc0refChr5 20546 48 + 87904 AAAAGACAGATCTGTCTATGTCCCACTCTCTGCACTTCCATAAAATGC- -s Anc1.Anc1refChr8 34371 49 + 57822 AAAAGACAGATCTGTCTATGTCCCACTCTCTGCACTTCCATAAAATGCC -s Anc2.Anc2refChr15 14521 48 + 86568 AAAAGACAGATCTGTCTGTGTCCCACTCTCTGAACTTCCATAAAATGC- -s mr.mrrefChr5 53757 49 + 294540 AAAAAACATTCCTGCCCAGGTCCCACTTTCTGCACTCCAACAAAATGCC -s simCow_chr6.simCow.chr6 197787 48 + 602619 AAAAGACAGATCTTTCTGTGATCCATGCTCTGTGCTGCCATAAAATGT- -s simDog_chr6.simDog.chr6 479352 45 - 593897 ---GGACAGGTCTGTCTGTTTCCCACTCTCTGAACTTCCATAAAATGC- -s simHuman_chr6.simHuman.chr6 201415 46 + 601863 AAAAGACACATTTGTCTATGCCCCACTATCTGCAATTCCATAAA---CC -s simRat_chr6.simRat.chr6 189181 49 + 647215 AAAAAACATTCCTGCCCGGGTCCCACTCTCTGCACCCCAACAAAATGCC - -a -s simMouse_chr6.simMouse.chr6 199157 3 + 636262 CTG -s Anc0.Anc0refChr5 20596 3 + 87904 TAA -s Anc1.Anc1refChr8 34423 3 + 57822 TAA -s Anc2.Anc2refChr15 14571 3 + 86568 TAA -s mr.mrrefChr5 53809 3 + 294540 TTA -s simCow_chr6.simCow.chr6 197837 3 + 602619 TCA -s simDog_chr6.simDog.chr6 479399 3 - 593897 TAA -s simHuman_chr6.simHuman.chr6 201464 3 + 601863 TAA -s simRat_chr6.simRat.chr6 189233 3 + 647215 TGA - -a -s simMouse_chr6.simMouse.chr6 199160 99 + 636262 CTATGGATCTATTGGACATTCTTTTACCACAGACAATGCAAGGTTCTGTGATTGGTCAAATACAGTTGAGGATTATCATAATCCCACATTGCAAATAAC -s Anc0.Anc0refChr5 20599 99 + 87904 CAACAGATCTAATGGACATTATGTAAACACAGACAACCCTAGGTCATCTGCTTTGTCTAGTTGTGTCCAGTACTTTCACTATCCCACATCAAAAATATC -s Anc1.Anc1refChr8 34426 99 + 57822 CAACAGATCTAATGGACATTATGTAAACACAGACAACCCTAGGTCATCTGCTTTGTCTAGTTGTGTCCAGTACTTTCACTATCCCACATCAAAAATATC -s Anc2.Anc2refChr15 14574 99 + 86568 CAACAGTTCTAATGGACATTATGAAAATACAGACAACCCTAGGTCATCTGCTTTGTCTAGTTGTGACCAGTTCTTTCACTGTCCCATATCAAAAATATC -s mr.mrrefChr5 53812 99 + 294540 CTATGGATCTATTGGACATTCTTTAACCACAGACAACGCAAGGTCCTGTGATTGGTCAAATACAGTTGAGTATTATCATAATCCCACATTGCAAATAAC -s simCow_chr6.simCow.chr6 197840 92 + 602619 CACCAGTTCAAATGGACATTATGCAGAGACAGACAACCCTAGGTCATCTGCTTTGTCTGGTTGTGACCGGTTCTTTCACC-------CTCAAAAATATC -s simDog_chr6.simDog.chr6 479402 87 - 593897 CAA----TCTAATGGCTATGATGAAAATACAGACAACCTT--------TGCTTTGTCAAGTTGTGACCACTTTTTTCACTGTCCCATATGGAAAGCATC -s simHuman_chr6.simHuman.chr6 201467 84 + 601863 CAACAGATCTACTGGACATTTTCTAAACACAGACAACCCTTGATCATCTGCTTTGTC--------TCTAGTAC-------ATCCCACATCAAAAATATC -s simRat_chr6.simRat.chr6 189241 99 + 647215 CTATTGCACTATTGCACACTCTTTAACCACAGACAACATAAGGTCCTGTGATTGGTCAGATACGGATGAGTATTATCACAATCCCACGTTGCAAATAAC - -a -s simMouse_chr6.simMouse.chr6 199259 7 + 636262 ACCTTAT -s Anc0.Anc0refChr5 20701 7 + 87904 ATCACCT -s Anc1.Anc1refChr8 34528 7 + 57822 ATCACCT -s Anc2.Anc2refChr15 14676 7 + 86568 ATCACCT -s mr.mrrefChr5 53911 7 + 294540 ACCTTAT -s simCow_chr6.simCow.chr6 197935 7 + 602619 ATCACCT -s simDog_chr6.simDog.chr6 479492 7 - 593897 GTCACAT -s simHuman_chr6.simHuman.chr6 201554 7 + 601863 ATCACCT -s simRat_chr6.simRat.chr6 189340 7 + 647215 ACCTTGT - -a -s simMouse_chr6.simMouse.chr6 199266 46 + 636262 ATGGAGCTTATGGCTGGTGACTAGTGCTCTAAATGTGGCAAGAACT -s Anc0.Anc0refChr5 20708 25 + 87904 ATCGACAATATGACTGGTG---------------------AGAACT -s Anc1.Anc1refChr8 34535 25 + 57822 ATCGACAATATGACTGGTG---------------------AGAACT -s Anc2.Anc2refChr15 14686 25 + 86568 GTCGACAATATGACTGGTG---------------------AGTACT -s mr.mrrefChr5 53918 46 + 294540 ATGGAGCATATGGCTGGTGACTAGTGCTCTAAATGTGGCAAGAACT -s simCow_chr6.simCow.chr6 197946 23 + 602619 GTGGACAATGTGACTGGTA---------------------AG--CT -s simDog_chr6.simDog.chr6 479502 25 - 593897 GTCGACAATATGACTGGTG---------------------GGTACT -s simHuman_chr6.simHuman.chr6 201561 24 + 601863 ATAGACGATATGAGTAGTG---------------------AGAAC- -s simRat_chr6.simRat.chr6 189347 46 + 647215 ATGGAGAATATGGCTGGTGACCAGTGCTCTAAACGTGGGGAGAAAT - -a -s simMouse_chr6.simMouse.chr6 199312 44 + 636262 CTAAAGGTGGGGCAAAGGACAAACATCTCGCAATTGTGGGGATT -s Anc0.Anc0refChr5 20733 42 + 87904 CTAAATGT-GGGAGAAGGACAAACATCT-GCAAATTGAGGGATT -s Anc1.Anc1refChr8 34560 42 + 57822 CTAAATGT-GGGAGAAGGACAAACATCT-GCAAATTGAGGGATT -s Anc2.Anc2refChr15 14714 42 + 86568 CTAAATGT-GGGAGAAGAACAAATACCT-GCAAATTGAGGGATT -s mr.mrrefChr5 53964 44 + 294540 CTAAATGTGGGGAGAAGGACAAACATCTCGCAATTGTGGGGATT -s simCow_chr6.simCow.chr6 197972 42 + 602619 CTAAATGT-GGGAGGAGCACAAATCGGA-GCAAATTGAGGGATT -s simDog_chr6.simDog.chr6 479530 42 - 593897 CTAAATGT-GGGAGAAGAACAAATACCT-GAAAATGGAGGGATT -s simHuman_chr6.simHuman.chr6 201585 38 + 601863 ----ATGT-GGGAGAAGGACAAACATCT-GCAAACTGAGGGATT -s simRat_chr6.simRat.chr6 189393 44 + 647215 CTAGATGTGAGGAGAAGGACAAACATCTTGAAATTGTGGGGAGT - -a -s simMouse_chr6.simMouse.chr6 199356 2 + 636262 AT -s Anc0.Anc0refChr5 20777 2 + 87904 AT -s Anc1.Anc1refChr8 34604 2 + 57822 AT -s Anc2.Anc2refChr15 14758 2 + 86568 AT -s mr.mrrefChr5 54008 2 + 294540 AT -s simCow_chr6.simCow.chr6 198016 2 + 602619 AT -s simDog_chr6.simDog.chr6 479574 2 - 593897 AT -s simHuman_chr6.simHuman.chr6 201625 2 + 601863 AT -s simRat_chr6.simRat.chr6 189437 2 + 647215 AT - -a -s simMouse_chr6.simMouse.chr6 199358 21 + 636262 ATACTGGAGGAGGGTGTCAGT -s Anc0.Anc0refChr5 20780 21 + 87904 GTACTAGAAGAGGATGTCAGT -s Anc1.Anc1refChr8 34607 21 + 57822 GTACTAGAAGAGGATGTCAGT -s Anc2.Anc2refChr15 14761 21 + 86568 GTACTAGATGACGATGTCAGT -s mr.mrrefChr5 54011 21 + 294540 ATACTGGAAGAGGGTGTCAGT -s simCow_chr6.simCow.chr6 198019 21 + 602619 GAACTAAAGGAATATGTCAGC -s simDog_chr6.simDog.chr6 479577 21 - 593897 GTACTAGATGACGATGTCAGT -s simHuman_chr6.simHuman.chr6 201628 21 + 601863 GTACTAGAATAGAAAGCCAGT -s simRat_chr6.simRat.chr6 189440 21 + 647215 ATACCGGAAGAGGGTGTTGGT - -a -s simMouse_chr6.simMouse.chr6 199379 5 + 636262 TAGTC -s Anc0.Anc0refChr5 20801 5 + 87904 TAGTC -s Anc1.Anc1refChr8 34628 5 + 57822 TAGTC -s Anc2.Anc2refChr15 14782 5 + 86568 TAGTC -s mr.mrrefChr5 54032 5 + 294540 TAGTC -s simCow_chr6.simCow.chr6 198040 4 + 602619 TAGT- -s simDog_chr6.simDog.chr6 479598 5 - 593897 TAGTC -s simHuman_chr6.simHuman.chr6 201652 5 + 601863 TATTC -s simRat_chr6.simRat.chr6 189461 5 + 647215 TAGTT - -a -s simMouse_chr6.simMouse.chr6 199384 88 + 636262 AGTTTTCTCTATTCTCTATTTAATTACTAGTAGGTGCTAAGTGAGCATATGCTACCTTTGATTTTAGATGGCCAAAGTTGTAATGGTA -s Anc0.Anc0refChr5 20807 87 + 87904 ATATCTCTCTTTTATCTATTCTATCACTGTTAAGTACTAGTTGAGCATATACCACCTTTGGTCTTAGGTGACTACTGTTGTAATAA-A -s Anc1.Anc1refChr8 34634 87 + 57822 ATATCTCTCTTTTATCTATTCTATCACTGTTAAGTACTAGTTGAGCATATACCACCTTTGGTCTTAGGTGACTACTGTTGTAATAA-A -s Anc2.Anc2refChr15 14788 87 + 86568 CTATCTATCATATATCTATTCTATCACTATTAAGTACTAGTTGAGTATATACCACCTTTGGTCTCAGGTGACCACTGTTGCAATAA-A -s mr.mrrefChr5 54037 88 + 294540 AGTTTTCTCTATTCTCTATTTAATCACTGGTAAGTGCTAGGTGAGCATATGCCACCTTTGATCTTAGATGGCTAAAGTTGTAATGGTA -s simCow_chr6.simCow.chr6 198045 82 + 602619 CTATCTATCATATATCTATT---TTACTATGAAGTACTGGTTGAGAATAGACCACTTTTG--TTCAGGCAGCAACTGTTGCGATTG-C -s simDog_chr6.simDog.chr6 479604 75 - 593897 ------------TATTTACTCTATCACCATTAAGTACTAGTTGACTGTATGCCAACTTTGGTCTCAGGTGACCACTGGTGCAAAAA-A -s simHuman_chr6.simHuman.chr6 201658 86 + 601863 ATCTCTCTCTTTTATCTATTCTATCTCTGTTAAGTACTAGTTGAGCATGTACCACCTTTGGTC-TAGGAGATTAGTATTGTTATCA-A -s simRat_chr6.simRat.chr6 189466 88 + 647215 AGTTTTTTCTATTCTTGATTTAATCACTGGTAAGTGCTAGGTGATCATATGTCACCTTTAATCTTAGATGGCTAAAGCTGCAATGGTA - -a -s simMouse_chr6.simMouse.chr6 199472 23 + 636262 CATAAACAGAGCAAGCATATAGT -s Anc0.Anc0refChr5 20894 23 + 87904 CATAAACAGAGCAAGCATGTAGT -s Anc1.Anc1refChr8 34721 23 + 57822 CATAAACAGAGCAAGCATGTAGT -s Anc2.Anc2refChr15 14878 23 + 86568 CATGAACAGAGCAAGCATGTAAT -s mr.mrrefChr5 54125 23 + 294540 CATAAACAGAGCAAGCATATAGT -s simCow_chr6.simCow.chr6 198130 22 + 602619 AATGTACAT-GAAAGGATGTATT -s simDog_chr6.simDog.chr6 479682 23 - 593897 CATGAACAGAGCAAGCATGTAAT -s simHuman_chr6.simHuman.chr6 201744 23 + 601863 CATAAACAGAGCAATCATGCAGT -s simRat_chr6.simRat.chr6 189554 22 + 647215 CATGGACAGAGTTAGCATA-AGT - -a -s simMouse_chr6.simMouse.chr6 199495 79 + 636262 TCTTCTGTTTGGTCATCCCATCTTACAGACAGGTGACTTTGATGTACTTCTACTTCTACTAGTGTGCTGCTGATCACAG -s Anc0.Anc0refChr5 20919 69 + 87904 TCCACCATTTGATCAAACAATATTACTGACA----ACTTGGATATACTTCTAC------GAGTGCGTTGATGCACTCAA -s Anc1.Anc1refChr8 34746 69 + 57822 TCCACCATTTGATCAAACAATATTACTGACA----ACTTGGATATACTTCTAC------GAGTGCGTTGATGCACTCAA -s Anc2.Anc2refChr15 14903 69 + 86568 TCCACCAATTGATCAAACAATACTACTGACA----ACTTGGATAGACTTCTAC------GAGTGCGTTGATGCACTCAA -s mr.mrrefChr5 54148 73 + 294540 TCTTCCATTTGATCATCCAATCTTACAGACAGGTGACTTTGATGTACTTCTAC------TAGTGTGCTGCTGAACTCAG -s simCow_chr6.simCow.chr6 198154 69 + 602619 TCCACCAATTGGCCATACACTACTACTGACA----ACTTGGATAGGCTTCAAT------GAGTACCTTGATGCACTCAA -s simDog_chr6.simDog.chr6 479707 69 - 593897 TCCATCAATTGATCTAACTATACTGCTAACA----CCTTGGATAGAATTCTAC------GGGTGTGTTGATGCACACAA -s simHuman_chr6.simHuman.chr6 201769 69 + 601863 CCCACCATTTGATCACGCAATATTACGGACA----ACTTGGATATTCCTCTAG------AAGCGCATTGATGCACTCAA -s simRat_chr6.simRat.chr6 189576 73 + 647215 TCTGGCATTTGATCATCCAACCTTACAGACAGGTGACTTTGATGTACTTCTAC------TAGTGTGCTGTTGAACTCCG - -a -s simMouse_chr6.simMouse.chr6 199574 8 + 636262 TCCACAAG -s Anc0.Anc0refChr5 20988 8 + 87904 TCCAAAAG -s Anc1.Anc1refChr8 34815 8 + 57822 TCCAAAAG -s Anc2.Anc2refChr15 14973 8 + 86568 TCCAAGAG -s mr.mrrefChr5 54221 8 + 294540 TCCACAAG -s simCow_chr6.simCow.chr6 198224 8 + 602619 TCCAAGAG -s simDog_chr6.simDog.chr6 479777 8 - 593897 TCTAAGAG -s simHuman_chr6.simHuman.chr6 201838 8 + 601863 TCCAAAAA -s simRat_chr6.simRat.chr6 189649 8 + 647215 TCCAGAAG - -a -s simMouse_chr6.simMouse.chr6 199582 12 + 636262 ACAATTCTCAAT -s Anc0.Anc0refChr5 20996 12 + 87904 ACAAGTGTCCAT -s Anc1.Anc1refChr8 34823 12 + 57822 ACAAGTGTCCAT -s Anc2.Anc2refChr15 14981 12 + 86568 ATAAGTGTCCAC -s mr.mrrefChr5 54229 12 + 294540 ACAATTCTCAAT -s simCow_chr6.simCow.chr6 198232 12 + 602619 ATAAGTGTCTAC -s simDog_chr6.simDog.chr6 479785 12 - 593897 ATAAGTGTCCAC -s simHuman_chr6.simHuman.chr6 201846 12 + 601863 GCAACCATCCAT -s simRat_chr6.simRat.chr6 189659 12 + 647215 ACAATTCTCAAC - -a -s simMouse_chr6.simMouse.chr6 199594 25 + 636262 CATGGCAGCAATTAGTTATGAGTCA -s Anc0.Anc0refChr5 21015 25 + 87904 GAAGGTGGCAATTAGTCATGAGTGA -s Anc1.Anc1refChr8 34842 25 + 57822 GAAGGTGGCAATTAGTCATGAGTGA -s Anc2.Anc2refChr15 15000 25 + 86568 GAAAATGGCCATGAATCATGAGCAA -s Anc2.Anc2refChr15 15084 25 + 86568 GAAGGTGGCAATAAGTCATGAGTGA -s mr.mrrefChr5 54246 25 + 294540 CATGGCGGCAATTAGTTATGAGTGA -s simCow_chr6.simCow.chr6 198340 25 + 602619 GAAAGTCGCAATAAGTCATGGGTGA -s simCow_chr6.simCow.chr6 198251 25 + 602619 CAAGGTGGTGAAGAGTCATGAGTGA -s simDog_chr6.simDog.chr6 479888 25 - 593897 GAAGGTGGCAAAAACTCATGAGTGA -s simDog_chr6.simDog.chr6 479804 25 - 593897 GAAAATGGCCATGAATCATGAGCAA -s simHuman_chr6.simHuman.chr6 201865 25 + 601863 GAAGGAGGCAGTTAGTCATGAGTGA -s simRat_chr6.simRat.chr6 189676 25 + 647215 CATGGTGGCAATTAGTTATGAGTGA - -a -s simMouse_chr6.simMouse.chr6 199619 4 + 636262 TGGG -s Anc0.Anc0refChr5 21040 4 + 87904 TAGG -s Anc1.Anc1refChr8 34867 4 + 57822 TAGG -s Anc2.Anc2refChr15 15025 4 + 86568 TAGG -s Anc2.Anc2refChr15 15109 4 + 86568 TAGG -s mr.mrrefChr5 54271 4 + 294540 TGGG -s simCow_chr6.simCow.chr6 198365 4 + 602619 TGGG -s simCow_chr6.simCow.chr6 198277 4 + 602619 TAGG -s simDog_chr6.simDog.chr6 479913 4 - 593897 TAGG -s simDog_chr6.simDog.chr6 479829 4 - 593897 TAGG -s simHuman_chr6.simHuman.chr6 201890 4 + 601863 TTGG -s simRat_chr6.simRat.chr6 189701 4 + 647215 AGGA - -a -s simMouse_chr6.simMouse.chr6 199623 13 + 636262 TAATCTGTAGCAA -s Anc0.Anc0refChr5 21046 13 + 87904 TAATCTGTGATAA -s Anc1.Anc1refChr8 34873 13 + 57822 TAATCTGTGACAA -s Anc2.Anc2refChr15 15031 13 + 86568 TAATCTGTGATAA -s Anc2.Anc2refChr15 15115 13 + 86568 TAATCTGTGATGA -s mr.mrrefChr5 54275 13 + 294540 TAATCTGTAGCAA -s simCow_chr6.simCow.chr6 198371 13 + 602619 TCATCTGTTATGA -s simCow_chr6.simCow.chr6 198283 13 + 602619 TAATCTGCGATGA -s simDog_chr6.simDog.chr6 479919 13 - 593897 AAATCTGTGATGA -s simDog_chr6.simDog.chr6 479835 13 - 593897 TAATCTGTGATAA -s simHuman_chr6.simHuman.chr6 201896 13 + 601863 TAAACTATGACAA -s simRat_chr6.simRat.chr6 189705 13 + 647215 TAATCTGTCGCAA - -a -s simMouse_chr6.simMouse.chr6 199636 4 + 636262 ATGT -s Anc0.Anc0refChr5 21059 4 + 87904 ATGG -s Anc1.Anc1refChr8 34886 4 + 57822 ATGG -s Anc2.Anc2refChr15 15128 4 + 86568 ATGG -s mr.mrrefChr5 54288 4 + 294540 ATGT -s simCow_chr6.simCow.chr6 198384 4 + 602619 GTGG -s simDog_chr6.simDog.chr6 479932 4 - 593897 ATGG -s simHuman_chr6.simHuman.chr6 201909 4 + 601863 ATGA -s simRat_chr6.simRat.chr6 189718 4 + 647215 TTGT - -a -s simMouse_chr6.simMouse.chr6 199640 5 + 636262 CAGCA -s Anc0.Anc0refChr5 21063 5 + 87904 AATCA -s Anc1.Anc1refChr8 34890 5 + 57822 AATCA -s Anc2.Anc2refChr15 15044 5 + 86568 AAGCA -s Anc2.Anc2refChr15 15132 5 + 86568 AATCA -s mr.mrrefChr5 54292 5 + 294540 CAGCA -s simCow_chr6.simCow.chr6 198388 5 + 602619 AATCA -s simCow_chr6.simCow.chr6 198300 5 + 602619 AATCA -s simDog_chr6.simDog.chr6 479936 5 - 593897 GATCA -s simDog_chr6.simDog.chr6 479848 5 - 593897 AAGCA -s simHuman_chr6.simHuman.chr6 201913 5 + 601863 AATTA -s simRat_chr6.simRat.chr6 189722 5 + 647215 CAGCC - -a -s simMouse_chr6.simMouse.chr6 199645 12 + 636262 TTACAACTGACA -s Anc0.Anc0refChr5 21068 12 + 87904 TCACACCTGGGA -s Anc1.Anc1refChr8 34895 12 + 57822 TCACACCTGGGA -s Anc2.Anc2refChr15 15049 12 + 86568 TCACACCTGGCC -s Anc2.Anc2refChr15 15137 12 + 86568 TCACACCTGGGG -s mr.mrrefChr5 54297 12 + 294540 TTACAACTGGCA -s simCow_chr6.simCow.chr6 198393 12 + 602619 TCACACCTGAGG -s simCow_chr6.simCow.chr6 198305 12 + 602619 CTCCTCCTGACA -s simDog_chr6.simDog.chr6 479950 12 - 593897 TCACACCTGGGG -s simDog_chr6.simDog.chr6 479853 12 - 593897 TCACACCTGGCC -s simHuman_chr6.simHuman.chr6 201918 12 + 601863 TCACACCTGGTA -s simRat_chr6.simRat.chr6 189727 12 + 647215 TTACAACTGGCA - -a -s simMouse_chr6.simMouse.chr6 199657 8 + 636262 TGGACACT -s Anc0.Anc0refChr5 21080 8 + 87904 TATCCGCT -s Anc1.Anc1refChr8 34907 8 + 57822 TATCCACT -s Anc2.Anc2refChr15 15061 8 + 86568 TAGCCGCT -s Anc2.Anc2refChr15 15149 8 + 86568 TATCAGCT -s mr.mrrefChr5 54309 8 + 294540 TGGACACT -s simCow_chr6.simCow.chr6 198405 8 + 602619 TAGTAGCT -s simCow_chr6.simCow.chr6 198317 8 + 602619 TAGCTGTT -s simDog_chr6.simDog.chr6 479962 8 - 593897 TATCAGTT -s simDog_chr6.simDog.chr6 479865 8 - 593897 TAGCCGCT -s simHuman_chr6.simHuman.chr6 201930 8 + 601863 TAACCACT -s simRat_chr6.simRat.chr6 189740 8 + 647215 TGGGCACT - -a -s simMouse_chr6.simMouse.chr6 199665 10 + 636262 GACAATGACG -s Anc0.Anc0refChr5 21088 10 + 87904 GCCAATTAGG -s Anc1.Anc1refChr8 34915 10 + 57822 GCCAATTAGG -s Anc2.Anc2refChr15 15069 10 + 86568 GCCAACTAGG -s Anc2.Anc2refChr15 15157 10 + 86568 GCCAATTAGG -s mr.mrrefChr5 54317 10 + 294540 GACAATGACG -s simCow_chr6.simCow.chr6 198413 10 + 602619 CCCAATTAGG -s simCow_chr6.simCow.chr6 198325 10 + 602619 GCCAATTAGG -s simDog_chr6.simDog.chr6 479970 10 - 593897 GCCAAGTAGG -s simDog_chr6.simDog.chr6 479873 10 - 593897 GCCAACTAGG -s simHuman_chr6.simHuman.chr6 201938 10 + 601863 GCCAATTAAG -s simRat_chr6.simRat.chr6 189749 10 + 647215 GACAATGACA - -a -s simMouse_chr6.simMouse.chr6 199675 1 + 636262 G -s Anc0.Anc0refChr5 21098 1 + 87904 G -s Anc1.Anc1refChr8 34925 1 + 57822 G -s Anc2.Anc2refChr15 15079 1 + 86568 G -s Anc2.Anc2refChr15 15167 1 + 86568 G -s mr.mrrefChr5 54327 1 + 294540 G -s simCow_chr6.simCow.chr6 198335 1 + 602619 G -s simDog_chr6.simDog.chr6 479980 1 - 593897 G -s simDog_chr6.simDog.chr6 479883 1 - 593897 G -s simHuman_chr6.simHuman.chr6 201948 1 + 601863 G -s simRat_chr6.simRat.chr6 189759 1 + 647215 G - -a -s simMouse_chr6.simMouse.chr6 199676 25 + 636262 GGTTTTGATTTATGAAGTCTGACCA -s Anc0.Anc0refChr5 21099 11 + 87904 GAC--------------TCTGACCA -s Anc1.Anc1refChr8 34926 11 + 57822 GAC--------------TCTGACCA -s Anc2.Anc2refChr15 15168 11 + 86568 GAC--------------GCTGAACC -s mr.mrrefChr5 54328 25 + 294540 GATTTTGATTTATGAAGTCTGACCA -s simDog_chr6.simDog.chr6 479981 11 - 593897 GAC--------------GCTGAACC -s simHuman_chr6.simHuman.chr6 201949 11 + 601863 GAC--------------TCAGACCA -s simRat_chr6.simRat.chr6 189760 25 + 647215 GATTATGTTTTATGAAGCCTGACCA - -a -s simMouse_chr6.simMouse.chr6 199701 16 + 636262 TTTGTAGGCAAGTCTC -s Anc0.Anc0refChr5 21112 16 + 87904 TTTATAGGCAAGTCTC -s Anc1.Anc1refChr8 34939 16 + 57822 TTTATAGGCAAGTCTC -s Anc2.Anc2refChr15 15181 16 + 86568 ATTAGAGGCAACTCTC -s mr.mrrefChr5 54353 16 + 294540 TTTGTAGGCAAGTCTC -s simCow_chr6.simCow.chr6 198423 11 + 602619 -----AGGCAACAGTC -s simDog_chr6.simDog.chr6 479994 16 - 593897 ATTAGAGGCAACTCTA -s simHuman_chr6.simHuman.chr6 201962 16 + 601863 TTTATAGACAAGTCTC -s simRat_chr6.simRat.chr6 189785 16 + 647215 TGTGTATGCAAGTCTC - -a -s simMouse_chr6.simMouse.chr6 199717 40 + 636262 ATTTGGAGAGGTGTTTGCTTATTTCTGCTTATTTGTACAA -s Anc0.Anc0refChr5 21128 30 + 87904 ATGTGGAGAGGTGTTTGCTTAGTTC----------TACAA -s Anc1.Anc1refChr8 34955 30 + 57822 ATGTGGAGAGGTGTTTGCTTAGTTC----------TACAA -s Anc2.Anc2refChr15 15197 30 + 86568 ATGTGGAGAGGTGTTTGCTTAGTTC----------TAAAA -s mr.mrrefChr5 54369 40 + 294540 ATTTGGAGAGGTGTTTGCTTATTTCTGCTTATTTGTACAA -s simCow_chr6.simCow.chr6 198435 30 + 602619 AGGTGGAGGGTCATTTGCTTCTGTC----------TAGAA -s simDog_chr6.simDog.chr6 480010 30 - 593897 ATGTGGAGAGGTGACGGCTTAGTTC----------TAAAA -s simHuman_chr6.simHuman.chr6 201978 30 + 601863 ATGCGGCGAGGTGTTTGCTTAATCC----------TACAA -s simRat_chr6.simRat.chr6 189801 23 + 647215 ATTTGG-----------------TTTGCTTATTTGTACAA - -a -s simMouse_chr6.simMouse.chr6 199757 39 + 636262 CCAACTTCTTTATGCCCCCTAATCAGAATGTAGTTTGGA -s Anc0.Anc0refChr5 21159 39 + 87904 CTGTTTTCTTTATATCCCTCAATAGGAATGTAATTAAGA -s Anc1.Anc1refChr8 34986 39 + 57822 CTGTTTTCTTTATATCCCTCAATAGGAATGTAATTAAGA -s Anc2.Anc2refChr15 15228 39 + 86568 CTGTTTTCTTTATATGCCTCAATAGGAATGGAATTAAGA -s mr.mrrefChr5 54410 39 + 294540 CTGACTTCTTTATGTCCCCCAATCAGAATGTAGTTTGGA -s simCow_chr6.simCow.chr6 198466 39 + 602619 CTGTTCTCTTTACATGCCTCAATTGGAATGAAATCTAGA -s simDog_chr6.simDog.chr6 480041 39 - 593897 TTGTATTCTCTATATGACTCAATAGGTATGGAATTAAGA -s simHuman_chr6.simHuman.chr6 202009 39 + 601863 CTGTTTTCTTTATCTCCTTCAATAGGAATGTAATTGAGA -s simRat_chr6.simRat.chr6 189825 39 + 647215 CTGAGTTCTTTATGTCCCCCAATCAAAATGTAGTTTGGA - -a -s simMouse_chr6.simMouse.chr6 199796 50 + 636262 ATTTTCCCAGTGGTTGACCCTTTAAACATGAAACCCTGAGGTTAAGTGCT -s Anc0.Anc0refChr5 21202 50 + 87904 GTGTTCCCAGATGTTAGACCTTAAGCTATAAATTCCTAATCTCAAGTGTT -s Anc1.Anc1refChr8 35029 50 + 57822 GTGTTCCCAGATGTTAGACCTTAAGCTATAAATTCCTAATCTCAAGTGTT -s Anc2.Anc2refChr15 15271 50 + 86568 GTGTTCTCAGAAGTTAGATGTTAAGCTGTAAATTCCTAATCTCAAGTGAT -s mr.mrrefChr5 54449 50 + 294540 ATTTTCCCAGTTGTTGAACCTTTAAACATGAAACCCTGAGGTTAAGTGTT -s simCow_chr6.simCow.chr6 198514 48 + 602619 GTATTTTCAGAAGTTAGATGTTAAGCTCTAAATTTCT--TCCCAAGTGAT -s simDog_chr6.simDog.chr6 480084 50 - 593897 GTGTTCTGAGAAGTCAGATGTTAAGCTGTGAATTCCTAATCTCAAGTGAT -s simHuman_chr6.simHuman.chr6 202052 50 + 601863 GTGTTCCCTGATGTTAGACCTTAACCTATAAATTCCTAAACTGTGATGTT -s simRat_chr6.simRat.chr6 189864 50 + 647215 ATTTTTCCAGTTGTTGAACCTCTAAACCTGAAACCCGGAGGTTAAGTGTT - -a -s simMouse_chr6.simMouse.chr6 199846 9 + 636262 GGTAGAGAC -s Anc0.Anc0refChr5 21252 9 + 87904 GTTGGAGAC -s Anc1.Anc1refChr8 35079 9 + 57822 GTTGGAGAC -s Anc2.Anc2refChr15 15321 9 + 86568 GTTGGACAC -s mr.mrrefChr5 54499 9 + 294540 GGTGGAGAC -s simCow_chr6.simCow.chr6 198562 9 + 602619 GTGCGTCAC -s simDog_chr6.simDog.chr6 480134 9 - 593897 GTTGGACAA -s simHuman_chr6.simHuman.chr6 202103 9 + 601863 GTTGGAGAC -s simRat_chr6.simRat.chr6 189914 9 + 647215 GCTGGAGAC - -a -s simMouse_chr6.simMouse.chr6 199855 103 + 636262 AGGGCTTCACTCTACAAAAGACACACTTAGCCTCGTTTATACAGTATACTATTTTTGGGTACTACCTGGAGGATCTTTACTCACTACCTACATTTTCCCTATT -s Anc0.Anc0refChr5 21261 53 + 87904 AGGACTTCATTCTGTAGAG--CA---------------------------------------------GAGGATATGCAATACCTACCCAAGTATTGCCT--- -s Anc1.Anc1refChr8 35088 58 + 57822 AGGACTTCATTCTGTAGAGTCCA---------------------------------------------GAGGATATGCAATACCTACCCAAGTATTGCCTATT -s Anc2.Anc2refChr15 15330 53 + 86568 AGGACTTTATTCTGTAGAG--CA---------------------------------------------GAGGATATGCAATACCTACCCAGGTATTGCCT--- -s mr.mrrefChr5 54508 103 + 294540 AGGACTTCACTCTATAAAGTACACACTTAGCCTCGTTTATACAGTATACTATGTCTGGGTACTACCTGGAGGATCTTTACTCACTACCTAAGTATTCCCTATT -s simCow_chr6.simCow.chr6 198571 52 + 602619 AGGAGGTTGCTCTGAAGAG--CT---------------------------------------------GAGTAAATGCAATACCTACCCAGGTGATACC---- -s simDog_chr6.simDog.chr6 480143 53 - 593897 AGGACTTTATTCTGTGGAG--CA---------------------------------------------GAGGATAGGCAATACCTGCCCAGGTATTGCCT--- -s simHuman_chr6.simHuman.chr6 202112 57 + 601863 AGGACTTCATTCTGTAGGGTCCA---------------------------------------------GAGGATATACAATGCCAATCCAAGTATTGCCTAT- -s simRat_chr6.simRat.chr6 189927 103 + 647215 ATGACTTCAATGTATAAAGTACACACTTAGCTTTATTTATACAGTGCACTATGTCTGGGTACTACTTGGTGGATCTCTGCTCCCTACCTAAGTACTCCCTATT - -a -s simMouse_chr6.simMouse.chr6 199958 17 + 636262 GACTCAGATTGATCCAA -s Anc0.Anc0refChr5 21314 17 + 87904 GATTTTGATTGGTTCAA -s Anc1.Anc1refChr8 35146 17 + 57822 GATTTTGATTGGTTCAA -s Anc2.Anc2refChr15 15383 17 + 86568 GATTTTGATTGGTTCAA -s mr.mrrefChr5 54611 17 + 294540 GACTCTGATTGATCCAA -s simCow_chr6.simCow.chr6 198623 17 + 602619 GATTTAGTTTGATTCAA -s simDog_chr6.simDog.chr6 480199 17 - 593897 GATTTTGATTGGTTCAA -s simHuman_chr6.simHuman.chr6 202169 2 + 601863 ---------------GA -s simRat_chr6.simRat.chr6 190030 17 + 647215 GACTTTGATTGTTCCAA - -a -s simMouse_chr6.simMouse.chr6 199975 44 + 636262 CACCATCTCAGATTACACGCCTGAGAAAGAAGATAAGATGTAGT -s Anc0.Anc0refChr5 21331 44 + 87904 CACCATCTTGTACATAATGCCTGTTGAAGGTGATAAGAGATGAT -s Anc1.Anc1refChr8 35163 44 + 57822 CACCATCTTGTACATAATGCCTGTTGAAGGTGATAAGAGATGAT -s Anc2.Anc2refChr15 15400 44 + 86568 CGCAATCTTGTACATAATGCCTGTTGAAGGTGAAAAGAGATGAT -s mr.mrrefChr5 54628 44 + 294540 CACCATCTCAGATTACACGCCTGAGAAAGAAGATAAGATGTAGT -s simCow_chr6.simCow.chr6 198640 44 + 602619 CGCAATCTTGCACTAAATGCCCATCACGGGTGAAAAGTGACGAT -s simDog_chr6.simDog.chr6 480216 44 - 593897 CACAATCTTGTACATCATGTCTGTTGAAGGTGAAAATAGATGAT -s simHuman_chr6.simHuman.chr6 202171 40 + 601863 AACCTTCTAGTA----ATCCCTGTTGAATGTAATATGAGATGAC -s simRat_chr6.simRat.chr6 190054 44 + 647215 CACAATCTCAGATTCAAGGTGTGACGAAGGGGATAGGATGTAGT - -a -s simMouse_chr6.simMouse.chr6 200019 5 + 636262 TACAG -s Anc0.Anc0refChr5 21382 5 + 87904 TATGA -s Anc1.Anc1refChr8 35214 5 + 57822 TATGA -s Anc2.Anc2refChr15 15451 5 + 86568 TATGA -s mr.mrrefChr5 54672 5 + 294540 TACAG -s simCow_chr6.simCow.chr6 198691 5 + 602619 TGTGA -s simDog_chr6.simDog.chr6 480267 5 - 593897 TATGA -s simHuman_chr6.simHuman.chr6 202218 5 + 601863 TATGA -s simRat_chr6.simRat.chr6 190098 5 + 647215 TACAG - -a -s simMouse_chr6.simMouse.chr6 200024 7 + 636262 GGGCAGA -s Anc0.Anc0refChr5 21387 7 + 87904 GGGCAGA -s Anc1.Anc1refChr8 35219 7 + 57822 GGGCAGA -s Anc2.Anc2refChr15 15457 7 + 86568 GGGCAGA -s mr.mrrefChr5 54677 7 + 294540 GGGCAGA -s simCow_chr6.simCow.chr6 198697 7 + 602619 GGGCAGA -s simDog_chr6.simDog.chr6 480273 7 - 593897 GGGCAGA -s simHuman_chr6.simHuman.chr6 202223 7 + 601863 GGGCAGA -s simRat_chr6.simRat.chr6 190103 7 + 647215 GGGCAGA - -a -s simMouse_chr6.simMouse.chr6 200031 1 + 636262 G -s Anc0.Anc0refChr5 21395 1 + 87904 G -s Anc1.Anc1refChr8 35227 1 + 57822 G -s Anc2.Anc2refChr15 15465 1 + 86568 A -s mr.mrrefChr5 54684 1 + 294540 G -s simCow_chr6.simCow.chr6 198705 1 + 602619 A -s simDog_chr6.simDog.chr6 480281 1 - 593897 A -s simHuman_chr6.simHuman.chr6 202231 1 + 601863 G -s simRat_chr6.simRat.chr6 190110 1 + 647215 G - -a -s simMouse_chr6.simMouse.chr6 200032 53 + 636262 TTGTAGTCTAGACACAGTGACCGTAGTCTAGACACAGTGACCATGGTGCCTTG -s Anc0.Anc0refChr5 21414 32 + 87904 TAGTGGTCTAAACACAT-------------------G--ACACTGGTGTTATC -s Anc1.Anc1refChr8 35246 34 + 57822 TAGTGGTCTAAACACAT-------------------GTGACACTGGTGTTATC -s Anc2.Anc2refChr15 15484 32 + 86568 TAGTGGTCTAAACACAT-------------------G--ACACTGGTATTATC -s mr.mrrefChr5 54703 53 + 294540 TTGTGGTCTAGACACAGTGACCGTAGTCTAGACACAGTGACCATGGTGTTTTC -s simCow_chr6.simCow.chr6 198724 32 + 602619 TAGTAGTCTAAGTACAT-------------------A--CCACTGGTATTATC -s simDog_chr6.simDog.chr6 480299 32 - 593897 TAGTGGTCTAAACACAT-------------------G--ACACTAATATTATC -s simHuman_chr6.simHuman.chr6 202250 34 + 601863 TAGTGATTAAAACACAT-------------------GTGAAACTGGCGTTCTC -s simRat_chr6.simRat.chr6 190129 53 + 647215 TTGTGGTCTAGGCACAGTGACCATAGTCTAGACACAGTGACCATGGTGTTTTC - -a -s simMouse_chr6.simMouse.chr6 200085 19 + 636262 AAGTCAACTCAGTCAGGAT -s Anc0.Anc0refChr5 21448 19 + 87904 AATCCACTACAATGAAGAT -s Anc1.Anc1refChr8 35282 19 + 57822 AATCCACTACAATGAAGAT -s Anc2.Anc2refChr15 15518 19 + 86568 AATCCACTACAATGATGTT -s mr.mrrefChr5 54756 19 + 294540 AAGTCAACACAGTGAAGAT -s simCow_chr6.simCow.chr6 198758 6 + 602619 GATCCA------------- -s simDog_chr6.simDog.chr6 480333 19 - 593897 AATCCCCTACAATGATGTT -s simHuman_chr6.simHuman.chr6 202286 19 + 601863 AATCCACTAAAACGAACAT -s simRat_chr6.simRat.chr6 190182 19 + 647215 AAGTTGACACAGTGGAGAT - -a -s simMouse_chr6.simMouse.chr6 200104 42 + 636262 ATAGATTCTAATGGAGTATACTATAGTGAGTAGCAGAGAATG -s Anc0.Anc0refChr5 21468 37 + 87904 ACAGTTTCTAGTTGAATATACAATTGTAAGTAGC----A-GA -s Anc1.Anc1refChr8 35302 38 + 57822 ACAGTTTCTAGTTGAATATACAATTGTAAGTAGC----AAGA -s Anc2.Anc2refChr15 15538 37 + 86568 ACAGTTTCTAGTTGAATATACAATTGTAACTAGC----A-GA -s mr.mrrefChr5 54776 42 + 294540 ATAGATTCTAATTGAGTATACAATAGTGAGTAGCAGAGAATG -s simCow_chr6.simCow.chr6 198765 37 + 602619 ATAGTTTCTAGGGGAAGATACAAGTATATATAGC----A-GA -s simDog_chr6.simDog.chr6 480353 37 - 593897 ACAGATTCTAGTTGAATGTACATTTGTAACTAGC----A-GA -s simHuman_chr6.simHuman.chr6 202306 38 + 601863 ACAGTTTCTAGTTGAATATACAATTGTAAGTAGC----AAGA -s simRat_chr6.simRat.chr6 190202 42 + 647215 ATAGATTCTAATTGAGTATACAATATTGGTTAGCGGATCACA - -a -s simMouse_chr6.simMouse.chr6 200146 26 + 636262 CTCTCTCCATTATCTATGTATTTAAA -s Anc0.Anc0refChr5 21524 23 + 87904 ---ACTCCCTTACCTACAAATCTAAA -s Anc1.Anc1refChr8 35359 26 + 57822 CCAACTCCCTTACCTACAAATCTAAA -s Anc2.Anc2refChr15 15594 23 + 86568 ---ACTCCCTTACCTACAAATCTAAA -s mr.mrrefChr5 54837 26 + 294540 CTCTCTCCATTATCTATGTATTTAAA -s simCow_chr6.simCow.chr6 198822 20 + 602619 ------CCCTCACCTACAAATTTAAA -s simDog_chr6.simDog.chr6 480409 23 - 593897 ---ACTCCCTTACCTACAAATCTAAA -s simHuman_chr6.simHuman.chr6 202363 26 + 601863 CCAACTCCTTTACCTACAAATCTAAA -s simRat_chr6.simRat.chr6 190336 26 + 647215 CTGTCTCCATTATCTATGTATTTTAA - -a -s simMouse_chr6.simMouse.chr6 200172 13 + 636262 GAGAGTTTGACTA -s Anc0.Anc0refChr5 21547 13 + 87904 AAGGAATTTGAAA -s Anc1.Anc1refChr8 35385 13 + 57822 AAGGAATTTGAAA -s Anc2.Anc2refChr15 15617 13 + 86568 AAGAAATTTGAAA -s mr.mrrefChr5 54863 13 + 294540 GAGGGTTTGACAA -s simCow_chr6.simCow.chr6 198842 13 + 602619 ATGAAATTTGAAA -s simDog_chr6.simDog.chr6 480432 13 - 593897 AAGAAATTTGTAA -s simHuman_chr6.simHuman.chr6 202389 13 + 601863 AAGGAATTTGAAA -s simRat_chr6.simRat.chr6 190363 13 + 647215 GAGGGTTTGACAA - -a -s simMouse_chr6.simMouse.chr6 200185 23 + 636262 CAAAAGCAAGGTAACACTTACAC -s Anc0.Anc0refChr5 21560 22 + 87904 TGAAAGCAAAGTAACCCTTATA- -s Anc1.Anc1refChr8 35398 22 + 57822 TGAAAGCAAAGTAACCCTTATA- -s Anc2.Anc2refChr15 15630 22 + 86568 TGAAAGCAAAGTAACCCTTGTA- -s mr.mrrefChr5 54876 23 + 294540 CAAAAGCAAAGTAACCCTTACAC -s simCow_chr6.simCow.chr6 198861 22 + 602619 TGAAAGCAAAGTAACCCTTGCA- -s simDog_chr6.simDog.chr6 480445 22 - 593897 TGAAGATAAAGTAACCCTTGTA- -s simHuman_chr6.simHuman.chr6 202402 22 + 601863 TGGAAGCAAAACAATCCTTATA- -s simRat_chr6.simRat.chr6 190376 21 + 647215 CAAAGGCAAA--AACCCTTACAC - -a -s simMouse_chr6.simMouse.chr6 200208 14 + 636262 CTTGTGTCTCTTCC -s Anc0.Anc0refChr5 21582 9 + 87904 -----GTCTCTTCC -s Anc1.Anc1refChr8 35420 9 + 57822 -----GTCTCTTCC -s Anc2.Anc2refChr15 15652 9 + 86568 -----GTCTCTTCC -s mr.mrrefChr5 54899 14 + 294540 CTTGTGTCTCTTCC -s simCow_chr6.simCow.chr6 198883 9 + 602619 -----GTCTCTTCC -s simDog_chr6.simDog.chr6 480467 9 - 593897 -----GTCTCTTGC -s simHuman_chr6.simHuman.chr6 202424 9 + 601863 -----GTCTCTCCC -s simRat_chr6.simRat.chr6 190399 14 + 647215 CTTGTGTCTCGTCA - -a -s simMouse_chr6.simMouse.chr6 200222 15 + 636262 CATTCATGGTTGAAT -s Anc0.Anc0refChr5 21592 15 + 87904 AATACAAGTTTGAAT -s Anc1.Anc1refChr8 35430 15 + 57822 AATACAAGTTTGAAT -s Anc2.Anc2refChr15 15662 15 + 86568 AATATAAGTTTGAAT -s mr.mrrefChr5 54913 15 + 294540 CATTCATGGTTGAAT -s simCow_chr6.simCow.chr6 198893 15 + 602619 AATATAAGACTAAAT -s simDog_chr6.simDog.chr6 480477 15 - 593897 AATATAAGTTTGACT -s simHuman_chr6.simHuman.chr6 202434 15 + 601863 TATACAAGTTCGAAT -s simRat_chr6.simRat.chr6 190413 15 + 647215 CATTCATGGTTGAAT - -a -s simMouse_chr6.simMouse.chr6 200237 33 + 636262 GCAGAGAACCTGTGACAGACTCAAAACAGAGAG -s Anc0.Anc0refChr5 21607 33 + 87904 GCAGAGAACCCCTGACAGTCTTAAAAAAGGGAA -s Anc1.Anc1refChr8 35445 33 + 57822 GCAGAGAACCCCTGACAGTCTTAAAAAAGGGAA -s Anc2.Anc2refChr15 15677 33 + 86568 GCAGAGGACCCCTGACAGTCTTAACAAAGGGAA -s mr.mrrefChr5 54928 33 + 294540 GCAGAGAACCTGTGACAGTCTCAAAACAGAGAA -s simCow_chr6.simCow.chr6 198908 33 + 602619 GCAGAGGACCCCTGACAGTCTTATCAGAGGAAA -s simDog_chr6.simDog.chr6 480493 33 - 593897 GCAGAGGGCCCCTGACAGTCTTAACGATGAGAA -s simHuman_chr6.simHuman.chr6 202449 33 + 601863 GCAGGGAACCCCTGACAGTCTAAAAAAAGGGAA -s simRat_chr6.simRat.chr6 190428 33 + 647215 GCAGAGAACCTGTGACAGTCTCAAAACAGAGAA - -a -s simMouse_chr6.simMouse.chr6 200270 5 + 636262 GTGAA -s Anc0.Anc0refChr5 21640 5 + 87904 GTAGA -s Anc1.Anc1refChr8 35478 5 + 57822 GTAGA -s Anc2.Anc2refChr15 15710 5 + 86568 GTAGA -s mr.mrrefChr5 54961 5 + 294540 GTGGA -s simCow_chr6.simCow.chr6 198941 4 + 602619 -TAGA -s simDog_chr6.simDog.chr6 480528 5 - 593897 GTAGA -s simHuman_chr6.simHuman.chr6 202482 5 + 601863 GTAGA -s simRat_chr6.simRat.chr6 190461 5 + 647215 GTGGA - -a -s simMouse_chr6.simMouse.chr6 200275 41 + 636262 GAGCATGTACAGTGTGTAGCATTCATCCTTTCACTTTATGA -s Anc0.Anc0refChr5 21649 39 + 87904 GAGCATGTAAGGCCT--GGCTTTTATCCTCTTCCTTTACGT -s Anc1.Anc1refChr8 35487 39 + 57822 GAGCATGTAAGGCCT--GGCTTTTATCCTCTTCCTTTACGT -s Anc2.Anc2refChr15 15719 39 + 86568 GAGCACATAAGGCCT--GGCTTTTATCCTCTTCTGTTACTT -s mr.mrrefChr5 54970 39 + 294540 GAGCATGTACAGTGT--AGCATTCATCCTTTTACTTTATGA -s simCow_chr6.simCow.chr6 198949 39 + 602619 GAGAAAATAAGGTTT--GGCTTTCATCCTCTTCTGTTACTT -s simDog_chr6.simDog.chr6 480537 27 - 593897 GACCACATAAGGCCT--AGCTTTTAACCC------------ -s simHuman_chr6.simHuman.chr6 202491 39 + 601863 GAGCCTGTAAGGCCT--GGCTTTAATCCTCTTCCTTTAGGC -s simRat_chr6.simRat.chr6 190471 39 + 647215 AAGCATGTACAGTGT--AGCATTCATCCTTTTACTTTGTGA - -a -s simMouse_chr6.simMouse.chr6 200316 9 + 636262 ATGATGATT -s Anc0.Anc0refChr5 21688 9 + 87904 AAAACAATT -s Anc1.Anc1refChr8 35526 9 + 57822 AAAACAATT -s Anc2.Anc2refChr15 15758 9 + 86568 AAAACAACT -s mr.mrrefChr5 55009 9 + 294540 AAGACAATT -s simCow_chr6.simCow.chr6 198997 9 + 602619 AAAACAACT -s simHuman_chr6.simHuman.chr6 202530 9 + 601863 AAAACAATT -s simRat_chr6.simRat.chr6 190510 9 + 647215 AAGACAATT - -a -s simMouse_chr6.simMouse.chr6 200325 15 + 636262 TAGTAGGACACCAGT -s Anc0.Anc0refChr5 21697 13 + 87904 GGGAAAG--CCCAGG -s Anc1.Anc1refChr8 35535 13 + 57822 GGGAAAG--CCCAGG -s Anc2.Anc2refChr15 15767 13 + 86568 GGGAGAA--CTTGGG -s mr.mrrefChr5 55018 15 + 294540 TAGAAGGACACCAGT -s simCow_chr6.simCow.chr6 199011 13 + 602619 GGGAGAA--CTTGGG -s simHuman_chr6.simHuman.chr6 202539 13 + 601863 AGGAAAG--GCCAGG -s simRat_chr6.simRat.chr6 190519 15 + 647215 TAGAAGGACACCAGT - -a -s simMouse_chr6.simMouse.chr6 200340 17 + 636262 TCACTACTTGTCAGATT -s Anc0.Anc0refChr5 21712 17 + 87904 TCACTACTAGTCAGATT -s Anc1.Anc1refChr8 35550 17 + 57822 TCACTACTAGTCAGATT -s Anc2.Anc2refChr15 15782 17 + 86568 TCACTACTAGTCAGATT -s mr.mrrefChr5 55035 17 + 294540 TCACTACTTGTCAGATT -s simCow_chr6.simCow.chr6 199026 17 + 602619 TCACTACTAGTCAGATT -s simHuman_chr6.simHuman.chr6 202554 17 + 601863 TCAATACTAGTCAGATT -s simRat_chr6.simRat.chr6 190536 17 + 647215 TCACTACCTGTTAGATT - -a -s simMouse_chr6.simMouse.chr6 200357 10 + 636262 TAGGAGATTT -s Anc0.Anc0refChr5 21744 10 + 87904 TAGGAAATTT -s Anc1.Anc1refChr8 35582 10 + 57822 TAGGAAATTT -s Anc2.Anc2refChr15 15814 10 + 86568 TAGGAAGTTG -s mr.mrrefChr5 55052 10 + 294540 TAGGAGATTT -s simCow_chr6.simCow.chr6 199058 10 + 602619 TAGGAAGTTG -s simDog_chr6.simDog.chr6 480572 10 - 593897 TAGGAAGTTG -s simHuman_chr6.simHuman.chr6 202586 10 + 601863 TAGGCAATTT -s simRat_chr6.simRat.chr6 190553 10 + 647215 TAGGAGATTT - -a -s simMouse_chr6.simMouse.chr6 200367 94 + 636262 TTACCAAGGTATTTGGGTTTGCCATTACCCATGTGTCCATTAGTAACCAGATTGTCACCAATCTTCATTTGTTCCAGGTTTCCCATTATGTGAG -s Anc0.Anc0refChr5 21754 34 + 87904 TTACCTAGGTT------------------------------------------------------------TTACAGGTTTGATATTTTGTGTG -s Anc1.Anc1refChr8 35592 34 + 57822 TTACCTAGGTT------------------------------------------------------------TTACAGGTTTGATATTTTGTGTG -s Anc2.Anc2refChr15 15824 34 + 86568 TTACCTAGGTT------------------------------------------------------------TTATAGGTTTGATATTTTGTGTG -s mr.mrrefChr5 55062 88 + 294540 TTACCAAGGTTTTTGGGTTTGCCATTACCCATGTGT--ATTAGTAACCAGATTGTCA----TCTTCATTTGTTCCAGGTTTGCTATTATGTGAG -s simCow_chr6.simCow.chr6 199068 34 + 602619 TTACCTAGGCT------------------------------------------------------------TTGTGGGAATGACATTTTGTGTG -s simDog_chr6.simDog.chr6 480582 33 - 593897 TTACCTAGATT------------------------------------------------------------TTATAGGTTTGATATTT-GTGTG -s simHuman_chr6.simHuman.chr6 202596 34 + 601863 TTATCTAGGTT------------------------------------------------------------TTACAGGTTTGATGTTTTGTGCG -s simRat_chr6.simRat.chr6 190572 88 + 647215 CTACCAAGGTTTTTGGGTTTGCCATCACGCATGCAT--ACTATTTACCAGATTGTCA----TCCGCATCTGTTCCAGGGTTGCTATTATGTGGG - -a -s simMouse_chr6.simMouse.chr6 200461 20 + 636262 TGTACAATGCTTAATTCAGC -s Anc0.Anc0refChr5 21788 15 + 87904 TGTACAA-----GAGTAATT -s Anc1.Anc1refChr8 35626 15 + 57822 TGTACAA-----GAGTAATT -s Anc2.Anc2refChr15 15858 15 + 86568 TGTACAA-----GAGTAGTT -s mr.mrrefChr5 55150 20 + 294540 TGTACAATGCTTGAGTAAGC -s simCow_chr6.simCow.chr6 199103 15 + 602619 TGTACAA-----AAATAGTT -s simDog_chr6.simDog.chr6 480615 15 - 593897 TGTACAA-----GAGTAGTC -s simHuman_chr6.simHuman.chr6 202630 15 + 601863 TGCACAG-----GAGTAATT -s simRat_chr6.simRat.chr6 190660 18 + 647215 TGTACGATGCTTGAGTAG-- - -a -s simMouse_chr6.simMouse.chr6 200481 2 + 636262 AA -s Anc0.Anc0refChr5 21803 2 + 87904 GA -s Anc1.Anc1refChr8 35641 2 + 57822 GA -s Anc2.Anc2refChr15 15873 2 + 86568 GA -s mr.mrrefChr5 55170 2 + 294540 AA -s simCow_chr6.simCow.chr6 199118 2 + 602619 AA -s simDog_chr6.simDog.chr6 480655 2 - 593897 GA -s simHuman_chr6.simHuman.chr6 202645 2 + 601863 GC - -a -s simMouse_chr6.simMouse.chr6 200483 105 + 636262 AGTGTCACCAATCTGAATTTGTATTTACTGTAAACACAGAGCAATCTATGAGCCTTAATTCAAGCAATACTTCATCCACAGTCTGTTGATGCTCAATCCATGTAG -s Anc0.Anc0refChr5 21805 103 + 87904 ATGGTCACCACACTGCATTTCTATTTGCTGTA--CACAGAGTGATCTATGACCCTTAATTAATGGAAGGTTTTATCCACAACCTGTTGATGCGCAATTCACATCT -s Anc1.Anc1refChr8 35643 103 + 57822 ATGGTCACCACACTGCATTTCTATTTGCTGTA--CACAGAGTGATCTATGACCCTTAATTAATGGAAGGTTTTATCCACAACCTGTTGATGCGCAATTCACATCT -s Anc2.Anc2refChr15 15875 103 + 86568 ATGGTCACCACACTGCATTTCGATTTGCTGTA--CACAGAGTGATCTATCACCAGTAATTAATGGAAGGTTTTATTCACAACCTGTTAATGCGCAATTCACATCT -s mr.mrrefChr5 55172 103 + 294540 AGTGTCACCAATCTGCATTTGTATTTACTGTA--CACAGAGTAATCTATGACCCTTAATTCAAGCAATACTTCATCCACAGTCTGTTGATGCTCAATCCACATCG -s simCow_chr6.simCow.chr6 199124 102 + 602619 GTGGTCTCCACACTGCATCTCGGGTTGCTGTA--CACAGAGCGATTCATCACCAGTAATAAATAGATGGTCCTATT-ATAACCATTTCATGCTCAATTCACACCT -s simDog_chr6.simDog.chr6 480657 100 - 593897 ATGGTCACCACA-TGCATTTTGATTTGCTGCA--CACAAAGTGATCTATCGCCAGTAATTAATGGAAGGTTTTATTCACAACCTGTTAATGCGCAATTGA--TTA -s simHuman_chr6.simHuman.chr6 202647 103 + 601863 ATGGTCACCACACTGCAGTGCTATTAGCTGTA--CACAGAGTGGTCTATGACCCTTAATTAATGGAGGGTTTTGTCCACAAACTGTTGATGCACAAGTCACATCT -s simRat_chr6.simRat.chr6 190678 93 + 647215 ----------ATCTGCATTTGTATTTACTGTT--CACAGAGTAATCTACAACCCTTAATTCTAGCAATACCTCATTCACAGTCTGTTGATGCTCAATCCACATCG - -a -s simMouse_chr6.simMouse.chr6 200588 56 + 636262 GTTGCAGAGGAGGTGCAACCTAAGTAAAGCTACCAAGAGCTGTCTGAACTCAGTTT -s Anc0.Anc0refChr5 21908 39 + 87904 GTTGCAGTG-----------TAAATCAATCCACCAAAAATTGTCTG------GTTG -s Anc1.Anc1refChr8 35746 51 + 57822 GTTGCAGTGCAGGTGCAACCTAAATCAATCCACCAAAAATTGTCTG-----AGTTG -s Anc2.Anc2refChr15 15978 39 + 86568 GGTGCAGTG-----------TAAATCAATCCACCAAAAATTGTCTG------GTTG -s mr.mrrefChr5 55275 56 + 294540 GTTGCAGAGCAGGTGCAACCTAAGTAAAGCTACCAAGAGCTGTCTGAACTCAGTTG -s simCow_chr6.simCow.chr6 199237 39 + 602619 GGTGCAACG-----------TAAACCAATCCACCGAAAATTGTCTT------AATG -s simDog_chr6.simDog.chr6 480757 39 - 593897 GGTGCAGTG-----------TAAATCAATCCACCAAAAATTGTCTG------GTTG -s simHuman_chr6.simHuman.chr6 202750 27 + 601863 GTTGCTGGGCAGGTGCAACCTA-----------------------------AATTG -s simRat_chr6.simRat.chr6 190771 56 + 647215 GTTGCAGAGCGGGTGCAACCTAAGTCAAGGTACAAAAAAGTGTCAGAACTGAGTTG - -a -s simMouse_chr6.simMouse.chr6 200644 14 + 636262 AAGAGCAGGACATG -s Anc0.Anc0refChr5 21947 14 + 87904 AACAACAAGACATG -s Anc1.Anc1refChr8 35797 14 + 57822 AACAACAAGACATG -s Anc2.Anc2refChr15 16022 14 + 86568 AACAACTAGACATG -s mr.mrrefChr5 55331 14 + 294540 AAGAGCAAGACATG -s simCow_chr6.simCow.chr6 199281 14 + 602619 ATCAACTAGGCATG -s simDog_chr6.simDog.chr6 480801 14 - 593897 AACAACTAGACATG -s simHuman_chr6.simHuman.chr6 202777 14 + 601863 AACAACAAAACATG -s simRat_chr6.simRat.chr6 190827 14 + 647215 GAGAGCAAGACATG - -a -s simMouse_chr6.simMouse.chr6 200658 23 + 636262 GAATGTCTGAGGATCTGCTCTGA -s Anc0.Anc0refChr5 21961 23 + 87904 GAAGATTTTAGGATGTGCCCTGA -s Anc1.Anc1refChr8 35811 23 + 57822 GAAGATTTTAGGATGTGCCCTGA -s Anc2.Anc2refChr15 16036 23 + 86568 GAAGATTTTAGGATGTGCCCTGA -s mr.mrrefChr5 55345 23 + 294540 GAATGTCTTAGGATCTGCCCTGA -s simCow_chr6.simCow.chr6 199295 23 + 602619 AAAAATTTTAGGACATGTCCTGA -s simDog_chr6.simDog.chr6 480817 23 - 593897 GAAGACTCTAGGATGTGCTCTGA -s simHuman_chr6.simHuman.chr6 202791 23 + 601863 GAAGATTTTAATATGTACCCTGA -s simRat_chr6.simRat.chr6 190841 23 + 647215 GAATGTCTTAGGTACTGCCCTGA - -a -s simMouse_chr6.simMouse.chr6 200681 5 + 636262 TGAAC -s Anc0.Anc0refChr5 21984 5 + 87904 TGAAC -s Anc1.Anc1refChr8 35834 5 + 57822 TGAAC -s Anc2.Anc2refChr15 16060 5 + 86568 TGAGC -s mr.mrrefChr5 55368 5 + 294540 TGAAC -s simCow_chr6.simCow.chr6 199319 5 + 602619 TAAGC -s simDog_chr6.simDog.chr6 480841 5 - 593897 TGAGC -s simHuman_chr6.simHuman.chr6 202814 5 + 601863 TGAAC -s simRat_chr6.simRat.chr6 190864 5 + 647215 TGAAC - -a -s simMouse_chr6.simMouse.chr6 200686 10 + 636262 TGTCTAGATG -s Anc0.Anc0refChr5 21989 10 + 87904 TGTCTAGGTA -s Anc1.Anc1refChr8 35839 10 + 57822 TGTCTAGGTA -s Anc2.Anc2refChr15 16065 10 + 86568 TGTCTAGGTA -s mr.mrrefChr5 55373 10 + 294540 TGTCTAGATG -s simCow_chr6.simCow.chr6 199324 9 + 602619 TGTCTAGGT- -s simDog_chr6.simDog.chr6 480846 10 - 593897 TGTCTAGGTA -s simHuman_chr6.simHuman.chr6 202821 10 + 601863 TGTCCAGGTA -s simRat_chr6.simRat.chr6 190869 10 + 647215 TGTCTAGATG - -a -s simMouse_chr6.simMouse.chr6 200696 27 + 636262 TTGGCAAAGACAACTGGGCTGCATACT -s Anc0.Anc0refChr5 22000 27 + 87904 TTTGCAATGACAACTGGGCTGCATACT -s Anc1.Anc1refChr8 35850 27 + 57822 TTTGCAATGACAACTGGGCTGCATACT -s Anc2.Anc2refChr15 16076 27 + 86568 TTTGCAATGGCAACTGGGCTGCATACT -s mr.mrrefChr5 55383 27 + 294540 TTGGCAAAGACAACTGGGCTGCATACT -s simCow_chr6.simCow.chr6 199333 23 + 602619 -TTACAA---CAACATGGCTGCAGACT -s simDog_chr6.simDog.chr6 480857 27 - 593897 TTTGCAATGGCAACTGAGCTGCATGCT -s simHuman_chr6.simHuman.chr6 202832 24 + 601863 TTAGC--CGATGACTGGGCT-CATACT -s simRat_chr6.simRat.chr6 190879 27 + 647215 TTGGCAAAAACAACTGGGCTGCATTCT - -a -s simMouse_chr6.simMouse.chr6 200723 2 + 636262 AT -s Anc0.Anc0refChr5 22027 2 + 87904 AT -s Anc1.Anc1refChr8 35877 2 + 57822 AT -s Anc2.Anc2refChr15 16103 2 + 86568 AT -s mr.mrrefChr5 55410 2 + 294540 AT -s simCow_chr6.simCow.chr6 199357 2 + 602619 AT -s simDog_chr6.simDog.chr6 480884 2 - 593897 AT -s simHuman_chr6.simHuman.chr6 202856 2 + 601863 AT -s simRat_chr6.simRat.chr6 190906 2 + 647215 AT - -a -s simMouse_chr6.simMouse.chr6 200725 33 + 636262 CACCTCACAGCAAGATGAGGACAGGAAAGGTCT -s Anc0.Anc0refChr5 22035 33 + 87904 TGCCTGAAGGGGAAATGGGACCAGGAAAGGTCT -s Anc1.Anc1refChr8 35887 33 + 57822 TGCCTGAAGGGGAAATGGGACCAGGAAAGGTCT -s Anc2.Anc2refChr15 16111 33 + 86568 TGCCTGAAGGGGAAATGGGACCAGGAAAGGTCT -s mr.mrrefChr5 55412 33 + 294540 TACCTCACGGCAAGATGGGGACAGGAAAGGTCT -s simCow_chr6.simCow.chr6 199365 33 + 602619 TGTCTGCAGGGGAGATGGGACCAGAAAAGGTCT -s simDog_chr6.simDog.chr6 480892 31 - 593897 TGCCTGAAG--GCAATGGGACCAGGAAACGACT -s simHuman_chr6.simHuman.chr6 202866 33 + 601863 TGCATTAAGCAGACATGGGACCAGGACAGGTCA -s simRat_chr6.simRat.chr6 190908 33 + 647215 TAACTCAGGGCAGGATGGGGACAGGAAAGGTCT - -a -s simMouse_chr6.simMouse.chr6 200758 12 + 636262 TGTTGGTTCAGA -s Anc0.Anc0refChr5 22070 12 + 87904 TGTTGGTTCAGA -s Anc1.Anc1refChr8 35922 12 + 57822 TGTTGGTTCAGA -s Anc2.Anc2refChr15 16146 12 + 86568 TGTTGGTTCAGA -s mr.mrrefChr5 55447 12 + 294540 TGTTGGTTCAGA -s simCow_chr6.simCow.chr6 199401 12 + 602619 CGTTGGTTCAGA -s simDog_chr6.simDog.chr6 480925 12 - 593897 TGTTGGTACAGA -s simHuman_chr6.simHuman.chr6 202901 12 + 601863 TGTTGATTCAGA -s simRat_chr6.simRat.chr6 190943 12 + 647215 TGTTGGTTCAGA - -a -s simMouse_chr6.simMouse.chr6 200770 34 + 636262 GTCTTTTCAAGAAATCCAGTTTGGAAATTGGGCT -s Anc0.Anc0refChr5 22103 34 + 87904 GTCTTTTCAAGAAAGCCAGTTTGGGAGTTTGGAT -s Anc1.Anc1refChr8 35955 34 + 57822 GTCTTTTCAAGAAAGCCAGTTTGGGAGTTTGGAT -s Anc2.Anc2refChr15 16179 34 + 86568 GTCTTTTCAAAAAAGACAGTTTGGGAGTTTGGAT -s mr.mrrefChr5 55480 34 + 294540 GTCTTTTCAAGAAATCCAGTTTGGAAATTGGGCT -s simCow_chr6.simCow.chr6 199434 34 + 602619 GTCTTTTCAAAAAATACAATTTGGGAGTTTCCAT -s simDog_chr6.simDog.chr6 480958 34 - 593897 GTCCCCTCAAAAAAGACAGTTAGGGAATTTGGAT -s simHuman_chr6.simHuman.chr6 202934 34 + 601863 GTCTTTTCAAGAAAGCCAGTTTGGGAGTTTGGAT -s simRat_chr6.simRat.chr6 190976 33 + 647215 GTCTTTCCAACAAATACAGTTTGGAAACTGG-CT - -a -s simMouse_chr6.simMouse.chr6 200804 6 + 636262 CATATG -s Anc0.Anc0refChr5 22137 6 + 87904 TACATA -s Anc1.Anc1refChr8 35989 6 + 57822 TACATA -s Anc2.Anc2refChr15 16213 6 + 86568 TACATA -s mr.mrrefChr5 55514 6 + 294540 CATATG -s simCow_chr6.simCow.chr6 199468 6 + 602619 TACGTA -s simDog_chr6.simDog.chr6 480999 6 - 593897 TACATA -s simHuman_chr6.simHuman.chr6 202968 6 + 601863 TACATA -s simRat_chr6.simRat.chr6 191009 6 + 647215 GATATG - -a -s simMouse_chr6.simMouse.chr6 200810 48 + 636262 GAAACATATGACACCTAGTTAAAATAAATAAGAACCTGGTTCCCAGTC -s Anc0.Anc0refChr5 22150 48 + 87904 GTAACAAATCACACCTAGTTGCAATAAATGAGAACATGTTTCCCACCC -s Anc1.Anc1refChr8 36002 48 + 57822 GTAACAAATCACACCTAGTTGCAATAAATGAGAACATGTTTCCCACCC -s Anc2.Anc2refChr15 16226 48 + 86568 GTAACAAATCACACCTAGTTGCAATAAATGAGAACATGTTTCCCACCC -s mr.mrrefChr5 55520 48 + 294540 GAAACATATGACACCTAGTTAAAATAAATAAGAACCTGGTTCCCAGTC -s simCow_chr6.simCow.chr6 199481 42 + 602619 GTAACAAA---CACCTAGTTGCAATGTATGAGAACATGTTTCCC---C -s simDog_chr6.simDog.chr6 481012 48 - 593897 GTAACAAATCACACCTAACTGCACAAAATAAGAATGGGTTGCCCACCC -s simHuman_chr6.simHuman.chr6 202981 48 + 601863 GTAACAAATAGCACCTAGTTGTAATAAATGAGGGCATGTTTCCCATCC -s simRat_chr6.simRat.chr6 191015 39 + 647215 GAAA----TTACACCTAGTCAAAGTA-----GACCGTGGTTCCCAGTC - -a -s simMouse_chr6.simMouse.chr6 200858 31 + 636262 ATCTGTGGGAATGGTAATGAGAGGACTTGAC -s Anc0.Anc0refChr5 22198 31 + 87904 ATCCCTGGGGATGGCAATGAGTGGATGTGAG -s Anc1.Anc1refChr8 36050 31 + 57822 ATCCCTGGGGATGGCAATGAGTGGATGTGAG -s Anc2.Anc2refChr15 16274 31 + 86568 ATCCCTGGGGATGGCAATGAGTGGATGTGAG -s mr.mrrefChr5 55568 31 + 294540 ATCCGTGGGAATGGTAATGAGTGGACTTGAC -s simCow_chr6.simCow.chr6 199523 30 + 602619 GTCTCTGGTGCTGGCAA-GAGTGGATGTGAG -s simDog_chr6.simDog.chr6 481075 31 - 593897 ATCCCTTGGGATAGCAATGAGTTGATGTGAG -s simHuman_chr6.simHuman.chr6 203029 31 + 601863 ATCCCTGGGGATGGCAATGAGTGGATGTCAG -s simRat_chr6.simRat.chr6 191054 25 + 647215 ACCC------AAGGTAATGGGTGGACTTGAC - -a -s simMouse_chr6.simMouse.chr6 200889 61 + 636262 ATTCTGAGGTGACACAATTGTGTTTTTTATCAGGTTCCTTTTTACTGTTATTTTTATTATG -s Anc0.Anc0refChr5 22229 61 + 87904 GTTCTGAGATGACACACCTGTGTTTTTTCTCAGGTTTCCTTTTACTCCTATTTGAGTTATG -s Anc1.Anc1refChr8 36081 61 + 57822 GTTCTGAGATGACACACCTGTGTTTTTTCTCAGGTTTCCTTTTACTCCTATTTGAGTTATG -s Anc2.Anc2refChr15 16305 61 + 86568 GCTCCTAGATGCCGCACCTGTGTTCTTTCTCAGGTTTCCTTTTACTCCTATTTGAGTTATG -s mr.mrrefChr5 55599 61 + 294540 ATTCTGAGGTGACACAACTGTGTTTTTTCTCAGGTTCCTTTTTACTCCTATTTGTATTATG -s simCow_chr6.simCow.chr6 199553 61 + 602619 ACTCCCAGATGGGTCACCTGTACTGTTTCTCAGGTCTCCCTTTACCCCTATTTGGGTTGTA -s simDog_chr6.simDog.chr6 481118 61 - 593897 GCACCTGGATGCCGGACCTGTGTTCTTTCTCAAGATTCCTTTTACTCCTATTTGAGTTATG -s simHuman_chr6.simHuman.chr6 203060 61 + 601863 GTTCTGAGAAGATACATCTATGTTTTTTCTCAGGTTTCCTTTTACTCCTATTTGAGTTATG -s simRat_chr6.simRat.chr6 191079 61 + 647215 ATTCTCAGGTGACACAACGGTGTTTTTTCTCAGGTTCCTCTTTACTCCTATTTGTATTATG - -a -s simMouse_chr6.simMouse.chr6 200950 8 + 636262 GAATTTGA -s Anc0.Anc0refChr5 22290 8 + 87904 GAATCTGA -s Anc1.Anc1refChr8 36142 8 + 57822 GAATCTGA -s Anc2.Anc2refChr15 16390 8 + 86568 GAATCTGA -s mr.mrrefChr5 55660 8 + 294540 GAATTTGA -s simCow_chr6.simCow.chr6 199638 6 + 602619 GAACCT-- -s simDog_chr6.simDog.chr6 481203 8 - 593897 GAATCTGA -s simHuman_chr6.simHuman.chr6 203121 8 + 601863 GAAACTGA -s simRat_chr6.simRat.chr6 191140 8 + 647215 GGATTTGA - -a -s simMouse_chr6.simMouse.chr6 200958 16 + 636262 CAGCAACACTTGATCC -s Anc0.Anc0refChr5 22301 16 + 87904 CAGCAACATCGAGTGC -s Anc1.Anc1refChr8 36153 16 + 57822 CAGCAACATCGAGTGC -s Anc2.Anc2refChr15 16401 16 + 86568 CAGCAACATCGAGTAC -s mr.mrrefChr5 55668 16 + 294540 CAGCAACACTTGATGC -s simCow_chr6.simCow.chr6 199644 16 + 602619 CAGCAACATCGAATAT -s simDog_chr6.simDog.chr6 481214 11 - 593897 CGGCAAC-----GTAC -s simHuman_chr6.simHuman.chr6 203132 16 + 601863 CAGCAGCATCCAGTGC -s simRat_chr6.simRat.chr6 191148 10 + 647215 GAGGA------GATGC - -a -s simMouse_chr6.simMouse.chr6 200974 11 + 636262 CTAAGCATTCT -s Anc0.Anc0refChr5 22317 10 + 87904 CTGAGTACAG- -s Anc1.Anc1refChr8 36169 10 + 57822 CTGAGTACAG- -s Anc2.Anc2refChr15 16417 10 + 86568 CTGAGTACAG- -s mr.mrrefChr5 55684 11 + 294540 CTAAGTATAGT -s simCow_chr6.simCow.chr6 199661 10 + 602619 TTGACTACAG- -s simDog_chr6.simDog.chr6 481225 10 - 593897 CTGAGTACAG- -s simHuman_chr6.simHuman.chr6 203148 10 + 601863 CTGAGTACAG- -s simRat_chr6.simRat.chr6 191158 11 + 647215 CTAAGTATAGT - -a -s simMouse_chr6.simMouse.chr6 200985 67 + 636262 GGACCTAGTGTGTAGTTGAAAGCAGGTCTAAGGGACTTATATGAAATTAGCATTCTAGAGATGGCCC -s Anc0.Anc0refChr5 22327 63 + 87904 GGCTCT---CTAAAGCTGAGGTCAAGTGTAAGTAACCTATGTGAAATCAGTATTCTGGAGTTGG-CC -s Anc1.Anc1refChr8 36179 67 + 57822 GGCTCTGATCTAAAGCTGAGGTCAAGTGTAAGTAACCTATGTGAAATCAGTATTCTGGAGTTGGACC -s Anc2.Anc2refChr15 16427 63 + 86568 GGCTCT---CTAAAGCTGAGGTCAAGTGTAAGTAACCTATGTGAAATCAGTATTCTGGAGATGG-CC -s mr.mrrefChr5 55695 67 + 294540 GGACCTAGTGTGTAGTTGAAGTCAGGTCTAAGGAACCTATATGAAATTAGCATTCTAGAGTTGGCCC -s simCow_chr6.simCow.chr6 199671 53 + 602619 -------------AGCTGAGGTCAAGTGCATGCTACCTATATGAAATCAGTATCCTACAGAAAG-CC -s simDog_chr6.simDog.chr6 481236 63 - 593897 GGCTCT---CTAAAGCTGAGGTTAGGCGTAAGTAACTTATGTAAAATCAGTATTCTGGACATGG-CA -s simHuman_chr6.simHuman.chr6 203158 67 + 601863 AGCTCTGATCTACAGCTGAGGTCAACTGTGAGTAACCTATGTGAAGTCAGTATTCTGAAGTCGGACC -s simRat_chr6.simRat.chr6 191169 67 + 647215 GGTCCTAGTGTGTAGTAGGAGTCAGGTCTAAGGAAACTATATGAAATTAACATTCTAGAGTTGGCCT - -a -s simMouse_chr6.simMouse.chr6 201052 19 + 636262 TGCCTGTGTTGTTTGTGAG -s Anc0.Anc0refChr5 22399 19 + 87904 TAACTATGTTGTTAGTGAT -s Anc1.Anc1refChr8 36255 19 + 57822 TAACTATGTTGTTAGTGAT -s Anc2.Anc2refChr15 16499 19 + 86568 TAACTATGTTGTTAGAGAT -s mr.mrrefChr5 55762 19 + 294540 TGCCTGTGTTGTTTGTGAG -s simCow_chr6.simCow.chr6 199733 13 + 602619 CAACTGTATTCTT------ -s simDog_chr6.simDog.chr6 481308 19 - 593897 TAACTATGTTGTTAGAGAT -s simHuman_chr6.simHuman.chr6 203234 19 + 601863 TAACTATGTTGTGAGTGAT -s simRat_chr6.simRat.chr6 191236 19 + 647215 TGCCTGTGTTGTTTGTGAG - -a -s simMouse_chr6.simMouse.chr6 201071 12 + 636262 ATCTTTCGTCAT -s Anc0.Anc0refChr5 22418 7 + 87904 ATCATTC----- -s Anc1.Anc1refChr8 36274 12 + 57822 ATCATTCGTTAT -s Anc2.Anc2refChr15 16518 7 + 86568 TGCATTC----- -s mr.mrrefChr5 55781 12 + 294540 ATCTTTCGTTAT -s simDog_chr6.simDog.chr6 481327 7 - 593897 TGCATTC----- -s simHuman_chr6.simHuman.chr6 203256 12 + 601863 ATTAGACGTTAT -s simRat_chr6.simRat.chr6 191255 12 + 647215 ATCCTTCATTAT - -a -s simMouse_chr6.simMouse.chr6 201083 15 + 636262 TAATTGTAGACTGGT -s Anc0.Anc0refChr5 22429 15 + 87904 TAACTATAGCCTAGT -s Anc1.Anc1refChr8 36290 15 + 57822 TAACTATAGCCTAGT -s Anc2.Anc2refChr15 16529 15 + 86568 TAACTATAACCTAGT -s mr.mrrefChr5 55793 15 + 294540 TAATTATAGACTGGT -s simDog_chr6.simDog.chr6 481338 15 - 593897 TAACTATAACCTAGT -s simHuman_chr6.simHuman.chr6 203272 15 + 601863 TAACTACAGTCTAGC -s simRat_chr6.simRat.chr6 191267 15 + 647215 TAATTATAGACTGGT - -a -s simMouse_chr6.simMouse.chr6 201098 5 + 636262 AGTTA -s Anc0.Anc0refChr5 22447 5 + 87904 AGTTA -s Anc1.Anc1refChr8 36308 5 + 57822 AGTTA -s Anc2.Anc2refChr15 16547 5 + 86568 ACTAA -s mr.mrrefChr5 55808 5 + 294540 AGTTA -s simDog_chr6.simDog.chr6 481356 5 - 593897 ACTAA -s simHuman_chr6.simHuman.chr6 203290 5 + 601863 AGTTG -s simRat_chr6.simRat.chr6 191282 5 + 647215 AGTTA - -a -s simMouse_chr6.simMouse.chr6 201103 37 + 636262 TTAGTGTCTTAATCTGGACTATTTCAGCTTGACACAT -s Anc0.Anc0refChr5 22455 28 + 87904 TGGGTGTAATAATCCAGGTGATTTCAGC--------- -s Anc1.Anc1refChr8 36316 28 + 57822 TGGGTGTAATAATCCAGGTGATTTCAGC--------- -s Anc2.Anc2refChr15 16555 28 + 86568 TATGTGTAACAATCCAGGTGCTTTTAGC--------- -s mr.mrrefChr5 55813 37 + 294540 TGGGTGTCTTAATCTGGATTATTTCAGCTTGACACAT -s simDog_chr6.simDog.chr6 481368 28 - 593897 TATGTGTAACAATCCAGGTGCTTTTAGC--------- -s simHuman_chr6.simHuman.chr6 203298 28 + 601863 TGGGTGGAATTATCCCAGTGATATCAGC--------- -s simRat_chr6.simRat.chr6 191287 37 + 647215 TGGATGCCTTAATCTGGATTATTTCAGCTTGACACAT - -a -s simMouse_chr6.simMouse.chr6 201140 76 + 636262 CATGGATTTCAGCCTTATGCATCAGTTCCCATTCCCTTTCAAAAGATCTAAGGGAATAAGTGTTCCACGGAGGATT -s Anc0.Anc0refChr5 22483 72 + 87904 CATTGATTTTAGCTTCATGCATCATCTACCCTTATTTTTCAAAAGCTCTAGGG----AAATGCTCTAGGGAGGACT -s Anc1.Anc1refChr8 36344 72 + 57822 CATTGATTTTAGCTTCATGCATCATCTACCCTTATTTTTCAAAAGCTCTAGGG----AAATGCTCTAGGGAGGACT -s Anc2.Anc2refChr15 16583 72 + 86568 CATTGATTTTAACTTCATGCATCATCTACCCTTATTGTTCAAAAGCTCCAGGG----AAATGCTCTAGGGAGGACT -s mr.mrrefChr5 55850 76 + 294540 CATGGATTTTAGCCTTATGCATCAGTTACCATTACCTTTCAAAAGATCTAAGGGAATAAGTGTTCCACGGAGGATT -s simCow_chr6.simCow.chr6 199746 59 + 602619 ------------CTTCATGCATCATCTACCCTTATTGCTCAAAAGCTGCAGGA----AAATGC-CTAGTAAGGGTT -s simDog_chr6.simDog.chr6 481405 70 - 593897 CATTGATTTTAACTCCATGCAT--TCTATCCGTATTGTTCAAAACGTCCAAGG----AAATGCTCTAGGGAGGACT -s simHuman_chr6.simHuman.chr6 203326 70 + 601863 AGTTGATTTTAGCTTCATCCATCATCTACCCTTATTTTTCAAAAGCTTTAGGG----AACTTCTATTGGGAAG--A -s simRat_chr6.simRat.chr6 191324 76 + 647215 CATGAATTTTAGCCTTATGCATCAGTTACCATTACCTTTCAAAAGAACTAAGGGAACAAATTTTCAAGGGAGGATC - -a -s simMouse_chr6.simMouse.chr6 201216 30 + 636262 CTTCAAGCAAAAGATAACACTGAAGCACTT -s Anc0.Anc0refChr5 22555 30 + 87904 TTTAAAGCAACAGATAACACTGAAGCACTT -s Anc1.Anc1refChr8 36416 30 + 57822 TTTAAAGCAACAGATAACACTGAAGCACTT -s Anc2.Anc2refChr15 16656 30 + 86568 TTTAGAGCTACAGATAACACTGAAGCACTT -s mr.mrrefChr5 55926 30 + 294540 CTTCAAGCAAAAGATAACACTGAAGCACTT -s simCow_chr6.simCow.chr6 199806 30 + 602619 CCTAGAGTGACAAATAATACTGAAACACTC -s simDog_chr6.simDog.chr6 481476 29 - 593897 TTTAGAACTATGGATAAC-CTGAAGTACTT -s simHuman_chr6.simHuman.chr6 203396 30 + 601863 TTTAAAGCAACAGATAACGCTGAAGCACTT -s simRat_chr6.simRat.chr6 191400 30 + 647215 CTTCAAGCAAAAGATAATACTGAAGCACTT - -a -s simMouse_chr6.simMouse.chr6 201246 7 + 636262 TACCCCC -s Anc0.Anc0refChr5 22598 7 + 87904 TCCCCCC -s Anc1.Anc1refChr8 36459 7 + 57822 TCCCCCC -s Anc2.Anc2refChr15 16699 7 + 86568 TCCCCCC -s mr.mrrefChr5 55956 7 + 294540 TACCCCC -s simCow_chr6.simCow.chr6 199848 7 + 602619 TCCCTCC -s simDog_chr6.simDog.chr6 481518 7 - 593897 ACCCCCC -s simHuman_chr6.simHuman.chr6 203439 7 + 601863 TCCCCCC -s simRat_chr6.simRat.chr6 191430 7 + 647215 TATCCCC - -a -s simMouse_chr6.simMouse.chr6 201253 25 + 636262 TATTGATCTTGTTACCCAGTCGTTA -s Anc0.Anc0refChr5 22616 24 + 87904 CATTGATCTTGTTACCTAGACGTC- -s Anc1.Anc1refChr8 36477 24 + 57822 CATTGATCTTGTTACCTAGACGTC- -s Anc2.Anc2refChr15 16718 24 + 86568 CATTGATCTTATTACCTAGACATC- -s mr.mrrefChr5 55963 24 + 294540 TATTGATCTTGTTACCCAGTCGTC- -s simCow_chr6.simCow.chr6 199867 24 + 602619 CATAGATCTTATTACCTAGGCGTT- -s simDog_chr6.simDog.chr6 481537 24 - 593897 CATTGATCTTACTACCTAGACATC- -s simHuman_chr6.simHuman.chr6 203457 18 + 601863 CATTGATCTTGTTA------AGCC- -s simRat_chr6.simRat.chr6 191437 24 + 647215 TATTGATCTTGTTACCCACCCATC- - -a -s simMouse_chr6.simMouse.chr6 201278 8 + 636262 TGGTGTTA -s Anc0.Anc0refChr5 22640 8 + 87904 TGGTATCA -s Anc1.Anc1refChr8 36501 8 + 57822 TGGTATCA -s Anc2.Anc2refChr15 16743 8 + 86568 TGGTATCA -s mr.mrrefChr5 55987 8 + 294540 TGGTGTTA -s simCow_chr6.simCow.chr6 199892 8 + 602619 TGGTATCA -s simDog_chr6.simDog.chr6 481562 8 - 593897 TGGCATCA -s simHuman_chr6.simHuman.chr6 203475 8 + 601863 CAGTATCA -s simRat_chr6.simRat.chr6 191461 8 + 647215 TGCTGCTA - -a -s simMouse_chr6.simMouse.chr6 201286 33 + 636262 TCCCGGCAGACCACATTCAGATCCTTCAGGATG -s Anc0.Anc0refChr5 22649 33 + 87904 TCCCAGACAGTTAAATTCAGATTCTGCTGGATG -s Anc1.Anc1refChr8 36510 33 + 57822 TCCCAGACAGTTAAATTCAGATTCTGCTGGATG -s Anc2.Anc2refChr15 16752 33 + 86568 TCCCAGACAGTTAAATTCAGATTCTGCTGGATG -s mr.mrrefChr5 55996 33 + 294540 TCCCAGAAGACTACATTCAGATTCTTCAGGATG -s simCow_chr6.simCow.chr6 199901 32 + 602619 TTCCAAACAAGTACATTCAG-TTCTGCTCGATG -s simDog_chr6.simDog.chr6 481575 33 - 593897 TCCCAGACAGTTAAATTCAGATTCTGCTGGATT -s simHuman_chr6.simHuman.chr6 203484 33 + 601863 TCTAAGACATTTAGATTCAGGTTCTGCTGGATG -s simRat_chr6.simRat.chr6 191470 33 + 647215 TCCCAGAAGACTGCATTCAGATTCTTTGGGATG - -a -s simMouse_chr6.simMouse.chr6 201319 28 + 636262 TAGTATAGTCTGGATAGTTGTAGCCCTT -s Anc0.Anc0refChr5 22688 28 + 87904 TGCTATAGCCTGGATAGTTATAATTCTT -s Anc1.Anc1refChr8 36549 28 + 57822 TGCTATAGCCTGGATAGTTATAATTCTT -s Anc2.Anc2refChr15 16791 28 + 86568 TGCTATAGCCTGGATAGTTACAATTCTT -s mr.mrrefChr5 56029 28 + 294540 TAGTATAGCCTGGATAGTTGTAGCCCTT -s simCow_chr6.simCow.chr6 199939 28 + 602619 TGCTATAGCATGGATAGTTAGAGTTCTT -s simDog_chr6.simDog.chr6 481610 28 - 593897 TCCTATAGCCTGGATAGTTACAATTCTT -s simHuman_chr6.simHuman.chr6 203524 28 + 601863 TGCCATAGCCTCGATAGTTATATTTCTT -s simRat_chr6.simRat.chr6 191503 28 + 647215 TAGTATAGCCTGGATAGTTGTAGCCCTT - -a -s simMouse_chr6.simMouse.chr6 201347 5 + 636262 GAAGC -s Anc0.Anc0refChr5 22727 5 + 87904 GGAGC -s Anc1.Anc1refChr8 36588 5 + 57822 GGAGC -s Anc2.Anc2refChr15 16830 5 + 86568 GGAGG -s mr.mrrefChr5 56057 5 + 294540 GAAGC -s simCow_chr6.simCow.chr6 199978 5 + 602619 GGAAG -s simDog_chr6.simDog.chr6 481649 5 - 593897 GGAGG -s simHuman_chr6.simHuman.chr6 203569 5 + 601863 GGAGC -s simRat_chr6.simRat.chr6 191531 5 + 647215 GAAGC - -a -s simMouse_chr6.simMouse.chr6 201352 11 + 636262 AAAATGGATAA -s Anc0.Anc0refChr5 22733 11 + 87904 AAAGTGGTCAG -s Anc1.Anc1refChr8 36594 11 + 57822 AAAGTGGTCAG -s Anc2.Anc2refChr15 16836 11 + 86568 AAAGTTGTAAG -s mr.mrrefChr5 56062 11 + 294540 AAAATGGACAA -s simCow_chr6.simCow.chr6 199984 11 + 602619 AAAGTTGTAGG -s simDog_chr6.simDog.chr6 481655 11 - 593897 AAAGTTGTAAT -s simHuman_chr6.simHuman.chr6 203575 9 + 601863 AAA--GGTCAG -s simRat_chr6.simRat.chr6 191536 11 + 647215 AAAAAGGACAA - -a -s simMouse_chr6.simMouse.chr6 201363 1 + 636262 A -s Anc0.Anc0refChr5 22744 1 + 87904 A -s Anc1.Anc1refChr8 36605 1 + 57822 A -s Anc2.Anc2refChr15 16849 1 + 86568 A -s mr.mrrefChr5 56073 1 + 294540 A -s simCow_chr6.simCow.chr6 199997 1 + 602619 A -s simDog_chr6.simDog.chr6 481668 1 - 593897 A -s simHuman_chr6.simHuman.chr6 203584 1 + 601863 A -s simRat_chr6.simRat.chr6 191547 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 201364 2 + 636262 CA -s Anc0.Anc0refChr5 22745 2 + 87904 GA -s Anc1.Anc1refChr8 36606 2 + 57822 GA -s Anc2.Anc2refChr15 16850 2 + 86568 GA -s mr.mrrefChr5 56074 2 + 294540 CA -s simCow_chr6.simCow.chr6 199998 2 + 602619 AA -s simDog_chr6.simDog.chr6 481669 2 - 593897 GA -s simHuman_chr6.simHuman.chr6 203596 2 + 601863 GA -s simRat_chr6.simRat.chr6 191548 2 + 647215 CA - -a -s simMouse_chr6.simMouse.chr6 201366 84 + 636262 CGGCAGCCTAGTTTGACTTTAAATAAAATAAGAAGTATCATTATATACCACTCTGGAGTGCATCCAAAGCATTTAATTTTAGTA -s Anc0.Anc0refChr5 22747 39 + 87904 GGGCAGCCCGGTGTTTCTATAAAT---------------------------------------------TGTGTCATTTTAGTA -s Anc1.Anc1refChr8 36608 39 + 57822 GGGCAGCCCGGTGTTTCTATAAAT---------------------------------------------TGTGTCATTTTAGTA -s Anc2.Anc2refChr15 16852 39 + 86568 GGGTAGCCCGGTGTTTCTATAAAT---------------------------------------------TGTGTCATTTTAGTG -s mr.mrrefChr5 56076 39 + 294540 CGGCAGCCTAGTTTGACTATAAAT---------------------------------------------CATTTAATTTTAGTA -s simCow_chr6.simCow.chr6 200012 39 + 602619 GGGTATCCCGGTGTTTGCATAAAT---------------------------------------------TGTGTCATTTTAGTG -s simDog_chr6.simDog.chr6 481671 37 - 593897 GGGTAGGCTGGT--TTCTATAAAT---------------------------------------------CGTGTCATTTTAGTG -s simHuman_chr6.simHuman.chr6 203598 39 + 601863 GGGCCGCCCGATATTTCTATAAAT---------------------------------------------TGTGTGATTTTAGTA -s simRat_chr6.simRat.chr6 191550 37 + 647215 TGGC--CCTAGTTTGACTATAAAT---------------------------------------------CATTTAATTTTGGTA - -a -s simMouse_chr6.simMouse.chr6 201450 2 + 636262 CA -s Anc0.Anc0refChr5 22786 2 + 87904 CA -s Anc1.Anc1refChr8 36647 2 + 57822 CA -s Anc2.Anc2refChr15 16891 2 + 86568 CA -s mr.mrrefChr5 56115 2 + 294540 CA -s simCow_chr6.simCow.chr6 200051 2 + 602619 CA -s simDog_chr6.simDog.chr6 481708 2 - 593897 CA -s simHuman_chr6.simHuman.chr6 203637 2 + 601863 CA -s simRat_chr6.simRat.chr6 191588 2 + 647215 CA - -a -s simMouse_chr6.simMouse.chr6 201452 4 + 636262 AGAA -s Anc0.Anc0refChr5 22788 4 + 87904 CGAT -s Anc1.Anc1refChr8 36649 4 + 57822 CGAT -s Anc2.Anc2refChr15 16893 4 + 86568 CGAT -s mr.mrrefChr5 56117 4 + 294540 AGAA -s simCow_chr6.simCow.chr6 200053 4 + 602619 AGAT -s simDog_chr6.simDog.chr6 481732 4 - 593897 CGAT -s simHuman_chr6.simHuman.chr6 203639 4 + 601863 CGAG -s simRat_chr6.simRat.chr6 191590 4 + 647215 AGAA - -a -s simMouse_chr6.simMouse.chr6 201456 4 + 636262 GTAT -s Anc0.Anc0refChr5 22793 4 + 87904 GTAT -s Anc1.Anc1refChr8 36654 4 + 57822 GTAT -s Anc2.Anc2refChr15 16898 4 + 86568 GTAT -s mr.mrrefChr5 56122 4 + 294540 GTAT -s simCow_chr6.simCow.chr6 200058 4 + 602619 GTAT -s simDog_chr6.simDog.chr6 481737 4 - 593897 CTAT -s simHuman_chr6.simHuman.chr6 203644 4 + 601863 GCAT -s simRat_chr6.simRat.chr6 191595 4 + 647215 GTAT - -a -s simMouse_chr6.simMouse.chr6 201460 38 + 636262 GTGTTTTTAGTGTACATCTTATAGGTAGTGTACAATTA -s Anc0.Anc0refChr5 22797 38 + 87904 GTGTTGTTAGTGTATGTGTTACGGGAAGTGTACAATTA -s Anc1.Anc1refChr8 36658 38 + 57822 GTGTTGTTAGTGTATGTGTTACGGGAAGTGTACAATTA -s Anc2.Anc2refChr15 16902 38 + 86568 GTGTTGTTAGTGTATGTGCTACGGGAAGTGTACAATTA -s mr.mrrefChr5 56126 38 + 294540 GTGTTGTTAGTGTACATCTTATGGGTAGTGTACAATTA -s simCow_chr6.simCow.chr6 200063 38 + 602619 GTGCTGTTAGCGTATGTGCTGCAGAAAGTGTACAATTA -s simDog_chr6.simDog.chr6 481741 33 - 593897 GTGTTGTTAGTGTATGAGCTATGGGAAGTGTAC----- -s simHuman_chr6.simHuman.chr6 203648 38 + 601863 GTATTGCTAGTGTATGTGTTACGGGAAGCATACGACTA -s simRat_chr6.simRat.chr6 191599 38 + 647215 GTGTTGTCAGTGTGCATTTTATGGGGAGGGTACAAGTA - -a -s simMouse_chr6.simMouse.chr6 201498 66 + 636262 TGCAACTACATAGCCCCAGCTATGAAAAGGACATGTAATTTGAAGAGTCTGTGTTTCCGATCATTA -s Anc0.Anc0refChr5 22842 65 + 87904 GGACATCACAAAGGCCTGGCCATGAAAGGGATAGATATGTTGGAAAGTCTGCATT-CCTACCTCTT -s Anc1.Anc1refChr8 36703 65 + 57822 GGACATCACAAAGGCCTGGCCATGAAAGGGATAGATATGTTGGAAAGTCTGCATT-CCTACCTCTT -s Anc2.Anc2refChr15 16947 65 + 86568 GTACATCACAAAGGCCTGGCCATGAAAGGGATAGATATGTTTGAAAGTCTGCATT-CCTACCTCTT -s mr.mrrefChr5 56164 65 + 294540 GGCAACTACATAGGCCCAGCTATGAAAAGGACAGGTAATTTGAAGAGTCTGTGTT-CCGACCATTT -s simCow_chr6.simCow.chr6 200133 65 + 602619 GCACATCACAAAGGCCTGGCCATGAAAGGGATGGATACGTTTGGGAGTCCGCATT-CCTCCCTCTT -s simDog_chr6.simDog.chr6 481778 65 - 593897 GTACATCACAAAGGTCTGGCCATGAAAGGGACAGATATATCTGAAAGTCTGTGTT-TCTAGCTCTT -s simHuman_chr6.simHuman.chr6 203693 65 + 601863 GGACATCACAAAGGCCTGGGCATGAAAGGGATAGATATGTTGGAACGCCTGCATT-CCTACCTCTT -s simRat_chr6.simRat.chr6 191637 65 + 647215 GGCAAATACATAGGCCCAGCTATGAAACGGTCAGGTCATTTGAAGAGTCTGTGTT-CCGACCGTTT - -a -s simMouse_chr6.simMouse.chr6 201564 26 + 636262 CATCCACATGAAACTCATGAGGATCA -s Anc0.Anc0refChr5 22907 26 + 87904 TATCCACACCAAATTCACAAGGATCA -s Anc1.Anc1refChr8 36768 26 + 57822 TATCCACACCAAATTCACAAGGATCA -s Anc2.Anc2refChr15 17012 26 + 86568 TGTACACACCAAATGCACAAGGATCA -s mr.mrrefChr5 56229 26 + 294540 CATCCACATGAAACTCACAAGGATCA -s simCow_chr6.simCow.chr6 200199 26 + 602619 TGTACACACCAAATGTACAGTGATCC -s simDog_chr6.simDog.chr6 481843 26 - 593897 AGTACACACCAAATGCACAAGGGACA -s simHuman_chr6.simHuman.chr6 203758 26 + 601863 TATCCACACCAAATTCACAAGGATCA -s simRat_chr6.simRat.chr6 191702 26 + 647215 CATCCACATGAAACTCACAAGGATCA - -a -s simMouse_chr6.simMouse.chr6 201590 18 + 636262 GACACAGTGTTACTGCAG -s Anc0.Anc0refChr5 22934 18 + 87904 AACTCAGTGCTACTGCAG -s Anc1.Anc1refChr8 36795 18 + 57822 AACTCAGTGCTACTGCAG -s Anc2.Anc2refChr15 17039 18 + 86568 AACTCAGTGCTATTGCAG -s mr.mrrefChr5 56256 18 + 294540 AACACAGTGTTACTGCAG -s simCow_chr6.simCow.chr6 200226 18 + 602619 AACTCAGTGCTATTGCAG -s simDog_chr6.simDog.chr6 481870 18 - 593897 AGCTCAGTGTTATTGCTG -s simHuman_chr6.simHuman.chr6 203785 18 + 601863 AACTCAGTGCTACTACAG -s simRat_chr6.simRat.chr6 191729 18 + 647215 AACACAGTATTAATGCAG - -a -s simMouse_chr6.simMouse.chr6 201608 6 + 636262 ATTGGG -s Anc0.Anc0refChr5 22952 2 + 87904 GT---- -s Anc1.Anc1refChr8 36813 2 + 57822 GT---- -s Anc2.Anc2refChr15 17057 2 + 86568 GT---- -s mr.mrrefChr5 56274 6 + 294540 ATTGGG -s simCow_chr6.simCow.chr6 200246 2 + 602619 GA---- -s simDog_chr6.simDog.chr6 481888 2 - 593897 AT---- -s simHuman_chr6.simHuman.chr6 203803 2 + 601863 GT---- -s simRat_chr6.simRat.chr6 191747 6 + 647215 ATTGGG - -a -s simMouse_chr6.simMouse.chr6 201614 78 + 636262 GCCTGGTGCTATGGCAGAGGGGGGTTCTAAGATCTCTGGACTTGTACGGAAGAGTTTGGATATTATGTGCATTTTCAA -s Anc0.Anc0refChr5 22954 76 + 87904 GCTCAGTACTATGCCAGAGTGG--TTGTGAGATCTCTGTGTTTGCACGAAAGAATTTAGATTTTATGTGCATTTTCAA -s Anc1.Anc1refChr8 36815 76 + 57822 GCTCAGTACTATGCCAGAGTGG--TTGTGAGATCTCTGTGTTTGCACGAAAGAATTTAGATTTTATGTGCATTTTCAA -s Anc2.Anc2refChr15 17059 76 + 86568 GCTCAGTACTATGCCAGAGTGG--TTGTGAGATCTCTGTGTTTACATGAAATAATTTAGATTCTATGGGCATTTGCAA -s mr.mrrefChr5 56280 76 + 294540 GCCTGGTGCTATGGCAGAGGGG--TTCTGAGATCTCTGGACTTGTACGGAAGAGTTTAGATATTATGTGCATTTTCAA -s simCow_chr6.simCow.chr6 200248 76 + 602619 GCTCAGTAGTATGGTAGAGTGG--TTGTGAGATCTCTGGGTTTACATGAAATAGTTTAGATTCCATGGGCATCAGCAA -s simDog_chr6.simDog.chr6 481906 73 - 593897 GCCCAGT-CTATGCCTGAGTGG--TTGTAAGATCTCTGTATTTATCTGAAATAAT--AGATTCTATGGGTATTTGAAA -s simHuman_chr6.simHuman.chr6 203805 76 + 601863 GCTCAGGACTATGACAGAGTTA--TTGTGTAATCTCTATGTTTGCACCAAAGAACTAAGATTTTGTGTACATTTTCAA -s simRat_chr6.simRat.chr6 191753 76 + 647215 GCCTGGTGCTATGGCAGAGGGG--TTCTGAGATCGCTGGACTTGTATGGAAGGGTTTAGATATTATGTGCATTTCCAA - -a -s simMouse_chr6.simMouse.chr6 201692 85 + 636262 GTTAACAACTCTCTGTGTTGAGCTAGCAATTTTCTTGGAGATAAAGGGAGCAGGTTTAGAAGGAACTGCCAGTTCTCAGACCATT -s Anc0.Anc0refChr5 23030 76 + 87904 GTTAAAAACTCTCTGTGTTGAGCTAGCAATTATCTTGGAGATAAAGGGAGCAGTTCTAGAAGAAACTGCCTGT-------C--CT -s Anc1.Anc1refChr8 36891 76 + 57822 GTTAAAAACTCTCTGTGTTGAGCTAGCAATTATCTTGGAGATAAAGGGAGCAGTTCTAGAAGAAACTGCCTGT-------C--CT -s Anc2.Anc2refChr15 17135 76 + 86568 GTTAAAAACTCTCTGTGTTGAGCTAGCAATTATCTTGGGGATAAAGGGAGCAGTTCTAGAAAGAACTGACTGT-------C--CT -s mr.mrrefChr5 56356 83 + 294540 GTTAACAACTCTCTGTGTTGAGCTAGCAATTATCTTGGAGATAAAGGGAGCAGGTTTAGAAGAAACTGCCAGTTCTCAGAC--TT -s simCow_chr6.simCow.chr6 200324 76 + 602619 GGTAAAAATATTTTGTGTTGAACTAACAATTAGCTTGGAAATAAAGGTAGCTGCTCTAGAAAGAATTGACTGT-------C--TT -s simDog_chr6.simDog.chr6 481979 76 - 593897 GTTAAAAACTCTCTGTGTTGAGATAGCAATTATCTGGGGGATAAAGGGGACAGTTGCACAAAGAACTGACTGT-------T--CT -s simHuman_chr6.simHuman.chr6 203882 74 + 601863 TTTAAGAACTCTCTGTGTAGAGCTAGCGATCATCTT--AGGTAAAAGGAGCAGTTCTAGAAGAAACTGCCCAT-------C--CT -s simRat_chr6.simRat.chr6 191829 81 + 647215 GTTAGCAACTC-CTGTGTT-CGCTAGCTATTATCTTGGAGAGAAAGGGAGCAGGTTTAGAAGAAACTGTCAGCTCTCAGCC--TG - -a -s simMouse_chr6.simMouse.chr6 201777 21 + 636262 GAAGAACAAGCTGGTGGGGTT -s Anc0.Anc0refChr5 23106 21 + 87904 GAAGAGCAAGCAGGAGAAGCT -s Anc1.Anc1refChr8 36967 21 + 57822 GAAGAGCAAGCAGGAGAAGCT -s Anc2.Anc2refChr15 17213 21 + 86568 GAAGACGAAGAAGGAGAAGCT -s mr.mrrefChr5 56439 21 + 294540 GAAGAGCAAGCAGGTGGGGCT -s simCow_chr6.simCow.chr6 200402 18 + 602619 GAGCATGAA---GGAGAAGCC -s simDog_chr6.simDog.chr6 482057 21 - 593897 GCAGACGAAGAAAGAGAAGCT -s simHuman_chr6.simHuman.chr6 203956 21 + 601863 GATGAGCATGCAGGAGAAGCT -s simRat_chr6.simRat.chr6 191910 21 + 647215 GAAGAGCAAGCAGGTGGGGCT - -a -s simMouse_chr6.simMouse.chr6 201798 14 + 636262 GTCTGTGGCCTTTG -s Anc0.Anc0refChr5 23165 10 + 87904 GTTTG----CAGTG -s Anc1.Anc1refChr8 37026 11 + 57822 GTTTGT---CAGTG -s Anc2.Anc2refChr15 17275 10 + 86568 GTTTG----CAGTG -s mr.mrrefChr5 56460 14 + 294540 GTCTGTGGCCTTTG -s simCow_chr6.simCow.chr6 200465 9 + 602619 GCCTA-----AGTG -s simDog_chr6.simDog.chr6 482119 10 - 593897 GTTTG----CAGCG -s simHuman_chr6.simHuman.chr6 204015 11 + 601863 GTTTGT---CGGTG -s simRat_chr6.simRat.chr6 191931 14 + 647215 GTCTGTGGCCTTTT - -a -s simMouse_chr6.simMouse.chr6 201812 25 + 636262 GCTTTTATAGCTTGCCTTACAGCTC -s Anc0.Anc0refChr5 23175 25 + 87904 GCCTTTATAGCTCTCTTTATAGCCC -s Anc1.Anc1refChr8 37037 25 + 57822 GCCTTTATAGCTCTCTTTATAGCCC -s Anc2.Anc2refChr15 17285 25 + 86568 GCCTTTATAGCTCTCTTGATAGCCC -s mr.mrrefChr5 56474 25 + 294540 GCCTTTATAGCTTGCCTTACAGCTC -s simCow_chr6.simCow.chr6 200481 25 + 602619 GCCCTTATAGCCCTCATAATAGCCC -s simDog_chr6.simDog.chr6 482129 25 - 593897 GCCTTTATAGCTCTCTTGATAGCTC -s simHuman_chr6.simHuman.chr6 204026 25 + 601863 ACCTTTATAGCTAACTTTATAGCCC -s simRat_chr6.simRat.chr6 191945 25 + 647215 GCCTTTATAGCTTGCCTTAAAGCTC - -a -s simMouse_chr6.simMouse.chr6 201837 102 + 636262 AGTGCTAAACACTAGTCAAGATGGAATAAGGGCATGAATACAATGGTATCAGCCAAGCAAACTGGGCAAGAGCTGGACAGGGTTGCTGTATCCACCAAGGGC -s Anc0.Anc0refChr5 23202 80 + 87904 AGTGCTAAACACTAGTGAAGATGAAATTAGAGCATGGATGCAA----------------------GAAAGAGTTGGACAGGCTTGCTGTATCTATCAAAAAA -s Anc1.Anc1refChr8 37064 101 + 57822 AGTGCTAAACACTAGTGAAGATGAAATTAGAGCATGGATGCAACACTGCCAGTCAAACAGCCT-AGAAAGAGTTGGACAGGCTTGCTGTATCTATCAAAAAA -s Anc2.Anc2refChr15 17312 80 + 86568 ATTCTTAAACACTAGTGGAGATGAAATTAGAGCATAGATGCAA----------------------GAAAGAGTTGCACAGGCTTGCTGTATCTATCAAAAAA -s mr.mrrefChr5 56499 102 + 294540 AGTGCTAAACACTAGTCAAGATGAAATAAGGGCATGAATACAATGGTACCAGTCAAGCAAACTGGGAAAGAGCTGGACAGGGTTGCTGTATCTACCAAGGGC -s simCow_chr6.simCow.chr6 200508 80 + 602619 ATTATCAAATATTAGTGGAGACGAAATGAGGGCATAGATGTAG----------------------GAAAGAGTTGCACAGGCTTGCTGTATCTATCAAAAAA -s simDog_chr6.simDog.chr6 482156 75 - 593897 A-TCTTAAACACTAGCGGAGATGAAAGTAGAGCATAGATGCAA----------------------GAAAGAGCTGCACAGGCTTGCTGTATTTATCAA---- -s simHuman_chr6.simHuman.chr6 204053 101 + 601863 AGTGCTATCCACTAGTGAAGATGAAATCACATCATGGAGGCAACACTGCCAGTCAAACAGCCT-AGAAAGGGTTGGATATGCTTGCTATATCTATCAAAAAA -s simRat_chr6.simRat.chr6 191970 102 + 647215 AGTGTTAAACACTAGACAAGATGAAACAAGGGCATGAATAGAATGGTTCCAGTTAAGCATACTGGTAAAGAGCTGGACAGGATTGCTGTATCTACCAAGGGC - -a -s simMouse_chr6.simMouse.chr6 201939 39 + 636262 AAGAGCTTCACTAAATAGGACACTAGTAATGAAGCAGAT -s Anc0.Anc0refChr5 23283 34 + 87904 AAAAGCTTTATTAGTTAA----CTACTAATGGGGGAGG- -s Anc1.Anc1refChr8 37166 38 + 57822 AAAAGCTTTATTAGTTAAGACACTACTAATGGGGGAGG- -s Anc2.Anc2refChr15 17393 34 + 86568 AAAAGCTTTATTGGTTAA----CTGCTAATGGGGGAGG- -s mr.mrrefChr5 56601 39 + 294540 AAGAGCTTTACTAAATAGGACACTACTAATGAGGCAGAT -s simCow_chr6.simCow.chr6 200589 34 + 602619 AAAAACTTTATTGGTTAA----CTGCTTATGGGGGAGG- -s simDog_chr6.simDog.chr6 482232 34 - 593897 AAAAGCTTTATTGACTAA----CTGTGAATGAGGGACC- -s simHuman_chr6.simHuman.chr6 204155 38 + 601863 AAAAGCTTTATTAGTTAAGACACCACTAATGGGGGAGG- -s simRat_chr6.simRat.chr6 192072 39 + 647215 AAGAGCTTTACTCAATAGGACATTACTAATGAGGCAAAT - -a -s simMouse_chr6.simMouse.chr6 201978 2 + 636262 AC -s Anc0.Anc0refChr5 23317 2 + 87904 CT -s Anc1.Anc1refChr8 37204 2 + 57822 CT -s Anc2.Anc2refChr15 17427 2 + 86568 CT -s mr.mrrefChr5 56640 2 + 294540 CC -s simCow_chr6.simCow.chr6 200625 2 + 602619 CT -s simDog_chr6.simDog.chr6 482266 2 - 593897 CT -s simHuman_chr6.simHuman.chr6 204193 2 + 601863 CT -s simRat_chr6.simRat.chr6 192111 2 + 647215 CC - -a -s simMouse_chr6.simMouse.chr6 201980 26 + 636262 AAACCAACCCATTCAAGACTTGTTTG -s Anc0.Anc0refChr5 23319 26 + 87904 GAACCAACACATTTATGACATGTTTG -s Anc1.Anc1refChr8 37206 26 + 57822 GAACCAACACATTTATGACATGTTTG -s Anc2.Anc2refChr15 17431 26 + 86568 GAACCAACACATTTATGGCATGTTTG -s mr.mrrefChr5 56642 26 + 294540 AAACCAACCCATTCATGACTTGTTTG -s simCow_chr6.simCow.chr6 200629 26 + 602619 TAACTGACATATTTATGGCATGTTTG -s simDog_chr6.simDog.chr6 482270 23 - 593897 GAACCAACACATTTGCT---TGTTTG -s simHuman_chr6.simHuman.chr6 204195 26 + 601863 GATCCAACACATTTATGAGGTGTCTG -s simRat_chr6.simRat.chr6 192113 26 + 647215 AAACCAACCCATTCATGACTTGTTTG - -a -s simMouse_chr6.simMouse.chr6 202006 66 + 636262 GTATTGCCCTATGAGTAGGTCATGGAGGGCTCAGCCATAGGCCACGGCAGGCTCAGCAAACACCCG -s Anc0.Anc0refChr5 23345 47 + 87904 GTCTTATCCTATGAACAGGCCATGGAAAGCTCAGTTAGCACCTACTG------------------- -s Anc1.Anc1refChr8 37232 47 + 57822 GTCTTATCCTATGAACAGGCCATGGAAAGCTCAGTTAGCACCTACTG------------------- -s Anc2.Anc2refChr15 17457 47 + 86568 GTCTTATCCCATTAACAGGCCATGGAAATCTCAGTTAGCACCTACTG------------------- -s mr.mrrefChr5 56668 66 + 294540 GTATTACCCTATGAGTAGGTCATGGAGGGCTCAGTCATAGGCCACGGCAGGCTCAGCAAACACCCG -s simCow_chr6.simCow.chr6 200655 47 + 602619 GTCTTATCCAATTGACAGGCCATGGAATTCTCAGTTGGCACTTACTG------------------- -s simDog_chr6.simDog.chr6 482293 45 - 593897 GTCTTATCCCACTAACAGGCCATGTAAA--CCCATTAGCACCTGCTG------------------- -s simHuman_chr6.simHuman.chr6 204222 47 + 601863 ATCTTATACTATGAACAGCCCATGGAAAGCTCAGTGAGGACCTACTG------------------- -s simRat_chr6.simRat.chr6 192139 65 + 647215 GTATTACCCTGTGAGTAGGTCATG-AGGGCTCAGTCAAAGGCCATGGCAGGCTCAGTGAACACCCA - -a -s simMouse_chr6.simMouse.chr6 202072 17 + 636262 AAGTTCATATGACAGCG -s Anc0.Anc0refChr5 23392 1 + 87904 ----------------G -s Anc1.Anc1refChr8 37279 1 + 57822 ----------------G -s Anc2.Anc2refChr15 17504 1 + 86568 ----------------G -s mr.mrrefChr5 56734 17 + 294540 AAGTTCATATGACAGCG -s simCow_chr6.simCow.chr6 200702 1 + 602619 ----------------G -s simDog_chr6.simDog.chr6 482338 1 - 593897 ----------------G -s simHuman_chr6.simHuman.chr6 204269 1 + 601863 ----------------G -s simRat_chr6.simRat.chr6 192205 17 + 647215 AAGTTCACATGACAGAG - -a -s simMouse_chr6.simMouse.chr6 202089 117 + 636262 ATGTATTGTTATTGAATAGTATCATTAGGGTGATAAAAGTTCACCAAACATCTGTATGTTTATGGACTAAAGTCCAATGGTAAACTGTATAAATTCACTGCTATCACCATTCAAACA -s Anc0.Anc0refChr5 23393 117 + 87904 ATGCATTGTTAATCAACAGTATCATTAGTGTCAGAAGAATTCACAATACCCCTATATTTCTATGGACTATGGTCCAATGGAGAACTAGATAAGTTCACTGCTATCACTGTGCAAATA -s Anc1.Anc1refChr8 37280 117 + 57822 ATGCATTGTTAATCAACAGTATCATTAGTGTCAGAAGAATTCACAATACCCCTATATTTCTATGGACTATGGTCCAATGGAGAACTAGATAAGTTCACTGCTATCACTGTGCAAATA -s Anc2.Anc2refChr15 17519 117 + 86568 ATTCATTATTAATCAACAGTATGATTGGTGTCAGACGAATTCACAATACCCCTATATTTCTATGGAATATGACCCATTGGAGAACAAGATAAGTTCACTGCTATCACTGTGCAAATA -s mr.mrrefChr5 56751 117 + 294540 ATGTATTGTTAATGAATAGTATCATTAGGGTGATAAGAGTTCACCAAACATCTGTATTTTTATGGACTAAAGTCCAATGGTAAACTGTATAAGTTCACTGCTATCACTGTGCAAACA -s simCow_chr6.simCow.chr6 200717 106 + 602619 ATTCATACTTAATCGACAATATGATTGGTGTTAGAGGAATTCACAATACCCCTATGTTTCTATGGA-----------TGGAGAGCAAGATAAGTTCACTCCAATCACTGTGCAAATA -s simDog_chr6.simDog.chr6 482353 115 - 593897 ATTCATTATTAGTCAACAGTATGATTGGTCTCGGACAAATTCACAAT-CCCCCATATTTCTATGTAATATGACCCATTAG-GAACAAGATAAATTCACGGCTATCACTGTGTAAACA -s simHuman_chr6.simHuman.chr6 204270 117 + 601863 ATGCATTGCTAACCAACTGTATCCTTAGCGTCACAAGAATTCACAATACCCCTATTTTTCTATGGACTATGGTCCAATGGAGAACTAGGTAAGTTCAATGCTATCTCTGTGCAGATG -s simRat_chr6.simRat.chr6 192222 115 + 647215 ATATATTGTTAATTAATAATATCATCAGGGTGAAAGGAGTTCACCAAACATCTGTATTTTTAT--ACTAATGTCTAATGGTAACCCGTACATGTTCGCTGCTATCACTGAGCAAACA - -a -s simMouse_chr6.simMouse.chr6 202206 11 + 636262 AAGCTTTTCCA -s Anc0.Anc0refChr5 23510 11 + 87904 AAGTTGATATA -s Anc1.Anc1refChr8 37397 11 + 57822 AAGTTGATATA -s Anc2.Anc2refChr15 17644 11 + 86568 AAATTGATATA -s mr.mrrefChr5 56868 11 + 294540 AAGCTTATCTA -s simCow_chr6.simCow.chr6 200831 5 + 602619 AA-----TAT- -s simDog_chr6.simDog.chr6 482476 11 - 593897 AAATTGACTTA -s simHuman_chr6.simHuman.chr6 204387 11 + 601863 AAGTTGATATA -s simRat_chr6.simRat.chr6 192337 11 + 647215 AAGCTTACTTA - -a -s simMouse_chr6.simMouse.chr6 202217 51 + 636262 ACATTAAATTTGCCTTGTGATTTGTACAGCTTTGTCTCATAGGGCCACCAG -s Anc0.Anc0refChr5 23521 51 + 87904 ACATTAAATTTTCCTTACACTTTGTACCGCTTTCTCTCTTAGGGCCACCAG -s Anc1.Anc1refChr8 37408 51 + 57822 ACATTAAATTTTCCTTACACTTTGTACCGCTTTCTCTCTTAGGGCCACCAG -s Anc2.Anc2refChr15 17655 51 + 86568 ACGTTAAATCTTCCTCACACATTGTACCCCTTTCTCTCTTGGGGCCACCAG -s mr.mrrefChr5 56879 51 + 294540 ACATTAAATTTGCCTTGTAATTTGTACAGCTTTGTCTCATAGGGCCACCAG -s simCow_chr6.simCow.chr6 200836 41 + 602619 ----------CTCCTCACACATTATGCCCCTCGCTTACTTGGGGCCACCAG -s simDog_chr6.simDog.chr6 482487 51 - 593897 ACGTTAAATCTTCCTCACAGAGTGCATCCCTTTCTCTCTTGGGGTCACCAG -s simHuman_chr6.simHuman.chr6 204569 51 + 601863 acATTTAATTTTCCTTACACTTTGTACTGCTTTCTCCCTTAGGGCCACCAG -s simRat_chr6.simRat.chr6 192348 51 + 647215 ACATTAAATCTGCCTTGTAATTTCTGCAGCTTTGTCTTATAGGGTCACCAG - -a -s simMouse_chr6.simMouse.chr6 202268 43 + 636262 GTCTGTCATCAAATCTGCAGATTCCTCAGTTTTTTAGCTTCAG -s Anc0.Anc0refChr5 23572 43 + 87904 GTCTTTTGTCAAATTTGCAGATTCCACAGTTTTTTTGCTATAT -s Anc1.Anc1refChr8 37459 43 + 57822 GTCTTTTGTCAAATTTGCAGATTCCACAGTTTTTTTGCTATAT -s Anc2.Anc2refChr15 17706 43 + 86568 GTCTTTTGTCAAATTTGCAGATTCCACAGTTTTTTTGTTATAT -s mr.mrrefChr5 56930 43 + 294540 GTCTTTCATCAAATCTGCAGATTCCTCAGTTTTTTAGCTTCAT -s simCow_chr6.simCow.chr6 200878 43 + 602619 GTCTTACGGCAAGTTTGCAGGTTCCACATCTTTTTTGTTGCAT -s simDog_chr6.simDog.chr6 482538 42 - 593897 GTCTTTTGTCAAATTTGCAGATTACACAGTCATTTTGTAATA- -s simHuman_chr6.simHuman.chr6 204620 42 + 601863 GTTGTTTGTCAAACTTGCAGATTCC-CAGTTTGTTTGCTAGAT -s simRat_chr6.simRat.chr6 192399 43 + 647215 GTCCTTCATCAAATCTGTAGGTTCCTCAGTTTTTTAACTCCGT - -a -s simMouse_chr6.simMouse.chr6 202311 18 + 636262 GAAACATACTAGACTTTG -s Anc0.Anc0refChr5 23616 14 + 87904 AAAACATATTA----CTG -s Anc1.Anc1refChr8 37503 14 + 57822 AAAACATATTA----CTG -s Anc2.Anc2refChr15 17750 14 + 86568 AAAACATATTA----CTG -s mr.mrrefChr5 56973 17 + 294540 GAAACATACTA-ACTTTG -s simCow_chr6.simCow.chr6 200922 14 + 602619 AAACCATACCA----CTG -s simDog_chr6.simDog.chr6 482580 13 - 593897 -AAACATATTA----CTG -s simHuman_chr6.simHuman.chr6 204663 14 + 601863 AAAACATGTTA----CTG -s simRat_chr6.simRat.chr6 192442 17 + 647215 GAATCGTACTA-ACTTTG - -a -s simMouse_chr6.simMouse.chr6 202329 7 + 636262 TCAGTGA -s Anc0.Anc0refChr5 23630 7 + 87904 TCATTGT -s Anc1.Anc1refChr8 37517 7 + 57822 TCATTGT -s Anc2.Anc2refChr15 17768 7 + 86568 TTATTGT -s mr.mrrefChr5 56990 7 + 294540 TCATTGA -s simCow_chr6.simCow.chr6 200940 7 + 602619 TTACTGT -s simDog_chr6.simDog.chr6 482597 7 - 593897 TTATTGT -s simHuman_chr6.simHuman.chr6 204677 6 + 601863 -CATTGT -s simRat_chr6.simRat.chr6 192459 7 + 647215 TGATTGA - -a -s simMouse_chr6.simMouse.chr6 202336 18 + 636262 CAAGAGGAACTCGCCTGA -s Anc0.Anc0refChr5 23637 18 + 87904 GAGAAGGAAAGTGCCTGA -s Anc1.Anc1refChr8 37524 18 + 57822 GAGAAGGAAAGTGCCTGA -s Anc2.Anc2refChr15 17787 18 + 86568 GAGAAGGAAAGTGCCTGC -s mr.mrrefChr5 56997 18 + 294540 CAAGAGGAACTTGCCTGA -s simCow_chr6.simCow.chr6 200959 16 + 602619 GAGAAGGAAAG--CCTAT -s simDog_chr6.simDog.chr6 482616 18 - 593897 GAGAATCAAAGTGTCTGC -s simHuman_chr6.simHuman.chr6 204683 18 + 601863 GAGAAGGAAAGTGCCTGA -s simRat_chr6.simRat.chr6 192466 18 + 647215 TAAGATGAACTTGCCTGA - -a -s simMouse_chr6.simMouse.chr6 202354 5 + 636262 AGAAT -s Anc0.Anc0refChr5 23658 5 + 87904 AGAAT -s Anc1.Anc1refChr8 37545 5 + 57822 AGAAT -s Anc2.Anc2refChr15 17808 5 + 86568 AGAAT -s mr.mrrefChr5 57015 5 + 294540 AGAAT -s simCow_chr6.simCow.chr6 200978 5 + 602619 CGAAT -s simDog_chr6.simDog.chr6 482637 5 - 593897 AGAAG -s simHuman_chr6.simHuman.chr6 204704 5 + 601863 AGAAT -s simRat_chr6.simRat.chr6 192484 5 + 647215 AGAAT - -a -s simMouse_chr6.simMouse.chr6 202359 26 + 636262 TGCACTTATAACTGTAATTGGCATGT -s Anc0.Anc0refChr5 23666 24 + 87904 TGCGCCTGTAAC--TAGTTGGCATGT -s Anc1.Anc1refChr8 37553 24 + 57822 TGCGCCTGTAAC--TAGTTGGCATGT -s Anc2.Anc2refChr15 17816 24 + 86568 TGGGCCTGTAAC--TAGTTGGCATGT -s mr.mrrefChr5 57020 26 + 294540 TGCACTTATAACTATAATTGGCATGT -s simCow_chr6.simCow.chr6 200986 22 + 602619 --GGCCTGTAAC--TTCTTGACATGT -s simDog_chr6.simDog.chr6 482657 24 - 593897 TGGGCCTGTAAC--TAGTAGGCATGC -s simHuman_chr6.simHuman.chr6 204712 24 + 601863 TGCTCCTGTAAC--TAGTTGGCATGT -s simRat_chr6.simRat.chr6 192489 26 + 647215 TGCAGTTATTATTATAATTGGCATGT - -a -s simMouse_chr6.simMouse.chr6 202385 1 + 636262 C -s Anc0.Anc0refChr5 23693 1 + 87904 C -s Anc1.Anc1refChr8 37580 1 + 57822 C -s Anc2.Anc2refChr15 17843 1 + 86568 C -s mr.mrrefChr5 57046 1 + 294540 C -s simCow_chr6.simCow.chr6 201011 1 + 602619 C -s simDog_chr6.simDog.chr6 482683 1 - 593897 C -s simHuman_chr6.simHuman.chr6 204739 1 + 601863 C -s simRat_chr6.simRat.chr6 192515 1 + 647215 C - -a -s simMouse_chr6.simMouse.chr6 202386 5 + 636262 TCAAG -s Anc0.Anc0refChr5 23695 5 + 87904 CCAAG -s Anc1.Anc1refChr8 37582 5 + 57822 CCAAG -s Anc2.Anc2refChr15 17845 5 + 86568 TCAAG -s mr.mrrefChr5 57048 5 + 294540 CCAAG -s simCow_chr6.simCow.chr6 201013 5 + 602619 TCAAG -s simDog_chr6.simDog.chr6 482685 5 - 593897 TCATG -s simHuman_chr6.simHuman.chr6 204741 5 + 601863 CCAAT -s simRat_chr6.simRat.chr6 192517 5 + 647215 CCCTG - -a -s simMouse_chr6.simMouse.chr6 202391 66 + 636262 ATTAAATTTTCTGAAAATTTAGTAGTTGGGGTACGACATAAATAGACATGGACCACTGGCTTAACT -s Anc0.Anc0refChr5 23716 66 + 87904 ATTGAATTATGTGAAAATTCAATAGTCATGGTGCTACATAAATAATGGGGGACCATTGGCTTAACT -s Anc1.Anc1refChr8 37603 66 + 57822 ATTGAATTATGTGAAAATTCAATAGTCATGGTGCTACATAAATAATGGGGGACCATTGGCTTAACT -s Anc2.Anc2refChr15 17866 66 + 86568 ATTGAATTATGCGAAAATTCTATAGTCATGGTGCTGCATAAATAGTGGGGGACCATTGGCTTAACT -s mr.mrrefChr5 57053 66 + 294540 ATTAAATTTTCTGAAAATTCAGTAGTTGGGGTGCGACATAAATAAACATGGACCACTGGCTTAACT -s simCow_chr6.simCow.chr6 201034 66 + 602619 ATTGAATAATGAGAAAATTCTGTAGCCACAGGACTGCATAAATAGTGAGGGACCATTGGCTTAACT -s simDog_chr6.simDog.chr6 482705 66 - 593897 ATTGAATTATGCGGAAATTCTATAATCATGGTGCTGCACAAATAGTGGTGGACCATTGGCTTAACT -s simHuman_chr6.simHuman.chr6 204762 66 + 601863 AGTGAGTTATGTAAAAATCCAATAGTCTTGGTGCTATATAAATAACGGGGAACCATTGTCATAACT -s simRat_chr6.simRat.chr6 192522 64 + 647215 ATTAAATTTTCTGAAAGTACTGTAGTTGGGGTGCAACATAACTAATCATGGACCACT--CTTAACT - -a -s simMouse_chr6.simMouse.chr6 202457 8 + 636262 AAGATTTG -s Anc0.Anc0refChr5 23782 6 + 87904 AAGATC-- -s Anc1.Anc1refChr8 37669 8 + 57822 AAGATCTG -s Anc2.Anc2refChr15 17932 6 + 86568 AAGATC-- -s mr.mrrefChr5 57119 8 + 294540 AAGATTTG -s simCow_chr6.simCow.chr6 201102 6 + 602619 AATATC-- -s simDog_chr6.simDog.chr6 482771 6 - 593897 CAGATC-- -s simHuman_chr6.simHuman.chr6 204828 8 + 601863 AAGATCTG -s simRat_chr6.simRat.chr6 192586 8 + 647215 AGGATTTG - -a -s simMouse_chr6.simMouse.chr6 202465 25 + 636262 CAAAGGGGTTTACTAGTGTGAAAAC -s Anc0.Anc0refChr5 23792 25 + 87904 CATAGGGGTCTACTAATGTGAAAAT -s Anc1.Anc1refChr8 37681 25 + 57822 CATAGGGGTCTACTAATGTGAAAAT -s Anc2.Anc2refChr15 17942 25 + 86568 CATAGGGGTCTACTAATGTCAAAAT -s mr.mrrefChr5 57127 25 + 294540 CAAAGGGGTCTACTAGTGTGAAAAC -s simCow_chr6.simCow.chr6 201112 25 + 602619 CATAGGGAATTACTAATGTCAAAGT -s simDog_chr6.simDog.chr6 482781 25 - 593897 CATAGGGGTCTACTAATGCCAAAAT -s simHuman_chr6.simHuman.chr6 204840 25 + 601863 CATAAGGGCCTACAAATGTGAATAT -s simRat_chr6.simRat.chr6 192594 25 + 647215 CAAAGGGGTCTACTAGTGTGAAGAC - -a -s simMouse_chr6.simMouse.chr6 202490 41 + 636262 TTGTAGTGCTACATAAACAGTGAGTGGCTATAGGTTTACTT -s Anc0.Anc0refChr5 23824 32 + 87904 TCATAGTACTACATAAACAGTGGGGGACCATA--------- -s Anc1.Anc1refChr8 37713 41 + 57822 TCATAGTACTACATAAACAGTGGGGGACCATAGGGTTACAT -s Anc2.Anc2refChr15 17974 32 + 86568 TCATAGTACTACATATACAGTGGGGGACCATA--------- -s mr.mrrefChr5 57152 41 + 294540 TTATAGTGCTACATAAACAGTGAGTGGCTATAGGTTTACAT -s simCow_chr6.simCow.chr6 201142 28 + 602619 TCATAGTACTG----GACAGTAGGGGACCATA--------- -s simDog_chr6.simDog.chr6 482813 32 - 593897 CCATAGTAGAACATATACAATGTGGGACCATA--------- -s simHuman_chr6.simHuman.chr6 204872 41 + 601863 TCATAGCACTACATAAACAGTGGGGGACCATAGGGTTACAT -s simRat_chr6.simRat.chr6 192619 41 + 647215 TTATAATGCTACATAAACAGTGAGTGGTAATAGGTTTGCAT - -a -s simMouse_chr6.simMouse.chr6 202531 36 + 636262 AAGGTCTATTTACAGCGGGACCTACCTTCATGTTAC -s Anc0.Anc0refChr5 23856 36 + 87904 AAGGTCTACTTTCATAGGGATCTATTTGTATGTCAC -s Anc1.Anc1refChr8 37754 36 + 57822 AAGGTCTACTTTCATAGGGATCTATTTGTATGTCAC -s Anc2.Anc2refChr15 18006 36 + 86568 AAGATCTACTTTCATAGGGATCTATTTGTATGTCAC -s mr.mrrefChr5 57193 36 + 294540 AAGGTCTATTTACAGCGGGACCTACCTTCATGTTAC -s simCow_chr6.simCow.chr6 201171 36 + 602619 AAGATCTATTTTCATAGAGATGTACTTTTATGTTAC -s simDog_chr6.simDog.chr6 482845 35 - 593897 AAGATCTACTTTGGAAGGGG-CTATTTGTATGTCAC -s simHuman_chr6.simHuman.chr6 204913 36 + 601863 ATGGTCTACCTGCATAGGGAACTAATTGTATGTAAC -s simRat_chr6.simRat.chr6 192660 36 + 647215 AAGGTTTATTTATAGGGGGATCTACCTTCATGTTAC - -a -s simMouse_chr6.simMouse.chr6 202567 29 + 636262 ACATGCTGGACCATGAGATTGTTTTTCTT -s Anc0.Anc0refChr5 23914 29 + 87904 GCATGCTTGGTTACGAGATTCTCTCTCCT -s Anc1.Anc1refChr8 37812 29 + 57822 GCATGCTTGGTTACGAGATTCTCTCTCCT -s Anc2.Anc2refChr15 18065 29 + 86568 GCATGCTTGGTTACAAGATTCTCTCTCCT -s mr.mrrefChr5 57229 29 + 294540 ACATGCTTGACCATGAGATTGTTTTTCTT -s simCow_chr6.simCow.chr6 201230 29 + 602619 GGATGCTTGGTTACAAGATTCCCCCTCCT -s simDog_chr6.simDog.chr6 482904 29 - 593897 GCATGCTTGGCCTCAAAATTCTCTTTTGT -s simHuman_chr6.simHuman.chr6 204971 29 + 601863 GCATGCTTGGTTACGAGAGTCTCTCTCCT -s simRat_chr6.simRat.chr6 192696 29 + 647215 ACATGCTTGACCATGAGATTGTTTTTCTT - -a -s simMouse_chr6.simMouse.chr6 202596 3 + 636262 TAT -s Anc0.Anc0refChr5 23979 3 + 87904 TGT -s Anc1.Anc1refChr8 37877 3 + 57822 TGT -s Anc2.Anc2refChr15 18130 3 + 86568 TGT -s mr.mrrefChr5 57258 3 + 294540 TAT -s simCow_chr6.simCow.chr6 201287 3 + 602619 TGT -s simDog_chr6.simDog.chr6 482969 3 - 593897 TGT -s simHuman_chr6.simHuman.chr6 205036 3 + 601863 TGT -s simRat_chr6.simRat.chr6 192725 3 + 647215 TAT - -a -s simMouse_chr6.simMouse.chr6 202599 13 + 636262 GCAAGAGGAGATT -s Anc0.Anc0refChr5 23986 13 + 87904 TCAGGAGGATCTT -s Anc1.Anc1refChr8 37884 13 + 57822 TCAGGAGGATCTT -s Anc2.Anc2refChr15 18137 13 + 86568 TTAGGGCAATCTT -s mr.mrrefChr5 57265 13 + 294540 GCAAGAGGAGATT -s simCow_chr6.simCow.chr6 201293 2 + 602619 -----------TT -s simDog_chr6.simDog.chr6 482976 13 - 593897 TTAGGGCAATCTT -s simHuman_chr6.simHuman.chr6 205043 13 + 601863 ACACAAGGATTTT -s simRat_chr6.simRat.chr6 192732 13 + 647215 GCAAGGGGAAACT - -a -s simMouse_chr6.simMouse.chr6 202612 23 + 636262 CTAAAGAATTAGGGCTCTAGGAG -s Anc0.Anc0refChr5 24004 17 + 87904 CTG------TAGGACTTAAGAGG -s Anc1.Anc1refChr8 37902 23 + 57822 CTGAACATTTAGGACTTAAGAGG -s Anc2.Anc2refChr15 18155 17 + 86568 CTG------TAAGACTTAAGAGG -s mr.mrrefChr5 57283 23 + 294540 CTGAAGAATTAGGGCTCTAGAAG -s simCow_chr6.simCow.chr6 201300 17 + 602619 CTG------TATGACATATGAGG -s simDog_chr6.simDog.chr6 482994 17 - 593897 CTG------TAAGACTTGAGAGG -s simHuman_chr6.simHuman.chr6 205061 23 + 601863 CTGAACATTTAGGACTGAAGAGG -s simRat_chr6.simRat.chr6 192750 23 + 647215 CTGAAGAATTAGGGCTCTAGAAG - -a -s simMouse_chr6.simMouse.chr6 202635 24 + 636262 CAGGATAAACTCTCCCTCTATAGT -s Anc0.Anc0refChr5 24021 24 + 87904 CAGGCTTAATCCCCTCTCTCTAAT -s Anc1.Anc1refChr8 37925 24 + 57822 CAGGCTTAATCCCCTCTCTCTAAT -s Anc2.Anc2refChr15 18172 24 + 86568 CAGGCTTAATCCCCTCTCTCTAAT -s mr.mrrefChr5 57306 24 + 294540 CAGGCTAAACTCTCCCTCTATAGT -s simCow_chr6.simCow.chr6 201317 24 + 602619 CACACTTAATCCCCTCTCTCTAAT -s simDog_chr6.simDog.chr6 483011 24 - 593897 CAGGCTTAATCCCCTCTCACTAAT -s simHuman_chr6.simHuman.chr6 205087 24 + 601863 CAGGCTTAATCCCCTTTCTCTGAT -s simRat_chr6.simRat.chr6 192773 24 + 647215 CAGACTAAACTCTCCCTCTATAGT - -a -s simMouse_chr6.simMouse.chr6 202659 5 + 636262 CAAAT -s Anc0.Anc0refChr5 24045 5 + 87904 AGAGT -s Anc1.Anc1refChr8 37949 5 + 57822 AGAGT -s Anc2.Anc2refChr15 18196 5 + 86568 AGAGT -s mr.mrrefChr5 57330 5 + 294540 CAAGT -s simCow_chr6.simCow.chr6 201341 5 + 602619 AGAGG -s simCow_chr6.simCow.chr6 201550 5 + 602619 AGAGG -s simDog_chr6.simDog.chr6 483035 5 - 593897 ATAGT -s simHuman_chr6.simHuman.chr6 205111 5 + 601863 TGAGT -s simRat_chr6.simRat.chr6 192797 5 + 647215 CAAGT - -a -s simMouse_chr6.simMouse.chr6 202664 118 + 636262 AATTTGTGTATGCTGTCCTATCTTACATCATGGTGAAGAGTGGAGTTTCTTGAAAACTTAGGTGGTATTACCGAATTATAAAACTACAGAATTATAAACAAGATTAATAAATGAGATT -s Anc0.Anc0refChr5 24063 97 + 87904 AATTCATGTATTGTGTTCTATCTTATACCATGAGGAAGAGTAGGATTTCTACATAAGTTAGCTGAGAATATTAAATC---A-------GGTCTACAAAAGAGAATA-----------T -s Anc1.Anc1refChr8 37967 103 + 57822 AATTCATGTATTGTGTTCTATCTTATACCATGAGGAAGAGTAGGATTTCTACATAAGTTAGCTGAGAATATTAAATC---AAACT-CAGGTCTACAAAAGAGAATA-----------T -s Anc2.Anc2refChr15 18214 97 + 86568 AACTCATGTATTGTGTTCTATCTTATACCATGAAAAAGAGTAGGATTTCTACATAAGTTTGCTGAGAATATTAAATC---A-------GGTCTACAAAAGAGAATA-----------T -s mr.mrrefChr5 57335 118 + 294540 AATTTGTGTATGCTGTCCTATCTTACACCATGGGGAAGAGTGGAGTTTCTTGAAAAGTTAGGTGATATTACCAAATTATAAAACTACAGAATTATAAACAAGATTAATAAATGAGATT -s simCow_chr6.simCow.chr6 201363 97 + 602619 AACTCATGTATTGTGTTCTCTTTCATACCATGAGAAAGAGTAGGAATTCTACGCAAGTTTGTTGAGAAAACTAAATC---A-------TGTTTACAAAGAAGAATA-----------T -s simCow_chr6.simCow.chr6 201568 96 + 602619 AACTCTTGTATTGTGTTCTATCTTGTGCCATGAAAAAGAGTAGGA-ACCTACGGAGGTTTGCTGAGAAAACTAAATC---A-------TGTCTACAAAAGAGAATA-----------T -s simDog_chr6.simDog.chr6 483053 94 - 593897 AACTGATGTACGTTGTTTTA--TTATACCATAAAAAAGAGTATGATTTCTACATAAGGTTGCTGACAATGTTAAATC---G-------GGTCTGCAAAAGA-AATG-----------T -s simHuman_chr6.simHuman.chr6 205129 101 + 601863 AATTCATGTCT--TGCTCTATCTTGTACCACGAGGAACAGTTGGATTTCTACATAAGTTAGCTGAAAATATGAAATC---AAACT-CAGGTCCACAAAAGAGAATA-----------T -s simRat_chr6.simRat.chr6 192802 115 + 647215 AATTTGTGGATGTTGTCCTATCTTACACCATGGGGAAGAG---AGTTTCTGGAAAAGTTAGATAATATTACAAAATTATAAAACTACAAAATTATGAACCAGACCAGCAAATGAGATT - -a -s simMouse_chr6.simMouse.chr6 202782 5 + 636262 TTATC -s Anc0.Anc0refChr5 24160 5 + 87904 TTGTC -s Anc1.Anc1refChr8 38070 5 + 57822 TTGTC -s Anc2.Anc2refChr15 18311 5 + 86568 TTGCC -s mr.mrrefChr5 57453 5 + 294540 TTGTC -s simCow_chr6.simCow.chr6 201460 5 + 602619 TTGTC -s simCow_chr6.simCow.chr6 201664 5 + 602619 TTGCC -s simDog_chr6.simDog.chr6 483147 4 - 593897 TTG-C -s simHuman_chr6.simHuman.chr6 205230 5 + 601863 TTGTC -s simRat_chr6.simRat.chr6 192919 5 + 647215 TTGTC - -a -s simMouse_chr6.simMouse.chr6 202787 11 + 636262 ACCTAATGATG -s Anc0.Anc0refChr5 24165 10 + 87904 TACAAGT-ATG -s Anc1.Anc1refChr8 38075 10 + 57822 TACAAGT-ATG -s Anc2.Anc2refChr15 18317 10 + 86568 TACAAGT-ATG -s mr.mrrefChr5 57458 11 + 294540 AACTAATGATG -s simCow_chr6.simCow.chr6 201466 10 + 602619 TACAAGT-CTA -s simCow_chr6.simCow.chr6 201670 7 + 602619 TAAAAGT---- -s simDog_chr6.simDog.chr6 483152 10 - 593897 TACAAGT-ATG -s simHuman_chr6.simHuman.chr6 205235 10 + 601863 TACAAGT-ATG -s simRat_chr6.simRat.chr6 192924 11 + 647215 CACTAATGATG - -a -s simMouse_chr6.simMouse.chr6 202798 9 + 636262 GTAATGAAC -s Anc0.Anc0refChr5 24177 9 + 87904 GTGATGAAT -s Anc1.Anc1refChr8 38087 9 + 57822 GTGATGAAT -s Anc2.Anc2refChr15 18329 9 + 86568 GTGAGGAAT -s mr.mrrefChr5 57469 9 + 294540 GTGATGAAC -s simCow_chr6.simCow.chr6 201478 9 + 602619 GTAAGGAAT -s simCow_chr6.simCow.chr6 201679 9 + 602619 ATGAGGAAC -s simDog_chr6.simDog.chr6 483164 9 - 593897 GTGAGGAAT -s simHuman_chr6.simHuman.chr6 205247 8 + 601863 GTGATGAA- -s simRat_chr6.simRat.chr6 192935 9 + 647215 GTGATGAAT - -a -s simMouse_chr6.simMouse.chr6 202807 26 + 636262 TTTGACAACTTAGACAACTTAGTAAG -s Anc0.Anc0refChr5 24186 16 + 87904 CT----------GGTGACTTAGTAAG -s Anc1.Anc1refChr8 38096 16 + 57822 CT----------GGTGACTTAGTAAG -s Anc2.Anc2refChr15 18339 16 + 86568 CT----------GGTGACTTGGTAAG -s mr.mrrefChr5 57478 16 + 294540 TT----------GACAACTTAGTAAG -s simCow_chr6.simCow.chr6 201488 16 + 602619 CT----------GATGACTTGGTAAG -s simCow_chr6.simCow.chr6 201689 16 + 602619 CT----------GATGATTTAGTAAG -s simDog_chr6.simDog.chr6 483174 16 - 593897 TT----------GGTGTCTTGGTAAG -s simHuman_chr6.simHuman.chr6 205255 16 + 601863 GT----------GGTGACCTAGTGAG -s simRat_chr6.simRat.chr6 192944 16 + 647215 TT----------GACAATTTAGTAAG - -a -s simMouse_chr6.simMouse.chr6 202833 39 + 636262 CATCCAAATTCAAAACCAGCCAATTAGCTATGCCTGCAC -s Anc0.Anc0refChr5 24202 26 + 87904 TATC------CAAATCCTGTTAATGAGGT-------TAC -s Anc1.Anc1refChr8 38112 33 + 57822 TATC------CAAATCCTGTTAATGAGGTATGCTTGTAC -s Anc2.Anc2refChr15 18355 26 + 86568 TATC------CAAATCCTGTTAATGAGGT-------TCC -s mr.mrrefChr5 57494 39 + 294540 CATCCAAATTCAAAACCAGCCAATTAGCTATGCCTGCAC -s simCow_chr6.simCow.chr6 201504 26 + 602619 TCTC------CAAACCCTGTCGATGAGGT-------TCC -s simCow_chr6.simCow.chr6 201705 26 + 602619 TATC------CAAACCCTGTTGATGAGGT-------TCC -s simDog_chr6.simDog.chr6 483206 26 - 593897 TATC------CAAATCCTGTTAATCAGCT-------TCC -s simHuman_chr6.simHuman.chr6 205271 29 + 601863 ----------TAAATCCTGTTAATAAGGTATGCTTGTAC -s simRat_chr6.simRat.chr6 192960 34 + 647215 CATCAAAATTAAAAATCAGCCAATCAGTT--GCCTG--- - -a -s simMouse_chr6.simMouse.chr6 202872 9 + 636262 TGTTTGTAC -s Anc0.Anc0refChr5 24239 9 + 87904 TGTTTGTAT -s Anc1.Anc1refChr8 38156 9 + 57822 TGTTTGTAT -s Anc2.Anc2refChr15 18392 9 + 86568 TGTTTGTAT -s mr.mrrefChr5 57533 9 + 294540 TGTTTGTAC -s simCow_chr6.simCow.chr6 201541 9 + 602619 TGCATTTGT -s simCow_chr6.simCow.chr6 201742 9 + 602619 TGTTTTTGT -s simDog_chr6.simDog.chr6 483245 9 - 593897 TGTTTGTAC -s simHuman_chr6.simHuman.chr6 205311 9 + 601863 TGTTTGAAG -s simRat_chr6.simRat.chr6 192994 9 + 647215 TGTTTGTAC - -a -s simMouse_chr6.simMouse.chr6 202881 2 + 636262 TC -s Anc0.Anc0refChr5 24248 2 + 87904 TC -s Anc1.Anc1refChr8 38165 2 + 57822 TC -s Anc2.Anc2refChr15 18401 2 + 86568 TC -s mr.mrrefChr5 57542 2 + 294540 TC -s simCow_chr6.simCow.chr6 201751 2 + 602619 CC -s simDog_chr6.simDog.chr6 483254 2 - 593897 TC -s simHuman_chr6.simHuman.chr6 205320 2 + 601863 TC -s simRat_chr6.simRat.chr6 193003 2 + 647215 TC - -a -s simMouse_chr6.simMouse.chr6 202883 33 + 636262 CCCCTGAGTCTCTGACAGATAACTCCTTACGCG -s Anc0.Anc0refChr5 24250 33 + 87904 CAGTAAATTCTATAAGAGACAACTTCTTATCTG -s Anc1.Anc1refChr8 38167 33 + 57822 CAGTAAATTCTATAAGAGACAACTTCTTATCTG -s Anc2.Anc2refChr15 18403 33 + 86568 CAGTAAATTCTATAAGAGACAATTTCTTATCTG -s mr.mrrefChr5 57544 33 + 294540 CCCTTGAGTCTCTAACAGATAACTTCTTATGTG -s simCow_chr6.simCow.chr6 201755 30 + 602619 CAGTAAATTCTCTG---GACAATTTCTTATCTG -s simDog_chr6.simDog.chr6 483256 33 - 593897 CAGTAAATTCTATAAGATACAATTTCTTATCTG -s simHuman_chr6.simHuman.chr6 205322 28 + 601863 CAGCAAA-----TAAAAGACAACTTCTTATCTG -s simRat_chr6.simRat.chr6 193005 33 + 647215 CCCTTGATTCTTTAATAGATAGCTTTTTATGTG - -a -s simMouse_chr6.simMouse.chr6 202916 8 + 636262 CAGATGGT -s Anc0.Anc0refChr5 24289 8 + 87904 TAGATGGT -s Anc1.Anc1refChr8 38206 8 + 57822 TAGATGGT -s Anc2.Anc2refChr15 18442 8 + 86568 TAGATGGT -s mr.mrrefChr5 57577 8 + 294540 CAGATGGT -s simCow_chr6.simCow.chr6 201791 8 + 602619 TAGATGGT -s simDog_chr6.simDog.chr6 483295 8 - 593897 TAGACAAT -s simHuman_chr6.simHuman.chr6 205356 8 + 601863 TAGATGGT -s simRat_chr6.simRat.chr6 193038 8 + 647215 CAGATGGT - -a -s simMouse_chr6.simMouse.chr6 202924 45 + 636262 TGGGATGTTTCCTGAGGATGGCAGAAGGCTAATTAGTGGTCATGG -s Anc0.Anc0refChr5 24297 45 + 87904 CGGAGTGTTTTCTGAGGATGGGGAAAAGCTAACAAGCAATCTTGG -s Anc1.Anc1refChr8 38214 45 + 57822 CGGAGTGTTTTCTGAGGATGGGGAAAAGCTAACAAGCAATCTTGG -s Anc2.Anc2refChr15 18450 45 + 86568 CGGAGTGTTTTCTCAGAACGGGGAAGAGCTAACAAGCAACCTCGC -s mr.mrrefChr5 57585 45 + 294540 TGGGATGTTTCCTGAGGATGGGGGAAAGCTAATTAGTGGTCTTGG -s simCow_chr6.simCow.chr6 201799 45 + 602619 TGCAGTGTTTTCTCAGCACGGGGGAGAGCTAACTGGTGACTTCGT -s simDog_chr6.simDog.chr6 483303 41 - 593897 CGGAGTGTTTTCTCACAAC----AAGAGCTAACAAGCAACCTCGC -s simHuman_chr6.simHuman.chr6 205403 45 + 601863 AGGAGTGTTTTCTGAGGATGGGGAAAAGCTAAACACCAATCTTGG -s simRat_chr6.simRat.chr6 193046 45 + 647215 GATGATGTTTCTAGAGGGTGGGGGAAAGCTAATTAGTGGTCTTGG - -a -s simMouse_chr6.simMouse.chr6 202969 21 + 636262 TTAGCTCTACAGAAGTGGAGT -s Anc0.Anc0refChr5 24342 21 + 87904 TTATCCCTGCCGTGGTGGTAT -s Anc1.Anc1refChr8 38259 21 + 57822 TTATCCCTGCCGTGGTGGTAT -s Anc2.Anc2refChr15 18495 21 + 86568 TTATCCCTGCCATGGTGGTAT -s mr.mrrefChr5 57630 21 + 294540 TTATCTCTACAGAAGTGGAAT -s simCow_chr6.simCow.chr6 201844 21 + 602619 TTATCCACGCCATGGTGGCAT -s simDog_chr6.simDog.chr6 483344 21 - 593897 CTATCCCTGCCATCGTGCTAT -s simHuman_chr6.simHuman.chr6 205459 21 + 601863 TTATCCCTTCCGTGGTGGTAT -s simRat_chr6.simRat.chr6 193091 21 + 647215 TTATGTCTACTGAAGTGGCAC - -a -s simMouse_chr6.simMouse.chr6 202990 15 + 636262 GGTCCCTTGGCACTG -s Anc0.Anc0refChr5 24363 15 + 87904 GGTCTTTTGGCGCTA -s Anc1.Anc1refChr8 38280 15 + 57822 GGTCTTTTGGCGCTA -s Anc2.Anc2refChr15 18519 15 + 86568 AGTCTTTTGGCGCTC -s mr.mrrefChr5 57651 15 + 294540 GGTCTCTTGGCACTA -s simCow_chr6.simCow.chr6 201868 15 + 602619 AGTCTTTTGGCAATC -s simDog_chr6.simDog.chr6 483368 15 - 593897 AGTCTTTTGGCGCTC -s simHuman_chr6.simHuman.chr6 205480 15 + 601863 GGTGTTATGGCCCCA -s simRat_chr6.simRat.chr6 193112 15 + 647215 AGTCTCTTGGCACTA - -a -s simMouse_chr6.simMouse.chr6 203005 11 + 636262 AGTTGTCACGA -s Anc0.Anc0refChr5 24378 11 + 87904 AGCTGTGATCT -s Anc1.Anc1refChr8 38295 11 + 57822 AGCTGTGATCT -s Anc2.Anc2refChr15 18534 11 + 86568 AGCTGTGATCT -s mr.mrrefChr5 57666 11 + 294540 AGTTGTGATGT -s simCow_chr6.simCow.chr6 201883 11 + 602619 ACCTGGGAACT -s simDog_chr6.simDog.chr6 483383 11 - 593897 AGCTGTCATCT -s simHuman_chr6.simHuman.chr6 205496 11 + 601863 AGCTGTGATCT -s simRat_chr6.simRat.chr6 193127 11 + 647215 AGTTGTGATTT - -a -s simMouse_chr6.simMouse.chr6 203016 3 + 636262 ACA -s Anc0.Anc0refChr5 24389 3 + 87904 ATA -s Anc1.Anc1refChr8 38306 3 + 57822 ATA -s Anc2.Anc2refChr15 18551 3 + 86568 ATA -s mr.mrrefChr5 57677 3 + 294540 ACA -s simCow_chr6.simCow.chr6 201900 3 + 602619 TTA -s simDog_chr6.simDog.chr6 483400 3 - 593897 AGA -s simHuman_chr6.simHuman.chr6 205507 3 + 601863 ATA -s simRat_chr6.simRat.chr6 193138 3 + 647215 ACA - -a -s simMouse_chr6.simMouse.chr6 203019 34 + 636262 TGAAGCTAAACTTGAAAATCTGCAAGCACAAACT -s Anc0.Anc0refChr5 24393 34 + 87904 TGAAGTCAAACATGAACATTTTCAGATTGCAACT -s Anc1.Anc1refChr8 38310 34 + 57822 TGAAGTCAAACATGAACATTTTCAGATTGCAACT -s Anc2.Anc2refChr15 18555 34 + 86568 TGAAGTCACACACAAGCATTTTCAGATTGCAACA -s mr.mrrefChr5 57680 34 + 294540 TGAAGTCAAACTTGAAAATCTGCAAGCACAAACT -s simCow_chr6.simCow.chr6 201904 34 + 602619 TGATGTCATACACAAGAATTTTCAGATTGCAGCT -s simDog_chr6.simDog.chr6 483404 34 - 593897 CAAAGTCACACACAGGCATTTCCAGATTGCAACA -s simHuman_chr6.simHuman.chr6 205511 34 + 601863 TGAAGTCAAAAATGAAGATTTTCAGATCACAACT -s simRat_chr6.simRat.chr6 193141 34 + 647215 TAAAGTCAAACTTGAAAATCTGCAAGCACAAACT - -a -s simMouse_chr6.simMouse.chr6 203053 1 + 636262 A -s Anc0.Anc0refChr5 24427 1 + 87904 A -s Anc1.Anc1refChr8 38344 1 + 57822 A -s Anc2.Anc2refChr15 18589 1 + 86568 A -s mr.mrrefChr5 57714 1 + 294540 A -s simCow_chr6.simCow.chr6 201938 1 + 602619 A -s simDog_chr6.simDog.chr6 483438 1 - 593897 A -s simHuman_chr6.simHuman.chr6 205553 1 + 601863 A -s simRat_chr6.simRat.chr6 193175 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 203054 17 + 636262 GTAACCCATCGATGTGC -s Anc0.Anc0refChr5 24434 16 + 87904 ATAAGCCATCATTATG- -s Anc1.Anc1refChr8 38351 17 + 57822 ATAAGCCATCATTATGC -s Anc2.Anc2refChr15 18596 16 + 86568 ATAAGCCAGTACCAAG- -s mr.mrrefChr5 57721 17 + 294540 ATAACCCATCATTATGC -s simCow_chr6.simCow.chr6 201945 11 + 602619 ATAAGTCAGT-----G- -s simDog_chr6.simDog.chr6 483445 16 - 593897 ATAAGCCAGTACCAAG- -s simHuman_chr6.simHuman.chr6 205560 17 + 601863 ATAAGCCATCATTATGC -s simRat_chr6.simRat.chr6 193182 17 + 647215 ATAACCCATCATTATGC - -a -s simMouse_chr6.simMouse.chr6 203071 25 + 636262 TGATGCTGGACAATAAATCAAAACC -s Anc0.Anc0refChr5 24450 25 + 87904 TTATGCTAGACAATAAATGGCAAAC -s Anc1.Anc1refChr8 38368 25 + 57822 TTATGCTAGACAATAAATGGCAAAC -s Anc2.Anc2refChr15 18612 25 + 86568 TTATGCTAGACAATAAATGGCGCAC -s mr.mrrefChr5 57738 25 + 294540 TGATGCTGGACAATAAATCAAAACC -s simCow_chr6.simCow.chr6 201956 25 + 602619 TTATGTTTGACAATAAACGCATCAC -s simDog_chr6.simDog.chr6 483461 25 - 593897 TCATGCTAGACAATAAATGGCGCAA -s simHuman_chr6.simHuman.chr6 205650 25 + 601863 TTATGCTAGACAATGAAGGGCAAAC -s simRat_chr6.simRat.chr6 193199 25 + 647215 TGATGCTGAACAATAAATCAAAACC - -a -s simMouse_chr6.simMouse.chr6 203096 7 + 636262 AACTGCA -s Anc0.Anc0refChr5 24475 2 + 87904 CA----- -s Anc1.Anc1refChr8 38393 7 + 57822 CACTCCA -s Anc2.Anc2refChr15 18637 2 + 86568 CA----- -s mr.mrrefChr5 57763 7 + 294540 AACTGCA -s simCow_chr6.simCow.chr6 201982 2 + 602619 TA----- -s simDog_chr6.simDog.chr6 483486 2 - 593897 CA----- -s simHuman_chr6.simHuman.chr6 205675 7 + 601863 CACTCCA -s simRat_chr6.simRat.chr6 193224 7 + 647215 AACTGCC - -a -s simMouse_chr6.simMouse.chr6 203103 20 + 636262 TACAACACTCTTTCGGCCTA -s Anc0.Anc0refChr5 24477 16 + 87904 TAGCACTTTCTTTTAG---- -s Anc1.Anc1refChr8 38400 16 + 57822 TAGCACTTTCTTTTAG---- -s Anc2.Anc2refChr15 18639 16 + 86568 TAGCACTTTCTTTTAG---- -s mr.mrrefChr5 57770 20 + 294540 TACAACACTCTTTCGGCCTA -s simCow_chr6.simCow.chr6 201984 16 + 602619 TGACACTTTTTTGTAG---- -s simDog_chr6.simDog.chr6 483488 16 - 593897 TAGAACGCTCTTTTAG---- -s simHuman_chr6.simHuman.chr6 205683 16 + 601863 TTGCACTTTCTTCTAG---- -s simRat_chr6.simRat.chr6 193231 20 + 647215 CACAACACTTTTTCAGCCGA - -a -s simMouse_chr6.simMouse.chr6 203123 68 + 636262 GTGGGGTGTTTGTGTATAATCAGTATTATGATGGGTTTGATATATTTAGTGGCCTGGTGACAGTCCGA -s Anc0.Anc0refChr5 24493 68 + 87904 TTGGGAAGTAGGTGCATAATCAGTATTAAGATGGGTTTGATATGATGAGTGGCATGGTGACAGTCTCA -s Anc1.Anc1refChr8 38416 68 + 57822 TTGGGAAGTAGGTGCATAATCAGTATTAAGATGGGTTTGATATGATGAGTGGCATGGTGACAGTCTCA -s Anc2.Anc2refChr15 18655 68 + 86568 TTGGAAAGTAGGTGCATAGTCAGTATTAAAGTGGGTTTGATATGATGAGTGGCATAGTGGCCGTCTCA -s mr.mrrefChr5 57790 68 + 294540 GTGGGGTGTTTGTGTATAATCAGTATTAAGATGGGTTTGATATATTTAGTGGCCTGGTGACAGTCTGA -s simCow_chr6.simCow.chr6 202000 67 + 602619 TTGAAAAGTTG-TGCCTAGTCAGTATTTAAGTGGGTTTGGTATGATGAGTGGCATAGTGGCCACCTCA -s simDog_chr6.simDog.chr6 483509 68 - 593897 TTGGAATGTAGGTGCATAGTTAGTATTAAAGTGGGATTGATATGATTAGTGGCATAGTGGCCGTCTCA -s simHuman_chr6.simHuman.chr6 205699 68 + 601863 TTGGGAAGTGGGTGCATTATCAGTCCTAAGATGGATTTGATATCATGAGTGGCTTGGTGATAGTCTCA -s simRat_chr6.simRat.chr6 193251 68 + 647215 GTGGGGTGTTTGTGTATAATCAGTATTAAGATGGGTTTGATATATACGGTGGCCTGGTGAGAGCCTGA - -a -s simMouse_chr6.simMouse.chr6 203191 67 + 636262 TATTTGAGAATCTCTTCTTAGTTCAATTTCTTAGTTCAACAAAAATGTAGATTTTCAATCTCACCAA -s Anc0.Anc0refChr5 24567 52 + 87904 TATTTGAGCACCTCT---------------TTAGGCCACTGAAAAGGCAGACCTTGGATCTCATGAA -s Anc1.Anc1refChr8 38490 52 + 57822 TATTTGAGCACCTCT---------------TTAGGCCACTGAAAAGGCAGACCTTGGATCTCATGAA -s Anc2.Anc2refChr15 18729 52 + 86568 TATTTGAGCACCTCT---------------TTAGGCCACTGAAAAGGCAGACCTTGGATCTCATGAA -s mr.mrrefChr5 57858 67 + 294540 TATTTGAGAATCTCTTCTTAGTTCAATTTCTTAGTTCAACAAAAATGTAGATTTTCAATCTCACCAA -s simCow_chr6.simCow.chr6 202073 52 + 602619 TATTTGAGCAATTCT---------------TTAGGTTACTGAAAAGGCAGAGCTTGGATCTCATCAA -s simDog_chr6.simDog.chr6 483583 52 - 593897 TATTTGGGCACCTCT---------------TTAAGCCACTGTAAAGGCAGACCTTGGATCTCATGAA -s simHuman_chr6.simHuman.chr6 205773 52 + 601863 TATTTGAGCACCTCT---------------TTAGACCACTGAAAAGACAGACCTTGGATTACATTAA -s simRat_chr6.simRat.chr6 193319 67 + 647215 TCTTTGAGAATCTCTTCTTAGTTCAACTCTTTAGTTCAACAAAAATGTAGATTTTCAATCTCACCAA - -a -s simMouse_chr6.simMouse.chr6 203258 1 + 636262 C -s Anc0.Anc0refChr5 24623 1 + 87904 T -s Anc1.Anc1refChr8 38546 1 + 57822 T -s Anc2.Anc2refChr15 18785 1 + 86568 T -s mr.mrrefChr5 57925 1 + 294540 T -s simCow_chr6.simCow.chr6 202129 1 + 602619 T -s simDog_chr6.simDog.chr6 483639 1 - 593897 T -s simHuman_chr6.simHuman.chr6 205829 1 + 601863 T -s simRat_chr6.simRat.chr6 193386 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 203259 11 + 636262 AATTTCAATTG -s Anc0.Anc0refChr5 24624 11 + 87904 AATTACAATTG -s Anc1.Anc1refChr8 38547 11 + 57822 AATTACAATTG -s Anc2.Anc2refChr15 18786 11 + 86568 ACTCACAATTG -s mr.mrrefChr5 57926 11 + 294540 AATTTCAATTG -s simCow_chr6.simCow.chr6 202132 11 + 602619 ACTCACAATTG -s simHuman_chr6.simHuman.chr6 205830 11 + 601863 AATTACAACTG -s simRat_chr6.simRat.chr6 193387 11 + 647215 AATTTCAATCA - -a -s simMouse_chr6.simMouse.chr6 203270 67 + 636262 CAGCCAATAACCTGGCTGTAGTTTGGGAAGGGTCCAATACATGAGATAACCTACCACCGACCCAGCA -s Anc0.Anc0refChr5 24664 67 + 87904 CAACTGATATCTCAGCAGGGCTTTGGGAGGGGTCCAATACCTGTGATTGATTGCCACTGACCCAGTA -s Anc1.Anc1refChr8 38587 67 + 57822 CAACTGATATCTCAGCAGGGCTTTGGGAGGGGTCCAATACCTGTGATTGATTGCCACTGACCCAGTA -s Anc2.Anc2refChr15 18826 67 + 86568 CAACTGATATTTCAGCAGGGCTTAGGGAGGGGTTCAATACCTGTGATTGATTGCCACAGACCCAGTG -s mr.mrrefChr5 57937 67 + 294540 CAACCAATATCCTGGCAGTAGTTTGGGAAGGGTCCAATACATGTGATAACCTACCACTGACCCAGTA -s simCow_chr6.simCow.chr6 202200 67 + 602619 CAACTGATATTTCAGTAGGGCTTGGGCAGGGGTTCAATACCTATGCTTGATTGGCAAAGGCCCATTG -s simDog_chr6.simDog.chr6 483647 67 - 593897 CAACTGATATTACAGCAGGGGTTAGGGGGGAATTGACTACCTGTCATTGATTGCCACAGACCAAGTG -s simHuman_chr6.simHuman.chr6 205870 67 + 601863 CAACTGATATCTCAGCAGGGCCTTCGGATGGGTCCAATACCTGTGGCGGATTCCCACTGACCCAGTA -s simRat_chr6.simRat.chr6 193398 67 + 647215 CTACCAGTATCCTGGCAGTAGTTTGGGAAGGGCCCAATACATATGATAAGCTACCACTGTCCCCGTG - -a -s simMouse_chr6.simMouse.chr6 203337 6 + 636262 TGTCTT -s Anc0.Anc0refChr5 24732 6 + 87904 TGTCTG -s Anc1.Anc1refChr8 38655 6 + 57822 TGTCTG -s Anc2.Anc2refChr15 18894 6 + 86568 AGTGTG -s mr.mrrefChr5 58004 6 + 294540 TGTCTT -s simCow_chr6.simCow.chr6 202268 6 + 602619 ATCTTA -s simDog_chr6.simDog.chr6 483715 6 - 593897 AGTGTG -s simHuman_chr6.simHuman.chr6 205938 6 + 601863 TGTCTG -s simRat_chr6.simRat.chr6 193465 6 + 647215 TGTCTT - -a -s simMouse_chr6.simMouse.chr6 203343 56 + 636262 ATTTTAAGACTTGGGAGGGTGATGTTAGCTGTATGAAACGTCTGTGAGTAAAATGT -s Anc0.Anc0refChr5 24744 56 + 87904 CTGCTAAGTCTTGTAGGGATGATGTCAGCTGTATGGAAGGCTGGTAAATAACATGT -s Anc1.Anc1refChr8 38667 56 + 57822 CTGCTAAGTCTTGTAGGGATGATGTCAGCTGTATGGAAGGCTGGTAAATAACATGT -s Anc2.Anc2refChr15 18906 56 + 86568 CTGCTAAGTCTTGTAGGGACAATGTCAGCGGTATGGAGGGCTGGTAAATAACATGT -s mr.mrrefChr5 58010 56 + 294540 ATTTTAAGACTTGGAAGGGTGATGTCAGCTGTATGAAACGCCTGTGAGTAAAATGT -s simCow_chr6.simCow.chr6 202275 53 + 602619 ---CCAAGTCTTGTAGGGACAATGTCAGCGGTACAGAGGGCTGGTAGATAATATGT -s simDog_chr6.simDog.chr6 483777 49 - 593897 CTGCTAAGTCATGTATG-------TCAGTGGTGTGTAGGGCTGGTGAATAACATGC -s simHuman_chr6.simHuman.chr6 205950 56 + 601863 GTCATAAGTCTTGTAGGGATGATTTCAGCTGTATGGAAGGCTGATAAATAACATGT -s simRat_chr6.simRat.chr6 193471 47 + 647215 ATTT--AAGTTTTAATAGGTGATGTCAGC------AAAC-CCTGTCAGTAAAAATT - -a -s simMouse_chr6.simMouse.chr6 203399 10 + 636262 TTCATCTTTG -s Anc0.Anc0refChr5 24800 10 + 87904 TCTGTCTATG -s Anc1.Anc1refChr8 38723 10 + 57822 TCTGTCTATG -s Anc2.Anc2refChr15 18962 10 + 86568 TCTGTCTAGG -s mr.mrrefChr5 58066 10 + 294540 TTCATCTTTG -s simCow_chr6.simCow.chr6 202328 10 + 602619 CCTGACTAAG -s simDog_chr6.simDog.chr6 483836 10 - 593897 TCTGTCCAGG -s simHuman_chr6.simHuman.chr6 206006 10 + 601863 TCTGTCTATG -s simRat_chr6.simRat.chr6 193518 10 + 647215 TTCAACTTTG - -a -s simMouse_chr6.simMouse.chr6 203409 21 + 636262 TATAATTTATGTCAGCCTGAT -s Anc0.Anc0refChr5 24816 21 + 87904 TACAATTTGTGTCAGTCTTCC -s Anc1.Anc1refChr8 38739 21 + 57822 TACAATTTGTGTCAGTCTTCC -s Anc2.Anc2refChr15 18978 21 + 86568 TACATTTTGTGTCAGTCTTCC -s mr.mrrefChr5 58076 21 + 294540 TATAATTTATGTCAGTCTGAT -s simCow_chr6.simCow.chr6 202344 21 + 602619 AACATTTCATGTCAGTCTCCC -s simDog_chr6.simDog.chr6 483852 21 - 593897 TATATTTTGTGTTATGCTTCC -s simHuman_chr6.simHuman.chr6 206022 20 + 601863 CACAA-TTGAGTCAGTCTTCC -s simRat_chr6.simRat.chr6 193528 21 + 647215 TATAATTTATGTCAGTCTGAT - -a -s simMouse_chr6.simMouse.chr6 203430 42 + 636262 AATGCTAGGCTGGAAGGCCTGAGCGCTTCCCCCGGCCTTAGT -s Anc0.Anc0refChr5 24838 33 + 87904 AACACTAGGCTTGAA--------CAGTCCAA-TGGCCTTAAT -s Anc1.Anc1refChr8 38761 34 + 57822 AACACTAGGCTTGAA--------CAGTCCAAATGGCCTTAAT -s Anc2.Anc2refChr15 19000 33 + 86568 AGCACTAGGCTCAAA--------CAGTCCAA-TGGTCTTAAT -s mr.mrrefChr5 58097 42 + 294540 AATGCTAGGCTTGAAGGCCTGAGCGCTTCCCCCGGCCTTAGT -s simCow_chr6.simCow.chr6 202366 12 + 602619 TGCCCT----------------------------GTCTTA-- -s simDog_chr6.simDog.chr6 483874 33 - 593897 AGCACTAGGCTCAAA--------CAGTCCAA-TGCTCTTAAT -s simHuman_chr6.simHuman.chr6 206043 34 + 601863 AACACTAGGTTTGAA--------CAATGCAAATGGCCCTAAT -s simRat_chr6.simRat.chr6 193549 42 + 647215 TATGCTAGGCTTGAAAGCCTGAGGCCTTCCCCCAGCATTAGT - -a -s simMouse_chr6.simMouse.chr6 203472 7 + 636262 GATCCGT -s Anc0.Anc0refChr5 24871 6 + 87904 AACCCC- -s Anc1.Anc1refChr8 38795 7 + 57822 AACCCCT -s Anc2.Anc2refChr15 19033 6 + 86568 AACCCC- -s mr.mrrefChr5 58139 7 + 294540 GATCCGT -s simCow_chr6.simCow.chr6 202378 2 + 602619 ----CA- -s simDog_chr6.simDog.chr6 483907 6 - 593897 AACCCC- -s simHuman_chr6.simHuman.chr6 206077 7 + 601863 AACCCCT -s simRat_chr6.simRat.chr6 193592 7 + 647215 TATTCGT - -a -s simMouse_chr6.simMouse.chr6 203479 3 + 636262 TTT -s Anc0.Anc0refChr5 24877 2 + 87904 -CT -s Anc1.Anc1refChr8 38802 3 + 57822 CCT -s Anc2.Anc2refChr15 19039 2 + 86568 -CT -s mr.mrrefChr5 58146 3 + 294540 TTT -s simCow_chr6.simCow.chr6 202380 2 + 602619 -GT -s simDog_chr6.simDog.chr6 483913 2 - 593897 -CT -s simHuman_chr6.simHuman.chr6 206084 3 + 601863 CCT -s simRat_chr6.simRat.chr6 193650 3 + 647215 TTT - -a -s simMouse_chr6.simMouse.chr6 203482 5 + 636262 ATTAT -s Anc0.Anc0refChr5 24888 5 + 87904 GGTAT -s Anc1.Anc1refChr8 38814 5 + 57822 GGTAT -s Anc2.Anc2refChr15 19050 5 + 86568 GGTAT -s mr.mrrefChr5 58149 5 + 294540 ATTAT -s simCow_chr6.simCow.chr6 202391 5 + 602619 GGCAT -s simDog_chr6.simDog.chr6 483924 5 - 593897 GGTGT -s simHuman_chr6.simHuman.chr6 206096 5 + 601863 TGTAT -s simRat_chr6.simRat.chr6 193653 5 + 647215 ATTAA - -a -s simMouse_chr6.simMouse.chr6 203487 25 + 636262 TACCTAAGGATGAATTCAATGCGAT -s Anc0.Anc0refChr5 24929 24 + 87904 TAC-AGGAGACATATGGTATGTGAT -s Anc1.Anc1refChr8 38855 25 + 57822 TACCAGGAGACATATGGTATGTGAT -s Anc2.Anc2refChr15 19091 24 + 86568 TAC-AGGAGACATATGGTATGTAAT -s mr.mrrefChr5 58154 25 + 294540 TACCTGGGGAGAAATTCAATGCGAT -s simCow_chr6.simCow.chr6 202432 24 + 602619 TAC-TTGAGACATATGCTATTGATT -s simDog_chr6.simDog.chr6 483965 24 - 593897 TAG-AGGAAGCATATGGTTTGTAAT -s simHuman_chr6.simHuman.chr6 206137 25 + 601863 TACCAGGAGACTTACAATATGTGAT -s simRat_chr6.simRat.chr6 193658 25 + 647215 TACCTGGGGAGAAAGTCAATGCAAT - -a -s simMouse_chr6.simMouse.chr6 203512 18 + 636262 TTGGGTTTATGCAGGTGG -s Anc0.Anc0refChr5 24953 17 + 87904 TGAA-TTCATGCAGGTGG -s Anc1.Anc1refChr8 38880 17 + 57822 TGAA-TTCATGCAGGTGG -s Anc2.Anc2refChr15 19115 17 + 86568 TGAA-TTCATGCAGGTGG -s mr.mrrefChr5 58179 17 + 294540 TTGG-TTCATGCAGGTGG -s simCow_chr6.simCow.chr6 202456 14 + 602619 TAAA-TTCATGCAGG--- -s simDog_chr6.simDog.chr6 483990 17 - 593897 GGAA-TTCATACAGGTGG -s simHuman_chr6.simHuman.chr6 206162 17 + 601863 TGAA-TTCATGCAGGTGG -s simRat_chr6.simRat.chr6 193683 17 + 647215 TTGG-TTCAGGCAGGTGA - -a -s simMouse_chr6.simMouse.chr6 203530 11 + 636262 GATCAGAACAG -s Anc0.Anc0refChr5 24970 9 + 87904 GATCAGACA-- -s Anc1.Anc1refChr8 38897 9 + 57822 GATCAGACA-- -s Anc2.Anc2refChr15 19132 9 + 86568 GATCAGACA-- -s mr.mrrefChr5 58196 11 + 294540 GATCAGACCAG -s simCow_chr6.simCow.chr6 202470 9 + 602619 GGTCAAACA-- -s simDog_chr6.simDog.chr6 484007 9 - 593897 GATCAGACA-- -s simHuman_chr6.simHuman.chr6 206179 9 + 601863 GTTCAGACA-- -s simRat_chr6.simRat.chr6 193787 11 + 647215 TCATGGACCAA - -a -s simMouse_chr6.simMouse.chr6 203541 12 + 636262 AACTACCTTATT -s Anc0.Anc0refChr5 24980 12 + 87904 AACACCCTTACT -s Anc1.Anc1refChr8 38907 12 + 57822 AACACCCTTACT -s Anc2.Anc2refChr15 19142 12 + 86568 AACACACATACT -s mr.mrrefChr5 58215 12 + 294540 AACAACCTTATT -s simCow_chr6.simCow.chr6 202480 12 + 602619 AACACTCCTATT -s simDog_chr6.simDog.chr6 484019 12 - 593897 GATACAGATACT -s simHuman_chr6.simHuman.chr6 206189 12 + 601863 ACCACCCTTACT -s simRat_chr6.simRat.chr6 193806 12 + 647215 AACAACCTTATC - -a -s simMouse_chr6.simMouse.chr6 203553 54 + 636262 GTTAACTAAAAGACATTGAGATCTCTATCCAGATTAAATAACAATGGAGAGAAA -s Anc0.Anc0refChr5 24992 46 + 87904 A----CCAAAGGACATATAAAGATTTCACAAGATTGAATAACAAGG----GAAA -s Anc1.Anc1refChr8 38919 46 + 57822 A----CCAAAGGACATATAAAGATTTCACAAGATTGAATAACAAGG----GAAA -s Anc2.Anc2refChr15 19154 46 + 86568 A----CCAAAGGATATATAAAGAATTCACAAGATTGAACAACAAGG----GAAA -s mr.mrrefChr5 58227 54 + 294540 GTTACCTAAAGGACATTGAGGTTTCTATCAAGATTGAATAACAATGGAAAGAAA -s simCow_chr6.simCow.chr6 202535 46 + 602619 A----CAAAAGGAAACATAAAAAATGCATAAGATTGAAAAGCACGG----GAAA -s simDog_chr6.simDog.chr6 484031 45 - 593897 A----CCAAAGGATATATAAAGA-TTCACAAGATTGAACAACAAGA----GAAA -s simHuman_chr6.simHuman.chr6 206201 46 + 601863 A----CGAAAGGACATATAAAGGTTTCAAAACATTGAATGCCAAGG----GAAA -s simRat_chr6.simRat.chr6 193818 53 + 647215 GTTACCTAAAGGACATTGAGGTTTCTGTCAAGATTGAATAACACTGGAA-GAAA - -a -s simMouse_chr6.simMouse.chr6 203607 28 + 636262 TGGTGAAGATGTACTTTATAAGTTAGTC -s Anc0.Anc0refChr5 25038 28 + 87904 TGGGGGTGATTTATCTTATAAGTTAGCT -s Anc1.Anc1refChr8 38965 28 + 57822 TGGGGGTGATTTATCTTATAAGTTAGCT -s Anc2.Anc2refChr15 19200 28 + 86568 TGAGGGTGATTTATCTCATAAGTTAGCT -s mr.mrrefChr5 58281 28 + 294540 TGGGGAAGATGTACTTTATAAGTTAGTC -s simCow_chr6.simCow.chr6 202581 28 + 602619 TGAGGGTGACTTTTCTCCTAAGCTAGCT -s simDog_chr6.simDog.chr6 484080 28 - 593897 TGAAGGTGATTTATTTCATAAGTTCTCT -s simHuman_chr6.simHuman.chr6 206247 28 + 601863 TGGGAGTGGTTTATCTTGTAAGGTAGGT -s simRat_chr6.simRat.chr6 193871 28 + 647215 TGGGGAAGATCTACTTCATAAGTTAATC - -a -s simMouse_chr6.simMouse.chr6 203635 22 + 636262 CAAAGAGTTCTACACTTGATGT -s Anc0.Anc0refChr5 25067 21 + 87904 CAGGCA-CTCTACACTTAATGT -s Anc1.Anc1refChr8 38994 22 + 57822 CAGGCAACTCTACACTTAATGT -s Anc2.Anc2refChr15 19229 21 + 86568 CAGGCA-CTCTATGCTTAATGA -s mr.mrrefChr5 58310 22 + 294540 CAGACAGTTCTACACTTGATGT -s simCow_chr6.simCow.chr6 202610 20 + 602619 GAGGCA-CACTATCCTTA-TGC -s simDog_chr6.simDog.chr6 484109 21 - 593897 CAGGCA-CTCTATGCTTAATGA -s simHuman_chr6.simHuman.chr6 206276 22 + 601863 CAGGCAACTGTACACTAAATGT -s simRat_chr6.simRat.chr6 193900 22 + 647215 CAGACCGTTCTACACTTGATGT - -a -s simMouse_chr6.simMouse.chr6 203657 41 + 636262 AGGTTGAATGACATTTCAGATAATAAAAAGAGAAGGTCTGA -s Anc0.Anc0refChr5 25094 41 + 87904 GGGTAGCATGAGATTTCAGATAATTGAAAGATAAGGTCTGA -s Anc1.Anc1refChr8 39022 41 + 57822 GGGTAGCATGAGATTTCAGATAATTGAAAGATAAGGTCTGA -s Anc2.Anc2refChr15 19256 41 + 86568 GGGTAGCATGAGATTACAGATAATTGAAAGATTAGGTCTGA -s mr.mrrefChr5 58332 41 + 294540 AGGTTGAATGAGATTTCAGATAATAAAAAGAGAAGGTCTGA -s simCow_chr6.simCow.chr6 202636 40 + 602619 GGGTATCAGGAGATTACAAGCTATTGAAAG-TTAGGTCCAA -s simDog_chr6.simDog.chr6 484136 41 - 593897 GGGTAGCATCAGACTACAGATAACTGAAAGATTAGGTATGA -s simHuman_chr6.simHuman.chr6 206304 41 + 601863 GGGTGGCATGGTATTTCAGATAATTGGAGGATAAGGTCTGA -s simRat_chr6.simRat.chr6 193922 41 + 647215 AGGTTGAATGAGATTTCAGATAACCAAAAGAGAAGGTCTGA - -a -s simMouse_chr6.simMouse.chr6 203698 9 + 636262 CAGTTCTCA -s Anc0.Anc0refChr5 25135 4 + 87904 CA-----TA -s Anc1.Anc1refChr8 39063 4 + 57822 CA-----TA -s Anc2.Anc2refChr15 19297 4 + 86568 CA-----TA -s mr.mrrefChr5 58373 9 + 294540 CAGTTCCTA -s simCow_chr6.simCow.chr6 202676 4 + 602619 CA-----TA -s simDog_chr6.simDog.chr6 484181 4 - 593897 CC-----TG -s simHuman_chr6.simHuman.chr6 206345 4 + 601863 CA-----TA -s simRat_chr6.simRat.chr6 193963 9 + 647215 CAGTTCCTA - -a -s simMouse_chr6.simMouse.chr6 203707 6 + 636262 TCTTTA -s Anc0.Anc0refChr5 25139 6 + 87904 TCCATA -s Anc1.Anc1refChr8 39067 6 + 57822 TCCATA -s Anc2.Anc2refChr15 19301 6 + 86568 TCCATA -s mr.mrrefChr5 58382 6 + 294540 TCTTTA -s simCow_chr6.simCow.chr6 202684 6 + 602619 TCCGTA -s simDog_chr6.simDog.chr6 484185 6 - 593897 TCGACA -s simHuman_chr6.simHuman.chr6 206349 6 + 601863 TCCCTA -s simRat_chr6.simRat.chr6 193972 6 + 647215 TCTTTA - -a -s simMouse_chr6.simMouse.chr6 203713 40 + 636262 AAACAATTCTCTTGAAGTGAAGCATATGTGTAATGACTGA -s Anc0.Anc0refChr5 25149 40 + 87904 TAACAATTGTCTTGAAGTGTAGTATGTGTGCAATGACCAA -s Anc1.Anc1refChr8 39077 40 + 57822 TAACAATTGTCTTGAAGTGTAGTATGTGTGCAATGACCAA -s Anc2.Anc2refChr15 19311 40 + 86568 TAACAATTGTCTTGAAGTGTAGTATGTGTGCAAGGACCAA -s mr.mrrefChr5 58392 40 + 294540 AAACAATTCTCTTGAAGTGAAGCATGTGTGTAATGACTGA -s simCow_chr6.simCow.chr6 202694 40 + 602619 TAACAATTGTTTTGAAGTGTAGTATGTCTGCAACGAGCAA -s simDog_chr6.simDog.chr6 484195 38 - 593897 TAACAATTGTCTTGAAGAGTAGTATGCG--CAAGGACCAA -s simHuman_chr6.simHuman.chr6 206359 40 + 601863 TAGCAATTTTCTTGAAGTGTAGTATGTGTGCAATGACCAA -s simRat_chr6.simRat.chr6 193982 40 + 647215 AAACAACTCTTTTGAAGTGAAGCGTGTGTGTAATGGCTGA - -a -s simMouse_chr6.simMouse.chr6 203753 25 + 636262 TGATTTGCTCAGTTATTCTGTGTCA -s Anc0.Anc0refChr5 25196 25 + 87904 TAACTTGTTCAGTTATCCTGTGTGA -s Anc1.Anc1refChr8 39124 25 + 57822 TAACTTGTTCAGTTATCCTGTGTGA -s Anc2.Anc2refChr15 19358 25 + 86568 TAACTTGTTAAGTTATCCTGTGTCA -s mr.mrrefChr5 58432 25 + 294540 TGATTTGTTCAGTTATTCTGTGTGA -s simCow_chr6.simCow.chr6 202741 23 + 602619 CAACTTA--AAGTTATCCTGTGTTA -s simDog_chr6.simDog.chr6 484240 25 - 593897 TGACTAGTTAAGTTAGCCTGTGTCA -s simHuman_chr6.simHuman.chr6 206406 25 + 601863 TAACTTGTTCAGCTATCCTGTGTGA -s simRat_chr6.simRat.chr6 194022 25 + 647215 TGATTCATTTGGATATTCTGTGTGA - -a -s simMouse_chr6.simMouse.chr6 203778 3 + 636262 CAT -s Anc0.Anc0refChr5 25222 3 + 87904 CAT -s Anc1.Anc1refChr8 39150 3 + 57822 CAT -s Anc2.Anc2refChr15 19384 3 + 86568 CAT -s mr.mrrefChr5 58458 3 + 294540 CAT -s simCow_chr6.simCow.chr6 202765 3 + 602619 CCT -s simDog_chr6.simDog.chr6 484266 3 - 593897 CAT -s simHuman_chr6.simHuman.chr6 206432 3 + 601863 CAG -s simRat_chr6.simRat.chr6 194067 3 + 647215 CAT - -a -s simMouse_chr6.simMouse.chr6 203781 50 + 636262 ATTCTCTAGTACCTCACAAGGCCATGCTATGTATTCGAGATTTGCCCAGC -s Anc0.Anc0refChr5 25225 38 + 87904 TCTCTCCAGTACCTCACAGAATCATCCCATGTGCTGGA------------ -s Anc1.Anc1refChr8 39153 50 + 57822 TCTCTCCAGTACCTCACAGAATCATCCCATGTGCTGGACACTCAGCTATT -s Anc2.Anc2refChr15 19387 38 + 86568 TCTCTTTGGTACCTCACAGAATCATCCCATGTGCTAGA------------ -s mr.mrrefChr5 58461 50 + 294540 TTTCTCCAGTACCTCACAAAATCATGCTATGTACTGGAGATTTGCCCAGT -s simCow_chr6.simCow.chr6 202768 38 + 602619 CCTCTTGGGTACCTCCCAGAATCATCCCATGTGCTAGA------------ -s simDog_chr6.simDog.chr6 484269 38 - 593897 TCTCTTTGGTACCTCACAGAATTGGCCCATGTGCTAGA------------ -s simHuman_chr6.simHuman.chr6 206435 50 + 601863 TGTCTCCAGTTCCCCACAGAATCATCCCATATGATGGACACTCAGCTATT -s simRat_chr6.simRat.chr6 194071 50 + 647215 TTTCTCCAGTACCACACAAAATCATGCTATGTACTGGAGATTTGACCAGT - -a -s simMouse_chr6.simMouse.chr6 203831 9 + 636262 AAAGTTATG -s Anc0.Anc0refChr5 25263 7 + 87904 --AGTTATG -s Anc1.Anc1refChr8 39203 9 + 57822 AAAGTTATG -s Anc2.Anc2refChr15 19425 7 + 86568 --AGTCATG -s mr.mrrefChr5 58511 9 + 294540 AAAGTTATG -s simCow_chr6.simCow.chr6 202807 7 + 602619 --ACTCAAG -s simDog_chr6.simDog.chr6 484307 7 - 593897 --AGTCATG -s simHuman_chr6.simHuman.chr6 206545 9 + 601863 AAGGTTATG -s simRat_chr6.simRat.chr6 194121 9 + 647215 ACAGTTATG - -a -s simMouse_chr6.simMouse.chr6 203840 51 + 636262 AGACATGAAGTGTCAATATGTCCAAGGACATATGATGTCCTTACTCAAAAG -s Anc0.Anc0refChr5 25270 51 + 87904 AGATATGAAGTGTCAGTGTGTCCTAGGCCATGTGAAATCTTCACTTGGAGA -s Anc1.Anc1refChr8 39212 51 + 57822 AGATATGAAGTGTCAGTGTGTCCTAGGCCATGTGAAATCTTCACTTGGAGA -s Anc2.Anc2refChr15 19432 51 + 86568 AGTTATGAAGTGCCAGTGTGTCCTAGGCCCTGTGAAATCTTCACTTAGAGA -s mr.mrrefChr5 58520 51 + 294540 AGACATGAAGTGTCAATATGTCCAAGGACATATGATGTCCTCACTCGAAGG -s simCow_chr6.simCow.chr6 202820 51 + 602619 AGTTACGAAGCGCTGGCGTGCCCTAGTTGTTGAGAATTCTTCGATTAGAGG -s simDog_chr6.simDog.chr6 484314 48 - 593897 ---TGTGAAGTGCCAGTGTGTCCTAGGCCCAGTGAAATATTCACTTAGAAA -s simHuman_chr6.simHuman.chr6 206554 51 + 601863 AGATATGAAGTGTCTGTGTTTTCTAGGCCATGTGAAATCTTCATTTGGGGA -s simRat_chr6.simRat.chr6 194130 50 + 647215 GGTCATGAAGTGTCAATATGTCCAGGG-CATATGACGTCCTCACTCGAAGG - -a -s simMouse_chr6.simMouse.chr6 203891 34 + 636262 TATAATTGCATGATGTGTGAAGTGGTGCCTGCTC -s Anc0.Anc0refChr5 25321 34 + 87904 TATAACTGTATTATGTGTGAAGTGGTGTCTACCC -s Anc1.Anc1refChr8 39263 34 + 57822 TATAACTGTATTATGTGTGAAGTGGTGTCTACCC -s Anc2.Anc2refChr15 19483 34 + 86568 TATCACTGTATTATGTGTGAAGTGGTGTCTATCT -s mr.mrrefChr5 58571 34 + 294540 TATAATTGTATGATGTGTGAAGTGGTGCCTGCTC -s simCow_chr6.simCow.chr6 202871 26 + 602619 -------GTATTATGTGTGAAGTGGTGCCTA-CG -s simDog_chr6.simDog.chr6 484363 33 - 593897 TATCACTGTAT-ATCTGTGAAGTGATGTCCGTCT -s simHuman_chr6.simHuman.chr6 206605 34 + 601863 TATAACTGGATTATGTGTGAGATGGTGTCTACAC -s simRat_chr6.simRat.chr6 194180 25 + 647215 TATATTTGTATGATGTGTGATG---------CCC - -a -s simMouse_chr6.simMouse.chr6 203925 11 + 636262 TAATAGAATCT -s Anc0.Anc0refChr5 25372 11 + 87904 TGCCAAATTGC -s Anc1.Anc1refChr8 39314 11 + 57822 TGCCAAATTGC -s Anc2.Anc2refChr15 19534 11 + 86568 TGCCAAATTGC -s mr.mrrefChr5 58605 11 + 294540 TAATAGAATCT -s simCow_chr6.simCow.chr6 202914 11 + 602619 GGCCAATTTGC -s simDog_chr6.simDog.chr6 484413 11 - 593897 TGCCGAATTGC -s simHuman_chr6.simHuman.chr6 206656 9 + 601863 --CCAAATTGC -s simRat_chr6.simRat.chr6 194205 11 + 647215 TAACAGAATCT - -a -s simMouse_chr6.simMouse.chr6 203936 51 + 636262 CTTTATAGCTATAGCACTATGTAAATTATGACTTCATCAGAGGTACAATGA -s Anc0.Anc0refChr5 25383 51 + 87904 CTCTATAGATATAGAACTGTGTAAATTATTGCTTCATTGTAGGTACGATGA -s Anc1.Anc1refChr8 39325 51 + 57822 CTCTATAGATATAGAACTGTGTAAATTATTGCTTCATTGTAGGTACGATGA -s Anc2.Anc2refChr15 19545 51 + 86568 CTCTATAGATATAGAACTGTGTAAATTATTGCTACATTGTAGGTAAGATGA -s mr.mrrefChr5 58616 51 + 294540 CTTTATAGCTATAGCACTATGTAAATTATGACTTCATTGGAGGTACAATGA -s simCow_chr6.simCow.chr6 202927 51 + 602619 CTCTATGGATATAGAATTGAGTAAATTATGGCTGCATTGTAGGTAAGATGA -s simDog_chr6.simDog.chr6 484424 51 - 593897 TTCTATAGATGTAGAACTGTGTATATTATTGCTACATTGTAGGTAAGATGA -s simHuman_chr6.simHuman.chr6 206665 50 + 601863 CTCTATAGATATAGAACT-TGTGAATTAATTCTTCCTTGTTGGTACGATGA -s simRat_chr6.simRat.chr6 194216 50 + 647215 TTTTATAGCTATGACACTATGTAAATTATGACTTC-TTGAAGGGAAAATGA - -a -s simMouse_chr6.simMouse.chr6 203987 31 + 636262 CTGGCTCAAATTCCCATGTGATGACCATTGG -s Anc0.Anc0refChr5 25445 31 + 87904 CTGGTTAAAATTCCCATGTGATGACCAAAGG -s Anc1.Anc1refChr8 39387 31 + 57822 CTGGTTAAAATTCCCATGTGATGACCAAAGG -s Anc2.Anc2refChr15 19607 31 + 86568 CCCGTTAGGGTTCCCATGTGATGACCAAAGG -s mr.mrrefChr5 58667 31 + 294540 CTGGCTAAAATTCCCATGTGATGACCATTGG -s simCow_chr6.simCow.chr6 202989 31 + 602619 CCCGTTAGGGTTCCCATCTGATGACCAAAGG -s simDog_chr6.simDog.chr6 484475 19 - 593897 ------------CCCATGTGATGACTAAAGG -s simHuman_chr6.simHuman.chr6 206726 31 + 601863 CTGGTTAAAATTCCCATGTGATGACCAGAGG -s simRat_chr6.simRat.chr6 194266 31 + 647215 CTGGCTAAAATTCCCATGTGTTGACCATTGG - -a -s simMouse_chr6.simMouse.chr6 204018 4 + 636262 AGCA -s Anc0.Anc0refChr5 25477 4 + 87904 AGCA -s Anc1.Anc1refChr8 39419 4 + 57822 AGCA -s Anc2.Anc2refChr15 19639 4 + 86568 ACCA -s mr.mrrefChr5 58698 4 + 294540 AGCA -s simCow_chr6.simCow.chr6 203021 4 + 602619 ACTG -s simDog_chr6.simDog.chr6 484495 4 - 593897 ACCA -s simHuman_chr6.simHuman.chr6 206758 4 + 601863 AGCA -s simRat_chr6.simRat.chr6 194297 4 + 647215 AGTG - -a -s simMouse_chr6.simMouse.chr6 204022 5 + 636262 CATTG -s Anc0.Anc0refChr5 25491 5 + 87904 AGTTG -s Anc1.Anc1refChr8 39433 5 + 57822 AGTTG -s Anc2.Anc2refChr15 19653 5 + 86568 AGTTG -s mr.mrrefChr5 58702 5 + 294540 CATTG -s simCow_chr6.simCow.chr6 203035 5 + 602619 AGTTC -s simDog_chr6.simDog.chr6 484509 5 - 593897 AGTTG -s simHuman_chr6.simHuman.chr6 206773 5 + 601863 AGTTG -s simRat_chr6.simRat.chr6 194301 5 + 647215 CATTG - -a -s simMouse_chr6.simMouse.chr6 204027 7 + 636262 GGCTTTC -s Anc0.Anc0refChr5 25496 7 + 87904 TGCTTTT -s Anc1.Anc1refChr8 39438 7 + 57822 TGCTTTT -s Anc2.Anc2refChr15 19658 7 + 86568 TGCTTTT -s mr.mrrefChr5 58707 7 + 294540 TGCTTTT -s simCow_chr6.simCow.chr6 203040 7 + 602619 TACCTTT -s simDog_chr6.simDog.chr6 484514 7 - 593897 TGCTTTT -s simHuman_chr6.simHuman.chr6 206778 7 + 601863 TGCTTTT -s simRat_chr6.simRat.chr6 194317 7 + 647215 TGCATTT - -a -s simMouse_chr6.simMouse.chr6 204034 30 + 636262 CAGACCATTGTTGCCACTACATCTATGGTG -s Anc0.Anc0refChr5 25504 27 + 87904 CAGTC---TGTTGCCACTGCATCTATTGTA -s Anc1.Anc1refChr8 39446 27 + 57822 CAGTC---TGTTGCCACTGCATCTATTGTA -s Anc2.Anc2refChr15 19666 27 + 86568 CAGTC---CCTTGCCACTGCATCTATTGTA -s mr.mrrefChr5 58715 30 + 294540 CAGACCATTGTTGCCACTACATCTATGGTA -s simCow_chr6.simCow.chr6 203048 27 + 602619 CAGTC---CTTTGCCACTGCATCTATTTTA -s simDog_chr6.simDog.chr6 484522 27 - 593897 CAGTC---CCTTACCACTACATCTATTGAA -s simHuman_chr6.simHuman.chr6 206786 27 + 601863 TAGGC---TGTTGTCACTGCATTTATTATA -s simRat_chr6.simRat.chr6 194325 30 + 647215 CAGCCCATTGTTGCCACTACATCTATGGTA - -a -s simMouse_chr6.simMouse.chr6 204064 116 + 636262 TGGGACCACTCCGTAAGCATTTTGGAGTTTAGAGCAATAGTGAAATCGGGAGGTATTCCTATGGAACGCGTTGACAGCATGGTCCTAACCCCGGAATCCACGTCTCGACCCATCAG -s Anc0.Anc0refChr5 25531 1 + 87904 T------------------------------------------------------------------------------------------------------------------- -s Anc1.Anc1refChr8 39473 1 + 57822 T------------------------------------------------------------------------------------------------------------------- -s Anc2.Anc2refChr15 19693 1 + 86568 T------------------------------------------------------------------------------------------------------------------- -s mr.mrrefChr5 58745 1 + 294540 T------------------------------------------------------------------------------------------------------------------- -s simCow_chr6.simCow.chr6 203076 1 + 602619 T------------------------------------------------------------------------------------------------------------------- -s simDog_chr6.simDog.chr6 484549 1 - 593897 C------------------------------------------------------------------------------------------------------------------- -s simHuman_chr6.simHuman.chr6 206813 1 + 601863 T------------------------------------------------------------------------------------------------------------------- -s simRat_chr6.simRat.chr6 194355 1 + 647215 T------------------------------------------------------------------------------------------------------------------- - -a -s simMouse_chr6.simMouse.chr6 204180 7 + 636262 AGTGATG -s Anc0.Anc0refChr5 25534 7 + 87904 AGTAATG -s Anc1.Anc1refChr8 39476 7 + 57822 AGTAATG -s Anc2.Anc2refChr15 19696 7 + 86568 CATAATG -s mr.mrrefChr5 58746 7 + 294540 AGTGATG -s simCow_chr6.simCow.chr6 203079 7 + 602619 CATAATG -s simDog_chr6.simDog.chr6 484552 5 - 593897 --TAATG -s simHuman_chr6.simHuman.chr6 206816 7 + 601863 AGTAATG -s simRat_chr6.simRat.chr6 194356 7 + 647215 AGTTATG - -a -s simMouse_chr6.simMouse.chr6 204187 7 + 636262 GACCTGT -s Anc0.Anc0refChr5 25541 7 + 87904 GGCCTGT -s Anc1.Anc1refChr8 39483 7 + 57822 GGCCTGT -s Anc2.Anc2refChr15 19703 7 + 86568 AGCCTGT -s mr.mrrefChr5 58753 7 + 294540 GACCTGT -s simCow_chr6.simCow.chr6 203086 7 + 602619 AACCTGT -s simDog_chr6.simDog.chr6 484557 7 - 593897 AGCCTGT -s simHuman_chr6.simHuman.chr6 206940 7 + 601863 GTCCTGT -s simRat_chr6.simRat.chr6 194363 7 + 647215 AACCTGT - -a -s simMouse_chr6.simMouse.chr6 204194 7 + 636262 GGCAGAA -s Anc0.Anc0refChr5 25548 7 + 87904 GGCAAAT -s Anc1.Anc1refChr8 39490 7 + 57822 GGCAAAT -s Anc2.Anc2refChr15 19710 7 + 86568 GGCAAAT -s mr.mrrefChr5 58760 7 + 294540 GGCAGAA -s simCow_chr6.simCow.chr6 203097 7 + 602619 GCCAAAT -s simDog_chr6.simDog.chr6 484564 7 - 593897 GGCAAGG -s simHuman_chr6.simHuman.chr6 206947 7 + 601863 GGCAAAT -s simRat_chr6.simRat.chr6 194370 7 + 647215 GGCAGAA - -a -s simMouse_chr6.simMouse.chr6 204201 11 + 636262 CATACACTTCC -s Anc0.Anc0refChr5 25555 11 + 87904 TACATACTTCC -s Anc1.Anc1refChr8 39497 11 + 57822 TACATACTTCC -s Anc2.Anc2refChr15 19717 11 + 86568 TACATACTTCC -s mr.mrrefChr5 58767 11 + 294540 CATATACTTCC -s simCow_chr6.simCow.chr6 377615 11 - 602619 TACACACTTCC -s simDog_chr6.simDog.chr6 484571 11 - 593897 TACATACTTCC -s simHuman_chr6.simHuman.chr6 206954 11 + 601863 TACATACTACC -s simRat_chr6.simRat.chr6 194377 11 + 647215 CATATACTTCC - -a -s simMouse_chr6.simMouse.chr6 204212 35 + 636262 TGTCTATAAGAGTCACATGCTTGCGGGCCTGAAGG -s Anc0.Anc0refChr5 25566 35 + 87904 TTCCTACAGGAGTCACATATCAGAGGGCTTCACGG -s Anc1.Anc1refChr8 39508 35 + 57822 TTCCTACAGGAGTCACATATCAGAGGGCTTCACGG -s Anc2.Anc2refChr15 19728 35 + 86568 TTCCTACAGGAGACACATACCAGAGGGCTTCACAG -s mr.mrrefChr5 58778 35 + 294540 TTTCTATAGGAGTCACATGTTTGAGGGCCTGAAGG -s simCow_chr6.simCow.chr6 377647 35 - 602619 TTTCTACAGGAGACTCATGCCATAGGGCTTCACAG -s simDog_chr6.simDog.chr6 484582 35 - 593897 TTCCTACAGGAGACACATACCAGCGGGCATCACAG -s simHuman_chr6.simHuman.chr6 206965 34 + 601863 TTG-TACAGGATTCACATATCAGAGGGATTCATGG -s simRat_chr6.simRat.chr6 194388 35 + 647215 CTTCTATGGGAGTCACCTGTTTGAGGGCCTGAAAG - -a -s simMouse_chr6.simMouse.chr6 204247 29 + 636262 GGCTAACCCCTCCATTGAAGCTTTCATGG -s Anc0.Anc0refChr5 25607 23 + 87904 ACGTAGCTCCCACATCAA------CATGG -s Anc1.Anc1refChr8 39549 23 + 57822 ACGTAGCTCCCACATCAA------CATGG -s Anc2.Anc2refChr15 19769 23 + 86568 ACGTAGCTCCCACATCAA------CATGG -s mr.mrrefChr5 58819 29 + 294540 GGCTAACCCCTCCATTGAAGCTTTCATGG -s simCow_chr6.simCow.chr6 377688 21 - 602619 AGGTACCTCCCACAT-AT------TAT-G -s simDog_chr6.simDog.chr6 484623 23 - 593897 ACGTAGCTCCCACATCAA------CATGG -s simHuman_chr6.simHuman.chr6 207005 23 + 601863 ATTTATCTCTCACATCAG------CACAG -s simRat_chr6.simRat.chr6 194429 29 + 647215 GGCTAACCCCTGCATTGAAGCTTTCATGG - -a -s simMouse_chr6.simMouse.chr6 204276 23 + 636262 ATCAATAGATAAACTTTTACCTG -s Anc0.Anc0refChr5 25630 23 + 87904 ATATGGTGACAACCTTTTGTCTG -s Anc1.Anc1refChr8 39572 23 + 57822 ATATGGTGACAACCTTTTGTCTG -s Anc2.Anc2refChr15 19792 23 + 86568 ATACGGTGACTACCTTTTGGCTG -s mr.mrrefChr5 58848 23 + 294540 ATCTAGTGATAAACTTTTATCTG -s simCow_chr6.simCow.chr6 377709 23 - 602619 ATACGGTGACTACCTTTTGCCTG -s simDog_chr6.simDog.chr6 484651 23 - 593897 ATACCGTGACTAAGTTTCGGTGG -s simHuman_chr6.simHuman.chr6 207028 23 + 601863 ATATGGTGACAACCTTATGTCTG -s simRat_chr6.simRat.chr6 194458 23 + 647215 ATCTAGTGATTAACTTTTATCTG - -a -s simMouse_chr6.simMouse.chr6 204299 104 + 636262 CACTTCAGCAGACTTCACACACTGTAGCTATGCCACACATCAGGGGTGTCATAGCTCCAATTACCAGTCAGTCATGGGGACGGATACTATTACCTCCTGCCTTA -s Anc0.Anc0refChr5 25658 51 + 87904 C------------------------------------------------TATAACTCTAATTACCAGTCAGTCATAAA-----ATGACAATATCCTCCACCTTA -s Anc1.Anc1refChr8 39600 51 + 57822 C------------------------------------------------TATAACTCTAATTACCAGTCAGTCATAAA-----ATGACAATATCCTCCACCTTA -s Anc2.Anc2refChr15 19820 51 + 86568 C------------------------------------------------TATAACTCTAATTACCAGTCAGTCATAAA-----ATGACAATATCCTCCACCTTA -s mr.mrrefChr5 58876 99 + 294540 CACTTCAGCAGACTTCACACACTGTAGCTATGCCACACATCAGGGGTGTCATAACTCTAATTACCAGTCAGTCATGGG-----ATACTATTACCTCCTACCTTA -s simCow_chr6.simCow.chr6 377737 51 - 602619 C------------------------------------------------TAAGACTCTATTTATCAGTTAGTCATAAG-----ATGACAATCTCCTCCACCTTA -s simDog_chr6.simDog.chr6 484679 51 - 593897 C------------------------------------------------TATAACTCTAATTACTAGTCAGTTGTACA-----AAGACAATATCCTCCACCTTA -s simHuman_chr6.simHuman.chr6 207056 51 + 601863 C------------------------------------------------TAGAACTCTAATTACCTGTCAGTCATAAA-----GTGGCAATTTCCTCCACCTTA -s simRat_chr6.simRat.chr6 194486 99 + 647215 CACTTCAGAGCACTTCACACACTGTAGTCATGTCACACATCAGGGGTGTCACAACTCTAATTACCAGTCAGTCATGGG-----ATACTATTACCTCCTACCCTA - -a -s simMouse_chr6.simMouse.chr6 204403 35 + 636262 AAATGCCATCAGACGCCAGCATAACAGCCCTTAAA -s Anc0.Anc0refChr5 25711 35 + 87904 GAACACCTACAGACGCAAACTTCCCAGCACCAAAA -s Anc1.Anc1refChr8 39653 35 + 57822 GAACACCTACAGACGCAAACTTCCCAGCACCAAAA -s Anc2.Anc2refChr15 19873 35 + 86568 GGACACCTACAGACACAAACTTCCCAGCACCAAAA -s mr.mrrefChr5 58975 35 + 294540 AAACGTCATCAGACGCCAGCATCACAGCCCTTAAA -s simCow_chr6.simCow.chr6 377790 35 - 602619 GTACACCTCCAGAAACAGACTGCCCAGCACCAAAT -s simDog_chr6.simDog.chr6 484732 34 - 593897 GGAAACCTA-AGACACAAACTTCCTAGCCCCACAA -s simHuman_chr6.simHuman.chr6 207109 35 + 601863 GAACACTTACAGACGCACACTTCCCCCCACCAAAA -s simRat_chr6.simRat.chr6 194585 35 + 647215 AAACGTCGTCAGATGCTAGCATCACAGCCCTTAAA - -a -s simMouse_chr6.simMouse.chr6 204438 21 + 636262 GTGCCTGTGATTTCCTAAACA -s Anc0.Anc0refChr5 25746 21 + 87904 GTGCCTATGACCCTCCCAATC -s Anc1.Anc1refChr8 39688 21 + 57822 GTGCCTATGACCCTCCCAATC -s Anc2.Anc2refChr15 19908 21 + 86568 GTGTCTATGACCCTCTCACTC -s mr.mrrefChr5 59010 21 + 294540 GTGCCTGTGATTTCCCAAACG -s simCow_chr6.simCow.chr6 377832 21 - 602619 GTGTCTTTGGCCCCCTCACTC -s simDog_chr6.simDog.chr6 484766 21 - 593897 GTGTCTATGACCTTCTCACTG -s simHuman_chr6.simHuman.chr6 207144 21 + 601863 GTACCTATGACCCTACCAATC -s simRat_chr6.simRat.chr6 194620 21 + 647215 GTGCCTGTGATTTCCCAAACG - -a -s simMouse_chr6.simMouse.chr6 204459 6 + 636262 CCAGTC -s Anc0.Anc0refChr5 25767 6 + 87904 CCAGTT -s Anc1.Anc1refChr8 39709 6 + 57822 CCAGTT -s Anc2.Anc2refChr15 19929 6 + 86568 CCAGTT -s mr.mrrefChr5 59031 6 + 294540 CCAGTC -s simCow_chr6.simCow.chr6 377856 6 - 602619 CCAGTT -s simDog_chr6.simDog.chr6 484787 6 - 593897 CCAGTT -s simHuman_chr6.simHuman.chr6 207165 6 + 601863 CCAGTT -s simRat_chr6.simRat.chr6 194641 6 + 647215 CCAGTC - -a -s simMouse_chr6.simMouse.chr6 204465 32 + 636262 ATTGTGGCCCAATCATCAATACAGTACATAAA -s Anc0.Anc0refChr5 25778 15 + 87904 -----------------CATTATAACCATGAA -s Anc1.Anc1refChr8 39720 15 + 57822 -----------------CATTATAACCATGAA -s Anc2.Anc2refChr15 19940 15 + 86568 -----------------CATTATAACCATGAA -s mr.mrrefChr5 59042 32 + 294540 ATTGTGGCCCAATCATCCATTCTGTACATGAA -s simCow_chr6.simCow.chr6 377867 15 - 602619 -----------------CAGTACAACCAAGAA -s simDog_chr6.simDog.chr6 484798 15 - 593897 -----------------CATTATGACCATTAA -s simHuman_chr6.simHuman.chr6 207176 15 + 601863 -----------------CATTATAATCATGAA -s simRat_chr6.simRat.chr6 194700 32 + 647215 ATTGCATCCCAATTATGCATTCTGTGCATGAA - -a -s simMouse_chr6.simMouse.chr6 204497 51 + 636262 TGGTCCTCCAAACACAATGTATTAAACTATGCCCAAATTGGTGTTATGATG -s Anc0.Anc0refChr5 25793 39 + 87904 TGATTCTCCAAACACGGTGTATTAAATCATGCCAAATTT------------ -s Anc1.Anc1refChr8 39735 39 + 57822 TGATTCTCCAAACACGGTGTATTAAATCATGCCAAATTT------------ -s Anc2.Anc2refChr15 19965 39 + 86568 TGATTCTCCAAACACGGTGTATTACATCATGCCAAATTT------------ -s mr.mrrefChr5 59074 51 + 294540 TGGTCCTCCAAACACAATGTATTAAACTATGCCAAATTTGGTGTTATGATG -s simCow_chr6.simCow.chr6 377895 30 - 602619 TGATTCTCTGCACGCGGTGTATT---------CAGATTT------------ -s simDog_chr6.simDog.chr6 484823 39 - 593897 TGATTCTCCAAACAAAGTGTATAACATCATGCCAAATTT------------ -s simHuman_chr6.simHuman.chr6 207191 32 + 601863 -------CACAACACGGTGTATTAAATCATGACAAATTT------------ -s simRat_chr6.simRat.chr6 194732 51 + 647215 TGGTCCTCTAAACACACTGTATCAAACTATGCTAAATTTGGTGTTATGATG - -a -s simMouse_chr6.simMouse.chr6 204548 59 + 636262 CATTAGGATGCCAATGGTCCTCCAAACCCAATGTATTAAATCACACTGGATTCAGTTCT -s Anc0.Anc0refChr5 25832 5 + 87904 ------------------------------------------------------ATTAT -s Anc1.Anc1refChr8 39774 5 + 57822 ------------------------------------------------------ATTAT -s Anc2.Anc2refChr15 20004 5 + 86568 ------------------------------------------------------AGTAT -s mr.mrrefChr5 59134 59 + 294540 TATTAGGATGCCAATGGTCCTCCAAACACAATGTATTAATTCACACTGGATTTGGTTCT -s simCow_chr6.simCow.chr6 377925 5 - 602619 ------------------------------------------------------AGAAT -s simDog_chr6.simDog.chr6 484862 5 - 593897 ------------------------------------------------------AGTAT -s simHuman_chr6.simHuman.chr6 207223 5 + 601863 ------------------------------------------------------ATTAT -s simRat_chr6.simRat.chr6 194792 59 + 647215 TATTAGGATGCCAATGGTTCTCCAAACACAATCTATTAATCCACACCAAATTTGGTTCT - -a -s simMouse_chr6.simMouse.chr6 204607 59 + 636262 TAGGGTGCAATAGGCCAGTTGATAGAAGATTAATGCCTGCACTTTAAGATTGTCCTTAG -s Anc0.Anc0refChr5 25837 57 + 87904 TTGGAT--AATGGGTGAGTTGATTGAAGAGTACTGTTTGTGTTTTGAGATTGTCCTTAG -s Anc1.Anc1refChr8 39779 59 + 57822 TTGGATTCAATGGGTGAGTTGATTGAAGAGTACTGTTTGTGTTTTGAGATTGTCCTTAG -s Anc2.Anc2refChr15 20009 57 + 86568 TTGAAT--AATGGGTGATTTGACTGAAGAGTACTGTTTGTGTTTTGGGATTGTCCCTAG -s mr.mrrefChr5 59193 59 + 294540 TAGGATGCAATAGGCCAGTTGATAGAAGAGTAATGCCTGCACTTTAAGATTGTCCTTAG -s simCow_chr6.simCow.chr6 377932 52 - 602619 TCCAAT--AATGGGTAACT-----GAAGAGTACTGTTTGTGTTTTGAGATTATCCCTAC -s simDog_chr6.simDog.chr6 484867 57 - 593897 TTGAAT--AATAGGTGATTTGACTCTAGAGTACTGTTAGTTTTTTGGGATTGTCCTTAG -s simHuman_chr6.simHuman.chr6 207228 59 + 601863 TGGGATTCAATGGGTGAGTTGATCGAAGAGTACTGTTTGTGTTTTGAGAGTGTTTTTGG -s simRat_chr6.simRat.chr6 194851 59 + 647215 TAGGATGCAATAGGCCAGTTGCTAGAAGAGTAATGCCTTCACTTTCATATTGTCACTAG - -a -s simMouse_chr6.simMouse.chr6 204666 66 + 636262 TATTCAAAGTGTATATTCTGTGGTGGGTACCTTGCTGTTCTATCCTATTCTTACCAAATATCCTCT -s Anc0.Anc0refChr5 25894 66 + 87904 TATTCAGTGTGTATGTTCTGTGTTGGGTGTGTTGTTGTTCTATTAAAATCTCTTCAGACATCACCT -s Anc1.Anc1refChr8 39844 66 + 57822 TATTCAGTGTGTATGTTCTGTGTTGGGTGTGTTGTTGTTCTATTAAAATCTCTTCAGACATCACCT -s Anc2.Anc2refChr15 20066 66 + 86568 CATTCAGTGTGTATGTTCTGTGTGGGGTGTGTTGTTGTTCTATTAACATCTCTTCAGACACCACCT -s mr.mrrefChr5 59258 66 + 294540 TATTCAATGTGTATATTCTGTGGTGGGTACCTTGTTGTTCTATCCTATTCTTACCAAATATCCCCT -s simCow_chr6.simCow.chr6 377984 44 - 602619 CATTCAGTGTATATGT----------------------TCCATTACTATCTATCCAGACACCACCT -s simDog_chr6.simDog.chr6 484924 65 - 593897 CATTCAGTGTGTATGTTCTGTGTGGGGTGTGTTGTTGTACTGTTAACATCTC-TCAAACACCACCT -s simHuman_chr6.simHuman.chr6 207299 65 + 601863 TATCCAGTGTGTTATTACTGTGTTGGGTGTGTTGTTGTTCTATTTAA-TCTCTTCAGACCTTACCT -s simRat_chr6.simRat.chr6 194916 66 + 647215 TATTCAATGTGTACATTCTGTGGTGGGCACTTTGTTCTTATGTCCCAGTCTCACCAAATATCCCCT - -a -s simMouse_chr6.simMouse.chr6 204732 77 + 636262 CTTTCACTGTATTACTATGCTGTTGTGGTAAAATTGACCATGTGCTACTTGACCATATACTGTAATTGGCCCAGGTA -s Anc0.Anc0refChr5 25961 72 + 87904 TTTTTGCTG--TTGCTGTGATGCTATTGTTAATTTGCTGATATGACATTTAACCATAGAC---AATTGGCACAGAAG -s Anc1.Anc1refChr8 39911 72 + 57822 TTTTTGCTG--TTGCTGTGATGCTATTGTTAATTTGCTGATATGACATTTAACCATAGAC---AATTGGCACAGAAG -s Anc2.Anc2refChr15 20133 72 + 86568 TTTTTGCTG--TTGCTGTGATGCTATTGTTACTTTGCTGATATGACATTTAACCATAAAC---AGTTGGCACAGAAG -s mr.mrrefChr5 59324 77 + 294540 CTTTTACTGTATTACTATGCTGTTGTGGTAAAATTGATCATGTGATATTTGACCATAGACTGTAATTGGCACAGGAA -s simCow_chr6.simCow.chr6 378029 72 - 602619 TTCTTTCTG--TTGATGTAATGCTATTGTGAGTTTGCTGGTATCGCATTTAACCATAAAC---GATTGGCAGAGAAA -s simDog_chr6.simDog.chr6 484990 72 - 593897 TTTTTGCTG--TAGCTGTGATGTTATTAGTACTTTGCTGATATGATATTTAACCATAAGC---AGTTGGCACAGAAG -s simHuman_chr6.simHuman.chr6 207365 71 + 601863 TTTTTGCTG--TTCCTGTGATGCTCTTGTTGATTTGCTGAGATGACATTCAGCCATAGAT----ATTGGCACAGAAC -s simRat_chr6.simRat.chr6 194982 77 + 647215 CTTTTACTGTCTTACTATGCTGTTATGGTCAAATTGATCATGTGATATTTGAGCGTAGGCTGTAATTGGCACAGGAA - -a -s simMouse_chr6.simMouse.chr6 204809 2 + 636262 AG -s Anc0.Anc0refChr5 26040 2 + 87904 CA -s Anc1.Anc1refChr8 39990 2 + 57822 CA -s Anc2.Anc2refChr15 20212 2 + 86568 CA -s mr.mrrefChr5 59408 2 + 294540 AG -s simCow_chr6.simCow.chr6 378108 2 - 602619 CA -s simDog_chr6.simDog.chr6 485069 2 - 593897 CA -s simHuman_chr6.simHuman.chr6 207443 2 + 601863 CT -s simRat_chr6.simRat.chr6 195066 2 + 647215 AG - -a -s simMouse_chr6.simMouse.chr6 204811 40 + 636262 ATGTTTGCAATTATCATCTTGATCATCACAGTACTGTGAT -s Anc0.Anc0refChr5 26043 29 + 87904 TTGTCTGTA------ATT---CTCATTGCAGTACTG--AT -s Anc1.Anc1refChr8 39993 29 + 57822 TTGTCTGTA------ATT---CTCATTGCAGTACTG--AT -s Anc2.Anc2refChr15 20215 29 + 86568 TTGTCTGTA------ATT---CTCATTGCAGTACTG--AT -s mr.mrrefChr5 59410 35 + 294540 ATGTTTGCAATTATCATT---ATCATCACAGTACTG--AT -s simCow_chr6.simCow.chr6 378111 29 - 602619 TTATCTCTT------ATA---CCCATTGCAGGTCTG--GT -s simDog_chr6.simDog.chr6 485072 29 - 593897 TTGTTAGTA------ATT---CTCATTGCAGTACTG--AT -s simHuman_chr6.simHuman.chr6 207446 29 + 601863 TTGACTGTA------ATT---CTCATTGCAGTACTA--AT -s simRat_chr6.simRat.chr6 195068 35 + 647215 ATGTTTGCAATAATCATT---ATCATCATAGTACTG--GT - -a -s simMouse_chr6.simMouse.chr6 204851 43 + 636262 CTTTATAACTGAACATAACAAGATTATGCTGTTTGTTGGAACA -s Anc0.Anc0refChr5 26072 43 + 87904 CTTTACAGCTGAACATTACAAGATTAAGCTGCTTCTTGGACCA -s Anc1.Anc1refChr8 40022 43 + 57822 CTTTACAGCTGAACATTACAAGATTAAGCTGCTTCTTGGACCA -s Anc2.Anc2refChr15 20244 43 + 86568 CTTTACAGCTGAATATTACAAGATTAAGCTGCTTCTTGGCCCA -s mr.mrrefChr5 59445 43 + 294540 CTTTATAACTGAACATAACAAGATTATGCTGTTTGTTGGAACA -s simCow_chr6.simCow.chr6 378140 43 - 602619 CTTTACTGCTGAATATTACAAGATGAAGCGGCTTCTTGGTCCA -s simDog_chr6.simDog.chr6 485118 43 - 593897 CTTTACAGCTGTATATTAGAAGATTAAGGTGCTTCTCGGCTTA -s simHuman_chr6.simHuman.chr6 207475 43 + 601863 CTTTAAAGCTGAACATTACAAGATCAAGCTACATCTTGGACCA -s simRat_chr6.simRat.chr6 195103 43 + 647215 CTTTATAACTGCATGTAACAAGATTATGCTGTTTGTTGGTACA - -a -s simMouse_chr6.simMouse.chr6 204894 9 + 636262 GCAATTAAG -s Anc0.Anc0refChr5 26115 9 + 87904 ATAACTAAG -s Anc1.Anc1refChr8 40065 9 + 57822 ATAACTAAG -s Anc2.Anc2refChr15 20287 9 + 86568 ATAACTAAG -s mr.mrrefChr5 59488 9 + 294540 ACAATTAAG -s simCow_chr6.simCow.chr6 378183 7 - 602619 ACAA--GAC -s simDog_chr6.simDog.chr6 485166 9 - 593897 ATAACTAAG -s simHuman_chr6.simHuman.chr6 207518 9 + 601863 ATAACCAAG -s simRat_chr6.simRat.chr6 195146 9 + 647215 ACAAATAAG - -a -s simMouse_chr6.simMouse.chr6 204903 2 + 636262 CA -s Anc0.Anc0refChr5 26135 2 + 87904 CA -s Anc1.Anc1refChr8 40085 2 + 57822 CA -s Anc2.Anc2refChr15 20315 2 + 86568 CA -s mr.mrrefChr5 59497 2 + 294540 CA -s simCow_chr6.simCow.chr6 378216 2 - 602619 CA -s simDog_chr6.simDog.chr6 485194 2 - 593897 CA -s simHuman_chr6.simHuman.chr6 207538 2 + 601863 CA -s simRat_chr6.simRat.chr6 195155 2 + 647215 TA - -a -s simMouse_chr6.simMouse.chr6 204905 53 + 636262 AGTGGTATATATAACTCCTGGTGCAACTAATTAAAGTAACAATTTTGTTAAAC -s Anc0.Anc0refChr5 26137 52 + 87904 CATGAACCAAATGAG-CCAGGTGCACTTAAAAAAAGTAAAGTTTTTATGAAAC -s Anc1.Anc1refChr8 40087 52 + 57822 CATGAACCAAATGAG-CCAGGTGCACTTAAAAAAAGTAAAGTTTTTATGAAAC -s Anc2.Anc2refChr15 20335 52 + 86568 CATAAACCAAATGAG-CCAGGTGCTCTTAAAAAAAGTAAAGTTTTTATGAAAC -s mr.mrrefChr5 59499 53 + 294540 AGTGGAATATATAACTCCTGGTGCACCTAATAAAAGTAACGATTTTGTTAAAC -s simCow_chr6.simCow.chr6 378236 50 - 602619 --TAAACCAAATGGG-CTAGGTGCTCTTAAAAAAAGTAAAGTTTTCATAAAAC -s simDog_chr6.simDog.chr6 485221 52 - 593897 CAGAAGCCAAATGAG-CCAGGTGCTCTTAAAAAAAGTGCTGTATTTGTGAACT -s simHuman_chr6.simHuman.chr6 207540 52 + 601863 CATGAACCAAATGAG-CCATGTGTACTCAAAAAAAGTAAAGTTTTTATGCAAC -s simRat_chr6.simRat.chr6 195157 48 + 647215 AGTGGAATATA-----CCCAGCACACCTAATAAAATTAATGATTTTGTTAAGC - -a -s simMouse_chr6.simMouse.chr6 204958 4 + 636262 CAAT -s Anc0.Anc0refChr5 26192 4 + 87904 CAAT -s Anc1.Anc1refChr8 40142 4 + 57822 CAAT -s Anc2.Anc2refChr15 20390 4 + 86568 CAAT -s mr.mrrefChr5 59552 4 + 294540 CAAT -s simCow_chr6.simCow.chr6 378289 4 - 602619 CAAT -s simDog_chr6.simDog.chr6 485276 4 - 593897 CAAA -s simHuman_chr6.simHuman.chr6 207595 4 + 601863 CAAT -s simRat_chr6.simRat.chr6 195205 4 + 647215 CAAT - -a -s simMouse_chr6.simMouse.chr6 204962 44 + 636262 CCAGAGCAATTGGTACATAGGGAAGAAGAGATCTCACCTCTGAG -s Anc0.Anc0refChr5 26196 42 + 87904 CCAGAGTCATTGGTACATAGGGAAGAAAAGAGCATAC--CAGAG -s Anc1.Anc1refChr8 40146 44 + 57822 CCAGAGTCATTGGTACATAGGGAAGAAAAGAGCATACGTCAGAG -s Anc2.Anc2refChr15 20394 42 + 86568 CCAGAGTCAGTGGTACATAGGGAAGAAAAGAGCATAC--CAGAG -s mr.mrrefChr5 59556 44 + 294540 CCAGAGCAATTGGTACATAGGGAAGAAGAGATCTCACCTCTGAG -s simCow_chr6.simCow.chr6 378310 42 - 602619 CCAGAGTCAGTGGTCCCCAGGGAAGCAAAGAGGGAAC--CGGAG -s simDog_chr6.simDog.chr6 485280 42 - 593897 CCAGAGTCAGTGGTACATAGGGAAAAAAAGAGCATAC--CAGAG -s simHuman_chr6.simHuman.chr6 207599 43 + 601863 CCAGAGTCATTGGTTCATA-GGAAGAAAAGGGCATATGTCATAG -s simRat_chr6.simRat.chr6 195209 44 + 647215 CCAGAGCAATCGATACATAGGGAAGAAGAGATCTCACCTCTGAG - -a -s simMouse_chr6.simMouse.chr6 205006 16 + 636262 ATCAGTGAAGCTATAT -s Anc0.Anc0refChr5 26251 16 + 87904 GTAAGTGGAGCTATAA -s Anc1.Anc1refChr8 40203 16 + 57822 GTAAGTGGAGCTATAA -s Anc2.Anc2refChr15 20449 16 + 86568 GTAAGTGGAGCTACAA -s mr.mrrefChr5 59600 16 + 294540 ATCAGTGGAGCTATAT -s simCow_chr6.simCow.chr6 378365 16 - 602619 GTAAGTGGAGCTGCAA -s simDog_chr6.simDog.chr6 485335 16 - 593897 GTAAGTGGAGCTACAA -s simHuman_chr6.simHuman.chr6 207655 16 + 601863 CTAACTGGAGCTATAA -s simRat_chr6.simRat.chr6 195253 16 + 647215 ATCAGTGGAGCTATAT - -a -s simMouse_chr6.simMouse.chr6 205022 21 + 636262 GAAGATGAGTGTAACTGGCAA -s Anc0.Anc0refChr5 26267 21 + 87904 GAGGATGACTGTAACTGGTAA -s Anc1.Anc1refChr8 40219 21 + 57822 GAGGATGACTGTAACTGGTAA -s Anc2.Anc2refChr15 20468 21 + 86568 GAGGATGACTGTAACTGGTAA -s mr.mrrefChr5 59616 21 + 294540 GAGGATGAGTGTAACTGGTAA -s simCow_chr6.simCow.chr6 378384 12 - 602619 GA---------TAATTGGCAA -s simDog_chr6.simDog.chr6 485354 21 - 593897 GAGGATGACTGTAACTGGTGG -s simHuman_chr6.simHuman.chr6 207671 21 + 601863 GAGGATGACTTTAACTGGTAA -s simRat_chr6.simRat.chr6 195269 21 + 647215 GAGGATGAGTGTAACTGATAA - -a -s simMouse_chr6.simMouse.chr6 205043 3 + 636262 GCC -s Anc0.Anc0refChr5 26289 3 + 87904 GCC -s Anc1.Anc1refChr8 40241 3 + 57822 GCC -s Anc2.Anc2refChr15 20490 3 + 86568 ACC -s mr.mrrefChr5 59637 3 + 294540 GGC -s simCow_chr6.simCow.chr6 378397 3 - 602619 ACA -s simDog_chr6.simDog.chr6 485376 3 - 593897 ACC -s simHuman_chr6.simHuman.chr6 207693 3 + 601863 GTT -s simRat_chr6.simRat.chr6 195290 3 + 647215 GGC - -a -s simMouse_chr6.simMouse.chr6 205046 9 + 636262 TTTATGAGC -s Anc0.Anc0refChr5 26292 9 + 87904 TTTATGAGC -s Anc1.Anc1refChr8 40244 9 + 57822 TTTATGAGC -s Anc2.Anc2refChr15 20493 9 + 86568 TTTATGAGC -s mr.mrrefChr5 59640 9 + 294540 TTTATGAGC -s simCow_chr6.simCow.chr6 378400 9 - 602619 TCTATGTCT -s simDog_chr6.simDog.chr6 485417 9 - 593897 TTTATGAGC -s simHuman_chr6.simHuman.chr6 207696 9 + 601863 TTTAGGAGC -s simRat_chr6.simRat.chr6 195293 9 + 647215 TTTATGAGC - -a -s simMouse_chr6.simMouse.chr6 205055 21 + 636262 CTAGTAGCAAGTAAAAAGAGG -s Anc0.Anc0refChr5 26331 21 + 87904 CTAGCAGCAAGTAAGAGGAAA -s Anc1.Anc1refChr8 40283 21 + 57822 CTAGCAGCAAGTAAGAGGAAA -s Anc2.Anc2refChr15 20532 21 + 86568 CTAGCAGCAAGTAAGAGGAAA -s mr.mrrefChr5 59668 21 + 294540 CTAGTAGCAAGTAAAAAGAAG -s simCow_chr6.simCow.chr6 378436 21 - 602619 CCAGAAGCAAGTAAGAAGAAA -s simDog_chr6.simDog.chr6 485457 20 - 593897 CTAGCAGCAAGTAAGAG-AAA -s simHuman_chr6.simHuman.chr6 207735 21 + 601863 CTAACAGCAAGTAAGATCAAA -s simRat_chr6.simRat.chr6 195321 21 + 647215 CTAGTAGCAAGTAAAAAGAAG - -a -s simMouse_chr6.simMouse.chr6 205076 3 + 636262 CAT -s Anc0.Anc0refChr5 26358 3 + 87904 TAC -s Anc1.Anc1refChr8 40310 3 + 57822 TAC -s Anc2.Anc2refChr15 20559 3 + 86568 TAC -s mr.mrrefChr5 59695 3 + 294540 CAC -s simCow_chr6.simCow.chr6 378463 3 - 602619 TAC -s simDog_chr6.simDog.chr6 485483 3 - 593897 TAC -s simHuman_chr6.simHuman.chr6 207762 3 + 601863 TCC -s simRat_chr6.simRat.chr6 195348 3 + 647215 CAC - -a -s simMouse_chr6.simMouse.chr6 205079 53 + 636262 ATTATTCCCCAGATAAAGGGGCTTCAGTAACTCCAATGGATAAACATATGAAG -s Anc0.Anc0refChr5 26367 52 + 87904 ATAGTTCCTAGCATGGGGCAACCTTAGTAA-TTCAATGAATAAAAGTATGAAG -s Anc1.Anc1refChr8 40319 52 + 57822 ATAGTTCCTAGCATGGGGCAACCTTAGTAA-TTCAATGAATAAAAGTATGAAG -s Anc2.Anc2refChr15 20568 52 + 86568 ATAGGTCCTAGCATGGGGCAACCTTAGTAA-TTCAATGAATAAAAGTATGAAG -s mr.mrrefChr5 59698 53 + 294540 ATTATTCCCCAGATAAAGGGGCTTTAGTAACTCCAATGAATAAACGTATGAAG -s simCow_chr6.simCow.chr6 378472 52 - 602619 ATAGATACTAGCAGAGGGCAACCTTAGCAA-TTCAATGGATAAAAGCCTGAAG -s simDog_chr6.simDog.chr6 485492 51 - 593897 ATAGGTCAT-GCATGGAACAACTTTAGTAA-TTCAATGAATAAAAGTATGAAG -s simHuman_chr6.simHuman.chr6 207771 51 + 601863 ATAGTTCCTAGCATGGGGCAACCTTAGTGA-TTCAGTGAATAAG-GTACAAAG -s simRat_chr6.simRat.chr6 195351 53 + 647215 ATTATACCCCAGATATAGGGTCGTTAGTTACTCCAATGAATAAAAGTATGAAG - -a -s simMouse_chr6.simMouse.chr6 205132 16 + 636262 GTCAGGGCCTCCCATA -s Anc0.Anc0refChr5 26425 16 + 87904 GCCAAGGCCTCCTACA -s Anc1.Anc1refChr8 40377 16 + 57822 GCCAAGGCCTCCTACA -s Anc2.Anc2refChr15 20626 16 + 86568 GCCAAGGCCCTTTACA -s mr.mrrefChr5 59751 16 + 294540 GTCAGGGCCTCCTATA -s simCow_chr6.simCow.chr6 378530 16 - 602619 GCCAAGGCCATGTACA -s simDog_chr6.simDog.chr6 485549 16 - 593897 GCAAAGGCCCTTTACA -s simHuman_chr6.simHuman.chr6 207828 16 + 601863 GCCAAGGCCTCCTACA -s simRat_chr6.simRat.chr6 195404 16 + 647215 GTCAGGGCCTCCTATA - -a -s simMouse_chr6.simMouse.chr6 205148 8 + 636262 CTACTGAT -s Anc0.Anc0refChr5 26446 8 + 87904 CATCTGAT -s Anc1.Anc1refChr8 40398 8 + 57822 CATCTGAT -s Anc2.Anc2refChr15 20647 8 + 86568 CATCTGAT -s mr.mrrefChr5 59772 8 + 294540 CAACTGAT -s simCow_chr6.simCow.chr6 378551 8 - 602619 TGTCTGAT -s simDog_chr6.simDog.chr6 485570 8 - 593897 CATCTGGT -s simHuman_chr6.simHuman.chr6 207849 8 + 601863 CAGCCGAT -s simRat_chr6.simRat.chr6 195425 8 + 647215 CATCTGGT - -a -s simMouse_chr6.simMouse.chr6 205156 6 + 636262 GTAGCA -s Anc0.Anc0refChr5 26454 6 + 87904 ATATCA -s Anc1.Anc1refChr8 40406 6 + 57822 ATATCA -s Anc2.Anc2refChr15 20655 6 + 86568 ATATCA -s mr.mrrefChr5 59780 6 + 294540 GTAGCA -s simCow_chr6.simCow.chr6 378563 6 - 602619 ATATCA -s simDog_chr6.simDog.chr6 485578 6 - 593897 ATATGA -s simHuman_chr6.simHuman.chr6 207857 6 + 601863 ATATCA -s simRat_chr6.simRat.chr6 195433 6 + 647215 GTAGCG - -a -s simMouse_chr6.simMouse.chr6 205162 12 + 636262 CAAGGCATCTGA -s Anc0.Anc0refChr5 26460 12 + 87904 CAGGGCATCAAA -s Anc1.Anc1refChr8 40412 12 + 57822 CAGGGCATCAAA -s Anc2.Anc2refChr15 20661 12 + 86568 TGGGGCAACAAA -s mr.mrrefChr5 59786 12 + 294540 CAAGGCATCTGA -s simCow_chr6.simCow.chr6 378569 12 - 602619 TGCGGCAACAAA -s simDog_chr6.simDog.chr6 485584 12 - 593897 TGGGGCAACAAA -s simHuman_chr6.simHuman.chr6 207865 9 + 601863 CA---CATCAAA -s simRat_chr6.simRat.chr6 195439 12 + 647215 CAGGGTATTGGA - -a -s simMouse_chr6.simMouse.chr6 205174 2 + 636262 TA -s Anc0.Anc0refChr5 26472 2 + 87904 AT -s Anc1.Anc1refChr8 40424 2 + 57822 AT -s Anc2.Anc2refChr15 20674 2 + 86568 AT -s mr.mrrefChr5 59798 2 + 294540 TA -s simCow_chr6.simCow.chr6 378585 2 - 602619 AT -s simDog_chr6.simDog.chr6 485597 2 - 593897 AG -s simHuman_chr6.simHuman.chr6 207874 2 + 601863 AT -s simRat_chr6.simRat.chr6 195451 2 + 647215 TA - -a -s simMouse_chr6.simMouse.chr6 205176 13 + 636262 CTGTAATCCTGGA -s Anc0.Anc0refChr5 26474 13 + 87904 CTTTAATCCTGGA -s Anc1.Anc1refChr8 40426 13 + 57822 CTTTAATCCTGGA -s Anc2.Anc2refChr15 20676 13 + 86568 CTTTAATCCTGGA -s mr.mrrefChr5 59800 13 + 294540 CTGTAATCCTGGA -s simCow_chr6.simCow.chr6 378587 13 - 602619 CTCTAAAATTGGA -s simDog_chr6.simDog.chr6 485599 13 - 593897 ATTGAATCCTCGA -s simHuman_chr6.simHuman.chr6 207876 13 + 601863 CTATGATCCTGGA -s simRat_chr6.simRat.chr6 195465 13 + 647215 CTGTAACCCTGGA - -a -s simMouse_chr6.simMouse.chr6 205189 14 + 636262 TACTGAAGCATGCA -s Anc0.Anc0refChr5 26507 14 + 87904 AACAGCAGCATGCA -s Anc1.Anc1refChr8 40459 14 + 57822 AACAGCAGCATGCA -s Anc2.Anc2refChr15 20709 14 + 86568 AATAGCTGCATGTA -s mr.mrrefChr5 59813 14 + 294540 AACTGAAGCATGCA -s simCow_chr6.simCow.chr6 378622 13 - 602619 -ATAGCTGCATGCC -s simDog_chr6.simDog.chr6 485632 14 - 593897 AATGGCTGCATGTA -s simHuman_chr6.simHuman.chr6 207913 14 + 601863 AACAGCAGCATGCT -s simRat_chr6.simRat.chr6 195478 14 + 647215 AACTGAAGCATGCG - -a -s simMouse_chr6.simMouse.chr6 205203 18 + 636262 TGAAATCAGACTGTGTAA -s Anc0.Anc0refChr5 26525 18 + 87904 TGAAATCAGAATCTGGAA -s Anc1.Anc1refChr8 40477 18 + 57822 TGAAATCAGAATCTGGAA -s Anc2.Anc2refChr15 20733 18 + 86568 TGAAATCACAATCTGGAT -s mr.mrrefChr5 59831 18 + 294540 TGAAATCAGACTGTGTAA -s simCow_chr6.simCow.chr6 378645 18 - 602619 TGAAATCATAATCTGGAG -s simDog_chr6.simDog.chr6 485656 18 - 593897 CAAAACCGCAATGTGGAT -s simHuman_chr6.simHuman.chr6 207931 18 + 601863 TGAAATCAGGATCTGCCA -s simRat_chr6.simRat.chr6 195499 18 + 647215 TGTAATCAGACTGTGTAA - -a -s simMouse_chr6.simMouse.chr6 205221 19 + 636262 CCTGTGTTGCATTGCTAGA -s Anc0.Anc0refChr5 26543 19 + 87904 CCTGTGGTGTATAGTTACA -s Anc1.Anc1refChr8 40495 19 + 57822 CCTGTGGTGTATAGTTACA -s Anc2.Anc2refChr15 20751 19 + 86568 CCTGTGGTGTATAGTTACA -s mr.mrrefChr5 59849 19 + 294540 CCTGTGGTGCATTGCTACA -s simCow_chr6.simCow.chr6 378663 19 - 602619 CCTGTGGTGTACGATTACC -s simDog_chr6.simDog.chr6 485674 19 - 593897 CCTGTAGTGTATAGTTACA -s simHuman_chr6.simHuman.chr6 207949 19 + 601863 CCCGCGGTGTATAGTTACA -s simRat_chr6.simRat.chr6 195518 19 + 647215 CTTGTGGTGCATTGCTACA - -a -s simMouse_chr6.simMouse.chr6 205240 60 + 636262 TAGAGGATTTATGATGCTTACAGCATACTTATCTACATAACACAGTACCCACATTCCCTA -s Anc0.Anc0refChr5 26571 58 + 87904 TAGAGTATTCGCAA-GTTAATATGATA-TCATTTATATAATACAGTAAACACACTTCCTA -s Anc1.Anc1refChr8 40523 58 + 57822 TAGAGTATTCGCAA-GTTAATATGATA-TCATTTATATAATACAGTAAACACACTTCCTA -s Anc2.Anc2refChr15 20779 58 + 86568 TAGAGTATCCGCAT-GTTAATATGATA-TCATTTATATAATACAGTAAACACACTTCCTC -s mr.mrrefChr5 59868 60 + 294540 TAGAGGATTTACGATGCTTACAGCATACTTATCTACATAACACAGTACCCACATTCCCTA -s simCow_chr6.simCow.chr6 378691 58 - 602619 TAAATCATCCACAT-GTTAGTATGATA-TTATTTATATAATACAATAAATACATTTCCTC -s simDog_chr6.simDog.chr6 485702 58 - 593897 TAGAGTATCTGCAT-GTTAATATGATA-TCATTTATATAATACAGTGGACACACTTCCTC -s simHuman_chr6.simHuman.chr6 207977 58 + 601863 TAGAGTATTCGCAA-GTTAATATGATA-TCATTTATATATTATAGTAAACGGGCTTCCTA -s simRat_chr6.simRat.chr6 195537 60 + 647215 TAGAGGATTTACTATGCTTACACCATACTTATCTACATAACACAGTACCCACATTCCCTA - -a -s simMouse_chr6.simMouse.chr6 205300 13 + 636262 TTGAATTGCTTGC -s Anc0.Anc0refChr5 26629 13 + 87904 TTTCATTGTCTCC -s Anc1.Anc1refChr8 40581 13 + 57822 TTTCATTGTCTCC -s Anc2.Anc2refChr15 20837 13 + 86568 TTTCTTTGTCTCC -s mr.mrrefChr5 59928 13 + 294540 TTGAATTGCTTGC -s simCow_chr6.simCow.chr6 378749 12 - 602619 CTTC-TTTTCTCT -s simDog_chr6.simDog.chr6 485761 13 - 593897 TTGTTTTGTCTCC -s simHuman_chr6.simHuman.chr6 208035 13 + 601863 TTTCATTGTCTCC -s simRat_chr6.simRat.chr6 195597 13 + 647215 TTGAATTGCTTGC - -a -s simMouse_chr6.simMouse.chr6 205313 5 + 636262 TTGAG -s Anc0.Anc0refChr5 26642 5 + 87904 TTAAT -s Anc1.Anc1refChr8 40594 5 + 57822 TTAAT -s Anc2.Anc2refChr15 20853 5 + 86568 CTAAT -s mr.mrrefChr5 59941 5 + 294540 TTGAG -s simCow_chr6.simCow.chr6 378764 5 - 602619 CTGCT -s simDog_chr6.simDog.chr6 485777 5 - 593897 CTAAT -s simHuman_chr6.simHuman.chr6 208048 5 + 601863 TCAAC -s simRat_chr6.simRat.chr6 195615 5 + 647215 TTTAG - -a -s simMouse_chr6.simMouse.chr6 205318 25 + 636262 GCTACATACCATGATGTTGTGCCGC -s Anc0.Anc0refChr5 26647 18 + 87904 TCTACTAACTATAAT-------CAT -s Anc1.Anc1refChr8 40599 18 + 57822 TCTACTAACTATAAT-------CAT -s Anc2.Anc2refChr15 20868 18 + 86568 TCTACTAACTATAAT-------CAT -s mr.mrrefChr5 59946 25 + 294540 GCTACACACCATGATGTTGTGCCGC -s simCow_chr6.simCow.chr6 378779 18 - 602619 TCTACTATCTATAAT-------CAT -s simDog_chr6.simDog.chr6 485792 18 - 593897 TCTACTAACTATAAT-------CAT -s simHuman_chr6.simHuman.chr6 208053 6 + 601863 CCTCCT------------------- -s simRat_chr6.simRat.chr6 195620 18 + 647215 GCTACACACCATGATATT------- - -a -s simMouse_chr6.simMouse.chr6 205343 94 + 636262 TTGAGCCAGAAGCTTTCATTCTTTAGGCATCCTTCAATAACCTTGTGAGGATGACACTGGCTGCCCTGAATTCTTTACTTCTTAGCCAGTTCAC -s Anc0.Anc0refChr5 26665 51 + 87904 TTGAGCTAG-------------------------------------------GACATCCGCTGAGCTATATTTTTCACTTACAACACAGCACCC -s Anc1.Anc1refChr8 40617 51 + 57822 TTGAGCTAG-------------------------------------------GACATCCGCTGAGCTATATTTTTCACTTACAACACAGCACCC -s Anc2.Anc2refChr15 20886 51 + 86568 TTGAGCTAG-------------------------------------------GACATCCGCTGAGCTATATTTTTCACTTACAACACAGCACCC -s mr.mrrefChr5 59971 93 + 294540 TTGAGCCAGA-GCTTTCATTCTTTAGGCATCCTTCGATAACCTTGTGGGGACGACACTGGCTGCCCTGAATTCTTTACTTCTTAGCCAGTTCAC -s simCow_chr6.simCow.chr6 378819 49 - 602619 TTAACCTAA-------------------------------------------GAC--CCACTCAGCTATATTTTTCACTTTTCATACCGCAGCC -s simDog_chr6.simDog.chr6 485810 51 - 593897 TTGAGCTAG-------------------------------------------GACATTGGCTGATCTATATTTTTCATTTACAACACAGCTCCC -s simHuman_chr6.simHuman.chr6 208059 42 + 601863 -----CTGT-------------------------------------------GATGTCCGTTGGGCTATATTTTTCACTT----CACAGCATCC -s simRat_chr6.simRat.chr6 195638 79 + 647215 ---------------TCATTCTTTAGGCACCTTTCGATAACCTTGTGGGTACGACACTGGCTGTCCTAAATTCTTTACTTCTCAGCCAGCTTGC - -a -s simMouse_chr6.simMouse.chr6 205437 20 + 636262 TGACTTCAGAGAGTCAGAGA -s Anc0.Anc0refChr5 26734 20 + 87904 TGACTCCTGAGATTAGGATA -s Anc1.Anc1refChr8 40686 20 + 57822 TGACTCCTGAGATTAGGATA -s Anc2.Anc2refChr15 20958 20 + 86568 TGACTCCTGAGATCAGGATA -s mr.mrrefChr5 60064 20 + 294540 TGACTTCAGAGAGTCGGAGA -s simCow_chr6.simCow.chr6 378888 20 - 602619 TGTCTCGTGTGATCAGGAGA -s simDog_chr6.simDog.chr6 485882 20 - 593897 TGACTCCTGAAATCATGATA -s simHuman_chr6.simHuman.chr6 208119 19 + 601863 -GACTCCTGAGACTAGGATA -s simRat_chr6.simRat.chr6 195717 16 + 647215 TGAC----GAGGATTGGAGG - -a -s simMouse_chr6.simMouse.chr6 205457 10 + 636262 TTTTACAGGC -s Anc0.Anc0refChr5 26754 10 + 87904 TTTTTCAGGC -s Anc1.Anc1refChr8 40706 10 + 57822 TTTTTCAGGC -s Anc2.Anc2refChr15 20978 10 + 86568 TTTATCAGGC -s mr.mrrefChr5 60084 10 + 294540 TTTTACAGGC -s simCow_chr6.simCow.chr6 378908 10 - 602619 TTTATCAAGC -s simDog_chr6.simDog.chr6 485902 10 - 593897 TTTATTAGGC -s simHuman_chr6.simHuman.chr6 208138 10 + 601863 TTGTTCAGAC -s simRat_chr6.simRat.chr6 195734 10 + 647215 TTTTCCAGGC - -a -s simMouse_chr6.simMouse.chr6 205467 28 + 636262 TTACTGTGATAACACTGCAGTATGTTTA -s Anc0.Anc0refChr5 26764 28 + 87904 TTGATGTGATAACACCGAAGTATATTTA -s Anc1.Anc1refChr8 40716 28 + 57822 TTGATGTGATAACACCGAAGTATATTTA -s Anc2.Anc2refChr15 20988 28 + 86568 TTGACATGATAACGTCAAAGTATATTTA -s mr.mrrefChr5 60094 28 + 294540 TTGCTGTGATAACACCGCAGTATGTTTA -s simCow_chr6.simCow.chr6 378937 27 - 602619 TTGACATAAAAAC-TCAAAGTATATTTA -s simDog_chr6.simDog.chr6 485912 28 - 593897 TTGACATGGTAATGTCAAATTAAATTTA -s simHuman_chr6.simHuman.chr6 208148 28 + 601863 TTGATGTGATAACACCGAAGTATCTTTA -s simRat_chr6.simRat.chr6 195744 28 + 647215 TTGCTGTGATAACACCGCAGTATGTTTA - -a -s simMouse_chr6.simMouse.chr6 205495 15 + 636262 TGAGCATGTTGGTGG -s Anc0.Anc0refChr5 26792 15 + 87904 TAAGCATGTTAGTGA -s Anc1.Anc1refChr8 40744 15 + 57822 TAAGCATGTTAGTGA -s Anc2.Anc2refChr15 21016 15 + 86568 TAAGGATGTTAGTGA -s mr.mrrefChr5 60122 15 + 294540 TGAGCATGTTGGTGG -s simCow_chr6.simCow.chr6 378964 15 - 602619 TAGGAATGTTACTGG -s simDog_chr6.simDog.chr6 485940 15 - 593897 TAAGGATCTTAGTGA -s simHuman_chr6.simHuman.chr6 208176 15 + 601863 TAAGCATGTGAATGA -s simRat_chr6.simRat.chr6 195839 15 + 647215 TGAGCATGTTGGTGG - -a -s simMouse_chr6.simMouse.chr6 205510 10 + 636262 AGCTATATAC -s Anc0.Anc0refChr5 26809 10 + 87904 ATTAAAAAAC -s Anc1.Anc1refChr8 40761 10 + 57822 ATTAAAAAAC -s Anc2.Anc2refChr15 21033 10 + 86568 ATTAAAAAAC -s mr.mrrefChr5 60137 10 + 294540 AGCAATATAC -s simCow_chr6.simCow.chr6 378981 10 - 602619 ATTAAAAAGC -s simDog_chr6.simDog.chr6 485957 10 - 593897 ATCAAAAAAC -s simHuman_chr6.simHuman.chr6 208193 10 + 601863 ATTAAAAACC -s simRat_chr6.simRat.chr6 195854 10 + 647215 AGCAACATAT - -a -s simMouse_chr6.simMouse.chr6 205520 4 + 636262 TACT -s Anc0.Anc0refChr5 26821 4 + 87904 TACT -s Anc1.Anc1refChr8 40773 4 + 57822 TACT -s Anc2.Anc2refChr15 21045 4 + 86568 TTCT -s mr.mrrefChr5 60147 4 + 294540 TACT -s simCow_chr6.simCow.chr6 378993 4 - 602619 TCCT -s simDog_chr6.simDog.chr6 485969 4 - 593897 TTCT -s simHuman_chr6.simHuman.chr6 208205 4 + 601863 TACT -s simRat_chr6.simRat.chr6 195864 4 + 647215 TACT - -a -s simMouse_chr6.simMouse.chr6 205524 11 + 636262 AGCCCAACAAG -s Anc0.Anc0refChr5 26827 11 + 87904 AGTCAACCAAA -s Anc1.Anc1refChr8 40779 11 + 57822 AGTCAACCAAA -s Anc2.Anc2refChr15 21068 11 + 86568 AGTCAACCGAA -s mr.mrrefChr5 60151 11 + 294540 AGTCAAACAAG -s simCow_chr6.simCow.chr6 379016 7 - 602619 ----ATCCGAA -s simDog_chr6.simDog.chr6 485992 7 - 593897 AGTCAAC---- -s simHuman_chr6.simHuman.chr6 208211 11 + 601863 AGTCAACCAAA -s simRat_chr6.simRat.chr6 195868 11 + 647215 AGTCAGACAAG - -a -s simMouse_chr6.simMouse.chr6 205535 9 + 636262 GAAGTAAGC -s Anc0.Anc0refChr5 26841 9 + 87904 GAAGTTCAA -s Anc1.Anc1refChr8 40793 9 + 57822 GAAGTTCAA -s Anc2.Anc2refChr15 21082 9 + 86568 GAAGTTCAA -s mr.mrrefChr5 60162 9 + 294540 GAAGTAAGC -s simCow_chr6.simCow.chr6 379026 9 - 602619 GAAGTTTAA -s simDog_chr6.simDog.chr6 485999 7 - 593897 --TGGTCAA -s simHuman_chr6.simHuman.chr6 208225 9 + 601863 GAAGTTCAA -s simRat_chr6.simRat.chr6 195879 9 + 647215 GCAGTAAGC - -a -s simMouse_chr6.simMouse.chr6 205544 26 + 636262 TGGTTATTTCCAACCATACCCCTAGC -s Anc0.Anc0refChr5 26856 26 + 87904 TGGAAATTTCTAACAATACTCCTAAT -s Anc1.Anc1refChr8 40808 26 + 57822 TGGAAATTTCTAACAATACTCCTAAT -s Anc2.Anc2refChr15 21097 26 + 86568 TGCAAATTTCTAACAATTCTCTTAAT -s mr.mrrefChr5 60171 26 + 294540 TGGTTATTTCTAACCATACCCCTAGC -s simCow_chr6.simCow.chr6 379041 21 - 602619 TG-----CTCTAACAATGCTCTTAAA -s simDog_chr6.simDog.chr6 486013 26 - 593897 TACAAATTTCTAGCAATTTTCTTGAT -s simHuman_chr6.simHuman.chr6 208240 26 + 601863 TGGAAATTTCTAACAATACTCCTAAT -s simRat_chr6.simRat.chr6 195888 26 + 647215 TGGTTATTTTTAACCATACCCTTAGC - -a -s simMouse_chr6.simMouse.chr6 205570 72 + 636262 CTTGGTGGTCCAGACCAAATCCTTTTCTAAACCGGATCCTTTTGGTTTGTCGCCAAAACTAAACAGGGCAGT -s Anc0.Anc0refChr5 26882 25 + 87904 CTCATTGGTTTAGACCAAATCCTTT----------------------------------------------- -s Anc1.Anc1refChr8 40834 55 + 57822 CTCATTGGTTTAGACCAAATCCTTT-----------------TATTTGGTCGCCCCAACTAACCTCGACAGG -s Anc2.Anc2refChr15 21123 25 + 86568 CTCATTGGTTTAGACCAAATCCTTT----------------------------------------------- -s mr.mrrefChr5 60197 72 + 294540 CTTAGTGGTCTAGACCAAATCCTTTTCTAAACCGGATCCTTTTGGTTTGTCGCCAAAACTAAACAGGGCAGT -s simCow_chr6.simCow.chr6 379062 25 - 602619 TTCATTAGTCCAGACCAAATTCTCT----------------------------------------------- -s simDog_chr6.simDog.chr6 486039 25 - 593897 CTAGTAGGTTTAGATCAAATCCTTT----------------------------------------------- -s simHuman_chr6.simHuman.chr6 208267 49 + 601863 CTCATTGGTTTACACCAGA-----------------------TATTTGGTCGCCCCAACTAACCTCGACAGG -s simRat_chr6.simRat.chr6 195914 72 + 647215 CTTAGTGGTCTAGACCAAATCCTCTTCTAGACCAAATCCTTTTGGTTTGTCCCCAAAACAAAACAGGGTAGT - -a -s simMouse_chr6.simMouse.chr6 205642 14 + 636262 GGAGTCTCACTTTC -s Anc0.Anc0refChr5 26907 13 + 87904 -AAGTCTCACTTTC -s Anc1.Anc1refChr8 40889 14 + 57822 GAAGTCTCACTTTC -s Anc2.Anc2refChr15 21148 13 + 86568 -AAGTCTCACCTTC -s mr.mrrefChr5 60269 14 + 294540 GGAGTCTCACTTTC -s simCow_chr6.simCow.chr6 379087 13 - 602619 -AGGTCCCACATTC -s simDog_chr6.simDog.chr6 486064 13 - 593897 -AAGTCTCACCTTC -s simHuman_chr6.simHuman.chr6 208317 14 + 601863 GAAGCCTTACTTTC -s simRat_chr6.simRat.chr6 195986 14 + 647215 GGAGTCTCACTTTC - -a -s simMouse_chr6.simMouse.chr6 205656 27 + 636262 CTGCCCGGTGTGACCAGCCCTTGTAAG -s Anc0.Anc0refChr5 26922 27 + 87904 CTGCTCAGCATGACCAACCCTTGTAAG -s Anc1.Anc1refChr8 40905 27 + 57822 CTGCTCAGCATGACCAACCCTTGTAAG -s Anc2.Anc2refChr15 21163 27 + 86568 CTGCTGAGCATGACCAACCCTTGTAGA -s mr.mrrefChr5 60283 27 + 294540 CTGCTCGGTGTGACCAGCCCTTGTAAG -s simCow_chr6.simCow.chr6 379102 27 - 602619 CTGCCGAGCATAACACGCCCTTGTAAG -s simDog_chr6.simDog.chr6 486079 27 - 593897 CTGCTGAGTATGACCAACCATTGTAGA -s simHuman_chr6.simHuman.chr6 208333 27 + 601863 CTGCTCAGCATGACCACCCCTTGTTAG -s simRat_chr6.simRat.chr6 196000 27 + 647215 CTGCTTGGTGTGACTATCCCTTGTAAC - -a -s simMouse_chr6.simMouse.chr6 205683 10 + 636262 GAAACCACAT -s Anc0.Anc0refChr5 26949 10 + 87904 GAACCCCCAT -s Anc1.Anc1refChr8 40932 10 + 57822 GAACCCCCAT -s Anc2.Anc2refChr15 21190 10 + 86568 GAACCCCCAT -s mr.mrrefChr5 60310 10 + 294540 GAAACCACAT -s simCow_chr6.simCow.chr6 379129 10 - 602619 GGAACCCCAT -s simDog_chr6.simDog.chr6 486106 9 - 593897 GAACTCTCA- -s simHuman_chr6.simHuman.chr6 208361 10 + 601863 AAACCCCCAT -s simRat_chr6.simRat.chr6 196027 9 + 647215 -AAACCTCAG - -a -s simMouse_chr6.simMouse.chr6 205693 25 + 636262 GACGCAAAGTAAAAGTGCTCTTCAA -s Anc0.Anc0refChr5 26967 25 + 87904 GATTGCAAGTAAAAGCACCCTTTAA -s Anc1.Anc1refChr8 40950 25 + 57822 GATTGCAAGTAAAAGCACCCTTTAA -s Anc2.Anc2refChr15 21208 25 + 86568 GATTGCAAGTAAAAACACCCTTTAA -s mr.mrrefChr5 60320 25 + 294540 GATGCAAAGTAAAAGCACTCTTCAA -s simCow_chr6.simCow.chr6 379147 25 - 602619 GATTGGAGGTAAAAACACTTTTTAT -s simDog_chr6.simDog.chr6 486122 25 - 593897 GATTGCAAATGAAAACACCCTTTAA -s simHuman_chr6.simHuman.chr6 208379 25 + 601863 GATTGCAAGTATAAGCACCCCTTGG -s simRat_chr6.simRat.chr6 196036 25 + 647215 GATGCAAAATAAAAGCAGTCTTCAA - -a -s simMouse_chr6.simMouse.chr6 205718 36 + 636262 GTCCCCATCCTATATCTAGAAAGGAGAAAGAATGCT -s Anc0.Anc0refChr5 26992 36 + 87904 GTCCCCAACTTTTATTCAAGACGAAGAAAAAATGCA -s Anc1.Anc1refChr8 40975 36 + 57822 GTCCCCAACTTTTATTCAAGACGAAGAAAAAATGCA -s Anc2.Anc2refChr15 21233 36 + 86568 GTCCCCAACTTTTATTCAAGACGGAGAAAAAACCCA -s mr.mrrefChr5 60345 36 + 294540 GTCCCCATCTTATATCTAAAAAGAAGAAAGAATGCA -s simCow_chr6.simCow.chr6 379172 36 - 602619 GTCCCCAACTTCTATTCAAGAAGGAAAAGACAAATA -s simDog_chr6.simDog.chr6 486148 36 - 593897 GTCCCCAACTTTTGATCAAGACGGAGAAAAAACCCA -s simHuman_chr6.simHuman.chr6 208404 36 + 601863 GTCCCCAGCTTTTATTCAAGAGGAAGAAAAAATGCA -s simRat_chr6.simRat.chr6 196061 36 + 647215 GTCCCCATCTTATATCTGAAAAGAAGAAAGGATGTA - -a -s simMouse_chr6.simMouse.chr6 205754 10 + 636262 TGAAGTTGGT -s Anc0.Anc0refChr5 27040 10 + 87904 TCAGGGTGGT -s Anc1.Anc1refChr8 41023 10 + 57822 TCAGGGTGGT -s Anc2.Anc2refChr15 21282 10 + 86568 TCAGGGTTGC -s mr.mrrefChr5 60381 10 + 294540 TGAAGTTGGT -s simCow_chr6.simCow.chr6 379221 10 - 602619 TCAGGATCGA -s simDog_chr6.simDog.chr6 486197 10 - 593897 CCAGGGTTGC -s simHuman_chr6.simHuman.chr6 208452 10 + 601863 TCAGGGTGTT -s simRat_chr6.simRat.chr6 196097 10 + 647215 TGAATTTGGT - -a -s simMouse_chr6.simMouse.chr6 205764 10 + 636262 TATGAAATCC -s Anc0.Anc0refChr5 27050 10 + 87904 TTTGAAATCC -s Anc1.Anc1refChr8 41033 10 + 57822 TTTGAAATCC -s Anc2.Anc2refChr15 21292 10 + 86568 TTTGATACCT -s mr.mrrefChr5 60391 10 + 294540 TATGAAATCC -s simCow_chr6.simCow.chr6 379271 10 - 602619 TCTGACTCCT -s simDog_chr6.simDog.chr6 486207 7 - 593897 TTTGATA--- -s simHuman_chr6.simHuman.chr6 208462 10 + 601863 TTTGAAATCC -s simRat_chr6.simRat.chr6 196107 10 + 647215 TATGATATCC - -a -s simMouse_chr6.simMouse.chr6 205774 38 + 636262 AGCTGAGTCTTGTGTCTAGCTTGATATATTTTTTTCCC -s Anc0.Anc0refChr5 27077 38 + 87904 GGCTAATTTTTGAACCTAGGTTGATTTTTTTTGTCAGC -s Anc1.Anc1refChr8 41060 38 + 57822 GGCTAATTTTTGAACCTAGGTTGATTTTTTTTGTCAGC -s Anc2.Anc2refChr15 21319 38 + 86568 GACTAATATTTGAACCTAGGTTGATTTTTTTTGTCAGC -s mr.mrrefChr5 60401 38 + 294540 GGCTGAGTCTTGTGCCTAGCTTGATATATTTTTTTCCC -s simCow_chr6.simCow.chr6 379298 38 - 602619 CACTGGTATTTGAACCTAGGTTTATTTTTTTTGTCAGC -s simDog_chr6.simDog.chr6 486223 38 - 593897 GACTAACATTTGAACCTAAGTTGACCTTTTTTGTCAGC -s simHuman_chr6.simHuman.chr6 208489 38 + 601863 GGTTAATTGCTGCACCTAGGTTGATTTCTTTTGTCAGC -s simRat_chr6.simRat.chr6 196117 38 + 647215 GGCTGAGTTTTGTGCCTAGCTTGATATATTTTTTTCCC - -a -s simMouse_chr6.simMouse.chr6 205812 99 + 636262 TTGGCTGTAATCATGTATTCATGCCTGCTTTTGCTGGCCTCCCACTTATTTGCTGGCCTCCCACTTAGTCTGCATAGCAGTAGCCAACTGATTTGGATT -s Anc0.Anc0refChr5 27115 77 + 87904 TTGGCTGTAATCA--TACTCATGTCTGTCTTTCCTGGC--------------------TCAAATTCACCCTGGGTATCAGTTGCCAACAGGATTGGCTT -s Anc1.Anc1refChr8 41098 77 + 57822 TTGGCTGTAATCA--TACTCATGTCTGTCTTTCCTGGC--------------------TCAAATTCACCCTGGGTATCAGTTGCCAACAGGATTGGCTT -s Anc2.Anc2refChr15 21371 77 + 86568 TTGGCTGTAATCA--TACTCATGTATGTCTTTCCTGGC--------------------TCAAATTCACCCTGGGTATTAGTTGCCAACAAGATTGCCTT -s mr.mrrefChr5 60439 79 + 294540 TTGGCTGTAATCATGTATTCATGCCTGCCTTTGCTGGC--------------------TCCCACTTAGCCTGCATAGCAGTAGCCAACTGGTTTGGCTT -s simCow_chr6.simCow.chr6 379350 77 - 602619 TTTGCAGTAATCA--TACTCATGTATGTCTTTCCCAGC--------------------TCACATTCGCCCTGGATATTAGTTGTCAACATGATTGCCCT -s simDog_chr6.simDog.chr6 486275 77 - 593897 TTGGCTGTAATCA--TCCTCATGGATGTCTTTCCTGCC--------------------TCAAATTCACCCTGGGTGTTAGTGTCCAACAAGATTTCCTT -s simHuman_chr6.simHuman.chr6 208527 77 + 601863 TCGGCTGTAATCA--TACTCATGTCTGTCTTCTGTGGC--------------------TCATATTCACCTTGAGTATCAGTTGCCAACAGGATTGGCTC -s simRat_chr6.simRat.chr6 196155 78 + 647215 TTGGCTGCAATAATGT-TCCCTGCCTTCCTTTGCCAGC--------------------GCCCACTTAGCCTGGATAGCAGTAGCCAACTGGTTTGGCGT - -a -s simMouse_chr6.simMouse.chr6 205911 30 + 636262 ATGGAATATATTTCTTGTAATGTTGAGTAC -s Anc0.Anc0refChr5 27193 28 + 87904 AT--TATATATGTTTTATAATGTCAAGTAT -s Anc1.Anc1refChr8 41176 30 + 57822 ATGCTATATATGTTTTATAATGTCAAGTAT -s Anc2.Anc2refChr15 21449 28 + 86568 AT--TTTATATGGTCTATAATGTCAAGTAT -s mr.mrrefChr5 60518 30 + 294540 ATGGAATATATTTCTTGTAATGTTGAGTAC -s simCow_chr6.simCow.chr6 379428 28 - 602619 AT--CTCACATGGTCTATGGTATCAAGTGT -s simDog_chr6.simDog.chr6 486353 28 - 593897 AT--TTTATATGGTCTATAATGCCTAGTAA -s simHuman_chr6.simHuman.chr6 208605 29 + 601863 ATGCTAT-TATCTTTTATCATGTCAAGTAT -s simRat_chr6.simRat.chr6 196233 30 + 647215 ATGAAATATATTTATTGTAATGATGAGTGC - -a -s simMouse_chr6.simMouse.chr6 205941 45 + 636262 AATATTCGACTCATGGTTATAATGATTATTGTTTTGCTTTAATGT -s Anc0.Anc0refChr5 27241 45 + 87904 AATACTTCAGCTTTGGTTAAAATTATTTTTGTTTCACTCTAACAT -s Anc1.Anc1refChr8 41226 45 + 57822 AATACTTCAGCTTTGGTTAAAATTATTTTTGTTTCACTCTAACAT -s Anc2.Anc2refChr15 21506 45 + 86568 AATACTTCAGCTTTGGTTAAAATTATTTTTGTTCCACTCTAACAT -s mr.mrrefChr5 60548 45 + 294540 AATATTTGACTCATGGTTATAATGATTATTGTTTTACTTTAATGT -s simCow_chr6.simCow.chr6 379483 44 - 602619 AATACTCCACCTTTGGTCA-AATCATTTTTGTTCCACTCTAACAT -s simDog_chr6.simDog.chr6 486414 45 - 593897 AATACTTCAGCTTTGGTTAAAGTTATTTTCATTCCACATGAATAT -s simHuman_chr6.simHuman.chr6 208654 45 + 601863 AATACTTCATCTTTGGTTAGAATTGTTTTTGTTTCATTCTAACAT -s simRat_chr6.simRat.chr6 196263 45 + 647215 AATATTTGACTCATGGTTATATTGATTGTTGTTTAACTTTAATGC - -a -s simMouse_chr6.simMouse.chr6 205986 2 + 636262 AG -s Anc0.Anc0refChr5 27286 1 + 87904 G- -s Anc1.Anc1refChr8 41271 2 + 57822 GG -s Anc2.Anc2refChr15 21551 1 + 86568 G- -s mr.mrrefChr5 60593 2 + 294540 AG -s simCow_chr6.simCow.chr6 379528 1 - 602619 G- -s simDog_chr6.simDog.chr6 486459 1 - 593897 G- -s simHuman_chr6.simHuman.chr6 208699 2 + 601863 TG -s simRat_chr6.simRat.chr6 196308 2 + 647215 AG - -a -s simMouse_chr6.simMouse.chr6 205988 68 + 636262 GAGTACCATCTACACTGGGCTAGGGTCAAACAATTAGCTCTGTGCACACTTATTTCATTACCTGTTGA -s Anc0.Anc0refChr5 27287 68 + 87904 TAGTATTTTCTGGGGTGGAATTGTGTCAGACAATTAGCTCTGTGCACACTTGATTCATTACCTGTTGG -s Anc1.Anc1refChr8 41273 68 + 57822 TAGTATTTTCTGGGGTGGAATTGTGTCAGACAATTAGCTCTGTGCACACTTGATTCATTACCTGTTGG -s Anc2.Anc2refChr15 21552 68 + 86568 TAGTATTTTCTGGGGTGGAATTGTGTCAGACAATTATCTCTGTGCACACTTGATTTGTTACTTGTTGG -s mr.mrrefChr5 60595 68 + 294540 GAGTACCATCTACACTGGGCTTGGGTCAGACAATTAGCTCTGTGCACACTTATTTCATTACCTGTTGA -s simCow_chr6.simCow.chr6 379529 50 - 602619 GAGTATTTTTTGG-----AATTGCGTCAGACAAT-ATCTCTGTGCACACTT------------ATGGG -s simDog_chr6.simDog.chr6 486460 66 - 593897 TAGTATCTCCTAGGGTGGGCT--TGACAAACAAATATCTCTGTGCACACTTGATTTGTTACTTGTTGC -s simHuman_chr6.simHuman.chr6 208702 68 + 601863 TAGTATTGTCTGTGTTGCAATTATGTCAGACAATCAGCTATGTGCACACTTGAGTCATTGCCCGTTGG -s simRat_chr6.simRat.chr6 196310 66 + 647215 CAGTACCCTCTACACTGGGCTTGGGTCAGACAAT-AGCTCTGTGCGCAGTTATTTC-TTACCTGTTGA - -a -s simMouse_chr6.simMouse.chr6 206056 63 + 636262 AATTAGCCAAGACTAAGCCTGAGGGACTGTCTGTGCTTGTCTCCTGCTAAATCAGGGAGCAAT -s Anc0.Anc0refChr5 27378 63 + 87904 AATTAGCTTACATTTACACTAAGGGACTGTCTGTACTTATCTCCAGCTGAATCAGTGAGCAAT -s Anc1.Anc1refChr8 41371 63 + 57822 AATTAGCTTACATTTACACTAAGGGACTGTCTGTACTTATCTCCAGCTGAATCAGTGAGCAAT -s Anc2.Anc2refChr15 21643 63 + 86568 AACTAGCTTACAATTACACTAAGGAACTGTCTATACTCATCTCCAGCTGAATCAGTGAGCAAT -s mr.mrrefChr5 60693 63 + 294540 AATTAGCCAAGATTAAGCCTGAGGGACTGTCTGTGCTTGTCTCCAGCTAAATCAGGGAGCAAT -s simCow_chr6.simCow.chr6 379602 56 - 602619 AACTAGT------TCACATTGAGGAACTGGCT-TATTCGACTCCAGCTGAATCAGTGAGTCAT -s simDog_chr6.simDog.chr6 486549 63 - 593897 AACTAGCTTACAATTACTCTAAGAAACTGTCTATGCTCATCTCCATCTGAATCAGTGAGCAGT -s simHuman_chr6.simHuman.chr6 208802 63 + 601863 ATTTAGCTTACATTTACACTAAGGGACTGTCTGTACTTATCACCAGCTGTAGTCATGAGCAAT -s simRat_chr6.simRat.chr6 196406 63 + 647215 AATTAGCAAAGATTAGGCATGAGGGACTGTCTGTGCTTGTCTCCAGCTAAATCAGGGAGCAAT - -a -s simMouse_chr6.simMouse.chr6 206119 8 + 636262 ATAAAAGC -s Anc0.Anc0refChr5 27470 8 + 87904 ATGTTAGC -s Anc1.Anc1refChr8 41463 8 + 57822 ATGTTAGC -s Anc2.Anc2refChr15 21735 8 + 86568 ATGTCCGC -s mr.mrrefChr5 60785 8 + 294540 ATATTAGC -s simCow_chr6.simCow.chr6 379684 8 - 602619 ATGTCTGC -s simDog_chr6.simDog.chr6 486638 7 - 593897 -TGTCCAC -s simHuman_chr6.simHuman.chr6 208894 8 + 601863 ATGTTAGC -s simRat_chr6.simRat.chr6 196498 8 + 647215 ATATTAGC - -a -s simMouse_chr6.simMouse.chr6 206127 6 + 636262 CAAAAT -s Anc0.Anc0refChr5 27478 6 + 87904 AGAATT -s Anc1.Anc1refChr8 41471 6 + 57822 AGAATT -s Anc2.Anc2refChr15 21743 6 + 86568 AGAATT -s mr.mrrefChr5 60793 6 + 294540 AGAAAT -s simCow_chr6.simCow.chr6 379693 6 - 602619 AGAATC -s simDog_chr6.simDog.chr6 486645 6 - 593897 AGAACT -s simHuman_chr6.simHuman.chr6 208902 6 + 601863 AGAATT -s simRat_chr6.simRat.chr6 196506 6 + 647215 AGGAAT - -a -s simMouse_chr6.simMouse.chr6 206133 16 + 636262 TAATAATACCACTGCA -s Anc0.Anc0refChr5 27485 6 + 87904 TAATAA---------- -s Anc1.Anc1refChr8 41478 16 + 57822 TAATAATACAGCAAAA -s Anc2.Anc2refChr15 21750 6 + 86568 TGATAA---------- -s mr.mrrefChr5 60799 16 + 294540 TAATAATACCACAGCA -s simCow_chr6.simCow.chr6 379700 6 - 602619 TGATTG---------- -s simDog_chr6.simDog.chr6 486652 6 - 593897 TGATAA---------- -s simHuman_chr6.simHuman.chr6 208909 16 + 601863 TAATAATACAGCAAAA -s simRat_chr6.simRat.chr6 196512 16 + 647215 TAATAATACAACAGCA - -a -s simMouse_chr6.simMouse.chr6 206149 2 + 636262 CT -s Anc1.Anc1refChr8 41505 2 + 57822 GG -s mr.mrrefChr5 60826 2 + 294540 CG -s simHuman_chr6.simHuman.chr6 208936 2 + 601863 GG -s simRat_chr6.simRat.chr6 196539 2 + 647215 TG - -a -s simMouse_chr6.simMouse.chr6 206151 7 + 636262 AGCAGCA -s Anc1.Anc1refChr8 41507 7 + 57822 AGCTGCA -s mr.mrrefChr5 60828 7 + 294540 AGCAGCA -s simHuman_chr6.simHuman.chr6 208939 7 + 601863 AGCTGCA -s simRat_chr6.simRat.chr6 196541 7 + 647215 AGCGGCA - -a -s simMouse_chr6.simMouse.chr6 206158 58 + 636262 GTAGACCAGGTTCCACAGAGATCTGTTTATTCCAGAATTACTTTGATCCTGATTGCTA -s Anc0.Anc0refChr5 27491 27 + 87904 -------------------------ATTCTTTCAGAATCACTTTGATC---A---CTA -s Anc1.Anc1refChr8 41516 55 + 57822 GTATATTTAGTGTCACCCAAAGTTGATTCTTTCAGAATCACTTTGATCCTAA---CTA -s Anc2.Anc2refChr15 21756 27 + 86568 -------------------------ACTCTTTCATAATCACTTTGATC---A---CCA -s mr.mrrefChr5 60837 58 + 294540 GTAGATCAGGTTTCACAGAAATCTGTTTATTCCAGAATTACTTTGATCCTGATTGCTA -s simCow_chr6.simCow.chr6 379706 25 - 602619 -------------------------ACTCTTTCGTCATCCCTTTGAT--------CCA -s simDog_chr6.simDog.chr6 486658 27 - 593897 -------------------------ACTTTGTCATAATCATGCAGATC---A---CCA -s simHuman_chr6.simHuman.chr6 208948 55 + 601863 GTATATTTAGTGTCACCCAAAGTTGATTCTTTCAGAATCACTTTGATCCTAA---CTA -s simRat_chr6.simRat.chr6 196550 57 + 647215 GTAGATCAGGTTTCATAGAAAT-TGGTTATTCCAGAATTGATTTTATCCTGATTGCTA - -a -s simMouse_chr6.simMouse.chr6 206216 42 + 636262 ATTGGGGTGTTGGTACATGGGCAAGTCAATCTTTTCTTTGAG -s Anc0.Anc0refChr5 27518 42 + 87904 ATTGTAATCATTGCACATAGGTAATTTAAACTTTCCTTTGAG -s Anc1.Anc1refChr8 41571 42 + 57822 ATTGTAATCATTGCACATAGGTAATTTAAACTTTCCTTTGAG -s Anc2.Anc2refChr15 21783 42 + 86568 ATTGTAATCATTGCACACAGGTAATTTAAACTCTCATTTGAG -s mr.mrrefChr5 60895 42 + 294540 ATTGGGGTCTTTGTACATAGGCAAGTTAATCTTTTCTTTGAG -s simCow_chr6.simCow.chr6 379738 42 - 602619 ATGATAATTGTTTCACACAGTTAATCTAAACACTCATTTGAG -s simDog_chr6.simDog.chr6 486685 42 - 593897 ACTGTAATCAATGCAGACAAGTAATTTAAACTCTCATTCAAT -s simHuman_chr6.simHuman.chr6 209003 42 + 601863 ATTGCAATCATTGCACATAGGTGATTTAAACTTTCCTTTGAG -s simRat_chr6.simRat.chr6 196607 42 + 647215 ATTGGGGTCTTTGTACATAGGCAAGCTAATCTCTTGTAGGAG - -a -s simMouse_chr6.simMouse.chr6 206258 27 + 636262 AGTATCTTGTGCATACTGATTTTAACC -s Anc0.Anc0refChr5 27560 27 + 87904 AGAGTCTTTAGCATACTGACTTTAATC -s Anc1.Anc1refChr8 41613 27 + 57822 AGAGTCTTTAGCATACTGACTTTAATC -s Anc2.Anc2refChr15 21825 27 + 86568 AGAGTCTTTAGCATACTGACTTTTATC -s mr.mrrefChr5 60937 27 + 294540 AGTATCTTGTGCATACTGATTTTAACC -s simCow_chr6.simCow.chr6 379780 27 - 602619 AGAGCCATTATCATACTGCCCTTTATC -s simDog_chr6.simDog.chr6 486727 26 - 593897 AGAGTCTTTAGTG-ACTAAGTTTTATC -s simHuman_chr6.simHuman.chr6 209046 27 + 601863 AGAGTCTTTAGCATAATGACTTTAATC -s simRat_chr6.simRat.chr6 196649 27 + 647215 AGTATCTTGTGCATACTGATATTAACC - -a -s simMouse_chr6.simMouse.chr6 206285 69 + 636262 TCTAGATAAATGATGGTCTGAGGGACTAAATTTGACAAGAGTCCCAGACAAAAGAACAGATGAATGACA -s Anc0.Anc0refChr5 27600 63 + 87904 ------TAAGTGATGGCCTGAGGGGTAAAGTATGCCATGATTCCCAAACATAAGAACAGATGTCAGAAA -s Anc1.Anc1refChr8 41653 63 + 57822 ------TAAGTGATGGCCTGAGGGGTAAAGTATGCCATGATTCCCAAACATAAGAACAGATGTCAGAAA -s Anc2.Anc2refChr15 21865 63 + 86568 ------TAAGTTATGGCCTGAGGGGTAAAGTATGCCATGATTCCCAAACGTAAGAACTGATGTCAGAAA -s mr.mrrefChr5 60978 69 + 294540 TTTAGATAAATGATGGTCTGAGGGACTAAATATGACAAGATTCCCAAACAAAAGAACAGATGTAAGACA -s simCow_chr6.simCow.chr6 379820 63 - 602619 ------TAAGTTATGGCCTGAGGGGCAATGAGTGACATAATTCCCAAACGTAAGAACTGATGTCAGAAA -s simDog_chr6.simDog.chr6 486766 53 - 593897 ------TAAGTTATGGCCTGGGGGGTGCAGTATGCTATGATTCCCAAAC----------ACGTCTGAGA -s simHuman_chr6.simHuman.chr6 209086 63 + 601863 ------TATGTGATGGCCTGAGGGGTAAAGTATGCCACGGTTCCCAAACATAACAACAGATGTCAAAAA -s simRat_chr6.simRat.chr6 196690 69 + 647215 TTTAGCTGAATGATAGACTGAGGGACTAAATATGATATGATTCCCAAACAAAAAAACAAATGTAAGATA - -a -s simMouse_chr6.simMouse.chr6 206354 38 + 636262 CATCAATGTTCTTCCTTACACTCATGACATTATAGGAT -s Anc0.Anc0refChr5 27664 38 + 87904 CAACCACATTCTTCCTCAGATCCTTGATACTAAAGGAT -s Anc1.Anc1refChr8 41717 38 + 57822 CAACCACATTCTTCCTCAGATCCTTGATACTAAAGGAT -s Anc2.Anc2refChr15 21929 38 + 86568 CAACCACATTCTTCATCAGATCCTTGATACTAAAGGAT -s mr.mrrefChr5 61048 38 + 294540 CATCAATGTTCTTCCTTACATTCATGACATTATAGGAT -s simCow_chr6.simCow.chr6 379884 38 - 602619 CAACCACATTCTTCATCAGATCTGTGATACTAAAGGAT -s simDog_chr6.simDog.chr6 486820 38 - 593897 AAACTTCATTCTTCATCAGATCCTTCGTACTAAAGGAG -s simHuman_chr6.simHuman.chr6 209150 37 + 601863 CAACCACACTCTTCCTCA-ATCGTTGATTGTGAAGGAT -s simRat_chr6.simRat.chr6 196760 38 + 647215 TATCAATGTTATTCCCTACATTCATGACGTTATAGGGT - -a -s simMouse_chr6.simMouse.chr6 206392 12 + 636262 CCCTTCAGTGCC -s Anc0.Anc0refChr5 27704 12 + 87904 TCCTGCAATCCC -s Anc1.Anc1refChr8 41757 12 + 57822 TCCTGCAATCCC -s Anc2.Anc2refChr15 21969 12 + 86568 TCCTGCAATCCC -s mr.mrrefChr5 61088 12 + 294540 TCCTTCAGTGCC -s simCow_chr6.simCow.chr6 379923 12 - 602619 TCCTGCAGTCCC -s simDog_chr6.simDog.chr6 486860 12 - 593897 TCCAGCAATCCC -s simHuman_chr6.simHuman.chr6 209189 12 + 601863 TCTTGCAATCCC -s simRat_chr6.simRat.chr6 196800 12 + 647215 TCCTTTTGTGCT - -a -s simMouse_chr6.simMouse.chr6 206404 12 + 636262 CTCTATTACACA -s Anc0.Anc0refChr5 27716 12 + 87904 TTAAATTGCACA -s Anc1.Anc1refChr8 41769 12 + 57822 TTAAATTGCACA -s Anc2.Anc2refChr15 21983 12 + 86568 TTAAGTTGCACC -s mr.mrrefChr5 61100 12 + 294540 CTCTATTACACA -s simCow_chr6.simCow.chr6 379937 12 - 602619 TTAAGTTGTATC -s simDog_chr6.simDog.chr6 486874 12 - 593897 TTAAGTTGCACC -s simHuman_chr6.simHuman.chr6 209201 12 + 601863 TTAAATTGCACA -s simRat_chr6.simRat.chr6 196812 12 + 647215 CTCTATTACACA - -a -s simMouse_chr6.simMouse.chr6 206416 16 + 636262 ATGGACTTATGTATTT -s Anc0.Anc0refChr5 27728 16 + 87904 ATGGTCTCATGTGTCT -s Anc1.Anc1refChr8 41781 16 + 57822 ATGGTCTCATGTGTCT -s Anc2.Anc2refChr15 21995 16 + 86568 ATAGTCTCATGTGTCT -s mr.mrrefChr5 61112 16 + 294540 ATGGACTCATGTATTT -s simCow_chr6.simCow.chr6 379996 16 - 602619 ATAAACTCATGTCTTT -s simDog_chr6.simDog.chr6 486886 16 - 593897 ATAGTCTCAGGTGTCT -s simHuman_chr6.simHuman.chr6 209219 16 + 601863 ATGGTCGCATATGTCT -s simRat_chr6.simRat.chr6 196824 16 + 647215 ATTGACTCATGTATTT - -a -s simMouse_chr6.simMouse.chr6 206432 43 + 636262 TCAACTTAGGGTGGAGCTCACCGTTACTTTAGCTCTCCTAACT -s Anc0.Anc0refChr5 27744 43 + 87904 TCAACTTAGGCTACACTTCACCATAATTTTATGTCTCTTAACC -s Anc1.Anc1refChr8 41797 43 + 57822 TCAACTTAGGCTACACTTCACCATAATTTTATGTCTCTTAACC -s Anc2.Anc2refChr15 22011 43 + 86568 TCAACTTAGGCTACACTTCACCATAATTTTATGTCCCTTAACC -s mr.mrrefChr5 61128 43 + 294540 TCAACTTAGGCTGCAGCTCACCGTTACTTTAGGTCTCCTAACT -s simCow_chr6.simCow.chr6 380012 43 - 602619 TCATCTTAGGCTACACTTCACCACAATTTCATGTACCTTAATC -s simDog_chr6.simDog.chr6 486902 43 - 593897 TTGACTTAGGCTACACGTCACCATAATTTTATGTCCCTTGACC -s simHuman_chr6.simHuman.chr6 209239 43 + 601863 TCAACTTAGGCTACACTTCAACATAATTTTATGTCTCTTAAGC -s simRat_chr6.simRat.chr6 196840 43 + 647215 TCAACTTAGGCTGCAGCTCACTGTTACTTTAGGTCTCCTAACT - -a -s simMouse_chr6.simMouse.chr6 206475 8 + 636262 TGATAACT -s Anc0.Anc0refChr5 27787 6 + 87904 AAAGG--T -s Anc1.Anc1refChr8 41840 6 + 57822 AAAGG--T -s Anc2.Anc2refChr15 22054 6 + 86568 AAAGG--T -s mr.mrrefChr5 61171 6 + 294540 TGATA--T -s simCow_chr6.simCow.chr6 380055 2 - 602619 AA------ -s simDog_chr6.simDog.chr6 486945 6 - 593897 AGAGG--T -s simHuman_chr6.simHuman.chr6 209282 6 + 601863 AAAGG--T -s simRat_chr6.simRat.chr6 196884 6 + 647215 TGATA--T - -a -s simMouse_chr6.simMouse.chr6 206483 7 + 636262 GTCAAAT -s Anc0.Anc0refChr5 27798 5 + 87904 GTCAA-- -s Anc1.Anc1refChr8 41851 5 + 57822 GTCAA-- -s Anc2.Anc2refChr15 22067 5 + 86568 GTCAA-- -s mr.mrrefChr5 61177 7 + 294540 GTCAAAT -s simCow_chr6.simCow.chr6 380064 2 - 602619 GT----- -s simDog_chr6.simDog.chr6 486958 5 - 593897 GTCAA-- -s simRat_chr6.simRat.chr6 196890 7 + 647215 GTCAAAT - -a -s simMouse_chr6.simMouse.chr6 206490 44 + 636262 CTTAACCTTATTCGGTGATTCTTTCTGTAATATGTTCAAGTTTT -s Anc0.Anc0refChr5 27803 25 + 87904 CTTAACCTCAATTGGTGATTCT-------------------TTC -s Anc1.Anc1refChr8 41856 44 + 57822 CTTAACCTCAATTGGTGATTCTATCTTTAATATGTACCAGTTTC -s Anc2.Anc2refChr15 22072 25 + 86568 CTTAACCTCAATTGGCTGTTTT-------------------TTC -s mr.mrrefChr5 61184 44 + 294540 CTTAAGCTTATTCGGTGATTCTTTCTGTAATATGTTCAAGTTTT -s simDog_chr6.simDog.chr6 486965 25 - 593897 CTTAACCTCAATTGGCTGTTTT-------------------TTC -s simHuman_chr6.simHuman.chr6 209293 32 + 601863 ------------TGGTGAGCCTATCTTTAATATGTACCAGCTTC -s simRat_chr6.simRat.chr6 196897 44 + 647215 CTTAAGCTTTTTTGGTGATTATTTCTGTAATATGTTCAAGTTCT - -a -s simMouse_chr6.simMouse.chr6 206534 28 + 636262 CCCCTAGTATGGCAGTACTAATACGCTT -s Anc0.Anc0refChr5 27828 24 + 87904 CCACTAA----GCAGTACCATTCAGCCT -s Anc1.Anc1refChr8 41900 28 + 57822 CCACTAATTGAGCAGTACCATTCAGCCT -s Anc2.Anc2refChr15 22097 24 + 86568 CCACCAA----GCGGTACCATTCACCCT -s mr.mrrefChr5 61228 28 + 294540 CCCCTAGTATGGCAGTACTAATAAGCTT -s simCow_chr6.simCow.chr6 380066 10 - 602619 ------------------CATTCACCCT -s simDog_chr6.simDog.chr6 486995 24 - 593897 CCACCAA----GCGGTACCCTTCACCCT -s simHuman_chr6.simHuman.chr6 209325 28 + 601863 CCACTAATTGTGCAGTACCATTCAGCCT -s simRat_chr6.simRat.chr6 196941 25 + 647215 CC---AGTATGGCAGTACTAATAAGTTT - -a -s simMouse_chr6.simMouse.chr6 206562 9 + 636262 TAAAGCCCA -s Anc0.Anc0refChr5 27863 8 + 87904 CAGA-CCCA -s Anc1.Anc1refChr8 41939 8 + 57822 CAGA-CCCA -s Anc2.Anc2refChr15 22132 8 + 86568 CCGG-GCCA -s mr.mrrefChr5 61256 8 + 294540 TAAA-CCCA -s simCow_chr6.simCow.chr6 380087 8 - 602619 CCTG-GTTT -s simDog_chr6.simDog.chr6 487030 8 - 593897 CCGG-GCCA -s simHuman_chr6.simHuman.chr6 209364 8 + 601863 CAGA-CCCA -s simRat_chr6.simRat.chr6 196966 8 + 647215 TAAA-CCCA - -a -s simMouse_chr6.simMouse.chr6 206571 51 + 636262 GTTATACCTACCCTGCAATAACTCCTACCAAGCATGACATCACCACTACTA -s Anc0.Anc0refChr5 27871 51 + 87904 GTTGTATCAACCAGGCAATAACTTATACCAACCATGCCATCACCACCACTA -s Anc1.Anc1refChr8 41947 51 + 57822 GTTGTATCAACCAGGCAATAACTTATACCAACCATGCCATCACCACCACTA -s Anc2.Anc2refChr15 22148 51 + 86568 GTTGTACCAACCAGGCAATGACCTATACCTACCATGCCATCACCACCACTA -s mr.mrrefChr5 61264 51 + 294540 GTTATATCTACCATGCAATAACTCCTACCAAGCATGACATCACCACTACTA -s simCow_chr6.simCow.chr6 380103 51 - 602619 GTTGTACCACCCAGGCAATGACATGTACCTACCATGCCATTAGTGCCACTA -s simDog_chr6.simDog.chr6 487046 51 - 593897 GTTGTACCAACCAGGCAATGACCTATACCTACCATGCCATCACCACTAGCA -s simHuman_chr6.simHuman.chr6 209372 51 + 601863 TCTGTATACACCAGGCAATAACTTATACCAATCATCCCAACAACAACACTA -s simRat_chr6.simRat.chr6 196974 47 + 647215 GTTATATCTACCATGCAGTTACTCCTACCAAGCATGACATCACCACT---- - -a -s simMouse_chr6.simMouse.chr6 206622 21 + 636262 GCCAGCTGTGCTGAAGACCCT -s Anc0.Anc0refChr5 27922 21 + 87904 GCCAGCTGTGTGGAGGACCCT -s Anc1.Anc1refChr8 41998 21 + 57822 GCCAGCTGTGTGGAGGACCCT -s Anc2.Anc2refChr15 22199 21 + 86568 GACAGGTGTGTGGAGGACCCT -s mr.mrrefChr5 61315 21 + 294540 GCCAGCTGTGCTGAGGACCCT -s simCow_chr6.simCow.chr6 380154 21 - 602619 CCCAGGTGTGCGGAGGGTCCT -s simDog_chr6.simDog.chr6 487097 21 - 593897 GATAGGTGTGTGGAGGACCCT -s simHuman_chr6.simHuman.chr6 209424 21 + 601863 GCCAGCTGTGGGGAGGACCCT -s simRat_chr6.simRat.chr6 197021 19 + 647215 --CAGCTGTGCAGAGGACCCA - -a -s simMouse_chr6.simMouse.chr6 206643 39 + 636262 GCGTCAGGAGTGTCCATTCTAAGCATTGTAGAACACCCA -s Anc0.Anc0refChr5 27943 39 + 87904 GTATCAGGGATGTGAGTTCCAAGCATTGTAGAGCACCCA -s Anc1.Anc1refChr8 42019 39 + 57822 GTATCAGGGATGTGAGTTCCAAGCATTGTAGAGCACCCA -s Anc2.Anc2refChr15 22220 39 + 86568 GTATAAGGGATGTGAGGTCCAAGCATTGTAGAGCACCCA -s mr.mrrefChr5 61336 39 + 294540 GTGTCAGGAGTGTCCATTCTAAGCATTGTAGAACACCCA -s simCow_chr6.simCow.chr6 380175 39 - 602619 GTATTAAGGATCCGAGGTCTCAGCATTGTAGAGCATACA -s simDog_chr6.simDog.chr6 487118 34 - 593897 ATATAAGGGTTGTAGCGTCCAAGCATTGT-----ACCCA -s simHuman_chr6.simHuman.chr6 209445 38 + 601863 GTTGC-GGGATGTGAGTACAAAACATTGTAGATCACCCA -s simRat_chr6.simRat.chr6 197043 39 + 647215 GTGTCAGGAGTGTCCATTCTAAGCATTGTAGAACAACCA - -a -s simMouse_chr6.simMouse.chr6 206682 7 + 636262 ATGTGGT -s Anc0.Anc0refChr5 27982 6 + 87904 TT-TGGT -s Anc1.Anc1refChr8 42058 7 + 57822 TTGTGGT -s Anc2.Anc2refChr15 22259 6 + 86568 TT-TGGC -s mr.mrrefChr5 61375 7 + 294540 ATGTGGT -s simCow_chr6.simCow.chr6 380215 6 - 602619 TT-TGGA -s simDog_chr6.simDog.chr6 487152 6 - 593897 TT-TAGC -s simHuman_chr6.simHuman.chr6 209483 7 + 601863 TTGTGGT -s simRat_chr6.simRat.chr6 197082 7 + 647215 GTGTGGT - -a -s simMouse_chr6.simMouse.chr6 206689 11 + 636262 GCATTGTTATT -s Anc0.Anc0refChr5 27988 11 + 87904 ACATCGTTGTT -s Anc1.Anc1refChr8 42065 11 + 57822 ACATCGTTGTT -s Anc2.Anc2refChr15 22265 11 + 86568 ACATCGTTCTT -s mr.mrrefChr5 61382 11 + 294540 GCATTGTTGTT -s simCow_chr6.simCow.chr6 380221 11 - 602619 ACATCACTATT -s simDog_chr6.simDog.chr6 487158 11 - 593897 TCATTGTTCTT -s simHuman_chr6.simHuman.chr6 209504 11 + 601863 ACATCCTAGAT -s simRat_chr6.simRat.chr6 197089 11 + 647215 GCATTGTTGTT - -a -s simMouse_chr6.simMouse.chr6 206700 12 + 636262 TCTTGAATAACT -s Anc0.Anc0refChr5 27999 12 + 87904 TCTTGTATAACT -s Anc1.Anc1refChr8 42076 12 + 57822 TCTTGTATAACT -s Anc2.Anc2refChr15 22276 12 + 86568 TCTTGTATAACT -s mr.mrrefChr5 61393 12 + 294540 TCTTGAATAACT -s simCow_chr6.simCow.chr6 380234 12 - 602619 TCTCCTACACCT -s simDog_chr6.simDog.chr6 487169 12 - 593897 TTTTGTATAACT -s simHuman_chr6.simHuman.chr6 209515 12 + 601863 TCTTATATAACT -s simRat_chr6.simRat.chr6 197100 12 + 647215 TCTTGGATAACT - -a -s simMouse_chr6.simMouse.chr6 206712 25 + 636262 ACAATAGAGGTATTCCATCATATCT -s Anc0.Anc0refChr5 28011 25 + 87904 Acaataagggtgttccatctcatca -s Anc1.Anc1refChr8 42088 25 + 57822 Acaataagggtgttccatctcatca -s Anc2.Anc2refChr15 22309 25 + 86568 Acaataagggtgttccatctcatca -s mr.mrrefChr5 61405 25 + 294540 ACAATAGAGGTATTCCATCACATCT -s simCow_chr6.simCow.chr6 380267 25 - 602619 acaataagggtgttccatcttatca -s simDog_chr6.simDog.chr6 487202 23 - 593897 ACAATAAGGGTGTTCCA--TCATGA -s simHuman_chr6.simHuman.chr6 209527 25 + 601863 Acgataagggtgttcaatctcatca -s simRat_chr6.simRat.chr6 197112 25 + 647215 AAAGTAGAGGTATTCGATCACATCT - -a -s simMouse_chr6.simMouse.chr6 206737 4 + 636262 CTCA -s Anc0.Anc0refChr5 28036 4 + 87904 ctca -s Anc1.Anc1refChr8 42113 4 + 57822 ctca -s Anc2.Anc2refChr15 22334 4 + 86568 ctca -s mr.mrrefChr5 61430 4 + 294540 CTCA -s simCow_chr6.simCow.chr6 380292 4 - 602619 ctca -s simDog_chr6.simDog.chr6 487230 4 - 593897 CACA -s simHuman_chr6.simHuman.chr6 209552 4 + 601863 ctca -s simRat_chr6.simRat.chr6 197137 4 + 647215 ATCA - -a -s simMouse_chr6.simMouse.chr6 206741 30 + 636262 TGTTTGGTATCATCTTAGACCTATCAAGCT -s Anc0.Anc0refChr5 28040 24 + 87904 tgtttggcatcgtcttggacttg------t -s Anc1.Anc1refChr8 42117 24 + 57822 tgtttggcatcgtcttggacttg------t -s Anc2.Anc2refChr15 22338 24 + 86568 tgttcggcatcgtcttggacttg------t -s mr.mrrefChr5 61434 30 + 294540 TGTTTGGTATCATCTTAGACCTGTCAAGCT -s simCow_chr6.simCow.chr6 380296 24 - 602619 tgttcggcatagccttggacctg------t -s simDog_chr6.simDog.chr6 487248 24 - 593897 TGTTCCATCTCGTTCCAGATTTG------T -s simHuman_chr6.simHuman.chr6 209556 24 + 601863 tgtttggcacggtcttggtcttg------t -s simRat_chr6.simRat.chr6 197141 30 + 647215 TGTTTGGTATCATCTTAGACCTGTTAAGGT - -a -s simMouse_chr6.simMouse.chr6 206771 70 + 636262 AATTTGTCAATAGAAAGATGGACACAAGGCTTTTGACTGGATGAAACAGGATGCTGACCTGTCCATAATC -s Anc0.Anc0refChr5 28074 68 + 87904 aatttgtcaatagaaacatggaca--aggcatttgactggatgaaacggaactctgacctgtccatattc -s Anc1.Anc1refChr8 42151 68 + 57822 aatttgtcaatagaaacatggaca--aggcatttgactggatgaaacggaactctgacctgtccatattc -s Anc2.Anc2refChr15 22372 68 + 86568 attctgtcaaaagaaacatgggtg--aggcatttgactggatgaaagggaactctgacctgtccatattc -s mr.mrrefChr5 61474 68 + 294540 AATTTGTCAATAGAAAGATGGACA--AGGCTTTTGACTGGATGAAAcagGATGCTGACCTGTCCATAATC -s simCow_chr6.simCow.chr6 380330 56 - 602619 agtctgttgaaagaaagatggttg--aggcatttaacttgatgaaagggaacattgac------------ -s simDog_chr6.simDog.chr6 487282 68 - 593897 ATTCTGTCAAATGAAACATGGGTG--AGGCATTAGACAGGATCAAAGGGAACTCTAACCTGTCCATATTC -s simHuman_chr6.simHuman.chr6 209590 68 + 601863 aatttgccaatagaaaattggaca--aggcatttgattggatgaaacggaactccgacctattcatactt -s simRat_chr6.simRat.chr6 197181 65 + 647215 AATCTGTCAATAGAAAGATGGACA--AGGCTTTTAACTCGATGACA---GATGCTGACCTGTCCATAATC - -a -s simMouse_chr6.simMouse.chr6 206841 27 + 636262 GGAATTATATATGTAGTGTACTTTTTT -s Anc0.Anc0refChr5 28143 27 + 87904 tggataagatatgtagcttaccttttc -s Anc1.Anc1refChr8 42220 27 + 57822 tggataagatatgtagcttaccttttc -s Anc2.Anc2refChr15 22441 27 + 86568 tggataagataagtagcctgcctctcc -s mr.mrrefChr5 61543 27 + 294540 GGAATTATATATGTAGCTTACTTTTTT -s simDog_chr6.simDog.chr6 487351 27 - 593897 TGGATAAGATAAGTAGCCTGCCTCTCC -s simHuman_chr6.simHuman.chr6 209659 27 + 601863 tggatgaggtatgtagcttacctttta -s simRat_chr6.simRat.chr6 197247 27 + 647215 GGAATTATATATGTAGCTTACTTTTTT - -a -s simMouse_chr6.simMouse.chr6 206868 7 + 636262 AGTGGTG -s Anc0.Anc0refChr5 28170 7 + 87904 aacggtg -s Anc1.Anc1refChr8 42247 7 + 57822 aacggtg -s Anc2.Anc2refChr15 22468 7 + 86568 aacggtg -s mr.mrrefChr5 61570 7 + 294540 AATGGTG -s simCow_chr6.simCow.chr6 380386 3 - 602619 ----atg -s simDog_chr6.simDog.chr6 487379 7 - 593897 AACGGTG -s simHuman_chr6.simHuman.chr6 209686 7 + 601863 aagggag -s simRat_chr6.simRat.chr6 197274 7 + 647215 AATGGTG - -a -s simMouse_chr6.simMouse.chr6 206875 8 + 636262 TGCTGATC -s Anc0.Anc0refChr5 28183 8 + 87904 tgattatc -s Anc1.Anc1refChr8 42260 8 + 57822 tgattatc -s Anc2.Anc2refChr15 22481 8 + 86568 tgattatc -s mr.mrrefChr5 61577 8 + 294540 TGATTATC -s simCow_chr6.simCow.chr6 380395 8 - 602619 tgattacc -s simDog_chr6.simDog.chr6 487392 8 - 593897 TAATTATC -s simHuman_chr6.simHuman.chr6 209699 8 + 601863 tgattatc -s simRat_chr6.simRat.chr6 197281 8 + 647215 TGATTATC - -a -s simMouse_chr6.simMouse.chr6 206883 7 + 636262 AGGTAAA -s Anc0.Anc0refChr5 28196 7 + 87904 agggaac -s Anc1.Anc1refChr8 42273 7 + 57822 agggaac -s Anc2.Anc2refChr15 22494 7 + 86568 ggggaat -s mr.mrrefChr5 61585 7 + 294540 AGGTAAA -s simCow_chr6.simCow.chr6 380408 7 - 602619 ggggaat -s simDog_chr6.simDog.chr6 487405 7 - 593897 GGGGAAT -s simHuman_chr6.simHuman.chr6 209712 7 + 601863 agggaac -s simRat_chr6.simRat.chr6 197289 7 + 647215 AGGTAGA - -a -s simMouse_chr6.simMouse.chr6 206890 4 + 636262 CCCT -s Anc0.Anc0refChr5 28203 4 + 87904 cctt -s Anc1.Anc1refChr8 42280 4 + 57822 cctt -s Anc2.Anc2refChr15 22501 4 + 86568 cctt -s mr.mrrefChr5 61592 4 + 294540 CCCT -s simCow_chr6.simCow.chr6 380419 4 - 602619 cctt -s simDog_chr6.simDog.chr6 487412 4 - 593897 CTTT -s simHuman_chr6.simHuman.chr6 209719 4 + 601863 cctc -s simRat_chr6.simRat.chr6 197296 4 + 647215 CCCT - -a -s simMouse_chr6.simMouse.chr6 206894 24 + 636262 TGTCATTTATCTGAGAATTGTGCA -s Anc0.Anc0refChr5 28207 10 + 87904 tgtcattcat-------------- -s Anc1.Anc1refChr8 42284 10 + 57822 tgtcattcat-------------- -s Anc2.Anc2refChr15 22506 10 + 86568 tgtcattcat-------------- -s mr.mrrefChr5 61596 24 + 294540 TGTCATTTATCTGAGAATTGTGCA -s simCow_chr6.simCow.chr6 380424 10 - 602619 tgttactcat-------------- -s simDog_chr6.simDog.chr6 487417 10 - 593897 TGCCATTCAT-------------- -s simHuman_chr6.simHuman.chr6 209723 10 + 601863 tgtcagtcat-------------- -s simRat_chr6.simRat.chr6 197300 24 + 647215 TGTCATTTATCTGAGAACTGTGTG - -a -s simMouse_chr6.simMouse.chr6 206918 45 + 636262 CAGTAAACACTATACCATACTTAAATAGCACCTTAACTGAGTGAC -s Anc0.Anc0refChr5 28217 45 + 87904 cagctgataatataccatacctgattagcaatttaagtaagatat -s Anc1.Anc1refChr8 42294 45 + 57822 cagctgataatataccatacctgattagcaatttaagtaagatat -s Anc2.Anc2refChr15 22516 45 + 86568 cagctgataatagagtatacctgactagcaatttaagtgagatat -s mr.mrrefChr5 61620 45 + 294540 CAGCAAACACTATACCATACTTAATTAGCACCTTAACTAAGTTAT -s simCow_chr6.simCow.chr6 380446 45 - 602619 ccgctggtaatagagtatacctgactggcaagttaagtgaggtat -s simDog_chr6.simDog.chr6 487427 40 - 593897 CACATGATA-----GTCTACTTGACTAGCAATTTAAGTGAGACAT -s simHuman_chr6.simHuman.chr6 209733 45 + 601863 tagctgataacataccatatctgattagcagtttaagcaacatat -s simRat_chr6.simRat.chr6 197324 45 + 647215 CAGCAAACACTATACCATACTTAATTAGCAACTTAACTAAGTTAT - -a -s simMouse_chr6.simMouse.chr6 206963 9 + 636262 CTAGTAACA -s Anc0.Anc0refChr5 28262 9 + 87904 ctggtgaca -s Anc1.Anc1refChr8 42339 9 + 57822 ctggtgaca -s Anc2.Anc2refChr15 22561 9 + 86568 atggcacca -s mr.mrrefChr5 61665 9 + 294540 CTAGTGACA -s simCow_chr6.simCow.chr6 380516 9 - 602619 atggatcca -s simDog_chr6.simDog.chr6 487467 9 - 593897 ATGGCACCA -s simHuman_chr6.simHuman.chr6 209778 9 + 601863 ctggtgaca -s simRat_chr6.simRat.chr6 197369 9 + 647215 CTCGTGACA - -a -s simMouse_chr6.simMouse.chr6 206972 44 + 636262 ATGAAAATGCTAGATCCCCTTTTTTTTTTAACAAGAATAACCAA -s Anc0.Anc0refChr5 28271 44 + 87904 atcaacatgctcaagtccctgttgtttttaacaagaataaccaa -s Anc1.Anc1refChr8 42348 44 + 57822 atcaacatgctcaagtccctgttgtttttaacaagaataaccaa -s Anc2.Anc2refChr15 22570 44 + 86568 atcaacatgctcaagtccctgttgtttgtagcaagaatgaccaa -s mr.mrrefChr5 61674 44 + 294540 ATCAAAATGCTAGATTCCCTTTTTtttttaacaAGAATAACCAA -s simCow_chr6.simCow.chr6 380531 44 - 602619 attaacatgctcacgtccctgttgtttgtagcaagaattaccaa -s simDog_chr6.simDog.chr6 487476 39 - 593897 AGC----TGCTCAAGTCCATG-TGTTTGTAGCAAGAATGACCAA -s simHuman_chr6.simHuman.chr6 209787 44 + 601863 atcaacatgctctagtccccattgttcttaacaaggataaccaa -s simRat_chr6.simRat.chr6 197378 35 + 647215 ATCAAAATGGGAGAATCCCTCTCT---------AGAATAACCAA - -a -s simMouse_chr6.simMouse.chr6 207016 3 + 636262 GGA -s Anc0.Anc0refChr5 28315 3 + 87904 gaa -s Anc1.Anc1refChr8 42392 3 + 57822 gaa -s Anc2.Anc2refChr15 22614 3 + 86568 gaa -s mr.mrrefChr5 61718 3 + 294540 GGA -s simCow_chr6.simCow.chr6 380575 3 - 602619 gaa -s simDog_chr6.simDog.chr6 487515 3 - 593897 GAA -s simHuman_chr6.simHuman.chr6 209831 3 + 601863 gaa -s simRat_chr6.simRat.chr6 197413 3 + 647215 GGA -s simRat_chr6.simRat.chr6 355274 3 - 647215 AAA - -a -s simMouse_chr6.simMouse.chr6 207019 2 + 636262 TT -s Anc0.Anc0refChr5 28318 2 + 87904 ct -s Anc1.Anc1refChr8 42395 2 + 57822 ct -s Anc2.Anc2refChr15 22617 2 + 86568 ct -s mr.mrrefChr5 61721 2 + 294540 TT -s simCow_chr6.simCow.chr6 380578 2 - 602619 ct -s simDog_chr6.simDog.chr6 193272 2 + 593897 CA -s simHuman_chr6.simHuman.chr6 209834 2 + 601863 ct -s simRat_chr6.simRat.chr6 197416 2 + 647215 TT -s simRat_chr6.simRat.chr6 355277 2 - 647215 AC - -a -s simMouse_chr6.simMouse.chr6 207021 5 + 636262 GCAGG -s Anc0.Anc0refChr5 28327 5 + 87904 catga -s Anc1.Anc1refChr8 42404 5 + 57822 catga -s Anc2.Anc2refChr15 22626 5 + 86568 catga -s mr.mrrefChr5 61723 5 + 294540 GGAGG -s simCow_chr6.simCow.chr6 380587 5 - 602619 catgg -s simDog_chr6.simDog.chr6 193281 5 + 593897 CATGA -s simHuman_chr6.simHuman.chr6 209843 5 + 601863 catga -s simRat_chr6.simRat.chr6 197418 5 + 647215 GGAGG -s simRat_chr6.simRat.chr6 355279 5 - 647215 TGTGG - -a -s simMouse_chr6.simMouse.chr6 207026 7 + 636262 TGTTTAA -s Anc0.Anc0refChr5 28333 7 + 87904 tgattag -s Anc1.Anc1refChr8 42410 7 + 57822 tgattag -s Anc2.Anc2refChr15 22632 7 + 86568 tcattag -s mr.mrrefChr5 61729 7 + 294540 TGTTTAG -s simCow_chr6.simCow.chr6 380593 7 - 602619 caattag -s simDog_chr6.simDog.chr6 193287 7 + 593897 TCATTAG -s simHuman_chr6.simHuman.chr6 209849 7 + 601863 tgatttg -s simRat_chr6.simRat.chr6 197424 7 + 647215 TGTTGAG -s simRat_chr6.simRat.chr6 355285 7 - 647215 TGTCTAG - -a -s simMouse_chr6.simMouse.chr6 207033 8 + 636262 AATGCAAT -s Anc0.Anc0refChr5 28342 3 + 87904 -----aat -s Anc1.Anc1refChr8 42423 8 + 57822 aatctaat -s Anc2.Anc2refChr15 22641 3 + 86568 -----aac -s mr.mrrefChr5 61742 8 + 294540 AATGCAAT -s simCow_chr6.simCow.chr6 380602 3 - 602619 -----aac -s simHuman_chr6.simHuman.chr6 209862 8 + 601863 aatctgat -s simRat_chr6.simRat.chr6 197437 8 + 647215 AGTGCAAT -s simRat_chr6.simRat.chr6 355298 4 - 647215 AAT----T - -a -s simMouse_chr6.simMouse.chr6 207041 10 + 636262 TGGAATCACA -s Anc0.Anc0refChr5 28348 10 + 87904 tagaaacaca -s Anc1.Anc1refChr8 42434 10 + 57822 tagaaacaca -s Anc2.Anc2refChr15 22647 10 + 86568 cagaaaccca -s mr.mrrefChr5 61753 10 + 294540 TGGAATCACA -s simCow_chr6.simCow.chr6 380608 10 - 602619 cagaaaccca -s simHuman_chr6.simHuman.chr6 209873 10 + 601863 tatagaaaca -s simRat_chr6.simRat.chr6 197448 10 + 647215 TGGAGTCACA -s simRat_chr6.simRat.chr6 355305 10 - 647215 TGGAATCACA - -a -s simMouse_chr6.simMouse.chr6 207051 31 + 636262 CTTGATAAACATAGGAGAAGCCTAGTAACTA -s Anc0.Anc0refChr5 28359 31 + 87904 ctgactaaacatagtaaaggcctactaattg -s Anc1.Anc1refChr8 42445 31 + 57822 ctgactaaacatagtaaaggcctactaattg -s Anc2.Anc2refChr15 22658 31 + 86568 ctgactaaatatagtaaaggcctactaattg -s mr.mrrefChr5 61763 31 + 294540 CTTAATAAACATAGTAGAGGCCTAGTAACTG -s simCow_chr6.simCow.chr6 380619 31 - 602619 ctgactaaatatagtaaagacctactaatcg -s simDog_chr6.simDog.chr6 193296 15 + 593897 ----------------AACGCCCAGTAATTG -s simHuman_chr6.simHuman.chr6 209884 31 + 601863 atgacaggacatattaaaggcctactaattg -s simRat_chr6.simRat.chr6 197458 31 + 647215 CTTAATAAACATAGTAGACATCTAGTAACTG -s simRat_chr6.simRat.chr6 355315 31 - 647215 CTTAATAAACCTAGTAGAGGCCTAGAAACCG - -a -s simMouse_chr6.simMouse.chr6 207082 54 + 636262 AAATACCTAATCAACCGTTGTTTTAAGTAGACGGGCAGGGGGTTCCATGCGCTG -s Anc0.Anc0refChr5 28390 27 + 87904 tgatacttaatccactactggaataag--------------------------- -s Anc1.Anc1refChr8 42476 27 + 57822 tgatacttaatccactactggaataag--------------------------- -s Anc2.Anc2refChr15 22689 27 + 86568 tgatacttaatccactactggaatcaa--------------------------- -s mr.mrrefChr5 61794 54 + 294540 TGATACCTAATCAACTATTGTTTTAAGTAGACTGGCAGGGGGTTCCATGCGGTG -s simCow_chr6.simCow.chr6 380650 27 - 602619 ggatacttaactcactacttgaattaa--------------------------- -s simDog_chr6.simDog.chr6 193317 27 + 593897 TGATGTTtaatctaatactggaatcaa--------------------------- -s simHuman_chr6.simHuman.chr6 209915 27 + 601863 tgatacttagtccactactgaaataag--------------------------- -s simRat_chr6.simRat.chr6 197489 54 + 647215 CGATACCTGATCAACTATTGTTTCAAGTAGACTGGCACGGGGTTCCATGCGGGG -s simRat_chr6.simRat.chr6 355346 54 - 647215 TGATACCTAATCAACTATTGTTTTGAGTAGACTGGAAAGGGGATCCATGGGGTG - -a -s simMouse_chr6.simMouse.chr6 207136 45 + 636262 TGCACCCTGGCCCTGGTGTTACTTCAATTAATGAGGAGGCTACAA -s mr.mrrefChr5 61848 37 + 294540 T--------GCCCTGGTGTTACTTCAATTAATGAGGAGGCTACAA -s simRat_chr6.simRat.chr6 197548 37 + 647215 T--------GCCCTGGTGTTACCCTAATTAATGAGGAGGCTACAA -s simRat_chr6.simRat.chr6 355400 4 - 647215 T--------TTT--------------------------------- - -a -s simMouse_chr6.simMouse.chr6 207181 52 + 636262 TTTGGTGGTTGGTGGATGCCACCTTAGTCCTCCATATGATGAATAATGTGGG -s Anc0.Anc0refChr5 28417 9 + 87904 -------------------------------------------tgatggagg -s Anc1.Anc1refChr8 42503 9 + 57822 -------------------------------------------tgatggagg -s Anc2.Anc2refChr15 22716 9 + 86568 -------------------------------------------tgagggagg -s mr.mrrefChr5 61885 52 + 294540 TTTGGTGGTTGGTGGATGCCACCTTAGTCCTCCATATGATGAATAATGTGGG -s simCow_chr6.simCow.chr6 380677 7 - 602619 -------------------------------------------tgagggg-- -s simDog_chr6.simDog.chr6 193344 9 + 593897 -------------------------------------------tgagggagg -s simHuman_chr6.simHuman.chr6 209942 9 + 601863 -------------------------------------------tgatggagg -s simRat_chr6.simRat.chr6 197603 52 + 647215 TTTGGTGGTTGGTGGATGCCACCTTACTACTCCAGATGATGAATAATGTGGG - -a -s simMouse_chr6.simMouse.chr6 207233 37 + 636262 ATCTGCTAACCACCAGCAGGCTTGCAAAAGAACACCT -s Anc1.Anc1refChr8 42512 37 + 57822 atctgttgacctccagaaggcctccagaaaaaaacct -s mr.mrrefChr5 61937 37 + 294540 ATCTGTTAACCACCAGCAGGCTTGCAGAAGAACACCT -s simHuman_chr6.simHuman.chr6 210623 37 + 601863 atctgttgacctccagaaggcctccagaaaaaaacct -s simRat_chr6.simRat.chr6 197655 37 + 647215 ATCTGTTAACCACCAGTAGGTTTGTGGAAGAACACCT - -a -s simMouse_chr6.simMouse.chr6 207270 73 + 636262 AGGAATAAATTTGATATAGTGGTACGTGCAGGACTTGCTCTGGAACCTTGGTGTTTGTAAGTATTGGCTTTAT -s Anc0.Anc0refChr5 28426 7 + 87904 ------------------------------------------------------------------gctccag -s Anc1.Anc1refChr8 42549 72 + 57822 aggatctaatttgagatattggtatttacaagacgcgctccagaatattcgtacttgcaa-cacttgctccag -s Anc2.Anc2refChr15 22725 7 + 86568 ------------------------------------------------------------------tctctag -s mr.mrrefChr5 61974 73 + 294540 AGGAATAAATTTGATATAGTGGTACGTGCAAGACTTGCTCTGGAACCTTGGTACTTGCAAGCATTGGCTTTAT -s simDog_chr6.simDog.chr6 193353 7 + 593897 ------------------------------------------------------------------tctctag -s simHuman_chr6.simHuman.chr6 210660 72 + 601863 aggatctaatttgagatattggtatttacaagacgcgctccagaatattcgtacttgcaa-cacttgctccag -s simRat_chr6.simRat.chr6 197694 73 + 647215 AGGAATAAATTTGACATAGTGGTACGTTCAAGACTTGCTTTGGGACCTTGGTACTTACAAGCAGTGGCCTTGT - -a -s simMouse_chr6.simMouse.chr6 207343 3 + 636262 ATA -s Anc0.Anc0refChr5 28433 3 + 87904 aaa -s Anc1.Anc1refChr8 42621 3 + 57822 aaa -s Anc2.Anc2refChr15 23139 3 + 86568 aaa -s mr.mrrefChr5 62047 3 + 294540 ATA -s simCow_chr6.simCow.chr6 380951 3 - 602619 aaa -s simDog_chr6.simDog.chr6 193769 3 + 593897 gaa -s simHuman_chr6.simHuman.chr6 210732 3 + 601863 aca -s simRat_chr6.simRat.chr6 197767 3 + 647215 ATA - -a -s simMouse_chr6.simMouse.chr6 207346 5 + 636262 TCAAC -s Anc0.Anc0refChr5 28436 5 + 87904 tcaat -s Anc1.Anc1refChr8 42624 5 + 57822 tcaat -s Anc2.Anc2refChr15 23142 5 + 86568 ttgat -s mr.mrrefChr5 62050 5 + 294540 TCAAC -s simCow_chr6.simCow.chr6 380954 5 - 602619 ttcat -s simDog_chr6.simDog.chr6 193772 5 + 593897 ttgat -s simHuman_chr6.simHuman.chr6 210737 5 + 601863 ttgta -s simRat_chr6.simRat.chr6 197770 5 + 647215 TCACC - -a -s simMouse_chr6.simMouse.chr6 207351 23 + 636262 AGAAATGATAACAAATTGGACAG -s Anc0.Anc0refChr5 28441 23 + 87904 aaaaaTGGTAGCAAATTGGAGAT -s Anc1.Anc1refChr8 42629 23 + 57822 aaaaaTGGTAGCAAATTGGAGAT -s Anc2.Anc2refChr15 23150 23 + 86568 aaaaaTGGTAGCAAACTGAAGAT -s mr.mrrefChr5 62055 23 + 294540 AAAAATGATAACAAATTGGAGAT -s simCow_chr6.simCow.chr6 380962 23 - 602619 aaaagTGGTATTAAACTGAAGAT -s simDog_chr6.simDog.chr6 193780 23 + 593897 gaaaATGGTAGCAAACTGAAGAT -s simHuman_chr6.simHuman.chr6 210742 23 + 601863 aaaaatggtagcaagttggagat -s simRat_chr6.simRat.chr6 197775 23 + 647215 AAAAATGATAACAAATTCAAGAT - -a -s simMouse_chr6.simMouse.chr6 207374 17 + 636262 AACAGTCAAAAATGATA -s Anc0.Anc0refChr5 28464 17 + 87904 GATGATcaAAAGTGGAa -s Anc1.Anc1refChr8 42652 17 + 57822 GATGATcaAAAGTGGAa -s Anc2.Anc2refChr15 23173 17 + 86568 GATGATtaAAAGTGGAa -s mr.mrrefChr5 62078 17 + 294540 GACAGTCAAAAATGATA -s simCow_chr6.simCow.chr6 380986 15 - 602619 GATGAT--GATCTGGGA -s simDog_chr6.simDog.chr6 193803 16 + 593897 GATGATTAAGAGTGGA- -s simHuman_chr6.simHuman.chr6 210765 17 + 601863 gatgaacaaaagtggaa -s simRat_chr6.simRat.chr6 197798 17 + 647215 GACAGTCCAAAAACAAA - -a -s simMouse_chr6.simMouse.chr6 207391 1 + 636262 G -s Anc0.Anc0refChr5 28482 1 + 87904 A -s Anc1.Anc1refChr8 42670 1 + 57822 A -s Anc2.Anc2refChr15 23191 1 + 86568 A -s mr.mrrefChr5 62095 1 + 294540 A -s simCow_chr6.simCow.chr6 381002 1 - 602619 A -s simDog_chr6.simDog.chr6 193820 1 + 593897 A -s simHuman_chr6.simHuman.chr6 210783 1 + 601863 a -s simRat_chr6.simRat.chr6 197815 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 207392 50 + 636262 CACTCATCTTTCTACAAGAGCACTCATATACCAAATCCGCAATGAAGGTA -s Anc0.Anc0refChr5 28558 50 + 87904 cacttgtttttccagaagaggactcgtttcccaagtctaaaataaactca -s Anc1.Anc1refChr8 42746 50 + 57822 cacttgtttttccagaagaggactcgtttcccaagtctaaaataaactca -s Anc2.Anc2refChr15 23267 50 + 86568 ctcttgttttaccagaagaggactcatttcccaagtctaaaataaactca -s mr.mrrefChr5 62135 50 + 294540 CACTCATCTTTCTACAAGAGCACTCGTATACCAAGTCCACAATGAACTCA -s simCow_chr6.simCow.chr6 381106 50 - 602619 CTCTTGTTTCGCCAGAAGAGGACTGCTTTTCCAAGTCTAAAGTAAACTCA -s simDog_chr6.simDog.chr6 193944 50 + 593897 ctcttgttttaccaggagaggactcatttcgcaagcctgaaataaactta -s simHuman_chr6.simHuman.chr6 210867 50 + 601863 cacttgtttttccagatgatgactcgtttcccaagtctaaaataaactca -s simRat_chr6.simRat.chr6 197855 50 + 647215 CACTCATCTTTCTACAAGAGCATTCGTAATCCAAGTCCACAATGAACTCA - -a -s simMouse_chr6.simMouse.chr6 207442 1 + 636262 T -s Anc0.Anc0refChr5 28728 1 + 87904 C -s Anc1.Anc1refChr8 42916 1 + 57822 C -s Anc2.Anc2refChr15 23437 1 + 86568 C -s mr.mrrefChr5 62185 1 + 294540 T -s simDog_chr6.simDog.chr6 194261 1 + 593897 C -s simHuman_chr6.simHuman.chr6 211037 1 + 601863 C -s simRat_chr6.simRat.chr6 197905 1 + 647215 G - -a -s simMouse_chr6.simMouse.chr6 207443 9 + 636262 ACTATCCTC -s Anc0.Anc0refChr5 28729 9 + 87904 ACTGTCCAT -s Anc1.Anc1refChr8 42917 9 + 57822 ACTGTCCAT -s Anc2.Anc2refChr15 23438 9 + 86568 ACCGTACAT -s mr.mrrefChr5 62186 9 + 294540 ACTGTCCTC -s simDog_chr6.simDog.chr6 194262 9 + 593897 ACCGTACAT -s simHuman_chr6.simHuman.chr6 211040 9 + 601863 ACTGTCCAT -s simRat_chr6.simRat.chr6 197906 9 + 647215 ACTGTACCC - -a -s simMouse_chr6.simMouse.chr6 207452 31 + 636262 TTTAATAGATAAAGATTCATTGTCCTAACAC -s Anc0.Anc0refChr5 28738 31 + 87904 TTTAACAAGTAAAGATTCATTATCCTTACAC -s Anc1.Anc1refChr8 42926 31 + 57822 TTTAACAAGTAAAGATTCATTATCCTTACAC -s Anc2.Anc2refChr15 23447 31 + 86568 TCTAACAAGTAAAAATCCATTATCCTTACAC -s mr.mrrefChr5 62195 31 + 294540 TTTAATAAATAAAGATTCATTGTCCTAACAC -s simDog_chr6.simDog.chr6 194271 31 + 593897 TCTAACAAGTAAAAATCCATTATCCTTACAC -s simHuman_chr6.simHuman.chr6 211049 31 + 601863 TTCAAAAAGTAAAGATTCATTATCCTTACAC -s simRat_chr6.simRat.chr6 197976 31 + 647215 TTTAATAAAGAAAGACTCATTGTCCTAACAC - -a -s simMouse_chr6.simMouse.chr6 207483 2 + 636262 CT -s Anc0.Anc0refChr5 28769 2 + 87904 CT -s Anc1.Anc1refChr8 42957 2 + 57822 CT -s Anc2.Anc2refChr15 23478 2 + 86568 CT -s mr.mrrefChr5 62226 2 + 294540 CT -s simDog_chr6.simDog.chr6 194306 2 + 593897 CT -s simHuman_chr6.simHuman.chr6 211080 2 + 601863 CT -s simRat_chr6.simRat.chr6 198007 2 + 647215 CT - -a -s simMouse_chr6.simMouse.chr6 207485 12 + 636262 AACGATCCATTT -s Anc0.Anc0refChr5 28783 12 + 87904 ATGGCTAAACTT -s Anc1.Anc1refChr8 42971 12 + 57822 ATGGCTAAACTT -s Anc2.Anc2refChr15 23492 12 + 86568 ATGACTAAACTT -s mr.mrrefChr5 62228 12 + 294540 AACGATAAATTT -s simDog_chr6.simDog.chr6 194333 12 + 593897 ATGACTAAACTT -s simHuman_chr6.simHuman.chr6 211094 12 + 601863 AGGGCTAAACTT -s simRat_chr6.simRat.chr6 198009 12 + 647215 AAAGATAAATTT - -a -s simMouse_chr6.simMouse.chr6 207497 39 + 636262 AAGGGCCTCTGCCAGACAAGGAAACCACACACCAGGCCA -s Anc0.Anc0refChr5 28800 39 + 87904 AGGGGCCTCTACTAGAAAGGAGGATGGGACATCTGGACA -s Anc1.Anc1refChr8 42988 39 + 57822 AGGGGCCTCTACTAGAAAGGAGGATGGGACATCTGGACA -s Anc2.Anc2refChr15 23509 39 + 86568 AGGGGCCTCTACTTGAAAGGAGGATGGTACATCTGGACC -s mr.mrrefChr5 62240 39 + 294540 AAGGGCCTCTACCAGACAAGGAAACCAGACACCAGGCCA -s simDog_chr6.simDog.chr6 194350 39 + 593897 AGGGGCCTCTACTTGAAAGGAGGATGGTACATCTGGACC -s simHuman_chr6.simHuman.chr6 211111 39 + 601863 AGGGGCCTCTACTAAAAATGAGGATATGACATCTGGACA -s simRat_chr6.simRat.chr6 198021 39 + 647215 CAGGTCCTCTACCGGACAACGAAACCAGAGAGCAGGCCA - -a -s simMouse_chr6.simMouse.chr6 207536 62 + 636262 CAATTGCTGATTACCATGGTGTGAAACAGGAATGCGGCACTCTAGTCAACCTGAGGCAGTTA -s Anc0.Anc0refChr5 28866 43 + 87904 C----------------AGTATGAAA---AACTGCGGCATCCTAGTCAACGTAAGGAAGTGA -s Anc1.Anc1refChr8 43054 43 + 57822 C----------------AGTATGAAA---AACTGCGGCATCCTAGTCAACGTAAGGAAGTGA -s Anc2.Anc2refChr15 23575 43 + 86568 C----------------AGTATAAAA---AACTGCGGCCTCCTAGTCAATGTAAGGAAGTGG -s mr.mrrefChr5 62279 46 + 294540 C----------------GGTGTGAAACAGGAATGCGGCACTCTAGTCAACCTGAGGCAGTCA -s simCow_chr6.simCow.chr6 381164 23 - 602619 ---------------------------------------TCCTAGACAATGTAAGGAAGTGG -s simDog_chr6.simDog.chr6 194416 42 + 593897 C----------------AGTATAAAA---AACTGCGGCCTCCAAGTCAATCTAAGGAAGTT- -s simHuman_chr6.simHuman.chr6 211184 43 + 601863 C----------------AACCTGAAA---AACCACAGCATCCTAGTCAACGTAAGGAAGTGA -s simRat_chr6.simRat.chr6 198060 46 + 647215 C----------------GGTGTGAGACAGGAATGTGGCACTTTAATCAACCTGCGGCAATCA - -a -s simMouse_chr6.simMouse.chr6 207598 36 + 636262 GCATGCTCTGATCAAGCCATTCCAGGATTGTAGAGG -s Anc0.Anc0refChr5 28916 34 + 87904 GCATAT--TGTTATAGCCATTCCATTCTTGTAAGGG -s Anc1.Anc1refChr8 43104 34 + 57822 GCATAT--TGTTATAGCCATTCCATTCTTGTAAGGG -s Anc2.Anc2refChr15 23625 34 + 86568 TCATAT--TGTTATAGCCATTCCATTCTCCTAAGAG -s mr.mrrefChr5 62328 36 + 294540 GCATGTTCTGATCAAGCCATTCCATGATTGTAGAGG -s simCow_chr6.simCow.chr6 381194 34 - 602619 ACATAT--TGTTATAACCATTGCATTGTCCTGAAAA -s simDog_chr6.simDog.chr6 194465 34 + 593897 TCATAT--TGTAATAGCTGTTCCATCCTCCTAAGAG -s simHuman_chr6.simHuman.chr6 211234 28 + 601863 GCATCT--TGCTATAGCCATTCCAT--TTG----GG -s simRat_chr6.simRat.chr6 198109 36 + 647215 GCATGTTCTGAGCAAGCCATTCCATGATTGTAAAGG - -a -s simMouse_chr6.simMouse.chr6 207634 17 + 636262 CTTGAATGGGTGATAAG -s Anc0.Anc0refChr5 28950 17 + 87904 TTTGAAAGGGTGAAAAG -s Anc1.Anc1refChr8 43138 17 + 57822 TTTGAAAGGGTGAAAAG -s Anc2.Anc2refChr15 23659 17 + 86568 TTTGAAAGGGTGAAAAG -s mr.mrrefChr5 62364 17 + 294540 CTTGAATGGGTGATAAG -s simCow_chr6.simCow.chr6 381228 17 - 602619 TTTGAAAGGGTGAAAAG -s simDog_chr6.simDog.chr6 194499 17 + 593897 TTTAAAGGCGTAAAAAG -s simHuman_chr6.simHuman.chr6 211262 17 + 601863 TTTGAAAGGGTGGAGAG -s simRat_chr6.simRat.chr6 198151 17 + 647215 CTTGAATGGGTGATAAA - -a -s simMouse_chr6.simMouse.chr6 207651 14 + 636262 TAAAGGAATACTCA -s Anc0.Anc0refChr5 28975 12 + 87904 TAAAGGAATCTT-- -s Anc1.Anc1refChr8 43163 12 + 57822 TAAAGGAATCTT-- -s Anc2.Anc2refChr15 23684 12 + 86568 TAAAGGAATCTT-- -s mr.mrrefChr5 62381 14 + 294540 TAAAGGAATATTCA -s simCow_chr6.simCow.chr6 381253 12 - 602619 TAAAGGAATCTT-- -s simDog_chr6.simDog.chr6 194524 12 + 593897 TGAAAGAATCTT-- -s simHuman_chr6.simHuman.chr6 211287 12 + 601863 TAGAGGAATCTT-- -s simRat_chr6.simRat.chr6 198168 14 + 647215 TAAAGGAATGTCCA - -a -s simMouse_chr6.simMouse.chr6 207665 24 + 636262 CATATAAGAGAAATTTCAGCCTTC -s Anc0.Anc0refChr5 28993 24 + 87904 CATATAAGAGAAACTATAATGGTC -s Anc1.Anc1refChr8 43181 24 + 57822 CATATAAGAGAAACTATAATGGTC -s Anc2.Anc2refChr15 23702 24 + 86568 CATACAAGAGAAGCTATAATGGTC -s mr.mrrefChr5 62401 24 + 294540 CATATAAGAGAAACTTCAGCCTTC -s simCow_chr6.simCow.chr6 381271 24 - 602619 CATACAAGAGGAGTTACAATGGCC -s simDog_chr6.simDog.chr6 194542 24 + 593897 CATACAAGAGAAGCTATGATGGTC -s simHuman_chr6.simHuman.chr6 211305 24 + 601863 CGTATAAGAGAAACCATATTGGTC -s simRat_chr6.simRat.chr6 198192 24 + 647215 CATAGAAGAGAAACTTCAGCCTTC - -a -s simMouse_chr6.simMouse.chr6 207689 43 + 636262 CTTCAAAATCAAAGCATTTACTTCAGTCTCTCTAAAAGGTATA -s Anc0.Anc0refChr5 29017 40 + 87904 CT---CAACCTAACCATTTACCTTAGTTTATCTAAAAGATATA -s Anc1.Anc1refChr8 43205 40 + 57822 CT---CAACCTAACCATTTACCTTAGTTTATCTAAAAGATATA -s Anc2.Anc2refChr15 23726 40 + 86568 CT---CAACCTAACCATTAATCTTTGTTTATCGTAAAAATAAA -s mr.mrrefChr5 62425 43 + 294540 CTTCAAAATCTAAGCATTTACTTCAGTCTCTCTAAAAGATATA -s simCow_chr6.simCow.chr6 381297 12 - 602619 CA---CAATGTATTC---------------------------- -s simDog_chr6.simDog.chr6 194566 40 + 593897 CT---CCGCCTCACCATTAATCTTTGTTTATCGTAAAAATAAA -s simHuman_chr6.simHuman.chr6 211329 40 + 601863 CC---CAACCTAGCCATTTACCTTAGCTTATGTAAAAGATATA -s simRat_chr6.simRat.chr6 198216 43 + 647215 CTTCAAAATCTAAGCATTTACTTCAATCTCACTAAAAGATATA - -a -s simMouse_chr6.simMouse.chr6 207732 16 + 636262 TGTTCATCCCAGTCAG -s Anc0.Anc0refChr5 29059 16 + 87904 TATTCAATCCAGTCAT -s Anc1.Anc1refChr8 43247 16 + 57822 TATTCAATCCAGTCAT -s Anc2.Anc2refChr15 23768 16 + 86568 CACTCAATCCATTCAT -s mr.mrrefChr5 62468 16 + 294540 TGTTCATTCCAGTCAT -s simCow_chr6.simCow.chr6 381309 7 - 602619 ---------CATTCAT -s simDog_chr6.simDog.chr6 194609 16 + 593897 CACTCAATCCCTTCAT -s simHuman_chr6.simHuman.chr6 211371 16 + 601863 TATTCACTCCAGTCAT -s simRat_chr6.simRat.chr6 198259 16 + 647215 TGTTCATTTCAGTCAT - -a -s simMouse_chr6.simMouse.chr6 207748 30 + 636262 CCAATCAGCCAATGGCAGTAGGCTATAACT -s Anc0.Anc0refChr5 29079 30 + 87904 CCAATCAGTCATACCCTGCGGACCATAACT -s Anc1.Anc1refChr8 43267 30 + 57822 CCAATCAGTCATACCCTGCGGACCATAACT -s Anc2.Anc2refChr15 23788 30 + 86568 CCAATCAGTGATACCCTGCGGACCATAACT -s mr.mrrefChr5 62488 30 + 294540 CCAATCAGCCAATGGCTGTAGGCCATAACT -s simCow_chr6.simCow.chr6 381320 30 - 602619 CCAATCAGTAATACCTTGCAGGACATAACT -s simDog_chr6.simDog.chr6 194629 30 + 593897 CAAATCAGTGATACCCTGCGGACCATAACT -s simHuman_chr6.simHuman.chr6 211391 25 + 601863 CCAATGAGTCACACACTG-----CATAACT -s simRat_chr6.simRat.chr6 198279 30 + 647215 CCAATCAGCCAATGGCTATAGGCCATAACT - -a -s simMouse_chr6.simMouse.chr6 207778 1 + 636262 T -s Anc0.Anc0refChr5 29109 1 + 87904 T -s Anc1.Anc1refChr8 43297 1 + 57822 T -s Anc2.Anc2refChr15 23818 1 + 86568 T -s mr.mrrefChr5 62518 1 + 294540 T -s simCow_chr6.simCow.chr6 381389 1 - 602619 T -s simDog_chr6.simDog.chr6 194659 1 + 593897 T -s simHuman_chr6.simHuman.chr6 211416 1 + 601863 T -s simRat_chr6.simRat.chr6 198309 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 207779 39 + 636262 AAATTTTGAGTAAACAAATCATATCTGTAGGTCCAAACA -s Anc0.Anc0refChr5 29116 39 + 87904 AAATATTGTGTAAACCAATCTTATATCTAGTCCTGAACT -s Anc1.Anc1refChr8 43304 39 + 57822 AAATATTGTGTAAACCAATCTTATATCTAGTCCTGAACT -s Anc2.Anc2refChr15 23825 39 + 86568 ATATGTTGTGTGAACCAATCTTATATTTAGTCCTGAACT -s mr.mrrefChr5 62519 39 + 294540 AAATATTGAGTAAACAAATCATATCTCTAGGTCTAAACA -s simCow_chr6.simCow.chr6 381396 39 - 602619 ATATGTAGTGTGTACCAATCTTATATTTAGTCCTAAAGT -s simDog_chr6.simDog.chr6 194666 39 + 593897 GTATGTTGTATGAACCAGTCATATTTTTAGTTCTGAACA -s simHuman_chr6.simHuman.chr6 211423 39 + 601863 AAATATTGTGCAACCCAATCTTGTATCTGGTCCTTAACT -s simRat_chr6.simRat.chr6 198310 39 + 647215 AATAATTGAGTAAACAAATCGTATCTCTAGGTCTAAACA - -a -s simMouse_chr6.simMouse.chr6 207818 24 + 636262 TATGACACCAAAAAAAGTGGGGCA -s Anc0.Anc0refChr5 29155 24 + 87904 TAGGACAGCAGAAAAAAACAGGAA -s Anc1.Anc1refChr8 43343 24 + 57822 TAGGACAGCAGAAAAAAACAGGAA -s Anc2.Anc2refChr15 23864 24 + 86568 TAGGACAGCAGAAAAAAACAGGAA -s mr.mrrefChr5 62558 24 + 294540 TATGACACCAAAAAAAGTGGGGCA -s simCow_chr6.simCow.chr6 381435 24 - 602619 TAGGACAACAAAAAATAACAGGAA -s simDog_chr6.simDog.chr6 194706 22 + 593897 TAGGATGGTAG--AAAAACAGGAA -s simHuman_chr6.simHuman.chr6 211462 24 + 601863 TGGGACAGCAGTACAAAGAAGGAA -s simRat_chr6.simRat.chr6 198349 24 + 647215 TACGACACCAAAAAAAGTGGGGCA - -a -s simMouse_chr6.simMouse.chr6 207842 27 + 636262 CTTTCATGAGTCTCTCAACCAGCTCAG -s Anc0.Anc0refChr5 29180 26 + 87904 CCTTG-AGAGTATCACAACCAGCTCAG -s Anc1.Anc1refChr8 43368 27 + 57822 CCTTGGAGAGTATCACAACCAGCTCAG -s Anc2.Anc2refChr15 23889 26 + 86568 CCTTG-AGAGTATCACAACCAGCTCAG -s mr.mrrefChr5 62582 27 + 294540 CTTTCATGAGTCTCTCAACCAGCTCAG -s simDog_chr6.simDog.chr6 194729 26 + 593897 CCTTG-AGAGTATCACAACCAGCTCAG -s simHuman_chr6.simHuman.chr6 211487 27 + 601863 CCTTGTGGAGCACCATAGCCTGCCCAA -s simRat_chr6.simRat.chr6 198373 27 + 647215 CTTTCATGCGTCTCTCAATCAGCTCAG - -a -s simMouse_chr6.simMouse.chr6 207869 87 + 636262 AATGTAAGTTCGAGATCTGTAAGCTGGGTATTGATACTTGCATTCGCGTCCCCCTAGTAGGACTCCTCACACAACCTGTTTACCTCT -s Anc0.Anc0refChr5 29206 82 + 87904 TATGTAAGTTCAAAACCTGTAAGCTAGGTATTG-----TCCATTGGTAGCCCTCTAGTCGGACTACTCATATGACCTGTTTGCCTCT -s Anc1.Anc1refChr8 43395 85 + 57822 TATGTAAGTTCAAAACCTGTAAGCTAGGTATTGACA--TCCATTGGTAGCCCTCTAGTCGGACTACTCATATGACCTGTTTGCCTCT -s Anc2.Anc2refChr15 23915 82 + 86568 TATGTAAGTTCAAAACCTGCTCGCTAGGTATTG-----TCCATTGGTAGCCCTCTAGTCGGACTATTCACATGACCTGCTTGCCTCT -s mr.mrrefChr5 62609 87 + 294540 AATGTAAGTTCAAGATCTGTAAGCTGGGTATTGATATTTCCATTGGCGTCCCCCTAGTAGGACTCCTCATACAACCTGTTTACCTCT -s simCow_chr6.simCow.chr6 381687 76 - 602619 ---GTAAGTTCAAACCCTCCTCGCTAGGTATT--------TATGGGTAGCCGACTAGTAGGACTATTAACATGACCTGCTTGCCTCT -s simDog_chr6.simDog.chr6 194756 72 + 593897 TATGTAACCTCAAAACCTGCTCGCTTGGTATTG-----TCCATTGGTAGCCCTCT-ATCGGACT-TTCGCAGGACA--------TGT -s simHuman_chr6.simHuman.chr6 211514 85 + 601863 CATGTAAGTTCAAAACCTGTAAGCCAGGTATTAACA--TCCATTGGTTGCCCTCTCGTTGGACTGCTCATATGACCCATTTGCCTCT -s simRat_chr6.simRat.chr6 198400 87 + 647215 AATGTAAGTTCAAGATCTGGAAGCTGGGTATTGATATTCCCAGTGGCATCCCCCTAGTAGGACTCCTCATACAACCTGTTAACCACT - -a -s simMouse_chr6.simMouse.chr6 207956 115 + 636262 TTAGTATGTCCCATTACATTATCAGTCGCATGAGTCTTCACTTACCTTGTTATGATGTGCTCCTTGATGCTCTTGGTGTTCAATCGGATGCTCCTGGTGCTCAATCTGACGCAAA -s Anc0.Anc0refChr5 29288 82 + 87904 TTTGTTTGTTCTATTACATCATCAATCACACCAGTTTGCACTTACTTTGCTATAACGGGCTCCTTGATG---T------------------------------ATCTGACACAAA -s Anc1.Anc1refChr8 43480 91 + 57822 TTTGTTTGTTCTATTACATCATCAATCACACCAGTTTGCACTTACTTTGCTATAACGGGCTCCTTGATG---T---------------------TGGTACTCAATCTGACACAAA -s Anc2.Anc2refChr15 23997 82 + 86568 TTTGTTTGTTCTATTACATCATCAATCAGACCAGTTTGCACTTACTTTGCTATAACGGGCTCCCTGATG---T------------------------------ATCTGACACAAA -s mr.mrrefChr5 62696 94 + 294540 TTAGTATGTCCCATTACATTATCAGTCACATGAGTTTTCACTTACCTTGCTATGATGTGCTCCTTGATGCTCT---------------------TGGTGCTCAATCTGACACAAA -s simCow_chr6.simCow.chr6 381765 82 - 602619 TTTGCTTTTTCCGCTACATTGTTAAGGAGTCCAGTTTGCACTTACTTTGCTATAGCATCCTACCTGATG---A------------------------------TTCTGACACCAA -s simDog_chr6.simDog.chr6 194828 81 + 593897 TGTGTCTGTTCTATTACGTCATCACTCAGACCAGTGTGCACTTGCTTTGCTA-AATGGGCTCCCTGATG---T------------------------------ACCTGACATAAA -s simHuman_chr6.simHuman.chr6 211599 91 + 601863 TTTATTTGTACTATTACATCATCAATCACGCCAGATTGCACTTACTTTACTATAACGCGCTTTTTGATG---T---------------------TGGTACTCAATCTGACACAAA -s simRat_chr6.simRat.chr6 198487 94 + 647215 CTGGTATGTCCCATTGCATTATCAGTCAAATGAGTTTTTACTTACCTTGCTGTGCTGTGCTCCCTGATGTTCT---------------------TGGTGCTCAGTCTGACATAAA - -a -s simMouse_chr6.simMouse.chr6 208071 40 + 636262 GTGGCTCCCCACTGTGACTTAAATCAATCTCAGTCTTGTG -s Anc0.Anc0refChr5 29374 18 + 87904 GT---TCTCCATTATGACTTC------------------- -s Anc1.Anc1refChr8 43575 18 + 57822 GT---TCTCCATTATGACTTC------------------- -s Anc2.Anc2refChr15 24083 18 + 86568 GT---TCTCCATTATGACTTC------------------- -s mr.mrrefChr5 62794 21 + 294540 GTGGCTCCCCACTGTGACTTA------------------- -s simCow_chr6.simCow.chr6 381851 18 - 602619 GT---TCCCCATCACATCTTC------------------- -s simDog_chr6.simDog.chr6 194913 17 + 593897 GT---TCTCCATTATGACTT-------------------- -s simHuman_chr6.simHuman.chr6 211694 18 + 601863 GT---TCGCAATTATCACTTT------------------- -s simRat_chr6.simRat.chr6 198585 21 + 647215 GTGGCTCCCGACTGTGCCTTA------------------- - -a -s simMouse_chr6.simMouse.chr6 208111 31 + 636262 GTATTTTTTACTCTTCAAGTTTCTCAGTGTT -s Anc0.Anc0refChr5 56455 14 - 87904 GTTTCTT---------A--T------GTGTT -s Anc1.Anc1refChr8 12088 16 - 57822 GTTTCTT---------AAGT------GTGTT -s Anc2.Anc2refChr15 60350 14 - 86568 GTTTCTT---------C--C------ATGTT -s mr.mrrefChr5 229433 31 - 294540 GTATTTTTTACTCTTCAAGTTTCTCAGTGTT -s simCow_chr6.simCow.chr6 218547 14 + 602619 GTTTCTT---------C--C------TTGTT -s simDog_chr6.simDog.chr6 396875 14 - 593897 GTTCCTC---------C--C------ATGCT -s simHuman_chr6.simHuman.chr6 388026 16 - 601863 GTTTCTT---------AAGT------GGGTT -s simRat_chr6.simRat.chr6 445787 31 - 647215 GTATTTTTTACTCTTCAACTTTCTCAGTGTT - -a -s simMouse_chr6.simMouse.chr6 208142 111 + 636262 GTAGTATTTTTTACTAACATTTAGAGTGCACAAGGTTAAGTCTCATTTCTATCATTTCCTTGGTTAGCGTTTCAATCAGATTACATGCAGCATGACAGTCCATTACTTCTT -s Anc0.Anc0refChr5 56470 111 - 87904 GTTGTCTTTTTTATTAACATCTGAGGTCCATGAGGTTAACTGTCATTTTTATCAGATCCTTGGTCAGTGTTTCAATCAGCGTGTAGTGTGCATTACAGTACAGTACTTGTT -s Anc1.Anc1refChr8 12105 111 - 57822 GTTGTCTTTTTTATTAACATCTGAGGTCCATGAGGTTAACTGTCATTTTTATCAGATCCTTGGTCAGTGTTTCAATCAGCGTGTAGTGTGCATTACAGTACAGTACTTGTT -s Anc2.Anc2refChr15 60365 111 - 86568 GTTGTCTTTTTTATTAACATCTGAGGTCCATGAGTTAAACTGTCATTTTTATCAGATCCTAGGTCAGTGTTTCAATCAGCGTGTAGTGTGCATTACAGTATAGTACTTGTT -s mr.mrrefChr5 229464 111 - 294540 GTAGTATTTTTTACTAACATTTAGAGTGCACAAGGTTAAGTGTCATTTCTATCATTTCCTTGGTCAGTGTTTCAATCAGAATACATGGAGCATGACAGTACAGTACTTCTT -s simCow_chr6.simCow.chr6 218562 111 + 602619 GTTGTCTTTTTCATTAACCTCTGAGGTCCATGAACTGTAATGTCATATTTATGAGGTCCCCAGTCAGTGTTTCACTCAGTGTGTGGGGTGCCTTGCAGTATAGTACTTGGT -s simDog_chr6.simDog.chr6 396890 111 - 593897 GTCGTCACATTTAATACCATCTGAGGTCCATGAGTTAAACTGTCATTTTTATCAGATCCTAGGTCAGTGTTTCAATTAGCATGTAGTGTGCATTACAGTATAGTACTTGTT -s simHuman_chr6.simHuman.chr6 388043 84 - 601863 GTTGTCTTTTTTATTAATGTCTGAGGTCCATGGTGTTA--------------------CTTGGTCAGTGTTTTAATCAGCGTGTAAA-------ACAGTACAGTACTTTTT -s simRat_chr6.simRat.chr6 445818 110 - 647215 GTGGTATTTTTTACTAACACTTAGAGTGCACAAGTTTAAATGCCATTTCCATCATTTCCTTGG-CAGTGCTCCAATCAGTATACATGGGGCATGACAGTATGGTACTTCTA - -a -s simMouse_chr6.simMouse.chr6 208253 1 + 636262 T -s Anc0.Anc0refChr5 56581 1 - 87904 T -s Anc1.Anc1refChr8 12216 1 - 57822 T -s Anc2.Anc2refChr15 60476 1 - 86568 T -s mr.mrrefChr5 229575 1 - 294540 T -s simCow_chr6.simCow.chr6 218708 1 + 602619 T -s simDog_chr6.simDog.chr6 397001 1 - 593897 T -s simHuman_chr6.simHuman.chr6 388127 1 - 601863 A -s simRat_chr6.simRat.chr6 445928 1 - 647215 T - -a -s simMouse_chr6.simMouse.chr6 208254 9 + 636262 CCTAGGGAG -s Anc0.Anc0refChr5 56582 9 - 87904 CCTAAGTAG -s Anc1.Anc1refChr8 12217 9 - 57822 CCTAAGTAG -s Anc2.Anc2refChr15 60478 9 - 86568 CCCAAGTAG -s mr.mrrefChr5 229576 9 - 294540 CCTAGGGAG -s simCow_chr6.simCow.chr6 218710 9 + 602619 CCCAATTTG -s simDog_chr6.simDog.chr6 397003 9 - 593897 CCCAAGAAG -s simHuman_chr6.simHuman.chr6 388128 9 - 601863 GTTACATAG -s simRat_chr6.simRat.chr6 445929 9 - 647215 CCTAGGGAG - -a -s simMouse_chr6.simMouse.chr6 208263 40 + 636262 CTGCCATTGGGTGTAACTACCTGGGTAGTAAAGCTTGATA -s Anc0.Anc0refChr5 56591 37 - 87904 TCATCATGGGCTGCAACAACCAATGTA---AAGCTTGATA -s Anc1.Anc1refChr8 12226 37 - 57822 TCATCATGGGCTGCAACAACCAATGTA---AAGCTTGATA -s Anc2.Anc2refChr15 60487 37 - 86568 TCATCATGGGCTGCAACAACCAATGTA---AAGCTTGATA -s mr.mrrefChr5 229585 37 - 294540 CTGCCATTGGGTGTAACTACCAGTGTA---AAGCTTGATA -s simCow_chr6.simCow.chr6 218721 35 + 602619 TCATCATGGGCTGCAACAGCCAATGGA---AAGCAGG--A -s simDog_chr6.simDog.chr6 397012 37 - 593897 TTATAGTGTACTGCAACAACTGATGTA---AAGCTTGATA -s simHuman_chr6.simHuman.chr6 388137 37 - 601863 TCATCAGGGGCTGCAACAACCAATGTA---AAGCTTGATA -s simRat_chr6.simRat.chr6 445938 37 - 647215 ATGCCATTGGGTGTTACTACCAGTGTA---AAGAGTGATA - -a -s simMouse_chr6.simMouse.chr6 208303 55 + 636262 GGATTAGCACATAAATGGCTTACAAGTGTAAACCTACACCAGGATACCTGGAGGT -s Anc0.Anc0refChr5 56628 54 - 87904 GGATTAGCACACTACTGACT-ACAGTGGTAAACCACCACCTAGATACCTAGAGAT -s Anc1.Anc1refChr8 12263 54 - 57822 GGATTAGCACACTACTGACT-ACAGTGGTAAACCACCACCTAGATACCTAGAGAT -s Anc2.Anc2refChr15 60524 54 - 86568 GGATTAGCACACTACTGACT-ACAGTGGTAAACCACCACCTAGATACCTAGAGAT -s mr.mrrefChr5 229622 55 - 294540 GGATTAGCACATTAATGGCTTACAAGTGTAAACCTACACCTGGATACCTGGAGGT -s simCow_chr6.simCow.chr6 218756 54 + 602619 GGATTAACATACTGATTACT-ACAGGGGTAAACTACGACTTGGATGCCTAGAGAT -s simDog_chr6.simDog.chr6 397049 54 - 593897 GGACTAGCACTCTACTGACT-ACAGTGGTAAACCCCCACCTAGCTACCTAGAGAT -s simHuman_chr6.simHuman.chr6 388176 54 - 601863 GGATTAGCACACTAGTGACA-GCAGAGGGTAACCATCATACAGATCCCTAGAAAT -s simRat_chr6.simRat.chr6 445975 54 - 647215 GGATTAGCACATTAATGGCTTACAAGTGTAAACC-ACACCTGGATACCTGGAGGT - -a -s simMouse_chr6.simMouse.chr6 208358 7 + 636262 ATGAGAG -s Anc0.Anc0refChr5 56682 7 - 87904 CCTAGAG -s Anc1.Anc1refChr8 12317 7 - 57822 CCTAGAG -s Anc2.Anc2refChr15 60578 7 - 86568 CCTAAAG -s mr.mrrefChr5 229677 7 - 294540 ACGAGAG -s simCow_chr6.simCow.chr6 218886 7 + 602619 CTTAAAG -s simDog_chr6.simDog.chr6 397103 7 - 593897 GCTGAAG -s simHuman_chr6.simHuman.chr6 388230 7 - 601863 CCCAGAG -s simRat_chr6.simRat.chr6 446029 7 - 647215 ACAAGAG - -a -s simMouse_chr6.simMouse.chr6 208365 25 + 636262 AATTACTGCTCTACCTGACACAGCC -s Anc0.Anc0refChr5 56689 25 - 87904 AATTACTGCTCTCCCTGACATAGCC -s Anc1.Anc1refChr8 12324 25 - 57822 AATTACTGCTCTCCCTGACATAGCC -s Anc2.Anc2refChr15 60585 25 - 86568 ACTTACTGCTCTCCCTGACATAGCC -s mr.mrrefChr5 229684 25 - 294540 AATTACTGCTCTACCTGACACAGCC -s simCow_chr6.simCow.chr6 218893 25 + 602619 ATCTATTGCTTTCCATTACACAGCC -s simDog_chr6.simDog.chr6 397111 24 - 593897 TCTTACTACTCTCCCTGACAT-GTC -s simHuman_chr6.simHuman.chr6 388237 25 - 601863 AATTACTGCTCTCCCTGACAAAGCC -s simRat_chr6.simRat.chr6 446036 25 - 647215 AGTTACTGCTCTACCCAACACAGCC - -a -s simMouse_chr6.simMouse.chr6 208390 45 + 636262 TTACATTATGTTGAATGTCCTCCTGCCTCATTTATACTAATTGGG -s Anc0.Anc0refChr5 56716 44 - 87904 CT-CACTATGTAGAGTGCCTTCCTCCCTCATTAATCCTAACCAGG -s Anc1.Anc1refChr8 12351 44 - 57822 CT-CACTATGTAGAGTGCCTTCCTCCCTCATTAATCCTAACCAGG -s Anc2.Anc2refChr15 60612 44 - 86568 CT-CACTATGTAGAGTACCTTCCTCCCTGATTAAGCCCAACCAGG -s mr.mrrefChr5 229709 45 - 294540 CTACATTATGTTGAATGTCCTCCTGCCTCATTAATACTAATTGGG -s simCow_chr6.simCow.chr6 218920 44 + 602619 CT-CACTATGTGGAGTACCTTCCTCCCTAATTAAGCCCAACCAGG -s simDog_chr6.simDog.chr6 397137 33 - 593897 CT-CACTATGCAGAGTACCCTCGTCCCTGA-----------AAGG -s simHuman_chr6.simHuman.chr6 388264 44 - 601863 CT-CACTATGTAGAGTGCCTTCCTCCCTCATTAATCCTAGCCAGG -s simRat_chr6.simRat.chr6 446061 45 - 647215 CTGCATTATATTGAATGTTCTCCTGCATCATTAATTCTAATTGGG - -a -s simMouse_chr6.simMouse.chr6 208435 3 + 636262 TGC -s Anc0.Anc0refChr5 56760 3 - 87904 TAC -s Anc1.Anc1refChr8 12395 3 - 57822 TAC -s Anc2.Anc2refChr15 60656 3 - 86568 TAC -s mr.mrrefChr5 229754 3 - 294540 TGC -s simCow_chr6.simCow.chr6 218964 3 + 602619 TAC -s simDog_chr6.simDog.chr6 397170 3 - 593897 TGC -s simHuman_chr6.simHuman.chr6 388330 3 - 601863 TAC -s simRat_chr6.simRat.chr6 446106 3 - 647215 TGC - -a -s simMouse_chr6.simMouse.chr6 208438 5 + 636262 ATTCC -s Anc0.Anc0refChr5 56763 5 - 87904 ATTAC -s Anc1.Anc1refChr8 12398 5 - 57822 ATTAC -s Anc2.Anc2refChr15 60659 5 - 86568 ATTAT -s mr.mrrefChr5 229757 5 - 294540 ATTCC -s simCow_chr6.simCow.chr6 218967 5 + 602619 ATTAG -s simDog_chr6.simDog.chr6 397174 5 - 593897 ATTAT -s simHuman_chr6.simHuman.chr6 388333 5 - 601863 ATTAC -s simRat_chr6.simRat.chr6 446109 5 - 647215 ATTCC - -a -s simMouse_chr6.simMouse.chr6 208443 32 + 636262 AGGATATTACAGTCTGGCTCCTCATCTCACTG -s Anc0.Anc0refChr5 56769 32 - 87904 AGGATATTACAATCCAGCTTCCCAACTCACCA -s Anc1.Anc1refChr8 12404 32 - 57822 AGGATATTACAATCCAGCTTCCCAACTCACCA -s Anc2.Anc2refChr15 60665 32 - 86568 AGGATATTACAATCCAGTGTCCCAACTCACCA -s mr.mrrefChr5 229763 32 - 294540 AGGATATTACAGTCTGGCTCCCCATCTCACTG -s simCow_chr6.simCow.chr6 218973 32 + 602619 AGAACACCACAATCCAGTGTCCCAACTTACCA -s simDog_chr6.simDog.chr6 397180 32 - 593897 AGGATATTACAATTCAGTGTCCCAACTCTCCA -s simHuman_chr6.simHuman.chr6 388339 32 - 601863 AGGATATTATAAACCAGCTTCCCAACTCACCA -s simRat_chr6.simRat.chr6 446115 32 - 647215 AGAATATTACAGTCTGGTTCCCCACCTCACTG - -a -s simMouse_chr6.simMouse.chr6 208475 9 + 636262 TTTAACATC -s Anc0.Anc0refChr5 56803 9 - 87904 TTATACATC -s Anc1.Anc1refChr8 12438 9 - 57822 TTATACATC -s Anc2.Anc2refChr15 60699 9 - 86568 TCATACATC -s mr.mrrefChr5 229795 9 - 294540 TTTAACATC -s simCow_chr6.simCow.chr6 219007 9 + 602619 TCATACATC -s simDog_chr6.simDog.chr6 397214 9 - 593897 TCATTCACC -s simHuman_chr6.simHuman.chr6 388373 9 - 601863 TTGTACATC -s simRat_chr6.simRat.chr6 446147 9 - 647215 TTTCACATC - -a -s simMouse_chr6.simMouse.chr6 208484 33 + 636262 TCATGCTGTCCTTTATGTTTGAATAATCCGGGG -s Anc0.Anc0refChr5 56812 30 - 87904 TGGTGCTGTCCTTTGTGTTCAAATCAT---GAG -s Anc1.Anc1refChr8 12447 30 - 57822 TGGTGCTGTCCTTTGTGTTCAAATCAT---GAG -s Anc2.Anc2refChr15 60708 30 - 86568 TGGTGCTGTCCTTTGTGTTCAAATCAT---GAG -s mr.mrrefChr5 229804 30 - 294540 TTATGCTGTCCTTTATGTTTGAATAAT---GGG -s simCow_chr6.simCow.chr6 219016 30 + 602619 TGGCACTGTCGTTTGTGGTAAAAACAT---GAG -s simDog_chr6.simDog.chr6 397224 30 - 593897 TGGTGCTGTTCTTTGTGTTCGAATCAT---GAG -s simHuman_chr6.simHuman.chr6 388382 30 - 601863 TGGAGCTATCCTTTGTGTACAAATGAT---GAG -s simRat_chr6.simRat.chr6 446156 30 - 647215 TTATGTTGTCCTTTATGTTTGAATAAT---GGG - -a -s simMouse_chr6.simMouse.chr6 208517 45 + 636262 ATTCCAGTCTTTCTTAGTGTGTCCCTTGGCACTGTTAGAAGGATT -s Anc0.Anc0refChr5 56842 45 - 87904 ATTACAGTCATTCTTAGTGGGTCCTCTGGCTCTGTTAGAAGAATG -s Anc1.Anc1refChr8 12477 45 - 57822 ATTACAGTCATTCTTAGTGGGTCCTCTGGCTCTGTTAGAAGAATG -s Anc2.Anc2refChr15 60743 45 - 86568 ATTACAGGCATTCTTAGTGGGCCCTCTGGCACTGATAGAAAAATG -s mr.mrrefChr5 229834 45 - 294540 ATTCCAGTCTTTCTTAGTGGGTCCTTTGGCTCTGTTAGAAGGATT -s simCow_chr6.simCow.chr6 219051 43 + 602619 ATTATGGGCATTCTCAGCGCGCC--CTGGCACCCATAGAAAAATG -s simDog_chr6.simDog.chr6 397259 45 - 593897 ATTGCAGGCATTCTTAGTCGGCCCTCTAGCACTGATAGAAAGATG -s simHuman_chr6.simHuman.chr6 388412 45 - 601863 ATTACAGTCATTCTTTGTGGGTCCTCTGGCTATGTTATAAGAATG -s simRat_chr6.simRat.chr6 446186 44 - 647215 ATTCCAGCCCTTTTTAGTGGG-CCTTTGGATCTGTTAGAAGGATT - -a -s simMouse_chr6.simMouse.chr6 208562 36 + 636262 GATTACAGACAGGCTTATTCACAAATCCAAGTCTGT -s Anc0.Anc0refChr5 56888 36 - 87904 GATTACAGGCAGTCTTACTGTCAAGTCCAAGTCCCT -s Anc1.Anc1refChr8 12523 36 - 57822 GATTACAGGCAGTCTTACTGTCAAGTCCAAGTCCCT -s Anc2.Anc2refChr15 60789 36 - 86568 GATCACAGGCACTCTTACTGTCAAGTGTAAGTCCCT -s mr.mrrefChr5 229879 36 - 294540 GATTACAGACAGGCTTATTGACAAATCCAAGTCCGT -s simCow_chr6.simCow.chr6 219095 35 + 602619 GTTCACAGGTACTCTTACTTACAAAT-TAAGTCCCT -s simDog_chr6.simDog.chr6 397305 36 - 593897 GATCACAGGCACTCTCACTGTCAGGTGTAAGTCCCT -s simHuman_chr6.simHuman.chr6 388458 36 - 601863 GAATACAGGCAGTCTTACTGGCAAGACCAGGTCCCT -s simRat_chr6.simRat.chr6 446230 31 - 647215 GATTTCAGACAGGTTTAATGACAAA-----GTCCAT - -a -s simMouse_chr6.simMouse.chr6 208598 6 + 636262 TTGATT -s Anc0.Anc0refChr5 56925 6 - 87904 TTGGTT -s Anc1.Anc1refChr8 12560 6 - 57822 TTGGTT -s Anc2.Anc2refChr15 60826 6 - 86568 TGGGTT -s mr.mrrefChr5 229915 6 - 294540 TTGGTT -s simCow_chr6.simCow.chr6 219131 6 + 602619 TGGGTT -s simDog_chr6.simDog.chr6 397342 6 - 593897 TGGGTT -s simHuman_chr6.simHuman.chr6 388495 6 - 601863 TTGGTC -s simRat_chr6.simRat.chr6 446261 6 - 647215 TTGGTT - -a -s simMouse_chr6.simMouse.chr6 208604 62 + 636262 GGACCGGTTTGATTGAACCATATTTCTAATAAGTTATTCAAGATGTTATTTCTGCAAGGAAA -s Anc0.Anc0refChr5 56931 48 - 87904 GGACTG--------------TACTTGTAATAAGTTATTTGAGATGTTATTTCTGAGGGGACA -s Anc1.Anc1refChr8 12566 48 - 57822 GGACTG--------------TACTTGTAATAAGTTATTTGAGATGTTATTTCTGAGGGGACA -s Anc2.Anc2refChr15 60832 48 - 86568 GGACTG--------------TACTTGTAATAAATTAACTGAGATGTTATTTCTAAGGGGACA -s mr.mrrefChr5 229921 48 - 294540 GGACCG--------------TATTTCTAATAAGTTATTCAAGATGTTATTTCTGAGAGGAAA -s simCow_chr6.simCow.chr6 219138 48 + 602619 GGACTG--------------TACTTGTAATAAACTAACTGTTATGTTACTTCTAAGGGAACA -s simDog_chr6.simDog.chr6 397348 48 - 593897 AGACTG--------------TACTTGTAATAAATTAACTGAGATGTTTTTTCTAAGGTGCCA -s simHuman_chr6.simHuman.chr6 388501 41 - 601863 GG---------------------TTATGATGAGTTGTTTGAGATGCTATGTCTGGGGGGACA -s simRat_chr6.simRat.chr6 446267 48 - 647215 GGACCG--------------TATTTCTAATAAGCTATCCAAAATGTTATTTCTGAGAAGAAA - -a -s simMouse_chr6.simMouse.chr6 208666 8 + 636262 GAATTATG -s Anc0.Anc0refChr5 56979 8 - 87904 AAGTGCCA -s Anc1.Anc1refChr8 12614 8 - 57822 AAGTGCCA -s Anc2.Anc2refChr15 60880 8 - 86568 AAGTGCCA -s mr.mrrefChr5 229969 8 - 294540 GAATGATG -s simCow_chr6.simCow.chr6 219186 8 + 602619 AGGTGCCA -s simDog_chr6.simDog.chr6 397396 2 - 593897 AA------ -s simHuman_chr6.simHuman.chr6 388542 8 - 601863 AAGTGCCA -s simRat_chr6.simRat.chr6 446316 8 - 647215 GAATGATG - -a -s simMouse_chr6.simMouse.chr6 208674 7 + 636262 TATCTGC -s Anc0.Anc0refChr5 56987 7 - 87904 TATCTGC -s Anc1.Anc1refChr8 12622 7 - 57822 TATCTGC -s Anc2.Anc2refChr15 60888 7 - 86568 TATTTGC -s mr.mrrefChr5 229977 7 - 294540 TATCTGC -s simCow_chr6.simCow.chr6 219196 7 + 602619 TATTTGC -s simDog_chr6.simDog.chr6 397398 6 - 593897 -ATTTGC -s simHuman_chr6.simHuman.chr6 388550 7 - 601863 TATCTGC -s simRat_chr6.simRat.chr6 446324 7 - 647215 TATCTGC - -a -s simMouse_chr6.simMouse.chr6 208681 28 + 636262 TACTAAAAGATGACTGGACAACTGGAGA -s Anc0.Anc0refChr5 56995 28 - 87904 TGTTAGAACTTCACTGGCCAATTTGAAA -s Anc1.Anc1refChr8 12630 28 - 57822 TGTTAGAACTTCACTGGCCAATTTGAAA -s Anc2.Anc2refChr15 60896 28 - 86568 TGTTAGAACTCCAGAGGCCAATTTAAAA -s mr.mrrefChr5 229984 28 - 294540 TATTAAAACATGACTGGACAATTGGAAA -s simCow_chr6.simCow.chr6 219204 4 + 602619 TGTT------------------------ -s simDog_chr6.simDog.chr6 397405 28 - 593897 TGCTAGAACTCCAGAGGCCAATTTAAAA -s simHuman_chr6.simHuman.chr6 388558 28 - 601863 TGTTAGAACTTCACTGGGTAATTTGAAA -s simRat_chr6.simRat.chr6 446331 28 - 647215 TATTAAAACGTAACTGGACAATTCGGAA - -a -s simMouse_chr6.simMouse.chr6 208709 8 + 636262 CTCCGAAT -s Anc0.Anc0refChr5 57100 6 - 87904 CTT--AAT -s Anc1.Anc1refChr8 12735 6 - 57822 CTT--AAT -s Anc2.Anc2refChr15 61001 6 - 86568 CTT--ACT -s mr.mrrefChr5 230087 8 - 294540 CTCCGAAT -s simCow_chr6.simCow.chr6 219250 6 + 602619 TTC--ACT -s simDog_chr6.simDog.chr6 397510 6 - 593897 CTT--ACT -s simHuman_chr6.simHuman.chr6 388663 6 - 601863 CTT--AAT -s simRat_chr6.simRat.chr6 446434 8 - 647215 CTCTGAAT - -a -s simMouse_chr6.simMouse.chr6 208717 21 + 636262 CCAACAAAATAAGAGGTAGGT -s Anc0.Anc0refChr5 57106 8 - 87904 GCATC-------------GGC -s Anc1.Anc1refChr8 12741 8 - 57822 GCATC-------------GGC -s Anc2.Anc2refChr15 61007 8 - 86568 GCGTT-------------GGC -s mr.mrrefChr5 230095 21 - 294540 CCAACAAAATAAGAGGTAGGT -s simCow_chr6.simCow.chr6 219256 8 + 602619 GCTAT-------------GGC -s simDog_chr6.simDog.chr6 397518 8 - 593897 GTGTT-------------GGG -s simHuman_chr6.simHuman.chr6 388669 8 - 601863 GCAGC-------------AGC -s simRat_chr6.simRat.chr6 446442 21 - 647215 CCAACAAAATAAAAGGTAGGT - -a -s simMouse_chr6.simMouse.chr6 208738 15 + 636262 GGATAAGAAGTAGAT -s Anc0.Anc0refChr5 57115 15 - 87904 AAGTAGGAAGTAGGT -s Anc1.Anc1refChr8 12750 15 - 57822 AAGTAGGAAGTAGGT -s Anc2.Anc2refChr15 61016 15 - 86568 AAGCAGGAAGTAGGA -s mr.mrrefChr5 230116 15 - 294540 GGATAAGAAGTAGGT -s simCow_chr6.simCow.chr6 219265 15 + 602619 AAGCAGGAAGTAGGA -s simDog_chr6.simDog.chr6 397527 15 - 593897 AAACAGGAAATAGGA -s simHuman_chr6.simHuman.chr6 388678 15 - 601863 AAGTAGGAAGTAGGT -s simRat_chr6.simRat.chr6 446463 15 - 647215 GGATAAGAAATTGGT - -a -s simMouse_chr6.simMouse.chr6 208753 2 + 636262 TA -s Anc0.Anc0refChr5 57137 2 - 87904 TA -s Anc1.Anc1refChr8 12772 2 - 57822 TA -s Anc2.Anc2refChr15 61038 2 - 86568 TA -s mr.mrrefChr5 230138 2 - 294540 TA -s simCow_chr6.simCow.chr6 219287 2 + 602619 TA -s simDog_chr6.simDog.chr6 397549 2 - 593897 TG -s simHuman_chr6.simHuman.chr6 388700 2 - 601863 TA -s simRat_chr6.simRat.chr6 446485 2 - 647215 TA - -a -s simMouse_chr6.simMouse.chr6 208755 14 + 636262 TCTATGTCCGATAC -s Anc0.Anc0refChr5 57140 14 - 87904 TCTTTGTCAGCAAC -s Anc1.Anc1refChr8 12775 14 - 57822 TCTTTGTCAGCAAC -s Anc2.Anc2refChr15 61041 14 - 86568 TCTTTGCCAGCATC -s mr.mrrefChr5 230140 14 - 294540 TCTATGTCAGATAC -s simCow_chr6.simCow.chr6 219290 14 + 602619 TCTTTGCCAGCATT -s simDog_chr6.simDog.chr6 397552 14 - 593897 TCTTTACTGGCTTC -s simHuman_chr6.simHuman.chr6 388703 14 - 601863 TCTTTGTCAGCAAC -s simRat_chr6.simRat.chr6 446487 14 - 647215 TCCATGTCAGATAC - -a -s simMouse_chr6.simMouse.chr6 208769 57 + 636262 ATTCATTGGAGTATAGTATTTTAAAGACTACACAACTTTGAGACATAGGCATATCTA -s Anc0.Anc0refChr5 57154 57 - 87904 AATCAATGGAGCAGGGTAGCCTGAACATTGCCCGACAACTCGAGTTATGCTTATTTG -s Anc1.Anc1refChr8 12789 57 - 57822 AATCAATGGAGCAGGGTAGCCTGAACATTGCCCGACAACTCGAGTTATGCTTATTTG -s Anc2.Anc2refChr15 61055 57 - 86568 AATCAATGGAGCAGGGTGGCCTGAACATTGCCCGACAACTCGAGTTATGCTTATTAG -s mr.mrrefChr5 230154 57 - 294540 ATTCATTGGAGTATAGTATCCTAAAGACTACCCAACTACGAGACATAGGCATATCTG -s simCow_chr6.simCow.chr6 219304 55 + 602619 AAACAATGGAGCAGGGTGGCCTGAACATAGCCCAACAATTCAAGCTAT--TTCTTAG -s simDog_chr6.simDog.chr6 397566 54 - 593897 AATCAATGGAGCAGGGTGGCTTGAACCATGCCCGACAACT-GACTTATGCCTATT-- -s simHuman_chr6.simHuman.chr6 388717 57 - 601863 AATTAATGGAGCAGGGTAGCCTGAACATTGCCTGACAACTGGAGGTATGCTTATTTG -s simRat_chr6.simRat.chr6 446502 53 - 647215 ATTCATTGGAGTAC----TCCTAAAAACTACCCAAGTACGAGACATAGACATACCTG - -a -s simMouse_chr6.simMouse.chr6 208826 18 + 636262 TGCTTTTCTGGAGCCTGA -s Anc0.Anc0refChr5 57216 18 - 87904 TGCTTTTCTGAAGATTAT -s Anc1.Anc1refChr8 12851 18 - 57822 TGCTTTTCTGAAGATTAT -s Anc2.Anc2refChr15 61117 18 - 86568 CGCTTTTCTGAAGATTAT -s mr.mrrefChr5 230211 18 - 294540 TGCTTTTCTGAAGCCTGA -s simCow_chr6.simCow.chr6 219364 17 + 602619 AGCTTTTCTG-AGAGTAT -s simDog_chr6.simDog.chr6 397625 18 - 593897 CCCTTTTCTGAAGTTTAT -s simHuman_chr6.simHuman.chr6 388779 18 - 601863 TGCTTTCCTGAAGAATAC -s simRat_chr6.simRat.chr6 446555 18 - 647215 TGTCTTTCTGAAGCCTTA - -a -s simMouse_chr6.simMouse.chr6 208844 3 + 636262 CTT -s Anc0.Anc0refChr5 57234 3 - 87904 CTT -s Anc1.Anc1refChr8 12869 3 - 57822 CTT -s Anc2.Anc2refChr15 61135 3 - 86568 CAC -s mr.mrrefChr5 230229 3 - 294540 CTT -s simCow_chr6.simCow.chr6 219387 3 + 602619 CAC -s simDog_chr6.simDog.chr6 397643 3 - 593897 CAC -s simHuman_chr6.simHuman.chr6 388797 3 - 601863 CTT -s simRat_chr6.simRat.chr6 446573 3 - 647215 CTT - -a -s simMouse_chr6.simMouse.chr6 208847 69 + 636262 TGAGAAAAGTCTACATGAAAAGGGTGCAAGTACAATCCATAGATATATTCTGTATACCTTGATGATGAA -s Anc0.Anc0refChr5 57237 65 - 87904 TAAGAAGAATTTAAATGAGAGGAGTGAAAGTACAG----TAGATATAATCTGTAAACTTACATAAAGAA -s Anc1.Anc1refChr8 12872 69 - 57822 TAAGAAGAATTTAAATGAGAGGAGTGAAAGTACAGTTCATAGATATAATCTGTAAACTTACATAAAGAA -s Anc2.Anc2refChr15 61161 65 - 86568 TAAGAAGAATTTAAATGAGAGGAGTGAAAGCACAG----TAGGTGTAATCTGTCAACTCACACAAAGAA -s mr.mrrefChr5 230232 69 - 294540 TAAGAAAAGTTTAAATGAAAAGGGTGCAAGTACAATCCATAGATATAATCTGTATACCTAGATGATGAA -s simCow_chr6.simCow.chr6 219413 61 + 602619 TAAGAAGAATTT-AATGAGAGGAGTGAAAGCAC-------AGGTGTAATCTGTCAACTCACACAAAGAA -s simDog_chr6.simDog.chr6 397669 36 - 593897 TAAGAAGAATTTAAATGAGAGTAGTGAAAGCACAG----T----------------------------- -s simHuman_chr6.simHuman.chr6 388800 69 - 601863 TAAGAACAATTTGAATGACAGGATAGAAAATACAGTTCATAGATATGATCTGTAGACTTACATTAAGAA -s simRat_chr6.simRat.chr6 446576 67 - 647215 TAAGCAAA--TTAAATGAAAAGGGTGCAACTACAATCCATGGATGTAATCTGTATACCTAGATGGTGAA - -a -s simMouse_chr6.simMouse.chr6 208916 12 + 636262 AGACATCCAAGT -s Anc0.Anc0refChr5 57302 12 - 87904 AATCATCTAAAT -s Anc1.Anc1refChr8 12941 12 - 57822 AATCATCTAAAT -s Anc2.Anc2refChr15 61226 12 - 86568 CATCATCTAAAT -s mr.mrrefChr5 230301 12 - 294540 AGACATCCAAGT -s simCow_chr6.simCow.chr6 219487 12 + 602619 CATCATCTAAAT -s simHuman_chr6.simHuman.chr6 388869 12 - 601863 AATCATCTAAAT -s simRat_chr6.simRat.chr6 446643 12 - 647215 AGACATTCAAGT - -a -s simMouse_chr6.simMouse.chr6 208928 78 + 636262 CTTTTTACTTCCAGAATGGATTACTCAACCATTACGATCTAGGGCACCTATAGGGAGTGTGGATCACAATCCATTATA -s Anc0.Anc0refChr5 57314 78 - 87904 TTTTTTACCTCCAGAGTCGATGTCCCAACCATTCTGCTCTAGAGCATCTATCTGAAGTGTAGGCTGTATTCTATTATA -s Anc1.Anc1refChr8 12953 78 - 57822 TTTTTTACCTCCAGAGTCGATGTCCCAACCATTCTGCTCTAGAGCATCTATCTGAAGTGTAGGCTGTATTCTATTATA -s Anc2.Anc2refChr15 61238 78 - 86568 TTTTTTACCTCCAGAGTCGGTGTCCCAACTATTCAGTTCCAGAGCATCCATCTAAACTGTAGGCTGTATTCTATTATA -s mr.mrrefChr5 230313 78 - 294540 CTTTTTACTTCCAGAGTGGATTACTCAACCATTCTGCTCTAGGGCACCTATAGGAAGTGTGGACTGTATTCCATTATA -s simCow_chr6.simCow.chr6 219500 78 + 602619 TTTTTTACCTCCAGAGTCGGTGTCCCAACTATTCAGTTCCAGAGCATCCATCTAAACTGTATGCTGTATTCTATTGTA -s simDog_chr6.simDog.chr6 397705 17 - 593897 -------------------------------------------------------------GGCCATATTCTATTATA -s simHuman_chr6.simHuman.chr6 388881 78 - 601863 TTTCTCACCTCCAGCGTATATGTCCCAATCAGCCTGCTCTAGAGCATCTATCAGAAGTGTAGGCTGTATTCTATCATA -s simRat_chr6.simRat.chr6 446655 78 - 647215 CTGTTTATGTCCAGAGTGGATTACTCACCCATTCTGCTCTAGGGCACCTATGGGAAGTTTGGACTGTATTCCAATATA - -a -s simMouse_chr6.simMouse.chr6 209006 4 + 636262 CTAT -s Anc0.Anc0refChr5 57392 4 - 87904 TTAT -s Anc1.Anc1refChr8 13031 4 - 57822 TTAT -s Anc2.Anc2refChr15 61317 4 - 86568 TTAA -s mr.mrrefChr5 230391 4 - 294540 TTAT -s simCow_chr6.simCow.chr6 219579 4 + 602619 TTAC -s simDog_chr6.simDog.chr6 397723 4 - 593897 TTAA -s simHuman_chr6.simHuman.chr6 388959 4 - 601863 TTAT -s simRat_chr6.simRat.chr6 446733 4 - 647215 TTAT - -a -s simMouse_chr6.simMouse.chr6 209010 11 + 636262 GCTTATACAGG -s Anc0.Anc0refChr5 57397 11 - 87904 GATTATGCAGG -s Anc1.Anc1refChr8 13036 11 - 57822 GATTATGCAGG -s Anc2.Anc2refChr15 61322 11 - 86568 GATTATGCAGG -s mr.mrrefChr5 230395 11 - 294540 GATTATGCAGG -s simCow_chr6.simCow.chr6 219584 11 + 602619 GATGATGTAGG -s simDog_chr6.simDog.chr6 397728 11 - 593897 GCTTATTCAGG -s simHuman_chr6.simHuman.chr6 388964 11 - 601863 GATTATGGAGG -s simRat_chr6.simRat.chr6 446737 11 - 647215 GATTATGCAGG - -a -s simMouse_chr6.simMouse.chr6 209021 14 + 636262 CTGATCACTGTGGT -s Anc0.Anc0refChr5 57429 14 - 87904 TTAACTGCTGTGAT -s Anc1.Anc1refChr8 13068 14 - 57822 TTAACTGCTGTGAT -s Anc2.Anc2refChr15 61354 14 - 86568 TTAACTGCTCTAAG -s mr.mrrefChr5 230406 14 - 294540 CTGATCACTGTGGT -s simCow_chr6.simCow.chr6 219616 14 + 602619 TTAACTGCTTTTGG -s simDog_chr6.simDog.chr6 397760 14 - 593897 GTACCCACTCTAAG -s simHuman_chr6.simHuman.chr6 388996 11 - 601863 TTAACT---GTGCT -s simRat_chr6.simRat.chr6 446748 14 - 647215 CTGATCACTATAGC - -a -s simMouse_chr6.simMouse.chr6 209035 16 + 636262 GCCTGGGCATGAAAAT -s Anc0.Anc0refChr5 57443 16 - 87904 GCCTGGGCATGAAAAT -s Anc1.Anc1refChr8 13082 16 - 57822 GCCTGGGCATGAAAAT -s Anc2.Anc2refChr15 61368 16 - 86568 GCCTGGGCATGAAAAT -s mr.mrrefChr5 230420 16 - 294540 GCCTGGGCATGAAAAT -s simCow_chr6.simCow.chr6 219630 16 + 602619 GCCTGGCCATACAAAC -s simDog_chr6.simDog.chr6 397774 16 - 593897 GCCTGGGCATGAGAAT -s simHuman_chr6.simHuman.chr6 389009 16 - 601863 GCCTGGGCATGAAAAT -s simRat_chr6.simRat.chr6 446762 16 - 647215 ACCTGGGCATGATAAT - -a -s simMouse_chr6.simMouse.chr6 209051 22 + 636262 CAGATTATTAACCCCTTAAGCA -s Anc0.Anc0refChr5 57460 22 - 87904 CATAGTATGGAACCTTGCAGTA -s Anc1.Anc1refChr8 13099 22 - 57822 CATAGTATGGAACCTTGCAGTA -s Anc2.Anc2refChr15 61385 22 - 86568 TATAGTATGGAACCTTGCAGTA -s mr.mrrefChr5 230437 22 - 294540 CATATTATTAAACCCTTAAGCA -s simCow_chr6.simCow.chr6 219666 22 + 602619 TATAGTATGGAACCTGGCACTA -s simDog_chr6.simDog.chr6 397791 22 - 593897 TATAGTATGGAACCTTTCAGGA -s simHuman_chr6.simHuman.chr6 389026 22 - 601863 CATACTATGGAACCTTGTGGTA -s simRat_chr6.simRat.chr6 446779 22 - 647215 TATATTATTAAACCCTTCAGCA - -a -s simMouse_chr6.simMouse.chr6 209073 20 + 636262 ATTGTGCTGTCTTACTAATT -s Anc0.Anc0refChr5 57482 20 - 87904 ACTGTGCTGATTTCCTAATT -s Anc1.Anc1refChr8 13121 20 - 57822 ACTGTGCTGATTTCCTAATT -s Anc2.Anc2refChr15 61407 20 - 86568 ACTGTGCTGATTTCTTGATT -s mr.mrrefChr5 230459 20 - 294540 ATTGTGCTGTTTTACTAATT -s simCow_chr6.simCow.chr6 219689 20 + 602619 CCTGTGCTGATTTATTCATT -s simDog_chr6.simDog.chr6 397813 20 - 593897 ACTGTGCTCATTTCTAGATT -s simHuman_chr6.simHuman.chr6 389048 20 - 601863 ACTGTGCTGATTTGCTAATT -s simRat_chr6.simRat.chr6 446801 20 - 647215 ATTGTGCTATTTTACTGATT - -a -s simMouse_chr6.simMouse.chr6 209093 12 + 636262 CAAAACAATATG -s Anc0.Anc0refChr5 57503 12 - 87904 CAAAGCAATGTG -s Anc1.Anc1refChr8 13142 12 - 57822 CAAAGCAATGTG -s Anc2.Anc2refChr15 61428 12 - 86568 CAGAGTAATGTG -s mr.mrrefChr5 230480 12 - 294540 CAAAGCAATATG -s simCow_chr6.simCow.chr6 219710 12 + 602619 CAGAGTAATGCG -s simDog_chr6.simDog.chr6 397834 12 - 593897 CAGAGTGATGTA -s simHuman_chr6.simHuman.chr6 389069 12 - 601863 CAAAGCAACGTG -s simRat_chr6.simRat.chr6 446822 12 - 647215 CAAAGCAATATC - -a -s simMouse_chr6.simMouse.chr6 209105 21 + 636262 ATCATCTGAATATTTTTACTT -s Anc0.Anc0refChr5 57515 19 - 87904 AATA-CTGTAG-TTTCAAATT -s Anc1.Anc1refChr8 13154 20 - 57822 AATA-CTGTAGATTTCAAATT -s Anc2.Anc2refChr15 61440 19 - 86568 GATT-CTGTAG-CTTCAGACC -s mr.mrrefChr5 230492 21 - 294540 AACATCTGAATATTTTTACTT -s simCow_chr6.simCow.chr6 219723 19 + 602619 TATG-CTTAAG-CATCAGAAT -s simDog_chr6.simDog.chr6 397846 19 - 593897 GTGT-CTGTAA-CTTCAGACC -s simHuman_chr6.simHuman.chr6 389081 20 - 601863 AATA-CCATAGATTTCAAGTT -s simRat_chr6.simRat.chr6 446834 21 - 647215 AACAGCTGAATATTTTTGAAT - -a -s simMouse_chr6.simMouse.chr6 209126 13 + 636262 GCTTTATTTGTAG -s Anc0.Anc0refChr5 57535 2 - 87904 GC----------- -s Anc1.Anc1refChr8 13175 13 - 57822 GCTTTACTAATTG -s Anc2.Anc2refChr15 61461 2 - 86568 GC----------- -s mr.mrrefChr5 230513 13 - 294540 GCTTTATTTGTTG -s simCow_chr6.simCow.chr6 219744 2 + 602619 GC----------- -s simDog_chr6.simDog.chr6 397867 2 - 593897 GC----------- -s simHuman_chr6.simHuman.chr6 389113 13 - 601863 GCTTTACTAATTG -s simRat_chr6.simRat.chr6 446855 13 - 647215 GCCTTATTTCTTG - -a -s simMouse_chr6.simMouse.chr6 209139 52 + 636262 TCAGTGCAAAGGGCAAAATTATGCTGCTTCTCACTTCTTAAATAGAATGTAT -s Anc1.Anc1refChr8 13188 52 - 57822 CCAGTGCAAAAGGTAAGATCATGTTGTTACCTGATTATTAAATAGTATGCAT -s mr.mrrefChr5 230526 52 - 294540 TCAGTGCAAAGGGTAAAATTATGCTGCTTCTCACTTCTTAAATAGAATGCAT -s simHuman_chr6.simHuman.chr6 389127 52 - 601863 CCAGTGCAAAAGGTAAGATCATGTTGTTACCTGATTTTTATTTAGTATGCAT -s simRat_chr6.simRat.chr6 446868 52 - 647215 TTAGCATAAAGGGTAAAAGTATGCTGCTTCTCACTTCTTAAATGGAATGCAT - -a -s simMouse_chr6.simMouse.chr6 209191 32 + 636262 AAGCACCAGACCAGATCCTCTTCACCTTTCAG -s Anc0.Anc0refChr5 57537 27 - 87904 -----AGTTGATATTTCCTCTTCTCCTTTCAG -s Anc1.Anc1refChr8 13240 32 - 57822 AGGTTAGTTGATATTTCCTCTTCTCCTTTCAG -s Anc2.Anc2refChr15 61463 27 - 86568 -----AAATGATATTTCCTCTTCACCTTTCAG -s mr.mrrefChr5 230578 32 - 294540 AAGCACCAGACCAGTTCCTCTTCTCCTTTCAG -s simCow_chr6.simCow.chr6 219746 27 + 602619 -----AACTGGTATTTCCTCTACACCTCTCAG -s simDog_chr6.simDog.chr6 397869 25 - 593897 -----AAATGATATATCCTCTTCAGGTTT--G -s simHuman_chr6.simHuman.chr6 389179 32 - 601863 AGGTTAGTTGATATTTCTTCTTCTCCTTTGAG -s simRat_chr6.simRat.chr6 446921 29 - 647215 AAACACCAGCCCAGTTCCCCTCCTTCCTT--- - -a -s simMouse_chr6.simMouse.chr6 209223 40 + 636262 ATTTAAGCTATTTGTTGTAATAGTTCCTGGTCATGATACT -s Anc0.Anc0refChr5 57565 40 - 87904 ACTTAAGCCATATGTTTTATTTGTTCTCTGTTTTGGTTTT -s Anc1.Anc1refChr8 13273 40 - 57822 ACTTAAGCCATATGTTTTATTTGTTCTCTGTTTTGGTTTT -s Anc2.Anc2refChr15 61491 40 - 86568 ACTTAAGCTATATGTTTTATTTGTTCTCTGTTTTGGTTTT -s mr.mrrefChr5 230610 40 - 294540 ATTTAAGCCATTTGTTGTAATAGTTCCTGGTCATGATTCT -s simCow_chr6.simCow.chr6 219777 40 + 602619 ACTTAAGCTATATGTATTATTTGTCCTTTGTTTAGGTTTT -s simDog_chr6.simDog.chr6 397895 40 - 593897 ACTTGAGCTATATGTTTTATTGGTTCTCTCCTCTGGCTTT -s simHuman_chr6.simHuman.chr6 389212 40 - 601863 AGTTAAGCCATCTGTTTTATTTACTCTCTGTTTTGGTTTT -s simRat_chr6.simRat.chr6 446950 35 - 647215 -----AGGCATATGTTATAATAGTTCCTGGTCATGATTCT - -a -s simMouse_chr6.simMouse.chr6 209263 64 + 636262 TGAATGCAATCTGCGGCACTATGCCGCCCCAACGCGGAAAGCTTCAAGTCAAACCTCCACTATC -s Anc0.Anc0refChr5 57608 58 - 87904 TGAAGCCAATCTGCGCCCTTATGCCACTTCAT-TTGAAAAGGTTAAAA-----CCTTCAATATC -s Anc1.Anc1refChr8 13316 58 - 57822 TGAAGCCAATCTGCGCCCTTATGCCACTTCAT-TTGAAAAGGTTAAAA-----CCTTCAATATC -s Anc2.Anc2refChr15 61534 58 - 86568 TGAAGCCAATCTGTGCCCTTGTGCCACTTAAT-TTGAAAGGGTTAAAA-----CCTTCAATATC -s mr.mrrefChr5 230650 59 - 294540 TGAATGCAATCTGCGGCATTATGCCACCCCAACGCGGAAAGGTTCAAG-----CCTTCACTATC -s simCow_chr6.simCow.chr6 219820 58 + 602619 TGAAGCCAATCCGTGCCTTTATGCCACTTGAT-TAGAAAGGAATAAAG-----CCTTCAATATC -s simDog_chr6.simDog.chr6 397938 58 - 593897 TGAAGTCAATTTGTGCCCTTGTGCCACTCAGT-TTGAAAGGGTTAAAA-----CCTGCAATATT -s simHuman_chr6.simHuman.chr6 389255 56 - 601863 TGAAGCCAATCGGCGCCCTTA--CCACTTCAG-TGGAAAAGGTGAAAA-----CCTTCAATATC -s simRat_chr6.simRat.chr6 446985 59 - 647215 TGAATGCAATCTGCAGCATTATTCTACCCCAACTTGGGGAAGTTCAAG-----CCTTCACTGTC - -a -s simMouse_chr6.simMouse.chr6 209327 1 + 636262 T -s Anc0.Anc0refChr5 57666 1 - 87904 T -s Anc1.Anc1refChr8 13374 1 - 57822 T -s Anc2.Anc2refChr15 61592 1 - 86568 T -s mr.mrrefChr5 230709 1 - 294540 T -s simCow_chr6.simCow.chr6 219885 1 + 602619 T -s simDog_chr6.simDog.chr6 397996 1 - 593897 T -s simHuman_chr6.simHuman.chr6 389311 1 - 601863 G -s simRat_chr6.simRat.chr6 447044 1 - 647215 T - -a -s simMouse_chr6.simMouse.chr6 209328 7 + 636262 GAATCAT -s Anc0.Anc0refChr5 57667 7 - 87904 TGCTTAT -s Anc1.Anc1refChr8 13375 7 - 57822 TGCTTAT -s Anc2.Anc2refChr15 61593 7 - 86568 TGCTTAT -s mr.mrrefChr5 230710 7 - 294540 GAATCAT -s simCow_chr6.simCow.chr6 219886 7 + 602619 TGCTTTT -s simDog_chr6.simDog.chr6 398022 7 - 593897 TGCTTAT -s simHuman_chr6.simHuman.chr6 389312 7 - 601863 TGCTTAT -s simRat_chr6.simRat.chr6 447045 7 - 647215 GAATCAT - -a -s simMouse_chr6.simMouse.chr6 209335 38 + 636262 AGTCAATAAGTTTCCTATTTCTATTGGTGCTGTGTCTC -s Anc0.Anc0refChr5 57675 38 - 87904 AATCAATATATTGCCTATGCCTTTTGCTTCTAGATCTA -s Anc1.Anc1refChr8 13383 38 - 57822 AATCAATATATTGCCTATGCCTTTTGCTTCTAGATCTA -s Anc2.Anc2refChr15 61601 38 - 86568 AATCAATATATTGCCTGTGCCTTTTGCTTCTAAATCTA -s mr.mrrefChr5 230717 38 - 294540 AGTCAATAAGTTTCCTATTTCTATTGGTTCTGGGTCTC -s simCow_chr6.simCow.chr6 219894 38 + 602619 AGTCAATATATTGCTTGTGCCTTTTGTGTCTACATCTA -s simDog_chr6.simDog.chr6 398030 37 - 593897 GATCAA-ATGTTGCCTGTGCCTACTGCTTCTAAATCTA -s simHuman_chr6.simHuman.chr6 389320 38 - 601863 AACTAATAGATTGCCTATGACTTTTAATTCCAGAGCTA -s simRat_chr6.simRat.chr6 447052 38 - 647215 AGTCAATAAGTTTCCTATTTCTATTGGTTCTGGGTCTC - -a -s simMouse_chr6.simMouse.chr6 209373 26 + 636262 ATTGACTTATAAAAACTAGACTCAAT -s Anc0.Anc0refChr5 57714 26 - 87904 TTCAATCAATATTAGTTAGACTCAAT -s Anc1.Anc1refChr8 13422 26 - 57822 TTCAATCAATATTAGTTAGACTCAAT -s Anc2.Anc2refChr15 61640 26 - 86568 TCCAATCAATATTAGTAAGACTCAGT -s mr.mrrefChr5 230755 26 - 294540 TTCGATTTATAAAAGCTAGACTCAAT -s simCow_chr6.simCow.chr6 219933 24 + 602619 TCTAATCCAAATTAGT--GAATTAGT -s simDog_chr6.simDog.chr6 398068 26 - 593897 CCCAATCAATATTAGTAAGACTCAGT -s simHuman_chr6.simHuman.chr6 389359 26 - 601863 TTCAATCAATATTAGTTGGACTGAAT -s simRat_chr6.simRat.chr6 447090 26 - 647215 TTCCATTTTTAAAAGCTAGACTCAAT - -a -s simMouse_chr6.simMouse.chr6 209399 4 + 636262 AACA -s Anc0.Anc0refChr5 57740 4 - 87904 AACA -s Anc1.Anc1refChr8 13448 4 - 57822 AACA -s Anc2.Anc2refChr15 61666 4 - 86568 AACA -s mr.mrrefChr5 230781 4 - 294540 AACA -s simCow_chr6.simCow.chr6 219957 4 + 602619 GACA -s simDog_chr6.simDog.chr6 398150 4 - 593897 AACA -s simHuman_chr6.simHuman.chr6 389385 4 - 601863 AACA -s simRat_chr6.simRat.chr6 447116 4 - 647215 AACA - -a -s simMouse_chr6.simMouse.chr6 209403 4 + 636262 CCCT -s Anc0.Anc0refChr5 57744 4 - 87904 CCTT -s Anc1.Anc1refChr8 13452 4 - 57822 CCTT -s Anc2.Anc2refChr15 61670 4 - 86568 CTTT -s mr.mrrefChr5 230785 4 - 294540 CCCT -s simCow_chr6.simCow.chr6 219961 4 + 602619 ATTT -s simDog_chr6.simDog.chr6 398154 4 - 593897 CTTG -s simHuman_chr6.simHuman.chr6 389389 4 - 601863 CCTT -s simRat_chr6.simRat.chr6 447642 4 - 647215 CCCT - -a -s simMouse_chr6.simMouse.chr6 209407 48 + 636262 CTGCTAATTCACTTCCCAGTATTGATATCACATGGACCATTGACATCA -s Anc0.Anc0refChr5 57758 29 - 87904 CTGCTTATTCACTGACCAGTATT------ACCTGG------------- -s Anc1.Anc1refChr8 13466 29 - 57822 CTGCTTATTCACTGACCAGTATT------ACCTGG------------- -s Anc2.Anc2refChr15 61684 29 - 86568 CTACTTATTCACTGACCCGTATT------ATCTGG------------- -s mr.mrrefChr5 230789 48 - 294540 CTGCTAATTCACTTCCCAGTATTGATATCACATGGACCATTGACATCA -s simCow_chr6.simCow.chr6 219975 25 + 602619 CTTCTTATTCACTTATCTGTATT------A----G------------- -s simDog_chr6.simDog.chr6 398168 29 - 593897 CTACTCATTCACTGACCCATATC------ATCTGA------------- -s simHuman_chr6.simHuman.chr6 389403 29 - 601863 CTGCTTATTCACTGACAAGTATT------ACCTGG------------- -s simRat_chr6.simRat.chr6 447646 48 - 647215 CTGCTAATTCACTTCCCAGCATTCATATCACAGTGACCATTGATATCA - -a -s simMouse_chr6.simMouse.chr6 209455 32 + 636262 CACGGCAGCATCATTTACAGATTCAATCCGGG -s mr.mrrefChr5 230837 32 - 294540 CACGGCAGCATCATTTACAGATTCAATCCGGG -s simRat_chr6.simRat.chr6 447719 32 - 647215 CAGGGCATCATCATTTACAGGTTCAACCCTGG - -a -s simMouse_chr6.simMouse.chr6 209487 66 + 636262 AGACCCAGAAGGctcctggaggcaccaggaaacagcacaaccagtcatgggctggctcatgatagg -s Anc0.Anc0refChr5 57787 29 - 87904 -------------------------------------CAGCCATTCATAGGTATGACCATGGGAGG -s Anc1.Anc1refChr8 13495 29 - 57822 -------------------------------------CAGCCATTCATAGGTATGACCATGGGAGG -s Anc2.Anc2refChr15 61713 29 - 86568 -------------------------------------TAGCGATACATAGGTATGACCATGGGAGA -s mr.mrrefChr5 230869 66 - 294540 AGACCCAGaaggctcctggaggcaccaggaaacagcacaaccagtcatgggctggctcatgatagg -s simCow_chr6.simCow.chr6 220000 25 + 602619 -------------------------------------AAGC---AGATAGGTATGACCATAGGAG- -s simDog_chr6.simDog.chr6 398197 28 - 593897 -------------------------------------TAG-GATACATAGGTATGACTGTGGGAGA -s simHuman_chr6.simHuman.chr6 389432 29 - 601863 -------------------------------------CAGCCATTCATAGGTATGACCATGGGAGG -s simRat_chr6.simRat.chr6 447752 66 - 647215 AGACCTAAaagtctcccggagacgccagaaaacaacacaaccagtcatgggctggctcatgatagt - -a -s simMouse_chr6.simMouse.chr6 209553 205 + 636262 aagtgggcaagacctcagattcacttcatatgcagaagatggcactccctttacatcagtactacttcgcatgtgccaggtcactgggtaagtacagatgccataggcaacaaaccacccacCAACTAAAGGGAATACCTCACTTTGTATTCCTGTAGCACTTTGTATTCCTGTAGCTGATACACCCAGTTTGATGGTGTTGTGC -s Anc0.Anc0refChr5 57819 61 - 87904 AAGTG-----------------------------------------------------------------------------------------------------------------------ATTAGATGGTATATCTCACTTTGTATTTCCCTGAT------------------T---ACTGCCA---AGCTGGTTTGG-TC -s Anc1.Anc1refChr8 13527 62 - 57822 AAGTG-----------------------------------------------------------------------------------------------------------------------ATTAGATGGTATATCTCACTTTGTATTTCCCTGAT------------------T---ACTGCCA---AGCTGGTTTGGTTC -s Anc2.Anc2refChr15 61745 61 - 86568 AAATG-----------------------------------------------------------------------------------------------------------------------ATTAGATGGTATATATCACTTTGTATTTCCCTGAT------------------T---GCTACCA---AGCTGGTTTGG-TC -s mr.mrrefChr5 230935 165 - 294540 aagtgggcaagacctcagattcacttcatatgcagaagatggcactccctttacatcagtactacttcgcatgtgccaggtcactgggtaa----------------------accacccacCAACTAAAGGGAATATCTCACTTTGTATTCCTGTGGT------------------TGATACAGCCAGTTAGATGGTGTTGTGC -s simCow_chr6.simCow.chr6 220027 61 + 602619 AAATG-----------------------------------------------------------------------------------------------------------------------ATTAGATGGTGTATATCAGTCTGTGTTTCTCTGTT------------------T---GCTACCA---AGCTGGTTTGG-TC -s simDog_chr6.simDog.chr6 398228 61 - 593897 AAACG-----------------------------------------------------------------------------------------------------------------------TGTAGATGGTATATATCACTTTATATTTCCTTGAT------------------A---GCTATTA---ACCTGGTTTGG-TA -s simHuman_chr6.simHuman.chr6 389464 62 - 601863 AAGTG-----------------------------------------------------------------------------------------------------------------------ATTATATGGTATGTCTCACTTTGTACTTCCCTGAT------------------T---ACTGCCA---AGCTGGTTTGTCTC -s simRat_chr6.simRat.chr6 447818 165 - 647215 gagtgggcaagacctcagattaacttcacttgcaaaagatggcactgcctgtacatcagtactacttcacatgaggcaggtcactgggtAA----------------------ACCACCCTCCAACTAAACAGAATATCTCACCTTGTATTCCTGTGGT------------------TGATACAGCTGGTTAGATGGTGTTGTGC - -a -s simMouse_chr6.simMouse.chr6 209758 35 + 636262 CGTTGAAATCCCAGTGCAATCACCTCAGTATTTGT -s Anc0.Anc0refChr5 57880 31 - 87904 C----ATGTTACATTATAATCACCTAAGTCTTTGC -s Anc1.Anc1refChr8 13589 31 - 57822 C----ATGTTACATTATAATCACCTAAGTCTTTGC -s Anc2.Anc2refChr15 61806 31 - 86568 C----ATGTTACAATATAATCACCTAAGTCTTTGC -s mr.mrrefChr5 231100 35 - 294540 CGTTGATATCCCATTACAATCACCTCAGTATTTGT -s simCow_chr6.simCow.chr6 220089 22 + 602619 C----ATGATTCTATATAATCACCTA--------- -s simDog_chr6.simDog.chr6 398289 31 - 593897 C----ATTTTACAATATAATCACCTAAGTCTTTGC -s simHuman_chr6.simHuman.chr6 389526 31 - 601863 C----ATGCTACATTATAATCACCTAAGCGTTTGC -s simRat_chr6.simRat.chr6 447983 35 - 647215 CTTTGATATCCCCTTACAATCACCACAGTATTGGT - -a -s simMouse_chr6.simMouse.chr6 209793 2 + 636262 TT -s Anc0.Anc0refChr5 57911 2 - 87904 AG -s Anc1.Anc1refChr8 13620 2 - 57822 AG -s Anc2.Anc2refChr15 61837 2 - 86568 AG -s mr.mrrefChr5 231135 2 - 294540 TG -s simDog_chr6.simDog.chr6 398330 2 - 593897 AG -s simHuman_chr6.simHuman.chr6 389557 2 - 601863 AG -s simRat_chr6.simRat.chr6 448018 2 - 647215 TG - -a -s simMouse_chr6.simMouse.chr6 209795 26 + 636262 TGACCTGGATTGGTCAACCTGATACT -s Anc0.Anc0refChr5 57913 26 - 87904 TAGCCTGGAGTGATCAACTTGGTACT -s Anc1.Anc1refChr8 13622 26 - 57822 TAGCCTGGAGTGATCAACTTGGTACT -s Anc2.Anc2refChr15 61839 26 - 86568 TAGCCTGGAGTGATCAACTTGGTATT -s mr.mrrefChr5 231137 26 - 294540 TGACCTGGATTGATCAACCTGATACT -s simCow_chr6.simCow.chr6 220111 25 + 602619 -AGCCTGGAGTGATCAACTTGGCATG -s simDog_chr6.simDog.chr6 398334 26 - 593897 TAGCCTGGAGTGATCAACTTGGTATT -s simHuman_chr6.simHuman.chr6 389559 26 - 601863 TAGCCTGGAGTAATCAACTTAGTACC -s simRat_chr6.simRat.chr6 448020 26 - 647215 TCACCTGGATGGATCAACCTGATACT - -a -s simMouse_chr6.simMouse.chr6 209821 33 + 636262 AGCAGATGTGGAGTTGTACGAGGTATGGAAAGA -s Anc0.Anc0refChr5 57939 33 - 87904 ATCAGATGTGGAGTTGTATAAAGTATGGAAAGA -s Anc1.Anc1refChr8 13648 33 - 57822 ATCAGATGTGGAGTTGTATAAAGTATGGAAAGA -s Anc2.Anc2refChr15 61871 33 - 86568 ACCAGATGTGGAGTTGTGTAAAGTATGGAAAGA -s mr.mrrefChr5 231163 33 - 294540 AGCAGATGTGGAGTTGTATAAGGTATGGAAAGA -s simCow_chr6.simCow.chr6 220142 33 + 602619 AGCAGATGTGGAGTTGTGTAAAGTGTGCAAAGA -s simDog_chr6.simDog.chr6 398366 33 - 593897 ACCAGATGTGGAGTTGTGTAAAGTATGGAAAGA -s simHuman_chr6.simHuman.chr6 389585 33 - 601863 ATCGGATGCAGAGTTGTATAAAGTATGGAAAGA -s simRat_chr6.simRat.chr6 448046 33 - 647215 AGCAGATGTGGAGTTGTATAAGGTATGGAAAGA - -a -s simMouse_chr6.simMouse.chr6 209854 13 + 636262 TCCCTTAGACTTT -s Anc0.Anc0refChr5 57972 13 - 87904 ACTCTTGGACTTT -s Anc1.Anc1refChr8 13681 13 - 57822 ACTCTTGGACTTT -s Anc2.Anc2refChr15 61904 13 - 86568 ACTCTTGGACTTT -s mr.mrrefChr5 231196 13 - 294540 TCCCTTAGACTTT -s simCow_chr6.simCow.chr6 220186 13 + 602619 ACTCTTGGACTTT -s simDog_chr6.simDog.chr6 398399 13 - 593897 ACTCTTGGACTTT -s simHuman_chr6.simHuman.chr6 389618 13 - 601863 ACTCTTGGACTTT -s simRat_chr6.simRat.chr6 448079 13 - 647215 TCATTTAGACTTT - -a -s simMouse_chr6.simMouse.chr6 209867 5 + 636262 GAGCT -s Anc0.Anc0refChr5 57989 5 - 87904 GAGCA -s Anc1.Anc1refChr8 13698 5 - 57822 GAGCA -s Anc2.Anc2refChr15 61921 5 - 86568 GAGCA -s mr.mrrefChr5 231213 5 - 294540 GAGCT -s simCow_chr6.simCow.chr6 220203 5 + 602619 GAGTA -s simDog_chr6.simDog.chr6 398416 5 - 593897 GAGCA -s simHuman_chr6.simHuman.chr6 389635 5 - 601863 GAGCA -s simRat_chr6.simRat.chr6 448096 5 - 647215 GAGCT - -a -s simMouse_chr6.simMouse.chr6 209872 1 + 636262 G -s Anc0.Anc0refChr5 58001 1 - 87904 G -s Anc1.Anc1refChr8 13710 1 - 57822 G -s Anc2.Anc2refChr15 61933 1 - 86568 T -s mr.mrrefChr5 231218 1 - 294540 G -s simCow_chr6.simCow.chr6 220215 1 + 602619 T -s simDog_chr6.simDog.chr6 398428 1 - 593897 T -s simHuman_chr6.simHuman.chr6 389647 1 - 601863 G -s simRat_chr6.simRat.chr6 448101 1 - 647215 G - -a -s simMouse_chr6.simMouse.chr6 209873 43 + 636262 ATCACTTGCGGCCATATTGAAGGTGCAGTAAGGCACTCTATGC -s Anc0.Anc0refChr5 58002 43 - 87904 GTAACTTGCAACCACATTGAAGATGAAGTAGTGCACTCTTCTC -s Anc1.Anc1refChr8 13711 43 - 57822 GTAACTTGCAACCACATTGAAGATGAAGTAGTGCACTCTTCTC -s Anc2.Anc2refChr15 61935 43 - 86568 GTAACTTGCAACCACATTGAAGATGAAGTAGTGCACTCTTCTC -s mr.mrrefChr5 231219 43 - 294540 ATCACTTGCGGCCATATTGAAGGTGCAGTAGGGCACTCTATGC -s simCow_chr6.simCow.chr6 220217 43 + 602619 GTAACCTGTAACCACATGGCAGGCGAAAAAGTGGACTCTTCTC -s simDog_chr6.simDog.chr6 398430 43 - 593897 GGGACTTGCCAGCACATTGAAGATTAAGTAGTGCAGACTTCTA -s simHuman_chr6.simHuman.chr6 389648 43 - 601863 GTAGCTTGCAACAAGATTGAAGATGAAGTAGTGTACTCTTCAC -s simRat_chr6.simRat.chr6 448102 43 - 647215 ATCACTTGCGGCCACATTGAAGGTACAGTAGGGGACTCTCTGC - -a -s simMouse_chr6.simMouse.chr6 209916 7 + 636262 TTTAAAT -s Anc0.Anc0refChr5 58051 7 - 87904 TGTAAAT -s Anc1.Anc1refChr8 13760 7 - 57822 TGTAAAT -s Anc2.Anc2refChr15 61984 7 - 86568 TGTAAGT -s mr.mrrefChr5 231262 7 - 294540 TGTAAAT -s simCow_chr6.simCow.chr6 220266 7 + 602619 TGTAAGT -s simDog_chr6.simDog.chr6 398479 7 - 593897 CATAAGT -s simHuman_chr6.simHuman.chr6 389697 7 - 601863 TGTAAAT -s simRat_chr6.simRat.chr6 448145 7 - 647215 TGTAAAT - -a -s simMouse_chr6.simMouse.chr6 209923 43 + 636262 TTGTCTAGATGATTTCCACACAAATGGGCATAGTCCACAGGTG -s Anc0.Anc0refChr5 58058 6 - 87904 TTATCT------------------------------------- -s Anc1.Anc1refChr8 13767 6 - 57822 TTATCT------------------------------------- -s Anc2.Anc2refChr15 61996 6 - 86568 TTATCT------------------------------------- -s mr.mrrefChr5 231269 43 - 294540 TTGTCTAGATGATTTCCACACAAATGGGCATAGTCCACAGGTG -s simCow_chr6.simCow.chr6 220278 6 + 602619 CTATCC------------------------------------- -s simDog_chr6.simDog.chr6 398491 6 - 593897 TTATCT------------------------------------- -s simHuman_chr6.simHuman.chr6 389704 6 - 601863 TTATCT------------------------------------- -s simRat_chr6.simRat.chr6 448152 43 - 647215 TTGTCTAGATGATTTCCACTCAAATGGGCATAGTCCACAGCTA - -a -s simMouse_chr6.simMouse.chr6 209966 50 + 636262 CCCTGCTACTTATCGGCAGTATTACCAGAGACTTGCCTAGTGCCTGAGTT -s Anc0.Anc0refChr5 58064 17 - 87904 ---------------------------------TGCCTACTGCTTTAGTT -s Anc1.Anc1refChr8 13773 17 - 57822 ---------------------------------TGCCTACTGCTTTAGTT -s Anc2.Anc2refChr15 62002 17 - 86568 ---------------------------------TGCCTACTGCTTTAGTC -s mr.mrrefChr5 231312 50 - 294540 CCCTGCTACTTATCGGCAGTATTACCAGAGACTTGCCTACTGCTTGAGTT -s simCow_chr6.simCow.chr6 220284 17 + 602619 ---------------------------------TTCTTACTGTCTTAGTC -s simDog_chr6.simDog.chr6 398497 17 - 593897 ---------------------------------TGCCTACTACTTAAGTC -s simHuman_chr6.simHuman.chr6 389710 17 - 601863 ---------------------------------TGCCTACTGCTTTAGTT -s simRat_chr6.simRat.chr6 448196 50 - 647215 CCCTACTGCTTATGAGCTGCAGGGCCAGAGACTTGCCTACTGCTTAAGTT - -a -s simMouse_chr6.simMouse.chr6 210016 49 + 636262 GACCTGAACTGAACTTAATGAATGAAAATTAATTTCTCATTAACCATTG -s Anc0.Anc0refChr5 58082 48 - 87904 GACCTGAATTGAACTACACAT-TTAAGCTTAATTTCTAAAGTACCGTTG -s Anc1.Anc1refChr8 13791 48 - 57822 GACCTGAATTGAACTACACAT-TTAAGCTTAATTTCTAAAGTACCGTTG -s Anc2.Anc2refChr15 62020 48 - 86568 GACCTGAATTGCACCACACAT-CTAAGCTTGATTTCAAAAGTCCTGCTG -s mr.mrrefChr5 231362 48 - 294540 GACCTGAACTGAACTTAATGA-TGAAAATTAATTTCTCATTAACCATTG -s simCow_chr6.simCow.chr6 220302 47 + 602619 GA-CTAAATTGCACAACACAT-ATAAGATTGATTTCACAAGTCCTACTG -s simDog_chr6.simDog.chr6 398515 48 - 593897 GACCTGAATTACACCACACAT-CTAAGCTTGATTTCAAGAGTCCTGCTG -s simHuman_chr6.simHuman.chr6 389728 45 - 601863 GACCTGAAGTGAACTACACAT-TTAA---TAATTCCTAAAGTACCGTTG -s simRat_chr6.simRat.chr6 448246 48 - 647215 GACCTGAACTGAAATTAATGA-TGAAAACTAATTTCTCATAAACCCGTG - -a -s simMouse_chr6.simMouse.chr6 210065 7 + 636262 AGCCCTC -s Anc0.Anc0refChr5 58130 7 - 87904 ATCCTCC -s Anc1.Anc1refChr8 13839 7 - 57822 ATCCTCC -s Anc2.Anc2refChr15 62080 7 - 86568 ATCCTCC -s mr.mrrefChr5 231410 7 - 294540 AGCCCCC -s simCow_chr6.simCow.chr6 220361 7 + 602619 ATCTTCC -s simDog_chr6.simDog.chr6 398575 7 - 593897 ATCCTCC -s simHuman_chr6.simHuman.chr6 389773 3 - 601863 A----CC -s simRat_chr6.simRat.chr6 448294 7 - 647215 AGCCCCC - -a -s simMouse_chr6.simMouse.chr6 210072 1 + 636262 C -s Anc0.Anc0refChr5 58138 1 - 87904 T -s Anc1.Anc1refChr8 13847 1 - 57822 T -s Anc2.Anc2refChr15 62088 1 - 86568 T -s mr.mrrefChr5 231417 1 - 294540 C -s simCow_chr6.simCow.chr6 220369 1 + 602619 T -s simDog_chr6.simDog.chr6 398583 1 - 593897 T -s simHuman_chr6.simHuman.chr6 389777 1 - 601863 T -s simRat_chr6.simRat.chr6 448301 1 - 647215 C - -a -s simMouse_chr6.simMouse.chr6 210073 122 + 636262 TATGGTAGTGTAGCCTTTGTTGTTTCCTCAGGTTGAACATTTCAACTTTCAATACAGAATTATAAGTATTTCAATAGCAAGCATGGGTATTAGTTCAATGGATTCATACAGGGATAGGCCCT -s Anc0.Anc0refChr5 58140 106 - 87904 TACAGTAGTGAAGCTTTCATTATTTCAATAGGTTCAACATTTCATCTTTTAGTATTGGATTCTACCTAGTTCAATAGCAAGGATGGGT---------------TTATA-GGGGATAGCCTCT -s Anc1.Anc1refChr8 13849 107 - 57822 TACAGTAGTGAAGCTTTCATTATTTCAATAGGTTCAACATTTCATCTTTTAGTATTGGATTCTACCTAGTTCAATAGCAAGGATGGGT---------------TTATATGGGGATAGCCTCT -s Anc2.Anc2refChr15 62090 106 - 86568 TACAGCAGTGAAGCTTTCATTATTTCAATTGGCTCAACATTTCATCTCTTAGTATTGGATTCTACCTAGTTCAATAGCAAGGATGGGT---------------TTATA-GTGGGTAGCCTTT -s mr.mrrefChr5 231419 122 - 294540 TATGGTAGTGTAGCCTTTGTTGTTTCCTCAGGTTGAACATTTCAACTTTCAATACAGAATTATAAGTATTTCAATAGCAAGCATGGGTATTAGTTCAATGGATTCATACAGGGATAGGCCCT -s simCow_chr6.simCow.chr6 220371 106 + 602619 TATTGCAGTGAAGCTTCCATTATTTCATTCAGCTCAACATTTCATCTCCTGATATTGGACTCTATCTATTCCAATACTAAGCATGGGT---------------TTACA-TAACGCCCGCTTT -s simDog_chr6.simDog.chr6 398585 104 - 593897 TACAGTAGCGAAGCTTTCATTATTT--ATTGGCTCAACATTTCATCTCTTAGTATTGGATTCTACCTTGTTCAATAGCAAGGATGGGT---------------TTATT-GTGGGTAGCCTTT -s simHuman_chr6.simHuman.chr6 389779 96 - 601863 TCCACTAT---AGCTCTCAGTATTTCACTAGGTCCAACAATTGATGTT--------GGATTGTCCCTACTTGTATAGCAAGTACAGGT---------------TTATATGGGGATAGACTCT -s simRat_chr6.simRat.chr6 448303 122 - 647215 TGTGATAGTGTAGCCTTTGTTGTCTCCTCAGGCTGAACATTTCAACTTTCAATACAGAATTATAAGTATCACAATAGCAAGCCTGGGTATTGTCTTAATGGGTTCATACAGGGATAGGCCCT - -a -s simMouse_chr6.simMouse.chr6 210195 16 + 636262 ATTCTTATTCTAGAAT -s Anc0.Anc0refChr5 58247 13 - 87904 ATTGTAACTCT---AT -s Anc1.Anc1refChr8 13957 16 - 57822 ATTGTAACTCTATAAT -s Anc2.Anc2refChr15 62197 13 - 86568 ATTGTAACTCT---AT -s mr.mrrefChr5 231541 16 - 294540 ATTCTAATTCTAGAAT -s simCow_chr6.simCow.chr6 220478 13 + 602619 ATTGTAACTCC---AT -s simDog_chr6.simDog.chr6 398690 13 - 593897 GTTGTAACTGT---AT -s simHuman_chr6.simHuman.chr6 389876 16 - 601863 ATTGTAACACTATAAT -s simRat_chr6.simRat.chr6 448425 16 - 647215 ATTCTAATTCTAGAAA - -a -s simMouse_chr6.simMouse.chr6 210211 2 + 636262 GC -s Anc0.Anc0refChr5 58264 2 - 87904 GC -s Anc1.Anc1refChr8 13977 2 - 57822 GC -s Anc2.Anc2refChr15 62214 2 - 86568 GC -s mr.mrrefChr5 231557 2 - 294540 GC -s simCow_chr6.simCow.chr6 220495 2 + 602619 GC -s simDog_chr6.simDog.chr6 398707 2 - 593897 GC -s simHuman_chr6.simHuman.chr6 389896 2 - 601863 GC -s simRat_chr6.simRat.chr6 448441 2 - 647215 GC - -a -s simMouse_chr6.simMouse.chr6 210213 19 + 636262 TGTTGCAGTTATTTACTTG -s Anc0.Anc0refChr5 58266 19 - 87904 GGTTGTAATCAGTTGCTTA -s Anc1.Anc1refChr8 13979 19 - 57822 GGTTGTAATCAGTTGCTTA -s Anc2.Anc2refChr15 62216 19 - 86568 GGTTATAATCAGTTGTTTA -s mr.mrrefChr5 231559 19 - 294540 TGTTGCAGTTATTTACTTG -s simCow_chr6.simCow.chr6 220497 19 + 602619 TATTATGATCAATTGTGTA -s simDog_chr6.simDog.chr6 398709 19 - 593897 GGCTATAATCAGTTATTTA -s simHuman_chr6.simHuman.chr6 389898 19 - 601863 CGTTGTAATCAGTTGCTTA -s simRat_chr6.simRat.chr6 448444 19 - 647215 TGTTACAGTTATTTACTTG - -a -s simMouse_chr6.simMouse.chr6 210232 9 + 636262 AATTTCCAT -s Anc0.Anc0refChr5 58299 9 - 87904 AACTTACAA -s Anc1.Anc1refChr8 14012 9 - 57822 AACTTACAA -s Anc2.Anc2refChr15 62249 9 - 86568 AACTCACAA -s mr.mrrefChr5 231578 9 - 294540 AATTTCCAT -s simCow_chr6.simCow.chr6 220531 9 + 602619 AACTCACAA -s simDog_chr6.simDog.chr6 398742 9 - 593897 ACCTCACAA -s simHuman_chr6.simHuman.chr6 389931 9 - 601863 AACGTACAA -s simRat_chr6.simRat.chr6 448463 9 - 647215 AATCTCCAC - -a -s simMouse_chr6.simMouse.chr6 210241 4 + 636262 GACC -s Anc0.Anc0refChr5 58308 4 - 87904 GACC -s Anc1.Anc1refChr8 14021 4 - 57822 GACC -s Anc2.Anc2refChr15 62262 4 - 86568 CACC -s mr.mrrefChr5 231587 4 - 294540 GACC -s simCow_chr6.simCow.chr6 220544 4 + 602619 CAGC -s simDog_chr6.simDog.chr6 398761 4 - 593897 CACC -s simHuman_chr6.simHuman.chr6 389940 4 - 601863 GACC -s simRat_chr6.simRat.chr6 448472 4 - 647215 AACT - -a -s simMouse_chr6.simMouse.chr6 210245 4 + 636262 TAGC -s Anc0.Anc0refChr5 58320 4 - 87904 TAGC -s Anc1.Anc1refChr8 14033 4 - 57822 TAGC -s Anc2.Anc2refChr15 62274 4 - 86568 TAGC -s mr.mrrefChr5 231591 4 - 294540 TAGC -s simCow_chr6.simCow.chr6 220556 4 + 602619 TATA -s simDog_chr6.simDog.chr6 398773 4 - 593897 TGGC -s simHuman_chr6.simHuman.chr6 389952 4 - 601863 TAGC -s simRat_chr6.simRat.chr6 448476 4 - 647215 TAGC - -a -s simMouse_chr6.simMouse.chr6 210249 7 + 636262 TATGACA -s Anc0.Anc0refChr5 58388 7 - 87904 TGTGAGA -s Anc1.Anc1refChr8 14101 7 - 57822 TGTGAGA -s Anc2.Anc2refChr15 62343 7 - 86568 TGTGAGA -s mr.mrrefChr5 231595 7 - 294540 TATGACA -s simCow_chr6.simCow.chr6 220625 7 + 602619 TGGGAGA -s simDog_chr6.simDog.chr6 398842 7 - 593897 TGTTAGA -s simHuman_chr6.simHuman.chr6 390020 7 - 601863 TGTGGGA -s simRat_chr6.simRat.chr6 448480 7 - 647215 TATGACA - -a -s simMouse_chr6.simMouse.chr6 210256 19 + 636262 TGCTGCATGTGAATCAAGA -s Anc0.Anc0refChr5 58395 17 - 87904 GATTGCATG--AATCAAGA -s Anc1.Anc1refChr8 14108 17 - 57822 GATTGCATG--AATCAAGA -s Anc2.Anc2refChr15 62350 17 - 86568 GATTGCATG--AAGCAAGC -s mr.mrrefChr5 231602 19 - 294540 TGCTGCATGTGAATCAAGA -s simCow_chr6.simCow.chr6 220632 17 + 602619 GATTGCATA--AACCAAAT -s simDog_chr6.simDog.chr6 398850 17 - 593897 GACTGCATG--AAGCAAGC -s simHuman_chr6.simHuman.chr6 390027 17 - 601863 GATTGCATG--AATCAAGA -s simRat_chr6.simRat.chr6 448487 19 - 647215 TGCTGCATGTAAATCAAGA - -a -s simMouse_chr6.simMouse.chr6 210275 1 + 636262 G -s Anc0.Anc0refChr5 58412 1 - 87904 G -s Anc1.Anc1refChr8 14125 1 - 57822 G -s Anc2.Anc2refChr15 62367 1 - 86568 C -s mr.mrrefChr5 231621 1 - 294540 G -s simCow_chr6.simCow.chr6 220649 1 + 602619 C -s simDog_chr6.simDog.chr6 398867 1 - 593897 C -s simHuman_chr6.simHuman.chr6 390047 1 - 601863 G -s simRat_chr6.simRat.chr6 448506 1 - 647215 G - -a -s simMouse_chr6.simMouse.chr6 210276 101 + 636262 ATTACCCACTATTGTAGACCCCCTAGCTCAACAATACAATATCATCTAGATGAGGATACTGATTGTAGGAGACATGATGCTCACACCCCCATGGCTATAAC -s Anc0.Anc0refChr5 58413 94 - 87904 AGTACC----CTTGTAGACCCTCTAGCCCCACAATACAGTACCATCTAGGTGTGGATAATGATTGCAGGAGATTTATTACTCACACCCGCCAGGCAAT--- -s Anc1.Anc1refChr8 14126 98 - 57822 AGTACCCGCTCTTGTAGACCCTCTAGCCCCACAATACAGTACCATCTAGGTGTGGATAATGATTGCAGGAGATTTATTACTCACACCCGCCAGGCAAT--- -s Anc2.Anc2refChr15 62368 94 - 86568 AACACC----CTTGTAGACCCTCTAGCCCCACAATACAGTCCCATCTAGGTGTGCATAATGATTGCAGGAGATTTATTACTCACACCCGCCAGGCAAT--- -s mr.mrrefChr5 231622 98 - 294540 AGTACCCACTCTTGTAGACCCCCTAGCCCAACAATACAGTATCATCTAGATGAGGATACTGATTGTAGGAGATATAATGCTCACACCCCCAAGGCTAT--- -s simCow_chr6.simCow.chr6 220652 93 + 602619 CACACC----CTTGTAGGCCCTATAACGCTGCAATACAGTCCTATCTAGATGTACATAATGATTGCAGGAAATTTATTACTCA-AGCTGCCAGGCAAT--- -s simDog_chr6.simDog.chr6 398868 94 - 593897 AACACC----CCTGCAGACCCTCTAGCCCCACAATACAGTCCCATCTAGGTGTGCATAATGATTTCAGAAGATTTATTACCCACACCCACCAGGCAAT--- -s simHuman_chr6.simHuman.chr6 390048 98 - 601863 AGTACCTGCTCTTGTAAACCCTCTACCCCCACAATACAGTACCATCTAGGTGTGGGTAATGATTGCAGGAGATTTATTACTCACACCCGCCAGGCAAT--- -s simRat_chr6.simRat.chr6 448507 97 - 647215 GGTAACCACTCTTGTAGACCTGCTAGCCCAATAATACAGTATCATTTAAATAAGGA-ACTGATTGTAGGGGATGTAATGCTCACACCCACAAGGCTAT--- - -a -s simMouse_chr6.simMouse.chr6 210377 5 + 636262 TTAAG -s Anc0.Anc0refChr5 31449 5 + 87904 TTCAG -s Anc1.Anc1refChr8 45734 5 + 57822 TTCAG -s Anc2.Anc2refChr15 26218 5 + 86568 TCCAA -s mr.mrrefChr5 65107 5 + 294540 TTAAG -s simCow_chr6.simCow.chr6 384072 4 - 602619 TCCA- -s simDog_chr6.simDog.chr6 197022 5 + 593897 TCCAA -s simHuman_chr6.simHuman.chr6 213837 5 + 601863 TTCAG -s simRat_chr6.simRat.chr6 201445 5 + 647215 TGAAG - -a -s simMouse_chr6.simMouse.chr6 210382 4 + 636262 ACCT -s Anc0.Anc0refChr5 31455 4 + 87904 ACCT -s Anc1.Anc1refChr8 45740 4 + 57822 ACCT -s Anc2.Anc2refChr15 26224 4 + 86568 ATGT -s mr.mrrefChr5 65112 4 + 294540 ACCT -s simDog_chr6.simDog.chr6 197028 4 + 593897 ATGT -s simHuman_chr6.simHuman.chr6 213843 4 + 601863 ACCT -s simRat_chr6.simRat.chr6 201450 4 + 647215 ACCT - -a -s simMouse_chr6.simMouse.chr6 210386 37 + 636262 TTTATGGCTGAACCCTGCCAATTCATTACAAACACAG -s Anc0.Anc0refChr5 31460 17 + 87904 GTTATGGCC-------------------CAA-CACTA -s Anc1.Anc1refChr8 45745 18 + 57822 GTTATGGCC-------------------CAAACACTA -s Anc2.Anc2refChr15 26229 17 + 86568 GTTATGGCC-------------------CAA-CACTA -s mr.mrrefChr5 65117 36 + 294540 TTTATGGCTGAACCCTGCCAATT-ATTACAAACACTG -s simCow_chr6.simCow.chr6 384076 12 - 602619 -----GACT-------------------CAC-CACCA -s simDog_chr6.simDog.chr6 197033 17 + 593897 GTTATAGTC-------------------CAA-CACTA -s simHuman_chr6.simHuman.chr6 213848 18 + 601863 GTTATGGCC-------------------CAAACACTA -s simRat_chr6.simRat.chr6 201455 36 + 647215 TTTTTGGCTGTACACTGCCAATT-GTTACGAACGCTG - -a -s simMouse_chr6.simMouse.chr6 210423 20 + 636262 CCAATATGTTACCCTGGAAT -s Anc0.Anc0refChr5 31478 20 + 87904 CCAATTCCTTTCCCTGAAAC -s Anc1.Anc1refChr8 45764 20 + 57822 CCAATTCCTTTCCCTGAAAC -s Anc2.Anc2refChr15 26247 20 + 86568 CCAATTCCTTTCCCTGGAAC -s mr.mrrefChr5 65153 20 + 294540 CCAATTTGTTACCCTGAAAT -s simCow_chr6.simCow.chr6 384089 20 - 602619 CCAATTCCTTTCCCTGGAAC -s simDog_chr6.simDog.chr6 197051 6 + 593897 CCACTT-------------- -s simHuman_chr6.simHuman.chr6 213867 20 + 601863 CCAATTCATATCCCTGAAAC -s simRat_chr6.simRat.chr6 201491 20 + 647215 CCAATTTGTTACCCTGAAAT - -a -s simMouse_chr6.simMouse.chr6 210443 18 + 636262 CTATGGAGGTCTAAGCAG -s Anc0.Anc0refChr5 31530 17 + 87904 ATATGGA-GTTAAGGAAG -s Anc1.Anc1refChr8 45816 17 + 57822 ATATGGA-GTTAAGGAAG -s Anc2.Anc2refChr15 26299 17 + 86568 ATATGGA-GTTAAGAAAG -s mr.mrrefChr5 65205 17 + 294540 ATATGGA-GTCAAGGCAG -s simCow_chr6.simCow.chr6 384145 17 - 602619 ATAGAGA-GTTAAGAAAG -s simDog_chr6.simDog.chr6 197083 17 + 593897 ATTTGAA-AGTAAGAAAG -s simHuman_chr6.simHuman.chr6 213919 17 + 601863 ATATGGA-GTGAAGGGAG -s simRat_chr6.simRat.chr6 201544 17 + 647215 ATATGGA-GTTAAGGCAG - -a -s simMouse_chr6.simMouse.chr6 210461 36 + 636262 GGCATTCATGATGTGGTACAAGTGTGTACCAGGATC -s Anc0.Anc0refChr5 31547 30 + 87904 GTGATCCA------GATTCATGTGCTTACCTGGACC -s Anc1.Anc1refChr8 45833 30 + 57822 GTGATCCA------GATTCATGTGCTTACCTGGACC -s Anc2.Anc2refChr15 26322 30 + 86568 GTGATCCA------GATTCTTGTGCTTACCTGGACC -s mr.mrrefChr5 65222 36 + 294540 GGCATTCATGATGTGGTACAAGTGCGTACCAGGATC -s simCow_chr6.simCow.chr6 384168 30 - 602619 GTGATCCA------GACTCTTGAGCATACCTAGACC -s simDog_chr6.simDog.chr6 197106 30 + 593897 GGGAGTCA------GATTCTTGTGCTTACCTGGACC -s simHuman_chr6.simHuman.chr6 213936 30 + 601863 GTGATCCA------GCTTCATGTGCTTACCTGGACT -s simRat_chr6.simRat.chr6 201561 36 + 647215 GGCATTCGCAATGTGGTACAAGTGCACACCAGGATC - -a -s simMouse_chr6.simMouse.chr6 210497 4 + 636262 TGCA -s Anc0.Anc0refChr5 31577 4 + 87904 TGCA -s Anc1.Anc1refChr8 45863 4 + 57822 TGCA -s Anc2.Anc2refChr15 26352 4 + 86568 TGCA -s mr.mrrefChr5 65258 4 + 294540 TGCA -s simCow_chr6.simCow.chr6 384198 4 - 602619 TGCA -s simDog_chr6.simDog.chr6 197140 4 + 593897 TGCA -s simHuman_chr6.simHuman.chr6 213966 4 + 601863 TGCA -s simRat_chr6.simRat.chr6 201597 4 + 647215 TGCA - -a -s simMouse_chr6.simMouse.chr6 210501 5 + 636262 TAATC -s Anc0.Anc0refChr5 31582 5 + 87904 TGAGC -s Anc1.Anc1refChr8 45868 5 + 57822 TGAGC -s Anc2.Anc2refChr15 26357 5 + 86568 TGAGC -s mr.mrrefChr5 65262 5 + 294540 TAATC -s simCow_chr6.simCow.chr6 384203 5 - 602619 TGACC -s simDog_chr6.simDog.chr6 197145 5 + 593897 TGTGC -s simHuman_chr6.simHuman.chr6 213971 5 + 601863 TGAGC -s simRat_chr6.simRat.chr6 201601 5 + 647215 TAACC - -a -s simMouse_chr6.simMouse.chr6 210506 3 + 636262 AGT -s Anc0.Anc0refChr5 31587 3 + 87904 ATT -s Anc1.Anc1refChr8 45873 3 + 57822 ATT -s Anc2.Anc2refChr15 26371 3 + 86568 ATC -s mr.mrrefChr5 65267 3 + 294540 ATT -s simCow_chr6.simCow.chr6 384217 3 - 602619 ACC -s simDog_chr6.simDog.chr6 197159 3 + 593897 ATC -s simHuman_chr6.simHuman.chr6 213976 3 + 601863 ATT -s simRat_chr6.simRat.chr6 201606 3 + 647215 ATT - -a -s simMouse_chr6.simMouse.chr6 210509 33 + 636262 ACCTTTGCTGGACCTGTTTTAAGGAAGGCAAAA -s Anc0.Anc0refChr5 31590 33 + 87904 ACCATTTCGGGATCTCCTCTGAGGGAGGTCAAA -s Anc1.Anc1refChr8 45876 33 + 57822 ACCATTTCGGGATCTCCTCTGAGGGAGGTCAAA -s Anc2.Anc2refChr15 26379 33 + 86568 ACCATCTTGGAATTTCCTCTGAGGGAGGTCAAA -s mr.mrrefChr5 65270 33 + 294540 ACCATTGCGGGATCTGTTTTAAGGAAGGCAAAA -s simCow_chr6.simCow.chr6 384225 33 - 602619 ACTGTCTTGGAATTTCCTATGAGGAAGGTCAAA -s simDog_chr6.simDog.chr6 197167 31 + 593897 ACCAACTTAGA--TACCTCTGAGGGAGGTGAAA -s simHuman_chr6.simHuman.chr6 213979 33 + 601863 ACCATTTCGGGATCTCCTCTGAGGGAAGTCAAA -s simRat_chr6.simRat.chr6 201609 33 + 647215 ACCATTGTGGAATTTGTTTTAAGGAAGGCAAAA - -a -s simMouse_chr6.simMouse.chr6 210542 50 + 636262 TGAAGTTCTATATACCCATCAATGGTCACACACAGCACATGACATTCATG -s Anc0.Anc0refChr5 31649 31 + 87904 TGATATATTAAA-------------------GCAGCACACAATATTGGAG -s Anc1.Anc1refChr8 45935 31 + 57822 TGATATATTAAA-------------------GCAGCACACAATATTGGAG -s Anc2.Anc2refChr15 26438 31 + 86568 TGATATATAAAA-------------------GCAGCATACAATGTTGGAG -s mr.mrrefChr5 65303 31 + 294540 TGAAATATTATA-------------------GCAGCACATGACATTCAAG -s simCow_chr6.simCow.chr6 384283 31 - 602619 TGGTATATAAAA-------------------GCAGCATACAATGTTAAAG -s simDog_chr6.simDog.chr6 197224 31 + 593897 TGATGTATAAAA-------------------GTATCATATGATGTTGGAG -s simHuman_chr6.simHuman.chr6 214038 31 + 601863 TGATAGATTAAA-------------------GCAGCACACAATATTTCAG -s simRat_chr6.simRat.chr6 201642 31 + 647215 TGACATATTACA-------------------GCAGCACATGACATCCAAT - -a -s simMouse_chr6.simMouse.chr6 210592 29 + 636262 GCTTTGCATTGCTTCTTGGCAATTTTTAC -s Anc0.Anc0refChr5 31680 24 + 87904 GCT-----TTCCTGGGTGGCAGTTTGTGT -s Anc1.Anc1refChr8 45966 24 + 57822 GCT-----TTCCTGGGTGGCAGTTTGTGT -s Anc2.Anc2refChr15 26469 24 + 86568 GCT-----TTGCTGGGTGTCAGTTTGTGT -s mr.mrrefChr5 65334 29 + 294540 GCTTTGCATTCCTTGTTGGCAATTTTTAC -s simCow_chr6.simCow.chr6 384322 24 - 602619 AAT-----ATTCAGGGTTCTACTTGCTGT -s simDog_chr6.simDog.chr6 197255 24 + 593897 GCC-----TTGCTTGGTGTCAGTTTGTTT -s simHuman_chr6.simHuman.chr6 214069 24 + 601863 GCT-----TTCCTGGCTCGCAGTTTGTGT -s simRat_chr6.simRat.chr6 201673 29 + 647215 GCTTTGCTTGCCTTGTTGGTGATTGCTCC - -a -s simMouse_chr6.simMouse.chr6 210621 29 + 636262 TCTATCCATGAGCTTTAAGCATGGTTCAC -s Anc0.Anc0refChr5 31706 25 + 87904 ----TCCATGAACTTTACCCACAGCCTAC -s Anc1.Anc1refChr8 45992 25 + 57822 ----TCCATGAACTTTACCCACAGCCTAC -s Anc2.Anc2refChr15 26495 25 + 86568 ----CTCATGAACTTTACCCACAGCCTAC -s mr.mrrefChr5 65365 29 + 294540 TCTATCCATGAGCTTTAACCATAGTTTAC -s simCow_chr6.simCow.chr6 384348 25 - 602619 ----CTCATGAACTATAACCACAGCCCAC -s simDog_chr6.simDog.chr6 197281 24 + 593897 ----CTCTTCAACTTTACCCAT-GCCTAC -s simHuman_chr6.simHuman.chr6 214095 25 + 601863 ----TCCATGAACTTTACCCACAGCCTAC -s simRat_chr6.simRat.chr6 201704 29 + 647215 TCCATCCGTGAGCTTTAACCATAGTTTGC - -a -s simMouse_chr6.simMouse.chr6 210650 6 + 636262 TTTTAG -s Anc0.Anc0refChr5 31737 2 + 87904 ----AA -s Anc1.Anc1refChr8 46023 6 + 57822 TCTTAA -s Anc2.Anc2refChr15 26526 2 + 86568 ----AA -s mr.mrrefChr5 65394 6 + 294540 TTTTAG -s simCow_chr6.simCow.chr6 384379 2 - 602619 ----AA -s simDog_chr6.simDog.chr6 197311 2 + 593897 ----AA -s simHuman_chr6.simHuman.chr6 214131 6 + 601863 TCTTAA -s simRat_chr6.simRat.chr6 201733 6 + 647215 TTTTAG - -a -s simMouse_chr6.simMouse.chr6 210656 16 + 636262 TTTGTGGTGCTGGTGC -s Anc0.Anc0refChr5 31742 16 + 87904 CTTGAGTCCATGGTGC -s Anc1.Anc1refChr8 46032 16 + 57822 CTTGAGTCCATGGTGC -s Anc2.Anc2refChr15 26531 16 + 86568 CTTGAGTCCATGGTGC -s mr.mrrefChr5 65400 16 + 294540 TTTGTGTTGCTGGTGC -s simCow_chr6.simCow.chr6 384384 16 - 602619 CTTGAGTTAGTGGTGC -s simDog_chr6.simDog.chr6 197316 16 + 593897 CTTGAGTCCATCTTGC -s simHuman_chr6.simHuman.chr6 214140 16 + 601863 CTCAAGTCCATGGTGC -s simRat_chr6.simRat.chr6 201739 16 + 647215 TTTGTGTTGCTGGTGC - -a -s simMouse_chr6.simMouse.chr6 210672 66 + 636262 CTAACTTATTATGTGATCAATCCTAACCTTAGTACTCTTGGGCAGCATTCACTTCTCCACTATGAT -s Anc0.Anc0refChr5 31759 62 + 87904 CTGGTTTATTATGTGGTCAATTCTAGCCCAGG----ATAGCTCAACATTAACTTCTCCACTATCAT -s Anc1.Anc1refChr8 46049 62 + 57822 CTGGTTTATTATGTGGTCAATTCTAGCCCAGG----ATAGCTCAACATTAACTTCTCCACTATCAT -s Anc2.Anc2refChr15 26548 62 + 86568 CTGGTTTATTATGTGGTCAATTCTAGCGCAGG----ATAGCTCCACATTAACTTCTCCACTATCAT -s mr.mrrefChr5 65417 66 + 294540 CTAATTTATTATGTGATCAATCCTAACCTTAGTACTCTTGGGCAACATTAACTTCTCCACTATGAT -s simCow_chr6.simCow.chr6 384401 62 - 602619 TTGATTTATTATGTTGTCAAGGCTATCTCAGA----ATAGCTCCACAGGAACGTCTCCACAATCAT -s simDog_chr6.simDog.chr6 197333 62 + 593897 CTGGTTTATAATGTGGTTACTTCTGGTGGGCG----ATGGCCCCACATTACCTTCTCTACTATCAT -s simHuman_chr6.simHuman.chr6 214157 62 + 601863 CTGGTTCATTATGTGGCCAATTCTAGCCCAGG----ATAGCTCAACCCTAACTTCTGCGCTACCAT -s simRat_chr6.simRat.chr6 201756 65 + 647215 CTAATTTATCATGTGATCAATCCTAACCTTAGTACTCTTGGCTAACATCAACCTCTCGA-TATGAT - -a -s simMouse_chr6.simMouse.chr6 210738 8 + 636262 CTTGCTTG -s Anc0.Anc0refChr5 31825 8 + 87904 CTTGACTG -s Anc1.Anc1refChr8 46115 8 + 57822 CTTGACTG -s Anc2.Anc2refChr15 26614 8 + 86568 CTCCACTG -s mr.mrrefChr5 65487 8 + 294540 CTTGCTTG -s simCow_chr6.simCow.chr6 384467 8 - 602619 CGCAACTG -s simDog_chr6.simDog.chr6 197399 8 + 593897 ATCCAATG -s simHuman_chr6.simHuman.chr6 214223 8 + 601863 CTTGACTG -s simRat_chr6.simRat.chr6 201825 8 + 647215 CTTGCTTG - -a -s simMouse_chr6.simMouse.chr6 210746 39 + 636262 CCAGGTTGATAATGGACTCATCTTGCACATCTGTCCTTT -s Anc0.Anc0refChr5 31834 39 + 87904 CCAGGCTGATAATCAACTCATTTTGTCTTCATGTTATTT -s Anc1.Anc1refChr8 46124 39 + 57822 CCAGGCTGATAATCAACTCATTTTGTCTTCATGTTATTT -s Anc2.Anc2refChr15 26623 39 + 86568 CCAGGCTGATAGTCAACTCATTTTGTCTTCATGTTATCT -s mr.mrrefChr5 65495 39 + 294540 CCAGGTTGATAATGGACTCATCTTGCACATCTGTTCTTT -s simCow_chr6.simCow.chr6 384476 35 - 602619 CCAGGCTG----TCAACTCATCTCAGCTTCATGTTGACT -s simDog_chr6.simDog.chr6 197408 39 + 593897 CCAGGCTGATAGTCAACTCATTTTGTCTTAATGTTATCT -s simHuman_chr6.simHuman.chr6 214232 39 + 601863 CCAGGCTGATAATAAACTCATTTTGACTTCATGTTATTT -s simRat_chr6.simRat.chr6 201833 39 + 647215 CCAGATTGATAATGGATTCATCTTGCACATCTGTTCTTT - -a -s simMouse_chr6.simMouse.chr6 210785 13 + 636262 ATGAATCCCCCTT -s Anc0.Anc0refChr5 31875 12 + 87904 -TGAACCCCTCTT -s Anc1.Anc1refChr8 46165 13 + 57822 ATGAACCCCTCTT -s Anc2.Anc2refChr15 26664 12 + 86568 -TGAACCCCCCTT -s mr.mrrefChr5 65534 13 + 294540 ATGAATCCCTCTT -s simCow_chr6.simCow.chr6 384513 12 - 602619 -TAAACTTCCCTT -s simDog_chr6.simDog.chr6 197449 12 + 593897 -TGAACCCCCCTT -s simHuman_chr6.simHuman.chr6 214275 13 + 601863 ATGAACCCCTCTT -s simRat_chr6.simRat.chr6 201872 12 + 647215 AT-AATTCCTCTT - -a -s simMouse_chr6.simMouse.chr6 210798 26 + 636262 CATTGCCCTGCAATGTGAGACAGGAA -s Anc0.Anc0refChr5 31887 23 + 87904 CACTGCC---CAGTGTGAGATGGGAG -s Anc1.Anc1refChr8 46178 26 + 57822 CACTGCCTGGCAGTGTGAGATGGGAG -s Anc2.Anc2refChr15 26692 23 + 86568 CACTGCC---CAGTGTGAGCTGGGAG -s mr.mrrefChr5 65547 26 + 294540 CACTGCCCTGCAATGTGAGATAGGAA -s simCow_chr6.simCow.chr6 384541 15 - 602619 TGC-----------ATGAAGTGTGAG -s simDog_chr6.simDog.chr6 197477 23 + 593897 CACTGCC---CAGTGTGAGCTGGGGA -s simHuman_chr6.simHuman.chr6 214288 25 + 601863 CAC-ACCTGGCAGTGTGAGATGGGAG -s simRat_chr6.simRat.chr6 201884 26 + 647215 CACTGCCCTGCAATATGAGATAGGAA - -a -s simMouse_chr6.simMouse.chr6 210824 7 + 636262 TAGCATT -s Anc0.Anc0refChr5 31910 7 + 87904 TAGAGTT -s Anc1.Anc1refChr8 46204 7 + 57822 TAGAGTT -s Anc2.Anc2refChr15 26715 7 + 86568 TAGAGTT -s mr.mrrefChr5 65573 7 + 294540 TAGCATT -s simCow_chr6.simCow.chr6 384568 7 - 602619 TAGAGTT -s simDog_chr6.simDog.chr6 197500 7 + 593897 TAGAGTT -s simHuman_chr6.simHuman.chr6 214313 7 + 601863 TAAAGTT -s simRat_chr6.simRat.chr6 201910 7 + 647215 TAGCGTA - -a -s simMouse_chr6.simMouse.chr6 210831 3 + 636262 CAA -s Anc0.Anc0refChr5 31919 3 + 87904 GAA -s Anc1.Anc1refChr8 46213 3 + 57822 GAA -s Anc2.Anc2refChr15 26724 3 + 86568 GAA -s mr.mrrefChr5 65580 3 + 294540 CAA -s simCow_chr6.simCow.chr6 384577 3 - 602619 GGA -s simDog_chr6.simDog.chr6 197509 3 + 593897 GAA -s simHuman_chr6.simHuman.chr6 214322 3 + 601863 AAA -s simRat_chr6.simRat.chr6 201917 3 + 647215 CAA - -a -s simMouse_chr6.simMouse.chr6 210834 2 + 636262 GG -s Anc0.Anc0refChr5 31922 2 + 87904 GG -s Anc1.Anc1refChr8 46216 2 + 57822 GG -s Anc2.Anc2refChr15 26728 2 + 86568 GG -s mr.mrrefChr5 65583 2 + 294540 GG -s simCow_chr6.simCow.chr6 384581 2 - 602619 GG -s simDog_chr6.simDog.chr6 197513 2 + 593897 GG -s simHuman_chr6.simHuman.chr6 214325 2 + 601863 GG -s simRat_chr6.simRat.chr6 201920 2 + 647215 TA - -a -s simMouse_chr6.simMouse.chr6 210836 44 + 636262 GGGGATATCTTTAGATTTTTTTCCACTGACCCCTGTCAGTTCAC -s Anc0.Anc0refChr5 31924 42 + 87904 GGATATAT--TTAGATATTTCTTCACTGACCACTGTCAGTTGAC -s Anc1.Anc1refChr8 46218 42 + 57822 GGATATAT--TTAGATATTTCTTCACTGACCACTGTCAGTTGAC -s Anc2.Anc2refChr15 26730 42 + 86568 AGATATAT--TTAGACATTTCTTCACTGACCATTGTCTGTTGAC -s mr.mrrefChr5 65585 42 + 294540 GGGGATAT--TTAGATTTTTTTCCACTGACCCCTGTCAGTTCAC -s simCow_chr6.simCow.chr6 384583 42 - 602619 AGATATAG--TTGGACATTTCTTCACTAATCAATGTCGGTTGAT -s simDog_chr6.simDog.chr6 197515 41 + 593897 -GATATAT--TTAGACATTCCTTTACTGACCATTGTCTGTCGAC -s simHuman_chr6.simHuman.chr6 214427 41 + 601863 GGATATAT--TTAG-TGCTTCTTCACTGAACACGCTCAGTTGAC -s simRat_chr6.simRat.chr6 201922 42 + 647215 GGGGATAT--GCAGAGTTTTTTCCACTGAGCTCTGTCAGTTCAC - -a -s simMouse_chr6.simMouse.chr6 210880 4 + 636262 TGGT -s Anc0.Anc0refChr5 31966 4 + 87904 TAGT -s Anc1.Anc1refChr8 46260 4 + 57822 TAGT -s Anc2.Anc2refChr15 26772 4 + 86568 TAGT -s mr.mrrefChr5 65627 4 + 294540 TGGT -s simCow_chr6.simCow.chr6 384625 4 - 602619 TAGT -s simDog_chr6.simDog.chr6 197556 4 + 593897 TAGT -s simHuman_chr6.simHuman.chr6 214468 4 + 601863 TAGT -s simRat_chr6.simRat.chr6 201966 4 + 647215 TGGT - -a -s simMouse_chr6.simMouse.chr6 210884 5 + 636262 GGACA -s Anc0.Anc0refChr5 31974 5 + 87904 GGACA -s Anc1.Anc1refChr8 46268 5 + 57822 GGACA -s Anc2.Anc2refChr15 26780 5 + 86568 GGACA -s mr.mrrefChr5 65631 5 + 294540 GGACA -s simCow_chr6.simCow.chr6 384633 5 - 602619 AGACA -s simDog_chr6.simDog.chr6 197564 5 + 593897 GGACA -s simHuman_chr6.simHuman.chr6 214476 5 + 601863 GGAAA -s simRat_chr6.simRat.chr6 201970 5 + 647215 GCACA - -a -s simMouse_chr6.simMouse.chr6 210889 26 + 636262 ACCTCTGGAGTCAGGGGCAAACAGAC -s Anc0.Anc0refChr5 31979 26 + 87904 GCCCCCAGAGTGATAGGCAAAGAGAC -s Anc1.Anc1refChr8 46273 26 + 57822 GCCCCCAGAGTGATAGGCAAAGAGAC -s Anc2.Anc2refChr15 26785 26 + 86568 GCCCCCAGAGTGATAGGCAAAGAGAC -s mr.mrrefChr5 65636 26 + 294540 ACCTCTGGAGTCAGGGGCAAACAGAC -s simCow_chr6.simCow.chr6 384638 26 - 602619 CCCCCCAAGGTAATCAGCATAGAGCC -s simDog_chr6.simDog.chr6 197589 26 + 593897 GCCCCATGAGAGATAGGCAATGAGAC -s simHuman_chr6.simHuman.chr6 214481 26 + 601863 GCCCCCACTGTGATAGGCAAATAGAC -s simRat_chr6.simRat.chr6 201975 26 + 647215 ACCTCTGGAGTTAGGGGCAAACAGAC - -a -s simMouse_chr6.simMouse.chr6 210915 38 + 636262 TGGATTAGGGGAACATGGCCAGGAGAGTAATACGCAGC -s Anc0.Anc0refChr5 32007 32 + 87904 TGGGCTA----AAC-GGGCCAGTAAAGTAATAGGAAG- -s Anc1.Anc1refChr8 46301 36 + 57822 TGGGCTATGTGAAC-GGGCCAGTAAAGTAATAGGAAG- -s Anc2.Anc2refChr15 26813 32 + 86568 TGGGCTA----AAC-GGGCCAGTAAAGTAATAGGAAA- -s mr.mrrefChr5 65662 38 + 294540 TGGATTAGGGGAACATGGCCAGGAGAGTAATACGCAGC -s simCow_chr6.simCow.chr6 384666 16 - 602619 TGGGCTA----AAC-AGGCCA----------------- -s simDog_chr6.simDog.chr6 197617 32 + 593897 TGGGCTA----AAC-GGGCCGGTAAAGTAATAGGAAA- -s simHuman_chr6.simHuman.chr6 214509 36 + 601863 TGGGCTATGTGAAT-CGGCCAGCAAAATAATAGGAAG- -s simRat_chr6.simRat.chr6 202001 38 + 647215 TGGATTAGGGGAACATGATCAGGAGAGTGATACGCAGT - -a -s simMouse_chr6.simMouse.chr6 210953 14 + 636262 ACAAGCATGTGATA -s Anc0.Anc0refChr5 32039 14 + 87904 GCAAGCATGTGATA -s Anc1.Anc1refChr8 46337 14 + 57822 GCAAGCATGTGATA -s Anc2.Anc2refChr15 26845 14 + 86568 GCAAGCATGTGTTA -s mr.mrrefChr5 65700 14 + 294540 ACAAGCATGTGATA -s simDog_chr6.simDog.chr6 197650 14 + 593897 GCAAGCATGTGTTA -s simHuman_chr6.simHuman.chr6 214545 14 + 601863 GCAAGCATGTGATA -s simRat_chr6.simRat.chr6 202039 14 + 647215 ACAAGCATGTGGGA - -a -s simMouse_chr6.simMouse.chr6 210967 45 + 636262 TCCTACAGTCAAAGATGTAAGAACCATTGTGTCTAGTCTTACTGT -s Anc0.Anc0refChr5 32057 39 + 87904 TACTATGTTCAGAGAGGTAAGAATGATAGTGTCCA------CTGT -s Anc1.Anc1refChr8 46357 39 + 57822 TACTATGTTCAGAGAGGTAAGAATGATAGTGTCCA------CTGT -s Anc2.Anc2refChr15 26863 39 + 86568 CACTATGTTCAGAGAGGTGAGAATGACAGTGTCCA------CTAT -s mr.mrrefChr5 65714 39 + 294540 TCCTACAGTCAAAGATGTAAGAACCATTGTGTCTA------CTGT -s simCow_chr6.simCow.chr6 384685 39 - 602619 CACTCTGTTCAGAGAAGTGAGACTCACAGTCTCCA------CTAT -s simDog_chr6.simDog.chr6 197668 39 + 593897 CACTATGTGCAGCAAGGTGAGAATGGCAGTGTCCA------CTAT -s simHuman_chr6.simHuman.chr6 214565 39 + 601863 TACTATGTTCAGAGAGGCAAGAATGATAGTGTACA------CTGT -s simRat_chr6.simRat.chr6 202053 39 + 647215 TCCTACAGTCAAAGATGAAAGAACGATTGTGTCTA------CTGT - -a -s simMouse_chr6.simMouse.chr6 211012 68 + 636262 GTTTACTACTCATCCATGTATACAATTCACATTGTACTTGTTGTGCTAGCAAATACAAGTAGAATTTG -s Anc0.Anc0refChr5 32096 68 + 87904 GCTTGCTAGTCATTCATATAAACATGTCATGTGGCACATGTCATGTTTGCCAACACAATGAGAATTTG -s Anc1.Anc1refChr8 46396 68 + 57822 GCTTGCTAGTCATTCATATAAACATGTCATGTGGCACATGTCATGTTTGCCAACACAATGAGAATTTG -s Anc2.Anc2refChr15 26919 68 + 86568 ACTTGCTAGCCATTCATATCAACATGTCATGTGGCACATGTCATGTTTGCCGGCACAATGAGGGTTTG -s mr.mrrefChr5 65753 68 + 294540 GTTTACTACTCATCCATGTATACAATTCACATTGTACTTGTTGTGCTAGCAAATACAAGTAGAATTTG -s simCow_chr6.simCow.chr6 384741 67 - 602619 AATTGCT-GCCATTCATAGTCACATGTGATGCTGCACAAGTCATGTTTGCCGGCACAATGAGGGTTTG -s simDog_chr6.simDog.chr6 197724 48 + 593897 ACTTGCTAGCCATTCAGATCAACATATCATGTG-CACATGTTATGTTGG------------------- -s simHuman_chr6.simHuman.chr6 214604 68 + 601863 GCTTGGTAGTCATTCATATAAACATGTCATGTGGCACATGTCATGTTTGCTAACACGATAAGAACTTG -s simRat_chr6.simRat.chr6 202092 68 + 647215 GTTTACTACTCATTCATATATCCAAATCACATTAAACTTGTTCTGCTAGGAAATACATGTAGAATTTT - -a -s simMouse_chr6.simMouse.chr6 211080 12 + 636262 GAATAATGGTAC -s Anc0.Anc0refChr5 32164 11 + 87904 GAAGA-GGATAC -s Anc1.Anc1refChr8 46464 11 + 57822 GAAGA-GGATAC -s Anc2.Anc2refChr15 27005 11 + 86568 GAAGA-GGATAC -s mr.mrrefChr5 65821 11 + 294540 GAATA-TGGTAC -s simCow_chr6.simCow.chr6 384826 11 - 602619 GAAGA-GGATAC -s simHuman_chr6.simHuman.chr6 214732 11 + 601863 GATCA-GGATAC -s simRat_chr6.simRat.chr6 202160 11 + 647215 AAATA-TAGTAC - -a -s simMouse_chr6.simMouse.chr6 211092 14 + 636262 AACAGATGTGTCTG -s Anc0.Anc0refChr5 32181 14 + 87904 TAAAGGTGTGCCTA -s Anc1.Anc1refChr8 46481 14 + 57822 TAAAGGTGTGCCTA -s Anc2.Anc2refChr15 27022 14 + 86568 TAAAGGTGTGCCTA -s mr.mrrefChr5 65832 14 + 294540 AACAGATGTGTCTG -s simCow_chr6.simCow.chr6 384843 14 - 602619 TAAAGGTGTGCCTA -s simDog_chr6.simDog.chr6 197776 14 + 593897 TAAAGGTGTACCTA -s simHuman_chr6.simHuman.chr6 214749 14 + 601863 TAAAGGTGTGCCTA -s simRat_chr6.simRat.chr6 202171 14 + 647215 AAAAGGTGTGTTTG - -a -s simMouse_chr6.simMouse.chr6 211106 43 + 636262 TATGGTTCCAAATCTTGTTTGTAAGCATTTGTTAGTGCTCTGT -s Anc0.Anc0refChr5 32195 40 + 87904 TATGGTTCCAATTTTTGTATGAAGGCTTCTATTAGTGC---TT -s Anc1.Anc1refChr8 46495 40 + 57822 TATGGTTCCAATTTTTGTATGAAGGCTTCTATTAGTGC---TT -s Anc2.Anc2refChr15 27036 40 + 86568 TATGGTTCCAATTTTTGTATGATGGCTTCTATTAGTGC---TT -s mr.mrrefChr5 65846 40 + 294540 TATGGTTCCAAATCTTGTTTGTAAGCATTTGTTAGTGC---GT -s simCow_chr6.simCow.chr6 384857 40 - 602619 TATGGTGTTAATTTCTGTATGCTGGCTTCTACTGGTGC---TT -s simDog_chr6.simDog.chr6 197811 40 + 593897 TATGGTTCCTAACTTTGTATAATGGCTTGTGTTAGTGT---TT -s simHuman_chr6.simHuman.chr6 214763 40 + 601863 TATGGTTCCAATTTTTGTGTGAAGGCTTCTATTAGTGC---TT -s simRat_chr6.simRat.chr6 202185 40 + 647215 TATGGTTCCAACTCTTATCTGTAAGTGTTTGTTAGTGC---GA - -a -s simMouse_chr6.simMouse.chr6 211149 7 + 636262 GGCCGTG -s Anc0.Anc0refChr5 32238 7 + 87904 GGACCCA -s Anc1.Anc1refChr8 46538 7 + 57822 GGACCCA -s Anc2.Anc2refChr15 27079 7 + 86568 GGACCCA -s mr.mrrefChr5 65886 7 + 294540 GGCCGTG -s simCow_chr6.simCow.chr6 384900 7 - 602619 GGATCCC -s simDog_chr6.simDog.chr6 197854 7 + 593897 GGACCCA -s simHuman_chr6.simHuman.chr6 214806 7 + 601863 GGACACA -s simRat_chr6.simRat.chr6 202225 7 + 647215 GGCCACA - -a -s simMouse_chr6.simMouse.chr6 211156 2 + 636262 TT -s Anc0.Anc0refChr5 32245 2 + 87904 TT -s Anc1.Anc1refChr8 46545 2 + 57822 TT -s Anc2.Anc2refChr15 27086 2 + 86568 TT -s mr.mrrefChr5 65893 2 + 294540 TT -s simCow_chr6.simCow.chr6 384907 2 - 602619 TT -s simDog_chr6.simDog.chr6 197861 2 + 593897 TT -s simHuman_chr6.simHuman.chr6 214813 2 + 601863 TT -s simRat_chr6.simRat.chr6 202233 2 + 647215 TT - -a -s simMouse_chr6.simMouse.chr6 211158 5 + 636262 ATTTG -s Anc0.Anc0refChr5 32248 5 + 87904 ACGTG -s Anc1.Anc1refChr8 46548 5 + 57822 ACGTG -s Anc2.Anc2refChr15 27089 5 + 86568 CCGAG -s mr.mrrefChr5 65895 5 + 294540 ATTTG -s simCow_chr6.simCow.chr6 384910 5 - 602619 CTGGG -s simDog_chr6.simDog.chr6 197864 5 + 593897 CCAAG -s simHuman_chr6.simHuman.chr6 214816 5 + 601863 ACGTG -s simRat_chr6.simRat.chr6 202235 5 + 647215 ATTTG - -a -s simMouse_chr6.simMouse.chr6 211163 9 + 636262 CATCTAAGC -s Anc0.Anc0refChr5 32253 9 + 87904 CATCTAAGC -s Anc1.Anc1refChr8 46553 9 + 57822 CATCTAAGC -s Anc2.Anc2refChr15 27095 9 + 86568 CATCTAAGC -s mr.mrrefChr5 65900 9 + 294540 CATCTAAGC -s simCow_chr6.simCow.chr6 384916 9 - 602619 CATTTAAGC -s simDog_chr6.simDog.chr6 197870 9 + 593897 CATCTAAGC -s simHuman_chr6.simHuman.chr6 214821 9 + 601863 AATCTAAAC -s simRat_chr6.simRat.chr6 202240 9 + 647215 CATCTAAGC - -a -s simMouse_chr6.simMouse.chr6 211172 8 + 636262 ACACACAG -s Anc0.Anc0refChr5 32263 8 + 87904 GCAGACAG -s Anc1.Anc1refChr8 46563 8 + 57822 GCAGACAG -s Anc2.Anc2refChr15 27105 8 + 86568 GCAGACAG -s mr.mrrefChr5 65909 8 + 294540 ACACACAG -s simCow_chr6.simCow.chr6 384926 8 - 602619 GCTAACAG -s simDog_chr6.simDog.chr6 197880 8 + 593897 ACAGATAG -s simHuman_chr6.simHuman.chr6 214831 8 + 601863 GCAGACAA -s simRat_chr6.simRat.chr6 202249 8 + 647215 ACAGATAG - -a -s simMouse_chr6.simMouse.chr6 211180 18 + 636262 CATGGATTCTATAACCAT -s Anc0.Anc0refChr5 32271 18 + 87904 TTGTAGGTCAATAAGCGT -s Anc1.Anc1refChr8 46571 18 + 57822 TTGTAGGTCAATAAGCGT -s Anc2.Anc2refChr15 27113 18 + 86568 TTGTAGGTCAATAAGCGC -s mr.mrrefChr5 65917 18 + 294540 CATGGATTCTATAACCAT -s simCow_chr6.simCow.chr6 384934 18 - 602619 GTCGAGGTCAGTAAGGGC -s simDog_chr6.simDog.chr6 197888 18 + 593897 TTGTACCTCAATAAACAC -s simHuman_chr6.simHuman.chr6 214839 18 + 601863 TTGTAGGTCAATAAGTGT -s simRat_chr6.simRat.chr6 202258 18 + 647215 CATGGGCTCCATAAGGAT - -a -s simMouse_chr6.simMouse.chr6 211198 14 + 636262 CACTGTTACCAGTG -s Anc0.Anc0refChr5 32289 14 + 87904 CACTGTTGCTGAGG -s Anc1.Anc1refChr8 46589 14 + 57822 CACTGTTGCTGAGG -s Anc2.Anc2refChr15 27131 14 + 86568 TACTGTTGCTGAGG -s mr.mrrefChr5 65935 14 + 294540 CACTGTTACCAGTG -s simCow_chr6.simCow.chr6 384958 14 - 602619 TACTTTTGCTAAGA -s simDog_chr6.simDog.chr6 197906 14 + 593897 TACTGTTGCTGAAG -s simHuman_chr6.simHuman.chr6 214857 14 + 601863 CGCTACTGCTGAGG -s simRat_chr6.simRat.chr6 202276 14 + 647215 CACTGTTACCAGTG - -a -s simMouse_chr6.simMouse.chr6 211212 12 + 636262 TTGCTGTTGATA -s Anc0.Anc0refChr5 32323 5 + 87904 TT-------ATA -s Anc1.Anc1refChr8 46623 11 + 57822 TTGC-GTGGATA -s Anc2.Anc2refChr15 27165 5 + 86568 TC-------ATA -s mr.mrrefChr5 65949 12 + 294540 TTGCTGTTGATA -s simCow_chr6.simCow.chr6 384992 5 - 602619 TC-------ATA -s simDog_chr6.simDog.chr6 197940 5 + 593897 TC-------ATA -s simHuman_chr6.simHuman.chr6 214901 11 + 601863 TTGC-GTGGATC -s simRat_chr6.simRat.chr6 202290 12 + 647215 TTACTGTTCATA - -a -s simMouse_chr6.simMouse.chr6 211224 10 + 636262 GGGACACCGT -s Anc0.Anc0refChr5 32328 10 + 87904 GAGACCACGT -s Anc1.Anc1refChr8 46634 10 + 57822 GAGACCACGT -s Anc2.Anc2refChr15 27170 10 + 86568 GAGACCACGT -s mr.mrrefChr5 65961 10 + 294540 GGGACACCGT -s simCow_chr6.simCow.chr6 384997 9 - 602619 GGG-CCACGT -s simDog_chr6.simDog.chr6 197945 10 + 593897 GAGACCACAT -s simHuman_chr6.simHuman.chr6 214913 10 + 601863 GAGAATGCGT -s simRat_chr6.simRat.chr6 202302 10 + 647215 GGGGCACAGA - -a -s simMouse_chr6.simMouse.chr6 211234 27 + 636262 TCACATGGAGCGGTGGATGTCACCACT -s Anc0.Anc0refChr5 32338 6 + 87904 GGA---------------------GCT -s Anc1.Anc1refChr8 46644 6 + 57822 GGA---------------------GCT -s Anc2.Anc2refChr15 27180 6 + 86568 GGA---------------------GCT -s mr.mrrefChr5 65971 6 + 294540 TCA---------------------ACT -s simCow_chr6.simCow.chr6 385009 6 - 602619 ACA---------------------ACG -s simDog_chr6.simDog.chr6 197955 6 + 593897 GGA---------------------GCT -s simHuman_chr6.simHuman.chr6 214923 6 + 601863 GGA---------------------GCT -s simRat_chr6.simRat.chr6 202312 6 + 647215 TTG---------------------ACT - -a -s simMouse_chr6.simMouse.chr6 211261 6 + 636262 TGTCAC -s Anc0.Anc0refChr5 32348 6 + 87904 TGTCAC -s Anc1.Anc1refChr8 46654 6 + 57822 TGTCAC -s Anc2.Anc2refChr15 27191 6 + 86568 TGTCAC -s mr.mrrefChr5 65977 6 + 294540 TGTCAC -s simCow_chr6.simCow.chr6 385020 6 - 602619 TGTCAC -s simDog_chr6.simDog.chr6 197966 6 + 593897 TGTCAT -s simHuman_chr6.simHuman.chr6 214933 6 + 601863 TGTCAC -s simRat_chr6.simRat.chr6 202318 6 + 647215 CGTCAC - -a -s simMouse_chr6.simMouse.chr6 211267 74 + 636262 CTTTTTAACGCTACTTAGACTTCCCACAGCGCCTTGCACAAATCTCCAAAAAAAGGCATATGCGGCCTTGTGAC -s Anc0.Anc0refChr5 32372 10 + 87904 CTTTC----------------------------------------------------------------TTAAC -s Anc1.Anc1refChr8 46678 10 + 57822 CTTTC----------------------------------------------------------------TTAAC -s Anc2.Anc2refChr15 27215 10 + 86568 TTTTC----------------------------------------------------------------TTAAC -s mr.mrrefChr5 65983 10 + 294540 CTTTT----------------------------------------------------------------GTGAC -s simCow_chr6.simCow.chr6 385050 10 - 602619 TTTTC----------------------------------------------------------------TTAAC -s simHuman_chr6.simHuman.chr6 214958 10 + 601863 CTTTG----------------------------------------------------------------TTAAC -s simRat_chr6.simRat.chr6 202324 10 + 647215 CATTT----------------------------------------------------------------GTGAT - -a -s simMouse_chr6.simMouse.chr6 211341 10 + 636262 ATTTTGGTAG -s Anc0.Anc0refChr5 32382 10 + 87904 CTTGTTATAG -s Anc1.Anc1refChr8 46688 10 + 57822 CTTGTTATAG -s Anc2.Anc2refChr15 27225 10 + 86568 CTTGCTATAG -s mr.mrrefChr5 65993 10 + 294540 ATTTTGGTAG -s simCow_chr6.simCow.chr6 385061 10 - 602619 CTTGCTATAG -s simHuman_chr6.simHuman.chr6 214968 10 + 601863 TTAGTTATAG -s simRat_chr6.simRat.chr6 202334 10 + 647215 TTTTTGGTGG - -a -s simMouse_chr6.simMouse.chr6 211351 3 + 636262 TCT -s Anc0.Anc0refChr5 32392 3 + 87904 TGT -s Anc1.Anc1refChr8 46698 3 + 57822 TGT -s Anc2.Anc2refChr15 27240 3 + 86568 TGT -s mr.mrrefChr5 66003 3 + 294540 TCT -s simCow_chr6.simCow.chr6 385076 3 - 602619 TGT -s simHuman_chr6.simHuman.chr6 214978 3 + 601863 TAT -s simRat_chr6.simRat.chr6 202344 3 + 647215 TCT - -a -s simMouse_chr6.simMouse.chr6 211354 33 + 636262 CAATTCAGTTGCAGCACAAATGTACAGGGTAAG -s Anc0.Anc0refChr5 32395 32 + 87904 TAACTTAGTTGTAGCATTCATTTACAGGATAA- -s Anc1.Anc1refChr8 46701 32 + 57822 TAACTTAGTTGTAGCATTCATTTACAGGATAA- -s Anc2.Anc2refChr15 27243 32 + 86568 TAACTTAGTTGTAGCATTCATTTACAAGATTA- -s mr.mrrefChr5 66006 33 + 294540 CAATTCAGTTGCAGCACAAATGTACAGGGTAAG -s simCow_chr6.simCow.chr6 385079 32 - 602619 TAACTTAGTTGTAGCATTCATCTACAAGCTTA- -s simDog_chr6.simDog.chr6 197974 28 + 593897 ----TTAGTTGTAGCATTCATTTACAAGATTA- -s simHuman_chr6.simHuman.chr6 215013 32 + 601863 TAACTTAGTTATAGTATTCATTTACAGGTTAA- -s simRat_chr6.simRat.chr6 202347 33 + 647215 CAATTCAGTTGTAGCACACATGTACAAGGTAAG - -a -s simMouse_chr6.simMouse.chr6 211387 16 + 636262 ATTAACACATCTATAG -s Anc0.Anc0refChr5 32427 13 + 87904 A---ATACATATATAG -s Anc1.Anc1refChr8 46733 16 + 57822 ATTAATACATATATAG -s Anc2.Anc2refChr15 27275 13 + 86568 A---ATATATATATAG -s mr.mrrefChr5 66039 16 + 294540 ATTAACACATCTATAG -s simCow_chr6.simCow.chr6 385116 13 - 602619 A---ATATGTATATTG -s simDog_chr6.simDog.chr6 198002 13 + 593897 G---ATATATATATAG -s simHuman_chr6.simHuman.chr6 215045 9 + 601863 ACTAATACC------- -s simRat_chr6.simRat.chr6 202380 16 + 647215 ATTAATACATATATAA - -a -s simMouse_chr6.simMouse.chr6 211403 42 + 636262 TTTAACCCTGATGTCAGTTTTGTATTAGTCATTATGACTAGC -s Anc0.Anc0refChr5 32440 42 + 87904 TTTCTCCCCAACCTCTGTTTTATAGTGATCCTCATGACTAGG -s Anc1.Anc1refChr8 46749 42 + 57822 TTTCTCCCCAACCTCTGTTTTATAGTGATCCTCATGACTAGG -s Anc2.Anc2refChr15 27288 42 + 86568 TTTCTCCCCAACCTCTGTTTTATAGTGATCCTCATGACTAGA -s mr.mrrefChr5 66055 42 + 294540 TTTAACCCTGATGTCTGTTTTGTATTAGTCATTATGACTAGG -s simCow_chr6.simCow.chr6 385129 41 - 602619 TTTCTCCC-AAGCTCTGGTTTATAGTAGTCCTCATGACAAGA -s simDog_chr6.simDog.chr6 198015 42 + 593897 TTTCATTCCAACCTCTGTTTTACAGTGAGTATCATAACTAGA -s simHuman_chr6.simHuman.chr6 385718 42 - 601863 CCTCTCCCCATCCTCTGTTTCATAGCCCTCCTCGTGACTAGG -s simRat_chr6.simRat.chr6 202396 41 + 647215 GTTAACCCCGAGGCCTGTAT-GTATTAGGCATTATGACTAGG - -a -s simMouse_chr6.simMouse.chr6 211445 26 + 636262 AGTTCCTTAAGAAATTCACACTAGCT -s Anc0.Anc0refChr5 32482 26 + 87904 TCTTCCCCAACAGATTTATAATTGAT -s Anc1.Anc1refChr8 46791 26 + 57822 TCTTCCCCAACAGATTTATAATTGAT -s Anc2.Anc2refChr15 27330 26 + 86568 CCTTCCCCAACAGATTTATAATTGAT -s mr.mrrefChr5 66097 26 + 294540 TGTTCCTTAAGAAATTTACAATAGCT -s simCow_chr6.simCow.chr6 385170 26 - 602619 CCTTCCCCAACAGTTTTATAATTGAT -s simDog_chr6.simDog.chr6 198057 26 + 593897 CCTTCCCCAACTAATTTATAATTGAT -s simHuman_chr6.simHuman.chr6 385761 26 - 601863 TCTCCCCCAACAGACTTAGAATTGAT -s simRat_chr6.simRat.chr6 202437 26 + 647215 TGTTCCTTAAGCAATTTACAATAGCT - -a -s simMouse_chr6.simMouse.chr6 211471 66 + 636262 TGTATCTCCCAGGGTTACCTGATGCTTATCATTATAGGCTTCTAAACAATGAAAACATGGATGATC -s Anc0.Anc0refChr5 32508 66 + 87904 CATGTTCTCTAGGGTTACCTAATGCTGTTCATTATAGGCTTCCAAACAATGAAACCATGGATTATC -s Anc1.Anc1refChr8 46817 66 + 57822 CATGTTCTCTAGGGTTACCTAATGCTGTTCATTATAGGCTTCCAAACAATGAAACCATGGATTATC -s Anc2.Anc2refChr15 27356 66 + 86568 CATGTTCTCTAGGGTCAGCTAATGCTGTTTATGATAGGCTTCCAAACTATGAAACCATGGATTATC -s mr.mrrefChr5 66123 66 + 294540 TATATTTCCCAGGGTTACCTAATGCTTATCATTATAGGCTTCTAAACAATGAAAACATGGATGATC -s simCow_chr6.simCow.chr6 385198 66 - 602619 CAAGTTCTCTAGGGTCAGCTGATGCTGTGTATGATAGGCTTCCAGATTGTGAAACCATGGATTATC -s simDog_chr6.simDog.chr6 198083 60 + 593897 CATGTTGTCTAAGGTCAGCTAATGGTGTT------AGGCTTACAAACTATGAAAACATGGATTATC -s simHuman_chr6.simHuman.chr6 385787 66 - 601863 GATGCTCTCTAGGGTTACATAATGCTGTTCATTATGGGCTTCCAAACAATGAAACCATGGATTATC -s simRat_chr6.simRat.chr6 202463 61 + 647215 TATATTTGCCAGGGCTGCCTAATGCTTACCATTGTAG-----TACACAATGAAAACATAGATGATC - -a -s simMouse_chr6.simMouse.chr6 211537 14 + 636262 ACTAGATCCCAGAA -s Anc0.Anc0refChr5 32575 14 + 87904 ACCAAATCTCAATA -s Anc1.Anc1refChr8 46884 14 + 57822 ACCAAATCTCAATA -s Anc2.Anc2refChr15 27423 14 + 86568 ACCAATTCTCAATA -s mr.mrrefChr5 66189 14 + 294540 ACTAGATCCCAGAA -s simCow_chr6.simCow.chr6 385265 14 - 602619 ACCAATTCTCAATA -s simDog_chr6.simDog.chr6 198144 14 + 593897 ACCAGTCTCAAACA -s simHuman_chr6.simHuman.chr6 385854 14 - 601863 ACCAAATCTCAATA -s simRat_chr6.simRat.chr6 202524 14 + 647215 ACTAGATCCCAGAC - -a -s simMouse_chr6.simMouse.chr6 211551 16 + 636262 ATTGTGACATCTAGAG -s Anc0.Anc0refChr5 32590 16 + 87904 GTTAGGACATCTAAAG -s Anc1.Anc1refChr8 46899 16 + 57822 GTTAGGACATCTAAAG -s Anc2.Anc2refChr15 27438 16 + 86568 GTTAGGACATCTAAAG -s mr.mrrefChr5 66203 16 + 294540 ATTGGGACATCTAGAG -s simCow_chr6.simCow.chr6 385280 16 - 602619 GTTAGGACATCTACAG -s simDog_chr6.simDog.chr6 198159 14 + 593897 --CTGGCCATCTAAAG -s simHuman_chr6.simHuman.chr6 385869 16 - 601863 GTTAGGACATGTAAAG -s simRat_chr6.simRat.chr6 202538 16 + 647215 TTTGGAACATCTAGAG - -a -s simMouse_chr6.simMouse.chr6 211567 1 + 636262 C -s Anc0.Anc0refChr5 32609 1 + 87904 C -s Anc1.Anc1refChr8 46918 1 + 57822 C -s Anc2.Anc2refChr15 27457 1 + 86568 C -s mr.mrrefChr5 66222 1 + 294540 C -s simCow_chr6.simCow.chr6 385299 1 - 602619 C -s simDog_chr6.simDog.chr6 198176 1 + 593897 C -s simHuman_chr6.simHuman.chr6 385888 1 - 601863 C -s simRat_chr6.simRat.chr6 202557 1 + 647215 C - -a -s simMouse_chr6.simMouse.chr6 211568 4 + 636262 AGAG -s Anc0.Anc0refChr5 32619 4 + 87904 AGAA -s Anc1.Anc1refChr8 46928 4 + 57822 AGAA -s Anc2.Anc2refChr15 27467 4 + 86568 AGAA -s mr.mrrefChr5 66223 4 + 294540 AGAG -s simCow_chr6.simCow.chr6 385309 4 - 602619 AGAC -s simDog_chr6.simDog.chr6 198186 4 + 593897 AGAA -s simHuman_chr6.simHuman.chr6 385898 4 - 601863 AGTA -s simRat_chr6.simRat.chr6 202558 4 + 647215 GGGG - -a -s simMouse_chr6.simMouse.chr6 211572 50 + 636262 GACATGCAAGTTATAACCAGCAAATTAGACATGTGCAATAAAATGGCGTT -s Anc0.Anc0refChr5 32623 50 + 87904 GACAGACAAATTATGACCAATAATCAAGATATGTGTAATAAAATATTTTT -s Anc1.Anc1refChr8 46932 50 + 57822 GACAGACAAATTATGACCAATAATCAAGATATGTGTAATAAAATATTTTT -s Anc2.Anc2refChr15 27471 50 + 86568 GACAGACAAATTGTGACCAATAATCAAGATATGTGTTATAAAATATTTTT -s mr.mrrefChr5 66227 50 + 294540 GACATGCAAATTATAACCAGCAAATTAGACATGTGCAATAAAATAGTTTT -s simCow_chr6.simCow.chr6 385321 49 - 602619 GACAGACAAGTTGCAACTAACAACCAAGTTATATATCATGAA-TATTTTT -s simDog_chr6.simDog.chr6 198190 41 + 593897 ---------ATTGTGACCAATCATTGAGATTTGTGTTATAAAATATTTTC -s simHuman_chr6.simHuman.chr6 385902 50 - 601863 GACAGACTAATTATGACCAATATTCAAGATATGTGAAATAAAATATTTTT -s simRat_chr6.simRat.chr6 202562 50 + 647215 GAAATGCAAATTATAAACAGCAAATTAGACATGGTTAATATAATAGTTTT - -a -s simMouse_chr6.simMouse.chr6 211622 62 + 636262 AACATTTATTGTCCTGTCTGTTGGTTTTATCAAGTGCAGGTTATGATTCACTCTAACAATTT -s Anc0.Anc0refChr5 32673 61 + 87904 ATCATCTGTTGTCCCACCTGTTATTTTTATTGAGCACAG-TCATCATTCAATCTAGCAATTT -s Anc1.Anc1refChr8 46982 61 + 57822 ATCATCTGTTGTCCCACCTGTTATTTTTATTGAGCACAG-TCATCATTCAATCTAGCAATTT -s Anc2.Anc2refChr15 27521 61 + 86568 ATTCTCTGTTGTCCCACCTGTTATTCTTGTTGAGCACAG-TCATCATTCAATTTAGCAATTT -s mr.mrrefChr5 66277 62 + 294540 ATCATTTATTGTCCTGTCTGTTAGTTTTATTAAGCGCAGGTCATCATTCACTCTAACAATTT -s simCow_chr6.simCow.chr6 385370 58 - 602619 ATG---TACAGTCCCAGTTGTTATTCTGGCCGGGCACTG-TTATCATTTAATGTAGCAACTT -s simDog_chr6.simDog.chr6 198232 61 + 593897 AGTCTCTGTTGTCCTACCTGTTGCTCTTGTTGAGCACAG-TCATCATTCAATTCAGCAATTT -s simHuman_chr6.simHuman.chr6 385952 61 - 601863 ATCACCTGTTGTCCCACCTGTTATTTTCATTGAGCCCAG-TCATCATTCAGTCTACCAATTT -s simRat_chr6.simRat.chr6 202612 62 + 647215 GTGATTTATTGTCCTGTTTGTTAGTTTTACTTAGCGCTGTTCATCATTCATGCTAATAATTT - -a -s simMouse_chr6.simMouse.chr6 211684 14 + 636262 ATTCCAAATATATT -s Anc0.Anc0refChr5 32734 3 + 87904 ATT----------- -s Anc1.Anc1refChr8 47043 3 + 57822 ATT----------- -s Anc2.Anc2refChr15 27582 3 + 86568 ATT----------- -s mr.mrrefChr5 66339 14 + 294540 ATTCCAAATATATT -s simCow_chr6.simCow.chr6 385437 3 - 602619 ATC----------- -s simDog_chr6.simDog.chr6 198293 3 + 593897 ATT----------- -s simHuman_chr6.simHuman.chr6 386013 3 - 601863 ATT----------- -s simRat_chr6.simRat.chr6 202674 14 + 647215 ATTCCAAATATATT - -a -s simMouse_chr6.simMouse.chr6 211698 12 + 636262 AGAGATAATACA -s Anc0.Anc0refChr5 32737 12 + 87904 AGAGACAATAAA -s Anc1.Anc1refChr8 47046 12 + 57822 AGAGACAATAAA -s Anc2.Anc2refChr15 27585 12 + 86568 AGAGACAATAAA -s mr.mrrefChr5 66353 12 + 294540 AGAGATAATACA -s simCow_chr6.simCow.chr6 385440 12 - 602619 AGAGACAATAAA -s simDog_chr6.simDog.chr6 198299 12 + 593897 AATGACAATAAG -s simHuman_chr6.simHuman.chr6 386016 12 - 601863 AGAGCCGATAAA -s simRat_chr6.simRat.chr6 202688 12 + 647215 AGAGATAATACA - -a -s simMouse_chr6.simMouse.chr6 211710 10 + 636262 GGAGCCTAAG -s Anc0.Anc0refChr5 32749 10 + 87904 GATATCCAAC -s Anc1.Anc1refChr8 47058 10 + 57822 GATATCCAAC -s Anc2.Anc2refChr15 27597 10 + 86568 GATATTCAAC -s mr.mrrefChr5 66365 10 + 294540 GGAGCCTAAG -s simCow_chr6.simCow.chr6 385452 10 - 602619 GATATTCTAC -s simDog_chr6.simDog.chr6 198311 10 + 593897 GACATTCAAC -s simHuman_chr6.simHuman.chr6 386028 10 - 601863 GATATCGAAC -s simRat_chr6.simRat.chr6 202704 10 + 647215 GGAGCCCAAG - -a -s simMouse_chr6.simMouse.chr6 211720 18 + 636262 TTACTGGTGATTTCATGG -s Anc0.Anc0refChr5 32760 18 + 87904 TTACTAGTGAATTCATGG -s Anc1.Anc1refChr8 47069 18 + 57822 TTACTAGTGAATTCATGG -s Anc2.Anc2refChr15 27608 18 + 86568 TTACTAGTGAATTCATGG -s mr.mrrefChr5 66375 18 + 294540 TTACTGGTGATTTCATGG -s simCow_chr6.simCow.chr6 385463 18 - 602619 TTACTAGTGAATCTATAG -s simDog_chr6.simDog.chr6 198322 18 + 593897 TTACTAGTGAATTCATGG -s simHuman_chr6.simHuman.chr6 386039 18 - 601863 TTACTAGTGAATTCATGA -s simRat_chr6.simRat.chr6 202714 9 + 647215 T---------TTTCATGG - -a -s simMouse_chr6.simMouse.chr6 211738 13 + 636262 TATCTTGATTTGC -s Anc1.Anc1refChr8 47087 13 + 57822 TATGTTGATCTAA -s mr.mrrefChr5 66393 13 + 294540 TATCTTGATTTGA -s simHuman_chr6.simHuman.chr6 386066 13 - 601863 TATGTTGATCTAA -s simRat_chr6.simRat.chr6 202723 13 + 647215 TATCTGGATTTGA - -a -s simMouse_chr6.simMouse.chr6 211751 7 + 636262 CCTACAT -s Anc1.Anc1refChr8 47100 7 + 57822 CCTAGGT -s mr.mrrefChr5 66406 7 + 294540 CCTACAT -s simHuman_chr6.simHuman.chr6 386084 7 - 601863 CCTAGGT -s simRat_chr6.simRat.chr6 202736 7 + 647215 CCTACAT - -a -s simMouse_chr6.simMouse.chr6 211758 31 + 636262 TACCGTTGTTACAACCAGTGGCGATCCATAG -s Anc0.Anc0refChr5 32803 31 + 87904 TACCATTGTTACAATTTCTGCAGACCTACAG -s Anc1.Anc1refChr8 47132 31 + 57822 TACCATTGTTACAATTTCTGCAGACCTACAG -s Anc2.Anc2refChr15 27651 31 + 86568 TACCACTGTTACAATTTCTGCAGACCTACAG -s mr.mrrefChr5 66413 31 + 294540 TACCGTTGTTACAACCAGTGGAGATCCATAG -s simCow_chr6.simCow.chr6 385500 29 - 602619 --CCAATGTTACAACTTCTGCAGACCTATAA -s simDog_chr6.simDog.chr6 198364 31 + 593897 TACCACTGTTGCAATTTCTGCAGACCTACAG -s simHuman_chr6.simHuman.chr6 386171 31 - 601863 TGCCATTGTTACAAATTCTACAGGCCTACAG -s simRat_chr6.simRat.chr6 202743 31 + 647215 TACCTATGTTACAATCAGTGGAGATCCATAG - -a -s simMouse_chr6.simMouse.chr6 211789 64 + 636262 CAGCAACAAGACAAGCAAAACAGTGGCGTACTTTAATGTTGCAGCTTTTTCCTTGTAGTGTTAC -s Anc0.Anc0refChr5 32834 58 + 87904 CAACAAAGAGGCAAGGGGAAAAGTGGTGTATTCTA------CAGCTTTTTTCTTGTAGTGACAT -s Anc1.Anc1refChr8 47163 58 + 57822 CAACAAAGAGGCAAGGGGAAAAGTGGTGTATTCTA------CAGCTTTTTTCTTGTAGTGACAT -s Anc2.Anc2refChr15 27682 58 + 86568 AAACAAAGAGGCAAGGGGAAAAGTGGTGTGTTCTA------CAGCTGTTTTCTTGTAGTGACAT -s mr.mrrefChr5 66444 64 + 294540 CAGCAACGAGGCAAGGAAAACAGTGGCGTACTTTAATGTTGCAGCTTTTTCCTTGTAGTGTTAC -s simCow_chr6.simCow.chr6 385532 58 - 602619 AAACAAAGAGTCGAGGGGGGAGGTGATGTGTTCTT------CAGCTGTTCTCTTGTAGTGACAC -s simDog_chr6.simDog.chr6 198395 58 + 593897 AAACAAAACAGTAAGGGGAAAAGTGGTGTGTTCTA------CAGCTGTTTTCTTGTAGTGACAT -s simHuman_chr6.simHuman.chr6 386202 58 - 601863 CAATAGAGAGGCAAGGGTAAAAGTGGTGCATTCAA------CAGCTTTTTTCTTGTAGCGACAT -s simRat_chr6.simRat.chr6 202774 64 + 647215 CATCAATGATGCAAGGAAAACGGTGGCATACGTTAATGTTGCAGGTTTTTCATTGCAATGCAAC - -a -s simMouse_chr6.simMouse.chr6 211853 23 + 636262 AATTGTCCACTGCCAGGAAGCTA -s Anc0.Anc0refChr5 32892 23 + 87904 GGTTACCTACTGCCAGGAAGCCA -s Anc1.Anc1refChr8 47221 23 + 57822 GGTTACCTACTGCCAGGAAGCCA -s Anc2.Anc2refChr15 27740 23 + 86568 GGTTACCTTCTGCCAGGAAGCCA -s mr.mrrefChr5 66508 23 + 294540 AATTGTCCACTGCCAGGAAGCTA -s simCow_chr6.simCow.chr6 385590 23 - 602619 AATTACCCTCTGCAAGGAAGCCA -s simDog_chr6.simDog.chr6 198462 23 + 593897 GGTTACCTTCTGCCAGGAAGCCA -s simHuman_chr6.simHuman.chr6 386260 15 - 601863 GGTTACCTAATGT--------GA -s simRat_chr6.simRat.chr6 202838 23 + 647215 AATTGATCACTGCCAGGGAGCCA - -a -s simMouse_chr6.simMouse.chr6 211876 7 + 636262 GGTTCCT -s Anc0.Anc0refChr5 32915 7 + 87904 GGTCCTT -s Anc1.Anc1refChr8 47244 7 + 57822 GGTCCTT -s Anc2.Anc2refChr15 27764 7 + 86568 TTTCTTT -s mr.mrrefChr5 66531 7 + 294540 GGTCCCT -s simCow_chr6.simCow.chr6 385614 7 - 602619 TTTCTTT -s simDog_chr6.simDog.chr6 198486 7 + 593897 TTTCTTT -s simHuman_chr6.simHuman.chr6 386275 7 - 601863 GGTCTTT -s simRat_chr6.simRat.chr6 202861 7 + 647215 GTTCCAT - -a -s simMouse_chr6.simMouse.chr6 211883 40 + 636262 TTATGTTGTGGTCAAAGAGCTTTCTTTTAAAGATTCACTA -s Anc0.Anc0refChr5 32922 38 + 87904 GTGTGTTGTGAACAAG--GCTTTCCTGTAAAGGGCCACTA -s Anc1.Anc1refChr8 47251 38 + 57822 GTGTGTTGTGAACAAG--GCTTTCCTGTAAAGGGCCACTA -s Anc2.Anc2refChr15 27771 38 + 86568 GTGTGTTGTGAAAAGG--GCTTTCCTGTAAAGGGCCACTA -s mr.mrrefChr5 66538 40 + 294540 TTGTGTTGTGGTCAAAGAGCTTTCTTTTAAAGATTCACTA -s simCow_chr6.simCow.chr6 385623 38 - 602619 GTGTGTTGTGAAAAGG--GCCTTCCTGTAAAGGGCCACTG -s simDog_chr6.simDog.chr6 198493 36 + 593897 GTATGTTGTCAA--GG--TCTTTCCTGTATAGGGCCACTA -s simHuman_chr6.simHuman.chr6 386282 38 - 601863 GTGTGTTGTGAACAAG--GCTTTTCTGTAAGGGGCCACCA -s simRat_chr6.simRat.chr6 202868 39 + 647215 TGGTGTTGT-GTCAACGAGCTTTCTACTAAAGATTCACTA - -a -s simMouse_chr6.simMouse.chr6 211923 12 + 636262 GAATTGTGTTGC -s Anc0.Anc0refChr5 32960 12 + 87904 CTACTTTGCTGC -s Anc1.Anc1refChr8 47289 12 + 57822 CTACTTTGCTGC -s Anc2.Anc2refChr15 27809 12 + 86568 CTACTTTGCTGT -s mr.mrrefChr5 66578 12 + 294540 GAATTGTGTTGC -s simCow_chr6.simCow.chr6 385661 12 - 602619 CTACTTTGTTGT -s simDog_chr6.simDog.chr6 198529 12 + 593897 CTACTTTGCTGT -s simHuman_chr6.simHuman.chr6 386320 12 - 601863 TTAGTTTACTGC -s simRat_chr6.simRat.chr6 202914 12 + 647215 GAATTGTGTTGT - -a -s simMouse_chr6.simMouse.chr6 211935 31 + 636262 TTAAAGACCCTGTTCTGGGTGGACAACACAA -s Anc0.Anc0refChr5 32978 31 + 87904 TTTAATACTGTCTTCAGGGTGACCAACACAT -s Anc1.Anc1refChr8 47307 31 + 57822 TTTAATACTGTCTTCAGGGTGACCAACACAT -s Anc2.Anc2refChr15 27827 31 + 86568 TTTAATACTGTCTTCAGGGTGACCAAAACTG -s mr.mrrefChr5 66590 31 + 294540 TTAAAGACCCTGTTCTGGGTGAACAACACAT -s simCow_chr6.simCow.chr6 385679 24 - 602619 TTTCATATTGTCTTCAGGGTGACC------- -s simDog_chr6.simDog.chr6 198547 30 + 593897 TTTAA-ACTGTCTTCAGTGTGACCAAAACTG -s simHuman_chr6.simHuman.chr6 386338 31 - 601863 TTTAATACTGTCTTCAGGGTGACCAACACAT -s simRat_chr6.simRat.chr6 202926 31 + 647215 TTAAAGACCTCGTGCTGGGTGAACAACACAT - -a -s simMouse_chr6.simMouse.chr6 211966 7 + 636262 CTGACTG -s Anc0.Anc0refChr5 33010 7 + 87904 CTTACTG -s Anc1.Anc1refChr8 47339 7 + 57822 CTTACTG -s Anc2.Anc2refChr15 27859 7 + 86568 ATTACTG -s mr.mrrefChr5 66621 7 + 294540 CTGACTG -s simCow_chr6.simCow.chr6 385849 1 - 602619 ------G -s simDog_chr6.simDog.chr6 198578 7 + 593897 ATTACTA -s simHuman_chr6.simHuman.chr6 386370 7 - 601863 CATACTG -s simRat_chr6.simRat.chr6 202957 7 + 647215 CTGACTG - -a -s simMouse_chr6.simMouse.chr6 211973 15 + 636262 ATGAGGGTTCATACC -s Anc0.Anc0refChr5 33017 8 + 87904 ATGTGGG-------C -s Anc1.Anc1refChr8 47346 8 + 57822 ATGTGGG-------C -s Anc2.Anc2refChr15 27869 8 + 86568 CTGTGGG-------C -s mr.mrrefChr5 66628 15 + 294540 ATGAGGGTGCATACC -s simCow_chr6.simCow.chr6 385853 8 - 602619 CTGCAGG-------C -s simDog_chr6.simDog.chr6 198588 8 + 593897 CTGTGGG-------C -s simHuman_chr6.simHuman.chr6 386377 3 - 601863 ATC------------ -s simRat_chr6.simRat.chr6 202964 14 + 647215 ATGA-ATTGCATACC - -a -s simMouse_chr6.simMouse.chr6 211988 8 + 636262 ACCAATGG -s Anc0.Anc0refChr5 33025 8 + 87904 AATATTAG -s Anc1.Anc1refChr8 47354 8 + 57822 AATATTAG -s Anc2.Anc2refChr15 27877 8 + 86568 AATATTAG -s mr.mrrefChr5 66643 8 + 294540 ACCAATGG -s simCow_chr6.simCow.chr6 385862 8 - 602619 AATATTAG -s simDog_chr6.simDog.chr6 198596 8 + 593897 AATATTAG -s simRat_chr6.simRat.chr6 202978 8 + 647215 ACCAATGG - -a -s simMouse_chr6.simMouse.chr6 211996 14 + 636262 GTAGGTAGGCCTAG -s Anc0.Anc0refChr5 33033 3 + 87904 GTA----------- -s Anc1.Anc1refChr8 47362 3 + 57822 GTA----------- -s Anc2.Anc2refChr15 27885 3 + 86568 GTA----------- -s mr.mrrefChr5 66651 14 + 294540 GTAGGTAGGCCTAG -s simCow_chr6.simCow.chr6 385870 3 - 602619 GCA----------- -s simDog_chr6.simDog.chr6 198604 3 + 593897 GTA----------- -s simRat_chr6.simRat.chr6 203057 14 + 647215 GTGGGTATGCTTAG - -a -s simMouse_chr6.simMouse.chr6 212010 14 + 636262 TGACTCTGAGCAAG -s Anc0.Anc0refChr5 33036 14 + 87904 TGACTTTGAGCAAG -s Anc1.Anc1refChr8 47365 14 + 57822 TGACTTTGAGCAAG -s Anc2.Anc2refChr15 27888 14 + 86568 TGACTTTGAGCAAG -s mr.mrrefChr5 66665 14 + 294540 TGACTCTGAGCAAG -s simCow_chr6.simCow.chr6 385873 14 - 602619 TAACTCTGAGCAAG -s simDog_chr6.simDog.chr6 198614 14 + 593897 TGACTTTGAGCAAG -s simRat_chr6.simRat.chr6 203071 14 + 647215 TGACTCTGAGCAAA - -a -s simMouse_chr6.simMouse.chr6 212024 38 + 636262 AGGTATACTCAGTAACTGTCACAAACAGTCACTTTTTA -s Anc0.Anc0refChr5 33050 27 + 87904 AGGTACATTCAGCAACTATCAC------CCAT-T---- -s Anc1.Anc1refChr8 47379 27 + 57822 AGGTACATTCAGCAACTATCAC------CCAT-T---- -s Anc2.Anc2refChr15 27905 27 + 86568 AGGTACATTCAGCAACTATCAC------CCAT-T---- -s mr.mrrefChr5 66679 36 + 294540 AGGTATACTCAGTAACTGTCAC-AACAGTCAC-TTTTA -s simCow_chr6.simCow.chr6 385890 27 - 602619 AGGTAACCTCAGCAACTATCAC------TCAT-T---- -s simDog_chr6.simDog.chr6 198631 27 + 593897 AGGTACATTCAGCAACTATCAC------CCAT-T---- -s simRat_chr6.simRat.chr6 203085 36 + 647215 TGGTATATTCAGTAAGTATCAC-AACAGTCAC-TTTTA - -a -s simMouse_chr6.simMouse.chr6 212062 29 + 636262 CATGTGAAACTTAAAAATTAACTGAGTAA -s Anc0.Anc0refChr5 33077 29 + 87904 CATGTGGAGGTTAGAAGGTATTCAAGTAA -s Anc1.Anc1refChr8 47406 29 + 57822 CATGTGGAGGTTAGAAGGTATTCAAGTAA -s Anc2.Anc2refChr15 27932 29 + 86568 CATGAGGAGGTTAGTAGGTATTCAAGTAA -s mr.mrrefChr5 66715 29 + 294540 CATGTGAAACTTAAAAAGTAACTGAGTAA -s simCow_chr6.simCow.chr6 385917 29 - 602619 CATGAGGGGGCTAGTAGGTATTCAAGCAA -s simDog_chr6.simDog.chr6 198659 29 + 593897 CATGAGGAGGTTGGTAAGTATTCAAGTAT -s simHuman_chr6.simHuman.chr6 386380 25 - 601863 ----TGGATGTTAGAAGGTATTCAACTAA -s simRat_chr6.simRat.chr6 203121 29 + 647215 TATGAGAAACTTAATCAGTAGCTGAGTAA - -a -s simMouse_chr6.simMouse.chr6 212091 41 + 636262 ACTGAAACCACCATCAACATATATCATGTTGACCCTTCACA -s Anc0.Anc0refChr5 33112 39 + 87904 ACTGGAACCACCAAGATCATATACTATGTTGACCCTTCA-- -s Anc1.Anc1refChr8 47441 40 + 57822 ACTGGAACCACCAAGATCATATACTATGTTGACCCTTCA-A -s Anc2.Anc2refChr15 27967 39 + 86568 ATTAGAACAACCAAGATCATATACTATGTTGATCATTCA-- -s mr.mrrefChr5 66744 41 + 294540 ACTGAAACCACCATCAACATATATCATGTTGACCCTTCACA -s simCow_chr6.simCow.chr6 385952 33 - 602619 ATTAGAACTACTTACAT------CTATGTTGATCATTCA-- -s simDog_chr6.simDog.chr6 198694 35 + 593897 A----AACAACCAAGATCATATACTATGTTGATCATTTA-- -s simHuman_chr6.simHuman.chr6 386411 36 - 601863 ACTGGAACCGCCCATATTATCTACTATGACAACTC-----A -s simRat_chr6.simRat.chr6 203150 41 + 647215 ATTGAAGCCACCATCAACATATATCATGTTGACCCTTTACA - -a -s simMouse_chr6.simMouse.chr6 212132 153 + 636262 AGAGGAGATCATTCCCATGGAGGCATTGGTTTATAGATTTATCACCTGTTGAGGCTTGGACCCCATGGAGACATTAGCCCAGAGATTTCGCACCTGTCTAGACTGGGGATGGAATGGCCTAATCTGGAGAGTGGCAAGGAAAGCTCCCTAGTG -s Anc0.Anc0refChr5 33152 62 + 87904 GGAGGAGGTCCTCTTTGTGGAGGCATGAGTTCACAGATTCCTTGTCTGTTGGGGGTGGGA-------------------------------------------------------------------------------------------TG -s Anc1.Anc1refChr8 47482 62 + 57822 GGAGGAGGTCCTCTTTGTGGAGGCATGAGTTCACAGATTCCTTGTCTGTTGGGGGTGGGA-------------------------------------------------------------------------------------------TG -s Anc2.Anc2refChr15 28007 62 + 86568 GGAGGAGGTCCTCTTTGTGGAGGCATGACTTCACAGTTTCCTTGTCTGTTGGTGGTGGGA-------------------------------------------------------------------------------------------CA -s mr.mrrefChr5 66786 152 + 294540 GGAGGAGATCATCCCCATGGAGGCATTGGTTCATAGATTTATTGCCTGTTGAGGCTTGGACCCCATGGAGACATTAGCCCAGAGATTTCGCACCTGTCTAGACTGGGGATGGAATGGCCTAATCTGGA-AGTGGCAAGGAAAGCTCCCTAGTG -s simCow_chr6.simCow.chr6 385986 51 - 602619 GGAGGGGGTCTTGTTTGTGGAGGCATGGCTTCACTGTTACCTTGTTTGTTG------------------------------------------------------------------------------------------------------ -s simDog_chr6.simDog.chr6 198730 62 + 593897 GGAGGAGGTCCCCTTCGTGGAGGCATGACTTAACACTTTCTTTGTCTGTTGGTGGTGGGA-------------------------------------------------------------------------------------------CA -s simHuman_chr6.simHuman.chr6 386448 62 - 601863 GGAGGAGGTCCTCTTTGTGGAGGCATGAGTTCACAGATTCCTTGTATGTTGGGGTTGGGA-------------------------------------------------------------------------------------------TG -s simRat_chr6.simRat.chr6 203192 151 + 647215 GGATGAGATCATCCCCACAGAGGCATTGGTTCGTAGA-TTATTGCCTGTTGAAGCTAGGACCCTATGGAGGCATTAGTTCATAGATTTCTTACCTGTCTAAACTGGGGATGGAATGACCTAATCTGGA-AGTGGCAAGGAAAGCTCCTCAATG - -a -s simMouse_chr6.simMouse.chr6 212285 3 + 636262 TAC -s Anc0.Anc0refChr5 33438 3 + 87904 TAC -s Anc1.Anc1refChr8 47768 3 + 57822 TAC -s Anc2.Anc2refChr15 28440 3 + 86568 TAC -s mr.mrrefChr5 66938 3 + 294540 TAC -s simCow_chr6.simCow.chr6 386443 3 - 602619 AAT -s simDog_chr6.simDog.chr6 199207 3 + 593897 TAC -s simHuman_chr6.simHuman.chr6 386739 3 - 601863 TAC -s simRat_chr6.simRat.chr6 203343 3 + 647215 TAC - -a -s simMouse_chr6.simMouse.chr6 212288 32 + 636262 CTCACCTTGAATAGGCTGAAGTAAAGTATCAT -s Anc0.Anc0refChr5 33441 32 + 87904 CTCACCTTGAATGGGCCATGGAAAAGTATAGT -s Anc1.Anc1refChr8 47771 32 + 57822 CTCACCTTGAATGGGCCATGGAAAAGTATAGT -s Anc2.Anc2refChr15 28443 32 + 86568 CTCACCTTGAATGAGCCATGGAAAAGTTTAGT -s mr.mrrefChr5 66941 32 + 294540 CTCACCTTGAATAGGCTGAAGTAAAGTATCAT -s simCow_chr6.simCow.chr6 386446 32 - 602619 CTCACCTTGAATGAGCTGTGGAAAAGTTTAAT -s simDog_chr6.simDog.chr6 199210 32 + 593897 CTCACCCTGAACGAACCACAGAAAAGTTTAGT -s simHuman_chr6.simHuman.chr6 386742 32 - 601863 CTCACCTTGAATGGGCCATGAAATAGTATAGT -s simRat_chr6.simRat.chr6 203349 32 + 647215 CTCACCTTGAATAGGCTGAAGTAGAGTGGAGT - -a -s simMouse_chr6.simMouse.chr6 212320 18 + 636262 TAGGCTCCATATGTCATT -s Anc0.Anc0refChr5 33473 18 + 87904 TGGGTTACTCACATAATT -s Anc1.Anc1refChr8 47803 18 + 57822 TGGGTTACTCACATAATT -s Anc2.Anc2refChr15 28479 18 + 86568 TGGGTTACTCACATAATT -s mr.mrrefChr5 66973 18 + 294540 TAGGCTCCATATGTCATT -s simCow_chr6.simCow.chr6 386526 18 - 602619 TGGGTTACTTACATAATT -s simDog_chr6.simDog.chr6 199246 18 + 593897 TGGGTTACTCAATTAATT -s simHuman_chr6.simHuman.chr6 386774 18 - 601863 TGGTTTGCTCACATAATT -s simRat_chr6.simRat.chr6 203381 18 + 647215 TAGGCTCCCTACGTCATT - -a -s simMouse_chr6.simMouse.chr6 212338 17 + 636262 GCTCCTTGTCTTTGGTA -s Anc0.Anc0refChr5 33491 13 + 87904 GCTACTTAGGATT---- -s Anc1.Anc1refChr8 47821 13 + 57822 GCTACTTAGGATT---- -s Anc2.Anc2refChr15 28497 13 + 86568 GCTACTTAGGATT---- -s mr.mrrefChr5 66991 17 + 294540 GCTCCTTGTCTTTGGTA -s simCow_chr6.simCow.chr6 386544 13 - 602619 GCTAATTAAGATT---- -s simDog_chr6.simDog.chr6 199265 13 + 593897 ACTACCTAGGATT---- -s simHuman_chr6.simHuman.chr6 386792 13 - 601863 GCTGCTTAGTATT---- -s simRat_chr6.simRat.chr6 203399 17 + 647215 GCTACTTGTCTTTGGTA - -a -s simMouse_chr6.simMouse.chr6 212355 33 + 636262 CTTGGAGACCTTGGTTGACTTTGGTTGCATACA -s Anc0.Anc0refChr5 33504 19 + 87904 ----TAGAC----------TTTAGTAGCAAGTA -s Anc1.Anc1refChr8 47834 23 + 57822 CCTATAGAC----------TTTAGTAGCAAGTA -s Anc2.Anc2refChr15 28510 19 + 86568 ----TGGAC----------TTTAGTAGTGAGTA -s mr.mrrefChr5 67008 23 + 294540 CTTGGAGAC----------TTTGGTTGCATATA -s simCow_chr6.simCow.chr6 386557 19 - 602619 ----TGGAA----------TCTAGTTGTGAGTA -s simDog_chr6.simDog.chr6 199278 19 + 593897 ----TGGAC----------TTCAGTAGTGAATA -s simHuman_chr6.simHuman.chr6 216145 23 + 601863 CCTATAGAC----------TTTTGTGGCAAGTA -s simRat_chr6.simRat.chr6 203416 23 + 647215 CTTGGAGAC----------TCTGGTTGCACATA - -a -s simMouse_chr6.simMouse.chr6 212388 18 + 636262 AGAACTTCTGGCCCAACT -s Anc0.Anc0refChr5 33526 18 + 87904 AGGACTTCTGGTCCATTC -s Anc1.Anc1refChr8 47860 18 + 57822 AGGACTTCTGGTCCATTC -s Anc2.Anc2refChr15 28532 18 + 86568 AGGACTTCTGGTCTATTC -s mr.mrrefChr5 67031 18 + 294540 AGGACTTCTGGTCCAACT -s simCow_chr6.simCow.chr6 386579 18 - 602619 AGTACTTCTGGTCTACCC -s simDog_chr6.simDog.chr6 199300 17 + 593897 AGGACTGCTG-TATATTC -s simHuman_chr6.simHuman.chr6 216171 18 + 601863 AGGACTTCTGGTCCATTC -s simRat_chr6.simRat.chr6 203439 18 + 647215 TGGACTTCTGGTCCAACT - -a -s simMouse_chr6.simMouse.chr6 212406 11 + 636262 GAGCTTGACTT -s Anc0.Anc0refChr5 33545 10 + 87904 GGGCTTGA-TG -s Anc1.Anc1refChr8 47879 10 + 57822 GGGCTTGA-TG -s Anc2.Anc2refChr15 28551 10 + 86568 GGGTTTGC-TG -s mr.mrrefChr5 67049 11 + 294540 GAGCTTGACTT -s simCow_chr6.simCow.chr6 386598 10 - 602619 GGGTTCAC-TG -s simDog_chr6.simDog.chr6 199318 10 + 593897 GAGTCTGC-TG -s simHuman_chr6.simHuman.chr6 216190 10 + 601863 GGGCTTGA-TG -s simRat_chr6.simRat.chr6 203457 11 + 647215 GAGCTCGACTT - -a -s simMouse_chr6.simMouse.chr6 212417 1 + 636262 C -s Anc0.Anc0refChr5 33562 1 + 87904 T -s Anc1.Anc1refChr8 47896 1 + 57822 T -s Anc2.Anc2refChr15 28568 1 + 86568 T -s mr.mrrefChr5 67060 1 + 294540 T -s simCow_chr6.simCow.chr6 386615 1 - 602619 T -s simDog_chr6.simDog.chr6 199335 1 + 593897 T -s simHuman_chr6.simHuman.chr6 216207 1 + 601863 T -s simRat_chr6.simRat.chr6 203468 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 212418 3 + 636262 TCA -s Anc0.Anc0refChr5 33563 3 + 87904 TTG -s Anc1.Anc1refChr8 47897 3 + 57822 TTG -s Anc2.Anc2refChr15 28569 3 + 86568 TTG -s mr.mrrefChr5 67061 3 + 294540 TCA -s simCow_chr6.simCow.chr6 386616 3 - 602619 TTG -s simDog_chr6.simDog.chr6 199337 3 + 593897 TTC -s simHuman_chr6.simHuman.chr6 216208 3 + 601863 TTG -s simRat_chr6.simRat.chr6 203469 3 + 647215 TCA - -a -s simMouse_chr6.simMouse.chr6 212421 35 + 636262 TTTCAGAAATAGACTGATGCCCTCCTATTGAAAGG -s Anc0.Anc0refChr5 33567 29 + 87904 TTTC------AGAGTGATGCCCCCCTATCAAAagg -s Anc1.Anc1refChr8 47901 29 + 57822 TTTC------AGAGTGATGCCCCCCTATCAAAagg -s Anc2.Anc2refChr15 28573 29 + 86568 TACC------AGAGTGATGCCCTCCTACCAGAagg -s mr.mrrefChr5 67065 35 + 294540 TTTCAGAAATAGAGTGATGCCCCCCTATTGAAAGG -s simCow_chr6.simCow.chr6 386620 1 - 602619 T---------------------------------- -s simDog_chr6.simDog.chr6 199341 29 + 593897 AACC------AGAGTGATGCCCTCCTACCAGAagg -s simHuman_chr6.simHuman.chr6 216212 29 + 601863 TTTC------AGAGTGCTGCCCCCCTATCAAAagg -s simRat_chr6.simRat.chr6 203473 35 + 647215 TTTCAGAGGTAGAGTGAGGCCCCCCTATTGAAAGG - -a -s simMouse_chr6.simMouse.chr6 212456 31 + 636262 catattactctattttaattcagttaggagg -s Anc0.Anc0refChr5 33602 29 + 87904 catattac--tctcctagcttggttatgagg -s Anc1.Anc1refChr8 47936 29 + 57822 catattac--tctcctagcttggttatgagg -s Anc2.Anc2refChr15 28608 29 + 86568 cagatcac--tctcctagcttggttatatga -s mr.mrrefChr5 67100 31 + 294540 catattactctctcttaattcagttaggagg -s simDog_chr6.simDog.chr6 199378 29 + 593897 cagatcac--tctcctagcttggttatatga -s simHuman_chr6.simHuman.chr6 216247 29 + 601863 catattgc--tctcctagcgtggtgatgagg -s simRat_chr6.simRat.chr6 203508 31 + 647215 CATAATACTctctcttaattcagttaggagg - -a -s simMouse_chr6.simMouse.chr6 212487 15 + 636262 caggccaggtgatcc -s Anc0.Anc0refChr5 33632 15 + 87904 cagtccaaggggtcc -s Anc1.Anc1refChr8 47966 15 + 57822 cagtccaaggggtcc -s Anc2.Anc2refChr15 28638 15 + 86568 cagtcggaggggtta -s mr.mrrefChr5 67131 15 + 294540 caggccaagtgatcc -s simDog_chr6.simDog.chr6 199409 15 + 593897 cagtcggaggggtta -s simHuman_chr6.simHuman.chr6 216277 15 + 601863 tagctcaaggggtcc -s simRat_chr6.simRat.chr6 203539 15 + 647215 ccgaccaagtgatcc - -a -s simMouse_chr6.simMouse.chr6 212502 7 + 636262 taggttt -s Anc0.Anc0refChr5 33647 4 + 87904 cagg--- -s Anc1.Anc1refChr8 47981 7 + 57822 caggttt -s Anc2.Anc2refChr15 28653 4 + 86568 cagg--- -s mr.mrrefChr5 67146 7 + 294540 caggttt -s simCow_chr6.simCow.chr6 386621 2 - 602619 --Gg--- -s simDog_chr6.simDog.chr6 199424 2 + 593897 ca----- -s simHuman_chr6.simHuman.chr6 216292 7 + 601863 cagtttt -s simRat_chr6.simRat.chr6 203569 7 + 647215 caggttt - -a -s simMouse_chr6.simMouse.chr6 212509 81 + 636262 agatttccaagtttcgattaggattaaatacagctcatggagtcagagctttaggaacaccatgcagtgagtgcagggagg -s Anc0.Anc0refChr5 33651 54 + 87904 ---------------------------atacagcttaaggggtcccagttttaagactttcaggttataagtgctgggggg -s Anc1.Anc1refChr8 47988 81 + 57822 aggcttttgggtcatgattgggattgaatacagcttaaggggtcccagttttaagactttcaggttataagtgctgggggg -s Anc2.Anc2refChr15 28657 54 + 86568 ---------------------------atacaactcaaggggtcccagttttaagactttcaggatgcaagtgctgggggg -s mr.mrrefChr5 67153 81 + 294540 agatttccaggtttcgattaggattaaatacagcttatggggtcccagttttaggaacaccatgtaatgagtgcagggagg -s simCow_chr6.simCow.chr6 386623 54 - 602619 ---------------------------atacaactcaaggggtcccagttttaagactttcaggatgcaagtgctgggggg -s simHuman_chr6.simHuman.chr6 216300 81 + 601863 aggcttttgggtcatgattgggattgaatatagcttgaggggtcccagttttaagactctcaggtcataagtgatgggggg -s simRat_chr6.simRat.chr6 203576 81 + 647215 agattcccaggtttcaattaggattaaatacagcttatgaggtccctgttttaggatcaccatgtaatgagcatggggagg - -a -s simMouse_chr6.simMouse.chr6 212590 14 + 636262 tagcaaataaactg -s Anc0.Anc0refChr5 33706 14 + 87904 tagcaaataacctt -s Anc1.Anc1refChr8 48070 14 + 57822 tagcaaataacctt -s Anc2.Anc2refChr15 28712 14 + 86568 ttgcaaataacctt -s mr.mrrefChr5 67234 14 + 294540 tagcaaataaactg -s simCow_chr6.simCow.chr6 386678 14 - 602619 ttgcaaataaattt -s simDog_chr6.simDog.chr6 199426 9 + 593897 -----gagagcctt -s simHuman_chr6.simHuman.chr6 216382 14 + 601863 tagtaaataatctt -s simRat_chr6.simRat.chr6 203657 14 + 647215 tagcaaaaaaactg - -a -s simMouse_chr6.simMouse.chr6 212604 7 + 636262 gagacat -s Anc0.Anc0refChr5 33720 7 + 87904 aggctat -s Anc1.Anc1refChr8 48084 7 + 57822 aggctat -s Anc2.Anc2refChr15 28726 7 + 86568 aggctat -s mr.mrrefChr5 67248 7 + 294540 gagacat -s simCow_chr6.simCow.chr6 386692 7 - 602619 aggacaa -s simDog_chr6.simDog.chr6 199438 7 + 593897 aggcttt -s simHuman_chr6.simHuman.chr6 216396 7 + 601863 aggctat -s simRat_chr6.simRat.chr6 203671 7 + 647215 gagacat - -a -s simMouse_chr6.simMouse.chr6 212611 106 + 636262 gtacacTGCTATCTGGAGTCTTATCCCTACTGTTCCTTTTGTTATCCACTTCCATACTGTACACTGGCTGTAGGCTCTTTTTGAGAGCTCCAGTGAGAGCACAATT -s Anc0.Anc0refChr5 33727 103 + 87904 gtatgtg-ctATCCAGAG--TTATCCCTACTGATCCTTTTGTTCTCCAATCTCATTGTGTACACCAGCAATAGGCTCTTGTGGAGAGCTTCAGTGAGAGCACAAGC -s Anc1.Anc1refChr8 48091 106 + 57822 gtatgtGGCTATCCAGAGACTTATCCCTACTGATCCTTTTGTTCTCCAATCTCATTGTGTACACCAGCAATAGGCTCTTGTGGAGAGCTTCAGTGAGAGCACAAGC -s Anc2.Anc2refChr15 28733 103 + 86568 gtatgtg-caATTCAGAG--TTATCGCTACTGATCCTTTTGTTCTCCAATCTCATTGTGTACACCAGCAATAGGCTCTTGTGGAGAGCTTCAGTAAGAGCACAAGC -s mr.mrrefChr5 67255 106 + 294540 gtacacTGCTATCTGGAGTCTTATCCCTACTGTTCCTTTTGTTATCCACTTCCATTCTGTACACTAGCTGTAGGCTCTTTTGGAGAGCTCCAGTGAGAGCACAATT -s simCow_chr6.simCow.chr6 386699 99 - 602619 gta-----caATTCAGAG--TTATCACTGCTGTTCTTTTTGTTTTCCAATCTCATTGTCTACAGCAGCAATAGACTCTTGTGGAATGCTTCAATAAGAGCACAAGC -s simDog_chr6.simDog.chr6 199452 101 + 593897 ggatgtg---attcaGAG--TTATCGCTACTCATCCTTTTGTTCTCCAATCCCATTGTGTACACCAGCAATAGGTTCTTGGGGAGAGCTTCCGTAAGAGCACAAGC -s simHuman_chr6.simHuman.chr6 216403 106 + 601863 gtaTGTGGCTATCCAGAGACTTGTCCCTACTGATCCTTTTGTTCTTCAATCTCCCTGCAGACACAAGCAATAGGCTCTTGTGGAGAGCTTCAGTGAAAGCACTAGG -s simRat_chr6.simRat.chr6 203678 104 + 647215 gtacacTGCTATCTGGAGTCTTATCACTACTATTCTTTTTGTTTTCCACTTCTATTCTG--CACCAGTTGTAGGCTCTTTTGGAGAGCTCCAGTGGGAGCACAATC - -a -s simMouse_chr6.simMouse.chr6 212717 11 + 636262 ATGCTGCTTTA -s Anc0.Anc0refChr5 33832 11 + 87904 ATGCCACCTTA -s Anc1.Anc1refChr8 48199 11 + 57822 ATGCCACCTTA -s Anc2.Anc2refChr15 28838 11 + 86568 ATGCCACCTTA -s mr.mrrefChr5 67361 11 + 294540 ATGCCACTTTA -s simCow_chr6.simCow.chr6 386800 11 - 602619 ATGTTGCCTTA -s simDog_chr6.simDog.chr6 199555 11 + 593897 ATGCCACCTTG -s simHuman_chr6.simHuman.chr6 216511 11 + 601863 ATGCCACCTTA -s simRat_chr6.simRat.chr6 203782 11 + 647215 ATGCCACTTTA - -a -s simMouse_chr6.simMouse.chr6 212728 15 + 636262 CCAGCCCTAGGGTGC -s Anc0.Anc0refChr5 33843 15 + 87904 CCATTCCTAAGGTGC -s Anc1.Anc1refChr8 48210 15 + 57822 CCATTCCTAAGGTGC -s Anc2.Anc2refChr15 28849 15 + 86568 CCATTCCTAAGGTGC -s mr.mrrefChr5 67372 15 + 294540 CCATTCCTAGGGTGC -s simCow_chr6.simCow.chr6 386811 15 - 602619 CCACTCCTAGGACGC -s simDog_chr6.simDog.chr6 199566 15 + 593897 CCATTCCAAAGGTGC -s simHuman_chr6.simHuman.chr6 216525 15 + 601863 TCCTTCCTAAGGTGT -s simRat_chr6.simRat.chr6 203793 15 + 647215 CCATTCCCAGGGTGC - -a -s simMouse_chr6.simMouse.chr6 212743 115 + 636262 TTGCATGGGGACCGTTCCGTAAGCACTTTTGAGTTTAGAGCATTAGTGAAATTGGGAGGTAGCACTACATATTTGACTTACCAATCCAGAGTGTTTCAGAGATCAGGGTCAATCA -s Anc0.Anc0refChr5 33858 57 + 87904 TTGAGTG----------------------------------------------------------TACATGTTCAACTTGCCAATTCATACTGTTTCCAAGATCAGGGGTAATCA -s Anc1.Anc1refChr8 48225 57 + 57822 TTGAGTG----------------------------------------------------------TACATGTTCAACTTGCCAATTCATACTGTTTCCAAGATCAGGGGTAATCA -s Anc2.Anc2refChr15 28864 57 + 86568 TTTAGTG----------------------------------------------------------TACATGTTCAAATTGCCAATTCATACTGAATCCAAGGCCAGGGGTTATCA -s mr.mrrefChr5 67387 57 + 294540 TTGCATG----------------------------------------------------------TACATGTTTGACTTACCAATCCAGAGTGTTTCAGAGATCAGGGTCAATCA -s simCow_chr6.simCow.chr6 386826 26 - 602619 TTTAA-G----------------------------------------------------------TACATATTCATAT------------------------------GTAATTA -s simDog_chr6.simDog.chr6 199581 57 + 593897 TTTAGTG----------------------------------------------------------TACATGCTCAAATTGCCAATTCATACTGAATCCAAGGCCAGGGGTTATCA -s simHuman_chr6.simHuman.chr6 216540 56 + 601863 TTGGGTG----------------------------------------------------------TACTTGTCCAACTTTCCAATTTACACTCTTTCCAACATCATGGATAATC- -s simRat_chr6.simRat.chr6 203809 57 + 647215 TTGCATG----------------------------------------------------------TACCTGTTTTACTTGCACATCCAAAGTGTTTCTGAGATCAGGGTCAATCA - -a -s simMouse_chr6.simMouse.chr6 212858 54 + 636262 TTACAGTCCAAGTACCTACTGATGGCTGAGATGACTCTTTATACATAATGCAAA -s Anc0.Anc0refChr5 33915 53 + 87904 CTTCAGT-TAAATATTTTCTAAAGGTTGAGATGATTTTTCATAGATAATCCAAA -s Anc1.Anc1refChr8 48282 54 + 57822 CTTCAGTCTAAATATTTTCTAAAGGTTGAGATGATTTTTCATAGATAATCCAAA -s Anc2.Anc2refChr15 29053 53 + 86568 CTTCAGT-TAAATTTTTTCTAAAGGTTGAGATGATTTTTCATAGATAACCCAAA -s mr.mrrefChr5 67444 54 + 294540 TTACAGTCCAAGTATCTACTGAAGGCTGAGATGATTCTTTATACATAATCCAAA -s simCow_chr6.simCow.chr6 386987 53 - 602619 TCTTAGT-TGAGATATTTCTAAAGGTTTAGATGATTTTTCATAGATAAAACAGA -s simDog_chr6.simDog.chr6 199777 53 + 593897 CTTCAGT-GAAATTTCTTCTACAGGCTGAAGTGATTTTTCATAGATAACCCAAA -s simHuman_chr6.simHuman.chr6 216596 53 + 601863 -TCAAGTCTAAATATTTTCCAAAGATTGAGAGGATCTTGCACAGATGATCCAAA -s simRat_chr6.simRat.chr6 203866 54 + 647215 TTACAGGCCAAGTGTCTACTGAAGGCAAAGATTATTCTTTATCCATAATCCAAA - -a -s simMouse_chr6.simMouse.chr6 212912 24 + 636262 ACTAAACCCTAGAGAGTTTCTATT -s Anc0.Anc0refChr5 33968 24 + 87904 CCTAAACCCTAAAGAACACACATT -s Anc1.Anc1refChr8 48336 24 + 57822 CCTAAACCCTAAAGAACACACATT -s Anc2.Anc2refChr15 29106 24 + 86568 CCTCAACCCTAAAGAACACACATT -s mr.mrrefChr5 67498 24 + 294540 ACTAAACCCTAGAGAGCATCTATT -s simCow_chr6.simCow.chr6 387040 24 - 602619 CCTGAAACCCAAAGACCATACATT -s simDog_chr6.simDog.chr6 199832 23 + 593897 TCTCAAC-CTAAAGAACACACATT -s simHuman_chr6.simHuman.chr6 216649 24 + 601863 CCTAAACCCTAAAGAACACACATT -s simRat_chr6.simRat.chr6 203920 24 + 647215 ACTAAACCCTGGAGAGCATTTATT - -a -s simMouse_chr6.simMouse.chr6 212936 57 + 636262 CCCTTCCATCACTTCACACCATCACATCACCCACCTAGACATGCCCCAAGCCACCAG -s Anc0.Anc0refChr5 34015 57 + 87904 CTCTGCCAAGGCTCCACACCAGCACATTACCCAACTTAGTATGCCCCCAGCCATTTG -s Anc1.Anc1refChr8 48383 57 + 57822 CTCTGCCAAGGCTCCACACCAGCACATTACCCAACTTAGTATGCCCCCAGCCATTTG -s Anc2.Anc2refChr15 29153 57 + 86568 CTCTGCCAAGGCTCCACACCAGCACATTACCCAACTTAGTATGCCTCCAGCCATTTG -s mr.mrrefChr5 67522 57 + 294540 CTCTTCCATCACTTCACACCAGCACATTACCCACCTTGACATGCCCCAAGCCACCAG -s simCow_chr6.simCow.chr6 387088 56 - 602619 CTCTGCTCTGGCTTCACACT-GCACATTACCCAACTTACTATGCCTCCAGCCATTTG -s simDog_chr6.simDog.chr6 199878 56 + 593897 CTCTGCCAAAGCTCCACACCAGCACATTGACCTACTTGGTATGCTTATGGCT-TTTG -s simHuman_chr6.simHuman.chr6 216696 57 + 601863 CTGTGTCACGGCTACACACCAGCACATTACCCAGCTTATTATGCCCCCAGCCATGTG -s simRat_chr6.simRat.chr6 203944 57 + 647215 CTCTTCCATTACTTCACCCCAGCACATTGCCCGTCTTGACTTGCCCCAAGCTGCCGG - -a -s simMouse_chr6.simMouse.chr6 212993 15 + 636262 TATTAATGTACTACT -s Anc0.Anc0refChr5 34160 15 + 87904 CATAAATGTACTGTG -s Anc1.Anc1refChr8 48528 15 + 57822 CATAAATGTACTGTG -s Anc2.Anc2refChr15 29306 15 + 86568 CATAAATGTACTGTG -s mr.mrrefChr5 67579 15 + 294540 TATTAATGTACTGTT -s simCow_chr6.simCow.chr6 387249 15 - 602619 CGTAATTGGACCGTT -s simDog_chr6.simDog.chr6 200030 15 + 593897 GATGAATGTACTATG -s simHuman_chr6.simHuman.chr6 216841 15 + 601863 CATACATGTACTGTG -s simRat_chr6.simRat.chr6 204001 15 + 647215 TATTAATGTGCTGTC - -a -s simMouse_chr6.simMouse.chr6 213008 19 + 636262 GTTTTCTCTTGATTATCAT -s Anc0.Anc0refChr5 34175 19 + 87904 GCCTTCTCTTGACTATCAA -s Anc1.Anc1refChr8 48543 19 + 57822 GCCTTCTCTTGACTATCAA -s Anc2.Anc2refChr15 29321 19 + 86568 GCCTTCTCTTTACTAGCAA -s mr.mrrefChr5 67594 19 + 294540 GTTTTCTCTTGATTATCAT -s simCow_chr6.simCow.chr6 387264 19 - 602619 GCTTTTTTTTCACTAGCAA -s simDog_chr6.simDog.chr6 200045 19 + 593897 GGCTTCTCTTTACTAGCAG -s simHuman_chr6.simHuman.chr6 216858 19 + 601863 GCCTTCTCTGGACTATCAA -s simRat_chr6.simRat.chr6 204016 18 + 647215 GTTTTCTCTTG-TTATGGT - -a -s simMouse_chr6.simMouse.chr6 213027 2 + 636262 TG -s Anc0.Anc0refChr5 34194 2 + 87904 TG -s Anc1.Anc1refChr8 48562 2 + 57822 TG -s Anc2.Anc2refChr15 29340 2 + 86568 TG -s mr.mrrefChr5 67613 2 + 294540 TG -s simCow_chr6.simCow.chr6 387283 2 - 602619 TG -s simDog_chr6.simDog.chr6 200064 2 + 593897 TG -s simHuman_chr6.simHuman.chr6 216877 2 + 601863 TG -s simRat_chr6.simRat.chr6 204035 2 + 647215 TG - -a -s simMouse_chr6.simMouse.chr6 213029 36 + 636262 ACCATACAATCCCATCAAATGGATGCCCATGGTCAA -s Anc0.Anc0refChr5 34197 36 + 87904 ACTGTACTGCCCCAACAAATGGATGCCCAAACCCAA -s Anc1.Anc1refChr8 48565 36 + 57822 ACTGTACTGCCCCAACAAATGGATGCCCAAACCCAA -s Anc2.Anc2refChr15 29343 36 + 86568 ACCATACTGCCCCTACAAATGTATGCCCAAACCCAA -s mr.mrrefChr5 67615 36 + 294540 ACTGTACAATCCCATCAAATGGATGCCCATGGTCAA -s simCow_chr6.simCow.chr6 387286 33 - 602619 AC---ACTGCCCCTCCAGATAACCCCCCGTACCCAA -s simDog_chr6.simDog.chr6 200067 36 + 593897 ACCATACTGCCCCTACAAATGTATGCCTAAACCCAA -s simHuman_chr6.simHuman.chr6 216880 28 + 601863 ACTGTACTGCCCCAACAAATGGATGCCC-------- -s simRat_chr6.simRat.chr6 204037 36 + 647215 CCTGTACAATACCATCAAATGGATACCCGTGGTCAA - -a -s simMouse_chr6.simMouse.chr6 213065 14 + 636262 CAATCAAATGCGTC -s Anc0.Anc0refChr5 34233 14 + 87904 CAATTTAATTCATG -s Anc1.Anc1refChr8 48601 14 + 57822 CAATTTAATTCATG -s Anc2.Anc2refChr15 29379 14 + 86568 CAATTTAATTTGTG -s mr.mrrefChr5 67651 14 + 294540 CAATTAAATGCATG -s simCow_chr6.simCow.chr6 387319 14 - 602619 CAGTCCAATTGGTG -s simDog_chr6.simDog.chr6 200103 14 + 593897 CAATTTAATTTGTG -s simDog_chr6.simDog.chr6 201804 14 + 593897 CAATTTAATTTGTG -s simHuman_chr6.simHuman.chr6 216908 11 + 601863 ---CTCTGTACATG -s simRat_chr6.simRat.chr6 204073 14 + 647215 CAATTAGATGTATG - -a -s simMouse_chr6.simMouse.chr6 213079 53 + 636262 CCTCAATGACACCGTTGACCCATTGATTAGTATGTTACACCCCAATCACCATT -s Anc0.Anc0refChr5 34247 40 + 87904 CTTCCATGG---TGCTGCCCCATGGATGAGTGTGTTGC-TTCTC--------- -s Anc1.Anc1refChr8 48615 52 + 57822 CTTCCATGGGGCTGCTGCCCCATGGATGAGTGTGTTGC-TTCTCATTACCTTT -s Anc2.Anc2refChr15 29393 40 + 86568 GTGCCATGG---TGCGGTCCTGTGGATGAGTGTTTTGC-TTTTC--------- -s mr.mrrefChr5 67665 53 + 294540 CCTCAATGACACTGTTGCCCCATGGATGAGTATGTTGCACCCCCATCACCATT -s simCow_chr6.simCow.chr6 387341 35 - 602619 GGGC--------TACTGTGCCATGGATGAGTGTGTTGC-TCTGT--------- -s simDog_chr6.simDog.chr6 200117 40 + 593897 GTGCCATGG---TGCGGTCCTGTGGATGAGTGTTTTGC-TTTTC--------- -s simDog_chr6.simDog.chr6 201818 40 + 593897 GTGCCATGG---TGCGGTCCTGTGGATGAGTGTTTTGC-TTTTC--------- -s simHuman_chr6.simHuman.chr6 216919 52 + 601863 CATTCATAGGGCTGCTGCCCCATGGATGAGTGTGTTGC-TTCTCATTACCTTT -s simRat_chr6.simRat.chr6 204087 53 + 647215 CCTCAATGACCCTGTTGCCCCATGGATGAGTATGTTGCACCCCCAACACCCTT - -a -s simMouse_chr6.simMouse.chr6 213132 6 + 636262 CCCGGT -s Anc1.Anc1refChr8 48690 6 + 57822 CTTGCT -s mr.mrrefChr5 67741 6 + 294540 CCTGGT -s simHuman_chr6.simHuman.chr6 216994 6 + 601863 CTTGCT -s simRat_chr6.simRat.chr6 204163 6 + 647215 CCTGGT - -a -s simMouse_chr6.simMouse.chr6 213138 4 + 636262 GAGT -s Anc1.Anc1refChr8 48696 4 + 57822 GGGT -s mr.mrrefChr5 67747 4 + 294540 GAGT -s simHuman_chr6.simHuman.chr6 217000 4 + 601863 GGGT -s simRat_chr6.simRat.chr6 204170 4 + 647215 GAAT - -a -s simMouse_chr6.simMouse.chr6 213142 28 + 636262 GCTGCCACCACTGCACTTCCCTTACCTA -s Anc0.Anc0refChr5 34287 18 + 87904 -----CATCTAAG-----CCCTAACCTA -s Anc1.Anc1refChr8 48700 23 + 57822 GCTGCCATCTAAG-----CCCTAACCTA -s Anc2.Anc2refChr15 29433 18 + 86568 -----TATCTAAG-----CCCTAACCCA -s mr.mrrefChr5 67751 28 + 294540 GCTGCCACCACTGCACTTCCCTTACCTA -s simCow_chr6.simCow.chr6 387376 18 - 602619 -----TGTCTCAG-----CCTAACCTCA -s simDog_chr6.simDog.chr6 200157 18 + 593897 -----TATCTAAG-----CCCTAACCCA -s simDog_chr6.simDog.chr6 201858 18 + 593897 -----TATCTAAG-----CCCTAACCCA -s simHuman_chr6.simHuman.chr6 217005 23 + 601863 GCTGTCATCTAAG-----CCCTAACCTA -s simRat_chr6.simRat.chr6 204174 28 + 647215 GCTGCCACCACTGCACTTCCCTTACCTA - -a -s simMouse_chr6.simMouse.chr6 213170 79 + 636262 CATGTTGTTTTCAAGATTTCACATAAAATTCCAGGTCTTACTGAATGATCATTATCTCTTTCATCTGGTGTAGGATTGG -s Anc0.Anc0refChr5 34305 77 + 87904 GGAATTATTTTGAAGACCTCCAAGGAAATGCCAGGCCTTACTGCATGATAATCATGTCTTTCATTTGATGGTGCATC-- -s Anc1.Anc1refChr8 48723 77 + 57822 GGAATTATTTTGAAGACCTCCAAGGAAATGCCAGGCCTTACTGCATGATAATCATGTCTTTCATTTGATGGTGCATC-- -s Anc2.Anc2refChr15 29451 77 + 86568 GGAATCATTTTGTAGACCTCCAAGGAAATGCCCAACCTTACTGCTTAACAATTTTGTTTTTGGTTTGATTGTGCATC-- -s mr.mrrefChr5 67779 79 + 294540 CATGTTGTTTTCAAGATCTCACATAAAATTCCAGGTCTTACTGAATGATCATCATCTCTTTCATCTGGTGGAGGATTGG -s simCow_chr6.simCow.chr6 387396 64 - 602619 GGAAATATTTTGAA-------------CTTCCAAACCCCACTGCTTAATAATCGTATCTTTACTTTGATGGAGAAGC-- -s simDog_chr6.simDog.chr6 200175 76 + 593897 GGAATCATTTTGTAGTCCTCCAAGGAAATGCCCAACCTTACTGCTTAACAATTTTGTT-TTGGTTTGATTGTGCATC-- -s simDog_chr6.simDog.chr6 201876 76 + 593897 GGAATCATTTTGTAGACCTCCAAGGAAATGCCCAACCTTACTGCTTAACAATTTTGTT-TTGGTTTGATTGTGCATC-- -s simHuman_chr6.simHuman.chr6 217028 77 + 601863 GGAATTAGTTTGAAGACCCCTAAAGAAATGACAGGCCTCACTGCATGATATTCATACCCTTCAATTGATGGGCAATC-- -s simRat_chr6.simRat.chr6 204202 78 + 647215 CCTGTTGATTTCAAGATCTCACATAGAACTCCAGGTCTGACTGAATCAT-ATCATTTCTTTCATGTGGTAGAGGATTGG - -a -s simMouse_chr6.simMouse.chr6 213249 22 + 636262 TGTTTGAGGAGTTTGCTCTAAA -s Anc0.Anc0refChr5 34382 20 + 87904 --TCTGAGAAGTCCATTCTAAA -s Anc1.Anc1refChr8 48800 20 + 57822 --TCTGAGAAGTCCATTCTAAA -s Anc2.Anc2refChr15 29528 20 + 86568 --TCGGACAAGTCCATGCTAAA -s mr.mrrefChr5 67858 22 + 294540 TGTTTGAGGAGTTTGCTCTAAA -s simCow_chr6.simCow.chr6 387460 18 - 602619 --TCTGAGAGATTCATG--AGA -s simDog_chr6.simDog.chr6 200251 20 + 593897 --TCGGACAAGTCCATGCTAAA -s simDog_chr6.simDog.chr6 201952 20 + 593897 --TCGGACAAGTCCATGCTAAA -s simHuman_chr6.simHuman.chr6 217105 20 + 601863 --TCTGAGAGGTCCATTTCAAA -s simRat_chr6.simRat.chr6 204282 18 + 647215 TGCTGGTGGATTTT----TGAG - -a -s simMouse_chr6.simMouse.chr6 213271 16 + 636262 GAGAGTGTGGGTCCAT -s Anc0.Anc0refChr5 34417 16 + 87904 GAGATTTTAGGTTTAG -s Anc1.Anc1refChr8 48835 16 + 57822 GAGATTTTAGGTTTAG -s Anc2.Anc2refChr15 29563 16 + 86568 AAGATTTTAGCTTTGG -s mr.mrrefChr5 67880 16 + 294540 GAGAGTGTGGGTCCAT -s simCow_chr6.simCow.chr6 387493 16 - 602619 GAGACTTTATCTTTAG -s simDog_chr6.simDog.chr6 200286 16 + 593897 AAGATTTTAGCTTTGG -s simDog_chr6.simDog.chr6 201987 16 + 593897 AAGATTTTAGCTTTGG -s simHuman_chr6.simHuman.chr6 217140 16 + 601863 GAGAATTTAGGTTTAC -s simRat_chr6.simRat.chr6 204300 6 + 647215 AAG----------CGT - -a -s simMouse_chr6.simMouse.chr6 213287 7 + 636262 GCATCTT -s Anc0.Anc0refChr5 34458 7 + 87904 GCATCTT -s Anc1.Anc1refChr8 48876 7 + 57822 GCATCTT -s Anc2.Anc2refChr15 29604 7 + 86568 GAAACTT -s mr.mrrefChr5 67896 7 + 294540 GCATCTT -s simCow_chr6.simCow.chr6 387536 7 - 602619 GCATCTT -s simDog_chr6.simDog.chr6 200321 7 + 593897 GAAACTT -s simDog_chr6.simDog.chr6 202022 7 + 593897 GAAACTT -s simHuman_chr6.simHuman.chr6 217181 7 + 601863 GCATCTT -s simRat_chr6.simRat.chr6 204306 7 + 647215 ACATCTT - -a -s simMouse_chr6.simMouse.chr6 213294 87 + 636262 TATAGAACAACAAGATAATTAGCCCTTTTTTGAAGGGCCCTTTTTTGAAGGAATGTACGTCAATGTACCTCAGTTACGGAGAGGACC -s Anc0.Anc0refChr5 34465 73 + 87904 TGTATGACACCAAGATAATT----CTT--------AGCCCTATTTTGAAGGAATGGA-GTCAAGAGACCACAGTTA-GGGGGGGATC -s Anc1.Anc1refChr8 48883 75 + 57822 TGTATGACACCAAGATAATT----CTT--------AGCCCTATTTTGAAGGAATGGATGTCAAGAGACCACAGTTATGGGGGGGATC -s Anc2.Anc2refChr15 29613 73 + 86568 TGTATGACACCAGTATAATT----CTT--------AGCCCTACTTTGAAAGAATGGA-GCTAAGAGACCACAGTGG-GGGGGAGATC -s mr.mrrefChr5 67903 87 + 294540 TATAGAACACCAAGATAATTAGCCCTTTTTTGAAGGGCCCTTTTTTGAAGGAATGTACGTCAATGTACCTCAGTTACGGAGAGGACC -s simCow_chr6.simCow.chr6 387543 39 - 602619 TGTATGAAATCAAGATACTT----ATT--------AGTCAGAC------------------------------------GAGAGATC -s simDog_chr6.simDog.chr6 200330 73 + 593897 TGTATGACACCAGTATAATT----CTT--------AGCCCTACTTTGAAAGAATGGA-GCTAAGAGACCACAGTGG-GGGGGAGATC -s simDog_chr6.simDog.chr6 202031 73 + 593897 TGTATGACACCAGTATAATT----CTT--------AGCCCTACTTTGAAAGAATGGA-GCTAAGAGACCACAGTGG-GGGGGAGATC -s simHuman_chr6.simHuman.chr6 217188 75 + 601863 TGTACCACACCAAGATAATT----CTT--------AACCATATTCTGCAGGAATGGATGTCAGCAGGCCACAGTTATGGGGGGGATC -s simRat_chr6.simRat.chr6 204313 53 + 647215 TATAGGATACCAAGATATTTAGCCCTATTTTGAAGGGCCCTT----------------------------------AGGAGAGGAAC - -a -s simMouse_chr6.simMouse.chr6 213381 32 + 636262 AATAAGTGTGTGATCATGATTCTAAACAAGGA -s Anc0.Anc0refChr5 35130 32 + 87904 AGTGAGTCTGTGACCATGACTCCAGAGAGCAA -s Anc1.Anc1refChr8 49550 32 + 57822 AGTGAGTCTGTGACCATGACTCCAGAGAGCAA -s Anc2.Anc2refChr15 30367 32 + 86568 AGTGAGTCTGTGACCATGGCCCCAGTGAGCAA -s mr.mrrefChr5 67990 32 + 294540 AATAAGTGTGTGATCATGATTCTAAACAGGGA -s simDog_chr6.simDog.chr6 201075 32 + 593897 AGTGAGTCCGTGACCATGGCCCCAGTGAGCAA -s simDog_chr6.simDog.chr6 202776 32 + 593897 AGTGAGTCTGTGACCATGGCCCCAGTGAGCAA -s simHuman_chr6.simHuman.chr6 217870 32 + 601863 AGCGAGTCTGTGGCCATGACTGCAGAGAGCAA -s simRat_chr6.simRat.chr6 204366 32 + 647215 AATAAGTGTGTGATGATGATTCTAAACAGGGA - -a -s simMouse_chr6.simMouse.chr6 213413 81 + 636262 AATGAAATGAATAGAGTGGTGAACACATTGGTTTAGCTGCATAGGAGGTTAAAAGAAGTGAGGGCCAGAGACCCCCTCAGA -s Anc0.Anc0refChr5 35168 76 + 87904 AACTAAATGAATG-----TCAAAAGCATTGGTTGATCTCCATGAGAGGTCAAAAGAAAAGAGAGCCAGAGAGCCCATCAGT -s Anc1.Anc1refChr8 49588 81 + 57822 AACTAAATGAATGGCTTGTCAAAAGCATTGGTTGATCTCCATGAGAGGTCAAAAGAAAAGAGAGCCAGAGAGCCCATCAGT -s Anc2.Anc2refChr15 30405 76 + 86568 AACTAATTGAATC-----TCAATAGCATTAGCTGATCCCCATGAGAGGTCAAAAGAAAAGAGAGCCTGGATGCAAATGAGT -s mr.mrrefChr5 68022 81 + 294540 AACGAAATGAATAGAGTGGTGAACACATTGGTTGAGCTGCATAAGAGGTTAAAAGAAGTGAGGGCCAGAGACCCCCTCAGA -s simCow_chr6.simCow.chr6 388079 15 - 602619 ------------------------------------------------------GAAAAGAGAGCCC--------AC---- -s simDog_chr6.simDog.chr6 201113 76 + 593897 AACTAATTGAATC-----TCAATAGCATTAGCTGATCCCCATGAGAGGTCAAAAGAAAAGAGAGCCTGGATGCAAATGAGT -s simDog_chr6.simDog.chr6 202814 76 + 593897 AACTAATTGAATC-----TCAATAGCATTAGCTGATCCCCATGAGAGGTCAAAAGAAAAGAGAGCCTGGATGCAAATGAGT -s simHuman_chr6.simHuman.chr6 217909 68 + 601863 AACTAAATGAATGGCTTGTCAAATGCATTGGTTGATGTACATTAGATGTCAAA-------------AGAGAGCCCATCAGT -s simRat_chr6.simRat.chr6 204398 77 + 647215 AACAAAATGGATAGAGTGGTGAACACATTGGTTGAGCTGCATAAGA----AAAAGAAGTGGGAGCCATAGACCCTCTCAGA - -a -s simMouse_chr6.simMouse.chr6 213494 7 + 636262 ATGAGGA -s Anc0.Anc0refChr5 35244 7 + 87904 ATTAGGA -s Anc1.Anc1refChr8 49669 7 + 57822 ATTAGGA -s Anc2.Anc2refChr15 30497 7 + 86568 ATTAGAA -s mr.mrrefChr5 68103 7 + 294540 ATGAGGA -s simCow_chr6.simCow.chr6 388096 3 - 602619 ----GAC -s simDog_chr6.simDog.chr6 201205 7 + 593897 ATTAGAA -s simDog_chr6.simDog.chr6 202906 7 + 593897 ATTAGAA -s simHuman_chr6.simHuman.chr6 217977 7 + 601863 ATTCAGA -s simRat_chr6.simRat.chr6 204475 7 + 647215 ATGAGGA - -a -s simMouse_chr6.simMouse.chr6 213501 60 + 636262 TGGTTCATCCTGTCGCAAATTTTTTGAGCAAACCAAACCAATAAGTCTGCCTGACAAGGA -s Anc0.Anc0refChr5 35251 37 + 87904 TGGTGCTCCATGTCACAA-----------------------TGAGCATGCCTGGGAAGGA -s Anc1.Anc1refChr8 49676 60 + 57822 TGGTGCTCCATGTCACAAGATTGTTGAATAAGCCAGACCAATGAGCATGCCTGGGAAGGA -s Anc2.Anc2refChr15 30504 37 + 86568 TGGTGCTCCATGTCATAA-----------------------TGAACATGTCTGGGAAGGA -s mr.mrrefChr5 68110 60 + 294540 TGGTTCATCCTGTCACAAATTTTTTGAGCAAACCAAACCAATGAGTCTGCCTGGCAAGGA -s simCow_chr6.simCow.chr6 388099 37 - 602619 TGGTACTCCATGGCATAA-----------------------GGAGGACACCTGGGGTGGA -s simDog_chr6.simDog.chr6 201212 37 + 593897 TGGTGCTCCATGTCATAA-----------------------TGAACATGTCTGGGAAGGA -s simDog_chr6.simDog.chr6 202913 37 + 593897 TGGTGCTCCATGTCATAA-----------------------TGAACATGTCTGGGAAGGA -s simHuman_chr6.simHuman.chr6 217985 60 + 601863 TGGTACTCCATATCACAAGATTGTTGAATAAGCCAGACCAATGAGCATGCCCGGGAAGGA -s simRat_chr6.simRat.chr6 204482 59 + 647215 TGGTTTATCCTGTCACAAATTTTTTGAGC-AACCAAACCAATGAGTCCACCTGGCAAGGA - -a -s simMouse_chr6.simMouse.chr6 213561 50 + 636262 AATTCAAAGAGGGAGAAGATGTAGAAAAGAAACCTTGTAGGAAGTGTTGC -s Anc0.Anc0refChr5 35298 45 + 87904 GATACAAGGAGGGGGAGCATGT-----AGAAACATAGTAGGAAGTGTTGC -s Anc1.Anc1refChr8 49746 45 + 57822 GATACAAGGAGGGGGAGCATGT-----AGAAACATAGTAGGAAGTGTTGC -s Anc2.Anc2refChr15 30551 45 + 86568 GATACACGCAGGGGAAGCATGT-----AGATACATAGTCAGAAGCGTTGT -s mr.mrrefChr5 68170 45 + 294540 AATTCAAGGAGGGAGAAGATGT-----AGAAACCTAGTAGGAAGTGTTGC -s simCow_chr6.simCow.chr6 388146 45 - 602619 GATACAAGGAGGGTGAACATGT-----AGATCCATAGTCAGAAGTGCTGC -s simDog_chr6.simDog.chr6 201259 45 + 593897 AATACACGCAGGGGAAGCATGT-----AGATACATAGTCAGAAGCGTTGT -s simDog_chr6.simDog.chr6 202960 45 + 593897 GATACACGCAGGGGAAGCATGT-----AGATACATAGTCAGAAGCGTTGT -s simHuman_chr6.simHuman.chr6 218055 45 + 601863 GATACAAGGAGGATGACCATGC-----AGGAAGATAGTAGGAAGTGTTGC -s simRat_chr6.simRat.chr6 204541 45 + 647215 AATTCAAGGAAGGAGAAGATAT-----AGAAACCCAGCAGGAAGTCTTGC - -a -s simMouse_chr6.simMouse.chr6 213611 73 + 636262 ACATAAAGGAGGGCAAGAGTAAACTAAAGAGCACATTTCCAAACCCAAAGTCATAAGCTAAAGGGCATAGAAT -s Anc0.Anc0refChr5 35343 45 + 87904 ATATCCAGG-----------------------CCACCTGAAGG--CAAAG---TAATTTAAAGAGTATAGAAC -s Anc1.Anc1refChr8 49791 45 + 57822 ATATCCAGG-----------------------CCACCTGAAGG--CAAAG---TAATTTAAAGAGTATAGAAC -s Anc2.Anc2refChr15 30596 45 + 86568 GTAACCAGA-----------------------CTACCTGAGGG--CGAAG---TAATTGAAACAGCAGAGAAC -s mr.mrrefChr5 68215 71 + 294540 ACATAAAGGAGGGCAAGAGTAAACTAGAGAGCACATTTCCAAA--CAAAGTCATAAGCTAAAGGGTATAGAAT -s simCow_chr6.simCow.chr6 388194 45 - 602619 ATAATAAGA-----------------------CTACCTGAGGG--GGATG---CAATCTTAGGAGTTGAGAAC -s simDog_chr6.simDog.chr6 201304 45 + 593897 GTAACCAGA-----------------------CTACCTGAGGG--CGAAG---TAATTGAAACAGCAGAGAAC -s simDog_chr6.simDog.chr6 203005 45 + 593897 GTAACCAGA-----------------------CTACCTGAGGG--CGAAG---TAATTGAAACAGCAGAGAAC -s simHuman_chr6.simHuman.chr6 218100 45 + 601863 ATGTTGAGG-----------------------CCACCTGAAGG--CAGAG---TAATGTAGTGAGTATAGAAC -s simRat_chr6.simRat.chr6 204586 71 + 647215 ACATAACGGGGGGCAAGAGAAAACTAGAGAGCATAATTCCAAA--CAAAGTCATAAACTAAAGGGTATAGACT - -a -s simMouse_chr6.simMouse.chr6 213684 42 + 636262 CTAAACCTAAAGTTGTAATATAGGAACCACAGTATGGCGTGA -s Anc0.Anc0refChr5 35388 41 + 87904 CTGAACCCAGAGTCATAATATAGGAACCACAGTACAGGC-GT -s Anc1.Anc1refChr8 49836 42 + 57822 CTGAACCCAGAGTCATAATATAGGAACCACAGTACAGGCTGT -s Anc2.Anc2refChr15 30643 41 + 86568 TTTAACCCAGAGTCACAATATAGGAACTACAGTGCAGGC-AT -s mr.mrrefChr5 68286 42 + 294540 CTGAACCTAAAGTTGTAATATAGGAACCACAGTATGGCGTGA -s simCow_chr6.simCow.chr6 388239 41 - 602619 ATGAACCTAGAGTCATAATAGACCGTAAACGATTCAGGG-AT -s simDog_chr6.simDog.chr6 201351 41 + 593897 TTTAACCCAGAGTCACAATATAGGAACTACAGTGCAGGC-AT -s simDog_chr6.simDog.chr6 203052 41 + 593897 TTTAACCCAGAGTCACAATATAGGAACTACAGTGCAGGC-AT -s simHuman_chr6.simHuman.chr6 218145 42 + 601863 CTGAACCCAGGGTCTTAACATAGGAACCGCAGTACAAACTGT -s simRat_chr6.simRat.chr6 204657 42 + 647215 CCGAACCTAAAGTTGCAATATAGGAACCACAGTATGGGGTGA - -a -s simMouse_chr6.simMouse.chr6 213726 21 + 636262 GTATTTGGTGCAAGAGCATTT -s Anc0.Anc0refChr5 35429 21 + 87904 ATATTTGCTGGAAAAACATCT -s Anc1.Anc1refChr8 49878 21 + 57822 ATATTTGCTGGAAAAACATCT -s Anc2.Anc2refChr15 30684 21 + 86568 ATATTCGCCGGAAAAACATCC -s mr.mrrefChr5 68328 21 + 294540 GTATTTGGTGCAAGAGCATTT -s simCow_chr6.simCow.chr6 388281 16 - 602619 ATAAT-----GGGAATCATAT -s simDog_chr6.simDog.chr6 201392 21 + 593897 ATATTCGCCGGAAAAACATCC -s simDog_chr6.simDog.chr6 203093 21 + 593897 ATATTCGCCGGAAAAACATCC -s simHuman_chr6.simHuman.chr6 218187 21 + 601863 ATATTTGTTGAAAAAACAACT -s simRat_chr6.simRat.chr6 204699 21 + 647215 GTGTTTGCTGCGAGAGCATAT - -a -s simMouse_chr6.simMouse.chr6 213747 2 + 636262 AA -s Anc0.Anc0refChr5 35450 2 + 87904 AA -s Anc1.Anc1refChr8 49899 2 + 57822 AA -s Anc2.Anc2refChr15 30708 2 + 86568 AA -s mr.mrrefChr5 68349 2 + 294540 AA -s simDog_chr6.simDog.chr6 201416 2 + 593897 AA -s simDog_chr6.simDog.chr6 203117 2 + 593897 AA -s simHuman_chr6.simHuman.chr6 218208 2 + 601863 AA -s simRat_chr6.simRat.chr6 204720 2 + 647215 AA - -a -s simMouse_chr6.simMouse.chr6 213749 50 + 636262 GATGTTTCTTCATGATACTCTTAATGAAAAAATGTTGATTACAACCTAAA -s Anc0.Anc0refChr5 35452 48 + 87904 G--GTTTTGAGATGATATTCTTAATCAAAAAATGTTGATTACAACCTAAA -s Anc1.Anc1refChr8 49901 48 + 57822 G--GTTTTGAGATGATATTCTTAATCAAAAAATGTTGATTACAACCTAAA -s Anc2.Anc2refChr15 30710 48 + 86568 G--GTTATGAGATGGTATTCTTAATCAAATAACGTTGATTACAACCTAAA -s mr.mrrefChr5 68351 50 + 294540 GATGTTTCTTCATGATATTCTTAATGAAAAAATGTTGATTACAACCTAAA -s simCow_chr6.simCow.chr6 388300 25 - 602619 --------------GTACACTCAATCAAACGATGTTAAT----------- -s simDog_chr6.simDog.chr6 201418 48 + 593897 G--GTTATGAGATGGTATTCTTAATCAAATAACGTTGATTACAACCTAAA -s simDog_chr6.simDog.chr6 203119 48 + 593897 G--GTTATGAGATGGTATTCTTAATCAAATAACGTTGATTACAACCTAAA -s simHuman_chr6.simHuman.chr6 218210 48 + 601863 G--GTCTTGAGCTGATATTTTTAATTAAAAGATGTTGATTACAACCTACA -s simRat_chr6.simRat.chr6 204723 47 + 647215 AATGTTTCTTCATGATATTCTTAATGAAAAAATTTTGGTTACGACCT--- - -a -s simMouse_chr6.simMouse.chr6 213799 40 + 636262 AACACGTTGATTGGGTAGATTACAAATTGAAGATGTGTGT -s Anc0.Anc0refChr5 35500 40 + 87904 AAGAGGTTGATTAGGTAGTTTACAGTCTAAAAACATATGT -s Anc1.Anc1refChr8 49949 40 + 57822 AAGAGGTTGATTAGGTAGTTTACAGTCTAAAAACATATGT -s Anc2.Anc2refChr15 30775 40 + 86568 AAGAGGTTGATTAGGTAGTTTACAGTCTAATAACATATGC -s mr.mrrefChr5 68401 40 + 294540 AACACGTTGATTAGGTAGATTACAAATTGAAGATATATGT -s simCow_chr6.simCow.chr6 388325 26 - 602619 --------------GTAGATTGCAGCCTAATAATACATGC -s simDog_chr6.simDog.chr6 201483 40 + 593897 AAGAGGTTGATTAGGTAGTTTACAGTCTAATAACATATGC -s simDog_chr6.simDog.chr6 203184 40 + 593897 AAGAGGTTGATTGGGTAGTTTACAGTCTAATAACATATGC -s simHuman_chr6.simHuman.chr6 218258 40 + 601863 AAGAGGTTCATTAGGAGGGTTATAGCCTAAAAAAATATGT -s simRat_chr6.simRat.chr6 204770 40 + 647215 AGCACGTTGATTAGGTAGATTACAAATTGAGGATATATGT - -a -s simMouse_chr6.simMouse.chr6 213839 35 + 636262 GGTCCCAACAGTCAACTGGGAGCACACTAACTAGA -s Anc0.Anc0refChr5 35541 35 + 87904 GGTTTCAAGTTTCAACTGGAAGCAGATTAACCAGG -s Anc1.Anc1refChr8 49990 35 + 57822 GGTTTCAAGTTTCAACTGGAAGCAGATTAACCAGG -s Anc2.Anc2refChr15 30816 35 + 86568 GATTTCCGGTTTCATCTGAAAACAGCATAACCAGG -s mr.mrrefChr5 68442 35 + 294540 GGTCCCAACAGTCAACTGGAAGCACATTAACCAGA -s simCow_chr6.simCow.chr6 388352 35 - 602619 GGTTCCAGGTCTTGACTGAGAATGTATTAACCAAG -s simDog_chr6.simDog.chr6 201524 35 + 593897 GATTTCCGGTTTCATCTGAAAACAGCACAACCAGG -s simDog_chr6.simDog.chr6 203225 35 + 593897 GATTTCCGGTTTCATCTGAAAACAGCATAACCAGG -s simHuman_chr6.simHuman.chr6 218299 34 + 601863 GGTTTCAAATCCCAATT-GAAGCGTATCGACCAAG -s simRat_chr6.simRat.chr6 204811 32 + 647215 GGTC---ACACTTAACTGAAAACACCTTAACCAGT - -a -s simMouse_chr6.simMouse.chr6 213874 26 + 636262 TAAGTGTAGTATTGAAGTTTGGTGAT -s Anc0.Anc0refChr5 35577 26 + 87904 TAAGCATAGTATTTGAATTTATCCAT -s Anc1.Anc1refChr8 50026 26 + 57822 TAAGCATAGTATTTGAATTTATCCAT -s Anc2.Anc2refChr15 30852 26 + 86568 TAAGCATAGTATTTGAAGTCATCCAG -s mr.mrrefChr5 68477 26 + 294540 TAAGTGTAGTATTGAAGTTTGGTGAT -s simCow_chr6.simCow.chr6 388388 25 - 602619 CAAGCATAGTTGTTGAGGTCATCTT- -s simDog_chr6.simDog.chr6 201560 23 + 593897 T---CATAGTATTTGAAGTCATCCAG -s simDog_chr6.simDog.chr6 203261 23 + 593897 T---CATAGTATTTGAAGTCATCCAG -s simHuman_chr6.simHuman.chr6 218334 26 + 601863 CAAGCATAGTGGTTGAATTTATCCAT -s simRat_chr6.simRat.chr6 204843 26 + 647215 TAAGTGTATTATTGAAGTTTGGTGAT - -a -s simMouse_chr6.simMouse.chr6 213900 64 + 636262 CTGTACAATTATGTGATGAAATGAACTCAACTATCCAGGCACATAGTGGAACCACTCAAGTTAC -s Anc0.Anc0refChr5 35604 64 + 87904 CCATACAATGATGTAAGGGAATTGACTCAAATATCTGGGCACATAGAGGAAGTACCTAACCTAC -s Anc1.Anc1refChr8 50053 64 + 57822 CCATACAATGATGTAAGGGAATTGACTCAAATATCTGGGCACATAGAGGAAGTACCTAACCTAC -s Anc2.Anc2refChr15 30879 64 + 86568 CCAAATAATGATGTAAGGGAATTGACCTAAATACTTGGGCAATTAGAGCAAGTACCTAACCTAC -s mr.mrrefChr5 68503 64 + 294540 CTGTACAATGATGTGAGGGAATGAACTCAACTATCCGGGCACATAGTGGAACCACTCAAGTTAC -s simCow_chr6.simCow.chr6 388413 60 - 602619 ----ATAATCATGTAAGGGGATTAACTTAGATACCAGGCCACATAAAGGAAGAACCTAACCTAC -s simDog_chr6.simDog.chr6 201584 64 + 593897 CCAAATAATGATGTAAGGGAATTGACCTAAATACTTGGGCAATTAGAGCAAGTACCTAACCTAC -s simDog_chr6.simDog.chr6 203285 64 + 593897 CCAAATAATGATGTAAGAGAATTGACCTAAATACTTGGGCAATTAGAGCAAGTACCTAACCTAC -s simHuman_chr6.simHuman.chr6 218361 64 + 601863 GCATGCAATGATGTAAGGGAATTGACTCAAATATCTGGGCACATAGAGGAAGTACCTGACACAC -s simRat_chr6.simRat.chr6 204869 64 + 647215 TTGTATAATGATGTGAGGGAATAATCTCAACTATCCGGGCGCATAGTGGTACCACTCAATCTAC - -a -s simMouse_chr6.simMouse.chr6 213964 22 + 636262 TTCAGAGTGCTTAACATTCAAG -s Anc0.Anc0refChr5 35668 22 + 87904 TTCACAATGCTTGAAATTCTAA -s Anc1.Anc1refChr8 50117 22 + 57822 TTCACAATGCTTGAAATTCTAA -s Anc2.Anc2refChr15 30943 22 + 86568 TTCACAGTCCTTGAAATGCTGA -s mr.mrrefChr5 68567 22 + 294540 TTCAGAATGCTTGACATTCAAG -s simCow_chr6.simCow.chr6 388473 22 - 602619 TTCACAGTGCTTGAAATTCTGG -s simDog_chr6.simDog.chr6 201648 22 + 593897 TTCACAGTCCTTGAAATGCTGA -s simDog_chr6.simDog.chr6 203349 22 + 593897 TTCACAGTCCTTGAAATGCTGA -s simHuman_chr6.simHuman.chr6 218447 22 + 601863 TTCACAATGCAGGAAATTCCAT -s simRat_chr6.simRat.chr6 204933 22 + 647215 TTCAGAATGCTTGACATTCTAG - -a -s simMouse_chr6.simMouse.chr6 213986 43 + 636262 GTGCATATGATATTATATCTCAGGTCTTACGTTTACATCATAA -s Anc0.Anc0refChr5 35690 37 + 87904 -----TCTGCCACAATGTGTAAGCTCTTACATTTACCTCA-AA -s Anc1.Anc1refChr8 50139 37 + 57822 -----TCTGCCACAATGTGTAAGCTCTTACATTTACCTCA-AA -s Anc2.Anc2refChr15 30965 37 + 86568 -----TCTGCCACAATGTGTAAGCTATCATATTCACCTCA-AA -s mr.mrrefChr5 68589 42 + 294540 GTGCATATGATATTATATCTCAGGTCTTACATTTACATCA-AA -s simCow_chr6.simCow.chr6 388495 34 - 602619 -----TCTACCATAATGTGTACTCCCTTACATTTGCCTA---- -s simDog_chr6.simDog.chr6 201670 37 + 593897 -----TCTGCCACAATGTGTAAGCTATCATATTCACCTCA-AA -s simDog_chr6.simDog.chr6 203371 37 + 593897 -----TCTGCCACAATGTGTAAGCTATCATATTCACCTCA-AA -s simHuman_chr6.simHuman.chr6 218469 37 + 601863 -----TCTGCCAAAATGTGTAAGATCTTGCATTTACTTCA-AA -s simRat_chr6.simRat.chr6 204961 40 + 647215 GTGCATAAGGTATTACA--TCATGTCTTACATTTACCACA-AA - -a -s simMouse_chr6.simMouse.chr6 214029 4 + 636262 TGCA -s Anc0.Anc0refChr5 35727 4 + 87904 TGTG -s Anc1.Anc1refChr8 50176 4 + 57822 TGTG -s Anc2.Anc2refChr15 31097 4 + 86568 TGTG -s mr.mrrefChr5 68631 4 + 294540 TGCA -s simCow_chr6.simCow.chr6 388535 4 - 602619 TGTG -s simDog_chr6.simDog.chr6 203503 4 + 593897 TTGG -s simHuman_chr6.simHuman.chr6 218506 4 + 601863 TGTG -s simRat_chr6.simRat.chr6 205001 4 + 647215 TACA - -a -s simMouse_chr6.simMouse.chr6 214033 10 + 636262 TCGATACTTT -s Anc0.Anc0refChr5 35737 10 + 87904 TTTACAATTG -s Anc1.Anc1refChr8 50186 10 + 57822 TTTACAATTG -s Anc2.Anc2refChr15 31107 10 + 86568 CTTACCATTG -s mr.mrrefChr5 68635 10 + 294540 TCGATACTTT -s simCow_chr6.simCow.chr6 388554 10 - 602619 CTTATGATTG -s simDog_chr6.simDog.chr6 203513 10 + 593897 CTTACCTTTG -s simHuman_chr6.simHuman.chr6 218516 10 + 601863 TTTACAATTA -s simRat_chr6.simRat.chr6 205005 10 + 647215 TCGATATTTT - -a -s simMouse_chr6.simMouse.chr6 214043 4 + 636262 TTTA -s Anc0.Anc0refChr5 35747 4 + 87904 CTTA -s Anc1.Anc1refChr8 50196 4 + 57822 CTTA -s Anc2.Anc2refChr15 31117 4 + 86568 CCTC -s mr.mrrefChr5 68645 4 + 294540 TTTA -s simCow_chr6.simCow.chr6 388564 4 - 602619 CCCC -s simDog_chr6.simDog.chr6 201800 4 + 593897 CCAA -s simDog_chr6.simDog.chr6 203523 4 + 593897 CTTC -s simHuman_chr6.simHuman.chr6 218526 4 + 601863 CTTA -s simRat_chr6.simRat.chr6 205015 4 + 647215 TTTA - -a -s simMouse_chr6.simMouse.chr6 214047 3 + 636262 AGA -s Anc0.Anc0refChr5 35751 3 + 87904 AGA -s Anc1.Anc1refChr8 50200 3 + 57822 AGA -s Anc2.Anc2refChr15 31121 3 + 86568 AGA -s mr.mrrefChr5 68649 3 + 294540 AGA -s simCow_chr6.simCow.chr6 388568 3 - 602619 AGA -s simDog_chr6.simDog.chr6 203527 3 + 593897 ACA -s simHuman_chr6.simHuman.chr6 218530 3 + 601863 AGA -s simRat_chr6.simRat.chr6 205019 3 + 647215 AGA - -a -s simMouse_chr6.simMouse.chr6 214050 7 + 636262 GGGAGCC -s Anc0.Anc0refChr5 35754 7 + 87904 TGCAGCG -s Anc1.Anc1refChr8 50203 7 + 57822 TGCAGCG -s Anc2.Anc2refChr15 31124 7 + 86568 TGCAGCG -s mr.mrrefChr5 68652 7 + 294540 TGCAGCC -s simCow_chr6.simCow.chr6 388571 7 - 602619 TGCAGCG -s simDog_chr6.simDog.chr6 203546 7 + 593897 TACAGCA -s simHuman_chr6.simHuman.chr6 218533 7 + 601863 TGCAGTG -s simRat_chr6.simRat.chr6 205022 7 + 647215 TGCAGCC - -a -s simMouse_chr6.simMouse.chr6 214057 12 + 636262 TACTGATGCTTG -s Anc0.Anc0refChr5 35761 12 + 87904 ATCTGGTGCTTG -s Anc1.Anc1refChr8 50210 12 + 57822 ATCTGGTGCTTG -s Anc2.Anc2refChr15 31131 12 + 86568 ATCTGGTGCTTG -s mr.mrrefChr5 68659 12 + 294540 TACTGATGCTTG -s simCow_chr6.simCow.chr6 388590 12 - 602619 ACTTGGGGCTTG -s simDog_chr6.simDog.chr6 203553 12 + 593897 ATCTGGTGCTTG -s simHuman_chr6.simHuman.chr6 218540 12 + 601863 AGCTGGTGCTTG -s simRat_chr6.simRat.chr6 205029 12 + 647215 CACTGATGCTTG - -a -s simMouse_chr6.simMouse.chr6 214069 22 + 636262 ACCTTGATTACGCCACATGTAT -s Anc0.Anc0refChr5 35795 22 + 87904 GCCCTGATTCTGCCACTTGCAT -s Anc1.Anc1refChr8 50244 22 + 57822 GCCCTGATTCTGCCACTTGCAT -s Anc2.Anc2refChr15 31165 22 + 86568 GCCCTGATTCTGCCACTTGCAT -s mr.mrrefChr5 68671 22 + 294540 ACCTTGATTATGCCACATGTAT -s simCow_chr6.simCow.chr6 388624 22 - 602619 GCCATGATTCCACAACTTACCA -s simDog_chr6.simDog.chr6 203587 22 + 593897 GCCCTGATTATGCCACTTGCAT -s simHuman_chr6.simHuman.chr6 218574 22 + 601863 GCACTGATTCTGCCACTTGCAT -s simRat_chr6.simRat.chr6 205041 22 + 647215 ACCTTGATTGTGCCACATGTAT - -a -s simMouse_chr6.simMouse.chr6 214091 23 + 636262 AAGAATAGGGGCCTGCAGAGTTG -s Anc0.Anc0refChr5 35823 23 + 87904 AAAAATAGGGGCGTGCAGAGTTG -s Anc1.Anc1refChr8 50272 23 + 57822 AAAAATAGGGGCGTGCAGAGTTG -s Anc2.Anc2refChr15 31193 23 + 86568 AAAAATAGGGGTGTGCACAGTTG -s mr.mrrefChr5 68693 23 + 294540 AAAAATAGGGGCCTGCAGAGTTG -s simCow_chr6.simCow.chr6 388652 23 - 602619 AAAAGTAGGGGTGTTCACAGTTG -s simDog_chr6.simDog.chr6 203615 16 + 593897 GAAAATAGGGATGTGT------- -s simHuman_chr6.simHuman.chr6 218602 23 + 601863 AAAAATAGGGGCGTGCAGAGTTA -s simRat_chr6.simRat.chr6 205063 23 + 647215 AAAAATAGGGATTTGCAGAGTTG - -a -s simMouse_chr6.simMouse.chr6 214114 59 + 636262 CATGATGTGTTGATCTTGAAACCTTGTTAAAAATAGCACGGAATAATTCTGGGTATTTA -s Anc0.Anc0refChr5 35847 59 + 87904 CATGATGTGTTGACCTGTAAACTATGATAAGAATAGCCCAGAATAAGTATGTGTATTTA -s Anc1.Anc1refChr8 50296 59 + 57822 CATGATGTGTTGACCTGTAAACTATGATAAGAATAGCCCAGAATAAGTATGTGTATTTA -s Anc2.Anc2refChr15 31217 59 + 86568 CATGATGTGTTGACCTGTAAACTATGATAAGAATAGCCCAGAATAAGGATGTTTACTTG -s mr.mrrefChr5 68716 59 + 294540 CATGATGTGTTGATCTTGAAACCTTGATAAAAATAGCCCGGAATAATTCTGTGTATTTA -s simCow_chr6.simCow.chr6 388676 53 - 602619 CATGACGTGTCAAAGTGTAGACTATGTTAAGAATAGCCCTGAATAAG------TACTTG -s simDog_chr6.simDog.chr6 203631 59 + 593897 CATGATGTGTTGACCTCTAAACTATGACAAGAATAGTCCAGACTAAGGATGTTCACTTG -s simHuman_chr6.simHuman.chr6 218626 59 + 601863 CATGATGTGTTGACTCGTAAACTATGATAAGAATAGCCCAGAATAAGTGTGTGTATTTA -s simRat_chr6.simRat.chr6 205086 59 + 647215 CATGATGTGTTGATCTTGGAACCTTGACAAAAAGAGCCAGGAACAATTCTATGTATTTG - -a -s simMouse_chr6.simMouse.chr6 214173 17 + 636262 AATACACTCATAATAAA -s Anc0.Anc0refChr5 35907 5 + 87904 GAT-------T-----A -s Anc1.Anc1refChr8 50356 5 + 57822 GAT-------T-----A -s Anc2.Anc2refChr15 31277 5 + 86568 GAT-------T-----A -s mr.mrrefChr5 68775 12 + 294540 AATACACTCAT-----A -s simCow_chr6.simCow.chr6 388730 5 - 602619 GAG-------A-----A -s simDog_chr6.simDog.chr6 203691 5 + 593897 GAT-------T-----G -s simHuman_chr6.simHuman.chr6 218686 5 + 601863 GAT-------T-----A -s simRat_chr6.simRat.chr6 205145 12 + 647215 AATACACTCAT-----A - -a -s simMouse_chr6.simMouse.chr6 214190 1 + 636262 A -s Anc0.Anc0refChr5 35912 1 + 87904 A -s Anc1.Anc1refChr8 50361 1 + 57822 A -s Anc2.Anc2refChr15 31282 1 + 86568 A -s mr.mrrefChr5 68787 1 + 294540 A -s simCow_chr6.simCow.chr6 388735 1 - 602619 A -s simDog_chr6.simDog.chr6 203728 1 + 593897 G -s simHuman_chr6.simHuman.chr6 218691 1 + 601863 A -s simRat_chr6.simRat.chr6 205157 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 214191 44 + 636262 GATTATTAGTCAGGCAAGATCTAATAAGATCTAATGGGTCTGGA -s Anc0.Anc0refChr5 35913 34 + 87904 GATTATAAGTCATGCAAGAC----------CACATGGATCTGAA -s Anc1.Anc1refChr8 50362 34 + 57822 GATTATAAGTCATGCAAGAC----------CACATGGATCTGAA -s Anc2.Anc2refChr15 31283 34 + 86568 GACTATAGGTCATGCAAGGC----------CACATGGAACTGAA -s mr.mrrefChr5 68788 44 + 294540 GATTATTAGTCAGGCAAGATCTAATAAGATCTAATGGGTCTGAA -s simCow_chr6.simCow.chr6 388737 33 - 602619 GAGTATTGGT-ATGCAAGGC----------GGTATGGAAATGGA -s simDog_chr6.simDog.chr6 203729 34 + 593897 AACTATAGGTCAGGCAGAGC----------CACATGGAACTGAA -s simHuman_chr6.simHuman.chr6 218692 34 + 601863 GATTATGAATCATGCAAGAC----------CCCATGGATCTCAA -s simRat_chr6.simRat.chr6 205158 44 + 647215 GATTATTATTCAGGCAAGATCTAAGAAAATCTAATGAGTCTGAA - -a -s simMouse_chr6.simMouse.chr6 214235 19 + 636262 CGAAATTGTTTGCCAGTGT -s Anc0.Anc0refChr5 35947 19 + 87904 CCATAGTGTTTGCCAGTGT -s Anc1.Anc1refChr8 50396 19 + 57822 CCATAGTGTTTGCCAGTGT -s Anc2.Anc2refChr15 31317 19 + 86568 CCATTGTGTTTGCCAGTGT -s mr.mrrefChr5 68832 19 + 294540 CGAAATTGTTTGCCAGTGT -s simCow_chr6.simCow.chr6 388780 19 - 602619 CCACGTAGTTTGCCAGTAA -s simDog_chr6.simDog.chr6 203763 19 + 593897 CCATTGTGTTTGCCAGTGT -s simHuman_chr6.simHuman.chr6 218726 19 + 601863 CCATAGTTTTTGCCAGTGT -s simRat_chr6.simRat.chr6 205202 19 + 647215 CAAAATTGTTTACCAGTGT - -a -s simMouse_chr6.simMouse.chr6 214254 13 + 636262 GGGTCTAGCTTTG -s Anc0.Anc0refChr5 35968 13 + 87904 GGAGTTAGCTTGA -s Anc1.Anc1refChr8 50417 13 + 57822 GGAGTTAGCTTGA -s Anc2.Anc2refChr15 31338 13 + 86568 GCAGTTAGCTCGA -s mr.mrrefChr5 68851 13 + 294540 GGGTCTAGCTTTG -s simCow_chr6.simCow.chr6 388801 13 - 602619 GCAGTTAGCTCGA -s simDog_chr6.simDog.chr6 203794 13 + 593897 GCAGTGAGCTCAT -s simHuman_chr6.simHuman.chr6 218747 13 + 601863 GGAGTTAGCTTGA -s simRat_chr6.simRat.chr6 205221 13 + 647215 TGGTCTAGCTCTT - -a -s simMouse_chr6.simMouse.chr6 214267 6 + 636262 TTTTTT -s Anc0.Anc0refChr5 35981 6 + 87904 TCTTCC -s Anc1.Anc1refChr8 50430 6 + 57822 TCTTCC -s Anc2.Anc2refChr15 31351 6 + 86568 TCTTCC -s mr.mrrefChr5 68864 6 + 294540 TTTTTT -s simCow_chr6.simCow.chr6 388819 6 - 602619 TCTTCC -s simDog_chr6.simDog.chr6 203807 6 + 593897 TCTTCC -s simHuman_chr6.simHuman.chr6 218760 6 + 601863 TCTCCA -s simRat_chr6.simRat.chr6 205234 6 + 647215 TTTTTT - -a -s simMouse_chr6.simMouse.chr6 214273 23 + 636262 GGTTTAGTGTGTGCCTAGGATTC -s Anc0.Anc0refChr5 35987 23 + 87904 TTTTGTGTCTGTGCCTGGGATAC -s Anc1.Anc1refChr8 50436 23 + 57822 TTTTGTGTCTGTGCCTGGGATAC -s Anc2.Anc2refChr15 31363 23 + 86568 TTGTGTGCCTATGCCTGGGATAA -s mr.mrrefChr5 68870 23 + 294540 GGTTTAGTGTGTGCCTAGGATTC -s simCow_chr6.simCow.chr6 388831 23 - 602619 ATGTGTGCCAATGCGCGGGATAA -s simDog_chr6.simDog.chr6 203819 23 + 593897 TTGTGTGCCTATGCCTGGGATAA -s simHuman_chr6.simHuman.chr6 218766 23 + 601863 TTTCAGGTTTGTGCCTTAGATAC -s simRat_chr6.simRat.chr6 205240 23 + 647215 GGTTTAGTATGTGCCTAGAATGC - -a -s simMouse_chr6.simMouse.chr6 214296 2 + 636262 TG -s Anc0.Anc0refChr5 36011 2 + 87904 CC -s Anc1.Anc1refChr8 50460 2 + 57822 CC -s Anc2.Anc2refChr15 31387 2 + 86568 CC -s mr.mrrefChr5 68893 2 + 294540 CG -s simCow_chr6.simCow.chr6 388855 2 - 602619 CC -s simDog_chr6.simDog.chr6 203843 2 + 593897 CC -s simHuman_chr6.simHuman.chr6 218790 2 + 601863 CC -s simRat_chr6.simRat.chr6 205263 2 + 647215 CA - -a -s simMouse_chr6.simMouse.chr6 214298 18 + 636262 CTATACACTCCAGAGAGT -s Anc0.Anc0refChr5 36013 18 + 87904 CTATACTTTCGAGAAAGT -s Anc1.Anc1refChr8 50462 18 + 57822 CTATACTTTCGAGAAAGT -s Anc2.Anc2refChr15 31389 18 + 86568 TTCTACTTTGGAGAAAGT -s mr.mrrefChr5 68895 18 + 294540 CTATACACTCCAGAGAGT -s simCow_chr6.simCow.chr6 388857 4 - 602619 --------------AAGT -s simDog_chr6.simDog.chr6 203856 18 + 593897 TTCTACTTTGGAGAAAGT -s simHuman_chr6.simHuman.chr6 218792 18 + 601863 CTATGCTTTCAAGAAAAT -s simRat_chr6.simRat.chr6 205265 18 + 647215 CTATACACTTCAGTGAGT - -a -s simMouse_chr6.simMouse.chr6 214316 37 + 636262 TACTAATTTGTGAAGATTCCAATGTGGTATGCTAGTT -s Anc0.Anc0refChr5 36031 31 + 87904 TCTT-TCTTGTGAATATTCCAA-----TGTGCTAGTC -s Anc1.Anc1refChr8 50480 32 + 57822 TCTTATCTTGTGAATATTCCAA-----TGTGCTAGTC -s Anc2.Anc2refChr15 31407 31 + 86568 TCTT-TCATGTGAATATTCCAA-----TGTGCTAGTC -s mr.mrrefChr5 68913 37 + 294540 TACTAACTTGTGAATATTCCAATGTGGTGTGCTAGTT -s simCow_chr6.simCow.chr6 388862 31 - 602619 TCTT-ACATGTGATTATCCTGA-----TGTGCTAGGC -s simDog_chr6.simDog.chr6 203874 31 + 593897 TCTT-TCAGGTGAATAGTCCAA-----TGTGCTAGTC -s simHuman_chr6.simHuman.chr6 218810 32 + 601863 TCTTATCTTGTGAATATTCCAA-----TGTGCTAGTC -s simRat_chr6.simRat.chr6 205283 37 + 647215 TGCTAACTTGTGAATATTTCAATGTGTAGTGTTAGTT - -a -s simMouse_chr6.simMouse.chr6 214353 57 + 636262 TTTCCATATAATGCGCTGATACTTTACAGAGACATACTACCAGGATTGTCTATTGAT -s Anc0.Anc0refChr5 36063 55 + 87904 TTCCCATATATGAAA--GGTAATTTACAGCCATATGCTATCAGGATCATCTATTGAT -s Anc1.Anc1refChr8 50513 55 + 57822 TTCCCATATATGAAA--GGTAATTTACAGCCATATGCTATCAGGATCATCTATTGAT -s Anc2.Anc2refChr15 31439 55 + 86568 TTCCCATAAGGGAAA--GGTAAATTACAGCCATATGCTGTCAGGATCATATATTGAT -s mr.mrrefChr5 68951 57 + 294540 TTCCCATATATTGCACTGATACTTTACAGAGATATACTATCAGGATTATCTATTGAT -s simCow_chr6.simCow.chr6 388894 55 - 602619 TTCCCACAATGGAAG--GGTAACTTACAGAGATGTGCTGCCGGGATCATATATTGAT -s simDog_chr6.simDog.chr6 203906 54 + 593897 TCTCCATAAGGGAAA--GGTAAATCACAGCCATATGCTGTCAGGATCAT-TATTGAT -s simHuman_chr6.simHuman.chr6 218843 55 + 601863 TTCCCATATATGAAA--AGTAATTTACAGCTATATGCTATCAGGATCATCTATCGAT -s simRat_chr6.simRat.chr6 205321 57 + 647215 TTCCCATGTATTGCACTGACATTTTACAGGGATACACTATCAGGATTATCTATTGAT - -a -s simMouse_chr6.simMouse.chr6 214410 15 + 636262 GATGGTGCAAGTTAT -s Anc0.Anc0refChr5 36118 15 + 87904 TCTCGTCAGCTTTTG -s Anc1.Anc1refChr8 50568 15 + 57822 TCTCGTCAGCTTTTG -s Anc2.Anc2refChr15 31494 15 + 86568 TCTCGTCAGCTTTTG -s mr.mrrefChr5 69008 15 + 294540 GATGGTGCAAGTTAT -s simCow_chr6.simCow.chr6 388949 15 - 602619 TCTGGTGAGGGTTAT -s simDog_chr6.simDog.chr6 203961 15 + 593897 TCTCTTCATCTATTG -s simHuman_chr6.simHuman.chr6 218898 15 + 601863 CCTTGTAAGCATTTG -s simRat_chr6.simRat.chr6 205378 15 + 647215 GATAGTGCAAGATAT - -a -s simMouse_chr6.simMouse.chr6 214425 60 + 636262 CTCTTGCTCTCCTGCATAGAGGGTTTCTTCAGAAAACAGTGGTTCTCAACATTCAGTCTC -s Anc0.Anc0refChr5 36133 59 + 87904 CTCTTGCTCTGCTGCATTGAGGGATGCATCAT-AAACAGTGGTCCTTGACACACAGTCTC -s Anc1.Anc1refChr8 50583 59 + 57822 CTCTTGCTCTGCTGCATTGAGGGATGCATCAT-AAACAGTGGTCCTTGACACACAGTCTC -s Anc2.Anc2refChr15 31509 59 + 86568 CTCTTGCTCTGCTGCATTGAGGGATGCATCAT-AAACAGTGGTCTTTGACACACAGTCTC -s mr.mrrefChr5 69023 60 + 294540 CTCTTGCTCTCCTGCATAGAGGGTTTCTTCAGAAAACAGTGGTTCTCAACATTCAGTCTC -s simCow_chr6.simCow.chr6 388964 57 - 602619 GTCTTGCTCTGGC-CATTCAGCAATGCTTTAT-AAACTG-GGTTTTGGATACACAGCCTC -s simDog_chr6.simDog.chr6 203980 59 + 593897 CTCTTGCCCTCCTGCATTGAGGGCTGCATCAT-AAATAGTGGTCTTTGACACACAGTGTC -s simHuman_chr6.simHuman.chr6 218913 59 + 601863 CTTTTGCTCTGCTGCATTGAGGGATGCCCCAT-AAACAGTGGTACTTGACACATAGTCTC -s simRat_chr6.simRat.chr6 205393 60 + 647215 CTCTTGCTCTTCTGCATAGAGGGTTTCTTCAGAAAACAGTGGTTCTCACCATTCAGTCTC - -a -s simMouse_chr6.simMouse.chr6 214485 8 + 636262 GAATGATG -s Anc0.Anc0refChr5 36200 8 + 87904 GAGTGACT -s Anc1.Anc1refChr8 50650 8 + 57822 GAGTGACT -s Anc2.Anc2refChr15 31576 8 + 86568 GAGTGACT -s mr.mrrefChr5 69091 8 + 294540 GAATGATG -s simCow_chr6.simCow.chr6 389029 8 - 602619 GAGTGATG -s simDog_chr6.simDog.chr6 204047 8 + 593897 GGGTGGCT -s simHuman_chr6.simHuman.chr6 218980 8 + 601863 GAGTGACA -s simRat_chr6.simRat.chr6 205461 8 + 647215 GAATGATG - -a -s simMouse_chr6.simMouse.chr6 214493 10 + 636262 CACAACTATA -s Anc0.Anc0refChr5 36208 10 + 87904 CAGGATTGTA -s Anc1.Anc1refChr8 50658 10 + 57822 CAGGATTGTA -s Anc2.Anc2refChr15 31584 10 + 86568 CAGGATTGTA -s mr.mrrefChr5 69099 10 + 294540 CACAACTATA -s simCow_chr6.simCow.chr6 389042 10 - 602619 CAGGAGTGTA -s simDog_chr6.simDog.chr6 204055 10 + 593897 AAGGTTTTTA -s simHuman_chr6.simHuman.chr6 218988 10 + 601863 CAGGATTGTA -s simRat_chr6.simRat.chr6 205469 9 + 647215 CAAAACTAC- - -a -s simMouse_chr6.simMouse.chr6 214503 93 + 636262 CCTGAGTCCCAGCAGAGTGACAGTCAGTGCAGCAGCAGGAGCAACGGAATACCCTACAATATGGAGCACAATATAGAGAGGTTGATAGGCAAC -s Anc0.Anc0refChr5 36219 66 + 87904 CCTGGGTCCCAACAAAGTAAGAGTCCATGCAGCAGCAGTTGCAGAAGTATACCCCACAGTGT---------------------------CAAC -s Anc1.Anc1refChr8 50669 66 + 57822 CCTGGGTCCCAACAAAGTAAGAGTCCATGCAGCAGCAGTTGCAGAAGTATACCCCACAGTGT---------------------------CAAC -s Anc2.Anc2refChr15 31595 66 + 86568 CCTGGGTCCCAACAAAGGAAGAGTCCATGCAGCAGCAGTTGGAGAACTATACCCCACAGTGT---------------------------GAGT -s mr.mrrefChr5 69109 93 + 294540 CCTGAGTCCCAGCAAAGTGACAGTCAGTGCAGCAGCAGGAGCAACGGAATACCCTACAATATGGAGCACAATATAGAGAGGTTGATAGGCAAC -s simCow_chr6.simCow.chr6 389053 61 - 602619 TTGGAGTCCCAACGAAGGATGAGTCAATGCA-CAGCAGTTGGAGATCTAGACCCCACAGTGT------------------------------- -s simDog_chr6.simDog.chr6 204066 66 + 593897 CCTGGGTCATATCAAAGGAAGAGTACATGCAGCAGCAGTTGGAGAACTATATCCCATAGTGA---------------------------GAGT -s simHuman_chr6.simHuman.chr6 218999 66 + 601863 CCTGGGTCCCAACAAAGTAGGAGTCTATTCAGCAGCAGTTGCACAAGGATACCCCACAGTGT---------------------------CAAC -s simRat_chr6.simRat.chr6 205478 93 + 647215 TCTGAGTCCCGGCAAAGTGACGATCAGTGCAGCAGCAGGAGCAATGGAATACACTACAATATGGAGTACAATATGGAGCGGTTGACAGGCAAC - -a -s simMouse_chr6.simMouse.chr6 214596 4 + 636262 AAAG -s Anc0.Anc0refChr5 36285 4 + 87904 AAAG -s Anc1.Anc1refChr8 50735 4 + 57822 AAAG -s Anc2.Anc2refChr15 31661 4 + 86568 AAAG -s mr.mrrefChr5 69202 4 + 294540 AAAG -s simDog_chr6.simDog.chr6 204138 4 + 593897 AAAG -s simHuman_chr6.simHuman.chr6 219065 3 + 601863 AAA- -s simRat_chr6.simRat.chr6 205571 4 + 647215 AAAG - -a -s simMouse_chr6.simMouse.chr6 214600 5 + 636262 TGCTA -s Anc0.Anc0refChr5 36289 4 + 87904 C-CTA -s Anc1.Anc1refChr8 50739 4 + 57822 C-CTA -s Anc2.Anc2refChr15 31665 4 + 86568 C-CTA -s mr.mrrefChr5 69206 5 + 294540 TGCTA -s simCow_chr6.simCow.chr6 179598 4 - 602619 C-CTA -s simDog_chr6.simDog.chr6 204143 4 + 593897 C-CTA -s simRat_chr6.simRat.chr6 205575 5 + 647215 TGTTA - -a -s simMouse_chr6.simMouse.chr6 214605 22 + 636262 CGGAAAGGTTGGCATAGGGCCT -s Anc0.Anc0refChr5 36293 22 + 87904 TAGGAAAATTGGCATGGGGGCG -s Anc1.Anc1refChr8 50743 22 + 57822 TAGGAAAATTGGCATGGGGGCG -s Anc2.Anc2refChr15 31669 22 + 86568 TATGACAATCAGCCTGGGGGTG -s mr.mrrefChr5 69211 22 + 294540 CGGAAAGGTTGGCATGGGGCCT -s simCow_chr6.simCow.chr6 179607 22 - 602619 TAAGAGAATCAGCTTAGGAGGA -s simDog_chr6.simDog.chr6 204147 22 + 593897 TATGACAATCAGTCTGGGGGTG -s simHuman_chr6.simHuman.chr6 219068 20 + 601863 --GGAAAATTGGCATGGGGGCC -s simRat_chr6.simRat.chr6 205580 22 + 647215 CATAAAGGTTGGCATGGGGCCT - -a -s simMouse_chr6.simMouse.chr6 214627 72 + 636262 GCAATTGAAGGGTAAATTTGCAGATCCAATAGCAAAAAGAGAAGCACGCTAGTAAGAGAAGATAGGGCCAAG -s Anc0.Anc0refChr5 36318 71 + 87904 AAAATTGAAGAGTAAAATCGAAAGTCCAATGGCTAAAAGAGAAGGGGAGTAGCAAAAGAAAAGAGGGCCAA- -s Anc1.Anc1refChr8 50768 71 + 57822 AAAATTGAAGAGTAAAATCGAAAGTCCAATGGCTAAAAGAGAAGGGGAGTAGCAAAAGAAAAGAGGGCCAA- -s Anc2.Anc2refChr15 31694 71 + 86568 AAAATTGAAGAGTAAAATTGAAAGTCCAATGGCTAAGAGAGAAGGGGAGTAGAAAATGAAAAGTGAGTTAA- -s mr.mrrefChr5 69233 72 + 294540 GCAATTGAAGGGTAAAATCGCAGGTCCAATAGCAAAAAGAGAAGCGCGCTAGCAAGAGAAAATAGGGCCAAG -s simCow_chr6.simCow.chr6 179632 54 - 602619 AAAATTGAAAAGCAAGATTGAAGGTCTAATGGCTAAGAGAGAAGGGGACTAGAA------------------ -s simDog_chr6.simDog.chr6 204172 71 + 593897 AAAATTGAAGAATGAAATTGAAAGCCCAACAGCTAAGAGATAAGGGGGGTAGAAAATGAAAAGTGAGTTAA- -s simHuman_chr6.simHuman.chr6 219091 71 + 601863 AAAATTGAAGAGTAAAATCAAATGTCCAATGGCTAAAAGAGAAGGGGATTAGCTAAAGAAAAAAGGGCCAC- -s simRat_chr6.simRat.chr6 205602 71 + 647215 GCAATTGAGGGGTAAAATCGCAGGTCCAATAGCAAAAAGAGAAGTGAG-CGGCAAGAGTAAAGAGGGACAAG - -a -s simMouse_chr6.simMouse.chr6 214699 59 + 636262 ACCTAAATAAAGAAAAGCAATAGTTGAGTATGTCATTGGCATTAGATGAGTGCTCTAGT -s Anc0.Anc0refChr5 36389 59 + 87904 ACCTACATAAAGACAGGCATTAATTGAACACCTTATTGGCATTAGATGAGTACCTCATT -s Anc1.Anc1refChr8 50839 59 + 57822 ACCTACATAAAGACAGGCATTAATTGAACACCTTATTGGCATTAGATGAGTACCTCATT -s Anc2.Anc2refChr15 31765 59 + 86568 ACCTACCTAAAGGCAGGCATTGAATGAACACCTTATTGGCATTAGATGAGTACCTCATT -s mr.mrrefChr5 69305 59 + 294540 ACCTACATAAAGAAAAGCATTAATTGAGTATGTCATTGGCATTAGATGAGTGCTCTAGT -s simCow_chr6.simCow.chr6 179686 58 - 602619 GCCTACCTGAAGG-AGAGATTGAATGAACAACTAATTGGCATTAGATGAGTACGTTATT -s simDog_chr6.simDog.chr6 204244 59 + 593897 ACCTATCTAAAGGCAGGCACTGAATGAACACCTTATTGGCATTAGACGAATACCTCATA -s simHuman_chr6.simHuman.chr6 219162 59 + 601863 ACCTACATAAAGACAGGCATTAATTGAACACCTTATTGGCAGTGGATGAGAATCTCACT -s simRat_chr6.simRat.chr6 205673 52 + 647215 ACCTACATAACGGAAAGCATTGATTGGGTATAACA-------TAGGTAAGTGCTCTAGT - -a -s simMouse_chr6.simMouse.chr6 214758 48 + 636262 AACCCCTCTCAAGGAGAGTCTCTACCCATATCATGGGAGGGTTGGTAA -s Anc0.Anc0refChr5 36449 48 + 87904 AACACCTCCCAGGGAGAGTTTTTGCTGCTATCCTGGAAGAGATGTGAA -s Anc1.Anc1refChr8 50899 48 + 57822 AACACCTCCCAGGGAGAGTTTTTGCTGCTATCCTGGAAGAGATGTGAA -s Anc2.Anc2refChr15 31825 48 + 86568 GACACCTCCCAAAGAGAGTTTTTGCTGCCATCTTGGAAGAGATGTGAA -s mr.mrrefChr5 69365 48 + 294540 AACCCCTCTCAGGGAGAGTCTTTACCCATATCCTGGGAGGGTTGGGAA -s simCow_chr6.simCow.chr6 179745 48 - 602619 GACACCTCCCACAGAGAGTTTTTGCTCCCATCGTAGAAGAGGTGCGAA -s simDog_chr6.simDog.chr6 204304 48 + 593897 GACACCTCTCAAAGAGAGTTTTGACTGCCATCTTGTAAGAGATGTGAT -s simHuman_chr6.simHuman.chr6 219222 48 + 601863 AACACCTCCCAGGTAGAGTTTTTGCTTCTAGCCTGGAAGAGATGTGAA -s simRat_chr6.simRat.chr6 205726 48 + 647215 AACCCCTCTCAGAGAGAGTCTTTACCCTTATTCTGCGAGGGTTGGGAA - -a -s simMouse_chr6.simMouse.chr6 214806 28 + 636262 TGTTGGTTTAAACAGTAAAATGGACATA -s Anc0.Anc0refChr5 36499 28 + 87904 TTATGTTTAATACTGCAGAATGGGGATA -s Anc1.Anc1refChr8 50949 28 + 57822 TTATGTTTAATACTGCAGAATGGGGATA -s Anc2.Anc2refChr15 31875 28 + 86568 TTATGTTTAATACTACAGAATGGGGACA -s mr.mrrefChr5 69413 28 + 294540 TGATGGTTTAAACAGTAAAATGGACATA -s simCow_chr6.simCow.chr6 179795 18 - 602619 TTATGTTTAATACTACA----------A -s simDog_chr6.simDog.chr6 204354 27 + 593897 TTATGTTTAATACTACAGAATGGGGAC- -s simHuman_chr6.simHuman.chr6 219272 28 + 601863 TTATGCTTAATACTGCTGAATGGGAATA -s simRat_chr6.simRat.chr6 205774 28 + 647215 TGATGGTTTAAATGGTAAAATGGACATA - -a -s simMouse_chr6.simMouse.chr6 214834 1 + 636262 T -s Anc0.Anc0refChr5 36527 1 + 87904 T -s Anc1.Anc1refChr8 50977 1 + 57822 T -s Anc2.Anc2refChr15 31903 1 + 86568 C -s mr.mrrefChr5 69441 1 + 294540 T -s simCow_chr6.simCow.chr6 179813 1 - 602619 C -s simHuman_chr6.simHuman.chr6 219321 1 + 601863 T -s simRat_chr6.simRat.chr6 205802 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 214835 70 + 636262 AAGTATTATATGTGATGGTTGCAGAAACACGAGTAAGCAGATCAGGTTGGGAGAGAAGCTAATCAAATTT -s Anc0.Anc0refChr5 36528 66 + 87904 AAGTATCATATGTGATCATTATGAAAACTCCAGGCAACA-ATCAGTTTG---GAAGAATTTTTCAAATCT -s Anc1.Anc1refChr8 50978 67 + 57822 AAGTATCATATGTGATCATTATGAAAACTCCAGGCAACATATCAGTTTG---GAAGAATTTTTCAAATCT -s Anc2.Anc2refChr15 31910 66 + 86568 AAGTATCATATATGAGCATTAATAAAAATCCAGGCCACA-ATCAGTTTG---GAAGAATTTTTCAAATCT -s mr.mrrefChr5 69442 70 + 294540 AAGTATTATATGTGATGGTTGTGGAAACACCAGTAAGCATATCAGGTTGGGAGAAGAATTTATCAAATCT -s simCow_chr6.simCow.chr6 179820 65 - 602619 AAGTATCATATATGACAGCAACTAAAAGACCAGGCCTC--ATCAGTTTG---GAAGAATATTTCAAATAT -s simDog_chr6.simDog.chr6 204381 54 + 593897 ------------TGGGCATTAATGAAAATCAAGCCCACA-ATCAGTTTG---GAAGAATTTTTCGAATCT -s simHuman_chr6.simHuman.chr6 219322 67 + 601863 AAGTATCATATGTGATCATTATGATAACGCCAGGCAACATATGAGTTTG---AAAGAATTTTTCAAATCT -s simRat_chr6.simRat.chr6 205803 69 + 647215 AGCTATTATATGTGAT-GCTGTGGAAACACCAATATGCATATCAGGTTGGGAGGAGAATTTATCAAATCT - -a -s simMouse_chr6.simMouse.chr6 214905 8 + 636262 TGTATGCC -s Anc0.Anc0refChr5 36594 7 + 87904 TGCAT-TC -s Anc1.Anc1refChr8 51045 7 + 57822 TGCAT-TC -s Anc2.Anc2refChr15 31977 7 + 86568 TGCAT-TC -s mr.mrrefChr5 69512 8 + 294540 TGTATGCC -s simCow_chr6.simCow.chr6 179886 7 - 602619 TGCAT-AC -s simDog_chr6.simDog.chr6 204436 7 + 593897 CGCAT-TC -s simHuman_chr6.simHuman.chr6 219389 7 + 601863 TGCAT-TG -s simRat_chr6.simRat.chr6 205872 8 + 647215 TGTGTGCC - -a -s simMouse_chr6.simMouse.chr6 214913 43 + 636262 CATTGGTTGAGAGATGGAATGCCCACAATGCTCTGCTAGGGAC -s Anc0.Anc0refChr5 36601 43 + 87904 CATTGGTTGAGAGATGAAACAGGCACAATGTTCTGCCAGAGAG -s Anc1.Anc1refChr8 51052 43 + 57822 CATTGGTTGAGAGATGAAACAGGCACAATGTTCTGCCAGAGAG -s Anc2.Anc2refChr15 31984 43 + 86568 CCTTAGTTGAGAGATGAAACAGGCACAATGTTCTGCCACAATG -s mr.mrrefChr5 69520 43 + 294540 CATTGGTTGAGAGATGGAATGCCCACAATGCTCTGCTAGAGAC -s simCow_chr6.simCow.chr6 179893 38 - 602619 CCATTGTTGATAGCTGAAATGGGCACAATGTTCTGCCA----- -s simDog_chr6.simDog.chr6 204444 43 + 593897 CCTTAGCTGAGAGATGAAACAGGCTCAATGTACAGGCCCAATG -s simHuman_chr6.simHuman.chr6 219396 43 + 601863 CATTGATTGAGAGATGAAACAGACATAATGTTCTGCCAGAGAG -s simRat_chr6.simRat.chr6 205880 43 + 647215 CTGTGGTTGAGAGGTGGACTGTTCACAATGCTCTGCTAGAGAC - -a -s simMouse_chr6.simMouse.chr6 214956 17 + 636262 ATACAACATACTCTCTA -s Anc0.Anc0refChr5 36651 17 + 87904 TTGAAACAAACCCCCTA -s Anc1.Anc1refChr8 51102 17 + 57822 TTGAAACAAACCCCCTA -s Anc2.Anc2refChr15 32034 17 + 86568 TTAAAACAAACCCCCTA -s mr.mrrefChr5 69563 17 + 294540 TTGCAACATACTCTCTA -s simCow_chr6.simCow.chr6 179936 17 - 602619 TTAAAACAACTCCTCTA -s simDog_chr6.simDog.chr6 204500 17 + 593897 TTAAAGCAAACCCCCTA -s simHuman_chr6.simHuman.chr6 219446 17 + 601863 TTGAAACAAACCCCCTA -s simRat_chr6.simRat.chr6 205923 17 + 647215 TTGCAACATACTCACTA - -a -s simMouse_chr6.simMouse.chr6 214973 47 + 636262 TCACGTGTACCAATGGCCCTGAAATCTTAGGAATGAAAACTTTTGTT -s Anc0.Anc0refChr5 36668 47 + 87904 TCATGCACAGCAATGGTCTTGAGACCTTATGATTGCAAACTTTAGTC -s Anc1.Anc1refChr8 51119 47 + 57822 TCATGCACAGCAATGGTCTTGAGACCTTATGATTGCAAACTTTAGTC -s Anc2.Anc2refChr15 32051 47 + 86568 TCATGCACAGCAATGGTCTTGAGACCTTATCATTGCAAACTTTAGTC -s mr.mrrefChr5 69580 47 + 294540 TCATGTGTACCAATGGCCCTGAAATCTTAGGAATGAAAACTTTTGTT -s simCow_chr6.simCow.chr6 179953 45 - 602619 TC--GCCTAGCAATGGTCTTGAGACCTTATAATTGCAAGCTTTAGTC -s simDog_chr6.simDog.chr6 204517 47 + 593897 TCATGCACAGCAACAGCCTTTAGACCTTAGCATTGTAAACTCTAGTC -s simHuman_chr6.simHuman.chr6 219464 47 + 601863 GCTTGCAGAGTAATGTTCTTGAGACCTTATGGTTGCAAACTTTAGTC -s simRat_chr6.simRat.chr6 205940 47 + 647215 TCATGTGTACCAATGGCCCAAAAATCTTAGGAATAGAAACTTTTGTT - -a -s simMouse_chr6.simMouse.chr6 215020 5 + 636262 TGCCT -s Anc0.Anc0refChr5 36718 5 + 87904 TGACT -s Anc1.Anc1refChr8 51169 5 + 57822 TGACT -s Anc2.Anc2refChr15 32101 5 + 86568 AGACA -s mr.mrrefChr5 69627 5 + 294540 TGCCT -s simCow_chr6.simCow.chr6 180001 5 - 602619 AGACA -s simDog_chr6.simDog.chr6 204567 5 + 593897 AAGCA -s simHuman_chr6.simHuman.chr6 219514 5 + 601863 TGATT -s simRat_chr6.simRat.chr6 205987 5 + 647215 TGCCT - -a -s simMouse_chr6.simMouse.chr6 215025 47 + 636262 GTATCCCATGAGCTAATCAGCCCATAACCCATGCTGTCAAATAAGGT -s Anc0.Anc0refChr5 36723 39 + 87904 CTATCACAAGAACTAAT-------TAACCAATTCAGCCAA-CCAGGT -s Anc1.Anc1refChr8 51174 39 + 57822 CTATCACAAGAACTAAT-------TAACCAATTCAGCCAA-CCAGGT -s Anc2.Anc2refChr15 32106 39 + 86568 CTATCACAAGAACTAAT-------TAACCAACTCAGCCAA-CCAGGT -s mr.mrrefChr5 69632 47 + 294540 GTATCACATGAGCTAATCAGCCCATAACCCATGCTGTCAAATAAGAT -s simCow_chr6.simCow.chr6 180006 39 - 602619 GTATCCAAAGACTTAAT-------CAACCAACTCAGCCAA-CCAGGT -s simDog_chr6.simDog.chr6 204572 39 + 593897 CTGTCACGAGAACTAAT-------TATCCAGCTTGGCAAA-CTAGGT -s simHuman_chr6.simHuman.chr6 219519 39 + 601863 CTATCATAAGAACTGAT-------GAACCAATTCAGCCAA-CCAGGA -s simRat_chr6.simRat.chr6 206042 47 + 647215 TTAACACATGAGATAATCACCCCATAAACTCTGCTGTTAAATTAGAT - -a -s simMouse_chr6.simMouse.chr6 215072 27 + 636262 AGAGAAACTAAACAGCAACGAAGTCAT -s Anc0.Anc0refChr5 36762 27 + 87904 AGAGAAACTAAATAGGTACAAAGTAGT -s Anc1.Anc1refChr8 51213 27 + 57822 AGAGAAACTAAATAGGTACAAAGTAGT -s Anc2.Anc2refChr15 32145 27 + 86568 AGAGAAACTTAATTGGTACAAAGTAGT -s mr.mrrefChr5 69679 27 + 294540 AGAGAAACTAAACAGCAACAAAGTCGT -s simCow_chr6.simCow.chr6 180045 27 - 602619 AGAGAAGCTGAATGGGTACAAAGTAAT -s simDog_chr6.simDog.chr6 204611 27 + 593897 AGAAAAACTTAATTGGGGCAAAGTAGC -s simHuman_chr6.simHuman.chr6 219560 27 + 601863 AGAGGAACTAGATAGGTATAAAGTAGT -s simRat_chr6.simRat.chr6 206089 27 + 647215 AGAGAAACTAAACAGCAACAAAGTGGT - -a -s simMouse_chr6.simMouse.chr6 215099 4 + 636262 TTTG -s Anc0.Anc0refChr5 36790 4 + 87904 TTTG -s Anc1.Anc1refChr8 51241 4 + 57822 TTTG -s Anc2.Anc2refChr15 32173 4 + 86568 TATG -s mr.mrrefChr5 69706 4 + 294540 TTTG -s simCow_chr6.simCow.chr6 180073 4 - 602619 TCCA -s simDog_chr6.simDog.chr6 204639 4 + 593897 TATG -s simHuman_chr6.simHuman.chr6 219588 4 + 601863 TTTG -s simRat_chr6.simRat.chr6 206116 4 + 647215 TTTG - -a -s simMouse_chr6.simMouse.chr6 215103 39 + 636262 CTCTCCAGAATTGGTGCAAAAAAAATTGAAATCCTTGTA -s Anc0.Anc0refChr5 36797 29 + 87904 TTTTCCAGAATTGGTACCACAATGACTGA---------- -s Anc1.Anc1refChr8 51248 29 + 57822 TTTTCCAGAATTGGTACCACAATGACTGA---------- -s Anc2.Anc2refChr15 32180 29 + 86568 TTTTCCAGAATTGGTACCACGATGACTAA---------- -s mr.mrrefChr5 69710 39 + 294540 CTTTCCAGAATTGGTACAAAAAAAATTGAAGTCCTTGTA -s simCow_chr6.simCow.chr6 180080 29 - 602619 TCTTCCAGAATTGGTATCACGATGACTAA---------- -s simDog_chr6.simDog.chr6 204645 20 + 593897 TTTCCCATAATTGATACCAT------------------- -s simHuman_chr6.simHuman.chr6 219595 29 + 601863 TTTTCCAGGACTGGTACTGCAATGACTGA---------- -s simRat_chr6.simRat.chr6 206120 39 + 647215 CTTACCAGAATTGGTACAAAGACAATTGAAGTCCTTATA - -a -s simMouse_chr6.simMouse.chr6 215142 55 + 636262 TAAGCAGGCCTTTAAGGCGAGTGTAGCTGGTATGTTACAATTTGGTGTGATAAGT -s Anc0.Anc0refChr5 36826 33 + 87904 -------------------AGTGTAGTTGGCATATTACAATC---TGCAGTAAGT -s Anc1.Anc1refChr8 51277 33 + 57822 -------------------AGTGTAGTTGGCATATTACAATC---TGCAGTAAGT -s Anc2.Anc2refChr15 32209 33 + 86568 -------------------AGTGTAGTTGGCATATCAAAATC---TGCAGTCAGT -s mr.mrrefChr5 69749 54 + 294540 TAAGCAGGCCTTTAAGGCGAGTGTAGCTGGCATGTTACAATTT-GTGTAATAAGT -s simCow_chr6.simCow.chr6 180109 33 - 602619 -------------------AGTGTAGTGGGCATACCAAAATC---TGCAGTCAGT -s simDog_chr6.simDog.chr6 204665 33 + 593897 -------------------AGTGTAGTTAACATATCAAAATG---TGCAGTCAGT -s simHuman_chr6.simHuman.chr6 219624 33 + 601863 -------------------AGTGTAGTTGGCATATTACCATC---TGCAGTAAGT -s simRat_chr6.simRat.chr6 206168 54 + 647215 TAAGCAGGCTTTAATGGGGAATGTAGATGGCGTGTTACAATTT-ATGTATCAAGT - -a -s simMouse_chr6.simMouse.chr6 215197 34 + 636262 GAATCAGGTTTTGCTACAAGACTGGCTAATTCTC -s Anc0.Anc0refChr5 36862 29 + 87904 GAATTA-GCTTAGGTGCAAGGCTAG----TTCTC -s Anc1.Anc1refChr8 51313 29 + 57822 GAATTA-GCTTAGGTGCAAGGCTAG----TTCTC -s Anc2.Anc2refChr15 32245 29 + 86568 GAATTA-GCTTAGGTGCGAGGCTAA----TTCTC -s mr.mrrefChr5 69803 33 + 294540 GAATCA-GTTTTGCTACAAGGCTGGCTAATTCTC -s simCow_chr6.simCow.chr6 180145 28 - 602619 GAATTA-GCTTAGGTGC-ATGCTAA----TTCTC -s simDog_chr6.simDog.chr6 204701 29 + 593897 GAATTG-GCTTAGGTGCGAGACTAA----TTCAC -s simHuman_chr6.simHuman.chr6 219660 29 + 601863 GGAGTA-GCTTAGGTGCAAGGCTAG----TTCTT -s simRat_chr6.simRat.chr6 206222 33 + 647215 GAATCA-GTTTTGCTACAAGGCTGGCTAATTCTC - -a -s simMouse_chr6.simMouse.chr6 215231 32 + 636262 ATCTAGCCCCATTTGGGACGCTTATTAGAGCC -s Anc0.Anc0refChr5 36891 23 + 87904 ATTCATCCCCATTTGGGA---TTTTT------ -s Anc1.Anc1refChr8 51342 23 + 57822 ATTCATCCCCATTTGGGA---TTTTT------ -s Anc2.Anc2refChr15 32274 23 + 86568 ATTCACCCCCATTTGGGA---TTTTT------ -s mr.mrrefChr5 69836 32 + 294540 ATTTATCCCCATTTGGGACGCTTATTAGAGCC -s simCow_chr6.simCow.chr6 180174 23 - 602619 ATTCACCACCATGTTGGA---CTTTT------ -s simDog_chr6.simDog.chr6 204730 23 + 593897 ATTCGCCCCCATTTGGGA---TTTTT------ -s simHuman_chr6.simHuman.chr6 219689 23 + 601863 ATTCATCCCAATTTGGGA---TTTTT------ -s simRat_chr6.simRat.chr6 206255 32 + 647215 TGTTATCCCCATTTGAGACGCTTATTAGAGCC - -a -s simMouse_chr6.simMouse.chr6 215263 34 + 636262 GTCCTTTCTAGTCCTTACTTGCCTCTAGTGCCAT -s Anc0.Anc0refChr5 36920 34 + 87904 ATTGTTTCTAGTCCTTACTTGCCTCTATTGCCAC -s Anc1.Anc1refChr8 51371 34 + 57822 ATTGTTTCTAGTCCTTACTTGCCTCTATTGCCAC -s Anc2.Anc2refChr15 32303 34 + 86568 ATTGTTTCTAGTCCTTACTTGCCTCTATCACCAC -s mr.mrrefChr5 69868 34 + 294540 ATTGTTTCTAGTCCTTACTTGCCTCTAGTGCCAC -s simCow_chr6.simCow.chr6 180203 34 - 602619 ATTGTTTCTCGTCCTTACTTGCCTGTGTCACCAC -s simDog_chr6.simDog.chr6 204759 33 + 593897 ATTG-TTCTAGTCCTTACTTGCCTCTATCACCAC -s simHuman_chr6.simHuman.chr6 219718 34 + 601863 ATTGTTTCTAGTCCTTACCTGCCTATATTGTCAC -s simHuman_chr6.simHuman.chr6 294055 34 + 601863 ATTGATCCTAGTCCTTACCAGCCTCTGTTTCCAC -s simRat_chr6.simRat.chr6 206287 34 + 647215 ATTGTTTCCAGTCCTTACTTGCCTCTAGTGCCAC - -a -s simMouse_chr6.simMouse.chr6 215297 38 + 636262 TTTGATAATGGTTGCAGGTATGAGTATCTTGAGCTGTT -s Anc0.Anc0refChr5 36954 25 + 87904 TCTTGTGAGGGTTGCAAGTATTTGT------------- -s Anc1.Anc1refChr8 51405 38 + 57822 TCTTGTGAGGGTTGCAAGTATTTGTGTCTTGCGTTGTT -s Anc2.Anc2refChr15 32337 25 + 86568 TCTTGTGAGGGTTGCAAGTATTTGT------------- -s mr.mrrefChr5 69902 38 + 294540 TTTGATAAGGGTTGCAAGTATGAGTATCTTGAGTTGTT -s simCow_chr6.simCow.chr6 180237 25 - 602619 TCTTGTGAGGGTACGAAGTAAGTGT------------- -s simDog_chr6.simDog.chr6 204792 25 + 593897 TCATGTGAGGGTTGCAAGTATTTTT------------- -s simHuman_chr6.simHuman.chr6 219752 38 + 601863 TCTTGTGAGGGTTGCAAGTATTTGTGTCTTGCGTTATT -s simHuman_chr6.simHuman.chr6 294089 38 + 601863 TCTTATGAGGGTTGCCACTACTTGTGTCTTGTGTTGCT -s simRat_chr6.simRat.chr6 206322 38 + 647215 GTTGATAAGGGACGCAAGTATGAGTATCTTAAGTTGCT - -a -s simMouse_chr6.simMouse.chr6 215335 33 + 636262 GTGAAGTCTGTTGTATGATGGTTATCCTTTAGA -s Anc1.Anc1refChr8 51443 11 + 57822 GT-ACGTCGGCC--------------------- -s mr.mrrefChr5 69940 32 + 294540 GTGAAGTCTGTTGTATGATGGTTATCC-TTAGA -s simHuman_chr6.simHuman.chr6 294127 11 + 601863 GT-ACGTCGGCC--------------------- -s simRat_chr6.simRat.chr6 206360 32 + 647215 GTGCAATCTGGTGTATGATGGTTCGCC-TTATA - -a -s simMouse_chr6.simMouse.chr6 215368 41 + 636262 TATATCTTGGGCTGCTGTATAACCTGGTGTAGGATGGCTAG -s Anc0.Anc0refChr5 36979 38 + 87904 ---TTCTTGCATTGCTGTATAACCTGGTGTATGATGGCCTG -s Anc1.Anc1refChr8 51454 41 + 57822 TGTTTCTTGCATTGCTGTATAACCTGGTGTATGATGGCCTG -s Anc2.Anc2refChr15 32362 38 + 86568 ---TTCTTGCATTGCTATATAACCTGGTGTATGATGGCCTG -s mr.mrrefChr5 69972 41 + 294540 TGTATCTTGGGCTGCTGTATAACCTGGTGTAGGATGGCCAG -s simCow_chr6.simCow.chr6 180262 38 - 602619 ---TTCTTGCATTGCTATATAACCTGGTGTATGATAGCTTG -s simDog_chr6.simDog.chr6 204817 38 + 593897 ---ATATTGCATAACTATATAACCTGGTATATGATGATCTG -s simHuman_chr6.simHuman.chr6 219790 41 + 601863 TGTTTCTTGCATTGCTGTATTACCTGGTGTATGATGGCCTG -s simHuman_chr6.simHuman.chr6 294138 7 + 601863 ----------------------------------TGACTAG -s simRat_chr6.simRat.chr6 206392 41 + 647215 TGTATCTTGGGCGGCTGTATAACCTGCTGTAGGATGGTCAG - -a -s simMouse_chr6.simMouse.chr6 215409 19 + 636262 CCTCAGATGCAAAAACCCA -s Anc0.Anc0refChr5 37022 19 + 87904 CATCAAATGTAAAAACAAA -s Anc1.Anc1refChr8 51500 19 + 57822 CATCAAATGTAAAAACAAA -s Anc2.Anc2refChr15 32413 19 + 86568 CATCAAATGTAAAAACAAA -s mr.mrrefChr5 70013 19 + 294540 CCTCAAATGCAAAAACCCA -s simCow_chr6.simCow.chr6 180314 19 - 602619 CATCAGGTGGAAAGGCAAA -s simDog_chr6.simDog.chr6 204872 19 + 593897 CATCGAATGTAAAAACTTA -s simHuman_chr6.simHuman.chr6 219836 19 + 601863 CATCAAATGTTAAAACAAA -s simHuman_chr6.simHuman.chr6 294145 19 + 601863 CATCTGGTGTAAAGACACA -s simRat_chr6.simRat.chr6 206433 14 + 647215 -CTCTAATGC----ACCCG - -a -s simMouse_chr6.simMouse.chr6 215428 2 + 636262 AT -s Anc0.Anc0refChr5 37042 2 + 87904 AT -s Anc1.Anc1refChr8 51520 2 + 57822 AT -s Anc2.Anc2refChr15 32433 2 + 86568 AT -s mr.mrrefChr5 70032 2 + 294540 AT -s simCow_chr6.simCow.chr6 180334 2 - 602619 AT -s simDog_chr6.simDog.chr6 204892 2 + 593897 CC -s simHuman_chr6.simHuman.chr6 219856 2 + 601863 AT -s simHuman_chr6.simHuman.chr6 294165 2 + 601863 AT -s simRat_chr6.simRat.chr6 206447 2 + 647215 AT - -a -s simMouse_chr6.simMouse.chr6 215430 2 + 636262 TC -s Anc0.Anc0refChr5 37044 2 + 87904 TC -s Anc1.Anc1refChr8 51522 2 + 57822 TC -s Anc2.Anc2refChr15 32435 2 + 86568 TC -s mr.mrrefChr5 70034 2 + 294540 TC -s simCow_chr6.simCow.chr6 180338 2 - 602619 TC -s simDog_chr6.simDog.chr6 204894 2 + 593897 TC -s simHuman_chr6.simHuman.chr6 219858 2 + 601863 TC -s simHuman_chr6.simHuman.chr6 294167 2 + 601863 TC -s simRat_chr6.simRat.chr6 206449 2 + 647215 TC - -a -s simMouse_chr6.simMouse.chr6 215432 18 + 636262 TCATCTAAAATTAGTGGT -s Anc0.Anc0refChr5 37046 13 + 87904 TTA-----AATTAGTGTT -s Anc1.Anc1refChr8 51524 13 + 57822 TTA-----AATTAGTGTT -s Anc2.Anc2refChr15 32440 13 + 86568 TTA-----AATTAGTGTT -s mr.mrrefChr5 70036 16 + 294540 TCATCT--AATTAGTGGT -s simCow_chr6.simCow.chr6 180343 13 - 602619 TTA-----AATTAGAGTT -s simDog_chr6.simDog.chr6 204899 13 + 593897 TTA-----AATTAGTGTT -s simHuman_chr6.simHuman.chr6 219860 13 + 601863 TTA-----AATTAGTGTT -s simHuman_chr6.simHuman.chr6 294169 13 + 601863 TCA-----AATTAGTGTT -s simRat_chr6.simRat.chr6 206451 16 + 647215 TCATCT--AATTACTGGT - -a -s simMouse_chr6.simMouse.chr6 215450 51 + 636262 GTTTGTGGACAATCATGGAACATACATGTTCTAAATCTATGTTACCAGCAG -s Anc0.Anc0refChr5 37059 51 + 87904 GTTGGTGAAGGTCAACGGACTTTACATAGTCTAAATCTATGTTATAGGCAG -s Anc1.Anc1refChr8 51537 51 + 57822 GTTGGTGAAGGTCAACGGACTTTACATAGTCTAAATCTATGTTATAGGCAG -s Anc2.Anc2refChr15 32453 51 + 86568 GTTGGTGAAGGTCAACAGACTTTACACAGTCTAAAGCCAAATTATAGACAG -s mr.mrrefChr5 70052 51 + 294540 GTTTGTGGAGGTTCACGGAACATACATATTCTAAATCTATGTTACCAGCAG -s simCow_chr6.simCow.chr6 180400 51 - 602619 GTTGGTGAAACTTCACAGATTTCACACAGTTTAGAGCCAAATTATAGACAG -s simDog_chr6.simDog.chr6 204912 40 + 593897 GCTGGTAGAGGTCAACAGACTTTACACAGTCTGAGGC-----------CAG -s simHuman_chr6.simHuman.chr6 219873 51 + 601863 GTTGGTGAAGGTCTACGGACGTTCCATACTCTAAATCTATGTTGTAGGCAG -s simHuman_chr6.simHuman.chr6 294182 10 + 601863 TGTTGGAACT----------------------------------------- -s simRat_chr6.simRat.chr6 206467 51 + 647215 GTTTGTGCAGGTTCACGGAATATACATATTCTAAATTTATGTTACCAGGAG - -a -s simMouse_chr6.simMouse.chr6 215501 47 + 636262 TGAGTCATCAATATAGGGTCTAGAACGGCATGTCTGATCTGTTCTGA -s Anc0.Anc0refChr5 37111 47 + 87904 TAAGTCTTCTATAGAGGGTATGGAAGGGCATGTCTGATCTGTTCTGA -s Anc1.Anc1refChr8 51589 47 + 57822 TAAGTCTTCTATAGAGGGTATGGAAGGGCATGTCTGATCTGTTCTGA -s Anc2.Anc2refChr15 32505 47 + 86568 CAAGTCTTCTGTAGAGGGTATGGAAAGGCATGTCTGATCTGTTCTGA -s mr.mrrefChr5 70103 47 + 294540 TGAGTCATCAATATAGGGTCTAGAAGGGCATGTCTGATCTGTTCTGA -s simCow_chr6.simCow.chr6 180452 45 - 602619 CCTGTTT--TGTAGAGGGCATGAAAAAGCATGTCTGTTCTATCCTGA -s simDog_chr6.simDog.chr6 204953 47 + 593897 CAAGTCTTCTGCACAGGGTATGGAGAGGCACGTCTGATCTGTTCTGA -s simHuman_chr6.simHuman.chr6 219925 47 + 601863 TAAGTCTTCTATGGAAGGTGTGGAAGTACATGTCTGATCAGTTCTAA -s simRat_chr6.simRat.chr6 206518 47 + 647215 TGAGTCATCAATACAGGGTCCAGAAGGGCATGTCTGATCTGTTCTCA - -a -s simMouse_chr6.simMouse.chr6 215548 18 + 636262 GTAAACTGACTTTTATAA -s Anc0.Anc0refChr5 37158 18 + 87904 GCAAAATGACTTTTTTAT -s Anc1.Anc1refChr8 51636 18 + 57822 GCAAAATGACTTTTTTAT -s Anc2.Anc2refChr15 32553 18 + 86568 GCAAAATGACTTTTTTAT -s mr.mrrefChr5 70150 18 + 294540 GTAAACTGACTTTTATAA -s simCow_chr6.simCow.chr6 180498 18 - 602619 GCAAGATGTCTTTTTCAC -s simDog_chr6.simDog.chr6 205001 18 + 593897 GCAGAATGACTTTTTTAT -s simHuman_chr6.simHuman.chr6 219972 18 + 601863 GCAAAATGACTCTCTAAG -s simRat_chr6.simRat.chr6 206565 18 + 647215 GTAAATTGACTTTTATAA - -a -s simMouse_chr6.simMouse.chr6 215566 22 + 636262 TTCCTTTCATAGCAGTCAGTTG -s Anc0.Anc0refChr5 37176 22 + 87904 TTCCTTTGCTAGTTGTCAGATG -s Anc1.Anc1refChr8 51654 22 + 57822 TTCCTTTGCTAGTTGTCAGATG -s Anc2.Anc2refChr15 32571 22 + 86568 TTCCTTTGCTAGTTGTCAGATG -s mr.mrrefChr5 70168 22 + 294540 TTCCTTTCATAGCTGTCAGATG -s simCow_chr6.simCow.chr6 180516 22 - 602619 TTCCTTTGCTAGTTGTTAGATG -s simDog_chr6.simDog.chr6 205019 22 + 593897 TTCCTTTTCTCGTTGTCAAATT -s simHuman_chr6.simHuman.chr6 219990 22 + 601863 TCCCTTTGCTAGTTGTCAGATG -s simRat_chr6.simRat.chr6 206584 22 + 647215 TTTCTTTCATAGCTGTCAGATG - -a -s simMouse_chr6.simMouse.chr6 215588 19 + 636262 GTCATAGAAGCCAACCTAC -s Anc0.Anc0refChr5 37198 19 + 87904 TTCACAGAATCCAACCTTC -s Anc1.Anc1refChr8 51676 19 + 57822 TTCACAGAATCCAACCTTC -s Anc2.Anc2refChr15 32593 19 + 86568 TTCACAGATTCCAACCTTC -s mr.mrrefChr5 70190 19 + 294540 GTCATAGAAGCCAACCTAC -s simCow_chr6.simCow.chr6 180538 19 - 602619 TTCACAGATGCCAACTTTA -s simDog_chr6.simDog.chr6 205042 19 + 593897 CTCTCAGATTCCAACCTCC -s simHuman_chr6.simHuman.chr6 220012 19 + 601863 TTCACAGAATCCAACCTTC -s simRat_chr6.simRat.chr6 206606 19 + 647215 GTCATAGAAGCCAACCTAC - -a -s simMouse_chr6.simMouse.chr6 215607 6 + 636262 TCTAAC -s Anc0.Anc0refChr5 37217 6 + 87904 TCTAAA -s Anc1.Anc1refChr8 51695 6 + 57822 TCTAAA -s Anc2.Anc2refChr15 32612 6 + 86568 TGTAAA -s mr.mrrefChr5 70209 6 + 294540 TCTAAA -s simCow_chr6.simCow.chr6 180557 6 - 602619 TTTAAA -s simDog_chr6.simDog.chr6 205063 6 + 593897 TGTAAA -s simHuman_chr6.simHuman.chr6 220031 6 + 601863 TCTAAA -s simRat_chr6.simRat.chr6 206625 6 + 647215 TCTAAA - -a -s simMouse_chr6.simMouse.chr6 215613 2 + 636262 AA -s Anc0.Anc0refChr5 37223 2 + 87904 AA -s Anc1.Anc1refChr8 51701 2 + 57822 AA -s Anc2.Anc2refChr15 32618 2 + 86568 AA -s mr.mrrefChr5 70215 2 + 294540 AA -s simCow_chr6.simCow.chr6 180563 2 - 602619 AA -s simDog_chr6.simDog.chr6 205072 2 + 593897 AA -s simHuman_chr6.simHuman.chr6 220037 2 + 601863 AT -s simRat_chr6.simRat.chr6 206631 2 + 647215 AA - -a -s simMouse_chr6.simMouse.chr6 215615 4 + 636262 ACAA -s Anc0.Anc0refChr5 37225 4 + 87904 CCAC -s Anc1.Anc1refChr8 51703 4 + 57822 CCAC -s Anc2.Anc2refChr15 32621 4 + 86568 CCAC -s mr.mrrefChr5 70217 4 + 294540 ACAA -s simCow_chr6.simCow.chr6 180566 4 - 602619 GCAC -s simDog_chr6.simDog.chr6 205075 4 + 593897 CCAC -s simHuman_chr6.simHuman.chr6 220039 4 + 601863 TCAC -s simRat_chr6.simRat.chr6 206633 4 + 647215 ACAA - -a -s simMouse_chr6.simMouse.chr6 215619 21 + 636262 ATCCACATGTACTAGGTTGAA -s Anc0.Anc0refChr5 37229 20 + 87904 AGCCTGAT-TGCTAGATCAAA -s Anc1.Anc1refChr8 51707 21 + 57822 AGCCTGATGTGCTAGATCAAA -s Anc2.Anc2refChr15 32625 20 + 86568 AGGCTGAT-TGTTAGATCAAA -s mr.mrrefChr5 70221 21 + 294540 ATCCACATGTACTAGGTTGAA -s simCow_chr6.simCow.chr6 389156 20 - 602619 AGGCCTAT-TGTTAGATCAAA -s simDog_chr6.simDog.chr6 205079 20 + 593897 AGGCTGAT-TGTTAGATTCCA -s simHuman_chr6.simHuman.chr6 220043 21 + 601863 ACCCTATTGTGCTAGATCAAA -s simRat_chr6.simRat.chr6 206637 21 + 647215 AGTCACATGCACGAGGTTGAA - -a -s simMouse_chr6.simMouse.chr6 215640 7 + 636262 CTCAATA -s Anc0.Anc0refChr5 37252 7 + 87904 CTCCATA -s Anc1.Anc1refChr8 51731 7 + 57822 CTCCATA -s Anc2.Anc2refChr15 32648 7 + 86568 AGCCATA -s mr.mrrefChr5 70242 7 + 294540 CTCAATA -s simCow_chr6.simCow.chr6 389178 7 - 602619 AACTGAG -s simDog_chr6.simDog.chr6 205102 7 + 593897 AGCCATA -s simHuman_chr6.simHuman.chr6 220067 7 + 601863 CTGGTTG -s simRat_chr6.simRat.chr6 206658 7 + 647215 CTCAATA - -a -s simMouse_chr6.simMouse.chr6 215647 3 + 636262 TAC -s Anc0.Anc0refChr5 37259 3 + 87904 TCC -s Anc1.Anc1refChr8 51738 3 + 57822 TCC -s Anc2.Anc2refChr15 32661 3 + 86568 TCC -s mr.mrrefChr5 70249 3 + 294540 TAC -s simCow_chr6.simCow.chr6 389191 3 - 602619 TCC -s simDog_chr6.simDog.chr6 205115 3 + 593897 TTC -s simHuman_chr6.simHuman.chr6 220074 3 + 601863 TCC -s simRat_chr6.simRat.chr6 206665 3 + 647215 TAC - -a -s simMouse_chr6.simMouse.chr6 215650 28 + 636262 AGCCCTCCCGGTATTTCACGCTGGCCAA -s Anc0.Anc0refChr5 37263 28 + 87904 GGCCTTACCTACTACTCACACTGGCTCA -s Anc1.Anc1refChr8 51742 28 + 57822 GGCCTTACCTACTACTCACACTGGCTCA -s Anc2.Anc2refChr15 32665 28 + 86568 GCCATTACCTACTACTCACACTGGCCCA -s mr.mrrefChr5 70252 28 + 294540 AGCCCTCCCGGTATTTCACGCTGGCTCA -s simCow_chr6.simCow.chr6 389195 28 - 602619 TCTAGTACCTAATACTCACACTGGCCCA -s simDog_chr6.simDog.chr6 205119 28 + 593897 GCCATTGCCTACTACTCACACTGGCCCA -s simHuman_chr6.simHuman.chr6 220078 28 + 601863 GGCCTTACCTACTACTCACACAGGCTCA -s simRat_chr6.simRat.chr6 206668 21 + 647215 AGTCCTCCAG-------ATGCTGGCTCA - -a -s simMouse_chr6.simMouse.chr6 215678 22 + 636262 ACATGGGTTATCATGTGCACAA -s Anc0.Anc0refChr5 37291 22 + 87904 ATATGGACTTTCACCTATACTA -s Anc1.Anc1refChr8 51770 22 + 57822 ATATGGACTTTCACCTATACTA -s Anc2.Anc2refChr15 32696 22 + 86568 ATGTGGACTTTCTTCTATACTA -s mr.mrrefChr5 70280 22 + 294540 ACATGGGTTATCACGTGCACTA -s simCow_chr6.simCow.chr6 389223 16 - 602619 ------ACATTTTTCTATACTA -s simDog_chr6.simDog.chr6 205152 22 + 593897 ATGTGGGTTCTCTTCTAAACCA -s simHuman_chr6.simHuman.chr6 220106 22 + 601863 AGACGTACCTTCACCTATATTA -s simRat_chr6.simRat.chr6 206689 22 + 647215 ACATGGGTTATCACGTGCACTA - -a -s simMouse_chr6.simMouse.chr6 215700 29 + 636262 GATAAATATTCTCTGGTTATTAGCTGTGG -s Anc0.Anc0refChr5 37313 29 + 87904 CATATATATTGGCTGTTCACTTGCTGAGG -s Anc1.Anc1refChr8 51792 29 + 57822 CATATATATTGGCTGTTCACTTGCTGAGG -s Anc2.Anc2refChr15 32718 29 + 86568 CATATATATTAGCTGTTCACTTGCTGAGG -s mr.mrrefChr5 70302 29 + 294540 GATAAATATTGTCTGGTTACTAGCTGTGG -s simCow_chr6.simCow.chr6 389239 29 - 602619 CATATATATCATCTGCTCACTAGCTGAGG -s simDog_chr6.simDog.chr6 205174 26 + 593897 CATATATATTAGCTGTT---TTGCTGAGG -s simHuman_chr6.simHuman.chr6 220129 29 + 601863 AATACATATTGACTGTTCTCTCGTTGAGG -s simRat_chr6.simRat.chr6 206711 29 + 647215 GATAAATATTGCCTGGTTACGATCTGTGG - -a -s simMouse_chr6.simMouse.chr6 215729 16 + 636262 ATATTGAGTTGTCACA -s Anc0.Anc0refChr5 37344 16 + 87904 ATATTAGGTTGTCTCA -s Anc1.Anc1refChr8 51823 16 + 57822 ATATTAGGTTGTCTCA -s Anc2.Anc2refChr15 32749 16 + 86568 AAATTAAGTTGCCTCA -s mr.mrrefChr5 70331 16 + 294540 ATATTAGGTTGTCTCA -s simCow_chr6.simCow.chr6 389270 16 - 602619 AAATTCAATTGCCTTA -s simDog_chr6.simDog.chr6 205202 16 + 593897 AAATTAAGTTGCCTCA -s simHuman_chr6.simHuman.chr6 220160 16 + 601863 ATATTAGGTTGTCTCA -s simRat_chr6.simRat.chr6 206740 16 + 647215 AGATTAGGCCGTCTCA - -a -s simMouse_chr6.simMouse.chr6 215745 4 + 636262 TACG -s Anc0.Anc0refChr5 37362 4 + 87904 TACG -s Anc1.Anc1refChr8 51841 4 + 57822 TACG -s Anc2.Anc2refChr15 32767 4 + 86568 TTTG -s mr.mrrefChr5 70347 4 + 294540 TACG -s simCow_chr6.simCow.chr6 389288 4 - 602619 TTTC -s simDog_chr6.simDog.chr6 205220 4 + 593897 TTTG -s simHuman_chr6.simHuman.chr6 220178 4 + 601863 TACT -s simRat_chr6.simRat.chr6 206756 4 + 647215 TATG - -a -s simMouse_chr6.simMouse.chr6 215749 9 + 636262 AGCCCCCTC -s Anc0.Anc0refChr5 37366 9 + 87904 AGCCTCTAC -s Anc1.Anc1refChr8 51845 9 + 57822 AGCCTCTAC -s Anc2.Anc2refChr15 32772 9 + 86568 AGCCTCTAT -s mr.mrrefChr5 70351 9 + 294540 AGCCTCTTC -s simCow_chr6.simCow.chr6 389293 3 - 602619 TGC------ -s simDog_chr6.simDog.chr6 205225 9 + 593897 AGCCTCTAT -s simHuman_chr6.simHuman.chr6 220182 9 + 601863 AGCCTCTAC -s simRat_chr6.simRat.chr6 206760 9 + 647215 AGCCTCTTC - -a -s simMouse_chr6.simMouse.chr6 215758 107 + 636262 ATAAGCGTATACATTATTGTGATCAGGTACTAAAGATATTACTGTGAAGATAAGGCCTAGATTACAAAATCTCAAAGCCCTGACAGGGAAGTCCAGAATCAAGAGTC -s Anc0.Anc0refChr5 37378 80 + 87904 ATG----TATATGTTATTGTGAGTAGGTACCAATGAAATTATTGTGAAGAAAAAGTCTAGAATG-----------------------GAAGTCTAGAATGCAGAATC -s Anc1.Anc1refChr8 51857 102 + 57822 ATGA-TGTATATGTTATTGTGAGTAGGTACCAATGAAATTATTGTGAAGAAAAAGTCTAGAATG----ATCACAGAGTACTGAAGAGGAAGTCTAGAATGCAGAATC -s Anc2.Anc2refChr15 32784 80 + 86568 ATG----TATATGTTGTTGAGAGCAGGTACCAATAAAATTATTGTGAAGAAAAAGTCAAGAATG-----------------------GAAGTCTATAATGCAGAATT -s mr.mrrefChr5 70363 107 + 294540 ATAAGTGTATACATTATTGTGAGTAGGTACTAAAGATATTACTGTGAAGATAAAGCCTAGATTACAAAATCTCAAAGCCCTGACAGGGAAGTCCAGAATCAAGAGTC -s simCow_chr6.simCow.chr6 389298 67 - 602619 ATG----TATATGTTGTTGATAGCAGGTACTGGTTAACTTAGTAGGAAGAA------------------------------------GAAGTCTATAATGCAGAATT -s simDog_chr6.simDog.chr6 205235 51 + 593897 -------------GCGTTGAGAACAGGTACCAATAAAATTATTGTGAAGACAAAGTCAAGAATG------------------------------------------- -s simHuman_chr6.simHuman.chr6 220194 102 + 601863 ATGA-TGTATATGTTATCATGAGTGGGTACCAATGGCATAATTGTGAAGAAAAAGTCTGGGATG----ATCACAGAGTACTGAAGAGGAAGTCTAGAGTGCAGAATC -s simRat_chr6.simRat.chr6 206772 107 + 647215 ATAAGTGTATACATTATTGTGAGTAGGAGCTAAAGATATCACTGTGAAGATGAAGGCTAGAGTACAAAATCTCAAAACCCTGACAGGGGAGTCCAGAATCAGGAGTC - -a -s simMouse_chr6.simMouse.chr6 215865 31 + 636262 TCCCTAATACAGTCCATGCTGAGATAATTGG -s Anc0.Anc0refChr5 37464 31 + 87904 TCCATAATAAAGTCCAGGCAGAGATAATTGA -s Anc1.Anc1refChr8 51965 31 + 57822 TCCATAATAAAGTCCAGGCAGAGATAATTGA -s Anc2.Anc2refChr15 32870 31 + 86568 CCCATAATAAAGTCCCGGCAGAGATAATTGA -s mr.mrrefChr5 70470 31 + 294540 TCCATAATACAGTCCATGCTGAGATAATTGG -s simCow_chr6.simCow.chr6 389371 31 - 602619 CCCATAATATAGTCCTGACAGAGATAATTTA -s simDog_chr6.simDog.chr6 205286 23 + 593897 --------AAAGTCCCAGCAGAGATAATTGA -s simHuman_chr6.simHuman.chr6 220302 31 + 601863 TCCATAATAGAGTCCAGGCAGAGATAATTGA -s simRat_chr6.simRat.chr6 206879 31 + 647215 TTCATAATACAGTCCTTGCTGGGATAATCAG - -a -s simMouse_chr6.simMouse.chr6 215896 5 + 636262 CATGA -s Anc0.Anc0refChr5 37495 4 + 87904 TC-AA -s Anc1.Anc1refChr8 51996 5 + 57822 TCTAA -s Anc2.Anc2refChr15 32901 4 + 86568 TC-AA -s mr.mrrefChr5 70501 5 + 294540 CCTGA -s simCow_chr6.simCow.chr6 389403 4 - 602619 TC-AA -s simDog_chr6.simDog.chr6 205309 4 + 593897 TC-AA -s simHuman_chr6.simHuman.chr6 220333 5 + 601863 TCTAA -s simRat_chr6.simRat.chr6 206910 5 + 647215 CCTGA - -a -s simMouse_chr6.simMouse.chr6 215901 11 + 636262 CTTAGAGAGTC -s Anc0.Anc0refChr5 37499 11 + 87904 CATAAAGAGTC -s Anc1.Anc1refChr8 52001 11 + 57822 CATAAAGAGTC -s Anc2.Anc2refChr15 32905 11 + 86568 CACAAAGAGTC -s mr.mrrefChr5 70506 11 + 294540 CATAGAGAGTC -s simCow_chr6.simCow.chr6 389407 11 - 602619 CACAAAGAGTC -s simDog_chr6.simDog.chr6 205313 11 + 593897 CACAGAGAGTC -s simHuman_chr6.simHuman.chr6 220339 11 + 601863 CATAAAGAGTT -s simRat_chr6.simRat.chr6 206915 11 + 647215 CACAGAGACTC - -a -s simMouse_chr6.simMouse.chr6 215912 56 + 636262 ATACAGTAATTTTGACATGCAGAATAATCTGCACTCATCAATCCTTCAATTGTAGC -s Anc0.Anc0refChr5 37678 56 + 87904 ATTTAATAGTTTTGACATGCAGAAAGATGTAAATACAGCAACCAGTCTATTGTAGC -s Anc1.Anc1refChr8 52180 56 + 57822 ATTTAATAGTTTTGACATGCAGAAAGATGTAAATACAGCAACCAGTCTATTGTAGC -s Anc2.Anc2refChr15 33085 56 + 86568 ATTTAATAGTTTTGACATTCAGAAAGATGTAAATACAGCAACCAGTCTATTGTAGC -s mr.mrrefChr5 70517 56 + 294540 ATACAGTAATTTTGACATGCAGAATAATCTGCACTCATCAATCCTTCAATTGTAGC -s simCow_chr6.simCow.chr6 389593 56 - 602619 ATGCAATAGTTTTGACATTTGGAAAGATGTCTACACATTAACCAGTCTAATGTAGC -s simDog_chr6.simDog.chr6 205428 56 + 593897 AATTAATAGTCTTGACATTCAGAAGGAGGTAAATACAGCAACCAGTCTATTGTAGC -s simHuman_chr6.simHuman.chr6 220518 40 + 601863 ATTTATTAGTTTTGATATGCAGAAAGAT----------------GTTTATTGTAGC -s simRat_chr6.simRat.chr6 206926 56 + 647215 ACAGAGTAATTTTGACATGCAGAATAATCTGCACTCATTAATCCTTCAATTCTAAC - -a -s simMouse_chr6.simMouse.chr6 215968 1 + 636262 A -s Anc0.Anc0refChr5 37737 1 + 87904 A -s Anc1.Anc1refChr8 52239 1 + 57822 A -s Anc2.Anc2refChr15 33144 1 + 86568 A -s mr.mrrefChr5 70573 1 + 294540 A -s simCow_chr6.simCow.chr6 389652 1 - 602619 A -s simDog_chr6.simDog.chr6 205487 1 + 593897 A -s simHuman_chr6.simHuman.chr6 220561 1 + 601863 A -s simRat_chr6.simRat.chr6 206982 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 215969 54 + 636262 AAATAAAACTGACTGTCTGTTATAAAAGAGAACTCATTTATTGTCTGCAATCAA -s Anc0.Anc0refChr5 37738 50 + 87904 ACATAAAACTGATTGTCCGCTATAAAAAAAAACTCATT----GTCCGCTATAAA -s Anc1.Anc1refChr8 52240 50 + 57822 ACATAAAACTGATTGTCCGCTATAAAAAAAAACTCATT----GTCCGCTATAAA -s Anc2.Anc2refChr15 33145 50 + 86568 ACATAAAACTGATTGTCCGCTATCAAAAAAAACTCATT----GTCCGCTGTAAA -s mr.mrrefChr5 70574 54 + 294540 AAATAAAACTGATTGTCTGTTATAAAAGAGAACTCATTTATTGTCTGCAATCAA -s simCow_chr6.simCow.chr6 389667 50 - 602619 ACATAAAACTGATTGTCTGGTATCAAAAGAGACTGATT----GTCTGCTCTAAA -s simDog_chr6.simDog.chr6 205488 50 + 593897 ACATAAAGCTGATTGTCCGCTATCAAAAAAAACTCATT----GTCCGCTGTGAA -s simHuman_chr6.simHuman.chr6 220562 45 + 601863 GGATAGAACTGATTGCCC-CTATAAAAAAAAAGTTATT--------GCTATAAA -s simRat_chr6.simRat.chr6 206983 54 + 647215 AAATAAAACTTATTGTCTGGTATAAAAGAGAACTCATTTATTGTATGCAATCTA - -a -s simMouse_chr6.simMouse.chr6 216023 96 + 636262 GATAGACTACCCAATCTCCAACCACATTCAGTAATACTGCACCTAATCAGCCAGGCTGTTATGTATGACCAAATTATCAACACCTGATAGATTCTC -s Anc0.Anc0refChr5 37788 95 + 87904 AATAGACCACCCAATCTCCAATCCCATACATTGAGGCTGAACCAAATGTACCA-ATCACCCTCTATAAACAAAGCATCAAAGCTTGATGGATTCTA -s Anc1.Anc1refChr8 52290 95 + 57822 AATAGACCACCCAATCTCCAATCCCATACATTGAGGCTGAACCAAATGTACCA-ATCACCCTCTATAAACAAAGCATCAAAGCTTGATGGATTCTA -s Anc2.Anc2refChr15 33195 95 + 86568 AATAGACCCCCCAATCCCCAATCCCATACATTGGGGCTAAACCAAATGTACCA-ATCACCCTCTACAAACAAAGCATCAAAGGTTGATGGATACTA -s mr.mrrefChr5 70628 95 + 294540 GATAGACTACCCAATCTCCAACCACATTCAGTAATACTGCACCTAATGAGCCA-GCTGTCATGTATGACCAAAGTATCAACACCTGATAGATTCTA -s simCow_chr6.simCow.chr6 389717 95 - 602619 AATAGACCTCCTGATCACTGATCCCCTCCATTGAGGCTAGACCGAATGTAGCA-ATCACCCTTTCCAAATAAAGCATCAAATGTTAATCGATCCTA -s simDog_chr6.simDog.chr6 205562 95 + 593897 AACAGACCCCCCAACTCCCAATCCCATAGATTGGGGCTAAACTAAATGTACCA-ATCACCCTCTACAAGCAAAGTATCAAAGGTTGATGGATACTA -s simHuman_chr6.simHuman.chr6 220607 94 + 601863 AATTGTCCACCCAATCTGCAATCCCTTACATTGA-GCTGAACCAAATGTACCA-ATCACCCTCTATAAACGAAGCATCAAACCTTGATGGATTCTA -s simRat_chr6.simRat.chr6 207037 92 + 647215 CATAGACTACCCAATCTCCAACTACATTCAGTAATACTGCACCTAATGAGCCA-GCTGTCA--TATGA-CAAAGTACCAAGACCTGACAGAGTTTA - -a -s simMouse_chr6.simMouse.chr6 216119 3 + 636262 CTC -s Anc0.Anc0refChr5 37885 3 + 87904 GTC -s Anc1.Anc1refChr8 52387 3 + 57822 GTC -s Anc2.Anc2refChr15 33292 3 + 86568 GTC -s mr.mrrefChr5 70723 3 + 294540 CTC -s simCow_chr6.simCow.chr6 389814 3 - 602619 GTG -s simDog_chr6.simDog.chr6 205659 3 + 593897 GGC -s simHuman_chr6.simHuman.chr6 220703 3 + 601863 ATT -s simRat_chr6.simRat.chr6 207129 3 + 647215 TTC - -a -s simMouse_chr6.simMouse.chr6 216122 19 + 636262 TCCAACCTATCTGTTACTA -s Anc0.Anc0refChr5 37888 15 + 87904 TTCAACCACCATA----CA -s Anc1.Anc1refChr8 52390 15 + 57822 TTCAACCACCATA----CA -s Anc2.Anc2refChr15 33295 15 + 86568 TTCAACCACCATA----CT -s mr.mrrefChr5 70726 15 + 294540 TCCAACCAACCTG----TA -s simCow_chr6.simCow.chr6 389817 15 - 602619 TTCAGCTACCATA----CT -s simDog_chr6.simDog.chr6 205662 15 + 593897 TCCAACCATGATA----CT -s simHuman_chr6.simHuman.chr6 220706 15 + 601863 TTCAATCACCATA----CA -s simRat_chr6.simRat.chr6 207189 15 + 647215 TCCAAATAACGTG----AA - -a -s simMouse_chr6.simMouse.chr6 216141 45 + 636262 AACTAAACAAAACTTATTAGGTATGTATAACGAGCAGGGGCTCAG -s Anc0.Anc0refChr5 37905 45 + 87904 AGTCATACAAAACTTATTATATATCTATAATGTGCAGAGACTCAA -s Anc1.Anc1refChr8 52407 45 + 57822 AGTCATACAAAACTTATTATATATCTATAATGTGCAGAGACTCAA -s Anc2.Anc2refChr15 33312 45 + 86568 AGTCATACAAAACTTATTATATATCTATAATGTGCACAGACTCAA -s mr.mrrefChr5 70741 45 + 294540 AGCTAAACAAAACTTATTAGATATGTATAATGAGCAGGGACTCAA -s simCow_chr6.simCow.chr6 389834 45 - 602619 GGTCATACAAAACTTATTATAGATCTAGAATGTGTGAAGAACCAA -s simDog_chr6.simDog.chr6 205679 43 + 593897 AGTGATACAAAACTTACTATATATCTGTTATATGCACAGACTC-- -s simHuman_chr6.simHuman.chr6 220723 45 + 601863 AGTCATACAAAACTTATTATATATCTATAATGCACAGAGACTCAA -s simRat_chr6.simRat.chr6 207204 45 + 647215 AGCTAAACAAAAACTACTAGATATGTATAATGAGCAAGGACTGAA - -a -s simMouse_chr6.simMouse.chr6 216186 35 + 636262 TCCTTTCTCACAGTTGTTAACCAGGACTTGCTCTC -s Anc0.Anc0refChr5 37950 32 + 87904 T--TGTCTCACAATTGC-AGTAGAGACTAGCTCTC -s Anc1.Anc1refChr8 52452 32 + 57822 T--TGTCTCACAATTGC-AGTAGAGACTAGCTCTC -s Anc2.Anc2refChr15 33357 32 + 86568 T--TGTCTCACAAGTGC-AGTAGAGACAAGAACTC -s mr.mrrefChr5 70786 35 + 294540 TCCTTTCTCACAATTGTTAATCAGGACTTGCTCTC -s simCow_chr6.simCow.chr6 389882 32 - 602619 T--TGTTTCAAAAGTAA-AGTAGAGACAAGAACTC -s simDog_chr6.simDog.chr6 205722 25 + 593897 T--TGTCTCACAAGCGC-AGTAGAG-------CTC -s simHuman_chr6.simHuman.chr6 220768 32 + 601863 T--GGTCTCACAATTGC-AGTAGAGAGTAGCTCTC -s simRat_chr6.simRat.chr6 207249 35 + 647215 TACTATATCATAATTGTAAATCAGGACTTGCCCTC - -a -s simMouse_chr6.simMouse.chr6 216221 8 + 636262 CCACCCTG -s Anc0.Anc0refChr5 37986 8 + 87904 CATCCTCA -s Anc1.Anc1refChr8 52488 8 + 57822 CATCCTCA -s Anc2.Anc2refChr15 33393 8 + 86568 CATCCTCA -s mr.mrrefChr5 70821 8 + 294540 CCACCCTG -s simCow_chr6.simCow.chr6 389918 8 - 602619 CATCCTTA -s simDog_chr6.simDog.chr6 205751 8 + 593897 CATCCTCG -s simHuman_chr6.simHuman.chr6 220804 8 + 601863 CACCTTCA -s simRat_chr6.simRat.chr6 207284 8 + 647215 CTACCCTG - -a -s simMouse_chr6.simMouse.chr6 216229 61 + 636262 TTGCTGCTAATTTAAGGTGAAAGGTGTCAGCATAGAAATGGAAGAAGCTCCCTATCTTTAT -s Anc0.Anc0refChr5 37994 36 + 87904 TGGCCGCCAATTTC-------ATTG-TTG------AAA---------CTCCATAT--ACAT -s Anc1.Anc1refChr8 52496 49 + 57822 TGGCCGCCAATTTCCAGTGAAATTG-TTGGCATAGAAA---------CTCCATAT--ACAT -s Anc2.Anc2refChr15 33401 36 + 86568 TGGCCGCGAAGTTC-------ATTG-TTG------ATA---------CTCCATGT--ACAT -s mr.mrrefChr5 70829 60 + 294540 TGGCTGCCAATTTAAGGTGAAAGTT-TCAGCATAGAAATGGAAGAAGCTCCCTATCTTTAT -s simCow_chr6.simCow.chr6 390123 14 - 602619 TGGCCGCGAAGCTT----------------------------------------------- -s simCow_chr6.simCow.chr6 389926 14 - 602619 GGGCCGCGAAGTTC----------------------------------------------- -s simDog_chr6.simDog.chr6 205759 23 + 593897 T--------------------ATTG-TTG------ATA---------CTCCATGT--ACAT -s simHuman_chr6.simHuman.chr6 220812 49 + 601863 TGGCCTCCAATTTCCAGTGAAATTG-CTGGCATAGGAA---------CTCCATAT--GAAT -s simRat_chr6.simRat.chr6 207292 60 + 647215 TGGCTGCCAATCTAAGGTGAGCATT-TACACATAGAAATGGAAGCAGCTCCCTATCTTTAT - -a -s simMouse_chr6.simMouse.chr6 216290 6 + 636262 GTCTTA -s Anc0.Anc0refChr5 38030 6 + 87904 TCTTTC -s Anc1.Anc1refChr8 52545 6 + 57822 TCTTTC -s Anc2.Anc2refChr15 33437 6 + 86568 TCTCTC -s mr.mrrefChr5 70889 6 + 294540 GTCTTA -s simDog_chr6.simDog.chr6 205783 6 + 593897 TCTCTC -s simHuman_chr6.simHuman.chr6 220861 6 + 601863 TCTTTC -s simRat_chr6.simRat.chr6 207352 6 + 647215 GTCTTT - -a -s simMouse_chr6.simMouse.chr6 216296 22 + 636262 CTGGAAGAGACATAATAGATGA -s Anc0.Anc0refChr5 38036 21 + 87904 TTGGAAGAGACACTACAGG-GA -s Anc1.Anc1refChr8 52551 21 + 57822 TTGGAAGAGACACTACAGG-GA -s Anc2.Anc2refChr15 33444 21 + 86568 TTTGAAGAGACACTACAGG-AA -s mr.mrrefChr5 70895 22 + 294540 CTGGAAGAGACATAATAGATGA -s simCow_chr6.simCow.chr6 390137 19 - 602619 --GGAAATGATACCGCAGA-GG -s simCow_chr6.simCow.chr6 389940 19 - 602619 --TGAAATGGCACCACAGA-AG -s simDog_chr6.simDog.chr6 205790 21 + 593897 TTTGAGGAGACACTACAGG-AA -s simHuman_chr6.simHuman.chr6 220867 21 + 601863 ATGGAAGAGCCACTCGGAG-GA -s simRat_chr6.simRat.chr6 207358 22 + 647215 CTGGAGGAGACATAATAGATGA - -a -s simMouse_chr6.simMouse.chr6 216318 13 + 636262 AGCTCTAGGGCCT -s Anc0.Anc0refChr5 38057 13 + 87904 GGCTTTGGGGCCT -s Anc1.Anc1refChr8 52572 13 + 57822 GGCTTTGGGGCCT -s Anc2.Anc2refChr15 33466 13 + 86568 GACTTTGGGGCCT -s mr.mrrefChr5 70917 13 + 294540 GGCTTTAGGGCCT -s simCow_chr6.simCow.chr6 390157 13 - 602619 GGCTCTGGAGCCT -s simCow_chr6.simCow.chr6 389960 13 - 602619 GACTTTGGAGCCT -s simDog_chr6.simDog.chr6 205811 13 + 593897 TACCTCGGGGCCT -s simHuman_chr6.simHuman.chr6 220888 13 + 601863 GGATTTGGGGTAT -s simRat_chr6.simRat.chr6 207380 13 + 647215 GGCTTAAGGGCCT - -a -s simMouse_chr6.simMouse.chr6 216331 91 + 636262 GACTTGATCATTACCGACTGAGGCCCGTGCTGTTGTCATTTGTATGTCATGTCTTCTTATAAGATGAATTAGTCATTTCATCCTTCCTAGA -s Anc0.Anc0refChr5 38070 86 + 87904 GACTTATTCATCACAGACTGAGGCCCTTCCTGCTGTCATGCCTCTGTCTTGTT-----ATATGACAGGTCTGTAGTTTCAACTTTCATAAG -s Anc1.Anc1refChr8 52585 88 + 57822 GACTTATTCATCACAGACTGAGGCCCTTCCTGCTGTCATGCCTCTGTCTTGTTT---TATATGACAGGTCTGTAGTTTCAACTTTCATAAG -s Anc2.Anc2refChr15 33479 86 + 86568 GACTTATTCATCCCAGACTGAGGCCTTTCTTGCTGTCCTGCCTCTGTCTTGTT-----ATATGACAGGTCTGTAGATTCAACTTTCATAAG -s mr.mrrefChr5 70930 91 + 294540 GACTTGATCATCACCGACTGAGGCCCGTGCTGTTGTCATTCCTATGTCATGTCTTCTTATAAGACAAACTAGTCATTTCATCCTTCCTAGA -s simCow_chr6.simCow.chr6 390170 86 - 602619 GACTTATTCAGCCCAGACTGTGGCTCTTGTTGCTGTCCTGCATCTGTCTTGTG-----ATAAGCTGGGTCTGTAGATTCAACTTTCATAAG -s simCow_chr6.simCow.chr6 389974 86 - 602619 GACTTATTCAGCCCAGACTGTGGCTTTTGTTGCTGTCCTGCATCTGTCTTGTT-----ATGAGACGAGTCTGTAGATTCAACTTTCATAAG -s simDog_chr6.simDog.chr6 205824 78 + 593897 GACATATTCTTCCTGCACTGAGCTCTGTC--------CTGCCTCTGTCTTGTT-----ATATGACAGACTTGTAGTTTCAGTGTTCCCAAG -s simHuman_chr6.simHuman.chr6 220901 64 + 601863 GAGTTATTCATCACAGACTGAGGCCCTTCCTGCAATTATGCCTCTGTCTTGTTT--------------------GTTTCA-------GCCG -s simRat_chr6.simRat.chr6 207393 91 + 647215 GACTTGATCATCACTGACTGAGGCTCGGGCTGTTGTCATTCCTATGTCATGTCTTCTTATAAGACAAACTTGTCATTTTATCCTTCCTAGA - -a -s simMouse_chr6.simMouse.chr6 216422 15 + 636262 CTTCTTCTTGTCCGT -s Anc0.Anc0refChr5 38156 14 + 87904 CTTCTT-TTGTCCTT -s Anc1.Anc1refChr8 52673 15 + 57822 CTTCTTCTTGTCCTT -s Anc2.Anc2refChr15 33565 14 + 86568 CTTCCT-TTGTTTTT -s mr.mrrefChr5 71021 15 + 294540 CTTCTTCTTGTCCAT -s simCow_chr6.simCow.chr6 390258 14 - 602619 TTTCAT-AAGTTTCC -s simCow_chr6.simCow.chr6 390060 13 - 602619 TTTCCT-AACTCTC- -s simDog_chr6.simDog.chr6 205902 14 + 593897 CTTCCT-TTGTTGTT -s simHuman_chr6.simHuman.chr6 220965 15 + 601863 CTTCTTCTTGTCCTT -s simRat_chr6.simRat.chr6 207484 15 + 647215 CTTCTTCATATCCAT - -a -s simMouse_chr6.simMouse.chr6 216437 29 + 636262 GTTAAGTGTTGTGCAGGGTGTAACTATGT -s Anc0.Anc0refChr5 38182 29 + 87904 GATAAGTGTTTTGATGGGTTAGACCAAAT -s Anc1.Anc1refChr8 52700 29 + 57822 GATAAGTGTTTTGATGGGTTAGACCAAAT -s Anc2.Anc2refChr15 33591 29 + 86568 GATAAGTGTTTTCATGGGTTAGACCAAAT -s mr.mrrefChr5 71036 29 + 294540 GTTAAGTGTTGTGCAGGGTGAGACCATGT -s simCow_chr6.simCow.chr6 390284 29 - 602619 GATAAGTGTTTTCCTGGATCAGGCCAAAT -s simDog_chr6.simDog.chr6 205928 29 + 593897 GATAAGTGCTTTCATGGGTTAGACCAAAT -s simHuman_chr6.simHuman.chr6 220992 29 + 601863 GCTGAGTGTCTGGTGAGGTAAGACCGAAT -s simRat_chr6.simRat.chr6 207499 29 + 647215 GTTAAGTGTTGTGCAGGGTGAGACCATGT - -a -s simMouse_chr6.simMouse.chr6 216466 55 + 636262 AATTTATTTACTGTCTCTAGTTTTATTTTTTATGATTATAATATTACACATAAAG -s Anc0.Anc0refChr5 38211 53 + 87904 AATTCATCTA--GCATATAGTTTGATTTATTATGATTGTAATTTTACACATAAAG -s Anc1.Anc1refChr8 52729 55 + 57822 AATTCATCTATTGCATATAGTTTGATTTATTATGATTGTAATTTTACACATAAAG -s Anc2.Anc2refChr15 33621 53 + 86568 GATTCATCCA--GCACATAGTTTGATTTATTATGATTGTAATTTTACAGATAAAG -s mr.mrrefChr5 71065 55 + 294540 AATTTATTTACTGTATCTAGTTTTATTTTTTATGATTATAATTTTACACATAAAG -s simCow_chr6.simCow.chr6 390314 53 - 602619 GATTTATTCA--GCACATAATTTGATTTATTATGATTGTAGTTCTACAGATAAAG -s simDog_chr6.simDog.chr6 205958 39 + 593897 GATTCATC----------AGTTTGATAT------ATTATAATTTTACAGATAATG -s simHuman_chr6.simHuman.chr6 221021 55 + 601863 AATTCATCTATTGCATGTAGTTTGATTTCTTATGATTGTAATTTTACACATAAAG -s simRat_chr6.simRat.chr6 207528 55 + 647215 AATTTATTTACTGTATTTAGTTTTATTTTTTATGAATATAATTTTACACATAAAG - -a -s simMouse_chr6.simMouse.chr6 216521 53 + 636262 ATAGCTCTGATTGTGTTCTCTGTGTACCAAGTAAATCAGGATCAATGGTTAGT -s Anc0.Anc0refChr5 38264 53 + 87904 ATAGCTCTGTTTGTGTTCTTTCTGTACCAAGTTAAACAGGATCAACAGTTAAT -s Anc1.Anc1refChr8 52784 53 + 57822 ATAGCTCTGTTTGTGTTCTTTCTGTACCAAGTTAAACAGGATCAACAGTTAAT -s Anc2.Anc2refChr15 33674 53 + 86568 ATAGTTCTGTTTGTGTTCTTCCTGTACCAAGTTAAACTGGATCAACAGTTAAT -s mr.mrrefChr5 71120 53 + 294540 ATAGCTCTGATTGTGTTCTCTGTGTACCAAGTTAATCAGGATCAATGGTTAGT -s simCow_chr6.simCow.chr6 390367 53 - 602619 ATAGTTCTGTTTGTGTTCTTCCTGTACAAAGTTAAGGTAAACACTCATTTCAT -s simDog_chr6.simDog.chr6 205997 53 + 593897 ACAGTTCTGGTTGTGTAGGTCCAGTACCCAGTTACACTGGGTCAACAGTCATT -s simHuman_chr6.simHuman.chr6 221076 53 + 601863 ATAGCTCTGTTTGTGTTCTTTTTGTACCAGGTTAACTAGGATCAACAGCTGAT -s simRat_chr6.simRat.chr6 207584 53 + 647215 ATAGGTCTGATTGGGTTCTCTCTGTGCCGAGCTAATCAGGATCAATGGTTAGT - -a -s simMouse_chr6.simMouse.chr6 216574 27 + 636262 TGTGGCACTTAAATTGTTGTACAACAG -s Anc0.Anc0refChr5 38321 27 + 87904 TGCAATATTCAGAGTAGTTGGCAACAA -s Anc1.Anc1refChr8 52841 27 + 57822 TGCAATATTCAGAGTAGTTGGCAACAA -s Anc2.Anc2refChr15 33731 27 + 86568 TGCAATATTCAGAGTAGTTGGCCACAA -s mr.mrrefChr5 71173 27 + 294540 TGTGGCACTGAAATTATTGTACAACAG -s simCow_chr6.simCow.chr6 390424 27 - 602619 TGTAATATTTGCAGTGATTGGCCACAA -s simDog_chr6.simDog.chr6 206060 27 + 593897 TGCAATAATCAGAGAAGTTGGCCACAA -s simHuman_chr6.simHuman.chr6 221133 27 + 601863 TGCAATTTTCATGGTAGACAGCAACAA -s simRat_chr6.simRat.chr6 207637 27 + 647215 GGTGGCACTGAAATTATTGTACAACAG - -a -s simMouse_chr6.simMouse.chr6 216601 20 + 636262 CCACCAGTGGGTGGCAGGTC -s Anc0.Anc0refChr5 38350 20 + 87904 CCACCAGTCGATGAGACATC -s Anc1.Anc1refChr8 52870 20 + 57822 CCACCAGTCGATGAGACATC -s Anc2.Anc2refChr15 33760 20 + 86568 CCACCAGTCAATGAGACATC -s mr.mrrefChr5 71200 20 + 294540 CCACCAGTGGGTGGCAGGTC -s simCow_chr6.simCow.chr6 390453 20 - 602619 CCACCAGTCATTCGGAGGTC -s simDog_chr6.simDog.chr6 206089 20 + 593897 CTACCAGACAATGAGACATC -s simHuman_chr6.simHuman.chr6 221162 12 + 601863 CCACTAGTTGAT-------- -s simRat_chr6.simRat.chr6 207664 20 + 647215 TCACCGGTGGGCGGCAGGTC - -a -s simMouse_chr6.simMouse.chr6 216621 7 + 636262 CCTGTTA -s Anc0.Anc0refChr5 38370 6 + 87904 CCATTT- -s Anc1.Anc1refChr8 52890 6 + 57822 CCATTT- -s Anc2.Anc2refChr15 33781 6 + 86568 CCATTT- -s mr.mrrefChr5 71220 6 + 294540 CCTGTT- -s simCow_chr6.simCow.chr6 390474 6 - 602619 CCCTTT- -s simDog_chr6.simDog.chr6 206110 6 + 593897 CCATTT- -s simHuman_chr6.simHuman.chr6 221174 2 + 601863 ----TT- -s simRat_chr6.simRat.chr6 207684 6 + 647215 CCTGTC- - -a -s simMouse_chr6.simMouse.chr6 216628 22 + 636262 TTCCCTATCTAAACACTGTTGC -s Anc0.Anc0refChr5 38376 22 + 87904 TTCCCTAGCTATTAGCTGCCAC -s Anc1.Anc1refChr8 52896 22 + 57822 TTCCCTAGCTATTAGCTGCCAC -s Anc2.Anc2refChr15 33787 22 + 86568 TTCCCTAGCTATTAGCTGCCAC -s mr.mrrefChr5 71226 22 + 294540 TTCCCTATCTAATAACTGTCAC -s simCow_chr6.simCow.chr6 390567 22 - 602619 TTCCCTAGACATTAGCTGCCAC -s simDog_chr6.simDog.chr6 206116 22 + 593897 TTCACTAGCTATTAGCTGCCAC -s simHuman_chr6.simHuman.chr6 221176 22 + 601863 TTTCCTAGTTTTTAGCTGCCAC -s simRat_chr6.simRat.chr6 207690 22 + 647215 TTCCCTATCTAATAACTGGCAC - -a -s simMouse_chr6.simMouse.chr6 216650 21 + 636262 TTTTAGCATCAGGATTATAAT -s Anc0.Anc0refChr5 38398 21 + 87904 TTTTATCATCAGGATAAATAA -s Anc1.Anc1refChr8 52918 21 + 57822 TTTTATCATCAGGATAAATAA -s Anc2.Anc2refChr15 33810 21 + 86568 TTTTATCATCAGGATAAATAA -s mr.mrrefChr5 71248 21 + 294540 TTTTAGCATCAGGATTATAAT -s simCow_chr6.simCow.chr6 390590 21 - 602619 TTTTATCATTGAAATATATAA -s simDog_chr6.simDog.chr6 206139 21 + 593897 TCTTATCATCAGGACAATAAA -s simHuman_chr6.simHuman.chr6 221198 21 + 601863 TTTTATCATCAGTATAAATAA -s simRat_chr6.simRat.chr6 207712 21 + 647215 TTTTGCCATCAGGACTATAAT - -a -s simMouse_chr6.simMouse.chr6 216671 28 + 636262 TGATGCAGGTGTTAAACAGCGTCCCTGG -s Anc0.Anc0refChr5 38419 27 + 87904 TGAATTGTGGGTTGAACAGGGTCTTA-G -s Anc1.Anc1refChr8 52939 28 + 57822 TGAATTGTGGGTTGAACAGGGTCTTAAG -s Anc2.Anc2refChr15 33831 27 + 86568 TGAATTGTGGGTTGAACAGGGTCTTA-G -s mr.mrrefChr5 71269 28 + 294540 TGATGCATGTGTTGAACAGCGTCCCTGG -s simCow_chr6.simCow.chr6 390742 27 - 602619 TGAGTTGAGGATTGAACAGGGTCTTA-G -s simDog_chr6.simDog.chr6 206160 27 + 593897 TCAATCGTGGGTTGAACAAGGTCCTC-G -s simHuman_chr6.simHuman.chr6 221219 28 + 601863 TGAACTGTGCCTTGAACGGGGTCTTAAG -s simRat_chr6.simRat.chr6 207733 28 + 647215 TAACACATGTGTTGGACATCATCCCTGG - -a -s simMouse_chr6.simMouse.chr6 216699 45 + 636262 CAGAAAGATGAGTTAGCACAGTCTTGGATACTTCTCATTCAATGG -s Anc0.Anc0refChr5 38453 45 + 87904 CAGAAAACTCAATCACCAAGGTCTTAGTTACTTCTAATTTAATGT -s Anc1.Anc1refChr8 52974 45 + 57822 CAGAAAACTCAATCACCAAGGTCTTAGTTACTTCTAATTTAATGT -s Anc2.Anc2refChr15 33865 45 + 86568 CAGGAAACTCAATCACCAAGGTCTTAGTTACTTTTAATTTAATGT -s mr.mrrefChr5 71297 45 + 294540 CAGAAAGCTGAGTTAGCACAGTCTTGGTTACTTCTAATTCAATGG -s simCow_chr6.simCow.chr6 390776 45 - 602619 CAGGAGACTCAATCACCAAGACCTTGGTTAATTTTGATTTAATAT -s simDog_chr6.simDog.chr6 206194 41 + 593897 CAGGAAACTCTTTTACAAAAGTCTTAGTCACTT-TAATTT---GT -s simHuman_chr6.simHuman.chr6 221254 45 + 601863 CAAAAAACTCAATCAACAAGGTCTTAGTTACTTCTAATTTAAGGT -s simRat_chr6.simRat.chr6 207761 45 + 647215 CAGAAAGCTGAGTTAGCACAGTCTTGGTTACTTCTAATTCAATGG - -a -s simMouse_chr6.simMouse.chr6 216744 32 + 636262 GCACAACCAAGTGGCACATAGGATACACCTTT -s Anc0.Anc0refChr5 38498 32 + 87904 GCAACAATAGGAGGTGTGTAGGATATACCCTT -s Anc1.Anc1refChr8 53019 32 + 57822 GCAACAATAGGAGGTGTGTAGGATATACCCTT -s Anc2.Anc2refChr15 33910 32 + 86568 ACAACAATAGGAGGTGTGTAGAATATACCCTG -s mr.mrrefChr5 71342 32 + 294540 GCACAACCAAGTGGCACATAGGATACACCTTT -s simCow_chr6.simCow.chr6 390821 32 - 602619 GCACTAATAGGAGGTGGGTAGAATATACCTTG -s simDog_chr6.simDog.chr6 206235 32 + 593897 ACAACAATGGGAAGAGTGTAGAACATGCCCTG -s simHuman_chr6.simHuman.chr6 221302 32 + 601863 GCAATAATAGGAGGTGTGTATGTTATACCCCT -s simRat_chr6.simRat.chr6 207806 32 + 647215 GCGCCGCCAAGTGGCACATAGGATAACCCTTT - -a -s simMouse_chr6.simMouse.chr6 216776 1 + 636262 A -s Anc0.Anc0refChr5 38530 1 + 87904 A -s Anc1.Anc1refChr8 53051 1 + 57822 A -s Anc2.Anc2refChr15 33942 1 + 86568 C -s mr.mrrefChr5 71374 1 + 294540 A -s simCow_chr6.simCow.chr6 390853 1 - 602619 C -s simDog_chr6.simDog.chr6 206267 1 + 593897 C -s simHuman_chr6.simHuman.chr6 221335 1 + 601863 A -s simRat_chr6.simRat.chr6 207838 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 216777 5 + 636262 TGTTG -s Anc0.Anc0refChr5 38535 5 + 87904 TTTTT -s Anc1.Anc1refChr8 53056 5 + 57822 TTTTT -s Anc2.Anc2refChr15 33947 5 + 86568 TTTTT -s mr.mrrefChr5 71379 5 + 294540 TGTTG -s simCow_chr6.simCow.chr6 390858 5 - 602619 TTTTT -s simDog_chr6.simDog.chr6 206272 5 + 593897 TTTTT -s simHuman_chr6.simHuman.chr6 221340 5 + 601863 TTTTT -s simRat_chr6.simRat.chr6 207843 5 + 647215 TGTTA - -a -s simMouse_chr6.simMouse.chr6 216782 36 + 636262 TGGGCTTGTTCTGTAGCATATGGTAGTAAACAATGT -s Anc0.Anc0refChr5 38540 36 + 87904 TAGGTTTGCTCTATAGAATATGGTAGTAATTGACAT -s Anc1.Anc1refChr8 53061 36 + 57822 TAGGTTTGCTCTATAGAATATGGTAGTAATTGACAT -s Anc2.Anc2refChr15 33953 36 + 86568 TAGGTTTGCTCTATAAAATATGGTAGTAATTCACAT -s mr.mrrefChr5 71384 36 + 294540 TGGGCTTGTTCTATAGCATATGGTAGTAAATGACAT -s simCow_chr6.simCow.chr6 390864 36 - 602619 GAGGCTCGCTCTATAAAATATGGTAGCAATTCACCT -s simDog_chr6.simDog.chr6 206278 36 + 593897 TAGGTTTCCTCTATAAAATATGGTAGTAATTCACAT -s simHuman_chr6.simHuman.chr6 221345 36 + 601863 TAGGTCTGCTCCATAGTAAATGGTAATAATTGGCAT -s simRat_chr6.simRat.chr6 207848 36 + 647215 TGGGCTTGTTCTATAGCAGATGGTAGCAAATGACAT - -a -s simMouse_chr6.simMouse.chr6 216818 36 + 636262 GATTTGAACCAACAGATGGAGCTCAACCTACACAAT -s Anc0.Anc0refChr5 38578 34 + 87904 GGTTTGAACCAACACATACAGATTAACCTGAT--AT -s Anc1.Anc1refChr8 53099 34 + 57822 GGTTTGAACCAACACATACAGATTAACCTGAT--AT -s Anc2.Anc2refChr15 33991 34 + 86568 GGTTTGAACCAACACATACAGATTAACCTGAT--AT -s mr.mrrefChr5 71420 36 + 294540 GATTTGAACCAACAGATGCAGCTCAACCTACACAAT -s simCow_chr6.simCow.chr6 390902 31 - 602619 GGCTTGA---AGCACATGGAGATTAACCTAAT--AT -s simDog_chr6.simDog.chr6 206316 34 + 593897 GGTTTGAACCAACATATACAGACTATGCTGAT--AT -s simHuman_chr6.simHuman.chr6 221383 34 + 601863 GGTCTTCACCAACACATACAGATTAACCTGAT--AG -s simRat_chr6.simRat.chr6 207884 36 + 647215 GATTTGAACCAACAAAGGCAGCTCAACCTCCATAAT - -a -s simMouse_chr6.simMouse.chr6 216854 2 + 636262 TA -s Anc0.Anc0refChr5 38612 2 + 87904 TA -s Anc1.Anc1refChr8 53133 2 + 57822 TA -s Anc2.Anc2refChr15 34030 2 + 86568 TA -s mr.mrrefChr5 71456 2 + 294540 TA -s simCow_chr6.simCow.chr6 390938 2 - 602619 TA -s simDog_chr6.simDog.chr6 206355 2 + 593897 TA -s simHuman_chr6.simHuman.chr6 221417 2 + 601863 TA -s simRat_chr6.simRat.chr6 207920 2 + 647215 TA - -a -s simMouse_chr6.simMouse.chr6 216856 47 + 636262 CCACACCTGTAAGTTTTAATCAGTAGCAATCATGTTAGTTAATGAAA -s Anc0.Anc0refChr5 38614 43 + 87904 CCAATATGGTAACTTTCAATCTGTCTCAACCATTTTA----CTGAAA -s Anc1.Anc1refChr8 53135 47 + 57822 CCAATATGGTAACTTTCAATCTGTCTCAACCATTTTAGTTACTGAAA -s Anc2.Anc2refChr15 34032 43 + 86568 CAAATATGGTAACTTTCAATCTGTCTCAACCATTTTA----CCGAAA -s mr.mrrefChr5 71458 47 + 294540 CCACACCTGTAAGTTTTAGTCAGTAGCAATCATGTTAGTTAATGAAA -s simCow_chr6.simCow.chr6 390941 43 - 602619 CAAGTCTAGCAACTTTCAATCCATATCAATCATTTTA----CCGAAA -s simDog_chr6.simDog.chr6 206357 43 + 593897 CAAATATGGTAACTTTCAATCTGTCTCAACCATTTCA----CCGAGA -s simHuman_chr6.simHuman.chr6 221419 17 + 601863 CCA------------------------------ATATGTTACTGAAA -s simRat_chr6.simRat.chr6 207922 47 + 647215 CCATACCAGTAAGTTTTAGTCAGTAACAATCATGTTAGTTAATGAAA - -a -s simMouse_chr6.simMouse.chr6 216903 137 + 636262 AAGTAAGTCCCTCCCACCTAAATTAACGATTAGATGCACCTGGATTACACCCTACTTGAGTATTGAAGTCCGCCTTGTGCACATATTGCATGCCCTGATATTGCTATAACTGAAGACATGACCCTCATGACCATACA -s Anc0.Anc0refChr5 38665 137 + 87904 AAATAAGTTACTCCCACCTAGACTAAATATTAGATGTGCCTGGATCACACCCAATTTGAGTATTGAAATCTGTTTAGCGTACATAGGGATCACCCTGATGTTACTTTTACCGGGGACACGAGCTTCAGGACCCTACA -s Anc1.Anc1refChr8 53190 137 + 57822 AAATAAGTTACTCCCACCTAGACTAAATATTAGATGTGCCTGGATCACACCCAATTTGAGTATTGAAATCTGTTTAGCGTACATAGGGATCACCCTGATGTTACTTTTACCGGGGACACGAGCTTCAGGACCCTACA -s Anc2.Anc2refChr15 34083 137 + 86568 AAATAAGTTATTCCCACCTAGACTAAACATTAGCTGTGCCCAGATCACACCCAATTCAAGTATTGGAATCTGTTTAGCATACATAGGGATCACCCTGATGTTACTTTTACCAGGGACACAAGCTTCAGGACCCTACA -s mr.mrrefChr5 71505 137 + 294540 AAGTAAGTCCCTCCCACCTAAATTAACTATTAGATGCACCTGGATTACACCCAACTTGAGTATTGAAGTCTGCCTAGTGCACATATTGAATACCCTGATATTGCTTTAACTGAGGACATGACCCTCATGACCATACA -s simCow_chr6.simCow.chr6 390992 134 - 602619 AAATAAGTTCACACCACTGAGACTAGTCATTAGCTGTACCCAGATCACACCC-ATTCAAGCATTGGAATCTGTTTAGCATTCATAGGGGTAACCCTGATGTTACTGTTGCCA--GACACAATCTTCAGGGCCCTACA -s simDog_chr6.simDog.chr6 206406 137 + 593897 AAATGAGTTATTCCCACCTTGATTAAACATTGGCTGTGACCAGATCACACCCAATTCAAGTAGTGGAATCTGTTTAACATACATAGGGATCACCCTAATGTTACCTCTACCAGGGTGACAAGCCTCAGAACCCTACA -s simHuman_chr6.simHuman.chr6 221444 136 + 601863 AAAAAAGTTACTCCCACCTAGACTAAATATTAGATGTGCCTGGATCATACTCAATATGGGTATTGAAATTTGTTCAGAGTACATAGAGATCAACTTGATGTTACTTTTATAGTGGACGCGAGCTTCAGGACTGTAC- -s simRat_chr6.simRat.chr6 207969 128 + 647215 AAGTAAGTCCTTCCTGCCTTCATTAACTATT------ACCCGGATTGCACGCAACTTGAGTATGGAA---TGCCTAGTGCACATAATGAATACCCTGATATTGCTTTAACTAAGGACATGACCCTCATGACCATACA - -a -s simMouse_chr6.simMouse.chr6 217040 23 + 636262 TGTGAGTTGAGGTTACCATAATC -s Anc0.Anc0refChr5 38802 23 + 87904 TAGGAGTTCCTGTCACATTGTTC -s Anc1.Anc1refChr8 53327 23 + 57822 TAGGAGTTCCTGTCACATTGTTC -s Anc2.Anc2refChr15 34221 23 + 86568 CAGGAGTTCCTGTCACATTGTCC -s mr.mrrefChr5 71642 23 + 294540 TATGAGTTGAGGTTACCATAATC -s simCow_chr6.simCow.chr6 391127 20 - 602619 C---AGTTCCTATCACATTGTCC -s simDog_chr6.simDog.chr6 206544 23 + 593897 CAGGAGTTCCTGTCACATTGCCC -s simHuman_chr6.simHuman.chr6 221580 23 + 601863 TAGGAGTTACTGTCACATTGTTC -s simRat_chr6.simRat.chr6 208097 23 + 647215 CAAGAGTTGTGGTTACCATAATC - -a -s simMouse_chr6.simMouse.chr6 217063 3 + 636262 CAG -s Anc0.Anc0refChr5 38826 3 + 87904 CCA -s Anc1.Anc1refChr8 53351 3 + 57822 CCA -s Anc2.Anc2refChr15 34245 3 + 86568 CCA -s mr.mrrefChr5 71665 3 + 294540 CAG -s simCow_chr6.simCow.chr6 391148 3 - 602619 CTA -s simDog_chr6.simDog.chr6 206568 3 + 593897 TCA -s simHuman_chr6.simHuman.chr6 221604 3 + 601863 CCA -s simRat_chr6.simRat.chr6 208120 3 + 647215 CAG - -a -s simMouse_chr6.simMouse.chr6 217066 17 + 636262 AATGCAGACTGATATCC -s Anc0.Anc0refChr5 38829 17 + 87904 AGTGTATATCTATTAAT -s Anc1.Anc1refChr8 53354 17 + 57822 AGTGTATATCTATTAAT -s Anc2.Anc2refChr15 34287 17 + 86568 AGTGTATATCTATTAAT -s mr.mrrefChr5 71668 17 + 294540 AATGCAGACCGATAACC -s simCow_chr6.simCow.chr6 391264 17 - 602619 AGCATATGTCTGTTAAT -s simDog_chr6.simDog.chr6 206610 17 + 593897 AGTGTATACCTATCAAT -s simHuman_chr6.simHuman.chr6 221607 17 + 601863 AGTGACTATCTATTAAT -s simRat_chr6.simRat.chr6 208123 17 + 647215 AATGCAGACCAATAACC - -a -s simMouse_chr6.simMouse.chr6 217083 49 + 636262 TGGCAGCAATGCATATCTAATGATGTAGTCATGCATGAAAGTTAGAGGT -s Anc0.Anc0refChr5 38846 38 + 87904 GTGCATTGTTGCTTAGCCAATG-----------CTTGACAGTTGGAGGC -s Anc1.Anc1refChr8 53371 38 + 57822 GTGCATTGTTGCTTAGCCAATG-----------CTTGACAGTTGGAGGC -s Anc2.Anc2refChr15 34304 38 + 86568 GTGCATTGTTGCTTAGTCAATG-----------TTTAACAGTTGAAGGC -s mr.mrrefChr5 71685 49 + 294540 TGGCAGCAATGCATATCTAATGATGTAGTCATGCTTGACAGTTAGAGGT -s simCow_chr6.simCow.chr6 391281 38 - 602619 GTGCATTGTTGCCAAGTCAACC-----------TTTAACAACTGAAGGT -s simDog_chr6.simDog.chr6 206627 38 + 593897 GTGCATTGTTGCTTAGTCAATG-----------TTTAATGGTTGAAGGC -s simHuman_chr6.simHuman.chr6 221624 38 + 601863 GTGCACTGTTGCTTAGCCAAAG-----------CTCGACAGTCGGAGGC -s simRat_chr6.simRat.chr6 208141 49 + 647215 TGGCAGCAATGCGTATCTAATGATGTAGTCATTCTTGACAGTTTGAGGT - -a -s simMouse_chr6.simMouse.chr6 217132 13 + 636262 TGGTTACATCTTG -s Anc0.Anc0refChr5 38884 13 + 87904 TGGTTATGTTCCA -s Anc1.Anc1refChr8 53409 13 + 57822 TGGTTATGTTCCA -s Anc2.Anc2refChr15 34342 13 + 86568 TGGTTGTGTTCCA -s mr.mrrefChr5 71734 13 + 294540 TGGTTACATCTTG -s simCow_chr6.simCow.chr6 391319 13 - 602619 TGGTCTTGTTCCT -s simDog_chr6.simDog.chr6 206673 13 + 593897 CAGTTGTGTTCTA -s simHuman_chr6.simHuman.chr6 221662 13 + 601863 TGGCTATGTTCCA -s simRat_chr6.simRat.chr6 208190 13 + 647215 TGGTTACATCTTG - -a -s simMouse_chr6.simMouse.chr6 217145 9 + 636262 AAGCACTGA -s Anc0.Anc0refChr5 38897 9 + 87904 AAGTGCTGA -s Anc1.Anc1refChr8 53422 9 + 57822 AAGTGCTGA -s Anc2.Anc2refChr15 34355 9 + 86568 AAGTGCTGA -s mr.mrrefChr5 71747 9 + 294540 AAGTACTGA -s simCow_chr6.simCow.chr6 391332 9 - 602619 AAGTGCGGA -s simDog_chr6.simDog.chr6 206688 9 + 593897 AACTGCTGA -s simHuman_chr6.simHuman.chr6 221675 9 + 601863 AAGTGCTGA -s simRat_chr6.simRat.chr6 208203 9 + 647215 AGGTATTGA - -a -s simMouse_chr6.simMouse.chr6 217154 42 + 636262 AACCTGAGAATGTGCTAGTTATTCATTTTAGTTGTGTCTATA -s Anc0.Anc0refChr5 38906 6 + 87904 GGGCTG------------------------------------ -s Anc1.Anc1refChr8 53431 6 + 57822 GGGCTG------------------------------------ -s Anc2.Anc2refChr15 34364 6 + 86568 GGGCCC------------------------------------ -s mr.mrrefChr5 71756 6 + 294540 AGCCTG------------------------------------ -s simCow_chr6.simCow.chr6 391371 6 - 602619 GGGCAT------------------------------------ -s simDog_chr6.simDog.chr6 206697 6 + 593897 GACCCC------------------------------------ -s simHuman_chr6.simHuman.chr6 221684 6 + 601863 GGGCTG------------------------------------ -s simRat_chr6.simRat.chr6 208212 6 + 647215 AGCCTG------------------------------------ - -a -s simMouse_chr6.simMouse.chr6 217196 7 + 636262 AGCTATC -s Anc0.Anc0refChr5 38918 7 + 87904 ATCTATC -s Anc1.Anc1refChr8 53443 7 + 57822 ATCTATC -s Anc2.Anc2refChr15 34376 7 + 86568 AGCTATC -s mr.mrrefChr5 71762 7 + 294540 ATCTATC -s simCow_chr6.simCow.chr6 391383 7 - 602619 GGCTATC -s simDog_chr6.simDog.chr6 206709 7 + 593897 AGCTATC -s simHuman_chr6.simHuman.chr6 221696 7 + 601863 ATCTATC -s simRat_chr6.simRat.chr6 208218 7 + 647215 ATCTGGC - -a -s simMouse_chr6.simMouse.chr6 217203 34 + 636262 ATAGTGTGGTGGGAATAGTTAGTAAATGTTGGCT -s Anc0.Anc0refChr5 38925 30 + 87904 ATTATGTCATGTGTATAGTCAATAAAAGT----T -s Anc1.Anc1refChr8 53450 30 + 57822 ATTATGTCATGTGTATAGTCAATAAAAGT----T -s Anc2.Anc2refChr15 34383 30 + 86568 ATTGTGTCATGTGTATAGTCAATAAAAGT----G -s mr.mrrefChr5 71769 30 + 294540 ATAATGTGATGGGTATAGTTAGTAAATGT----T -s simCow_chr6.simCow.chr6 391390 30 - 602619 ATTGTGTCATGTGTACAGTTGACAAAAGT----G -s simDog_chr6.simDog.chr6 206716 30 + 593897 ATTGTGTCATGTGTTTAGTCATTAAAAGT----G -s simHuman_chr6.simHuman.chr6 221703 30 + 601863 ACCATGTCATGTGTATGGTCAATACAAGT----T -s simRat_chr6.simRat.chr6 208291 20 + 647215 ATAACGTGAAAATTCTAGTT-------------- - -a -s simMouse_chr6.simMouse.chr6 217237 19 + 636262 TTTGATTAAATGAAACCAT -s Anc0.Anc0refChr5 38955 13 + 87904 TTGAATTAAGT------AG -s Anc1.Anc1refChr8 53480 17 + 57822 TTGAATTAAGTGAA--CAG -s Anc2.Anc2refChr15 34422 13 + 86568 TTGAGTTAAGT------AG -s mr.mrrefChr5 71799 17 + 294540 TTTGATTAAATGAA--CAT -s simCow_chr6.simCow.chr6 391429 13 - 602619 TTTGGTTAAGC------AG -s simDog_chr6.simDog.chr6 206755 13 + 593897 TTGAGTTAAGT------AG -s simHuman_chr6.simHuman.chr6 221733 17 + 601863 TTGCATTAAGTGAA--CAG - -a -s simMouse_chr6.simMouse.chr6 217256 39 + 636262 TTTCATAGCAAGGATGGACATTCAAACATGGGACTGGCT -s Anc0.Anc0refChr5 38969 38 + 87904 TTTGACACAATAGGTG-GAATATCAGCATGGGACATGGT -s Anc1.Anc1refChr8 53498 38 + 57822 TTTGACACAATAGGTG-GAATATCAGCATGGGACATGGT -s Anc2.Anc2refChr15 34436 38 + 86568 TTTGACACAATAGGTG-GAATATCAGTGTGAGACATGGT -s mr.mrrefChr5 71816 39 + 294540 TTTCATAGCAAGGATGGACATTCAAACATGGGACTGGCT -s simCow_chr6.simCow.chr6 391443 38 - 602619 TTTGACACCATGGATG-GAATATCAGTGTGAGACATGGT -s simDog_chr6.simDog.chr6 206769 15 + 593897 TTTGATCAAATAGGT------------------------ -s simHuman_chr6.simHuman.chr6 221751 38 + 601863 TTCGACACAACAACTG-CAATATGAGCATAGGACGTGTT - -a -s simMouse_chr6.simMouse.chr6 217295 11 + 636262 GCATACATGTC -s Anc0.Anc0refChr5 39009 11 + 87904 ACATCCATGTT -s Anc1.Anc1refChr8 53538 11 + 57822 ACATCCATGTT -s Anc2.Anc2refChr15 34476 11 + 86568 ACATCCATGTT -s mr.mrrefChr5 71855 11 + 294540 GCATACATGTC -s simCow_chr6.simCow.chr6 391483 11 - 602619 ACATCCATGTT -s simHuman_chr6.simHuman.chr6 221791 11 + 601863 ACATCCCTGTT - -a -s simMouse_chr6.simMouse.chr6 217306 14 + 636262 ACTTTCTGGTTTCT -s Anc0.Anc0refChr5 39022 13 + 87904 ACTTACAT-TTTTC -s Anc1.Anc1refChr8 53551 14 + 57822 ACTTACATATTTTC -s Anc2.Anc2refChr15 34489 13 + 86568 ACTTACAT-CTTTC -s mr.mrrefChr5 71866 14 + 294540 ACTTTCTTGTTTCT -s simCow_chr6.simCow.chr6 391496 13 - 602619 ACTTACAT-CTTTC -s simHuman_chr6.simHuman.chr6 221804 14 + 601863 ACTTCCATATTTTC -s simRat_chr6.simRat.chr6 208311 12 + 647215 --TCTCTTGTTTCT - -a -s simMouse_chr6.simMouse.chr6 217320 19 + 636262 GTCTCTATAACAGTTAACA -s Anc0.Anc0refChr5 39043 17 + 87904 TTCTCTATTACAG--AACA -s Anc1.Anc1refChr8 53573 17 + 57822 TTCTCTATTACAG--AACA -s Anc2.Anc2refChr15 34510 17 + 86568 TTCCCTATTACTG--AATA -s mr.mrrefChr5 71880 19 + 294540 TTCTCTATAACAGTTAACA -s simCow_chr6.simCow.chr6 391517 17 - 602619 TTCCCTATTACTG--AATA -s simHuman_chr6.simHuman.chr6 221826 17 + 601863 TGATCTATCACAG--AACA -s simRat_chr6.simRat.chr6 208323 19 + 647215 TTCTCTGTAACAGTTAACA - -a -s simMouse_chr6.simMouse.chr6 217339 1 + 636262 A -s Anc0.Anc0refChr5 39060 1 + 87904 A -s Anc1.Anc1refChr8 53590 1 + 57822 A -s Anc2.Anc2refChr15 34527 1 + 86568 A -s mr.mrrefChr5 71899 1 + 294540 A -s simCow_chr6.simCow.chr6 391545 1 - 602619 A -s simHuman_chr6.simHuman.chr6 221843 1 + 601863 A -s simRat_chr6.simRat.chr6 208342 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 217340 122 + 636262 GCTACTAAACAGATTGAGACTGAGAGGAATTCCCAAAGCATCCTATTTAAGTGCTCCTTCCAATGGAGGTCATAGGTAGCTTGACTTATAGGTTTCATGAATAAGAATGGATTATCTAAAAA -s Anc0.Anc0refChr5 39066 110 + 87904 GCTACCAAATAGATGGAAACAGAGAGGGAGTGACAGAGCACCACATTCAGGTGCTCCCACCATAGGAA------------TTGACTTGTACATAAAATGGGTAAGACCTGATTATCCATAAA -s Anc1.Anc1refChr8 53596 110 + 57822 GCTACCAAATAGATGGAAACAGAGAGGGAGTGACAGAGCACCACATTCAGGTGCTCCCACCATAGGAA------------TTGACTTGTACATAAAATGGGTAAGACCTGATTATCCATAAA -s Anc2.Anc2refChr15 34533 110 + 86568 GCTCTCAGATAGGCGAAAATTGAGAGGGAGTGACAGAGCTCCACATTCAGTTGCTCCCACCATAGGAA------------TTGACTTGTACACAAAATGGGTAAGACCTGATTACCCATAAA -s mr.mrrefChr5 71900 113 + 294540 GCTACTAAACAGATTGAGACAGAGAGGGAGTCCCAGAGCACCCTATTTAGGTGCTCCTTCCAATGGAAGT---------CTTGACTTATAGGTTTCATGAATAAGAATGGATTATCTAAAAA -s simCow_chr6.simCow.chr6 391551 98 - 602619 GCTCTCAGATAGGCGAAAATTGAGAGGGAATGACAGGGCGCTACA-----TTACTCCCATTATAGGAA------------TTGACTTGCACA-------GACAAGACCTGATTACCAGTAAA -s simDog_chr6.simDog.chr6 206784 94 + 593897 ----------------AAATTAAGAGGAAGTGACCAAGCTCCACATTCAGTTGTTCCTGCCATAGCAA------------TTGACTTGTACACAAAATGGGTAAGACCTTATTACCCATAAA -s simHuman_chr6.simHuman.chr6 221849 110 + 601863 GCTACAAAGTAGATAGAAACAGAGAAGGAGTGACAGAGCACCACATTCAGGTGCTCCCACCATAAGAA------------TTGACTAGTATATGAAATGGGTAAGACCTGATTATCCATAAA -s simRat_chr6.simRat.chr6 208343 113 + 647215 GCTACTAAACAGATTGAGACAGAGACGGAGTCCCAGAGCACCCTATTTAGGTGCTCCTTCCAGTGGAAGC---------GTTGACTTATAGGTTTCATGAATAAGAATGGATTGTCTAAAAG - -a -s simMouse_chr6.simMouse.chr6 217462 22 + 636262 CAGACTTTCCTTAACTCTTGTT -s Anc0.Anc0refChr5 39183 22 + 87904 CAGGCTTTTTTTAACTCTTGTT -s Anc1.Anc1refChr8 53713 22 + 57822 CAGGCTTTTTTTAACTCTTGTT -s Anc2.Anc2refChr15 34650 22 + 86568 CAGGCTTCTTTTAACTATTGTT -s mr.mrrefChr5 72013 22 + 294540 CAGGCTTTCCTTAACTCTTGTT -s simCow_chr6.simCow.chr6 391656 22 - 602619 CAGGTTTCTTTGAACAATTGTT -s simDog_chr6.simDog.chr6 206885 22 + 593897 CAGGCTTCTCTTAACTATTGCT -s simHuman_chr6.simHuman.chr6 221966 22 + 601863 CAGGCGTTTTTTAGCTCTTGTA -s simRat_chr6.simRat.chr6 208456 22 + 647215 CAGGCTTTCATTAACTCTTGTT - -a -s simMouse_chr6.simMouse.chr6 217484 51 + 636262 GGTGTGTTCTGTTTCAGTGATCCCCCCAATGGTCCAGAACTTGCTGGGTCT -s Anc0.Anc0refChr5 39219 48 + 87904 GGTTTGTTATGTTTTAAAGAT---CCCATAGTTCCAGAACTGGGTGGGTCT -s Anc1.Anc1refChr8 53749 48 + 57822 GGTTTGTTATGTTTTAAAGAT---CCCATAGTTCCAGAACTGGGTGGGTCT -s Anc2.Anc2refChr15 34686 48 + 86568 GCCTTGTTATGTTTTAAAGAT---TCCATAGTTCCAGAACTGAGTGGGTCT -s mr.mrrefChr5 72035 48 + 294540 GGTGTGTTCTGTTTCAGTGAT---CCCAATGGTCCAGAACTTGCTGGGTCT -s simCow_chr6.simCow.chr6 391692 48 - 602619 GCCTTATTAGGTTTTAAAGAG---GCCGGAGTATCATGACTGAGTGTGTAT -s simDog_chr6.simDog.chr6 206921 48 + 593897 GCCTTGTTATGTTTCAAAGAT---TCCATAGTTCAAGAACTGAGTGGGTCT -s simHuman_chr6.simHuman.chr6 222002 48 + 601863 AGTTTGTTATGTTTTAAGGAC---CCCATGGTTCCAGAACTGGGCGAGTCT -s simRat_chr6.simRat.chr6 208478 48 + 647215 GGTCTGTTCTGCTTCAGTGAT---CCCAATGGGCCAGAACTTGCTGGGTCA - -a -s simMouse_chr6.simMouse.chr6 217535 22 + 636262 TGGGTGGTTGTACTAGTGTGTC -s Anc0.Anc0refChr5 39268 22 + 87904 TGGGTGGGTGTACAAGTGTGTC -s Anc1.Anc1refChr8 53798 22 + 57822 TGGGTGGGTGTACAAGTGTGTC -s Anc2.Anc2refChr15 34735 22 + 86568 TGGGTGGGTGTACAAGTGTGTG -s mr.mrrefChr5 72083 22 + 294540 TGGGTGGTTGTACTAGTGTGTC -s simCow_chr6.simCow.chr6 391741 22 - 602619 TGGGTGGGGGTACAGGTGTGTG -s simDog_chr6.simDog.chr6 206970 22 + 593897 CAGGTGGATGTACAAGTGTGTG -s simHuman_chr6.simHuman.chr6 222051 22 + 601863 TGGGTGGGTGTAAGAGCATGTC -s simRat_chr6.simRat.chr6 208526 22 + 647215 TGAGTGGCTTTACTAGTGTGAC - -a -s simMouse_chr6.simMouse.chr6 217557 15 + 636262 TGCTTCTTTGGTAAG -s Anc0.Anc0refChr5 39294 13 + 87904 TG--TGATTAGGTAG -s Anc1.Anc1refChr8 53824 13 + 57822 TG--TGATTAGGTAG -s Anc2.Anc2refChr15 34761 13 + 86568 TG--TGATTAAGTAG -s mr.mrrefChr5 72109 15 + 294540 TGCTTGTTTGGTAAG -s simCow_chr6.simCow.chr6 391767 5 - 602619 TG--TGA-------- -s simDog_chr6.simDog.chr6 206996 13 + 593897 TG--TGATTAAGTAG -s simHuman_chr6.simHuman.chr6 222077 12 + 601863 T---TGCTTAGATAG -s simRat_chr6.simRat.chr6 208552 15 + 647215 TGCTTGTTTGGGACG - -a -s simMouse_chr6.simMouse.chr6 217572 6 + 636262 TTCCTC -s Anc0.Anc0refChr5 39307 6 + 87904 TTCTTT -s Anc1.Anc1refChr8 53837 6 + 57822 TTCTTT -s Anc2.Anc2refChr15 34774 6 + 86568 TCCTTC -s mr.mrrefChr5 72124 6 + 294540 TTCCTT -s simDog_chr6.simDog.chr6 207028 6 + 593897 TCCTTC -s simHuman_chr6.simHuman.chr6 222089 6 + 601863 TTCTTT -s simRat_chr6.simRat.chr6 208567 6 + 647215 TTCCTT - -a -s simMouse_chr6.simMouse.chr6 217578 85 + 636262 AGGAAAAGAAAAAGGAGACCGTGACTATTTGGGAGAAAAATAAACACTGTGAGAAGTTTTTAGCAGTTGGGCATGACACCAAAAT -s Anc0.Anc0refChr5 39313 84 + 87904 AGTAGAGGAAGGAGGAGACTATGATCATCCAGGAGAAAA-TGAGCATTGTGGGAGCTTTTTAGCTGTTGGGCATAACATCAAATC -s Anc1.Anc1refChr8 53843 84 + 57822 AGTAGAGGAAGGAGGAGACTATGATCATCCAGGAGAAAA-TGAGCATTGTGGGAGCTTTTTAGCTGTTGGGCATAACATCAAATC -s Anc2.Anc2refChr15 34780 84 + 86568 AGTAGAGGAGGGAGGAGACTATGATCATCCAGGAGAAAA-TGGGCATTGTGGGAGCTTTTTAGCTGTTGGGCATAACATCAAATC -s mr.mrrefChr5 72130 85 + 294540 AGGAGAAGAAAAAGGAGACCATGACTATTTGGGAGAAAAATGAACACTGTGAGAAGTTTTTAGCAGTTGGGCATGACACCAAATT -s simCow_chr6.simCow.chr6 391772 77 - 602619 -------TAGGGTGGAGACTATGATCATCCAGGAGAAAA-TGGGCACTGTGGACGCCTTTTAGCTGGTGGGCATAACATCAAATC -s simDog_chr6.simDog.chr6 207036 84 + 593897 AGTAGAGGCGGGAGGAGACTGTGATCATTCAGGAAAAGA-TAGGCATTGTGGGAACTTTTTAGCTGTTGGGCCTAACATCAAACC -s simHuman_chr6.simHuman.chr6 222095 84 + 601863 AGTAGAGGAAGGAGGAGACTATGATCACCCAGGAGAAAA-TGAGCATTGCAGGAGATTTTTAGCTGTTAGGCATAACATTAAATC -s simRat_chr6.simRat.chr6 208573 85 + 647215 AGGAGAAGAAAAAGGAGACCATGACTATTTGGTAAAAAAATGAACACTGTCTAAAGTTTTTAGTAGTTGGGCATGACACCAAATT - -a -s simMouse_chr6.simMouse.chr6 217663 45 + 636262 AACCATCCAGTGGATTCAGTAATTGCAGACATTAGATTGAAGCAA -s Anc0.Anc0refChr5 39397 45 + 87904 AGCCATTCAATAGATTCAGTAATTGCTAATGCTAGATTGAATCCA -s Anc1.Anc1refChr8 53927 45 + 57822 AGCCATTCAATAGATTCAGTAATTGCTAATGCTAGATTGAATCCA -s Anc2.Anc2refChr15 34864 45 + 86568 AGCCATTCAATAGATTCAGTAATTGCTAATGCTAGATTGAATCCA -s mr.mrrefChr5 72215 45 + 294540 AACCATTCAATGGATTCAGTAATTGCAGACATTAGATTGAAGCAA -s simCow_chr6.simCow.chr6 391849 45 - 602619 CGCCATTGGATAGATTCAGAGATTGCCAGTGCCAGATTCAATGAA -s simDog_chr6.simDog.chr6 207125 45 + 593897 AGCCATTCACTAGACACAGTAATTGCTGAAGCTAGATTGGAACCA -s simHuman_chr6.simHuman.chr6 222179 45 + 601863 AGTTATTCAAAAAATTCAGTAATTGCTAATGCTGGATTGAATTGA -s simRat_chr6.simRat.chr6 208658 45 + 647215 GACCATTCAATGGATTTGGTAACTGCAGACATTAGATTGAAGAAA - -a -s simMouse_chr6.simMouse.chr6 217708 29 + 636262 GATAGATGTTGGACACCAAAGATATGCCA -s Anc0.Anc0refChr5 39460 29 + 87904 GGTACATTTTGGACACTAAAGATATTCCA -s Anc1.Anc1refChr8 53990 29 + 57822 GGTACATTTTGGACACTAAAGATATTCCA -s Anc2.Anc2refChr15 34927 29 + 86568 GGTACATTTTGAACACTAAAGACATTCCA -s mr.mrrefChr5 72277 29 + 294540 GATAGATTTTGGACACCAAAGATATGCCA -s simCow_chr6.simCow.chr6 391913 29 - 602619 AGTACACTTTGATCACTAAAGACATTCCA -s simDog_chr6.simDog.chr6 207309 29 + 593897 GGTACATTTTGAACAACAAGGACATTCCA -s simHuman_chr6.simHuman.chr6 222242 29 + 601863 TGTACATTTTGGACCCTAAAGATATTCCA -s simRat_chr6.simRat.chr6 208720 29 + 647215 CATAGAGTGTGTACTCCAAAGATATGCCA - -a -s simMouse_chr6.simMouse.chr6 217737 53 + 636262 TTATTTATGCCCAAATTTGAACTTTTCCAGAGCCCAGAATAGTTAAGCCACAT -s Anc0.Anc0refChr5 39491 19 + 87904 ATTT----------------------------------ATAGTTGACCCACAT -s Anc1.Anc1refChr8 54021 19 + 57822 ATTT----------------------------------ATAGTTGACCCACAT -s Anc2.Anc2refChr15 34958 19 + 86568 GTTT----------------------------------ATAGTTGACCCACCT -s mr.mrrefChr5 72306 19 + 294540 ATTT----------------------------------ATAGTTGACCCACAT -s simCow_chr6.simCow.chr6 210398 19 + 602619 TCTT----------------------------------ATAACTAACCCATGT -s simDog_chr6.simDog.chr6 207340 19 + 593897 GTTT----------------------------------ATAGTTGACCCACCT -s simHuman_chr6.simHuman.chr6 222273 19 + 601863 ATTT----------------------------------ATAGTTGACGCACAT -s simRat_chr6.simRat.chr6 208749 19 + 647215 ATTT----------------------------------ATAGTTGACCCACAT - -a -s simMouse_chr6.simMouse.chr6 217790 36 + 636262 TTGGTCCCAAACTACCCCCATGCAAGGTATCCCTAC -s Anc0.Anc0refChr5 39510 35 + 87904 TTGGCAAC-ACTTACCTCCACTTATGGCATAATCAG -s Anc1.Anc1refChr8 54040 35 + 57822 TTGGCAAC-ACTTACCTCCACTTATGGCATAATCAG -s Anc2.Anc2refChr15 34981 35 + 86568 TTGGCAAC-ACTTACCTCCACTTGTGATATAATCAG -s mr.mrrefChr5 72325 35 + 294540 TTGGTCCC-AACTACCCCCATGCAAGGCATCCCCAG -s simCow_chr6.simCow.chr6 210421 35 + 602619 TTGGCAAC-ACTTACCTCCACTTGTGATATAATCAG -s simHuman_chr6.simHuman.chr6 222315 35 + 601863 TTGGCAAC-AGTTACCTCCACTGATAGCATAATCAG -s simRat_chr6.simRat.chr6 208768 16 + 647215 TTGGT--------------------TGCATCCCCAG - -a -s simMouse_chr6.simMouse.chr6 217826 6 + 636262 ATGATT -s Anc0.Anc0refChr5 39545 6 + 87904 ATGATT -s Anc1.Anc1refChr8 54075 6 + 57822 ATGATT -s Anc2.Anc2refChr15 35016 6 + 86568 GTTGTT -s mr.mrrefChr5 72360 6 + 294540 ATGATT -s simCow_chr6.simCow.chr6 210457 6 + 602619 GTTGTT -s simHuman_chr6.simHuman.chr6 222350 6 + 601863 ATGATT -s simRat_chr6.simRat.chr6 208784 6 + 647215 ATGATT - -a -s simMouse_chr6.simMouse.chr6 217832 14 + 636262 CTGGTAGGCCAGTA -s Anc0.Anc0refChr5 39552 14 + 87904 TTAGCAGGTCAGGA -s Anc1.Anc1refChr8 54082 14 + 57822 TTAGCAGGTCAGGA -s Anc2.Anc2refChr15 35023 14 + 86568 TTAGCACGTCAAGA -s mr.mrrefChr5 72366 14 + 294540 CTGGTAGGCCAGTA -s simCow_chr6.simCow.chr6 210464 14 + 602619 TTAGCACGTCAAGA -s simHuman_chr6.simHuman.chr6 222357 14 + 601863 TTAGAAGGTCAGGA -s simRat_chr6.simRat.chr6 208790 14 + 647215 CTGGTAGACCAGTA - -a -s simMouse_chr6.simMouse.chr6 217846 18 + 636262 GCCACCTTAGGTTAAAGA -s Anc0.Anc0refChr5 39566 18 + 87904 GCCAGGTGGGGTCTTAGG -s Anc1.Anc1refChr8 54096 18 + 57822 GCCAGGTGGGGTCTTAGG -s Anc2.Anc2refChr15 35037 18 + 86568 GCAAGGTGGGGACTTAAG -s mr.mrrefChr5 72380 18 + 294540 GCCACCTTAGGTTTAAGA -s simCow_chr6.simCow.chr6 210478 18 + 602619 GCAAGGTGGGGACTTAAG -s simHuman_chr6.simHuman.chr6 222372 18 + 601863 GCCTGTTCGGGTCTTGGG -s simRat_chr6.simRat.chr6 208804 18 + 647215 GCTCACATAGACTTAAGA - -a -s simMouse_chr6.simMouse.chr6 217864 25 + 636262 AAGCAAAATCTGAGGAGTATACAAG -s Anc0.Anc0refChr5 39584 25 + 87904 AAGTAAAATCCCAGTGGTAAGTGAG -s Anc1.Anc1refChr8 54114 25 + 57822 AAGTAAAATCCCAGTGGTAAGTGAG -s Anc2.Anc2refChr15 35055 25 + 86568 GAGTAAAATCCCAGTGGCAAGTGAA -s mr.mrrefChr5 72398 25 + 294540 AAGCAAAATCTGAGGAGTATACAAG -s simCow_chr6.simCow.chr6 210498 25 + 602619 GAGTAAAATCCCAGTGGCAAGTGAA -s simDog_chr6.simDog.chr6 207361 4 + 593897 ---------------------TGAA -s simHuman_chr6.simHuman.chr6 222390 25 + 601863 AGCTATAGTTCCAGTCTTAAGTGAG -s simRat_chr6.simRat.chr6 208822 25 + 647215 AAGCGAAATCTGAGGAGTATACAAG - -a -s simMouse_chr6.simMouse.chr6 217889 3 + 636262 TAA -s Anc0.Anc0refChr5 39609 3 + 87904 TAA -s Anc1.Anc1refChr8 54139 3 + 57822 TAA -s Anc2.Anc2refChr15 35080 3 + 86568 CAG -s mr.mrrefChr5 72423 3 + 294540 TAA -s simCow_chr6.simCow.chr6 210561 3 + 602619 CAG -s simDog_chr6.simDog.chr6 207365 3 + 593897 CAG -s simHuman_chr6.simHuman.chr6 222415 3 + 601863 TAA -s simRat_chr6.simRat.chr6 208847 3 + 647215 TAA - -a -s simMouse_chr6.simMouse.chr6 217892 41 + 636262 GCTAATGTCTGTTGATGTACTCTTGTGGTTCGAGCCTAAGT -s Anc0.Anc0refChr5 39612 25 + 87904 GCTATGTTCTTATGAAGTACCCTTG---------------- -s Anc1.Anc1refChr8 54142 25 + 57822 GCTATGTTCTTATGAAGTACCCTTG---------------- -s Anc2.Anc2refChr15 35083 25 + 86568 GCTATGTTCTTAAGGATGACCCTGG---------------- -s mr.mrrefChr5 72426 25 + 294540 GCTAATGTCTGTTGATGTACTCTTG---------------- -s simCow_chr6.simCow.chr6 210567 22 + 602619 GCTACATTCTTAAGAATATCC---A---------------- -s simDog_chr6.simDog.chr6 207368 25 + 593897 CCTGTGTTCTTAAGGCTGACTCTGG---------------- -s simHuman_chr6.simHuman.chr6 222418 24 + 601863 GCTATGTT-TAATGAGGTACCCTTG---------------- -s simRat_chr6.simRat.chr6 208850 25 + 647215 GCTAATGTCTGTCGACATACTCTTG---------------- - -a -s simMouse_chr6.simMouse.chr6 217933 8 + 636262 GTGCCAAG -s Anc0.Anc0refChr5 39639 8 + 87904 GTCCTGAA -s Anc1.Anc1refChr8 54169 8 + 57822 GTCCTGAA -s Anc2.Anc2refChr15 35110 8 + 86568 GTCCTGAA -s mr.mrrefChr5 72451 8 + 294540 GTGCTGAG -s simCow_chr6.simCow.chr6 210591 8 + 602619 ATCCTGAA -s simDog_chr6.simDog.chr6 207395 8 + 593897 GGCCTGAA -s simHuman_chr6.simHuman.chr6 222444 8 + 601863 GTCCTGAA -s simRat_chr6.simRat.chr6 208875 8 + 647215 GTGCTGAG - -a -s simMouse_chr6.simMouse.chr6 217941 79 + 636262 GAGGGGCAAGCACCTAGTGTGAGACTGTGACTATTTCTCCTGCTGCTTGGATTTGCTTTTTCACCCCAATAACTGTCAG -s Anc0.Anc0refChr5 39649 75 + 87904 GCAGGGGGGGAACTTTGTATGAAACTTTGTATATTTCCC---CTGCTAGGATTTCCTCCTTCGTACCA-CAACTAGAGG -s Anc1.Anc1refChr8 54179 76 + 57822 GCAGGGGGGGAACTTTGTATGAAACTTTGTATATTTCCC---CTGCTAGGATTTCCTCCTTCGTACCAACAACTAGAGG -s Anc2.Anc2refChr15 35120 75 + 86568 GCAGGGGCGGAACTTTATATGAAGCATTATATATTTCCC---CTGCTAGGATCTCCTCCTTCGTACCA-CAACTAGAGG -s mr.mrrefChr5 72459 76 + 294540 GAGGGGGGAGCACCTAGTGTGAGACTGTGAATATTTCTC---CTGCTTGGATTTGCTCTTTCACCCCAATAACTATCAG -s simCow_chr6.simCow.chr6 210601 68 + 602619 GGAGGGGTGGAACTTTATAAGAAGCCTTATATATTTCCT---CTGCTAGAATCAACTCCTTCGGTCCA-GAA------- -s simDog_chr6.simDog.chr6 207405 75 + 593897 GCGGGGGCGGAACTTTATATGAGGCATCATATAGTTCCC---CTGCTAGGATCTCCTCCTTCATACCA-CAACTAGAGG -s simHuman_chr6.simHuman.chr6 222454 72 + 601863 GCAGGGGGGGAACTCTGTATAAAACTCTGTAGATTT-------TGCTAGTATTTCCTCCTTCGTGCTGACAAATAGAGG -s simRat_chr6.simRat.chr6 208883 76 + 647215 GGGAGGGGAGCACCTAGTGTGAGACTGTGAATATTTCTC---CTGCTTGGATTTGCTCTATCACCCCAATAACTATCAG - -a -s simMouse_chr6.simMouse.chr6 218020 32 + 636262 AATGGCAAATGCTCTAAGCCAAATGAGGAGAA -s Anc0.Anc0refChr5 39724 32 + 87904 ATTGGCAGATGCTCTGAATATAATGCAGAGAA -s Anc1.Anc1refChr8 54255 32 + 57822 ATTGGCAGATGCTCTGAATATAATGCAGAGAA -s Anc2.Anc2refChr15 35195 32 + 86568 ATTGGCAGATGCTCTGAATATAATGCAGATAA -s mr.mrrefChr5 72535 32 + 294540 AATGGCAGATGCTCTAAGCCAAATGAGGAGAA -s simCow_chr6.simCow.chr6 392223 26 - 602619 ATTCACAGATGCTC------AAATGCAGAAGA -s simDog_chr6.simDog.chr6 207480 32 + 593897 ATTGGCAGATGCACTGAATATAATTGAGCTAA -s simHuman_chr6.simHuman.chr6 222526 32 + 601863 ATTGGCAGAGGCTCTGAATGGAGTGCAGAGAA -s simRat_chr6.simRat.chr6 208959 32 + 647215 AATGGCAGATGCTACCTGCCAAAAGTGGAGAA - -a -s simMouse_chr6.simMouse.chr6 218052 4 + 636262 ACTG -s Anc0.Anc0refChr5 39756 4 + 87904 ACTA -s Anc1.Anc1refChr8 54287 4 + 57822 ACTA -s Anc2.Anc2refChr15 35227 4 + 86568 ACTA -s mr.mrrefChr5 72567 4 + 294540 ACTG -s simCow_chr6.simCow.chr6 392249 4 - 602619 ACTA -s simDog_chr6.simDog.chr6 207512 4 + 593897 ACTA -s simHuman_chr6.simHuman.chr6 222595 4 + 601863 ACTA -s simRat_chr6.simRat.chr6 208991 4 + 647215 ACTG - -a -s simMouse_chr6.simMouse.chr6 218056 52 + 636262 ATTACCAGCAGGGCCGGTCAGTGCTTGTGGTGGAGTGGTTATGTACATGTAT -s Anc0.Anc0refChr5 39760 50 + 87904 ATGACCAACAGGACTGGGC--AGCTCGTGGTGGAGTGGTTAAGGACATGTAT -s Anc1.Anc1refChr8 54291 50 + 57822 ATGACCAACAGGACTGGGC--AGCTCGTGGTGGAGTGGTTAAGGACATGTAT -s Anc2.Anc2refChr15 35238 50 + 86568 ATGACCAACAGGACTGGGC--AGCTCGTGGTGGAATAGTTAAGGACATGTTT -s mr.mrrefChr5 72571 50 + 294540 ATTACCAGCAGGACCGGTC--TGCTTGTGGTGGAGTGGTTAAGTACATGTAT -s simCow_chr6.simCow.chr6 392254 49 - 602619 -TGACGAACATGACTAGGC--AGCTGGTGGCGGAATAGTTAAGGACATGTTT -s simDog_chr6.simDog.chr6 207523 50 + 593897 ATGACCAATAGGACTGGGT--ACCCCGGGGTGGTATACTTAAGGACATGTTT -s simHuman_chr6.simHuman.chr6 222599 50 + 601863 ATGACCAACAGGACTGGGC--AGCTAGTGGTGGAGTGGTTAAGGACATGTAT -s simRat_chr6.simRat.chr6 208995 50 + 647215 ATTACCAGCAGGACCGGAC--TGCTTGTGGTGGGGTGGTTAAGTACATGTAT - -a -s simMouse_chr6.simMouse.chr6 218108 4 + 636262 CTGG -s Anc0.Anc0refChr5 39810 4 + 87904 CAGG -s Anc1.Anc1refChr8 54341 4 + 57822 CAGG -s Anc2.Anc2refChr15 35288 4 + 86568 CTGG -s mr.mrrefChr5 72621 4 + 294540 CAGG -s simCow_chr6.simCow.chr6 392303 4 - 602619 CTGG -s simHuman_chr6.simHuman.chr6 222650 4 + 601863 AAGA -s simRat_chr6.simRat.chr6 209045 4 + 647215 CAGG - -a -s simMouse_chr6.simMouse.chr6 218112 17 + 636262 CTGTCCCTTTTCACTTA -s Anc0.Anc0refChr5 39814 17 + 87904 ATCTCCCTTTACACTTA -s Anc1.Anc1refChr8 54345 17 + 57822 ATCTCCCTTTACACTTA -s Anc2.Anc2refChr15 35293 17 + 86568 ATCTCCCTTTACACCTC -s mr.mrrefChr5 72625 17 + 294540 ATGTCCCTTTTCACTTA -s simCow_chr6.simCow.chr6 392308 17 - 602619 ATCTCCCTTTTTACCTC -s simDog_chr6.simDog.chr6 207573 12 + 593897 -----CCTGAACTCCTC -s simHuman_chr6.simHuman.chr6 222654 17 + 601863 ATATCCCCTTACATTTA -s simRat_chr6.simRat.chr6 209049 17 + 647215 ACCTCCCATTTCACTTG - -a -s simMouse_chr6.simMouse.chr6 218129 9 + 636262 GTTTCATCC -s Anc0.Anc0refChr5 39831 9 + 87904 TTTTCTCCT -s Anc1.Anc1refChr8 54362 9 + 57822 TTTTCTCCT -s Anc2.Anc2refChr15 35310 9 + 86568 TTCTCTCCT -s mr.mrrefChr5 72642 9 + 294540 GTTTCAACC -s simCow_chr6.simCow.chr6 392326 9 - 602619 TTCGATCCT -s simDog_chr6.simDog.chr6 207585 9 + 593897 TTCTCTCTT -s simHuman_chr6.simHuman.chr6 222671 9 + 601863 TTTTGtcct -s simRat_chr6.simRat.chr6 209066 9 + 647215 ATTTCAACC - -a -s simMouse_chr6.simMouse.chr6 218138 73 + 636262 TGATTTAACAAATCCTCTGTCGCTTCCCACATGAATGACATTCAAATGGGAATCCTTGAGTTGCACTACATCC -s Anc0.Anc0refChr5 39845 72 + 87904 ttactAATTAA-CCCTCCAGTGCTTGCAACATGAAAGTTATCAAACTGGGACTCCTTGAGATATATTGTATcc -s Anc1.Anc1refChr8 54376 72 + 57822 ttactAATTAA-CCCTCCAGTGCTTGCAACATGAAAGTTATCAAACTGGGACTCCTTGAGATATATTGTATcc -s Anc2.Anc2refChr15 35324 72 + 86568 ttactAATTAA-CCCTGCAGTGCTTGCAACATGAAAGTTATCAAACTGGGACTCATTGGGATATTTTGTATct -s mr.mrrefChr5 72651 73 + 294540 TGATTTATCAAATCCTCTGTCGCTTCCCACATGAATGACATCAAAATGGGAATCCTTGAGTTGTATTACATCc -s simCow_chr6.simCow.chr6 392340 72 - 602619 TTACTAATTAA-CCCTACAGTGCTGGCAAGATAAAAGCTATCAAGCTGGGGCTCTTTGGGTGATGTTGTATCT -s simDog_chr6.simDog.chr6 207595 65 + 593897 -----ACTTAA-CCCTGCAGTAGTTGCAACATGAAAGTCAGCAAAATGGAACTCATTGGGATATTTTATGT-- -s simHuman_chr6.simHuman.chr6 222685 72 + 601863 ttactaattaa-cccgccagtgcttgcagcatgacagttatcaaactgggactccttgagctctattggatcc -s simRat_chr6.simRat.chr6 209075 72 + 647215 TGATTTATCAAATCCTCTGTCACTTCCCACATGAATGGCATCAAATTGGGAATCTTTGAGTTGTATTACATC- - -a -s simMouse_chr6.simMouse.chr6 218211 7 + 636262 AATAACT -s Anc0.Anc0refChr5 39917 7 + 87904 aataacc -s Anc1.Anc1refChr8 54448 7 + 57822 aataacC -s Anc2.Anc2refChr15 35396 7 + 86568 catagcc -s mr.mrrefChr5 72724 7 + 294540 aataaCT -s simCow_chr6.simCow.chr6 392412 7 - 602619 CATAGCC -s simHuman_chr6.simHuman.chr6 222758 7 + 601863 aataacc -s simRat_chr6.simRat.chr6 209147 2 + 647215 -----CT - -a -s simMouse_chr6.simMouse.chr6 218218 13 + 636262 AAATCACAATAGT -s Anc0.Anc0refChr5 39924 13 + 87904 AAactagaAGAGG -s Anc1.Anc1refChr8 54455 13 + 57822 AAactagaAGAGG -s Anc2.Anc2refChr15 35404 13 + 86568 GAACTAGAAGAGG -s mr.mrrefChr5 72731 13 + 294540 AAatcacaATAGT -s simCow_chr6.simCow.chr6 392420 13 - 602619 CAACTAGAAGAGG -s simDog_chr6.simDog.chr6 207661 13 + 593897 GAACTAGAAAGGG -s simHuman_chr6.simHuman.chr6 222765 13 + 601863 aaactagaagaGA -s simRat_chr6.simRat.chr6 209149 2 + 647215 AA----------- - -a -s simMouse_chr6.simMouse.chr6 218231 60 + 636262 AATATTAAAAGTCTATGTTCTCAGTCAGCAACTTGGAGTGATTATCATCACTAAGCAGTT -s Anc0.Anc0refChr5 39947 60 + 87904 AATACTAAGAGTCTATGTTCCCATTGAGCAACTAGGAGTAATTGCCATCACTAAGCAGTT -s Anc1.Anc1refChr8 54478 60 + 57822 AATACTAAGAGTCTATGTTCCCATTGAGCAACTAGGAGTAATTGCCATCACTAAGCAGTT -s Anc2.Anc2refChr15 35428 60 + 86568 AATACTAAGAGGCTATGTTCTTATTGAGCAACTAGGGGTAATTGCCATCACTAAGGAGTT -s mr.mrrefChr5 72744 60 + 294540 AATATTAAAAGTCTATGTTCCCATTGAGCAACTTGGAGTGATTACCATCACTAAGCAGTT -s simCow_chr6.simCow.chr6 392444 46 - 602619 AATGTT--GATGCT----TCTTATTGAGCAACTAACGGTAATTGCCATCGCT-------- -s simDog_chr6.simDog.chr6 207685 60 + 593897 AATACTAAGAGGCTATGTTGTTAGTGGGCAACTAGGGGTGATTGCTACCACTAAGGAGTT -s simHuman_chr6.simHuman.chr6 222790 58 + 601863 AATAGTCACAGTCTATCCTCCCATTGAGCGACTAGTAA--ATTGCCATCACTAAGCAATT -s simRat_chr6.simRat.chr6 209151 60 + 647215 GATATTAAAAGTCTATATTCCCATTGAGCAACTTGGAGTGATAACCATCACTAAGCAGTT - -a -s simMouse_chr6.simMouse.chr6 218291 26 + 636262 TAACAGTCAAGGGAGAATAACACCGC -s Anc0.Anc0refChr5 40008 26 + 87904 TAGCAGTTGAGGAGTAATAACACAAA -s Anc1.Anc1refChr8 54539 26 + 57822 TAGCAGTTGAGGAGTAATAACACAAA -s Anc2.Anc2refChr15 35489 26 + 86568 TAGCAGTTGAGGAGGAATACAACAAA -s mr.mrrefChr5 72804 26 + 294540 TAACAGTCAAGGGATAATAACACCGC -s simCow_chr6.simCow.chr6 392490 26 - 602619 TATCAGTCAAGGACAAATACAGCAAA -s simDog_chr6.simDog.chr6 207746 26 + 593897 TAGCAATTGAGGGGGAATACAACAAA -s simHuman_chr6.simHuman.chr6 222849 22 + 601863 TAGCAGTGTAGGAGTAATAACC---- -s simRat_chr6.simRat.chr6 209211 26 + 647215 TAACAGTTGAGGGATAATCCCACCAA - -a -s simMouse_chr6.simMouse.chr6 218317 44 + 636262 CCAAAGCGAATGCACAATTGAGGAAACACACTAAGTCGCAACCC -s Anc0.Anc0refChr5 40034 44 + 87904 CAAAGGTGTATGATCAATTGAGGAGACACATTCAGTGACCACTT -s Anc1.Anc1refChr8 54565 44 + 57822 CAAAGGTGTATGATCAATTGAGGAGACACATTCAGTGACCACTT -s Anc2.Anc2refChr15 35515 44 + 86568 CAAAGAAGTATGATAAATTGAGGAGACACATTCAGTGACCACTT -s mr.mrrefChr5 72830 44 + 294540 CCAAAGTGAATGCACAATTGAGGAAACACACTAAGTGGCAACCT -s simCow_chr6.simCow.chr6 392517 44 - 602619 CAAAGTAGTATGATTAATTGAGGAGACAGATTCAGTCACGATTT -s simDog_chr6.simDog.chr6 207772 44 + 593897 CAAAGAAGTATGTTAAAGTGAAGAGACCCATTCAGTGACCACTC -s simHuman_chr6.simHuman.chr6 222871 41 + 601863 ---AGGTGTATGATCAATTGAGGAGACACATTTAGTGACCACTT -s simRat_chr6.simRat.chr6 209237 44 + 647215 CCAAAGTGATTGCACAATTGAGGAAACACACCAAGTGGCAACCT - -a -s simMouse_chr6.simMouse.chr6 218361 74 + 636262 GACAAGTGTGAGCATTCCCTTGGAAAGAATGTTTTAAATGTGAGTAGGCCACAACCATCTATGCTGTTGATTGT -s Anc0.Anc0refChr5 40078 59 + 87904 GACAAGTGTGAATATCCCTT-----AAAATATTTTACATGTTGGTGTGCCTCCACCA-------TG---AATGC -s Anc1.Anc1refChr8 54609 59 + 57822 GACAAGTGTGAATATCCCTT-----AAAATATTTTACATGTTGGTGTGCCTCCACCA-------TG---AATGC -s Anc2.Anc2refChr15 35559 59 + 86568 GACAAGTGTGAATATCCCTT-----AAAATATCTTACATGTTGGTGTGCCTCCACCA-------TG---TATGC -s mr.mrrefChr5 72874 62 + 294540 GACAAGTGTGAGCATTCCCT-----AGAATGTTTTAAATGTGGGTAGGCCACAACCA-------TGTTGATTGT -s simCow_chr6.simCow.chr6 392561 59 - 602619 GACAAGTGTGAATATCCCTT-----AAAATATCTTACATATTGGAGTATCACCACCA-------TA---TATGC -s simDog_chr6.simDog.chr6 207816 54 + 593897 ACTAAGTGAGGGTACCCCTC-----AACATGTCCTACTTGTTGGTGTGCCTTCACCA-------TG-------- -s simHuman_chr6.simHuman.chr6 222915 59 + 601863 GACAAGTGTAAATATCCCTT-----AAAATATTTTACATGTCGGTGTGCCGCCAGCA-------TG---AGTCC -s simRat_chr6.simRat.chr6 209281 57 + 647215 AACAAATGCGAGCATT---------AGAATGTCCTAAACGTTGGTAGGGCCCAACCA-------TGTTGATTG- - -a -s simMouse_chr6.simMouse.chr6 218435 14 + 636262 AATTTTCAACAAGA -s Anc0.Anc0refChr5 40137 13 + 87904 AATCA-CCACAACA -s Anc1.Anc1refChr8 54668 13 + 57822 AATCA-CCACAACA -s Anc2.Anc2refChr15 35618 13 + 86568 AATCA-CCACACCA -s mr.mrrefChr5 72936 14 + 294540 AATTTTCAACAACA -s simCow_chr6.simCow.chr6 392653 13 - 602619 AATCA-CCACACCA -s simDog_chr6.simDog.chr6 207870 5 + 593897 ---------TACCA -s simHuman_chr6.simHuman.chr6 222974 13 + 601863 AATCA-CTACAACA -s simRat_chr6.simRat.chr6 209338 12 + 647215 --TTTTCAACAACA - -a -s simMouse_chr6.simMouse.chr6 218449 15 + 636262 ACTTTAATCTTTCTC -s Anc0.Anc0refChr5 40150 14 + 87904 ACTT-ATTCTTCCTC -s Anc1.Anc1refChr8 54681 14 + 57822 ACTT-ATTCTTCCTC -s Anc2.Anc2refChr15 35631 14 + 86568 CTTT-ATTCTACCTC -s mr.mrrefChr5 72950 15 + 294540 ACTTTAATCTTTCTC -s simCow_chr6.simCow.chr6 392667 14 - 602619 CTTT-ATACTATCTC -s simDog_chr6.simDog.chr6 207875 14 + 593897 CTTT-ATTCTACCTT -s simHuman_chr6.simHuman.chr6 222987 14 + 601863 ACTT-ATTCTTCCTC -s simRat_chr6.simRat.chr6 209350 15 + 647215 ACTTTAATCTTTCTT - -a -s simMouse_chr6.simMouse.chr6 218464 3 + 636262 TAT -s Anc0.Anc0refChr5 40164 3 + 87904 CAC -s Anc1.Anc1refChr8 54695 3 + 57822 CAC -s Anc2.Anc2refChr15 35645 3 + 86568 CAC -s mr.mrrefChr5 72965 3 + 294540 CAT -s simCow_chr6.simCow.chr6 392682 3 - 602619 TAG -s simDog_chr6.simDog.chr6 207889 3 + 593897 CAC -s simHuman_chr6.simHuman.chr6 223001 3 + 601863 CAC -s simRat_chr6.simRat.chr6 209365 3 + 647215 CAT - -a -s simMouse_chr6.simMouse.chr6 218467 69 + 636262 GGCAATGTTTGGATTTTCAGAATGCTGATTGTAATTTTCAACAACAACTTTAATCTTTCTTCGTATGCG -s Anc0.Anc0refChr5 40168 18 + 87904 GGCAATATTTGGGTTTTC--------------------------------------------------- -s Anc1.Anc1refChr8 54699 18 + 57822 GGCAATATTTGGGTTTTC--------------------------------------------------- -s Anc2.Anc2refChr15 35649 18 + 86568 GGCAACATTTGGGTTTTC--------------------------------------------------- -s mr.mrrefChr5 72969 69 + 294540 GGCAATGTTTGGATTTTCAGAATGCTGATTGTAATTTTCAACAACAACTTTAATCTTTCTTCGTATGCG -s simCow_chr6.simCow.chr6 392686 18 - 602619 GGCAACAATTGGGTTTTC--------------------------------------------------- -s simDog_chr6.simDog.chr6 207893 18 + 593897 GGCAACATTTGGGTTTCC--------------------------------------------------- -s simHuman_chr6.simHuman.chr6 223005 18 + 601863 GGCAATTTTTGGGTTCTC--------------------------------------------------- -s simRat_chr6.simRat.chr6 209369 69 + 647215 AACAATGTTTGGATTTTCAGAATGCTGATTGAAATTTTCAACAACAATTTTAATCTTTCTCCATAGGTG - -a -s simMouse_chr6.simMouse.chr6 218536 65 + 636262 CTTGGATTTTCTGAATACTATCTCCTGGTATCCCTTTGCTGGCCGATACCTCATCCACTATTTGG -s Anc0.Anc0refChr5 40186 54 + 87904 ----------T-GGTTACTATCTCCTGTTAGCCCTTTGTTTGTCCATACCTCACCCACCATTTAG -s Anc1.Anc1refChr8 54717 54 + 57822 ----------T-GGTTACTATCTCCTGTTAGCCCTTTGTTTGTCCATACCTCACCCACCATTTAG -s Anc2.Anc2refChr15 35667 54 + 86568 ----------T-GGTTACTATCTCCTGTTGGCCCTTTGTTTGTCCTTACCTCACCCACCATTTAG -s mr.mrrefChr5 73038 64 + 294540 CTTGGATTTTC-GAATACTATCTCCTGGTATCCCTTTGCTGGTCGATACCTCATCCACTATTTAG -s simCow_chr6.simCow.chr6 392704 54 - 602619 ----------T-GGTTACTATCTCCTGTTGGCCCTTTATCTATCCTTATCTCACCCACTGTTTAG -s simDog_chr6.simDog.chr6 207911 54 + 593897 ----------T-GGTTACTATGTCATGTTGGCCCATTGTTTGTCCTTACCTTACTCACCATTAAG -s simHuman_chr6.simHuman.chr6 223023 54 + 601863 ----------T-GGTCACCACCACCTGCTAGCCCTTTGTTTGTCCATACCTCGCCCACCATCTAG -s simRat_chr6.simRat.chr6 209480 60 + 647215 CTTGGATTTTC-GAATACTATCTCCTGGCATCCCCTTGCTGGTCAA----TCATCCACTATTTAG - -a -s simMouse_chr6.simMouse.chr6 218601 59 + 636262 CCATATGTCAATCACACACCTATAAATCCCTTAACTACTACTTCTGGATACTCCTGAGC -s Anc0.Anc0refChr5 40240 38 + 87904 ACATATGTCAATAACACACTCATAAATCACTTACCT---------------------GC -s Anc1.Anc1refChr8 54771 38 + 57822 ACATATGTCAATAACACACTCATAAATCACTTACCT---------------------GC -s Anc2.Anc2refChr15 35721 38 + 86568 ACATATGTCAAAAACACACTCATAAATCACATACCT---------------------GC -s mr.mrrefChr5 73102 59 + 294540 ACATATGTCAATCACACACCTATAAATCCCTTAACTACTACTTCTGGATACTCATGAGC -s simCow_chr6.simCow.chr6 392758 37 - 602619 AC-TGTGTCAAAAACACTCTCATAAATCACACACCT---------------------GA -s simDog_chr6.simDog.chr6 207965 38 + 593897 ACATATGTCAAAAAAACACTCATAAATCACATACCT---------------------GC -s simHuman_chr6.simHuman.chr6 223095 38 + 601863 ACATATATCAATAACACACTCGTAAATCACTTATCT---------------------GC -s simRat_chr6.simRat.chr6 209540 59 + 647215 ACATATGTCAATCACACACCTATAAATCCCTTAACTACTACTTCTGGATACTCACCAGC - -a -s simMouse_chr6.simMouse.chr6 218660 36 + 636262 TACTACTGGCTCCTCATGTTATTACAGTCGTTATCA -s Anc0.Anc0refChr5 40278 35 + 87904 TAGTACTGAGTACTCATGATG-TGCAGTCATTATCA -s Anc1.Anc1refChr8 54809 35 + 57822 TAGTACTGAGTACTCATGATG-TGCAGTCATTATCA -s Anc2.Anc2refChr15 35763 35 + 86568 TAGTACTGAGTACCCATGATG-TGCAGTAATTACTG -s mr.mrrefChr5 73161 35 + 294540 TACTACTGGCTCCTCATGTTA-TACAGTCATTATCA -s simCow_chr6.simCow.chr6 392799 35 - 602619 TAGTACTGGGTACCCATGAGG-TACAACAATTACTG -s simDog_chr6.simDog.chr6 208007 35 + 593897 AAGTACAGAGTACCCATGATG-AGCTGTAATTACTG -s simHuman_chr6.simHuman.chr6 223133 35 + 601863 TAGTATTGTGCACTCATGATG-TGCAGTCATTATCA -s simRat_chr6.simRat.chr6 209599 35 + 647215 TACTTCTGGTTACTCGTGTTA-TACAGTCATTATCA - -a -s simMouse_chr6.simMouse.chr6 218696 14 + 636262 TGCTTTGGAGCTTT -s Anc0.Anc0refChr5 40317 14 + 87904 CTCTTTGAAGTTCT -s Anc1.Anc1refChr8 54848 14 + 57822 CTCTTTGAAGTTCT -s Anc2.Anc2refChr15 35802 14 + 86568 CTCTTTGAAGTTCT -s mr.mrrefChr5 73196 14 + 294540 TGCTTTGGAGCTTT -s simCow_chr6.simCow.chr6 392838 14 - 602619 CTCTTTGAAGTTCC -s simDog_chr6.simDog.chr6 208046 14 + 593897 CTCTTTGAAGTTCT -s simHuman_chr6.simHuman.chr6 223172 14 + 601863 CTCTTTGAAGTTCT -s simRat_chr6.simRat.chr6 209634 14 + 647215 TGCTTTGGAGCTTT - -a -s simMouse_chr6.simMouse.chr6 218710 26 + 636262 CTAGTGTACACAGTATATAGCATTAG -s Anc0.Anc0refChr5 40339 21 + 87904 CTAGTGTTTACAGCATACAG-----G -s Anc1.Anc1refChr8 54870 26 + 57822 CTAGTGTTTACAGCATACAGCATAAG -s Anc2.Anc2refChr15 35824 21 + 86568 CTAGTGTTTACAACATACAG-----G -s mr.mrrefChr5 73210 26 + 294540 CTAGTGTACACAGTATATAGCATTAG -s simCow_chr6.simCow.chr6 392860 21 - 602619 CTAATGTTTACAACATACAG-----G -s simDog_chr6.simDog.chr6 208069 21 + 593897 CTAGTGTTTACAATATACAG-----G -s simHuman_chr6.simHuman.chr6 223194 26 + 601863 CTAGTGTTTGCAGCATACAGCATAAG -s simRat_chr6.simRat.chr6 209648 26 + 647215 CTAGTGTACACAGTATATAGCATTAG - -a -s simMouse_chr6.simMouse.chr6 218736 82 + 636262 ATTCCCTTGGACCTTGGACCACCACGATCAAGGGCTGTCACTACCTATCTTTTACCTCATGTGCATTTGCAAGTATAGAGAA -s Anc0.Anc0refChr5 40360 73 + 87904 ATACCCTTGGACA----ACCACCAGAATCACAGGCCCTC-----CAAACTACTACCCAGCTTTCACCTGTAAGTCCAAAGAA -s Anc1.Anc1refChr8 54896 73 + 57822 ATACCCTTGGACA----ACCACCAGAATCACAGGCCCTC-----CAAACTACTACCCAGCTTTCACCTGTAAGTCCAAAGAA -s Anc2.Anc2refChr15 35845 73 + 86568 ATACACTTGGACA----ATCCCCAGAATTACAGGCCCTC-----AAAACTACTACCCAGCTTTTACCTGTAAGCCCAAAGAA -s mr.mrrefChr5 73236 82 + 294540 ATTCCCTTGGACCTTGGACCACCACGATCAAGGGCCCTCACTACCTATCTTTTACCTCATTTGCACTTGCAAGTATAGAGAA -s simCow_chr6.simCow.chr6 392926 66 - 602619 ATACGCTTGGACA----ATCTCCAGAATTACATGCCCTC-----AAAATTACTATCCAGCT-------ATGAGCACAAAGAA -s simDog_chr6.simDog.chr6 208090 73 + 593897 ATACACTTGAACA----ATCCCCAGAATTGCAGGCTTTC-----AATACTACTACCCAGCTTTTACCTGTAAGCCCAGAGAA -s simHuman_chr6.simHuman.chr6 223220 72 + 601863 AT-ACCTTGGACT----ACCACCAGAATCACTGGCCCTC-----CAAGCTACTACTCAGCTTACACCAGTAAGTGCAAAGAA -s simRat_chr6.simRat.chr6 209674 75 + 647215 ATTC-------ACTGGGATGACCACGATTAAAGGCCCTCACTACCTATCTTTTACCTCTTTTGCACTTGCAAGTATTGAGAA - -a -s simMouse_chr6.simMouse.chr6 218818 24 + 636262 GCTAGGCTCTCTAAGGACGTCAGT -s Anc0.Anc0refChr5 40433 24 + 87904 GCTAAGCTCTCTATGGAGGTCTGT -s Anc1.Anc1refChr8 54969 24 + 57822 GCTAAGCTCTCTATGGAGGTCTGT -s Anc2.Anc2refChr15 35918 24 + 86568 GCTAAGCTCTCTCTGGAGGTCTGT -s mr.mrrefChr5 73318 24 + 294540 GCTAGGCTCTCTAAGGAGGTCAGT -s simCow_chr6.simCow.chr6 392992 23 - 602619 GTTAAGCTATCT-TAGAGGTCTGT -s simDog_chr6.simDog.chr6 208163 24 + 593897 GCTAAGCTCTCTCTGAAGGCATGT -s simHuman_chr6.simHuman.chr6 223293 24 + 601863 GCTAAGCTCTTTACGGAGGTCTGT -s simRat_chr6.simRat.chr6 209749 17 + 647215 GC-AGGCT------GGAGGTCAGT - -a -s simMouse_chr6.simMouse.chr6 218842 6 + 636262 CTGAGA -s Anc0.Anc0refChr5 40457 6 + 87904 CAGCAA -s Anc1.Anc1refChr8 54993 6 + 57822 CAGCAA -s Anc2.Anc2refChr15 35943 6 + 86568 CAGCAG -s mr.mrrefChr5 73342 6 + 294540 CTGAGA -s simCow_chr6.simCow.chr6 393016 6 - 602619 CTGCAG -s simDog_chr6.simDog.chr6 208188 6 + 593897 CAGCAG -s simHuman_chr6.simHuman.chr6 223317 6 + 601863 CAGCAA - -a -s simMouse_chr6.simMouse.chr6 218848 13 + 636262 CTCCAATGGTTTA -s Anc0.Anc0refChr5 40472 13 + 87904 CTCCAATGGTTTG -s Anc1.Anc1refChr8 55008 13 + 57822 CTCCAATGGTTTG -s Anc2.Anc2refChr15 35958 13 + 86568 TCCCAATGGTTTG -s mr.mrrefChr5 73348 13 + 294540 CTCCAATGGTTTA -s simCow_chr6.simCow.chr6 393031 13 - 602619 TCCCAATGGTTTG -s simDog_chr6.simDog.chr6 208203 13 + 593897 TCCGGCTGGTTTG -s simHuman_chr6.simHuman.chr6 223332 13 + 601863 CTCCAATGGTTTG - -a -s simMouse_chr6.simMouse.chr6 218861 11 + 636262 GTTTGCAACAG -s Anc0.Anc0refChr5 40485 8 + 87904 -TTTGCA--AG -s Anc1.Anc1refChr8 55021 9 + 57822 GTTTGCA--AG -s Anc2.Anc2refChr15 35971 8 + 86568 -TTTGCA--AC -s mr.mrrefChr5 73361 9 + 294540 GTTTGCA--AG -s simCow_chr6.simCow.chr6 393044 8 - 602619 -TGTGCA--AC -s simDog_chr6.simDog.chr6 208216 8 + 593897 -TTTGCA--AC -s simHuman_chr6.simHuman.chr6 223366 9 + 601863 GTTTTCA--AG - -a -s simMouse_chr6.simMouse.chr6 218872 11 + 636262 AACCCATGACA -s Anc0.Anc0refChr5 40493 11 + 87904 CACCCATAAAA -s Anc1.Anc1refChr8 55030 11 + 57822 CACCCATAAAA -s Anc2.Anc2refChr15 35981 11 + 86568 CACCCATAAAA -s mr.mrrefChr5 73370 11 + 294540 AACCCATGACA -s simCow_chr6.simCow.chr6 393054 11 - 602619 CGCCCATAAAG -s simDog_chr6.simDog.chr6 208226 11 + 593897 CACCCATGTAA -s simHuman_chr6.simHuman.chr6 223375 11 + 601863 CACCCATAAAA - -a -s simMouse_chr6.simMouse.chr6 218883 40 + 636262 TTATATCTAAGACTAGCTTTGATGCTGGTAGAGGAACATA -s Anc0.Anc0refChr5 40505 39 + 87904 CTATATCT-AGAATAACTGTAAAGGTGGTAGAGGGACATA -s Anc1.Anc1refChr8 55042 39 + 57822 CTATATCT-AGAATAACTGTAAAGGTGGTAGAGGGACATA -s Anc2.Anc2refChr15 35993 39 + 86568 CTATATAT-AGAATAACTGTAAAGGTGGTAGAGCGATATA -s mr.mrrefChr5 73381 39 + 294540 TTATATCT-AGACTAACTGTGATGCTGGTAGAGGAACATA -s simCow_chr6.simCow.chr6 393066 39 - 602619 CTATATAT-AGAACAACTGTAAAGGTGGTAGAGCGATATA -s simDog_chr6.simDog.chr6 208238 19 + 593897 -TATCTAT-AGAATAATTGTA------------------- -s simHuman_chr6.simHuman.chr6 223387 39 + 601863 CTATATCT-GGATTAACTGTAAGGGTGGTAGAGGGGCATA -s simRat_chr6.simRat.chr6 209766 28 + 647215 ------------CTAACTGTGACGTTGGTAGAAGAACATA - -a -s simMouse_chr6.simMouse.chr6 218923 11 + 636262 CCCATGCATTT -s Anc0.Anc0refChr5 40544 11 + 87904 CCCAGACACTT -s Anc1.Anc1refChr8 55081 11 + 57822 CCCAGACACTT -s Anc2.Anc2refChr15 36035 11 + 86568 CCCAGACACTT -s mr.mrrefChr5 73420 11 + 294540 CCCATGCATTT -s simCow_chr6.simCow.chr6 393107 9 - 602619 --TAGATGCTC -s simDog_chr6.simDog.chr6 208258 11 + 593897 CCCTGACACTT -s simHuman_chr6.simHuman.chr6 223426 11 + 601863 TCCAGACACTT -s simRat_chr6.simRat.chr6 209794 11 + 647215 CTGATGCATTT - -a -s simMouse_chr6.simMouse.chr6 218934 7 + 636262 ATCACCT -s Anc0.Anc0refChr5 40555 1 + 87904 A------ -s Anc1.Anc1refChr8 55092 7 + 57822 AACACTT -s Anc2.Anc2refChr15 36046 1 + 86568 A------ -s mr.mrrefChr5 73431 7 + 294540 ATCACCT -s simCow_chr6.simCow.chr6 393116 1 - 602619 A------ -s simDog_chr6.simDog.chr6 208269 1 + 593897 A------ -s simHuman_chr6.simHuman.chr6 223452 7 + 601863 GACACTT -s simRat_chr6.simRat.chr6 209805 7 + 647215 ATCACCT - -a -s simMouse_chr6.simMouse.chr6 218941 13 + 636262 TATCATAAGGATC -s Anc0.Anc0refChr5 40562 10 + 87904 TATCAGAGGG--- -s Anc1.Anc1refChr8 55105 10 + 57822 TATCAGAGGG--- -s Anc2.Anc2refChr15 36053 10 + 86568 TATCAGAGGG--- -s mr.mrrefChr5 73438 10 + 294540 TACAATTAGG--- -s simCow_chr6.simCow.chr6 393122 10 - 602619 TATCATAGGG--- -s simDog_chr6.simDog.chr6 208276 10 + 593897 CATCAGAGGG--- -s simHuman_chr6.simHuman.chr6 223466 10 + 601863 TATCAGAGGA--- -s simRat_chr6.simRat.chr6 209812 10 + 647215 TACAATTATG--- - -a -s simMouse_chr6.simMouse.chr6 218954 13 + 636262 CAAGGTCAAATGA -s Anc0.Anc0refChr5 40575 13 + 87904 CAAATTTAAGTGA -s Anc1.Anc1refChr8 55118 13 + 57822 CAAATTTAAGTGA -s Anc2.Anc2refChr15 36066 13 + 86568 AAGATTTAAGTGA -s mr.mrrefChr5 73448 13 + 294540 CAAGGTTAAATGA -s simCow_chr6.simCow.chr6 393135 13 - 602619 TAGATTTAAGTGA -s simDog_chr6.simDog.chr6 208289 13 + 593897 AAGATTTAAATGA -s simHuman_chr6.simHuman.chr6 223479 13 + 601863 CAAAATTAGGTGA -s simRat_chr6.simRat.chr6 209822 13 + 647215 CAAGGTTAAATGG - -a -s simMouse_chr6.simMouse.chr6 218967 27 + 636262 CCAGATATTAAGCTCTGGGTGGTGATT -s Anc0.Anc0refChr5 40594 25 + 87904 CCAGGTTTTAAGCT--GAATGGTGATT -s Anc1.Anc1refChr8 55137 25 + 57822 CCAGGTTTTAAGCT--GAATGGTGATT -s Anc2.Anc2refChr15 36085 25 + 86568 CCAGGTTTTAAGCT--GAATGGTGATT -s mr.mrrefChr5 73461 27 + 294540 CCAGGTATTAAGCTCTGGGTGGTGATT -s simCow_chr6.simCow.chr6 393154 25 - 602619 CCAGCTTTTAGGCT--GGATGGTCATT -s simDog_chr6.simDog.chr6 208308 25 + 593897 CCAGGTCTTCAGCT--GAGTGGTGATT -s simHuman_chr6.simHuman.chr6 223499 25 + 601863 CCAGGTTTTAAGCT--GAATGGCAATT -s simRat_chr6.simRat.chr6 209835 26 + 647215 CCAGGTGACAAGCTCTGGG-AGTGATT - -a -s simMouse_chr6.simMouse.chr6 218994 25 + 636262 TGTGTCCAACAACCAAACTGACGAA -s Anc0.Anc0refChr5 40619 22 + 87904 TCTGC---CTAACAGAACTGCCAGT -s Anc1.Anc1refChr8 55162 22 + 57822 TCTGC---CTAACAGAACTGCCAGT -s Anc2.Anc2refChr15 36110 22 + 86568 TCTGC---CTAACAGAACTGCTAGT -s mr.mrrefChr5 73488 22 + 294540 TGTGT---ACAACCGAACTGACGAA -s simCow_chr6.simCow.chr6 393179 22 - 602619 TTTGC---CTAACAGAACCTCTAAT -s simDog_chr6.simDog.chr6 208333 22 + 593897 TCTGC---ATAATAGAACTGCTAGT -s simHuman_chr6.simHuman.chr6 223525 22 + 601863 CTTGC---CTGACAGAACTGCCAGT -s simRat_chr6.simRat.chr6 209861 22 + 647215 TGTGT---ACAACTGACCTAACAAA - -a -s simMouse_chr6.simMouse.chr6 219019 31 + 636262 TTGGGCTAAGTTGCAAACTAAATCACATATA -s Anc0.Anc0refChr5 40646 22 + 87904 CTGGGCTAGGTTGAACTCCAA---------A -s Anc1.Anc1refChr8 55189 22 + 57822 CTGGGCTAGGTTGAACTCCAA---------A -s Anc2.Anc2refChr15 36137 22 + 86568 CTCAGCTAGCTTGAACTCCAA---------A -s mr.mrrefChr5 73510 22 + 294540 TTGGGCTAAGTTGCAAACTAA---------A -s simCow_chr6.simCow.chr6 393206 22 - 602619 TTTTGTTAGCTTGAACTCTAC---------A -s simDog_chr6.simDog.chr6 208360 22 + 593897 CTCAGCTAGCTTGAACTCCAA---------A -s simHuman_chr6.simHuman.chr6 223552 22 + 601863 CTGGACTAGGTTAAACTCCAG---------A -s simRat_chr6.simRat.chr6 209883 22 + 647215 TTGGGCTAAGTTGCACATTAA---------A - -a -s simMouse_chr6.simMouse.chr6 219050 61 + 636262 TCACTTGAGAACGCCCGTTATTAAGCATTTTAGTCCATTCATTACGGGGTAAAATAGCTGG -s Anc0.Anc0refChr5 40668 61 + 87904 ATGCTCGAGGACTCCCAGTGGTTTGCTTTTTAGTTCGGTTATTAGGGTGCAATGTGGCTGG -s Anc1.Anc1refChr8 55211 61 + 57822 ATGCTCGAGGACTCCCAGTGGTTTGCTTTTTAGTTCGGTTATTAGGGTGCAATGTGGCTGG -s Anc2.Anc2refChr15 36159 61 + 86568 ATGCTCGAGGACTCCCAGTGTTTTGCTTTTTAGTTTGGATATTAGGATGCAATGTGGCGGG -s mr.mrrefChr5 73532 61 + 294540 TCACTTGAGAACGCCCATTAGTAAGCATTTTAGTCCATTCATTACGGGGTAAAATAGCTGG -s simCow_chr6.simCow.chr6 393229 61 - 602619 TTGCTTGAGGACTCCCAGTGCTCTGCTCTTTAGTTTGGATATTAGGATGCAATGTAGCAAG -s simDog_chr6.simDog.chr6 208382 61 + 593897 AGAGTCAAGAACTTCCACTGTTTTGTTTTTTAGTTTGGATATTGAGATGCAATGTGGCGGG -s simHuman_chr6.simHuman.chr6 223574 61 + 601863 GTGCTCGAGGCCTCTGAGTGGTTTGCTTTTTAGTTCGCTTATTAGGGTACAATTCGGCTGG -s simRat_chr6.simRat.chr6 209905 56 + 647215 TCACTTGAGAACCCCCATTAG-----ATTTGAGTCCAGTCATTATGGGGTAAAATAGCTGG - -a -s simMouse_chr6.simMouse.chr6 219111 13 + 636262 ACATTTTTTACAT -s Anc0.Anc0refChr5 40738 12 + 87904 -AGATTTATCCAT -s Anc1.Anc1refChr8 55281 13 + 57822 CAGATTTATCCAT -s Anc2.Anc2refChr15 36229 12 + 86568 -AGATTCATCTAC -s mr.mrrefChr5 73602 13 + 294540 ACGTTTTTTACAT -s simCow_chr6.simCow.chr6 393299 12 - 602619 -GGATTCATCTGC -s simDog_chr6.simDog.chr6 208452 12 + 593897 -AGATTCACCTAC -s simHuman_chr6.simHuman.chr6 223644 13 + 601863 CAGATTTATCCAT -s simRat_chr6.simRat.chr6 209970 13 + 647215 AGGTTCTCTATAT - -a -s simMouse_chr6.simMouse.chr6 219124 14 + 636262 GAGATTGGAGATTT -s Anc0.Anc0refChr5 40804 14 + 87904 GAGTTTTGGTATTT -s Anc1.Anc1refChr8 55348 14 + 57822 GAGTTTTGGTATTT -s Anc2.Anc2refChr15 36295 14 + 86568 GAGTTTTGGTATTT -s mr.mrrefChr5 73615 14 + 294540 GAGATTGGAGATTT -s simCow_chr6.simCow.chr6 395189 14 - 602619 CAGTTCAGGTATTT -s simDog_chr6.simDog.chr6 208531 14 + 593897 GAGTTTTGGTATTT -s simHuman_chr6.simHuman.chr6 223711 14 + 601863 GAGCTTTGGTATTT -s simRat_chr6.simRat.chr6 209983 14 + 647215 GAGATTGGAGATTT - -a -s simMouse_chr6.simMouse.chr6 219138 20 + 636262 GCCACACGTATCATGCCGCT -s Anc0.Anc0refChr5 40821 20 + 87904 GCCATCAGTCACTAGGCATT -s Anc1.Anc1refChr8 55365 20 + 57822 GCCATCAGTCACTAGGCATT -s Anc2.Anc2refChr15 36312 20 + 86568 GCCATCAGTCACTAGGCATT -s mr.mrrefChr5 73632 20 + 294540 GCCACCAGTAACATGCCACT -s simCow_chr6.simCow.chr6 395206 20 - 602619 GCTACCAGTCACTAGGCATT -s simDog_chr6.simDog.chr6 208549 13 + 593897 GCCCTAAGT-----AGCA-- -s simHuman_chr6.simHuman.chr6 223728 20 + 601863 GCCATCAGTCATTAGGCATT -s simRat_chr6.simRat.chr6 210000 20 + 647215 GCCACCAGTTACATGCCACT - -a -s simMouse_chr6.simMouse.chr6 219158 10 + 636262 TAATATAGTA -s Anc0.Anc0refChr5 40855 9 + 87904 TAATATAAT- -s Anc1.Anc1refChr8 55399 9 + 57822 TAATATAAT- -s Anc2.Anc2refChr15 36346 9 + 86568 TAATATAAT- -s mr.mrrefChr5 73652 10 + 294540 TAATATAGTA -s simCow_chr6.simCow.chr6 395241 9 - 602619 TAAAATAAT- -s simDog_chr6.simDog.chr6 208566 5 + 593897 TAATG----- -s simHuman_chr6.simHuman.chr6 223762 9 + 601863 TAATATAAT- -s simRat_chr6.simRat.chr6 210020 10 + 647215 TACTACAGTA - -a -s simMouse_chr6.simMouse.chr6 219168 15 + 636262 TGTTCATTTATCCAT -s Anc0.Anc0refChr5 40864 15 + 87904 CATTAGTTTGTCCAC -s Anc1.Anc1refChr8 55408 15 + 57822 CATTAGTTTGTCCAC -s Anc2.Anc2refChr15 36355 15 + 86568 CATTAGTTTGTCCAC -s mr.mrrefChr5 73662 15 + 294540 TGTTCATTTATCCAT -s simCow_chr6.simCow.chr6 395251 15 - 602619 CATTAGCTTGTCCAC -s simDog_chr6.simDog.chr6 208571 15 + 593897 CATTAGTTCGTCCAC -s simHuman_chr6.simHuman.chr6 223771 15 + 601863 CATTAGTTTGTCCCC -s simRat_chr6.simRat.chr6 210030 15 + 647215 TGTTCATTTATCCAT - -a -s simMouse_chr6.simMouse.chr6 219183 55 + 636262 GGCTATATGCCTGTGAGACCACAACCTAATTTGAAGCCTCCCTTGTCGCATCAGC -s Anc0.Anc0refChr5 40879 55 + 87904 AGCTGTATAATTGTGGGACCACTACCTTGTTTGAAGTGCTCTTTGTACCATCAAT -s Anc1.Anc1refChr8 55423 55 + 57822 AGCTGTATAATTGTGGGACCACTACCTTGTTTGAAGTGCTCTTTGTACCATCAAT -s Anc2.Anc2refChr15 36370 55 + 86568 ATCTGTACAATTGTGGGACCACTACGTTGTTTGAAGTGCTTTTTGTACCATCAGT -s mr.mrrefChr5 73677 55 + 294540 GGCTATATGCCTGTGAGACCACAACCTTATTTGAAGCCTCCCTTGTCCCATCAAT -s simCow_chr6.simCow.chr6 395266 54 - 602619 AGCAGTACAATTGTGGGACCACTACATTATTTGAAATGCTACTCGCACCA-CAGC -s simDog_chr6.simDog.chr6 208586 53 + 593897 ATCTGTACAGTTGTGGGACCACTACGTTGTTT--AGTGCTTTTTGTACCATCAGT -s simHuman_chr6.simHuman.chr6 223789 55 + 601863 AGTTGTATAATTGTGGCACTATTACCTTTTTTGAAGTGCTCTTTGTACCATTGAT -s simRat_chr6.simRat.chr6 210045 55 + 647215 GGCTATATGCCTGTGAGACCACAACCTTATTTGAAGCCTCCCTTGTGCCATCAAT - -a -s simMouse_chr6.simMouse.chr6 219238 1 + 636262 A -s Anc0.Anc0refChr5 40934 1 + 87904 G -s Anc1.Anc1refChr8 55478 1 + 57822 G -s Anc2.Anc2refChr15 36441 1 + 86568 G -s mr.mrrefChr5 73732 1 + 294540 G -s simCow_chr6.simCow.chr6 395338 1 - 602619 G -s simDog_chr6.simDog.chr6 208655 1 + 593897 G -s simHuman_chr6.simHuman.chr6 223844 1 + 601863 G -s simRat_chr6.simRat.chr6 210100 1 + 647215 G - -a -s simMouse_chr6.simMouse.chr6 219239 3 + 636262 ACC -s Anc0.Anc0refChr5 40963 3 + 87904 ACA -s Anc1.Anc1refChr8 55507 3 + 57822 ACA -s Anc2.Anc2refChr15 36470 3 + 86568 ACA -s mr.mrrefChr5 73760 3 + 294540 ACC -s simCow_chr6.simCow.chr6 395367 3 - 602619 TTG -s simDog_chr6.simDog.chr6 208684 3 + 593897 ACA -s simHuman_chr6.simHuman.chr6 223873 3 + 601863 ACT -s simRat_chr6.simRat.chr6 210128 3 + 647215 ACC - -a -s simMouse_chr6.simMouse.chr6 219242 8 + 636262 CTTCCTCT -s Anc0.Anc0refChr5 40966 8 + 87904 CCTAATCT -s Anc1.Anc1refChr8 55510 8 + 57822 CCTAATCT -s Anc2.Anc2refChr15 36476 8 + 86568 CTTAATCT -s mr.mrrefChr5 73763 8 + 294540 CCTCCTCT -s simCow_chr6.simCow.chr6 395373 8 - 602619 CTAAATCT -s simDog_chr6.simDog.chr6 208690 8 + 593897 CTTAATCA -s simHuman_chr6.simHuman.chr6 223876 8 + 601863 CCTAATCT -s simRat_chr6.simRat.chr6 210131 8 + 647215 CCTCCTCT - -a -s simMouse_chr6.simMouse.chr6 219250 8 + 636262 ACTTTCCA -s Anc0.Anc0refChr5 40975 8 + 87904 ATTTTACA -s Anc1.Anc1refChr8 55519 8 + 57822 ATTTTACA -s Anc2.Anc2refChr15 36485 8 + 86568 ATTTTACA -s mr.mrrefChr5 73771 8 + 294540 ATTTTCCA -s simCow_chr6.simCow.chr6 395382 8 - 602619 ATTTTTCA -s simDog_chr6.simDog.chr6 208699 8 + 593897 AGTTTACA -s simHuman_chr6.simHuman.chr6 223885 8 + 601863 ATTTTACA -s simRat_chr6.simRat.chr6 210139 8 + 647215 ATTTTCTA - -a -s simMouse_chr6.simMouse.chr6 219258 24 + 636262 CCCTATATCTAGATGGTGACACTA -s Anc0.Anc0refChr5 41007 24 + 87904 CCCTATATTTGGATGGTGTGCAGA -s Anc1.Anc1refChr8 55551 24 + 57822 CCCTATATTTGGATGGTGTGCAGA -s Anc2.Anc2refChr15 36517 24 + 86568 CCCTATATTTGGATGGTGTGCAAA -s mr.mrrefChr5 73779 24 + 294540 CCCTATATCTAGATGGTGACACTA -s simCow_chr6.simCow.chr6 395414 24 - 602619 CCCTATACTTGGATGATGTACAAA -s simDog_chr6.simDog.chr6 208731 23 + 593897 CCCTATATGTGGA-GGCATGCAAA -s simHuman_chr6.simHuman.chr6 223917 24 + 601863 CCTGATATTTGGATGGTGTGCAGA -s simRat_chr6.simRat.chr6 210147 24 + 647215 CCCTATATCTAGATGGTGACACTA - -a -s simMouse_chr6.simMouse.chr6 219282 1 + 636262 A -s Anc0.Anc0refChr5 41031 1 + 87904 A -s Anc1.Anc1refChr8 55575 1 + 57822 A -s Anc2.Anc2refChr15 36545 1 + 86568 A -s mr.mrrefChr5 73803 1 + 294540 A -s simCow_chr6.simCow.chr6 395442 1 - 602619 A -s simDog_chr6.simDog.chr6 208758 1 + 593897 A -s simHuman_chr6.simHuman.chr6 223941 1 + 601863 A -s simRat_chr6.simRat.chr6 210171 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 219283 40 + 636262 GTGAACAATTTACCATCCCTTTTGTTGGCTGTTGTCAAGC -s Anc0.Anc0refChr5 41037 40 + 87904 ATGAACAATTTATCTTCCCTTTTAGTGTCTATTGTAGGAC -s Anc1.Anc1refChr8 55581 40 + 57822 ATGAACAATTTATCTTCCCTTTTAGTGTCTATTGTAGGAC -s Anc2.Anc2refChr15 36551 40 + 86568 ATGAACAATTTATCTTCCTTTTTAGTGTCTATTATAGGAC -s mr.mrrefChr5 73809 40 + 294540 GTGAACAATTTACCATCCCTTTTGTTGGCTGTTGTCAAGC -s simCow_chr6.simCow.chr6 395448 40 - 602619 ATGAACAATTCATCGTCCTTTTTAGTGTCTATTTGAGGAC -s simDog_chr6.simDog.chr6 208764 40 + 593897 ATGAACAATTTATCTTGCTTTTTATTGTCTATAATAGGAC -s simHuman_chr6.simHuman.chr6 223947 40 + 601863 ATGAGCAATTTATCTTCTCTTTTAGTCTCAATTGTAGGAC -s simRat_chr6.simRat.chr6 210177 40 + 647215 GTGAACAATTTACCCTCCTTTCTGTTGGCTGTTGTCAAGC - -a -s simMouse_chr6.simMouse.chr6 219323 60 + 636262 GATTTTGCTGTCTCAGGTGCCCAGTGATTAGATAATGATTTTGGCTCTTATTTATGTCCC -s Anc0.Anc0refChr5 41083 60 + 87904 AATTTGGCTGCCCCAGGTGCCCATCCAGTAGACAATGATGATGGGTCTCATTTCTGGCCC -s Anc1.Anc1refChr8 55627 60 + 57822 AATTTGGCTGCCCCAGGTGCCCATCCAGTAGACAATGATGATGGGTCTCATTTCTGGCCC -s Anc2.Anc2refChr15 36598 60 + 86568 TATTTGACTGCCCCAGGTGCTCATCCAGTAGCCAATGATGATGGGTCTCATCTCTGGCCT -s mr.mrrefChr5 73855 60 + 294540 AATTTTGCTGTCTCAGGTGCCCAGCAATTAGATAATAATTTTGGCTCTTATTTATGTCCC -s simCow_chr6.simCow.chr6 395495 58 - 602619 CGTTTGTCTGCCCCAGGTGCTCATCCAGTATGCAATGATGATGGATCTCATCTCTGGC-- -s simDog_chr6.simDog.chr6 208811 60 + 593897 TATTTGACTGGCCCAGGTGCTCATTCAGTAGCCAATGATGATGGGTCGCATCTCTGGCCT -s simHuman_chr6.simHuman.chr6 223994 52 + 601863 AATTTGGCTGCTCTAGGCACC-ATCTAGTTAACAAT-------GGTCTCATTTCTGGCCC -s simRat_chr6.simRat.chr6 210223 58 + 647215 AATTTTGCTGTCTCAGGTGCT--GCAAGGAGATAATAATTATGGTTCTTGTTTATGTCCT - -a -s simMouse_chr6.simMouse.chr6 219383 6 + 636262 TTTGTC -s Anc0.Anc0refChr5 41160 6 + 87904 TCTATA -s Anc1.Anc1refChr8 55704 6 + 57822 TCTATA -s Anc2.Anc2refChr15 36675 6 + 86568 TCTATA -s mr.mrrefChr5 73929 6 + 294540 TCTATC -s simCow_chr6.simCow.chr6 395568 6 - 602619 TCTATC -s simDog_chr6.simDog.chr6 208888 6 + 593897 TCTATA -s simHuman_chr6.simHuman.chr6 224063 6 + 601863 TCTATT -s simRat_chr6.simRat.chr6 210295 6 + 647215 TCTATC - -a -s simMouse_chr6.simMouse.chr6 219389 28 + 636262 TTCTCGCGTATCCTTAGTAGAGGGCTCT -s Anc0.Anc0refChr5 41246 27 + 87904 TTT-CAGCAATCCTTAATGGAATGCTGT -s Anc1.Anc1refChr8 55790 28 + 57822 TTTTCAGCAATCCTTAATGGAATGCTGT -s Anc2.Anc2refChr15 36761 27 + 86568 TTT-CGGCAATCTTTAATGCAATGCTGT -s mr.mrrefChr5 73935 28 + 294540 TTCTCAGGTATCCTTAATAGAGGGCTCT -s simCow_chr6.simCow.chr6 395654 27 - 602619 TTT-CGGCAATCTTTGATGCAATGATGT -s simDog_chr6.simDog.chr6 208973 27 + 593897 TCT-TGACAATCTTTAATGCAATGCTCG -s simHuman_chr6.simHuman.chr6 224157 28 + 601863 TTTTCAGCAATCCTTAATGGAACACTGT -s simRat_chr6.simRat.chr6 210301 28 + 647215 TTCTCAGGTATCTTTAATAGAGGGCTCT - -a -s simMouse_chr6.simMouse.chr6 219417 8 + 636262 GATTTTCT -s Anc0.Anc0refChr5 41276 8 + 87904 TTTTTTTT -s Anc1.Anc1refChr8 55821 8 + 57822 TTTTTTTT -s Anc2.Anc2refChr15 36791 8 + 86568 TTTTTTTT -s mr.mrrefChr5 73966 8 + 294540 GATTTTCT -s simCow_chr6.simCow.chr6 395684 8 - 602619 TTCTGGTT -s simDog_chr6.simDog.chr6 209003 8 + 593897 TTTTTTTT -s simHuman_chr6.simHuman.chr6 224188 8 + 601863 TTTTTCTT -s simRat_chr6.simRat.chr6 210332 8 + 647215 GATTTTCT - -a -s simMouse_chr6.simMouse.chr6 219425 36 + 636262 TATGCCCTATTGAGTGGGTTATAAGTTCTCTCATAC -s Anc0.Anc0refChr5 41285 36 + 87904 TAGGCACTATTAAGGTTGTATTGGGTTTACAAATCC -s Anc1.Anc1refChr8 55830 36 + 57822 TAGGCACTATTAAGGTTGTATTGGGTTTACAAATCC -s Anc2.Anc2refChr15 36800 36 + 86568 TAGGCACTATTAAGGTTGTATTGGGTTTAAAAGTCC -s mr.mrrefChr5 73974 36 + 294540 TATGCCCTATTGAGTGGGTTTTAGGTTCACTCATCC -s simCow_chr6.simCow.chr6 395693 36 - 602619 TATGCACTATTATAGGTGTGTTGGGTTTATAAGTCC -s simDog_chr6.simDog.chr6 209012 36 + 593897 TAGGCACTATTAAGGTTGTAGTGGGTTTAAAAGTCC -s simHuman_chr6.simHuman.chr6 224197 36 + 601863 TACGCACTATTAACGTTGTATTGGCTTTACAAAATT -s simRat_chr6.simRat.chr6 210340 36 + 647215 TGTGCTCCATTGAGTGGGTGTTAGGTTCACCGATCC - -a -s simMouse_chr6.simMouse.chr6 219461 4 + 636262 CCAC -s Anc0.Anc0refChr5 41323 4 + 87904 TCAC -s Anc1.Anc1refChr8 55868 4 + 57822 TCAC -s Anc2.Anc2refChr15 36838 4 + 86568 TCAC -s mr.mrrefChr5 74012 4 + 294540 CCAC -s simCow_chr6.simCow.chr6 395731 4 - 602619 ACAC -s simDog_chr6.simDog.chr6 209050 4 + 593897 TCAC -s simHuman_chr6.simHuman.chr6 224235 4 + 601863 TCAC -s simRat_chr6.simRat.chr6 210378 4 + 647215 CCAC - -a -s simMouse_chr6.simMouse.chr6 219465 5 + 636262 CACAA -s Anc0.Anc0refChr5 41332 4 + 87904 C-CAA -s Anc1.Anc1refChr8 55877 5 + 57822 CGCAA -s Anc2.Anc2refChr15 36847 4 + 86568 C-CAA -s mr.mrrefChr5 74016 5 + 294540 CACAA -s simCow_chr6.simCow.chr6 395742 4 - 602619 C-CAA -s simDog_chr6.simDog.chr6 209059 4 + 593897 C-CAA -s simHuman_chr6.simHuman.chr6 224244 5 + 601863 TGTAA -s simRat_chr6.simRat.chr6 210382 4 + 647215 CA-AA - -a -s simMouse_chr6.simMouse.chr6 219470 4 + 636262 CCAC -s Anc0.Anc0refChr5 41336 4 + 87904 CAGC -s Anc1.Anc1refChr8 55882 4 + 57822 CAGC -s Anc2.Anc2refChr15 36851 4 + 86568 CAGC -s mr.mrrefChr5 74021 4 + 294540 CCAC -s simCow_chr6.simCow.chr6 395748 4 - 602619 CAAC -s simDog_chr6.simDog.chr6 209063 4 + 593897 CAGC -s simHuman_chr6.simHuman.chr6 224249 4 + 601863 CAGC -s simRat_chr6.simRat.chr6 210386 4 + 647215 CCAC - -a -s simMouse_chr6.simMouse.chr6 219474 23 + 636262 CAGTTGTCTTTGCTGTATAAAAT -s Anc0.Anc0refChr5 41340 23 + 87904 TAGTTGTCTTCACTGCATCTAAT -s Anc1.Anc1refChr8 55886 23 + 57822 TAGTTGTCTTCACTGCATCTAAT -s Anc2.Anc2refChr15 36855 23 + 86568 TAGATGTCTTCACTGCATCTAAT -s mr.mrrefChr5 74025 23 + 294540 TAGTTGTCTTTGCTGTATAAAAT -s simCow_chr6.simCow.chr6 395752 23 - 602619 TAGATGCCTTCACTGCATCAAGT -s simDog_chr6.simDog.chr6 209067 18 + 593897 TATACGTCTTCATT-----TTAT -s simHuman_chr6.simHuman.chr6 224253 23 + 601863 TAGTTATCTTCACTCCATGTAAT -s simRat_chr6.simRat.chr6 210400 23 + 647215 TAGTTGTCTTTGCTGTATAAAAT - -a -s simMouse_chr6.simMouse.chr6 219497 17 + 636262 ATACGACCCTGCATTAT -s Anc0.Anc0refChr5 41364 17 + 87904 AGGCCATCCAAAGTTAT -s Anc1.Anc1refChr8 55910 17 + 57822 AGGCCATCCAAAGTTAT -s Anc2.Anc2refChr15 36879 17 + 86568 AGGCCATCCAAAGCTCT -s mr.mrrefChr5 74048 17 + 294540 AGACCACCCTGCATTAT -s simCow_chr6.simCow.chr6 395776 17 - 602619 AGGCCTTTCAAAGATCT -s simDog_chr6.simDog.chr6 209086 17 + 593897 AGGCCACCCAAAGCTCC -s simHuman_chr6.simHuman.chr6 224277 17 + 601863 AGGCCATCCAAAGTTAT -s simRat_chr6.simRat.chr6 210423 17 + 647215 AGACCACCCTGCATTAT - -a -s simMouse_chr6.simMouse.chr6 219514 26 + 636262 TGCATCCCAAGGTTTCCAGGTCCTTA -s Anc0.Anc0refChr5 41381 26 + 87904 TGTGTCTCAATGTTCTTAGAGTTTGA -s Anc1.Anc1refChr8 55927 26 + 57822 TGTGTCTCAATGTTCTTAGAGTTTGA -s Anc2.Anc2refChr15 36896 26 + 86568 TGTGTCTCAATGTTCTTAGAGTTTGA -s mr.mrrefChr5 74065 26 + 294540 TGCATCCCAAGGTTTTCAGGTCCTTA -s simCow_chr6.simCow.chr6 395797 26 - 602619 TGTGTTTCAATGTCCTTGGATTTTGA -s simDog_chr6.simDog.chr6 209103 26 + 593897 TATGTCTCAATGTTCTTAGAGTTTGA -s simHuman_chr6.simHuman.chr6 224294 26 + 601863 TGTGTCTAAATGTTCTTAGACTTTGA -s simRat_chr6.simRat.chr6 210440 26 + 647215 CTCATCCCAAGATTTTCAGGTGCTTA - -a -s simMouse_chr6.simMouse.chr6 219540 56 + 636262 CTCTCATTTTTCTTGCATCTTGTGTGTGGTTCGTATTAATTTTAATAGGTGTGAAT -s Anc0.Anc0refChr5 41407 48 + 87904 CTTTAATTTTTATTGCGTCTTGCTTGTTGCTAGTTGTAGTAT-----GGTGT---C -s Anc1.Anc1refChr8 55953 48 + 57822 CTTTAATTTTTATTGCGTCTTGCTTGTTGCTAGTTGTAGTAT-----GGTGT---C -s Anc2.Anc2refChr15 36922 48 + 86568 CTTTAATTTTCATTGCGTCTTGCTTGTTGCTAGTTGTAGTAT-----GGTGT---C -s mr.mrrefChr5 74091 56 + 294540 CTCTCATTTTTCTTGCATCTTGTGTGTGGTTCGTATTAGTTTTAATAGATGTGAAT -s simCow_chr6.simCow.chr6 489263 48 - 602619 CTTTAATTTACACTGCATCTTGCTTGTGGCTAGTTGTAGCAT-----GGTGT---C -s simDog_chr6.simDog.chr6 209129 48 + 593897 CTTTATGCTTCATTGCGTCTTCCTTCTTGCCAGTTGTAGTAT-----GGTGT---C -s simHuman_chr6.simHuman.chr6 224320 48 + 601863 CCTTTATTTCTGTTGTGTCTTGCTTGTAGCTAGTTGTAGTAT-----GGTGT---C -s simRat_chr6.simRat.chr6 210466 56 + 647215 TTCTCATTTTTCTTGCACCTTGTATGTGGTTTGTAATAGTTATTATAGATGTAAAT - -a -s simMouse_chr6.simMouse.chr6 219596 3 + 636262 TGG -s Anc0.Anc0refChr5 41455 3 + 87904 TGG -s Anc1.Anc1refChr8 56001 3 + 57822 TGG -s Anc2.Anc2refChr15 36973 3 + 86568 TTG -s mr.mrrefChr5 74147 3 + 294540 TGG -s simCow_chr6.simCow.chr6 489314 3 - 602619 TCG -s simDog_chr6.simDog.chr6 209180 3 + 593897 TTG -s simHuman_chr6.simHuman.chr6 224368 3 + 601863 TGG -s simRat_chr6.simRat.chr6 210522 3 + 647215 TGG - -a -s simMouse_chr6.simMouse.chr6 219599 18 + 636262 TGTTATACTACTTTTCTT -s Anc0.Anc0refChr5 41458 18 + 87904 TGTTATTCTATTTTTTTC -s Anc1.Anc1refChr8 56004 18 + 57822 TGTTATTCTATTTTTTTC -s Anc2.Anc2refChr15 36976 18 + 86568 TGTTATTCTATTTGTTTC -s mr.mrrefChr5 74150 18 + 294540 TGTTATACTACTTTTCTT -s simCow_chr6.simCow.chr6 489465 18 - 602619 TGTCATCCTATTTGTTTC -s simDog_chr6.simDog.chr6 209183 18 + 593897 TGTTATTCTATTTGTTTC -s simHuman_chr6.simHuman.chr6 224371 18 + 601863 TGTTATTCTATTATTTTC -s simRat_chr6.simRat.chr6 210525 18 + 647215 TGTTATACTACTTTTCTT - -a -s simMouse_chr6.simMouse.chr6 219617 27 + 636262 TTCTAAATCTGTGAGTCTGCTGAGGGT -s Anc0.Anc0refChr5 41612 25 + 87904 TCTTGA--CTTTGATCTTGCTAAGGGT -s Anc1.Anc1refChr8 56158 25 + 57822 TCTTGA--CTTTGATCTTGCTAAGGGT -s Anc2.Anc2refChr15 37148 25 + 86568 TCTTGG--CTTTTATCTTGCTATGGGA -s mr.mrrefChr5 74168 27 + 294540 TCCTGAATCTGTGAGTCTGCTGAGGGT -s simCow_chr6.simCow.chr6 489634 25 - 602619 TCTTAG--CTTTTATCCTGCTATGGGA -s simDog_chr6.simDog.chr6 209355 25 + 593897 TACTGG--AGTTTATCTGGCTATGGGA -s simHuman_chr6.simHuman.chr6 224538 25 + 601863 TCTTGA--CTTTGATCTTGAAAAGGGT -s simRat_chr6.simRat.chr6 210543 27 + 647215 TCCTGAATCTGTGAGGCTGCTGAGGGT - -a -s simMouse_chr6.simMouse.chr6 219644 1 + 636262 A -s Anc0.Anc0refChr5 41647 1 + 87904 A -s Anc1.Anc1refChr8 56193 1 + 57822 A -s Anc2.Anc2refChr15 37183 1 + 86568 G -s mr.mrrefChr5 74195 1 + 294540 A -s simCow_chr6.simCow.chr6 489669 1 - 602619 G -s simDog_chr6.simDog.chr6 209390 1 + 593897 G -s simHuman_chr6.simHuman.chr6 224573 1 + 601863 A -s simRat_chr6.simRat.chr6 210570 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 219645 15 + 636262 TTCTGTATGTCCATT -s Anc0.Anc0refChr5 41648 15 + 87904 TCTTGTACATCCATT -s Anc1.Anc1refChr8 56194 15 + 57822 TCTTGTACATCCATT -s Anc2.Anc2refChr15 37195 15 + 86568 TCTTGGACATCCATC -s mr.mrrefChr5 74196 15 + 294540 TTCTGTATGTCCATT -s simCow_chr6.simCow.chr6 489681 15 - 602619 TCTTGGACATCCATC -s simDog_chr6.simDog.chr6 209402 15 + 593897 TCTTGGACATCCATC -s simHuman_chr6.simHuman.chr6 224574 15 + 601863 TCATATACATTCATT -s simRat_chr6.simRat.chr6 210571 15 + 647215 TTCTGTATGTCCATT - -a -s simMouse_chr6.simMouse.chr6 219660 2 + 636262 AT -s Anc0.Anc0refChr5 41663 2 + 87904 AT -s Anc1.Anc1refChr8 56209 2 + 57822 AT -s Anc2.Anc2refChr15 37210 2 + 86568 AT -s mr.mrrefChr5 74211 2 + 294540 AT -s simCow_chr6.simCow.chr6 489779 2 - 602619 AT -s simDog_chr6.simDog.chr6 209417 2 + 593897 AT -s simHuman_chr6.simHuman.chr6 224589 2 + 601863 GT -s simRat_chr6.simRat.chr6 210586 2 + 647215 AT - -a -s simMouse_chr6.simMouse.chr6 219662 12 + 636262 TTAGACTAGGAT -s Anc0.Anc0refChr5 41669 12 + 87904 TTAGATCAGGAT -s Anc1.Anc1refChr8 56215 12 + 57822 TTAGATCAGGAT -s Anc2.Anc2refChr15 37216 12 + 86568 TTACATCAGGAT -s mr.mrrefChr5 74217 12 + 294540 TTAGACTAGGAT -s simCow_chr6.simCow.chr6 489785 12 - 602619 TTACATCCGGAT -s simDog_chr6.simDog.chr6 209419 6 + 593897 ------CAGGAT -s simHuman_chr6.simHuman.chr6 224595 12 + 601863 TTAGCTCTGGAT -s simRat_chr6.simRat.chr6 210592 12 + 647215 TTAGACTAGGAT - -a -s simMouse_chr6.simMouse.chr6 219674 22 + 636262 CAGTAGCATCTGATCTGAGAGG -s Anc0.Anc0refChr5 41682 21 + 87904 CAG-GCCATTTGATCTGAGAGG -s Anc1.Anc1refChr8 56228 22 + 57822 CAGTGCCATTTGATCTGAGAGG -s Anc2.Anc2refChr15 37229 21 + 86568 CAG-GCCATTCGATCTGAGAGG -s mr.mrrefChr5 74229 22 + 294540 CAGTAGCATCTGATCTGAGAGG -s simCow_chr6.simCow.chr6 489798 21 - 602619 GAG-GCCATTGAATGGGAGAAG -s simDog_chr6.simDog.chr6 209426 21 + 593897 CAG-GCCATCCGATCTGAGAGG -s simHuman_chr6.simHuman.chr6 224608 22 + 601863 CTGTGTCTTTTGATCTTAGAGG -s simRat_chr6.simRat.chr6 210604 22 + 647215 CAGTAGCATCTGGTCTGAGAGG - -a -s simMouse_chr6.simMouse.chr6 219696 2 + 636262 TA -s Anc0.Anc0refChr5 41703 2 + 87904 TA -s Anc1.Anc1refChr8 56250 2 + 57822 TA -s Anc2.Anc2refChr15 37250 2 + 86568 TA -s mr.mrrefChr5 74251 2 + 294540 TA -s simCow_chr6.simCow.chr6 489822 2 - 602619 TA -s simDog_chr6.simDog.chr6 209447 2 + 593897 TA -s simHuman_chr6.simHuman.chr6 224630 2 + 601863 TA -s simRat_chr6.simRat.chr6 210626 2 + 647215 TA - -a -s simMouse_chr6.simMouse.chr6 219698 28 + 636262 GTTTATGGCAGTATTGTTTGCCTTGCAC -s Anc0.Anc0refChr5 41705 28 + 87904 GTTTACGACAGTATTATTTTCTTTGCAT -s Anc1.Anc1refChr8 56252 28 + 57822 GTTTACGACAGTATTATTTTCTTTGCAT -s Anc2.Anc2refChr15 37252 28 + 86568 GCTTACGACAACATTATTTTCTTTGAGT -s mr.mrrefChr5 74253 28 + 294540 GTTTATGGCAGTATTGTTTGCCTTGCAT -s simCow_chr6.simCow.chr6 489825 28 - 602619 GCTTATGGCAAAATTGTTTTCCTTAAGT -s simDog_chr6.simDog.chr6 209449 28 + 593897 GCTTACGACAACATTATTTTCTTTGAGT -s simHuman_chr6.simHuman.chr6 224632 28 + 601863 GTTTACCACAGTACTATTTTATTTGCAT -s simRat_chr6.simRat.chr6 210628 28 + 647215 TTTCATGGCAGTATTGTTTGCCATGCAT - -a -s simMouse_chr6.simMouse.chr6 219726 1 + 636262 T -s Anc0.Anc0refChr5 41734 1 + 87904 T -s Anc1.Anc1refChr8 56281 1 + 57822 T -s Anc2.Anc2refChr15 37281 1 + 86568 T -s mr.mrrefChr5 74282 1 + 294540 T -s simCow_chr6.simCow.chr6 489854 1 - 602619 T -s simDog_chr6.simDog.chr6 209478 1 + 593897 T -s simHuman_chr6.simHuman.chr6 224661 1 + 601863 T -s simRat_chr6.simRat.chr6 210657 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 219727 90 + 636262 ATCAAAAAGAGCCCTTGCTTAGTAAATCATGCCCAGTCTCTTAATGTAAAAGCTCTGGAAACCCCCATTTGGGAGTGGCAGTAGAGGAGG -s Anc0.Anc0refChr5 41735 69 + 87904 ATCAAAGAGG-GTCTTGCTTGGTAAATCATGCCCAGTTTTTTAATATGAAAGATGTGAA--------------------GCAGAAGAAGG -s Anc1.Anc1refChr8 56282 69 + 57822 ATCAAAGAGG-GTCTTGCTTGGTAAATCATGCCCAGTTTTTTAATATGAAAGATGTGAA--------------------GCAGAAGAAGG -s Anc2.Anc2refChr15 37282 69 + 86568 ATCAAAGAGG-GTCTTGCTTGGTATACCATGCCCAGTTTTTTAATATGAAAGAAGCGAA--------------------GCAGAAGAAGG -s mr.mrrefChr5 74283 69 + 294540 ATCAAAAAGA-GCCTTGCTTAGTAAATCATGCCCAGTCTCTTAATGTAAAAGCTCTGGA--------------------AGCAGAGGAGG -s simCow_chr6.simCow.chr6 489860 65 - 602619 ATCAAGTAGG-GCCTTGCTTGGTAT----TGGGCAGTTTTTTAATATGAAAGACGCGTA--------------------GCAGGAGAAGG -s simDog_chr6.simDog.chr6 209479 69 + 593897 ATCAAAGAGG-GTTTTGCTTGGTGTACCATGCCCAGTTTTCCAATTTGGGAGAAGCAAA--------------------GCGGATGAAGT -s simHuman_chr6.simHuman.chr6 224662 69 + 601863 ATCAAAGGGG-GTCTTGCTTGGTAAATCACACCCAGTTTTTTAACATGAAAGATTTGAA--------------------GCATAAGAGGG -s simRat_chr6.simRat.chr6 210658 69 + 647215 ATCAAAAAGA-GCCTTGCTTAGTAAATCATTCCCAGACTCTTAAGGTATAAGCTCCAGA--------------------AGCAGAGGAGG - -a -s simMouse_chr6.simMouse.chr6 219817 8 + 636262 ACATGGTA -s Anc0.Anc0refChr5 41804 8 + 87904 ACATGGAA -s Anc1.Anc1refChr8 56351 8 + 57822 ACATGGAA -s Anc2.Anc2refChr15 37351 8 + 86568 ATATCTAG -s mr.mrrefChr5 74352 8 + 294540 ACATGGTA -s simCow_chr6.simCow.chr6 489935 8 - 602619 ATAGCTAG -s simDog_chr6.simDog.chr6 209548 8 + 593897 ATATCCAG -s simHuman_chr6.simHuman.chr6 224731 8 + 601863 ACATGGGA -s simRat_chr6.simRat.chr6 210727 8 + 647215 ACATGGTA - -a -s simMouse_chr6.simMouse.chr6 219825 24 + 636262 GAAGTACAACATAGATCTCCCTTT -s Anc0.Anc0refChr5 41812 24 + 87904 ATGGTATAACATGGATCTTCCTTT -s Anc1.Anc1refChr8 56359 24 + 57822 ATGGTATAACATGGATCTTCCTTT -s Anc2.Anc2refChr15 37359 24 + 86568 ATGGTATAACATGGATCTTCTTGT -s mr.mrrefChr5 74360 24 + 294540 GAAGTACAACATAGATCTCCCTTT -s simCow_chr6.simCow.chr6 489943 24 - 602619 ATGGTAAACCATGGATCTCATTCT -s simDog_chr6.simDog.chr6 209556 24 + 593897 ATGGTATTACATGGATCTTCTTGT -s simHuman_chr6.simHuman.chr6 224763 24 + 601863 ATGGTATAACATGGATTTTCCTTT -s simRat_chr6.simRat.chr6 210735 24 + 647215 CACGTACAACATAGGTCTCTCTTT - -a -s simMouse_chr6.simMouse.chr6 219849 10 + 636262 AGCAATTAAT -s Anc0.Anc0refChr5 41836 10 + 87904 ACCTGTGAAT -s Anc1.Anc1refChr8 56383 10 + 57822 ACCTGTGAAT -s Anc2.Anc2refChr15 37383 10 + 86568 ACCTGTGAAT -s mr.mrrefChr5 74384 10 + 294540 AGCAATTAAT -s simCow_chr6.simCow.chr6 489967 10 - 602619 ACCTGTGAAT -s simDog_chr6.simDog.chr6 209580 10 + 593897 ACCAGTGAAT -s simHuman_chr6.simHuman.chr6 224788 10 + 601863 ACCTGTGAGT -s simRat_chr6.simRat.chr6 210759 10 + 647215 ATCAATTAAT - -a -s simMouse_chr6.simMouse.chr6 219859 24 + 636262 ATGACAGACTTGGCACATTGTCAA -s Anc0.Anc0refChr5 41846 24 + 87904 AGGACAGGCTTGATGCCATGTTGA -s Anc1.Anc1refChr8 56393 24 + 57822 AGGACAGGCTTGATGCCATGTTGA -s Anc2.Anc2refChr15 37393 24 + 86568 AGGGCAGGCTTGATGGCATGTTGA -s mr.mrrefChr5 74394 24 + 294540 ATGACAGACTTGGCACATTGTTAA -s simCow_chr6.simCow.chr6 489977 24 - 602619 ATGGCAGGTTTGATGGCACGTTGA -s simDog_chr6.simDog.chr6 209590 17 + 593897 AGGGCATGCT-------ATGTTGA -s simHuman_chr6.simHuman.chr6 224842 24 + 601863 AGGACAGGCTGGATGCGATGTTGA -s simRat_chr6.simRat.chr6 210769 24 + 647215 AGGACAGACTCGGCACATTGTTAA - -a -s simMouse_chr6.simMouse.chr6 219883 19 + 636262 AAGACATTAGGCTACCCAA -s Anc0.Anc0refChr5 41891 19 + 87904 CACACAGTAGTCTACCCAA -s Anc1.Anc1refChr8 56438 19 + 57822 CACACAGTAGTCTACCCAA -s Anc2.Anc2refChr15 37438 19 + 86568 CACACAGTAGTCTACCCAA -s mr.mrrefChr5 74439 19 + 294540 AAGACAGTAGGCTACCCAA -s simCow_chr6.simCow.chr6 490022 19 - 602619 CACACAATGGACTACTCAA -s simDog_chr6.simDog.chr6 209628 19 + 593897 CACACAGTAGTCTACCCAA -s simHuman_chr6.simHuman.chr6 224887 19 + 601863 TACACAGTATTCTACCCAA -s simRat_chr6.simRat.chr6 210814 19 + 647215 AAGGTCGTAGGCTACCCAA - -a -s simMouse_chr6.simMouse.chr6 219902 10 + 636262 TCTTCAGCAT -s Anc0.Anc0refChr5 41910 10 + 87904 CCTCTAGCAT -s Anc1.Anc1refChr8 56457 10 + 57822 CCTCTAGCAT -s Anc2.Anc2refChr15 37457 10 + 86568 CCTCTAGGAT -s mr.mrrefChr5 74458 10 + 294540 CCTTCAGCAT -s simCow_chr6.simCow.chr6 490041 1 - 602619 C--------- -s simDog_chr6.simDog.chr6 209647 10 + 593897 CCTCTAGGAT -s simHuman_chr6.simHuman.chr6 224906 10 + 601863 CCTCTAGCAT -s simRat_chr6.simRat.chr6 210834 10 + 647215 CCTTCAGCAT - -a -s simMouse_chr6.simMouse.chr6 219912 49 + 636262 GACTGACTGCACCAAACATGTAAATCCCTGGGTAAAAGTAGGAGGGTAA -s Anc0.Anc0refChr5 42105 47 + 87904 GACTGTTTGCACCAAGCATTCAAATACCTGGGTAAGGGTAA--GGGTAA -s Anc1.Anc1refChr8 56652 49 + 57822 GACTGTTTGCACCAAGCATTCAAATACCTGGGTAAGGGTAAAAGGGTAA -s Anc2.Anc2refChr15 37654 47 + 86568 GACTGTTTGCACCAAGCATTCAAATACATGGGCAAGGGTAA--GGGTAA -s mr.mrrefChr5 74468 49 + 294540 GACTGATTGCACCAAACATTTAAATCCCTGGGTAAGGGTAGGAGGGTAA -s simCow_chr6.simCow.chr6 490241 39 - 602619 GACTGTTTGGATCAATCATTTAAATACATGGGCAAGGGT---------- -s simDog_chr6.simDog.chr6 209842 45 + 593897 GACCGTTTGCTCCAAGCTCTCAAATATATGGTCAAGG--AA--GGGTAA -s simHuman_chr6.simHuman.chr6 225137 49 + 601863 GACTGCTTTCAGCAAGCATTAAAATTCCTGGGTAAGGGTAAAAGGGTAC -s simRat_chr6.simRat.chr6 210844 49 + 647215 GGCTGATTGCACTAAACATTTAAATACCTGGGTAAGGGTAGGAGGGTAA - -a -s simMouse_chr6.simMouse.chr6 219961 23 + 636262 ACAAAACTACATCTCCTGCTTTA -s Anc0.Anc0refChr5 42154 22 + 87904 ACAAATTGACATGC-CTGCCTTA -s Anc1.Anc1refChr8 56703 22 + 57822 ACAAATTGACATGC-CTGCCTTA -s Anc2.Anc2refChr15 37703 22 + 86568 ACAAATTGAGAGGC-CTACCTGA -s mr.mrrefChr5 74517 22 + 294540 ACAAAACGACATCT-CTGCCTTA -s simCow_chr6.simCow.chr6 490280 13 - 602619 ---------GAGGC-CTACCTGA -s simDog_chr6.simDog.chr6 209889 22 + 593897 ACAAATTGAGAGGC-TAACCTGA -s simHuman_chr6.simHuman.chr6 225188 22 + 601863 ACAAATTGACATAC-CTGCCTTA -s simRat_chr6.simRat.chr6 210893 22 + 647215 ACAAAACGACGTGT-CTGCCTTA - -a -s simMouse_chr6.simMouse.chr6 219984 18 + 636262 CACTAAAGCTAACAATAT -s Anc0.Anc0refChr5 42178 15 + 87904 CAC---AGTTAACAGTAG -s Anc1.Anc1refChr8 56727 18 + 57822 CACTGCAGTTAACAGTAG -s Anc2.Anc2refChr15 37727 15 + 86568 CAC---AGTTAACAGTAG -s mr.mrrefChr5 74539 18 + 294540 CACTGAAGCTAACAATAT -s simCow_chr6.simCow.chr6 490295 15 - 602619 CAC---ATTTAGCAGCAG -s simDog_chr6.simDog.chr6 209913 15 + 593897 CCC---AGTTAACAGTAG -s simHuman_chr6.simHuman.chr6 225212 18 + 601863 CACTGCAGTTAACAGTAC -s simRat_chr6.simRat.chr6 210915 18 + 647215 CACTGAAGGTAATGATAT - -a -s simMouse_chr6.simMouse.chr6 220002 105 + 636262 CACGAGATCAGCAACCAAAAGATTACAAGAAGCGACTTGCATAAACGGATGGCAGTGAAATGCAGGACCATAATTGTTCTGCTTCAATCGCTATACAAGCTATGC -s Anc0.Anc0refChr5 42202 105 + 87904 CATGAGGTCAGCAACCAAAAGATTTCAAGGAATGGCTCTCATAAACAGATGACAGTGAAATGCAGGACCATAATTGTTCCATTTCATTTAATATAAAATCAAAGA -s Anc1.Anc1refChr8 56754 105 + 57822 CATGAGGTCAGCAACCAAAAGATTTCAAGGAATGGCTCTCATAAACAGATGACAGTGAAATGCAGGACCATAATTGTTCCATTTCATTTAATATAAAATCAAAGA -s Anc2.Anc2refChr15 37751 105 + 86568 CAAGAGGTCAGCAGCCAAAAGATTTCAAGGAATGGATCTTATAAACAGATGACAGTAAAATGCAGGACCATAATTGTTCCATTTCATTTAATATAAAATCAAAGA -s mr.mrrefChr5 74566 105 + 294540 CATGAGGTCAGCAACCAAAAGATTACAAGAAACGACTTGCATAAACAGATGGCAGTGAAATGCAGGACCATAATTGTTCCACTTCAATCACTATAAAAGCTATGA -s simCow_chr6.simCow.chr6 490317 89 - 602619 ------------AGCCAAAAGATTTCAAGGAATGGATCTTACAAACTGATGACAGTCAAATGCGGGACCAT----GTTCCGTTTCATTTAATATAAAATCAGAGA -s simDog_chr6.simDog.chr6 209937 105 + 593897 CAAGAGGTCAGCCGCCCAATTGTTTCAAGGAATGGATCTTTTAAACAGATGACAGTAAAATGCAGGACCATAATTGTTCCACTTCATTTAATATGAAATTAAAAA -s simHuman_chr6.simHuman.chr6 225239 105 + 601863 CATGAGGTTAGCAACCAAAAGATTTCAATGAATGGCCCTCATAAACAGATGACAGTGAAATGCAGGACCGTAATTATTCCATTTCATTTAATATAAAATCAAAGA -s simRat_chr6.simRat.chr6 210942 105 + 647215 TATGAAGTCAGCAACCAAAAGATGACAAGAAACAACTTGCATAAAAAGATGGCAGTGGGATGCAGGACCATAATTGTTCCACTTCAATCACTATAAAAGCTATGA - -a -s simMouse_chr6.simMouse.chr6 220107 2 + 636262 TT -s Anc0.Anc0refChr5 42307 2 + 87904 TT -s Anc1.Anc1refChr8 56859 2 + 57822 TT -s Anc2.Anc2refChr15 37867 2 + 86568 TC -s mr.mrrefChr5 74671 2 + 294540 TT -s simCow_chr6.simCow.chr6 490417 2 - 602619 TC -s simDog_chr6.simDog.chr6 210053 2 + 593897 TC -s simHuman_chr6.simHuman.chr6 225344 2 + 601863 TT -s simRat_chr6.simRat.chr6 211047 2 + 647215 TA - -a -s simMouse_chr6.simMouse.chr6 220109 69 + 636262 GACACAGTCCAGCGCATTGTGGCTCATGACTATGCTCCTATCTATCTCTGTCGAGACCTTTTTTCAAGC -s Anc0.Anc0refChr5 42310 33 + 87904 GACCCTGGCT--------------------------CCTATCTA------TCAGGAGGCTTTTT----G -s Anc1.Anc1refChr8 56862 50 + 57822 GACCCTGGCTATGATATTGCAG-------------TCCTATCTA------TCAGGAGGCTTTTTTGATG -s Anc2.Anc2refChr15 37870 33 + 86568 GACCCTTGCT--------------------------CCTATCTC------TCAGGAGGCCTATT----G -s mr.mrrefChr5 74673 63 + 294540 GACCCTGTCCAGGGCATTGTGGCTCATGACTGTGGTCCTATCTA------TCGAGACCTTTTTTCAAGC -s simCow_chr6.simCow.chr6 490420 33 - 602619 GGCCTGTGCT--------------------------CCTATCTC------TCAGGAGGCCTATT----G -s simDog_chr6.simDog.chr6 210056 16 + 593897 CACCCTTGCT--------------------------CCTATC--------------------------- -s simHuman_chr6.simHuman.chr6 225347 50 + 601863 GACCCTGGCTATGATATTGCAG-------------TCCTATCTA------TCAGGAAGATTTTTTGATT -s simRat_chr6.simRat.chr6 211049 63 + 647215 GACCCTGTCCAGGTCATTGTGGCTCAAGACTGTGGTCCTATCTA------TGGAGAGCTGTTTTCAAGC - -a -s simMouse_chr6.simMouse.chr6 220178 11 + 636262 TTCTGATACCA -s Anc0.Anc0refChr5 42352 11 + 87904 TTCTTATACCA -s Anc1.Anc1refChr8 56921 11 + 57822 TTCTTATACCA -s Anc2.Anc2refChr15 37912 11 + 86568 CTGTTGTACCA -s mr.mrrefChr5 74736 11 + 294540 TTCTTATACCA -s simCow_chr6.simCow.chr6 490462 11 - 602619 CTGTTGTACCA -s simHuman_chr6.simHuman.chr6 225406 11 + 601863 TTCTTATACCA -s simRat_chr6.simRat.chr6 211112 11 + 647215 TCCTTATACCA - -a -s simMouse_chr6.simMouse.chr6 220189 10 + 636262 ACAACCAAAT -s Anc0.Anc0refChr5 42363 10 + 87904 ACATGCTAAT -s Anc1.Anc1refChr8 56932 10 + 57822 ACATGCTAAT -s Anc2.Anc2refChr15 37923 10 + 86568 TCATGCTAGT -s mr.mrrefChr5 74747 10 + 294540 ACAACCAAAT -s simCow_chr6.simCow.chr6 490473 10 - 602619 TCATGCTAGT -s simHuman_chr6.simHuman.chr6 225430 10 + 601863 AGATGCCAAT -s simRat_chr6.simRat.chr6 211123 10 + 647215 GCAACCAAAC - -a -s simMouse_chr6.simMouse.chr6 220199 1 + 636262 G -s Anc0.Anc0refChr5 42373 1 + 87904 G -s Anc1.Anc1refChr8 56942 1 + 57822 G -s Anc2.Anc2refChr15 37933 1 + 86568 A -s mr.mrrefChr5 74757 1 + 294540 G -s simCow_chr6.simCow.chr6 490483 1 - 602619 A -s simHuman_chr6.simHuman.chr6 225455 1 + 601863 G -s simRat_chr6.simRat.chr6 211133 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 220200 13 + 636262 CAATGCCCCCCTG -s Anc0.Anc0refChr5 42374 13 + 87904 CAATACCCCCCTG -s Anc1.Anc1refChr8 56943 13 + 57822 CAATACCCCCCTG -s Anc2.Anc2refChr15 37935 13 + 86568 CAATACTCTCCTC -s mr.mrrefChr5 74758 13 + 294540 CAATGCCCCCCTG -s simCow_chr6.simCow.chr6 490485 13 - 602619 CAATACTCTCCTC -s simHuman_chr6.simHuman.chr6 225456 13 + 601863 CAATCCCCCCCTG -s simRat_chr6.simRat.chr6 211134 13 + 647215 CAATGACCCCCTG - -a -s simMouse_chr6.simMouse.chr6 220213 20 + 636262 TACAGGACAGTGCCCACAGT -s Anc0.Anc0refChr5 42393 20 + 87904 TTTCATGCAGTGCTCACTGT -s Anc1.Anc1refChr8 56962 20 + 57822 TTTCATGCAGTGCTCACTGT -s Anc2.Anc2refChr15 37954 20 + 86568 TTTCATGCAGAACTTGCTGT -s mr.mrrefChr5 74771 20 + 294540 TACAAGGCAGTGCTCACTGT -s simCow_chr6.simCow.chr6 490504 20 - 602619 TTTCATGCAGAACTTGCTGT -s simHuman_chr6.simHuman.chr6 225475 20 + 601863 TTTCATGCTGTGCTCACTGT -s simRat_chr6.simRat.chr6 211147 20 + 647215 TACAAGGCAGTGCTCACTGT - -a -s simMouse_chr6.simMouse.chr6 220233 13 + 636262 TAGGACCCACCAT -s Anc0.Anc0refChr5 42421 13 + 87904 TAAAACTTATCAC -s Anc1.Anc1refChr8 56990 13 + 57822 TAAAACTTATCAC -s Anc2.Anc2refChr15 37982 13 + 86568 CAAAACTTATCAC -s mr.mrrefChr5 74791 13 + 294540 TAGGACCCACCAT -s simCow_chr6.simCow.chr6 490532 13 - 602619 CAAAACTTATCAC -s simHuman_chr6.simHuman.chr6 225503 13 + 601863 TAAAACTTATCGC -s simRat_chr6.simRat.chr6 211167 13 + 647215 TACGACCCACCAT - -a -s simMouse_chr6.simMouse.chr6 220246 19 + 636262 TTTTCAGAAAGCTCCACAG -s Anc0.Anc0refChr5 42476 19 + 87904 TTTGGGGAAAGCTGCATTG -s Anc1.Anc1refChr8 57045 19 + 57822 TTTGGGGAAAGCTGCATTG -s Anc2.Anc2refChr15 38037 19 + 86568 TTTGGGGAAAGCTGCATTG -s mr.mrrefChr5 74804 19 + 294540 TTTGCAGAAAGCTGCACAG -s simCow_chr6.simCow.chr6 490667 19 - 602619 TTTAGGGAAAGCTGCATTG -s simDog_chr6.simDog.chr6 210072 16 + 593897 ---GGGGAAAGCTGCCTGT -s simHuman_chr6.simHuman.chr6 225559 19 + 601863 TTTGGGGAAGGCTGCATTG -s simRat_chr6.simRat.chr6 211180 19 + 647215 TGTGCAGAAAGCTGCTCAA - -a -s simMouse_chr6.simMouse.chr6 220265 34 + 636262 CCTTAGCTGGCTATCTTGGGAAAGCTCAAGTGGG -s Anc0.Anc0refChr5 42496 34 + 87904 CCTTGGCTGCCTATATCCAGAAACCTCTAATTGG -s Anc1.Anc1refChr8 57065 34 + 57822 CCTTGGCTGCCTATATCCAGAAACCTCTAATTGG -s Anc2.Anc2refChr15 38057 34 + 86568 CCTTGGCTGCCTATATCCAGGAACCTCTAACTGG -s mr.mrrefChr5 74824 34 + 294540 CCTTGGCTGGCTATCTTGGGAAAGCTCTAGTGGG -s simCow_chr6.simCow.chr6 490687 34 - 602619 CCTTGGCAGCCAATCTGCAGGTACCCTAAAGTTG -s simDog_chr6.simDog.chr6 210089 34 + 593897 CCTTAGCTGCCTACATCCAGGAATCTCTAACTGG -s simHuman_chr6.simHuman.chr6 225579 34 + 601863 CCTTGGCTGCCTATTCCCAGAAACATCTCATTGG -s simRat_chr6.simRat.chr6 211200 34 + 647215 CCTTGGCTGACTAGCTGGGGAAGATTCTAGCAGG - -a -s simMouse_chr6.simMouse.chr6 220299 8 + 636262 CTCTTTAG -s Anc0.Anc0refChr5 42536 8 + 87904 CTCTTTAT -s Anc1.Anc1refChr8 57105 8 + 57822 CTCTTTAT -s Anc2.Anc2refChr15 38097 8 + 86568 CCCTTTAT -s mr.mrrefChr5 74858 8 + 294540 CTCTTTAG -s simCow_chr6.simCow.chr6 490727 8 - 602619 TCCTTTAT -s simDog_chr6.simDog.chr6 210129 8 + 593897 CCATTTAT -s simHuman_chr6.simHuman.chr6 225620 8 + 601863 CTCTTTAT -s simRat_chr6.simRat.chr6 211234 8 + 647215 CTCTTTAG - -a -s simMouse_chr6.simMouse.chr6 220307 5 + 636262 GTAGT -s Anc0.Anc0refChr5 42544 5 + 87904 GTAGT -s Anc1.Anc1refChr8 57113 5 + 57822 GTAGT -s Anc2.Anc2refChr15 38105 5 + 86568 GTAGT -s mr.mrrefChr5 74866 5 + 294540 GTAGT -s simCow_chr6.simCow.chr6 490735 5 - 602619 GTGGT -s simDog_chr6.simDog.chr6 210137 5 + 593897 GTAGT -s simHuman_chr6.simHuman.chr6 225628 5 + 601863 GGAGT -s simRat_chr6.simRat.chr6 211323 5 + 647215 GTAGT - -a -s simMouse_chr6.simMouse.chr6 220312 26 + 636262 TTGATGCTATGCCACCACATGCCAAT -s Anc0.Anc0refChr5 42549 21 + 87904 TTGATG-----CCACCAGATATCAAT -s Anc1.Anc1refChr8 57118 21 + 57822 TTGATG-----CCACCAGATATCAAT -s Anc2.Anc2refChr15 38111 21 + 86568 TTGATG-----TCACTAGATATCAAT -s mr.mrrefChr5 74871 26 + 294540 TTGATGCTATGCCACCAGATGCCAAT -s simCow_chr6.simCow.chr6 490741 21 - 602619 CTGATG-----TCACGAGATATCAAT -s simDog_chr6.simDog.chr6 210143 21 + 593897 TTGATG-----TCACTAAATAACCAT -s simHuman_chr6.simHuman.chr6 225633 21 + 601863 TTGTTG-----CCACCAGATTTCAAT -s simRat_chr6.simRat.chr6 211328 26 + 647215 TTGATGCTATGCCACTAGATGACGAT - -a -s simMouse_chr6.simMouse.chr6 220338 9 + 636262 ATCGAGTGA -s Anc0.Anc0refChr5 42570 9 + 87904 GTCCAGTGA -s Anc1.Anc1refChr8 57139 9 + 57822 GTCCAGTGA -s Anc2.Anc2refChr15 38132 9 + 86568 GTCTAGAGA -s mr.mrrefChr5 74897 9 + 294540 ATCCAGTGA -s simCow_chr6.simCow.chr6 490763 9 - 602619 GTCTAGAGG -s simDog_chr6.simDog.chr6 210164 9 + 593897 GTCTAGAGA -s simHuman_chr6.simHuman.chr6 225654 9 + 601863 GTCCAGTGA -s simRat_chr6.simRat.chr6 211354 9 + 647215 ATCCAATGA - -a -s simMouse_chr6.simMouse.chr6 220347 2 + 636262 CT -s Anc0.Anc0refChr5 42709 2 + 87904 GT -s Anc1.Anc1refChr8 57278 2 + 57822 GT -s Anc2.Anc2refChr15 38343 2 + 86568 GT -s mr.mrrefChr5 74906 2 + 294540 TT -s simCow_chr6.simCow.chr6 490974 2 - 602619 GT -s simDog_chr6.simDog.chr6 210375 2 + 593897 GT -s simHuman_chr6.simHuman.chr6 225793 2 + 601863 GT -s simRat_chr6.simRat.chr6 211363 2 + 647215 TT - -a -s simMouse_chr6.simMouse.chr6 220349 20 + 636262 GTGTCAACAAGTTTAAGCCT -s Anc0.Anc0refChr5 42711 20 + 87904 CTAAGAACAAGTTTAAGCCT -s Anc1.Anc1refChr8 57280 20 + 57822 CTAAGAACAAGTTTAAGCCT -s Anc2.Anc2refChr15 38345 20 + 86568 CTAAGAACAAGTTCAGGCCC -s mr.mrrefChr5 74908 20 + 294540 GTGTCAACAAGTTTAAGCCT -s simCow_chr6.simCow.chr6 490976 20 - 602619 CTATGTACAGGTTCAAGCTC -s simDog_chr6.simDog.chr6 210377 20 + 593897 CTAAGAACAAGTTCAGGCCC -s simHuman_chr6.simHuman.chr6 225795 18 + 601863 TTAAGAACAG--TTCAGCCT -s simRat_chr6.simRat.chr6 211366 20 + 647215 GTCTCAACAAGTTTAAGCCT - -a -s simMouse_chr6.simMouse.chr6 220369 6 + 636262 CCCTGA -s Anc0.Anc0refChr5 42744 6 + 87904 CCCTGA -s Anc1.Anc1refChr8 57313 6 + 57822 CCCTGA -s Anc2.Anc2refChr15 38378 6 + 86568 CCCCTA -s mr.mrrefChr5 74928 6 + 294540 CCCTGA -s simCow_chr6.simCow.chr6 491009 6 - 602619 CCACCA -s simDog_chr6.simDog.chr6 210410 6 + 593897 CCCCTA -s simHuman_chr6.simHuman.chr6 225826 6 + 601863 CCCTGA -s simRat_chr6.simRat.chr6 211386 5 + 647215 -GCTGA - -a -s simMouse_chr6.simMouse.chr6 220375 17 + 636262 TTGTCTCACACAGTTGT -s Anc0.Anc0refChr5 42753 17 + 87904 TTGTCACACACAGTGGT -s Anc1.Anc1refChr8 57322 17 + 57822 TTGTCACACACAGTGGT -s Anc2.Anc2refChr15 38387 17 + 86568 TTGTCACACACAGTGCT -s mr.mrrefChr5 74934 17 + 294540 TTGTCTCACACAGTTGT -s simCow_chr6.simCow.chr6 491018 17 - 602619 TCAATACACACAGTGCC -s simDog_chr6.simDog.chr6 210419 17 + 593897 TTGTCTCACACAGTGCT -s simHuman_chr6.simHuman.chr6 225835 17 + 601863 TTGTCACACACAGCAGT -s simRat_chr6.simRat.chr6 211391 17 + 647215 TTGTCACACAAGGCTGT - -a -s simMouse_chr6.simMouse.chr6 220392 74 + 636262 GCCTTGCGTAACTGAGAGATATCATGGAACTTACTGTTAGTCATTAACTTCATGGACGCTTTAGTTCAAAGGCC -s Anc0.Anc0refChr5 42770 74 + 87904 ACCTTGTATAACTGCAAGATAAGATTGAACTTACTGTAAGTCATTTAGTTCTTGTATGCTTAAGGTCTAAAGAC -s Anc1.Anc1refChr8 57339 74 + 57822 ACCTTGTATAACTGCAAGATAAGATTGAACTTACTGTAAGTCATTTAGTTCTTGTATGCTTAAGGTCTAAAGAC -s Anc2.Anc2refChr15 38404 74 + 86568 ACCTTGTATAACTGCAAGATAAGATTGAACTTACTGTAAGCCATTTAGTTCTTGTATGCTTAAGGCTTAAAGAC -s mr.mrrefChr5 74951 74 + 294540 GCCTTGTGTAACTGAGAGATATGATGGAACTTACTGTTAGTCATTAAGTTCATGTATGCTTTAGTTCAAAGGCC -s simCow_chr6.simCow.chr6 491035 74 - 602619 ACCTTGTATAACTACAAGATAAGATTGAACTTACTGTAAGACATTTGGTTCTTGTATGATTCCAGCTTAGGGAC -s simDog_chr6.simDog.chr6 210436 74 + 593897 ACCTTGTATAACTGCATGAAAGGATTGAACTTGCTGTAAGCCCACTAGTTCTTGTATGCTTAAGTCTTAAAGAC -s simHuman_chr6.simHuman.chr6 225855 74 + 601863 ACCTTGTATAACTGCAAGATGAGACTGAACCAACTGTAAGTCATTTAGTTCTTCCATGCTTAAGGTCCAAAGAT -s simRat_chr6.simRat.chr6 211408 74 + 647215 GGCTTGTGTAAATGAGGGATAAGATGGAACTTACTGTTAGTTGTTATGTTCATGTATGCTTTAGGTCAGAGGCC - -a -s simMouse_chr6.simMouse.chr6 220466 1 + 636262 T -s Anc0.Anc0refChr5 42844 1 + 87904 T -s Anc1.Anc1refChr8 57413 1 + 57822 T -s Anc2.Anc2refChr15 38478 1 + 86568 T -s mr.mrrefChr5 75025 1 + 294540 T -s simCow_chr6.simCow.chr6 491109 1 - 602619 T -s simDog_chr6.simDog.chr6 210510 1 + 593897 T -s simHuman_chr6.simHuman.chr6 225929 1 + 601863 T -s simRat_chr6.simRat.chr6 211508 1 + 647215 G - -a -s simMouse_chr6.simMouse.chr6 220467 17 + 636262 GTTCCAGTCCAGTAACC -s Anc0.Anc0refChr5 42860 17 + 87904 GTTCCAGTCCCATAACC -s Anc1.Anc1refChr8 57429 17 + 57822 GTTCCAGTCCCATAACC -s Anc2.Anc2refChr15 38494 17 + 86568 GTTCCAGTCCCATAACC -s mr.mrrefChr5 75026 17 + 294540 GTTCCAGTCCCATGACC -s simCow_chr6.simCow.chr6 491125 15 - 602619 GTTT--GTCCTGTAACT -s simDog_chr6.simDog.chr6 210526 17 + 593897 GTTCCAGTCCCATGACC -s simHuman_chr6.simHuman.chr6 225945 17 + 601863 GTTCCAGTCCAATAACC -s simRat_chr6.simRat.chr6 211509 17 + 647215 GTTCCAGTCCCATGACC - -a -s simMouse_chr6.simMouse.chr6 220484 176 + 636262 TGTACTGGGGACCGCTCCATAAGCATTTTGGAGTTTAGAGCAATAGTGAAATCGGGAGGTATTCCTATGGAACGCGTCGACAGCATGGTCCTAACCCCGGAATCCACATCTCGACCCATCAGCGCTACTATATAGGCTCGCGATGAGAGTTCGAACCATTTAACCCTACCCTCGGT -s Anc0.Anc0refChr5 42877 11 + 87904 TGATCT---------------------------------------------------------------------------------------------------------------------------------------------------------------CTTC------C -s Anc1.Anc1refChr8 57446 15 + 57822 TGATCTG-----------------------------------------------------------------------------------------------------------------------------------------------------------ATCCTTC------C -s Anc2.Anc2refChr15 38511 11 + 86568 CGATTT---------------------------------------------------------------------------------------------------------------------------------------------------------------CTTG------C -s mr.mrrefChr5 75043 24 + 294540 TGTCCTG--------------------------------------------------------------------------------------------------------------------------------------------------------TTTACCCTACACACGGT -s simCow_chr6.simCow.chr6 491140 10 - 602619 GGAT-T---------------------------------------------------------------------------------------------------------------------------------------------------------------CTCT------C -s simDog_chr6.simDog.chr6 210543 8 + 593897 C---TT---------------------------------------------------------------------------------------------------------------------------------------------------------------CTTG------T -s simHuman_chr6.simHuman.chr6 225962 15 + 601863 TGATCTG-----------------------------------------------------------------------------------------------------------------------------------------------------------ATCCTGC------C -s simRat_chr6.simRat.chr6 211527 24 + 647215 TGTCCTG--------------------------------------------------------------------------------------------------------------------------------------------------------TTTACCCGGCACACGGT - -a -s simMouse_chr6.simMouse.chr6 220660 50 + 636262 TTATACATTACATAGATGTCACGGTTGTAGGTATTAGGAGCATCATTGGA -s Anc0.Anc0refChr5 42888 50 + 87904 TGATAGGTTATATAGGTGCAACCCTTTTAGGTATTAGGACCACTTTTGCA -s Anc1.Anc1refChr8 57461 50 + 57822 TGATAGGTTATATAGGTGCAACCCTTTTAGGTATTAGGACCACTTTTGCA -s Anc2.Anc2refChr15 38522 50 + 86568 TGGTAGGTTATATAGGTGCAACCCTTTTAGGTATTAGAACCACTTTTGCA -s mr.mrrefChr5 75067 50 + 294540 TTATACATTACATAGATGTCACGGTTGTAGGTATTAGGAGCATCATTGGA -s simCow_chr6.simCow.chr6 491150 50 - 602619 TAGTAGATTATATAGGTGTAACCCTTTTAGGTAGAAACACCACTTCTGCA -s simDog_chr6.simDog.chr6 210551 49 + 593897 TGGTAGGTTATATAGACGCAACTTTCTTAGGTATTAGAACCACT-TGGTA -s simHuman_chr6.simHuman.chr6 225977 50 + 601863 TGATAGGCTGTATAGGTGAAACCCTTTTAGGTGTTAGGATCACTGTTGCA -s simRat_chr6.simRat.chr6 211579 50 + 647215 TCATAGATTACACAGATGTTGTTCTTGTAGGTATTAGGGTAATCATTGGA - -a -s simMouse_chr6.simMouse.chr6 220710 17 + 636262 ACTGGTTGACCCAATCG -s Anc0.Anc0refChr5 42940 16 + 87904 ACTTGTTGATCCTATT- -s Anc1.Anc1refChr8 57513 16 + 57822 ACTTGTTGATCCTATT- -s Anc2.Anc2refChr15 38574 16 + 86568 ACTTGTTGATCCTATT- -s mr.mrrefChr5 75117 16 + 294540 ACTGGTTGACCCAATC- -s simCow_chr6.simCow.chr6 491202 16 - 602619 ACTAGTCGATCCTATT- -s simDog_chr6.simDog.chr6 210602 16 + 593897 ACTTGTTGATCCTACT- -s simHuman_chr6.simHuman.chr6 226029 16 + 601863 ACTTGTTGTTCCTATT- -s simRat_chr6.simRat.chr6 211629 16 + 647215 ACTGGTTGATCCAATC- - -a -s simMouse_chr6.simMouse.chr6 220727 41 + 636262 AACCCCAGCTGATTCAGCAGATGGGACCACCATTCTGAAAG -s Anc0.Anc0refChr5 42995 40 + 87904 AACTTCACCGCATTCAGCTGATGGGTTCACCATCATA-AAA -s Anc1.Anc1refChr8 57568 40 + 57822 AACTTCACCGCATTCAGCTGATGGGTTCACCATCATA-AAA -s Anc2.Anc2refChr15 38629 40 + 86568 GACTTCACAGCATTCAGCTGATGGGTTCACCATCATA-AAA -s mr.mrrefChr5 75133 40 + 294540 AACCCCAGCTGATTCAGCAGATGGGACCACCATTCTG-AAG -s simCow_chr6.simCow.chr6 491257 40 - 602619 GACTTCACAGCATTCATCTGATGGTTTTGGGATTATA-AAA -s simDog_chr6.simDog.chr6 210657 33 + 593897 GAGTTC-------TGAGCTGATGGGTTCACCATCATA-AAA -s simHuman_chr6.simHuman.chr6 226084 24 + 601863 AACTTCATCAAATTCAGCTGA-----------------AAA -s simRat_chr6.simRat.chr6 211645 40 + 647215 CACTCCAGGTGATTCAGCAGATGGGGCCACCATTATG-AAG - -a -s simMouse_chr6.simMouse.chr6 220768 67 + 636262 ATGGTGATGCCTTATCAAAAACCCTGCCCTCCATGAGGAGGTTTAGTCCGGATAAAGTACGGACTAA -s Anc0.Anc0refChr5 43035 46 + 87904 GGGGCTATACCTCATCAAAAACCCTGCCCTTTAGCAGGAAGTTTAG--------------------- -s Anc1.Anc1refChr8 57608 46 + 57822 GGGGCTATACCTCATCAAAAACCCTGCCCTTTAGCAGGAAGTTTAG--------------------- -s Anc2.Anc2refChr15 38671 46 + 86568 GGGGCTACACCTCATCAAAAACCCTGTCCTTTAGCAGGGAGTTTAG--------------------- -s mr.mrrefChr5 75173 46 + 294540 ATGGTGATGCCTTATCAAAAACCCTGCCCTCCATGAGGAGGTTTAG--------------------- -s simCow_chr6.simCow.chr6 491299 46 - 602619 GGGGCTACACCTCTTCAAAGACCCTGACCTTTAGCAGGGAGTTGCG--------------------- -s simDog_chr6.simDog.chr6 210692 46 + 593897 GGGGCTACACCTTATCAAAAACCCTGTCCTTTAGCAGGGTGATTAG--------------------- -s simHuman_chr6.simHuman.chr6 226108 46 + 601863 GGGGCTATACCTCATTCAAAACCCTCCCCTTTACCAGGAAGTTTAG--------------------- -s simRat_chr6.simRat.chr6 211685 46 + 647215 ATGGTGATGCCTTATCAAAAACCCTGTCCTCCATCAGGAAGTTTGG--------------------- - -a -s simMouse_chr6.simMouse.chr6 220835 19 + 636262 AGACTATGGCATTCCACCT -s Anc0.Anc0refChr5 43081 19 + 87904 AGGCTCAGGTGTGGAACAT -s Anc1.Anc1refChr8 57654 19 + 57822 AGGCTCAGGTGTGGAACAT -s Anc2.Anc2refChr15 38719 19 + 86568 AGGCTCAGGTGTGGAACAT -s mr.mrrefChr5 75219 19 + 294540 AGACTATGGCATTCCACCT -s simCow_chr6.simCow.chr6 491347 19 - 602619 AAGATCAGGAATGTAACAT -s simDog_chr6.simDog.chr6 210740 19 + 593897 AGGCTTGGGTGTGGAACAT -s simHuman_chr6.simHuman.chr6 226169 19 + 601863 GGGCTCAGGTTTGGGGCAT -s simRat_chr6.simRat.chr6 211731 19 + 647215 AAGCTATGGCATTCCACCC - -a -s simMouse_chr6.simMouse.chr6 220854 196 + 636262 CCTAGAATTCCACCCCCCTATACACTTGAGTACCAGTGCGTAAATCCGAACAGGGAATTTACAATGTATGTGCTGTGATCACTCAGCACTTCATCACACGGGGCAGACTTGTAGCCAAGCCCTGACCATTCTACATCGCTTCGCGGGGCAAACGTAGCCAAGCACTGACCATTTATCCATGGCTGCCTCTGGCAGG -s Anc0.Anc0refChr5 43104 28 + 87904 TCTGGCATTCCTTCCCCCTGCAC------------------------------------------------------------------------------------------------------------------------------------------------------------------------CCTAG -s Anc1.Anc1refChr8 57677 28 + 57822 TCTGGCATTCCTTCCCCCTGCAC------------------------------------------------------------------------------------------------------------------------------------------------------------------------CCTAG -s Anc2.Anc2refChr15 38742 28 + 86568 TCTGGCATTCCTTCCCCCTGCAC------------------------------------------------------------------------------------------------------------------------------------------------------------------------CCTAG -s mr.mrrefChr5 75238 28 + 294540 CCTAGAATTCCACCCCCCTATAC------------------------------------------------------------------------------------------------------------------------------------------------------------------------GCAGG -s simCow_chr6.simCow.chr6 491370 28 - 602619 TCTGGCATTCCATCCCCCTGCAC------------------------------------------------------------------------------------------------------------------------------------------------------------------------CCCAG -s simDog_chr6.simDog.chr6 210759 21 + 593897 ---GGCATTCCTACCCTCTAC----------------------------------------------------------------------------------------------------------------------------------------------------------------------------TAG -s simHuman_chr6.simHuman.chr6 226192 28 + 601863 TCTGACATTCCGTCTCCTTGCAC------------------------------------------------------------------------------------------------------------------------------------------------------------------------TCTAG -s simRat_chr6.simRat.chr6 211750 28 + 647215 CCCACCATTCCACCCCCTTATAC------------------------------------------------------------------------------------------------------------------------------------------------------------------------TCAGA - -a -s simMouse_chr6.simMouse.chr6 221050 13 + 636262 TCTAAGTCACAGG -s Anc0.Anc0refChr5 43142 13 + 87904 TCTAAATCAGGGG -s Anc1.Anc1refChr8 57715 13 + 57822 TCTAAATCAGGGG -s Anc2.Anc2refChr15 38780 13 + 86568 TCTGAATCGGGGG -s mr.mrrefChr5 75266 13 + 294540 TCTAAGTCACAGG -s simCow_chr6.simCow.chr6 491410 13 - 602619 TCTGAAAAAGGGG -s simDog_chr6.simDog.chr6 210790 13 + 593897 TCTGAATCGGGTG -s simHuman_chr6.simHuman.chr6 226230 13 + 601863 TCAAAATTAGGGG -s simRat_chr6.simRat.chr6 211778 13 + 647215 TCTAAGTCACAGG - -a -s simMouse_chr6.simMouse.chr6 221063 24 + 636262 CATGCATTACAGCCATCTTCTCTA -s Anc0.Anc0refChr5 43159 22 + 87904 TATAAATTATAGCCATCCATCC-- -s Anc1.Anc1refChr8 57732 22 + 57822 TATAAATTATAGCCATCCATCC-- -s Anc2.Anc2refChr15 38798 22 + 86568 TATAAATTATGGCCATCCATCC-- -s mr.mrrefChr5 75279 24 + 294540 CATGCATTACAGCCATCTTCTCTA -s simCow_chr6.simCow.chr6 491428 22 - 602619 TATAAAGTATGGCCATCCACAC-- -s simDog_chr6.simDog.chr6 210808 22 + 593897 TATAAATTATGACCGTCAATCC-- -s simHuman_chr6.simHuman.chr6 226247 22 + 601863 TATATATTATAGCCATCCATCC-- -s simRat_chr6.simRat.chr6 211792 24 + 647215 TATGCATTACAGCCATCTCATCTA - -a -s simMouse_chr6.simMouse.chr6 221087 69 + 636262 ACAGACGGTTATTGTGAGTATGTGCATCAATATGCCCTCCTTTCAATTATACCAAGCCAATGCGACTGT -s Anc0.Anc0refChr5 43181 68 + 87904 -CTGTTAGTTATTGAGAGCATGTGCATTACAATACCTTCCCTTCAAATGTGACAAGCTCATGTGATTAT -s Anc1.Anc1refChr8 57754 68 + 57822 -CTGTTAGTTATTGAGAGCATGTGCATTACAATACCTTCCCTTCAAATGTGACAAGCTCATGTGATTAT -s Anc2.Anc2refChr15 38820 68 + 86568 -CTGTTAGTTATTGAGAGCCTGTGCATTACAATACCTTCCCTTCAAATGTGACAAGCTCATGTGATTAT -s mr.mrrefChr5 75303 69 + 294540 ACAGACGGTTATTGTGAGTATGTGCATCAATATGCCCTCCTTTCAATTATACCAAGCCAATGCGACTGT -s simCow_chr6.simCow.chr6 491450 67 - 602619 -CTGTTAGTTATTGAGAGCCTGTGCATCAAAATACCTTGCCTTCAAAGGAGACAAG-TCATGTGTTTAT -s simDog_chr6.simDog.chr6 210830 68 + 593897 -CTGTTAATTATTGAGTGCCAGTGCATTACAATAGTATCCCTTAAAATGTGACATGCTCATGTGATCAT -s simHuman_chr6.simHuman.chr6 226269 68 + 601863 -CTGTAAGTTATTGAAAGCATGTGCCTAACAATACCTTCCCTTCAAATGTGACAAGCTCATGTGATTAT -s simRat_chr6.simRat.chr6 211821 69 + 647215 ACAGATGGATGTTTTGAGTATGTGCAACAATATGCCCTCCCTTCAATTATGCCAGGCCAATGCAACCGT - -a -s simMouse_chr6.simMouse.chr6 221156 4 + 636262 AGAA -s Anc0.Anc0refChr5 43249 4 + 87904 GGAA -s Anc1.Anc1refChr7 0 4 - 47259 GGAA -s Anc2.Anc2refChr15 38888 4 + 86568 GGAA -s mr.mrrefChr5 75372 4 + 294540 AGAA -s simCow_chr6.simCow.chr6 491517 4 - 602619 GGTA -s simDog_chr6.simDog.chr6 210898 4 + 593897 GGAA -s simHuman_chr6.simHuman.chr6 300752 4 - 601863 GGAA -s simRat_chr6.simRat.chr6 211890 4 + 647215 AGAA - -a -s simMouse_chr6.simMouse.chr6 221160 9 + 636262 TACACCCCT -s Anc0.Anc0refChr5 43255 7 + 87904 T--ACCCCT -s Anc1.Anc1refChr7 6 7 - 47259 T--ACCCCT -s Anc2.Anc2refChr15 38894 7 + 86568 C--ACCCCT -s mr.mrrefChr5 75376 7 + 294540 T--ACCCCT -s simCow_chr6.simCow.chr6 491523 7 - 602619 C--ACCCAT -s simDog_chr6.simDog.chr6 210904 7 + 593897 C--ACCCCT -s simHuman_chr6.simHuman.chr6 300758 7 - 601863 T--ACCCCT -s simRat_chr6.simRat.chr6 211894 7 + 647215 T--ACCCCT - -a -s simMouse_chr6.simMouse.chr6 221169 6 + 636262 GGATCA -s Anc0.Anc0refChr5 43264 6 + 87904 AGATCA -s Anc1.Anc1refChr7 15 6 - 47259 AGATCA -s Anc2.Anc2refChr15 38903 6 + 86568 AGATCA -s mr.mrrefChr5 75383 6 + 294540 GGATCA -s simCow_chr6.simCow.chr6 491533 4 - 602619 AGAT-- -s simDog_chr6.simDog.chr6 210913 6 + 593897 AGATCA -s simHuman_chr6.simHuman.chr6 300767 6 - 601863 AGATCA -s simRat_chr6.simRat.chr6 211901 6 + 647215 AGATCA - -a -s simMouse_chr6.simMouse.chr6 221175 36 + 636262 GTCTTGCTTGCTCTCTTATTGCAGTGCAATGACCGT -s Anc0.Anc0refChr5 43270 36 + 87904 GTCATGCTTGCTTTTTAGTTGCAGTGCAAAGATTTT -s Anc1.Anc1refChr7 21 36 - 47259 GTCATGCTTGCTTTTTAGTTGCAGTGCAAAGATTTT -s Anc2.Anc2refChr15 38909 36 + 86568 GTCATGTTTGCATCTTAGTTGCAGTGCAAAGATTTT -s mr.mrrefChr5 75389 36 + 294540 GTCTTGCTTGCTCTCTTATTGCAGTGCAATGACCGT -s simCow_chr6.simCow.chr6 491537 31 - 602619 -----GTTTGCATCTTAGTTGCAGTGCAATGATTTT -s simDog_chr6.simDog.chr6 210919 23 + 593897 GTCAT-------------TTGCAGTGTAAAAATTTT -s simHuman_chr6.simHuman.chr6 300780 36 - 601863 GTCACACTTTCTTTGTGGTTGCAGTGCCAAGCTGTT -s simRat_chr6.simRat.chr6 211907 36 + 647215 GTTATGCTTGTTCCTTTATTGCAGTGTAATCACTTT - -a -s simMouse_chr6.simMouse.chr6 221211 79 + 636262 TAGTCTCTCAGTGTAAGACTTATCAAAGGGGTGAGTTCTCATATGTACTAACAGTACCCTGACATGTCATTAACTCCAA -s Anc0.Anc0refChr5 43306 73 + 87904 TAGTCT---AAAGAAATACTTATCACAGGA---AGCTCCCATATGTGCTAACAATTCCCTGTTATGTAAATAATACCAA -s Anc1.Anc1refChr7 57 73 - 47259 TAGTCT---AAAGAAATACTTATCACAGGA---AGCTCCCATATGTGCTAACAATTCCCTGTTATGTAAATAATACCAA -s Anc2.Anc2refChr15 38945 73 + 86568 TAGCCT---AAAGAAATACTTATCACAGGA---AGCTCCCATATGTGCTAACAATTCCCTGTTATGCATATAATACCAA -s mr.mrrefChr5 75425 79 + 294540 TAGTCTCTCAGTGTAAGACTTATCAAAGGGGTGAGTTCTCATATGTACTAACAGTACCCTGACATGTCATTAACTCCAA -s simCow_chr6.simCow.chr6 491570 72 - 602619 CAGCCT---GGCAAAATGCCTATCATAGGA---AGCCCCAATGTGTGCTAACAATTCACTGTTATGCATAT-CTAACAA -s simDog_chr6.simDog.chr6 210942 73 + 593897 TAGCCT---AAAGAAATACTTATCACAAGA---AGCTCCCATACGTGTCAACAACTTCCTGTCATGCATATAACCCCAA -s simHuman_chr6.simHuman.chr6 300816 68 - 601863 TGGT--------AAGAAACTTATCACAGAA---AGCTCCCGTATGTGCTAACAATGCCCTGTTATGTGAGTAATACGAA -s simRat_chr6.simRat.chr6 211943 79 + 647215 TAGTCTCCCGGTGTAAATCTTGTTAAAGGGGTGAGTTCTCATATGTACTAATAGTACCCTGTCAAGTTAGTAACTCCAA - -a -s simMouse_chr6.simMouse.chr6 221290 38 + 636262 TATTATTGAAGAAGTGGGCTCGGGGAGTGAATTTCCAC -s Anc0.Anc0refChr5 43383 19 + 87904 TATCCTAGAAG-AGTGGGCT------------------ -s Anc1.Anc1refChr7 134 19 - 47259 TATCCTAGAAG-AGTGGGCT------------------ -s Anc2.Anc2refChr15 39022 19 + 86568 TATCCTAGAAG-AGTGGGCT------------------ -s mr.mrrefChr5 75504 19 + 294540 TATTATTGAAG-AGTGGGCT------------------ -s simCow_chr6.simCow.chr6 491665 19 - 602619 TACCCTAGAAG-AGTGGGCT------------------ -s simDog_chr6.simDog.chr6 211019 19 + 593897 TATCCCAGAAG-AGTGGGTA------------------ -s simHuman_chr6.simHuman.chr6 300888 19 - 601863 TATCTTAGAAG-AGTGGGCT------------------ -s simRat_chr6.simRat.chr6 212022 19 + 647215 TATTGTTGAAG-AGTGGGCT------------------ - -a -s simMouse_chr6.simMouse.chr6 221328 10 + 636262 ATTGTGTGGG -s Anc0.Anc0refChr5 43419 10 + 87904 ATTATATGGG -s Anc1.Anc1refChr7 170 10 - 47259 ATTATATGGG -s Anc2.Anc2refChr15 39058 10 + 86568 ATTATATTGG -s mr.mrrefChr5 75523 10 + 294540 ATTGTGTGGG -s simCow_chr6.simCow.chr6 491701 6 - 602619 ATTATA---- -s simDog_chr6.simDog.chr6 211055 10 + 593897 ATTATATTGG -s simHuman_chr6.simHuman.chr6 300924 10 - 601863 ACTATTTGGG -s simRat_chr6.simRat.chr6 212041 10 + 647215 ATTGTGTGGG - -a -s simMouse_chr6.simMouse.chr6 221338 2 + 636262 AT -s Anc0.Anc0refChr5 43429 2 + 87904 AT -s Anc1.Anc1refChr7 180 2 - 47259 AT -s Anc2.Anc2refChr15 39068 2 + 86568 AT -s mr.mrrefChr5 75533 2 + 294540 AT -s simDog_chr6.simDog.chr6 211065 2 + 593897 AT -s simHuman_chr6.simHuman.chr6 300934 2 - 601863 AT -s simRat_chr6.simRat.chr6 212076 2 + 647215 AT - -a -s simMouse_chr6.simMouse.chr6 221340 7 + 636262 TATAACC -s Anc0.Anc0refChr5 43456 7 + 87904 CACAACT -s Anc1.Anc1refChr7 207 7 - 47259 CACAACT -s Anc2.Anc2refChr15 39095 7 + 86568 CACAACT -s mr.mrrefChr5 75535 7 + 294540 TATAACC -s simCow_chr6.simCow.chr6 491732 7 - 602619 TACAACC -s simDog_chr6.simDog.chr6 211090 7 + 593897 CACAACT -s simHuman_chr6.simHuman.chr6 300961 7 - 601863 aacaact -s simRat_chr6.simRat.chr6 212078 7 + 647215 CATAACC - -a -s simMouse_chr6.simMouse.chr6 221347 18 + 636262 TCAGCATTAGACACATTG -s Anc0.Anc0refChr5 43463 18 + 87904 CTGGCATTGGAAATTCTG -s Anc1.Anc1refChr7 214 18 - 47259 CTGGCATTGGAAATTCTG -s Anc2.Anc2refChr15 39102 18 + 86568 CTGGCATTGGAAATTCTG -s mr.mrrefChr5 75542 18 + 294540 TCAGCATTAGACACATTG -s simCow_chr6.simCow.chr6 491739 18 - 602619 CTGACATTGGAAATTCTG -s simDog_chr6.simDog.chr6 211097 18 + 593897 CTGGTATTGGAAATTCTG -s simHuman_chr6.simHuman.chr6 301124 18 - 601863 CTGGCATTGAAGATTCTG -s simRat_chr6.simRat.chr6 212085 18 + 647215 TTGGCATTAGACACATCG - -a -s simMouse_chr6.simMouse.chr6 221365 2 + 636262 GT -s Anc0.Anc0refChr5 43481 2 + 87904 GT -s Anc1.Anc1refChr7 232 2 - 47259 GT -s Anc2.Anc2refChr15 39120 2 + 86568 AA -s mr.mrrefChr5 75560 2 + 294540 GT -s simCow_chr6.simCow.chr6 491760 2 - 602619 AA -s simDog_chr6.simDog.chr6 211115 2 + 593897 AA -s simHuman_chr6.simHuman.chr6 301142 2 - 601863 GT -s simRat_chr6.simRat.chr6 212103 2 + 647215 AT - -a -s simMouse_chr6.simMouse.chr6 221367 15 + 636262 AGGTTGTTTGCAGCC -s Anc0.Anc0refChr5 43483 15 + 87904 ATTTTGTATCTTACT -s Anc1.Anc1refChr7 234 15 - 47259 ATTTTGTATCTTACT -s Anc2.Anc2refChr15 39122 15 + 86568 ATTTTGTATCTTACT -s mr.mrrefChr5 75562 15 + 294540 AGGTTGTTTGCAGCC -s simCow_chr6.simCow.chr6 491762 15 - 602619 ATTTTGTATCGTACT -s simDog_chr6.simDog.chr6 211117 15 + 593897 ACTTTGTATCTTACT -s simHuman_chr6.simHuman.chr6 301147 15 - 601863 ATCTTGTAATTTACT -s simRat_chr6.simRat.chr6 212105 15 + 647215 AGGATGTTTACAGCC - -a -s simMouse_chr6.simMouse.chr6 221382 51 + 636262 CCCCAATATTCATCAACACACTATGCTTGGAGATTTGTGATCATCACTCAA -s Anc0.Anc0refChr5 43507 50 + 87904 CTTTTATGTCCTTGATCACCTTACTCTTGCAGATTTATGATCATCACTAA- -s Anc1.Anc1refChr7 258 51 - 47259 CTTTTATGTCCTTGATCACCTTACTCTTGCAGATTTATGATCATCACTAAA -s Anc2.Anc2refChr15 39146 50 + 86568 CTTTTATGTCCTTGATCACCTTACTCTTGCAGATTTATGATCATCACTAA- -s mr.mrrefChr5 75577 51 + 294540 CCCCAATATTCATCAACACACTATGCTTGGAGATTTGTGATCATCACTCAA -s simCow_chr6.simCow.chr6 491786 50 - 602619 TAAATATGTCCGTGATAACCTTACTCTTGCAGATTTATGATCATGACTAA- -s simDog_chr6.simDog.chr6 211141 50 + 593897 CTTTAATGTCCTCAATCACCTTACACTTGCAGATTTACAATCATCACTAA- -s simHuman_chr6.simHuman.chr6 301171 51 - 601863 CTTTTCTGTGCCTGATCACCTTACTCTTGCAGATTTATGATTATCATTAAA -s simRat_chr6.simRat.chr6 212120 51 + 647215 CCCCACTATTCACCTACTCCCTATGCTTGGAGATTTGTGACCATCACTCAA - -a -s simMouse_chr6.simMouse.chr6 221433 35 + 636262 CAGACCTTATAATTTATCATAATCATTTAAGAATG -s Anc0.Anc0refChr5 43557 19 + 87904 ---------TAATTG-------TCACTGAAGAATA -s Anc1.Anc1refChr7 309 28 - 47259 TAGACCTGATAATTG-------TCACTGAAGAATA -s Anc2.Anc2refChr15 39196 19 + 86568 ---------TAATTG-------GCACTGAAGATTA -s mr.mrrefChr5 75628 28 + 294540 CAGACCTTATAATTT-------TCATTTAAGAATG -s simCow_chr6.simCow.chr6 491836 19 - 602619 ---------TAAGTG-------GCACTGAAGATTA -s simDog_chr6.simDog.chr6 211191 17 + 593897 ---------TAATTG---------ACTGAAGATTA -s simHuman_chr6.simHuman.chr6 301223 27 - 601863 TAGACCTGATAAATG-------TCACAGAAGAAT- -s simRat_chr6.simRat.chr6 212171 28 + 647215 TTAGCCTTTTCATTT-------TCATTTAAGAATG - -a -s simMouse_chr6.simMouse.chr6 221468 34 + 636262 GACTCCAAAGGCCCGGTTTTAGTTTAGCTCTCAA -s Anc0.Anc0refChr5 43576 33 + 87904 GTCTTCAAATGCTTGGTTT-GGTCTAGCTCTCAA -s Anc1.Anc1refChr7 337 33 - 47259 GTCTTCAAATGCTTGGTTT-GGTCTAGCTCTCAA -s Anc2.Anc2refChr15 39215 33 + 86568 GTCTTCTAATGCTTGATTT-GGTCTAGTTCTCAA -s mr.mrrefChr5 75656 34 + 294540 GACTCCAAAGGCCCGGTTTTAGTTTAGCTCTCAA -s simCow_chr6.simCow.chr6 491859 33 - 602619 GTCTTCTGATGCTTGATTA-GGTTGAGTTTTCAA -s simDog_chr6.simDog.chr6 211208 33 + 593897 GTCTTCTAATGCTTGATTT-GGTCTAGTTCTCAA -s simHuman_chr6.simHuman.chr6 301250 30 - 601863 -CCATCAAATGCTTGGGTT-GGTATAGCCCTC-- -s simRat_chr6.simRat.chr6 212199 34 + 647215 GACTCCAAAGGGCCGGTTTTAGTTTAGGTCTTAA - -a -s simMouse_chr6.simMouse.chr6 221502 18 + 636262 AGGAGCAGCACAGCCTCG -s Anc0.Anc0refChr5 43609 17 + 87904 AAGCGAAGTGCAGCC-TG -s Anc1.Anc1refChr7 370 17 - 47259 AAGCGAAGTGCAGCC-TG -s Anc2.Anc2refChr15 39249 17 + 86568 AAGCGAAGTGAAGCC-TG -s mr.mrrefChr5 75690 17 + 294540 AGGAGCAGCACAGCC-CG -s simCow_chr6.simCow.chr6 491893 17 - 602619 AGGGACAGTGGAGCC-TG -s simDog_chr6.simDog.chr6 211242 17 + 593897 AAGCGAAGTGAAACC-TA -s simHuman_chr6.simHuman.chr6 301280 7 - 601863 ----------CAGCC-TG -s simRat_chr6.simRat.chr6 212233 17 + 647215 AGGAGCAGCACAGCC-AG - -a -s simMouse_chr6.simMouse.chr6 221520 64 + 636262 AGGTAGAACACCATCGCCTCAGAAATTCCCCTGATCATATCCTCCATCTAGTAGAGGTACATCT -s Anc0.Anc0refChr5 43626 59 + 87904 G-ACAGAACAACATCAACTTAGAAAATCCACTGATCCTGAGTTCCAT---GTAGGGCTATGC-T -s Anc1.Anc1refChr7 387 60 - 47259 GTACAGAACAACATCAACTTAGAAAATCCACTGATCCTGAGTTCCAT---GTAGGGCTATGC-T -s Anc2.Anc2refChr15 39266 59 + 86568 G-ACAGAACAACACCAACTTAGCCTATCCATTGATCCTGAGTTCCAT---GCAAGGCCATGC-T -s mr.mrrefChr5 75707 63 + 294540 AGGTAGAACACCATCGCCTCAGAAATTCCCCTGATCATATCCTCCATCTAGTAGAGGTACAT-T -s simCow_chr6.simCow.chr6 491912 59 - 602619 G-ACAGAACAACACCAACATAGACATTCGAGTGATCGTGAGTTCCAT---GCAAGGCCATGC-T -s simDog_chr6.simDog.chr6 211259 43 + 593897 G-ACGGAATAGCACTAACTCCGCCTATCCATTGATCCTAGGTTA-------------------- -s simHuman_chr6.simHuman.chr6 301287 57 - 601863 GTACAGAACAACATCAACGTAGAAA---AACTGATCCTGAGTTCCAC---ATAGGGTTATGG-T -s simRat_chr6.simRat.chr6 212250 63 + 647215 AGGTAGGACACCTTCACCACAGAAACTCCCCTGATCATAACCTCCATCTAGTAGAGGTATAT-T - -a -s simMouse_chr6.simMouse.chr6 221584 559 + 636262 AATCTTACCAACTCTTTTAGTAACAGAGATTTCAATAGATATACAGAAACTGGCTGGGAGGTTGGAATCAATTCAAAGCAACCTGATTGATCAATTGAGTGAAGACAAGGGCCAGTTAGTCCAGGAGTGAGCCCCATTCTTTTTACCACTGTATTTTAAAATGATACAATGGGTACGAGCGGACTGGTCTCTTTGGTCTCCGGAGATATTTTTGCACAGGGGGGTTGGTCTCTGGAGATATTTTTACAGTATCTATGGAATTGATCAAGCACCCGACTGCTCCAGCATCAGCAATGTTTGCCAAAATGACCCGTGGAAGGTTGGAGCTAACCATTGTTCACAGAACCAGCACTTGACTGCCCCAACATTGACAATTTATGCTGAGTAATTTGTGCTTAGACTACCCATTGAAGGTTGGATTGGACATTGCCCCAAAGAGTTCTGGCACTTTAACTTTTTAAATTTTGGGTTGGACGAAGAAAAGAAGGATTTTCCCATCAGCAGCTATGTGCTATGAAGTGATAGGAACTCACTTCTCATACTATCTGTGCTTCTAACA -s Anc0.Anc0refChr5 43689 138 + 87904 AATGTTATCACCTCTATGAGAAGCTGACCTTTTAATAAATATACAGAAACTAGCTGGGATGTTGCACTCTATTGTAAGCAACTTGATTGC-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CTATGAAGTGATAGGAACTCACTTCTCATACCATCAGTGCTTATAGCA -s Anc1.Anc1refChr7 451 138 - 47259 AATGTTATCACCTCTATGAGAAGCTGACCTTTTAATAAATATACAGAAACTAGCTGGGATGTTGCACTCTATTGTAAGCAACTTGATTGC-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CTATGAAGTGATAGGAACTCACTTCTCATACCATCAGTGCTTATAGCA -s Anc2.Anc2refChr15 39329 138 + 86568 AATGTTGTCACCTCTATGAGAAGCTTACCTTTTAATAAATATCCACAAACTAGCTGGAATGTTGCACTTTATTGTAAGCAACTTGACTGC-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CTATGAAGTGATAGGGACTCACGTATCATACCTTCAGTACTTATAGCA -s mr.mrrefChr5 75770 548 + 294540 AATCTTACCAACTCTTTTAGTAACAGAGATTTCAATAGATATACAGAAACTGGCTGGGAGGTTGGAATCAATTCAAAGCAACCTGATTGATCAATTGAGTGAAGACAAGGGCCAGTTAGTCCAGGAGTGAGCCCCATTCTTTTTACCACTGTATTTTAAAATGATACAATGGGTACGAGCGGACTGGTCTCT---------GGAGATATTTTTGCACAGGGGGGTTGGTCTCTGGAGATATTTTTACAGTATCTATGGAATTGATCAAGCACCCGACTGCTCCAGCATCAGCAATGTTTGCCAAAATGACCCGTGGAAGGTTGGAGCTAA-CATTGTTCACAGAACCAGCACTTGACTGCCCCAACATTGACAATTTATGCTGAGTAATTTGTGCTTAGACTACCCATTGAAGGTTGGATTGGACATTG-CCCAAAGAGTTCTGGCACTTTAACTTTTTAAATTTTGGGTTGGACGAAGAAAAGAAGGATTTTCCTATCAGCAGCTATGTGCTATGAAGTGATAGGAACTCACTTCTCATACTATCTGTGCTTCTAGCA -s simCow_chr6.simCow.chr6 491975 132 - 602619 AATGTTGTCACCTCTATGAGAACGTTACCTTATTATAAATATACACAAACTAGCTAGAA------AATGTATTGTAAACAACTTGACTGC-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CTATGAAGTGATAGGGACTCACCTAGCTTAATTTTCGTACACATAACA -s simDog_chr6.simDog.chr6 211306 138 + 593897 GATGTTGTCACCTCTGTGAGAAGCTTAACTTTTAGTAAATATCCACAAGCTAGCTGGAATGTTGCACTTTATTGTAAGGAACTTGACTGC-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GTATGAAGTGCTAGGGACTCATGCATCATACCTTCAGTATTTATAGCA -s simHuman_chr6.simHuman.chr6 301348 135 - 601863 AGTGTCATCACCTCTATGAGAAGCTGACCTTTGAATAAATATACAGA---CTACTGGGATGTTCCACACTATGGTAAGCAACTAGATGGC-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CTATGAAGTGATAGAAACTCACTTCTCATACCAACAGTGCTTGTAGCA -s simRat_chr6.simRat.chr6 212313 548 + 647215 GATCTTACCAACTCTATTAGAAACCCACATTTCAATAGACCTACAGGAACTGGCTAGGTGATTGGAAACTATTCAAAGCAACCTGCTCGATTAATCGAGTGAAGACAAGGGCCATTCAGTGCAGGATGGAGCCCCATTCTTCTTACCACTGAATTTTAAAATGATACAATGGGCACAAGGGGATTGGTCTCT---------GGAGATATCTTTGCACAAGGGGATTGGTCTCTGGAGATATTTTTACATATTCTGTGGAATTGATCAAGCACTTGACTGCTCCAGCAGTAGCAATGCTTGCTAAAACAACCCATGGAAGGTTGGATTCAA-CATTGTTCACAGATCCAGCACTTGACTGCCCCAACATTGGCAGTTTATGCTGAGAAATTTGTGCCGAGACTACCCGTTGAAGGTTGGATTGAACATTG-CTCAAGGAGTTCTATCACTTTGACTTTTTAGATTTTGGGTTGGACAAGGGAAAGAAGGATTTTCCTATCAGCAGCTACGAGCTAGGAAGTGATAAGAACTCACTTCTCATGCTATTGGTGCTTTTGGCA - -a -s simMouse_chr6.simMouse.chr6 222143 16 + 636262 TGAAGTGATTTCAACC -s Anc0.Anc0refChr5 43828 16 + 87904 TGAAATGATTTTGGAC -s Anc1.Anc1refChr7 590 16 - 47259 TGAAATGATTTTGGAC -s Anc2.Anc2refChr15 39468 16 + 86568 TGAAATGATTTTGGAC -s mr.mrrefChr5 76318 16 + 294540 TGAAGTGATTTCAACC -s simCow_chr6.simCow.chr6 492108 16 - 602619 TGAAATGATTTTTGAT -s simDog_chr6.simDog.chr6 211445 16 + 593897 CCAAATGATTTTGGGC -s simHuman_chr6.simHuman.chr6 301484 16 - 601863 TGAAATGATTCTGGAC -s simRat_chr6.simRat.chr6 212861 16 + 647215 TGAAGTGATTTCAACC - -a -s simMouse_chr6.simMouse.chr6 222159 11 + 636262 AAGCCCAATCA -s Anc0.Anc0refChr5 43844 11 + 87904 TAGCTCAGTCA -s Anc1.Anc1refChr7 606 11 - 47259 TAGCTCAGTCA -s Anc2.Anc2refChr15 39484 11 + 86568 TAGTTCAGTCA -s mr.mrrefChr5 76334 11 + 294540 TAGCTCAATCA -s simCow_chr6.simCow.chr6 492125 11 - 602619 TTGTTCAGTCA -s simDog_chr6.simDog.chr6 211461 11 + 593897 TAGTTTAGTTA -s simHuman_chr6.simHuman.chr6 301500 11 - 601863 TAGCTCACTCA -s simRat_chr6.simRat.chr6 212877 11 + 647215 TAGCTCAATCA - -a -s simMouse_chr6.simMouse.chr6 222170 11 + 636262 TCACCTTTCCC -s Anc0.Anc0refChr5 43860 11 + 87904 TCATTTTTTTT -s Anc1.Anc1refChr7 622 11 - 47259 TCATTTTTTTT -s Anc2.Anc2refChr15 39500 11 + 86568 CCATTTTTTTT -s mr.mrrefChr5 76345 11 + 294540 TCACTTTTCTC -s simCow_chr6.simCow.chr6 492141 11 - 602619 CCCTTTTTTTA -s simDog_chr6.simDog.chr6 211477 8 + 593897 CCAT---CTCT -s simHuman_chr6.simHuman.chr6 301516 11 - 601863 TCATTTTTTTT -s simRat_chr6.simRat.chr6 212888 11 + 647215 TCACTTTTCTC - -a -s simMouse_chr6.simMouse.chr6 222181 38 + 636262 CATTTAATACTGCTGCCAATATGAAAAAGGTTGCAGAC -s Anc0.Anc0refChr5 43887 34 + 87904 CAACTAGTACAGCTGAGAAAGAA--AAAG--TGCAGCC -s Anc1.Anc1refChr7 649 34 - 47259 CAACTAGTACAGCTGAGAAAGAA--AAAG--TGCAGCC -s Anc2.Anc2refChr15 39527 34 + 86568 CAACCAGTACAGATGAGAATGAA--AAAG--TGCAGCC -s mr.mrrefChr5 76356 36 + 294540 CATTTAATACTGCTGAGAAAGTG--AAAGGTTGCAGAC -s simCow_chr6.simCow.chr6 492168 32 - 602619 TAACCAGTACTGTT--TCAGAAA--ACAG--TGCATTC -s simDog_chr6.simDog.chr6 211500 34 + 593897 CTACCAGTACAGATGAGAATGAA--AAAG--AGCAGCC -s simHuman_chr6.simHuman.chr6 301543 34 - 601863 CAACTAGTACCACTGAGAAAGAA--AAAG--TGCAGCC -s simRat_chr6.simRat.chr6 212899 36 + 647215 CACTTAATACTGCTAAGAGAGTG--AAAGGTTGCAGAG - -a -s simMouse_chr6.simMouse.chr6 222219 18 + 636262 GGCACAAGCATGTGTCCA -s Anc0.Anc0refChr5 43925 18 + 87904 GACACAATCATGTTCTCA -s Anc1.Anc1refChr7 687 18 - 47259 GACACAATCATGTTCTCA -s Anc2.Anc2refChr15 39565 18 + 86568 AACACAATCATGTTCTCA -s mr.mrrefChr5 76392 18 + 294540 GGCACAAGCATGTTTTCA -s simCow_chr6.simCow.chr6 492204 18 - 602619 AACACAATGATGTTGTCA -s simDog_chr6.simDog.chr6 211537 11 + 593897 ------ACCAT-CTCTCA -s simHuman_chr6.simHuman.chr6 301581 18 - 601863 GACATAATCATGTTCTCA -s simRat_chr6.simRat.chr6 212935 18 + 647215 GCCACAAGCATGTTTTCA - -a -s simMouse_chr6.simMouse.chr6 222237 14 + 636262 TCCCCTAATATCAG -s Anc0.Anc0refChr5 43943 14 + 87904 TCCCCTGATCACAG -s Anc1.Anc1refChr7 705 14 - 47259 TCCCCTGATCACAG -s Anc2.Anc2refChr15 39583 14 + 86568 TCCCCTGATCACAG -s mr.mrrefChr5 76410 14 + 294540 TCCCCTAATATCAG -s simCow_chr6.simCow.chr6 492222 13 - 602619 TCCACTGATC-CAG -s simDog_chr6.simDog.chr6 211548 14 + 593897 TTTCCTGATCACAG -s simHuman_chr6.simHuman.chr6 301599 14 - 601863 TCCCCTGATCACAG -s simRat_chr6.simRat.chr6 212957 14 + 647215 TCCTCTAATATCAG - -a -s simMouse_chr6.simMouse.chr6 222251 1 + 636262 C -s Anc0.Anc0refChr5 43963 1 + 87904 C -s Anc1.Anc1refChr7 725 1 - 47259 C -s Anc2.Anc2refChr15 39603 1 + 86568 C -s mr.mrrefChr5 76424 1 + 294540 C -s simCow_chr6.simCow.chr6 492241 1 - 602619 C -s simDog_chr6.simDog.chr6 211568 1 + 593897 C -s simHuman_chr6.simHuman.chr6 301619 1 - 601863 C -s simRat_chr6.simRat.chr6 212971 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 222252 35 + 636262 TGTGAATTTCCTGGACAGGTTTGGGCTTACAGCCA -s Anc0.Anc0refChr5 43964 35 + 87904 TGTAAATTTCCTGGGCATGTTTGAGCCTACAGCTT -s Anc1.Anc1refChr7 726 35 - 47259 TGTAAATTTCCTGGGCATGTTTGAGCCTACAGCTT -s Anc2.Anc2refChr15 39604 35 + 86568 TGTAAGTTTCCTGGGCATGTTTGAGTCTACAGCTT -s mr.mrrefChr5 76425 35 + 294540 TGTGAATTTCCTGGACAGGTTTGGGCCTACAGCCA -s simCow_chr6.simCow.chr6 492242 35 - 602619 TGTAAGCATTCTGGGTATGTGTGAGTCTACAAGTT -s simDog_chr6.simDog.chr6 211569 35 + 593897 TGTAAGTTTCCCGGGCATGTTTAAGTCAACAGCTT -s simHuman_chr6.simHuman.chr6 301620 35 - 601863 TGTAAATTTCTTGGGCATTCTTGAGCCTACAGCTT -s simRat_chr6.simRat.chr6 212982 35 + 647215 TGTGAATTCCCTGGACAGGTTTGGGCCTACAGCCA - -a -s simMouse_chr6.simMouse.chr6 222287 7 + 636262 CTGGCTT -s Anc0.Anc0refChr5 44005 7 + 87904 CTTACTA -s Anc1.Anc1refChr7 767 7 - 47259 CTTACTA -s Anc2.Anc2refChr15 39645 7 + 86568 CTTACTA -s mr.mrrefChr5 76460 7 + 294540 CTGGCTT -s simCow_chr6.simCow.chr6 492283 7 - 602619 CTTACTA -s simDog_chr6.simDog.chr6 211610 7 + 593897 CTTGCTA -s simHuman_chr6.simHuman.chr6 301661 7 - 601863 CTCACTA -s simRat_chr6.simRat.chr6 213017 7 + 647215 CTGGCTT - -a -s simMouse_chr6.simMouse.chr6 222294 5 + 636262 TAGAA -s Anc0.Anc0refChr5 44012 5 + 87904 GAGAA -s Anc1.Anc1refChr7 774 5 - 47259 GAGAA -s Anc2.Anc2refChr15 39652 5 + 86568 GAGAA -s mr.mrrefChr5 76467 5 + 294540 TAGAA -s simCow_chr6.simCow.chr6 492298 5 - 602619 GGGCA -s simDog_chr6.simDog.chr6 211617 5 + 593897 GAGAA -s simHuman_chr6.simHuman.chr6 301668 5 - 601863 GAGAA -s simRat_chr6.simRat.chr6 213024 5 + 647215 TAGAA - -a -s simMouse_chr6.simMouse.chr6 222299 4 + 636262 TTAC -s Anc0.Anc0refChr5 44017 4 + 87904 GTGT -s Anc1.Anc1refChr7 779 4 - 47259 GTGT -s Anc2.Anc2refChr15 39658 4 + 86568 GTGT -s mr.mrrefChr5 76472 4 + 294540 TTAT -s simCow_chr6.simCow.chr6 492304 4 - 602619 GTGT -s simDog_chr6.simDog.chr6 211623 4 + 593897 TTGT -s simHuman_chr6.simHuman.chr6 301673 4 - 601863 GTGT -s simRat_chr6.simRat.chr6 213029 4 + 647215 TTAT - -a -s simMouse_chr6.simMouse.chr6 222303 16 + 636262 TGTGAATTCAATAGGA -s Anc0.Anc0refChr5 44021 16 + 87904 CTTGAATTGGAGAGTG -s Anc1.Anc1refChr7 783 16 - 47259 CTTGAATTGGAGAGTG -s Anc2.Anc2refChr15 39662 16 + 86568 CTTTAATTGGGGAGTG -s mr.mrrefChr5 76476 16 + 294540 TGTGAATTCAATAGGA -s simCow_chr6.simCow.chr6 492310 16 - 602619 GTCTACACGTTGGATG -s simDog_chr6.simDog.chr6 211627 16 + 593897 CTTTAATTGGGGAGTG -s simHuman_chr6.simHuman.chr6 301677 16 - 601863 CCTGAATGGGAAAGTG -s simRat_chr6.simRat.chr6 213033 16 + 647215 TGTGGATTCAATAGGT - -a -s simMouse_chr6.simMouse.chr6 222319 2 + 636262 TG -s Anc0.Anc0refChr5 44037 2 + 87904 TG -s Anc1.Anc1refChr7 799 2 - 47259 TG -s Anc2.Anc2refChr15 39678 2 + 86568 TG -s mr.mrrefChr5 76492 2 + 294540 TG -s simCow_chr6.simCow.chr6 492359 2 - 602619 TG -s simDog_chr6.simDog.chr6 211643 2 + 593897 TG -s simHuman_chr6.simHuman.chr6 301693 2 - 601863 TG -s simRat_chr6.simRat.chr6 213049 2 + 647215 TG - -a -s simMouse_chr6.simMouse.chr6 222321 11 + 636262 AGGAGTAGTAA -s Anc0.Anc0refChr5 44045 8 + 87904 AGGATTAA--- -s Anc1.Anc1refChr7 807 11 - 47259 AGGATTAATAA -s Anc2.Anc2refChr15 39686 8 + 86568 AGGATTAA--- -s mr.mrrefChr5 76494 11 + 294540 AGGAGTAGTAA -s simCow_chr6.simCow.chr6 492367 8 - 602619 AGGATTGA--- -s simDog_chr6.simDog.chr6 211651 8 + 593897 TTGGTTAA--- -s simHuman_chr6.simHuman.chr6 301701 11 - 601863 AGGATTATTAA -s simRat_chr6.simRat.chr6 213051 11 + 647215 GGGAATAGTAA - -a -s simMouse_chr6.simMouse.chr6 222332 10 + 636262 TGACAGCAAT -s Anc0.Anc0refChr5 44053 5 + 87904 ----AAC-AT -s Anc1.Anc1refChr7 818 10 - 47259 TGACAACAAT -s Anc2.Anc2refChr15 39694 5 + 86568 ----AAC-AT -s mr.mrrefChr5 76505 10 + 294540 TGACAGCAAT -s simCow_chr6.simCow.chr6 492385 5 - 602619 ----AAC-AT -s simDog_chr6.simDog.chr6 211659 5 + 593897 ----AAC-AT -s simHuman_chr6.simHuman.chr6 301714 10 - 601863 TGACAACAAT -s simRat_chr6.simRat.chr6 213062 10 + 647215 TGACAGCAAT - -a -s simMouse_chr6.simMouse.chr6 222342 10 + 636262 ATAATTTATC -s Anc0.Anc0refChr5 36247 10 - 87904 ATAATTTATA -s Anc1.Anc1refChr7 828 10 - 47259 ATAATTTATA -s Anc2.Anc2refChr15 38651 10 - 86568 ATAATTTATA -s mr.mrrefChr5 76515 10 + 294540 ATAATTTATA -s simCow_chr6.simCow.chr6 229261 10 + 602619 ATAATTTATA -s simDog_chr6.simDog.chr6 374073 10 - 593897 ATATTTTATA -s simHuman_chr6.simHuman.chr6 301724 10 - 601863 ACAATTTACA -s simRat_chr6.simRat.chr6 213072 10 + 647215 ATAATATATA - -a -s simMouse_chr6.simMouse.chr6 222352 20 + 636262 TCAGTAACCCTGTAGCTTTA -s Anc0.Anc0refChr5 36258 20 - 87904 TTAGTAAGCCTGAAGCCTTA -s Anc1.Anc1refChr7 839 20 - 47259 TTAGTAAGCCTGAAGCCTTA -s Anc2.Anc2refChr15 38662 20 - 86568 TTAGTAAGTCTGAAGCCCTA -s mr.mrrefChr5 76525 20 + 294540 TCAGTAACCCTGTAGCTTTA -s simCow_chr6.simCow.chr6 229272 20 + 602619 TTAGTAAGTGTGAAGCCCTA -s simDog_chr6.simDog.chr6 374084 20 - 593897 TCAGTAAGTCTAGAGCCCTA -s simHuman_chr6.simHuman.chr6 301735 20 - 601863 TTAGTAAGCCAGAAGGCTCA -s simRat_chr6.simRat.chr6 213082 20 + 647215 TCAGTAACTCTGTAGCTCTA - -a -s simMouse_chr6.simMouse.chr6 222372 112 + 636262 TTAGCATACTCCAACTTTGATTGAAATCATTTTGATGGACAAAAGGTATATTTTGCAAGACAAAGGGGCAAACTTGATGGTAGGATTAGGAGTGTCTGAGTAGCAACCAGGA -s Anc0.Anc0refChr5 36278 110 - 87904 TAAGCACATCCCAACTTAAATTGAAATAAGTATGGTGTAC-AAAGATATATTTTGCCAGAACAA-GGGCCATCTGGATAACAGATTAAGGACAGTCTGAGAACAGTTCAGGA -s Anc1.Anc1refChr7 859 110 - 47259 TAAGCACATCCCAACTTAAATTGAAATAAGTATGGTGTAC-AAAGATATATTTTGCCAGAACAA-GGGCCATCTGGATAACAGATTAAGGACAGTCTGAGAACAGTTCAGGA -s Anc2.Anc2refChr15 38682 110 - 86568 TAAGCACATCCTAACTTAAATTATAATAAGTATGGTGTAC-AAAGATATATTTTGCCAGAATGA-GGGCCATCTGGATAACAGATTAACTACAGTCTGAGAACAGTTCAGGA -s mr.mrrefChr5 76545 111 + 294540 TTAGCATATTCCAACTTAGATTGAAATCATTTTGATGGACAAAAGGTATATTTTGCCAGACCAA-GGGCCAACTTGATGATAGAATTAGGACAGTCTGAGTAGCAACCAGGA -s simCow_chr6.simCow.chr6 229293 110 + 602619 TTAGCACATCCTAACTTAAATTATAATAAGTATGGTGAAC-AAAGGTATATTTTGCCAGAATGA-GGGCCATCTGGATAACATATAAACTTCAGTCCGAGGACAGTTCAGGA -s simDog_chr6.simDog.chr6 374104 88 - 593897 TAAGCACACTCTGACTTATAACATAAT--GTATGATGTTT-GGATAGAT---------------------GTCTGGATAACAGATTAACTACAGTCTGAGACCAGTTCTGGA -s simHuman_chr6.simHuman.chr6 301755 110 - 601863 TGAGCACATCCCAACTCAAATTGAAATGAGTATGGTGTAC-AAAGATATATTTTGCCAGATCAG-CGGCCAGCTGGATCACAGATTAAGGGCAGTCTGAGAATGGTTCAGAG -s simRat_chr6.simRat.chr6 213102 111 + 647215 TTAGCATCTTCAAACTTAGATTGAAATCATTTTGATGGACAAGAAGTATATTTTGCCAGACCAA-GGGCCAACTTTCTGATAGAATTAGTCCAGACTGAAGAACAACTAGGA - -a -s simMouse_chr6.simMouse.chr6 222484 3 + 636262 AGT -s Anc0.Anc0refChr5 36393 3 - 87904 AGT -s Anc1.Anc1refChr7 974 3 - 47259 AGT -s Anc2.Anc2refChr15 38797 3 - 86568 AGT -s mr.mrrefChr5 76661 3 + 294540 AGT -s simCow_chr6.simCow.chr6 229408 3 + 602619 ATT -s simDog_chr6.simDog.chr6 374197 3 - 593897 TGT -s simHuman_chr6.simHuman.chr6 301870 3 - 601863 AGT -s simRat_chr6.simRat.chr6 213218 3 + 647215 AGT - -a -s simMouse_chr6.simMouse.chr6 222487 4 + 636262 GTGC -s Anc0.Anc0refChr5 36396 4 - 87904 TTGT -s Anc1.Anc1refChr7 977 4 - 47259 TTGT -s Anc2.Anc2refChr15 38800 4 - 86568 TTGT -s mr.mrrefChr5 76664 4 + 294540 GTGT -s simCow_chr6.simCow.chr6 373362 4 - 602619 TTGT -s simDog_chr6.simDog.chr6 374200 4 - 593897 TTGT -s simHuman_chr6.simHuman.chr6 301873 4 - 601863 TTGT -s simRat_chr6.simRat.chr6 213221 4 + 647215 GTAT - -a -s simMouse_chr6.simMouse.chr6 222491 48 + 636262 AGAGATCAGTGTCGTCAACCCCTTCTATTAGCCAGAATCGATGTGTCT -s Anc0.Anc0refChr5 36400 42 - 87904 AAGTATAAA------CCAGCCCTTGAATTAGCCAAAATGGATGTGTCT -s Anc1.Anc1refChr7 981 43 - 47259 AAGTATAAAG-----CCAGCCCTTGAATTAGCCAAAATGGATGTGTCT -s Anc2.Anc2refChr15 38804 42 - 86568 AAGTATAAA------CCAGCCCTTGAATTAGACAAAATGCATGTGTCT -s mr.mrrefChr5 76668 48 + 294540 AGGGATCAGTGTCGTCAACCCCTTCAATTAGCCAGAATGGATGTGTCT -s simCow_chr6.simCow.chr6 373423 42 - 602619 CAGTACACA------CCACCCCTTAAATTAGACAGAATGAAAGTTTCT -s simDog_chr6.simDog.chr6 374204 41 - 593897 AATTATAAA------CCAGCCCTTGAATTAGACAAAAA-CATGTGTCT -s simHuman_chr6.simHuman.chr6 301877 36 - 601863 AAGTATTAAG------------TTTAATTAGCCACAATGGATGGGTCT -s simRat_chr6.simRat.chr6 213225 48 + 647215 GGGGATCAGTGTAGTAAACCCCTTCAATTAGTCAGAATGGATGCGTCT - -a -s simMouse_chr6.simMouse.chr6 222539 34 + 636262 TAGATTTTGAATTAATTAACTCCTTCGATAAACT -s Anc0.Anc0refChr5 36442 34 - 87904 GGGTCTTTGAGTGAGCTAACTCCCTCAACAAAAT -s Anc1.Anc1refChr7 1024 34 - 47259 GGGTCTTTGAGTGAGCTAACTCCCTCAACAAAAT -s Anc2.Anc2refChr15 38846 34 - 86568 GGGTCTTTGAGTGAGCTAACTCCCTTAACATAAT -s mr.mrrefChr5 76716 34 + 294540 TAGATTTTGAATTAATTAACTCCCTCAATAAACT -s simCow_chr6.simCow.chr6 373465 34 - 602619 TAGTCTTTAAATTAGTTAACTCCCTTGAAGCAAT -s simDog_chr6.simDog.chr6 374246 34 - 593897 GGGTCTTTGAGTGAGCTAACTCATTTAGCATAAT -s simHuman_chr6.simHuman.chr6 301913 19 - 601863 ---------------CTAACTCCCTCAACAAAGT -s simRat_chr6.simRat.chr6 213273 34 + 647215 TAGTCTTCGAATTAATTAACTCCCTCAATGAACT - -a -s simMouse_chr6.simMouse.chr6 222573 34 + 636262 GGTGGTTGTCCAACTTGGGTTCTAAGGAGTTTTA -s Anc0.Anc0refChr5 36495 17 - 87904 GGTGGATCACACACATG----------------- -s Anc1.Anc1refChr7 1077 17 - 47259 GGTGGATCACACACATG----------------- -s Anc2.Anc2refChr15 38906 17 - 86568 GTGTGATCACACACATG----------------- -s mr.mrrefChr5 76769 34 + 294540 GGTGGTTGTCCAACTTGGGTTCTAAGGAGTTTTA -s simCow_chr6.simCow.chr6 373549 17 - 602619 ATGTGATCACACACTCA----------------- -s simDog_chr6.simDog.chr6 374306 17 - 593897 GTGTAATCATACACATG----------------- -s simHuman_chr6.simHuman.chr6 301951 17 - 601863 TGTGGCCCGCACACATG----------------- -s simRat_chr6.simRat.chr6 213326 34 + 647215 GATGGTTGTCCAATTTGGGAGTTAAGGAGTATCA - -a -s simMouse_chr6.simMouse.chr6 222607 48 + 636262 TTTATGCCCATCTTGCTACTGGCATATAACCGTAAAAGCAGAAGGTCC -s Anc0.Anc0refChr5 36512 36 - 87904 --------CGTGTTGCTACTGTCCCATAACAGCAAAAGC--AATGT-- -s Anc1.Anc1refChr7 1094 36 - 47259 --------CGTGTTGCTACTGTCCCATAACAGCAAAAGC--AATGT-- -s Anc2.Anc2refChr15 38923 36 - 86568 --------TGTGTAGGTACTGTCCCATTACAGCAAAAGC--ACTAT-- -s mr.mrrefChr5 76803 46 + 294540 TTTATGCCCATGTTGCTACTGGCATATAACAGTAAAAGC--AAAGTCC -s simCow_chr6.simCow.chr6 373566 36 - 602619 --------TCTGTAGTTACTGTCCAATTACTGCAAAAGT--GCTAT-- -s simDog_chr6.simDog.chr6 374323 36 - 593897 --------TGTGTAGGCACTATCCCATTATAGCAAAATC--ACAAT-- -s simHuman_chr6.simHuman.chr6 301968 36 - 601863 --------CTTGTTGCTACTGACCCATAACATCAAAGGA--AATGT-- -s simRat_chr6.simRat.chr6 213361 46 + 647215 TTTATGGCCATGTTGCTACTGGCATATAGCAGTAAAAGC--AAAGTCC - -a -s simMouse_chr6.simMouse.chr6 222655 47 + 636262 AACAATGCCAGGGCATTCATGTAATCTAATTAATTGCTATATACTGT -s Anc0.Anc0refChr5 36548 47 - 87904 AACAAAGCCTGTGAGTATATACAATCTGATTCATTGCTATACAATAT -s Anc1.Anc1refChr7 1130 47 - 47259 AACAAAGCCTGTGAGTATATACAATCTGATTCATTGCTATACAATAT -s Anc2.Anc2refChr15 38959 47 - 86568 AACAAAGCCTGTGAGTATATACAACCTGATTCATTGACCTACAATAT -s mr.mrrefChr5 76849 47 + 294540 AACAATGCCAGGGCATTCATGCAATCTAATTAATTGCTATATACTAT -s simCow_chr6.simCow.chr6 373602 36 - 602619 G-----------GAGTATATCTAGCCTGTTTTGTTGACCTACAACAC -s simDog_chr6.simDog.chr6 374362 47 - 593897 AACAAAGCCTGTGGGCATATACCACCGGATTCATTGACCTACAATAT -s simHuman_chr6.simHuman.chr6 302004 47 - 601863 AATAAAGCCTGTGAGTATCTACAATCTGATTCATTGCTATACAGTAG -s simRat_chr6.simRat.chr6 213407 47 + 647215 AACAATGCCAGGGCATTAATTCAATCTAATTAATTGCTATATACTAT - -a -s simMouse_chr6.simMouse.chr6 222702 4 + 636262 TGCA -s Anc0.Anc0refChr5 36605 4 - 87904 TGCA -s Anc1.Anc1refChr7 1187 4 - 47259 TGCA -s Anc2.Anc2refChr15 39016 4 - 86568 TGCA -s mr.mrrefChr5 76896 4 + 294540 TGCA -s simCow_chr6.simCow.chr6 373659 4 - 602619 AACA -s simDog_chr6.simDog.chr6 374419 4 - 593897 TGCA -s simHuman_chr6.simHuman.chr6 302061 4 - 601863 TGCA -s simRat_chr6.simRat.chr6 213454 4 + 647215 TGCA - -a -s simMouse_chr6.simMouse.chr6 222706 14 + 636262 TCCACAAACAGTCC -s Anc0.Anc0refChr5 36626 14 - 87904 CCTACAAACAGTCC -s Anc1.Anc1refChr7 1208 14 - 47259 CCTACAAACAGTCC -s Anc2.Anc2refChr15 39037 14 - 86568 CCTACAAACAGTCA -s mr.mrrefChr5 76900 14 + 294540 TCTACAAACAGTCC -s simCow_chr6.simCow.chr6 373680 8 - 602619 CCTACAGA------ -s simDog_chr6.simDog.chr6 374440 13 - 593897 CCTAC-AACAGTCA -s simHuman_chr6.simHuman.chr6 302082 14 - 601863 CCTGCAAATAGTTC -s simRat_chr6.simRat.chr6 213458 14 + 647215 TCTACAAACAGTCC - -a -s simMouse_chr6.simMouse.chr6 222720 34 + 636262 CTTACAATACATATCAAACTCATAAAGTATTGCT -s Anc0.Anc0refChr5 36676 34 - 87904 TTTACTCTACATATTACAATTGTAAAATTCTACC -s Anc1.Anc1refChr7 1258 34 - 47259 TTTACTCTACATATTACAATTGTAAAATTCTACC -s Anc2.Anc2refChr15 39087 34 - 86568 TTTACTCTACATATTACAATTGTAAAATTCTATC -s mr.mrrefChr5 76914 34 + 294540 CTTACAATACATATCAAACTCATAAAATATTGCT -s simCow_chr6.simCow.chr6 373709 30 - 602619 TTTAC----CATATTACAATTGTAAAATACAAAC -s simDog_chr6.simDog.chr6 374488 34 - 593897 TTTTCTCTACATATTACAAATATAAAATTCTATC -s simHuman_chr6.simHuman.chr6 302132 34 - 601863 TCTACCCTACATATTAGAATTGTAAAATTCTCCC -s simRat_chr6.simRat.chr6 213472 34 + 647215 CTTACAATACACATCAAATTCATAAAATATCGCT - -a -s simMouse_chr6.simMouse.chr6 222754 39 + 636262 CTCTCTGAAGCCAATTTGGACCTAGATGCCATCTATGGT -s Anc0.Anc0refChr5 36712 39 - 87904 TTCTTTGAAACCAATATGGACATAGTCAGCACATATCCT -s Anc1.Anc1refChr7 1294 39 - 47259 TTCTTTGAAACCAATATGGACATAGTCAGCACATATCCT -s Anc2.Anc2refChr15 39123 39 - 86568 TTCTTTGAAACCAATATGGACATGATCAGCACATATCCT -s mr.mrrefChr5 76948 39 + 294540 CTCTTTGAAGCCAATTTGGACCTAGATGCCATCTATCGT -s simCow_chr6.simCow.chr6 373741 39 - 602619 TTCTTTGAAACGAATATAGACATGACCAGCACGCATACT -s simDog_chr6.simDog.chr6 374524 32 - 593897 TTCTTTGAAACCAATATGATCATGATC-----ATATC-- -s simHuman_chr6.simHuman.chr6 302168 39 - 601863 TTATTTCAAACCATTGTGGACATAGTCAACAAATATCCT -s simRat_chr6.simRat.chr6 213506 39 + 647215 CTCTTTGAAGCCAATTTAGACCTAGATGCCATCTATCAT - -a -s simMouse_chr6.simMouse.chr6 222793 12 + 636262 TAAGCAATGATC -s Anc0.Anc0refChr5 36800 10 - 87904 TAAGC--TTATC -s Anc1.Anc1refChr7 1382 10 - 47259 TAAGC--TTATC -s Anc2.Anc2refChr15 39211 10 - 86568 TAAGC--TTATC -s mr.mrrefChr5 76987 12 + 294540 TAAGCAATAATC -s simCow_chr6.simCow.chr6 373833 10 - 602619 TAAAC--TGACC -s simDog_chr6.simDog.chr6 374605 10 - 593897 TTAGC--TTATC -s simHuman_chr6.simHuman.chr6 302258 10 - 601863 TAAGC--TCATC -s simRat_chr6.simRat.chr6 213545 12 + 647215 TAAGCAATAATA - -a -s simMouse_chr6.simMouse.chr6 222805 6 + 636262 TGTATC -s Anc0.Anc0refChr5 36810 6 - 87904 TCTAGC -s Anc1.Anc1refChr7 1392 6 - 47259 TCTAGC -s Anc2.Anc2refChr15 39221 6 - 86568 TCCAGC -s mr.mrrefChr5 76999 6 + 294540 TGTATC -s simCow_chr6.simCow.chr6 373843 6 - 602619 TTCAGC -s simDog_chr6.simDog.chr6 374615 6 - 593897 TCCAGC -s simHuman_chr6.simHuman.chr6 302268 6 - 601863 TCTAGC -s simRat_chr6.simRat.chr6 213603 6 + 647215 TGTAGC - -a -s simMouse_chr6.simMouse.chr6 222811 22 + 636262 TCTAATACAATAGACCTTCTGC -s Anc0.Anc0refChr5 36817 22 - 87904 TCTAGTTCAATAAAACTTCTTC -s Anc1.Anc1refChr7 1399 22 - 47259 TCTAGTTCAATAAAACTTCTTC -s Anc2.Anc2refChr15 39228 22 - 86568 TCTAGTTCAATAAAACTTCTTC -s mr.mrrefChr5 77005 22 + 294540 TCTAATACAATAGACCTTCTGC -s simCow_chr6.simCow.chr6 373850 22 - 602619 TCTAGCTCAATAGAACTTCTTC -s simDog_chr6.simDog.chr6 374622 21 - 593897 TCTAGTT-AATAAAACTTCTAC -s simHuman_chr6.simHuman.chr6 302275 22 - 601863 CCTAGTTCAATACAACTGTTTC -s simRat_chr6.simRat.chr6 213609 21 + 647215 TCTAATATGATAG-CCTTCCAC - -a -s simMouse_chr6.simMouse.chr6 222833 35 + 636262 CTGGCTCAATAGAACCATGCCATCAGGTTTACCTA -s Anc0.Anc0refChr5 36840 34 - 87904 CAATCC-AATAGAACCATCCCATCCGGTTTACCTA -s Anc1.Anc1refChr7 1422 35 - 47259 CAATCCCAATAGAACCATCCCATCCGGTTTACCTA -s Anc2.Anc2refChr15 39251 34 - 86568 CAATCC-AATAGAACCATCCTATCCGGTTTACCTA -s mr.mrrefChr5 77027 35 + 294540 CTGGCTCAATAGAACCATGCCATCAGGTTTACCTA -s simCow_chr6.simCow.chr6 373873 34 - 602619 CAAACC-AATAGAGCCATCCAGTCAGGTCCACCTC -s simDog_chr6.simDog.chr6 374644 34 - 593897 CAGTCC-AATAGAACCATCCTATCCAGTTTACCTA -s simHuman_chr6.simHuman.chr6 302298 34 - 601863 CAATCCCAACAGAACTTTCCCATTGGGTGT-CTAA -s simRat_chr6.simRat.chr6 213630 35 + 647215 CTGGATCAATAAAACCATGCCATGAGGCTTACCTA - -a -s simMouse_chr6.simMouse.chr6 222868 13 + 636262 ACCATAACAGAAC -s Anc0.Anc0refChr5 36874 13 - 87904 TCCACACCAGAAC -s Anc1.Anc1refChr7 1457 13 - 47259 TCCACACCAGAAC -s Anc2.Anc2refChr15 39286 13 - 86568 TCCACACCTGAAC -s mr.mrrefChr5 77062 13 + 294540 TCCACACCAGAAC -s simCow_chr6.simCow.chr6 373908 13 - 602619 TTCACGCCTGAAG -s simDog_chr6.simDog.chr6 374679 13 - 593897 CCCACACCTCAAC -s simHuman_chr6.simHuman.chr6 302332 13 - 601863 TCTACACCAGAAC -s simRat_chr6.simRat.chr6 213665 13 + 647215 TCCACACCAGAGT - -a -s simMouse_chr6.simMouse.chr6 222881 11 + 636262 GCACATAGACA -s Anc0.Anc0refChr5 36889 11 - 87904 GAACACAAACA -s Anc1.Anc1refChr7 1472 11 - 47259 GAACACAAACA -s Anc2.Anc2refChr15 39301 11 - 86568 GAACACAAACA -s mr.mrrefChr5 77075 11 + 294540 GCACATAGACA -s simCow_chr6.simCow.chr6 373923 10 - 602619 GCCCA-AAAGA -s simDog_chr6.simDog.chr6 374694 11 - 593897 GAACACAAACA -s simHuman_chr6.simHuman.chr6 302347 11 - 601863 GAACACAAACA -s simRat_chr6.simRat.chr6 213678 11 + 647215 GCACATAGACA - -a -s simMouse_chr6.simMouse.chr6 222892 33 + 636262 CACCCTCCTAACATGATGTCATCAGAGTATGAA -s Anc0.Anc0refChr5 36910 30 - 87904 AACACTCTCAGCTTATAGTCATAAG---ATGAA -s Anc1.Anc1refChr7 1493 30 - 47259 AACACTCTCAGCTTATAGTCATAAG---ATGAA -s Anc2.Anc2refChr15 39322 30 - 86568 ACCACTGTCAGATTATAGTAATAAG---ATGAA -s mr.mrrefChr5 77086 33 + 294540 CACCCTCCTAGCATGATGTCATAAGAGTATGAA -s simCow_chr6.simCow.chr6 373943 30 - 602619 ACCACTGTCAAATTATAGTAATAAG---ATGAA -s simDog_chr6.simDog.chr6 374715 14 - 593897 ACCACTGTCAGACT------------------- -s simHuman_chr6.simHuman.chr6 302368 30 - 601863 AACATTCTCAGCTTATAGTCATAAG---ATGAA -s simRat_chr6.simRat.chr6 213689 33 + 647215 TACCCTCCTAGCATGATGTCATAAGAGTATGAA - -a -s simMouse_chr6.simMouse.chr6 222925 12 + 636262 AGGTCTTGCACT -s Anc0.Anc0refChr5 36946 12 - 87904 AGGTTTTGCATT -s Anc1.Anc1refChr7 1529 12 - 47259 AGGTTTTGCATT -s Anc2.Anc2refChr15 39358 12 - 86568 AGGTTTTGCATT -s mr.mrrefChr5 77119 12 + 294540 AGGTTTTGCACT -s simCow_chr6.simCow.chr6 373979 12 - 602619 ATGTTTTCCATT -s simDog_chr6.simDog.chr6 374734 12 - 593897 AGGTTTTGCATT -s simHuman_chr6.simHuman.chr6 302404 12 - 601863 AGGTTTGGCATC -s simRat_chr6.simRat.chr6 213722 12 + 647215 AGGTTTTGCACT - -a -s simMouse_chr6.simMouse.chr6 222937 3 + 636262 GTA -s Anc0.Anc0refChr5 36960 3 - 87904 GTG -s Anc1.Anc1refChr7 1543 3 - 47259 GTG -s Anc2.Anc2refChr15 39372 3 - 86568 GTG -s mr.mrrefChr5 77131 3 + 294540 GTA -s simCow_chr6.simCow.chr6 373993 3 - 602619 GTG -s simDog_chr6.simDog.chr6 374748 3 - 593897 TTT -s simHuman_chr6.simHuman.chr6 302418 3 - 601863 GTG - -a -s simMouse_chr6.simMouse.chr6 222940 57 + 636262 TCGACCTCAGGAAACCACTCCGGGACTCTTTAGGTGGGATATTACTGCCTTCCAGAA -s Anc0.Anc0refChr5 36963 55 - 87904 TTTACCTCAGGAAACGACC-AAACCTACTGTATAT-GTATATTACTGCCTTCCACAA -s Anc1.Anc1refChr7 1546 55 - 47259 TTTACCTCAGGAAACGACC-AAACCTACTGTATAT-GTATATTACTGCCTTCCACAA -s Anc2.Anc2refChr15 39375 55 - 86568 GTTACCTAAGAACACGACC-AAACCTACTGTATAT-GTATATTACTGCCTTCTACAA -s mr.mrrefChr5 77134 55 + 294540 TCGACCTCAGGAAACCACT-CGAGACTCTGTAGGT-GGATATTACTGCCTTCCAGAA -s simCow_chr6.simCow.chr6 373997 51 - 602619 ATCACAGAACAACACCACC-CAAGCTGCTCTTTGC-GTATATAA----CTTCTGTAA -s simDog_chr6.simDog.chr6 374751 55 - 593897 GTTACCTACGAACACGACC-AAACCCACTGGATAT-GTATATTACTGCCTTCTACAA -s simHuman_chr6.simHuman.chr6 302421 52 - 601863 TATATCCCAAGAAACTGCC-AAAACTACTGTA----TTATATTACTGCCTTCCGCAA -s simRat_chr6.simRat.chr6 213734 49 + 647215 ------TCAGGAAACCACT-GGAGACTTTGCAGGT-GGATATTACTTCCTTCTAGAA - -a -s simMouse_chr6.simMouse.chr6 222997 4 + 636262 TGAG -s Anc0.Anc0refChr5 37018 4 - 87904 TGAC -s Anc1.Anc1refChr7 1601 4 - 47259 TGAC -s Anc2.Anc2refChr15 39433 4 - 86568 TAAG -s mr.mrrefChr5 77189 4 + 294540 TGAC -s simCow_chr6.simCow.chr6 374051 4 - 602619 TAAG -s simDog_chr6.simDog.chr6 374809 4 - 593897 TAAG -s simHuman_chr6.simHuman.chr6 302473 4 - 601863 TGAC -s simRat_chr6.simRat.chr6 213783 4 + 647215 TGAC - -a -s simMouse_chr6.simMouse.chr6 223001 12 + 636262 AATTAGTTATAC -s Anc0.Anc0refChr5 37055 12 - 87904 AATTAGCTATAC -s Anc1.Anc1refChr7 1638 12 - 47259 AATTAGCTATAC -s Anc2.Anc2refChr15 39470 12 - 86568 AACTAGCTATAC -s mr.mrrefChr5 77193 12 + 294540 AATTAGTTATAC -s simCow_chr6.simCow.chr6 374089 12 - 602619 AACTAGCTATAC -s simDog_chr6.simDog.chr6 374846 12 - 593897 AACAAGCAATAC -s simHuman_chr6.simHuman.chr6 302510 12 - 601863 AATTAGGTGTTC -s simRat_chr6.simRat.chr6 213787 12 + 647215 AATTTGCTATAC - -a -s simMouse_chr6.simMouse.chr6 223013 3 + 636262 TTG -s Anc0.Anc0refChr5 37069 3 - 87904 CTG -s Anc1.Anc1refChr7 1652 3 - 47259 CTG -s Anc2.Anc2refChr15 39484 3 - 86568 CTG -s mr.mrrefChr5 77207 3 + 294540 TTG -s simCow_chr6.simCow.chr6 374103 3 - 602619 CTG -s simDog_chr6.simDog.chr6 374860 3 - 593897 CTT -s simHuman_chr6.simHuman.chr6 302524 3 - 601863 CTG -s simRat_chr6.simRat.chr6 213801 3 + 647215 TTG - -a -s simMouse_chr6.simMouse.chr6 223016 7 + 636262 TGCCATC -s Anc0.Anc0refChr5 37081 7 - 87904 TGCCACT -s Anc1.Anc1refChr7 1664 7 - 47259 TGCCACT -s Anc2.Anc2refChr15 39496 7 - 86568 TTTCCCT -s mr.mrrefChr5 77219 7 + 294540 TGCCATC -s simCow_chr6.simCow.chr6 374154 7 - 602619 TTTCCCT -s simDog_chr6.simDog.chr6 374872 7 - 593897 TTTCCCT -s simHuman_chr6.simHuman.chr6 302538 7 - 601863 TGCCACT -s simRat_chr6.simRat.chr6 213813 7 + 647215 TGTCATC - -a -s simMouse_chr6.simMouse.chr6 223023 5 + 636262 TGAGT -s Anc0.Anc0refChr5 37092 5 - 87904 CAAGT -s Anc1.Anc1refChr7 1675 5 - 47259 CAAGT -s Anc2.Anc2refChr15 39507 5 - 86568 CAAAT -s mr.mrrefChr5 77226 5 + 294540 CAAGT -s simCow_chr6.simCow.chr6 374165 5 - 602619 GGTAT -s simDog_chr6.simDog.chr6 374883 5 - 593897 CAAAT -s simHuman_chr6.simHuman.chr6 302549 5 - 601863 CAAGT -s simRat_chr6.simRat.chr6 213820 5 + 647215 CAAGT - -a -s simMouse_chr6.simMouse.chr6 223028 39 + 636262 GTAAGCTCCAGAGTGGGGTAACTAAATGTGGTTGCATGT -s Anc0.Anc0refChr5 37097 37 - 87904 GTAAGCTCCACAGTAAGTTAGGTAG-TGTGGCTG-ATAT -s Anc1.Anc1refChr7 1680 38 - 47259 GTAAGCTCCACAGTAAGTTAGGTAG-TGTGGCTGCATAT -s Anc2.Anc2refChr15 39518 37 - 86568 GTAAGCCCCACAGTAAGTTAGGTAG-TGTGGCTG-ATAT -s mr.mrrefChr5 77231 39 + 294540 GTAAGCTCCAGAGTAAGGTAACTAGATGTGGTTGCATGT -s simCow_chr6.simCow.chr6 374176 37 - 602619 GTAAGCAACTCAGGTCATTAGGTGT-GGTATCTT-ATAT -s simDog_chr6.simDog.chr6 374894 37 - 593897 GTAAGCCCCACAGTAAGTTAGGTAG-TGTGGCTG-ATAT -s simHuman_chr6.simHuman.chr6 302554 38 - 601863 GTAAGCTTCCAAGTAACTTAGGTAG-TGTTGCTACATAT -s simRat_chr6.simRat.chr6 213825 39 + 647215 GAAAGCTCCAGAGTAAGACAAATAGACGTGGTTGCGTGT - -a -s simMouse_chr6.simMouse.chr6 223067 7 + 636262 CCTACAC -s Anc0.Anc0refChr5 37134 7 - 87904 CTTTTTC -s Anc1.Anc1refChr7 1718 7 - 47259 CTTTTTC -s Anc2.Anc2refChr15 39555 7 - 86568 CTTTTTG -s mr.mrrefChr5 77270 7 + 294540 CCTACAC -s simCow_chr6.simCow.chr6 374213 6 - 602619 CT-TTCA -s simDog_chr6.simDog.chr6 374933 7 - 593897 CTTTTTG -s simHuman_chr6.simHuman.chr6 302592 7 - 601863 CTTTTGC -s simRat_chr6.simRat.chr6 213864 7 + 647215 CCTACAC - -a -s simMouse_chr6.simMouse.chr6 223074 19 + 636262 TCTGATGCATACTCACGTA -s Anc0.Anc0refChr5 37145 19 - 87904 TGTGATATGTGCAAGAGTA -s Anc1.Anc1refChr7 1729 19 - 47259 TGTGATATGTGCAAGAGTA -s Anc2.Anc2refChr15 39566 19 - 86568 TGTGATATGTGCAAGAGTG -s mr.mrrefChr5 77277 19 + 294540 TCTGATGCATGCTCGCGTA -s simCow_chr6.simCow.chr6 374223 19 - 602619 TGTAATATGTCGAAGAGTC -s simDog_chr6.simDog.chr6 374944 19 - 593897 TGTGATATGTGCTAGCGTG -s simHuman_chr6.simHuman.chr6 302603 19 - 601863 TGTGATATGTGTAAGAGTA -s simRat_chr6.simRat.chr6 213871 19 + 647215 TCTGATGCATGCTTGCATA - -a -s simMouse_chr6.simMouse.chr6 223093 7 + 636262 TATTAGA -s Anc0.Anc0refChr5 37164 6 - 87904 TATTAC- -s Anc1.Anc1refChr7 1748 7 - 47259 TATTACA -s Anc2.Anc2refChr15 39585 6 - 86568 CATTAC- -s mr.mrrefChr5 77296 7 + 294540 TATTAGA -s simCow_chr6.simCow.chr6 374242 6 - 602619 CTTTAC- -s simDog_chr6.simDog.chr6 374963 6 - 593897 CATTAC- -s simHuman_chr6.simHuman.chr6 302625 7 - 601863 TTTTACA -s simRat_chr6.simRat.chr6 213890 7 + 647215 TACTAGA - -a -s simMouse_chr6.simMouse.chr6 223100 20 + 636262 ATCTACCTCTGGTAAAGCTA -s Anc0.Anc0refChr5 37174 20 - 87904 ATCTGCCTTTGGTAAAGTTA -s Anc1.Anc1refChr7 1759 20 - 47259 ATCTGCCTTTGGTAAAGTTA -s Anc2.Anc2refChr15 39595 20 - 86568 ATCTGCCTTTGGTAAAGTTA -s mr.mrrefChr5 77303 20 + 294540 ATCTACCTCTGGTAAAGCTA -s simCow_chr6.simCow.chr6 374260 20 - 602619 ATCTACCTTTCGTAAAGTTG -s simDog_chr6.simDog.chr6 374973 20 - 593897 GTGAGTATTTGGTAAAGTTA -s simHuman_chr6.simHuman.chr6 302636 20 - 601863 ATCTGCCTTTGAGAAAGTTT -s simRat_chr6.simRat.chr6 213897 20 + 647215 ATCTACCTCTAGTAAAGCTA - -a -s simMouse_chr6.simMouse.chr6 223120 8 + 636262 GGCAGTTA -s Anc0.Anc0refChr5 37195 8 - 87904 GGCAGCCA -s Anc1.Anc1refChr7 1780 8 - 47259 GGCAGCCA -s Anc2.Anc2refChr15 39616 8 - 86568 GGCAGCCA -s mr.mrrefChr5 77324 8 + 294540 GGCAGCTA -s simCow_chr6.simCow.chr6 374281 7 - 602619 GACAGCC- -s simDog_chr6.simDog.chr6 374994 8 - 593897 GGAAGCCA -s simHuman_chr6.simHuman.chr6 302657 8 - 601863 GGCAGCCA -s simRat_chr6.simRat.chr6 213918 8 + 647215 GGCAGCTA - -a -s simMouse_chr6.simMouse.chr6 223128 40 + 636262 GTGAAGTAAGAACCCTCATTCCAACCATTTCTCATGACAA -s Anc1.Anc1refChr7 1788 25 - 47259 G---------------GACTCCAACCATTTCTAGTGACAA -s mr.mrrefChr5 77332 40 + 294540 GTGAAGTAAGAACCCTGATTCCAACCATTTCTCATGACAA -s simHuman_chr6.simHuman.chr6 302665 25 - 601863 G---------------GACTCCAACCATTTCTAGTGACAA -s simRat_chr6.simRat.chr6 213927 40 + 647215 GTGAAGTAGGAATCCTGATTCCAACCATTTCTCATGACAA - -a -s simMouse_chr6.simMouse.chr6 223168 96 + 636262 ACCCCAGAACTATACAAACCGACTATTCCAACCGTTTCTGATAGCCAAACTTAGAATGACACACCCCTACAACAAGTAAGAAAGATAACACAATGC -s Anc0.Anc0refChr5 37203 91 - 87904 ----AGGAGAAATAAGATCT-TCTATTCCAACCATTTCTAATGACAAACCCTAGAACTCTACAATCCTACACTAAGTGAGAATGATAACACTATGC -s Anc1.Anc1refChr7 1813 95 - 47259 AGCCAGGAGAAATAAGATCT-TCTATTCCAACCATTTCTAATGACAAACCCTAGAACTCTACAATCCTACACTAAGTGAGAATGATAACACTATGC -s Anc2.Anc2refChr15 39624 91 - 86568 ----AGGAGAAATAAGATCT-TTTATTCCAACCATTTCTAGTGACAAACTCCAGAACTCCACAATCCTACACTAAGTGAGAATGATAACACTATGC -s mr.mrrefChr5 77372 96 + 294540 ACCCCAGAACTATACAAACTAACTATTCCAACCGTTTCTAATAGCCAAACCTAGAATGATACACTCCTACAACAAGTAAGAAAGATAACACTATGC -s simCow_chr6.simCow.chr6 374288 90 - 602619 ----AGGAGAAACAATATCT-CTTCTTTTAACCATTTCTGGTGACAAACTCCAGGA-TTCACAGTTCTAAACTTAGTTAGAATGAAAACACTATGC -s simDog_chr6.simDog.chr6 375002 91 - 593897 ----AGAAGAAATAAGATCT-TTTATTCCAAGCATTTCTAGTTACAAAATCCAGATCTCCACAATCCTACATTAAGTGAGAATGATAACACTATGC -s simHuman_chr6.simHuman.chr6 302747 94 - 601863 AGCCAGGAGAAATAAGAGCT-GCTATTCCAACCCTTTCTAAAGAGAAACCCTAGTACTCTGCGATCCTACACTAAGTGAGAA-GATGACACTATTC -s simRat_chr6.simRat.chr6 213967 96 + 647215 GCCCCAGAATTATACAAACTAAGTATTCCAACCATTTCTAATAGTCAAGCCTAGAATGATATACTCCAACAACAAGTAAGAAACATAACACTATGC - -a -s simMouse_chr6.simMouse.chr6 223264 112 + 636262 CAATGGTTTTAGATAACAAGTACTTGTGGAAAAAAACGTGCCCCCAAATCAAACATAATCAGATGAGGCGGGGAATAAAATAACTTGAGATTGTAGATGATAACCTCATTTA -s Anc0.Anc0refChr5 37294 108 - 87904 CAATAGTTGAAGATGACAAGTACTCCTGA---ACTACATGCTCCTGAATCAAACATAACCAGATGGGACAAGGAATAAAGTAATTTGAGTTTATACATGATAGTTTCA-TTA -s Anc1.Anc1refChr7 1908 108 - 47259 CAATAGTTGAAGATGACAAGTACTCCTGA---ACTACATGCTCCTGAATCAAACATAACCAGATGGGACAAGGAATAAAGTAATTTGAGTTTATACATGATAGTTTCA-TTA -s Anc2.Anc2refChr15 39715 108 - 86568 CAATAGTTGAAGATGATAAGTACTCCTGA---CCTACATGCTCCTGAATCAAACATAACCAGATGGGACAAGGAATAAAGTAATTTGAGTTTATACATGATAGTTTCA-TTA -s mr.mrrefChr5 77468 109 + 294540 CAATGGTTTTAGATGACAAGTACTTCTGG---ACAACATGCCCCCAAATCAAACATAACCAGATGAGACGGGGAATAAAATAACTTGAGATTGTAGATGATAGCCTCATTTA -s simCow_chr6.simCow.chr6 374378 104 - 602619 CAATCGTTGAAGAT---AAGTACTCCTGA---CCCACATGATCCTGAATCAATCATAACCAGATGGGACAAGGAGCAAAGTGATTTGAGTTTGTACATGAC-GTTTTA-TTA -s simDog_chr6.simDog.chr6 375096 104 - 593897 CAATAGTTGAAGATGATAA----TGATGA---CCTACATGCTTCTGAACCGAACATAACCAGGCAGGCCGTGGAATCAAGTAATTTGAGCTTATACATAATAGTTTCA-TCA -s simHuman_chr6.simHuman.chr6 302841 108 - 601863 CAACAGTTGAAGATGACAAGTGCTCCTGA---ACTATATGCTCGTGAATCAAACTTAACCAGATGGGACAAGGAATAAAGTAGATTGAGTTTATACATGATAGTTTCA-TTA -s simRat_chr6.simRat.chr6 214063 109 + 647215 CAATGGTTTTAAATGACAAATACTTCTGG---ACAACATGCCCCCAAATCAAACATAACCAGATGAGATGGGGAACGAAATAACTTGAGATCCTGGATGATAGCCTCATTTA - -a -s simMouse_chr6.simMouse.chr6 223376 16 + 636262 TTCATCATGATGGTTC -s Anc0.Anc0refChr5 37402 8 - 87904 TC----ATGAG----C -s Anc1.Anc1refChr7 2016 9 - 47259 TC---CATGAG----C -s Anc2.Anc2refChr15 39823 8 - 86568 TC----ATGAA----T -s mr.mrrefChr5 77577 16 + 294540 TCCATCATGAGGGTTC -s simCow_chr6.simCow.chr6 374485 8 - 602619 TC----ATGAA----T -s simDog_chr6.simDog.chr6 375200 8 - 593897 TC----ATGAA----T -s simHuman_chr6.simHuman.chr6 302949 9 - 601863 TC---CATGAG----C -s simRat_chr6.simRat.chr6 214172 16 + 647215 TCCGCCATGAGTGTTC - -a -s simMouse_chr6.simMouse.chr6 223392 10 + 636262 ATTAATGCTA -s Anc0.Anc0refChr5 37411 2 - 87904 AT-------- -s Anc1.Anc1refChr7 2026 4 - 47259 ATTG------ -s Anc2.Anc2refChr15 39832 2 - 86568 AT-------- -s mr.mrrefChr5 77594 10 + 294540 ATTGATGCTA -s simCow_chr6.simCow.chr6 374494 2 - 602619 AT-------- -s simDog_chr6.simDog.chr6 375209 2 - 593897 AT-------- -s simHuman_chr6.simHuman.chr6 302959 4 - 601863 AATG------ -s simRat_chr6.simRat.chr6 214189 10 + 647215 ATTGATGCCA - -a -s simMouse_chr6.simMouse.chr6 223402 20 + 636262 GCACAGTGTACGGGACTAAC -s Anc0.Anc0refChr5 37413 20 - 87904 GTAAAGTATACGGGATTAAC -s Anc1.Anc1refChr7 2030 20 - 47259 GTAAAGTATACGGGATTAAC -s Anc2.Anc2refChr15 39834 20 - 86568 GTAAAGTATACGGGATTAAC -s mr.mrrefChr5 77604 20 + 294540 GTACAGTGTACGGGACTAAC -s simCow_chr6.simCow.chr6 374497 20 - 602619 GCAAAGCATACAGGATTAAC -s simDog_chr6.simDog.chr6 375211 20 - 593897 GTACAGTGTGCGGGATTAAA -s simHuman_chr6.simHuman.chr6 302963 20 - 601863 GTAAAGTATATGGGATTAAC -s simRat_chr6.simRat.chr6 214199 20 + 647215 GTACAGTTTGCAGGACTAAT - -a -s simMouse_chr6.simMouse.chr6 223422 79 + 636262 GTAACCTCAGATAGCCAAGCATCCAAAAAGTATATTAATTGGCATGCAGTTCAATAGGGTAACAACATGTGCACATCTC -s Anc0.Anc0refChr5 37433 41 - 87904 GTACCTTCAGGTGGCCATTCATCCTAAAAGTATATGAATTG-------------------------------------- -s Anc1.Anc1refChr7 2050 41 - 47259 GTACCTTCAGGTGGCCATTCATCCTAAAAGTATATGAATTG-------------------------------------- -s Anc2.Anc2refChr15 39854 41 - 86568 ATACCTTGCGGTGGCCATTCATCCTAAAAGTATATGAATTG-------------------------------------- -s mr.mrrefChr5 77624 79 + 294540 GTAACCTCAGATGGCCAAGCATCCAAAAAGTATATTAATTGGCATGCAGTTCAATAGGGTAACAACATGTGCACATCTC -s simCow_chr6.simCow.chr6 374517 40 - 602619 ATACCATTCGGTGGCCATGCACCCT-AAAGTATACAAATTG-------------------------------------- -s simDog_chr6.simDog.chr6 375232 41 - 593897 ATACCTAGCAGTCGCCATTCATCCTAAAAGTATATGACTTG-------------------------------------- -s simHuman_chr6.simHuman.chr6 302983 41 - 601863 GGTTCTTCAGGTGGACATACATCCTAAAAGTATAGGAATTA-------------------------------------- -s simRat_chr6.simRat.chr6 214219 79 + 647215 ATAACCTCAGATGGCCAAGCATCCAAAAAGTATATTAATTGGCATAGAGTTCAATAGGGTAACAACATGTGCACATCTC - -a -s simMouse_chr6.simMouse.chr6 223501 37 + 636262 TGCTCAGGGCATGACGAGGAAATAATTGTTGCACTAT -s Anc0.Anc0refChr5 37474 25 - 87904 ------------GACAAGGAAATAAATGGTGCACTTT -s Anc1.Anc1refChr7 2091 25 - 47259 ------------GACAAGGAAATAAATGGTGCACTTT -s Anc2.Anc2refChr15 39895 25 - 86568 ------------GACAAGGAAATAAATGGTGCACTTT -s mr.mrrefChr5 77703 37 + 294540 TGCTCAGGGCATGACAAGGAAATAATTGTTGCACTAT -s simCow_chr6.simCow.chr6 374557 25 - 602619 ------------GACAAGGAAATAGATAGTGCACTTT -s simDog_chr6.simDog.chr6 375273 25 - 593897 ------------GATAAGGAAATAAATGGTGCCATTT -s simHuman_chr6.simHuman.chr6 303024 25 - 601863 ------------GACAAGGATATAAATGGTGCACTTT -s simRat_chr6.simRat.chr6 214309 37 + 647215 TATTTGGAGCATGACAAGGAAATAATTGTTGCATTCT - -a -s simMouse_chr6.simMouse.chr6 223538 5 + 636262 GTGGC -s Anc0.Anc0refChr5 37499 5 - 87904 GTGAC -s Anc1.Anc1refChr7 2116 5 - 47259 GTGAC -s Anc2.Anc2refChr15 39920 5 - 86568 GTTAC -s mr.mrrefChr5 77740 5 + 294540 GTGGC -s simCow_chr6.simCow.chr6 374583 5 - 602619 GTAAC -s simDog_chr6.simDog.chr6 375298 5 - 593897 GTTAC -s simHuman_chr6.simHuman.chr6 303049 5 - 601863 GTGAC -s simRat_chr6.simRat.chr6 214346 5 + 647215 GTGGC - -a -s simMouse_chr6.simMouse.chr6 223543 7 + 636262 ATTCATT -s Anc0.Anc0refChr5 37506 7 - 87904 GTTCATT -s Anc1.Anc1refChr7 2123 7 - 47259 GTTCATT -s Anc2.Anc2refChr15 39927 7 - 86568 GTTCATT -s mr.mrrefChr5 77745 7 + 294540 ATTCATT -s simCow_chr6.simCow.chr6 374590 7 - 602619 GTTCATC -s simDog_chr6.simDog.chr6 375305 7 - 593897 GTTCATT -s simHuman_chr6.simHuman.chr6 303056 7 - 601863 GTTCATA -s simRat_chr6.simRat.chr6 214351 7 + 647215 ATTCATT - -a -s simMouse_chr6.simMouse.chr6 223550 25 + 636262 GGTGCGAGGCATATCATGTTAAGGT -s Anc0.Anc0refChr5 37513 25 - 87904 TGTACATGATATATTGTCTTCAAGT -s Anc1.Anc1refChr7 2130 25 - 47259 TGTACATGATATATTGTCTTCAAGT -s Anc2.Anc2refChr15 39934 25 - 86568 TGTACATGATATATTGTCTTCAAGT -s mr.mrrefChr5 77752 25 + 294540 GGTGCAAGGCATATTATGTTAAGGT -s simCow_chr6.simCow.chr6 374603 25 - 602619 TGTGCATGATATATTGTGTCAAAGT -s simDog_chr6.simDog.chr6 375312 25 - 593897 TGTACATGATATATTACCTTCAAGT -s simHuman_chr6.simHuman.chr6 303063 25 - 601863 CATATATGATATATTGTTTTGAAGT -s simRat_chr6.simRat.chr6 214358 25 + 647215 TGTGCAAGGCATATTATGTTAAGGT - -a -s simMouse_chr6.simMouse.chr6 223575 7 + 636262 GGCTTCC -s Anc0.Anc0refChr5 37538 7 - 87904 GGCTTCC -s Anc1.Anc1refChr7 2155 7 - 47259 GGCTTCC -s Anc2.Anc2refChr15 39959 7 - 86568 GGCTTCT -s mr.mrrefChr5 77777 7 + 294540 GGCTTCC -s simCow_chr6.simCow.chr6 374647 7 - 602619 GGCTCCC -s simDog_chr6.simDog.chr6 375337 7 - 593897 GGCTTTT -s simHuman_chr6.simHuman.chr6 303088 7 - 601863 CGTTTCC -s simRat_chr6.simRat.chr6 214383 7 + 647215 GGCTTCC - -a -s simMouse_chr6.simMouse.chr6 223582 35 + 636262 AAAAACTTAACACGCAGATAGGACTTGATTTCTAA -s Anc0.Anc0refChr5 37545 35 - 87904 AAAAACTTAAAACTAAGAGAGCACATAAATTCTAT -s Anc1.Anc1refChr7 2162 35 - 47259 AAAAACTTAAAACTAAGAGAGCACATAAATTCTAT -s Anc2.Anc2refChr15 39966 35 - 86568 AAAAGCTTAAAACAAATAGAGCCCATAGATTCTAT -s mr.mrrefChr5 77784 35 + 294540 AAAAACTTAACACTCAGATAGGACTTGATTTCTAA -s simCow_chr6.simCow.chr6 374654 35 - 602619 AGAGTGTTACAACAAACTGAGCCCAAATACTTTAT -s simDog_chr6.simDog.chr6 375344 35 - 593897 AAGAGCTTAATACAAATAGAGCCCATAGATTCAAT -s simHuman_chr6.simHuman.chr6 303096 35 - 601863 AAAAACTTGAAACTTGGAGAGCACATAAATTCTAT -s simRat_chr6.simRat.chr6 214390 34 + 647215 AAAAAC-TAACACTCATATAGGACTTGATTTCTAA - -a -s simMouse_chr6.simMouse.chr6 223617 25 + 636262 TTAGATTCAGTCCAGCTTAACGTGG -s Anc0.Anc0refChr5 37580 25 - 87904 TTAGATCCTATCCATCTTAGTGTGG -s Anc1.Anc1refChr7 2197 25 - 47259 TTAGATCCTATCCATCTTAGTGTGG -s Anc2.Anc2refChr15 40001 25 - 86568 TTAGATCCTATCCATATTATTGTGA -s mr.mrrefChr5 77819 25 + 294540 TTAGATTCAGTCCAGCTTAGTGTGG -s simCow_chr6.simCow.chr6 374689 25 - 602619 ATGTATCCCATCCAAATGATAGTGA -s simDog_chr6.simDog.chr6 375379 25 - 593897 TTAGATTCTATCCATATTATTGTGA -s simHuman_chr6.simHuman.chr6 303148 25 - 601863 TTAGATCCTATCCATCTTAGTGAGG -s simRat_chr6.simRat.chr6 214424 25 + 647215 TTTGATTTGGTCCAGCTCAGTGTGG - -a -s simMouse_chr6.simMouse.chr6 223642 33 + 636262 AAGTTTGTGATTGTAGATTGATAGAGGCACAGG -s Anc0.Anc0refChr5 37606 26 - 87904 GGGGTCCT-------GAATGATAGAGGCACAGG -s Anc1.Anc1refChr7 2223 26 - 47259 GGGGTCCT-------GAATGATAGAGGCACAGG -s Anc2.Anc2refChr15 40027 26 - 86568 GGTGCCCT-------GAACGATTGAGGTGCAGG -s mr.mrrefChr5 77844 26 + 294540 GAGTTCGT-------GATTGATAGAGGCACAGG -s simCow_chr6.simCow.chr6 374714 21 - 602619 -----CTT-------GACAGTTTTAGGAGCAGG -s simDog_chr6.simDog.chr6 375405 23 - 593897 GGTGCCC---------GACGATTGAG-TGCAGG -s simHuman_chr6.simHuman.chr6 303174 26 - 601863 GGGGTCCT-------GAATGATAGAGCCACAGG -s simRat_chr6.simRat.chr6 214449 26 + 647215 GAGTTCTT-------GATTGACAGAGGCACAGG - -a -s simMouse_chr6.simMouse.chr6 223675 1 + 636262 G -s Anc0.Anc0refChr5 37632 1 - 87904 G -s Anc1.Anc1refChr7 2249 1 - 47259 G -s Anc2.Anc2refChr15 40054 1 - 86568 G -s mr.mrrefChr5 77870 1 + 294540 G -s simCow_chr6.simCow.chr6 374736 1 - 602619 G -s simDog_chr6.simDog.chr6 375429 1 - 593897 G -s simHuman_chr6.simHuman.chr6 303200 1 - 601863 G -s simRat_chr6.simRat.chr6 214475 1 + 647215 G - -a -s simMouse_chr6.simMouse.chr6 223676 22 + 636262 ACATGAAATGCCATTCATTCAA -s Anc0.Anc0refChr5 37633 22 - 87904 CCATGAAATCCTGGTCTTTTAA -s Anc1.Anc1refChr7 2250 22 - 47259 CCATGAAATCCTGGTCTTTTAA -s Anc2.Anc2refChr15 40055 22 - 86568 CCATGAAATCCTGGTCTTTTAG -s mr.mrrefChr5 77871 22 + 294540 ACATGAAATGCTGTTCATTCAA -s simCow_chr6.simCow.chr6 374737 22 - 602619 GCATGAAAACTTGGTCATTTAT -s simDog_chr6.simDog.chr6 375430 22 - 593897 CCATGAAATCCTGGTCTTTTAG -s simHuman_chr6.simHuman.chr6 303206 22 - 601863 GAATGAAAGCCTGGTCGTTTAA -s simRat_chr6.simRat.chr6 214476 22 + 647215 ACATGAAATGCTGTCCATTCAA - -a -s simMouse_chr6.simMouse.chr6 223698 38 + 636262 TTTAATCTACTGATTCAAGCATGTTTAGTCTGGGAAAT -s Anc0.Anc0refChr5 37655 37 - 87904 TTTT-TCTACTGGTCCAAGCATGTTCAGTCCAAGAGAG -s Anc1.Anc1refChr7 2272 38 - 47259 TTTTCTCTACTGGTCCAAGCATGTTCAGTCCAAGAGAG -s Anc2.Anc2refChr15 40077 37 - 86568 TTTT-TCTACTGGTCCAAGAGTGTTCAGTCCAAGAGAG -s mr.mrrefChr5 77893 38 + 294540 TTTAATCTACTGATTCAAGCATGTTTAGTCCAAGAAAT -s simCow_chr6.simCow.chr6 374759 37 - 602619 TTTC-TCTGCTGGTTCAAGAGTGTTCAGTCAAAGAGAG -s simDog_chr6.simDog.chr6 375452 37 - 593897 CTCT-TTTACTGGTCCAAGAGTGGTCAGTCCAAGAGAC -s simHuman_chr6.simHuman.chr6 303230 38 - 601863 TTTTCTCTACTGGTCCAAGCATGTTGAGTCCAAGCGAG -s simRat_chr6.simRat.chr6 214498 37 + 647215 TCTGAG-TACTGATTCAAGCATGTTCAGTCCAAGGAAT - -a -s simMouse_chr6.simMouse.chr6 223736 20 + 636262 TTACAATAACGAATATAGAT -s Anc0.Anc0refChr5 37692 20 - 87904 TTATGATAACCATTATGGGT -s Anc1.Anc1refChr7 2310 20 - 47259 TTATGATAACCATTATGGGT -s Anc2.Anc2refChr15 40114 20 - 86568 TTATGATAACCATTTTGGGT -s mr.mrrefChr5 77931 20 + 294540 TTACAATAACCAATATAGAT -s simCow_chr6.simCow.chr6 374796 20 - 602619 TTATGAGGATCATTTCGGTT -s simDog_chr6.simDog.chr6 375489 20 - 593897 TTATGATAACCATTTTGGGT -s simHuman_chr6.simHuman.chr6 303268 20 - 601863 TTATGATAACCGTTATGGGT -s simRat_chr6.simRat.chr6 214544 20 + 647215 TTACAATACCCAATATAGAT - -a -s simMouse_chr6.simMouse.chr6 223756 53 + 636262 CTTTTTTTACTAACTATTCTAGTGAAAAGCATACTTACACATGTTGGTGCTGC -s Anc0.Anc0refChr5 37712 51 - 87904 TTTTCTCAACTAACTATTCTAATAAAAAGTATACTTACAGA--TTGATGCTGC -s Anc1.Anc1refChr7 2330 51 - 47259 TTTTCTCAACTAACTATTCTAATAAAAAGTATACTTACAGA--TTGATGCTGC -s Anc2.Anc2refChr15 40134 51 - 86568 TTTTCTCAACTAGCTGTTCTTAAAAAAAGTATACTTACAGA--TTGATACTGT -s mr.mrrefChr5 77951 53 + 294540 CTTTTTTTACTAACTATTCTAGTAAAAAGCATACTTACACATGTTGATGCTGC -s simCow_chr6.simCow.chr6 374816 50 - 602619 TCTTTTCAATTAGCTGTTCCTGCAAGAAGTA-ACTTACATC--TTAATACTGT -s simDog_chr6.simDog.chr6 375509 51 - 593897 TTTTCTCTACTAGCTGTCTTTAAAAAAAGTATACTTACAGA--TTGATACTGT -s simHuman_chr6.simHuman.chr6 303290 51 - 601863 TTTTCTCAACTAACTATTCTAATAAAAAGTATAGTTATAGA--TTGATGCTGC -s simRat_chr6.simRat.chr6 214564 53 + 647215 CTTTTTTGACTAACTATTCTAGTAAAAAGCATACTTACACATGGTGATACTGC - -a -s simMouse_chr6.simMouse.chr6 223809 8 + 636262 TTAACCAT -s Anc0.Anc0refChr5 37763 8 - 87904 TTAACCAT -s Anc1.Anc1refChr7 2381 8 - 47259 TTAACCAT -s Anc2.Anc2refChr15 40185 8 - 86568 TTAACCAT -s mr.mrrefChr5 78004 8 + 294540 TTAACCAT -s simCow_chr6.simCow.chr6 374873 8 - 602619 TTAACCAT -s simDog_chr6.simDog.chr6 375560 8 - 593897 TCAACCGT -s simHuman_chr6.simHuman.chr6 303341 8 - 601863 TTAACCAT -s simRat_chr6.simRat.chr6 214617 8 + 647215 ATAACCAT - -a -s simMouse_chr6.simMouse.chr6 223817 9 + 636262 CTATATCCA -s Anc0.Anc0refChr5 37772 9 - 87904 ATACATCCC -s Anc1.Anc1refChr7 2390 9 - 47259 ATACATCCC -s Anc2.Anc2refChr15 40194 9 - 86568 ATCCCACCA -s mr.mrrefChr5 78012 9 + 294540 CTATATCCC -s simCow_chr6.simCow.chr6 374882 9 - 602619 ATCTTCCCA -s simDog_chr6.simDog.chr6 375569 9 - 593897 ATCCCACTA -s simHuman_chr6.simHuman.chr6 303350 9 - 601863 ATACATCCC -s simRat_chr6.simRat.chr6 214625 9 + 647215 CTATGTCCC - -a -s simMouse_chr6.simMouse.chr6 223826 75 + 636262 TTGCACGCTTCAGCAGTCTAATACCCCTCCGAATTTCAATGTCCAAGGCACCTCAGGCTGACTGAATGAGTTGTT -s Anc0.Anc0refChr5 37781 40 - 87904 C---------------------------------TTCAACATCCAGGGCACCTTGAGC-GGCTTAATGAATT-TT -s Anc1.Anc1refChr7 2399 40 - 47259 C---------------------------------TTCAACATCCAGGGCACCTTGAGC-GGCTTAATGAATT-TT -s Anc2.Anc2refChr15 40205 40 - 86568 C---------------------------------TTCAACATCCAGGGCACCTTTAGC-AGATTAATGAATT-TT -s mr.mrrefChr5 78021 75 + 294540 CTGCACGCTTCAGCAGTCTAATACCCCTCCGAATTTCAATGTCCAAGGCACCTTGGGCTGACTGAATGAATTGTT -s simCow_chr6.simCow.chr6 374893 39 - 602619 T---------------------------------TACAGCATCCAGCACGCTTTTAGC-AGATTAGTGT-TT-TT -s simDog_chr6.simDog.chr6 375580 40 - 593897 C---------------------------------TTGAACACCAGGGGCACCAGTAGC-AGATTAATAAATT-CT -s simHuman_chr6.simHuman.chr6 303359 40 - 601863 C---------------------------------CCCAACATCCAGGGCACCTTGTGC-GGCTTAATGCATT-TT -s simRat_chr6.simRat.chr6 214634 75 + 647215 CTACATGCTCCATCAGTCTGAAACCCCTCCGAATTTCAATGTCCATGGCACCTTGGGCAGACTGAATGAATCATT - -a -s simMouse_chr6.simMouse.chr6 223901 15 + 636262 AATCATCTAAATATT -s Anc0.Anc0refChr5 37821 14 - 87904 GATTGTCTAAATA-T -s Anc1.Anc1refChr7 2439 14 - 47259 GATTGTCTAAATA-T -s Anc2.Anc2refChr15 40245 14 - 86568 GATTGTCTAAATA-T -s mr.mrrefChr5 78096 15 + 294540 AATCATCTAAATATT -s simCow_chr6.simCow.chr6 374932 14 - 602619 GATTATCTAAATA-T -s simDog_chr6.simDog.chr6 375623 13 - 593897 TATTGTCAAAGCA-- -s simHuman_chr6.simHuman.chr6 303399 14 - 601863 GATTGTCTAAATA-T -s simRat_chr6.simRat.chr6 214709 15 + 647215 AATCATCTCAATATT - -a -s simMouse_chr6.simMouse.chr6 223916 60 + 636262 TATTGAACCTATTCCACTGTACCACTGAGCCTTAGCCTTTTGAGCTTTAGCCATGTAAAG -s Anc0.Anc0refChr5 37835 45 - 87904 TGTTACACCTAACCTGCTGTCC---------------TCTTGAGATTGAGTGATTTAAAA -s Anc1.Anc1refChr7 2453 45 - 47259 TGTTACACCTAACCTGCTGTCC---------------TCTTGAGATTGAGTGATTTAAAA -s Anc2.Anc2refChr15 40259 45 - 86568 TGTTACACCTAACCTGCTGTCC---------------TCTTGAGATGGAGTGACTTAAAA -s mr.mrrefChr5 78111 45 + 294540 TATTGAACCTAATCCACTGTAC---------------TTTTGAGCTTTAGCCATGTAAAG -s simCow_chr6.simCow.chr6 374947 41 - 602619 TGTTACACCTAACCTGCTGT-------------------TTGAGGTAGAGTGACTTAACA -s simDog_chr6.simDog.chr6 375636 44 - 593897 -ATTACATCTGACCTACTGTCC---------------TCTGGACATGGAGTGACTTGAAA -s simHuman_chr6.simHuman.chr6 303413 45 - 601863 TGTTATACCTAACCTGCTGCCC---------------TCCTGAGATTGATTGATATAAAA -s simRat_chr6.simRat.chr6 214724 41 + 647215 T----AACTTAATCCACTGTAC---------------TTTTAAGCCTTAGCCATGTAAAG - -a -s simMouse_chr6.simMouse.chr6 223976 16 + 636262 TTGGGTGTAGTGTCAT -s Anc0.Anc0refChr5 37892 15 - 87904 ATGGGCGTAATGTTA- -s Anc1.Anc1refChr7 2510 16 - 47259 ATGGGCGTAATGTTAT -s Anc2.Anc2refChr15 40318 15 - 86568 ATGGGCGTAATGTTA- -s mr.mrrefChr5 78156 16 + 294540 TTGGGTGTAGTGTCAT -s simCow_chr6.simCow.chr6 375002 15 - 602619 ATGGGCGAAATGTTA- -s simDog_chr6.simDog.chr6 375694 15 - 593897 ATAGGCATAATGTTT- -s simHuman_chr6.simHuman.chr6 303470 16 - 601863 ATGGCGGTAATGCTAT -s simRat_chr6.simRat.chr6 214765 16 + 647215 TTGGGTGTAGTGTCAT - -a -s simMouse_chr6.simMouse.chr6 223992 1 + 636262 T -s Anc0.Anc0refChr5 37919 1 - 87904 C -s Anc1.Anc1refChr7 2540 1 - 47259 C -s Anc2.Anc2refChr15 40345 1 - 86568 C -s mr.mrrefChr5 78172 1 + 294540 T -s simCow_chr6.simCow.chr6 375029 1 - 602619 C -s simDog_chr6.simDog.chr6 375710 1 - 593897 C -s simHuman_chr6.simHuman.chr6 303502 1 - 601863 C -s simRat_chr6.simRat.chr6 214781 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 223993 79 + 636262 ATAACACAGTGATACCAAGATGCATATTGCCGTTTCTGCAGCATGATGTGGGATGATCAAAATAAGGAGTAGTGCATGA -s Anc0.Anc0refChr5 37920 74 - 87904 ATGGAACAGGGGTACCAAGATGTTTTCTG--GTTTCT---ACATGATATCAGATGATCAAAATAGGGAATAATCCATGC -s Anc1.Anc1refChr7 2541 76 - 47259 ATGGAACAGGGGTACCAAGATGTTTTCTGTGGTTTCT---ACATGATATCAGATGATCAAAATAGGGAATAATCCATGC -s Anc2.Anc2refChr15 40346 74 - 86568 ATGGACCAGGGGTACCGAGATGTTTTCTG--GTTTCT---ACACGATATCAGATGATCAAAATAGGCAATAATCCATCC -s mr.mrrefChr5 78173 76 + 294540 ATAACACAGGGATACCAAGATGCATTTTGTCGTTTCT---GCATGATATCGGATGATCAAAATAAGGAGTAGTGCATGA -s simCow_chr6.simCow.chr6 375078 74 - 602619 ATGAACCAGGGGTATCTAGATGCTTTCTG--GTTTCT---ACAAGATATCAGATGATCAAAACAGGCAGCAATCTATCC -s simDog_chr6.simDog.chr6 375711 73 - 593897 ATGGACCAGGGGTACCGAGATGTTGTAAG--GTTTAG---ACTCGATATTGCACTATCAAAATAGGCAATAATCCCC-T -s simHuman_chr6.simHuman.chr6 303503 76 - 601863 AAGGAACAGGGGTACCAAGACGTTTTCTGTGGTTTCT---ACATGATACCAGATGATCAAAATAGGGAATAAGCCATGC -s simRat_chr6.simRat.chr6 214782 71 + 647215 ATAACGCAGGAACACCAAGGTGCATTTTGTTGTTTCT---GCATTATATCTGATGATC-AAATAAGGAGTAGTGC---- - -a -s simMouse_chr6.simMouse.chr6 224072 92 + 636262 CAGACTACTAATCCTTAAGAGATGTTGTCTTATTGTTGTTTAGATTTCATCAAGTGCCTTTGAAAGGCAATAACGGTAGAGCAACGAAAGCT -s Anc0.Anc0refChr5 37994 44 - 87904 AAGACTAATAATCATCAAGAG------------------------------------------------ATAATGAATGAACCATGAATGCT -s Anc1.Anc1refChr7 2617 44 - 47259 AAGACTAATAATCATCAAGAG------------------------------------------------ATAATGAATGAACCATGAATGCT -s Anc2.Anc2refChr15 40420 44 - 86568 AAGACTAATAATCATCAAGAG------------------------------------------------ATGATGAATGAACCATGCATGCT -s mr.mrrefChr5 78249 92 + 294540 CAGACTACTAATCCTTAAGAGATGTTGTCTTATTGTTGTTTAGATTTCATCAAGTGCCTTTGAAAGATAATAACGGAAGAACCATGAAAGCT -s simCow_chr6.simCow.chr6 375158 43 - 602619 AAGGCTTATAATCATCAAGAG------------------------------------------------ATGATGAATGAAGCATGCA-GCT -s simDog_chr6.simDog.chr6 375784 44 - 593897 AAGACTAATAATCAACAAGAG------------------------------------------------ATGAGGAATGAACCATGCATGTT -s simHuman_chr6.simHuman.chr6 303579 44 - 601863 AAGATGAATAAACATCAAGAG------------------------------------------------ATAATGAATGAATCATGAATGCT -s simRat_chr6.simRat.chr6 214853 78 + 647215 --------------TTGAGACATGTTGTCTTATCATTGTTTAGATTTTGCAAAGTGCTTTTGAAAGATAAACATGGAAGAACCATGAAAGAC - -a -s simMouse_chr6.simMouse.chr6 224164 10 + 636262 ACCAGAGCAC -s Anc0.Anc0refChr5 38038 9 - 87904 A-CAGTGCAT -s Anc1.Anc1refChr7 2661 9 - 47259 A-CAGTGCAT -s Anc2.Anc2refChr15 40464 9 - 86568 A-AAGTGGAT -s mr.mrrefChr5 78341 10 + 294540 ACCAGAGCAC -s simCow_chr6.simCow.chr6 375201 9 - 602619 A-AAGTGAAT -s simDog_chr6.simDog.chr6 375828 9 - 593897 A-AAGTGGAT -s simHuman_chr6.simHuman.chr6 303623 9 - 601863 A-CAGTGCAT -s simRat_chr6.simRat.chr6 214958 10 + 647215 AACAGAGCAC - -a -s simMouse_chr6.simMouse.chr6 224174 8 + 636262 TTGGGGTA -s Anc0.Anc0refChr5 38052 8 - 87904 CTGGGGTA -s Anc1.Anc1refChr7 2675 8 - 47259 CTGGGGTA -s Anc2.Anc2refChr15 40478 8 - 86568 CTGGGGTA -s mr.mrrefChr5 78351 8 + 294540 TTGGGGTA -s simCow_chr6.simCow.chr6 375215 8 - 602619 TTGGGGTA -s simDog_chr6.simDog.chr6 375842 8 - 593897 CTGGGGTA -s simHuman_chr6.simHuman.chr6 303637 8 - 601863 ATGGGCTA -s simRat_chr6.simRat.chr6 214968 8 + 647215 TTGGAGTA - -a -s simMouse_chr6.simMouse.chr6 224182 49 + 636262 AATTAAGACAAGAATATGTGAACAATACAACTCGCTGTCTACCTGGACC -s Anc0.Anc0refChr5 38062 29 - 87904 AATTAAGAAAAGAAA-------------------CTATCT-GTAATATC -s Anc1.Anc1refChr7 2685 30 - 47259 AATTAAGAAAAGAAA-------------------CTATCTAGTAATATC -s Anc2.Anc2refChr15 40488 29 - 86568 AATGAAGAAAAGAAA-------------------ATATCT-GTAATATC -s mr.mrrefChr5 78359 49 + 294540 AATTAAGACAAGAATATGTGAACAATACAACTCACTATCTAGCTGGACC -s simCow_chr6.simCow.chr6 375225 29 - 602619 AATGAAGAAAAGATA-------------------ATATTA-GTAGTATC -s simDog_chr6.simDog.chr6 375852 29 - 593897 AATGAAGAAAAGCAA-------------------ATATCT-GCAATATC -s simHuman_chr6.simHuman.chr6 303647 30 - 601863 AATTAAGAATAGAAA-------------------CTATCCAGTAATATC -s simRat_chr6.simRat.chr6 214976 49 + 647215 AATGAGAACAAGAACATGTGAACAATACAACTCACTATCTCGCTGGACC - -a -s simMouse_chr6.simMouse.chr6 224231 43 + 636262 CCCCTATGGCCTGTGGCTTTTGTTAGTTTAGCTAGCAAAGATC -s Anc0.Anc0refChr5 38092 30 - 87904 CCCCT-------------TTGATTAGCTTGGCTAGCTAAGATC -s Anc1.Anc1refChr7 2716 30 - 47259 CCCCT-------------TTGATTAGCTTGGCTAGCTAAGATC -s Anc2.Anc2refChr15 40518 30 - 86568 CCCCT-------------TTGACTAGCCTGGCTAACTAAGATC -s mr.mrrefChr5 78408 43 + 294540 CCCCTATGGCCTGTGGCTTTTGTTAGTTTAGCTAGCAAAGATC -s simCow_chr6.simCow.chr6 375255 30 - 602619 CCCGA-------------TTGACTAGCCTGGCCAACTAAAATC -s simDog_chr6.simDog.chr6 375882 30 - 593897 CTCCT-------------TGAGCCAGCCTGGCTAACTGAGATT -s simHuman_chr6.simHuman.chr6 303678 30 - 601863 CCCTC-------------TTGATTAGCTTGGTTGGCTAAGAAC -s simRat_chr6.simRat.chr6 215025 43 + 647215 CCCCTATGCCCTGTGGCTTTTGTTAATTTAGCCAGCAGTGATC - -a -s simMouse_chr6.simMouse.chr6 224274 9 + 636262 TATACAAAG -s Anc0.Anc0refChr5 38122 9 - 87904 TATACAGAG -s Anc1.Anc1refChr7 2746 9 - 47259 TATACAGAG -s Anc2.Anc2refChr15 40550 9 - 86568 TATACAGAG -s mr.mrrefChr5 78451 9 + 294540 TATACAAAG -s simCow_chr6.simCow.chr6 375287 9 - 602619 TATGCAGAG -s simDog_chr6.simDog.chr6 375914 9 - 593897 TATAGAGAG -s simHuman_chr6.simHuman.chr6 303708 9 - 601863 TATACAGCG -s simRat_chr6.simRat.chr6 215068 9 + 647215 TATACAAAG - -a -s simMouse_chr6.simMouse.chr6 224283 39 + 636262 ACAGCAATCACTAAACTTATGTTGGGGAACCAGTTAGGA -s Anc0.Anc0refChr5 38132 38 - 87904 ACTGCAGTCACTAAACATATGTT-CGGAGTCAGTTAGGA -s Anc1.Anc1refChr7 2756 38 - 47259 ACTGCAGTCACTAAACATATGTT-CGGAGTCAGTTAGGA -s Anc2.Anc2refChr15 40560 38 - 86568 ACTGCAGTCACTAATCATATGTT-CAGAGTCAGTTAGGA -s mr.mrrefChr5 78460 38 + 294540 ACAGCAATCACTAAACATATGTT-GGGAACCAGTTAGGA -s simCow_chr6.simCow.chr6 375297 38 - 602619 ACTGCAGTCACTAAGCATCTGTT-GAGACTCAGTTAGGA -s simDog_chr6.simDog.chr6 375924 38 - 593897 GCTGTAGTCACTAATCATATGTT-CAGAGTCAGTTAGGA -s simHuman_chr6.simHuman.chr6 303718 38 - 601863 ACTTCAGTCATTAAAAATATGTC-TGAAGTCAGGTAAGA -s simRat_chr6.simRat.chr6 215077 38 + 647215 ATGGCAAACACTAAACATATGTT-GGGAACCAGTTAGGA - -a -s simMouse_chr6.simMouse.chr6 224322 4 + 636262 ATGA -s Anc0.Anc0refChr5 38175 4 - 87904 ATAA -s Anc1.Anc1refChr7 2799 4 - 47259 ATAA -s Anc2.Anc2refChr15 40603 4 - 86568 ACAA -s mr.mrrefChr5 78503 4 + 294540 ATAA -s simCow_chr6.simCow.chr6 375340 4 - 602619 AGAA -s simDog_chr6.simDog.chr6 375967 4 - 593897 ACAG -s simHuman_chr6.simHuman.chr6 303761 4 - 601863 ATAA -s simRat_chr6.simRat.chr6 215120 4 + 647215 TTAA - -a -s simMouse_chr6.simMouse.chr6 224326 17 + 636262 GCTTTCTAATTGATAAT -s Anc0.Anc0refChr5 38188 17 - 87904 ACTTTCTAGCTGATAAC -s Anc1.Anc1refChr7 2812 17 - 47259 ACTTTCTAGCTGATAAC -s Anc2.Anc2refChr15 40620 17 - 86568 ACTTTCTAGCCAATAGC -s mr.mrrefChr5 78507 17 + 294540 GCTTTCTAGTTGATAAT -s simCow_chr6.simCow.chr6 375357 17 - 602619 AATTCGTAATCAATAGG -s simDog_chr6.simDog.chr6 375984 17 - 593897 TCCTTCTAGCCAATAGC -s simHuman_chr6.simHuman.chr6 303774 17 - 601863 ACTTTCTAGCTGAAAAC -s simRat_chr6.simRat.chr6 215124 17 + 647215 GCTTTCTAGATTTTAAT - -a -s simMouse_chr6.simMouse.chr6 224343 6 + 636262 CTGCAG -s Anc0.Anc0refChr5 38205 6 - 87904 CTGAGG -s Anc1.Anc1refChr7 2829 6 - 47259 CTGAGG -s Anc2.Anc2refChr15 40643 6 - 86568 CTGAGG -s mr.mrrefChr5 78524 6 + 294540 CTGCAG -s simCow_chr6.simCow.chr6 375380 6 - 602619 CTGAGG -s simDog_chr6.simDog.chr6 376007 6 - 593897 TTGAGG -s simHuman_chr6.simHuman.chr6 303791 6 - 601863 CTGAGG -s simRat_chr6.simRat.chr6 215141 6 + 647215 CTGCCG - -a -s simMouse_chr6.simMouse.chr6 224349 29 + 636262 CGTTTGCAGGGCAACTGTGAGTATCCTCT -s Anc0.Anc0refChr5 38213 28 - 87904 T-TCTACAGGGCAATTGTCAGTGTCCTCT -s Anc1.Anc1refChr7 2837 28 - 47259 T-TCTACAGGGCAATTGTCAGTGTCCTCT -s Anc2.Anc2refChr15 40651 28 - 86568 T-TCTACAGGGCAATTGTCAGTGTCCTCT -s mr.mrrefChr5 78530 28 + 294540 T-TTTGCAGGGCAACTGTGAGTATCCTCT -s simCow_chr6.simCow.chr6 375388 28 - 602619 T-TCTACACGGCAAATCTCAGTGTCCGCT -s simDog_chr6.simDog.chr6 376015 28 - 593897 T-TCTACAGGGCAATTGTCAATGTCCTGT -s simHuman_chr6.simHuman.chr6 303799 28 - 601863 T-TCTACAGTGCACTTGTCAGTGTCTTCT -s simRat_chr6.simRat.chr6 215147 28 + 647215 T-TTTGCAGGGCAACTGTGAGTATCCTCT - -a -s simMouse_chr6.simMouse.chr6 224378 1 + 636262 A -s Anc0.Anc0refChr5 38243 1 - 87904 C -s Anc1.Anc1refChr7 2867 1 - 47259 C -s Anc2.Anc2refChr15 40681 1 - 86568 C -s mr.mrrefChr5 78558 1 + 294540 A -s simCow_chr6.simCow.chr6 375418 1 - 602619 C -s simDog_chr6.simDog.chr6 376045 1 - 593897 C -s simHuman_chr6.simHuman.chr6 303829 1 - 601863 C -s simRat_chr6.simRat.chr6 215175 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 224379 175 + 636262 CCAATCCTTGTTCTAAGTTTTATCCAAGCATTGTCTTCTTGGAgagcagggtgtgcaactgcgtgaggactcacactggcagggtaacagaatatgtactttggacaagtgctgcaactggacctacccccctcaaactattcagtactctgtgtgatgtttttgagaaattaat -s Anc0.Anc0refChr5 38244 48 - 87904 -CAATTCTTCTTTTAGGCTTTATTCAAACATTATATTTTTGGAGA------------------------------------------------------------------------------------------------------------------------------TAAT -s Anc1.Anc1refChr7 2868 49 - 47259 TCAATTCTTCTTTTAGGCTTTATTCAAACATTATATTTTTGGAGA------------------------------------------------------------------------------------------------------------------------------TAAT -s Anc2.Anc2refChr15 40682 48 - 86568 -CAATTCTTCTTTTTGGCTTTATTCAAAAATTATATTTTTGGAGA------------------------------------------------------------------------------------------------------------------------------TTAT -s mr.mrrefChr5 78559 175 + 294540 CCAATCCTTGTTCTAAGTTTTATTCAAACATTGTCTTCTTGGAGAgcagggtgtgcaactgcgtgaggactcacactggcagggtaacagaatatgtactttggacaagtgctgcaactggacctacccccctcaaactattcagtactctgtgtgatgtttttgagaaattaat -s simCow_chr6.simCow.chr6 375419 47 - 602619 -CAATTCTTCTTTTTGGCTTTATTCAAAAATTAT-CTTTTAGAGA------------------------------------------------------------------------------------------------------------------------------TGGT -s simDog_chr6.simDog.chr6 376046 48 - 593897 -CAATTCACCTTTTTGTCTCTATTCAAGAGTTATATCTTTGGAGC------------------------------------------------------------------------------------------------------------------------------TTAT -s simHuman_chr6.simHuman.chr6 303830 49 - 601863 TCAATTCTTCTTTTAGGCTTTATTCAAACATGATATTTCTGGAGA------------------------------------------------------------------------------------------------------------------------------TAAT -s simRat_chr6.simRat.chr6 215182 175 + 647215 CCAATCCTTGTTCTAAGTTTTGTTCAAACATTGCCTTCTTGGAACGCAGGGTGTGCAACTGAGTGAGGAGCCACGCTGGCAGCATAACAGGATGCGTACGTTGAACAAGGGCTGCAAGAGGGTCTATccccctcaagctattcagtaatctgtgtgatgtttctatgaaatcaat - -a -s simMouse_chr6.simMouse.chr6 224554 10 + 636262 gtgctcaaca -s Anc0.Anc0refChr5 38295 9 - 87904 ATGC-CAACA -s Anc1.Anc1refChr7 2920 9 - 47259 ATGC-CAACA -s Anc2.Anc2refChr15 40733 9 - 86568 ATGC-CAACA -s mr.mrrefChr5 78734 10 + 294540 gtgctcaaca -s simCow_chr6.simCow.chr6 375469 9 - 602619 ATGC-CAATA -s simDog_chr6.simDog.chr6 376097 9 - 593897 ATGC-CAACA -s simHuman_chr6.simHuman.chr6 303882 9 - 601863 ATGC-CAACA -s simRat_chr6.simRat.chr6 215357 10 + 647215 gtgcccaact - -a -s simMouse_chr6.simMouse.chr6 224564 5 + 636262 aacaa -s Anc0.Anc0refChr5 38304 5 - 87904 AAGTA -s Anc1.Anc1refChr7 2929 5 - 47259 AAGTA -s Anc2.Anc2refChr15 40770 5 - 86568 AAGTA -s mr.mrrefChr5 78744 5 + 294540 aacaa -s simCow_chr6.simCow.chr6 375513 5 - 602619 AGGTA -s simDog_chr6.simDog.chr6 376134 5 - 593897 AAGTA -s simHuman_chr6.simHuman.chr6 303891 5 - 601863 AAGTA -s simRat_chr6.simRat.chr6 215367 5 + 647215 cacaa - -a -s simMouse_chr6.simMouse.chr6 224569 146 + 636262 cagaagaataaccaacaaatgattcaaagaatgactggatccccttctatggttgacctggtgtgcagtaggctcttaggaacacagtttgcacaatacaggtacctacataataggatttgcagccctgccttgaaactaataag -s Anc0.Anc0refChr5 38309 22 - 87904 CAGAAGa---CACAA------ATTGAAAGAA------------------------------------------------------------------------------------------------------------------- -s Anc1.Anc1refChr7 2934 25 - 47259 CAGAAGaatACACAA------ATTGAAAGAA------------------------------------------------------------------------------------------------------------------- -s Anc2.Anc2refChr15 40775 22 - 86568 CATAAGA---CACAC------AGTGAAAGAG------------------------------------------------------------------------------------------------------------------- -s mr.mrrefChr5 78749 146 + 294540 cagaagaataaccaacaaatgattcaaagaatgactggatccccttctatggttgacctggtgtgcagtaggctcttaggaacacagtttgcacaatacaggtacctacataataggatttgcagccctgccttgaaactaataag -s simCow_chr6.simCow.chr6 375518 19 - 602619 CATTAGA---AACAC------AGTGTAA---------------------------------------------------------------------------------------------------------------------- -s simDog_chr6.simDog.chr6 376139 22 - 593897 CATAAGA---CACAC------AGCGAAGGAG------------------------------------------------------------------------------------------------------------------- -s simHuman_chr6.simHuman.chr6 303896 25 - 601863 TTGTATAATACACAA------ATTGAAAGAA------------------------------------------------------------------------------------------------------------------- -s simRat_chr6.simRat.chr6 215381 146 + 647215 caacagagtaaccaacaaatgattcaaagaatagatggatcaccttctatggttcacctagagggaagttagttcttaggaacacagcttgcacaatacagggaccaacatactaagatttgcaaccctctcttgagattaataag - -a -s simMouse_chr6.simMouse.chr6 224715 39 + 636262 acacaagctaatatgcagatttagcaggaccaccaacaa -s mr.mrrefChr5 78895 39 + 294540 acacaagctaatatgcagatttagcaggaccaccaacaa -s simRat_chr6.simRat.chr6 215669 39 + 647215 acacaagctaatatgcagatttagcacgaccaccaacaa - -a -s simMouse_chr6.simMouse.chr6 224754 9 + 636262 caccaatgg -s mr.mrrefChr5 78934 9 + 294540 caccaatgg -s simRat_chr6.simRat.chr6 215710 9 + 647215 cactgatgg - -a -s simMouse_chr6.simMouse.chr6 224763 100 + 636262 cgtaaaaaaaccactgtcaaattagcctggaatcaaaaaagagaacctatggcaaacttagttctaggtaaaaaaaattgagctggttggatcatgttgc -s mr.mrrefChr5 78943 100 + 294540 cgtaaaaaaaccactgtcaaattagcctggaatcaaaaaagagaacctatggcaaacttagttctaggtaaaaaaaattgagctggttggatcatgttgc -s simRat_chr6.simRat.chr6 215722 100 + 647215 tgcaaaaaagccactgtcaaatcagcctggaaacaaaaaagagaacccatggcaaaattaattctatgtaaaagaaattgagctggtgggaccatgttgc - -a -s simMouse_chr6.simMouse.chr6 224863 93 + 636262 AGattacaatcaatgtttcatataggtaggggccaaggattcactagttgatagtggtgttggaggaactggttgtctatcttccaagagcta -s mr.mrrefChr5 79043 92 + 294540 AGattacaatcaatgtt-catataggtaggggccaaggattcactagttgatagtggtgttggaggaactggttgtctatcttccaagagcta -s simRat_chr6.simRat.chr6 215828 92 + 647215 ACATTACAATCAATGTT-CGTATAGGTGGgggccaagaattcactatttgatagcagtgttggaggaactggttgtctatctagcaagaggta - -a -s simMouse_chr6.simMouse.chr6 224956 25 + 636262 ttcttagtgccttatacaggtttag -s mr.mrrefChr5 79135 25 + 294540 ttcttagtgccttatacaggtttag -s simRat_chr6.simRat.chr6 215932 25 + 647215 ttcttaatgctttatacaggtttaa - -a -s simMouse_chr6.simMouse.chr6 224981 115 + 636262 aaaagggtctaaatgttagtggatgatcccagaaacactgtccaagatattggcatgggacaacatctatttagataccaaagtcaactgctgtgaattgcaaaatcgatgagca -s mr.mrrefChr5 79160 115 + 294540 aaaagggtctaaatgttagtggatgatcccagaaacactgtccaagatattggcatgggacaacatctatttagataccaaagtcaactgctgtgaattgcaaaatcgatgagca -s simRat_chr6.simRat.chr6 215972 115 + 647215 AGAGAAGACTAAACCTTCGCGGATGATCtcagaaacaccatctgggatattggcatagaagaacatctgtttagtcaccaaagtcaactgcagctaaactcaaaatcgatgagca - -a -s simMouse_chr6.simMouse.chr6 225096 213 + 636262 caagtgagatatggacaggttaaagagcctgcatggattgaaagaaaagaagtctgtggttacaataaacagtgatatttgaacttggcatgagatctttccaacttattcctctcacacagttacacaaaaggaaaaccaataacaggattaaatgataggttagggacatgaacaggtgctaactggcaagggaagatgttgcagtgaaaa -s mr.mrrefChr5 79275 177 + 294540 caagtgagatatggaca------agagcctgcatggattgaaagaa----------tggttacaa-----------atttgaacttggcatgagatctttccaacttattcctctcacacagttacacaaaaggaaaaccaataacaggattaaatgataggttagggacatgaacaggtgctaactggcaa---------ttgcagtgaaaa -s simRat_chr6.simRat.chr6 216094 177 + 647215 caactgagacataaaca------aaagcctgagtggattgatagaa----------TGGTTAAAA-----------ATTTAAATTTGGAATGAGAGCTTTGCAACTTATTCCTctcacacaattacccaagaagaagaccaataacatgaacaaatgatgggctcgggacatgaacaggcactaactggcaa---------ttgtggcgaaaa - -a -s simMouse_chr6.simMouse.chr6 225309 97 + 636262 agcaccagaggaaatgtaattttccttgaacagtttgtcacaggtctattgcatggggagtcatggtagaacaatgccactatgatgcACTACAATA -s mr.mrrefChr5 79452 97 + 294540 agcaccagaggaaatgtaattttccttgaacagtttgtcacaggtctattgcatggggagtcatggtagaacaatgccactatgatgcACTACAATA -s simRat_chr6.simRat.chr6 216276 97 + 647215 agcaccagaggaaatgtaatttttcttgaACAGTTCGTCACAGATCTATTGCATGGGGCGTCATGGTAGAACAATGCCACTATGATGCACTATAATG - -a -s simMouse_chr6.simMouse.chr6 225406 71 + 636262 TAAAGTAGACGCCAGTATGGGTGCACTCCAGGAAGGCGTTTTCCTGGTCCCAAAGCCACAAACAAAGTTTT -s mr.mrrefChr5 79549 67 + 294540 TAAAGTAGACGCCAG----GGTGCACTCCAGGAAGGCGTTTTCCTGGTCCCAAAGCCACAAACAAAGTTTT -s simRat_chr6.simRat.chr6 216375 67 + 647215 TAAAGTAGGCGCCAG----GGCGTGCTGCAGGAAGGCCTTTTCCTGGTCCCGAGGCCACAAATAAAGTTTT - -a -s simMouse_chr6.simMouse.chr6 225477 176 + 636262 ATGCAACAATACTGGACAACACTATTTTGAGACATAATAGAACGGGTGAACACACTAGGCTGTATATGCAGGAAGCCAACAGTCCAGGCAGTACTTCCTAGGCTGCCAACCAACCGATGCCTGTTAGAAATCCGACTAGTCCCAGTGGCTCAGGGAGGTAGGTGAGTATCTTCGCT -s Anc0.Anc0refChr5 38331 9 - 87904 -----------------------------------------------------------------------------------------------------------------------------------------------------------------------AGTTTGGCC -s Anc1.Anc1refChr7 2959 9 - 47259 -----------------------------------------------------------------------------------------------------------------------------------------------------------------------AGTTTGGCC -s Anc2.Anc2refChr15 40797 9 - 86568 -----------------------------------------------------------------------------------------------------------------------------------------------------------------------AGTCTGCCC -s mr.mrrefChr5 79616 174 + 294540 ATGCAACAATACTGGACAACACTATTTTGAGACATAATAGAACGGGTGAACACACTAGGCTGTATATGCAGGAAGCCAACAGTCCAG-CAGTACTTCCTAGGCTGCCAACCAACCGATGCCTGTTAGAAATCCGACTAGTCCCAGTG-CTCAGGGAGGTAGGTGAGTATCTTCGCT -s simDog_chr6.simDog.chr6 376161 9 - 593897 -----------------------------------------------------------------------------------------------------------------------------------------------------------------------AGTCTGCCC -s simHuman_chr6.simHuman.chr6 303921 9 - 601863 -----------------------------------------------------------------------------------------------------------------------------------------------------------------------AGTTTAGCC -s simRat_chr6.simRat.chr6 216443 174 + 647215 ATGCGACAATACTGGATAAGACTATTTTGAGACATAATAGAAGGGGTGAACAAATCAGGCTGTATTTGCGCAAAGCCAACAAACCAG-TGGTACTTTCTAGGCTGCCAACTAACCAATGCCTGTGAGAAATCCAACTAGTCCCAGTG-CTCAGGGAGGCAGGCAAGAATTTTGGCT - -a -s simMouse_chr6.simMouse.chr6 225653 314 + 636262 CATAGTTGTGCTCAGCATGATGATGTAGGACTATAGTAAATAAGAAATCACATAAACCTTTTCATAATTCTAGTACATGAGAAGACACAAGCTCCAAGAGTGGGAGCATCATGGAGCCCCAAAGAATGTTGGTTACAAATATCGTGCGATGGATGGCATCCCATTTGTTTTATCGGGTAATGTGTGTTGGTCCCATCAACAGGTGCCTGTGGTCACCTAACATTGTATGAGGCCAGCATGCTCTTTCTACAGGTGTCTCAGATTACTTGACGGGCATGGGAGGTCAGGCAAGCTCAGCAACTAATTGAGCACAT -s Anc0.Anc0refChr5 38340 69 - 87904 CATTGCTGTGCTCAGCAGGA----------C--TAGAACACAAGATATCTCATA-------TCATAATTCTAATACATGATAAGACAC---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- -s Anc1.Anc1refChr7 2968 86 - 47259 CATTGCTGTGCTCAGCAGGATGATGTAAGAC--TAGAACACAAGATATCTCATAGACCTTTTCATAATTCTAATACATGATAAGACAC---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- -s Anc2.Anc2refChr15 40806 69 - 86568 TATTGCTGCACTCCGCGGGA----------C--TATGACACAAGGTATCTCATA-------TCATAATTCCGATACATGATAACACAC---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- -s mr.mrrefChr5 79790 303 + 294540 CATAGTTGTGCTCAGCATGATGATGTAGGACTATAGTAAATAAGAAATCACATAAACCTTTTCATAATTCTAGTACATGAGAAGACACAA------AGAGTGGGAG----ATGGAGCCCCAAAGAATGTTGGTTACAAATATCGTGCGATGGATGGCATCCCATTTGTTTTATCGGGTAATGTGTGTTGGTCCCATCAACAGGTGCCTGTGGTCACCTAACATTGTATGAGGCCAGCATGCTCTTTCTACAGGTGTCTCAGATTACTTGACGG-CATGGGAGGTCAGGCAAGCTCAGCAACTAATTGAGCACAT -s simCow_chr6.simCow.chr6 375537 4 - 602619 ------------------------------------------------------------------------------------CCAC---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- -s simDog_chr6.simDog.chr6 376171 69 - 593897 TATTGCTGCACTCCGCGGGA----------C--TATGACACAAGGTATCTCATA-------TCATAATTCCGATACATGATAACACAC---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- -s simHuman_chr6.simHuman.chr6 303930 86 - 601863 CATTGCTCTGCTCAGCAGGATGATGTAAGAC--TAGAACACAAGACATGTTATAGACCTTTTCCTAATTTTAATACATGACAAGACAC---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- -s simRat_chr6.simRat.chr6 216617 303 + 647215 AATAGTTGTGCTCGGTATGATGATGCAGGACTATAGTAAATAAGATATCACATAAACCTTGCCATAATTCTAGTACATGAGAAGACACAA------AGAGTGTGAG----ATGGAGCCCCAAAAAATATTCGTTACAAGTGTCAAGTGATGGATAGCATACCACTTGTTTTATGGGGTAATGTGTTTTGGGCCTACCAACAGGTGACTGTGGTTGCCTGCCAGTGTGTGAGGCCAGCTTGCTCTTTCTACAGGTGTCTCCAATTGCTTGACAG-TAAAAGGTGTCAGGCAAGCTCAGCAGCCAAATGAGCACAT - -a -s simMouse_chr6.simMouse.chr6 225967 3 + 636262 TTG -s mr.mrrefChr5 80100 3 + 294540 TTG -s simRat_chr6.simRat.chr6 216927 3 + 647215 TTG - -a -s simMouse_chr6.simMouse.chr6 225970 53 + 636262 TATTATTGGAGATTTCCACAAGGTGCTGTTTGAAATCTCAACATTGTTAAGTG -s Anc0.Anc0refChr5 38409 5 - 87904 ------------------------------------------------AAGCA -s Anc1.Anc1refChr7 3054 5 - 47259 ------------------------------------------------AAGCA -s Anc2.Anc2refChr15 40875 5 - 86568 ------------------------------------------------AAGAA -s mr.mrrefChr5 80103 53 + 294540 TATTAATGGAGCTTTCCACAAGGTGCTGTTTTAATTCTCAACATTGTTAAGCA -s simCow_chr6.simCow.chr6 375541 5 - 602619 ------------------------------------------------AAGTG -s simDog_chr6.simDog.chr6 376240 5 - 593897 ------------------------------------------------AAGAA -s simHuman_chr6.simHuman.chr6 304016 5 - 601863 ------------------------------------------------AAGCA -s simRat_chr6.simRat.chr6 216932 53 + 647215 TTTTAATGGAGCTTTGCACAGGGTGCCGTTTTAATTCCCAACATTGTTACGCA - -a -s simMouse_chr6.simMouse.chr6 226023 65 + 636262 AGTGATCCTTAGTGATACAGAATGGGCTCAATTATGGTTTTATCCTTGAGGAACCTGTTCCTGGA -s Anc0.Anc0refChr5 38414 58 - 87904 GGTAATCCTGAGTGATATAGGATGGTCTCTATTATGGTTTTATGGTT-------CTGTTCCTGGA -s Anc1.Anc1refChr7 3059 65 - 47259 GGTAATCCTGAGTGATATAGGATGGTCTCTATTATGGTTTTATGGTTTGTCAACCTGTTCCTGGA -s Anc2.Anc2refChr15 40880 58 - 86568 GGTAATCCTGAGTGATATAGGGAGGTCTCTGGCATGGTTTTATGGTT-------CTGTTGATGAA -s mr.mrrefChr5 80156 65 + 294540 AGTGATCCTGAGTGATACAGAATGGTCTCTATTATGGTTTTATCCTTGAGGAACCTGTTCCTGGA -s simCow_chr6.simCow.chr6 375546 50 - 602619 GGTGGTCCTGAGCGGTGTAGGGAGGTCTATGGCA--------TGGTT-------ATGCTGGAGAA -s simDog_chr6.simDog.chr6 376247 58 - 593897 GGCAATCCTGCGTGATATAGGGAGGGCTCTGGCATGGTTTTATGTTT-------CTGTTGATGAA -s simHuman_chr6.simHuman.chr6 304021 65 - 601863 GGTAAGCCCGAGTGATATAGGATGGTCTTTATTATGGCTTTATGGTTTGTCAACCTGTTCCTGGA -s simRat_chr6.simRat.chr6 216985 65 + 647215 ATTGATCCTGCATGACACAGAAAGGTTTCTAATACGATTTTATTCTTGAGAAACCTGTTCCTGGA - -a -s simMouse_chr6.simMouse.chr6 226088 2 + 636262 TA -s Anc0.Anc0refChr5 38472 2 - 87904 TA -s Anc1.Anc1refChr7 3124 2 - 47259 TA -s Anc2.Anc2refChr15 40938 2 - 86568 TA -s mr.mrrefChr5 80221 2 + 294540 TA -s simCow_chr6.simCow.chr6 375598 2 - 602619 CA -s simDog_chr6.simDog.chr6 376305 2 - 593897 TA -s simHuman_chr6.simHuman.chr6 304086 2 - 601863 TA -s simRat_chr6.simRat.chr6 217050 2 + 647215 TA - -a -s simMouse_chr6.simMouse.chr6 226090 6 + 636262 AAACAT -s Anc0.Anc0refChr5 38477 6 - 87904 AAAAGT -s Anc1.Anc1refChr7 3129 6 - 47259 AAAAGT -s Anc2.Anc2refChr15 40943 6 - 86568 AAAAGT -s mr.mrrefChr5 80223 6 + 294540 AAACAT -s simCow_chr6.simCow.chr6 375603 6 - 602619 CCAGGT -s simDog_chr6.simDog.chr6 376310 6 - 593897 AAAAGT -s simHuman_chr6.simHuman.chr6 304091 6 - 601863 AAATGT -s simRat_chr6.simRat.chr6 217052 6 + 647215 GCACAG - -a -s simMouse_chr6.simMouse.chr6 226096 19 + 636262 TGATCCTGATCTTAAGTGC -s Anc0.Anc0refChr5 38483 17 - 87904 TGATCCCGATCCTAAGT-- -s Anc1.Anc1refChr7 3135 19 - 47259 TGATCCCGATCCTAAGTTC -s Anc2.Anc2refChr15 40949 17 - 86568 TGATCCCGATCCTAAGT-- -s mr.mrrefChr5 80229 19 + 294540 TGATCCTGATCTTAAGTGC -s simCow_chr6.simCow.chr6 375612 17 - 602619 GGATTCTGATCCTAAGT-- -s simDog_chr6.simDog.chr6 376316 17 - 593897 TTATCCCGTACCCAAGT-- -s simHuman_chr6.simHuman.chr6 304097 19 - 601863 TGACCCAGATCCTAAGTTC -s simRat_chr6.simRat.chr6 217058 19 + 647215 TGATCCGGATCTTGAGTAC - -a -s simMouse_chr6.simMouse.chr6 226115 15 + 636262 AAGCTCTCTTACGAG -s Anc0.Anc0refChr5 38500 11 - 87904 ----ACTGTTATGAG -s Anc1.Anc1refChr7 3154 15 - 47259 AGGGACTGTTATGAG -s Anc2.Anc2refChr15 40966 11 - 86568 ----ACTGTTATGAA -s mr.mrrefChr5 80248 15 + 294540 AAGCTCTGTTACGAG -s simCow_chr6.simCow.chr6 375629 11 - 602619 ----AATGTTATGAT -s simDog_chr6.simDog.chr6 376333 11 - 593897 ----ACTGTTATGAA -s simHuman_chr6.simHuman.chr6 304184 15 - 601863 AGGGACTGTTATGAG -s simRat_chr6.simRat.chr6 217077 15 + 647215 ATGCTCTGTTTCAAG - -a -s simMouse_chr6.simMouse.chr6 226130 59 + 636262 TTGCTAGAGTTGGGTAGTTAAGGAATCACCTCAATTTGGATTGGTTGGGAAAATGTCTT -s Anc0.Anc0refChr5 38511 58 - 87904 TTGGGAGAATTGTTTAGCTAAGGAATCACCTGAATTTGG-TTGGATGGGAAAGCGTCTG -s Anc1.Anc1refChr7 3169 59 - 47259 TTGGGAGAATTGTTTAGCTAAGGAATCACCTGAATTTGGATTGGATGGGAAAGCGTCTG -s Anc2.Anc2refChr15 40977 58 - 86568 TTGGGAGAATTGTTTAGCTAAGGAATCACCTGTATTTGG-TTGGATGGGAAAGTGTCTG -s mr.mrrefChr5 80263 59 + 294540 TTGCTAGAGTTGGGTAGCTAAGGAATCACCTCAATTTGGATTGGTTGGGAAAACGTCTT -s simCow_chr6.simCow.chr6 375641 58 - 602619 TTGGTGGAACTGTCCTGCTGAGGAATCCCCTGTATTTGT-TTGGATGCGAAAGTGTCTT -s simDog_chr6.simDog.chr6 376344 58 - 593897 TTGGGAGAGTTGTTTAGCTAAGGAATCACTCATATTTGG-TTAGATGGGAAAGTGTCTG -s simHuman_chr6.simHuman.chr6 304199 55 - 601863 CTGGCAAAATTATTTAGCT----AACAACCTGAATTTGGATTGGATGGGAAGGCGTCCC -s simRat_chr6.simRat.chr6 217092 59 + 647215 TTGCTAGAGTTGGATAGCTAAGGAATCACCTCAATTCGGATTGGTTGAGGAAACATCTT - -a -s simMouse_chr6.simMouse.chr6 226189 5 + 636262 GGTTA -s Anc0.Anc0refChr5 38570 5 - 87904 GGTCT -s Anc1.Anc1refChr7 3229 5 - 47259 GGTCT -s Anc2.Anc2refChr15 41036 5 - 86568 GTTCT -s mr.mrrefChr5 80322 5 + 294540 GGTTA -s simCow_chr6.simCow.chr6 375700 5 - 602619 GCTCT -s simDog_chr6.simDog.chr6 376403 5 - 593897 GTTCT -s simHuman_chr6.simHuman.chr6 304255 5 - 601863 GGTAT -s simRat_chr6.simRat.chr6 217151 5 + 647215 GGTTA - -a -s simMouse_chr6.simMouse.chr6 226194 31 + 636262 TGAAGATGGGTCCCTGCACCATGTATGTATG -s Anc0.Anc0refChr5 38575 30 - 87904 TTAAGTTTGTCTCA-GCAGTATGCATGTATG -s Anc1.Anc1refChr7 3234 30 - 47259 TTAAGTTTGTCTCA-GCAGTATGCATGTATG -s Anc2.Anc2refChr15 41041 30 - 86568 TTAGCTTTGTCTCA-GCAGTGTGCATGTATG -s mr.mrrefChr5 80327 30 + 294540 TGAAGATTGGTCCC-GCAGCATGTATGTATG -s simCow_chr6.simCow.chr6 375705 30 - 602619 GGAGCTTTATCTCA-GTAGTGTTCACGTGTG -s simDog_chr6.simDog.chr6 376409 30 - 593897 TTAGCCTTGTTTCA-GCAGTGTGCATGTATG -s simHuman_chr6.simHuman.chr6 304260 30 - 601863 TCAAGTTTGTCTCA-GCAGAATGCATGTACG -s simRat_chr6.simRat.chr6 217156 30 + 647215 TGAAGCTTGGTCCC-TCAGTGCGGATGTATG - -a -s simMouse_chr6.simMouse.chr6 226225 8 + 636262 AATTGTAG -s Anc0.Anc0refChr5 38605 6 - 87904 TGTTG--A -s Anc1.Anc1refChr7 3264 8 - 47259 TGTTGCAA -s Anc2.Anc2refChr15 41071 6 - 86568 TGTAG--A -s mr.mrrefChr5 80357 8 + 294540 AATTGTAG -s simCow_chr6.simCow.chr6 375738 6 - 602619 TCTAG--A -s simDog_chr6.simDog.chr6 376439 6 - 593897 TGTAG--A -s simHuman_chr6.simHuman.chr6 304290 8 - 601863 TGCTGCAA -s simRat_chr6.simRat.chr6 217186 8 + 647215 AATTGTAG - -a -s simMouse_chr6.simMouse.chr6 226233 14 + 636262 ATACCATTAACAAA -s Anc0.Anc0refChr5 38612 14 - 87904 AAACCACTAACAAA -s Anc1.Anc1refChr7 3273 14 - 47259 AAACCACTAACAAA -s Anc2.Anc2refChr15 41078 14 - 86568 AAGCCACTAATAAA -s mr.mrrefChr5 80366 14 + 294540 AAACCATTAACAAA -s simCow_chr6.simCow.chr6 375745 14 - 602619 AACCCAGTTATAAA -s simDog_chr6.simDog.chr6 376446 14 - 593897 AAGCCACTAATAAA -s simHuman_chr6.simHuman.chr6 304299 14 - 601863 AAACCACTAACAAA -s simRat_chr6.simRat.chr6 217195 14 + 647215 AAACCATTAACAAG - -a -s simMouse_chr6.simMouse.chr6 226247 3 + 636262 AAT -s Anc0.Anc0refChr5 38651 3 - 87904 GAT -s Anc1.Anc1refChr7 3312 3 - 47259 GAT -s Anc2.Anc2refChr15 41117 3 - 86568 GAT -s mr.mrrefChr5 80385 3 + 294540 GAT -s simCow_chr6.simCow.chr6 375790 3 - 602619 TGA -s simDog_chr6.simDog.chr6 376485 3 - 593897 GAT -s simHuman_chr6.simHuman.chr6 304338 3 - 601863 GAT -s simRat_chr6.simRat.chr6 217214 3 + 647215 GAT - -a -s simMouse_chr6.simMouse.chr6 226250 5 + 636262 CATGG -s Anc0.Anc0refChr5 38654 5 - 87904 TACAA -s Anc1.Anc1refChr7 3315 5 - 47259 TACAA -s Anc2.Anc2refChr15 41125 5 - 86568 TACAA -s mr.mrrefChr5 80388 5 + 294540 CATAA -s simCow_chr6.simCow.chr6 375798 5 - 602619 CACAA -s simDog_chr6.simDog.chr6 376493 5 - 593897 TACAA -s simHuman_chr6.simHuman.chr6 304341 5 - 601863 TACAA -s simRat_chr6.simRat.chr6 217217 5 + 647215 CATAA - -a -s simMouse_chr6.simMouse.chr6 226255 18 + 636262 CTTTCTCAAGAATTTGCA -s Anc0.Anc0refChr5 38663 17 - 87904 CTTTATCAAAAA-CTGCA -s Anc1.Anc1refChr7 3324 17 - 47259 CTTTATCAAAAA-CTGCA -s Anc2.Anc2refChr15 41134 17 - 86568 CTTTATCAAAAA-CTGCA -s mr.mrrefChr5 80393 18 + 294540 CTTTCTCAAGAATTTGCA -s simCow_chr6.simCow.chr6 375807 17 - 602619 CTTCATCAAAAT-TTGCG -s simDog_chr6.simDog.chr6 376502 17 - 593897 CTGTATCAAAAA-CTGCA -s simHuman_chr6.simHuman.chr6 304350 14 - 601863 CTTTATCAAAAA----CA -s simRat_chr6.simRat.chr6 217222 18 + 647215 CTTTCTCTAGATTTTGCA - -a -s simMouse_chr6.simMouse.chr6 226273 11 + 636262 TAGTGCCAATT -s Anc0.Anc0refChr5 38680 11 - 87904 TAGTGTTAGTT -s Anc1.Anc1refChr7 3341 11 - 47259 TAGTGTTAGTT -s Anc2.Anc2refChr15 41151 11 - 86568 TAGTGTTAGTC -s mr.mrrefChr5 80411 11 + 294540 TAGTGCTAATT -s simCow_chr6.simCow.chr6 375826 11 - 602619 TAGTGTTAGTC -s simDog_chr6.simDog.chr6 376519 11 - 593897 TAGTGTTAGTC -s simHuman_chr6.simHuman.chr6 304364 11 - 601863 TAGTGTTAGTT -s simRat_chr6.simRat.chr6 217240 11 + 647215 TAGTGCTAATT - -a -s simMouse_chr6.simMouse.chr6 226284 9 + 636262 AGTGTAGGT -s Anc0.Anc0refChr5 38693 5 - 87904 GGTG----G -s Anc1.Anc1refChr7 3354 9 - 47259 GGTGTAAAG -s Anc2.Anc2refChr15 41164 5 - 86568 GGTG----G -s mr.mrrefChr5 80422 9 + 294540 AGTGTAGGT -s simCow_chr6.simCow.chr6 375839 5 - 602619 GATA----G -s simDog_chr6.simDog.chr6 376532 5 - 593897 TGTG----G -s simHuman_chr6.simHuman.chr6 304377 9 - 601863 GGTCTAAAG -s simRat_chr6.simRat.chr6 217251 9 + 647215 AGTGCAGGT - -a -s simMouse_chr6.simMouse.chr6 226293 4 + 636262 TAAC -s Anc0.Anc0refChr5 38698 4 - 87904 TAAC -s Anc1.Anc1refChr7 3363 4 - 47259 TAAC -s Anc2.Anc2refChr15 41169 4 - 86568 TAAA -s mr.mrrefChr5 80431 4 + 294540 TAAC -s simCow_chr6.simCow.chr6 375844 4 - 602619 AAAA -s simDog_chr6.simDog.chr6 376537 4 - 593897 TTAA -s simHuman_chr6.simHuman.chr6 304386 4 - 601863 TAAC -s simRat_chr6.simRat.chr6 217262 4 + 647215 TAAC - -a -s simMouse_chr6.simMouse.chr6 226297 69 + 636262 CCAAGATATGACACGTCTTCTTATTCACTTACTGTCAAAAAGTTGAGTTACTGCGGTTACACCTTTAAT -s Anc0.Anc0refChr5 38702 69 - 87904 TCAAGATATGACACATTGTTTTATTCTTTAACTATTAGCAAGTTGAGTAATTGCAGTCACACCTTTTAT -s Anc1.Anc1refChr7 3367 69 - 47259 TCAAGATATGACACATTGTTTTATTCTTTAACTATTAGCAAGTTGAGTAATTGCAGTCACACCTTTTAT -s Anc2.Anc2refChr15 41173 69 - 86568 TCAACATATGATACATTGTTTTATTCTTTAACTATTAGCAAGTTAAGTAATTGCAGTCACACCTTTTAT -s mr.mrrefChr5 80435 69 + 294540 TCAAGATATGACACATCTTTTTATTCATTTACTGTCAAAAAGTTGAGTTACTGCGGTCACACCTTTAAT -s simCow_chr6.simCow.chr6 375848 61 - 602619 TCAACATATGG------GTTTTATTCTTGAACTAGTGTCAAGTTAAGTAATTT--GTCACACCTTTCAT -s simDog_chr6.simDog.chr6 376541 69 - 593897 TCAACATATGATACATTGTTTTATTCTTTAGCTATTAGCAAGTTAAGTAATTGCAGGCATGCCTATTAT -s simHuman_chr6.simHuman.chr6 304393 69 - 601863 TGATGATATGACACACTGTTTTATTCTTTAACTATTACCAAGTTGAGTAATTACAGTCACACCTTTTAT -s simRat_chr6.simRat.chr6 217266 64 + 647215 TCAGTATATGACACATCTTTCTATTCGTTTACC-----AAAGTTGAGCTACTGTGGTCACACCTTTGAT - -a -s simMouse_chr6.simMouse.chr6 226366 19 + 636262 TGTCTAACCCACAAATAGC -s Anc0.Anc0refChr5 38771 19 - 87904 GCTTTGACCCACAAATAGC -s Anc1.Anc1refChr7 3436 19 - 47259 GCTTTGACCCACAAATAGC -s Anc2.Anc2refChr15 41242 19 - 86568 GCTTTGACCCACAAATAGT -s mr.mrrefChr5 80504 19 + 294540 TGTTTAACCCACAAATAGC -s simCow_chr6.simCow.chr6 375909 19 - 602619 GCTTTGACCCACAAATAGT -s simDog_chr6.simDog.chr6 376610 12 - 593897 GCTTTGACTCAC------- -s simHuman_chr6.simHuman.chr6 304462 19 - 601863 GCTTTGACCCACAAATGGC -s simRat_chr6.simRat.chr6 217333 19 + 647215 CATTTAATCCACAAATAGC - -a -s simMouse_chr6.simMouse.chr6 226385 3 + 636262 TGA -s Anc0.Anc0refChr5 38792 3 - 87904 TAA -s Anc1.Anc1refChr7 3457 3 - 47259 TAA -s Anc2.Anc2refChr15 41263 3 - 86568 AAA -s mr.mrrefChr5 80523 3 + 294540 TAA -s simCow_chr6.simCow.chr6 375930 3 - 602619 AAA -s simHuman_chr6.simHuman.chr6 304483 3 - 601863 TAA -s simRat_chr6.simRat.chr6 217352 3 + 647215 TAA - -a -s simMouse_chr6.simMouse.chr6 226388 29 + 636262 AGGAGACAAACATTTGCTACTTGCAAACA -s Anc0.Anc0refChr5 38795 29 - 87904 AAGAGACAAACACTTGCAATTTGCAAACT -s Anc1.Anc1refChr7 3460 29 - 47259 AAGAGACAAACACTTGCAATTTGCAAACT -s Anc2.Anc2refChr15 41274 29 - 86568 AAGAGACAAACACTTGCAATTTGCAAACT -s mr.mrrefChr5 80526 29 + 294540 AGGAGACAAACATTTGCTACTTGCAAACA -s simCow_chr6.simCow.chr6 375946 29 - 602619 AAAAGACAAACACTTGCAATTTGCAAACT -s simDog_chr6.simDog.chr6 376630 29 - 593897 AAGAAACAAACACTTGCTATTTGCAAACT -s simHuman_chr6.simHuman.chr6 304486 22 - 601863 AAGAGACAAACGCTTGCAGATT------- -s simRat_chr6.simRat.chr6 217355 29 + 647215 AGGAAACAAACATTTGCTACTTGCAAACA - -a -s simMouse_chr6.simMouse.chr6 226417 23 + 636262 ACAATTAGACAAATATGCTGGGA -s Anc0.Anc0refChr5 38824 23 - 87904 ACAATTACACACTTAAGCTGACA -s Anc1.Anc1refChr7 3489 23 - 47259 ACAATTACACACTTAAGCTGACA -s Anc2.Anc2refChr15 41305 23 - 86568 ACAATTACACACTTAAGCTAACA -s mr.mrrefChr5 80555 23 + 294540 ACAATTAGACAAATATGCTGGGA -s simCow_chr6.simCow.chr6 375977 23 - 602619 ACAATTACACACTTATGCTGAAA -s simDog_chr6.simDog.chr6 376661 23 - 593897 ACAATTACACACTTAAGCTAACA -s simHuman_chr6.simHuman.chr6 304508 7 - 601863 -------------TAATCTG--- -s simRat_chr6.simRat.chr6 217384 23 + 647215 AGAGTTAGACAAATATGTTGGAA - -a -s simMouse_chr6.simMouse.chr6 226440 5 + 636262 ACCCA -s Anc0.Anc0refChr5 38847 5 - 87904 ACCCA -s Anc1.Anc1refChr7 3512 5 - 47259 ACCCA -s Anc2.Anc2refChr15 41340 5 - 86568 ACCCA -s mr.mrrefChr5 80578 5 + 294540 ACCCA -s simCow_chr6.simCow.chr6 376012 5 - 602619 ACTTA -s simDog_chr6.simDog.chr6 376697 5 - 593897 ACCCA -s simHuman_chr6.simHuman.chr6 304515 2 - 601863 ---TA -s simRat_chr6.simRat.chr6 217407 5 + 647215 ACCCA - -a -s simMouse_chr6.simMouse.chr6 226445 44 + 636262 GTAGGCCAAAAGGAGATAGATCTGAGAAGTGACTATCAGGAGCG -s Anc1.Anc1refChr7 3522 32 - 47259 GTGGGC-----------AGGGCTGTGAACTGG-TCTTAAGCATA -s mr.mrrefChr5 80588 44 + 294540 GTAGGCCAAAAGGAGATAGAGCTGAGAAGTGGCTATCAGGAGCA -s simHuman_chr6.simHuman.chr6 304522 32 - 601863 GTGGGC-----------AGGGCTGTGAACTGG-TCTTAAGCATA -s simRat_chr6.simRat.chr6 217417 44 + 647215 GTAGGCTAAAAGGAGATAGAGCTGAGAAGTGGCTATCAGGGGCA - -a -s simMouse_chr6.simMouse.chr6 226489 47 + 636262 GTGCCTGTAGAGCTAAATTCCAATTTGTAGTACCAAACATGAAGTTA -s Anc1.Anc1refChr7 3621 44 - 47259 GTCCTTTTAAACCAAGATTTCAATGTGTAACAT---ATGTAAAGTTA -s mr.mrrefChr5 80699 47 + 294540 GTGCCTGTAGAGCTAAATTCCAATGTGTAGTATCAAATATGAAGTTA -s simHuman_chr6.simHuman.chr6 304621 44 - 601863 GTCCTTTTAAACCAAGATTTCAATGTGTAACAT---ATGTAAAGTTA -s simRat_chr6.simRat.chr6 217528 47 + 647215 GTGCCTGTAGATCTAAATTACGATGTGTAGTATCAAATATGAAGTTA - -a -s simMouse_chr6.simMouse.chr6 226536 25 + 636262 TGTTCACAATAGGAACTGAAAATAC -s Anc1.Anc1refChr7 3665 25 - 47259 TATCAGCAATGAGATTTGCAAGTAT -s mr.mrrefChr5 80746 25 + 294540 TGTCAGCAATAGGAACTGAAAATAC -s simHuman_chr6.simHuman.chr6 304665 25 - 601863 TATCAGCAATGAGATTTGCAAGTAT -s simRat_chr6.simRat.chr6 217582 25 + 647215 TGTCAGCAATAGGAACTGAAAATAC - -a -s simMouse_chr6.simMouse.chr6 226561 44 + 636262 AAGAATCTTATTGGTTGCATTCATTACCATTAATCCTGTACTCA -s Anc1.Anc1refChr7 3690 44 - 47259 GAAAATTTTGTTGGTAGCCTTTGTCCACATTAGTCCTATACTCA -s mr.mrrefChr5 80771 44 + 294540 AAGAATTTTATTGGTTGCATTCATCACCATTAATCCTGTACTCA -s simHuman_chr6.simHuman.chr6 304717 44 - 601863 GAAAATTTTGTTGGTAGCCTTTGTCCACATTAGTCCTATACTCA -s simRat_chr6.simRat.chr6 217607 44 + 647215 AAGAATTTTATTGGTGGTATTGATCACCATTAATCCTGTACTCA - -a -s simMouse_chr6.simMouse.chr6 226605 123 + 636262 TTATCAATGAGGCTTTAAGGGAAAATAATAGAGTGAAGCATGATATTACACTTGGGAGGAGTGACACTCTGTTGAAGATAGAGATAGATAGTTCTAATCTTGCAGCATTCTGTAATAGGCACA -s Anc1.Anc1refChr7 3734 86 - 47259 TTATCAATGGGGCTCTTAGAGAATACCATGGAGTGGGTCTT-----------------------------------TATAGAGGGAGGTAGCTATAAGCTTG-AGCA-TCTATGATTGGCACA -s mr.mrrefChr5 80815 123 + 294540 TTATCAATGAGGCTTTAAGAGAAAATAATAGAGTGAAGCATGATATTACACTTGGGAGGAGTGACACTCTGTTGAAGATAGAGATAGATAGTTCTAATCTTGCAGCATTCTGTAATAGGCACA -s simHuman_chr6.simHuman.chr6 304781 86 - 601863 TTATCAATGGGGCTCTTAGAGAATACCATGGAGTGGGTCTT-----------------------------------TATAGAGGGAGGTAGCTATAAGCTTG-AGCA-TCTATGATTGGCACA -s simRat_chr6.simRat.chr6 217651 123 + 647215 TTATCATTGAGGTTTTAAGAGAGGAGTATTAAGTGAAGCATGATATTTCACTTGGGCTGAGTGACACTCTGCTGAAGATAGAGATTGATAATTCGAATCTTGGAGCATTCTGTAATAGGCATG - -a -s simMouse_chr6.simMouse.chr6 226728 19 + 636262 TAGTATCCATTACCCATCC -s Anc0.Anc0refChr5 38853 6 - 87904 -------------ATGTCC -s Anc1.Anc1refChr7 3820 19 - 47259 TAGTAGCTGGTGCATGTCC -s Anc2.Anc2refChr15 41346 6 - 86568 -------------ATGAAC -s mr.mrrefChr5 80938 19 + 294540 TAGTATCCAGTACCCATCC -s simCow_chr6.simCow.chr6 376018 6 - 602619 -------------CTGATC -s simDog_chr6.simDog.chr6 376703 6 - 593897 -------------ATGAAC -s simHuman_chr6.simHuman.chr6 304870 19 - 601863 TAGTAGCTGGTGCATGTCC -s simRat_chr6.simRat.chr6 217774 19 + 647215 TAGTCTCCAGTTCCCATCC - -a -s simMouse_chr6.simMouse.chr6 226747 46 + 636262 CAACCTATGGGCCAATACACGGCAAAAACTGAAAGAAGCTTGAAGT -s Anc0.Anc0refChr5 38859 46 - 87904 TGACGATTGGGCTGATACACCCCAAAAACCAATAAGTCATAGAAAT -s Anc1.Anc1refChr7 3839 46 - 47259 TGACGATTGGGCTGATACACCCCAAAAACCAATAAGTCATAGAAAT -s Anc2.Anc2refChr15 41354 46 - 86568 TCATGCTTGGTGTGATACACGCTAGAAACCAATAAGTCATACAAAT -s mr.mrrefChr5 80957 46 + 294540 CAACCATTGGGCCAATACACCCCAAAAACTGACAGAAGCTTGAAAT -s simCow_chr6.simCow.chr6 376026 46 - 602619 TTGTGCCTAGCAGATTAGATCCTACAAAATGATAAGTCGTATAAAC -s simDog_chr6.simDog.chr6 376711 46 - 593897 TCATGCTTGGTGTGATACACGCTAGAAACCAATAAGTCATACAAGT -s simHuman_chr6.simHuman.chr6 304889 38 - 601863 TGACGATTGGGCAGACACACCCCAA--------ATGCCATAGAAAT -s simRat_chr6.simRat.chr6 217793 46 + 647215 CAACCATCGGACCCATACACCCCAAAAACTGGCAGAAGCTTGAAAT - -a -s simMouse_chr6.simMouse.chr6 226793 84 + 636262 TAGCAAGACCTACTGGACAAAGCTCCACTGAGGGGGCATAAGGTGGAGTGCGGTGCATCTACAACCTGCTTGTTTTACAGTGTA -s Anc0.Anc0refChr5 38915 84 - 87904 TAGCAAGACCTACTGGACAAAGCTCTACTGGGGGATCATAAGGGGGAGCACGGTACATCTTGAACCTTCTAGTTTTACAGTGTG -s Anc1.Anc1refChr7 3895 84 - 47259 TAGCAAGACCTACTGGACAAAGCTCTACTGGGGGATCATAAGGGGGAGCACGGTACATCTTGAACCTTCTAGTTTTACAGTGTG -s Anc2.Anc2refChr15 41410 84 - 86568 TAGCAAGACCTAATGGACAAAGCTCTACTGGGGGATCATAAGGGGGAGCAAGGAACATCTTGAACCTTCTAGCCCTACAGTGTG -s mr.mrrefChr5 81003 84 + 294540 TAGCAAGACCTACTGGACAAAGCTCCACTGGGGGGGCATAAGGTGGAGTGCGGTGCATCTTCAACCTGCTTGTTTTACAGTGTA -s simCow_chr6.simCow.chr6 376087 84 - 602619 TAGCAAGACCTATTGGATGAAACTTTACCGGGGGTTCATAAGGGGGAGCAAGGAACATCCTGGACCTTCTAGCCCTACAGTGTG -s simDog_chr6.simDog.chr6 376767 84 - 593897 TAGCAAGACATAATGGACAAAGTTCTACTGGGCAACCATAAGGGGGAGCAAGGAGCATCTTGAACCTTCTAGCCCTACAGTGTG -s simHuman_chr6.simHuman.chr6 304937 84 - 601863 TAGCAAGACCTACTGGACATAGCTCTAGTGGGGGATCATAAGGGGGAGCACAGTACATCTTGAACCATTAAGTTTTATAGTGGG -s simRat_chr6.simRat.chr6 217839 84 + 647215 TAGCAAGACCTACTGGACAAAGCTCCACTGGGGGGATAGAAGGTGGAGTGTGGTGCATCTTAGACCTGCTCGTTTTACAGTATA - -a -s simMouse_chr6.simMouse.chr6 226877 61 + 636262 TCAGATGTACTGAATATAGCCTACAGAGATTAATTTTAAGCTATACCATGGAGTACCCAAC -s Anc0.Anc0refChr5 39010 60 - 87904 TTAGATGTGCTAAGTATAATCTACAGAGATTAA-TTTAAGCTATACCAGGCAGTAGCTAGC -s Anc1.Anc1refChr7 3990 60 - 47259 TTAGATGTGCTAAGTATAATCTACAGAGATTAA-TTTAAGCTATACCAGGCAGTAGCTAGC -s Anc2.Anc2refChr15 41505 60 - 86568 TTAGATGCGCTAAGTATAATCTACAGAGTTTAA-TTTAAGCTATACTAGGCAGTAGTTAGC -s mr.mrrefChr5 81098 61 + 294540 TTAGATGTGCTGAATATAGCCTACAGAGATTAATTTTAAGCTATACCATGGAGTAGCCAAC -s simCow_chr6.simCow.chr6 376182 60 - 602619 TTGGATGAACTAAGTATAATCTACAAAGTTTAA-TTTAGGCTATACTAGGCAGTAATTAGC -s simDog_chr6.simDog.chr6 376862 60 - 593897 TTAGATGCGCTAAGTATGATTTACAGAGTTTAA-TTTAAGATATACTAGCCAATAGTTAGC -s simHuman_chr6.simHuman.chr6 305032 58 - 601863 GTAGAGGTGCTTAG-ATAATCTATGTA-ATTAG-TTTAAGCTATACCAGGCAGTAGCTAGC -s simRat_chr6.simRat.chr6 217934 61 + 647215 TTAGATGTGCTGAACATAGCCCACAGAGATTAATTTTAAGCTATGCCATGGAGTAGCCACC - -a -s simMouse_chr6.simMouse.chr6 226938 4 + 636262 TCTA -s Anc0.Anc0refChr5 39070 4 - 87904 TCTC -s Anc1.Anc1refChr7 4050 4 - 47259 TCTC -s Anc2.Anc2refChr15 41566 4 - 86568 TCTC -s mr.mrrefChr5 81159 4 + 294540 TCTA -s simCow_chr6.simCow.chr6 376243 4 - 602619 TCTC -s simDog_chr6.simDog.chr6 376923 4 - 593897 TCTC -s simHuman_chr6.simHuman.chr6 305090 4 - 601863 TCTC -s simRat_chr6.simRat.chr6 217995 4 + 647215 TCTA - -a -s simMouse_chr6.simMouse.chr6 226942 18 + 636262 TTTTAGATGCCAAATTAT -s Anc0.Anc0refChr5 39076 18 - 87904 TTTTAAACGCCCAATTAG -s Anc1.Anc1refChr7 4056 18 - 47259 TTTTAAACGCCCAATTAG -s Anc2.Anc2refChr15 41572 18 - 86568 ATTTAAACGCCCAATCAG -s mr.mrrefChr5 81163 18 + 294540 TTTTAGATGCCAAATTAT -s simCow_chr6.simCow.chr6 376249 18 - 602619 CTTTCAACACCCAATGAG -s simDog_chr6.simDog.chr6 376929 18 - 593897 ATTTAGATGTCAAATCAA -s simHuman_chr6.simHuman.chr6 305096 18 - 601863 TTTTAAACGCCCAATTAG -s simRat_chr6.simRat.chr6 217999 18 + 647215 TTTTAGATGCCAAATTAT - -a -s simMouse_chr6.simMouse.chr6 226960 56 + 636262 ATTAAGACTAACACTTGGTGGCCTGGAAGTGAACACAGGACGCTTGTAATAGTTCG -s Anc0.Anc0refChr5 39096 56 - 87904 TTTAAGATGGACACTTAGTGGCCTGGAGATGCACATAGGACACTTTTAATGATTTG -s Anc1.Anc1refChr7 4076 56 - 47259 TTTAAGATGGACACTTAGTGGCCTGGAGATGCACATAGGACACTTTTAATGATTTG -s Anc2.Anc2refChr15 41592 56 - 86568 TTTAATATGGACAGTTAGTGGCCTGGGGATGCACATAGGATACTTTCAATGATTTG -s mr.mrrefChr5 81183 56 + 294540 ATTAAGACTAACACTTGGTGGCCTGGAAGTGAACACAGGACGCTTTTAATGGTTCG -s simCow_chr6.simCow.chr6 376269 56 - 602619 TTTAAATCAGACAGTTAGTGGCCGTGGGACACACATAGGATACTTTCAATGACTAG -s simDog_chr6.simDog.chr6 376949 56 - 593897 TTCAATATGGACGGTTAGTGGCCTGGGGATGCACATAGGATACTTTCCATGATTTG -s simHuman_chr6.simHuman.chr6 305116 56 - 601863 TGTGAGAAGGACACATAATGGCTTGAAGCTGCACATAAGACACTTTTAATGTTTGG -s simRat_chr6.simRat.chr6 218019 56 + 647215 ATTATGACTATTGTTTGGTAGCCTGGAATAGAACACAGGAGGCCTTTAGTGATTAG - -a -s simMouse_chr6.simMouse.chr6 227016 7 + 636262 ATATTAT -s Anc0.Anc0refChr5 39155 7 - 87904 ATATTAT -s Anc1.Anc1refChr7 4135 7 - 47259 ATATTAT -s Anc2.Anc2refChr15 41651 7 - 86568 AGATCAT -s mr.mrrefChr5 81242 7 + 294540 ATATTAT -s simCow_chr6.simCow.chr6 376328 7 - 602619 AACTCAG -s simDog_chr6.simDog.chr6 377008 7 - 593897 AGATCAT -s simHuman_chr6.simHuman.chr6 305175 7 - 601863 ATATTAT -s simRat_chr6.simRat.chr6 218078 7 + 647215 ACATTAT - -a -s simMouse_chr6.simMouse.chr6 227023 2 + 636262 GG -s Anc0.Anc0refChr5 39162 2 - 87904 GG -s Anc1.Anc1refChr7 4142 2 - 47259 GG -s Anc2.Anc2refChr15 41658 2 - 86568 GG -s mr.mrrefChr5 81249 2 + 294540 GG -s simCow_chr6.simCow.chr6 376409 2 - 602619 GG -s simDog_chr6.simDog.chr6 377015 2 - 593897 GG -s simHuman_chr6.simHuman.chr6 305182 2 - 601863 GG -s simRat_chr6.simRat.chr6 218085 2 + 647215 GC - -a -s simMouse_chr6.simMouse.chr6 227025 41 + 636262 CCATCTTGTGCTTGTCACCAAAAAGTACCCACATTTATACC -s Anc0.Anc0refChr5 39165 39 - 87904 CCATCATGTGCTTGTCACT--AAAGTACCTGTGTTTATATC -s Anc1.Anc1refChr7 4145 39 - 47259 CCATCATGTGCTTGTCACT--AAAGTACCTGTGTTTATATC -s Anc2.Anc2refChr15 41661 39 - 86568 GCATCATGTGCTTGGCACT--AAAGTATCTGTGTGTACATC -s mr.mrrefChr5 81251 39 + 294540 CCATCTTGTGCTTGTCACC--AAAGTACCCGCATTTATACC -s simCow_chr6.simCow.chr6 376412 38 - 602619 GCACCTTGTGCTTGCCACT--AAAG-ATCGGTGTCTACATT -s simDog_chr6.simDog.chr6 377018 38 - 593897 GCATCATGTGCGTGGCATC---AAGTATCTGTATGCACATC -s simHuman_chr6.simHuman.chr6 305185 39 - 601863 CCATCCTGTGCTCATCACT--AAAGTTCCTGTGTTTATATC -s simRat_chr6.simRat.chr6 218087 39 + 647215 ACATCTTGTGCCAGTCACC--AAAGGACCCGCATTTATACC - -a -s simMouse_chr6.simMouse.chr6 227066 66 + 636262 TATGATCTAGTGTATATGTCATTGGAATCCTAAAAGAACGCCACAAGAATCAGTATGTGTTGGTTA -s Anc0.Anc0refChr5 39204 63 - 87904 AATTATGTAGTATATATGTCATGGCAATGCTAAAAGAACATC---GTAGTCAGTATATGTTGGTTA -s Anc1.Anc1refChr7 4184 63 - 47259 AATTATGTAGTATATATGTCATGGCAATGCTAAAAGAACATC---GTAGTCAGTATATGTTGGTTA -s Anc2.Anc2refChr15 41700 63 - 86568 AATTATGGACTAAATATGTCATGGCAATGCTAAAAGAACATT---GTAATCAGTATATGTTGGTAA -s mr.mrrefChr5 81290 66 + 294540 TATGATCTAGTGTATATGTCATTGGAATCCTAAAAGAACACCACAGGAGTCAGTATATGTTGGTTA -s simCow_chr6.simCow.chr6 376451 63 - 602619 AATTATGGACTAAATATGTCATGGCAATGCTAAAAGAACACT---GTAATCACTATATGTTGGTCA -s simDog_chr6.simDog.chr6 377056 43 - 593897 --------------------ATGGCAATCCTAAAGGATTATT---GTAATCTGTATATGTTGGTAA -s simHuman_chr6.simHuman.chr6 305224 63 - 601863 AATTGTGTAGCATATATGTTATAGCAATGCTTAAAGCACATC---GTAGTCAGTATATATTAGTTA -s simRat_chr6.simRat.chr6 218126 66 + 647215 TATGATCTAGTGTATATGTCACTGTAATCCTAAAAGAACACCACAGGAGTCAGTATATGTTGGTTA - -a -s simMouse_chr6.simMouse.chr6 227132 32 + 636262 GAACAGATAGTAGTAATTGAATCAGTGACTGT -s Anc0.Anc0refChr5 39268 32 - 87904 CAGGAGATAGTAGTAATGAGATCAGTTACTGT -s Anc1.Anc1refChr7 4248 32 - 47259 CAGGAGATAGTAGTAATGAGATCAGTTACTGT -s Anc2.Anc2refChr15 41764 32 - 86568 CAGGAGATAGTAGTAATGAGATCAGTTACTGT -s mr.mrrefChr5 81356 32 + 294540 GAACAGATAGTAGTAATTAAATCAGTGACTGT -s simCow_chr6.simCow.chr6 376515 32 - 602619 TGGAGGATAGTAGTAATTAGATCAATGACCAT -s simDog_chr6.simDog.chr6 377100 32 - 593897 CATGAGATAGTAGTAAAGAGATCTGTTACTGT -s simHuman_chr6.simHuman.chr6 305288 32 - 601863 CAGGAGATAGTAGTAATAAGATCAGCAACTGT -s simRat_chr6.simRat.chr6 218192 32 + 647215 GAACAGATAGTAGTAATTAAATGAGTGATCAT - -a -s simMouse_chr6.simMouse.chr6 227164 3 + 636262 CCT -s Anc0.Anc0refChr5 39303 3 - 87904 CAG -s Anc1.Anc1refChr7 4283 3 - 47259 CAG -s Anc2.Anc2refChr15 41799 3 - 86568 CAG -s mr.mrrefChr5 81388 3 + 294540 CCT -s simCow_chr6.simCow.chr6 376550 3 - 602619 TAG -s simDog_chr6.simDog.chr6 377135 3 - 593897 CAG -s simHuman_chr6.simHuman.chr6 305323 3 - 601863 CAG -s simRat_chr6.simRat.chr6 218224 3 + 647215 CCA - -a -s simMouse_chr6.simMouse.chr6 227167 4 + 636262 GCAT -s Anc0.Anc0refChr5 39306 4 - 87904 GTAT -s Anc1.Anc1refChr7 4286 4 - 47259 GTAT -s Anc2.Anc2refChr15 41803 4 - 86568 ATAT -s mr.mrrefChr5 81391 4 + 294540 GCAT -s simCow_chr6.simCow.chr6 376554 4 - 602619 ATAT -s simDog_chr6.simDog.chr6 377139 4 - 593897 ATAT -s simHuman_chr6.simHuman.chr6 305326 4 - 601863 GTAT -s simRat_chr6.simRat.chr6 218227 4 + 647215 GCAT - -a -s simMouse_chr6.simMouse.chr6 227171 9 + 636262 AACCAATGC -s Anc0.Anc0refChr5 39312 9 - 87904 AACCAATTC -s Anc1.Anc1refChr7 4292 9 - 47259 AACCAATTC -s Anc2.Anc2refChr15 41809 9 - 86568 TACCTATTA -s mr.mrrefChr5 81395 9 + 294540 AACCAATGC -s simCow_chr6.simCow.chr6 376560 9 - 602619 TGCCCTCTA -s simDog_chr6.simDog.chr6 377145 9 - 593897 TACCTATTA -s simHuman_chr6.simHuman.chr6 305332 9 - 601863 AACCAATCC -s simRat_chr6.simRat.chr6 218231 9 + 647215 AACCAATGC - -a -s simMouse_chr6.simMouse.chr6 227180 6 + 636262 ATCTCA -s Anc0.Anc0refChr5 39398 6 - 87904 AACTCA -s Anc1.Anc1refChr7 4378 6 - 47259 AACTCA -s Anc2.Anc2refChr15 41901 6 - 86568 AATTCA -s mr.mrrefChr5 81404 6 + 294540 ATCTCA -s simCow_chr6.simCow.chr6 376638 6 - 602619 AATTCA -s simDog_chr6.simDog.chr6 377237 6 - 593897 AATTCA -s simHuman_chr6.simHuman.chr6 305418 6 - 601863 AACTCA -s simRat_chr6.simRat.chr6 218240 6 + 647215 ATCTCA - -a -s simMouse_chr6.simMouse.chr6 227186 18 + 636262 ATTCATATTTTAAGGCAA -s Anc0.Anc0refChr5 39405 18 - 87904 ACTGAGGGTATAAGCGGA -s Anc1.Anc1refChr7 4385 18 - 47259 ACTGAGGGTATAAGCGGA -s Anc2.Anc2refChr15 41908 18 - 86568 ACTGAGGGTATGAGCGGC -s mr.mrrefChr5 81410 18 + 294540 ATTCATAGTTTAAGGCAA -s simCow_chr6.simCow.chr6 376645 18 - 602619 ATTGAGGGTATTATGGGC -s simDog_chr6.simDog.chr6 377244 18 - 593897 ACTGAGGGTATGAGCAGC -s simHuman_chr6.simHuman.chr6 305425 18 - 601863 ACTGAGGGTATAAGAGGA -s simRat_chr6.simRat.chr6 218246 18 + 647215 ATTTATAGTCTAAGGTAA - -a -s simMouse_chr6.simMouse.chr6 227204 5 + 636262 CAGTA -s Anc0.Anc0refChr5 39428 5 - 87904 CAGTA -s Anc1.Anc1refChr7 4408 5 - 47259 CAGTA -s Anc2.Anc2refChr15 42029 5 - 86568 TAGCC -s mr.mrrefChr5 81428 5 + 294540 CAGTA -s simCow_chr6.simCow.chr6 376771 5 - 602619 TAGCT -s simDog_chr6.simDog.chr6 377365 5 - 593897 TAGCC -s simHuman_chr6.simHuman.chr6 305448 5 - 601863 CAGTA -s simRat_chr6.simRat.chr6 218264 5 + 647215 TAGTA - -a -s simMouse_chr6.simMouse.chr6 227209 12 + 636262 GGTTAGTATCTT -s Anc0.Anc0refChr5 39433 10 - 87904 G-TTAGTCTCT- -s Anc1.Anc1refChr7 4413 12 - 47259 GGTTAGTCTCTT -s Anc2.Anc2refChr15 42034 10 - 86568 G-TTAGTCTCT- -s mr.mrrefChr5 81433 12 + 294540 GGTTAGTATCTT -s simCow_chr6.simCow.chr6 376776 10 - 602619 G-TAAGTCTCT- -s simDog_chr6.simDog.chr6 377374 10 - 593897 G-TTAGTCTCT- -s simHuman_chr6.simHuman.chr6 305453 12 - 601863 GTTTAGCCTCTT -s simRat_chr6.simRat.chr6 218269 12 + 647215 GGTTAGTATCGC - -a -s simMouse_chr6.simMouse.chr6 227221 31 + 636262 TACCTACACTGAAGAGAAAACAGACATGTAC -s Anc0.Anc0refChr5 39443 31 - 87904 CACCTACACAGAAGATAAAACAGACATGTCC -s Anc1.Anc1refChr7 4425 31 - 47259 CACCTACACAGAAGATAAAACAGACATGTCC -s Anc2.Anc2refChr15 42044 31 - 86568 CACCTACGCAGAAGATAAAACATGCACGTCC -s mr.mrrefChr5 81445 31 + 294540 CACCTACACTGAAGAGAAAACAGACATGTAC -s simCow_chr6.simCow.chr6 376786 31 - 602619 CACCTATGCAGAGGATAGAACCAACACTTCC -s simDog_chr6.simDog.chr6 377385 31 - 593897 CACCTACGCAGAAGATAAAACATGCACGTCC -s simHuman_chr6.simHuman.chr6 305465 28 - 601863 CACCCCCAC---AGACAAAACAGACATGTCC -s simRat_chr6.simRat.chr6 218281 31 + 647215 CACCTACACTGAAGAGAAAACAGACATGTAC - -a -s simMouse_chr6.simMouse.chr6 227252 5 + 636262 ATGCA -s Anc0.Anc0refChr5 39474 3 - 87904 ATA-- -s Anc1.Anc1refChr7 4456 5 - 47259 ATAGA -s Anc2.Anc2refChr15 42075 3 - 86568 GCA-- -s mr.mrrefChr5 81476 5 + 294540 ATGCA -s simCow_chr6.simCow.chr6 376817 3 - 602619 GCA-- -s simDog_chr6.simDog.chr6 377418 3 - 593897 GCA-- -s simHuman_chr6.simHuman.chr6 305493 5 - 601863 ATAGA -s simRat_chr6.simRat.chr6 218312 5 + 647215 ATGCA - -a -s simMouse_chr6.simMouse.chr6 227257 9 + 636262 TATGGCCCT -s Anc0.Anc0refChr5 39477 4 - 87904 -----CCCT -s Anc1.Anc1refChr7 4461 9 - 47259 CACAGCCCT -s Anc2.Anc2refChr15 42078 4 - 86568 -----CCCC -s mr.mrrefChr5 81481 9 + 294540 CATGGCCCT -s simCow_chr6.simCow.chr6 376820 4 - 602619 -----TCCC -s simDog_chr6.simDog.chr6 377421 4 - 593897 -----CCCC -s simHuman_chr6.simHuman.chr6 305502 9 - 601863 CACAGCTCT -s simRat_chr6.simRat.chr6 218317 9 + 647215 CATGGCCCT - -a -s simMouse_chr6.simMouse.chr6 227266 20 + 636262 TTCTAAGATTCATGTCTCTA -s Anc0.Anc0refChr5 39488 13 - 87904 GTTCATGTCTC-------TA -s Anc1.Anc1refChr7 4477 20 - 47259 GTTCATGTCTCATGTCTCTA -s Anc2.Anc2refChr15 42089 13 - 86568 GTTCATGTCTT-------TA -s mr.mrrefChr5 81490 20 + 294540 GTCTAAGGTTCATGTCTCTA -s simCow_chr6.simCow.chr6 376831 13 - 602619 GATCATGTCTC-------TA -s simDog_chr6.simDog.chr6 377458 13 - 593897 GTTCATGTCTT-------TA -s simHuman_chr6.simHuman.chr6 305518 20 - 601863 GTTCATGTCTCATGTCTCTA -s simRat_chr6.simRat.chr6 218326 20 + 647215 GTCTAAGGTTCATGTCTTTA - -a -s simMouse_chr6.simMouse.chr6 227286 14 + 636262 TGTAGTAAGGATAG -s Anc0.Anc0refChr5 39502 14 - 87904 GGGAGTAAGGAGAT -s Anc1.Anc1refChr7 4498 14 - 47259 GGGAGTAAGGAGAT -s Anc2.Anc2refChr15 42103 14 - 86568 GGGAGTAATGATTT -s mr.mrrefChr5 81510 14 + 294540 TGGAGTAAGGAGAG -s simCow_chr6.simCow.chr6 376845 14 - 602619 GTGGGTAAGGCTTT -s simDog_chr6.simDog.chr6 377472 14 - 593897 GGGAGTAATGATTT -s simHuman_chr6.simHuman.chr6 305539 14 - 601863 GGGAGCAAGGAGAT -s simRat_chr6.simRat.chr6 218346 14 + 647215 TGGAGTAAGGAGAG - -a -s simMouse_chr6.simMouse.chr6 227300 4 + 636262 ACCC -s Anc0.Anc0refChr5 39516 4 - 87904 AATC -s Anc1.Anc1refChr7 4512 4 - 47259 AATC -s Anc2.Anc2refChr15 42160 4 - 86568 AATC -s mr.mrrefChr5 81524 4 + 294540 ACCC -s simCow_chr6.simCow.chr6 376903 4 - 602619 AGGC -s simDog_chr6.simDog.chr6 377530 4 - 593897 GATC -s simHuman_chr6.simHuman.chr6 305553 4 - 601863 AATC -s simRat_chr6.simRat.chr6 218360 4 + 647215 TCCT - -a -s simMouse_chr6.simMouse.chr6 227304 109 + 636262 TGAAGTAGCAGAACAAGTCTGACTCTTTTGCTGTTCTATTGTGCATCTAATGCCCATAGTGTCCTGGTGAGTTATAAAGATTTAAATAGTGTTTGGGCTGGGAGAAGAC -s mr.mrrefChr5 81528 78 + 294540 TGAAGTAGCAGAACAAGTCTGACTCTTTTGCTGTTCTATTGTGCATCTA------------------------------ATTTAAATAGTG-TTGGGCTGGGAGAAGAC -s simRat_chr6.simRat.chr6 218365 78 + 647215 TGAAGTATCAGAACAAGTCTGGCTCTTTTGCTGTTTCGTTGTGCATGCA------------------------------ATTAAACCAGTA-TTGGGCTGGGAAAAGGC - -a -s simMouse_chr6.simMouse.chr6 227413 19 + 636262 AGGTCAGCTAAAAAAGCGA -s Anc0.Anc0refChr5 39520 1 - 87904 ------------------A -s Anc1.Anc1refChr7 4516 1 - 47259 ------------------A -s Anc2.Anc2refChr15 42164 1 - 86568 ------------------A -s mr.mrrefChr5 81606 19 + 294540 AGGTCAGCTAAAAAAGCGA -s simCow_chr6.simCow.chr6 376907 1 - 602619 ------------------A -s simDog_chr6.simDog.chr6 377534 1 - 593897 ------------------A -s simHuman_chr6.simHuman.chr6 305557 1 - 601863 ------------------A -s simRat_chr6.simRat.chr6 218450 19 + 647215 TGGTCAGCTAAAAAAACCA - -a -s simMouse_chr6.simMouse.chr6 227432 4 + 636262 ACCA -s Anc0.Anc0refChr5 39521 4 - 87904 GTTA -s Anc1.Anc1refChr7 4517 4 - 47259 GTTA -s Anc2.Anc2refChr15 42165 4 - 86568 GTTA -s mr.mrrefChr5 81625 4 + 294540 ACCA -s simCow_chr6.simCow.chr6 376908 4 - 602619 GCTA -s simDog_chr6.simDog.chr6 377552 4 - 593897 GTTA -s simHuman_chr6.simHuman.chr6 305558 4 - 601863 GTTA -s simRat_chr6.simRat.chr6 218469 4 + 647215 ACCA - -a -s simMouse_chr6.simMouse.chr6 227436 30 + 636262 AGTAAGGGGGACCATTTACAGGGGTTGATG -s Anc0.Anc0refChr5 39525 30 - 87904 AGTAAGTGAGGCCATTCATAGAAGTTGATG -s Anc1.Anc1refChr7 4521 30 - 47259 AGTAAGTGAGGCCATTCATAGAAGTTGATG -s Anc2.Anc2refChr15 42169 30 - 86568 AGTAAGTGAGGCTATTCATAGAAGTTGATG -s mr.mrrefChr5 81629 30 + 294540 AGTAAGGGGGACCATTTACAGGGGTTGATG -s simCow_chr6.simCow.chr6 376914 30 - 602619 AGTAAGTGAGGCTATTCATAGAAGTTGATG -s simDog_chr6.simDog.chr6 377556 30 - 593897 AGTAAGTGAGGCTATTCACAGAAGTTGATG -s simHuman_chr6.simHuman.chr6 305562 27 - 601863 AGTAAGCAAGGCCATTCATAGAAGTTG--- -s simRat_chr6.simRat.chr6 218473 30 + 647215 AGTAAGTGAGAGTATTTACGGGGATTGATG - -a -s simMouse_chr6.simMouse.chr6 227466 44 + 636262 ACTATTGATATCATGGGTGGTGTCTGAACCCTCCAGGCAGGTGG -s Anc0.Anc0refChr5 39555 21 - 87904 ACAATTGACCTGATGGGA-----------------------TGG -s Anc1.Anc1refChr7 4551 21 - 47259 ACAATTGACCTGATGGGA-----------------------TGG -s Anc2.Anc2refChr15 42201 21 - 86568 ACAATTGACCTGATGGGA-----------------------TGG -s mr.mrrefChr5 81659 21 + 294540 ACTATTGATATCATGGGT-----------------------TGG -s simCow_chr6.simCow.chr6 376946 21 - 602619 AATATTGACCTTATGGGA-----------------------TGG -s simDog_chr6.simDog.chr6 377588 21 - 593897 ACAATTGACCTGATGGGA-----------------------TGG -s simRat_chr6.simRat.chr6 218505 21 + 647215 ACCATTGAGATTATGGAC-----------------------TGG - -a -s simMouse_chr6.simMouse.chr6 227510 36 + 636262 TGTCTGAACCCTCCAGGCAGGATTAGAAATTATCCT -s Anc0.Anc0refChr5 39576 1 - 87904 T----------------------------------- -s Anc1.Anc1refChr7 4572 1 - 47259 T----------------------------------- -s Anc2.Anc2refChr15 42222 1 - 86568 T----------------------------------- -s mr.mrrefChr5 81680 30 + 294540 TGTCTGAA------AGGCAGGATTAGAAATTATCCT -s simDog_chr6.simDog.chr6 377723 1 - 593897 T----------------------------------- -s simRat_chr6.simRat.chr6 218526 30 + 647215 TGTCTGAG------AGGCAGTATTAGCGAATATCCT - -a -s simMouse_chr6.simMouse.chr6 227546 65 + 636262 TCACAATTGAGATCATGATGTCACTTTTGAATCCTCACTAGATATCCAGATGCCACCCTGTTAGT -s Anc0.Anc0refChr5 39577 22 - 87904 -------------------------------------------ATCCAGATGTCGCACTGTTAGT -s Anc1.Anc1refChr7 4573 25 - 47259 ----------------------------------TTT------ATCCAGATGTCGCACTGTTAGT -s Anc2.Anc2refChr15 42223 22 - 86568 -------------------------------------------ATTCAAGTGTCGCACTGTTAGT -s mr.mrrefChr5 81710 59 + 294540 TCACAATTGAGATCATGATGTCACTTTTGAATCCTCA------ATCCAGATGTCACCCTGTTAGT -s simCow_chr6.simCow.chr6 376967 16 - 602619 -------------------------------------------------GTGTCACACTGTTATT -s simDog_chr6.simDog.chr6 377724 22 - 593897 -------------------------------------------ATTCAAGTGTCGCACTTCTAGT -s simHuman_chr6.simHuman.chr6 305589 25 - 601863 ----------------------------------TTT------ATCCAGATGTTGCACTGTTGAT -s simRat_chr6.simRat.chr6 218561 59 + 647215 CCACCATTTACGTCATGGTGTAGCTTTTGAATCCTAA------ATCCAGATGTCACCCTGTTAGT - -a -s simMouse_chr6.simMouse.chr6 227611 15 + 636262 CAATATGGTATTATG -s Anc0.Anc0refChr5 39619 12 - 87904 CTATAT---CATATA -s Anc1.Anc1refChr7 4618 15 - 47259 CTATATAGTCATATA -s Anc2.Anc2refChr15 42265 12 - 86568 CTATAT---CATATA -s mr.mrrefChr5 81782 15 + 294540 CAATATGGTATTATG -s simCow_chr6.simCow.chr6 377003 12 - 602619 CTTTAT---CCTATA -s simDog_chr6.simDog.chr6 377765 12 - 593897 ATATAT---CATATA -s simHuman_chr6.simHuman.chr6 305634 15 - 601863 CTATATAGTTATATT -s simRat_chr6.simRat.chr6 218633 15 + 647215 TAATATGGTATTATG - -a -s simMouse_chr6.simMouse.chr6 227626 7 + 636262 TAAGCCA -s Anc0.Anc0refChr5 39631 7 - 87904 TAATCGA -s Anc1.Anc1refChr7 4633 7 - 47259 TAATCGA -s Anc2.Anc2refChr15 42277 7 - 86568 TAATTGC -s mr.mrrefChr5 81797 7 + 294540 TAAGCCA -s simCow_chr6.simCow.chr6 377015 7 - 602619 TAATTGC -s simDog_chr6.simDog.chr6 377777 7 - 593897 TAATTGC -s simHuman_chr6.simHuman.chr6 305658 7 - 601863 CTATCTA -s simRat_chr6.simRat.chr6 218648 7 + 647215 TAAGCCA - -a -s simMouse_chr6.simMouse.chr6 227633 2 + 636262 GA -s Anc0.Anc0refChr5 39638 2 - 87904 GA -s Anc1.Anc1refChr7 4640 2 - 47259 GA -s Anc2.Anc2refChr15 42284 2 - 86568 CA -s mr.mrrefChr5 81804 2 + 294540 GA -s simCow_chr6.simCow.chr6 377022 2 - 602619 CA -s simDog_chr6.simDog.chr6 377784 2 - 593897 CA -s simHuman_chr6.simHuman.chr6 305665 2 - 601863 GA -s simRat_chr6.simRat.chr6 218673 2 + 647215 GA - -a -s simMouse_chr6.simMouse.chr6 227635 76 + 636262 GTACTTGCTCAATCCCTCACACTCATTCTACCATGTGTGAAAGTATATACTATTGTAGCAACATGTGTAAACATTG -s Anc0.Anc0refChr5 39641 75 - 87904 GCCCCTATTTAGTCCCTCACAATCTTTCCATCATGAAGGTAATTGTATACCATCATAGCAATATGTGTCATCATT- -s Anc1.Anc1refChr7 4643 76 - 47259 GCCCCTATTTAGTCCCTCACAATCTTTCCATCATGAAGGTAATTGTATACCATCATAGCAATATGTGTCATCATTG -s Anc2.Anc2refChr15 42287 75 - 86568 GCCCCTATTTAGTCCCTTACAATCTTTCCATCATGAAGGTAATTGTATACCATCATAGCATTATGTATCATCATT- -s mr.mrrefChr5 81806 76 + 294540 GTCCCTGTTCAATCCCTCACACTCATTCTACCATGAGTGAAAGTATATACTATTGTAGCAACATGTGTAAACATTG -s simCow_chr6.simCow.chr6 377025 75 - 602619 GGCCCTATTTAGTCCCTTAGATCCTTTCCATCATGAATGAACATATACACCAGCATAGCATTATGTATCATCATT- -s simDog_chr6.simDog.chr6 377787 75 - 593897 GCCCCTATTTAGTCCCTTGCCATCTTTCCATCATGAAGGTAATTGTATACCATCATAGCATTATGTATCATCATT- -s simHuman_chr6.simHuman.chr6 305668 62 - 601863 GCCCCTATCTAGTAATTCACAATCTTTTCATCATGA--------------CACCATAGCTATATGTGTCACCATTG -s simRat_chr6.simRat.chr6 218675 76 + 647215 GTCCCTGTTCAATCCCTCACACTCGTCCTACCATGAGCGAAAGTATATACTATTGTGGCAAAATGTATAAACATTG - -a -s simMouse_chr6.simMouse.chr6 227711 81 + 636262 GGGCACTATTGAGAGTATGGCAATGTCCATACAGGTCGTTAATGTTCATACAGCGTCATTATTTAGGGTGGCTTCAGGTTC -s Anc0.Anc0refChr5 39742 61 - 87904 GGGCACTATTGGGAGTATGGCAATGGCCGTACAT--------------------ATCTTCACTTTGGGTCTCTCCAGGTTC -s Anc1.Anc1refChr7 4745 61 - 47259 GGGCACTATTGGGAGTATGGCAATGGCCGTACAT--------------------ATCTTCACTTTGGGTCTCTCCAGGTTC -s Anc2.Anc2refChr15 42388 61 - 86568 ATGCACTATTGGGAGTAGGGCAATGGCCGTAAAT--------------------ATCTTCCCTTTAGGTCTCTCCAGGTTC -s mr.mrrefChr5 81882 61 + 294540 GGGCACTATTGAGAGTATGGCAATGTCCATACAG--------------------GTCATTATTTAGGGTCGCTTCAGGTTC -s simCow_chr6.simCow.chr6 377126 61 - 602619 AAGCACCATTGGGAGTAAGACAATGGCCGAAGAT--------------------ATCTTCCCTTTAGATCTCTCCAGGTTC -s simDog_chr6.simDog.chr6 377888 60 - 593897 ATGCACTATTGGGAGTAGGGCAATGGCC-TAAAT--------------------ATCTTCCCTTTAGGTCTCTTCAGGCTC -s simHuman_chr6.simHuman.chr6 305756 61 - 601863 GGGCACTATTGGGAGTTTGGGAATGGCTGTACAT--------------------ATCTTCACTTTGGGTCTCTCCAGGTTC -s simRat_chr6.simRat.chr6 218751 60 + 647215 AGGCGC-ATTGTGAGTATGGCAATGTCCATACAG--------------------GTCACTATTGAGGGGCGCTTCAGGTTC - -a -s simMouse_chr6.simMouse.chr6 227792 5 + 636262 AGAAA -s Anc0.Anc0refChr5 39804 5 - 87904 AAAAA -s Anc1.Anc1refChr7 4807 5 - 47259 AAAAA -s Anc2.Anc2refChr15 42450 5 - 86568 AAAAA -s mr.mrrefChr5 81943 5 + 294540 AAAAA -s simCow_chr6.simCow.chr6 377188 5 - 602619 AAAAC -s simDog_chr6.simDog.chr6 377949 5 - 593897 AAAAA -s simHuman_chr6.simHuman.chr6 305818 5 - 601863 AAAAA -s simRat_chr6.simRat.chr6 218811 5 + 647215 AAAAA - -a -s simMouse_chr6.simMouse.chr6 227797 27 + 636262 TACATGGGGCTGAACATTGAAATTATC -s Anc0.Anc0refChr5 39809 27 - 87904 CACATGGGGCTAAACATTGAAAAGATA -s Anc1.Anc1refChr7 4812 27 - 47259 CACATGGGGCTAAACATTGAAAAGATA -s Anc2.Anc2refChr15 42456 27 - 86568 CACAGGGGGCTAAACATTGAAAAGATA -s mr.mrrefChr5 81948 27 + 294540 TACATGGGGCTGAACATTGAAATTATA -s simCow_chr6.simCow.chr6 377194 27 - 602619 CATGGGGGGCTAAACATTGAAAAACTG -s simDog_chr6.simDog.chr6 377955 27 - 593897 CACAGAGGGCTAAACACTGAAAAGATA -s simHuman_chr6.simHuman.chr6 305823 27 - 601863 CACATGGGACTAGACATTGAAAAGATA -s simRat_chr6.simRat.chr6 218816 27 + 647215 TACATGGGGCTGTACATTGAAACTATA - -a -s simMouse_chr6.simMouse.chr6 227824 22 + 636262 GTTCCATTATGGAGGGTTCATA -s Anc0.Anc0refChr5 39836 11 - 87904 GAT-----------GATCTATA -s Anc1.Anc1refChr7 4839 11 - 47259 GAT-----------GATCTATA -s Anc2.Anc2refChr15 42483 11 - 86568 GAA-----------GATCTATA -s mr.mrrefChr5 81975 22 + 294540 GTTCCATTATGGAGGGTCCATA -s simCow_chr6.simCow.chr6 377221 11 - 602619 GAA-----------GGTTTATA -s simDog_chr6.simDog.chr6 377993 11 - 593897 GAA-----------AATCTATA -s simHuman_chr6.simHuman.chr6 305850 11 - 601863 GGT-----------GATCTATA -s simRat_chr6.simRat.chr6 218843 22 + 647215 GTTTCATTGTGGAGGGTCCATA - -a -s simMouse_chr6.simMouse.chr6 227846 50 + 636262 TGTTAATAATCACCATACAGAAAATTAGAAATAATATTAGAAATGACAAA -s Anc0.Anc0refChr5 39850 38 - 87904 TGTTAATAACCCCACTACAG------------AATACTAGAAATGTCAAA -s Anc1.Anc1refChr7 4853 38 - 47259 TGTTAATAACCCCACTACAG------------AATACTAGAAATGTCAAA -s Anc2.Anc2refChr15 42497 38 - 86568 TGTTAATGACCCCACTACAG------------AATACTAGAAATGTCAAA -s mr.mrrefChr5 81997 50 + 294540 TGTTAATAATCCCCATACAGAAAATTAGAAATAATATTAGAAATGTCAAA -s simCow_chr6.simCow.chr6 377235 37 - 602619 TGTTAATGACCCCACTTCAG------------AATAC-AGAAACAACAAA -s simDog_chr6.simDog.chr6 378006 38 - 593897 TGATAACGACCCTACTACAG------------AATACTAGAAATGTCAAA -s simHuman_chr6.simHuman.chr6 305864 38 - 601863 TGTTAATAACTCCACTACAG------------AATACTAGAAATGTCAAA -s simRat_chr6.simRat.chr6 218865 50 + 647215 TGTAGATAATCCCCATACAGAATATCATAGATGATATTAGCAATGTCAAA - -a -s simMouse_chr6.simMouse.chr6 227896 5 + 636262 CGGTG -s Anc0.Anc0refChr5 39889 5 - 87904 CTATG -s Anc1.Anc1refChr7 4892 5 - 47259 CTATG -s Anc2.Anc2refChr15 42536 5 - 86568 CTATG -s mr.mrrefChr5 82047 5 + 294540 CTATG -s simCow_chr6.simCow.chr6 377273 5 - 602619 CTATG -s simDog_chr6.simDog.chr6 378045 5 - 593897 ATATG -s simHuman_chr6.simHuman.chr6 305903 5 - 601863 CTATA -s simRat_chr6.simRat.chr6 218915 5 + 647215 TTATG - -a -s simMouse_chr6.simMouse.chr6 227901 9 + 636262 CCTATATAT -s Anc0.Anc0refChr5 39894 9 - 87904 TTTTTACAC -s Anc1.Anc1refChr7 4897 9 - 47259 TTTTTACAC -s Anc2.Anc2refChr15 42548 9 - 86568 TTTTTACAT -s mr.mrrefChr5 82052 9 + 294540 CTTATATAC -s simCow_chr6.simCow.chr6 377285 9 - 602619 TTTTGGCAT -s simDog_chr6.simDog.chr6 378057 9 - 593897 TTTTTACAT -s simHuman_chr6.simHuman.chr6 305908 9 - 601863 ATTCTACAC -s simRat_chr6.simRat.chr6 218920 9 + 647215 CTGATGTAC - -a -s simMouse_chr6.simMouse.chr6 227910 8 + 636262 ACTGCATG -s Anc0.Anc0refChr5 39905 8 - 87904 GTTGTATG -s Anc1.Anc1refChr7 4908 8 - 47259 GTTGTATG -s Anc2.Anc2refChr15 42559 8 - 86568 GTTGTATG -s mr.mrrefChr5 82061 8 + 294540 ATTGCATG -s simCow_chr6.simCow.chr6 377296 8 - 602619 GTTGCATG -s simDog_chr6.simDog.chr6 378068 8 - 593897 ACCATTAG -s simHuman_chr6.simHuman.chr6 305919 8 - 601863 GTTGGATG -s simRat_chr6.simRat.chr6 218929 8 + 647215 ATTGCATA - -a -s simMouse_chr6.simMouse.chr6 227918 49 + 636262 TGCTGTGTGGATAGATACTCCAACCTTTATAATATCTTTATAATATTCT -s Anc0.Anc0refChr5 39914 32 - 87904 TGTTGCATAGGGAAATGTTACAAA-----------CTTTTTT------G -s Anc1.Anc1refChr7 4917 37 - 47259 TGTTGCATAGGGAAATGTTACAAA-----------CTTTTTTCTA-GCG -s Anc2.Anc2refChr15 42568 32 - 86568 TGTTGCATAGGGAAATGTTACAAA-----------CTTTTTT------G -s mr.mrrefChr5 82069 38 + 294540 TGCTGTGTGGATAGATATTCCAAC-----------CTTTATAATATTCT -s simCow_chr6.simCow.chr6 377305 32 - 602619 TGTTGCATAGGCAAATGTTCCAAA-----------CTTTTTA------G -s simDog_chr6.simDog.chr6 378077 25 - 593897 CTTT-------GAAATGTCACATA-----------TGATTTT------G -s simHuman_chr6.simHuman.chr6 305928 37 - 601863 TGTTGCATAGGGAAATGTTGCAAA-----------CTTTTTTCTA-GCA -s simRat_chr6.simRat.chr6 218937 38 + 647215 TGATGTGTGGTTAGATCTTCCAGC-----------CCTTATAATATTCT - -a -s simMouse_chr6.simMouse.chr6 227967 38 + 636262 TTCTGTAGTGGAGTTATCAACACGTCAAGCATCTTCCT -s Anc0.Anc0refChr5 39946 38 - 87904 GTCTGTAGTGAAGGTATTAGCCTGTTAAAGACCTTCCT -s Anc1.Anc1refChr7 4954 38 - 47259 GTCTGTAGTGAAGGTATTAGCCTGTTAAAGACCTTCCT -s Anc2.Anc2refChr15 42600 38 - 86568 ATCTTTAGTTAAGGTATTAGCCTGTTAAAGACTTTCCT -s mr.mrrefChr5 82107 38 + 294540 GTCTGTAGTGGAGTTATCAACATGTCAAGCATCTTCCT -s simCow_chr6.simCow.chr6 377338 38 - 602619 ATCTATAGTTGAGGTATCAACATGTTACAGATTTTCCG -s simDog_chr6.simDog.chr6 378102 37 - 593897 ATTTTTACATAAACGATTAGGCT-TTAAAGGCTACCGT -s simHuman_chr6.simHuman.chr6 305965 37 - 601863 GTCTGTAGTGACGGTATTACCCTGTTATTGA-CTTCCT -s simRat_chr6.simRat.chr6 218975 36 + 647215 GTCTGTAGTCGAGTTAT--ACATGTCAAGCATTTTCAT - -a -s simMouse_chr6.simMouse.chr6 228005 7 + 636262 GGTGTTC -s Anc0.Anc0refChr5 39997 7 - 87904 GGGGTTT -s Anc1.Anc1refChr7 5005 7 - 47259 GGGGTTT -s Anc2.Anc2refChr15 42651 7 - 86568 GGGGTTT -s mr.mrrefChr5 82145 7 + 294540 GGTGTTT -s simCow_chr6.simCow.chr6 377389 7 - 602619 GGGGTTT -s simDog_chr6.simDog.chr6 378152 3 - 593897 TGA---- -s simHuman_chr6.simHuman.chr6 306015 7 - 601863 GGGGTTT -s simRat_chr6.simRat.chr6 219011 7 + 647215 GGTGTTT - -a -s simMouse_chr6.simMouse.chr6 228012 2 + 636262 TA -s Anc0.Anc0refChr5 40004 2 - 87904 TA -s Anc1.Anc1refChr7 5012 2 - 47259 TA -s Anc2.Anc2refChr15 42658 2 - 86568 TC -s mr.mrrefChr5 82152 2 + 294540 TA -s simCow_chr6.simCow.chr6 377396 2 - 602619 TC -s simHuman_chr6.simHuman.chr6 306022 2 - 601863 TA -s simRat_chr6.simRat.chr6 219058 2 + 647215 TA - -a -s simMouse_chr6.simMouse.chr6 228014 69 + 636262 GAGTAGCTTAGGTCTTGGTCATTTTGCGGGTCAATATGCTCTAGAGTGTATATGGATCCAATTTAGCTG -s Anc0.Anc0refChr5 40006 65 - 87904 GAG----TTTTGTCTTAGTCACTCTGTGAGTCACTAGGCTCTAGAGGATATATTGACCCAAATTATCAG -s Anc1.Anc1refChr7 5014 65 - 47259 GAG----TTTTGTCTTAGTCACTCTGTGAGTCACTAGGCTCTAGAGGATATATTGACCCAAATTATCAG -s Anc2.Anc2refChr15 42660 65 - 86568 GAG----TCTTGTTGTAGGCACTCAGTGAATCACTAGGCTCTAGAGGATAAATTGACCCAAATTATCAG -s mr.mrrefChr5 82154 69 + 294540 GAGTAGCTTAGGTCTTGGTCATTTTGTGGGTCAATATGCTCTAGAGTGTATATGGATCCAATTTAGCTG -s simCow_chr6.simCow.chr6 377404 63 - 602619 GAG----TCTTGTTGTAGGCAC--GGTCAATTGATAAGCTCTAGAGGATACATTCACCCATATTATCAG -s simDog_chr6.simDog.chr6 378155 52 - 593897 ----------------AGGCCCTCATTGAATCACTAGGCACTAAAGGATAAATTGGCCCAAA-TATCAT -s simHuman_chr6.simHuman.chr6 306024 64 - 601863 GAG----TTCTGTCTTAGTCACTGTGTGAGTCAGTAGGCTC-AGAGGATATATTGACCTGAATTATCAG -s simRat_chr6.simRat.chr6 219060 69 + 647215 GAGTAGCTTAGGTCTTGGTTGTTTTGTGGGTCAATATGCTCTAGAGTGTATATGGATCCAACTTAGCTG - -a -s simMouse_chr6.simMouse.chr6 228083 13 + 636262 GGTCCTAATTTGT -s Anc0.Anc0refChr5 40072 13 - 87904 CGGCCTAAATCAT -s Anc1.Anc1refChr7 5080 13 - 47259 CGGCCTAAATCAT -s Anc2.Anc2refChr15 42726 13 - 86568 CGGCCTAAATCAT -s mr.mrrefChr5 82223 13 + 294540 GGTCCTAATTTGT -s simCow_chr6.simCow.chr6 377468 13 - 602619 TGGCCTAAATCAT -s simDog_chr6.simDog.chr6 378208 13 - 593897 CAGCCTAATTCAT -s simHuman_chr6.simHuman.chr6 306089 13 - 601863 AGGCCTAAATAAT -s simRat_chr6.simRat.chr6 219129 13 + 647215 GGTCCTAATGTGT - -a -s simMouse_chr6.simMouse.chr6 228096 16 + 636262 GACAAGACAGCTGTTT -s Anc0.Anc0refChr5 40086 15 - 87904 GGC-AGACAGCTGTCT -s Anc1.Anc1refChr7 5094 15 - 47259 GGC-AGACAGCTGTCT -s Anc2.Anc2refChr15 42740 15 - 86568 TGC-AGACGGCTGTCT -s mr.mrrefChr5 82237 16 + 294540 GGCAAGACAGCTGTTT -s simCow_chr6.simCow.chr6 377482 15 - 602619 TGC-AGAGTGCTGTCT -s simDog_chr6.simDog.chr6 378222 15 - 593897 TGT-GGACGGCTGTCT -s simHuman_chr6.simHuman.chr6 306103 15 - 601863 GGC-AGACAGCTATCT -s simRat_chr6.simRat.chr6 219143 16 + 647215 GGCAAGACAGCCGTTT - -a -s simMouse_chr6.simMouse.chr6 228112 14 + 636262 TAACAGTCCTACTT -s Anc0.Anc0refChr5 40105 14 - 87904 TAACAGTCCTACTT -s Anc1.Anc1refChr7 5113 14 - 47259 TAACAGTCCTACTT -s Anc2.Anc2refChr15 42759 14 - 86568 TCACAGGTCTGCTT -s mr.mrrefChr5 82253 14 + 294540 TAACAGTCCTACTT -s simCow_chr6.simCow.chr6 377499 14 - 602619 TTGCAGGTCTGCTC -s simDog_chr6.simDog.chr6 378241 14 - 593897 TCACAGGTCTGCTT -s simHuman_chr6.simHuman.chr6 306122 14 - 601863 CAACAGTCCTACTT -s simRat_chr6.simRat.chr6 219159 14 + 647215 TAAAAGTCCAACTT - -a -s simMouse_chr6.simMouse.chr6 228126 91 + 636262 ACTGATGGCTATCTTTAGCAATGAGGTCATATTGAGTGTAGTCATAGCTCATGCTATTAGTTGTTCGTGATCATCTTAGAGCCCACTGATC -s Anc0.Anc0refChr5 40120 91 - 87904 ACTACTTGTTATCTCTAGCAATGAGATGATATTGAATGTAGTAACTGAGCCTGTTATTGGTTGATGCCAGACACCTTAGGCCCCTTTAATC -s Anc1.Anc1refChr7 5128 91 - 47259 ACTACTTGTTATCTCTAGCAATGAGATGATATTGAATGTAGTAACTGAGCCTGTTATTGGTTGATGCCAGACACCTTAGGCCCCTTTAATC -s Anc2.Anc2refChr15 42774 91 - 86568 ACTACTTATTATCTCTGGCTATCATATGGTATTGAATGTAATAACTGAGCCTGTTATTGGTTGATGCGAGACACCTTAGGCCCCTTTAATC -s mr.mrrefChr5 82267 91 + 294540 ACCGATGGCTATCTTTAGCAATGAGGTCATATTGAGTGTAGTCATAGCTCATGCTATTAGTTGTTGGCGATCACCTTAGACCCCATTGATC -s simCow_chr6.simCow.chr6 377514 90 - 602619 ACTACTTACTGTCTCTGACTATCAAATGGTA-TGAATGCAATACCTGAGCCTGTTATTGGCTGATGCTGGACACCTTAGGCCCCTTTACTC -s simDog_chr6.simDog.chr6 378256 89 - 593897 ACTGCTTATTATGTTTGGCTATCCTGAG-TATTGAATGTAATAACTAAGCCTGCTATTGGTTTATGCGATATAACTTATACTCCTTTAAC- -s simHuman_chr6.simHuman.chr6 306137 91 - 601863 ACTACTCGATATCTCTAGCAAAGAGATGATATTGTATGTAGTAAGTGAGCCTGTTATTCGTTGATGCCAGACACCTTAGGCCCCTTTCATT -s simRat_chr6.simRat.chr6 219173 91 + 647215 ACCGAGGCTTATCTTTAGCAATGAGGCCATATTGCGTGTAGTCACGGCTCATGCTATCAGTTGTTGGCGACCACCTTAGACCCCATTGATC - -a -s simMouse_chr6.simMouse.chr6 228217 7 + 636262 AAACACA -s Anc0.Anc0refChr5 40212 4 - 87904 AAA---A -s Anc1.Anc1refChr7 5220 4 - 47259 AAA---A -s Anc2.Anc2refChr15 42866 4 - 86568 AAC---A -s mr.mrrefChr5 82359 7 + 294540 AAACACA -s simCow_chr6.simCow.chr6 377605 1 - 602619 A------ -s simDog_chr6.simDog.chr6 378348 3 - 593897 -AC---A -s simHuman_chr6.simHuman.chr6 306229 4 - 601863 AAA---A -s simRat_chr6.simRat.chr6 219265 7 + 647215 AAACATG - -a -s simMouse_chr6.simMouse.chr6 228224 20 + 636262 ATCAACCCCTACTAGGTTTC -s Anc0.Anc0refChr5 40216 15 - 87904 GTCA-----TACTAAGTTTC -s Anc1.Anc1refChr7 5224 20 - 47259 GTCAACCCCTACTAAGTTTC -s Anc2.Anc2refChr15 42870 15 - 86568 GTCA-----TACTAAGTTTT -s mr.mrrefChr5 82366 20 + 294540 GTCAACCCCTACTAGGTTTC -s simCow_chr6.simCow.chr6 203104 3 + 602619 -----------------TTT -s simDog_chr6.simDog.chr6 378353 15 - 593897 GTCA-----TACTAAGTTTT -s simHuman_chr6.simHuman.chr6 306233 20 - 601863 GTCAACCCCTACTAAGATTC -s simRat_chr6.simRat.chr6 219272 20 + 647215 GTCAACCCGTACTAGGTTTC - -a -s simMouse_chr6.simMouse.chr6 228244 1 + 636262 G -s Anc0.Anc0refChr5 40232 1 - 87904 G -s Anc1.Anc1refChr7 5245 1 - 47259 G -s Anc2.Anc2refChr15 42886 1 - 86568 G -s mr.mrrefChr5 82386 1 + 294540 G -s simCow_chr6.simCow.chr6 203108 1 + 602619 G -s simDog_chr6.simDog.chr6 378369 1 - 593897 G -s simHuman_chr6.simHuman.chr6 306254 1 - 601863 G -s simRat_chr6.simRat.chr6 219292 1 + 647215 G - -a -s simMouse_chr6.simMouse.chr6 228245 37 + 636262 TACTTTTTGAGAGTAGACCTTATGAGAGCTGAGGTAA -s Anc0.Anc0refChr5 40233 9 - 87904 TATCTTATG---------------------------- -s Anc1.Anc1refChr7 5246 37 - 47259 TATCTTATGAGAGTGGACCCTAGGAGCACAGAGATGA -s Anc2.Anc2refChr15 42887 9 - 86568 TATCTTATG---------------------------- -s mr.mrrefChr5 82387 37 + 294540 TACTTTTTGAGAGTAGACCTTATGAGAGCAGAGGTAA -s simCow_chr6.simCow.chr6 203109 9 + 602619 CATCTTGTG---------------------------- -s simDog_chr6.simDog.chr6 378371 9 - 593897 TATCTTATA---------------------------- -s simHuman_chr6.simHuman.chr6 306255 37 - 601863 TATCTTCTGAGAGTGGACCCTAGGAGCACAGAGATGA -s simRat_chr6.simRat.chr6 219293 37 + 647215 TACTTTATGAGAGTAGACTTTATGGGAGCAGAAGCAA - -a -s simMouse_chr6.simMouse.chr6 228282 2 + 636262 GA -s Anc1.Anc1refChr7 5283 2 - 47259 GA -s mr.mrrefChr5 82424 2 + 294540 GA -s simHuman_chr6.simHuman.chr6 306325 2 - 601863 GA -s simRat_chr6.simRat.chr6 219330 2 + 647215 CA - -a -s simMouse_chr6.simMouse.chr6 228284 46 + 636262 GACTATAACCAAGGGCCATTATTTTTCCAGGAGGGAGTAGCATAAC -s Anc0.Anc0refChr5 40242 1 - 87904 ---------------------------------------------C -s Anc1.Anc1refChr7 5287 46 - 47259 AACTATAACTAATGATCCTTATTTTTACAAGAGTGAGAAGTATTGC -s Anc2.Anc2refChr15 42896 1 - 86568 ---------------------------------------------C -s mr.mrrefChr5 82428 46 + 294540 GACTATAACCAAGGGCCCTTATTTTTCCAGGAGGGAGTAGTATAAC -s simCow_chr6.simCow.chr6 203118 1 + 602619 ---------------------------------------------C -s simDog_chr6.simDog.chr6 378380 1 - 593897 ---------------------------------------------C -s simHuman_chr6.simHuman.chr6 306329 46 - 601863 AACTATAACTAATGATCCTTATTTTTACAAGAGTGAGAAGTATTGC -s simRat_chr6.simRat.chr6 219334 46 + 647215 GATTCTGACCAAGGGCCCTTACTTTCCCAGGAGGGAGTAGTGTAAC - -a -s simMouse_chr6.simMouse.chr6 228330 7 + 636262 ATAGTAC -s Anc0.Anc0refChr5 40249 7 - 87904 ATAGTAC -s Anc1.Anc1refChr7 5339 7 - 47259 ATAGTAC -s Anc2.Anc2refChr15 42903 7 - 86568 ATAGTAC -s mr.mrrefChr5 82474 7 + 294540 ATAGTAC -s simCow_chr6.simCow.chr6 203125 7 + 602619 GTAGTGT -s simDog_chr6.simDog.chr6 378387 7 - 593897 ATAGTAC -s simHuman_chr6.simHuman.chr6 306381 7 - 601863 ATAGTAC -s simRat_chr6.simRat.chr6 219380 7 + 647215 ATAACTC - -a -s simMouse_chr6.simMouse.chr6 228337 21 + 636262 AAAACACAAGCTTAATCTAAG -s Anc0.Anc0refChr5 40256 16 - 87904 AAAACCCATTCTTAAT----- -s Anc1.Anc1refChr7 5346 16 - 47259 AAAACCCATTCTTAAT----- -s Anc2.Anc2refChr15 42910 16 - 86568 AAAACCCATTCTTAGT----- -s mr.mrrefChr5 82481 21 + 294540 AAAACCCAAGCTTAATCCAAG -s simCow_chr6.simCow.chr6 203132 16 + 602619 AAAGCCTATTCTGAGC----- -s simDog_chr6.simDog.chr6 378394 16 - 593897 AAAAACCATCCTTAGT----- -s simHuman_chr6.simHuman.chr6 306388 16 - 601863 AATACCCATTCTTAAT----- -s simRat_chr6.simRat.chr6 219388 21 + 647215 AAAACCCAAACTTAACCCAAG - -a -s simMouse_chr6.simMouse.chr6 228358 6 + 636262 TCAGGC -s Anc0.Anc0refChr5 40272 6 - 87904 CCAGGC -s Anc1.Anc1refChr7 5362 6 - 47259 CCAGGC -s Anc2.Anc2refChr15 42926 6 - 86568 CCATGC -s mr.mrrefChr5 82505 6 + 294540 CCAGGC -s simCow_chr6.simCow.chr6 203148 6 + 602619 CCAAGC -s simDog_chr6.simDog.chr6 378410 6 - 593897 CCATGC -s simHuman_chr6.simHuman.chr6 306404 6 - 601863 CCAGGC -s simRat_chr6.simRat.chr6 219412 6 + 647215 CAAGTC - -a -s simMouse_chr6.simMouse.chr6 228364 1 + 636262 T -s Anc0.Anc0refChr5 40278 1 - 87904 T -s Anc1.Anc1refChr7 5368 1 - 47259 T -s Anc2.Anc2refChr15 42932 1 - 86568 T -s mr.mrrefChr5 82511 1 + 294540 T -s simCow_chr6.simCow.chr6 203154 1 + 602619 T -s simDog_chr6.simDog.chr6 378421 1 - 593897 C -s simHuman_chr6.simHuman.chr6 306410 1 - 601863 T -s simRat_chr6.simRat.chr6 219418 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 228365 3 + 636262 TGA -s Anc0.Anc0refChr5 40279 3 - 87904 AGA -s Anc1.Anc1refChr7 5369 3 - 47259 AGA -s Anc2.Anc2refChr15 42933 3 - 86568 AAA -s mr.mrrefChr5 82512 3 + 294540 TGA -s simCow_chr6.simCow.chr6 203158 3 + 602619 ATA -s simDog_chr6.simDog.chr6 378422 3 - 593897 TAA -s simHuman_chr6.simHuman.chr6 306411 3 - 601863 AGA -s simRat_chr6.simRat.chr6 219419 3 + 647215 TGC - -a -s simMouse_chr6.simMouse.chr6 228368 49 + 636262 CTCTGTTTGACAACATGCTATGCAGGCACATTGTTCAGCTGCTGCTATT -s Anc0.Anc0refChr5 40282 46 - 87904 C---GTTTGACAACAGACTATACACTTACACTATTCAGCAGCTGCTATT -s Anc1.Anc1refChr7 5372 46 - 47259 C---GTTTGACAACAGACTATACACTTACACTATTCAGCAGCTGCTATT -s Anc2.Anc2refChr15 42936 46 - 86568 T---GTTTGACAGCAGACTATACACTTACACTATTCAACAGCTGCTATT -s mr.mrrefChr5 82515 49 + 294540 CTCTGTTTGACAACATGCTATGCAGTCACACTGTTCAGCTGCTGCTATT -s simCow_chr6.simCow.chr6 203161 46 + 602619 T---GTTTGATAGCAGACTATACACTTACACTATCCACCAGCTGCTATT -s simDog_chr6.simDog.chr6 378425 46 - 593897 T---GTTTGACAGCAGACTATACACTTATACTATTCGACTGCCACTATT -s simHuman_chr6.simHuman.chr6 306414 46 - 601863 C---ATTTGCCGACAAACAGTACGCTTACACTATTCAGCAGCTGCTATG -s simRat_chr6.simRat.chr6 219426 49 + 647215 CTCTGTTTGACAACATGCTATGCAGTCACACTGTTCAGCTGCTGATATT - -a -s simMouse_chr6.simMouse.chr6 228417 23 + 636262 TTCTGATACAATATTGTTCTGAG -s Anc0.Anc0refChr5 40328 23 - 87904 TTCATATTCAACACCCTTCTGAG -s Anc1.Anc1refChr7 5418 23 - 47259 TTCATATTCAACACCCTTCTGAG -s Anc2.Anc2refChr15 42982 23 - 86568 TTCATATTCAACACCCTTCTGAG -s mr.mrrefChr5 82564 23 + 294540 TTCTGATTCAATACTCTTCTGAG -s simCow_chr6.simCow.chr6 203207 23 + 602619 TTCATATGCAACACTCTTTCAAG -s simDog_chr6.simDog.chr6 378471 23 - 593897 TTCATCTTCAATGCCCCTCTGAG -s simHuman_chr6.simHuman.chr6 306509 23 - 601863 TTCATATTCAACACCCTTCTGAG -s simRat_chr6.simRat.chr6 219475 23 + 647215 TTCTGGTTCAAAACTCTTCTGAG - -a -s simMouse_chr6.simMouse.chr6 228440 12 + 636262 TGCTAGTTTTAT -s Anc0.Anc0refChr5 40439 9 - 87904 TGATTGTTC--- -s Anc1.Anc1refChr7 5529 9 - 47259 TGATTGTTC--- -s Anc2.Anc2refChr15 43093 9 - 86568 TGATTGTTT--- -s mr.mrrefChr5 82587 12 + 294540 TGTTTGTTTCAT -s simCow_chr6.simCow.chr6 203307 9 + 602619 TGTTTGTTT--- -s simDog_chr6.simDog.chr6 378582 9 - 593897 TGATTATTT--- -s simHuman_chr6.simHuman.chr6 306643 9 - 601863 TGGTTGTTC--- -s simRat_chr6.simRat.chr6 219498 12 + 647215 TATTTGTTTCAT - -a -s simMouse_chr6.simMouse.chr6 228452 47 + 636262 GCTACATTCTGCACACCACACAATCGAATCATAATATACTTGCTGAG -s Anc0.Anc0refChr5 40448 40 - 87904 ------TT-TGCAGACCACACACTAAAAGAATCATTCACTAGCCCAG -s Anc1.Anc1refChr7 5538 41 - 47259 ------TTCTGCAGACCACACACTAAAAGAATCATTCACTAGCCCAG -s Anc2.Anc2refChr15 43102 40 - 86568 ------TT-TGCAGACCACACACTAAAAGAATCACTCACTAGCCAAG -s mr.mrrefChr5 82603 47 + 294540 GCCACATTCTGCACACCACACAATCGAATAATAATTTACTTGCTCAG -s simCow_chr6.simCow.chr6 203316 32 + 602619 ------CT-TGCACACCACAAATGCAAG-------GCACTAGCTGA- -s simDog_chr6.simDog.chr6 378591 40 - 593897 ------TT-TGCAGACCACACACTAAAAGAATCACTCACTAACCAAG -s simHuman_chr6.simHuman.chr6 306652 41 - 601863 ------TTCTGCCTGCCATACACTAAAAAAATCATTCACTAGCCCAG -s simRat_chr6.simRat.chr6 219514 47 + 647215 GCCACATTCTGCACATCACACAATTGAATAATAATTGACTTGAACTC - -a -s simMouse_chr6.simMouse.chr6 228499 1 + 636262 T -s Anc0.Anc0refChr5 40488 1 - 87904 T -s Anc1.Anc1refChr7 5579 1 - 47259 T -s Anc2.Anc2refChr15 43142 1 - 86568 T -s mr.mrrefChr5 82650 1 + 294540 T -s simDog_chr6.simDog.chr6 378631 1 - 593897 T -s simHuman_chr6.simHuman.chr6 306693 1 - 601863 C -s simRat_chr6.simRat.chr6 219782 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 228500 47 + 636262 GGAGCCGGCTTGATCCTCTGTGCTAAATTTGTTTTAAACACTTCTGG -s Anc0.Anc0refChr5 40489 47 - 87904 GGAGCAGTCTAAATTCTCTGTGCCATATTTGTTTTAAACACTTCTGG -s Anc1.Anc1refChr7 5580 47 - 47259 GGAGCAGTCTAAATTCTCTGTGCCATATTTGTTTTAAACACTTCTGG -s Anc2.Anc2refChr15 43144 47 - 86568 GGAGCAGTCTAATTTCTCTATGCTATATATGTTTTAAACACTTCTTG -s mr.mrrefChr5 82651 47 + 294540 GGAGCCGTCTTGATCCTCTGTGCCATATTTGTTTTAAACACTTCTGG -s simCow_chr6.simCow.chr6 203349 47 + 602619 GGAGCAATCTAATTTCCGTATGCTATATCTGTTTTAAACGCTTTTTC -s simDog_chr6.simDog.chr6 378633 47 - 593897 GGAGCAGTCTAGTTTATCTATGCTATATAAGTTTTAAACACCTCTTG -s simHuman_chr6.simHuman.chr6 306694 47 - 601863 AGCACAGTCTAAATTCTCTGTGCCATATTTGTTTTAAACACTTCTGG -s simRat_chr6.simRat.chr6 219783 47 + 647215 GGAGACGTCTTCATCCTCTGTGCCATATTTGTTTTAAACACTTCCGG - -a -s simMouse_chr6.simMouse.chr6 228547 33 + 636262 TTAGGTCCAGTGTGGGATCTAGCCAACTAATTG -s Anc0.Anc0refChr5 40536 33 - 87904 TTTGGTGCAGTGTGGGATTTAGCCGACCAAATG -s Anc1.Anc1refChr7 5627 33 - 47259 TTTGGTGCAGTGTGGGATTTAGCCGACCAAATG -s Anc2.Anc2refChr15 43191 33 - 86568 TTTGGTGCAGTATGGGATTTAACTGACCAAATG -s mr.mrrefChr5 82698 33 + 294540 TTTGGTCCAGTGTGGGATCTAGCCAACTAATTG -s simCow_chr6.simCow.chr6 203396 33 + 602619 TTTGGTGCAGTATGGGATTTAACTGACCTAATG -s simDog_chr6.simDog.chr6 378682 33 - 593897 TTTGTTGCATTATGGGGTTTAACTAACTAGATG -s simHuman_chr6.simHuman.chr6 306741 33 - 601863 TCTGGTGCAGTGTGGGATTTAGCCGACCCAATG -s simRat_chr6.simRat.chr6 219830 33 + 647215 TTTGGTCTAGTATGGGATCTAGCCAGCTAATCA - -a -s simMouse_chr6.simMouse.chr6 228580 1 + 636262 T -s Anc0.Anc0refChr5 40569 1 - 87904 T -s Anc1.Anc1refChr7 5660 1 - 47259 T -s Anc2.Anc2refChr15 43237 1 - 86568 T -s mr.mrrefChr5 82731 1 + 294540 T -s simCow_chr6.simCow.chr6 203442 1 + 602619 T -s simDog_chr6.simDog.chr6 378728 1 - 593897 T -s simHuman_chr6.simHuman.chr6 306774 1 - 601863 T -s simRat_chr6.simRat.chr6 219863 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 228581 5 + 636262 TGACT -s Anc0.Anc0refChr5 40573 5 - 87904 TGACT -s Anc1.Anc1refChr7 5664 5 - 47259 TGACT -s Anc2.Anc2refChr15 43241 5 - 86568 TGACT -s mr.mrrefChr5 82732 5 + 294540 TGACT -s simCow_chr6.simCow.chr6 203446 5 + 602619 TGGCT -s simDog_chr6.simDog.chr6 378732 5 - 593897 TGACT -s simHuman_chr6.simHuman.chr6 306778 5 - 601863 AGACT -s simRat_chr6.simRat.chr6 219864 5 + 647215 TGACT - -a -s simMouse_chr6.simMouse.chr6 228586 6 + 636262 ACATGG -s Anc0.Anc0refChr5 40580 6 - 87904 ACATAA -s Anc1.Anc1refChr7 5671 6 - 47259 ACATAA -s Anc2.Anc2refChr15 43248 6 - 86568 GCATAA -s mr.mrrefChr5 82737 6 + 294540 ACATGG -s simCow_chr6.simCow.chr6 203453 6 + 602619 GCATAA -s simDog_chr6.simDog.chr6 378739 6 - 593897 GCATAA -s simHuman_chr6.simHuman.chr6 306785 6 - 601863 ACATAA -s simRat_chr6.simRat.chr6 219869 6 + 647215 ACATGG - -a -s simMouse_chr6.simMouse.chr6 228592 17 + 636262 ATAATTGACTTCCCATA -s Anc0.Anc0refChr5 40586 10 - 87904 T-------GTTCCTCTA -s Anc1.Anc1refChr7 5677 10 - 47259 T-------GTTCCTCTA -s Anc2.Anc2refChr15 43256 10 - 86568 T-------GTTCTTCTA -s mr.mrrefChr5 82743 10 + 294540 A-------CTTCCTATA -s simCow_chr6.simCow.chr6 203461 10 + 602619 T-------ATTCTTCTA -s simDog_chr6.simDog.chr6 378747 10 - 593897 T-------GTTGTTCAA -s simHuman_chr6.simHuman.chr6 306791 10 - 601863 T-------GTCCCTCTA -s simRat_chr6.simRat.chr6 219875 10 + 647215 A-------CTTCCTATA - -a -s simMouse_chr6.simMouse.chr6 228609 8 + 636262 ACATAAAC -s Anc0.Anc0refChr5 40602 8 - 87904 ACATAAAC -s Anc1.Anc1refChr7 5693 8 - 47259 ACATAAAC -s Anc2.Anc2refChr15 43272 8 - 86568 ACATGAAC -s mr.mrrefChr5 82753 8 + 294540 ACATAAAC -s simCow_chr6.simCow.chr6 203477 8 + 602619 ACCTGTAT -s simDog_chr6.simDog.chr6 378763 8 - 593897 ACATGAAC -s simHuman_chr6.simHuman.chr6 306807 8 - 601863 ACATAACC -s simRat_chr6.simRat.chr6 219885 8 + 647215 ACATAAAC - -a -s simMouse_chr6.simMouse.chr6 228617 4 + 636262 CACT -s Anc0.Anc0refChr5 40610 4 - 87904 GAAT -s Anc1.Anc1refChr7 5701 4 - 47259 GAAT -s Anc2.Anc2refChr15 43282 4 - 86568 GAAT -s mr.mrrefChr5 82761 4 + 294540 CACT -s simCow_chr6.simCow.chr6 203487 4 + 602619 GAAT -s simDog_chr6.simDog.chr6 378773 4 - 593897 AAGT -s simHuman_chr6.simHuman.chr6 306815 4 - 601863 GAAT -s simRat_chr6.simRat.chr6 219893 4 + 647215 CACA - -a -s simMouse_chr6.simMouse.chr6 228621 6 + 636262 GTCAAG -s Anc0.Anc0refChr5 40657 6 - 87904 GCCTTG -s Anc1.Anc1refChr7 5748 6 - 47259 GCCTTG -s Anc2.Anc2refChr15 43329 6 - 86568 GCCTTA -s mr.mrrefChr5 82765 6 + 294540 GTCAAG -s simCow_chr6.simCow.chr6 203534 6 + 602619 GCCTCA -s simDog_chr6.simDog.chr6 378816 6 - 593897 GCCTTA -s simHuman_chr6.simHuman.chr6 306862 6 - 601863 GCCGTG -s simRat_chr6.simRat.chr6 219897 6 + 647215 ATCAAG - -a -s simMouse_chr6.simMouse.chr6 228627 1 + 636262 T -s Anc0.Anc0refChr5 40663 1 - 87904 T -s Anc1.Anc1refChr7 5754 1 - 47259 T -s Anc2.Anc2refChr15 43335 1 - 86568 T -s mr.mrrefChr5 82771 1 + 294540 T -s simCow_chr6.simCow.chr6 203540 1 + 602619 T -s simDog_chr6.simDog.chr6 378822 1 - 593897 T -s simHuman_chr6.simHuman.chr6 306868 1 - 601863 T -s simRat_chr6.simRat.chr6 219908 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 228628 3 + 636262 CTC -s Anc0.Anc0refChr5 40664 3 - 87904 TTA -s Anc1.Anc1refChr7 5755 3 - 47259 TTA -s Anc2.Anc2refChr15 43339 3 - 86568 TCA -s mr.mrrefChr5 82772 3 + 294540 CTC -s simCow_chr6.simCow.chr6 203544 3 + 602619 TCA -s simDog_chr6.simDog.chr6 378826 3 - 593897 TCA -s simHuman_chr6.simHuman.chr6 306869 3 - 601863 TTA -s simRat_chr6.simRat.chr6 219909 3 + 647215 CTC - -a -s simMouse_chr6.simMouse.chr6 228631 6 + 636262 AACTTC -s Anc0.Anc0refChr5 40667 6 - 87904 CACTTC -s Anc1.Anc1refChr7 5758 6 - 47259 CACTTC -s Anc2.Anc2refChr15 43342 6 - 86568 CACGTT -s mr.mrrefChr5 82775 6 + 294540 AACTTC -s simCow_chr6.simCow.chr6 203550 6 + 602619 CACAGA -s simDog_chr6.simDog.chr6 378829 6 - 593897 CACGTT -s simHuman_chr6.simHuman.chr6 306872 6 - 601863 CACTTC -s simRat_chr6.simRat.chr6 219912 6 + 647215 ACCTTC - -a -s simMouse_chr6.simMouse.chr6 228637 9 + 636262 ATGGAAGAT -s Anc0.Anc0refChr5 40673 9 - 87904 ACAGAAGAC -s Anc1.Anc1refChr7 5764 9 - 47259 ACAGAAGAC -s Anc2.Anc2refChr15 43348 9 - 86568 ACAGAAGAT -s mr.mrrefChr5 82781 9 + 294540 ACAGAAGAC -s simCow_chr6.simCow.chr6 203556 9 + 602619 ACAGAAGAT -s simDog_chr6.simDog.chr6 378835 9 - 593897 AAAGCAGAT -s simHuman_chr6.simHuman.chr6 306879 9 - 601863 ACAGAAGAC -s simRat_chr6.simRat.chr6 219918 9 + 647215 ACAGAAAAC - -a -s simMouse_chr6.simMouse.chr6 228646 2 + 636262 TT -s Anc0.Anc0refChr5 40686 2 - 87904 TT -s Anc1.Anc1refChr7 5777 2 - 47259 TT -s Anc2.Anc2refChr15 43361 2 - 86568 TT -s mr.mrrefChr5 82790 2 + 294540 TT -s simCow_chr6.simCow.chr6 203569 2 + 602619 TT -s simDog_chr6.simDog.chr6 378848 2 - 593897 TT -s simHuman_chr6.simHuman.chr6 306892 2 - 601863 TT -s simRat_chr6.simRat.chr6 219927 2 + 647215 TT - -a -s simMouse_chr6.simMouse.chr6 228648 20 + 636262 AGACAGGATATTCATATTGG -s Anc0.Anc0refChr5 40688 20 - 87904 AAACAGGACTTACATCCTGG -s Anc1.Anc1refChr7 5779 20 - 47259 AAACAGGACTTACATCCTGG -s Anc2.Anc2refChr15 43363 20 - 86568 AAACATGACTTACATCCTGG -s mr.mrrefChr5 82792 20 + 294540 AGACAGGATATTCATCCTGG -s simCow_chr6.simCow.chr6 203577 20 + 602619 AAACATGACTTACATTCTAG -s simDog_chr6.simDog.chr6 378850 20 - 593897 AAACATAAATTCCATCCTGG -s simHuman_chr6.simHuman.chr6 306894 20 - 601863 AAACAGGTCTTACATCCTGG -s simRat_chr6.simRat.chr6 219929 20 + 647215 GGACAGGATACGCATCCTGG - -a -s simMouse_chr6.simMouse.chr6 228668 30 + 636262 CTAGACTGTTGTCTAGACAGTCTTGGGTGA -s Anc0.Anc0refChr5 40722 30 - 87904 CTAGACAGCCATCTAGACATTATTGGATGA -s Anc1.Anc1refChr7 5813 30 - 47259 CTAGACAGCCATCTAGACATTATTGGATGA -s Anc2.Anc2refChr15 43397 30 - 86568 CTAAGCAGCCATCTGGACATTATTGGATGA -s mr.mrrefChr5 82826 30 + 294540 CTAGACAGTTGTCTAGACAGTATTGGGTGA -s simCow_chr6.simCow.chr6 203611 30 + 602619 CTAAGCAGCCTTCTGGACATTATGGGCTAA -s simDog_chr6.simDog.chr6 378884 30 - 593897 CTGAGCAGCGACCTGGACATTATTGAATGA -s simHuman_chr6.simHuman.chr6 306928 30 - 601863 CTAGACAGCCATCTAGACATTATTGGATGA -s simRat_chr6.simRat.chr6 219963 30 + 647215 CTAGACAGTTGTCTAGACAGTAATGGGTGA - -a -s simMouse_chr6.simMouse.chr6 228698 9 + 636262 AACATATTG -s Anc0.Anc0refChr5 40752 9 - 87904 AGTATATTC -s Anc1.Anc1refChr7 5843 9 - 47259 AGTATATTC -s Anc2.Anc2refChr15 43428 9 - 86568 AGTATATTC -s mr.mrrefChr5 82856 9 + 294540 AACATATTG -s simCow_chr6.simCow.chr6 203642 9 + 602619 AATATATTC -s simDog_chr6.simDog.chr6 378915 9 - 593897 AGTATATTC -s simHuman_chr6.simHuman.chr6 306958 9 - 601863 AGTATCGTC -s simRat_chr6.simRat.chr6 219993 9 + 647215 AACAAATTT - -a -s simMouse_chr6.simMouse.chr6 228707 5 + 636262 ATGGA -s Anc0.Anc0refChr5 40761 5 - 87904 ATTGA -s Anc1.Anc1refChr7 5852 5 - 47259 ATTGA -s Anc2.Anc2refChr15 43437 5 - 86568 ATTGA -s mr.mrrefChr5 82865 5 + 294540 ATGGA -s simCow_chr6.simCow.chr6 203651 5 + 602619 ACTGA -s simCow_chr6.simCow.chr6 262403 5 + 602619 GCCAA -s simDog_chr6.simDog.chr6 378924 5 - 593897 ATTGA -s simHuman_chr6.simHuman.chr6 306967 5 - 601863 ATTGA -s simRat_chr6.simRat.chr6 220002 5 + 647215 GCAGA - -a -s simMouse_chr6.simMouse.chr6 228712 30 + 636262 TGTATGGTCTTAGGAATCTACAATACGTTC -s Anc0.Anc0refChr5 40766 30 - 87904 TGTATTATCTTAGGAATATACAACACGCCC -s Anc1.Anc1refChr7 5857 30 - 47259 TGTATTATCTTAGGAATATACAACACGCCC -s Anc2.Anc2refChr15 43442 30 - 86568 TGTATTATCTTAGGAATATACAACATGCCA -s mr.mrrefChr5 82870 30 + 294540 TGTATGGTCTTAGGAATATACAATACGTTC -s simCow_chr6.simCow.chr6 203656 24 + 602619 TGT------TTAAGAATATACAACATGCCA -s simCow_chr6.simCow.chr6 262408 20 + 602619 TGT----------GAATATACAACATGCCA -s simDog_chr6.simDog.chr6 378931 30 - 593897 TGTATTATCTCAGGAATATACCACATACCA -s simHuman_chr6.simHuman.chr6 306972 30 - 601863 TGTATTATCCTAGGAATATACAACACGCCC -s simRat_chr6.simRat.chr6 220007 30 + 647215 TATATGGTATTAGGAATACACAATAGGTTC - -a -s simMouse_chr6.simMouse.chr6 228742 2 + 636262 AT -s Anc0.Anc0refChr5 40796 2 - 87904 CT -s Anc1.Anc1refChr7 5887 2 - 47259 CT -s Anc2.Anc2refChr15 43472 2 - 86568 CT -s mr.mrrefChr5 82900 2 + 294540 AT -s simCow_chr6.simCow.chr6 262428 2 + 602619 CT -s simDog_chr6.simDog.chr6 378961 2 - 593897 CT -s simHuman_chr6.simHuman.chr6 307002 2 - 601863 CT -s simRat_chr6.simRat.chr6 220037 2 + 647215 AT - -a -s simMouse_chr6.simMouse.chr6 228744 13 + 636262 GTCCTATTGTGAC -s Anc0.Anc0refChr5 40805 13 - 87904 GTTCTCCTGTGGC -s Anc1.Anc1refChr7 5896 13 - 47259 GTTCTCCTGTGGC -s Anc2.Anc2refChr15 43485 13 - 86568 GTTCTGCTGTGGC -s mr.mrrefChr5 82902 13 + 294540 GTCCTCTTGTGAC -s simCow_chr6.simCow.chr6 262441 13 + 602619 GATCTACTTTGGC -s simDog_chr6.simDog.chr6 378974 13 - 593897 GTTGTGCTGTGGC -s simHuman_chr6.simHuman.chr6 307011 13 - 601863 GTTCACCTGTGGT -s simRat_chr6.simRat.chr6 220039 13 + 647215 GTCCTCTTGTGAC - -a -s simMouse_chr6.simMouse.chr6 228757 44 + 636262 AGCAGTGATAATATGTAGGACATGTAAGAAAGAGATAATCATCA -s Anc0.Anc0refChr5 40915 18 - 87904 AACAATGATAATATGTAG-------------------------- -s Anc1.Anc1refChr7 6006 18 - 47259 AACAATGATAATATGTAG-------------------------- -s Anc2.Anc2refChr15 43597 18 - 86568 AACAATGATTATGTGTAG-------------------------- -s mr.mrrefChr5 82915 44 + 294540 AGCACTGATAATATGTAGGACATATAAGAAAGAGATGATCATCA -s simCow_chr6.simCow.chr6 203740 18 + 602619 ACCAATGAGTATGTGTTG-------------------------- -s simCow_chr6.simCow.chr6 262551 18 + 602619 ATCGATGATTATGTGTTG-------------------------- -s simDog_chr6.simDog.chr6 379086 18 - 593897 AATAACGATTCTTTGTAG-------------------------- -s simHuman_chr6.simHuman.chr6 307123 18 - 601863 AACAATGATAATACATAG-------------------------- -s simRat_chr6.simRat.chr6 220052 44 + 647215 AGCACTGATAATATGTAGGACATATAAGAAAGAGATGATCATCA - -a -s simMouse_chr6.simMouse.chr6 228801 19 + 636262 TTGTACTTTTACTTGCGCT -s Anc0.Anc0refChr5 40959 19 - 87904 TTGCATTTTTAATTGCATT -s Anc1.Anc1refChr7 6052 19 - 47259 TTGCATTTTTAATTGCATT -s Anc2.Anc2refChr15 43641 19 - 86568 TTGCATTTTTAATTGCTTT -s mr.mrrefChr5 83016 19 + 294540 TTGTACTTTTACTTGCACT -s simCow_chr6.simCow.chr6 203784 19 + 602619 TTGCATTTTTAATCGCTCG -s simCow_chr6.simCow.chr6 262595 19 + 602619 TTGCATTTTTAATCGGATT -s simDog_chr6.simDog.chr6 379128 19 - 593897 TTGCATTTTTACTTGCTTT -s simHuman_chr6.simHuman.chr6 307169 19 - 601863 TTGCATTTTTATTTGCATT -s simRat_chr6.simRat.chr6 220153 19 + 647215 CTGTACTTTTACTTGCACT - -a -s simMouse_chr6.simMouse.chr6 228820 7 + 636262 TTCTTAT -s Anc0.Anc0refChr5 40978 7 - 87904 TTCTTAT -s Anc1.Anc1refChr7 6071 7 - 47259 TTCTTAT -s Anc2.Anc2refChr15 43660 7 - 86568 TTCTTCT -s mr.mrrefChr5 83035 7 + 294540 TTCTTAT -s simCow_chr6.simCow.chr6 203805 7 + 602619 TTTTTCT -s simCow_chr6.simCow.chr6 262614 7 + 602619 TTTTTCT -s simDog_chr6.simDog.chr6 379147 7 - 593897 TTCTTCT -s simHuman_chr6.simHuman.chr6 307188 7 - 601863 TCCTTAT -s simRat_chr6.simRat.chr6 220172 7 + 647215 TTCTTAT - -a -s simMouse_chr6.simMouse.chr6 228827 65 + 636262 AATAGGTCCAACCAACTGGACTCAACTGAATCTTGCCTTCAGAAAAAAATGTTATAACATGGTAT -s Anc0.Anc0refChr5 40985 60 - 87904 AA-AGGCCCAACTAAGTGAACTCAACTGAATCCTGGATTTAGAAGTAAATACTATAA----GCAT -s Anc1.Anc1refChr7 6078 60 - 47259 AA-AGGCCCAACTAAGTGAACTCAACTGAATCCTGGATTTAGAAGTAAATACTATAA----GCAT -s Anc2.Anc2refChr15 43667 60 - 86568 AA-AAGCCCAAATAAGTGAACTCAACTGGATCCTGGATTTAGAAGTAAATACTATAA----GCAT -s mr.mrrefChr5 83042 65 + 294540 AATAGGTCCAACCAACTGGACTCAACTGAATCTTGCATTTAGAAGTAAATGTTATAACACTGTAT -s simCow_chr6.simCow.chr6 203812 60 + 602619 AA-AAAGCCCTACAAGTGGACTCATCTGGATGTTGCATTTAGAAGTAAATACTATAA----GCAT -s simCow_chr6.simCow.chr6 262621 60 + 602619 AA-GACGCCCTATGGGTGGACTCAACTGGATGTTGGATTTAGAAGTAAATACTATAA----GCAT -s simDog_chr6.simDog.chr6 379155 60 - 593897 AA-AAGCCCAATTAAGTGAACTTCATTGCAGCCTGGATTAAGAAGTAAATACTATGA----GCAT -s simHuman_chr6.simHuman.chr6 307195 60 - 601863 AA-AGGCCCAACTAAGTGAACTCAGCTAAGTCCTGGATTTAGAAGTACACACTATAA----GCAC -s simRat_chr6.simRat.chr6 220179 62 + 647215 AATAGGTCCAACCAACTGG---CAACTGCATTTTGCATTTAGAAGTAAATGTTTTAACACTGTAC - -a -s simMouse_chr6.simMouse.chr6 228892 19 + 636262 TACCATGATTCCGTTTCAA -s Anc0.Anc0refChr5 41045 19 - 87904 TGAGTTTATTACATTTCAA -s Anc1.Anc1refChr7 6138 19 - 47259 TGAGTTTATTACATTTCAA -s Anc2.Anc2refChr15 43727 19 - 86568 TGAGTTTATTACATTTCAA -s mr.mrrefChr5 83107 19 + 294540 TACCATGATTCCGTTTCAA -s simCow_chr6.simCow.chr6 203945 19 + 602619 TGAATTTATTACATTTCAA -s simCow_chr6.simCow.chr6 262681 19 + 602619 TGAATTTATTACATTTCAA -s simDog_chr6.simDog.chr6 379215 18 - 593897 TGAGTTTCCTA-ATTTCAA -s simHuman_chr6.simHuman.chr6 307255 19 - 601863 TGAGTTTATTACATTTTAA -s simRat_chr6.simRat.chr6 220241 18 + 647215 TATCATGATTCC-TTTCAA - -a -s simMouse_chr6.simMouse.chr6 228911 13 + 636262 CCCATGGAAGATC -s Anc0.Anc0refChr5 41064 13 - 87904 TTCCTGTTAACAC -s Anc1.Anc1refChr7 6157 13 - 47259 TTCCTGTTAACAC -s Anc2.Anc2refChr15 43746 13 - 86568 TTCCTGTTAACAC -s mr.mrrefChr5 83126 13 + 294540 CCCATGGAAGTTC -s simCow_chr6.simCow.chr6 203964 13 + 602619 TCCCGGTTAACAC -s simCow_chr6.simCow.chr6 262700 13 + 602619 TTCCAGTTAACAC -s simDog_chr6.simDog.chr6 379242 13 - 593897 TTCCTTTTAACAC -s simHuman_chr6.simHuman.chr6 307274 13 - 601863 TGCCTGTCAACAC -s simRat_chr6.simRat.chr6 220259 13 + 647215 CCCATGGAAGTTC - -a -s simMouse_chr6.simMouse.chr6 228924 106 + 636262 CCATGGAGGTTCCAGTAACATTGCCCTCACGCTGAATTGGCTTGGTAACATTTTATCACAAAAATTTAGGTAAAAGCAAGTCACTCGAAATGGCTAATATGGATGA -s Anc0.Anc0refChr5 41081 6 - 87904 TCTT----------------------------------------------------------------------------------------------------GT -s Anc1.Anc1refChr7 6174 52 - 47259 TCTTAGAGGGTAGGATACCATTGCCTTCAGATGAACCTG---------------------------------------------------TGCCTCTTCT---TGT -s Anc2.Anc2refChr15 43763 6 - 86568 TCTT----------------------------------------------------------------------------------------------------TT -s mr.mrrefChr5 83139 106 + 294540 CCATGGAGGTTCCAGTACCATTGCCCTCACACTAAATTGGCTTGGTAACATTTTATCACAAAAATTTAGGTAAAAGCAAGTCACTCGAAATGGCTAATGTGGATGA -s simCow_chr6.simCow.chr6 203981 6 + 602619 TCTT----------------------------------------------------------------------------------------------------TT -s simCow_chr6.simCow.chr6 262717 6 + 602619 TCTT----------------------------------------------------------------------------------------------------TT -s simDog_chr6.simDog.chr6 379259 6 - 593897 TCTT----------------------------------------------------------------------------------------------------TT -s simHuman_chr6.simHuman.chr6 307294 52 - 601863 TCTTAGAGGGTAGGATACCATTGCCTTCAGATGAACCTG---------------------------------------------------TGCCTCTTCT---TGT -s simRat_chr6.simRat.chr6 220272 99 + 647215 CCATGGAGGTTCCAGTACCATTGCCCTTGCACTAAATTG-------AACGTTTAATCACAAAAATATAGGTAAAAGCGGGTCACATTAAATGGCTAATGTGGATCA - -a -s simMouse_chr6.simMouse.chr6 229030 55 + 636262 AATTCCAGAACCATTGCCCTCACATTAAAATGATTTTGTAACATTTTACTGCAAA -s Anc0.Anc0refChr5 41087 55 - 87904 AGGTCCAGTACCATTGCCTTCAGATTAGCCTGACTCTGTAACATTCTACCACAAG -s Anc1.Anc1refChr7 6226 55 - 47259 AGGTCCAGTACCATTGCCTTCAGATTAGCCTGACTCTGTAACATTCTACCACAAG -s Anc2.Anc2refChr15 43769 55 - 86568 GGGTCCAGTACCATTGCCTTCAGAATGGCCAGACTCTGTAACACTCTACCACAAG -s mr.mrrefChr5 83245 55 + 294540 AGTTCCAGTACCATTGCCCTCACATTAAAATGACTTTGTAACATTTTACCGCAAA -s simCow_chr6.simCow.chr6 203987 55 + 602619 GGGTCCAGTATCATTCTGTTCAGAATGGCCAGACTCTGGAACACTCTACCACAAG -s simCow_chr6.simCow.chr6 262723 55 + 602619 GGGTCCAGTATCATTCTGTTAAGAATGGCCAGACTCTGGATCACTCTACCACAAG -s simDog_chr6.simDog.chr6 379269 41 - 593897 GGGTCCAGTACCAATGCCCTCAGACTGG-CATACTCTGTAAC------------- -s simHuman_chr6.simHuman.chr6 307346 55 - 601863 AGGTCTGATACCATCGCCTTCAGATGAGCCTGACTCAGTAACTTTCTGCCACAAG -s simRat_chr6.simRat.chr6 220371 55 + 647215 AGTTCCCGTACCATTGTCCTCACACTAAATTGACTTTATAATATTTTACCGAAAA - -a -s simMouse_chr6.simMouse.chr6 229085 50 + 636262 ATATAGGTAAAAGCAGATCACTCTAACTGGCTAATGTAGAAAATTCTTTT -s Anc0.Anc0refChr5 41142 48 - 87904 ATATAGGGTAAATCAGGTTATTCTGAATGTCTAATGGGGTGGA--CTCTT -s Anc1.Anc1refChr7 6281 48 - 47259 ATATAGGGTAAATCAGGTTATTCTGAATGTCTAATGGGGTGGA--CTCTT -s Anc2.Anc2refChr15 43824 48 - 86568 ATATAGGGTAAATCAGAATTTTCTGAGTGTATAACAGGGTGGA--CTCTT -s mr.mrrefChr5 83300 50 + 294540 ATATAGGTAAAAGCAGGTCACTCTAAATGGCTAATGTGGAGAATTCTTTT -s simCow_chr6.simCow.chr6 204042 48 + 602619 ATATAAGGTAAATCAGAATTTTTTGAGTTTATAATAGAATGGA--CTCTC -s simCow_chr6.simCow.chr6 262778 48 + 602619 ATATAAGGTAAATCAGAATTTTTTGAATCTATAACGGAGTGGA--CTCTC -s simDog_chr6.simDog.chr6 379310 48 - 593897 ATCTAGAGTAGACCAGATTTTGCTGAGCGTTTAACAAGGTGGA--CTATT -s simHuman_chr6.simHuman.chr6 307401 47 - 601863 ATATAGCATAAATCAGGTTA-TCTGAATGTCTCATGGGGTGGC--CTGTT -s simRat_chr6.simRat.chr6 220427 50 + 647215 ACATAGGTAAAGGCAGGTCAATCTAAATGGCTAATGTGGAGAATTCTTTT - -a -s simMouse_chr6.simMouse.chr6 229135 6 + 636262 CAATTC -s Anc0.Anc0refChr5 41190 5 - 87904 CTTTT- -s Anc1.Anc1refChr7 6329 6 - 47259 CTTTTC -s Anc2.Anc2refChr15 43872 5 - 86568 CTGTT- -s mr.mrrefChr5 83350 6 + 294540 CATTTC -s simCow_chr6.simCow.chr6 204090 5 + 602619 TTGTT- -s simCow_chr6.simCow.chr6 262826 5 + 602619 TTGTT- -s simDog_chr6.simDog.chr6 379359 5 - 593897 CTGTC- -s simHuman_chr6.simHuman.chr6 307448 6 - 601863 CTTTTC -s simRat_chr6.simRat.chr6 220477 6 + 647215 CATTTC - -a -s simMouse_chr6.simMouse.chr6 229141 82 + 636262 TGGATGTCTGCGCATGAAAAAATATTCGAGACTATACGGGATTTATCGCTCTGGGCACACTTGCCAGTGTCGCGATAGCCAA -s Anc0.Anc0refChr5 41200 7 - 87904 C---------------------------------------------------------------------------AGTCAA -s Anc1.Anc1refChr7 6340 7 - 47259 C---------------------------------------------------------------------------AGTCAA -s Anc2.Anc2refChr15 43882 7 - 86568 C---------------------------------------------------------------------------AGTCAA -s mr.mrrefChr5 83356 7 + 294540 C---------------------------------------------------------------------------AGCCAA -s simCow_chr6.simCow.chr6 204100 7 + 602619 C---------------------------------------------------------------------------AGTCAA -s simCow_chr6.simCow.chr6 262836 7 + 602619 C---------------------------------------------------------------------------AGTCAA -s simDog_chr6.simDog.chr6 379369 7 - 593897 T---------------------------------------------------------------------------GGCCAA -s simHuman_chr6.simHuman.chr6 307460 7 - 601863 C---------------------------------------------------------------------------AGTCAA -s simRat_chr6.simRat.chr6 220483 7 + 647215 C---------------------------------------------------------------------------AGCCAA - -a -s simMouse_chr6.simMouse.chr6 229223 14 + 636262 CTAATTGGAACAGA -s Anc0.Anc0refChr5 41207 14 - 87904 TTGATTGGACCAGG -s Anc1.Anc1refChr7 6347 14 - 47259 TTGATTGGACCAGG -s Anc2.Anc2refChr15 43889 14 - 86568 TTGATTGGACTGGG -s mr.mrrefChr5 83363 14 + 294540 TTAATTGGAACAGA -s simCow_chr6.simCow.chr6 262843 14 + 602619 TCGACTGGACTGGG -s simDog_chr6.simDog.chr6 379376 14 - 593897 CTGATTGGACTGGG -s simHuman_chr6.simHuman.chr6 307467 14 - 601863 TTGATTGGACCAGG -s simRat_chr6.simRat.chr6 220490 14 + 647215 TAAATTGGATCAGA - -a -s simMouse_chr6.simMouse.chr6 229237 26 + 636262 CATTTGTCAATCAGATTGGAAAAATG -s Anc0.Anc0refChr5 41221 26 - 87904 CATTTGTCAATCAGATTGCAAAAATG -s Anc1.Anc1refChr7 6361 26 - 47259 CATTTGTCAATCAGATTGCAAAAATG -s Anc2.Anc2refChr15 43903 26 - 86568 CATTTGTCAATCAGATTGCAAGAATG -s mr.mrrefChr5 83377 26 + 294540 CATTTGTCAATCAGATTGGAAAAATG -s simCow_chr6.simCow.chr6 204107 26 + 602619 CATCTGTCAATCAGATTAAAAGAGGG -s simCow_chr6.simCow.chr6 262857 22 + 602619 TATCTGTCAATCTGAGGTAAGG---- -s simDog_chr6.simDog.chr6 379390 26 - 593897 CATTTGTCAATTAGATTGCAAGAATG -s simHuman_chr6.simHuman.chr6 307481 26 - 601863 CATTTGTCAATCAGACTGCAAAAATG -s simRat_chr6.simRat.chr6 220504 26 + 647215 CATTTGTCAATCAGATTGGAAAAATG - -a -s simMouse_chr6.simMouse.chr6 229263 15 + 636262 ATGAACCTAAATTGA -s Anc0.Anc0refChr5 41248 15 - 87904 ATGAACCCAAAATGA -s Anc1.Anc1refChr7 6388 15 - 47259 ATGAACCCAAAATGA -s Anc2.Anc2refChr15 43930 15 - 86568 ATGAACACAAAATGA -s mr.mrrefChr5 83403 15 + 294540 ATGAACCCAAATTGA -s simCow_chr6.simCow.chr6 204134 15 + 602619 CTGAAGTCAAAGTGA -s simDog_chr6.simDog.chr6 379417 15 - 593897 AAGAACACAAGATGA -s simHuman_chr6.simHuman.chr6 307510 15 - 601863 ATGAACCCAAACTGA -s simRat_chr6.simRat.chr6 220530 15 + 647215 ATGAACCCACATTGA - -a -s simMouse_chr6.simMouse.chr6 229278 14 + 636262 CTCAGTTTGGCCAA -s Anc0.Anc0refChr5 41263 14 - 87904 CTCAGTTTGGCCAG -s Anc1.Anc1refChr7 6403 14 - 47259 CTCAGTTTGGCCAG -s Anc2.Anc2refChr15 43945 14 - 86568 CTCAGTATGGCCAT -s mr.mrrefChr5 83418 14 + 294540 CTCAGTTTGGCCAG -s simCow_chr6.simCow.chr6 204153 14 + 602619 CCCAGTCTGGCCAA -s simDog_chr6.simDog.chr6 379432 11 - 593897 CTCGAAAT---CAT -s simHuman_chr6.simHuman.chr6 307525 14 - 601863 CACAGTTTGGCCAG -s simRat_chr6.simRat.chr6 220545 14 + 647215 CTCAGCTTGGCCAG - -a -s simMouse_chr6.simMouse.chr6 229292 94 + 636262 GAGACGATACTAGATTGCATTGGTATGGCTAGCTTTTGCCTAACACCAGACACCCTCAAAACCCCTTAATTTTGATGGTGTTCTTCATAATATG -s Anc0.Anc0refChr5 41277 15 - 87904 TATAGTGTGGTA-------------------------------------------------------------------------------ATG -s Anc1.Anc1refChr7 6417 15 - 47259 TATAGTGTGGTA-------------------------------------------------------------------------------ATG -s Anc2.Anc2refChr15 43959 15 - 86568 TATAGTGGTGTA-------------------------------------------------------------------------------TAA -s mr.mrrefChr5 83432 20 + 294540 GAGACTATGCTAGATTG--------------------------------------------------------------------------ATG -s simCow_chr6.simCow.chr6 204174 15 + 602619 TATAGTAGTGTA-------------------------------------------------------------------------------TAA -s simDog_chr6.simDog.chr6 379443 15 - 593897 TATAGTGGTGTA-------------------------------------------------------------------------------TAA -s simHuman_chr6.simHuman.chr6 307539 15 - 601863 TAAAGTTTGGTA-------------------------------------------------------------------------------ATG -s simRat_chr6.simRat.chr6 220559 20 + 647215 GAGACTATGCTAGATTG--------------------------------------------------------------------------ATG - -a -s simMouse_chr6.simMouse.chr6 229386 208 + 636262 GCAGCAGTACCATCTAGTCAAAAACTCCGGCTATCTCTGTGCTGACTTGGAGCATATATAATTATTCATCTGTGCCATCAACAGCGTGTCTTCAAAACAATTGGTGGCACTACTGGTCTTACAAGGCATCATTCTCCTTCAGGCAATGGGGTATCCCAGTTAAAGTACTCGTTGCATCCTAAGCATAAGAGCTAGAATATGATATTAG -s Anc0.Anc0refChr5 41377 26 - 87904 GCACCAGTACCATCTTATTAAAAACT-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- -s Anc1.Anc1refChr7 6517 26 - 47259 GCACCAGTACCATCTTATTAAAAACT-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- -s Anc2.Anc2refChr15 44072 26 - 86568 GCACCAGTACCATCTTATTAAAAACT-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- -s mr.mrrefChr5 83452 203 + 294540 GCAGCAGTACCATCTAGTCAAAAACTCCGGCTATCTCTGTGCTGACTTGGAGCATATATAATTATTCA-----GCCATCAACAGCGTGTCTTCAAAACAATTGGTGGCACTACTGGTCTTACAAGGCATCATTCTCCTTCAGGCAATGGGGTATCCCAGTTAAAGTACTCGTTGCATCCTAAGCATAAGAGCTAGAATATGATATTAG -s simCow_chr6.simCow.chr6 204311 26 + 602619 GCAGCAGTACTATATTATTAACAACG-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- -s simDog_chr6.simDog.chr6 379550 26 - 593897 GCACCAGTACCATCATATTACAAACT-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- -s simHuman_chr6.simHuman.chr6 307639 26 - 601863 GCACCAGTACAATTTTATTAAAATCT-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- -s simRat_chr6.simRat.chr6 220579 203 + 647215 GCAGCAGTACCATCTAGTCAAAAACTCTGGCTATCTCTGTGGTGTCTTGGGGTATATATATTTATTCA-----GCCGTCAAGAAGGCACCTTCAAAAGGATCGGTGGCACTACTGGTCTTACAAGGCATCATTCTCCTTCAGGCAATGAGGTATCCCAGTTGAAGTCCTCTTTGCAACCTCTGCATGAGAGCTTGAATATGATATTAG - -a -s simMouse_chr6.simMouse.chr6 229594 108 + 636262 AAAATTTGGCGGTATATCAACCCTCATTGCTGAAGTCAATTTTCATTTAGATTTGGCTGTGGAAATGTACAGAGTCAGGTCCGGTGATAGACCTGACTTAGATAAAGG -s mr.mrrefChr5 83655 107 + 294540 AAAATTTGGCGGTATATCAACCCTCATTGCTGAAGTCAATTTTCATTTAGATTTGGCTGT-GAAATGTACAGAGTCAGGTCCGGTGATAGACCTGACTTAGATAAAGG -s simRat_chr6.simRat.chr6 220783 107 + 647215 AAAATTTGGGGGTATATTAACCTTCGTCGCAGAAGTCAATTTTCATTTAGATTTGGCTGT-GCAATGTACAGAGTCAGGTCAGGTGATAGAACTGATTTACATAAAGG - -a -s simMouse_chr6.simMouse.chr6 229702 25 + 636262 AAAACATGCTTGTATCAACACTATG -s Anc0.Anc0refChr5 41923 6 - 87904 -------------------ACTATA -s Anc1.Anc1refChr7 6913 6 - 47259 -------------------ACTATA -s Anc2.Anc2refChr15 44658 6 - 86568 -------------------ACTGTA -s mr.mrrefChr5 83762 25 + 294540 AAAACATGCTTGTATCAACACTATG -s simCow_chr6.simCow.chr6 204697 6 + 602619 -------------------GCTGCA -s simDog_chr6.simDog.chr6 380135 6 - 593897 -------------------ACTGTA -s simHuman_chr6.simHuman.chr6 308180 6 - 601863 -------------------ACCATA -s simRat_chr6.simRat.chr6 220893 25 + 647215 AAAACATGCTTGTATCAACACTATG - -a -s simMouse_chr6.simMouse.chr6 229727 15 + 636262 TACAGCATAAAGCTA -s Anc0.Anc0refChr5 41929 9 - 87904 TACAGCAGA------ -s Anc1.Anc1refChr7 6919 15 - 47259 TACAGCAGAAAGATA -s Anc2.Anc2refChr15 44666 9 - 86568 TACAGCAGA------ -s mr.mrrefChr5 83787 15 + 294540 TACAGCATAAAGCTA -s simCow_chr6.simCow.chr6 204704 7 + 602619 --CAGTGGA------ -s simDog_chr6.simDog.chr6 380143 9 - 593897 TACAGCATG------ -s simHuman_chr6.simHuman.chr6 308186 15 - 601863 TGCAGCAGAAAGATA -s simRat_chr6.simRat.chr6 220918 15 + 647215 TACGGTAGAAAGCTA - -a -s simMouse_chr6.simMouse.chr6 229742 2 + 636262 GG -s Anc0.Anc0refChr5 41938 2 - 87904 GA -s Anc1.Anc1refChr7 6934 2 - 47259 GA -s Anc2.Anc2refChr15 44675 2 - 86568 GA -s mr.mrrefChr5 83802 2 + 294540 GG -s simCow_chr6.simCow.chr6 204713 2 + 602619 GA -s simDog_chr6.simDog.chr6 380152 2 - 593897 AA -s simHuman_chr6.simHuman.chr6 308218 2 - 601863 GA -s simRat_chr6.simRat.chr6 220933 2 + 647215 GA - -a -s simMouse_chr6.simMouse.chr6 229744 30 + 636262 GCCTTTTCCTGTTTTATCCTTAAGCAATGA -s Anc0.Anc0refChr5 41940 27 - 87904 GGTTTATCTCGCCTTGACCTGGAGCA--A- -s Anc1.Anc1refChr7 6936 29 - 47259 GGTTTATCTCGCCTTGACCTGGAGCAACA- -s Anc2.Anc2refChr15 44677 27 - 86568 GGTTTATCTCGCCTTGACCTGGAGCA--A- -s mr.mrrefChr5 83804 29 + 294540 GCCTTTTCCTGTTTTATCCTTAAGCAATG- -s simCow_chr6.simCow.chr6 204715 27 + 602619 GGTTTATCTTGACTTGACCCGGAGCA--A- -s simDog_chr6.simDog.chr6 380154 27 - 593897 GGTGTATCTCGCCTTGACCTGGAGCA--C- -s simHuman_chr6.simHuman.chr6 308220 29 - 601863 GATTTATCTGGCCTTGACCTGGAGCAACA- -s simRat_chr6.simRat.chr6 220936 29 + 647215 GCCTTTTCCTGATTTATCCTCAAGCAACT- - -a -s simMouse_chr6.simMouse.chr6 229774 16 + 636262 CCTCTTGGGAAACCAC -s Anc0.Anc0refChr5 41970 11 - 87904 CCTCATGGTAA----- -s Anc1.Anc1refChr7 6968 11 - 47259 CCTCATGGTAA----- -s Anc2.Anc2refChr15 44707 11 - 86568 ATTCACAGTAA----- -s mr.mrrefChr5 83833 11 + 294540 CCTCTTGGGAA----- -s simCow_chr6.simCow.chr6 204745 11 + 602619 GTTCACAGTAA----- -s simDog_chr6.simDog.chr6 380184 11 - 593897 ATTCACAGTAA----- -s simHuman_chr6.simHuman.chr6 308253 11 - 601863 CCTCATGGTAG----- -s simRat_chr6.simRat.chr6 220965 11 + 647215 CCTCTTGGTAA----- - -a -s simMouse_chr6.simMouse.chr6 229790 48 + 636262 AACACAGGGTGTCACATCATTAATTAAAGCACACTGATGTGATGCATA -s Anc0.Anc0refChr5 41989 47 - 87904 AACAAAAGGTGTCACTCCACTAAATAAAGCTCTCTGATTTGATATA-G -s Anc1.Anc1refChr7 6987 47 - 47259 AACAAAAGGTGTCACTCCACTAAATAAAGCTCTCTGATTTGATATA-G -s Anc2.Anc2refChr15 44726 47 - 86568 AACAAAAGGTGTCACTCCACTAAACAAAGCTCTCTGATTTGATATA-G -s mr.mrrefChr5 83844 48 + 294540 AACACAGGGTGTCACATCATTAATTAAAGCACACTGATGTGATGCATA -s simCow_chr6.simCow.chr6 204757 46 + 602619 -AAACAGGGTATCACTCCACTAAACGAAACTGTCTGATATGGTTCA-C -s simDog_chr6.simDog.chr6 380203 47 - 593897 AACAAAAGATGTCGTTCCACTGAACAAAGCTCTCTGATTTGATATA-G -s simHuman_chr6.simHuman.chr6 308272 36 - 601863 AACATATGGTGTCACTCCACTAAATAAAGTGTTCTG------------ -s simRat_chr6.simRat.chr6 220976 48 + 647215 AACACAGGGTGTCACATCTTTAAATAAAGCATACTGGTGGGATGTATA - -a -s simMouse_chr6.simMouse.chr6 229838 49 + 636262 ATCTATGCTCAGGTGCCACTTTAAACATCGAACAGTAACTACATCTCAT -s Anc0.Anc0refChr5 42036 40 - 87904 ATCTATTCTCCGACTCCACTTCAAACATTGAACATTGAC---------T -s Anc1.Anc1refChr7 7034 40 - 47259 ATCTATTCTCCGACTCCACTTCAAACATTGAACATTGAC---------T -s Anc2.Anc2refChr15 44773 40 - 86568 ATCTATTCTCCGACTCCACTTCAAGCATTAAACATTGAC---------T -s mr.mrrefChr5 83892 40 + 294540 ATCTATGCTCAGGTGCCACTTTAAACATCGAACAGTAAC---------T -s simCow_chr6.simCow.chr6 204803 40 + 602619 ACCTATTCCCCGATACCATTTCAAGTATTAAACATGGAC---------T -s simDog_chr6.simDog.chr6 380250 39 - 593897 ATCTATTCTCAGACTGCACTTTAAGCATTAAACATTGAC---------- -s simHuman_chr6.simHuman.chr6 308308 39 - 601863 -TCTATTCTCCGACCCTACCTCAAACCTTGAACACTGAC---------T -s simRat_chr6.simRat.chr6 221025 40 + 647215 ATCTATGCACAGGTGCCACTTTAAAGATCAAATGGTAAC---------T - -a -s simMouse_chr6.simMouse.chr6 229887 17 + 636262 CCCTATGGATTTCATAC -s Anc0.Anc0refChr5 42085 17 - 87904 CCCTATGAATCTCACAC -s Anc1.Anc1refChr7 7083 17 - 47259 CCCTATGAATCTCACAC -s Anc2.Anc2refChr15 44822 17 - 86568 CCCTATGAATCTCACAC -s mr.mrrefChr5 83932 17 + 294540 CCCTATGGATTTCATAC -s simCow_chr6.simCow.chr6 204852 16 + 602619 CCCTA-GGATCTCATGC -s simDog_chr6.simDog.chr6 380296 17 - 593897 CCCTGTGAGTCTCACAT -s simHuman_chr6.simHuman.chr6 308357 17 - 601863 CTCTATGAATGTCACAC -s simRat_chr6.simRat.chr6 221065 17 + 647215 CCCTATGAATTTCATAC - -a -s simMouse_chr6.simMouse.chr6 229904 5 + 636262 AAGAA -s Anc0.Anc0refChr5 42102 5 - 87904 AAGAA -s Anc1.Anc1refChr7 7100 5 - 47259 AAGAA -s Anc2.Anc2refChr15 44839 5 - 86568 AAAAA -s mr.mrrefChr5 83949 5 + 294540 AAGAA -s simCow_chr6.simCow.chr6 204868 5 + 602619 AAAAA -s simDog_chr6.simDog.chr6 380313 5 - 593897 TCAAA -s simHuman_chr6.simHuman.chr6 308374 5 - 601863 AAGAA -s simRat_chr6.simRat.chr6 221083 5 + 647215 AAGAA - -a -s simMouse_chr6.simMouse.chr6 229909 17 + 636262 TTCACAGCTCCAACAGG -s Anc0.Anc0refChr5 42108 17 - 87904 TGCACAAGTCTAGAGGG -s Anc1.Anc1refChr7 7106 17 - 47259 TGCACAAGTCTAGAGGG -s Anc2.Anc2refChr15 44845 17 - 86568 TGCACAAGCCTAGAGGG -s mr.mrrefChr5 83954 17 + 294540 TTCACAGCTCCAACAGG -s simCow_chr6.simCow.chr6 204874 17 + 602619 TGCACAACCCTATCGGG -s simDog_chr6.simDog.chr6 380319 17 - 593897 TGCACAAGCCTAGAGGG -s simHuman_chr6.simHuman.chr6 308380 17 - 601863 TGCACACATCTAGTGGG -s simRat_chr6.simRat.chr6 221088 17 + 647215 TGCGCAGCTTCAACAGG - -a -s simMouse_chr6.simMouse.chr6 229926 24 + 636262 TTTGTAAGTCCCAAGAAGATTTCA -s Anc0.Anc0refChr5 42128 14 - 87904 TTTATGATTCCC----------CA -s Anc1.Anc1refChr7 7126 14 - 47259 TTTATGATTCCC----------CA -s Anc2.Anc2refChr15 44865 14 - 86568 TTTATGATTCCC----------CA -s mr.mrrefChr5 83971 14 + 294540 TTTGTAAGTCCC----------CA -s simCow_chr6.simCow.chr6 204894 13 + 602619 TTTATGATTCCC-----------A -s simDog_chr6.simDog.chr6 380339 14 - 593897 GTTGTGATTCAC----------CA -s simHuman_chr6.simHuman.chr6 308400 14 - 601863 TTTATGAATCCC----------CA -s simRat_chr6.simRat.chr6 221105 14 + 647215 TTTGCAAGTCCC----------CA - -a -s simMouse_chr6.simMouse.chr6 229950 33 + 636262 GTTGAGTGGTATCCACACAGAACCAAATACTGT -s Anc0.Anc0refChr5 42157 30 - 87904 GA---GTGGTACTCACACAAAGCCAAATACTGT -s Anc1.Anc1refChr7 7155 30 - 47259 GA---GTGGTACTCACACAAAGCCAAATACTGT -s Anc2.Anc2refChr15 44894 30 - 86568 GA---GTGGTACTCACTCAAAGCCAAATACTAT -s mr.mrrefChr5 83985 30 + 294540 GT---GTGGTATCCACACAGAACCAAATACTGT -s simCow_chr6.simCow.chr6 204922 30 + 602619 GA---GAGGTACTTACCCAAAGCCAAACACTTT -s simDog_chr6.simDog.chr6 380368 30 - 593897 GA---GTGGAACTCACTCAAAGCCAAATATCAT -s simHuman_chr6.simHuman.chr6 308429 30 - 601863 GA---GTGGTACTCGCAGAAAGCAAAATACTGT -s simRat_chr6.simRat.chr6 221119 30 + 647215 GT---GAGGTATCCACACAAAGCCAAATACTGT - -a -s simMouse_chr6.simMouse.chr6 229983 3 + 636262 CTG -s Anc0.Anc0refChr5 42187 2 - 87904 CC- -s Anc1.Anc1refChr7 7185 2 - 47259 CC- -s Anc2.Anc2refChr15 44924 2 - 86568 TC- -s mr.mrrefChr5 84015 2 + 294540 CT- -s simCow_chr6.simCow.chr6 204962 2 + 602619 TC- -s simDog_chr6.simDog.chr6 380398 2 - 593897 TC- -s simHuman_chr6.simHuman.chr6 308459 2 - 601863 CC- -s simRat_chr6.simRat.chr6 221149 2 + 647215 CT- - -a -s simMouse_chr6.simMouse.chr6 229986 2 + 636262 GA -s Anc0.Anc0refChr5 42190 2 - 87904 GA -s Anc1.Anc1refChr7 7188 2 - 47259 GA -s Anc2.Anc2refChr15 44927 2 - 86568 GA -s mr.mrrefChr5 84017 2 + 294540 GA -s simCow_chr6.simCow.chr6 204965 2 + 602619 GA -s simDog_chr6.simDog.chr6 380401 2 - 593897 GA -s simHuman_chr6.simHuman.chr6 308462 2 - 601863 GC -s simRat_chr6.simRat.chr6 221151 2 + 647215 GA - -a -s simMouse_chr6.simMouse.chr6 229988 20 + 636262 TATCAACTTTGGGGCATTGG -s Anc0.Anc0refChr5 42192 20 - 87904 TATCAAAACAGATGTGTTGG -s Anc1.Anc1refChr7 7190 20 - 47259 TATCAAAACAGATGTGTTGG -s Anc2.Anc2refChr15 44929 20 - 86568 CATCAAAACAGATGTGTTGG -s mr.mrrefChr5 84019 20 + 294540 TATCAACTTTGGGGCATTGG -s simCow_chr6.simCow.chr6 204967 20 + 602619 CATCAAAACAGATGTGTTAA -s simDog_chr6.simDog.chr6 380431 20 - 593897 CATCAAAACAGATGTATTGG -s simHuman_chr6.simHuman.chr6 308464 20 - 601863 TATCAAAGCAGATGTGTTGT -s simRat_chr6.simRat.chr6 221153 20 + 647215 CATCAGTGTGGACGCGTCAG - -a -s simMouse_chr6.simMouse.chr6 230008 6 + 636262 AGTCTT -s Anc0.Anc0refChr5 42212 6 - 87904 AAATTT -s Anc1.Anc1refChr7 7210 6 - 47259 AAATTT -s Anc2.Anc2refChr15 44949 6 - 86568 AAATCT -s mr.mrrefChr5 84039 6 + 294540 agtctt -s simCow_chr6.simCow.chr6 204987 6 + 602619 AAATCT -s simDog_chr6.simDog.chr6 380451 6 - 593897 AAATCA -s simHuman_chr6.simHuman.chr6 308484 6 - 601863 AAGTTT -s simRat_chr6.simRat.chr6 221182 6 + 647215 agtctt - -a -s simMouse_chr6.simMouse.chr6 230014 15 + 636262 AACTAGGACCCTACA -s Anc0.Anc0refChr5 42221 15 - 87904 AACTAGGACCCCTCA -s Anc1.Anc1refChr7 7219 15 - 47259 AACTAGGACCCCTCA -s Anc2.Anc2refChr15 44958 15 - 86568 AACTAGGGCCCCTTA -s mr.mrrefChr5 84045 15 + 294540 aactaggaccctaca -s simCow_chr6.simCow.chr6 204996 15 + 602619 AAGAAgggccccttg -s simDog_chr6.simDog.chr6 380460 15 - 593897 AACTAGGGTCCCTTA -s simHuman_chr6.simHuman.chr6 308493 15 - 601863 AACTAGGACCTCTCA -s simRat_chr6.simRat.chr6 221188 15 + 647215 aactaggacaccaca - -a -s simMouse_chr6.simMouse.chr6 230029 41 + 636262 AGTAATATTACATCCAAATATCTACACCAAGAGACGATGTG -s Anc0.Anc0refChr5 42236 37 - 87904 AGCAATATTGCATCCTAATATCCAAACCAGAAGA----GTG -s Anc1.Anc1refChr7 7234 37 - 47259 AGCAATATTGCATCCTAATATCCAAACCAGAAGA----GTG -s Anc2.Anc2refChr15 44973 37 - 86568 AGCAATATGGCATCCTAATAACCAAACCTGAAGA----GTG -s mr.mrrefChr5 84060 41 + 294540 agtaatattacatccaaatatctacaccaagagacgatgtg -s simCow_chr6.simCow.chr6 205011 37 + 602619 agcagtctcacatcctagtaactaaacccgaaga----gga -s simDog_chr6.simDog.chr6 380476 37 - 593897 AGCAATATGGCACCTGAATAACCAAACCTGAAGA----GTG -s simHuman_chr6.simHuman.chr6 308508 37 - 601863 AGCAAAATTGCATCCTAATATCCAAATCAGTAGA----GTG -s simRat_chr6.simRat.chr6 221203 41 + 647215 agcaatattacatcctaatagttaaaccaagagacgatatg - -a -s simMouse_chr6.simMouse.chr6 230070 117 + 636262 GCTCGAGTTTCAGTGTTTCAGAGAGGGCTATGTCTTGAAAGAAATTCAGTCCGGGTGGATCATCAGCACACAACATATTTCGGTAGGACAGTACCAGTTGTTAGGCAGGATAATTTG -s Anc0.Anc0refChr5 42273 17 - 87904 ACATGGATTCCA----------------------------------------------------------------------------------------------------ACTTG -s Anc1.Anc1refChr7 7271 17 - 47259 ACATGGATTCCA----------------------------------------------------------------------------------------------------ACTTG -s Anc2.Anc2refChr15 45010 17 - 86568 ATATGGAATCTA----------------------------------------------------------------------------------------------------ACCTG -s mr.mrrefChr5 84101 104 + 294540 GCTCGAGTTTCAGTGTTTCAGAGAGGGCTATGTCTTGAAAGAAA-------------GATCATCAGCACACAACATATTTCGGTAGGACAGTACCAGTTGTTAGGCAGGATAATTTG -s simCow_chr6.simCow.chr6 205048 17 + 602619 atatggaattta----------------------------------------------------------------------------------------------------acctC -s simDog_chr6.simDog.chr6 380513 17 - 593897 ATATGACATCTA----------------------------------------------------------------------------------------------------ACCTG -s simHuman_chr6.simHuman.chr6 308545 17 - 601863 ACATGGATTCCA----------------------------------------------------------------------------------------------------ACTTG -s simRat_chr6.simRat.chr6 221256 104 + 647215 GCTCAAGTTTAAGTGTTTCAGAGAGGGCCACACATTGAAAGAAA-------------GATTACTAGGGCATAACATATTTTGATATGACAATACTAGTTGCTAGCCAGAATTATTTG - -a -s simMouse_chr6.simMouse.chr6 230187 4 + 636262 AGCT -s Anc0.Anc0refChr5 42290 4 - 87904 AGCT -s Anc1.Anc1refChr7 7288 4 - 47259 AGCT -s Anc2.Anc2refChr15 45032 4 - 86568 AGCT -s mr.mrrefChr5 84205 4 + 294540 AGCT -s simCow_chr6.simCow.chr6 205070 4 + 602619 AGCT -s simDog_chr6.simDog.chr6 380535 4 - 593897 AGCT -s simRat_chr6.simRat.chr6 221360 4 + 647215 AGTT - -a -s simMouse_chr6.simMouse.chr6 230191 9 + 636262 TGAGGAGGT -s Anc0.Anc0refChr5 42294 9 - 87904 tgAGTAGTT -s Anc1.Anc1refChr7 7292 9 - 47259 TGAGTAGTT -s Anc2.Anc2refChr15 45045 9 - 86568 ccAGTAGTA -s mr.mrrefChr5 84209 9 + 294540 TGAGGAGGT -s simCow_chr6.simCow.chr6 205083 9 + 602619 TGAGTAGGA -s simDog_chr6.simDog.chr6 380550 9 - 593897 ccaacagta -s simHuman_chr6.simHuman.chr6 308562 9 - 601863 TGAGTAGAT -s simRat_chr6.simRat.chr6 221364 9 + 647215 TGAGGGGGT - -a -s simMouse_chr6.simMouse.chr6 230200 12 + 636262 GCAAGGAAGAAT -s Anc0.Anc0refChr5 42307 12 - 87904 GGGAGGAAGAAT -s Anc1.Anc1refChr7 7305 12 - 47259 GGGAGGAAGAAT -s Anc2.Anc2refChr15 45058 12 - 86568 GGGGGGTATAGT -s mr.mrrefChr5 84218 12 + 294540 GCAAGGAAGAAT -s simCow_chr6.simCow.chr6 205096 12 + 602619 GGGGGGTATAGT -s simHuman_chr6.simHuman.chr6 308575 12 - 601863 GGGAGGAAGAAT -s simRat_chr6.simRat.chr6 221373 12 + 647215 GCAAGGAATAAT - -a -s simMouse_chr6.simMouse.chr6 230212 21 + 636262 ATGGATAAGAAATAAGTATGT -s Anc0.Anc0refChr5 42321 20 - 87904 ATGTATAAAGAATATTTA-GA -s Anc1.Anc1refChr7 7319 20 - 47259 ATGTATAAAGAATATTTA-GA -s Anc2.Anc2refChr15 45072 20 - 86568 ATGTAGAAAGATTATTTT-GA -s mr.mrrefChr5 84230 21 + 294540 ATGGATAAGAAATAAGTATGT -s simCow_chr6.simCow.chr6 205110 20 + 602619 ATGTAGAAAGGGTATTTT-TA -s simDog_chr6.simDog.chr6 380561 14 - 593897 ------agagattatttt-gg -s simHuman_chr6.simHuman.chr6 308589 20 - 601863 ATGAATAAAGAATATTTA-GA -s simRat_chr6.simRat.chr6 221385 21 + 647215 ATGCATGAGAAAAAAATATGT - -a -s simMouse_chr6.simMouse.chr6 230233 12 + 636262 ACAGCATGTGGG -s Anc0.Anc0refChr5 42341 7 - 87904 ACA-----TGAG -s Anc1.Anc1refChr7 7339 7 - 47259 ACA-----TGAG -s Anc2.Anc2refChr15 45092 7 - 86568 ACA-----TGAG -s mr.mrrefChr5 84251 7 + 294540 ACA-----TGGG -s simCow_chr6.simCow.chr6 205131 7 + 602619 AGA-----TGAG -s simDog_chr6.simDog.chr6 380575 7 - 593897 gca-----taat -s simHuman_chr6.simHuman.chr6 308609 7 - 601863 ACA-----TGAG -s simRat_chr6.simRat.chr6 221406 7 + 647215 AGA-----TGGG - -a -s simMouse_chr6.simMouse.chr6 230245 4 + 636262 TTAT -s Anc0.Anc0refChr5 42350 4 - 87904 TAAC -s Anc1.Anc1refChr7 7348 4 - 47259 TAAC -s Anc2.Anc2refChr15 45101 4 - 86568 TAAC -s mr.mrrefChr5 84258 4 + 294540 TTAT -s simCow_chr6.simCow.chr6 205140 4 + 602619 AAAC -s simDog_chr6.simDog.chr6 380584 4 - 593897 tttg -s simHuman_chr6.simHuman.chr6 308618 4 - 601863 TAAC -s simRat_chr6.simRat.chr6 221413 4 + 647215 TTAT - -a -s simMouse_chr6.simMouse.chr6 230249 4 + 636262 AACC -s Anc0.Anc0refChr5 42354 4 - 87904 AACC -s Anc1.Anc1refChr7 7352 4 - 47259 AACC -s Anc2.Anc2refChr15 45105 4 - 86568 AACT -s mr.mrrefChr5 84262 4 + 294540 AACC -s simCow_chr6.simCow.chr6 205145 4 + 602619 AACT -s simDog_chr6.simDog.chr6 380588 4 - 593897 tact -s simHuman_chr6.simHuman.chr6 308622 4 - 601863 AACC -s simRat_chr6.simRat.chr6 221417 4 + 647215 AACC - -a -s simMouse_chr6.simMouse.chr6 230253 2 + 636262 TG -s Anc0.Anc0refChr5 42359 2 - 87904 TC -s Anc1.Anc1refChr7 7357 2 - 47259 TC -s Anc2.Anc2refChr15 45110 2 - 86568 TC -s mr.mrrefChr5 84266 2 + 294540 TG -s simCow_chr6.simCow.chr6 205150 2 + 602619 TC -s simDog_chr6.simDog.chr6 380593 2 - 593897 ga -s simHuman_chr6.simHuman.chr6 308627 2 - 601863 TC -s simRat_chr6.simRat.chr6 221421 2 + 647215 TG - -a -s simMouse_chr6.simMouse.chr6 230255 4 + 636262 ATTA -s Anc0.Anc0refChr5 42361 4 - 87904 ATCC -s Anc1.Anc1refChr7 7359 4 - 47259 ATCC -s Anc2.Anc2refChr15 45112 4 - 86568 ATCC -s mr.mrrefChr5 84268 4 + 294540 ATTA -s simCow_chr6.simCow.chr6 205152 4 + 602619 ATCA -s simDog_chr6.simDog.chr6 380595 4 - 593897 atcc -s simHuman_chr6.simHuman.chr6 308629 4 - 601863 ATCC -s simRat_chr6.simRat.chr6 221424 4 + 647215 ATTA - -a -s simMouse_chr6.simMouse.chr6 230259 3 + 636262 TAG -s Anc0.Anc0refChr5 42365 3 - 87904 TAG -s Anc1.Anc1refChr7 7363 3 - 47259 TAG -s Anc2.Anc2refChr15 45116 3 - 86568 TAG -s mr.mrrefChr5 84272 3 + 294540 TAG -s simCow_chr6.simCow.chr6 205156 3 + 602619 TAG -s simDog_chr6.simDog.chr6 380599 3 - 593897 tag -s simHuman_chr6.simHuman.chr6 308633 3 - 601863 TAG -s simRat_chr6.simRat.chr6 221433 3 + 647215 TAG - -a -s simMouse_chr6.simMouse.chr6 230262 19 + 636262 GGGAATCGTAATTGCACAA -s Anc0.Anc0refChr5 42368 19 - 87904 GTCAATTGTATTAGCTTGA -s Anc1.Anc1refChr7 7366 19 - 47259 GTCAATTGTATTAGCTTGA -s Anc2.Anc2refChr15 45119 19 - 86568 GTCAATTGTATTAGCTTGC -s mr.mrrefChr5 84275 19 + 294540 GGGAATCGTAATTGCACAA -s simCow_chr6.simCow.chr6 205159 19 + 602619 GTCAATTGTATTAGCTTTC -s simDog_chr6.simDog.chr6 380639 17 - 593897 GTCAAGTGTTGTACC--GC -s simHuman_chr6.simHuman.chr6 308636 19 - 601863 GTCAATTGTATTAGCTTGA -s simRat_chr6.simRat.chr6 221436 19 + 647215 GGTAGTCATAATAGCACAG - -a -s simMouse_chr6.simMouse.chr6 230281 39 + 636262 AAAGCAATGTTTAGTCTATGAAGTTTTATGTTTGACCAT -s Anc0.Anc0refChr5 42389 34 - 87904 GAATCAATGCTGAGTCTGTT---CATCATGCCT--CCAT -s Anc1.Anc1refChr7 7387 35 - 47259 GAATCAATGCTGAGTCTGTT--GCATCATGCCT--CCAT -s Anc2.Anc2refChr15 45140 34 - 86568 GAATCAATGCTGAGTCTGCT---CATCATACCT--CCAT -s mr.mrrefChr5 84294 39 + 294540 AAAGCAATGTTTAGTCTATGAAGTTTTATGTTTGACCAT -s simCow_chr6.simCow.chr6 205180 34 + 602619 GAAGCAATGCTGAGTCTGCT---CATCAAACCG--CCAT -s simDog_chr6.simDog.chr6 380658 30 - 593897 GCAT----GCCGAGTCTGCT---CAACATACCT--CCAT -s simHuman_chr6.simHuman.chr6 308657 35 - 601863 GAATTGATGCTGAGTCCGTT--GCATAATGCCC--CCAT -s simRat_chr6.simRat.chr6 221455 39 + 647215 AAAGCTATGTTTAGTCTATGCAATATTATGTTGCACCAT - -a -s simMouse_chr6.simMouse.chr6 230320 20 + 636262 GGTTCTAGTATGTACTAAAA -s Anc0.Anc0refChr5 42423 5 - 87904 GATTC--------------- -s Anc1.Anc1refChr7 7422 18 - 47259 GATTCTAGTGTGTATTAA-- -s Anc2.Anc2refChr15 45174 5 - 86568 GATTC--------------- -s mr.mrrefChr5 84333 20 + 294540 GGTTCTAGTATGTACTAAAA -s simCow_chr6.simCow.chr6 205216 5 + 602619 GAGTC--------------- -s simDog_chr6.simDog.chr6 380688 5 - 593897 GATGC--------------- -s simHuman_chr6.simHuman.chr6 308692 18 - 601863 GATTCTAGTGTGTATTAA-- -s simRat_chr6.simRat.chr6 221494 20 + 647215 GGTTCTAGTAAGTACTAACA - -a -s simMouse_chr6.simMouse.chr6 230340 3 + 636262 CGG -s Anc1.Anc1refChr7 7440 3 - 47259 CGG -s mr.mrrefChr5 84353 3 + 294540 CGG -s simHuman_chr6.simHuman.chr6 308710 3 - 601863 CGG -s simRat_chr6.simRat.chr6 221517 3 + 647215 TGA - -a -s simMouse_chr6.simMouse.chr6 230343 22 + 636262 CAGCACTTCAGCACCTTAACTT -s Anc0.Anc0refChr5 42448 22 - 87904 TAGCCTTCCAACATACTAACTT -s Anc1.Anc1refChr7 7463 22 - 47259 TAGCCTTCCAACATACTAACTT -s Anc2.Anc2refChr15 45199 22 - 86568 TAGCCTTCCGACATACAACTTT -s mr.mrrefChr5 84356 22 + 294540 CAGCACTTCAGCACCTTAACTT -s simCow_chr6.simCow.chr6 205241 19 + 602619 ---CCTGCTGACGTACAAGTTA -s simDog_chr6.simDog.chr6 380713 22 - 593897 TAGCCTTCCGACATACAACTTT -s simHuman_chr6.simHuman.chr6 308792 22 - 601863 TAGCCTTCCAACATAATAACCT -s simRat_chr6.simRat.chr6 221520 22 + 647215 CAGCACTTCAGCATATTAACTT - -a -s simMouse_chr6.simMouse.chr6 230365 5 + 636262 GTCTT -s Anc0.Anc0refChr5 42470 5 - 87904 GTCTT -s Anc1.Anc1refChr7 7485 5 - 47259 GTCTT -s Anc2.Anc2refChr15 45221 5 - 86568 GTATC -s mr.mrrefChr5 84378 5 + 294540 GTCTT -s simCow_chr6.simCow.chr6 205260 5 + 602619 GTATC -s simDog_chr6.simDog.chr6 380735 5 - 593897 GTATT -s simHuman_chr6.simHuman.chr6 308817 5 - 601863 ATCTT -s simRat_chr6.simRat.chr6 221542 5 + 647215 GTCTT - -a -s simMouse_chr6.simMouse.chr6 230370 13 + 636262 TTATTGATAGTTT -s Anc0.Anc0refChr5 42475 13 - 87904 TTAATGATAGTTT -s Anc1.Anc1refChr7 7490 13 - 47259 TTAATGATAGTTT -s Anc2.Anc2refChr15 45226 13 - 86568 TTAATGACAGTTT -s mr.mrrefChr5 84383 13 + 294540 TTATTGATAGTTT -s simCow_chr6.simCow.chr6 205265 13 + 602619 TTCATGACAGTTT -s simDog_chr6.simDog.chr6 380740 13 - 593897 TTAATGGCAGTTT -s simHuman_chr6.simHuman.chr6 308829 13 - 601863 TTAATGATAGTTT -s simRat_chr6.simRat.chr6 221547 13 + 647215 TTATTGATAGCTT - -a -s simMouse_chr6.simMouse.chr6 230383 16 + 636262 ATTTTAAACCTAGTCT -s Anc0.Anc0refChr5 42490 16 - 87904 ATTTTGCACTTAGTCT -s Anc1.Anc1refChr7 7505 16 - 47259 ATTTTGCACTTAGTCT -s Anc2.Anc2refChr15 45241 16 - 86568 ATTTTGCACTTAGTCT -s mr.mrrefChr5 84396 16 + 294540 ATTTTAAACCTAGTCT -s simCow_chr6.simCow.chr6 205280 16 + 602619 ATTTTGCACTCAGTCT -s simDog_chr6.simDog.chr6 380755 16 - 593897 ATTTTGCACCTAGTCT -s simHuman_chr6.simHuman.chr6 308844 16 - 601863 ATTTTGCACTTGGTTT -s simRat_chr6.simRat.chr6 221560 16 + 647215 ATTTTAAACCTAGTCT - -a -s simMouse_chr6.simMouse.chr6 230399 22 + 636262 GGATTTGTCACATAGTTGAGTT -s Anc0.Anc0refChr5 42507 22 - 87904 TAAGTAGCCGCATAATTGAGTT -s Anc1.Anc1refChr7 7522 22 - 47259 TAAGTAGCCGCATAATTGAGTT -s Anc2.Anc2refChr15 45258 22 - 86568 TAAGTAGCTGCATAATTGAGTT -s mr.mrrefChr5 84412 22 + 294540 GGATTTGTCACATAGTTGAGTT -s simCow_chr6.simCow.chr6 205297 22 + 602619 TAACTAGCTGCATAATTGAGTT -s simDog_chr6.simDog.chr6 380772 22 - 593897 TAAGTAGCTGCCTAATTGAGTT -s simHuman_chr6.simHuman.chr6 308861 22 - 601863 TAAGTAGCCGCATAATAGAGTC -s simRat_chr6.simRat.chr6 221576 22 + 647215 GTATTTGTCATATAGTTGGGTT - -a -s simMouse_chr6.simMouse.chr6 230421 21 + 636262 CTTGGTGTAAAATCGCAACTG -s Anc0.Anc0refChr5 42529 21 - 87904 CAAGGCATAGAATGACTACTG -s Anc1.Anc1refChr7 7544 21 - 47259 CAAGGCATAGAATGACTACTG -s Anc2.Anc2refChr15 45280 21 - 86568 CAAGGCATAGAGTGACTACTT -s mr.mrrefChr5 84434 21 + 294540 CTTGGTGTAAAATCGCAACTG -s simCow_chr6.simCow.chr6 205319 21 + 602619 CAAGACAAAGGTTAACAAATC -s simDog_chr6.simDog.chr6 380795 20 - 593897 CAAGGCATAGAGTGAGTAC-T -s simHuman_chr6.simHuman.chr6 308883 21 - 601863 CCAGGCATAGAATGACTACAG -s simRat_chr6.simRat.chr6 221598 21 + 647215 CTTGATGTAAAATGGCAACTG - -a -s simMouse_chr6.simMouse.chr6 230442 16 + 636262 CTATAGGGTCTTAAGA -s Anc0.Anc0refChr5 42550 16 - 87904 CTATAGGGTCTTAAGG -s Anc1.Anc1refChr7 7565 16 - 47259 CTATAGGGTCTTAAGG -s Anc2.Anc2refChr15 45301 16 - 86568 CCATAGGGTCTTAGTG -s mr.mrrefChr5 84455 16 + 294540 CTATAGGGTCTTAAGA -s simCow_chr6.simCow.chr6 205340 16 + 602619 CCATAAGATCTTTGAG -s simDog_chr6.simDog.chr6 380815 16 - 593897 CCATAGGGTCTTAGTA -s simHuman_chr6.simHuman.chr6 308904 13 - 601863 CTGTAGG---CTTAGG -s simRat_chr6.simRat.chr6 221640 16 + 647215 CTATAGGGTCTTAAAA - -a -s simMouse_chr6.simMouse.chr6 230458 23 + 636262 GCGACCGTGCAGGTTGCTCAGAA -s Anc0.Anc0refChr5 42566 20 - 87904 GCGATAGTGT---CTGCTGAGAA -s Anc1.Anc1refChr7 7581 20 - 47259 GCGATAGTGT---CTGCTGAGAA -s Anc2.Anc2refChr15 45325 20 - 86568 GCCATAGTGT---CTGCTGAGAA -s mr.mrrefChr5 84471 23 + 294540 GCGACCGTGCAGGTTGCTCAGAA -s simCow_chr6.simCow.chr6 205364 20 + 602619 GCCATAGTGT---CTGCTGAGAA -s simDog_chr6.simDog.chr6 380839 20 - 593897 GCCATAGGGT---CTGCTGAGAG -s simHuman_chr6.simHuman.chr6 308917 20 - 601863 GTGATAGTGT---CTGCTGACAA -s simRat_chr6.simRat.chr6 221656 23 + 647215 GCGACCATCAGGGTTACTGAGAG - -a -s simMouse_chr6.simMouse.chr6 230481 26 + 636262 CCATTGATCAACATCATTATGTGAGC -s Anc0.Anc0refChr5 42587 26 - 87904 CCATAGATCAACAGCACTATGTGAGC -s Anc1.Anc1refChr7 7602 26 - 47259 CCATAGATCAACAGCACTATGTGAGC -s Anc2.Anc2refChr15 45346 26 - 86568 CCATAGATCAACAGCACTATGTGAGC -s mr.mrrefChr5 84494 26 + 294540 CCATTGATCAACATCATTATGTGAGC -s simCow_chr6.simCow.chr6 205385 16 + 602619 CCA----------GCACTATGCGGTC -s simDog_chr6.simDog.chr6 380860 26 - 593897 CTGTAGATCAACAGCACTATGTGAGC -s simHuman_chr6.simHuman.chr6 308938 25 - 601863 CCATAGATGAACAGCACTA-GAGAGC -s simRat_chr6.simRat.chr6 221679 26 + 647215 TCATTAATCAACATCATTATGTGAGC - -a -s simMouse_chr6.simMouse.chr6 230507 140 + 636262 TTCTGAGAGTTACCACAATTGTGGACTGTGTAATAGGTTAGGCACAGCCTACGGAACATGTAAGTACAGTATTTTGGTTGGAGCCATTCAAGTAGGCAATTGGCCTGAGGGAGATTGGATTGCACCCTTGTTTACCAAAC -s Anc0.Anc0refChr5 43393 26 - 87904 TTCTAATGTTT-------CTGTTG-----GTAATAAGT------------------------------------------------------------------------------------------------------ -s Anc1.Anc1refChr7 8408 26 - 47259 TTCTAATGTTT-------CTGTTG-----GTAATAAGT------------------------------------------------------------------------------------------------------ -s Anc2.Anc2refChr15 46416 26 - 86568 TCCTAATGTTT-------CTGTTG-----GTGTTCAGA------------------------------------------------------------------------------------------------------ -s mr.mrrefChr5 84520 119 + 294540 TTCTGAGAGTTA-CACAATTGTGGAC--TGTAATAGGTTAGGCACAGCCTACGGAACATGTAAGTACA---------------CCATTCAAGTAGGCAATTGGCCTGAGGGAGATTGGATTGCACC---GTTTACCAAAC -s simCow_chr6.simCow.chr6 206429 26 + 602619 CACGAATGTTT-------ATGTTG-----ATGTTCAGC------------------------------------------------------------------------------------------------------ -s simDog_chr6.simDog.chr6 381847 20 - 593897 TCCTAATGTTT-------CTGTCT-----G------GA------------------------------------------------------------------------------------------------------ -s simHuman_chr6.simHuman.chr6 309761 26 - 601863 TTCTAATGTTT-------CTGTTG-----GTAATAAGT------------------------------------------------------------------------------------------------------ -s simRat_chr6.simRat.chr6 221705 119 + 647215 TACTGAGAGTTG-CACAACAGTGAAT--CGTAATGGGTTGGACACAGTCTGGGGAACGTGTAAGTACA---------------CCATTTGAGTTGGCAATTGGCCTGGGGGATATCAGGTTATACC---GTGTATCAAAC - -a -s simMouse_chr6.simMouse.chr6 230647 87 + 636262 ACCCGACCAGTTGAACTAGGGGACTAAAATGGATTCAACTGAGAATGGAGGTATGTCACACACGGGTGTTTGCCAGCCTGTGAAGTT -s mr.mrrefChr5 84639 87 + 294540 ACCCGACCAGTTGAACTAGGGGACTAAAATGGATTCAACTGAGAATGGAGGTATGTCACACACGGGTGTTTGCCAGCCTGTGAAGTT -s simRat_chr6.simRat.chr6 221825 87 + 647215 CCCCAATCAGTTGAACTAGAGAACTAAGATGGATTCAACTGAGGATGGAGGTCTGTCACATAAGGGTGCCTGCCAGTCTGTGAAGTT - -a -s simMouse_chr6.simMouse.chr6 230734 10 + 636262 TACAGGTTTG -s mr.mrrefChr5 84726 10 + 294540 TACAGGTTTG -s simRat_chr6.simRat.chr6 221922 10 + 647215 CACAGATTTG - -a -s simMouse_chr6.simMouse.chr6 230744 467 + 636262 CCTGTTAGGATTGGTAAGAACAACTAAGTGCGTGCAACATGAGGGGGGATGTAGGGGTATAGGTAAATAAATCTAGGATGCTACATTTAGTCTAACATATCATTGTAACATCAAGTATCAATGTTAACATCCCCCATTCATACATTAAGATAAGAATTGGCTAAACAGCTATGGTGTGTATTATTATCTTATAAAGTTTTAAGTGGTGCTTCGCAGAGTAAGTCATAGATTAGTCCAATCTATCAGAGTACCTTGTAAGACTATATTTCATCACACTCATTTCTAATAAAGGGATGAACAACAATTAATCCATATTACCCATATCGTCCACACATTACAGTGTAGCACTCACTGGTTATAACAACTCTCTTACCTGGACCCGACTTATCACATTCATGGTTACCAACGAACTGTGGAATTATCAATCACAATGGCAGCACTCATTGGAAGCTCTCTATCATGATTCT -s Anc0.Anc0refChr5 43419 19 - 87904 --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GGAGCTCT--ATCATGATCCT -s Anc1.Anc1refChr7 8434 19 - 47259 --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GGAGCTCT--ATCATGATCCT -s Anc2.Anc2refChr15 46442 19 - 86568 --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GGAGCTCT--ATCATTATCCT -s mr.mrrefChr5 84736 112 + 294540 CCTGTTAGGATTGGTAAGAACAACTAA----GTGCAACATGAGGGGGGATGTAGGGGTATAGGTAAATAAATCTAGG------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TCACAATG-CAGCACTCATTGGGAGCTCT--ATCATGATTCT -s simCow_chr6.simCow.chr6 206455 19 + 602619 --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AGAGCTCT--CTCATTATACT -s simDog_chr6.simDog.chr6 381867 19 - 593897 --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GGAGCTCT--ATCATTACCCT -s simHuman_chr6.simHuman.chr6 309787 19 - 601863 --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GGAGCCCT--ACCATGATCCT -s simRat_chr6.simRat.chr6 221940 112 + 647215 CCTGTTAGGACTGGTAAGTACAACTAA----GTGCAACATGAGTGGGGATGTCAGGGTATAAGCATGTAGAGCAGGG------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TCACAATG-CGGCACTCATTGGGAGCTCT--ATCATGATTCT - -a -s simMouse_chr6.simMouse.chr6 231211 6 + 636262 TCCATT -s Anc0.Anc0refChr5 43441 6 - 87904 TCCATT -s Anc1.Anc1refChr7 8456 6 - 47259 TCCATT -s Anc2.Anc2refChr15 46464 6 - 86568 TTCTGT -s mr.mrrefChr5 84848 6 + 294540 TCCATT -s simDog_chr6.simDog.chr6 381889 6 - 593897 TTCTGT -s simHuman_chr6.simHuman.chr6 309809 6 - 601863 TCCATT -s simRat_chr6.simRat.chr6 222052 6 + 647215 TCCATC - -a -s simMouse_chr6.simMouse.chr6 231217 36 + 636262 CTTCTCTGCCTCTTCTTGCTGGCAAGTTTTGTGCCT -s Anc0.Anc0refChr5 43467 34 - 87904 CTTCTCAGTTTCCTCTTGTTGGCAGGTTT--TGCCT -s Anc1.Anc1refChr7 8482 36 - 47259 CTTCTCAGTTTCCTCTTGTTGGCAGGTTTTGTGCCT -s Anc2.Anc2refChr15 46490 34 - 86568 TTTCTCAGTTTCCCCTTGTAGGCAGGTTT--TGCCT -s mr.mrrefChr5 84854 36 + 294540 CTTCTCTGCTTCTTCTTGCTGGCAAGTTTTGTGCCT -s simCow_chr6.simCow.chr6 206488 22 + 602619 ------------CCCTTGTAGGTAGGTTT--GATCA -s simDog_chr6.simDog.chr6 381915 34 - 593897 TTTCTCAGTTTCCCCTTGCACGCAGGTTT--TGCCT -s simHuman_chr6.simHuman.chr6 309836 36 - 601863 CTTCACAGATTTCTCTTGTTGGCAGGTCTTTTGCCG -s simRat_chr6.simRat.chr6 222058 36 + 647215 CTGCTCGGCTTCATCTTGCTGGCAAGTTTTGTGCCT - -a -s simMouse_chr6.simMouse.chr6 231253 1 + 636262 A -s Anc0.Anc0refChr5 43501 1 - 87904 C -s Anc1.Anc1refChr7 8518 1 - 47259 C -s Anc2.Anc2refChr15 46524 1 - 86568 C -s mr.mrrefChr5 84890 1 + 294540 A -s simCow_chr6.simCow.chr6 206547 1 + 602619 C -s simDog_chr6.simDog.chr6 381949 1 - 593897 A -s simHuman_chr6.simHuman.chr6 309872 1 - 601863 C -s simRat_chr6.simRat.chr6 222094 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 231254 253 + 636262 ACACCAATGTGCTTCCTAGGAATTGTGGTGCTGCTGTGCTAAGTTAAGGGGTTGATAGTTCACAACTTTTACCTGTTCTTAACTATGCTGAGAGGGGGCTAATTATCACCTTAGAGACGGTGAAGGGGACCTTGGGATAATTTCTAACACACATCAGAGATCGCAACCTATACAGGACTATTGTTCCCCAAGACCTTGGGATAATTTCTAACACACATCAGAGATCGCAACCTATACAGGACTATTGTTCCCT -s Anc0.Anc0refChr5 43502 122 - 87904 TCACCAATTTGATTACAATCAAATATCACACTGCTGTG-----TTAAAGGTTTGAAATTTCACAATCTTTATCTGTG-----------------------------------------------------------------------------------------------------------------------TGG-ATTATTTCTATCACAAATCAGAGGGCACTACT------TGACTATTATTCTCC -s Anc1.Anc1refChr7 8519 128 - 47259 TCACCAATTTGATTACAATCAAATATCACACTGCTGTG-----TTAAAGGTTTGAAATTTCACAATCTTTATCTGTG-----------------------------------------------------------------------------------------------------------------------TGG-ATTATTTCTATCACAAATCAGAGGGCACTACTTATACATGACTATTATTCTCC -s Anc2.Anc2refChr15 46525 122 - 86568 GCACCAATTTGATTACAATCAAATATCACATTGCTGTG-----TTAAAGGTTTCAAATTTCACAATCTTTATCTGTG-----------------------------------------------------------------------------------------------------------------------GGG-ATTATTTCTATCACAAATCAGAGGGCACTCCT------TGAAAATTATTCTCA -s mr.mrrefChr5 84891 134 + 294540 TCACCAATGTGCTTCCAAGCAATTATCATGCTGCTGTGCTAAGTTAAGGGGTTGATAGTTCACAACTTTTACCTGTT-----------------------------------------------------------------------------------------------------------------------TGGGATAATTTCTATCACACATCAGAGATCGCTACCTATACATGACTATTATTCCCC -s simCow_chr6.simCow.chr6 206548 110 + 602619 ACCCCAAGTTGATTAAAATTGAATGCCACATTACTGTG-----TTGAAGCTTTCAAATTCCACAATCTTTATCTGTG-----------------------------------------------------------------------------------------------------------------------CGG-ACTATTCCTATCACAAATAAGAGCGCA------------------TATTCTCA -s simDog_chr6.simDog.chr6 381950 114 - 593897 GCACCAATTTGACTTCAATCAAATATCACATTGATGTG-----TTAAAGGTTTCAAATTTCACAACCTTTATTTGTT-----------------------------------------------------------------------------------------------------------------------GAG-ATTATTTCTAGCACAAATCAGAGGGCACTCCT------TGAAAAT-------- -s simHuman_chr6.simHuman.chr6 309873 127 - 601863 TCACCAATTTGTTGATAATCAAATATCACACAGCCATG-----TTAATGGTTTGAAATTTCACAATCATGGTCTGCG-----------------------------------------------------------------------------------------------------------------------TGG-ATTATTTCTGTCACAAAT-AGAAGGCACTACTTATACATTACTATTATTCTCC -s simRat_chr6.simRat.chr6 222105 134 + 647215 TCATCAATGTGCTTCCAAGCAATTATCATGTTGCTGCATTAAGTTAGGGGCTTGATAGTCCACAACTTTTACCTGTT-----------------------------------------------------------------------------------------------------------------------TGGGATAACTTCTATCACATATCAGAGATCGCTACCTATAGATGACTATTATTCCCC - -a -s simMouse_chr6.simMouse.chr6 231507 6 + 636262 AAGGTG -s Anc0.Anc0refChr5 43625 6 - 87904 TAGGCT -s Anc1.Anc1refChr7 8648 6 - 47259 TAGGCT -s Anc2.Anc2refChr15 46648 6 - 86568 TAGGCT -s mr.mrrefChr5 85026 6 + 294540 AAGGCG -s simCow_chr6.simCow.chr6 206659 6 + 602619 TAGGCT -s simHuman_chr6.simHuman.chr6 310001 6 - 601863 CAGGCT -s simRat_chr6.simRat.chr6 222240 6 + 647215 AAGGCG - -a -s simMouse_chr6.simMouse.chr6 231513 25 + 636262 CATCTGCATGGGTAAATTCACAGCA -s Anc0.Anc0refChr5 43631 24 - 87904 TATCTGGATA-GGGTAATCACTACA -s Anc1.Anc1refChr7 8654 25 - 47259 TATCTGGATAGGGGTAATCACTACA -s Anc2.Anc2refChr15 46654 24 - 86568 TATCTGGATA-GGATAATCACTACA -s mr.mrrefChr5 85032 25 + 294540 CATCTGGATGGGTGAATTCACAGCA -s simCow_chr6.simCow.chr6 206667 24 + 602619 TATCTGGATA-GGATAATCACTACA -s simHuman_chr6.simHuman.chr6 310007 25 - 601863 TTCCTGGATTGAGGCAATTACGACA -s simRat_chr6.simRat.chr6 222246 25 + 647215 CATCTGGATGGGTGAATTCACACCA - -a -s simMouse_chr6.simMouse.chr6 231538 5 + 636262 AGTCA -s Anc0.Anc0refChr5 43674 5 - 87904 AGTCA -s Anc1.Anc1refChr7 8698 5 - 47259 AGTCA -s Anc2.Anc2refChr15 46697 5 - 86568 AATCC -s mr.mrrefChr5 85057 5 + 294540 AGTCA -s simCow_chr6.simCow.chr6 206712 5 + 602619 AATTC -s simDog_chr6.simDog.chr6 382064 2 - 593897 ---CC -s simHuman_chr6.simHuman.chr6 310051 5 - 601863 AGGCA -s simRat_chr6.simRat.chr6 222271 5 + 647215 AGTCT - -a -s simMouse_chr6.simMouse.chr6 231543 6 + 636262 TACAAC -s Anc0.Anc0refChr5 43681 6 - 87904 TACAAC -s Anc1.Anc1refChr7 8705 6 - 47259 TACAAC -s Anc2.Anc2refChr15 46704 6 - 86568 ACAGGC -s mr.mrrefChr5 85062 6 + 294540 TACAAC -s simCow_chr6.simCow.chr6 206719 6 + 602619 ACAAGC -s simDog_chr6.simDog.chr6 382068 6 - 593897 ACAGGC -s simHuman_chr6.simHuman.chr6 310058 6 - 601863 TACAAC -s simRat_chr6.simRat.chr6 222276 6 + 647215 TACAAC - -a -s simMouse_chr6.simMouse.chr6 231549 29 + 636262 CATCTGGAGAGAGTTATACAGAAGGCATA -s Anc0.Anc0refChr5 43687 28 - 87904 CACATGGGAAGAGCACCATAGCATACG-A -s Anc1.Anc1refChr7 8711 29 - 47259 CACATGGGAAGAGCACCATAGCATACGCA -s Anc2.Anc2refChr15 46710 28 - 86568 AACATGGGAATAGCACCATAGCACACA-G -s mr.mrrefChr5 85068 29 + 294540 CATCTGGAGAGAGTTATACAGAATGCGTA -s simCow_chr6.simCow.chr6 206725 28 + 602619 AGCATTCAAGCAGCACCATGGCACACA-G -s simDog_chr6.simDog.chr6 382074 28 - 593897 AACATGGGAATAGCACCATAGCGCACA-G -s simHuman_chr6.simHuman.chr6 310072 29 - 601863 CACATGGGAAGGGCACCATAGCATACGCA -s simRat_chr6.simRat.chr6 222282 29 + 647215 CATCTGGCGAGTGTCGTACAGAATGTGTA - -a -s simMouse_chr6.simMouse.chr6 231578 2 + 636262 GC -s Anc0.Anc0refChr5 43715 2 - 87904 AC -s Anc1.Anc1refChr7 8740 2 - 47259 AC -s Anc2.Anc2refChr15 46738 2 - 86568 AC -s mr.mrrefChr5 85097 2 + 294540 AC -s simCow_chr6.simCow.chr6 206753 2 + 602619 AC -s simDog_chr6.simDog.chr6 382102 2 - 593897 AC -s simHuman_chr6.simHuman.chr6 310103 2 - 601863 AT -s simRat_chr6.simRat.chr6 222311 2 + 647215 AC - -a -s simMouse_chr6.simMouse.chr6 231580 56 + 636262 TTGAAAACACAGCAAGCGGGTGTAAATGCAATAGTGAAAGGTTATGCCTACATACA -s Anc0.Anc0refChr5 43717 39 - 87904 TTTGAAAC----CAAGCAGATATGATTG-------------TTCTGCCACCATGCA -s Anc1.Anc1refChr7 8742 43 - 47259 TTTGAAACAAATCAAGCAGATATGATTG-------------TTCTGCCACCATGCA -s Anc2.Anc2refChr15 46740 39 - 86568 TTTGAAAC----CAAGCAGACATGATTA-------------TGCTGCCACCATGCA -s mr.mrrefChr5 85099 56 + 294540 TTGAAAACACAGCAAGCAGGTGTAAATGCAATAGTGAAAGGTTATGCCTACATGCA -s simCow_chr6.simCow.chr6 206756 37 + 602619 TTTGGAAC----CAAGCCGTCATGAATA-------------TGCTGGCCCCATG-- -s simDog_chr6.simDog.chr6 382104 39 - 593897 TTTGAAAC----CAAGCAGACATGATTA-------------TGCCCCCACCACTCA -s simHuman_chr6.simHuman.chr6 310105 43 - 601863 TTTGAAACAAATCAAGCAGATATGGCTG-------------TTCTGTCACCGTGTA -s simRat_chr6.simRat.chr6 222313 56 + 647215 TTGAAAACACAGCAAGTAGTTGTAAATGCAACAGTGAAAGGTTTTGCCCACATGCA - -a -s simMouse_chr6.simMouse.chr6 231636 103 + 636262 TATCAACTTTAGAGCTCCAGAGTTGGCTGTCACTTATGACATAAAGTGTGAGTCCCCAACTATCAGCATAAAGTGTAATCTTAGCATGACTGCCGTACTGGGA -s Anc0.Anc0refChr5 43757 88 - 87904 TATCAACATTATAGCTCCAGAGTTGGCTAT-----ATCAGACAG----------CTCACCTATTCACATAAAGTGTAATCTTTACACAACTCCACTATTGGGA -s Anc1.Anc1refChr7 8786 88 - 47259 TATCAACATTATAGCTCCAGAGTTGGCTAT-----ATCAGACAG----------CTCACCTATTCACATAAAGTGTAATCTTTACACAACTCCACTATTGGGA -s Anc2.Anc2refChr15 46780 88 - 86568 TATCAACAGTGTAGCTCCAGAGTTAGCTAT-----ATCAGACAG----------CTCGCGTATTCAAACAAAATGTAAGCTTTACACAACTCCTCTATTGTAA -s mr.mrrefChr5 85155 103 + 294540 TATCAACTTTAGAGCTCCAGAGTTGGCTATCACTTATGACATAGAGTGTGAGTCCCCAACTATTAGCATAAAGTGTAATCTTAGCATGACTGCAGTACTGGGA -s simCow_chr6.simCow.chr6 110213 13 + 602619 ------------------------------------------------------------------------------------------TCCATTACTGTTA -s simDog_chr6.simDog.chr6 382144 88 - 593897 TATCAACAGTGTAGCTCCAGAGTTAGCTAT-----ATCAGACAG----------CTCGCGTATTCAAACAAAATGTAAGCTTTACACAACTCCTCTATTGTAA -s simHuman_chr6.simHuman.chr6 310149 88 - 601863 TATCAACATTATAGCTCCAGAGTTGGCTAT-----ATCAGACAG----------CTCACCTAATGACATAAAGTGCAATCTTGACACAACACCACTATTGGGA -s simRat_chr6.simRat.chr6 222369 102 + 647215 TATCAACTTTAGCGCTCCAGAGTCAGCTATCACCTATGACATAGAGTGCGATTCCCCAAATATT-GCATAACGTGTAATGTTACCATGACTGCAGTACTGGGA - -a -s simMouse_chr6.simMouse.chr6 231739 1 + 636262 T -s Anc0.Anc0refChr5 43845 1 - 87904 C -s Anc1.Anc1refChr7 8874 1 - 47259 C -s Anc2.Anc2refChr15 46868 1 - 86568 C -s mr.mrrefChr5 85258 1 + 294540 T -s simCow_chr6.simCow.chr6 110228 1 + 602619 C -s simDog_chr6.simDog.chr6 382232 1 - 593897 C -s simHuman_chr6.simHuman.chr6 310237 1 - 601863 C -s simRat_chr6.simRat.chr6 222471 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 231740 1 + 636262 C -s Anc0.Anc0refChr5 51657 1 + 87904 C -s Anc1.Anc1refChr7 8875 1 - 47259 C -s Anc2.Anc2refChr15 47917 1 + 86568 A -s mr.mrrefChr5 85259 1 + 294540 C -s simCow_chr6.simCow.chr6 373358 1 - 602619 A -s simDog_chr6.simDog.chr6 219824 1 + 593897 A -s simHuman_chr6.simHuman.chr6 310238 1 - 601863 C -s simRat_chr6.simRat.chr6 222472 1 + 647215 C - -a -s simMouse_chr6.simMouse.chr6 231741 1 + 636262 A -s Anc0.Anc0refChr5 51660 1 + 87904 A -s Anc1.Anc1refChr7 8878 1 - 47259 A -s Anc2.Anc2refChr15 47920 1 + 86568 G -s mr.mrrefChr5 85260 1 + 294540 A -s simCow_chr6.simCow.chr6 373361 1 - 602619 G -s simDog_chr6.simDog.chr6 219827 1 + 593897 G -s simHuman_chr6.simHuman.chr6 310246 1 - 601863 A -s simRat_chr6.simRat.chr6 222473 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 231742 8 + 636262 CTTCAGCC -s Anc0.Anc0refChr5 51661 8 + 87904 CTTCAGCA -s Anc1.Anc1refChr7 8879 8 - 47259 CTTCAGCA -s Anc2.Anc2refChr15 47921 8 + 86568 TTTCGGCG -s mr.mrrefChr5 85261 8 + 294540 CTTCAGCA -s simDog_chr6.simDog.chr6 219881 8 + 593897 TTTCGGCG -s simHuman_chr6.simHuman.chr6 310247 8 - 601863 CTTCAGCA -s simRat_chr6.simRat.chr6 222474 8 + 647215 CTTCAGCA - -a -s simMouse_chr6.simMouse.chr6 231750 14 + 636262 ATGATACGCAATGT -s Anc0.Anc0refChr5 51669 14 + 87904 ATGATACACAGTGC -s Anc1.Anc1refChr7 8887 14 - 47259 ATGATACACAGTGC -s Anc2.Anc2refChr15 47929 14 + 86568 ATTACACACAGTGC -s mr.mrrefChr5 85269 14 + 294540 ATGATACGCAGTGT -s simDog_chr6.simDog.chr6 219893 14 + 593897 ATTACACACAGTGC -s simHuman_chr6.simHuman.chr6 310255 14 - 601863 ATGATACACAGTGC -s simRat_chr6.simRat.chr6 222482 13 + 647215 A-GATATGCTGCGT - -a -s simMouse_chr6.simMouse.chr6 231764 12 + 636262 CACCAATCTGAG -s Anc0.Anc0refChr5 51688 12 + 87904 AACAAGTATAAA -s Anc1.Anc1refChr7 8906 12 - 47259 AACAAGTATAAA -s Anc2.Anc2refChr15 47948 12 + 86568 AACAAGCATAAA -s mr.mrrefChr5 85283 12 + 294540 CACCAATCTGAG -s simDog_chr6.simDog.chr6 219912 12 + 593897 AACAAGCATAAA -s simHuman_chr6.simHuman.chr6 310274 12 - 601863 AACAAGTATAAA -s simRat_chr6.simRat.chr6 222495 12 + 647215 CACCAATCTGAG - -a -s simMouse_chr6.simMouse.chr6 231776 47 + 636262 GCATATGCCTTACTAATTCTAGCACCATAGACAGTAAACTCGAGTCA -s Anc0.Anc0refChr5 51701 44 + 87904 GCATATGTGGTACCAATTT--AACCCTGGCTTATTAATTCTAACTC- -s Anc1.Anc1refChr7 8919 47 - 47259 GCATATGTGGTACCAATTTTAAACCCTGGCTTATTAATTCTAACTCC -s Anc2.Anc2refChr15 47961 44 + 86568 GCATCTATGGCACCAATTT--AACAGTGGCTAATTAATTCTAGCTC- -s mr.mrrefChr5 85295 47 + 294540 GCATATGCCTTACTAATTTTAGAACCTTAGATAGTAAACTCAAGTCA -s simDog_chr6.simDog.chr6 219925 44 + 593897 GCATCTATGGCACCAATTT--AACAGTGGCTAATTAATTCTAGCTC- -s simHuman_chr6.simHuman.chr6 310287 46 - 601863 GCATATGTGATACC-GTTTTAAACCCTGGCTTACTAATTCTAACTCC -s simRat_chr6.simRat.chr6 222507 47 + 647215 GCATATGCCTTACTAATTTTAGATCTTCAGATGGTAAACTCAAGTTA - -a -s simMouse_chr6.simMouse.chr6 231823 66 + 636262 GTCAGCTAGAAGAGTTCCGCAATGTCCCGGAACCAGCCAAAAATGCGAATGGGTGTTCTACGGCTC -s Anc0.Anc0refChr5 51755 49 + 87904 GTCAGCTAGAGGAGGT------------AGAAGCAGCCATAA-----AATGAGTGCTTTACAATTC -s Anc1.Anc1refChr7 8978 49 - 47259 GTCAGCTAGAGGAGGT------------AGAAGCAGCCATAA-----AATGAGTGCTTTACAATTC -s Anc2.Anc2refChr15 48015 49 + 86568 GTCATCTATAGGGGGT------------AGGAGCAGCCATGA-----AATGAGAGCTTTACAACCC -s mr.mrrefChr5 85354 66 + 294540 GTCAGCTAGAAGAGTTCCGCAATGTCCCAGAACCAGCCAAAAATGCGAATGAGTGTTCTACAGTTC -s simDog_chr6.simDog.chr6 219979 49 + 593897 GTCATCTATAGGGGGT------------AGGAGCAGCCATGA-----AATGAGAGCTTTACAACCC -s simHuman_chr6.simHuman.chr6 310346 49 - 601863 GTCAGCTAGAGGAGGT------------AGAAGCAGCCGTAA-----AATGAATGCCTTACAATTC -s simRat_chr6.simRat.chr6 222566 66 + 647215 GTTAGCTGAAAGAGTTCTACAATGTCCCAGAACCAGCAAAAAGTGCAAATGAGTGTTCTACATTTC - -a -s simMouse_chr6.simMouse.chr6 231889 3 + 636262 ATG -s Anc0.Anc0refChr5 51804 3 + 87904 ATG -s Anc1.Anc1refChr7 9027 3 - 47259 ATG -s Anc2.Anc2refChr15 48064 3 + 86568 ACA -s mr.mrrefChr5 85420 3 + 294540 ATG -s simDog_chr6.simDog.chr6 220029 3 + 593897 ACA -s simHuman_chr6.simHuman.chr6 310395 3 - 601863 ATG -s simRat_chr6.simRat.chr6 222632 3 + 647215 ATG - -a -s simMouse_chr6.simMouse.chr6 231892 2 + 636262 TA -s Anc0.Anc0refChr5 51809 2 + 87904 TA -s Anc1.Anc1refChr7 9032 2 - 47259 TA -s Anc2.Anc2refChr15 48069 2 + 86568 TA -s mr.mrrefChr5 85423 2 + 294540 TA -s simDog_chr6.simDog.chr6 220034 2 + 593897 TA -s simHuman_chr6.simHuman.chr6 310400 2 - 601863 TA -s simRat_chr6.simRat.chr6 222635 2 + 647215 TA - -a -s simMouse_chr6.simMouse.chr6 231894 11 + 636262 TCATGGAATAC -s Anc0.Anc0refChr5 51811 7 + 87904 TCACAGA---- -s Anc1.Anc1refChr7 9034 11 - 47259 TCACAGAACAC -s Anc2.Anc2refChr15 48071 7 + 86568 TCATATA---- -s mr.mrrefChr5 85425 11 + 294540 TCATGGAATAC -s simDog_chr6.simDog.chr6 220037 7 + 593897 TCATATA---- -s simHuman_chr6.simHuman.chr6 310402 11 - 601863 TCACAGAACAC -s simRat_chr6.simRat.chr6 222637 11 + 647215 TCATGGAATAT - -a -s simMouse_chr6.simMouse.chr6 231905 54 + 636262 GTTCTAGCCAATTCGAAAGGATATAGCTTAGTACCTCTTTGCATTGTGATGTCC -s Anc0.Anc0refChr5 51818 8 + 87904 -GTTTAGCC--------------------------------------------- -s Anc1.Anc1refChr7 9045 54 - 47259 GGTTTAGCCAATTCAAAAGTATATATCTTAGTGCCTCTTTACACGGGAATGATC -s Anc2.Anc2refChr15 48078 8 + 86568 -TTTCAGCC--------------------------------------------- -s mr.mrrefChr5 85436 54 + 294540 GTTCTAGCCAATTCAAAAGGATATATCTTAGTACCTCTTTGCATTGGGATGACC -s simDog_chr6.simDog.chr6 220044 8 + 593897 -TTTCAGCC--------------------------------------------- -s simHuman_chr6.simHuman.chr6 310414 54 - 601863 GGTTTAGCCAATTCAAAAGTGGATATCCTAGTGCCTCTTTACACGGGAATGATC -s simRat_chr6.simRat.chr6 222648 54 + 647215 GTTATAGCCAATACAAAAGGATATATCTTTGTACCTCCTTGCATTGGGATGACC - -a -s simMouse_chr6.simMouse.chr6 231959 92 + 636262 GACCAGCTTCATGATTGCTGTGAGGCTCATGCGTAATAATGTTTTGGTTAAACAGTAGATAGTCTGCCTCCTACTCATTCTGGCTATGTCTC -s Anc0.Anc0refChr5 51827 71 + 87904 GACCAGCTTCATGA-TGCTGTGAG-----TGTATGATAATGGTTTGGACAAGCAC-------GCTGCCTCTTACTCATC--------CTGTG -s Anc1.Anc1refChr7 9101 91 - 47259 GACCAGCTTCATGA-TGCTGTGAGGCTCATGTATGATAATGGTTTGGACAAGCACTAAATAGGCTGCCTCTTACTCATCTACTCATTCTGTG -s Anc2.Anc2refChr15 48087 71 + 86568 GATCAGTTTCATAG-TACCGTGAG-----TGTATGATAAGTGTTTTGACAAGAAC-------GATGCCTGTTATTCATC--------CTGTG -s mr.mrrefChr5 85492 92 + 294540 GACCAGCTTCATGATTGCTGTGAGGCTCATGCATAATAATGTTTTGGTTAAACAGTAGATAGTCTGCCTCCTACTCATTCTGTCAATGTCTG -s simDog_chr6.simDog.chr6 220053 71 + 593897 GATCAGTTTCATAG-TACCGTGAG-----TGTATGATAAGTGTTTTGACAAGAAC-------GATGCCTGTTATTCATC--------CTGTG -s simHuman_chr6.simHuman.chr6 310470 91 - 601863 GACTAACTTAATGA-TGCTGTGAGGCTCATGAATGGTAATGATTTGGACAAGCACTAAATAGGCAGCCTCTTACTCATCTACTCATTCTGTG -s simRat_chr6.simRat.chr6 222704 92 + 647215 GACCAGCTTCATAATTGATGTGAGGCTTACTCATAATAATGTTTTGGTTAAACAGTAGGTAGCTTGCCTCCTGCTCATTCTGTCAGTGTATG - -a -s simMouse_chr6.simMouse.chr6 232051 59 + 636262 ATCAAGATGTGTAATTTAGAACTATTTTTTCCATTCATGACTCCATGAAGCCCCGCACT -s Anc0.Anc0refChr5 51908 32 + 87904 GTTG--ATGTGTATTTTTGAACTATTCCTCCC-----------------------CA-- -s Anc1.Anc1refChr7 9202 32 - 47259 GTTG--ATGTGTATTTTTGAACTATTCCTCCC-----------------------CA-- -s Anc2.Anc2refChr15 48168 32 + 86568 GTTG--ATATGTGTTTTTAAACTAGTCCGCCC-----------------------CA-- -s mr.mrrefChr5 85584 57 + 294540 ATTGAGATGTGTAATTTTGAACTATTTTTTCCATTCATGACTCCATGAAGCCCCGCA-- -s simDog_chr6.simDog.chr6 220134 32 + 593897 GTTG--ATATGTGTTTTTAAACTAGTCCGCCC-----------------------CA-- -s simHuman_chr6.simHuman.chr6 310571 32 - 601863 GTGG--ATGGGTATTTTTGAACTTTTCCTCCC-----------------------CA-- -s simRat_chr6.simRat.chr6 222796 57 + 647215 ATTGAGATGTTTAATTTTGAACTATTTTTTCCATTCGTGACTCCATTAAGCCCCTCA-- - -a -s simMouse_chr6.simMouse.chr6 232110 12 + 636262 GATGATACCACT -s Anc0.Anc0refChr5 51940 12 + 87904 CACAACTCGTTA -s Anc1.Anc1refChr7 9234 12 - 47259 CACAACTCGTTA -s Anc2.Anc2refChr15 48200 12 + 86568 CACAACTCGTTA -s mr.mrrefChr5 85641 12 + 294540 GACAACACCACT -s simDog_chr6.simDog.chr6 220178 12 + 593897 CACAACTCGTTA -s simHuman_chr6.simHuman.chr6 310603 12 - 601863 CTCAACCCTGTG -s simRat_chr6.simRat.chr6 222853 12 + 647215 GACAACACCACT - -a -s simMouse_chr6.simMouse.chr6 232122 45 + 636262 GAAACAACCATGTGTAAAAAGTATCAACTCGAAAATGAAAATCAT -s Anc0.Anc0refChr5 51952 44 + 87904 AACAT-ACCAAGTGTAAAGAGGATCAACTTCAGAATGAAAAGCTT -s Anc1.Anc1refChr7 9246 45 - 47259 AACATAACCAAGTGTAAAGAGGATCAACTTCAGAATGAAAAGCTT -s Anc2.Anc2refChr15 48212 44 + 86568 AACGT-ACCAAGTGTAAAGGGGATCAACTTCAGAATGAGAAGCTT -s mr.mrrefChr5 85653 45 + 294540 AAAATAACCATGTGTAAAGAGTATCAACTTGAAAATGAAAAGCAT -s simDog_chr6.simDog.chr6 220197 44 + 593897 AACGT-ACCAAGTGTAAAGGGGATCAACTTCAGAATGAGAAGCTT -s simHuman_chr6.simHuman.chr6 310615 45 - 601863 AACATAACCAAGTGTAAAGAGAGTCAACTTCTGAATTAAAGGATT -s simRat_chr6.simRat.chr6 222865 45 + 647215 AAAATAACCATGTATAAAGAGCATCAACTTGAAGATGAAAAGCAT - -a -s simMouse_chr6.simMouse.chr6 232167 14 + 636262 GTGGCCAAACCAGA -s Anc0.Anc0refChr5 51998 14 + 87904 GTGGTTAGACCAGA -s Anc1.Anc1refChr7 9293 14 - 47259 GTGGTTAGACCAGA -s Anc2.Anc2refChr15 48258 14 + 86568 AGGGTTAGACCAGA -s mr.mrrefChr5 85698 14 + 294540 GTGGCCAAACCAGA -s simDog_chr6.simDog.chr6 220243 14 + 593897 AGGGTTAGACCAGA -s simHuman_chr6.simHuman.chr6 310662 14 - 601863 GTGGTTAGACCAGA -s simRat_chr6.simRat.chr6 222910 14 + 647215 GTGGCCAACCCAGA - -a -s simMouse_chr6.simMouse.chr6 232181 28 + 636262 ACATGTGAATGCATAGTCTCTGAAGACT -s Anc0.Anc0refChr5 52024 28 + 87904 ATATGTAAAAGCATAGCCTCTAATGACT -s Anc1.Anc1refChr7 9319 28 - 47259 ATATGTAAAAGCATAGCCTCTAATGACT -s Anc2.Anc2refChr15 48284 28 + 86568 GTATGTAAAAGCATAGCCTTTAATGACT -s mr.mrrefChr5 85712 28 + 294540 ACATGTGAATGCATAGTCTCTGAAGACT -s simCow_chr6.simCow.chr6 229425 28 + 602619 GCACGTAAATGCCTAGCCCTTAATGACT -s simDog_chr6.simDog.chr6 220269 28 + 593897 GTGTGTCAAAGCATAGCCTTTAAGAACT -s simHuman_chr6.simHuman.chr6 310688 28 - 601863 ATATGTAAAAACATAGCCACTAATGACT -s simRat_chr6.simRat.chr6 222924 28 + 647215 ACATGTGAATGCATAGTCTCTGAAGACT - -a -s simMouse_chr6.simMouse.chr6 232209 24 + 636262 ATGCACTTGTTATGCAATTTGTGC -s Anc0.Anc0refChr5 52053 24 + 87904 ATGTGATTGTTATGCATTTTATAC -s Anc1.Anc1refChr7 9348 24 - 47259 ATGTGATTGTTATGCATTTTATAC -s Anc2.Anc2refChr15 48313 24 + 86568 ATATGATTGTTATTCATTATATAC -s mr.mrrefChr5 85740 24 + 294540 ATGCACTTGTTATGCAATTTGTGC -s simCow_chr6.simCow.chr6 229454 22 + 602619 GTAC--TTGTTATACATTATATAC -s simDog_chr6.simDog.chr6 220298 24 + 593897 ATATGATTGTTATTCATTATATAC -s simHuman_chr6.simHuman.chr6 310717 24 - 601863 ATGTGATTGTGATGCATTTTATAC -s simRat_chr6.simRat.chr6 222952 24 + 647215 ATGCACTTGTTATGCAATTTGTGT - -a -s simMouse_chr6.simMouse.chr6 232233 21 + 636262 TCTGTTAGAAGCTGTGAACAA -s Anc0.Anc0refChr5 52092 21 + 87904 TCTGTTAGGAGTTGTCAACAG -s Anc1.Anc1refChr7 9387 21 - 47259 TCTGTTAGGAGTTGTCAACAG -s Anc2.Anc2refChr15 48352 21 + 86568 TTTGTTAGGAGTTGTCAACAG -s mr.mrrefChr5 85764 21 + 294540 TCTGTTAGGAGTTGTGAACAA -s simCow_chr6.simCow.chr6 229491 21 + 602619 CATATTAGGAGCAGTCAACAG -s simDog_chr6.simDog.chr6 220338 21 + 593897 TTTGTTAGGAGTTGTCAACAG -s simHuman_chr6.simHuman.chr6 310756 21 - 601863 TCTGTTAGGAGTTGTCAACAG -s simRat_chr6.simRat.chr6 222976 21 + 647215 TCCATTAGGCATTGTTAACAA - -a -s simMouse_chr6.simMouse.chr6 232254 20 + 636262 TTAGATAGGTATGTAATATC -s Anc0.Anc0refChr5 52233 19 + 87904 TAACCTAGGTATGCAATGC- -s Anc1.Anc1refChr7 9530 20 - 47259 TAACCTAGGTATGCAATGCC -s Anc2.Anc2refChr15 48498 19 + 86568 TGACCTAGGTATGCAATGC- -s mr.mrrefChr5 85900 20 + 294540 TAAGATAGGTATGTAATATC -s simCow_chr6.simCow.chr6 229629 19 + 602619 TGACCTAGGTATACAATGA- -s simDog_chr6.simDog.chr6 220471 19 + 593897 TGACCCAGGTACGTATTGC- -s simHuman_chr6.simHuman.chr6 310899 20 - 601863 TAACTTGCGTATGCAATGCC -s simRat_chr6.simRat.chr6 223112 20 + 647215 TAAGCTAGGTATGTAGTATC - -a -s simMouse_chr6.simMouse.chr6 232274 24 + 636262 TGGAACTATAGGATTACAGGGCAA -s Anc0.Anc0refChr5 52252 17 + 87904 -------ATAGGTCAACAGGGCAA -s Anc1.Anc1refChr7 9550 24 - 47259 TGAAATTATAGGTCAACAGGGCAA -s Anc2.Anc2refChr15 48517 17 + 86568 -------ATGGGTCAACAGAGCAA -s mr.mrrefChr5 85920 24 + 294540 TGGAACTATAGGATTACAGGGCAA -s simCow_chr6.simCow.chr6 229648 14 + 602619 -------GTGAATCAA---AGCAA -s simDog_chr6.simDog.chr6 220490 17 + 593897 -------ATGGGTCAACAGAGCAA -s simHuman_chr6.simHuman.chr6 310920 24 - 601863 TGAAATTGCAAGTCAACAGGACAA -s simRat_chr6.simRat.chr6 223132 24 + 647215 TGGAACTCTAGGATTATAGGGCAA - -a -s simMouse_chr6.simMouse.chr6 232298 5 + 636262 GTAAA -s Anc0.Anc0refChr5 52269 5 + 87904 GTAAA -s Anc1.Anc1refChr7 9574 5 - 47259 GTAAA -s Anc2.Anc2refChr15 48534 5 + 86568 GCAGA -s mr.mrrefChr5 85944 5 + 294540 GTAAA -s simCow_chr6.simCow.chr6 229662 5 + 602619 GCAGA -s simDog_chr6.simDog.chr6 220508 5 + 593897 GCGGA -s simHuman_chr6.simHuman.chr6 310944 5 - 601863 GTAAA -s simRat_chr6.simRat.chr6 223156 4 + 647215 GTAG- - -a -s simMouse_chr6.simMouse.chr6 232303 39 + 636262 CATATTATGTGACCAATTAGAAGACATGTAGCAGCAGTC -s Anc0.Anc0refChr5 52274 39 + 87904 CATATTATATACCAAGTCAGAAGGGGAATAACCGCAGTC -s Anc1.Anc1refChr7 9579 39 - 47259 CATATTATATACCAAGTCAGAAGGGGAATAACCGCAGTC -s Anc2.Anc2refChr15 48539 39 + 86568 CATATTATATACCATGTTAGAACGGGAGTAACCACAGTG -s mr.mrrefChr5 85949 39 + 294540 CATATTATGTGACCAGTCAGAAGACATATAGCAGCAGTC -s simCow_chr6.simCow.chr6 229668 39 + 602619 TGTATTATATGTGATGTTAGAACAGGTGCAACCACAGCG -s simDog_chr6.simDog.chr6 220513 39 + 593897 CATAAGATATACCATGTTAGAACGTGAGTATCCACAGTG -s simHuman_chr6.simHuman.chr6 310949 39 - 601863 CATATTATATACCAAGTCAGAAGGGGAATAACGGCTGTC -s simRat_chr6.simRat.chr6 223160 39 + 647215 CATCTTATTTGTGCTGACAGAAGACATACGGCAGCAGTC - -a -s simMouse_chr6.simMouse.chr6 232342 62 + 636262 ATATTATGCACCCCTCCCCACACACCAGGTGACCTGTGTGTAAACCAGGTAAGCCAGTGGCA -s Anc0.Anc0refChr5 52316 24 + 87904 ACTTTATGCAC------------ACCAG--------------------------CACAAGCA -s Anc1.Anc1refChr7 9621 50 - 47259 ACTTTATGCAC------------ACCAGGTTATGTGCTTCTAAGCCAAGTTAGTCACAAGCA -s Anc2.Anc2refChr15 48581 24 + 86568 ACTTGATGCAT------------ACCAG--------------------------CACAAGCA -s mr.mrrefChr5 85988 50 + 294540 ATATTATGCAC------------ACCAGGTGACCTGTTTGTAAACCAAGTAAGCCAGAGGCA -s simCow_chr6.simCow.chr6 229710 24 + 602619 GCTTCATGTGT------------ACCAG--------------------------AACAAGCT -s simDog_chr6.simDog.chr6 220555 24 + 593897 ATTTGATGCAT------------ACCAG--------------------------CACAAGCA -s simHuman_chr6.simHuman.chr6 310991 50 - 601863 ACTTTATGCAC------------ACCAGGTTATGTGCTTCTAAGCCAAGTTAGTTACAAGCA -s simRat_chr6.simRat.chr6 223199 50 + 647215 ATATTGTGCAC------------ACCAAGTGACCTGTTTGTAAACCAAGTAAGCCAGAGGCA - -a -s simMouse_chr6.simMouse.chr6 232404 15 + 636262 ACCATGCTGACTTAC -s Anc0.Anc0refChr5 52342 14 + 87904 ACCAGGCTGA-TTAT -s Anc1.Anc1refChr7 9673 14 - 47259 ACCAGGCTGA-TTAT -s Anc2.Anc2refChr15 48607 14 + 86568 ACCAGGCTGA-TTAT -s mr.mrrefChr5 86038 15 + 294540 ACCAGGCTGACTTAC -s simCow_chr6.simCow.chr6 229736 14 + 602619 ACCTGTCTGA-TTAT -s simDog_chr6.simDog.chr6 220581 14 + 593897 ACAAGGATGa-ttat -s simHuman_chr6.simHuman.chr6 311043 14 - 601863 ACCAGGCTTA-TTAT -s simRat_chr6.simRat.chr6 223249 15 + 647215 ACCAGGCTGAGTTAC - -a -s simMouse_chr6.simMouse.chr6 232419 8 + 636262 AAACTATG -s Anc0.Anc0refChr5 52356 8 + 87904 AAATTTAG -s Anc1.Anc1refChr7 9687 8 - 47259 AAATTTAG -s Anc2.Anc2refChr15 48621 8 + 86568 AAATTTAG -s mr.mrrefChr5 86053 8 + 294540 AAACTAAG -s simCow_chr6.simCow.chr6 229751 8 + 602619 AAATTTAG -s simDog_chr6.simDog.chr6 220595 8 + 593897 aaatttaa -s simHuman_chr6.simHuman.chr6 311057 8 - 601863 GAATTCAG -s simRat_chr6.simRat.chr6 223264 8 + 647215 AAACTAAG - -a -s simMouse_chr6.simMouse.chr6 232427 14 + 636262 GTATCTTCACAATA -s Anc0.Anc0refChr5 52364 14 + 87904 GTTCCTTCTGTACA -s Anc1.Anc1refChr7 9695 14 - 47259 GTTCCTTCTGTACA -s Anc2.Anc2refChr15 48629 14 + 86568 GTTGCTTCTGTACA -s mr.mrrefChr5 86061 14 + 294540 GTTCCTTCACAACA -s simCow_chr6.simCow.chr6 229759 14 + 602619 GTTGCTTCTGTCCA -s simDog_chr6.simDog.chr6 220612 14 + 593897 GTTGCTTCCATACA -s simHuman_chr6.simHuman.chr6 311065 14 - 601863 GTTCCTTCTGTACA -s simRat_chr6.simRat.chr6 223272 14 + 647215 GTTCCTTCACAACA - -a -s simMouse_chr6.simMouse.chr6 232441 11 + 636262 TCTTAATTTCT -s Anc0.Anc0refChr5 52424 11 + 87904 TATTGACTTGT -s Anc1.Anc1refChr7 9755 11 - 47259 TATTGACTTGT -s Anc2.Anc2refChr15 48689 11 + 86568 CATTGACTGGT -s mr.mrrefChr5 86075 11 + 294540 TATTAACTTCT -s simCow_chr6.simCow.chr6 229819 11 + 602619 CATTGACTGGT -s simDog_chr6.simDog.chr6 220672 7 + 593897 CGTTGAC---- -s simHuman_chr6.simHuman.chr6 311125 11 - 601863 TATTGACCTAT -s simRat_chr6.simRat.chr6 223286 11 + 647215 TATTAACTTCT - -a -s simMouse_chr6.simMouse.chr6 232452 117 + 636262 GAATTTGATTTAACATCTAAATGAACAGGCCTTACAGAAAGATAGTGTACCTAATCAATTTTTTGTTGGAATATGTGTGGTTCTTGTTTGTCGCTAGCTAGATTAATTCATGATATC -s Anc0.Anc0refChr5 52443 110 + 87904 GAATCTATCTTCACATCCAAG-----AGTTCTTCCATGAAGATAGTGAACCTTAGCAATTCTCTG--GGCATACTTGTGATTTGTGTATGTAGCCAGCTAGATTAACTTATGATATC -s Anc1.Anc1refChr7 9774 115 - 47259 GAATCTATCTTCACATCCAAGAAAGCAGTTCTTCCATGAAGATAGTGAACCTTAGCAATTCTCTG--GGCATACTTGTGATTTGTGTATGTAGCCAGCTAGATTAACTTATGATATC -s Anc2.Anc2refChr15 48708 110 + 86568 GGATCCATCTTCACATCCAAG-----AGTTCTTCCATGAAGATAGTGAACCTTAGCAATTCTCTT--GGCATACTCAGGATTTGTGTATTTAGTCAGCTAAATCAACTTATGATATC -s mr.mrrefChr5 86086 117 + 294540 GAATCTGATTTAACATCTAAATGAACAGGCCTTACATAAAGATAGTGAACCTAATCAATTTTTTGTTGGAATATGTGTGGTTCTTGTATGTCGCTAGCTAGATTAATTTATGATATC -s simCow_chr6.simCow.chr6 229838 97 + 602619 GGATCCATCTTCACATCCAAG-----AGTTCTTCCATGAAGATAGTGAACCTTAGCAATTGTGTT--CGCATACCCACGATCCGTGTATTT-------------AAGTTATGACATG -s simDog_chr6.simDog.chr6 220679 56 + 593897 ----------------------------------------------------------TTCGCCT--GGTA-ACTCAGGATTTGTGTATTTAGTCAGCTAAATCAACTGATGGTGCC -s simHuman_chr6.simHuman.chr6 311144 115 - 601863 GAATCTTTCTTCACATCCAGCAAAGCAGTTCTTCCATTAAGATGGTGAAACCTAGTAATTCTATG--GGCAGACTTGTGATTTGTTTATGTAGCCAGCTAGATTAAATTATGATATC -s simRat_chr6.simRat.chr6 223297 117 + 647215 GAATCTGATTTAATATCTAAATGAACAGGGCTTACATGAAGAGAGTGAACCTAATCAATTTTTTGTTTGGATATATGTGCTTCTTGTATGTTGTTAACTAGATTAATTTAAAATATC - -a -s simMouse_chr6.simMouse.chr6 232569 9 + 636262 ACCTTTCTG -s Anc0.Anc0refChr5 52553 9 + 87904 ACTTTTCTA -s Anc1.Anc1refChr7 9889 9 - 47259 ACTTTTCTA -s Anc2.Anc2refChr15 48818 9 + 86568 ACTGTTCTA -s mr.mrrefChr5 86203 9 + 294540 ACCTTTCTG -s simCow_chr6.simCow.chr6 229936 9 + 602619 ACTATTCTA -s simDog_chr6.simDog.chr6 220735 9 + 593897 ACTGTTCTA -s simHuman_chr6.simHuman.chr6 311259 9 - 601863 ACTTTTCTA -s simRat_chr6.simRat.chr6 223414 9 + 647215 ACCTCCATG - -a -s simMouse_chr6.simMouse.chr6 232578 1 + 636262 G -s Anc0.Anc0refChr5 52562 1 + 87904 A -s Anc1.Anc1refChr7 9898 1 - 47259 A -s Anc2.Anc2refChr15 48832 1 + 86568 A -s mr.mrrefChr5 86212 1 + 294540 A -s simDog_chr6.simDog.chr6 220750 1 + 593897 A -s simHuman_chr6.simHuman.chr6 311268 1 - 601863 A -s simRat_chr6.simRat.chr6 223423 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 232579 10 + 636262 TTAGTTATAA -s Anc0.Anc0refChr5 52589 10 + 87904 CTAGCTATAA -s Anc1.Anc1refChr7 9925 10 - 47259 CTAGCTATAA -s Anc2.Anc2refChr15 48859 10 + 86568 CTAACTAGAA -s mr.mrrefChr5 86213 10 + 294540 TTAGTTATAA -s simCow_chr6.simCow.chr6 229969 10 + 602619 CGAACTACAT -s simDog_chr6.simDog.chr6 220777 10 + 593897 CTGAGTAGAA -s simHuman_chr6.simHuman.chr6 311295 10 - 601863 CTAGCTATAA -s simRat_chr6.simRat.chr6 223424 10 + 647215 TAAAGCATAA - -a -s simMouse_chr6.simMouse.chr6 232589 60 + 636262 GCTTACATGTGGTAATGTATATTGTCATCTATTTCCATTTTAAGGTAACTATCCACATAA -s Anc0.Anc0refChr5 52602 57 + 87904 GGATATATGTT---ATTCATACCTTTATGTACTTCCATATTAGGGTGACTTTATAGATAT -s Anc1.Anc1refChr7 9938 60 - 47259 GGATATATGTTGTGATTCATACCTTTATGTACTTCCATATTAGGGTGACTTTATAGATAT -s Anc2.Anc2refChr15 48872 57 + 86568 GGATATGTTTT---ATTCACACCTTTATGTACCTCCATATTGGGATGCCTTTATAGATCT -s mr.mrrefChr5 86223 60 + 294540 GCTTACATGTGGTAATGTATACCGTCATGTATTTCCATATTAAGGTAACTATCCACATAA -s simCow_chr6.simCow.chr6 229982 52 + 602619 GGATATC--------TTCACACCTTTATGTATCTCCCTATTCGGCTAGCTTTATAGATCT -s simDog_chr6.simDog.chr6 220790 33 + 593897 GGATGTGTTTT---A-----------ATGTAC--CCATCTTGAGATGCC----------- -s simHuman_chr6.simHuman.chr6 311308 60 - 601863 GGATATATGTTGTGGTTCATACCTCTATGTACTTCCATATTAGGGTTACTCTATGTATAT -s simRat_chr6.simRat.chr6 223434 60 + 647215 GATGACATGTGGTAATGTATACCATCATGTATTGCCATATTAAGGTAACTATCCTCATGA - -a -s simMouse_chr6.simMouse.chr6 232649 9 + 636262 TCCATTAAG -s Anc0.Anc0refChr5 52659 7 + 87904 TCA--CAAG -s Anc1.Anc1refChr7 9998 7 - 47259 TCA--CAAG -s Anc2.Anc2refChr15 48929 7 + 86568 TTA--CAAG -s mr.mrrefChr5 86283 9 + 294540 TCCATCAAG -s simCow_chr6.simCow.chr6 230060 7 + 602619 TTA--TGTG -s simDog_chr6.simDog.chr6 220823 7 + 593897 TTA--CAAG -s simHuman_chr6.simHuman.chr6 311368 7 - 601863 TCA--CAAG -s simRat_chr6.simRat.chr6 223494 9 + 647215 CTCATCAAG - -a -s simMouse_chr6.simMouse.chr6 232658 165 + 636262 CCTGGGATACTTAATGGGGATACTTAACCTAACTTGTCTTGCCTATGTTAATTAAATGATATGTTTACGTAAGTGCCAAGTTTTGCTGGGGTAACTATCCTCATAATCCATCAAGCCTGGGTACTTAATGGGGATACTTAACCCAACTTGTCCCTATGTTAACTA -s Anc0.Anc0refChr5 52666 22 + 87904 CC--------------------------------TGTCCTGCCTCTGATAA---------------------------------------------------------------------------------------------------------------CTA -s Anc1.Anc1refChr7 10005 22 - 47259 CC--------------------------------TGTCCTGCCTCTGATAA---------------------------------------------------------------------------------------------------------------CTA -s Anc2.Anc2refChr15 48939 22 + 86568 TT--------------------------------TGTCCTGCCTCAAATAA---------------------------------------------------------------------------------------------------------------CTA -s mr.mrrefChr5 86292 54 + 294540 CCTGGGATACTTAATGGGGATACTTAACCTAACTTGTCCTGCCTATGTTAA---------------------------------------------------------------------------------------------------------------CTA -s simCow_chr6.simCow.chr6 230070 22 + 602619 TA--------------------------------TGTCCTGCCTTCAACAA---------------------------------------------------------------------------------------------------------------CTA -s simDog_chr6.simDog.chr6 220833 22 + 593897 TT--------------------------------TGTCTTGTCCCAAATAA---------------------------------------------------------------------------------------------------------------CTA -s simHuman_chr6.simHuman.chr6 311375 22 - 601863 CC--------------------------------TGTCCACCCTCTGGTAC---------------------------------------------------------------------------------------------------------------CTT -s simRat_chr6.simRat.chr6 223503 54 + 647215 CCTGGGACACTTAATGGGAAATCTTAATCTAACTTGTCCTGCCTAAGATAA---------------------------------------------------------------------------------------------------------------CTA - -a -s simMouse_chr6.simMouse.chr6 232823 96 + 636262 AATGATATGTTTACATAAGTGCCAAATTTTGCTGGTGTTAAATGCTTATCACAGCTGGATTTGCAATTCTGAACCACAGCTACTTAACCCTACAAC -s Anc0.Anc0refChr5 52688 88 + 87904 ATAGATAGATTTACATAAGTGCTGAATTTTGCTGGTTTGAAGTGCTCACTGCAACCAGCTT-GCAAGTCAAAAACATA-------TTTCCTACAAT -s Anc1.Anc1refChr7 10027 88 - 47259 ATAGATAGATTTACATAAGTGCTGAATTTTGCTGGTTTGAAGTGCTCACTGCAACCAGCTT-GCAAGTCAAAAACATA-------TTTCCTACAAT -s Anc2.Anc2refChr15 48963 88 + 86568 ATAGATAGATTTACATAAGTGCTGAGTGGTGCTGGTTTGAAGTACTCACTGCAACCAGCTT-GCAAGCCAAAAACATA-------TTTCCGACAAT -s mr.mrrefChr5 86346 88 + 294540 ATTGATATGTTTACATAAGTGCCAAATTTTGCTGGTGTTAAATGCTTATCACAGCTAGATT-GCAATTCTGAACCACA-------ATCCCTACAAT -s simCow_chr6.simCow.chr6 230094 84 + 602619 ----ATGGATTTACATTGATGCTTGGTGTAGGCGGTTTAAAGTACTCACCACAAACAGCTT-GGAAGCCAAGACCATA-------TTTCCAACAAT -s simDog_chr6.simDog.chr6 220857 88 + 593897 ATAGATAGATTTACATAAGTGCTGAGTGGTACTGGTTTGAAGTACTCACTGCAGCCAGCTT-GCAAGCCAAAAACATA-------TTTCCGACAAT -s simHuman_chr6.simHuman.chr6 311397 70 - 601863 ATATATA------------------ACTTTGCTGGTTTGAAGGGCTCACTGCAACCAGCTT-GCACGTCACAAACATA-------TTGCCTACCAT -s simRat_chr6.simRat.chr6 223557 88 + 647215 ATTCATACGTTTACATAAGTGCCAAGTTTCGCCGGTGCTAAATGCTTATCACTGCTAGATT-GCAATTCTGAACCACA-------ATCCCTACAAT - -a -s simMouse_chr6.simMouse.chr6 232919 17 + 636262 ATACAGGTATAATTTGA -s Anc0.Anc0refChr5 52776 16 + 87904 GTA-TGGACAAAGTTAC -s Anc1.Anc1refChr7 10115 16 - 47259 GTA-TGGACAAAGTTAC -s Anc2.Anc2refChr15 49051 16 + 86568 GTA-TGGACAAAGTTTA -s mr.mrrefChr5 86434 16 + 294540 ATA-AGGTATAATTTGC -s simCow_chr6.simCow.chr6 230178 12 + 602619 GTA-TGGACACAG---- -s simDog_chr6.simDog.chr6 220945 16 + 593897 ATA-CAGACAAAATTTA -s simHuman_chr6.simHuman.chr6 311467 16 - 601863 GTA-TGGACAAAGTGAC -s simRat_chr6.simRat.chr6 223648 16 + 647215 ATA-AGGCTTAATTTGC - -a -s simMouse_chr6.simMouse.chr6 232936 51 + 636262 CTTATTAACTGTTGTGATAACATATACATAGGACCTAGCATGAAGGTCCCC -s Anc0.Anc0refChr5 52793 45 + 87904 C------TTTGTTCTGGTAATACGTTCATAGGATTGAGGTAGAAGCTCACC -s Anc1.Anc1refChr7 10132 51 - 47259 CTTACTATTTGTTCTGGTAATACGTTCATAGGATTGAGGTAGAAGCTCACC -s Anc2.Anc2refChr15 49068 45 + 86568 C------TTTGTTCTGGTAATCCGTTCATAGGATTGAGGTAGAGACTCACC -s mr.mrrefChr5 86450 51 + 294540 CTTATTATCTGTTGTGATAACATATACATAGGATTGAGCTAGAAGCTCCCC -s simCow_chr6.simCow.chr6 230190 35 + 602619 --------TTGCTATTGTAATGAGTTCATAAAATTGG--------CTCAGC -s simDog_chr6.simDog.chr6 220962 45 + 593897 C------TTAATTCTGGTAATCCGTTCATAGGATTGAGGTAGAGACTCACC -s simHuman_chr6.simHuman.chr6 311485 51 - 601863 CTTACTATTTGTGCTGGTAATAGGTTCATGGGATTGAGTTAGAAGCTCACC -s simRat_chr6.simRat.chr6 223664 47 + 647215 CTTATTATCT----TGATAACGCATGCATAGGATTGAGATAGAAGCTCCCA - -a -s simMouse_chr6.simMouse.chr6 232987 8 + 636262 TAAATATT -s Anc0.Anc0refChr5 52838 6 + 87904 AAAAT--T -s Anc1.Anc1refChr7 10183 6 - 47259 AAAAT--T -s Anc2.Anc2refChr15 49113 6 + 86568 AAAAT--T -s mr.mrrefChr5 86501 6 + 294540 TAAAT--T -s simCow_chr6.simCow.chr6 230225 6 + 602619 AATAT--T -s simDog_chr6.simDog.chr6 221008 6 + 593897 AAAAT--T -s simHuman_chr6.simHuman.chr6 311536 6 - 601863 AAAAT--C -s simRat_chr6.simRat.chr6 223711 3 + 647215 TAA----- - -a -s simMouse_chr6.simMouse.chr6 232995 14 + 636262 TTCTTTACGCTGCA -s Anc0.Anc0refChr5 52844 14 + 87904 TTCTTTACACTACT -s Anc1.Anc1refChr7 10189 14 - 47259 TTCTTTACACTACT -s Anc2.Anc2refChr15 49119 14 + 86568 CTCTTTATACTACT -s mr.mrrefChr5 86507 14 + 294540 TTCTTTACGCTGCA -s simCow_chr6.simCow.chr6 230234 14 + 602619 CTCTGCATACTACT -s simDog_chr6.simDog.chr6 221014 14 + 593897 CTCTTTATACTACT -s simHuman_chr6.simHuman.chr6 311542 14 - 601863 TTCATTACACTACT - -a -s simMouse_chr6.simMouse.chr6 233009 15 + 636262 TATGCAGATATAGAT -s Anc0.Anc0refChr5 52858 15 + 87904 TATGCAGAAATAGAT -s Anc1.Anc1refChr7 10203 15 - 47259 TATGCAGAAATAGAT -s Anc2.Anc2refChr15 49133 15 + 86568 TATGCAGGAATGGAT -s mr.mrrefChr5 86521 15 + 294540 TATGCAGATATAGAT -s simCow_chr6.simCow.chr6 230250 15 + 602619 TATGTAGGAATGGAT -s simDog_chr6.simDog.chr6 221028 15 + 593897 GATGCAAGAATGGAT -s simHuman_chr6.simHuman.chr6 311556 15 - 601863 TATGCAGACATAGAT - -a -s simMouse_chr6.simMouse.chr6 233024 5 + 636262 AAGAA -s Anc0.Anc0refChr5 52873 3 + 87904 AAG-- -s Anc1.Anc1refChr7 10218 3 - 47259 AAG-- -s Anc2.Anc2refChr15 49148 3 + 86568 AAG-- -s mr.mrrefChr5 86536 3 + 294540 AAG-- -s simCow_chr6.simCow.chr6 230265 3 + 602619 AAG-- -s simDog_chr6.simDog.chr6 221045 3 + 593897 AAG-- -s simHuman_chr6.simHuman.chr6 311571 3 - 601863 AAG-- - -a -s simMouse_chr6.simMouse.chr6 233029 38 + 636262 GTAGATGGGTTTGCCAATTTTACACATGAGGGGCCTGA -s Anc0.Anc0refChr5 52876 38 + 87904 GCAGAAGGATTTGTCGATTTTAAACTTGAGGGGCCTAA -s Anc1.Anc1refChr7 10221 38 - 47259 GCAGAAGGATTTGTCGATTTTAAACTTGAGGGGCCTAA -s Anc2.Anc2refChr15 49151 38 + 86568 GCAGGAGGATTTGTCTATTTCAAACTTGAGGGGCCTAA -s mr.mrrefChr5 86539 38 + 294540 GTAGATGGGTTTGCCGATTTTACACATGAGGGGCCTGA -s simCow_chr6.simCow.chr6 230269 38 + 602619 ATAGGAAGGATCTTCCCTCTCAAACTTGAGAGGCCTAA -s simDog_chr6.simDog.chr6 221048 38 + 593897 GCAGGAGGATTTGCCTATTTCAAACTTTAGGGACCTAA -s simHuman_chr6.simHuman.chr6 311574 38 - 601863 GCAGAATGATTTGTCGGTTTTAAATTTGAGGAGCCTAA -s simRat_chr6.simRat.chr6 223714 38 + 647215 GTAAATGGGACAGCTGCATTTTCACATAAGAGGTCTGA - -a -s simMouse_chr6.simMouse.chr6 233067 3 + 636262 GTG -s Anc0.Anc0refChr5 52914 3 + 87904 GTT -s Anc1.Anc1refChr7 10259 3 - 47259 GTT -s Anc2.Anc2refChr15 49189 3 + 86568 GTT -s mr.mrrefChr5 86577 3 + 294540 GTG -s simCow_chr6.simCow.chr6 230310 3 + 602619 GTT -s simDog_chr6.simDog.chr6 221086 3 + 593897 GTA -s simHuman_chr6.simHuman.chr6 311612 3 - 601863 GTT -s simRat_chr6.simRat.chr6 223752 3 + 647215 GTC - -a -s simMouse_chr6.simMouse.chr6 233070 11 + 636262 GTGCATTCTGA -s Anc0.Anc0refChr5 52919 11 + 87904 ATACTTACTGC -s Anc1.Anc1refChr7 10264 11 - 47259 ATACTTACTGC -s Anc2.Anc2refChr15 49194 11 + 86568 ATATTTACTGC -s mr.mrrefChr5 86580 11 + 294540 ATGCATTCTGA -s simCow_chr6.simCow.chr6 230315 8 + 602619 ATATTAAC--- -s simDog_chr6.simDog.chr6 221091 11 + 593897 ATATTTACTGC -s simHuman_chr6.simHuman.chr6 311617 11 - 601863 ATACTTACTGC -s simRat_chr6.simRat.chr6 223755 11 + 647215 ATGCATTCTGA - -a -s simMouse_chr6.simMouse.chr6 233081 9 + 636262 ATAACCTTC -s Anc0.Anc0refChr5 52936 9 + 87904 ATCAGTTTT -s Anc1.Anc1refChr7 10281 9 - 47259 ATCAGTTTT -s Anc2.Anc2refChr15 49211 9 + 86568 ATCTGTTTT -s mr.mrrefChr5 86591 9 + 294540 ATAACCTTC -s simDog_chr6.simDog.chr6 221108 9 + 593897 ATCTGTTTT -s simHuman_chr6.simHuman.chr6 311634 9 - 601863 ATCAGTTTT -s simRat_chr6.simRat.chr6 223766 9 + 647215 ATATCCTTC - -a -s simMouse_chr6.simMouse.chr6 233090 13 + 636262 AACTACTTGTATG -s Anc0.Anc0refChr5 52945 13 + 87904 AACTACTCTTATG -s Anc1.Anc1refChr7 10290 13 - 47259 AACTACTCTTATG -s Anc2.Anc2refChr15 49220 13 + 86568 AATTACTCTTTTG -s mr.mrrefChr5 86600 13 + 294540 AACTACTTGTATG -s simDog_chr6.simDog.chr6 221118 13 + 593897 AATTACTCTTTTG -s simHuman_chr6.simHuman.chr6 311643 13 - 601863 AACTAGTCCTATG -s simRat_chr6.simRat.chr6 223775 13 + 647215 AACTACTTGTATG - -a -s simMouse_chr6.simMouse.chr6 233103 16 + 636262 GGAAGCCTTTACCAGC -s Anc0.Anc0refChr5 52967 16 + 87904 GGTACCCTTTACTGGC -s Anc1.Anc1refChr7 10312 16 - 47259 GGTACCCTTTACTGGC -s Anc2.Anc2refChr15 49242 16 + 86568 GGTACAATTCTCTGGC -s mr.mrrefChr5 86613 16 + 294540 GGAACCCTTTACCAGC -s simDog_chr6.simDog.chr6 221140 16 + 593897 GGTACAATTCTCTGGC -s simHuman_chr6.simHuman.chr6 311665 16 - 601863 GGTGCCCTTTACTGGC -s simRat_chr6.simRat.chr6 223788 16 + 647215 GGAACCTTTTACCAAC - -a -s simMouse_chr6.simMouse.chr6 233119 27 + 636262 TCGAGTTCTGAGTAGCTTGATGTGCCA -s Anc0.Anc0refChr5 52983 22 + 87904 TTGAGTCCTTATGAGCTTGA-----CA -s Anc1.Anc1refChr7 10328 27 - 47259 TTGAGTCCTTATGAGCTTGATGTGCCA -s Anc2.Anc2refChr15 49258 22 + 86568 TTGAGTCTTTATGGGCTTCA-----CA -s mr.mrrefChr5 86629 27 + 294540 TCGAGTTCTGAGTAGCTTGATGTGCCA -s simDog_chr6.simDog.chr6 221156 22 + 593897 TTGAGTCTTTATGGGCTTCA-----CA -s simHuman_chr6.simHuman.chr6 311683 27 - 601863 TTGAGTCCTTAAGAGCTTGATGTGCCA -s simRat_chr6.simRat.chr6 223804 27 + 647215 TCAAGTTCTGAGTAACTCAATGTGCCG - -a -s simMouse_chr6.simMouse.chr6 233146 126 + 636262 GCCATGCACCTATTCCTGGTTCTGCTCCTCTCATCCACTCAAGTGGAGGCTAATATAACAATAATCTAATATCATTAATAGGAGGGACAGTGCTAGAAACAGAGACAGTTTTTGATAAAGATTGAT -s Anc0.Anc0refChr5 53014 95 + 87904 GCCTTGCACTCTCTCTTGGCTGTGCTA-TTTCTGACCCT-GGTTGAAGGTTAGCATAATAATGACTTTCTACCACTAAGAGCA---------CTAGCAGC--------------------ACTCAT -s Anc1.Anc1refChr7 10364 97 - 47259 GCCTTGCACTCTCTCTTGGCTGTGCTACTTTCTGACCCTCGGTTGAAGGTTAGCATAATAATGACTTTCTACCACTAAGAGCA---------CTAGCAGC--------------------ACTCAT -s Anc2.Anc2refChr15 49289 95 + 86568 CCTTTGCGCACTATCTTGGCAGTGCTA-TGTCTGACCCT-GGTTGAATGTTAGCATTATAATGACTGTCTACCACTAAGAGCA---------GGGGCAGC--------------------ACTCAG -s mr.mrrefChr5 86656 106 + 294540 GCCATGCACTTACTCCTGGTTGTGCTCCTTTCATCCACTCAAGTGGAGGCTAATATAACAATAATCTAATATCATTAATAGGA---------CTAGAAACAG-----------GATAAAGATTGAT -s simDog_chr6.simDog.chr6 221187 95 + 593897 CCTTTGCGCACTATCTTGGCAGTGCTA-TGTCTGACCCT-GGTTGAATGTTAGCATTATAATGACTGTCTACCACTAAGAGCA---------GGGGCAGC--------------------ACTCAG -s simHuman_chr6.simHuman.chr6 311719 97 - 601863 GCCCTGCACTCTCTCTTGGCTGAGCTACTTTCCGGCCCTCTGATACAGGATAGCATAATAATGACATCTTACCACTAAGAGCA---------CTAAGAGC--------------------AGTTAT -s simRat_chr6.simRat.chr6 223831 62 + 647215 GCCTTGCACTTACTCCTGGTTGTGCTTCTTGCATTCACTCAAGTGGAGG----------------------------------------------------------------GATAAAGATGGAT - -a -s simMouse_chr6.simMouse.chr6 233272 43 + 636262 TCTAAGGACTGAGACCTTGTCTTGGTTAGGATCCCAGTCCTGC -s Anc0.Anc0refChr5 53109 35 + 87904 TGTAAA-ACTGTCATCTTGTCTT-GTTAGC-T-----ATATGC -s Anc1.Anc1refChr7 10461 41 - 47259 TGTAAA-ACTGTCATCTTGTCTTGGTTAGC-TCCCAGATATGC -s Anc2.Anc2refChr15 49384 35 + 86568 GGTAAA-ACTGTCATCTCGTCTT-GTAAGC-T-----ATATGC -s mr.mrrefChr5 86762 42 + 294540 TCTAAG-ACTGAGACCTTGTCTTGGTTAGGATCCCAGTCATGC -s simCow_chr6.simCow.chr6 230323 1 + 602619 ----------------------------------------C-- -s simDog_chr6.simDog.chr6 221303 35 + 593897 GGTAAA-ACTGTCATCTCGTCTT-GTAAGC-T-----ATATGC -s simHuman_chr6.simHuman.chr6 311816 41 - 601863 TGTAAA-ACTCCCATATTGTCTGGGTTAGT-TCCCAGCTATGC -s simRat_chr6.simRat.chr6 223893 42 + 647215 TCTACG-ACTGGGACCTTGTCTTGGTTAGGATCCCAGTCATGC - -a -s simMouse_chr6.simMouse.chr6 233315 14 + 636262 CTGTTCTTTAGTAA -s Anc0.Anc0refChr5 53144 14 + 87904 CTATTCTTTATTAA -s Anc1.Anc1refChr7 10502 14 - 47259 CTATTCTTTATTAA -s Anc2.Anc2refChr15 49419 14 + 86568 CTATTCTTTATTAA -s mr.mrrefChr5 86804 14 + 294540 CTGTTCTTTAGTAA -s simCow_chr6.simCow.chr6 230780 11 + 602619 CTATTC---ATTAA -s simDog_chr6.simDog.chr6 221338 14 + 593897 TCATTCTTTATTAA -s simHuman_chr6.simHuman.chr6 311857 14 - 601863 CTATTGTCTAACAA -s simRat_chr6.simRat.chr6 223935 14 + 647215 TTGTTCTTCAGTAA - -a -s simMouse_chr6.simMouse.chr6 233329 19 + 636262 TCAGAGTTGTCTACCTTTT -s Anc0.Anc0refChr5 53158 19 + 87904 TCAGAGCTTCCCTCACTTT -s Anc1.Anc1refChr7 10516 19 - 47259 TCAGAGCTTCCCTCACTTT -s Anc2.Anc2refChr15 49433 19 + 86568 TCAGAGCTTCCCTCACTTT -s mr.mrrefChr5 86818 19 + 294540 TCAGAGTTTTCCTCCCTTT -s simCow_chr6.simCow.chr6 230791 19 + 602619 TTGGAGCTTCCCTCCCTTT -s simDog_chr6.simDog.chr6 221352 19 + 593897 TCAGAGCTTATCAAAATCT -s simHuman_chr6.simHuman.chr6 311872 19 - 601863 TCAAAGCTTCCCTCACTTT -s simRat_chr6.simRat.chr6 223949 19 + 647215 TCAGAGTTTTCCTCCCTTT - -a -s simMouse_chr6.simMouse.chr6 233348 2 + 636262 TC -s Anc0.Anc0refChr5 53177 2 + 87904 CC -s Anc1.Anc1refChr7 10535 2 - 47259 CC -s Anc2.Anc2refChr15 49452 2 + 86568 CC -s mr.mrrefChr5 86837 2 + 294540 TC -s simCow_chr6.simCow.chr6 230810 2 + 602619 GC -s simDog_chr6.simDog.chr6 221389 2 + 593897 CA -s simHuman_chr6.simHuman.chr6 311891 2 - 601863 CC -s simRat_chr6.simRat.chr6 223968 2 + 647215 TT - -a -s simMouse_chr6.simMouse.chr6 233350 5 + 636262 GCAGG -s Anc0.Anc0refChr5 53184 5 + 87904 AGAGG -s Anc1.Anc1refChr7 10542 5 - 47259 AGAGG -s Anc2.Anc2refChr15 49459 5 + 86568 AGAGG -s mr.mrrefChr5 86843 5 + 294540 GCAGG -s simCow_chr6.simCow.chr6 230817 5 + 602619 AGAGG -s simDog_chr6.simDog.chr6 221396 5 + 593897 AGATG -s simHuman_chr6.simHuman.chr6 311898 5 - 601863 AAAGG -s simRat_chr6.simRat.chr6 223974 5 + 647215 GCAGG - -a -s simMouse_chr6.simMouse.chr6 233355 34 + 636262 TCTCAATAGGAAATTGGTTAGTACATTATATGGT -s Anc0.Anc0refChr5 53189 32 + 87904 TT--AATAGGATGTTGATTAGAACATTATATTGT -s Anc1.Anc1refChr7 10547 34 - 47259 TTTCAATAGGATGTTGATTAGAACATTATATTGT -s Anc2.Anc2refChr15 49464 32 + 86568 TT--GGTAGGATGCTGATTGGAACATTATATTGG -s mr.mrrefChr5 86848 34 + 294540 TCTCAATAGGAAATTGATTAGTACATTATATGGT -s simCow_chr6.simCow.chr6 230824 32 + 602619 TT--GATAGGACGCTAATTGGAACATTATATTGC -s simDog_chr6.simDog.chr6 221401 32 + 593897 TT--GGTAGGATTCTGATTGGAAAATTATATTGG -s simHuman_chr6.simHuman.chr6 311903 34 - 601863 TTTCAACTGGATGTTGATTAGAACATTATATAGT -s simRat_chr6.simRat.chr6 223979 34 + 647215 TCTCTATAGGAAACTGATTAGCACATTATCTGGT - -a -s simMouse_chr6.simMouse.chr6 233389 158 + 636262 ATCAATTCGAACTAATTGAACTGACATCTCCTCAGCAGAACTCTTGTGAGTGGTGCCAGACAAATCATACTTAGGTTGCTCAAGCTTGTATTTAGTTCAATCATAGGAATACAGGTCATTCTTGACTGCATTAGAGCCCCCCAAAGATGGTATTTTAC -s Anc0.Anc0refChr5 53221 134 + 87904 AATCATTTGAACTAATTGAACTTATTTCTCCCTAACAAAATTCTTGTGAGTTGGCATAGACAAATTATACTTAGGCAG---------------------ACCATAACAATATTGGTCTTTCATGATTA-ATTAGAGCCCT--GGCACTGGTATTTTTA -s Anc1.Anc1refChr7 10581 135 - 47259 AATCATTTGAACTAATTGAACTTATTTCTCCCTAACAAAATTCTTGTGAGTTGGCATAGACAAATTATACTTAGGCAG---------------------ACCATAACAATATTGGTCTTTCATGATTACATTAGAGCCCT--GGCACTGGTATTTTTA -s Anc2.Anc2refChr15 49496 134 + 86568 AATCATTTGTACTAAGTGAACTTATTTCTCCCTAACAAAATGCTTGTGAGTTGGCATAGCCAAACTATATGTAGGCAG---------------------ACCCTAACAACATTGGTCTTTCATGATCA-ATTGGAGCCCT--GGCACTGGTACTTTTA -s mr.mrrefChr5 86882 156 + 294540 AACAATTTGAACTAATTGAACTGACATCTCCTCAGCAGAACTCTTGTGAGTTGTGCTAGACAAATCATACTTAGGCTGCTCAAGCTTGTATTTAGTTCAATCATAGCAATACAGGTCATTCTTGACTGCATTAGAGCCCC--AAAAATGGTATTTTTA -s simCow_chr6.simCow.chr6 230856 129 + 602619 AATCATTTGTACTAA-----CTCATTTCTCCCTAAATAAATGCTCGTGAGTTGGCATGGCCAAAATATCTGAAGGCAG---------------------ACACTAAGAACATAGATCTCTCATGATCC-ATTGGAGCCCT--GGCTCTGGTACTTTTA -s simDog_chr6.simDog.chr6 221433 131 + 593897 CATCATTTGTATTAAGTGAACTTATTTCTCCTTAGCAAAATGCATGTGAGTAGGCAGAGCCAAACTATATGTAGGAAG---------------------ACCCTAACA---TTGGTCTTTCATGATCA-ATTGGAGCTCT--TGCACCTGTACTTATA -s simHuman_chr6.simHuman.chr6 311937 134 - 601863 AATTATTTGAACTAATTGAACTAATGTCTCGCTAACACGCTTTTTGTGACTTGGCATAGACAAAT-ATACTCAGGCAG---------------------AACATAACAATATGGGTCTTTCATGATTACATTAGAGCCCT--GGTAGTGGTATTTTTA -s simRat_chr6.simRat.chr6 224014 149 + 647215 AACAATTTGAACTAATTGACCTGACATCTCTTCAGCGGAACTCTTGTGAATTGTGTTGGGCAAATCATACTTAGGCCAACCAAATTTGTTTTAAGGCCAATCATAGCAACACAGGTCATTCTTGACTGCATTAGA---------AAATGGTATTTTTA - -a -s simMouse_chr6.simMouse.chr6 233547 20 + 636262 CTAATATTAAGAAGTATGGT -s Anc0.Anc0refChr5 53358 14 + 87904 CTATTATTATTAT------T -s Anc1.Anc1refChr7 10719 14 - 47259 CTATTATTATTAT------T -s Anc2.Anc2refChr15 49633 14 + 86568 CTATTACTATTAT------T -s mr.mrrefChr5 87041 20 + 294540 CTAATATTAATAAGTATGGT -s simCow_chr6.simCow.chr6 230988 14 + 602619 CTATTACTATTAT------T -s simDog_chr6.simDog.chr6 221567 1 + 593897 C------------------- -s simHuman_chr6.simHuman.chr6 312074 14 - 601863 CCATAATTACTAC------T -s simRat_chr6.simRat.chr6 224166 20 + 647215 CTAATATTAATAAGTATGGT - -a -s simMouse_chr6.simMouse.chr6 233567 17 + 636262 TATCTGTTTTATTGTCT -s Anc0.Anc0refChr5 53372 17 + 87904 TATAAGTCTTGTTGTCC -s Anc1.Anc1refChr7 10733 17 - 47259 TATAAGTCTTGTTGTCC -s Anc2.Anc2refChr15 49647 17 + 86568 TACAAGGCCTATTGTCC -s mr.mrrefChr5 87061 17 + 294540 TATCTGTTTTGTTGTCT -s simCow_chr6.simCow.chr6 231011 17 + 602619 TACAAGGCCTATTGTCC -s simHuman_chr6.simHuman.chr6 312088 17 - 601863 CATAGGTATTGCTGTCC -s simRat_chr6.simRat.chr6 224186 17 + 647215 TATCTGTTTTGTTGTCT - -a -s simMouse_chr6.simMouse.chr6 233584 3 + 636262 GTG -s Anc0.Anc0refChr5 53390 3 + 87904 GTC -s Anc1.Anc1refChr7 10751 3 - 47259 GTC -s Anc2.Anc2refChr15 49665 3 + 86568 ATC -s mr.mrrefChr5 87078 3 + 294540 GTG -s simCow_chr6.simCow.chr6 231029 3 + 602619 ACC -s simDog_chr6.simDog.chr6 221568 2 + 593897 -TC -s simHuman_chr6.simHuman.chr6 312106 3 - 601863 GTC -s simRat_chr6.simRat.chr6 224203 3 + 647215 GTG - -a -s simMouse_chr6.simMouse.chr6 233587 48 + 636262 ATTGCATGTTTTCAGAACCTGTTCTAAGGGCTGTTCATCTCAGTTTGA -s Anc0.Anc0refChr5 53393 19 + 87904 ATTGTGAGCTATGAG-----------------------------TTGA -s Anc1.Anc1refChr7 10754 37 - 47259 ATTGTGAGCTATGAGCATCGAATATAAGGGCC-----------CTTGA -s Anc2.Anc2refChr15 49668 19 + 86568 ATCTTGATCTATGAG-----------------------------TTGA -s mr.mrrefChr5 87081 46 + 294540 ATTGCATGCTATCAGAACCTGTTCTAAGGGCTGTTCATC--AGTTTGA -s simCow_chr6.simCow.chr6 231036 19 + 602619 ACCTTGATCTATGAA-----------------------------TTGA -s simDog_chr6.simDog.chr6 221570 19 + 593897 ATCTTGATCTCTGAG-----------------------------TTGA -s simHuman_chr6.simHuman.chr6 312109 37 - 601863 ATTGTGGGCTATTGCCATCGAATATAAGGGCC-----------CTTGA -s simRat_chr6.simRat.chr6 224206 46 + 647215 ATTGCCTGCTATCAGAACCTGGTGTAAGGGCTGTTCATC--AGTTCGA - -a -s simMouse_chr6.simMouse.chr6 233635 41 + 636262 TCTATGTGTGTGTAGGTTATTAAGTAACAGAGATCAGACTC -s Anc0.Anc0refChr5 53412 37 + 87904 TCTATGAGTGTGTAAGTTAT---GCAATTGAGATGGGA-TC -s Anc1.Anc1refChr7 10791 37 - 47259 TCTATGAGTGTGTAAGTTAT---GCAATTGAGATGGGA-TC -s Anc2.Anc2refChr15 49687 37 + 86568 TCTATGAGTGTGTAAGCTAT---GCACTTGAGATGGGA-TT -s mr.mrrefChr5 87127 41 + 294540 TCTATGAGTGTGTAGGTTATTAAGTAACTGAGATCGGACTC -s simCow_chr6.simCow.chr6 231055 33 + 602619 TCTATGAGTGTATAAGGTAT---ACACTTGAGA----A-TT -s simDog_chr6.simDog.chr6 221589 37 + 593897 TCTATGAGTGTGTGAGCTAT---GCACTTGAGGTGGGA-TT -s simHuman_chr6.simHuman.chr6 312146 37 - 601863 TCTATGAGTGTGTAAGTTAT---GCAATTGAGATGGGA-TC -s simRat_chr6.simRat.chr6 224276 41 + 647215 TCTAAGAGTGTGTAGGTTATTAAGAAACTGAGATCGGACTC - -a -s simMouse_chr6.simMouse.chr6 233676 10 + 636262 ACCTTTTTCT -s Anc0.Anc0refChr5 53462 10 + 87904 ACCATTTTCT -s Anc1.Anc1refChr7 10841 10 - 47259 ACCATTTTCT -s Anc2.Anc2refChr15 49737 10 + 86568 ACCATCTTCT -s mr.mrrefChr5 87181 10 + 294540 ACCATTTTCT -s simCow_chr6.simCow.chr6 231101 10 + 602619 ACCATGTTAT -s simDog_chr6.simDog.chr6 221639 10 + 593897 ACCATCTTCT -s simHuman_chr6.simHuman.chr6 312196 10 - 601863 ACCACTTTCT -s simRat_chr6.simRat.chr6 224330 10 + 647215 ACCATTTACT - -a -s simMouse_chr6.simMouse.chr6 233686 11 + 636262 AAAACTAATTT -s Anc0.Anc0refChr5 53473 3 + 87904 --------TTT -s Anc1.Anc1refChr7 10864 11 - 47259 AAAACAAATTT -s Anc2.Anc2refChr15 49748 3 + 86568 --------TTT -s mr.mrrefChr5 87204 11 + 294540 AAAACTAATTT -s simCow_chr6.simCow.chr6 231112 3 + 602619 --------ATT -s simDog_chr6.simDog.chr6 221650 3 + 593897 --------TTT -s simHuman_chr6.simHuman.chr6 312220 11 - 601863 AAAACAAATTT -s simRat_chr6.simRat.chr6 224353 11 + 647215 AAGACTAGTTT - -a -s simMouse_chr6.simMouse.chr6 233697 20 + 636262 CTTGAATGGTTACTCAATTG -s Anc0.Anc0refChr5 53476 20 + 87904 GTCCAGTGGTCACTTGATTG -s Anc1.Anc1refChr7 10875 20 - 47259 GTCCAGTGGTCACTTGATTG -s Anc2.Anc2refChr15 49751 20 + 86568 GTCCAGTGGTCACTTGATTG -s mr.mrrefChr5 87215 20 + 294540 CTTGAATGGTCACTTGATTG -s simCow_chr6.simCow.chr6 231118 20 + 602619 GGCAGGTGGTCACTTGATTG -s simDog_chr6.simDog.chr6 221653 20 + 593897 CTCCAGTGGTCACTTGCTTG -s simHuman_chr6.simHuman.chr6 312231 20 - 601863 GTCCAGTGGTCACTTGATTG -s simRat_chr6.simRat.chr6 224364 20 + 647215 ATTGAATGGCCACTTGATTG - -a -s simMouse_chr6.simMouse.chr6 233717 27 + 636262 CATGGAGTGGAATCCTAATAGCTTAAT -s Anc0.Anc0refChr5 53498 26 + 87904 CATGAACT-GAGTCACAAGGGCTCAAT -s Anc1.Anc1refChr7 10897 26 - 47259 CATGAACT-GAGTCACAAGGGCTCAAT -s Anc2.Anc2refChr15 49773 26 + 86568 CATGAACT-AAGTCACAAGGGCTCAAT -s mr.mrrefChr5 87237 27 + 294540 CATGGAGTGGAATCCTAATAGCTTAAT -s simCow_chr6.simCow.chr6 231140 25 + 602619 CATGGACT-AAGTC-CAAGGGTTCAAT -s simDog_chr6.simDog.chr6 221676 26 + 593897 CATCAACC-AAGTCACAATCGCCTGAT -s simHuman_chr6.simHuman.chr6 312253 26 - 601863 CATGTACT-GAGTCACAAGGGCTCAAT -s simRat_chr6.simRat.chr6 224386 27 + 647215 CTTGAAGTGGAAGCCTAATAGCTTAAA - -a -s simMouse_chr6.simMouse.chr6 233744 2 + 636262 GA -s Anc0.Anc0refChr5 53524 2 + 87904 GA -s Anc1.Anc1refChr7 10923 2 - 47259 GA -s Anc2.Anc2refChr15 49800 2 + 86568 GA -s mr.mrrefChr5 87264 2 + 294540 GA -s simCow_chr6.simCow.chr6 231166 2 + 602619 GA -s simDog_chr6.simDog.chr6 221703 2 + 593897 GA -s simHuman_chr6.simHuman.chr6 312279 2 - 601863 GA -s simRat_chr6.simRat.chr6 224413 2 + 647215 GA - -a -s simMouse_chr6.simMouse.chr6 233746 38 + 636262 TGACCATCAATCTGGAAAATCTGAGTACACTATCGGGA -s Anc0.Anc0refChr5 53529 33 + 87904 AGACCATCAATCTTGGCAATCTGAGCAAACT-----TA -s Anc1.Anc1refChr7 10928 33 - 47259 AGACCATCAATCTTGGCAATCTGAGCAAACT-----TA -s Anc2.Anc2refChr15 49805 33 + 86568 AGACCATCAATCTTGGCAATCTGAGCAAACT-----TA -s mr.mrrefChr5 87269 38 + 294540 TGACCATCAATCTGGAAAATCTGAGTACACTATCGGGA -s simCow_chr6.simCow.chr6 231171 31 + 602619 AGACAATCAATCTTGACAACCTGAGTAAACT------- -s simDog_chr6.simDog.chr6 221708 29 + 593897 TGACCATCACTCATGGCAATC----CAACTT-----TA -s simHuman_chr6.simHuman.chr6 312284 33 - 601863 AGACTATCAATCTTGGCAATCTGAGCAAACT-----TA -s simRat_chr6.simRat.chr6 224418 38 + 647215 TGAACATCAATCTGGAGGTTCTGAGTACACTATAGGGA - -a -s simMouse_chr6.simMouse.chr6 233784 93 + 636262 GAGATTGAACTGGGGTTAAAGACATGGAAGATACAATGCCCTTTGACGTTTGACCTCAAAATGCAATAACTTTTGCTTGCTCTTGTCTTGGTG -s Anc0.Anc0refChr5 53562 58 + 87904 GAGATTGAAC-AAGGTTAAAAGGATGGAAGA------------------------------TGCAATAAC--TT--TTGATCTCATCTAGGTG -s Anc1.Anc1refChr7 10961 60 - 47259 GAGATTGAAC-AAGGTTAAAAGGATGGAAGA------------------------------TGCAATAACTTTT--TTGATCTCATCTAGGTG -s Anc2.Anc2refChr15 49845 58 + 86568 GAGATTGAAC-AAGGTTGAAAGAATGGAAGA------------------------------TGTAATAAC--TT--TTGATCTCATCTAGGTG -s mr.mrrefChr5 87307 86 + 294540 GAGATTGAACTGGGGTTAAAAGGATGGAAGATACAATGCCCTTTGAC-------CTCAAAATGCAATAACTTTTGCTTGCTCTTGTCTTGGTG -s simCow_chr6.simCow.chr6 231209 58 + 602619 GAGGTTGAAC-AAGGTTGAAAGAATGGAGGG------------------------------TGTAATAAC--TC--TTGATCACATCTGGGTG -s simDog_chr6.simDog.chr6 221748 58 + 593897 GAGATTGAAG-TAGGTTGAAACAATGGAAGA------------------------------TGTGATAAC--TT--ATGATCTCATCTAGGCA -s simHuman_chr6.simHuman.chr6 312317 56 - 601863 GAGATCAAAC-AAGGTCAAAAGGATGGAAGA------------------------------TGCAACAACTTTT------CATCATCTAGGTG -s simRat_chr6.simRat.chr6 224456 86 + 647215 GAGATTGAACTGGGGTTAAAAGGATCAAATACACAACACCCTTTGAC-------TTCAAAATGCAATAACTTTTGCTTGCTCTATTCTTGGTG - -a -s simMouse_chr6.simMouse.chr6 233877 61 + 636262 TGAACAAAATTGGTTGTGGGTGTAAAGCCAAATTGTGCAAACTAATCCTAGGGGCATAGGC -s Anc0.Anc0refChr5 53620 61 + 87904 TGGATAAAATTGCTGGGAGATCTAAAGCCAAGTGTTGTAAATTAAACCTTGGGACACAGGC -s Anc1.Anc1refChr7 11021 61 - 47259 TGGATAAAATTGCTGGGAGATCTAAAGCCAAGTGTTGTAAATTAAACCTTGGGACACAGGC -s Anc2.Anc2refChr15 49903 61 + 86568 TGGGTAAAATTGCTGGGAGATCTAAAGCTAAGGGTTGTAAATGAAACCTTGGGACACAGGC -s mr.mrrefChr5 87393 61 + 294540 TGAACAAAATTGGTTGTGGATGTAAAGCCAAGTTTTGCAAACTAAACCTAGGGGCATAGGC -s simCow_chr6.simCow.chr6 231285 60 + 602619 TGGGTAAAATTTATGCGAGATCTAAAGCTAAGGGTTGTAAATGAAAGCTTGG-ACACAGGC -s simDog_chr6.simDog.chr6 221806 42 + 593897 TGTGTAAAATTGCTTGGAGA-------------------AATGAAACCTTGGGACACAGGC -s simHuman_chr6.simHuman.chr6 312373 61 - 601863 TGGATAATGTTGCTGGGAGATCTAACGCCAAGTCTCATGGATTAAACCCTGGGACACAAAC -s simRat_chr6.simRat.chr6 224542 61 + 647215 TGAACAAAATTGGCAGTGGATGTAAAGCTAGGTTTTGCAAACTAAACCTAGGGGCATAGGC - -a -s simMouse_chr6.simMouse.chr6 233938 28 + 636262 TGCTAAGGTCAACAAGGGCTAAGAAAGG -s Anc0.Anc0refChr5 53682 28 + 87904 CACTGAGGTCAACAGGGTAAAAGAAAGG -s Anc1.Anc1refChr7 11083 28 - 47259 CACTGAGGTCAACAGGGTAAAAGAAAGG -s Anc2.Anc2refChr15 49965 28 + 86568 CACTGAGGTCAGCAAGGTAAGAGAAAGG -s mr.mrrefChr5 87455 28 + 294540 TGCTAAGGTCAACAGGGTCTAAGAAAGG -s simCow_chr6.simCow.chr6 231346 28 + 602619 CACTGAGGACAGCAAGGTAAGAGAAAGG -s simDog_chr6.simDog.chr6 221849 28 + 593897 CACTGAGGTTGGCAAGGTAAGAGAAAGG -s simHuman_chr6.simHuman.chr6 312435 28 - 601863 CACTGAGGTCAACAGGGTAAAAGAAAAG -s simRat_chr6.simRat.chr6 224604 28 + 647215 TGCGATGGTCAACAGGGTCTAAGAATGG - -a -s simMouse_chr6.simMouse.chr6 233966 84 + 636262 GCATTTGCTGCGAGTGAAGTGACCTTCTAGGTTCGTAGACCACATGATTCTGCCTGTTGTCTACTCTGAATTAAACGTAAACAT -s Anc0.Anc0refChr5 53711 77 + 87904 ACAGCAGCCTTAAGTAACTCAGAGAGTGGGGCTAGCAGA--GCTTGCTTCTGCCTGTTGTTAGCACTGAACCAGACC-----AT -s Anc1.Anc1refChr7 11112 77 - 47259 ACAGCAGCCTTAAGTAACTCAGAGAGTGGGGCTAGCAGA--GCTTGCTTCTGCCTGTTGTTAGCACTGAACCAGACC-----AT -s Anc2.Anc2refChr15 49994 77 + 86568 ACAGCAGCCTTAAGAAACTCAGAGAGTGGGGCTAGCAGA--GCTTGCTTCTGCCTGTTGCTAGCACTGAACCAGACC-----AT -s mr.mrrefChr5 87483 79 + 294540 GCATTTGCCTTGAGTGAAGCAACCTTCTAGGTTCGTAGACCACATGATTCTGCCTGTTGTCTGCTCTGAATTAAACG-----AT -s simCow_chr6.simCow.chr6 231375 69 + 602619 ACAACAGCCA------ACTCAGAG--TGGAGCTAGCAGA--GCTTGCTTCTGCCTGTTACTAGCACTGAAGCAGACC-----AT -s simDog_chr6.simDog.chr6 221878 77 + 593897 ACAGTAGCCTTAAGAAGTTCAGAGAGTGGGGCTATCAGA--GCTTGATTCAGCGTGTTGCGAGCAGTGAACCAGACC-----AT -s simHuman_chr6.simHuman.chr6 312464 77 - 601863 TCAGCAGCCTTAAGTTACTCAGAGGCTAGGGCTAGCAGA--GCTTGCTGCTGCCCGTGGTTAGCACTGAACCAGACC-----AT -s simRat_chr6.simRat.chr6 224632 79 + 647215 GCATTTGTCTTGAATGAAGCAACCTACTAGGTTTGTATACCACAAGGTTCTGCCTATTGTCTGCTATGAATTAAACG-----AT - -a -s simMouse_chr6.simMouse.chr6 234050 48 + 636262 GTTTATGTAGCAACAAGAACATGCCCACTCAAAAAAGCTACATGGGTG -s Anc0.Anc0refChr5 53792 48 + 87904 GGTTATGTAGCAACAAGAACATGCCCACCCAGAAAAGCTACACAAGCA -s Anc1.Anc1refChr7 11193 48 - 47259 GGTTATGTAGCAACAAGAACATGCCCACCCAGAAAAGCTACACAAGCA -s Anc2.Anc2refChr15 50075 48 + 86568 GGTTATGTAGCAACAAGAACATGCTTACCCAGAAAGGCTACACAAGCA -s mr.mrrefChr5 87562 48 + 294540 GTTTATGTAGCAACAAGAACATGCCCACTCAGAAAAGCTACATGGGTG -s simCow_chr6.simCow.chr6 231447 48 + 602619 GGTAATGTAGTAACAAGAACATACTAGCCCAGAAAGGCCACACAGGCA -s simDog_chr6.simDog.chr6 221959 48 + 593897 GGCTCTGTAGCAACAAGAACAGGCTTACCCAGAAAGGCTACACAAGCA -s simHuman_chr6.simHuman.chr6 312547 48 - 601863 GGTCATGTAGCAACCAGAACATGCCCACCCAGAAAAGCTACACAAGCA -s simRat_chr6.simRat.chr6 224711 47 + 647215 -TTTATGTAGCAACAAGAACATGCTCACTCAGAAAAGCTACATGGGTC - -a -s simMouse_chr6.simMouse.chr6 234098 29 + 636262 CACCACCTGCATGATATGAAAGAAGGGTT -s Anc0.Anc0refChr5 53841 11 + 87904 TCCCATCTGTG------------------ -s Anc1.Anc1refChr7 11242 28 - 47259 TCCCATCTGTGCCATCC-AATGGAGGGTT -s Anc2.Anc2refChr15 50124 11 + 86568 CCTAATCTATG------------------ -s mr.mrrefChr5 87610 29 + 294540 TACCACCTGCATCATATGAAAGGAGGGTT -s simCow_chr6.simCow.chr6 231496 11 + 602619 CCTAATCCATT------------------ -s simDog_chr6.simDog.chr6 222008 11 + 593897 CCTAATCTATG------------------ -s simHuman_chr6.simHuman.chr6 312596 28 - 601863 TGCCAATTGTGCCATCC-AATGGAGGGTT -s simRat_chr6.simRat.chr6 224758 29 + 647215 TACCACCTGCATCCTATAAACAGAGGGTT - -a -s simMouse_chr6.simMouse.chr6 234127 36 + 636262 CAAGTAGTCTTTAGAATTAGATCCATATTGGTATAT -s Anc0.Anc0refChr5 53857 36 + 87904 CAAGTAGTCTTCAGAATCAGATCTAAATAGTTATAG -s Anc1.Anc1refChr7 11275 36 - 47259 CAAGTAGTCTTCAGAATCAGATCTAAATAGTTATAG -s Anc2.Anc2refChr15 50140 36 + 86568 CAAGTAGTCTTCAGAATCAGATCTAAATAGTTACAG -s mr.mrrefChr5 87639 36 + 294540 CAAGTAGTCTTTAGAATTAGATCCATATTGGTATAT -s simCow_chr6.simCow.chr6 231512 36 + 602619 TAAGTAGTCTTTAAAATCAAATCTAAATAGTTGCAG -s simDog_chr6.simDog.chr6 222024 36 + 593897 CAAGTAGTCTTCAGAATCAGATCTAGATAGTTACAG -s simHuman_chr6.simHuman.chr6 312630 36 - 601863 CAAGTAGTCTTCAGAATCAGATCTAAATAGTTATAG -s simRat_chr6.simRat.chr6 224787 36 + 647215 CAAGAAGTCTTTAGAATTAGATCCATATTGGTATAT - -a -s simMouse_chr6.simMouse.chr6 234163 34 + 636262 CATGCCACTCCTTTTTCTTGAGTAGGTAGGTGAA -s Anc0.Anc0refChr5 53899 32 + 87904 CAGTCCACCCCTCTT--CTGAGTAGGTAGACAAA -s Anc1.Anc1refChr7 11317 32 - 47259 CAGTCCACCCCTCTT--CTGAGTAGGTAGACAAA -s Anc2.Anc2refChr15 50182 32 + 86568 CAGTCCATCCTTCTT--CTGAGTAGGTAGACAAA -s mr.mrrefChr5 87675 32 + 294540 CATTCCACCCCTTTT--TTGAGTAGGTAGGCGAA -s simCow_chr6.simCow.chr6 231554 31 + 602619 CAGTTC-TCCTTGTT--CTGAGTAGGTGGACAAA -s simDog_chr6.simDog.chr6 222066 32 + 593897 CAGTCCATCCTTCTC--CTGAGTAGGCAGACAGA -s simHuman_chr6.simHuman.chr6 312672 32 - 601863 CAGTCCACCCCTCTT--CTGAGTAGGTATACAAA -s simRat_chr6.simRat.chr6 224823 32 + 647215 CATTCTACCCCTTTT--TTGAGTAGGTAGGCGAA - -a -s simMouse_chr6.simMouse.chr6 234197 12 + 636262 TCTGACTTCTTT -s Anc0.Anc0refChr5 53932 12 + 87904 TCTAATTTTCTT -s Anc1.Anc1refChr7 11350 12 - 47259 TCTAATTTTCTT -s Anc2.Anc2refChr15 50215 12 + 86568 TCTAATTTCCTT -s mr.mrrefChr5 87707 12 + 294540 TCTAACTTTTTT -s simCow_chr6.simCow.chr6 231586 12 + 602619 TCTAATCCCCTT -s simDog_chr6.simDog.chr6 222099 12 + 593897 CCTGATTTCTGT -s simHuman_chr6.simHuman.chr6 312705 12 - 601863 TCTAATTTTCTT -s simRat_chr6.simRat.chr6 224855 12 + 647215 TCTAACTTTTCT - -a -s simMouse_chr6.simMouse.chr6 234209 66 + 636262 TTATCTGAGTAAATACAAGATCTATATAGGAAAGGTCTGGGCCTTACCATCTCCAGACTAGAAAAT -s Anc0.Anc0refChr5 53946 66 + 87904 ATATATGAGCAAATACACTATCAATATAGGAAAAGTTTATGCCGTACCATTTCCAGACTAGATAAT -s Anc1.Anc1refChr7 11364 66 - 47259 ATATATGAGCAAATACACTATCAATATAGGAAAAGTTTATGCCGTACCATTTCCAGACTAGATAAT -s Anc2.Anc2refChr15 50229 66 + 86568 ATCTATGAGCAAATACACTATCAATATAGGAACAGTTTATGCTGTAGCATTTCCAGACTGGATAAT -s mr.mrrefChr5 87719 66 + 294540 ATATCTGAGTAAATACAAGATCTATATAGGAAAGGTCTGGGCCTTACCATTTCCAGACTAGAAAAT -s simCow_chr6.simCow.chr6 231600 66 + 602619 ACCCATGAGCAAATACACCATCCATATAGGAACGGTTTATGCTGAAGTATTTCCTGTCTGGATAAT -s simDog_chr6.simDog.chr6 222113 64 + 593897 ATCTATGAATGAATACACTGTCACTATAGGAACAGTTTATGC--TAGCACTTCCAGACTGGATATC -s simHuman_chr6.simHuman.chr6 312719 66 - 601863 ATATATGAGCAAATACACAATCAATATAGGGAAAGTTTATGCCATACCATTTACAGACTAGATAAT -s simRat_chr6.simRat.chr6 224867 66 + 647215 ATATGTGAGTAAATACAAGATCTATGTAGGAAAGGTCTGGGCCTTACCATTTCCAGACTAGAGAAT - -a -s simMouse_chr6.simMouse.chr6 234275 12 + 636262 TTCCTGTATATA -s Anc0.Anc0refChr5 54012 12 + 87904 TTTGTGTCAGTG -s Anc1.Anc1refChr7 11430 12 - 47259 TTTGTGTCAGTG -s Anc2.Anc2refChr15 50295 12 + 86568 TTTGTTTCAGTG -s mr.mrrefChr5 87785 12 + 294540 TTCCTGTATATA -s simCow_chr6.simCow.chr6 231666 8 + 602619 TT-GTTTCA--- -s simDog_chr6.simDog.chr6 222182 12 + 593897 TTTGTTTAAGTG -s simHuman_chr6.simHuman.chr6 312785 12 - 601863 TTTGTGTCAGTT -s simRat_chr6.simRat.chr6 224933 11 + 647215 TTCCAGT-TATA - -a -s simMouse_chr6.simMouse.chr6 234287 29 + 636262 CACAGGGATGTTTCCATAGGATTTACAGC -s Anc0.Anc0refChr5 54024 19 + 87904 CAGAGGGCTATGACC----------TAGC -s Anc1.Anc1refChr7 11442 19 - 47259 CAGAGGGCTATGACC----------TAGC -s Anc2.Anc2refChr15 50307 19 + 86568 CAGTGGGCTATGATC----------TAGC -s mr.mrrefChr5 87797 29 + 294540 CACAGGGATGTGTCCATGGGATTTACAGC -s simCow_chr6.simCow.chr6 231674 19 + 602619 CAGGGGGTTATGATC----------AAGC -s simDog_chr6.simDog.chr6 222206 19 + 593897 CAGTGGGCTATGATC----------TAGA -s simHuman_chr6.simHuman.chr6 312797 19 - 601863 CAGAGGGCTATGACC----------TAGC -s simRat_chr6.simRat.chr6 224944 29 + 647215 CACAGGGGTGTGGCCATGGGATATACAGC - -a -s simMouse_chr6.simMouse.chr6 234316 56 + 636262 TCTGCCTGGGGGCTTGATTGGGGACTCTGTGTGCATGTCGAGGCATGACAGTCTGG -s Anc0.Anc0refChr5 54045 46 + 87904 TCGGCCTT-GGGCAGGATT------G---TGTGGTTGTCCAGGCATTTCAGACTGG -s Anc1.Anc1refChr7 11463 47 - 47259 TCGGCCTTGGGGCAGGATT------G---TGTGGTTGTCCAGGCATTTCAGACTGG -s Anc2.Anc2refChr15 50328 46 + 86568 TAGGCCTT-GGGCAGGACT------G---TGTAGTTGTTCAGGCATTTCAGACTGG -s mr.mrrefChr5 87826 53 + 294540 TCTGCCTGGGGGCTTGATTGGGGACT---TGTGCATGTCCAGGCATTACAGTCTGG -s simCow_chr6.simCow.chr6 231695 26 + 602619 T---------GGCA---------------------TGTGCAGGCACTTCAAACTGG -s simDog_chr6.simDog.chr6 222227 46 + 593897 TAGGCCTT-GAGCAGGACT------G---TGTAGTTGTTCAGGCATTTTAGACTAG -s simHuman_chr6.simHuman.chr6 312818 47 - 601863 TCGGCTTTGTGGCAGGATT------G---TGTGTGTGACCAGGCATTTCAGATTGC -s simRat_chr6.simRat.chr6 224973 50 + 647215 TCTGACAGGGGGCTCGACTGGGGACT------GCAAGTCCAGGCATTACAGTCTGG - -a -s simMouse_chr6.simMouse.chr6 234372 20 + 636262 GACCATTGTGATTGAAAATA -s Anc0.Anc0refChr5 54091 9 + 87904 AGCCTTTGT----------- -s Anc1.Anc1refChr7 11510 20 - 47259 AGCCTTTGTGATTAATAATA -s Anc2.Anc2refChr15 50374 9 + 86568 AGCCTTTGT----------- -s mr.mrrefChr5 87879 20 + 294540 AACCTTTGTGATTGAAAATA -s simCow_chr6.simCow.chr6 231722 9 + 602619 AGTATTTGT----------- -s simDog_chr6.simDog.chr6 222273 9 + 593897 AGCCTTTGC----------- -s simHuman_chr6.simHuman.chr6 312865 20 - 601863 AGCCTTTGTGATTAATAATA -s simRat_chr6.simRat.chr6 225023 20 + 647215 AACCTTTGTGATGGACAATA - -a -s simMouse_chr6.simMouse.chr6 234392 10 + 636262 GTCCCTCACT -s Anc0.Anc0refChr5 54117 10 + 87904 GTTTCTCACA -s Anc1.Anc1refChr7 11547 10 - 47259 GTTTCTCACA -s Anc2.Anc2refChr15 50400 10 + 86568 GTTTCTTACA -s mr.mrrefChr5 87899 10 + 294540 GTCCCTCACT -s simCow_chr6.simCow.chr6 231748 10 + 602619 GTTTTTTACA -s simDog_chr6.simDog.chr6 222299 10 + 593897 GTTTCTTACC -s simHuman_chr6.simHuman.chr6 312903 10 - 601863 GTTTCTCACA -s simRat_chr6.simRat.chr6 225043 10 + 647215 GTCCCTCACC - -a -s simMouse_chr6.simMouse.chr6 234402 26 + 636262 ACCAACAACGCAGTCGGCTGATACCC -s Anc0.Anc0refChr5 54127 26 + 87904 AAAATAAACGGTATCGCCTAATAGTT -s Anc1.Anc1refChr7 11557 26 - 47259 AAAATAAACGGTATCGCCTAATAGTT -s Anc2.Anc2refChr15 50411 26 + 86568 AAAATAAACGGTATCACCTAATAGTT -s mr.mrrefChr5 87909 26 + 294540 ACCAACAACGCAATCGGCTGATACCC -s simCow_chr6.simCow.chr6 231759 26 + 602619 AAAATAAACAGTACCTCCTAATAGTT -s simDog_chr6.simDog.chr6 222311 26 + 593897 AAAATAGATGGTATCACCTAATAGTT -s simHuman_chr6.simHuman.chr6 312913 26 - 601863 GAAATAAACGGTATGGCTTAATAGTT -s simRat_chr6.simRat.chr6 225053 26 + 647215 ACCAACAATGCAATTGGCTGATACGC - -a -s simMouse_chr6.simMouse.chr6 234428 28 + 636262 TGGGGGCCTCACATTTTACATAAAGAGG -s Anc0.Anc0refChr5 54158 28 + 87904 TAGGGGCCTTGCATTTTTCATAACAAAA -s Anc1.Anc1refChr7 11588 28 - 47259 TAGGGGCCTTGCATTTTTCATAACAAAA -s Anc2.Anc2refChr15 50442 28 + 86568 TAGGAGCCTTGCATTTTTCATAACAAAA -s mr.mrrefChr5 87935 28 + 294540 TAGGGGCCTCGCATTTTACATAAAGAGG -s simCow_chr6.simCow.chr6 231790 28 + 602619 TATGTTCCTTGCATTTTTCATAATGAGA -s simDog_chr6.simDog.chr6 222342 28 + 593897 TAGGAGCCCTGCATTTTTCATAACAAAA -s simHuman_chr6.simHuman.chr6 312944 28 - 601863 TAGGGACCTTGCATTTTTCATAACAAAA -s simRat_chr6.simRat.chr6 225079 28 + 647215 TAGGGGCCTCGCATTTTACTTAAAGAGG - -a -s simMouse_chr6.simMouse.chr6 234456 74 + 636262 AGTCTGATATTAAGTGAGCCACAACTGAGGGGAGACACTGAAGGTGAGGAATAACACCCTGGGCCTGGAACAAA -s Anc0.Anc0refChr5 54186 70 + 87904 GGTCCCATATTCAATGAATTATGACTGATGGCTAACACTGAAGGCTGGAAA--ACACC--AAACCTGGCATAAA -s Anc1.Anc1refChr7 11616 72 - 47259 GGTCCCATATTCAATGAATTATGACTGATGGCTAACACTGAAGGCTGGAAA--ACACCTAAAACCTGGCATAAA -s Anc2.Anc2refChr15 50470 70 + 86568 GGTCCCAGGTTCAACATGTTATGACTGATGGCTAATGCCAAAGGCTGGAAA--ACACC--AAATCTGGCATAAA -s mr.mrrefChr5 87963 74 + 294540 AGTCTGATATTAAGTGAACCACAACTGAGGGGAGACACTGAAGGTTGGGAATAACCCCCTGGGCCTGGAATAAA -s simCow_chr6.simCow.chr6 231818 59 + 602619 GCTCTCACGTTCAACATGTCATGACTGATCGTAAATGCCAACAGCTGGGA---------------TGGCATAAA -s simDog_chr6.simDog.chr6 222370 70 + 593897 GGGCCCAGGTTCAACATGTTGTGGCTGCTGGCTGATGCCAAAGGCTCGAAA--ACACC--AAATCTCACATTAA -s simHuman_chr6.simHuman.chr6 312972 72 - 601863 GGTCCTATATTCAATGAATTATGACTGATGGCTAACACTGAAGGCTGGAAA--ACAACTAAAACCTGGCATAAA -s simRat_chr6.simRat.chr6 225122 74 + 647215 AGTCTGATATCAAGTAAACCACTACAGAAGGGAGACACTAAGGGTTGGGAATAAGCCCCTCGGCCTGGAATAAA - -a -s simMouse_chr6.simMouse.chr6 234530 22 + 636262 AAAACATAAGGCATGTTTGGAG -s Anc0.Anc0refChr5 54262 20 + 87904 AGAACATGAAGCCTTCTC--TG -s Anc1.Anc1refChr7 11694 20 - 47259 AGAACATGAAGCCTTCTC--TG -s Anc2.Anc2refChr15 50546 20 + 86568 AGAACATGAAGCCTTCTC--TG -s mr.mrrefChr5 88043 22 + 294540 AAAACATAAAGCCTGCTTGGAG -s simCow_chr6.simCow.chr6 231883 20 + 602619 AATACATGAAGCCTTCTC--TG -s simDog_chr6.simDog.chr6 222446 20 + 593897 AGAACATAAAGCCTTCTC--TG -s simHuman_chr6.simHuman.chr6 313050 20 - 601863 AGAACATGAAGCCTTCTC--CG -s simRat_chr6.simRat.chr6 225202 22 + 647215 AAAACATAAAGCCTGCTTGGAT - -a -s simMouse_chr6.simMouse.chr6 234552 30 + 636262 TAACTGAGAGGACAAAATGCTCCCACCCAT -s Anc0.Anc0refChr5 54282 30 + 87904 TAACTGAGTGGTCAAAATGCTCCAGCCCTT -s Anc1.Anc1refChr7 11714 30 - 47259 TAACTGAGTGGTCAAAATGCTCCAGCCCTT -s Anc2.Anc2refChr15 50566 30 + 86568 TAGCTGAGTAATAAAAATGCTCCAGTCCTT -s mr.mrrefChr5 88065 30 + 294540 TAACTGAGAGGACAAAATGCTCCCGCCCTT -s simCow_chr6.simCow.chr6 231905 30 + 602619 TAGCTGAGTAATAAAAATGCTCCAGTGCTC -s simDog_chr6.simDog.chr6 222466 16 + 593897 --------------AAATGTTCCTGTCCTT -s simHuman_chr6.simHuman.chr6 313070 30 - 601863 TGACTGAGGGGTCAAAATGCTCAAGCCTTT -s simRat_chr6.simRat.chr6 225224 29 + 647215 TAACTGAGAGG-TGAAATGCTTCTGCCCTT - -a -s simMouse_chr6.simMouse.chr6 234582 2 + 636262 GA -s Anc0.Anc0refChr5 54312 2 + 87904 GA -s Anc1.Anc1refChr7 11744 2 - 47259 GA -s Anc2.Anc2refChr15 50596 2 + 86568 TA -s mr.mrrefChr5 88095 2 + 294540 GA -s simCow_chr6.simCow.chr6 231935 2 + 602619 TA -s simDog_chr6.simDog.chr6 222482 2 + 593897 TA -s simHuman_chr6.simHuman.chr6 313112 2 - 601863 GA -s simRat_chr6.simRat.chr6 225253 2 + 647215 GA - -a -s simMouse_chr6.simMouse.chr6 234584 22 + 636262 CCCTTGCTAGGGGGAGGCAATT -s Anc0.Anc0refChr5 54314 22 + 87904 CTCCTGCTAAAGAGGAGGTAAT -s Anc1.Anc1refChr7 11746 22 - 47259 CTCCTGCTAAAGAGGAGGTAAT -s Anc2.Anc2refChr15 50598 22 + 86568 CTCCTGCTAAAAAGGAGGTAAT -s mr.mrrefChr5 88097 22 + 294540 CCCCTGCTAGGGAGAGGCAATT -s simCow_chr6.simCow.chr6 231937 22 + 602619 CTCCTTCTAAAAAGGAGGTTAT -s simDog_chr6.simDog.chr6 222484 22 + 593897 CTCCTGCTAAAAAGGAGGTAAT -s simHuman_chr6.simHuman.chr6 313119 22 - 601863 CTCCTGCTAAAGAGGAGGTAAT -s simRat_chr6.simRat.chr6 225255 22 + 647215 CCCCTGCTAGGGAGAGGCAATT - -a -s simMouse_chr6.simMouse.chr6 234606 58 + 636262 TGTCAACAATGAGCAACAAATCGGCAAGTTCTTATCTAGGATGGGGATGATGTATGAG -s Anc0.Anc0refChr5 54337 58 + 87904 TATCAACAATGAGCAACAAATCAGCAAACTCTTATTTTGTCCGGAGATGATGTGTGAG -s Anc1.Anc1refChr7 11769 58 - 47259 TATCAACAATGAGCAACAAATCAGCAAACTCTTATTTTGTCCGGAGATGATGTGTGAG -s Anc2.Anc2refChr15 50621 58 + 86568 TATAAACAATGAGCAAGAAATCAACAAACTCTTATTTTGTCCGGAGATGATGTGTGAG -s mr.mrrefChr5 88120 58 + 294540 TGTCAACAATGAGCAACAAATCGGCAAGTTCTTATCTAGGATGGGGATGATGTATGAG -s simCow_chr6.simCow.chr6 231960 56 + 602619 TATAAATGTTTAGAAAGA--TCAATAAACTCTTATTTTGTCTGGAGATGATGTGTGAG -s simDog_chr6.simDog.chr6 222507 57 + 593897 TATAAACAATGAGCAGGAAATTAACCA-CTCTTATTTTGTACGGACTTGATGTGTGAG -s simHuman_chr6.simHuman.chr6 313142 58 - 601863 TATCAACAATGAGCAACTCATCAGCAAACCCTTATTTTGTCAGGAGATGATGTGTGTG -s simRat_chr6.simRat.chr6 225278 58 + 647215 TGCTACCAATGAGCTACAGATTGACAAGTTCTTATCTGGGTTGGGGATGATGTATGAG - -a -s simMouse_chr6.simMouse.chr6 234664 24 + 636262 AGTACACCATGAATTAATAGTTGC -s Anc0.Anc0refChr5 54396 24 + 87904 AGTAAATTGTGAATTAATAATAGC -s Anc1.Anc1refChr7 11828 24 - 47259 AGTAAATTGTGAATTAATAATAGC -s Anc2.Anc2refChr15 50680 24 + 86568 AGTAAATTGTGAGTTAATAATAGC -s mr.mrrefChr5 88178 24 + 294540 AGTACATCATGAATTAATAGTTGC -s simCow_chr6.simCow.chr6 232017 24 + 602619 AGTCAATTGTGAGTTAGTAATAGC -s simDog_chr6.simDog.chr6 222565 24 + 593897 AGTAAATTGTGAGTTGATAATAGC -s simHuman_chr6.simHuman.chr6 313201 24 - 601863 AGTGTATTGTGAAGTAATATTAGC -s simRat_chr6.simRat.chr6 225336 24 + 647215 AGTACGTCATAAGTTATTAGTTGC - -a -s simMouse_chr6.simMouse.chr6 234688 19 + 636262 AGGAAAGATAAGCTTGGGT -s Anc0.Anc0refChr5 54420 19 + 87904 AGCAGAAATAAACTTGGGA -s Anc1.Anc1refChr7 11852 19 - 47259 AGCAGAAATAAACTTGGGA -s Anc2.Anc2refChr15 50704 19 + 86568 AGCAGAAATAAACTTGGGA -s mr.mrrefChr5 88202 19 + 294540 AGGAAAGATAAGCTTGGGT -s simCow_chr6.simCow.chr6 232041 19 + 602619 AGCATAATCAAGCTTGGGA -s simDog_chr6.simDog.chr6 222589 19 + 593897 AGCAGAAATAAACTTGGGA -s simHuman_chr6.simHuman.chr6 313228 19 - 601863 AGAAGAAATAAACTTGGGA -s simRat_chr6.simRat.chr6 225360 19 + 647215 AGGAAAGCTAAGCTTGGGT - -a -s simMouse_chr6.simMouse.chr6 234707 5 + 636262 CTCTG -s Anc0.Anc0refChr5 54439 5 + 87904 ATCCA -s Anc1.Anc1refChr7 11871 5 - 47259 ATCCA -s Anc2.Anc2refChr15 50723 5 + 86568 ACCCA -s mr.mrrefChr5 88221 5 + 294540 CTCCA -s simCow_chr6.simCow.chr6 232077 5 + 602619 AACCA -s simDog_chr6.simDog.chr6 222612 5 + 593897 CCCTA -s simHuman_chr6.simHuman.chr6 313247 5 - 601863 ATCCA -s simRat_chr6.simRat.chr6 225379 5 + 647215 CTCCA - -a -s simMouse_chr6.simMouse.chr6 234712 11 + 636262 ACCCAGCCCCA -s Anc0.Anc0refChr5 54444 8 + 87904 ATCTGACC--- -s Anc1.Anc1refChr7 11876 11 - 47259 ATCTGACCCCA -s Anc2.Anc2refChr15 50777 8 + 86568 ATCTGACC--- -s mr.mrrefChr5 88226 11 + 294540 ACCCAACCCCA -s simCow_chr6.simCow.chr6 232131 8 + 602619 ACTGGACA--- -s simDog_chr6.simDog.chr6 222668 8 + 593897 ATCTGACC--- -s simHuman_chr6.simHuman.chr6 313252 11 - 601863 ATCTGATCCCA -s simRat_chr6.simRat.chr6 225384 11 + 647215 ACCCAAACCCA - -a -s simMouse_chr6.simMouse.chr6 234723 5 + 636262 CATGT -s Anc0.Anc0refChr5 54452 1 + 87904 ----T -s Anc1.Anc1refChr7 11887 5 - 47259 CATGT -s Anc2.Anc2refChr15 50785 1 + 86568 ----T -s mr.mrrefChr5 88237 5 + 294540 CATGT -s simCow_chr6.simCow.chr6 232139 1 + 602619 ----T -s simDog_chr6.simDog.chr6 222676 1 + 593897 ----T -s simHuman_chr6.simHuman.chr6 313263 5 - 601863 CATGT -s simRat_chr6.simRat.chr6 225401 5 + 647215 CATGT - -a -s simMouse_chr6.simMouse.chr6 234728 2 + 636262 TA -s Anc0.Anc0refChr5 54453 2 + 87904 CG -s Anc1.Anc1refChr7 11892 2 - 47259 CG -s Anc2.Anc2refChr15 50786 2 + 86568 CC -s mr.mrrefChr5 88242 2 + 294540 TA -s simCow_chr6.simCow.chr6 232140 2 + 602619 TC -s simDog_chr6.simDog.chr6 222679 2 + 593897 CC -s simHuman_chr6.simHuman.chr6 313268 2 - 601863 CG -s simRat_chr6.simRat.chr6 225406 2 + 647215 TA - -a -s simMouse_chr6.simMouse.chr6 234730 9 + 636262 ATACCACCT -s Anc0.Anc0refChr5 54457 7 + 87904 ATACCAC-- -s Anc1.Anc1refChr7 11896 9 - 47259 ATACCACAT -s Anc2.Anc2refChr15 50790 7 + 86568 ACACCAC-- -s mr.mrrefChr5 88244 9 + 294540 ATACCACAT -s simCow_chr6.simCow.chr6 232144 7 + 602619 ATATCAT-- -s simDog_chr6.simDog.chr6 222683 7 + 593897 ACACCAC-- -s simHuman_chr6.simHuman.chr6 313273 9 - 601863 ATACCACAT -s simRat_chr6.simRat.chr6 225408 5 + 647215 ----TATAT - -a -s simMouse_chr6.simMouse.chr6 234739 6 + 636262 CCCATT -s Anc0.Anc0refChr5 54464 6 + 87904 CCAATT -s Anc1.Anc1refChr7 11905 6 - 47259 CCAATT -s Anc2.Anc2refChr15 50797 6 + 86568 TCAGTT -s mr.mrrefChr5 88253 6 + 294540 CCAATT -s simCow_chr6.simCow.chr6 232153 6 + 602619 CCATTT -s simDog_chr6.simDog.chr6 222690 6 + 593897 TCAGTT -s simHuman_chr6.simHuman.chr6 313282 6 - 601863 CCAATT -s simRat_chr6.simRat.chr6 225413 6 + 647215 ACAATT - -a -s simMouse_chr6.simMouse.chr6 234745 2 + 636262 TA -s Anc0.Anc0refChr5 54470 2 + 87904 TG -s Anc1.Anc1refChr7 11911 2 - 47259 TG -s Anc2.Anc2refChr15 50803 2 + 86568 CG -s mr.mrrefChr5 88259 2 + 294540 TA -s simCow_chr6.simCow.chr6 232161 2 + 602619 CA -s simDog_chr6.simDog.chr6 222696 2 + 593897 CG -s simHuman_chr6.simHuman.chr6 313288 2 - 601863 TG -s simRat_chr6.simRat.chr6 225419 2 + 647215 TA - -a -s simMouse_chr6.simMouse.chr6 234747 122 + 636262 GTGCAGCGAAGGTGGATACGAAGTCATTTCAAGTAGAATTAACACAAAGAAGCCAATTCTGATGAATTTCCATAGGAAAACTGATTCTGACCATTCAGTAATGACGCTCACAATGACGCCCA -s Anc0.Anc0refChr5 54472 18 + 87904 GTGCAGC--------------------------------------------------------------------------------------------------------AGTGATGGCCA -s Anc1.Anc1refChr7 11913 18 - 47259 GTGCAGC--------------------------------------------------------------------------------------------------------AGTGATGGCCA -s Anc2.Anc2refChr15 50809 18 + 86568 ATCCAGT--------------------------------------------------------------------------------------------------------AGTGATGGCCA -s mr.mrrefChr5 88261 122 + 294540 GTGCAGCGAAGGTATATACGAAGTCATTTCAAGTAGAATTAACACAAAGAAGCCAATTCTGATGAATTTCCATAGGAAAACTGATTCTGACCATTCAGTAATGACGCTCACAATGACGCCCA -s simCow_chr6.simCow.chr6 232170 18 + 602619 AACCTAT--------------------------------------------------------------------------------------------------------TTTGGCACCCA -s simDog_chr6.simDog.chr6 222702 18 + 593897 ATCCAGT--------------------------------------------------------------------------------------------------------AGTGATGGCCA -s simHuman_chr6.simHuman.chr6 313290 7 - 601863 GTGCAGC------------------------------------------------------------------------------------------------------------------- -s simRat_chr6.simRat.chr6 225421 122 + 647215 GTGCAGTGAAGGTATATATGAAGTCATTTCAAGTAGAATTAACACTAAGAAGCCAATTCTCATGAATTCCCACGTAAAAACCGATTCTTACCCTTCAGTGATGATGCTCACAATGATGCTCA - -a -s simMouse_chr6.simMouse.chr6 234869 9 + 636262 GGAGTTTCT -s Anc0.Anc0refChr5 54490 8 + 87904 GAAG-TCCC -s Anc1.Anc1refChr7 11931 8 - 47259 GAAG-TCCC -s Anc2.Anc2refChr15 50827 8 + 86568 GAAG-TCCC -s mr.mrrefChr5 88383 8 + 294540 GGAG-TTCT -s simCow_chr6.simCow.chr6 232191 8 + 602619 GGTG-TCCC -s simDog_chr6.simDog.chr6 222720 8 + 593897 GAAG-TCCC -s simRat_chr6.simRat.chr6 225543 8 + 647215 GGAG-TCCT - -a -s simMouse_chr6.simMouse.chr6 234878 20 + 636262 ATGTTAACTGGCTGTCCCAC -s Anc0.Anc0refChr5 54498 20 + 87904 ATGTTAACTAGCTATCCCAT -s Anc1.Anc1refChr7 11939 20 - 47259 ATGTTAACTAGCTATCCCAT -s Anc2.Anc2refChr15 50836 20 + 86568 ATGTTAACTAGCTATCCCAT -s mr.mrrefChr5 88391 20 + 294540 ATGTTAACTGGCTGTCCCAC -s simCow_chr6.simCow.chr6 232200 20 + 602619 GAGTTAACTGGCTGTCCCAT -s simDog_chr6.simDog.chr6 222729 20 + 593897 ATGTTAACTAGCTATCCCAT -s simRat_chr6.simRat.chr6 225551 20 + 647215 ATGTTAACTGGCTGTGCAAC - -a -s simMouse_chr6.simMouse.chr6 234898 3 + 636262 ATT -s Anc0.Anc0refChr5 54518 3 + 87904 ATT -s Anc1.Anc1refChr7 11959 3 - 47259 ATT -s Anc2.Anc2refChr15 50856 3 + 86568 ATT -s mr.mrrefChr5 88411 3 + 294540 ATT -s simCow_chr6.simCow.chr6 232220 3 + 602619 AAT -s simDog_chr6.simDog.chr6 222749 3 + 593897 ATT -s simRat_chr6.simRat.chr6 225577 3 + 647215 ATA - -a -s simMouse_chr6.simMouse.chr6 234901 26 + 636262 AAGATATGGCTAGCAATCTCATGATC -s Anc0.Anc0refChr5 54521 22 + 87904 ATGATTGAACTAGTGATCTC----CC -s Anc1.Anc1refChr7 11962 22 - 47259 ATGATTGAACTAGTGATCTC----CC -s Anc2.Anc2refChr15 50865 22 + 86568 ATGATTGAACTAGTGATCTC----CC -s mr.mrrefChr5 88414 26 + 294540 AAGATATGGCTAGCAATCTCATGATC -s simCow_chr6.simCow.chr6 232229 22 + 602619 AAGATCAGCCTAGTTACCTC----AC -s simDog_chr6.simDog.chr6 222758 22 + 593897 ATGATTGAACTAGTGATCTC----CC -s simRat_chr6.simRat.chr6 225580 26 + 647215 ACAATATGACTAGCAATCTCAAGATC - -a -s simMouse_chr6.simMouse.chr6 234927 7 + 636262 AATTTTG -s Anc0.Anc0refChr5 54543 7 + 87904 CATTCAG -s Anc1.Anc1refChr7 11984 7 - 47259 CATTCAG -s Anc2.Anc2refChr15 50887 7 + 86568 CATTCAG -s mr.mrrefChr5 88440 7 + 294540 AATTTTG -s simCow_chr6.simCow.chr6 232251 7 + 602619 CATTCAG -s simDog_chr6.simDog.chr6 222780 7 + 593897 CATTCAG -s simRat_chr6.simRat.chr6 225619 7 + 647215 AATTTCG - -a -s simMouse_chr6.simMouse.chr6 234934 2 + 636262 AG -s Anc0.Anc0refChr5 54550 2 + 87904 AG -s Anc1.Anc1refChr7 11991 2 - 47259 AG -s Anc2.Anc2refChr15 50894 2 + 86568 AG -s mr.mrrefChr5 88447 2 + 294540 AG -s simCow_chr6.simCow.chr6 232258 2 + 602619 AG -s simDog_chr6.simDog.chr6 222793 2 + 593897 AG -s simHuman_chr6.simHuman.chr6 313297 1 - 601863 -A -s simRat_chr6.simRat.chr6 225626 2 + 647215 AA - -a -s simMouse_chr6.simMouse.chr6 234936 7 + 636262 CTGAGCT -s Anc0.Anc0refChr5 54552 7 + 87904 CCGAGCT -s Anc1.Anc1refChr7 11993 7 - 47259 CCGAGCT -s Anc2.Anc2refChr15 50896 7 + 86568 CCAAGTT -s mr.mrrefChr5 88449 7 + 294540 CTGAGCT -s simCow_chr6.simCow.chr6 232260 7 + 602619 CTGAGCT -s simDog_chr6.simDog.chr6 222797 7 + 593897 CCAAGTT -s simHuman_chr6.simHuman.chr6 313298 7 - 601863 CAGAGCT -s simRat_chr6.simRat.chr6 225628 7 + 647215 CTGGGCT - -a -s simMouse_chr6.simMouse.chr6 234943 14 + 636262 TAACAACCCCATTA -s Anc0.Anc0refChr5 54559 14 + 87904 TAACAGCCCCACTG -s Anc1.Anc1refChr7 12000 14 - 47259 TAACAGCCCCACTG -s Anc2.Anc2refChr15 50903 14 + 86568 CAACAGTCCCACTG -s mr.mrrefChr5 88456 14 + 294540 TAACAACCCCATTG -s simCow_chr6.simCow.chr6 232267 14 + 602619 GAACAGTCCCACTG -s simDog_chr6.simDog.chr6 222804 14 + 593897 CAACGGTCCCATCG -s simHuman_chr6.simHuman.chr6 313307 14 - 601863 TAACAGCCCTACTG -s simRat_chr6.simRat.chr6 225635 14 + 647215 TAACAACCCCATTG - -a -s simMouse_chr6.simMouse.chr6 234957 93 + 636262 GGTCACACGATTATCATTCATGTGCTTCGTTTCCACTTTCCCATTAGGCATCCAGGGACTAATTAGAGGGCTATTAGCCGCTATTAACCTTGG -s Anc0.Anc0refChr5 54576 90 + 87904 ACTCACACCGTTCTCATCTATATGCTTTGCTTGCAGTTTCTTATTAGGTAAACAGGGAGCTATTAGAGAGCTATTAGCCAC---TTACCCCAG -s Anc1.Anc1refChr7 12017 90 - 47259 ACTCACACCGTTCTCATCTATATGCTTTGCTTGCAGTTTCTTATTAGGTAAACAGGGAGCTATTAGAGAGCTATTAGCCAC---TTACCCCAG -s Anc2.Anc2refChr15 50920 90 + 86568 ACTCACACCGTTCTCATCTATATGCTTTGCTTGCAGATCATTATTAGGTAAACAGGGAGCTATTAGTGAGCTATTAGCCAC---TTACCCCAG -s mr.mrrefChr5 88470 93 + 294540 GCTCACACGATTATCATTCATGTGCTTTGTTTCCACTTTCCTATTAGGCATCCAGGGACTAATTAGAGGGCTATTAGCCGCTATTAACCTTGG -s simCow_chr6.simCow.chr6 232284 85 + 602619 -CTCACACCATACTCATCTATATACTTTGCTTGCAGAT----GTTAGGTAAACAGGGTGCGATTGGGGTGCTATCTGCCAC---TTACTCTGA -s simDog_chr6.simDog.chr6 222821 89 + 593897 ACTCACACTGTTCTCATCCACATGCTTTGCTTGTAAATCATTATTGGTTAAGGAGGGAAGTACTAGTTA-TTAGTAGCCAC---ATACCTCAG -s simHuman_chr6.simHuman.chr6 313324 90 - 601863 ACTCAAATCGTTCTCATCTATATGCTTTGCTTACCGTTTCTTAGTAGGTAAACAGGGAGCTATTAGAGAGCTATTAGCCAC---TTACCCCAG -s simRat_chr6.simRat.chr6 225649 93 + 647215 GCTCACACGATTATCATTCATCTGCTTTGTCTCCACTTTCCTATTTGGCATCCAGGGACTAATTAGGGGGCTAGTAGCAGCTATTAACCTTGG - -a -s simMouse_chr6.simMouse.chr6 235050 27 + 636262 GATTATAGCTAAAGACAATTCAGGCCA -s Anc0.Anc0refChr5 54666 18 + 87904 AATTATTGC---------TGCTGACCA -s Anc1.Anc1refChr7 12107 20 - 47259 AATTATTGCTG-------TGCTGACCA -s Anc2.Anc2refChr15 51010 18 + 86568 AATTATTGC---------TGCTGACTA -s mr.mrrefChr5 88563 27 + 294540 GATTATTGCTGAAGACAATTCAGGCCA -s simCow_chr6.simCow.chr6 232369 15 + 602619 AATTATTGC---------TG---ACTG -s simDog_chr6.simDog.chr6 223023 18 + 593897 AATAATTGC---------TGCTGAATA -s simHuman_chr6.simHuman.chr6 313414 20 - 601863 AATTATTGCTG-------TGCTGACCA -s simRat_chr6.simRat.chr6 225742 27 + 647215 GATTATTGCTGAAGACAGTTGAGGCCA - -a -s simMouse_chr6.simMouse.chr6 235077 1 + 636262 A -s Anc0.Anc0refChr5 54686 1 + 87904 A -s Anc1.Anc1refChr7 12129 1 - 47259 A -s Anc2.Anc2refChr15 51030 1 + 86568 A -s mr.mrrefChr5 88590 1 + 294540 A -s simCow_chr6.simCow.chr6 232386 1 + 602619 G -s simDog_chr6.simDog.chr6 223043 1 + 593897 A -s simHuman_chr6.simHuman.chr6 313436 1 - 601863 A -s simRat_chr6.simRat.chr6 225769 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 235078 44 + 636262 TCACCGACCTATGATATACCATTAGTTAATAGGTTACCAATAAT -s Anc0.Anc0refChr5 54687 40 + 87904 GTACCAACCTCCCATAGGCT----GTTAATAGATAACCAGCAAT -s Anc1.Anc1refChr7 12130 40 - 47259 GTACCAACCTCCCATAGGCT----GTTAATAGATAACCAGCAAT -s Anc2.Anc2refChr15 51041 40 + 86568 GTACTAACCTCCCGTAGGCT----GTTAATAGATAACCAGCACA -s mr.mrrefChr5 88591 40 + 294540 TCACCGACCTATGATATACC----GTTAATAGGTTACCAATAAT -s simCow_chr6.simCow.chr6 232397 32 + 602619 GCACT---CTCTC-----CT----GTTAATAGATAACCAATAAA -s simDog_chr6.simDog.chr6 223055 40 + 593897 GTAGTAACCTCCTGTAGGCT----GTTAATAGATAACCAGCACA -s simHuman_chr6.simHuman.chr6 313437 40 - 601863 GTACCAACCTGCCATAGGGT----GTTAATAGATAACCAGCGAT -s simRat_chr6.simRat.chr6 225770 20 + 647215 TCACCGACCTATGATATACC------------------------ - -a -s simMouse_chr6.simMouse.chr6 235122 26 + 636262 TAGTTTGAGGTATGTCTGTTTAGAGG -s Anc0.Anc0refChr5 54727 8 + 87904 TAGCT------------------AGA -s Anc1.Anc1refChr7 12170 11 - 47259 TAGCTTGA---------------AGA -s Anc2.Anc2refChr15 51081 8 + 86568 TAACT------------------GAA -s mr.mrrefChr5 88631 24 + 294540 TAGTTTGAGGTATGTCTG--TAGAGG -s simCow_chr6.simCow.chr6 232429 8 + 602619 TAGCT------------------GAA -s simDog_chr6.simDog.chr6 223095 8 + 593897 TAACT------------------GAA -s simHuman_chr6.simHuman.chr6 313580 11 - 601863 CAGGTTGA---------------AGA -s simRat_chr6.simRat.chr6 225790 6 + 647215 --------------------TAGAGG - -a -s simMouse_chr6.simMouse.chr6 235148 52 + 636262 TATGTCTGTTTATGATTGGACTCCAGTTGTAAGGTCTGCCTTCCCCTATGTG -s Anc0.Anc0refChr5 54735 50 + 87904 TATGTCTGATCATGCCTGAACCACAGTTGTAAGGGCTGC--TCCCCTCTGTA -s Anc1.Anc1refChr7 12181 52 - 47259 TATGTCTGATCATGCCTGAACCACAGTTGTAAGGGCTGCTATCCCCTCTGTA -s Anc2.Anc2refChr15 51089 50 + 86568 CACGTCTGATCATGCCTGAACCACAGTTGTAAGGGCTGC--TCTCCTCTGTA -s mr.mrrefChr5 88655 52 + 294540 TATGTCTGTTTATGATTGGACTCCAGTTGTAAGGTCTGCCTTCCCCTATGTG -s simCow_chr6.simCow.chr6 232438 50 + 602619 CACCTCTGATCATGCCTAAACAACAGACGTATGGGCTGC--TTTCTTCTGTA -s simDog_chr6.simDog.chr6 223103 45 + 593897 CACGTCTGTTCATGACTGAACCACAGTTGGAAGG-------CCCCCTCTGTA -s simHuman_chr6.simHuman.chr6 313591 49 - 601863 TATGTCTGAGCATGCCTGAACCACAGTTGTAAGGGTTGTTATCCATTGT--- -s simRat_chr6.simRat.chr6 225796 52 + 647215 TATGTCCATTTAAGATTGGACCCCAGTTGTAAGGTCTGCCTTCCCCTATGTG - -a -s simMouse_chr6.simMouse.chr6 235200 13 + 636262 AGTGTGTAGTGGG -s Anc0.Anc0refChr5 54785 13 + 87904 AGTGTATGGTGGG -s Anc1.Anc1refChr7 12233 13 - 47259 AGTGTATGGTGGG -s Anc2.Anc2refChr15 51139 13 + 86568 AGTGTATGGTGGG -s mr.mrrefChr5 88707 13 + 294540 AGTGTGTAGTGGG -s simCow_chr6.simCow.chr6 232490 13 + 602619 AGTGCATTGCCAC -s simDog_chr6.simDog.chr6 223148 13 + 593897 AGTGTATGGTGGG -s simHuman_chr6.simHuman.chr6 313640 12 - 601863 -GTATATGGTGGG -s simRat_chr6.simRat.chr6 225848 13 + 647215 AGTGTATAGCGGG - -a -s simMouse_chr6.simMouse.chr6 235213 45 + 636262 TGTTTTCCCCCCATTATCTATTGTGACCAATCTGGCTTTGCCCAG -s Anc0.Anc0refChr5 54801 44 + 87904 TGTTTTCCCGCCATTATCTGTTATGACCAATCTGGTTTTGGTC-T -s Anc1.Anc1refChr7 12249 45 - 47259 TGTTTTCCCGCCATTATCTGTTATGACCAATCTGGTTTTGGTCAT -s Anc2.Anc2refChr15 51155 44 + 86568 TGTTTTCCCGCCATTATCTGTTAGGACTAATCTGGTTTTGGTC-T -s mr.mrrefChr5 88720 45 + 294540 TGTTTTCCCCCCATTATCTATTGTGACCAATCTGGCTTTGCCCAG -s simCow_chr6.simCow.chr6 232506 40 + 602619 TGTTTTCCTGTCAGTATCTGAGTG----AATCTGGTTTTCACC-T -s simDog_chr6.simDog.chr6 223164 44 + 593897 TTTTTGCCCACCATAATCTGTTAGGACTAATCTGGTTTTGGTC-T -s simHuman_chr6.simHuman.chr6 313655 45 - 601863 TGTTTTCCCGCTATTATCTGTTATGACCAATCTGGTTGTGGGCAT -s simRat_chr6.simRat.chr6 225861 45 + 647215 TGTTTTCCCCCCATTATCTATTGTGACCAATCCGGCTTTGCCCAG - -a -s simMouse_chr6.simMouse.chr6 235258 5 + 636262 AGTTT -s Anc0.Anc0refChr5 54845 5 + 87904 AGCTT -s Anc1.Anc1refChr7 12294 5 - 47259 AGCTT -s Anc2.Anc2refChr15 51199 5 + 86568 AGCTT -s mr.mrrefChr5 88765 5 + 294540 AGTTT -s simCow_chr6.simCow.chr6 232547 5 + 602619 AGCTT -s simDog_chr6.simDog.chr6 223208 5 + 593897 AGCTT -s simHuman_chr6.simHuman.chr6 313700 5 - 601863 AGCTT -s simRat_chr6.simRat.chr6 225906 5 + 647215 TGTTT - -a -s simMouse_chr6.simMouse.chr6 235263 7 + 636262 TCAATAC -s Anc0.Anc0refChr5 54851 7 + 87904 TCAATAT -s Anc1.Anc1refChr7 12300 7 - 47259 TCAATAT -s Anc2.Anc2refChr15 51205 7 + 86568 TTAATAT -s mr.mrrefChr5 88770 7 + 294540 TCAATAC -s simCow_chr6.simCow.chr6 232553 7 + 602619 TCAGTGT -s simDog_chr6.simDog.chr6 223214 7 + 593897 TTAATAT -s simHuman_chr6.simHuman.chr6 313706 7 - 601863 TCAATAG -s simRat_chr6.simRat.chr6 225911 7 + 647215 TCAATAC - -a -s simMouse_chr6.simMouse.chr6 235270 9 + 636262 TGTACTCAA -s Anc0.Anc0refChr5 54858 8 + 87904 TAAACT-AC -s Anc1.Anc1refChr7 12307 9 - 47259 TAAACTCAC -s Anc2.Anc2refChr15 51212 8 + 86568 CAAACT-AC -s mr.mrrefChr5 88777 9 + 294540 TGTACTCAA -s simCow_chr6.simCow.chr6 232560 8 + 602619 CAAACC-CC -s simDog_chr6.simDog.chr6 223268 8 + 593897 CAAACT-AC -s simHuman_chr6.simHuman.chr6 313713 8 - 601863 TAAACCCA- -s simRat_chr6.simRat.chr6 225918 9 + 647215 TGGACTTAA - -a -s simMouse_chr6.simMouse.chr6 235279 32 + 636262 GTTATATTGGCAGAGACAACCATCTCAAATGC -s Anc0.Anc0refChr5 54866 30 + 87904 GTTGTATTGTCAGAGACAATAATCTTAAA--T -s Anc1.Anc1refChr7 12316 30 - 47259 GTTGTATTGTCAGAGACAATAATCTTAAA--T -s Anc2.Anc2refChr15 51220 30 + 86568 GTTGTATTGTCAGAGACAATAATCTTAAA--T -s mr.mrrefChr5 88786 30 + 294540 GTTATATTGGCAGAGACAACCATCTCAAA--C -s simCow_chr6.simCow.chr6 232573 30 + 602619 GTTGAATGGACAGAGGCAATAGCTTCAAA--T -s simDog_chr6.simDog.chr6 223276 30 + 593897 GTTGTATTGTCAGAGACAATAATCTTAAA--T -s simRat_chr6.simRat.chr6 225927 30 + 647215 ATTATATTGACACAGGCTACCACCTCAAA--C - -a -s simMouse_chr6.simMouse.chr6 235311 2 + 636262 TG -s Anc0.Anc0refChr5 54896 2 + 87904 TA -s Anc1.Anc1refChr7 12346 2 - 47259 TA -s Anc2.Anc2refChr15 51268 2 + 86568 TA -s mr.mrrefChr5 88816 2 + 294540 TG -s simCow_chr6.simCow.chr6 232621 2 + 602619 CA -s simDog_chr6.simDog.chr6 223324 2 + 593897 TA -s simRat_chr6.simRat.chr6 225957 2 + 647215 TG - -a -s simMouse_chr6.simMouse.chr6 235313 61 + 636262 TATTACTAGTTCACCAATTTACACCCACATCACATGGTCTTTATGTGTATTTTACTAATGG -s Anc0.Anc0refChr5 54898 59 + 87904 TATTAGTGGGT-ACC-ATTTACACCCATGGTGTATGGTATTGCCATGTATTTTGCTATTGG -s Anc1.Anc1refChr7 12348 59 - 47259 TATTAGTGGGT-ACC-ATTTACACCCATGGTGTATGGTATTGCCATGTATTTTGCTATTGG -s Anc2.Anc2refChr15 51270 59 + 86568 TATTAGTGGGT-ACC-ATTTACACCCATGGTGTATGGTATTGCCATGTATTTTGCTATTGG -s mr.mrrefChr5 88818 61 + 294540 TATTACTAGTTCACCAATTTACACCCACATCACATGGTCTTTATGTGTATTTTACTAATGG -s simCow_chr6.simCow.chr6 232635 59 + 602619 CACTAGTGGAT-ACC-ATCCGCACCCATGGGGCATGGTCCTCCCATGTATTTTACTATTGG -s simDog_chr6.simDog.chr6 223326 59 + 593897 TATTAGTGGGT-ACC-ATTTACACCCATGGTGTATGGTATTGCCATGTATTTTGCTATTGA -s simRat_chr6.simRat.chr6 225959 61 + 647215 CATTACTAGTTCACCGATTTAGACCCACATTGCATAGTCTTTTTGTGTATTTTACTATTGG - -a -s simMouse_chr6.simMouse.chr6 235374 17 + 636262 CCCCATGTGAACCCTGA -s Anc0.Anc0refChr5 54957 17 + 87904 CCCCACATGTACATTGA -s Anc1.Anc1refChr7 12407 17 - 47259 CCCCACATGTACATTGA -s Anc2.Anc2refChr15 51331 17 + 86568 CCCCACATGTACATTGA -s mr.mrrefChr5 88879 17 + 294540 CCCCATGTGAACCCTGA -s simCow_chr6.simCow.chr6 232696 15 + 602619 CCCCA--TGTACATCAG -s simDog_chr6.simDog.chr6 223387 17 + 593897 CCCCACATGTTCATTGA -s simHuman_chr6.simHuman.chr6 313721 13 - 601863 ----GGTTGTATATTGA -s simRat_chr6.simRat.chr6 226020 17 + 647215 CCCCATGTGAACCTTGC - -a -s simMouse_chr6.simMouse.chr6 235391 5 + 636262 ACCAG -s Anc0.Anc0refChr5 54974 5 + 87904 TTCAG -s Anc1.Anc1refChr7 12424 5 - 47259 TTCAG -s Anc2.Anc2refChr15 51348 5 + 86568 TTAGG -s mr.mrrefChr5 88896 5 + 294540 ACCAG -s simCow_chr6.simCow.chr6 232711 5 + 602619 ATGGG -s simDog_chr6.simDog.chr6 223404 5 + 593897 TTAAG -s simHuman_chr6.simHuman.chr6 313734 5 - 601863 GACAG -s simRat_chr6.simRat.chr6 226038 5 + 647215 ACCAG - -a -s simMouse_chr6.simMouse.chr6 235396 14 + 636262 TGGAGTTTACTCTG -s Anc0.Anc0refChr5 54979 11 + 87904 TAGAGTCTG-TC-- -s Anc1.Anc1refChr7 12429 13 - 47259 TAGAGTCTG-TCTA -s Anc2.Anc2refChr15 51353 11 + 86568 TAGTGTCTG-TC-- -s mr.mrrefChr5 88901 14 + 294540 TGGAGTTTACTCTG -s simCow_chr6.simCow.chr6 232716 11 + 602619 TGGTGTTTG-TC-- -s simDog_chr6.simDog.chr6 223409 11 + 593897 TAGAGTCTG-TC-- -s simHuman_chr6.simHuman.chr6 313742 13 - 601863 GAGAGTGTG-TCTA -s simRat_chr6.simRat.chr6 226043 14 + 647215 TGGAGTTTACTCTA - -a -s simMouse_chr6.simMouse.chr6 235410 46 + 636262 ATCAGAGTGAAACCACAAGGATTCTGCTCCAAACCATAAAGTTCAT -s Anc0.Anc0refChr5 54990 46 + 87904 ATCAAAGCAAAACCATATGGAGACCGCTCCTAATGGTAAAACTCAT -s Anc1.Anc1refChr7 12442 46 - 47259 ATCAAAGCAAAACCATATGGAGACCGCTCCTAATGGTAAAACTCAT -s Anc2.Anc2refChr15 51364 46 + 86568 GTCAAAGCAAGACTGTGTGGAGACCGCTCCTAATGGTAAAACTCAT -s mr.mrrefChr5 88915 46 + 294540 ATCAGAGTGAAACCACAAGGATTCTGCTCCAAACCATAAAGTTCAT -s simCow_chr6.simCow.chr6 232727 46 + 602619 TTCAAAGCAAGACTGTGTGTAGATCGCTCCTAATGGTAAAATTCAT -s simDog_chr6.simDog.chr6 223424 46 + 593897 GTCAAAGCAAGACTGTGAGGAAACTGCTCCTAATGGTAAAACATAT -s simHuman_chr6.simHuman.chr6 313755 46 - 601863 ATCAAAGCAGAACCATATGGAGACCGCTCCTGATAGTATCACTCAT -s simRat_chr6.simRat.chr6 226057 46 + 647215 ATCAAAGCAAAACCACAAGGATTCTGCTTCAAATGATAAAGTTCAT - -a -s simMouse_chr6.simMouse.chr6 235456 50 + 636262 GGGATATTACAGCATGCTTAGATGTGAATCAACATCCTTAGATGTGAAGC -s Anc0.Anc0refChr5 55038 46 + 87904 GGGATAGTCCAGGCTGCTTACATGTGGAGTAA----GTCATATACAAAAC -s Anc1.Anc1refChr7 12490 46 - 47259 GGGATAGTCCAGGCTGCTTACATGTGGAGTAA----GTCATATACAAAAC -s Anc2.Anc2refChr15 51412 46 + 86568 GGGATAGTCCAGGCTGCTTACATGTGGAGTGA----GTCATATACAAAAC -s mr.mrrefChr5 88961 50 + 294540 GGGATATTACAGCATGCTTAGATGTGAATCAACATCCTTAGATGTGAAGC -s simCow_chr6.simCow.chr6 232775 46 + 602619 GGCAAGTCCCAGGCTGCTAACATGTGGAGTTG----GTCATATATAAGAC -s simDog_chr6.simDog.chr6 223472 46 + 593897 TGGATAGTCCATGCTACTTACATGTGGAATGA----GTCATACACAAAAC -s simHuman_chr6.simHuman.chr6 313803 46 - 601863 GGAATAGGCCAGATTGCTTAAACATGGAGTAA----GTCATATACAGAAC -s simRat_chr6.simRat.chr6 226105 50 + 647215 GGGATATTACAACATTCTTAGATGTGGGGCAACGTCCTTAGATGTGGAGC - -a -s simMouse_chr6.simMouse.chr6 235506 18 + 636262 ACGGAATATATTTAAGTT -s Anc0.Anc0refChr5 55090 17 + 87904 -CAGAGTATATTTAAAGT -s Anc1.Anc1refChr7 12542 18 - 47259 ACAGAGTATATTTAAAGT -s Anc2.Anc2refChr15 51464 17 + 86568 -CAGAGTATATTTAAAGT -s mr.mrrefChr5 89011 18 + 294540 ACGGAATATATTTAAGTT -s simCow_chr6.simCow.chr6 232827 16 + 602619 -CAGAGGTTATTTAA-GT -s simDog_chr6.simDog.chr6 223524 17 + 593897 -CAGAGTATATTTAAAGT -s simHuman_chr6.simHuman.chr6 313871 18 - 601863 ACAAATTATACTCAAAGT -s simRat_chr6.simRat.chr6 226155 18 + 647215 ACGGGATATATTTAAGTT - -a -s simMouse_chr6.simMouse.chr6 235524 17 + 636262 CTCTGCCACACGCCAAA -s Anc0.Anc0refChr5 55172 1 + 87904 C---------------- -s Anc1.Anc1refChr7 12625 13 - 47259 CCCTGACGGAGGC---- -s Anc2.Anc2refChr15 51546 1 + 86568 T---------------- -s mr.mrrefChr5 89029 17 + 294540 CTCTGCCACACGCCAAA -s simCow_chr6.simCow.chr6 232907 1 + 602619 T---------------- -s simHuman_chr6.simHuman.chr6 314026 13 - 601863 CCCTGACGGAGGC---- -s simRat_chr6.simRat.chr6 226173 17 + 647215 CTCTGCCATACACTAAA - -a -s simMouse_chr6.simMouse.chr6 235541 4 + 636262 CTTA -s mr.mrrefChr5 89046 4 + 294540 CTTA -s simRat_chr6.simRat.chr6 226191 4 + 647215 CTTA - -a -s simMouse_chr6.simMouse.chr6 235545 44 + 636262 ACAGTATGCCGCACTCCCCCATTTTGCTCTATCATGATACATGC -s Anc0.Anc0refChr5 55173 36 + 87904 --------CCATACTCCCCTATTTTGCTCTATCTTGATGTGTGA -s Anc1.Anc1refChr7 12638 43 - 47259 -TCGTATGCCATACTCCCCTATTTTGCTCTATCTTGATGTGTGA -s Anc2.Anc2refChr15 51547 36 + 86568 --------CCATGCTCCCCTACTTTTCCCTACGTTGATGTGTGA -s mr.mrrefChr5 89050 44 + 294540 ACAGTATGCCGCACTCCCCCATTTTGCTCTATCATGATATATGC -s simCow_chr6.simCow.chr6 232908 36 + 602619 --------CCATGCTCCCCTACTTTTCCCTACGTTGATATGTGG -s simDog_chr6.simDog.chr6 223598 6 + 593897 --------------------------------------GTGTGA -s simHuman_chr6.simHuman.chr6 314039 43 - 601863 -TCGTATGCCATATTCTCCTATTTTGCTCCATCTTGAAGTGTGA -s simRat_chr6.simRat.chr6 226268 43 + 647215 ATGGATTGCCGCACTCCCCCATCTTACTCTAGCCTGATAT-TGC - -a -s simMouse_chr6.simMouse.chr6 235589 5 + 636262 ATTAT -s Anc0.Anc0refChr5 55209 5 + 87904 TTGAT -s Anc1.Anc1refChr7 12681 5 - 47259 TTGAT -s Anc2.Anc2refChr15 51583 5 + 86568 TTGAA -s mr.mrrefChr5 89094 5 + 294540 TTTAT -s simCow_chr6.simCow.chr6 232950 5 + 602619 TTGGA -s simDog_chr6.simDog.chr6 223604 4 + 593897 TTGA- -s simHuman_chr6.simHuman.chr6 314082 5 - 601863 TTGAT -s simRat_chr6.simRat.chr6 226311 5 + 647215 TTTAT - -a -s simMouse_chr6.simMouse.chr6 235594 10 + 636262 CTCACAATGA -s Anc0.Anc0refChr5 55215 10 + 87904 CTCACAATAA -s Anc1.Anc1refChr7 12687 10 - 47259 CTCACAATAA -s Anc2.Anc2refChr15 51589 10 + 86568 CTCACAATAA -s mr.mrrefChr5 89099 10 + 294540 CTCACAATAA -s simCow_chr6.simCow.chr6 232956 10 + 602619 CTCACAATAG -s simDog_chr6.simDog.chr6 223608 8 + 593897 --AACAATAA -s simHuman_chr6.simHuman.chr6 314088 10 - 601863 CTCACACTAA -s simRat_chr6.simRat.chr6 226316 10 + 647215 CTCACAATAA - -a -s simMouse_chr6.simMouse.chr6 235604 18 + 636262 GTGTTGGACCCTTGGGCT -s Anc0.Anc0refChr5 55226 13 + 87904 GTTTTAGA-----GGGCT -s Anc1.Anc1refChr7 12698 18 - 47259 GTTTTAGACCCTTGGGCT -s Anc2.Anc2refChr15 51600 13 + 86568 GTTTTATA-----GAGCT -s mr.mrrefChr5 89109 18 + 294540 GTGTTGGACCCTTGGGCT -s simCow_chr6.simCow.chr6 232967 13 + 602619 GTTATATA-----GAGCT -s simDog_chr6.simDog.chr6 223617 8 + 593897 GTTTT----------GCT -s simHuman_chr6.simHuman.chr6 314099 18 - 601863 GCATTAGACCCTTGGGCT -s simRat_chr6.simRat.chr6 226326 16 + 647215 GTGTTGGACCCT--GGCT - -a -s simMouse_chr6.simMouse.chr6 235622 37 + 636262 ATAAGAATATTCAGCATTAACTTACATTTTGTCTTCA -s Anc0.Anc0refChr5 55239 37 + 87904 TTAAGTATTTTCAGATTTGATTTGCATTTTGTCTTCA -s Anc1.Anc1refChr7 12716 37 - 47259 TTAAGTATTTTCAGATTTGATTTGCATTTTGTCTTCA -s Anc2.Anc2refChr15 51613 37 + 86568 TTAAGTATTTTCAGATTTGATTAGCATTCTGTCTGCA -s mr.mrrefChr5 89127 37 + 294540 ATAAGAATATTCAGAATTAATTTGCATTTTGTCTTCA -s simCow_chr6.simCow.chr6 232980 37 + 602619 TCAAGAGTTTTCAGATTTGATTCGCATTCTGTCGGTA -s simDog_chr6.simDog.chr6 223625 37 + 593897 TTAAGTATTCTCAGATTTGGTTAGCATTCTGTGTGCA -s simHuman_chr6.simHuman.chr6 314119 37 - 601863 TTAAGTATTTTCAGAGTTGATTTGCATTTTGTCTTCA -s simRat_chr6.simRat.chr6 226342 28 + 647215 ATAAGAATCTTCAGAATTAATTTGCAT---------A - -a -s simMouse_chr6.simMouse.chr6 235659 33 + 636262 CTTTGTGTGTTTAATATTAAGTGATTTCCATCA -s Anc0.Anc0refChr5 55276 33 + 87904 CTTAGTGAGTTAAATGTTAAGTGATTTCCATCA -s Anc1.Anc1refChr7 12753 33 - 47259 CTTAGTGAGTTAAATGTTAAGTGATTTCCATCA -s Anc2.Anc2refChr15 51650 33 + 86568 CTTAATGATTTAAATGTTAAGTGATTTCAATCA -s mr.mrrefChr5 89164 33 + 294540 CTTTGTGTGTTTAATATTAAGTGATTTCCATCA -s simCow_chr6.simCow.chr6 233017 33 + 602619 CTTAATGATTTAAATGTTAAGTGATTTTAACAA -s simDog_chr6.simDog.chr6 223662 33 + 593897 CTCAACATTTTAAATGTTAAATGACTTCAATCA -s simHuman_chr6.simHuman.chr6 314162 33 - 601863 CTTAGTGAGTGAAATTTTAAGTGGTTCCCATCC -s simRat_chr6.simRat.chr6 226370 33 + 647215 CTTTGTGCATTTAATATTAAGCGATTTCCATCT - -a -s simMouse_chr6.simMouse.chr6 235692 12 + 636262 GTGTGTGTGGAT -s Anc0.Anc0refChr5 55309 12 + 87904 GTGTGTGTAGGT -s Anc1.Anc1refChr7 12786 12 - 47259 GTGTGTGTAGGT -s Anc2.Anc2refChr15 51683 12 + 86568 GGTTGTGTAGGT -s mr.mrrefChr5 89197 12 + 294540 GTGTGTGTGGAT -s simCow_chr6.simCow.chr6 233050 12 + 602619 GTGTGTGTAGGC -s simDog_chr6.simDog.chr6 223695 10 + 593897 GGTTGTG--TGT -s simHuman_chr6.simHuman.chr6 314202 12 - 601863 GTGTGTGAAGGT -s simRat_chr6.simRat.chr6 226403 12 + 647215 GTGTGTGTGGAT - -a -s simMouse_chr6.simMouse.chr6 235704 57 + 636262 TTTTTATCACTCTTCCTATTGTGTATAAATATGTGATACCCCAGAACAGATCACTTT -s Anc0.Anc0refChr5 55321 50 + 87904 T--TTATTATTCTTGCTAAT-----GAAACACATGATGCTCAAGACTAGTCTACTCT -s Anc1.Anc1refChr7 12798 55 - 47259 T--TTATTATTCTTGCTAATGTGTGGAAACACATGATGCTCAAGACTAGTCTACTCT -s Anc2.Anc2refChr15 51695 50 + 86568 T--TTATCTTTCTTGCTAAT-----GAACCACATGATGCTCAAGACTAGTCTACTCT -s mr.mrrefChr5 89209 57 + 294540 TTTTTATTACTCTTCCTATTGTGTATAAACATGTGATACCCCAGAACAGATCACTTT -s simCow_chr6.simCow.chr6 233063 50 + 602619 T--TTGTCTTTCTTCATAAT-----GAAACATATGATGCTCCAGACTAATCTACTCA -s simDog_chr6.simDog.chr6 223705 50 + 593897 T--TTATCTTTCTTGCTAAT-----GAACCACATGATGCTCAAGACTAGTCTACTCT -s simHuman_chr6.simHuman.chr6 314214 29 - 601863 T--TTATTATTCTTTCTAATGTGTGGAAACA-------------------------- -s simRat_chr6.simRat.chr6 226415 57 + 647215 TTTTTATTAGTCTTCCTATTGTGTATAAACATGTGATACCCCAGAACAGACCACTTT - -a -s simMouse_chr6.simMouse.chr6 235761 8 + 636262 CACCAGTG -s Anc0.Anc0refChr5 55371 8 + 87904 CCCCAATG -s Anc1.Anc1refChr7 12853 8 - 47259 CCCCAATG -s Anc2.Anc2refChr15 51746 8 + 86568 CCCCAATG -s mr.mrrefChr5 89266 8 + 294540 CACCAGTG -s simCow_chr6.simCow.chr6 233114 8 + 602619 CTCCAGTG -s simDog_chr6.simDog.chr6 223756 8 + 593897 CCCCAATG -s simHuman_chr6.simHuman.chr6 314243 2 - 601863 ------TG -s simRat_chr6.simRat.chr6 226472 8 + 647215 CACGAGTG - -a -s simMouse_chr6.simMouse.chr6 235769 11 + 636262 ATGAATAGAAA -s Anc0.Anc0refChr5 55379 11 + 87904 AATGCTAGGGG -s Anc1.Anc1refChr7 12861 11 - 47259 AATGCTAGGGG -s Anc2.Anc2refChr15 51767 11 + 86568 AATGCTAGGGG -s mr.mrrefChr5 89274 11 + 294540 AATAATAGAAA -s simCow_chr6.simCow.chr6 233123 10 + 602619 -ATGCTAGGGG -s simDog_chr6.simDog.chr6 223886 1 + 593897 A---------- -s simHuman_chr6.simHuman.chr6 314245 11 - 601863 AATGGTAGGGG -s simRat_chr6.simRat.chr6 226480 11 + 647215 AATAATAGAAA - -a -s simMouse_chr6.simMouse.chr6 235780 85 + 636262 TTAGCGGCAGAAGCAACACTTTGTTTACTACCTTAGGACAATATGGGTTGTGTAAATGCCCTGCCTTAAGATGAGGGATCTCCAA -s Anc0.Anc0refChr5 55390 61 + 87904 TTGGCAGTAG------T-----GTCC------------TAAAATGGGCTCCTCATG-AACCTGCCTTAAGGTGAGGGACATTCCC -s Anc1.Anc1refChr7 12872 61 - 47259 TTGGCAGTAG------T-----GTCC------------TAAAATGGGCTCCTCATG-AACCTGCCTTAAGGTGAGGGACATTCCC -s Anc2.Anc2refChr15 51778 61 + 86568 TTGACAGTAG------T-----GCTC------------TAAAACAGACTCCTCATG-AACCCGCTTCAAGGTGACGGACATTCCC -s mr.mrrefChr5 89285 85 + 294540 TTAGCAGCAGAAGCAACACTTTGTCCACTACCTTAGGACAATATGGGTTGTGTAAGTACCCTGCCTTAAGATGAGGGATCTCCAA -s simCow_chr6.simCow.chr6 233136 61 + 602619 TTGACAGTAG------T-----GCTC------------TAAAACAGACTCCTCATG-AACCCGCTTCAAGGTGACGGACATTCCC -s simHuman_chr6.simHuman.chr6 314256 61 - 601863 TTGGCAGTAT------T-----GTCC------------TAAAATGGGCTCCTCATG-AACCTGCCTTGAAGTGAGAGACATTTTC -s simRat_chr6.simRat.chr6 226491 80 + 647215 TTAGCAGGAGAAGCTACACTTTGTCCACTACCTTGTGAGAAGATG-----TGTAGGTACCCTGCCTTAAGATGACCGATTTCCAA - -a -s simMouse_chr6.simMouse.chr6 235865 99 + 636262 CTTATTTACCCAGCAGGTTCAATAATGGTGTTCTTAGCCATGCCCATGCACAGATGAGTTGGGTTTCATTTGATGCACTGTTGAATTGTTTGGTGTGAA -s Anc0.Anc0refChr5 55451 88 + 87904 TTTATTTACCTAGCAGATTCAATGATGGTGTCCTTAAC------CACACAC---TGCATTGTGCTAGATTTAATGCACTATTGAATTGTCTTATGTG-- -s Anc1.Anc1refChr7 12933 93 - 47259 TTTATTTACCTAGCAGATTCAATGATGGTGTCCTTAAC------CACACACTGATGCATTGTGCTAGATTTAATGCACTATTGAATTGTCTTATGTGGA -s Anc2.Anc2refChr15 51839 88 + 86568 TTTGTTTACTGAGCAGACTCAATGATGGTGACTTTAAC------CACACAC---TACATTGTGTTAGATTTAATGCACTATTGAATTGTCTTATGTG-- -s mr.mrrefChr5 89370 99 + 294540 CTTATTTACCTAGCAGGTTCAATAATGGTGTTCTTAGCCATGCCCATACACAGATGAGTTGGGCTTGATTTGATGCACTGTTGAATTGTTTGGTGTGAA -s simCow_chr6.simCow.chr6 233200 88 + 602619 TTTGTTTACTGAGCAGACTCAATAATGGTGCCTTTAAC------CACACCT---TACATTGTGTTAAATTTAATGCCTTATTGAATGGTCTTCTGTG-- -s simDog_chr6.simDog.chr6 223887 76 + 593897 ------------GCAGACTTAAAGATGGTGACTTTAAC------CACACAC---TACATTGTGTTAGATTTAATACACTATTGAATTGTCTTATGTG-- -s simHuman_chr6.simHuman.chr6 314317 93 - 601863 TTCATTCACCTAGCAGATTCAATGATGGTGTCCTTAAT------CACACACTGATGTATTGCGCTAGATTTCATGCACTATTGATTTCTGCTATGTGGA -s simRat_chr6.simRat.chr6 226571 98 + 647215 -TTACTTGCCTAGCAGTATCAATAATGCTGTTTTTGGCCATGTCCATACACAAATGAGTTGGGCCTGATTTAATGCACTGTTAAATTGTCTGGTGTGAA - -a -s simMouse_chr6.simMouse.chr6 235964 46 + 636262 GAGTTAGCACCTTGGTAAAAGGTGATTTGTAATTTTGGCTAAGAAT -s Anc0.Anc0refChr5 55547 45 + 87904 GATTCAA-TCTAAGGTGTTAGGTGAGCTGTCGTTTTGGCTACCACT -s Anc1.Anc1refChr7 13034 46 - 47259 GATTCAATTCTAAGGTGTTAGGTGAGCTGTCGTTTTGGCTACCACT -s Anc2.Anc2refChr15 51935 45 + 86568 TATTCAG-TCTAAGATGTTAGGTGAGCTGTCGTTATGGTCACCACT -s mr.mrrefChr5 89469 46 + 294540 GAGTTAACACCTTGGTGAAAGGTGATCTGTAATTTTGGCTAACAAT -s simCow_chr6.simCow.chr6 233296 45 + 602619 TATTCAG-TCCAAGATGTGAGGTGATCTGTAATTATGGTCACCACT -s simDog_chr6.simDog.chr6 223965 37 + 593897 TATTCAG-CCTAAGATGGTAGGTGAGTTGTCGT--------CCATT -s simHuman_chr6.simHuman.chr6 314425 46 - 601863 GATTCAATGCTAAGGTGTCAGGTGGCCTGTGGTTTTAGCTACCACT -s simRat_chr6.simRat.chr6 226669 46 + 647215 GAGTTAACTCCTTGATGATAGGTGATCTGTAATTTTGGCTAACATT - -a -s simMouse_chr6.simMouse.chr6 236010 31 + 636262 ATCCATTAAATTTGTAACTGTCCATTCTGCA -s Anc0.Anc0refChr5 55595 31 + 87904 ATCTATTTCAACTGCCTCTCTCCATTCTACA -s Anc1.Anc1refChr7 13083 31 - 47259 ATCTATTTCAACTGCCTCTCTCCATTCTACA -s Anc2.Anc2refChr15 51983 31 + 86568 ATCTATTTCAACTGCCTCTCTCCACTCAACT -s mr.mrrefChr5 89515 31 + 294540 ATCCATTAAATCTGCAACTGTCCATTCTGCA -s simCow_chr6.simCow.chr6 233344 31 + 602619 TTCATCTTCAACTGCAGCTCTCCGTTTGACT -s simDog_chr6.simDog.chr6 224005 31 + 593897 ACCTATTTCAAATGCCTTTCCCCACTCAACT -s simHuman_chr6.simHuman.chr6 314474 31 - 601863 ATCTATTTCAGCCACCTCTTTCCATTCTCCA -s simRat_chr6.simRat.chr6 226715 31 + 647215 ATCCATTAAATCTGCAACTCTCCATTAAGCA - -a -s simMouse_chr6.simMouse.chr6 236041 2 + 636262 AT -s Anc0.Anc0refChr5 55626 2 + 87904 TT -s Anc1.Anc1refChr7 13114 2 - 47259 TT -s Anc2.Anc2refChr15 52014 2 + 86568 TT -s mr.mrrefChr5 89546 2 + 294540 AT -s simCow_chr6.simCow.chr6 233375 2 + 602619 TT -s simDog_chr6.simDog.chr6 224036 2 + 593897 TT -s simHuman_chr6.simHuman.chr6 314512 2 - 601863 TT -s simRat_chr6.simRat.chr6 226746 2 + 647215 AT - -a -s simMouse_chr6.simMouse.chr6 236043 35 + 636262 CAAGTCTGTATGACGGGTAAACCTGAACACAGACT -s Anc0.Anc0refChr5 55628 31 + 87904 CTAA---GTGTTACAAGTACAC-TGAATACAGGCT -s Anc1.Anc1refChr7 13116 32 - 47259 CTAA--CGTGTTACAAGTACAC-TGAATACAGGCT -s Anc2.Anc2refChr15 52016 31 + 86568 CTAA---GTTTTATGAGTACAC-TGAATACAGGCT -s mr.mrrefChr5 89548 35 + 294540 CAAGTCTGTGTGACAGGTAAACCTGAACACAGACT -s simCow_chr6.simCow.chr6 233378 31 + 602619 CTTA---GTTTTATGAGTACAC-TGAATACAGGCT -s simDog_chr6.simDog.chr6 224038 30 + 593897 CTAA---GTTTTCTGAGTACAC-TGAATACAG-CT -s simHuman_chr6.simHuman.chr6 314514 32 - 601863 CCAA--CGTGTTACAATTACAC-TCAAAACAGGCT -s simRat_chr6.simRat.chr6 226748 35 + 647215 CAAGTCTGTGTCACAGGTAAACCTGAACACAGACT - -a -s simMouse_chr6.simMouse.chr6 236078 102 + 636262 CTGCCATAGTAACCTTGTTCACCTTAACTGTAACTGATCACAACCCTATCAATATGTCATAGAAAACCATTCAATATTCTTTCACATTCTACAAATCTGGTA -s Anc0.Anc0refChr5 55659 96 + 87904 CTGCCATGATAAGCTTGTTTACCTCAGTTTCGACCTATTACAACCACCTCAACGTGTCATGGTCACACATTCAATATACTTTCA------ACAAACCTGATA -s Anc1.Anc1refChr7 13148 96 - 47259 CTGCCATGATAAGCTTGTTTACCTCAGTTTCGACCTATTACAACCACCTCAACGTGTCATGGTCACACATTCAATATACTTTCA------ACAAACCTGATA -s Anc2.Anc2refChr15 52047 96 + 86568 CTGCCATGATAAGCTTGTCTACCTCAGTTTTGACCAATTACAACCACCTCAATGTGTCATGGTCACACATTCAATATATTTTCA------ACAAACCTGATA -s mr.mrrefChr5 89583 102 + 294540 CTGCCATAGTAACCTTGTTTACCTTAACTGCAACCTATCACAACCCTATCAACATGTCATAGAAACCCATTCAATATTCTTTCACATTCTACAAACCTGGTA -s simCow_chr6.simCow.chr6 233450 80 + 602619 CTGCCATGATAAGCTTGTCCATGTCACTTTTGACCAATTGCAACCATCTCA---TGTTGTGGTCACA-------------TTGA------ACAAACCTGGTA -s simDog_chr6.simDog.chr6 224068 96 + 593897 CTCCCATGATAAGCTTGTCTACCTCTGTTTTGACCAATTAAATCCACCTCAATGTGTCATGGTTGCACATTCAATATATTTTCT------ACGAACCTGATA -s simHuman_chr6.simHuman.chr6 314546 90 - 601863 CTGCCGTGATAAGCTTGTTTAGCTCA--TTCGACCTATTACAACC----GGTCGTGTCATGGTCACACATTCAATATCCTTTCA------ACATACCTGTTA -s simRat_chr6.simRat.chr6 226783 101 + 647215 TT-CCATAGTAACCTTGTTTATTTTACCTGCAACCTAACACAACCCTATCAACATGTCATAGCAACCCACTTAATATTCTTTCACATTCTACAAGCCTGGTA - -a -s simMouse_chr6.simMouse.chr6 236180 5 + 636262 CAGGA -s Anc0.Anc0refChr5 55759 5 + 87904 CTGAA -s Anc1.Anc1refChr7 13248 5 - 47259 CTGAA -s Anc2.Anc2refChr15 52147 5 + 86568 ATGCA -s mr.mrrefChr5 89685 5 + 294540 CAGAA -s simCow_chr6.simCow.chr6 233534 5 + 602619 ATGCA -s simDog_chr6.simDog.chr6 224168 5 + 593897 ATGCA -s simHuman_chr6.simHuman.chr6 314640 5 - 601863 CTGAA -s simRat_chr6.simRat.chr6 226884 5 + 647215 CAGAA - -a -s simMouse_chr6.simMouse.chr6 236185 14 + 636262 GTAGCCCTTGGACA -s Anc0.Anc0refChr5 55764 14 + 87904 GTAACCCTTGGTCA -s Anc1.Anc1refChr7 13253 14 - 47259 GTAACCCTTGGTCA -s Anc2.Anc2refChr15 52152 14 + 86568 GTGACCTTTGGTTA -s mr.mrrefChr5 89690 14 + 294540 GTAGCCCTTGGACA -s simCow_chr6.simCow.chr6 233539 13 + 602619 GTGACATTTGGT-A -s simDog_chr6.simDog.chr6 224174 14 + 593897 GTGACCTTTGGTTC -s simHuman_chr6.simHuman.chr6 314645 14 - 601863 GTAACCCCTGGTCA -s simRat_chr6.simRat.chr6 226889 14 + 647215 GTACCCCTTGGACA - -a -s simMouse_chr6.simMouse.chr6 236199 6 + 636262 TAATAC -s Anc0.Anc0refChr5 55894 6 + 87904 TGTTTC -s Anc1.Anc1refChr7 13383 6 - 47259 TGTTTC -s Anc2.Anc2refChr15 52333 6 + 86568 TGTTTC -s mr.mrrefChr5 89704 6 + 294540 TAATAC -s simCow_chr6.simCow.chr6 233717 4 + 602619 T--TTA -s simDog_chr6.simDog.chr6 224347 6 + 593897 TGTTTC -s simHuman_chr6.simHuman.chr6 314776 6 - 601863 TGGTTT -s simRat_chr6.simRat.chr6 226903 6 + 647215 TAATCC - -a -s simMouse_chr6.simMouse.chr6 236205 21 + 636262 AGCTCACAGACTGGCTGTCAA -s Anc0.Anc0refChr5 55900 21 + 87904 ACCTTTCAGTTTGGCTGTTAA -s Anc1.Anc1refChr7 13389 21 - 47259 ACCTTTCAGTTTGGCTGTTAA -s Anc2.Anc2refChr15 52339 21 + 86568 ACCTTTCAGTTTGACTGTTAA -s mr.mrrefChr5 89710 21 + 294540 AGCTCACAGACTGGCTGTCAA -s simCow_chr6.simCow.chr6 233721 21 + 602619 ACCCTTCAGGTTGTCTGCTAA -s simDog_chr6.simDog.chr6 224353 21 + 593897 ACCTTTTAGTTTGACTATCGA -s simHuman_chr6.simHuman.chr6 314782 21 - 601863 ACCTTTCAGTTTGGCTGTTAA -s simRat_chr6.simRat.chr6 227145 21 + 647215 AGTTCACATTCTCACTATCAA - -a -s simMouse_chr6.simMouse.chr6 236226 10 + 636262 TCTGCAATGG -s Anc0.Anc0refChr5 55921 9 + 87904 AATG-AATGG -s Anc1.Anc1refChr7 13410 10 - 47259 AATGTAATGG -s Anc2.Anc2refChr15 52360 9 + 86568 AATG-AATAG -s mr.mrrefChr5 89731 10 + 294540 TCTGCAATGG -s simCow_chr6.simCow.chr6 233742 9 + 602619 AATG-AATAG -s simDog_chr6.simDog.chr6 224379 9 + 593897 AATG-AAGAG -s simHuman_chr6.simHuman.chr6 314803 10 - 601863 AATGTGATGG -s simRat_chr6.simRat.chr6 227166 10 + 647215 ACTGCAATGG - -a -s simMouse_chr6.simMouse.chr6 236236 28 + 636262 AGACTCATTTATGGTAGTAACATAATGT -s Anc0.Anc0refChr5 55930 28 + 87904 AGAGTGATTAATGTTAGCAACATAAGCT -s Anc1.Anc1refChr7 13420 28 - 47259 AGAGTGATTAATGTTAGCAACATAAGCT -s Anc2.Anc2refChr15 52369 28 + 86568 AGAGTGATTAATGTTAGCAACATAAGCT -s mr.mrrefChr5 89741 28 + 294540 AGACTCATTTATGGTAGTAACATAATGT -s simCow_chr6.simCow.chr6 233751 28 + 602619 AGATGCATTAATGTTAATAACATAAGGT -s simDog_chr6.simDog.chr6 224426 28 + 593897 AGAGTGATATATGCTAGCAACATAAGCC -s simHuman_chr6.simHuman.chr6 314813 28 - 601863 CGAGTGATTAACGTTAGCAACATAAGCT -s simRat_chr6.simRat.chr6 227176 28 + 647215 AGGCTCATTAATGCTAGCCACAAGATCT - -a -s simMouse_chr6.simMouse.chr6 236264 27 + 636262 TGATTGAGAATAAGCCCCATTGATGCT -s Anc0.Anc0refChr5 55960 26 + 87904 TTACTGGGAATAAGGCCCGTGGATG-A -s Anc1.Anc1refChr7 13450 26 - 47259 TTACTGGGAATAAGGCCCGTGGATG-A -s Anc2.Anc2refChr15 52399 26 + 86568 TTACTGGTAGTAAGGCCCGGGGATG-A -s mr.mrrefChr5 89769 26 + 294540 TGATTGAGAATAAGCCCCATTGATG-T -s simCow_chr6.simCow.chr6 233781 21 + 602619 AGACTGGTAGCAAG-----GGGATG-A -s simDog_chr6.simDog.chr6 224457 26 + 593897 TTACTGGTAGTAAGGCCCGGGGATG-A -s simHuman_chr6.simHuman.chr6 314843 26 - 601863 TTACTGGGAATGAGACCTCTGGATG-A -s simRat_chr6.simRat.chr6 227204 26 + 647215 TGGCTGAGAATATGCCCCATTGATG-T - -a -s simMouse_chr6.simMouse.chr6 236291 2 + 636262 CC -s Anc0.Anc0refChr5 55986 2 + 87904 CC -s Anc1.Anc1refChr7 13476 2 - 47259 CC -s Anc2.Anc2refChr15 52426 2 + 86568 CC -s mr.mrrefChr5 89795 2 + 294540 CC -s simCow_chr6.simCow.chr6 233803 2 + 602619 TG -s simDog_chr6.simDog.chr6 224484 2 + 593897 CC -s simHuman_chr6.simHuman.chr6 314869 2 - 601863 CC -s simRat_chr6.simRat.chr6 227230 2 + 647215 CC - -a -s simMouse_chr6.simMouse.chr6 236293 278 + 636262 TGTTTCTCATCAGTAATTGCAGAGAACAATGCCAGTATGGTGCATTCCACCGGGTAAAGCAGATGGCCAGTATGGGTACACTGTGGGAAGGCCCTTTGTGCACTGTGGGAAGGCCCCTTCCTAATACCTAAGTTCACAAATATAGGTTTATGATGTACAATTGAGCAATACTATAATAGAGGGAGCTGACAAATCAGGCTGTATTTCCAGGGACCCAATAAACCATGCTGTGGTGTGTCTCCAGGGCCCCTGTGTGCCGAGTCCATATATTGGTTGCT -s Anc0.Anc0refChr5 55988 36 + 87904 TGTTTCTTAC--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TGTGCAGAGTCCATGTATTGACAGCT -s Anc1.Anc1refChr7 13478 36 - 47259 TGTTTCTTAC--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TGTGCAGAGTCCATGTATTGACAGCT -s Anc2.Anc2refChr15 52428 36 + 86568 TGTTTCTTAC--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TGTACAGAGTCCATGAGTTGACAGCT -s mr.mrrefChr5 89797 264 + 294540 TGTTTCTCATCAGTAATT--------CAATGCCAGTATGGTGCATTCCACCGGGTAAAGCAGATGGCCAGTATGGGTACACTGTGGGAAGGCCCTTTGTGCACTGTGGGAAGGCCCCTTCCTAATACCTAAGTTCACAAATATAGGTTTAT-ATGTACAATTGAGCAATACTATAATAGAGGGAGCTGACAAATCAGGCTGTATTTCCAGGGACCCAATAAACCATGC-----TGTGTCTCCAGGGCCCCTGTGTGCCGAGTCCATATATTGGTTGCT -s simCow_chr6.simCow.chr6 233805 32 + 602619 TGTTTCT------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GTACAGGGTGCATGAGTTGGCAGCT -s simDog_chr6.simDog.chr6 224486 36 + 593897 TGTTTCCTAC--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TGTACAAAGTCCATAAGTTGACAGCT -s simHuman_chr6.simHuman.chr6 314878 36 - 601863 TGTTTCTTAC--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TGTGCAGAGTCCATGTATTGACAGCA -s simRat_chr6.simRat.chr6 227232 264 + 647215 TGCTTTTCATCAGAAATC--------TAATGCTAGAGTGGTGCATTCCACTAGGTAAACCAGATGCCCAGTATGGGTGCATTATGGAAAGGCCCCTTGTGCACTGTGGGAAGGCCCTTTCCTAATACCTAAGTTCACATATAAAGGTTTAT-AGGTACAATTGAGCAATACCATAATAGAGGGAGCCGACAAACCAGGCCGTATTTCCAGGGACCCAATAAACCATAC-----TGTATCTCCTAGGTCCCCATGCGCTGAGTCCATATATTGGTTGCT - -a -s simMouse_chr6.simMouse.chr6 236571 3 + 636262 GCT -s Anc0.Anc0refChr5 56024 3 + 87904 GCT -s Anc1.Anc1refChr7 13514 3 - 47259 GCT -s Anc2.Anc2refChr15 52464 3 + 86568 CCT -s mr.mrrefChr5 90061 3 + 294540 GCT -s simCow_chr6.simCow.chr6 233837 3 + 602619 ACT -s simDog_chr6.simDog.chr6 224522 3 + 593897 CCT -s simHuman_chr6.simHuman.chr6 314914 3 - 601863 GCT -s simRat_chr6.simRat.chr6 227497 3 + 647215 GCG - -a -s simMouse_chr6.simMouse.chr6 236574 7 + 636262 TGTGGAC -s Anc0.Anc0refChr5 56028 7 + 87904 TGTGGGC -s Anc1.Anc1refChr7 13518 7 - 47259 TGTGGGC -s Anc2.Anc2refChr15 52468 7 + 86568 TATGGGC -s mr.mrrefChr5 90064 7 + 294540 TGTGGAC -s simCow_chr6.simCow.chr6 233841 7 + 602619 TATAGGC -s simDog_chr6.simDog.chr6 224526 7 + 593897 TATGGGT -s simHuman_chr6.simHuman.chr6 314918 7 - 601863 TGTGGGC -s simRat_chr6.simRat.chr6 227500 7 + 647215 TGTGGAC - -a -s simMouse_chr6.simMouse.chr6 236581 7 + 636262 CTAATAA -s Anc0.Anc0refChr5 56037 7 + 87904 CTAAGAG -s Anc1.Anc1refChr7 13527 7 - 47259 CTAAGAG -s Anc2.Anc2refChr15 52477 7 + 86568 CTAAGAG -s mr.mrrefChr5 90071 7 + 294540 CTAATAA -s simCow_chr6.simCow.chr6 233850 7 + 602619 CTATGAG -s simDog_chr6.simDog.chr6 224535 7 + 593897 CTGAGAC -s simHuman_chr6.simHuman.chr6 314927 7 - 601863 CCAGGGG -s simRat_chr6.simRat.chr6 227507 7 + 647215 CTAATAA - -a -s simMouse_chr6.simMouse.chr6 236588 57 + 636262 GGAGCCCAAGTTGGTGAAACTTGTGACCGCTTCACTACCAGTCGCCTGATGTAACAT -s Anc0.Anc0refChr5 56044 57 + 87904 GGATCCCAACATGAAGAAAATTGTGACAGCTTCACAGCCAGTCTTCTGATGTGACAT -s Anc1.Anc1refChr7 13534 57 - 47259 GGATCCCAACATGAAGAAAATTGTGACAGCTTCACAGCCAGTCTTCTGATGTGACAT -s Anc2.Anc2refChr15 52484 57 + 86568 GGATCACAACATGAAGAAAAATGTAACAGCTTCACAGCCAGTCTTCTGATGTGACAT -s mr.mrrefChr5 90078 57 + 294540 GGAGCCCAAGTTGGTGAAACTTGTGACCGCTTCACTACCAGTCGCCTGATGTAACAT -s simCow_chr6.simCow.chr6 233857 57 + 602619 GGGACACAAAATGAAGAAACTTGTAACAGCCTCACAACCGGTCTTCTGATGTGACAT -s simDog_chr6.simDog.chr6 224542 45 + 593897 GGATCACAACACGAAGTAAAATGTAACAGCTTCACAGACAGTCTT------------ -s simHuman_chr6.simHuman.chr6 314934 55 - 601863 GGATCCCAGCATGAAGAAGGT--TGACAGCTTCACAGCCAGTCTTTTGATGTGAAAT -s simRat_chr6.simRat.chr6 227571 57 + 647215 GGAGCCTAAGTTGGCAAAACTTGTGACTGCCTCCCTACCATTCACCAGATGTAACAT - -a -s simMouse_chr6.simMouse.chr6 236645 6 + 636262 ATAATT -s Anc0.Anc0refChr5 56101 6 + 87904 GTCATT -s Anc1.Anc1refChr7 13591 6 - 47259 GTCATT -s Anc2.Anc2refChr15 52541 6 + 86568 GCCGTT -s mr.mrrefChr5 90135 6 + 294540 ATAATT -s simCow_chr6.simCow.chr6 233920 6 + 602619 GCCGTT -s simHuman_chr6.simHuman.chr6 314989 6 - 601863 GTCATT -s simRat_chr6.simRat.chr6 227628 6 + 647215 GTAATT - -a -s simMouse_chr6.simMouse.chr6 236651 6 + 636262 TTCCCG -s Anc0.Anc0refChr5 56109 6 + 87904 TGGCCA -s Anc1.Anc1refChr7 13599 6 - 47259 TGGCCA -s Anc2.Anc2refChr15 52549 6 + 86568 TGGCCA -s mr.mrrefChr5 90141 6 + 294540 TTCCCG -s simCow_chr6.simCow.chr6 233928 6 + 602619 TGGCCA -s simHuman_chr6.simHuman.chr6 314997 6 - 601863 TGGCCA -s simRat_chr6.simRat.chr6 227634 6 + 647215 TTGGTG - -a -s simMouse_chr6.simMouse.chr6 236657 41 + 636262 ACTTTTTACTGATACCCTCTCCTCACAAATCTTATATTGGG -s Anc0.Anc0refChr5 56117 41 + 87904 GCTTTTTATTCATGCCTTCCCTTTAGATATCTTGTATCAGG -s Anc1.Anc1refChr7 13607 41 - 47259 GCTTTTTATTCATGCCTTCCCTTTAGATATCTTGTATCAGG -s Anc2.Anc2refChr15 52557 41 + 86568 GCTTTTTATTCATGCCTTCCCTTTAGATATCTTGTGTCAGG -s mr.mrrefChr5 90147 41 + 294540 ACTTTTTACTGATACCCTCTCCTCACAAATCTTATATTGGG -s simCow_chr6.simCow.chr6 233936 41 + 602619 GTTTTCTACTCATGCTTTCCCTTGAGATCTCACATGTCAGA -s simDog_chr6.simDog.chr6 224587 40 + 593897 -CTTTTTATTGATGGCTTCTCTTTAGATATCTTGTGTCAAG -s simHuman_chr6.simHuman.chr6 315005 41 - 601863 GCTTTTTATTCATGCGTTCCTTTTGGATATCTTGTATCAGG -s simRat_chr6.simRat.chr6 227640 41 + 647215 GTTTTTTACTAATATCCTCCCTTCACACATCTTATATCAGG - -a -s simMouse_chr6.simMouse.chr6 236698 21 + 636262 ATGATCACAGATTTGTCCCAA -s Anc0.Anc0refChr5 56159 21 + 87904 AGGACTACATGTTTGTCCCAA -s Anc1.Anc1refChr7 13649 21 - 47259 AGGACTACATGTTTGTCCCAA -s Anc2.Anc2refChr15 52599 21 + 86568 AGGACTACATGTTTGTCCCAA -s mr.mrrefChr5 90188 21 + 294540 ATGATCACAGATTTGTCCCAA -s simCow_chr6.simCow.chr6 233978 21 + 602619 AAGACCACATGTTTCTACCAA -s simDog_chr6.simDog.chr6 224628 18 + 593897 AG---TGCATCCTGGTCCCAA -s simHuman_chr6.simHuman.chr6 315047 21 - 601863 AGGGCTACATGTTTGTGCCAA -s simRat_chr6.simRat.chr6 227681 21 + 647215 ATGATCACAGAATTGTCTCAA - -a -s simMouse_chr6.simMouse.chr6 236719 9 + 636262 AATGATCTG -s Anc0.Anc0refChr5 56181 9 + 87904 ACTGATCAG -s Anc1.Anc1refChr7 13671 9 - 47259 ACTGATCAG -s Anc2.Anc2refChr15 52621 9 + 86568 ACTGATCAG -s mr.mrrefChr5 90209 9 + 294540 AATGATCTG -s simCow_chr6.simCow.chr6 234000 9 + 602619 ACTGACCCA -s simDog_chr6.simDog.chr6 224647 9 + 593897 ACTGATCAG -s simHuman_chr6.simHuman.chr6 315069 9 - 601863 ACTGGTTAG -s simRat_chr6.simRat.chr6 227702 9 + 647215 AATGGCCTG - -a -s simMouse_chr6.simMouse.chr6 236728 15 + 636262 CCCTCTATTGCCATC -s Anc0.Anc0refChr5 56190 15 + 87904 CCCTCTATTGCCATT -s Anc1.Anc1refChr7 13680 15 - 47259 CCCTCTATTGCCATT -s Anc2.Anc2refChr15 52630 15 + 86568 ACCTCTATTGCCATT -s mr.mrrefChr5 90218 15 + 294540 CCCTCTATTGCCATC -s simCow_chr6.simCow.chr6 234009 15 + 602619 GCCTCTATTGCCATT -s simDog_chr6.simDog.chr6 224656 15 + 593897 ACCTCTATTGCCATT -s simHuman_chr6.simHuman.chr6 315078 15 - 601863 CCCTCTACTGCCACT -s simRat_chr6.simRat.chr6 227713 15 + 647215 CCCTCTATCGCCATC - -a -s simMouse_chr6.simMouse.chr6 236743 141 + 636262 TCCTGCATCCTACATCTTTCATTATTCTCTATGCAGCCCTAGCACTAGTAGACCCAGTGGGAGATTGGCTTCCAGAACACATTACGGTTCAATTTACCCCGCAAAATTCCAACAAACATTGTAGGTAAAGATATAAGGTAT -s Anc0.Anc0refChr5 56211 40 + 87904 TCCTACATCATGCATTCTTCATGAGACA-----------------------------------------------------------------------------------------------------CTTGTAACTTAT -s Anc1.Anc1refChr7 13701 40 - 47259 TCCTACATCATGCATTCTTCATGAGACA-----------------------------------------------------------------------------------------------------CTTGTAACTTAT -s Anc2.Anc2refChr15 52651 40 + 86568 TCTTACATCATGCATTCCTCATGAGACA-----------------------------------------------------------------------------------------------------CTTGTAACTAAT -s mr.mrrefChr5 90233 40 + 294540 TCCTGCATCCTACATCTTTCATTATTCT-----------------------------------------------------------------------------------------------------GATATAAGGTAT -s simDog_chr6.simDog.chr6 224677 40 + 593897 TCTTACATCATGCATTCCTCATGAGACA-----------------------------------------------------------------------------------------------------CTTGTAACTAAT -s simHuman_chr6.simHuman.chr6 315100 40 - 601863 TCCTACATCTTGCATTCTGCATGAGCCC-----------------------------------------------------------------------------------------------------CTGGAAACTTAT -s simRat_chr6.simRat.chr6 227728 40 + 647215 TCCTACATCCTACATCTTTCATCATTCT-----------------------------------------------------------------------------------------------------GATATACGGTAT - -a -s simMouse_chr6.simMouse.chr6 236884 13 + 636262 AACTAGAATTTGT -s Anc0.Anc0refChr5 56253 13 + 87904 AACTTGTCCTTGT -s Anc1.Anc1refChr7 13743 13 - 47259 AACTTGTCCTTGT -s Anc2.Anc2refChr15 52693 13 + 86568 AACTTGTCCTTAC -s mr.mrrefChr5 90273 13 + 294540 AACTAGAATTTGT -s simDog_chr6.simDog.chr6 224719 13 + 593897 AACTTGTCCTTAC -s simHuman_chr6.simHuman.chr6 315142 13 - 601863 AACTTGTCCTTGT -s simRat_chr6.simRat.chr6 227768 13 + 647215 AACTAGAATACGT - -a -s simMouse_chr6.simMouse.chr6 236897 28 + 636262 AGAAACCAAGTACCTCAGTGATTCCCCC -s Anc0.Anc0refChr5 56269 13 + 87904 ACAAA---------------ATTCTACC -s Anc1.Anc1refChr7 13759 13 - 47259 ACAAA---------------ATTCTACC -s Anc2.Anc2refChr15 52709 13 + 86568 CCAAA---------------AACCTATC -s mr.mrrefChr5 90286 28 + 294540 AGAAACCAAGTACCTCAGTGATTCCCCC -s simDog_chr6.simDog.chr6 224735 13 + 593897 CCAAA---------------AACCTATC -s simHuman_chr6.simHuman.chr6 315158 13 - 601863 ACAAA---------------ATTCTACC -s simRat_chr6.simRat.chr6 227781 28 + 647215 AGAAACCAAATACCTGAGTGATTCCGCC - -a -s simMouse_chr6.simMouse.chr6 236925 31 + 636262 ATATAAATTATGCATAGATGCTGCTCTCATA -s Anc0.Anc0refChr5 56282 31 + 87904 ATACCAATTATGTCTAGATACTTCTCTCACA -s Anc1.Anc1refChr7 13772 31 - 47259 ATACCAATTATGTCTAGATACTTCTCTCACA -s Anc2.Anc2refChr15 52805 31 + 86568 ATACCAATTATGTCTAGAAACTTCTCTCACA -s mr.mrrefChr5 90314 31 + 294540 ATATAAATTATGCATAGATGCTGCTCTCATA -s simCow_chr6.simCow.chr6 234117 31 + 602619 ATACCAATCATGTCTAGAAACTGCTCTCATA -s simDog_chr6.simDog.chr6 224950 31 + 593897 ATACCGATTATGTCTAGAAACTTCTCTCACA -s simHuman_chr6.simHuman.chr6 315171 27 - 601863 ----CAATTATATCCAGATACTTCTCTTACA -s simRat_chr6.simRat.chr6 227809 31 + 647215 AGGTGAATTATGGATAGATGCTGCTCTCATT - -a -s simMouse_chr6.simMouse.chr6 236956 16 + 636262 GGGCTACCTACTTAAA -s Anc0.Anc0refChr5 56313 16 + 87904 GGGCTATCCACTTAAA -s Anc1.Anc1refChr7 13803 16 - 47259 GGGCTATCCACTTAAA -s Anc2.Anc2refChr15 52836 16 + 86568 GGGCTATCCACTTAAA -s mr.mrrefChr5 90345 16 + 294540 GGGCTACCTACTTAAA -s simCow_chr6.simCow.chr6 234148 13 + 602619 GGGCTATCTACTT--- -s simDog_chr6.simDog.chr6 224981 16 + 593897 GGGCTAGCCAGTTAAA -s simHuman_chr6.simHuman.chr6 315199 16 - 601863 GGGCTATCCACTTAAA -s simRat_chr6.simRat.chr6 227840 16 + 647215 GGGCTACCCACTTAAA - -a -s simMouse_chr6.simMouse.chr6 236972 7 + 636262 TGCAATG -s Anc0.Anc0refChr5 56349 7 + 87904 TACAATG -s Anc1.Anc1refChr7 13839 7 - 47259 TACAATG -s Anc2.Anc2refChr15 52872 7 + 86568 TACAATG -s mr.mrrefChr5 90361 7 + 294540 TGCAATG -s simCow_chr6.simCow.chr6 234169 7 + 602619 TACAATC -s simDog_chr6.simDog.chr6 225017 7 + 593897 TACAATG -s simHuman_chr6.simHuman.chr6 315235 7 - 601863 TACAATG -s simRat_chr6.simRat.chr6 227856 7 + 647215 TGCAATG - -a -s simMouse_chr6.simMouse.chr6 236979 6 + 636262 CTCCTT -s Anc0.Anc0refChr5 56369 6 + 87904 CTCCTT -s Anc1.Anc1refChr7 13859 6 - 47259 CTCCTT -s Anc2.Anc2refChr15 52892 6 + 86568 CTACTT -s mr.mrrefChr5 90368 6 + 294540 CTCCTT -s simCow_chr6.simCow.chr6 234189 6 + 602619 TGACTT -s simDog_chr6.simDog.chr6 225037 6 + 593897 CTACTT -s simHuman_chr6.simHuman.chr6 315255 6 - 601863 CTCCTT -s simRat_chr6.simRat.chr6 227863 6 + 647215 CTCCTT - -a -s simMouse_chr6.simMouse.chr6 236985 68 + 636262 TCAACCTAAGCTGCCTGATTAAAGATCATTCCATGGTTACATAAATATGGGTAGCTGTTGGTCACAGG -s Anc0.Anc0refChr5 56375 68 + 87904 TCAATTTCAGCAGCCCAATGAAGTACTATTCCCTGCTTACATAAACCTGTGTAGCTGTTGGTTACAGG -s Anc1.Anc1refChr7 13865 68 - 47259 TCAATTTCAGCAGCCCAATGAAGTACTATTCCCTGCTTACATAAACCTGTGTAGCTGTTGGTTACAGG -s Anc2.Anc2refChr15 52898 68 + 86568 TCAATTTCAACAGCCCAATGAAGTACTATTCCCTGCTTACATAAACCTCTGTAGCTGTTGGATACAGG -s mr.mrrefChr5 90374 68 + 294540 TCAACCTAAGCTGCCTGATTAAAGATCATTCCATGGTTACATAAATATGGGTAGCTGTTGGTCACAGG -s simCow_chr6.simCow.chr6 234195 68 + 602619 GCAATTTTGATGGTTCAATGAGGGACCATTTCTGGCTTACATAAGTGCCTGTAGCTGTTGAATGCAGG -s simDog_chr6.simDog.chr6 225110 68 + 593897 TCAATTTCAACAGCCCAATGAAATACTCTTCCCTTCTTATATGGACCTCTGTAGCTGTTGGATACAGG -s simHuman_chr6.simHuman.chr6 315261 67 - 601863 TCAATTTCAGCAGCCCAATGAAGAACAATCCCCTGCTTACATAAACCTGTGTAGCTGTCGAT-ACAGG -s simRat_chr6.simRat.chr6 227869 68 + 647215 TCAACTTCAACTGCCAAATTAAAGATCATTCCATGGTTCCATAAATGTGTGCAGCTGCTGGCCACAGG - -a -s simMouse_chr6.simMouse.chr6 237053 25 + 636262 TTTTATCAAAGAGCATGGCCCAGAT -s Anc0.Anc0refChr5 56443 25 + 87904 ATATATCAAAGGTAACTGACTAGAT -s Anc1.Anc1refChr7 13933 25 - 47259 ATATATCAAAGGTAACTGACTAGAT -s Anc2.Anc2refChr15 52966 25 + 86568 ATATATCAAAGGTAACTGACTAGAT -s mr.mrrefChr5 90442 25 + 294540 TTTTATCAAAGAGCATGGCCCAGAT -s simCow_chr6.simCow.chr6 234263 25 + 602619 ATATATCAAAAGTAATTCCCTAGAC -s simDog_chr6.simDog.chr6 225178 25 + 593897 ATATATTAAAGGTAACGGACTAGGT -s simHuman_chr6.simHuman.chr6 315330 25 - 601863 ATATATCCAAGGTGACTATTTAGAT -s simRat_chr6.simRat.chr6 227937 25 + 647215 TTATATCAAAGAGAGCAGCCCAGAT - -a -s simMouse_chr6.simMouse.chr6 237078 5 + 636262 GCTGA -s Anc0.Anc0refChr5 56468 5 + 87904 TCTGT -s Anc1.Anc1refChr7 13958 5 - 47259 TCTGT -s Anc2.Anc2refChr15 52991 5 + 86568 TCTCT -s mr.mrrefChr5 90467 5 + 294540 GCTGA -s simCow_chr6.simCow.chr6 234288 5 + 602619 ACTCT -s simDog_chr6.simDog.chr6 225203 5 + 593897 TCTCT -s simHuman_chr6.simHuman.chr6 315355 5 - 601863 TCTGC -s simRat_chr6.simRat.chr6 227973 5 + 647215 GCTGA - -a -s simMouse_chr6.simMouse.chr6 237083 5 + 636262 AGAGT -s Anc0.Anc0refChr5 56490 5 + 87904 AGACT -s Anc1.Anc1refChr7 13980 5 - 47259 AGACT -s Anc2.Anc2refChr15 53013 5 + 86568 AGACT -s mr.mrrefChr5 90472 5 + 294540 AGAGT -s simCow_chr6.simCow.chr6 234310 5 + 602619 AGACT -s simDog_chr6.simDog.chr6 225225 5 + 593897 AGGCT -s simHuman_chr6.simHuman.chr6 315377 5 - 601863 AAACT -s simRat_chr6.simRat.chr6 227978 5 + 647215 AGAGA - -a -s simMouse_chr6.simMouse.chr6 237088 12 + 636262 CTAGTGCAGATT -s Anc0.Anc0refChr5 56495 11 + 87904 GTAATACC-ATA -s Anc1.Anc1refChr7 13985 11 - 47259 GTAATACC-ATA -s Anc2.Anc2refChr15 53018 11 + 86568 GTAATACC-ATA -s mr.mrrefChr5 90477 11 + 294540 CTAGTGCA-ATT -s simCow_chr6.simCow.chr6 234315 11 + 602619 GTAATACC-ATA -s simDog_chr6.simDog.chr6 225232 11 + 593897 GTAATACC-ATA -s simHuman_chr6.simHuman.chr6 315382 11 - 601863 GTAATACC-ATA -s simRat_chr6.simRat.chr6 227983 11 + 647215 CTAGTGGA-ATT - -a -s simMouse_chr6.simMouse.chr6 237100 11 + 636262 TTGTACCCTGG -s Anc0.Anc0refChr5 56506 2 + 87904 TT--------- -s Anc1.Anc1refChr7 13996 2 - 47259 TT--------- -s Anc2.Anc2refChr15 53029 2 + 86568 TT--------- -s mr.mrrefChr5 90488 11 + 294540 TTGTACCCTGG -s simCow_chr6.simCow.chr6 234326 2 + 602619 TT--------- -s simDog_chr6.simDog.chr6 225264 2 + 593897 TT--------- -s simHuman_chr6.simHuman.chr6 315393 2 - 601863 TT--------- -s simRat_chr6.simRat.chr6 227994 11 + 647215 TTGCCCCCGGG - -a -s simMouse_chr6.simMouse.chr6 237111 11 + 636262 GTGGTTGCCAT -s Anc0.Anc0refChr5 56508 11 + 87904 TTGAATGTCAT -s Anc1.Anc1refChr7 13998 11 - 47259 TTGAATGTCAT -s Anc2.Anc2refChr15 53031 11 + 86568 TTGAATGTCAT -s mr.mrrefChr5 90499 11 + 294540 GTGGTTGCCAT -s simCow_chr6.simCow.chr6 234342 11 + 602619 TTGAATGTCAT -s simDog_chr6.simDog.chr6 225266 11 + 593897 TTGAATGTCAT -s simHuman_chr6.simHuman.chr6 315395 11 - 601863 TTGAATGTCAT -s simRat_chr6.simRat.chr6 228005 11 + 647215 GTGGTTTCCAT - -a -s simMouse_chr6.simMouse.chr6 237122 14 + 636262 CCAGTGTGTTTCCT -s Anc0.Anc0refChr5 56547 12 + 87904 --AGTGTCTTTCCT -s Anc1.Anc1refChr7 14037 14 - 47259 TTAGTGTCTTTCCT -s Anc2.Anc2refChr15 53078 12 + 86568 --AGCATCTCTCCT -s mr.mrrefChr5 90510 14 + 294540 CCAGTGTGTTTCCT -s simCow_chr6.simCow.chr6 234388 7 + 602619 -------CTTTCCC -s simDog_chr6.simDog.chr6 225313 12 + 593897 --AGCATCTCCCCT -s simHuman_chr6.simHuman.chr6 315656 13 - 601863 TTACTGT-TTTCCT -s simRat_chr6.simRat.chr6 228016 14 + 647215 TAACTGCGTTTCCT - -a -s simMouse_chr6.simMouse.chr6 237136 20 + 636262 TCATTAAGCTTTGATTAATC -s Anc0.Anc0refChr5 56567 16 + 87904 TCAATAAACTTC----GGTC -s Anc1.Anc1refChr7 14059 16 - 47259 TCAATAAACTTC----GGTC -s Anc2.Anc2refChr15 53098 16 + 86568 TCAACAAACCTC----GGTC -s mr.mrrefChr5 90524 20 + 294540 TCATTAAGCTTTGATTAATC -s simCow_chr6.simCow.chr6 234403 16 + 602619 TCAACAAATCTT----GGCC -s simDog_chr6.simDog.chr6 225333 16 + 593897 TTAACAAACCTC----GGTC -s simHuman_chr6.simHuman.chr6 315677 16 - 601863 TCAGTAAACTAC----CGTC -s simRat_chr6.simRat.chr6 228030 20 + 647215 TCATGAAGCTTTAATTAATC - -a -s simMouse_chr6.simMouse.chr6 237156 2 + 636262 AC -s Anc0.Anc0refChr5 56583 2 + 87904 AC -s Anc1.Anc1refChr7 14075 2 - 47259 AC -s Anc2.Anc2refChr15 53115 2 + 86568 AC -s mr.mrrefChr5 90544 2 + 294540 AC -s simCow_chr6.simCow.chr6 234420 2 + 602619 AC -s simDog_chr6.simDog.chr6 225350 2 + 593897 AC -s simHuman_chr6.simHuman.chr6 315693 2 - 601863 AC -s simRat_chr6.simRat.chr6 228050 2 + 647215 AC - -a -s simMouse_chr6.simMouse.chr6 237158 98 + 636262 CCTCTTCCACCCATGTTTTTTCAGTGTGGCCAGGTAGACTACATTTACTCACATAAGGTCGTTACCTTGTCCATTCACCAAGATGTTGTTCATTGTGT -s Anc0.Anc0refChr5 56643 13 + 87904 CC-------------------------------------------------------------------------------------ATTCACTGTAG -s Anc1.Anc1refChr7 14135 13 - 47259 CC-------------------------------------------------------------------------------------ATTCACTGTAG -s Anc2.Anc2refChr15 53179 13 + 86568 TC-------------------------------------------------------------------------------------ACCCACTGGAG -s mr.mrrefChr5 90546 13 + 294540 CC-------------------------------------------------------------------------------------GTTCATTGTGT -s simDog_chr6.simDog.chr6 225414 13 + 593897 TC-------------------------------------------------------------------------------------ACCCACTGGAG -s simHuman_chr6.simHuman.chr6 315822 13 - 601863 CC-------------------------------------------------------------------------------------ATTCACTATAG -s simRat_chr6.simRat.chr6 228052 13 + 647215 CC-------------------------------------------------------------------------------------GCTCATTGCAT - -a -s simMouse_chr6.simMouse.chr6 237256 21 + 636262 CTGACACATATTATGATACTC -s Anc0.Anc0refChr5 56657 21 + 87904 TTGGCACATATGAGGATACTC -s Anc1.Anc1refChr7 14149 21 - 47259 TTGGCACATATGAGGATACTC -s Anc2.Anc2refChr15 53193 21 + 86568 TTGGCACATATGAGGGTATTC -s mr.mrrefChr5 90559 21 + 294540 CTGACACATATTATGATACTC -s simDog_chr6.simDog.chr6 225428 21 + 593897 TTGGCACATATGAGGGTATTC -s simHuman_chr6.simHuman.chr6 315837 21 - 601863 TTGGCACATATGAGGATACTT -s simRat_chr6.simRat.chr6 228065 21 + 647215 CTGACACATATTATGAAACTC - -a -s simMouse_chr6.simMouse.chr6 237277 24 + 636262 ATGAAAGGTCTACTTCCATGTTTC -s Anc0.Anc0refChr5 56682 20 + 87904 ATGCAAGGCCAACTTCC----TAT -s Anc1.Anc1refChr7 14174 20 - 47259 ATGCAAGGCCAACTTCC----TAT -s Anc2.Anc2refChr15 53218 20 + 86568 TTGCAAGGTCTACTTCC----TAT -s mr.mrrefChr5 90584 24 + 294540 ATGAAAGGCCAACTTCCATGTTTC -s simDog_chr6.simDog.chr6 225453 20 + 593897 TTGCAAGGTCTACTTCC----TAT -s simHuman_chr6.simHuman.chr6 315862 20 - 601863 ATGCAAGGCCAACTTCC----TAT -s simRat_chr6.simRat.chr6 228090 24 + 647215 ATGAAAGGCCAACTTCCATATCTC - -a -s simMouse_chr6.simMouse.chr6 237301 22 + 636262 TAATAGTGATGGGTAGGAATAG -s Anc0.Anc0refChr5 56702 15 + 87904 TGATGGTGGGTAAT-------G -s Anc1.Anc1refChr7 14194 22 - 47259 TGATGGTGGGTAATGTAGTTAG -s Anc2.Anc2refChr15 53238 15 + 86568 TAATGGTGGGTAAT-------G -s mr.mrrefChr5 90608 22 + 294540 TGATAGTGGTGGGTAGGAATAG -s simDog_chr6.simDog.chr6 225481 15 + 593897 TAATGGTGGGTAAT-------G -s simHuman_chr6.simHuman.chr6 315882 22 - 601863 TGATGGTGGGCATTGTAGTTAG -s simRat_chr6.simRat.chr6 228114 22 + 647215 TGATAGTGGTGGGTAGGAATAG - -a -s simMouse_chr6.simMouse.chr6 237323 10 + 636262 TTAAAGCATC -s Anc0.Anc0refChr5 56717 10 + 87904 TTTAAACAAA -s Anc1.Anc1refChr7 14216 10 - 47259 TTTAAACAAA -s Anc2.Anc2refChr15 53253 10 + 86568 CTTGAACAAA -s mr.mrrefChr5 90630 10 + 294540 TTTAAGCATA -s simDog_chr6.simDog.chr6 225496 10 + 593897 CTTGAACAAA -s simHuman_chr6.simHuman.chr6 315905 10 - 601863 TTTAAACAAA -s simRat_chr6.simRat.chr6 228136 10 + 647215 TTTAAGCATA - -a -s simMouse_chr6.simMouse.chr6 237333 18 + 636262 AAGTGTATGAATCAACAG -s Anc0.Anc0refChr5 56727 16 + 87904 TAGTATGTGAAC--ACAG -s Anc1.Anc1refChr7 14226 16 - 47259 TAGTATGTGAAC--ACAG -s Anc2.Anc2refChr15 53263 16 + 86568 TAGTATGGGAAC--ATAT -s mr.mrrefChr5 90640 18 + 294540 AAGTGTATGAATCAACAG -s simDog_chr6.simDog.chr6 225506 16 + 593897 TAGTATGGGAAC--ATAT -s simHuman_chr6.simHuman.chr6 315918 16 - 601863 CAGCATGTGAAC--ACAG -s simRat_chr6.simRat.chr6 228146 18 + 647215 AAGTGTATGAATCTCCAG - -a -s simMouse_chr6.simMouse.chr6 237351 26 + 636262 CCCCCTTTCCTTGAGCTGCAATTTAT -s Anc0.Anc0refChr5 56743 26 + 87904 CTTCCATAGACTGAGCTTTAGTTTAT -s Anc1.Anc1refChr7 14242 26 - 47259 CTTCCATAGACTGAGCTTTAGTTTAT -s Anc2.Anc2refChr15 53279 26 + 86568 CTTTCATAGAATGAGCTTTAGTATAT -s mr.mrrefChr5 90658 26 + 294540 CCCCCTTACCCTGAGCTGTAATTTAT -s simDog_chr6.simDog.chr6 225548 26 + 593897 CTTTCATAGAATGAGCTTTAGTATAT -s simHuman_chr6.simHuman.chr6 315934 26 - 601863 CTTCCATAGACTGACCTTTAGTTTGT -s simRat_chr6.simRat.chr6 228164 26 + 647215 CCCCTTTACCCTGAGCTATGATTTAT - -a -s simMouse_chr6.simMouse.chr6 237377 10 + 636262 TGTGGATAGT -s Anc0.Anc0refChr5 56770 10 + 87904 TGTGGATAGT -s Anc1.Anc1refChr7 14269 10 - 47259 TGTGGATAGT -s Anc2.Anc2refChr15 53306 10 + 86568 TCTAGATAGT -s mr.mrrefChr5 90684 10 + 294540 TGTGGATAGT -s simDog_chr6.simDog.chr6 225575 10 + 593897 TCTAGATAGT -s simHuman_chr6.simHuman.chr6 315961 10 - 601863 TGTGAGTAGT -s simRat_chr6.simRat.chr6 228190 10 + 647215 TGTGGACAGT - -a -s simMouse_chr6.simMouse.chr6 237387 38 + 636262 TGCATTATGCAAGTATGAGAAACTAGTGTGCGATCTGG -s Anc0.Anc0refChr5 56780 31 + 87904 ATCACTATGCAGGCATTAGGTATTAGTGTGC------- -s Anc1.Anc1refChr7 14279 31 - 47259 ATCACTATGCAGGCATTAGGTATTAGTGTGC------- -s Anc2.Anc2refChr15 53316 31 + 86568 ATCACTTTGCAGCCATTGGGTATCAGTGTGC------- -s mr.mrrefChr5 90694 38 + 294540 TGCATTATGCAAGCATGAGAAACTAGTGTGCGATCTGG -s simDog_chr6.simDog.chr6 225589 31 + 593897 ATCACTTTGCAGCCATTGGGTATCAGTGTGC------- -s simHuman_chr6.simHuman.chr6 315971 31 - 601863 ATCACTATGCAGGCACCAGGTATTTGTGTGC------- -s simRat_chr6.simRat.chr6 228200 38 + 647215 CGCATTGTGCAAGCATGTGAAACTAGTGTTTGATCTGG - -a -s simMouse_chr6.simMouse.chr6 237425 20 + 636262 ATCGGTTTTACTGTCAGTTA -s Anc0.Anc0refChr5 56812 20 + 87904 ATCTGCTTTACTGTCTGTTA -s Anc1.Anc1refChr7 14311 20 - 47259 ATCTGCTTTACTGTCTGTTA -s Anc2.Anc2refChr15 53348 20 + 86568 ACCTGCTTTGCTGTCCGTCA -s mr.mrrefChr5 90733 20 + 294540 ATCGGCTTTACTGTCTGTTA -s simDog_chr6.simDog.chr6 225621 20 + 593897 ACCTGCTTTGCTGTCCGTCA -s simHuman_chr6.simHuman.chr6 316003 20 - 601863 ATCTGCTTTACTGCCTGTTA -s simRat_chr6.simRat.chr6 228239 20 + 647215 ATCCGCCTTACTGTCTGTTA - -a -s simMouse_chr6.simMouse.chr6 237445 37 + 636262 TCTGGGGCATTTTCCAGCAGTTACAGGCTGAGAATCG -s Anc0.Anc0refChr5 56832 37 + 87904 TCTGGTGAATTTTCCAACAGCCACTGGATCAGTTTTG -s Anc1.Anc1refChr7 14331 37 - 47259 TCTGGTGAATTTTCCAACAGCCACTGGATCAGTTTTG -s Anc2.Anc2refChr15 53368 37 + 86568 TCTGGTTAATTTTCCAACAGCCATTGGAGGTGTTTTG -s mr.mrrefChr5 90753 37 + 294540 TCTGGGGCATTTTCCAGCAGTTACAGGCTCAGAATTG -s simDog_chr6.simDog.chr6 225641 37 + 593897 TCTGGTTAATTTTCCAACAGCCATTGGAGGTGTTTTG -s simHuman_chr6.simHuman.chr6 316028 37 - 601863 TCTGGTGAATTTTCCAAAGGCCTCTGTATCAGCTTTG -s simRat_chr6.simRat.chr6 228259 37 + 647215 TCTGGGGCATTTTCCAGCAGTTGCAGGCTCAGGATTG - -a -s simMouse_chr6.simMouse.chr6 237482 26 + 636262 ATAACTCACAAGTAAACCTTCTTACA -s Anc0.Anc0refChr5 56873 26 + 87904 ATGAACCACAAGCTAACCTCCTCACA -s Anc1.Anc1refChr7 14372 26 - 47259 ATGAACCACAAGCTAACCTCCTCACA -s Anc2.Anc2refChr15 53409 26 + 86568 ATGAACCACAAGCTAACTTCCTCATA -s mr.mrrefChr5 90790 26 + 294540 ATAACTCACAAGTAAACCTTCTTACA -s simDog_chr6.simDog.chr6 225682 26 + 593897 ATGAACCACAAGCTAACTTCCTCATA -s simHuman_chr6.simHuman.chr6 316069 26 - 601863 ATGAAGCATGAGCTAATCTCCTCACA -s simRat_chr6.simRat.chr6 228296 26 + 647215 ATTACTCACAAGTAAACCTTATTACA - -a -s simMouse_chr6.simMouse.chr6 237508 1 + 636262 G -s Anc0.Anc0refChr5 56899 1 + 87904 C -s Anc1.Anc1refChr7 14398 1 - 47259 C -s Anc2.Anc2refChr15 53435 1 + 86568 C -s mr.mrrefChr5 90816 1 + 294540 G -s simDog_chr6.simDog.chr6 225708 1 + 593897 C -s simHuman_chr6.simHuman.chr6 316096 1 - 601863 T -s simRat_chr6.simRat.chr6 228322 1 + 647215 G - -a -s simMouse_chr6.simMouse.chr6 237509 22 + 636262 CCCAGAACCATAAAAGGTTATT -s Anc0.Anc0refChr5 56900 22 + 87904 TCCAGAACATTAAAAGGTCTTC -s Anc1.Anc1refChr7 14399 22 - 47259 TCCAGAACATTAAAAGGTCTTC -s Anc2.Anc2refChr15 53436 22 + 86568 TCCAGAACATTCAAGGCCCTTC -s mr.mrrefChr5 90817 22 + 294540 TCCAGAACCATAAAAGGTTATC -s simDog_chr6.simDog.chr6 225709 22 + 593897 TCCAGAACATTCAAGGCCCTTC -s simHuman_chr6.simHuman.chr6 316097 22 - 601863 TCCAGAAGACCAAAAGGTCTTC -s simRat_chr6.simRat.chr6 228354 22 + 647215 TCCAGAACCATAAAAGCTTATC - -a -s simMouse_chr6.simMouse.chr6 237531 121 + 636262 TATTGCCATTTGGAAGAAATACTAATTTACACCCTCTTCTTTATTTCTAGCACACAACTATTCGAATCATATTCCAAGTGGTTGCCAGCTAACAAGTCATATTGCAAGTGTTTGAATGATA -s Anc0.Anc0refChr5 56966 55 + 87904 TTTTGCCATTTGGAAGAAATACTAAATGACACCCTCTTCTTTATTTCTATCAAAT------------------------------------------------------------------ -s Anc1.Anc1refChr7 14465 55 - 47259 TTTTGCCATTTGGAAGAAATACTAAATGACACCCTCTTCTTTATTTCTATCAAAT------------------------------------------------------------------ -s Anc2.Anc2refChr15 53502 55 + 86568 ATTTGCCATTTGGAAGAAATAATAAATGACACCCTCTTATTTGTCTCTATGAAAT------------------------------------------------------------------ -s mr.mrrefChr5 90875 121 + 294540 TATTGCCATTTGGAAGAAATACTAATTTACACCCTCTTCTTTATTTCTAGCACACAACTATTCGAATCATATTCCAAGTGGTTGCCAGCTAACAAGTCATATTGCAAGTGTTTGAATGATA -s simDog_chr6.simDog.chr6 225776 55 + 593897 ATTTGCCATTTGGAAGAAATAATAAATGACACCCTCTTATTTGTCTCTATGAAAT------------------------------------------------------------------ -s simHuman_chr6.simHuman.chr6 316163 55 - 601863 TTTTGCTGTTTGGAAGAAATACCAACTGTCATCCTTTACTTCACTTCTATCAAAT------------------------------------------------------------------ -s simRat_chr6.simRat.chr6 228414 121 + 647215 TATTGCCACTTGGGAGAAATACTAATTTACACCCTCTTCTTGATCTCTAGTATACAACTATTTGAATCATATAGTAAGTGGTTGCCAGCTACCAAGTCATGTTACAAGTGTTTGAATGAAC - -a -s simMouse_chr6.simMouse.chr6 237652 16 + 636262 TTGTGCCCATTCCCCT -s Anc0.Anc0refChr5 57021 16 + 87904 TTGTGCTCATGGACCT -s Anc1.Anc1refChr7 14520 16 - 47259 TTGTGCTCATGGACCT -s Anc2.Anc2refChr15 53557 16 + 86568 GTGTACTCATGGACCT -s mr.mrrefChr5 90996 16 + 294540 TTGTGCCCATTCCCCT -s simDog_chr6.simDog.chr6 225839 16 + 593897 GTGTACTCATGGACCT -s simHuman_chr6.simHuman.chr6 316218 16 - 601863 TTGTGCTCATCGACCT -s simRat_chr6.simRat.chr6 228535 16 + 647215 TTGTGGCCATTCCCCT - -a -s simMouse_chr6.simMouse.chr6 237668 9 + 636262 CAAAATCTT -s Anc0.Anc0refChr5 57038 8 + 87904 GAAA-TGTA -s Anc1.Anc1refChr7 14537 9 - 47259 GAAACTGTA -s Anc2.Anc2refChr15 53574 8 + 86568 GAAA-TGTA -s mr.mrrefChr5 91012 9 + 294540 GAAACTCTT -s simDog_chr6.simDog.chr6 225856 8 + 593897 GAAA-TGTA -s simHuman_chr6.simHuman.chr6 316235 9 - 601863 GAAACTGTA -s simRat_chr6.simRat.chr6 228551 9 + 647215 GAAACTCTG - -a -s simMouse_chr6.simMouse.chr6 237677 14 + 636262 TAGCAACCCTCATA -s Anc0.Anc0refChr5 57046 14 + 87904 TGGATACCCCCTTA -s Anc1.Anc1refChr7 14546 14 - 47259 TGGATACCCCCTTA -s Anc2.Anc2refChr15 53582 14 + 86568 TGAAAACACTCTTA -s mr.mrrefChr5 91021 14 + 294540 TGGCTACCCCCATA -s simDog_chr6.simDog.chr6 225866 14 + 593897 TGAAAACACTCTTA -s simHuman_chr6.simHuman.chr6 316244 14 - 601863 TGGGTACCCCCTTA -s simRat_chr6.simRat.chr6 228560 14 + 647215 TGACTACCCCCATA - -a -s simMouse_chr6.simMouse.chr6 237691 5 + 636262 CAAGC -s Anc0.Anc0refChr5 57060 5 + 87904 CACAA -s Anc1.Anc1refChr7 14560 5 - 47259 CACAA -s Anc2.Anc2refChr15 53596 5 + 86568 CACAA -s mr.mrrefChr5 91035 5 + 294540 CAAAC -s simDog_chr6.simDog.chr6 225933 5 + 593897 CACAA -s simHuman_chr6.simHuman.chr6 316258 5 - 601863 CACAA -s simRat_chr6.simRat.chr6 228574 5 + 647215 CAAAC - -a -s simMouse_chr6.simMouse.chr6 237696 77 + 636262 TTAGGCAGCGTACTTGACTGCTTCCCATGTGGCAAGTCCTAGTTCAGCTTTCATAAGAACCATCAAGTGTTTACCAG -s Anc0.Anc0refChr5 57071 47 + 87904 TTA----------------------------GCACATCCTAGCTCAGCTTT-AGGAGAACTATCAACTG-TTAGCAG -s Anc1.Anc1refChr7 14571 71 - 47259 TTAAACCGTATACTCGACTA----CCCTGTGGCACATCCTAGCTCAGCTTT-AGGAGAACTATCAACTG-TTAGCAG -s Anc2.Anc2refChr15 53607 47 + 86568 TTA----------------------------GCACATCTTAGCTCAGCTTC-AGGAGAACTATCAGCCA-ATAGCAG -s mr.mrrefChr5 91040 77 + 294540 TTAGGCAGCATACTTGACTGCTTCCCATGTGGCAAGTCCTAGTTCAGCTTTCATGAGAACCATCAAGTGTTTACCAG -s simDog_chr6.simDog.chr6 225944 47 + 593897 TTA----------------------------GCACATCTTAGCTCAGCTTC-AGGAGAACTATCAGCCA-ATAGCAG -s simHuman_chr6.simHuman.chr6 316269 71 - 601863 TTCAACCGTATACTCGACTA----CCCTGTGGCAGTTCCTTGCACATCTTT-AGGAGAACTATAAATTG-TTAACTG -s simRat_chr6.simRat.chr6 228579 72 + 647215 CTAGGCAGCATAAC-----GCTTCCCATGTGGCAAGTCCTAGTTCAGCCCTCATGAGAACCATCAGCTGTTGACCAG - -a -s simMouse_chr6.simMouse.chr6 237773 52 + 636262 TGTTGCAAGCATTCACAAGGTCTTCTTAAACTAACTCACAAGACCTTCTTAA -s Anc0.Anc0refChr5 57118 37 + 87904 TATTGCAAGTATT-ACAAGATCTTTTTAAACC--------------TATCAG -s Anc1.Anc1refChr7 14642 38 - 47259 TATTGCAAGTATTCACAAGATCTTTTTAAACC--------------TATCAG -s Anc2.Anc2refChr15 53654 37 + 86568 TATTGCTGGTATT-ATAAGATGTTTCTAAGCC--------------TATCAG -s mr.mrrefChr5 91117 38 + 294540 TGTTGCAAGCATTCACAAGGTCTTCTTAAACC--------------TATTAG -s simDog_chr6.simDog.chr6 225995 37 + 593897 TATTGCTGGTATT-ATAAGATGTTTCTAAGCC--------------TATCAG -s simHuman_chr6.simHuman.chr6 316340 38 - 601863 TATTGCAAGTATTCACAAGATCTTTTCAAACC--------------TATCAG -s simRat_chr6.simRat.chr6 228651 38 + 647215 TGTTGCAAGCATTCACAAGGTATTCTTAAACC--------------TATGAG - -a -s simMouse_chr6.simMouse.chr6 237825 37 + 636262 ACTAACAGATAGGTCAGGAGAGTTGTGAGAAGATAAG -s Anc0.Anc0refChr5 57195 34 + 87904 ATTAATATAAAGTG--GAG-AGTGGTGCCAAGATGGG -s Anc1.Anc1refChr7 14720 36 - 47259 ATTAATATAAAGTGGAGAG-AGTGGTGCCAAGATGGG -s Anc2.Anc2refChr15 53731 34 + 86568 ATTAATATAAGGTG--GAG-AGTGGTGCCTACATGGG -s mr.mrrefChr5 91155 36 + 294540 ACTAACAGAAAGGTCAGGA-AGTTGTGAGAAGATAGG -s simDog_chr6.simDog.chr6 226072 34 + 593897 ATTAATATAAGGTG--GAG-AGTGGTGCCTACATGGG -s simHuman_chr6.simHuman.chr6 316438 36 - 601863 ATTAATATAAATTGGAGAG-AGTGGTGCCAAGATGGG -s simRat_chr6.simRat.chr6 228689 36 + 647215 AGTAACACAAAGGTCAGGA-AGTTGTGAGAAGATAGG - -a -s simMouse_chr6.simMouse.chr6 237862 49 + 636262 TGGCCCATGTAAAGCTAGGTCATAACATGGCACATCATATTCCACTTAG -s Anc0.Anc0refChr5 57237 46 + 87904 TGGCCCAGCTTAATCCAGGGC---ACATGATAAAACATATTCCACTTGG -s Anc1.Anc1refChr7 14764 46 - 47259 TGGCCCAGCTTAATCCAGGGC---ACATGATAAAACATATTCCACTTGG -s Anc2.Anc2refChr15 53773 46 + 86568 ACGCCCAGCTTACTCCAGGGT---GCTTGATAACACCTATGTCACTTGG -s mr.mrrefChr5 91191 49 + 294540 TGGCCCATGTAAAGCTAGGTCATAACATGGCACATCATATTCCACTTAG -s simDog_chr6.simDog.chr6 226114 46 + 593897 ACGCCCAGCTTACTCCAGGGT---GCTTGATAACACCTATGTCACTTGG -s simHuman_chr6.simHuman.chr6 316482 46 - 601863 TGGCCTAATATAATCCAGGCC---ACATGATAAAACATATTCCACTTGG -s simRat_chr6.simRat.chr6 228725 49 + 647215 TGGCCCATGTAAAGCTAGGTCATAATACGGCACATTGTATTCCACTTAG - -a -s simMouse_chr6.simMouse.chr6 237911 39 + 636262 CTCCATGAGTATCTCTATCCCACATAAATCTTGCTGGTT -s Anc0.Anc0refChr5 57291 36 + 87904 TGCTTTAAGTAACCCTATCCAATGAGAATATTGC---AT -s Anc1.Anc1refChr7 14818 36 - 47259 TGCTTTAAGTAACCCTATCCAATGAGAATATTGC---AT -s Anc2.Anc2refChr15 53827 36 + 86568 TGCTTCAAGTAACACTATCCAATGAGAATCTTAC---AT -s mr.mrrefChr5 91240 39 + 294540 CTCTATGAGTAACCCTATCCCATGAAAATATTGCTGGTT -s simDog_chr6.simDog.chr6 226168 36 + 593897 TGCTTCAAGTAACACTATCCAATGAGAATCTTAC---AT -s simHuman_chr6.simHuman.chr6 316536 36 - 601863 TGCTTTAGGTAACCCTATTCGATGACAATATTGC---AT -s simRat_chr6.simRat.chr6 228774 39 + 647215 CTCTATGAGTAACCCTATCCCATGAGAATATTGTGGGTT - -a -s simMouse_chr6.simMouse.chr6 237950 23 + 636262 GTTTCTATAAATAGGGTCCCACC -s Anc0.Anc0refChr5 57327 23 + 87904 GTCTCTATCAATCTGTACCTACC -s Anc1.Anc1refChr7 14854 23 - 47259 GTCTCTATCAATCTGTACCTACC -s Anc2.Anc2refChr15 53863 23 + 86568 GTCTCTATCAATCTGTACCTACC -s mr.mrrefChr5 91279 23 + 294540 GTTTCTATAAATAGGGTCCCACC -s simCow_chr6.simCow.chr6 234461 22 + 602619 -TCGCTATCAATCGGTACCTAAC -s simDog_chr6.simDog.chr6 226207 23 + 593897 GTCTCTATCAATCTGTACCTACC -s simHuman_chr6.simHuman.chr6 316572 21 - 601863 GTCTCCATGAACCAG--CCTACC -s simRat_chr6.simRat.chr6 228813 23 + 647215 GTTTCTATTAATAGAGTCCCACC - -a -s simMouse_chr6.simMouse.chr6 237973 2 + 636262 TG -s Anc0.Anc0refChr5 57353 2 + 87904 CA -s Anc1.Anc1refChr7 14880 2 - 47259 CA -s Anc2.Anc2refChr15 53889 2 + 86568 CA -s mr.mrrefChr5 91302 2 + 294540 TG -s simCow_chr6.simCow.chr6 234486 2 + 602619 CA -s simDog_chr6.simDog.chr6 226233 2 + 593897 CA -s simHuman_chr6.simHuman.chr6 316596 2 - 601863 CA -s simRat_chr6.simRat.chr6 228836 2 + 647215 TG - -a -s simMouse_chr6.simMouse.chr6 237975 6 + 636262 TTCTGC -s Anc0.Anc0refChr5 57355 6 + 87904 TTCTGT -s Anc1.Anc1refChr7 14882 6 - 47259 TTCTGT -s Anc2.Anc2refChr15 53891 6 + 86568 TTCTGT -s mr.mrrefChr5 91304 6 + 294540 TTCTGC -s simCow_chr6.simCow.chr6 234488 6 + 602619 TTCTGC -s simDog_chr6.simDog.chr6 226236 6 + 593897 TTCCTT -s simHuman_chr6.simHuman.chr6 316598 6 - 601863 TTCTGT -s simRat_chr6.simRat.chr6 228838 6 + 647215 TTTTGC - -a -s simMouse_chr6.simMouse.chr6 237981 15 + 636262 ATGATGAATACTTGG -s Anc0.Anc0refChr5 57361 12 + 87904 ATGATG-ATAC--GG -s Anc1.Anc1refChr7 14888 12 - 47259 ATGATG-ATAC--GG -s Anc2.Anc2refChr15 53897 12 + 86568 GTTACT-ATAT--GG -s mr.mrrefChr5 91310 15 + 294540 ATGATGAATACTTGG -s simCow_chr6.simCow.chr6 234497 12 + 602619 GTTCCT-ACAT--GG -s simDog_chr6.simDog.chr6 226242 12 + 593897 GTTACT-ATAT--GG -s simHuman_chr6.simHuman.chr6 316604 12 - 601863 ATGGTG-GTAC--AG -s simRat_chr6.simRat.chr6 228844 15 + 647215 ATGATGAATACTTGG - -a -s simMouse_chr6.simMouse.chr6 237996 12 + 636262 TTATCTTAATCG -s Anc0.Anc0refChr5 57373 12 + 87904 CTATCTTCATCT -s Anc1.Anc1refChr7 14900 12 - 47259 CTATCTTCATCT -s Anc2.Anc2refChr15 53909 12 + 86568 CAATCTTCATCT -s mr.mrrefChr5 91325 12 + 294540 TTATCTTAATCT -s simCow_chr6.simCow.chr6 234555 12 + 602619 CAATCCTTATCT -s simDog_chr6.simDog.chr6 226254 12 + 593897 CAATCTCCATCT -s simHuman_chr6.simHuman.chr6 316616 11 - 601863 CTTTCTTCATC- -s simRat_chr6.simRat.chr6 228859 12 + 647215 TTATTTCAATCT - -a -s simMouse_chr6.simMouse.chr6 238008 24 + 636262 TGGTATGTACCTCCACATGTATGC -s Anc0.Anc0refChr5 57385 24 + 87904 TAATGTATATTTCCACATGTATGT -s Anc1.Anc1refChr7 14912 24 - 47259 TAATGTATATTTCCACATGTATGT -s Anc2.Anc2refChr15 53921 24 + 86568 TAATGTACATTTCAACATGTATGT -s mr.mrrefChr5 91337 24 + 294540 TGGTATGTATTTCCACATGTATGC -s simCow_chr6.simCow.chr6 234573 24 + 602619 TAATGTAGATTTCAACATCTATGT -s simDog_chr6.simDog.chr6 226266 24 + 593897 TAATTTCCGCTTCAACATGTAGAT -s simHuman_chr6.simHuman.chr6 316627 23 - 601863 TAATGTATATTT-CACATGTATGT -s simRat_chr6.simRat.chr6 228871 24 + 647215 TGGTATGCATTGCCAGATGTATGC - -a -s simMouse_chr6.simMouse.chr6 238032 6 + 636262 ACCTGT -s Anc0.Anc0refChr5 57411 6 + 87904 ACCTCT -s Anc1.Anc1refChr7 14938 6 - 47259 ACCTCT -s Anc2.Anc2refChr15 53947 6 + 86568 ACCTCT -s mr.mrrefChr5 91361 6 + 294540 ACCTGT -s simCow_chr6.simCow.chr6 234599 6 + 602619 ATCTCT -s simDog_chr6.simDog.chr6 226292 6 + 593897 ACCTCT -s simHuman_chr6.simHuman.chr6 316652 6 - 601863 ACCTCT -s simRat_chr6.simRat.chr6 228895 6 + 647215 ACCTGT - -a -s simMouse_chr6.simMouse.chr6 238038 5 + 636262 AAGAG -s Anc0.Anc0refChr5 57424 5 + 87904 AACAA -s Anc1.Anc1refChr7 14951 5 - 47259 AACAA -s Anc2.Anc2refChr15 53960 5 + 86568 AACAA -s mr.mrrefChr5 91367 5 + 294540 AACAG -s simCow_chr6.simCow.chr6 234612 5 + 602619 AACAA -s simDog_chr6.simDog.chr6 226305 5 + 593897 AACAA -s simHuman_chr6.simHuman.chr6 316665 5 - 601863 AACAC -s simRat_chr6.simRat.chr6 228901 5 + 647215 AACAG - -a -s simMouse_chr6.simMouse.chr6 238043 10 + 636262 GAGTTAGATA -s Anc0.Anc0refChr5 57451 10 + 87904 GGATTCGATA -s Anc1.Anc1refChr7 14978 10 - 47259 GGATTCGATA -s Anc2.Anc2refChr15 53987 10 + 86568 GGAGCCAATA -s mr.mrrefChr5 91390 10 + 294540 GGGTTAGATA -s simCow_chr6.simCow.chr6 234639 7 + 602619 G---CCAGCA -s simDog_chr6.simDog.chr6 226332 10 + 593897 GGAGCCAATA -s simHuman_chr6.simHuman.chr6 316692 10 - 601863 GGCTTCGATA -s simRat_chr6.simRat.chr6 228924 10 + 647215 GGTTCGGATA - -a -s simMouse_chr6.simMouse.chr6 238053 13 + 636262 CAATGACCGGAGT -s Anc0.Anc0refChr5 57462 13 + 87904 CAATGAAGGTTTT -s Anc1.Anc1refChr7 14989 13 - 47259 CAATGAAGGTTTT -s Anc2.Anc2refChr15 53998 13 + 86568 CAATCAAGGTTTT -s mr.mrrefChr5 91400 13 + 294540 CAATGACCGGAGT -s simCow_chr6.simCow.chr6 234647 11 + 602619 C--TTAATGTTTT -s simDog_chr6.simDog.chr6 226343 13 + 593897 CAATCAAGGTTTA -s simHuman_chr6.simHuman.chr6 316703 13 - 601863 CAATGAAGGTCTT -s simRat_chr6.simRat.chr6 228934 12 + 647215 -AATGACCAGAAT - -a -s simMouse_chr6.simMouse.chr6 238066 3 + 636262 GAA -s Anc0.Anc0refChr5 57475 2 + 87904 TA- -s Anc1.Anc1refChr7 15002 3 - 47259 TAA -s Anc2.Anc2refChr15 54011 2 + 86568 TA- -s mr.mrrefChr5 91413 3 + 294540 GAA -s simCow_chr6.simCow.chr6 234667 2 + 602619 TG- -s simDog_chr6.simDog.chr6 226356 2 + 593897 CA- -s simHuman_chr6.simHuman.chr6 316716 3 - 601863 TAA -s simRat_chr6.simRat.chr6 228946 3 + 647215 GAA - -a -s simMouse_chr6.simMouse.chr6 238069 85 + 636262 CATGTGATTAGCACAATCATCATGTTGTTGTGTTTATCCCAGGACAGATACACCAAAAACAGCCCTCTCATAAATATTATCCCTG -s Anc0.Anc0refChr5 57477 40 + 87904 ------------------------------------------GACAAATACACAAAAAATGGGTCTCTCATA---ATTACTCTTC -s Anc1.Anc1refChr7 15005 85 - 47259 TGTTCGGATAATGGAATTATCACTTCTTTGCCTTTTTCCCAGGACAAATACACAAAAAATGGGTCTCTCATAAATATTACTCTTC -s Anc2.Anc2refChr15 54013 40 + 86568 ------------------------------------------GACAGATACACAAAAAATGGGTCTCTCATA---ATCACTCTTC -s mr.mrrefChr5 91416 85 + 294540 CATGTGATTAGCACAATTATCATGTTGTTGCGTTTATCCCAGGACAAATACACCAAAAATGGCCCTCTCATAAATATTATCCCTC -s simCow_chr6.simCow.chr6 234669 40 + 602619 ------------------------------------------GAAAGATACACAAAAAGTGGGCCTCTTATA---ATCACTCCTT -s simDog_chr6.simDog.chr6 226358 40 + 593897 ------------------------------------------GACAGATACACAGAAAAGAGGTCTCTCATT---ATCATTCTTC -s simHuman_chr6.simHuman.chr6 316720 85 - 601863 TGTTCGGATAATGGAATTATCACTTCTTTGCCTTTTTCCCAGGACAATTAGATGAAAAATGGGTCTCTCATAAATACTACTCTTC -s simRat_chr6.simRat.chr6 228949 85 + 647215 CACCTGATTAGCACAGTTATCAGGTTGTTGCTATTATCCTGAGACAAATACACCAAAAATGGCCCTCTCGTAAATATTATCCCTC - -a -s simMouse_chr6.simMouse.chr6 238154 4 + 636262 AGTT -s Anc0.Anc0refChr5 57518 4 + 87904 ATTT -s Anc1.Anc1refChr7 15091 4 - 47259 ATTT -s Anc2.Anc2refChr15 54054 4 + 86568 ATTT -s mr.mrrefChr5 91501 4 + 294540 AGTT -s simCow_chr6.simCow.chr6 234710 2 + 602619 AT-- -s simDog_chr6.simDog.chr6 226399 4 + 593897 ATTT -s simHuman_chr6.simHuman.chr6 316806 4 - 601863 ATTT -s simRat_chr6.simRat.chr6 229034 4 + 647215 AGTT - -a -s simMouse_chr6.simMouse.chr6 238158 5 + 636262 GAGAC -s Anc0.Anc0refChr5 57522 5 + 87904 GGAGG -s Anc1.Anc1refChr7 15095 5 - 47259 GGAGG -s Anc2.Anc2refChr15 54058 5 + 86568 GGAGG -s mr.mrrefChr5 91505 5 + 294540 GAGAC -s simCow_chr6.simCow.chr6 234712 5 + 602619 GGAGG -s simDog_chr6.simDog.chr6 226403 5 + 593897 GGAGG -s simHuman_chr6.simHuman.chr6 316810 5 - 601863 GTAGG -s simRat_chr6.simRat.chr6 229060 5 + 647215 GAGAC - -a -s simMouse_chr6.simMouse.chr6 238163 9 + 636262 ATCTACACC -s Anc0.Anc0refChr5 57527 9 + 87904 ATCTACACT -s Anc1.Anc1refChr7 15100 9 - 47259 ATCTACACT -s Anc2.Anc2refChr15 54064 9 + 86568 ATCTACACT -s mr.mrrefChr5 91510 9 + 294540 ATCTACACC -s simCow_chr6.simCow.chr6 234718 9 + 602619 ATTTACACT -s simDog_chr6.simDog.chr6 226409 9 + 593897 ATCTACACT -s simHuman_chr6.simHuman.chr6 316815 9 - 601863 AGCTACACT -s simRat_chr6.simRat.chr6 229065 9 + 647215 ATCTACACC - -a -s simMouse_chr6.simMouse.chr6 238172 62 + 636262 TTCTGTCAGACCCTATATAAGGCCGACCAGTGGAGCTTCTTTCTGAGTTAGCTTTGGCAAGA -s Anc0.Anc0refChr5 57542 13 + 87904 TTTTGTAACATCC------------------------------------------------- -s Anc1.Anc1refChr7 15115 13 - 47259 TTTTGTAACATCC------------------------------------------------- -s Anc2.Anc2refChr15 54079 13 + 86568 TTTTGTAACATCC------------------------------------------------- -s mr.mrrefChr5 91525 57 + 294540 TTCTGTCACACCCTATATAAGGC-----AGTGGAGCTTCTTTCTGAGTTAGCTTTGGCAAGA -s simCow_chr6.simCow.chr6 234733 13 + 602619 TTCTATCACATCC------------------------------------------------- -s simDog_chr6.simDog.chr6 226424 13 + 593897 TGTTGTAACACCT------------------------------------------------- -s simHuman_chr6.simHuman.chr6 316830 13 - 601863 TTTTGTTACATCC------------------------------------------------- -s simRat_chr6.simRat.chr6 229080 57 + 647215 TTCTGTCACACCTTATATAAGGC-----AGTGGGGCGTCTTTCTGAGTTAGCTTTGGCATGA - -a -s simMouse_chr6.simMouse.chr6 238234 20 + 636262 CCTAGTAGAGTGTCCCTGAA -s Anc0.Anc0refChr5 57555 5 + 87904 ------AAAAT--------- -s Anc1.Anc1refChr7 15128 14 - 47259 ------AAAATTACATCCAA -s Anc2.Anc2refChr15 54092 5 + 86568 ------AATAT--------- -s mr.mrrefChr5 91582 20 + 294540 CCTAGTAGAATGACACTGAA -s simCow_chr6.simCow.chr6 234746 5 + 602619 ------AATGT--------- -s simDog_chr6.simDog.chr6 226437 5 + 593897 ------GATAT--------- -s simHuman_chr6.simHuman.chr6 316843 14 - 601863 ------AAAATTACATCCAA -s simRat_chr6.simRat.chr6 229139 20 + 647215 CTTAGCAGAATGACACTGAA - -a -s simMouse_chr6.simMouse.chr6 238254 29 + 636262 ATTCTATCAATTTGCCGAACGACTGCACA -s Anc0.Anc0refChr5 57560 27 + 87904 --ATTGTCAACAAGCTAAGTAGAAGAGCA -s Anc1.Anc1refChr7 15142 29 - 47259 ACATTGTCAACAAGCTAAGTAGAAGAGCA -s Anc2.Anc2refChr15 54097 27 + 86568 --ATGGTCAACAAGCTAAGTAGAAGATCA -s mr.mrrefChr5 91602 29 + 294540 ATTTTATCAATATGCCAAATGACTGCGCA -s simCow_chr6.simCow.chr6 234751 27 + 602619 --ATAGTCAACAAGCTAAGTAGAGGATCA -s simDog_chr6.simDog.chr6 226442 27 + 593897 --GTGGTCAGCAAGCTAAGTAGAAGATCA -s simHuman_chr6.simHuman.chr6 316863 29 - 601863 ACATTGTCTACAGGCTAACTAGACAGGCA -s simRat_chr6.simRat.chr6 229159 29 + 647215 ATTTTATCAATATGCCAAATGACTGCGCA - -a -s simMouse_chr6.simMouse.chr6 238283 51 + 636262 TATATCCAATTTGAAGGGTGATTTGATGTTCAAGGGTATTTAATTTCCACA -s Anc0.Anc0refChr5 57588 50 + 87904 TGCATCCAAATTGAAGGCTGATTTGATGTT-AAAGGTATTTATTTCCCCCA -s Anc1.Anc1refChr7 15172 50 - 47259 TGCATCCAAATTGAAGGCTGATTTGATGTT-AAAGGTATTTATTTCCCCCA -s Anc2.Anc2refChr15 54125 50 + 86568 TGCATCCAAATCGAAGGCTGATTTTATGTC-AAAGGTATTTATGTCTTCCA -s mr.mrrefChr5 91631 51 + 294540 TATATCCAATTTGAAGGGTGATTTGATGTTCAAGGGTATTTATTTTCCACA -s simCow_chr6.simCow.chr6 234779 48 + 602619 TGCATCCAAATAGAAGGCTGATTTTATGTC-AAAGATATT--TGTTTTCCA -s simDog_chr6.simDog.chr6 226470 43 + 593897 TGCATCCAAATCGAGGACTGGTC--------ATAAGTACATATGGCTTCCA -s simHuman_chr6.simHuman.chr6 316893 50 - 601863 TCCATCCAAATTGAAGGCTAATTTGATGTT-AAAGGTATTTATTTCCCTCA -s simRat_chr6.simRat.chr6 229188 51 + 647215 TATGTCCAATTTGAAGGTTGATTTGATGTTCAAGGGTCTTTATTTTCCATA - -a -s simMouse_chr6.simMouse.chr6 238334 4 + 636262 GATG -s Anc0.Anc0refChr5 57638 4 + 87904 GTTA -s Anc1.Anc1refChr7 15222 4 - 47259 GTTA -s Anc2.Anc2refChr15 54175 4 + 86568 GTTA -s mr.mrrefChr5 91682 4 + 294540 GATG -s simCow_chr6.simCow.chr6 234829 4 + 602619 GTTA -s simDog_chr6.simDog.chr6 226513 4 + 593897 ATTA -s simHuman_chr6.simHuman.chr6 316943 4 - 601863 GTTA -s simRat_chr6.simRat.chr6 229239 4 + 647215 GATT - -a -s simMouse_chr6.simMouse.chr6 238338 10 + 636262 GTGTAGTCGC -s Anc0.Anc0refChr5 57642 8 + 87904 GCATATAC-- -s Anc1.Anc1refChr7 15226 10 - 47259 GCATATACTC -s Anc2.Anc2refChr15 54179 8 + 86568 GCATATAC-- -s mr.mrrefChr5 91686 10 + 294540 GCATAGTCTC -s simCow_chr6.simCow.chr6 234833 8 + 602619 GCAAACAC-- -s simDog_chr6.simDog.chr6 226518 7 + 593897 GCATATA--- -s simHuman_chr6.simHuman.chr6 316947 10 - 601863 GCATATACTC -s simRat_chr6.simRat.chr6 229243 10 + 647215 GCATAGTCTC - -a -s simMouse_chr6.simMouse.chr6 238348 1 + 636262 A -s Anc0.Anc0refChr5 57650 1 + 87904 A -s Anc1.Anc1refChr7 15236 1 - 47259 A -s Anc2.Anc2refChr15 31970 1 - 86568 A -s mr.mrrefChr5 91696 1 + 294540 A -s simDog_chr6.simDog.chr6 366858 1 - 593897 A -s simHuman_chr6.simHuman.chr6 316957 1 - 601863 A -s simRat_chr6.simRat.chr6 229253 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 238349 1 + 636262 T -s Anc0.Anc0refChr5 57651 1 + 87904 T -s Anc1.Anc1refChr7 15237 1 - 47259 T -s Anc2.Anc2refChr15 31971 1 - 86568 G -s mr.mrrefChr5 91697 1 + 294540 T -s simDog_chr6.simDog.chr6 366863 1 - 593897 G -s simHuman_chr6.simHuman.chr6 316958 1 - 601863 T -s simRat_chr6.simRat.chr6 229254 1 + 647215 C - -a -s simMouse_chr6.simMouse.chr6 238350 7 + 636262 CATGATG -s Anc0.Anc0refChr5 57652 7 + 87904 GATGATA -s Anc1.Anc1refChr7 15238 7 - 47259 GATGATA -s Anc2.Anc2refChr15 31972 7 - 86568 GAGCATA -s mr.mrrefChr5 91698 7 + 294540 CATGATG -s simCow_chr6.simCow.chr6 367303 7 - 602619 GAGTATA -s simDog_chr6.simDog.chr6 366869 7 - 593897 GAGCAGA -s simHuman_chr6.simHuman.chr6 316959 7 - 601863 GATGATA -s simRat_chr6.simRat.chr6 229255 7 + 647215 TATGATG - -a -s simMouse_chr6.simMouse.chr6 238357 9 + 636262 CTAACATGT -s Anc0.Anc0refChr5 57659 9 + 87904 TAATTATGT -s Anc1.Anc1refChr7 15245 9 - 47259 TAATTATGT -s Anc2.Anc2refChr15 31979 9 - 86568 TACTTATGT -s mr.mrrefChr5 91705 9 + 294540 CTAACATGT -s simCow_chr6.simCow.chr6 367310 9 - 602619 CACTAATAT -s simDog_chr6.simDog.chr6 366879 9 - 593897 TACTTATGT -s simHuman_chr6.simHuman.chr6 316966 9 - 601863 TGATTATGT -s simRat_chr6.simRat.chr6 229262 9 + 647215 CTAACATGT - -a -s simMouse_chr6.simMouse.chr6 238366 3 + 636262 TGC -s Anc0.Anc0refChr5 57673 3 + 87904 TGC -s Anc1.Anc1refChr7 15259 3 - 47259 TGC -s Anc2.Anc2refChr15 31993 3 - 86568 TAC -s mr.mrrefChr5 91714 3 + 294540 TGC -s simCow_chr6.simCow.chr6 367324 3 - 602619 CAC -s simDog_chr6.simDog.chr6 366893 3 - 593897 TAC -s simHuman_chr6.simHuman.chr6 316980 3 - 601863 TGC -s simRat_chr6.simRat.chr6 229271 3 + 647215 TGC - -a -s simMouse_chr6.simMouse.chr6 238369 35 + 636262 TACTATTGGATTGGGCCTCTCTAGTGGGATGTTTG -s Anc0.Anc0refChr5 57691 32 + 87904 TCCAATGGGAAATGTTTATTCTTGTTCGAAGT--- -s Anc1.Anc1refChr7 15277 35 - 47259 TCCAATGGGAAATGTTTATTCTTGTTCGAAGTagg -s Anc2.Anc2refChr15 32011 32 - 86568 TCCAATGGGAAATGTTTATTCATGTTCCAAAT--- -s mr.mrrefChr5 91717 35 + 294540 TACTATTGGATTAGGCTTCTCTAGTGGGATGTATG -s simCow_chr6.simCow.chr6 367345 29 - 602619 TTCAATAGGAAATGTTTATTCATGTTCCA------ -s simDog_chr6.simDog.chr6 366911 31 - 593897 TCCAATGGGAGATGTT-ATACATGATGCAAAT--- -s simHuman_chr6.simHuman.chr6 316998 35 - 601863 TCCAATGGGAAATGTTCATTCTTGTTCGAAGAagg -s simRat_chr6.simRat.chr6 229274 35 + 647215 TACTATTGGTTTAGGCTTCTCTAGCGGGATGTATG - -a -s simMouse_chr6.simMouse.chr6 238404 15 + 636262 GTCACAGCTATAGTT -s Anc1.Anc1refChr7 15312 15 - 47259 attgcttgtttagtt -s mr.mrrefChr5 91752 15 + 294540 GTTGCATCTATAGTT -s simHuman_chr6.simHuman.chr6 317046 15 - 601863 attgcttgtttagtt -s simRat_chr6.simRat.chr6 229309 15 + 647215 CTTGCATCTGTAGTT - -a -s simMouse_chr6.simMouse.chr6 238419 92 + 636262 GGATTCTGGATGCTGTTCATGAATACTTCTCACTTAAGGATAATACACTGTAATAAATCTTTAGGATAACTTTGAGAAAACTATTATATTAA -s Anc0.Anc0refChr5 57723 43 + 87904 -------------------------------------------------GCATTAATTCTTCAGAATAAATTTGGGGAAACTAGAATCTTAA -s Anc1.Anc1refChr7 15327 82 - 47259 ggattccatataactcttccagt-tcTTCCAATTTGGTGG---------GCATTAATTCTTCAGAATAAATTTGGGGAAACTAGAATCTTAA -s Anc2.Anc2refChr15 32043 43 - 86568 -------------------------------------------------GCATTAAATCTTCAGATTAAATTTGGAGAAACTAGAATCTTAA -s mr.mrrefChr5 91767 91 + 294540 GGATTCTGGATGCCGTTTATGAA-ACTTCTCACTTAAGGATAATACACTGTAATAATTCTTTAGGATAAATTTGGGAAAACTAGTATATTAA -s simCow_chr6.simCow.chr6 367374 38 - 602619 -------------------------------------------------GTCTTAAATCTTCA-----AATTTGGAGAAGCTAGAATCCAAA -s simDog_chr6.simDog.chr6 366942 43 - 593897 -------------------------------------------------GCATTAAAATTTCAGATTAAATTTGGAGAAACTAGAATCTTAA -s simHuman_chr6.simHuman.chr6 317065 82 - 601863 ggattccatataactcttccagt-tcTTCCAATTTGGTGG---------GCATTAATTCATCAGAATAAATCTGGGGAAACTAGAATCTTAA -s simRat_chr6.simRat.chr6 229324 91 + 647215 GGATTCTGGATGCCGTTTATGAA-ACTTTTCACTTAAGGATAATACACTGTAATAATTCTTTAGGATAAATTTAGGAAAACTAGTATATTAA - -a -s simMouse_chr6.simMouse.chr6 238511 49 + 636262 AAAGGTGTCAGGTGAAACAATGCATGGGGTTGCAGTCCAAATAAAAAGA -s Anc0.Anc0refChr5 57767 45 + 87904 AAAGATGTCAGGTGAAAC----CATGGGATTGCAGTTAGTGTAAAAATA -s Anc1.Anc1refChr7 15410 45 - 47259 AAAGATGTCAGGTGAAAC----CATGGGATTGCAGTTAGTGTAAAAATA -s Anc2.Anc2refChr15 32087 45 - 86568 GAAGATGTCAGGTGAAGG----CATGGGATTGCAGTTAGTGTAAAAATA -s mr.mrrefChr5 91858 49 + 294540 AAAGATGTCAGGTGAAACAATGCATGGGGTTGCAGTTCAAGTAAAAAGA -s simCow_chr6.simCow.chr6 367413 45 - 602619 GAAGATGTCAGATAAAGG----AATGGGATTACAGTAGATGTGTAAACA -s simDog_chr6.simDog.chr6 366986 45 - 593897 GAAGATGTCAGGTGTAGG----CATGGGATTGCAGTTAGCTTAAAAATA -s simHuman_chr6.simHuman.chr6 317148 45 - 601863 AAAGATGTCAGCTGACAC----CATGGGATTGTAGTTAGTGTAAAAAAG -s simRat_chr6.simRat.chr6 229415 49 + 647215 AGAGATGTCTGGTGAAATAATGCATGGGGTTGCAGTTCAAGTTAAAAGA - -a -s simMouse_chr6.simMouse.chr6 238560 12 + 636262 TTCCCACACCTA -s Anc0.Anc0refChr5 57812 9 + 87904 TTCCC---TCTA -s Anc1.Anc1refChr7 15455 9 - 47259 TTCCC---TCTA -s Anc2.Anc2refChr15 32134 9 - 86568 TTCCC---TCAA -s mr.mrrefChr5 91907 12 + 294540 TTCCCACACCTA -s simCow_chr6.simCow.chr6 367460 9 - 602619 CTCTC---TCAA -s simDog_chr6.simDog.chr6 367033 9 - 593897 TTTCC---TCAA -s simHuman_chr6.simHuman.chr6 317193 9 - 601863 TTCCC---TCTA -s simRat_chr6.simRat.chr6 229464 12 + 647215 TATTCACACCTA - -a -s simMouse_chr6.simMouse.chr6 238572 3 + 636262 ACC -s Anc0.Anc0refChr5 57826 3 + 87904 ACC -s Anc1.Anc1refChr7 15469 3 - 47259 ACC -s Anc2.Anc2refChr15 32148 3 - 86568 GCC -s mr.mrrefChr5 91919 3 + 294540 ACC -s simCow_chr6.simCow.chr6 367474 3 - 602619 GTC -s simDog_chr6.simDog.chr6 367047 3 - 593897 GCC -s simHuman_chr6.simHuman.chr6 317207 3 - 601863 ACC -s simRat_chr6.simRat.chr6 229476 3 + 647215 ACC - -a -s simMouse_chr6.simMouse.chr6 238575 48 + 636262 TACTCATATCTAGGAGTGAAGCAGAGACTGCCTATTGAGAGAAGGATT -s Anc0.Anc0refChr5 57831 48 + 87904 TACAATCACCCAGGAGTGAAACAGAGATTGTCTATTGAGGGCAGGGCT -s Anc1.Anc1refChr7 15474 48 - 47259 TACAATCACCCAGGAGTGAAACAGAGATTGTCTATTGAGGGCAGGGCT -s Anc2.Anc2refChr15 32153 48 - 86568 TTCAATCACCCAAGAGTAAAACAAAAATTGTCTATTGAGGGCAGGGCT -s mr.mrrefChr5 91922 48 + 294540 TACTCATACCTAGGAGTGAAGCAGAGACTGCCTATTGAGAGAAGGACT -s simCow_chr6.simCow.chr6 367479 48 - 602619 TTCAATCACCACAGAGTAAAACAAAATTTGTCAATTGAGGGCTGGGTT -s simDog_chr6.simDog.chr6 367052 44 - 593897 TTTCATCATCCAAGAGTAAAA----AATTGTCTATTGAGGGGAGGGCT -s simHuman_chr6.simHuman.chr6 317212 48 - 601863 TACAATCACCCAGGAGTGAAACGGAGATTGTCTATTGAAGTCAGGGCT -s simRat_chr6.simRat.chr6 229479 48 + 647215 TACTCATACCTAGCAGTGAAGCAGAGACAGCCTCTTGAGAGAAGCACC - -a -s simMouse_chr6.simMouse.chr6 238623 21 + 636262 GATACTTACTTCACATCCCAG -s Anc0.Anc0refChr5 57880 21 + 87904 GATATTTAGTCCATACCCCAG -s Anc1.Anc1refChr7 15523 21 - 47259 GATATTTAGTCCATACCCCAG -s Anc2.Anc2refChr15 32202 21 - 86568 GATATTTAGTCCACACCCTAG -s mr.mrrefChr5 91971 21 + 294540 GATACTTACTTCATACCCCAG -s simCow_chr6.simCow.chr6 367528 21 - 602619 GCTACTTAGTTCACACCCTAG -s simDog_chr6.simDog.chr6 367097 18 - 593897 GATATA-AATCCA--CTCTAG -s simHuman_chr6.simHuman.chr6 317261 21 - 601863 GATATTTGGTCCATACCCCAG -s simRat_chr6.simRat.chr6 229528 21 + 647215 GATACTTACTTCATGCCCCAG - -a -s simMouse_chr6.simMouse.chr6 238644 22 + 636262 CAGTACAGTATTATGCATTATA -s Anc0.Anc0refChr5 57901 21 + 87904 TAGTCAATTATT-TACACTATA -s Anc1.Anc1refChr7 15544 22 - 47259 TAGTCAATTATTATACACTATA -s Anc2.Anc2refChr15 32223 21 - 86568 TAGTCAATCATT-TACAATATA -s mr.mrrefChr5 91992 22 + 294540 CAGTACAGTATTATACACTATA -s simCow_chr6.simCow.chr6 367550 21 - 602619 TAGTCACTCTTA-TATAATATA -s simDog_chr6.simDog.chr6 367115 21 - 593897 TAGTCCATCATT-CTCCACTTA -s simHuman_chr6.simHuman.chr6 317282 22 - 601863 TAGTCAGATATCATACACTACA -s simRat_chr6.simRat.chr6 229549 22 + 647215 CAGTACAGTATTATACACTATA - -a -s simMouse_chr6.simMouse.chr6 238666 39 + 636262 TTATGTTCTATTACTCAATCTCATAGTCAGCCAGAAGTA -s Anc0.Anc0refChr5 57922 39 + 87904 TTATGTACCACTATGTGATCTCAAATTAAGACATAGGTA -s Anc1.Anc1refChr7 15566 39 - 47259 TTATGTACCACTATGTGATCTCAAATTAAGACATAGGTA -s Anc2.Anc2refChr15 32245 39 - 86568 TTATGTACCACTATGTGATCTCAAATTAAGACATAGGCA -s mr.mrrefChr5 92014 39 + 294540 TTATGTACTATTACTCAATCTCATAGTCAGCCATAGGTA -s simCow_chr6.simCow.chr6 367572 33 - 602619 TAAAG---CCCTATGTAATCTCAAATTAAGACATAG--- -s simDog_chr6.simDog.chr6 367137 39 - 593897 TTATGTACCACTACATGACCTCAAATTAAGAAATAGGCA -s simHuman_chr6.simHuman.chr6 317304 39 - 601863 TTATGTACCAGTATGTGATCTCAAATTAGGACATAGATA -s simRat_chr6.simRat.chr6 229571 36 + 647215 A---GTACTATTACTCAATCTTATAATCAGGCATAGGTA - -a -s simMouse_chr6.simMouse.chr6 238705 42 + 636262 GGAATAGAAGTTAGTTGGGCAGAATAGTAAACTGATATGAGT -s Anc0.Anc0refChr5 57961 42 + 87904 GGAACAGTAACTAATCGGACAGAGTAGTAAGCTGGCATAAGT -s Anc1.Anc1refChr7 15605 42 - 47259 GGAACAGTAACTAATCGGACAGAGTAGTAAGCTGGCATAAGT -s Anc2.Anc2refChr15 32288 42 - 86568 GGAACAGTAACTAATCGGACAGAGTAGCAAGCTGGCATAAGT -s mr.mrrefChr5 92053 42 + 294540 GGAATAGAAGTTAGTTGGGCAGAATAGTAAACTGATATGAGT -s simCow_chr6.simCow.chr6 367608 42 - 602619 GGAACGGTAATTAATTGGGCAGAGTAGAAAGCCAGCATAAGT -s simDog_chr6.simDog.chr6 367186 42 - 593897 GGAACAGTAACTAATCAGACAGAGTTGCAAGCTGGTTGATGT -s simHuman_chr6.simHuman.chr6 317343 30 - 601863 GA------------TCGGACAGAGTAGTGAGCTGTCATAAGT -s simRat_chr6.simRat.chr6 229607 42 + 647215 GGAATAGCACTCATTTAGGAAGAATAGTAAACTGATATGAGT - -a -s simMouse_chr6.simMouse.chr6 238747 5 + 636262 ACATA -s Anc0.Anc0refChr5 58003 5 + 87904 ACATA -s Anc1.Anc1refChr7 15647 5 - 47259 ACATA -s Anc2.Anc2refChr15 32330 5 - 86568 ACATA -s mr.mrrefChr5 92095 5 + 294540 ACATA -s simCow_chr6.simCow.chr6 367650 5 - 602619 ACATA -s simDog_chr6.simDog.chr6 367231 5 - 593897 GGATA -s simHuman_chr6.simHuman.chr6 317373 5 - 601863 ACATA -s simRat_chr6.simRat.chr6 229649 5 + 647215 ACATA - -a -s simMouse_chr6.simMouse.chr6 238752 17 + 636262 CACTCTGTGTCCGTACC -s Anc0.Anc0refChr5 58033 17 + 87904 TACACTGTGCAAGTACC -s Anc1.Anc1refChr7 15677 17 - 47259 TACACTGTGCAAGTACC -s Anc2.Anc2refChr15 32360 17 - 86568 TTCACAGAACAGATACT -s mr.mrrefChr5 92100 17 + 294540 CACTCTGTGTCAGTACC -s simCow_chr6.simCow.chr6 367684 17 - 602619 TGTGCAGCATAGATAGC -s simDog_chr6.simDog.chr6 367355 17 - 593897 ATCACAGAACAGATACT -s simHuman_chr6.simHuman.chr6 317403 17 - 601863 TACACTGTGCAAGTACC -s simRat_chr6.simRat.chr6 229654 17 + 647215 CACTCCGTGTGAGTACC - -a -s simMouse_chr6.simMouse.chr6 238769 7 + 636262 TGACCAG -s Anc0.Anc0refChr5 58050 4 + 87904 TA---CT -s Anc1.Anc1refChr7 15694 4 - 47259 TA---CT -s Anc2.Anc2refChr15 32377 4 - 86568 AT---AA -s mr.mrrefChr5 92117 7 + 294540 TGACCAG -s simCow_chr6.simCow.chr6 367774 4 - 602619 AT---AA -s simHuman_chr6.simHuman.chr6 317420 2 - 601863 TA----- -s simRat_chr6.simRat.chr6 229671 7 + 647215 TGACCCG - -a -s simMouse_chr6.simMouse.chr6 238776 36 + 636262 TTAAGCCACACGAGTGTCTGTTGATGCTACATGCTA -s Anc0.Anc0refChr5 58054 36 + 87904 TTATGTCATACGAATGTCTGTTGTTGCTACATGCTA -s Anc1.Anc1refChr7 15698 36 - 47259 TTATGTCATACGAATGTCTGTTGTTGCTACATGCTA -s Anc2.Anc2refChr15 54598 36 + 86568 TCATCTCATACGAATGTCTGTTGTTGCTACATGCTA -s mr.mrrefChr5 92124 36 + 294540 TTAAGCCACACGAGTGTCTGTTGATGCTACATGCTA -s simCow_chr6.simCow.chr6 235316 30 + 602619 ------TATACGGGTGTCTGTTGTTTATAAATGCTA -s simDog_chr6.simDog.chr6 227039 36 + 593897 TCATCTCATACAAATGTCCATTGTTGCTACATGCTA -s simHuman_chr6.simHuman.chr6 317422 31 - 601863 -TATGTCATACGAATGTCTGTTG----CATACGTGT -s simRat_chr6.simRat.chr6 229678 36 + 647215 TTAAGCCACACAATCATCTGTTGATGCTACATGCTA - -a -s simMouse_chr6.simMouse.chr6 238812 26 + 636262 GTTGCTGGCTTTGATCTGAGAGTGAA -s Anc0.Anc0refChr5 58090 21 + 87904 ATT-----CTGTGATTCTGGGGTGAA -s Anc1.Anc1refChr7 15734 21 - 47259 ATT-----CTGTGATTCTGGGGTGAA -s Anc2.Anc2refChr15 54667 21 + 86568 GTT-----CTGTGAATCTGGGGTTCA -s mr.mrrefChr5 92160 26 + 294540 ATTGCTGGCTTTGATCTGAGGGTGAA -s simCow_chr6.simCow.chr6 235379 21 + 602619 GTT-----CAGTGAATCTGGGGCACA -s simDog_chr6.simDog.chr6 227125 21 + 593897 GTT-----CTGTGAATCTGGGGTTCA -s simHuman_chr6.simHuman.chr6 317453 21 - 601863 ATT-----CTGTGATTCTGGGGTGAA -s simRat_chr6.simRat.chr6 229714 26 + 647215 ATTGCTGGTTTTGATCTAAAGGTGAA - -a -s simMouse_chr6.simMouse.chr6 238838 3 + 636262 AAT -s Anc0.Anc0refChr5 58111 3 + 87904 TGT -s Anc1.Anc1refChr7 15755 3 - 47259 TGT -s Anc2.Anc2refChr15 54688 3 + 86568 TGT -s mr.mrrefChr5 92186 3 + 294540 AAT -s simCow_chr6.simCow.chr6 235400 3 + 602619 AGC -s simDog_chr6.simDog.chr6 227165 3 + 593897 TGT -s simHuman_chr6.simHuman.chr6 317474 3 - 601863 TGG -s simRat_chr6.simRat.chr6 229740 3 + 647215 AAT - -a -s simMouse_chr6.simMouse.chr6 238841 98 + 636262 AAAATGCTTTTTATCTTGACATATATGTGGACACAGAAATGATTAGTTAGTTCTCACCTGAACATGTTTGTTTAGAATGCACAATGCAAAAACACATG -s Anc0.Anc0refChr5 58114 86 + 87904 CAAATACCTTTCATCTTGACATCTAAATGGAT------GTGACTTAT----TTTTACTTCAACAAGTCCTCTTAG--TGTATTATGCAAAAAACCATG -s Anc1.Anc1refChr7 15758 86 - 47259 CAAATACCTTTCATCTTGACATCTAAATGGAT------GTGACTTAT----TTTTACTTCAACAAGTCCTCTTAG--TGTATTATGCAAAAAACCATG -s Anc2.Anc2refChr15 54691 86 + 86568 CAAATACCTTTCATCTTGGCATCTAAATGGAT------GTGACTTAT----TTTTACTTCAACAAGCCCTCTTAG--TGCATTATGTAAAAAACCATG -s mr.mrrefChr5 92189 94 + 294540 AAAATGCTTTTCATCTTGACATATATGTGGATACAGAAATGATTAGT----TTTTACCTGAACATGTTTGTGTAGAATATACAATGCAAAAACACATG -s simCow_chr6.simCow.chr6 235406 86 + 602619 CAAATACCTTTCATCTTGGCATCTAAATGGAT------GTGACTTAT----TTTTACCTCAACCAACCCTATTAT--GGCATTGTGTAGAGAACTATG -s simDog_chr6.simDog.chr6 227168 86 + 593897 CGAATGCTTTTCATCCTGGTGTCTAAATGGAT------CTGACTTTT----TTTTACTTTAACAAGCCCTCTTAG--TGCATTATATAAAAAACCACG -s simHuman_chr6.simHuman.chr6 317477 86 - 601863 CAAAAACCATTCATTTTTACATCTAAATGGAT------GTGACTTAC----TTTTAATTCAACAGGTGCTGTTAG--TGTATTATGCAAAAAACCATG -s simRat_chr6.simRat.chr6 229743 94 + 647215 AAAATCCGTTTCATCTAGACATTTATGTGGATACAGAAATGATTAGT----TTTTACCTGAACATGTTTATGTGGAATATACAATGCAAAAACACATG - -a -s simMouse_chr6.simMouse.chr6 238939 38 + 636262 TACATGCTGTTTCTATGACATACCTGTGAAGTATTACT -s Anc0.Anc0refChr5 58202 37 + 87904 GACA-GCTGTTTCTGTAACATACCTGTAAAGGGTCAAT -s Anc1.Anc1refChr7 15846 38 - 47259 GACATGCTGTTTCTGTAACATACCTGTAAAGGGTCAAT -s Anc2.Anc2refChr15 54779 37 + 86568 GGCA-ACTATTTCCGTAACATACCTGGACATGGTCAAT -s mr.mrrefChr5 92283 38 + 294540 TACATGCTGTTTCTATAACATACCTGTGAAGTATTACT -s simCow_chr6.simCow.chr6 235494 29 + 602619 A---------TTCCAGAACATACCTGCACAAGGTCAGT -s simDog_chr6.simDog.chr6 227256 37 + 593897 GGCA-ACTATTTCCGTAACATACCTGGGCATGGTCTAT -s simHuman_chr6.simHuman.chr6 317565 38 - 601863 CACATGCTGTTTCTGTAATGCACCTGTAAAGGGTCAAT -s simRat_chr6.simRat.chr6 229837 38 + 647215 TACATGACATTTCTAAAACATACCTGTGAAGCATTGCT - -a -s simMouse_chr6.simMouse.chr6 238977 34 + 636262 TTCCATAAAAACACTGGCACACTGGCACAAGGAG -s Anc0.Anc0refChr5 58257 25 + 87904 TTCCATGAACACAAT--------GG-ACAAATAT -s Anc1.Anc1refChr7 15902 26 - 47259 TTCCATGAACACAAT--------GGCACAAATAT -s Anc2.Anc2refChr15 54834 25 + 86568 TTCCATGAACTCAAT--------GG-GCAAATAT -s mr.mrrefChr5 92321 26 + 294540 TTCCATAAAAACACT--------GGCACAAGGAG -s simCow_chr6.simCow.chr6 235541 25 + 602619 TTTCATGAACTCAAT--------GA-GCAAATAT -s simDog_chr6.simDog.chr6 227311 25 + 593897 TCCCATGAACTCAAT--------GG-GCACACTT -s simHuman_chr6.simHuman.chr6 317621 26 - 601863 TTCCATGAACACTAT--------GTCACAAATAT -s simRat_chr6.simRat.chr6 229875 26 + 647215 TTCCACAAAAACACT--------GGCACAAGGAG - -a -s simMouse_chr6.simMouse.chr6 239011 39 + 636262 ACTATCGCCCCCCCATGCTTAAATATCACCATGTTTGCA -s Anc0.Anc0refChr5 58288 33 + 87904 ATCT------CCTCATTCTTAAATATTACCATATTTGTA -s Anc1.Anc1refChr7 15934 39 - 47259 ATCTTCCCCCCCTCATTCTTAAATATTACCATATTTGTA -s Anc2.Anc2refChr15 54865 33 + 86568 ATCT------CCTCATTCTCAAATATTACCATATTTGTG -s mr.mrrefChr5 92347 39 + 294540 ACTATCGCCCCCTCATGCTTAAATATCACCATGTTTGCA -s simCow_chr6.simCow.chr6 235572 13 + 602619 ATCT------CCTCATTCT-------------------- -s simDog_chr6.simDog.chr6 227342 33 + 593897 ATCT------CCTCATTCTCAAATATTACCATATTTGTG -s simHuman_chr6.simHuman.chr6 317653 39 - 601863 ATCTTCCCCCCCTCATTCTTAAATGCTACCACATTTGTA -s simRat_chr6.simRat.chr6 229901 35 + 647215 ACTAATTCCTCCTCATGCGTAAATAT----ATGTTTGCA - -a -s simMouse_chr6.simMouse.chr6 239050 265 + 636262 GTAGGTTTGTTCTGAACTTGGAAAGGAGAGCTGTGTGTTAGGTCATCATCTTTGCACGAAAAGAATTCCAAGCACAGCTTTACCGTGCTGTACGCCATGGGTAGGGTTAAATGGTTAACTCTCATCGCGAGACTATATAGTAGAGCTGACGGGTCGAGATGTGGATTCCGGGGTTAGGACCATGCTGTCGACGCGTTCCATAGGAATACCTCCCGATTTCACTATTGCTCTAAACGAGATGTGGTCAATTCAAAATGTATCTTGG -s Anc0.Anc0refChr5 58328 57 + 87904 ACAGGTCTGCTCTGAACTTGGAAAAGTGAGGTATATCTTTGTTCATTCT----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GATCTGAG -s Anc1.Anc1refChr7 15980 57 - 47259 ACAGGTCTGCTCTGAACTTGGAAAAGTGAGGTATATCTTTGTTCATTCT----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GATCTGAG -s Anc2.Anc2refChr15 54905 57 + 86568 ACATGTCTGCAATGAACTTAGAAAAGTGAGGTTTGTCTTTGTTCATTCT----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GATCAGAG -s mr.mrrefChr5 92386 57 + 294540 ACAGGTTTGCTCTGAACTTGGAAAAGAGAGCTATATGTTTGGTCATCAT----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TATCTTGG -s simCow_chr6.simCow.chr6 235585 39 + 602619 ------------------TAGAAGAGTCCGATTCCTCATTGTTCATTCT----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TATAAGAA -s simDog_chr6.simDog.chr6 227382 57 + 593897 ACATGTCTGCAATGAACTTAGAAAGGTGAGGCTTGTCTTTGTTGATTCT----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GATCAGAG -s simHuman_chr6.simHuman.chr6 317699 56 - 601863 ACAGGAGTGCTCTGAACTTGCAAAAG-GAGGTATATCCTTGTTCATTGT----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GATCTGAG -s simRat_chr6.simRat.chr6 229936 38 + 647215 ACAGGTTTGCTCTGAGCTTGGGAAAG-AAG--AGAAGGTTG-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- - -a -s simMouse_chr6.simMouse.chr6 239315 7 + 636262 AAGATAG -s Anc0.Anc0refChr5 58385 7 + 87904 CACATAT -s Anc1.Anc1refChr7 16037 7 - 47259 CACATAT -s Anc2.Anc2refChr15 54972 7 + 86568 CACATAT -s mr.mrrefChr5 92443 7 + 294540 AAGATAG -s simCow_chr6.simCow.chr6 235634 7 + 602619 CAGATTG -s simDog_chr6.simDog.chr6 227449 7 + 593897 CACATAT -s simHuman_chr6.simHuman.chr6 317755 7 - 601863 CATATAC - -a -s simMouse_chr6.simMouse.chr6 239322 29 + 636262 TGTGGAAGATCAGCATATGCCAAGTTTTG -s Anc0.Anc0refChr5 58392 29 + 87904 TATGTTGGATCAGCATATACTAAGTTTTG -s Anc1.Anc1refChr7 16044 29 - 47259 TATGTTGGATCAGCATATACTAAGTTTTG -s Anc2.Anc2refChr15 54979 29 + 86568 TATGTTGGATCAGCCTATACTAAGTTTTG -s mr.mrrefChr5 92450 29 + 294540 TGTGGAAGATCAGCATATGCCAAGTTTTG -s simCow_chr6.simCow.chr6 235641 29 + 602619 TAGGGTGGATCAGCGTATACTATGTCTTG -s simDog_chr6.simDog.chr6 227460 29 + 593897 TGTGTGGGACCATCCTATGCTAAGTTTTG -s simHuman_chr6.simHuman.chr6 317762 29 - 601863 TATGCTGGGTTTGCATATACTAAGTTTTG - -a -s simMouse_chr6.simMouse.chr6 239351 1 + 636262 T -s Anc0.Anc0refChr5 58421 1 + 87904 T -s Anc1.Anc1refChr7 16073 1 - 47259 T -s Anc2.Anc2refChr15 55018 1 + 86568 T -s mr.mrrefChr5 92479 1 + 294540 T -s simCow_chr6.simCow.chr6 235680 1 + 602619 T -s simDog_chr6.simDog.chr6 227499 1 + 593897 T -s simHuman_chr6.simHuman.chr6 317791 1 - 601863 T - -a -s simMouse_chr6.simMouse.chr6 239352 102 + 636262 CTATTGTCTGGGACTTTCCCTACATGTGGGTAAAATAATTCCCCCAGTTATTGCCAAAAGAACTGCACTGTTGACTTAGATCCTCTGTCTCAGTGCCAAGAG -s Anc0.Anc0refChr5 58422 93 + 87904 CTAAT-------ACTTTCCCCACATGTGAGCAACATAACTCTTCCAGCTATTGTCAAAGGTACATCACTGTTAGCTCATATCC--TGTCTTGGTCTCAAGAG -s Anc1.Anc1refChr7 16074 93 - 47259 CTAAT-------ACTTTCCCCACATGTGAGCAACATAACTCTTCCAGCTATTGTCAAAGGTACATCACTGTTAGCTCATATCC--TGTCTTGGTCTCAAGAG -s Anc2.Anc2refChr15 55019 93 + 86568 CTGAT-------ACTTTCCCCACATGTGAGTAACATACCTCTTCCAGCTATTGTTAAAGGTACATCACTGTTAGCTCATATCT--TGTGTTGATCTCAAGAG -s mr.mrrefChr5 92480 95 + 294540 CTATT-------ACTTTCCCTACATGTGGGCAAAATAATTCCCCCAGTTATTGCCAAAGGAACTGCACTGTTAACTCAGATCCTCTGTCTTGGTGCCAAGAG -s simCow_chr6.simCow.chr6 235682 91 + 602619 CTGAT-------ACTTTCCTC-CATGTGAGTGGCATGCTTCTTCCAGCTATTAGTAGAGGTACCCCACTGTCCACTCATACCT--CACTTTG-TCTTGGGAG -s simDog_chr6.simDog.chr6 227500 93 + 593897 CTGAT-------ACTTTCCCCACACGAGCGTAATATACCTCATCCAGTTATTGTTGAGAGTACATCACTGTTAGCTCATATCT--TGTGTTGATCTCAAGAG -s simHuman_chr6.simHuman.chr6 317792 82 - 601863 CCAAT-------ACTTTCCCCACATGTGAGCAACATAACTATTCCAGCTATTGTCAAAGG-----------TAGCTCATATCC--TGTCTTGGGCTCCAGAG -s simRat_chr6.simRat.chr6 229974 80 + 647215 ----------------------CAAGTGGGCAAAGTAATTCCCCCAGTTATTGCCAAAGGGCCTGTACTGTTATCTCAAATCCTCTGTCTTGGTGCCTAGAG - -a -s simMouse_chr6.simMouse.chr6 239454 37 + 636262 GCAGGCTACAATTTTTGCAGATTTGTTGCTCTATGAT -s Anc0.Anc0refChr5 58515 36 + 87904 CCAAGTTAGTATC-TTGAGGACTTGTTCCTCTAGACT -s Anc1.Anc1refChr7 16167 37 - 47259 CCAAGTTAGTATCTTTGAGGACTTGTTCCTCTAGACT -s Anc2.Anc2refChr15 55115 36 + 86568 CCAAGTTAGTATC-TTGAGGACTTGATCCTCTAGACT -s mr.mrrefChr5 92575 37 + 294540 GCAGGCTAGTATCTTTGCAGATTTGTTGCTCTAGGAT -s simCow_chr6.simCow.chr6 235776 36 + 602619 CTGAGTAAGTATC-TTCAACGCTTGCTCCTCTAGACT -s simDog_chr6.simDog.chr6 227596 36 + 593897 CCAAGTTAGTATC-TTGAGGACTCGATCCTCTAGACT -s simHuman_chr6.simHuman.chr6 317874 26 - 601863 CC------GTTTCTT-----ACTTGTTCCTCTAGACT -s simRat_chr6.simRat.chr6 230054 37 + 647215 GCAGGCTAGTATCTTTGCAGATTTGTCACTCTAGGAT - -a -s simMouse_chr6.simMouse.chr6 239491 18 + 636262 CAGTATGCAGATAGAGCA -s Anc0.Anc0refChr5 58566 15 + 87904 TGTTATGGAACTA-AG-- -s Anc1.Anc1refChr7 16219 16 - 47259 TGTTATGGAACTAGAG-- -s Anc2.Anc2refChr15 55166 15 + 86568 TGTTATGGAACTA-AG-- -s mr.mrrefChr5 92612 16 + 294540 TGGTATGCAGATAGAG-- -s simCow_chr6.simCow.chr6 235826 15 + 602619 TGGTATGGCACAA-AG-- -s simDog_chr6.simDog.chr6 227647 15 + 593897 TGTTATGGAATTG-AG-- -s simHuman_chr6.simHuman.chr6 317915 16 - 601863 TGAAATGGAACTAGTG-- -s simRat_chr6.simRat.chr6 230091 16 + 647215 TGGTATGCAGATAGAG-- - -a -s simMouse_chr6.simMouse.chr6 239509 67 + 636262 GGCTCTTAAGGATCCCAACATCTGCTATGTGCAATTCAATCCTCCTGAGATTCTGGGTTGCAAAATT -s Anc0.Anc0refChr5 58581 67 + 87904 GATTCTTAAGGAATCCATCATCTGCTATGTGCTAGTCTGCCCTCCTGTGAATCTGGGTTGCAAAAGT -s Anc1.Anc1refChr7 16235 67 - 47259 GATTCTTAAGGAATCCATCATCTGCTATGTGCTAGTCTGCCCTCCTGTGAATCTGGGTTGCAAAAGT -s Anc2.Anc2refChr15 55181 67 + 86568 GATTCTTATGGAATCCATCATCTTGTATGTGCTAGTCTGTACTCTTGTGTATCTGGGTTGCATAGGA -s mr.mrrefChr5 92628 67 + 294540 GACTCTTAAGGATTCCAACATCTGCTATGTGCAATTCAACCCTCCTGAGATTCTGGGTTGCAAAATT -s simCow_chr6.simCow.chr6 235841 15 + 602619 GATACTTGCAGAATC---------------------------------------------------- -s simDog_chr6.simDog.chr6 227662 67 + 593897 CATTCCAATGGAATCCATCATCTTGTATGTGCTAGTCTGTACTCTTGTGTATCTGGGTTGCATAGGA -s simHuman_chr6.simHuman.chr6 317931 66 - 601863 GATTTTTAAGGAGTCCATCATCTGCTATATGCTAGTCTGCCTTCCTGCGAAACCAGCTT-CAAAAGT -s simRat_chr6.simRat.chr6 230108 65 + 647215 AACTCCTAAGGATTCCAACATC--CAATGTGCAATTTGCCCCCCCTGACATTCTGGTTTGCAAAATC - -a -s simMouse_chr6.simMouse.chr6 239576 29 + 636262 CGAAATATCATTGAGATATTCCTCAATTT -s Anc0.Anc0refChr5 58648 23 + 87904 AG------TATTAAGATTTTGCTTAATTT -s Anc1.Anc1refChr7 16302 25 - 47259 AGGA----TATTAAGATTTTGCTTAATTT -s Anc2.Anc2refChr15 55248 23 + 86568 AG------TATTAAGATTTTGCTCAATTT -s mr.mrrefChr5 92695 29 + 294540 AGAAATATCATTGAGATATTCCTTAATTT -s simCow_chr6.simCow.chr6 235856 23 + 602619 AT------TATTATTACATTACTCACTTT -s simDog_chr6.simDog.chr6 227732 23 + 593897 AG------TATTAAGATTGTGTTCAATTT -s simHuman_chr6.simHuman.chr6 317997 25 - 601863 AGGA----TATTAAGATCTCGCTTAATTT -s simRat_chr6.simRat.chr6 230173 29 + 647215 AGAAATATCATTGAGATATTCCTTAATCT - -a -s simMouse_chr6.simMouse.chr6 239605 1 + 636262 A -s Anc0.Anc0refChr5 58671 1 + 87904 A -s Anc1.Anc1refChr7 16327 1 - 47259 A -s Anc2.Anc2refChr15 55271 1 + 86568 A -s mr.mrrefChr5 92724 1 + 294540 A -s simCow_chr6.simCow.chr6 235879 1 + 602619 A -s simDog_chr6.simDog.chr6 227757 1 + 593897 A -s simHuman_chr6.simHuman.chr6 318022 1 - 601863 A -s simRat_chr6.simRat.chr6 230202 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 239606 14 + 636262 TGTGGACATGAATT -s Anc0.Anc0refChr5 58676 14 + 87904 AGACGACACAAATT -s Anc1.Anc1refChr7 16332 14 - 47259 AGACGACACAAATT -s Anc2.Anc2refChr15 55276 14 + 86568 AGACAACACAAATT -s mr.mrrefChr5 92725 14 + 294540 AGTGGACATGAATT -s simCow_chr6.simCow.chr6 235883 14 + 602619 TTACAACACAAATT -s simDog_chr6.simDog.chr6 227762 14 + 593897 AGACAAAATAAATT -s simHuman_chr6.simHuman.chr6 318027 14 - 601863 AGACGACACAAACT -s simRat_chr6.simRat.chr6 230203 14 + 647215 AGTGGACATGTATT - -a -s simMouse_chr6.simMouse.chr6 239620 32 + 636262 AGCAAATGATATGACATCAGTGATCCTAACTA -s Anc0.Anc0refChr5 58690 32 + 87904 AATACAAGGTATGACATCAGTGACCCTAACTA -s Anc1.Anc1refChr7 16346 32 - 47259 AATACAAGGTATGACATCAGTGACCCTAACTA -s Anc2.Anc2refChr15 55290 32 + 86568 AATACAAGGTATGACATCAGCAACCCTAATTG -s mr.mrrefChr5 92739 32 + 294540 AGCAAATGATATGACATCAGTGACCCTAACTA -s simCow_chr6.simCow.chr6 235901 32 + 602619 AATACAATGCATTACATCATGTACCCTCATTG -s simDog_chr6.simDog.chr6 227776 32 + 593897 AATACAAGGTATGACAACAGCAACCCTAGTTG -s simHuman_chr6.simHuman.chr6 318041 32 - 601863 AATGCAAGGTGTGTTGTCAGTGAGCCTGACTA -s simRat_chr6.simRat.chr6 230217 32 + 647215 AGCAAATGATATCACATCAGTGACCCCAACTA - -a -s simMouse_chr6.simMouse.chr6 239652 12 + 636262 TGTGTCCACCAG -s Anc0.Anc0refChr5 58724 11 + 87904 TG-ACCCACCAG -s Anc1.Anc1refChr7 16380 12 - 47259 TGTACCCACCAG -s Anc2.Anc2refChr15 55324 11 + 86568 TG-ACCCACCAG -s mr.mrrefChr5 92773 12 + 294540 TGTGTCCACCAG -s simCow_chr6.simCow.chr6 235935 11 + 602619 TG-ATCCACCAG -s simDog_chr6.simDog.chr6 227810 11 + 593897 TG-ACCCACCAG -s simHuman_chr6.simHuman.chr6 318075 12 - 601863 TGTACCCACCAG -s simRat_chr6.simRat.chr6 230251 12 + 647215 TGTGTCCGCCAG - -a -s simMouse_chr6.simMouse.chr6 239664 48 + 636262 ATTAACTTCATTTTCTGTGAGGACTCAATTGTCTCTCATCAGGGCTGA -s Anc0.Anc0refChr5 58735 48 + 87904 ACTGACTCTATATCCTGTGATATCAAAATTGTTTGTCATCAGCCCCAA -s Anc1.Anc1refChr7 16392 48 - 47259 ACTGACTCTATATCCTGTGATATCAAAATTGTTTGTCATCAGCCCCAA -s Anc2.Anc2refChr15 55340 48 + 86568 GCTGACTCTATATCCTGTGATATCAAAATTGTTCGTCATCAGCCTCAG -s mr.mrrefChr5 92785 48 + 294540 ATTAACTTCATTTTCTGTGATGACAAAATTGTTTGTCATCAGGGCTGA -s simCow_chr6.simCow.chr6 235951 48 + 602619 GCTGACTCTATATCCTGTGGTATCAAAACTATTTGTCATCAGCGTCAG -s simDog_chr6.simDog.chr6 227826 47 + 593897 GCTGACCTTATATTTTATGATATCAAAATTGTTCGTCATCGGTCTC-G -s simHuman_chr6.simHuman.chr6 318087 47 - 601863 ACTGACTCTATGTCCTGTGATATCAGAATTG-TTGTCAGAAGCCCCCA -s simRat_chr6.simRat.chr6 230263 48 + 647215 ATTAACTTCATTTTCTGTGATGACAAAATTGTTTGTCTTCAGGGCTGA - -a -s simMouse_chr6.simMouse.chr6 239712 14 + 636262 CTGTAGGTGGTCTA -s Anc0.Anc0refChr5 58783 14 + 87904 TTGTAAATAATCTG -s Anc1.Anc1refChr7 16440 14 - 47259 TTGTAAATAATCTG -s Anc2.Anc2refChr15 55388 14 + 86568 TTGTAAATAATCTG -s mr.mrrefChr5 92833 14 + 294540 TTGTAGATGGTCTA -s simCow_chr6.simCow.chr6 235999 14 + 602619 TTGTAGATAATTTG -s simDog_chr6.simDog.chr6 227873 14 + 593897 TTGTAAATAATCTG -s simHuman_chr6.simHuman.chr6 318135 14 - 601863 TTGTAAATAATCTG -s simRat_chr6.simRat.chr6 230311 13 + 647215 TTGTAGATGGT-TA - -a -s simMouse_chr6.simMouse.chr6 239726 46 + 636262 TGACCCGAAAAGATAGCCAAGGCAGACAATGAACAACTACTTTGAC -s Anc0.Anc0refChr5 58797 44 + 87904 TGGCCTCAGAAGATAGACAAAGCCCCAGATAAACAA--GCTTTGAT -s Anc1.Anc1refChr7 16454 44 - 47259 TGGCCTCAGAAGATAGACAAAGCCCCAGATAAACAA--GCTTTGAT -s Anc2.Anc2refChr15 55402 44 + 86568 TGGTCTCAGAAGATAAACAAGGCCCCAGATAAACAA--GCTTTGAC -s mr.mrrefChr5 92847 46 + 294540 TGGCCTGAAAAGATAGCCAAAGCAGAAAATGAACAACTACTTTGAT -s simCow_chr6.simCow.chr6 236027 44 + 602619 TGGTCTCAGGAGATAAACAAGGGTCCAGATAACCCA--TCCTTGAG -s simDog_chr6.simDog.chr6 227887 40 + 593897 TGGT----GAAGATAACCAAGGCCCCAAATAAAGAA--GCTTTGAC -s simHuman_chr6.simHuman.chr6 318149 44 - 601863 TGGCCTCAGAAGATGGACAAAGCCCTAGATAAACAA--GCTTTGAT -s simRat_chr6.simRat.chr6 230324 46 + 647215 TGGCCTGAAAAGATACCCAGAGCAGAAAATGAACAACTACTTTTGT - -a -s simMouse_chr6.simMouse.chr6 239772 10 + 636262 TCAAAGGCCT -s Anc0.Anc0refChr5 58841 10 + 87904 TCAAAGCCCT -s Anc1.Anc1refChr7 16498 10 - 47259 TCAAAGCCCT -s Anc2.Anc2refChr15 55446 10 + 86568 TCAAAGCCCT -s mr.mrrefChr5 92893 10 + 294540 TCAAAGGCCT -s simCow_chr6.simCow.chr6 236071 10 + 602619 TCAAAGTCTT -s simDog_chr6.simDog.chr6 227927 10 + 593897 ACAAAGCCCT -s simHuman_chr6.simHuman.chr6 318193 10 - 601863 TCAAAGCCCT -s simRat_chr6.simRat.chr6 230372 10 + 647215 TCAAAGACCT - -a -s simMouse_chr6.simMouse.chr6 239782 6 + 636262 CAACAT -s Anc0.Anc0refChr5 58883 6 + 87904 CTTCAT -s Anc1.Anc1refChr7 16540 6 - 47259 CTTCAT -s Anc2.Anc2refChr15 55488 6 + 86568 CTTAGT -s mr.mrrefChr5 92903 6 + 294540 CAACAT -s simCow_chr6.simCow.chr6 236113 6 + 602619 TTTATT -s simDog_chr6.simDog.chr6 227967 6 + 593897 CTTAGT -s simHuman_chr6.simHuman.chr6 318235 6 - 601863 CCGCAT -s simRat_chr6.simRat.chr6 230382 6 + 647215 CAACAT - -a -s simMouse_chr6.simMouse.chr6 239788 1 + 636262 T -s Anc0.Anc0refChr5 58889 1 + 87904 A -s Anc1.Anc1refChr7 16546 1 - 47259 A -s Anc2.Anc2refChr15 55494 1 + 86568 A -s mr.mrrefChr5 92909 1 + 294540 T -s simCow_chr6.simCow.chr6 236122 1 + 602619 A -s simDog_chr6.simDog.chr6 227973 1 + 593897 A -s simHuman_chr6.simHuman.chr6 318241 1 - 601863 A -s simRat_chr6.simRat.chr6 230388 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 239789 6 + 636262 TGAAGC -s Anc0.Anc0refChr5 58890 6 + 87904 TCTGAA -s Anc1.Anc1refChr7 16547 6 - 47259 TCTGAA -s Anc2.Anc2refChr15 55495 6 + 86568 TCTGAA -s mr.mrrefChr5 92910 6 + 294540 TCAAGC -s simCow_chr6.simCow.chr6 236123 6 + 602619 TCAGAA -s simDog_chr6.simDog.chr6 228011 6 + 593897 TCTGAA -s simHuman_chr6.simHuman.chr6 318242 6 - 601863 TCTGAA -s simRat_chr6.simRat.chr6 230389 6 + 647215 TCAACT - -a -s simMouse_chr6.simMouse.chr6 239795 18 + 636262 TGTACTGAGATGTTAGCC -s Anc0.Anc0refChr5 58896 18 + 87904 TGTACTGAGACATTGGCC -s Anc1.Anc1refChr7 16553 18 - 47259 TGTACTGAGACATTGGCC -s Anc2.Anc2refChr15 55503 18 + 86568 TGTACTGAGACATTGGCC -s mr.mrrefChr5 92916 18 + 294540 TGTACTGAGATGTTAGCC -s simCow_chr6.simCow.chr6 236131 18 + 602619 TGTACTGATACATTGGTC -s simDog_chr6.simDog.chr6 228019 18 + 593897 TGTACCAAGACATCAGCC -s simHuman_chr6.simHuman.chr6 318248 18 - 601863 TACACTGAGACATTGGCC -s simRat_chr6.simRat.chr6 230395 18 + 647215 TGTACTGAGATGTTAGCC - -a -s simMouse_chr6.simMouse.chr6 239813 162 + 636262 CAACTTGCAATACTAACCAGTAGTACTTCCTGGCCAGACAACAATAGTTTACTCCCATCAATTTGGGGGATAATTATACAAAGTATTACAACTGGTGCCATTTGAGTTAGCTATCAGCCTGGAGGATGCTGGGATTGCACCCTCAGATACTCATGTTACCTG -s Anc0.Anc0refChr5 58914 56 + 87904 CAACTTCCAGGCCT----AGTAGTACTTCCAGGCCTAATAGTAATAGTTCACTTCCA------------------------------------------------------------------------------------------------------CTG -s Anc1.Anc1refChr7 16571 56 - 47259 CAACTTCCAGGCCT----AGTAGTACTTCCAGGCCTAATAGTAATAGTTCACTTCCA------------------------------------------------------------------------------------------------------CTG -s Anc2.Anc2refChr15 55524 56 + 86568 CAACTTCCAGGCCC----AATGGTACTTCCAGGCCTAATAGTAATAGCTCACTTCCA------------------------------------------------------------------------------------------------------ATG -s mr.mrrefChr5 92934 151 + 294540 CAACTTCCAGTCCTAACCAGTAGTACTTCCAGGCCAGACAACAATAGTTTACTCCCATCAATTTGGGGG----TTATACAAAGTATTACAACTGGTGCCA------TTAGCTATCAGCCTGGAGGATGCT-GGATTGCACCCTCATATACTCATGTTACCTG -s simCow_chr6.simCow.chr6 236152 56 + 602619 CAACTTCCAGGCCC----AATGGTACTTCCAGGCCTATTAGTAATAGCTCATGTCTA------------------------------------------------------------------------------------------------------ATG -s simDog_chr6.simDog.chr6 228040 55 + 593897 CAACTTCCAGGACC----AATGGTACTTCCAGGACAAATAGTA-TAGCTCACTTCCA------------------------------------------------------------------------------------------------------ATG -s simHuman_chr6.simHuman.chr6 318266 56 - 601863 CAATGTCTGGGCCT----AGTAGTACTTCCAGGCCTAATAGTAGTAGTTCACTTCCA------------------------------------------------------------------------------------------------------CTG -s simRat_chr6.simRat.chr6 230413 140 + 647215 CAACTTCCAGTCCTACATAGTAGTACTTCCAGACCAGACAACACTAGTTTACTCCCATCACTTTGGGGG----TTATACAAAGTATCACAACTGGTGTCA------TTAGCTATCAGTCTGAAGGATGCT-GGATTGCACCCTCATATATT----------- - -a -s simMouse_chr6.simMouse.chr6 239975 2 + 636262 TC -s Anc0.Anc0refChr5 58970 2 + 87904 TA -s Anc1.Anc1refChr7 16627 2 - 47259 TA -s Anc2.Anc2refChr15 55581 2 + 86568 TA -s mr.mrrefChr5 93085 2 + 294540 TC -s simCow_chr6.simCow.chr6 236209 2 + 602619 TA -s simDog_chr6.simDog.chr6 228096 2 + 593897 TA -s simHuman_chr6.simHuman.chr6 318322 2 - 601863 TA - -a -s simMouse_chr6.simMouse.chr6 239977 15 + 636262 TCCTGTTACCTGTTT -s Anc0.Anc0refChr5 58975 15 + 87904 CCATGTTACCTGTTT -s Anc1.Anc1refChr7 16632 15 - 47259 CCATGTTACCTGTTT -s Anc2.Anc2refChr15 55586 15 + 86568 CCATGTTACCTGTGT -s mr.mrrefChr5 93087 15 + 294540 TCCTGTTACCTGTTT -s simCow_chr6.simCow.chr6 236214 15 + 602619 CCCTAATACTGGTGT -s simDog_chr6.simDog.chr6 228101 15 + 593897 CCATGTTACCTGTGT -s simHuman_chr6.simHuman.chr6 318327 15 - 601863 ACATGTCACCTGTTT -s simRat_chr6.simRat.chr6 230553 14 + 647215 -TGTGTAACCTGTGT - -a -s simMouse_chr6.simMouse.chr6 239992 23 + 636262 GCAGTAGATGCTTTGGTAAAATA -s Anc0.Anc0refChr5 58990 23 + 87904 GCAGTAGTAACCAGGGTAAAGCA -s Anc1.Anc1refChr7 16647 23 - 47259 GCAGTAGTAACCAGGGTAAAGCA -s Anc2.Anc2refChr15 55601 23 + 86568 GCAGTAGTAACCAGGGTAAAGCA -s mr.mrrefChr5 93102 23 + 294540 GCAGTAGATGCTTGGGTAAAGTA -s simCow_chr6.simCow.chr6 236230 23 + 602619 GCTGTAGTGAGCAGGGTAAAGTA -s simDog_chr6.simDog.chr6 228116 22 + 593897 GCAGT-GTAACCAATGGAAAGCA -s simHuman_chr6.simHuman.chr6 318342 23 - 601863 GCAGTAGTCACCAGGGTAATGCA -s simRat_chr6.simRat.chr6 230567 23 + 647215 GCAGTAGATGGTTGGGTAAAGTA - -a -s simMouse_chr6.simMouse.chr6 240015 6 + 636262 CAGCTA -s Anc0.Anc0refChr5 59014 6 + 87904 CAGTGG -s Anc1.Anc1refChr7 16671 6 - 47259 CAGTGG -s Anc2.Anc2refChr15 55625 6 + 86568 CAGTGG -s mr.mrrefChr5 93126 6 + 294540 CAGCTA -s simCow_chr6.simCow.chr6 236254 6 + 602619 CAATGG -s simDog_chr6.simDog.chr6 228139 6 + 593897 CAGTGC -s simHuman_chr6.simHuman.chr6 318366 6 - 601863 CAGTGG -s simRat_chr6.simRat.chr6 230591 6 + 647215 CAGCCA - -a -s simMouse_chr6.simMouse.chr6 240021 5 + 636262 AAGGC -s Anc0.Anc0refChr5 59021 5 + 87904 AAGGC -s Anc1.Anc1refChr7 16678 5 - 47259 AAGGC -s Anc2.Anc2refChr15 55632 5 + 86568 AAGGC -s mr.mrrefChr5 93132 5 + 294540 AAGGC -s simCow_chr6.simCow.chr6 236261 5 + 602619 AAGGC -s simDog_chr6.simDog.chr6 228146 5 + 593897 AAGGC -s simHuman_chr6.simHuman.chr6 318373 5 - 601863 AAGGC -s simRat_chr6.simRat.chr6 230597 5 + 647215 GAGGC - -a -s simMouse_chr6.simMouse.chr6 240026 16 + 636262 TATGATCCGCCATTCA -s Anc0.Anc0refChr5 59026 16 + 87904 TAAAACCTACCATCTA -s Anc1.Anc1refChr7 16683 16 - 47259 TAAAACCTACCATCTA -s Anc2.Anc2refChr15 55637 16 + 86568 TAAAGCCTACTATCTA -s mr.mrrefChr5 93137 16 + 294540 TATGATCCACCATTCA -s simCow_chr6.simCow.chr6 236270 16 + 602619 TAAAGCCTTCAATCTA -s simDog_chr6.simDog.chr6 228151 16 + 593897 TAAAGCCTACTATCAA -s simHuman_chr6.simHuman.chr6 318378 16 - 601863 TAATACTGACCATCTA -s simRat_chr6.simRat.chr6 230602 16 + 647215 CACAATCCACCATTCA - -a -s simMouse_chr6.simMouse.chr6 240042 23 + 636262 CTGCTTATAAGAGTGAACATGGA -s Anc0.Anc0refChr5 59042 23 + 87904 CTGCTCATGCAGGCAGATACGGA -s Anc1.Anc1refChr7 16699 23 - 47259 CTGCTCATGCAGGCAGATACGGA -s Anc2.Anc2refChr15 55660 23 + 86568 CTGCTCATGCAGGCAGATACAGC -s mr.mrrefChr5 93153 23 + 294540 CTGCTCATAAGAGTGAACATGGA -s simCow_chr6.simCow.chr6 236293 23 + 602619 CTGCTCATGAAGGCAGATAGGGC -s simDog_chr6.simDog.chr6 228174 23 + 593897 CTGCTCATGCAGGCAGATACAGC -s simHuman_chr6.simHuman.chr6 318394 10 - 601863 CCATTCA-------------GAA -s simRat_chr6.simRat.chr6 230618 23 + 647215 CTGCTCATAAGAGTGAATATGCA - -a -s simMouse_chr6.simMouse.chr6 240065 26 + 636262 TCCCAGTGAAGCAGGCTAGTGAGGTT -s Anc0.Anc0refChr5 59065 26 + 87904 CCCCAATAAAACAGGCTTGTAAGGTT -s Anc1.Anc1refChr7 16722 26 - 47259 CCCCAATAAAACAGGCTTGTAAGGTT -s Anc2.Anc2refChr15 55683 26 + 86568 CCCCAATAAAACAGGCTTGTAAGGTT -s mr.mrrefChr5 93176 26 + 294540 TCCCAATGAAGCAGGCTAGTGAGGTT -s simCow_chr6.simCow.chr6 236335 26 + 602619 CCTGAATAAAGCAGGTTTGTAAGGTT -s simDog_chr6.simDog.chr6 228197 26 + 593897 CCCCAATAAAACAGGCTTGTAATGTC -s simHuman_chr6.simHuman.chr6 318404 26 - 601863 CCCCAATAAAACAGGCTTGTAAGGTT -s simRat_chr6.simRat.chr6 230641 26 + 647215 TCCCAATGAAGCAGGCTAGTGAGGTT - -a -s simMouse_chr6.simMouse.chr6 240091 8 + 636262 AGAATCTA -s Anc0.Anc0refChr5 59091 8 + 87904 GGACTCCA -s Anc1.Anc1refChr7 16748 8 - 47259 GGACTCCA -s Anc2.Anc2refChr15 55709 8 + 86568 GGATTCCA -s mr.mrrefChr5 93202 8 + 294540 AGACTCCA -s simCow_chr6.simCow.chr6 236361 7 + 602619 GGGTATC- -s simDog_chr6.simDog.chr6 228224 8 + 593897 GGATTCCA -s simHuman_chr6.simHuman.chr6 318430 8 - 601863 GGACTCCA -s simRat_chr6.simRat.chr6 230667 8 + 647215 AGACTCCA - -a -s simMouse_chr6.simMouse.chr6 240099 10 + 636262 AATTACTATA -s Anc0.Anc0refChr5 59099 10 + 87904 AATTACTAGA -s Anc1.Anc1refChr7 16756 10 - 47259 AATTACTAGA -s Anc2.Anc2refChr15 55717 10 + 86568 TATCACTAGA -s mr.mrrefChr5 93210 10 + 294540 AATTACTATA -s simCow_chr6.simCow.chr6 236368 7 + 602619 ---CACTAGA -s simDog_chr6.simDog.chr6 228232 10 + 593897 TATCACTAGA -s simHuman_chr6.simHuman.chr6 318439 10 - 601863 ATTTGCTAGA -s simRat_chr6.simRat.chr6 230675 10 + 647215 AATTAATTTA - -a -s simMouse_chr6.simMouse.chr6 240109 9 + 636262 GGGGTGCCA -s Anc0.Anc0refChr5 59109 9 + 87904 GGATTGCCA -s Anc1.Anc1refChr7 16766 9 - 47259 GGATTGCCA -s Anc2.Anc2refChr15 55727 9 + 86568 GTATTGCCA -s mr.mrrefChr5 93220 9 + 294540 GGGGTGCCA -s simCow_chr6.simCow.chr6 236375 9 + 602619 GCATTACCA -s simDog_chr6.simDog.chr6 228242 9 + 593897 GTATTGCCA -s simHuman_chr6.simHuman.chr6 318449 9 - 601863 TGATTGTCA -s simRat_chr6.simRat.chr6 230687 9 + 647215 GGGCTGCCA - -a -s simMouse_chr6.simMouse.chr6 240118 32 + 636262 ATAAATGGTGAGCCGACTGCCCTCTTGGGCTA -s Anc0.Anc0refChr5 59119 32 + 87904 TACAATGGTGAATGGATGTCCCTCTGGAGCTA -s Anc1.Anc1refChr7 16776 32 - 47259 TACAATGGTGAATGGATGTCCCTCTGGAGCTA -s Anc2.Anc2refChr15 55737 32 + 86568 TATAATGGTGAATGGATGTCTCTCTGGAGCTA -s mr.mrrefChr5 93230 32 + 294540 AACAATGGTGAATCGACTGCCCTCTGGGGCTA -s simCow_chr6.simCow.chr6 236385 32 + 602619 TATAATGGTGAATGGATATCACTGTGAAGCTA -s simDog_chr6.simDog.chr6 228252 32 + 593897 TATGGTGGTGAATGGATGCCTCTCTGGAACTA -s simHuman_chr6.simHuman.chr6 318459 32 - 601863 TACAATGGTGAATGGATGTCCCTATGGAGCTA -s simRat_chr6.simRat.chr6 230697 32 + 647215 AACAATGGTGAATCAACTGTCCTCTGGGGCTA - -a -s simMouse_chr6.simMouse.chr6 240150 16 + 636262 TAATCTTCTCACCTAT -s Anc0.Anc0refChr5 59154 16 + 87904 TAATCTTCTCACATAC -s Anc1.Anc1refChr7 16811 16 - 47259 TAATCTTCTCACATAC -s Anc2.Anc2refChr15 55772 16 + 86568 TAATCTTCTCACATGC -s mr.mrrefChr5 93262 16 + 294540 TAATCTTCTCACATAC -s simCow_chr6.simCow.chr6 236420 16 + 602619 TCATCTTCTCCTGCCC -s simDog_chr6.simDog.chr6 228287 16 + 593897 TAATCTTATCACATGC -s simHuman_chr6.simHuman.chr6 318494 16 - 601863 TACTCTTCCCACATAC -s simRat_chr6.simRat.chr6 230729 16 + 647215 TAATCTTCTCACATAC - -a -s simMouse_chr6.simMouse.chr6 240166 4 + 636262 CTCA -s Anc0.Anc0refChr5 59170 4 + 87904 TTCA -s Anc1.Anc1refChr7 16827 4 - 47259 TTCA -s Anc2.Anc2refChr15 55788 4 + 86568 TTCA -s mr.mrrefChr5 93278 4 + 294540 CTCA -s simCow_chr6.simCow.chr6 236437 4 + 602619 TTTG -s simDog_chr6.simDog.chr6 228303 4 + 593897 TTCA -s simHuman_chr6.simHuman.chr6 318510 4 - 601863 TTCA -s simRat_chr6.simRat.chr6 230745 4 + 647215 CTCA - -a -s simMouse_chr6.simMouse.chr6 240170 11 + 636262 CCGCAATCATC -s Anc0.Anc0refChr5 59175 11 + 87904 CCACAACCAAC -s Anc1.Anc1refChr7 16832 11 - 47259 CCACAACCAAC -s Anc2.Anc2refChr15 55793 11 + 86568 CCACAACCAAC -s mr.mrrefChr5 93282 11 + 294540 CCGCAACCATC -s simCow_chr6.simCow.chr6 236442 11 + 602619 CCGCAACCAAC -s simDog_chr6.simDog.chr6 228308 11 + 593897 CCACAACCAAT -s simHuman_chr6.simHuman.chr6 318515 11 - 601863 CCATAACCAGC -s simRat_chr6.simRat.chr6 230749 11 + 647215 CCGCAACCAAC - -a -s simMouse_chr6.simMouse.chr6 240181 15 + 636262 TTGACTATGTCCACG -s Anc0.Anc0refChr5 59200 15 + 87904 TAAAGCATGTCCATC -s Anc1.Anc1refChr7 16858 15 - 47259 TAAAGCATGTCCATC -s Anc2.Anc2refChr15 55818 15 + 86568 TAAAGCATCTCCATC -s mr.mrrefChr5 93308 15 + 294540 TTAACTATGTCCACG -s simCow_chr6.simCow.chr6 236467 15 + 602619 TTGAACATACCCTTC -s simDog_chr6.simDog.chr6 228333 15 + 593897 TAAAGCATCTCCATC -s simHuman_chr6.simHuman.chr6 318541 15 - 601863 CAAAGCTTGGCCATC -s simRat_chr6.simRat.chr6 230775 15 + 647215 TTAACTATGTCCACG - -a -s simMouse_chr6.simMouse.chr6 240196 23 + 636262 TTGGTCTTGAGTATTACCCCTTC -s Anc0.Anc0refChr5 59215 23 + 87904 TAGGTCTCGAGTATTACTCCTTC -s Anc1.Anc1refChr7 16873 23 - 47259 TAGGTCTCGAGTATTACTCCTTC -s Anc2.Anc2refChr15 55833 23 + 86568 TAGGTATCGAGTATTACTCCCTC -s mr.mrrefChr5 93323 23 + 294540 TAGGTCTTGAGTATTACCCCTTC -s simCow_chr6.simCow.chr6 236532 23 + 602619 TAGGCATCAAGTATTACTCCCTC -s simDog_chr6.simDog.chr6 228348 21 + 593897 TAATTATTG--TGCTACTCCCTC -s simHuman_chr6.simHuman.chr6 318556 23 - 601863 TAGGTCTCGAGTATTACACCTTC -s simRat_chr6.simRat.chr6 230790 23 + 647215 TAGGTGTTGAGTATTACCCCTTC - -a -s simMouse_chr6.simMouse.chr6 240219 11 + 636262 CCCATTGAGGG -s Anc0.Anc0refChr5 59253 11 + 87904 TCCATAGGGGG -s Anc1.Anc1refChr7 16911 11 - 47259 TCCATAGGGGG -s Anc2.Anc2refChr15 55871 11 + 86568 TCCATAGGGGG -s mr.mrrefChr5 93346 11 + 294540 CCCATTGAGGG -s simCow_chr6.simCow.chr6 236570 11 + 602619 TCCATAAGAGG -s simDog_chr6.simDog.chr6 228384 11 + 593897 TCCATAGGGGG -s simHuman_chr6.simHuman.chr6 318594 11 - 601863 TCCATAGGGGG -s simRat_chr6.simRat.chr6 230813 11 + 647215 CAGATTGAGGG - -a -s simMouse_chr6.simMouse.chr6 240230 10 + 636262 GATCTTATAC -s Anc0.Anc0refChr5 59264 10 + 87904 GATTTTAAAC -s Anc1.Anc1refChr7 16922 10 - 47259 GATTTTAAAC -s Anc2.Anc2refChr15 55888 10 + 86568 GATTTTAAAC -s mr.mrrefChr5 93357 10 + 294540 GATCTTATAC -s simCow_chr6.simCow.chr6 236587 10 + 602619 GATTTCATAC -s simDog_chr6.simDog.chr6 228401 10 + 593897 GATTTTAAAC -s simHuman_chr6.simHuman.chr6 318605 10 - 601863 AATTTTAGAC -s simRat_chr6.simRat.chr6 230824 10 + 647215 GATCTTATAC - -a -s simMouse_chr6.simMouse.chr6 240240 59 + 636262 AGGAGAAAATTTCCTTATGGATACTTTTAGAGTAAACTCTGATAATACGGTCAGCCCAT -s Anc0.Anc0refChr5 59275 59 + 87904 GGGAGACAACCTCCTTACAGCTACTTTTGGAGTATGCTCAAACAATACAGACAGCCCAC -s Anc1.Anc1refChr7 16933 59 - 47259 GGGAGACAACCTCCTTACAGCTACTTTTGGAGTATGCTCAAACAATACAGACAGCCCAC -s Anc2.Anc2refChr15 55899 59 + 86568 GGGAGACAACCTCCTCACAGCTACTTCTGGAGTATGCCCAAACAATACAGACAGCCCAC -s mr.mrrefChr5 93368 59 + 294540 GGGAGAAAATTTCCTTATGGATACTTTTAGAGTATACTCTGATAATACGGTCAGCCCAT -s simCow_chr6.simCow.chr6 236598 59 + 602619 AGGAGATAAACTCCCCAGTGCTACTTCTGGGGTATACCCATACAATACAGTCAGCCCAC -s simDog_chr6.simDog.chr6 228412 58 + 593897 GGAAGACAGCCTCCTCACAGCAATGTCTGGAGTATGCCTAAACAATCAAGACAG-CTAC -s simHuman_chr6.simHuman.chr6 318616 58 - 601863 GGGGTACAACCTCCTTAC-GCTACTTTTGGAGTATGCTCACACAATACAGGCAGTCCAC -s simRat_chr6.simRat.chr6 230835 59 + 647215 GGGAGAAAATTTCCCTATAGACATTTTTAGAGTATACTCTGATAACACTGTCAGCCCAT - -a -s simMouse_chr6.simMouse.chr6 240299 55 + 636262 TTATATATGCTTTGCCTTGCAACAACCCAGCAGAGTTCAAGCGCACTCAGCTGGC -s Anc0.Anc0refChr5 59366 55 + 87904 TTACACATACTTTGCATTGTCAAAACCTTGTGGAGTGCAGGAGTATTCAGTGAGC -s Anc1.Anc1refChr7 17024 55 - 47259 TTACACATACTTTGCATTGTCAAAACCTTGTGGAGTGCAGGAGTATTCAGTGAGC -s Anc2.Anc2refChr15 55990 55 + 86568 TTACACAGACTTTGCATTTTCAAAACCCTGTGGAGTGCAGGAGTATTCAGTGAGC -s mr.mrrefChr5 93427 55 + 294540 TTATATATGCTTTGCCTTGCAACAACCTAGCAGAGTTCAAGCGCACTCAGCTGGC -s simCow_chr6.simCow.chr6 236695 55 + 602619 TTACACAAACTTTGCATTTTCGCAACCCAATGGAGTGCAGGATTATTCAATGGGC -s simDog_chr6.simDog.chr6 228502 52 + 593897 TTACACAGACATTGCATC---AAAACCCTGCGGAGTTCAGGAGCATTCAGTTAGA -s simHuman_chr6.simHuman.chr6 318706 55 - 601863 TTAGACATAATTTGCATTGTTATAAACTTGTCGGGTGCAGGAGTATTCAGTGAGC -s simRat_chr6.simRat.chr6 230894 54 + 647215 TTATATATGCTTTGCCCTGCAACAACCTAGCA-AATTCAAGGGCACTCAGCTGAC - -a -s simMouse_chr6.simMouse.chr6 240354 29 + 636262 AGGATTATTGACCCTATGAGTGAATTAAA -s Anc0.Anc0refChr5 59423 29 + 87904 AAAATGTGGGCCCTACTGAGTAAATTAAG -s Anc1.Anc1refChr7 17081 29 - 47259 AAAATGTGGGCCCTACTGAGTAAATTAAG -s Anc2.Anc2refChr15 56047 29 + 86568 GAATTGTGGGCCCTACTGAGTAAATTAAG -s mr.mrrefChr5 93482 29 + 294540 AGGATTATTGACCCTATGAGTGAATTAAG -s simCow_chr6.simCow.chr6 236752 26 + 602619 GAAGTA---GCCCTACTGAGTAAATTAAG -s simDog_chr6.simDog.chr6 228555 27 + 593897 --ATTGTGGGCCGTACTGAGTAAATTAAG -s simHuman_chr6.simHuman.chr6 318763 29 - 601863 AAAATGGGCGCCCTACTGAGTAAATTAAG -s simRat_chr6.simRat.chr6 230948 29 + 647215 AGGGTTATTGACCCTATGAGTGAATTAAG - -a -s simMouse_chr6.simMouse.chr6 240383 32 + 636262 GGTCGCATTGTGGGTACTAATGATGTGTCCAA -s Anc0.Anc0refChr5 59452 32 + 87904 GGTAAGGCTGCTGGTAATAATGATGTCTCTAA -s Anc1.Anc1refChr7 17110 32 - 47259 GGTAAGGCTGCTGGTAATAATGATGTCTCTAA -s Anc2.Anc2refChr15 56076 32 + 86568 GGTAAGGCTGCTGGTATTAGTGATGTCTCTTA -s mr.mrrefChr5 93511 32 + 294540 GGTCGCATTGTGGGTAATAATGATGTGTCCAA -s simCow_chr6.simCow.chr6 236778 32 + 602619 GGTAAATCTGCAGGTATCATTGTTGTCACTTA -s simDog_chr6.simDog.chr6 228584 28 + 593897 GGCAAGGCTGCTGGTATTAGTGATGTCT---- -s simHuman_chr6.simHuman.chr6 318792 32 - 601863 GGTGAGGCTGCCAGTAATAATGATGTCTCTAA -s simRat_chr6.simRat.chr6 230977 19 + 647215 GGT-------------ATAATGATGCGTCCAG - -a -s simMouse_chr6.simMouse.chr6 240415 34 + 636262 AATTGCATTCAGGTTTAAAGTGGTCTCCAAGTCT -s Anc0.Anc0refChr5 59485 34 + 87904 AATAGCATTCAAATCTAAAGTGGTATCCAAATTT -s Anc1.Anc1refChr7 17143 34 - 47259 AATAGCATTCAAATCTAAAGTGGTATCCAAATTT -s Anc2.Anc2refChr15 56109 34 + 86568 GATAGCATTCAAATCTAAAGCAGTATCTAAATTT -s mr.mrrefChr5 93543 34 + 294540 AATAGCATTCAGATTTAAAGTGGTCTCCAAGTCT -s simCow_chr6.simCow.chr6 236811 34 + 602619 GATAGCATTTAAACCTCAAGCAGCATCAAAATTT -s simDog_chr6.simDog.chr6 228612 28 + 593897 ------AGTCAAATTTAGAGCACTATCTTTAGTT -s simHuman_chr6.simHuman.chr6 318825 34 - 601863 AATAGAATTCAAATCTAAAGTGGTATCCAAATTT -s simRat_chr6.simRat.chr6 230996 34 + 647215 AATAGCATTCAGATTTAAAGTGGTCTCCAAGTCT - -a -s simMouse_chr6.simMouse.chr6 240449 45 + 636262 CTCCTGTCAGAACTATAACGAACGCTCCTGTCAGAGTTATAATGT -s Anc0.Anc0refChr5 59523 16 + 87904 CTCCTCTTAGAAA-----------------------------TCT -s Anc1.Anc1refChr7 17181 16 - 47259 CTCCTCTTAGAAA-----------------------------TCT -s Anc2.Anc2refChr15 56147 16 + 86568 CTCCTCCTAGAAA-----------------------------TCT -s mr.mrrefChr5 93577 16 + 294540 CTCCTGTCAGAAC-----------------------------TGT -s simCow_chr6.simCow.chr6 236849 16 + 602619 ATACTTCTAGAAA-----------------------------TCT -s simDog_chr6.simDog.chr6 228644 16 + 593897 CTCGTCCTAGAAA-----------------------------TCT -s simHuman_chr6.simHuman.chr6 318863 16 - 601863 CTCCTCTTGGAAA-----------------------------TCT -s simRat_chr6.simRat.chr6 231030 16 + 647215 CTCCTGTCAGAAT-----------------------------TGT - -a -s simMouse_chr6.simMouse.chr6 240494 20 + 636262 ATAAATAAAAATCAATGTGG -s Anc0.Anc0refChr5 59545 20 + 87904 ATAAATGCTAATCAATGTGA -s Anc1.Anc1refChr7 17203 20 - 47259 ATAAATGCTAATCAATGTGA -s Anc2.Anc2refChr15 56169 20 + 86568 ATAAATGCTAATCTATGTGA -s mr.mrrefChr5 93593 20 + 294540 ATAAATGATAATCAATGTGA -s simCow_chr6.simCow.chr6 236872 20 + 602619 ATAAATGCTAGTCTATTTGA -s simDog_chr6.simDog.chr6 228666 20 + 593897 ATAATTCCTAATCTATGTGA -s simHuman_chr6.simHuman.chr6 318885 20 - 601863 ACAAATGCTAATTAATGTGA -s simRat_chr6.simRat.chr6 231046 20 + 647215 ATAAATGGTAGTCAATATGA - -a -s simMouse_chr6.simMouse.chr6 240514 15 + 636262 CTTCAGCCTTTTTTA -s Anc0.Anc0refChr5 59567 15 + 87904 TATAGGCTTGTTTAA -s Anc1.Anc1refChr7 17225 15 - 47259 TATAGGCTTGTTTAA -s Anc2.Anc2refChr15 56191 15 + 86568 TATAGACTTGGTTAA -s mr.mrrefChr5 93613 15 + 294540 CTTCGGCCTTTTTTA -s simCow_chr6.simCow.chr6 236894 14 + 602619 T-TAGATGTGGTTAA -s simDog_chr6.simDog.chr6 228688 15 + 593897 TATAGACTTGGATAA -s simHuman_chr6.simHuman.chr6 318907 15 - 601863 TATAGGCTTATTTAA -s simRat_chr6.simRat.chr6 231066 15 + 647215 CTTTGGCCTTTCTTA - -a -s simMouse_chr6.simMouse.chr6 240529 133 + 636262 AGTCCCAAGCACTTATAGAACTCGATCCAAATTGTACTTAGTTACGGGTCCTTCTCCTTGCCATTTCCCCAGGATCTAGTGTCCATAGCCACCCCTTGTTCCTCTCTGACAGGGAAGATTACATCCACACTTT -s Anc0.Anc0refChr5 59583 90 + 87904 GGTCCTGAGCACTTACAGAACTCAATTGAAATTGTACTTA-----AA--------------------------------------CAAATAAAAAAAGTTCCTCTCTGAAAAGGAACATCACTTCAACATTTT -s Anc1.Anc1refChr7 17241 90 - 47259 GGTCCTGAGCACTTACAGAACTCAATTGAAATTGTACTTA-----AA--------------------------------------CAAATAAAAAAAGTTCCTCTCTGAAAAGGAACATCACTTCAACATTTT -s Anc2.Anc2refChr15 56207 90 + 86568 GGTCATAAGCACTTACAGAACTCAATTGAAATTGTACTTA-----AA--------------------------------------CAAATAAAAAAAGTTCCTCTGTAAAAAGGAACATCACTTCAACATTTT -s mr.mrrefChr5 93629 97 + 294540 AGTCCCGAGCACTTATAGAACTCAATCCAAATTGTACTTA-----GGGTCCTTC-------------------------------TAGCCACCCCTTGTTCCTCTCTGACAGGGAAGATTACATCAACACTTT -s simCow_chr6.simCow.chr6 236909 84 + 602619 GG------ACACCTACAGCACTCAATTGATATTGTACTTA-----AA--------------------------------------CTAATAAAAAAAGTTCCTCTATAGAAAGGAACATCACTTCAACAATTT -s simDog_chr6.simDog.chr6 228704 90 + 593897 GGTCATAAGTACTTACAGAACTCAATTGAAATTGAACTTA-----AA--------------------------------------CAAATTAAAAAAGTTCCTCTGCAAAAAGAAACATTACTTCAATCTTCT -s simHuman_chr6.simHuman.chr6 318923 90 - 601863 GGTCCTGAGCACTCACAGAACTCAATTGTAGTTGTACTTA-----AA--------------------------------------CAAATAAAAAGAGTTCCTCTCTGAAAAAGAACATCACTTCAACATTTT -s simRat_chr6.simRat.chr6 231082 97 + 647215 AGCCCCGAGCACTTATAGAGCTCAATCCAAATTGTACTTA-----GGGTCCTTC-------------------------------TAGCCACCCCTTGTTCCTCTCTGACAGGGAAGATTACATCAACACTTT - -a -s simMouse_chr6.simMouse.chr6 240662 11 + 636262 TACATGATTAT -s Anc0.Anc0refChr5 59677 11 + 87904 TTCATGATCAG -s Anc1.Anc1refChr7 17335 11 - 47259 TTCATGATCAG -s Anc2.Anc2refChr15 56301 11 + 86568 TTCATGAACAG -s mr.mrrefChr5 93730 11 + 294540 TACATGATTAT -s simCow_chr6.simCow.chr6 236997 4 + 602619 ATCA------- -s simDog_chr6.simDog.chr6 228798 11 + 593897 TTCATGAACAG -s simHuman_chr6.simHuman.chr6 319017 11 - 601863 TTCATGATCAG -s simRat_chr6.simRat.chr6 231183 11 + 647215 TCTATGATAAT - -a -s simMouse_chr6.simMouse.chr6 240673 2 + 636262 TC -s Anc0.Anc0refChr5 59688 2 + 87904 AT -s Anc1.Anc1refChr7 17346 2 - 47259 AT -s Anc2.Anc2refChr15 56314 2 + 86568 AT -s mr.mrrefChr5 93741 2 + 294540 TC -s simCow_chr6.simCow.chr6 237003 2 + 602619 AT -s simDog_chr6.simDog.chr6 228812 2 + 593897 AT -s simHuman_chr6.simHuman.chr6 319028 2 - 601863 GT -s simRat_chr6.simRat.chr6 231194 2 + 647215 TC - -a -s simMouse_chr6.simMouse.chr6 240675 22 + 636262 TAGTTCTTGGCGCATTTTTCTG -s Anc0.Anc0refChr5 59690 8 + 87904 AA--------------TTTCTG -s Anc1.Anc1refChr7 17348 8 - 47259 AA--------------TTTCTG -s Anc2.Anc2refChr15 56316 8 + 86568 AA--------------TTTCTG -s mr.mrrefChr5 93743 22 + 294540 TAGTTCTTGGCGCATTTTTCTG -s simCow_chr6.simCow.chr6 237005 8 + 602619 AG--------------TTTTTG -s simDog_chr6.simDog.chr6 228814 8 + 593897 AA--------------TTTCTG -s simHuman_chr6.simHuman.chr6 319030 8 - 601863 AA--------------CTTCTA -s simRat_chr6.simRat.chr6 231197 22 + 647215 TAGTCCCTGATCCATTTTTCTC - -a -s simMouse_chr6.simMouse.chr6 240697 17 + 636262 TACTAGCCATATCATAA -s Anc0.Anc0refChr5 59698 17 + 87904 TACTACTCATTTCATAA -s Anc1.Anc1refChr7 17356 17 - 47259 TACTACTCATTTCATAA -s Anc2.Anc2refChr15 56328 17 + 86568 TACTACTCATTTCATAA -s mr.mrrefChr5 93765 17 + 294540 TACTAGTCATATCATAA -s simCow_chr6.simCow.chr6 237017 17 + 602619 AACTACTTATTACATAA -s simDog_chr6.simDog.chr6 228832 17 + 593897 TACTACTCATCTCATAA -s simHuman_chr6.simHuman.chr6 319038 17 - 601863 TACTACTCATTGCATAA -s simRat_chr6.simRat.chr6 231219 17 + 647215 TACTAGTCATATCATAA - -a -s simMouse_chr6.simMouse.chr6 240714 21 + 636262 CTAAGGTAGGCCTAGAATGGA -s Anc0.Anc0refChr5 59727 18 + 87904 CTAAGGTAAG-TTATTAT--A -s Anc1.Anc1refChr7 17385 18 - 47259 CTAAGGTAAG-TTATTAT--A -s Anc2.Anc2refChr15 56357 18 + 86568 CTCAGGTAAG-TTATTAT--A -s mr.mrrefChr5 93782 20 + 294540 CTAAGGTAAG-CTAGAATGGA -s simDog_chr6.simDog.chr6 228904 18 + 593897 CTCAGGTAAG-TTATTAT--A -s simHuman_chr6.simHuman.chr6 319067 18 - 601863 CCAGGGTAAG-TTATTAT--A -s simRat_chr6.simRat.chr6 231236 20 + 647215 CTAAGGTAAG-CTAGAATGGA - -a -s simMouse_chr6.simMouse.chr6 240735 18 + 636262 ATCAGGACCTAGGAGACT -s Anc0.Anc0refChr5 59745 11 + 87904 AGCAGAGCC-------CA -s Anc1.Anc1refChr7 17403 11 - 47259 AGCAGAGCC-------CA -s Anc2.Anc2refChr15 56375 11 + 86568 AGTAAAGCT-------CA -s mr.mrrefChr5 93802 18 + 294540 ATCAGGACCTAGGAGACT -s simDog_chr6.simDog.chr6 228924 11 + 593897 AGTAAAGCT-------CA -s simHuman_chr6.simHuman.chr6 319085 11 - 601863 AGCAGAGCC-------CC -s simRat_chr6.simRat.chr6 231256 18 + 647215 ATCAGGATCTAGGAGACT - -a -s simMouse_chr6.simMouse.chr6 240753 17 + 636262 GGACCATCTAAAACACA -s Anc0.Anc0refChr5 59756 17 + 87904 AAACTGTCAAAACCACA -s Anc1.Anc1refChr7 17414 17 - 47259 AAACTGTCAAAACCACA -s Anc2.Anc2refChr15 56386 17 + 86568 AAACTGTCAAAACCATG -s mr.mrrefChr5 93820 17 + 294540 GAACCATCTAAAACACA -s simCow_chr6.simCow.chr6 237035 8 + 602619 -AACTGTCA-------- -s simDog_chr6.simDog.chr6 228943 17 + 593897 AAGCTATCCAAACCATG -s simHuman_chr6.simHuman.chr6 319096 17 - 601863 AAACTGTCAAAACAGCA -s simRat_chr6.simRat.chr6 231274 17 + 647215 GAACCATCTAAAGCACA - -a -s simMouse_chr6.simMouse.chr6 240770 26 + 636262 AAGGTATATACCCATACTCTGAGTGG -s Anc0.Anc0refChr5 59774 26 + 87904 AAGGTGTAACCCTATACTCTTACTGG -s Anc1.Anc1refChr7 17432 26 - 47259 AAGGTGTAACCCTATACTCTTACTGG -s Anc2.Anc2refChr15 56404 26 + 86568 AAGGTGTAACCCTGTGCTCTTACCTG -s mr.mrrefChr5 93838 26 + 294540 AAGGTATATCCCCATACTCTTACTGG -s simCow_chr6.simCow.chr6 237044 26 + 602619 AAGATGTAAACGTGCGCTATCATGTG -s simDog_chr6.simDog.chr6 228961 26 + 593897 AAGGTATAACCCTGTGCTCTTACCTG -s simHuman_chr6.simHuman.chr6 319114 26 - 601863 AAGGTGTAACCTGATACCCTTACTGG -s simRat_chr6.simRat.chr6 231292 26 + 647215 AAGGTATAGCACCATACTATTACTGG - -a -s simMouse_chr6.simMouse.chr6 240796 7 + 636262 TGATGCG -s Anc0.Anc0refChr5 59816 7 + 87904 CAATGTG -s Anc1.Anc1refChr7 17474 7 - 47259 CAATGTG -s Anc2.Anc2refChr15 56446 7 + 86568 CAACATG -s mr.mrrefChr5 93864 7 + 294540 TGATGTG -s simCow_chr6.simCow.chr6 237086 7 + 602619 CAACCGG -s simDog_chr6.simDog.chr6 229003 7 + 593897 CAACATA -s simHuman_chr6.simHuman.chr6 319156 7 - 601863 CAATGTG -s simRat_chr6.simRat.chr6 231318 7 + 647215 TGATGTG - -a -s simMouse_chr6.simMouse.chr6 240803 11 + 636262 ATGAAGCATTC -s Anc0.Anc0refChr5 59823 11 + 87904 ATAGAGTGTCC -s Anc1.Anc1refChr7 17481 11 - 47259 ATAGAGTGTCC -s Anc2.Anc2refChr15 56454 11 + 86568 GTAGAATGTCC -s mr.mrrefChr5 93871 11 + 294540 ATGAAGTATTC -s simCow_chr6.simCow.chr6 237094 11 + 602619 GAAGAATGTCC -s simDog_chr6.simDog.chr6 229011 11 + 593897 GTCGAATGTCC -s simHuman_chr6.simHuman.chr6 319163 11 - 601863 ATAGAGTGTCC -s simRat_chr6.simRat.chr6 231325 11 + 647215 AGGAAGTATAC - -a -s simMouse_chr6.simMouse.chr6 240814 1 + 636262 A -s Anc0.Anc0refChr5 59834 1 + 87904 A -s Anc1.Anc1refChr7 17492 1 - 47259 A -s Anc2.Anc2refChr15 56466 1 + 86568 A -s mr.mrrefChr5 93882 1 + 294540 A -s simCow_chr6.simCow.chr6 237106 1 + 602619 A -s simDog_chr6.simDog.chr6 229023 1 + 593897 A -s simHuman_chr6.simHuman.chr6 319174 1 - 601863 A -s simRat_chr6.simRat.chr6 231336 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 240815 4 + 636262 CATG -s Anc0.Anc0refChr5 59835 4 + 87904 CATG -s Anc1.Anc1refChr7 17493 4 - 47259 CATG -s Anc2.Anc2refChr15 56467 4 + 86568 CATG -s mr.mrrefChr5 93883 4 + 294540 CATG -s simCow_chr6.simCow.chr6 237107 4 + 602619 CATG -s simDog_chr6.simDog.chr6 229024 4 + 593897 CATG -s simHuman_chr6.simHuman.chr6 319213 4 - 601863 CATG -s simRat_chr6.simRat.chr6 231337 4 + 647215 CATG - -a -s simMouse_chr6.simMouse.chr6 240819 23 + 636262 CTTAAGTCTTGTGAGCATTTAGG -s Anc0.Anc0refChr5 59843 18 + 87904 CCTAAGAC-----TGCTTTTAGG -s Anc1.Anc1refChr7 17501 23 - 47259 CCTAAGACTTGTGTGCTTTTAGG -s Anc2.Anc2refChr15 56475 18 + 86568 CCTAAGAC-----TGCTTTTAGG -s mr.mrrefChr5 93887 23 + 294540 CTTAAGTCTTGTGAGCATTTAGG -s simCow_chr6.simCow.chr6 237115 13 + 602619 CCT----------TGCTATTAGG -s simDog_chr6.simDog.chr6 229032 18 + 593897 CCTAAGAC-----TGATTTTAGG -s simHuman_chr6.simHuman.chr6 319221 23 - 601863 CCTAAGACTTGTGTGCTTTCAGG -s simRat_chr6.simRat.chr6 231341 23 + 647215 TTTAAGTCTTGTGAGTATTTAGG - -a -s simMouse_chr6.simMouse.chr6 240842 16 + 636262 TAATAATAAGCTACTG -s Anc0.Anc0refChr5 59862 16 + 87904 TGATAAAGAGCTACTG -s Anc1.Anc1refChr7 17525 16 - 47259 TGATAAAGAGCTACTG -s Anc2.Anc2refChr15 56494 16 + 86568 TGATAAAGAGCTACTG -s mr.mrrefChr5 93910 16 + 294540 TAATAATAAGCTACTG -s simCow_chr6.simCow.chr6 237129 15 + 602619 GGAAGAAGAGCTACT- -s simDog_chr6.simDog.chr6 229051 16 + 593897 TGATAAAGAGCTACTG -s simHuman_chr6.simHuman.chr6 319245 16 - 601863 TGATAAACAGCTGCTG -s simRat_chr6.simRat.chr6 231364 16 + 647215 TAATAATGAGCTACTG - -a -s simMouse_chr6.simMouse.chr6 240858 106 + 636262 GAGTAATCAACTTGCAACCTTGTTACTTGTTAATAAGTAACATAGAGCATAGAAATTAGTAGCTATCTTAGAAGGACACCAGCCACATCATTACATGTCTACAAGT -s Anc0.Anc0refChr5 59879 99 + 87904 AAATAATCAACTTGCAAC-------CTAATTAAGAGTTGACATAGAGCCTAGACGTTAGAAACATTCTGGTGAGGACACCAGTCACATCATTATATGCCTACAAGA -s Anc1.Anc1refChr7 17542 99 - 47259 AAATAATCAACTTGCAAC-------CTAATTAAGAGTTGACATAGAGCCTAGACGTTAGAAACATTCTGGTGAGGACACCAGTCACATCATTATATGCCTACAAGA -s Anc2.Anc2refChr15 56511 99 + 86568 AAATTATCAATTTGCAAC-------ATAATTCAGAGTTGACATAGAGCCTAAACGTTAAAAAAATTCTGGTGAGGACACCAGTCACATCATTATATGCCTACAAGA -s mr.mrrefChr5 93926 101 + 294540 GAGTAATCAACTTGCAAC-----TACTTGTTAATAAGTGACATAGAGCCTAGAAATTAGTAGCTTTCTTAGAAGGACACCAGCCACATCATTACATGTCTACAAGA -s simCow_chr6.simCow.chr6 237145 99 + 602619 AGATTATCAATATGCAAC-------ATAATTGATAGTTGGCACAGAGCCTAAGAGTTGAAGATTTTTTGGAGGAGACACCAATCACTTCATTGTATGTCTAGAAGA -s simDog_chr6.simDog.chr6 229068 94 + 593897 AA----TCACTTTGCAAC-------ATAGTTCAGAGTTGATATAGAGCCTAAACATTAAAAAAATTCTGGT-AGGACACCAGTCACATCATTATATGCCTACAGGA -s simHuman_chr6.simHuman.chr6 319262 99 - 601863 AAATAATCAACTCGCAAC-------CTAATTAAAACTTGACATAGAGTCTAGATGCTAGGAACCTTCTAGTGAGGACACCACTCACACTATTATATGCCTACAAAA -s simRat_chr6.simRat.chr6 231380 84 + 647215 GA---------------------TCCTTCTTAATAAGTGACATAGAGCCTAGAAATTAGTAGCTTTCTTAGAA-GACACCAGCTACATCATTACATGTCTACAAGA - -a -s simMouse_chr6.simMouse.chr6 240964 59 + 636262 ATTGAGGGCATCAAAAGCATGAGTGAGTGGGGACTCTTCAAGGTCAGTGAAATGAGGAG -s Anc0.Anc0refChr5 59978 56 + 87904 GTTCAGTGCCTGCAAAACAAGGGAGAGTGAGGACTCTACAGGGTCAGCAAAAC---AAG -s Anc1.Anc1refChr7 17641 56 - 47259 GTTCAGTGCCTGCAAAACAAGGGAGAGTGAGGACTCTACAGGGTCAGCAAAAC---AAG -s Anc2.Anc2refChr15 56610 56 + 86568 GTTCAGTGCCTGCAAAACAAGGGAGAGTGAGGACTCTATAGGGTCTGCAAAAC---AAG -s mr.mrrefChr5 94027 59 + 294540 ATTCAGGGCATCAAAAACATGAGAGAGTGGGGACTCTTCAAGGTCAGTGAAACGAGGAG -s simCow_chr6.simCow.chr6 237244 56 + 602619 GTTCAGTGCCTGTAAAAAAAGGGAAAGTGAGGACTCTATACAGGCTGCAAAAC---CAG -s simDog_chr6.simDog.chr6 229162 56 + 593897 GTTCAGTGTTTGCAACACAAGGGAGATTGAGGACCCTATAGGGTCTCCAAAAT---AAG -s simHuman_chr6.simHuman.chr6 319362 54 - 601863 GTTCAGAGCCTGCAAAACAAGGAAGAGTAAGGACTC--CATGGTCAGCATAAC---AAG -s simRat_chr6.simRat.chr6 231464 59 + 647215 ATTCAGGGCATTAAAAACATGAGAGAGTGGGGGCTCTTCAGGGTCAGTGAAACAGGGAG - -a -s simMouse_chr6.simMouse.chr6 241023 19 + 636262 ATTTAGGATGTTGATAGTT -s Anc0.Anc0refChr5 60034 19 + 87904 ATTGAGGATGTTGAGGAAG -s Anc1.Anc1refChr7 17697 19 - 47259 ATTGAGGATGTTGAGGAAG -s Anc2.Anc2refChr15 56666 19 + 86568 AGTGAGGGTGTTAAGGAAG -s mr.mrrefChr5 94086 19 + 294540 ATTTAGGATGTTGATAGTT -s simCow_chr6.simCow.chr6 237304 19 + 602619 ACTGACGGTGTTAATGGAG -s simDog_chr6.simDog.chr6 229221 19 + 593897 GGTGGGAGTGCTAAGGAAG -s simHuman_chr6.simHuman.chr6 319416 19 - 601863 ATTGAGGATGTTGAGGAGG -s simRat_chr6.simRat.chr6 231523 19 + 647215 ATCTATGATGTTGATAGTT - -a -s simMouse_chr6.simMouse.chr6 241042 11 + 636262 ATAATCACCTG -s Anc0.Anc0refChr5 60053 11 + 87904 ATAAACACCTG -s Anc1.Anc1refChr7 17716 11 - 47259 ATAAACACCTG -s Anc2.Anc2refChr15 56685 11 + 86568 ATAAACACCTG -s mr.mrrefChr5 94105 11 + 294540 ATAATCACCTG -s simCow_chr6.simCow.chr6 237323 11 + 602619 ATAAACACCTG -s simDog_chr6.simDog.chr6 229240 11 + 593897 TTAAACCCCAG -s simHuman_chr6.simHuman.chr6 319435 11 - 601863 ATACACACCTG -s simRat_chr6.simRat.chr6 231543 11 + 647215 ACAGTCACCCG - -a -s simMouse_chr6.simMouse.chr6 241053 33 + 636262 TTATTCTTCCTACAGTATTTTGTCTCAGTGTGG -s Anc0.Anc0refChr5 60064 33 + 87904 TTATTCATCAAAGAGCATTTTCTCTCAGTGTGG -s Anc1.Anc1refChr7 17727 33 - 47259 TTATTCATCAAAGAGCATTTTCTCTCAGTGTGG -s Anc2.Anc2refChr15 56697 33 + 86568 TTATTCATCAAAGAGCATTTTCACTCAGTTTGG -s mr.mrrefChr5 94116 33 + 294540 TTATTCTTCCTACAGTATTTTGTCTCAGTGTGG -s simCow_chr6.simCow.chr6 237336 33 + 602619 CTATTTATCAAATAGCATTGTTCCTCAGTTTGG -s simDog_chr6.simDog.chr6 229252 33 + 593897 TTAGTCATCAAAGAGCATTTTCAGTCAGTTTGG -s simHuman_chr6.simHuman.chr6 319446 33 - 601863 TTATTCGTCAAGGATCTTTTCCTCCCAGTGTGG -s simRat_chr6.simRat.chr6 231554 33 + 647215 TTATTCTTCTTAAAGGGTTTTGTCTCACTATGG - -a -s simMouse_chr6.simMouse.chr6 241086 10 + 636262 CAAATGTTTG -s Anc0.Anc0refChr5 60098 10 + 87904 CAAAAGTTTG -s Anc1.Anc1refChr7 17761 10 - 47259 CAAAAGTTTG -s Anc2.Anc2refChr15 56731 10 + 86568 TAAAAGTTTG -s mr.mrrefChr5 94149 10 + 294540 CAAATGTTTG -s simCow_chr6.simCow.chr6 237370 10 + 602619 TAAAGGTTTG -s simDog_chr6.simDog.chr6 229286 10 + 593897 TGAAAGTTTG -s simHuman_chr6.simHuman.chr6 319480 10 - 601863 CAAAAGCTTG -s simRat_chr6.simRat.chr6 231587 10 + 647215 CAAGTGTTTA - -a -s simMouse_chr6.simMouse.chr6 241096 7 + 636262 ATACTTT -s Anc0.Anc0refChr5 60108 7 + 87904 ATACTCT -s Anc1.Anc1refChr7 17771 7 - 47259 ATACTCT -s Anc2.Anc2refChr15 56741 7 + 86568 ATACTCT -s mr.mrrefChr5 94159 7 + 294540 ATACTTT -s simCow_chr6.simCow.chr6 237383 7 + 602619 ATACTCT -s simDog_chr6.simDog.chr6 229296 7 + 593897 ATATACT -s simHuman_chr6.simHuman.chr6 319490 7 - 601863 ACACTCT -s simRat_chr6.simRat.chr6 231597 7 + 647215 ATACTTT - -a -s simMouse_chr6.simMouse.chr6 241103 18 + 636262 TCTAATCCTATGAAGGAG -s Anc0.Anc0refChr5 60117 18 + 87904 TTTAGTTCTATGAAAGAG -s Anc1.Anc1refChr7 17780 18 - 47259 TTTAGTTCTATGAAAGAG -s Anc2.Anc2refChr15 56750 18 + 86568 TTTAGTCCTATGAAAGAG -s mr.mrrefChr5 94168 18 + 294540 TCTAATTCTATGAAGGAG -s simCow_chr6.simCow.chr6 237392 18 + 602619 TTTAGTCCCATGAAGGAG -s simDog_chr6.simDog.chr6 229305 18 + 593897 TTGTGTCCTATGAAAGAG -s simHuman_chr6.simHuman.chr6 319499 18 - 601863 TTTAGTTCTATGACAGAT -s simRat_chr6.simRat.chr6 231607 18 + 647215 TCTAATTCTCCGGAGGAG - -a -s simMouse_chr6.simMouse.chr6 241121 18 + 636262 TATTGTACCGTTGATCTA -s Anc0.Anc0refChr5 60147 18 + 87904 TATTCTCCTGTTGATCTA -s Anc1.Anc1refChr7 17810 18 - 47259 TATTCTCCTGTTGATCTA -s Anc2.Anc2refChr15 56780 18 + 86568 TATTCTCCTGTCAATCTA -s mr.mrrefChr5 94186 18 + 294540 TATTGTACTGTTGATCTA -s simCow_chr6.simCow.chr6 237422 18 + 602619 CAATCTACTGTCAATCTA -s simDog_chr6.simDog.chr6 229332 8 + 593897 TCTTTTCC---------- -s simHuman_chr6.simHuman.chr6 319529 18 - 601863 TACTCTCCTGTTGATCTA -s simRat_chr6.simRat.chr6 231625 18 + 647215 TATTGTACTGTTGATCTA - -a -s simMouse_chr6.simMouse.chr6 241139 12 + 636262 GGGAAAAAACTT -s Anc0.Anc0refChr5 60169 12 + 87904 AGCAAAAGGCAC -s Anc1.Anc1refChr7 17832 12 - 47259 AGCAAAAGGCAC -s Anc2.Anc2refChr15 56802 12 + 86568 AGCGAAAGGCAC -s mr.mrrefChr5 94208 12 + 294540 AGGAAAAAACTT -s simCow_chr6.simCow.chr6 237444 12 + 602619 AGTGAACGGTAC -s simDog_chr6.simDog.chr6 229341 12 + 593897 CGCGGAAGGCAC -s simHuman_chr6.simHuman.chr6 319551 12 - 601863 AGCAACAGGCAC -s simRat_chr6.simRat.chr6 231647 12 + 647215 AGGAAAAAACTT - -a -s simMouse_chr6.simMouse.chr6 241151 7 + 636262 TTGTTAG -s Anc0.Anc0refChr5 60184 7 + 87904 TTGTTAA -s Anc1.Anc1refChr7 17847 7 - 47259 TTGTTAA -s Anc2.Anc2refChr15 56817 7 + 86568 TTGTTAA -s mr.mrrefChr5 94220 7 + 294540 TTGTTAG -s simCow_chr6.simCow.chr6 237459 7 + 602619 TTGGTAA -s simDog_chr6.simDog.chr6 229356 7 + 593897 TTGTCAG -s simHuman_chr6.simHuman.chr6 319566 7 - 601863 TTGTTAA -s simRat_chr6.simRat.chr6 231659 7 + 647215 TTGTTAG - -a -s simMouse_chr6.simMouse.chr6 241158 8 + 636262 GAAAGAAA -s Anc0.Anc0refChr5 60193 8 + 87904 TCAGGCAA -s Anc1.Anc1refChr7 17856 8 - 47259 TCAGGCAA -s Anc2.Anc2refChr15 56829 8 + 86568 TCAGGCAA -s mr.mrrefChr5 94227 8 + 294540 GAAAGCAA -s simCow_chr6.simCow.chr6 237471 8 + 602619 TCAGGCAA -s simDog_chr6.simDog.chr6 229368 8 + 593897 TCAGCAAA -s simHuman_chr6.simHuman.chr6 319575 8 - 601863 TCAGGCAA -s simRat_chr6.simRat.chr6 231666 8 + 647215 GAAAGCAA - -a -s simMouse_chr6.simMouse.chr6 241166 40 + 636262 TGACTAGCATCCTTAATGATGTGGTTAATGGAATTTGGTT -s Anc0.Anc0refChr5 60201 40 + 87904 TCACTATCATCATCAATGAGTTGGCCAACGGCACCTGGTT -s Anc1.Anc1refChr7 17864 40 - 47259 TCACTATCATCATCAATGAGTTGGCCAACGGCACCTGGTT -s Anc2.Anc2refChr15 56837 40 + 86568 TCATTATCATCATCAATGAGTGGGCCAACAGCACCTGGTT -s mr.mrrefChr5 94235 40 + 294540 TCACTATCATCCTTAATGATGTGGCTAACGGCATCTGGTT -s simCow_chr6.simCow.chr6 237502 40 + 602619 TCATTATCATCATCAATGAGTGGGCTAACAACACCTGGTT -s simDog_chr6.simDog.chr6 229376 40 + 593897 TCATTATGCTCATCAGTGAGTGGGCCAGCAGCACCTGGTT -s simHuman_chr6.simHuman.chr6 319583 40 - 601863 TCACTATCATCATCAATGAGTTGGCCAACGCCACCTGGTT -s simRat_chr6.simRat.chr6 231674 40 + 647215 TCACTATCGTCCTTAATGATATGGCTAACGGCTTCTAGTT - -a -s simMouse_chr6.simMouse.chr6 241206 8 + 636262 CATTGGTA -s Anc0.Anc0refChr5 60290 7 + 87904 CATT-GTC -s Anc1.Anc1refChr7 17953 7 - 47259 CATT-GTC -s Anc2.Anc2refChr15 56928 7 + 86568 CACT-GTC -s mr.mrrefChr5 94275 8 + 294540 CATTGGTA -s simCow_chr6.simCow.chr6 237593 7 + 602619 CACT-GTC -s simDog_chr6.simDog.chr6 229498 7 + 593897 CACT-GTC -s simHuman_chr6.simHuman.chr6 319672 7 - 601863 CATT-GTC -s simRat_chr6.simRat.chr6 231714 8 + 647215 CATTGGTA - -a -s simMouse_chr6.simMouse.chr6 241214 76 + 636262 TTTCACTAACTTAACCTTGGGTAGATACTCTAACTACTACATCTTTCCTCCCCCCTAGTAGAGACCGTACACCTTT -s Anc0.Anc0refChr5 60297 66 + 87904 TGTCACTAACTCAATCTTTGGTAGACATTCAAGCTACTACATCATTCCA----------TCATGCACTAGATATTT -s Anc1.Anc1refChr7 17960 75 - 47259 TGTCACTAACTCAATCTTTGGTAGACATTCAAGCTACTACATCATTCCATCACCC-AATTCATGCACTAGATATTT -s Anc2.Anc2refChr15 56939 66 + 86568 TGTCACTAACCCAATCTTTAGTAGACATTCAAGCTACTACATCACTCCA----------TCATGCACTAGATATTG -s mr.mrrefChr5 94283 75 + 294540 TTTCACTAACTCAACCTTGGGTAGATACTCTAGCTACTACATCTTTCCTCCCCCC-AGTAGAGGCCGTACACATTT -s simCow_chr6.simCow.chr6 237604 59 + 602619 TGTCACGAACCCAATCTTTAGTAGACATTCAAGCTATTACCTC----------------TCCTCCAGT-GATATTA -s simDog_chr6.simDog.chr6 229509 66 + 593897 TGTCACTAACCAAACCTTCAGTAAATATTCAATCTACTACATCACTCCA----------TCATGCACTAGGTATTG -s simHuman_chr6.simHuman.chr6 319679 75 - 601863 TGTCACTTAATCAATTTTTGGTAGACATTCAAGCCACTACATCATTCCATCACCC-AATTCACGCACTAGATATTT -s simRat_chr6.simRat.chr6 231722 75 + 647215 TTTCACTAACTCAACCTTGGATAGATGCTCTAGCTACTACATCTTTCCTCCCCCC-AGTAGATGCGGTACACATTC - -a -s simMouse_chr6.simMouse.chr6 241290 8 + 636262 GGGAACTG -s Anc0.Anc0refChr5 60372 8 + 87904 GGAAAATG -s Anc1.Anc1refChr7 18044 8 - 47259 GGAAAATG -s Anc2.Anc2refChr15 57015 8 + 86568 GGAAAATG -s mr.mrrefChr5 94358 8 + 294540 GGGAACTG -s simCow_chr6.simCow.chr6 237673 8 + 602619 GGAAAACA -s simDog_chr6.simDog.chr6 229585 8 + 593897 GGAAAATG -s simHuman_chr6.simHuman.chr6 319763 8 - 601863 GGTAAGTG -s simRat_chr6.simRat.chr6 231797 8 + 647215 GGGGAATG - -a -s simMouse_chr6.simMouse.chr6 241298 3 + 636262 AGG -s Anc0.Anc0refChr5 60380 3 + 87904 GGG -s Anc1.Anc1refChr7 18052 3 - 47259 GGG -s Anc2.Anc2refChr15 57023 3 + 86568 GGG -s mr.mrrefChr5 94366 3 + 294540 GGG -s simCow_chr6.simCow.chr6 237681 3 + 602619 GTG -s simDog_chr6.simDog.chr6 229593 3 + 593897 GGG -s simHuman_chr6.simHuman.chr6 319771 3 - 601863 GGG -s simRat_chr6.simRat.chr6 231812 3 + 647215 GGA - -a -s simMouse_chr6.simMouse.chr6 241301 21 + 636262 ATACTGGCAGATATGGCTCCA -s Anc0.Anc0refChr5 60384 21 + 87904 GCACTTGAAACTATGGTTCCA -s Anc1.Anc1refChr7 18056 21 - 47259 GCACTTGAAACTATGGTTCCA -s Anc2.Anc2refChr15 57027 21 + 86568 GCACTTGAAACTATGGTTTCA -s mr.mrrefChr5 94369 21 + 294540 ACACTGGCAGATATGGCTCCA -s simCow_chr6.simCow.chr6 237685 20 + 602619 -CACTTGAAGCTATTGCTGCA -s simDog_chr6.simDog.chr6 229597 21 + 593897 GCACTTGAAACTATGGTTTCA -s simHuman_chr6.simHuman.chr6 319775 21 - 601863 GCACTTGAATTCATAGTCCCA -s simRat_chr6.simRat.chr6 231815 21 + 647215 ACACTGGTAAATATGGCTCCA - -a -s simMouse_chr6.simMouse.chr6 241322 23 + 636262 GAAAGATCGACTTTGGTTGACAT -s Anc0.Anc0refChr5 60406 23 + 87904 GAAAGATTAACTGTGGTTGATAT -s Anc1.Anc1refChr7 18078 23 - 47259 GAAAGATTAACTGTGGTTGATAT -s Anc2.Anc2refChr15 57049 23 + 86568 GAAAGATTAACTGTGATTGATAT -s mr.mrrefChr5 94390 23 + 294540 GAAAGATTGACTTTGGTTGACAT -s simCow_chr6.simCow.chr6 237706 23 + 602619 AAAAGATTAACTGTTATTGATAT -s simDog_chr6.simDog.chr6 229619 23 + 593897 GCAAGATTAATTGTGATTGTCGT -s simHuman_chr6.simHuman.chr6 319797 23 - 601863 GAAAGATTAACAGTGGTTGATAT -s simRat_chr6.simRat.chr6 231836 23 + 647215 GATAACATGACTTTGGTTAACAT - -a -s simMouse_chr6.simMouse.chr6 241345 13 + 636262 AAGGGGTACATCA -s Anc0.Anc0refChr5 60429 13 + 87904 AAAGGAAACACCA -s Anc1.Anc1refChr7 18101 13 - 47259 AAAGGAAACACCA -s Anc2.Anc2refChr15 57072 13 + 86568 GAAGGAAACACCA -s mr.mrrefChr5 94413 13 + 294540 AAGGGGTACATCA -s simCow_chr6.simCow.chr6 237729 13 + 602619 GCAGGAGACACAA -s simDog_chr6.simDog.chr6 229642 13 + 593897 GAGGGAAACACCA -s simHuman_chr6.simHuman.chr6 319857 13 - 601863 AAAGGAAACAACA -s simRat_chr6.simRat.chr6 231859 13 + 647215 TGGGGGTACATCA - -a -s simMouse_chr6.simMouse.chr6 241358 7 + 636262 GAGCTGG -s Anc0.Anc0refChr5 60442 7 + 87904 GATCTGG -s Anc1.Anc1refChr7 18114 7 - 47259 GATCTGG -s Anc2.Anc2refChr15 57085 7 + 86568 GATCTGG -s mr.mrrefChr5 94426 7 + 294540 GAGCTGG -s simCow_chr6.simCow.chr6 237742 7 + 602619 GATCTAG -s simDog_chr6.simDog.chr6 229655 7 + 593897 GATCTGG -s simHuman_chr6.simHuman.chr6 319873 7 - 601863 GATCTGG -s simRat_chr6.simRat.chr6 231872 7 + 647215 GACCTGG - -a -s simMouse_chr6.simMouse.chr6 241365 37 + 636262 GCTCAGTGGTAATCAACAAGTCTTCACAACAAAAATT -s Anc0.Anc0refChr5 60454 32 + 87904 GAT-GGTGGCAGCTAA----CTCTCACAACAACAATT -s Anc1.Anc1refChr7 18126 32 - 47259 GAT-GGTGGCAGCTAA----CTCTCACAACAACAATT -s Anc2.Anc2refChr15 57097 32 + 86568 GCT-GGTGGCAGCTAA----CTCTCACTACAACAATT -s mr.mrrefChr5 94433 33 + 294540 GATCAGTGGTAATCAA----CCCTCACAACAAAAATT -s simCow_chr6.simCow.chr6 237754 32 + 602619 GCT-GGTGGCAGCTAA----CTCTTACTACAACAATT -s simDog_chr6.simDog.chr6 229667 32 + 593897 GCC-AGTGGCAGTTAA----TTATCACTAAAGCAAGT -s simHuman_chr6.simHuman.chr6 319885 32 - 601863 GAT-GGTGGCAGCTTA----CTCTCGCAACAACAATT -s simRat_chr6.simRat.chr6 231879 33 + 647215 GATCAGTGGTAATCAA----CCCTCACAACAAGAATT - -a -s simMouse_chr6.simMouse.chr6 241402 23 + 636262 AAGGATGCAATGGCAATCATGCC -s Anc0.Anc0refChr5 60486 23 + 87904 AAGGATGCCATGGCAGTAGCCCC -s Anc1.Anc1refChr7 18158 23 - 47259 AAGGATGCCATGGCAGTAGCCCC -s Anc2.Anc2refChr15 57129 23 + 86568 AAGGATGCCATGGGAGTAACCCC -s mr.mrrefChr5 94466 23 + 294540 AAGGATGCAATGGCAATCGTGCC -s simCow_chr6.simCow.chr6 237791 16 + 602619 AAAGATACCAT-------ATGCC -s simDog_chr6.simDog.chr6 229699 23 + 593897 AAGGATGCCATGGGAGTAacccc -s simHuman_chr6.simHuman.chr6 319917 23 - 601863 AAGGATGCCATGGCACTAGCACC -s simRat_chr6.simRat.chr6 231912 23 + 647215 AAGGAGGCAATTGCAATTGTGCC - -a -s simMouse_chr6.simMouse.chr6 241425 44 + 636262 ATCCATTGAGTGGGTAGGCTTTTGATGATACCATCACTGCCTTA -s Anc0.Anc0refChr5 60509 44 + 87904 ATCCATTGAGCACTTGAGCTTTTGATGACAGAATGACTGACTCA -s Anc1.Anc1refChr7 18181 44 - 47259 ATCCATTGAGCACTTGAGCTTTTGATGACAGAATGACTGACTCA -s Anc2.Anc2refChr15 57152 44 + 86568 ATCCATTGAGCACTTGAGCTTTTAATGACAGAATGGCTGACTCA -s mr.mrrefChr5 94489 44 + 294540 ATCCATTGAGTGGGTAAGCTTTTGATGATACCATGACTGCCTTA -s simCow_chr6.simCow.chr6 237807 44 + 602619 ATCCATCGAGCAATTGAGCTTTTCCTGACAAAACAGCTGACTCA -s simDog_chr6.simDog.chr6 229997 44 + 593897 ATTCATTCAGCGCTTGAGCTTTTAATGATAGAATGGCTGACTTA -s simHuman_chr6.simHuman.chr6 319940 44 - 601863 GTCCACTGAGCATCTGAGATTTTGATGACAGGATGACTGACTCA -s simRat_chr6.simRat.chr6 231935 38 + 647215 ATCC------TGAGCAAGCTTCTGGTGATTCCAGGGTGGCCTTA - -a -s simMouse_chr6.simMouse.chr6 241469 7 + 636262 TTGGAAA -s Anc0.Anc0refChr5 60553 7 + 87904 TTGACAA -s Anc1.Anc1refChr7 18225 7 - 47259 TTGACAA -s Anc2.Anc2refChr15 57196 7 + 86568 TTGACAA -s mr.mrrefChr5 94533 7 + 294540 TTGAAAA -s simCow_chr6.simCow.chr6 237852 7 + 602619 TTGCCAA -s simDog_chr6.simDog.chr6 230041 7 + 593897 TTGACTA -s simHuman_chr6.simHuman.chr6 319984 7 - 601863 TTGACAG -s simRat_chr6.simRat.chr6 231973 7 + 647215 TTGAAAA - -a -s simMouse_chr6.simMouse.chr6 241476 116 + 636262 TCTAAACACATTGATAGTAAGAGCTGTAATCCAATGCCATGAGTAGGAAGCTGCACTTGTTTATTTGCACACCTGGATGCATTTGACTGCATTCTTCACCCCTTAATATCCTCACA -s Anc0.Anc0refChr5 60561 102 + 87904 GCTAAACACACCAAGGGCACAAAAGATAGTT-----TCATGGGTAGTAAGC-CCACCTTTTTAGTTTCATACCTTCATAC------CTTCTTGTTTTACCCCCTGATAT--TTTTA -s Anc1.Anc1refChr7 18233 103 - 47259 GCTAAACACACCAAGGGCACAAAAGATAGTT-----TCATGGGTAGTAAGCACCACCTTTTTAGTTTCATACCTTCATAC------CTTCTTGTTTTACCCCCTGATAT--TTTTA -s Anc2.Anc2refChr15 57204 102 + 86568 GCTAAACACACCAAGGGTACAGAAGATAGTT-----TCATGGGTAGTATGC-CCACCTTTTTAGTTTCATACCTTCATAC------CTTCTTGTTCTACCCCCTGATAT--CTTTA -s mr.mrrefChr5 94540 114 + 294540 GCTAAACACACTGATAGCAAAAACTGTAATCCAA--CCATGAGTAGGAAGCAGCACCTGTTTATTTGCACACCTGGATGCATTTGACTGCATTCTTCACCCCTTAATATCCTCACA -s simCow_chr6.simCow.chr6 237860 97 + 602619 ACTAAGCACCCCAAGAGTATAGAATATAGTT-----TCATGTGTAGTATGC-CTACCTTTATAGTTTCAATCTT-----C------CTTCTTGTTCTACCCCTTGATAT--CTTTA -s simDog_chr6.simDog.chr6 230049 102 + 593897 GCTCGACACAGCAAGGGTGCTGAAGATAGTC-----TCATGGGAAGCATGC-CCACCTTTTCGGTCTCATACCTTCATAC------CTTCTTATTCTGCCCCCTAATAT--CTTCA -s simHuman_chr6.simHuman.chr6 319992 103 - 601863 GCTAAACACACCAAGGGCACAAAAGATAGCT-----TCATGGGTAATAAGCATCACCTTTTTAGTTTCAGACCTTCATAC------CTTCTCGTTTTATCCCCTGATGT--TTGTA -s simRat_chr6.simRat.chr6 231980 114 + 647215 GCTAAACACACTGATAGCAAAAACTGTAATGCAA--CCATGAGTAGGAGGCAGCACCTCGTTATTTGCATGCCTGGATGGCTTTGACTGCATTCTTCACCCCTTAATATCTTCACA - -a -s simMouse_chr6.simMouse.chr6 241592 5 + 636262 GATCT -s Anc0.Anc0refChr5 60663 3 + 87904 GA--T -s Anc1.Anc1refChr7 18336 3 - 47259 GA--T -s Anc2.Anc2refChr15 57306 3 + 86568 GA--T -s mr.mrrefChr5 94654 3 + 294540 GA--T -s simCow_chr6.simCow.chr6 237957 3 + 602619 GA--T -s simDog_chr6.simDog.chr6 230171 3 + 593897 GC--C -s simHuman_chr6.simHuman.chr6 320095 3 - 601863 GA--T -s simRat_chr6.simRat.chr6 232094 3 + 647215 GA--T - -a -s simMouse_chr6.simMouse.chr6 241597 25 + 636262 CCAGGAGGTCACATCTTGATCTCCA -s Anc0.Anc0refChr5 60666 25 + 87904 CCAAAGGGCCTCATCCTGATGCCCA -s Anc1.Anc1refChr7 18339 25 - 47259 CCAAAGGGCCTCATCCTGATGCCCA -s Anc2.Anc2refChr15 57309 25 + 86568 CAGAAGGGCCTCATCCTGATGTTCC -s mr.mrrefChr5 94657 25 + 294540 CCAGGAGGTCACATCTTGATCCCCA -s simCow_chr6.simCow.chr6 237962 25 + 602619 CAGAAGGGCCTCATCCTGATGTTCC -s simDog_chr6.simDog.chr6 230174 25 + 593897 CAGGAGGGCCTCATCCTGATGTTCC -s simHuman_chr6.simHuman.chr6 320098 25 - 601863 CCAAAGGACCTCATCCCGGTGCCCA -s simRat_chr6.simRat.chr6 232097 25 + 647215 GCAGGCGGTCACATCTTGATCCACA - -a -s simMouse_chr6.simMouse.chr6 241622 15 + 636262 CTCAGAATGGAGAGC -s Anc0.Anc0refChr5 60691 15 + 87904 CTCAGAATGGTGAGT -s Anc1.Anc1refChr7 18364 15 - 47259 CTCAGAATGGTGAGT -s Anc2.Anc2refChr15 57334 15 + 86568 TCCAGAATGTTATGT -s mr.mrrefChr5 94682 15 + 294540 CTCAGAATGGAGAGC -s simCow_chr6.simCow.chr6 237988 15 + 602619 TCCAGAATGTGATGT -s simDog_chr6.simDog.chr6 230199 15 + 593897 TCCTGAATGTTATGT -s simHuman_chr6.simHuman.chr6 320123 15 - 601863 CTCAGAATGGTGAGT -s simRat_chr6.simRat.chr6 232122 15 + 647215 CTCAGAATGGAAAGC - -a -s simMouse_chr6.simMouse.chr6 241637 9 + 636262 TTTGGTTTC -s Anc0.Anc0refChr5 60706 9 + 87904 TTCATTTTT -s Anc1.Anc1refChr7 18379 9 - 47259 TTCATTTTT -s Anc2.Anc2refChr15 57349 9 + 86568 TTCATTTTT -s mr.mrrefChr5 94697 9 + 294540 TTTGGTTTC -s simCow_chr6.simCow.chr6 238003 9 + 602619 TTCATCTTT -s simDog_chr6.simDog.chr6 230240 9 + 593897 TTCAATTTC -s simHuman_chr6.simHuman.chr6 320138 9 - 601863 TTCCTTTTT -s simRat_chr6.simRat.chr6 232137 9 + 647215 TTTGGTTTC - -a -s simMouse_chr6.simMouse.chr6 241646 73 + 636262 AGTTGAAGTCTTGGCTGGTCACTTACATATTGGGCAGCCAAGTTCTCAAGTTTGTCTCTCACATGTGGCATAT -s Anc0.Anc0refChr5 60715 38 + 87904 AGTTGATG-----------------------------------TCTCAACTGAGTCTCTCACATAGGGGTAAT -s Anc1.Anc1refChr7 18388 38 - 47259 AGTTGATG-----------------------------------TCTCAACTGAGTCTCTCACATAGGGGTAAT -s Anc2.Anc2refChr15 57358 38 + 86568 AGTTGATG-----------------------------------TCTCAACTGAGTCCCTCACATAGGGGCAAT -s mr.mrrefChr5 94706 73 + 294540 AGTTGAAGTCTTGGCTGGTCACTTACATATTGGGCAGCCAAGTTCTCAAGTGTGTCTCTCACATGTGGCTTAT -s simCow_chr6.simCow.chr6 238012 36 + 602619 AGTTGATG-----------------------------------TCC--ACTGGGTGCCTCACATATGGGCAGT -s simDog_chr6.simDog.chr6 230249 38 + 593897 AGTCGATG-----------------------------------TCTCAACCAAGTCCCTCACAGAGTGGCAAT -s simHuman_chr6.simHuman.chr6 320147 38 - 601863 AGTTGAGG-----------------------------------TCTCAAATGAGTTTCCCACATAGGGTTAAT -s simRat_chr6.simRat.chr6 232147 73 + 647215 AGTAGAAGTCACAGCTGGTCACTCACTTATTGGGCAGTTAAGTTCTCAATTGTGTCCCTCACATGTAGCTGAT - -a -s simMouse_chr6.simMouse.chr6 241719 8 + 636262 TGGAGGAC -s Anc0.Anc0refChr5 60754 8 + 87904 TACAGGAC -s Anc1.Anc1refChr7 18427 8 - 47259 TACAGGAC -s Anc2.Anc2refChr15 57397 8 + 86568 CACAGGAT -s mr.mrrefChr5 94779 8 + 294540 TGCAGGAC -s simCow_chr6.simCow.chr6 238049 6 + 602619 CA--GGAT -s simDog_chr6.simDog.chr6 230288 8 + 593897 CACAGGGT -s simHuman_chr6.simHuman.chr6 320186 8 - 601863 TTCAGGAC -s simRat_chr6.simRat.chr6 232220 8 + 647215 TGCAGGAC - -a -s simMouse_chr6.simMouse.chr6 241727 7 + 636262 AGTCTAA -s Anc0.Anc0refChr5 60762 7 + 87904 AGTCAAA -s Anc1.Anc1refChr7 18435 7 - 47259 AGTCAAA -s Anc2.Anc2refChr15 57405 7 + 86568 AGTCAAA -s mr.mrrefChr5 94787 7 + 294540 AGTCTAA -s simCow_chr6.simCow.chr6 238055 7 + 602619 GATAAAA -s simDog_chr6.simDog.chr6 230316 7 + 593897 AGTCAAA -s simHuman_chr6.simHuman.chr6 320194 7 - 601863 AGTCAAA -s simRat_chr6.simRat.chr6 232228 7 + 647215 AGTCTAA - -a -s simMouse_chr6.simMouse.chr6 241734 35 + 636262 CCGTTCCAAAAAGTTTTAAAGGAACCTGTATCGTG -s Anc0.Anc0refChr5 60790 34 + 87904 -TGCTCTATACAGTTTTGAAGCACCTAGTAGCATG -s Anc1.Anc1refChr7 18463 34 - 47259 -TGCTCTATACAGTTTTGAAGCACCTAGTAGCATG -s Anc2.Anc2refChr15 57433 34 + 86568 -TGCTCTATACAGTTTTGAAGCACCTAGTAGCACA -s mr.mrrefChr5 94802 35 + 294540 CCGTTCCATAAAGTTTTAAAGGAACCTGTATCATG -s simCow_chr6.simCow.chr6 238082 34 + 602619 -TGCTCTATAAAGTTTTGAAGGACCTAGTAGCACA -s simDog_chr6.simDog.chr6 230344 34 + 593897 -TGCTCTATACAGTTTTGGAGCACCCAGTAGCACA -s simHuman_chr6.simHuman.chr6 320222 33 - 601863 -TGCTCTATATAAT-TTGAAGAACCTGGTAGCATG -s simRat_chr6.simRat.chr6 232246 35 + 647215 CCGTTCCATAGAGTTTTAAATGAACCTGTATCATG - -a -s simMouse_chr6.simMouse.chr6 241769 8 + 636262 AAGTGGAC -s Anc0.Anc0refChr5 60825 8 + 87904 AAGTGGAC -s Anc1.Anc1refChr7 18498 8 - 47259 AAGTGGAC -s Anc2.Anc2refChr15 57468 8 + 86568 AAATGGAC -s mr.mrrefChr5 94837 8 + 294540 AAGTGGAC -s simCow_chr6.simCow.chr6 238117 8 + 602619 AAATGGGC -s simDog_chr6.simDog.chr6 230379 8 + 593897 TAATGGAC -s simHuman_chr6.simHuman.chr6 320256 8 - 601863 AAGTGGAC -s simRat_chr6.simRat.chr6 232281 8 + 647215 ATGCGAAC - -a -s simMouse_chr6.simMouse.chr6 241777 10 + 636262 CTCAGCATGG -s Anc0.Anc0refChr5 60835 10 + 87904 CTCAATATGT -s Anc1.Anc1refChr7 18508 10 - 47259 CTCAATATGT -s Anc2.Anc2refChr15 57498 10 + 86568 CTCAATACGT -s mr.mrrefChr5 94845 10 + 294540 CTCAATATGG -s simCow_chr6.simCow.chr6 238147 10 + 602619 CTCAATACTT -s simDog_chr6.simDog.chr6 230410 10 + 593897 CTAAATACGT -s simHuman_chr6.simHuman.chr6 320266 10 - 601863 CTCAATATGT -s simRat_chr6.simRat.chr6 232289 10 + 647215 CTCAATATGG - -a -s simMouse_chr6.simMouse.chr6 241787 2 + 636262 TG -s Anc0.Anc0refChr5 60845 2 + 87904 TT -s Anc1.Anc1refChr7 18518 2 - 47259 TT -s Anc2.Anc2refChr15 57508 2 + 86568 TT -s mr.mrrefChr5 94855 2 + 294540 TG -s simCow_chr6.simCow.chr6 238161 2 + 602619 TT -s simDog_chr6.simDog.chr6 230420 2 + 593897 TT -s simHuman_chr6.simHuman.chr6 320276 2 - 601863 TC -s simRat_chr6.simRat.chr6 232299 2 + 647215 TG - -a -s simMouse_chr6.simMouse.chr6 241789 56 + 636262 ACTTCTTTTCTCAATGTACTAGTGGGTAAATAAATGTGGGAATGTACAAAGCCAGT -s Anc0.Anc0refChr5 60847 46 + 87904 A-TGCTTTT---ACGATGCCA-----TATATAAATGTCAGGATTTACAAAGGT-GT -s Anc1.Anc1refChr7 18520 46 - 47259 A-TGCTTTT---ACGATGCCA-----TATATAAATGTCAGGATTTACAAAGGT-GT -s Anc2.Anc2refChr15 57510 46 + 86568 A-TGGTATT---ACGATGTCA-----TATATAAATGTCAGGATTTACAAAGGT-GT -s mr.mrrefChr5 94857 56 + 294540 ACTTCTTTTCTCAATGTACTAGTGGGTAAATAAATGTGGGAATGTACAAAGCCAGT -s simCow_chr6.simCow.chr6 238163 44 + 602619 A-GGATCTT-----GATGTCA-----TAAATAAATGTCAGGATTTACAAAAGT-GT -s simDog_chr6.simDog.chr6 230422 31 + 593897 T-TGGTATC---ACGATGTTG-----TATTTA---------------AAAGGT-GT -s simHuman_chr6.simHuman.chr6 320278 46 - 601863 A-TGCTTTT---AGAATGCCA-----TACATATATGCCATGATTTACAAAGGT-GT -s simRat_chr6.simRat.chr6 232302 51 + 647215 ACTTCTTTTCTCAATGTACTAGTGGGTAAATGAATGTGGGAATGTA-----CCAGT - -a -s simMouse_chr6.simMouse.chr6 241845 74 + 636262 AAAAACATGCCTCTGTAATGACATCGACTGTTACACAGTACGCAGTGAGCTCAACTGTAACACAGTACGCAATG -s Anc0.Anc0refChr5 60895 47 + 87904 ATGAACATTACTCTCTAATGGCACACACTGTTACACTGTCAGCAT---------------------------TA -s Anc1.Anc1refChr7 18568 47 - 47259 ATGAACATTACTCTCTAATGGCACACACTGTTACACTGTCAGCAT---------------------------TA -s Anc2.Anc2refChr15 57558 47 + 86568 TTGAACATTACTCTCTAATGGCACACACTGTTACACTGTCAGCAT---------------------------CA -s mr.mrrefChr5 94915 47 + 294540 AAAAACATGCCTCTGTAATGACATCGACTGTTACACTGTAAGCAG---------------------------TG -s simCow_chr6.simCow.chr6 238209 47 + 602619 TTGAACATGGCTCTATAACAGCACACCCCACTAAAATGTCAGCAT---------------------------CA -s simDog_chr6.simDog.chr6 230455 47 + 593897 TGGAACTTTACTCTCTAATGGTACACACTGTTGCACCGTCAGCAT---------------------------CA -s simHuman_chr6.simHuman.chr6 320326 46 - 601863 ATGAATATAACCCC-TAATGTCACACACTGTTACACTGTCAGCAT---------------------------TA -s simRat_chr6.simRat.chr6 232355 47 + 647215 AAAAACATGTCTCTTTAATAACATCGACTGTTACACTGTTAGCAG---------------------------TG - -a -s simMouse_chr6.simMouse.chr6 241919 112 + 636262 AGCTACAGCAGGAGTAGATCTCAGAATTATCTAGGATAACATGCAGTAATCTGCCCACGGAGTGAATCAGCTAACCTTGTCAGTCGTGATTTTAACTTAATACTTCCAGTAC -s Anc0.Anc0refChr5 60954 112 + 87904 AGCTACAGCAGGAGTAAACTTCAGAATGACCTGGGATTACAGACGGTGACCGCCACAGGAAGTGGATCAGCTAGCCATGGGGGTTGTGGGTCTTGTTTAATACTTCTAGCAC -s Anc1.Anc1refChr7 18627 112 - 47259 AGCTACAGCAGGAGTAAACTTCAGAATGACCTGGGATTACAGACGGTGACCGCCACAGGAAGTGGATCAGCTAGCCATGGGGGTTGTGGGTCTTGTTTAATACTTCTAGCAC -s Anc2.Anc2refChr15 57617 112 + 86568 AGCTACAGAGGGAGTAAACTTCAGAATGACCTGGGATTATAGATGGTGACCTCCACAGGTAGTGGATCAGCTAGCCGTAGGGGCTGTGGGTCCTGTTTAATACTTCTAGCAC -s mr.mrrefChr5 94962 112 + 294540 AGCTACAGCAGGAGTAGACCTCAGAATGACCTAGGATAACATACGGTAATCGGCCCACGAAGTGAATCAGCTAACCATGTGAGTTGTGAGTTTAACTTAATACTTCTAGTAC -s simCow_chr6.simCow.chr6 238268 100 + 602619 AGCTACAGTGAGAATAAACTTCTGAATAACCTG----TATAGATAGTAACCTC------GAGTGAACCACCTAGCC--AGGGGCTGTGGGTCCTGTGGAATACCTCTGGTCC -s simDog_chr6.simDog.chr6 230512 106 + 593897 ---TACAGAGGAAGTGAACTTCAAAA-GACCTGGGATTATAGGTGGTGGTT-CCACAGGTAGGGGATCGGCCTGCTGTAGGGA-TGTGGATCCTCTTTAGTACTGCTAACAC -s simHuman_chr6.simHuman.chr6 320384 112 - 601863 AGCTACAACAGGAGTAAACTTCAGAATGACCTGGGCTTACAGACGATGACCGCCAAGGAAAGTGGATCAGCTAGGCATGGGGGTTGTGGGACTCGTTTGATACTTCTAGCAC -s simRat_chr6.simRat.chr6 232402 112 + 647215 GACTACAGCAGCATTAGGCCTCAGAATGCCCAAGGATAACATATGGTAAGCGGCCCAAGAAGTGACTCGGCTTACCACATGAGTTGTGAGTTTTACTTAATACTTCTAGTAC - -a -s simMouse_chr6.simMouse.chr6 242031 13 + 636262 TCACACAATGCTA -s Anc0.Anc0refChr5 61072 13 + 87904 TTACACCATACAA -s Anc1.Anc1refChr7 18745 13 - 47259 TTACACCATACAA -s Anc2.Anc2refChr15 57735 13 + 86568 TTACACCATACAA -s mr.mrrefChr5 95074 13 + 294540 TCACACAATGCAA -s simCow_chr6.simCow.chr6 238374 13 + 602619 TTATGCCATACAA -s simDog_chr6.simDog.chr6 230620 13 + 593897 TTACACCATACAA -s simHuman_chr6.simHuman.chr6 320502 13 - 601863 TTACACCATTCAG -s simRat_chr6.simRat.chr6 232514 13 + 647215 TCTCACAATGCAA - -a -s simMouse_chr6.simMouse.chr6 242044 23 + 636262 GGTATCATTTAAAGCCCCCAGCT -s Anc0.Anc0refChr5 61086 23 + 87904 GGCACCATTTTGAGCTCCCAGCG -s Anc1.Anc1refChr7 18759 23 - 47259 GGCACCATTTTGAGCTCCCAGCG -s Anc2.Anc2refChr15 57749 23 + 86568 GGCACCATGTTGAGCTCCCAGCG -s mr.mrrefChr5 95087 23 + 294540 GGTATCATTTAGAGCCCCCAGCT -s simCow_chr6.simCow.chr6 238388 23 + 602619 TGCATGATGTTGAGTTCCCAGCT -s simDog_chr6.simDog.chr6 230634 23 + 593897 GGCACCATGTTGTGCTCCCAACG -s simHuman_chr6.simHuman.chr6 320516 23 - 601863 GCCACCATTTTGAGCTCCCAGCG -s simRat_chr6.simRat.chr6 232527 23 + 647215 GGAATCGTTTGGAGCCCCCAGCT - -a -s simMouse_chr6.simMouse.chr6 242067 12 + 636262 GTGGTGAGGGTT -s Anc0.Anc0refChr5 61109 12 + 87904 ACAGTGGGAGTA -s Anc1.Anc1refChr7 18782 12 - 47259 ACAGTGGGAGTA -s Anc2.Anc2refChr15 57772 12 + 86568 ACAGTGGAAGTA -s mr.mrrefChr5 95110 12 + 294540 GTAGTGAGGGTT -s simCow_chr6.simCow.chr6 238411 12 + 602619 ACAGTAGAAGTA -s simDog_chr6.simDog.chr6 230671 12 + 593897 ATAGTGCAAGTA -s simHuman_chr6.simHuman.chr6 320539 12 - 601863 ACAGGGGGAGTA -s simRat_chr6.simRat.chr6 232550 12 + 647215 GTAGTGAGGGGT - -a -s simMouse_chr6.simMouse.chr6 242079 26 + 636262 AAGACCCTGGGATTACACATGGAGAG -s Anc0.Anc0refChr5 61129 26 + 87904 AGTGACCAGGGATTACAGATGGTGAC -s Anc1.Anc1refChr7 18802 26 - 47259 AGTGACCAGGGATTACAGATGGTGAC -s Anc2.Anc2refChr15 57792 26 + 86568 AGTGACTAGGGATTACAGATGGTGAC -s mr.mrrefChr5 95130 26 + 294540 AAGACCCTGGGATTACACATGGAGAC -s simCow_chr6.simCow.chr6 238431 26 + 602619 AACAGTGAGTGATTGCAGATGGTGAC -s simDog_chr6.simDog.chr6 230691 25 + 593897 AGTGACT-GGGACTACAGATAGTTAC -s simHuman_chr6.simHuman.chr6 320559 26 - 601863 AGTGACCCAGGATTACAGACGGTGAC -s simRat_chr6.simRat.chr6 232570 26 + 647215 AAGAGCCTGGGATTACATATGGAAAC - -a -s simMouse_chr6.simMouse.chr6 242105 12 + 636262 TCCTGGAGAGGT -s Anc0.Anc0refChr5 61156 12 + 87904 TCCATAAGAAGT -s Anc1.Anc1refChr7 18829 12 - 47259 TCCATAAGAAGT -s Anc2.Anc2refChr15 57819 12 + 86568 TCTATAGGAAAT -s mr.mrrefChr5 95156 12 + 294540 TCCTGGAGAGGT -s simCow_chr6.simCow.chr6 238458 2 + 602619 TC---------- -s simDog_chr6.simDog.chr6 230717 12 + 593897 TCTATAGGAAAT -s simHuman_chr6.simHuman.chr6 320586 12 - 601863 TCCATCAGAAGT -s simRat_chr6.simRat.chr6 232596 12 + 647215 TACTGGAAAGGT - -a -s simMouse_chr6.simMouse.chr6 242117 36 + 636262 ATGTTTTGAATTTTACAGTGATGGATGGCACATGCC -s Anc0.Anc0refChr5 61197 36 + 87904 TTGTTTTGAACTTTACAGTGATGGATGGGACATGCC -s Anc1.Anc1refChr7 18870 36 - 47259 TTGTTTTGAACTTTACAGTGATGGATGGGACATGCC -s Anc2.Anc2refChr15 57860 36 + 86568 TTGTTTAGTACTTTATAGTGATGGATGGGACATGCC -s mr.mrrefChr5 95196 36 + 294540 ATGTTTTGAACTTTACAGTGATGGATGGCACATGCC -s simCow_chr6.simCow.chr6 238485 23 + 602619 TAGTTT-------------GATGGATGGGACATGCC -s simDog_chr6.simDog.chr6 230758 36 + 593897 CTGTTTAGTACTTTATAGTAATGGATGGGACATGCC -s simHuman_chr6.simHuman.chr6 320627 36 - 601863 TTGTTTTCAACATCACAGTGAGGGATGGGACGTGCA -s simRat_chr6.simRat.chr6 232644 36 + 647215 ATGTTTTGAACTTTACAGTGATAGGTGACACATGCC - -a -s simMouse_chr6.simMouse.chr6 242153 7 + 636262 ATGAATA -s Anc0.Anc0refChr5 61233 7 + 87904 ATGACTA -s Anc1.Anc1refChr7 18906 7 - 47259 ATGACTA -s Anc2.Anc2refChr15 57896 7 + 86568 ATGACTA -s mr.mrrefChr5 95232 7 + 294540 ATGAATA -s simCow_chr6.simCow.chr6 238509 7 + 602619 ATGTCTA -s simDog_chr6.simDog.chr6 230794 7 + 593897 ATGACTA -s simHuman_chr6.simHuman.chr6 320663 7 - 601863 ATGATGA -s simRat_chr6.simRat.chr6 232680 7 + 647215 ATGAATA - -a -s simMouse_chr6.simMouse.chr6 242160 14 + 636262 TACCGCAAATACCT -s Anc0.Anc0refChr5 61240 14 + 87904 AACTGCAAGCCACT -s Anc1.Anc1refChr7 18913 14 - 47259 AACTGCAAGCCACT -s Anc2.Anc2refChr15 57903 14 + 86568 AACTGCAAGCCACT -s mr.mrrefChr5 95239 14 + 294540 TACCGCAAATACCT -s simCow_chr6.simCow.chr6 238584 13 + 602619 AACT-CAAGCCCCT -s simDog_chr6.simDog.chr6 230801 13 + 593897 AACTGCAAAT-ACT -s simHuman_chr6.simHuman.chr6 320670 14 - 601863 AACTGCAAGCCACC -s simRat_chr6.simRat.chr6 232687 14 + 647215 GACCACAAATACCT - -a -s simMouse_chr6.simMouse.chr6 242174 8 + 636262 CTCGAATA -s Anc0.Anc0refChr5 61254 8 + 87904 CTTTACCA -s Anc1.Anc1refChr7 18927 8 - 47259 CTTTACCA -s Anc2.Anc2refChr15 57917 8 + 86568 TTTTACCA -s mr.mrrefChr5 95253 8 + 294540 CTTGAATA -s simCow_chr6.simCow.chr6 238600 8 + 602619 TTTTTCCA -s simDog_chr6.simDog.chr6 230814 8 + 593897 TTTTATGA -s simHuman_chr6.simHuman.chr6 320684 8 - 601863 CTTTACCA -s simRat_chr6.simRat.chr6 232701 8 + 647215 ATTAAATA - -a -s simMouse_chr6.simMouse.chr6 242182 44 + 636262 ACTGTAATTTACCTGTAATTTACTTAATCCATCTTGTGATACAG -s Anc0.Anc0refChr5 61264 33 + 87904 A-----------CTGTAGTCTAAACACTTCATCATGTGATACAG -s Anc1.Anc1refChr7 18937 33 - 47259 A-----------CTGTAGTCTAAACACTTCATCATGTGATACAG -s Anc2.Anc2refChr15 57927 33 + 86568 A-----------CTGTAGTCTAAACACTTCATCATGTGATACAG -s mr.mrrefChr5 95261 33 + 294540 A-----------CTGTAGTCTACTTAATCCATCTTGTGATACAG -s simCow_chr6.simCow.chr6 238610 33 + 602619 A-----------ATGTAGTCTACATACTTGATTATGTGATACAG -s simDog_chr6.simDog.chr6 230824 33 + 593897 C-----------CTGTAATCTGAACACTTCATCATGTGATACAG -s simHuman_chr6.simHuman.chr6 320694 33 - 601863 A-----------CTATGGTCTAGAGACTTCATCATGTGATGCAA -s simRat_chr6.simRat.chr6 232709 33 + 647215 A-----------GTGTAGTCTACTCAATCCATCTTGTGATACAG - -a -s simMouse_chr6.simMouse.chr6 242226 31 + 636262 GACATGAGGGCGAGGCCCATTTTCTAAGGTT -s Anc0.Anc0refChr5 61297 31 + 87904 CTGTGGGGTGTAAAGCCCATTTGTCAAGGTT -s Anc1.Anc1refChr7 18970 31 - 47259 CTGTGGGGTGTAAAGCCCATTTGTCAAGGTT -s Anc2.Anc2refChr15 57962 31 + 86568 CTGTGGGGTGTAAAGCCCATTAGTCAAGATT -s mr.mrrefChr5 95294 31 + 294540 GACATGAGGGTGAGGCCCATTTTCTAAGGTT -s simCow_chr6.simCow.chr6 238645 31 + 602619 CCATGGGGTGTGAAGCCTACTAGTAAATATT -s simDog_chr6.simDog.chr6 230859 31 + 593897 CTGTGGGGTGTAAAGCCCTTTACTCAAGATT -s simHuman_chr6.simHuman.chr6 320727 31 - 601863 ATGTAGTGTGTAAAGCCCATTTGACGAGGTT -s simRat_chr6.simRat.chr6 232742 31 + 647215 GACATGAGGGTGAGGCCCATTTCCTAAGGTC - -a -s simMouse_chr6.simMouse.chr6 242257 66 + 636262 CCCAGCACCATAAAGAAATCCAGCAGGGTGCAGTGTGAGTGAACAAGCCTATCAATTTGTAGATAT -s Anc0.Anc0refChr5 61328 60 + 87904 CCCACCCCTCCAAAAAAAACTAACAGTACGCA------GTGATCTGGACTCTCAATCTGTGAATGT -s Anc1.Anc1refChr7 19001 60 - 47259 CCCACCCCTCCAAAAAAAACTAACAGTACGCA------GTGATCTGGACTCTCAATCTGTGAATGT -s Anc2.Anc2refChr15 57994 60 + 86568 CCCACCCCTCCAAAAAAAACTAACAGTATACA------GTGATTTGGACTCTCAATCTGTGAATGT -s mr.mrrefChr5 95325 62 + 294540 CCCAGCACCATAAAGAAATCCAGCAGGGCGCAGT----GTGAACAAGCCTATCAATTTGTGAATGT -s simCow_chr6.simCow.chr6 238677 60 + 602619 CCCACCCCCCTGAAAAAAATTAACAGTATACA------GAGATTTAGACTCACAATCTGTGAATGT -s simDog_chr6.simDog.chr6 230891 60 + 593897 CCCACCTCTACAAAAAAAACCTACAGTATACA------GTGATTTGAACTCTCAATCTGCGAATGT -s simHuman_chr6.simHuman.chr6 320758 60 - 601863 CCCACCCCTCCTAAAAGAACTAACAGTTCGCA------GTGATCTTGGCTCCCAATCTGTGAATGT -s simRat_chr6.simRat.chr6 232773 62 + 647215 CCCAGCATCATAGAGAAATCCAGCAGGGCGCAAT----GTCAATAAGCCTATCAATTTGTGAATGT - -a -s simMouse_chr6.simMouse.chr6 242323 115 + 636262 GGTCAGAACACGCATGTTCTGAGATCTGGATGTTCTGAGATCTTGACCCAGAATACATTTAGTACGATTCTTCTGTGGGCTTTCAGCCAGATGAAACAAGAGACATGCAAGATTC -s Anc0.Anc0refChr5 61408 101 + 87904 GGTCAGAACAGGCATGTCCTTAGACCTTG--ACCTAGAGCCCTTG------------TTTAGTACCAAGCTTTTTTGAGCTCTCAGTAAGATGAAAGAAGAGACATGCAAGATTC -s Anc1.Anc1refChr7 19081 101 - 47259 GGTCAGAACAGGCATGTCCTTAGACCTTG--ACCTAGAGCCCTTG------------TTTAGTACCAAGCTTTTTTGAGCTCTCAGTAAGATGAAAGAAGAGACATGCAAGATTC -s Anc2.Anc2refChr15 58074 101 + 86568 GGTCAGAACAGGCATGTCCTTAGACCTTG--ACCTAGAGCCCCTG------------TTTTGTACCAAGCTTTTTTGAGCTCACAGCAAGATGAAAGAAGAGACATGCAAGATTC -s mr.mrrefChr5 95407 113 + 294540 GGTCAGAACAGGCATGTTCTGAGATCTGG--GTTCTGAGATCTTGACCCAGAATACATTTAGTACGATTCTTTTGTGAGCTCTCAGTCAGATGAAACAAGAGACATGCAAGATTC -s simCow_chr6.simCow.chr6 238757 101 + 602619 GGTCCAAACAGGCATGTCCTTAAACCACG--ACCTAGCACCCATA------------TTTTGTACTGAGCTTTTTTGAGCTAACAGCAAGACGAAAGACGAGACATGCAAGATTC -s simDog_chr6.simDog.chr6 230971 90 + 593897 AGTCAGAACAGGCATGTCCTCAGACCTTG--ATCTACAGCC-CTG------------CCTTGTATCATGCTGTTTTGAGCCCACAGCAAGATGAAAGAAGA----------GCTC -s simHuman_chr6.simHuman.chr6 320838 101 - 601863 GTTTAGAACAGGCTTGTCCTTAGGGCTTT--ACCTAGAGCCCTTG------------TTCAGTACCAAGCTTTTTTAAGCTCTCAGTGAGATGAAATAAGAGATATGCAAGATTC -s simRat_chr6.simRat.chr6 232855 71 + 647215 GGTCAGAAAAGGCATGTTCTGAGATCTGG--------------------------------GTACACTTCTTTTGCGAGCTCCCAGTTAGATGAAACTGGATA------------ - -a -s simMouse_chr6.simMouse.chr6 242438 6 + 636262 TAAATG -s Anc0.Anc0refChr5 61513 6 + 87904 TTAATG -s Anc1.Anc1refChr7 19186 6 - 47259 TTAATG -s Anc2.Anc2refChr15 58179 6 + 86568 TTATTG -s mr.mrrefChr5 95520 6 + 294540 TAAATG -s simCow_chr6.simCow.chr6 238862 6 + 602619 TTTTTG -s simDog_chr6.simDog.chr6 231065 6 + 593897 TGATTG -s simHuman_chr6.simHuman.chr6 320943 6 - 601863 TTAATG -s simRat_chr6.simRat.chr6 232926 5 + 647215 -AAATG - -a -s simMouse_chr6.simMouse.chr6 242444 58 + 636262 CCTTGAGGAGTAAGTCAGTTTGTGAGGACCCAGATTAGGAGACATGTATGGATTGACA -s Anc0.Anc0refChr5 61619 57 + 87904 TCTTGTTAAGTACATCA-ACTGGGAGTACACAAATTGGGATACACATTTGGATTGAGT -s Anc1.Anc1refChr7 19292 57 - 47259 TCTTGTTAAGTACATCA-ACTGGGAGTACACAAATTGGGATACACATTTGGATTGAGT -s Anc2.Anc2refChr15 58285 57 + 86568 TCTTGTTAAGTACATCA-ACTGGGCATACACAAATTGGGATACACATTTGGATTGAGT -s mr.mrrefChr5 95526 58 + 294540 CCTTGTGAAGTAAGTCAGATTGTGAGGACCCAGATTAGGAGACATATATGGATTGACT -s simCow_chr6.simCow.chr6 238968 57 + 602619 TCTTATTAAGTACATCA-ACCAGGCATACACAAACTGGGATACACCTTAGGGTTGAGT -s simDog_chr6.simDog.chr6 231088 54 + 593897 ---TGTTAGGTACATCA-ACTGAGCATACGCAAATTGGGACAGACATTTGGATTGAAT -s simHuman_chr6.simHuman.chr6 321061 57 - 601863 TCTTGTTAAGTATATCA-ACTGGGAGTACACAAATTGGGATACACAGCTTGATTGAGT -s simRat_chr6.simRat.chr6 232931 58 + 647215 CCTTGTGAAGTGAGTCAGATTGTGAGGTCCCAGATTAGGAGACATATATGGATTGACT - -a -s simMouse_chr6.simMouse.chr6 242502 19 + 636262 GTCCCACCACGCTTGCTGC -s Anc0.Anc0refChr5 61677 19 + 87904 GTCCCACTAAGCTTGCTGC -s Anc1.Anc1refChr7 19350 19 - 47259 GTCCCACTAAGCTTGCTGC -s Anc2.Anc2refChr15 58343 19 + 86568 GTCCCATCAAGCTTGCTGT -s mr.mrrefChr5 95584 19 + 294540 GTCCCACTAAGCTTGCTGC -s simCow_chr6.simCow.chr6 239047 19 + 602619 GTGCCTTCAAGCTTGCTGT -s simDog_chr6.simDog.chr6 231143 19 + 593897 GTCCCATCAAGCTTGGCGT -s simHuman_chr6.simHuman.chr6 321119 19 - 601863 GTCCCACTAAGCTTGCTGC -s simRat_chr6.simRat.chr6 232989 19 + 647215 GTCTGATTAAGCTTGCTGC - -a -s simMouse_chr6.simMouse.chr6 242521 15 + 636262 ACATCACTAGGCGAG -s Anc0.Anc0refChr5 61697 15 + 87904 ATTTCACTGAGCATG -s Anc1.Anc1refChr7 19370 15 - 47259 ATTTCACTGAGCATG -s Anc2.Anc2refChr15 58363 15 + 86568 ATTTCATTGAGCATG -s mr.mrrefChr5 95603 15 + 294540 ACATCACTAAGCGAG -s simCow_chr6.simCow.chr6 239067 12 + 602619 ATTTCATTGA---TG -s simDog_chr6.simDog.chr6 231163 15 + 593897 GGTCCATTGGGCACA -s simHuman_chr6.simHuman.chr6 321139 15 - 601863 ATTTCACTGAGCTTG -s simRat_chr6.simRat.chr6 233008 15 + 647215 ACATCGCTAAGCAAG - -a -s simMouse_chr6.simMouse.chr6 242536 97 + 636262 CCTCCAGATGATTTACATCTTACCATAGTTCTTCCTTTGACATTGCGAAAGGCTACAAAACATATTGCATACTTTCTAACAATGATGTGAGTCAGTC -s Anc0.Anc0refChr5 61733 97 + 87904 CCCCCATATGGTTTACATCTTACCACAATTTTACCATTACCATTGTGAAAGGCTAGGAAAAGTAAGGTGTACTCTATAAAAATGTTGTGAAGCTGTC -s Anc1.Anc1refChr7 19408 97 - 47259 CCCCCATATGGTTTACATCTTACCACAATTTTACCATTACCATTGTGAAAGGCTAGGAAAAGTAAGGTGTACTCTATAAAAATGTTGTGAAGCTGTC -s Anc2.Anc2refChr15 58399 97 + 86568 CCCCCATATGGTTTACATCTTACCACAATTTTACCATTACCATTGTGAAAGGCTAGGAAAAGTAAGGTGTACTTTATAAAAATGTTGTGAAGCTGTC -s mr.mrrefChr5 95618 97 + 294540 CCTCCAGATGATTTACATCTTACCATAGTTTTTCCTTTGCCATTGTGAAAGGCTACAAAAAGTAATGCGTACTCTCTAACAATGATGTGAGTCAGTC -s simCow_chr6.simCow.chr6 239097 92 + 602619 ACCCCATGTGGTTTATATCTTAGCACA----TTCCATTGCCATTGTGAAAGGCTAGGAAAAGCAAGGTGT-CTTTCTAAAAATGTTGTGAAGCTGTC -s simDog_chr6.simDog.chr6 231199 97 + 593897 CCCCCATATAGTTTACATCTTACCACAATTTTATCATTACCCTTGTGGAAGGCTAGGAAAAGTAAGGTGTACTTTATAAAAATATCGTGAAACTGTC -s simHuman_chr6.simHuman.chr6 321177 97 - 601863 CCCCCATATGGTTTACATCTCATCACAATTTTGCCACTTCCATTGTGAAAGGCTATGAAGAGTAAATGGTATTCTATAAAAATGTTATTAAGCTGTC -s simRat_chr6.simRat.chr6 233023 97 + 647215 CTGCCAAATGATTTATATATTACCATAGTTTTTCCTTCGCCATTGTGAAAGGCTACAAAAAGTAATGCGTACTCTCTAACAATGATGTGACTCAGTC - -a -s simMouse_chr6.simMouse.chr6 242633 13 + 636262 TCGACAGGTTGTC -s Anc0.Anc0refChr5 61832 13 + 87904 GTGATAGGTTTTC -s Anc1.Anc1refChr7 19507 13 - 47259 GTGATAGGTTTTC -s Anc2.Anc2refChr15 58498 13 + 86568 GTGATAGGTTTTG -s mr.mrrefChr5 95715 13 + 294540 TTGATAGGTTGTC -s simCow_chr6.simCow.chr6 239191 13 + 602619 GTGAATGGTGCAG -s simDog_chr6.simDog.chr6 231298 13 + 593897 GTGATAGCTTTTG -s simHuman_chr6.simHuman.chr6 321276 13 - 601863 GTGATAGGTATTC -s simRat_chr6.simRat.chr6 233120 13 + 647215 TTGTTAGGTTGTC - -a -s simMouse_chr6.simMouse.chr6 242646 17 + 636262 AGGATTAAGTGATGTAT -s Anc0.Anc0refChr5 61851 17 + 87904 AAGAATGAACAGTGTAT -s Anc1.Anc1refChr7 19526 17 - 47259 AAGAATGAACAGTGTAT -s Anc2.Anc2refChr15 58517 17 + 86568 AAGAATGAACAGTGTAT -s mr.mrrefChr5 95728 17 + 294540 AGGATTAAGTGATATAT -s simCow_chr6.simCow.chr6 239210 17 + 602619 AAGAATGAACAGTGTAT -s simDog_chr6.simDog.chr6 231317 17 + 593897 AGGAATGAACAGTGTAT -s simHuman_chr6.simHuman.chr6 321295 17 - 601863 AATGATGAACAGTGTAT -s simRat_chr6.simRat.chr6 233133 17 + 647215 AGGATCAAGTGATACAT - -a -s simMouse_chr6.simMouse.chr6 242663 7 + 636262 ATCAGTA -s Anc0.Anc0refChr5 61920 7 + 87904 GTGAATG -s Anc1.Anc1refChr7 19595 7 - 47259 GTGAATG -s Anc2.Anc2refChr15 58641 7 + 86568 GTGAATG -s mr.mrrefChr5 95745 7 + 294540 ATCAGTA -s simCow_chr6.simCow.chr6 239347 7 + 602619 GTGAATG -s simDog_chr6.simDog.chr6 231441 7 + 593897 GTGAATA -s simHuman_chr6.simHuman.chr6 321364 7 - 601863 GTGAATG -s simRat_chr6.simRat.chr6 233150 7 + 647215 CTCAGTT - -a -s simMouse_chr6.simMouse.chr6 242670 7 + 636262 GATGATA -s Anc0.Anc0refChr5 61927 7 + 87904 AGTGATA -s Anc1.Anc1refChr7 19602 7 - 47259 AGTGATA -s Anc2.Anc2refChr15 58676 7 + 86568 AGTGATA -s mr.mrrefChr5 95752 7 + 294540 GATGATA -s simCow_chr6.simCow.chr6 239382 6 + 602619 AGT-ATG -s simDog_chr6.simDog.chr6 231476 7 + 593897 AGCGAGA -s simHuman_chr6.simHuman.chr6 321371 7 - 601863 AGTGATA -s simRat_chr6.simRat.chr6 233157 7 + 647215 AATGATA - -a -s simMouse_chr6.simMouse.chr6 242677 32 + 636262 CACTAGATAATATGAAACACTAGACCTCTTAT -s Anc0.Anc0refChr5 61939 32 + 87904 CACTAGATGATATGAAATGCTGGACCTCTTAC -s Anc1.Anc1refChr7 19614 32 - 47259 CACTAGATGATATGAAATGCTGGACCTCTTAC -s Anc2.Anc2refChr15 58688 32 + 86568 CACTAGATTATATGAAATGCTGGACCTCTTAT -s mr.mrrefChr5 95759 32 + 294540 CACTAGATGATATGAAACGCTAGACCTCTTAC -s simCow_chr6.simCow.chr6 239393 31 + 602619 TGCCAGAATAGATGAAATGCTGGACC-CTTCT -s simDog_chr6.simDog.chr6 231488 32 + 593897 CACTAGATTATATGAAATGCTGAACCTCTTAT -s simHuman_chr6.simHuman.chr6 321383 32 - 601863 CAGTAGATGATATGAAATTCTGGACCTCTTAC -s simRat_chr6.simRat.chr6 233164 32 + 647215 CATTAGATGATGTAAAACGCTAGACCTCTTCC - -a -s simMouse_chr6.simMouse.chr6 242709 9 + 636262 AATCATGGG -s Anc0.Anc0refChr5 61971 9 + 87904 AATCAGGGT -s Anc1.Anc1refChr7 19646 9 - 47259 AATCAGGGT -s Anc2.Anc2refChr15 58720 9 + 86568 AATCAGGGT -s mr.mrrefChr5 95791 9 + 294540 AATCATGGG -s simCow_chr6.simCow.chr6 239424 9 + 602619 GATAAGGGT -s simDog_chr6.simDog.chr6 231521 9 + 593897 AATCAGCGT -s simHuman_chr6.simHuman.chr6 321415 9 - 601863 AATCGGGGA -s simRat_chr6.simRat.chr6 233196 9 + 647215 AATCATGGG - -a -s simMouse_chr6.simMouse.chr6 242718 2 + 636262 GA -s Anc1.Anc1refChr6 121938 2 + 197743 GG -s mr.mrrefChr3 24551 2 + 181027 GG -s mr.mrrefChr5 95813 2 + 294540 GA -s simMouse_chr6.simMouse.chr6 468843 2 + 636262 GG -s simMouse_chr6.simMouse.chr6 697 2 - 636262 GA -s simRat_chr6.simRat.chr6 478783 2 + 647215 GG -s simRat_chr6.simRat.chr6 352588 2 + 647215 GG -s simRat_chr6.simRat.chr6 66883 2 - 647215 GG - -a -s simMouse_chr6.simMouse.chr6 242720 4 + 636262 CTTC -s Anc1.Anc1refChr6 121940 4 + 197743 CTTC -s mr.mrrefChr3 24553 4 + 181027 CTTC -s mr.mrrefChr5 95815 4 + 294540 CTTC -s simMouse_chr6.simMouse.chr6 468846 4 + 636262 CTTC -s simMouse_chr6.simMouse.chr6 699 4 - 636262 CTTC -s simRat_chr6.simRat.chr6 478785 4 + 647215 CTTC -s simRat_chr6.simRat.chr6 352590 4 + 647215 CTTC - -a -s simMouse_chr6.simMouse.chr6 242724 1 + 636262 A -s Anc1.Anc1refChr6 121944 1 + 197743 A -s mr.mrrefChr3 24557 1 + 181027 A -s mr.mrrefChr3 157148 1 + 181027 G -s mr.mrrefChr5 95819 1 + 294540 A -s simMouse_chr6.simMouse.chr6 468850 1 + 636262 A -s simMouse_chr6.simMouse.chr6 609224 1 + 636262 G -s simMouse_chr6.simMouse.chr6 703 1 - 636262 G -s simRat_chr6.simRat.chr6 478789 1 + 647215 A -s simRat_chr6.simRat.chr6 83776 1 - 647215 G -s simRat_chr6.simRat.chr6 352594 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 242725 17 + 636262 AATTCACAAACAAAGCG -s Anc1.Anc1refChr6 121945 17 + 197743 AAGTCGCAAACAAAGCA -s mr.mrrefChr3 24558 17 + 181027 AAGTTGCAAACAGAGCA -s mr.mrrefChr3 157149 17 + 181027 AAGCCGCAAACAAAGCA -s mr.mrrefChr5 95820 17 + 294540 AAGTCGCAAACAAAGCG -s simMouse_chr6.simMouse.chr6 468851 17 + 636262 AAGTTGCAAACAGAGCA -s simMouse_chr6.simMouse.chr6 609225 17 + 636262 AAGCCGCAAACAAAGCA -s simMouse_chr6.simMouse.chr6 704 17 - 636262 AAGTCGTGAACAAAGCG -s simRat_chr6.simRat.chr6 478790 17 + 647215 AAGTTGCAAGCAAAGTA -s simRat_chr6.simRat.chr6 83777 17 - 647215 AAGTCACAAACAAGGCA -s simRat_chr6.simRat.chr6 352595 17 + 647215 AAGTCGCAAACAATGTA -s simRat_chr6.simRat.chr6 66885 17 - 647215 AAGTCGCAAACGAAGCA - -a -s simMouse_chr6.simMouse.chr6 242742 4 + 636262 TACA -s Anc1.Anc1refChr6 121962 4 + 197743 TACG -s mr.mrrefChr3 24575 4 + 181027 TACG -s mr.mrrefChr3 157166 4 + 181027 TACG -s mr.mrrefChr5 95837 4 + 294540 TACG -s simMouse_chr6.simMouse.chr6 468868 4 + 636262 TACG -s simMouse_chr6.simMouse.chr6 609242 4 + 636262 TACG -s simMouse_chr6.simMouse.chr6 721 4 - 636262 TACG -s simRat_chr6.simRat.chr6 478807 4 + 647215 TACA -s simRat_chr6.simRat.chr6 83794 4 - 647215 TACA -s simRat_chr6.simRat.chr6 66902 4 - 647215 TATG - -a -s simMouse_chr6.simMouse.chr6 242746 61 + 636262 CGAGGCAGTCGTATACAAGAGTGTTCAGTTAGCAAATCGTCTCGAGCGAGTCATGACCGTG -s Anc1.Anc1refChr6 121966 61 + 197743 CAAGGCAATTGCATACCAGAGCCCTCAAATGGCAAATAGTCTTGAGCTAATAATGACTGTG -s mr.mrrefChr3 24579 61 + 181027 CAAGTCAATTGCATACCGGAGCCCTCAAATGGCAATTAGTCCCAAGCCAACAATGATTGTG -s mr.mrrefChr3 157170 61 + 181027 CAAGGCAATTGCATACTAGAGCACTCAAATGGCAAATAGTCTTGAGTTAATAATGACTGTG -s mr.mrrefChr5 95841 61 + 294540 CAAGGCAGTCGCATACCAGAGTGCTCAGTTAGCAAATCGTCTTGAGCGAATCATGACCGTG -s simMouse_chr6.simMouse.chr6 468872 61 + 636262 CAAGTCAATTGCATACCGGAGCCCTCAAATGGCAATTAGTCCCAAGCCAACAATGATTGTG -s simMouse_chr6.simMouse.chr6 609246 61 + 636262 CAAGGCAATTGCATACTAGAGCACTCAAATGGCAAATAGTCTTGAGTTAATAATGACTGTG -s simMouse_chr6.simMouse.chr6 725 61 - 636262 CAAGGCGGTCGCATACCAGAGCGCTCAGTTAGCAAATCGTCTTGAGCGAATCATGACCGTG -s simRat_chr6.simRat.chr6 478811 61 + 647215 CAAAGCAATTGCATACTGGAGCACTCAAATGGCAGATAGCCCCAAGCCAATAATGACTGTG -s simRat_chr6.simRat.chr6 83798 61 - 647215 CAAGGCAACCGAATACCAGGATGCTTAAATGGCTAATATTCCTGAGTGATTAATGACTGTG -s simRat_chr6.simRat.chr6 352612 61 + 647215 CAAGGCTATAGCAGACCAGAGGACTCAAATGGTGGATAATCCCGAGCCAATAATGGCTGTG -s simRat_chr6.simRat.chr6 66906 61 - 647215 GGAGGCCATAGCATACCAGAGTGCTCAAGTGGCAGATAGTCCTGAGCTAATAATGACTGTG - -a -s simMouse_chr6.simMouse.chr6 242807 13 + 636262 GGCCCAGACAGTA -s Anc1.Anc1refChr6 122027 13 + 197743 GGCCCACACATTA -s mr.mrrefChr3 24640 13 + 181027 GGCCCACACGTTA -s mr.mrrefChr3 157231 13 + 181027 GGCCCACACATTA -s mr.mrrefChr5 95902 13 + 294540 GGCCCAGACAGTA -s simMouse_chr6.simMouse.chr6 468933 13 + 636262 GGCCCACACGTTA -s simMouse_chr6.simMouse.chr6 609307 13 + 636262 GGCCCACACATTA -s simMouse_chr6.simMouse.chr6 786 13 - 636262 GGCCCAGACAGTA -s simRat_chr6.simRat.chr6 478872 13 + 647215 GGCCCACCCGTTA -s simRat_chr6.simRat.chr6 83859 13 - 647215 GGCCCACACATTA -s simRat_chr6.simRat.chr6 66967 13 - 647215 GGGCCACACAATT - -a -s simMouse_chr6.simMouse.chr6 242820 2 + 636262 TA -s Anc1.Anc1refChr6 122040 2 + 197743 CG -s mr.mrrefChr3 24653 2 + 181027 TG -s mr.mrrefChr5 95915 2 + 294540 CG -s simMouse_chr6.simMouse.chr6 468946 2 + 636262 TG -s simMouse_chr6.simMouse.chr6 799 2 - 636262 CG -s simRat_chr6.simRat.chr6 478885 2 + 647215 TG -s simRat_chr6.simRat.chr6 66980 2 - 647215 CG - -a -s simMouse_chr6.simMouse.chr6 242822 4 + 636262 ATGT -s Anc1.Anc1refChr6 122042 4 + 197743 ATGT -s mr.mrrefChr3 24655 4 + 181027 TTGT -s mr.mrrefChr3 157244 4 + 181027 ATGT -s mr.mrrefChr5 95917 4 + 294540 ATGT -s simMouse_chr6.simMouse.chr6 468948 4 + 636262 TTGT -s simMouse_chr6.simMouse.chr6 609320 4 + 636262 ATGT -s simMouse_chr6.simMouse.chr6 801 4 - 636262 ATGT -s simRat_chr6.simRat.chr6 478887 4 + 647215 ATGT -s simRat_chr6.simRat.chr6 83874 4 - 647215 ATTT -s simRat_chr6.simRat.chr6 66982 4 - 647215 ATGT - -a -s simMouse_chr6.simMouse.chr6 242826 15 + 636262 AGCACTCACTGGTTA -s Anc1.Anc1refChr6 122046 15 + 197743 AGCACTCACTGGTTA -s mr.mrrefChr3 24659 15 + 181027 AGAATTCATTGGTTA -s mr.mrrefChr3 157248 15 + 181027 AGCACTCACTGGTTA -s mr.mrrefChr5 95921 15 + 294540 AGCACTCACTGGTTA -s simMouse_chr6.simMouse.chr6 468952 15 + 636262 AGAATTCATTGGTTA -s simMouse_chr6.simMouse.chr6 609324 15 + 636262 AGCACTCACTGGTTA -s simMouse_chr6.simMouse.chr6 805 15 - 636262 AGCACTCACTGGTTA -s simRat_chr6.simRat.chr6 478891 15 + 647215 AGCACTGACTGGTTA -s simRat_chr6.simRat.chr6 83878 15 - 647215 AGGACTCACTGGTTA -s simRat_chr6.simRat.chr6 67036 12 - 647215 AGCACTCATTAG--- - -a -s simMouse_chr6.simMouse.chr6 242841 1 + 636262 T -s Anc1.Anc1refChr6 122061 1 + 197743 T -s mr.mrrefChr3 24674 1 + 181027 T -s mr.mrrefChr5 95936 1 + 294540 T -s simMouse_chr6.simMouse.chr6 468967 1 + 636262 T -s simMouse_chr6.simMouse.chr6 820 1 - 636262 T -s simRat_chr6.simRat.chr6 478906 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 242842 3 + 636262 TAA -s Anc1.Anc1refChr6 122062 3 + 197743 TAA -s mr.mrrefChr3 24675 3 + 181027 AAC -s mr.mrrefChr3 157263 3 + 181027 TAA -s mr.mrrefChr5 95937 3 + 294540 TAA -s simMouse_chr6.simMouse.chr6 468968 3 + 636262 AAC -s simMouse_chr6.simMouse.chr6 609339 3 + 636262 TAA -s simMouse_chr6.simMouse.chr6 821 3 - 636262 AAC -s simRat_chr6.simRat.chr6 478907 3 + 647215 AAC -s simRat_chr6.simRat.chr6 83893 3 - 647215 TAG - -a -s simMouse_chr6.simMouse.chr6 242845 5 + 636262 GACTT -s Anc1.Anc1refChr6 122065 5 + 197743 GACTT -s mr.mrrefChr3 24678 5 + 181027 GACTT -s mr.mrrefChr3 157266 5 + 181027 CACTC -s mr.mrrefChr5 95940 5 + 294540 GACTT -s simMouse_chr6.simMouse.chr6 468971 5 + 636262 GACTT -s simMouse_chr6.simMouse.chr6 609343 5 + 636262 CACTC -s simMouse_chr6.simMouse.chr6 824 5 - 636262 GACTT -s simRat_chr6.simRat.chr6 478910 5 + 647215 GACTT -s simRat_chr6.simRat.chr6 83896 5 - 647215 TGCTC - -a -s simMouse_chr6.simMouse.chr6 242850 29 + 636262 TCGTGCCCGGGCCAGACTTGTCATACTCA -s Anc1.Anc1refChr6 122070 9 + 197743 TCATACC--------------------CA -s mr.mrrefChr3 24695 9 + 181027 TCACACC--------------------CC -s mr.mrrefChr3 157271 9 + 181027 ACATACC--------------------CA -s mr.mrrefChr5 95945 9 + 294540 TCGTGCC--------------------CA -s simMouse_chr6.simMouse.chr6 468996 9 + 636262 TCACACC--------------------CC -s simMouse_chr6.simMouse.chr6 609348 9 + 636262 ACATACC--------------------CA -s simMouse_chr6.simMouse.chr6 829 9 - 636262 TCGTGCC--------------------CA -s simRat_chr6.simRat.chr6 478927 9 + 647215 TCACACT--------------------AT -s simRat_chr6.simRat.chr6 83901 9 - 647215 ACATACC--------------------GG - -a -s simMouse_chr6.simMouse.chr6 242879 2 + 636262 TG -s Anc1.Anc1refChr6 122079 2 + 197743 TG -s mr.mrrefChr3 24704 2 + 181027 TG -s mr.mrrefChr3 157280 2 + 181027 GA -s mr.mrrefChr5 95954 2 + 294540 TG -s simMouse_chr6.simMouse.chr6 469006 2 + 636262 TG -s simMouse_chr6.simMouse.chr6 609357 2 + 636262 GA -s simMouse_chr6.simMouse.chr6 838 2 - 636262 CT -s simRat_chr6.simRat.chr6 478936 2 + 647215 TG -s simRat_chr6.simRat.chr6 83910 2 - 647215 GA - -a -s simMouse_chr6.simMouse.chr6 242881 12 + 636262 GTTACCAACGAA -s Anc1.Anc1refChr6 122081 12 + 197743 GTTACCAACGAA -s mr.mrrefChr3 24706 12 + 181027 ATTACCAACAAA -s mr.mrrefChr3 157297 12 + 181027 GTTACCAACGAA -s mr.mrrefChr5 95956 12 + 294540 GTTTCCAAAGAA -s simMouse_chr6.simMouse.chr6 469008 12 + 636262 ATTACCAATGAA -s simMouse_chr6.simMouse.chr6 609374 12 + 636262 GTTACCAACGAA -s simMouse_chr6.simMouse.chr6 840 12 - 636262 ATTTGCAAAGAA -s simRat_chr6.simRat.chr6 478938 12 + 647215 GTTACCAACAAA -s simRat_chr6.simRat.chr6 83932 12 - 647215 GTTACCAACAAA - -a -s simMouse_chr6.simMouse.chr6 242893 1 + 636262 G -s Anc1.Anc1refChr6 122093 1 + 197743 C -s mr.mrrefChr3 24718 1 + 181027 C -s mr.mrrefChr3 157309 1 + 181027 C -s mr.mrrefChr5 95968 1 + 294540 T -s simMouse_chr6.simMouse.chr6 609386 1 + 636262 C -s simMouse_chr6.simMouse.chr6 852 1 - 636262 T -s simRat_chr6.simRat.chr6 478950 1 + 647215 C -s simRat_chr6.simRat.chr6 83944 1 - 647215 C - -a -s simMouse_chr6.simMouse.chr6 242894 6 + 636262 TTTGTA -s Anc1.Anc1refChr6 122094 6 + 197743 TGTGGA -s mr.mrrefChr3 24719 6 + 181027 TGTGGA -s mr.mrrefChr3 157310 6 + 181027 TGCGGA -s mr.mrrefChr5 95969 6 + 294540 TTTATA -s simMouse_chr6.simMouse.chr6 469020 6 + 636262 TGTGGA -s simMouse_chr6.simMouse.chr6 609387 6 + 636262 TGCGGA -s simMouse_chr6.simMouse.chr6 853 6 - 636262 TTTAGA -s simRat_chr6.simRat.chr6 478951 6 + 647215 TGTGGA -s simRat_chr6.simRat.chr6 83945 6 - 647215 TGCAGA - -a -s simMouse_chr6.simMouse.chr6 242900 2 + 636262 TT -s Anc1.Anc1refChr6 122100 2 + 197743 TT -s mr.mrrefChr3 24725 2 + 181027 TT -s mr.mrrefChr3 157316 2 + 181027 TT -s mr.mrrefChr5 95975 2 + 294540 TT -s simMouse_chr6.simMouse.chr6 469026 2 + 636262 TT -s simMouse_chr6.simMouse.chr6 609393 2 + 636262 TT -s simMouse_chr6.simMouse.chr6 859 2 - 636262 TT -s simRat_chr6.simRat.chr6 83951 2 - 647215 TT - -a -s simMouse_chr6.simMouse.chr6 242902 6 + 636262 TCCCCA -s Anc1.Anc1refChr6 122102 6 + 197743 TACCCA -s mr.mrrefChr3 24727 6 + 181027 TACTGA -s mr.mrrefChr3 157318 6 + 181027 TACCCA -s mr.mrrefChr5 95977 6 + 294540 TCCCCA -s simMouse_chr6.simMouse.chr6 469028 6 + 636262 TACTGA -s simMouse_chr6.simMouse.chr6 609395 6 + 636262 TACCCA -s simMouse_chr6.simMouse.chr6 958 6 - 636262 TCTCCA -s simRat_chr6.simRat.chr6 83953 6 - 647215 TACCCA - -a -s simMouse_chr6.simMouse.chr6 242908 2 + 636262 CA -s Anc1.Anc1refChr6 122108 2 + 197743 CA -s mr.mrrefChr3 24734 2 + 181027 CA -s mr.mrrefChr3 157324 2 + 181027 TC -s mr.mrrefChr5 95983 2 + 294540 CA -s simMouse_chr6.simMouse.chr6 469035 2 + 636262 CA -s simMouse_chr6.simMouse.chr6 609401 2 + 636262 TC -s simMouse_chr6.simMouse.chr6 964 2 - 636262 AT -s simRat_chr6.simRat.chr6 83959 2 - 647215 TC - -a -s simMouse_chr6.simMouse.chr6 242910 5 + 636262 CAAAG -s Anc1.Anc1refChr6 122110 5 + 197743 CAATG -s mr.mrrefChr3 24736 5 + 181027 CTATA -s mr.mrrefChr3 157326 5 + 181027 CATTG -s mr.mrrefChr5 95985 5 + 294540 CAAGG -s simMouse_chr6.simMouse.chr6 469037 5 + 636262 CTATA -s simMouse_chr6.simMouse.chr6 609404 5 + 636262 CATTG -s simMouse_chr6.simMouse.chr6 966 5 - 636262 CAAGA -s simRat_chr6.simRat.chr6 83961 5 - 647215 CAATG - -a -s simMouse_chr6.simMouse.chr6 242915 6 + 636262 CACCAG -s Anc1.Anc1refChr6 122115 6 + 197743 CAGCAC -s mr.mrrefChr3 24741 6 + 181027 CAGCAC -s mr.mrrefChr3 157331 6 + 181027 CAGCAC -s mr.mrrefChr5 95990 6 + 294540 CACAAG -s simMouse_chr6.simMouse.chr6 469042 6 + 636262 CAGCAC -s simMouse_chr6.simMouse.chr6 609409 6 + 636262 CAGCAC -s simMouse_chr6.simMouse.chr6 971 6 - 636262 AACAAG -s simRat_chr6.simRat.chr6 478957 6 + 647215 CAGCAC -s simRat_chr6.simRat.chr6 83966 6 - 647215 CACAAC - -a -s simMouse_chr6.simMouse.chr6 242921 2 + 636262 GC -s Anc1.Anc1refChr6 122121 2 + 197743 TC -s mr.mrrefChr3 24747 2 + 181027 TC -s mr.mrrefChr3 157337 2 + 181027 TC -s mr.mrrefChr5 95996 2 + 294540 GC -s simMouse_chr6.simMouse.chr6 469048 2 + 636262 TC -s simMouse_chr6.simMouse.chr6 609415 2 + 636262 TC -s simMouse_chr6.simMouse.chr6 987 2 - 636262 GC -s simRat_chr6.simRat.chr6 478963 2 + 647215 TC -s simRat_chr6.simRat.chr6 83972 2 - 647215 TC - -a -s simMouse_chr6.simMouse.chr6 242923 1 + 636262 C -s Anc1.Anc1refChr6 122125 1 + 197743 T -s mr.mrrefChr3 24751 1 + 181027 T -s mr.mrrefChr3 157341 1 + 181027 T -s mr.mrrefChr5 95998 1 + 294540 C -s simMouse_chr6.simMouse.chr6 469052 1 + 636262 T -s simMouse_chr6.simMouse.chr6 609419 1 + 636262 T -s simMouse_chr6.simMouse.chr6 989 1 - 636262 C -s simRat_chr6.simRat.chr6 478967 1 + 647215 T -s simRat_chr6.simRat.chr6 83976 1 - 647215 T - -a -s simMouse_chr6.simMouse.chr6 242924 1 + 636262 A -s Anc1.Anc1refChr6 122126 1 + 197743 G -s mr.mrrefChr3 24752 1 + 181027 G -s mr.mrrefChr3 157342 1 + 181027 G -s mr.mrrefChr5 95999 1 + 294540 A -s simMouse_chr6.simMouse.chr6 469053 1 + 636262 G -s simMouse_chr6.simMouse.chr6 609421 1 + 636262 G -s simMouse_chr6.simMouse.chr6 990 1 - 636262 A -s simRat_chr6.simRat.chr6 478968 1 + 647215 G -s simRat_chr6.simRat.chr6 83977 1 - 647215 G - -a -s simMouse_chr6.simMouse.chr6 242925 10 + 636262 CGTTAGTCAC -s Anc1.Anc1refChr6 122129 10 + 197743 CGTTTATCAT -s mr.mrrefChr3 24756 10 + 181027 CGTTTATCAT -s mr.mrrefChr3 157345 10 + 181027 CATTTATCAT -s mr.mrrefChr5 96002 10 + 294540 CGTTTATCAC -s simMouse_chr6.simMouse.chr6 469057 10 + 636262 TGTTTATCAT -s simMouse_chr6.simMouse.chr6 609424 10 + 636262 CATTTATCAT -s simMouse_chr6.simMouse.chr6 996 7 - 636262 TGCTTTT--- -s simRat_chr6.simRat.chr6 478972 10 + 647215 CGTTTATCAC -s simRat_chr6.simRat.chr6 83980 10 - 647215 CATTTATCAC -s simRat_chr6.simRat.chr6 352675 10 + 647215 CGTTTATCAC -s simRat_chr6.simRat.chr6 67050 10 - 647215 CGTTTATCAC - -a -s simMouse_chr6.simMouse.chr6 242935 19 + 636262 CGCCACATGAGTCCTCCTT -s Anc1.Anc1refChr6 122139 19 + 197743 GGCCACATGAGTCCCCCTA -s mr.mrrefChr3 157355 19 + 181027 GGTCACAGGAGTCCCCCTA -s mr.mrrefChr5 96012 19 + 294540 GGCCACATGAGTCCCCCTA -s simMouse_chr6.simMouse.chr6 609434 19 + 636262 GGTCACAGGAGTCCCCCTA -s simRat_chr6.simRat.chr6 83990 19 - 647215 AGCTATGTGAATCCCTCTA -s simRat_chr6.simRat.chr6 352685 19 + 647215 GGTGACATGAGTCCCTTTA -s simRat_chr6.simRat.chr6 67060 19 - 647215 GGCCACGTGGGTCCCCCTA - -a -s simMouse_chr6.simMouse.chr6 242954 2 + 636262 TC -s mr.mrrefChr5 96031 2 + 294540 TC -s simRat_chr6.simRat.chr6 352704 2 + 647215 TC -s simRat_chr6.simRat.chr6 67079 2 - 647215 TC - -a -s simMouse_chr6.simMouse.chr6 242956 66 + 636262 TGTcagtcatgggctcgcttatgatggccagtggtcaaggcctcggattcaccttgcacatgaaag -s mr.mrrefChr5 96046 66 + 294540 TGTcactcatgggctcgcttatgatggccagtggtcaaggcctcggattcacctcgcacatgaaag -s simRat_chr6.simRat.chr6 352719 66 + 647215 TGgcacttagggggtcgtctatgatggcctgtggccaaggcctcggattcacctcgcacatgaaag -s simRat_chr6.simRat.chr6 67094 66 - 647215 TGAcactcatgggctcacttatgagggccagtggtcagggcttcggattcacctcacacacaaaag - -a -s simMouse_chr6.simMouse.chr6 243022 109 + 636262 atggaacttcctgtacaatggttccagcgaatatgatgtcaggtcactgggtcagtactgatgccgagggcagagtcccccccacagaatcgcctaccccattgcTTAC -s mr.mrrefChr5 96112 103 + 294540 atggtacttcctgtacaacggttccaccgaacatgatgtcaggtcactgggtcagtacagatgccgagggcagagtcccccccacagaatcgcctaccccatt------ -s simRat_chr6.simRat.chr6 353021 103 + 647215 atggtccttcgtgtacaacggtaccaccaaacatgatgtcaggtcactgcgtcagtacagatgccgagggtggcgtcccacccacaaagtcacccaccccact------ -s simRat_chr6.simRat.chr6 67160 65 - 647215 atggtacttcctgtacaacagtgccactgtacatgatgtcaggtcgctgggtcagtacagatacc-------------------------------------------- - -a -s simMouse_chr6.simMouse.chr6 243131 7 + 636262 CAAGTAT -s Anc0.Anc0refChr5 61990 2 + 87904 -----AT -s Anc1.Anc1refChr7 19665 2 - 47259 -----AT -s Anc2.Anc2refChr15 58739 2 + 86568 -----AT -s mr.mrrefChr5 96215 7 + 294540 TAGGTAT -s simCow_chr6.simCow.chr6 239443 2 + 602619 -----AT -s simDog_chr6.simDog.chr6 231540 2 + 593897 -----AT -s simHuman_chr6.simHuman.chr6 321434 2 - 601863 -----AC -s simRat_chr6.simRat.chr6 233210 7 + 647215 TAGGTAT - -a -s simMouse_chr6.simMouse.chr6 243138 71 + 636262 AGTTTCAAGAAGAGTTAGGGTGCTTCGTGGTGAATTTCTTGACAGCCTATCTTCCATTAGGAGAACCAACT -s Anc0.Anc0refChr5 61996 61 + 87904 AGTCTCAAGAAGGGTTAGGGTGCTACCTGGTG-----CGTA-----CCATCTGAGAATGTGACACCTGACT -s Anc1.Anc1refChr7 19671 61 - 47259 AGTCTCAAGAAGGGTTAGGGTGCTACCTGGTG-----CGTA-----CCATCTGAGAATGTGACACCTGACT -s Anc2.Anc2refChr15 58746 61 + 86568 AGTCTCAAGAAGGGCTAGGGTGCTACCTGGTA-----TGTA-----CCATCTGAGAATCTGACACCTGACT -s mr.mrrefChr5 96226 66 + 294540 AGTCTCAAGAAGAGTTAGGGTGCTTCGTGGTGAATTTCTTG-----CTATCTTCCATTGTGAGACCCAACT -s simCow_chr6.simCow.chr6 239450 56 + 602619 AGTCTCAAGAAGCACTAGGACACGACCTAGTA---------------CATTTGAGAATATAGCACCTGACT -s simDog_chr6.simDog.chr6 231547 59 + 593897 AGTCCCAAGAACGGCTAGGGTGCTA--TGGTA-----TGTA-----CCATCTGAGAATCAGACACCTGACT -s simHuman_chr6.simHuman.chr6 321440 61 - 601863 AGTCTCAAGAAGGGTTAGGGTGCTCACTGGTG-----CGTA-----CAATCTGAGAATGTGACACCTGACT -s simRat_chr6.simRat.chr6 233222 66 + 647215 AGTCTGAAGAAGAGTTAGGGTGCTTTGTGGTGAATTCTTGG-----CTATCTTCTGTTGTGAGACCCAACT - -a -s simMouse_chr6.simMouse.chr6 243209 20 + 636262 GGGTTCTATCTGAAGCTTTA -s Anc0.Anc0refChr5 62057 19 + 87904 AGGTCTTGT-TGAAGTTGTA -s Anc1.Anc1refChr7 19732 19 - 47259 AGGTCTTGT-TGAAGTTGTA -s Anc2.Anc2refChr15 58807 19 + 86568 AGGTCTTGT-TGAAGTTGTA -s mr.mrrefChr5 96292 20 + 294540 GGGTTCTATCTGAAGCTTTA -s simCow_chr6.simCow.chr6 239519 19 + 602619 AGGTCTTGT-TGAACTTGTA -s simDog_chr6.simDog.chr6 231606 19 + 593897 ACGTCTTGT-TAAAGTTGTA -s simHuman_chr6.simHuman.chr6 321501 19 - 601863 AGGTCTTGT-TGAAGTTGTA -s simRat_chr6.simRat.chr6 233288 20 + 647215 GGGTTCTATTTGAGGCTTTA - -a -s simMouse_chr6.simMouse.chr6 243229 9 + 636262 CTTCATCAA -s Anc0.Anc0refChr5 62078 9 + 87904 CTGCATCAA -s Anc1.Anc1refChr7 19753 9 - 47259 CTGCATCAA -s Anc2.Anc2refChr15 58828 9 + 86568 CTGCATCAA -s mr.mrrefChr5 96312 9 + 294540 CTGCATCAA -s simCow_chr6.simCow.chr6 239540 9 + 602619 CTGCATCAA -s simDog_chr6.simDog.chr6 231627 9 + 593897 CTACATCAG -s simHuman_chr6.simHuman.chr6 321522 9 - 601863 CTGCATCAA -s simRat_chr6.simRat.chr6 233308 4 + 647215 CTGC----- - -a -s simMouse_chr6.simMouse.chr6 243238 17 + 636262 TCAGGCAGTGAACTATA -s Anc0.Anc0refChr5 62087 17 + 87904 AGAAGTAGTGAACTATA -s Anc1.Anc1refChr7 19762 17 - 47259 AGAAGTAGTGAACTATA -s Anc2.Anc2refChr15 58837 17 + 86568 AGAAGTAGTGAACTATA -s mr.mrrefChr5 96321 17 + 294540 TCAGGCAGTGAACTATA -s simCow_chr6.simCow.chr6 239549 17 + 602619 AGAAGTAGTGAACTATA -s simDog_chr6.simDog.chr6 231637 4 + 593897 AGAA------------- -s simHuman_chr6.simHuman.chr6 321531 17 - 601863 AGAAGTGGTGACCTATA -s simRat_chr6.simRat.chr6 233312 13 + 647215 ----GCAGTGAACTATA - -a -s simMouse_chr6.simMouse.chr6 243255 39 + 636262 GTCTGGTTTTGTTCTTTAACAAGTGATAATCAGAAGGTC -s Anc0.Anc0refChr5 62104 39 + 87904 AAATTGTTCTGTCTTTCAACAGGTGATAATAAGAAGGTC -s Anc1.Anc1refChr7 19779 39 - 47259 AAATTGTTCTGTCTTTCAACAGGTGATAATAAGAAGGTC -s Anc2.Anc2refChr15 58854 39 + 86568 AAATTTTTCCGTCTTTCAACAGGTGATAATAGGAAGGTC -s mr.mrrefChr5 96338 39 + 294540 GTCTTGTTTTGTCTTTTAACAAGTGATAATCAGAAGGTC -s simCow_chr6.simCow.chr6 239567 39 + 602619 AAATTTTTCCGTCTTTAAACAAGTGATGATAGGAAGGTC -s simDog_chr6.simDog.chr6 231641 26 + 593897 -------------TTTCAACAGGTGATAATAGTAAGGTC -s simHuman_chr6.simHuman.chr6 321548 39 - 601863 AAATTGTTCTGTCTTTCAGCAGGTGACAAGTAGAAGGTC -s simRat_chr6.simRat.chr6 233325 39 + 647215 GTCTTGCTTTTTCTTTTGACAAGTGATAATCAGAAGGTC - -a -s simMouse_chr6.simMouse.chr6 243294 39 + 636262 TAAAATAGGGGCTTTAAGCGTTTGCATGTATTAATACAT -s Anc0.Anc0refChr5 62143 38 + 87904 AGAAATAGGGTATTTAAGCTTTTGCATGTATTCATACA- -s Anc1.Anc1refChr7 19818 38 - 47259 AGAAATAGGGTATTTAAGCTTTTGCATGTATTCATACA- -s Anc2.Anc2refChr15 58894 38 + 86568 AGAAATAGGGTATTTAAGCTTTCACATGTATTCATACA- -s mr.mrrefChr5 96377 38 + 294540 TAAAATAGGGGCTTTAAGCGTTTGCATGTATTAATACA- -s simCow_chr6.simCow.chr6 239607 36 + 602619 GGA--TAGGAGATTTGAGCGTGAACATGTATTCATACA- -s simDog_chr6.simDog.chr6 231668 38 + 593897 AGAAATAGGGTATTTAAGCTTTCACATGTATTCATACA- -s simHuman_chr6.simHuman.chr6 321587 38 - 601863 AGAAATAGGGCATTTAAGCTATTGCATGTATTCATACA- -s simRat_chr6.simRat.chr6 233364 35 + 647215 TAAAACA---GCTTTAAGTGTTTGCATGTATTGATACA- - -a -s simMouse_chr6.simMouse.chr6 243333 104 + 636262 TTCCCTGGCACATACATTTAAGAGTCAAGAAGAATAATTGAGAGAGAAGTGATGCTTGAACTCAAGAACGCAGAACTGGAATGTATAAATGACTTAACCATGAA -s Anc0.Anc0refChr5 62226 103 + 87904 TTCCCTAGCACATTCTTTTAAGTGTCAGAGTGAATGATTGAGACAGAAGTAGCACTTGAACGCAGGAATGCA-GACTGGAATGTAAGCATGACTAACCCATGAA -s Anc1.Anc1refChr7 19901 103 - 47259 TTCCCTAGCACATTCTTTTAAGTGTCAGAGTGAATGATTGAGACAGAAGTAGCACTTGAACGCAGGAATGCA-GACTGGAATGTAAGCATGACTAACCCATGAA -s Anc2.Anc2refChr15 58977 103 + 86568 TTCCCTATCACACTCTTTTAAGTGCCAGAGTAAATGATTGAGACAGAAGTAGCACTTGAACGCAGGAATGCA-GACTGGAATGTAAGCATGACTAACCCAGGAA -s mr.mrrefChr5 96415 104 + 294540 TTCCCTAGCACATACATTTAAGAGTCAGGATGAATAATTGAGAGAGAAGTGATGCTTGAACTCAAGAACGCAGAACTGGAATGTATGAATGACTTAACCATGAA -s simCow_chr6.simCow.chr6 239663 69 + 602619 --------------------------------AATGATTGACACAG--GTAGCTCTTAAACTGAGGTATGCA-GGCTGGAATTTAAGCATGACTAACCCAAGAA -s simDog_chr6.simDog.chr6 231753 103 + 593897 TTCCCTATCACACTCTTTTAAGTGCCAGAGTAAATGATTGCGACAGAAGTAGCACTTGAATGCAGGAACGCA-GACTGGAGTGTAACCATGATTAACCTGGGAA -s simHuman_chr6.simHuman.chr6 321679 103 - 601863 TTCCCTAGTGGATTCTTTTAAGGGTCAGAGTGGATGATTGATATGGAGGTAGCACTTGAACCCATGAATGCA-CACTGGAATGTAGGCATGACTAACCCATGAA -s simRat_chr6.simRat.chr6 233399 103 + 647215 TTCCCTAGCACATACCATTAGGAGCCAGGATGAATAACTGAGAGTGAAGTTATGCTTGAATTCAAGAA-ACAGAACTGGAATATATGAATGACTTAACCATAAA - -a -s simMouse_chr6.simMouse.chr6 243437 7 + 636262 AACAGTC -s Anc0.Anc0refChr5 62329 7 + 87904 TTCAGAC -s Anc1.Anc1refChr7 20004 7 - 47259 TTCAGAC -s Anc2.Anc2refChr15 59081 7 + 86568 TTCAGAC -s mr.mrrefChr5 96519 7 + 294540 TTCAGAC -s simCow_chr6.simCow.chr6 239733 7 + 602619 TTCAGAT -s simDog_chr6.simDog.chr6 231857 7 + 593897 TTCAGAC -s simHuman_chr6.simHuman.chr6 321782 7 - 601863 TTCAGAC -s simRat_chr6.simRat.chr6 233502 7 + 647215 TTCAAAC - -a -s simMouse_chr6.simMouse.chr6 243444 5 + 636262 TAATG -s Anc0.Anc0refChr5 62338 5 + 87904 TAATG -s Anc1.Anc1refChr7 20013 5 - 47259 TAATG -s Anc2.Anc2refChr15 59090 5 + 86568 TAGTG -s mr.mrrefChr5 96528 5 + 294540 TAATG -s simCow_chr6.simCow.chr6 239742 5 + 602619 TTGTG -s simDog_chr6.simDog.chr6 231866 5 + 593897 TAGTG -s simHuman_chr6.simHuman.chr6 321791 5 - 601863 TAATG -s simRat_chr6.simRat.chr6 233511 5 + 647215 TAATG - -a -s simMouse_chr6.simMouse.chr6 243449 28 + 636262 CACTCCTACGCCAGATATCCTAGACTCT -s Anc0.Anc0refChr5 62347 28 + 87904 CACAACTACCCTAGTTATTCTAGACTCC -s Anc1.Anc1refChr7 20022 28 - 47259 CACAACTACCCTAGTTATTCTAGACTCC -s Anc2.Anc2refChr15 59099 28 + 86568 CAGAACTACCCTAGTTATTCTAGACTTC -s mr.mrrefChr5 96533 28 + 294540 CACTCCTACGCTAGATATCCTAGACTCT -s simCow_chr6.simCow.chr6 239751 28 + 602619 CATGACTACCCTAATTTTTGTAGACTGC -s simDog_chr6.simDog.chr6 231875 28 + 593897 CAGACCTACCCTAGTAATCCTAGACTTC -s simHuman_chr6.simHuman.chr6 321800 28 - 601863 CACAATTACCCTAGTTATTCTAGCCTCC -s simRat_chr6.simRat.chr6 233516 28 + 647215 CACTCCTTCTCTAGATATCCTAGACTCT - -a -s simMouse_chr6.simMouse.chr6 243477 23 + 636262 TGTCAATGAGAGCTGCAACCTAG -s Anc0.Anc0refChr5 62376 23 + 87904 TATCAGTGAGGGCTGCAGGTGCA -s Anc1.Anc1refChr7 20051 23 - 47259 TATCAGTGAGGGCTGCAGGTGCA -s Anc2.Anc2refChr15 59128 23 + 86568 TATTAGTGAGGGCTACAGGTGCA -s mr.mrrefChr5 96562 23 + 294540 TATCAATGAGAGCTGCAGCCGAG -s simCow_chr6.simCow.chr6 239780 23 + 602619 TAGTAGTGCATGCTACAGGTGCT -s simDog_chr6.simDog.chr6 231904 23 + 593897 TGTTGGTGAGGGCTACAGGCGCA -s simHuman_chr6.simHuman.chr6 321829 23 - 601863 TACCAGTGTGGGCTGCAGGTGTC -s simRat_chr6.simRat.chr6 233545 23 + 647215 CATCAATGAGAGCTACAGTAGAG - -a -s simMouse_chr6.simMouse.chr6 243500 1 + 636262 C -s Anc0.Anc0refChr5 62402 1 + 87904 C -s Anc1.Anc1refChr7 20077 1 - 47259 C -s Anc2.Anc2refChr15 59154 1 + 86568 C -s mr.mrrefChr5 96593 1 + 294540 T -s simCow_chr6.simCow.chr6 239806 1 + 602619 T -s simDog_chr6.simDog.chr6 231930 1 + 593897 C -s simHuman_chr6.simHuman.chr6 321855 1 - 601863 C -s simRat_chr6.simRat.chr6 233576 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 243501 26 + 636262 ATCTTCAATGCTCCCACTGACTCCTA -s Anc0.Anc0refChr5 62403 26 + 87904 ATCTTGGAGACCCCCACTGACTCTTA -s Anc1.Anc1refChr7 20078 26 - 47259 ATCTTGGAGACCCCCACTGACTCTTA -s Anc2.Anc2refChr15 59156 26 + 86568 ATCTTGGAGACCCCCACTGTTTCTTA -s mr.mrrefChr5 96594 26 + 294540 ATCTTCAATGCTCCCACTGACTCCTA -s simCow_chr6.simCow.chr6 239808 26 + 602619 GTCATGGAGACCCCCACTGCTTCATA -s simDog_chr6.simDog.chr6 231932 26 + 593897 ATCTTGGAAATCCCCACTGTTTCTTA -s simHuman_chr6.simHuman.chr6 321856 26 - 601863 ATCTTGGTGCCCCCAACTGACTCTTA -s simRat_chr6.simRat.chr6 233577 26 + 647215 ATCTTCAATGCTCCCACTGACTCCTA - -a -s simMouse_chr6.simMouse.chr6 243527 28 + 636262 TACCTTCGCCCTGTTAAGCCTTACGTTG -s Anc0.Anc0refChr5 62429 28 + 87904 TACCTTTCCACTGTTAAGTCTTATTTTA -s Anc1.Anc1refChr7 20104 28 - 47259 TACCTTTCCACTGTTAAGTCTTATTTTA -s Anc2.Anc2refChr15 59182 28 + 86568 TACCTTCCTACTGTTATGTGTTATTTTA -s mr.mrrefChr5 96620 28 + 294540 TACCTTTGCCCTGTTAAGCCTTACTTTG -s simCow_chr6.simCow.chr6 239834 28 + 602619 TACCTTTCTCTTGTTATGTGTTATTTTA -s simDog_chr6.simDog.chr6 231958 28 + 593897 TACCTTCCTACTGTTATGTGTTATTCTA -s simHuman_chr6.simHuman.chr6 321892 27 - 601863 TAACTTTCCTCAGT-AAGTCTTATTACA -s simRat_chr6.simRat.chr6 233603 28 + 647215 TACCTTTGCCCTGTTAAGCCTTACTTTG - -a -s simMouse_chr6.simMouse.chr6 243555 5 + 636262 TATGT -s Anc0.Anc0refChr5 62457 2 + 87904 ---GT -s Anc1.Anc1refChr7 20133 5 - 47259 TTTGT -s Anc2.Anc2refChr15 59210 2 + 86568 ---GT -s mr.mrrefChr5 96649 5 + 294540 TATGT -s simCow_chr6.simCow.chr6 239862 2 + 602619 ---AT -s simDog_chr6.simDog.chr6 231986 2 + 593897 ---GT -s simHuman_chr6.simHuman.chr6 321920 5 - 601863 TTTGT -s simRat_chr6.simRat.chr6 233632 5 + 647215 TGTGT - -a -s simMouse_chr6.simMouse.chr6 243560 49 + 636262 TTCCCTGGGACTATCGTGATTTGGGACTATCATGATCGCACACCCTTAT -s Anc0.Anc0refChr5 62459 32 + 87904 CTCCTTCAGACTATCT----------------TGATTGTACAC-AGTAC -s Anc1.Anc1refChr7 20138 32 - 47259 CTCCTTCAGACTATCT----------------TGATTGTACAC-AGTAC -s Anc2.Anc2refChr15 59212 32 + 86568 CTCCTTCAGACTATCT----------------TGACTGTGAAC-AGTAC -s mr.mrrefChr5 96654 33 + 294540 TTCCTTGAGACTATCG----------------TGATCGCACACCATTAT -s simCow_chr6.simCow.chr6 239939 26 + 602619 CTTCTCCAGACTATCT----------------TGACTG-------GTAC -s simDog_chr6.simDog.chr6 231988 27 + 593897 CTCCTTCACACTATTT----------------T-----TGAAC-AGTAC -s simHuman_chr6.simHuman.chr6 321925 32 - 601863 CTCCTTCAGACTATCT----------------TGATTGTACAT-AGTAC -s simRat_chr6.simRat.chr6 233637 33 + 647215 TTCCTTGAGACTATCG----------------TGATCGCACACCATTAT - -a -s simMouse_chr6.simMouse.chr6 243609 7 + 636262 CATTACT -s Anc0.Anc0refChr5 62493 7 + 87904 TCTTACT -s Anc1.Anc1refChr7 20172 7 - 47259 TCTTACT -s Anc2.Anc2refChr15 59246 7 + 86568 TCTCATT -s mr.mrrefChr5 96689 7 + 294540 CATTACT -s simCow_chr6.simCow.chr6 239967 7 + 602619 TTGCATT -s simDog_chr6.simDog.chr6 232017 5 + 593897 TCTCA-- -s simHuman_chr6.simHuman.chr6 321959 7 - 601863 GCTTACC -s simRat_chr6.simRat.chr6 233672 7 + 647215 CATTACT - -a -s simMouse_chr6.simMouse.chr6 243616 10 + 636262 GTTGGGTTGG -s Anc0.Anc0refChr5 62501 9 + 87904 GCT-GGTTCA -s Anc1.Anc1refChr7 20180 10 - 47259 GCTGGGTTCA -s Anc2.Anc2refChr15 59254 9 + 86568 GCT-GGTTCA -s mr.mrrefChr5 96697 10 + 294540 GTTGGGTTGG -s simCow_chr6.simCow.chr6 239975 9 + 602619 GCT-GGTTCA -s simHuman_chr6.simHuman.chr6 321967 10 - 601863 TCTAAGTTCA -s simRat_chr6.simRat.chr6 233680 10 + 647215 GTTGGGTTGG - -a -s simMouse_chr6.simMouse.chr6 243626 7 + 636262 CCTTCTC -s Anc0.Anc0refChr5 62510 7 + 87904 CCTTCTT -s Anc1.Anc1refChr7 20190 7 - 47259 CCTTCTT -s Anc2.Anc2refChr15 59263 7 + 86568 CATTCCT -s mr.mrrefChr5 96707 7 + 294540 CCTTCTC -s simCow_chr6.simCow.chr6 240063 7 + 602619 CATTCCT -s simHuman_chr6.simHuman.chr6 321977 7 - 601863 CCTTCTT -s simRat_chr6.simRat.chr6 233690 7 + 647215 TCTTCTC - -a -s simMouse_chr6.simMouse.chr6 243633 9 + 636262 TTATCACAT -s Anc0.Anc0refChr5 62519 9 + 87904 TCATCACAT -s Anc1.Anc1refChr7 20199 9 - 47259 TCATCACAT -s Anc2.Anc2refChr15 59272 9 + 86568 TCATTCCAT -s mr.mrrefChr5 96714 9 + 294540 TCATCACAT -s simCow_chr6.simCow.chr6 240072 9 + 602619 TCATGCCAT -s simDog_chr6.simDog.chr6 232024 9 + 593897 TCAATCCAC -s simHuman_chr6.simHuman.chr6 321986 9 - 601863 TCATCACAT -s simRat_chr6.simRat.chr6 233697 9 + 647215 TCATCACAT - -a -s simMouse_chr6.simMouse.chr6 243642 35 + 636262 TATTGTCTAACACGGAGTTACACAAAGTTTTAGTA -s Anc0.Anc0refChr5 62529 35 + 87904 TAATGCCTAATGCGTACTTGCATGAAGCTTTAGTA -s Anc1.Anc1refChr7 20209 35 - 47259 TAATGCCTAATGCGTACTTGCATGAAGCTTTAGTA -s Anc2.Anc2refChr15 59282 35 + 86568 TAATGCCTAATGCATACTTGCATGAAGCTCTAGTG -s mr.mrrefChr5 96724 35 + 294540 TAATGTCTAATACGGAGTTGCACAAAGTTTTAGTA -s simCow_chr6.simCow.chr6 240082 35 + 602619 TAGTGCCTAATGCATACTTGCATGAAGCTGTAATG -s simDog_chr6.simDog.chr6 232034 28 + 593897 TAATGCATA-------GTTGCATGAAACTCTAGTG -s simHuman_chr6.simHuman.chr6 321996 35 - 601863 TAATGGCTAATGTGCACTTGGATGAAGCTTTAGTA -s simRat_chr6.simRat.chr6 233707 35 + 647215 TAATGTGTAATACAGAGTTGCACAAAGTTTTAGTA - -a -s simMouse_chr6.simMouse.chr6 243677 94 + 636262 GTTGGTTATTAGGGAAACATAAAGTGATATTTAAAGTAGAAGACGGTGGTCTTGTCCTGCCTCATTCTTGAGATCTACATTTTATTAGTAAAAA -s Anc0.Anc0refChr5 62570 16 + 87904 GTTGGCCATTGGGG------------------------------------------------------------------------------AA -s Anc1.Anc1refChr7 20250 94 - 47259 GTTGGCCATTGGGGAAACAGAGTTGGATTTTCAGGTTTGAACATGATAACCTTGTCCTGTCTCATTCTTGTGATCCGCAATTTATTAATGCAAA -s Anc2.Anc2refChr15 59323 16 + 86568 GTTGGCCATTGGGG------------------------------------------------------------------------------AA -s mr.mrrefChr5 96765 94 + 294540 GTTGGTCATTAGGGAAACATAATGTGATATTTAAAGTAGAAGATGATGGCCTTGTCCTGCCTCATTCTTGAGATCTACATTTTATTAGTAAAAA -s simCow_chr6.simCow.chr6 240123 11 + 602619 GTTGGCCATTG----------------------------------------------------------------------------------- -s simDog_chr6.simDog.chr6 232068 16 + 593897 GTTGGCCGTTGGGG------------------------------------------------------------------------------AA -s simHuman_chr6.simHuman.chr6 322037 94 - 601863 GTAGGCCATTGGAGAAACAGAGTTGGATTTTCAGGTTTGAACATGATAACCTTGTCCTGTCTCATTCTTGTGATCCGCAATTTATTAATGCAAC -s simRat_chr6.simRat.chr6 233748 94 + 647215 GTTGGTCATTAGGGAAACATAATCTGATATTTAAAGTAGAAGATGATGGCCTTGTCCAACCTCATTCCTGAGATCTACATTTTAACACTAAAAA - -a -s simMouse_chr6.simMouse.chr6 243771 6 + 636262 TCGGGT -s Anc0.Anc0refChr5 62586 4 + 87904 TTGG-- -s Anc1.Anc1refChr7 20344 4 - 47259 TTGG-- -s Anc2.Anc2refChr15 59339 4 + 86568 TTGG-- -s mr.mrrefChr5 96859 6 + 294540 TTGGGT -s simDog_chr6.simDog.chr6 232116 4 + 593897 TTGG-- -s simHuman_chr6.simHuman.chr6 322131 4 - 601863 TTGG-- -s simRat_chr6.simRat.chr6 233842 6 + 647215 TTGGGG - -a -s simMouse_chr6.simMouse.chr6 243777 36 + 636262 TCACCTATCACCTGTAGATGAAATTCATAGTTGTGG -s Anc0.Anc0refChr5 62590 36 + 87904 TAACTCTTCACCTGTATAGATAATTCATATTTGTGA -s Anc1.Anc1refChr7 20348 36 - 47259 TAACTCTTCACCTGTATAGATAATTCATATTTGTGA -s Anc2.Anc2refChr15 59343 36 + 86568 TAACTCTTCACCTCTATGTATAATTCATATTTGGGA -s mr.mrrefChr5 96865 36 + 294540 TCACCTATCACCTGTATAGATAATTCATAGTTGTGG -s simCow_chr6.simCow.chr6 240733 17 + 602619 -------------------ATTATTCATATTTGGGT -s simDog_chr6.simDog.chr6 232122 36 + 593897 TAACTCTTCACCTCTATGTATAGTTCATATTCGGGA -s simHuman_chr6.simHuman.chr6 322135 36 - 601863 TAAGTCTTCACCCGTATAGATCATTCATATTTATGA -s simRat_chr6.simRat.chr6 233848 35 + 647215 GCACCTATCACCTGTATAGATAATTTATAGTT-TGG - -a -s simMouse_chr6.simMouse.chr6 243813 1 + 636262 T -s Anc0.Anc0refChr5 62626 1 + 87904 T -s Anc1.Anc1refChr7 20384 1 - 47259 T -s Anc2.Anc2refChr15 59379 1 + 86568 T -s mr.mrrefChr5 96901 1 + 294540 T -s simCow_chr6.simCow.chr6 240750 1 + 602619 T -s simDog_chr6.simDog.chr6 232160 1 + 593897 T -s simHuman_chr6.simHuman.chr6 322171 1 - 601863 T -s simRat_chr6.simRat.chr6 233883 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 243814 50 + 636262 AGATGCACCACCACCCTAAACATGGAAATTCAACCGATTGAGTGACTTCA -s Anc0.Anc0refChr5 62627 38 + 87904 ATA--CACTTTTACCCTG----------TTCAAGAGATTTAGTAACTTTA -s Anc1.Anc1refChr7 20385 38 - 47259 ATA--CACTTTTACCCTG----------TTCAAGAGATTTAGTAACTTTA -s Anc2.Anc2refChr15 59380 38 + 86568 ATG--TACTTTTATCCTG----------TTCAAGAGATTTAGTAACTTTA -s mr.mrrefChr5 96902 50 + 294540 AGATGCACCTTTACCCTAAACATGGAAATTCAACAGATTGAGTGACTTTA -s simCow_chr6.simCow.chr6 240760 32 + 602619 ACG--TAATTTTATCCTG----------T------GATTTAGTAACTTTA -s simDog_chr6.simDog.chr6 232161 38 + 593897 ATG--TACTTTTATCCCA----------CTCAAGAGCTTTAGTAGCTTTA -s simHuman_chr6.simHuman.chr6 322172 38 - 601863 AAA--CACTTTTACCCTG----------TTCAAGAGACTTGGTAACTTTA -s simRat_chr6.simRat.chr6 233884 50 + 647215 AGATGCATCTTTACCCTAAACATGAAAATCCAACAGATTCAGTGACTTTG - -a -s simMouse_chr6.simMouse.chr6 243864 3 + 636262 ATG -s Anc0.Anc0refChr5 62665 2 + 87904 G-T -s Anc1.Anc1refChr7 20423 3 - 47259 GTT -s Anc2.Anc2refChr15 59418 2 + 86568 G-T -s mr.mrrefChr5 96952 3 + 294540 GTG -s simCow_chr6.simCow.chr6 240792 2 + 602619 G-T -s simDog_chr6.simDog.chr6 232199 2 + 593897 G-T -s simHuman_chr6.simHuman.chr6 322216 3 - 601863 GTT -s simRat_chr6.simRat.chr6 233934 3 + 647215 GTG - -a -s simMouse_chr6.simMouse.chr6 243867 12 + 636262 ACCATACGATGG -s Anc0.Anc0refChr5 62667 12 + 87904 ACCACATGATGA -s Anc1.Anc1refChr7 20426 12 - 47259 ACCACATGATGA -s Anc2.Anc2refChr15 59420 12 + 86568 ACTACATGATGA -s mr.mrrefChr5 96955 12 + 294540 ACCACATGATGG -s simCow_chr6.simCow.chr6 240795 12 + 602619 ACTACATGATGA -s simDog_chr6.simDog.chr6 232201 12 + 593897 ACTACATGATGC -s simHuman_chr6.simHuman.chr6 322219 12 - 601863 ACCACATGACGA -s simRat_chr6.simRat.chr6 233937 12 + 647215 ACCGCATGATGG - -a -s simMouse_chr6.simMouse.chr6 243879 61 + 636262 GTCAGTCCTGCCCTTTAGCACAGCAAGTGGAGGAAGGACATTCACTACAAGATATGATTAC -s Anc0.Anc0refChr5 62682 55 + 87904 GTCAG-----CCCCTTAGCATG-CAAATAGACGGAGAACATTCACTTCAAGATATAATCAT -s Anc1.Anc1refChr7 20441 55 - 47259 GTCAG-----CCCCTTAGCATG-CAAATAGACGGAGAACATTCACTTCAAGATATAATCAT -s Anc2.Anc2refChr15 59435 55 + 86568 GTCAG-----CCCCTTAGCATG-TAAATAGACAGAGAACATTCACCTCAAGACATAATCAT -s mr.mrrefChr5 96967 60 + 294540 GTCAGTCCTGCCCTTTAGCACA-CAAATGGAGGAAGGACATTCACTACAAGATATAATTAT -s simCow_chr6.simCow.chr6 240810 55 + 602619 ACCAG-----CCCTTCAGAAAA-GAAATAGACAGAGAACATTCATGTCAATGCATAATCAT -s simDog_chr6.simDog.chr6 232216 42 + 593897 GTCG---------CTTAGCATG-TGAATAGACAGAGAACATTCACCTCAAGA--------- -s simHuman_chr6.simHuman.chr6 322234 55 - 601863 GTCAC-----CCCCTTAGCATG-CAAATAGACGGAGAACATTCACTGCAAGATATAACAAT -s simRat_chr6.simRat.chr6 233949 60 + 647215 GTCTGTCCTGCCGTTTAGCACA-CAAATGGAGGTAGGATATTCACTACAAGACATAATCAT - -a -s simMouse_chr6.simMouse.chr6 243940 15 + 636262 TCACACTACAGGATT -s Anc0.Anc0refChr5 62738 15 + 87904 CCACATTACATGATT -s Anc1.Anc1refChr7 20497 15 - 47259 CCACATTACATGATT -s Anc2.Anc2refChr15 59491 15 + 86568 CCACACTGCATGACT -s mr.mrrefChr5 97027 15 + 294540 TCACATTACAGGATT -s simCow_chr6.simCow.chr6 240866 15 + 602619 CCACACTGCATGACT -s simHuman_chr6.simHuman.chr6 322290 15 - 601863 CCACTTCACGTGATT -s simRat_chr6.simRat.chr6 234009 15 + 647215 TCACATTACACGCCT - -a -s simMouse_chr6.simMouse.chr6 243955 47 + 636262 TTTCGTTGTTTATACTCCTTGGCTTGTGGTTTATCAAGGTGAAAGTT -s Anc0.Anc0refChr5 23775 46 - 87904 TGCTAATATTGACCCTCCCTGGGCTGTGATTCATCCAGATT-AAGCT -s Anc1.Anc1refChr7 25267 46 + 47259 TGCTAATATTGACCCTCCCTGGGCTGTGATTCATCCAGATT-AAGCT -s Anc2.Anc2refChr15 25641 46 - 86568 TGCTAATATTGACCCTCCCTGGGCTGTGATTCACCCAGATT-TAGCT -s mr.mrrefChr5 97042 47 + 294540 TTTCGTTGTTTATCCTCCTTGGGTTGTGGTTCATCAAGATGAAAGTT -s simCow_chr6.simCow.chr6 360307 46 - 602619 TGCTAACATTTAACCTCCCTGGACTGCGATTCACCTATCAT-GAGCT -s simDog_chr6.simDog.chr6 360392 44 - 593897 TGTTAATATTGACTCTCCCTGGGCTGTGGTACACCCAGATT-TAG-- -s simHuman_chr6.simHuman.chr6 278044 46 + 601863 TGCTAATATTCACCCTCCCTGGGCTGTGAATCATCCAGATT-AAGCT -s simRat_chr6.simRat.chr6 234024 47 + 647215 CTTCATTGTGTATCCCCTTTGGGTTATGGTTCATCAAGATGAAGCTT - -a -s simMouse_chr6.simMouse.chr6 244002 12 + 636262 CTTCTCCAGTTG -s Anc0.Anc0refChr5 23821 12 - 87904 CTTGTCTACTGG -s Anc1.Anc1refChr7 25313 12 + 47259 CTTGTCTACTGG -s Anc2.Anc2refChr15 25687 12 - 86568 CGTGTCTCCTGG -s mr.mrrefChr5 97089 12 + 294540 CTTCTCCAGTTG -s simCow_chr6.simCow.chr6 360354 12 - 602619 CCTCTCTTCTGG -s simDog_chr6.simDog.chr6 360436 11 - 593897 -GTGCCTCTCTG -s simHuman_chr6.simHuman.chr6 278090 12 + 601863 CTTGTCTACTGG -s simRat_chr6.simRat.chr6 234071 12 + 647215 CTTCTCCAGTTG - -a -s simMouse_chr6.simMouse.chr6 244014 20 + 636262 GGTATGTTGGAACTGAGATA -s Anc0.Anc0refChr5 23834 20 - 87904 GGGACATTGGGACTAGAGTA -s Anc1.Anc1refChr7 25326 20 + 47259 GGGACATTGGGACTAGAGTA -s Anc2.Anc2refChr15 25700 20 - 86568 GGGACATTGGGACTAGAGTA -s mr.mrrefChr5 97102 20 + 294540 GGTATGTTGGAACTAAGATA -s simCow_chr6.simCow.chr6 360367 19 - 602619 GGGATATTGAGCCTAG-GTA -s simDog_chr6.simDog.chr6 360448 20 - 593897 GGGACATTGGGACTAAAGTA -s simHuman_chr6.simHuman.chr6 278103 20 + 601863 GGGACACTGGGACTAGAGTA -s simRat_chr6.simRat.chr6 234084 20 + 647215 GGAATGTTGGAACTAAGATT - -a -s simMouse_chr6.simMouse.chr6 244034 64 + 636262 CCATTAAACAAGAATAGTGAACAATATATCACCCCGTTTCGTTACTTGATGGAAAGATAGCTAG -s Anc0.Anc0refChr5 23855 64 - 87904 CTATTAAACAAAACCAGCAAGCAATGTATCACCTTCTCTCGTGACATGCTGGAAACATGGCCAG -s Anc1.Anc1refChr7 25347 64 + 47259 CTATTAAACAAAACCAGCAAGCAATGTATCACCTTCTCTCGTGACATGCTGGAAACATGGCCAG -s Anc2.Anc2refChr15 25721 64 - 86568 CTATTAAACAGAACCACCAAGCAAGGTATCACCTTCTCTCATGACATGCTGGAAACATGGCCAG -s mr.mrrefChr5 97122 64 + 294540 CCATTAAACAAAAATAGTGAACAATATATCACCTCCTCTCGTGACTTGATGGAAAGATAGCTAG -s simCow_chr6.simCow.chr6 360387 64 - 602619 CCGCTAAACAGAACCACCAGGCAAAGTATTGCCTTCTCTCTTGACATGCTGGAATCCTGGCCAG -s simDog_chr6.simDog.chr6 360469 64 - 593897 CTATTAAACAGAACCACCAAGTGAGGCATCACTTCCTCTCAAGATATTTTGGAAACATGGCCAG -s simHuman_chr6.simHuman.chr6 278124 64 + 601863 CTATTAAACAAAACAAGCAAGCAATGTATCACCTTCTCTCGTGACATGCTGGAAGCATGGCCAG -s simRat_chr6.simRat.chr6 234104 64 + 647215 CCATTAAACAAAAATATTGACCAACATATCACCTCCTCTCATGACTTGATGAAAAGATTGCTAG - -a -s simMouse_chr6.simMouse.chr6 244098 44 + 636262 AGAGTTATTATTGACTAAACCAATATATTTTCCAGCAAGAAAAG -s Anc0.Anc0refChr5 23919 37 - 87904 AG------TATTGAGT-AACCAAGATTTTTTTAAGCAAGAGAAT -s Anc1.Anc1refChr7 25411 37 + 47259 AG------TATTGAGT-AACCAAGATTTTTTTAAGCAAGAGAAT -s Anc2.Anc2refChr15 25785 37 - 86568 AG------TGCTGGGT-AACCAAGATTTTTTTAAGCAAGAGAAT -s mr.mrrefChr5 97186 43 + 294540 AGA-TTATTATTGAGTAAACCAAGATATTTTTCAGCAAGAAAAG -s simCow_chr6.simCow.chr6 360457 37 - 602619 AT------TGCTGGGT-AACTAAGATTTTTTTAAGCAAGAGAGC -s simDog_chr6.simDog.chr6 360533 31 - 593897 AG------------GC-TATCAGGAATTTTTTAAGCAAGGGAAT -s simHuman_chr6.simHuman.chr6 278188 37 + 601863 AG------TATTGAGT-AACCAAGATTTTTTTGAGCAAGAGAAA -s simRat_chr6.simRat.chr6 234168 43 + 647215 GGA-TTATTATTGCGTAAACAAAGATATTTTTCAGCAAGAAAAG - -a -s simMouse_chr6.simMouse.chr6 244142 29 + 636262 TGTAATCATAGAAGCAGGAGAAGAAACAA -s Anc0.Anc0refChr5 23956 29 - 87904 TGCAATAGTAGAAGCATGAAATCTAACAA -s Anc1.Anc1refChr7 25448 29 + 47259 TGCAATAGTAGAAGCATGAAATCTAACAA -s Anc2.Anc2refChr15 25822 29 - 86568 TGCAATAGTAGAATCATGATATCTAACAA -s mr.mrrefChr5 97229 29 + 294540 TGTAATAGTAGAAGCAGGAAATGAAACAA -s simCow_chr6.simCow.chr6 360494 29 - 602619 TGCAATAGTGGAATAATGAGATCTAATAA -s simDog_chr6.simDog.chr6 360564 29 - 593897 TGCAATAGTAGAATCATGATATGTAACAA -s simHuman_chr6.simHuman.chr6 278229 29 + 601863 TGCTATAGTAGAGGTATGAAATCTAACGG -s simRat_chr6.simRat.chr6 234211 29 + 647215 TATAATAGCAGAAGCAGGAAATGAAACAA - -a -s simMouse_chr6.simMouse.chr6 244171 19 + 636262 ATCAGTTAAAGATTGGTGT -s Anc0.Anc0refChr5 23985 19 - 87904 ATTGGTTAAAGATTGGAGT -s Anc1.Anc1refChr7 25477 19 + 47259 ATTGGTTAAAGATTGGAGT -s Anc2.Anc2refChr15 25851 19 - 86568 ATTGGTTAAAGATTGGAGT -s mr.mrrefChr5 97258 19 + 294540 ATCAGTTAAAGATTGGTGT -s simCow_chr6.simCow.chr6 360531 19 - 602619 ATTGGTGAAAAATTAGAGT -s simDog_chr6.simDog.chr6 360593 19 - 593897 ATTGGTTAAAGATTGGGGT -s simHuman_chr6.simHuman.chr6 278258 19 + 601863 ATTTGTTAAATATTGGAGT -s simRat_chr6.simRat.chr6 234240 19 + 647215 ATCAGTTAAAGATTGGTGT - -a -s simMouse_chr6.simMouse.chr6 244190 5 + 636262 TAGAT -s Anc0.Anc0refChr5 24007 3 - 87904 TG-A- -s Anc1.Anc1refChr7 25499 4 + 47259 TGGA- -s Anc2.Anc2refChr15 25873 3 - 86568 TA-A- -s mr.mrrefChr5 97277 5 + 294540 TGGAT -s simCow_chr6.simCow.chr6 360553 3 - 602619 TA-C- -s simDog_chr6.simDog.chr6 360615 3 - 593897 TA-A- -s simHuman_chr6.simHuman.chr6 278280 4 + 601863 TGGA- -s simRat_chr6.simRat.chr6 234259 5 + 647215 TGGAT - -a -s simMouse_chr6.simMouse.chr6 244195 10 + 636262 TATTGGTGTT -s Anc0.Anc0refChr5 24020 9 - 87904 CATT-TTATT -s Anc1.Anc1refChr7 25513 9 + 47259 CATT-TTATT -s Anc2.Anc2refChr15 25886 9 - 86568 CATC-TGATT -s mr.mrrefChr5 97296 10 + 294540 TATTGGTGTT -s simCow_chr6.simCow.chr6 360566 9 - 602619 CATC-TGTGC -s simDog_chr6.simDog.chr6 360628 9 - 593897 TATC-TGATT -s simHuman_chr6.simHuman.chr6 278294 9 + 601863 CATT-TTATT -s simRat_chr6.simRat.chr6 234279 10 + 647215 TATCCGTGTC - -a -s simMouse_chr6.simMouse.chr6 244205 21 + 636262 CATGAAACTTCACTGGGATGG -s Anc0.Anc0refChr5 24029 21 - 87904 CATAAAACTTCACTGAATTGG -s Anc1.Anc1refChr7 25522 21 + 47259 CATAAAACTTCACTGAATTGG -s Anc2.Anc2refChr15 25896 21 - 86568 CATAAACCTTCACTGAATTAG -s mr.mrrefChr5 97306 21 + 294540 CATGAAACTTCACTGGGATGG -s simCow_chr6.simCow.chr6 360576 21 - 602619 CATAAAGCTTCATTGAATTAG -s simDog_chr6.simDog.chr6 360638 21 - 593897 CACAAACCGTCACTGAACTAG -s simHuman_chr6.simHuman.chr6 278303 21 + 601863 CATAAAACTTCACTTAATTGG -s simRat_chr6.simRat.chr6 234289 21 + 647215 CATGAAACTTCACTGGGGTGG - -a -s simMouse_chr6.simMouse.chr6 244226 22 + 636262 ATGAACTTGACTGCATATTATA -s Anc0.Anc0refChr5 24050 21 - 87904 ATGAGCTCCTCTGTGG-TCATA -s Anc1.Anc1refChr7 25543 21 + 47259 ATGAGCTCCTCTGTGG-TCATA -s Anc2.Anc2refChr15 25917 21 - 86568 ATGAGCTCCTCTGTGG-TCATA -s mr.mrrefChr5 97327 22 + 294540 ATGAACTCGACTGTGGTTTATA -s simCow_chr6.simCow.chr6 360600 21 - 602619 ACCGGCTCCTCTGTGG-TCATA -s simDog_chr6.simDog.chr6 360659 21 - 593897 ATGAACTCCTTTGTGG-TCGCA -s simHuman_chr6.simHuman.chr6 278324 21 + 601863 ATGAGTCCCTCAATGG-TCATA -s simRat_chr6.simRat.chr6 234310 22 + 647215 ATGAACTCGACTGTGGTTCATA - -a -s simMouse_chr6.simMouse.chr6 244248 11 + 636262 AAACCCACTGA -s Anc0.Anc0refChr5 24078 9 - 87904 A--CCCACTGA -s Anc1.Anc1refChr7 25571 9 + 47259 A--CCCACTGA -s Anc2.Anc2refChr15 25949 9 - 86568 A--ATTAATGC -s mr.mrrefChr5 97349 9 + 294540 A--CCCACTGA -s simCow_chr6.simCow.chr6 360634 9 - 602619 G--ATTAGTGA -s simDog_chr6.simDog.chr6 360691 9 - 593897 A--ATTAATGC -s simHuman_chr6.simHuman.chr6 278352 9 + 601863 A--CCCACTGA -s simRat_chr6.simRat.chr6 234332 9 + 647215 A--CCCACTGA - -a -s simMouse_chr6.simMouse.chr6 244259 46 + 636262 AACAGATGATAGGGGTATAGTCAAGTGCGCAATGCGAATTCTCAGT -s Anc0.Anc0refChr5 24087 43 - 87904 ATTATATGAAAGGAGGATTTTCAAGTGCAGATAGCCATTTCTC--- -s Anc1.Anc1refChr7 25580 43 + 47259 ATTATATGAAAGGAGGATTTTCAAGTGCAGATAGCCATTTCTC--- -s Anc2.Anc2refChr15 25958 43 - 86568 ATTATATCAAGGGATGATTTTGAAGTGAAGATAGCAGTTTCTC--- -s mr.mrrefChr5 97358 46 + 294540 ATCAGATGAAAGGGGTATTGTCAAGTGCACATTGCCAATTCTCAGT -s simCow_chr6.simCow.chr6 360643 28 - 602619 AGTAGGTAAAGGGC---------------GATAGCAGTTTCTC--- -s simDog_chr6.simDog.chr6 360700 33 - 593897 ATTATAGCAAGGGATGATTTTGAAGTGAAGCTA------------- -s simHuman_chr6.simHuman.chr6 278367 43 + 601863 ATTATATGAAAGGAGAATTATCAAGTGCAGATAGCCAGGTCTC--- -s simRat_chr6.simRat.chr6 234341 46 + 647215 ATCTGATGAAAGGGGTAATGCCAAGTGCACATTGCCAATTTTCAGT - -a -s simMouse_chr6.simMouse.chr6 244305 35 + 636262 TGTGTCGTGATTGACCATTAGGCACTACTATAAGT -s Anc0.Anc0refChr5 24133 35 - 87904 AGTGGAGTGAATGACCATCAGGCACTTCTATCAGA -s Anc1.Anc1refChr7 25626 35 + 47259 AGTGGAGTGAATGACCATCAGGCACTTCTATCAGA -s Anc2.Anc2refChr15 26004 35 - 86568 AGGGGAGTAAATGACCAGCAGGCACTTCTATCAGA -s mr.mrrefChr5 97409 35 + 294540 AGTGTAGTGATTGACCATCAGGCACTACTATCAGT -s simCow_chr6.simCow.chr6 360674 35 - 602619 AGGGGAGTAGATGATCTGCAGGCACCACTCTCAGA -s simDog_chr6.simDog.chr6 360733 33 - 593897 --GGGAGTAAATGACTAGCAGGCATTTCTATCAGA -s simHuman_chr6.simHuman.chr6 278413 34 + 601863 AGTGGGGTGAGT-ACCATCACACACTGCTATTAGC -s simRat_chr6.simRat.chr6 234392 32 + 647215 AATGTAGTGACTGAC---CATGCACTACTATCAGT - -a -s simMouse_chr6.simMouse.chr6 244340 2 + 636262 GT -s Anc0.Anc0refChr5 24179 2 - 87904 GT -s Anc1.Anc1refChr7 25672 2 + 47259 GT -s Anc2.Anc2refChr15 26050 2 - 86568 GT -s mr.mrrefChr5 97444 2 + 294540 GT -s simCow_chr6.simCow.chr6 360742 2 - 602619 GT -s simDog_chr6.simDog.chr6 360777 2 - 593897 GT -s simHuman_chr6.simHuman.chr6 278459 2 + 601863 GT -s simRat_chr6.simRat.chr6 234424 2 + 647215 GT - -a -s simMouse_chr6.simMouse.chr6 244342 15 + 636262 GAACATCAGTGTGAA -s Anc0.Anc0refChr5 24181 15 - 87904 GACTATCAGTGTGAA -s Anc1.Anc1refChr7 25674 15 + 47259 GACTATCAGTGTGAA -s Anc2.Anc2refChr15 26052 15 - 86568 GACTATCAGTGTGAA -s mr.mrrefChr5 97446 15 + 294540 GAACATCAGTGTGAA -s simCow_chr6.simCow.chr6 360744 15 - 602619 TAGCATCAGCGTGAA -s simDog_chr6.simDog.chr6 360780 15 - 593897 GACTATCAATGTGAT -s simHuman_chr6.simHuman.chr6 278461 15 + 601863 AACTATTAGTGTGAA -s simRat_chr6.simRat.chr6 234426 15 + 647215 GAACATCAGTGTCAG - -a -s simMouse_chr6.simMouse.chr6 244357 3 + 636262 CAG -s Anc0.Anc0refChr5 24196 3 - 87904 CAC -s Anc1.Anc1refChr7 25689 3 + 47259 CAC -s Anc2.Anc2refChr15 26067 3 - 86568 CAC -s mr.mrrefChr5 97461 3 + 294540 CAG -s simCow_chr6.simCow.chr6 360759 3 - 602619 TAC -s simDog_chr6.simDog.chr6 360800 3 - 593897 CAC -s simHuman_chr6.simHuman.chr6 278476 3 + 601863 CAC -s simRat_chr6.simRat.chr6 234441 3 + 647215 CAG - -a -s simMouse_chr6.simMouse.chr6 244360 16 + 636262 TCATTAACAATTAAGC -s Anc0.Anc0refChr5 24199 16 - 87904 TCTTTGGTGTTTATTC -s Anc1.Anc1refChr7 25692 16 + 47259 TCTTTGGTGTTTATTC -s Anc2.Anc2refChr15 26070 16 - 86568 TCCTTGACATTTATTC -s mr.mrrefChr5 97467 16 + 294540 TCTTTAGTGATTAAGC -s simCow_chr6.simCow.chr6 360762 14 - 602619 TA--TACCATTTAGTT -s simDog_chr6.simDog.chr6 360803 16 - 593897 CCCTTGACATGTATTC -s simHuman_chr6.simHuman.chr6 278479 16 + 601863 TCTTTGGTGTTTATCC -s simRat_chr6.simRat.chr6 234447 16 + 647215 TCTTTAGTGATTAAGC - -a -s simMouse_chr6.simMouse.chr6 244376 37 + 636262 TTTTGATAGAAGACAGCTTGATTGAGAGCACATGAGG -s Anc0.Anc0refChr5 24217 32 - 87904 CTTTGATAGTAGACATCCT----GAGAGTACATA-TG -s Anc1.Anc1refChr7 25710 37 + 47259 CTTTGATAGTAGACATCCTCATTGAGAGTACATAATG -s Anc2.Anc2refChr15 26088 32 - 86568 CTTTGATAGTAGACATCCT----GAGAGTATATA-TG -s mr.mrrefChr5 97483 37 + 294540 TTTTGATAGAAGACAGCTTCATTGAGAGCACATGAGG -s simCow_chr6.simCow.chr6 360778 32 - 602619 CTTTGGTAGTACACAACTT----GAGAGTAGAGA-TG -s simDog_chr6.simDog.chr6 360821 32 - 593897 CTTTGATATTAGACATCCT----GAGAGTATATA-TG -s simHuman_chr6.simHuman.chr6 278497 37 + 601863 CTTTGATAGTAGACATCCTCATTGAGAGTGCATAATG -s simRat_chr6.simRat.chr6 234463 37 + 647215 TTGTGATAGAAGACAGCTTCATTGAAAGCACATGAGG - -a -s simMouse_chr6.simMouse.chr6 244413 7 + 636262 TATCTTT -s Anc0.Anc0refChr5 24255 7 - 87904 TATCTTT -s Anc1.Anc1refChr7 25753 7 + 47259 TATCTTT -s Anc2.Anc2refChr15 26126 7 - 86568 TATCTTT -s mr.mrrefChr5 97520 7 + 294540 TATCTTT -s simCow_chr6.simCow.chr6 360816 7 - 602619 TATCTTT -s simDog_chr6.simDog.chr6 360859 7 - 593897 TATCTCC -s simHuman_chr6.simHuman.chr6 278540 7 + 601863 TATCTTT -s simRat_chr6.simRat.chr6 234500 7 + 647215 TATCTTT - -a -s simMouse_chr6.simMouse.chr6 244420 18 + 636262 TGCTTTCAATAGCAGATG -s Anc0.Anc0refChr5 24263 18 - 87904 TGTTCTTAATGGCACATT -s Anc1.Anc1refChr7 25761 18 + 47259 TGTTCTTAATGGCACATT -s Anc2.Anc2refChr15 26134 18 - 86568 TGTTCCTAATGGCACATT -s mr.mrrefChr5 97527 18 + 294540 TGCTTTCAATAGCAGATG -s simCow_chr6.simCow.chr6 360824 18 - 602619 TATTCCTAATGACACATT -s simDog_chr6.simDog.chr6 360867 18 - 593897 CGATCCTAATGGCACAAC -s simHuman_chr6.simHuman.chr6 278548 18 + 601863 TGTTCTTAATGGCACATT -s simRat_chr6.simRat.chr6 234507 18 + 647215 TGCTTTCAATAGCAGATG - -a -s simMouse_chr6.simMouse.chr6 244438 172 + 636262 GCCTACAAGCTAAAGTATTTGAATTTCTTTTTTGCACAAATTAATGAGTGCCAGATTGCCACAACGTCAGTAGCCCCTACAAAGAGGATGTTTGTTTTACAAGTATGGGAACCAGAGTGTACTCACTGCCGGTGCGTTGCAGCATCTAATAAGAATACAGATCAGGATGTTA -s Anc0.Anc0refChr5 24281 85 - 87904 ACCTATCCACTAAAGTTTTCCAATTTCTTTTTTTCAAGCATAAAA-----------------------GG-------TTTAAGAAGGTTA---------CATACCAAGATACTGGAGA------------------------------------------------ACGTTA -s Anc1.Anc1refChr7 25779 108 + 47259 ACCTATCCACTAAAGTTTTCCAATTTCTTTTTTTCAAGCATAAAACAGTGCCACACAGCTGCAAATTTGG-------TTTAAGAAGGTTA---------CATACCAAGATACTGGAGA------------------------------------------------ACGTTA -s Anc2.Anc2refChr15 26152 85 - 86568 ACCTATCCACTAATGTTCACCAACTTCTTTTTTTCAAGCTAAAAA-----------------------GG-------GTTAAGAAGGTTA---------CATACCAACATGCTGGAGA------------------------------------------------ACATTA -s mr.mrrefChr5 97545 172 + 294540 TCCTACCAACTAGAGTCTTTCAATTTCTTTTGTGCACAAATTAATGAGTGCCACATTGCCACAATGTTCGTAGCCCCTATAAGGAGGTTGTTTGTCTTACAAGCATGGGAACCAGAGTGTACTCACTGCCGGTGCTTTCCAGCATCTAGAAAGAATACAGATCAGGATGTTA -s simCow_chr6.simCow.chr6 360842 77 - 602619 GCCTACCCG---ATGT----CAACTTTTTTTTTTCAAGCTCTAAA-----------------------AG-------GTTAAAAAGGTTA---------CGTACCAAAATGCCAGAGA------------------------------------------------A-ATGG -s simDog_chr6.simDog.chr6 360885 82 - 593897 ACCAATCCACTAATGTTCACCAA---CTTCTTATACAGCTAATTA-----------------------GG-------TTTAAGAAGGTTT---------CATGCCAACATGGTGGATA------------------------------------------------ACATTA -s simHuman_chr6.simHuman.chr6 278566 108 + 601863 AACTAGCCACTAAAGTTTTCTGATTTCTTTTTTTCAGGCATGAAACAGTGCCACACAGCTGCAAATTTGG-------TTTGAGAAGATTA---------CACACCAAGACACTGGAGA------------------------------------------------ACGTTA -s simRat_chr6.simRat.chr6 234525 172 + 647215 TCCTACCAACTAGAGTCTTTCAATTTCTTTTGTGCACAAATTAACGAGTGCCACATTGCCACAATGTTCGTAGCCCCTATAAGGAGGTTGTTTGTCTTACAAGCATGGGAACCAGAGTGTACTCACTGCGGGTGCTTTCCAGCATCTAGAAAGAATACAGATCAGGATGTTA -s simRat_chr6.simRat.chr6 234880 172 + 647215 TCCTACCAACTAGAGTCTTTCAATTTCTTTTGTGCACAAATTAATGAGTGCCACATTGCCACAATGTTCGTAGCCCCTATAAGGAGGTTGTTTGTCTTACAAGCATGGGAACCAGGGTGTACTCACTACCGGTGCTTTCCGGCATCTAGAAAGAATACAGATCAGGATGTTA - -a -s simMouse_chr6.simMouse.chr6 244610 60 + 636262 AGATCACTCAGGTATTAGAGAATTTATGTGGTCATCTTGGTTCTCATGCTCTTACTATGT -s Anc0.Anc0refChr5 24367 11 - 87904 GGTA---TCAGG----------------------------------------------GT -s Anc1.Anc1refChr7 25888 11 + 47259 GGTA---TCAGG----------------------------------------------GT -s Anc2.Anc2refChr15 26238 11 - 86568 GGTA---TTGGA----------------------------------------------GC -s mr.mrrefChr5 97718 14 + 294540 AGAGCACTCAGG----------------------------------------------GT -s simCow_chr6.simCow.chr6 360920 11 - 602619 GGTC---TTGGA----------------------------------------------GC -s simDog_chr6.simDog.chr6 360968 11 - 593897 GGTA---TTGAA----------------------------------------------GC -s simHuman_chr6.simHuman.chr6 278675 11 + 601863 GGTA---TCAGG----------------------------------------------GT -s simRat_chr6.simRat.chr6 234698 14 + 647215 AAAGCACTCAGG----------------------------------------------GT -s simRat_chr6.simRat.chr6 235053 14 + 647215 AGAGCACTCAGG----------------------------------------------GT - -a -s simMouse_chr6.simMouse.chr6 244670 16 + 636262 AACACCTCTACTTGAT -s Anc0.Anc0refChr5 24396 15 - 87904 AACACCTCCACATG-T -s Anc1.Anc1refChr7 25917 15 + 47259 AACACCTCCACATG-T -s Anc2.Anc2refChr15 26287 15 - 86568 AACACCCCCACATG-C -s mr.mrrefChr5 97732 16 + 294540 AACACCTTTTCATGAT -s simCow_chr6.simCow.chr6 360968 15 - 602619 AACACCCCCACATG-C -s simDog_chr6.simDog.chr6 361035 15 - 593897 GACACCCCCACATG-C -s simHuman_chr6.simHuman.chr6 278704 15 + 601863 AACACCTCCACATG-T -s simRat_chr6.simRat.chr6 234712 16 + 647215 AACACCTTTTCATGAT -s simRat_chr6.simRat.chr6 235067 10 + 647215 AACACCTTTT------ - -a -s simMouse_chr6.simMouse.chr6 244686 8 + 636262 ATATTCAC -s Anc0.Anc0refChr5 24411 8 - 87904 ATATTGAA -s Anc1.Anc1refChr7 25932 8 + 47259 ATATTGAA -s Anc2.Anc2refChr15 26302 8 - 86568 ATATTGAA -s mr.mrrefChr5 97748 8 + 294540 ATATTGAA -s simCow_chr6.simCow.chr6 360984 8 - 602619 ATATAGAA -s simDog_chr6.simDog.chr6 361050 8 - 593897 ACAGTGAA -s simHuman_chr6.simHuman.chr6 278719 8 + 601863 ATATTGAA -s simRat_chr6.simRat.chr6 234728 8 + 647215 ATATTAAA -s simRat_chr6.simRat.chr6 235077 7 + 647215 -TATTGAA - -a -s simMouse_chr6.simMouse.chr6 244694 34 + 636262 CATGAAAATCCTTCATGAAGCTGAGATTGGTTAG -s Anc0.Anc0refChr5 24419 33 - 87904 CAGGAAAAT-CTTCATGAAGCTGAGACAGTTTTG -s Anc1.Anc1refChr7 25940 33 + 47259 CAGGAAAAT-CTTCATGAAGCTGAGACAGTTTTG -s Anc2.Anc2refChr15 26310 33 - 86568 CAGGAAAAT-CTTCATGAGGCTGGGACAATCTTG -s mr.mrrefChr5 97756 33 + 294540 CATGAAGAT-CTTCATGAAGTTGAGACTGGTTAG -s simCow_chr6.simCow.chr6 360993 28 - 602619 CAGGAATAT-CTTCATGAG-CAGGGACAAT---- -s simDog_chr6.simDog.chr6 361058 33 - 593897 CAGGAAAAT-CTTCATGAGGCTGGGACAATCTTG -s simHuman_chr6.simHuman.chr6 278727 33 + 601863 CAGAAAAAT-CCTCATGAAGCTGAGACAGTTTTG -s simRat_chr6.simRat.chr6 234736 33 + 647215 CATGAAGAT-CTTCATGAAGTTGAGACTGGTTAG -s simRat_chr6.simRat.chr6 235084 33 + 647215 CATGAAGAT-CTTCATGAAGTTGGGACTGGTTAG - -a -s simMouse_chr6.simMouse.chr6 244728 4 + 636262 TGGT -s Anc0.Anc0refChr5 24452 4 - 87904 GTGT -s Anc1.Anc1refChr7 25973 4 + 47259 GTGT -s Anc2.Anc2refChr15 26343 4 - 86568 GTGT -s mr.mrrefChr5 97789 4 + 294540 CACT -s simCow_chr6.simCow.chr6 361021 3 - 602619 -TGC -s simDog_chr6.simDog.chr6 361092 4 - 593897 GTTT -s simHuman_chr6.simHuman.chr6 278760 4 + 601863 GTGT -s simRat_chr6.simRat.chr6 234769 4 + 647215 CACT -s simRat_chr6.simRat.chr6 235117 4 + 647215 CACT - -a -s simMouse_chr6.simMouse.chr6 244732 23 + 636262 GGGATAATGTGGCTTGTCACAGT -s Anc0.Anc0refChr5 24456 23 - 87904 GGGCAATTTTGGCTCATCACAGT -s Anc1.Anc1refChr7 25977 23 + 47259 GGGCAATTTTGGCTCATCACAGT -s Anc2.Anc2refChr15 26354 23 - 86568 GGACAATTTTGGCTCATCACAGT -s mr.mrrefChr5 97793 23 + 294540 GGGATGATATGGCTTGCCACAGT -s simCow_chr6.simCow.chr6 361031 23 - 602619 GGACAATTTTGGCTCATCACAGT -s simDog_chr6.simDog.chr6 361103 23 - 593897 GGACAATTATGGATCATCACAGT -s simHuman_chr6.simHuman.chr6 278764 23 + 601863 CGACCATTTTGGCTCATGCCAGT -s simRat_chr6.simRat.chr6 234773 23 + 647215 GGGATGATATGGCTTGCCACAGT -s simRat_chr6.simRat.chr6 235121 23 + 647215 GGGACGATATGGCTTGCCACAGT - -a -s simMouse_chr6.simMouse.chr6 244755 24 + 636262 CAAGTCCCTTGCGCTAAGCCTAAG -s Anc0.Anc0refChr5 24499 24 - 87904 TAAGTCCCCTGCCCTAAGCCTAAG -s Anc1.Anc1refChr7 26020 24 + 47259 TAAGTCCCCTGCCCTAAGCCTAAG -s Anc2.Anc2refChr15 26397 24 - 86568 TCAGTCCCCTGCCCTGACCCTAAG -s mr.mrrefChr5 97816 24 + 294540 CAAGTCCCCTGTGCGAAGCCTAAG -s simCow_chr6.simCow.chr6 361074 24 - 602619 ACAGTTCACTGCCCTGACCCATTG -s simDog_chr6.simDog.chr6 361146 24 - 593897 TCAGTCCCCTGCTTTGACACTAAG -s simHuman_chr6.simHuman.chr6 278807 24 + 601863 TAAGTCTTCTGCCCTAAGCCTAAG -s simRat_chr6.simRat.chr6 234796 24 + 647215 CAAGTCCCCTGTGTGAAGCCTAAG -s simRat_chr6.simRat.chr6 235144 24 + 647215 CAAGTCCCCTGTGCGAAGCCTAAG - -a -s simMouse_chr6.simMouse.chr6 244779 43 + 636262 GAAGTTGACAGATCAGATCGTTCTGACTGTCTTCATAAAGTTG -s Anc0.Anc0refChr5 24523 42 - 87904 GAA-TTGATAGGTTAGATCATTTTTACTGTCTTCATAAAGTTG -s Anc1.Anc1refChr7 26044 43 + 47259 GAAGTTGATAGGTTAGATCATTTTTACTGTCTTCATAAAGTTG -s Anc2.Anc2refChr15 26421 42 - 86568 CAA-TTGATAGGTTGCATCATTTTTACTGTCTTAACAAAACTT -s mr.mrrefChr5 97840 43 + 294540 GAAGTTAATAGATCAGATCATTCTGACTTTCTTCATAAAGTTG -s simCow_chr6.simCow.chr6 361098 31 - 602619 CAA-TTGATGGATTGTGTCATTTTGACTGTCT----------- -s simDog_chr6.simDog.chr6 361170 42 - 593897 TGA-TTGATAGGATGCATCATTCTTACTGTCTTAACAAAACTT -s simHuman_chr6.simHuman.chr6 278843 43 + 601863 GGCGTTGATAGCTTAGATCATTTTTACTGTCTTCATTGAGTTG -s simRat_chr6.simRat.chr6 234820 43 + 647215 GAAGTTAATAGATCAGATCATACTGACTTTCTTCATAAAGTTG -s simRat_chr6.simRat.chr6 235168 43 + 647215 GAAGTTAATAGATCAGATCATTCTGACTTTCTTCATAAAGTTG - -a -s simMouse_chr6.simMouse.chr6 244822 17 + 636262 ACTTTGAAAGTCATGTG -s Anc0.Anc0refChr5 24566 17 - 87904 ACTTTAAAAATTATGTG -s Anc1.Anc1refChr7 26088 17 + 47259 ACTTTAAAAATTATGTG -s Anc2.Anc2refChr15 26464 17 - 86568 ACTCTAAAAATTATGTG -s mr.mrrefChr5 97883 17 + 294540 ACTTTGAAAATCATGTG -s simCow_chr6.simCow.chr6 361130 17 - 602619 ACTCCAAAAATCATATG -s simDog_chr6.simDog.chr6 361213 17 - 593897 ACTCTGAAAATTACGTA -s simHuman_chr6.simHuman.chr6 278887 17 + 601863 ACTTTAGAAATTATGCG -s simRat_chr6.simRat.chr6 234863 17 + 647215 GCTTTCAATAGCAGATG -s simRat_chr6.simRat.chr6 235211 17 + 647215 ACTTTGACAATCATGAG - -a -s simMouse_chr6.simMouse.chr6 244839 17 + 636262 TATTCAAACAAGCCTAG -s Anc0.Anc0refChr5 24583 17 - 87904 GATTCAGACAAGCTCAC -s Anc1.Anc1refChr7 26105 17 + 47259 GATTCAGACAAGCTCAC -s Anc2.Anc2refChr15 26481 17 - 86568 GATTCAGACAAGCTCAC -s mr.mrrefChr5 97900 17 + 294540 TATTCAAACAAGCCTAG -s simCow_chr6.simCow.chr6 361147 17 - 602619 GATTCCGACAAGCTTAC -s simDog_chr6.simDog.chr6 361230 17 - 593897 GATTCAAACAAGCCCAC -s simHuman_chr6.simHuman.chr6 278904 17 + 601863 CATTCAGACAAGCTCAC -s simRat_chr6.simRat.chr6 235228 17 + 647215 AAGGCAAACATGACTAG - -a -s simMouse_chr6.simMouse.chr6 244856 12 + 636262 CAATCTATATTT -s Anc0.Anc0refChr5 24604 12 - 87904 CACTCCCTACTC -s Anc1.Anc1refChr7 26126 12 + 47259 CACTCCCTACTC -s Anc2.Anc2refChr15 26504 12 - 86568 CACTCCATACTC -s mr.mrrefChr5 97917 12 + 294540 CAATCTCTACTC -s simCow_chr6.simCow.chr6 361170 12 - 602619 TACTCCAGATTG -s simDog_chr6.simDog.chr6 361253 12 - 593897 CACTTCATTCTC -s simHuman_chr6.simHuman.chr6 278925 12 + 601863 CACACCCTACTC -s simRat_chr6.simRat.chr6 235245 12 + 647215 CAATCTCTACTC - -a -s simMouse_chr6.simMouse.chr6 244868 6 + 636262 ACCACA -s Anc0.Anc0refChr5 24616 6 - 87904 TGCACA -s Anc1.Anc1refChr7 26138 6 + 47259 TGCACA -s Anc2.Anc2refChr15 26516 6 - 86568 TGCACA -s mr.mrrefChr5 97929 6 + 294540 ACCACA -s simCow_chr6.simCow.chr6 361182 5 - 602619 TGCAC- -s simDog_chr6.simDog.chr6 361265 6 - 593897 TGTACA -s simHuman_chr6.simHuman.chr6 278937 6 + 601863 TACACA -s simRat_chr6.simRat.chr6 235261 6 + 647215 ACCACA - -a -s simMouse_chr6.simMouse.chr6 244874 41 + 636262 TTGAGCCTCAGATTCAACTGTTATTCTAATCTCCTACTTTT -s Anc0.Anc0refChr5 24630 41 - 87904 TTGAGCCTCAGTTTCTACTGCAATTCTGATCTCCTAATTTT -s Anc1.Anc1refChr7 26152 41 + 47259 TTGAGCCTCAGTTTCTACTGCAATTCTGATCTCCTAATTTT -s Anc2.Anc2refChr15 26530 41 - 86568 TTAAGCCTCAGTTTCTGCTGCAATTTTGTTCCCCTAATTTT -s mr.mrrefChr5 97935 41 + 294540 TTGAGCCTCAGATTCAACTGTTATTCTAATCTCCTAATTTT -s simCow_chr6.simCow.chr6 361188 41 - 602619 TTAAGCCTCACTTTCTGGTGCAGTTTAGTTCCCCTAATCTT -s simDog_chr6.simDog.chr6 361295 41 - 593897 TTAAACCTCAGTTCCTGCTGCAATTTTGTTCCCCTAATTTT -s simHuman_chr6.simHuman.chr6 278951 41 + 601863 TTGAGTGTCAGTTTCTATTACAATTCTGATCTCTTAATTTT -s simRat_chr6.simRat.chr6 235267 40 + 647215 TTGAGCCTCAGATTCAACTG-TACTCCAATCTCCTAATTTT - -a -s simMouse_chr6.simMouse.chr6 244915 80 + 636262 GAAAGGGGCCTTAATGCATTGTCCCAGACCAGCAAGGAAGAAGCCCTTCTTGAGACACTTGTTGCTCCCACTCACTTATT -s Anc0.Anc0refChr5 24671 19 - 87904 CACCGGAGCCTCAA------------------------------------------------------------T-TATT -s Anc1.Anc1refChr7 26193 77 + 47259 CACCGGAGCCTCAACAGACTGTGCCAAACTGACAAAGAAGATGCCCTTCATTAG--TATCTTTGTTCCCACCTAT-TATT -s Anc2.Anc2refChr15 26571 19 - 86568 CACCGGAGCCTCAA------------------------------------------------------------T-TTTC -s mr.mrrefChr5 97976 79 + 294540 GAAAGGGGCCTTAATGCACTGTGCCAGACTGGCAAGGAAGAAGCCCTTCATGAGACACTCGTTGCTCCCACTCAC-TATT -s simCow_chr6.simCow.chr6 361229 19 - 602619 CACAGGAGCCTCCA------------------------------------------------------------C-TTTC -s simDog_chr6.simDog.chr6 361338 19 - 593897 CACCGAGGTCTCAA------------------------------------------------------------T-TTTC -s simHuman_chr6.simHuman.chr6 278992 77 + 601863 CACTGGAGCCTGGACAGACTGTGCCAAACTGACAAAGAAGATGCCCTTCATTAG--TATCTTTGTTCCCACCTAT-TATT -s simRat_chr6.simRat.chr6 235307 79 + 647215 GAAAGGGGCCTTAATGCACTGTGCTGGTTTGGCAAGGAAGAAGCCCTTCATGAGACGCTCATTGCTCCCACTCAC-TATG - -a -s simMouse_chr6.simMouse.chr6 244995 13 + 636262 TAGGTTGAGCTAC -s Anc0.Anc0refChr5 24697 13 - 87904 AAAGTTGAGCCAC -s Anc1.Anc1refChr7 26277 13 + 47259 AAAGTTGAGCCAC -s Anc2.Anc2refChr15 26597 13 - 86568 AAAGCTGAGCCAC -s mr.mrrefChr5 98055 13 + 294540 TAAGTTGAGCTAC -s simCow_chr6.simCow.chr6 361255 13 - 602619 AAAGCTGAGCCAC -s simDog_chr6.simDog.chr6 361364 4 - 593897 AAAG--------- -s simHuman_chr6.simHuman.chr6 279076 13 + 601863 AAAGTTGAGTGGC -s simRat_chr6.simRat.chr6 235386 13 + 647215 TAAGTTGAGCTAC - -a -s simMouse_chr6.simMouse.chr6 245008 8 + 636262 ATTGGGGA -s Anc0.Anc0refChr5 24710 8 - 87904 ATTGAGCA -s Anc1.Anc1refChr7 26290 8 + 47259 ATTGAGCA -s Anc2.Anc2refChr15 26610 8 - 86568 ATTGAGCG -s mr.mrrefChr5 98068 8 + 294540 ATTGGGGA -s simCow_chr6.simCow.chr6 361268 8 - 602619 ATTGAGCG -s simHuman_chr6.simHuman.chr6 279090 8 + 601863 ACTGCAAA -s simRat_chr6.simRat.chr6 235399 8 + 647215 ATTGGGGA - -a -s simMouse_chr6.simMouse.chr6 245016 3 + 636262 CCT -s Anc0.Anc0refChr5 24718 3 - 87904 CCT -s Anc1.Anc1refChr7 26298 3 + 47259 CCT -s Anc2.Anc2refChr15 26618 3 - 86568 CCT -s mr.mrrefChr5 98076 3 + 294540 CCT -s simCow_chr6.simCow.chr6 361276 3 - 602619 CCT -s simHuman_chr6.simHuman.chr6 279107 3 + 601863 CTA -s simRat_chr6.simRat.chr6 235407 3 + 647215 CCT - -a -s simMouse_chr6.simMouse.chr6 245019 22 + 636262 TGAACAACAACTGCCTAGGTCT -s Anc0.Anc0refChr5 24721 19 - 87904 ---ACAGCAATTACCTGGGTCT -s Anc1.Anc1refChr7 26302 22 + 47259 TGCACAGCAATTACCTGGGTCT -s Anc2.Anc2refChr15 26621 19 - 86568 ---ACTGCAATTACTCGGGTCT -s mr.mrrefChr5 98080 22 + 294540 TGAACAACAATTACCTGGGTCT -s simCow_chr6.simCow.chr6 361279 19 - 602619 ---ACTGCAATTACTCGGGTCT -s simHuman_chr6.simHuman.chr6 279111 22 + 601863 TGCAAAGCAATTACCTGGGGCT -s simRat_chr6.simRat.chr6 235411 22 + 647215 TGAACAACAATTACCTGAGTCT - -a -s simMouse_chr6.simMouse.chr6 245041 20 + 636262 ACCTGTTAGGTGAACATCCA -s Anc0.Anc0refChr5 24745 8 - 87904 ATGT------------TCCA -s Anc1.Anc1refChr7 26329 8 + 47259 ATGT------------TCCA -s Anc2.Anc2refChr15 26645 8 - 86568 ATGT------------GTCA -s mr.mrrefChr5 98107 20 + 294540 ACCTGTTAGGTGAACATCCA -s simCow_chr6.simCow.chr6 361303 8 - 602619 ATGT------------GTCA -s simHuman_chr6.simHuman.chr6 279138 8 + 601863 ATAT------------TCCA -s simRat_chr6.simRat.chr6 235438 20 + 647215 ACCTGTTAGGTGAACATCCA - -a -s simMouse_chr6.simMouse.chr6 245061 2 + 636262 AC -s Anc0.Anc0refChr5 24753 2 - 87904 AC -s Anc1.Anc1refChr7 26337 2 + 47259 AC -s Anc2.Anc2refChr15 26653 2 - 86568 AC -s mr.mrrefChr5 98127 2 + 294540 AC -s simCow_chr6.simCow.chr6 361323 2 - 602619 AC -s simHuman_chr6.simHuman.chr6 279146 2 + 601863 AT -s simRat_chr6.simRat.chr6 235458 2 + 647215 GC - -a -s simMouse_chr6.simMouse.chr6 245063 28 + 636262 ATAGCAGTTTTATTTTCCCTTGGCCTCT -s Anc0.Anc0refChr5 24755 28 - 87904 ATAGCATTTCTATTGTCACCCAATCTCT -s Anc1.Anc1refChr7 26339 28 + 47259 ATAGCATTTCTATTGTCACCCAATCTCT -s Anc2.Anc2refChr15 26655 28 - 86568 ACAGCATTTCTTCTGTCACCCAATCTCT -s mr.mrrefChr5 98129 28 + 294540 ATAGCAGTTTTATTTTCCCCTGGCCTCT -s simCow_chr6.simCow.chr6 361325 28 - 602619 ACAGCATTTCTTCTGTCACCCAATCTCT -s simHuman_chr6.simHuman.chr6 279148 28 + 601863 ATAGCACTACTATTGTCACCCACTCTCT -s simRat_chr6.simRat.chr6 235474 28 + 647215 ATACCAGTTTTACTTTTCCCTGTCTTAC - -a -s simMouse_chr6.simMouse.chr6 245091 49 + 636262 ACTCACATACATGATGCATGCAGCTGCTAGAAACTGGAACAGTTGAACA -s Anc0.Anc0refChr5 24783 24 - 87904 GCTG-----------------------TAATAACCA-AAGA-TTGAACA -s Anc1.Anc1refChr7 26367 26 + 47259 GCTG-----------------------TAATAACCATAAGAGTTGAACA -s Anc2.Anc2refChr15 26683 24 - 86568 GCTG-----------------------TCATAACCA-AAGA-TCAAATA -s mr.mrrefChr5 98157 49 + 294540 ACTCACATACATGATGCATGCAGCTGCTAGAAACTGGAACAGTTGAACA -s simCow_chr6.simCow.chr6 361360 24 - 602619 GCTG-----------------------TCATAACCA-AAGA-TCAAATA -s simHuman_chr6.simHuman.chr6 279176 26 + 601863 GTTG-----------------------TAATAGCCATAAGAGTTGAACA -s simRat_chr6.simRat.chr6 235502 49 + 647215 ACTCACATATATGACGCATTCAACTGCGAGAAACTGGAACAGTTGAATA - -a -s simMouse_chr6.simMouse.chr6 245140 30 + 636262 TGCTAATCCCAATGATTGACTGTGCTCAAC -s Anc0.Anc0refChr5 24815 20 - 87904 AG----------TGATTCACTGTGCTCAAC -s Anc1.Anc1refChr7 26401 30 + 47259 AGCAGAACTTAATGATTCACTGTGCTCAAC -s Anc2.Anc2refChr15 26715 20 - 86568 AG----------TGATTCACCTTGCTCAAC -s mr.mrrefChr5 98206 30 + 294540 AGCTAATCCCAATGATTGACTGTGCTCAAC -s simCow_chr6.simCow.chr6 361392 20 - 602619 AG----------TGATTCACCTTGCTCAAC -s simHuman_chr6.simHuman.chr6 279210 30 + 601863 AGCAGAACTTAACGATTCACTGTGCTTAGC -s simRat_chr6.simRat.chr6 235551 30 + 647215 AGCTAATCCCAATGATTGACTGTCCTCAAC - -a -s simMouse_chr6.simMouse.chr6 245170 14 + 636262 CACGACCTTAGCTG -s Anc0.Anc0refChr5 24851 14 - 87904 CCTCACCCTAGCTT -s Anc1.Anc1refChr7 26447 14 + 47259 CCTCACCCTAGCTT -s Anc2.Anc2refChr15 26751 14 - 86568 CCTCACCCTAGCTT -s mr.mrrefChr5 98252 14 + 294540 CATGACCTTAGCTT -s simCow_chr6.simCow.chr6 361428 14 - 602619 CCTCACCCTAGCTT -s simHuman_chr6.simHuman.chr6 279256 14 + 601863 TCTCACCCTAGCTT -s simRat_chr6.simRat.chr6 235599 14 + 647215 CATGACCTTAGCTT - -a -s simMouse_chr6.simMouse.chr6 245184 5 + 636262 GGCCA -s Anc0.Anc0refChr5 24865 5 - 87904 GAACA -s Anc1.Anc1refChr7 26461 5 + 47259 GAACA -s Anc2.Anc2refChr15 26765 5 - 86568 AAACA -s mr.mrrefChr5 98266 5 + 294540 GACCA -s simCow_chr6.simCow.chr6 361442 5 - 602619 AAACA -s simHuman_chr6.simHuman.chr6 279270 5 + 601863 GAACA -s simRat_chr6.simRat.chr6 235614 5 + 647215 GACCA - -a -s simMouse_chr6.simMouse.chr6 245189 42 + 636262 TAAATTGACTATATACTGGGGCCTCAATACAGAACAAGCATT -s Anc0.Anc0refChr5 24888 40 - 87904 CAAAAAGAGAGTACACTAGGGTTTCAATACAGAAT--GCATG -s Anc1.Anc1refChr7 26484 40 + 47259 CAAAAAGAGAGTACACTAGGGTTTCAATACAGAAT--GCATG -s Anc2.Anc2refChr15 26799 40 - 86568 CAAAAAGAAAGTACACTAGGGTCCCAATACAGAAT--GCATG -s mr.mrrefChr5 98271 42 + 294540 TAAATAGAGAGTATACTGGGGCTTCAATACAGAATAAGCATT -s simCow_chr6.simCow.chr6 361476 40 - 602619 CAAATATAATGTACACTAGGGTCCCAATACAGAAC--AGATG -s simDog_chr6.simDog.chr6 361386 40 - 593897 CAAGAAGAAAGTAGACTAGGGTCCCAATATAGATT--GCATG -s simHuman_chr6.simHuman.chr6 279293 40 + 601863 CAAAAAGAGAGGACACTAGGGTTTCGATACAGAAT--GCATG -s simRat_chr6.simRat.chr6 235619 42 + 647215 TAAATAGCGAGTATACTGGGGCTTCAATACAGAATATGCATT - -a -s simMouse_chr6.simMouse.chr6 245231 4 + 636262 CCTC -s Anc0.Anc0refChr5 24929 4 - 87904 TCCC -s Anc1.Anc1refChr7 26525 4 + 47259 TCCC -s Anc2.Anc2refChr15 26840 4 - 86568 TCCC -s mr.mrrefChr5 98313 4 + 294540 CCCC -s simCow_chr6.simCow.chr6 361517 4 - 602619 TCCC -s simDog_chr6.simDog.chr6 361444 4 - 593897 TTTT -s simHuman_chr6.simHuman.chr6 279334 4 + 601863 TCCC -s simRat_chr6.simRat.chr6 235661 4 + 647215 CCCC - -a -s simMouse_chr6.simMouse.chr6 245235 8 + 636262 AACATTGC -s Anc0.Anc0refChr5 24979 8 - 87904 TATGTTAC -s Anc1.Anc1refChr7 26575 8 + 47259 TATGTTAC -s Anc2.Anc2refChr15 26890 8 - 86568 TATGTTAC -s mr.mrrefChr5 98363 8 + 294540 AACATTGC -s simCow_chr6.simCow.chr6 361567 8 - 602619 TATGTTAC -s simDog_chr6.simDog.chr6 361495 8 - 593897 TATGTTAC -s simHuman_chr6.simHuman.chr6 279385 8 + 601863 TATGTGAC -s simRat_chr6.simRat.chr6 235711 8 + 647215 AACATTGC - -a -s simMouse_chr6.simMouse.chr6 245243 100 + 636262 TGATAATTTGTCCTTCTTCCCCAGCCGGTGAGGCAGGCACATAACTGCAGCACATTAGTGGTCTAACTACTCCCAAGGTAACTTTTTGTACAAGGAGCAC -s Anc0.Anc0refChr5 24987 100 - 87904 TAATAATTTGCCCTTCTGCCCCTGATGGTCAGGCAGGCACATAATTGCACTCCATCTGTGTGACATCTGCTGCCATAGTGGCTTTTTTTACAAAGAGTCA -s Anc1.Anc1refChr7 26583 100 + 47259 TAATAATTTGCCCTTCTGCCCCTGATGGTCAGGCAGGCACATAATTGCACTCCATCTGTGTGACATCTGCTGCCATAGTGGCTTTTTTTACAAAGAGTCA -s Anc2.Anc2refChr15 26898 100 - 86568 TGATAATTTGCCCTTCTGCCCCTGATTGTCAGGCAGGCACATAATTGCCCTCCATCTGTGTGACATCAGCCGCCATAGTGGCTTTTTTTACAAAGAGTCA -s mr.mrrefChr5 98371 100 + 294540 TAATAATTTGTCCTTCTTCCCCAGCTGGTGAGGCAGGCACATAACTGCAGCACATTAGTGGTCTAACTGCTCCCATGGTAACTTTTTGTACAAGGAGTAC -s simCow_chr6.simCow.chr6 361577 96 - 602619 TGTCAGTCTGCCCTTCTGCCCCTGATTGTCAGGCAGGCACTTAATTGCCCTCCCTCTGTTTCACATAAGCCGCCATAGTG----TCTTCACAAAGAGTCC -s simDog_chr6.simDog.chr6 361503 96 - 593897 TGATAATTTGTCCTTCTGCCCGTGATTGTCAGGCAGTCACATAATTGC----CATCTGTGTGACAACAGCCACCATAGTGGCTTTTTATACAAAGAGTCA -s simHuman_chr6.simHuman.chr6 279393 100 + 601863 CAATAATTTGCCCTTCTGTCCCTAATGGTCCAACAGGGACATAATTGCATACCATCTGTGAAACATCTGCTGCCATAGTGGCCTTTTTTATAAAGAGTGT -s simRat_chr6.simRat.chr6 235719 99 + 647215 TAATAATTTGTCCTT-TTCCCCGGCTGGTAAGGCAGGCGCATAACTGGAGCGCATGAGTGGTCAAACTGCTTCCATGGTCACTTTTTGTACAAGAAGTCC - -a -s simMouse_chr6.simMouse.chr6 245343 13 + 636262 CTTGCAGAATTGT -s Anc0.Anc0refChr5 25087 13 - 87904 CTTGGTTAATGGC -s Anc1.Anc1refChr7 26683 13 + 47259 CTTGGTTAATGGC -s Anc2.Anc2refChr15 26998 13 - 86568 CTTGGTTAATGGC -s mr.mrrefChr5 98471 13 + 294540 CTTGCTGAATTGT -s simCow_chr6.simCow.chr6 361673 13 - 602619 CTTGATCAATAGC -s simDog_chr6.simDog.chr6 361599 13 - 593897 CCTGGTTAATGGC -s simHuman_chr6.simHuman.chr6 279494 13 + 601863 CTCAGTTAATGGC -s simRat_chr6.simRat.chr6 235818 13 + 647215 CTTGATGAATTGT - -a -s simMouse_chr6.simMouse.chr6 245356 1 + 636262 G -s Anc0.Anc0refChr5 25120 1 - 87904 G -s Anc1.Anc1refChr7 26716 1 + 47259 G -s Anc2.Anc2refChr15 27031 1 - 86568 G -s mr.mrrefChr5 98504 1 + 294540 G -s simCow_chr6.simCow.chr6 361706 1 - 602619 G -s simDog_chr6.simDog.chr6 361632 1 - 593897 G -s simHuman_chr6.simHuman.chr6 279527 1 + 601863 G -s simRat_chr6.simRat.chr6 235851 1 + 647215 G - -a -s simMouse_chr6.simMouse.chr6 245357 1 + 636262 A -s Anc0.Anc0refChr5 25126 1 - 87904 A -s Anc1.Anc1refChr7 26722 1 + 47259 A -s Anc2.Anc2refChr15 27037 1 - 86568 A -s mr.mrrefChr5 98505 1 + 294540 A -s simCow_chr6.simCow.chr6 361712 1 - 602619 G -s simDog_chr6.simDog.chr6 361638 1 - 593897 A -s simHuman_chr6.simHuman.chr6 279533 1 + 601863 A -s simRat_chr6.simRat.chr6 235852 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 245358 24 + 636262 ACAAGATTTGTCACACTTATGGCA -s Anc0.Anc0refChr5 25127 24 - 87904 ACAAGATTTATCACACTTAAGAAA -s Anc1.Anc1refChr7 26723 24 + 47259 ACAAGATTTATCACACTTAAGAAA -s Anc2.Anc2refChr15 27038 24 - 86568 ACAAAATTCATCACACATAAGAAA -s mr.mrrefChr5 98506 24 + 294540 ACAAGATTTGTCACACTTATGGCA -s simCow_chr6.simCow.chr6 361714 24 - 602619 ACAAAATTCATCACACATAAGAAA -s simHuman_chr6.simHuman.chr6 279534 24 + 601863 ACAGGATTTATCGCACTTAAGAAA -s simRat_chr6.simRat.chr6 235853 24 + 647215 ACAAGACTTGTCACACTTATGGAA - -a -s simMouse_chr6.simMouse.chr6 245382 33 + 636262 CCATTATTAACGTGGTATCTAATCTTTTGTACC -s Anc0.Anc0refChr5 64159 33 + 87904 CCCATGTTAGCATGCCAGCTAACTTTTAGTACC -s Anc1.Anc1refChr7 22022 33 - 47259 CCCATGTTAGCATGCCAGCTAACTTTTAGTACC -s Anc2.Anc2refChr15 60957 33 + 86568 CCCATGTTAGCATGCCAGCTAACTTTTAGTACC -s mr.mrrefChr5 98530 33 + 294540 CCATTATTAACGTGGTATCTAATCTTTTGTACC -s simCow_chr6.simCow.chr6 242342 32 + 602619 CGCATGTTAGCATAGGAGCTAACTTGTAGTAC- -s simDog_chr6.simDog.chr6 233532 33 + 593897 CCCATGTCAGCATGCCACTTAACTTTTAGCACC -s simHuman_chr6.simHuman.chr6 323849 33 - 601863 CCCCTGTTAGCATGTCAGCTGGCTTTCAGTACA -s simRat_chr6.simRat.chr6 235877 33 + 647215 CTATTATTAACATGGTATCTAACCTGTTACACT - -a -s simMouse_chr6.simMouse.chr6 245415 10 + 636262 TGAAACTTGA -s Anc0.Anc0refChr5 64192 10 + 87904 TTAAACTTAA -s Anc1.Anc1refChr7 22055 10 - 47259 TTAAACTTAA -s Anc2.Anc2refChr15 60990 10 + 86568 TTAAACTTAA -s mr.mrrefChr5 98563 10 + 294540 TGAAACTTGA -s simCow_chr6.simCow.chr6 242374 8 + 602619 --AAACTTAA -s simDog_chr6.simDog.chr6 233566 10 + 593897 TTAAACTTAA -s simHuman_chr6.simHuman.chr6 323882 10 - 601863 TTAAACTTAA -s simRat_chr6.simRat.chr6 235910 10 + 647215 TGAAACCTGC - -a -s simMouse_chr6.simMouse.chr6 245425 38 + 636262 TGTCTAGCTGACAACTGTTGGTGGATGTGTATGGAAGA -s Anc0.Anc0refChr5 64203 36 + 87904 T--ATAGCAGACAACTCTTGGTGCACATGGCTGGAGTA -s Anc1.Anc1refChr7 22066 38 - 47259 TGCATAGCAGACAACTCTTGGTGCACATGGCTGGAGTA -s Anc2.Anc2refChr15 61001 36 + 86568 T--ATACCAGACAACTCTTGGTGCACATGGCTGAAGTA -s mr.mrrefChr5 98573 38 + 294540 TGTCTAGCTGACAACTGTTGGTGGATGTGTATGGAAGA -s simCow_chr6.simCow.chr6 242383 36 + 602619 T--GGACCAAGCAACTTTTGGTGCACATGGTTGAAGTG -s simDog_chr6.simDog.chr6 233577 36 + 593897 T--ATACCTGACAACTCTTGGTCCACATCACTGAAGCA -s simHuman_chr6.simHuman.chr6 323893 38 - 601863 TGCATAGCAGACAATTCGTGGTGCACATGGCTGGAGTA -s simRat_chr6.simRat.chr6 235920 38 + 647215 CGTCTAGCTGACAACTGTTGGTGGATGTGTATGGAAGG - -a -s simMouse_chr6.simMouse.chr6 245463 105 + 636262 ACCATACCCATGAGGATTTGTTGGTATTCTATTACATCGCTTGTTTCCCTACATCCTAACCTTCTGAAGGTCAAAGATGAGATCCAATTTCAATAAGCTATGGCA -s Anc0.Anc0refChr5 64245 56 + 87904 ACTACAC---T----------------------------------------------AAACTTCTGAAGGTCAAAGATCAGATCCAAATCAACTAAGTTATGACG -s Anc1.Anc1refChr7 22110 59 - 47259 ACTACACAAAT----------------------------------------------AAACTTCTGAAGGTCAAAGATCAGATCCAAATCAACTAAGTTATGACG -s Anc2.Anc2refChr15 61043 56 + 86568 ATTACAC---T----------------------------------------------AAACTTCTGAAGGTCAAAGATCAGATCCAAATCAGCTAAGTTATGATG -s mr.mrrefChr5 98611 101 + 294540 ACCATACCCATGAGGATTTGTTGGTATTC----ACATCGCTTGTTTCCCTACATCCTAACCTTCTGAAGGTCAAAGATGAGATCCAATTTCAATAAGCTATGGCA -s simCow_chr6.simCow.chr6 242425 56 + 602619 ATTACAA---T----------------------------------------------AAACTTCTGAAGGTCAAAGATCAGGTCCAAACCAGCCAAGTTATGATG -s simDog_chr6.simDog.chr6 233619 56 + 593897 ATTACGC---T----------------------------------------------AACCTTTTGAAGGTTAAAGAACAGATCCAAATCAGCTCAAGTATAATG -s simHuman_chr6.simHuman.chr6 323937 58 - 601863 ACTAAACAAAT----------------------------------------------AAACTGCTGAAGTTCAAA-ATTAGATCCAAATCAACTAGGTTATGACC -s simRat_chr6.simRat.chr6 235958 101 + 647215 ACCATACACATTAGGGTTTGTTGGTATCA----GCATGACTTGTTTCCCCACATCCTAACCTTCTGAAGGTCAAAAATGGGATCCAATTTCGATAAGCTATGGTG - -a -s simMouse_chr6.simMouse.chr6 245568 6 + 636262 TTGCAC -s Anc0.Anc0refChr5 64302 6 + 87904 TTGCAC -s Anc1.Anc1refChr7 22170 6 - 47259 TTGCAC -s Anc2.Anc2refChr15 61100 6 + 86568 TTGCAC -s mr.mrrefChr5 98712 6 + 294540 TTGCAC -s simCow_chr6.simCow.chr6 242482 6 + 602619 TTGCAC -s simDog_chr6.simDog.chr6 233676 6 + 593897 TTACAC -s simHuman_chr6.simHuman.chr6 323996 6 - 601863 TTGCAC -s simRat_chr6.simRat.chr6 236059 6 + 647215 TTGCAC - -a -s simMouse_chr6.simMouse.chr6 245574 2 + 636262 AC -s Anc0.Anc0refChr5 64314 2 + 87904 AC -s Anc1.Anc1refChr7 22182 2 - 47259 AC -s Anc2.Anc2refChr15 61112 2 + 86568 AC -s mr.mrrefChr5 98718 2 + 294540 AC -s simCow_chr6.simCow.chr6 242494 2 + 602619 CC -s simDog_chr6.simDog.chr6 233688 2 + 593897 AC -s simHuman_chr6.simHuman.chr6 324008 2 - 601863 AC -s simRat_chr6.simRat.chr6 236065 2 + 647215 AC - -a -s simMouse_chr6.simMouse.chr6 245576 23 + 636262 TCAAGGCCCCATTAAACCTTAGG -s Anc0.Anc0refChr5 64316 23 + 87904 AGAAAGACCCATTGAATCGTAAG -s Anc1.Anc1refChr7 22184 23 - 47259 AGAAAGACCCATTGAATCGTAAG -s Anc2.Anc2refChr15 61114 23 + 86568 AGAAAGACCCCTTGAATTGTAAG -s mr.mrrefChr5 98720 23 + 294540 TCAAGGCCCCATTAAACCTTAGG -s simCow_chr6.simCow.chr6 242496 23 + 602619 AGAAACACCCCTTGACTTCTAAA -s simDog_chr6.simDog.chr6 233691 23 + 593897 AGGAAGACCCCTTGAATTGTAAG -s simHuman_chr6.simHuman.chr6 324010 23 - 601863 AGAAAGGCCTATCGAGTCCTATA -s simRat_chr6.simRat.chr6 236067 23 + 647215 TCAAGGGCCCATTAAACTCTAAG - -a -s simMouse_chr6.simMouse.chr6 245599 18 + 636262 TGAATATTGCTGTTCCAT -s Anc0.Anc0refChr5 64339 12 + 87904 TGA------CTATTGTAT -s Anc1.Anc1refChr7 22207 13 - 47259 TGA-----CCTATTGTAT -s Anc2.Anc2refChr15 61137 12 + 86568 TGA------CTATGGTTG -s mr.mrrefChr5 98743 13 + 294540 TGA-----GCTGTTCCAT -s simCow_chr6.simCow.chr6 242519 12 + 602619 TGA------CTATGACTG -s simDog_chr6.simDog.chr6 233714 12 + 593897 TGA------CTATGGTTG -s simHuman_chr6.simHuman.chr6 324035 13 - 601863 TGG-----CCTATTGAAT -s simRat_chr6.simRat.chr6 236090 13 + 647215 TGA-----GTTATTTCAT - -a -s simMouse_chr6.simMouse.chr6 245617 2 + 636262 GC -s Anc0.Anc0refChr5 64351 2 + 87904 TC -s Anc1.Anc1refChr7 22220 2 - 47259 TC -s Anc2.Anc2refChr15 61149 2 + 86568 TC -s mr.mrrefChr5 98756 2 + 294540 GC -s simCow_chr6.simCow.chr6 242533 2 + 602619 TC -s simDog_chr6.simDog.chr6 233726 2 + 593897 TC -s simHuman_chr6.simHuman.chr6 324048 2 - 601863 CC -s simRat_chr6.simRat.chr6 236103 2 + 647215 GC - -a -s simMouse_chr6.simMouse.chr6 245619 12 + 636262 ATTGAGGGACTG -s Anc0.Anc0refChr5 64357 12 + 87904 ACTGAGGGACTG -s Anc1.Anc1refChr7 22226 12 - 47259 ACTGAGGGACTG -s Anc2.Anc2refChr15 61155 12 + 86568 ACTGAGGGACTG -s mr.mrrefChr5 98758 12 + 294540 ATTGAGGGACTG -s simCow_chr6.simCow.chr6 242539 12 + 602619 ACTGAGGGACTA -s simDog_chr6.simDog.chr6 233732 12 + 593897 ACCGCAGGACTG -s simHuman_chr6.simHuman.chr6 324054 12 - 601863 ACTGAGGGACTG -s simRat_chr6.simRat.chr6 236105 12 + 647215 ATTGAGGGACTG - -a -s simMouse_chr6.simMouse.chr6 245631 42 + 636262 ATCCAGTTGTCAGAATTTTTGTTACGTGTGACACAATCACAT -s Anc0.Anc0refChr5 64369 32 + 87904 TTCAGGTTGTCAAATT---------GTGTGACCCA-TCGTAT -s Anc1.Anc1refChr7 22238 32 - 47259 TTCAGGTTGTCAAATT---------GTGTGACCCA-TCGTAT -s Anc2.Anc2refChr15 61167 32 + 86568 TTCAGGTTGTCAAATT---------GTTGGACCCA-TCGTAT -s mr.mrrefChr5 98770 41 + 294540 ATCCAGTTGTCAGAATTTTTGTTACGTGTGACACA-TCACAT -s simCow_chr6.simCow.chr6 242551 32 + 602619 TTCAGCTCGTCAAATT---------GTTGGTCCCA-ACATAT -s simDog_chr6.simDog.chr6 233750 26 + 593897 TTCAGGTTGTAAAGT---------------ACCCA-TTGTAT -s simHuman_chr6.simHuman.chr6 324066 32 - 601863 TCCAGGTTGTCACATT---------ATGTGACCCA-TCTTAT -s simRat_chr6.simRat.chr6 236117 41 + 647215 TTCCCGTTGTCAGAATTTCTGTTATGTTTGACACA-TCATGT - -a -s simMouse_chr6.simMouse.chr6 245673 16 + 636262 TTGAGGTAAATATGAG -s Anc0.Anc0refChr5 64403 16 + 87904 TTAGGATACATGAGAT -s Anc1.Anc1refChr7 22272 16 - 47259 TTAGGATACATGAGAT -s Anc2.Anc2refChr15 61201 16 + 86568 TGAGGATACATGAGAT -s mr.mrrefChr5 98811 16 + 294540 TTGAGGTAAATATGAG -s simCow_chr6.simCow.chr6 242585 16 + 602619 TGAGGATACATGAGAT -s simDog_chr6.simDog.chr6 233778 16 + 593897 GGAGGATACATGAGGT -s simHuman_chr6.simHuman.chr6 324100 15 - 601863 TTAGGAGACACGCGA- -s simRat_chr6.simRat.chr6 236158 16 + 647215 CTGAGCCAAATATGAG - -a -s simMouse_chr6.simMouse.chr6 245689 24 + 636262 CTGCCACTACTTCGGTGGAATCCC -s Anc0.Anc0refChr5 64419 24 + 87904 CCACCAATATTTTGGTGGATCCTC -s Anc1.Anc1refChr7 22288 24 - 47259 CCACCAATATTTTGGTGGATCCTC -s Anc2.Anc2refChr15 61217 24 + 86568 CCACCAATATTTTGGTGGATCCTC -s mr.mrrefChr5 98827 24 + 294540 CTGCCACTACTTCGGTGGAATCCC -s simCow_chr6.simCow.chr6 242601 24 + 602619 CCACCAATACTTTGGTGGATCCTC -s simDog_chr6.simDog.chr6 233794 24 + 593897 CCACCAATATTTTGGTGGATCCTC -s simHuman_chr6.simHuman.chr6 324115 14 - 601863 ----------TTTGGTGGGTCCTC -s simRat_chr6.simRat.chr6 236176 24 + 647215 CCGCCAGCATTCTGGTGGAATCTC - -a -s simMouse_chr6.simMouse.chr6 245713 8 + 636262 ATAGGATT -s Anc0.Anc0refChr5 64443 8 + 87904 ATATAATA -s Anc1.Anc1refChr7 22312 8 - 47259 ATATAATA -s Anc2.Anc2refChr15 61244 8 + 86568 ATATAATA -s mr.mrrefChr5 98851 8 + 294540 ATAGGATT -s simCow_chr6.simCow.chr6 242628 8 + 602619 GTCTAGGA -s simDog_chr6.simDog.chr6 233821 8 + 593897 ATATGATA -s simHuman_chr6.simHuman.chr6 324129 8 - 601863 ATATAATA -s simRat_chr6.simRat.chr6 236200 8 + 647215 ATATGATT - -a -s simMouse_chr6.simMouse.chr6 245721 4 + 636262 ATAA -s Anc0.Anc0refChr5 64451 4 + 87904 AAAT -s Anc1.Anc1refChr7 22320 4 - 47259 AAAT -s Anc2.Anc2refChr15 61256 4 + 86568 AAAT -s mr.mrrefChr5 98859 4 + 294540 ATAA -s simCow_chr6.simCow.chr6 242640 4 + 602619 AAAT -s simDog_chr6.simDog.chr6 233833 4 + 593897 AAGT -s simHuman_chr6.simHuman.chr6 324137 4 - 601863 AAAT -s simRat_chr6.simRat.chr6 236208 4 + 647215 ATAA - -a -s simMouse_chr6.simMouse.chr6 245725 16 + 636262 CAACCTGGACAGTAGG -s Anc0.Anc0refChr5 64460 15 + 87904 CAACCTGGATGGTAA- -s Anc1.Anc1refChr7 22329 16 - 47259 CAACCTGGATGGTAAC -s Anc2.Anc2refChr15 61267 15 + 86568 CAACCTGGATGGTAA- -s mr.mrrefChr5 98863 16 + 294540 CAACCTGGACAGTAGG -s simCow_chr6.simCow.chr6 242653 15 + 602619 CAACCTGAATGGCAA- -s simDog_chr6.simDog.chr6 233844 15 + 593897 CAACCTGGATGGTAA- -s simHuman_chr6.simHuman.chr6 324146 16 - 601863 TACCCTGGATGGTACC -s simRat_chr6.simRat.chr6 236212 16 + 647215 CAACACAGACAGTCGG - -a -s simMouse_chr6.simMouse.chr6 245741 5 + 636262 TTACT -s Anc1.Anc1refChr7 22345 5 - 47259 TTACT -s mr.mrrefChr5 98879 5 + 294540 TTACT -s simHuman_chr6.simHuman.chr6 324163 5 - 601863 TTACT -s simRat_chr6.simRat.chr6 236228 5 + 647215 TTGCT - -a -s simMouse_chr6.simMouse.chr6 245746 21 + 636262 CTTAACACAGCCATACCTACT -s Anc0.Anc0refChr5 64475 19 + 87904 --TGACACAGCCATACCTATT -s Anc1.Anc1refChr7 22350 21 - 47259 CCTGACACAGCCATACCTATT -s Anc2.Anc2refChr15 61282 19 + 86568 --TGAGACAACCATACCTATT -s mr.mrrefChr5 98884 21 + 294540 CTTAACACAGCCATACCTACT -s simCow_chr6.simCow.chr6 242669 19 + 602619 --CAAGACAACCATACCTATT -s simDog_chr6.simDog.chr6 233859 19 + 593897 --TGAGACAATCATAATCAAT -s simHuman_chr6.simHuman.chr6 324169 21 - 601863 CCTGACAGAGCCATCCCTATT -s simRat_chr6.simRat.chr6 236234 21 + 647215 CTTGACACAGCTATACCTACT - -a -s simMouse_chr6.simMouse.chr6 245767 5 + 636262 ATTCA -s Anc0.Anc0refChr5 64498 5 + 87904 ATTCA -s Anc1.Anc1refChr7 22375 5 - 47259 ATTCA -s Anc2.Anc2refChr15 61305 5 + 86568 ATTCA -s mr.mrrefChr5 98905 5 + 294540 ATTCA -s simCow_chr6.simCow.chr6 242692 5 + 602619 ATTCA -s simDog_chr6.simDog.chr6 233882 5 + 593897 ATTCA -s simHuman_chr6.simHuman.chr6 324194 5 - 601863 AGTCA -s simRat_chr6.simRat.chr6 236255 5 + 647215 ATTCA - -a -s simMouse_chr6.simMouse.chr6 245772 17 + 636262 TGGGGTTAATTTGGATT -s Anc0.Anc0refChr5 64519 7 + 87904 T----------TTGATT -s Anc1.Anc1refChr7 22396 7 - 47259 T----------TTGATT -s Anc2.Anc2refChr15 61326 7 + 86568 T----------TTGATT -s mr.mrrefChr5 98910 7 + 294540 T----------TGGATT -s simCow_chr6.simCow.chr6 242707 7 + 602619 T----------TTGATT -s simDog_chr6.simDog.chr6 233899 3 + 593897 --------------ATT -s simHuman_chr6.simHuman.chr6 324218 7 - 601863 T----------TCGATT -s simRat_chr6.simRat.chr6 236260 7 + 647215 A----------TGGACT - -a -s simMouse_chr6.simMouse.chr6 245789 38 + 636262 CTGACCGGTAATCTTCAAAAGTCTGTAAATAAGTCTAT -s Anc0.Anc0refChr5 64529 38 + 87904 CTGACCTGTAATCTTCAAAAGTTTGTACATAGGTCTAC -s Anc1.Anc1refChr7 22406 38 - 47259 CTGACCTGTAATCTTCAAAAGTTTGTACATAGGTCTAC -s Anc2.Anc2refChr15 61336 38 + 86568 CTGACCTGTAGTCTTCAAAAGTTTGTACATAGGTCTAC -s mr.mrrefChr5 98917 38 + 294540 CTGACCGGTAATCTTCAAAAGTCTGTAAATAAGTCTAT -s simCow_chr6.simCow.chr6 242717 38 + 602619 CTTACCTGTAGTCCTCAAAAGTATGTAAATATGTCTAT -s simDog_chr6.simDog.chr6 233905 38 + 593897 CTGACCTGTAGTCTACAAAAGTTTGTACATAGGTCTAC -s simHuman_chr6.simHuman.chr6 324228 32 - 601863 CTGACCTGTAATCTTCAAAAATTTGTACATA------C -s simRat_chr6.simRat.chr6 236267 38 + 647215 CTGACCAGTAATCTTCACAAGTCTGTAATCAAGTCTAT - -a -s simMouse_chr6.simMouse.chr6 245827 13 + 636262 TGTTTTGTGCACT -s Anc0.Anc0refChr5 64567 13 + 87904 TGCTTCATAAGCT -s Anc1.Anc1refChr7 22444 13 - 47259 TGCTTCATAAGCT -s Anc2.Anc2refChr15 61374 13 + 86568 TGCTTCATAAGCT -s mr.mrrefChr5 98955 13 + 294540 TGTTTTGTGCACT -s simCow_chr6.simCow.chr6 242755 13 + 602619 TGCTTCACAAGCT -s simDog_chr6.simDog.chr6 233943 13 + 593897 TACTTCATGAGCT -s simHuman_chr6.simHuman.chr6 324260 13 - 601863 TGCTTCAGAACCT -s simRat_chr6.simRat.chr6 236350 13 + 647215 GGTTCTGTGCACT - -a -s simMouse_chr6.simMouse.chr6 245840 60 + 636262 TCCAGTTCCCATTCTCAAAGTCACATTGTCTGGCTATACATGTTGGCAATATACCGAGGT -s Anc0.Anc0refChr5 64584 45 + 87904 TACTGTTCAAGTTCTCA--------------AACTATATGTGTTGTCAATTCAT-GGGGA -s Anc1.Anc1refChr7 22461 45 - 47259 TACTGTTCAAGTTCTCA--------------AACTATATGTGTTGTCAATTCAT-GGGGA -s Anc2.Anc2refChr15 61391 45 + 86568 CACTTTCCAAGTTGTCA--------------AACTATATGTGTTGTCGATTCAT-GGGGA -s mr.mrrefChr5 98968 60 + 294540 TCCAGTTCCCATTCTCAAAGTCACATTGTCTGGCTATACATGTTGGCAATATACCGAGGT -s simCow_chr6.simCow.chr6 242772 20 + 602619 CACT----------TCA--------------CACT-TATGGTTTG--------------- -s simDog_chr6.simDog.chr6 233960 45 + 593897 CACTTTCCAAGTTGCCA--------------AACTATATGTGTTGTCGATTCAT-GGGGA -s simHuman_chr6.simHuman.chr6 324277 45 - 601863 TACTGTTGAAGCTCTCA--------------AATTATATGTGTTGTCAATTCAT-GGGTA -s simRat_chr6.simRat.chr6 236363 60 + 647215 CCCAGCTCCCATTCTCAAACTCACATTCTCCAACAATAAATCTTGGCAATATACTGAGGT - -a -s simMouse_chr6.simMouse.chr6 245900 13 + 636262 CCATAAGCAGTTT -s Anc0.Anc0refChr5 64629 13 + 87904 CCATAAGCAGTTT -s Anc1.Anc1refChr7 22506 13 - 47259 CCATAAGCAGTTT -s Anc2.Anc2refChr15 61436 13 + 86568 CCATAAAGGATCT -s mr.mrrefChr5 99028 13 + 294540 CCATAAGCAGTTT -s simDog_chr6.simDog.chr6 234006 13 + 593897 CCATAAAGGATCT -s simHuman_chr6.simHuman.chr6 324322 13 - 601863 TCATGAGCAGTTT -s simRat_chr6.simRat.chr6 236423 13 + 647215 CCATGAGCATTAT - -a -s simMouse_chr6.simMouse.chr6 245913 5 + 636262 GGAGT -s Anc0.Anc0refChr5 64642 5 + 87904 GGTGT -s Anc1.Anc1refChr7 22519 5 - 47259 GGTGT -s Anc2.Anc2refChr15 61449 5 + 86568 AGTGT -s mr.mrrefChr5 99041 5 + 294540 GGAGT -s simDog_chr6.simDog.chr6 234022 5 + 593897 AGTGT -s simHuman_chr6.simHuman.chr6 324335 5 - 601863 GGTCT -s simRat_chr6.simRat.chr6 236436 5 + 647215 GGAGT - -a -s simMouse_chr6.simMouse.chr6 245918 1 + 636262 T -s Anc0.Anc0refChr5 64647 1 + 87904 T -s Anc1.Anc1refChr7 22524 1 - 47259 T -s Anc2.Anc2refChr15 61454 1 + 86568 T -s mr.mrrefChr5 99046 1 + 294540 T -s simDog_chr6.simDog.chr6 234027 1 + 593897 T -s simHuman_chr6.simHuman.chr6 324340 1 - 601863 T -s simRat_chr6.simRat.chr6 236442 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 245919 65 + 636262 TCTTCAGCAATGGGCTGGGGACTACACTTTGGAGATGGGTTCATGACTTACACAAACTTCCTCCT -s Anc0.Anc0refChr5 64651 52 + 87904 TAGT-TCAAACAGGCTGGAGACTACACTTTGGAGGCAGGTTT---GCTTACA----CCTC----- -s Anc1.Anc1refChr7 22528 60 - 47259 TAGTCTCAAACAGGCTGGAGACTACACTTTGGAGGCAGGTTTGGGGCTTACACAACCCTC----- -s Anc2.Anc2refChr15 61458 52 + 86568 TAGT-TCAGCCATGCTTGAGACTACACCCTGGAGGCAGGTTT---GCCTACA----CCTC----- -s mr.mrrefChr5 99047 60 + 294540 TCTTCAGCAATGGGCTGGGGACTACACTTTGGAGATGGGTTCATGACTTACACAAACTTC----- -s simDog_chr6.simDog.chr6 234031 52 + 593897 TAGT-TCAGCCATGCTTGAGACTACACCCTGGAGGCAGGTTT---GCCTACA----CCTC----- -s simHuman_chr6.simHuman.chr6 324344 60 - 601863 TAGTCTCAAACAGGCTGGTGACCACATTTCGAAGGCAGGTTTGGGGCTTACAAAACCCTC----- -s simRat_chr6.simRat.chr6 236443 60 + 647215 TCTTCAGCAATGGACTGGCACCTGCAATCTGGGGATGGATTCATGACTTACACAAACTTC----- - -a -s simMouse_chr6.simMouse.chr6 245984 3 + 636262 GAT -s Anc0.Anc0refChr0 11634 3 - 26507 GAT -s Anc1.Anc1refChr6 182362 3 - 197743 GAT -s Anc2.Anc2refChr17 20198 3 - 28526 GAT -s mr.mrrefChr5 200131 3 + 294540 GAT -s simCow_chr6.simCow.chr6 278684 3 - 602619 GAT -s simDog_chr6.simDog.chr6 278052 3 - 593897 GAT -s simHuman_chr6.simHuman.chr6 266022 3 - 601863 GAT -s simRat_chr6.simRat.chr6 344309 3 + 647215 GAT - -a -s simMouse_chr6.simMouse.chr6 245987 2 + 636262 CA -s Anc0.Anc0refChr0 11637 2 - 26507 CA -s Anc1.Anc1refChr6 182365 2 - 197743 CA -s Anc2.Anc2refChr17 20209 2 - 28526 CA -s mr.mrrefChr5 200134 2 + 294540 CA -s simCow_chr6.simCow.chr6 278695 2 - 602619 CA -s simDog_chr6.simDog.chr6 278063 2 - 593897 CA -s simHuman_chr6.simHuman.chr6 266025 2 - 601863 CA -s simRat_chr6.simRat.chr6 344312 2 + 647215 CA - -a -s simMouse_chr6.simMouse.chr6 245989 4 + 636262 TGTG -s Anc0.Anc0refChr0 11817 4 - 26507 TGTG -s Anc1.Anc1refChr6 182545 4 - 197743 TGTG -s Anc2.Anc2refChr17 20390 4 - 28526 TATA -s mr.mrrefChr5 200136 4 + 294540 TGTG -s simCow_chr6.simCow.chr6 278870 4 - 602619 TATA -s simDog_chr6.simDog.chr6 278244 4 - 593897 CATA -s simHuman_chr6.simHuman.chr6 266340 4 - 601863 TGTG -s simRat_chr6.simRat.chr6 344314 4 + 647215 TGTG - -a -s simMouse_chr6.simMouse.chr6 245993 73 + 636262 GGATAAAAATCTTGAGGCCCTATGAGAGGTATATTGATTGTCTAGATAAAATGTAGCCTGTCAAGAGCTATGT -s Anc0.Anc0refChr0 11821 1 - 26507 C------------------------------------------------------------------------ -s Anc1.Anc1refChr6 182549 1 - 197743 C------------------------------------------------------------------------ -s Anc2.Anc2refChr17 20481 1 - 28526 C------------------------------------------------------------------------ -s mr.mrrefChr5 200140 73 + 294540 GGATAAAAATCTTGAGGCCCTATGAGAGGTATATTGATTGTCTAGATAAAATGTAGCCTGTCAAGAGCTATGT -s simCow_chr6.simCow.chr6 278959 1 - 602619 C------------------------------------------------------------------------ -s simDog_chr6.simDog.chr6 278477 1 - 593897 C------------------------------------------------------------------------ -s simHuman_chr6.simHuman.chr6 266344 1 - 601863 A------------------------------------------------------------------------ -s simRat_chr6.simRat.chr6 344318 73 + 647215 GGACAAAAATCTTGAGGCCCTATGAGAGGTAAATTGATTGCCTAGATAAAATGAAGCCTGTCAAGAGCTATGT - -a -s simMouse_chr6.simMouse.chr6 246066 40 + 636262 TGTCCTCAAACCTCATAGCTGCAACCCTTTGACTTATTTT -s mr.mrrefChr5 200213 40 + 294540 TGTCCTCAAACCTCATAGCTGCAACCCTTTGACTTATTTT -s simRat_chr6.simRat.chr6 344393 40 + 647215 TGTACTTAAACCTCATAGCTACAACCATCTGACTTATTTT - -a -s simMouse_chr6.simMouse.chr6 246106 207 + 636262 GGCACCCTTTGAGTTAGCTATCAGTCAGGGAGACATGAGGTTGCTTCTTAATTGGTCACAATGTAGGAGTGGGACAGAATTGACTGAATTGGAAGCCTTGTGCACATACCTGGCCTCCTTGTTAATCAGACTGGACTAGTTAGACGGATTCTGTTGAGCAAGGGGCTTCATTCATGAGATCCTTTACCCACCTTGTCACCAAACTTG -s mr.mrrefChr5 200253 194 + 294540 GGCACCCTTTGAGTTAGCTATCAGTCAGGGAGACATGAGGTTGCTTCT-----------AATGTAGGAGTGGGACAGAATTG-CTGAATTGGAAGCCTTGTGCACATACCTGGCCTCCTTGTTAATCAGACTGGACTAGTTAGACGGATTCTGTTGAGC-AGGGGCTTCATTCATGAGATCCTTTACCCACCTTGTCACCAAACTTG -s simRat_chr6.simRat.chr6 344455 194 + 647215 GGCACCCTTTGATTTGGCTATCAGTCCGGGGGACATGAGGTTGATCCT-----------GATGTAGGAGTGCGACAGAATTG-CTGAATTGAAAGCCTTGTGCACAGACCTGGCCCCCTCGTCAAGTGCTCTGGAGTAGTTAGATGGATTACATTGAGC-CGGGCCTTTATTGAAGAGATCCTTCACCAGACTTGTCACCAAACTTG - -a -s simMouse_chr6.simMouse.chr6 246313 1 + 636262 T -s Anc0.Anc0refChr5 64703 1 + 87904 T -s Anc1.Anc1refChr7 22588 1 - 47259 T -s Anc2.Anc2refChr15 61510 1 + 86568 T -s mr.mrrefChr5 99107 1 + 294540 T -s simDog_chr6.simDog.chr6 234083 1 + 593897 T -s simHuman_chr6.simHuman.chr6 324404 1 - 601863 T -s simRat_chr6.simRat.chr6 236503 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 246314 3 + 636262 ACT -s Anc0.Anc0refChr5 64705 2 + 87904 AC- -s Anc1.Anc1refChr7 22590 2 - 47259 AC- -s Anc2.Anc2refChr15 61512 2 + 86568 AC- -s mr.mrrefChr5 99108 2 + 294540 AC- -s simDog_chr6.simDog.chr6 234102 2 + 593897 AC- -s simHuman_chr6.simHuman.chr6 324406 2 - 601863 CC- -s simRat_chr6.simRat.chr6 236504 2 + 647215 TC- - -a -s simMouse_chr6.simMouse.chr6 246317 13 + 636262 GCATGGGAAGGCA -s Anc0.Anc0refChr5 64719 10 + 87904 ---AGAGAGGGCA -s Anc1.Anc1refChr7 22605 13 - 47259 GCAAGAGAGGGCA -s Anc2.Anc2refChr15 61526 10 + 86568 ---AGAGAGGGCA -s mr.mrrefChr5 99110 13 + 294540 GCATGGGAAGGCA -s simCow_chr6.simCow.chr6 242792 10 + 602619 ---AGGGAGGGAC -s simDog_chr6.simDog.chr6 234116 8 + 593897 -----AGGGGCCA -s simHuman_chr6.simHuman.chr6 324443 13 - 601863 GCAAGAGAGGGCA - -a -s simMouse_chr6.simMouse.chr6 246330 14 + 636262 GTTAAAGCTTGCAT -s Anc0.Anc0refChr5 64736 14 + 87904 GCTAGAGTTTACCT -s Anc1.Anc1refChr7 22625 14 - 47259 GCTAGAGTTTACCT -s Anc2.Anc2refChr15 61543 14 + 86568 GCTAGAGTTTACCT -s mr.mrrefChr5 99123 14 + 294540 GTTAAAGCTTGCAT -s simCow_chr6.simCow.chr6 242809 14 + 602619 GCTGGAGTTTGCCT -s simDog_chr6.simDog.chr6 234131 14 + 593897 GCTAGCATTGACCT -s simHuman_chr6.simHuman.chr6 324463 14 - 601863 GCTAGAGTTTACCC - -a -s simMouse_chr6.simMouse.chr6 246344 36 + 636262 TTACTTAAGCAAGCTAGTGAATACCAGAAATGTCGT -s Anc0.Anc0refChr5 64750 36 + 87904 CTAATTAGGTTAGCTAATGAACACAAGAAATGTTAT -s Anc1.Anc1refChr7 22639 36 - 47259 CTAATTAGGTTAGCTAATGAACACAAGAAATGTTAT -s Anc2.Anc2refChr15 61557 36 + 86568 CAAATTAGGTTAGCTAATGAACAGAGAAAATGCTAT -s mr.mrrefChr5 99137 36 + 294540 TTACTTAAGCAAGCTAGTGAATACCAGAAATGTTGT -s simCow_chr6.simCow.chr6 242824 36 + 602619 TAAATTAGGTCAGCTAATGAACAGAGAAAATGCTAT -s simDog_chr6.simDog.chr6 234145 20 + 593897 CAAATTAGGTTAGCTGATGA---------------- -s simHuman_chr6.simHuman.chr6 324477 36 - 601863 ATAATTGGTATAGCTAATGAACACTAGAAATGTTAT -s simRat_chr6.simRat.chr6 236506 10 + 647215 --------------------------ATAATGTTGT - -a -s simMouse_chr6.simMouse.chr6 246380 82 + 636262 ATGGTACAGCCACATGAAATGGTGTCCACAAACAACAGACTATGCAGGATGACCAAAGGTGATGATGGGAATTGCACACCAC -s Anc0.Anc0refChr5 64786 79 + 87904 ATGGTACTGTCACATAAACTAGGG---ACGAAAAACAAACCATGCAGGATCATAAATGGTGATGATGGAAATTATATACTGC -s Anc1.Anc1refChr7 22675 82 - 47259 ATGGTACTGTCACATAAACTAGGGTATACGAAAAACAAACCATGCAGGATCATAAATGGTGATGATGGAAATTATATACTGC -s Anc2.Anc2refChr15 61593 79 + 86568 GTGGTGCTGTCATCTAGACTAGGG---ATGGCTGACAAACCATGCAGAATCATAAATAGTGAAGATGGAAATTATATACTGC -s mr.mrrefChr5 99173 82 + 294540 ATGGTACTGCCACATGAAATGGTGTCCACAAAAAACAGACTATGCAGGATGACCAATGGTGATGATGGGAATTGTACACCAC -s simCow_chr6.simCow.chr6 242861 79 + 602619 GTGGTGCTGTCATCTAGACTAGGG---ATGGCTGACAAACCATGCAGAATCATAAATAGTGAAGATGGAAATTATATACTGC -s simHuman_chr6.simHuman.chr6 324513 82 - 601863 ATGGTACTGTCACATTAACTAGAGTATACGAAAAACAAACAATGCGGGACTATACATGATAATGATGGTAATTATATACAGC -s simRat_chr6.simRat.chr6 236516 82 + 647215 ATGGTAGTGCCACAGAAAATGGTCTCCACAAAATACAGACTATGCAGGATCACCAATGGTGATGAAGGGAATTGTACACCAC - -a -s simMouse_chr6.simMouse.chr6 246462 14 + 636262 CATGGTGAAGTTAT -s Anc0.Anc0refChr5 64865 14 + 87904 CATGGTGAGGTCAT -s Anc1.Anc1refChr7 22757 14 - 47259 CATGGTGAGGTCAT -s Anc2.Anc2refChr15 61672 14 + 86568 AACAATGAGATCAT -s mr.mrrefChr5 99255 14 + 294540 CATGGTGAAGTTAT -s simCow_chr6.simCow.chr6 242956 14 + 602619 AACAATGAGATCAT -s simHuman_chr6.simHuman.chr6 324595 14 - 601863 CATGGTGAGGTCAT -s simRat_chr6.simRat.chr6 236598 14 + 647215 CACGGTGAAGTTAT - -a -s simMouse_chr6.simMouse.chr6 246476 35 + 636262 CAACAACAACTCTGTGCAAGATTATCATTCGCTGT -s Anc0.Anc0refChr5 64881 35 + 87904 CAATAACAACTTGGTACATGGTTATCCTGTGCTGT -s Anc1.Anc1refChr7 22773 35 - 47259 CAATAACAACTTGGTACATGGTTATCCTGTGCTGT -s Anc2.Anc2refChr15 61688 35 + 86568 CAATGACAGCTTGGTACATGGTTATCCTGTGGTGT -s mr.mrrefChr5 99269 35 + 294540 CAACAACAACTCTGTGCAAGATTATCATTTGCTGT -s simCow_chr6.simCow.chr6 242973 35 + 602619 CAATGACAGCTTGGTACATGGTTATCCTGTGGTGT -s simHuman_chr6.simHuman.chr6 324611 35 - 601863 CAATAACAACCTGGTACATGCTTATCCTGTCCTGT -s simRat_chr6.simRat.chr6 236612 35 + 647215 CAACAACAACTCAGTGCAAGGTTATCATTTGCTGT - -a -s simMouse_chr6.simMouse.chr6 246511 1 + 636262 A -s Anc0.Anc0refChr5 64916 1 + 87904 G -s Anc1.Anc1refChr7 22808 1 - 47259 G -s Anc2.Anc2refChr15 61723 1 + 86568 G -s mr.mrrefChr5 99304 1 + 294540 A -s simCow_chr6.simCow.chr6 243009 1 + 602619 G -s simHuman_chr6.simHuman.chr6 324646 1 - 601863 G -s simRat_chr6.simRat.chr6 236647 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 246512 4 + 636262 TGTC -s Anc0.Anc0refChr5 64926 4 + 87904 TGGT -s Anc1.Anc1refChr7 22818 4 - 47259 TGGT -s Anc2.Anc2refChr15 61733 4 + 86568 TGGT -s mr.mrrefChr5 99305 4 + 294540 TGTC -s simCow_chr6.simCow.chr6 243019 4 + 602619 TGGT -s simHuman_chr6.simHuman.chr6 324656 4 - 601863 TGGT -s simRat_chr6.simRat.chr6 236648 4 + 647215 TGTC - -a -s simMouse_chr6.simMouse.chr6 246516 4 + 636262 CACA -s Anc0.Anc0refChr5 64930 4 + 87904 CATA -s Anc1.Anc1refChr7 22822 4 - 47259 CATA -s Anc2.Anc2refChr15 61737 4 + 86568 CATA -s mr.mrrefChr5 99309 4 + 294540 CACA -s simCow_chr6.simCow.chr6 243029 4 + 602619 CATA -s simDog_chr6.simDog.chr6 234165 3 + 593897 -ATA -s simHuman_chr6.simHuman.chr6 324660 4 - 601863 CATA -s simRat_chr6.simRat.chr6 236652 4 + 647215 CACA - -a -s simMouse_chr6.simMouse.chr6 246520 6 + 636262 CAAAGC -s Anc0.Anc0refChr5 64942 6 + 87904 CCCAGT -s Anc1.Anc1refChr7 22834 6 - 47259 CCCAGT -s Anc2.Anc2refChr15 61749 6 + 86568 CCCAGT -s mr.mrrefChr5 99313 6 + 294540 CAAAGC -s simCow_chr6.simCow.chr6 243041 6 + 602619 CCCAGT -s simDog_chr6.simDog.chr6 234176 6 + 593897 CCCAGT -s simHuman_chr6.simHuman.chr6 324672 6 - 601863 AGCAGT -s simRat_chr6.simRat.chr6 236656 6 + 647215 CAAAGT - -a -s simMouse_chr6.simMouse.chr6 246526 18 + 636262 GAAATATCAATCTGTAAG -s Anc0.Anc0refChr5 64951 18 + 87904 GTAATGTCAATCTCTCAG -s Anc1.Anc1refChr7 22843 18 - 47259 GTAATGTCAATCTCTCAG -s Anc2.Anc2refChr15 61758 18 + 86568 GTAATGTCAATCTCTCAG -s mr.mrrefChr5 99319 18 + 294540 GAAATATCAATCTGTAAG -s simCow_chr6.simCow.chr6 243050 18 + 602619 GTAATGTCAATCACTCAG -s simDog_chr6.simDog.chr6 234185 18 + 593897 GTAATGTGAATCTTTTTG -s simHuman_chr6.simHuman.chr6 324684 18 - 601863 GTAGTGCCAATCTCTCAG -s simRat_chr6.simRat.chr6 236662 18 + 647215 GACATATCAATATGATAG - -a -s simMouse_chr6.simMouse.chr6 246544 1 + 636262 T -s Anc0.Anc0refChr5 64972 1 + 87904 C -s Anc1.Anc1refChr7 22864 1 - 47259 C -s Anc2.Anc2refChr15 61779 1 + 86568 C -s mr.mrrefChr5 99337 1 + 294540 T -s simCow_chr6.simCow.chr6 243071 1 + 602619 C -s simDog_chr6.simDog.chr6 234206 1 + 593897 C -s simHuman_chr6.simHuman.chr6 324705 1 - 601863 C -s simRat_chr6.simRat.chr6 236680 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 246545 101 + 636262 AGTGAGTACAGGTCTGTGAATGACTACAGTGCCTTCTGTCTGCTCAGAGTCTCCACTGTAAGGGCCTTACTGAGACATGTAGCACACCTCTTGTTTGTGAT -s Anc0.Anc0refChr5 64973 98 + 87904 AGAGAATACAGGTCTG--GATTACTACACTACCTTCTATCTTCTCACAGTTTCCACTGTAAGAGGCATGGTAAGACATGGATCAA-CCCTTTGTTTGTTAA -s Anc1.Anc1refChr7 22865 98 - 47259 AGAGAATACAGGTCTG--GATTACTACACTACCTTCTATCTTCTCACAGTTTCCACTGTAAGAGGCATGGTAAGACATGGATCAA-CCCTTTGTTTGTTAA -s Anc2.Anc2refChr15 61781 98 + 86568 AGAGAATTCAGGTCTG--GATTACTACACTACCTTCTATCTTCTCACAGTTTCCTCTGTAAGGGGCATGGTAAGACATGGATCAA-CCCTTTGTTTGTTAA -s mr.mrrefChr5 99338 99 + 294540 AGTGAGTACAGGTCTG--GATGACTACAGTGCCTTCTGTCTTCTCACAGTCTCCACTGTAAGAGCCATACTGAGACATGGAGCACACCTTTTGTTTGTTAT -s simCow_chr6.simCow.chr6 243073 97 + 602619 AGAGAATTCGGGTCTG--GACCGCTACAATACC-CCTATCTTCTCACAGTCTCCTTACCAGGGGGCATGGTATAACATGGACCAC-CCCTTTGTTTGTTAA -s simDog_chr6.simDog.chr6 234208 97 + 593897 AGAAAAGTCAGGTCTG--GATTAGTACACTACCTTCTATCTTCTCACAGGTTCATCTGTAAGGGGCATGGCAAGAC-TAGATCAA-CCCATTGTCTGTAAA -s simHuman_chr6.simHuman.chr6 324706 97 - 601863 AGCGAATACAGGCATG--GATTACCACACTACCTTCTATTTTCTCACAGTTTCCACTGTAAGAGGCATGGTAAGACATGGATGAT-CCCTTTGTTTGTTA- -s simRat_chr6.simRat.chr6 236681 97 + 647215 AGTGAGTACAGGTCTG--GATGGCTAGAGTGCCTCCTGTCTTCTCACAGTCTCCACTGCAAGAGCCATACTGG--CATGGAGCACACCTTTTGTCCATTAT - -a -s simMouse_chr6.simMouse.chr6 246646 10 + 636262 CAAAATAAAC -s Anc0.Anc0refChr5 65071 10 + 87904 GGAAATGAAC -s Anc1.Anc1refChr7 22963 10 - 47259 GGAAATGAAC -s Anc2.Anc2refChr15 61879 10 + 86568 GGAAATGAGC -s mr.mrrefChr5 99437 10 + 294540 CAAAATAAAC -s simCow_chr6.simCow.chr6 243176 10 + 602619 GGAAATGAGC -s simDog_chr6.simDog.chr6 234305 10 + 593897 GGAAATGAGC -s simHuman_chr6.simHuman.chr6 324803 7 - 601863 ---AGTTAAC -s simRat_chr6.simRat.chr6 236778 10 + 647215 TAGAATAAAC - -a -s simMouse_chr6.simMouse.chr6 246656 26 + 636262 ACCCTCTTCACCTCAGTTACCCACTA -s Anc0.Anc0refChr5 65081 26 + 87904 ATCCTCCTGTCCTCAGTTACCCAATA -s Anc1.Anc1refChr7 22973 26 - 47259 ATCCTCCTGTCCTCAGTTACCCAATA -s Anc2.Anc2refChr15 61889 26 + 86568 ATCCTCCTGTCCTCAGTCACCCAACA -s mr.mrrefChr5 99447 26 + 294540 ACCCTCTTCACCTCAGTTACCCACTA -s simCow_chr6.simCow.chr6 243186 26 + 602619 ATCCTACTGTCCTCAGTCACCAAACA -s simDog_chr6.simDog.chr6 234315 23 + 593897 ATCCTCTTG---TCAGTCATCCAACA -s simHuman_chr6.simHuman.chr6 324810 26 - 601863 ATCCTCCTGTCCTCAGTTGCCCAATA -s simRat_chr6.simRat.chr6 236790 12 + 647215 AACTCCTGCATC-------------- - -a -s simMouse_chr6.simMouse.chr6 246682 2 + 636262 AG -s Anc0.Anc0refChr5 65107 2 + 87904 AG -s Anc1.Anc1refChr7 22999 2 - 47259 AG -s Anc2.Anc2refChr15 61917 2 + 86568 AG -s mr.mrrefChr5 99473 2 + 294540 AG -s simCow_chr6.simCow.chr6 243215 2 + 602619 AG -s simDog_chr6.simDog.chr6 234340 2 + 593897 AG -s simHuman_chr6.simHuman.chr6 324836 2 - 601863 AG -s simRat_chr6.simRat.chr6 236802 2 + 647215 AG - -a -s simMouse_chr6.simMouse.chr6 246684 89 + 636262 CTCTCTCTACTTAAAGGCAAAGGACAGTGAAACTAGAGATTGTGGCAGGTTAGCTCATTAGAAGGCTGACATATAACATGCTTGCTTGG -s Anc0.Anc0refChr5 65119 89 + 87904 CTACCATTACTCAATACCAACAGTCAACCACATTAGAGATTGAGACAGGTTGGTCCTTCAGACGACCTACATATAACATGCTTGGTTGG -s Anc1.Anc1refChr7 23011 89 - 47259 CTACCATTACTCAATACCAACAGTCAACCACATTAGAGATTGAGACAGGTTGGTCCTTCAGACGACCTACATATAACATGCTTGGTTGG -s Anc2.Anc2refChr15 61929 89 + 86568 CTACCATTACTCAATACTGACAGTCAACCACATTAGAGATTGAGACAGGTTGGTCCTTCAGACAACCTACATATAACATGCTTGGTTGG -s mr.mrrefChr5 99475 89 + 294540 CTATCTTTACTTAATGGCAACGGACAGTGAAACTAGAGATTGTGGCAGGTTAGCTCATTAGAAGACTGACATATAACATGCTTGCTTGG -s simCow_chr6.simCow.chr6 243227 89 + 602619 ATAGCATTACTCAATATTGACAGTCACCCACGTTCGAAATTGAGAGAGATTGGTCTTTCAGACAACTTACATGTAACATGCCTGGTGGA -s simDog_chr6.simDog.chr6 234352 86 + 593897 CGACCATTACTCAATAC---CAATAAAACACATTAGAGATTGAGACAGGTTGGTCCTTCAGTCAACCTGCATAAAACATGCTTGATTGG -s simHuman_chr6.simHuman.chr6 324848 86 - 601863 CTACCATCACTCAATTCCAACAGTCAACCACTTTTGA---TGAAACAGGTTGGTCCTTCAGATGACCCACATATAACATGCTTGGATGG -s simRat_chr6.simRat.chr6 236804 88 + 647215 CTATCTTTACTTAATGGTAACGGACAGTGAAACTAGAGAGTGTGG-AGATCAGCTCATTAGAGGACTGACATGTGACATGCTTGCTTGG - -a -s simMouse_chr6.simMouse.chr6 246773 26 + 636262 TTTGGTAGATGTATTTAAGAATGCAT -s Anc0.Anc0refChr5 65208 21 + 87904 AT-----GATGTATTGAAGAATGCAT -s Anc1.Anc1refChr7 23100 21 - 47259 AT-----GATGTATTGAAGAATGCAT -s Anc2.Anc2refChr15 62018 21 + 86568 AT-----GATATATTGAAGAATGCAT -s mr.mrrefChr5 99564 26 + 294540 TTTGGTAGATGTATTTAAGAATGCAT -s simCow_chr6.simCow.chr6 243316 21 + 602619 AT-----GATATATTGGAGAATGCAT -s simDog_chr6.simDog.chr6 234439 21 + 593897 GT-----CTTATAGTGAAGAATGCAT -s simHuman_chr6.simHuman.chr6 324934 21 - 601863 AT-----GATGGATTCAAGAATGCAT -s simRat_chr6.simRat.chr6 236892 26 + 647215 TTTGGTAGATGTATTTGAGAATACAT - -a -s simMouse_chr6.simMouse.chr6 246799 3 + 636262 AAA -s Anc0.Anc0refChr5 65229 3 + 87904 GAA -s Anc1.Anc1refChr7 23121 3 - 47259 GAA -s Anc2.Anc2refChr15 62039 3 + 86568 GAA -s mr.mrrefChr5 99590 3 + 294540 AAA -s simCow_chr6.simCow.chr6 243337 3 + 602619 GAA -s simDog_chr6.simDog.chr6 234462 3 + 593897 GAA -s simHuman_chr6.simHuman.chr6 324955 3 - 601863 GCA -s simRat_chr6.simRat.chr6 236918 3 + 647215 TAA - -a -s simMouse_chr6.simMouse.chr6 246802 22 + 636262 TCCACCTTGCCTCAAAGATGAG -s Anc0.Anc0refChr5 65232 18 + 87904 TC----TTGCCTCAAAGTTGAG -s Anc1.Anc1refChr7 23124 18 - 47259 TC----TTGCCTCAAAGTTGAG -s Anc2.Anc2refChr15 62046 18 + 86568 TC----TTGCCTCAAAGTTGAG -s mr.mrrefChr5 99593 18 + 294540 TC----TTGCCTCAAAGATGAG -s simCow_chr6.simCow.chr6 243344 18 + 602619 TC----TTGCCTCAAAATTGAG -s simDog_chr6.simDog.chr6 234469 18 + 593897 TC----TTGCCTCAGAGTTGAG -s simHuman_chr6.simHuman.chr6 324958 16 - 601863 TT----TTTCC--AAAGTTGGT -s simRat_chr6.simRat.chr6 236921 18 + 647215 TC----TCACCTCAAAGATGAG - -a -s simMouse_chr6.simMouse.chr6 246824 43 + 636262 TGCCTGTAATTTTCGCCACGCCACATCACTATTATATTCCTTT -s Anc0.Anc0refChr5 65250 43 + 87904 TGTCTGTGAATTTAGACAGGCCTCATCACTGGTGGATTCCTTT -s Anc1.Anc1refChr7 23142 43 - 47259 TGTCTGTGAATTTAGACAGGCCTCATCACTGGTGGATTCCTTT -s Anc2.Anc2refChr15 62064 43 + 86568 TGTCTGTGAATTTAGAAGTGCCTCATCACTAGTGGATTCCTTT -s mr.mrrefChr5 99611 43 + 294540 TGTCTGTAATTTTCGCCAGGCCACATCACTGGTATATTCCTTT -s simCow_chr6.simCow.chr6 243362 37 + 602619 TGTGTGTGAACTTA------CCCCCTAACGAGTAGATTCCTTT -s simDog_chr6.simDog.chr6 234489 43 + 593897 TGTCTGTGGATTTAGAAGTGCCTCACCACTAGTGGCTTCCTTT -s simHuman_chr6.simHuman.chr6 324974 43 - 601863 TGTCTATGAATTTTGACAGGCCTCATCACTGGTGGATTCCTTC -s simRat_chr6.simRat.chr6 236939 43 + 647215 TGTCTGTAATTTCAGCCAGGCTGCATTACTGGTATGTCCCTTT - -a -s simMouse_chr6.simMouse.chr6 246867 62 + 636262 CATGTTGTGTGTTGTTCAATTGCTCAGAACTTTACTAACCAAGAAGTGTGTGCAAGAAGCCC -s Anc0.Anc0refChr5 65303 56 + 87904 CATGTTGCATGTT---TG---ATTCAGAGCTCCACTAACTAAGGGCTGTGTGCAGGACACCT -s Anc1.Anc1refChr7 23195 59 - 47259 CATGTTGCATGTT---TGATTATTCAGAGCTCCACTAACTAAGGGCTGTGTGCAGGACACCT -s Anc2.Anc2refChr15 62117 56 + 86568 TATGTTGCCTATT---TG---ATTCAGAGCTCCACTAACTAAGGGCTGTGTGCAGGACACCT -s mr.mrrefChr5 99664 59 + 294540 CATGTTGTATGTT---CAATTGCTCAGAGCTTTACTAACTAAGAAGTGTGTGCAAGAAGCCC -s simCow_chr6.simCow.chr6 243409 56 + 602619 TATGTTGCCTATT---TG---ATTCAGAGCCCCACTAACTAAAAGCTGGGTGTAGGACATCC -s simDog_chr6.simDog.chr6 234541 34 + 593897 ----------------------------GCTCCACTGACTAAGGGCTGTCTGCAGTACTCCT -s simHuman_chr6.simHuman.chr6 325027 59 - 601863 CATGTTGCATGTT---TGATTATTCAGAGCTCCACTAACTACGGGCTGTGTGCAGGACACCT -s simRat_chr6.simRat.chr6 236992 58 + 647215 CAGGTTGTATGTT---CAATTGCTCAGAGCTTTGCTAATTAAGAAGTGTGTTCAAGAAGGC- - -a -s simMouse_chr6.simMouse.chr6 246929 6 + 636262 ATAGAC -s Anc0.Anc0refChr5 65359 6 + 87904 TTAAAC -s Anc1.Anc1refChr7 23254 6 - 47259 TTAAAC -s Anc2.Anc2refChr15 62176 6 + 86568 TTAAAC -s mr.mrrefChr5 99723 6 + 294540 ATAGAC -s simCow_chr6.simCow.chr6 243468 6 + 602619 TTACAC -s simDog_chr6.simDog.chr6 234578 6 + 593897 ATAAGC -s simHuman_chr6.simHuman.chr6 325086 6 - 601863 TTAAAC - -a -s simMouse_chr6.simMouse.chr6 246935 23 + 636262 ACAATTTGTGTAAGGCTCTTGTA -s Anc0.Anc0refChr5 65366 23 + 87904 ACAATTTGTGTGAGGCTCTGGTT -s Anc1.Anc1refChr7 23261 23 - 47259 ACAATTTGTGTGAGGCTCTGGTT -s Anc2.Anc2refChr15 62183 23 + 86568 ACAATTTTACTGAGGCTCTGGTT -s mr.mrrefChr5 99729 23 + 294540 ACAATTTGTGTAAGGCTCTTGTA -s simCow_chr6.simCow.chr6 243475 18 + 602619 ACAAT-----TGAGGTTTTGGTA -s simDog_chr6.simDog.chr6 234585 23 + 593897 ACGATTTTACTGAGGCTCTGGCT -s simHuman_chr6.simHuman.chr6 325093 23 - 601863 ACAATCTGTGTGAGGCTCTGGTG -s simRat_chr6.simRat.chr6 237050 20 + 647215 ---ACTTGTATTAGCTTGTCGTA - -a -s simMouse_chr6.simMouse.chr6 246958 96 + 636262 TTACCTTGTGGGAAGGTAACTATAGATACATACCTCTATGTGTTCAAGGCCTTCACTTTGTCATAACTTCAATCTGCTTACAAAGGTTTAATGCAG -s Anc0.Anc0refChr5 65389 96 + 87904 TTACATTATGGTGATGTCACTATAGATACTTACCACTACGCATGCGTGGCATCAACTTTACATTAATTTTAATCTCCTTATATGGGTTTACTGCAG -s Anc1.Anc1refChr7 23284 96 - 47259 TTACATTATGGTGATGTCACTATAGATACTTACCACTACGCATGCGTGGCATCAACTTTACATTAATTTTAATCTCCTTATATGGGTTTACTGCAG -s Anc2.Anc2refChr15 62206 96 + 86568 TTACATTATGGTGATACCACTCTAGATGCTTACTACTACACATGCGTGGCATCGATTTTACATTAATTTTAACCTCCATATATGGGTTTACTCCAT -s mr.mrrefChr5 99752 96 + 294540 TTACCTTGTGGTAAGGTAACTATAGATACATACCTCTATGTGTTCATGGCATTAACTTTGTCATAACTTCAATCTGCTTATAAGGGTTTACTGCAG -s simCow_chr6.simCow.chr6 243493 88 + 602619 TTATAGTCTTGCAACACCACTC--------TACTACTACACATGCATCGCATCGTTTATACACTAATTTTAACCTCAATATGTGGGTTTGGTACAT -s simDog_chr6.simDog.chr6 234608 96 + 593897 TTACATTATGGTGATACCACTCTAGATGCTATGTACTACACATGTGCGGCATTGATTTTACATTAATTTTAACCTCCATATATCGGTTTACTCCAT -s simHuman_chr6.simHuman.chr6 325116 95 - 601863 TTACATTATGGTGATGTC-CTAGGCATACTTACCACTACGCATCCTTGGCACCAACTTTACATTAATTTTGATCATCTTATATGAGTTTACTGCAG -s simRat_chr6.simRat.chr6 237078 96 + 647215 TCAGCTTGTGCTAAGGTAATTATAGTTCCATACATCTATATGTTCATGGCATTAATTTTGTCATGACTTCAATCTGCTTATAAGGGTTTACTACAG - -a -s simMouse_chr6.simMouse.chr6 247054 34 + 636262 TCACACTCCACAAGGAAATATGATAACTACTACA -s Anc0.Anc0refChr5 65504 34 + 87904 TTACAATTCACAAGGGAACTGGATGATTAAACCA -s Anc1.Anc1refChr7 23399 34 - 47259 TTACAATTCACAAGGGAACTGGATGATTAAACCA -s Anc2.Anc2refChr15 62321 34 + 86568 TTACAATTCACAAGGGAACTGGACAACTAAACCC -s mr.mrrefChr5 99848 34 + 294540 TTACACTTCACAAGGAAATATGATGATTACAACA -s simCow_chr6.simCow.chr6 243600 34 + 602619 TTATAATTCACAAGGGAATTGGAGTACTTAACCC -s simDog_chr6.simDog.chr6 234723 33 + 593897 TCACACTTCAGAAGGGAACTGGACAACTAAATC- -s simHuman_chr6.simHuman.chr6 325230 34 - 601863 TTACAATTCACAAGGGAACTGGATGATTAAACCA -s simRat_chr6.simRat.chr6 237174 34 + 647215 TTACACTTCACAAAGAAATATGACGATTACAACA - -a -s simMouse_chr6.simMouse.chr6 247088 25 + 636262 GGAGAAATCAAAATAACTTCAGTAA -s Anc0.Anc0refChr5 65595 25 + 87904 GGAAAGACCAAGATAACATAAACAA -s Anc1.Anc1refChr7 23490 25 - 47259 GGAAAGACCAAGATAACATAAACAA -s Anc2.Anc2refChr15 62412 25 + 86568 GGAAAGACCAAGATAACATAAGCAA -s mr.mrrefChr5 99882 25 + 294540 GGAGAAATCAAGATAACTTCAATAA -s simCow_chr6.simCow.chr6 243691 25 + 602619 GGAAAGACCAAGATAACACAAATAA -s simDog_chr6.simDog.chr6 234810 25 + 593897 GGAGAGACAAAGATAACGTAAGCAA -s simHuman_chr6.simHuman.chr6 325321 25 - 601863 GGAAAGACCAAGATAACATAAACAC -s simRat_chr6.simRat.chr6 237208 25 + 647215 GGAGAAGTTGAGATAGCTTCAATCA - -a -s simMouse_chr6.simMouse.chr6 247113 55 + 636262 AATAAAGACATGGCAGCTTCATTTAGTGTAACCTTGAAGTGCATATTCAATTAAA -s Anc0.Anc0refChr5 65620 55 + 87904 AAAAGAGACATGGCTGCTCCATTTGGTATAACTCTAAACTGCATATTCAATTGAA -s Anc1.Anc1refChr7 23515 55 - 47259 AAAAGAGACATGGCTGCTCCATTTGGTATAACTCTAAACTGCATATTCAATTGAA -s Anc2.Anc2refChr15 62437 55 + 86568 AAAAGAGACACAGCTGCTCCATCTGGTATGACTCTACAGTGCAGGTTCAATTGAA -s mr.mrrefChr5 99907 55 + 294540 AATAAAGACATGGCAGCTTCATTTAGTGTAACCTTGAACTGCATATTCAATTAAA -s simCow_chr6.simCow.chr6 243716 43 + 602619 AGAAAGGACACAGCCGCTCCAACTGGCATGACTC------------TTAATTGAA -s simDog_chr6.simDog.chr6 234835 55 + 593897 AATAGAGACACAGCTGCTCCATCTGGTATGACTCTACAGTGCAGGTTCAATTGGA -s simHuman_chr6.simHuman.chr6 325350 55 - 601863 AAAAGAGACATGGCTGCTCCATTTGGTTTAACTCCAAACTGCATAGTCAGTAGAA -s simRat_chr6.simRat.chr6 237233 55 + 647215 AATAAAAACATGACAGCTTCACTTATCATAATCTTGAACAGCATAATCAATCAAA - -a -s simMouse_chr6.simMouse.chr6 247168 7 + 636262 TATAACC -s Anc0.Anc0refChr5 65698 7 + 87904 TATAACC -s Anc1.Anc1refChr7 23593 7 - 47259 TATAACC -s Anc2.Anc2refChr15 62515 7 + 86568 TATAACC -s mr.mrrefChr5 99962 7 + 294540 TATAACC -s simCow_chr6.simCow.chr6 243782 7 + 602619 TATAACC -s simDog_chr6.simDog.chr6 234913 7 + 593897 TATAACC -s simHuman_chr6.simHuman.chr6 325428 7 - 601863 TATAACC -s simRat_chr6.simRat.chr6 237288 7 + 647215 CATAACC - -a -s simMouse_chr6.simMouse.chr6 247175 16 + 636262 AGCTCCTAGAGACAGG -s Anc0.Anc0refChr5 65707 16 + 87904 GGCTGCTGTATGCAGC -s Anc1.Anc1refChr7 23602 16 - 47259 GGCTGCTGTATGCAGC -s Anc2.Anc2refChr15 62524 16 + 86568 GGCTGCTTTATGCAGC -s mr.mrrefChr5 99969 16 + 294540 AGCTCCTGGAGACAGG -s simCow_chr6.simCow.chr6 243835 16 + 602619 GGTTGTTTTATGCAGC -s simDog_chr6.simDog.chr6 234922 15 + 593897 GACTGCTTTATA-GGC -s simHuman_chr6.simHuman.chr6 325437 16 - 601863 GGCCGCTGTATGTAGC -s simRat_chr6.simRat.chr6 237295 16 + 647215 ACCTACTGGAAACAGG - -a -s simMouse_chr6.simMouse.chr6 247191 27 + 636262 TTAGAACCATTGCTAAGCTTCCTGTTC -s Anc0.Anc0refChr5 65725 27 + 87904 TTAGAACAGTTGTTAGGCTCCCTGTTC -s Anc1.Anc1refChr7 23620 27 - 47259 TTAGAACAGTTGTTAGGCTCCCTGTTC -s Anc2.Anc2refChr15 62542 27 + 86568 TTAGAAAAGTTGTTAGGCTCTCTGTTC -s mr.mrrefChr5 99985 27 + 294540 TTAGAACCATTGCTAAGCTTCCTGTTC -s simCow_chr6.simCow.chr6 243853 27 + 602619 TTAGAATAGTTGCTAGACTCTTTGTTT -s simDog_chr6.simDog.chr6 234939 27 + 593897 TTAGAAAAATTGTTGGGCTCTCTGTGC -s simHuman_chr6.simHuman.chr6 325455 27 - 601863 TTAGAACAGTTCTTAGCCCCCCTGTTC -s simRat_chr6.simRat.chr6 237311 18 + 647215 TT---------GATAAGCTTTCTGTTC - -a -s simMouse_chr6.simMouse.chr6 247218 43 + 636262 CTTTTTGAGGACATTAGGGACACTGGGGATCCCAGTTGGGTGT -s Anc0.Anc0refChr5 65756 35 + 87904 CGTT-------CAACTGGGCCACTAGT-ATCCCTGTTGCCTCT -s Anc1.Anc1refChr7 23651 35 - 47259 CGTT-------CAACTGGGCCACTAGT-ATCCCTGTTGCCTCT -s Anc2.Anc2refChr15 62577 35 + 86568 CGTC-------CAACTGGGCTACTAGT-ATGCCTGTGGCCTCG -s mr.mrrefChr5 100012 43 + 294540 CTTTTTGAGGACATTAGGGACACTGGGGATCCCAGTTGGGTGT -s simCow_chr6.simCow.chr6 243888 35 + 602619 TGTC-------CAACTGGCCTACTAGT-ATGCCTGTGGCATCA -s simDog_chr6.simDog.chr6 234974 24 + 593897 CGTC-------TAACTGGG------------TCTGTGGCCTCG -s simHuman_chr6.simHuman.chr6 325486 35 - 601863 CATT-------CGACTGGGCCACCAGC-ATCCCTATTGCCTCT -s simRat_chr6.simRat.chr6 237329 42 + 647215 CTTTTTGAGGACAT-AGGGACACTGGGGATCCCAGTTGGGTGT - -a -s simMouse_chr6.simMouse.chr6 247261 7 + 636262 TGAGCTA -s Anc0.Anc0refChr5 65793 7 + 87904 CAGGCAA -s Anc1.Anc1refChr7 23688 7 - 47259 CAGGCAA -s Anc2.Anc2refChr15 62614 7 + 86568 CAGGCAA -s mr.mrrefChr5 100055 7 + 294540 TGAGCTA -s simCow_chr6.simCow.chr6 243925 7 + 602619 CAGACGG -s simDog_chr6.simDog.chr6 235000 7 + 593897 TGGGGAA -s simHuman_chr6.simHuman.chr6 325523 7 - 601863 CAGGCAA -s simRat_chr6.simRat.chr6 237371 7 + 647215 TGAGCTA - -a -s simMouse_chr6.simMouse.chr6 247268 16 + 636262 AAGTATGCTGGCCAGT -s Anc0.Anc0refChr5 65801 16 + 87904 AAGTAGGCTGGTCAGT -s Anc1.Anc1refChr7 23696 16 - 47259 AAGTAGGCTGGTCAGT -s Anc2.Anc2refChr15 62622 16 + 86568 AAGTGGGCTGGTCAGT -s mr.mrrefChr5 100063 16 + 294540 AAGTATGCTGGCCAGT -s simCow_chr6.simCow.chr6 243933 16 + 602619 AAATTGGCTGCTCAGT -s simDog_chr6.simDog.chr6 235008 16 + 593897 AAGTGGGCTCGTCAGT -s simHuman_chr6.simHuman.chr6 325531 16 - 601863 AAGTAGGCAGGTCAGT -s simRat_chr6.simRat.chr6 237379 16 + 647215 AAGTACGCTGGCCAGT - -a -s simMouse_chr6.simMouse.chr6 247284 3 + 636262 ATA -s Anc0.Anc0refChr5 65817 3 + 87904 ATA -s Anc1.Anc1refChr7 23712 3 - 47259 ATA -s Anc2.Anc2refChr15 62638 3 + 86568 AAA -s mr.mrrefChr5 100079 3 + 294540 ATA -s simCow_chr6.simCow.chr6 243965 3 + 602619 AAA -s simDog_chr6.simDog.chr6 235024 3 + 593897 AAA -s simHuman_chr6.simHuman.chr6 325547 3 - 601863 ATG -s simRat_chr6.simRat.chr6 237395 3 + 647215 ATA - -a -s simMouse_chr6.simMouse.chr6 247287 34 + 636262 CAGTGAGAGTTGGTTCCAATAGGGTTATAGCATT -s Anc0.Anc0refChr5 65820 30 + 87904 CA----GCTTTGTTTCCAACAAGGCCAGAGACTT -s Anc1.Anc1refChr7 23715 33 - 47259 CAG-ATGCTTTGTTTCCAACAAGGCCAGAGACTT -s Anc2.Anc2refChr15 62641 30 + 86568 TA----GCTTTGTTTCCAACAAGGCCAGAGACAT -s mr.mrrefChr5 100082 34 + 294540 CAGTAAGAGTTGGTTCCAATAGGGTTATAGCATT -s simCow_chr6.simCow.chr6 243968 29 + 602619 TG----GCTTTGGCACCAAT-AGGCCAGAGGCAT -s simDog_chr6.simDog.chr6 235029 30 + 593897 TA----GCTGTGTTTCCAACAAGACCTGAGACAT -s simHuman_chr6.simHuman.chr6 325550 33 - 601863 CAG-ATGCTTTGATTCTAACAAGGCCAAGGACTT -s simRat_chr6.simRat.chr6 237398 34 + 647215 CAGTAAGACTAGGTTCCAGGAGGGTTAGAGCATT - -a -s simMouse_chr6.simMouse.chr6 247321 15 + 636262 CTTTCCACTTGTTGG -s Anc0.Anc0refChr5 65850 15 + 87904 CTTTGCACTGGTGGG -s Anc1.Anc1refChr7 23748 15 - 47259 CTTTGCACTGGTGGG -s Anc2.Anc2refChr15 62671 15 + 86568 ATTTGCACTGGCGGG -s mr.mrrefChr5 100116 15 + 294540 CTTTCCACTTGTGGG -s simCow_chr6.simCow.chr6 243997 8 + 602619 A-------TGTCGGG -s simDog_chr6.simDog.chr6 235059 15 + 593897 ATTTGCACTGGCGGG -s simHuman_chr6.simHuman.chr6 325584 15 - 601863 CTTTGCACTGATGTG -s simRat_chr6.simRat.chr6 237432 15 + 647215 CTTTCCACCTGTGGG - -a -s simMouse_chr6.simMouse.chr6 247336 27 + 636262 GTAGGAGCTGTTGTATTCTGCAAAATT -s Anc0.Anc0refChr5 65865 19 + 87904 GCAGGAGCTAACATATT--------TG -s Anc1.Anc1refChr7 23763 19 - 47259 GCAGGAGCTAACATATT--------TG -s Anc2.Anc2refChr15 62686 19 + 86568 GCAGGAGATAACATGTT--------TG -s mr.mrrefChr5 100131 19 + 294540 GTAGGAGCTGACATATT--------TT -s simCow_chr6.simCow.chr6 244005 19 + 602619 GCAGGACGTAACCTGTT--------AG -s simDog_chr6.simDog.chr6 235077 19 + 593897 GCAGGAGATAGCATGTT--------TG -s simHuman_chr6.simHuman.chr6 325599 19 - 601863 GCAGGAGCTAACATATT--------TG -s simRat_chr6.simRat.chr6 237447 19 + 647215 GTAGGAGCTGACATATT--------TT - -a -s simMouse_chr6.simMouse.chr6 247363 10 + 636262 TTGAAGGGTG -s Anc0.Anc0refChr5 20299 8 - 87904 GGC--CTGCT -s Anc1.Anc1refChr7 20926 8 + 47259 GGC--CTGCT -s Anc2.Anc2refChr15 22082 8 - 86568 GGC--CTGGT -s mr.mrrefChr5 100150 8 + 294540 TTG--GGGTG -s mr.mrrefChr5 191383 8 - 294540 GGC--CTGCA -s simCow_chr6.simCow.chr6 356568 8 - 602619 GGT--CTGGT -s simDog_chr6.simDog.chr6 357033 8 - 593897 TGC--ATGGT -s simHuman_chr6.simHuman.chr6 273198 7 + 601863 GGC--CT-CT -s simMouse_chr6.simMouse.chr6 385814 8 - 636262 GGC--CTGCA -s simRat_chr6.simRat.chr6 406724 8 - 647215 GGC--CTGCG -s simRat_chr6.simRat.chr6 237466 8 + 647215 CTG--GGGTG - -a -s simMouse_chr6.simMouse.chr6 247373 20 + 636262 ACCTGATATAAGACTATATA -s Anc0.Anc0refChr5 20307 8 - 87904 ACCTGGTA------------ -s Anc1.Anc1refChr7 20934 10 + 47259 ACCTGGTATA---------- -s Anc2.Anc2refChr15 22090 8 - 86568 ACCTGGAA------------ -s mr.mrrefChr5 100158 10 + 294540 ACCTGATATA---------- -s mr.mrrefChr5 191391 10 - 294540 ACCTGGTATA---------- -s simCow_chr6.simCow.chr6 356581 8 - 602619 GGTTGGAA------------ -s simDog_chr6.simDog.chr6 357041 8 - 593897 ACCTGGAA------------ -s simHuman_chr6.simHuman.chr6 273205 8 + 601863 ACCTGGTA------------ -s simMouse_chr6.simMouse.chr6 385822 10 - 636262 ACCTGATATA---------- -s simRat_chr6.simRat.chr6 406732 10 - 647215 ACCTGGTATA---------- -s simRat_chr6.simRat.chr6 237474 10 + 647215 ACCTGATATA---------- - -a -s simMouse_chr6.simMouse.chr6 247393 1 + 636262 A -s mr.mrrefChr5 100168 1 + 294540 A -s simRat_chr6.simRat.chr6 237484 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 247394 17 + 636262 GACTTCATTCTTTGACA -s Anc0.Anc0refChr5 20315 17 - 87904 AATTGTGTTTCTTAACA -s Anc1.Anc1refChr7 20944 17 + 47259 AATTGTGTTTCTTAACA -s Anc2.Anc2refChr15 22098 17 - 86568 AATTGTGTGTCTTAACA -s mr.mrrefChr5 100169 17 + 294540 GACTTCATTCTTTGACA -s mr.mrrefChr5 191401 17 - 294540 GACTTTGTTGTTTGACA -s simCow_chr6.simCow.chr6 356589 17 - 602619 GATTGTGTGTGTTAACA -s simDog_chr6.simDog.chr6 357049 17 - 593897 AATTGTGTGTCTTAACA -s simHuman_chr6.simHuman.chr6 273213 17 + 601863 AATTGTGCTTCCTAACA -s simMouse_chr6.simMouse.chr6 385832 17 - 636262 GACTTCGTTGTTTGATA -s simRat_chr6.simRat.chr6 406742 17 - 647215 GACCCTGTTCTTTGGCA -s simRat_chr6.simRat.chr6 237485 17 + 647215 GACTTTGTTCTTTGACA - -a -s simMouse_chr6.simMouse.chr6 247411 19 + 636262 TGTCAGCTGGGTAGCATTC -s Anc0.Anc0refChr5 20351 19 - 87904 GGTCGGTTGGGTAGCCCTA -s Anc1.Anc1refChr7 20980 19 + 47259 GGTCGGTTGGGTAGCCCTA -s Anc2.Anc2refChr15 22134 19 - 86568 GGTAGGTTGGGTAGCCCTG -s mr.mrrefChr5 100186 19 + 294540 TGTCAGCTGGGTAGCATTC -s mr.mrrefChr5 191418 19 - 294540 GGTCAGTTGGGTAGCCTTA -s simCow_chr6.simCow.chr6 356625 19 - 602619 GGTCGGTTGGGTAGCCCTG -s simDog_chr6.simDog.chr6 357086 19 - 593897 GTTAGGTTGAGTAGCCTTG -s simHuman_chr6.simHuman.chr6 273249 19 + 601863 AGTTGGTTGGGTAGCCCTA -s simMouse_chr6.simMouse.chr6 385849 19 - 636262 GGTCAGTTGGGTAGCCTTA -s simRat_chr6.simRat.chr6 406759 19 - 647215 GGTCTGCTGGGTAGCCTTG -s simRat_chr6.simRat.chr6 237502 19 + 647215 AGTCAGCCACATAGCCCTG - -a -s simMouse_chr6.simMouse.chr6 247430 1 + 636262 A -s Anc0.Anc0refChr5 20370 1 - 87904 A -s Anc1.Anc1refChr7 20999 1 + 47259 A -s Anc2.Anc2refChr15 22153 1 - 86568 A -s mr.mrrefChr5 100205 1 + 294540 A -s mr.mrrefChr5 191437 1 - 294540 T -s simCow_chr6.simCow.chr6 356644 1 - 602619 A -s simDog_chr6.simDog.chr6 357105 1 - 593897 A -s simHuman_chr6.simHuman.chr6 273268 1 + 601863 A -s simMouse_chr6.simMouse.chr6 385868 1 - 636262 T -s simRat_chr6.simRat.chr6 237521 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 247431 30 + 636262 ACTTATATCATTTTTGCTCAGTGTACTGAA -s Anc0.Anc0refChr5 20371 30 - 87904 AGTTGCATCATATTAGTTAAGTGCTCTTAA -s Anc1.Anc1refChr7 21000 30 + 47259 AGTTGCATCATATTAGTTAAGTGCTCTTAA -s Anc2.Anc2refChr15 22154 30 - 86568 AGTTTCTTCATATTAGTTGAGTGCTCTTCA -s mr.mrrefChr5 100206 30 + 294540 ACTTATATCATTTTTGCTCAGTGTACTGAA -s mr.mrrefChr5 191438 30 - 294540 ATTTGTATCATTTTAGCTAATGGCCCTGAA -s simCow_chr6.simCow.chr6 356645 30 - 602619 AGTTTCCTAATGTTAGTTGAGTACTCTTCA -s simDog_chr6.simDog.chr6 357106 30 - 593897 AGTTTGTTCATATTGGTCGAGTGCTCTTCA -s simHuman_chr6.simHuman.chr6 273269 30 + 601863 AGTGGCATTATATTAGTTAAGTGCTCTTAA -s simMouse_chr6.simMouse.chr6 385869 22 - 636262 ATTTGTATCATTTTAGCTA--------GGA -s simRat_chr6.simRat.chr6 406778 30 - 647215 ACTTGTATCATTTTAGCTAATGGCCCTGAA -s simRat_chr6.simRat.chr6 237522 30 + 647215 ACTCATGACGTCTTAGCTAGGTGCACTGAA - -a -s simMouse_chr6.simMouse.chr6 247461 5 + 636262 CAACT -s Anc0.Anc0refChr5 20402 5 - 87904 CTACT -s Anc1.Anc1refChr7 21031 5 + 47259 CTACT -s Anc2.Anc2refChr15 22185 5 - 86568 ATCCT -s mr.mrrefChr5 100236 5 + 294540 CAACT -s mr.mrrefChr5 191469 5 - 294540 CAACT -s simCow_chr6.simCow.chr6 356676 5 - 602619 ATCCC -s simDog_chr6.simDog.chr6 357137 5 - 593897 ATCCT -s simHuman_chr6.simHuman.chr6 273300 5 + 601863 CTACT -s simMouse_chr6.simMouse.chr6 385892 5 - 636262 CAACT -s simRat_chr6.simRat.chr6 406809 5 - 647215 CAGCT -s simRat_chr6.simRat.chr6 237552 5 + 647215 CAACT - -a -s simMouse_chr6.simMouse.chr6 247466 25 + 636262 CTTTCAGACACCCCTATAGTGGCAT -s Anc0.Anc0refChr5 20407 23 - 87904 CCTCTTGACACCGGTATAGTGCT-- -s Anc1.Anc1refChr7 21036 23 + 47259 CCTCTTGACACCGGTATAGTGCT-- -s Anc2.Anc2refChr15 22195 23 - 86568 CCTCTTAACACTGGTATAGTGCT-- -s mr.mrrefChr5 100241 23 + 294540 CTTTCAGACACCCCTATAGTGGC-- -s mr.mrrefChr5 191474 23 - 294540 CGTTCAGACACCTGTATAATGGC-- -s simCow_chr6.simCow.chr6 356686 23 - 602619 CCTCTTAACACTGGTATAGTCTT-- -s simDog_chr6.simDog.chr6 357147 23 - 593897 CCTCTAAACACTGGTATAGTGCT-- -s simHuman_chr6.simHuman.chr6 273305 23 + 601863 CCTCTTCAGACCGGTATAGTGCT-- -s simMouse_chr6.simMouse.chr6 385897 16 - 636262 CGTTCAGACACCTGTA--------- -s simRat_chr6.simRat.chr6 406814 23 - 647215 TATTCAGACACCCATATAATGGC-- -s simRat_chr6.simRat.chr6 237557 23 + 647215 CCTCTGGACACTGGTATAGTGGC-- - -a -s simMouse_chr6.simMouse.chr6 247491 14 + 636262 CATATTTGCTTAAT -s Anc0.Anc0refChr5 20437 14 - 87904 GTTATTTCATTATA -s Anc1.Anc1refChr7 21066 14 + 47259 GTTATTTCATTATA -s Anc2.Anc2refChr15 22225 14 - 86568 GTTATTTCATTATA -s mr.mrrefChr5 100264 14 + 294540 CATATTTGCTTAAT -s mr.mrrefChr5 191499 14 - 294540 CATATTTGTTGAAT -s simCow_chr6.simCow.chr6 356716 14 - 602619 GTTGTCTCATTGTG -s simDog_chr6.simDog.chr6 357178 14 - 593897 TTTATTTAATTATA -s simHuman_chr6.simHuman.chr6 273335 14 + 601863 GTTATTTCATGATA -s simMouse_chr6.simMouse.chr6 385913 14 - 636262 CATATTTGTTGAAT -s simRat_chr6.simRat.chr6 406839 14 - 647215 CATATTAGTTGAAT -s simRat_chr6.simRat.chr6 237580 14 + 647215 TCTATTTGTTTAAT - -a -s simMouse_chr6.simMouse.chr6 247505 2 + 636262 TC -s Anc0.Anc0refChr5 20451 2 - 87904 TT -s Anc1.Anc1refChr7 21080 2 + 47259 TT -s Anc2.Anc2refChr15 22239 2 - 86568 TT -s mr.mrrefChr5 100278 2 + 294540 TC -s mr.mrrefChr5 191513 2 - 294540 TC -s simCow_chr6.simCow.chr6 356730 2 - 602619 CT -s simDog_chr6.simDog.chr6 357192 2 - 593897 TT -s simHuman_chr6.simHuman.chr6 273349 2 + 601863 TT -s simMouse_chr6.simMouse.chr6 385927 2 - 636262 TC -s simRat_chr6.simRat.chr6 237594 2 + 647215 TC - -a -s simMouse_chr6.simMouse.chr6 247507 1 + 636262 T -s Anc0.Anc0refChr5 20462 1 - 87904 T -s Anc1.Anc1refChr7 21091 1 + 47259 T -s Anc2.Anc2refChr15 22250 1 - 86568 T -s mr.mrrefChr5 100280 1 + 294540 T -s mr.mrrefChr5 191524 1 - 294540 C -s simCow_chr6.simCow.chr6 356741 1 - 602619 T -s simHuman_chr6.simHuman.chr6 273360 1 + 601863 T -s simMouse_chr6.simMouse.chr6 385940 1 - 636262 C -s simRat_chr6.simRat.chr6 406854 1 - 647215 C -s simRat_chr6.simRat.chr6 237596 1 + 647215 C - -a -s simMouse_chr6.simMouse.chr6 247508 6 + 636262 ATTAAG -s Anc0.Anc0refChr5 20463 6 - 87904 AGTTAA -s Anc1.Anc1refChr7 21092 6 + 47259 AGTTAA -s Anc2.Anc2refChr15 22251 6 - 86568 AGTTAA -s mr.mrrefChr5 100281 6 + 294540 ATTAAG -s mr.mrrefChr5 191525 6 - 294540 ATTAAA -s simCow_chr6.simCow.chr6 356742 6 - 602619 AGATAA -s simDog_chr6.simDog.chr6 357196 5 - 593897 -GTTAA -s simHuman_chr6.simHuman.chr6 273361 6 + 601863 GGTTAA -s simMouse_chr6.simMouse.chr6 385941 6 - 636262 ATTAAG -s simRat_chr6.simRat.chr6 406856 6 - 647215 ATTAAA -s simRat_chr6.simRat.chr6 237597 6 + 647215 ATTAAG - -a -s simMouse_chr6.simMouse.chr6 247514 23 + 636262 AAACTCACTCCCGACTATCTAGG -s Anc0.Anc0refChr5 20469 23 - 87904 GAACCTACTCCTGATTATCTAGA -s Anc1.Anc1refChr7 21098 23 + 47259 GAACCTACTCCTGATTATCTAGA -s Anc2.Anc2refChr15 22259 23 - 86568 GACCCTACCCCTGATTATCAAGA -s mr.mrrefChr5 100287 23 + 294540 AAACTCACTCCCGACTATCTAGG -s mr.mrrefChr5 191531 23 - 294540 AAACCCACTCTTAACTATCTAAG -s simCow_chr6.simCow.chr6 356750 23 - 602619 AGCCGTATCCCTATTTATCAAGA -s simDog_chr6.simDog.chr6 357203 23 - 593897 GACCCTACCCTTGATGATCAAGA -s simHuman_chr6.simHuman.chr6 273367 23 + 601863 GAACTTACTCCTTATTATCCAGA -s simMouse_chr6.simMouse.chr6 385947 23 - 636262 AAACCCACTCTTAACTATCTAAG -s simRat_chr6.simRat.chr6 406862 23 - 647215 AAACCCACTCTTAACTATCTAAG -s simRat_chr6.simRat.chr6 237603 23 + 647215 AATCCCACTCTTGACTATCTAGG - -a -s simMouse_chr6.simMouse.chr6 247537 21 + 636262 TGCCTTTGAGACCCACTGCTC -s Anc0.Anc0refChr5 20492 21 - 87904 TGACTCCAAGACCCATTGCTT -s Anc1.Anc1refChr7 21121 21 + 47259 TGACTCCAAGACCCATTGCTT -s Anc2.Anc2refChr15 22282 21 - 86568 TGACTCCAAGTCCCATTGCTT -s mr.mrrefChr5 100310 21 + 294540 TGCCTTTGAGACCCACTGCTC -s mr.mrrefChr5 191554 21 - 294540 TGTCTCCACGACCCACTGCTT -s simCow_chr6.simCow.chr6 356773 19 - 602619 TGAC--AAAGTCCCATTGCTA -s simDog_chr6.simDog.chr6 357226 21 - 593897 TGACTCCAAGTCCTATTGCTT -s simHuman_chr6.simHuman.chr6 273390 21 + 601863 CAACTCCAAAACCCATTGCAT -s simMouse_chr6.simMouse.chr6 385970 21 - 636262 TGTCTCCACGACCGACTCCTT -s simRat_chr6.simRat.chr6 406890 21 - 647215 TGCCTCCGTGACCCAGGGCTT -s simRat_chr6.simRat.chr6 237626 21 + 647215 TGCCTTCAAGACCCACCGCTG - -a -s simMouse_chr6.simMouse.chr6 247558 20 + 636262 GCAGAAAAGATGAGCCCCCA -s Anc0.Anc0refChr5 20513 20 - 87904 GGTATCACAAAGGGCCACCA -s Anc1.Anc1refChr7 21142 20 + 47259 GGTATCACAAAGGGCCACCA -s Anc2.Anc2refChr15 22303 20 - 86568 GGTATCACAAAGGGCCACCA -s mr.mrrefChr5 100331 20 + 294540 GCAGAAAAGATGAGCCCCCA -s mr.mrrefChr5 191575 20 - 294540 GTTATCACAGTGGGCCCCCA -s simCow_chr6.simCow.chr6 356792 20 - 602619 GGTACCACAAGGGGCCATGT -s simDog_chr6.simDog.chr6 357247 19 - 593897 TGTATCAC-AAGAGCCACCA -s simHuman_chr6.simHuman.chr6 273420 20 + 601863 GGTATCACTAAGGGCCACCA -s simMouse_chr6.simMouse.chr6 385991 20 - 636262 GTTATAACAGTGGGCCCCCA -s simRat_chr6.simRat.chr6 406911 20 - 647215 GTTGTCACAGGGGGCCCCCA -s simRat_chr6.simRat.chr6 237647 20 + 647215 CCAGAAAAGATGAGCCCCCC - -a -s simMouse_chr6.simMouse.chr6 247578 95 + 636262 CATACCAGCTAGCTACTGAATGCACACAATGGAATATACTCAGTCACAAACTGAAGTTCTGCATCCAGTTGTCACACTGGTATGACCAAAATGCA -s Anc0.Anc0refChr5 66929 2 + 87904 ca--------------------------------------------------------------------------------------------- -s Anc1.Anc1refChr7 24637 73 - 47259 caaactgg--ggtgaggtatttcacact--------tattcagcttgaaagaggggtagt--------ttcacacacaggt----ccacaatgaa -s Anc2.Anc2refChr15 63803 2 + 86568 CC--------------------------------------------------------------------------------------------- -s mr.mrrefChr5 100351 95 + 294540 CATACCAGCTAGCTACTGAATGCACACAATGGAATATACTCAGTCACAAACTGAAGTTCTGCATCCAGTTGTCACACTGGTATGACCAAAATGCA -s simCow_chr6.simCow.chr6 245054 2 + 602619 CT--------------------------------------------------------------------------------------------- -s simDog_chr6.simDog.chr6 236213 2 + 593897 CC--------------------------------------------------------------------------------------------- -s simHuman_chr6.simHuman.chr6 326755 73 - 601863 caaactgg--ggtgaggtatttcacact--------tattcagcttgaaagaggggtagt--------ttcacacacaggt----ccacaatgaa -s simRat_chr6.simRat.chr6 237667 95 + 647215 TGTTCCAGCTAAATACTGAATGCACACAATAGAATATGCTTAGCCACGAGCTGTAGTTCTGCATCCAGTTGTGACACTGGTATGACCAAAAAGCA - -a -s simMouse_chr6.simMouse.chr6 247673 7 + 636262 AAAGAAA -s Anc1.Anc1refChr7 24710 7 - 47259 aaacaaa -s mr.mrrefChr5 100446 7 + 294540 AAAGAAA -s simHuman_chr6.simHuman.chr6 326831 7 - 601863 aaacaaa -s simRat_chr6.simRat.chr6 237762 7 + 647215 AAAGAAA - -a -s simMouse_chr6.simMouse.chr6 247680 210 + 636262 TGCATATTTTCTATGATTCAATGGATAAATAGCTACATACAACACTTGTTGACTATCATTCATTAAACATATGTATTGAAGAAAGGGCTTCATACATAGCTGCTTTATTCTTGGCAAATCTTGGTAAGCAGGAATCATCAGAAACATGCAGTCCACATCTCAACTGTCCATTGGTGTATTTCTAGACCCTGCAAGAATGTATTATCACAG -s Anc1.Anc1refChr7 24717 5 - 47259 tacat------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- -s mr.mrrefChr5 100453 202 + 294540 TGCATATTTTCTATGATTCA----ATAAATAGCTACATACAACACTTGTTGACTATCATTCATTAAACATATGTATTGAAGAAA---CTTCA-ACATAGCTGCTTTATTCTTGGCAAATCTTGGTAAGCAGGAATCATCAGAAACATGCAGTCCACATCTCAACTGTCCATTGGTGTATTTCTAGACCCTGCAAGAATGTATTATCACAG -s simHuman_chr6.simHuman.chr6 326838 5 - 601863 tacat------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- -s simRat_chr6.simRat.chr6 237770 202 + 647215 TACATATTTTCTATGATTCA----ATAAATAGCTCCGTACAGCGTTGGTTGACTATCACTCATTAGACATGTGTATTGATAAAA---CCTCA-GCATAGCCCTTTTAATCTTGGCAAATCTTGGTAGACAGAGGTCATCAGAGACTTGCAGTCAGCTTCTCACTTGTCCATTGGTATATTCCTATACCCTACAAGACTGTATTATCACAG - -a -s simMouse_chr6.simMouse.chr6 247890 604 + 636262 GGAATGAAAGACAAAAAAAATGAAAGTCATTCTTAGTTTTGATTCCTTAGACTTCCACTGAAGCTACCAGAGGTGGGCGGTTAGATAGTCCATGTGTATTAACAAAGTAACTGATCAATGATACCCTATTGATCAATGATACCCTACCCCCTACCAGCATTGTGATCTGCTGAAACAACAGGTGATGAAACTAATATAACCAATGTGTTGTAGAGGTCAAGAAGAATTGGTTTCAGATGTAACCTCATGACTGACTAACTGATTGGTTGAGGCAGGTGTTGCCTCATGACTCACTAACTGATTGTTTGGGGTTGGGCAGTCTTGGGGGGCACAAGCTGATTTGGTTGGGGTTGGTCAGTCTTGGGAGGTTTGCCCCTCAGAGTTTGCCCCCACTGTTTAATGGTGAGTGAATTATGAGTACAGATGTGACGGGTTGAGTGAGGCAAAAAAGAAGGTAGGTGCGTGATAGTCATAAAACCAAATGTGGGCCTCAAAATTTCATAGTAGTTTTAGAGAAGTAGCTACAAATTGGAAGGGTGAAAACACCGGTTCAAGGCTGTGAATACTAAGTCTATTTTTGCTAGCCACCATATTTTCAAGTGAA -s mr.mrrefChr5 100655 572 + 294540 GGAATGAAAGACAAAAAAAATGAAAGTCATTCTTAGTTTTGATTCCTTAGACTTCCACTGAAGCTACCAGAGGTGGGCGGTTAGATAGTCCATGTGTATTAACAAAGTAACTGATCAATGATACCCTATTG------------------CCTACCAGCATTGTGATCTGCTGAAACAACAGGTGATGAAACT-ATATAACCAATGTGTTGT---GGTCAAGAAGAATTGGTTTCAGATGTAACCTCATGACTGACTAACTGATTGGTTGAGGCAGGTGTTGCCTCATGACTCACTAACTGATTGTTTGGGGTTGGGCAGTCTTGGGGGGCACAAGCTG-TTTGGTTGGGGTTGGTCAGTCTTGGGAGGTTTGCCCCTCAGAGTTTGCCCCCACTGTTTAATGGTGAGTGAATTATGAGTACAGATG-GACGGGTTGAGTGAGGCAAAAAAGAAGGTAGGTGCGTGATAGTCATAAAACCA--------CCTCAAAATTTCATAGTAGTTTTAGAGAAGTAGCTACAAATTGGAAGGGTGAAAACACCGGTTCAAGGCTGTGAATACTAAGTCTATTTTTGCTAGCCACCATATTTTCAAGTGAA -s simRat_chr6.simRat.chr6 238006 572 + 647215 GGAGTGAAAGACAAAAAAAACTAAAGTTATTCTTAGGTTAGATTCCTTACACTTCCACTGAAGCTACCAGAGCTGGGCAACTAGATAGTCCATGTATAATAACACAGTAACTGATCAATAACACCCTACTG------------------CCTACCCGAGTTGTGATCTGCTGAAACAATAGGTGATGACACT-ATATAATCAATGTGTTGT---GGTCAAGAAGAATCCTTTTCAGATGTAAACTCATAACTCACTAACTGATTGGTTGGGGCAGATGTAACCCTAAGACTCACTATCTGATTGGTTGGGGTTGGGCAGTCCTGGGTGGCACTAACTG-TTTGGGAGGGGTCGGGCAGTCTTGGGAAGATTGCCCTTCAGAGTTTGCCCCCACCGCTCAACAGTGAGTACATTATAAGTACAGATG-GACAGGTTGAGTGAGGCAAAAAAGAAATTGGATGCATGGTAGTCATAAAACCA--------CCTCAAAATCTCATAGTAGCTTTAGAGAAGTAGCTATGAGTTGGAAGGATGAAAGCACCAGTTCAATCCTGTGTATACTAAGTCTATCTTTGCTAGCCAACCTATTTTCAAGTAAA - -a -s simMouse_chr6.simMouse.chr6 248494 11 + 636262 GACATGTTTCT -s mr.mrrefChr5 101227 11 + 294540 GACATGTTTCT -s simRat_chr6.simRat.chr6 238585 11 + 647215 AACATGCTTCT - -a -s simMouse_chr6.simMouse.chr6 248505 134 + 636262 TTATCTATTGTCCCCCAGGCCAATAGCCGATTCAAATGGCAGTAGCTGTAATGCTAATGCTTTTTTAGGTCTGAATCCTCCAAGCTAGTAGTTAACTCACAAACAGTGCCAATGGAACAGTAAGGAACAATGTA -s mr.mrrefChr5 101238 128 + 294540 TTATCTATTGTCCCCCAGGCCAATAGCCGATTCAAATGGCAGTAGCTGTA------ATGCTTTTTTAGGTCTGAATCCTCCAAGCTAGTAGTTAACTCACAAACAGTGCCAATGGAACAGTAAGGAACAATGTA -s simRat_chr6.simRat.chr6 238621 128 + 647215 TGATCTATTGTCCCCCAGACAAATAGCCAACTCACATGGCAGCAGCCATA------ATACTTTTTTAGGTATGGGTCCCTCAAGCTAGTAGCCAACTCACAAACGATGCCAATGAAGCAGTAAGGAACGATGTA - -a -s simMouse_chr6.simMouse.chr6 248639 140 + 636262 TGAATCACAGTGTCTGCTTAAACTCTTTGTGCGCACTAGTATTTAATATGTGACTTGCCCAGTTTGCCTTGGTACAATTGCATGACCAATAATACAAGAGCTAAATCATCAGGGGGAAGTACAGCAATCAGGAACCTACA -s Anc1.Anc1refChr7 24722 21 - 47259 -----------------------------------------------------------------------------------------------------------------gagaagaaaaccaataa------taca -s mr.mrrefChr5 101366 94 + 294540 TGAATCACAGTGTCTGCTTAAACTCTTTGTGCGCACTAGTATTTAATATGTGACTTGCCCAGTT----------------------------------------------AGGGGGAAGTACAGCAATCAGGAACCTACA -s simHuman_chr6.simHuman.chr6 326843 21 - 601863 -----------------------------------------------------------------------------------------------------------------gagaagaaaaccaataa------taca -s simRat_chr6.simRat.chr6 238762 94 + 647215 TGAATCACAGTGTTAGCTTAAGCTTTTTCCAAGCACTAATATTCAATGTTTGACTTGCCCAGTT----------------------------------------------AGGGTTAAGTACAGCAATCAGGAACCTACA - -a -s simMouse_chr6.simMouse.chr6 248779 5 + 636262 GGGTg -s Anc1.Anc1refChr7 24743 5 - 47259 gatag -s mr.mrrefChr5 101460 5 + 294540 GGGTg -s simHuman_chr6.simHuman.chr6 326867 5 - 601863 gatag -s simRat_chr6.simRat.chr6 238856 5 + 647215 GGGTG - -a -s simMouse_chr6.simMouse.chr6 248784 3 + 636262 cac -s Anc1.Anc1refChr7 24749 3 - 47259 cat -s mr.mrrefChr5 101466 3 + 294540 cac -s simHuman_chr6.simHuman.chr6 326873 3 - 601863 cat -s simRat_chr6.simRat.chr6 238862 3 + 647215 CAC - -a -s simMouse_chr6.simMouse.chr6 248787 22 + 636262 tctcttgctaggggagatgtct -s Anc1.Anc1refChr7 24752 22 - 47259 cctcttgctagggaagaggtct -s mr.mrrefChr5 101469 22 + 294540 tctcttgctaggggagaggtct -s simHuman_chr6.simHuman.chr6 326876 22 - 601863 cctcttgctagggaagaggtct -s simRat_chr6.simRat.chr6 238872 19 + 647215 TTCATTTCAAAGGGAGGGA--- - -a -s simMouse_chr6.simMouse.chr6 248809 4 + 636262 tgtc -s Anc1.Anc1refChr7 24774 4 - 47259 tgtt -s mr.mrrefChr5 101491 4 + 294540 tgtc -s simHuman_chr6.simHuman.chr6 326899 4 - 601863 tgtt - -a -s simMouse_chr6.simMouse.chr6 248813 49 + 636262 cctagcgaacatgtcttgtcctgaaaggactgaacggaactgagttcag -s Anc1.Anc1refChr7 24778 47 - 47259 cttaaaatgtataccttcttgtaacccatctga--gtaggtgagctcag -s mr.mrrefChr5 101495 49 + 294540 cctagcatacatatcttgtcctgaaacaactgaacggaactgagctcag -s simHuman_chr6.simHuman.chr6 326914 47 - 601863 cttaaaatgtataccttcttgtaacccatctga--gtaggtgagctcag -s simRat_chr6.simRat.chr6 238891 37 + 647215 -ATAGCATAAGTAT-----------ACAACAAACTTACACAGATCCCAC - -a -s simMouse_chr6.simMouse.chr6 248862 4 + 636262 tgtc -s Anc1.Anc1refChr7 24825 4 - 47259 tgtc -s mr.mrrefChr5 101544 4 + 294540 tgtc -s simHuman_chr6.simHuman.chr6 326964 4 - 601863 tgtc -s simRat_chr6.simRat.chr6 238928 4 + 647215 ATAC - -a -s simMouse_chr6.simMouse.chr6 248866 47 + 636262 atcctacagatgttgcagataagcactcacaaaggtgggctgtctct -s Anc1.Anc1refChr7 24829 47 - 47259 aacttagagatatgggagaaaagctctcacaaaagtcgacggtctca -s mr.mrrefChr5 101548 47 + 294540 atcctacagatgttgcagataagcactcacaaaggtgggctgtctct -s simHuman_chr6.simHuman.chr6 326974 47 - 601863 aacttagagatatgggagaaaagctctcacaaaagtcgacggtctca -s simRat_chr6.simRat.chr6 238932 47 + 647215 ATTCAAACTatgttgcagatcagcacacacaaaggtgggctgactct - -a -s simMouse_chr6.simMouse.chr6 248913 219 + 636262 cccctatagagtagcaccgcaccacatccctgctaagtagcaacagcctaaaagctagactcggccacatcttgctaaccccaaaagcacatcttacccatcccaaaggtattgaagagaggaccatagtgttaagatatacaatcaggcaacctatggcaacctaagcaggaggactactataggcgggaagacctcagtggaaagatacccactctg -s Anc1.Anc1refChr7 24878 136 - 47259 gc-------------------------ccctcctaagtagtaccc-cctaatagatgagctcacccacaccttaatcatccaa------------------------------ggggagagggccatatt--taggatatacaagtaggtg---tatggt----------------------caggcgggaagatcatactggaaagacattcactcaa -s mr.mrrefChr5 101597 217 + 294540 cccctatagagtagcaccgcaccacatccctcctaagtagcaacagcctaaaagctagactcagccacatcttactaatcccaaaagcacatcttacccatcccagaggtattgaagagaggaccatagt--taggatatacaatcaggcaacctatggcaacctaagcaggaggactactataggcgggaagacctcagtggaaagatatccactctg -s simHuman_chr6.simHuman.chr6 327023 136 - 601863 gc-------------------------ccctcctaagtagtaccc-cctaatagatgagctcacccacaccttaatcatccaa------------------------------ggggagagggccatatt--taggatatacaagtaggtg---tatggt----------------------caggcgggaagatcatactggaaagacattcactcaa -s simRat_chr6.simRat.chr6 238981 214 + 647215 cccttatgaagtagcactgcaccacatccctcctaaatagcaaagacctaaaagctagacccagccacatcttactaatcccaaaagcacatcttacgcatcccagaggtattgtag---ggaccatagc--taggatatccaataagacaacctgtggcaacctgagcaggaagactaccattggtgagaagacctcagtggaaagatatccactctg - -a -s simMouse_chr6.simMouse.chr6 249132 7 + 636262 ctacctt -s Anc1.Anc1refChr7 25014 7 - 47259 ttatttt -s mr.mrrefChr5 101814 7 + 294540 ctacttt -s simHuman_chr6.simHuman.chr6 327183 7 - 601863 ttatttt -s simRat_chr6.simRat.chr6 239195 7 + 647215 caacttt - -a -s simMouse_chr6.simMouse.chr6 249139 25 + 636262 gggaccccctgctaacctgggggag -s Anc1.Anc1refChr7 25025 25 - 47259 aacacccacacccaacctagggggg -s mr.mrrefChr5 101825 25 + 294540 gggacccactcctaacctgggggag -s simHuman_chr6.simHuman.chr6 327194 25 - 601863 aacacccacacccaacctagggggg -s simRat_chr6.simRat.chr6 239206 25 + 647215 gggaccaactcctaacctgggtgag - -a -s simMouse_chr6.simMouse.chr6 249164 42 + 636262 gatctgcaaacatgaaatggagttgatatgccactctgttgc -s Anc1.Anc1refChr7 25050 37 - 47259 ggttcataaacagggaacgcgattgaagcacccact-----c -s mr.mrrefChr5 101850 37 + 294540 gatttgcaaacatgaaatgggattgatatgccaatt-----c -s simHuman_chr6.simHuman.chr6 327220 37 - 601863 ggttcataaacagggaacgcgattgaagcacccact-----c -s simRat_chr6.simRat.chr6 239231 37 + 647215 gatttgcaagcatgaaatgggattgaTATGCTAATT-----C - -a -s simMouse_chr6.simMouse.chr6 249206 63 + 636262 tagacaggaaacctagctcagtcagagggagaggctcatatgtaaacattcaaggggaaatga -s Anc1.Anc1refChr7 25087 63 - 47259 tagacagaaagcttggctcaatctgagggaggagcctgtatgtatacacacaaaggaaaataa -s mr.mrrefChr5 101887 63 + 294540 tagacaggaaacctggctcaatctgagggagaggctcatatgtaaacattcaaggggaaatga -s simHuman_chr6.simHuman.chr6 327307 63 - 601863 tagacagaaagcttggctcaatctgagggaggagcctgtatgtatacacacaaaggaaaataa -s simRat_chr6.simRat.chr6 239268 63 + 647215 TAGACAGGAcacctggctcaatttgagggagcggctcatatgtaaacatccaaggggaaatga - -a -s simMouse_chr6.simMouse.chr6 249269 91 + 636262 catatgtaaacattcaaggggaaatgaagggatgcatgtttatgtaaacgcataagaagaagcaagagagagtcagtatgtaatgatcccc -s Anc1.Anc1refChr7 25150 88 - 47259 tgtatgtaaatacacaaaggaaaatgatgggatgttcttgtacgtaagc-cataaaggaaaataagagaaa--cagtttgtagttaaactc -s mr.mrrefChr5 101950 91 + 294540 catatgtaaacattcaaggggaaatgaagggatgcatgtttatgtaaacgcataagagaaagcaagagagagtcagtatgtaattataccc -s simHuman_chr6.simHuman.chr6 327376 88 - 601863 tgtatgtaaatacacaaaggaaaatgatgggatgttcttgtacgtaagc-cataaaggaaaataagagaaa--cagtttgtagttaaactc -s simRat_chr6.simRat.chr6 239331 64 + 647215 ---------------------------agggatgcatgttcatgtaaatgcataacagaaagcaagagagaatcagtatgtcattgtaccc - -a -s simMouse_chr6.simMouse.chr6 249360 63 + 636262 agtatgtctgtgcaacacccattagaattagagtagtggctcatattgagtatgacaaaaagg -s Anc1.Anc1refChr7 25238 63 - 47259 ggagcagcagtgagctacccatttaatttagagaactgacacgtatttagagacccaaagaag -s mr.mrrefChr5 102041 63 + 294540 agtgcgtctgtgcaacacccattagaattagagtagtggctcatattgagtatgacaaaaaag -s simHuman_chr6.simHuman.chr6 327468 63 - 601863 ggagcagcagtgagctacccatttaatttagagaactgacacgtatttagagacccaaagaag -s simRat_chr6.simRat.chr6 239395 63 + 647215 agtgcgtctgtgcaagacccactagagttagagtagtggctcatattgagtatgaccaaaaag - -a -s simMouse_chr6.simMouse.chr6 249423 56 + 636262 tacagggccaaggcttgaactagatttttatcatcctcaaggctgacttaaagcct -s Anc1.Anc1refChr7 25301 48 - 47259 tccaaggggaaggcttgtactaaaact--------ctctaggtctaagaggagtct -s mr.mrrefChr5 102104 56 + 294540 tacagggccaaggcttgaactagaactttatcatcctcaaggctgacttagagcct -s simHuman_chr6.simHuman.chr6 327535 48 - 601863 tccaaggggaaggcttgtactaaaact--------ctctaggtctaagaggagtct -s simRat_chr6.simRat.chr6 239458 55 + 647215 tacagggccaaggcttgcactagaactttatcatcctaaaaggtgacttagagcc- - -a -s simMouse_chr6.simMouse.chr6 249479 25 + 636262 ttaaagcctcaaggtctaggaggag -s Anc1.Anc1refChr7 25349 25 - 47259 ttaaacctcctaggtctaagaagag -s mr.mrrefChr5 102160 25 + 294540 ttaaagcctcaaggtctaggaagag -s simHuman_chr6.simHuman.chr6 327590 25 - 601863 ttaaacctcctaggtctaagaagag -s simRat_chr6.simRat.chr6 239513 17 + 647215 --------tcaaggtctaggcagag - -a -s simMouse_chr6.simMouse.chr6 249504 74 + 636262 gtgtgaggtgaaacattcaccacctcaggacattcccccttagtgaattcgagacctacattgactggttagga -s Anc1.Anc1refChr7 25374 66 - 47259 atttgagaagaaggatacactcccagag--------tccctcatcaattcagggcctgtagtggggaggtagta -s mr.mrrefChr5 102185 74 + 294540 gtgtgaggtgaaacattcaccacctcaggacattcccccttagtcaattcaaggcctacattgggtggttagga -s simHuman_chr6.simHuman.chr6 327630 66 - 601863 atttgagaagaaggatacactcccagag--------tccctcatcaattcagggcctgtagtggggaggtagta -s simRat_chr6.simRat.chr6 239530 72 + 647215 gtg--aggggaaacacttacctcctcaggacattccctcttagtcaattcaaggactaccatgggtggttatga - -a -s simMouse_chr6.simMouse.chr6 249578 21 + 636262 taaattcaaattacaggaaag -s Anc1.Anc1refChr7 25440 21 - 47259 ggaatttgaattacaggagag -s mr.mrrefChr5 102259 21 + 294540 tgaatttgaattacaggaaag -s simHuman_chr6.simHuman.chr6 327698 21 - 601863 ggaatttgaattacaggagag -s simRat_chr6.simRat.chr6 239602 21 + 647215 tgaacttgaattacgggaaaa - -a -s simMouse_chr6.simMouse.chr6 249599 5 + 636262 ttacc -s Anc1.Anc1refChr7 25461 5 - 47259 ttacc -s mr.mrrefChr5 102280 5 + 294540 ttacc -s simHuman_chr6.simHuman.chr6 327721 5 - 601863 ttacc -s simRat_chr6.simRat.chr6 239623 5 + 647215 ttact - -a -s simMouse_chr6.simMouse.chr6 249604 1 + 636262 t -s Anc1.Anc1refChr7 25466 1 - 47259 g -s mr.mrrefChr5 102285 1 + 294540 t -s simHuman_chr6.simHuman.chr6 327743 1 - 601863 g -s simRat_chr6.simRat.chr6 239628 1 + 647215 t - -a -s simMouse_chr6.simMouse.chr6 249605 44 + 636262 gtggtttcagagttataactcgatctacatgagaagcccatggt -s Anc1.Anc1refChr7 25484 44 - 47259 gcagccacggagtcaaaattcaatttacaggagaaacttgtatt -s mr.mrrefChr5 102303 44 + 294540 gtggtttcagagttaaaactcgatctacatgagaagctcatggt -s simHuman_chr6.simHuman.chr6 327761 44 - 601863 gcagccacggagtcaaaattcaatttacaggagaaacttgtatt -s simRat_chr6.simRat.chr6 239647 44 + 647215 gtggtttcagagttgaaacttgatctacatgaggagctcaaggt - -a -s simMouse_chr6.simMouse.chr6 249649 70 + 636262 ctcccgggaagtggagacagtatgatctgttgatggattccctagacctgatatagacttttcttaccta -s Anc1.Anc1refChr7 25528 69 - 47259 tttctggtaagtggagatggtgggacctgtccagggagtcc-tagacctgctgcaaattgtggtcatcta -s mr.mrrefChr5 102347 69 + 294540 cttctgggaagtggagacagtatgacctgttgatggattcc-tagacctgatgcagacttttcttaccta -s simHuman_chr6.simHuman.chr6 327812 69 - 601863 tttctggtaagtggagatggtgggacctgtccagggagtcc-tagacctgctgcaaattgtggtcatcta -s simRat_chr6.simRat.chr6 239691 69 + 647215 cttctggggagtggagacagtatgacctgttggtggattac-tagacctgatgcagactttttttaccta - -a -s simMouse_chr6.simMouse.chr6 249719 29 + 636262 caacaaagttaaagcaagggttacctcct -s Anc1.Anc1refChr7 25597 29 - 47259 aaacaagattaaaggaaacgtcaccttat -s mr.mrrefChr5 102416 29 + 294540 caacaaagttaaagcaagggttacctcct -s simHuman_chr6.simHuman.chr6 327884 29 - 601863 aaacaagattaaaggaaacgtcaccttat -s simRat_chr6.simRat.chr6 239760 27 + 647215 caacaacgttaggg--aggattacctcct - -a -s simMouse_chr6.simMouse.chr6 249748 25 + 636262 caGACAGCTATGGTCAAAAGATAAT -s Anc1.Anc1refChr7 25626 25 - 47259 caggcacgtatttgttgcacAtgac -s mr.mrrefChr5 102445 25 + 294540 caGACAGCTATGGTCAAAAGATAAT -s simHuman_chr6.simHuman.chr6 327921 25 - 601863 caggcacgtatttgttgcacatgac -s simRat_chr6.simRat.chr6 239787 25 + 647215 caGACAGCTATGGTCATAAGATAAT - -a -s simMouse_chr6.simMouse.chr6 249773 85 + 636262 TGCCTGACTCAACTAAATGCACTGGTTCTACATACAATGTTCAACTCTTCTATTCTACTATGGAACACGTAACAATGGCTACAAT -s Anc0.Anc0refChr5 66931 79 + 87904 -----AACTTGACTAAGCTTATTGATTCTGCATTCTTC-TTCAACTTTTCTATTTTACTGTGAAATAGGTAACTATGTCTAATAT -s Anc1.Anc1refChr7 25651 84 - 47259 tgtaCAACTTGACTAAGCTTATTGATTCTGCATTCTTC-TTCAACTTTTCTATTTTACTGTGAAATAGGTAACTATGTCTAATAT -s Anc2.Anc2refChr15 63805 79 + 86568 -----AACTTGACTAAGCTTATTGATTCTGCATTCTTC-CTCAACTTTTCTATTTTACTGTGAAATAGTTAACTACGTCTAATAA -s mr.mrrefChr5 102470 85 + 294540 TGTCTGACTCAACTAAGTGCACTGGTTCTACATACAATGTTCAACTCTTCTATTTTACTGTGGAACACGTAACAATGGCTAAAAT -s simCow_chr6.simCow.chr6 245056 79 + 602619 -----GGCCTGAGTAAGGCAATTGATTCCGTGTTTGTC-CTCAACATCTCTATATTACTGTGAAATAGATAACAACGTCTAATAA -s simDog_chr6.simDog.chr6 236215 79 + 593897 -----AACTTGACTAAGCTTATTGATTGTGCATTCTTC-CTCAACTTTTCTATTGTACTGTGAAATAGTCAACTACAGCTAATAA -s simHuman_chr6.simHuman.chr6 327948 84 - 601863 tgtacaacttgACTAAGCTGATTAATTCTGCATGCTCC-TTCAACTTTCGTATTTTACTGTGAAATAGGTAACGATGTCTAATAT -s simRat_chr6.simRat.chr6 239812 85 + 647215 TGTCTGACTCAACTAAGTGCAATGGTTCTACATACAATGTTCAACAATTTTATTTTACTGTGGGACATATAACAATGGCTAAGAT - -a -s simMouse_chr6.simMouse.chr6 249858 35 + 636262 GCCTCTGCAAGTTTAAAAATTTTTATTCCCCAGTT -s Anc0.Anc0refChr5 67011 13 + 87904 AGC----------------------TTCCACAGTT -s Anc1.Anc1refChr7 25736 13 - 47259 AGC----------------------TTCCACAGTT -s Anc2.Anc2refChr15 63885 13 + 86568 AGC----------------------TTCCACAGTT -s mr.mrrefChr5 102556 35 + 294540 GCCTCTGCAAGTTTAAAAATTTTTATTCCCCAGTT -s simCow_chr6.simCow.chr6 245136 13 + 602619 AGT----------------------TTCCACAGTT -s simDog_chr6.simDog.chr6 236295 13 + 593897 AGC----------------------ATCCCTAGTT -s simHuman_chr6.simHuman.chr6 328033 13 - 601863 AGC----------------------TTCCACTGTT -s simRat_chr6.simRat.chr6 239898 35 + 647215 GCCTCCGCCAGTTCAAAAATTTTTATTCCCCAGTT - -a -s simMouse_chr6.simMouse.chr6 249893 15 + 636262 GAAGATTTCTACAGC -s Anc0.Anc0refChr5 67025 15 + 87904 GAAAATTTTTGCAAC -s Anc1.Anc1refChr7 25750 15 - 47259 GAAAATTTTTGCAAC -s Anc2.Anc2refChr15 63899 15 + 86568 GAAAATTTTTGCAAC -s mr.mrrefChr5 102592 15 + 294540 GAAGATTTTTACAGC -s simCow_chr6.simCow.chr6 245150 15 + 602619 CTAAATTCTACAAAC -s simDog_chr6.simDog.chr6 236309 15 + 593897 GATAATTTTTGCAAC -s simHuman_chr6.simHuman.chr6 328047 15 - 601863 GAAAATTTTTGCAAC -s simRat_chr6.simRat.chr6 239934 15 + 647215 GAATATTTTTACAGC - -a -s simMouse_chr6.simMouse.chr6 249908 13 + 636262 TCTGAAAAACTGC -s Anc0.Anc0refChr5 67040 13 + 87904 TCTCAAAAACTGT -s Anc1.Anc1refChr7 25765 13 - 47259 TCTCAAAAACTGT -s Anc2.Anc2refChr15 63914 13 + 86568 TCCCAAAAACTGT -s mr.mrrefChr5 102607 13 + 294540 TCTGAAAAACTGC -s simCow_chr6.simCow.chr6 245461 13 + 602619 TCCCAAAAACTGC -s simDog_chr6.simDog.chr6 236324 11 + 593897 TCCCAAAAA--GT -s simHuman_chr6.simHuman.chr6 328062 13 - 601863 TCTCGCAAACTGT -s simRat_chr6.simRat.chr6 239949 13 + 647215 TCTGAAAAACTGC - -a -s simMouse_chr6.simMouse.chr6 249921 28 + 636262 GTGGTATACTAAGCACCAGTAGTAAAAG -s Anc0.Anc0refChr5 67054 27 + 87904 TGG-AATATTAAGAATAAGTCTTAAAGG -s Anc1.Anc1refChr7 25779 28 - 47259 TGGAAATATTAAGAATAAGTCTTAAAGG -s Anc2.Anc2refChr15 63928 27 + 86568 TGG-AATATTAAGAATAAGCCTTAAAGA -s mr.mrrefChr5 102620 28 + 294540 TGGGTATATTAAGCATAAGTAGTAAAAG -s simCow_chr6.simCow.chr6 245475 27 + 602619 TGG-AATCTCAAGAATAAGCCTTAAAGA -s simDog_chr6.simDog.chr6 236336 26 + 593897 TGG-AATATT-AGAATGAGCCTTAAAGA -s simHuman_chr6.simHuman.chr6 328076 28 - 601863 TGGAACTATTAAGAATAAATGCTAAGGG -s simRat_chr6.simRat.chr6 239962 28 + 647215 TGGGTATATTACGCATAAGTATTAAAAG - -a -s simMouse_chr6.simMouse.chr6 249949 102 + 636262 AAGTGCTAGTTGGATGCAAAAGCACAACTTTACAAATCTCCACAAGCTGAGTAAACCTGGCCATATTCGCCCCTTTACCCTGTGCATTGCAGTTCTGAAGAC -s Anc0.Anc0refChr5 67081 86 + 87904 GAGTACATGTTGAATT-----GCCCAACTCCACAAACCTATGCTAGCTGAATT--CC---------TCCCCGTTGTACCCAGCATACTGTAATTCTGAAGGC -s Anc1.Anc1refChr7 25807 86 - 47259 GAGTACATGTTGAATT-----GCCCAACTCCACAAACCTATGCTAGCTGAATT--CC---------TCCCCGTTGTACCCAGCATACTGTAATTCTGAAGGC -s Anc2.Anc2refChr15 63955 86 + 86568 GAGTACATGTTGAATT-----GCCCAACTCCACAAACCTATGCTAGCTGAATT--CC---------TCCCCGTTGTACCCAGCATACTGTAATTCTGAATGC -s mr.mrrefChr5 102648 100 + 294540 AAGTGCTAGTTGGATGCAAAAGCACAACTTTACAAATCTCTACAAGCTGAGTT--CCTGGCCATATTCGCCCCTTTACCCTGTGCACTGTAGTTCTGAAGAC -s simCow_chr6.simCow.chr6 245518 84 + 602619 GAGTACATGTTGAATT-----GCCCAACTCCACACACCTATGCTAGATGAATC--CC---------ACCCAGTTGCGCCCAGCATACTGTAATTCTGA--GC -s simDog_chr6.simDog.chr6 236362 75 + 593897 GAGTACAAATTGAATT-----GCCCAACTTCACAA-----------CTGAATT--CC---------TTCCCGTTGTACCCAGCATACTGTAATTCTGAATAC -s simHuman_chr6.simHuman.chr6 328104 86 - 601863 GAGTACATGTTGAATT-----GCCCGACTCCACAACCCTGTGCTAGCTGAACT--CC---------TCACCAATATACCCAGCATACTGTAATACTGAAGGC -s simRat_chr6.simRat.chr6 239990 100 + 647215 AAGTGCTAGTGGGATGCAAACATACAGCTTTACACATGCCTACAAGCTGAGTT--CGTGGCCCTCAGCCCCCCTGTACCTGCTGCACTGTAGTTCTGAGGAC - -a -s simMouse_chr6.simMouse.chr6 250051 36 + 636262 CCTAAGATTGAGTACTAGTTCATTCCAAAACAATCA -s Anc0.Anc0refChr5 67167 36 + 87904 ATTAAGATTGAGTATTAGTTTGTTCCTAAACAATTG -s Anc1.Anc1refChr7 25893 36 - 47259 ATTAAGATTGAGTATTAGTTTGTTCCTAAACAATTG -s Anc2.Anc2refChr15 64041 36 + 86568 ATTGAGATTGAGTATTAGTTTGTTCTTAAGCAATTG -s mr.mrrefChr5 102748 36 + 294540 CCTAAGATTGAGTACTAGTTCATTCCAAAACAATTG -s simCow_chr6.simCow.chr6 245602 36 + 602619 ATTTAGATTGAGTATTAGTTTGTTTTTAAGCAATTG -s simDog_chr6.simDog.chr6 236437 36 + 593897 ATTGAGATTGACTATTAGTCTGTCCTTAAGCAATTG -s simHuman_chr6.simHuman.chr6 328211 36 - 601863 TTTAAGGTTGAGTCTTAGTTTGTTCCTAAATGATTG -s simRat_chr6.simRat.chr6 240090 36 + 647215 CCTAAGATTGAGTACAGGTTCATTCCAAAACAGTTG - -a -s simMouse_chr6.simMouse.chr6 250087 39 + 636262 CTTAACTACTTCCTTCTAAGTCTGATTTCCTCCTGAAGA -s Anc0.Anc0refChr5 67207 39 + 87904 TTTAAGTACTTCCTTCTAAGTTTAATCTCCTCTTTAATG -s Anc1.Anc1refChr7 25933 39 - 47259 TTTAAGTACTTCCTTCTAAGTTTAATCTCCTCTTTAATG -s Anc2.Anc2refChr15 64081 39 + 86568 TCCAAGTACTACCTTCTAAGTTTAATCTCCTCTTTAGTG -s mr.mrrefChr5 102784 39 + 294540 TTTAACTACTTCCTTCTAAGTCTGATTTCCTCCTTAAGA -s simCow_chr6.simCow.chr6 245642 34 + 602619 ----AGTATTACCTTCTGA-TATAATCTCCTCTTTAGTG -s simDog_chr6.simDog.chr6 236477 37 + 593897 TCCAAGTACTACCTTTTAAGTTTAATCTCCCTATTA--T -s simHuman_chr6.simHuman.chr6 328251 39 - 601863 TTTAAGTACTTCCTTCTAAGCTTAATCTCCTCTTTAATG -s simRat_chr6.simRat.chr6 240126 39 + 647215 TTTAACTACTTCCTTCTAAGTCTGATTTCCTCCTTAAGA - -a -s simMouse_chr6.simMouse.chr6 250126 1 + 636262 G -s Anc0.Anc0refChr5 67250 1 + 87904 G -s Anc1.Anc1refChr7 25976 1 - 47259 G -s Anc2.Anc2refChr15 64124 1 + 86568 G -s mr.mrrefChr5 102823 1 + 294540 G -s simCow_chr6.simCow.chr6 245680 1 + 602619 G -s simHuman_chr6.simHuman.chr6 328294 1 - 601863 G -s simRat_chr6.simRat.chr6 240165 1 + 647215 G - -a -s simMouse_chr6.simMouse.chr6 250127 33 + 636262 ATCAGAGGGGTCTGAGATACTCAAGTAGCTCCA -s Anc0.Anc0refChr5 67251 32 + 87904 ATCA-AGGGGTCTGAGACACTAAAGTAGCTCCA -s Anc1.Anc1refChr7 25977 32 - 47259 ATCA-AGGGGTCTGAGACACTAAAGTAGCTCCA -s Anc2.Anc2refChr15 64125 32 + 86568 ATCA-AGGGGTCTGAGACACTAAAGTAGCTGCT -s mr.mrrefChr5 102824 33 + 294540 ATCAGAGGGGTCTGAGATACTCAAGTAGCTCCA -s simCow_chr6.simCow.chr6 245685 32 + 602619 ATCC-AGGGGTCTGAGGCACTAAAGCAACTGCC -s simDog_chr6.simDog.chr6 236517 26 + 593897 -TCA-AA-----TAACACACCAAAGTAGCTGCT -s simHuman_chr6.simHuman.chr6 328295 32 - 601863 ATCA-AGGGGTCTGAGACACTAAAGTAGCTCCA -s simRat_chr6.simRat.chr6 240166 33 + 647215 ATCAGAGGGGTCTGAGATACTCAAGTAGTTCCA - -a -s simMouse_chr6.simMouse.chr6 250160 22 + 636262 AACCTGTGAGGTTCTATTTCAA -s Anc0.Anc0refChr5 67284 22 + 87904 AACCCATGAAGTTCTACTTCAA -s Anc1.Anc1refChr7 26010 22 - 47259 AACCCATGAAGTTCTACTTCAA -s Anc2.Anc2refChr15 64158 22 + 86568 AACCCATGAAGTTCTACTTAAA -s mr.mrrefChr5 102857 22 + 294540 AACCTGTGAGGTTCTATTTCAA -s simCow_chr6.simCow.chr6 245718 22 + 602619 AAGCTACGAAATTCTACCTGAA -s simDog_chr6.simDog.chr6 236544 22 + 593897 AACCCATGGAGTTCTATTTAAG -s simHuman_chr6.simHuman.chr6 328328 22 - 601863 AACCCATGAAGTTCTACTTCAA -s simRat_chr6.simRat.chr6 240199 22 + 647215 AACCTGTGAGGTTCTATTTCAA - -a -s simMouse_chr6.simMouse.chr6 250182 11 + 636262 TTGTGATATGG -s Anc0.Anc0refChr5 67307 11 + 87904 TTGTGTTATGG -s Anc1.Anc1refChr7 26033 11 - 47259 TTGTGTTATGG -s Anc2.Anc2refChr15 64181 11 + 86568 ATGTGTTATGG -s mr.mrrefChr5 102879 11 + 294540 TTGTGATATGG -s simCow_chr6.simCow.chr6 245741 11 + 602619 ATGTGTGATGG -s simDog_chr6.simDog.chr6 236567 10 + 593897 AT-CGTTATGG -s simHuman_chr6.simHuman.chr6 328354 11 - 601863 TGGTGCTATGG -s simRat_chr6.simRat.chr6 240221 9 + 647215 TTGTGATA--G - -a -s simMouse_chr6.simMouse.chr6 250193 17 + 636262 GACTTCTTGAAACGAGG -s Anc0.Anc0refChr5 67318 14 + 87904 GACTT---GAAACAAAG -s Anc1.Anc1refChr7 26044 14 - 47259 GACTT---GAAACAAAG -s Anc2.Anc2refChr15 64192 14 + 86568 GACTT---GAAACAAAG -s mr.mrrefChr5 102890 14 + 294540 GACTT---GAAACGAGG -s simCow_chr6.simCow.chr6 245753 14 + 602619 AATTT---GAGCCAAAG -s simDog_chr6.simDog.chr6 236577 14 + 593897 GACTT---GAAACAAGG -s simHuman_chr6.simHuman.chr6 328365 14 - 601863 GACTT---GATACAAAA -s simRat_chr6.simRat.chr6 240230 14 + 647215 GACTT---GAAATGAGG - -a -s simMouse_chr6.simMouse.chr6 250210 12 + 636262 TCTAGGTATGAG -s Anc0.Anc0refChr5 67332 12 + 87904 TCTAGGTATTGG -s Anc1.Anc1refChr7 26058 12 - 47259 TCTAGGTATTGG -s Anc2.Anc2refChr15 64206 12 + 86568 TCTAGGTAGTGG -s mr.mrrefChr5 102904 12 + 294540 TCTAGGTATGAG -s simCow_chr6.simCow.chr6 245767 12 + 602619 TCTAGGTAGTGG -s simDog_chr6.simDog.chr6 236591 12 + 593897 TTTAGGTAGTGG -s simHuman_chr6.simHuman.chr6 328381 12 - 601863 TCTAAGTATTGG -s simRat_chr6.simRat.chr6 240244 11 + 647215 TCTAGGT-TGAG - -a -s simMouse_chr6.simMouse.chr6 250222 3 + 636262 AAA -s Anc0.Anc0refChr5 67344 3 + 87904 AGA -s Anc1.Anc1refChr7 26070 3 - 47259 AGA -s Anc2.Anc2refChr15 64218 3 + 86568 AGA -s mr.mrrefChr5 102916 3 + 294540 AAA -s simCow_chr6.simCow.chr6 245779 3 + 602619 AGA -s simDog_chr6.simDog.chr6 236604 3 + 593897 AGT -s simHuman_chr6.simHuman.chr6 328393 3 - 601863 AGA -s simRat_chr6.simRat.chr6 240255 3 + 647215 AAA - -a -s simMouse_chr6.simMouse.chr6 250225 22 + 636262 GTGCACCCTAAAAATTGTGACA -s Anc0.Anc0refChr5 67347 20 + 87904 GTGCACC--AAAAACTGTAACA -s Anc1.Anc1refChr7 26073 20 - 47259 GTGCACC--AAAAACTGTAACA -s Anc2.Anc2refChr15 64221 20 + 86568 GTACACC--AAAAACTGTAGAA -s mr.mrrefChr5 102919 22 + 294540 GTGCACCCTAAAAATTGTGACA -s simCow_chr6.simCow.chr6 245784 19 + 602619 GTACACC--AAAAACTACAT-A -s simDog_chr6.simDog.chr6 236607 20 + 593897 ACACACC--AAGAAATGTAGAA -s simHuman_chr6.simHuman.chr6 328396 20 - 601863 GTGCGCC--AAAAGCTGTAACA -s simRat_chr6.simRat.chr6 240258 22 + 647215 GTGCACCCTAAACATTGTGACA - -a -s simMouse_chr6.simMouse.chr6 250247 4 + 636262 GGAG -s Anc0.Anc0refChr5 67367 4 + 87904 CTAG -s Anc1.Anc1refChr7 26093 4 - 47259 CTAG -s Anc2.Anc2refChr15 64241 4 + 86568 CTAG -s mr.mrrefChr5 102941 4 + 294540 GGAG -s simCow_chr6.simCow.chr6 245803 4 + 602619 CTGG -s simDog_chr6.simDog.chr6 236627 4 + 593897 CTAG -s simHuman_chr6.simHuman.chr6 328419 4 - 601863 TTTG -s simRat_chr6.simRat.chr6 240280 4 + 647215 GGAG - -a -s simMouse_chr6.simMouse.chr6 250322 11 + 636262 GTTTCTTAATG -s Anc0.Anc0refChr5 67442 9 + 87904 AATTCT--ATG -s Anc1.Anc1refChr7 26168 9 - 47259 AATTCT--ATG -s Anc2.Anc2refChr15 64318 9 + 86568 AATTCA--CTA -s mr.mrrefChr5 103016 9 + 294540 ATTTCT--ATG -s simCow_chr6.simCow.chr6 245878 9 + 602619 AATTCA--CCA -s simDog_chr6.simDog.chr6 236701 2 + 593897 ---------TA -s simHuman_chr6.simHuman.chr6 328503 9 - 601863 AATTCT--ATG -s simRat_chr6.simRat.chr6 240361 1 + 647215 A---------- - -a -s simMouse_chr6.simMouse.chr6 250370 1 + 636262 T -s Anc0.Anc0refChr5 67502 1 + 87904 T -s Anc1.Anc1refChr7 26228 1 - 47259 T -s Anc2.Anc2refChr15 64383 1 + 86568 T -s mr.mrrefChr5 103071 1 + 294540 T -s simCow_chr6.simCow.chr6 245943 1 + 602619 T -s simDog_chr6.simDog.chr6 236760 1 + 593897 T -s simHuman_chr6.simHuman.chr6 328563 1 - 601863 C -s simRat_chr6.simRat.chr6 240406 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 250448 11 + 636262 TATGACATATC -s Anc0.Anc0refChr5 67605 11 + 87904 TGTGACACATA -s Anc1.Anc1refChr7 26333 11 - 47259 TGTGACACATA -s Anc2.Anc2refChr15 64486 11 + 86568 TGTAACACATA -s mr.mrrefChr5 103157 11 + 294540 TATGACACATC -s simCow_chr6.simCow.chr6 246051 11 + 602619 TGTAACACATA -s simDog_chr6.simDog.chr6 236864 11 + 593897 TGTAATACATA -s simHuman_chr6.simHuman.chr6 328665 11 - 601863 TGTGACACACA -s simRat_chr6.simRat.chr6 240491 11 + 647215 TATGACACATC - -a -s simMouse_chr6.simMouse.chr6 250459 4 + 636262 CATT -s Anc0.Anc0refChr5 67618 4 + 87904 CCTT -s Anc1.Anc1refChr7 26346 4 - 47259 CCTT -s Anc2.Anc2refChr15 64499 4 + 86568 CCTT -s mr.mrrefChr5 103170 4 + 294540 CATT -s simCow_chr6.simCow.chr6 246064 4 + 602619 CCTT -s simDog_chr6.simDog.chr6 236877 4 + 593897 CCTT -s simHuman_chr6.simHuman.chr6 328678 4 - 601863 CCTT -s simRat_chr6.simRat.chr6 240504 4 + 647215 CATT - -a -s simMouse_chr6.simMouse.chr6 250463 58 + 636262 GAGCAAGCCATAGACCCACCAGCGAATTGATTCCGCGTTTTACAGGTTTGTGGCAAGT -s Anc0.Anc0refChr5 67622 56 + 87904 CAGTGACCCATAGGCCCACTGACAATTTGA--TTGCACTTAACTGGTGCATGGGAAGT -s Anc1.Anc1refChr7 26350 58 - 47259 CAGTGACCCATAGGCCCACTGACAATTTGATTTTGCACTTAACTGGTGCATGGGAAGT -s Anc2.Anc2refChr15 64503 56 + 86568 CAGTGACCCATAGGCCCACTGACAAGTTGA--TTGCACTTAACTGGTGCATGGGAAGT -s mr.mrrefChr5 103174 58 + 294540 GAGCAACCCATAGACCCACCAGCGATTTGATTCTGCATTTTACAGGTTTGTGGCAAGT -s simCow_chr6.simCow.chr6 246069 55 + 602619 AAGTGATACATGGGCACACTGGCAGGTTGA--TTGCA-TAAGCTGGTGCATGGGAACT -s simDog_chr6.simDog.chr6 236881 56 + 593897 CAGGGACCCATAGGCCAACTGACGAGTTGA--TTGTACTTAACTGGTGCATGGGGAGT -s simHuman_chr6.simHuman.chr6 328682 54 - 601863 CAGTGGCCCATAGGCCCACTGACAAT----GTTTGCACTTAACTGGTACATGGGAAGC -s simRat_chr6.simRat.chr6 240508 58 + 647215 GTGCAACCGATAGTCCCACCAGTGATTTGATTCTGTATTTTACAGGTTTGTGGCAAGT - -a -s simMouse_chr6.simMouse.chr6 250521 2 + 636262 GT -s Anc0.Anc0refChr5 67679 2 + 87904 GT -s Anc1.Anc1refChr7 26409 2 - 47259 GT -s Anc2.Anc2refChr15 64560 2 + 86568 CT -s mr.mrrefChr5 103232 2 + 294540 GT -s simCow_chr6.simCow.chr6 246125 2 + 602619 TT -s simDog_chr6.simDog.chr6 236938 2 + 593897 CT -s simHuman_chr6.simHuman.chr6 328737 2 - 601863 GT -s simRat_chr6.simRat.chr6 240566 2 + 647215 GT - -a -s simMouse_chr6.simMouse.chr6 250523 25 + 636262 AGTTCTGCTCAAAGGCCTCATAAGA -s Anc0.Anc0refChr5 67681 25 + 87904 ATTTATACTCCCTGGTCTCCTAAGT -s Anc1.Anc1refChr7 26411 25 - 47259 ATTTATACTCCCTGGTCTCCTAAGT -s Anc2.Anc2refChr15 64562 25 + 86568 ATTTATACTCCCAGGTCTCCTAAGT -s mr.mrrefChr5 103234 25 + 294540 AGTTCTGCTCAATGGCCTCATAAGA -s simCow_chr6.simCow.chr6 246131 25 + 602619 TTTTATAATCCTAGGTCACCTAAGT -s simDog_chr6.simDog.chr6 236940 25 + 593897 ATTTGTACTCTCAGGTCTCCTGAGT -s simHuman_chr6.simHuman.chr6 328739 25 - 601863 ATTTATACTCCCTGGACTCCTAAGT -s simRat_chr6.simRat.chr6 240568 23 + 647215 AGTT--GCTCAATGGCCTCATACGA - -a -s simMouse_chr6.simMouse.chr6 250548 18 + 636262 AAGTGCTGTTGACTAACA -s Anc0.Anc0refChr5 67706 18 + 87904 AGGTGTTATTTACTAACA -s Anc1.Anc1refChr7 26436 18 - 47259 AGGTGTTATTTACTAACA -s Anc2.Anc2refChr15 64587 18 + 86568 AGGTGTTATTTACTAACA -s mr.mrrefChr5 103259 18 + 294540 AAGTGTTGTTGACTAACA -s simCow_chr6.simCow.chr6 246156 18 + 602619 AAGTATTATTTACCAACC -s simDog_chr6.simDog.chr6 236966 18 + 593897 AGGTGCTGTTTGCTAAAA -s simHuman_chr6.simHuman.chr6 328764 18 - 601863 AGATGTTATTTACTAACA -s simRat_chr6.simRat.chr6 240591 18 + 647215 AAGTATTGTTGACTAACA - -a -s simMouse_chr6.simMouse.chr6 250566 5 + 636262 TCATA -s Anc0.Anc0refChr5 67724 5 + 87904 TGTTG -s Anc1.Anc1refChr7 26454 5 - 47259 TGTTG -s Anc2.Anc2refChr15 64605 5 + 86568 TGTTG -s mr.mrrefChr5 103277 5 + 294540 TCATA -s simCow_chr6.simCow.chr6 246175 5 + 602619 TGTTG -s simDog_chr6.simDog.chr6 236984 5 + 593897 TGTTG -s simHuman_chr6.simHuman.chr6 328782 5 - 601863 AGTTG -s simRat_chr6.simRat.chr6 240609 5 + 647215 TCCTA - -a -s simMouse_chr6.simMouse.chr6 250571 12 + 636262 TGGAACTGAATA -s Anc0.Anc0refChr5 67744 12 + 87904 TTGAAATGAATA -s Anc1.Anc1refChr7 26474 12 - 47259 TTGAAATGAATA -s Anc2.Anc2refChr15 64625 12 + 86568 TTGAAATCAATA -s mr.mrrefChr5 103296 12 + 294540 TGGAACTGAATA -s simCow_chr6.simCow.chr6 246195 12 + 602619 TTGAAATCAATA -s simDog_chr6.simDog.chr6 236993 12 + 593897 TTGAAATCAATA -s simHuman_chr6.simHuman.chr6 328802 12 - 601863 TTGAAATGAATG -s simRat_chr6.simRat.chr6 240628 12 + 647215 TCGAACTGAACA - -a -s simMouse_chr6.simMouse.chr6 250583 68 + 636262 TATATAACGTGCCAGTAACTAATTTATTGGGGGGACTATATTACATAAAAGTTTTGGTCTGCCCTAGG -s Anc0.Anc0refChr5 67756 62 + 87904 TATAGAAAAT----GTCATAAGTTTATTGGGGGGAC--TATTATATAAGAGATTTGGTCTGCCCTAGG -s Anc1.Anc1refChr7 26486 68 - 47259 TATAGAAAATATCAGTCATAAGTTTATTGGGGGGACTATATTATATAAGAGATTTGGTCTGCCCTAGG -s Anc2.Anc2refChr15 64637 62 + 86568 CAGAGAAAAT----GTCATAAGTTTATTGGGGGTAC--TATTATTTTAGAGATTTGGTCTGCCCCCGG -s mr.mrrefChr5 103308 68 + 294540 TATATAAAGTGCCAGTCACTAATTTATTGGGGGGACTATATTACATAAGAGATTTGGTCTGCCCTAGG -s simCow_chr6.simCow.chr6 246207 51 + 602619 CAAAGAAAAA----GTCAT-AGTTCATTGGGGGATC--TATACTTTTAGAGATTTGGT---------- -s simDog_chr6.simDog.chr6 237005 62 + 593897 CAGACAAAAT----GTCACAAGTTTATTGGAGCTAT--TATTATTTTAGAGATTCGGTCTGCCCCCGG -s simHuman_chr6.simHuman.chr6 328841 68 - 601863 TGTAGAAAATATCAGTCATGGGTCTGTTGTGGGGACTATATTATATACGAGATTTGGTCTCCCCTAGG -s simRat_chr6.simRat.chr6 240640 64 + 647215 TA----AAGTGGCAGTCACCAATTTATTGGGGGAACTATATTAGATAAGAGATTTGGTCTGCCCTAGG - -a -s simMouse_chr6.simMouse.chr6 250651 17 + 636262 CTTAGTTTATTGAACCC -s Anc0.Anc0refChr5 67818 17 + 87904 CTTAGTTTATTAAACCC -s Anc1.Anc1refChr7 26554 17 - 47259 CTTAGTTTATTAAACCC -s Anc2.Anc2refChr15 64699 17 + 86568 ATTAGTTTATTAAACCC -s mr.mrrefChr5 103376 17 + 294540 CTTAGTTTATTGAACCC -s simCow_chr6.simCow.chr6 246258 12 + 602619 -----TTTATGAAATCC -s simDog_chr6.simDog.chr6 237067 17 + 593897 ATTAGTTTATTAAACCC -s simHuman_chr6.simHuman.chr6 328909 17 - 601863 CTTGGTTTTTCAGACCA -s simRat_chr6.simRat.chr6 240705 17 + 647215 CTTAGTTTATTGAACCC - -a -s simMouse_chr6.simMouse.chr6 250668 9 + 636262 ATGGCAACC -s Anc0.Anc0refChr5 67835 4 + 87904 AT-----TC -s Anc1.Anc1refChr7 26571 4 - 47259 AT-----TC -s Anc2.Anc2refChr15 64720 4 + 86568 AT-----CC -s mr.mrrefChr5 103393 9 + 294540 ATGGCAATC -s simCow_chr6.simCow.chr6 246274 4 + 602619 GC-----CC -s simDog_chr6.simDog.chr6 237088 4 + 593897 AT-----CC -s simHuman_chr6.simHuman.chr6 328926 4 - 601863 AT-----TC -s simRat_chr6.simRat.chr6 240722 9 + 647215 ATGGTTATC - -a -s simMouse_chr6.simMouse.chr6 250677 39 + 636262 TTGGATGGATATTATAGACTAAGACACAACTGTCTAGGT -s Anc0.Anc0refChr5 67839 36 + 87904 CTGGA---ATATTCTAAACTGGGAAACCACTACCTGTGT -s Anc1.Anc1refChr7 26575 36 - 47259 CTGGA---ATATTCTAAACTGGGAAACCACTACCTGTGT -s Anc2.Anc2refChr15 64724 36 + 86568 CTGGA---ATATTCTAAACTGGGAAACCACTACCTGTGT -s mr.mrrefChr5 103402 39 + 294540 TTGGATGGATATTATAGACTAGGACACAACTGTCTAGGT -s simCow_chr6.simCow.chr6 246279 36 + 602619 CTGGA---ATATTCCAAACTGGGAAACCACTACCTATGT -s simDog_chr6.simDog.chr6 237092 36 + 593897 CTGGA---ATGTTCTAGACTTGGAAACCACTACCCGTGT -s simHuman_chr6.simHuman.chr6 328930 36 - 601863 CTGGA---ATATTCTCAAATGGGAAACTACTAGCTGTGT -s simRat_chr6.simRat.chr6 240731 39 + 647215 TTGGATGGATATTTAAGACTAGGACACAACTGTTTAGGT - -a -s simMouse_chr6.simMouse.chr6 250716 4 + 636262 ATCA -s Anc0.Anc0refChr5 67876 4 + 87904 ATCA -s Anc1.Anc1refChr7 26612 4 - 47259 ATCA -s Anc2.Anc2refChr15 64761 4 + 86568 ATCC -s mr.mrrefChr5 103441 4 + 294540 ATCA -s simCow_chr6.simCow.chr6 246316 4 + 602619 ATCT -s simDog_chr6.simDog.chr6 237129 4 + 593897 ATCC -s simHuman_chr6.simHuman.chr6 328967 4 - 601863 ATCA -s simRat_chr6.simRat.chr6 240770 4 + 647215 ATCA - -a -s simMouse_chr6.simMouse.chr6 250720 6 + 636262 TTAACT -s Anc0.Anc0refChr5 67880 6 + 87904 ATTACT -s Anc1.Anc1refChr7 26616 6 - 47259 ATTACT -s Anc2.Anc2refChr15 64765 6 + 86568 ATTACT -s mr.mrrefChr5 103445 6 + 294540 TTAACT -s simCow_chr6.simCow.chr6 246324 6 + 602619 ACTACT -s simDog_chr6.simDog.chr6 237133 4 + 593897 ATTA-- -s simHuman_chr6.simHuman.chr6 328971 6 - 601863 CTTACT -s simRat_chr6.simRat.chr6 240774 6 + 647215 TTAACT - -a -s simMouse_chr6.simMouse.chr6 250726 8 + 636262 GACAATAG -s Anc0.Anc0refChr5 67904 8 + 87904 GGTACTTG -s Anc1.Anc1refChr7 26640 8 - 47259 GGTACTTG -s Anc2.Anc2refChr15 64789 8 + 86568 GGTGCTTG -s mr.mrrefChr5 103451 8 + 294540 GACAATAG -s simCow_chr6.simCow.chr6 246352 8 + 602619 GGTTCTAG -s simDog_chr6.simDog.chr6 237147 8 + 593897 TGTGTTTT -s simHuman_chr6.simHuman.chr6 328995 8 - 601863 GGTACTTG -s simRat_chr6.simRat.chr6 240780 8 + 647215 GACAATAG - -a -s simMouse_chr6.simMouse.chr6 250734 9 + 636262 ACACCCCAG -s Anc0.Anc0refChr5 67914 9 + 87904 ACCCCCCAG -s Anc1.Anc1refChr7 26650 9 - 47259 ACCCCCCAG -s Anc2.Anc2refChr15 64811 9 + 86568 ACCCTCCTG -s mr.mrrefChr5 103459 9 + 294540 ACACCCCAG -s simCow_chr6.simCow.chr6 246376 9 + 602619 ATTCTCTGT -s simDog_chr6.simDog.chr6 237172 9 + 593897 ACCCTCCTG -s simHuman_chr6.simHuman.chr6 329005 9 - 601863 ACCCCCCAG -s simRat_chr6.simRat.chr6 240788 9 + 647215 ACACCCCAG - -a -s simMouse_chr6.simMouse.chr6 250743 20 + 636262 TCTAACTGGAAGCTCCCAGC -s Anc0.Anc0refChr5 67923 20 + 87904 CCAAAATAGAAACATCAAGC -s Anc1.Anc1refChr7 26659 20 - 47259 CCAAAATAGAAACATCAAGC -s Anc2.Anc2refChr15 64820 20 + 86568 TAAAAAAAAACACATCAAGC -s mr.mrrefChr5 103468 20 + 294540 CCTAACTGGAAGCTTCAAGC -s simCow_chr6.simCow.chr6 246385 20 + 602619 TAAAAAAAAACACATGACGC -s simDog_chr6.simDog.chr6 237183 18 + 593897 TAACTAAAAACAC--CGAGC -s simHuman_chr6.simHuman.chr6 329014 20 - 601863 CCCAAGTAGAAACATCAAGT -s simRat_chr6.simRat.chr6 240797 20 + 647215 CCTAACTGGAAGCTTCAAGC - -a -s simMouse_chr6.simMouse.chr6 250763 13 + 636262 ACATAAGTTATCA -s Anc0.Anc0refChr5 67943 10 + 87904 ACATAGGTT---A -s Anc1.Anc1refChr7 26679 10 - 47259 ACATAGGTT---A -s Anc2.Anc2refChr15 64840 10 + 86568 ATGTAGGTT---A -s mr.mrrefChr5 103488 13 + 294540 ACATAAGTTATCA -s simCow_chr6.simCow.chr6 246406 10 + 602619 ATGTAGGTT---A -s simDog_chr6.simDog.chr6 237201 10 + 593897 ATGTATGTT---A -s simHuman_chr6.simHuman.chr6 329034 10 - 601863 ACATAGTTT---A -s simRat_chr6.simRat.chr6 240817 13 + 647215 ACCTGAATTGTCA - -a -s simMouse_chr6.simMouse.chr6 250776 59 + 636262 ATACTTATGTACGTCCAGCTAGGCAAACAGCAATGGTGGATGCTAGGCAAACAGCATAG -s Anc0.Anc0refChr5 67953 49 + 87904 ATATTTGTGCACATGCAGCTTGGAAAACAGCAATGATGAATGCTAGTCA---------- -s Anc1.Anc1refChr7 26689 49 - 47259 ATATTTGTGCACATGCAGCTTGGAAAACAGCAATGATGAATGCTAGTCA---------- -s Anc2.Anc2refChr15 64850 49 + 86568 ATATTTGTGCCAATGCAGCTTGGAAAACAGCAATGATGAATGCTAGTCA---------- -s mr.mrrefChr5 103501 59 + 294540 ATACTTATGTACATCCAGCTAGGCAAACAGCAATGGTGGATGCTAGGCAAACAGCATAG -s simCow_chr6.simCow.chr6 246421 48 + 602619 ATATTTGTGCCAAT-CATCTTAGAAAATAGCAATGATGGATGCTAGTCA---------- -s simDog_chr6.simDog.chr6 237211 49 + 593897 AGATTTGTGCCAAAGCAGCTTGGACAACAGCAAAAATGAATGCTAGTCA---------- -s simHuman_chr6.simHuman.chr6 329044 49 - 601863 ATGTTTGTGCACATGCAGCTTGGAAAACAGTAATGATGAATGCTAGCCA---------- -s simRat_chr6.simRat.chr6 240830 59 + 647215 ATACTTATGTATATCCATCTAGCCAAACGGCAATGGTGGATGCTAGGCAAACATCATGG - -a -s simMouse_chr6.simMouse.chr6 250835 68 + 636262 ATGCTAGCTAAAGTCCATCCCAAACTACTACTGGTGTGGCCATGCCTGCCCACTACACTCCATAAGAA -s Anc0.Anc0refChr5 68002 49 + 87904 ---------GTACTCCATCTCAA---ACTT---GTGTGGCCATGCTTAC----CACACTCCCTAAATG -s Anc1.Anc1refChr7 26738 52 - 47259 ---------GTACTCCATCTCAA---ACTTGTGGTGTGGCCATGCTTAC----CACACTCCCTAAATG -s Anc2.Anc2refChr15 64899 49 + 86568 ---------GTACTTTATCTCAA---ACTT---GTGTGGCCACGCTTAC----CTGACGCCATATATG -s mr.mrrefChr5 103560 64 + 294540 ATGCTAGCTAAAGTCCATCCCAAACTACTACTGGTGTGGCCATGCCTGC----TACACTCCCTAAGTA -s simCow_chr6.simCow.chr6 246469 49 + 602619 ---------GTACGTTATCTCAA---GCTT---GTGTGGCCACGCTTAC----CCAGCACCATATGTG -s simDog_chr6.simDog.chr6 237260 49 + 593897 ---------GTACTTTATCTCAA---ACTT---GTGTAGCCACACTTAC----TTGATGCCATATATG -s simHuman_chr6.simHuman.chr6 329093 52 - 601863 ---------GTACTCCATCTCAA---ATTTGTGTGGTGGCCATGCTTAC----CACACTCCCTAATTG -s simRat_chr6.simRat.chr6 240890 64 + 647215 ATGCTAGGTAAAGTCCATCCCAAACAACTACTGGTGTGGCCATGCCCGC----TATGCTCCCTAAGTA - -a -s simMouse_chr6.simMouse.chr6 250903 24 + 636262 CAAATGTTAACTATAAGAGACCCT -s Anc0.Anc0refChr5 68051 17 + 87904 TAAATGTCAACTAT-------TAT -s Anc1.Anc1refChr7 26790 24 - 47259 TAAATGTCAACTATAATAAACTAT -s Anc2.Anc2refChr15 64948 17 + 86568 TAAATGTCAACTAT-------TAT -s mr.mrrefChr5 103624 24 + 294540 CAAATGTTAACTATAAGAGACTCT -s simCow_chr6.simCow.chr6 246518 17 + 602619 TAAGTGCCAACTAC-------TAT -s simDog_chr6.simDog.chr6 237309 17 + 593897 CAAATGTAAACTAT-------TAT -s simHuman_chr6.simHuman.chr6 329177 24 - 601863 TAAATGTCAACTATAATAAACTAT -s simRat_chr6.simRat.chr6 240954 24 + 647215 CAGACGTTAACTATAAGAGACTCT - -a -s simMouse_chr6.simMouse.chr6 250927 24 + 636262 GTCAACACTAAACTAGAATGTGGA -s Anc0.Anc0refChr5 68068 24 + 87904 GACGACAATAAACTAAAATTTAGT -s Anc1.Anc1refChr7 26814 24 - 47259 GACGACAATAAACTAAAATTTAGT -s Anc2.Anc2refChr15 64965 24 + 86568 TACGACAATAAACTAAAATTTAGT -s mr.mrrefChr5 103648 24 + 294540 GTCAACACTAAACTAAAATGTGGA -s simCow_chr6.simCow.chr6 246538 24 + 602619 TACAAAAATATACTGAAATTTAGT -s simDog_chr6.simDog.chr6 237326 24 + 593897 TACGACAATGAACTAGAATTGAGT -s simHuman_chr6.simHuman.chr6 329201 24 - 601863 GACGACAATAAACTAAAATTTAGT -s simRat_chr6.simRat.chr6 240978 24 + 647215 GTCAACACTAAACTAAAATGTGGC - -a -s simMouse_chr6.simMouse.chr6 250951 42 + 636262 TTTAATTTGCCACAGTGGAACTTGTTTTGAGCATGCCACCAG -s Anc0.Anc0refChr5 68092 40 + 87904 TGTAATTTGCTACAATGGATCCAG--TTGACCAGGTCCTGTG -s Anc1.Anc1refChr7 26838 42 - 47259 TGTAATTTGCTACAATGGATCCAGTATTGACCAGGTCCTGTG -s Anc2.Anc2refChr15 64989 40 + 86568 TGTAATTTGCTATGATGGATTCAG--TTTACTGGGTGCTGTG -s mr.mrrefChr5 103672 42 + 294540 TGTAATTTGCCACAGTGGAACTTGTTTTGACCATGCCACCAG -s simCow_chr6.simCow.chr6 246564 40 + 602619 TGTAATCTGCTATGATGGATTCAG--TTTACTGGGTGCTGTG -s simDog_chr6.simDog.chr6 237350 13 + 593897 CATAATTTGCAAT----------------------------- -s simHuman_chr6.simHuman.chr6 329225 42 - 601863 TGTGATTTGCTACAATGGATCCAACATTGTCCAGGTCCTGTG -s simRat_chr6.simRat.chr6 241002 42 + 647215 TGTAATTTGCCACAGTGGAGCTTGTTTTGGCCATGCTACCAG - -a -s simMouse_chr6.simMouse.chr6 250993 2 + 636262 TT -s Anc0.Anc0refChr5 68134 2 + 87904 AT -s Anc1.Anc1refChr7 26882 2 - 47259 AT -s Anc2.Anc2refChr15 65031 2 + 86568 AT -s mr.mrrefChr5 103714 2 + 294540 TT -s simCow_chr6.simCow.chr6 246606 2 + 602619 AT -s simHuman_chr6.simHuman.chr6 329269 2 - 601863 GG -s simRat_chr6.simRat.chr6 241044 2 + 647215 CT - -a -s simMouse_chr6.simMouse.chr6 250995 22 + 636262 ATAGAAACACTGAGAGCTATTA -s Anc0.Anc0refChr5 68136 22 + 87904 ATATGAACACTGACAGATATTA -s Anc1.Anc1refChr7 26884 22 - 47259 ATATGAACACTGACAGATATTA -s Anc2.Anc2refChr15 65033 22 + 86568 ACATGCACACCAACAGATATTA -s mr.mrrefChr5 103716 22 + 294540 ATAGAAACACTGAGAGCTATTA -s simCow_chr6.simCow.chr6 246608 22 + 602619 ACATGCACACCAACAGATATTA -s simHuman_chr6.simHuman.chr6 329273 22 - 601863 ATAAGAATGCTGACAGGTATTC -s simRat_chr6.simRat.chr6 241046 22 + 647215 GTAGAAACACTGAGAGTTGTTA - -a -s simMouse_chr6.simMouse.chr6 251017 11 + 636262 AGACCAATCTA -s Anc0.Anc0refChr5 68158 11 + 87904 ACACTAATCTT -s Anc1.Anc1refChr7 26906 11 - 47259 ACACTAATCTT -s Anc2.Anc2refChr15 65055 11 + 86568 ACACTTATCTT -s mr.mrrefChr5 103738 11 + 294540 AGACCAATCTA -s simCow_chr6.simCow.chr6 246630 11 + 602619 ACACTTAGCTT -s simDog_chr6.simDog.chr6 237363 4 + 593897 -------TCTT -s simHuman_chr6.simHuman.chr6 329296 11 - 601863 ACACTAATCTT -s simRat_chr6.simRat.chr6 241068 11 + 647215 AGACCAATCTA - -a -s simMouse_chr6.simMouse.chr6 251028 1 + 636262 A -s Anc0.Anc0refChr5 68171 1 + 87904 A -s Anc1.Anc1refChr7 26919 1 - 47259 A -s Anc2.Anc2refChr15 65068 1 + 86568 A -s mr.mrrefChr5 103749 1 + 294540 A -s simCow_chr6.simCow.chr6 246643 1 + 602619 A -s simDog_chr6.simDog.chr6 237369 1 + 593897 G -s simHuman_chr6.simHuman.chr6 329309 1 - 601863 A -s simRat_chr6.simRat.chr6 241079 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 251029 16 + 636262 GTATCTCCAAACGCTA -s Anc0.Anc0refChr5 68172 15 + 87904 GTATAT-CAAACACTA -s Anc1.Anc1refChr7 26920 16 - 47259 GTATATCCAAACACTA -s Anc2.Anc2refChr15 65069 15 + 86568 ATCTAT-CAAACGTTC -s mr.mrrefChr5 103750 16 + 294540 GTATCTCCAAACACTA -s simCow_chr6.simCow.chr6 246644 15 + 602619 ATGTAT-CAAACGTTC -s simDog_chr6.simDog.chr6 237370 4 + 593897 ATCT------------ -s simHuman_chr6.simHuman.chr6 329310 16 - 601863 GTATATCCAAACACTA -s simRat_chr6.simRat.chr6 241081 16 + 647215 GTATCTCCAAGCACTA - -a -s simMouse_chr6.simMouse.chr6 251045 17 + 636262 CCCTTATTATTTGCACA -s Anc0.Anc0refChr5 68195 17 + 87904 CGCTCACAATTCACATA -s Anc1.Anc1refChr7 26944 17 - 47259 CGCTCACAATTCACATA -s Anc2.Anc2refChr15 65092 17 + 86568 TGTTCACAATCCACATA -s mr.mrrefChr5 103766 17 + 294540 CCCTTACTATTTGCACA -s simCow_chr6.simCow.chr6 246667 17 + 602619 TGTTCACAATCCACATA -s simHuman_chr6.simHuman.chr6 329334 17 - 601863 CTCTCACATTTCACATA -s simRat_chr6.simRat.chr6 241097 17 + 647215 CCCTTACTATTTCCACA - -a -s simMouse_chr6.simMouse.chr6 251062 3 + 636262 TCA -s Anc0.Anc0refChr5 68214 3 + 87904 TCT -s Anc1.Anc1refChr7 26963 3 - 47259 TCT -s Anc2.Anc2refChr15 65111 3 + 86568 TCT -s mr.mrrefChr5 103783 3 + 294540 TCA -s simCow_chr6.simCow.chr6 246686 3 + 602619 TCT -s simDog_chr6.simDog.chr6 237381 1 + 593897 --T -s simHuman_chr6.simHuman.chr6 329353 3 - 601863 TCT -s simRat_chr6.simRat.chr6 241114 3 + 647215 TTA - -a -s simMouse_chr6.simMouse.chr6 251065 83 + 636262 CAACATTGTTTTACATAAGGACATAAGATGGTTATAGTGACCATTGTTTGAGACTACCCAGTGAGTAATAGACATGATCTGGT -s Anc0.Anc0refChr5 68217 83 + 87904 TAAGATCTTCTTACTTTAACACCTAAAATGGTGATTGTGGCCATGGTTTGAGACTACCTACTAAATAACAGACATGATATGGT -s Anc1.Anc1refChr7 26966 83 - 47259 TAAGATCTTCTTACTTTAACACCTAAAATGGTGATTGTGGCCATGGTTTGAGACTACCTACTAAATAACAGACATGATATGGT -s Anc2.Anc2refChr15 65114 83 + 86568 TAAGATCTTCTTGCTTTAACACCTACAATGGTGATTGCGGCCATGGTGTGATACTACCTACTAAATAACAGACATGATATGGT -s mr.mrrefChr5 103786 83 + 294540 TAACATTGTTTTACATTAGGACATAAGATGGTTATAGTGACCATTGTTTGAGACTACCCAGTGAGTAATAGACATGATCTGGT -s simCow_chr6.simCow.chr6 246689 80 + 602619 TTAGATTTTCTTTCTTTAACATCCACTATGGTGACTGAGGCTG---TGTGATACTACCTGTTAAGTAACATACAGAATATGGT -s simDog_chr6.simDog.chr6 237382 82 + 593897 TATCATCTTCTTGCTTAAACACCTGCAATGGTGATTGCAGCCATGGTGTGATATTACCTACTAAATAACAGATATG-TATGGT -s simHuman_chr6.simHuman.chr6 329356 75 - 601863 TAAGATATTCCTACCTTAATACCTAAAATGGTAATTGTGGCCATGGTTTGAGACC--------AATAGCAGACATGAGAGGGT -s simRat_chr6.simRat.chr6 241122 80 + 647215 TAACACCATTGTAAATTAGGGCAGAAGA---TTATAGTGACCATTGTTTGAGACTACTCAATATGTTATAGACATGATCTGGT - -a -s simMouse_chr6.simMouse.chr6 251148 22 + 636262 GTTAGTTAACAGTATTAAAATA -s Anc0.Anc0refChr5 68301 22 + 87904 GTTAGTTAATGGTATTAAAATA -s Anc1.Anc1refChr7 27050 22 - 47259 GTTAGTTAATGGTATTAAAATA -s Anc2.Anc2refChr15 65198 22 + 86568 GTTAGTTAATGGTATTGAAATA -s mr.mrrefChr5 103869 22 + 294540 GTTAGTTAACAGTATTAAAATA -s simCow_chr6.simCow.chr6 246770 22 + 602619 GTTAGTTAATGATAGGGGAATA -s simDog_chr6.simDog.chr6 237465 22 + 593897 GGTAGTTAATGGCATTGAGATA -s simHuman_chr6.simHuman.chr6 329432 22 - 601863 GTTAGTTAATGGTATTAAAATA -s simRat_chr6.simRat.chr6 241202 22 + 647215 GTTAGTTAACAGTATTAAAATA - -a -s simMouse_chr6.simMouse.chr6 251170 3 + 636262 GAC -s Anc0.Anc0refChr5 68323 3 + 87904 GTC -s Anc1.Anc1refChr7 27072 3 - 47259 GTC -s Anc2.Anc2refChr15 65220 3 + 86568 GTC -s mr.mrrefChr5 103891 3 + 294540 GAC -s simCow_chr6.simCow.chr6 246792 3 + 602619 GTC -s simDog_chr6.simDog.chr6 237491 3 + 593897 GGC -s simHuman_chr6.simHuman.chr6 329454 3 - 601863 GTC -s simRat_chr6.simRat.chr6 241224 3 + 647215 GAT - -a -s simMouse_chr6.simMouse.chr6 251173 4 + 636262 TGTG -s Anc0.Anc0refChr5 68326 1 + 87904 C--- -s Anc1.Anc1refChr7 27075 1 - 47259 C--- -s Anc2.Anc2refChr15 65223 1 + 86568 C--- -s mr.mrrefChr5 103894 4 + 294540 TGTG -s simCow_chr6.simCow.chr6 246798 1 + 602619 C--- -s simDog_chr6.simDog.chr6 237494 1 + 593897 C--- -s simHuman_chr6.simHuman.chr6 329457 1 - 601863 C--- -s simRat_chr6.simRat.chr6 241227 4 + 647215 TGCA - -a -s simMouse_chr6.simMouse.chr6 251177 7 + 636262 ATCTGCT -s Anc0.Anc0refChr5 68327 7 + 87904 ATCTGTT -s Anc1.Anc1refChr7 27076 7 - 47259 ATCTGTT -s Anc2.Anc2refChr15 65224 7 + 86568 ATGTGTT -s mr.mrrefChr5 103898 7 + 294540 ATCTGCT -s mr.mrrefChr5 189941 7 - 294540 ATCTGTC -s simCow_chr6.simCow.chr6 246799 7 + 602619 ATCCGCT -s simDog_chr6.simDog.chr6 237495 7 + 593897 ATGTGTT -s simHuman_chr6.simHuman.chr6 329458 7 - 601863 ATTTGTT -s simMouse_chr6.simMouse.chr6 384321 7 - 636262 ATCTGTC -s simRat_chr6.simRat.chr6 405336 7 - 647215 ATCTGTC -s simRat_chr6.simRat.chr6 241231 7 + 647215 ATCTGCT - -a -s simMouse_chr6.simMouse.chr6 251184 14 + 636262 GCTAAGACATCTTA -s Anc0.Anc0refChr5 68334 5 + 87904 G---------CTTA -s Anc1.Anc1refChr7 27083 14 - 47259 GCTAAGATGTCTTA -s Anc2.Anc2refChr15 65231 5 + 86568 G---------CTTA -s mr.mrrefChr5 103905 14 + 294540 GCTAAGACATCTTA -s mr.mrrefChr5 189948 14 - 294540 ACTAAGATGTCCAG -s simCow_chr6.simCow.chr6 246806 5 + 602619 G---------CTCA -s simDog_chr6.simDog.chr6 237504 5 + 593897 G---------GGTA -s simHuman_chr6.simHuman.chr6 329465 5 - 601863 GCT---------TA -s simMouse_chr6.simMouse.chr6 384328 14 - 636262 ACTAAGATGTCCAG -s simRat_chr6.simRat.chr6 405343 14 - 647215 ACTAAGATGTCCAG -s simRat_chr6.simRat.chr6 241238 14 + 647215 GTTTAGACATCCTA - -a -s simMouse_chr6.simMouse.chr6 251198 10 + 636262 TACCACTTCT -s Anc0.Anc0refChr5 68339 10 + 87904 TACCACTCCT -s Anc1.Anc1refChr7 27097 10 - 47259 TACCACTCCT -s Anc2.Anc2refChr15 65236 10 + 86568 TACCACTCAT -s mr.mrrefChr5 103919 10 + 294540 TACCACTTCT -s mr.mrrefChr5 189962 10 - 294540 TACCACTCCC -s simCow_chr6.simCow.chr6 246818 10 + 602619 TACCACTCAT -s simDog_chr6.simDog.chr6 237509 6 + 593897 TATCAT---- -s simHuman_chr6.simHuman.chr6 329470 10 - 601863 CCCCACCCCT -s simMouse_chr6.simMouse.chr6 384342 10 - 636262 TACCACTCCC -s simRat_chr6.simRat.chr6 405357 10 - 647215 TACCACTCCT -s simRat_chr6.simRat.chr6 241252 10 + 647215 TACCACTTCT - -a -s simMouse_chr6.simMouse.chr6 251208 1 + 636262 G -s Anc0.Anc0refChr5 68349 1 + 87904 G -s Anc1.Anc1refChr7 27107 1 - 47259 G -s Anc2.Anc2refChr15 65246 1 + 86568 G -s mr.mrrefChr5 103929 1 + 294540 G -s simCow_chr6.simCow.chr6 246828 1 + 602619 G -s simHuman_chr6.simHuman.chr6 329480 1 - 601863 G -s simRat_chr6.simRat.chr6 241262 1 + 647215 G - -a -s simMouse_chr6.simMouse.chr6 251209 9 + 636262 TCCTGGGTG -s Anc0.Anc0refChr5 68350 9 + 87904 TACTGGACG -s Anc1.Anc1refChr7 27108 9 - 47259 TACTGGACG -s Anc2.Anc2refChr15 65247 9 + 86568 CACTGGGCG -s mr.mrrefChr5 103930 9 + 294540 TCCTGGATG -s mr.mrrefChr5 189972 9 - 294540 TACTGGATG -s simCow_chr6.simCow.chr6 246829 9 + 602619 CACTGGGCG -s simDog_chr6.simDog.chr6 237515 7 + 593897 --CTAGGCG -s simHuman_chr6.simHuman.chr6 329481 9 - 601863 TGCTGGACA -s simMouse_chr6.simMouse.chr6 384352 9 - 636262 TACTGGATG -s simRat_chr6.simRat.chr6 405368 9 - 647215 TACTGGATA -s simRat_chr6.simRat.chr6 241263 9 + 647215 TACTGGATG - -a -s simMouse_chr6.simMouse.chr6 251218 13 + 636262 CAATGCTTCTTGT -s Anc0.Anc0refChr5 68361 13 + 87904 CTTAGCTACTTGC -s Anc1.Anc1refChr7 27119 13 - 47259 CTTAGCTACTTGC -s Anc2.Anc2refChr15 65258 13 + 86568 CTTAGCTACTTGC -s mr.mrrefChr5 103939 13 + 294540 CAATGCTTCTTGT -s mr.mrrefChr5 189983 13 - 294540 CGTAGCTACTTTT -s simCow_chr6.simCow.chr6 246840 13 + 602619 CTTAGCTACATGC -s simDog_chr6.simDog.chr6 237524 13 + 593897 CTTAGCTACTTGC -s simHuman_chr6.simHuman.chr6 329492 13 - 601863 CTCAGCTACGTGC -s simMouse_chr6.simMouse.chr6 384363 13 - 636262 CGTAGCTACTTTT -s simRat_chr6.simRat.chr6 405379 13 - 647215 CTAAGCTATTTCT -s simRat_chr6.simRat.chr6 241272 13 + 647215 CAATGCTTCTTGT - -a -s simMouse_chr6.simMouse.chr6 251231 2 + 636262 GA -s Anc0.Anc0refChr5 68382 2 + 87904 AA -s Anc1.Anc1refChr7 27140 2 - 47259 AA -s Anc2.Anc2refChr15 65279 2 + 86568 AA -s mr.mrrefChr5 103952 2 + 294540 GA -s mr.mrrefChr5 189996 2 - 294540 GA -s simDog_chr6.simDog.chr6 237545 2 + 593897 AA -s simHuman_chr6.simHuman.chr6 329513 2 - 601863 AA -s simMouse_chr6.simMouse.chr6 384376 2 - 636262 GA -s simRat_chr6.simRat.chr6 405392 2 - 647215 GA -s simRat_chr6.simRat.chr6 241285 2 + 647215 GA - -a -s simMouse_chr6.simMouse.chr6 251233 3 + 636262 CTC -s Anc0.Anc0refChr5 68384 3 + 87904 GTC -s Anc1.Anc1refChr7 27142 3 - 47259 GTC -s Anc2.Anc2refChr15 65281 3 + 86568 GTC -s mr.mrrefChr5 103954 3 + 294540 CTC -s simDog_chr6.simDog.chr6 237547 3 + 593897 GTC -s simHuman_chr6.simHuman.chr6 329515 3 - 601863 GTC -s simRat_chr6.simRat.chr6 241287 3 + 647215 CTC - -a -s simMouse_chr6.simMouse.chr6 251236 39 + 636262 AAAGTTTGAACTACATATGCTACATGTTACTTAGTTGGA -s Anc0.Anc0refChr5 68387 39 + 87904 AGAGTTTGGAATACTTATTCCACATGTTACTTAGTAGGA -s Anc1.Anc1refChr7 27145 39 - 47259 AGAGTTTGGAATACTTATTCCACATGTTACTTAGTAGGA -s Anc2.Anc2refChr15 65284 39 + 86568 AGAGTTTGGAATACTTATTCCATATGTTACTTAGTAGGA -s mr.mrrefChr5 103957 39 + 294540 AAAGTTTGAACTACATATGCTACATGTTACTTAGTTGGA -s mr.mrrefChr5 189998 39 - 294540 AGGGTTTGAATTACTGATTCCACATGCTATCTAGTAGGA -s simCow_chr6.simCow.chr6 246861 34 + 602619 -----CTTGGCTGCTTATTCCATATCTTCCTTTGTAGGA -s simDog_chr6.simDog.chr6 237550 39 + 593897 AGAGTTTGAAATACTTATTTCATATGATACCTAGGAGGA -s simHuman_chr6.simHuman.chr6 329518 39 - 601863 AGAATTTAGAATACTTATGCCACATGTTGCTTAGTAGGA -s simMouse_chr6.simMouse.chr6 384378 39 - 636262 AGGGTTTGAATTACTGATTCCACATGCTATCTAGTAGGA -s simRat_chr6.simRat.chr6 405394 39 - 647215 AGGGTTTGAATTACTTATTTCCCATGTTACGTAGTCGGA -s simRat_chr6.simRat.chr6 241290 39 + 647215 AAAGTTTGAACGACATATTCTACATGTTATTTCGTCAAA - -a -s simMouse_chr6.simMouse.chr6 251275 15 + 636262 AAATGCACTAATTTT -s Anc0.Anc0refChr5 68426 15 + 87904 AAGTGTACTAATTTG -s Anc1.Anc1refChr7 27184 15 - 47259 AAGTGTACTAATTTG -s Anc2.Anc2refChr15 65323 15 + 86568 AAGTGTACTAATTTG -s mr.mrrefChr5 103996 15 + 294540 AAATGCACTAATTTT -s mr.mrrefChr5 190037 15 - 294540 AGATTCACTAATTTT -s simCow_chr6.simCow.chr6 246895 15 + 602619 AAGTGTACTAATTTG -s simDog_chr6.simDog.chr6 237589 15 + 593897 AAGTGTACTGATATG -s simHuman_chr6.simHuman.chr6 329557 15 - 601863 AAGTGTACTAACTTG -s simMouse_chr6.simMouse.chr6 384419 15 - 636262 AGATTCACTAATTTT -s simRat_chr6.simRat.chr6 405433 15 - 647215 AGATTAACTAATTTT -s simRat_chr6.simRat.chr6 241329 15 + 647215 AACTGCACTAATTTT - -a -s simMouse_chr6.simMouse.chr6 251290 26 + 636262 ATAACACCCCACACAAGTGCACACAG -s Anc0.Anc0refChr5 68446 15 + 87904 AGAACGCCCCA---------ACA--A -s Anc1.Anc1refChr7 27204 24 - 47259 AGAACGCCCCACACAGGTGGACA--A -s Anc2.Anc2refChr15 65343 15 + 86568 AGAACGCCCCA---------ATA--G -s mr.mrrefChr5 104016 24 + 294540 ATAACACCCCACACAAGTGCACA--G -s mr.mrrefChr5 190057 24 - 294540 ATAACGTCCAACACAGGTGGACA--A -s simCow_chr6.simCow.chr6 246915 15 + 602619 CGAACTCCCCA---------CAA--G -s simDog_chr6.simDog.chr6 237609 15 + 593897 AGAATGCCCCA---------ATA--G -s simHuman_chr6.simHuman.chr6 329577 18 - 601863 TGAACGCCCCACACAGGT-------- -s simMouse_chr6.simMouse.chr6 384439 24 - 636262 ATAACGTCCAACACAGGTGGACA--A -s simRat_chr6.simRat.chr6 405453 24 - 647215 ATAACATCCAACACAGGTGCACA--A -s simRat_chr6.simRat.chr6 241349 24 + 647215 ATAACACCCCACACAAGTGCACA--A - -a -s simMouse_chr6.simMouse.chr6 251316 12 + 636262 GAGATTCCAATG -s Anc0.Anc0refChr5 68461 12 + 87904 GAGTTTCCAATC -s Anc1.Anc1refChr7 27228 12 - 47259 GAGTTTCCAATC -s Anc2.Anc2refChr15 65358 12 + 86568 GTGTTTTGAATC -s mr.mrrefChr5 104040 12 + 294540 GAGTTTCCAATG -s mr.mrrefChr5 190083 12 - 294540 GGGTTTCCAGTG -s simCow_chr6.simCow.chr6 246930 12 + 602619 GTGGTTTGTATC -s simDog_chr6.simDog.chr6 237624 12 + 593897 GGTTTTTGAATC -s simHuman_chr6.simHuman.chr6 329595 10 - 601863 --GTTTCCAATC -s simMouse_chr6.simMouse.chr6 384465 12 - 636262 GGGTTTCCAGTG -s simRat_chr6.simRat.chr6 405479 12 - 647215 GAGTTGCCAATG -s simRat_chr6.simRat.chr6 241373 12 + 647215 GAGTTTCCAATG - -a -s simMouse_chr6.simMouse.chr6 251328 1 + 636262 T -s Anc0.Anc0refChr5 68473 1 + 87904 T -s Anc1.Anc1refChr7 27240 1 - 47259 T -s Anc2.Anc2refChr15 65370 1 + 86568 T -s mr.mrrefChr5 104052 1 + 294540 T -s simCow_chr6.simCow.chr6 246942 1 + 602619 T -s simDog_chr6.simDog.chr6 237636 1 + 593897 T -s simHuman_chr6.simHuman.chr6 329605 1 - 601863 A -s simRat_chr6.simRat.chr6 241385 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 251329 1 + 636262 T -s Anc0.Anc0refChr5 68474 1 + 87904 T -s Anc1.Anc1refChr7 27241 1 - 47259 T -s Anc2.Anc2refChr15 65371 1 + 86568 T -s mr.mrrefChr5 104053 1 + 294540 T -s mr.mrrefChr5 190095 1 - 294540 C -s simCow_chr6.simCow.chr6 246943 1 + 602619 T -s simDog_chr6.simDog.chr6 237637 1 + 593897 T -s simHuman_chr6.simHuman.chr6 329606 1 - 601863 T -s simMouse_chr6.simMouse.chr6 384477 1 - 636262 C -s simRat_chr6.simRat.chr6 405491 1 - 647215 C -s simRat_chr6.simRat.chr6 241386 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 251330 14 + 636262 CCTGTACAGGGGCA -s Anc0.Anc0refChr5 68475 14 + 87904 CCTATACCTGGCTA -s Anc1.Anc1refChr7 27242 14 - 47259 CCTATACCTGGCTA -s Anc2.Anc2refChr15 65372 14 + 86568 CCTATACCTGGCTA -s mr.mrrefChr5 104054 14 + 294540 CCTGTACATGGGCA -s mr.mrrefChr5 190096 14 - 294540 CCTGTGCCTGGTCC -s simCow_chr6.simCow.chr6 246944 14 + 602619 CCCATACCTGTCTA -s simDog_chr6.simDog.chr6 237638 13 + 593897 CCTGTACCTGGC-A -s simHuman_chr6.simHuman.chr6 329607 14 - 601863 TCTATACCTGGCTA -s simMouse_chr6.simMouse.chr6 384479 14 - 636262 CCTGTGCCTGGTCC -s simRat_chr6.simRat.chr6 405492 14 - 647215 CCTGTGCCTGCTCC -s simRat_chr6.simRat.chr6 241387 14 + 647215 CCTGTACATGGGCA - -a -s simMouse_chr6.simMouse.chr6 251344 4 + 636262 ACTT -s Anc0.Anc0refChr5 68489 4 + 87904 ACTT -s Anc1.Anc1refChr7 27256 4 - 47259 ACTT -s Anc2.Anc2refChr15 65386 4 + 86568 ACTT -s mr.mrrefChr5 104068 4 + 294540 ACTT -s mr.mrrefChr5 190110 4 - 294540 ACTT -s simCow_chr6.simCow.chr6 246958 4 + 602619 ACAT -s simDog_chr6.simDog.chr6 237651 4 + 593897 ACTT -s simHuman_chr6.simHuman.chr6 329621 4 - 601863 ACTT -s simMouse_chr6.simMouse.chr6 384493 4 - 636262 ACTT -s simRat_chr6.simRat.chr6 405609 4 - 647215 ATTT -s simRat_chr6.simRat.chr6 241401 4 + 647215 ATTT - -a -s simMouse_chr6.simMouse.chr6 251348 2 + 636262 AA -s Anc0.Anc0refChr5 68493 2 + 87904 GA -s Anc1.Anc1refChr7 27260 2 - 47259 GA -s Anc2.Anc2refChr15 65390 2 + 86568 GA -s mr.mrrefChr5 104072 2 + 294540 AA -s mr.mrrefChr5 190114 2 - 294540 AA -s simCow_chr6.simCow.chr6 246974 2 + 602619 TA -s simDog_chr6.simDog.chr6 237655 2 + 593897 GA -s simHuman_chr6.simHuman.chr6 329625 2 - 601863 GG -s simMouse_chr6.simMouse.chr6 384497 2 - 636262 AA -s simRat_chr6.simRat.chr6 405613 2 - 647215 CA -s simRat_chr6.simRat.chr6 241405 2 + 647215 AA - -a -s simMouse_chr6.simMouse.chr6 251350 10 + 636262 TCACAAGTAT -s Anc0.Anc0refChr5 68500 10 + 87904 TCACATGGTG -s Anc1.Anc1refChr7 27267 10 - 47259 TCACATGGTG -s Anc2.Anc2refChr15 65397 10 + 86568 TAACATGGTG -s mr.mrrefChr5 104079 10 + 294540 TCACAAGTAT -s mr.mrrefChr5 190121 10 - 294540 TCAGAAGTCT -s simCow_chr6.simCow.chr6 246981 10 + 602619 TCACACTGTG -s simDog_chr6.simDog.chr6 237662 8 + 593897 TAA--TGGTG -s simHuman_chr6.simHuman.chr6 329630 10 - 601863 TGACATGGTG -s simMouse_chr6.simMouse.chr6 384504 10 - 636262 TCAGAAGTCT -s simRat_chr6.simRat.chr6 405620 10 - 647215 CCAGAAGTTT -s simRat_chr6.simRat.chr6 241412 10 + 647215 TCACAAGTAT - -a -s simMouse_chr6.simMouse.chr6 251360 1 + 636262 T -s Anc0.Anc0refChr5 68510 1 + 87904 T -s Anc1.Anc1refChr7 27277 1 - 47259 T -s Anc2.Anc2refChr15 65407 1 + 86568 T -s mr.mrrefChr5 104089 1 + 294540 T -s mr.mrrefChr5 190131 1 - 294540 C -s simCow_chr6.simCow.chr6 246992 1 + 602619 C -s simDog_chr6.simDog.chr6 237670 1 + 593897 T -s simHuman_chr6.simHuman.chr6 329640 1 - 601863 T -s simMouse_chr6.simMouse.chr6 384514 1 - 636262 C -s simRat_chr6.simRat.chr6 405630 1 - 647215 T -s simRat_chr6.simRat.chr6 241422 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 251361 5 + 636262 ATTCA -s Anc0.Anc0refChr5 68511 4 + 87904 ATCT- -s Anc1.Anc1refChr7 27278 5 - 47259 ATCTA -s Anc2.Anc2refChr15 65408 4 + 86568 ATCT- -s mr.mrrefChr5 104090 5 + 294540 ATTTA -s mr.mrrefChr5 190132 5 - 294540 GTCGA -s simCow_chr6.simCow.chr6 246993 4 + 602619 ATAT- -s simDog_chr6.simDog.chr6 237671 4 + 593897 ATCT- -s simHuman_chr6.simHuman.chr6 329641 5 - 601863 ATCTA -s simMouse_chr6.simMouse.chr6 384515 5 - 636262 GTCGA -s simRat_chr6.simRat.chr6 405631 5 - 647215 GTTCA -s simRat_chr6.simRat.chr6 241439 5 + 647215 ACTTA - -a -s simMouse_chr6.simMouse.chr6 251366 2 + 636262 AA -s Anc0.Anc0refChr5 68515 2 + 87904 AA -s Anc1.Anc1refChr7 27283 2 - 47259 AA -s Anc2.Anc2refChr15 65412 2 + 86568 AA -s mr.mrrefChr5 104095 2 + 294540 AA -s mr.mrrefChr5 190137 2 - 294540 AA -s simCow_chr6.simCow.chr6 246997 2 + 602619 AA -s simDog_chr6.simDog.chr6 237675 1 + 593897 A- -s simHuman_chr6.simHuman.chr6 329646 2 - 601863 AG -s simMouse_chr6.simMouse.chr6 384520 2 - 636262 AA -s simRat_chr6.simRat.chr6 405636 2 - 647215 CA -s simRat_chr6.simRat.chr6 241449 2 + 647215 AA - -a -s simMouse_chr6.simMouse.chr6 251368 3 + 636262 CTT -s Anc0.Anc0refChr5 68523 3 + 87904 CTT -s Anc1.Anc1refChr7 27291 3 - 47259 CTT -s Anc2.Anc2refChr15 65420 3 + 86568 CTA -s mr.mrrefChr5 104097 3 + 294540 CTT -s mr.mrrefChr5 190139 3 - 294540 GTT -s simCow_chr6.simCow.chr6 247010 3 + 602619 CAA -s simDog_chr6.simDog.chr6 237676 3 + 593897 CTA -s simHuman_chr6.simHuman.chr6 329656 3 - 601863 CTC -s simMouse_chr6.simMouse.chr6 384522 3 - 636262 GTT -s simRat_chr6.simRat.chr6 405638 3 - 647215 GTG -s simRat_chr6.simRat.chr6 241451 3 + 647215 CTT - -a -s simMouse_chr6.simMouse.chr6 251371 3 + 636262 GTG -s Anc0.Anc0refChr5 68526 3 + 87904 ATG -s Anc1.Anc1refChr7 27294 3 - 47259 ATG -s Anc2.Anc2refChr15 65423 3 + 86568 ACA -s mr.mrrefChr5 104100 3 + 294540 ATG -s simCow_chr6.simCow.chr6 247013 3 + 602619 GCA -s simDog_chr6.simDog.chr6 237679 3 + 593897 ACA -s simHuman_chr6.simHuman.chr6 329659 3 - 601863 ATG -s simRat_chr6.simRat.chr6 241454 3 + 647215 AAG - -a -s simMouse_chr6.simMouse.chr6 251374 12 + 636262 CTCTAGCAGTCT -s Anc0.Anc0refChr5 68529 12 + 87904 TTCTAGAAGTCT -s Anc1.Anc1refChr7 27297 12 - 47259 TTCTAGAAGTCT -s Anc2.Anc2refChr15 65426 12 + 86568 GTCTTGATGTCT -s mr.mrrefChr5 104103 12 + 294540 TTCTAGCAGTCT -s mr.mrrefChr5 190142 12 - 294540 TTCCAGCAGTCT -s simCow_chr6.simCow.chr6 247016 12 + 602619 GTCTTAATGGCT -s simDog_chr6.simDog.chr6 237682 10 + 593897 GTCTTGA--TCT -s simHuman_chr6.simHuman.chr6 329662 12 - 601863 TTCCAGAAGTCT -s simMouse_chr6.simMouse.chr6 384525 12 - 636262 TTCCAGCAGTCT -s simRat_chr6.simRat.chr6 405641 12 - 647215 TTCCAGCAATCT -s simRat_chr6.simRat.chr6 241457 8 + 647215 TTCAAGCA---- - -a -s simMouse_chr6.simMouse.chr6 251386 1 + 636262 C -s Anc0.Anc0refChr5 68542 1 + 87904 G -s Anc1.Anc1refChr7 27310 1 - 47259 G -s Anc2.Anc2refChr15 65439 1 + 86568 G -s mr.mrrefChr5 104115 1 + 294540 C -s mr.mrrefChr5 190155 1 - 294540 T -s simCow_chr6.simCow.chr6 247029 1 + 602619 A -s simDog_chr6.simDog.chr6 237693 1 + 593897 G -s simHuman_chr6.simHuman.chr6 329675 1 - 601863 G -s simMouse_chr6.simMouse.chr6 384538 1 - 636262 T -s simRat_chr6.simRat.chr6 405654 1 - 647215 G - -a -s simMouse_chr6.simMouse.chr6 251387 2 + 636262 AA -s Anc0.Anc0refChr5 68543 2 + 87904 AC -s Anc1.Anc1refChr7 27311 2 - 47259 AC -s Anc2.Anc2refChr15 65440 2 + 86568 AT -s mr.mrrefChr5 104116 2 + 294540 AA -s mr.mrrefChr5 190156 2 - 294540 AC -s simCow_chr6.simCow.chr6 247030 2 + 602619 AT -s simDog_chr6.simDog.chr6 237694 2 + 593897 AT -s simHuman_chr6.simHuman.chr6 329676 2 - 601863 AC -s simMouse_chr6.simMouse.chr6 384539 2 - 636262 AC -s simRat_chr6.simRat.chr6 405656 2 - 647215 AC - -a -s simMouse_chr6.simMouse.chr6 251389 5 + 636262 ATCAT -s Anc0.Anc0refChr5 68546 5 + 87904 GTCAT -s Anc1.Anc1refChr7 27314 5 - 47259 GTCAT -s Anc2.Anc2refChr15 65443 5 + 86568 GTCAT -s mr.mrrefChr5 104118 5 + 294540 ATCAT -s mr.mrrefChr5 190158 4 - 294540 ATCA- -s simCow_chr6.simCow.chr6 247033 5 + 602619 GTTAT -s simDog_chr6.simDog.chr6 237697 5 + 593897 GTCAT -s simHuman_chr6.simHuman.chr6 329679 5 - 601863 GTCAT -s simMouse_chr6.simMouse.chr6 384541 4 - 636262 ATCA- -s simRat_chr6.simRat.chr6 405658 4 - 647215 ATCA- - -a -s simMouse_chr6.simMouse.chr6 251394 6 + 636262 ATCTTG -s Anc0.Anc0refChr5 68551 6 + 87904 ATTATG -s Anc1.Anc1refChr7 27319 6 - 47259 ATTATG -s Anc2.Anc2refChr15 65448 6 + 86568 ATTATC -s mr.mrrefChr5 104123 6 + 294540 ATCTTG -s mr.mrrefChr5 190162 6 - 294540 ATTTTG -s simCow_chr6.simCow.chr6 247038 6 + 602619 ATTATC -s simDog_chr6.simDog.chr6 237702 6 + 593897 ATTGTC -s simHuman_chr6.simHuman.chr6 329684 6 - 601863 ATTATG -s simMouse_chr6.simMouse.chr6 384545 6 - 636262 ATTTTG -s simRat_chr6.simRat.chr6 405663 6 - 647215 ATCTTG - -a -s simMouse_chr6.simMouse.chr6 251400 8 + 636262 CTCTCTGT -s Anc0.Anc0refChr5 68557 8 + 87904 CTTTCTGT -s Anc1.Anc1refChr7 27325 8 - 47259 CTTTCTGT -s Anc2.Anc2refChr15 65454 8 + 86568 CTTTCTGT -s mr.mrrefChr5 104129 8 + 294540 CTCTCTGT -s mr.mrrefChr5 190170 8 - 294540 CTCTCTGC -s simCow_chr6.simCow.chr6 247044 8 + 602619 CTTTCTTT -s simDog_chr6.simDog.chr6 237708 8 + 593897 CTTTCTGT -s simHuman_chr6.simHuman.chr6 329690 8 - 601863 CCTTTTGA -s simMouse_chr6.simMouse.chr6 384553 8 - 636262 CTCTCTGC -s simRat_chr6.simRat.chr6 405671 8 - 647215 CTCTCTGC - -a -s simMouse_chr6.simMouse.chr6 251408 71 + 636262 TTTCACAAGTATTCTTCAAAGTTGCTTTAGCAATTTAAAAAATCATATCTTGCTCTCTTTATTGTTATGCA -s Anc0.Anc0refChr5 68565 7 + 87904 TCTCC----------------------------------------------------------------TA -s Anc1.Anc1refChr7 27333 7 - 47259 TCTCC----------------------------------------------------------------TA -s Anc2.Anc2refChr15 65465 7 + 86568 TCACC----------------------------------------------------------------TA -s mr.mrrefChr5 104137 7 + 294540 TTTCA----------------------------------------------------------------CA -s mr.mrrefChr5 190178 7 - 294540 TTTGC----------------------------------------------------------------TA -s simCow_chr6.simCow.chr6 247055 7 + 602619 TCACC----------------------------------------------------------------TA -s simDog_chr6.simDog.chr6 237720 7 + 593897 TCACC----------------------------------------------------------------TA -s simHuman_chr6.simHuman.chr6 329698 7 - 601863 ACTCC----------------------------------------------------------------TA -s simMouse_chr6.simMouse.chr6 384561 7 - 636262 TTTGC----------------------------------------------------------------TA -s simRat_chr6.simRat.chr6 405679 7 - 647215 ATTAT----------------------------------------------------------------TG - -a -s simMouse_chr6.simMouse.chr6 251479 28 + 636262 GATTTCTAGTTTAGATGACCCTAGTGTT -s Anc0.Anc0refChr5 68572 28 + 87904 GATTTCTAGTTTAGATGACCTCAGTGTT -s Anc1.Anc1refChr7 27340 28 - 47259 GATTTCTAGTTTAGATGACCTCAGTGTT -s Anc2.Anc2refChr15 65472 28 + 86568 GATTTCTAGTTTAGATGACATCTGTGTT -s mr.mrrefChr5 104144 28 + 294540 GATTTCTAGTTTAGATGACCCTAGTGTT -s mr.mrrefChr5 190188 28 - 294540 AGTTTCTGGGTTAGATGACCCGAGTGTT -s simCow_chr6.simCow.chr6 247062 28 + 602619 GACTTCTAATTGGGATGACATTAGTATT -s simDog_chr6.simDog.chr6 237727 24 + 593897 GATTTCTTGTTTAG----CATCTGTGTC -s simHuman_chr6.simHuman.chr6 329705 28 - 601863 GATTTCAAGTTTAGATGACCTACATGTT -s simMouse_chr6.simMouse.chr6 384571 28 - 636262 AGTTTCTGGGTTAGATGACCCGAGTGTT -s simRat_chr6.simRat.chr6 405689 28 - 647215 AGTTTCTAGTTCAGATGACCCAACTGTT - -a -s simMouse_chr6.simMouse.chr6 251507 14 + 636262 TCAAGGATAAATGA -s Anc0.Anc0refChr5 68601 14 + 87904 TGAAGGATGACTAA -s Anc1.Anc1refChr7 27369 14 - 47259 TGAAGGATGACTAA -s Anc2.Anc2refChr15 65501 14 + 86568 TGAAGGATGACTAA -s mr.mrrefChr5 104172 14 + 294540 TCAAGGATAAATGA -s mr.mrrefChr5 190217 14 - 294540 TCAGGGATGAGTAA -s simCow_chr6.simCow.chr6 247091 14 + 602619 TGAAGAATAACGAA -s simDog_chr6.simDog.chr6 237752 14 + 593897 TGAAGGATGACTAG -s simHuman_chr6.simHuman.chr6 329734 14 - 601863 TGAAGGATGACTAA -s simMouse_chr6.simMouse.chr6 384600 14 - 636262 TCAGGGATGAGTAA -s simRat_chr6.simRat.chr6 405718 14 - 647215 TCAAGGATGAGTAA - -a -s simMouse_chr6.simMouse.chr6 251521 7 + 636262 AAAATGC -s Anc0.Anc0refChr5 68615 7 + 87904 AAAATGC -s Anc1.Anc1refChr7 27383 7 - 47259 AAAATGC -s Anc2.Anc2refChr15 65515 7 + 86568 AAAATGC -s mr.mrrefChr5 104186 7 + 294540 AAAATGC -s mr.mrrefChr5 190232 7 - 294540 AGAAAGA -s simCow_chr6.simCow.chr6 247105 7 + 602619 AAAATGC -s simDog_chr6.simDog.chr6 237766 7 + 593897 CAAATGC -s simHuman_chr6.simHuman.chr6 329748 7 - 601863 AAAATGC -s simMouse_chr6.simMouse.chr6 384615 7 - 636262 AGAAAGA -s simRat_chr6.simRat.chr6 405733 7 - 647215 AGATGCA - -a -s simMouse_chr6.simMouse.chr6 251528 12 + 636262 TGTCAATAATCG -s Anc0.Anc0refChr5 68622 12 + 87904 CGTCAGTAATGG -s Anc1.Anc1refChr7 27390 12 - 47259 CGTCAGTAATGG -s Anc2.Anc2refChr15 65522 12 + 86568 CATCAGTAATGG -s mr.mrrefChr5 104193 12 + 294540 TGTCAATAATCG -s mr.mrrefChr5 190239 3 - 294540 TGT--------- -s simCow_chr6.simCow.chr6 247112 12 + 602619 TATCAGTAATGG -s simDog_chr6.simDog.chr6 237773 12 + 593897 CAACAGTAATGG -s simHuman_chr6.simHuman.chr6 329755 12 - 601863 CTTCAGTAATGG -s simMouse_chr6.simMouse.chr6 384622 3 - 636262 TGT--------- -s simRat_chr6.simRat.chr6 405741 3 - 647215 TGT--------- - -a -s simMouse_chr6.simMouse.chr6 251540 7 + 636262 GGACTTG -s Anc0.Anc0refChr5 68650 7 + 87904 GAGCTTG -s Anc1.Anc1refChr7 27418 7 - 47259 GAGCTTG -s Anc2.Anc2refChr15 65553 7 + 86568 GAGCTTG -s mr.mrrefChr5 104205 7 + 294540 GGACTTG -s simCow_chr6.simCow.chr6 247143 7 + 602619 GAGCTTG -s simDog_chr6.simDog.chr6 237804 7 + 593897 GAGCTTG -s simHuman_chr6.simHuman.chr6 329783 7 - 601863 GAGCTTG - -a -s simMouse_chr6.simMouse.chr6 251547 75 + 636262 AGTTGCTACATAGTCTCTGTGTGGTTTTGAGGCGAGGGTATACAGGTAGTGGTGCTAGTGTCCACCAACAACACT -s Anc0.Anc0refChr5 68657 71 + 87904 AATTGTTACTTAGTGTGGGTGTGTTTAAGAGGATAGAGTACACA-GCAGTGTTGCTAGTGG--ATCAAAACC-CT -s Anc1.Anc1refChr7 27425 71 - 47259 AATTGTTACTTAGTGTGGGTGTGTTTAAGAGGATAGAGTACACA-GCAGTGTTGCTAGTGG--ATCAAAACC-CT -s Anc2.Anc2refChr15 65560 71 + 86568 AATTGTTACTTGGTGTGGTTGTGTTTAAGAGGGTAGAGTACACA-ACAGTGTTGGTGGTGG--ATCAAAGCT-CT -s mr.mrrefChr5 104212 71 + 294540 AGTTGCTACATAGTCTCTGTGTGGTTTTGAGGCGAGGGTATACA-GTAGTGGTGCTAGTGT--ACCAACAAC-CT -s mr.mrrefChr5 190242 15 - 294540 -------------------------------GAGAGGGTACACA-GT---------------------------- -s simCow_chr6.simCow.chr6 247151 71 + 602619 AATTGATACTTGGTGAGGTTGTGTTCAAGAGGTTAGGGTACATG-CCAGTGTTGGTGGTGG--ATCAAAGCT-CT -s simDog_chr6.simDog.chr6 237811 70 + 593897 AATTTTTACTTGGTATGGTAGTGTTTAAGAGGGTAGAGTACACA-ATAG-GTTGGTGGTGG--ATCAAAGCT-CT -s simHuman_chr6.simHuman.chr6 329790 71 - 601863 AATTGTTACTTAGTGTGGGTGTGTTTAAAAGGATAGAGTATACA-TCAGTTTTACTAGTGG--ATCAAAAGC-CT -s simMouse_chr6.simMouse.chr6 384625 15 - 636262 -------------------------------GAGAGGGTACACA-GT---------------------------- -s simRat_chr6.simRat.chr6 405744 6 - 647215 -------------------------------GATAGA-------------------------------------- - -a -s simMouse_chr6.simMouse.chr6 251647 1 + 636262 A -s mr.mrrefChr5 104308 1 + 294540 A -s simRat_chr6.simRat.chr6 241482 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 251662 1 + 636262 G -s Anc0.Anc0refChr5 19303 1 - 87904 T -s Anc1.Anc1refChr7 19890 1 + 47259 T -s Anc2.Anc2refChr15 21067 1 - 86568 T -s mr.mrrefChr5 104323 1 + 294540 G -s simCow_chr6.simCow.chr6 355528 1 - 602619 T -s simDog_chr6.simDog.chr6 356145 1 - 593897 C -s simHuman_chr6.simHuman.chr6 272129 1 + 601863 T -s simRat_chr6.simRat.chr6 241497 1 + 647215 G - -a -s simMouse_chr6.simMouse.chr6 251691 3 + 636262 GGA -s mr.mrrefChr5 104352 3 + 294540 GGA -s simRat_chr6.simRat.chr6 241526 3 + 647215 GGA - -a -s simMouse_chr6.simMouse.chr6 251709 2 + 636262 AG -s mr.mrrefChr5 104370 2 + 294540 AG -s simRat_chr6.simRat.chr6 241544 2 + 647215 AG - -a -s simMouse_chr6.simMouse.chr6 251724 1 + 636262 T -s Anc0.Anc0refChr5 19362 1 - 87904 A -s Anc1.Anc1refChr7 19949 1 + 47259 A -s Anc2.Anc2refChr15 21129 1 - 86568 A -s mr.mrrefChr5 104385 1 + 294540 T -s simCow_chr6.simCow.chr6 355590 1 - 602619 A -s simDog_chr6.simDog.chr6 356204 1 - 593897 A -s simHuman_chr6.simHuman.chr6 272188 1 + 601863 A -s simRat_chr6.simRat.chr6 241561 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 251758 5 + 636262 AAAAA -s Anc0.Anc0refChr5 19404 5 - 87904 AAAAA -s Anc1.Anc1refChr7 19992 5 + 47259 AAAAA -s Anc2.Anc2refChr15 21171 5 - 86568 TAAAT -s mr.mrrefChr5 104419 5 + 294540 AAAAA -s mr.mrrefChr5 190461 5 - 294540 AAAAA -s simCow_chr6.simCow.chr6 355638 5 - 602619 AAAAT -s simDog_chr6.simDog.chr6 356235 5 - 593897 TAAAT -s simHuman_chr6.simHuman.chr6 272233 3 + 601863 --AAA -s simRat_chr6.simRat.chr6 405803 5 - 647215 AAAAA -s simRat_chr6.simRat.chr6 241595 5 + 647215 ACAAA - -a -s simMouse_chr6.simMouse.chr6 251783 1 + 636262 A - -a -s simMouse_chr6.simMouse.chr6 251797 2 + 636262 AT -s mr.mrrefChr5 104457 2 + 294540 AT -s simRat_chr6.simRat.chr6 241736 2 + 647215 AT - -a -s simMouse_chr6.simMouse.chr6 251823 5 + 636262 GCTGC -s Anc0.Anc0refChr5 19458 5 - 87904 ACTGA -s Anc1.Anc1refChr7 20055 5 + 47259 ACTGA -s Anc2.Anc2refChr15 21225 5 - 86568 ACTCA -s mr.mrrefChr5 104483 5 + 294540 GCTGC -s mr.mrrefChr5 190524 5 - 294540 ACTGC -s simCow_chr6.simCow.chr6 355704 5 - 602619 ACCAA -s simDog_chr6.simDog.chr6 356288 5 - 593897 ACTCA -s simHuman_chr6.simHuman.chr6 272286 5 + 601863 GCTGA -s simRat_chr6.simRat.chr6 405866 5 - 647215 ACTGC -s simRat_chr6.simRat.chr6 241762 5 + 647215 ACCGC - -a -s simMouse_chr6.simMouse.chr6 251843 2 + 636262 CT - -a -s simMouse_chr6.simMouse.chr6 251899 2 + 636262 AG -s Anc0.Anc0refChr5 19543 2 - 87904 TG -s Anc1.Anc1refChr7 20140 2 + 47259 TG -s Anc2.Anc2refChr15 21310 2 - 86568 TG -s mr.mrrefChr5 104557 2 + 294540 AG -s simCow_chr6.simCow.chr6 355779 2 - 602619 TG -s simDog_chr6.simDog.chr6 356373 2 - 593897 CA -s simHuman_chr6.simHuman.chr6 272371 2 + 601863 TG -s simRat_chr6.simRat.chr6 241836 2 + 647215 AG - -a -s simMouse_chr6.simMouse.chr6 251941 31 + 636262 TGCAGAATTTTAGCTCTAAAGGTTAAAGGAA -s Anc0.Anc0refChr5 68728 7 + 87904 -----------------GATGG-------AA -s Anc1.Anc1refChr7 27496 7 - 47259 -----------------GATGG-------AA -s Anc2.Anc2refChr15 65631 7 + 86568 -----------------GATGG-------AG -s mr.mrrefChr5 104599 24 + 294540 TGCAGAATTTTAGCTCTAAAGG-------AA -s simCow_chr6.simCow.chr6 247222 7 + 602619 -----------------GATGG-------AC -s simDog_chr6.simDog.chr6 237881 7 + 593897 -----------------GATGA-------AG -s simHuman_chr6.simHuman.chr6 329861 7 - 601863 -----------------GATGG-------AA -s simRat_chr6.simRat.chr6 241879 24 + 647215 CGCAGAATTTTAGCTCTAAAGT-------AA - -a -s simMouse_chr6.simMouse.chr6 251972 38 + 636262 TCAATTGTCACAACTGTAGGACAAACAGTTATCCCTTA -s Anc0.Anc0refChr5 68735 27 + 87904 TGAACT-TCTCTACT-TAGAGTAGACAGT--------- -s Anc1.Anc1refChr7 27503 31 - 47259 TGAACT-TCTCTACT-TAGAGTAGACAGT-----CTCA -s Anc2.Anc2refChr15 65638 27 + 86568 TGATCT-TCTCTACT-TAGAGTAGACAGT--------- -s mr.mrrefChr5 104623 38 + 294540 TCAATTGTCACAACTGTAGGACAAACAGTTATCCCTTA -s simCow_chr6.simCow.chr6 247229 27 + 602619 TGATCT-CATCTACC-TAGAGCAGACAGT--------- -s simDog_chr6.simDog.chr6 237893 27 + 593897 TGGTCT-TCTCTACT-TAGAGTAGACAGT--------- -s simHuman_chr6.simHuman.chr6 329868 13 - 601863 CTAACT-TGT------------------------CTCA -s simRat_chr6.simRat.chr6 241903 38 + 647215 TCACTTGTCACAACTGTAGAGCAAACAGCTATTAATTA - -a -s simMouse_chr6.simMouse.chr6 252010 71 + 636262 AGTACTAAGATATGTATTTTTAATTAATTTCACCATCCTTTCACTTATAGGATGGTATGGATGGGCCTCTT -s Anc0.Anc0refChr5 68762 59 + 87904 ---------ATATGTG---TTAATTAATATCATCATCCTTACATTTATAGAATAGCATACATGGGCTTCTT -s Anc1.Anc1refChr7 27534 66 - 47259 A-----TGGATATGTGTTTTTAATTAATATCATCATCCTTACATTTATAGAATAGCATACATGGGCTTCTT -s Anc2.Anc2refChr15 65665 59 + 86568 ---------ATATGTG---TTAATTAATATCATCATCCTAACATTTAAAGAATAGCATACATGGGCTTCTT -s mr.mrrefChr5 104661 71 + 294540 AGTACTTAGATATGTATTTTTAATTAATTTCATCATCCTTACACTTATAGAATGGTATGGATGGGCCTCTT -s simCow_chr6.simCow.chr6 247256 52 + 602619 -------------------TTAATTAATTTCATCATCCTAACATTTAAAGAACAGCATACATGGGCCTCCT -s simDog_chr6.simDog.chr6 237939 58 + 593897 ---------ATATGTG---TTAATTAA-ATCATCATCCTAACATTTAAACAATAGCATACATGGGCTTCTC -s simHuman_chr6.simHuman.chr6 329881 66 - 601863 A-----TGGGTATGTGTTTTTAATTAATCTCATCGTCCTTACATTTATAGAATAGCATACATGGGCTCCTT -s simRat_chr6.simRat.chr6 241942 71 + 647215 AGTACTTAGTTATGTATCTTCAATTAATTTCATCATCCTTACACTGATCGAGTGGTATGGATGGGCCTCTT - -a -s simMouse_chr6.simMouse.chr6 252081 58 + 636262 GATATGTCACCCTAGGAAAACGATAGTAGAAACACTGTACGTTTACAAGCAATCTGAT -s Anc0.Anc0refChr5 68821 58 + 87904 GGTATGTCACCAGAAAATAACAATACTAGCAATACTGTATGTTTACAGGCAGTCTGGT -s Anc1.Anc1refChr7 27600 58 - 47259 GGTATGTCACCAGAAAATAACAATACTAGCAATACTGTATGTTTACAGGCAGTCTGGT -s Anc2.Anc2refChr15 65724 58 + 86568 GGTATAACTCCAGAAAATAACAATGCTAACAATACTGTATGTTTACAGGCAGTCTGGC -s mr.mrrefChr5 104732 58 + 294540 GATATGTCACCCTAAGAAAACAATAGTAGAAACACTGTATGTTTACAAGCAATCTGAT -s simCow_chr6.simCow.chr6 247346 58 + 602619 GGTACACCTCTAGAAAATAATAATGCTAACAAGACTATATGTTTCCAGGTAGGCTGAA -s simDog_chr6.simDog.chr6 237997 58 + 593897 GGTATAACTCCAGAAAATAACGATGCTAAAAATACTGTAGATATACAGGCAGTCTGGC -s simHuman_chr6.simHuman.chr6 329947 57 - 601863 GGTATGTGACCACAAACTAACAATACTAGCAATACTGTATGTTTACATG-AGTCTGGT -s simRat_chr6.simRat.chr6 242013 58 + 647215 GAGATGCTACCCTAACAGAACAATGGTAGAAACATTGTATGGTTACAAGCAATCTAAT - -a -s simMouse_chr6.simMouse.chr6 252139 15 + 636262 CACTATTCTTATGTG -s Anc0.Anc0refChr5 68881 15 + 87904 CACCATTCTAAAGTA -s Anc1.Anc1refChr7 27660 15 - 47259 CACCATTCTAAAGTA -s Anc2.Anc2refChr15 65784 15 + 86568 CACCATTCTAAAGTA -s mr.mrrefChr5 104790 15 + 294540 CACTATTCTTATGTG -s simCow_chr6.simCow.chr6 247406 11 + 602619 C----TCCTAAAGTA -s simDog_chr6.simDog.chr6 238057 15 + 593897 CACCATTCTAGAGTA -s simHuman_chr6.simHuman.chr6 330006 15 - 601863 CACCATTCTAAGGTA -s simRat_chr6.simRat.chr6 242071 15 + 647215 CGCTACTCTTATGTG - -a -s simMouse_chr6.simMouse.chr6 252154 7 + 636262 TGAATAG -s Anc0.Anc0refChr5 68901 7 + 87904 TGAGTAG -s Anc1.Anc1refChr7 27680 7 - 47259 TGAGTAG -s Anc2.Anc2refChr15 65804 7 + 86568 TGAGTAG -s mr.mrrefChr5 104805 7 + 294540 TGAATAG -s simDog_chr6.simDog.chr6 238077 7 + 593897 TGAGTAG -s simHuman_chr6.simHuman.chr6 330026 7 - 601863 TGAGTAG -s simRat_chr6.simRat.chr6 242086 7 + 647215 TGAATAG - -a -s simMouse_chr6.simMouse.chr6 252161 22 + 636262 AAATAGAATGTCCATTGTACTA -s Anc0.Anc0refChr5 68914 18 + 87904 AAATACAATTCATAATGC---- -s Anc1.Anc1refChr7 27693 19 - 47259 AAATACAATTCATAATGCA--- -s Anc2.Anc2refChr15 65817 18 + 86568 AAATACAATTCATAATGC---- -s mr.mrrefChr5 104812 22 + 294540 AAATAGAATTTCTATTGTACTA -s simCow_chr6.simCow.chr6 247419 18 + 602619 AAATACAATTCATACTGT---- -s simDog_chr6.simDog.chr6 238090 18 + 593897 AAATATAATTCATAACAC---- -s simHuman_chr6.simHuman.chr6 330039 19 - 601863 GAATACAATTCATAATGCA--- -s simRat_chr6.simRat.chr6 242093 22 + 647215 AAATAAAATTTGTATTGTATTT - -a -s simMouse_chr6.simMouse.chr6 252183 9 + 636262 ATGCCTGAC -s Anc0.Anc0refChr5 68932 9 + 87904 ATGTGTGAG -s Anc1.Anc1refChr7 27712 9 - 47259 ATGTGTGAG -s Anc2.Anc2refChr15 65835 9 + 86568 ATGTGTGAG -s mr.mrrefChr5 104834 9 + 294540 ATGCCTGAC -s simCow_chr6.simCow.chr6 247441 9 + 602619 ATGTGTAAT -s simDog_chr6.simDog.chr6 238108 9 + 593897 ATGTATGTG -s simHuman_chr6.simHuman.chr6 330058 7 - 601863 --GTGTGAG -s simRat_chr6.simRat.chr6 242115 9 + 647215 ATGCATAAC - -a -s simMouse_chr6.simMouse.chr6 252192 103 + 636262 AAGTTTTTGGGGCAAGATCCAGTACAAATGATGGGTCAAAGGAACGGAATGTTATCAGAATTATGAGAGACCGCCCGTAAGTATTGTTGAGTATTATATGAAA -s Anc0.Anc0refChr5 68941 92 + 87904 AAGTTTGCCGGGT--GACCAAG--CATATGATGGGTCAAAGT----GAAGTTCATTAGAAA---AAGAACCACCCTGTTGGTATTGGCAAGGATAAGATGGAA -s Anc1.Anc1refChr7 27721 96 - 47259 AAGTTTGCCGGGTA-GACCAAG--CATATGATGGGTCAAAGT----GAAGTTCATTAGAAACATAAGAACCACCCTGTTGGTATTGGCAAGGATAAGATGGAA -s Anc2.Anc2refChr15 65844 92 + 86568 AAGTTTGCCAGGT--GACCAAG--CATATGATGAGTCAACTT----GAAGTTCATTAGAAA---AAAAACCACCCTGTTGGTATTGGCAAGGATAAGATGGAA -s mr.mrrefChr5 104843 103 + 294540 AAGTTTTTGGGGTAAGATCCAGTACAAATGATGGGTCAAAGTAACGGAATGTTATCAGAATTATGAGAGACCGCCTGTAAGTATTGTCAAGTATTACATGAAA -s simCow_chr6.simCow.chr6 247450 92 + 602619 AGATTTATTAGGT--AGCCGAG--CATATGATGAGTCAACTT----GATGGTCATCACAAG---AGAAACCACCCTATTGGTAGTTTCAATTTTAAGGTGTAA -s simDog_chr6.simDog.chr6 238120 92 + 593897 AAGTTTGCCAGGT--GACCAAG--CATATGATGAGTCACCTT----AGAGTTCATTAGAAA---AAATACCACTCTGTTGGTATTGGCAAGGATAAGATGGAA -s simHuman_chr6.simHuman.chr6 330065 73 - 601863 AAGTTTGCAGGGTA-------------------GGTCAAAGT----GAACATCATTAAAAACATCAGAATCACCTTGTTGGCATTGCCA-------GATGGAA -s simRat_chr6.simRat.chr6 242124 102 + 647215 AAGTTTTTGGGGTAAGATCCAGTGCAATTGATGAGCCAAAGTAACAGAATGTTATGAGAATTATGAGAGACCGCCTGTAAGTGTTGTCAAGTATTACATGAA- - -a -s simMouse_chr6.simMouse.chr6 252295 40 + 636262 TTCTTTCTGTTAGATCCTTATTTTTGAGGATGCAATTAAA -s Anc0.Anc0refChr5 69041 40 + 87904 TTCTTTCTGCTGCATCCTGATTTTTGAGAATGTAATTGAA -s Anc1.Anc1refChr7 27825 40 - 47259 TTCTTTCTGCTGCATCCTGATTTTTGAGAATGTAATTGAA -s Anc2.Anc2refChr15 65944 40 + 86568 TTCTTTCTGCTGCAACCTGATTTTTGAGAATGTAATTGGA -s mr.mrrefChr5 104946 40 + 294540 TTCTTTCTGTTGGATCCTGATTTTTGAGGATGCAATTAAA -s simCow_chr6.simCow.chr6 247550 40 + 602619 CTCTTTCTGCTAAAACCTGGTTTTTGAGAATGTCATTAGA -s simDog_chr6.simDog.chr6 238220 40 + 593897 TTCTTTTTGCTGCAACCTGACTCTCGAGACTGTAATTGGA -s simHuman_chr6.simHuman.chr6 330146 38 - 601863 TTCTCTCTGCTG--TGCTGATTTTTGAGAATGGAATTGAA -s simRat_chr6.simRat.chr6 242226 38 + 647215 --CTTTCTGTTGGATCCTGCTTTTTGAGGATGTAACTAAA - -a -s simMouse_chr6.simMouse.chr6 252335 29 + 636262 TTCTGAGTAAGTGCACATTGTCTCCATAG -s Anc0.Anc0refChr5 69081 23 + 87904 TTCAGAGCTAATGAGCAAAGCC------G -s Anc1.Anc1refChr7 27865 29 - 47259 TTCAGAGCTAATGAGCAAAGCCTTTGTTG -s Anc2.Anc2refChr15 65986 23 + 86568 TGCAGAGCTAATCAGCAAAGCC------G -s mr.mrrefChr5 104986 29 + 294540 TTCTGAGCGAGTGCACATTGTCTCCATAG -s simCow_chr6.simCow.chr6 247592 23 + 602619 TGCAGAGCTAATTAGCCTAGCT------G -s simDog_chr6.simDog.chr6 238262 23 + 593897 TCCAGAGTTGATCAGCAAAGTC------G -s simHuman_chr6.simHuman.chr6 330184 25 - 601863 TTCC----CAACGAGCACAGCCTTTGTTG -s simRat_chr6.simRat.chr6 242264 29 + 647215 TTCTGAGCGAGTCCATAATGTCTCAGTAG - -a -s simMouse_chr6.simMouse.chr6 252364 37 + 636262 GACATACCTAGTAATGGACCCCTGTTGTTGAGATGTG -s Anc0.Anc0refChr5 69104 34 + 87904 CACATGCCTGGAAAAGGATCCCTATTG---ATAGGAA -s Anc1.Anc1refChr7 27894 34 - 47259 CACATGCCTGGAAAAGGATCCCTATTG---ATAGGAA -s Anc2.Anc2refChr15 66009 34 + 86568 CACATGTCTGGAAAAGGATAACTATTG---ATAGGAA -s mr.mrrefChr5 105015 34 + 294540 CACATACCTAGTAATGGATCCCTGTTG---AGATGTG -s simCow_chr6.simCow.chr6 247619 34 + 602619 TACATGTCTAGGAAAGGATATCTATTC---ATAGGAA -s simDog_chr6.simDog.chr6 238285 27 + 593897 CACATATCTGGAAAAGGATAACTATTG---------- -s simHuman_chr6.simHuman.chr6 330210 34 - 601863 CACATGCCTGGAACAGTATCCCTATTG---ACAGGCT -s simRat_chr6.simRat.chr6 242293 34 + 647215 CACATACCTAGGAATGGATCCCTGTCG---AGATGTG - -a -s simMouse_chr6.simMouse.chr6 252401 2 + 636262 AA -s Anc0.Anc0refChr5 69230 2 + 87904 AA -s Anc1.Anc1refChr7 28023 2 - 47259 AA -s Anc2.Anc2refChr15 66135 2 + 86568 AA -s mr.mrrefChr5 105149 2 + 294540 AA -s simCow_chr6.simCow.chr6 247742 2 + 602619 AA -s simDog_chr6.simDog.chr6 238399 2 + 593897 AA -s simHuman_chr6.simHuman.chr6 330338 2 - 601863 AA -s simRat_chr6.simRat.chr6 242427 2 + 647215 AA - -a -s simMouse_chr6.simMouse.chr6 252403 15 + 636262 GGGTACTCACGCAAA -s Anc0.Anc0refChr5 69245 3 + 87904 ------------AAG -s Anc1.Anc1refChr7 28038 15 - 47259 AAGTGTGTGGGCAAG -s Anc2.Anc2refChr15 66150 3 + 86568 ------------AAG -s mr.mrrefChr5 105151 15 + 294540 AAGTACTCACGCAAA -s simCow_chr6.simCow.chr6 247756 3 + 602619 ------------GTA -s simDog_chr6.simDog.chr6 238411 3 + 593897 ------------AAG -s simHuman_chr6.simHuman.chr6 330353 15 - 601863 AAGTGTGTGGGCAAG -s simRat_chr6.simRat.chr6 242429 15 + 647215 AAGTACTCATGCAAA - -a -s simMouse_chr6.simMouse.chr6 252418 5 + 636262 GGAGG -s Anc0.Anc0refChr5 69250 5 + 87904 GAATG -s Anc1.Anc1refChr7 28055 5 - 47259 GAATG -s Anc2.Anc2refChr15 66155 5 + 86568 GAATG -s mr.mrrefChr5 105166 5 + 294540 GGAGG -s simCow_chr6.simCow.chr6 247761 5 + 602619 GAATG -s simDog_chr6.simDog.chr6 238416 5 + 593897 GAGTG -s simHuman_chr6.simHuman.chr6 330372 5 - 601863 GTAAG -s simRat_chr6.simRat.chr6 242444 5 + 647215 GGAGG - -a -s simMouse_chr6.simMouse.chr6 252423 14 + 636262 CAGTACAAGTTTAA -s Anc0.Anc0refChr5 69256 14 + 87904 CAGTACTAGCTTAA -s Anc1.Anc1refChr7 28061 14 - 47259 CAGTACTAGCTTAA -s Anc2.Anc2refChr15 66161 14 + 86568 CAGTACTAGTTTAA -s mr.mrrefChr5 105172 14 + 294540 CAGTACAAGCTTAA -s simCow_chr6.simCow.chr6 247767 14 + 602619 CAGTACTGGTTTAA -s simDog_chr6.simDog.chr6 238422 14 + 593897 CAGCAATACTTTAA -s simHuman_chr6.simHuman.chr6 330378 14 - 601863 CAGTACTAGCTTAA -s simRat_chr6.simRat.chr6 242450 14 + 647215 CAGTACAAGCTTAA - -a -s simMouse_chr6.simMouse.chr6 252437 5 + 636262 ATTGA -s Anc0.Anc0refChr5 69284 1 + 87904 ----A -s Anc1.Anc1refChr7 28089 5 - 47259 ATTGA -s Anc2.Anc2refChr15 66189 1 + 86568 ----A -s mr.mrrefChr5 105186 5 + 294540 ATTGA -s simCow_chr6.simCow.chr6 247795 1 + 602619 ----A -s simDog_chr6.simDog.chr6 238449 1 + 593897 ----A -s simHuman_chr6.simHuman.chr6 330598 5 - 601863 ATTGA -s simRat_chr6.simRat.chr6 242464 5 + 647215 ATGGA - -a -s simMouse_chr6.simMouse.chr6 252442 2 + 636262 AA -s Anc0.Anc0refChr5 69285 2 + 87904 AA -s Anc1.Anc1refChr7 28094 2 - 47259 AA -s Anc2.Anc2refChr15 66190 2 + 86568 AA -s mr.mrrefChr5 105191 2 + 294540 AA -s simCow_chr6.simCow.chr6 247796 2 + 602619 AA -s simDog_chr6.simDog.chr6 238450 2 + 593897 AA -s simHuman_chr6.simHuman.chr6 330607 2 - 601863 AA -s simRat_chr6.simRat.chr6 242469 2 + 647215 AA - -a -s simMouse_chr6.simMouse.chr6 252444 28 + 636262 GGGTTCCAATGTCCATGATGCATAAGGC -s Anc0.Anc0refChr5 69287 28 + 87904 GGGTCCCAATGTATGTAATCCATAGGTC -s Anc1.Anc1refChr7 28096 28 - 47259 GGGTCCCAATGTATGTAATCCATAGGTC -s Anc2.Anc2refChr15 66192 28 + 86568 GGGTCCCAATGTATGTAATCCATAGGTC -s mr.mrrefChr5 105193 28 + 294540 GGGTTCCAATGTCTATAATGCATAAGGC -s simCow_chr6.simCow.chr6 247798 26 + 602619 GGCTCCCAATGTATGTATTCCATGGG-- -s simDog_chr6.simDog.chr6 238452 28 + 593897 GAGTTCCAATGTATGTAATAAAAACTTC -s simHuman_chr6.simHuman.chr6 330609 28 - 601863 GGGTCCAAATGAATGTAATCCATAGGCC -s simRat_chr6.simRat.chr6 242510 28 + 647215 GGGTTCCAATGTCTATAACACATAAGAT - -a -s simMouse_chr6.simMouse.chr6 252472 3 + 636262 TGA -s Anc0.Anc0refChr5 69316 3 + 87904 TAA -s Anc1.Anc1refChr7 28125 3 - 47259 TAA -s Anc2.Anc2refChr15 66221 3 + 86568 TAA -s mr.mrrefChr5 105221 3 + 294540 TGA -s simCow_chr6.simCow.chr6 247824 3 + 602619 TAT -s simDog_chr6.simDog.chr6 238481 3 + 593897 TGA -s simHuman_chr6.simHuman.chr6 330638 3 - 601863 TAA -s simRat_chr6.simRat.chr6 242538 3 + 647215 TGA - -a -s simMouse_chr6.simMouse.chr6 252475 6 + 636262 ATATAC -s Anc0.Anc0refChr5 69319 6 + 87904 ATCTAC -s Anc1.Anc1refChr7 28128 6 - 47259 ATCTAC -s Anc2.Anc2refChr15 66224 6 + 86568 ATCTAC -s mr.mrrefChr5 105224 6 + 294540 ATATAC -s simCow_chr6.simCow.chr6 247827 6 + 602619 AGATAC -s simDog_chr6.simDog.chr6 238621 6 + 593897 ATCTAC -s simHuman_chr6.simHuman.chr6 330641 6 - 601863 ATCAAC -s simRat_chr6.simRat.chr6 242541 6 + 647215 ATATAT - -a -s simMouse_chr6.simMouse.chr6 252481 11 + 636262 CACAACCTTAT -s Anc0.Anc0refChr5 69325 11 + 87904 AGCAACTCTGG -s Anc1.Anc1refChr7 28134 11 - 47259 AGCAACTCTGG -s Anc2.Anc2refChr15 66230 11 + 86568 AGCAACTCTGG -s mr.mrrefChr5 105230 11 + 294540 CACAACCTTAT -s simCow_chr6.simCow.chr6 247838 11 + 602619 GGCAACTCGAG -s simDog_chr6.simDog.chr6 238627 11 + 593897 AATAACTCTGG -s simHuman_chr6.simHuman.chr6 330647 5 - 601863 AGCAA------ -s simRat_chr6.simRat.chr6 242547 11 + 647215 CACAACTTTAG - -a -s simMouse_chr6.simMouse.chr6 252492 37 + 636262 CTATTGGTTATTTCTGGCCACGTATGACATTTCTCTG -s Anc0.Anc0refChr5 69336 37 + 87904 TTATTAGTTATTTTAGGCCACCTATGATGGTTGCCTG -s Anc1.Anc1refChr7 28145 37 - 47259 TTATTAGTTATTTTAGGCCACCTATGATGGTTGCCTG -s Anc2.Anc2refChr15 66244 37 + 86568 TTATTAGTTATTTTAGGCCAGCTATGATGGTTGCCTG -s mr.mrrefChr5 105241 37 + 294540 CTATTGGTTATTTCAGGCCACGTATGACGTTTCTCTG -s simCow_chr6.simCow.chr6 247852 37 + 602619 TTGTCAGTTATTTTAAGCTAGCCATGATGGTTGCCTG -s simDog_chr6.simDog.chr6 238641 36 + 593897 TTATTTGTTACTTGAGGCCAGCTATGATGGTTGCCT- -s simHuman_chr6.simHuman.chr6 330652 35 - 601863 --ATTAGTTATTCTAGGCCACATATGATGGTTGCTTG -s simRat_chr6.simRat.chr6 242558 37 + 647215 CTATCGGTTATTTCAGGCCACCTATGACGTTTCTCTG - -a -s simMouse_chr6.simMouse.chr6 252529 28 + 636262 ATCATACTTCAGGGTCTAAGTTGGCATT -s Anc0.Anc0refChr5 69377 28 + 87904 AGCCTACTTCAGAATTTGAACTGGCATC -s Anc1.Anc1refChr7 28186 28 - 47259 AGCCTACTTCAGAATTTGAACTGGCATC -s Anc2.Anc2refChr15 66285 28 + 86568 AGCCCACTTCAGAATTTGAACTGGCATC -s mr.mrrefChr5 105282 28 + 294540 ATCATACTTCAGGGTCTAAGTTGGCATT -s simCow_chr6.simCow.chr6 247893 22 + 602619 A------GTCAGAATCAAGACTGGCATC -s simDog_chr6.simDog.chr6 238677 28 + 593897 AGCCCACTTCAGAATTTGAACTGGCATC -s simHuman_chr6.simHuman.chr6 330691 28 - 601863 AGCCTATCTCAGAATTTTAACTGACATC -s simRat_chr6.simRat.chr6 242599 28 + 647215 ATCATACTTCAGGGTCTGAGTTGGCATT - -a -s simMouse_chr6.simMouse.chr6 252557 15 + 636262 GAGAGAAGTTGTAGT -s Anc0.Anc0refChr5 69407 15 + 87904 GATAGAAGTTGGAGT -s Anc1.Anc1refChr7 28216 15 - 47259 GATAGAAGTTGGAGT -s Anc2.Anc2refChr15 66315 15 + 86568 GGTAGAAGTTGGAGT -s mr.mrrefChr5 105310 15 + 294540 GAGAGAAGTTGGAGT -s simCow_chr6.simCow.chr6 247916 12 + 602619 ---AAAGGTCTAAGT -s simDog_chr6.simDog.chr6 238707 12 + 593897 GGTAGAAACTGG--- -s simHuman_chr6.simHuman.chr6 330721 15 - 601863 GAAAGAAGTTGGAGT -s simRat_chr6.simRat.chr6 242627 15 + 647215 GAGTGAAGTTGGAGT - -a -s simMouse_chr6.simMouse.chr6 252572 12 + 636262 GTATTTTAGCTA -s Anc0.Anc0refChr5 69437 12 + 87904 GCATTTTGGATA -s Anc1.Anc1refChr7 28246 12 - 47259 GCATTTTGGATA -s Anc2.Anc2refChr15 66345 12 + 86568 GCATTGTGGATA -s mr.mrrefChr5 105325 12 + 294540 GTATTTTAGCTA -s simCow_chr6.simCow.chr6 247943 12 + 602619 ACACTCTGGATA -s simDog_chr6.simDog.chr6 238719 12 + 593897 GTATTGTGGCTA -s simHuman_chr6.simHuman.chr6 330752 12 - 601863 GCATTTCGGATA -s simRat_chr6.simRat.chr6 242642 7 + 647215 GGATTTT----- - -a -s simMouse_chr6.simMouse.chr6 252584 44 + 636262 TTCCACCAGCTAAGCAGGCCTGACAGAGTGACTATACAAACCTT -s Anc0.Anc0refChr5 69449 43 + 87904 TTC-ACCAGCAAAGCGGGCCTCATAGAGTGACCATACAATCCTT -s Anc1.Anc1refChr7 28258 43 - 47259 TTC-ACCAGCAAAGCGGGCCTCATAGAGTGACCATACAATCCTT -s Anc2.Anc2refChr15 66357 43 + 86568 TTC-ACCAGCAAAGTGGGCCACATAGAGTGACCATACAGTCCTT -s mr.mrrefChr5 105337 43 + 294540 TTC-ACCAGCTAAGCAGGCCTGACAGAGTGACTATACAAACCTT -s simCow_chr6.simCow.chr6 247956 43 + 602619 TCC-ACCAGCAAAGTGGGCTAAACAAAGTGACCACACAGTCCTT -s simDog_chr6.simDog.chr6 238731 42 + 593897 GTC-ACCAGCTAAG-GTGCCACATAGAATGACCATACAGTCCTT -s simHuman_chr6.simHuman.chr6 330764 43 - 601863 TTC-ACCAGTAAAGCGGGCCTCATAGAGTGGCCAAACAATCCTT - -a -s simMouse_chr6.simMouse.chr6 252628 11 + 636262 GTAACTGCATA -s Anc0.Anc0refChr5 69493 1 + 87904 ----------A -s Anc1.Anc1refChr7 28302 11 - 47259 GCTACTACCTA -s Anc2.Anc2refChr15 66401 1 + 86568 ----------A -s mr.mrrefChr5 105380 11 + 294540 GTAACTGCATA -s simCow_chr6.simCow.chr6 248000 1 + 602619 ----------A -s simDog_chr6.simDog.chr6 238774 1 + 593897 ----------A -s simHuman_chr6.simHuman.chr6 330808 11 - 601863 GCTACTACCTA -s simRat_chr6.simRat.chr6 242649 4 + 647215 -------CATA - -a -s simMouse_chr6.simMouse.chr6 252639 9 + 636262 AACAAGACT -s Anc0.Anc0refChr5 69494 9 + 87904 CACAAGACT -s Anc1.Anc1refChr7 28313 9 - 47259 CACAAGACT -s Anc2.Anc2refChr15 66402 9 + 86568 CACACAGTT -s mr.mrrefChr5 105391 9 + 294540 AACAAGACT -s simCow_chr6.simCow.chr6 248022 9 + 602619 CACACAGTC -s simDog_chr6.simDog.chr6 238775 9 + 593897 CAGACAGTT -s simHuman_chr6.simHuman.chr6 330819 9 - 601863 CACAAGACT -s simRat_chr6.simRat.chr6 242653 9 + 647215 AACAAGACT - -a -s simMouse_chr6.simMouse.chr6 252648 96 + 636262 AACCACTACCTTAGGACTTAGAACAGTTACATTGGGAATCTGGACATGGTTCACCTGGAAAATGCTTGGGAGTCAATTTCCCTTACTGAATTATCA -s Anc0.Anc0refChr5 69503 95 + 87904 ATCAGATACCTAGGGACTTAGATCAGATGCATTGGGAATGTTAAAACCA-TCATTTGGAAAATGCTTTGGGGTAAATAACCCTTCCTTAATTATCA -s Anc1.Anc1refChr7 28322 95 - 47259 ATCAGATACCTAGGGACTTAGATCAGATGCATTGGGAATGTTAAAACCA-TCATTTGGAAAATGCTTTGGGGTAAATAACCCTTCCTTAATTATCA -s Anc2.Anc2refChr15 66411 95 + 86568 TTCAGATACCTAGGGACTTAAATCAGATGCATTGGGAATGTTAAAACCA-TCATTTGGAAAATGCTTTGGGGTAAACAACACTTCCTTAGGAAGCA -s mr.mrrefChr5 105400 96 + 294540 AACCACTACCTTAGGACTTAGAACAGTTACATTGGGAATCTGGACACGGTTCATCTGGAAAATGCTTGGGAGTCAATTTCCCTTACTGAATTATCA -s simCow_chr6.simCow.chr6 248041 57 + 602619 TTCAGATACCTAAGGACTCAAATCAGATGTATTGGGAAC-----AACCT-TCCTTCGTAAA---------------------------------CA -s simDog_chr6.simDog.chr6 238784 95 + 593897 TCCAGATACCCAGGGATTTAAATCAGATGCATTGGGAATGTTAAAACTA-TCATTTGGAAGATGCTTTGGGGTAAACAACACTTCCTTAGGAAGCA -s simHuman_chr6.simHuman.chr6 330828 95 - 601863 ATCAGATACCTGGACACATAGAGCAGATGCATTAGTAATGTTCAAACCA-TCATTTGGAAAATGCTCTGGGGTGAATGACCCTTCCTTAATTATGA -s simRat_chr6.simRat.chr6 242662 81 + 647215 GACCACTACCTTAGGACTT-------TTACATTGGGAATCTAGAGACGGTTCATCT-----ATGC---GGAGTCAGTTTCCCTTACCAAATTATCA - -a -s simMouse_chr6.simMouse.chr6 252744 31 + 636262 GGTCTCTGGGTCAGTCCCCAGACCATTTCAG -s Anc0.Anc0refChr5 69598 18 + 87904 GGTCTCTGAGCC-------------ACCTAG -s Anc1.Anc1refChr7 28417 18 - 47259 GGTCTCTGAGCC-------------ACCTAG -s Anc2.Anc2refChr15 66513 18 + 86568 GGTCTCTGGGCC-------------ACCTAG -s mr.mrrefChr5 105496 18 + 294540 GGTCTCTGAGCC-------------TTTCAG -s simCow_chr6.simCow.chr6 248105 18 + 602619 GGACTCTGGTCC-------------ACCTAG -s simDog_chr6.simDog.chr6 238886 18 + 593897 GATCTCTGGGCC-------------ACCTAG -s simHuman_chr6.simHuman.chr6 330923 18 - 601863 GGTCTCTTAGCC-------------ACCTAG -s simRat_chr6.simRat.chr6 242743 18 + 647215 GGTCTCTGAGCC-------------TTTCAG - -a -s simMouse_chr6.simMouse.chr6 252775 9 + 636262 CACAATAGA -s Anc0.Anc0refChr5 69617 9 + 87904 CACAACAGG -s Anc1.Anc1refChr7 28436 9 - 47259 CACAACAGG -s Anc2.Anc2refChr15 66532 9 + 86568 CACAACAGG -s mr.mrrefChr5 105515 9 + 294540 CACAATAGG -s simCow_chr6.simCow.chr6 248124 9 + 602619 CACAACAGA -s simDog_chr6.simDog.chr6 238905 9 + 593897 CACAACAGG -s simHuman_chr6.simHuman.chr6 330942 9 - 601863 CACTACAGG -s simRat_chr6.simRat.chr6 242762 9 + 647215 CACAATAGG - -a -s simMouse_chr6.simMouse.chr6 252784 37 + 636262 GATGAACAGGCAGGAAGGAGTTGCTCTATATAGGAAT -s Anc0.Anc0refChr5 69626 37 + 87904 ATTACACAGGCAGCAAGAAATGGCATTTCGAAGGAAT -s Anc1.Anc1refChr7 28445 37 - 47259 ATTACACAGGCAGCAAGAAATGGCATTTCGAAGGAAT -s Anc2.Anc2refChr15 66541 37 + 86568 ATTACACAGGCAGCAAGAAATGGCATTTCGAAGGAAT -s mr.mrrefChr5 105524 37 + 294540 GATGAACAGGCAGCAAGGAGTTGCTCTTCATAGGAAT -s simCow_chr6.simCow.chr6 248133 37 + 602619 GTTACACAGGCAGCAAGAAATAGCATTTAGAAGGAAT -s simDog_chr6.simDog.chr6 238919 37 + 593897 ATTACACAGGCAGCAAGAAATGGCATTTCAAAGGAAT -s simHuman_chr6.simHuman.chr6 330951 37 - 601863 ATTACCCAAACAGCAAGAAATGGTAGTTCGAAGGAAG -s simRat_chr6.simRat.chr6 242771 37 + 647215 GATGAACAGGTGGCAAGGAGTTGCTTTTCATAAGAAT - -a -s simMouse_chr6.simMouse.chr6 252821 19 + 636262 CCAGGGACCCAATGTTCAG -s Anc0.Anc0refChr5 69663 18 + 87904 CTAGTAA-CCAACATTCTG -s Anc1.Anc1refChr7 28482 18 - 47259 CTAGTAA-CCAACATTCTG -s Anc2.Anc2refChr15 66578 18 + 86568 CTATTAA-ACAACATTCTG -s mr.mrrefChr5 105561 19 + 294540 CCAGGGACCCAATATTCAG -s simCow_chr6.simCow.chr6 248173 18 + 602619 TTAATGA-ACAACATTGTG -s simDog_chr6.simDog.chr6 238956 16 + 593897 CCATTAA-ACAACACTC-- -s simHuman_chr6.simHuman.chr6 330988 18 - 601863 CTTGTAA-CCAACATTATG -s simRat_chr6.simRat.chr6 242808 19 + 647215 GCAGGGACCCAATATTCAG - -a -s simMouse_chr6.simMouse.chr6 252840 6 + 636262 TAGGAC -s Anc0.Anc0refChr5 69687 6 + 87904 TAGGGA -s Anc1.Anc1refChr7 28506 6 - 47259 TAGGGA -s Anc2.Anc2refChr15 66602 6 + 86568 TAATGA -s mr.mrrefChr5 105580 6 + 294540 TAGGAC -s simCow_chr6.simCow.chr6 248197 6 + 602619 TGAAGA -s simDog_chr6.simDog.chr6 238978 6 + 593897 TAATGA -s simHuman_chr6.simHuman.chr6 331012 6 - 601863 TAGGGA -s simRat_chr6.simRat.chr6 242827 6 + 647215 TAAGAC - -a -s simMouse_chr6.simMouse.chr6 252846 15 + 636262 GTGTGCATAACGTAA -s Anc0.Anc0refChr5 69693 15 + 87904 ATCTGTACAATATAG -s Anc1.Anc1refChr7 28512 15 - 47259 ATCTGTACAATATAG -s Anc2.Anc2refChr15 66608 15 + 86568 AACTGTACAATACAG -s mr.mrrefChr5 105586 15 + 294540 GTGTGTATAATATAA -s simCow_chr6.simCow.chr6 248203 15 + 602619 ACCTGTACAATAGAG -s simDog_chr6.simDog.chr6 238984 15 + 593897 AACTGTGCAATACAG -s simHuman_chr6.simHuman.chr6 331018 15 - 601863 ATCTGTACAATATAG -s simRat_chr6.simRat.chr6 242834 15 + 647215 GTGGGTATAATATAT - -a -s simMouse_chr6.simMouse.chr6 252861 60 + 636262 CTCTTCTCTGTAGCTAAACAGTCAGTGAATCTAATTTGCTAAATATCTCTTATGAATCTC -s Anc0.Anc0refChr5 69708 59 + 87904 TTTGTGTTTGTAGCTAAACAGTCAGTTACTCCAATTTTCTAAATATCTCTTGTGTATCC- -s Anc1.Anc1refChr7 28527 59 - 47259 TTTGTGTTTGTAGCTAAACAGTCAGTTACTCCAATTTTCTAAATATCTCTTGTGTATCC- -s Anc2.Anc2refChr15 66624 59 + 86568 TTTGTGTTTATAGCTAAACAGTTAGTTACTCCAATTTTCTAAATATCTGATGTGTATCC- -s mr.mrrefChr5 105601 60 + 294540 CTCGTGTCTGTAGCTAAACAGTCAGTGACTCTAATTTGCTAAATATCTCTTATGAATCTC -s simCow_chr6.simCow.chr6 248219 59 + 602619 TTTGTAATTACAACTAGAGAGTTAGTAATTCCAATCTCCTAAATGTCTGATCTGTGTCC- -s simDog_chr6.simDog.chr6 239000 59 + 593897 TTTGTGTTTATAGCTAAACAGTTAGTTACTCCAACTTTCTAGATATCTGATGTGTATGT- -s simHuman_chr6.simHuman.chr6 331033 59 - 601863 TTTGTGTTTGTAGCTAAAAAGTCAGTTACTCCAATTGTCTTAATATCCCTTGTGTAGCC- -s simRat_chr6.simRat.chr6 242849 60 + 647215 CTCGTGTCTGTAGCTAAACAGTCAGTGACTGTAATTTGCTAAATATCTCTTATGAATCTC - -a -s simMouse_chr6.simMouse.chr6 252921 3 + 636262 CGG -s Anc0.Anc0refChr5 69767 3 + 87904 CTG -s Anc1.Anc1refChr7 28586 3 - 47259 CTG -s Anc2.Anc2refChr15 66683 3 + 86568 CTG -s mr.mrrefChr5 105661 3 + 294540 CGG -s simCow_chr6.simCow.chr6 248279 3 + 602619 TTG -s simDog_chr6.simDog.chr6 239059 3 + 593897 CTG -s simHuman_chr6.simHuman.chr6 331092 3 - 601863 CAG -s simRat_chr6.simRat.chr6 242909 3 + 647215 CTC - -a -s simMouse_chr6.simMouse.chr6 252924 21 + 636262 GGTCTTCTAACGTTCAGATAC -s Anc0.Anc0refChr5 69770 21 + 87904 TGACTTCTTATGCCTACATAC -s Anc1.Anc1refChr7 28589 21 - 47259 TGACTTCTTATGCCTACATAC -s Anc2.Anc2refChr15 66686 21 + 86568 TAACTTCTTATGCCTACATAC -s mr.mrrefChr5 105664 21 + 294540 GGTCTTCTAATGTCCAGATAC -s simCow_chr6.simCow.chr6 248282 21 + 602619 CAACTTCTTACGCCTAGGTAC -s simDog_chr6.simDog.chr6 239065 21 + 593897 TAACTTTTTATGCCTACATAC -s simHuman_chr6.simHuman.chr6 331095 21 - 601863 TGACTTCTTGTGCCTACATAC -s simRat_chr6.simRat.chr6 242912 21 + 647215 GGTCTTCTAATGACCAGATAC - -a -s simMouse_chr6.simMouse.chr6 252945 1 + 636262 A -s Anc0.Anc0refChr5 69791 1 + 87904 A -s Anc1.Anc1refChr7 28610 1 - 47259 A -s Anc2.Anc2refChr15 66707 1 + 86568 A -s mr.mrrefChr5 105685 1 + 294540 A -s simCow_chr6.simCow.chr6 248303 1 + 602619 A -s simDog_chr6.simDog.chr6 239086 1 + 593897 A -s simHuman_chr6.simHuman.chr6 331116 1 - 601863 A -s simRat_chr6.simRat.chr6 242935 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 252946 6 + 636262 AGAGTA -s Anc0.Anc0refChr5 69850 6 + 87904 AGAGTC -s Anc1.Anc1refChr7 28669 6 - 47259 AGAGTC -s Anc2.Anc2refChr15 66766 6 + 86568 AAAGTC -s mr.mrrefChr5 105686 6 + 294540 AGAGTA -s simCow_chr6.simCow.chr6 248355 6 + 602619 AAAGTC -s simHuman_chr6.simHuman.chr6 331175 6 - 601863 AGAGTC -s simRat_chr6.simRat.chr6 242936 6 + 647215 AAAGTG - -a -s simMouse_chr6.simMouse.chr6 252952 14 + 636262 AGGAACTAAATTGT -s Anc0.Anc0refChr5 69856 11 + 87904 ACGTACTAGGG--- -s Anc1.Anc1refChr7 28675 11 - 47259 ACGTACTAGGG--- -s Anc2.Anc2refChr15 66772 11 + 86568 ACATGCTAGGG--- -s mr.mrrefChr5 105692 11 + 294540 AGGAACTAAAT--- -s simCow_chr6.simCow.chr6 248361 11 + 602619 ACATGCTAGGG--- -s simHuman_chr6.simHuman.chr6 331181 11 - 601863 ATGTACTAGGG--- -s simRat_chr6.simRat.chr6 242946 11 + 647215 AGGAACCCAAT--- - -a -s simMouse_chr6.simMouse.chr6 252966 12 + 636262 GTTGAATGGGTG -s Anc0.Anc0refChr5 69867 11 + 87904 ACTG-ATGGGAG -s Anc1.Anc1refChr7 28686 12 - 47259 ACTGAATGGGAG -s Anc2.Anc2refChr15 66783 11 + 86568 ACTG-GTGGGAG -s mr.mrrefChr5 105703 12 + 294540 GTTGAATGGGTG -s simCow_chr6.simCow.chr6 248376 11 + 602619 ACTG-GTGGGAG -s simHuman_chr6.simHuman.chr6 331192 12 - 601863 ACTGAATGGGAG -s simRat_chr6.simRat.chr6 242957 7 + 647215 GTTAATT----- - -a -s simMouse_chr6.simMouse.chr6 252978 17 + 636262 TGCACAGAGTGTTTTCA -s Anc0.Anc0refChr5 69882 17 + 87904 TATAGAAAATGTCTTCA -s Anc1.Anc1refChr7 28702 17 - 47259 TATAGAAAATGTCTTCA -s Anc2.Anc2refChr15 66798 17 + 86568 TATAGAAAATGTCTTCA -s mr.mrrefChr5 105715 17 + 294540 TGCACAGAGTGTTTTCA -s simCow_chr6.simCow.chr6 248391 17 + 602619 TATAGAAAATGTCTTCA -s simHuman_chr6.simHuman.chr6 331208 17 - 601863 TATAAAAAATATCTTCA - -a -s simMouse_chr6.simMouse.chr6 252995 18 + 636262 GGTCTATCACAAGTATTT -s Anc0.Anc0refChr5 69934 12 + 87904 A------CATAAGTATAT -s Anc1.Anc1refChr7 28754 18 - 47259 AATCCATCATAAGTATAT -s Anc2.Anc2refChr15 66850 12 + 86568 A------CATTAGTAGAT -s mr.mrrefChr5 105732 18 + 294540 GGTCTATCACAAGTATTT -s simCow_chr6.simCow.chr6 248443 11 + 602619 -------CATTAGTAGAT -s simDog_chr6.simDog.chr6 239172 1 + 593897 A----------------- -s simHuman_chr6.simHuman.chr6 331260 18 - 601863 AATCCATCATAAGTGTGT - -a -s simMouse_chr6.simMouse.chr6 253013 19 + 636262 CAAATAGATGGTGCGCAAG -s Anc0.Anc0refChr5 69947 13 + 87904 CGAACAGGTGG------AG -s Anc1.Anc1refChr7 28773 13 - 47259 CGAACAGGTGG------AG -s Anc2.Anc2refChr15 66863 13 + 86568 TGATCAGGTGG------AG -s mr.mrrefChr5 105750 13 + 294540 CAAATAGATGG------AG -s simCow_chr6.simCow.chr6 248455 13 + 602619 TGATCAGGTGG------GG -s simDog_chr6.simDog.chr6 239173 4 + 593897 ---------GG------AG -s simHuman_chr6.simHuman.chr6 331279 13 - 601863 CCAACAGGTGG------AG - -a -s simMouse_chr6.simMouse.chr6 253032 26 + 636262 TAAAGGAGGTTAAGCATTCAGCAATA -s Anc0.Anc0refChr5 69960 13 + 87904 GCAAGATGGATAG------------- -s Anc1.Anc1refChr7 28786 13 - 47259 GCAAGATGGATAG------------- -s Anc2.Anc2refChr15 66876 13 + 86568 GCAAGATCAATAG------------- -s mr.mrrefChr5 105763 13 + 294540 TAAAGGAGGTTAA------------- -s simCow_chr6.simCow.chr6 248469 13 + 602619 GGAAGAAAAATAG------------- -s simDog_chr6.simDog.chr6 239177 12 + 593897 GCACTATCAA-AA------------- -s simHuman_chr6.simHuman.chr6 331292 13 - 601863 GTAAGATGGATAG------------- - -a -s simMouse_chr6.simMouse.chr6 253058 103 + 636262 AGGTTGCCAGATTAGTGGTTTTATCTCCATGCCCTAAGAAGACTACTGAATTGTTAGGGTCTATTTTCACAGTCATGAGACTGCAATTGGAGTAAGTAGAACT -s Anc0.Anc0refChr5 69973 102 + 87904 AGGTCCCCATATTCACTGTTTTGCCTCCATGCCCTGAGGAGACTACAGAGAGGTTAGAGGCTATTCTTACAGTCATGATACTACCATTGGGG-AAGTAGGACT -s Anc1.Anc1refChr7 28799 102 - 47259 AGGTCCCCATATTCACTGTTTTGCCTCCATGCCCTGAGGAGACTACAGAGAGGTTAGAGGCTATTCTTACAGTCATGATACTACCATTGGGG-AAGTAGGACT -s Anc2.Anc2refChr15 66889 102 + 86568 AGGTCCCCATATTCACTCTTTTGCCTCCATGCCCTGATGGGACCACAGGGAGGTTAGAGGCTATTCTTAAAGTCATGATACTACCATTGGGA-AGGTAGGACT -s mr.mrrefChr5 105776 102 + 294540 AGGTTGCCAGATTAGTGGTTTTATCTCCATGCCCTAAGAAGACTACTGAATTGTTAGGGTCTATTTTCACAGTCATGAGACTGCCATTGGAG-AAGTAGAACT -s simCow_chr6.simCow.chr6 248500 102 + 602619 AGGTTCCCATATTCACTCTTTTGCCTCCGTGCCCTGATGGGACCACAGGGAGGTTAGAGGCTATTCTTAAAGTCATGATACTACCATTGGGA-AGGTAGGACT -s simDog_chr6.simDog.chr6 239189 40 + 593897 AGGTC--------CACTCTTTTGCCTCCATACCCTGA------------------------------------------------------A-AGGTATGACT -s simHuman_chr6.simHuman.chr6 331305 102 - 601863 AGGTCCCCATATTCACTGCTTTGCCTCTATGCCCTGAGGAGATTACAGAGAGGTTAGTGGTTATTCTTACAGTCATGGTGCTACCATTGTGG-AAGTAGGACT -s simRat_chr6.simRat.chr6 242964 26 + 647215 ----------------------------------------------------------------------AGTCTAGACAACGCCAT-------GGTAAAACT - -a -s simMouse_chr6.simMouse.chr6 253161 28 + 636262 TTCAGTGAGGACGATGAAGTCACTAACC -s Anc0.Anc0refChr5 70076 27 + 87904 TTCAGTGACAATGATGAAGTCACT-AAC -s Anc1.Anc1refChr7 28902 28 - 47259 TTCAGTGACAATGATGAAGTCACTAAAC -s Anc2.Anc2refChr15 66992 27 + 86568 TTCAGCGACAATGATGAAGTCCAT-GGC -s mr.mrrefChr5 105878 28 + 294540 TTCAGTGAGAATGATGAAGTCACTAACC -s simCow_chr6.simCow.chr6 248603 27 + 602619 TTCAGAGACATTGATGAAGTCCAT-GGC -s simDog_chr6.simDog.chr6 239230 21 + 593897 TTTAGCAACAATTATGAAGTC------- -s simHuman_chr6.simHuman.chr6 331408 28 - 601863 TTCAGTGACAATGATGGAGTCACTAAAC -s simRat_chr6.simRat.chr6 242990 28 + 647215 TACAGTGAGAATGATGAACTCACTAACC - -a -s simMouse_chr6.simMouse.chr6 253189 14 + 636262 AATCATACATCTGT -s Anc0.Anc0refChr5 70105 14 + 87904 AATCACAAATCTGG -s Anc1.Anc1refChr7 28932 14 - 47259 AATCACAAATCTGG -s Anc2.Anc2refChr15 67021 14 + 86568 AATTACAAATCTGG -s mr.mrrefChr5 105906 14 + 294540 AATCATACATCTGT -s simCow_chr6.simCow.chr6 248632 14 + 602619 AATTACAAATCTCG -s simDog_chr6.simDog.chr6 239251 10 + 593897 ----ACAAATCTGG -s simHuman_chr6.simHuman.chr6 331438 14 - 601863 AATCACAAATCTGG -s simRat_chr6.simRat.chr6 243018 14 + 647215 AACCATACATCTGT - -a -s simMouse_chr6.simMouse.chr6 253203 13 + 636262 ATTGCAGTGGAAG -s Anc0.Anc0refChr5 70119 10 + 87904 GTT---GTGGAGG -s Anc1.Anc1refChr7 28946 10 - 47259 GTT---GTGGAGG -s Anc2.Anc2refChr15 67035 10 + 86568 GTT---GTGGAGG -s mr.mrrefChr5 105920 13 + 294540 ATTGCAGTGGAAG -s simCow_chr6.simCow.chr6 248646 10 + 602619 ACT---GTGGTGG -s simDog_chr6.simDog.chr6 239264 10 + 593897 GTA---GTGGAAG -s simHuman_chr6.simHuman.chr6 331452 10 - 601863 GTT---GTGGAGG -s simRat_chr6.simRat.chr6 243032 13 + 647215 ATTGCAGTGGAAG - -a -s simMouse_chr6.simMouse.chr6 253216 38 + 636262 ATATTCAAAGTGGGGTCTAGTGTACAGTTATTACCTGC -s Anc0.Anc0refChr5 70129 37 + 87904 ATCTACAA-GTGTAGTCTAGTGAACAGCTATTGACTGT -s Anc1.Anc1refChr7 28956 37 - 47259 ATCTACAA-GTGTAGTCTAGTGAACAGCTATTGACTGT -s Anc2.Anc2refChr15 67045 37 + 86568 CTATACAA-GTGTAGTCTAGTGAACAGCTATTGACTGT -s mr.mrrefChr5 105933 37 + 294540 ATCTTCAA-GTGTAGTCTAGTGTACAGTTATTACCTGC -s simCow_chr6.simCow.chr6 248660 37 + 602619 CTACACAA-GTGTAGTCTAGTGACCAGCTATTGACAGT -s simDog_chr6.simDog.chr6 239274 36 + 593897 CTATACGA-GTCTAATCTAGTGAACAGCTATTAACTG- -s simHuman_chr6.simHuman.chr6 331462 37 - 601863 AGCTAGAA-CTGTAGTCTAGCGCACAGCTATTGACTGT -s simRat_chr6.simRat.chr6 243045 36 + 647215 GCCTTCAA-GTGTAGTA-AGTGTACAGTTATTACCTGC - -a -s simMouse_chr6.simMouse.chr6 253254 9 + 636262 ACGTCACTT -s Anc0.Anc0refChr5 70166 8 + 87904 ATG-CACTT -s Anc1.Anc1refChr7 28993 9 - 47259 ATGCCACTT -s Anc2.Anc2refChr15 67082 8 + 86568 ATG-CACCT -s mr.mrrefChr5 105970 9 + 294540 ACGTCACTT -s simCow_chr6.simCow.chr6 248697 8 + 602619 ATG-CACCT -s simHuman_chr6.simHuman.chr6 331499 9 - 601863 ATGCCGCTT -s simRat_chr6.simRat.chr6 243085 9 + 647215 ACATCACTT - -a -s simMouse_chr6.simMouse.chr6 253263 1 + 636262 C -s Anc0.Anc0refChr5 70178 1 + 87904 T -s Anc1.Anc1refChr7 29006 1 - 47259 T -s Anc2.Anc2refChr15 67094 1 + 86568 T -s mr.mrrefChr5 105983 1 + 294540 T -s simCow_chr6.simCow.chr6 248709 1 + 602619 T -s simDog_chr6.simDog.chr6 239313 1 + 593897 T -s simHuman_chr6.simHuman.chr6 331512 1 - 601863 T -s simRat_chr6.simRat.chr6 243098 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 253264 48 + 636262 AGTAACAGCTCAATACTGTAATAGTGGCTACAGATATTAGTATTACCT -s Anc0.Anc0refChr5 70183 35 + 87904 AGTGACAGGTC-------------TTGCAACAGACATCAGTTTTTCCT -s Anc1.Anc1refChr7 29011 35 - 47259 AGTGACAGGTC-------------TTGCAACAGACATCAGTTTTTCCT -s Anc2.Anc2refChr15 67099 35 + 86568 AGTGACAGGTA-------------TTGCAACAGACATCAGTTGCTCCT -s mr.mrrefChr5 105984 48 + 294540 AGTAACAGCTCAATACTGTAATAGTGGCTACAGATATTAGTATTACCT -s simCow_chr6.simCow.chr6 248714 35 + 602619 AGTGCCACTGA-------------TGGCAGCAGACGTCAGTTGCTCCT -s simDog_chr6.simDog.chr6 239318 35 + 593897 ATTGACAGGTA-------------TTGCAACAGACATCAGTTGCCCCT -s simHuman_chr6.simHuman.chr6 331517 35 - 601863 AGTGACAGATC-------------TTGCCACAGAAAGCAGTTTTTCAT -s simRat_chr6.simRat.chr6 243099 48 + 647215 ACCAATTGCCAGCTACTGCAACAGTCGTGATAGTTACTGGTACTACCT - -a -s simMouse_chr6.simMouse.chr6 253312 13 + 636262 ACTATTTTTTGAC -s Anc0.Anc0refChr5 70220 13 + 87904 CTTGTTTTTTGCC -s Anc1.Anc1refChr7 29048 13 - 47259 CTTGTTTTTTGCC -s Anc2.Anc2refChr15 67136 13 + 86568 CTTGTTTTTTGCC -s mr.mrrefChr5 106034 13 + 294540 ACTATTTTTTGCC -s simCow_chr6.simCow.chr6 248751 13 + 602619 CCTGTTTTTTGCA -s simDog_chr6.simDog.chr6 239355 13 + 593897 CTTGTTTTATGCC -s simHuman_chr6.simHuman.chr6 331554 13 - 601863 CTTGTTTTTTGCT -s simRat_chr6.simRat.chr6 243149 13 + 647215 ACTATCTTTTGCC - -a -s simMouse_chr6.simMouse.chr6 253325 9 + 636262 CCACATTGT -s Anc0.Anc0refChr5 70239 9 + 87904 CCAAAGTGT -s Anc1.Anc1refChr7 29067 9 - 47259 CCAAAGTGT -s Anc2.Anc2refChr15 67155 9 + 86568 CCAAAGTGT -s mr.mrrefChr5 106053 9 + 294540 CCACATTGT -s simCow_chr6.simCow.chr6 248770 9 + 602619 TCACAGTGT -s simDog_chr6.simDog.chr6 239374 9 + 593897 CCAAAGTGT -s simHuman_chr6.simHuman.chr6 331573 9 - 601863 CCATAGCGT -s simRat_chr6.simRat.chr6 243168 9 + 647215 CCACAATGT - -a -s simMouse_chr6.simMouse.chr6 253334 5 + 636262 AATCA -s Anc0.Anc0refChr5 70249 5 + 87904 AATCA -s Anc1.Anc1refChr7 29077 5 - 47259 AATCA -s Anc2.Anc2refChr15 67165 5 + 86568 AATCA -s mr.mrrefChr5 106063 5 + 294540 AATCA -s simCow_chr6.simCow.chr6 248780 5 + 602619 AATTA -s simDog_chr6.simDog.chr6 239384 5 + 593897 AATCG -s simHuman_chr6.simHuman.chr6 331583 5 - 601863 AATCA -s simRat_chr6.simRat.chr6 243178 5 + 647215 AATCA - -a -s simMouse_chr6.simMouse.chr6 253339 104 + 636262 GGTGAGAATGAAGAATTGGCAAAAGCTGACCCCCAAACTGGAGGAGTGTGAGAGTATGGTTCAGATTTACTTACTAGTACGGTTATTGCCTATTGAGATTTGGT -s Anc0.Anc0refChr5 70257 17 + 87904 AGTGGTGACCCAGATTT--------------------------------------------------------------------------------------- -s Anc1.Anc1refChr7 29085 17 - 47259 AGTGGTGACCCAGATTT--------------------------------------------------------------------------------------- -s Anc2.Anc2refChr15 67173 17 + 86568 AGTGGTGACCCAGATTT--------------------------------------------------------------------------------------- -s mr.mrrefChr5 106071 67 + 294540 GGTGAGAATGAAGAATTGGCAAAAGCTGACCCCCAAACTGGAGGAGTGTGAG-------------------------------------CTATTGAGATTTGGT -s simCow_chr6.simCow.chr6 248788 17 + 602619 AGTGGTCACCCAGTTTT--------------------------------------------------------------------------------------- -s simDog_chr6.simDog.chr6 239392 17 + 593897 AGTGGTGACCCAGATTT--------------------------------------------------------------------------------------- -s simHuman_chr6.simHuman.chr6 331591 4 - 601863 AGTG---------------------------------------------------------------------------------------------------- -s simRat_chr6.simRat.chr6 243189 67 + 647215 GGTGAGAATGAAGAATTGGCAAAACCCGACACCAAAACTGGAGGAGTGTGAG-------------------------------------CAAGTGAGATTTGAT - -a -s simMouse_chr6.simMouse.chr6 253443 71 + 636262 CCCATCAAAAATTTGTGATCACACTCTGCATTATTTCAGGGGCCCTGGGTTTAAAGGCCGCTAAGGTGTGG -s mr.mrrefChr5 106138 71 + 294540 CCCATCAAAAATTTGTGATCACACTCTGCATTATTTCAGGGGCCCTGGGTTTAAAGGCCGCTAAGGTGTGG -s simRat_chr6.simRat.chr6 243261 71 + 647215 ACCATCAAAATTTTGTGATCACAATCTGCATTATTTCAGGGGTACTGGGTTTAAAGGTCATTAAGTTGTGG - -a -s simMouse_chr6.simMouse.chr6 253514 47 + 636262 TAATAGTAACCACCAATCCAGTAAACTACAACAGACAGCATTTTTAT -s Anc0.Anc0refChr5 70274 9 + 87904 --------------------------------------CATTTTCAT -s Anc1.Anc1refChr7 29102 9 - 47259 --------------------------------------CATTTTCAT -s Anc2.Anc2refChr15 67190 9 + 86568 --------------------------------------CATTTTCAT -s mr.mrrefChr5 106209 46 + 294540 TAATAGTAACCACCAATCCAGTAAACT-CAACAGACAGCATTTTTAT -s simCow_chr6.simCow.chr6 248805 9 + 602619 --------------------------------------TATTTTTAT -s simDog_chr6.simDog.chr6 239409 9 + 593897 --------------------------------------CATTTTCAT -s simRat_chr6.simRat.chr6 243359 46 + 647215 TAACAGTAACCTCCAACCCAGTAAACC-CAAAAGAGATTATTTTTAT - -a -s simMouse_chr6.simMouse.chr6 253561 35 + 636262 TCTAATGTACCTGCCGTAGTAAGAAATGGCTCAAT -s Anc0.Anc0refChr5 70283 33 + 87904 TC--ATGTTCTCACTGTAGTAGGAAGTAGCTCAAC -s Anc1.Anc1refChr7 29111 35 - 47259 TCTGATGTTCTCACTGTAGTAGGAAGTAGCTCAAC -s Anc2.Anc2refChr15 67199 33 + 86568 TC--ATGGTTTCACTGTAGTAGGAAGTAGCTCAAC -s mr.mrrefChr5 106255 35 + 294540 TCTGATGTACCTGCCGTAGTAAGAAATAGCTCAAC -s simCow_chr6.simCow.chr6 248814 28 + 602619 -------GTTTCACTGTAGTAGGAAGTAGCTCAAC -s simDog_chr6.simDog.chr6 239428 33 + 593897 TC--ATGGTTTCACTGTAGTAGGCAGTAGCCCAAT -s simHuman_chr6.simHuman.chr6 331595 35 - 601863 CTTGTTGTTCTCACTGTACTAGGAAGTAGCTCAAC -s simRat_chr6.simRat.chr6 243405 35 + 647215 TCTGCTGTACCTGTCATAGTAAGAAATAGCTCAAC - -a -s simMouse_chr6.simMouse.chr6 253596 22 + 636262 AGCCGATTAATTTTGTCAACTT -s Anc0.Anc0refChr5 70332 16 + 87904 AACTGATTTAC---TTCA---T -s Anc1.Anc1refChr7 29162 16 - 47259 AACTGATTTAC---TTCA---T -s Anc2.Anc2refChr15 67248 16 + 86568 AAATGATTTGC---TACA---T -s mr.mrrefChr5 106306 19 + 294540 AACCGATTAATTTTGTCA---T -s simCow_chr6.simCow.chr6 248856 15 + 602619 AAATGATGTGC---T-CA---T -s simDog_chr6.simDog.chr6 239477 16 + 593897 AAATGGTTTGC---TACA---T -s simHuman_chr6.simHuman.chr6 331646 16 - 601863 AACTGATTCAG---ATCA---T -s simRat_chr6.simRat.chr6 243456 18 + 647215 AACCAATTAACTTTGTCA---- - -a -s simMouse_chr6.simMouse.chr6 253618 110 + 636262 TCGACTTGGAGGGCTTTGGCAAACTCTCTTAGCATAAACCAGGGTTGTCATTGTTTAGCCAATTATGACAAAAGAAGGTCAAACCAAGAAGATCCATATATTCATACACT -s Anc0.Anc0refChr5 70349 101 + 87904 TCCACTTGGCAGATTTTGAGAGATACTTTTAGCATAACCCATAGTTGTCAGTGTTTAGCTAGTTATCACAAAAGAGTGTCAAACTAAGAAGATCCATA---------ATG -s Anc1.Anc1refChr7 29179 101 - 47259 TCCACTTGGCAGATTTTGAGAGATACTTTTAGCATAACCCATAGTTGTCAGTGTTTAGCTAGTTATCACAAAAGAGTGTCAAACTAAGAAGATCCATA---------ATG -s Anc2.Anc2refChr15 67265 101 + 86568 TCCACTTGGCAGATTTTGAGAGATACTTTTAGCATAACCCATAGTTATCAGTGTTTAGCTAGTTATCACAAAAGAGTGTCAAACTGAGAAGATCCATA---------GTG -s mr.mrrefChr5 106325 110 + 294540 TCGACTTGGAAGGCTTTGGGAAATTCTTTTAGCATAAACCAGGGTTGTCATTGTTTAGCCAATTATGACAAAAGAAGGTCAAACCAAGAAGATCCATATATTCATACATT -s simCow_chr6.simCow.chr6 248872 100 + 602619 TACACTTGGAAGATTTTGAGAGATACTTTTAGCAGAACCCATAGTTATCTTTGTTTAGCTGACATTCACAAAGGAGTGTCAAA-TGAGAAGATCCATA---------GTG -s simDog_chr6.simDog.chr6 239494 101 + 593897 TCCAATTGGCAGTTTTTGAGAGATACTTTTAGAATCACCCATAATTATCAGTGTTTGGCAAGTTATCATAAAAGAGTGTCATACCGAGAAGATCCATA---------GTG -s simHuman_chr6.simHuman.chr6 331663 101 - 601863 TCCACTTGGGAGATTTGAAGAGTTACTTTTAGCATACCCCGTAGTTGTCAGAGTTTAGCTAGTTATCACAAAAGAGTGTCAAGCTAAGAAGATCAATA---------ATG -s simRat_chr6.simRat.chr6 243474 104 + 647215 ------TGGAAGGCTTTGGGAAATTCTTTTAGCATAAACCAGGGGTGTCATTGTTTAGCCAATGATGACAAAAGAAGGTGAAACCAAGAAGATTCATAAATTCATAAATT - -a -s simMouse_chr6.simMouse.chr6 253728 5 + 636262 TTGCA -s Anc0.Anc0refChr5 70450 5 + 87904 TTGCA -s Anc1.Anc1refChr7 29280 5 - 47259 TTGCA -s Anc2.Anc2refChr15 67367 5 + 86568 TTACA -s mr.mrrefChr5 106435 5 + 294540 TTGCA -s simCow_chr6.simCow.chr6 248973 5 + 602619 CTTCA -s simDog_chr6.simDog.chr6 239596 5 + 593897 TTACA -s simHuman_chr6.simHuman.chr6 331764 5 - 601863 TTGCA -s simRat_chr6.simRat.chr6 243578 5 + 647215 CTGCA - -a -s simMouse_chr6.simMouse.chr6 253733 19 + 636262 TAGAAGCCCATAACACTCC -s Anc0.Anc0refChr5 70455 19 + 87904 TAGGAGACCATAATACTCT -s Anc1.Anc1refChr7 29285 19 - 47259 TAGGAGACCATAATACTCT -s Anc2.Anc2refChr15 67374 19 + 86568 TAGGAGACCATAATACTCT -s mr.mrrefChr5 106440 19 + 294540 TAGAAGCCCATAACACTCC -s simCow_chr6.simCow.chr6 248980 18 + 602619 TAGAAGACTGTAATAGTT- -s simDog_chr6.simDog.chr6 239603 19 + 593897 TAGGAGACCATAACACTCT -s simHuman_chr6.simHuman.chr6 331769 12 - 601863 -------CCATCATACTCT -s simRat_chr6.simRat.chr6 243583 19 + 647215 TAGAAGACGATAACACTCC - -a -s simMouse_chr6.simMouse.chr6 253752 45 + 636262 GTGCCAGAGACATTTAATTACAGAACTCCTTGGTACTACCTTTAT -s Anc0.Anc0refChr5 70474 45 + 87904 GGTCTGAAGACAATTAATTTCAGAGTTCTTTGGCCCTACATTTGT -s Anc1.Anc1refChr7 29304 45 - 47259 GGTCTGAAGACAATTAATTTCAGAGTTCTTTGGCCCTACATTTGT -s Anc2.Anc2refChr15 67393 45 + 86568 GGTCTGAAGGCAATTAATTTCAGAGTTCTTTGGCCCTACATTTGT -s mr.mrrefChr5 106459 45 + 294540 GTGCCAGAGACATTTAATTACAGAACTCCTTGGTACTACCTTTGT -s simCow_chr6.simCow.chr6 248998 43 + 602619 -GTCAGAAGTCAATGAATTTTAGAAATCTTTGTCCCTACACTTG- -s simDog_chr6.simDog.chr6 239624 45 + 593897 GGTCTGAAGGCAATTAGTTTCAGAGTTCTTTGGCACTACATTTGT -s simHuman_chr6.simHuman.chr6 331781 45 - 601863 GGTCGGAAGACAATTAACTTCAGAGGTCTTTCACCCTATATTTGT -s simRat_chr6.simRat.chr6 243602 45 + 647215 ATGCTAGAGACATTTGATTACAGAACTCCTCAGGACTGCCTTTGT - -a -s simMouse_chr6.simMouse.chr6 253797 42 + 636262 TCTTTTTTATGTGCTATCAGAGGCAGGTTAATTACCAGGCCC -s Anc0.Anc0refChr5 70521 40 + 87904 TGATTATTGTGTGCTAACAGA-CCAGGCTAATCCCCAAG-CA -s Anc1.Anc1refChr7 29351 42 - 47259 TGATTATTGTGTGCTAACAGAGCCAGGCTAATCCCCAAGTCA -s Anc2.Anc2refChr15 67440 40 + 86568 CCATTATTGTGTGTTAACAGA-CCAGGCTAATCCCCAAG-CA -s mr.mrrefChr5 106504 42 + 294540 TGTTTTTTATGTGCTATCAGAGGCAGGTTAATTACCAGGCCC -s simCow_chr6.simCow.chr6 249041 26 + 602619 --ATCATTGTGTGTTAACAGA-------------TGAAA-TA -s simDog_chr6.simDog.chr6 239671 26 + 593897 CCATTGT---------------CCAGGCTAATCCCCAAG-CA -s simHuman_chr6.simHuman.chr6 331828 42 - 601863 TGGTTATTGTGTGCTGGCAGAGTCAGGCTAATGCACAAGTCA -s simRat_chr6.simRat.chr6 243647 42 + 647215 TGTTTTTTCTGTGCTATCAGAGGCAGGTTCATTACCAGGCCC - -a -s simMouse_chr6.simMouse.chr6 253839 6 + 636262 AACCAA -s Anc0.Anc0refChr5 70566 6 + 87904 AAACAA -s Anc1.Anc1refChr7 29398 6 - 47259 AAACAA -s Anc2.Anc2refChr15 67485 6 + 86568 AAACAA -s mr.mrrefChr5 106546 6 + 294540 AAACAA -s simCow_chr6.simCow.chr6 249072 6 + 602619 AAACAA -s simDog_chr6.simDog.chr6 239702 6 + 593897 AAACAT -s simHuman_chr6.simHuman.chr6 331875 6 - 601863 AAACAA -s simRat_chr6.simRat.chr6 243689 6 + 647215 AGACAA - -a -s simMouse_chr6.simMouse.chr6 253845 45 + 636262 ACCTACATAAGCGAGATTGTATTGTCAATTAGCTGTGGTCTACTA -s Anc0.Anc0refChr5 70572 45 + 87904 ACCAATATGAATGGGGTAACTAACTCACCTAGCTGTGAACTACTA -s Anc1.Anc1refChr7 29404 45 - 47259 ACCAATATGAATGGGGTAACTAACTCACCTAGCTGTGAACTACTA -s Anc2.Anc2refChr15 67491 45 + 86568 ACCAATATGAATGGTGTAACTAACTCACCTAGGTGTGAACTACTA -s mr.mrrefChr5 106552 45 + 294540 ACCAATATAAGCGAGATAGTAATGTCACTTAGCTGTGGTCTACTA -s simCow_chr6.simCow.chr6 249078 45 + 602619 ACAAATATGAGTGGTGTAACTAACTCACCTAGGTGTGGACTACCA -s simDog_chr6.simDog.chr6 239708 45 + 593897 ACCTATATGAATAATGTAACTAACTCATATATGTGTCAATTACTA -s simHuman_chr6.simHuman.chr6 331881 45 - 601863 ACCAATATTACTGGGGTAACTAACTCCCCTAGCGGTGAACTATTA -s simRat_chr6.simRat.chr6 243701 45 + 647215 ACCAATACAAGGGAGATAGTAACATCACTTTGCTGTGGTCTCCTA - -a -s simMouse_chr6.simMouse.chr6 253890 21 + 636262 ATAATCACCTGAGGAGAAATA -s Anc0.Anc0refChr5 70617 20 + 87904 ACAGTCACCTGAGG-GAAATA -s Anc1.Anc1refChr7 29449 20 - 47259 ACAGTCACCTGAGG-GAAATA -s Anc2.Anc2refChr15 67536 20 + 86568 ACAGTCACCTGAGG-GAAATA -s mr.mrrefChr5 106597 21 + 294540 ATAATCACCTGAGGAGAAATA -s simCow_chr6.simCow.chr6 249124 20 + 602619 GCAGTCACCTGAAG-GAAACA -s simDog_chr6.simDog.chr6 239753 19 + 593897 ACAGTCACCTG-GG-GAAATA -s simHuman_chr6.simHuman.chr6 331926 20 - 601863 ACAGTCACCTGAGG-GAAATA -s simRat_chr6.simRat.chr6 243746 21 + 647215 ATAATCACCTGATGAACGATC - -a -s simMouse_chr6.simMouse.chr6 253911 120 + 636262 AGTACTAAAGAGTACAGCCGTCAGATTAGTAGGGCAACTAAGAGCAACATATGAGTGTTAGAGAAGATGCAGATGGCAATAAACGTCCCCCATTGAGATTAAGCAAAGGAAATTTGACTT -s Anc0.Anc0refChr5 70641 115 + 87904 AG-GC----AAGTCAGGCGGTGAGATTAGTAGGGCAACTAAGAGCAAGATAAGACAGTTACAGAAAATGCTGATGGCAACAAATACACACAATTGAGATCAAGTAAGGCAAAACTGATTT -s Anc1.Anc1refChr7 29473 115 - 47259 AG-GC----AAGTCAGGCGGTGAGATTAGTAGGGCAACTAAGAGCAAGATAAGACAGTTACAGAAAATGCTGATGGCAACAAATACACACAATTGAGATCAAGTAAGGCAAAACTGATTT -s Anc2.Anc2refChr15 67573 115 + 86568 AG-AC----AAGTCAGGTGGTCAGATTAGTAGGGCAACTAAGAGCAAGATAAAACATTTACAGAAAATGCTGGTGGCAACAAATATAAACACTTGGGATCAAGTTAGGCAAAACTGATTT -s mr.mrrefChr5 106618 119 + 294540 AG-GCTAAAGAGTACAGCCGTGAGATTAGTAGGGCAACTAAGAGCAAGATATGAGTGTTAGAGAAAATGCTGATGGCAATAAACGCCCCCCATTGAGATTAAGCAAAGGAAATTTGACTT -s simCow_chr6.simCow.chr6 249161 114 + 602619 AG-AC----AAGTCA-GTGGTCAGATCAGAAGGGCAACTAAGACCAAGATAAAATGCTTACAGAAAATGCTGGTGGCAATAAGTATAAACATTTGGGATAAAGTGAGACAAAACTGAGGT -s simDog_chr6.simDog.chr6 239789 106 + 593897 AG-AC----AAGTCAGG---------TAATAGGGCAACTAAGAGCAAGATAAAACATTTACAGAAAATGCTGGTGGCAACAAATATAAGCACTTGGGATCAAATTAGGCAAAGCTGATTT -s simHuman_chr6.simHuman.chr6 331950 115 - 601863 AG-GC----AAGTCAGGCTGTGAGATTAGTAGGGGAAATAAGAGCAAGATAAGGCAGTTACAGAAAATACTGATGGCAACAGATCCACACAATTGAGATCAAGTAAGGCAAAACTGATCT -s simRat_chr6.simRat.chr6 243767 119 + 647215 AG-GCTAAAGAGTATAGCCGTGAGATTAGTAGGGTAACTAAGAGCAAGATACAAGTGTTAGAGAAAACGCTGATAGCAATCAAAGCCCCCTGTTGAGATTAAGCAAATGAAGTTTAACTT - -a -s simMouse_chr6.simMouse.chr6 254031 53 + 636262 AGGAATGACAATAGAAGTGGAATCTAAGTTTCTTAGGAATGACAATAGAAGTG -s Anc0.Anc0refChr5 70756 19 + 87904 A-GCA---------------------------------ATAACAATGGAAGTG -s Anc1.Anc1refChr7 29588 19 - 47259 A-GCA---------------------------------ATAACAATGGAAGTG -s Anc2.Anc2refChr15 67688 19 + 86568 A-GCA---------------------------------ATAACAATGGAAGTG -s mr.mrrefChr5 106737 20 + 294540 AGGAA---------------------------------ATGACAATAGAAGTG -s simCow_chr6.simCow.chr6 249275 19 + 602619 T-GCA---------------------------------ATAACAATGGAAGTG -s simDog_chr6.simDog.chr6 239896 19 + 593897 A-GCA---------------------------------ATGACAATGGAAGCA -s simHuman_chr6.simHuman.chr6 332065 19 - 601863 A-GCA---------------------------------ATAACAATGGAAGTG -s simRat_chr6.simRat.chr6 243886 20 + 647215 AGGAA---------------------------------ATGACAATAGAAGTG - -a -s simMouse_chr6.simMouse.chr6 254084 18 + 636262 GAATCTAAGTTTGTGCTA -s Anc0.Anc0refChr5 70776 18 + 87904 AAAATTAAGTTACTGCTA -s Anc1.Anc1refChr7 29608 18 - 47259 AAAATTAAGTTACTGCTA -s Anc2.Anc2refChr15 67708 18 + 86568 AAAATTATGTTACTGTTA -s mr.mrrefChr5 106757 18 + 294540 GAATCTAAGTTTCTGCTA -s simCow_chr6.simCow.chr6 249295 18 + 602619 AAAATTTTGATTCTGTTA -s simDog_chr6.simDog.chr6 239916 18 + 593897 ATAAATATGTTAATGTTA -s simHuman_chr6.simHuman.chr6 332085 18 - 601863 AAAATTAAGTTACTGCTA -s simRat_chr6.simRat.chr6 243906 18 + 647215 GAATCTAAGTTTCTGCTA - -a -s simMouse_chr6.simMouse.chr6 254102 50 + 636262 TTAAAGTTTTCCGATATTGACTATTGCGCAAGCAAGCTACTTAAAAAGTG -s Anc0.Anc0refChr5 70794 50 + 87904 TCAGAGTCTGCCACTATCGAATATGGTGCAAGCTGGCTACTTAATAAGTG -s Anc1.Anc1refChr7 29626 50 - 47259 TCAGAGTCTGCCACTATCGAATATGGTGCAAGCTGGCTACTTAATAAGTG -s Anc2.Anc2refChr15 67726 50 + 86568 TCAGCGTCTGCCAGTATCGAATATGGTGCAAGCTAGCTACTTATTAAGTG -s mr.mrrefChr5 106775 50 + 294540 TTAAAGTTTTCCACTATTGACTATGGTGCAAGCTGGCTACTTAAAAAGTG -s simCow_chr6.simCow.chr6 249313 50 + 602619 TCAGGGTCTGCCATGATCAAACTTGGTCCAAGATATCTACTTATTAAGTG -s simDog_chr6.simDog.chr6 239940 50 + 593897 TCAGCGTCTGCCAGTATAGATTATGGTGTAAGCTAGCTACCTATTAGATG -s simHuman_chr6.simHuman.chr6 332103 50 - 601863 TCTGAGACTGCCACTTTCCAATATGGTGCCAGCTGCCTACTTAATAAGTG -s simRat_chr6.simRat.chr6 243924 45 + 647215 TT-----TTTCTACTATTGACTATGGTGCAAGCTGGCTACTCAAAAAGTG - -a -s simMouse_chr6.simMouse.chr6 254152 134 + 636262 TTTATAGGGCCGTAGGAACATAATAGTCTGCAGTGGTCCTAGATCAATACTAAGCAATAATGACCGTAAGAGATGTTTACTGCTCTGGTAAGTACAGGGTAGTCCATGTAGAGATGCTGCAAGTGTCTACCTAT -s Anc0.Anc0refChr5 70855 129 + 87904 TTTAGAAGGCTGCAGGAGCATAATAGTCTGCACTGG-CCTAAATGACTATTAAGTAATAGCAACAGTAAGAGGTGTTGGCTGGTCTAGCAAGTATGGGATAGCAGATATGAT--TGCTGCCAT--TGTACCTTC -s Anc1.Anc1refChr7 29687 132 - 47259 TTTAGAAGGCTGCAGGAGCATAATAGTCTGCACTGGTCCTAAATGACTATTAAGTAATAGCAACAGTAAGAGGTGTTGGCTGGTCTAGCAAGTATGGGATAGCAGATATGAT--TGCTGCCATTGTGTACCTTC -s Anc2.Anc2refChr15 67787 129 + 86568 TTTAGGAGGCTGCAGGAGCATAATAGCATGCACTGG-CCTAAATGACTATTAAGTAATAGCAACAGTAAGAGGTGTTGGCTGGTCTAGCAAGTGTGAGATAGTAGATATGAT--TGATGCCAT--TATACCTTC -s mr.mrrefChr5 106825 132 + 294540 TTTATAAGGCTGTAGGAGCATAATAGTCTGCAGTGGTCCTAAATGAATACTAAGCAATAGCGACCGTAAGAGATGTTTACTGGTCTAGTAAGTACAGGGTAGCCGATGTGGA--TGCTGCAATTGTCTACCTAT -s simCow_chr6.simCow.chr6 249374 128 + 602619 TTCAGCAGGTTGCAGGAGCACAATAACTTGCATCGG-CC-GAATTACTATTAAGTAATATCCAGAGTAAGAGGAGTTGGCTGGTCTAACAAGTGGGAGATAGTAGATACAAT--TGTTCCCAT--TCTACCATC -s simDog_chr6.simDog.chr6 240007 129 + 593897 CGTAGGGGTCTGCAGGAGCATAATAGCATGCACTGG-CCTAAATGACAATTAAGTAACAGCAACAGTTAGAGATGTTGGATGATCTAGCAAGTGTCAGATAGTAGATGTGGT--TGATGCCAT--TATACCTTC -s simHuman_chr6.simHuman.chr6 332164 132 - 601863 TTTACAAAGCTGCAGGAGCAGAGTAGTCTGCCCTGGTCCTAAATGACTATAAAGTAATAGCAACAGTAACAGGTGTTGGCTGGTCTAGCAAGCATGGGATAGCAGACATGAC--CACTGCCATTGTGCACCTGC -s simRat_chr6.simRat.chr6 243969 128 + 647215 TTTATAAGGCTCTAGGAG----ATGGTCTGCATCGGTCTTAAATGAATACTAAGCAACAGCGACCATACGAGATGCTTACTGGTCTAGTAGCTACAAGGTGGCCGATCTGGA--TGCTGCAATTCTCTACCTAT - -a -s simMouse_chr6.simMouse.chr6 254286 4 + 636262 ACCA -s Anc0.Anc0refChr5 70999 4 + 87904 AGCA -s Anc1.Anc1refChr7 29834 4 - 47259 AGCA -s Anc2.Anc2refChr15 67931 4 + 86568 TGCA -s mr.mrrefChr5 106970 4 + 294540 ACCA -s simCow_chr6.simCow.chr6 249517 4 + 602619 CTTA -s simDog_chr6.simDog.chr6 240151 4 + 593897 TGCA -s simHuman_chr6.simHuman.chr6 332311 4 - 601863 AGCA -s simRat_chr6.simRat.chr6 244110 4 + 647215 ACCA - -a -s simMouse_chr6.simMouse.chr6 254290 8 + 636262 ACCATCAT -s Anc0.Anc0refChr5 71005 8 + 87904 ACCAGGTT -s Anc1.Anc1refChr7 29840 8 - 47259 ACCAGGTT -s Anc2.Anc2refChr15 67937 8 + 86568 ACAAGGTT -s mr.mrrefChr5 106974 8 + 294540 ACCATCAT -s simCow_chr6.simCow.chr6 249523 8 + 602619 ACAGAGTT -s simDog_chr6.simDog.chr6 240157 8 + 593897 AGAAGGTG -s simHuman_chr6.simHuman.chr6 332317 8 - 601863 ACCAGGTT -s simRat_chr6.simRat.chr6 244114 8 + 647215 ACCATCCT - -a -s simMouse_chr6.simMouse.chr6 254298 2 + 636262 TC -s Anc0.Anc0refChr5 71013 2 + 87904 AC -s Anc1.Anc1refChr7 29848 2 - 47259 AC -s Anc2.Anc2refChr15 67945 2 + 86568 AC -s mr.mrrefChr5 106982 2 + 294540 TC -s simCow_chr6.simCow.chr6 249531 2 + 602619 AC -s simDog_chr6.simDog.chr6 240177 2 + 593897 AC -s simHuman_chr6.simHuman.chr6 332325 2 - 601863 AC -s simRat_chr6.simRat.chr6 244122 2 + 647215 TC - -a -s simMouse_chr6.simMouse.chr6 254300 61 + 636262 ATGGCTTTTGCCAGGGACATACATGATCCAGCAATACACCCAAACAAACTCTGGGATGCAG -s Anc0.Anc0refChr5 71015 59 + 87904 ATGGCTTCCGCCAACAACATACATGACCTATCA--ACACCCAAACAAATTCTGACACACAG -s Anc1.Anc1refChr7 29850 61 - 47259 ATGGCTTCCGCCAACAACATACATGACCTATCAACACACCCAAACAAATTCTGACACACAG -s Anc2.Anc2refChr15 67947 59 + 86568 ATGGCTTCCGCTAACAACATACATGACCTATCA--AAACCTAAACAAATCCCAACACACAG -s mr.mrrefChr5 106984 61 + 294540 ATGGCTTTTGCCAGGGACATACATGATCTAGCAACACACCCAAACAAACTCTGACATGCAG -s simCow_chr6.simCow.chr6 249534 59 + 602619 ATGAATTCTACTAACAAAATAAATGACATATCA--AAACTTAAACAAATCTCCAAATAGAA -s simDog_chr6.simDog.chr6 240179 59 + 593897 ATGGCTTCCGCTAACTACATACATGATCTATCA--AAACCTAAATAAATCCCAACACACTG -s simHuman_chr6.simHuman.chr6 332327 61 - 601863 ATGGCTTCAGCCGACAACATACATGACCTATCAACACTTCCAAACAAATTCTGACACACAG -s simRat_chr6.simRat.chr6 244124 61 + 647215 ATGGGTTTTGCCAGTGATATACATGATCTAGCAACACACCCAAACAAACTCCGACATGCAG - -a -s simMouse_chr6.simMouse.chr6 254361 47 + 636262 TTGGAGTCAACTGGCCAATAAAGCGGGTAGTTGGTTAGTGAGATATA -s Anc0.Anc0refChr5 71075 47 + 87904 CTGAAGTAAACTGAAAAAAAAAGCAAATAGTTAGGTTGGGAGAGATA -s Anc1.Anc1refChr7 29912 47 - 47259 CTGAAGTAAACTGAAAAAAAAAGCAAATAGTTAGGTTGGGAGAGATA -s Anc2.Anc2refChr15 68007 47 + 86568 CTGAGCTAAGCTGAAAAAAAAAGCAAATAGTTAGGTTGGAAGAGATA -s mr.mrrefChr5 107045 47 + 294540 CTGAAGTCAACTGGCCAATAAAGCAGGTAGTTAGTTTGTGAGATATA -s simCow_chr6.simCow.chr6 249594 47 + 602619 GTGAGTTATGCTGACAAATGAAGCAAATAGTTAGTTTGGAAAAGATG -s simDog_chr6.simDog.chr6 240239 47 + 593897 CTAAGCTCAGCTGAAACAAAAGGCAAATAGTTGGGCTGGAAGAGATA -s simHuman_chr6.simHuman.chr6 332389 47 - 601863 CCGAAGTAAACTGAATAACAAAGCAAATAGTGAGGTTGGGAGAGGTA -s simRat_chr6.simRat.chr6 244185 47 + 647215 CTTAACTCAAATGGCCAATAAAGCAGGTAATTAGATTGTGAGACTTA - -a -s simMouse_chr6.simMouse.chr6 254408 4 + 636262 TGTT -s Anc0.Anc0refChr5 71122 4 + 87904 GGTT -s Anc1.Anc1refChr7 29959 4 - 47259 GGTT -s Anc2.Anc2refChr15 68054 4 + 86568 GGTT -s mr.mrrefChr5 107092 4 + 294540 TGTT -s simCow_chr6.simCow.chr6 249649 4 + 602619 GGTT -s simDog_chr6.simDog.chr6 240286 4 + 593897 GGCT -s simHuman_chr6.simHuman.chr6 332436 4 - 601863 GGTT -s simRat_chr6.simRat.chr6 244232 4 + 647215 TGTT - -a -s simMouse_chr6.simMouse.chr6 254412 9 + 636262 ATTGCATGT -s Anc0.Anc0refChr5 71129 9 + 87904 GTTGCATCT -s Anc1.Anc1refChr7 29966 9 - 47259 GTTGCATCT -s Anc2.Anc2refChr15 68061 9 + 86568 ATTGCATCT -s mr.mrrefChr5 107096 9 + 294540 GTTGCATGT -s simCow_chr6.simCow.chr6 249656 9 + 602619 ATTGCATCG -s simDog_chr6.simDog.chr6 240293 9 + 593897 ATTACATCT -s simHuman_chr6.simHuman.chr6 332443 9 - 601863 GTTGCATTT -s simRat_chr6.simRat.chr6 244236 9 + 647215 GTTGCATGT - -a -s simMouse_chr6.simMouse.chr6 254421 65 + 636262 TTAATGGACAAGGTTCCAAACTTGCTACTCTGATCAGACATCATATATCCCCAGGTCACTTGGCT -s Anc0.Anc0refChr5 71138 60 + 87904 TTAGTGGGCAAAGCTCTACTCTTATTACTTCGCTCA-----CATATACCCCAAAATTACCTTACT -s Anc1.Anc1refChr7 29975 60 - 47259 TTAGTGGGCAAAGCTCTACTCTTATTACTTCGCTCA-----CATATACCCCAAAATTACCTTACT -s Anc2.Anc2refChr15 68076 60 + 86568 TTAGTGAGCATATCTCTACTCTTATTACTTCACTCA-----CATATACCCCAAAATTACCTTACT -s mr.mrrefChr5 107105 65 + 294540 TTAATGGACAAGGTTCCACACTTACTACTCCGATCAGACATCATATATCCCCAGGTCACTTGGCT -s simCow_chr6.simCow.chr6 249671 60 + 602619 CTAGTGAGTAGACCTCTACTTTTATTTCTTCACCCA-----CATACCCCCAAATTCTACCTTACC -s simDog_chr6.simDog.chr6 240308 58 + 593897 TTAGTGAGCATATCTCTACTCTTATTACTTCATTT-------GTATACCCCCAAATTATCTTACT -s simHuman_chr6.simHuman.chr6 332452 60 - 601863 TTAGTGGGCAAAGCACTGCTCTTATTACTTCGCTCA-----CATATACCCCAAAATTGCCTTACT -s simRat_chr6.simRat.chr6 244245 65 + 647215 TTAATGGACAAGGTTCCACACTTACTACTCCGATCAGACATCACATATCCCCAGGTCACTTGGTT - -a -s simMouse_chr6.simMouse.chr6 254486 41 + 636262 AAACTAAACAGTTGCCTACCCCAAAATTACCTTATTAGAAT -s Anc0.Anc0refChr5 71198 41 + 87904 AAACTGTACAGTTGTATGTCCCAAAATTCCCTTATTAGACT -s Anc1.Anc1refChr7 30035 41 - 47259 AAACTGTACAGTTGTATGTCCCAAAATTCCCTTATTAGACT -s Anc2.Anc2refChr15 68136 41 + 86568 AAACTGTACAGTTGAATGTCCTGAGACTCCTTCATTAATCT -s mr.mrrefChr5 107170 41 + 294540 AAACTGAACAGTTGTCTACCCCAAAATTACCTTATTAGAAT -s simCow_chr6.simCow.chr6 249731 19 + 602619 AAACTGTATGGTTGACTGT---------------------- -s simDog_chr6.simDog.chr6 240369 41 + 593897 AAACTGTACAGCTGAATATCCTGAGACTCCTTCATTAATCT -s simHuman_chr6.simHuman.chr6 332512 39 - 601863 AAACTGGACAGTTGTGT--TCCAAAATTCCCTTATCAGACT -s simRat_chr6.simRat.chr6 244310 41 + 647215 AAACCGAACAGTTGTCTACCTCATAATTACCTTATTAGAAT - -a -s simMouse_chr6.simMouse.chr6 254527 8 + 636262 CTAGCTGA -s Anc0.Anc0refChr5 71242 7 + 87904 -TAGCTGA -s Anc1.Anc1refChr7 30079 8 - 47259 CTAGCTGA -s Anc2.Anc2refChr15 68180 7 + 86568 -TGGCTGG -s mr.mrrefChr5 107211 8 + 294540 CTAGCTGA -s simCow_chr6.simCow.chr6 249750 5 + 602619 ---GCAGG -s simDog_chr6.simDog.chr6 240413 7 + 593897 -TGGCTGG -s simHuman_chr6.simHuman.chr6 332554 8 - 601863 CAAGCTGA -s simRat_chr6.simRat.chr6 244351 8 + 647215 CTTATTGG - -a -s simMouse_chr6.simMouse.chr6 254535 28 + 636262 CCATGGGAATATCATTTGATATCTAAAC -s Anc0.Anc0refChr5 71253 28 + 87904 TCATCGAGATGTGGCTCAATAGCTACAC -s Anc1.Anc1refChr7 30091 28 - 47259 TCATCGAGATGTGGCTCAATAGCTACAC -s Anc2.Anc2refChr15 68191 28 + 86568 TCATCGAGATGTGGCTCAATGGGCACAT -s mr.mrrefChr5 107219 28 + 294540 CCATGGGAATATCACTTGATAGCTAAAC -s simCow_chr6.simCow.chr6 249759 28 + 602619 TCATGGAGATGTGGTTCAATTGTCACAT -s simDog_chr6.simDog.chr6 240424 28 + 593897 TCATCGAGATTCGGCTTTATGGGCACAT -s simHuman_chr6.simHuman.chr6 332566 28 - 601863 TCTTAGAGATGTGGCTCAATAGCTACAC -s simRat_chr6.simRat.chr6 244359 28 + 647215 CTATGGGAATATCACTTGCTAGCCAAAC - -a -s simMouse_chr6.simMouse.chr6 254563 7 + 636262 AATGTAC -s Anc0.Anc0refChr5 71281 7 + 87904 AATATAT -s Anc1.Anc1refChr7 30119 7 - 47259 AATATAT -s Anc2.Anc2refChr15 68219 7 + 86568 AATGTAT -s mr.mrrefChr5 107247 7 + 294540 AATATAC -s simCow_chr6.simCow.chr6 249788 7 + 602619 AATGTAT -s simDog_chr6.simDog.chr6 240452 7 + 593897 GATGTGT -s simHuman_chr6.simHuman.chr6 332594 5 - 601863 ACTAT-- -s simRat_chr6.simRat.chr6 244387 7 + 647215 AACACAC - -a -s simMouse_chr6.simMouse.chr6 254570 30 + 636262 TTTGAGTAGGCGGACAACCAATACACAACC -s Anc0.Anc0refChr5 71288 30 + 87904 CTTGTATAGGTATGGAATTAAAATGTGACA -s Anc1.Anc1refChr7 30126 30 - 47259 CTTGTATAGGTATGGAATTAAAATGTGACA -s Anc2.Anc2refChr15 68226 30 + 86568 CTAGTATAGGTATGGAATTAAAGTGTAACA -s mr.mrrefChr5 107254 30 + 294540 TTTGTATAGGTGTGGAATTAAAATATGACA -s simCow_chr6.simCow.chr6 249801 30 + 602619 TTAGTATAGGTATGGAATTGAAGGTTAACA -s simDog_chr6.simDog.chr6 240459 30 + 593897 CTAGTATAGGTATGGAATTAAAGTGCAACA -s simHuman_chr6.simHuman.chr6 332599 30 - 601863 CTTGTATAGGTATGGAATTAAAATGTGTCA -s simRat_chr6.simRat.chr6 244394 30 + 647215 TTTGTATAGGTGTGGAATTAAAATATGACA - -a -s simMouse_chr6.simMouse.chr6 254600 1 + 636262 C -s Anc0.Anc0refChr5 71318 1 + 87904 C -s Anc1.Anc1refChr7 30156 1 - 47259 C -s Anc2.Anc2refChr15 68257 1 + 86568 C -s mr.mrrefChr5 107284 1 + 294540 C -s simCow_chr6.simCow.chr6 249832 1 + 602619 C -s simDog_chr6.simDog.chr6 240490 1 + 593897 C -s simHuman_chr6.simHuman.chr6 332629 1 - 601863 C -s simRat_chr6.simRat.chr6 244424 1 + 647215 C - -a -s simMouse_chr6.simMouse.chr6 254601 102 + 636262 CTGTGATCCTACCCCAAAATTACCTTATTAGAATCTTGCTGACCATGGGGATATTATTTGATAGCTAAACAATGTACTTTGAGTAGGTGGACAACCAATACA -s Anc0.Anc0refChr5 71328 35 + 87904 CTGTGACCT------------------------------------------------------GCTGATATACATA--T-----------GCAACCAACTGA -s Anc1.Anc1refChr7 30166 35 - 47259 CTGTGACCT------------------------------------------------------GCTGATATACATA--T-----------GCAACCAACTGA -s Anc2.Anc2refChr15 68267 35 + 86568 CTGCGACCT------------------------------------------------------GCTGACATACATA--T-----------GCAACTAACTGA -s mr.mrrefChr5 107294 37 + 294540 CTGTGATCT------------------------------------------------------GCTGATCTACGTACTC-----------ACAACCAATACA -s simCow_chr6.simCow.chr6 249839 34 + 602619 -TGCAACCT------------------------------------------------------GCTTACATACATA--T-----------GCAATTAATGGA -s simDog_chr6.simDog.chr6 240500 35 + 593897 CCACGACCT------------------------------------------------------ACTGACATATGTA--T-----------GCAACTAACTGA -s simHuman_chr6.simHuman.chr6 332639 35 - 601863 CTGTGACCT------------------------------------------------------GCTGATGTACATA--T-----------GCGACCAACTGA -s simRat_chr6.simRat.chr6 244434 37 + 647215 CTGTGATCT------------------------------------------------------GCTGGTCTACGTACAC-----------ACAACCAATACA - -a -s simMouse_chr6.simMouse.chr6 254703 51 + 636262 CAACCCCTGTGATCTCAGTAAACTAAGTTTCCTGACTTGGTCCTATAACTT -s Anc0.Anc0refChr5 71363 45 + 87904 CATTCCTGTTT------TCATACCAAGGTTCATCACTTTGTTCTATAAGTT -s Anc1.Anc1refChr7 30201 51 - 47259 CATTCCTGTTTTTTTCATCATACCAAGGTTCATCACTTTGTTCTATAAGTT -s Anc2.Anc2refChr15 68303 45 + 86568 CATTCCTGTAT------TCATACCAAGGTTCATCACCTAGATTTATAAGTT -s mr.mrrefChr5 107331 51 + 294540 CAACCCCTGTGATCTCATTAAACTAAGTTTCATGACTTTGTCCTATAAGTT -s simCow_chr6.simCow.chr6 249874 45 + 602619 GGTCCCTGTAT------TCATACCAAGGTTTGTCATCTAGACTTATAAGTT -s simDog_chr6.simDog.chr6 240536 45 + 593897 CATTCATGTAT------TCAAACCAAAGTTCATCACCTAGATTTATAAGTT -s simHuman_chr6.simHuman.chr6 332674 49 - 601863 CATGCCTGTTTTTTTCATCATACCAGGGTTCATA--TTTGTTCTATAAGTT -s simRat_chr6.simRat.chr6 244471 51 + 647215 CAACCCCTGTGATCTCATTAAACTAAGTTTCATGACTTTGTCCTATAAGTT - -a -s simMouse_chr6.simMouse.chr6 254754 11 + 636262 GTAACTATTGG -s Anc0.Anc0refChr5 71418 3 + 87904 --------TGT -s Anc1.Anc1refChr7 30262 11 - 47259 GTACCTCTTGT -s Anc2.Anc2refChr15 68358 3 + 86568 --------TGT -s mr.mrrefChr5 107382 11 + 294540 GTAACTATTGG -s simCow_chr6.simCow.chr6 249929 3 + 602619 --------TGT -s simDog_chr6.simDog.chr6 240591 3 + 593897 --------TGT -s simHuman_chr6.simHuman.chr6 332739 11 - 601863 GTACCTCTTGT -s simRat_chr6.simRat.chr6 244522 11 + 647215 GTAACTATTGG - -a -s simMouse_chr6.simMouse.chr6 254765 20 + 636262 GTTAGGTATCTGTCAACCTG -s Anc0.Anc0refChr5 71421 20 + 87904 GTTAGGTATTTCTTGACCTA -s Anc1.Anc1refChr7 30273 20 - 47259 GTTAGGTATTTCTTGACCTA -s Anc2.Anc2refChr15 68361 20 + 86568 GTTAGGTATTTCTTGACCTG -s mr.mrrefChr5 107393 20 + 294540 GTTAGGTATCTGTCAACCTA -s simCow_chr6.simCow.chr6 249977 19 + 602619 ATTAGGTATTTC-TGGCCTG -s simDog_chr6.simDog.chr6 240594 20 + 593897 GACAGGTATTTTTTGACCAG -s simHuman_chr6.simHuman.chr6 332750 20 - 601863 GTTAGGTATTTCTAGACCTA -s simRat_chr6.simRat.chr6 244533 6 + 647215 CTT--------------CCA - -a -s simMouse_chr6.simMouse.chr6 254785 34 + 636262 CTGGTATTTAAGGTCCTTGATAGAGTATGAAGTC -s Anc0.Anc0refChr5 71442 34 + 87904 CTAGAGGTTAAGGTCATTGATACAGTATGAAATA -s Anc1.Anc1refChr7 30294 34 - 47259 CTAGAGGTTAAGGTCATTGATACAGTATGAAATA -s Anc2.Anc2refChr15 68382 34 + 86568 CTAGAAGTTAAAGTCATTGATACAGTATGAAAGA -s mr.mrrefChr5 107413 34 + 294540 CTGGTGTTTAAGGTCCTTGATAGAGTATGAAGTC -s simCow_chr6.simCow.chr6 249997 32 + 602619 TTAGAAGTAAAAGTCATTGGGACAGT--GTCAAA -s simDog_chr6.simDog.chr6 240615 33 + 593897 CTACAAGCTAAAGTC-TTGATACAGTATGAAAGG -s simHuman_chr6.simHuman.chr6 332771 34 - 601863 CTAGGGGTTAAGGTCATTGATACAGGATGCTATA -s simRat_chr6.simRat.chr6 244539 34 + 647215 CTGGAGTTCAAGATCCTTGATAGGGTATGAGGTG - -a -s simMouse_chr6.simMouse.chr6 254819 6 + 636262 CTCATG -s Anc0.Anc0refChr5 71476 6 + 87904 TTGGTG -s Anc1.Anc1refChr7 30328 6 - 47259 TTGGTG -s Anc2.Anc2refChr15 68416 6 + 86568 TAGTAG -s mr.mrrefChr5 107447 6 + 294540 CTCGTG -s simCow_chr6.simCow.chr6 250030 6 + 602619 TAGTAG -s simDog_chr6.simDog.chr6 240648 6 + 593897 TAGTAG -s simHuman_chr6.simHuman.chr6 332805 6 - 601863 TTGGTG -s simRat_chr6.simRat.chr6 244573 6 + 647215 CTTGTG - -a -s simMouse_chr6.simMouse.chr6 254825 5 + 636262 CCATG -s Anc0.Anc0refChr5 71518 5 + 87904 CCATA -s Anc1.Anc1refChr7 30370 5 - 47259 CCATA -s Anc2.Anc2refChr15 68458 5 + 86568 CCATA -s mr.mrrefChr5 107453 5 + 294540 CCATG -s simCow_chr6.simCow.chr6 250072 5 + 602619 CCATA -s simDog_chr6.simDog.chr6 240687 5 + 593897 CCAGA -s simHuman_chr6.simHuman.chr6 332847 5 - 601863 CCATA -s simRat_chr6.simRat.chr6 244579 5 + 647215 CCATG - -a -s simMouse_chr6.simMouse.chr6 254830 18 + 636262 TTGTAGGTGGAGATGTGC -s Anc0.Anc0refChr5 71526 17 + 87904 TTGTA-GTGGAGCTGTGC -s Anc1.Anc1refChr7 30378 17 - 47259 TTGTA-GTGGAGCTGTGC -s Anc2.Anc2refChr15 68466 17 + 86568 TTGTA-GTGGAGCTGTGC -s mr.mrrefChr5 107458 18 + 294540 TTGTAGGTGGAGATGTGC -s simCow_chr6.simCow.chr6 250080 17 + 602619 TTGTA-GCGGAGCTGCGC -s simDog_chr6.simDog.chr6 240695 17 + 593897 TTGTA-GTAGAGCAGTAC -s simHuman_chr6.simHuman.chr6 332855 17 - 601863 TTGTA-AGGGAGTTGTGC -s simRat_chr6.simRat.chr6 244584 18 + 647215 TTGTAGGTGGAGCTGTGC - -a -s simMouse_chr6.simMouse.chr6 254848 5 + 636262 CTGCA -s Anc0.Anc0refChr5 71546 5 + 87904 CTGCA -s Anc1.Anc1refChr7 30398 5 - 47259 CTGCA -s Anc2.Anc2refChr15 68486 5 + 86568 CTGCA -s mr.mrrefChr5 107479 5 + 294540 CTGCA -s simCow_chr6.simCow.chr6 250100 5 + 602619 CTGCA -s simDog_chr6.simDog.chr6 240715 5 + 593897 CTACA -s simHuman_chr6.simHuman.chr6 332875 5 - 601863 TTGCA -s simRat_chr6.simRat.chr6 244605 5 + 647215 CTGCA - -a -s simMouse_chr6.simMouse.chr6 254853 6 + 636262 ACCTTG -s Anc0.Anc0refChr5 71551 6 + 87904 AAATTG -s Anc1.Anc1refChr7 30403 6 - 47259 AAATTG -s Anc2.Anc2refChr15 68491 6 + 86568 AAATTG -s mr.mrrefChr5 107484 6 + 294540 ACCTTG -s simCow_chr6.simCow.chr6 250105 6 + 602619 AAATTT -s simDog_chr6.simDog.chr6 240720 6 + 593897 AAGTTG -s simHuman_chr6.simHuman.chr6 332881 6 - 601863 AATTTG -s simRat_chr6.simRat.chr6 244610 6 + 647215 ACGTCG - -a -s simMouse_chr6.simMouse.chr6 254859 5 + 636262 TATGC -s Anc0.Anc0refChr5 71558 5 + 87904 TATCA -s Anc1.Anc1refChr7 30410 5 - 47259 TATCA -s Anc2.Anc2refChr15 68498 5 + 86568 TATCA -s mr.mrrefChr5 107491 5 + 294540 TATGC -s simCow_chr6.simCow.chr6 250112 5 + 602619 TATCA -s simDog_chr6.simDog.chr6 240727 5 + 593897 TATCA -s simHuman_chr6.simHuman.chr6 332888 5 - 601863 TATCA -s simRat_chr6.simRat.chr6 244617 5 + 647215 TATGG - -a -s simMouse_chr6.simMouse.chr6 254864 12 + 636262 CATTTTACCAGC -s Anc0.Anc0refChr5 71563 12 + 87904 TGTCTCACCAGT -s Anc1.Anc1refChr7 30415 12 - 47259 TGTCTCACCAGT -s Anc2.Anc2refChr15 68503 12 + 86568 TGTCTCACCAGT -s mr.mrrefChr5 107496 12 + 294540 CATTTTACCAGC -s simCow_chr6.simCow.chr6 250117 12 + 602619 TGTCTGTCTGAT -s simDog_chr6.simDog.chr6 240732 12 + 593897 CACCTCACCAGT -s simHuman_chr6.simHuman.chr6 332917 12 - 601863 TGTCCCACCAGT -s simRat_chr6.simRat.chr6 244622 12 + 647215 CATTTTACCAGC - -a -s simMouse_chr6.simMouse.chr6 254876 73 + 636262 ACATAGATTCTAGCTTTGCCCAAATAGTTGTAGTGAAATCATTCTGTTGGCTGGCAAGATGATGATACAAGAA -s Anc0.Anc0refChr5 71575 62 + 87904 -----GACTCAGACGTATTCCAAATGTTTGTAGTGGAGTCATCC---AGGCTGGTAAAT---TGATACCATGT -s Anc1.Anc1refChr7 30427 62 - 47259 -----GACTCAGACGTATTCCAAATGTTTGTAGTGGAGTCATCC---AGGCTGGTAAAT---TGATACCATGT -s Anc2.Anc2refChr15 68515 62 + 86568 -----CACTCAGACGTATTCCAAATGTTTGTAGTGGAGTTATCC---GAGGTGGTAAAT---TTATAGCATGT -s mr.mrrefChr5 107508 73 + 294540 ACATAGATTCTAGCTTTGTCCAAACAGTTGTAGTGGAGTCATTCTGTAGGCTGGCAAGATGATGATACAAGAA -s simCow_chr6.simCow.chr6 250129 62 + 602619 -----CACTCTGAAGTATTCCAAATGTTTGTAGTGGAGTTAGCT---GAGTGGAAAATT---TAATAGCATGT -s simDog_chr6.simDog.chr6 240744 62 + 593897 -----CACTCAGACTTTTTCCAAATGTTTGTAGCAGAGTTGTGC---GACGTGGTAAAT---TTATAGCATGT -s simHuman_chr6.simHuman.chr6 332929 53 - 601863 -----GACTCA---GTATTT------TTTGTATTGGAGTCATCC---AGGCTGGTAGAT---TGATACCATGT -s simRat_chr6.simRat.chr6 244635 73 + 647215 ACAGAGGTTCTAGCTTTCTCCTAACAACTGTAGTGGAGTCAAGCTGGAGGCTGGCAAGATGATGATAGAAGAG - -a -s simMouse_chr6.simMouse.chr6 254949 13 + 636262 CTCTTACCCACCA -s Anc0.Anc0refChr5 71637 13 + 87904 CCTCTGGCCACTC -s Anc1.Anc1refChr7 30489 13 - 47259 CCTCTGGCCACTC -s Anc2.Anc2refChr15 68578 13 + 86568 CCTCTGGCCACTC -s mr.mrrefChr5 107581 13 + 294540 CTTCTACCCACCA -s simCow_chr6.simCow.chr6 250192 12 + 602619 CCTCT-GACAACT -s simDog_chr6.simDog.chr6 240807 13 + 593897 ACTCTGGCTACTC -s simHuman_chr6.simHuman.chr6 332982 13 - 601863 CCTCTGGGCACTC -s simRat_chr6.simRat.chr6 244708 13 + 647215 CTTCTACCCACCA - -a -s simMouse_chr6.simMouse.chr6 254962 3 + 636262 AAG -s Anc0.Anc0refChr5 71650 3 + 87904 CAG -s Anc1.Anc1refChr7 30502 3 - 47259 CAG -s Anc2.Anc2refChr15 68591 3 + 86568 CAA -s mr.mrrefChr5 107594 3 + 294540 AAG -s simCow_chr6.simCow.chr6 250204 2 + 602619 CA- -s simDog_chr6.simDog.chr6 240823 3 + 593897 AAA -s simHuman_chr6.simHuman.chr6 332995 3 - 601863 CAG -s simRat_chr6.simRat.chr6 244721 3 + 647215 AAG - -a -s simMouse_chr6.simMouse.chr6 254965 18 + 636262 AAAGGTCATATCCTTCTT -s Anc0.Anc0refChr5 71654 18 + 87904 AAAGCTCATATCTATCTT -s Anc1.Anc1refChr7 30506 18 - 47259 AAAGCTCATATCTATCTT -s Anc2.Anc2refChr15 68595 18 + 86568 AAAGCTCATATCTATCTT -s mr.mrrefChr5 107597 18 + 294540 AAAGGTCATATCCATCTT -s simCow_chr6.simCow.chr6 250206 9 + 602619 ---------ATTAACATG -s simDog_chr6.simDog.chr6 240827 18 + 593897 AAAGCTCATATCTATCTT -s simHuman_chr6.simHuman.chr6 332999 18 - 601863 ATCGCTCATGTCTATCTT -s simRat_chr6.simRat.chr6 244724 18 + 647215 AAGGGTCGTCTCCATCTT - -a -s simMouse_chr6.simMouse.chr6 254983 39 + 636262 GTATATGAATATCAACACAGGCTTGCGTGTTTTTGGAAC -s Anc0.Anc0refChr5 71677 10 + 87904 GAACATCTAT----------------------------- -s Anc1.Anc1refChr7 30529 10 - 47259 GAACATCTAT----------------------------- -s Anc2.Anc2refChr15 68618 10 + 86568 TAACATCTAC----------------------------- -s mr.mrrefChr5 107620 22 + 294540 GTATATGAATATCA-----------------TTTGGAAC -s simCow_chr6.simCow.chr6 250220 10 + 602619 TGACATCCAC----------------------------- -s simDog_chr6.simDog.chr6 240850 10 + 593897 TAACATCTAC----------------------------- -s simHuman_chr6.simHuman.chr6 333022 10 - 601863 GCACATCTAT----------------------------- -s simRat_chr6.simRat.chr6 244747 22 + 647215 GTATCAGAATATCA-----------------CTTGGAAC - -a -s simMouse_chr6.simMouse.chr6 255022 7 + 636262 AAGAAAG -s Anc0.Anc0refChr5 71687 7 + 87904 TAGAAAG -s Anc1.Anc1refChr7 30539 7 - 47259 TAGAAAG -s Anc2.Anc2refChr15 68634 7 + 86568 TGGAAAG -s mr.mrrefChr5 107642 7 + 294540 AAGAAAG -s simCow_chr6.simCow.chr6 250236 7 + 602619 TGAAAAG -s simDog_chr6.simDog.chr6 240866 7 + 593897 TGGAAAG -s simHuman_chr6.simHuman.chr6 333032 7 - 601863 TAGAAAG -s simRat_chr6.simRat.chr6 244769 7 + 647215 AGGGAAG - -a -s simMouse_chr6.simMouse.chr6 255029 7 + 636262 GTCATTT -s Anc0.Anc0refChr5 71694 7 + 87904 ATACTAT -s Anc1.Anc1refChr7 30546 7 - 47259 ATACTAT -s Anc2.Anc2refChr15 68641 7 + 86568 ATACTAT -s mr.mrrefChr5 107649 7 + 294540 GTCATAT -s simCow_chr6.simCow.chr6 250243 7 + 602619 CTACTAT -s simDog_chr6.simDog.chr6 240873 7 + 593897 ATACTAT -s simHuman_chr6.simHuman.chr6 333039 7 - 601863 ATACTAC -s simRat_chr6.simRat.chr6 244777 7 + 647215 GTCATAT - -a -s simMouse_chr6.simMouse.chr6 255036 54 + 636262 CCATTTTATGCAAGTACATGAATATGGCTTGGAACATCCTCCCATTTGGTAGCA -s Anc0.Anc0refChr5 71702 35 + 87904 CCACCTAAT-----------------AGTTGAAACA--CTCCCATTTGCTAGCA -s Anc1.Anc1refChr7 30554 37 - 47259 CCACCTAAT-----------------AGTTGAAACATCCTCCCATTTGCTAGCA -s Anc2.Anc2refChr15 68649 35 + 86568 TCACTTATA-----------------AGTTAAGACA--CTCACATTTGCTAACA -s mr.mrrefChr5 107656 53 + 294540 CCATCTTATGCA-GTACATGAATATGACTTGGAACATCCTCCCATTTGGTAGCA -s simCow_chr6.simCow.chr6 250251 35 + 602619 TCACTTATA-----------------AGTTAAGACA--CTCACATTTGCTAACA -s simHuman_chr6.simHuman.chr6 333047 36 - 601863 CCACCTGAT-----------------AGCTGAAACATCCT-CCATCTGCTAGCA -s simRat_chr6.simRat.chr6 244784 53 + 647215 CTATCTTACGCA-GTCTATGAATATGACTTGGAACATTCCCCCATTTGGTAGCA - -a -s simMouse_chr6.simMouse.chr6 255090 37 + 636262 CTGTTAGGGTTAGGGCTAGACCTTTGGCTCTCAGCAA -s Anc0.Anc0refChr5 71737 31 + 87904 CTGTCAG------AGCTATATCCTTGGCTCTCAGCAA -s Anc1.Anc1refChr7 30591 31 - 47259 CTGTCAG------AGCTATATCCTTGGCTCTCAGCAA -s Anc2.Anc2refChr15 68684 31 + 86568 CTGCCTG------AAGTATATCCAAGGCCCTTGGCAA -s mr.mrrefChr5 107709 31 + 294540 CTGTTAG------GGCTAGACCTTTGGCTCTCAGCAA -s simCow_chr6.simCow.chr6 250290 31 + 602619 CTGCCTG------AAGTATATCCAAGGCCCTTGGCAA -s simHuman_chr6.simHuman.chr6 333083 31 - 601863 CTTTCAA------AGCTATAACCTTGGCTCTCAGCAA -s simRat_chr6.simRat.chr6 244837 30 + 647215 CTGTTAG------GACTAGACCTTTGGCTTTCAGCA- - -a -s simMouse_chr6.simMouse.chr6 255127 37 + 636262 CTGCTACTCAGCAAGGTATTAATTTCCTTAATCAGAA -s Anc0.Anc0refChr5 71783 34 + 87904 TTGCAATGGAGTGAGAGATTA---TGCTTGCTAAAAA -s Anc1.Anc1refChr7 30637 34 - 47259 TTGCAATGGAGTGAGAGATTA---TGCTTGCTAAAAA -s Anc2.Anc2refChr15 68730 34 + 86568 TTGCAATGGAGTGAGAGATTA---GGCTTGCTAAAAA -s mr.mrrefChr5 107740 37 + 294540 CTGCTACTGAGTAAGATATTAATTTCCTTGATCAGAA -s simCow_chr6.simCow.chr6 250336 34 + 602619 CTGCAGTGGAAAGAGAGTTTA---GGCTGGTTAAAAA -s simDog_chr6.simDog.chr6 240893 34 + 593897 TCGCGATGGCGTGACAGATTA---GGCTTGCTAAAAA -s simHuman_chr6.simHuman.chr6 333129 34 - 601863 TTGCAATGGACTCAGAAATTA---TACTTGGTAGAAA -s simRat_chr6.simRat.chr6 244867 37 + 647215 CTGCTGCTGGGTAAGATATTAACTTGCTTGATTAGAA - -a -s simMouse_chr6.simMouse.chr6 255164 22 + 636262 TATATCCCGGATATGACTTTCT -s Anc0.Anc0refChr5 71818 22 + 87904 TACATCAAGGCTATTAATTTAG -s Anc1.Anc1refChr7 30672 22 - 47259 TACATCAAGGCTATTAATTTAG -s Anc2.Anc2refChr15 68765 22 + 86568 GACATCATGGCTATTAATTTAG -s mr.mrrefChr5 107777 22 + 294540 TATATCCATGATATCACTTTCT -s simCow_chr6.simCow.chr6 250371 22 + 602619 GACATCATGGCTGTTGATTTAG -s simDog_chr6.simDog.chr6 240928 16 + 593897 GACTTC------ATTAATTTAG -s simHuman_chr6.simHuman.chr6 333164 22 - 601863 TACATCAAGGCTATTAATTTAG -s simRat_chr6.simRat.chr6 244904 22 + 647215 GATATTCATGATATCACTTCCT - -a -s simMouse_chr6.simMouse.chr6 255186 1 + 636262 T -s Anc0.Anc0refChr5 71840 1 + 87904 T -s Anc1.Anc1refChr7 30694 1 - 47259 T -s Anc2.Anc2refChr15 68789 1 + 86568 T -s mr.mrrefChr5 107799 1 + 294540 T -s simCow_chr6.simCow.chr6 250395 1 + 602619 T -s simDog_chr6.simDog.chr6 240946 1 + 593897 T -s simHuman_chr6.simHuman.chr6 333186 1 - 601863 T -s simRat_chr6.simRat.chr6 244926 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 255187 39 + 636262 CATGCTTGATGGAGTCCGTTCAGGATATAGCTTTTTCGC -s Anc0.Anc0refChr5 71843 33 + 87904 AAT------TGGAATCCATCTAGGATATAACTTCTTTCC -s Anc1.Anc1refChr7 30697 33 - 47259 AAT------TGGAATCCATCTAGGATATAACTTCTTTCC -s Anc2.Anc2refChr15 68792 33 + 86568 AAT------TGGAACCCATCTAGGATATAACTCCTTTCC -s mr.mrrefChr5 107800 39 + 294540 CATGCTTGATGGAGTCCGTTCAGGATATAGCTTCTTTGC -s simCow_chr6.simCow.chr6 250398 33 + 602619 AAT------TGGAACCCATCTAGGATATAACTCCCTTCC -s simDog_chr6.simDog.chr6 240949 33 + 593897 AAT------TGGAACCCATCTAGGATATAGCTCCTTTCC -s simHuman_chr6.simHuman.chr6 333189 33 - 601863 AAT------TGGACTCCAACTAGTATATAAGTTCTTTCC -s simRat_chr6.simRat.chr6 244927 39 + 647215 CATGCTTGATGGAATCCGTTCAGGATATAGCTTCTTTGC - -a -s simMouse_chr6.simMouse.chr6 255226 132 + 636262 TGCTGAGGGTGTTATTAGTGTTGTTCAAGGTTCCTCTAGGTGTTTTAGCTACGCAGTCTAGACTCCACTCCAATCTCCCCAATTTAATAGTTGTAGGCCCAAGCTTCCTGCTACTGTTTAAGAGACCCATTT -s Anc0.Anc0refChr5 71876 52 + 87904 TGCTGAA---------AGCCTTGCTTATGGTTCCTCTGAGTATTTTAGCCGTGCAATCATG----------------------------------------------------------------------- -s Anc1.Anc1refChr7 30730 52 - 47259 TGCTGAA---------AGCCTTGCTTATGGTTCCTCTGAGTATTTTAGCCGTGCAATCATG----------------------------------------------------------------------- -s Anc2.Anc2refChr15 68825 52 + 86568 TGCTGAA---------TGCCTTGCTTATGGTTCCTGTGAATATTTTAGCTGTGTAATCATG----------------------------------------------------------------------- -s mr.mrrefChr5 107839 123 + 294540 TGCTGAG---------AGTGTTGTTCAAGGTTCCTCTAGGTATTTTAGCCACGCAGTCAAGACTCCACTCCAATCTCCCCAATTTAATAGTTGTAGGCCCAAGCTTCCTGCTACTGTTTAAGAGACCCATTT -s simCow_chr6.simCow.chr6 250432 52 + 602619 TGCTGGA---------TACCTTGCATATGGTTCCTGCAAGTGTTGTAGCTATATAATCGTT----------------------------------------------------------------------- -s simDog_chr6.simDog.chr6 240982 49 + 593897 TGCTGAA---------TGCCTTGCTTATGGACC---TGAATATTTTAGCTGTGTAATCATG----------------------------------------------------------------------- -s simHuman_chr6.simHuman.chr6 333222 52 - 601863 AGCTAAA---------AGCCTTGCTTGTGATTCCACTTTGAATTTTAGCCGTGCATTGATG----------------------------------------------------------------------- -s simRat_chr6.simRat.chr6 244966 123 + 647215 TGCTGAG---------AGTGTTGTTCAAGGTTCCCCTAGGCATTTTGGCCACGCAGTCAAATCTCCACTCTGATCTCCCTAACCTAATAATTGTAGGCTCAAGCTTCCCAATACTGTTTGGGAGACCCATTT - -a -s simMouse_chr6.simMouse.chr6 255358 72 + 636262 ATGTAGCTTCATTTATGGTTCTCGTAGGTGCTTTAGGTGCACAGTGAACACTCCTATCTCCACAGCTTGAAG -s Anc0.Anc0refChr5 71928 23 + 87904 -------------------------------------------------ACTCCCAAATCCCCAGCTTGAGG -s Anc1.Anc1refChr7 30782 23 - 47259 -------------------------------------------------ACTCCCAAATCCCCAGCTTGAGG -s Anc2.Anc2refChr15 68877 23 + 86568 -------------------------------------------------ACACCCAAATCCCCAGCTTGAGG -s mr.mrrefChr5 107962 72 + 294540 ATGTAGCTTCATTTATGGTTCTCGTAGGTGCTTTAGGTGCACAGTGAACACTCCTATCTCCACAGCTTGAAG -s simCow_chr6.simCow.chr6 250484 23 + 602619 -------------------------------------------------ACACCCAAATTGCCAGCTTAAGG -s simDog_chr6.simDog.chr6 241031 23 + 593897 -------------------------------------------------ATACCCGAATCCCCTGCTTGGGG -s simHuman_chr6.simHuman.chr6 333274 23 - 601863 -------------------------------------------------ACTCCCAAATCCCTAGTTTGAGG -s simRat_chr6.simRat.chr6 245091 72 + 647215 ACGTAGCTTCATTTATGTTTCCCATAGGTGCTTTAGCTGCACAGTGAAGACTCCCATCTCCACAACTTGAAG - -a -s simMouse_chr6.simMouse.chr6 255430 8 + 636262 AAAGCCCC -s Anc0.Anc0refChr5 71951 8 + 87904 ATGCCCTC -s Anc1.Anc1refChr7 30805 8 - 47259 ATGCCCTC -s Anc2.Anc2refChr15 68900 8 + 86568 ATGCCCTC -s mr.mrrefChr5 108034 8 + 294540 AAAGCCCC -s simCow_chr6.simCow.chr6 250509 8 + 602619 AGGAACCC -s simDog_chr6.simDog.chr6 241054 8 + 593897 ATGCCCTC -s simHuman_chr6.simHuman.chr6 333297 2 - 601863 G------C -s simRat_chr6.simRat.chr6 245163 8 + 647215 AAAGCCCC - -a -s simMouse_chr6.simMouse.chr6 255438 31 + 636262 AAGCTTGCTCCATGGTATGAAAAGTCCTATG -s Anc0.Anc0refChr5 71959 27 + 87904 AAGCTTGCCCCATGGTATGAAAATTCC---- -s Anc1.Anc1refChr7 30813 28 - 47259 AAGCTTGCCCCATGGTATGAAAATTCC---A -s Anc2.Anc2refChr15 68934 27 + 86568 AAGTTTGCCATGTGGTATGAAAATTCC---- -s mr.mrrefChr5 108042 31 + 294540 AAGCTTGCTCCATGGTATGAAAAGTCCTATG -s simCow_chr6.simCow.chr6 250560 27 + 602619 AAGTTTGCCTTGTGGTATGACAACTTC---- -s simDog_chr6.simDog.chr6 241110 27 + 593897 AAGTTTGCCATGTGGCATGAAAATTCC---- -s simHuman_chr6.simHuman.chr6 333299 28 - 601863 AAGCTTGCCCCATGATCTGGAAATTCC---A -s simRat_chr6.simRat.chr6 245171 31 + 647215 AAGCTTGCTCCATGGTATGAAAAGTCCTATG - -a -s simMouse_chr6.simMouse.chr6 255469 12 + 636262 CTTACTATTCAA -s Anc0.Anc0refChr5 71986 12 + 87904 CACAATATTAAC -s Anc1.Anc1refChr7 30841 12 - 47259 CACAATATTAAC -s Anc2.Anc2refChr15 68961 12 + 86568 CACAATATTAAC -s mr.mrrefChr5 108073 12 + 294540 CTTACTATTCAA -s simCow_chr6.simCow.chr6 250591 12 + 602619 CCCAATATTAAC -s simDog_chr6.simDog.chr6 241137 5 + 593897 CAT-------GC -s simHuman_chr6.simHuman.chr6 333327 12 - 601863 CACAGTATTGAC -s simRat_chr6.simRat.chr6 245202 12 + 647215 CTTACTATTAAG - -a -s simMouse_chr6.simMouse.chr6 255481 9 + 636262 TCCATCGTC -s Anc0.Anc0refChr5 71998 9 + 87904 TCCACTGTC -s Anc1.Anc1refChr7 30853 9 - 47259 TCCACTGTC -s Anc2.Anc2refChr15 68973 9 + 86568 TCCACTGTC -s mr.mrrefChr5 108085 9 + 294540 TCCACTGTC -s simCow_chr6.simCow.chr6 250603 9 + 602619 CCTACTGTC -s simDog_chr6.simDog.chr6 241142 9 + 593897 TCCACTGTC -s simHuman_chr6.simHuman.chr6 333339 9 - 601863 TCCACTGTC -s simRat_chr6.simRat.chr6 245267 9 + 647215 TTCACTATC - -a -s simMouse_chr6.simMouse.chr6 255490 17 + 636262 ATCATGGAGTCTAATTA -s Anc0.Anc0refChr5 72007 17 + 87904 ACCATGAACAATCATTA -s Anc1.Anc1refChr7 30862 17 - 47259 ACCATGAACAATCATTA -s Anc2.Anc2refChr15 68982 17 + 86568 ACCATAAACAATCATTA -s mr.mrrefChr5 108094 17 + 294540 ATCATGGACTCTAATTA -s simCow_chr6.simCow.chr6 250612 17 + 602619 ACCACTAGCAATCATTA -s simDog_chr6.simDog.chr6 241151 17 + 593897 ACAATAAACAGTCATTT -s simHuman_chr6.simHuman.chr6 333348 17 - 601863 CCCAAGAACAATCATTA -s simRat_chr6.simRat.chr6 245278 17 + 647215 ATGATGGACTCTAACTA - -a -s simMouse_chr6.simMouse.chr6 255507 52 + 636262 TAGCTTCATCATATACTGTTCCTGTGACTCTATTTTGCACTGAAGTGTAGTA -s Anc0.Anc0refChr5 72033 51 + 87904 AAGCTTCGTCATGGACTGTTCTTCTGT-TCTTCTTTACACTCAAGTGTAGTA -s Anc1.Anc1refChr7 30888 51 - 47259 AAGCTTCGTCATGGACTGTTCTTCTGT-TCTTCTTTACACTCAAGTGTAGTA -s Anc2.Anc2refChr15 69008 51 + 86568 AAGCTTTGTCATGGACTGTTCTTCGGT-CCTTCTATACACTCAAGTGTAGTA -s mr.mrrefChr5 108120 52 + 294540 TAGCTTCATCATATACTGTTCCTCTGACTCTACTTTGCACTCAAGTGTAGTA -s simCow_chr6.simCow.chr6 250638 51 + 602619 AAGCTTTGTCGTGGACTGTTATCCGGT-CCTTCTATGCACCCAAATGTAGTA -s simDog_chr6.simDog.chr6 241177 40 + 593897 AAGCTTTGTCACAGACTGTTCTTC------------ACACTCAAGTGTAGTA -s simHuman_chr6.simHuman.chr6 333374 51 - 601863 AAGATTCGTCATGGACTGTTTTTCTGG-TTTTCGTTACACTCATGTGTATTC -s simRat_chr6.simRat.chr6 245304 52 + 647215 TGGCTCCATCACATACCGTTGCTCTGACCCTACTCTGCACTCAAGTGTAGTA - -a -s simMouse_chr6.simMouse.chr6 255559 7 + 636262 CACAAGC -s Anc0.Anc0refChr5 72086 7 + 87904 TACAAGC -s Anc1.Anc1refChr7 30941 7 - 47259 TACAAGC -s Anc2.Anc2refChr15 69061 7 + 86568 TACAAGC -s mr.mrrefChr5 108172 7 + 294540 CACAAGC -s simCow_chr6.simCow.chr6 250691 7 + 602619 TACAAGC -s simDog_chr6.simDog.chr6 241219 7 + 593897 TACAACC -s simHuman_chr6.simHuman.chr6 333427 7 - 601863 TACAAGC -s simRat_chr6.simRat.chr6 245356 7 + 647215 CACATGC - -a -s simMouse_chr6.simMouse.chr6 255566 74 + 636262 TATCTTATTATCTATCACAGCCTGATGGGGCCAGCAGGTGCTCGATGTCATATATCTAGTTATGGGTAAGAGTA -s Anc0.Anc0refChr5 72095 64 + 87904 TTTCTTGTTGTCTATCACAGATTCATGTGGCTGGC-------TGGTACTATGTATTTAATTTTGG---ATGAAA -s Anc1.Anc1refChr7 30950 64 - 47259 TTTCTTGTTGTCTATCACAGATTCATGTGGCTGGC-------TGGTACTATGTATTTAATTTTGG---ATGAAA -s Anc2.Anc2refChr15 69070 64 + 86568 TTTCTTGTTGTCCATCAGAGATTCATGTGGCTGGC-------TGGTACTATGTATTTAATTTTGG---ATGAAA -s mr.mrrefChr5 108179 65 + 294540 TATCTTATTATCTATCACAGCCTCATGGGGCTAGCA------TGATGTCATGTATTTAATTATGG---AGGGTA -s simCow_chr6.simCow.chr6 250700 51 + 602619 TTTCTTGTTGCCCATCAGAGATTCATGTGGCTAGC-------TGGTACTATGTATCTA---------------- -s simDog_chr6.simDog.chr6 241228 64 + 593897 TTTCTCGTTGTCCATCAGAGATTCATGTGGCTGGC-------TGGTACAGTGTATTCAATTTTGG---ATGAAA -s simHuman_chr6.simHuman.chr6 333436 64 - 601863 TTTCTTGCTGTCTATCACAGATTCATGTGACTTGC-------TGGTACTATGTATTTAATCTTGG---ATGAAA -s simRat_chr6.simRat.chr6 245363 64 + 647215 TGTCCTATTATCTATCACAGTCTCATGGGGCTGTCA------TGATGTCACGTATTTAATTATA----AGGGTA - -a -s simMouse_chr6.simMouse.chr6 255640 11 + 636262 AGGGTGTCCTT -s Anc0.Anc0refChr5 72159 11 + 87904 AAGTTATCCTA -s Anc1.Anc1refChr7 31014 11 - 47259 AAGTTATCCTA -s Anc2.Anc2refChr15 69134 11 + 86568 GAGTTATCCTA -s mr.mrrefChr5 108244 11 + 294540 AGGGTGTCCTT -s simCow_chr6.simCow.chr6 250751 7 + 602619 ---TAAGCCT- -s simDog_chr6.simDog.chr6 241298 11 + 593897 GAGTTATCCTA -s simHuman_chr6.simHuman.chr6 333500 11 - 601863 AAGTTATTCTG -s simRat_chr6.simRat.chr6 245427 11 + 647215 AGGGTGTCCTT - -a -s simMouse_chr6.simMouse.chr6 255651 13 + 636262 ACATGGTTTCGGT -s Anc0.Anc0refChr5 72170 13 + 87904 ACGGGGACTTTGT -s Anc1.Anc1refChr7 31025 13 - 47259 ACGGGGACTTTGT -s Anc2.Anc2refChr15 69145 13 + 86568 ATGGGGACTTTGT -s mr.mrrefChr5 108255 13 + 294540 ACTTGGTCTCAGT -s simCow_chr6.simCow.chr6 250758 5 + 602619 --------TTTCT -s simDog_chr6.simDog.chr6 241310 13 + 593897 ATGGGGACTTTGT -s simHuman_chr6.simHuman.chr6 333511 13 - 601863 GCAATGACTTGGT -s simRat_chr6.simRat.chr6 245438 13 + 647215 ACTTGGTCTCAGT - -a -s simMouse_chr6.simMouse.chr6 255664 46 + 636262 AGTTTAGGAAGATAAGGTTTCAGCATTAGATGGCTTGACATCAGGC -s Anc0.Anc0refChr5 72183 44 + 87904 AGTAGAAGAAGATAAA--TTCAAGATTGGATAGCTTGGCATCAGGT -s Anc1.Anc1refChr7 31038 44 - 47259 AGTAGAAGAAGATAAA--TTCAAGATTGGATAGCTTGGCATCAGGT -s Anc2.Anc2refChr15 69158 44 + 86568 TGTTGAAGAAGACAAA--TTCAAGATTGGATAGCTTGGCATCATGT -s mr.mrrefChr5 108268 45 + 294540 AGTATAGGAAGATAAG-TTTCAGCATTAGATGGCTTGACATCAGGC -s simCow_chr6.simCow.chr6 250763 41 + 602619 TGTTGCCCATCAGAGA--TTCATG--TGGCTAGC-TGGTACTATGT -s simDog_chr6.simDog.chr6 241323 44 + 593897 TGTTGAAGAAGACAAG--CTCAACATTAGATAGCTTGGCATCATAT -s simHuman_chr6.simHuman.chr6 333528 42 - 601863 AGAAGACGAAGATA----TTCAAGATTGGATAGTCTGGCATCAGGT -s simRat_chr6.simRat.chr6 245451 45 + 647215 AGTATAGGATGATAAG-TCTCAGCATCAGATGGCTTGACATCAGGC - -a -s simMouse_chr6.simMouse.chr6 255710 26 + 636262 TTGGAAGAGAAGAGAGAAGCACCATG -s Anc0.Anc0refChr5 72227 26 + 87904 TCAGAACACAGATGAGAAGTTCCGCA -s Anc1.Anc1refChr7 31082 26 - 47259 TCAGAACACAGATGAGAAGTTCCGCA -s Anc2.Anc2refChr15 69202 26 + 86568 TCAAAACACAGATCAAAAGTTCCGCA -s mr.mrrefChr5 108313 26 + 294540 TCAGAACACAGGAGAGAAGTACCACG -s simCow_chr6.simCow.chr6 250805 26 + 602619 TTAAGGCCTGGATCATATGTCTAGAA -s simDog_chr6.simDog.chr6 241367 26 + 593897 TCAAAACACAGGACAAAAGTTCCACA -s simHuman_chr6.simHuman.chr6 333570 26 - 601863 TCAGAACACAGATGAGAAGTGCGGCA -s simRat_chr6.simRat.chr6 245496 26 + 647215 TCAGAACACAGGAGAGAAGTACCACG - -a -s simMouse_chr6.simMouse.chr6 255736 18 + 636262 GAGACAGTAGGTGGTCCC -s Anc0.Anc0refChr5 72310 18 + 87904 AAGACAGTAGGTGGTCCC -s Anc1.Anc1refChr7 31165 18 - 47259 AAGACAGTAGGTGGTCCC -s Anc2.Anc2refChr15 69285 18 + 86568 AAGACAGTAGGTGGTCCA -s mr.mrrefChr5 108396 18 + 294540 GAGACAGTAGGTGGTCCC -s simCow_chr6.simCow.chr6 250862 18 + 602619 AGGACGGGAGGTGGTCCT -s simDog_chr6.simDog.chr6 241450 18 + 593897 GAGACAGTAGGTGGTCCA -s simHuman_chr6.simHuman.chr6 333653 18 - 601863 AAGACAATAGGTGGTCCC -s simRat_chr6.simRat.chr6 245579 18 + 647215 GAGACAGTAGTTGGTCCC - -a -s simMouse_chr6.simMouse.chr6 255754 14 + 636262 TACTAATAGAGTTC -s Anc0.Anc0refChr5 72332 14 + 87904 AACTAACAGAGGTT -s Anc1.Anc1refChr7 31187 14 - 47259 AACTAACAGAGGTT -s Anc2.Anc2refChr15 69307 14 + 86568 AACTAGCTAAGGTT -s mr.mrrefChr5 108414 14 + 294540 TACTAACAGAGTTC -s simCow_chr6.simCow.chr6 250884 14 + 602619 TAATAGTTAAGGTC -s simDog_chr6.simDog.chr6 241472 14 + 593897 AACTAGCTAAGGTT -s simHuman_chr6.simHuman.chr6 333675 14 - 601863 CACCAACAGAGGTT -s simRat_chr6.simRat.chr6 245597 14 + 647215 TACTAACAGAGTTC - -a -s simMouse_chr6.simMouse.chr6 255768 15 + 636262 AAACTAACTGAGTTC -s Anc0.Anc0refChr5 72346 15 + 87904 TAACTAACTGAGGTC -s Anc1.Anc1refChr7 31201 15 - 47259 TAACTAACTGAGGTC -s Anc2.Anc2refChr15 69321 15 + 86568 TAACTAACTGAGGTC -s mr.mrrefChr5 108428 15 + 294540 AAACTAACTGAGTTC -s simCow_chr6.simCow.chr6 250898 15 + 602619 TGACCAACTGAGGCC -s simDog_chr6.simDog.chr6 241487 15 + 593897 CAACTAACTGAGGTC -s simHuman_chr6.simHuman.chr6 333689 15 - 601863 TAACTAACTGAGGTC -s simRat_chr6.simRat.chr6 245611 15 + 647215 CAACTAACTGGATCT - -a -s simMouse_chr6.simMouse.chr6 255783 5 + 636262 AACCA -s Anc0.Anc0refChr5 72362 5 + 87904 AACTA -s Anc1.Anc1refChr7 31217 5 - 47259 AACTA -s Anc2.Anc2refChr15 69337 5 + 86568 AACTA -s mr.mrrefChr5 108443 5 + 294540 AACTA -s simCow_chr6.simCow.chr6 250914 5 + 602619 AACTA -s simDog_chr6.simDog.chr6 241503 5 + 593897 AACTA -s simHuman_chr6.simHuman.chr6 333705 5 - 601863 AACTA -s simRat_chr6.simRat.chr6 245626 5 + 647215 CACTA - -a -s simMouse_chr6.simMouse.chr6 255788 51 + 636262 TAGGTCACAAGCACGATATTGTCTGTTCAACCATAGGTCACAAGCACAATA -s Anc0.Anc0refChr5 72370 18 + 87904 GAGGT---------------------------------CTCCAGTGCAATA -s Anc1.Anc1refChr7 31225 18 - 47259 GAGGT---------------------------------CTCCAGTGCAATA -s Anc2.Anc2refChr15 69345 18 + 86568 GAGGT---------------------------------CTCTAATGCAATA -s mr.mrrefChr5 108448 18 + 294540 TAGGT---------------------------------CACCAGTACAATA -s simCow_chr6.simCow.chr6 250922 10 + 602619 GTGGG-----------------------------------------CAATA -s simDog_chr6.simDog.chr6 241511 18 + 593897 GAGAT---------------------------------CTCTAATGGAACA -s simHuman_chr6.simHuman.chr6 333713 18 - 601863 GAGGT---------------------------------CTACAGTGCAATG -s simRat_chr6.simRat.chr6 245631 18 + 647215 TATGT---------------------------------CACCAGTAGAATA - -a -s simMouse_chr6.simMouse.chr6 255839 10 + 636262 TCGTCTTATT -s Anc0.Anc0refChr5 72388 10 + 87904 TTGAGCCATC -s Anc1.Anc1refChr7 31243 10 - 47259 TTGAGCCATC -s Anc2.Anc2refChr15 69363 10 + 86568 TTGAGCCATC -s mr.mrrefChr5 108466 10 + 294540 TTGTCTCATT -s simCow_chr6.simCow.chr6 250932 10 + 602619 TTGAGCCATT -s simDog_chr6.simDog.chr6 241531 10 + 593897 TTCAACAAAC -s simHuman_chr6.simHuman.chr6 333731 10 - 601863 TTGAGCCATC -s simRat_chr6.simRat.chr6 245649 10 + 647215 TTGTCTCATT - -a -s simMouse_chr6.simMouse.chr6 255849 95 + 636262 CTCTGCAACAGACAAAACATCCTAGGAATTTAACCATTTAATGCACTAGATACAGCAGCCTCTACCTCAACCGCAGGGGGGTACTGTATACAATG -s Anc0.Anc0refChr5 72398 95 + 87904 AACTGTCACAAACTGAATGTCTTAGAAACTAAACCATCCACTACACAGGGTAAGGCGGCCAGTATCCAAGCTGCCAGGGTGCACTGTACAGAATG -s Anc1.Anc1refChr7 31253 95 - 47259 AACTGTCACAAACTGAATGTCTTAGAAACTAAACCATCCACTACACAGGGTAAGGCGGCCAGTATCCAAGCTGCCAGGGTGCACTGTACAGAATG -s Anc2.Anc2refChr15 69373 95 + 86568 AACTGCCATAAACTGAATGTCTTAAAAACTAAATCATCCACTACACAGGGAAAGGCGGCCAGTATCCAAGCTGCCAGGGTGCACTGTACAGAATG -s mr.mrrefChr5 108476 95 + 294540 CTCTGTAACAAACAAAACATCCTAGGAACTTAACCATTTAATGCACAAGATACAGCAGCCTGTACCTAAGCTGCAGGGGGGTACTGTATACAATG -s simCow_chr6.simCow.chr6 250942 90 + 602619 TATGAGCATCAACTGAAAGTCTTACCAACTAAAACATCCACTACACAGAGAAA---GGCCATCA--CAAGCTGCTAGGGTGCACTTTACAGAATG -s simDog_chr6.simDog.chr6 241543 95 + 593897 AACTGCAATAAACTAGATGTCCTGAAAGGTAAATCGTTCACAACACAGGGAAAGGCCGCCTGTGTCCAAGCCGCCGGGGTGCATTGTACAGAATG -s simHuman_chr6.simHuman.chr6 333741 95 - 601863 AACTGTCACAAATTGAGTGACTTAGAAACTAAACCATCCACTACACAGGGTAAGCAGGCCAGTAACCAAGTTGCCAGGCAGCACCGTACAGAGTG -s simRat_chr6.simRat.chr6 245659 92 + 647215 C-CTCTAACGAACAATACATG-CAGGAACTTAGCCATTTAGTGCACAAGATACAGCAGCCGGTAGCTAAGCTGCAGAGTG-TACTGTATACAATG - -a -s simMouse_chr6.simMouse.chr6 255944 24 + 636262 TTCCAGAACTCACAAGTTTACAAA -s Anc0.Anc0refChr5 72497 23 + 87904 TTTCGGGACTCACAAGTTTAT-AC -s Anc1.Anc1refChr7 31352 23 - 47259 TTTCGGGACTCACAAGTTTAT-AC -s Anc2.Anc2refChr15 69472 23 + 86568 TTTTGGGACTCACAAGTTTAT-GC -s mr.mrrefChr5 108571 24 + 294540 TTCCAGGACTCACAAGTTTACAAA -s simCow_chr6.simCow.chr6 251036 11 + 602619 TTCTGGGACTC------------- -s simDog_chr6.simDog.chr6 241642 23 + 593897 TTTTAGGACTCACAAGTTTAT-GC -s simHuman_chr6.simHuman.chr6 333840 23 - 601863 TTTCGGGACTCACAAGTTCAT-AC -s simRat_chr6.simRat.chr6 245751 24 + 647215 ATCCAGGACTCACAAGTTTACAAA - -a -s simMouse_chr6.simMouse.chr6 255968 1 + 636262 T -s Anc0.Anc0refChr5 72520 1 + 87904 T -s Anc1.Anc1refChr7 31375 1 - 47259 T -s Anc2.Anc2refChr15 69495 1 + 86568 T -s mr.mrrefChr5 108595 1 + 294540 T -s simDog_chr6.simDog.chr6 241666 1 + 593897 T -s simHuman_chr6.simHuman.chr6 333863 1 - 601863 T -s simRat_chr6.simRat.chr6 245775 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 255969 33 + 636262 CGTGATCTAATATATGACAAGGCACCTAATGGA -s Anc0.Anc0refChr5 72523 33 + 87904 CATGATCTAATATATGATAAGACACATAGTGGA -s Anc1.Anc1refChr7 31378 33 - 47259 CATGATCTAATATATGATAAGACACATAGTGGA -s Anc2.Anc2refChr15 69498 33 + 86568 CACAATCTAATATAGGATGAGATTCATAGTGGA -s mr.mrrefChr5 108598 33 + 294540 CATGATCTAATATATGACAAGGCACCTAATGGA -s simCow_chr6.simCow.chr6 251047 14 + 602619 -------------------AGAATCATAGTGGA -s simDog_chr6.simDog.chr6 241669 33 + 593897 CACAATCTAATATAGGATGAAATTCTTAGAGGA -s simHuman_chr6.simHuman.chr6 333866 33 - 601863 CATGATCTAATATATTAGAAGACACATAGTGGG -s simRat_chr6.simRat.chr6 245778 33 + 647215 CATGATCTAGTATCTGACAAGGTGCTTAACGGA - -a -s simMouse_chr6.simMouse.chr6 256002 69 + 636262 AAAGCCTGTTGCATCAAGTGACCTTAGCTATCTTACATAACAAACTGCCATGAACCCAATGCCCTGGAT -s Anc0.Anc0refChr5 72558 69 + 87904 AAAGCCTGCCACATTGAGTGACTGTGGCCTTTGTTTATATCACACTGCCATGAACCCCATGTATTGAAT -s Anc1.Anc1refChr7 31413 69 - 47259 AAAGCCTGCCACATTGAGTGACTGTGGCCTTTGTTTATATCACACTGCCATGAACCCCATGTATTGAAT -s Anc2.Anc2refChr15 69533 69 + 86568 AAAGCCTGCCATGCTGAGTGACTGTGGTCTTTGTTTATATCACATTGCCATGAACCCCATGTATTGAAT -s mr.mrrefChr5 108633 69 + 294540 AAAGCCTGCTGCATCAAGTGACCTTAGCCATTTTACATATCAAACTGCCATGAACCCAATGCCCTGGAT -s simCow_chr6.simCow.chr6 251063 63 + 602619 AAAGCCTTCCAT-----GTGAATGTAGTCTTAGTTTATGTCACATTGCCATGAACCCCATGTATTGAA- -s simDog_chr6.simDog.chr6 241704 68 + 593897 GAGGCCTGCTATGCTGAGTGACTTTGGTCTTTGTTTATATT-CATTGCCATGAACCCCACATATTCAAT -s simHuman_chr6.simHuman.chr6 333901 69 - 601863 ATAGCCTGCCACATTGAGTGACTGTGCCCTTTGTTTATATCACACTGCCATGAACCCCATGTATTGAAT -s simRat_chr6.simRat.chr6 245813 65 + 647215 AAAGCCTGCTGTGTCAAGTGACCTTTACCACTTTACATATCAAACTGCCATGAAC----TGCCCAGGAT - -a -s simMouse_chr6.simMouse.chr6 256071 2 + 636262 CC -s Anc0.Anc0refChr5 72627 1 + 87904 T- -s Anc1.Anc1refChr7 31482 1 - 47259 T- -s Anc2.Anc2refChr15 69603 1 + 86568 T- -s mr.mrrefChr5 108702 1 + 294540 T- -s simDog_chr6.simDog.chr6 241773 1 + 593897 T- -s simHuman_chr6.simHuman.chr6 333970 1 - 601863 T- -s simRat_chr6.simRat.chr6 245878 1 + 647215 T- - -a -s simMouse_chr6.simMouse.chr6 256073 16 + 636262 ATACAGACTCCCATTG -s Anc0.Anc0refChr5 72628 16 + 87904 AGACAGACTCCCATGG -s Anc1.Anc1refChr7 31483 16 - 47259 AGACAGACTCCCATGG -s Anc2.Anc2refChr15 69604 16 + 86568 AGTCCGACTCCTATGG -s mr.mrrefChr5 108703 16 + 294540 ATACAGACTCCCATTG -s simCow_chr6.simCow.chr6 251126 6 + 602619 ---------CCTAT-G -s simDog_chr6.simDog.chr6 241774 16 + 593897 AGTCCGACTCCTATGG -s simHuman_chr6.simHuman.chr6 333976 16 - 601863 AGACAGACCCCCATGG -s simRat_chr6.simRat.chr6 245879 15 + 647215 ATACAGGC-CTCTGTG - -a -s simMouse_chr6.simMouse.chr6 256089 12 + 636262 ATTAGAATTAGG -s Anc0.Anc0refChr5 72644 11 + 87904 -TTAGAATTAGG -s Anc1.Anc1refChr7 31499 12 - 47259 ATTAGAATTAGG -s Anc2.Anc2refChr15 69620 11 + 86568 -CTAGAATTAGG -s mr.mrrefChr5 108719 12 + 294540 ATTAGAATTAGG -s simCow_chr6.simCow.chr6 251132 11 + 602619 -CTAGAATTAGT -s simDog_chr6.simDog.chr6 241790 11 + 593897 -CTAGAATTAGG -s simHuman_chr6.simHuman.chr6 333995 12 - 601863 ATTGAATTTAGG -s simRat_chr6.simRat.chr6 245894 12 + 647215 ATTAGAACTGGG - -a -s simMouse_chr6.simMouse.chr6 256101 28 + 636262 CTGAAGTGAAATATGCTCTAGCTCCGTT -s Anc0.Anc0refChr5 72655 22 + 87904 CTGTGATGAACCAAGATCT---A---TT -s Anc1.Anc1refChr7 31511 25 - 47259 CTGTGATGAACCAAGATCTAACA---TT -s Anc2.Anc2refChr15 69631 22 + 86568 CTGTGATGAACCAAGATCT---A---TT -s mr.mrrefChr5 108731 25 + 294540 CTGAAGTGAAATACGCTCTAGCT---TT -s simCow_chr6.simCow.chr6 251143 22 + 602619 CCATAACAATACAAGCTCT---A---TT -s simDog_chr6.simDog.chr6 241801 22 + 593897 CTGTGGTGAACCAAGATCT---A---TT -s simHuman_chr6.simHuman.chr6 334015 22 - 601863 CTCCCATGGATAAAA---TGACA---TT -s simRat_chr6.simRat.chr6 245906 25 + 647215 CTGCAGTGAAATACGCTCTAGCT---CT - -a -s simMouse_chr6.simMouse.chr6 256129 19 + 636262 CACCTTCTAGTGTAGATTA -s Anc0.Anc0refChr5 72678 19 + 87904 ACCTATCTAATATAGATTA -s Anc1.Anc1refChr7 31537 19 - 47259 ACCTATCTAATATAGATTA -s Anc2.Anc2refChr15 69654 19 + 86568 ACATATCTAATATAGATTA -s mr.mrrefChr5 108757 19 + 294540 CACCTTCTAGTGTAGATTA -s simCow_chr6.simCow.chr6 251166 19 + 602619 ACATAGCTAATATAGATTA -s simDog_chr6.simDog.chr6 241824 19 + 593897 ACATATCTAATATAGACTA -s simHuman_chr6.simHuman.chr6 334038 19 - 601863 ACCAATCTAATATACATGA -s simRat_chr6.simRat.chr6 245932 19 + 647215 CACCTTCTAGTGTAGATTA - -a -s simMouse_chr6.simMouse.chr6 256148 19 + 636262 CATTGTGATTTATAGTACA -s Anc0.Anc0refChr5 72698 17 + 87904 CATTGTTATTTCTAGTG-- -s Anc1.Anc1refChr7 31557 19 - 47259 CATTGTTATTTCTAGTGCA -s Anc2.Anc2refChr15 69674 17 + 86568 CATTGTTATTTCTAGTG-- -s mr.mrrefChr5 108776 19 + 294540 CATTGTGATTTATAGTACA -s simCow_chr6.simCow.chr6 251186 17 + 602619 CATTGTTATTTCTAGTG-- -s simDog_chr6.simDog.chr6 241844 17 + 593897 CATTGTTATTTCTAGTA-- -s simHuman_chr6.simHuman.chr6 334058 18 - 601863 CATTGTTATTT-TAGTGCA -s simRat_chr6.simRat.chr6 245951 19 + 647215 TACTGTGATTTATCATACA - -a -s simMouse_chr6.simMouse.chr6 256167 2 + 636262 AC -s Anc0.Anc0refChr5 72715 1 + 87904 -C -s Anc1.Anc1refChr7 31576 2 - 47259 AC -s Anc2.Anc2refChr15 69691 1 + 86568 -C -s mr.mrrefChr5 108795 2 + 294540 AC -s simCow_chr6.simCow.chr6 251203 1 + 602619 -C -s simDog_chr6.simDog.chr6 241861 1 + 593897 -C -s simHuman_chr6.simHuman.chr6 334084 2 - 601863 AC -s simRat_chr6.simRat.chr6 245970 2 + 647215 GC - -a -s simMouse_chr6.simMouse.chr6 256169 37 + 636262 AGAGTAGCTCATGGTACTAACTATCATCACACTGAGC -s Anc0.Anc0refChr5 72716 37 + 87904 AGAGTAGCCTGTGGTTCTAAACATAAGCACACTAAGC -s Anc1.Anc1refChr7 31578 37 - 47259 AGAGTAGCCTGTGGTTCTAAACATAAGCACACTAAGC -s Anc2.Anc2refChr15 69692 37 + 86568 AGAGTAGCCTGTGGTTCTAAACATAAGCACACTAAGC -s mr.mrrefChr5 108797 37 + 294540 AGAGTAGCTCATGGTTCTAAATATCATCACACTGAGC -s simCow_chr6.simCow.chr6 251207 37 + 602619 AGGGTGGCCTGTGGTTCTAAACATGAGCACACTAAGC -s simDog_chr6.simDog.chr6 241862 37 + 593897 AGAGTAGCCTGTGGTTCTAAACCTAAGCACACTAAGC -s simHuman_chr6.simHuman.chr6 334086 37 - 601863 TGAATAATCTGCGGCTCTATACATATGCACACTAAGC -s simRat_chr6.simRat.chr6 245972 37 + 647215 AGAGTAGCTCATGGTTCTAAATATGATTACACTGAGC - -a -s simMouse_chr6.simMouse.chr6 256206 21 + 636262 GGGAACCCCTACTTCAATACA -s Anc0.Anc0refChr5 72757 21 + 87904 GAGGCCATCTACTTCAATCTA -s Anc1.Anc1refChr7 31619 21 - 47259 GAGGCCATCTACTTCAATCTA -s Anc2.Anc2refChr15 69733 21 + 86568 GAGGCCATCTACTTCAATCTA -s mr.mrrefChr5 108837 21 + 294540 GAGAACCCCTACTTCAATACA -s simCow_chr6.simCow.chr6 251248 20 + 602619 GAGGCCATCTAC-TCAATCTA -s simDog_chr6.simDog.chr6 241903 21 + 593897 GAGGCCATCTATTTTAGCCTA -s simHuman_chr6.simHuman.chr6 334127 21 - 601863 GAGGCCATCTACTTCAATCTA -s simRat_chr6.simRat.chr6 246012 21 + 647215 GAGCACCCTTACTTCAACACA - -a -s simMouse_chr6.simMouse.chr6 256227 62 + 636262 ATCAGCAGAATGGTAATTAAGACCTAATAGTTGTTACCTCAGTCCCTGGAAGAGATTAGAGC -s Anc0.Anc0refChr5 72778 62 + 87904 TGCAGAAGAGTGGTAATTAAGGCCCAATAGTCAGAACCATGGTCCCTGGAGGATGTTAGAGT -s Anc1.Anc1refChr7 31640 62 - 47259 TGCAGAAGAGTGGTAATTAAGGCCCAATAGTCAGAACCATGGTCCCTGGAGGATGTTAGAGT -s Anc2.Anc2refChr15 69758 62 + 86568 TGCAGAAGAGTGGTAATTAAGGCCCAATAATCAGAACCATGGTCCGTTGAGGATGTTAGAGT -s mr.mrrefChr5 108858 62 + 294540 ATCAGCAGAATGGTAATTAAGACCTAATAGTTGTAACCTCGGTCCCTGGAAGAGGTTAGAGT -s simCow_chr6.simCow.chr6 251272 62 + 602619 GGCAGAAGAGTCATAATTAAGACCCAATAATCAGAACCATGGTCCGTTGAGGATCCTAGAAT -s simDog_chr6.simDog.chr6 241928 56 + 593897 TGCAGCAGAATGGTAAGTAAGGCCCAATAATCAGGACCTCAG----TTGC--ATGTCAGAGT -s simHuman_chr6.simHuman.chr6 334148 62 - 601863 TGCAGAACAGTGGTAGTTAAGGCCCAATAGTCAGAACCATGGTCCCTGGAGGATGTTAGAGT -s simRat_chr6.simRat.chr6 246033 62 + 647215 ATCAGCAGAATGTTAATTAAGACCTAATAGTTGCAACCTCGGTCCTTGGGAGAGGTTAGAGT - -a -s simMouse_chr6.simMouse.chr6 256289 18 + 636262 GTTGCTTCAAAGTGTTTA -s Anc0.Anc0refChr5 72840 12 + 87904 GATGCT------TGTTAT -s Anc1.Anc1refChr7 31702 12 - 47259 GATGCT------TGTTAT -s Anc2.Anc2refChr15 69820 12 + 86568 GAATTT------TGTTAT -s mr.mrrefChr5 108920 18 + 294540 GTTGCTTCAAAGTGTTTA -s simCow_chr6.simCow.chr6 251343 12 + 602619 GAGTTT------TGTTAT -s simDog_chr6.simDog.chr6 241984 12 + 593897 GAATTT------TGTTAT -s simHuman_chr6.simHuman.chr6 334210 6 - 601863 GCTGCT------------ -s simRat_chr6.simRat.chr6 246095 18 + 647215 GTTTCTTCAAAGTGTTAA - -a -s simMouse_chr6.simMouse.chr6 256307 20 + 636262 CCATGATAGGATGCCTGTGG -s Anc0.Anc0refChr5 72852 20 + 87904 TGATTATAGTCTGCCTGTGC -s Anc1.Anc1refChr7 31714 20 - 47259 TGATTATAGTCTGCCTGTGC -s Anc2.Anc2refChr15 69832 20 + 86568 TGATTATAGTCTGCCTGTGC -s mr.mrrefChr5 108938 20 + 294540 CCATGATAGGATGCCTGTGG -s simCow_chr6.simCow.chr6 251355 20 + 602619 TCACTTCAGTCTGCCTTTAC -s simDog_chr6.simDog.chr6 241996 20 + 593897 TGATTATAGTCTGCCTGTGC -s simHuman_chr6.simHuman.chr6 334216 7 - 601863 -------------ACTATGA -s simRat_chr6.simRat.chr6 246151 20 + 647215 CCATGATAGGATGCCTGTGG - -a -s simMouse_chr6.simMouse.chr6 256327 8 + 636262 TCAACAAA -s Anc0.Anc0refChr5 72887 8 + 87904 CCAACAAA -s Anc1.Anc1refChr7 31749 8 - 47259 CCAACAAA -s Anc2.Anc2refChr15 69867 8 + 86568 CCAACAGA -s mr.mrrefChr5 108958 8 + 294540 TCAACAAA -s simCow_chr6.simCow.chr6 251390 8 + 602619 CCAACAGA -s simDog_chr6.simDog.chr6 242031 8 + 593897 CCATCAGA -s simHuman_chr6.simHuman.chr6 334238 8 - 601863 CCAACAAA -s simRat_chr6.simRat.chr6 246171 8 + 647215 TGAACAAA - -a -s simMouse_chr6.simMouse.chr6 256335 25 + 636262 CGATGCACTTGTTATTTAAATAACA -s Anc0.Anc0refChr5 72896 25 + 87904 TAATGTACTCATTATTTAAATAGAA -s Anc1.Anc1refChr7 31758 25 - 47259 TAATGTACTCATTATTTAAATAGAA -s Anc2.Anc2refChr15 69876 25 + 86568 TAATGAACTCATTATTCAAATAGAA -s mr.mrrefChr5 108966 25 + 294540 CGATGTACTTGTTATTTAAATAACA -s simCow_chr6.simCow.chr6 251399 25 + 602619 TTATGCACCTATTATTGAAGTACAA -s simDog_chr6.simDog.chr6 242040 25 + 593897 TAATGAACTCATTATTCAAATTGAA -s simHuman_chr6.simHuman.chr6 334247 25 - 601863 TAATGTACTCATTATTTAAATAGAA -s simRat_chr6.simRat.chr6 246179 25 + 647215 CGAAGTACTTGTTATTTAAATATCA - -a -s simMouse_chr6.simMouse.chr6 256360 47 + 636262 GAGTAGTTGCTGAGTTGTGCCACACTAGAGCTCACTTATGCATGTGG -s Anc0.Anc0refChr5 72921 8 + 87904 GAATAGTT--------------------------------------- -s Anc1.Anc1refChr7 31783 8 - 47259 GAATAGTT--------------------------------------- -s Anc2.Anc2refChr15 69901 8 + 86568 GAATAGTT--------------------------------------- -s mr.mrrefChr5 108991 47 + 294540 GAGTAGTTGCTGAGGTGTGCCACACTAGAGCTCACTTATGCATGTGG -s simCow_chr6.simCow.chr6 251424 8 + 602619 GAATAGTT--------------------------------------- -s simDog_chr6.simDog.chr6 242098 8 + 593897 GAATAGTT--------------------------------------- -s simHuman_chr6.simHuman.chr6 334272 8 - 601863 GAATACTT--------------------------------------- -s simRat_chr6.simRat.chr6 246204 47 + 647215 GAGTAGTTGCTGAGGTGTGCCCCACTAGAGCTTGCTCATGCCTGTGG - -a -s simMouse_chr6.simMouse.chr6 256407 123 + 636262 TAGCAAATAAGCTACCCATTATATAAATAACAAACTTTATGCTTAAGGTGTGCTCCAGTAAAGATCCTTTGATTTGTAAACCCTTACTTTATGGCCCAGAATAACAAAGAACAACAAATGTGA -s Anc0.Anc0refChr5 72929 75 + 87904 -----------------------------------------CTTTAGGTGTGCTCCACTAAAGATCCCTTGGTTCATCAGCCATCATTTCCTGG-------TAGCAAGGAATGATTAATGCAA -s Anc1.Anc1refChr7 31791 75 - 47259 -----------------------------------------CTTTAGGTGTGCTCCACTAAAGATCCCTTGGTTCATCAGCCATCATTTCCTGG-------TAGCAAGGAATGATTAATGCAA -s Anc2.Anc2refChr15 69909 75 + 86568 -----------------------------------------GATTAGGTGTGCTCTGCTAAAAATCCCTTGGTTCATCAGCCATCATTTCCTGG-------TAGAAGGGAATGATTAATGCAA -s mr.mrrefChr5 109038 123 + 294540 TAGCAAATAAGCTACCCATTATATAAATAACAAACTTTATGCTTAAGGTGTGCTCCAGTAAAGATCCTTTGATTCATAAACCCTTACTTTATGGCCCAGAATAACAAAGAACAACAAATGTGA -s simCow_chr6.simCow.chr6 251432 75 + 602619 -----------------------------------------GATTAGTTGTGCCCTGCTAGAAAGCCTTCGGTTCAGAAGCCATCTTTTCCTGG-------TGGAAGGGGAGGATGAATGCAA -s simDog_chr6.simDog.chr6 242106 75 + 593897 -----------------------------------------GATTATGTGTGCTCTGCTAAAATTTCCTTGGTTCATCAGCCATCATTTCCTGA-------TAGAAGGGAATGATTGATGCAA -s simHuman_chr6.simHuman.chr6 334280 75 - 601863 -----------------------------------------CTTTAGGTGTGTTACACTAAAGATCCATTGGTTCATTAGCCATCATTTCCTGG-------TAGCAAGGAGTGAGTAATACAA -s simRat_chr6.simRat.chr6 246252 113 + 647215 TAGCAAGCAATATACCCATAATTTAAATAACAAACTTGTTGTTTAAGGTGTGCTCTGCTAAAGATCCTCTGATTCATAAACCCTTACTTTATGGACCAGAGTAACAAA----------CGTGA - -a -s simMouse_chr6.simMouse.chr6 256530 17 + 636262 ATAAATAAATGTTAGAG -s Anc0.Anc0refChr5 73005 17 + 87904 ATACCTAAATCTCTGCG -s Anc1.Anc1refChr7 31867 17 - 47259 ATACCTAAATCTCTGCG -s Anc2.Anc2refChr15 69985 17 + 86568 AGCCCTAAATCTCTACA -s mr.mrrefChr5 109161 17 + 294540 ATACATAAATGTCAGAG -s simCow_chr6.simCow.chr6 251508 14 + 602619 AGGCCTAAATCTCT--- -s simDog_chr6.simDog.chr6 242182 15 + 593897 AGCCCTCAATCT--ACA -s simHuman_chr6.simHuman.chr6 334356 17 - 601863 ATACCTAAATCTCTGTG -s simRat_chr6.simRat.chr6 246365 17 + 647215 ATGCATAAATGTCAGAG - -a -s simMouse_chr6.simMouse.chr6 256547 34 + 636262 TCTCAGAGGAGTCCCTGACTAGCTTAAGCCCTGG -s Anc0.Anc0refChr5 73022 32 + 87904 --TCAGAGGATTCCCAAACCAGATCAAGTCCTAA -s Anc1.Anc1refChr7 31884 34 - 47259 TCTCAGAGGATTCCCAAACCAGATCAAGTCCTAA -s Anc2.Anc2refChr15 70002 32 + 86568 --TCAGAGGATTCCCAAACCAGAGCAAGTCCTAA -s mr.mrrefChr5 109178 34 + 294540 TCTCAGAGGAGTCCCTGACTAGCTTAAGCCCTGA -s simCow_chr6.simCow.chr6 251522 29 + 602619 -----GAGACTTCTCATGCCAGACTAAGTCATAT -s simDog_chr6.simDog.chr6 242197 32 + 593897 --TCAAGGGATGTCCAAACCAGAGCAAGTCCTAA -s simHuman_chr6.simHuman.chr6 334376 33 - 601863 TCATAGAGGATTCCCAAACC-GATCAAGTCCTAA -s simRat_chr6.simRat.chr6 246382 34 + 647215 TCTCAAAGGAGGCCCCGACTAGCTTAGGCCCTGA - -a -s simMouse_chr6.simMouse.chr6 256581 8 + 636262 GGATACAT -s Anc0.Anc0refChr5 73056 8 + 87904 GGTTATGT -s Anc1.Anc1refChr7 31920 8 - 47259 GGTTATGT -s Anc2.Anc2refChr15 70036 8 + 86568 GGTTATGT -s mr.mrrefChr5 109212 8 + 294540 GGATACAT -s simCow_chr6.simCow.chr6 251553 8 + 602619 GGTTATGT -s simDog_chr6.simDog.chr6 242231 8 + 593897 GGTTATGT -s simHuman_chr6.simHuman.chr6 334411 8 - 601863 GGCTATGT -s simRat_chr6.simRat.chr6 246416 8 + 647215 GGATACAT - -a -s simMouse_chr6.simMouse.chr6 256589 23 + 636262 CACCCAGTTAGGATCTAAGAATG -s Anc0.Anc0refChr5 73065 23 + 87904 TTCTCTGGTAGGATGTGAGAAAG -s Anc1.Anc1refChr7 31929 23 - 47259 TTCTCTGGTAGGATGTGAGAAAG -s Anc2.Anc2refChr15 70045 23 + 86568 TTCTCTGGTAGGATGTGGGAAAG -s mr.mrrefChr5 109220 23 + 294540 CTCCCAGTTAGGATCTAAGAATG -s simCow_chr6.simCow.chr6 251562 23 + 602619 GTCTCTGGTAGGATTTTGGAAAG -s simDog_chr6.simDog.chr6 242240 21 + 593897 TTCCTCAGC--GATGTGGGAAAG -s simHuman_chr6.simHuman.chr6 334420 23 - 601863 TTCTCTGGTAGGATATCAGAAAG -s simRat_chr6.simRat.chr6 246424 23 + 647215 CTCCCACTTAGGATCTAGAAATG - -a -s simMouse_chr6.simMouse.chr6 256612 26 + 636262 ACATATCATAGTTCTTGCTGAGTTTA -s Anc0.Anc0refChr5 73088 26 + 87904 ACCTATCATAGCTTTTACTGAGTTTA -s Anc1.Anc1refChr7 31952 26 - 47259 ACCTATCATAGCTTTTACTGAGTTTA -s Anc2.Anc2refChr15 70068 26 + 86568 ACCTATCATAGCTTTTACTGAGTTCA -s mr.mrrefChr5 109243 26 + 294540 ACATATCATAGTTCTTGCTGAGTTTA -s simCow_chr6.simCow.chr6 251598 26 + 602619 ACTTATCATAGCTTTTACTCAATTCG -s simDog_chr6.simDog.chr6 242261 26 + 593897 ATCTACCATGGTTTTTACTGAGTTCA -s simHuman_chr6.simHuman.chr6 334443 26 - 601863 ACCTATCATAGCTTTTACTGAGTCTA -s simRat_chr6.simRat.chr6 246447 26 + 647215 ACATATCATAGTTCTTGCTGAGTTTA - -a -s simMouse_chr6.simMouse.chr6 256638 57 + 636262 GACTTTGTCACCTTTGAATTGCTTCGCCTGTAACCTTTAGATTTGGTGTAATTCTAT -s Anc0.Anc0refChr5 73114 54 + 87904 GGCTTTGTCACCTTTGCATTTTGCCGCCTGTTA--TTGGGACTTTGTAC-ATTCTTT -s Anc1.Anc1refChr7 31978 55 - 47259 GGCTTTGTCACCTTTGCATTTTGCCGCCTGTTA--TTGGGACTTTGTACAATTCTTT -s Anc2.Anc2refChr15 70094 54 + 86568 GGCTTTGTCACCTTTGCATTTTGCCACCTGTTA--TTGGGACTTTGTAC-ATTTTTT -s mr.mrrefChr5 109269 55 + 294540 GACTTTGTCACCTTTGCATTGCTCCGCCTGTTA--TTTGGATTTGGTACAATTCTAT -s simCow_chr6.simCow.chr6 251627 52 + 602619 AGCTTTATCAACTTTGCA-CCTGCCA-ATGTTA--TTGGGACTTTGTAC-ATTTTTT -s simDog_chr6.simDog.chr6 242287 34 + 593897 GGCTTTGTCACCTTTGCATTTTGCCACCCGTTA--T--------------------- -s simHuman_chr6.simHuman.chr6 334469 55 - 601863 TGCTTTGTCACCTTCGCATTTTGCCGCCTGTTA--TTGGGACTTTATACAATTCCCT -s simRat_chr6.simRat.chr6 246473 55 + 647215 AACTTTGTCACCTTAGCATTGCTCCGCCTGTTA--TTTGGATTTGGTACAATTCTAT - -a -s simMouse_chr6.simMouse.chr6 256695 8 + 636262 CTACAAAA -s Anc0.Anc0refChr5 73168 8 + 87904 CTACAAAA -s Anc1.Anc1refChr7 32033 8 - 47259 CTACAAAA -s Anc2.Anc2refChr15 70148 8 + 86568 CTATAAAA -s mr.mrrefChr5 109324 8 + 294540 CTACAAAA -s simCow_chr6.simCow.chr6 251679 8 + 602619 CTATAAAA -s simHuman_chr6.simHuman.chr6 334545 8 - 601863 CTTCAAGA -s simRat_chr6.simRat.chr6 246528 8 + 647215 CTAGAAAA - -a -s simMouse_chr6.simMouse.chr6 256703 2 + 636262 AG -s Anc0.Anc0refChr5 73177 2 + 87904 AT -s Anc1.Anc1refChr7 32042 2 - 47259 AT -s Anc2.Anc2refChr15 70157 2 + 86568 AT -s mr.mrrefChr5 109332 2 + 294540 AG -s simCow_chr6.simCow.chr6 251688 2 + 602619 AT -s simHuman_chr6.simHuman.chr6 334554 2 - 601863 AT -s simRat_chr6.simRat.chr6 246536 2 + 647215 AG - -a -s simMouse_chr6.simMouse.chr6 256705 6 + 636262 AACTTG -s Anc0.Anc0refChr5 73179 6 + 87904 AAGGTG -s Anc1.Anc1refChr7 32044 6 - 47259 AAGGTG -s Anc2.Anc2refChr15 70161 6 + 86568 AAAGTG -s mr.mrrefChr5 109334 6 + 294540 AAGTTG -s simCow_chr6.simCow.chr6 251692 6 + 602619 AAAGTG -s simHuman_chr6.simHuman.chr6 334556 6 - 601863 AAGCTG -s simRat_chr6.simRat.chr6 246538 6 + 647215 AAGTTG - -a -s simMouse_chr6.simMouse.chr6 256711 5 + 636262 TTTTT -s Anc0.Anc0refChr5 73187 5 + 87904 TTTTT -s Anc1.Anc1refChr7 32052 5 - 47259 TTTTT -s Anc2.Anc2refChr15 70169 5 + 86568 TTTTT -s mr.mrrefChr5 109340 5 + 294540 TTTTT -s simCow_chr6.simCow.chr6 251700 5 + 602619 TTTTT -s simHuman_chr6.simHuman.chr6 334564 5 - 601863 TTTTT -s simRat_chr6.simRat.chr6 246544 5 + 647215 TTTTT - -a -s simMouse_chr6.simMouse.chr6 256716 10 + 636262 ATTAGAGGTC -s Anc0.Anc0refChr5 73192 10 + 87904 GAAAAGGGAC -s Anc1.Anc1refChr7 32057 10 - 47259 GAAAAGGGAC -s Anc2.Anc2refChr15 70174 10 + 86568 GAAAATGGAC -s mr.mrrefChr5 109345 10 + 294540 ATAAAGGGTC -s simCow_chr6.simCow.chr6 251731 10 + 602619 GAAAATGGAC -s simDog_chr6.simDog.chr6 242321 4 + 593897 ------GGAC -s simHuman_chr6.simHuman.chr6 334569 10 - 601863 GAAAAGGGAC -s simRat_chr6.simRat.chr6 246549 10 + 647215 AGAAAGGTTC - -a -s simMouse_chr6.simMouse.chr6 256726 6 + 636262 CACCTG -s Anc0.Anc0refChr5 73206 6 + 87904 CCCATA -s Anc1.Anc1refChr7 32071 6 - 47259 CCCATA -s Anc2.Anc2refChr15 70188 6 + 86568 CCCATA -s mr.mrrefChr5 109355 6 + 294540 CACCTG -s simCow_chr6.simCow.chr6 251745 6 + 602619 CCTATA -s simDog_chr6.simDog.chr6 242333 6 + 593897 CTCAAA -s simHuman_chr6.simHuman.chr6 334583 6 - 601863 CCCGTA -s simRat_chr6.simRat.chr6 246559 6 + 647215 CACATG - -a -s simMouse_chr6.simMouse.chr6 256732 11 + 636262 AAAGCCACCCA -s Anc0.Anc0refChr5 73212 11 + 87904 AGGGTCATCCA -s Anc1.Anc1refChr7 32077 11 - 47259 AGGGTCATCCA -s Anc2.Anc2refChr15 70194 11 + 86568 AGGGTCATCCA -s mr.mrrefChr5 109361 11 + 294540 AAGGCCACCCA -s simCow_chr6.simCow.chr6 251751 11 + 602619 AAGATCATCCA -s simDog_chr6.simDog.chr6 242344 11 + 593897 AGCGTCATCCA -s simHuman_chr6.simHuman.chr6 334589 11 - 601863 AGGGTCATCTA -s simRat_chr6.simRat.chr6 246565 11 + 647215 AAGGCCACCCA - -a -s simMouse_chr6.simMouse.chr6 256743 1 + 636262 A -s Anc0.Anc0refChr5 73227 1 + 87904 A -s Anc1.Anc1refChr7 32092 1 - 47259 A -s Anc2.Anc2refChr15 70209 1 + 86568 A -s mr.mrrefChr5 109375 1 + 294540 A -s simCow_chr6.simCow.chr6 251765 1 + 602619 A -s simDog_chr6.simDog.chr6 242362 1 + 593897 A -s simHuman_chr6.simHuman.chr6 334604 1 - 601863 A -s simRat_chr6.simRat.chr6 246579 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 256744 31 + 636262 TAGATCACTCATGAGTTCACTGATACGAAGA -s Anc0.Anc0refChr5 73230 29 + 87904 TAGATGACCCATGAGTTCACCCCTACAAA-- -s Anc1.Anc1refChr7 32095 29 - 47259 TAGATGACCCATGAGTTCACCCCTACAAA-- -s Anc2.Anc2refChr15 70212 29 + 86568 TAGATGACCCATGGGTTCACCCCTACGAA-- -s mr.mrrefChr5 109376 30 + 294540 TAGATGACTCATGAGTTCACTGATACAAAG- -s simCow_chr6.simCow.chr6 251768 29 + 602619 TTGATGACCCATGGGTTTACCCCTACTGA-- -s simDog_chr6.simDog.chr6 242365 29 + 593897 TAAATAACCCATGGGTTCGCCAGTACGAA-- -s simHuman_chr6.simHuman.chr6 334607 29 - 601863 TAGATGACCCATGAGTTCATCCCTACAAA-- -s simRat_chr6.simRat.chr6 246580 30 + 647215 TAGATGACTCACGGGTTCACTGATATAGAC- - -a -s simMouse_chr6.simMouse.chr6 256775 8 + 636262 ACACACTG -s Anc0.Anc0refChr5 73259 8 + 87904 ATACGCTC -s Anc1.Anc1refChr7 32124 8 - 47259 ATACGCTC -s Anc2.Anc2refChr15 70241 8 + 86568 ATACGCTC -s mr.mrrefChr5 109406 8 + 294540 ATACACTG -s simCow_chr6.simCow.chr6 251797 8 + 602619 ATACACTC -s simDog_chr6.simDog.chr6 242394 8 + 593897 TTATGCTC -s simHuman_chr6.simHuman.chr6 334636 8 - 601863 ATACGCTA -s simRat_chr6.simRat.chr6 400048 8 - 647215 TTTTTCTG - -a -s simMouse_chr6.simMouse.chr6 256783 25 + 636262 CAACAGCTCTACTGTCTGCAGCAGG -s Anc0.Anc0refChr5 73267 21 + 87904 C-ACAGTTCTACTGTTTACAGC--- -s Anc1.Anc1refChr7 32132 24 - 47259 C-ACAGTTCTACTGTTTACAGCTGG -s Anc2.Anc2refChr15 70249 21 + 86568 A-ACAGTTCTAATATTTACAAC--- -s mr.mrrefChr5 109414 25 + 294540 CAACAGCTCTACTGTTTACAGCAGG -s simCow_chr6.simCow.chr6 251805 19 + 602619 A-ACAGG--TGACATTTGCACC--- -s simDog_chr6.simDog.chr6 242402 21 + 593897 A-ACAGTTCTAATATTTACAAC--- -s simHuman_chr6.simHuman.chr6 334644 23 - 601863 C-ACACATCTACTGCTTA-AGATGG -s simRat_chr6.simRat.chr6 400057 25 - 647215 CGTCATCTCTACTGTTTACAGCAGG - -a -s simMouse_chr6.simMouse.chr6 256808 13 + 636262 TATACAACTAAAA -s Anc0.Anc0refChr5 73320 13 + 87904 TATACAACTAAAA -s Anc1.Anc1refChr7 32188 13 - 47259 TATACAACTAAAA -s Anc2.Anc2refChr15 70302 13 + 86568 TGTACAACTAAAA -s mr.mrrefChr5 109439 13 + 294540 TATACAACTAAAA -s simCow_chr6.simCow.chr6 251858 13 + 602619 TGTACAGCTAAAA -s simDog_chr6.simDog.chr6 242446 13 + 593897 TGAGCAACAAAAC -s simHuman_chr6.simHuman.chr6 334704 13 - 601863 TATACAACTAAAA -s simRat_chr6.simRat.chr6 400082 13 - 647215 TATACAATTGCGG - -a -s simMouse_chr6.simMouse.chr6 256821 5 + 636262 CGACT -s Anc0.Anc0refChr5 73335 5 + 87904 TGATT -s Anc1.Anc1refChr7 32203 5 - 47259 TGATT -s Anc2.Anc2refChr15 70317 5 + 86568 TGTTT -s mr.mrrefChr5 109452 5 + 294540 TGACT -s simCow_chr6.simCow.chr6 251873 5 + 602619 TGTTT -s simDog_chr6.simDog.chr6 242461 5 + 593897 TATTT -s simHuman_chr6.simHuman.chr6 334719 5 - 601863 TGATT -s simRat_chr6.simRat.chr6 400095 5 - 647215 TGACA - -a -s simMouse_chr6.simMouse.chr6 256826 13 + 636262 ATATTTTCCAGGA -s Anc0.Anc0refChr5 73340 13 + 87904 AAAGCTGCCAATA -s Anc1.Anc1refChr7 32208 13 - 47259 AAAGCTGCCAATA -s Anc2.Anc2refChr15 70322 13 + 86568 AAAGCTGCCAATG -s mr.mrrefChr5 109457 13 + 294540 ATATTTTCCAGGA -s simCow_chr6.simCow.chr6 251878 13 + 602619 AAGGCTGCTGATG -s simDog_chr6.simDog.chr6 242469 13 + 593897 AAAGCTGCCAATG -s simHuman_chr6.simHuman.chr6 334724 13 - 601863 AAAGCTGCCAACA -s simRat_chr6.simRat.chr6 400100 13 - 647215 ATATTTCTCAGGA - -a -s simMouse_chr6.simMouse.chr6 256839 37 + 636262 TATTTAACGAGTTACTAGATTGAAGCCAAGAAAATAG -s Anc0.Anc0refChr5 73355 37 + 87904 TATTTAACAATTTACTGGACCAAATCCAAGAAAATAG -s Anc1.Anc1refChr7 32223 37 - 47259 TATTTAACAATTTACTGGACCAAATCCAAGAAAATAG -s Anc2.Anc2refChr15 70337 37 + 86568 TGTTTAACACTCTACTGGACCAAATCCAAGAAAATAG -s mr.mrrefChr5 109470 37 + 294540 TATTTAACAAGTTACTAGACTAAAGCCAAGAAAATAG -s simCow_chr6.simCow.chr6 251893 34 + 602619 TGTTTAAAAGTCTACTTGACC---TCTAAGGAAATAG -s simDog_chr6.simDog.chr6 242484 33 + 593897 AGTTTAACACT----TGGACTAAATCCAAGATTATAG -s simHuman_chr6.simHuman.chr6 334739 37 - 601863 TATCTAATAATTTACTGAACCAAATCCAAGAAAATAG -s simRat_chr6.simRat.chr6 400113 37 - 647215 TATTTAGCAAGCTGCTAGACTAATGCCAAGAAAATAG - -a -s simMouse_chr6.simMouse.chr6 256876 1 + 636262 T -s Anc0.Anc0refChr5 73438 1 + 87904 T -s Anc1.Anc1refChr7 32306 1 - 47259 T -s Anc2.Anc2refChr15 70421 1 + 86568 C -s mr.mrrefChr5 109507 1 + 294540 T -s simCow_chr6.simCow.chr6 251974 1 + 602619 C -s simDog_chr6.simDog.chr6 242559 1 + 593897 C -s simHuman_chr6.simHuman.chr6 334823 1 - 601863 t -s simRat_chr6.simRat.chr6 400150 1 - 647215 T - -a -s simMouse_chr6.simMouse.chr6 256877 60 + 636262 AAGTTCAAATGAATATGGTTTGGTCAGTCAAGTATGGGACCTATCAGTCAATGTGTTGAC -s Anc0.Anc0refChr5 73439 38 + 87904 AAGTACAATTACCTATGGTTT----TGA------------------GTGAATATATTGAC -s Anc1.Anc1refChr7 32307 38 - 47259 AAGTACAATTACCTATGGTTT----TGA------------------GTGAATATATTGAC -s Anc2.Anc2refChr15 70426 38 + 86568 CAATACACTAACCAATGGCTT----TCA------------------GTGAATATATTGAC -s mr.mrrefChr5 109508 56 + 294540 AAGTTCAAATGAATATGGTTT----AGTCAAGTATGGGACCTATCAGTCAATGTGTTGAC -s simCow_chr6.simCow.chr6 251979 38 + 602619 CAATACACTAACCGTTGACTT----CCA------------------GTAAATGCCTTGAC -s simDog_chr6.simDog.chr6 242564 38 + 593897 CAATACACTGACCAATGGCTT----TCA------------------GTGAATATATTGAC -s simHuman_chr6.simHuman.chr6 334824 38 - 601863 aagtgccacttcctattttgt----tgc------------------acaactatagaaac -s simRat_chr6.simRat.chr6 400151 56 - 647215 AAGTTCAAATGAATATGGTGT----AGGTAAGTGTGGGAACTTTCAGTCAATGTGTTGAC - -a -s simMouse_chr6.simMouse.chr6 256937 10 + 636262 CAAAATACAT -s Anc0.Anc0refChr5 73477 9 + 87904 CAAAGTGCG- -s Anc1.Anc1refChr7 32345 10 - 47259 CAAAGTGCGc -s Anc2.Anc2refChr15 70464 9 + 86568 CAAAGTGTG- -s mr.mrrefChr5 109564 10 + 294540 CAAAATACAT -s simCow_chr6.simCow.chr6 252017 9 + 602619 CAAATGGTG- -s simDog_chr6.simDog.chr6 242602 9 + 593897 CAAAGTGTG- -s simHuman_chr6.simHuman.chr6 334863 10 - 601863 tcaattgccc -s simRat_chr6.simRat.chr6 400207 10 - 647215 CAAAATCCAT - -a -s simMouse_chr6.simMouse.chr6 256947 33 + 636262 GCCAAGGGGCCAGGAGACTTTGCAAGAGTGGAC -s Anc0.Anc0refChr5 73530 26 + 87904 ACTAAGACACT----GAATTTGGAAGAATG--- -s Anc1.Anc1refChr7 32399 29 - 47259 ACTAAGACACT----GAATTTGGAAGAATGACC -s Anc2.Anc2refChr15 70519 26 + 86568 ACTAAGACACT----GAAACTAGAAGAATG--- -s mr.mrrefChr5 109574 33 + 294540 GCCAAGGGGCCAGGAGACTTTGCAAGAGTGGAC -s simCow_chr6.simCow.chr6 252074 26 + 602619 GGTAAGCCATT----GAAACTAGCAGAATG--- -s simDog_chr6.simDog.chr6 242662 26 + 593897 ACTAAGACACT----GAAACTAGAAGAATG--- -s simHuman_chr6.simHuman.chr6 334998 29 - 601863 ACTAAGACACT----GAATTTGAAAGAATGACC -s simRat_chr6.simRat.chr6 400217 33 - 647215 CCGAGGGGGCCTGGAGACTATGCAAGGGTGGAC - -a -s simMouse_chr6.simMouse.chr6 256980 12 + 636262 TGCTGGCTTTTA -s Anc1.Anc1refChr7 32428 8 - 47259 TGCTG----TTA -s mr.mrrefChr5 109607 12 + 294540 TGCTGGCTTTTA -s simHuman_chr6.simHuman.chr6 335027 8 - 601863 TGCTG----TTA -s simRat_chr6.simRat.chr6 400251 12 - 647215 CACGGGTGTTTA - -a -s simMouse_chr6.simMouse.chr6 256992 1 + 636262 C -s Anc0.Anc0refChr5 73662 1 + 87904 C -s Anc1.Anc1refChr7 32542 1 - 47259 C -s Anc2.Anc2refChr15 70652 1 + 86568 C -s mr.mrrefChr5 109619 1 + 294540 C -s simCow_chr6.simCow.chr6 252202 1 + 602619 T -s simDog_chr6.simDog.chr6 242804 1 + 593897 C -s simHuman_chr6.simHuman.chr6 335276 1 - 601863 C -s simRat_chr6.simRat.chr6 400263 1 - 647215 C - -a -s simMouse_chr6.simMouse.chr6 256993 39 + 636262 TGATACAAATTGCTCTATGGCCTATGGACGACCAAGACA -s Anc0.Anc0refChr5 73663 32 + 87904 TGATACAGAATGC-------ACTGTGGGCGACTGAGACA -s Anc1.Anc1refChr7 32543 32 - 47259 TGATACAGAATGC-------ACTGTGGGCGACTGAGACA -s Anc2.Anc2refChr15 70653 32 + 86568 TGATACAGAATGC-------AGTGTGAGCAGCTGAGACA -s mr.mrrefChr5 109620 39 + 294540 TGATACAAATTGCTCTATGGCCTATGGACGACCAAGACA -s simCow_chr6.simCow.chr6 252206 32 + 602619 TGATACAGAATGA-------AGTGTGAGCAGCTGAGACT -s simDog_chr6.simDog.chr6 242805 17 + 593897 TGATATAGAATGC-------A---------------GAA -s simHuman_chr6.simHuman.chr6 335277 32 - 601863 TGATACAGAATGC-------ACTGCAGGCGACTGAGACA -s simRat_chr6.simRat.chr6 400264 39 - 647215 TGATACAGATTGCTCTTTGGCCAATGGACAACCAAGACA - -a -s simMouse_chr6.simMouse.chr6 257032 10 + 636262 TGAGACTAAA -s Anc0.Anc0refChr5 73696 10 + 87904 TGAAACTAAA -s Anc1.Anc1refChr7 32576 10 - 47259 TGAAACTAAA -s Anc2.Anc2refChr15 70686 10 + 86568 TGTAACTGAA -s mr.mrrefChr5 109659 10 + 294540 TGAGACTAAA -s simCow_chr6.simCow.chr6 252243 10 + 602619 TGTAACTGAA -s simDog_chr6.simDog.chr6 242823 10 + 593897 TTTAACTGAA -s simHuman_chr6.simHuman.chr6 335310 10 - 601863 TGAAACTAAA -s simRat_chr6.simRat.chr6 400303 10 - 647215 TGAGACTGGA - -a -s simMouse_chr6.simMouse.chr6 257042 6 + 636262 ATTATG -s Anc0.Anc0refChr5 73709 5 + 87904 ATGAT- -s Anc1.Anc1refChr7 32589 6 - 47259 ATGATA -s Anc2.Anc2refChr15 70699 5 + 86568 ATGAT- -s mr.mrrefChr5 109669 6 + 294540 ATTATG -s simCow_chr6.simCow.chr6 252256 5 + 602619 ATGAT- -s simDog_chr6.simDog.chr6 242836 5 + 593897 ATGAT- -s simHuman_chr6.simHuman.chr6 335323 6 - 601863 ATGATA -s simRat_chr6.simRat.chr6 400313 6 - 647215 ATTATG - -a -s simMouse_chr6.simMouse.chr6 257048 10 + 636262 TGGAACTCTA -s Anc0.Anc0refChr5 73714 8 + 87904 --GAACTCTG -s Anc1.Anc1refChr7 32595 10 - 47259 TGGAACTCTG -s Anc2.Anc2refChr15 70704 8 + 86568 --GAACTCTG -s mr.mrrefChr5 109675 10 + 294540 TGGAACTCTA -s simCow_chr6.simCow.chr6 252261 8 + 602619 --GTGCTCTT -s simDog_chr6.simDog.chr6 242841 6 + 593897 --GAA--CCG -s simHuman_chr6.simHuman.chr6 335329 10 - 601863 TGGAACTCTG -s simRat_chr6.simRat.chr6 400322 10 - 647215 GGGAACTCTA - -a -s simMouse_chr6.simMouse.chr6 257058 7 + 636262 TGCGGTG -s Anc0.Anc0refChr5 73781 7 + 87904 TGTGGTG -s Anc1.Anc1refChr7 32664 7 - 47259 TGTGGTG -s Anc2.Anc2refChr15 70771 7 + 86568 TGTGGTG -s mr.mrrefChr5 109685 7 + 294540 TGCGGTG -s simCow_chr6.simCow.chr6 252330 7 + 602619 AGTGATG -s simDog_chr6.simDog.chr6 242906 5 + 593897 TGTGG-- -s simHuman_chr6.simHuman.chr6 335398 7 - 601863 TGTGGTG -s simRat_chr6.simRat.chr6 400332 7 - 647215 TGGTCTG - -a -s simMouse_chr6.simMouse.chr6 257065 55 + 636262 CTGCATGTCCACAATTAGCTTCTACCTTTGAATATGGTTATGATTATGGTAGTGA -s Anc0.Anc0refChr5 73794 55 + 87904 CTGAATGCCTGCAGTTAACTTCTGCCTTTGAATCTGGTTATGATTCTTGTGGTGG -s Anc1.Anc1refChr7 32677 55 - 47259 CTGAATGCCTGCAGTTAACTTCTGCCTTTGAATCTGGTTATGATTCTTGTGGTGG -s Anc2.Anc2refChr15 70784 55 + 86568 TTGAATCCCTGCAGTTAACTTCTGCCTTTGAATCTGGTTATGATTCTTGTGGTGG -s mr.mrrefChr5 109692 55 + 294540 CTGCATGTCCACAATTAGCTTCTACCTTTGAATATGGTTATGATTATGGTAGTGA -s simCow_chr6.simCow.chr6 252343 55 + 602619 TTGAATCCTTTCACTCGACTCTTGTCTTGGAATCTGGCCATGGTTCTGGTAGTGG -s simDog_chr6.simDog.chr6 242911 47 + 593897 --------CTGCAGATACCTTCTGCCTTTGAGCCTGGTTATCATTCTTGTGGTAT -s simHuman_chr6.simHuman.chr6 335411 55 - 601863 CTGAATGCCTGCATTTAACTTGTGCCTTTGAATCTGGTTATGATTCTTGTGGTGG -s simRat_chr6.simRat.chr6 400339 55 - 647215 CTGCAAGTCCATAATTAGCTTCCACCTTGGAGCATGGTTATGATTTTGGTAGTGA - -a -s simMouse_chr6.simMouse.chr6 257120 10 + 636262 GATTTGTAAT -s Anc0.Anc0refChr5 73849 10 + 87904 CTTTGGTGAT -s Anc1.Anc1refChr7 32732 10 - 47259 CTTTGGTGAT -s Anc2.Anc2refChr15 70839 10 + 86568 CTTTGGTGAT -s mr.mrrefChr5 109747 10 + 294540 GATTTGTAAT -s simCow_chr6.simCow.chr6 252399 10 + 602619 CATTGTTGAT -s simDog_chr6.simDog.chr6 242958 10 + 593897 GTTTGGTGAT -s simHuman_chr6.simHuman.chr6 335466 10 - 601863 CTTCCATGAT -s simRat_chr6.simRat.chr6 400394 10 - 647215 GATTTGATTT - -a -s simMouse_chr6.simMouse.chr6 257130 7 + 636262 CTATCAG -s Anc0.Anc0refChr5 73859 7 + 87904 CTTTTAG -s Anc1.Anc1refChr7 32742 7 - 47259 CTTTTAG -s Anc2.Anc2refChr15 70849 7 + 86568 CTTTTAG -s mr.mrrefChr5 109757 7 + 294540 CTATTAG -s simCow_chr6.simCow.chr6 252409 7 + 602619 CTTTAAG -s simDog_chr6.simDog.chr6 242968 7 + 593897 CTTTTAG -s simHuman_chr6.simHuman.chr6 335476 7 - 601863 CTTTTAG -s simRat_chr6.simRat.chr6 400408 7 - 647215 CTATTAC - -a -s simMouse_chr6.simMouse.chr6 257137 13 + 636262 CTTTGTACAAAGT -s Anc0.Anc0refChr5 73867 13 + 87904 CTAAGTACAGAGT -s Anc1.Anc1refChr7 32750 13 - 47259 CTAAGTACAGAGT -s Anc2.Anc2refChr15 70857 13 + 86568 CTAACTACAGAAT -s mr.mrrefChr5 109764 13 + 294540 CTTTGTACAAAGT -s simCow_chr6.simCow.chr6 252417 13 + 602619 CTGAATACAGAAT -s simDog_chr6.simDog.chr6 242976 9 + 593897 CTAACTACA---- -s simHuman_chr6.simHuman.chr6 335484 13 - 601863 CTAAGAACATAGT -s simRat_chr6.simRat.chr6 400415 13 - 647215 CTTTGTACAACAT - -a -s simMouse_chr6.simMouse.chr6 257150 35 + 636262 GAACTTAAAGTGAACTTTATCTTGACTGAAGGAAC -s Anc0.Anc0refChr5 73880 24 + 87904 GAACCT-----------AAACTTGACTAAAGGAAC -s Anc1.Anc1refChr7 32763 24 - 47259 GAACCT-----------AAACTTGACTAAAGGAAC -s Anc2.Anc2refChr15 70870 24 + 86568 GAACCT-----------AAACTTGACTAAAGAAAT -s mr.mrrefChr5 109777 24 + 294540 GAACTT-----------TATCTTGACTGAAGGAAC -s simCow_chr6.simCow.chr6 252449 24 + 602619 GAACTT-----------AAACTTGACTAAAAAAAT -s simDog_chr6.simDog.chr6 242985 21 + 593897 GTATCA-----------GAA---GACTAGAGAAAT -s simHuman_chr6.simHuman.chr6 335497 24 - 601863 GAACCT-----------AAACTTGACTAAAGGAGC -s simRat_chr6.simRat.chr6 400428 24 - 647215 AAACTT-----------TGTCTTGACTGAAGGAAC - -a -s simMouse_chr6.simMouse.chr6 257185 11 + 636262 TAATAACTGAT -s Anc0.Anc0refChr5 73906 11 + 87904 TATTGACAGAT -s Anc1.Anc1refChr7 32789 11 - 47259 TATTGACAGAT -s Anc2.Anc2refChr15 70896 11 + 86568 TATTGACAGAT -s mr.mrrefChr5 109801 11 + 294540 TAATAACTGAT -s simCow_chr6.simCow.chr6 252475 10 + 602619 TAGTGAT-GAT -s simDog_chr6.simDog.chr6 243008 11 + 593897 TATTAACAGAT -s simHuman_chr6.simHuman.chr6 335523 11 - 601863 TATTGACAGAT -s simRat_chr6.simRat.chr6 400452 11 - 647215 TAATAACTGAT - -a -s simMouse_chr6.simMouse.chr6 257196 40 + 636262 AGAGATGTGATGTGCAGCTACAGTTGAGTTGCCCATGTAC -s Anc0.Anc0refChr5 73918 40 + 87904 AGGGATGTGATGCTCAACTGCATTTAAGTTACCCATGCAC -s Anc1.Anc1refChr7 32801 40 - 47259 AGGGATGTGATGCTCAACTGCATTTAAGTTACCCATGCAC -s Anc2.Anc2refChr15 70908 40 + 86568 AGGGATGTGATGCTCACCTGCATTTAAGTTACCAGTGCAC -s mr.mrrefChr5 109813 40 + 294540 AGAGATGTGATGTGCAACTACAGTTGAGTTGCCCATGCAC -s simCow_chr6.simCow.chr6 252486 30 + 602619 A-GGATGCGATGCTCACCTGAATTTA---------TGCAC -s simDog_chr6.simDog.chr6 243020 40 + 593897 AGGGTTGTGATGCTCACCTGCACTTAAGTTACCAGTCTAC -s simHuman_chr6.simHuman.chr6 335535 40 - 601863 AGGGATGTGCTGCTCAACTGCATTTAAATTATCCATGCAC -s simRat_chr6.simRat.chr6 400464 40 - 647215 ATAGATGTGATGTATGACTACAGTTGAGTTGCCCATGCAT - -a -s simMouse_chr6.simMouse.chr6 257236 1 + 636262 T -s Anc0.Anc0refChr5 73958 1 + 87904 T -s Anc1.Anc1refChr7 32841 1 - 47259 T -s Anc2.Anc2refChr15 70949 1 + 86568 T -s mr.mrrefChr5 109853 1 + 294540 T -s simCow_chr6.simCow.chr6 252517 1 + 602619 T -s simDog_chr6.simDog.chr6 243061 1 + 593897 T -s simHuman_chr6.simHuman.chr6 335575 1 - 601863 T -s simRat_chr6.simRat.chr6 400504 1 - 647215 T - -a -s simMouse_chr6.simMouse.chr6 257237 20 + 636262 GCATTCAAGATACCTATGGC -s Anc0.Anc0refChr5 73959 20 + 87904 GCATTTAAATTACCCATGGC -s Anc1.Anc1refChr7 32842 20 - 47259 GCATTTAAATTACCCATGGC -s Anc2.Anc2refChr15 70950 20 + 86568 GCATTTAAATTACCCATGGC -s mr.mrrefChr5 109854 20 + 294540 GCATTCAAGATACCTATGGC -s simCow_chr6.simCow.chr6 252518 18 + 602619 G--TGTAAATTACCAATGGC -s simDog_chr6.simDog.chr6 243062 20 + 593897 GCATTCAAATGATTCAGGGC -s simHuman_chr6.simHuman.chr6 335576 20 - 601863 TCATTTAAATTACCCATAGC -s simRat_chr6.simRat.chr6 400506 20 - 647215 GCATCCAAGATACCTATGGC - -a -s simMouse_chr6.simMouse.chr6 257257 9 + 636262 TTGTTCAGG -s Anc0.Anc0refChr5 73979 9 + 87904 TTGTCCAAG -s Anc1.Anc1refChr7 32862 9 - 47259 TTGTCCAAG -s Anc2.Anc2refChr15 70970 9 + 86568 TTGTCCAAG -s mr.mrrefChr5 109874 9 + 294540 TTGTTCAGG -s simCow_chr6.simCow.chr6 252536 9 + 602619 TTGTGCAAG -s simDog_chr6.simDog.chr6 243082 5 + 593897 TTGTC---- -s simHuman_chr6.simHuman.chr6 335596 9 - 601863 TTGTCCAAG -s simRat_chr6.simRat.chr6 400527 9 - 647215 TTGTTCAGG - -a -s simMouse_chr6.simMouse.chr6 257266 32 + 636262 GGCAAGAGTTATGTGATGAGGTGGTCCCAAGC -s Anc0.Anc0refChr5 73988 32 + 87904 GGCATGAGTAATGTGATTAGGTGGTCCCAGGC -s Anc1.Anc1refChr7 32871 32 - 47259 GGCATGAGTAATGTGATTAGGTGGTCCCAGGC -s Anc2.Anc2refChr15 70979 32 + 86568 GGCATGAGTAATGTGATTAGGTGGTCCCCGGC -s mr.mrrefChr5 109883 32 + 294540 GGCATGAGTTATGTGATGAGGTGGTCCCAAGC -s simCow_chr6.simCow.chr6 252545 32 + 602619 GGTATGTGTAATCTGATTAGGTGGTCCCCAAC -s simDog_chr6.simDog.chr6 243437 32 + 593897 GGCACAAGTAATGTGATTAGGTGGGCCCCGGG -s simHuman_chr6.simHuman.chr6 335605 32 - 601863 GGCATGAGTGGTGGGATTAAATGATCTCAGGC -s simRat_chr6.simRat.chr6 400536 32 - 647215 GGCATGAATAATGTGATGAGGTGGTTCCAAGC - -a -s simMouse_chr6.simMouse.chr6 257298 37 + 636262 CCAGCCAACAATGTTACAGGTTGGATAGTCAGAACAG -s Anc0.Anc0refChr5 74022 33 + 87904 CCAGTCAGCACCAGGACATGCTGGATAGTTA-AA--- -s Anc1.Anc1refChr7 32905 34 - 47259 CCAGTCAGCACCAGGACATGCTGGATAGTTAGAA--- -s Anc2.Anc2refChr15 71013 33 + 86568 CCAGTCAGCACCAGGACATGCTGGATGGTTA-AA--- -s mr.mrrefChr5 109915 37 + 294540 CCAGCCAACAATGTGACATGCTGGATAGTCAGAACAG -s simCow_chr6.simCow.chr6 252579 31 + 602619 CCA--CAACACCAGGGCATGCTGGATGATAA-AA--- -s simDog_chr6.simDog.chr6 243471 33 + 593897 CCAGTCAGCACCAGGACATGGTGAGTGGTTA-AA--- -s simHuman_chr6.simHuman.chr6 335639 31 - 601863 CCAGTCACTAG---GACATGCTGGATAGTTAGAA--- -s simRat_chr6.simRat.chr6 400568 36 - 647215 CCAGCCAACAATGTGAAATGCTGCATGG-CAGTGTGT - -a -s simMouse_chr6.simMouse.chr6 257335 1 + 636262 C -s Anc0.Anc0refChr5 74055 1 + 87904 C -s Anc1.Anc1refChr7 32939 1 - 47259 C -s Anc2.Anc2refChr15 71046 1 + 86568 C -s mr.mrrefChr5 109952 1 + 294540 C -s simCow_chr6.simCow.chr6 252612 1 + 602619 C -s simDog_chr6.simDog.chr6 243504 1 + 593897 C -s simHuman_chr6.simHuman.chr6 335670 1 - 601863 C -s simRat_chr6.simRat.chr6 400604 1 - 647215 T - -a -s simMouse_chr6.simMouse.chr6 257336 38 + 636262 TGCAAGTCTCAACCAACAGAGTGACAACTATAATCATG -s Anc0.Anc0refChr5 74056 26 + 87904 CCCAAGTTGCA------------ACAACCATCACCATA -s Anc1.Anc1refChr7 32940 26 - 47259 CCCAAGTTGCA------------ACAACCATCACCATA -s Anc2.Anc2refChr15 71047 26 + 86568 CCCAAGTTGCA------------ACAACCATCGCCATA -s mr.mrrefChr5 109953 38 + 294540 TGCAAGTTTCAACAAACAGAGTGACAACTATAATCATG -s simCow_chr6.simCow.chr6 252613 26 + 602619 CTCCAAGTGCA------------TCAACCATACTCATA -s simDog_chr6.simDog.chr6 243505 26 + 593897 TCCAAGTTGCA------------ACTACAATCGCTATA -s simHuman_chr6.simHuman.chr6 335671 26 - 601863 CCCAGGTTGCA------------ATAACCATTACCAAA -s simRat_chr6.simRat.chr6 247168 38 + 647215 TGCAAGCTTCAACAAACCTAGTGACAACTATAATCATG - -a -s simMouse_chr6.simMouse.chr6 257374 9 + 636262 TCTCAGTGG -s Anc0.Anc0refChr5 74082 9 + 87904 TATAAATAG -s Anc1.Anc1refChr7 32966 9 - 47259 TATAAATAG -s Anc2.Anc2refChr15 71073 9 + 86568 TATAAATAG -s mr.mrrefChr5 109991 9 + 294540 TCTAAGTGG -s simCow_chr6.simCow.chr6 252639 9 + 602619 TGTAAATGG -s simDog_chr6.simDog.chr6 243531 9 + 593897 TATAAATAG -s simHuman_chr6.simHuman.chr6 335697 9 - 601863 TATAAATAG -s simRat_chr6.simRat.chr6 247207 9 + 647215 TCTAAGTGG - -a -s simMouse_chr6.simMouse.chr6 257383 15 + 636262 TGATAGGTTCCTCCC -s Anc0.Anc0refChr5 74091 12 + 87904 TGATGGGTTTCT--- -s Anc1.Anc1refChr7 32975 15 - 47259 TGATGGGTTTCTCCC -s Anc2.Anc2refChr15 71082 12 + 86568 TGATGGCTTTCT--- -s mr.mrrefChr5 110000 15 + 294540 TGATAGGTTCCTCCC -s simCow_chr6.simCow.chr6 252648 12 + 602619 TGATGGCTTTCT--- -s simDog_chr6.simDog.chr6 243540 7 + 593897 TG-----TTTTT--- -s simHuman_chr6.simHuman.chr6 335706 15 - 601863 TGATGGGTTTCTCCC -s simRat_chr6.simRat.chr6 247217 15 + 647215 TGATAGGTTCCTTCA - -a -s simMouse_chr6.simMouse.chr6 257398 18 + 636262 AGGAAAGTAGTACAGGGG -s Anc0.Anc0refChr5 74110 18 + 87904 AGAAGTATTTCCTCAAGT -s Anc1.Anc1refChr7 32997 18 - 47259 AGAAGTATTTCCTCAAGT -s Anc2.Anc2refChr15 71101 18 + 86568 AAAAGTATTTCCTCAAGT -s mr.mrrefChr5 110015 18 + 294540 AGGAAAGTAGCACAGGGG -s simCow_chr6.simCow.chr6 252665 18 + 602619 AAAAGTATTTCCTCAAGT -s simDog_chr6.simDog.chr6 243554 18 + 593897 AAAAGTATTTCCTCATGT -s simHuman_chr6.simHuman.chr6 335728 18 - 601863 AGAATTATGTCCTCAAGT -s simRat_chr6.simRat.chr6 247232 18 + 647215 AGGAAAGTAGCACAGGGG - -a -s simMouse_chr6.simMouse.chr6 257416 30 + 636262 CTGATAGCAGAGCTCTTTGTACCTATGATT -s Anc0.Anc0refChr5 74129 27 + 87904 CTGATAGAAGAGCCACCCATACCTATG--- -s Anc1.Anc1refChr7 33016 30 - 47259 CTGATAGAAGAGCCACCCATACCTATGGTT -s Anc2.Anc2refChr15 71120 27 + 86568 CTGAGAGGAGAGCCACCCATACCTATG--- -s mr.mrrefChr5 110034 30 + 294540 CTGATAGAAGAGCTCCCTGTACCTATGATT -s simCow_chr6.simCow.chr6 252684 27 + 602619 CCAAGAGGAGGTCCATGCATACCTATG--- -s simDog_chr6.simDog.chr6 243573 27 + 593897 CTGAGGGGAGAGCCACCTGTACCTATG--- -s simHuman_chr6.simHuman.chr6 335747 28 - 601863 CT--TAGAAGAGCAACCCATACCTATGGTT -s simRat_chr6.simRat.chr6 247251 30 + 647215 CTGACAGAGGAGCTCCCTGTACCTATGACT - -a -s simMouse_chr6.simMouse.chr6 257446 7 + 636262 GTCAGCT -s Anc0.Anc0refChr5 74156 7 + 87904 GTTTACA -s Anc1.Anc1refChr7 33046 7 - 47259 GTTTACA -s Anc2.Anc2refChr15 71147 7 + 86568 GTTTACG -s mr.mrrefChr5 110064 7 + 294540 GTCAGCA -s simCow_chr6.simCow.chr6 252714 7 + 602619 GTTTACA -s simDog_chr6.simDog.chr6 243600 7 + 593897 GTTTACG -s simHuman_chr6.simHuman.chr6 335775 7 - 601863 GTTCACA -s simRat_chr6.simRat.chr6 247281 7 + 647215 GTCTGCA - -a -s simMouse_chr6.simMouse.chr6 257453 37 + 636262 TATGCCAGACCTCCTGTTTGGGATGTACGTACTGCCC -s Anc0.Anc0refChr5 74163 34 + 87904 TATGCCAGGCCACCTGTTCTGAATGTATGC---TACA -s Anc1.Anc1refChr7 33053 34 - 47259 TATGCCAGGCCACCTGTTCTGAATGTATGC---TACA -s Anc2.Anc2refChr15 71154 34 + 86568 TATGCCAGGCCACCTGGTCTGAATGTATGC---TACA -s mr.mrrefChr5 110071 37 + 294540 TATGCCAGACCTCCTGTTTGGGATGTATGCACTGCCA -s simCow_chr6.simCow.chr6 252721 31 + 602619 TATGCTGGGCCATCTGGTTTGAATGTCTGC---T--- -s simDog_chr6.simDog.chr6 243607 34 + 593897 TACGTCAGGCCACCTGGTCAGACAGTATGC---TACA -s simHuman_chr6.simHuman.chr6 335789 34 - 601863 TATACCAGGCTACTTGTTCTGAATGTATGC---TACA -s simRat_chr6.simRat.chr6 247288 37 + 647215 TATGCCAGACCTCCTGTTTGGGATGTATGCCCTGCCA - -a -s simMouse_chr6.simMouse.chr6 257490 22 + 636262 AACTGTCTATAGATTACATTGA -s Anc0.Anc0refChr5 74197 22 + 87904 AACTGGCTACAGGTCTCAATGA -s Anc1.Anc1refChr7 33087 22 - 47259 AACTGGCTACAGGTCTCAATGA -s Anc2.Anc2refChr15 71188 22 + 86568 ATCTGGTTACAGGTCTCAATGA -s mr.mrrefChr5 110108 22 + 294540 AACTGGCTATAGATTACATTGA -s simCow_chr6.simCow.chr6 252752 13 + 602619 ---------CAGGTGTCAATGA -s simDog_chr6.simDog.chr6 243644 22 + 593897 ATCTGGTTACAGGTCTCAATGA -s simHuman_chr6.simHuman.chr6 335823 22 - 601863 AACTGGCTACAGGTCTCAAAGA -s simRat_chr6.simRat.chr6 247325 22 + 647215 AACTGGCTATAAATAACATTGG - -a -s simMouse_chr6.simMouse.chr6 257512 143 + 636262 ATTAATTCCTTGAGCCCATTAATGCAGCAGCCAGGTATTGATTGGACTAGAGTTGGTCTTCTAAACACCAAGATAAAGGAGAGTACATTTGTTAAGAAGGATTCTACATACTACCGACCACACTAGTTAATCTGCTGTATCAA -s Anc0.Anc0refChr5 74222 140 + 87904 ATTAGCTCCATGTGCTCAACAATACAGCAGCCTGGCATTGATT-GGCTGGCGTTGGGACCTTAAACACCAAGAGAAAGGAG-GAACACATTCTAAGTGGGATGCTACATGCTACAATCTGTCCTAGCAAATCTTCTGT-TTGA -s Anc1.Anc1refChr7 33112 142 - 47259 ATTAGCTCCATGTGCTCAACAATACAGCAGCCTGGCATTGATTGGGCTGGCGTTGGGACCTTAAACACCAAGAGAAAGGAG-GAACACATTCTAAGTGGGATGCTACATGCTACAATCTGTCCTAGCAAATCTTCTGTATTGA -s Anc2.Anc2refChr15 71213 140 + 86568 ATTAGCTCCATGTGCTCAACATTAGAGCAGCCAGGCATTGATT-AGCTGGCATTGGGACCTTAAATATCAAGAGAAAGGAG-GTACACATTCTAAGTGGGGTGCTACCTGCTACAATCTGTCCTAGCAAAGCTTCTGT-TTGA -s mr.mrrefChr5 110133 143 + 294540 ATTAATTCCTTGAGCCCATTAATGCAGCAGCCTGGTATTGATTGGACTAGAGTTGGGCCTCTAAACACCAAGAGAAAGGAGAGAACATTTGTTAAGAAGGATTCTACATGCTACCGACCACACTAGTTAATCTGCTGTATCAA -s simCow_chr6.simCow.chr6 252768 140 + 602619 ATTACCGCTGTGTACTTGAGATTTGAGCAACAAGACATTGATT-TGTTGGCCTTAGGACCTTGAAGATCAAGAGAAAGGAG-GTGCCTATTCTAAGTGGGGTGCCACCTGCTACACTTCATCCCAGCAGAGCTTCTGT-ATGA -s simDog_chr6.simDog.chr6 243678 139 + 593897 ATTAGCTCCATGTGCTCAACATTAGAGCAGCCAGGCATAGATT-AGCTGGCATTGGGTTCTTAAATATTAAGAGAAAGTAG-GTACACATTC-AAATGGAGTGCTACCTCCTACAATCTGTCCTAGCAAAGCTTCTGT-TTGA -s simHuman_chr6.simHuman.chr6 335848 117 - 601863 ATAAGCCTCATGTTCAC----ATACAGCAGCCTGGCATTGATTGGGCTGATGTTGGGACCTTAAACACCAAGAGAAAGGAG-GAATACATTCTAAG-TGGATGCTACATGCTAC----------------TCT----CATAGA -s simRat_chr6.simRat.chr6 247350 143 + 647215 AATAATTCCTTGAGCCCATCAATGCAGCAGCCTAGTATTGATTGGACTAGCATTGGGCCTCTAAACACCAGAAGAGAGGAGAGAACATTTGTTAAGGAGGATCATACATGCTATCAACCACACTAGTTAATCTTCTGTATCAA - -a -s simMouse_chr6.simMouse.chr6 257655 24 + 636262 AATGACCCAGTCTACAACATTAAA -s Anc0.Anc0refChr5 74362 24 + 87904 AAAAACCCAGTTGACAACATCAAA -s Anc1.Anc1refChr7 33254 24 - 47259 AAAAACCCAGTTGACAACATCAAA -s Anc2.Anc2refChr15 71353 24 + 86568 AAAAACTTGGTTGACAACATCAAA -s mr.mrrefChr5 110276 24 + 294540 AATAACCCAGTCTACAACATTAAA -s simCow_chr6.simCow.chr6 252909 17 + 602619 ATAAACTTGGCTGACAA------- -s simDog_chr6.simDog.chr6 243817 24 + 593897 GAAAACTTGGTTGACAACATCAAA -s simHuman_chr6.simHuman.chr6 335965 24 - 601863 AAGAACCCAATTGCCAACATCAAA -s simRat_chr6.simRat.chr6 247493 24 + 647215 AATAACTCAGTCTACAATATTGAA - -a -s simMouse_chr6.simMouse.chr6 257679 3 + 636262 ATC -s Anc0.Anc0refChr5 74386 3 + 87904 ATA -s Anc1.Anc1refChr7 33278 3 - 47259 ATA -s Anc2.Anc2refChr15 71383 3 + 86568 ATA -s mr.mrrefChr5 110300 3 + 294540 ATC -s simCow_chr6.simCow.chr6 349070 3 - 602619 AAC -s simDog_chr6.simDog.chr6 243847 3 + 593897 GTA -s simHuman_chr6.simHuman.chr6 335989 3 - 601863 AGT -s simRat_chr6.simRat.chr6 247517 3 + 647215 GAC - -a -s simMouse_chr6.simMouse.chr6 257682 13 + 636262 TAACTTAGCCTGT -s Anc0.Anc0refChr5 74389 13 + 87904 TCACTTGATCTGT -s Anc1.Anc1refChr7 33281 13 - 47259 TCACTTGATCTGT -s Anc2.Anc2refChr15 71386 13 + 86568 TCATGTGATATGT -s mr.mrrefChr5 110303 13 + 294540 TAACTTAGCCTGT -s simCow_chr6.simCow.chr6 349073 13 - 602619 TCATGTGACCTGT -s simDog_chr6.simDog.chr6 243850 13 + 593897 TCATGTGATATGT -s simHuman_chr6.simHuman.chr6 336051 13 - 601863 TCACTTGATCTGT -s simRat_chr6.simRat.chr6 247520 13 + 647215 TAGCTTACCCTGT - -a -s simMouse_chr6.simMouse.chr6 257695 4 + 636262 TACT -s Anc0.Anc0refChr5 74402 4 + 87904 GTCA -s Anc1.Anc1refChr7 33294 4 - 47259 GTCA -s Anc2.Anc2refChr15 71404 4 + 86568 GTTA -s mr.mrrefChr5 110316 4 + 294540 TACT -s simCow_chr6.simCow.chr6 349099 4 - 602619 GTTA -s simDog_chr6.simDog.chr6 243868 4 + 593897 GTTA -s simHuman_chr6.simHuman.chr6 336064 4 - 601863 GGCA -s simRat_chr6.simRat.chr6 247533 4 + 647215 TCCC - -a -s simMouse_chr6.simMouse.chr6 257699 66 + 636262 CATGACACACCACTAAGTCATTGCTTTGAAGGCCATAACTTCTGTAGAAGCTACAGTAGAAAAATG -s Anc0.Anc0refChr5 74406 23 + 87904 CTTGACACAC-------------------------------------------CACTAGTTTAATG -s Anc1.Anc1refChr7 33298 23 - 47259 CTTGACACAC-------------------------------------------CACTAGTTTAATG -s Anc2.Anc2refChr15 71408 23 + 86568 CTTGATACAC-------------------------------------------CACTGGTTTAATG -s mr.mrrefChr5 110320 66 + 294540 CGTGACACACCACTAAGTCATTGCTTTGAAGGCCATAACTTCTGTAGAAGCTACACTAGAAAAATG -s simCow_chr6.simCow.chr6 349104 23 - 602619 CTTGACAAAC-------------------------------------------CACTGGTTTAATG -s simDog_chr6.simDog.chr6 243872 23 + 593897 CTTGATACAC-------------------------------------------CACTGGTTTAATG -s simHuman_chr6.simHuman.chr6 336068 23 - 601863 TTTGACACAC-------------------------------------------CACTAGTTGAATG -s simRat_chr6.simRat.chr6 247537 58 + 647215 TGTGACA--------AGTCATCGCTTTGAAGACCATAACTTCTGTAGAAGCTATACTAGAAAGATG - -a -s simMouse_chr6.simMouse.chr6 257765 1 + 636262 A -s Anc0.Anc0refChr5 74429 1 + 87904 G -s Anc1.Anc1refChr7 33321 1 - 47259 G -s Anc2.Anc2refChr15 71431 1 + 86568 G -s mr.mrrefChr5 110386 1 + 294540 A -s simCow_chr6.simCow.chr6 349127 1 - 602619 G -s simDog_chr6.simDog.chr6 243895 1 + 593897 G -s simHuman_chr6.simHuman.chr6 336091 1 - 601863 G -s simRat_chr6.simRat.chr6 247617 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 257766 15 + 636262 TAAGGAGCTAGATGG -s Anc0.Anc0refChr5 74431 15 + 87904 TGAAGAGCAAAATTG -s Anc1.Anc1refChr7 33323 15 - 47259 TGAAGAGCAAAATTG -s Anc2.Anc2refChr15 71433 15 + 86568 TGAAGACCAAAATTT -s mr.mrrefChr5 110387 15 + 294540 TAAGGAGCTAGATGG -s simCow_chr6.simCow.chr6 349129 15 - 602619 GGATGACCAAAATTT -s simDog_chr6.simDog.chr6 243897 15 + 593897 TGAAGACCCAAATTT -s simHuman_chr6.simHuman.chr6 336093 15 - 601863 TGAAGAGCAACATTG -s simRat_chr6.simRat.chr6 247618 15 + 647215 TAAGGAGCTAGGTGG - -a -s simMouse_chr6.simMouse.chr6 257781 55 + 636262 GAGAGATCAGGGTGATCTTCCTTAGCCAGGCTGGTTCTTTCACAAGTGGGGAGAC -s Anc0.Anc0refChr5 74446 16 + 87904 ---------------------------------------TCACAAGCAGGGAGAT -s Anc1.Anc1refChr7 33338 16 - 47259 ---------------------------------------TCACAAGCAGGGAGAT -s Anc2.Anc2refChr15 71448 16 + 86568 ---------------------------------------TCACAAGCAGGGAGAT -s mr.mrrefChr5 110402 55 + 294540 GAGAGATCAGGGTGATCTTCCTTAGCCAGGCTGGTTCTTTCACAAGTAGGGAGAC -s simCow_chr6.simCow.chr6 349144 16 - 602619 ---------------------------------------TCACAAGCAGGGAGGT -s simDog_chr6.simDog.chr6 243912 16 + 593897 ---------------------------------------TCATAGGCAGGGAGAT -s simHuman_chr6.simHuman.chr6 336108 16 - 601863 ---------------------------------------TCACAAACACTGAGAT -s simRat_chr6.simRat.chr6 247645 55 + 647215 AAGAAATCAGTGTGGTCCTCCTTAGCCAGGCTGGTCCTTTCAGAAGTAGGGAGAC - -a -s simMouse_chr6.simMouse.chr6 257836 29 + 636262 GAAAAGGTTAACAGCTGTGGTAATATGTG -s Anc0.Anc0refChr5 74462 29 + 87904 GAAAAGGTTAACATCTGTGCTAGAGTATT -s Anc1.Anc1refChr7 33354 29 - 47259 GAAAAGGTTAACATCTGTGCTAGAGTATT -s Anc2.Anc2refChr15 71464 29 + 86568 GAAACGGTTAACATCTGTGCTAGAATATT -s mr.mrrefChr5 110457 29 + 294540 GAAAAGGTTAACAGCTGTGGTAATGTGTG -s simCow_chr6.simCow.chr6 349188 29 - 602619 GAAAGGGTTAACATCTATCCCAGAATATG -s simDog_chr6.simDog.chr6 243928 29 + 593897 GAAACTGCTAACATCTGTGCTAGAATATT -s simHuman_chr6.simHuman.chr6 336124 29 - 601863 GAAGAGGTTAACATCTGTGCTAGAGTATT -s simRat_chr6.simRat.chr6 247700 27 + 647215 AAAAAGGTT--CAGCTGTGATAATGCGTG - -a -s simMouse_chr6.simMouse.chr6 257865 39 + 636262 GTTGTCTAAAAGGGAAGATTGAAGCTCAACTGTAAGCTC -s Anc0.Anc0refChr5 74491 38 + 87904 -TTGTCTAGGAGGGGGTGTCGCAGCCTAACTGTAAGCTA -s Anc1.Anc1refChr7 33385 39 - 47259 GTTGTCTAGGAGGGGGTGTCGCAGCCTAACTGTAAGCTA -s Anc2.Anc2refChr15 71493 38 + 86568 -TTGTCTAGGAGGGGGTGTCGCAGCCTCAATGTAAGCTA -s mr.mrrefChr5 110488 39 + 294540 GTTGTTTAAAAGGGAAGGTTGAAGCTCAACTGTAAGCTC -s simCow_chr6.simCow.chr6 349217 38 - 602619 -TTCTCTAGGAGGGTGTGTTGCAACTTCATGGTAAGCTA -s simDog_chr6.simDog.chr6 243957 38 + 593897 -TTGTCTGGGAGGGGGGAACACAGCCTCAATGTAGGCTA -s simHuman_chr6.simHuman.chr6 336169 39 - 601863 GTTATCTAGGGAGGGGTGTGGCAGCCTAACTGTAAGCTA -s simRat_chr6.simRat.chr6 247729 31 + 647215 GTTGTTTCAAAGGGAAGGTTGAAGCT--------AGCTC - -a -s simMouse_chr6.simMouse.chr6 257904 37 + 636262 ACACACTGTTTTGCTAGATTCTTCCGCCTTGATACCT -s Anc0.Anc0refChr5 74529 36 + 87904 GTACACCATTTTTATTGATTC-CCTGCCTTGGAAGTT -s Anc1.Anc1refChr7 33424 36 - 47259 GTACACCATTTTTATTGATTC-CCTGCCTTGGAAGTT -s Anc2.Anc2refChr15 71533 36 + 86568 GTATACCATTTTTATTGATTC-TCTGCCTTGGAAGTC -s mr.mrrefChr5 110527 37 + 294540 ACACACTGTTTTGCTAGATTCTCCTGCCTTGGAACCT -s simCow_chr6.simCow.chr6 349257 36 - 602619 TTATGCCATTTTTATTGATTC-GCTGCCATGTATCTC -s simDog_chr6.simDog.chr6 243997 36 + 593897 GTATACCATCTTTATTGATTT-TCTGCCTTGGCAGTC -s simHuman_chr6.simHuman.chr6 336208 36 - 601863 CTACACCATTTTTATTGATTC-CCTGCCTCAGAATTT -s simRat_chr6.simRat.chr6 247760 37 + 647215 ACACATTGTTTTGCCAGATTCTCCTGCCTTGGAACCT - -a -s simMouse_chr6.simMouse.chr6 257941 6 + 636262 TGTACT -s Anc0.Anc0refChr5 74565 6 + 87904 AGTGGT -s Anc1.Anc1refChr7 33460 6 - 47259 AGTGGT -s Anc2.Anc2refChr15 71569 6 + 86568 AGTGGT -s mr.mrrefChr5 110564 6 + 294540 TGTACT -s simCow_chr6.simCow.chr6 349293 6 - 602619 AGGGGT -s simDog_chr6.simDog.chr6 244033 6 + 593897 ATTAGT -s simHuman_chr6.simHuman.chr6 336244 6 - 601863 GGTGGT -s simRat_chr6.simRat.chr6 247812 6 + 647215 TCTACT - -a -s simMouse_chr6.simMouse.chr6 257947 21 + 636262 TGGAGATATCAGGTTTCCAAC -s Anc0.Anc0refChr5 74576 7 + 87904 TGCAGAT-------------- -s Anc1.Anc1refChr7 33471 15 - 47259 TGCAGATAGCGG------AAC -s Anc2.Anc2refChr15 71580 7 + 86568 TGCAGAT-------------- -s mr.mrrefChr5 110575 21 + 294540 TGGAGATATCAGGTTTCCAAC -s simCow_chr6.simCow.chr6 349304 7 - 602619 TGCAGAT-------------- -s simDog_chr6.simDog.chr6 244044 7 + 593897 TGCAGAT-------------- -s simHuman_chr6.simHuman.chr6 336255 15 - 601863 TGCAGATAGCGG------AAC -s simRat_chr6.simRat.chr6 247823 21 + 647215 TGGAGATATCAGATTTCCAAC - -a -s simMouse_chr6.simMouse.chr6 257968 29 + 636262 CCTTATTAAACCCTTAATAAGATCACAGC -s Anc0.Anc0refChr5 74583 24 + 87904 CCAT-----ACTCCTAGCAAGACTATGGC -s Anc1.Anc1refChr7 33486 24 - 47259 CCAT-----ACTCCTAGCAAGACTATGGC -s Anc2.Anc2refChr15 71587 24 + 86568 TCAT-----GCTTCATGCTTTACTATGAC -s mr.mrrefChr5 110596 29 + 294540 CCTTATTAAACCCTTAGTAAGACCACGGC -s simCow_chr6.simCow.chr6 349331 22 - 602619 TAAT-----GCTTCATCCTTTATTATG-- -s simDog_chr6.simDog.chr6 244051 24 + 593897 TCAT-----GCTTCATGCTTTACTGTCAC -s simHuman_chr6.simHuman.chr6 336270 24 - 601863 CTCT-----ACTCCTAGCAAGACTATGGC -s simRat_chr6.simRat.chr6 247844 29 + 647215 CCTTATTAAGCCCTTAGTAAGACCACGGC - -a -s simMouse_chr6.simMouse.chr6 257997 25 + 636262 TCATGGTTTTTACTTCAATATCATG -s Anc0.Anc0refChr5 74607 23 + 87904 TCATGCTTTTTA--TCTGTTTCATG -s Anc1.Anc1refChr7 33510 25 - 47259 TCATGCTTTTTATTTCTGTTTCATG -s Anc2.Anc2refChr15 71614 23 + 86568 TCATGCTTTTTA--TCTGATTCGTG -s mr.mrrefChr5 110625 25 + 294540 TCATGGTTTTTACTTCAATATCATG -s simCow_chr6.simCow.chr6 349356 23 - 602619 TCACACTTTAAG--TCTCATTTATG -s simDog_chr6.simDog.chr6 244078 23 + 593897 TCATGCTTTTTA--TCTGATTCGTG -s simHuman_chr6.simHuman.chr6 336294 25 - 601863 TCCTGACATGCTTTACTGTTTCATA -s simRat_chr6.simRat.chr6 247873 25 + 647215 TCTTGGTTTTTACTTCAATATCATG - -a -s simMouse_chr6.simMouse.chr6 258022 5 + 636262 ATCAA -s Anc0.Anc0refChr5 74630 5 + 87904 ATAAA -s Anc1.Anc1refChr7 33535 5 - 47259 ATAAA -s Anc2.Anc2refChr15 71695 5 + 86568 ATATC -s mr.mrrefChr5 110650 5 + 294540 ATCAA -s simCow_chr6.simCow.chr6 349437 5 - 602619 GTATT -s simDog_chr6.simDog.chr6 244159 5 + 593897 ATATC -s simHuman_chr6.simHuman.chr6 336319 5 - 601863 CTAAA -s simRat_chr6.simRat.chr6 247898 5 + 647215 ATCAA - -a -s simMouse_chr6.simMouse.chr6 258027 5 + 636262 TACCC -s Anc0.Anc0refChr5 74635 5 + 87904 CATCC -s Anc1.Anc1refChr7 33540 5 - 47259 CATCC -s Anc2.Anc2refChr15 71700 5 + 86568 CATCA -s mr.mrrefChr5 110655 5 + 294540 TACCC -s simCow_chr6.simCow.chr6 349463 5 - 602619 CATCA -s simDog_chr6.simDog.chr6 244164 5 + 593897 CATCA -s simHuman_chr6.simHuman.chr6 336324 5 - 601863 CATCC -s simRat_chr6.simRat.chr6 247903 5 + 647215 TACTC - -a -s simMouse_chr6.simMouse.chr6 258032 14 + 636262 TACATCAGGTTCTT -s Anc0.Anc0refChr5 74646 14 + 87904 CAAGACAGATTCTC -s Anc1.Anc1refChr7 33551 14 - 47259 CAAGACAGATTCTC -s Anc2.Anc2refChr15 71711 14 + 86568 CAAGACAAATTCTC -s mr.mrrefChr5 110660 14 + 294540 TACATCAGATTCTT -s simCow_chr6.simCow.chr6 349474 14 - 602619 CAAAACAAATTCTC -s simDog_chr6.simDog.chr6 244175 14 + 593897 CAAGAAGAATTCCC -s simHuman_chr6.simHuman.chr6 336335 14 - 601863 CAAGCCAGATTCTC -s simRat_chr6.simRat.chr6 247908 14 + 647215 TACATCAGATTCTT - -a -s simMouse_chr6.simMouse.chr6 258046 51 + 636262 GTGCTGTAAGAAATGGGTGAATTAGGAAAAATGCTTGTAATGGATAGAGAT -s Anc0.Anc0refChr5 74706 50 + 87904 GTGCTGTAATAAATGAGTGAATTA-TAAAAATACTTGTAATGAATAAACAT -s Anc1.Anc1refChr7 33611 50 - 47259 GTGCTGTAATAAATGAGTGAATTA-TAAAAATACTTGTAATGAATAAACAT -s Anc2.Anc2refChr15 71783 50 + 86568 GTGCTGTAATAAATGAGTGAATTA-TAAAAACACTTGCAATGAATAAACAT -s mr.mrrefChr5 110674 51 + 294540 GTGCTGTAAGAAATGGGTGAATTAGTAAAAATGCTTGTAATGGATAAAGAT -s simCow_chr6.simCow.chr6 349548 50 - 602619 ATGCTGTAATAAAAGGGTGAACTA-TAAAAACACCTGCATTGAATAGGCAT -s simDog_chr6.simDog.chr6 244247 47 + 593897 GCACTGTAATAAATGAG---ATTA-TAATGACACTTGCAATGAATAAACAT -s simHuman_chr6.simHuman.chr6 336398 50 - 601863 GTGCTGTAATAAATGAGTGAAATA-TAAAAATACTTGTCCTGAATAAACAA -s simRat_chr6.simRat.chr6 247922 50 + 647215 CTGCTGTAAGAAATTGGG-AATTAGTAAAAAGGCTTGTATTGGATAAAGAT - -a -s simMouse_chr6.simMouse.chr6 258097 12 + 636262 CTAGGCTTTTTA -s Anc0.Anc0refChr5 74756 12 + 87904 CTGAGCTATTTG -s Anc1.Anc1refChr7 33661 12 - 47259 CTGAGCTATTTG -s Anc2.Anc2refChr15 71833 12 + 86568 CTGATCCATTTG -s mr.mrrefChr5 110725 12 + 294540 CTAGGCTTTTTA -s simCow_chr6.simCow.chr6 349598 12 - 602619 CTAATCCTTTCA -s simDog_chr6.simDog.chr6 244310 12 + 593897 CTGATCCATTTG -s simHuman_chr6.simHuman.chr6 336448 12 - 601863 CTGAGCTCTTTG -s simRat_chr6.simRat.chr6 247972 12 + 647215 CTAGGCTTTTTA - -a -s simMouse_chr6.simMouse.chr6 258109 51 + 636262 GAGAGGAAGCAGCAAGTGAGCACCTAAAATTTAATTTTGCGGGGCTATCTA -s Anc0.Anc0refChr5 74770 51 + 87904 TAGTGGAAGCAGCAAACAAGCACATACAATTTAATTCTACAGGGCTATCTG -s Anc1.Anc1refChr7 33675 51 - 47259 TAGTGGAAGCAGCAAACAAGCACATACAATTTAATTCTACAGGGCTATCTG -s Anc2.Anc2refChr15 71847 51 + 86568 TAGTGGAAGCAGCAAATTAGCACATACAATTTAATTCTACAGGGCTATCTG -s mr.mrrefChr5 110737 51 + 294540 TAGAGGAAGCAGCAAGCAAGCACCTAAAATTTAATTTTGCGGGGCTATCTA -s simCow_chr6.simCow.chr6 349612 51 - 602619 TATTGGATGCAACAAATGAGCACATACAAATTAATTCTGCAGGGCTATCTG -s simDog_chr6.simDog.chr6 244324 51 + 593897 TAGTGGAAGTAGCAAGTTAACACATACAATTTAGTTCTACAGAGCTATCTG -s simHuman_chr6.simHuman.chr6 336462 51 - 601863 TAGTGGAAGCAGCTAACAAGTACATACAATTTAACTCCACAGGGCTATGTG -s simRat_chr6.simRat.chr6 247984 50 + 647215 TAG-GGAAGCCGCAAGCAAGCACTTAAAATTCAATTTTGTTGGGCTATCTA - -a -s simMouse_chr6.simMouse.chr6 258160 14 + 636262 CACTCAAAAAACAC -s Anc0.Anc0refChr5 74835 7 + 87904 -------AAGACAA -s Anc1.Anc1refChr7 33743 14 - 47259 CACTCCAAAGACAA -s Anc2.Anc2refChr15 71912 7 + 86568 -------AAGATAA -s mr.mrrefChr5 110788 14 + 294540 CACTCCAAAAACAC -s simCow_chr6.simCow.chr6 349677 7 - 602619 -------AAGATAA -s simDog_chr6.simDog.chr6 244389 7 + 593897 -------AAGGTAA -s simHuman_chr6.simHuman.chr6 336533 14 - 601863 CACTCCAAAGACAA -s simRat_chr6.simRat.chr6 248034 14 + 647215 CACTCCAAAAACAC - -a -s simMouse_chr6.simMouse.chr6 258174 8 + 636262 TCCAGCAA -s Anc0.Anc0refChr5 74842 8 + 87904 TCCAACAA -s Anc1.Anc1refChr7 33757 8 - 47259 TCCAACAA -s Anc2.Anc2refChr15 71919 8 + 86568 TCCAAACT -s mr.mrrefChr5 110802 8 + 294540 TCCAGCAA -s simCow_chr6.simCow.chr6 349685 8 - 602619 GCCTGATG -s simDog_chr6.simDog.chr6 244396 8 + 593897 TGTAAACT -s simHuman_chr6.simHuman.chr6 336547 8 - 601863 TCCAACAA -s simRat_chr6.simRat.chr6 248048 8 + 647215 TCCAGAAA - -a -s simMouse_chr6.simMouse.chr6 258182 45 + 636262 GTTCAAGTGACAGAATGGTTTTTTCATCTTGCAACTATCATGTGG -s Anc0.Anc0refChr5 74850 45 + 87904 TTTCAAGTGGCGGAGTGGTAACTTTACTCTGTAACTATCACATGG -s Anc1.Anc1refChr7 33765 45 - 47259 TTTCAAGTGGCGGAGTGGTAACTTTACTCTGTAACTATCACATGG -s Anc2.Anc2refChr15 71927 45 + 86568 TTTCAAGTGGCGGAGTGGTAACTTCACTCTGTAACTATCCCATGG -s mr.mrrefChr5 110810 45 + 294540 GTTCAAGTGACAGAATGGTTTTTTTATTTTGCAACTATCATGTGG -s simCow_chr6.simCow.chr6 253556 45 + 602619 TTTCAAGTGCTGAAGTAGTAATTTCACTCTGTAACTATCCCATGG -s simDog_chr6.simDog.chr6 244404 31 + 593897 ATTGAAGTGGCAGATTGGTAAC--------------ATCCCATGG -s simHuman_chr6.simHuman.chr6 336555 45 - 601863 TTTCAGGTGGCGGAGTGATAACTTTGCTCGGTAAAAATCACAGGG -s simRat_chr6.simRat.chr6 248056 45 + 647215 GTTCAAGTAACAGAATGGTTTTTTTAGTTTGCAACTATCGTGTGG - -a -s simMouse_chr6.simMouse.chr6 258227 72 + 636262 TTGCTATCAAAAGATTGAATCCTCAAATTCCCCCTTAGTGCAAGAGTATCTGTATGTGGTGCAGTAGCCAAG -s Anc0.Anc0refChr5 74897 71 + 87904 T-GCTTTAAAGAGGGAGCATTCTCAAATTCTTCCTTAGTGCGAGATTATCAGTATGCAGTGCAGTATTCAGG -s Anc1.Anc1refChr7 33812 71 - 47259 T-GCTTTAAAGAGGGAGCATTCTCAAATTCTTCCTTAGTGCGAGATTATCAGTATGCAGTGCAGTATTCAGG -s Anc2.Anc2refChr15 71974 71 + 86568 T-GCTTTAAAGAGGGAGCATTCCCAAATTTTTCCTTAGTACGAGTTTACCAGTATGCAGTGTAGTATTCAGA -s mr.mrrefChr5 110855 71 + 294540 T-GCTATCAAAAGATTGAATTCTCAAATTCCTCCTTAGTGCAAGATTATCAGTATGTGGTGCAGTAGCCAGG -s simCow_chr6.simCow.chr6 253603 70 + 602619 T-GCTT-AAAGATGGAGCATTCCCAAATAGTTCCTTAGTACGAGTTTACCAGTATGCAGTGTAGTATTCAGA -s simDog_chr6.simDog.chr6 244437 38 + 593897 T-G--TTGAAGGGGAAGCATGCCCAAATTTTTC-------------------------------TATTCAAA -s simHuman_chr6.simHuman.chr6 336602 71 - 601863 T-GCTTTAAAGAGGGAGCATTCTCACATCCTTCCTTAGTGCGAGATTGTCAGTATGCAGTACACTATGCAGG -s simRat_chr6.simRat.chr6 248101 71 + 647215 T-GCTATCAAAAGATTCAGTTCGCAAATTCCTCCTTAGTGCAAGATTATCAGTATATGGTGCAGCAGTCAGG - -a -s simMouse_chr6.simMouse.chr6 258299 10 + 636262 TCTATTAATC -s Anc0.Anc0refChr5 74969 10 + 87904 TGTCTTAATC -s Anc1.Anc1refChr7 33884 10 - 47259 TGTCTTAATC -s Anc2.Anc2refChr15 72046 10 + 86568 TGCCTTAGTC -s mr.mrrefChr5 110926 10 + 294540 TCTATTAATC -s simCow_chr6.simCow.chr6 253674 10 + 602619 TGCATTACTC -s simDog_chr6.simDog.chr6 244476 10 + 593897 TGCCTTAGGC -s simHuman_chr6.simHuman.chr6 336674 10 - 601863 TGTTTTAATC -s simRat_chr6.simRat.chr6 248172 10 + 647215 TCCAGTAATC - -a -s simMouse_chr6.simMouse.chr6 258309 20 + 636262 TTTTAAGAGTCCGGTGCTAA -s Anc0.Anc0refChr5 74979 20 + 87904 TACTAAAAGTCCTATCCTAA -s Anc1.Anc1refChr7 33894 20 - 47259 TACTAAAAGTCCTATCCTAA -s Anc2.Anc2refChr15 72056 20 + 86568 TACTAAAAGTCCTATCCTAA -s mr.mrrefChr5 110936 20 + 294540 TTTTAAGAGTCCTGTGCTAA -s simCow_chr6.simCow.chr6 253687 20 + 602619 TACTAGAAGTCCTATCTCAA -s simDog_chr6.simDog.chr6 244486 20 + 593897 TACTAAAAGTTGTATTCTTG -s simHuman_chr6.simHuman.chr6 336684 20 - 601863 TACTAAAAGTCCTATCCTAA -s simRat_chr6.simRat.chr6 248182 13 + 647215 TTTTAACAAGCAT------- - -a -s simMouse_chr6.simMouse.chr6 258329 4 + 636262 AGCA -s Anc0.Anc0refChr5 74999 4 + 87904 AGTA -s Anc1.Anc1refChr7 33914 4 - 47259 AGTA -s Anc2.Anc2refChr15 72076 4 + 86568 AGTA -s mr.mrrefChr5 110956 4 + 294540 AGCA -s simCow_chr6.simCow.chr6 253707 4 + 602619 AGTA -s simDog_chr6.simDog.chr6 244511 4 + 593897 AGTG -s simHuman_chr6.simHuman.chr6 336704 4 - 601863 AATA - -a -s simMouse_chr6.simMouse.chr6 258333 10 + 636262 CCCAACAATG -s Anc0.Anc0refChr5 75005 10 + 87904 ACCCTCAATC -s Anc1.Anc1refChr7 33920 10 - 47259 ACCCTCAATC -s Anc2.Anc2refChr15 72082 10 + 86568 ACCCTCAATC -s mr.mrrefChr5 110960 10 + 294540 CCCAACAATG -s simCow_chr6.simCow.chr6 253713 10 + 602619 AACCTCCATC -s simDog_chr6.simDog.chr6 244517 10 + 593897 GCCCTCAGTC -s simHuman_chr6.simHuman.chr6 336710 10 - 601863 ACCCTCAATC -s simRat_chr6.simRat.chr6 248195 9 + 647215 -CCACCAATA - -a -s simMouse_chr6.simMouse.chr6 258343 17 + 636262 TGGTGACTTCCCTGAGT -s Anc0.Anc0refChr5 75015 15 + 87904 CCA--GTTCTCATGAAT -s Anc1.Anc1refChr7 33930 15 - 47259 CCA--GTTCTCATGAAT -s Anc2.Anc2refChr15 72092 15 + 86568 CCA--GTTCTCATGAAT -s mr.mrrefChr5 110970 17 + 294540 CGATGACTTCCATGAGT -s simCow_chr6.simCow.chr6 253723 15 + 602619 ATA--GTTCCCATGAAT -s simDog_chr6.simDog.chr6 244530 13 + 593897 CCA--A--CTCACACAT -s simHuman_chr6.simHuman.chr6 336720 15 - 601863 CCA--GTTCTCATGAAT -s simRat_chr6.simRat.chr6 248204 17 + 647215 CGAAGAGTTCCATGAGT - -a -s simMouse_chr6.simMouse.chr6 258360 31 + 636262 CTAAAATGATTGCAGGCAATAGACTTAAAAG -s Anc0.Anc0refChr5 75031 31 + 87904 TTGAAATACTTACAGGAGTCAGGTGCACAGT -s Anc1.Anc1refChr7 33946 31 - 47259 TTGAAATACTTACAGGAGTCAGGTGCACAGT -s Anc2.Anc2refChr15 72108 31 + 86568 TTGAAATACTTACAAGAGTCAGGTGCACAGT -s mr.mrrefChr5 110987 31 + 294540 TTGAAATGATTGCAGGCAACAGGCTCACAGG -s simCow_chr6.simCow.chr6 253748 31 + 602619 TTGAAATACTTGCGAGAGTCAGGTGCACAGT -s simDog_chr6.simDog.chr6 244544 22 + 593897 CTCACATACTGAAA------AAGTA---AGT -s simHuman_chr6.simHuman.chr6 336736 31 - 601863 TTGAAATACTTACAGGTGCCAGGTGCACAGT -s simRat_chr6.simRat.chr6 248221 31 + 647215 TTGAAATGATTGCAGGCAGCAGGCTCACAGG - -a -s simMouse_chr6.simMouse.chr6 258391 11 + 636262 AGCAATAGACC -s Anc0.Anc0refChr5 75062 11 + 87904 AAAAATAGACC -s Anc1.Anc1refChr7 33977 11 - 47259 AAAAATAGACC -s Anc2.Anc2refChr15 72139 11 + 86568 AAAAATAGACC -s mr.mrrefChr5 111018 11 + 294540 AGCAATAGACC -s simCow_chr6.simCow.chr6 253779 11 + 602619 AAAAGTAGACC -s simDog_chr6.simDog.chr6 244571 11 + 593897 AAAGACAGTCC -s simHuman_chr6.simHuman.chr6 336767 11 - 601863 AAAAATAGACC -s simRat_chr6.simRat.chr6 248252 11 + 647215 GGCAATAGACT - -a -s simMouse_chr6.simMouse.chr6 258402 10 + 636262 GATCTAGGAG -s Anc0.Anc0refChr5 75073 10 + 87904 AATCTAAGGG -s Anc1.Anc1refChr7 33988 10 - 47259 AATCTAAGGG -s Anc2.Anc2refChr15 72150 10 + 86568 AATCTAAGGG -s mr.mrrefChr5 111029 10 + 294540 GATCTAGGAG -s simCow_chr6.simCow.chr6 253790 10 + 602619 AATCTAAGGG -s simDog_chr6.simDog.chr6 244584 10 + 593897 ATTCTAAGGG -s simHuman_chr6.simHuman.chr6 336778 10 - 601863 AATCCAAGGG -s simRat_chr6.simRat.chr6 248263 10 + 647215 GATCTAGGAG - -a -s simMouse_chr6.simMouse.chr6 258412 4 + 636262 ATTG -s Anc0.Anc0refChr5 75084 4 + 87904 TTTG -s Anc1.Anc1refChr7 33999 4 - 47259 TTTG -s Anc2.Anc2refChr15 72161 4 + 86568 TTCG -s mr.mrrefChr5 111039 4 + 294540 ATTG -s simCow_chr6.simCow.chr6 253801 4 + 602619 ATCG -s simDog_chr6.simDog.chr6 244595 4 + 593897 TTCA -s simHuman_chr6.simHuman.chr6 336789 4 - 601863 CTTG -s simRat_chr6.simRat.chr6 248273 4 + 647215 ATTG - -a -s simMouse_chr6.simMouse.chr6 258416 44 + 636262 AGATTATCAGTGGAAAGAGTTCATGTTCTGGAGATACTCTACTA -s Anc0.Anc0refChr5 75088 44 + 87904 AGATTATCAGTGGAAAGAGTTCATGCCGTGCAGATATTGGACTA -s Anc1.Anc1refChr7 34003 44 - 47259 AGATTATCAGTGGAAAGAGTTCATGCCGTGCAGATATTGGACTA -s Anc2.Anc2refChr15 72165 44 + 86568 AGATTAACAGTGGAAAGAGTTCAGCCCGTGCAGATGTCTGACTA -s mr.mrrefChr5 111043 44 + 294540 AGATTATCAGTGGAAAGAGTTCATGTTCTGGAGATATTGTACTA -s simCow_chr6.simCow.chr6 253865 44 + 602619 GGATAAACCATGGAAAGAGTTCAGCCCGCGCTGATGGCTGGCTA -s simDog_chr6.simDog.chr6 244599 38 + 593897 AGATTAACAGTGGAAAGAGTTC------TGGAGATGTCTGACTA -s simHuman_chr6.simHuman.chr6 336793 44 - 601863 AGATTATCAGTGAAATGAGTTCATGGCTTGCAGATATTGCACAA -s simRat_chr6.simRat.chr6 248277 38 + 647215 AGATTATTAGTGGAAAGAGTTCATGC------AATCTTGTACTA - -a -s simMouse_chr6.simMouse.chr6 258460 14 + 636262 TAATTGTGTCAGGA -s Anc0.Anc0refChr5 75134 14 + 87904 TAGTTTAGTCAGAG -s Anc1.Anc1refChr7 34049 14 - 47259 TAGTTTAGTCAGAG -s Anc2.Anc2refChr15 72211 14 + 86568 TAGTTTAGTCAGAG -s mr.mrrefChr5 111087 14 + 294540 TAATTGTGTCAGGG -s simCow_chr6.simCow.chr6 253911 11 + 602619 TTGTTGAGT---AG -s simDog_chr6.simDog.chr6 244639 14 + 593897 TAATTTAGTCAGAG -s simHuman_chr6.simHuman.chr6 336839 14 - 601863 TAGTTAAGTCAGAG -s simRat_chr6.simRat.chr6 248315 14 + 647215 TAATTTTGTCAGGG - -a -s simMouse_chr6.simMouse.chr6 258474 10 + 636262 ATTAGCTGTT -s Anc0.Anc0refChr5 75161 10 + 87904 ATTAGCTGTT -s Anc1.Anc1refChr7 34076 10 - 47259 ATTAGCTGTT -s Anc2.Anc2refChr15 72238 10 + 86568 ATTAGCTGTT -s mr.mrrefChr5 111101 10 + 294540 ATTAGCTGTT -s simCow_chr6.simCow.chr6 253935 10 + 602619 ATTAGCTGTT -s simDog_chr6.simDog.chr6 244664 10 + 593897 ATTAGTGGTT -s simHuman_chr6.simHuman.chr6 336878 10 - 601863 ATTAGCTGTG -s simRat_chr6.simRat.chr6 248329 10 + 647215 ATTAGCTGTT - -a -s simMouse_chr6.simMouse.chr6 258484 10 + 636262 CTTCCTTCCT -s Anc0.Anc0refChr5 75172 10 + 87904 CTTCCCATCT -s Anc1.Anc1refChr7 34087 10 - 47259 CTTCCCATCT -s Anc2.Anc2refChr15 72249 10 + 86568 CTTCCCATCT -s mr.mrrefChr5 111111 10 + 294540 CTTCCTTTCT -s simCow_chr6.simCow.chr6 253946 10 + 602619 CTACCCCTCT -s simDog_chr6.simDog.chr6 244675 10 + 593897 CTTCCCAACT -s simHuman_chr6.simHuman.chr6 336889 10 - 601863 CTTCCCATCT -s simRat_chr6.simRat.chr6 248339 10 + 647215 CTTCCTTTCT - -a -s simMouse_chr6.simMouse.chr6 258494 12 + 636262 TCAGAGTATGAC -s Anc0.Anc0refChr5 75199 12 + 87904 TGGGAGTCTGAC -s Anc1.Anc1refChr7 34114 12 - 47259 TGGGAGTCTGAC -s Anc2.Anc2refChr15 72276 12 + 86568 TGGGAGTCTGAC -s mr.mrrefChr5 111121 12 + 294540 TCAGAGTATGAC -s simCow_chr6.simCow.chr6 253973 12 + 602619 CGGGAGTCTGAC -s simDog_chr6.simDog.chr6 244702 12 + 593897 TGGGGGTCTGAC -s simHuman_chr6.simHuman.chr6 336916 12 - 601863 TGGGAGTTTGAT -s simRat_chr6.simRat.chr6 248349 12 + 647215 TCAGGATATGAC - -a -s simMouse_chr6.simMouse.chr6 258506 26 + 636262 AGAATTTGGTTATAGAGTAATCGCTC -s Anc0.Anc0refChr5 75211 26 + 87904 AAAGTTTGGTTAGAGAACAATTGCTC -s Anc1.Anc1refChr7 34126 26 - 47259 AAAGTTTGGTTAGAGAACAATTGCTC -s Anc2.Anc2refChr15 72288 26 + 86568 AATGTTTGGTTAGAGAACAATTACTC -s mr.mrrefChr5 111133 26 + 294540 AGAATTTGGTTATAGAATAATTGCTC -s simCow_chr6.simCow.chr6 253985 26 + 602619 AGGGTCTGGTTAGGGAACAATTACTT -s simDog_chr6.simDog.chr6 244714 26 + 593897 AATGTTTGGCTAAAGAACAATCATTC -s simHuman_chr6.simHuman.chr6 336965 26 - 601863 GAAGTTTGGTTAGAGAAAAATTGCTC -s simRat_chr6.simRat.chr6 248361 26 + 647215 AGAACTTGGTTATAGAATAATTGCCC - -a -s simMouse_chr6.simMouse.chr6 258532 80 + 636262 AAGGAAGTATGAGTACAGTAGGCCCTGTGCCTTTACTTGAATCTGTATTGTCTATAGGGTAGTCTTCTGTGTAATTCTGC -s Anc0.Anc0refChr5 75238 80 + 87904 ACGGAACTATGACGATCTAAGACCCTGCATCTCTGCCTGATTTTACAGTGTCTGTTGGGTGGTCTTCCATGTCATTCTGC -s Anc1.Anc1refChr7 34153 80 - 47259 ACGGAACTATGACGATCTAAGACCCTGCATCTCTGCCTGATTTTACAGTGTCTGTTGGGTGGTCTTCCATGTCATTCTGC -s Anc2.Anc2refChr15 72315 80 + 86568 ACGGAACTATTACGATCTAACACCCTGCATTTTTGCCTGATTTTGCAGTGTCTGTTGAGTGGTCTTCCACGACATTCTGC -s mr.mrrefChr5 111159 80 + 294540 AAGGAAGTATGAGTATAGTAGGCCCTGTGCCTCTACCTGAATTTATATTGTCTATAGGGTAGTCTTCTGTGTAATTCTGC -s simCow_chr6.simCow.chr6 254012 65 + 602619 TTGTGGGTATTAC--------ACCTTGCCTTTTCGCCTGGTTTTGAAGTATCCATTGAGCGGTCTT-------ATTCTGC -s simDog_chr6.simDog.chr6 244741 80 + 593897 ACAGAACTTTTAGGATCTAACTCCCTGCACTTTTGCCTTATTTTGCAGTGTTTGTTGAGTGGTCTTCCACGACATTGTGC -s simHuman_chr6.simHuman.chr6 336992 78 - 601863 ACGGAACTACGACAATTTCAGACTCTGCATCTCTGCCTGATTTCACAGTGTCTGTTGGGTG--CTTCCATGTCATTCTAC -s simRat_chr6.simRat.chr6 248387 80 + 647215 ATGGAAGTATGAATATGGTAGTCCCTGTGCTTCTACCTAAATTTATTTTGTTGATATGGTAGTCTTCTGTGTAATGCTGC - -a -s simMouse_chr6.simMouse.chr6 258612 26 + 636262 AAAGCTGTGAGGAGCAAACACCCGCG -s Anc0.Anc0refChr5 75322 24 + 87904 AAAGCTGCAACATG-AACCACCA-CA -s Anc1.Anc1refChr7 34237 24 - 47259 AAAGCTGCAACATG-AACCACCA-CA -s Anc2.Anc2refChr15 72399 24 + 86568 AATGCGGCAACATA-AACTACCA-CA -s mr.mrrefChr5 111239 26 + 294540 AAAGCTGCAACAAGCAAACACCAGCG -s simCow_chr6.simCow.chr6 254081 24 + 602619 AATGCATCGATATA-AACTACCA-CA -s simDog_chr6.simDog.chr6 244825 24 + 593897 AATGCGGCAACATA-AATTACAA-CA -s simHuman_chr6.simHuman.chr6 337074 24 - 601863 AAAGCTACAACAGG-AACCACCA-CA -s simRat_chr6.simRat.chr6 248467 26 + 647215 TAAGCTGCAACAAATGAACACCAGCA - -a -s simMouse_chr6.simMouse.chr6 258638 8 + 636262 CTTTTAAC -s Anc0.Anc0refChr5 75346 7 + 87904 CT-TTAAA -s Anc1.Anc1refChr7 34261 7 - 47259 CT-TTAAA -s Anc2.Anc2refChr15 72423 7 + 86568 CT-TTAAA -s mr.mrrefChr5 111265 8 + 294540 CTTTTAAC -s simCow_chr6.simCow.chr6 254105 7 + 602619 CT-TTAAA -s simDog_chr6.simDog.chr6 244849 7 + 593897 CC-TTATA -s simHuman_chr6.simHuman.chr6 337098 7 - 601863 GT-TCAAG -s simRat_chr6.simRat.chr6 248494 8 + 647215 CTTTTAAC - -a -s simMouse_chr6.simMouse.chr6 258646 26 + 636262 TAATCTGCCTGTTTAGAACAGCTATG -s Anc0.Anc0refChr5 75353 26 + 87904 TGATTAGCCTATTTGCAGCAGCTATG -s Anc1.Anc1refChr7 34268 26 - 47259 TGATTAGCCTATTTGCAGCAGCTATG -s Anc2.Anc2refChr15 72432 26 + 86568 TGATTAGCCTATTTGCTGCTGATATG -s mr.mrrefChr5 111273 26 + 294540 TAATCTGCCTGTTTAGAACAGCTATG -s simCow_chr6.simCow.chr6 254114 26 + 602619 TGATCAGCCTATTTGCTGCTGATATG -s simDog_chr6.simDog.chr6 244858 14 + 593897 TGATTGGCCTTTTT------------ -s simHuman_chr6.simHuman.chr6 337105 26 - 601863 TCCCAAGCCTATTTGCAGCAGCTATG -s simRat_chr6.simRat.chr6 248502 26 + 647215 TGATCTGTCTGTTTAGAACAGGTATG - -a -s simMouse_chr6.simMouse.chr6 258672 19 + 636262 TTTATATAGGCTGGTCCAT -s Anc0.Anc0refChr5 75379 19 + 87904 TTTCTGCACAATGGTCCAG -s Anc1.Anc1refChr7 34294 19 - 47259 TTTCTGCACAATGGTCCAG -s Anc2.Anc2refChr15 72458 19 + 86568 TTTCTGCACAATGGTCCAG -s mr.mrrefChr5 111299 19 + 294540 TTTATACAGGATGGTCCAT -s simCow_chr6.simCow.chr6 254140 19 + 602619 TTTCTGCATGATGGTCCAA -s simDog_chr6.simDog.chr6 245095 19 + 593897 TTTCTGCACAATGGTCCAG -s simHuman_chr6.simHuman.chr6 337131 19 - 601863 TTTTTGCACAATGGTCCAG -s simRat_chr6.simRat.chr6 248528 19 + 647215 TTTATACAGGATGGTCCAT - -a -s simMouse_chr6.simMouse.chr6 258691 45 + 636262 CTGGCCCCAGACTTCTATGACCTATTGGGGTCAGAATTCTGTGGT -s Anc0.Anc0refChr5 75398 45 + 87904 CTGGCCTCAGACTTCTATGTCCACTATAACTCACAACTCTGTGAA -s Anc1.Anc1refChr7 34313 45 - 47259 CTGGCCTCAGACTTCTATGTCCACTATAACTCACAACTCTGTGAA -s Anc2.Anc2refChr15 72477 45 + 86568 CAGGTCTCAGACTTCTATGTCCACTATAACTCACAACTCTGTGAA -s mr.mrrefChr5 111318 45 + 294540 CTGGCCCCAGACTTCTATGACCAATTGGAGTCACAATTCTGTGGT -s simCow_chr6.simCow.chr6 254160 44 + 602619 CAGGTGTCACACTTCTGTGTCCAATAGATGTCTCAACTCC-TGCA -s simDog_chr6.simDog.chr6 245114 45 + 593897 CAGGTCTCAGACTTCTATGTCCACTATAACTCATAACTATGCGAA -s simHuman_chr6.simHuman.chr6 337150 45 - 601863 CTGACCTCAAGCTTCTATGTCCACTACAAACCACAACCCTATGTA -s simRat_chr6.simRat.chr6 248547 45 + 647215 CTGGCCCCAGACTTCCATGACTAATTGGAGTCACAATTCTGTGGT - -a -s simMouse_chr6.simMouse.chr6 258736 30 + 636262 TGTTGGGCCTCTAGCACACAGGTGGACAAG -s Anc0.Anc0refChr5 75444 30 + 87904 TGTTGGTCCCCTAGCTCTCAGGCAGACTGA -s Anc1.Anc1refChr7 34359 30 - 47259 TGTTGGTCCCCTAGCTCTCAGGCAGACTGA -s Anc2.Anc2refChr15 72523 30 + 86568 TGTTGGTCCCCTAGCTCTCAGGCAGACTGA -s mr.mrrefChr5 111364 30 + 294540 TGTTGGTCCCCTAGCACACAGGTGGACTAG -s simCow_chr6.simCow.chr6 254204 26 + 602619 TGATGGTCCAATAGGT----GACAGACTTC -s simDog_chr6.simDog.chr6 245160 30 + 593897 TGTTGGTCCCCTAGCTCTCAGGCAGACTGA -s simHuman_chr6.simHuman.chr6 337196 30 - 601863 TGTTGGTCCCCCAGCGCTCAGGCAGACTGA -s simRat_chr6.simRat.chr6 248593 30 + 647215 TGCTGGTCCCCTAGTACACAGGTGGACTAG - -a -s simMouse_chr6.simMouse.chr6 258766 13 + 636262 CAGTCCAAGATAA -s Anc0.Anc0refChr5 75474 13 + 87904 CAGTTCAAGACAA -s Anc1.Anc1refChr7 34389 13 - 47259 CAGTTCAAGACAA -s Anc2.Anc2refChr15 72553 13 + 86568 CAGTTCAAGACAA -s mr.mrrefChr5 111394 13 + 294540 CAGTCCAAGATAA -s simCow_chr6.simCow.chr6 254236 13 + 602619 CACTACATGTCAG -s simDog_chr6.simDog.chr6 245190 13 + 593897 CAGTTTAAGATAA -s simHuman_chr6.simHuman.chr6 337226 13 - 601863 CAGTTCAAAACAA -s simRat_chr6.simRat.chr6 248623 13 + 647215 CAGTCCAAGATAA - -a -s simMouse_chr6.simMouse.chr6 258779 3 + 636262 TTG -s Anc0.Anc0refChr5 75487 3 + 87904 TTG -s Anc1.Anc1refChr7 34402 3 - 47259 TTG -s Anc2.Anc2refChr15 72566 3 + 86568 TTG -s mr.mrrefChr5 111407 3 + 294540 TTG -s simCow_chr6.simCow.chr6 254250 3 + 602619 TTG -s simHuman_chr6.simHuman.chr6 337239 3 - 601863 TTG -s simRat_chr6.simRat.chr6 248636 3 + 647215 TTG - -a -s simMouse_chr6.simMouse.chr6 258782 16 + 636262 AGTAGTCCTCATTCTA -s Anc0.Anc0refChr5 75573 16 + 87904 AGCAGTGCTCATTCTA -s Anc1.Anc1refChr7 34489 16 - 47259 AGCAGTGCTCATTCTA -s Anc2.Anc2refChr15 72662 16 + 86568 AGCAGTGCTCATTCTA -s mr.mrrefChr5 111491 16 + 294540 AGTAGTGCTCATTCTA -s simCow_chr6.simCow.chr6 254330 11 + 602619 AAAAGCGCTCA----- -s simDog_chr6.simDog.chr6 245292 16 + 593897 AGCAGTGTTCCTTCTA -s simHuman_chr6.simHuman.chr6 337326 16 - 601863 ATGAGTGCTCATTCTA -s simRat_chr6.simRat.chr6 248725 16 + 647215 AGTAATGCTCATTCTA - -a -s simMouse_chr6.simMouse.chr6 258798 33 + 636262 GAATGGAACTCCTCTTGCACAGCTAGCTGGGGG -s Anc0.Anc0refChr5 75590 33 + 87904 GGATGGAACTCCACTTACACAGCTACCTGGAGA -s Anc1.Anc1refChr7 34506 33 - 47259 GGATGGAACTCCACTTACACAGCTACCTGGAGA -s Anc2.Anc2refChr15 72679 33 + 86568 GGATGGAATTCCACTTACACAACAACCTGGAGA -s mr.mrrefChr5 111507 33 + 294540 GGATGGAACTCCTCTTGCACAGCTAGCTGGGGG -s simCow_chr6.simCow.chr6 254341 31 + 602619 GTATGGAAT--CACTTACACACCAACCTGGAGA -s simDog_chr6.simDog.chr6 245309 32 + 593897 GGATGGAATTCC-CTTACACAATAACCTGGAGA -s simHuman_chr6.simHuman.chr6 337343 33 - 601863 GGATGGAACTCCACTTACACAGCTACCTAGAGA -s simRat_chr6.simRat.chr6 248741 16 + 647215 GGATGCAACTCCT-----------------GCG - -a -s simMouse_chr6.simMouse.chr6 258831 13 + 636262 GTCATACACAGAT -s Anc0.Anc0refChr5 75623 13 + 87904 CTGACACACAAAG -s Anc1.Anc1refChr7 34539 13 - 47259 CTGACACACAAAG -s Anc2.Anc2refChr15 72713 13 + 86568 CATGCACACAAAG -s mr.mrrefChr5 111540 13 + 294540 GTGATACACAGAT -s simCow_chr6.simCow.chr6 254373 13 + 602619 CATGCACACCAAG -s simDog_chr6.simDog.chr6 245342 13 + 593897 CATGCACACAAAG -s simHuman_chr6.simHuman.chr6 337376 13 - 601863 CTGACACACAAAG -s simRat_chr6.simRat.chr6 248757 13 + 647215 GTGATACACAGAT - -a -s simMouse_chr6.simMouse.chr6 258844 2 + 636262 AC -s Anc0.Anc0refChr5 75636 2 + 87904 AC -s Anc1.Anc1refChr7 34552 2 - 47259 AC -s Anc2.Anc2refChr15 72726 2 + 86568 AC -s mr.mrrefChr5 111553 2 + 294540 AC -s simCow_chr6.simCow.chr6 254386 2 + 602619 AC -s simDog_chr6.simDog.chr6 245355 2 + 593897 AC -s simHuman_chr6.simHuman.chr6 337392 2 - 601863 CT -s simRat_chr6.simRat.chr6 248770 2 + 647215 AC - -a -s simMouse_chr6.simMouse.chr6 258846 27 + 636262 ATCAGTTACCCAGTTAAAAGAATACTA -s Anc0.Anc0refChr5 75643 23 + 87904 ATCAGT----CTGATACAGAAGTATCA -s Anc1.Anc1refChr7 34559 23 - 47259 ATCAGT----CTGATACAGAAGTATCA -s Anc2.Anc2refChr15 72733 23 + 86568 ATCAGT----CTGATACAGAAGTATCA -s mr.mrrefChr5 111555 27 + 294540 ATCAGTTACCCAGTTAAAAGAATATTA -s simCow_chr6.simCow.chr6 254393 23 + 602619 ATCGAT----TTGATACAAAATTATCA -s simDog_chr6.simDog.chr6 245362 23 + 593897 ATCAGT----CTGATACAGAAGTATCA -s simHuman_chr6.simHuman.chr6 337399 5 - 601863 AACAG---------------------- -s simRat_chr6.simRat.chr6 248772 27 + 647215 ATCAGTTACCTGTTTAAAATAATATTA - -a -s simMouse_chr6.simMouse.chr6 258873 54 + 636262 CTAATAGTCTTCTAGTGTTCTGAGTGACCTTGGGAGTGGGGGATTCAACAGTAC -s Anc0.Anc0refChr5 75666 50 + 87904 CCA----TCTCCTGGTGTTCTGCTTGTCCTTGGCAATGGGAGATTCAACAGCAC -s Anc1.Anc1refChr7 34582 50 - 47259 CCA----TCTCCTGGTGTTCTGCTTGTCCTTGGCAATGGGAGATTCAACAGCAC -s Anc2.Anc2refChr15 72756 50 + 86568 CCA----TATCCCGGTGTTCTGCTTGTCCTTGGCAATGGGAGATTCAACATCAC -s mr.mrrefChr5 111582 54 + 294540 CTAGTAGTCTTCTGGTGTTCTGATTGACCTTGGGAGTGGGGGATTCAACAGCAC -s simCow_chr6.simCow.chr6 254417 50 + 602619 CCA----TGGGTGTTTGTTCTGCTGGTCCTTTGAGATGGGAGATTCAACAACAC -s simDog_chr6.simDog.chr6 245385 50 + 593897 CCA----TATCCCGGTTTTCTGCTTGTCCTCGGCATTGTGTGATTCAACATCAC -s simHuman_chr6.simHuman.chr6 337404 50 - 601863 CCA----TCTCATGGTGTTCTGTTTGTCCTTAGCAATGGGAAATTTAACAGCAC -s simRat_chr6.simRat.chr6 248799 54 + 647215 CTAGTAGTCTTCTGGTGTTCTCATTGACCTTTGGAGTGGGGGATTCAACAGCAC - -a -s simMouse_chr6.simMouse.chr6 258927 16 + 636262 TGCACAAATGATGGAG -s Anc0.Anc0refChr5 75725 16 + 87904 TCTATAAATGCTGCAG -s Anc1.Anc1refChr7 34641 16 - 47259 TCTATAAATGCTGCAG -s Anc2.Anc2refChr15 72815 16 + 86568 TCTATGAATGCTGCAG -s mr.mrrefChr5 111636 16 + 294540 TGCACAAATGATGGAG -s simCow_chr6.simCow.chr6 254476 16 + 602619 TCTATGAATGCTTCAG -s simDog_chr6.simDog.chr6 245444 16 + 593897 TCTATGAATGCTGGGG -s simHuman_chr6.simHuman.chr6 337463 16 - 601863 TCTATAAGTGTTGCAG -s simRat_chr6.simRat.chr6 248853 12 + 647215 TGCA----TGATGGAG - -a -s simMouse_chr6.simMouse.chr6 258943 12 + 636262 TACATAGTGCAC -s Anc0.Anc0refChr5 75747 12 + 87904 TAGTTTGTGCAC -s Anc1.Anc1refChr7 34663 12 - 47259 TAGTTTGTGCAC -s Anc2.Anc2refChr15 72837 12 + 86568 TAGTTTCAGCAC -s mr.mrrefChr5 111652 12 + 294540 TACATAGTGCAC -s simCow_chr6.simCow.chr6 254498 12 + 602619 TAATTTTAGTGC -s simDog_chr6.simDog.chr6 245466 12 + 593897 TAGTATCAGCAC -s simHuman_chr6.simHuman.chr6 337485 12 - 601863 TATTTGGTGCAC -s simRat_chr6.simRat.chr6 248865 12 + 647215 TACATAGTGCAC - -a -s simMouse_chr6.simMouse.chr6 258955 14 + 636262 CTTCTGCAGCATTT -s Anc0.Anc0refChr5 75763 14 + 87904 CTTTGTTGGCATTT -s Anc1.Anc1refChr7 34679 14 - 47259 CTTTGTTGGCATTT -s Anc2.Anc2refChr15 72855 14 + 86568 CTTTGTTGGCATTT -s mr.mrrefChr5 111664 14 + 294540 CTTCTGCAGCATTT -s simCow_chr6.simCow.chr6 254516 14 + 602619 CTTCTTTGGTATTT -s simDog_chr6.simDog.chr6 245484 14 + 593897 CTTTGGTGGCTTTT -s simHuman_chr6.simHuman.chr6 337501 14 - 601863 CTTTGTTGGCATTT -s simRat_chr6.simRat.chr6 248877 14 + 647215 CCTCTGCAGCATTT - -a -s simMouse_chr6.simMouse.chr6 258969 7 + 636262 TTACAGC -s Anc0.Anc0refChr5 75778 7 + 87904 GTATAAC -s Anc1.Anc1refChr7 34694 7 - 47259 GTATAAC -s Anc2.Anc2refChr15 72870 7 + 86568 GTATAAC -s mr.mrrefChr5 111678 7 + 294540 GTATAAC -s simCow_chr6.simCow.chr6 254531 7 + 602619 GTATAAC -s simDog_chr6.simDog.chr6 245499 7 + 593897 CTATAAC -s simHuman_chr6.simHuman.chr6 337516 7 - 601863 GTATAAC -s simRat_chr6.simRat.chr6 248891 7 + 647215 GTATAAC - -a -s simMouse_chr6.simMouse.chr6 258976 5 + 636262 AAGAG -s Anc0.Anc0refChr5 75785 5 + 87904 AAGAG -s Anc1.Anc1refChr7 34701 5 - 47259 AAGAG -s Anc2.Anc2refChr15 72877 5 + 86568 AAGAG -s mr.mrrefChr5 111685 5 + 294540 AAGAG -s simCow_chr6.simCow.chr6 254570 5 + 602619 AAGAG -s simDog_chr6.simDog.chr6 245506 5 + 593897 AAGAG -s simHuman_chr6.simHuman.chr6 337523 5 - 601863 AAGAG -s simRat_chr6.simRat.chr6 248898 5 + 647215 AAGAG - -a -s simMouse_chr6.simMouse.chr6 258981 67 + 636262 CATTTATAATCGGGTTCTTCTCTTGCCCAAGCCAGATATTCACCAGGCTTGTGGTGTATAAGTGACG -s Anc0.Anc0refChr5 75792 64 + 87904 CTTATATAAT-GGGCCC--TTGTTACCCAAGCCAGATATACACCATGTTTGCAGTGTATAATGGAAC -s Anc1.Anc1refChr7 34708 64 - 47259 CTTATATAAT-GGGCCC--TTGTTACCCAAGCCAGATATACACCATGTTTGCAGTGTATAATGGAAC -s Anc2.Anc2refChr15 72884 64 + 86568 CTTATATGTT-GGGCCC--TTTTTACCCAAGCCAGATATACACCATGTTTGCAGTGTATAATGGAAC -s mr.mrrefChr5 111690 65 + 294540 CATTTATAATCGGGCTC--CTGTTACCCAAGCCAGATATTCACCAGGCTTGTGGTGTATAAGGGACG -s simCow_chr6.simCow.chr6 254577 59 + 602619 CTTATATGTT-GGGCCC--TTTTTACCCAAGTC-----TACAAGATGTTTGCAGTGTATAATGGAAC -s simDog_chr6.simDog.chr6 245513 64 + 593897 CTTATATGTT-GGGCCC--TCTTTACCCTAGCCAGATATACACCATGTTTGCAGTGCATAATGGATT -s simHuman_chr6.simHuman.chr6 337531 64 - 601863 CCTATATAAT-GGGCCC--TTGTTAGCCAAGCCAGACATACACCATGTTTGCAGTGTATAATGGAAC -s simRat_chr6.simRat.chr6 248903 63 + 647215 CATTTATATTTGGGCTC--ATGTTACCCAAGCCAAATATGCACAGG--TTGTGGTGTATAAGGGATG - -a -s simMouse_chr6.simMouse.chr6 259048 7 + 636262 CGGATAG -s Anc0.Anc0refChr5 75856 5 + 87904 AGGAT-- -s Anc1.Anc1refChr7 34772 5 - 47259 AGGAT-- -s Anc2.Anc2refChr15 72948 5 + 86568 AGGAT-- -s mr.mrrefChr5 111755 7 + 294540 AGGATAG -s simCow_chr6.simCow.chr6 254637 5 + 602619 AGGAT-- -s simDog_chr6.simDog.chr6 245577 5 + 593897 GGGAC-- -s simHuman_chr6.simHuman.chr6 337595 5 - 601863 AGGAT-- -s simRat_chr6.simRat.chr6 248966 7 + 647215 AAGATAG - -a -s simMouse_chr6.simMouse.chr6 259055 27 + 636262 AGTTCAGAGGCAAAAGGTCAATAGCAC -s Anc0.Anc0refChr5 75861 27 + 87904 TGTTTAGAGGCAAAAAGTTGATATCAC -s Anc1.Anc1refChr7 34777 27 - 47259 TGTTTAGAGGCAAAAAGTTGATATCAC -s Anc2.Anc2refChr15 72953 27 + 86568 TGTTTAGAGGCAAAAAGTTGATATCAC -s mr.mrrefChr5 111762 27 + 294540 AGTTCAGAGGCAAAAGGTCAATAGCAC -s simCow_chr6.simCow.chr6 254644 27 + 602619 TGTTTAGATGCAAAAAGTTGATATCAT -s simDog_chr6.simDog.chr6 245582 27 + 593897 TGTTTAGAGGACAAAAGTTTATATCAC -s simHuman_chr6.simHuman.chr6 337600 27 - 601863 TGTTGAGAGGCAATAAGTTGATAACAC -s simRat_chr6.simRat.chr6 248973 27 + 647215 AGTTCAGAGGCAAAAGGTCAATAGCAC - -a -s simMouse_chr6.simMouse.chr6 259082 7 + 636262 CTTGGTC -s Anc0.Anc0refChr5 75890 6 + 87904 CTTGG-A -s Anc1.Anc1refChr7 34806 6 - 47259 CTTGG-A -s Anc2.Anc2refChr15 72982 6 + 86568 CTTGG-A -s mr.mrrefChr5 111789 6 + 294540 CTTGG-C -s simCow_chr6.simCow.chr6 254673 6 + 602619 CTTGT-A -s simDog_chr6.simDog.chr6 245611 6 + 593897 TTTGG-A -s simHuman_chr6.simHuman.chr6 337629 6 - 601863 CTTGG-A -s simRat_chr6.simRat.chr6 249000 4 + 647215 CTTG--- - -a -s simMouse_chr6.simMouse.chr6 259089 17 + 636262 AAAAGCAGAATCTTTCT -s Anc0.Anc0refChr5 75896 17 + 87904 ACATGCAGAATTCTTTT -s Anc1.Anc1refChr7 34812 17 - 47259 ACATGCAGAATTCTTTT -s Anc2.Anc2refChr15 72989 17 + 86568 GCATGCGGGATTCCTTG -s mr.mrrefChr5 111795 17 + 294540 AAAAGCAGAATCCTTCT -s simCow_chr6.simCow.chr6 254680 17 + 602619 GCATGCGGGATTGCTTG -s simDog_chr6.simDog.chr6 245618 17 + 593897 GTGTGTGGGGTTCCTTG -s simHuman_chr6.simHuman.chr6 337635 17 - 601863 ACATACAGAATTCTTTT -s simRat_chr6.simRat.chr6 249004 7 + 647215 ----------TCCTTCT - -a -s simMouse_chr6.simMouse.chr6 259106 59 + 636262 GATCTATGCATTTGGACTAATGACATTTTACTTCCTTACTCCCAGAGCTTCGCATTTCA -s Anc0.Anc0refChr5 75913 53 + 87904 GATTAACACATTTGAACTATTGACATTTCAC------ATTCCTAAAAGTTGATTTTTCC -s Anc1.Anc1refChr7 34829 53 - 47259 GATTAACACATTTGAACTATTGACATTTCAC------ATTCCTAAAAGTTGATTTTTCC -s Anc2.Anc2refChr15 73011 53 + 86568 GAGTATCACATTTAAACAATCAACACTTCAT------TTTCCTAAAAGCTGATTTTTCC -s mr.mrrefChr5 111812 59 + 294540 GATCTACACATTTGGACTATTGACATTTTACTTCCTTACTCCTAAAGCTTCGCTTTTCA -s simCow_chr6.simCow.chr6 254702 53 + 602619 GGGCAACACAGGTAAACCCTGAACACTTCTT------TTTCCTAAAACCTGATCTTTCC -s simDog_chr6.simDog.chr6 245640 53 + 593897 GAGTATCACATTTAAACAATCAACACTTCAT------TTATCTAAAAGCTGCTTTTTCC -s simHuman_chr6.simHuman.chr6 337652 52 - 601863 T-TTGACACATTTGAACTATTGACGTTTCGC------ATTCCTAAAAGTTGATTCTTCC -s simRat_chr6.simRat.chr6 249011 59 + 647215 AATCTACACATCAGGACTATTGACATTTTACTTCACTACTCCTAAAGCTTTGCTTTTCA - -a -s simMouse_chr6.simMouse.chr6 259165 22 + 636262 CTTTTGGCTTGGATGTTTCATC -s Anc0.Anc0refChr5 75966 21 + 87904 CTTTTGGCTTGGGT-CTTCATC -s Anc1.Anc1refChr7 34882 21 - 47259 CTTTTGGCTTGGGT-CTTCATC -s Anc2.Anc2refChr15 73064 21 + 86568 CTTTTGGCCTAGGT-CTTCATC -s mr.mrrefChr5 111871 21 + 294540 CTTTTGGCTTGGAT-TTTCATC -s simCow_chr6.simCow.chr6 254755 21 + 602619 TTTTTGGCCAAGGT-CTTCATC -s simDog_chr6.simDog.chr6 245694 21 + 593897 CTTTAGGCCTAGGT-TTTTGTC -s simHuman_chr6.simHuman.chr6 337704 21 - 601863 CTTTTGGCTTGGGT-CTACATC -s simRat_chr6.simRat.chr6 249070 17 + 647215 GTTTTGGCTTGGAT-----ATC - -a -s simMouse_chr6.simMouse.chr6 259187 3 + 636262 AGA -s Anc0.Anc0refChr5 75987 3 + 87904 TGA -s Anc1.Anc1refChr7 34903 3 - 47259 TGA -s Anc2.Anc2refChr15 73085 3 + 86568 TGA -s mr.mrrefChr5 111892 3 + 294540 TGA -s simCow_chr6.simCow.chr6 254780 3 + 602619 TAA -s simDog_chr6.simDog.chr6 245715 3 + 593897 TGA -s simHuman_chr6.simHuman.chr6 337725 3 - 601863 TGA -s simRat_chr6.simRat.chr6 249087 3 + 647215 TGT - -a -s simMouse_chr6.simMouse.chr6 259190 11 + 636262 TCCATGGCAAA -s Anc0.Anc0refChr5 75991 11 + 87904 TTTGTAGCAAA -s Anc1.Anc1refChr7 34907 11 - 47259 TTTGTAGCAAA -s Anc2.Anc2refChr15 73089 11 + 86568 TTTGTAGGAAA -s mr.mrrefChr5 111895 11 + 294540 TCTGTGGCAAA -s simCow_chr6.simCow.chr6 254784 1 + 602619 T---------- -s simDog_chr6.simDog.chr6 245719 11 + 593897 TTTGTAGGAAA -s simHuman_chr6.simHuman.chr6 337729 11 - 601863 TTTGTAGCAAG -s simRat_chr6.simRat.chr6 249090 11 + 647215 TCTGTGGTAAA - -a -s simMouse_chr6.simMouse.chr6 259201 23 + 636262 TGTTGAGGGCTCTCCAGACTTGT -s Anc0.Anc0refChr5 76002 23 + 87904 TGCTGAGGGTTCTCCAAATTTTT -s Anc1.Anc1refChr7 34918 23 - 47259 TGCTGAGGGTTCTCCAAATTTTT -s Anc2.Anc2refChr15 73100 23 + 86568 TGCCAAGGGTTCTCCAAATCCTT -s mr.mrrefChr5 111906 23 + 294540 TGTTGAGGGCTCTCCAGACTTGT -s simCow_chr6.simCow.chr6 254785 17 + 602619 ------GGGTGCGCCAAATCCTT -s simDog_chr6.simDog.chr6 245732 15 + 593897 TGCCAAGGGTTCTC--------T -s simHuman_chr6.simHuman.chr6 337740 23 - 601863 TGCTGAGGGTTATCCAAAATTTT -s simRat_chr6.simRat.chr6 249101 21 + 647215 TGTTGAGGGCCCTCTTG--TTGA - -a -s simMouse_chr6.simMouse.chr6 259224 2 + 636262 TT -s Anc0.Anc0refChr5 76025 2 + 87904 TT -s Anc1.Anc1refChr7 34941 2 - 47259 TT -s Anc2.Anc2refChr15 73123 2 + 86568 TA -s mr.mrrefChr5 111929 2 + 294540 TT -s simCow_chr6.simCow.chr6 254802 2 + 602619 TC -s simDog_chr6.simDog.chr6 245747 2 + 593897 GA -s simHuman_chr6.simHuman.chr6 259054 2 + 601863 TT -s simHuman_chr6.simHuman.chr6 337763 2 - 601863 TT -s simRat_chr6.simRat.chr6 249122 2 + 647215 TT - -a -s simMouse_chr6.simMouse.chr6 259226 2 + 636262 AT -s Anc0.Anc0refChr5 76030 2 + 87904 GT -s Anc1.Anc1refChr7 34946 2 - 47259 GT -s Anc2.Anc2refChr15 73128 2 + 86568 GT -s mr.mrrefChr5 111934 2 + 294540 AT -s simCow_chr6.simCow.chr6 254807 2 + 602619 GT -s simDog_chr6.simDog.chr6 245752 2 + 593897 GC -s simHuman_chr6.simHuman.chr6 259057 2 + 601863 AT -s simHuman_chr6.simHuman.chr6 337768 2 - 601863 GT -s simRat_chr6.simRat.chr6 249127 2 + 647215 AT - -a -s simMouse_chr6.simMouse.chr6 259228 47 + 636262 ATGGCCACGATAGATTACAGTTGGTTGCCATTTATTTCTCTTGCTTT -s Anc0.Anc0refChr5 76035 47 + 87904 ATGGCCACCATGCATCCCAATTGGTTTCTGTTTTTTCTCTTTGCTTT -s Anc1.Anc1refChr7 34951 47 - 47259 ATGGCCACCATGCATCCCAATTGGTTTCTGTTTTTTCTCTTTGCTTT -s Anc2.Anc2refChr15 73133 47 + 86568 ATGGCCACCATGCACCCCAATTGGTTTCTGTTTTTTCTCTTTGCTTT -s mr.mrrefChr5 111936 47 + 294540 ATGGCCACGATAGATTACAGTTGGTTGCCATTTATTCTCTTTGCTTT -s simCow_chr6.simCow.chr6 254812 47 + 602619 ACGGCCACCACACACTCCAACTGGTTTGTGTATTTCCTCTTCACTCC -s simDog_chr6.simDog.chr6 245757 47 + 593897 ATGGCCACGATGCACCACAATTGATCTTTGTTATTTCCCTTTGCTTT -s simHuman_chr6.simHuman.chr6 259059 47 + 601863 CTGGCAACCATGCATCCCAATTGGTTTCTGTTTTTACTCTTTTCTTT -s simHuman_chr6.simHuman.chr6 337773 47 - 601863 ATGGCCACCATGCTTTGTATTTGGTTTCTGATTTTTCTCTTCGCTCT -s simRat_chr6.simRat.chr6 249129 47 + 647215 ATGGCCACAATAGATTACAATTGGTTGCCATCTCTTCTCTTTGCATT - -a -s simMouse_chr6.simMouse.chr6 259275 2 + 636262 CT -s Anc0.Anc0refChr5 76090 2 + 87904 TT -s Anc1.Anc1refChr7 35006 2 - 47259 TT -s Anc2.Anc2refChr15 73188 2 + 86568 TT -s mr.mrrefChr5 111991 2 + 294540 CT -s simCow_chr6.simCow.chr6 254867 2 + 602619 CT -s simDog_chr6.simDog.chr6 245812 2 + 593897 TT -s simHuman_chr6.simHuman.chr6 259114 2 + 601863 TT -s simHuman_chr6.simHuman.chr6 337828 2 - 601863 TT -s simRat_chr6.simRat.chr6 249184 2 + 647215 CT - -a -s simMouse_chr6.simMouse.chr6 259277 2 + 636262 TC -s Anc0.Anc0refChr5 76092 2 + 87904 CT -s Anc1.Anc1refChr7 35008 2 - 47259 CT -s Anc2.Anc2refChr15 73191 2 + 86568 CT -s mr.mrrefChr5 111993 2 + 294540 TC -s simCow_chr6.simCow.chr6 254870 2 + 602619 CA -s simDog_chr6.simDog.chr6 245815 2 + 593897 CT -s simHuman_chr6.simHuman.chr6 259116 2 + 601863 AC -s simHuman_chr6.simHuman.chr6 337830 2 - 601863 CT -s simRat_chr6.simRat.chr6 249186 2 + 647215 TC - -a -s simMouse_chr6.simMouse.chr6 259279 2 + 636262 CA -s Anc0.Anc0refChr5 76094 2 + 87904 AA -s Anc1.Anc1refChr7 35010 2 - 47259 AA -s Anc2.Anc2refChr15 73193 2 + 86568 AA -s mr.mrrefChr5 111995 2 + 294540 CA -s simCow_chr6.simCow.chr6 254872 2 + 602619 AA -s simDog_chr6.simDog.chr6 245817 2 + 593897 AA -s simHuman_chr6.simHuman.chr6 337832 2 - 601863 AA -s simRat_chr6.simRat.chr6 249188 2 + 647215 CA - -a -s simMouse_chr6.simMouse.chr6 259281 26 + 636262 AACTTATGTCCTTAATACAAACAATC -s Anc0.Anc0refChr5 76096 26 + 87904 AACTTGTGTCCTTAATACAAGCAACT -s Anc1.Anc1refChr7 35012 26 - 47259 AACTTGTGTCCTTAATACAAGCAACT -s Anc2.Anc2refChr15 73195 26 + 86568 AACTTGTGTCCTTAATACAAGCAACT -s mr.mrrefChr5 111997 26 + 294540 AACTTATGTCCTTAATACAAACAATC -s simCow_chr6.simCow.chr6 254874 25 + 602619 AACTTGTGT-CTTAATACAAGCAACT -s simDog_chr6.simDog.chr6 245819 26 + 593897 CACCTGTGTCATTAATACAAGCAAAT -s simHuman_chr6.simHuman.chr6 259118 26 + 601863 AACTTATGTCCTCAATACAAGCAACT -s simHuman_chr6.simHuman.chr6 337834 26 - 601863 AACTTGGGTCCTTAATTCAAGCAACT -s simRat_chr6.simRat.chr6 249190 26 + 647215 AACTAATGTCCTTAATACAAACAATC - -a -s simMouse_chr6.simMouse.chr6 259307 4 + 636262 GCTG -s Anc0.Anc0refChr5 76122 4 + 87904 TCTG -s Anc1.Anc1refChr7 35038 4 - 47259 TCTG -s Anc2.Anc2refChr15 73221 4 + 86568 TCAA -s mr.mrrefChr5 112023 4 + 294540 GCTG -s simCow_chr6.simCow.chr6 254899 4 + 602619 TTAA -s simDog_chr6.simDog.chr6 245845 4 + 593897 TCAA -s simHuman_chr6.simHuman.chr6 337860 4 - 601863 TCTG -s simRat_chr6.simRat.chr6 249216 4 + 647215 GCTG - -a -s simMouse_chr6.simMouse.chr6 259311 4 + 636262 TCCA -s Anc0.Anc0refChr5 76126 4 + 87904 ATCT -s Anc1.Anc1refChr7 35042 4 - 47259 ATCT -s Anc2.Anc2refChr15 73225 4 + 86568 ATCT -s mr.mrrefChr5 112027 4 + 294540 TCCT -s simCow_chr6.simCow.chr6 254903 4 + 602619 ACCC -s simDog_chr6.simDog.chr6 245849 4 + 593897 ATCT -s simHuman_chr6.simHuman.chr6 259144 4 + 601863 TCCT -s simHuman_chr6.simHuman.chr6 337864 4 - 601863 ATCT -s simRat_chr6.simRat.chr6 249220 4 + 647215 CCCT - -a -s simMouse_chr6.simMouse.chr6 259315 2 + 636262 GA -s Anc0.Anc0refChr5 76130 2 + 87904 GA -s Anc1.Anc1refChr7 35046 2 - 47259 GA -s Anc2.Anc2refChr15 73229 2 + 86568 GA -s mr.mrrefChr5 112031 2 + 294540 GA -s simCow_chr6.simCow.chr6 254907 2 + 602619 AA -s simDog_chr6.simDog.chr6 245853 2 + 593897 GA -s simHuman_chr6.simHuman.chr6 337868 2 - 601863 GA -s simRat_chr6.simRat.chr6 249224 2 + 647215 GA - -a -s simMouse_chr6.simMouse.chr6 259317 20 + 636262 CATCCAATATTCCCAACATG -s Anc0.Anc0refChr5 76132 20 + 87904 CCTCCATTGTTCTCAACATA -s Anc1.Anc1refChr7 35048 20 - 47259 CCTCCATTGTTCTCAACATA -s Anc2.Anc2refChr15 73231 20 + 86568 CCTCCATTGTCTACAATAGC -s mr.mrrefChr5 112033 20 + 294540 CATCCAATATTCCCAACATG -s simCow_chr6.simCow.chr6 254909 20 + 602619 CCCCCATTGTCTTCAACAGT -s simDog_chr6.simDog.chr6 245855 20 + 593897 CCTCCATTATCTACAATAGC -s simHuman_chr6.simHuman.chr6 259148 20 + 601863 CACCCATTGTTCTCACCATA -s simHuman_chr6.simHuman.chr6 337870 20 - 601863 CCTCCATGGTTCTCAGCATA -s simRat_chr6.simRat.chr6 249226 20 + 647215 CATCCAGTATTCCCAACATG - -a -s simMouse_chr6.simMouse.chr6 259337 55 + 636262 CTCCCACTGACAGTAACCACATGACCAAACAGGAGTTGGAACCATCATGCAACTC -s Anc0.Anc0refChr5 76152 52 + 87904 CTCCTACTGACAGCAACCACTTAACTAAATGAAAGTCAGAACCATCA-GCCAC-- -s Anc1.Anc1refChr7 35068 52 - 47259 CTCCTACTGACAGCAACCACTTAACTAAATGAAAGTCAGAACCATCA-GCCAC-- -s Anc2.Anc2refChr15 73251 52 + 86568 CTCCTACTGACAGCAACCACTTAACTAAATGAAAGTCAGAACCATCA-GCCAA-- -s mr.mrrefChr5 112053 55 + 294540 CTCCCACTGACAGTAACCACATGACCAAACGGAAGTTAGAACCATCATGCAACTC -s simCow_chr6.simCow.chr6 254929 51 + 602619 CTCCTACTGAC-GCAATTGCTTATTTAACCAAAAGTTAGCACCATCA-ACCAA-- -s simDog_chr6.simDog.chr6 245875 52 + 593897 CTCCTACGAACGGCGACCACTTAAGTAAATGAAAGTCAGAATCATCA-GCCAA-- -s simHuman_chr6.simHuman.chr6 259174 52 + 601863 CCCCTACTGACAGAAACCACTTAACCAAATGAATGTCAGAACCATCA-GCCAC-- -s simHuman_chr6.simHuman.chr6 337890 51 - 601863 CTCCTA-TCACAGCAACCACTTAACTAAATGAAAGTAAGAGCCATCA-ACCAG-- -s simRat_chr6.simRat.chr6 249246 55 + 647215 CTCCCACTGACAGTAACCATGTGACCAAACGGAAGGTAGAACCATCACACAACTT - -a -s simMouse_chr6.simMouse.chr6 259392 15 + 636262 AAGCATTACAACTTA -s Anc0.Anc0refChr5 76204 4 + 87904 -----------CTTA -s Anc1.Anc1refChr7 35120 4 - 47259 -----------CTTA -s Anc2.Anc2refChr15 73303 4 + 86568 -----------CTTA -s mr.mrrefChr5 112108 15 + 294540 AAGCATTACAACTTA -s simCow_chr6.simCow.chr6 254980 2 + 602619 -----------CT-- -s simDog_chr6.simDog.chr6 245927 4 + 593897 -----------TTTT -s simHuman_chr6.simHuman.chr6 259226 4 + 601863 -----------CTTA -s simHuman_chr6.simHuman.chr6 337941 4 - 601863 -----------CTTA -s simRat_chr6.simRat.chr6 249302 15 + 647215 AAGCATTACAACTTA - -a -s simMouse_chr6.simMouse.chr6 259407 49 + 636262 GCACTCTTGTGTTATTGCTAATTTTTGGGTAGACCAATCTTTAGGTTGG -s Anc0.Anc0refChr5 76209 23 + 87904 GCATGCTGGTGTTATTGCCAATC-------------------------- -s Anc1.Anc1refChr7 35125 28 - 47259 GCATGCTGGTGTTATTGCCAATCTTTGG--------------------- -s Anc2.Anc2refChr15 73308 23 + 86568 GCATGCTGGTGTTATTGCCAATC-------------------------- -s mr.mrrefChr5 112124 28 + 294540 GCATTCTTGTGTTATTGCTAATTTTTGG--------------------- -s simCow_chr6.simCow.chr6 254982 17 + 602619 ---TGCTGGTGTTATTTCC---A-------------------------- -s simDog_chr6.simDog.chr6 245932 23 + 593897 GTATATGGGGGCTATTGCCAATC-------------------------- -s simHuman_chr6.simHuman.chr6 259231 28 + 601863 GCATGCTGGTTTTATTGGCAATCTTTGG--------------------- -s simHuman_chr6.simHuman.chr6 337946 22 - 601863 GCATGCTGATGTTATTGCCCCT--------------------------- -s simRat_chr6.simRat.chr6 249318 28 + 647215 GCATTTTTGTGTCATCATTGATTTTTCA--------------------- - -a -s simMouse_chr6.simMouse.chr6 259456 46 + 636262 TCATTTTGGGTAGGCCAATCTTTAGGTTGGTCATTTCTAATCTTGG -s Anc1.Anc1refChr7 35153 5 - 47259 TCAAT----------------------------------------- -s mr.mrrefChr5 112152 46 + 294540 TCATTTTGGGTAGGCCAATCTTTGGGTTGGTCATTTCTAATCTTGG -s simHuman_chr6.simHuman.chr6 259260 5 + 601863 TCAAT----------------------------------------- -s simRat_chr6.simRat.chr6 249346 46 + 647215 CCGCTTTGGGCAGACCAATTTTTGGGTTGGTCATTTCTAATCTTGG - -a -s simMouse_chr6.simMouse.chr6 259502 21 + 636262 CCAATCTTTGGGTTGGTTATT -s Anc0.Anc0refChr5 76232 14 + 87904 ---ATCTCTGGG-TG---ATC -s Anc1.Anc1refChr7 35158 16 - 47259 --AATCTCTGGGTTG---ATC -s Anc2.Anc2refChr15 73331 14 + 86568 ---ATCTCTGGG-TG---ATC -s mr.mrrefChr5 112198 18 + 294540 CCAATCTTTGGGTTG---ATT -s simCow_chr6.simCow.chr6 254999 14 + 602619 ---ATCTCTGGG-TG---ATC -s simDog_chr6.simDog.chr6 245955 12 + 593897 ---ATCTGTGGG-C-----TC -s simHuman_chr6.simHuman.chr6 259265 16 + 601863 --AATCTTTGGGTCA---ATC -s simHuman_chr6.simHuman.chr6 337968 13 - 601863 -----CTCTGGGTTG---CTT -s simRat_chr6.simRat.chr6 249397 18 + 647215 CCAATCTTTGGGTTG---ATT - -a -s simMouse_chr6.simMouse.chr6 259523 23 + 636262 CCTTACTATGGGGTCAATAGCTT -s Anc0.Anc0refChr5 76250 23 + 87904 CCTTAATTTGGGGTCAATTGCTC -s Anc1.Anc1refChr7 35178 23 - 47259 CCTTAATTTGGGGTCAATTGCTC -s Anc2.Anc2refChr15 73349 23 + 86568 ACCTAATTTGGGGTCAATTGCTC -s mr.mrrefChr5 112216 23 + 294540 CCTTACTCTGGGGTCAATAGCTT -s simCow_chr6.simCow.chr6 255017 23 + 602619 ACCACATTTGGGGTTAATAGCTC -s simDog_chr6.simDog.chr6 245971 22 + 593897 ACCTAATTTGGGG-CAATTGCTC -s simHuman_chr6.simHuman.chr6 259285 23 + 601863 CCTTAACTTGGGGTCAATTGATC -s simHuman_chr6.simHuman.chr6 337985 23 - 601863 CTTTAATCTGGGGACAATTGCTC -s simRat_chr6.simRat.chr6 249415 23 + 647215 CCTTACTCGGAGGTCAATAGCTT - -a -s simMouse_chr6.simMouse.chr6 259546 12 + 636262 GGGAATATAGAC -s Anc0.Anc0refChr5 76280 12 + 87904 GGAAATATAGAC -s Anc1.Anc1refChr7 35208 12 - 47259 GGAAATATAGAC -s Anc2.Anc2refChr15 73379 12 + 86568 GGAAATATAGAC -s mr.mrrefChr5 112246 12 + 294540 GGAAATATAGAC -s simCow_chr6.simCow.chr6 255047 12 + 602619 GGAAATATAGAA -s simDog_chr6.simDog.chr6 246000 12 + 593897 GGAAGTATAAAC -s simHuman_chr6.simHuman.chr6 259315 12 + 601863 GGAAAAATTTAC -s simHuman_chr6.simHuman.chr6 338015 12 - 601863 GGAAATATAGAC -s simRat_chr6.simRat.chr6 249445 12 + 647215 GGAAATATAAAC - -a -s simMouse_chr6.simMouse.chr6 259558 2 + 636262 AT -s Anc0.Anc0refChr5 76292 2 + 87904 CT -s Anc1.Anc1refChr7 35220 2 - 47259 CT -s Anc2.Anc2refChr15 73392 2 + 86568 CT -s mr.mrrefChr5 112258 2 + 294540 AT -s simCow_chr6.simCow.chr6 255060 2 + 602619 CT -s simDog_chr6.simDog.chr6 246013 2 + 593897 CT -s simHuman_chr6.simHuman.chr6 259327 2 + 601863 AC -s simHuman_chr6.simHuman.chr6 338027 2 - 601863 CT -s simRat_chr6.simRat.chr6 249457 2 + 647215 AT - -a -s simMouse_chr6.simMouse.chr6 259560 24 + 636262 ATTTATGCATAGCAATCTCCTACA -s Anc0.Anc0refChr5 76294 24 + 87904 CTTTTGCCATACTAATATCTTACA -s Anc1.Anc1refChr7 35222 24 - 47259 CTTTTGCCATACTAATATCTTACA -s Anc2.Anc2refChr15 73394 24 + 86568 CTTCTGCCATACTAATATCTTGTA -s mr.mrrefChr5 112260 24 + 294540 ATTTATGCATAGCAATCTCCTACA -s simCow_chr6.simCow.chr6 255062 24 + 602619 CTTCTGCCATACTAGTGTCTTGTA -s simDog_chr6.simDog.chr6 246015 24 + 593897 CTCCTGCCATGCTAATATCCTGTG -s simHuman_chr6.simHuman.chr6 338029 24 - 601863 CTTTTGCCATACTGATATCTCACA -s simRat_chr6.simRat.chr6 249459 24 + 647215 ACTTATGCATAGCAATCTCCTACA - -a -s simMouse_chr6.simMouse.chr6 259584 20 + 636262 CAAGCGTGCCCACAAACAGC -s Anc0.Anc0refChr5 76319 20 + 87904 CAAGAGTGACCTTATACAAC -s Anc1.Anc1refChr7 35247 20 - 47259 CAAGAGTGACCTTATACAAC -s Anc2.Anc2refChr15 73419 20 + 86568 CAAGAGAGACCTTATACAAC -s mr.mrrefChr5 112284 20 + 294540 CAAGCGTGCCCTCAAACAGC -s simCow_chr6.simCow.chr6 255087 20 + 602619 CAATAGGGACCTTATACGAC -s simDog_chr6.simDog.chr6 246040 20 + 593897 CAAAAGAGACCTCATACAAC -s simHuman_chr6.simHuman.chr6 259329 20 + 601863 CAAGAGCAACCTTGTACAAC -s simHuman_chr6.simHuman.chr6 338054 20 - 601863 CAAGAGTGACCTGATATGAC -s simRat_chr6.simRat.chr6 249483 20 + 647215 CAATTGTGCTTTCAAACAGC - -a -s simMouse_chr6.simMouse.chr6 259604 5 + 636262 TTCTA -s Anc0.Anc0refChr5 76339 5 + 87904 TTCTA -s Anc1.Anc1refChr7 35267 5 - 47259 TTCTA -s Anc2.Anc2refChr15 73439 5 + 86568 TTCTA -s mr.mrrefChr5 112304 5 + 294540 TTCTA -s simCow_chr6.simCow.chr6 255107 5 + 602619 CTCTA -s simDog_chr6.simDog.chr6 246060 5 + 593897 TTCAA -s simHuman_chr6.simHuman.chr6 338074 5 - 601863 TGCTA -s simRat_chr6.simRat.chr6 249503 5 + 647215 TTCTA - -a -s simMouse_chr6.simMouse.chr6 259609 109 + 636262 GAAAAGATGTATACATGTCCCCTCTGGACCACAAAAACTGATCATATAACTCATATCAATTACCCTACACTTCTTATTCAGCTTCGTATTTTCTAAACTGATTGACCAA -s Anc0.Anc0refChr5 76344 100 + 87904 CAAAAAATGTATGCTTGT---CTCAGAATTAAACAAACTGATTACATAACTAACATCTACTTCCCTA-----CTTATTTAGTTTTGGCTTTTGT-AACAGATTGACAGA -s Anc1.Anc1refChr7 35272 103 - 47259 CAAAAAATGTATGCTTGTAGCCTCAGAATTAAACAAACTGATTACATAACTAACATCTACTTCCCTA-----CTTATTTAGTTTTGGCTTTTGT-AACAGATTGACAGA -s Anc2.Anc2refChr15 73444 100 + 86568 CAAAAAATGTATGCTTGT---TTCAGAATTGAACAAACTGATTACATAACTAACATCTACTTCCCTA-----CTTATTTAGTTTTGACTTTTGT-AACAGATGGACAGA -s mr.mrrefChr5 112309 109 + 294540 GAAAAAATGTATACATGTCCCCTCTGGATCACAAAAACTGATCATATAACTCATATCAATTACCCTACACTTCTTATTCAGCTTTGGATTTTCTAAACTGATTGACCGA -s simCow_chr6.simCow.chr6 255114 100 + 602619 CAAAAAATATATGCTTGT---ATCAGAATCCAAAACATTGATTATGTAACTCATGTCTACTTCCCTA-----TCTATTTAGTTTTGTATCTTAT-AACAGATGGACGGA -s simDog_chr6.simDog.chr6 246065 96 + 593897 AA----ATGTATGTTTGT---TTCAGGATTGAACAAACTGATCACATAACTAACATCTACTTCCCCA-----CTTATTTAGTTTTGACTTTTGT-AACAGATGGACAGA -s simHuman_chr6.simHuman.chr6 338079 103 - 601863 CATATAATGTAGGCTTATAGCCGCAGAATTAAAGAAGCTGATTACATAGCTTACATCTACTTCCCTA-----CTGATTGAGTTTTGGTGTTTGT-AACAGATTAACAGA -s simRat_chr6.simRat.chr6 249508 109 + 647215 TAAAAAATGTATACGTGTCCCCTCTGGATGACAAAAACTGATCATATAACTCATATCAATTACCTTACACTTCTTATTTAGCTTTGGCTTTTCCAAATTGATTGACTGA - -a -s simMouse_chr6.simMouse.chr6 259718 65 + 636262 TCCAAACATAACATTGACCATAGACATACTTAATGACCCCTTACTAAGCACCTATCTCAATGTGA -s Anc0.Anc0refChr5 76459 65 + 87904 TTTGAGCATACTGTCCACCATACAAATACTTGATGACACCTTGCTAAGTGCCTGACTTGATGTGA -s Anc1.Anc1refChr7 35390 65 - 47259 TTTGAGCATACTGTCCACCATACAAATACTTGATGACACCTTGCTAAGTGCCTGACTTGATGTGA -s Anc2.Anc2refChr15 73559 65 + 86568 TTTGAGTATAATGTCCACCATACAAATACCTGATGACATCTTGCTAAGTGCCTGACTTGATGTGA -s mr.mrrefChr5 112418 65 + 294540 TTCAAACATACCATCGACCATAGACATACTTAATGACCCCTTACTAAGTACCTATCTCAATGTGA -s simCow_chr6.simCow.chr6 255229 64 + 602619 TTTGAG-ATAATGTCCACAAAACAAATACCTGATGACAACTAGTTAGGTGACTAACTTGATGTTA -s simDog_chr6.simDog.chr6 246176 65 + 593897 TTTGAATGAAATATCTACCATACAAATACCTGATGACATCTTGCTAAGTGCCTGACTTGATGTGA -s simHuman_chr6.simHuman.chr6 338197 65 - 601863 TTTGTGCATACTGTCCACCATACAAATACTTCATGACACCTTGACAAGTGGCTGACTTGATGTGA -s simRat_chr6.simRat.chr6 249617 65 + 647215 TTCAAACATACCCTCAACCATAGACATACCTGATGACCACTTACTAAATACCTATCTCAATGTTA - -a -s simMouse_chr6.simMouse.chr6 259783 196 + 636262 GGCATTAGGCAAGCAGATGCCTCATGAGATTGCATATGTTCTTAGCATGTTTAACACTACTTAGACTTTGCACAGCGTCTCGCGCAATTCTCTAAAAGAAGGCAAACGCGGGCCATGTACACACAGTCAGTGCTTGGCTATGCCCCTTCCCCACACGGCAGATCTGCATGGAGTTCATGGAAGTCCCTTCTTACCC -s Anc0.Anc0refChr5 76524 83 + 87904 GACA-TAGACTAAAGAATGCCTCACAAGATTACATATGTACTTGTCACT---A--TTTTCTT-----------------------------------------------------------------------------------------------------------GGTGTTGATGGAAGTTACTCCTTACCC -s Anc1.Anc1refChr7 35455 83 - 47259 GACA-TAGACTAAAGAATGCCTCACAAGATTACATATGTACTTGTCACT---A--TTTTCTT-----------------------------------------------------------------------------------------------------------GGTGTTGATGGAAGTTACTCCTTACCC -s Anc2.Anc2refChr15 73625 83 + 86568 AAGA-TAGACTAAAGAATGTCTCCCTAGAGTACATATGTACTTGTCACT---A--TTTTCTT-----------------------------------------------------------------------------------------------------------GGTGTTGATGGGAGTTACTCCTTACCT -s mr.mrrefChr5 112483 86 + 294540 GGCATTAGACTAGCGGATGCCTCATAAGATTGCATATGTTCTTAGCATG---AACTCTTCTT-----------------------------------------------------------------------------------------------------------GGAGTTCATGGAAGTCACTTCTTACCC -s simCow_chr6.simCow.chr6 255294 83 + 602619 AAGG-TAAGCCAACAGCTGTCTCCTCAGAGCACATATGTATATGTCATT---A--TTTTCCT-----------------------------------------------------------------------------------------------------------GGTGTTGATGGGAGTTACTCCTTAGCT -s simDog_chr6.simDog.chr6 246242 83 + 593897 AAGA-TAGACTAAAGAATGTCTCCCTAGAGTGCATATATACTTGTCACT---A--CTTTCTT-----------------------------------------------------------------------------------------------------------GGAATTGATGGGGGTTACTGCTTACCT -s simHuman_chr6.simHuman.chr6 338262 83 - 601863 GACA-TAGACTAATGAAGACCTGACATGATTACATATGTGCTTTTCACT---A--TTTTCTC-----------------------------------------------------------------------------------------------------------AGTGTCAATGCAAGTTACGCCTTACCC -s simRat_chr6.simRat.chr6 249682 80 + 647215 GTCATTGGACTAGCGGGTGCATCATAAG------TATGTACTTAGCATG---AGATCTTCTT-----------------------------------------------------------------------------------------------------------GGAGTTCATGGAAGTCATTTCTTACCC - -a -s simMouse_chr6.simMouse.chr6 259979 14 + 636262 TAGCACCCACATAT -s Anc0.Anc0refChr5 76612 14 + 87904 TAGCACCCACACAT -s Anc1.Anc1refChr7 35543 14 - 47259 TAGCACCCACACAT -s Anc2.Anc2refChr15 73713 14 + 86568 CAGCACTCACACAT -s mr.mrrefChr5 112569 14 + 294540 TAGCACCCACATAT -s simCow_chr6.simCow.chr6 255382 14 + 602619 CAGTACTCACACAT -s simDog_chr6.simDog.chr6 246330 14 + 593897 CCGCCCTCACACAT -s simHuman_chr6.simHuman.chr6 338350 14 - 601863 TAGCACCTACACAT -s simRat_chr6.simRat.chr6 249762 14 + 647215 TAGCACCCACATAG - -a -s simMouse_chr6.simMouse.chr6 259993 15 + 636262 GATCTTCATGCTGCA -s Anc0.Anc0refChr5 76626 15 + 87904 GATCTTGATGTTGCA -s Anc1.Anc1refChr7 35557 15 - 47259 GATCTTGATGTTGCA -s Anc2.Anc2refChr15 73727 15 + 86568 GATCTTGATGTTGCA -s mr.mrrefChr5 112583 15 + 294540 GATCTTCATGCTGCA -s simCow_chr6.simCow.chr6 255396 15 + 602619 GATCTTGATGTTACA -s simDog_chr6.simDog.chr6 246344 15 + 593897 GATCTTGATGTTGCA -s simHuman_chr6.simHuman.chr6 338364 14 - 601863 GACTTTGATGTTGT- -s simRat_chr6.simRat.chr6 249797 15 + 647215 GGTCTTCATGCTGCA - -a -s simMouse_chr6.simMouse.chr6 260008 33 + 636262 TGTCAATGGGAGTCAGGAACTTGTACTTATGCC -s Anc0.Anc0refChr5 76641 33 + 87904 TGGTTATGGGAATTAAGATCTTCCATTCATGGC -s Anc1.Anc1refChr7 35572 33 - 47259 TGGTTATGGGAATTAAGATCTTCCATTCATGGC -s Anc2.Anc2refChr15 73743 33 + 86568 TGGTTATGTGGATCAAGATCATCCATTCATGGC -s mr.mrrefChr5 112598 33 + 294540 TGTCAATGGGAGTTAGGATCTTGCACTTATGCC -s simCow_chr6.simCow.chr6 255412 33 + 602619 TGTCTTTGGGACTCAAGACCCTCCAATCATGGC -s simDog_chr6.simDog.chr6 246360 33 + 593897 TGGTTATGTGGATCGAGATCATTTATTCATAGC -s simHuman_chr6.simHuman.chr6 338378 28 - 601863 -----ATTGGATTTAAGATCTTCCATTCAAGGC -s simRat_chr6.simRat.chr6 249812 33 + 647215 TGTAAATAGGAATTAGGATTTTGCACTTATGCC - -a -s simMouse_chr6.simMouse.chr6 260041 18 + 636262 TGTCTCATTGCCTGAGTG -s Anc0.Anc0refChr5 76674 13 + 87904 TTTCTTATATCCC----- -s Anc1.Anc1refChr7 35605 18 - 47259 TTTCTTATATCCCAAGTG -s Anc2.Anc2refChr15 73776 13 + 86568 TTCCTTATATCCC----- -s mr.mrrefChr5 112631 18 + 294540 TTTCTCATTGCCTGAGTG -s simCow_chr6.simCow.chr6 255449 13 + 602619 TTCCTAATATCCC----- -s simDog_chr6.simDog.chr6 246393 13 + 593897 TTCCTTATATCCC----- -s simHuman_chr6.simHuman.chr6 338406 18 - 601863 TTTCTGCTATCCCAAGTG -s simRat_chr6.simRat.chr6 249845 18 + 647215 TTTCTCATCCCCTGAGTG - -a -s simMouse_chr6.simMouse.chr6 260059 1 + 636262 A -s Anc1.Anc1refChr7 35623 1 - 47259 A -s mr.mrrefChr5 112649 1 + 294540 A -s simHuman_chr6.simHuman.chr6 338428 1 - 601863 A -s simRat_chr6.simRat.chr6 249863 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 260060 13 + 636262 GACCACATAGCAC -s Anc0.Anc0refChr5 76687 12 + 87904 -ACAATAGCGCAC -s Anc1.Anc1refChr7 35625 13 - 47259 AACAATAGCGCAC -s Anc2.Anc2refChr15 73789 12 + 86568 -ACACTAGCACAC -s mr.mrrefChr5 112651 13 + 294540 GACCACAGAGCAC -s simCow_chr6.simCow.chr6 255462 12 + 602619 -ACACTAGCACAC -s simDog_chr6.simDog.chr6 246406 12 + 593897 -ACACTAGCACAC -s simHuman_chr6.simHuman.chr6 338430 13 - 601863 AACAATAGCGCAC -s simRat_chr6.simRat.chr6 249865 13 + 647215 GAGCACAGATCAC - -a -s simMouse_chr6.simMouse.chr6 260073 5 + 636262 AATGA -s Anc0.Anc0refChr5 76700 5 + 87904 AATCA -s Anc1.Anc1refChr7 35639 5 - 47259 AATCA -s Anc2.Anc2refChr15 73802 5 + 86568 TATCA -s mr.mrrefChr5 112665 5 + 294540 AATGA -s simCow_chr6.simCow.chr6 255475 5 + 602619 TATCA -s simDog_chr6.simDog.chr6 246419 5 + 593897 TATGA -s simHuman_chr6.simHuman.chr6 338444 5 - 601863 AATCA -s simRat_chr6.simRat.chr6 249879 5 + 647215 GATGA - -a -s simMouse_chr6.simMouse.chr6 260078 9 + 636262 TAATCTGTA -s Anc0.Anc0refChr5 76705 9 + 87904 TAATCAGTA -s Anc1.Anc1refChr7 35644 9 - 47259 TAATCAGTA -s Anc2.Anc2refChr15 73807 9 + 86568 TCATCAGTA -s mr.mrrefChr5 112670 9 + 294540 TAATCTGTA -s simCow_chr6.simCow.chr6 255480 9 + 602619 TGAGCAGTA -s simDog_chr6.simDog.chr6 246697 9 + 593897 TCATCAGTA -s simHuman_chr6.simHuman.chr6 338449 9 - 601863 TAATCAGTA -s simRat_chr6.simRat.chr6 249884 9 + 647215 TAATCGGTA - -a -s simMouse_chr6.simMouse.chr6 260087 20 + 636262 AATTAAGAAATACTAGAAGA -s Anc0.Anc0refChr5 76715 20 + 87904 AATTAGGAAGGGGTAAAAGA -s Anc1.Anc1refChr7 35654 20 - 47259 AATTAGGAAGGGGTAAAAGA -s Anc2.Anc2refChr15 73817 20 + 86568 AATTAGGAAGGGGTAAAAGA -s mr.mrrefChr5 112679 20 + 294540 AATTAAGAAATACTAAAAGA -s simCow_chr6.simCow.chr6 255490 20 + 602619 ATATTGGGAGGGGTAAAAAA -s simDog_chr6.simDog.chr6 246707 20 + 593897 AATTAGGATAAGGTAAAAGA -s simHuman_chr6.simHuman.chr6 338459 20 - 601863 AATTCGGAAGGGGCAAAAGA -s simRat_chr6.simRat.chr6 249893 20 + 647215 AATTAAGAAAAACTAAAAGA - -a -s simMouse_chr6.simMouse.chr6 260107 24 + 636262 GTGGAAACATCTGTAAGGTATGTA -s Anc0.Anc0refChr5 76735 24 + 87904 TTATGAACATCTGTATGGTATGCA -s Anc1.Anc1refChr7 35674 24 - 47259 TTATGAACATCTGTATGGTATGCA -s Anc2.Anc2refChr15 73837 24 + 86568 TTATGAACATCTGTATAGTATGCA -s mr.mrrefChr5 112699 24 + 294540 GTGGAAACATCTGTAAGGTATGTA -s simCow_chr6.simCow.chr6 255512 24 + 602619 TTATGAACATCTTTATAGTATGTG -s simDog_chr6.simDog.chr6 246727 24 + 593897 GTATGAAAATCTGTATAGTATGCA -s simHuman_chr6.simHuman.chr6 338479 18 - 601863 TTATGGACTTTTGCAGGG------ -s simRat_chr6.simRat.chr6 249913 24 + 647215 GTGGAAACACCCGTAAGGTATGTA - -a -s simMouse_chr6.simMouse.chr6 260131 25 + 636262 TTTCTTTCTAATAGTGGAATACACG -s Anc0.Anc0refChr5 76759 24 + 87904 TTTCCTTCTAATAATTAGATAC-TA -s Anc1.Anc1refChr7 35698 24 - 47259 TTTCCTTCTAATAATTAGATAC-TA -s Anc2.Anc2refChr15 73862 24 + 86568 TTTCCTTCTAATAATTAGACAA-TA -s mr.mrrefChr5 112723 24 + 294540 TTTCTTTCTAATAGTGGAATAC-CA -s simCow_chr6.simCow.chr6 255537 24 + 602619 TCTCCTTCTAATAATTTGAAGA-TG -s simDog_chr6.simDog.chr6 246752 24 + 593897 TTTCCTTCTAATACTTAGACAA-TA -s simHuman_chr6.simHuman.chr6 338497 22 - 601863 --TCCTTCTAATAATCAGATAC-TA -s simRat_chr6.simRat.chr6 249937 24 + 647215 TCTCTTTGTAATACTGTAATAC-CA - -a -s simMouse_chr6.simMouse.chr6 260156 1 + 636262 T -s Anc0.Anc0refChr5 76783 1 + 87904 T -s Anc1.Anc1refChr7 35722 1 - 47259 T -s Anc2.Anc2refChr15 73891 1 + 86568 T -s mr.mrrefChr5 112747 1 + 294540 T -s simCow_chr6.simCow.chr6 255566 1 + 602619 T -s simDog_chr6.simDog.chr6 246781 1 + 593897 T -s simHuman_chr6.simHuman.chr6 338519 1 - 601863 T -s simRat_chr6.simRat.chr6 249961 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 260157 53 + 636262 CCATTGCACAGAGTCAAGTAACTAGTGAAAACACAATCTTACACTACCTCCAA -s Anc0.Anc0refChr5 76784 53 + 87904 CTTTTTCAAGGAGTCAACCAACTGTTGCAAGCAAAATCTGAAACCACCTCTCA -s Anc1.Anc1refChr7 35723 53 - 47259 CTTTTTCAAGGAGTCAACCAACTGTTGCAAGCAAAATCTGAAACCACCTCTCA -s Anc2.Anc2refChr15 73892 53 + 86568 CTTTTTCAAGGAGTCAACCAATTGTAGCAAGCAAAATCTGAAACCACCTCTCA -s mr.mrrefChr5 112748 53 + 294540 CCATTTCACAGAGTCAAGTAACTATTGAAAACACAATCTTACACCACCTCCAA -s simCow_chr6.simCow.chr6 255567 30 + 602619 CTTT-----------------------AAAGCAAAATTTGAAACCACCTCTCA -s simDog_chr6.simDog.chr6 246782 53 + 593897 CTTTTTCAAGGAGTCAACCAATTGTAGCAAGCAAAATCTGTAACCCCCTCTCA -s simHuman_chr6.simHuman.chr6 338522 53 - 601863 CTGTCTCATGGAGCCAACCAACAGTTGCAAGCAAAATATGAAACCACCACTCA -s simRat_chr6.simRat.chr6 249962 53 + 647215 CCATTTCACAGAGTCAAGTGACTATCGGAAACACAATCATACACCATCTCCGA - -a -s simMouse_chr6.simMouse.chr6 260210 22 + 636262 GCCCCATAATATTCTGTTCTTG -s Anc0.Anc0refChr5 76837 21 + 87904 GTACCATGCAATGCTGTT-TTG -s Anc1.Anc1refChr7 35776 21 - 47259 GTACCATGCAATGCTGTT-TTG -s Anc2.Anc2refChr15 73945 21 + 86568 GTACTGTGCAATGCTGTT-GTG -s mr.mrrefChr5 112801 22 + 294540 GCCCCATAATATTCTGTTCTTG -s simCow_chr6.simCow.chr6 255597 20 + 602619 AT-CAGTACAATGCTGTT-GTG -s simDog_chr6.simDog.chr6 246846 21 + 593897 GTACTGTGCAACGGCATT-GTG -s simHuman_chr6.simHuman.chr6 338575 21 - 601863 GTGCCATGCAATGCTGTT-TTG -s simRat_chr6.simRat.chr6 250015 22 + 647215 GCCCCATATGTTTCTTTTCTTA - -a -s simMouse_chr6.simMouse.chr6 260232 21 + 636262 CCTTTAGGTGAGGTGGACCTA -s Anc0.Anc0refChr5 76858 21 + 87904 CTTCTAGGTAAGGTGCATATA -s Anc1.Anc1refChr7 35797 21 - 47259 CTTCTAGGTAAGGTGCATATA -s Anc2.Anc2refChr15 73966 21 + 86568 CTTCTAGGCAAAGTGCATATA -s mr.mrrefChr5 112823 21 + 294540 CCTTTAGGTGAGGTGGACATA -s simCow_chr6.simCow.chr6 255617 21 + 602619 CTTCTAGGCAAAGTGCATATA -s simDog_chr6.simDog.chr6 246868 21 + 593897 CTTTTAAGCAAAGTGCATATA -s simHuman_chr6.simHuman.chr6 338596 21 - 601863 CTGCTAGGTAAGGTGAATGCA -s simRat_chr6.simRat.chr6 250037 16 + 647215 CCTT-----GCAGCGGACATA - -a -s simMouse_chr6.simMouse.chr6 260253 68 + 636262 GTCACAAGGATTTATCTCATGCATGAATAAGGGTATGCCCCAAGAGTACAGGAGTAGCTGCGTCATGA -s Anc0.Anc0refChr5 76893 47 + 87904 ATCACAG-TATTTATCTCATA----AACAAGGTTCTGAG--------GCAGGAACAGTC--------A -s Anc1.Anc1refChr7 35832 48 - 47259 ATCACAGCTATTTATCTCATA----AACAAGGTTCTGAG--------GCAGGAACAGTC--------A -s Anc2.Anc2refChr15 74001 47 + 86568 ATCACAG-TCTTTATCTCATG----AACTAGGTTCTGAG--------GCAGGAACAGTC--------A -s mr.mrrefChr5 112844 60 + 294540 GTCACAACGATTTATCTCATACATGAATAAGGTTATGCC--------ACAGGAGTAGTTGCGTCATGA -s simCow_chr6.simCow.chr6 255653 47 + 602619 TTCACAG-ACTTTAGCGCCCC----ATCCAGGATGTGAG--------GCAGGAACAGGC--------A -s simDog_chr6.simDog.chr6 246903 47 + 593897 ATCACAA-TCCTTATCTCATG----AACTAGGTTCTGAG--------GCTGGACCAGTC--------A -s simHuman_chr6.simHuman.chr6 338631 48 - 601863 ATTACAGCTATTTATCTCAGA----AACAAGGTTCTGAG--------GCAGGAACAGTC--------A -s simRat_chr6.simRat.chr6 250053 60 + 647215 GTCACAACCATTTATCTCCTACATGAGTGGGGTTATGCC--------ACAGGAGTAGTTGCATCATGA - -a -s simMouse_chr6.simMouse.chr6 260321 3 + 636262 TTA -s Anc0.Anc0refChr5 76940 3 + 87904 TTG -s Anc1.Anc1refChr7 35880 3 - 47259 TTG -s Anc2.Anc2refChr15 74051 3 + 86568 TTG -s mr.mrrefChr5 112904 3 + 294540 TTG -s simCow_chr6.simCow.chr6 255703 3 + 602619 TTG -s simDog_chr6.simDog.chr6 246953 3 + 593897 TTG -s simHuman_chr6.simHuman.chr6 338679 3 - 601863 TTG -s simRat_chr6.simRat.chr6 250113 3 + 647215 TTG - -a -s simMouse_chr6.simMouse.chr6 260324 17 + 636262 TCCAGGTTCACGGTCAA -s Anc0.Anc0refChr5 76943 17 + 87904 TTCATGTTAACAGTTGC -s Anc1.Anc1refChr7 35883 17 - 47259 TTCATGTTAACAGTTGC -s Anc2.Anc2refChr15 74054 17 + 86568 TTCATGTTAACAGTTGT -s mr.mrrefChr5 112907 17 + 294540 TTCAGGTTCACAGTCAC -s simCow_chr6.simCow.chr6 255706 16 + 602619 TTCACGTCAATAGTTG- -s simDog_chr6.simDog.chr6 246956 17 + 593897 TTCATATTAACAATTGT -s simHuman_chr6.simHuman.chr6 338683 17 - 601863 TTCATGTTAACAGTTGC -s simRat_chr6.simRat.chr6 250116 17 + 647215 TTCAGGTTCACAGTCAC - -a -s simMouse_chr6.simMouse.chr6 260341 39 + 636262 GTTTATTCCTATTTATGACAATACCTAATGAAGATCCAT -s Anc0.Anc0refChr5 76961 32 + 87904 GTTTATTCCTATTTATAACAATAACCAATGA-------T -s Anc1.Anc1refChr7 35901 32 - 47259 GTTTATTCCTATTTATAACAATAACCAATGA-------T -s Anc2.Anc2refChr15 74072 32 + 86568 ATTTATTTCCATTTATAACAATAACCAATAA-------C -s mr.mrrefChr5 112924 32 + 294540 GTTTATTCCTATTTATGACAATACCTAATGA-------T -s simCow_chr6.simCow.chr6 255722 23 + 602619 ---------CATCTAGAGCAATAACCAATAA-------C -s simDog_chr6.simDog.chr6 246974 32 + 593897 ATTTATTTCCATTTATAACAGTAATGAATAA-------C -s simHuman_chr6.simHuman.chr6 338701 32 - 601863 GGTTATTCCTATTGATAACTATTACCAATGA-------T -s simRat_chr6.simRat.chr6 250133 32 + 647215 GTTTATTCCAATTTATGACAATACTTGATAA-------T - -a -s simMouse_chr6.simMouse.chr6 260380 3 + 636262 CAT -s Anc0.Anc0refChr5 76993 3 + 87904 CAT -s Anc1.Anc1refChr7 35933 3 - 47259 CAT -s Anc2.Anc2refChr15 74110 3 + 86568 CAT -s mr.mrrefChr5 112956 3 + 294540 CAT -s simCow_chr6.simCow.chr6 255751 3 + 602619 CAT -s simDog_chr6.simDog.chr6 247012 3 + 593897 CAT -s simHuman_chr6.simHuman.chr6 338733 3 - 601863 TAT -s simRat_chr6.simRat.chr6 250165 3 + 647215 CAT - -a -s simMouse_chr6.simMouse.chr6 260383 11 + 636262 TTATGGCAAAT -s Anc0.Anc0refChr5 76996 11 + 87904 TGATGGCAGCT -s Anc1.Anc1refChr7 35936 11 - 47259 TGATGGCAGCT -s Anc2.Anc2refChr15 74113 11 + 86568 TCATGTCTACT -s mr.mrrefChr5 112959 11 + 294540 TGATGGCAGAT -s simCow_chr6.simCow.chr6 255754 11 + 602619 TTGTGGCTACT -s simDog_chr6.simDog.chr6 247015 11 + 593897 TCATGTCTACT -s simHuman_chr6.simHuman.chr6 338814 11 - 601863 TGTAAGCAGCT -s simRat_chr6.simRat.chr6 250168 11 + 647215 TGATGGCAGAT - -a -s simMouse_chr6.simMouse.chr6 260394 5 + 636262 ACACT -s Anc0.Anc0refChr5 77007 5 + 87904 ACACT -s Anc1.Anc1refChr7 35947 5 - 47259 ACACT -s Anc2.Anc2refChr15 74124 5 + 86568 ACATG -s mr.mrrefChr5 112970 5 + 294540 ACACT -s simCow_chr6.simCow.chr6 255765 5 + 602619 ACTTG -s simDog_chr6.simDog.chr6 247026 5 + 593897 ACATG -s simHuman_chr6.simHuman.chr6 338826 5 - 601863 ATACT -s simRat_chr6.simRat.chr6 250179 5 + 647215 ACACT - -a -s simMouse_chr6.simMouse.chr6 260399 16 + 636262 GAGCGCTTGGTTGTAT -s Anc0.Anc0refChr5 77012 15 + 87904 GAAGGTT-GGTTGTCT -s Anc1.Anc1refChr7 35952 16 - 47259 GAAGGTTGGGTTGTCT -s Anc2.Anc2refChr15 74129 15 + 86568 GAAGGTT-GTTTGTCT -s mr.mrrefChr5 112975 16 + 294540 GAGCGTTGGGTTGTAT -s simCow_chr6.simCow.chr6 255783 15 + 602619 GAAGGTT-ACTTGAAT -s simDog_chr6.simDog.chr6 247031 15 + 593897 GAAAGTT-GTTCGTCT -s simHuman_chr6.simHuman.chr6 338831 16 - 601863 GAAGGTTGGGTTGCCT -s simRat_chr6.simRat.chr6 250184 14 + 647215 GAGTGTTGGCCTGT-- - -a -s simMouse_chr6.simMouse.chr6 260415 21 + 636262 GTGCCAGTGAATATTTCCATG -s Anc0.Anc0refChr5 77031 21 + 87904 ATGGCAGCATATATCTCCTCA -s Anc1.Anc1refChr7 35972 21 - 47259 ATGGCAGCATATATCTCCTCA -s Anc2.Anc2refChr15 74148 21 + 86568 ATTGCAGCATATATCTCCTCA -s mr.mrrefChr5 112991 21 + 294540 GTGGCAGTAAATATTTCCACA -s simCow_chr6.simCow.chr6 255802 21 + 602619 ATTGCAGCATATATCTCCTCA -s simDog_chr6.simDog.chr6 247050 21 + 593897 ATTGCGGCATATATCTCCTCT -s simHuman_chr6.simHuman.chr6 338851 21 - 601863 ATGGCAGCATATATCTCCTCA -s simRat_chr6.simRat.chr6 250198 20 + 647215 -TGGCAGTAAATATTTCCACA - -a -s simMouse_chr6.simMouse.chr6 260436 35 + 636262 TCAGGAGGAATAAGACCTACTACATCTTGAATTTG -s Anc0.Anc0refChr5 77055 30 + 87904 TCAGCAGGAGT-TGACTTACAACCTTTTGTA---- -s Anc1.Anc1refChr7 35996 32 - 47259 TCAGCAGGAGT-TGACTTACAACCTTTTGTATT-- -s Anc2.Anc2refChr15 74172 30 + 86568 TCAGCTGGAGT-TGACTTACAACCTTTTGTA---- -s mr.mrrefChr5 113015 35 + 294540 TCAGGAGGAGTAAGACCTACTACATTTTGAATTTG -s simCow_chr6.simCow.chr6 255826 30 + 602619 TCGGCTGGAGT-CGACTTACAACCCATTGTA---- -s simDog_chr6.simDog.chr6 247074 30 + 593897 TCAGCTGGAGT-TGGCTTACAACCTTCTGTA---- -s simHuman_chr6.simHuman.chr6 338875 32 - 601863 GGAGAAGGAGT-TGACTTACAACCTTTTGTATT-- -s simRat_chr6.simRat.chr6 250221 35 + 647215 TCAGGAGGAGCAAGACCTACCACATTTTGAATTTG - -a -s simMouse_chr6.simMouse.chr6 260471 36 + 636262 AAGGTCTTCATAAAACCTGTGCAACTAATGGTAAAT -s Anc0.Anc0refChr5 77085 25 + 87904 -----TGTAATACTAGCAATG---CTA---ACATAT -s Anc1.Anc1refChr7 36028 32 - 47259 -ACAGTGTAATACTAGCAATG---CTAATGACATAT -s Anc2.Anc2refChr15 74202 25 + 86568 -----TGTAAAACTGGCAATA---CTA---ACATAT -s mr.mrrefChr5 113050 36 + 294540 AAGGTTTTCATAAAACCAGTGCAACTAATGGTAAAT -s simCow_chr6.simCow.chr6 255856 25 + 602619 -----TGTAAAACTGGCAATA---CTA---ACATAT -s simDog_chr6.simDog.chr6 247104 24 + 593897 -----TGTAAAACTGGCAAGA---CTA---A-ATAT -s simHuman_chr6.simHuman.chr6 338907 32 - 601863 -ACAGTGTAATAGTAGCAATG---CTAATGACATAT -s simRat_chr6.simRat.chr6 250257 36 + 647215 AAGGTTTTTATAAAACCAGTGTAATTAATTGTAAAT - -a -s simMouse_chr6.simMouse.chr6 260507 33 + 636262 ATCTTCTCTAGTTCGCTTGAGAAAAGTGATCGC -s Anc0.Anc0refChr5 77110 25 + 87904 ATTTTCTCTAGT----CTAAAAATAGT----GT -s Anc1.Anc1refChr7 36060 25 - 47259 ATTTTCTCTAGT----CTAAAAATAGT----GT -s Anc2.Anc2refChr15 74227 25 + 86568 ATTTTCTCTAGT----TTAAAAATAGT----GT -s mr.mrrefChr5 113086 33 + 294540 ATCTTCTCTAGTTCGCCTGAGAAAAGTGATCGC -s simCow_chr6.simCow.chr6 255881 9 + 602619 ATCCTCTTT------------------------ -s simDog_chr6.simDog.chr6 247135 25 + 593897 ATTTTCTCAAGT----TTAAAAATAGT----GT -s simHuman_chr6.simHuman.chr6 338939 25 - 601863 ATTTCTTCTAGT----CTAAAAGGAGT----GT -s simRat_chr6.simRat.chr6 250293 33 + 647215 ATCTTCTCTAGTAAGTCTGAGAAAAGTGATCTC - -a -s simMouse_chr6.simMouse.chr6 260540 56 + 636262 ATGACCTTAGGCATATGTGTGATATTGAGTGGTGGAATTCATCTTTTACTTAATGG -s Anc0.Anc0refChr5 77135 43 + 87904 ACAACCTTTTGTATTTCTGTGTTAATTAGCAGTTGAGTTCATC------------- -s Anc1.Anc1refChr7 36085 43 - 47259 ACAACCTTTTGTATTTCTGTGTTAATTAGCAGTTGAGTTCATC------------- -s Anc2.Anc2refChr15 74252 43 + 86568 ACAACCTTTTGTTTTACTGTATGAGTTAGCAGTTGAGTTCATC------------- -s mr.mrrefChr5 113119 43 + 294540 ATAACCTTATGCATTTGTGTGATAATGAGTGGTGGAATTCATC------------- -s simDog_chr6.simDog.chr6 247164 43 + 593897 ACAACCTTTTGTTTTACTGTATGAGTTAGCAGTTGAGTTCATC------------- -s simHuman_chr6.simHuman.chr6 338964 43 - 601863 ACAACCTTTTGTATTTTTGTGTTAATTAGCAGTTGAGTTCATC------------- -s simRat_chr6.simRat.chr6 250326 43 + 647215 ATAACCTTATGCATTTGTGTGATAATGAGTGATGGAATTCATT------------- - -a -s simMouse_chr6.simMouse.chr6 260596 16 + 636262 GACGATAATTAGGCCC -s Anc0.Anc0refChr5 9674 16 - 87904 AATGGTGCTTAGGACT -s Anc1.Anc1refChr7 10062 16 + 47259 AATGGTGCTTAGGACT -s Anc2.Anc2refChr15 11139 16 - 86568 AATGGTGCTTAGGACT -s mr.mrrefChr5 180244 16 - 294540 AACGATAATTAGGCCT -s simCow_chr6.simCow.chr6 345523 16 - 602619 AATAGTGCTTAGGACT -s simDog_chr6.simDog.chr6 345547 16 - 593897 AATGCTGCTTAGGACT -s simHuman_chr6.simHuman.chr6 261914 16 + 601863 AAGGGTGTTTAGGACT -s simRat_chr6.simRat.chr6 395688 16 - 647215 AATGACAATTAGGCCT - -a -s simMouse_chr6.simMouse.chr6 260612 16 + 636262 GCTCTGTGCTAGCCAG -s mr.mrrefChr5 180315 16 - 294540 GCGCTGTGCTAGCCAG -s simRat_chr6.simRat.chr6 395774 16 - 647215 GTGCTGTGCTAGCCAG - -a -s simMouse_chr6.simMouse.chr6 260628 52 + 636262 AGCACAACCTTCATGGTGCTTTGCCTATGCTATTATTATGGCGCCAATACTT -s Anc0.Anc0refChr5 9741 16 - 87904 ------------------------------------TATGGCTGTAATATCT -s Anc1.Anc1refChr7 10129 16 + 47259 ------------------------------------TATGGCTGTAATATCT -s Anc2.Anc2refChr15 11206 16 - 86568 ------------------------------------TCTGGCTGTAGTATCT -s mr.mrrefChr5 180331 52 - 294540 AGCACAACCTTCATCGTGCTTTGCCTATGCTATTATTATGGCGCCAATACTT -s simCow_chr6.simCow.chr6 345588 11 - 602619 -----------------------------------------CTGTATTGTCT -s simDog_chr6.simDog.chr6 345614 16 - 593897 ------------------------------------TCTGGCTGTAGTATCT -s simHuman_chr6.simHuman.chr6 261981 16 + 601863 ------------------------------------TATGGCTGTAATATCT -s simRat_chr6.simRat.chr6 395798 52 - 647215 AGGAGAATCTTCATCGTGCTTTGCCTATTTTATCATTATGGCGCTAATACTT - -a -s simMouse_chr6.simMouse.chr6 260680 5 + 636262 ATCTA -s Anc0.Anc0refChr5 9766 2 - 87904 A--T- -s Anc1.Anc1refChr7 10154 3 + 47259 A--TA -s Anc2.Anc2refChr15 11231 2 - 86568 A--T- -s mr.mrrefChr5 180383 3 - 294540 A--TA -s simCow_chr6.simCow.chr6 345608 2 - 602619 A--T- -s simHuman_chr6.simHuman.chr6 262006 3 + 601863 A--TA -s simRat_chr6.simRat.chr6 395850 3 - 647215 A--TA - -a -s simMouse_chr6.simMouse.chr6 260685 13 + 636262 ATTATACAAAGCA -s Anc0.Anc0refChr5 9768 12 - 87904 -TCATACAAAGTG -s Anc1.Anc1refChr7 10157 13 + 47259 ATCATACAAAGTG -s Anc2.Anc2refChr15 11233 12 - 86568 -TCATACAAAGTG -s mr.mrrefChr5 180386 13 - 294540 ATTATACAAAGCA -s simCow_chr6.simCow.chr6 345610 12 - 602619 -TCATAGCAAGTG -s simDog_chr6.simDog.chr6 345638 10 - 593897 ---ATACAAAGTA -s simHuman_chr6.simHuman.chr6 262012 13 + 601863 ATCATACAAGGTG -s simRat_chr6.simRat.chr6 395853 13 - 647215 ATTATACAGAGCA - -a -s simMouse_chr6.simMouse.chr6 260698 57 + 636262 AGTGGTGCCACAGCTACAGGTTGCATCAAGTTCCATCCACAGCTTACAAAATGATGT -s Anc0.Anc0refChr5 9780 43 - 87904 AGTGGTGCTACTGCTACAGGTTGCATCAAGTTCCTTT--------------TGACAT -s Anc1.Anc1refChr7 10170 43 + 47259 AGTGGTGCTACTGCTACAGGTTGCATCAAGTTCCTTT--------------TGACAT -s Anc2.Anc2refChr15 11245 43 - 86568 AGTGGTGTTACTGCAACAGGTTGCATCAAGTTCCTTT--------------CAACAT -s mr.mrrefChr5 180399 57 - 294540 AGTGGTGCTACAGCTACAGGTTGCATCAAGTTCCATTCACAGCTTACAAAATGATGT -s simCow_chr6.simCow.chr6 345629 43 - 602619 AGTGGTGTTACTGCAACAGGTAGGATCAGGTCCCTTT--------------CAACAT -s simDog_chr6.simDog.chr6 345648 42 - 593897 AGTGGTG-TACTGAAACACGTTGCATCAAGTTCCCTC--------------CAACAT -s simHuman_chr6.simHuman.chr6 262025 43 + 601863 AGTGGTGCTACTGCTATGGGTTGTATCAAGTTCCTTT--------------TGACAT -s simRat_chr6.simRat.chr6 395866 57 - 647215 AGTGTTGCTACAGTTACAGACTGCATCATGTTCTGTTTACAGCTTACAAACTGATGT - -a -s simMouse_chr6.simMouse.chr6 260755 55 + 636262 TGCCAATATCCATCAAGACTCCCTAACCCCCTCTTTCGACCCTCTCCATTAGTGA -s Anc0.Anc0refChr5 9823 55 - 87904 CAGCAATATGTATCAGGTTTCCGAAGACCCCTTTTTCAACCCCCTCCATCAATGA -s Anc1.Anc1refChr7 10213 55 + 47259 CAGCAATATGTATCAGGTTTCCGAAGACCCCTTTTTCAACCCCCTCCATCAATGA -s Anc2.Anc2refChr15 11288 55 - 86568 CAGCAATATGTATCAGGTTTCTGAAGACCCCTTTTATTACCCCCTCCATCAAATA -s mr.mrrefChr5 180456 55 - 294540 TGCCAATATCCATCAAGACTCCCTAACCCCCTCTTTCAACCCTCTCCATTAGTGA -s simCow_chr6.simCow.chr6 345672 55 - 602619 CAGCAATATGTATTAGGTTTCTGAAGGCTCCTTGTATGACCCCCCCCATCAAATA -s simDog_chr6.simDog.chr6 345693 55 - 593897 CAGCAATATGCAGCAGGTTTCTGGAGACCACTTTTATTGCCCCCTCCATCACATA -s simHuman_chr6.simHuman.chr6 262068 55 + 601863 AAAGAATATATATCAGGTGCCCAAAGACCCCTTCCTCAACCCCTTCCATCAATGA -s simRat_chr6.simRat.chr6 395923 55 - 647215 TGCCAAAATCCATCAAGACTCCCTAACCCCCTCTTTCAACTCTATCTATTAGTGA - -a -s simMouse_chr6.simMouse.chr6 260810 24 + 636262 ACTAGAGGAGACTCTTTCTAACTC -s Anc0.Anc0refChr5 9878 24 - 87904 ACCAGAGAAGAATCGTTAGAACTT -s Anc1.Anc1refChr7 10268 24 + 47259 ACCAGAGAAGAATCGTTAGAACTT -s Anc2.Anc2refChr15 11345 24 - 86568 ACCAGAGAAGAAGTGTTAGAACTT -s mr.mrrefChr5 180511 24 - 294540 ACTAGAGGAGAATCTTTCTAACTC -s simCow_chr6.simCow.chr6 345729 24 - 602619 ATCAAAGTAGAACTGGCAGATCGT -s simDog_chr6.simDog.chr6 345750 24 - 593897 ACCAGAGAAGAAGTGTTAAAACTT -s simHuman_chr6.simHuman.chr6 262123 24 + 601863 GCCATAGCAGAATCATTGGAACTT -s simRat_chr6.simRat.chr6 395978 24 - 647215 ACTAGAGGAGAATCTTTCTAACTC - -a -s simMouse_chr6.simMouse.chr6 260834 47 + 636262 CCAGTCAGATTGTGTGCATATATTATAACATCACTGGGTATTGAAAA -s Anc0.Anc0refChr5 9907 39 - 87904 CCAATCAGATTGTGGGCATACCTTAGGACCCCTCCAGGC-------- -s Anc1.Anc1refChr7 10297 47 + 47259 CCAATCAGATTGTGGGCATACCTTAGGACCCCTCCAGGCTTTAGGTT -s Anc2.Anc2refChr15 11374 39 - 86568 CCAATCAGAACATGGGCATGCCTCAGGAACCCTCCAGGC-------- -s mr.mrrefChr5 180535 47 - 294540 CCAGTCAGATTGTGTGCATATATTAGAACATCACTGGGTATTAAGAA -s simCow_chr6.simCow.chr6 345758 33 - 602619 CCAATCGGAGCATGGGCATCCCCCAGAGGCTCT-------------- -s simDog_chr6.simDog.chr6 345779 38 - 593897 CCAATCACAACATGGGAAAGCCTCAGGAACCA-CCAGGC-------- -s simHuman_chr6.simHuman.chr6 262152 47 + 601863 CCAATCAGATTGTGGGCATACGTTAGCACCCCTCCAGGCTTTAGGTT -s simRat_chr6.simRat.chr6 396002 47 - 647215 CCAGTCAGATTGTGAGCCTATATTAGGAAATCACTGGGTATTAAGAA - -a -s simMouse_chr6.simMouse.chr6 260881 42 + 636262 ATTGTTTACTATATCATATACAAACAATTCCAGTAGATTCCT -s Anc0.Anc0refChr5 9951 40 - 87904 ATTGTCTATTCTATCTTAT-CAAATG-TTCCCATGGATTTCT -s Anc1.Anc1refChr7 10349 42 + 47259 ATTGTCTATTCTATCTTATACAAATGATTCCCATGGATTTCT -s Anc2.Anc2refChr15 11418 40 - 86568 ACCGTCTATTCTATCTTAT-CAAATG-TTCCCATGGACTTCT -s mr.mrrefChr5 180582 42 - 294540 ATTGTCTACTCTATCATATACAAACAATTCCAATGGATTCCT -s simCow_chr6.simCow.chr6 345796 40 - 602619 ACAGTCTACTCTATGTTAT-CAAATG-TTCCCATGCAGTTCT -s simDog_chr6.simDog.chr6 345822 37 - 593897 ACCCTTTATTCTAGCTTAT-CAAA----TCCCATGGACTTCT -s simHuman_chr6.simHuman.chr6 262213 42 + 601863 ATTGTCTATTCTATCTTATACAAATGATTCCCATGGATTTCT -s simRat_chr6.simRat.chr6 396049 42 - 647215 ACTGTCTACTCGATCATTTACAAACAATTTCAATGGATTCCT - -a -s simMouse_chr6.simMouse.chr6 260923 3 + 636262 GCA -s Anc0.Anc0refChr5 9993 3 - 87904 GCA -s Anc1.Anc1refChr7 10393 3 + 47259 GCA -s Anc2.Anc2refChr15 11460 3 - 86568 GCA -s mr.mrrefChr5 180626 3 - 294540 GCA -s simCow_chr6.simCow.chr6 345838 3 - 602619 GGA -s simDog_chr6.simDog.chr6 345861 3 - 593897 GCA -s simHuman_chr6.simHuman.chr6 262257 3 + 601863 GCA -s simRat_chr6.simRat.chr6 396093 3 - 647215 GCA - -a -s simMouse_chr6.simMouse.chr6 260926 5 + 636262 GCAAG -s Anc0.Anc0refChr5 9997 5 - 87904 GCATG -s Anc1.Anc1refChr7 10397 5 + 47259 GCATG -s Anc2.Anc2refChr15 11464 5 - 86568 GCATG -s mr.mrrefChr5 180629 5 - 294540 GCAAG -s simCow_chr6.simCow.chr6 345842 5 - 602619 GCATG -s simDog_chr6.simDog.chr6 345865 5 - 593897 GCATT -s simHuman_chr6.simHuman.chr6 262261 5 + 601863 GCATG -s simRat_chr6.simRat.chr6 396096 5 - 647215 GCAAG - -a -s simMouse_chr6.simMouse.chr6 260931 3 + 636262 CCC -s Anc0.Anc0refChr5 10002 3 - 87904 CCC -s Anc1.Anc1refChr7 10402 3 + 47259 CCC -s Anc2.Anc2refChr15 11469 3 - 86568 CCC -s mr.mrrefChr5 180634 3 - 294540 CCC -s simCow_chr6.simCow.chr6 345848 3 - 602619 CCC -s simDog_chr6.simDog.chr6 345870 3 - 593897 CCC -s simHuman_chr6.simHuman.chr6 262266 3 + 601863 CCT -s simRat_chr6.simRat.chr6 396101 3 - 647215 CCC - -a -s simMouse_chr6.simMouse.chr6 260934 44 + 636262 ATAGACTAAATACGTAACGAAGGGTATGTACAAGTACTGACCAG -s Anc0.Anc0refChr5 10006 43 - 87904 TTAGACTAAATAAGTGACCAAGGCTATGCA-AAGTACTGGCCAG -s Anc1.Anc1refChr7 10406 44 + 47259 TTAGACTAAATAAGTGACCAAGGCTATGCAGAAGTACTGGCCAG -s Anc2.Anc2refChr15 11473 43 - 86568 TTAGACTGAATGAGTGACAAAGGCTGTGCA-AAGTACTGGCCAG -s mr.mrrefChr5 180638 44 - 294540 ATAGACTAAATAAGTGACCAAGGGTATGTACAAGTACTGGCCAG -s simCow_chr6.simCow.chr6 345852 43 - 602619 TTAGACTCAATGAGTGGCTAAGGCTGTACA-AAGTACTGGCCAG -s simDog_chr6.simDog.chr6 345874 39 - 593897 TTAAACTGAA----TGACAAAGGGTGTGCA-AAGTACTGGCCAG -s simHuman_chr6.simHuman.chr6 262270 44 + 601863 TCAGACTAAACAATTGACCAAGGCTATGCAGAAGTACTGGCCAG -s simRat_chr6.simRat.chr6 396105 44 - 647215 ATAGACTAAATAAGTGACCAAGGGTATATACAAGTACTGGCCAG - -a -s simMouse_chr6.simMouse.chr6 260978 22 + 636262 TGGTCCAAGTGTTCATCCAAAC -s Anc0.Anc0refChr5 10049 22 - 87904 CTATCCAACTCTTCATCTGAAT -s Anc1.Anc1refChr7 10450 22 + 47259 CTATCCAACTCTTCATCTGAAT -s Anc2.Anc2refChr15 11516 22 - 86568 CTATCCATCTCTTTATCTGGAT -s mr.mrrefChr5 180682 22 - 294540 TGGTCCAAGTGTTCATCCGAAT -s simCow_chr6.simCow.chr6 345986 22 - 602619 TTATGCAGCTCTGGATCTGGAT -s simDog_chr6.simDog.chr6 345913 22 - 593897 CTATCCATCATTTTGATTGGAA -s simHuman_chr6.simHuman.chr6 262314 22 + 601863 CTTTCCAATTCTTCATCTGAAT -s simRat_chr6.simRat.chr6 396149 22 - 647215 TGGTCCAAGTATTCATCCGAAT - -a -s simMouse_chr6.simMouse.chr6 261000 13 + 636262 CCATGGCTCTTTC -s Anc0.Anc0refChr5 10075 12 - 87904 CCCC-ACTTTTTC -s Anc1.Anc1refChr7 10476 12 + 47259 CCCC-ACTTTTTC -s Anc2.Anc2refChr15 11542 12 - 86568 CCCC-ACTTTTTT -s mr.mrrefChr5 180704 12 - 294540 CCCC-GCTCTTTC -s simCow_chr6.simCow.chr6 346012 10 - 602619 CCCC-A--CTTTT -s simDog_chr6.simDog.chr6 345939 12 - 593897 CCCC-ACTTTTCT -s simHuman_chr6.simHuman.chr6 262340 12 + 601863 CCCC-ACTTTTTC -s simRat_chr6.simRat.chr6 396171 12 - 647215 CCCC-GCTCTTCC - -a -s simMouse_chr6.simMouse.chr6 261013 16 + 636262 GGTAACAAATATGAGA -s Anc0.Anc0refChr5 10087 16 - 87904 TATAACAAATATGAAA -s Anc1.Anc1refChr7 10488 16 + 47259 TATAACAAATATGAAA -s Anc2.Anc2refChr15 11554 16 - 86568 TATAACAAATTTGAAA -s mr.mrrefChr5 180716 16 - 294540 GGTAACAAATATGAGA -s simCow_chr6.simCow.chr6 346024 16 - 602619 TATAACAAATGTGAAA -s simDog_chr6.simDog.chr6 345951 15 - 593897 TATAACAAATT-GAGA -s simHuman_chr6.simHuman.chr6 262352 16 + 601863 TACAACAAATATGAAA -s simRat_chr6.simRat.chr6 396183 16 - 647215 AGTAACAAATATTAGA - -a -s simMouse_chr6.simMouse.chr6 261029 26 + 636262 TTGACTACTGTTCCTGCAATTTGATG -s Anc0.Anc0refChr5 10103 24 - 87904 TT--TTACTGTTCCTGTAGTTTAATG -s Anc1.Anc1refChr7 10504 24 + 47259 TT--TTACTGTTCCTGTAGTTTAATG -s Anc2.Anc2refChr15 11572 24 - 86568 TT--TTACTGTTCCTGTAGTTTAATG -s mr.mrrefChr5 180732 26 - 294540 TTGACTACTGTTCCTGCAATTTGATG -s simCow_chr6.simCow.chr6 346042 24 - 602619 TT--TTACTGTTCCTGTAGCTCAATG -s simDog_chr6.simDog.chr6 345968 24 - 593897 TA--TTACTGTTCCTGTTGTTTAATG -s simHuman_chr6.simHuman.chr6 262368 24 + 601863 TT--TTACTGTCTGTGTATTTTAATG -s simRat_chr6.simRat.chr6 396199 25 - 647215 TGGACTACTGTTCCTGCACTTT-ATG - -a -s simMouse_chr6.simMouse.chr6 261055 11 + 636262 AGCACATCAAC -s Anc0.Anc0refChr5 10127 9 - 87904 AG--CATAAGC -s Anc1.Anc1refChr7 10528 9 + 47259 AG--CATAAGC -s Anc2.Anc2refChr15 11596 9 - 86568 AC--CATAAGC -s mr.mrrefChr5 180758 9 - 294540 AG--CATCAAC -s simCow_chr6.simCow.chr6 346066 9 - 602619 AC--CCCAGGT -s simDog_chr6.simDog.chr6 345992 9 - 593897 AC--CATAAGC -s simHuman_chr6.simHuman.chr6 262393 9 + 601863 AG--CATAAGC -s simRat_chr6.simRat.chr6 396224 9 - 647215 AG--CATCAAC - -a -s simMouse_chr6.simMouse.chr6 261066 30 + 636262 AGATTGTTGACATTGAGAATTGCTGCCCTG -s Anc0.Anc0refChr5 10136 15 - 87904 AGATTATTGAC-TTG--------------G -s Anc1.Anc1refChr7 10537 15 + 47259 AGATTATTGAC-TTG--------------G -s Anc2.Anc2refChr15 11608 15 - 86568 AATTTAATGAT-TTT--------------G -s mr.mrrefChr5 180767 30 - 294540 AGATTGTTGACATTGAGAATTGCTGCCCTG -s simCow_chr6.simCow.chr6 346078 15 - 602619 ACTTTAATGAT-TTT--------------A -s simDog_chr6.simDog.chr6 346004 15 - 593897 AATTTAATGAT-TGT--------------G -s simHuman_chr6.simHuman.chr6 262402 15 + 601863 AGACTATTGAC-TTG--------------G -s simRat_chr6.simRat.chr6 396233 30 - 647215 AGCTTGTTGACATTGGGAAGTGCTGCCCTG - -a -s simMouse_chr6.simMouse.chr6 261096 77 + 636262 AGAGTGGTTATCTGCTCAATCTGCTAAGGTACCTAGCTTCATCACGGACTTCACTGTATCTCCATTCTGTAGTTGAA -s Anc0.Anc0refChr5 10151 68 - 87904 AAAGTGGATATT---------AGCTAAGTGTCCTAGCCTCATCAGACATTCCACTGTATCTCTGTTCTGCTGTTGAA -s Anc1.Anc1refChr7 10552 68 + 47259 AAAGTGGATATT---------AGCTAAGTGTCCTAGCCTCATCAGACATTCCACTGTATCTCTGTTCTGCTGTTGAA -s Anc2.Anc2refChr15 11629 68 - 86568 AAAGTAGATATT---------TGCTAAGTGTCCGAGCCTCATCAGACATTCCACTGTAACTCTGTTCTGCTGGTAAA -s mr.mrrefChr5 180797 77 - 294540 AGAGTGGATATCTGCTCAATCAGCTAAGTTTCCTAGCTTCATCACGGACTTCACTGTATCTCCATTCTGCTGTTGAA -s simCow_chr6.simCow.chr6 346099 68 - 602619 AAAGTAGATATT---------TGAAAAGGGTCCCAGCCTCAGGAGCCAGTCCACTGTACCTCTGCTGTGCTCGCAAT -s simDog_chr6.simDog.chr6 346025 65 - 593897 AAAGCAGATATT---------TGCTAACT---TGAGCCTCATCAGACATTCCACTATAACTCTGTTCTGATGGTAAA -s simHuman_chr6.simHuman.chr6 262417 68 + 601863 ATAGTGGATATT---------AGTTAAGTGTCCTAGCCTCATCAGACATTCCATTGTATCTCTGTTCTGCTGTTGTA -s simRat_chr6.simRat.chr6 396263 77 - 647215 CAAGTGGATATCTGCTCAACCATCTAAGTCTCCTAGCTTCATCATGGACTTCACTGTATCTCCATTCCACTGCTGAA - -a -s simMouse_chr6.simMouse.chr6 261173 11 + 636262 AACATGTAGAT -s Anc0.Anc0refChr5 10222 11 - 87904 AATGTGCAGAT -s Anc1.Anc1refChr7 10623 11 + 47259 AATGTGCAGAT -s Anc2.Anc2refChr15 11700 11 - 86568 AATGTGCAAAT -s mr.mrrefChr5 180874 11 - 294540 AACATGTAGAT -s simCow_chr6.simCow.chr6 346170 11 - 602619 AATGTGTACAT -s simDog_chr6.simDog.chr6 346093 11 - 593897 AATTTGCAAAC -s simHuman_chr6.simHuman.chr6 262488 11 + 601863 AATGTGCAGAT -s simRat_chr6.simRat.chr6 396340 11 - 647215 GCCACGTAGAT - -a -s simMouse_chr6.simMouse.chr6 261184 17 + 636262 TCACTAGGATGGAGTGC -s Anc0.Anc0refChr5 10235 17 - 87904 TAACTGGGGAGAATTGC -s Anc1.Anc1refChr7 10636 17 + 47259 TAACTGGGGAGAATTGC -s Anc2.Anc2refChr15 11713 17 - 86568 TAACTGGGGAGAATTGC -s mr.mrrefChr5 180885 17 - 294540 TAACTAGGAAGAAGTGC -s simCow_chr6.simCow.chr6 346183 17 - 602619 AAATTGAGGAGAATTGC -s simDog_chr6.simDog.chr6 346106 17 - 593897 TGACTGGGGAGAATTGT -s simHuman_chr6.simHuman.chr6 262501 17 + 601863 TAACTGGGGAGAACTGC -s simRat_chr6.simRat.chr6 396351 17 - 647215 TAACTAGGAAGAATTGC - -a -s simMouse_chr6.simMouse.chr6 261201 1 + 636262 T -s Anc0.Anc0refChr5 10252 1 - 87904 T -s Anc1.Anc1refChr7 10653 1 + 47259 T -s Anc2.Anc2refChr15 11731 1 - 86568 T -s mr.mrrefChr5 180902 1 - 294540 T -s simCow_chr6.simCow.chr6 346201 1 - 602619 T -s simDog_chr6.simDog.chr6 346124 1 - 593897 T -s simRat_chr6.simRat.chr6 396368 1 - 647215 T - -a -s simMouse_chr6.simMouse.chr6 261202 9 + 636262 CAAGGGTTA -s Anc0.Anc0refChr5 10253 6 - 87904 CAGGT---A -s Anc1.Anc1refChr7 10654 6 + 47259 CAGGT---A -s Anc2.Anc2refChr15 11732 6 - 86568 CAGGT---A -s mr.mrrefChr5 180903 6 - 294540 CAAGG---A -s simCow_chr6.simCow.chr6 346210 6 - 602619 TAGAT---A -s simDog_chr6.simDog.chr6 346125 6 - 593897 CAGGT---A -s simRat_chr6.simRat.chr6 396369 6 - 647215 CAAGG---A - -a -s simMouse_chr6.simMouse.chr6 261211 5 + 636262 TCAAT -s Anc0.Anc0refChr5 10259 5 - 87904 TCCCC -s Anc1.Anc1refChr7 10660 5 + 47259 TCCCC -s Anc2.Anc2refChr15 11738 5 - 86568 TCCCC -s mr.mrrefChr5 180909 5 - 294540 TCAAT -s simCow_chr6.simCow.chr6 346225 5 - 602619 GCCTC -s simDog_chr6.simDog.chr6 346131 5 - 593897 TCCCC -s simRat_chr6.simRat.chr6 396375 5 - 647215 TCAAT - -a -s simMouse_chr6.simMouse.chr6 261216 48 + 636262 CCTCAAGTGCTATCTCAACTATCTTGTCCAGGACGCTACTATAACAGT -s Anc0.Anc0refChr5 10264 46 - 87904 CCC--ATAGCAGTTACCCTTGTTTTGTCTTGCACGCTGCCATAACAGA -s Anc1.Anc1refChr7 10665 46 + 47259 CCC--ATAGCAGTTACCCTTGTTTTGTCTTGCACGCTGCCATAACAGA -s Anc2.Anc2refChr15 11744 46 - 86568 CCC--ATAGCAGTTACCCTTGTTTTGTCTTGCAGGATGACACAACAGA -s mr.mrrefChr5 180914 46 - 294540 CCT--AGTGCTATCTCAACTATCTTGTCCAGGACGCTGCCATAACAGA -s simCow_chr6.simCow.chr6 346231 45 - 602619 AGG--GTATCAGCTCCCCTTAACTAGTTCTGCAGCATGACAAACCAA- -s simDog_chr6.simDog.chr6 346137 46 - 593897 CCC--ATAGCAGTTACCCTTGTTTTGTCTTGCAGGATGACCCAACAGA -s simHuman_chr6.simHuman.chr6 262518 15 + 601863 ---------------------------------CTCTGCCATAACAGA -s simRat_chr6.simRat.chr6 396380 46 - 647215 CCT--AGTGCTATTTCAATCATCTTGTCCAAGATGCTGCCACAACAGA - -a -s simMouse_chr6.simMouse.chr6 261264 18 + 636262 CTGGGCTAGGGACATATG -s Anc0.Anc0refChr5 10311 17 - 87904 CTGTACCAAT-ACACATG -s Anc1.Anc1refChr7 10712 17 + 47259 CTGTACCAAT-ACACATG -s Anc2.Anc2refChr15 11791 17 - 86568 CTGTACCAAT-ACACATG -s mr.mrrefChr5 180961 18 - 294540 CTGTACTAGGGACACATG -s simCow_chr6.simCow.chr6 346276 13 - 602619 ----ACCAAT-GCACATG -s simDog_chr6.simDog.chr6 346184 17 - 593897 CTGTACCAAT-ACATGTG -s simHuman_chr6.simHuman.chr6 262534 17 + 601863 TAGTACCAAT-ACACATG -s simRat_chr6.simRat.chr6 396427 18 - 647215 CTGTACTAGGGACACATG - -a -s simMouse_chr6.simMouse.chr6 261282 42 + 636262 GCTGATGGAAATACAGACAACATTTTATTTGGTGCTAATACT -s Anc0.Anc0refChr5 10330 42 - 87904 ACTAACATAAGTAAGGACAACATGTCATCCAGTGCTGATACT -s Anc1.Anc1refChr7 10731 42 + 47259 ACTAACATAAGTAAGGACAACATGTCATCCAGTGCTGATACT -s Anc2.Anc2refChr15 11810 42 - 86568 ACTAACATAAGTAAGGACAACATGTCATCCAGTGCTGATACT -s mr.mrrefChr5 180979 42 - 294540 ACTGATGGAAATACAGACAACATTTCATTTGGTGCTAATACT -s simCow_chr6.simCow.chr6 346291 42 - 602619 ACTGACATAAGTATGGACAATGTGTCATCCAGTGCTGATACT -s simDog_chr6.simDog.chr6 346203 38 - 593897 ACTAACATAAGTAAGGGCAACATTTTGTCC----CTTTTACT -s simHuman_chr6.simHuman.chr6 262553 40 + 601863 ACTAACATAAGTA--GACAACATGTCATCCTGTGCTGATACT -s simRat_chr6.simRat.chr6 396445 39 - 647215 ACTGGTGGAAATATGGACAACATTTCATTAGGTGTT---ACT - -a -s simMouse_chr6.simMouse.chr6 261324 24 + 636262 CATCCAACTGCCTGCCATGCGGTA -s Anc0.Anc0refChr5 10373 24 - 87904 TACACTGGTGCCTGTCGTGCAGTA -s Anc1.Anc1refChr7 10774 24 + 47259 TACACTGGTGCCTGTCGTGCAGTA -s Anc2.Anc2refChr15 11854 24 - 86568 TACAATGGTGCCTGTTGTGCACTG -s mr.mrrefChr5 181021 24 - 294540 CATCCAACTGCCTGCCATGCAGTA -s simCow_chr6.simCow.chr6 346335 24 - 602619 TACAATGGTGCCTGATGTGCATTG -s simDog_chr6.simDog.chr6 346243 24 - 593897 TACAATGGTCCCTGTTGTGCACTG -s simHuman_chr6.simHuman.chr6 262594 24 + 601863 TACACTGGTGTCTGTCGCGCAGTA -s simRat_chr6.simRat.chr6 396484 24 - 647215 CATCCAACTGCTGCCAATGCACTA - -a -s simMouse_chr6.simMouse.chr6 261348 147 + 636262 TTTCTACCCCAGACCTCGGGACCGCTCCGTAAGCATTTTTGAGTTTAGGGCAATAGTGAAATTGGGAGGTAGCACATTTCCTATGGAGCCCGTCAACCACATGCCCGAGAATAATGCAAGGCTATTAGACCTCACTTATATTCGATT -s Anc0.Anc0refChr5 10401 50 - 87904 TTTCTACCCC------------------------------------------------------------------------------------------------GAGAATCATGGAG-GCTATCTGACCTCACTTATATTCAGTT -s Anc1.Anc1refChr7 10802 51 + 47259 TTTCTACCCCA-----------------------------------------------------------------------------------------------GAGAATCATGGAG-GCTATCTGACCTCACTTATATTCAGTT -s Anc2.Anc2refChr15 11882 50 - 86568 TTTCTGCCCT------------------------------------------------------------------------------------------------GAGAATCATGGAG-GCTATCTGACCCCACCTATTTTCAGTT -s mr.mrrefChr5 181045 60 - 294540 TTTCTACCCCAGACCTC--------------------------------------------------------------------------------------CCCGAGAATAATGCAA-GCTATTAGACCTCACTTATATTCGATT -s simCow_chr6.simCow.chr6 346367 50 - 602619 TTGCCCCCCT------------------------------------------------------------------------------------------------GACAATCTTGGAG-GCTATCTGACCCCACCTATTTTCAGTT -s simDog_chr6.simDog.chr6 346296 38 - 593897 TTTCTGCCCT------------------------------------------------------------------------------------------------GAGAATCATGGAG-GCTA------------TATTTTCAGTT -s simHuman_chr6.simHuman.chr6 262622 38 + 601863 TTTCTACCTCA-------------------------------------------------------------------------------------------------------TGGAG-GCTATCTGACCTTGCTCTTATT----- -s simRat_chr6.simRat.chr6 396508 60 - 647215 TTCCAACCCCACACCTC--------------------------------------------------------------------------------------CCCAAGAAAAATGCAA-GCTATGAGACCTCACTTATACTCAATT - -a -s simMouse_chr6.simMouse.chr6 261495 4 + 636262 TGCA -s Anc0.Anc0refChr5 10451 4 - 87904 TGCC -s Anc1.Anc1refChr7 10853 4 + 47259 TGCC -s Anc2.Anc2refChr15 11932 4 - 86568 TACC -s mr.mrrefChr5 181105 4 - 294540 TGCA -s simCow_chr6.simCow.chr6 346417 4 - 602619 TCCA -s simDog_chr6.simDog.chr6 346334 4 - 593897 TACC -s simHuman_chr6.simHuman.chr6 262660 3 + 601863 -GCC -s simRat_chr6.simRat.chr6 396572 4 - 647215 TGCA - -a -s simMouse_chr6.simMouse.chr6 261499 5 + 636262 ACTTT -s Anc0.Anc0refChr5 10455 5 - 87904 ACTTT -s Anc1.Anc1refChr7 10857 5 + 47259 ACTTT -s Anc2.Anc2refChr15 11939 5 - 86568 ACTTT -s mr.mrrefChr5 181109 5 - 294540 ACTTT -s simCow_chr6.simCow.chr6 346424 5 - 602619 ATTTT -s simDog_chr6.simDog.chr6 346341 5 - 593897 ACTTT -s simHuman_chr6.simHuman.chr6 262663 5 + 601863 AGTTT -s simRat_chr6.simRat.chr6 396576 5 - 647215 ACTTT - -a -s simMouse_chr6.simMouse.chr6 261504 3 + 636262 ACT -s Anc0.Anc0refChr5 10460 3 - 87904 ACT -s Anc1.Anc1refChr7 10862 3 + 47259 ACT -s Anc2.Anc2refChr15 11944 3 - 86568 ATT -s mr.mrrefChr5 181114 3 - 294540 ACT -s simCow_chr6.simCow.chr6 346429 3 - 602619 ATT -s simDog_chr6.simDog.chr6 346347 3 - 593897 ATT -s simHuman_chr6.simHuman.chr6 262668 3 + 601863 ACT -s simRat_chr6.simRat.chr6 396581 3 - 647215 ACT - -a -s simMouse_chr6.simMouse.chr6 261507 24 + 636262 ATCACCATAAAGAGCTTGGTTCTG -s Anc0.Anc0refChr5 10463 24 - 87904 ATCACTTTAAAGAGGCTGGTTCTG -s Anc1.Anc1refChr7 10865 24 + 47259 ATCACTTTAAAGAGGCTGGTTCTG -s Anc2.Anc2refChr15 11947 24 - 86568 ATCAATTTAAAGAGGCTGGTTCTG -s mr.mrrefChr5 181117 24 - 294540 ATCACCATAAAGAGCTTGGTTCTG -s simCow_chr6.simCow.chr6 346432 24 - 602619 GTCAATTTAATAAGGCAGGGTCTG -s simDog_chr6.simDog.chr6 346350 24 - 593897 ATCAATTTAAAGCGACTGATTCTG -s simHuman_chr6.simHuman.chr6 262678 24 + 601863 ATCACTTTAAAGAGGCTGGTTCAG -s simRat_chr6.simRat.chr6 396584 24 - 647215 ATCACCATAAAAAGCTTGGGTCTG - -a -s simMouse_chr6.simMouse.chr6 261531 15 + 636262 GAGTGTGAATGTGGG -s Anc0.Anc0refChr5 10487 15 - 87904 GAGTGTGGGCGTGGG -s Anc1.Anc1refChr7 10889 15 + 47259 GAGTGTGGGCGTGGG -s Anc2.Anc2refChr15 11973 15 - 86568 GAGTGTGGGCGTGGG -s mr.mrrefChr5 181141 15 - 294540 GAGTGTGAATGTGGG -s simCow_chr6.simCow.chr6 346458 15 - 602619 GAGTGTGGAGGTAAG -s simDog_chr6.simDog.chr6 346376 15 - 593897 GAGAGTGGGCATGGA -s simHuman_chr6.simHuman.chr6 262702 15 + 601863 GAGTGTGGGCGCGGG -s simRat_chr6.simRat.chr6 396608 15 - 647215 GAATGTGAATGTGGG - -a -s simMouse_chr6.simMouse.chr6 261546 69 + 636262 CAACTAGATGTCAGTACATGGATTTTTAAATCCACCTACAACTCTCTAAAAAGTAGGTGTAATTAGGGT -s Anc0.Anc0refChr5 10502 69 - 87904 AGACCAGATGTCATTGAATAGAGTTTTAAATCCGCCAGCACTTCTCCTAGACATAGATCTACTTACTAT -s Anc1.Anc1refChr7 10904 69 + 47259 AGACCAGATGTCATTGAATAGAGTTTTAAATCCGCCAGCACTTCTCCTAGACATAGATCTACTTACTAT -s Anc2.Anc2refChr15 11988 69 - 86568 AGACCAGATGTCATTGAACAGAGTTTTAAGTCCGTCAGCACTTCTCCTAGACATGGACCTCCTAGCTAT -s mr.mrrefChr5 181156 69 - 294540 CAACCAGATGTCAGTAAATGGATTTTTAAATCCACCTACAACTCTCTAAGACGTAGGTGTAATTAGGGT -s simCow_chr6.simCow.chr6 346474 69 - 602619 AGACCAGAAGGCATTGGACACAGTTTCAATTCCACCCACACATCTCCACAACATGGACCTCCTAGACAT -s simDog_chr6.simDog.chr6 346391 69 - 593897 TAACCAGATGTTGTTGAACAGAGTTTTAAGTCCGTCAGCACTTCTCCTAGACATGGCCCTCCTAGCTAT -s simHuman_chr6.simHuman.chr6 262717 58 + 601863 AGACCAGATGTCATTTAATAGAGTTTTAAATCCGCCCG-----------GACACAGATCTACTTACTAT -s simRat_chr6.simRat.chr6 396623 69 - 647215 CAGCCGGATGTCAATAAATGGATTTTTAAATCCAACTAAGACTCTCTTAGACGGAGGTGTAATTGGGGT - -a -s simMouse_chr6.simMouse.chr6 261615 22 + 636262 ATACTGCACATTTTCTGAGGGC -s Anc0.Anc0refChr5 10571 22 - 87904 ATGATACACATTTTCTTAGGCC -s Anc1.Anc1refChr7 10973 22 + 47259 ATGATACACATTTTCTTAGGCC -s Anc2.Anc2refChr15 12080 22 - 86568 ATGATACACATTTTCTTAGGCC -s mr.mrrefChr5 181225 22 - 294540 ATACTGCACATTTTCTGAGGGC -s simCow_chr6.simCow.chr6 346566 22 - 602619 ATAATTCACATTTTCTTAGGCC -s simDog_chr6.simDog.chr6 346484 22 - 593897 ATGATACACATTTTCTTAGGCC -s simHuman_chr6.simHuman.chr6 262775 1 + 601863 A--------------------- -s simRat_chr6.simRat.chr6 396692 22 - 647215 ATACGGCACATTTTCTCAGGGC - -a -s simMouse_chr6.simMouse.chr6 261637 17 + 636262 TAGCACTGATAAACTTA -s Anc0.Anc0refChr5 10593 17 - 87904 TAGCACTGTTACACTGA -s Anc1.Anc1refChr7 10995 17 + 47259 TAGCACTGTTACACTGA -s Anc2.Anc2refChr15 12103 17 - 86568 TAGCACTGTTACACTGA -s mr.mrrefChr5 181247 17 - 294540 TAGCACTGATAAACTTA -s simCow_chr6.simCow.chr6 346589 17 - 602619 TAGCACAATTACACTGA -s simDog_chr6.simDog.chr6 346507 17 - 593897 TAGCACTGTTACACTGA -s simHuman_chr6.simHuman.chr6 262776 1 + 601863 ----------------G -s simRat_chr6.simRat.chr6 396714 17 - 647215 TAGCACTGATAAACTGA - -a -s simMouse_chr6.simMouse.chr6 261654 3 + 636262 CCC -s Anc0.Anc0refChr5 10610 3 - 87904 CCC -s Anc1.Anc1refChr7 11012 3 + 47259 CCC -s Anc2.Anc2refChr15 12145 3 - 86568 CAC -s mr.mrrefChr5 181264 3 - 294540 CCC -s simCow_chr6.simCow.chr6 346631 3 - 602619 CAC -s simDog_chr6.simDog.chr6 346550 3 - 593897 CAC -s simHuman_chr6.simHuman.chr6 262777 3 + 601863 CCC -s simRat_chr6.simRat.chr6 396731 3 - 647215 CCC - -a -s simMouse_chr6.simMouse.chr6 261657 12 + 636262 CTGTACTATCTG -s Anc0.Anc0refChr5 10613 12 - 87904 CTGATCTATCTG -s Anc1.Anc1refChr7 11015 12 + 47259 CTGATCTATCTG -s Anc2.Anc2refChr15 12148 12 - 86568 TTGATCCATGTG -s mr.mrrefChr5 181267 12 - 294540 CTGTACTATCTG -s simCow_chr6.simCow.chr6 346638 12 - 602619 TTGATCCATGTA -s simDog_chr6.simDog.chr6 346553 12 - 593897 TTGATCCATGTG -s simHuman_chr6.simHuman.chr6 262780 12 + 601863 CTTCGTTGTCTG -s simRat_chr6.simRat.chr6 396734 12 - 647215 CCGTACTATCTG - -a -s simMouse_chr6.simMouse.chr6 261669 9 + 636262 CACTCTTTC -s Anc0.Anc0refChr5 10625 8 - 87904 CACTCCTT- -s Anc1.Anc1refChr7 11027 8 + 47259 CACTCCTT- -s Anc2.Anc2refChr15 12169 8 - 86568 CACTCCTT- -s mr.mrrefChr5 181279 8 - 294540 CACTCTTT- -s simCow_chr6.simCow.chr6 346659 8 - 602619 CACTACTT- -s simDog_chr6.simDog.chr6 346574 8 - 593897 CACTCCTT- -s simRat_chr6.simRat.chr6 396746 8 - 647215 CACTCTTT- - -a -s simMouse_chr6.simMouse.chr6 261678 3 + 636262 TTC -s Anc0.Anc0refChr5 10633 3 - 87904 CTC -s Anc1.Anc1refChr7 11035 3 + 47259 CTC -s Anc2.Anc2refChr15 12177 3 - 86568 CTC -s mr.mrrefChr5 181287 3 - 294540 TTC -s simCow_chr6.simCow.chr6 346667 3 - 602619 CTC -s simDog_chr6.simDog.chr6 346594 3 - 593897 CTC -s simRat_chr6.simRat.chr6 396754 3 - 647215 TTC - -a -s simMouse_chr6.simMouse.chr6 261681 35 + 636262 CAAGCTCCTCAGTACAGGTTTTACTCATTGACACA -s Anc0.Anc0refChr5 10636 35 - 87904 CGGTCTCCTGAGTACATGTTTCATTCATTGACATA -s Anc1.Anc1refChr7 11038 35 + 47259 CGGTCTCCTGAGTACATGTTTCATTCATTGACATA -s Anc2.Anc2refChr15 12183 35 - 86568 CGGTCTCCTGAGTACATGTTTCATTCATTGACATA -s mr.mrrefChr5 181290 35 - 294540 CAAGCTCCTCAGTACAGGTTTTACTCATTGACACA -s simCow_chr6.simCow.chr6 346673 35 - 602619 CTGTCCCCCAAGTATTAGTTACAATCAATAACATA -s simDog_chr6.simDog.chr6 346600 35 - 593897 CGGTCTCCTGAGTACATGTTTCATTCATTGCCATA -s simHuman_chr6.simHuman.chr6 262792 15 + 601863 --------------------CCTAGCATTGACATA -s simRat_chr6.simRat.chr6 396757 35 - 647215 CAAGCTCCTCAGTATAGGTTTCACTCATTGAAACA - -a -s simMouse_chr6.simMouse.chr6 261716 17 + 636262 ACATTAGACATAGAGCA -s Anc0.Anc0refChr5 10673 17 - 87904 ATGTTAGGCATGGAGTA -s Anc1.Anc1refChr7 11075 17 + 47259 ATGTTAGGCATGGAGTA -s Anc2.Anc2refChr15 12220 17 - 86568 ATGTTAGGCATGGGGTA -s mr.mrrefChr5 181325 17 - 294540 ACATTAGACATAGAGCA -s simCow_chr6.simCow.chr6 346710 17 - 602619 ATATCAGGCACAGGATA -s simDog_chr6.simDog.chr6 346637 17 - 593897 ATGTTAGGCATGGGGTA -s simHuman_chr6.simHuman.chr6 262809 8 + 601863 ATGC---------AGGA -s simRat_chr6.simRat.chr6 396792 17 - 647215 ACGTTAGACATAGAGCA - -a -s simMouse_chr6.simMouse.chr6 261733 24 + 636262 GTCCTGACAACAGTGCCCATTGGC -s Anc0.Anc0refChr5 10690 21 - 87904 GCCTTGAC--CAGT-CCCATTGGT -s Anc1.Anc1refChr7 11092 24 + 47259 GCCTTGACAACAGTGCCCATTGGT -s Anc2.Anc2refChr15 12237 21 - 86568 ACCTTGAC--CAGT-CCTATTGGC -s mr.mrrefChr5 181342 24 - 294540 GTCCTGACAACAGTGCCCATTGGT -s simCow_chr6.simCow.chr6 346727 2 - 602619 AC---------------------- -s simDog_chr6.simDog.chr6 346654 21 - 593897 ACCTTGAC--CAGT-CCTATTGGC -s simHuman_chr6.simHuman.chr6 262817 24 + 601863 GGCTTGACAACAGTGCCCATTGGT -s simRat_chr6.simRat.chr6 396810 24 - 647215 TTCCGGAGAACAGTGCCCATTGGT - -a -s simMouse_chr6.simMouse.chr6 261757 14 + 636262 AAAGGAATATTCTT -s Anc0.Anc0refChr5 10714 12 - 87904 CCATGTGCAGAA-- -s Anc1.Anc1refChr7 11119 12 + 47259 CCATGTGCAGAA-- -s Anc2.Anc2refChr15 12261 12 - 86568 CCATGTGCAGAA-- -s mr.mrrefChr5 181366 12 - 294540 CCATGAGTATTC-- -s simDog_chr6.simDog.chr6 346678 12 - 593897 CCATGTGCAGAA-- -s simHuman_chr6.simHuman.chr6 262844 12 + 601863 CCATGTGCTGGA-- -s simRat_chr6.simRat.chr6 396834 12 - 647215 CCATGAGTAAAC-- - -a -s simMouse_chr6.simMouse.chr6 261771 19 + 636262 CACCACCAAGGCAAATAAA -s Anc0.Anc0refChr5 78244 19 + 87904 CACCACCAGGACAAAGAGA -s Anc1.Anc1refChr7 37211 19 - 47259 CACCACCAGGACAAAGAGA -s Anc2.Anc2refChr15 75443 19 + 86568 AACCGCCAGGACACAGAGA -s mr.mrrefChr5 114310 19 + 294540 CACCACCAGGACAAATAAA -s simCow_chr6.simCow.chr6 257109 19 + 602619 ATCCCCCAGAACTTGGAGA -s simDog_chr6.simDog.chr6 248364 19 + 593897 AACCGCCTGGACACAGAGA -s simHuman_chr6.simHuman.chr6 339964 19 - 601863 CGCCACCAGGACAAAGAGA -s simRat_chr6.simRat.chr6 251541 19 + 647215 CACCACCAGGACAAATAAA - -a -s simMouse_chr6.simMouse.chr6 261790 16 + 636262 CCCATCATTGAGTCAG -s Anc0.Anc0refChr5 78263 16 + 87904 CCCCTCACTGAATCAG -s Anc1.Anc1refChr7 37230 16 - 47259 CCCCTCACTGAATCAG -s Anc2.Anc2refChr15 75462 16 + 86568 CCCCTCACTGAATCAG -s mr.mrrefChr5 114329 16 + 294540 CCCATCATTGAGTCAG -s simCow_chr6.simCow.chr6 257128 16 + 602619 TCCCTCACTGAATCAG -s simDog_chr6.simDog.chr6 248410 16 + 593897 CCCCTCACTGAATTGG -s simHuman_chr6.simHuman.chr6 339983 16 - 601863 CCCCCTACCGAATCAG -s simRat_chr6.simRat.chr6 251560 16 + 647215 CCCATCATTGAGTCAG - -a -s simMouse_chr6.simMouse.chr6 261806 1 + 636262 A -s Anc0.Anc0refChr5 78283 1 + 87904 A -s Anc1.Anc1refChr7 37250 1 - 47259 A -s Anc2.Anc2refChr15 75482 1 + 86568 A -s mr.mrrefChr5 114345 1 + 294540 A -s simCow_chr6.simCow.chr6 257148 1 + 602619 A -s simDog_chr6.simDog.chr6 248430 1 + 593897 A -s simHuman_chr6.simHuman.chr6 340003 1 - 601863 A -s simRat_chr6.simRat.chr6 251576 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 261807 2 + 636262 AT -s Anc0.Anc0refChr5 78290 2 + 87904 AT -s Anc1.Anc1refChr7 37257 2 - 47259 AT -s Anc2.Anc2refChr15 75489 2 + 86568 AT -s mr.mrrefChr5 114352 2 + 294540 AT -s simCow_chr6.simCow.chr6 257155 2 + 602619 AT -s simDog_chr6.simDog.chr6 248437 2 + 593897 AT -s simHuman_chr6.simHuman.chr6 340010 2 - 601863 AT -s simRat_chr6.simRat.chr6 251583 2 + 647215 AT - -a -s simMouse_chr6.simMouse.chr6 261809 1 + 636262 G -s Anc0.Anc0refChr5 78292 1 + 87904 G -s Anc1.Anc1refChr7 37259 1 - 47259 G -s Anc2.Anc2refChr15 75492 1 + 86568 G -s mr.mrrefChr5 114354 1 + 294540 G -s simCow_chr6.simCow.chr6 257158 1 + 602619 G -s simDog_chr6.simDog.chr6 248440 1 + 593897 G -s simHuman_chr6.simHuman.chr6 340012 1 - 601863 G -s simRat_chr6.simRat.chr6 251585 1 + 647215 G - -a -s simMouse_chr6.simMouse.chr6 261810 9 + 636262 GTCATCTCA -s Anc0.Anc0refChr5 78304 9 + 87904 ATAAGCATA -s Anc1.Anc1refChr7 37271 9 - 47259 ATAAGCATA -s Anc2.Anc2refChr15 75504 9 + 86568 ATAGGCATG -s mr.mrrefChr5 114355 9 + 294540 GTCATCTCA -s simCow_chr6.simCow.chr6 257170 9 + 602619 GTAGGCATC -s simDog_chr6.simDog.chr6 248452 9 + 593897 ATAGGCATG -s simHuman_chr6.simHuman.chr6 340024 9 - 601863 ACAAACATA -s simRat_chr6.simRat.chr6 251586 9 + 647215 GTCATCTCA - -a -s simMouse_chr6.simMouse.chr6 261819 49 + 636262 CTGACTACAACATATTTAACTTTTAGGAACAGTCATATATGCCAAACTT -s Anc0.Anc0refChr5 78326 49 + 87904 CTGACATCCACACATTTCACTTGTAAGAAAAGTCACATATACCAAACTT -s Anc1.Anc1refChr7 37293 49 - 47259 CTGACATCCACACATTTCACTTGTAAGAAAAGTCACATATACCAAACTT -s Anc2.Anc2refChr15 75526 49 + 86568 CTGATATCCACACATTTCACTTGTAAGAAAAGTAACATATACTAAACTT -s mr.mrrefChr5 114377 49 + 294540 CTGACTACAACATATTTAACTTGTAGGAACAGTCATATATGCCAAACTT -s simCow_chr6.simCow.chr6 257192 49 + 602619 CTGATATCCAGACATATCACTTGTAAGAAAAGTAGCATATACTAAACTT -s simDog_chr6.simDog.chr6 248474 49 + 593897 CTACTATCCACACATTTCACTTGTAAGAAAAGTAACATATACTACACTT -s simHuman_chr6.simHuman.chr6 340046 49 - 601863 CTGACACCGTCACATGTCACTTGTATGAAAACTCACATTCACCAAACTT -s simRat_chr6.simRat.chr6 251608 48 + 647215 CTAACTTCAACATATTTAACTTGTAGGA-CAGTCATATATGCCGAACCT - -a -s simMouse_chr6.simMouse.chr6 261868 99 + 636262 GACTTGTTGTATCCAACACTAGAGACAGCAACCAATTCAGTCTAGGGTAGGGAGTTTTAACAGAACAGCACCAAGCAGTATCCACAACATTGCTAAGAT -s Anc0.Anc0refChr5 78375 93 + 87904 CGCTTGTTATATTCAAGAGTAGAGACAGCAACCAATGCAGAAT-GG-----GAGTCTTAACGGAACTGCATCAATCAGTATCCAGCACGTTTCTAAGAT -s Anc1.Anc1refChr7 37342 94 - 47259 CGCTTGTTATATTCAAGAGTAGAGACAGCAACCAATGCAGAATAGG-----GAGTCTTAACGGAACTGCATCAATCAGTATCCAGCACGTTTCTAAGAT -s Anc2.Anc2refChr15 75575 93 + 86568 CACTTGTTAGATTCAAGAGTAGAGGCAGCAACCAATGCAGAAT-GG-----GAGTCTTAATGGAACTGCATCAATCAGTATACAGCACATTTCTAAGAT -s mr.mrrefChr5 114426 94 + 294540 GGCTTGTTGTATTCAAGACTAGAGACAGCAACCAATTCAGTCTAGG-----GAGTTTTAACAGAACAGCATCAAGCAGTATCCACAACGTTGCTAAGAT -s simCow_chr6.simCow.chr6 257241 93 + 602619 CACTTGTTAGATTCAAGAGTAGAAGCAGCAACCAACGCAAAAT-GG-----GAGTCTTAATAGAACTGTATCAATCAGTATACAGCACATTTCTGATAT -s simDog_chr6.simDog.chr6 248523 89 + 593897 CAGTTTTCAGATTGAAGAGTGGAG----CAACCAATGCGGAAT-GG-----GAGTCTTAATGGAACTGCATCAATCAGTATACAGCACATTTCTAAGGT -s simHuman_chr6.simHuman.chr6 340095 94 - 601863 TGCTTGTTATATTCAAGAGTAGAGACAGCAACCGATGCAGAACAAG-----GAGTCCTAACGGAACTGCATCAATCAGTACCCAGCATGTTCCCAAGAT -s simRat_chr6.simRat.chr6 251657 94 + 647215 GGCTTGTTGTATTCATGACTAGAGACAGTAACTAATACAGGCTAGG-----GAGTTTTAACAGAACAGCATCAAGCTGTATCCACAACGTTGCTAAGAT - -a -s simMouse_chr6.simMouse.chr6 261967 8 + 636262 TGATTGTG -s Anc0.Anc0refChr5 78468 8 + 87904 TGATACCA -s Anc1.Anc1refChr7 37436 8 - 47259 TGATACCA -s Anc2.Anc2refChr15 75668 8 + 86568 TGAGACCA -s mr.mrrefChr5 114520 8 + 294540 TGATCATG -s simCow_chr6.simCow.chr6 257334 8 + 602619 TGGGACCA -s simDog_chr6.simDog.chr6 248620 8 + 593897 TGAGACCA -s simHuman_chr6.simHuman.chr6 340189 8 - 601863 CAATACCA -s simRat_chr6.simRat.chr6 251751 8 + 647215 TGATCATG - -a -s simMouse_chr6.simMouse.chr6 261975 9 + 636262 AAGGAATAT -s Anc0.Anc0refChr5 78477 6 + 87904 ATGGAA--- -s Anc1.Anc1refChr7 37445 6 - 47259 ATGGAA--- -s Anc2.Anc2refChr15 75677 6 + 86568 ATGGTA--- -s mr.mrrefChr5 114529 9 + 294540 AAGGAATAT -s simCow_chr6.simCow.chr6 257343 6 + 602619 ATGGTA--- -s simDog_chr6.simDog.chr6 248629 6 + 593897 ATGGTC--- -s simHuman_chr6.simHuman.chr6 340198 6 - 601863 ACTAAA--- -s simRat_chr6.simRat.chr6 251760 9 + 647215 AAGGGATGT - -a -s simMouse_chr6.simMouse.chr6 261984 24 + 636262 GAAGTTTCATCATGGCGAATGCAA -s Anc0.Anc0refChr5 78483 16 + 87904 GAAGTAACATTATA--------AG -s Anc1.Anc1refChr7 37451 24 - 47259 GAAGTAACATTATAGAGGATGGAG -s Anc2.Anc2refChr15 75683 16 + 86568 AAGGTAACATTAAA--------AG -s mr.mrrefChr5 114538 24 + 294540 GAAGTTTCATCATGGAGAATGGAG -s simCow_chr6.simCow.chr6 257354 16 + 602619 AAGGGAATATCAAA--------AG -s simDog_chr6.simDog.chr6 248635 16 + 593897 AGGGTAACATTGAA--------AG -s simHuman_chr6.simHuman.chr6 340204 24 - 601863 GAAATCCCATTATAGAGGATGGAG -s simRat_chr6.simRat.chr6 251769 24 + 647215 GAAGTTTCATCATGGAGAATGGAG - -a -s simMouse_chr6.simMouse.chr6 262008 77 + 636262 AATGGACAAAGGAGAAGTGAGGAAACTTCTTGGACTTCTACATTTGACTGTGTAGCAGTGGCTGAGTCTACATTAAC -s Anc0.Anc0refChr5 78499 75 + 87904 AATGGAAGCAGGAAAAGTGAGTATACTTGTTGGATTATTAC-TGTGCATGTGTTG-GGTGACTGAGTATACATCAAC -s Anc1.Anc1refChr7 37475 75 - 47259 AATGGAAGCAGGAAAAGTGAGTATACTTGTTGGATTATTAC-TGTGCATGTGTTG-GGTGACTGAGTATACATCAAC -s Anc2.Anc2refChr15 75699 75 + 86568 AATGGAAGCAGTAAAAGTGAGTATACTTGTTGGATTATTAC-TGTGCATGTGTTG-GGTGACTGAGCATAAACCAAC -s mr.mrrefChr5 114562 77 + 294540 AATGGACACAGGAGAAGTGAGGAAACTTCTTGGACTACTACATTTGACTGTGTAGCGGTGGCTGAGTCTACATCAAC -s simCow_chr6.simCow.chr6 257385 73 + 602619 AATGGAAGCAGTAATATTGAGTATACTTGTTGGACTATTAC-GGTGCATATG--G-GGTGACTGAGCTTAAACCAAC -s simDog_chr6.simDog.chr6 248651 74 + 593897 AATGGAGGAAGTAGAAGTGAGTATACTTGTTGTAT-ATGAC-TGTGCATGTGTTA-AGTGACTGAGCATAAACCAAC -s simHuman_chr6.simHuman.chr6 340228 75 - 601863 AATGTAAGCAGGAAAAGTGAATACACTTGTTGGATTATTAC-TGTGCATGTGTTG-GGTGACAGAGTATACATCAAC -s simRat_chr6.simRat.chr6 251793 77 + 647215 GATGGACACTGGAGAAGTGGGGAAACTTCTTGGACTACTACCTTTGATTGTGTAATGCTGGCTAAGTTTACACCAAT - -a -s simMouse_chr6.simMouse.chr6 262085 54 + 636262 GGTATGTACCTCTGTTCGGAAAATATGTTTTGTATTTTAAGATGTTCCAGTATG -s Anc0.Anc0refChr5 78575 53 + 87904 GGTATGCACCTCAGTTCAACAGACGTGTTCTGTCA-ATAAAATCATCCAGTAAA -s Anc1.Anc1refChr7 37551 54 - 47259 GGTATGCACCTCAGTTCAACAGACGTGTTCTGTCATATAAAATCATCCAGTAAA -s Anc2.Anc2refChr15 75775 53 + 86568 GGTATGCACCTGAGTTCAACAGACGTGGTCTGTCA-ATCAAGTCATTCAGTAAA -s mr.mrrefChr5 114639 54 + 294540 GGTATGTACCTCTGTTCAGCAAATATGTTTTGTCTTTTAAGATGTTCCAGTATG -s simCow_chr6.simCow.chr6 257459 53 + 602619 GGTATGCACCTTGGTTCTGAAGACATGCACTGTCA-ATCAAGGCATTCAGTATA -s simDog_chr6.simDog.chr6 248726 49 + 593897 GGTATGCACCTGAGTTCAACATATGTGGTCTTTCA-ACCCTGTAG----GTGAA -s simHuman_chr6.simHuman.chr6 340304 54 - 601863 GGTTTGCATCTCAGTTCAACTGACGTGTTCTGTCATATAAAAACATCCAGTAAA -s simRat_chr6.simRat.chr6 251870 54 + 647215 GGTATGTACCTCTGTGCAGCAAATATGTTTTGTCTTCAACGATGTTCCAGTAGG - -a -s simMouse_chr6.simMouse.chr6 262139 30 + 636262 GGAATAGATTTGCTAAGATGTCATGCTTAG -s Anc0.Anc0refChr5 78628 27 + 87904 GGAACAGATTTGCTAAAGTGCCATTCC--- -s Anc1.Anc1refChr7 37605 27 - 47259 GGAACAGATTTGCTAAAGTGCCATTCC--- -s Anc2.Anc2refChr15 75834 27 + 86568 GGAACAGACTTGCTAAAGTGCCATTCC--- -s mr.mrrefChr5 114693 27 + 294540 GGAATAGATTTGCTAAGATGTCATGCT--- -s simCow_chr6.simCow.chr6 257514 27 + 602619 GGAAGAGACGTGCTAAAGTGCCATCCC--- -s simDog_chr6.simDog.chr6 248781 27 + 593897 GGAACAGTCTTGCTAAAGAGCTGTTCC--- -s simHuman_chr6.simHuman.chr6 340358 27 - 601863 GCAAAGGATTTGCTAAAGTGCCACTCC--- -s simRat_chr6.simRat.chr6 251924 27 + 647215 GGAATAGATTTGCTAAGACAGCAGGCC--- - -a -s simMouse_chr6.simMouse.chr6 262169 58 + 636262 AAGTCATAGTGGGTATTCAATACTTGCACCTCTAATCCAATTGATTGCCTGCATGTTT -s Anc0.Anc0refChr5 78655 56 + 87904 AAATTATTATGTGTATGCAATGTTTACTACTCCACTC--AGCGGATGGCTCAATGTGT -s Anc1.Anc1refChr7 37632 56 - 47259 AAATTATTATGTGTATGCAATGTTTACTACTCCACTC--AGCGGATGGCTCAATGTGT -s Anc2.Anc2refChr15 75868 56 + 86568 AAATTATTATGTGTATGCAATGTTTACTACTCCACTC--AGCGGATGGCTCAATGTGT -s mr.mrrefChr5 114720 58 + 294540 AAGTCATAGTGGGTATTCAATACTTGCACCTCCAATCCAATTGATTGCCTGCATGTTT -s simCow_chr6.simCow.chr6 257548 56 + 602619 CAATTGTCGTGTGTATGCATTGTTTTCTGATCTATTC--AGTAGACAGCTTTATGTGT -s simDog_chr6.simDog.chr6 248815 56 + 593897 AAATTATTATGTGTATGCAATGTTTACTACTCCACTC--AGCGGATGGCTCAATGTGT -s simHuman_chr6.simHuman.chr6 340385 2 - 601863 AA-------------------------------------------------------- -s simRat_chr6.simRat.chr6 251951 58 + 647215 AAGTCATCATGGGTATGCGATCCTTGCAACTCCATTCCAATTGATTGCCCACATGTTT - -a -s simMouse_chr6.simMouse.chr6 262227 45 + 636262 CTATTTCTAGGGTTCCCACATAGTTTGTTTTTGTTTTGACTAACT -s Anc0.Anc0refChr5 78711 31 + 87904 C---TTTCAGGAATTTCAGACCGTT-----------TGATAAACA -s Anc1.Anc1refChr7 37688 39 - 47259 C---TTTCAGGAATTTCAGACCGTT---CTTGGGACTGATAAACA -s Anc2.Anc2refChr15 75924 31 + 86568 C---TTTCAGGAATTTCAGACCGTT-----------TGATAAACA -s mr.mrrefChr5 114778 45 + 294540 CTATTTCTAGGGTTCCCACATAGTTTGTTTTTGGTCTGATAAACA -s simCow_chr6.simCow.chr6 257604 24 + 602619 T---TTTCAGGTTTTTCAGACAGTT-----------TG------- -s simDog_chr6.simDog.chr6 248872 31 + 593897 C---TTTCAGGAATTTCAGACCGTT-----------TGATAAACA -s simHuman_chr6.simHuman.chr6 340387 17 - 601863 ----------------------------CTTGGGACTAATAAACA -s simRat_chr6.simRat.chr6 252009 45 + 647215 CTATTTGCAGGATTCTCAGATAGTTTGTTTTTGGTCTGATAAATA - -a -s simMouse_chr6.simMouse.chr6 262272 3 + 636262 ATT -s Anc0.Anc0refChr5 78742 3 + 87904 ATC -s Anc1.Anc1refChr7 37727 3 - 47259 ATC -s Anc2.Anc2refChr15 75955 3 + 86568 ATC -s mr.mrrefChr5 114823 3 + 294540 ATC -s simCow_chr6.simCow.chr6 344426 3 - 602619 ATC -s simDog_chr6.simDog.chr6 248903 3 + 593897 ATC -s simHuman_chr6.simHuman.chr6 340404 3 - 601863 ATC -s simRat_chr6.simRat.chr6 252054 3 + 647215 ATC - -a -s simMouse_chr6.simMouse.chr6 262275 13 + 636262 TCCAACTTGGTTA -s Anc0.Anc0refChr5 78746 13 + 87904 TCCTACTTGGTTA -s Anc1.Anc1refChr7 37731 13 - 47259 TCCTACTTGGTTA -s Anc2.Anc2refChr15 75959 13 + 86568 TTCTACTTGGTTA -s mr.mrrefChr5 114826 13 + 294540 TCCAACTTGGTTA -s simCow_chr6.simCow.chr6 344430 13 - 602619 TTCCACCTGGCTA -s simDog_chr6.simDog.chr6 248907 13 + 593897 TTCTAGTTGGTTA -s simHuman_chr6.simHuman.chr6 340408 13 - 601863 TCCTCCTTTGTTG -s simRat_chr6.simRat.chr6 252057 12 + 647215 TCCAACTTGGTG- - -a -s simMouse_chr6.simMouse.chr6 262288 3 + 636262 CAC -s Anc0.Anc0refChr5 78759 2 + 87904 CA- -s Anc1.Anc1refChr7 37744 2 - 47259 CA- -s Anc2.Anc2refChr15 75972 2 + 86568 CA- -s mr.mrrefChr5 114839 3 + 294540 CAC -s simCow_chr6.simCow.chr6 344443 2 - 602619 AA- -s simDog_chr6.simDog.chr6 248923 2 + 593897 CA- -s simHuman_chr6.simHuman.chr6 340421 2 - 601863 CA- -s simRat_chr6.simRat.chr6 252069 3 + 647215 CAC - -a -s simMouse_chr6.simMouse.chr6 262291 56 + 636262 CCAACTAAATGAGCCTGGCACTCCCAGACGTCAAGAGGATTGATTAACAGACAATG -s Anc0.Anc0refChr5 78761 55 + 87904 CCACCTAGATGAGCCTGGAAGTTTTAAACCT-GAGAAGTTTGAATAACACCCAACT -s Anc1.Anc1refChr7 37746 55 - 47259 CCACCTAGATGAGCCTGGAAGTTTTAAACCT-GAGAAGTTTGAATAACACCCAACT -s Anc2.Anc2refChr15 75974 55 + 86568 CCACCTAGATGAATCTGGAAGCTTTAAGCCT-GAGAAGTTTGAATGACACCCAACT -s mr.mrrefChr5 114842 56 + 294540 CCAACTAAATGAGCCTGGCACTCCCAAACCTCAAGAAGTTTGAATAACAGACAATG -s simCow_chr6.simCow.chr6 344445 20 - 602619 CCACCTGGACGAATCGGGAA------------------------------------ -s simDog_chr6.simDog.chr6 248931 55 + 593897 CCACTTAGATGAATCTGAAAGCTTTAAGCCT-GAGAAGTTTGAATGACACCCAACT -s simHuman_chr6.simHuman.chr6 340423 55 - 601863 CCATCCAGATGAGCCTGGAAGTATTAAACCT-GACAAGTTGGAACAACACCCAACT -s simRat_chr6.simRat.chr6 252072 56 + 647215 CCACCTAAATGAGCCTGGCACTTCCAAACCTCATGAAGTTTGAATAACAGGCAATG - -a -s simMouse_chr6.simMouse.chr6 262347 15 + 636262 AAGATCATTCTGGAA -s Anc0.Anc0refChr5 78816 15 + 87904 AATAACATTGTAGAA -s Anc1.Anc1refChr7 37801 15 - 47259 AATAACATTGTAGAA -s Anc2.Anc2refChr15 76029 15 + 86568 AATAACATTGTAGAG -s mr.mrrefChr5 114898 15 + 294540 AAGATCATTCTAGAA -s simCow_chr6.simCow.chr6 344465 10 - 602619 -----TGTCGTAGAC -s simDog_chr6.simDog.chr6 248991 15 + 593897 AATAACATTGTAGAG -s simHuman_chr6.simHuman.chr6 340478 15 - 601863 AACAGCATTGTACAA -s simRat_chr6.simRat.chr6 252128 12 + 647215 GA-ATCATTCTAG-- - -a -s simMouse_chr6.simMouse.chr6 262362 5 + 636262 CCACT -s Anc0.Anc0refChr5 78834 5 + 87904 CCACT -s Anc1.Anc1refChr7 37819 5 - 47259 CCACT -s Anc2.Anc2refChr15 76047 5 + 86568 CCGAT -s mr.mrrefChr5 114913 5 + 294540 CCACT -s simCow_chr6.simCow.chr6 344478 3 - 602619 C--AT -s simDog_chr6.simDog.chr6 249008 5 + 593897 CCGAT -s simHuman_chr6.simHuman.chr6 340496 5 - 601863 CCACT - -a -s simMouse_chr6.simMouse.chr6 262367 58 + 636262 ATGGATAATAGCTAACCAGACTTTCAGATTCACAAATTGGGGGTACTCATTTGATTTA -s Anc0.Anc0refChr5 78845 58 + 87904 ATGGATAATAACTAACCAGACCTAGAGATTGGCATATTGGTGATGCCCATTTTGATTA -s Anc1.Anc1refChr7 37830 58 - 47259 ATGGATAATAACTAACCAGACCTAGAGATTGGCATATTGGTGATGCCCATTTTGATTA -s Anc2.Anc2refChr15 76058 58 + 86568 ATGGATAATAACTAACCAGACCTAGAGATTGGCATATTGGTGATGCCCATTTTGATTT -s mr.mrrefChr5 114918 58 + 294540 ATGGATAATAGCTAACCAGACTTTCAGATTCACATATTGGGGGTACTCATTTTATTTA -s simCow_chr6.simCow.chr6 344487 58 - 602619 ATGGATAATAGCTGACCACACCTAAACACTGGCATATTGGTGATGCCCATTTTATCTC -s simDog_chr6.simDog.chr6 249019 58 + 593897 ATGAATAATAACTAACCAGACCTAGAGGTTGACAGATTGGTGGTGCCCGTTCTGATTT -s simHuman_chr6.simHuman.chr6 340507 58 - 601863 ATAGATAATTACTAACCAGACCTAGAGATTGGGATACTGGTGATGCCCATTTTGATTA -s simRat_chr6.simRat.chr6 252140 51 + 647215 -----TAATAGCTAGCCAGAATTCCAGATTCACATAATGGGG--ACTCGTTTTATATA - -a -s simMouse_chr6.simMouse.chr6 262425 19 + 636262 GAGAGTATTACTAAATATT -s Anc0.Anc0refChr5 78909 19 + 87904 CAGGGGGATACCCAATTCA -s Anc1.Anc1refChr7 37894 19 - 47259 CAGGGGGATACCCAATTCA -s Anc2.Anc2refChr15 76122 19 + 86568 CAGGGGGATTCCCAATTCA -s mr.mrrefChr5 114976 19 + 294540 CAGAGTATTACCAAATATT -s simCow_chr6.simCow.chr6 344551 19 - 602619 CAAGTGTATTCCCCATCTC -s simDog_chr6.simDog.chr6 249083 19 + 593897 CAGGGGGATTTCCAATTCA -s simHuman_chr6.simHuman.chr6 340571 19 - 601863 CAGGGGGATACCTAATTAA -s simRat_chr6.simRat.chr6 252191 19 + 647215 CATAGTATCACCAATTATT - -a -s simMouse_chr6.simMouse.chr6 262444 25 + 636262 ATGGCATCATAATGGCTATTTAGCA -s Anc0.Anc0refChr5 78929 24 + 87904 GCATGATTATGATG-TTTCTTTGTT -s Anc1.Anc1refChr7 37914 24 - 47259 GCATGATTATGATG-TTTCTTTGTT -s Anc2.Anc2refChr15 76142 24 + 86568 GCATGAATATGATT-TTTCCTTGTT -s mr.mrrefChr5 114996 25 + 294540 GTAGCATCATAATGGCTTCTTAGTT -s simCow_chr6.simCow.chr6 344571 24 - 602619 GCATGAATACAATA-TATCGTTGTT -s simDog_chr6.simDog.chr6 249103 24 + 593897 ACATGCATGTGATT-TTTCCTTGTT -s simHuman_chr6.simHuman.chr6 340591 24 - 601863 GCATGATTATGATG-TTTCTTTGTT -s simRat_chr6.simRat.chr6 252211 22 + 647215 GTAC---CACAATGGCTTCTTAGTT - -a -s simMouse_chr6.simMouse.chr6 262469 23 + 636262 TCAAAGACATGTGCAATCCACAG -s Anc0.Anc0refChr5 78957 23 + 87904 TCCTGGAAATGTGTAATCTACAG -s Anc1.Anc1refChr7 37942 23 - 47259 TCCTGGAAATGTGTAATCTACAG -s Anc2.Anc2refChr15 76170 23 + 86568 TCCTGGAAATATGTAATCTACAG -s mr.mrrefChr5 115021 23 + 294540 TCAAAGACATGTGCAATCCACAG -s simCow_chr6.simCow.chr6 344599 23 - 602619 TCCTGAAAATACGGAACCTACAG -s simDog_chr6.simDog.chr6 249131 23 + 593897 CCCTAGAAATATGTAATCTATGG -s simHuman_chr6.simHuman.chr6 340619 23 - 601863 TCCTGGAGGTGTGTAATCTACAG -s simRat_chr6.simRat.chr6 252233 23 + 647215 TCAAAGACATGTGCAATCCACAG - -a -s simMouse_chr6.simMouse.chr6 262492 10 + 636262 GAGAAAAGGG -s Anc0.Anc0refChr5 78981 10 + 87904 AAGAAAAGAG -s Anc1.Anc1refChr7 37966 10 - 47259 AAGAAAAGAG -s Anc2.Anc2refChr15 76194 10 + 86568 AAGAAAAAAG -s mr.mrrefChr5 115044 10 + 294540 GAGAAAAGGG -s simCow_chr6.simCow.chr6 344623 10 - 602619 AAGAAAACAA -s simDog_chr6.simDog.chr6 249155 10 + 593897 AAGTGAGAGG -s simHuman_chr6.simHuman.chr6 340643 10 - 601863 AAGAAAAGAG -s simRat_chr6.simRat.chr6 252256 10 + 647215 GGGAAAAGGG - -a -s simMouse_chr6.simMouse.chr6 262502 130 + 636262 TCTAATGTCCTAACAAAGCAGATTGTTGTTTGTAGGTCATTTTTAACTCGACATCCCTTCAGAGACTTTTGAAGCTAAGTTCATCAACTTGGAGACCAGTGCACACCTCAGAGCTGTCCATCATGTAGAC -s Anc0.Anc0refChr5 78997 96 + 87904 TTTACTGTCTTAGCACA-TAG-GTGACCTTTTT-----ATTTTTGACT-------CCTTAAGAGACTTTTGAAGC--------------------CTAGTGCACACCGGAAACCTATCCACCTTATATAT -s Anc1.Anc1refChr7 37982 101 - 47259 TTTACTGTCTTAGCACA-TAG-GTGACCTTTTTAAAAGATTTTTGACT-------CCTTAAGAGACTTTTGAAGC--------------------CTAGTGCACACCGGAAACCTATCCACCTTATATAT -s Anc2.Anc2refChr15 76210 96 + 86568 TTTACTGTCTTAGCACA-TAG-GTGACCTTTTT-----GTATTGCACT-------CCTAAAGAGACTTTTGAAGC--------------------CTAGTGCACACCGGAAACCTATCCACCTTATATAT -s mr.mrrefChr5 115054 129 + 294540 TCTAATGTCCTAACACA-CAGATTGTTGTTTGTAGGTCATTTTTGACTCGACATCCCTTCAGAGACTTTTGAAGCTAAGTTCATCAACTTGGAGACTAGTGCACACCTCAGACCTGTCCATCATATAGAC -s simCow_chr6.simCow.chr6 344639 96 - 602619 TTTACTGTCTTAGCACA-TAG-GTGACCCTTTT-----GTATTACACA-------CCTAAAGAGACTTTTGAAAC--------------------CAAGTGCACACCAGTAACCCATCTACCTTATATAT -s simDog_chr6.simDog.chr6 249171 96 + 593897 TTTACTGTTTTAGCACA-TAG-GTGACCTTTTT-----GTATTGCACT-------CCTAAAGAGACTTTTGAAGC--------------------CTAGTGTGGACTGGAAGCTTATCCACCCCATATAT -s simHuman_chr6.simHuman.chr6 340659 101 - 601863 TTTATTGTCTTAGCACA-TAG-CTGCACTCCTTAAAAGACTTTTGACT-------CCTTAAAAGACTTTTGAATC--------------------CTAGTACACACCCAAAACCTATCCAACTTATATAT -s simRat_chr6.simRat.chr6 252266 129 + 647215 TCTAATGTCCTAACACA-CAGGGGTTCATTTGTAGGTCATTTTTGACTTGATAATACTTTAGAGACTTTGGGGGCCAAGTTTATCAACTTACAGCCTAGTGCACACCTCAGACCTGTTCATCACATAGAC - -a -s simMouse_chr6.simMouse.chr6 262632 8 + 636262 AGTTAGTA -s Anc0.Anc0refChr5 79093 8 + 87904 AAACAGTA -s Anc1.Anc1refChr7 38083 8 - 47259 AAACAGTA -s Anc2.Anc2refChr15 76306 8 + 86568 AAACAGTA -s mr.mrrefChr5 115183 8 + 294540 AGTTAGTA -s simCow_chr6.simCow.chr6 344742 8 - 602619 AAAAATAA -s simDog_chr6.simDog.chr6 249267 8 + 593897 AGTCAGTA -s simHuman_chr6.simHuman.chr6 340760 8 - 601863 AAACAGTA -s simRat_chr6.simRat.chr6 252395 8 + 647215 AGTGAGTA - -a -s simMouse_chr6.simMouse.chr6 262640 2 + 636262 AG -s Anc0.Anc0refChr5 79101 2 + 87904 AA -s Anc1.Anc1refChr7 38091 2 - 47259 AA -s Anc2.Anc2refChr15 76314 2 + 86568 AA -s mr.mrrefChr5 115191 2 + 294540 AA -s simCow_chr6.simCow.chr6 344750 2 - 602619 AA -s simDog_chr6.simDog.chr6 249275 2 + 593897 AA -s simHuman_chr6.simHuman.chr6 340768 2 - 601863 AA -s simRat_chr6.simRat.chr6 252404 2 + 647215 AA - -a -s simMouse_chr6.simMouse.chr6 262642 7 + 636262 ATGTTAT -s Anc0.Anc0refChr5 79103 7 + 87904 ATATTAT -s Anc1.Anc1refChr7 38093 7 - 47259 ATATTAT -s Anc2.Anc2refChr15 76316 7 + 86568 ATATTAT -s mr.mrrefChr5 115193 7 + 294540 ATATTAT -s simCow_chr6.simCow.chr6 344752 7 - 602619 ATATTAC -s simDog_chr6.simDog.chr6 249278 7 + 593897 GGATTGT -s simHuman_chr6.simHuman.chr6 340770 7 - 601863 ATATTAT -s simRat_chr6.simRat.chr6 252406 7 + 647215 GTATTAT - -a -s simMouse_chr6.simMouse.chr6 262649 7 + 636262 GTTAAAG -s Anc0.Anc0refChr5 79111 7 + 87904 GTTAAAA -s Anc1.Anc1refChr7 38101 7 - 47259 GTTAAAA -s Anc2.Anc2refChr15 76330 7 + 86568 GCTACAA -s mr.mrrefChr5 115200 7 + 294540 GTTAAAG -s simCow_chr6.simCow.chr6 344766 7 - 602619 GCTACAG -s simDog_chr6.simDog.chr6 249292 7 + 593897 GCTACAA -s simHuman_chr6.simHuman.chr6 340778 7 - 601863 GTTAAAA -s simRat_chr6.simRat.chr6 252413 7 + 647215 GTTAAAG - -a -s simMouse_chr6.simMouse.chr6 262656 47 + 636262 CAGGGTAACACAATTGTCGTGGGAACTGACCAAAATCCAGGGTGATG -s Anc0.Anc0refChr5 79132 47 + 87904 CAGGGTAATGGAGTTGCCTTGGGGATTGACCAAAAGTCAGGTTAATG -s Anc1.Anc1refChr7 38122 47 - 47259 CAGGGTAATGGAGTTGCCTTGGGGATTGACCAAAAGTCAGGTTAATG -s Anc2.Anc2refChr15 76351 47 + 86568 CAGGGTAATGGAGTTGCCTCAGGGATTGACCAAAAGTCAGGTTAATG -s mr.mrrefChr5 115207 47 + 294540 CAGGGTAACACAATTGTCGTGGGAACTGACCAAAAGTCAGGGTGATG -s simCow_chr6.simCow.chr6 344809 47 - 602619 CAGGGTAATGGAGTAGCCTCAGAGATTGACTGAAGGTCAGGTAGACG -s simDog_chr6.simDog.chr6 249313 45 + 593897 CAGACTAATGGAGTTGTC--AGGGATGGATCAAAAGTCAGGTTAATG -s simHuman_chr6.simHuman.chr6 340799 47 - 601863 CATGGTAATGGAGTTGCCTTGGGGATTAACCAAATGTCAGGTTAATG -s simRat_chr6.simRat.chr6 252420 47 + 647215 CAGGGTAACACAATTGTCATGGGAAATGACCAAAAGTCAGGGCGATG - -a -s simMouse_chr6.simMouse.chr6 262703 79 + 636262 AGGGTTCAGCGAGTTATCCAAGAGGCTAAATCTTTGCAGTGGATTCTCCCATCTTAGTATTCTTAAGAAATTGCACCCT -s Anc0.Anc0refChr5 79179 79 + 87904 AGGGTTCCACCAGTTGTCAAAGGAGCTAAATCTTTGCAGCTGATTCTCATGTTCCAGCATTCTTAGGAAGATGCACCCT -s Anc1.Anc1refChr7 38169 79 - 47259 AGGGTTCCACCAGTTGTCAAAGGAGCTAAATCTTTGCAGCTGATTCTCATGTTCCAGCATTCTTAGGAAGATGCACCCT -s Anc2.Anc2refChr15 76398 79 + 86568 AGGGTTCCATCAGTTGTCAAAGGAGCTAAATCTTTGCAGCTGATTCTCATGTTCCAGCATTCCTAGGGAGATGCACCCT -s mr.mrrefChr5 115254 79 + 294540 AGGGTTCAGCCAGTTATCCAAGAGGCTAAATCTTTGCAGTGGATTCTCCCATTTTAGTATTCTTAGGAAGTTGCACCCT -s simCow_chr6.simCow.chr6 344856 79 - 602619 AGGGTTCTGTCAGTTGTCCAGGGAGCTAACTCTTTGCAGCTGTTTACTATGTTCCTGCACTCCTAGGGAAATGCATCCT -s simDog_chr6.simDog.chr6 249359 72 + 593897 GGGGTCCCATGAGTTGTCAAAGGAGCTAAATCTTGGCAGCTGATTCTCATGTTCCAGCATT-------AGATGCACCCT -s simHuman_chr6.simHuman.chr6 340846 63 - 601863 AGGCCTCCACCAGTTGTTAAAGGAGCTAAATCCTT----------------TTCCAGCATCCTCAGGAAGGCGCAGCCC -s simRat_chr6.simRat.chr6 252467 79 + 647215 AGGGTTCTGCCAGTTATCCAAGCGGCTAATTCTTTGCAGCTGTTTCTCATATTTTACTACTCTTAGGAGGATGCACCCT - -a -s simMouse_chr6.simMouse.chr6 262782 5 + 636262 AGTGT -s Anc0.Anc0refChr5 79258 5 + 87904 AATGT -s Anc1.Anc1refChr7 38248 5 - 47259 AATGT -s Anc2.Anc2refChr15 76484 5 + 86568 AATGT -s mr.mrrefChr5 115333 5 + 294540 AATGT -s simCow_chr6.simCow.chr6 344942 5 - 602619 AATGT -s simDog_chr6.simDog.chr6 249438 5 + 593897 AATGT -s simHuman_chr6.simHuman.chr6 340909 5 - 601863 AATGT -s simRat_chr6.simRat.chr6 252546 5 + 647215 AAAGT - -a -s simMouse_chr6.simMouse.chr6 262787 9 + 636262 TACACCAGA -s Anc0.Anc0refChr5 79278 9 + 87904 TATACAAAA -s Anc1.Anc1refChr7 38268 9 - 47259 TATACAAAA -s Anc2.Anc2refChr15 76504 9 + 86568 AATATAAAA -s mr.mrrefChr5 115338 9 + 294540 TATACCAAA -s simDog_chr6.simDog.chr6 249450 9 + 593897 AATATAAAA -s simHuman_chr6.simHuman.chr6 340929 9 - 601863 TATGCAAAA -s simRat_chr6.simRat.chr6 252551 9 + 647215 TATACTAAA - -a -s simMouse_chr6.simMouse.chr6 262796 3 + 636262 GGG -s Anc0.Anc0refChr5 79288 3 + 87904 GGG -s Anc1.Anc1refChr7 38278 3 - 47259 GGG -s Anc2.Anc2refChr15 76514 3 + 86568 GGG -s mr.mrrefChr5 115347 3 + 294540 GGG -s simDog_chr6.simDog.chr6 249460 3 + 593897 GGG -s simHuman_chr6.simHuman.chr6 340939 3 - 601863 GGG -s simRat_chr6.simRat.chr6 252560 3 + 647215 GAA - -a -s simMouse_chr6.simMouse.chr6 262799 1 + 636262 C -s Anc0.Anc0refChr5 79291 1 + 87904 A -s Anc1.Anc1refChr7 38281 1 - 47259 A -s Anc2.Anc2refChr15 76517 1 + 86568 A -s mr.mrrefChr5 115350 1 + 294540 C -s simDog_chr6.simDog.chr6 249464 1 + 593897 A -s simHuman_chr6.simHuman.chr6 340942 1 - 601863 A -s simRat_chr6.simRat.chr6 252563 1 + 647215 C - -a -s simMouse_chr6.simMouse.chr6 262800 5 + 636262 CAACA -s Anc0.Anc0refChr5 79294 5 + 87904 TAACA -s Anc1.Anc1refChr7 38284 5 - 47259 TAACA -s Anc2.Anc2refChr15 76520 5 + 86568 GGACA -s mr.mrrefChr5 115351 5 + 294540 TAACA -s simCow_chr6.simCow.chr6 258193 2 + 602619 ---AA -s simDog_chr6.simDog.chr6 249467 5 + 593897 GGACA -s simHuman_chr6.simHuman.chr6 340945 5 - 601863 TAACA -s simRat_chr6.simRat.chr6 252564 5 + 647215 TATCA - -a -s simMouse_chr6.simMouse.chr6 262805 7 + 636262 CATGCAG -s Anc0.Anc0refChr5 79299 7 + 87904 TGCATTG -s Anc1.Anc1refChr7 38289 7 - 47259 TGCATTG -s Anc2.Anc2refChr15 76525 7 + 86568 TGCATTG -s mr.mrrefChr5 115356 7 + 294540 CATGCAG -s simCow_chr6.simCow.chr6 258195 7 + 602619 TGTAGAT -s simDog_chr6.simDog.chr6 249485 7 + 593897 TGCATTG -s simHuman_chr6.simHuman.chr6 340950 7 - 601863 TGCATTG -s simRat_chr6.simRat.chr6 252569 7 + 647215 CATGCAG - -a -s simMouse_chr6.simMouse.chr6 262812 11 + 636262 CTCAGGTAAAA -s Anc0.Anc0refChr5 79308 11 + 87904 CTCAAGTGAAA -s Anc1.Anc1refChr7 38298 11 - 47259 CTCAAGTGAAA -s Anc2.Anc2refChr15 76534 11 + 86568 CTCAAGTGAAA -s mr.mrrefChr5 115365 11 + 294540 CTCAGGTAAAA -s simCow_chr6.simCow.chr6 258204 11 + 602619 GTCAAGTGAAA -s simDog_chr6.simDog.chr6 249494 11 + 593897 CTCAAGTGCAA -s simHuman_chr6.simHuman.chr6 340959 11 - 601863 CTCAAGTGAAA -s simRat_chr6.simRat.chr6 252578 5 + 647215 CTCA------A - -a -s simMouse_chr6.simMouse.chr6 262823 14 + 636262 GAACCATCGGTACT -s Anc0.Anc0refChr5 79327 14 + 87904 AAATCATGGGTACT -s Anc1.Anc1refChr7 38317 14 - 47259 AAATCATGGGTACT -s Anc2.Anc2refChr15 76553 14 + 86568 AAATTATGGGTACT -s mr.mrrefChr5 115376 14 + 294540 GAACCATGGGTACT -s simCow_chr6.simCow.chr6 258223 14 + 602619 AGATTATTGGAACT -s simDog_chr6.simDog.chr6 249513 14 + 593897 AAATTATGGGTTCT -s simHuman_chr6.simHuman.chr6 340978 14 - 601863 AAATCAAGGCTACT -s simRat_chr6.simRat.chr6 252583 14 + 647215 GAACGATGGGTACT - -a -s simMouse_chr6.simMouse.chr6 262837 13 + 636262 CCGTTGTGAGCAC -s Anc0.Anc0refChr5 79341 13 + 87904 CTTTTGTAAGCAT -s Anc1.Anc1refChr7 38331 13 - 47259 CTTTTGTAAGCAT -s Anc2.Anc2refChr15 76567 13 + 86568 TCTTTGTAAGCAT -s mr.mrrefChr5 115390 13 + 294540 CTGTTGTGAGCAC -s simCow_chr6.simCow.chr6 258241 13 + 602619 TCTTTGCAGGCAT -s simDog_chr6.simDog.chr6 249527 13 + 593897 TCTTTGTAAGCAT -s simHuman_chr6.simHuman.chr6 340992 13 - 601863 CTTTTGTAAACAT -s simRat_chr6.simRat.chr6 252597 13 + 647215 CTGTTGTGAGCAC - -a -s simMouse_chr6.simMouse.chr6 262850 8 + 636262 AAGGGAGA -s Anc0.Anc0refChr5 79354 8 + 87904 GAGGGAAA -s Anc1.Anc1refChr7 38344 8 - 47259 GAGGGAAA -s Anc2.Anc2refChr15 76580 8 + 86568 GAGAGAAA -s mr.mrrefChr5 115403 8 + 294540 AAGGGAGA -s simCow_chr6.simCow.chr6 258256 8 + 602619 GAGAGAAA -s simHuman_chr6.simHuman.chr6 341005 8 - 601863 TAGGGACA -s simRat_chr6.simRat.chr6 252610 8 + 647215 AAGGGGGA - -a -s simMouse_chr6.simMouse.chr6 262858 17 + 636262 GCAACTAACTGGCTTGG -s Anc0.Anc0refChr5 79370 17 + 87904 GCCAGTAATTGGCCAGG -s Anc1.Anc1refChr7 38360 17 - 47259 GCCAGTAATTGGCCAGG -s Anc2.Anc2refChr15 76596 17 + 86568 GCCAGTGATTGGCCAGG -s mr.mrrefChr5 115411 17 + 294540 GCAACTAACTGGCTTGG -s simCow_chr6.simCow.chr6 258272 17 + 602619 CCCAGTGAATGGCCAGG -s simDog_chr6.simDog.chr6 249853 17 + 593897 GGGTATGATTGGCCAGG -s simHuman_chr6.simHuman.chr6 341021 17 - 601863 GCCAGTAATTGGCCAGG -s simRat_chr6.simRat.chr6 252618 17 + 647215 GTGAATAACGGGCTGGG - -a -s simMouse_chr6.simMouse.chr6 262875 4 + 636262 TTTT -s Anc0.Anc0refChr5 79388 4 + 87904 TCTT -s Anc1.Anc1refChr7 38378 4 - 47259 TCTT -s Anc2.Anc2refChr15 76614 4 + 86568 TCTT -s mr.mrrefChr5 115429 4 + 294540 TTTT -s simCow_chr6.simCow.chr6 258290 4 + 602619 TTTT -s simDog_chr6.simDog.chr6 249871 4 + 593897 TCTT -s simHuman_chr6.simHuman.chr6 341039 4 - 601863 TCTT -s simRat_chr6.simRat.chr6 252636 4 + 647215 TTCT - -a -s simMouse_chr6.simMouse.chr6 262879 15 + 636262 AGCAGGATATTAAAA -s Anc0.Anc0refChr5 79392 15 + 87904 AGTAAGAGATTACAA -s Anc1.Anc1refChr7 38382 15 - 47259 AGTAAGAGATTACAA -s Anc2.Anc2refChr15 76618 15 + 86568 AGTAAGAGATTACAA -s mr.mrrefChr5 115433 15 + 294540 AGCAGGATATTAAAA -s simCow_chr6.simCow.chr6 258294 14 + 602619 AGTAGGAG-TTACAA -s simDog_chr6.simDog.chr6 249875 15 + 593897 AGGCAGTGATTACAA -s simHuman_chr6.simHuman.chr6 341044 15 - 601863 AGTAAGAGATTACAA -s simRat_chr6.simRat.chr6 252640 14 + 647215 AGCAGGATATTAAG- - -a -s simMouse_chr6.simMouse.chr6 262894 22 + 636262 CCTTAGAGGAATAGCTCATAGC -s Anc0.Anc0refChr5 79436 22 + 87904 CCTTAGGGTTGTGGCTCATATC -s Anc1.Anc1refChr7 38426 22 - 47259 CCTTAGGGTTGTGGCTCATATC -s Anc2.Anc2refChr15 76662 22 + 86568 CCTTAAGGTTGTGGGTCACATC -s mr.mrrefChr5 115448 22 + 294540 CCTTAGAGTAATAGCTCATAGC -s simCow_chr6.simCow.chr6 258337 20 + 602619 CCTCAAGGTTATGGAT--CAGC -s simDog_chr6.simDog.chr6 249919 22 + 593897 CCATAAGGGTGTGGGCCACATC -s simHuman_chr6.simHuman.chr6 341088 22 - 601863 CCTTAGGGTTGAGGCTCATAAT -s simRat_chr6.simRat.chr6 252654 22 + 647215 CCTTGGAGTACTACTTCATAGC - -a -s simMouse_chr6.simMouse.chr6 262916 110 + 636262 AGAGATGAGTGACTATCATGTTCCAGAATATGAATCCAACTGGCATATCATCCCAGCACAAGGGTCAGGATAAATGAAGGCACCCTGTACTATTCATTGCAAACACCCCC -s Anc0.Anc0refChr5 79459 109 + 87904 AGGGATCAGTGACTATCTTGTTTCAGAGTATGAATCCAACAGGCATCTTATCCCAGC-CAAGGGTAAGTTTCTACGAAAGCACCCTGTGCCTTTCATTGCAAACATACCC -s Anc1.Anc1refChr7 38449 110 - 47259 AGGGATCAGTGACTATCTTGTTTCAGAGTATGAATCCAACAGGCATCTTATCCCAGCACAAGGGTAAGTTTCTACGAAAGCACCCTGTGCCTTTCATTGCAAACATACCC -s Anc2.Anc2refChr15 76685 109 + 86568 AGGGATCAGTGAATATCTTGTTTCAGAGTATGAATCCAACAGGCATCTTATCCCAGC-CAAGGATAAGTTTCTACAAAATCACCCTGTGCCTTTCATTGCAAACATACCC -s mr.mrrefChr5 115470 110 + 294540 AGAGATCAGTGACTATCATGTTTCAGAATATGAATCCAACAGGCATATCATCCCAGCACAAGGGTCAGGATAAATGAAGGCACCCTGTGCTTTTCATTGCAAACACACCC -s simCow_chr6.simCow.chr6 258358 103 + 602619 AGGGGTCAGTGATTATCTTATTT-AAGGTATGAGTGCAACAGGCATCT-----CAGT-CAAGGATAAATTTCTACAAAATCACTCTGTACCTTTCACTGCAAATATACCC -s simDog_chr6.simDog.chr6 249942 109 + 593897 AAGGATCAGTGCATATTGTGATTCAGAATATGAATCCAATAGGCATATTATCCCAGC-CAAGGATAAGTTTCCACAAACTCACCAAGCGATTTTCATTGCAAACACACCC -s simHuman_chr6.simHuman.chr6 341111 110 - 601863 GGGGAGCAGTGACTAACTTCTTTCAGAGTATGGATCCAACAGGCATCTGCTGCCAGCAAAAGGGTAAGTTTCTACGAAAGCGCCCTGTGCCTTTCAGTGAAAACATACCC -s simRat_chr6.simRat.chr6 252676 107 + 647215 AGAGATCAGTGACTATCGTGTTTCAGAATATGAAACCAACAGGCATATCATCCCAGCAGAAGGGATAGGAGAAATGAAGGCATCCTGTGCTTTTC---GCAAACACACCC - -a -s simMouse_chr6.simMouse.chr6 263026 2 + 636262 TT -s Anc0.Anc0refChr5 79568 2 + 87904 TG -s Anc1.Anc1refChr7 38559 2 - 47259 TG -s Anc2.Anc2refChr15 76794 2 + 86568 TG -s mr.mrrefChr5 115580 2 + 294540 TT -s simCow_chr6.simCow.chr6 258461 2 + 602619 TG -s simDog_chr6.simDog.chr6 250053 2 + 593897 TA -s simHuman_chr6.simHuman.chr6 341221 2 - 601863 TG -s simRat_chr6.simRat.chr6 252783 2 + 647215 TT - -a -s simMouse_chr6.simMouse.chr6 263028 39 + 636262 CTTTGTATTGACACTTAGTTGGGAGAAGAAAAGTAATTT -s Anc0.Anc0refChr5 79594 34 + 87904 CTTTGCATTGATGCTCAGTTATGA-----AAAGAGATAT -s Anc1.Anc1refChr7 38585 34 - 47259 CTTTGCATTGATGCTCAGTTATGA-----AAAGAGATAT -s Anc2.Anc2refChr15 76820 34 + 86568 CTTTGCATTGATGCTCAGTTATGA-----AAAGAGATAT -s mr.mrrefChr5 115606 34 + 294540 CTTTGTATTGACACTTAGTTGTGA-----AAAGTAATTT -s simCow_chr6.simCow.chr6 258486 34 + 602619 GTTAGCATTGAAGTTTAGTTATGA-----AAAGAGTCAT -s simDog_chr6.simDog.chr6 250079 34 + 593897 CTTTGCCTTTATGCTCAGTTATGA-----AAGGGAATAT -s simHuman_chr6.simHuman.chr6 341247 33 - 601863 ATTTGCATTGATGCTCAA-TATGA-----AAAGAGATAT -s simRat_chr6.simRat.chr6 252809 34 + 647215 CTTCGTATTGACACTAAGTTGTAA-----AAAATCATTT - -a -s simMouse_chr6.simMouse.chr6 263067 13 + 636262 AGAAATTCACCAG -s Anc0.Anc0refChr5 79628 13 + 87904 AGAAATTCACCCG -s Anc1.Anc1refChr7 38619 13 - 47259 AGAAATTCACCCG -s Anc2.Anc2refChr15 76854 13 + 86568 AGACATTCACCCG -s mr.mrrefChr5 115640 13 + 294540 AGAAATTCACCAG -s simCow_chr6.simCow.chr6 258525 13 + 602619 AAATATTCACCAG -s simDog_chr6.simDog.chr6 250113 13 + 593897 AGACATTCACCCG -s simHuman_chr6.simHuman.chr6 341280 4 - 601863 AGAA--------- -s simRat_chr6.simRat.chr6 252843 13 + 647215 AGGAATTCACCAA - -a -s simMouse_chr6.simMouse.chr6 263080 46 + 636262 GAGCTATTCACTCTGTCAATAGGGTGATTAGGTTCACACAATTTAT -s Anc0.Anc0refChr5 79653 46 + 87904 GGGTTACTCAACCTGTCAATAGGATGATTAGGTTCATCCCAATTAT -s Anc1.Anc1refChr7 38644 46 - 47259 GGGTTACTCAACCTGTCAATAGGATGATTAGGTTCATCCCAATTAT -s Anc2.Anc2refChr15 76882 46 + 86568 GGGTAACTCAACCTGTCATGAGGGTGATTAGGTTCATCCCAATTTT -s mr.mrrefChr5 115653 46 + 294540 GAGCTATTCACTCTGTCAATAGGATGATTAGGTTCACACAATTTAT -s simCow_chr6.simCow.chr6 258553 46 + 602619 GTGTAACTCAACCTGTCAGGAGGGTGATTTGGTTCGTCCCAATTTT -s simDog_chr6.simDog.chr6 250141 46 + 593897 GGGTAACTCAACCTGTCATGAGGGTGATTAGGTTCATCCCAATTTT -s simHuman_chr6.simHuman.chr6 341296 45 - 601863 GGGTTACTCAACCTGTAAATA-GACAATTAGATGCATCCCAATTAT -s simRat_chr6.simRat.chr6 252856 46 + 647215 GAGCTATTCTCTCTGTCGCTAGGATTATTAGGTTCACACGATTTAT - -a -s simMouse_chr6.simMouse.chr6 263126 33 + 636262 TTTAATGTAGCTTGATTATGCCGGGAACATCAG -s Anc0.Anc0refChr5 79704 30 + 87904 TATAATGTAGCATTATGATGTTTGGGACAT--- -s Anc1.Anc1refChr7 38695 30 - 47259 TATAATGTAGCATTATGATGTTTGGGACAT--- -s Anc2.Anc2refChr15 76933 30 + 86568 TATAATGTAGCATTATGGTGTTTGGGACAT--- -s mr.mrrefChr5 115699 33 + 294540 TTTAATGTAGCTTGATTATGCCGGGAACATCAG -s simCow_chr6.simCow.chr6 258604 30 + 602619 TATAATGTAGCATTATGGTGTTTGGGACAT--- -s simHuman_chr6.simHuman.chr6 341346 30 - 601863 TATAATGTCGCATAATCATGTTTGGTACAT--- -s simRat_chr6.simRat.chr6 252902 33 + 647215 TTTAATGTAGATTGATTATGCCGGGAACATTAG - -a -s simMouse_chr6.simMouse.chr6 263159 7 + 636262 GTTTCAA -s Anc0.Anc0refChr5 79734 7 + 87904 ATCTAAA -s Anc1.Anc1refChr7 38725 7 - 47259 ATCTAAA -s Anc2.Anc2refChr15 76963 7 + 86568 AGCTAAA -s mr.mrrefChr5 115732 7 + 294540 GTTTCAA -s simCow_chr6.simCow.chr6 258642 7 + 602619 AGCTAAA -s simHuman_chr6.simHuman.chr6 341376 7 - 601863 ATCTAAA -s simRat_chr6.simRat.chr6 252935 7 + 647215 GTTTCAA - -a -s simMouse_chr6.simMouse.chr6 263166 27 + 636262 AGTATGCCCACACTAACTAAGCTTTTA -s Anc0.Anc0refChr5 79741 26 + 87904 TTTATGGTGCCA-TAACCAGGTGTTAA -s Anc1.Anc1refChr7 38732 27 - 47259 TTTATGGTGCCATTAACCAGGTGTTAA -s Anc2.Anc2refChr15 76970 26 + 86568 TTCATGGTGCCA-TGTCCAGGTGATAA -s mr.mrrefChr5 115739 27 + 294540 TGTATGCCCACACTAACTAAGCTTTTA -s simCow_chr6.simCow.chr6 258649 26 + 602619 TTCATGGTGCCA-TGTCCAGGTGATAA -s simHuman_chr6.simHuman.chr6 341383 27 - 601863 TTTATGGTGCCATTAACCAGGTGTTAA -s simRat_chr6.simRat.chr6 252943 27 + 647215 TGTACGCCCACACTAACTAAGGTATTG - -a -s simMouse_chr6.simMouse.chr6 263193 5 + 636262 AAGCT -s Anc0.Anc0refChr5 79767 5 + 87904 GAGCT -s Anc1.Anc1refChr7 38759 5 - 47259 GAGCT -s Anc2.Anc2refChr15 76996 5 + 86568 GAGCT -s mr.mrrefChr5 115766 5 + 294540 GAGCT -s simCow_chr6.simCow.chr6 259227 5 + 602619 GAGCT -s simHuman_chr6.simHuman.chr6 341410 5 - 601863 GAGCT -s simRat_chr6.simRat.chr6 252970 5 + 647215 GACCT - -a -s simMouse_chr6.simMouse.chr6 263198 100 + 636262 AAGCATCCTCACTCACGCAAAATGGCTTGAGGAAATGGTTGAGCAGGGTAGGCCCACCATCAATATTGAGTTGATTTGAACTGGTGTGCTTCATGCCACT -s Anc0.Anc0refChr5 79772 5 + 87904 AAG--------CT--------------------------------------------------------------------------------------- -s Anc1.Anc1refChr7 38764 13 - 47259 AAGAAAAACCACT--------------------------------------------------------------------------------------- -s Anc2.Anc2refChr15 77001 5 + 86568 AAT--------CT--------------------------------------------------------------------------------------- -s mr.mrrefChr5 115771 99 + 294540 AAGCATCCTCACTCACGCAAAATGGCTTGAGGAAATGGTTGAGCAGGGTAGGCCCACCATCAATATTGAGTTGATTTGAACT-GTGTGCTTCATGCCACT -s simCow_chr6.simCow.chr6 259232 5 + 602619 AAT--------CT--------------------------------------------------------------------------------------- -s simHuman_chr6.simHuman.chr6 341416 13 - 601863 AAGAAAAACCACT--------------------------------------------------------------------------------------- -s simRat_chr6.simRat.chr6 252975 99 + 647215 AAGCATCCTCATTCAGGCAAAATGGCTTGAAGAGATGGTTGGGCAGGGTAGACCCGCCGTCAATATTGAGTTGATTTCAACT-GTGTGCTTCATGCCACT - -a -s simMouse_chr6.simMouse.chr6 263298 139 + 636262 CCAAGGCCCAAAATACAAGGGATTTTAGTTAAGGTGGCATTTGGTATTCAACAAAGAAAGAATTAAGCTTTTATGTGCAGCTTAATATGACGTGTGGAGTGATTTATAGAGTACATTTCCTTAGAACATCTTCACATAG -s mr.mrrefChr5 115870 136 + 294540 CCAAGGCCCAAAATACAAGGGATTTTAGTTAA---GGCATTTGGTATTCAACAAAGAAAGAATTAAGCTTTTATGTGCAGCTTAATATGACGTGTGGAGTGATTTATAGAGTACATTTCCTTAGAACATCTTCACATAG -s simRat_chr6.simRat.chr6 253075 136 + 647215 CCAAGGCCCAAATTATAAGGGATTTTAGTGAA---GGCATTTGGTATTCAATAAAGAAGGAAGTAAGCTTTGATGTACAGTTAAATATGGTATATCAAGTGGTTTATAGAGTACATTTTCCTAGAACATCTTGATATAG - -a -s simMouse_chr6.simMouse.chr6 263437 162 + 636262 TATTTCAATGAACACGAGGAATAGGTAGAATGCCTAAGAAATGGAGTTTTCACAGGATAAAGGTGATAATAGAATTACTGGAGATTACACCCCAGATAACTTTGGCACTGATTCACTAGTCAATAGTACCAACATGTAAGGCAGCTGATCACCTGTCAGCTC -s Anc0.Anc0refChr5 79777 40 + 87904 --------------------------------------------------------------------------------------------------------------------------ACAGTCTCAACATACAATGCACCTGGGAACCAGACTGCTC -s Anc1.Anc1refChr7 38777 40 - 47259 --------------------------------------------------------------------------------------------------------------------------ACAGTCTCAACATACAATGCACCTGGGAACCAGACTGCTC -s Anc2.Anc2refChr15 77006 40 + 86568 --------------------------------------------------------------------------------------------------------------------------GCAATCTTAGCATAAGATGCACCTGGGAACCAGACTTCTC -s mr.mrrefChr5 116006 162 + 294540 TATTTCAATGAACACGAGGAATAGGTAGAATGCCTAAGAAATGGAGTTTTCACAGGATAAAGGTGATAATAGAATTACTGGAGATTACACCCCAGATAACTTTGGCACTGATTCACTAGTCAATAGTATCAACATGCAAGGCAGCTGATCACCAGTCAGCTC -s simCow_chr6.simCow.chr6 259237 40 + 602619 --------------------------------------------------------------------------------------------------------------------------GCAATCTTAGCATAAGATGCACCTGGGAACCAGACTTCTC -s simHuman_chr6.simHuman.chr6 341429 40 - 601863 --------------------------------------------------------------------------------------------------------------------------ACAGTGTCAATATACAATGCACCTGGGGACCAGGCTGCTC -s simRat_chr6.simRat.chr6 253219 162 + 647215 TATTACAATTAGCATGAGGAATAGGTAGAATGCCCAAAAAATGAAGATTCCACAGGATAAAGGTGATAGTGGAATTATCGGAGATTACACCCCAGATAACTTTGGCACTGATTCACTAGTCAACAGTATCAACATGCAAGGCAACTGATCACCAGTCAGCTC - -a -s simMouse_chr6.simMouse.chr6 263599 49 + 636262 AGGTTTGGGGATTCTGACTCCATTCCCTGAAGTAATTACAACAGGGTAT -s Anc0.Anc0refChr5 79817 48 + 87904 ATATTTAGTCATC-TGCCTCTATACCCTGAGTTTATTACAGCAAGGTAG -s Anc1.Anc1refChr7 38817 48 - 47259 ATATTTAGTCATC-TGCCTCTATACCCTGAGTTTATTACAGCAAGGTAG -s Anc2.Anc2refChr15 77046 48 + 86568 ATATTTAGTCATC-TGCCTCTATCCTCTGAGTTTATTACAGCAAGTTAG -s mr.mrrefChr5 116168 48 + 294540 AGGTTTGGGCATT-TGACTCCATACCCTGAAGTAATTACAACAGGGTAT -s simCow_chr6.simCow.chr6 259278 36 + 602619 AAATTTAGTCATC-TGCCT------------GTTATTAGAGTGGGCTAG -s simDog_chr6.simDog.chr6 250187 47 + 593897 -TATTGGGACATC-TGCCTCTATCCTCTGAGTCTATCACAGCAAGTTGG -s simHuman_chr6.simHuman.chr6 341469 48 - 601863 ATATTTAGTCATC-TGCCTCAATACCCTGGGATTGTTACATCAAGGTAG -s simRat_chr6.simRat.chr6 253381 48 + 647215 AGGTCTGGGCATT-TAACTGTACACCCTGAAGTAATTACAGCAGGGTGA - -a -s simMouse_chr6.simMouse.chr6 263648 4 + 636262 TCCT -s Anc0.Anc0refChr5 79865 4 + 87904 TCCT -s Anc1.Anc1refChr7 38865 4 - 47259 TCCT -s Anc2.Anc2refChr15 77094 4 + 86568 TCCT -s mr.mrrefChr5 116216 4 + 294540 TCCT -s simCow_chr6.simCow.chr6 259314 4 + 602619 TTCT -s simDog_chr6.simDog.chr6 250235 4 + 593897 TCCT -s simHuman_chr6.simHuman.chr6 341517 4 - 601863 CCTT -s simRat_chr6.simRat.chr6 253429 4 + 647215 TCCT - -a -s simMouse_chr6.simMouse.chr6 263652 40 + 636262 GATGCTAGCATTGGGGGAGTAGGAGGCGCTAGGGAGAATG -s Anc0.Anc0refChr5 79878 40 + 87904 GGTACAAGCATTGTGGAAATAGTAGTCTCCAGAGACAATG -s Anc1.Anc1refChr7 38878 40 - 47259 GGTACAAGCATTGTGGAAATAGTAGTCTCCAGAGACAATG -s Anc2.Anc2refChr15 77107 40 + 86568 GGTACAAGCATTGTGGAAATATGACTCTCCAGAGACACTG -s mr.mrrefChr5 116229 40 + 294540 GATACTAGCATTGGGGAAGTAGTAGGCGCTAGGGAGAATG -s simCow_chr6.simCow.chr6 259327 39 + 602619 GGTACAAGCATCAGGGAAGTATAACTCCCCAGA-ACACTG -s simDog_chr6.simDog.chr6 250251 40 + 593897 GGTACAAGCATTGTGACAATATGACCCTCCAGAGGCACTG -s simHuman_chr6.simHuman.chr6 341530 40 - 601863 GGTACAAGCATTGTGGAATTGGTAGTCTCCAGTGACAATG -s simRat_chr6.simRat.chr6 253442 31 + 647215 GATACTGGCATTGGGTAAGTAGTAGG---------GAATG - -a -s simMouse_chr6.simMouse.chr6 263692 27 + 636262 TAGTGGTAATAAGTTCATGTAGATGCA -s Anc0.Anc0refChr5 79919 27 + 87904 TAGAAGCACTAACTTCATGTTGACACA -s Anc1.Anc1refChr7 38919 27 - 47259 TAGAAGCACTAACTTCATGTTGACACA -s Anc2.Anc2refChr15 77148 27 + 86568 TGAAAGCACTAACTTCATGTTGACACA -s mr.mrrefChr5 116269 27 + 294540 TAGTGGTAATAACTTCATGTAGATGCA -s simCow_chr6.simCow.chr6 259367 27 + 602619 TGAATACACTAACTTCAGGTAGATGCA -s simDog_chr6.simDog.chr6 250292 27 + 593897 TGAAAGCACTAACTTCATGTTGACACA -s simHuman_chr6.simHuman.chr6 341571 22 - 601863 TAGCAGCATTAACTTCATGT-----CA -s simRat_chr6.simRat.chr6 253473 20 + 647215 TA-------TAACTTCATGTAGGTGCA - -a -s simMouse_chr6.simMouse.chr6 263719 107 + 636262 ATCTTTGAACAAGACAAACCCTGTTAGGAGATTGCAGGGAGATGGCCTGATTGCAGGGAAATGGCCCACATCACTCTGAGTCTGCACCTGCACATATGCTTAAGCCT -s Anc0.Anc0refChr5 79946 56 + 87904 ATCTTTTAACAAAACAACACATGTCAGC-------------------TGAG-------------------------------TGAACCT-CATATGTGCTTAAGCCG -s Anc1.Anc1refChr7 38946 57 - 47259 ATCTTTTAACAAAACAACACATGTCAGC-------------------TGAG-------------------------------TGAACCTGCATATGTGCTTAAGCCG -s Anc2.Anc2refChr15 77175 56 + 86568 ATTTTTTAACAAAACAACACATGACAGC-------------------TGAG-------------------------------TGAACCC-CATATGTGCTTAAGCCG -s mr.mrrefChr5 116296 88 + 294540 ATCTTTGAACAAAACAAACCCTGTCAGG-------------------TGAGTGCAGGGAAATGGCCCACATCACTCTGAGTCTGCACCTGCACATGTGCTTAAGCCT -s simCow_chr6.simCow.chr6 259394 56 + 602619 ATTATATAAAAAAACTACACATGACAGC-------------------TAAA-------------------------------TGACCCC-TATATGGACTTTAGCCA -s simDog_chr6.simDog.chr6 250319 56 + 593897 ATTTTTTAACAAAACAACACATGACAGC-------------------TGAG-------------------------------TGAACCC-CATATTTGCTTAAACCG -s simHuman_chr6.simHuman.chr6 341593 57 - 601863 TTCGTTTACCAGAACAACACATGTCAGC-------------------CGAG-------------------------------TGAGCCTGCATATGTGCTTAAGCCC -s simRat_chr6.simRat.chr6 253495 88 + 647215 ATCTACGAACCAAACAAACCCTGTCAGG-------------------TGAGTGCAGGGGGATGGCCCACATCACTCTGAATCTGCATCTGCACATGTGCTTAAGCCT - -a -s simMouse_chr6.simMouse.chr6 263826 10 + 636262 AAGCTAACAC -s Anc0.Anc0refChr5 80004 10 + 87904 TAATTAACAC -s Anc1.Anc1refChr7 39005 10 - 47259 TAATTAACAC -s Anc2.Anc2refChr15 77233 10 + 86568 TAATTAACAC -s mr.mrrefChr5 116386 10 + 294540 AAGCTAACAC -s simCow_chr6.simCow.chr6 259452 10 + 602619 GAATTAACAC -s simDog_chr6.simDog.chr6 250377 10 + 593897 TAATTAACAC -s simRat_chr6.simRat.chr6 253585 10 + 647215 GAGCTAACAC - -a -s simMouse_chr6.simMouse.chr6 263836 14 + 636262 CCAAACGAGCCTGT -s Anc0.Anc0refChr5 80014 8 + 87904 T------AGGCTAA -s Anc1.Anc1refChr7 39015 8 - 47259 T------AGGCTAA -s Anc2.Anc2refChr15 77243 8 + 86568 T------AGGCTTA -s mr.mrrefChr5 116396 14 + 294540 CCAAACGAGCCTAT -s simCow_chr6.simCow.chr6 259467 8 + 602619 C------AAGCTTA -s simDog_chr6.simDog.chr6 250387 8 + 593897 T------AGGCTTA -s simHuman_chr6.simHuman.chr6 341651 5 - 601863 ---------TTTAC -s simRat_chr6.simRat.chr6 253595 14 + 647215 CCAGACATAGCTAT - -a -s simMouse_chr6.simMouse.chr6 263850 10 + 636262 TAGCTTGATA -s Anc0.Anc0refChr5 80022 10 + 87904 AATCTCCATA -s Anc1.Anc1refChr7 39023 10 - 47259 AATCTCCATA -s Anc2.Anc2refChr15 77251 10 + 86568 AATTTCCATA -s mr.mrrefChr5 116410 10 + 294540 TAGCTTGATA -s simCow_chr6.simCow.chr6 259476 10 + 602619 AATTGCCATA -s simDog_chr6.simDog.chr6 250395 10 + 593897 AATTTCCATA -s simHuman_chr6.simHuman.chr6 341656 10 - 601863 AATCTCCATA -s simRat_chr6.simRat.chr6 253609 10 + 647215 CAGCTTGACA - -a -s simMouse_chr6.simMouse.chr6 263860 36 + 636262 TACTATTCTTCAGTAGCCCTCAAGTTAGGGATGGTA -s Anc0.Anc0refChr5 80032 36 + 87904 TATTATTCTTCAGCAGCCTTCATGTTAGGACTGGTA -s Anc1.Anc1refChr7 39033 36 - 47259 TATTATTCTTCAGCAGCCTTCATGTTAGGACTGGTA -s Anc2.Anc2refChr15 77261 36 + 86568 TATTACTCTTCAGCAGCCTTCATATTAGGACTGGCG -s mr.mrrefChr5 116420 36 + 294540 TACTATTCTTCAGTAGCCCTCATGTTAGGACTGGTA -s simCow_chr6.simCow.chr6 259486 36 + 602619 TATTACTCTTTAGCAGCCTTTACATTAGGACTAGCC -s simDog_chr6.simDog.chr6 250405 36 + 593897 GATCACTCTTCAGCAGCCTTCATATCAGGACTGGCG -s simHuman_chr6.simHuman.chr6 341666 36 - 601863 TATTATTCTTCAGCAGCCTTCATGTTAGGACTGGTA -s simRat_chr6.simRat.chr6 253638 36 + 647215 TACTATTCTTCAGTAGCCCTTGTGTTAGGACTGACA - -a -s simMouse_chr6.simMouse.chr6 263896 74 + 636262 CTCTAGTAGTGTTTTCTAAATGCATGTGATTGTTGTTAGGGTTTGAATGAATGTAGCCAAGTGTGGAACCATGA -s Anc0.Anc0refChr5 80069 72 + 87904 ATGCAACAGTGTTTTCTAAATCTATGTGATGGTTATGAAGATTTGAATGAATGTAGCCAAGTGTGGAACCAT-- -s Anc1.Anc1refChr7 39070 74 - 47259 ATGCAACAGTGTTTTCTAAATCTATGTGATGGTTATGAAGATTTGAATGAATGTAGCCAAGTGTGGAACCATGA -s Anc2.Anc2refChr15 77298 72 + 86568 ATGCAACAGTGTTTTCTAATTCTATGTGATGGTTATGAAGATTTGAATACATGCAGCCAGGTGTGGAACCAC-- -s mr.mrrefChr5 116456 74 + 294540 CTCTAGTAGTGTTTTCTAAATGCATGTGATTGTTGTGAGGGTTTGAATGAATGTAGCCAAGTGTGGAACCATGA -s simCow_chr6.simCow.chr6 259523 72 + 602619 ATGCAACAGGGTTTTCTAATTCTATTTGATAGTTATGAGGATTTGAACCCATGAAGCCAGCCATGGAACCAC-- -s simDog_chr6.simDog.chr6 250442 72 + 593897 ATGCAATTGTGTTTTCTAATTCTATGTGATGGTTATGAAGTCTTGAATACATGCAGCCAGGTGCAGAACCAC-- -s simHuman_chr6.simHuman.chr6 341703 72 - 601863 ATGCAACAGTGTTTTCTAAATCTATGTGATCATTATGATGATTTGAATGAATGTAGTTAAGTGTGGAA--ATGA -s simRat_chr6.simRat.chr6 253674 74 + 647215 CTCTGGTGGTGTTTTCTAAATACATATGATTGTTGTGAGAGTTTCAATGAATGTAGCCAAGTGTGGAACTGTGA - -a -s simMouse_chr6.simMouse.chr6 263970 17 + 636262 TGATACAGTGTAATCCA -s Anc0.Anc0refChr5 80146 17 + 87904 TGATGCAGTGTAAGCGA -s Anc1.Anc1refChr7 39149 17 - 47259 TGATGCAGTGTAAGCGA -s Anc2.Anc2refChr15 77375 17 + 86568 TGAAGCAGTGTAAGAGA -s mr.mrrefChr5 116530 17 + 294540 TGATACAGTGTAATCCA -s simCow_chr6.simCow.chr6 259600 16 + 602619 TGAATTGGTGTAAG-GA -s simDog_chr6.simDog.chr6 250520 17 + 593897 TGAAGCAGTGTAAGAGA -s simHuman_chr6.simHuman.chr6 341780 17 - 601863 TGATGCAGTGTAAGCAA -s simRat_chr6.simRat.chr6 253748 17 + 647215 CGATATAGTGTAATCca - -a -s simMouse_chr6.simMouse.chr6 263987 10 + 636262 ATAGTGACAT -s Anc0.Anc0refChr5 80164 7 + 87904 ---ATAAGAT -s Anc1.Anc1refChr7 39167 10 - 47259 ATAATAAGAT -s Anc2.Anc2refChr15 77393 7 + 86568 ---ATAAGAT -s mr.mrrefChr5 116547 10 + 294540 ATAGTGACAT -s simCow_chr6.simCow.chr6 259617 7 + 602619 ---GTAAAAT -s simDog_chr6.simDog.chr6 250538 7 + 593897 ---ATAAGAT -s simHuman_chr6.simHuman.chr6 341798 10 - 601863 ATAATAAGAT -s simRat_chr6.simRat.chr6 253765 10 + 647215 acagtgacat - -a -s simMouse_chr6.simMouse.chr6 263997 1 + 636262 G -s Anc0.Anc0refChr3 195963 1 - 222631 G -s Anc1.Anc1refChr6 141484 1 - 197743 G -s Anc2.Anc2refChr13 66336 1 - 96486 G -s mr.mrrefChr5 116557 1 + 294540 G -s mr.mrrefChr5 46440 1 - 294540 A -s simCow_chr6.simCow.chr6 216302 1 - 602619 A -s simDog_chr6.simDog.chr6 217151 1 - 593897 G -s simHuman_chr6.simHuman.chr6 221207 1 - 601863 G -s simMouse_chr6.simMouse.chr6 241930 1 - 636262 A -s simRat_chr6.simRat.chr6 252629 1 - 647215 A -s simRat_chr6.simRat.chr6 253775 1 + 647215 g - -a -s simMouse_chr6.simMouse.chr6 263998 4 + 636262 CAGG -s Anc0.Anc0refChr3 195964 4 - 222631 CAAG -s Anc1.Anc1refChr6 141485 4 - 197743 CAAG -s Anc2.Anc2refChr13 66337 4 - 96486 CATG -s mr.mrrefChr5 116558 4 + 294540 cagg -s mr.mrrefChr5 46441 4 - 294540 CAGG -s simCow_chr6.simCow.chr6 216303 4 - 602619 CATG -s simDog_chr6.simDog.chr6 217152 4 - 593897 CATA -s simHuman_chr6.simHuman.chr6 221208 4 - 601863 CAAG -s simHuman_chr6.simHuman.chr6 156347 4 - 601863 CAAG -s simMouse_chr6.simMouse.chr6 241931 4 - 636262 CAGG -s simRat_chr6.simRat.chr6 252630 4 - 647215 CAGG -s simRat_chr6.simRat.chr6 253776 4 + 647215 cagg - -a -s simMouse_chr6.simMouse.chr6 264002 3 + 636262 TAC -s mr.mrrefChr5 116562 3 + 294540 tac -s simRat_chr6.simRat.chr6 253780 3 + 647215 tac - -a -s simMouse_chr6.simMouse.chr6 264005 1 + 636262 A -s Anc0.Anc0refChr3 195968 1 - 222631 A -s Anc1.Anc1refChr6 141489 1 - 197743 A -s Anc2.Anc2refChr13 66341 1 - 96486 A -s mr.mrrefChr5 116565 1 + 294540 a -s mr.mrrefChr5 46445 1 - 294540 A -s simCow_chr6.simCow.chr6 216307 1 - 602619 A -s simDog_chr6.simDog.chr6 217156 1 - 593897 T -s simHuman_chr6.simHuman.chr6 221212 1 - 601863 A -s simHuman_chr6.simHuman.chr6 156351 1 - 601863 A -s simMouse_chr6.simMouse.chr6 241935 1 - 636262 G -s simRat_chr6.simRat.chr6 252634 1 - 647215 A -s simRat_chr6.simRat.chr6 253783 1 + 647215 a - -a -s simMouse_chr6.simMouse.chr6 264006 7 + 636262 GCCTGtt -s Anc0.Anc0refChr3 195970 7 - 222631 AATTGAT -s Anc1.Anc1refChr6 141491 7 - 197743 AATTGAT -s Anc2.Anc2refChr13 66343 7 - 96486 AAGTGAT -s mr.mrrefChr5 116566 7 + 294540 gcctgtt -s mr.mrrefChr5 46447 7 - 294540 AACTAAT -s simCow_chr6.simCow.chr6 216309 7 - 602619 AACTGAT -s simDog_chr6.simDog.chr6 217158 7 - 593897 AGGTGAC -s simHuman_chr6.simHuman.chr6 221214 7 - 601863 AATTGAT -s simHuman_chr6.simHuman.chr6 156352 7 - 601863 ATTTGAT -s simMouse_chr6.simMouse.chr6 241937 7 - 636262 AACTAAT -s simRat_chr6.simRat.chr6 252636 7 - 647215 AAATAAT -s simRat_chr6.simRat.chr6 253784 7 + 647215 accagtt - -a -s simMouse_chr6.simMouse.chr6 264013 6 + 636262 cccaag -s Anc0.Anc0refChr3 195977 6 - 222631 CTTATG -s Anc1.Anc1refChr6 141498 6 - 197743 CTTATG -s Anc2.Anc2refChr13 66350 6 - 96486 CTTATG -s mr.mrrefChr5 116573 6 + 294540 cccaag -s mr.mrrefChr5 46454 6 - 294540 TTTATG -s simCow_chr6.simCow.chr6 216349 6 - 602619 CTTATG -s simDog_chr6.simDog.chr6 217165 6 - 593897 CTCACG -s simHuman_chr6.simHuman.chr6 221221 6 - 601863 CTGGTG -s simHuman_chr6.simHuman.chr6 156359 6 - 601863 CTTGTG -s simMouse_chr6.simMouse.chr6 241944 6 - 636262 TTTATG -s simRat_chr6.simRat.chr6 252643 6 - 647215 TTTATG -s simRat_chr6.simRat.chr6 253791 6 + 647215 cccaaa - -a -s simMouse_chr6.simMouse.chr6 264019 2 + 636262 gc -s Anc0.Anc0refChr3 195983 2 - 222631 AC -s Anc1.Anc1refChr6 141504 2 - 197743 AC -s Anc2.Anc2refChr13 66356 2 - 96486 AC -s mr.mrrefChr5 116579 2 + 294540 gc -s mr.mrrefChr5 46460 2 - 294540 AT -s simCow_chr6.simCow.chr6 216355 2 - 602619 AT -s simDog_chr6.simDog.chr6 217171 2 - 593897 AC -s simHuman_chr6.simHuman.chr6 221227 2 - 601863 AC -s simHuman_chr6.simHuman.chr6 156365 2 - 601863 AC -s simMouse_chr6.simMouse.chr6 241950 2 - 636262 AT -s simRat_chr6.simRat.chr6 253797 2 + 647215 gt - -a -s simMouse_chr6.simMouse.chr6 264021 4 + 636262 gcag -s Anc0.Anc0refChr3 195986 4 - 222631 GCAT -s Anc1.Anc1refChr6 141507 4 - 197743 GCAT -s Anc2.Anc2refChr13 66359 4 - 96486 GCAT -s mr.mrrefChr5 116581 4 + 294540 gcag -s mr.mrrefChr5 46463 4 - 294540 GCAG -s simCow_chr6.simCow.chr6 216358 4 - 602619 GCAC -s simDog_chr6.simDog.chr6 217174 4 - 593897 GCAT -s simHuman_chr6.simHuman.chr6 221230 4 - 601863 GCAT -s simHuman_chr6.simHuman.chr6 156368 4 - 601863 GCAT -s simMouse_chr6.simMouse.chr6 241953 4 - 636262 GCAG -s simRat_chr6.simRat.chr6 253799 4 + 647215 gcgg - -a -s simMouse_chr6.simMouse.chr6 264025 7 + 636262 tacaaag -s Anc0.Anc0refChr3 195990 7 - 222631 GTTTTAT -s Anc1.Anc1refChr6 141511 7 - 197743 GTTTTAT -s Anc2.Anc2refChr13 66363 7 - 96486 GTTTTAT -s mr.mrrefChr5 116585 7 + 294540 tacaaag -s mr.mrrefChr5 46467 7 - 294540 CCTCAAT -s simCow_chr6.simCow.chr6 216362 7 - 602619 ATTCTAT -s simDog_chr6.simDog.chr6 217178 6 - 593897 GTGTC-T -s simHuman_chr6.simHuman.chr6 221234 7 - 601863 GTTTTAC -s simHuman_chr6.simHuman.chr6 156372 7 - 601863 GTTTTAC -s simMouse_chr6.simMouse.chr6 241960 7 - 636262 CCTCAAT -s simRat_chr6.simRat.chr6 253803 7 + 647215 tacaaag - -a -s simMouse_chr6.simMouse.chr6 264032 13 + 636262 cgtatagcatacc -s Anc0.Anc0refChr3 195997 13 - 222631 TGCACATCACACC -s Anc1.Anc1refChr6 141518 13 - 197743 TGCACATCACACC -s Anc2.Anc2refChr13 66370 13 - 96486 TGCACATCACACC -s mr.mrrefChr5 116592 13 + 294540 cgtatagcatacc -s mr.mrrefChr5 46474 13 - 294540 TGTACATAATCCT -s simCow_chr6.simCow.chr6 216369 13 - 602619 TGCACATCACCCT -s simDog_chr6.simDog.chr6 217184 13 - 593897 TGCAAATCATACC -s simHuman_chr6.simHuman.chr6 221241 13 - 601863 TGCACATCACACT -s simHuman_chr6.simHuman.chr6 156379 13 - 601863 TGCACATCACACC -s simMouse_chr6.simMouse.chr6 241967 13 - 636262 TGTACGTAATCCT -s simRat_chr6.simRat.chr6 252649 13 - 647215 TGTACATAATCCT -s simRat_chr6.simRat.chr6 253810 13 + 647215 tgtatagaatatc - -a -s simMouse_chr6.simMouse.chr6 264045 1 + 636262 c -s Anc0.Anc0refChr3 196010 1 - 222631 G -s Anc1.Anc1refChr6 141531 1 - 197743 G -s Anc2.Anc2refChr13 66383 1 - 96486 G -s mr.mrrefChr5 116605 1 + 294540 c -s mr.mrrefChr5 46487 1 - 294540 G -s simCow_chr6.simCow.chr6 216382 1 - 602619 G -s simDog_chr6.simDog.chr6 217197 1 - 593897 A -s simHuman_chr6.simHuman.chr6 221254 1 - 601863 G -s simHuman_chr6.simHuman.chr6 156392 1 - 601863 T -s simMouse_chr6.simMouse.chr6 241980 1 - 636262 G -s simRat_chr6.simRat.chr6 252669 1 - 647215 A -s simRat_chr6.simRat.chr6 253823 1 + 647215 c - -a -s simMouse_chr6.simMouse.chr6 264046 6 + 636262 atcatc -s mr.mrrefChr5 116606 6 + 294540 atcatc -s simRat_chr6.simRat.chr6 253824 6 + 647215 atcatc - -a -s simMouse_chr6.simMouse.chr6 264052 4 + 636262 tatg -s Anc0.Anc0refChr3 196011 4 - 222631 TGAG -s Anc1.Anc1refChr6 141532 4 - 197743 TGAG -s Anc2.Anc2refChr13 66384 4 - 96486 TGAG -s mr.mrrefChr5 116612 4 + 294540 tatg -s mr.mrrefChr5 46488 4 - 294540 TGGG -s simCow_chr6.simCow.chr6 216383 4 - 602619 TGGT -s simDog_chr6.simDog.chr6 217198 4 - 593897 TGAG -s simHuman_chr6.simHuman.chr6 221255 4 - 601863 CGGG -s simHuman_chr6.simHuman.chr6 156393 4 - 601863 TGAG -s simMouse_chr6.simMouse.chr6 241981 4 - 636262 TGGG -s simRat_chr6.simRat.chr6 252670 4 - 647215 TGGA -s simRat_chr6.simRat.chr6 253830 4 + 647215 cgtg - -a -s simMouse_chr6.simMouse.chr6 264070 260 + 636262 ccccatggattgatgctggtcccctgatgatataattgtagaacttagaacCACATCTATGTGGTTAACGGAGTGCATGATCCTAGTGTATGACGGTGGTAacataatagtctgatatagtatgcatggattgttagttagaaatctcctaacactgaactgcttacaattgacactgtggagactgaaacactgataccatgcactcagatgatatttggctgttagcagggtccatacaggcaactttccagtgactg -s mr.mrrefChr5 116630 255 + 294540 ccccatggattgatgctggtcccctgatgatataattgtagaacttagaacCACATCTATGTGGTTAACGGAGTGCATGATCCTAGTGTatgacggtggtaacataatagtctgatatagtatgcatggatt----gttagaaatctcctaa-actgaactgcttacaattgacactgtggagactgaaacactgataccatgcactcagatgatatttggctgttagcagggtccatacaggcaactttccagtgactg -s simRat_chr6.simRat.chr6 253848 255 + 647215 ccccatgggttgatgctggttcccttatgatataattgtaaaacCTCGAGCCACACCTATGTGATTAAGCGAGTGCATGATTCCAGTGTgtgacgctggcaacataatagtctgatatagcatgcatggatt----gttataagtcccctaa-attgaactgctcacaattgacactgtgcggactaaaataccactatcatgcactctaacagtgttatgctcctaacggggtccatacaggcgacttcacagtgactg - -a -s simMouse_chr6.simMouse.chr6 264330 234 + 636262 gaggtactggcaaagctgtgacagaaaactgtgggggcacaaaatgctcaattgttgggatttgccgcgatgtaggctgtagaaaagggaaaaaattattcctaaaacaaaaggttgtaaaaacctctgataaactagcttgctgtcccaACAAACACCTGGATGAGATGACTGGGTAGTGCTAGAATTTGAGGACTTCGGTGACTATCACCAAGCACATGTACTAGAGTTTAC -s mr.mrrefChr5 116885 228 + 294540 gaggtactggcaaagctgtgacagaaaactgtgggggcacaaaatgctcaattgttgggatttgccgcga-gtaggctgtagaaaagggaaaaaattattcctaaaacaaaaggttgtaaaaacctctgataaactagcttgctgtcccaACAAACACCTG-----GATGACTGGGTAGTGCTAGAATTTGAGGACTTCGGTGACTATCACCAAGCACATGTACTAGAGTTTAC -s simRat_chr6.simRat.chr6 254119 228 + 647215 gaggtactgccaaagctatgacagaacaccgtgggggcacaaaatgcgtactttttggaatcatccgtga-gtaggctgtaaaaaagggaaaaagttattcctaaaacagaagattatcaaaacctctgataaaccagcttgctgtcccaAAAGACCCATG-----GATGACTGGGTTATGCTAGAACTTGAGGCTTTTGGCAACTATCACCAAGTACATATACTAAAGTTTAC - -a -s simMouse_chr6.simMouse.chr6 264564 298 + 636262 TTTGCTCAACGAATAATTGGGCATTTTCTTCCAGCAAGCCCATTTCCCCATTTGAGAGACTGCCATCACAAGAGTTGAGCAGGTTTACTCACAAAAATACGTGAACACTGGAGCACTTACCCTAGTGGGAGTCAAGACATCAAATTACCTAAATGTATCTCCCTGCCCCGCTTCCTGTACTCAGGCAGGTGGTGAAAACAGTGCTACGTGATGCATTCGTACAGCATGCTTTATTGTCCATAACCCTAAGTGTTGGTGTCTCATGGTGGTGTCCTCAATAGCTGCTTAAGAATGGAAA -s mr.mrrefChr5 117113 101 + 294540 TTTGCTCAACGAATAATTGGGC---------------------------------GAGACTGCCATCACAAGAGTTG--------------------------------------------------------------------------------------------------------------------------------------------------------------------AACCCTAAGTGTTGGTGTCTCATGGTGGTGTCCTCAATAGCTGCTTAAGAATGGAAA -s simRat_chr6.simRat.chr6 254348 101 + 647215 TTTGCTCAACGAATAATTAGGC---------------------------------GCGGCTGCCACCACAAGAGTTG--------------------------------------------------------------------------------------------------------------------------------------------------------------------AACTCTAAGTGTTGGTGTCTCATGGTGGTGTCCTCAATAGCTTGCTAAGAGTGGAAG - -a -s simMouse_chr6.simMouse.chr6 264862 62 + 636262 ATGTATATATCCCTACAGACTTGAGGAAAAAAACCTGCTCATATTATGGCATATAGAGTGAT -s mr.mrrefChr5 117214 62 + 294540 ATGTATATATCCCCACAGACTTGAGGAAAAAAACCTGCTCATATTATGGCATATAGAGTGAT -s simRat_chr6.simRat.chr6 254455 17 + 647215 ATGCATATATCCCCACA--------------------------------------------- - -a -s simMouse_chr6.simMouse.chr6 264925 22 + 636262 TCTTACTAGGAAGCCTTGCCAC -s Anc0.Anc0refChr3 196043 20 - 222631 TTTCA--AGGAATCTTTGCCAC -s Anc1.Anc1refChr6 141564 20 - 197743 TTTCA--AGGAATCTTTGCCAC -s Anc2.Anc2refChr13 66416 20 - 96486 TTTCA--AGGAATCTTTGTCAC -s mr.mrrefChr5 117277 21 + 294540 TCTTAC-AGGAAGCCTTGCCAC -s mr.mrrefChr5 46589 20 - 294540 TCTCA--AGGAAGCTTTACCAT -s simCow_chr6.simCow.chr6 216423 19 - 602619 TTTCA--AG-ACTATTTGCCAC -s simDog_chr6.simDog.chr6 217226 20 - 593897 TTTCA--AGGAATCTCTGTTAC -s simHuman_chr6.simHuman.chr6 221279 20 - 601863 TTTCA--AGGAATCTTTATCAC -s simHuman_chr6.simHuman.chr6 156425 20 - 601863 TTTCA--AGGAATCTTTGCCAC -s simMouse_chr6.simMouse.chr6 241990 20 - 636262 TCTCA--AGGAAGCTTCAATAT -s simRat_chr6.simRat.chr6 252838 20 - 647215 TCACA--AGGAAACATTGCCAT -s simRat_chr6.simRat.chr6 254472 1 + 647215 ---------------------C - -a -s simMouse_chr6.simMouse.chr6 264947 23 + 636262 AATACAATAGGGCTCTGTCTGTT -s Anc0.Anc0refChr3 196063 23 - 222631 AATATAAGAGGCCACCTTCTATC -s Anc1.Anc1refChr6 141584 23 - 197743 AATATAAGAGGCCACCTTCTATC -s Anc2.Anc2refChr13 66436 23 - 96486 AATATAAGAGACCACCTTCTATC -s mr.mrrefChr5 117298 23 + 294540 AATACAATAGGGCTCTGTCTGTT -s mr.mrrefChr5 46610 23 - 294540 AATACAAGAGGGCTCCTTCTGCC -s simCow_chr6.simCow.chr6 216442 23 - 602619 AATATAAGAGGCCTCCCTCTATC -s simDog_chr6.simDog.chr6 217246 23 - 593897 GATAGAAGAGACCACTTTCTATC -s simHuman_chr6.simHuman.chr6 221299 23 - 601863 AATATAAGGGACCATCTTCTATC -s simHuman_chr6.simHuman.chr6 156445 23 - 601863 AATATAAGTGGCCATCTTCTATC -s simMouse_chr6.simMouse.chr6 242011 23 - 636262 AATACAAGAGGGCTCCTTCTGCT -s simRat_chr6.simRat.chr6 252859 23 - 647215 AATACAAGAGGGCTCCTTCTGCC -s simRat_chr6.simRat.chr6 254473 23 + 647215 AGTACAATAGGGCTCTGTCTGTT - -a -s simMouse_chr6.simMouse.chr6 264970 1 + 636262 T -s Anc0.Anc0refChr3 196086 1 - 222631 C -s Anc1.Anc1refChr6 141607 1 - 197743 C -s Anc2.Anc2refChr13 66459 1 - 96486 C -s mr.mrrefChr5 117321 1 + 294540 T -s mr.mrrefChr5 46633 1 - 294540 G -s simDog_chr6.simDog.chr6 217278 1 - 593897 T -s simHuman_chr6.simHuman.chr6 221322 1 - 601863 C -s simHuman_chr6.simHuman.chr6 156468 1 - 601863 C -s simMouse_chr6.simMouse.chr6 242034 1 - 636262 G -s simRat_chr6.simRat.chr6 252882 1 - 647215 A -s simRat_chr6.simRat.chr6 254496 1 + 647215 C - -a -s simMouse_chr6.simMouse.chr6 264971 1 + 636262 G -s mr.mrrefChr5 117322 1 + 294540 G -s simRat_chr6.simRat.chr6 254497 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 264972 20 + 636262 GATGATATTGCTCAATAGAA -s Anc0.Anc0refChr3 196087 20 - 222631 AATAATATTGCTCAGTTGAG -s Anc1.Anc1refChr6 141608 20 - 197743 AATAATATTGCTCAGTTGAG -s Anc2.Anc2refChr13 66460 20 - 96486 TATAATATTGCTCAGTTGTG -s mr.mrrefChr5 117323 20 + 294540 GATGATATTGCTCAATAGAA -s mr.mrrefChr5 46634 20 - 294540 AATGATATTGCTCATTTGAG -s simCow_chr6.simCow.chr6 216465 16 - 602619 ----ATCTTGCTGAGTTTTG -s simDog_chr6.simDog.chr6 217279 20 - 593897 TAGCGTATTGCTAAGTTGTG -s simHuman_chr6.simHuman.chr6 221323 20 - 601863 AATAATATTGCTCAGTTGAG -s simHuman_chr6.simHuman.chr6 156469 20 - 601863 GATAATATTGATCAGTTGAG -s simMouse_chr6.simMouse.chr6 242035 20 - 636262 AATGATACTGCTCATTTGAG -s simRat_chr6.simRat.chr6 252883 20 - 647215 AATGATATTGCTCAATTGAG -s simRat_chr6.simRat.chr6 254498 20 + 647215 GATGATATTGCTCAATAGAA - -a -s simMouse_chr6.simMouse.chr6 264992 15 + 636262 TTACTTTCTAACAAA -s Anc0.Anc0refChr3 196107 15 - 222631 TTACTTTGTGAGAAA -s Anc1.Anc1refChr6 141628 15 - 197743 TTACTTTGTGAGAAA -s Anc2.Anc2refChr13 66480 15 - 96486 TTACTTTGTGAGAAA -s mr.mrrefChr5 117343 15 + 294540 TTACTTTCTAACAAA -s mr.mrrefChr5 46654 15 - 294540 TTACTTTCAGAGAAA -s simCow_chr6.simCow.chr6 216481 15 - 602619 TTACTTTCGGAGAAA -s simDog_chr6.simDog.chr6 217299 15 - 593897 TTACTTTGAGAGCAA -s simHuman_chr6.simHuman.chr6 221343 15 - 601863 TTACTTTGTGAGAAA -s simHuman_chr6.simHuman.chr6 156489 15 - 601863 TTACTTTGTGAGAAA -s simMouse_chr6.simMouse.chr6 242065 15 - 636262 TTACTTTCAGAGAAA -s simRat_chr6.simRat.chr6 252903 15 - 647215 TGACTTTCAGAGGAA -s simRat_chr6.simRat.chr6 254518 15 + 647215 TTACTTTCAAACAAA - -a -s simMouse_chr6.simMouse.chr6 265007 10 + 636262 ATTCCAAAAG -s Anc0.Anc0refChr3 196123 10 - 222631 ATTCCAAGAA -s Anc1.Anc1refChr6 141644 10 - 197743 ATTCCAAGAA -s Anc2.Anc2refChr13 66496 10 - 96486 ATTCCAAGCA -s mr.mrrefChr5 117358 10 + 294540 ATTCCAAAAG -s mr.mrrefChr5 46669 10 - 294540 ATTCCAAGAA -s simCow_chr6.simCow.chr6 216497 10 - 602619 AGCTCATGCA -s simDog_chr6.simDog.chr6 217315 10 - 593897 ATTCCACGCA -s simHuman_chr6.simHuman.chr6 221359 10 - 601863 ATTCCAAGAA -s simHuman_chr6.simHuman.chr6 156505 10 - 601863 ATTCCAAGAA -s simMouse_chr6.simMouse.chr6 242080 10 - 636262 ACCCCAAGAA -s simRat_chr6.simRat.chr6 252918 10 - 647215 ATTCCAAGAA -s simRat_chr6.simRat.chr6 254533 10 + 647215 ATTCCAAAAG - -a -s simMouse_chr6.simMouse.chr6 265017 4 + 636262 CTCC -s Anc0.Anc0refChr3 196133 4 - 222631 CTCC -s Anc1.Anc1refChr6 141654 4 - 197743 CTCC -s Anc2.Anc2refChr13 66510 4 - 96486 CTCT -s mr.mrrefChr5 117368 4 + 294540 CTCC -s mr.mrrefChr5 46679 4 - 294540 CTCT -s simCow_chr6.simCow.chr6 216511 4 - 602619 CTCC -s simDog_chr6.simDog.chr6 217329 4 - 593897 CTCT -s simHuman_chr6.simHuman.chr6 221369 4 - 601863 CTCC -s simHuman_chr6.simHuman.chr6 156515 4 - 601863 CTCC -s simMouse_chr6.simMouse.chr6 242090 4 - 636262 CTCT -s simRat_chr6.simRat.chr6 252928 4 - 647215 CTCT -s simRat_chr6.simRat.chr6 254543 4 + 647215 CTTC - -a -s simMouse_chr6.simMouse.chr6 265021 5 + 636262 TGGAC -s Anc0.Anc0refChr3 196144 5 - 222631 TGGAG -s Anc1.Anc1refChr6 141665 5 - 197743 TGGAG -s Anc2.Anc2refChr13 66521 5 - 96486 TTGAG -s mr.mrrefChr5 117379 5 + 294540 TGGAC -s mr.mrrefChr5 46690 5 - 294540 TACAG -s simCow_chr6.simCow.chr6 216522 5 - 602619 TTGAC -s simDog_chr6.simDog.chr6 217340 5 - 593897 TTGAG -s simHuman_chr6.simHuman.chr6 221380 5 - 601863 TGGAG -s simHuman_chr6.simHuman.chr6 156526 5 - 601863 TGGAA -s simMouse_chr6.simMouse.chr6 242101 5 - 636262 TACAG -s simRat_chr6.simRat.chr6 252939 5 - 647215 TACAG -s simRat_chr6.simRat.chr6 254554 5 + 647215 TGGAT - -a -s simMouse_chr6.simMouse.chr6 265026 8 + 636262 AGACCCAT -s Anc0.Anc0refChr3 196149 8 - 222631 AGACACAT -s Anc1.Anc1refChr6 141670 8 - 197743 AGACACAT -s Anc2.Anc2refChr13 66526 8 - 96486 AGACACAT -s mr.mrrefChr5 117384 8 + 294540 AGACCCAT -s mr.mrrefChr5 46695 8 - 294540 ACAACCAT -s simCow_chr6.simCow.chr6 216527 8 - 602619 AGACACAT -s simDog_chr6.simDog.chr6 217345 8 - 593897 ATACACTT -s simHuman_chr6.simHuman.chr6 156531 8 - 601863 AGGCATAT -s simMouse_chr6.simMouse.chr6 242106 8 - 636262 ACAACCAT -s simRat_chr6.simRat.chr6 252944 8 - 647215 ACAACCAT -s simRat_chr6.simRat.chr6 254559 8 + 647215 AGACCCAC - -a -s simMouse_chr6.simMouse.chr6 265034 8 + 636262 CCCAAGTA -s Anc0.Anc0refChr3 196157 8 - 222631 TGCAAGTA -s Anc1.Anc1refChr6 141678 8 - 197743 TGCAAGTA -s Anc2.Anc2refChr13 66534 8 - 96486 TGCAAATA -s mr.mrrefChr5 117392 8 + 294540 CTCAAGTA -s mr.mrrefChr5 46703 8 - 294540 TCTGAGTA -s simCow_chr6.simCow.chr6 216535 8 - 602619 TTCAAAGG -s simDog_chr6.simDog.chr6 217353 8 - 593897 TCCAAACA -s simHuman_chr6.simHuman.chr6 221385 8 - 601863 TGCAAGTA -s simHuman_chr6.simHuman.chr6 156539 8 - 601863 TGTAAGTA -s simMouse_chr6.simMouse.chr6 242114 8 - 636262 TCTGAGTA -s simRat_chr6.simRat.chr6 252952 8 - 647215 TCTGAGTG -s simRat_chr6.simRat.chr6 254567 8 + 647215 CTCAAGCA - -a -s simMouse_chr6.simMouse.chr6 265042 33 + 636262 TGCCCTCCCAGGTTTATCGACGAAGACCTTACC -s Anc0.Anc0refChr3 196165 33 - 222631 TGCCCTCCCAAGTTTATTGACAACATCATTATC -s Anc1.Anc1refChr6 141686 33 - 197743 TGCCCTCCCAAGTTTATTGACAACATCATTATC -s Anc2.Anc2refChr13 66542 33 - 96486 CACCCTCCCAAGTTTATTGATAACATTATTATC -s mr.mrrefChr5 117400 33 + 294540 TACCCTCCCAGGTTTATCGACGAAAGCCTTACC -s mr.mrrefChr5 46711 33 - 294540 TGCTGTCCCAGGTTTATTGACAACAACATTGTT -s simCow_chr6.simCow.chr6 216551 33 - 602619 CACCCTCCCAAGTTCATCAATGACAGTGTTATT -s simDog_chr6.simDog.chr6 217361 33 - 593897 CACCCTCCCAAGTTTATTGATAATGATATTATC -s simHuman_chr6.simHuman.chr6 221393 33 - 601863 TGCCCTTCGAAGTTTATTGACGACATCATTATC -s simHuman_chr6.simHuman.chr6 156547 27 - 601863 TG------GGAGTCTATTGACAACATCATTATC -s simMouse_chr6.simMouse.chr6 242122 33 - 636262 TGCTGTCCCAGGTTTATTGACACCAACATTGTT -s simRat_chr6.simRat.chr6 252960 33 - 647215 TGTTATCCCAGGTTTATTAACAATAACATTGTG -s simRat_chr6.simRat.chr6 254575 33 + 647215 TATCCACTGAGGTTTATTGACAAAAGCCTTACA - -a -s simMouse_chr6.simMouse.chr6 265075 8 + 636262 TAGCACTC -s Anc0.Anc0refChr3 196204 8 - 222631 TAGCACTC -s Anc1.Anc1refChr6 141725 8 - 197743 TAGCACTC -s Anc2.Anc2refChr13 66581 8 - 96486 TAGCACTC -s mr.mrrefChr5 117433 8 + 294540 TAGCACTC -s mr.mrrefChr5 46744 8 - 294540 TAGCACTC -s simCow_chr6.simCow.chr6 216590 8 - 602619 TAGCACTC -s simDog_chr6.simDog.chr6 217400 8 - 593897 TAATACTC -s simHuman_chr6.simHuman.chr6 221432 8 - 601863 TAGCACTC -s simHuman_chr6.simHuman.chr6 156580 8 - 601863 TAGCACTC -s simMouse_chr6.simMouse.chr6 242155 8 - 636262 TAGCACTC -s simRat_chr6.simRat.chr6 252993 8 - 647215 TAGCACTC -s simRat_chr6.simRat.chr6 254608 8 + 647215 TAGCATTC - -a -s simMouse_chr6.simMouse.chr6 265083 24 + 636262 TATTAAATTACTGATGCTGTACAA -s Anc0.Anc0refChr3 196212 24 - 222631 TATGCAATATCTGCATCTGTACAA -s Anc1.Anc1refChr6 141733 24 - 197743 TATGCAATATCTGCATCTGTACAA -s Anc2.Anc2refChr13 66589 24 - 96486 TATGCAATATCTGCATCTGTACAA -s mr.mrrefChr5 117441 24 + 294540 TATTAAATCACTGATGCTGTACAA -s simCow_chr6.simCow.chr6 216598 24 - 602619 TATGCAATCTCTGTTTCTGTACAA -s simDog_chr6.simDog.chr6 217408 17 - 593897 ACTGTAA-------AGCTGCCCAA -s simHuman_chr6.simHuman.chr6 221440 24 - 601863 TATGCGATATCTGCATCTGTACAA -s simHuman_chr6.simHuman.chr6 156588 24 - 601863 TATGCAATATCTGCATCTGTACAG -s simRat_chr6.simRat.chr6 254616 24 + 647215 TATTAAATCACTGATCCTGTATAA - -a -s simMouse_chr6.simMouse.chr6 265107 53 + 636262 GGTTCTAGCACAGTAATCTGTCACTTTCAAAGTCTGGGTTTAAACATTCATTA -s Anc0.Anc0refChr3 196237 53 - 222631 GGTTTTACCACAATAAGCTGTTACTTTCTAACACTGGGTTTAATTATACAGGG -s Anc1.Anc1refChr6 141758 53 - 197743 GGTTTTACCACAATAAGCTGTTACTTTCTAACACTGGGTTTAATTATACAGGG -s Anc2.Anc2refChr13 66614 53 - 96486 GGTTTTACTACAATAAGGTTTTGCTTTCTAACACTGGGTTTAATTATACAGGG -s mr.mrrefChr5 117465 53 + 294540 GGTTCTACCACAGTAAGCTGTCACTTTCAAAGTCTGGGTTTAAACATTCATTG -s mr.mrrefChr5 46753 53 - 294540 GGCTTTGGCACAACCAGCTGTTAATTCTAAATACTGGGTTTAATCATCCAGAG -s simCow_chr6.simCow.chr6 216622 53 - 602619 GGTTTTACCACATTAAGGTGTTTCTTTCTAACACTGGGTTTAATTATACAGGG -s simDog_chr6.simDog.chr6 217551 53 - 593897 GGTTTTACTACAATAAGGTTTTGCTTTCTAACATTGGGCTTAATTATACAGGG -s simHuman_chr6.simHuman.chr6 221465 25 - 601863 ----------------------------TAACACTGGGTTTCATTATACTTGG -s simHuman_chr6.simHuman.chr6 156613 25 - 601863 ----------------------------TAACACTGCGTTTAATTATATTGGG -s simMouse_chr6.simMouse.chr6 242164 53 - 636262 GGCTTTGGCACAACCAGCTGTTAATTCTAAATACTGGGTTTAATCATCGAGAG -s simRat_chr6.simRat.chr6 253026 53 - 647215 GGTTTTATCACAATCAGTTGTTAATCCTCAATACTGCGTTTAATCATCCAGAT -s simRat_chr6.simRat.chr6 254640 53 + 647215 GGTTCTACCACAGAAAGCTGTCACTTTCAAAGGCTGGGTTTAAACATTCATTG - -a -s simMouse_chr6.simMouse.chr6 265160 4 + 636262 GACA -s Anc0.Anc0refChr3 196295 3 - 222631 GAC- -s Anc1.Anc1refChr6 141816 3 - 197743 GAC- -s Anc2.Anc2refChr13 66672 3 - 96486 TAC- -s mr.mrrefChr5 117518 3 + 294540 GAC- -s mr.mrrefChr5 46811 3 - 294540 CAT- -s simCow_chr6.simCow.chr6 216680 3 - 602619 CAC- -s simDog_chr6.simDog.chr6 217609 3 - 593897 TAC- -s simHuman_chr6.simHuman.chr6 221490 3 - 601863 GAA- -s simHuman_chr6.simHuman.chr6 156643 3 - 601863 GAC- -s simMouse_chr6.simMouse.chr6 242222 3 - 636262 CAT- -s simRat_chr6.simRat.chr6 253084 3 - 647215 CAT- -s simRat_chr6.simRat.chr6 254693 3 + 647215 GAC- - -a -s simMouse_chr6.simMouse.chr6 265164 13 + 636262 AGTAGCAATTGAt -s Anc0.Anc0refChr3 196298 12 - 222631 ACAAT-ATTTGCt -s Anc1.Anc1refChr6 141819 12 - 197743 ACAAT-ATTTGCt -s Anc2.Anc2refChr13 66675 12 - 96486 ACAAT-ATTTGCT -s mr.mrrefChr5 117521 13 + 294540 AGTATCAATTGGt -s simCow_chr6.simCow.chr6 216683 12 - 602619 ACAAG-GTTCACA -s simDog_chr6.simDog.chr6 217612 12 - 593897 ACAAT-ATTTGCT -s simRat_chr6.simRat.chr6 254696 13 + 647215 AGTATCAATTGGT - -a -s simMouse_chr6.simMouse.chr6 265177 4 + 636262 gact -s Anc0.Anc0refChr3 196310 4 - 222631 gaca -s Anc1.Anc1refChr6 141831 4 - 197743 gaca -s Anc2.Anc2refChr13 66690 4 - 96486 GACA -s mr.mrrefChr5 117534 4 + 294540 gact -s simCow_chr6.simCow.chr6 216698 4 - 602619 GACA -s simDog_chr6.simDog.chr6 217627 4 - 593897 GACA -s simRat_chr6.simRat.chr6 254709 4 + 647215 GCCT - -a -s simMouse_chr6.simMouse.chr6 265181 5 + 636262 ggttg -s Anc0.Anc0refChr3 196314 5 - 222631 GCTAG -s Anc1.Anc1refChr6 141835 5 - 197743 GCTAG -s Anc2.Anc2refChr13 66694 5 - 96486 GCTGG -s mr.mrrefChr5 117538 5 + 294540 ggttg -s mr.mrrefChr5 46814 5 - 294540 ACTAG -s simCow_chr6.simCow.chr6 216702 5 - 602619 GTTGG -s simDog_chr6.simDog.chr6 217631 5 - 593897 GCTGG -s simHuman_chr6.simHuman.chr6 221493 5 - 601863 ACTAG -s simHuman_chr6.simHuman.chr6 156646 5 - 601863 GCTAG -s simMouse_chr6.simMouse.chr6 242225 5 - 636262 ACTAG -s simRat_chr6.simRat.chr6 253087 5 - 647215 GCTAG -s simRat_chr6.simRat.chr6 254713 5 + 647215 GGTTG - -a -s simMouse_chr6.simMouse.chr6 265186 7 + 636262 actggat -s Anc0.Anc0refChr3 196319 7 - 222631 ACTATAT -s Anc1.Anc1refChr6 141840 7 - 197743 ACTATAT -s Anc2.Anc2refChr13 66699 7 - 96486 TCTATAT -s mr.mrrefChr5 117543 7 + 294540 actggat -s mr.mrrefChr5 46819 7 - 294540 ACAGTAT -s simCow_chr6.simCow.chr6 216707 7 - 602619 CCTATAT -s simDog_chr6.simDog.chr6 217642 7 - 593897 TCTATAT -s simHuman_chr6.simHuman.chr6 221498 7 - 601863 ACTATAT -s simHuman_chr6.simHuman.chr6 156651 7 - 601863 ACTATAT -s simMouse_chr6.simMouse.chr6 242230 7 - 636262 ACAGTAT -s simRat_chr6.simRat.chr6 253092 7 - 647215 ACCGTAT -s simRat_chr6.simRat.chr6 254718 7 + 647215 ACTGgtg - -a -s simMouse_chr6.simMouse.chr6 265193 1 + 636262 c -s Anc0.Anc0refChr3 196326 1 - 222631 A -s Anc1.Anc1refChr6 141847 1 - 197743 A -s Anc2.Anc2refChr13 66706 1 - 96486 A -s mr.mrrefChr5 117550 1 + 294540 c -s mr.mrrefChr5 46837 1 - 294540 A -s simCow_chr6.simCow.chr6 216714 1 - 602619 A -s simDog_chr6.simDog.chr6 217649 1 - 593897 T -s simHuman_chr6.simHuman.chr6 221505 1 - 601863 A -s simHuman_chr6.simHuman.chr6 156658 1 - 601863 A -s simMouse_chr6.simMouse.chr6 242251 1 - 636262 A -s simRat_chr6.simRat.chr6 253108 1 - 647215 A -s simRat_chr6.simRat.chr6 254725 1 + 647215 c - -a -s simMouse_chr6.simMouse.chr6 265194 8 + 636262 ctggcatg -s Anc0.Anc0refChr3 196327 8 - 222631 TCGGCTTG -s Anc1.Anc1refChr6 141848 8 - 197743 TCGGCTTG -s Anc2.Anc2refChr13 66707 8 - 96486 TCAGCTTG -s mr.mrrefChr5 117551 8 + 294540 ctggcatg -s mr.mrrefChr5 46838 8 - 294540 TTGTGTTC -s simCow_chr6.simCow.chr6 216718 8 - 602619 TCGGCTTG -s simDog_chr6.simDog.chr6 217650 8 - 593897 TAAGCTTG -s simHuman_chr6.simHuman.chr6 221506 8 - 601863 TCGGCTTG -s simHuman_chr6.simHuman.chr6 156659 8 - 601863 TCAGTTTG -s simMouse_chr6.simMouse.chr6 242252 8 - 636262 TTGTGTTC -s simRat_chr6.simRat.chr6 253109 8 - 647215 TTGTGTGC -s simRat_chr6.simRat.chr6 254726 8 + 647215 ctggcatg - -a -s simMouse_chr6.simMouse.chr6 265202 1 + 636262 t -s Anc0.Anc0refChr3 196335 1 - 222631 C -s Anc1.Anc1refChr6 141856 1 - 197743 C -s Anc2.Anc2refChr13 66715 1 - 96486 C -s mr.mrrefChr5 117559 1 + 294540 t -s mr.mrrefChr5 46846 1 - 294540 C -s simCow_chr6.simCow.chr6 216726 1 - 602619 C -s simDog_chr6.simDog.chr6 217658 1 - 593897 C -s simHuman_chr6.simHuman.chr6 221514 1 - 601863 C -s simHuman_chr6.simHuman.chr6 156672 1 - 601863 C -s simMouse_chr6.simMouse.chr6 242260 1 - 636262 C -s simRat_chr6.simRat.chr6 253117 1 - 647215 C -s simRat_chr6.simRat.chr6 254734 1 + 647215 t - -a -s simMouse_chr6.simMouse.chr6 265203 22 + 636262 agcaggtgtattcagtgtcctt -s Anc0.Anc0refChr3 196338 22 - 222631 ATCACATCTATTAAGTTAATTT -s Anc1.Anc1refChr6 141859 22 - 197743 ATCACATCTATTAAGTTAATTT -s Anc2.Anc2refChr13 66718 22 - 96486 ATCACATCCATTAAGTTGATTT -s mr.mrrefChr5 117560 22 + 294540 agcaggtgtattcagtgtcctt -s mr.mrrefChr5 46849 22 - 294540 ATCACATCTAATAAGTTAACTC -s simCow_chr6.simCow.chr6 216729 22 - 602619 GTCACATCCGTTAAGTAGACTT -s simDog_chr6.simDog.chr6 217661 21 - 593897 ATT-TGTCCATTGAGTTGATTT -s simHuman_chr6.simHuman.chr6 221517 22 - 601863 ATCAAATTTATTAAGTTAATTT -s simHuman_chr6.simHuman.chr6 156675 22 - 601863 ATCACATCTATTAAGTTAATTT -s simMouse_chr6.simMouse.chr6 242263 22 - 636262 ATCACAACTAATAAGTTAACTC -s simRat_chr6.simRat.chr6 253120 22 - 647215 ATCACATCTAATAAGTTAGCTC -s simRat_chr6.simRat.chr6 254735 22 + 647215 agcaggtgtatttagtgtcttt - -a -s simMouse_chr6.simMouse.chr6 265225 5 + 636262 acaga -s Anc0.Anc0refChr3 196364 5 - 222631 GCAGA -s Anc1.Anc1refChr6 141885 5 - 197743 GCAGA -s Anc2.Anc2refChr13 66744 5 - 96486 GCTGA -s mr.mrrefChr5 117582 5 + 294540 acaga -s mr.mrrefChr5 46875 5 - 294540 GCAGG -s simCow_chr6.simCow.chr6 216755 5 - 602619 GCTGA -s simDog_chr6.simDog.chr6 217686 5 - 593897 GCTGT -s simHuman_chr6.simHuman.chr6 221543 5 - 601863 GCAGA -s simHuman_chr6.simHuman.chr6 156701 5 - 601863 GCAGA -s simMouse_chr6.simMouse.chr6 242289 5 - 636262 GTAGG -s simRat_chr6.simRat.chr6 253146 5 - 647215 GCAGG -s simRat_chr6.simRat.chr6 254757 5 + 647215 ccaga - -a -s simMouse_chr6.simMouse.chr6 265230 9 + 636262 gacaacatt -s Anc0.Anc0refChr3 196369 9 - 222631 GAATAAATT -s Anc1.Anc1refChr6 141890 9 - 197743 GAATAAATT -s Anc2.Anc2refChr13 66749 9 - 96486 GAGTAAATT -s mr.mrrefChr5 117587 9 + 294540 gacaacatt -s mr.mrrefChr5 46880 9 - 294540 GAATACATA -s simCow_chr6.simCow.chr6 216760 9 - 602619 GAGCAAGTT -s simDog_chr6.simDog.chr6 217691 9 - 593897 GAGTAAATT -s simHuman_chr6.simHuman.chr6 221548 9 - 601863 GAATAAATG -s simHuman_chr6.simHuman.chr6 156706 9 - 601863 GAATAAATG -s simMouse_chr6.simMouse.chr6 242298 9 - 636262 GAATACCTA -s simRat_chr6.simRat.chr6 253151 9 - 647215 GAACACATT -s simRat_chr6.simRat.chr6 254762 9 + 647215 gatggcctt - -a -s simMouse_chr6.simMouse.chr6 265239 46 + 636262 cttgggttatctctagcagccagcttcctgttgacagtataaggat -s Anc0.Anc0refChr3 196532 35 - 222631 CACTAGTTATATCCCAGGGCTCCCTTCC-----------TGTGGAT -s Anc1.Anc1refChr6 142053 35 - 197743 CACTAGTTATATCCCAGGGCTCCCTTCC-----------TGTGGAT -s Anc2.Anc2refChr13 66912 35 - 96486 CACTAGCTATATCCCAGGGATCCCTTCC-----------TGTGGAT -s mr.mrrefChr5 117596 35 + 294540 cttgggttatctctagcagccagcttcc-----------taaggat -s mr.mrrefChr5 46996 35 - 294540 CACCAGCCATCTCCCAGGCATTCTTTCC-----------TGTTGAG -s simCow_chr6.simCow.chr6 217045 35 - 602619 CACTAGCGATATCTCAGGGATCCCTTAC-----------TGTGGGC -s simDog_chr6.simDog.chr6 217815 35 - 593897 CACTAGCCATATCCCAGGAATCTCTTTC-----------TGTGGAT -s simHuman_chr6.simHuman.chr6 221720 35 - 601863 CACTAGTTATATCCCAAGGCTCCCGTCC-----------AGTAGAT -s simHuman_chr6.simHuman.chr6 156844 33 - 601863 CATTAGTTATGTCCCAGGGCTCCCGTCC-----------TGTAG-- -s simMouse_chr6.simMouse.chr6 242414 35 - 636262 CACCTACCATCTCCCAGGCATTATTTCC-----------TGTTGAG -s simRat_chr6.simRat.chr6 253267 35 - 647215 CACCAGCCATCTCCCAGGAATTCTTTCC-----------CATTGAG -s simRat_chr6.simRat.chr6 254771 35 + 647215 cttgggttatctctagcagctggcttcC-----------CAAGGat - -a -s simMouse_chr6.simMouse.chr6 265285 15 + 636262 tgataaaagcagtct -s Anc0.Anc0refChr3 196574 14 - 222631 TG-TAAAAGTAATCA -s Anc1.Anc1refChr6 142095 14 - 197743 TG-TAAAAGTAATCA -s Anc2.Anc2refChr13 66954 14 - 96486 TG-AAAAACTAATCA -s mr.mrrefChr5 117631 14 + 294540 tg-taaaagcagtct -s mr.mrrefChr5 47038 14 - 294540 TG-TAAAAATAGTCA -s simCow_chr6.simCow.chr6 217087 9 - 602619 TC-AAAAATT----- -s simDog_chr6.simDog.chr6 217857 14 - 593897 GG-AAAAACTAATCA -s simHuman_chr6.simHuman.chr6 221762 14 - 601863 TG-TCAGTATAATCA -s simHuman_chr6.simHuman.chr6 156883 14 - 601863 TG-TCAGAGTAATCC -s simMouse_chr6.simMouse.chr6 242456 14 - 636262 TT-AAAAAATAGTCA -s simRat_chr6.simRat.chr6 253309 14 - 647215 TG-TAAAAATAGTCA -s simRat_chr6.simRat.chr6 254806 14 + 647215 tg-tataagcagtct - -a -s simMouse_chr6.simMouse.chr6 265300 14 + 636262 attaaaataataat -s Anc0.Anc0refChr3 196588 14 - 222631 AGGGACATAACAGT -s Anc1.Anc1refChr6 142110 14 - 197743 AGGGACATAACAGT -s Anc2.Anc2refChr13 66968 14 - 96486 AGGGACATAACAGT -s mr.mrrefChr5 117645 14 + 294540 attaaaataataat -s mr.mrrefChr5 47053 14 - 294540 AAGAAAATAACAAT -s simDog_chr6.simDog.chr6 217871 14 - 593897 AAGGACATAACAGT -s simHuman_chr6.simHuman.chr6 221777 14 - 601863 AGGGACATGACAGT -s simHuman_chr6.simHuman.chr6 156898 14 - 601863 GGGGACATTACAGT -s simMouse_chr6.simMouse.chr6 242471 14 - 636262 AAGAAAATAATAAT -s simRat_chr6.simRat.chr6 253324 14 - 647215 AAGAAAATAACGAT -s simRat_chr6.simRat.chr6 254820 14 + 647215 attaaaataataac - -a -s simMouse_chr6.simMouse.chr6 265314 1 + 636262 g -s mr.mrrefChr5 117659 1 + 294540 g -s simRat_chr6.simRat.chr6 254834 1 + 647215 a - -a -s simMouse_chr6.simMouse.chr6 265315 20 + 636262 atgaatgttgcatccctcaa -s Anc0.Anc0refChr3 196602 17 - 222631 ATACTTATTGATTCTGT--- -s Anc1.Anc1refChr6 142124 20 - 197743 ATACTTATTGATTCTGTcaa -s Anc2.Anc2refChr13 66982 17 - 96486 ATACTTATTCATTCTGT--- -s mr.mrrefChr5 117660 20 + 294540 atgaatgttgcatccctcaa -s mr.mrrefChr5 47067 20 - 294540 ATGCATATTGTCTCTGTCCA -s simDog_chr6.simDog.chr6 217885 17 - 593897 ATACTTATTCATTCTGT--- -s simHuman_chr6.simHuman.chr6 221791 17 - 601863 ATACTTTTTCATTCTGT--- -s simHuman_chr6.simHuman.chr6 156912 17 - 601863 ATACTTGTTGACTCTGT--- -s simMouse_chr6.simMouse.chr6 242485 20 - 636262 AGGCATATTGTCTCTGTCCA -s simRat_chr6.simRat.chr6 253338 20 - 647215 ATGCATATTGTCTATATCCA -s simRat_chr6.simRat.chr6 254835 20 + 647215 aagaatgttgaatctctcaa - -a -s simMouse_chr6.simMouse.chr6 265335 2 + 636262 gg -s Anc0.Anc0refChr3 196619 2 - 222631 GT -s Anc1.Anc1refChr6 142144 2 - 197743 GT -s Anc2.Anc2refChr13 66999 2 - 96486 GT -s mr.mrrefChr5 117680 2 + 294540 gg -s mr.mrrefChr5 47087 2 - 294540 GT -s simDog_chr6.simDog.chr6 217905 2 - 593897 GT -s simHuman_chr6.simHuman.chr6 221808 2 - 601863 GT -s simHuman_chr6.simHuman.chr6 156929 2 - 601863 GT -s simMouse_chr6.simMouse.chr6 242505 2 - 636262 GT -s simRat_chr6.simRat.chr6 253358 2 - 647215 GT -s simRat_chr6.simRat.chr6 254855 2 + 647215 gg - -a -s simMouse_chr6.simMouse.chr6 265337 2 + 636262 ga -s mr.mrrefChr5 117682 2 + 294540 ga -s simRat_chr6.simRat.chr6 254857 2 + 647215 ga - -a -s simMouse_chr6.simMouse.chr6 265339 1 + 636262 t -s Anc0.Anc0refChr3 196621 1 - 222631 T -s Anc1.Anc1refChr6 142146 1 - 197743 T -s Anc2.Anc2refChr13 67001 1 - 96486 T -s mr.mrrefChr5 117684 1 + 294540 t -s mr.mrrefChr5 47089 1 - 294540 T -s simCow_chr6.simCow.chr6 217096 1 - 602619 T -s simDog_chr6.simDog.chr6 217907 1 - 593897 T -s simHuman_chr6.simHuman.chr6 221810 1 - 601863 T -s simHuman_chr6.simHuman.chr6 156931 1 - 601863 T -s simMouse_chr6.simMouse.chr6 242507 1 - 636262 T -s simRat_chr6.simRat.chr6 253360 1 - 647215 T -s simRat_chr6.simRat.chr6 254859 1 + 647215 t - -a -s simMouse_chr6.simMouse.chr6 265340 13 + 636262 cattttgggagct -s Anc0.Anc0refChr3 196627 13 - 222631 TCTTCTAAAGGAT -s Anc1.Anc1refChr6 142152 13 - 197743 TCTTCTAAAGGAT -s Anc2.Anc2refChr13 67007 13 - 96486 TCCTCTAAAGGAT -s mr.mrrefChr5 117685 13 + 294540 cattttgggagct -s mr.mrrefChr5 47095 13 - 294540 TCCCCTAAGAGAT -s simCow_chr6.simCow.chr6 217102 13 - 602619 TCCTCTAAAGGAT -s simDog_chr6.simDog.chr6 217913 13 - 593897 TCCTCGAAAGAAT -s simHuman_chr6.simHuman.chr6 221821 13 - 601863 TTTTCTAAAGGAT -s simHuman_chr6.simHuman.chr6 156932 13 - 601863 TCTTCTAAAGGAT -s simMouse_chr6.simMouse.chr6 242513 13 - 636262 TCCCCTAAGAGAT -s simRat_chr6.simRat.chr6 253366 13 - 647215 TCCCCTAAGAGAC -s simRat_chr6.simRat.chr6 254860 13 + 647215 cattttgcgagcc - -a -s simMouse_chr6.simMouse.chr6 265353 4 + 636262 agaa -s Anc0.Anc0refChr3 196640 4 - 222631 GGAG -s Anc1.Anc1refChr6 142165 4 - 197743 GGAG -s Anc2.Anc2refChr13 67020 4 - 96486 GGAG -s mr.mrrefChr5 117698 4 + 294540 agaa -s mr.mrrefChr5 47108 4 - 294540 AGTG -s simCow_chr6.simCow.chr6 217115 4 - 602619 AAAG -s simDog_chr6.simDog.chr6 217926 2 - 593897 --AG -s simHuman_chr6.simHuman.chr6 221834 4 - 601863 GGAG -s simHuman_chr6.simHuman.chr6 156945 4 - 601863 GGAG -s simMouse_chr6.simMouse.chr6 242562 4 - 636262 AGTG -s simRat_chr6.simRat.chr6 253379 4 - 647215 AGTG -s simRat_chr6.simRat.chr6 254873 4 + 647215 agaa - -a -s simMouse_chr6.simMouse.chr6 265357 17 + 636262 gtctgggctgcagtact -s Anc0.Anc0refChr3 196646 17 - 222631 GTCTAGACTACAATGCT -s Anc1.Anc1refChr6 142171 17 - 197743 GTCTAGACTACAATGCT -s Anc2.Anc2refChr13 67026 17 - 96486 GTCTAGACTACAAGGCT -s mr.mrrefChr5 117702 17 + 294540 gtctgggctgcagtact -s mr.mrrefChr5 47114 17 - 294540 GAATAGATCACAATGTT -s simCow_chr6.simCow.chr6 217121 17 - 602619 GTTAAGACCACAAGACC -s simDog_chr6.simDog.chr6 217930 17 - 593897 GTCCGGACTACAAGGCT -s simHuman_chr6.simHuman.chr6 221840 17 - 601863 GTCTAGACTAAAATGCT -s simHuman_chr6.simHuman.chr6 156951 17 - 601863 GTCTAGACTAAAAGGCT -s simMouse_chr6.simMouse.chr6 242568 17 - 636262 GAATAGATCACAACGTT -s simRat_chr6.simRat.chr6 253385 17 - 647215 GCATAAATCACAATCTT -s simRat_chr6.simRat.chr6 254877 17 + 647215 gtctgggctgcagtatt - -a -s simMouse_chr6.simMouse.chr6 265374 3 + 636262 gct -s Anc0.Anc0refChr3 196665 3 - 222631 GAT -s Anc1.Anc1refChr6 142190 3 - 197743 GAT -s Anc2.Anc2refChr13 67045 3 - 96486 GAT -s mr.mrrefChr5 117719 3 + 294540 gct -s mr.mrrefChr5 47133 3 - 294540 GAT -s simCow_chr6.simCow.chr6 217140 3 - 602619 CAT -s simDog_chr6.simDog.chr6 217949 3 - 593897 TAT -s simHuman_chr6.simHuman.chr6 221859 3 - 601863 GAT -s simHuman_chr6.simHuman.chr6 156970 3 - 601863 GAT -s simMouse_chr6.simMouse.chr6 242587 3 - 636262 CAT -s simRat_chr6.simRat.chr6 253404 3 - 647215 GAC -s simRat_chr6.simRat.chr6 254894 3 + 647215 act - -a -s simMouse_chr6.simMouse.chr6 265377 2 + 636262 gg -s Anc0.Anc0refChr3 196673 2 - 222631 AT -s Anc1.Anc1refChr6 142198 2 - 197743 AT -s Anc2.Anc2refChr13 67053 2 - 96486 AT -s mr.mrrefChr5 117722 2 + 294540 gg -s mr.mrrefChr5 47141 2 - 294540 AT -s simCow_chr6.simCow.chr6 217148 2 - 602619 AT -s simDog_chr6.simDog.chr6 217957 2 - 593897 AC -s simHuman_chr6.simHuman.chr6 221862 2 - 601863 AG -s simHuman_chr6.simHuman.chr6 156973 2 - 601863 AT -s simMouse_chr6.simMouse.chr6 242595 2 - 636262 AT -s simRat_chr6.simRat.chr6 253412 2 - 647215 AT -s simRat_chr6.simRat.chr6 254897 2 + 647215 ga - -a -s simMouse_chr6.simMouse.chr6 265379 1 + 636262 c -s Anc0.Anc0refChr3 196675 1 - 222631 A -s Anc1.Anc1refChr6 142200 1 - 197743 A -s Anc2.Anc2refChr13 67055 1 - 96486 A -s mr.mrrefChr5 117724 1 + 294540 c -s simCow_chr6.simCow.chr6 217150 1 - 602619 A -s simDog_chr6.simDog.chr6 217959 1 - 593897 A -s simHuman_chr6.simHuman.chr6 221864 1 - 601863 C -s simHuman_chr6.simHuman.chr6 156975 1 - 601863 A -s simRat_chr6.simRat.chr6 254899 1 + 647215 c - -a -s simMouse_chr6.simMouse.chr6 265380 7 + 636262 accatca -s Anc0.Anc0refChr3 196676 7 - 222631 GCTGGTG -s Anc1.Anc1refChr6 142201 7 - 197743 GCTGGTG -s Anc2.Anc2refChr13 67056 7 - 96486 GCTGGTG -s mr.mrrefChr5 117725 7 + 294540 accatca -s mr.mrrefChr5 47143 7 - 294540 GCTAGTT -s simCow_chr6.simCow.chr6 217151 7 - 602619 GCTCGTG -s simDog_chr6.simDog.chr6 217960 7 - 593897 GCTGGCG -s simHuman_chr6.simHuman.chr6 156976 7 - 601863 ACTGGTG -s simMouse_chr6.simMouse.chr6 242597 7 - 636262 GCTAGTT -s simRat_chr6.simRat.chr6 253414 7 - 647215 GCTAGAT -s simRat_chr6.simRat.chr6 254900 7 + 647215 accatca - -a -s simMouse_chr6.simMouse.chr6 265387 4 + 636262 gcat -s Anc0.Anc0refChr3 196683 4 - 222631 CTTT -s Anc1.Anc1refChr6 142208 4 - 197743 CTTT -s Anc2.Anc2refChr13 67063 4 - 96486 CTTT -s mr.mrrefChr5 117732 4 + 294540 gcat -s mr.mrrefChr5 47150 4 - 294540 TCTT -s simCow_chr6.simCow.chr6 217158 4 - 602619 TTTT -s simDog_chr6.simDog.chr6 217967 4 - 593897 CTTT -s simHuman_chr6.simHuman.chr6 221865 4 - 601863 CTTT -s simHuman_chr6.simHuman.chr6 156983 4 - 601863 TTTT -s simMouse_chr6.simMouse.chr6 242604 4 - 636262 TCTT -s simRat_chr6.simRat.chr6 253421 4 - 647215 TCTT -s simRat_chr6.simRat.chr6 254907 4 + 647215 gcat - -a -s simMouse_chr6.simMouse.chr6 265391 15 + 636262 cacatctccattttt -s Anc0.Anc0refChr3 196687 15 - 222631 CTCTTCCCCATGATT -s Anc1.Anc1refChr6 142212 15 - 197743 CTCTTCCCCATGATT -s Anc2.Anc2refChr13 67068 15 - 96486 CTCTCCTCCATGATT -s mr.mrrefChr5 117736 15 + 294540 cacatctccattttt -s mr.mrrefChr5 47154 15 - 294540 TCTCTCCCTATGATT -s simCow_chr6.simCow.chr6 217163 14 - 602619 CTCTCCTCCATGAT- -s simDog_chr6.simDog.chr6 217972 15 - 593897 CTCTCCTCCATGATT -s simHuman_chr6.simHuman.chr6 221869 15 - 601863 CTCTTCCCCATGATT -s simHuman_chr6.simHuman.chr6 156987 15 - 601863 CTCTCCCCCATGATT -s simMouse_chr6.simMouse.chr6 242608 15 - 636262 TCTCTTCCTATGATT -s simRat_chr6.simRat.chr6 253425 15 - 647215 TCTCTCCCTATGATT -s simRat_chr6.simRat.chr6 254911 15 + 647215 cacatttccatcttt - -a -s simMouse_chr6.simMouse.chr6 265406 2 + 636262 ta -s Anc0.Anc0refChr3 196703 2 - 222631 GG -s Anc1.Anc1refChr6 142228 2 - 197743 GG -s Anc2.Anc2refChr13 67084 2 - 96486 GA -s mr.mrrefChr5 117751 2 + 294540 ta -s mr.mrrefChr5 47169 2 - 294540 GG -s simCow_chr6.simCow.chr6 217178 2 - 602619 AA -s simDog_chr6.simDog.chr6 217988 2 - 593897 GA -s simHuman_chr6.simHuman.chr6 221922 2 - 601863 GG -s simHuman_chr6.simHuman.chr6 157003 2 - 601863 GG -s simMouse_chr6.simMouse.chr6 242623 2 - 636262 GG -s simRat_chr6.simRat.chr6 253440 2 - 647215 GG -s simRat_chr6.simRat.chr6 254926 2 + 647215 ta - -a -s simMouse_chr6.simMouse.chr6 265408 170 + 636262 aaagcactctatcaggaacttgcaattctcgtaaTGTAATGAAggtcattatggtaccccagtatttctgctatcgggaaggcttggtgtatgaccaaaccagacttggcatgcacccatgtatgTCCCCTGCACTTGCTCACCACAGATTAACAAAGGTGACCACGAGT -s mr.mrrefChr5 117753 170 + 294540 aaagcactctatcaggaacttgcaattctcgtaatgtaatGAAggtcattatggtaccccagtatttctgctatcgggaaggcttggtgtatgaccaaaccagacttggcatgcacccatgtatgTCCCCTGCACTTGCTCACCACAGATTAACAAAGGTGACCACGAGT -s simRat_chr6.simRat.chr6 254928 170 + 647215 aaagcaccctatcaggaacttgcaattttcataatataatGAAGATCATTATGGTAtgccagtatttctgctatctggaaggcttggtatatgaccagaccagacttggcatacacccaagtgtgCCCTCTGCACTTGCTTACCACAGGTTAAAAAGGGTGACCACATGT - -a -s simMouse_chr6.simMouse.chr6 265578 11 + 636262 CCTATACAGAC -s mr.mrrefChr5 117923 11 + 294540 CCTATACAGAC -s simRat_chr6.simRat.chr6 255100 11 + 647215 CCTATACTGAC - -a -s simMouse_chr6.simMouse.chr6 265589 7 + 636262 GGCTGAA -s Anc0.Anc0refChr3 196705 7 - 222631 GGCTCAA -s Anc1.Anc1refChr6 142230 7 - 197743 GGCTCAA -s Anc2.Anc2refChr13 67086 7 - 96486 GCCTCAA -s mr.mrrefChr5 117934 7 + 294540 GGCTGAA -s mr.mrrefChr5 47171 7 - 294540 GCCTTAA -s simCow_chr6.simCow.chr6 217180 7 - 602619 GCCTCAA -s simDog_chr6.simDog.chr6 217990 7 - 593897 GCCTCAA -s simHuman_chr6.simHuman.chr6 221924 7 - 601863 GGCTCAA -s simHuman_chr6.simHuman.chr6 157005 7 - 601863 GGCTCAA -s simMouse_chr6.simMouse.chr6 242625 7 - 636262 GCCTTAA -s simRat_chr6.simRat.chr6 253442 7 - 647215 GCCTTAA -s simRat_chr6.simRat.chr6 255111 7 + 647215 AGCTGAA - -a -s simMouse_chr6.simMouse.chr6 265596 3 + 636262 CAC -s Anc0.Anc0refChr3 196712 3 - 222631 CAT -s Anc1.Anc1refChr6 142237 3 - 197743 CAT -s Anc2.Anc2refChr13 67093 3 - 96486 CAT -s mr.mrrefChr5 117941 3 + 294540 CAC -s mr.mrrefChr5 47178 3 - 294540 GAT -s simCow_chr6.simCow.chr6 217187 2 - 602619 -AT -s simDog_chr6.simDog.chr6 217997 3 - 593897 CAT -s simHuman_chr6.simHuman.chr6 221931 3 - 601863 CAT -s simHuman_chr6.simHuman.chr6 157012 3 - 601863 CAT -s simMouse_chr6.simMouse.chr6 242632 3 - 636262 GAT -s simRat_chr6.simRat.chr6 255118 3 + 647215 CAT - -a -s simMouse_chr6.simMouse.chr6 265599 2 + 636262 GG -s Anc0.Anc0refChr3 196715 2 - 222631 GA -s Anc1.Anc1refChr6 142240 2 - 197743 GA -s Anc2.Anc2refChr13 67096 2 - 96486 GA -s mr.mrrefChr5 117944 2 + 294540 GG -s mr.mrrefChr5 47181 2 - 294540 GA -s simCow_chr6.simCow.chr6 217189 2 - 602619 GA -s simDog_chr6.simDog.chr6 218000 2 - 593897 GA -s simHuman_chr6.simHuman.chr6 221934 2 - 601863 GA -s simHuman_chr6.simHuman.chr6 157015 2 - 601863 GA -s simMouse_chr6.simMouse.chr6 242635 2 - 636262 GA -s simRat_chr6.simRat.chr6 253449 2 - 647215 GA -s simRat_chr6.simRat.chr6 255121 2 + 647215 AA - -a -s simMouse_chr6.simMouse.chr6 265601 7 + 636262 TGGATTC -s Anc0.Anc0refChr3 196726 7 - 222631 TGGCTGC -s Anc1.Anc1refChr6 142251 7 - 197743 TGGCTGC -s Anc2.Anc2refChr13 67107 7 - 96486 TGGCTGC -s mr.mrrefChr5 117946 7 + 294540 TGGATTC -s mr.mrrefChr5 47190 7 - 294540 TGGATGC -s simCow_chr6.simCow.chr6 217200 7 - 602619 TGGCTGC -s simDog_chr6.simDog.chr6 218011 5 - 593897 TAGCT-- -s simHuman_chr6.simHuman.chr6 221945 7 - 601863 TGGTTGC -s simHuman_chr6.simHuman.chr6 157026 5 - 601863 TGGCT-- -s simMouse_chr6.simMouse.chr6 242644 7 - 636262 TAGATGC -s simRat_chr6.simRat.chr6 253458 7 - 647215 TGGATGC -s simRat_chr6.simRat.chr6 255123 7 + 647215 TGGATTC - -a -s simMouse_chr6.simMouse.chr6 265608 2 + 636262 AT -s Anc0.Anc0refChr3 196738 2 - 222631 AT -s Anc1.Anc1refChr6 142263 2 - 197743 AT -s Anc2.Anc2refChr13 67119 2 - 96486 GT -s mr.mrrefChr5 117953 2 + 294540 AT -s mr.mrrefChr5 47202 2 - 294540 TT -s simCow_chr6.simCow.chr6 217212 2 - 602619 GT -s simHuman_chr6.simHuman.chr6 221952 2 - 601863 AT -s simHuman_chr6.simHuman.chr6 157031 1 - 601863 -C -s simMouse_chr6.simMouse.chr6 242656 2 - 636262 TT -s simRat_chr6.simRat.chr6 253470 2 - 647215 AT -s simRat_chr6.simRat.chr6 255130 2 + 647215 AT - -a -s simMouse_chr6.simMouse.chr6 265610 1 + 636262 A -s mr.mrrefChr5 117955 1 + 294540 A -s simRat_chr6.simRat.chr6 255132 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 265611 15 + 636262 GGCCTGTGCTACTCT -s Anc0.Anc0refChr3 196740 15 - 222631 GGCCAGAGGTAGTCT -s Anc1.Anc1refChr6 142265 15 - 197743 GGCCAGAGGTAGTCT -s Anc2.Anc2refChr13 67121 15 - 96486 GAGCAGAGGTAGGCT -s mr.mrrefChr5 117956 15 + 294540 GGCCTGTGCTACTCT -s mr.mrrefChr5 47204 15 - 294540 TGCCAGAGGCATTCT -s simCow_chr6.simCow.chr6 217214 15 - 602619 GAGCAGAGGTAGGCT -s simHuman_chr6.simHuman.chr6 221954 1 - 601863 G-------------- -s simHuman_chr6.simHuman.chr6 157032 1 - 601863 A-------------- -s simMouse_chr6.simMouse.chr6 242658 15 - 636262 TGCCAGAGGCATTCT -s simRat_chr6.simRat.chr6 253472 15 - 647215 TGCCAGAGGCGTTCT -s simRat_chr6.simRat.chr6 255133 15 + 647215 GGCCTGTGCTACACT - -a -s simMouse_chr6.simMouse.chr6 265626 2 + 636262 TT -s Anc0.Anc0refChr3 196755 2 - 222631 GC -s Anc1.Anc1refChr6 142280 2 - 197743 GC -s Anc2.Anc2refChr13 67136 2 - 96486 GC -s mr.mrrefChr5 117971 2 + 294540 TT -s simCow_chr6.simCow.chr6 217229 2 - 602619 GC -s simRat_chr6.simRat.chr6 255148 2 + 647215 TT - -a -s simMouse_chr6.simMouse.chr6 265628 4 + 636262 TACT -s Anc0.Anc0refChr3 196757 4 - 222631 TAAT -s Anc1.Anc1refChr6 142282 4 - 197743 TAAT -s Anc2.Anc2refChr13 67138 4 - 96486 TAAT -s mr.mrrefChr5 117973 4 + 294540 TACT -s mr.mrrefChr5 47219 4 - 294540 TAAG -s simCow_chr6.simCow.chr6 217231 4 - 602619 TAAG -s simDog_chr6.simDog.chr6 218016 3 - 593897 -ACT -s simHuman_chr6.simHuman.chr6 221955 1 - 601863 ---T -s simHuman_chr6.simHuman.chr6 157033 1 - 601863 ---T -s simMouse_chr6.simMouse.chr6 242673 4 - 636262 TAAG -s simRat_chr6.simRat.chr6 253487 4 - 647215 TAAG -s simRat_chr6.simRat.chr6 255150 4 + 647215 TAAT - -a -s simMouse_chr6.simMouse.chr6 265632 749 + 636262 CTGGAGTCATTATTTTGTGTAACACATCATTATCCAATACTGGCAATGATACCAGAGGCTACTATTTAATATCTGGTCAAGTTGTAAATATGCTCATAAGTCCCGATATCCTGTGCTCCATAGCATCCCAGTCTTCTTCATTGTACATAGAATGAGTTGCAAAGGGTGTGAGACCCTCTGAGTTGTAAGAATCAAGGGGTTGGCAAATAACCTGAGGACTTGAATACAATCCAAGTGCCATCCAAGTGCTATCCGGCTCTTTCCTAATCACAATCATCTTCAGGTGGATGTCAAGTCTAGGCCCTGGTTGACAGACAATTGTCATCACCCTCAGGCAAATGTAAGGTTATACATGGGAGAGTGCACAGCAATCACAGAATGTTGGTCCAGTCCAAACCCCTGGCTATACTTAGAATTTATCCACTAGACGTCCCAGTAAATGGTTGGTCACAATGTAACTCATACCCCACAGTCAGACATGAGTAATGTAATTCACTTAGATTCAAGGCCGCAAATCAGTTGTCTTGGTGCAGGAGGCATACAGCATGCACCTAATGAACATACATTTGAGGTAATCACTACAGTTAATTTTAATGCAGCTAGGCCAAAATGAGATAGTTAATCTTAGTGACTCCACATTGGCGAGCTTCTCTCTCTTCTGCTGCCTGAAGTTCAGACGCCCTGGAAGACTGGTGTTACCTAGGCTTGGGACTACCCACTGTAGGGAGACCAAACCCAGTATTATGATA -s Anc0.Anc0refChr3 196766 20 - 222631 GCAGAGGCATTATT----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AAGAGT----------- -s Anc1.Anc1refChr6 142291 20 - 197743 GCAGAGGCATTATT----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AAGAGT----------- -s Anc2.Anc2refChr13 67147 20 - 96486 GCAGAGGCATTATT----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AGGAGT----------- -s mr.mrrefChr5 117977 20 + 294540 CTGGAGTCATTATT----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AACCCA----------- -s mr.mrrefChr5 47228 20 - 294540 CCGGTGGCATTATT----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AATTAA----------- -s simCow_chr6.simCow.chr6 217240 20 - 602619 GCAGAGGTATTATT----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AGGATT----------- -s simDog_chr6.simDog.chr6 218027 20 - 593897 GCAGAGGCATCATT----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AGGAGT----------- -s simHuman_chr6.simHuman.chr6 221961 20 - 601863 GCAGAGGCATTATT----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AAGAGT----------- -s simHuman_chr6.simHuman.chr6 157039 20 - 601863 GTAGAGGCATTAAT----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AAGAGT----------- -s simMouse_chr6.simMouse.chr6 242682 4 - 636262 --GGTA----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- -s simRat_chr6.simRat.chr6 253496 20 - 647215 CCAGTGGCATTATT----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AATTAA----------- -s simRat_chr6.simRat.chr6 255154 20 + 647215 CGGGAGTCATCATT----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GACCCT----------- - -a -s simMouse_chr6.simMouse.chr6 266381 14 + 636262 GATATTGTTTCATT -s Anc0.Anc0refChr3 196786 14 - 222631 TAGATGGAGTTAAC -s Anc1.Anc1refChr6 142311 14 - 197743 TAGATGGAGTTAAC -s Anc2.Anc2refChr13 67167 14 - 96486 TAGATGGAGTTAAC -s mr.mrrefChr5 117997 14 + 294540 GATATTGTTTCATT -s mr.mrrefChr5 47248 14 - 294540 GGTATGAAGTAAGC -s simCow_chr6.simCow.chr6 217260 14 - 602619 CAGACAGAGTTAAC -s simDog_chr6.simDog.chr6 218047 14 - 593897 TAGATTGAGTTTAC -s simHuman_chr6.simHuman.chr6 221981 14 - 601863 TAGATGGAGTTGAC -s simHuman_chr6.simHuman.chr6 157088 14 - 601863 TAGACGGAGTCAAC -s simMouse_chr6.simMouse.chr6 242686 10 - 636262 ----TGAAGTAAGC -s simRat_chr6.simRat.chr6 253516 14 - 647215 GGTATGAAGTAAGC -s simRat_chr6.simRat.chr6 391942 14 - 647215 AAGATTGTTTCATT - -a -s simMouse_chr6.simMouse.chr6 266395 1 + 636262 T -s Anc0.Anc0refChr3 196842 1 - 222631 T -s Anc1.Anc1refChr6 142367 1 - 197743 T -s Anc2.Anc2refChr13 67223 1 - 96486 T -s mr.mrrefChr5 118011 1 + 294540 T -s mr.mrrefChr5 47319 1 - 294540 T -s simCow_chr6.simCow.chr6 217316 1 - 602619 T -s simDog_chr6.simDog.chr6 218117 1 - 593897 T -s simHuman_chr6.simHuman.chr6 222037 1 - 601863 T -s simHuman_chr6.simHuman.chr6 157144 1 - 601863 T -s simMouse_chr6.simMouse.chr6 242753 1 - 636262 T -s simRat_chr6.simRat.chr6 253587 1 - 647215 T -s simRat_chr6.simRat.chr6 391956 1 - 647215 T - -a -s simMouse_chr6.simMouse.chr6 266396 15 + 636262 CCCGGCTGCCCTCTA -s Anc0.Anc0refChr3 196843 15 - 222631 CTTGGGTTCCCCATA -s Anc1.Anc1refChr6 142368 15 - 197743 CTTGGGTTCCCCATA -s Anc2.Anc2refChr13 67224 15 - 96486 CTTGGGTTCCCCATA -s mr.mrrefChr5 118012 15 + 294540 CCCGGCTGCCCTCTA -s mr.mrrefChr5 47324 15 - 294540 CTAGAATTCCCCATA -s simCow_chr6.simCow.chr6 217317 15 - 602619 CTAGGATTCCCTATA -s simDog_chr6.simDog.chr6 218118 14 - 593897 CTTGGG-TCCCCATA -s simHuman_chr6.simHuman.chr6 222038 15 - 601863 GTTGGATTTCCCATA -s simHuman_chr6.simHuman.chr6 157145 15 - 601863 CTTGGGTTTCCCATA -s simMouse_chr6.simMouse.chr6 242758 15 - 636262 CTAGAATTCCCCATA -s simRat_chr6.simRat.chr6 253592 15 - 647215 CTAGAATTCCCCATA -s simRat_chr6.simRat.chr6 391957 15 - 647215 CCTGGTTGCCCTCTA - -a -s simMouse_chr6.simMouse.chr6 266411 1 + 636262 G -s Anc0.Anc0refChr3 196858 1 - 222631 T -s Anc1.Anc1refChr6 142383 1 - 197743 T -s Anc2.Anc2refChr13 67239 1 - 96486 T -s mr.mrrefChr5 118027 1 + 294540 G -s mr.mrrefChr5 47339 1 - 294540 G -s simCow_chr6.simCow.chr6 217347 1 - 602619 C -s simDog_chr6.simDog.chr6 218132 1 - 593897 T -s simHuman_chr6.simHuman.chr6 222053 1 - 601863 T -s simHuman_chr6.simHuman.chr6 157160 1 - 601863 T -s simMouse_chr6.simMouse.chr6 242773 1 - 636262 G -s simRat_chr6.simRat.chr6 253607 1 - 647215 G -s simRat_chr6.simRat.chr6 391972 1 - 647215 G - -a -s simMouse_chr6.simMouse.chr6 266412 5 + 636262 ATAAA -s Anc0.Anc0refChr3 196859 5 - 222631 GGAAA -s Anc1.Anc1refChr6 142384 5 - 197743 GGAAA -s Anc2.Anc2refChr13 67248 5 - 96486 GGAAA -s mr.mrrefChr5 118028 5 + 294540 ATAAA -s mr.mrrefChr5 47340 5 - 294540 GTAAA -s simCow_chr6.simCow.chr6 217356 5 - 602619 GGAAA -s simDog_chr6.simDog.chr6 218141 5 - 593897 GTCAA -s simHuman_chr6.simHuman.chr6 222054 5 - 601863 GGAAG -s simHuman_chr6.simHuman.chr6 157161 5 - 601863 GGAAA -s simMouse_chr6.simMouse.chr6 242774 5 - 636262 GTAAA -s simRat_chr6.simRat.chr6 253608 5 - 647215 GTCAA -s simRat_chr6.simRat.chr6 391973 5 - 647215 TCAAA - -a -s simMouse_chr6.simMouse.chr6 266417 8 + 636262 TGGAACTT -s Anc0.Anc0refChr3 196867 8 - 222631 AGGGGGTG -s Anc1.Anc1refChr6 142392 8 - 197743 AGGGGGTG -s Anc2.Anc2refChr13 67256 8 - 96486 AGAGGTTG -s mr.mrrefChr5 118033 8 + 294540 TGGAACTT -s mr.mrrefChr5 47348 8 - 294540 AGGAGCTG -s simCow_chr6.simCow.chr6 217364 8 - 602619 ACAGGTTG -s simDog_chr6.simDog.chr6 218149 8 - 593897 ATAGGTTG -s simHuman_chr6.simHuman.chr6 222062 8 - 601863 TGTGAGTG -s simHuman_chr6.simHuman.chr6 157169 8 - 601863 AGGGCGTG -s simMouse_chr6.simMouse.chr6 242782 8 - 636262 GGGAGCTG -s simRat_chr6.simRat.chr6 253616 8 - 647215 ACTACCTG -s simRat_chr6.simRat.chr6 391978 8 - 647215 TGGAACTT - -a -s simMouse_chr6.simMouse.chr6 266425 8 + 636262 GATGACCA -s Anc0.Anc0refChr3 196875 8 - 222631 GATGAGCT -s Anc1.Anc1refChr6 142400 8 - 197743 GATGAGCT -s Anc2.Anc2refChr13 67264 8 - 96486 GATGAGCT -s mr.mrrefChr5 118041 8 + 294540 GATGACCA -s mr.mrrefChr5 47372 8 - 294540 CATGAGCT -s simCow_chr6.simCow.chr6 217372 8 - 602619 GATGAGTT -s simDog_chr6.simDog.chr6 218157 8 - 593897 GATGAGCT -s simHuman_chr6.simHuman.chr6 222070 8 - 601863 AATGAGCT -s simHuman_chr6.simHuman.chr6 157177 8 - 601863 AATGATCT -s simMouse_chr6.simMouse.chr6 242806 8 - 636262 CATGAGCT -s simRat_chr6.simRat.chr6 253640 8 - 647215 CATGAGAT -s simRat_chr6.simRat.chr6 391986 8 - 647215 GATGACCA - -a -s simMouse_chr6.simMouse.chr6 266433 9 + 636262 TTCTGTCAT -s Anc0.Anc0refChr3 196883 7 - 222631 -T-TGGAGG -s Anc1.Anc1refChr6 142431 8 - 197743 CT-TGGAGG -s Anc2.Anc2refChr13 67272 7 - 96486 -C-TGTAGG -s mr.mrrefChr5 118049 8 + 294540 TT-TGTCAT -s mr.mrrefChr5 47405 8 - 294540 AT-TAGTTG -s simCow_chr6.simCow.chr6 217380 7 - 602619 -T-AGTGAG -s simDog_chr6.simDog.chr6 218165 7 - 593897 -C-TGTAGG -s simHuman_chr6.simHuman.chr6 222101 8 - 601863 CT-TAGAGG -s simHuman_chr6.simHuman.chr6 157208 7 - 601863 C--TGGCAT -s simRat_chr6.simRat.chr6 253673 8 - 647215 AT-TAGTTG -s simRat_chr6.simRat.chr6 391994 8 - 647215 TT-TGTCAT - -a -s simMouse_chr6.simMouse.chr6 266442 1 + 636262 T -s Anc0.Anc0refChr3 196890 1 - 222631 A -s Anc1.Anc1refChr6 142439 1 - 197743 A -s Anc2.Anc2refChr13 67279 1 - 96486 A -s mr.mrrefChr5 118057 1 + 294540 T -s mr.mrrefChr5 47413 1 - 294540 A -s simCow_chr6.simCow.chr6 217387 1 - 602619 A -s simDog_chr6.simDog.chr6 218172 1 - 593897 A -s simHuman_chr6.simHuman.chr6 222109 1 - 601863 G -s simHuman_chr6.simHuman.chr6 157215 1 - 601863 T -s simRat_chr6.simRat.chr6 253682 1 - 647215 A -s simRat_chr6.simRat.chr6 392002 1 - 647215 T - -a -s simMouse_chr6.simMouse.chr6 266443 3 + 636262 CTG -s mr.mrrefChr5 118058 3 + 294540 CTG -s simRat_chr6.simRat.chr6 392003 3 - 647215 CTG - -a -s simMouse_chr6.simMouse.chr6 266446 11 + 636262 TATGATTTATT -s Anc0.Anc0refChr3 196891 11 - 222631 TGTGGTCTACC -s Anc1.Anc1refChr6 142440 11 - 197743 TGTGGTCTACC -s Anc2.Anc2refChr13 67280 11 - 96486 TGTGGTCTACC -s mr.mrrefChr5 118061 11 + 294540 TATGATTTATT -s mr.mrrefChr5 47414 11 - 294540 TATGCCCTACC -s simCow_chr6.simCow.chr6 217388 11 - 602619 TGGGGTCTACC -s simDog_chr6.simDog.chr6 218173 11 - 593897 TGTGGTCTAGC -s simHuman_chr6.simHuman.chr6 222110 11 - 601863 TGTGGTCTACC -s simHuman_chr6.simHuman.chr6 157216 5 - 601863 TCTGG------ -s simRat_chr6.simRat.chr6 253683 11 - 647215 TATGCCCTACC -s simRat_chr6.simRat.chr6 392006 11 - 647215 TATGATTTATT - -a -s simMouse_chr6.simMouse.chr6 266457 8 + 636262 GTGTTTGA -s mr.mrrefChr5 118072 8 + 294540 GTGTTTGA -s simRat_chr6.simRat.chr6 392017 8 - 647215 GTATTTGA - -a -s simMouse_chr6.simMouse.chr6 266465 10 + 636262 AGTGAGTCTA -s Anc0.Anc0refChr3 196902 10 - 222631 AATACAACTA -s Anc1.Anc1refChr6 142451 10 - 197743 AATACAACTA -s Anc2.Anc2refChr13 67291 10 - 96486 AATACAACTA -s mr.mrrefChr5 118080 10 + 294540 AGTGAGTCTA -s mr.mrrefChr5 47425 10 - 294540 AGCATACCCA -s simCow_chr6.simCow.chr6 217399 10 - 602619 AATGTGACTA -s simDog_chr6.simDog.chr6 218184 10 - 593897 AATACAACTA -s simHuman_chr6.simHuman.chr6 222121 10 - 601863 AACACAACCA -s simMouse_chr6.simMouse.chr6 242839 10 - 636262 AGCATACCCA -s simRat_chr6.simRat.chr6 253694 10 - 647215 AGCATCCCCA -s simRat_chr6.simRat.chr6 392025 10 - 647215 AGTGAGTCTA - -a -s simMouse_chr6.simMouse.chr6 266475 2 + 636262 TT -s Anc0.Anc0refChr3 196912 2 - 222631 TC -s Anc1.Anc1refChr6 142461 2 - 197743 TC -s Anc2.Anc2refChr13 67302 2 - 96486 TC -s mr.mrrefChr5 118090 2 + 294540 TT -s mr.mrrefChr5 47435 2 - 294540 TT -s simCow_chr6.simCow.chr6 217453 2 - 602619 TC -s simDog_chr6.simDog.chr6 218195 2 - 593897 TT -s simHuman_chr6.simHuman.chr6 222131 2 - 601863 TC -s simMouse_chr6.simMouse.chr6 242849 2 - 636262 TT -s simRat_chr6.simRat.chr6 253704 2 - 647215 TT -s simRat_chr6.simRat.chr6 392035 2 - 647215 TA - -a -s simMouse_chr6.simMouse.chr6 266477 4 + 636262 GTCC -s Anc0.Anc0refChr3 196918 4 - 222631 CACA -s Anc1.Anc1refChr6 142467 4 - 197743 CACA -s Anc2.Anc2refChr13 67308 4 - 96486 CACA -s mr.mrrefChr5 118092 4 + 294540 GTCC -s mr.mrrefChr5 47441 4 - 294540 ATCA -s simCow_chr6.simCow.chr6 217459 4 - 602619 CATC -s simDog_chr6.simDog.chr6 218201 4 - 593897 CACA -s simHuman_chr6.simHuman.chr6 222137 4 - 601863 CACA -s simHuman_chr6.simHuman.chr6 157225 4 - 601863 TAAA -s simMouse_chr6.simMouse.chr6 242855 4 - 636262 ATCA -s simRat_chr6.simRat.chr6 253710 4 - 647215 GTCA -s simRat_chr6.simRat.chr6 392037 4 - 647215 CTGC - -a -s simMouse_chr6.simMouse.chr6 266481 2 + 636262 AG -s Anc0.Anc0refChr3 196922 2 - 222631 TA -s Anc1.Anc1refChr6 142471 2 - 197743 TA -s Anc2.Anc2refChr13 67312 2 - 96486 TA -s mr.mrrefChr5 118096 2 + 294540 AG -s mr.mrrefChr5 47445 2 - 294540 CT -s simCow_chr6.simCow.chr6 217463 2 - 602619 TA -s simDog_chr6.simDog.chr6 218205 2 - 593897 TA -s simHuman_chr6.simHuman.chr6 222141 2 - 601863 TA -s simHuman_chr6.simHuman.chr6 157229 2 - 601863 TG -s simMouse_chr6.simMouse.chr6 242859 2 - 636262 CT -s simRat_chr6.simRat.chr6 253714 2 - 647215 CG -s simRat_chr6.simRat.chr6 255284 2 + 647215 AG - -a -s simMouse_chr6.simMouse.chr6 266483 22 + 636262 CCCTTCAGAGATATGCTGTGAA -s Anc0.Anc0refChr3 160806 22 + 222631 CCTTTCGCGGACATGCTATGAA -s Anc1.Anc1refChr6 197070 22 + 197743 CCTTTCGCGGACATGCTATGAA -s Anc2.Anc2refChr1 75431 22 + 142988 TCTTGCGCGGACATGCTATGAG -s mr.mrrefChr3 109386 22 + 181027 CCCTTCGCAAACATGCTATGAA -s mr.mrrefChr5 118098 22 + 294540 CCCTTCAGAGATATGCTGTGAA -s simCow_chr6.simCow.chr6 534157 22 + 602619 GCTTATGCGGACACGCTATGGC -s simDog_chr6.simDog.chr6 522379 22 + 593897 TCTTGCGCGAGCGTGCTATGAG -s simHuman_chr6.simHuman.chr6 529218 22 + 601863 CCTTTCGCGGACATGCTATGAA -s simMouse_chr6.simMouse.chr6 559441 22 + 636262 CTCTTCGTAAACAGCTTATGAA -s simRat_chr6.simRat.chr6 34621 22 - 647215 CCCTTCGCCAACATGCTATGAA -s simRat_chr6.simRat.chr6 255286 22 + 647215 CCTTTCAGAGATTTGCTGTGAA - -a -s simMouse_chr6.simMouse.chr6 266505 3 + 636262 GGG -s Anc0.Anc0refChr3 160828 3 + 222631 GGA -s Anc1.Anc1refChr6 197092 3 + 197743 GGA -s Anc2.Anc2refChr1 75453 3 + 142988 GGA -s mr.mrrefChr3 109408 3 + 181027 GGG -s mr.mrrefChr5 118120 3 + 294540 GGG -s simCow_chr6.simCow.chr6 534179 3 + 602619 GGA -s simDog_chr6.simDog.chr6 522401 3 + 593897 GGA -s simHuman_chr6.simHuman.chr6 529240 3 + 601863 GGA -s simMouse_chr6.simMouse.chr6 559463 3 + 636262 GGG -s simRat_chr6.simRat.chr6 34643 3 - 647215 GGG -s simRat_chr6.simRat.chr6 255309 3 + 647215 GGG - -a -s simMouse_chr6.simMouse.chr6 266508 3 + 636262 TCA -s Anc0.Anc0refChr3 160836 3 + 222631 TCG -s Anc1.Anc1refChr6 197100 3 + 197743 TCG -s Anc2.Anc2refChr1 75461 3 + 142988 CCG -s mr.mrrefChr3 109416 3 + 181027 TCA -s mr.mrrefChr5 118123 3 + 294540 TCA -s simCow_chr6.simCow.chr6 534187 3 + 602619 ACT -s simDog_chr6.simDog.chr6 522409 3 + 593897 CCG -s simHuman_chr6.simHuman.chr6 529248 3 + 601863 TCG -s simMouse_chr6.simMouse.chr6 559471 3 + 636262 TCA -s simRat_chr6.simRat.chr6 34651 3 - 647215 TCA -s simRat_chr6.simRat.chr6 255312 3 + 647215 TCA - -a -s simMouse_chr6.simMouse.chr6 266511 33 + 636262 CTGAGAGAAAAACTCCTAGATGCAAATGTATTG -s Anc0.Anc0refChr3 160839 33 + 222631 CCGAGAGAAGGACTCCAGGACACAAATGTATCG -s Anc1.Anc1refChr6 197103 33 + 197743 CCGAGAGAAGGACTCCAGGACACAAATGTATCG -s Anc2.Anc2refChr1 75464 33 + 142988 CCGAGAGAAGGACTCCAGGACACAGATGTATCG -s mr.mrrefChr3 109419 33 + 181027 TCGAAAGAAGGGCTCCAGGACACACATGTATCG -s mr.mrrefChr5 118126 33 + 294540 CTGAGAGAAAAACTCCTAGATGCAAATGTATTG -s simCow_chr6.simCow.chr6 534190 33 + 602619 CCGAGTGAAGGATTCAAGGACACAGATGTGTAG -s simDog_chr6.simDog.chr6 522415 33 + 593897 CCGAGAGAAGGACTCCAGTACATAGATGCATCG -s simHuman_chr6.simHuman.chr6 529251 24 + 601863 CCAA---------TCCCGGACACAAGTGTATCG -s simMouse_chr6.simMouse.chr6 559474 33 + 636262 TCGAAAGAAGGGCTCCACGACAAACATGTATCA -s simRat_chr6.simRat.chr6 34654 33 - 647215 TCGAAAGAAGGTCTCTAGGACACACATGTATCG -s simRat_chr6.simRat.chr6 255315 33 + 647215 CTGAGAAAAGAATTCCTATATGTAAATGTATTG - -a -s simMouse_chr6.simMouse.chr6 266544 18 + 636262 CAAGGTCGGGTATTGTGG -s Anc0.Anc0refChr3 160872 18 + 222631 CGGGGTAATGTATCGCGG -s Anc1.Anc1refChr6 197136 18 + 197743 CGGGGTAATGTATCGCGG -s Anc2.Anc2refChr1 75497 18 + 142988 TGGGGTAATGTATCGCGG -s mr.mrrefChr5 118159 18 + 294540 CAAGGTCGGGTATTGTGG -s simCow_chr6.simCow.chr6 534223 17 + 602619 -GGGGTAATATATCGCAG -s simDog_chr6.simDog.chr6 522448 18 + 593897 TGGTCTGATGTATCGCGG -s simHuman_chr6.simHuman.chr6 529275 18 + 601863 CGGGGTAATGTATCGCGG -s simRat_chr6.simRat.chr6 255348 18 + 647215 CAATGCCATGTATTGTGG - -a -s simMouse_chr6.simMouse.chr6 266562 5 + 636262 GGTGG -s Anc0.Anc0refChr3 160890 5 + 222631 GGTGG -s Anc1.Anc1refChr6 197154 5 + 197743 GGTGG -s Anc2.Anc2refChr1 75515 5 + 142988 GGTGG -s mr.mrrefChr3 109452 5 + 181027 GGCGG -s mr.mrrefChr5 118177 5 + 294540 GGTGG -s simCow_chr6.simCow.chr6 534240 5 + 602619 GGTAG -s simDog_chr6.simDog.chr6 522466 5 + 593897 GGTGG -s simHuman_chr6.simHuman.chr6 529293 5 + 601863 GGTGT -s simMouse_chr6.simMouse.chr6 559507 5 + 636262 GGCGG -s simRat_chr6.simRat.chr6 34687 5 - 647215 GACGG -s simRat_chr6.simRat.chr6 255366 5 + 647215 GGCGA - -a -s simMouse_chr6.simMouse.chr6 266567 4 + 636262 ATAC -s Anc0.Anc0refChr3 160895 4 + 222631 ATAG -s Anc1.Anc1refChr6 197159 4 + 197743 ATAG -s Anc2.Anc2refChr1 75520 4 + 142988 ATAG -s mr.mrrefChr5 118182 4 + 294540 ATAC -s simCow_chr6.simCow.chr6 534245 4 + 602619 ATAG -s simDog_chr6.simDog.chr6 522471 4 + 593897 ATAG -s simHuman_chr6.simHuman.chr6 529298 4 + 601863 ATAG -s simRat_chr6.simRat.chr6 255371 4 + 647215 ATAC - -a -s simMouse_chr6.simMouse.chr6 266571 23 + 636262 ATTTTGCCCACTAATGAATAAGC -s Anc0.Anc0refChr3 160899 23 + 222631 TTTTAGACCACTAATGAATTGCC -s Anc1.Anc1refChr6 197163 23 + 197743 TTTTAGACCACTAATGAATTGCC -s Anc2.Anc2refChr1 75524 23 + 142988 TTTCAGACCACTAATGAATTGCG -s mr.mrrefChr3 109457 23 + 181027 TCTTCGACCACTTATGGATCGGC -s mr.mrrefChr5 118186 23 + 294540 ATTTTGCCCACTAATGAATAAGC -s simCow_chr6.simCow.chr6 534249 23 + 602619 TTTCAGACCACTATTGAATGGCC -s simDog_chr6.simDog.chr6 522475 23 + 593897 TTTCAAACCACTAATGAATTGCG -s simHuman_chr6.simHuman.chr6 529302 23 + 601863 TTTTAGACCACTAATGAATTGCT -s simMouse_chr6.simMouse.chr6 559512 23 + 636262 TCTTCGACCACTTCTGGATCGGC -s simRat_chr6.simRat.chr6 34692 23 - 647215 TCTTCTACCACTTATGGATCGGC -s simRat_chr6.simRat.chr6 255375 23 + 647215 GTGTTGTCCACTAATAAAGACAC - -a -s simMouse_chr6.simMouse.chr6 266594 1 + 636262 C -s mr.mrrefChr5 118209 1 + 294540 C -s simRat_chr6.simRat.chr6 255398 1 + 647215 C - -a -s simMouse_chr6.simMouse.chr6 266595 10 + 636262 AAGGATGGAT -s Anc0.Anc0refChr3 160922 10 + 222631 AAGAATGAGT -s Anc1.Anc1refChr6 197186 10 + 197743 AAGAATGAGT -s Anc2.Anc2refChr1 75547 10 + 142988 ACGAATGAGT -s mr.mrrefChr3 109480 10 + 181027 AGGGACGAAT -s mr.mrrefChr5 118210 10 + 294540 AAGGATGGAT -s simCow_chr6.simCow.chr6 534272 10 + 602619 GCGATTGAGT -s simDog_chr6.simDog.chr6 522498 10 + 593897 ACGAACGAGT -s simHuman_chr6.simHuman.chr6 529325 10 + 601863 AAGAATAAGT -s simMouse_chr6.simMouse.chr6 559535 10 + 636262 AGGGACGAAT -s simRat_chr6.simRat.chr6 34715 10 - 647215 AGGGACGAAT -s simRat_chr6.simRat.chr6 255399 10 + 647215 AAGGATGGGT - -a -s simMouse_chr6.simMouse.chr6 266605 1 + 636262 T -s Anc0.Anc0refChr3 160932 1 + 222631 T -s Anc1.Anc1refChr6 197196 1 + 197743 T -s Anc2.Anc2refChr1 75557 1 + 142988 C -s mr.mrrefChr3 109490 1 + 181027 T -s mr.mrrefChr5 118220 1 + 294540 T -s simCow_chr6.simCow.chr6 534282 1 + 602619 C -s simDog_chr6.simDog.chr6 522508 1 + 593897 C -s simHuman_chr6.simHuman.chr6 529335 1 + 601863 T -s simMouse_chr6.simMouse.chr6 559545 1 + 636262 T -s simRat_chr6.simRat.chr6 34725 1 - 647215 T -s simRat_chr6.simRat.chr6 255412 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 266606 10 + 636262 CCCTCTAATC -s mr.mrrefChr5 118221 10 + 294540 CCCTCTAATC -s simRat_chr6.simRat.chr6 255413 10 + 647215 CCCTCTAATC - -a -s simMouse_chr6.simMouse.chr6 266616 10 + 636262 AATCCCTTTG -s Anc0.Anc0refChr3 160933 10 + 222631 GACCACTCTA -s Anc1.Anc1refChr6 197197 10 + 197743 GACCACTCTA -s Anc2.Anc2refChr1 75558 10 + 142988 GACCACTCTA -s mr.mrrefChr3 109491 10 + 181027 GATCCCTCTA -s mr.mrrefChr5 118231 10 + 294540 AATCCCTTTG -s simCow_chr6.simCow.chr6 534283 10 + 602619 AACCACTCTA -s simDog_chr6.simDog.chr6 522509 10 + 593897 GACCACTCTA -s simHuman_chr6.simHuman.chr6 529336 10 + 601863 GACCACTCTA -s simMouse_chr6.simMouse.chr6 559546 10 + 636262 GATCCCTCTA -s simRat_chr6.simRat.chr6 34726 10 - 647215 AATCCCTCTA -s simRat_chr6.simRat.chr6 255423 10 + 647215 AATCCCATTG - -a -s simMouse_chr6.simMouse.chr6 266626 1 + 636262 T -s mr.mrrefChr5 118241 1 + 294540 T -s simRat_chr6.simRat.chr6 255433 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 266627 16 + 636262 AACACATGGAGCTCTT -s Anc0.Anc0refChr3 160943 16 + 222631 ACCACATGGAAACCGC -s Anc1.Anc1refChr6 197207 16 + 197743 ACCACATGGAAACCGC -s Anc2.Anc2refChr1 75568 16 + 142988 ACCACATGGAAACCGC -s mr.mrrefChr3 109501 16 + 181027 ACCACATGGAAGCCAT -s mr.mrrefChr5 118242 16 + 294540 AACACATGGAGCTCTT -s simCow_chr6.simCow.chr6 534293 16 + 602619 ACCACGCGGAAACCGC -s simDog_chr6.simDog.chr6 522519 16 + 593897 ACCACATGGAAACCGC -s simHuman_chr6.simHuman.chr6 529346 16 + 601863 AACACATGAAAACCGC -s simMouse_chr6.simMouse.chr6 559556 16 + 636262 ACCACATGGAAGCCAT -s simRat_chr6.simRat.chr6 34736 16 - 647215 ACCAGATGGCAGTCTT -s simRat_chr6.simRat.chr6 255434 16 + 647215 AACACATGGAGCCCTT - -a -s simMouse_chr6.simMouse.chr6 266643 17 + 636262 CAACCACATAGGCTTCC -s mr.mrrefChr5 118258 10 + 294540 CAAC-------GCTTCC -s simRat_chr6.simRat.chr6 255450 10 + 647215 GAAC-------GCTTCC - -a -s simMouse_chr6.simMouse.chr6 266660 30 + 636262 AATTTGAATGCAATGTGTTTTCTTGCATGG -s Anc0.Anc0refChr3 160959 29 + 222631 AATTTAACTGTTACGTG-TGTCTTGCGCGG -s Anc1.Anc1refChr6 197223 29 + 197743 AATTTAACTGTTACGTG-TGTCTTGCGCGG -s Anc2.Anc2refChr1 75584 29 + 142988 AATTTAACTGTTACGTG-TGTCTTGCGCAG -s mr.mrrefChr3 109517 29 + 181027 AATTTAATTGCTACGCG-TGTCTTGCGCGG -s mr.mrrefChr5 118268 29 + 294540 AATTTGAATGCAATGTG-TTTCTTGCATGG -s simCow_chr6.simCow.chr6 534309 29 + 602619 GAGTTAACTGCTACGTG-TGCCTTGCGTAG -s simDog_chr6.simDog.chr6 522535 29 + 593897 ATTTTAACTCTTACGTG-TGTCTTGCGCAT -s simHuman_chr6.simHuman.chr6 529362 29 + 601863 AATAAAACTGTTACTTG-TGTCTTGCGCCG -s simMouse_chr6.simMouse.chr6 559572 29 + 636262 AATTTAATTGCTACGCG-TGTCTTGCACGG -s simRat_chr6.simRat.chr6 34752 29 - 647215 AATTCAATTACTACGCG-TGTCTTGCGCGT -s simRat_chr6.simRat.chr6 255460 29 + 647215 AATTTGAGTGCAATGTG-TTTCTTGCATGG - -a -s simMouse_chr6.simMouse.chr6 266690 5 + 636262 ATTGA -s Anc0.Anc0refChr3 160988 5 + 222631 ATCGA -s Anc1.Anc1refChr6 197252 5 + 197743 ATCGA -s Anc2.Anc2refChr1 75613 5 + 142988 ATCGA -s mr.mrrefChr3 109546 5 + 181027 ATTAA -s mr.mrrefChr5 118297 5 + 294540 ATTGA -s simCow_chr6.simCow.chr6 534338 5 + 602619 ACTGA -s simDog_chr6.simDog.chr6 522564 5 + 593897 ATCGA -s simHuman_chr6.simHuman.chr6 529391 5 + 601863 ATCGA -s simMouse_chr6.simMouse.chr6 559601 2 + 636262 A---A -s simRat_chr6.simRat.chr6 34781 5 - 647215 ATTAA -s simRat_chr6.simRat.chr6 255497 5 + 647215 GTTGA - -a -s simMouse_chr6.simMouse.chr6 266695 20 + 636262 CCTGAAGTGTTTCCCAGTGG -s Anc0.Anc0refChr3 160993 20 + 222631 CACGTGGTGTTTCCCGGTGT -s Anc1.Anc1refChr6 197257 20 + 197743 CACGTGGTGTTTCCCGGTGT -s Anc2.Anc2refChr1 75618 20 + 142988 CACGTGGTGTTTACCGGTGT -s mr.mrrefChr3 109551 20 + 181027 CACGTTGCGTTTCTTACTGA -s mr.mrrefChr5 118302 20 + 294540 CCTGAAGTGTTTCCCAGTGG -s simCow_chr6.simCow.chr6 534343 20 + 602619 CGCGTGGTTTTTTCCGGTGT -s simDog_chr6.simDog.chr6 522569 20 + 593897 CACGTGGTGTTTACCGGTGC -s simHuman_chr6.simHuman.chr6 529400 20 + 601863 CAGGTGGTGTTTCACGGTTT -s simMouse_chr6.simMouse.chr6 559603 15 + 636262 CACGTTG--TTTC---CTGA -s simRat_chr6.simRat.chr6 34786 20 - 647215 TACGTTGCGTTTATTACTGA -s simRat_chr6.simRat.chr6 255502 20 + 647215 CCTGAAGTGTTTCCCCGTGG - -a -s simMouse_chr6.simMouse.chr6 266715 2 + 636262 TC -s mr.mrrefChr5 118322 2 + 294540 TC -s simRat_chr6.simRat.chr6 255522 2 + 647215 CT - -a -s simMouse_chr6.simMouse.chr6 266717 17 + 636262 ATTGACTTACCCTATGA -s Anc0.Anc0refChr3 161013 16 + 222631 ATTGGCTTA-CCCACGA -s Anc1.Anc1refChr6 197277 16 + 197743 ATTGGCTTA-CCCACGA -s Anc2.Anc2refChr1 75638 16 + 142988 ATTGGCTTA-CCCACGA -s mr.mrrefChr3 109571 16 + 181027 ATCATCGAT-TCCCCTA -s mr.mrrefChr5 118324 16 + 294540 ATTGACTTA-CCTATGA -s simCow_chr6.simCow.chr6 534363 16 + 602619 GCTGTCTTA-CCTGCGA -s simDog_chr6.simDog.chr6 522589 16 + 593897 ATTGGCTTA-CCCACAA -s simHuman_chr6.simHuman.chr6 529420 16 + 601863 ATTGGCTTA-CCCACGA -s simMouse_chr6.simMouse.chr6 559618 16 + 636262 TTCATCGAT-TTCCCTA -s simRat_chr6.simRat.chr6 34806 16 - 647215 ATCAACGAT-TCCCCTA -s simRat_chr6.simRat.chr6 255524 16 + 647215 ATTGACTTA-CCTACGA - -a -s simMouse_chr6.simMouse.chr6 266734 3 + 636262 TTG -s Anc0.Anc0refChr3 161029 2 + 222631 TG- -s Anc1.Anc1refChr6 197293 2 + 197743 TG- -s Anc2.Anc2refChr1 75654 2 + 142988 TG- -s mr.mrrefChr3 109587 2 + 181027 CT- -s mr.mrrefChr5 118340 2 + 294540 TT- -s simCow_chr6.simCow.chr6 534379 2 + 602619 TT- -s simDog_chr6.simDog.chr6 522606 2 + 593897 TG- -s simHuman_chr6.simHuman.chr6 529436 2 + 601863 GG- -s simMouse_chr6.simMouse.chr6 559634 2 + 636262 CT- -s simRat_chr6.simRat.chr6 34822 2 - 647215 CT- -s simRat_chr6.simRat.chr6 255540 2 + 647215 TT- - -a -s simMouse_chr6.simMouse.chr6 266737 1 + 636262 G -s mr.mrrefChr5 118342 1 + 294540 G -s simRat_chr6.simRat.chr6 255542 1 + 647215 G - -a -s simMouse_chr6.simMouse.chr6 266738 32 + 636262 CCCAACATAATTCCAGAATGCTATAGAGTATG -s Anc0.Anc0refChr3 161031 21 + 222631 GAAAACATAACTC-----------AGAGTATG -s Anc1.Anc1refChr6 197295 32 + 197743 GAAAACATAACTCCACACTGCTGTAGAGTATG -s Anc2.Anc2refChr1 75656 21 + 142988 GAAAACATAACTC-----------AGTATATA -s mr.mrrefChr3 109589 32 + 181027 CAAAACATAGCTTCACACCGCTGTAAAGGGCG -s mr.mrrefChr5 118343 32 + 294540 CCCAACATAATTCCAGAATGCTATAGAGTATG -s simCow_chr6.simCow.chr6 534381 15 + 602619 GTAAACATAACTC-----------AG------ -s simDog_chr6.simDog.chr6 522608 21 + 593897 GAAAACATGGCTC-----------AGTATATA -s simHuman_chr6.simHuman.chr6 529438 31 + 601863 GAAAGCATAACTCCACTCTGCGGTAGAGTA-G -s simMouse_chr6.simMouse.chr6 559636 32 + 636262 CAAAACATAGCTTCACACCGCTGTAAAGGGCG -s simRat_chr6.simRat.chr6 34824 32 - 647215 CAAAACATCGCTTCACAACGCTGTAAAGGGCG -s simRat_chr6.simRat.chr6 255543 32 + 647215 CCCAACATAACTCCAGAATGCTTTAGAGTATG - -a -s simMouse_chr6.simMouse.chr6 266770 36 + 636262 AAACCTCCACAACAGTGCGTTGGGGTAGTGAACTTC -s Anc0.Anc0refChr3 161052 36 + 222631 AAACCTCGACAACAGTATGGTAGGGTAGTAAACTTC -s Anc1.Anc1refChr6 197327 36 + 197743 AAACCTCGACAACAGTATGGTAGGGTAGTAAACTTC -s Anc2.Anc2refChr1 75677 36 + 142988 AAATCTCGACAGCAGTATAGTAGAGTAGTAAACTTC -s mr.mrrefChr3 109622 36 + 181027 AAACTTTGACGACAGTTCGGTAGGGAGGCGAACTTC -s mr.mrrefChr5 118375 36 + 294540 AAACCTCCACAACAGTGCGTTGGGGTAGTGAACTTC -s simCow_chr6.simCow.chr6 534396 36 + 602619 AAACCTCGACAGCAGTGTAGTAGAGTAGTGGAGTTC -s simDog_chr6.simDog.chr6 522629 35 + 593897 AAATCTCGACAGCA-TATAGTAGAGTAGTAAACTTC -s simHuman_chr6.simHuman.chr6 529469 36 + 601863 AATCTCCGACAACAGTATGGGAGTGTAGCAATCTTC -s simMouse_chr6.simMouse.chr6 559669 36 + 636262 AAACCTTGACGACAGTTCGGTAGGGAGGCGAACTTC -s simRat_chr6.simRat.chr6 34857 36 - 647215 AAACTTTGACTACAGTTCGATAGGGAGGCGAACTTC -s simRat_chr6.simRat.chr6 255575 36 + 647215 AAACCTCCCCAATAGTGGGTTAGGGTAGTGTACTTC - -a -s simMouse_chr6.simMouse.chr6 266806 1 + 636262 G -s mr.mrrefChr5 118411 1 + 294540 G -s simRat_chr6.simRat.chr6 255612 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 266807 9 + 636262 TATTAGCAC -s Anc0.Anc0refChr3 161088 9 + 222631 GATATTGAC -s Anc1.Anc1refChr6 197363 9 + 197743 GATATTGAC -s Anc2.Anc2refChr1 75713 9 + 142988 GATATTGGT -s mr.mrrefChr3 109658 9 + 181027 TATGATGAC -s mr.mrrefChr5 118412 9 + 294540 TATTAGCAC -s simCow_chr6.simCow.chr6 534432 9 + 602619 GATGTTAGT -s simDog_chr6.simDog.chr6 522664 9 + 593897 AATACTGGT -s simHuman_chr6.simHuman.chr6 529505 9 + 601863 GATATTGAC -s simMouse_chr6.simMouse.chr6 559705 9 + 636262 TATGATGAC -s simRat_chr6.simRat.chr6 34893 9 - 647215 TATGATGAC -s simRat_chr6.simRat.chr6 255613 9 + 647215 TATTAGCAT - -a -s simMouse_chr6.simMouse.chr6 266816 5 + 636262 CTCTG -s Anc0.Anc0refChr3 161098 4 + 222631 CTGC- -s Anc1.Anc1refChr6 197373 5 + 197743 CTGCG -s Anc2.Anc2refChr1 75723 4 + 142988 CTGC- -s mr.mrrefChr3 109667 5 + 181027 GTGCG -s mr.mrrefChr5 118421 5 + 294540 CTCTG -s simCow_chr6.simCow.chr6 534442 4 + 602619 CAGC- -s simDog_chr6.simDog.chr6 522674 4 + 593897 CTGC- -s simHuman_chr6.simHuman.chr6 529515 5 + 601863 CCGCC -s simMouse_chr6.simMouse.chr6 559714 5 + 636262 GTACG -s simRat_chr6.simRat.chr6 34902 5 - 647215 GTGCG -s simRat_chr6.simRat.chr6 255622 5 + 647215 CACTG - -a -s simMouse_chr6.simMouse.chr6 266821 3 + 636262 CCA -s Anc1.Anc1refChr6 197378 3 + 197743 ACA -s mr.mrrefChr5 118426 3 + 294540 CCA -s simHuman_chr6.simHuman.chr6 529520 3 + 601863 ACA -s simRat_chr6.simRat.chr6 255627 3 + 647215 CCA - -a -s simMouse_chr6.simMouse.chr6 266824 68 + 636262 GAAGATTGATTGAAGACACTGTAATACACGAACTGGCTTTATGAAATAACAATAGTGTTTAACAACAT -s Anc0.Anc0refChr3 161102 46 + 222631 ---------------------CAATGCGTGAACTAACTATATGGAGCGACAGTCGTGTTTAACAAC-T -s Anc1.Anc1refChr6 197381 63 + 197743 GGAG----ATCGGTGAAACGGCAATGCGTGAACTAACTATATGGAGCGACAGTCGTGTTTAACAAC-T -s Anc2.Anc2refChr1 75727 46 + 142988 ---------------------CAATGCGTGAACTAACTAATTAGAGCGACAGTCGTGTTTGACAAC-T -s mr.mrrefChr3 109672 63 + 181027 GGAG----TGCTCCGATACCATGAGCTGTGGACCGACTTTATGGGTCGACAATATTGTTTAACGAC-T -s mr.mrrefChr5 118429 63 + 294540 GAAG----ATTGAAGACACTGTAATACACGAACTGGCTTTATGAAATAACAATAGTGTTTAACAAC-T -s simCow_chr6.simCow.chr6 534446 46 + 602619 ---------------------CAATATGTAGACTAACTTTTTAGAGCGACAGTCGTGTTCTATGAC-T -s simDog_chr6.simDog.chr6 522678 42 + 593897 ---------------------CAATGCGTGAACTAACTAA----AACGACGGTCGTGTTTGACAAC-T -s simHuman_chr6.simHuman.chr6 529523 63 + 601863 GGAC----ATCGGTGAAACGGCAGCGGTTGAACTAACTACCTGTAGCGACAGTCTTGTTTAACAAC-C -s simMouse_chr6.simMouse.chr6 559719 63 + 636262 GGAG----TGCTCCGATACCATTAAGTGTGGGCCGTCTTTATGGGTCGACAATATCGTCTAACGAC-T -s simRat_chr6.simRat.chr6 34907 63 - 647215 GGAG----AGCTCCGATACCATGAGCTGCGGACCGACTTTATGGGACGACAATATTGTTTAACTAC-T -s simRat_chr6.simRat.chr6 255630 63 + 647215 GAAG----ATGGGAGACCCTGTAATACATAAACTGATGTTATGAAACAACAATAGTGTTTAACAAC-C - -a -s simMouse_chr6.simMouse.chr6 266892 9 + 636262 GGCTTGATG -s Anc0.Anc0refChr3 161149 6 + 222631 GGCTT---T -s Anc1.Anc1refChr6 197445 9 + 197743 GGCTTGTCT -s Anc2.Anc2refChr1 75774 6 + 142988 GGCTT---T -s mr.mrrefChr3 109736 9 + 181027 GGCTTCCCT -s mr.mrrefChr5 118492 9 + 294540 GGCTTGATG -s simCow_chr6.simCow.chr6 534493 6 + 602619 GGCTT---A -s simDog_chr6.simDog.chr6 522721 6 + 593897 GGCTT---T -s simHuman_chr6.simHuman.chr6 529587 9 + 601863 GGCTTGTCT -s simMouse_chr6.simMouse.chr6 559783 9 + 636262 GGCTTCCCT -s simRat_chr6.simRat.chr6 34971 9 - 647215 GGCTTCCCT -s simRat_chr6.simRat.chr6 255693 9 + 647215 AGCTTGACA - -a -s simMouse_chr6.simMouse.chr6 266901 5 + 636262 GCCTC -s Anc0.Anc0refChr3 161166 5 + 222631 GCATC -s Anc1.Anc1refChr6 197465 5 + 197743 GCATC -s Anc2.Anc2refChr1 75791 5 + 142988 GCGTC -s mr.mrrefChr3 109745 5 + 181027 GCATC -s mr.mrrefChr5 118501 5 + 294540 GCCTC -s simCow_chr6.simCow.chr6 534510 5 + 602619 GCGTC -s simDog_chr6.simDog.chr6 522738 5 + 593897 GTGTC -s simHuman_chr6.simHuman.chr6 529682 5 + 601863 GCATC -s simMouse_chr6.simMouse.chr6 559792 5 + 636262 GCATC -s simRat_chr6.simRat.chr6 34980 5 - 647215 GCTTC -s simRat_chr6.simRat.chr6 255702 5 + 647215 GTCTC - -a -s simMouse_chr6.simMouse.chr6 266906 2 + 636262 TT -s Anc0.Anc0refChr3 161171 2 + 222631 TT -s Anc1.Anc1refChr6 197470 2 + 197743 TT -s Anc2.Anc2refChr1 75796 2 + 142988 TT -s mr.mrrefChr3 109750 2 + 181027 TT -s mr.mrrefChr5 118506 2 + 294540 TT -s simCow_chr6.simCow.chr6 534515 2 + 602619 CT -s simDog_chr6.simDog.chr6 522743 2 + 593897 TT -s simHuman_chr6.simHuman.chr6 529687 2 + 601863 TC -s simMouse_chr6.simMouse.chr6 559797 2 + 636262 TT -s simRat_chr6.simRat.chr6 34985 2 - 647215 TT -s simRat_chr6.simRat.chr6 255708 2 + 647215 TT - -a -s simMouse_chr6.simMouse.chr6 266908 25 + 636262 TGCTGGCAAGTTGCAAAGTGGGGAG -s Anc0.Anc0refChr3 161177 25 + 222631 TTCTGGCAAGGTCTTAAGCGGGGGA -s Anc1.Anc1refChr6 197476 25 + 197743 TTCTGGCAAGGTCTTAAGCGGGGGA -s Anc2.Anc2refChr1 75802 25 + 142988 TTCTGTCAAGAGCTTAAGCGGGGGA -s mr.mrrefChr3 109756 25 + 181027 TGCTGGCGAAGCCTTAAGCGGAGGG -s mr.mrrefChr5 118508 25 + 294540 TGCTGGCAAGTTGCAAAGTGGGGAG -s simCow_chr6.simCow.chr6 534521 25 + 602619 TTCTGTCAAGAGCTTAAGCGGGGGA -s simDog_chr6.simDog.chr6 522749 10 + 593897 TTC---------------TGGGGGA -s simHuman_chr6.simHuman.chr6 529693 25 + 601863 CTCCGCCGAGGTTCTAAGCGGGGGA -s simMouse_chr6.simMouse.chr6 559803 25 + 636262 TTCTGGCGAAGCCTTAAGCGGAGGG -s simRat_chr6.simRat.chr6 34991 25 - 647215 TGCTGGCGAAGCCTTAAGCGGAGGG -s simRat_chr6.simRat.chr6 255710 25 + 647215 TGCTGTCAAGTTACAAAGTGGGGGG - -a -s simMouse_chr6.simMouse.chr6 266933 7 + 636262 ATCCTCT -s Anc0.Anc0refChr3 161202 7 + 222631 ACCCTGT -s Anc1.Anc1refChr6 197501 7 + 197743 ACCCTGT -s Anc2.Anc2refChr1 75827 7 + 142988 ACCCTGT -s mr.mrrefChr3 109841 7 + 181027 ATACTCT -s mr.mrrefChr5 118533 7 + 294540 ATCCTCT -s simCow_chr6.simCow.chr6 534546 7 + 602619 CCCCTTG -s simDog_chr6.simDog.chr6 522759 7 + 593897 ACCCTGT -s simHuman_chr6.simHuman.chr6 529718 7 + 601863 ACCCCGT -s simMouse_chr6.simMouse.chr6 559888 5 + 636262 ATACT-- -s simRat_chr6.simRat.chr6 35076 7 - 647215 ATACTCT -s simRat_chr6.simRat.chr6 255735 7 + 647215 ACCCTGT - -a -s simMouse_chr6.simMouse.chr6 266940 30 + 636262 TCTGTTGTCCATTATCTTTGAGCAATGTCT -s Anc0.Anc0refChr3 161209 25 + 222631 TCTGTTGTCTTCAGTTT-----CAACAACT -s Anc1.Anc1refChr6 197508 30 + 197743 TCTGTTGTCTTCAGTTTTTGAGCAACAACT -s Anc2.Anc2refChr1 75834 25 + 142988 TCTGTTGTCTTCAGTTT-----CAACAACT -s mr.mrrefChr3 109851 30 + 181027 TCTGTTGTCTGCAGTCATTGAGCAACATAT -s mr.mrrefChr5 118540 30 + 294540 TCTGTTGTCCATTATCTTTGAGCAATGTCT -s simCow_chr6.simCow.chr6 534553 23 + 602619 TCTGTTGTCTTCAGTT------CAAC-ACT -s simDog_chr6.simDog.chr6 522766 15 + 593897 TCAGTT----------T-----CAACACCT -s simHuman_chr6.simHuman.chr6 529725 30 + 601863 TCTGTTGCCTTCAGTTATTGAGCAACAACT -s simMouse_chr6.simMouse.chr6 559893 30 + 636262 TCTGTTGTCGGCTGTCATTGAGCAACATAT -s simRat_chr6.simRat.chr6 35086 30 - 647215 TCTGTTGTCTGCAGTCATTGAGCACCATGT -s simRat_chr6.simRat.chr6 255742 30 + 647215 TCTGTTGTCGGCAATCTTTGGGCAATGTCT - -a -s simMouse_chr6.simMouse.chr6 266970 21 + 636262 AGAACCCTCTATTCAGATACC -s Anc0.Anc0refChr3 161241 18 + 222631 AGTGCCCTCTATTCATA---G -s Anc1.Anc1refChr6 197545 21 + 197743 AGTGCCCTCTATTCATATATG -s Anc2.Anc2refChr1 75866 18 + 142988 AGTGCCCTCTATTCAGA---G -s mr.mrrefChr3 109888 21 + 181027 AGAGACATCTATCCATAGATC -s mr.mrrefChr5 118570 21 + 294540 AGAACCCTCTATTCAGATACC -s simCow_chr6.simCow.chr6 534583 18 + 602619 AGTTTCCTCTAATGAGA---A -s simDog_chr6.simDog.chr6 522788 18 + 593897 AGTGCCCTCTATTCAGA---G -s simHuman_chr6.simHuman.chr6 529762 18 + 601863 AGTGCCCTCTATTCA---ATG -s simMouse_chr6.simMouse.chr6 559930 21 + 636262 AGAGACATCTATCCATAGATC -s simRat_chr6.simRat.chr6 35123 21 - 647215 AGAGACATCTATCCAGAGACC -s simRat_chr6.simRat.chr6 255772 21 + 647215 AGAACCCTCTATTCAGATACC - -a -s simMouse_chr6.simMouse.chr6 266991 1 + 636262 T -s Anc0.Anc0refChr3 161259 1 + 222631 T -s Anc1.Anc1refChr6 197566 1 + 197743 T -s Anc2.Anc2refChr1 75884 1 + 142988 T -s mr.mrrefChr3 109909 1 + 181027 T -s mr.mrrefChr5 118591 1 + 294540 T -s simCow_chr6.simCow.chr6 534601 1 + 602619 T -s simDog_chr6.simDog.chr6 522809 1 + 593897 T -s simHuman_chr6.simHuman.chr6 529780 1 + 601863 T -s simMouse_chr6.simMouse.chr6 559951 1 + 636262 T -s simRat_chr6.simRat.chr6 35144 1 - 647215 T -s simRat_chr6.simRat.chr6 255793 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 266992 2 + 636262 GC -s Anc0.Anc0refChr3 161260 2 + 222631 GC -s Anc1.Anc1refChr6 197567 2 + 197743 GC -s Anc2.Anc2refChr1 75885 2 + 142988 GC -s mr.mrrefChr5 118592 2 + 294540 GC -s simDog_chr6.simDog.chr6 522810 2 + 593897 GC -s simHuman_chr6.simHuman.chr6 529781 2 + 601863 GC -s simRat_chr6.simRat.chr6 255794 2 + 647215 AC - -a -s simMouse_chr6.simMouse.chr6 266994 3 + 636262 AAC -s Anc0.Anc0refChr3 161262 3 + 222631 AAT -s Anc1.Anc1refChr6 197569 3 + 197743 AAT -s Anc2.Anc2refChr1 75887 3 + 142988 AAT -s mr.mrrefChr3 109910 3 + 181027 ATG -s mr.mrrefChr5 118594 3 + 294540 AAC -s simCow_chr6.simCow.chr6 534602 1 + 602619 --C -s simDog_chr6.simDog.chr6 522812 3 + 593897 AAT -s simHuman_chr6.simHuman.chr6 529783 3 + 601863 TAT -s simMouse_chr6.simMouse.chr6 559952 3 + 636262 ATG -s simRat_chr6.simRat.chr6 35145 3 - 647215 ATG -s simRat_chr6.simRat.chr6 255796 3 + 647215 GAC - -a -s simMouse_chr6.simMouse.chr6 266997 42 + 636262 CCTTGCTCTTTTGCCTCATTTGTAACACAGTCAGGACATCCA -s Anc0.Anc0refChr3 161265 42 + 222631 CCTTGAGATTGAGCCTTATTTGTGAGCCAGCCAGGAAAATCA -s Anc1.Anc1refChr6 197572 42 + 197743 CCTTGAGATTGAGCCTTATTTGTGAGCCAGCCAGGAAAATCA -s Anc2.Anc2refChr1 75890 42 + 142988 CCTAGAGATTGAGCCTTATTTGTGAGCCAGCCAGGAAAATCA -s mr.mrrefChr3 109913 42 + 181027 CTTTGAGATTGAGCCTTATGTGTGATGCAGCCATGAAAATTG -s mr.mrrefChr5 118597 42 + 294540 CCTTGCTCTTTTGCCTCATTTGTAACACAGTCAGGACATCCA -s simCow_chr6.simCow.chr6 534603 37 + 602619 AATAGAGATTGAG-----TTTGTGAGCCAGCCAGGAAACTTT -s simDog_chr6.simDog.chr6 522815 42 + 593897 CCTAGAGATTGAGCCTTATTTGTGAGCCAGCCAAGAAAATCA -s simHuman_chr6.simHuman.chr6 529786 42 + 601863 CTTGGAGATTGAACCTTTTCTGTGAGCCAGCCAGGAAAATGG -s simMouse_chr6.simMouse.chr6 559957 42 + 636262 CTTTGTGATTGAGCCTGATGTGTGATGCAACCATGAAAATTG -s simRat_chr6.simRat.chr6 35148 42 - 647215 CTTTGAGATTGAGCCTTCTATGTAATACAGCCACAAAAAGTG -s simRat_chr6.simRat.chr6 255799 42 + 647215 CCTTGCCCCTGTGTCTTATTTGTAATATGGCCTGGACATCCA - -a -s simMouse_chr6.simMouse.chr6 267039 3 + 636262 CTT -s Anc0.Anc0refChr3 161351 3 + 222631 TAT -s Anc1.Anc1refChr6 197659 3 + 197743 TAT -s Anc2.Anc2refChr1 75976 3 + 142988 TAC -s mr.mrrefChr3 110047 3 + 181027 CAT -s mr.mrrefChr5 118639 3 + 294540 CTT -s simCow_chr6.simCow.chr6 534682 2 + 602619 TA- -s simDog_chr6.simDog.chr6 522901 3 + 593897 TAC -s simHuman_chr6.simHuman.chr6 529880 3 + 601863 TAG -s simMouse_chr6.simMouse.chr6 560091 3 + 636262 CAT -s simRat_chr6.simRat.chr6 35300 3 - 647215 CAT -s simRat_chr6.simRat.chr6 255878 3 + 647215 CTT - -a -s simMouse_chr6.simMouse.chr6 267042 44 + 636262 CCGCATTGACTGTTAGCTTTTAACTGTCTCTATAATCTGTTGGG -s Anc0.Anc0refChr3 161354 44 + 222631 CTGTATTGACTGTTAGCTGTTATCTATCTCTATGATCTGGTGGG -s Anc1.Anc1refChr6 197662 44 + 197743 CTGTATTGACTGTTAGCTGTTATCTATCTCTATGATCTGGTGGG -s Anc2.Anc2refChr1 75979 44 + 142988 CTGTATTAACTGTTAGCTGTTGTCCATCTTTATGATCTGGTGGG -s mr.mrrefChr3 110050 44 + 181027 CTGCATTGACTGTGAGTGGTTATGTATCTGTATGATTTGGTGGG -s mr.mrrefChr5 118642 44 + 294540 CCGCATTGACTGTTAGCTTTTAACTGTCTCTATAATCTGTTGGG -s simCow_chr6.simCow.chr6 534684 39 + 602619 CTGTA-----TGTCAGCTGTTGTCCATCCTCATGATTTGGTGGT -s simDog_chr6.simDog.chr6 522904 40 + 593897 CTGTATTAACTGTTAGCTGTT----ATCTTTATGCTCTGCTGGG -s simHuman_chr6.simHuman.chr6 529884 44 + 601863 TTGTATTGACTGTTAGCTGTCATCTTTCTCTATTATCTGGTGGG -s simMouse_chr6.simMouse.chr6 560094 43 + 636262 CTGCATTGACTGTGAATG-TTATGTATCTGTATGATTTGGTGGG -s simRat_chr6.simRat.chr6 35303 44 - 647215 CTGCATTGACTGTGAGTGGTTATGTATCTTTATGATTTGGTGAG -s simRat_chr6.simRat.chr6 255881 44 + 647215 CTGCATTGACTATAAGCTTTTAACAATCTTTATAATCTGTTGAG - -a -s simMouse_chr6.simMouse.chr6 267086 6 + 636262 ACTGGG -s mr.mrrefChr5 118686 6 + 294540 ACTGGG -s simRat_chr6.simRat.chr6 255925 6 + 647215 GCAGGG - -a -s simMouse_chr6.simMouse.chr6 267092 5 + 636262 CTCAT -s Anc0.Anc0refChr3 161399 5 + 222631 CTTAT -s Anc1.Anc1refChr6 197707 5 + 197743 CTTAT -s Anc2.Anc2refChr1 76024 5 + 142988 CTTAT -s mr.mrrefChr3 110094 5 + 181027 CTTAT -s mr.mrrefChr5 118692 5 + 294540 CTCAT -s simCow_chr6.simCow.chr6 534724 5 + 602619 CTTAT -s simDog_chr6.simDog.chr6 522945 5 + 593897 CTTAT -s simHuman_chr6.simHuman.chr6 529930 5 + 601863 CTTAT -s simMouse_chr6.simMouse.chr6 560137 5 + 636262 CTTAT -s simRat_chr6.simRat.chr6 35347 5 - 647215 CTTAT -s simRat_chr6.simRat.chr6 255931 5 + 647215 CTCAT - -a -s simMouse_chr6.simMouse.chr6 267097 1 + 636262 G -s Anc0.Anc0refChr3 161404 1 + 222631 G -s Anc1.Anc1refChr6 197712 1 + 197743 G -s Anc2.Anc2refChr1 76029 1 + 142988 G -s mr.mrrefChr5 118697 1 + 294540 G -s simCow_chr6.simCow.chr6 534729 1 + 602619 G -s simDog_chr6.simDog.chr6 522950 1 + 593897 G -s simHuman_chr6.simHuman.chr6 529935 1 + 601863 G -s simRat_chr6.simRat.chr6 255936 1 + 647215 G - -a -s simMouse_chr6.simMouse.chr6 267098 26 + 636262 CAGGAAGCGTAATGTGATTACTGTTC -s Anc0.Anc0refChr3 161405 26 + 222631 CAGGAAGTGTAATGTGATTACTGTTT -s Anc1.Anc1refChr6 197713 26 + 197743 CAGGAAGTGTAATGTGATTACTGTTT -s Anc2.Anc2refChr1 76030 26 + 142988 CAGGAAGTTTAATGTGATTACTGTTT -s mr.mrrefChr3 110099 26 + 181027 CAAGAATTATAATGTGAATACTGTTC -s mr.mrrefChr5 118698 26 + 294540 CAGGAAGCGTAATGTGATTACTGTTC -s simCow_chr6.simCow.chr6 534730 10 + 602619 GATGG----------------TGTCT -s simDog_chr6.simDog.chr6 522951 26 + 593897 CAGGAAGTTTAATGTGATTACTGTTT -s simHuman_chr6.simHuman.chr6 529936 25 + 601863 TAAGAAGCGTAATGTGCTTACT-TTT -s simMouse_chr6.simMouse.chr6 560142 26 + 636262 CAAGGATTATGATGTGAATACTGTTC -s simRat_chr6.simRat.chr6 35352 26 - 647215 CAAAAAAAATAATGTGAATACTATTC -s simRat_chr6.simRat.chr6 255937 26 + 647215 CAGGAAGCATAATGTGGTTACTGTTT - -a -s simMouse_chr6.simMouse.chr6 267124 19 + 636262 TGAATTAGCAAAGTCACAT -s mr.mrrefChr5 118724 19 + 294540 TGAATTAGCAAAGTCACAT -s simRat_chr6.simRat.chr6 255963 19 + 647215 TGAATAAGCAGAGTTATAT - -a -s simMouse_chr6.simMouse.chr6 267143 74 + 636262 GAGTCTCTCCCGAGCCTAAGTGCCATGTGGAATTTGCTTGGAAGATTATGGTTCAACAATTCATATAGTTCccc -s mr.mrrefChr5 118743 74 + 294540 GAGTCTCTCCCGAGCCTAAGTGCCATGTGGAATTTGCTTGGAAGATTATGGTTCAACAATTCATATAGTTCccc -s simRat_chr6.simRat.chr6 256011 74 + 647215 GAGTCTCAGGCAAGCCTCAGTGCCATCGGGAATTTGGTTAGAAAATTATGGTGTAACAATTCATATAGTTCTCC - -a -s simMouse_chr6.simMouse.chr6 267217 61 + 636262 tgatgtttgacaacctttttacacaatcagttccatagcatcaccatgtttgtctcctgtt -s mr.mrrefChr5 118817 61 + 294540 tgatgtttgacaacctttttacacaatcagttccatagcatcaccatgtttgtctcctgtt -s simRat_chr6.simRat.chr6 256091 61 + 647215 TTATGTTTGACAACCTATTTGCACAATCAGTTCAATAGGGTCACCATGCTTGTCTCTTGTT - -a -s simMouse_chr6.simMouse.chr6 267278 334 + 636262 tactcagcAgagaatgagtaggttcctatctcctccacagttaaagtaaattcctacccttgctgaggctagtagggcttcaggtggaagTCTATAGGTGCCTCTGATAGCTTGACAGCACAACAAGCGGGGCCTGCTCACAGCCAAGTTACTAACTGCATGCACATGGCTACATTTGCCTTTTATTAGAGCTTTGCACAGTGCGCTGTGCTAAATCTAAACAaggttaagcattgctctctgtccctcaactgcaaaacacagtagtgcatggacactttagaaacttctcaaccaagaagcAAGACAAGGTGTATAAGGGAACTCTGTGTAG -s mr.mrrefChr5 118878 325 + 294540 tactcagcAgaga---agtaggttcctatctcctccacagttaaagtaaattcctacccttgctgaggctagtagggcttcaggtggaagTCTATAGGTGCCTCTGATAGCTTGACAGCACAACAAGCGGGGCCTGCTCACAGCCAAGTTACTAACTGCATGCACATGGCTACATTTGC-----ATTAGAGCTTTGCACAGTGCGCTGTGCTAAATCTAAACAaggttaagcattgctc-ctgtccctcaactgcaaaacacagtagtgcatggacactttagaaacttctcaaccaagaagcAAGACAAGGTGTATAAGGGAACTCTGTGTAG -s simRat_chr6.simRat.chr6 256176 325 + 647215 TAATCACCAGaga---aattagttcctatcccccccactgttggagtaaactcctacctttgctggggttagtaggacttcaggttgaagTCTATAGGTGCCTGTGATTACTTGACAGCACATCAAGCGGGGCAGGCTCAGAGCCAAATTACTAACTGCATGCACATGGTTTCATTTGC-----ATTAGGGCTCTGCACAAAGTGCTGTACTAAGACCAAACAAGGTTAAGCATTGCTC-CTGCCCCTTAATCCCAAAACACAGTAGTGCATGGACACTTTAGAAACTTCTCAACCAGGAAGCAAGACAGGGTGTATGAGGGAACTCTATGTAG - -a -s simMouse_chr6.simMouse.chr6 267612 41 + 636262 AATTGAAGCGGGTAAATTGATGGCCATTGATGCTTCACTAA -s mr.mrrefChr5 119203 40 + 294540 AATTGAAGCGGGTAAA-TGATGGCCATTGATGCTTCACTAA -s simRat_chr6.simRat.chr6 256503 40 + 647215 AATCAAAATCGATAAA-TGATGCCAATTGATAGTTCAACAA - -a -s simMouse_chr6.simMouse.chr6 267653 22 + 636262 ATTTAAAAGTTAGGTGCCAAAG -s mr.mrrefChr5 119243 22 + 294540 ATTTAAAAGTTAGGTGCCAAAG -s simRat_chr6.simRat.chr6 256547 22 + 647215 ATTTAAAAGTCAGGTGCCAAAG - -a -s simMouse_chr6.simMouse.chr6 267675 10 + 636262 TGATGCTATC -s mr.mrrefChr5 119265 10 + 294540 TGATGCTATC -s simRat_chr6.simRat.chr6 256576 10 + 647215 TGATGCTATC - -a -s simMouse_chr6.simMouse.chr6 267685 20 + 636262 ACCCTTTCTTTAGAAGAGTT -s mr.mrrefChr5 119275 20 + 294540 ACCCTTTCTTTAGAAGAGTT -s simRat_chr6.simRat.chr6 256610 20 + 647215 ATTTTTGCTTGAGAAGAATT - -a -s simMouse_chr6.simMouse.chr6 267705 4 + 636262 ATTT -s Anc0.Anc0refChr3 161431 3 + 222631 ACT- -s Anc1.Anc1refChr6 197739 4 + 197743 ACTT -s Anc2.Anc2refChr1 76056 3 + 142988 ACT- -s mr.mrrefChr3 110125 4 + 181027 ACTC -s mr.mrrefChr5 119295 4 + 294540 ATTT -s simCow_chr6.simCow.chr6 534740 3 + 602619 ACT- -s simDog_chr6.simDog.chr6 522977 3 + 593897 ACT- -s simHuman_chr6.simHuman.chr6 529961 4 + 601863 ACTT -s simMouse_chr6.simMouse.chr6 560168 4 + 636262 ACTC -s simRat_chr6.simRat.chr6 35378 4 - 647215 ACTC -s simRat_chr6.simRat.chr6 256630 4 + 647215 ATTT - -a -s simMouse_chr6.simMouse.chr6 267709 9 + 636262 TAGAACACG -s Anc0.Anc0refChr5 80389 9 + 87904 TAGGACAGG -s Anc1.Anc1refChr7 39395 9 - 47259 TAGGACAGG -s Anc2.Anc2refChr15 77622 9 + 86568 TAGGACAGG -s mr.mrrefChr5 119299 9 + 294540 TAGAACACG -s simCow_chr6.simCow.chr6 259842 9 + 602619 AAGAACAGA -s simDog_chr6.simDog.chr6 250768 9 + 593897 TAGGACAGG -s simHuman_chr6.simHuman.chr6 342033 9 - 601863 TAGGACATG -s simRat_chr6.simRat.chr6 256634 9 + 647215 TAGAACAGG - -a -s simMouse_chr6.simMouse.chr6 267718 11 + 636262 CCCTGAAAAGA -s Anc0.Anc0refChr5 80409 11 + 87904 CCCTGAAAAGA -s Anc1.Anc1refChr7 39415 11 - 47259 CCCTGAAAAGA -s Anc2.Anc2refChr15 77642 11 + 86568 CCCTGAAAAGA -s mr.mrrefChr5 119308 11 + 294540 CCCTGAAAAGA -s simCow_chr6.simCow.chr6 259862 11 + 602619 CCCTGAGAAGA -s simDog_chr6.simDog.chr6 250788 11 + 593897 TCCTGAAAAGA -s simHuman_chr6.simHuman.chr6 342053 11 - 601863 CCCTGAAAAGA -s simRat_chr6.simRat.chr6 256643 11 + 647215 CCCTGACAAGA - -a -s simMouse_chr6.simMouse.chr6 267729 2 + 636262 TA -s Anc0.Anc0refChr5 80420 2 + 87904 CA -s Anc1.Anc1refChr7 39426 2 - 47259 CA -s Anc2.Anc2refChr15 77653 2 + 86568 CA -s mr.mrrefChr5 119319 2 + 294540 TA -s simCow_chr6.simCow.chr6 259873 2 + 602619 CA -s simDog_chr6.simDog.chr6 250799 2 + 593897 CA -s simHuman_chr6.simHuman.chr6 342064 2 - 601863 CA -s simRat_chr6.simRat.chr6 256657 2 + 647215 TA - -a -s simMouse_chr6.simMouse.chr6 267731 8 + 636262 TATAGATT -s Anc0.Anc0refChr5 80423 8 + 87904 TACAGATA -s Anc1.Anc1refChr7 39429 8 - 47259 TACAGATA -s Anc2.Anc2refChr15 77656 8 + 86568 TGCAGATA -s mr.mrrefChr5 119321 8 + 294540 TATAGATT -s simCow_chr6.simCow.chr6 259880 8 + 602619 TTCAGGTA -s simDog_chr6.simDog.chr6 250802 8 + 593897 TGCAGATA -s simHuman_chr6.simHuman.chr6 342067 8 - 601863 TACAAATA -s simRat_chr6.simRat.chr6 256659 8 + 647215 TATATATT - -a -s simMouse_chr6.simMouse.chr6 267739 4 + 636262 TAGC -s Anc0.Anc0refChr5 80431 4 + 87904 TTGC -s Anc1.Anc1refChr7 39437 4 - 47259 TTGC -s Anc2.Anc2refChr15 77669 4 + 86568 TTTC -s mr.mrrefChr5 119329 4 + 294540 TAGC -s simCow_chr6.simCow.chr6 259893 4 + 602619 TTTA -s simDog_chr6.simDog.chr6 250815 4 + 593897 TTTC -s simHuman_chr6.simHuman.chr6 342075 4 - 601863 TTGC -s simRat_chr6.simRat.chr6 256667 4 + 647215 TAGC - -a -s simMouse_chr6.simMouse.chr6 267743 35 + 636262 TGGTATAATCTATGGTAGCTGCTGATTCCGTAGAG -s Anc0.Anc0refChr5 80437 35 + 87904 TGACCTGACCCCTAGCAGCGGCTGATTACGTAAAG -s Anc1.Anc1refChr7 39443 35 - 47259 TGACCTGACCCCTAGCAGCGGCTGATTACGTAAAG -s Anc2.Anc2refChr15 77675 35 + 86568 TGACCTGACCCCCAGCAGGGGTTGATTACCTAAAG -s mr.mrrefChr5 119333 35 + 294540 TGGTATAATCTATGGTAGCTGCTGATTCCGTAGAG -s simCow_chr6.simCow.chr6 259899 29 + 602619 TAA------TCCCAGCAGTGGTTGATTACTCAAAG -s simDog_chr6.simDog.chr6 250821 33 + 593897 TGACCTGACCTACGGCAGGGGTTGATTACCTTA-- -s simHuman_chr6.simHuman.chr6 342081 35 - 601863 TGACCTGACCCCTAGCAGCAGCCGATTACGTAAAG -s simRat_chr6.simRat.chr6 256671 35 + 647215 TGGTATGACCTATGGCAGCTGCTGATTCTGTAGAG - -a -s simMouse_chr6.simMouse.chr6 267778 50 + 636262 GCAAGACTCATATTCAATAGTCTGACCATGGAACATAATCAACAATGCTG -s Anc0.Anc0refChr5 80472 38 + 87904 TTAAG------------TGTTCTGGTCCTGGAACAACATCAACAGTGCTC -s Anc1.Anc1refChr7 39478 49 - 47259 TTAAGACTCAT-CTCAATGTTCTGGTCCTGGAACAACATCAACAGTGCTC -s Anc2.Anc2refChr15 77710 38 + 86568 TTTAG------------TGTTCTGGTTCTGGAACAACATCACCAGTGTAC -s mr.mrrefChr5 119368 50 + 294540 GCAAGACTCATATTCAATAGTCTGACCATGGAACATAATCAACAATGCTG -s simCow_chr6.simCow.chr6 259942 37 + 602619 TTCAG------------TGTTTTGGTTCTGGAACAACATCACCAG-GTAT -s simDog_chr6.simDog.chr6 250854 37 + 593897 TTTAG------------TGTTCTGGTTTTAGAACAAC-TCACCAGTGTAC -s simHuman_chr6.simHuman.chr6 342116 47 - 601863 TTAAGACTCAT-CTCAAC--CCTGGTCCTGGAACAACATCAACGGTGCTC -s simRat_chr6.simRat.chr6 256706 50 + 647215 GCAAGACTCATATTCAATAATCTGACAGTAGAACATAATCAACAATGCTT - -a -s simMouse_chr6.simMouse.chr6 267828 2 + 636262 GT -s Anc0.Anc0refChr5 80510 2 + 87904 GT -s Anc1.Anc1refChr7 39527 2 - 47259 GT -s Anc2.Anc2refChr15 77748 2 + 86568 GC -s mr.mrrefChr5 119418 2 + 294540 GT -s simCow_chr6.simCow.chr6 259979 2 + 602619 GC -s simDog_chr6.simDog.chr6 250895 2 + 593897 GC -s simHuman_chr6.simHuman.chr6 342163 2 - 601863 GT -s simRat_chr6.simRat.chr6 256756 2 + 647215 GT - -a -s simMouse_chr6.simMouse.chr6 267830 2 + 636262 CG -s Anc0.Anc0refChr5 80513 2 + 87904 CG -s Anc1.Anc1refChr7 39530 2 - 47259 CG -s Anc2.Anc2refChr15 77751 2 + 86568 CA -s mr.mrrefChr5 119420 2 + 294540 CG -s simDog_chr6.simDog.chr6 250898 2 + 593897 CA -s simHuman_chr6.simHuman.chr6 342166 2 - 601863 CG -s simRat_chr6.simRat.chr6 256759 2 + 647215 TG - -a -s simMouse_chr6.simMouse.chr6 267832 17 + 636262 CTTGACATGAGGCTTGC -s Anc0.Anc0refChr5 80527 12 + 87904 CTTGAAATT-----GTC -s Anc1.Anc1refChr7 39544 12 - 47259 CTTGAAATT-----GTC -s Anc2.Anc2refChr15 77765 12 + 86568 CTTGAAATT-----GTC -s mr.mrrefChr5 119422 12 + 294540 CTTGACATG-----TGC -s simCow_chr6.simCow.chr6 259998 12 + 602619 CTTGAAATT-----GTC -s simHuman_chr6.simHuman.chr6 342180 12 - 601863 CTTGGTATC-----ATC -s simRat_chr6.simRat.chr6 256761 12 + 647215 CTTGACATG-----TGC - -a -s simMouse_chr6.simMouse.chr6 267849 6 + 636262 TCCGTG -s Anc0.Anc0refChr5 80539 6 + 87904 TCCATG -s Anc1.Anc1refChr7 39556 6 - 47259 TCCATG -s Anc2.Anc2refChr15 77777 6 + 86568 TCCATG -s mr.mrrefChr5 119434 6 + 294540 TCCGTG -s simCow_chr6.simCow.chr6 260010 6 + 602619 TCCATG -s simHuman_chr6.simHuman.chr6 342192 6 - 601863 TCCATG -s simRat_chr6.simRat.chr6 256775 6 + 647215 TCCACG - -a -s simMouse_chr6.simMouse.chr6 267855 5 + 636262 CAATG -s Anc0.Anc0refChr5 80545 3 + 87904 --ATG -s Anc1.Anc1refChr7 39562 5 - 47259 AAATG -s Anc2.Anc2refChr15 77783 3 + 86568 --ATG -s mr.mrrefChr5 119440 5 + 294540 CAATG -s simCow_chr6.simCow.chr6 260016 3 + 602619 --ATG -s simHuman_chr6.simHuman.chr6 342198 5 - 601863 AACTG -s simRat_chr6.simRat.chr6 256787 5 + 647215 CAGAG - -a -s simMouse_chr6.simMouse.chr6 267860 83 + 636262 GGCATAACATTTGACAGAGCTATCGTCTGCATTCCCAGATCATCTGCAGCTATTATAAGTGTTTATTGTAATGGGCCAAGCTC -s Anc0.Anc0refChr5 80555 62 + 87904 GGTATAACATTTAACAGGGCTATC-----------------ACTTGCAGCTATTATAAGTGT---T-ATAATGGGCCAAGCTC -s Anc1.Anc1refChr7 39574 65 - 47259 GGTATAACATTTAACAGGGCTATC-----------------ACTTGCAGCTATTATAAGTGTTAAT-ATAATGGGCCAAGCTC -s Anc2.Anc2refChr15 77793 62 + 86568 GGTAGCACATTCAATAAGACCATC-----------------ACTTGCAGCTAGTGGCAGTGT---T-ATAATGTCCCAAGCTG -s mr.mrrefChr5 119445 78 + 294540 GGCATAACATTTGACAGAGCTATCGTCTGCATT-----ATCATCTGCAGCTATTATAAGTGTTTATTGTAATGGGCCAAGCTC -s simCow_chr6.simCow.chr6 260026 62 + 602619 GGTAGCACATTCAATAAGACCATC-----------------ACTTGCAGCTAGTGGCAGTGT---T-ATAATGTCCCAAGCTG -s simHuman_chr6.simHuman.chr6 342214 65 - 601863 GGGATAGCATTTAACAGGGCTATC-----------------ACTTGCAGCTATTATAAGTGTTAAT-ATAATGGGTTAAGCCC -s simRat_chr6.simRat.chr6 256792 78 + 647215 GGGATAACATTTGAAAGAGCTATCGTCTGCACT-----ATCATCTGCAGCTATTATAAGTTTCTATTGTAATGGGCCACGTTG - -a -s simMouse_chr6.simMouse.chr6 267943 30 + 636262 CACAGTAGAACTAGCCACAGGGGGGACATT -s Anc0.Anc0refChr5 80617 24 + 87904 CACAGT----CAAGCC--AGTGCGGTCATC -s Anc1.Anc1refChr7 39639 26 - 47259 CACAGT----CAAGCCATAGTGCGGTCATC -s Anc2.Anc2refChr15 77855 24 + 86568 GACAGT----CAGACC--AGTGCAGTCATC -s mr.mrrefChr5 119523 30 + 294540 CACAGTAGAACTAGCCACAGGGGGGACATT -s simCow_chr6.simCow.chr6 260088 24 + 602619 GACAGT----CAGACC--AGTGCAGTCATC -s simHuman_chr6.simHuman.chr6 342280 26 - 601863 CACAGT----CAAGCCATAGTAAGGTCACC -s simRat_chr6.simRat.chr6 256870 30 + 647215 CACAGGAGGGCCAGCCACAGAGAGGACATC - -a -s simMouse_chr6.simMouse.chr6 267973 27 + 636262 TGGTATCAAGCCAATCCCAGAGTCTTA -s Anc0.Anc0refChr5 80641 23 + 87904 TAGAATCAATTCAAT-CT---ATCTTC -s Anc1.Anc1refChr7 39665 26 - 47259 TAGAATCAATTCAAT-CTAGAATCTTC -s Anc2.Anc2refChr15 77879 23 + 86568 CAGAATCTATTGTAC-TT---ATCTAC -s mr.mrrefChr5 119553 26 + 294540 TGGTATCAAGCCAAT-CCAGAGTCTTA -s simCow_chr6.simCow.chr6 260114 23 + 602619 CAGAATCTATTGTAC-TT---ATCTAC -s simHuman_chr6.simHuman.chr6 342306 26 - 601863 TAGAATCAAATCAAT-CAAGAATCTTG -s simRat_chr6.simRat.chr6 256900 26 + 647215 TGGTGTCAATCCAAT-CCAGAGTCCTA - -a -s simMouse_chr6.simMouse.chr6 268000 16 + 636262 TCACCCTAGTGGTTTA -s Anc0.Anc0refChr5 80664 16 + 87904 TCCCACCTGTGATGTA -s Anc1.Anc1refChr7 39691 16 - 47259 TCCCACCTGTGATGTA -s Anc2.Anc2refChr15 77902 16 + 86568 TCCCATCTGTGATGTA -s mr.mrrefChr5 119579 16 + 294540 TCACCCTAGTGGTTTA -s simCow_chr6.simCow.chr6 260137 16 + 602619 TCCCATCTGTGATGTA -s simHuman_chr6.simHuman.chr6 342436 16 - 601863 TGCCACATACTATGTA -s simRat_chr6.simRat.chr6 256926 16 + 647215 CCCCCCTTGTGGTTTA - -a -s simMouse_chr6.simMouse.chr6 268016 44 + 636262 CTTTTGGTGGGTATCTGGCATCTAAATTAGAGAAGCTGCCTCAC -s Anc0.Anc0refChr5 80689 37 + 87904 ATTTTGGAGGGT-------GTCCATCTTAGAGGCACTGTCTCAT -s Anc1.Anc1refChr7 39716 37 - 47259 ATTTTGGAGGGT-------GTCCATCTTAGAGGCACTGTCTCAT -s Anc2.Anc2refChr15 77927 37 + 86568 ATTTTGGAGGGT-------GTCCATCTTAGAGGCACTGTCTCAT -s mr.mrrefChr5 119595 37 + 294540 CTTTTGGTGGGT-------ATCTAAATTAGAGAAGCTGCCTCAC -s simCow_chr6.simCow.chr6 260162 37 + 602619 ATTTTGGAGAGT-------GTCCATCTTAGAGGCACTGACTCAT -s simDog_chr6.simDog.chr6 250910 33 + 593897 ATTTTGGAGGGT-------GTCAATCTTAGAAGCACTGT----G -s simHuman_chr6.simHuman.chr6 342461 37 - 601863 TTATTGGAGGGT-------GTCCATCTTAGAGGCACTATTTCAT -s simRat_chr6.simRat.chr6 256942 37 + 647215 TTTTTGGTGGGT-------ACTCAAGTTAGAGATGCTGACTCAT - -a -s simMouse_chr6.simMouse.chr6 268060 27 + 636262 TTGGATGAGCAACTGAGGTGAGCAATT -s Anc0.Anc0refChr5 80726 16 + 87904 TGGGATGAACGACTGA----------- -s Anc1.Anc1refChr7 39753 16 - 47259 TGGGATGAACGACTGA----------- -s Anc2.Anc2refChr15 77964 16 + 86568 TGGGATGAACGATTTG----------- -s mr.mrrefChr5 119632 27 + 294540 TTGGATGAGCAACTGAGGTGAGCAATT -s simCow_chr6.simCow.chr6 260209 16 + 602619 TGGGATGAACAATTTG----------- -s simDog_chr6.simDog.chr6 250943 16 + 593897 TGGAATGAGCGATTTG----------- -s simHuman_chr6.simHuman.chr6 342498 16 - 601863 TGGCATGATTGGCTGA----------- -s simRat_chr6.simRat.chr6 256979 27 + 647215 TTGGGTGAGCAACTGAGACAAGCAATT - -a -s simMouse_chr6.simMouse.chr6 268087 92 + 636262 TTGCAGTTGTCCTACCTCCATGGGGCGCATTCTTCATAGATGACTAGAGAACCACAAAAGGCAAATCATATAGCCTGCATCTCCACCTCCAC -s Anc0.Anc0refChr5 80743 87 + 87904 CTGT---AGTCCTG--TCCATAGGGTGCATTAGTCGTACTTGACTAGTGTATCACAAAGGCCAAATCATATATCCTGAGGCTCCATGTCCAC -s Anc1.Anc1refChr7 39770 87 - 47259 CTGT---AGTCCTG--TCCATAGGGTGCATTAGTCGTACTTGACTAGTGTATCACAAAGGCCAAATCATATATCCTGAGGCTCCATGTCCAC -s Anc2.Anc2refChr15 77981 87 + 86568 CTGT---AGTCCTG--TCCATAAGGTGCATTAGTCGTACTTAACTAGTGTATCACAAAGGCCAAATCATACATCTTGAGGCTCCATGTCCCC -s mr.mrrefChr5 119659 89 + 294540 TTGC---TGTCCTACCTCCATGGGGCGCATTCTTCATAGATGACTAGAGAACCACAAAAGGCAAATCATATAGCCTGCATCTCCACCTCCAC -s simCow_chr6.simCow.chr6 260226 87 + 602619 CTGT---TGTCCTG--TCCTTAAGGTGCATTAGTCACAGTTTACCAGTGTATCAAAAAGCCTAAATCATACATCTTGAGTCTCCATATCCCC -s simDog_chr6.simDog.chr6 250960 87 + 593897 CTGA---AGTCATG--TCCATAAGGTGCATTAGGGGTACTTAACTACCATATCACAAGGGCCACATCATACATCTTGAGGCTCCATGTCCCC -s simHuman_chr6.simHuman.chr6 342817 81 - 601863 CTGT---AGTCCTG--TCCATTGGG------AGTCGTACTTGACTAGTGGATCACAAAGGCCAAATCATATATCCTGAGACTCTATGTCCAC -s simRat_chr6.simRat.chr6 257006 89 + 647215 TTGC---TGTCCTACCTCCGTGGGGTGCATTCATCACAGATGACTAATGAACCACAAAAGGCAAGTCATGTAGCCTGCATCACCATCTCCAC - -a -s simMouse_chr6.simMouse.chr6 268179 6 + 636262 TTATTA -s Anc0.Anc0refChr5 80830 6 + 87904 TTATTA -s Anc1.Anc1refChr7 39857 6 - 47259 TTATTA -s Anc2.Anc2refChr15 78069 6 + 86568 GTATTA -s mr.mrrefChr5 119748 6 + 294540 TTATTA -s simCow_chr6.simCow.chr6 260314 6 + 602619 GTCTTA -s simDog_chr6.simDog.chr6 251048 6 + 593897 GTATTA -s simHuman_chr6.simHuman.chr6 342898 6 - 601863 TTACTA -s simRat_chr6.simRat.chr6 257095 6 + 647215 TTATTA - -a -s simMouse_chr6.simMouse.chr6 268185 19 + 636262 CACAGACTGACCCCCTAGT -s Anc0.Anc0refChr5 80837 19 + 87904 CACAGCATGTCCCCTTTGT -s Anc1.Anc1refChr7 39864 19 - 47259 CACAGCATGTCCCCTTTGT -s Anc2.Anc2refChr15 78076 19 + 86568 CACAGCATGTCCCCTTTGT -s mr.mrrefChr5 119754 19 + 294540 CACAGACTGACCCCCTAGT -s simCow_chr6.simCow.chr6 260321 19 + 602619 CACAACTTGACCCCATTGT -s simDog_chr6.simDog.chr6 251055 19 + 593897 CACAGCATGTCTCCTTTGT -s simHuman_chr6.simHuman.chr6 342905 19 - 601863 CACAGCATGTCCCCTTTGT -s simRat_chr6.simRat.chr6 257101 19 + 647215 CACAGAGTGATCCCCTAGT - -a -s simMouse_chr6.simMouse.chr6 268204 7 + 636262 CATGCCC -s Anc0.Anc0refChr5 80859 7 + 87904 CACACCT -s Anc1.Anc1refChr7 39886 7 - 47259 CACACCT -s Anc2.Anc2refChr15 78098 7 + 86568 CACAGCT -s mr.mrrefChr5 119773 7 + 294540 CATGCCC -s simCow_chr6.simCow.chr6 260343 7 + 602619 CATGACT -s simDog_chr6.simDog.chr6 251077 7 + 593897 CACAGCT -s simHuman_chr6.simHuman.chr6 342927 7 - 601863 CACACCT -s simRat_chr6.simRat.chr6 257120 7 + 647215 CATACCC - -a -s simMouse_chr6.simMouse.chr6 268211 15 + 636262 CTGTTTTAGCTGCAG -s Anc0.Anc0refChr5 80867 15 + 87904 CCATTTTGACTGCAG -s Anc1.Anc1refChr7 39894 15 - 47259 CCATTTTGACTGCAG -s Anc2.Anc2refChr15 78106 15 + 86568 CCATTTTGACTGCAG -s mr.mrrefChr5 119780 15 + 294540 CTGTTTTAGCTGCAG -s simCow_chr6.simCow.chr6 260351 15 + 602619 GCGCATTGACTGCAG -s simDog_chr6.simDog.chr6 251085 15 + 593897 CCATTTCGACTGCAG -s simHuman_chr6.simHuman.chr6 342935 15 - 601863 CCATTTTGATTACAG -s simRat_chr6.simRat.chr6 257127 15 + 647215 CTGGTTTAGCTTGGG - -a -s simMouse_chr6.simMouse.chr6 268226 8 + 636262 AATCTTGG -s Anc0.Anc0refChr5 80882 8 + 87904 GATCTTGG -s Anc1.Anc1refChr7 39909 8 - 47259 GATCTTGG -s Anc2.Anc2refChr15 78121 8 + 86568 GATATTGG -s mr.mrrefChr5 119795 8 + 294540 AATCTTGG -s simCow_chr6.simCow.chr6 260366 8 + 602619 GGTATTGG -s simDog_chr6.simDog.chr6 251100 8 + 593897 GATATTGG -s simHuman_chr6.simHuman.chr6 342950 8 - 601863 GATCTTGG -s simRat_chr6.simRat.chr6 257144 8 + 647215 AATCCATG - -a -s simMouse_chr6.simMouse.chr6 268234 8 + 636262 CGTAGCTC -s Anc0.Anc0refChr5 80891 8 + 87904 CATCACTC -s Anc1.Anc1refChr7 39918 8 - 47259 CATCACTC -s Anc2.Anc2refChr15 78130 8 + 86568 CATCACTC -s mr.mrrefChr5 119803 8 + 294540 CGTAGCTC -s simCow_chr6.simCow.chr6 260375 8 + 602619 CATCACTC -s simDog_chr6.simDog.chr6 251109 8 + 593897 CAAAACTC -s simHuman_chr6.simHuman.chr6 342959 8 - 601863 CATCACTC -s simRat_chr6.simRat.chr6 257152 8 + 647215 TGGAACTT - -a -s simMouse_chr6.simMouse.chr6 268242 14 + 636262 CGACACAATGCGGG -s Anc0.Anc0refChr5 80899 14 + 87904 CACCACAATTGGGT -s Anc1.Anc1refChr7 39926 14 - 47259 CACCACAATTGGGT -s Anc2.Anc2refChr15 78138 14 + 86568 CACCACAATTGGAT -s mr.mrrefChr5 119811 14 + 294540 CGACACAATGCGGG -s simCow_chr6.simCow.chr6 260383 14 + 602619 CACCACAATTGGAT -s simDog_chr6.simDog.chr6 251117 14 + 593897 AACCACAATTGGAT -s simHuman_chr6.simHuman.chr6 342967 14 - 601863 CACCACAATTGGGT -s simRat_chr6.simRat.chr6 257171 14 + 647215 CGCTACAACATTCG - -a -s simMouse_chr6.simMouse.chr6 268256 10 + 636262 GAGGCATGGG -s Anc0.Anc0refChr5 80913 10 + 87904 GGAACACAGG -s Anc1.Anc1refChr7 39940 10 - 47259 GGAACACAGG -s Anc2.Anc2refChr15 78152 10 + 86568 GGAATACAGG -s mr.mrrefChr5 119825 10 + 294540 GAGGCATGGG -s simCow_chr6.simCow.chr6 260397 10 + 602619 GGGAAACAGA -s simDog_chr6.simDog.chr6 251131 10 + 593897 GGAATACAGG -s simHuman_chr6.simHuman.chr6 342981 10 - 601863 GGAACACAGG -s simRat_chr6.simRat.chr6 257188 10 + 647215 GTGCCATCAA - -a -s simMouse_chr6.simMouse.chr6 268266 4 + 636262 ATGA -s Anc0.Anc0refChr5 80927 4 + 87904 ATCA -s Anc1.Anc1refChr7 39954 4 - 47259 ATCA -s Anc2.Anc2refChr15 78166 4 + 86568 GTCA -s mr.mrrefChr5 119835 4 + 294540 ATGA -s simCow_chr6.simCow.chr6 260411 4 + 602619 GTCA -s simDog_chr6.simDog.chr6 251145 4 + 593897 GTCA -s simHuman_chr6.simHuman.chr6 342995 4 - 601863 ATCA -s simRat_chr6.simRat.chr6 257198 4 + 647215 GTAA - -a -s simMouse_chr6.simMouse.chr6 268270 24 + 636262 AATGTCTTTAGTCCAGGTATTAAT -s Anc0.Anc0refChr5 80931 21 + 87904 GATGTCTACAGTTCAGA---TAAT -s Anc1.Anc1refChr7 39958 21 - 47259 GATGTCTACAGTTCAGA---TAAT -s Anc2.Anc2refChr15 78170 21 + 86568 GATGTCTACAGTTCAGA---TATT -s mr.mrrefChr5 119839 21 + 294540 AATGTCTTTAGTCCAGG---TAAT -s simCow_chr6.simCow.chr6 260415 21 + 602619 GATGTCCGCAGTCCAGA---TACT -s simDog_chr6.simDog.chr6 251149 21 + 593897 GATCTCTACAGTTCAGC---TGTT -s simHuman_chr6.simHuman.chr6 342999 21 - 601863 GATGTTTACAGTTCAGA---CAAT -s simRat_chr6.simRat.chr6 257204 21 + 647215 CAGGTCTATAGTCCAGG---TAAT - -a -s simMouse_chr6.simMouse.chr6 268294 17 + 636262 AGTTTCATGACAACCAC -s Anc0.Anc0refChr5 80955 16 + 87904 AGTTTTGTGACTACTA- -s Anc1.Anc1refChr7 39982 16 - 47259 AGTTTTGTGACTACTA- -s Anc2.Anc2refChr15 78194 16 + 86568 AGTTTTGTGACTACTG- -s mr.mrrefChr5 119860 17 + 294540 AGTTTCATGACAACCAC -s simCow_chr6.simCow.chr6 260439 16 + 602619 AGATTGGTGACTACTG- -s simDog_chr6.simDog.chr6 251177 10 + 593897 AGTTTTGTGA------- -s simHuman_chr6.simHuman.chr6 343023 16 - 601863 AGCTTTGGGACTACTA- -s simRat_chr6.simRat.chr6 257225 17 + 647215 AGTTTCATGACAACTAC - -a -s simMouse_chr6.simMouse.chr6 268311 4 + 636262 ATGT -s Anc0.Anc0refChr5 80971 4 + 87904 ATGT -s Anc1.Anc1refChr7 39998 4 - 47259 ATGT -s Anc2.Anc2refChr15 78210 4 + 86568 ATGT -s mr.mrrefChr5 119877 4 + 294540 ATGT -s simCow_chr6.simCow.chr6 260456 4 + 602619 ATGT -s simHuman_chr6.simHuman.chr6 343039 4 - 601863 ATGT -s simRat_chr6.simRat.chr6 257242 4 + 647215 ATGT - -a -s simMouse_chr6.simMouse.chr6 268315 24 + 636262 GACAAACATAGTAGCCCAGACAGG -s Anc0.Anc0refChr5 80975 24 + 87904 GACAACCATAGTATCACAGACAGG -s Anc1.Anc1refChr7 40002 24 - 47259 GACAACCATAGTATCACAGACAGG -s Anc2.Anc2refChr15 78214 24 + 86568 GACAACCACAGTATCACAGACAGG -s mr.mrrefChr5 119881 24 + 294540 GACAAACATAGTAGCCCAGACAGG -s simCow_chr6.simCow.chr6 260461 21 + 602619 GACAACCACAGTATCACAGAC--- -s simDog_chr6.simDog.chr6 251187 15 + 593897 -ACAACCA--------CAGCCAGG -s simHuman_chr6.simHuman.chr6 343043 24 - 601863 GACAACAATAGTATCACAGATGAG -s simRat_chr6.simRat.chr6 257246 24 + 647215 GACAAACATAATAGCCCAGATAGG - -a -s simMouse_chr6.simMouse.chr6 268339 17 + 636262 ACTAGAAATGATAAGTA -s Anc0.Anc0refChr5 80999 12 + 87904 ACT-----TGAGTAGTA -s Anc1.Anc1refChr7 40026 17 - 47259 ACTATACATGAGTAGTA -s Anc2.Anc2refChr15 78238 12 + 86568 CAT-----TGAGTAGTC -s mr.mrrefChr5 119905 17 + 294540 ACTAGAAATGATAAGTA -s simCow_chr6.simCow.chr6 260482 10 + 602619 --T-----TAAGTAGTC -s simDog_chr6.simDog.chr6 251202 12 + 593897 CAT-----TGAGTAGTA -s simHuman_chr6.simHuman.chr6 343368 17 - 601863 ACGATACATGAATAGTA -s simRat_chr6.simRat.chr6 257270 17 + 647215 GATAGAAATGATAAGTA - -a -s simMouse_chr6.simMouse.chr6 268356 30 + 636262 TGCCAACCATTCTGCAGTGGACATTTAATT -s Anc0.Anc0refChr5 81015 19 + 87904 TGACAACCATAGTATAGTG----------- -s Anc1.Anc1refChr7 40047 30 - 47259 TGACAACCATAGTATAGTGAACATTTAAAT -s Anc2.Anc2refChr15 78254 19 + 86568 TGACATCCATAGTATAGTG----------- -s mr.mrrefChr5 119922 30 + 294540 TGCCAACCATTCTGCAGTGGACATTTAATT -s simCow_chr6.simCow.chr6 260496 19 + 602619 TGATATCCATAGAATAGTG----------- -s simDog_chr6.simDog.chr6 251218 19 + 593897 TTACCTCTGTAGTATAGTG----------- -s simHuman_chr6.simHuman.chr6 343389 30 - 601863 TGACAACCATAGTATAGTGAACATTTAAAT -s simRat_chr6.simRat.chr6 257287 30 + 647215 TGACAACCATAGAGCAGTGGACATTTGATT - -a -s simMouse_chr6.simMouse.chr6 268386 40 + 636262 TCAATCGAGAGACTATTCGATGAGTATTTCATATGGCTGT -s Anc0.Anc0refChr5 81034 40 + 87904 TCAGGCCAGTGGCTATTCAATGAGAAGTCAGTATGTTTGT -s Anc1.Anc1refChr7 40077 40 - 47259 TCAGGCCAGTGGCTATTCAATGAGAAGTCAGTATGTTTGT -s Anc2.Anc2refChr15 78273 40 + 86568 CCAGGCCAGTTGCTATTCAATGAGAAGTCAGTACGTTTGT -s mr.mrrefChr5 119952 40 + 294540 TCAATCGAGAGACTATTCGATGAGTATTTCATATGGCTGT -s simCow_chr6.simCow.chr6 260526 40 + 602619 CCAGACCGGATGGTATTCTAGGAACAATGAGTATGTTTGT -s simDog_chr6.simDog.chr6 251237 40 + 593897 CTAGGCCAGTTGCTATTCAATGAGAAGTCAGTACGTTTGT -s simHuman_chr6.simHuman.chr6 343419 39 - 601863 TCAGATCAG-GGCTATTGAGGAAACGGTCTGTATGTTTAT -s simRat_chr6.simRat.chr6 257317 40 + 647215 TCAGACAAGAGGCTATTCAATGAGTATTTCATATGGCTGT - -a -s simMouse_chr6.simMouse.chr6 268426 1 + 636262 T -s Anc0.Anc0refChr5 81075 1 + 87904 G -s Anc1.Anc1refChr7 40118 1 - 47259 G -s Anc2.Anc2refChr15 78314 1 + 86568 G -s mr.mrrefChr5 119992 1 + 294540 T -s simCow_chr6.simCow.chr6 260567 1 + 602619 A -s simDog_chr6.simDog.chr6 251278 1 + 593897 G -s simHuman_chr6.simHuman.chr6 343459 1 - 601863 C -s simRat_chr6.simRat.chr6 257357 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 268427 4 + 636262 CTGA -s Anc0.Anc0refChr5 81076 4 + 87904 CTAG -s Anc1.Anc1refChr7 40119 4 - 47259 CTAG -s Anc2.Anc2refChr15 78315 4 + 86568 TTAG -s mr.mrrefChr5 119993 4 + 294540 CTGA -s simCow_chr6.simCow.chr6 260568 4 + 602619 GTAG -s simDog_chr6.simDog.chr6 251279 4 + 593897 TTAG -s simHuman_chr6.simHuman.chr6 343460 4 - 601863 CTAG -s simRat_chr6.simRat.chr6 257380 4 + 647215 TTGA - -a -s simMouse_chr6.simMouse.chr6 268431 10 + 636262 TACTTCCAGT -s Anc0.Anc0refChr5 81080 10 + 87904 TAATTCCAGT -s Anc1.Anc1refChr7 40123 10 - 47259 TAATTCCAGT -s Anc2.Anc2refChr15 78319 10 + 86568 TAATTACAGT -s mr.mrrefChr5 119997 10 + 294540 TACTTCCAGT -s simCow_chr6.simCow.chr6 260573 10 + 602619 TAATTCTAGC -s simDog_chr6.simDog.chr6 251283 10 + 593897 TAATTACAGT -s simHuman_chr6.simHuman.chr6 343464 10 - 601863 CAATTCCAGG -s simRat_chr6.simRat.chr6 257384 10 + 647215 TATTTCCAGT - -a -s simMouse_chr6.simMouse.chr6 268441 6 + 636262 GGGGAA -s Anc0.Anc0refChr5 81090 6 + 87904 GGATAA -s Anc1.Anc1refChr7 40133 6 - 47259 GGATAA -s Anc2.Anc2refChr15 78330 6 + 86568 GGATAA -s mr.mrrefChr5 120007 6 + 294540 GGGGAA -s simCow_chr6.simCow.chr6 260584 6 + 602619 GGCCAA -s simDog_chr6.simDog.chr6 251294 6 + 593897 GGATAA -s simHuman_chr6.simHuman.chr6 343474 6 - 601863 GGATAA -s simRat_chr6.simRat.chr6 257394 6 + 647215 GGTGAA - -a -s simMouse_chr6.simMouse.chr6 268447 1 + 636262 T -s Anc0.Anc0refChr5 81098 1 + 87904 T -s Anc1.Anc1refChr7 40141 1 - 47259 T -s Anc2.Anc2refChr15 78338 1 + 86568 T -s mr.mrrefChr5 120013 1 + 294540 T -s simCow_chr6.simCow.chr6 260592 1 + 602619 T -s simDog_chr6.simDog.chr6 251302 1 + 593897 T -s simHuman_chr6.simHuman.chr6 343482 1 - 601863 T -s simRat_chr6.simRat.chr6 257404 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 268448 43 + 636262 AAATTTCTAGACAGCAGCGAAAGCTAGTCAGCATTAAATTAAA -s Anc0.Anc0refChr5 81099 34 + 87904 CA----TTAGAGATGCAAGAAAGTAAATCCACATCA-----CA -s Anc1.Anc1refChr7 40142 38 - 47259 CAAGTCTTAGAGATGCAAGAAAGTAAATCCACATCA-----CA -s Anc2.Anc2refChr15 78339 34 + 86568 CA----TTAGAGATGCAAGAAAGTAAATCCACATCA-----CA -s mr.mrrefChr5 120014 38 + 294540 AAATTTCTAGACAGCAGCGAAAGCTAGTCAGCATTA-----AA -s simCow_chr6.simCow.chr6 260598 34 + 602619 CC----TTAGACTTTGAAGAAAGTCGGGCCACATCA-----CA -s simDog_chr6.simDog.chr6 251303 34 + 593897 CA----TTAGAGATGCAAGAAAGTAAATCCACATCA-----CA -s simHuman_chr6.simHuman.chr6 343483 11 - 601863 CAAGTCTTAGA-------------------------------- -s simRat_chr6.simRat.chr6 257405 38 + 647215 AAATTTCTTGACATCAAGATAAGTTAGTCAGCATTA-----CG - -a -s simMouse_chr6.simMouse.chr6 268491 39 + 636262 TTATCATCACTTATTTTGTGCCTGACTGGAAATGTCCTC -s Anc0.Anc0refChr5 81133 37 + 87904 GTGT--TCACAACTTCCCTTCATGCTTGCAAATATCCCC -s Anc1.Anc1refChr7 40180 37 - 47259 GTGT--TCACAACTTCCCTTCATGCTTGCAAATATCCCC -s Anc2.Anc2refChr15 78373 37 + 86568 GTGT--TCACAACTTCCCTTCATGCTTGCAAATATCCCC -s mr.mrrefChr5 120052 39 + 294540 TTATCATCACTTATTTTGTGCCTGACTGGAAATGTCCTC -s simCow_chr6.simCow.chr6 260632 37 + 602619 GTGT--TCACAACTCCCCTTCATGCTTGCAAATATCCCC -s simCow_chr6.simCow.chr6 570413 37 + 602619 GTGT--TCACAACTTCCCTTCATGCTTGCAAATATCCCC -s simDog_chr6.simDog.chr6 251337 37 + 593897 GTGT--CCATCACTTTCCTTTGTGCTTGCAGTTCTCCCC -s simRat_chr6.simRat.chr6 257443 39 + 647215 TTATCATCACATATTTCGAGCCTGTCTGTACATGTCCTC - -a -s simMouse_chr6.simMouse.chr6 268530 13 + 636262 TGACTTAGACAGG -s Anc0.Anc0refChr5 81170 13 + 87904 TGCTTTAGACTTG -s Anc1.Anc1refChr7 40217 13 - 47259 TGCTTTAGACTTG -s Anc2.Anc2refChr15 78411 13 + 86568 TGCTTTAGACTTG -s mr.mrrefChr5 120091 13 + 294540 TGACTTAGACAGG -s simCow_chr6.simCow.chr6 260670 13 + 602619 TGCTTTAGACTTG -s simCow_chr6.simCow.chr6 570451 13 + 602619 TGCTTTAGACTTG -s simDog_chr6.simDog.chr6 251375 13 + 593897 TGGTTTATACCTG -s simRat_chr6.simRat.chr6 257483 13 + 647215 TGATTTAAACTGG - -a -s simMouse_chr6.simMouse.chr6 268543 23 + 636262 CATTTAGAAACTTTCTGGCTCCA -s Anc0.Anc0refChr5 81183 21 + 87904 A--TTGCAAATATTCTGGACCCA -s Anc1.Anc1refChr7 40230 21 - 47259 A--TTGCAAATATTCTGGACCCA -s Anc2.Anc2refChr15 78424 21 + 86568 A--TTGCAAATATTCTGGACCCA -s mr.mrrefChr5 120104 23 + 294540 CATTTAGAAACTTTCTGGCTCCA -s simCow_chr6.simCow.chr6 260683 21 + 602619 A--TTGCAAATATTCTGAACCCA -s simCow_chr6.simCow.chr6 570464 21 + 602619 A--TTGCAAATATTCTGGACCCA -s simDog_chr6.simDog.chr6 251390 21 + 593897 A--CTGCAGATATTCTGGGTCCA -s simRat_chr6.simRat.chr6 257500 23 + 647215 CATTCAGAGACTTTCTGGCACCA - -a -s simMouse_chr6.simMouse.chr6 268566 10 + 636262 CTTAGCATAG -s Anc0.Anc0refChr5 81204 8 + 87904 CT--GGACCG -s Anc1.Anc1refChr7 40251 8 - 47259 CT--GGACCG -s Anc2.Anc2refChr15 78446 8 + 86568 CT--GGACCG -s mr.mrrefChr5 120127 8 + 294540 CT--GCATAG -s simCow_chr6.simCow.chr6 260705 8 + 602619 CT--AGACCG -s simCow_chr6.simCow.chr6 570486 8 + 602619 CT--GGACTG -s simDog_chr6.simDog.chr6 251412 7 + 593897 -T--GACCCA -s simRat_chr6.simRat.chr6 257523 8 + 647215 CT--GCATAG - -a -s simMouse_chr6.simMouse.chr6 268576 49 + 636262 ATTTGTAGCTTTAGTGCGCAGCACCCAAGCCCACATGGTGAGCAACTTC -s Anc0.Anc0refChr5 81212 49 + 87904 CTCTGTAGCTTTACCAAGTGGAACCTTATTTCAAATGTTGAGCAACTTT -s Anc1.Anc1refChr7 40259 49 - 47259 CTCTGTAGCTTTACCAAGTGGAACCTTATTTCAAATGTTGAGCAACTTT -s Anc2.Anc2refChr15 78455 49 + 86568 CTCTGTAGCTTTACCAAGTGGAACCTTATTATGTATGTTGAGCAACTTT -s mr.mrrefChr5 120135 49 + 294540 ATTTGTAGCTTTAGTGCGCAGCACCCAAGCTCAAATGGTGAGCAACTTC -s simCow_chr6.simCow.chr6 260714 46 + 602619 CTCTGTAGCTTTACCAAGTGGAACGTTACTAC---TGCTGAGCAACTTC -s simCow_chr6.simCow.chr6 570495 25 + 602619 CTCTATAGGTTTACCAAGTGGAACA------------------------ -s simDog_chr6.simDog.chr6 251420 49 + 593897 ATTTGTACCTTTAATGAGTGGAGCCTTATTATGTATGTTGAGCAACTTT -s simHuman_chr6.simHuman.chr6 343494 19 - 601863 ------------------------------TCAAGTGTTGAGCAACTTT -s simRat_chr6.simRat.chr6 257531 49 + 647215 ATTGGTAGCTTTAGTGCGCAGCACCCAGGCTCAAATGGTGAGCGACTTC - -a -s simMouse_chr6.simMouse.chr6 268625 45 + 636262 AACATAGATATGTGATACATTAGTGGAAGATATTTGGCTCATCAG -s Anc0.Anc0refChr5 81261 45 + 87904 AACATAAATATGTGCTACATTAGTGGAAAATTTTTGGCTGATCAA -s Anc1.Anc1refChr7 40308 45 - 47259 AACATAAATATGTGCTACATTAGTGGAAAATTTTTGGCTGATCAA -s Anc2.Anc2refChr15 78504 45 + 86568 AACATAAATATGAGCTATATTAGTAGAAAATTTATGGCTGGAAAA -s mr.mrrefChr5 120184 45 + 294540 AACATAGATATGTGATACATTAGTGGAAGATATTTGGCTCATCAG -s simCow_chr6.simCow.chr6 260760 26 + 602619 TACCTAAATATTGGCTATGTCA-------------------AATG -s simDog_chr6.simDog.chr6 251471 45 + 593897 AACATAAATGTGAGCTATATTAGTAGAAAATTTATGGCTGGAAAA -s simHuman_chr6.simHuman.chr6 343513 45 - 601863 AACATAAATATATACTACATTAGTGGAAACTCTTCAGCCAATCAA -s simRat_chr6.simRat.chr6 257580 45 + 647215 AACATAGATATGTGGTACGTTAGTGCAAGATATTTGGCTTATCAG - -a -s simMouse_chr6.simMouse.chr6 268670 19 + 636262 ACACATGATTTTACTTTAC -s Anc0.Anc0refChr5 81306 19 + 87904 ATATACTCTTCTACCCTAT -s Anc1.Anc1refChr7 40353 19 - 47259 ATATACTCTTCTACCCTAT -s Anc2.Anc2refChr15 78549 19 + 86568 ATATACTCTTCCACCCTAT -s mr.mrrefChr5 120229 19 + 294540 ACACACGATTTTACTTTAC -s simCow_chr6.simCow.chr6 260786 19 + 602619 ATATCCTCTTCCACCCTAT -s simDog_chr6.simDog.chr6 251526 19 + 593897 ATATATTCTTCCAGTTTAC -s simHuman_chr6.simHuman.chr6 343558 19 - 601863 ATATACTCTTCTACCCTAT -s simRat_chr6.simRat.chr6 257625 17 + 647215 ACACACA--TTTACTTTAC - -a -s simMouse_chr6.simMouse.chr6 268689 25 + 636262 CCTGAGTGATTATTTTGTGACAATG -s Anc0.Anc0refChr5 81325 23 + 87904 CCTGAGTCTTCATT--TTAACAATG -s Anc1.Anc1refChr7 40372 23 - 47259 CCTGAGTCTTCATT--TTAACAATG -s Anc2.Anc2refChr15 78568 23 + 86568 CCTGAGTCTTCATT--TTATCAATG -s mr.mrrefChr5 120248 23 + 294540 CCTGAGTGATTATT--GTAACAATG -s simCow_chr6.simCow.chr6 260805 23 + 602619 CCTGAGCCTTCATT--TTAGCTATG -s simDog_chr6.simDog.chr6 251581 23 + 593897 CCTGAGTCGTCATT--CTATCAATG -s simHuman_chr6.simHuman.chr6 343577 23 - 601863 CCTGAATCTTCATT--TTAACAGAG -s simRat_chr6.simRat.chr6 257642 23 + 647215 CCTTAGTGCTTATT--GTAACAATG - -a -s simMouse_chr6.simMouse.chr6 268714 14 + 636262 CGTGGTTATCAGCT -s Anc0.Anc0refChr5 81348 14 + 87904 CATGGTTATCAGCT -s Anc1.Anc1refChr7 40395 14 - 47259 CATGGTTATCAGCT -s Anc2.Anc2refChr15 78591 14 + 86568 CATGTTTATCAGCT -s mr.mrrefChr5 120271 14 + 294540 CGTGGTTATCAGCT -s simCow_chr6.simCow.chr6 260834 14 + 602619 TATGTTTATCAGCT -s simDog_chr6.simDog.chr6 251604 14 + 593897 CATGTTTTTCAGCT -s simHuman_chr6.simHuman.chr6 343600 14 - 601863 CATGGTTATCAGTT -s simRat_chr6.simRat.chr6 257665 14 + 647215 TGTGATTATCAGCT - -a -s simMouse_chr6.simMouse.chr6 268728 167 + 636262 TAGTCCAACACTGCTCTATGTCCAGAACTATATCATAATGCTCATGTGATATTTTTATCATCCTATAGGTGCACCTGGCCCCCGTACTATAAAGTAGCAACTGCTGTACCTAGTTTTTGTTCTCTCCTAACCTGATGCTCCACAAAGGTTTACCTCCTTCGATACTA -s Anc0.Anc0refChr5 81362 128 + 87904 TAATTCAACATTGTTCTTTATCCAGAACTAGAATGTGATGCTTATTCTATCTTTTTACTATCCTATGG---------------------------------------ATCTGGTTTTTGTTTTCTCCTAACCTAATGCCTCCCCAGGCTTTACCCTCTACGATACTA -s Anc1.Anc1refChr7 40409 128 - 47259 TAATTCAACATTGTTCTTTATCCAGAACTAGAATGTGATGCTTATTCTATCTTTTTACTATCCTATGG---------------------------------------ATCTGGTTTTTGTTTTCTCCTAACCTAATGCCTCCCCAGGCTTTACCCTCTACGATACTA -s Anc2.Anc2refChr15 78605 128 + 86568 TAATTCAACATTGTTCTTTATCCAGTACTAGAATATGATGGCTATTCTATCTTTTTTCTATCCTATGG---------------------------------------ATCTGGTTTTTGTTTTCTCCTAACCTAAAGCCTCTGCAGGCTTTACCCTCTACGATACTG -s mr.mrrefChr5 120285 164 + 294540 TAGTCCAACATTGCTCTATGTCCAGAACTATATTGTGATGCTCATGTGATATTTTTATTATCCTATAGGTGCACCTGGCCCCCGTACTATAAAGTAGC--CTG-TGTACCTAGTTTTTGTTCTCTCCTAACCTGATGCTTCCCAAAGGTTTACCTTCTTCGATACTA -s simCow_chr6.simCow.chr6 260848 128 + 602619 TAATACAACATTGCTCTTTATCCAGCATTAGAAAATAATGGGTATTGTATTGTTTTTCTATCCCGTGG---------------------------------------ATCTGGTTTTTGTTTTCCCCTAACCTAAAGCCCCTTCAGGCTTTACCTTCTACAATTTTG -s simDog_chr6.simDog.chr6 251618 123 + 593897 TTATTCAACATTGTTCTTTATCCAGTACTAAAATATGATCGCTATTCTGTCTTTTTTCTATCCTA--------------------------------------------CAGGTTTCTGATTTCTCCCAACTGGAAGCCTCTGCATACTTTACCCCCTACGATACTG -s simHuman_chr6.simHuman.chr6 343614 128 - 601863 TAATTGACTTTTATTCTTTATCTACAACTAGAATGTGATGCTTATTCTATCTTTTTAATTTCCTATGG---------------------------------------ATCTGATTTTAGTTTTCTCCTGACCTAATGCCTCCCCTGGCTTTACCCTCTAAGATCCTA -s simRat_chr6.simRat.chr6 257681 164 + 647215 TAGTCCAACATTCCTCTACGTCCAGGACTATATTGTGATGCTCATGTGATATTTTTATTATCCTATAGGTGCACCTGACCCCCATACTATAATGTAGC--CTG-TGTGTCTAGTTTTTATTCTCTCCTAACCTGATGCTTTCCAAAGGTTTACCTTCTTTGATACTA - -a -s simMouse_chr6.simMouse.chr6 268895 6 + 636262 TTTCTA -s Anc0.Anc0refChr5 81490 6 + 87904 TTTCTA -s Anc1.Anc1refChr7 40537 6 - 47259 TTTCTA -s Anc2.Anc2refChr15 78733 6 + 86568 TTTCTA -s mr.mrrefChr5 120449 6 + 294540 TTTCTA -s simCow_chr6.simCow.chr6 260978 6 + 602619 TTTCTA -s simDog_chr6.simDog.chr6 251741 6 + 593897 TCTCTA -s simHuman_chr6.simHuman.chr6 343742 6 - 601863 TTTCTG -s simRat_chr6.simRat.chr6 257845 6 + 647215 TTTTTA - -a -s simMouse_chr6.simMouse.chr6 268901 8 + 636262 GAAAAAAT -s Anc0.Anc0refChr5 81497 8 + 87904 GATAAAAT -s Anc1.Anc1refChr7 40544 8 - 47259 GATAAAAT -s Anc2.Anc2refChr15 78740 8 + 86568 GATAATAT -s mr.mrrefChr5 120456 8 + 294540 GAAAAAAT -s simCow_chr6.simCow.chr6 260985 8 + 602619 AACAATAT -s simDog_chr6.simDog.chr6 251748 8 + 593897 GATAATAT -s simHuman_chr6.simHuman.chr6 343749 8 - 601863 GATGAAAT -s simRat_chr6.simRat.chr6 257852 8 + 647215 GAAAAAAT - -a -s simMouse_chr6.simMouse.chr6 268909 6 + 636262 GGTGGA -s Anc0.Anc0refChr5 81506 6 + 87904 GGTTGA -s Anc1.Anc1refChr7 40553 6 - 47259 GGTTGA -s Anc2.Anc2refChr15 78749 6 + 86568 GGTTGA -s mr.mrrefChr5 120464 6 + 294540 GGTGGA -s simCow_chr6.simCow.chr6 260994 6 + 602619 GGTGGA -s simDog_chr6.simDog.chr6 251757 6 + 593897 GGTTGA -s simHuman_chr6.simHuman.chr6 343758 6 - 601863 GGTAGA -s simRat_chr6.simRat.chr6 257860 6 + 647215 AGTGGA - -a -s simMouse_chr6.simMouse.chr6 268915 29 + 636262 TATTGGGCACACTTCAACATCCTCAATGT -s Anc0.Anc0refChr5 81512 29 + 87904 ATTCAGGCATCCTTCTACATCCTCATTGT -s Anc1.Anc1refChr7 40559 29 - 47259 ATTCAGGCATCCTTCTACATCCTCATTGT -s Anc2.Anc2refChr15 78755 29 + 86568 ATTCAGGCATCATTGTACATCCTCATTGT -s mr.mrrefChr5 120470 29 + 294540 TATTAGGCACACTTCAACATCCTCAATGT -s simCow_chr6.simCow.chr6 261000 29 + 602619 TTTCAGGCGTCATCGTACATCCTCATTGT -s simDog_chr6.simDog.chr6 251773 20 + 593897 ATTCAGGCATCATTGTACAT--------- -s simHuman_chr6.simHuman.chr6 343764 29 - 601863 GCTCAGGCAACCTTCTACATTCCTGGTGT -s simRat_chr6.simRat.chr6 257866 24 + 647215 TATTAAGCACACTTCA-----TTCAATGT - -a -s simMouse_chr6.simMouse.chr6 268944 44 + 636262 AACAAAGGTAGTTATCTGGGCAATTGTCATCTAGTTTACCGTTG -s Anc0.Anc0refChr5 81541 42 + 87904 AAC-AAGGTAGTTATCTGGGCAATAAT-ATGTGGTTCATAGTTG -s Anc1.Anc1refChr7 40588 43 - 47259 AAC-AAGGTAGTTATCTGGGCAATAATAATGTGGTTCATAGTTG -s Anc2.Anc2refChr15 78784 42 + 86568 ACC-AAGGTAGTTATTTGGGCAACAAT-ACGTGCTCCATAGTGG -s mr.mrrefChr5 120499 44 + 294540 AACAAAGGTAGTTATCTGGGCAATTGTCATCTAGTTTACCGTTG -s simCow_chr6.simCow.chr6 261030 42 + 602619 ACC-AAGGTAGTTATTTGGGCAACAAT-ACGTGCTCCATAGTGG -s simHuman_chr6.simHuman.chr6 343793 43 - 601863 AAT-GAGGAAGTTATCCGGGCAATAATAATGTGGTTCATAGTTG -s simRat_chr6.simRat.chr6 257890 44 + 647215 AGCAAAGGTAGCTATCTGGGCAATTGTCATATATTTTACCATTG - -a -s simMouse_chr6.simMouse.chr6 268988 42 + 636262 GTAAGATCAATCTATTATTCCCATTTTCTGCGATTATTTCTA -s Anc0.Anc0refChr5 81598 30 + 87904 CTAAGATCAACCTATTGTTGCCAT----T--------TTCTA -s Anc1.Anc1refChr7 40646 30 - 47259 CTAAGATCAACCTATTGTTGCCAT----T--------TTCTA -s Anc2.Anc2refChr15 78841 30 + 86568 CTAAGAGCAACCTATTGTTGCCAC----T--------TTCTA -s mr.mrrefChr5 120543 34 + 294540 GTAAGATCAATCTATTGTTGCCATTTTCT--------TTCTA -s simCow_chr6.simCow.chr6 261086 30 + 602619 CTAAGAACGGCCTATTGTTGCCAC----T--------TTCTA -s simDog_chr6.simDog.chr6 251807 30 + 593897 CTTCGGGCAATCTCTTGTTGCTGC----T--------TCCCA -s simHuman_chr6.simHuman.chr6 343851 30 - 601863 ATAAGATCAACCTAGTGTTGCCAT----T--------TTCTA -s simRat_chr6.simRat.chr6 257934 34 + 647215 GTAAGATCGATCTATTGATGCCAGTTTCT--------TTCTG - -a -s simMouse_chr6.simMouse.chr6 269030 46 + 636262 CTACTAGAGAGTGCACTGAAGTGCACCCAAGTGACCAGCCTTTCCA -s Anc0.Anc0refChr5 81628 33 + 87904 ACACTAGAGAATGC-----------CCCCAGA-TGGAGCAGTTCC- -s Anc1.Anc1refChr7 40676 35 - 47259 ACACTAGAGAATGC-----------CCCCAGAGTGGAGCAGTTCCA -s Anc2.Anc2refChr15 78871 33 + 86568 ACACTAGAGAACGC-----------CCCCAGA-TGGAACAGTTTC- -s mr.mrrefChr5 120577 46 + 294540 CTACTAGAGAGTGCACTGAAGTGCACCCAAGTGACCAGCCTTTCCA -s simCow_chr6.simCow.chr6 261116 33 + 602619 CCACTAGAGATGGT-----------TTCCTAC-CATGTCACCTTT- -s simDog_chr6.simDog.chr6 251838 33 + 593897 ACAGTAAAGAACTC-----------CCCCAGA-TGGAACAGTTTC- -s simHuman_chr6.simHuman.chr6 343881 35 - 601863 AAACTAGAGGATGA-----------CCCCAGAGTGGAGCAGTCCCA -s simRat_chr6.simRat.chr6 257968 46 + 647215 CTATTAGAGAGTGAACTGGGGTGCACCCAAGTGACCAGCCTTAAAT - -a -s simMouse_chr6.simMouse.chr6 269076 13 + 636262 GTGTTGTTAATTT -s Anc0.Anc0refChr5 81868 13 + 87904 GTATTGTCAATTT -s Anc1.Anc1refChr7 40918 13 - 47259 GTATTGTCAATTT -s Anc2.Anc2refChr15 79111 13 + 86568 GTATTGTCAATTT -s mr.mrrefChr5 120623 13 + 294540 GTGTTGTTAATTT -s simCow_chr6.simCow.chr6 261346 13 + 602619 GTATCATTAATTT -s simDog_chr6.simDog.chr6 252077 13 + 593897 GTATTGTCAATTT -s simHuman_chr6.simHuman.chr6 344155 11 - 601863 GTATTGT--ATTT -s simRat_chr6.simRat.chr6 258014 13 + 647215 GCATAGGTAATTT - -a -s simMouse_chr6.simMouse.chr6 269089 21 + 636262 GGTACGAAGACATGAAATGAA -s Anc0.Anc0refChr5 81881 21 + 87904 GGTCCAAAATCATTAAAGGAA -s Anc1.Anc1refChr7 40931 21 - 47259 GGTCCAAAATCATTAAAGGAA -s Anc2.Anc2refChr15 79124 21 + 86568 GGTCCAAGATCATTAAAGGAA -s mr.mrrefChr5 120636 21 + 294540 GGTACGAAGACATGAAATGAA -s simCow_chr6.simCow.chr6 261360 21 + 602619 GGTCAAATATCATGAAAGGGA -s simDog_chr6.simDog.chr6 252090 21 + 593897 GGTCCAAGACTATTAAAACAA -s simHuman_chr6.simHuman.chr6 344166 21 - 601863 GGTCCAAAATCATAAAGGGAG -s simRat_chr6.simRat.chr6 258027 21 + 647215 GGTACAGAAACATGAAATGAA - -a -s simMouse_chr6.simMouse.chr6 269110 5 + 636262 CATTG -s Anc0.Anc0refChr5 81902 5 + 87904 TCTTG -s Anc1.Anc1refChr7 40952 5 - 47259 TCTTG -s Anc2.Anc2refChr15 79145 5 + 86568 TCTTG -s mr.mrrefChr5 120657 5 + 294540 CATTG -s simCow_chr6.simCow.chr6 261381 5 + 602619 TCTTA -s simDog_chr6.simDog.chr6 252111 5 + 593897 TCTTG -s simHuman_chr6.simHuman.chr6 344187 5 - 601863 TCTTG -s simRat_chr6.simRat.chr6 258049 5 + 647215 CATTG - -a -s simMouse_chr6.simMouse.chr6 269115 51 + 636262 TGATCAACTTGACAGCTCGGGGAGTCAGTTACCTGGACAACCAGGGCAGGC -s Anc0.Anc0refChr5 81907 26 + 87904 TG-------TG------------------TACCTGGACTACCAGGGCAGAC -s Anc1.Anc1refChr7 40957 26 - 47259 TG-------TG------------------TACCTGGACTACCAGGGCAGAC -s Anc2.Anc2refChr15 79150 26 + 86568 GG-------GG------------------TACCTGGACTACCAGGGCAGAC -s mr.mrrefChr5 120662 50 + 294540 TGA-CAACTTGACAGCTCGGGGAGTCAGTTACCTGGACAACCAGGGCAGGC -s simCow_chr6.simCow.chr6 261387 26 + 602619 GG-------GG------------------TGCCTGGACTACCCTGGCAGAC -s simDog_chr6.simDog.chr6 252116 21 + 593897 GG-------GG------------------TA-----ACTACCAGGGCAGAT -s simHuman_chr6.simHuman.chr6 344192 26 - 601863 TG-------TG------------------TACCGGGACTACCAGGGCAGAC -s simRat_chr6.simRat.chr6 258054 50 + 647215 TGG-CTACCCGACAGCTAGGGCAGTCAGTTACCTGGACAACCAGGACAGGC - -a -s simMouse_chr6.simMouse.chr6 269166 12 + 636262 AATCACTCTTAG -s Anc0.Anc0refChr5 81939 12 + 87904 AACAACCTTGAG -s Anc1.Anc1refChr7 40989 12 - 47259 AACAACCTTGAG -s Anc2.Anc2refChr15 79182 12 + 86568 AACAACCTTGAG -s mr.mrrefChr5 120712 12 + 294540 AATCACTCTTAG -s simCow_chr6.simCow.chr6 261564 12 + 602619 AACAACCTTGAG -s simDog_chr6.simDog.chr6 252143 12 + 593897 AACAACCCCCAG -s simHuman_chr6.simHuman.chr6 344224 12 - 601863 AACTACCTTGAG -s simRat_chr6.simRat.chr6 258104 12 + 647215 AATGACACTTAG - -a -s simMouse_chr6.simMouse.chr6 269178 83 + 636262 ATCAAGGATTCAACACAATAGATCTTCAACAAGATAACCTATATCCTCGAAAAAGATATGTTACTTGTTGTTAGGTAGTGCAA -s Anc0.Anc0refChr5 81951 62 + 87904 GTCAATGATTTAATAC---------------------CATATATCCTCAACACAGAGTTGTAACTGGTTGTTAGGCAGTGTGA -s Anc1.Anc1refChr7 41001 62 - 47259 GTCAATGATTTAATAC---------------------CATATATCCTCAACACAGAGTTGTAACTGGTTGTTAGGCAGTGTGA -s Anc2.Anc2refChr15 79194 62 + 86568 GTCAATCATTTAATAC---------------------TATACATCTTCAACGCAGGGTTAAAACTGGATGTTAGGCAGTGTGA -s mr.mrrefChr5 120724 83 + 294540 ATCAAGGATTCAACACAATAGATCTTCAACAAGATAACCTATATCCTCGAAAAAGATATGTTACTTGTTGTTAGGTAGTGCAA -s simCow_chr6.simCow.chr6 261576 61 + 602619 GTCAAGCATTTAATAC---------------------TACACA-CATCAATGCAGGTTTAAAACTGGAAGTTAGGCAGTGCGA -s simDog_chr6.simDog.chr6 252155 58 + 593897 GTAAGTCATTTAATAC---------------------TATACATCTTCAACGCAGGGT----ACTGGATGTCAGGCACTGTGA -s simHuman_chr6.simHuman.chr6 344236 62 - 601863 GTCAAAGATTTAATAC---------------------CAGATATCCCCAACACAAAGTTGTCATTGGTTGTTAGGCAGTGTGA -s simRat_chr6.simRat.chr6 258152 83 + 647215 GTCAAGGATACAACACTATAGATCTTCAACAAGATAACCTATATCCTCAAAAAAGAAATGTTACTTGTAGTTAGGCAGTGTGA - -a -s simMouse_chr6.simMouse.chr6 269261 51 + 636262 GATCAGGTTGCAGGAACCATTAGCCTTATAGCTAGTTTGTTTTGTTCCATA -s Anc0.Anc0refChr5 82020 23 + 87904 GATCAGAAT---------------------------ACATCTTGCTCCAT- -s Anc1.Anc1refChr7 41070 23 - 47259 GATCAGAAT---------------------------ACATCTTGCTCCAT- -s Anc2.Anc2refChr15 79263 23 + 86568 GAGCAGAAT---------------------------ACATCTAGCTTCAT- -s mr.mrrefChr5 120807 23 + 294540 GATCAGGTT---------------------------TTGTTTTGTTCCAT- -s simCow_chr6.simCow.chr6 261644 23 + 602619 GAGCGGTAT---------------------------ACATTTAGCTTCAT- -s simDog_chr6.simDog.chr6 252220 21 + 593897 G--CAGAAT---------------------------ACTTCTAGCCTCAT- -s simHuman_chr6.simHuman.chr6 344305 23 - 601863 AATCAGAAT---------------------------ACATCTTGCTCCAT- -s simRat_chr6.simRat.chr6 258235 23 + 647215 TATCAGGTT---------------------------TTGTTTTGTTCCAT- - -a -s simMouse_chr6.simMouse.chr6 269312 41 + 636262 GTATAGCTTACTTACGTCGGGAGGCCTTCCCATTTACTATT -s Anc0.Anc0refChr5 82065 26 + 87904 GTACAGCACACCTACATCAGAAGGCT--------------- -s Anc1.Anc1refChr7 41115 26 - 47259 GTACAGCACACCTACATCAGAAGGCT--------------- -s Anc2.Anc2refChr15 79308 26 + 86568 GTACAGCACACCCACATCAGAAGGCT--------------- -s mr.mrrefChr5 120830 41 + 294540 GTATAGCTTACTTACGTCGGGAGGCCTTCCCATTTACTATT -s simCow_chr6.simCow.chr6 261689 26 + 602619 GTACAGTACACTCGTATTGGAAGGTA--------------- -s simDog_chr6.simDog.chr6 252263 26 + 593897 GTACAGCACACCCACATCAGAGGGCT--------------- -s simHuman_chr6.simHuman.chr6 344350 26 - 601863 ATACAGCACACCTACATCACAAGGCT--------------- -s simRat_chr6.simRat.chr6 258258 41 + 647215 GTACAGCTTACTTGCATCAGAAGGCTTTCCCATTTACTATT - -a -s simMouse_chr6.simMouse.chr6 269353 5 + 636262 TATGG -s mr.mrrefChr5 120871 5 + 294540 TGTGG -s simRat_chr6.simRat.chr6 258336 5 + 647215 TGTGG - -a -s simMouse_chr6.simMouse.chr6 269358 3 + 636262 GAT -s Anc0.Anc0refChr3 1904 3 + 222631 GAT -s Anc1.Anc1refChr5 4231 3 + 6477 GAT -s Anc2.Anc2refChr13 4066 3 + 96486 GAT -s mr.mrrefChr5 120876 3 + 294540 GAT -s simCow_chr6.simCow.chr6 359502 3 + 602619 GAT -s simDog_chr6.simDog.chr6 350139 3 + 593897 GAT -s simHuman_chr6.simHuman.chr6 248263 3 + 601863 GAT -s simRat_chr6.simRat.chr6 258341 3 + 647215 GTT - -a -s simMouse_chr6.simMouse.chr6 269361 28 + 636262 CCAAAAAGCAGGTTGAAGAGTTAGGTGA -s Anc0.Anc0refChr3 1907 28 + 222631 CCTAAAAGCAGGTTGAAGACCTAGGTAA -s Anc1.Anc1refChr5 4234 28 + 6477 CCTAAAAGCAGGTTGAAGACCTAGGTAA -s Anc2.Anc2refChr13 4069 28 + 96486 CCTCAAAGCAGGTTGAAGACCTAGTTAA -s mr.mrrefChr5 120879 28 + 294540 CCAAAAAGCAGGTTGAAGAGCTAGGTGA -s simCow_chr6.simCow.chr6 359525 28 + 602619 CCTCAAAGCAGGTTGAAGACCTAGTCAA -s simDog_chr6.simDog.chr6 350142 28 + 593897 CCTCAAAGCAGGTTGAAGACTTAGTTAA -s simHuman_chr6.simHuman.chr6 248266 19 + 601863 CCTAAATG---------GTACTAGGTAG -s simRat_chr6.simRat.chr6 258344 28 + 647215 CCCAAAAGCAGGTTGAAAAGCTAGGAGA - -a -s simMouse_chr6.simMouse.chr6 269389 43 + 636262 GGCAAGAAGCCCAGGCGGATGCTAGAAGATACAGTTCAGGATT -s Anc0.Anc0refChr3 1935 42 + 222631 GGAGCTAAATCCAGGCTGCCTCTAGATAAAACAGTTCT-CATG -s Anc1.Anc1refChr5 4262 42 + 6477 GGAGCTAAATCCAGGCTGCCTCTAGATAAAACAGTTCT-CATG -s Anc2.Anc2refChr13 4097 42 + 96486 GGAGCTAAATCCAGGCTGCCTCTAGATAAAACAGTACT-CATG -s mr.mrrefChr5 120907 43 + 294540 GGCAAGAAGCCCAGGCTGCTTCTAGAAAAAACAGTTCTGGATT -s simCow_chr6.simCow.chr6 359577 42 + 602619 GGAGCCAGATCCAGGCTGCTTCTAGATAAAACAGTACT-CATG -s simDog_chr6.simDog.chr6 350170 41 + 593897 AAGGCTAAATCCAGGCATTCTCTAGATGAAACA-TACT-CATT -s simHuman_chr6.simHuman.chr6 248285 42 + 601863 GGAGCTAAATCCAGGCTGCCTCTTGATAGAACAGTTCT-CATG -s simRat_chr6.simRat.chr6 258372 43 + 647215 GGCAGCAAGCCCAGGCTGCTTCAGGAAATAACAGTCCTGGCAT - -a -s simMouse_chr6.simMouse.chr6 269432 2 + 636262 GT -s Anc0.Anc0refChr3 1977 2 + 222631 GT -s Anc1.Anc1refChr5 4304 2 + 6477 GT -s Anc2.Anc2refChr13 4139 2 + 96486 GT -s mr.mrrefChr5 120950 2 + 294540 GT -s simCow_chr6.simCow.chr6 359623 2 + 602619 GT -s simDog_chr6.simDog.chr6 350211 2 + 593897 GT -s simHuman_chr6.simHuman.chr6 248327 2 + 601863 GT -s simRat_chr6.simRat.chr6 258415 2 + 647215 GT - -a -s simMouse_chr6.simMouse.chr6 269434 26 + 636262 GTAGCAAGGCTCCGGCTTTAATCTGG -s Anc0.Anc0refChr3 1979 26 + 222631 TAAGCCAGGCTTTAATTTTAATTTGG -s Anc1.Anc1refChr5 4306 26 + 6477 TAAGCCAGGCTTTAATTTTAATTTGG -s Anc2.Anc2refChr13 4141 26 + 96486 TAATCCAGGCTTTAATTTTAATTTGG -s mr.mrrefChr5 120952 26 + 294540 GTAGCAAGGCTTCAACTTTAATCTGG -s simCow_chr6.simCow.chr6 359625 26 + 602619 TAAACAAGGCCCTAACTTTCATTTGG -s simDog_chr6.simDog.chr6 350214 26 + 593897 TGTTTCAGGCTTTATTTTTAACTTGG -s simHuman_chr6.simHuman.chr6 248329 26 + 601863 TAAGCGAGCCTTTAATTTTAATTTGG -s simRat_chr6.simRat.chr6 258417 26 + 647215 GCAGTAAGGCTTCAACTTTTATCTGG - -a -s simMouse_chr6.simMouse.chr6 269460 26 + 636262 AGAACAGTATGCTATTCCATACTAGG -s Anc0.Anc0refChr3 2010 26 + 222631 AGATATGTACTCTATTCCATATTAGG -s Anc1.Anc1refChr5 4337 26 + 6477 AGATATGTACTCTATTCCATATTAGG -s Anc2.Anc2refChr13 4172 26 + 96486 AGATATGTACTCTATTCTATATTAGG -s mr.mrrefChr5 120978 26 + 294540 AGAACAGTATGCTATTCCATACTAGG -s simCow_chr6.simCow.chr6 359656 26 + 602619 AGATCTGTATTCTATTCTACATTAGG -s simDog_chr6.simDog.chr6 350245 26 + 593897 AGATATGTACTCAATTCTATGTTAGG -s simHuman_chr6.simHuman.chr6 248360 25 + 601863 AGAGATGTACCCTGTTCCA-ATTAGG -s simRat_chr6.simRat.chr6 258443 26 + 647215 AGAACAGTATGCTATTCCATACTGAG - -a -s simMouse_chr6.simMouse.chr6 269486 19 + 636262 TTAGGAATTTACTGTGTAC -s Anc0.Anc0refChr3 2036 19 + 222631 TTGGGGATCAATTGTGTAC -s Anc1.Anc1refChr5 4363 19 + 6477 TTGGGGATCAATTGTGTAC -s Anc2.Anc2refChr13 4198 19 + 96486 TTGGGGATCAATGTTGTAT -s mr.mrrefChr5 121004 19 + 294540 TTAGGAATTTACTGTGTAC -s mr.mrrefChr5 121169 19 + 294540 TTGGAAATTTGTTGTATAC -s simCow_chr6.simCow.chr6 359682 19 + 602619 TTGGGGATCAATGTTGTAC -s simDog_chr6.simDog.chr6 350271 19 + 593897 TTGGGGATCAATGTTGTAT -s simHuman_chr6.simHuman.chr6 248385 19 + 601863 TTTGGGATCAATTGTCTGC -s simMouse_chr6.simMouse.chr6 269671 19 + 636262 TTGAAAATTTGTTGTATAC -s simRat_chr6.simRat.chr6 258633 19 + 647215 TTGGAAATTTGTTGTGTAC -s simRat_chr6.simRat.chr6 258469 19 + 647215 TTAGAAGTTTGTTGTGTAC - -a -s simMouse_chr6.simMouse.chr6 269505 15 + 636262 TCAGCAACACATGAA -s mr.mrrefChr5 121023 15 + 294540 TCAGCAACACATGAA -s simRat_chr6.simRat.chr6 258488 15 + 647215 TCTGCAACACAAGAA - -a -s simMouse_chr6.simMouse.chr6 269520 16 + 636262 GTAGCAACACAAGAAG -s Anc0.Anc0refChr3 2055 16 + 222631 GTTGCAACACAAGATG -s Anc1.Anc1refChr5 4382 16 + 6477 GTTGCAACACAAGATG -s Anc2.Anc2refChr13 4217 16 + 96486 TTTGCAACACAAGATA -s mr.mrrefChr5 121038 16 + 294540 GTAGCAACACAAGAAG -s mr.mrrefChr5 121188 16 + 294540 GTTGCAACAGAAAGGC -s simCow_chr6.simCow.chr6 359701 3 + 602619 TTT------------- -s simDog_chr6.simDog.chr6 350290 16 + 593897 TTTGCAACACAAGATA -s simHuman_chr6.simHuman.chr6 248404 15 + 601863 -TTGCAACACAAGATG -s simMouse_chr6.simMouse.chr6 269690 16 + 636262 GTTGCAACAGAGAGGC -s simRat_chr6.simRat.chr6 258652 16 + 647215 ATTGCAGCAGAAAGGC -s simRat_chr6.simRat.chr6 258503 16 + 647215 GTAGCAACACAAGAAG - -a -s simMouse_chr6.simMouse.chr6 269536 29 + 636262 TATTTAATTGTCTGTCTTGGTACTATGTA -s Anc0.Anc0refChr3 2071 29 + 222631 TATTTAATTCTCCCTCTTAGTACTATGTA -s Anc1.Anc1refChr5 4398 29 + 6477 TATTTAATTCTCCCTCTTAGTACTATGTA -s Anc2.Anc2refChr13 4233 29 + 96486 TATGTAATCCGCCCTCTCAGTACTATGTA -s mr.mrrefChr5 121054 29 + 294540 TATTTAATTGTCTGTCTTGGTACTATGTA -s mr.mrrefChr5 121204 29 + 294540 TGTTTAACTCTCTGTCATAGTACTATGAA -s simDog_chr6.simDog.chr6 350306 29 + 593897 TATGTAATCCGCCCTCTCAGTACTATGTA -s simHuman_chr6.simHuman.chr6 248421 29 + 601863 TGTATAATTCTCCCTATGAGTACTATGCA -s simMouse_chr6.simMouse.chr6 269706 29 + 636262 TGTTTAACTCTCTGTCATAGTACTATGAA -s simRat_chr6.simRat.chr6 258668 29 + 647215 TGTTTAACTCTCTGTCATAGTACTATGAA -s simRat_chr6.simRat.chr6 258519 29 + 647215 TATATACTTGTCTGTCTTGGTACTATGTA - -a -s simMouse_chr6.simMouse.chr6 269565 22 + 636262 ACAATTGAGCATCCTATCCTAT -s Anc0.Anc0refChr3 2110 7 + 222631 A---------------TCCTAT -s Anc1.Anc1refChr5 4437 7 + 6477 A---------------TCCTAT -s Anc2.Anc2refChr13 4272 7 + 96486 A---------------TCCCAA -s mr.mrrefChr5 121083 7 + 294540 A---------------TCCTAT -s mr.mrrefChr5 121243 7 + 294540 A---------------TTCTAC -s simCow_chr6.simCow.chr6 359706 3 + 602619 A---------------TA---- -s simDog_chr6.simDog.chr6 350355 7 + 593897 A---------------TCCCAA -s simHuman_chr6.simHuman.chr6 248460 7 + 601863 A---------------TCCTAT -s simMouse_chr6.simMouse.chr6 269745 7 + 636262 A---------------TTCTAC -s simRat_chr6.simRat.chr6 258707 7 + 647215 A---------------TTCTAC -s simRat_chr6.simRat.chr6 258548 6 + 647215 ----------------TCCTAT - -a -s simMouse_chr6.simMouse.chr6 269587 16 + 636262 CTCATTTAATATCAAG -s Anc0.Anc0refChr3 2122 16 + 222631 ATTATTGAAAATCAGG -s Anc1.Anc1refChr5 4449 16 + 6477 ATTATTGAAAATCAGG -s Anc2.Anc2refChr13 4284 16 + 96486 ATTCTTGAAAATCAGG -s mr.mrrefChr5 121090 16 + 294540 CTCATTTAATATCAAG -s mr.mrrefChr5 121255 16 + 294540 CTTTTTGAAAATTGGG -s simCow_chr6.simCow.chr6 359709 13 + 602619 ---CTTGAAAATCAGG -s simDog_chr6.simDog.chr6 350367 16 + 593897 ATTCTGGCAAATCAGG -s simHuman_chr6.simHuman.chr6 248472 16 + 601863 AGTATTGAAGATCAGG -s simMouse_chr6.simMouse.chr6 269757 16 + 636262 CTTTTTTAAAGTTGGG -s simRat_chr6.simRat.chr6 258719 16 + 647215 CTTTTTGAAAATTGGG -s simRat_chr6.simRat.chr6 258554 16 + 647215 CTCATTTAAAATCAAG - -a -s simMouse_chr6.simMouse.chr6 269603 1 + 636262 T -s Anc0.Anc0refChr3 2138 1 + 222631 T -s Anc1.Anc1refChr5 4465 1 + 6477 T -s Anc2.Anc2refChr13 4300 1 + 96486 T -s mr.mrrefChr5 121106 1 + 294540 T -s simCow_chr6.simCow.chr6 359722 1 + 602619 T -s simDog_chr6.simDog.chr6 350383 1 + 593897 T -s simHuman_chr6.simHuman.chr6 248488 1 + 601863 T -s simRat_chr6.simRat.chr6 258570 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 269604 11 + 636262 AGCATTTATTG -s Anc0.Anc0refChr3 2139 11 + 222631 AGCATTTATCA -s Anc1.Anc1refChr5 4466 11 + 6477 AGCATTTATCA -s Anc2.Anc2refChr13 4301 11 + 96486 AGCATTTATCA -s mr.mrrefChr5 121107 11 + 294540 AGCATTTATTG -s mr.mrrefChr5 121271 11 + 294540 AGCATCTACTT -s simCow_chr6.simCow.chr6 359723 11 + 602619 AGCATTTATCA -s simDog_chr6.simDog.chr6 350384 11 + 593897 TGCATTTATCA -s simHuman_chr6.simHuman.chr6 248489 11 + 601863 AGCATTTATCA -s simMouse_chr6.simMouse.chr6 269773 7 + 636262 AG----TACTT -s simRat_chr6.simRat.chr6 258735 11 + 647215 AGCATCTACTT -s simRat_chr6.simRat.chr6 258571 11 + 647215 AGTATTTATTG - -a -s simMouse_chr6.simMouse.chr6 269615 4 + 636262 TCAA -s Anc0.Anc0refChr3 2150 4 + 222631 TCAA -s Anc1.Anc1refChr5 4477 4 + 6477 TCAA -s Anc2.Anc2refChr13 4312 4 + 96486 TCAA -s mr.mrrefChr5 121118 4 + 294540 TCAA -s mr.mrrefChr5 121282 4 + 294540 TCAA -s simCow_chr6.simCow.chr6 359734 4 + 602619 TCAA -s simDog_chr6.simDog.chr6 350395 4 + 593897 TCAA -s simHuman_chr6.simHuman.chr6 248500 4 + 601863 CCAA -s simMouse_chr6.simMouse.chr6 269780 4 + 636262 TCTA -s simRat_chr6.simRat.chr6 258747 4 + 647215 TCAA -s simRat_chr6.simRat.chr6 258582 4 + 647215 TCAA - -a -s simMouse_chr6.simMouse.chr6 269619 38 + 636262 AGACATCTAGGCAAGGCAGAAACACACTCTTTAACTAG -s Anc0.Anc0refChr3 2154 33 + 222631 ACACATT-----AAGACATAGACAAACTCTTCAACTAA -s Anc1.Anc1refChr5 4481 33 + 6477 ACACATT-----AAGACATAGACAAACTCTTCAACTAA -s Anc2.Anc2refChr13 4316 33 + 96486 ACACATT-----AAAACATAGACAAACTCTTCAACTAA -s mr.mrrefChr5 121122 33 + 294540 AGACATC-----AAGGCAGAAACACACTCTTTAACTAG -s mr.mrrefChr5 121286 33 + 294540 AGACATT-----AAGACAGAAACAAACTCCTCAACCAA -s simCow_chr6.simCow.chr6 359738 33 + 602619 ACACATT-----AGAACATAGACAAAATCTTTAACTAA -s simDog_chr6.simDog.chr6 350399 30 + 593897 GCATATT-----AA---CTAGACAAACTTTTCAACTAG -s simHuman_chr6.simHuman.chr6 248506 33 + 601863 ACACATT-----AAGACATAGACAAACTCTTCAACCAA -s simMouse_chr6.simMouse.chr6 269784 33 + 636262 AGACACT-----CAGACAGAAACAAACTCCTCAACCAA -s simRat_chr6.simRat.chr6 258751 33 + 647215 AGACATT-----AAGACAGAAACAAACTCCTCAAGTAG -s simRat_chr6.simRat.chr6 258586 33 + 647215 AGACATC-----AAGGTAGAAATAAACTCTTTAACTGG - -a -s simMouse_chr6.simMouse.chr6 269657 6 + 636262 AGATGT -s Anc0.Anc0refChr3 2188 4 + 222631 AGAA-- -s Anc1.Anc1refChr5 4515 6 + 6477 AGAACT -s Anc2.Anc2refChr13 4350 4 + 96486 TGAA-- -s mr.mrrefChr5 121155 6 + 294540 AGATGT -s mr.mrrefChr5 121323 6 + 294540 TGAACT -s simCow_chr6.simCow.chr6 359772 4 + 602619 TGAA-- -s simDog_chr6.simDog.chr6 350430 4 + 593897 TGAA-- -s simHuman_chr6.simHuman.chr6 248540 1 + 601863 -----T -s simMouse_chr6.simMouse.chr6 269821 6 + 636262 TGAACT -s simRat_chr6.simRat.chr6 258788 6 + 647215 TCAACT -s simRat_chr6.simRat.chr6 258619 6 + 647215 AGATGT - -a -s simMouse_chr6.simMouse.chr6 269663 1 + 636262 A -s Anc1.Anc1refChr5 4521 1 + 6477 G -s mr.mrrefChr5 121161 1 + 294540 A -s mr.mrrefChr5 121329 1 + 294540 A -s simHuman_chr6.simHuman.chr6 248541 1 + 601863 G -s simMouse_chr6.simMouse.chr6 269827 1 + 636262 A -s simRat_chr6.simRat.chr6 258625 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 269664 7 + 636262 CTTAAAG -s Anc0.Anc0refChr3 2192 5 + 222631 --ACAAA -s Anc1.Anc1refChr5 4522 7 + 6477 ATACAAA -s Anc2.Anc2refChr13 4354 5 + 96486 --AGAAA -s mr.mrrefChr5 121162 7 + 294540 CTTAAAG -s mr.mrrefChr5 121330 7 + 294540 ATTCAAG -s simCow_chr6.simCow.chr6 359776 5 + 602619 --AGAAG -s simDog_chr6.simDog.chr6 350434 5 + 593897 --AGAAA -s simHuman_chr6.simHuman.chr6 248542 7 + 601863 ATACAAA -s simMouse_chr6.simMouse.chr6 269828 7 + 636262 ATTCAAG -s simRat_chr6.simRat.chr6 258794 7 + 647215 ATTCAAG -s simRat_chr6.simRat.chr6 258626 7 + 647215 CCTAATA - -a -s simMouse_chr6.simMouse.chr6 269735 2 + 636262 GC -s Anc0.Anc0refChr3 2100 2 + 222631 GC -s Anc1.Anc1refChr5 4427 2 + 6477 GC -s Anc2.Anc2refChr13 4262 2 + 96486 GC -s mr.mrrefChr5 121233 2 + 294540 GC -s simDog_chr6.simDog.chr6 350335 2 + 593897 GC -s simHuman_chr6.simHuman.chr6 248450 2 + 601863 AC -s simRat_chr6.simRat.chr6 258697 2 + 647215 GC - -a -s simMouse_chr6.simMouse.chr6 269737 8 + 636262 AACTTAGT -s Anc0.Anc0refChr3 2102 8 + 222631 AACTTGGC -s Anc1.Anc1refChr5 4429 8 + 6477 AACTTGGC -s Anc2.Anc2refChr13 4264 8 + 96486 AACTTGGC -s mr.mrrefChr5 121235 8 + 294540 AACTTAGT -s simCow_chr6.simCow.chr6 359704 2 + 602619 ------GC -s simDog_chr6.simDog.chr6 350347 8 + 593897 AACTTGGC -s simHuman_chr6.simHuman.chr6 248452 8 + 601863 AACTTGGC -s simRat_chr6.simRat.chr6 258699 8 + 647215 AACTTAGT - -a -s simMouse_chr6.simMouse.chr6 269752 5 + 636262 ATCAA -s Anc0.Anc0refChr3 2117 5 + 222631 GCTAT -s Anc1.Anc1refChr5 4444 5 + 6477 GCTAT -s Anc2.Anc2refChr13 4279 5 + 96486 GCTAT -s mr.mrrefChr5 121250 5 + 294540 ATTAA -s simDog_chr6.simDog.chr6 350362 5 + 593897 GCTAT -s simHuman_chr6.simHuman.chr6 248467 5 + 601863 GCTAT -s simRat_chr6.simRat.chr6 258714 5 + 647215 ATTAA - -a -s simMouse_chr6.simMouse.chr6 269817 4 + 636262 TTCC -s Anc0.Anc0refChr3 2187 1 + 222631 T--- -s Anc1.Anc1refChr5 4514 1 + 6477 T--- -s Anc2.Anc2refChr13 4349 1 + 96486 T--- -s mr.mrrefChr5 121319 4 + 294540 TTCC -s simCow_chr6.simCow.chr6 359771 1 + 602619 T--- -s simDog_chr6.simDog.chr6 350429 1 + 593897 T--- -s simHuman_chr6.simHuman.chr6 248539 1 + 601863 T--- -s simRat_chr6.simRat.chr6 258784 4 + 647215 TTCC - -a -s simMouse_chr6.simMouse.chr6 269835 15 + 636262 GAAAGCCTCCTTTTA -s Anc0.Anc0refChr3 2197 9 + 222631 G------TCTTCTTT -s Anc1.Anc1refChr5 4529 9 + 6477 G------TCTTCTTT -s Anc2.Anc2refChr13 4359 9 + 96486 G------TCTTCTTT -s mr.mrrefChr5 121337 15 + 294540 GAAAGCCTCTTTTTA -s simCow_chr6.simCow.chr6 359781 9 + 602619 G------TTTTCTGT -s simDog_chr6.simDog.chr6 350439 9 + 593897 G------TCTTGTTT -s simHuman_chr6.simHuman.chr6 248549 9 + 601863 G------TCTTCTTT -s simRat_chr6.simRat.chr6 258801 15 + 647215 GAAAGCCTCTCTTTA - -a -s simMouse_chr6.simMouse.chr6 269850 12 + 636262 AGACTAATATTC -s Anc0.Anc0refChr3 2206 12 + 222631 ATACTAACATTC -s Anc1.Anc1refChr5 4538 12 + 6477 ATACTAACATTC -s Anc2.Anc2refChr13 4368 12 + 96486 ATATTAACACTC -s mr.mrrefChr5 121352 12 + 294540 AGACTAATATTC -s simCow_chr6.simCow.chr6 359792 12 + 602619 ATATTAACATCC -s simDog_chr6.simDog.chr6 350448 8 + 593897 ----TAATACTC -s simHuman_chr6.simHuman.chr6 248558 11 + 601863 ATGCTAACATG- -s simRat_chr6.simRat.chr6 258816 12 + 647215 AGACTAAAATTC - -a -s simMouse_chr6.simMouse.chr6 269862 37 + 636262 AGTTTAAAGAGCAAGCAATTGACCCAGCTCTTCCACA -s Anc0.Anc0refChr3 2221 32 + 222631 AATCAGCAAGCTAACAA-----CCCGGCTTCTACAGA -s Anc1.Anc1refChr5 4553 37 + 6477 AATCAGCAAGCTAACAAATTTACCCGGCTTCTACAGA -s Anc2.Anc2refChr13 4383 32 + 96486 AAGCAGCAAGCTAACAA-----CCCGACTTCTACAGA -s mr.mrrefChr5 121364 37 + 294540 AGTATAAAGGCCAAGCAATTGACCCAGCTCTTCCAGA -s simCow_chr6.simCow.chr6 359807 29 + 602619 CAAGGGCAAGCTCACAA-----GCCAAC---TACAGG -s simDog_chr6.simDog.chr6 350459 32 + 593897 AAGCAGCAGGCTAACAG-----CCCGACTTCTACACA -s simHuman_chr6.simHuman.chr6 248572 34 + 601863 AATCAGCAAGCTAATAAATTTTTTAGG---GTTCAGA -s simRat_chr6.simRat.chr6 258828 37 + 647215 AGTATAAAGGCCAAGCAGTTGACCCAGCTCTCCTAGG - -a -s simMouse_chr6.simMouse.chr6 269899 2 + 636262 AA -s Anc0.Anc0refChr3 2258 2 + 222631 AA -s Anc1.Anc1refChr5 4595 2 + 6477 AA -s Anc2.Anc2refChr13 4420 2 + 96486 AA -s mr.mrrefChr5 121406 2 + 294540 AA -s simCow_chr6.simCow.chr6 359841 2 + 602619 AT -s simDog_chr6.simDog.chr6 350496 2 + 593897 AA -s simHuman_chr6.simHuman.chr6 248611 2 + 601863 AA -s simRat_chr6.simRat.chr6 258870 2 + 647215 AA - -a -s simMouse_chr6.simMouse.chr6 269901 15 + 636262 TTATCAGCTTGACAC -s Anc0.Anc0refChr3 2261 15 + 222631 TCCTCAGGCTGATGT -s Anc1.Anc1refChr5 4598 15 + 6477 TCCTCAGGCTGATGT -s Anc2.Anc2refChr13 4423 15 + 96486 TCCTCAGGCTGATGT -s mr.mrrefChr5 121408 15 + 294540 TCATCAGCTTGACAT -s simCow_chr6.simCow.chr6 359844 15 + 602619 TCCTCGGTCTGACAT -s simDog_chr6.simDog.chr6 350499 15 + 593897 TCTTCAGGCTGATGT -s simHuman_chr6.simHuman.chr6 248614 14 + 601863 TCCTCAGACTG-TGT -s simRat_chr6.simRat.chr6 258872 15 + 647215 TCATCAGTTTGACAT - -a -s simMouse_chr6.simMouse.chr6 269916 14 + 636262 ATGAGCTATTTTTC -s Anc0.Anc0refChr3 2276 14 + 222631 ATGAGTAATTTGTT -s Anc1.Anc1refChr5 4613 14 + 6477 ATGAGTAATTTGTT -s Anc2.Anc2refChr13 4441 14 + 96486 ATGAGTAATTTGTT -s mr.mrrefChr5 121423 14 + 294540 ATGAGCTATTTGTC -s simCow_chr6.simCow.chr6 359862 14 + 602619 ATGAGCTATTTGAT -s simDog_chr6.simDog.chr6 350517 14 + 593897 ATGAGTATCTTGTA -s simHuman_chr6.simHuman.chr6 248628 14 + 601863 GGGAGGCATTTGTT -s simRat_chr6.simRat.chr6 258887 14 + 647215 ATGAGCTATTTGTC - -a -s simMouse_chr6.simMouse.chr6 269930 47 + 636262 AATCCTGCCATGCGCTTCCCCTTTTGCTTTTTTAAATGATAGTCCGA -s Anc0.Anc0refChr3 2291 45 + 222631 AATCCTGCTATGCACAT-CCCTTACACTTTGTC-AGTCATGGTCTAA -s Anc1.Anc1refChr5 4628 45 + 6477 AATCCTGCTATGCACAT-CCCTTACACTTTGTC-AGTCATGGTCTAA -s Anc2.Anc2refChr13 4456 45 + 96486 AATCCTGATATGCACAG-CCATCACACTTTGTC-AGTCATGGTCTAA -s mr.mrrefChr5 121437 46 + 294540 AATCCTGCCATGCACTTCCCCTTTTGCTTTTTT-AATGATAGTCTGA -s simCow_chr6.simCow.chr6 359877 39 + 602619 AATCCTGGTATGCAC-------CACACTTTGTC-AGTCATGGTTTAA -s simDog_chr6.simDog.chr6 350532 45 + 593897 AATCCTGACATGAACAG-CCATCACACTTTCTC-AGTCATGGTCTAA -s simHuman_chr6.simHuman.chr6 248643 45 + 601863 AATTCTGCTGTGCACAT-CCCTTAGACTCTGTC-AGTCAGGGTCTAA -s simRat_chr6.simRat.chr6 258901 46 + 647215 AATCATGCCATGCACTTCCCCTTTCGCTTTTTT-AATGACAGTCTGA - -a -s simMouse_chr6.simMouse.chr6 269977 8 + 636262 TGTGGCAA -s Anc0.Anc0refChr3 2372 8 + 222631 TTAAGCAA -s Anc1.Anc1refChr5 4709 8 + 6477 TTAAGCAA -s Anc2.Anc2refChr13 4537 8 + 96486 TTAAGCAC -s mr.mrrefChr5 121513 8 + 294540 TGAGGCAA -s simCow_chr6.simCow.chr6 359952 8 + 602619 TTAGGCAC -s simDog_chr6.simDog.chr6 350613 8 + 593897 TTAAGCAC -s simHuman_chr6.simHuman.chr6 248724 8 + 601863 TTAAGGAA -s simRat_chr6.simRat.chr6 258977 8 + 647215 TGAGGCAA - -a -s simMouse_chr6.simMouse.chr6 269985 15 + 636262 TGAAATACAGTTTAA -s Anc0.Anc0refChr3 2380 15 + 222631 TGAAACACAATTCGA -s Anc1.Anc1refChr5 4717 15 + 6477 TGAAACACAATTCGA -s Anc2.Anc2refChr13 4545 15 + 96486 TGAAACACAACTTGA -s mr.mrrefChr5 121521 15 + 294540 TGAAATACAGTTCGA -s simCow_chr6.simCow.chr6 359965 15 + 602619 TGAAACACAAATTGA -s simDog_chr6.simDog.chr6 350621 15 + 593897 TGAAACACGACCTGG -s simHuman_chr6.simHuman.chr6 248732 15 + 601863 TGAAACACAATTCGA -s simRat_chr6.simRat.chr6 258985 15 + 647215 CGAATTACAGTTCGA - -a -s simMouse_chr6.simMouse.chr6 270000 4 + 636262 TATG -s Anc0.Anc0refChr3 2395 4 + 222631 TATG -s Anc1.Anc1refChr5 4732 4 + 6477 TATG -s Anc2.Anc2refChr13 4560 4 + 96486 TATG -s mr.mrrefChr5 121536 4 + 294540 TATG -s simCow_chr6.simCow.chr6 359980 4 + 602619 TATG -s simDog_chr6.simDog.chr6 351086 4 + 593897 TGTG -s simHuman_chr6.simHuman.chr6 248747 4 + 601863 TATG -s simRat_chr6.simRat.chr6 259000 4 + 647215 TATG - -a -s simMouse_chr6.simMouse.chr6 270004 3 + 636262 AAA -s Anc0.Anc0refChr3 2399 3 + 222631 AAA -s Anc1.Anc1refChr5 4736 3 + 6477 AAA -s Anc2.Anc2refChr13 4564 3 + 96486 AAA -s mr.mrrefChr5 121540 3 + 294540 AAA -s simCow_chr6.simCow.chr6 359984 3 + 602619 AAA -s simDog_chr6.simDog.chr6 351090 3 + 593897 GAA -s simHuman_chr6.simHuman.chr6 248751 3 + 601863 ATA -s simRat_chr6.simRat.chr6 259005 3 + 647215 AAA - -a -s simMouse_chr6.simMouse.chr6 270007 3 + 636262 AAT -s Anc0.Anc0refChr3 2407 3 + 222631 AAT -s Anc1.Anc1refChr5 4744 3 + 6477 AAT -s Anc2.Anc2refChr13 4572 3 + 96486 AAT -s mr.mrrefChr5 121543 3 + 294540 AAT -s simCow_chr6.simCow.chr6 359992 3 + 602619 AAT -s simDog_chr6.simDog.chr6 351098 3 + 593897 ATT -s simHuman_chr6.simHuman.chr6 248759 3 + 601863 AAT -s simRat_chr6.simRat.chr6 259008 3 + 647215 AAT - -a -s simMouse_chr6.simMouse.chr6 270010 4 + 636262 GAAA -s Anc0.Anc0refChr3 2410 4 + 222631 GAAA -s Anc1.Anc1refChr5 4747 4 + 6477 GAAA -s Anc2.Anc2refChr13 4575 4 + 96486 GAAA -s mr.mrrefChr5 121546 4 + 294540 GAAA -s simCow_chr6.simCow.chr6 359995 4 + 602619 GGAA -s simDog_chr6.simDog.chr6 351101 4 + 593897 GAAA -s simHuman_chr6.simHuman.chr6 248764 4 + 601863 AAAA -s simRat_chr6.simRat.chr6 259011 4 + 647215 GATA - -a -s simMouse_chr6.simMouse.chr6 270014 19 + 636262 CCTCTTGTGAGCCAGGCCT -s Anc0.Anc0refChr3 2414 19 + 222631 AATCTTATGAGCCAGGCCT -s Anc1.Anc1refChr5 4751 19 + 6477 AATCTTATGAGCCAGGCCT -s Anc2.Anc2refChr13 4580 19 + 96486 AATCTCATCAGACCAGCTT -s mr.mrrefChr5 121550 19 + 294540 CCTCTTGTGAGCCAGGCCT -s simCow_chr6.simCow.chr6 360000 15 + 602619 -ATCTCATCAAAT---CAG -s simDog_chr6.simDog.chr6 351106 19 + 593897 ATCCTCATCAGACCAGCTT -s simHuman_chr6.simHuman.chr6 248768 19 + 601863 GATCTTATGGGCCAGGCCT -s simRat_chr6.simRat.chr6 259015 19 + 647215 CTTCTTGTGAGCCAGGGCC - -a -s simMouse_chr6.simMouse.chr6 270033 90 + 636262 GTTTCTTATACTGCTTTGGTTAAGAGGTCTACTATGTTTGCTTTTTGACATGTCAACCCATGTTCAAGGGAGGTATTGGTTTGATTACCT -s Anc0.Anc0refChr3 2434 89 + 222631 TTTT-TTGAGATGATTTGATTAAGAGGCCTATCATATTTGCTTTTTGACATGTCAACCTGTGTTTAAGGGGGGTACTGCCTTGATTGCCT -s Anc1.Anc1refChr5 4771 89 + 6477 TTTT-TTGAGATGATTTGATTAAGAGGCCTATCATATTTGCTTTTTGACATGTCAACCTGTGTTTAAGGGGGGTACTGCCTTGATTGCCT -s Anc2.Anc2refChr13 4600 89 + 96486 TTTC-TTGAGATGATTTGATTAAGAGGCCTATCATATTTGCTTTTTGACATGTCAACCTGCGTTTAAGTGGGGTACTGCCCTGATTTCCT -s mr.mrrefChr5 121570 90 + 294540 GTTTCTTATGCTGCTTTGGTTAAGAGGTCTACTATATTTGCTTTTTGACATGTCAACCCATGTTCAAGGGAGGTACTGGCTTGATTGCCT -s simCow_chr6.simCow.chr6 360016 89 + 602619 CTTC-TTGAGATGAAATGATTAAGAGGCCTATCATATTTGCTTTTTGACATGTCACTTTCGGATTCAGTAGAGTCCTGCCCTTATTACCT -s simDog_chr6.simDog.chr6 351126 86 + 593897 TTTC-TCAGGATGATTTGAATAAGGGGCCTAACAAATTTG-TCTTTGACATGTAAACCTGCATTCAA--GTGGTACTGCACCGATTTTCT -s simHuman_chr6.simHuman.chr6 248788 88 + 601863 TTTT-GTGAGAAGGTTTGATTTAGAGGCCTATGATATTTGCTTTTTGACATATCAA-CTGTGTTTAAGGGGGGTACTGTCTTGATTGCCT -s simRat_chr6.simRat.chr6 259035 90 + 647215 GTTTCTTATGCTGCTTTCGTTACCAGGTCTACTATATTCACTTTTTGACACGTCAACCCATGTTCAAGGGAGGTACTACCTTGATTGCCT - -a -s simMouse_chr6.simMouse.chr6 270123 9 + 636262 ACACAGAAA -s Anc0.Anc0refChr3 2530 8 + 222631 ACACA-AAA -s Anc1.Anc1refChr5 4867 9 + 6477 ACACAGAAA -s Anc2.Anc2refChr13 4696 8 + 96486 ATATA-AAA -s mr.mrrefChr5 121660 9 + 294540 ACACAGAAA -s simCow_chr6.simCow.chr6 360112 8 + 602619 ATAGA-AAA -s simDog_chr6.simDog.chr6 351219 8 + 593897 ATATA-AAA -s simHuman_chr6.simHuman.chr6 248883 9 + 601863 ACACGGAAA -s simRat_chr6.simRat.chr6 259125 9 + 647215 ACACAGAAA - -a -s simMouse_chr6.simMouse.chr6 270132 5 + 636262 AGAAC -s Anc0.Anc0refChr3 2541 5 + 222631 AAGAT -s Anc1.Anc1refChr5 4879 5 + 6477 AAGAT -s Anc2.Anc2refChr13 4707 5 + 96486 AAGAT -s mr.mrrefChr5 121669 5 + 294540 AGAAC -s simCow_chr6.simCow.chr6 360120 2 + 602619 ---AT -s simDog_chr6.simDog.chr6 351230 5 + 593897 AAGAT -s simHuman_chr6.simHuman.chr6 248895 5 + 601863 AAGAT -s simRat_chr6.simRat.chr6 259134 5 + 647215 AGAAC - -a -s simMouse_chr6.simMouse.chr6 270137 6 + 636262 CTCCAT -s Anc0.Anc0refChr3 2546 6 + 222631 CCCAAT -s Anc1.Anc1refChr5 4884 6 + 6477 CCCAAT -s Anc2.Anc2refChr13 4721 6 + 96486 CCCAGT -s mr.mrrefChr5 121674 6 + 294540 CTCCAT -s simCow_chr6.simCow.chr6 360131 6 + 602619 CTCAGT -s simDog_chr6.simDog.chr6 351244 6 + 593897 CCCAGT -s simHuman_chr6.simHuman.chr6 248900 6 + 601863 CCCAAT -s simRat_chr6.simRat.chr6 259139 6 + 647215 CTCCGA - -a -s simMouse_chr6.simMouse.chr6 270143 7 + 636262 CATTGTA -s Anc0.Anc0refChr3 2570 7 + 222631 CATCATA -s Anc1.Anc1refChr5 4908 7 + 6477 CATCATA -s Anc2.Anc2refChr13 4745 7 + 96486 CATCCTA -s mr.mrrefChr5 121680 7 + 294540 CATCATA -s simCow_chr6.simCow.chr6 360155 7 + 602619 CGTACTA -s simDog_chr6.simDog.chr6 351264 7 + 593897 CATCCTA -s simHuman_chr6.simHuman.chr6 248925 7 + 601863 CATCACA -s simRat_chr6.simRat.chr6 259145 7 + 647215 CATCATA - -a -s simMouse_chr6.simMouse.chr6 270150 3 + 636262 TAG -s Anc0.Anc0refChr3 2577 3 + 222631 TAG -s Anc1.Anc1refChr5 4915 3 + 6477 TAG -s Anc2.Anc2refChr13 4752 3 + 96486 TAT -s mr.mrrefChr5 121687 3 + 294540 TAG -s simCow_chr6.simCow.chr6 360170 3 + 602619 TAT -s simHuman_chr6.simHuman.chr6 248933 3 + 601863 TAG -s simRat_chr6.simRat.chr6 259152 3 + 647215 CAG - -a -s simMouse_chr6.simMouse.chr6 270153 226 + 636262 GTAAATGTACAGGGAAGCCTTCTAACACTCACCCAATATGTAGTATGGAATGGTCTTGCTAGACTCAATTGAGGACACAAGCCCAATTAGTTACTCATGGCACAAGGTCAATGAAATACTTGAGGCCCGCAAGATAAATGAGTTGAGCACTACAATTACAACCTGATCATTATTACTCTTGGGTTAGTAACATGCCACCAGGTACCGATCTATCATTCCATTCAGA -s Anc0.Anc0refChr3 2580 183 + 222631 CTAAATATA-AGGGATGCCCTCAAATACTTGGCCAATACATAATATGGAACAGTGTCACTAGACTCATGTGAAGGCACAAGCCCAATTATTT-----------------AATCGAGCACTGGA-------------------------ACTATAACAATAACAGTATCATTGGTACTCTTGGGGTAATAGCACTCACAGAGGTACCATCCTATCATTCCATTCAGA -s Anc1.Anc1refChr5 4918 183 + 6477 CTAAATATA-AGGGATGCCCTCAAATACTTGGCCAATACATAATATGGAACAGTGTCACTAGACTCATGTGAAGGCACAAGCCCAATTATTT-----------------AATCGAGCACTGGA-------------------------ACTATAACAATAACAGTATCATTGGTACTCTTGGGGTAATAGCACTCACAGAGGTACCATCCTATCATTCCATTCAGA -s Anc2.Anc2refChr13 4986 183 + 96486 CTAAAGATA-TTGGCATCCCTCAAATACTTGACCAATGCATAATATGGAACAGCGTCACTAGACTCATGTGAAGGCACAATCCCAATTATTT-----------------AATCGAGCACTGGA-------------------------ACTATAACAATAACAGTATCATTGGTACTCTTAGGGTAATAGCACTTACAGAGGTACCATCCTATCATTCCATTCAAA -s mr.mrrefChr5 121690 226 + 294540 GTAAATGTACAGGGATGCCTTCAAACACTCAGCCAATATATAATATGGAATAGTCTTGCTAGACTCAATTGAGGGCACAAGCCCAATTAGTTACTCATGGCACAAGGTCAATGAAATACTTGAGGCCCGCAAGATAAATGAGTTGAGCACTGCAATTACAACATTATCATTGTTACTCTTGGGTTAATAACATGCCACCAGGTACCAATCTATCATTCCATTCAGA -s simCow_chr6.simCow.chr6 360441 175 + 602619 TTGAAATTA-TTGGTATGCTGCAAATACTTCACCAATGCATAATATGGAAGA-CGTCACGAGACTCAAGTGAAGGGACAATGCCAATTGTTT-----------------AACCGAGTACTGGA-------------------------AGTATAACAGTGAG------ATTTGTACCCT-AGGGTAATAACACTTACACAAGTACCATCCTATCATTCCATTCAAA -s simDog_chr6.simDog.chr6 351275 163 + 593897 CTAAAGATG-TTAGCATCCCTCCAATACTTGACCTATGCATAATATGGAACAGCATCACTAGATTCATGTGAAGGCACAATCCCACTTATTT-----------------AATCAAGCACTGGA-------------------------GCTGAGATTATAACAGTATCAATGGTACTCTTAAGTTAATAGTGCTTACAGAGTTAAT-------------------- -s simHuman_chr6.simHuman.chr6 248936 183 + 601863 ATAAATACA-AGGTATGCCCTCAGATACTTGGCCAATACATCACATGAAAAAGTGTCACTAGACTCATATGACGGTACAAGACCAATTATTC-----------------AATTGAGCACTGGA-------------------------ACTATAACAATAACAATATCATTGGTACTCTTGGGGTAATAGCACTCACAGAGGTACCACCCTACCATTCCATTCAGA -s simRat_chr6.simRat.chr6 259155 225 + 647215 GTAGATGTACAGGGATGCCTTCAAACACTCAGCCAATATATGATAT-CAACAGCCTTGCTAGACTCAATTGAGGGCACAAGGCCAATTAGTGATTGTTGGCACAAGGCCAATGCAATACTTGACCACTGCAATATAAATTAGTTGAGCACTGCAATTAGAACATTAACATTGTTACTCTTGGGTCAATAACAAGTCACAAGGTACCAATCTATCATTTTATGCTGA - -a -s simMouse_chr6.simMouse.chr6 270379 18 + 636262 ATTCATGTAGGAAAGTAA -s Anc0.Anc0refChr3 2772 18 + 222631 ATTCATGATGGAAAGTAA -s Anc1.Anc1refChr5 5110 18 + 6477 ATTCATGATGGAAAGTAA -s Anc2.Anc2refChr13 5178 18 + 96486 ATTCATGATGGACAGTAA -s mr.mrrefChr5 121925 18 + 294540 ATTCATGTTGGAAAGTAA -s simCow_chr6.simCow.chr6 360625 18 + 602619 ATTCATGATGGACAGTAA -s simHuman_chr6.simHuman.chr6 249128 18 + 601863 ATCCATGATGGAAAGTAA -s simRat_chr6.simRat.chr6 259389 18 + 647215 ATTCATGTTGGAAAGTAG - -a -s simMouse_chr6.simMouse.chr6 270397 73 + 636262 ACAAAGTGTTCAAGATTCTAACTAATGATAATAAATTGGGACTGGTCTTATGCAAGGTATTGTGGTTCAATAC -s Anc0.Anc0refChr3 2790 37 + 222631 ACAAAGGGTTCAGGATTCTAACTGATGATCATAAACT------------------------------------ -s Anc1.Anc1refChr5 5128 73 + 6477 ACAAAGGGTTCAGGATTCTAACTGATGATCATAAACTGGAATTGGTTTTACTCAAAGTACTGTGGGTCCAAAC -s Anc2.Anc2refChr13 5196 37 + 96486 ACATAGGGTTCAGGATTCCAATGGATGATCATAAACT------------------------------------ -s mr.mrrefChr5 121943 73 + 294540 ACAAAGTGTTCAGGATTCTAACTAATGATCATAAATTGGGACTGGTCTTATGCAAAGTACTGTGGTTCAATAC -s simCow_chr6.simCow.chr6 360643 37 + 602619 ACATAGGGTCCAGGATTCCAATGAATGATCATAAACT------------------------------------ -s simDog_chr6.simDog.chr6 351438 30 + 593897 -------GTTCAGGATTCCAATGGATGATTATAAACT------------------------------------ -s simHuman_chr6.simHuman.chr6 249152 73 + 601863 ACAAAGGGTTCAGGATTCTAACTGATGATCATAAACTGGAATTGGTTTTACTCAAAGTACTGTGGGTCCAAAC -s simRat_chr6.simRat.chr6 259407 73 + 647215 ACAAAGTATTCTGAACTCTAACTCACGATCATAGATTGAGACGGGTCTTATGCGAAGTACTGTGGCTCAATAC - -a -s simMouse_chr6.simMouse.chr6 270470 20 + 636262 TTCAATTAGCAGCAGCATTT -s Anc0.Anc0refChr3 2827 18 + 222631 TTTAAA--GTAGAAGCATTT -s Anc1.Anc1refChr5 5201 20 + 6477 TTTAAATAGTAGAAGCATTT -s Anc2.Anc2refChr13 5233 18 + 96486 TTTAAA--GTGGAAGCATTT -s mr.mrrefChr5 122016 20 + 294540 TTCAATTAGTAGCAGCATTT -s simCow_chr6.simCow.chr6 360688 18 + 602619 TTTAAG--GTGGAAGCACTT -s simDog_chr6.simDog.chr6 351468 18 + 593897 TTTAAA--GTGAAAGCATTT -s simHuman_chr6.simHuman.chr6 249225 20 + 601863 TTTGAATGGTAGAAGAATTT -s simRat_chr6.simRat.chr6 259480 20 + 647215 TTCCATTAGTGGCAGCATCT - -a -s simMouse_chr6.simMouse.chr6 270490 12 + 636262 GTAATTATCTGT -s Anc0.Anc0refChr3 2845 12 + 222631 ATGGATAGCCCT -s Anc1.Anc1refChr5 5221 12 + 6477 ATGGATAGCCCT -s Anc2.Anc2refChr13 5251 12 + 96486 ATGGATAGCCCT -s mr.mrrefChr5 122036 12 + 294540 GTAATTATCTGT -s simCow_chr6.simCow.chr6 360706 12 + 602619 GTGGATAGCCCT -s simDog_chr6.simDog.chr6 351487 12 + 593897 ATAAATGGCCCT -s simHuman_chr6.simHuman.chr6 249245 12 + 601863 CTGGATAACCCT -s simRat_chr6.simRat.chr6 259500 12 + 647215 GTAATTATCTGT - -a -s simMouse_chr6.simMouse.chr6 270502 3 + 636262 GAC -s Anc0.Anc0refChr3 2857 3 + 222631 GAC -s Anc1.Anc1refChr5 5233 3 + 6477 GAC -s Anc2.Anc2refChr13 5263 3 + 96486 GAC -s mr.mrrefChr5 122048 3 + 294540 GAC -s simCow_chr6.simCow.chr6 360718 3 + 602619 GAC -s simDog_chr6.simDog.chr6 351500 3 + 593897 GTA -s simHuman_chr6.simHuman.chr6 249257 3 + 601863 GAC -s simRat_chr6.simRat.chr6 259512 3 + 647215 GAC - -a -s simMouse_chr6.simMouse.chr6 270505 11 + 636262 ACCACCCAGCT -s Anc0.Anc0refChr3 2860 11 + 222631 ACTAATCAGCC -s Anc1.Anc1refChr5 5236 11 + 6477 ACTAATCAGCC -s Anc2.Anc2refChr13 5266 11 + 96486 ACTAATTAGCA -s mr.mrrefChr5 122051 11 + 294540 ACTACCCAGCC -s simCow_chr6.simCow.chr6 360727 11 + 602619 ACTATTTAGCT -s simDog_chr6.simDog.chr6 351503 11 + 593897 ACTCATTGGCA -s simHuman_chr6.simHuman.chr6 249260 11 + 601863 ACTAATCAGCC -s simRat_chr6.simRat.chr6 259515 11 + 647215 ACTACGCAGCC - -a -s simMouse_chr6.simMouse.chr6 270516 29 + 636262 CCACCATAGCAGGGGTGCAAGTTTAAATA -s Anc0.Anc0refChr3 2871 29 + 222631 CTATCATTGCAGAGGTAGAGGTTTAAATA -s Anc1.Anc1refChr5 5247 29 + 6477 CTATCATTGCAGAGGTAGAGGTTTAAATA -s Anc2.Anc2refChr13 5277 29 + 96486 CTATCATTGCAGAAGTAGAGGTTTACATA -s mr.mrrefChr5 122062 29 + 294540 CCACCATAGCAGGGGTGCAAGTTTAAATA -s simCow_chr6.simCow.chr6 360738 29 + 602619 CTATCATTGCGGGAGTAGAGGTTTATTTA -s simDog_chr6.simDog.chr6 351515 29 + 593897 CTATCATTGCAGAAGTAGAGGTTTACATT -s simHuman_chr6.simHuman.chr6 249271 26 + 601863 CTATCATTGCAGTGG---AGGTTTAAATA -s simRat_chr6.simRat.chr6 259526 29 + 647215 CCACCATGGCAGAGGTGCAAGTTTAAATA - -a -s simMouse_chr6.simMouse.chr6 270545 46 + 636262 TTAGGTAGCTACAAAGCCTTCTAGGAGCTGGTCATTCACTCATTGA -s Anc0.Anc0refChr3 2900 46 + 222631 TTAGTTGGCTACAAAATCTTCAAGGAACTGGCTTTTCACTAATGGA -s Anc1.Anc1refChr5 5276 46 + 6477 TTAGTTGGCTACAAAATCTTCAAGGAACTGGCTTTTCACTAATGGA -s Anc2.Anc2refChr13 5306 46 + 96486 TTAGTTGGCTACAAAATCTTCAAGGAACTGGCTTTTTGCTAATGGA -s mr.mrrefChr5 122091 46 + 294540 TTAGGTGGCTACAAAACCTTCTAGGAGCTGGCCATTCACTCATTGA -s simCow_chr6.simCow.chr6 360771 46 + 602619 TAAGTTGGCTACAAAATCTTCAAGGAGCTGACCTTTTGCTGATGGA -s simDog_chr6.simDog.chr6 351544 46 + 593897 CTCGCTGGCTACAGAGTCCTCAAGGAAATGGCTCTTTGCTAATGGA -s simHuman_chr6.simHuman.chr6 249297 46 + 601863 TTAGTTGGCTACAAAATCTTCAAGGATCTAGCTTGTCACAAATGGA -s simRat_chr6.simRat.chr6 259555 46 + 647215 TTAGGTGGTTACAAAAGCTTCTAGAAGCTGGCCATGCACTTATCAA - -a -s simMouse_chr6.simMouse.chr6 270591 8 + 636262 GGCTTAAA -s Anc0.Anc0refChr3 2946 8 + 222631 CACTTGGA -s Anc1.Anc1refChr5 5322 8 + 6477 CACTTGGA -s Anc2.Anc2refChr13 5352 8 + 96486 CAATTGGG -s mr.mrrefChr5 122137 8 + 294540 GGCTTGGA -s simCow_chr6.simCow.chr6 360817 8 + 602619 GGATTGGG -s simDog_chr6.simDog.chr6 351597 7 + 593897 CA-TTGGG -s simHuman_chr6.simHuman.chr6 249343 8 + 601863 CACTTGGA -s simRat_chr6.simRat.chr6 259601 8 + 647215 GGCTTGGA - -a -s simMouse_chr6.simMouse.chr6 270599 12 + 636262 TGCGGTTGAGAT -s Anc0.Anc0refChr3 2958 12 + 222631 TTATATGGAGAA -s Anc1.Anc1refChr5 5334 12 + 6477 TTATATGGAGAA -s Anc2.Anc2refChr13 5364 12 + 96486 CTATATGGAGAA -s mr.mrrefChr5 122145 12 + 294540 TGAGGTTGAGAT -s simCow_chr6.simCow.chr6 360829 12 + 602619 ATATTTAGATAA -s simDog_chr6.simDog.chr6 351608 12 + 593897 CAATATGAAGAA -s simHuman_chr6.simHuman.chr6 249355 12 + 601863 TTATATGGAGAA -s simRat_chr6.simRat.chr6 259609 12 + 647215 TGAGGTTGAGAT - -a -s simMouse_chr6.simMouse.chr6 270611 37 + 636262 GTAGTGTAGGCAGCAGAGATTTACTTACTGTTAAAAA -s Anc0.Anc0refChr3 2970 34 + 222631 AAAATGTAGTGTGACAAG---CACTTACAGTTAAAAC -s Anc1.Anc1refChr5 5346 34 + 6477 AAAATGTAGTGTGACAAG---CACTTACAGTTAAAAC -s Anc2.Anc2refChr13 5376 34 + 96486 AAAATGTAGTGTGACAAC---CACTTACAGTTAAAAC -s mr.mrrefChr5 122157 37 + 294540 GAAGTGTAGGCAGCAGAGATTTACTTACTGTTAAAAA -s simCow_chr6.simCow.chr6 360841 33 + 602619 ATG-TGTACTGTGCCAGC---CACTTACAGTTAAAAC -s simDog_chr6.simDog.chr6 351621 34 + 593897 AAAATGTCGTGTGACCAC---CTGTTATAGTTAAAAC -s simHuman_chr6.simHuman.chr6 249367 34 + 601863 AAAATGTAGTGTGACAAG---AACTTACAGTTAGAAC -s simRat_chr6.simRat.chr6 259621 31 + 647215 GAAGTGCAAGCAGCAGAGAATCACTTAC------AAA - -a -s simMouse_chr6.simMouse.chr6 270648 8 + 636262 GGCACATT -s Anc0.Anc0refChr3 3004 8 + 222631 TGCACATG -s Anc1.Anc1refChr5 5380 8 + 6477 TGCACATG -s Anc2.Anc2refChr13 5410 8 + 96486 TGCATATG -s mr.mrrefChr5 122194 8 + 294540 GGCACATT -s simCow_chr6.simCow.chr6 360875 8 + 602619 TGCATACA -s simDog_chr6.simDog.chr6 351655 8 + 593897 TGAATGTG -s simHuman_chr6.simHuman.chr6 249401 8 + 601863 TGCACATG -s simRat_chr6.simRat.chr6 259652 8 + 647215 GACACATT - -a -s simMouse_chr6.simMouse.chr6 270656 7 + 636262 TGTTAAA -s Anc0.Anc0refChr3 3017 7 + 222631 TATCTAG -s Anc1.Anc1refChr5 5393 7 + 6477 TATCTAG -s Anc2.Anc2refChr13 5423 7 + 96486 TATCTAG -s mr.mrrefChr5 122202 7 + 294540 TGTTAAA -s simCow_chr6.simCow.chr6 360888 7 + 602619 TATCTAG -s simDog_chr6.simDog.chr6 351668 7 + 593897 CAACTAG -s simHuman_chr6.simHuman.chr6 249414 7 + 601863 TATCTAG -s simRat_chr6.simRat.chr6 259660 7 + 647215 TGTTAAA - -a -s simMouse_chr6.simMouse.chr6 270663 1 + 636262 T -s Anc0.Anc0refChr3 3043 1 + 222631 T -s Anc1.Anc1refChr5 5419 1 + 6477 T -s Anc2.Anc2refChr13 5449 1 + 96486 T -s mr.mrrefChr5 122209 1 + 294540 T -s simCow_chr6.simCow.chr6 360910 1 + 602619 T -s simDog_chr6.simDog.chr6 351694 1 + 593897 T -s simHuman_chr6.simHuman.chr6 249440 1 + 601863 T -s simRat_chr6.simRat.chr6 259667 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 270664 54 + 636262 AAACCCATTAGGTCAGGTGATGCACCCATTTTACTGGCCTACAGATCCCCAGAC -s Anc0.Anc0refChr3 3044 52 + 222631 GAAGATGTTAGATAGGGTGATGTGTCCACCTGACCT--CTACAGAGGTCCAGGT -s Anc1.Anc1refChr5 5420 52 + 6477 GAAGATGTTAGATAGGGTGATGTGTCCACCTGACCT--CTACAGAGGTCCAGGT -s Anc2.Anc2refChr13 5450 52 + 96486 GAAGATGTTAGATAGGTTGATGTGTCCACCTGACCT--CTACAGAGGTCCAGGT -s mr.mrrefChr5 122210 52 + 294540 AAACCTATTAGGTCAGGTGATGCACCCACTTTACTG--CTACAGATCTCCAGAC -s simCow_chr6.simCow.chr6 360911 52 + 602619 GAAGATTTTAGATAAGATGAAATGTCCATTTGAATG--CTACAGAGGTCAAGGT -s simDog_chr6.simDog.chr6 351696 51 + 593897 GAAGATGTTAGATAGATT-ATGTGTCCACCTGACCT--CTGCAGCGGTCCAGTT -s simHuman_chr6.simHuman.chr6 249441 52 + 601863 GAATGTGTTAGATAGGGTGACGTCTCCACATGCCCT--CTACAGAGGTCCAGGT -s simRat_chr6.simRat.chr6 259668 52 + 647215 AGACATATTAGGTCAGGTGATGCACCCACTTTACTG--CTATAAATCTGCAGAG - -a -s simMouse_chr6.simMouse.chr6 270718 7 + 636262 CAATTAT -s Anc0.Anc0refChr3 3101 7 + 222631 CATCTAC -s Anc1.Anc1refChr5 5477 7 + 6477 CATCTAC -s Anc2.Anc2refChr13 5507 7 + 96486 AATCTCC -s mr.mrrefChr5 122262 7 + 294540 CAATTAT -s simCow_chr6.simCow.chr6 360968 7 + 602619 AGTTTCC -s simDog_chr6.simDog.chr6 351752 7 + 593897 AATCTCC -s simHuman_chr6.simHuman.chr6 249498 7 + 601863 CATCTAC -s simRat_chr6.simRat.chr6 259720 7 + 647215 CAATTAT - -a -s simMouse_chr6.simMouse.chr6 270725 14 + 636262 GTTAATTAGTTGGT -s Anc0.Anc0refChr3 3110 14 + 222631 GGGCCCTAATTAGT -s Anc1.Anc1refChr5 5486 14 + 6477 GGGCCCTAATTAGT -s Anc2.Anc2refChr13 5516 14 + 96486 GGGCCCTAATAAGT -s mr.mrrefChr5 122271 14 + 294540 GTTAATTAGTTGGT -s simCow_chr6.simCow.chr6 360977 14 + 602619 GAGCCTTACTATGT -s simDog_chr6.simDog.chr6 351761 14 + 593897 GGGCACTAATAAGT -s simHuman_chr6.simHuman.chr6 249507 14 + 601863 GGGCCCTAATTAGT -s simRat_chr6.simRat.chr6 259729 14 + 647215 GTTAATTAGTTGAC - -a -s simMouse_chr6.simMouse.chr6 270739 27 + 636262 ATGGCATGTGTCTGTGCGGAGGTGATG -s Anc0.Anc0refChr3 3124 12 + 222631 GAGACACAT---------------CAA -s Anc1.Anc1refChr5 5500 12 + 6477 GAGACACAT---------------CAA -s Anc2.Anc2refChr13 5534 12 + 96486 AAGACCCAT---------------CAA -s mr.mrrefChr5 122285 27 + 294540 GTGGCATGTATCTGTGCGGAGGTGATG -s simCow_chr6.simCow.chr6 360995 11 + 602619 A-GATTCAT---------------CAA -s simDog_chr6.simDog.chr6 351779 12 + 593897 AAAACCCAT---------------CAA -s simHuman_chr6.simHuman.chr6 249521 12 + 601863 GAGACACAT---------------CCA -s simRat_chr6.simRat.chr6 259743 27 + 647215 GCGGTATGAATCTGTGAGGAGGTGGTG - -a -s simMouse_chr6.simMouse.chr6 270766 39 + 636262 ACGGTGCTACCCACTGCACTCTTCATTCTAAATGCCTAT -s Anc0.Anc0refChr3 3139 36 + 222631 GCCTTGGTTCATTGGGAACCT---ATTTTGCATGCCTAT -s Anc1.Anc1refChr5 5515 36 + 6477 GCCTTGGTTCATTGGGAACCT---ATTTTGCATGCCTAT -s Anc2.Anc2refChr13 5549 36 + 96486 GGCTTGGTTCATTGGGAACCC---ATTTTGCATGCCTAT -s mr.mrrefChr5 122315 39 + 294540 ACGTTGCTACCTACTGCACTTTTCATTCTACATGCCTAT -s simCow_chr6.simCow.chr6 361009 36 + 602619 GGCTTCACTCATTAGGAACCC---ATTTTGTATGCCTTT -s simDog_chr6.simDog.chr6 351794 36 + 593897 GGCTTGGTTTGTAGGGAACCC---ACTTTGCAAGACTAT -s simHuman_chr6.simHuman.chr6 249536 36 + 601863 GCCTTAGTTCATTGGGAACCT---ATTTTGCATGCCCAT -s simRat_chr6.simRat.chr6 259775 39 + 647215 ATGTTGCTACCTACTGCACTTTTCATTCTACATGCCTAT - -a -s simMouse_chr6.simMouse.chr6 270805 14 + 636262 ATATTGGTTAAGAA -s Anc0.Anc0refChr3 3175 14 + 222631 AAATTGATGAAGAA -s Anc1.Anc1refChr5 5551 14 + 6477 AAATTGATGAAGAA -s Anc2.Anc2refChr13 5585 14 + 96486 AAATTGATGAGGAG -s mr.mrrefChr5 122354 14 + 294540 ATATTGGTTAAGAA -s simCow_chr6.simCow.chr6 361046 14 + 602619 AAATTGATGTGGAG -s simDog_chr6.simDog.chr6 351830 13 + 593897 AA-TTAATGAGGAG -s simHuman_chr6.simHuman.chr6 249572 14 + 601863 AAATTGATGAAGAA -s simRat_chr6.simRat.chr6 259814 14 + 647215 ATATTGGTTAAGAA - -a -s simMouse_chr6.simMouse.chr6 270819 38 + 636262 ATTTATGCACAAACAGGGGCCTCAGCAGTATCTCCAGT -s Anc0.Anc0refChr3 3192 38 + 222631 ATTCATGCACAAACAAGAATCTCAGCAATGCCTCCAGT -s Anc1.Anc1refChr5 5568 38 + 6477 ATTCATGCACAAACAAGAATCTCAGCAATGCCTCCAGT -s Anc2.Anc2refChr13 5602 38 + 96486 ATTCATGCACAAATAAGAATCTCAGCAAGGCCTCCTGT -s mr.mrrefChr5 122368 38 + 294540 ATTTATGCACAAACAGGAGCCTCAGCAATATCTCCAGT -s simCow_chr6.simCow.chr6 361063 38 + 602619 TTTCATTTGTAAATAAGAATCTTAGCAAGTCCTCTAGT -s simDog_chr6.simDog.chr6 351846 38 + 593897 ATTCCTGCACAAATAAGACCCTCAGCAAGGCCTCCTGT -s simHuman_chr6.simHuman.chr6 249589 34 + 601863 GTTCATGCACAAACAAGAATCTCACCAATG----CAGT -s simRat_chr6.simRat.chr6 259828 38 + 647215 ATTTATGCACAAATGGGAGCCTCAGCAATACCTCCCGT - -a -s simMouse_chr6.simMouse.chr6 270857 62 + 636262 TTGACAGCATAAATAACTGTATTGAGTGTGGGTATGTGTAGAACTTACTGATTTATGCACGG -s Anc0.Anc0refChr3 3231 58 + 222631 TTGACAGCCTACAAAACTGTATTGGCTGTGGG----TGTAAGTTTTACAGTTTTATTCCTTG -s Anc1.Anc1refChr5 5607 58 + 6477 TTGACAGCCTACAAAACTGTATTGGCTGTGGG----TGTAAGTTTTACAGTTTTATTCCTTG -s Anc2.Anc2refChr13 5641 58 + 96486 TTGACAGCCTACAACACTGTATTGGCTGCGGG----CAAAAGTTATACAGTTCTATTCCTTG -s mr.mrrefChr5 122406 62 + 294540 TTGACAGCATAAATAACTGTATTGAGTGTGGGTATGTGTAGAACTTACTGATTTATGCACTG -s simCow_chr6.simCow.chr6 361102 56 + 602619 TTGACAGCCTACAACGCTGTATTGACTGCAGG----CAAATGTAATACAGTTCTATTCCT-- -s simDog_chr6.simDog.chr6 351885 57 + 593897 TTGACAGCCCACTACACTATATTGGTTG-GGG----CAAAAGTTATACAGTTCTATCCTTTG -s simHuman_chr6.simHuman.chr6 249624 58 + 601863 TTGAAAGCCTACAAAACTGTATTGGCTGTGGG----TGTAAGGTTTACAGTTTTACTCCTTC -s simRat_chr6.simRat.chr6 259866 62 + 647215 TTGACAGCATAAATAACTATATTGAGTGTGGGTATGCGTAGAAGTTACTGATTTATGTGCTG - -a -s simMouse_chr6.simMouse.chr6 270919 38 + 636262 ATGCTGGTGTGATTAGGGGAGATGTACCCAGATCTGCC -s Anc0.Anc0refChr3 3289 38 + 222631 ATGCTGGTGTGACTAGGGGAGATGAACCCAGCCCAGGC -s Anc1.Anc1refChr5 5665 38 + 6477 ATGCTGGTGTGACTAGGGGAGATGAACCCAGCCCAGGC -s Anc2.Anc2refChr13 5700 38 + 96486 ATGCTGGTGTGATTATGGGAGAGGAACCCAGCCCAGGC -s mr.mrrefChr5 122468 38 + 294540 ATGCTGGTGTGACTAGGGGAGATGTACCCAGCTCTGCC -s simCow_chr6.simCow.chr6 361159 38 + 602619 ATTCTGGTGTGATTATGGAAGAGGAACCCAGCTCAGGT -s simDog_chr6.simDog.chr6 351943 26 + 593897 ATGCTGGTGTGATTATAGG------------CCGAGGC -s simHuman_chr6.simHuman.chr6 249682 38 + 601863 ATGCTGGTGTGACTAGGGGAGTTGAACCCAGCCCCAGC -s simRat_chr6.simRat.chr6 259928 38 + 647215 ATGCTGGTGTGACTAGGGGAGATGTACCCTGCTCTGTC - -a -s simMouse_chr6.simMouse.chr6 270957 15 + 636262 TTCCTGTCCATCTAA -s Anc0.Anc0refChr3 3327 15 + 222631 GGCCTGTACATCTAA -s Anc1.Anc1refChr5 5703 15 + 6477 GGCCTGTACATCTAA -s Anc2.Anc2refChr13 5738 15 + 96486 GGCCTGAACATCTAA -s mr.mrrefChr5 122506 15 + 294540 TTCCTGTCCATCTAA -s simCow_chr6.simCow.chr6 361203 15 + 602619 GGCCCAACCATTCAA -s simDog_chr6.simDog.chr6 351969 15 + 593897 GGCCTGAACATCTGA -s simHuman_chr6.simHuman.chr6 249720 15 + 601863 AGCCTGTTCATCTAA -s simRat_chr6.simRat.chr6 259966 15 + 647215 TTCCTGTCCGCCTAA - -a -s simMouse_chr6.simMouse.chr6 270972 66 + 636262 TCACAACTACATATTTTTGTCTGGTTTCAGTAAAGTCCCCCCAAGCAAGCAGGAGTGATGGCATCA -s Anc0.Anc0refChr3 3342 66 + 222631 TTGTAACTACACAACTTCATCAAGTTACAGTAAAGTCCCTCCAAGTTAACAGGAGTGTGGAAATGA -s Anc1.Anc1refChr5 5718 66 + 6477 TTGTAACTACACAACTTCATCAAGTTACAGTAAAGTCCCTCCAAGTTAACAGGAGTGTGGAAATGA -s Anc2.Anc2refChr13 5753 66 + 96486 TTATAACTACACAACTTCATCAAGTTCCAGTGAAGGCCCTCCCAGTTAACAGGAGTGTGGAAATGA -s mr.mrrefChr5 122521 66 + 294540 TCGCAACTACATATTTTCGTCTGGTTACAGTAAAGTCCCCCCAAGCAAGCAGGAGTGATGACATCA -s simCow_chr6.simCow.chr6 361218 66 + 602619 TTATGACTACATAACTTCACCAAGTTCCGGTGGAGGCCCTCCCAGTTAACAGTAGTGTAGAAATGA -s simDog_chr6.simDog.chr6 351984 66 + 593897 TTACAACTATGCATCATCATCAGTCTCCATTGAAGGCCCACCCAGTTAACAGGAGTGTGCAAACAA -s simHuman_chr6.simHuman.chr6 249736 66 + 601863 TGGTAACTACACAACTTCATCAAGTTACAGTAAAGTTGCTCCAAGTTAACAGGAGTGTGGATATGA -s simRat_chr6.simRat.chr6 259981 60 + 647215 TTGCAACTA------GTCGTCTGGTTACAGTAAATTCCCCCCAAGCAAGCAGGAGTGATGACATCA - -a -s simMouse_chr6.simMouse.chr6 271038 30 + 636262 CCCACAGACTATGTAAAAGTACCAACGTAA -s Anc0.Anc0refChr3 3408 30 + 222631 ATCACAGACTAGGTGAAAGTTTCAACATGA -s Anc1.Anc1refChr5 5784 30 + 6477 ATCACAGACTAGGTGAAAGTTTCAACATGA -s Anc2.Anc2refChr13 5820 30 + 96486 ATCACGGACTAGGTGAAAGTCTCAACTTGA -s mr.mrrefChr5 122587 30 + 294540 CTCACAGACTAGGTAAAAGTTCCAACATGA -s simCow_chr6.simCow.chr6 361285 30 + 602619 ATTATTTACTAGGTGAAATTCTTAATGTGA -s simDog_chr6.simDog.chr6 352051 28 + 593897 ATCACGGACTAGGTAA--GTCTCAACTTAA -s simHuman_chr6.simHuman.chr6 249802 30 + 601863 ATCACAGACTAGATGAAAGTTTCAACATGA -s simRat_chr6.simRat.chr6 260041 30 + 647215 CTCATAGACTAGGTAAAAGGTACAACATGA - -a -s simMouse_chr6.simMouse.chr6 271068 3 + 636262 GGT -s Anc0.Anc0refChr3 3438 3 + 222631 GGT -s Anc1.Anc1refChr5 5814 3 + 6477 GGT -s Anc2.Anc2refChr13 5850 3 + 96486 GGT -s mr.mrrefChr5 122617 3 + 294540 GGT -s simCow_chr6.simCow.chr6 361315 3 + 602619 TGT -s simDog_chr6.simDog.chr6 352094 3 + 593897 GGT -s simHuman_chr6.simHuman.chr6 249832 3 + 601863 GGT -s simRat_chr6.simRat.chr6 260071 3 + 647215 GGT - -a -s simMouse_chr6.simMouse.chr6 271071 11 + 636262 AGGAGACCTGT -s Anc0.Anc0refChr3 3443 11 + 222631 AGGAGACCTGT -s Anc1.Anc1refChr5 5819 11 + 6477 AGGAGACCTGT -s Anc2.Anc2refChr13 5855 11 + 96486 AGGAGACCTGC -s mr.mrrefChr5 122620 11 + 294540 AGGAGACCTGT -s simCow_chr6.simCow.chr6 361320 11 + 602619 AAAAGACCTGC -s simDog_chr6.simDog.chr6 352099 11 + 593897 GGGAGACCTGC -s simHuman_chr6.simHuman.chr6 249837 11 + 601863 AGGAGACCCGT -s simRat_chr6.simRat.chr6 260074 11 + 647215 AGGAGACCTGT - -a -s simMouse_chr6.simMouse.chr6 271082 5 + 636262 GTTCT -s Anc0.Anc0refChr3 3456 5 + 222631 GTTCC -s Anc1.Anc1refChr5 5832 5 + 6477 GTTCC -s Anc2.Anc2refChr13 5868 5 + 96486 GTTCC -s mr.mrrefChr5 122631 5 + 294540 GTTCC -s simCow_chr6.simCow.chr6 361333 5 + 602619 GTTCC -s simDog_chr6.simDog.chr6 352112 5 + 593897 GTTAC -s simHuman_chr6.simHuman.chr6 249850 5 + 601863 GTTCC -s simRat_chr6.simRat.chr6 260085 5 + 647215 GTTCC - -a -s simMouse_chr6.simMouse.chr6 271087 2 + 636262 CT -s Anc0.Anc0refChr3 3462 2 + 222631 CC -s Anc1.Anc1refChr5 5838 2 + 6477 CC -s Anc2.Anc2refChr13 5874 2 + 96486 TC -s mr.mrrefChr5 122637 2 + 294540 CT -s simCow_chr6.simCow.chr6 361339 2 + 602619 TC -s simDog_chr6.simDog.chr6 352118 2 + 593897 TG -s simHuman_chr6.simHuman.chr6 249856 2 + 601863 CC -s simRat_chr6.simRat.chr6 260091 2 + 647215 CT - -a -s simMouse_chr6.simMouse.chr6 271089 69 + 636262 GCCTAGATGTTGGTACAGATCCATACAACTAAATGTTGCCACCATTCCTGTCTAGACATCTAGCTCATG -s Anc0.Anc0refChr3 3465 69 + 222631 GCCTAAATGTTGGTGCAAATCCATACAACTTAATGGTAACACCATTCCTGTCAAGCCATCTATATCATG -s Anc1.Anc1refChr5 5841 69 + 6477 GCCTAAATGTTGGTGCAAATCCATACAACTTAATGGTAACACCATTCCTGTCAAGCCATCTATATCATG -s Anc2.Anc2refChr13 5877 69 + 96486 GCCTAAATGTCAGTGCAAATCCATGCAACTTAATGGTAACACCATTCATGCCAAGCCGTCTTTATCACG -s mr.mrrefChr5 122639 69 + 294540 GCCTAGATGTTGGTACAGATCCATACAACTAAATGGTGACACCATTCCTGTCTAGACATCTATCTCATG -s simCow_chr6.simCow.chr6 361342 45 + 602619 ACCTAAATGTCAGTGCAAGTCCATGGAACTTAATGGTAACACCAT------------------------ -s simDog_chr6.simDog.chr6 352121 69 + 593897 GTCTAAATGTCAGAGCAAATCCATGCAACTTAATGATAACACCATTCATGCCAAGCCGTCTTTATCACG -s simHuman_chr6.simHuman.chr6 249859 69 + 601863 GCCTAAATGTTGGTTCAAATCCATACTACTTAATGGTAACTCAATTCCTGTTGAGCCATCTATTTCATG -s simRat_chr6.simRat.chr6 260093 69 + 647215 GACTAGATGTTCGTACAGATCCATACAACTAAATGGTGACACCCTTCCTGTCTAGATATCTATCTCATG - -a -s simMouse_chr6.simMouse.chr6 271158 21 + 636262 CATGTTACATAAGAACTGTGC -s Anc0.Anc0refChr3 3534 21 + 222631 CATGATGCATCAGAGTGGTGC -s Anc1.Anc1refChr5 5910 21 + 6477 CATGATGCATCAGAGTGGTGC -s Anc2.Anc2refChr13 5946 21 + 96486 CATGATGCATCAGAGTTTAGC -s mr.mrrefChr5 122708 21 + 294540 CATGATGCATAAGAACGGTGC -s simCow_chr6.simCow.chr6 361387 17 + 602619 ----ATATGTAAGAGTTTGGC -s simDog_chr6.simDog.chr6 352271 21 + 593897 CATGATGCATCAGAGTTTAGC -s simHuman_chr6.simHuman.chr6 249928 21 + 601863 CATGATGCAGGAGAGTGGTGT -s simRat_chr6.simRat.chr6 260162 21 + 647215 CATGATGCATAACACCGGTGC - -a -s simMouse_chr6.simMouse.chr6 271179 31 + 636262 CATGTGAAAGGTCCCTGGTCCCTTCAGATCC -s Anc0.Anc0refChr3 3555 24 + 222631 CATGTGTTAGGTCTTTTG-------AGGTCT -s Anc1.Anc1refChr5 5931 24 + 6477 CATGTGTTAGGTCTTTTG-------AGGTCT -s Anc2.Anc2refChr13 5968 24 + 96486 CATGTGTTAGGTCTTTTG-------AGGTAT -s mr.mrrefChr5 122729 24 + 294540 CATGTGAAAGGTCCCTTG-------AGATCC -s simCow_chr6.simCow.chr6 361406 24 + 602619 CATGTGTTAAATCTTTTG-------AGGTTT -s simDog_chr6.simDog.chr6 352293 16 + 593897 CATGTGTTAGG---------------GGTAT -s simHuman_chr6.simHuman.chr6 249949 24 + 601863 CATGTGTCAGGTATTTTG-------AGGTCT -s simRat_chr6.simRat.chr6 260183 24 + 647215 CATGTGAAAAGTCCCTTG-------AGATCC - -a -s simMouse_chr6.simMouse.chr6 271210 13 + 636262 CCTTCAAAACAGT -s Anc0.Anc0refChr3 3585 13 + 222631 CACTCAAAACAGT -s Anc1.Anc1refChr5 5961 13 + 6477 CACTCAAAACAGT -s Anc2.Anc2refChr13 5998 13 + 96486 CACTCAAAACAGT -s mr.mrrefChr5 122753 13 + 294540 CCTTCAAAACAGT -s simCow_chr6.simCow.chr6 361436 13 + 602619 CACTCAAAATAGT -s simDog_chr6.simDog.chr6 352315 13 + 593897 CACTTAGAACAGT -s simHuman_chr6.simHuman.chr6 249979 13 + 601863 CTGTCAAAACAGT -s simRat_chr6.simRat.chr6 260207 13 + 647215 CCTTCAAAACAGC - -a -s simMouse_chr6.simMouse.chr6 271223 17 + 636262 ATCCTATATAGTCTTCC -s Anc0.Anc0refChr3 3599 17 + 222631 AACCTATATAGTCTTCC -s Anc1.Anc1refChr5 5975 17 + 6477 AACCTATATAGTCTTCC -s Anc2.Anc2refChr13 6012 17 + 96486 AACCTATATAGTCTTCT -s mr.mrrefChr5 122767 17 + 294540 ATCCTATATAGTCTTCC -s simCow_chr6.simCow.chr6 361450 17 + 602619 AACCTGTATGGACTTCT -s simDog_chr6.simDog.chr6 352329 17 + 593897 AACCTATATAGTATTTT -s simHuman_chr6.simHuman.chr6 249993 17 + 601863 AACCTATATAGTCTGCC -s simRat_chr6.simRat.chr6 260221 17 + 647215 ATCCTATATAGTCTTCC - -a -s simMouse_chr6.simMouse.chr6 271240 6 + 636262 AGCCCT -s Anc0.Anc0refChr3 3617 6 + 222631 GGCCCT -s Anc1.Anc1refChr5 5993 6 + 6477 GGCCCT -s Anc2.Anc2refChr13 6030 6 + 96486 GTCCCT -s mr.mrrefChr5 122784 6 + 294540 AGCCCT -s simCow_chr6.simCow.chr6 361467 3 + 602619 ---CCT -s simDog_chr6.simDog.chr6 352347 6 + 593897 GTCCCT -s simHuman_chr6.simHuman.chr6 250011 6 + 601863 TGCCCT -s simRat_chr6.simRat.chr6 260238 5 + 647215 AA-CCT - -a -s simMouse_chr6.simMouse.chr6 271246 31 + 636262 TACAATGTCCACAGAAGAATCATGACGGTTG -s Anc0.Anc0refChr3 3623 21 + 222631 TAC----------TAAGAATCATGAAAGTGG -s Anc1.Anc1refChr5 5999 21 + 6477 TAC----------TAAGAATCATGAAAGTGG -s Anc2.Anc2refChr13 6044 21 + 96486 TAT----------TAGGAATCATGAAAGTGG -s mr.mrrefChr5 122790 31 + 294540 TACAATGTCCACAGAAGAATCATGACGGTTG -s simCow_chr6.simCow.chr6 361479 21 + 602619 TTA----------GAGGAATCCTGAGAGTGG -s simDog_chr6.simDog.chr6 352361 21 + 593897 TAT----------TAGGAATCATGAAAGTGG -s simHuman_chr6.simHuman.chr6 250017 21 + 601863 TAC----------TAAGAATCATAAAAGTGG -s simRat_chr6.simRat.chr6 260243 31 + 647215 TACAATGTCTACAGAGGAATCATGATGGTTG - -a -s simMouse_chr6.simMouse.chr6 271277 22 + 636262 AATTGTTGACTTTACCAAAGGT -s Anc0.Anc0refChr3 3684 21 + 222631 AATTGTCT-ACTTATAATAGGT -s Anc1.Anc1refChr5 6060 22 + 6477 AATTGTCTTACTTATAATAGGT -s Anc2.Anc2refChr13 6105 21 + 96486 AATTGTCT-ACTTATAATAGGT -s mr.mrrefChr5 122821 22 + 294540 AATTGTTGACTTTATCAAAGGT -s simCow_chr6.simCow.chr6 361535 18 + 602619 ---TGGCA-ACTGACTACAGAT -s simDog_chr6.simDog.chr6 352422 21 + 593897 AATTGTCT-ACTTATAATAGGT -s simHuman_chr6.simHuman.chr6 250079 22 + 601863 AATTGTCTTACTTGTAATAGGT -s simRat_chr6.simRat.chr6 260274 22 + 647215 AATTGTTGACTTTTTCAAAGGT - -a -s simMouse_chr6.simMouse.chr6 271299 13 + 636262 TGCAACTGTCCTT -s Anc0.Anc0refChr3 3707 13 + 222631 TGTAGCTGACTTT -s Anc1.Anc1refChr5 6084 13 + 6477 TGTAGCTGACTTT -s Anc2.Anc2refChr13 6128 13 + 96486 CATAGCTAACTTT -s mr.mrrefChr5 122843 13 + 294540 TGCAGCTGTCCTT -s simCow_chr6.simCow.chr6 361555 13 + 602619 CATAGCTAACTTT -s simDog_chr6.simDog.chr6 352445 13 + 593897 CAAAGCCAACTTT -s simHuman_chr6.simHuman.chr6 250103 13 + 601863 TGTAGCTGACTTT -s simRat_chr6.simRat.chr6 260296 13 + 647215 TGCAGCTGTCCTG - -a -s simMouse_chr6.simMouse.chr6 271312 30 + 636262 GAGTGCATTATTTTACTCTAGACATACATG -s Anc0.Anc0refChr3 3720 27 + 222631 GACTGT-TTA--TTATTTTAGGCATACTTG -s Anc1.Anc1refChr5 6097 27 + 6477 GACTGT-TTA--TTATTTTAGGCATACTTG -s Anc2.Anc2refChr13 6141 27 + 96486 CACTGC-TTG--TTATCTTAAGTATACTTG -s mr.mrrefChr5 122856 30 + 294540 GAGTGTATTATTTTACTCTAGACATACATG -s simCow_chr6.simCow.chr6 361568 26 + 602619 CACTGC-T-G--TTATCTTAAGTATACTTG -s simDog_chr6.simDog.chr6 352458 27 + 593897 CACTGC-TTG--TTATCTTAAATATACCTG -s simHuman_chr6.simHuman.chr6 250116 27 + 601863 GACTGT-TTA--TTATTTTAGGCATACTTG -s simRat_chr6.simRat.chr6 260310 30 + 647215 GTGTGTATTATTTTACACTAGACATACATG - -a -s simMouse_chr6.simMouse.chr6 271342 39 + 636262 TGTTAAACAGATTCTCTGCAAATGTGAGTGCCTTTCACA -s Anc0.Anc0refChr3 3747 38 + 222631 TGTTGAACAAAT-GTCTACCACAGTGAGCAATCGTTGTT -s Anc1.Anc1refChr5 6124 39 + 6477 TGTTGAACAAATTGTCTACCACAGTGAGCAATCGTTGTT -s Anc2.Anc2refChr13 6168 38 + 96486 TGTTGAACAAAT-GTCCACCCCAGTGAGCAATCATTGTT -s mr.mrrefChr5 122886 39 + 294540 TGTTAAACAGATTCTCTGCAAATGTGAGTAACTGTCACA -s simCow_chr6.simCow.chr6 361594 38 + 602619 TGTTGCAGAAAT-GTTAACCTCAGTGAGGAATCATTCTA -s simDog_chr6.simDog.chr6 352485 36 + 593897 TGTTAAACAA---GTCCACCCCAGTGAGCAATCATTGTT -s simHuman_chr6.simHuman.chr6 250143 39 + 601863 CGCTGAACAAATTGTCTACCAGAGTGAGCAATCGTTGTT -s simRat_chr6.simRat.chr6 260343 39 + 647215 TGTTAAACAGATCCTCTGCACATGTGAGTAACTGTCACA - -a -s simMouse_chr6.simMouse.chr6 271381 24 + 636262 TTTTAGGACCAGTTGGATTAAAGA -s Anc0.Anc0refChr3 3785 24 + 222631 TTTTATGACCAATAGGAAAAAATA -s Anc1.Anc1refChr5 6163 24 + 6477 TTTTATGACCAATAGGAAAAAATA -s Anc2.Anc2refChr13 6206 24 + 96486 TTTTATGACCAATAGGGAAAAATA -s mr.mrrefChr5 122925 24 + 294540 TTTTAGGACCAGTTGGATTAAAGA -s simCow_chr6.simCow.chr6 361632 24 + 602619 TTTTAGGAGCAGTACGGCAAAATA -s simDog_chr6.simDog.chr6 352522 24 + 593897 TTTGATGACCAATAGGGAGGAATG -s simHuman_chr6.simHuman.chr6 250182 24 + 601863 TTTTAAAACCATTGGGAAAAAGCA -s simRat_chr6.simRat.chr6 260382 24 + 647215 TTTTAGGACCAGTTGGACTAAAGA - -a -s simMouse_chr6.simMouse.chr6 271405 18 + 636262 CCTAATGCCTACAATTGG -s Anc0.Anc0refChr3 3810 18 + 222631 CCCAGTGCCTTCAATTGG -s Anc1.Anc1refChr5 6188 18 + 6477 CCCAGTGCCTTCAATTGG -s Anc2.Anc2refChr13 6231 18 + 96486 CCCAGTGCCTTCAATTAG -s mr.mrrefChr5 122950 18 + 294540 CCTAATGCCTACAATTGG -s simCow_chr6.simCow.chr6 361657 18 + 602619 TCCAGTGCCCTCAATTAG -s simDog_chr6.simDog.chr6 352547 18 + 593897 CCCAGTGCCTCCAATTAG -s simHuman_chr6.simHuman.chr6 250207 18 + 601863 CCCAGTGCCTTCAATTGG -s simRat_chr6.simRat.chr6 260407 18 + 647215 CCTAATGCCTAAAATTGG - -a -s simMouse_chr6.simMouse.chr6 271423 5 + 636262 TAGGA -s Anc0.Anc0refChr3 3828 5 + 222631 TTGGA -s Anc1.Anc1refChr5 6206 5 + 6477 TTGGA -s Anc2.Anc2refChr13 6249 5 + 96486 TTGGA -s mr.mrrefChr5 122968 5 + 294540 TAGGA -s simCow_chr6.simCow.chr6 361675 5 + 602619 TTAGA -s simDog_chr6.simDog.chr6 352565 5 + 593897 CAGGA -s simHuman_chr6.simHuman.chr6 250225 5 + 601863 TTGAA -s simRat_chr6.simRat.chr6 260426 5 + 647215 TAGGA - -a -s simMouse_chr6.simMouse.chr6 271428 3 + 636262 TAG -s Anc0.Anc0refChr3 3833 3 + 222631 TGA -s Anc1.Anc1refChr5 6211 3 + 6477 TGA -s Anc2.Anc2refChr13 6254 3 + 96486 TGA -s mr.mrrefChr5 122973 3 + 294540 TGG -s simCow_chr6.simCow.chr6 361682 3 + 602619 TGA -s simDog_chr6.simDog.chr6 352570 3 + 593897 TGA -s simHuman_chr6.simHuman.chr6 250230 3 + 601863 TGA -s simRat_chr6.simRat.chr6 260431 3 + 647215 TGG - -a -s simMouse_chr6.simMouse.chr6 271431 6 + 636262 TATAAA -s Anc0.Anc0refChr3 3836 6 + 222631 TAAAAA -s Anc1.Anc1refChr5 6214 6 + 6477 TAAAAA -s Anc2.Anc2refChr13 6257 6 + 96486 TAAAAA -s mr.mrrefChr5 122976 6 + 294540 TATAAA -s simCow_chr6.simCow.chr6 361685 6 + 602619 TATAAA -s simDog_chr6.simDog.chr6 352573 6 + 593897 TAAAAA -s simHuman_chr6.simHuman.chr6 250233 6 + 601863 TAGAAA -s simRat_chr6.simRat.chr6 260436 6 + 647215 TATAAA - -a -s simMouse_chr6.simMouse.chr6 271437 52 + 636262 CTCTTTGCTAGAGTTTATGAATCCCAAGTACATGGTGACAGTGAACATTACC -s Anc0.Anc0refChr3 3842 44 + 222631 CTTTCTGCTGGAGTTCATCAATGCTAAATAAATGGTGAGAATGA-------- -s Anc1.Anc1refChr5 6220 44 + 6477 CTTTCTGCTGGAGTTCATCAATGCTAAATAAATGGTGAGAATGA-------- -s Anc2.Anc2refChr13 6264 44 + 96486 CTTTCTGCTGGAGTTCATCAATGCTAAATAAATGGTTAGAATGA-------- -s mr.mrrefChr5 122982 52 + 294540 CTCTCTGCTAGAGTTTATGAATCCCAAATACATGGTGACAGTGAACATTACC -s simCow_chr6.simCow.chr6 361692 33 + 602619 CTTTCTGCTG-----------TGCTAAATAAATGAATAGAATGA-------- -s simDog_chr6.simDog.chr6 352580 36 + 593897 CTTTTTGCTGGAGTTCATCAATGCTGAACAAATGGT---------------- -s simHuman_chr6.simHuman.chr6 250239 44 + 601863 CTTTCTGCTGGGGTCCATCAATGCTAAATAAACGGCGGTAATGA-------- -s simRat_chr6.simRat.chr6 260442 52 + 647215 CTCTCTGCTAGAGTTTATAAATCCCAAATACATGGTGACATTGAATATTACC - -a -s simMouse_chr6.simMouse.chr6 271489 75 + 636262 CACATCAATTAGATGTCTGTCAGAAAAGGCCTGGAGAGAGTTGATATTCATAAGACCTGTATTAGTATTCAAGAT -s Anc0.Anc0refChr3 3886 75 + 222631 CTCATCAATCAGATGTTCCTCAAAGCAGGCTTGGAGAGAGTTGCTGTTCATAAAGCCTGCATTACTATTCCAGAT -s Anc1.Anc1refChr5 6264 75 + 6477 CTCATCAATCAGATGTTCCTCAAAGCAGGCTTGGAGAGAGTTGCTGTTCATAAAGCCTGCATTACTATTCCAGAT -s Anc2.Anc2refChr13 6308 75 + 96486 TTCTTCAATCAGGTGTTCCCTAAAGCAGGCATGGAGAGAGTTACTGTTGGTAAAGCCTCCATTACTACTTCAGAT -s mr.mrrefChr5 123034 75 + 294540 CACATCAATTAGATGTCCCTCAGAACAGGCTTGGAGAGAGTTGATATTCATAAGACCTGTATTAGTATTCAAGAT -s simCow_chr6.simCow.chr6 361733 52 + 602619 TTCTTCAATCAGGTGTTCCCTGAAGCAGGCATGGAAAGGGTTACTGAAAGTA----------------------- -s simDog_chr6.simDog.chr6 352616 55 + 593897 --------------------TAAAGCAGGTATGGAGAGAGTTACTGTTGGTGAAGCCTCCATTACTACTTCAGAT -s simHuman_chr6.simHuman.chr6 250283 75 + 601863 CTCATCAATCAGATGTTCCTCAAAGCAGGCTTGGAGAGACTCGCTGTCCATAAAGCCAGCATTACTATTCCAGAT -s simRat_chr6.simRat.chr6 260494 75 + 647215 CACATCCATTAGATGTCCCTTAGAACAGGCTTGGAGAGAGGTGATATTTATAGGACCCATATTAGTATTCTAGAT - -a -s simMouse_chr6.simMouse.chr6 271564 6 + 636262 TACTTC -s Anc0.Anc0refChr3 3973 6 + 222631 TACTGC -s Anc1.Anc1refChr5 6351 6 + 6477 TACTGC -s Anc2.Anc2refChr13 6395 6 + 96486 TTCTGA -s mr.mrrefChr5 123116 6 + 294540 TACTTC -s simDog_chr6.simDog.chr6 352683 6 + 593897 TTCTGA -s simHuman_chr6.simHuman.chr6 250370 6 + 601863 TATTGC -s simRat_chr6.simRat.chr6 260576 6 + 647215 TACTTC - -a -s simMouse_chr6.simMouse.chr6 271570 32 + 636262 GGTTCTTCACTCCCCATTGAGCTTGGCCTCCA -s Anc0.Anc0refChr3 3979 28 + 222631 GAT--TTCAATCCCCAC-GAGCTT-GCCTCCA -s Anc1.Anc1refChr5 6357 29 + 6477 GAT--TTCAATCCCCACTGAGCTT-GCCTCCA -s Anc2.Anc2refChr13 6401 28 + 96486 TCT--CTCAATCCCCAC-AAGCTT-GCCTCCA -s mr.mrrefChr5 123122 31 + 294540 GATTCTTCACTCCCCATTGAGCTT-GCCTCCA -s simDog_chr6.simDog.chr6 352689 28 + 593897 TCT--CTCAATCCCCAC-AAGCTT-GCCTCCA -s simHuman_chr6.simHuman.chr6 250376 29 + 601863 GAT--TTCTTTCCCTGCTGAGTTT-GCCTACA -s simRat_chr6.simRat.chr6 260583 31 + 647215 GATTCTTCACTCCCCATTGAGCTT-GCCGCCA - -a -s simMouse_chr6.simMouse.chr6 271602 3 + 636262 AGT -s Anc0.Anc0refChr3 4007 3 + 222631 AGT -s Anc1.Anc1refChr5 6386 3 + 6477 AGT -s Anc2.Anc2refChr13 6429 3 + 96486 GGT -s mr.mrrefChr5 123153 3 + 294540 AGT -s simDog_chr6.simDog.chr6 352722 3 + 593897 GGT -s simHuman_chr6.simHuman.chr6 250405 3 + 601863 AGT -s simRat_chr6.simRat.chr6 260614 3 + 647215 AGT - -a -s simMouse_chr6.simMouse.chr6 271605 23 + 636262 ATTGCAACTTAAAACATTGCCCC -s Anc0.Anc0refChr3 4015 23 + 222631 ATTGCAATTCATTGCTTACTCTT -s Anc1.Anc1refChr5 6394 23 + 6477 ATTGCAATTCATTGCTTACTCTT -s Anc2.Anc2refChr13 6437 23 + 96486 ACCTCAATTCATTGCTTACTCTT -s mr.mrrefChr5 123156 23 + 294540 ATTGCAACTTAATACATTGCCTC -s simCow_chr6.simCow.chr6 361785 20 + 602619 ---TCCATTCATTGCATACTCTT -s simDog_chr6.simDog.chr6 352730 23 + 593897 ACCTCAACTGGTTGCTTACACTT -s simHuman_chr6.simHuman.chr6 250413 23 + 601863 ATTGCTATTCATTGCTTGCTTTT -s simRat_chr6.simRat.chr6 260617 23 + 647215 ATTGCAACTTGATACATTGCCTC - -a -s simMouse_chr6.simMouse.chr6 271628 19 + 636262 TAGGAAATAGCGACTCTAC -s Anc0.Anc0refChr3 4038 19 + 222631 TGGGAAATGGAGAGTTTAT -s Anc1.Anc1refChr5 6417 19 + 6477 TGGGAAATGGAGAGTTTAT -s Anc2.Anc2refChr13 6460 19 + 96486 TGGGAAATGGAGAGTCTAT -s mr.mrrefChr5 123179 19 + 294540 TAGGAAATAGCGACTTTAC -s simCow_chr6.simCow.chr6 361807 19 + 602619 TGGGAAATGGAGAGTCTAT -s simDog_chr6.simDog.chr6 352753 7 + 593897 CT------------TCTAT -s simHuman_chr6.simHuman.chr6 250436 19 + 601863 TGGGTAATGGTGAATTTAT -s simRat_chr6.simRat.chr6 260640 19 + 647215 TAGGAAGTAGCAACTTTAC - -a -s simMouse_chr6.simMouse.chr6 271647 58 + 636262 TCTGTCAAGCATGTGGCGTTGTATCCACACAAGCAGGTTTAGTTAAGGCAAAACTAGC -s Anc0.Anc0refChr3 4069 21 + 222631 CCTTCCAAGTATGTGGCCTTG------------------------------------- -s Anc1.Anc1refChr5 6448 21 + 6477 CCTTCCAAGTATGTGGCCTTG------------------------------------- -s Anc2.Anc2refChr13 6492 21 + 96486 CCCTCCAAGTGTGTGGCCTTG------------------------------------- -s mr.mrrefChr5 123198 58 + 294540 TCTGCCAAGCATGTGGCGTTGTATCCACACAAGCAGGTTTAGTTAAGGCAAAACTAGC -s simCow_chr6.simCow.chr6 361834 20 + 602619 CCCTCCCAGTGTATGGCCT-A------------------------------------- -s simDog_chr6.simDog.chr6 352773 21 + 593897 CCCCCCAAGTGTGTGGCCTTG------------------------------------- -s simHuman_chr6.simHuman.chr6 250467 21 + 601863 CCTTCCAAGTATGTGGCCTTG------------------------------------- -s simRat_chr6.simRat.chr6 260659 58 + 647215 TTTGCCAAGCATGTGGTGTCACATCCACACAAATAGGTTTTGTCAAAGCAAAACTAGC - -a -s simMouse_chr6.simMouse.chr6 271705 8 + 636262 TGTTCAAG -s Anc0.Anc0refChr3 4090 8 + 222631 TGGTCCAG -s Anc1.Anc1refChr5 6469 8 + 6477 TGGTCCAG -s Anc2.Anc2refChr13 6513 8 + 96486 TGGTGCAG -s mr.mrrefChr5 123256 8 + 294540 TGTTCAAG -s simCow_chr6.simCow.chr6 361854 8 + 602619 TGGTGCAG -s simDog_chr6.simDog.chr6 352794 8 + 593897 TGTTGCAG -s simHuman_chr6.simHuman.chr6 250488 8 + 601863 TGGTCTAG -s simRat_chr6.simRat.chr6 260739 8 + 647215 TGTTCAAG - -a -s simMouse_chr6.simMouse.chr6 271713 63 + 636262 ATGATGCATCTTAATGTTGACTACTATCAAGAACAAAGGTGGTCACGTTAGAGGCATGGACAT -s Anc0.Anc0refChr5 0 56 - 87904 -------AGTGTAATGTCGTCTACTATAAATAACCAAGATGGTCAAATTAGAGGCATCTTTAC -s Anc1.Anc1refChr7 0 63 + 47259 GTGGTGCAGTGTAATGTCGTCTACTATAAATAACCAAGATGGTCAAATTAGAGGCATCTTTAC -s Anc2.Anc2refChr15 1232 56 - 86568 -------AGTGTATTAGCATCTACTACAAATAACAAAGATGGTCAAATTAGAGCCATCTTTAT -s mr.mrrefChr5 123264 63 + 294540 ATGGTGCATCTTAATGTTGACTACTATCAAGAACCAAGGTGGTCACATTAGAGGCATGGACAC -s simCow_chr6.simCow.chr6 334830 56 - 602619 -------ATTGTATCAGCAGCTATTACAAATAACAAAGATGGCCATGTTAGAGACATGTTTGT -s simDog_chr6.simDog.chr6 335489 55 - 593897 --------GTGTAGTAGCATCTACTGCAAATACCAACAACGGTCAAATTGGAGCCATCTGCAT -s simHuman_chr6.simHuman.chr6 250496 63 + 601863 GTGGTGCAAGCTAATGTAGGCTACTATGAATAACCAAGCTGGTCAAATTAGAAGCATATTTAC -s simRat_chr6.simRat.chr6 260748 63 + 647215 ATGGTGCATCTTAATTTTGACTACTATTGAGAACCAAGGTGGTCTCATTAGAGGCATGCACAC - -a -s simMouse_chr6.simMouse.chr6 271776 24 + 636262 TCCTATGGTAGGCAATTTGTAGGG -s Anc0.Anc0refChr5 56 24 - 87904 TTCTATTGTAGGTACTTAGTAAGG -s Anc1.Anc1refChr7 63 24 + 47259 TTCTATTGTAGGTACTTAGTAAGG -s Anc2.Anc2refChr15 1288 24 - 86568 TTCTATTGTACGTACTTAATTAGT -s mr.mrrefChr5 123327 24 + 294540 TCCTATGGTAGGCACTTTGTAGGG -s simCow_chr6.simCow.chr6 334886 17 - 602619 T-------TACATATTTCATGGCC -s simDog_chr6.simDog.chr6 335547 24 - 593897 TTCTATTGTACGCACTAAATTAGT -s simHuman_chr6.simHuman.chr6 250559 24 + 601863 TTCGATTATAGGTACTTAGTAAGG -s simRat_chr6.simRat.chr6 260811 24 + 647215 TCCTATCGTAGGCACATTGTAGGG - -a -s simMouse_chr6.simMouse.chr6 271800 9 + 636262 ATAGCTAAA -s Anc0.Anc0refChr5 84 9 - 87904 AGGGCAAAA -s Anc1.Anc1refChr7 91 9 + 47259 AGGGCAAAA -s Anc2.Anc2refChr15 1316 9 - 86568 AGGGCACAA -s mr.mrrefChr5 123351 9 + 294540 ATAGCTAAA -s simCow_chr6.simCow.chr6 334907 9 - 602619 ATGGCACAA -s simDog_chr6.simDog.chr6 335575 9 - 593897 GGGGCACAA -s simHuman_chr6.simHuman.chr6 250587 9 + 601863 ACGGCAAAA -s simRat_chr6.simRat.chr6 260835 9 + 647215 ATAGCTAAA - -a -s simMouse_chr6.simMouse.chr6 271809 31 + 636262 GTAGAAAACCAAAGACAAAACAAGCACAAAT -s Anc0.Anc0refChr5 95 22 - 87904 AAAGAAAAAAAAAAACAAAA---------GC -s Anc1.Anc1refChr7 102 22 + 47259 AAAGAAAAAAAAAAACAAAA---------GC -s Anc2.Anc2refChr15 1327 22 - 86568 AAAGTAAAAAAAAAACATAA---------GC -s mr.mrrefChr5 123360 31 + 294540 GAAGAAAACCAAAGACAAAACAAGCACAAAT -s simCow_chr6.simCow.chr6 334918 21 - 602619 CAAGTACAA-AAAAGCATAA---------TC -s simDog_chr6.simDog.chr6 335586 22 - 593897 AAAGTAAAAAGAAAACATAA---------GA -s simHuman_chr6.simHuman.chr6 250598 22 + 601863 AAAGAAAAATAAAAACAAAA---------GC -s simRat_chr6.simRat.chr6 260844 31 + 647215 GAGGAAAACCAGAGACAAGACTAGCACAAAC - -a -s simMouse_chr6.simMouse.chr6 271840 23 + 636262 AAATAACTTTTTACTTAGGAGAA -s Anc0.Anc0refChr5 117 23 - 87904 AACAAACCTTTTAACAATATGAA -s Anc1.Anc1refChr7 124 23 + 47259 AACAAACCTTTTAACAATATGAA -s Anc2.Anc2refChr15 1349 23 - 86568 AACAAACCTTTTAACAATACGAA -s mr.mrrefChr5 123391 23 + 294540 AAATAACTTTTTACTTAGGTGAA -s simCow_chr6.simCow.chr6 334939 23 - 602619 GATGAACCTTTTAACAATTCGAA -s simDog_chr6.simDog.chr6 335609 21 - 593897 AACAGA--TTTTAACAATACGGA -s simHuman_chr6.simHuman.chr6 250620 23 + 601863 AACAAACCTTTTAACAGTATGAA -s simRat_chr6.simRat.chr6 260875 21 + 647215 CAAT--CATTTTATTCAGGTGAA - -a -s simMouse_chr6.simMouse.chr6 271863 8 + 636262 TCCCATAA -s Anc0.Anc0refChr5 140 8 - 87904 TTCAATAA -s Anc1.Anc1refChr7 147 8 + 47259 TTCAATAA -s Anc2.Anc2refChr15 1372 8 - 86568 TTCAATAA -s mr.mrrefChr5 123414 8 + 294540 TTCCATAA -s simCow_chr6.simCow.chr6 334962 7 - 602619 CTCA-TAA -s simDog_chr6.simDog.chr6 335634 8 - 593897 TGCAAAAA -s simHuman_chr6.simHuman.chr6 250643 8 + 601863 TTCAATAA -s simRat_chr6.simRat.chr6 260896 8 + 647215 TTGCATAA - -a -s simMouse_chr6.simMouse.chr6 271871 3 + 636262 AGA -s Anc0.Anc0refChr5 150 3 - 87904 AGA -s Anc1.Anc1refChr7 157 3 + 47259 AGA -s Anc2.Anc2refChr15 1382 3 - 86568 AGA -s mr.mrrefChr5 123422 3 + 294540 AGA -s simCow_chr6.simCow.chr6 334971 3 - 602619 TGA -s simDog_chr6.simDog.chr6 335644 3 - 593897 AGA -s simHuman_chr6.simHuman.chr6 250653 3 + 601863 AGA -s simRat_chr6.simRat.chr6 260904 3 + 647215 AGA - -a -s simMouse_chr6.simMouse.chr6 271874 10 + 636262 AGTCTCTTAC -s Anc0.Anc0refChr5 174 10 - 87904 AGTCTCTTAC -s Anc1.Anc1refChr7 181 10 + 47259 AGTCTCTTAC -s Anc2.Anc2refChr15 1406 10 - 86568 AGTCTTTGAC -s mr.mrrefChr5 123425 10 + 294540 AGTCTCTTAC -s simCow_chr6.simCow.chr6 334995 10 - 602619 AGTCTTTAAC -s simDog_chr6.simDog.chr6 335668 10 - 593897 AGTCTTTGAC -s simHuman_chr6.simHuman.chr6 250677 10 + 601863 ACTCTCTTAC -s simRat_chr6.simRat.chr6 260907 10 + 647215 AGTCTATTAC - -a -s simMouse_chr6.simMouse.chr6 271884 44 + 636262 ATCCTATCAGCTACTAACCTTTAACTCTTTATGTACCAAATCAA -s Anc0.Anc0refChr5 184 43 - 87904 CTCCAATACACTAGTAACCT-CAACTCTTTACATACCAAATCAA -s Anc1.Anc1refChr7 191 44 + 47259 CTCCAATACACTAGTAACCTTCAACTCTTTACATACCAAATCAA -s Anc2.Anc2refChr15 1416 43 - 86568 CTCCACTACACTAGTAACCT-CAACTCTTTGCATACCAAACCAA -s mr.mrrefChr5 123435 44 + 294540 ATCCTATCAACTACTAACCTTCAACTCTTTATATACCAAATCAA -s simCow_chr6.simCow.chr6 335005 41 - 602619 ATCC--TACACTAGTAACCT-CAACTCTTTGCATACCAAAGCAA -s simDog_chr6.simDog.chr6 335683 36 - 593897 CTGCACTACACCA--------CAACTCTTTGTATACCAAACCAA -s simHuman_chr6.simHuman.chr6 250687 43 + 601863 TTCCAATACACTATTGAG-GTCAACTCCCTACATACTAAATCAA -s simRat_chr6.simRat.chr6 260917 44 + 647215 ATCCCATTAACTACTATCCTTCAACTCTTTATATACCAAATCAA - -a -s simMouse_chr6.simMouse.chr6 271928 6 + 636262 ATGGAC -s Anc0.Anc0refChr5 227 2 - 87904 AT---- -s Anc1.Anc1refChr7 235 2 + 47259 AT---- -s Anc2.Anc2refChr15 1459 2 - 86568 AT---- -s mr.mrrefChr5 123479 6 + 294540 ATGGAC -s simCow_chr6.simCow.chr6 335046 2 - 602619 AT---- -s simDog_chr6.simDog.chr6 335722 2 - 593897 AT---- -s simHuman_chr6.simHuman.chr6 250730 2 + 601863 AT---- -s simRat_chr6.simRat.chr6 260961 6 + 647215 ATAGAC - -a -s simMouse_chr6.simMouse.chr6 271934 14 + 636262 TCCAGGAAGCATAC -s Anc0.Anc0refChr5 229 10 - 87904 CCTTGGAAGC---- -s Anc1.Anc1refChr7 237 10 + 47259 CCTTGGAAGC---- -s Anc2.Anc2refChr15 1461 10 - 86568 CCTTGGAAGC---- -s mr.mrrefChr5 123485 14 + 294540 TCTAGGAAGCATAC -s simCow_chr6.simCow.chr6 335052 10 - 602619 TCTTAGGGGC---- -s simDog_chr6.simDog.chr6 335724 10 - 593897 CCTTGGAAGC---- -s simHuman_chr6.simHuman.chr6 250732 10 + 601863 CCTTGGAAGC---- -s simRat_chr6.simRat.chr6 260967 14 + 647215 TTTAGGAAGCATAC - -a -s simMouse_chr6.simMouse.chr6 271948 40 + 636262 TGGCTCCATTCAAGTTTCCCATCATTCTGACTCATACAGA -s Anc0.Anc0refChr5 239 40 - 87904 TAGTACCATTCAACTTTACCATCATTCTGACATGTGCAGA -s Anc1.Anc1refChr7 247 40 + 47259 TAGTACCATTCAACTTTACCATCATTCTGACATGTGCAGA -s Anc2.Anc2refChr15 1471 40 - 86568 TAGTACCATTCAGCATTACCATCATTCTGACATGTGCAGA -s mr.mrrefChr5 123499 40 + 294540 TGGCTCCATTCAAGTTTCCCATCATTCTGACTCATACAGA -s simCow_chr6.simCow.chr6 335090 40 - 602619 TAGTTCCCTTCAGCATTACCATCATTCTGACATCCACAGA -s simDog_chr6.simDog.chr6 335734 30 - 593897 ----ACAATTTA------CAATCGTACTGTCACGTGCAGT -s simHuman_chr6.simHuman.chr6 250742 40 + 601863 TAGTACCATTCAACTTTTCCATCATTTCAACATGTGCAGA -s simRat_chr6.simRat.chr6 260981 40 + 647215 TGGATTCATTCAAATATCCCATCATTCTGACTCATACAGA - -a -s simMouse_chr6.simMouse.chr6 271988 5 + 636262 ATCTA -s Anc0.Anc0refChr5 279 5 - 87904 ATTTT -s Anc1.Anc1refChr7 287 5 + 47259 ATTTT -s Anc2.Anc2refChr15 1511 5 - 86568 ATTTT -s mr.mrrefChr5 123539 5 + 294540 ATCTT -s mr.mrrefChr5 123702 5 + 294540 CTGTT -s simCow_chr6.simCow.chr6 335130 5 - 602619 ATTTA -s simDog_chr6.simDog.chr6 335764 5 - 593897 ATTTT -s simHuman_chr6.simHuman.chr6 250782 5 + 601863 ATTTT -s simMouse_chr6.simMouse.chr6 272147 5 + 636262 CTGTT -s simRat_chr6.simRat.chr6 261188 5 + 647215 CTGTT -s simRat_chr6.simRat.chr6 261021 5 + 647215 ATCTT - -a -s simMouse_chr6.simMouse.chr6 271993 3 + 636262 CTG -s mr.mrrefChr5 123544 3 + 294540 CTG -s simRat_chr6.simRat.chr6 261026 3 + 647215 CTT - -a -s simMouse_chr6.simMouse.chr6 271996 12 + 636262 ATGTTTCTTATA -s Anc0.Anc0refChr5 284 9 - 87904 -TATTACCCA-- -s Anc1.Anc1refChr7 292 12 + 47259 ATATTACCCAGA -s Anc2.Anc2refChr15 1516 9 - 86568 -TATTATCCA-- -s mr.mrrefChr5 123547 12 + 294540 ATGTTTCCTATA -s mr.mrrefChr5 123707 12 + 294540 AGATTACACAGA -s simCow_chr6.simCow.chr6 335135 9 - 602619 -TCTTATGCA-- -s simDog_chr6.simDog.chr6 335769 9 - 593897 -TATTATCCA-- -s simHuman_chr6.simHuman.chr6 250787 9 + 601863 -TGTTGCCTC-- -s simMouse_chr6.simMouse.chr6 272152 12 + 636262 AGATTACACAGA -s simRat_chr6.simRat.chr6 261193 12 + 647215 AGCTTACACAGA -s simRat_chr6.simRat.chr6 261029 12 + 647215 ATGTTTCCCACT - -a -s simMouse_chr6.simMouse.chr6 272008 1 + 636262 T -s Anc1.Anc1refChr7 304 1 + 47259 T -s mr.mrrefChr5 123559 1 + 294540 T -s mr.mrrefChr5 123719 1 + 294540 A -s simMouse_chr6.simMouse.chr6 272173 1 + 636262 A -s simRat_chr6.simRat.chr6 261205 1 + 647215 A -s simRat_chr6.simRat.chr6 261041 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 272009 3 + 636262 GTT -s mr.mrrefChr5 123560 3 + 294540 GTT -s simRat_chr6.simRat.chr6 261042 3 + 647215 ATT - -a -s simMouse_chr6.simMouse.chr6 272012 17 + 636262 TTCTAGTGCTAACATTC -s Anc0.Anc0refChr5 293 17 - 87904 TTTTAGTGCTAACCATC -s Anc1.Anc1refChr7 305 17 + 47259 TTTTAGTGCTAACCATC -s Anc2.Anc2refChr15 1525 17 - 86568 TTTTAGTGCTAACCATA -s mr.mrrefChr5 123563 17 + 294540 TTTTAGTGCTAACATTC -s mr.mrrefChr5 123720 17 + 294540 TTTTAGTGTGGACCAGC -s simCow_chr6.simCow.chr6 335144 17 - 602619 TTTAAGTGCTAACCATC -s simDog_chr6.simDog.chr6 335778 17 - 593897 TTTTAGTGCTAACCGTA -s simHuman_chr6.simHuman.chr6 250796 17 + 601863 TTTTAGTGGTAACTATT -s simMouse_chr6.simMouse.chr6 272174 17 + 636262 TTTTAGTGTGGACCAGC -s simRat_chr6.simRat.chr6 261206 17 + 647215 TTCTAGTGTGGACCAAC -s simRat_chr6.simRat.chr6 261045 17 + 647215 TTTTAGTGCCAAGCTTC - -a -s simMouse_chr6.simMouse.chr6 272029 2 + 636262 AG -s Anc0.Anc0refChr5 311 2 - 87904 AC -s Anc1.Anc1refChr7 323 2 + 47259 AC -s Anc2.Anc2refChr15 1543 2 - 86568 AC -s mr.mrrefChr5 123581 2 + 294540 AC -s mr.mrrefChr5 123738 2 + 294540 AC -s simCow_chr6.simCow.chr6 335162 2 - 602619 AC -s simDog_chr6.simDog.chr6 335796 2 - 593897 AC -s simHuman_chr6.simHuman.chr6 250814 2 + 601863 AC -s simMouse_chr6.simMouse.chr6 272192 2 + 636262 AC -s simRat_chr6.simRat.chr6 261224 2 + 647215 AC -s simRat_chr6.simRat.chr6 261063 2 + 647215 AC - -a -s simMouse_chr6.simMouse.chr6 272031 25 + 636262 CCTATTCAGCACACAGCAAAGCCGA -s Anc0.Anc0refChr5 318 23 - 87904 CTAACTCAA--CAAAGCAAAGCCAA -s Anc1.Anc1refChr7 330 23 + 47259 CTAACTCAA--CAAAGCAAAGCCAA -s Anc2.Anc2refChr15 1550 23 - 86568 CTAACTCAA--CAAGGCAAAGCAAG -s mr.mrrefChr5 123588 23 + 294540 CCAACTCAG--CACAGCAAAGCCAA -s mr.mrrefChr5 123745 23 + 294540 CCAAATCAG--CAAATCAATGTCAA -s simCow_chr6.simCow.chr6 335169 23 - 602619 CTAACCCAA--TAAGGCAAAGCAAC -s simDog_chr6.simDog.chr6 335803 23 - 593897 CTAAATCAA--CAAGGCAAAGCAAG -s simHuman_chr6.simHuman.chr6 250821 23 + 601863 ATAGCTCAA--CAAAGCGAAGCCAA -s simMouse_chr6.simMouse.chr6 272199 23 + 636262 CCAAATCAG--CAAATCAATGTCAA -s simRat_chr6.simRat.chr6 261231 23 + 647215 CCAAATCAG--CAAATCAATGTCAA -s simRat_chr6.simRat.chr6 261070 23 + 647215 CCAACTCAG--CACAGCAAAGCCAA - -a -s simMouse_chr6.simMouse.chr6 272056 20 + 636262 CCAGTGTTCACAACATTTCC -s Anc0.Anc0refChr5 341 20 - 87904 CCATTGTTTCCAACATTTAC -s Anc1.Anc1refChr7 353 20 + 47259 CCATTGTTTCCAACATTTAC -s Anc2.Anc2refChr15 1573 20 - 86568 CCATTGATTCCGGCATTTGC -s mr.mrrefChr5 123611 20 + 294540 CCATTGTTTACAACATTTAC -s simCow_chr6.simCow.chr6 335192 20 - 602619 CCATTGGTTCTGGAATTAGC -s simDog_chr6.simDog.chr6 335826 20 - 593897 CCATTGATTCCGGCATTTGC -s simHuman_chr6.simHuman.chr6 250844 20 + 601863 CCTTGGTTTTCAACATTCAC -s simRat_chr6.simRat.chr6 261093 20 + 647215 CCCTTGTATGCAAAATTTAC - -a -s simMouse_chr6.simMouse.chr6 272076 37 + 636262 ACTTCTGATCCCTGCAACATTAGTAGCAAATGCTTCT -s Anc0.Anc0refChr5 361 37 - 87904 AAGTCCCATCCCTTAAACATTGGTAGCAAATGCTACT -s Anc1.Anc1refChr7 373 37 + 47259 AAGTCCCATCCCTTAAACATTGGTAGCAAATGCTACT -s Anc2.Anc2refChr15 1593 37 - 86568 AAGTCCCATCCCTTAAACATTGGTAGGAAATGTTACT -s mr.mrrefChr5 123631 37 + 294540 ACTTCCCATCCCTGCAACATTAGTAGCAAATGCTTCT -s mr.mrrefChr5 123768 37 + 294540 GAGTCCCGTCCCTTAGATATTGGTAGCAAATGCTACT -s simCow_chr6.simCow.chr6 335212 37 - 602619 AAGACCCATCCATTAAACATTGGTAGTGAGTGTTACA -s simDog_chr6.simDog.chr6 335846 35 - 593897 ACGTCCTGTCCCTTTAGAAATGGTAGGAAAG--TACT -s simHuman_chr6.simHuman.chr6 250864 37 + 601863 AATTCCCATCCCTTAAACATTGGTAGCAAATGCTACT -s simMouse_chr6.simMouse.chr6 272222 37 + 636262 GAGTCCCGTCCCTTAGATATTGGTAGCAAATGTTACT -s simRat_chr6.simRat.chr6 261274 37 + 647215 AAGTCCCATTACTTAGATATAGGTAGCAAAGGCTACT -s simRat_chr6.simRat.chr6 261113 37 + 647215 ACTTCCCATCCCTGTAACATTGCAAGCAGATGCTACT - -a -s simMouse_chr6.simMouse.chr6 272113 3 + 636262 TGA -s Anc0.Anc0refChr5 402 3 - 87904 CAA -s Anc1.Anc1refChr7 414 3 + 47259 CAA -s Anc2.Anc2refChr15 1634 3 - 86568 CAA -s mr.mrrefChr5 123668 3 + 294540 TGA -s mr.mrrefChr5 123809 3 + 294540 CAA -s simCow_chr6.simCow.chr6 335253 3 - 602619 CAA -s simDog_chr6.simDog.chr6 335885 3 - 593897 CAA -s simHuman_chr6.simHuman.chr6 250905 3 + 601863 CAA -s simMouse_chr6.simMouse.chr6 272263 3 + 636262 CAA -s simRat_chr6.simRat.chr6 261315 3 + 647215 CAA -s simRat_chr6.simRat.chr6 261150 3 + 647215 TGA - -a -s simMouse_chr6.simMouse.chr6 272116 1 + 636262 G -s Anc0.Anc0refChr5 405 1 - 87904 T -s Anc1.Anc1refChr7 417 1 + 47259 T -s Anc2.Anc2refChr15 1637 1 - 86568 T -s mr.mrrefChr5 123671 1 + 294540 G -s mr.mrrefChr5 123812 1 + 294540 C -s simCow_chr6.simCow.chr6 335256 1 - 602619 T -s simDog_chr6.simDog.chr6 335889 1 - 593897 T -s simHuman_chr6.simHuman.chr6 250908 1 + 601863 T -s simMouse_chr6.simMouse.chr6 272266 1 + 636262 C -s simRat_chr6.simRat.chr6 261318 1 + 647215 C -s simRat_chr6.simRat.chr6 261153 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 272117 10 + 636262 CTAGTCTAAT -s Anc0.Anc0refChr5 406 10 - 87904 TTAATCTCCT -s Anc1.Anc1refChr7 418 10 + 47259 TTAATCTCCT -s Anc2.Anc2refChr15 1638 10 - 86568 TTAATCTCCT -s mr.mrrefChr5 123672 10 + 294540 CTAGTCTAAT -s mr.mrrefChr5 123813 10 + 294540 CTAATCTCAT -s simCow_chr6.simCow.chr6 335257 10 - 602619 TTAATCTCCT -s simDog_chr6.simDog.chr6 335890 10 - 593897 TTGATCTCCT -s simHuman_chr6.simHuman.chr6 250909 10 + 601863 TTAATCTCCC -s simMouse_chr6.simMouse.chr6 272267 10 + 636262 CTAATCTCAT -s simRat_chr6.simRat.chr6 261319 10 + 647215 CTAATCCCAT -s simRat_chr6.simRat.chr6 261158 10 + 647215 CTAGTCTAAT - -a -s simMouse_chr6.simMouse.chr6 272127 8 + 636262 CTTAGGAA -s Anc0.Anc0refChr5 416 8 - 87904 TTTAGAAA -s Anc1.Anc1refChr7 428 8 + 47259 TTTAGAAA -s Anc2.Anc2refChr15 1648 8 - 86568 TTTAGAAA -s mr.mrrefChr5 123682 8 + 294540 CTTAGGAA -s mr.mrrefChr5 123823 8 + 294540 TTCAAAAA -s simCow_chr6.simCow.chr6 335267 8 - 602619 TTTAGAAA -s simDog_chr6.simDog.chr6 335900 8 - 593897 TCTAGAAA -s simHuman_chr6.simHuman.chr6 250919 8 + 601863 TTTAGAAA -s simMouse_chr6.simMouse.chr6 272277 8 + 636262 TTCAAAAA -s simRat_chr6.simRat.chr6 261168 8 + 647215 TTTAGAAA - -a -s simMouse_chr6.simMouse.chr6 272135 12 + 636262 ACTACTGTACCT -s Anc0.Anc0refChr5 424 12 - 87904 ACCACTACATCT -s Anc1.Anc1refChr7 436 12 + 47259 ACCACTACATCT -s Anc2.Anc2refChr15 1656 12 - 86568 ACCACTACATCT -s mr.mrrefChr5 123690 12 + 294540 ACTACTGTACCT -s mr.mrrefChr5 123831 12 + 294540 ACCATTACATCT -s simCow_chr6.simCow.chr6 335275 12 - 602619 ACCACTACATCG -s simDog_chr6.simDog.chr6 335908 12 - 593897 ACCACACCATCT -s simHuman_chr6.simHuman.chr6 250927 12 + 601863 ACCACTACATCT -s simMouse_chr6.simMouse.chr6 272285 12 + 636262 ACCATTACATCT -s simRat_chr6.simRat.chr6 261329 12 + 647215 AACATGACATCT -s simRat_chr6.simRat.chr6 261176 12 + 647215 ACTACTGTATCT - -a -s simMouse_chr6.simMouse.chr6 272164 9 + 636262 ATTTTATGT - -a -s simMouse_chr6.simMouse.chr6 272191 1 + 636262 A -s Anc0.Anc0refChr5 310 1 - 87904 A -s Anc1.Anc1refChr7 322 1 + 47259 A -s Anc2.Anc2refChr15 1542 1 - 86568 A -s mr.mrrefChr5 123737 1 + 294540 A -s mr.mrrefChr5 123580 1 + 294540 A -s simCow_chr6.simCow.chr6 335161 1 - 602619 A -s simDog_chr6.simDog.chr6 335795 1 - 593897 A -s simHuman_chr6.simHuman.chr6 250813 1 + 601863 A -s simRat_chr6.simRat.chr6 261062 1 + 647215 A -s simRat_chr6.simRat.chr6 261223 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 272194 5 + 636262 TCTCA -s Anc0.Anc0refChr5 313 5 - 87904 TCTAG -s Anc1.Anc1refChr7 325 5 + 47259 TCTAG -s Anc2.Anc2refChr15 1545 5 - 86568 TCTAG -s mr.mrrefChr5 123740 5 + 294540 TCTCA -s mr.mrrefChr5 123583 5 + 294540 TAGGG -s simCow_chr6.simCow.chr6 335164 5 - 602619 TCTAG -s simDog_chr6.simDog.chr6 335798 5 - 593897 TTTAG -s simHuman_chr6.simHuman.chr6 250816 5 + 601863 TCAAG -s simRat_chr6.simRat.chr6 261065 5 + 647215 TAGGG -s simRat_chr6.simRat.chr6 261226 5 + 647215 TTTGA - -a -s simMouse_chr6.simMouse.chr6 272259 4 + 636262 CCCA -s Anc0.Anc0refChr5 398 4 - 87904 CCTA -s Anc1.Anc1refChr7 410 4 + 47259 CCTA -s Anc2.Anc2refChr15 1630 4 - 86568 CCTA -s mr.mrrefChr5 123805 4 + 294540 CCCA -s simCow_chr6.simCow.chr6 335249 4 - 602619 CCTA -s simDog_chr6.simDog.chr6 335881 4 - 593897 CCTA -s simHuman_chr6.simHuman.chr6 250901 4 + 601863 CCTA -s simRat_chr6.simRat.chr6 261311 4 + 647215 CCCA - -a -s simMouse_chr6.simMouse.chr6 272297 53 + 636262 AGAGTGTAGTCGATATGAATCTGATGTCTACCAACCAATTTCTATTGAGATGT -s Anc0.Anc0refChr5 436 53 - 87904 CCATTGTAGACAATGTGAATTAGATCTCTACCAACCTATGTCTATTAAGATGA -s Anc1.Anc1refChr7 448 53 + 47259 CCATTGTAGACAATGTGAATTAGATCTCTACCAACCTATGTCTATTAAGATGA -s Anc2.Anc2refChr15 1668 53 - 86568 CCATTGTAGATGATGTGCATTAGGGCTCTGCCAACCTCTGTCTATTAGGAGTA -s mr.mrrefChr5 123843 53 + 294540 AGAGTGTAGACAATATGAATCTGATGTCTACCAACCAATTTCTATTGAGATGT -s simCow_chr6.simCow.chr6 335287 23 - 602619 CCATTGTAGATGATTTGGATTAT------------------------------ -s simDog_chr6.simDog.chr6 335920 53 - 593897 CCCTTGTAGATGATGTGCATTAGGGCTCTGCCAACCTCTGTCTATTAGGAGTA -s simHuman_chr6.simHuman.chr6 250939 53 + 601863 TCATTGCAGACAATGGGAACTAGATCTCTACGAATCTATACCTATTAAGATGA -s simRat_chr6.simRat.chr6 261341 49 + 647215 AGAGTGTAGACAAT----ATCTCATTTTTGCCAACCAATGTCTATTGAGATAT - -a -s simMouse_chr6.simMouse.chr6 272350 37 + 636262 CTACAAATAGTCAGATGATCAATAGACATAGGTCTTT -s Anc0.Anc0refChr5 491 37 - 87904 TTACAAATAGACGGAGAATCAATAGACACAGGACTTT -s Anc1.Anc1refChr7 503 37 + 47259 TTACAAATAGACGGAGAATCAATAGACACAGGACTTT -s Anc2.Anc2refChr15 1723 37 - 86568 TTGCAAATAGACGGTGAATCAATAGACACAGGACTTT -s mr.mrrefChr5 123898 37 + 294540 CTACAAATAGTCAGATGATCAATAGACATAGGTCTTT -s simDog_chr6.simDog.chr6 335975 37 - 593897 TTGCAAATAGACGGTGAATCAATAGACACAGGACTTT -s simHuman_chr6.simHuman.chr6 250994 37 + 601863 TCACAAATAGGTGAAAAATCAATACACACAGGACACT -s simRat_chr6.simRat.chr6 261392 37 + 647215 CTATAAATAGTCAGTTTATCAATAGATATAGGCCTTT - -a -s simMouse_chr6.simMouse.chr6 272387 26 + 636262 CTGGACCCCAATGTCCCACTTGGCAG -s Anc0.Anc0refChr5 556 26 - 87904 CCGGACCCCACTGATCCATTTGGTGA -s Anc1.Anc1refChr7 568 26 + 47259 CCGGACCCCACTGATCCATTTGGTGA -s Anc2.Anc2refChr15 1788 26 - 86568 ACTTATGCCACTGATCCCCTTGGTGA -s mr.mrrefChr5 123935 26 + 294540 CTGGACCCCAATGACCCATTTGGCAA -s simDog_chr6.simDog.chr6 336040 26 - 593897 ACTTATGCCACTGATCCCCTTGGTGA -s simHuman_chr6.simHuman.chr6 251059 26 + 601863 CCGGACCCCACTGATCCATTTGGTGA -s simRat_chr6.simRat.chr6 261429 26 + 647215 CTGGACCCCAATGACCCATATGGCAA - -a -s simMouse_chr6.simMouse.chr6 272413 46 + 636262 ACGCAAGATGTGATGTTTCAGTTGATGAACTAGCATAACTTAGATT -s Anc0.Anc0refChr5 582 43 - 87904 ATGTAAGAAGACACCTTTCAAT---CAGATTACCATAGCTTAGACT -s Anc1.Anc1refChr7 594 43 + 47259 ATGTAAGAAGACACCTTTCAAT---CAGATTACCATAGCTTAGACT -s Anc2.Anc2refChr15 1814 43 - 86568 ATGTAAGAAGACACCTTTCTTT---CAGATTACCATAGTTCAGACT -s mr.mrrefChr5 123961 43 + 294540 ATGCAAGATGTGACGTTTCAAT---TGGACTAGCATAACTTAGACT -s simDog_chr6.simDog.chr6 336066 43 - 593897 ATGTAAGAAGACACCTTTCTTT---CAGATTACCATAGTTCAGACT -s simHuman_chr6.simHuman.chr6 251085 43 + 601863 ATGTAAGAGTGCACTTTTCAAT---CAGATTACCATGGCTTAGACT -s simRat_chr6.simRat.chr6 261457 43 + 647215 ATGCAAGATGCAACATTTCAAT---TGGACCAGCATAACTCAGACT - -a -s simMouse_chr6.simMouse.chr6 272459 12 + 636262 TACGTAATAAAT -s Anc0.Anc0refChr5 625 12 - 87904 TACGTAATCAAT -s Anc1.Anc1refChr7 637 12 + 47259 TACGTAATCAAT -s Anc2.Anc2refChr15 1857 12 - 86568 TATGTAGTCAAC -s mr.mrrefChr5 124004 12 + 294540 TACGTAATAAAT -s simDog_chr6.simDog.chr6 336109 12 - 593897 TATGTAGTCAAC -s simHuman_chr6.simHuman.chr6 251131 12 + 601863 TACATAATCAAT -s simRat_chr6.simRat.chr6 261500 12 + 647215 TACGTAATAAAT - -a -s simMouse_chr6.simMouse.chr6 272471 28 + 636262 GCAATTAATGGAAGAAATTAAAAGTACT -s Anc0.Anc0refChr5 637 25 - 87904 GC---TAGTGAGAGAAATTAAGAATACT -s Anc1.Anc1refChr7 649 25 + 47259 GC---TAGTGAGAGAAATTAAGAATACT -s Anc2.Anc2refChr15 1869 25 - 86568 AC---GAGTGAGAGCAATTCAGAATCCT -s mr.mrrefChr5 124016 28 + 294540 GCAATTAATGGAAGAAATTAAAAATACT -s simDog_chr6.simDog.chr6 336124 25 - 593897 AC---GAGTGAGAGCAATTCAGAATCCT -s simHuman_chr6.simHuman.chr6 251143 25 + 601863 GC---TAGTGACCAATATTAAGAATACT -s simRat_chr6.simRat.chr6 261512 28 + 647215 ACAATTGATGGGAGAAATTAAAAATACT - -a -s simMouse_chr6.simMouse.chr6 272499 5 + 636262 TTAAA -s Anc0.Anc0refChr5 664 5 - 87904 TTGAA -s Anc1.Anc1refChr7 676 5 + 47259 TTGAA -s Anc2.Anc2refChr15 1896 5 - 86568 GAGCA -s mr.mrrefChr5 124044 5 + 294540 TTAAA -s simDog_chr6.simDog.chr6 336151 5 - 593897 GAGCA -s simHuman_chr6.simHuman.chr6 251170 5 + 601863 TTGAA -s simRat_chr6.simRat.chr6 261540 5 + 647215 TTAAA - -a -s simMouse_chr6.simMouse.chr6 272504 20 + 636262 TTAAGAGGATGTGGATACTA -s Anc0.Anc0refChr5 676 20 - 87904 TTAAGAGGAGATTCATACTA -s Anc1.Anc1refChr7 688 20 + 47259 TTAAGAGGAGATTCATACTA -s Anc2.Anc2refChr15 1908 20 - 86568 CTAAGGGGAGACTCATACTA -s mr.mrrefChr5 124049 20 + 294540 TTAAGAGGATGTGGATACTA -s simDog_chr6.simDog.chr6 336164 20 - 593897 CTAAGGGGAGACTCATACTA -s simHuman_chr6.simHuman.chr6 251182 20 + 601863 TTAAAAGGTGATCTATAATA -s simRat_chr6.simRat.chr6 261545 20 + 647215 TTAAGAAGATGTGCATACTA - -a -s simMouse_chr6.simMouse.chr6 272524 13 + 636262 CATAAGGTGGGGG -s Anc0.Anc0refChr5 698 13 - 87904 CATAAGGCAGGGG -s Anc1.Anc1refChr7 710 13 + 47259 CATAAGGCAGGGG -s Anc2.Anc2refChr15 1930 13 - 86568 CATGAGGCAGGGG -s mr.mrrefChr5 124069 13 + 294540 CATAAGGTGGGGG -s simCow_chr6.simCow.chr6 335310 7 - 602619 ------GCAGGGT -s simDog_chr6.simDog.chr6 336186 13 - 593897 CATGAGGCAGGGG -s simHuman_chr6.simHuman.chr6 251208 13 + 601863 CATAAGGCAGGGA -s simRat_chr6.simRat.chr6 261565 13 + 647215 CATTAGGTGGGGG - -a -s simMouse_chr6.simMouse.chr6 272537 29 + 636262 CTGACTTGGGTTATGAATTCAATTCCAGT -s Anc0.Anc0refChr5 711 29 - 87904 ATGACTTAGGGTATATATTCAGGCCTAGT -s Anc1.Anc1refChr7 723 29 + 47259 ATGACTTAGGGTATATATTCAGGCCTAGT -s Anc2.Anc2refChr15 1943 29 - 86568 ATTACTTAGGGTATATATTCAGGCCTAGC -s mr.mrrefChr5 124082 29 + 294540 CTGACTTGGGTTATGTATTCAATTCCAGT -s simCow_chr6.simCow.chr6 335317 29 - 602619 ATTACTTAGGGTATATATTCAGGCCCTGC -s simDog_chr6.simDog.chr6 336199 29 - 593897 ATTATTCAGGGTATATATTCAGGTCTAAC -s simHuman_chr6.simHuman.chr6 251221 29 + 601863 TTGACTTAGGGTATATATTCAGGCCGGGT -s simRat_chr6.simRat.chr6 261580 29 + 647215 CTGACTTGGGTTAAGTATTCAATTCCAGT - -a -s simMouse_chr6.simMouse.chr6 272566 4 + 636262 TCCT -s Anc0.Anc0refChr5 750 4 - 87904 TCTT -s Anc1.Anc1refChr7 762 4 + 47259 TCTT -s Anc2.Anc2refChr15 1982 4 - 86568 TCTT -s mr.mrrefChr5 124111 4 + 294540 TCTT -s simCow_chr6.simCow.chr6 335356 3 - 602619 TCT- -s simDog_chr6.simDog.chr6 336238 4 - 593897 TCCT -s simHuman_chr6.simHuman.chr6 251260 4 + 601863 TCTT -s simRat_chr6.simRat.chr6 261609 4 + 647215 TCTT - -a -s simMouse_chr6.simMouse.chr6 272570 87 + 636262 GGGCCTCATCCTAAGTATAGTTTTACTTTGTACTGCATGTTGCCAATTTGCTTCCACCATATGATAGCAGAAGCCAGGCAGCTATTT -s Anc0.Anc0refChr5 777 83 - 87904 GGGCCTAGTCCTAAGTAAAGTACTATCTTGTACTGTATGTTGTCAATTCACTTTCACCAT----TAATGGTAGCAGATCAAATAACT -s Anc1.Anc1refChr7 789 83 + 47259 GGGCCTAGTCCTAAGTAAAGTACTATCTTGTACTGTATGTTGTCAATTCACTTTCACCAT----TAATGGTAGCAGATCAAATAACT -s Anc2.Anc2refChr15 2009 83 - 86568 GGGCCTAGTCCTAAGTAAAGTACTATCTTGTACTGTATGTATTCAATTCACTTTCACCAC----TAATGGTAGCAGATTAAATAACT -s mr.mrrefChr5 124133 87 + 294540 GGGCCTCATCCTAAGTATAGTTTTATCTTGTACTGTATGTTGCCAATTCGCTTCCACCATATGATAGTGGAAGCAGATCAGCTATTT -s simCow_chr6.simCow.chr6 335382 83 - 602619 GGGCCTAGTCCTAAGGAAAGTATTACCTTGTATTGTATGTACTCACTTCACTTTCACCAC----TGATGTTAGCAGATTACATGACT -s simDog_chr6.simDog.chr6 336265 83 - 593897 GGGATGAGGCCTAAGTAAAATACTATCTTGTACTGTACATATTCAAGTCAATTTCAGCAC----TAATGGTAGCAGCTTAAACAACT -s simHuman_chr6.simHuman.chr6 251287 83 + 601863 GGACCTAGTCCTAAGTAAAGTAGTATCTTGCACTGTATGTTGTCGATTCTCTTTTACTCT----TAATGGTAGCAGATCAAGTAACT -s simRat_chr6.simRat.chr6 261631 87 + 647215 GGGCCTCATCCTGAGTATAGTTTTATCTTGTACTGTATGTAGCCAGTTCGCTCCCACCATATGGCAGTGGAAGAAGATCAGCTATTA - -a -s simMouse_chr6.simMouse.chr6 272657 40 + 636262 CTATGTTGTATCCCTCTCTCCTAATCCCCTAGACTGTCAT -s Anc0.Anc0refChr5 860 38 - 87904 CTATGTCCTGTCCCTCTC--CTAATCCCCTAGACTAGCAC -s Anc1.Anc1refChr7 872 38 + 47259 CTATGTCCTGTCCCTCTC--CTAATCCCCTAGACTAGCAC -s Anc2.Anc2refChr15 2096 38 - 86568 CTATGTCCTGTCCCTCTC--CTAATCCCCTAGACCAGCAC -s mr.mrrefChr5 124220 40 + 294540 CTATGTTGTATCCCTCTCTCCTAATCCCCTAGACTATCAT -s simCow_chr6.simCow.chr6 335469 38 - 602619 CTATGTACCATTCCACTC--CTAATCCCCTAGATCAGCAC -s simDog_chr6.simDog.chr6 336352 38 - 593897 CTATGTCTTGTCCCTCTC--CTAATCCCCTAGACCAGCAA -s simHuman_chr6.simHuman.chr6 251370 38 + 601863 GTATGTCCTGTCCCTCTC--TTAATGCTCTAGGCTAGCAC -s simRat_chr6.simRat.chr6 261718 40 + 647215 CTCTGTTGTATCCCTCTCCCCTAATCCCCTAGACCATCAT - -a -s simMouse_chr6.simMouse.chr6 272697 25 + 636262 ATTAGTTATATTATATGGAAGGTTT -s Anc0.Anc0refChr5 898 23 - 87904 ATTAGTTTC-CTACA-GGTGAGACT -s Anc1.Anc1refChr7 910 23 + 47259 ATTAGTTTC-CTACA-GGTGAGACT -s Anc2.Anc2refChr15 2134 23 - 86568 ATTAGTTTC-CCACA-GGTGAGACT -s mr.mrrefChr5 124260 25 + 294540 ATTAGTTATACTATATGGAAGGATT -s simCow_chr6.simCow.chr6 335514 23 - 602619 ATTAGCTTC-CCACC-GGTGAGATT -s simDog_chr6.simDog.chr6 336390 21 - 593897 ATTAGTTTC-CCACA-G--GAGACT -s simHuman_chr6.simHuman.chr6 251408 23 + 601863 ATTAATTGC-CTACA-GATGAGACT -s simRat_chr6.simRat.chr6 261758 25 + 647215 ATTAGTTATACTATATGGAAGAATT - -a -s simMouse_chr6.simMouse.chr6 272722 30 + 636262 ATGACTCTTCATCTCATTCCACCAGAAAAT -s Anc0.Anc0refChr5 921 30 - 87904 ATAACTTTTCATGCAGCTCTACCAGAGGTT -s Anc1.Anc1refChr7 933 30 + 47259 ATAACTTTTCATGCAGCTCTACCAGAGGTT -s Anc2.Anc2refChr15 2157 30 - 86568 ATAACTTTTCATGCAGCTCTACCAGAGGTT -s mr.mrrefChr5 124285 30 + 294540 ATAACTTTTCATCTCATTCCACCAGAGAAT -s simCow_chr6.simCow.chr6 335537 30 - 602619 ATAACTTTTCACACAGCTCTACCAGAGGTT -s simDog_chr6.simDog.chr6 336434 30 - 593897 CCGACTTTACATGCAGCTCTACCAGAGGTT -s simHuman_chr6.simHuman.chr6 251431 30 + 601863 ATAACATATCATGCAGATCTACCAGAGTCT -s simRat_chr6.simRat.chr6 261783 30 + 647215 ATAACTTTTCATCTCACTCCACCAGAGAAT - -a -s simMouse_chr6.simMouse.chr6 272752 5 + 636262 TCTTC -s Anc0.Anc0refChr5 978 5 - 87904 TTTTC -s Anc1.Anc1refChr7 991 5 + 47259 TTTTC -s Anc2.Anc2refChr15 2214 5 - 86568 TTTTC -s mr.mrrefChr5 124339 5 + 294540 TCTTC -s simCow_chr6.simCow.chr6 335593 5 - 602619 TTTTC -s simDog_chr6.simDog.chr6 336491 5 - 593897 TTTTC -s simHuman_chr6.simHuman.chr6 251492 5 + 601863 TTTTT -s simRat_chr6.simRat.chr6 261837 5 + 647215 TCTTC - -a -s simMouse_chr6.simMouse.chr6 272757 33 + 636262 ATGCAACCCCATAAGTGGTTGAGGCATTTGTCT -s Anc0.Anc0refChr5 983 33 - 87904 ATGCAGCTCCACCAGAGGTTGAGGCATTTGTAT -s Anc1.Anc1refChr7 996 33 + 47259 ATGCAGCTCCACCAGAGGTTGAGGCATTTGTAT -s Anc2.Anc2refChr15 2219 33 - 86568 ATGCAGCTCCACCAGAGGTTGAGTCATTTGTAT -s mr.mrrefChr5 124344 33 + 294540 ATGCAACCCCATAAGTGGTTGAGGCATTTGTAT -s simCow_chr6.simCow.chr6 335598 33 - 602619 ATCTAGCGCTGCAAGAGGTTGAGTCATTTGTAT -s simDog_chr6.simDog.chr6 336496 33 - 593897 ATGCAGCTTCATCAGGGGTTGAGTCAGTCCTAT -s simHuman_chr6.simHuman.chr6 251498 33 + 601863 GTGCGGCTCCACCAGAGGTTGAGGCATTTGTAT -s simRat_chr6.simRat.chr6 261842 33 + 647215 ATACAACCCCTTAAGTGGCTGAGGCATTTGTAT - -a -s simMouse_chr6.simMouse.chr6 272790 4 + 636262 CATT -s Anc0.Anc0refChr5 1016 4 - 87904 CATT -s Anc1.Anc1refChr7 1029 4 + 47259 CATT -s Anc2.Anc2refChr15 2252 4 - 86568 CATT -s mr.mrrefChr5 124377 4 + 294540 CATT -s simCow_chr6.simCow.chr6 335635 4 - 602619 CATT -s simDog_chr6.simDog.chr6 336529 4 - 593897 CATC -s simHuman_chr6.simHuman.chr6 251531 4 + 601863 CAGT -s simRat_chr6.simRat.chr6 261875 4 + 647215 CGTA - -a -s simMouse_chr6.simMouse.chr6 272794 3 + 636262 GTC -s Anc0.Anc0refChr5 1023 3 - 87904 GGC -s Anc1.Anc1refChr7 1036 3 + 47259 GGC -s Anc2.Anc2refChr15 2262 3 - 86568 GGC -s mr.mrrefChr5 124381 3 + 294540 GGC -s simCow_chr6.simCow.chr6 335645 3 - 602619 GGC -s simDog_chr6.simDog.chr6 336539 3 - 593897 GGC -s simHuman_chr6.simHuman.chr6 251538 3 + 601863 GGC -s simRat_chr6.simRat.chr6 261879 3 + 647215 GGC - -a -s simMouse_chr6.simMouse.chr6 272797 57 + 636262 AACACAGAACCAATTCATTGCCAACAAAGAACCGACTTCAATTGCTATTTGTCTATT -s Anc0.Anc0refChr5 1026 35 - 87904 TAGCCAAAACCA----------------------ACCTCAATCGCTATTGTGCAAAT -s Anc1.Anc1refChr7 1039 35 + 47259 TAGCCAAAACCA----------------------ACCTCAATCGCTATTGTGCAAAT -s Anc2.Anc2refChr15 2265 35 - 86568 TAGCCAAAACCA----------------------ACCTTAATCGCTATTGTGCAAAT -s mr.mrrefChr5 124384 35 + 294540 AACACAAAACCA----------------------ACTTCAATTGCTATTTGTCTATT -s simCow_chr6.simCow.chr6 335661 35 - 602619 AAGCCATGATGG----------------------ACCTTAATTGCTATTGTGCAATT -s simDog_chr6.simDog.chr6 336542 33 - 593897 TATTGAAAACCA----------------------ACCTT--TCGCTATTGTGGAAAT -s simHuman_chr6.simHuman.chr6 251541 35 + 601863 TAGCCAAAACCA----------------------ACCACAATCGCTATTGTGCAAAT -s simRat_chr6.simRat.chr6 261882 35 + 647215 AACACAAAACCA----------------------ACTTCAGTTGCTATTTGTCTATT - -a -s simMouse_chr6.simMouse.chr6 272854 29 + 636262 TCAAGCATCTTTTCCAAGCAAGAGATTCT -s Anc0.Anc0refChr5 1148 29 - 87904 TCAAATATCCTTGTGAAGCAAGCGTTTAT -s Anc1.Anc1refChr7 1161 29 + 47259 TCAAATATCCTTGTGAAGCAAGCGTTTAT -s Anc2.Anc2refChr15 2388 29 - 86568 TCAGATACACTTGTGAGGCAAGCCTATAT -s mr.mrrefChr5 124419 29 + 294540 TCAAGCATCCTTTCCAAGCAAGAGATTAT -s simCow_chr6.simCow.chr6 335785 29 - 602619 TCAGTTACACTTGAAAGGCAAGCCTCCAT -s simDog_chr6.simDog.chr6 336662 26 - 593897 ---GATACACTTGTGAGGCAAGCCAATAT -s simHuman_chr6.simHuman.chr6 251665 29 + 601863 TCAAATATCCTTATGAAATGAGGGTTTAT -s simRat_chr6.simRat.chr6 261917 29 + 647215 TCAAGCATCCTTGCAAAGCAAGAGATTAT - -a -s simMouse_chr6.simMouse.chr6 272883 8 + 636262 GGTAAGGA -s Anc0.Anc0refChr5 1177 8 - 87904 GGTAAGTA -s Anc1.Anc1refChr7 1190 8 + 47259 GGTAAGTA -s Anc2.Anc2refChr15 2417 8 - 86568 GGCAAGTA -s mr.mrrefChr5 124448 8 + 294540 GGTAAGGA -s simCow_chr6.simCow.chr6 335814 8 - 602619 GGCAAGTC -s simDog_chr6.simDog.chr6 336688 7 - 593897 -GCAAGCA -s simHuman_chr6.simHuman.chr6 251695 8 + 601863 GGTAAGTA -s simRat_chr6.simRat.chr6 261946 8 + 647215 GGTAAGGA - -a -s simMouse_chr6.simMouse.chr6 272891 53 + 636262 ATCGACACTAATTGAGACGAGCAAGGTGTCAGGAGGAGGCATAGACATACATG -s Anc0.Anc0refChr5 1187 50 - 87904 ACTGACACTAGTTCAGAATAGCAAGGTGTCAGCGG---GCCTAGAAATACATG -s Anc1.Anc1refChr7 1200 50 + 47259 ACTGACACTAGTTCAGAATAGCAAGGTGTCAGCGG---GCCTAGAAATACATG -s Anc2.Anc2refChr15 2431 50 - 86568 ATTGACACCAGTTCAGAATAGCAAGGTGTCAGCGG---GTCTAGATATACCTA -s mr.mrrefChr5 124456 53 + 294540 ACTGACACTAATTGAGACGAGCAAGGTGTCAGGAGGAGGCATAGAAATACATG -s simCow_chr6.simCow.chr6 335828 42 - 602619 ATTGACACTAGTCCA--------AGGTGTCAGCAG---GTCTGGATATTCCTA -s simDog_chr6.simDog.chr6 336701 46 - 593897 ATTGACACCAGTTCAGAATAGCAAGATATCAGGGG---GTCTAGATATA---- -s simHuman_chr6.simHuman.chr6 251705 49 + 601863 ACTGAC-CTCGTTCAGATTAACAAGGTGTCAGCGG---GCCTATAAATACATG -s simRat_chr6.simRat.chr6 261954 53 + 647215 ACTGACACTAATTGAGACAAGCAAGATGTTAGGAGTAGGCATTGAAATACATG - -a -s simMouse_chr6.simMouse.chr6 272944 29 + 636262 GAATCGAAAATATTCTCCCAGGTGGCATT -s Anc0.Anc0refChr5 1238 29 - 87904 GAATTAAAGATATGCTCACAGGTGGCATT -s Anc1.Anc1refChr7 1251 29 + 47259 GAATTAAAGATATGCTCACAGGTGGCATT -s Anc2.Anc2refChr15 2482 29 - 86568 GAATTAAAGATATGCTCACAGGTGGCATT -s mr.mrrefChr5 124509 29 + 294540 GAATCGAAAATATTCTCCCAGGTGGCATT -s simCow_chr6.simCow.chr6 335871 29 - 602619 GAATTAAAGATATGGTCACAGGTGACATT -s simDog_chr6.simDog.chr6 336748 29 - 593897 GAACCACATATATGCTCACAGGCAGCATT -s simHuman_chr6.simHuman.chr6 251755 29 + 601863 GAATTAAAGGCATGCTCACAAGTGGCATT -s simRat_chr6.simRat.chr6 262007 18 + 647215 GAATC-----------CCCTGGTGGCATT - -a -s simMouse_chr6.simMouse.chr6 272973 4 + 636262 TATA -s Anc0.Anc0refChr5 1267 4 - 87904 TATG -s Anc1.Anc1refChr7 1280 4 + 47259 TATG -s Anc2.Anc2refChr15 2511 4 - 86568 TATG -s mr.mrrefChr5 124538 4 + 294540 TATA -s simCow_chr6.simCow.chr6 335900 4 - 602619 TATG -s simDog_chr6.simDog.chr6 336777 4 - 593897 TATA -s simHuman_chr6.simHuman.chr6 251785 4 + 601863 TGGG -s simRat_chr6.simRat.chr6 262025 4 + 647215 TCAT - -a -s simMouse_chr6.simMouse.chr6 272977 6 + 636262 TAGCAT -s Anc0.Anc0refChr5 1271 6 - 87904 TGGCAA -s Anc1.Anc1refChr7 1284 6 + 47259 TGGCAA -s Anc2.Anc2refChr15 2525 6 - 86568 TGGCAA -s mr.mrrefChr5 124542 6 + 294540 TAGCAA -s simCow_chr6.simCow.chr6 335927 6 - 602619 TGGCAA -s simDog_chr6.simDog.chr6 336791 6 - 593897 TGGCAA -s simHuman_chr6.simHuman.chr6 251789 6 + 601863 TGGCAA -s simRat_chr6.simRat.chr6 262029 6 + 647215 TAGCAA - -a -s simMouse_chr6.simMouse.chr6 272983 95 + 636262 CTCTTGTATGAAACGAGTTCTCAATTGGCAATTTCAATTTATGTATAACACAGAAACTTCGAGAAGATGGTTGAAAGAACAGATATTCCTGTATG -s Anc0.Anc0refChr5 1277 88 - 87904 ------TATGAAACAAGCTTTCAATTGTCAATATCAATGTACATGTAATGCC-ACTCTTCATGAAACTGTTTGAAAGATCAGATATTCCGATATG -s Anc1.Anc1refChr7 1290 94 + 47259 CTTTTGTATGAAACAAGCTTTCAATTGTCAATATCAATGTACATGTAATGCC-ACTCTTCATGAAACTGTTTGAAAGATCAGATATTCCGATATG -s Anc2.Anc2refChr15 2531 88 - 86568 ------TATGAAACAAGCTTTCAATCATCAACATAAATGTACATGTTATGCC-ACTCTTCATGAAACTGCTTGAAAGATCAGATAGTATGATATG -s mr.mrrefChr5 124548 94 + 294540 CTCTTGTATGAAACAAGTTCTCAATTGGCAATTTCAATTTATGTATAACACA-AATCTTCATGAAAATGTTTGAAAGAACAGATATTCCTGTATG -s simCow_chr6.simCow.chr6 335933 88 - 602619 ------TATGAAACAAGCTTTCAGCCATCAACATAGATGTACCTGTGATGCT-GCTCTTCTTGAAACCGCTTGCAAAAACAGATAGTATGAAATG -s simDog_chr6.simDog.chr6 336797 88 - 593897 ------TATGAGACAAGAATTCAATCATCAACATAAATGCACATGCTGAGGC-ATTCCTCATGAAACTGCTTGAAAGATCAGTTTGTATGATATG -s simHuman_chr6.simHuman.chr6 251799 94 + 601863 CTTTCATATGAAATAAGCTTTCAATTGTTGATGTCAATCTACATGTAATGCC-ACTTTTCATGACATTGTTTAAAAGAGCAGATATTCCGATATA -s simRat_chr6.simRat.chr6 262035 94 + 647215 CTCGTGTATGAAACAAGTTCTCTATTGGCAATTCCAATTTATGTATAAGACA-AATCTTTATGAAAATGTTTGAATGAACAGAAAGTCCTGTATC - -a -s simMouse_chr6.simMouse.chr6 273078 15 + 636262 TAGAAGATATAGTAT -s Anc0.Anc0refChr5 1365 15 - 87904 AACAAAGAATAGTAT -s Anc1.Anc1refChr7 1384 15 + 47259 AACAAAGAATAGTAT -s Anc2.Anc2refChr15 2619 15 - 86568 AGCAAAGAATAGTAT -s mr.mrrefChr5 124642 15 + 294540 TAGAAGATATAGTAT -s simCow_chr6.simCow.chr6 336073 15 - 602619 AGCAAATAATTGTAT -s simDog_chr6.simDog.chr6 336885 15 - 593897 GGCAAAGAATAGTAT -s simHuman_chr6.simHuman.chr6 251893 15 + 601863 AACGAAGAAAAGTAT -s simRat_chr6.simRat.chr6 262129 15 + 647215 CAGAAGAGATAGTAT - -a -s simMouse_chr6.simMouse.chr6 273093 46 + 636262 GGTCATTAGTAGTAATTTTGAGTCGAATAATTAATGAGCTATGGGT -s Anc0.Anc0refChr5 1380 42 - 87904 AGTCATTAGTAAT----TTGAGTCGAATGATTAGTAAGCTGTGGTT -s Anc1.Anc1refChr7 1399 42 + 47259 AGTCATTAGTAAT----TTGAGTCGAATGATTAGTAAGCTGTGGTT -s Anc2.Anc2refChr15 2634 42 - 86568 AGTCATTAGAAAT----TTGAGTTGAATGATTAGTAAGCTGTGGTT -s mr.mrrefChr5 124657 46 + 294540 GGTCATTAGTAGTAATTTTGAGTCGAATAATTAATGAGCTATGGGT -s simCow_chr6.simCow.chr6 336088 42 - 602619 AGTCATTAGAAAT----TTGAGTTGCATGATTAGTATGATAAGGTT -s simDog_chr6.simDog.chr6 336900 42 - 593897 AATAATTAAAAAT----TTGTGTTGAATGATTAGTAAGCTGTGGTT -s simHuman_chr6.simHuman.chr6 251908 42 + 601863 AGCCATTAGTAAT----TTGAGTCGAATGGTTAGTAAGCTGTGGCT -s simRat_chr6.simRat.chr6 262162 46 + 647215 GGTCATTGGTAGTAATGTGGAATTGAATAATTAATGACCTATGGTT - -a -s simMouse_chr6.simMouse.chr6 273139 2 + 636262 AA -s Anc0.Anc0refChr5 1422 2 - 87904 AA -s Anc1.Anc1refChr7 1441 2 + 47259 AA -s Anc2.Anc2refChr15 2676 2 - 86568 AA -s mr.mrrefChr5 124703 2 + 294540 AA -s simCow_chr6.simCow.chr6 336130 2 - 602619 GC -s simDog_chr6.simDog.chr6 336942 2 - 593897 AA -s simHuman_chr6.simHuman.chr6 251953 2 + 601863 AA -s simRat_chr6.simRat.chr6 262208 2 + 647215 AA - -a -s simMouse_chr6.simMouse.chr6 273141 9 + 636262 TGTTAACCA -s Anc0.Anc0refChr5 1424 9 - 87904 TGTTAGCCA -s Anc1.Anc1refChr7 1443 9 + 47259 TGTTAGCCA -s Anc2.Anc2refChr15 2678 9 - 86568 TGTTAGCCA -s mr.mrrefChr5 124705 9 + 294540 TGTTAACCA -s simCow_chr6.simCow.chr6 336132 9 - 602619 TGTTAGACA -s simDog_chr6.simDog.chr6 336944 9 - 593897 TGTTAGCCA -s simHuman_chr6.simHuman.chr6 251966 9 + 601863 TGTTACCCA -s simRat_chr6.simRat.chr6 262210 9 + 647215 TGTTAGCCA - -a -s simMouse_chr6.simMouse.chr6 273150 4 + 636262 CAGT -s Anc0.Anc0refChr5 1433 4 - 87904 CAGC -s Anc1.Anc1refChr7 1452 4 + 47259 CAGC -s Anc2.Anc2refChr15 2694 4 - 86568 CAGC -s mr.mrrefChr5 124714 4 + 294540 CAGC -s simCow_chr6.simCow.chr6 336148 4 - 602619 CAGC -s simDog_chr6.simDog.chr6 336960 4 - 593897 CAGC -s simHuman_chr6.simHuman.chr6 251975 4 + 601863 CCGC -s simRat_chr6.simRat.chr6 262219 4 + 647215 CAGC - -a -s simMouse_chr6.simMouse.chr6 273154 28 + 636262 GGTTTGAATGACAAATCTATGACAAATC -s Anc0.Anc0refChr5 1465 17 - 87904 AGTCTGA-----------ATTGGTAATA -s Anc1.Anc1refChr7 1484 17 + 47259 AGTCTGA-----------ATTGGTAATA -s Anc2.Anc2refChr15 2726 17 - 86568 AATCTCA-----------ATTGGTAATA -s mr.mrrefChr5 124736 17 + 294540 GGTTTGA-----------ATGACAAATC -s simCow_chr6.simCow.chr6 336176 17 - 602619 AAGTTCA-----------ATTGGCAAAA -s simDog_chr6.simDog.chr6 336992 10 - 593897 AATCT------------------TAATA -s simHuman_chr6.simHuman.chr6 252007 17 + 601863 AGTATGC-----------ATTGATAATA -s simRat_chr6.simRat.chr6 262241 17 + 647215 GGTTTGA-----------ACGACAGATC - -a -s simMouse_chr6.simMouse.chr6 273182 14 + 636262 TATCCAAAGAAAGA -s Anc0.Anc0refChr5 1484 14 - 87904 TAGCCTAAGAGAGT -s Anc1.Anc1refChr7 1503 14 + 47259 TAGCCTAAGAGAGT -s Anc2.Anc2refChr15 2745 14 - 86568 TAGCCTAAGAGAGT -s mr.mrrefChr5 124753 14 + 294540 TATCCAAAGAAAGA -s simCow_chr6.simCow.chr6 336195 14 - 602619 TAGCTTAAGTGTGA -s simDog_chr6.simDog.chr6 337004 14 - 593897 TAGCCTAAGAGAGT -s simHuman_chr6.simHuman.chr6 252026 14 + 601863 TAGCCTAAGGGGGG -s simRat_chr6.simRat.chr6 262258 14 + 647215 TACCCAAGGAAAGA - -a -s simMouse_chr6.simMouse.chr6 273196 4 + 636262 AAAC -s Anc0.Anc0refChr5 1501 4 - 87904 AAAC -s Anc1.Anc1refChr7 1520 4 + 47259 AAAC -s Anc2.Anc2refChr15 2762 4 - 86568 AAAT -s mr.mrrefChr5 124767 4 + 294540 AAAC -s simCow_chr6.simCow.chr6 336212 4 - 602619 AAAA -s simDog_chr6.simDog.chr6 337021 4 - 593897 ATAT -s simHuman_chr6.simHuman.chr6 252043 4 + 601863 AAAC -s simRat_chr6.simRat.chr6 262272 4 + 647215 AAAC - -a -s simMouse_chr6.simMouse.chr6 273200 1 + 636262 A -s Anc0.Anc0refChr5 1505 1 - 87904 A -s Anc1.Anc1refChr7 1524 1 + 47259 A -s Anc2.Anc2refChr15 2766 1 - 86568 A -s mr.mrrefChr5 124771 1 + 294540 A -s simCow_chr6.simCow.chr6 336216 1 - 602619 A -s simDog_chr6.simDog.chr6 337025 1 - 593897 A -s simHuman_chr6.simHuman.chr6 252049 1 + 601863 G -s simRat_chr6.simRat.chr6 262276 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 273201 16 + 636262 CATAAAAACTTATTAT -s Anc0.Anc0refChr5 1506 16 - 87904 CATAAAGGATTATGAT -s Anc1.Anc1refChr7 1525 16 + 47259 CATAAAGGATTATGAT -s Anc2.Anc2refChr15 2770 16 - 86568 CATTAAGGATTGTGAT -s mr.mrrefChr5 124772 16 + 294540 CATAAAAGCTTATTAT -s simCow_chr6.simCow.chr6 336220 16 - 602619 CATTAAGGATTGTGAT -s simDog_chr6.simDog.chr6 337029 16 - 593897 CGTTAAGGATTGTGAC -s simHuman_chr6.simHuman.chr6 252050 16 + 601863 CATAAAGGAAAATGAT -s simRat_chr6.simRat.chr6 262277 16 + 647215 CACAAAAGCTTATCAT - -a -s simMouse_chr6.simMouse.chr6 273217 21 + 636262 TGATCCAAATTGCGTATGAGG -s Anc0.Anc0refChr5 1522 21 - 87904 TAATCAAAACTGTGTATGTAA -s Anc1.Anc1refChr7 1541 21 + 47259 TAATCAAAACTGTGTATGTAA -s Anc2.Anc2refChr15 2786 21 - 86568 TAACCAAAACTGTGTCTGTAA -s mr.mrrefChr5 124788 21 + 294540 TGATCAAAATTGTGTATGAAG -s simCow_chr6.simCow.chr6 336238 21 - 602619 TAACCAAAACTGTATCTGTAA -s simDog_chr6.simDog.chr6 337045 21 - 593897 TAACTAAAACTGTGACTGTGA -s simHuman_chr6.simHuman.chr6 252066 21 + 601863 TAATCAAAACTGTGTATGCAA -s simRat_chr6.simRat.chr6 262293 21 + 647215 CGATCAAAATTGTGTATGAAG - -a -s simMouse_chr6.simMouse.chr6 273238 4 + 636262 ACTA -s Anc0.Anc0refChr5 1543 4 - 87904 ACTA -s Anc1.Anc1refChr7 1562 4 + 47259 ACTA -s Anc2.Anc2refChr15 2807 4 - 86568 ACTA -s mr.mrrefChr5 124809 4 + 294540 ACTA -s simCow_chr6.simCow.chr6 336259 4 - 602619 ACTA -s simDog_chr6.simDog.chr6 337072 4 - 593897 GCCA -s simHuman_chr6.simHuman.chr6 252087 4 + 601863 ACTA -s simRat_chr6.simRat.chr6 262314 4 + 647215 ACCA - -a -s simMouse_chr6.simMouse.chr6 273242 11 + 636262 AATTCACTCTG -s Anc0.Anc0refChr5 1548 11 - 87904 AATTCTCTCTG -s Anc1.Anc1refChr7 1567 11 + 47259 AATTCTCTCTG -s Anc2.Anc2refChr15 2812 11 - 86568 AGTTTTCTCTG -s mr.mrrefChr5 124813 11 + 294540 AATTCACTCTG -s simCow_chr6.simCow.chr6 336264 6 - 602619 A-----CTCTC -s simDog_chr6.simDog.chr6 337077 10 - 593897 AGTTTTCT-TG -s simHuman_chr6.simHuman.chr6 252092 11 + 601863 AATTCTCTCTG -s simRat_chr6.simRat.chr6 262318 11 + 647215 AATTTACTCGT - -a -s simMouse_chr6.simMouse.chr6 273253 23 + 636262 CAGTAGCCTAGAATATTTTGGCC -s Anc0.Anc0refChr5 1568 23 - 87904 CATCAGCCCAGGATATTCTGACA -s Anc1.Anc1refChr7 1587 23 + 47259 CATCAGCCCAGGATATTCTGACA -s Anc2.Anc2refChr15 2832 23 - 86568 CATCAGCCCAGGATATTCTAACA -s mr.mrrefChr5 124824 23 + 294540 CAGTAGCCCAGAATATTTTGGCC -s simCow_chr6.simCow.chr6 336279 23 - 602619 CATCACCCCAGGATATTCTTACA -s simDog_chr6.simDog.chr6 337096 23 - 593897 CATAAGCCCAAGACATCCTAACA -s simHuman_chr6.simHuman.chr6 252112 23 + 601863 CATCAGCCCAGGATACTATGACA -s simRat_chr6.simRat.chr6 262329 14 + 647215 CAGTAGCCCAGAA---------C - -a -s simMouse_chr6.simMouse.chr6 273276 24 + 636262 CTACGCTTAATACAACTAAGCCAT -s Anc0.Anc0refChr5 1594 24 - 87904 CAACATCTACAACACTCACACCAT -s Anc1.Anc1refChr7 1613 24 + 47259 CAACATCTACAACACTCACACCAT -s Anc2.Anc2refChr15 2858 24 - 86568 CAACATCTACAACACTCACAGCAT -s mr.mrrefChr5 124847 24 + 294540 CTACACTTAATACAACTAAGCCAT -s simCow_chr6.simCow.chr6 336305 23 - 602619 CAACATCTACA-CACCCACAGCAT -s simDog_chr6.simDog.chr6 337122 24 - 593897 CAATATCTACTACACTCACAGCAT -s simHuman_chr6.simHuman.chr6 252138 24 + 601863 CAACATGTACAACACACATACCAT -s simRat_chr6.simRat.chr6 262343 24 + 647215 TTACATTTAATACAACTAAGCCAT - -a -s simMouse_chr6.simMouse.chr6 273300 9 + 636262 GCTGCTGGC -s Anc0.Anc0refChr5 1623 7 - 87904 TCTGCTA-- -s Anc1.Anc1refChr7 1642 7 + 47259 TCTGCTA-- -s Anc2.Anc2refChr15 2888 7 - 86568 TCTGCTA-- -s mr.mrrefChr5 124871 9 + 294540 TCTGCTGGT -s simCow_chr6.simCow.chr6 336334 7 - 602619 TCTGCTA-- -s simDog_chr6.simDog.chr6 337152 7 - 593897 TCTGCTA-- -s simHuman_chr6.simHuman.chr6 252167 7 + 601863 TCTGCTA-- -s simRat_chr6.simRat.chr6 262367 9 + 647215 TCCGCTGGT - -a -s simMouse_chr6.simMouse.chr6 273309 8 + 636262 ATTGCAAA -s Anc0.Anc0refChr5 1630 8 - 87904 ACTGTAAA -s Anc1.Anc1refChr7 1649 8 + 47259 ACTGTAAA -s Anc2.Anc2refChr15 2896 8 - 86568 ACTGTAGA -s mr.mrrefChr5 124880 8 + 294540 ATTGCAAA -s simCow_chr6.simCow.chr6 336342 8 - 602619 ATTATAGA -s simDog_chr6.simDog.chr6 337160 8 - 593897 ACAGTGGA -s simHuman_chr6.simHuman.chr6 252174 8 + 601863 AGTGTAAA -s simRat_chr6.simRat.chr6 262376 8 + 647215 ATTACAAA - -a -s simMouse_chr6.simMouse.chr6 273317 10 + 636262 ACAAGTGGCA -s Anc0.Anc0refChr5 1644 10 - 87904 AAAAGTGACA -s Anc1.Anc1refChr7 1663 10 + 47259 AAAAGTGACA -s Anc2.Anc2refChr15 2910 10 - 86568 AAAAGTGACA -s mr.mrrefChr5 124888 10 + 294540 ACAAGTGACA -s simCow_chr6.simCow.chr6 336356 10 - 602619 AAAAATGACA -s simDog_chr6.simDog.chr6 337174 10 - 593897 AGAAGCAACA -s simHuman_chr6.simHuman.chr6 252188 10 + 601863 AAAAGTGCCA -s simRat_chr6.simRat.chr6 262384 10 + 647215 ATAAGTGACA - -a -s simMouse_chr6.simMouse.chr6 273327 28 + 636262 AACAGCACACTTGAGTAGGGAAATCACC -s Anc0.Anc0refChr5 1654 28 - 87904 TACTGCATGCTTGGGCAGGTAACATACC -s Anc1.Anc1refChr7 1673 28 + 47259 TACTGCATGCTTGGGCAGGTAACATACC -s Anc2.Anc2refChr15 2920 28 - 86568 TACTGCATGCTTGGGCAGGTATCATACC -s mr.mrrefChr5 124898 28 + 294540 AACTGCACACTTGAGTAGGTAACTTACC -s simCow_chr6.simCow.chr6 336366 28 - 602619 TACAGCATGCTTGGGCAGGTGGCATACC -s simDog_chr6.simDog.chr6 337184 28 - 593897 TACTGTATGCTCAGGTAGACATCATACC -s simHuman_chr6.simHuman.chr6 252202 28 + 601863 CATTGCAGGCTTGGGCAGGTAACATACC -s simRat_chr6.simRat.chr6 262394 28 + 647215 GACTGCACACTTTAGAAGGTAGCTTACC - -a -s simMouse_chr6.simMouse.chr6 273355 1 + 636262 C -s Anc0.Anc0refChr5 1685 1 - 87904 C -s Anc1.Anc1refChr7 1704 1 + 47259 C -s Anc2.Anc2refChr15 2951 1 - 86568 C -s mr.mrrefChr5 124929 1 + 294540 C -s simCow_chr6.simCow.chr6 336397 1 - 602619 C -s simDog_chr6.simDog.chr6 337215 1 - 593897 C -s simHuman_chr6.simHuman.chr6 252233 1 + 601863 C -s simRat_chr6.simRat.chr6 262425 1 + 647215 C - -a -s simMouse_chr6.simMouse.chr6 273356 66 + 636262 AGCAGCTCCCCTGGTCATGAATCAAGATTGGTTCTAATCATTTATATGCAGCTCAGCTCATTAAAC -s Anc0.Anc0refChr5 1686 63 - 87904 AGC---ACCCCTGGTCATGAATTATGATTGGTTCTAACTATTTACATCCTGCTCAGTTCATTATAT -s Anc1.Anc1refChr7 1705 66 + 47259 AGCAGCACCCCTGGTCATGAATTATGATTGGTTCTAACTATTTACATCCTGCTCAGTTCATTATAT -s Anc2.Anc2refChr15 2952 63 - 86568 ACC---ACTCCTGGTCATGAATTATGATTGGTTCTAACTATTTACAACCTCCTCAGTTCATTATAT -s mr.mrrefChr5 124930 66 + 294540 AGCAGCTCCCCTGGTCATGAATCAAGATTGGTTCTAATTATTTATATGCAGCTCAGTTCATTAAAC -s simCow_chr6.simCow.chr6 336398 63 - 602619 ATC---ACTCATGTTCATGAATTATGATTGTTTCTATTTATTTACGACCGTCTCAGTTCATTATAT -s simDog_chr6.simDog.chr6 337216 50 - 593897 TCC---ACTCCTGGTCATGAATCACAATTGGCTCTAACTATTGACAACCTCCT------------- -s simHuman_chr6.simHuman.chr6 252235 66 + 601863 GGCAGCGCCCCTGGTGGCGAATTATGATAGGTTCTAAATATTTACATCCTGCTCAGTTCATTATAT -s simRat_chr6.simRat.chr6 262426 66 + 647215 AGCAGCTCCCCTGGTCATGAATCAAGATTGGTTCTGACTATTTATATGCAGCTTAGTTCATTAAAC - -a -s simMouse_chr6.simMouse.chr6 273422 1 + 636262 A -s Anc0.Anc0refChr5 1749 1 - 87904 A -s Anc1.Anc1refChr7 1771 1 + 47259 A -s Anc2.Anc2refChr15 3015 1 - 86568 A -s mr.mrrefChr5 124996 1 + 294540 A -s simCow_chr6.simCow.chr6 336511 1 - 602619 A -s simDog_chr6.simDog.chr6 337266 1 - 593897 A -s simHuman_chr6.simHuman.chr6 252301 1 + 601863 A -s simRat_chr6.simRat.chr6 262492 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 273423 29 + 636262 TTCAGATTGCTGCAGGGCCAAGCTGAGGT -s Anc0.Anc0refChr5 1757 29 - 87904 ATGACATTGCCCAACAGCCCAGTTGAGGT -s Anc1.Anc1refChr7 1779 29 + 47259 ATGACATTGCCCAACAGCCCAGTTGAGGT -s Anc2.Anc2refChr15 3039 29 - 86568 CTGACATTGCCCAACAGCCCAGTCGAGGT -s mr.mrrefChr5 124997 29 + 294540 ATGAGATTGCTGCAGGGCCCAGCTGAGGT -s simCow_chr6.simCow.chr6 336535 29 - 602619 CTGACTTTGCTCAACAGCCCAGTCAAGGT -s simDog_chr6.simDog.chr6 337290 29 - 593897 CTTACACTGCCCAACAGCCCAGTCGAGGT -s simHuman_chr6.simHuman.chr6 252309 29 + 601863 ATGACATTGCCCACCAGCCCAGTTGAGGT -s simRat_chr6.simRat.chr6 262493 29 + 647215 ATGAGATTGTTACAGGGCCCAGCTGAGGT - -a -s simMouse_chr6.simMouse.chr6 273452 18 + 636262 TGTGTTCTTGAGTAGCTG -s Anc0.Anc0refChr5 1786 17 - 87904 TGTGCC-TTAGGGGGCCA -s Anc1.Anc1refChr7 1808 18 + 47259 TGTGCCCTTAGGGGGCCA -s Anc2.Anc2refChr15 3068 17 - 86568 TGTGCC-TTGGGGGGCCA -s mr.mrrefChr5 125026 18 + 294540 TGTGTTCTTAAGTAGCTG -s simCow_chr6.simCow.chr6 336564 17 - 602619 GATGCC-CTTTGGGGCCA -s simDog_chr6.simDog.chr6 337330 17 - 593897 TGGGCC-TTGGGGGACCG -s simHuman_chr6.simHuman.chr6 252338 18 + 601863 TGTGCCCTTAGGGGGCCA -s simRat_chr6.simRat.chr6 262522 18 + 647215 TGTGTTCTTAAGTAGCAG - -a -s simMouse_chr6.simMouse.chr6 273470 7 + 636262 GATACTC -s Anc0.Anc0refChr5 1805 7 - 87904 GATGCTA -s Anc1.Anc1refChr7 1828 7 + 47259 GATGCTA -s Anc2.Anc2refChr15 3087 7 - 86568 GATGCTA -s mr.mrrefChr5 125046 7 + 294540 GATACTC -s simCow_chr6.simCow.chr6 336583 7 - 602619 GATCCTA -s simDog_chr6.simDog.chr6 337349 7 - 593897 GATGTTT -s simHuman_chr6.simHuman.chr6 252358 7 + 601863 GATGCTA -s simRat_chr6.simRat.chr6 262542 7 + 647215 GATACTT - -a -s simMouse_chr6.simMouse.chr6 273477 18 + 636262 TGGCATTGTAAGTTGAAT -s Anc0.Anc0refChr5 1813 18 - 87904 GGGCAATGTAAGTTGAAC -s Anc1.Anc1refChr7 1836 18 + 47259 GGGCAATGTAAGTTGAAC -s Anc2.Anc2refChr15 3095 18 - 86568 GGGCAATGTAACTTGAAC -s mr.mrrefChr5 125053 18 + 294540 TGGCATTGTAAGTTGAAT -s simCow_chr6.simCow.chr6 336591 18 - 602619 AGGGAATGTGACTTGAAC -s simDog_chr6.simDog.chr6 337357 18 - 593897 GCGCAATGTAACTTGAGC -s simHuman_chr6.simHuman.chr6 252366 18 + 601863 GGGCAATGTATGTTGGAA -s simRat_chr6.simRat.chr6 262549 18 + 647215 TGGCATTGTAAGTTAAAT - -a -s simMouse_chr6.simMouse.chr6 273495 8 + 636262 CTTTATTG -s Anc0.Anc0refChr5 1831 8 - 87904 CTTTATCG -s Anc1.Anc1refChr7 1854 8 + 47259 CTTTATCG -s Anc2.Anc2refChr15 3113 8 - 86568 ATTTATCG -s mr.mrrefChr5 125071 8 + 294540 CTTTATTG -s simCow_chr6.simCow.chr6 336609 8 - 602619 ATTAATTG -s simDog_chr6.simDog.chr6 337375 8 - 593897 ATTTACCG -s simHuman_chr6.simHuman.chr6 252752 2 + 601863 CT------ -s simRat_chr6.simRat.chr6 262567 8 + 647215 CTTTATGA - -a -s simMouse_chr6.simMouse.chr6 273503 63 + 636262 CTCCAGCTTAGGACAATAGAATGTGATACAAGGTACCTAGTAGATCAATTGATAATAAACGGT -s Anc0.Anc0refChr5 1839 63 - 87904 CCCCAGCTTAGCACACTATAATGTGATATGAGCCACCTAATGGATCAATTTATATGAAACAAT -s Anc1.Anc1refChr7 1862 63 + 47259 CCCCAGCTTAGCACACTATAATGTGATATGAGCCACCTAATGGATCAATTTATATGAAACAAT -s Anc2.Anc2refChr15 3122 63 - 86568 CCCTAGCTTAGCACACTATAATGTGAAATGAGCCACCTAATGGATCAATTTATACGAAGCAAT -s mr.mrrefChr5 125079 63 + 294540 CCCCAGCTTAGGACAATATAATGTGATACAAGGTACCTAATAGATCAATTGATATTAAACGGT -s simCow_chr6.simCow.chr6 336618 56 - 602619 CCCTAGCTTAGATCACTATA-TGTGAAATGAGCTGCCTAAGGGATCAATTTCCAGG------C -s simDog_chr6.simDog.chr6 337384 63 - 593897 CCCTAGCTTAGCACACTATAAAGTGAAATGAGCCACCTAGTGGATCAATTTATACGAAGCAAT -s simHuman_chr6.simHuman.chr6 252754 60 + 601863 ---CAGCTTAACACACTATAATGTAATATCAGTCACCAAATGGGTTACTTTATTTAAAACAAT -s simRat_chr6.simRat.chr6 262575 60 + 647215 CCCAAGCTTAGGATAAAATAATGTGATACATGG---CTAATAGATCAATTGATATGAAACGGT - -a -s simMouse_chr6.simMouse.chr6 273566 7 + 636262 AGAACGT -s Anc0.Anc0refChr5 1902 7 - 87904 AAATGCT -s Anc1.Anc1refChr7 1925 7 + 47259 AAATGCT -s Anc2.Anc2refChr15 3185 7 - 86568 AAATGAT -s mr.mrrefChr5 125142 7 + 294540 AGAACCT -s simCow_chr6.simCow.chr6 336674 7 - 602619 CAGTGAT -s simDog_chr6.simDog.chr6 337455 7 - 593897 AAATGAT -s simHuman_chr6.simHuman.chr6 252814 7 + 601863 AAATGCT -s simRat_chr6.simRat.chr6 262635 7 + 647215 AGAACCT - -a -s simMouse_chr6.simMouse.chr6 273573 20 + 636262 GCCAAAAGACTGACTCCCCT -s Anc0.Anc0refChr5 1911 20 - 87904 GCCAAAAGAGCAGCTCCCCT -s Anc1.Anc1refChr7 1934 20 + 47259 GCCAAAAGAGCAGCTCCCCT -s Anc2.Anc2refChr15 3194 20 - 86568 GCCATAAGAGCAGCTCCCCT -s mr.mrrefChr5 125149 20 + 294540 GCCAAAAGAGCAACTCCCCT -s simCow_chr6.simCow.chr6 336683 20 - 602619 GATATAAAAGCTGCGCACCA -s simDog_chr6.simDog.chr6 337464 20 - 593897 GCCATAAGAGCAGTTCCCCT -s simHuman_chr6.simHuman.chr6 252823 20 + 601863 GCCAAAAGAGCAGCTCCCCC -s simRat_chr6.simRat.chr6 262642 20 + 647215 GCCAAAAGAGCAACTCCCCT - -a -s simMouse_chr6.simMouse.chr6 273593 1 + 636262 A -s Anc0.Anc0refChr5 1931 1 - 87904 A -s Anc1.Anc1refChr7 1954 1 + 47259 A -s Anc2.Anc2refChr15 3214 1 - 86568 G -s mr.mrrefChr5 125169 1 + 294540 A -s simCow_chr6.simCow.chr6 336704 1 - 602619 G -s simDog_chr6.simDog.chr6 337484 1 - 593897 G -s simHuman_chr6.simHuman.chr6 252843 1 + 601863 A -s simRat_chr6.simRat.chr6 262662 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 273594 3 + 636262 CTA -s Anc0.Anc0refChr5 1932 3 - 87904 CTA -s Anc1.Anc1refChr7 1955 3 + 47259 CTA -s Anc2.Anc2refChr15 3215 3 - 86568 TCA -s mr.mrrefChr5 125170 3 + 294540 CTA -s simCow_chr6.simCow.chr6 336705 3 - 602619 TCA -s simDog_chr6.simDog.chr6 337485 3 - 593897 TCA -s simHuman_chr6.simHuman.chr6 252844 3 + 601863 CTA -s simRat_chr6.simRat.chr6 262670 3 + 647215 TTA - -a -s simMouse_chr6.simMouse.chr6 273597 9 + 636262 AGAGGATGG -s Anc0.Anc0refChr5 1948 9 - 87904 AGAGGCTGT -s Anc1.Anc1refChr7 1971 9 + 47259 AGAGGCTGT -s Anc2.Anc2refChr15 3231 9 - 86568 AGAGGCTGT -s mr.mrrefChr5 125173 9 + 294540 AGAGGATGG -s simCow_chr6.simCow.chr6 336724 9 - 602619 AGAAGCTGT -s simDog_chr6.simDog.chr6 337501 9 - 593897 AGAGGCTGT -s simHuman_chr6.simHuman.chr6 252860 9 + 601863 AGAGGCTGT -s simRat_chr6.simRat.chr6 262673 9 + 647215 AGAGGATGG - -a -s simMouse_chr6.simMouse.chr6 273606 5 + 636262 CCAAT -s Anc0.Anc0refChr5 1965 5 - 87904 CCAAT -s Anc1.Anc1refChr7 1988 5 + 47259 CCAAT -s Anc2.Anc2refChr15 3248 5 - 86568 CCAAT -s mr.mrrefChr5 125182 5 + 294540 CCAAT -s simCow_chr6.simCow.chr6 336741 5 - 602619 CCAAT -s simDog_chr6.simDog.chr6 337518 5 - 593897 CTGTT -s simHuman_chr6.simHuman.chr6 252877 5 + 601863 TCAAT -s simRat_chr6.simRat.chr6 262682 5 + 647215 CCAAT - -a -s simMouse_chr6.simMouse.chr6 273611 20 + 636262 TTGAGGCTAAATGTAGGGAT -s Anc0.Anc0refChr5 1978 20 - 87904 TTGAGGCCAAAACTAAGGAA -s Anc1.Anc1refChr7 2001 20 + 47259 TTGAGGCCAAAACTAAGGAA -s Anc2.Anc2refChr15 3261 20 - 86568 TTGGGGCCAAAACTAAGACA -s mr.mrrefChr5 125187 20 + 294540 TTGAGGCTAAAAGTAGGGAT -s simCow_chr6.simCow.chr6 336754 20 - 602619 TTTGCACTAAAACTAAGACA -s simDog_chr6.simDog.chr6 337531 20 - 593897 TTGGGGCCAACACTAAGACA -s simHuman_chr6.simHuman.chr6 252891 20 + 601863 TTGAGGCCAAAACTAAAGAA -s simRat_chr6.simRat.chr6 262687 20 + 647215 TTGAGGCTAAAATGAGGGAT - -a -s simMouse_chr6.simMouse.chr6 273631 11 + 636262 CTTTGACTGCA -s Anc0.Anc0refChr5 1999 11 - 87904 CTGTGACCTCA -s Anc1.Anc1refChr7 2022 11 + 47259 CTGTGACCTCA -s Anc2.Anc2refChr15 3282 11 - 86568 CTGTGACTTCA -s mr.mrrefChr5 125207 11 + 294540 CTTTGACCGCA -s simCow_chr6.simCow.chr6 336775 11 - 602619 CTGTAACTTCA -s simDog_chr6.simDog.chr6 337552 11 - 593897 CTGTGACTTCA -s simHuman_chr6.simHuman.chr6 252912 11 + 601863 CTGTGACCTCC -s simRat_chr6.simRat.chr6 262707 11 + 647215 CTTTGACCACA - -a -s simMouse_chr6.simMouse.chr6 273642 26 + 636262 GTGTCTGAGTGGTCACAATACCTATG -s Anc0.Anc0refChr5 2010 25 - 87904 GTCTGTGAGTGGTAACAATATCT-TG -s Anc1.Anc1refChr7 2033 25 + 47259 GTCTGTGAGTGGTAACAATATCT-TG -s Anc2.Anc2refChr15 3293 25 - 86568 GTCTGCAAGTGGTAACAATATCT-GG -s mr.mrrefChr5 125218 26 + 294540 GTGTCTGAGTGGTCACAATACCTATG -s simCow_chr6.simCow.chr6 336786 25 - 602619 GTTTGCAAGTGGTAACAATATCG-GG -s simDog_chr6.simDog.chr6 337563 25 - 593897 GTCTGCAAGTAGTAACAATATCT-GG -s simHuman_chr6.simHuman.chr6 252923 25 + 601863 GTCTGTGGGTGGTAACAATATTT-TG -s simRat_chr6.simRat.chr6 262725 26 + 647215 GTGTATGAACAGTTACAATACCTATG - -a -s simMouse_chr6.simMouse.chr6 273668 24 + 636262 CTGACAATCAACCAAATGGTGGCG -s Anc0.Anc0refChr5 2035 24 - 87904 CTGGCAAACAGCCAAATGGCGGTG -s Anc1.Anc1refChr7 2058 24 + 47259 CTGGCAAACAGCCAAATGGCGGTG -s Anc2.Anc2refChr15 3318 24 - 86568 CTGGCAAACAGCCAAATCGCGGTG -s mr.mrrefChr5 125244 24 + 294540 CTGACAATCAGCCAAATGGTGGCG -s simCow_chr6.simCow.chr6 336811 24 - 602619 GTGGTAAACAGCCAAATTGCGTTG -s simDog_chr6.simDog.chr6 337589 24 - 593897 CTGGCACACAACCAAGTCATGGTG -s simHuman_chr6.simHuman.chr6 252948 24 + 601863 TTGGCAAACAGCTAAATGGCAGTG -s simRat_chr6.simRat.chr6 262751 13 + 647215 CTGAGAATCAGCC----------- - -a -s simMouse_chr6.simMouse.chr6 273692 33 + 636262 CAGGAAGCATTGTCTCGGTAAGGCACCTTGGAA -s Anc0.Anc0refChr5 2064 33 - 87904 CAAGAGTCACAGTCATGGCCAGGCCCCTTAAGA -s Anc1.Anc1refChr7 2087 33 + 47259 CAAGAGTCACAGTCATGGCCAGGCCCCTTAAGA -s Anc2.Anc2refChr15 3347 33 - 86568 CCATAGTCACAGTCATGGCCAGGCCCATTAAGA -s mr.mrrefChr5 125268 33 + 294540 CAGGAAGCACTGTCTCGGTAAGGCACCTTAGAA -s simCow_chr6.simCow.chr6 336840 33 - 602619 CCTAAGTTACTGTCATGGTCAGGCCCACTAAGA -s simDog_chr6.simDog.chr6 337618 33 - 593897 CCATAGACACAGTCATGGCCACACGCATTGAGA -s simHuman_chr6.simHuman.chr6 252977 33 + 601863 CAAGAGTCACCATCGTGGCCAGGCCCCATAAGA -s simRat_chr6.simRat.chr6 262764 33 + 647215 CAGGAAACACTCTCTCGGTTAGTCACCTTAGAA - -a -s simMouse_chr6.simMouse.chr6 273725 18 + 636262 TTGCAAACATTCAGGCAG -s Anc0.Anc0refChr5 2105 18 - 87904 TTGTAAACATTCAGACAG -s Anc1.Anc1refChr7 2128 18 + 47259 TTGTAAACATTCAGACAG -s Anc2.Anc2refChr15 3388 18 - 86568 TTGTAAGCATTCAGACAG -s mr.mrrefChr5 125301 18 + 294540 TTGCAAACATTCAGGCAG -s simCow_chr6.simCow.chr6 336881 13 - 602619 TTTTAA-----CAGACAG -s simDog_chr6.simDog.chr6 337659 18 - 593897 TTGTAAGCATTCACACAG -s simHuman_chr6.simHuman.chr6 253018 18 + 601863 TTGTGAACATTCAGACAG -s simRat_chr6.simRat.chr6 262797 17 + 647215 -TGCAAACATTCAGGGAG - -a -s simMouse_chr6.simMouse.chr6 273743 4 + 636262 TCAC -s Anc0.Anc0refChr5 2123 4 - 87904 TCAC -s Anc1.Anc1refChr7 2146 4 + 47259 TCAC -s Anc2.Anc2refChr15 3406 4 - 86568 TCAC -s mr.mrrefChr5 125319 4 + 294540 TCAC -s simCow_chr6.simCow.chr6 336896 4 - 602619 TCAG -s simDog_chr6.simDog.chr6 337677 4 - 593897 TCAC -s simHuman_chr6.simHuman.chr6 253036 4 + 601863 TCAC -s simRat_chr6.simRat.chr6 262814 4 + 647215 TCAC - -a -s simMouse_chr6.simMouse.chr6 273747 34 + 636262 TCAGTACATTGCAATTGTATTCACCAACCCATTT -s Anc0.Anc0refChr5 2127 34 - 87904 TCAGTACACTTCAATTGTACTCATCAACACATTT -s Anc1.Anc1refChr7 2150 34 + 47259 TCAGTACACTTCAATTGTACTCATCAACACATTT -s Anc2.Anc2refChr15 3410 34 - 86568 TCAGTATGCTTCAATTGTGCTCATCAACACATTT -s mr.mrrefChr5 125323 34 + 294540 TCAGTACATTGCAATTGTATTCATCAACCCATTT -s simCow_chr6.simCow.chr6 336900 28 - 602619 TCAGTAT------ATTGTGCTCATCAGCACATTT -s simDog_chr6.simDog.chr6 337697 34 - 593897 TAAGTATGCTTCAATTGTGTTCATCAACACATTT -s simHuman_chr6.simHuman.chr6 253040 34 + 601863 TCAGTACAGTTCAATTGTACTCATCAATACATTT -s simRat_chr6.simRat.chr6 262818 34 + 647215 TCAGTACGTTGTAATTGTATTCATCAACCCATTT - -a -s simMouse_chr6.simMouse.chr6 273781 12 + 636262 TTAGAAGAGAAG -s Anc0.Anc0refChr5 2161 12 - 87904 TTATAAGAGCAG -s Anc1.Anc1refChr7 2184 12 + 47259 TTATAAGAGCAG -s Anc2.Anc2refChr15 3444 12 - 86568 TTATAAGACCAG -s mr.mrrefChr5 125357 12 + 294540 TTAGAAGAGCAG -s simCow_chr6.simCow.chr6 336929 12 - 602619 TTATAAGATCCA -s simDog_chr6.simDog.chr6 337731 12 - 593897 TTATAAGACTAG -s simHuman_chr6.simHuman.chr6 253074 12 + 601863 TTATAAGAGCAT -s simRat_chr6.simRat.chr6 262852 12 + 647215 TTAGAAGAGCTG - -a -s simMouse_chr6.simMouse.chr6 273793 20 + 636262 CATGTTGCTAATGTGCCCCA -s Anc0.Anc0refChr5 2173 20 - 87904 CATGTAGTTAATGTTACTCA -s Anc1.Anc1refChr7 2196 20 + 47259 CATGTAGTTAATGTTACTCA -s Anc2.Anc2refChr15 3457 20 - 86568 CATTTGGTTAATGTTACTCA -s mr.mrrefChr5 125369 20 + 294540 CATGTAGCTAATGTGCCCCA -s simCow_chr6.simCow.chr6 336942 20 - 602619 TATTTGGTTAATGTTAATCA -s simDog_chr6.simDog.chr6 337744 20 - 593897 CACTTGGTTAATATCACTTA -s simHuman_chr6.simHuman.chr6 253086 20 + 601863 CATGTAGTTGATGTTGCTCA -s simRat_chr6.simRat.chr6 262864 20 + 647215 CATGTAGCTAATGTGCCCAA - -a -s simMouse_chr6.simMouse.chr6 273813 5 + 636262 GGTTC -s Anc0.Anc0refChr5 2195 5 - 87904 TGTTC -s Anc1.Anc1refChr7 2218 5 + 47259 TGTTC -s Anc2.Anc2refChr15 3479 5 - 86568 TGTTC -s mr.mrrefChr5 125389 5 + 294540 GGTTC -s simCow_chr6.simCow.chr6 336964 5 - 602619 TATTC -s simDog_chr6.simDog.chr6 337766 5 - 593897 TGTCC -s simHuman_chr6.simHuman.chr6 253108 5 + 601863 TGTTC -s simRat_chr6.simRat.chr6 262884 5 + 647215 GGTCC - -a -s simMouse_chr6.simMouse.chr6 273818 7 + 636262 CACATAA -s Anc0.Anc0refChr5 2200 7 - 87904 CACATTG -s Anc1.Anc1refChr7 2223 7 + 47259 CACATTG -s Anc2.Anc2refChr15 3484 7 - 86568 CACATTG -s mr.mrrefChr5 125394 7 + 294540 CACATAA -s simCow_chr6.simCow.chr6 336969 7 - 602619 CACAATG -s simDog_chr6.simDog.chr6 337771 6 - 593897 CA-GTTG -s simHuman_chr6.simHuman.chr6 253113 7 + 601863 GACATTG -s simRat_chr6.simRat.chr6 262901 7 + 647215 CACATAA - -a -s simMouse_chr6.simMouse.chr6 273825 65 + 636262 CCTTATGATCCTAGTGACCTGGATCCACCACAGCTACTTGGCAGAGAGCTCCTTTGTAAAAATGA -s Anc0.Anc0refChr5 2208 61 - 87904 CCTAATGATCCTATTGACCTGGCTACGCTTGATCTGCCTGTCTGAAAGC--GTCTTCAA--ATGC -s Anc1.Anc1refChr7 2231 64 + 47259 CCTAATGATCCTATTGACCTGGCTACGCTTGATCTGCCTGTCTGAAAGC-CGTCTTCAAGAATGC -s Anc2.Anc2refChr15 3492 61 - 86568 CCTACTGATCCTATTAACCTGCCTATGCTTGATCTGACTGTCTGAAAGC--GTCTTCAA--ATAC -s mr.mrrefChr5 125401 65 + 294540 CCTTATGATCCTATTGACCTGGATCCACCACAGCTACTTGGCAGAGAGCTCCTTTGTAAGAATGA -s simCow_chr6.simCow.chr6 336977 60 - 602619 CCTACTGATCCTACTAATCTG-CTATGCTTGATCTGTCTGACTAAAGGC--CTCTTCAA--ATAT -s simDog_chr6.simDog.chr6 337778 53 - 593897 CCTACTGATCTTATTATCTTACCTAT--------TGATTGTGAGAAAGC--GTCTTCAA--ATAC -s simHuman_chr6.simHuman.chr6 253121 62 + 601863 CCTGATGATCCTATTGACCTGGCTACCCATGATCTGCCTGTCTGAAA---CATCTTCAAGAGTGC -s simRat_chr6.simRat.chr6 262908 65 + 647215 CCTTATGATCCTATTGACCTAGTTCCATCACAGCTACTTGGCAGAGAGCTCCTTTGCAAGAATGA - -a -s simMouse_chr6.simMouse.chr6 273890 16 + 636262 AAATTGGTCATAGCTA -s Anc0.Anc0refChr5 2276 13 - 87904 AAATTGTT---GGCTA -s Anc1.Anc1refChr7 2302 13 + 47259 AAATTGTT---GGCTA -s Anc2.Anc2refChr15 3560 13 - 86568 GATGTATT---GGTTA -s mr.mrrefChr5 125466 16 + 294540 AAATTGGTCATAGCTA -s simCow_chr6.simCow.chr6 337044 13 - 602619 CACATATT---GGTTA -s simDog_chr6.simDog.chr6 337838 13 - 593897 GATGTATC---GGTTA -s simHuman_chr6.simHuman.chr6 253190 13 + 601863 AAATTGTT---GGCTA -s simRat_chr6.simRat.chr6 262973 16 + 647215 AAATTGGTCATAGCTA - -a -s simMouse_chr6.simMouse.chr6 273906 18 + 636262 GAAAGAGCTTTGTGTGTA -s Anc0.Anc0refChr5 2289 18 - 87904 GGCTGAGCTCAACATGTA -s Anc1.Anc1refChr7 2315 18 + 47259 GGCTGAGCTCAACATGTA -s Anc2.Anc2refChr15 3573 18 - 86568 TGCTGAGCTCAACATATA -s mr.mrrefChr5 125482 18 + 294540 GAAAGAGCTCAGTGTGTA -s simCow_chr6.simCow.chr6 337057 18 - 602619 TGCTGGGCTTTGCATATA -s simDog_chr6.simDog.chr6 337851 18 - 593897 TGCTGAGCTCAACATATA -s simHuman_chr6.simHuman.chr6 253204 18 + 601863 GGTGGAGCTCAACTTGTA -s simRat_chr6.simRat.chr6 262989 18 + 647215 GAAAGAGCTCAGTGTGTA - -a -s simMouse_chr6.simMouse.chr6 273924 26 + 636262 CAACTGTAAAAATGGAATAGAAGTAG -s Anc0.Anc0refChr5 2335 26 - 87904 CAATCAGAATGATAGAATAGAAGTGG -s Anc1.Anc1refChr7 2361 26 + 47259 CAATCAGAATGATAGAATAGAAGTGG -s Anc2.Anc2refChr15 3619 26 - 86568 CTATCAGAATGATGGAATAGAATTGG -s mr.mrrefChr5 125528 26 + 294540 CAACTGTAAAAATAGAATAGAAGTGG -s simCow_chr6.simCow.chr6 337103 26 - 602619 GTATCAGAATGATGGCATAGAACTGG -s simDog_chr6.simDog.chr6 337897 26 - 593897 CTATCAGTATAATGGAATAGAATTGG -s simHuman_chr6.simHuman.chr6 253250 26 + 601863 CAATCAGAATGACAGAATAGAAGTGG -s simRat_chr6.simRat.chr6 263035 26 + 647215 CAACTGTAAATATAGAATAGAAGTGG - -a -s simMouse_chr6.simMouse.chr6 273950 19 + 636262 GAATCTTTGGGGAATAGAC -s Anc0.Anc0refChr5 2361 19 - 87904 GAATAGTTGGAGAATAGAC -s Anc1.Anc1refChr7 2387 19 + 47259 GAATAGTTGGAGAATAGAC -s Anc2.Anc2refChr15 3645 19 - 86568 AAACAGTCTGAGAATAGAC -s mr.mrrefChr5 125554 19 + 294540 GAATCTTTGGGGAATAGAC -s simCow_chr6.simCow.chr6 337129 19 - 602619 AAACAATCAGAGTATAAAC -s simDog_chr6.simDog.chr6 337923 19 - 593897 AAACAGTCTCAGAATAGAC -s simHuman_chr6.simHuman.chr6 253277 19 + 601863 GCGTGGTTGGAGAATAGAC -s simRat_chr6.simRat.chr6 263061 19 + 647215 GAATTTTTGGGGAATAGAC - -a -s simMouse_chr6.simMouse.chr6 273969 11 + 636262 ACTTGACCATA -s Anc0.Anc0refChr5 2380 11 - 87904 ATTTGTCAATA -s Anc1.Anc1refChr7 2406 11 + 47259 ATTTGTCAATA -s Anc2.Anc2refChr15 3664 11 - 86568 ATCTGTCAGTA -s mr.mrrefChr5 125573 11 + 294540 ACTTGTCCATA -s simCow_chr6.simCow.chr6 337148 11 - 602619 ATCTATCAGTG -s simDog_chr6.simDog.chr6 337943 10 - 593897 ATCAGTCA-TA -s simHuman_chr6.simHuman.chr6 253296 10 + 601863 -TTTGTCAATA -s simRat_chr6.simRat.chr6 263080 11 + 647215 ACTTGTCTATA - -a -s simMouse_chr6.simMouse.chr6 273980 31 + 636262 GGTCTGTCGAGACTTAGCTGTCCAGTAGGCA -s Anc0.Anc0refChr5 2391 6 - 87904 GGTCTG------------------------- -s Anc1.Anc1refChr7 2417 6 + 47259 GGTCTG------------------------- -s Anc2.Anc2refChr15 3676 6 - 86568 GGTCTG------------------------- -s mr.mrrefChr5 125584 6 + 294540 GGTCTG------------------------- -s simCow_chr6.simCow.chr6 337160 6 - 602619 GGTTTG------------------------- -s simDog_chr6.simDog.chr6 337954 6 - 593897 GGTCTG------------------------- -s simHuman_chr6.simHuman.chr6 253306 5 + 601863 AG-CTG------------------------- -s simRat_chr6.simRat.chr6 263091 6 + 647215 GATCTG------------------------- - -a -s simMouse_chr6.simMouse.chr6 274011 30 + 636262 GATTCATTATGGGGTACCTAGGAAGCCATG -s Anc0.Anc0refChr5 2401 30 - 87904 GACTCATTATGAGGTAGTTAAGAAGCCCTA -s Anc1.Anc1refChr7 2427 30 + 47259 GACTCATTATGAGGTAGTTAAGAAGCCCTA -s Anc2.Anc2refChr15 3686 30 - 86568 GACTCGTTATGAGATAGTTTAGAAGCCCTA -s mr.mrrefChr5 125590 30 + 294540 GACTCATTATGGGGTAGCTAGGAAGCCATG -s simCow_chr6.simCow.chr6 337166 30 - 602619 GACTCGTTATAAGTTAGCTGAGCAGCCCTA -s simDog_chr6.simDog.chr6 337972 27 - 593897 GACTCGTTATGAGATTGTTTAGAAGC---A -s simHuman_chr6.simHuman.chr6 253315 30 + 601863 GACACACGTTGTAGTAGTTAAGAAGCCCCA -s simRat_chr6.simRat.chr6 263097 30 + 647215 GACTCATTATGGCGTTGCTAGAAAGCTATG - -a -s simMouse_chr6.simMouse.chr6 274041 87 + 636262 TCTTGTGGATGATATGGATACAGCAGGCCACTTGGGTATAAAATCAGCCAACCTCTGCCATGCTTAATGTAAGGCACAACAGCCGCA -s Anc0.Anc0refChr5 2431 77 - 87904 TCTGGGGGATTATATGGATACAGGGGGCCTCT--GATAGAAAATTAACCAACTTGTACAA---TAAATA-----GATACCAGCCGCA -s Anc1.Anc1refChr7 2457 82 + 47259 TCTGGGGGATTATATGGATACAGGGGGCCTCTTGGATAGAAAATTAACCAACTTGTACAAGTTTAAATA-----GATACCAGCCGCA -s Anc2.Anc2refChr15 3716 77 - 86568 TCTGGGGGATTATATGGATACAGGGGGCCTCT--GATTGAGAATTAACCAACTTGTACAA---CAAATA-----GATACAAGCTGCA -s mr.mrrefChr5 125620 87 + 294540 TCTTGTGGATGATATGGATACAGCAGGCCACTTGGGTATAAAATCAGCCAACTTGTGCAAGGTTTAATGTAAGGGACAACAGCCGCA -s simCow_chr6.simCow.chr6 337200 73 - 602619 TTTGGGGGATTATAGGGATACAGGGGGCCTCT--GA----GTATCAACCAGCTTATAAAA---GAATTA-----ATCACAAGCTGCA -s simDog_chr6.simDog.chr6 337999 77 - 593897 TCTTGGGGAGTATATGGATGGAGGGGGCCTCT--GATTGAGAATTAGCTAACATGTACAA---CAAATG-----GATACAACTTGCA -s simHuman_chr6.simHuman.chr6 253345 82 + 601863 ACTGGGGGATTATCTGGATACAGTGGGCCCATTGACTAGAAAATAAACCAACTTGTACAAGTTTAAATA-----GATATCAGCCCCG -s simRat_chr6.simRat.chr6 263127 78 + 647215 GCTTG---------TGGGTACAGCAGGCCACTTAGGTATAAAATCAGACAACTTGTGCAAGGTTCAATGTAAGGGACAACAGCTGCA - -a -s simMouse_chr6.simMouse.chr6 274128 76 + 636262 CTATTTCTTATTCTACCTGATTGAGAAGGATAGTTCTTGGAATAATGTGGGACAAAGTTGAACTGGATATATGATT -s Anc0.Anc0refChr5 2509 76 - 87904 CTATTTGTTATTCTACCTGACTGAAAATGTTAGTTCTTGGGAAAATATGGGACAAAGTTGAACTGGGTCTATTATT -s Anc1.Anc1refChr7 2540 76 + 47259 CTATTTGTTATTCTACCTGACTGAAAATGTTAGTTCTTGGGAAAATATGGGACAAAGTTGAACTGGGTCTATTATT -s Anc2.Anc2refChr15 3794 76 - 86568 CTATTTGTTATTCTACCTGACTAAAAATGTTAGTTCTTGGGGAAATATGGGACAAAGTTAAACTGGGTCTATTTTT -s mr.mrrefChr5 125707 76 + 294540 CTATTTCTTATTCTACCTGATTGAAAAGGATAGTTCTTGGAATAATGTGGGACAAAGTTGAACTGGATCTATGATT -s simCow_chr6.simCow.chr6 337274 76 - 602619 CTATTTGTTATTCTACCTGACTAAAATTGTTAGTTCTTGGGGAAATATGGAGCAAAGTTCAAATGGGTCCATTGCT -s simDog_chr6.simDog.chr6 338077 73 - 593897 CTATTTGTTATTCTACCTGAAT---AATGTCAGTTGTTGGGGAGATGTGGGATAAAGTCAAACTGGGTCTATTTTT -s simHuman_chr6.simHuman.chr6 253428 76 + 601863 CTATTTGCTGTTCTACCTGACTGAAAATGTTAGTCCTTGGGAAAATAGAGGACAAAGTTGAACTGGGTCTATTATT -s simRat_chr6.simRat.chr6 263205 76 + 647215 CTATTTCTTATTTTACCTGATACAAAAGGATGGATCTTGGAGTAATGTGGGACGAAGTTGAACTGGACCTACGATT - -a -s simMouse_chr6.simMouse.chr6 274204 10 + 636262 TAGCAGCATC -s Anc0.Anc0refChr5 2592 10 - 87904 TAGCAGCATC -s Anc1.Anc1refChr7 2623 10 + 47259 TAGCAGCATC -s Anc2.Anc2refChr15 3877 10 - 86568 TAGCAGCATC -s mr.mrrefChr5 125783 10 + 294540 TAGCAGCATC -s simCow_chr6.simCow.chr6 337357 10 - 602619 TGGCAGCAAC -s simDog_chr6.simDog.chr6 338157 9 - 593897 AAACA-CTTA -s simHuman_chr6.simHuman.chr6 253511 10 + 601863 TAGCAGCAGC -s simRat_chr6.simRat.chr6 263281 10 + 647215 TAGCAGCTTC - -a -s simMouse_chr6.simMouse.chr6 274214 1 + 636262 C -s Anc0.Anc0refChr5 2602 1 - 87904 C -s Anc1.Anc1refChr7 2633 1 + 47259 C -s Anc2.Anc2refChr15 3887 1 - 86568 C -s mr.mrrefChr5 125793 1 + 294540 C -s simCow_chr6.simCow.chr6 337370 1 - 602619 C -s simDog_chr6.simDog.chr6 338166 1 - 593897 A -s simHuman_chr6.simHuman.chr6 253521 1 + 601863 C -s simRat_chr6.simRat.chr6 263291 1 + 647215 C - -a -s simMouse_chr6.simMouse.chr6 274215 14 + 636262 CCCAAAAAAAGTGG -s Anc0.Anc0refChr5 2653 8 - 87904 ------AAGAATGG -s Anc1.Anc1refChr7 2684 14 + 47259 TCCAAAAAGAATGG -s Anc2.Anc2refChr15 3938 8 - 86568 ------GAGAATGG -s mr.mrrefChr5 125794 14 + 294540 CCCAAAAAAAGTGG -s simCow_chr6.simCow.chr6 337420 8 - 602619 ------GAGAATTG -s simDog_chr6.simDog.chr6 338209 8 - 593897 ------GTGAACGG -s simHuman_chr6.simHuman.chr6 253575 14 + 601863 TCCAAAAACAATGG -s simRat_chr6.simRat.chr6 263292 14 + 647215 CCCAAAGAAAGTGG - -a -s simMouse_chr6.simMouse.chr6 274229 26 + 636262 TAAGTTGCTTCCGCGATCCCCTGTTA -s Anc0.Anc0refChr5 2661 6 - 87904 AAA--------------------TAA -s Anc1.Anc1refChr7 2698 6 + 47259 AAA--------------------TAA -s Anc2.Anc2refChr15 3947 6 - 86568 AAA--------------------TAA -s mr.mrrefChr5 125808 6 + 294540 TAA--------------------TAA -s simCow_chr6.simCow.chr6 337429 6 - 602619 AAG--------------------GAA -s simDog_chr6.simDog.chr6 338218 6 - 593897 CAA--------------------TAA -s simHuman_chr6.simHuman.chr6 253589 6 + 601863 AAG--------------------AAA -s simRat_chr6.simRat.chr6 263306 6 + 647215 TAA--------------------TAA - -a -s simMouse_chr6.simMouse.chr6 274255 9 + 636262 ATACCCAAT -s Anc0.Anc0refChr5 2667 9 - 87904 ATACCCAAC -s Anc1.Anc1refChr7 2704 9 + 47259 ATACCCAAC -s Anc2.Anc2refChr15 3953 9 - 86568 ATACCCAAC -s mr.mrrefChr5 125814 9 + 294540 ATACCCAAT -s simCow_chr6.simCow.chr6 337435 9 - 602619 ATATCCAAC -s simDog_chr6.simDog.chr6 338224 9 - 593897 ATACCCAAC -s simHuman_chr6.simHuman.chr6 253596 9 + 601863 ATTCCCAAC -s simRat_chr6.simRat.chr6 263312 9 + 647215 GTATCCAAT - -a -s simMouse_chr6.simMouse.chr6 274264 4 + 636262 GGAC -s Anc0.Anc0refChr5 2677 4 - 87904 GGAC -s Anc1.Anc1refChr7 2714 4 + 47259 GGAC -s Anc2.Anc2refChr15 3963 4 - 86568 GGAC -s mr.mrrefChr5 125823 4 + 294540 GGAC -s simCow_chr6.simCow.chr6 337445 4 - 602619 GGAA -s simDog_chr6.simDog.chr6 338234 4 - 593897 GGAC -s simHuman_chr6.simHuman.chr6 253606 4 + 601863 GGAC -s simRat_chr6.simRat.chr6 263321 4 + 647215 GGAC - -a -s simMouse_chr6.simMouse.chr6 274268 2 + 636262 TT -s Anc0.Anc0refChr5 2681 2 - 87904 TC -s Anc1.Anc1refChr7 2718 2 + 47259 TC -s Anc2.Anc2refChr15 3967 2 - 86568 TC -s mr.mrrefChr5 125827 2 + 294540 TT -s simCow_chr6.simCow.chr6 337456 2 - 602619 TC -s simDog_chr6.simDog.chr6 338238 2 - 593897 CT -s simHuman_chr6.simHuman.chr6 253610 2 + 601863 TC -s simRat_chr6.simRat.chr6 263325 2 + 647215 TT - -a -s simMouse_chr6.simMouse.chr6 274270 1 + 636262 G -s Anc0.Anc0refChr5 2684 1 - 87904 A -s Anc1.Anc1refChr7 2721 1 + 47259 A -s Anc2.Anc2refChr15 3970 1 - 86568 A -s mr.mrrefChr5 125829 1 + 294540 G -s simCow_chr6.simCow.chr6 337459 1 - 602619 A -s simDog_chr6.simDog.chr6 338241 1 - 593897 A -s simHuman_chr6.simHuman.chr6 253613 1 + 601863 A -s simRat_chr6.simRat.chr6 263327 1 + 647215 G - -a -s simMouse_chr6.simMouse.chr6 274271 51 + 636262 TTGAGTAAGTAAACCCATAATAGAGACTCTTCTTTGATGAACACTTATGGA -s Anc0.Anc0refChr5 2685 49 - 87904 TCGAGTAGGAAAACCCATAATAG-GT-TTTTCTTTAATGAACACTTATGCA -s Anc1.Anc1refChr7 2722 50 + 47259 TCGAGTAGGAAAACCCATAATAG-GTCTTTTCTTTAATGAACACTTATGCA -s Anc2.Anc2refChr15 3971 49 - 86568 TCTAGTAGGAAAACCCATAATAG-GT-GTTTCTTTAATGGACACTTATGCA -s mr.mrrefChr5 125830 51 + 294540 TTGAGTAAGTAAACCCATAATAGAGACTCTTCTTTAATGAACACTTATGGA -s simCow_chr6.simCow.chr6 337470 49 - 602619 CCCAGTAGGAAAATAAATAACCG-GT-GTTTCTTTAATGGACACTTAGGCA -s simDog_chr6.simDog.chr6 338242 49 - 593897 TCTAGTAGGAAAACCCATAATAG-GT-GCTTCTTTGATAGACACTTATGCA -s simHuman_chr6.simHuman.chr6 253614 50 + 601863 TCGAGTAGGGGGAGCCACAATAG-GCCTTTCTGTTAATGAGCACTGATGCA -s simRat_chr6.simRat.chr6 263328 51 + 647215 TTGAGTAAGTAAACCCATAATAGAGACTCTTCTTTAATGGACACCTATGGA - -a -s simMouse_chr6.simMouse.chr6 274322 15 + 636262 AAAGACATAAGGTAC -s Anc0.Anc0refChr5 2747 1 - 87904 --------------G -s Anc1.Anc1refChr7 2785 15 + 47259 AGAACCATAATGTAG -s Anc2.Anc2refChr15 4033 1 - 86568 --------------G -s mr.mrrefChr5 125881 15 + 294540 AAAGACATAAGGTAC -s simCow_chr6.simCow.chr6 337532 1 - 602619 --------------G -s simDog_chr6.simDog.chr6 338304 1 - 593897 --------------G -s simHuman_chr6.simHuman.chr6 253775 15 + 601863 AGAACCATAATGTAG -s simRat_chr6.simRat.chr6 263379 15 + 647215 AAAGACATAAGGTAC - -a -s simMouse_chr6.simMouse.chr6 274337 5 + 636262 TTAGA -s Anc0.Anc0refChr5 2748 5 - 87904 TGTCA -s Anc1.Anc1refChr7 2800 5 + 47259 TGTCA -s Anc2.Anc2refChr15 4034 5 - 86568 TGTCA -s mr.mrrefChr5 125896 5 + 294540 TTTGA -s simCow_chr6.simCow.chr6 337535 5 - 602619 TGTTG -s simDog_chr6.simDog.chr6 338305 5 - 593897 TGTCA -s simHuman_chr6.simHuman.chr6 253790 5 + 601863 TGTAA -s simRat_chr6.simRat.chr6 263394 5 + 647215 TTTGA - -a -s simMouse_chr6.simMouse.chr6 274342 11 + 636262 ATTTAGGGTTG -s Anc0.Anc0refChr5 2764 10 - 87904 -GTTAGGTACC -s Anc1.Anc1refChr7 2816 11 + 47259 AGTTAGGTACC -s Anc2.Anc2refChr15 4050 10 - 86568 -GTTAGGTACC -s mr.mrrefChr5 125901 11 + 294540 ATTTAGGATTG -s simCow_chr6.simCow.chr6 337550 10 - 602619 -ATCAGGTACC -s simDog_chr6.simDog.chr6 338321 10 - 593897 -GTTAGGTACC -s simHuman_chr6.simHuman.chr6 253806 11 + 601863 AGTTTGGGACC -s simRat_chr6.simRat.chr6 263399 11 + 647215 ATTTAGGATTG - -a -s simMouse_chr6.simMouse.chr6 274353 6 + 636262 ATGCCT -s Anc0.Anc0refChr5 2774 6 - 87904 AGGCCT -s Anc1.Anc1refChr7 2827 6 + 47259 AGGCCT -s Anc2.Anc2refChr15 4060 6 - 86568 AGGCCT -s mr.mrrefChr5 125912 6 + 294540 ATGCCT -s simDog_chr6.simDog.chr6 338339 6 - 593897 AGGCCT -s simHuman_chr6.simHuman.chr6 253817 6 + 601863 AGTGCT -s simRat_chr6.simRat.chr6 263410 6 + 647215 ATGCCT - -a -s simMouse_chr6.simMouse.chr6 274359 20 + 636262 CCTCATCCCCTGTTACCAAA -s Anc0.Anc0refChr5 2781 20 - 87904 CCCCATCCCATCTTACCAAA -s Anc1.Anc1refChr7 2834 20 + 47259 CCCCATCCCATCTTACCAAA -s Anc2.Anc2refChr15 4067 20 - 86568 GCCCAACCCATCTTACCAGA -s mr.mrrefChr5 125918 20 + 294540 CCCCATCCCCTGTTACCAAA -s simCow_chr6.simCow.chr6 337560 12 - 602619 --------CATCTTAATGGA -s simDog_chr6.simDog.chr6 338346 20 - 593897 GCCCAACCCATCTTACCAGA -s simHuman_chr6.simHuman.chr6 253824 20 + 601863 CCCCATCTCATCTTACCAAA -s simRat_chr6.simRat.chr6 263416 19 + 647215 GCCCATCCCCTGTCACC-AA - -a -s simMouse_chr6.simMouse.chr6 274379 9 + 636262 ACTAATTTC -s Anc0.Anc0refChr5 2801 8 - 87904 -CAAATATC -s Anc1.Anc1refChr7 2854 9 + 47259 ACAAATATC -s Anc2.Anc2refChr15 4087 8 - 86568 -CAAATATT -s mr.mrrefChr5 125938 9 + 294540 ACTAATATC -s simCow_chr6.simCow.chr6 337572 8 - 602619 -CAAAGATC -s simDog_chr6.simDog.chr6 338366 8 - 593897 -CAAATATT -s simHuman_chr6.simHuman.chr6 253860 9 + 601863 ATAAGTATC -s simRat_chr6.simRat.chr6 263435 9 + 647215 ACTCATATC - -a -s simMouse_chr6.simMouse.chr6 274388 5 + 636262 ATCAA -s Anc0.Anc0refChr5 2809 5 - 87904 ATTCA -s Anc1.Anc1refChr7 2863 5 + 47259 ATTCA -s Anc2.Anc2refChr15 4095 5 - 86568 GTTCA -s mr.mrrefChr5 125947 5 + 294540 ATCAA -s simCow_chr6.simCow.chr6 337580 5 - 602619 ACTCA -s simDog_chr6.simDog.chr6 338375 5 - 593897 GTTCA -s simHuman_chr6.simHuman.chr6 253869 5 + 601863 ATTCA -s simRat_chr6.simRat.chr6 263444 5 + 647215 ATCAA - -a -s simMouse_chr6.simMouse.chr6 274393 11 + 636262 AAGCTGCATGA -s Anc0.Anc0refChr5 2814 4 - 87904 ATCC------- -s Anc1.Anc1refChr7 2868 11 + 47259 ATCCTGAGTGA -s Anc2.Anc2refChr15 4100 4 - 86568 ATCT------- -s mr.mrrefChr5 125952 11 + 294540 AAGCTGCATGA -s simCow_chr6.simCow.chr6 337598 4 - 602619 ATAT------- -s simDog_chr6.simDog.chr6 338380 4 - 593897 ATCT------- -s simHuman_chr6.simHuman.chr6 253874 11 + 601863 AGCCTGAGTGA -s simRat_chr6.simRat.chr6 263449 11 + 647215 AAGCTGCATAA - -a -s simMouse_chr6.simMouse.chr6 274404 41 + 636262 CAAATGTAACAAACTCAACATTAACAGAGTGTACCCAATGG -s Anc0.Anc0refChr5 2818 39 - 87904 AATGTTAAACTCACACCACATTAACAAAGTGTA--AGAGGG -s Anc1.Anc1refChr7 2879 39 + 47259 AATGTTAAACTCACACCACATTAACAAAGTGTA--AGAGGG -s Anc2.Anc2refChr15 4104 39 - 86568 AATGTTAAACTCACACCACATTAACAAAGTGTA--AGAGGG -s mr.mrrefChr5 125963 39 + 294540 AAAGTTTAACAAACTCAACATTAACAGAGTGTA--CGATGG -s simCow_chr6.simCow.chr6 337602 38 - 602619 AATGTTAAACTCACATCACCTTA-TAAAGCATG--AGGGGG -s simDog_chr6.simDog.chr6 338384 39 - 593897 AATGTTACACTCACACCATACTAACAAAGTGTA--AGAGGG -s simHuman_chr6.simHuman.chr6 253891 38 + 601863 AATGCTAAACTCACACCACATTAACGAAGTGTA---GAGGG -s simRat_chr6.simRat.chr6 263460 39 + 647215 AAAGTTTAACAAACTCAACAATAACAGAGTGTA--TGGTGG - -a -s simMouse_chr6.simMouse.chr6 274445 9 + 636262 GTGCCCTTC -s Anc0.Anc0refChr5 2857 9 - 87904 ATGCCCTTC -s Anc1.Anc1refChr7 2918 9 + 47259 ATGCCCTTC -s Anc2.Anc2refChr15 4145 9 - 86568 ATGCCCTTC -s mr.mrrefChr5 126002 9 + 294540 ATGCCCTTC -s simCow_chr6.simCow.chr6 337642 9 - 602619 ATGCCCTGC -s simDog_chr6.simDog.chr6 338425 9 - 593897 ATGCCCTTC -s simHuman_chr6.simHuman.chr6 253929 9 + 601863 AAGCCCTTC -s simRat_chr6.simRat.chr6 263499 9 + 647215 ATGCCCTTC - -a -s simMouse_chr6.simMouse.chr6 274454 56 + 636262 TTTGTGCAGTATGATGGATTCCCGCCCTCAATACAGCCTGACAGGAGGCAGCAGCT -s Anc0.Anc0refChr5 2866 54 - 87904 A--GAGGAGTATGATGGGTTGCAGTGCTCAGTAGGGGCTGATAGGAAACAGTATCT -s Anc1.Anc1refChr7 2927 54 + 47259 A--GAGGAGTATGATGGGTTGCAGTGCTCAGTAGGGGCTGATAGGAAACAGTATCT -s Anc2.Anc2refChr15 4154 54 - 86568 A--CAGGAGTATGATGGGGTGCAGTGCTCAGGAGGGGCTGATAGGAAACAGTATCT -s mr.mrrefChr5 126011 56 + 294540 TTTGTGCAGTATGATGGATTCCAGCCCTCAATACAGCCTGACAGGAGGCAGCAGCT -s simCow_chr6.simCow.chr6 337651 54 - 602619 G--CGGGAGTATGCTGGGATGCACTCCTTAGGGGGGGCTGCTAGGAGAAAGTATCT -s simDog_chr6.simDog.chr6 338436 54 - 593897 A--CAGGAGTATGATGGAGGTTAGTGTTCAGGAGGGGCTGATAGGAAACAGCATCT -s simHuman_chr6.simHuman.chr6 253938 54 + 601863 A--GAGGAGTATGATGGGTTGCAGTTCTCAGTAGGGGCTGATAGGAAACAGTGTCT -s simRat_chr6.simRat.chr6 263508 56 + 647215 TTTGTGCAGTATGATGGACTCCAGCCCTCAATACAGACTAACAAAAGGCTGCAACT - -a -s simMouse_chr6.simMouse.chr6 274510 2 + 636262 AA -s Anc0.Anc0refChr5 2921 2 - 87904 AA -s Anc1.Anc1refChr7 2982 2 + 47259 AA -s Anc2.Anc2refChr15 4209 2 - 86568 AA -s mr.mrrefChr5 126068 2 + 294540 AA -s simCow_chr6.simCow.chr6 337706 2 - 602619 AA -s simDog_chr6.simDog.chr6 338491 2 - 593897 AT -s simHuman_chr6.simHuman.chr6 253993 2 + 601863 AA -s simRat_chr6.simRat.chr6 263565 2 + 647215 AA - -a -s simMouse_chr6.simMouse.chr6 274512 98 + 636262 CACATAAATTGCAGTCAAATTGTCAATAGGTGGAATAGAAGCTTAGTGCTGTCATGGTGCAAGAAAATTCAAACATAGCAATATTAGGCAGCTTATGA -s Anc0.Anc0refChr5 2924 97 - 87904 CACATAAATTGCAGTCAAATTGTTGATAAGTGGGAGAGAAGCCTGATCATGCTCTGGTGCAAGAAAATTCAAACATAAGGACAT-ATGCAGCCTACTA -s Anc1.Anc1refChr7 2985 97 + 47259 CACATAAATTGCAGTCAAATTGTTGATAAGTGGGAGAGAAGCCTGATCATGCTCTGGTGCAAGAAAATTCAAACATAAGGACAT-ATGCAGCCTACTA -s Anc2.Anc2refChr15 4212 97 - 86568 CACACAAATTGCAGTCAAATTGTTGATAAGTGGGAGAGAAGCCTGATCATTCTCTGCTGCAAGAAAACTCAAACATAAGGATAT-ATACAGCCTACTA -s mr.mrrefChr5 126070 98 + 294540 CACATAAATTGCAGTCAAATTGTCAATAGGTGGAATAGAAGCTTAGTGCTGTTATGGTGCAAGAAAATTCAAACATAACAACATTAGGCAGCTTATGA -s simCow_chr6.simCow.chr6 337709 89 - 602619 CGCACAAATTGCAGTCCAATTGTTGATCAGCAGGCGAGAATCTTGATCATTCCTTG--------AGACTCAAACACAAGGATGT-ATACAGCTTGTTA -s simDog_chr6.simDog.chr6 338494 97 - 593897 CACACAAATTGCAGTCAAATTATTGATAAGTGGGAGAGAAGCCAGGTCATTCTCTGCTGCAAGAAAACTCACACATAAGGATAG-ATACAGCCTACTA -s simHuman_chr6.simHuman.chr6 253996 97 + 601863 CACATAAATTGCGGTCATATTGCTGATAAGTGGGAGAGAAGCCTGATTGTGCTCTGGTGCAAGAAAATTTAAGCATGAGGACAT-ATGCAGCCTACTA -s simRat_chr6.simRat.chr6 263567 98 + 647215 CACGTAAATTGCAGTTAAATTGTCAATAGGTGGACAAGAAGCTTAGTGCTGTTATGGTGCATGAAGATTCAAACATAACAACATTAAGCAGCTTATGA - -a -s simMouse_chr6.simMouse.chr6 274610 10 + 636262 GACAAGATGT -s Anc0.Anc0refChr5 3046 7 - 87904 GT---GGTAC -s Anc1.Anc1refChr7 3107 10 + 47259 GTTGAGGTAC -s Anc2.Anc2refChr15 4334 7 - 86568 GT---GGTAT -s mr.mrrefChr5 126168 10 + 294540 GATGAGATGC -s simCow_chr6.simCow.chr6 337823 7 - 602619 GT---GGTAT -s simDog_chr6.simDog.chr6 338616 7 - 593897 GT---GGTAT -s simHuman_chr6.simHuman.chr6 254118 10 + 601863 GCTGAGGTAC -s simRat_chr6.simRat.chr6 263665 10 + 647215 GATGAGATGC - -a -s simMouse_chr6.simMouse.chr6 274620 29 + 636262 GAACCTAGCCTAAAAAAGATATGTGCTGA -s Anc0.Anc0refChr5 3057 29 - 87904 GGACTGAGCATAAAAAAAGTATGTGCTGA -s Anc1.Anc1refChr7 3121 29 + 47259 GGACTGAGCATAAAAAAAGTATGTGCTGA -s Anc2.Anc2refChr15 4345 29 - 86568 GGACTGAGCATAAAAAAAATATGTGCTGA -s mr.mrrefChr5 126178 29 + 294540 GGACCTAGCCTAAAAAAGGTATGTGCTGA -s simCow_chr6.simCow.chr6 337834 29 - 602619 GGTCTTAGCATAAAGGAGATTTGTGCTGA -s simDog_chr6.simDog.chr6 338627 29 - 593897 GGACGGAGTATTAAAAAAATATCTGCTGA -s simHuman_chr6.simHuman.chr6 254132 29 + 601863 GGACTGAGCACAAAAAACGTGTGAGCTGA -s simRat_chr6.simRat.chr6 263675 29 + 647215 GGACCTAGCCTAAAAAAGGTATGTGCTGA - -a -s simMouse_chr6.simMouse.chr6 274649 49 + 636262 TATATATCATGTTCCACCCTTTGTAGAGGGGCCCTACATCCCCTGTGGT -s Anc0.Anc0refChr5 3086 47 - 87904 TATA--TCATGTTCTACCCATTGAAGTGGACCACTATATCCTCTGTGAT -s Anc1.Anc1refChr7 3150 47 + 47259 TATA--TCATGTTCTACCCATTGAAGTGGACCACTATATCCTCTGTGAT -s Anc2.Anc2refChr15 4374 47 - 86568 TATT--TCATGTTCTACCCATTGAAGTGGACCACTATATCCTCTGTGAT -s mr.mrrefChr5 126207 49 + 294540 TATATATCATGTTCCACCCTTTGTAGAGGGCCCCTACATCCTCTGTGAT -s simCow_chr6.simCow.chr6 337863 47 - 602619 TATG--TCATGTTCTACCCATTGAAGTGGACCACTTTATCCTCTGTGAT -s simDog_chr6.simDog.chr6 338656 47 - 593897 TATT--TCATGTTCTACCCATTGAAGTGGACCACTATCTCCTCTGTGAC -s simHuman_chr6.simHuman.chr6 254161 46 + 601863 TGAA--TCATGTTCTGCCCATTGAAGTGGACCACTATATCCTC-ATGAT -s simRat_chr6.simRat.chr6 263710 49 + 647215 TACATATCATGTTCCACCCTTTGTAGCAGGCCCCTACATCCTCTGTGAT - -a -s simMouse_chr6.simMouse.chr6 274698 10 + 636262 ATGGGATCTA -s Anc0.Anc0refChr5 3142 10 - 87904 ATGGAATTTA -s Anc1.Anc1refChr7 3206 10 + 47259 ATGGAATTTA -s Anc2.Anc2refChr15 4444 10 - 86568 ATGGAATTTA -s mr.mrrefChr5 126256 10 + 294540 ATGGGATTTA -s simCow_chr6.simCow.chr6 337933 10 - 602619 ATGGAATCTA -s simDog_chr6.simDog.chr6 338726 10 - 593897 ATGGAATTCT -s simHuman_chr6.simHuman.chr6 254216 10 + 601863 AGGGAATTTA -s simRat_chr6.simRat.chr6 263759 10 + 647215 ATAGGATTTA - -a -s simMouse_chr6.simMouse.chr6 274708 35 + 636262 TTGAAGATCATCATAGTATGTAAAACACAGTGGCA -s Anc0.Anc0refChr5 3152 35 - 87904 CAGAAGACCATTATAGCAGGAAAGACACAAGAGCA -s Anc1.Anc1refChr7 3216 35 + 47259 CAGAAGACCATTATAGCAGGAAAGACACAAGAGCA -s Anc2.Anc2refChr15 4454 35 - 86568 CAGAAGACCATTATAGCAGGAAAGACACAAGAGCA -s mr.mrrefChr5 126266 35 + 294540 TTGAAGATCATCATAGTATGTAAAACACAATGGCA -s simCow_chr6.simCow.chr6 337948 35 - 602619 CAGAAGACCATTATAGCAAAAAAAACACAAGGGCA -s simDog_chr6.simDog.chr6 338736 23 - 593897 C------------TAGCAGGAAAGACACAAGACAG -s simHuman_chr6.simHuman.chr6 254226 35 + 601863 CATAAGACAATGATAGAAGGAAAGACACAAGAGCA -s simRat_chr6.simRat.chr6 263769 35 + 647215 TTGAAGATCATCATGGTATATAAAACGCAATGGCA - -a -s simMouse_chr6.simMouse.chr6 274743 6 + 636262 ATCTGT -s Anc0.Anc0refChr5 3198 5 - 87904 ATC-TC -s Anc1.Anc1refChr7 3262 5 + 47259 ATC-TC -s Anc2.Anc2refChr15 4500 5 - 86568 ACT-TC -s mr.mrrefChr5 126301 5 + 294540 ATC-GT -s simCow_chr6.simCow.chr6 337987 5 - 602619 ACT-TC -s simDog_chr6.simDog.chr6 338770 5 - 593897 ACT-TC -s simHuman_chr6.simHuman.chr6 254275 5 + 601863 ATC-CC -s simRat_chr6.simRat.chr6 263804 5 + 647215 ATC-GG - -a -s simMouse_chr6.simMouse.chr6 274749 48 + 636262 AATCTGTATAAGAAGGGCACCAATAGTGAGTAGGGAGTAATGTATGTA -s Anc0.Anc0refChr5 3203 35 - 87904 AGTCTGCATAAGA---GCACTAATGGT-------GAGT---GTATGTA -s Anc1.Anc1refChr7 3267 35 + 47259 AGTCTGCATAAGA---GCACTAATGGT-------GAGT---GTATGTA -s Anc2.Anc2refChr15 4505 35 - 86568 AGTCTGCATAAGA---GCACTAATGGT-------GAGT---GTATGTA -s mr.mrrefChr5 126306 41 + 294540 AATCTGTATAAGAAGAGCACCAATAGT-------GAGTAATGTATGTA -s simCow_chr6.simCow.chr6 337993 35 - 602619 AGTCTCCATAATA---TCACTAATCGT-------GAGC---ATATGTA -s simDog_chr6.simDog.chr6 338775 35 - 593897 AGACTGCATAAGA---GCACTGTAGGT-------GATT---GTATATA -s simHuman_chr6.simHuman.chr6 254280 35 + 601863 AGTCTGCATAAGA---GCACTAATGGT-------GAGT---GTATGTG -s simRat_chr6.simRat.chr6 263809 41 + 647215 AATCTGTATAAGAAGAGCATCAATAGT-------GAATAATGTATATA - -a -s simMouse_chr6.simMouse.chr6 274797 35 + 636262 TGACCTAGGATTATCTTGGCACGCCTTAAGGCTAA -s Anc0.Anc0refChr5 3239 34 - 87904 TGATCTGGAATTACCTTGGTA-GCTTTAAGCCTAA -s Anc1.Anc1refChr7 3303 35 + 47259 TGATCTGGAATTACCTTGGTAAGCTTTAAGCCTAA -s Anc2.Anc2refChr15 4541 34 - 86568 TGATCTGGAATTACCTTGGTA-GCTTTAGGCCTAA -s mr.mrrefChr5 126347 35 + 294540 TGACCTGGGATTATCTTGGCACGCCTTAAGGCTAA -s simCow_chr6.simCow.chr6 338029 34 - 602619 TGATCTGGAATTATCTTGGTA-GCCTTAGGCCTAA -s simDog_chr6.simDog.chr6 338811 34 - 593897 TGATCTGGAATTACCTTGGTA-GTTTTAGGCCTAA -s simHuman_chr6.simHuman.chr6 254316 35 + 601863 TGATGTGGAATTAGCATGGTAAGCTATAACACTAA -s simRat_chr6.simRat.chr6 263850 35 + 647215 TGACCTGTGATTATATTGGCACACCTTAAGGCTAA - -a -s simMouse_chr6.simMouse.chr6 274832 7 + 636262 TCTGTTA -s Anc0.Anc0refChr5 3277 7 - 87904 TCAATGA -s Anc1.Anc1refChr7 3342 7 + 47259 TCAATGA -s Anc2.Anc2refChr15 4579 7 - 86568 TTAATGA -s mr.mrrefChr5 126386 7 + 294540 TCTGTTA -s simCow_chr6.simCow.chr6 338067 7 - 602619 TTAATGA -s simDog_chr6.simDog.chr6 338849 7 - 593897 TTAATGA -s simHuman_chr6.simHuman.chr6 254355 7 + 601863 TCAATGA -s simRat_chr6.simRat.chr6 263889 7 + 647215 TATGTTA - -a -s simMouse_chr6.simMouse.chr6 274839 11 + 636262 CCGAAAGTAAG -s Anc0.Anc0refChr5 3297 7 - 87904 CAGGAGG---- -s Anc1.Anc1refChr7 3362 11 + 47259 CAGGAGGTAAG -s Anc2.Anc2refChr15 4599 7 - 86568 TAAGAGA---- -s mr.mrrefChr5 126393 11 + 294540 CCGAAAGTAAG -s simCow_chr6.simCow.chr6 338087 7 - 602619 TAAGACA---- -s simDog_chr6.simDog.chr6 338869 7 - 593897 TAAGAGA---- -s simHuman_chr6.simHuman.chr6 254375 11 + 601863 CAGGAGGTAAG -s simRat_chr6.simRat.chr6 263896 11 + 647215 CCGAAAGTAAG - -a -s simMouse_chr6.simMouse.chr6 274850 3 + 636262 GTG -s Anc0.Anc0refChr5 3304 3 - 87904 GTG -s Anc1.Anc1refChr7 3373 3 + 47259 GTG -s Anc2.Anc2refChr15 4606 3 - 86568 GGG -s mr.mrrefChr5 126404 3 + 294540 GTG -s simCow_chr6.simCow.chr6 338095 3 - 602619 AGG -s simDog_chr6.simDog.chr6 338876 3 - 593897 GGG -s simHuman_chr6.simHuman.chr6 254386 3 + 601863 GTG -s simRat_chr6.simRat.chr6 263907 3 + 647215 GTG - -a -s simMouse_chr6.simMouse.chr6 274853 17 + 636262 TTGTAGCCTTGACATAA -s Anc0.Anc0refChr5 3307 17 - 87904 TTACATTCTTGACATAA -s Anc1.Anc1refChr7 3376 17 + 47259 TTACATTCTTGACATAA -s Anc2.Anc2refChr15 4609 17 - 86568 TTACATTCTTAACATAA -s mr.mrrefChr5 126407 17 + 294540 TTGTATCCTTGACATAA -s simCow_chr6.simCow.chr6 338098 17 - 602619 TTACATGCTTAACATAA -s simDog_chr6.simDog.chr6 338879 17 - 593897 CTGCATTTTTAACATAC -s simHuman_chr6.simHuman.chr6 254389 17 + 601863 TAACATTCTTGACATAA -s simRat_chr6.simRat.chr6 263911 17 + 647215 TTGTATCCTTTACATAA - -a -s simMouse_chr6.simMouse.chr6 274870 16 + 636262 GGGGCCCCACTTCTAG -s Anc0.Anc0refChr5 3333 16 - 87904 ATGGCCCCATGACTAG -s Anc1.Anc1refChr7 3402 16 + 47259 ATGGCCCCATGACTAG -s Anc2.Anc2refChr15 4635 16 - 86568 ATAGACCCATGACTAG -s mr.mrrefChr5 126424 16 + 294540 GTGGCCCCATGTCTAG -s simCow_chr6.simCow.chr6 338123 16 - 602619 ACAGTCCCATGTCTAG -s simDog_chr6.simDog.chr6 338905 16 - 593897 ATAGACCCAAGACAAG -s simHuman_chr6.simHuman.chr6 254415 16 + 601863 ATGGCCCCATGACTAG -s simRat_chr6.simRat.chr6 263928 15 + 647215 GTGGCCCCATGTCTA- - -a -s simMouse_chr6.simMouse.chr6 274886 47 + 636262 GGGGGGTGATACCTGCAGTATTTCAGGTAGAAAGCATTGCCTAGATG -s Anc0.Anc0refChr5 3355 47 - 87904 GGGGGGTAACACACACTGTATTTGGGTTAGTGAGCATTGCCTTGATG -s Anc1.Anc1refChr7 3424 47 + 47259 GGGGGGTAACACACACTGTATTTGGGTTAGTGAGCATTGCCTTGATG -s Anc2.Anc2refChr15 4657 47 - 86568 AGGGGGTAACATACACTGTATTTGGGTTAGTGTGCATTGCCTCAATG -s mr.mrrefChr5 126440 47 + 294540 GGGGGGTGACACCCACAGTATTTCAGGTAGTAAGCATTGCCTTGATG -s simCow_chr6.simCow.chr6 338141 45 - 602619 --GGGGTGACATGCACTGTATTTGGGTTGGTGTTCAATGCTGCAGTG -s simDog_chr6.simDog.chr6 338959 47 - 593897 AGGGGGTAACATACACTGTCTTTGGGGTAGTGTGCATTGCCTCAATG -s simHuman_chr6.simHuman.chr6 254437 47 + 601863 GGAGGGTAACCCACACTGTATTTGGGTTAGTGAGCACCGCCTTGATG -s simRat_chr6.simRat.chr6 263943 36 + 647215 -GGGGGTGACACCCACA----------TAGTAAGTCTTGCCCTGATG - -a -s simMouse_chr6.simMouse.chr6 274933 31 + 636262 GCCCATATGTAATGTCACCACTGAATATCAC -s Anc0.Anc0refChr5 3410 27 - 87904 GCCTATAAGCAATGTCACCA----ATACCAC -s Anc1.Anc1refChr7 3479 27 + 47259 GCCTATAAGCAATGTCACCA----ATACCAC -s Anc2.Anc2refChr15 4712 27 - 86568 GCCTATAAGCAACATCACCA----GTACTAC -s mr.mrrefChr5 126487 31 + 294540 GCCTATAAGTAATGTCACCACTGAATACCAC -s simCow_chr6.simCow.chr6 338194 27 - 602619 GCCTATAAGCAACATCATCG----GTATGCC -s simDog_chr6.simDog.chr6 339014 27 - 593897 GCCTATAAGTAACATCACCA----GTACTAC -s simHuman_chr6.simHuman.chr6 254492 27 + 601863 GCATATAAGCAATGTCGCCC----ATACCAC -s simRat_chr6.simRat.chr6 263979 31 + 647215 GCCTATAAGTAATGTCACCACTGAATACCAT - -a -s simMouse_chr6.simMouse.chr6 274964 21 + 636262 GGCATTTTGGCTGGGAACTTG -s Anc0.Anc0refChr5 3450 21 - 87904 AGCATTTTAGATATAAACTTA -s Anc1.Anc1refChr7 3519 21 + 47259 AGCATTTTAGATATAAACTTA -s Anc2.Anc2refChr15 4753 21 - 86568 AGCATTTTAGAGATAACCTCA -s mr.mrrefChr5 126518 21 + 294540 GGCATTTTGGCTGTGAACTTG -s simCow_chr6.simCow.chr6 338235 21 - 602619 AGCCCTATAAGCAACACACCG -s simDog_chr6.simDog.chr6 339055 21 - 593897 AGCATTTTAGAGATAACCTCA -s simHuman_chr6.simHuman.chr6 254532 21 + 601863 AGCATTTTAGATATTAACTTA -s simRat_chr6.simRat.chr6 264010 21 + 647215 GGCATTTTGGCTGTGAACTTG - -a -s simMouse_chr6.simMouse.chr6 274985 3 + 636262 AAC -s Anc0.Anc0refChr5 3471 3 - 87904 AAT -s Anc1.Anc1refChr7 3540 3 + 47259 AAT -s Anc2.Anc2refChr15 4774 3 - 86568 AAT -s mr.mrrefChr5 126539 3 + 294540 AAC -s simCow_chr6.simCow.chr6 338256 3 - 602619 GAA -s simDog_chr6.simDog.chr6 339087 3 - 593897 AGT -s simHuman_chr6.simHuman.chr6 254553 3 + 601863 AAT -s simRat_chr6.simRat.chr6 264031 3 + 647215 AAC - -a -s simMouse_chr6.simMouse.chr6 274988 6 + 636262 ATTATG -s Anc0.Anc0refChr5 3478 6 - 87904 CTGATA -s Anc1.Anc1refChr7 3547 6 + 47259 CTGATA -s Anc2.Anc2refChr15 4781 6 - 86568 CTGGTA -s mr.mrrefChr5 126542 6 + 294540 ATGATG -s simCow_chr6.simCow.chr6 338263 6 - 602619 CAAGTG -s simDog_chr6.simDog.chr6 339094 6 - 593897 ATGGTA -s simHuman_chr6.simHuman.chr6 254560 6 + 601863 CTGATA -s simRat_chr6.simRat.chr6 264034 6 + 647215 GTGATG - -a -s simMouse_chr6.simMouse.chr6 274994 6 + 636262 ATGATG -s Anc0.Anc0refChr5 3484 6 - 87904 CTAGTG -s Anc1.Anc1refChr7 3553 6 + 47259 CTAGTG -s Anc2.Anc2refChr15 4787 6 - 86568 CTAGTA -s mr.mrrefChr5 126548 6 + 294540 ATAATG -s simCow_chr6.simCow.chr6 338274 6 - 602619 CTGAGC -s simDog_chr6.simDog.chr6 339100 6 - 593897 TTAGTA -s simHuman_chr6.simHuman.chr6 254566 6 + 601863 CTAGTG -s simRat_chr6.simRat.chr6 264040 6 + 647215 GTAATG - -a -s simMouse_chr6.simMouse.chr6 275000 23 + 636262 CTGGATGTAAAAAGTGGATCCAA -s Anc0.Anc0refChr5 3491 23 - 87904 CTGGATGTATGAAGAGGATCCAA -s Anc1.Anc1refChr7 3560 23 + 47259 CTGGATGTATGAAGAGGATCCAA -s Anc2.Anc2refChr15 4794 23 - 86568 TTGGATGTATGAAAAGGATCCAA -s mr.mrrefChr5 126554 23 + 294540 CTGGATGTAAAAAGTGGATCCAA -s simCow_chr6.simCow.chr6 338281 23 - 602619 TTTTAGATATGAACTTAAGCATG -s simDog_chr6.simDog.chr6 339107 23 - 593897 TTGGATGTATGAAAAGGATCCAA -s simHuman_chr6.simHuman.chr6 254573 23 + 601863 CTGGATGTGTGAAGCAGATCCAA -s simRat_chr6.simRat.chr6 264046 23 + 647215 CTGGATGTAAAGAGTGGATCCAA - -a -s simMouse_chr6.simMouse.chr6 275023 4 + 636262 CATT -s Anc0.Anc0refChr5 3514 4 - 87904 CATT -s Anc1.Anc1refChr7 3583 4 + 47259 CATT -s Anc2.Anc2refChr15 4818 4 - 86568 CATT -s mr.mrrefChr5 126577 4 + 294540 CATT -s simCow_chr6.simCow.chr6 338305 4 - 602619 CATC -s simDog_chr6.simDog.chr6 339131 4 - 593897 CATT -s simHuman_chr6.simHuman.chr6 254596 4 + 601863 CATT -s simRat_chr6.simRat.chr6 264069 4 + 647215 CATT - -a -s simMouse_chr6.simMouse.chr6 275027 24 + 636262 GATTGAGTGAGTATAAGGAAACAT -s Anc0.Anc0refChr5 3518 24 - 87904 GTTTTAAAAAATATAAGGACACAT -s Anc1.Anc1refChr7 3587 24 + 47259 GTTTTAAAAAATATAAGGACACAT -s Anc2.Anc2refChr15 4822 24 - 86568 GTTTTAAAAAATCTAAGGACAAAT -s mr.mrrefChr5 126581 24 + 294540 GATTGAGTGAGTATAAGGAAACAT -s simCow_chr6.simCow.chr6 338310 24 - 602619 GTTTTAAAGAATGTAAGGACAAAT -s simDog_chr6.simDog.chr6 339135 24 - 593897 GTTTTAAAAAATCTGGGGACGAAT -s simHuman_chr6.simHuman.chr6 254600 24 + 601863 GTTTTAAAAAATATAAGGACACAT -s simRat_chr6.simRat.chr6 264073 24 + 647215 GATTGAGTGACTATAGGGGATATT - -a -s simMouse_chr6.simMouse.chr6 275051 16 + 636262 ACCAACCAGATGAGAA -s Anc0.Anc0refChr5 3546 16 - 87904 ACCAGGCAGATGGAAG -s Anc1.Anc1refChr7 3615 16 + 47259 ACCAGGCAGATGGAAG -s Anc2.Anc2refChr15 4850 16 - 86568 ACCAGGCAGATAGAAG -s mr.mrrefChr5 126605 16 + 294540 ACCAACCAGATGGGAG -s simCow_chr6.simCow.chr6 338338 16 - 602619 AATAGGTGGAAAGAAG -s simDog_chr6.simDog.chr6 339163 16 - 593897 ACCAGGCACATAGAAG -s simHuman_chr6.simHuman.chr6 254628 16 + 601863 ATCAGGCAGATGGAAG -s simRat_chr6.simRat.chr6 264097 16 + 647215 ACCAACCAGATGGGAG - -a -s simMouse_chr6.simMouse.chr6 275067 15 + 636262 TTGGTTCATTTGGCA -s Anc0.Anc0refChr5 3562 15 - 87904 TTCAGTACAATGATA -s Anc1.Anc1refChr7 3631 15 + 47259 TTCAGTACAATGATA -s Anc2.Anc2refChr15 4872 15 - 86568 TTCAGTACAAAGTTA -s mr.mrrefChr5 126621 15 + 294540 TTGGTTCATTTGACA -s simCow_chr6.simCow.chr6 338360 11 - 602619 ----GTACAAAGTTC -s simDog_chr6.simDog.chr6 339185 15 - 593897 TTCAGGACAAAGTTA -s simHuman_chr6.simHuman.chr6 254644 15 + 601863 TTCAGTACAATGAAA -s simRat_chr6.simRat.chr6 264113 15 + 647215 TTGGATCATGCGACA - -a -s simMouse_chr6.simMouse.chr6 275082 3 + 636262 ACT -s Anc0.Anc0refChr5 3579 3 - 87904 GCT -s Anc1.Anc1refChr7 3648 3 + 47259 GCT -s Anc2.Anc2refChr15 4889 3 - 86568 GCT -s mr.mrrefChr5 126638 3 + 294540 ACT -s simCow_chr6.simCow.chr6 338373 3 - 602619 ACT -s simDog_chr6.simDog.chr6 339202 3 - 593897 GTT -s simHuman_chr6.simHuman.chr6 254661 3 + 601863 GCT -s simRat_chr6.simRat.chr6 264130 3 + 647215 ACT - -a -s simMouse_chr6.simMouse.chr6 275085 43 + 636262 AAAGCATGTCTTATATTCTCCTACATCACTGACAAGTAGACCC -s Anc0.Anc0refChr5 3582 43 - 87904 AAATCATGTCTTGCACTATCCTGCATCACTGATGAGAAGATGT -s Anc1.Anc1refChr7 3651 43 + 47259 AAATCATGTCTTGCACTATCCTGCATCACTGATGAGAAGATGT -s Anc2.Anc2refChr15 4892 43 - 86568 GAATCATGCCTTGCACTATCCTGCATCACTGGTGAGAATATGT -s mr.mrrefChr5 126641 43 + 294540 AAAGCATGTCTTATATTCTCCTACATCACTGACAAGTAGACCC -s simCow_chr6.simCow.chr6 338376 43 - 602619 GAAACATGCCTCTTAGTATCCTGCATCAGTGGTAAGAATATGT -s simDog_chr6.simDog.chr6 339205 43 - 593897 TGATCATGCCATGCGCTATTCTGCATCACTGGTGAGGGTATGT -s simHuman_chr6.simHuman.chr6 254666 43 + 601863 AAACCATGTCTTGCACTATCCTGCATCATTGATGATAAGATTT -s simRat_chr6.simRat.chr6 264133 39 + 647215 GGAGCATGCCTTATA----CTTCCATCTCTGAGATGTACACCC - -a -s simMouse_chr6.simMouse.chr6 275128 25 + 636262 CCACAGCAAGGACTTGATCGAATTC -s Anc0.Anc0refChr5 3625 25 - 87904 TCATAGATTGGGATTGGCTGAATTT -s Anc1.Anc1refChr7 3694 25 + 47259 TCATAGATTGGGATTGGCTGAATTT -s Anc2.Anc2refChr15 4935 25 - 86568 TCATAGATTGGGATTGGCTGAATTT -s mr.mrrefChr5 126684 25 + 294540 CCACAGCAAGGAATTGATTGAATTT -s simCow_chr6.simCow.chr6 338419 25 - 602619 ATACAGATTGAGATTGGTATAATTC -s simDog_chr6.simDog.chr6 339256 25 - 593897 TCATAGATTGGGCTTGGCTGAGTTT -s simHuman_chr6.simHuman.chr6 254709 25 + 601863 GCATAGATTGGGATTGGCTGAATTT -s simRat_chr6.simRat.chr6 264172 25 + 647215 CCGCAGCAAGGAAGTGTTTTAATTT - -a -s simMouse_chr6.simMouse.chr6 275153 105 + 636262 ACAAGATGGTCTTCTCATGAAGTATAGCAAGCTACAAACCGGATAATGGTGAAACATGAGATATTTTAAGAAAATATACTAAGTGCTTTAGTTACCGTCTGAACA -s Anc0.Anc0refChr5 3650 48 - 87904 ACGAGAATGTTTTTTCATCAGATGTAAGAAG------ACTGTATA-------------------TGTAAGAAA-------------------------------- -s Anc1.Anc1refChr7 3719 80 + 47259 ACGAGAATGTTTTTTCATCAGATGTAAGAAG------ACTGTATA-------------------TGTAAGAAAGTCTTCTATTTGTCTAATTGAAGAGTTTAGTA -s Anc2.Anc2refChr15 4960 48 - 86568 ACGAAAATGTTTTTTCATCAGATGTAAGAAA------ATTGTATA-------------------TGTAAGAAA-------------------------------- -s mr.mrrefChr5 126709 105 + 294540 ACAAGATGGTTTTTTCATGAAGTATAGCAAGCTATAAACCGGATAATGGTGAAACATGAGATATTTTAAGAAAATATACTAAGTGCTTTAGTTACCGTCTGAACA -s simCow_chr6.simCow.chr6 338444 48 - 602619 ACTAAAATGTTTTTTCATCAGATGTAAGAAA------ATTGTACA-------------------TGTAAGAAA-------------------------------- -s simDog_chr6.simDog.chr6 339282 48 - 593897 ATGAAAATGCTTTTTCATCTGATCTAAGAGA------ATGGTGTA-------------------TGGAAGAAA-------------------------------- -s simHuman_chr6.simHuman.chr6 254734 80 + 601863 ACCAGAATGTTTTTTCATCAGATGTAAGAAG------ACTGTATA-------------------TGTAAGAAAGTCTTCTATTTGTCTAATTGAAGAGTTTAGTA -s simRat_chr6.simRat.chr6 264197 105 + 647215 AAAAGATGGTTTTTTTATGAAGTATAGCAAATTATGAACCAGATAATGGTCAAACATGAGCCATCTTAAGAAAATATACTAAGGGCTTTAGTTGCTGCCtgaaca - -a -s simMouse_chr6.simMouse.chr6 275258 24 + 636262 TATCCTAAAGGTCATATGCTAATC -s Anc1.Anc1refChr7 3799 24 + 47259 TATTCTAGCACTATTTCACTAACC -s mr.mrrefChr5 126814 24 + 294540 TATCCTAAAGGTCATTTGCTAATC -s simHuman_chr6.simHuman.chr6 254827 24 + 601863 TATTCTAGCACTATTTCACTAACC -s simRat_chr6.simRat.chr6 264302 24 + 647215 tatgctaaaggtcatttgctaatc - -a -s simMouse_chr6.simMouse.chr6 275282 80 + 636262 CCAAGCCTCACAACCTTACCGTATTGCAGCTAGCTCCCCTCAAGTAAATTTTTGGTCTATCCATTCTAAAGGTACTTGCT -s Anc1.Anc1refChr7 3824 78 + 47259 CCAGAACTCAGAATC-TGCaattcttgagctggggcccctcaagg-tgtattttgtacacatattctaaagttaattgcc -s mr.mrrefChr5 126839 79 + 294540 CCAAGCCTCACAACCtTGCagtattgcagctagctcccctcaagt-aatatttggtctacacattctaaagGTACTTGCT -s simHuman_chr6.simHuman.chr6 254852 78 + 601863 CCAGAACTCAGAATC-TGCaattcttgagctggggcccctcaagg-tgtattttgtacacatattctaaagttaattgcc -s simRat_chr6.simRat.chr6 264327 79 + 647215 ccaaggctttcagccttgcagaattgcagctcgctcccctcaagt-aatatttggtctacacattttaaagGTACTTGCT - -a -s simMouse_chr6.simMouse.chr6 275362 10 + 636262 ATGCCTATTT -s Anc1.Anc1refChr7 3902 10 + 47259 acccccgatt -s mr.mrrefChr5 126918 10 + 294540 ATGCCTATTT -s simHuman_chr6.simHuman.chr6 254931 10 + 601863 acccccgatt -s simRat_chr6.simRat.chr6 264406 10 + 647215 ATGCCTATTT - -a -s simMouse_chr6.simMouse.chr6 275372 1 + 636262 A -s Anc1.Anc1refChr7 3912 1 + 47259 A -s mr.mrrefChr5 126928 1 + 294540 A -s simHuman_chr6.simHuman.chr6 192997 1 + 601863 A -s simHuman_chr6.simHuman.chr6 254941 1 + 601863 a -s simRat_chr6.simRat.chr6 264416 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 275373 3 + 636262 CAT -s Anc1.Anc1refChr7 3913 3 + 47259 gat -s mr.mrrefChr5 126929 3 + 294540 GAT -s simHuman_chr6.simHuman.chr6 254942 3 + 601863 gat -s simRat_chr6.simRat.chr6 264417 3 + 647215 GAT - -a -s simMouse_chr6.simMouse.chr6 275376 26 + 636262 TAAGACATGGTGTCAAAACTTTTAAC -s Anc0.Anc0refChr5 3714 26 - 87904 TATGAGACTGTGTCAAAACCTGTAAC -s Anc1.Anc1refChr7 3932 26 + 47259 TATGAGACTGTGTCAAAACCTGTAAC -s Anc2.Anc2refChr15 5024 26 - 86568 CATGAGACTGTGTCAAAACCTGTAAC -s mr.mrrefChr5 126932 26 + 294540 TAAGACATGGTGTCAAAACCTTTAAC -s simCow_chr6.simCow.chr6 338508 26 - 602619 CATGAGACTGTGCCAAAACCTGTGTC -s simDog_chr6.simDog.chr6 339346 26 - 593897 CATGATACTGGGTCAAGACCTGTAAT -s simHuman_chr6.simHuman.chr6 255335 26 + 601863 TGTGAGACTGTATCATAACCTGTAAC -s simRat_chr6.simRat.chr6 264420 26 + 647215 TAATATGTGGTGTCAGAACCTTTAAC - -a -s simMouse_chr6.simMouse.chr6 275402 27 + 636262 CACTTAGTGTGAATGACTGGACATATT -s Anc0.Anc0refChr5 3740 27 - 87904 CTCTTACTATAAGTGACTGTACATAAT -s Anc1.Anc1refChr7 3958 27 + 47259 CTCTTACTATAAGTGACTGTACATAAT -s Anc2.Anc2refChr15 5050 27 - 86568 CTCTCACTATAAGTGACTGTACATAAT -s mr.mrrefChr5 126958 27 + 294540 CACTTAGTGTGAATGACTGGACATATT -s simCow_chr6.simCow.chr6 338534 12 - 602619 CTCTCACTATGA--------------- -s simDog_chr6.simDog.chr6 339374 27 - 593897 CCCTCACTATAAGTGACTGTACATAAT -s simHuman_chr6.simHuman.chr6 255361 27 + 601863 CTATTACTATAACTGACTGTACATAAT -s simRat_chr6.simRat.chr6 264446 27 + 647215 TACTTAGTGTGGATGACTGAACATATT - -a -s simMouse_chr6.simMouse.chr6 275429 22 + 636262 TTGGATTTCTTCTAGTGTGACA -s Anc0.Anc0refChr5 3863 9 - 87904 --GGAAT-----------GAGA -s Anc1.Anc1refChr7 4081 11 + 47259 TTGGAAT-----------GAGA -s Anc2.Anc2refChr15 5181 9 - 86568 --GGAAT-----------GAGA -s mr.mrrefChr5 126985 22 + 294540 TTGGATTTCTTCTAGTGTGACA -s simCow_chr6.simCow.chr6 338636 9 - 602619 --GGAAT-----------GAAT -s simDog_chr6.simDog.chr6 339508 9 - 593897 --GGAAT-----------GAGA -s simHuman_chr6.simHuman.chr6 255509 11 + 601863 TTGGACT-----------GAGA -s simRat_chr6.simRat.chr6 264473 22 + 647215 TTGGATTCATTCCAGCATGAGA - -a -s simMouse_chr6.simMouse.chr6 275451 4 + 636262 CTGC -s Anc0.Anc0refChr5 3872 4 - 87904 CCAC -s Anc1.Anc1refChr7 4092 4 + 47259 CCAC -s Anc2.Anc2refChr15 5190 4 - 86568 CCAC -s mr.mrrefChr5 127007 4 + 294540 CTGC -s simCow_chr6.simCow.chr6 338645 4 - 602619 CCAC -s simDog_chr6.simDog.chr6 339517 4 - 593897 CTAA -s simHuman_chr6.simHuman.chr6 192998 4 + 601863 CTGC -s simHuman_chr6.simHuman.chr6 255520 4 + 601863 CCAC -s simRat_chr6.simRat.chr6 264495 4 + 647215 CTGT - -a -s simMouse_chr6.simMouse.chr6 275455 14 + 636262 GCCATAGAGGTCAT -s Anc0.Anc0refChr5 3876 14 - 87904 ACCATCAAATGTGT -s Anc1.Anc1refChr7 4096 14 + 47259 ACCATCAAATGTGT -s Anc2.Anc2refChr15 5194 14 - 86568 ACAATCAAATGTGA -s mr.mrrefChr5 127011 14 + 294540 GCCATAGAGGTCAT -s simCow_chr6.simCow.chr6 338649 13 - 602619 ACACTCAA-TGTGA -s simDog_chr6.simDog.chr6 339521 14 - 593897 ATAATCAAATGTCA -s simHuman_chr6.simHuman.chr6 193004 14 + 601863 ACCAAAGAATCTTT -s simHuman_chr6.simHuman.chr6 255524 14 + 601863 ACGATCAAATGTGC -s simRat_chr6.simRat.chr6 264499 14 + 647215 ACAATTGGAGTCAT - -a -s simMouse_chr6.simMouse.chr6 275469 7 + 636262 TGTGTAG -s Anc0.Anc0refChr5 3890 7 - 87904 TATGTAG -s Anc1.Anc1refChr7 4110 7 + 47259 TATGTAG -s Anc2.Anc2refChr15 5208 7 - 86568 CATGTAG -s mr.mrrefChr5 127025 7 + 294540 TATGTAG -s simCow_chr6.simCow.chr6 338662 7 - 602619 CATGTAG -s simDog_chr6.simDog.chr6 339535 7 - 593897 CATGTAG -s simHuman_chr6.simHuman.chr6 193018 7 + 601863 GACACAG -s simHuman_chr6.simHuman.chr6 255540 7 + 601863 TATGTAG -s simRat_chr6.simRat.chr6 264513 7 + 647215 CATGTAG - -a -s simMouse_chr6.simMouse.chr6 275476 4 + 636262 CTGG -s Anc0.Anc0refChr5 3901 4 - 87904 CTAG -s Anc1.Anc1refChr7 4121 4 + 47259 CTAG -s Anc2.Anc2refChr15 5219 4 - 86568 CTAG -s mr.mrrefChr5 127036 4 + 294540 CTGG -s simCow_chr6.simCow.chr6 338673 4 - 602619 CAAG -s simDog_chr6.simDog.chr6 339546 4 - 593897 CTGG -s simHuman_chr6.simHuman.chr6 193030 4 + 601863 TTAG -s simHuman_chr6.simHuman.chr6 255551 4 + 601863 CTAG -s simRat_chr6.simRat.chr6 264524 4 + 647215 CTGG - -a -s simMouse_chr6.simMouse.chr6 275480 12 + 636262 AATAGGTTTTAA -s Anc0.Anc0refChr5 3905 12 - 87904 AATAAGTTTTAA -s Anc1.Anc1refChr7 4125 12 + 47259 AATAAGTTTTAA -s Anc2.Anc2refChr15 5223 12 - 86568 AATAAGTTTTCA -s mr.mrrefChr5 127040 12 + 294540 AATAGGTTTTAA -s simCow_chr6.simCow.chr6 338710 12 - 602619 AATAAGTTCTCA -s simDog_chr6.simDog.chr6 339550 12 - 593897 AATAAGTCTTCA -s simHuman_chr6.simHuman.chr6 193034 12 + 601863 AATAAGTTGGAG -s simHuman_chr6.simHuman.chr6 255555 12 + 601863 AATAAGTTGGAA -s simRat_chr6.simRat.chr6 264528 12 + 647215 AATATGTTTAAA - -a -s simMouse_chr6.simMouse.chr6 275492 36 + 636262 CCATAACCATCAAGCTGACCCTGAGGCATTGCTTGA -s Anc0.Anc0refChr5 3917 36 - 87904 CCATCAGGAGCAGGTTGGATCTGAGACTTCACTTGA -s Anc1.Anc1refChr7 4137 36 + 47259 CCATCAGGAGCAGGTTGGATCTGAGACTTCACTTGA -s Anc2.Anc2refChr15 5241 36 - 86568 CCATCAGGAGCAGGTTGGATCTGAGACTTTACTTGA -s mr.mrrefChr5 127052 36 + 294540 CCATAACCATCAAGCTGGCCCTGAGGCATCACTTGA -s simCow_chr6.simCow.chr6 338728 36 - 602619 CCATTGGGAGCAGGATGGATCTGAGCCTTTATGTGA -s simDog_chr6.simDog.chr6 339568 36 - 593897 CCATCAGGAGCAGGGTGAGTATGAGACTTTACTTGA -s simHuman_chr6.simHuman.chr6 193046 26 + 601863 C----------AGGTTGGATCTGAGACTTCACTTGA -s simHuman_chr6.simHuman.chr6 255567 26 + 601863 C----------AGGTTGGATCTGAGACTTCACTTGA -s simRat_chr6.simRat.chr6 264540 36 + 647215 CTATAACTGGCAAGCTGGCCCTGAGGCATCACTTGA - -a -s simMouse_chr6.simMouse.chr6 275528 7 + 636262 CCAAGCA -s Anc0.Anc0refChr5 3953 7 - 87904 CCAAACA -s Anc1.Anc1refChr7 4173 7 + 47259 CCAAACA -s Anc2.Anc2refChr15 5277 7 - 86568 CCAAACA -s mr.mrrefChr5 127088 7 + 294540 CCAAGCA -s simCow_chr6.simCow.chr6 338764 7 - 602619 CCAAATA -s simDog_chr6.simDog.chr6 339605 7 - 593897 CCAAACA -s simHuman_chr6.simHuman.chr6 193072 7 + 601863 CCAAACA -s simHuman_chr6.simHuman.chr6 255593 7 + 601863 CCAAACA -s simRat_chr6.simRat.chr6 264576 7 + 647215 CTAGGCA - -a -s simMouse_chr6.simMouse.chr6 275535 50 + 636262 TATCTCCTACTAAATGGTAACAGAGGGTTGTACCATAATTGCTTTCAGGA -s Anc0.Anc0refChr5 3960 47 - 87904 TATTTTCTACCAG-TTGTAGCAGGGGGTTTACCGGTAATTGCTAT--GTA -s Anc1.Anc1refChr7 4180 48 + 47259 TATTTTCTACCAGATTGTAGCAGGGGGTTTACCGGTAATTGCTAT--GTA -s Anc2.Anc2refChr15 5284 47 - 86568 TATTTTCTACCAG-TTGCAACAGGGGGTTAACCTGTAATTGCTAG--GTG -s mr.mrrefChr5 127095 48 + 294540 TATCTTCTACTAAATGGTAGCAGAGGGTTGTACCATAATTGCTTT--GGA -s simCow_chr6.simCow.chr6 338771 47 - 602619 GATTTTCTACCAA-TTGCAACAGGGGGTTAGTCTGCAATTGCCGG--GTG -s simDog_chr6.simDog.chr6 339614 47 - 593897 TATTATCTACCAG-CTGCAATAGGGATTTAACCTGTTATTTCTAG--GTG -s simHuman_chr6.simHuman.chr6 193079 48 + 601863 TACTTTCTACCAGATTGTAGCAGGGGGTTTACCGGTAAATGCTAT--GTA -s simHuman_chr6.simHuman.chr6 255600 48 + 601863 TACTTTCTACCAGATTGTAGCAGGGGGTTTACCGGTAAATGCTAT--GTA -s simRat_chr6.simRat.chr6 264583 47 + 647215 TATCTTCTGCTAAACGGTCGCAGAGCGTTGTAACATAAGTGCT-C--GGA - -a -s simMouse_chr6.simMouse.chr6 275585 138 + 636262 TCTTCCATAACAGAGTCATTGAAACTGTGGTAGCCTAATGCACATAAGGGTAGCACGAGCATTTGACGGCATGTCTAGGGGGGGCAGCTTCTACAAATTACAATAACAATAACAGTAGAGGGCTAAGTTGGGTGCAAG -s Anc0.Anc0refChr5 4010 104 - 87904 TTTTCCAAAACAGAGTCATT-AAATTATGGTAGCCT---GCCCATCAGGGTGGTACA----------GCCTTACCTATATTAGGACGCCCT-------------AACAATGACAGTAGAGGGCTAGATGGG------- -s Anc1.Anc1refChr7 4231 104 + 47259 TTTTCCAAAACAGAGTCATT-AAATTATGGTAGCCT---GCCCATCAGGGTGGTACA----------GCCTTACCTATATTAGGACGCCCT-------------AACAATGACAGTAGAGGGCTAGATGGG------- -s Anc2.Anc2refChr15 5334 104 - 86568 TTTTCCAAAACAGAGTCATT-AAATCATAGTAGCCT---GCCCATCAGGGTGGTGCA----------GTCTTACCTATATTAGGACGTGCT-------------AACAATGACAGTAGAGGGCTAGATGGG------- -s mr.mrrefChr5 127143 137 + 294540 TATTCCATAACAGAGTCATT-AAACTGTGGTAGCCTAATGCACATAAGGGTAGCACAAGCATTTGACGGCATATCTAGGGGGGGCAGCTTCTACAAACTACAAGAACAATAACAGTAGAGGGCTAGATTGGGTGCAAG -s simCow_chr6.simCow.chr6 338821 104 - 602619 TTTTCCAAAACGGAGTCATT-AAATCAGAGTAGCCT---GCCCATCACAGTGGGGCA----------GTCTTGCCTCCATTAGGACATGCT-------------AGCAACAACAGTAGAGGGCTAGATGGG------- -s simDog_chr6.simDog.chr6 339664 104 - 593897 TTTTCTAAAACAGAGTCATT-ATATCCTAGTGGCCT---GCTCACCAAGGTCAAGCA----------GTCTTACCTGTATTAGGATGTGCT-------------CACTATGACAATAGCGGGATAGATGTG------- -s simHuman_chr6.simHuman.chr6 193130 104 + 601863 TTTTCCAAGACAAAGTCATT-AAATTATGGTAGCCC---GCCCATCAGGGTAGTACA----------GCCTTACCTATATTAGGACGCCCT-------------AACAACGACAGTAAAGGGCTAGATTGG------- -s simHuman_chr6.simHuman.chr6 255651 104 + 601863 TTCTCCAAGACAAAGTCATT-AAATTATGGTAGCCC---GCCCATCAGGGTGGTATA----------GCCTTACCTATATTAGGACACCCT-------------AAGAATGACAGTAAAGGGCTAGATGGG------- -s simRat_chr6.simRat.chr6 264630 137 + 647215 TATTGCATAGCAGAGTTATC-GAACTGTGGTAGCCTAATGCACTTAAGGGTAGCACAAGCATTTGACAGCATATTTAGGGGGGGCAGCTTCTAAAAACTACAAGAACCCTAACAATAGAGGGTTAGATTGGGTGCAAG - -a -s simMouse_chr6.simMouse.chr6 275723 1 + 636262 A -s Anc0.Anc0refChr5 4122 1 - 87904 A -s Anc1.Anc1refChr7 4343 1 + 47259 A -s Anc2.Anc2refChr15 5446 1 - 86568 A -s mr.mrrefChr5 127289 1 + 294540 A -s simDog_chr6.simDog.chr6 339776 1 - 593897 A -s simHuman_chr6.simHuman.chr6 193242 1 + 601863 A -s simHuman_chr6.simHuman.chr6 255763 1 + 601863 A -s simRat_chr6.simRat.chr6 264776 1 + 647215 G - -a -s simMouse_chr6.simMouse.chr6 275724 14 + 636262 CAACCATATCACAT -s Anc0.Anc0refChr5 4123 10 - 87904 CAAACAA----TGT -s Anc1.Anc1refChr7 4344 14 + 47259 CAAACAAGTCATGT -s Anc2.Anc2refChr15 5447 10 - 86568 CAAACAA----TGT -s mr.mrrefChr5 127290 14 + 294540 CAAACATGTCACAT -s simCow_chr6.simCow.chr6 338933 1 - 602619 -------------T -s simDog_chr6.simDog.chr6 339777 10 - 593897 CAGACAA----TGT -s simHuman_chr6.simHuman.chr6 193243 14 + 601863 CAAACAAGTCATCT -s simHuman_chr6.simHuman.chr6 255764 14 + 601863 CAAACAAGTCATGT -s simRat_chr6.simRat.chr6 264799 14 + 647215 CAAACATGTCACAT - -a -s simMouse_chr6.simMouse.chr6 275738 12 + 636262 ACACCTTGGCAT -s Anc0.Anc0refChr5 4134 12 - 87904 ATGCCTTGGCAT -s Anc1.Anc1refChr7 4359 12 + 47259 ATGCCTTGGCAT -s Anc2.Anc2refChr15 5458 12 - 86568 ATGCCTTGGCAT -s mr.mrrefChr5 127305 12 + 294540 ACACCTTGGCAT -s simCow_chr6.simCow.chr6 338935 12 - 602619 CTGCCTTGGCAA -s simDog_chr6.simDog.chr6 339788 12 - 593897 GTGTCTTGGCAC -s simHuman_chr6.simHuman.chr6 193258 12 + 601863 ATGCCTCAGCAT -s simHuman_chr6.simHuman.chr6 255779 12 + 601863 ATGCCTTGGCGT -s simRat_chr6.simRat.chr6 264814 12 + 647215 ACACCTTGGCAT - -a -s simMouse_chr6.simMouse.chr6 275750 45 + 636262 GTAAGGGCTCCAGTTAGCGAATTATCTTGTTTCTCCCTAATGAAC -s Anc0.Anc0refChr5 4146 27 - 87904 GTAAGGACTCCGGTTTACAAATTCTCT------------------ -s Anc1.Anc1refChr7 4371 27 + 47259 GTAAGGACTCCGGTTTACAAATTCTCT------------------ -s Anc2.Anc2refChr15 5470 27 - 86568 GTAAGGAGTCCGGTTTACAAATTCTCT------------------ -s mr.mrrefChr5 127317 45 + 294540 GTAAGGGCTCCAGTTAGCGAATTCTCTTGTTACTCCCTTATGAAC -s simCow_chr6.simCow.chr6 338947 27 - 602619 GCAAGGAGTCTGGTCTACAAATTCTCT------------------ -s simDog_chr6.simDog.chr6 339811 27 - 593897 GTAAGGAGTCCAGTTTATAAGTTCTCA------------------ -s simHuman_chr6.simHuman.chr6 193270 27 + 601863 GTAAGGACTCCGGTTTACAAATTCTCT------------------ -s simHuman_chr6.simHuman.chr6 255791 27 + 601863 GTAAGGACTGCGGTTTACAAATTCTAT------------------ -s simRat_chr6.simRat.chr6 264826 45 + 647215 GTAAAGGCTCCAGTTAGTGAATTCTCTTGTTACTCCCTTATGAAC - -a -s simMouse_chr6.simMouse.chr6 275795 27 + 636262 CCAACCAAAGATAACATTTAATGGGTG -s Anc0.Anc0refChr5 4173 15 - 87904 -------AAGATCAATTTGAA-----G -s Anc1.Anc1refChr7 4398 20 + 47259 -------AAGATCAATTTGAATGTTCG -s Anc2.Anc2refChr15 5497 15 - 86568 -------AAGATCAATTTGAA-----G -s mr.mrrefChr5 127362 27 + 294540 TTGACCAAAGATAACATTTAATGGGTG -s simCow_chr6.simCow.chr6 338974 15 - 602619 -------AGGATCAATTTGAA-----G -s simDog_chr6.simDog.chr6 339838 15 - 593897 -------AAGATGAATTTGAG-----G -s simHuman_chr6.simHuman.chr6 193297 20 + 601863 -------AAAATCAATTTGAATGTTCG -s simHuman_chr6.simHuman.chr6 255818 20 + 601863 -------AAAATCAATTTGAATGTTCG -s simRat_chr6.simRat.chr6 264998 27 + 647215 TTGGCCAAAGATAACATTTAATAGGTG - -a -s simMouse_chr6.simMouse.chr6 275822 1 + 636262 A -s Anc1.Anc1refChr7 4466 1 + 47259 A -s mr.mrrefChr5 127389 1 + 294540 A -s simHuman_chr6.simHuman.chr6 193317 1 + 601863 A -s simHuman_chr6.simHuman.chr6 255897 1 + 601863 A -s simRat_chr6.simRat.chr6 265025 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 275823 15 + 636262 AGTACACCGTCGGAT -s Anc0.Anc0refChr5 4236 13 - 87904 --GTCTGCCACTGAA -s Anc1.Anc1refChr7 4467 15 + 47259 AGGTCTGCCACTGAA -s Anc2.Anc2refChr15 5560 13 - 86568 --GTATGCCACTGCA -s mr.mrrefChr5 127390 15 + 294540 AGTACAGCCTCGGAT -s simCow_chr6.simCow.chr6 339037 13 - 602619 --GTATGCCACTGCA -s simHuman_chr6.simHuman.chr6 255898 15 + 601863 AGGTCTGCCACTGAA -s simRat_chr6.simRat.chr6 265026 15 + 647215 AGTGCAGCCCTCGAT - -a -s simMouse_chr6.simMouse.chr6 275838 3 + 636262 TAG -s Anc0.Anc0refChr5 4249 3 - 87904 TAG -s Anc1.Anc1refChr7 4482 3 + 47259 TAG -s Anc2.Anc2refChr15 5573 3 - 86568 TAG -s mr.mrrefChr5 127405 3 + 294540 TAG -s simCow_chr6.simCow.chr6 339050 3 - 602619 TAG -s simHuman_chr6.simHuman.chr6 193318 3 + 601863 TAG -s simHuman_chr6.simHuman.chr6 255913 3 + 601863 TAG -s simRat_chr6.simRat.chr6 265041 3 + 647215 TAG - -a -s simMouse_chr6.simMouse.chr6 275841 4 + 636262 TAAT -s Anc0.Anc0refChr5 4253 4 - 87904 AACT -s Anc1.Anc1refChr7 4486 4 + 47259 AACT -s Anc2.Anc2refChr15 5577 4 - 86568 GACT -s mr.mrrefChr5 127408 4 + 294540 TAAT -s simCow_chr6.simCow.chr6 339054 4 - 602619 GACT -s simDog_chr6.simDog.chr6 339857 4 - 593897 GACT -s simHuman_chr6.simHuman.chr6 193321 4 + 601863 AACT -s simHuman_chr6.simHuman.chr6 255917 4 + 601863 AACT -s simRat_chr6.simRat.chr6 265044 4 + 647215 TAGT - -a -s simMouse_chr6.simMouse.chr6 275845 33 + 636262 ATTTCATCTCTATATGACTCTATGTAACTCTGT -s Anc0.Anc0refChr5 4257 23 - 87904 GTTTAGT----------CTCTATGTAACTCTGT -s Anc1.Anc1refChr7 4490 23 + 47259 GTTTAGT----------CTCTATGTAACTCTGT -s Anc2.Anc2refChr15 5581 23 - 86568 GTTTAGT----------CTCTATGTAACTCTGT -s mr.mrrefChr5 127412 33 + 294540 ATTTCATTTCTATATGACTCTATGTAACTCTGT -s simCow_chr6.simCow.chr6 339058 23 - 602619 GCTTAGT----------CTCTGTGTGGCTCTGT -s simDog_chr6.simDog.chr6 339893 23 - 593897 GTTTAGT----------CTCTATGTCACTCTGT -s simHuman_chr6.simHuman.chr6 193325 23 + 601863 GTTTAGT----------CTCTATGTAACCCTGT -s simHuman_chr6.simHuman.chr6 255921 23 + 601863 GTTTAGT----------CTCTATGTAACCCTGT -s simRat_chr6.simRat.chr6 265048 33 + 647215 ATTTCATTTCTAGATAACCCTATGTAACTCTGT - -a -s simMouse_chr6.simMouse.chr6 275878 13 + 636262 TCCATGTAACTCT -s Anc0.Anc0refChr5 4280 13 - 87904 TCCATGTAACTGT -s Anc1.Anc1refChr7 4513 13 + 47259 TCCATGTAACTGT -s Anc2.Anc2refChr15 5605 13 - 86568 TCCATGTAACTGT -s mr.mrrefChr5 127445 13 + 294540 TCCATGTAACTCT -s simCow_chr6.simCow.chr6 339082 13 - 602619 TTGATGTAGCTCT -s simDog_chr6.simDog.chr6 339917 13 - 593897 TCCATGTAACTGT -s simHuman_chr6.simHuman.chr6 193348 10 + 601863 TCCATGTGAT--- -s simHuman_chr6.simHuman.chr6 255944 10 + 601863 TCCATGTGAT--- -s simRat_chr6.simRat.chr6 265081 13 + 647215 TCCATGTAACTCT - -a -s simMouse_chr6.simMouse.chr6 275891 6 + 636262 AGTTTT -s Anc0.Anc0refChr5 4293 6 - 87904 AGGCTC -s Anc1.Anc1refChr7 4526 6 + 47259 AGGCTC -s Anc2.Anc2refChr15 5619 6 - 86568 AGTCTC -s mr.mrrefChr5 127458 6 + 294540 AGGTTT -s simCow_chr6.simCow.chr6 339096 6 - 602619 AGTCTC -s simDog_chr6.simDog.chr6 339931 6 - 593897 AGTTTC -s simHuman_chr6.simHuman.chr6 193358 4 + 601863 --GCTC -s simHuman_chr6.simHuman.chr6 255954 4 + 601863 --GCTC -s simRat_chr6.simRat.chr6 265094 6 + 647215 AGGTTT - -a -s simMouse_chr6.simMouse.chr6 275897 8 + 636262 CTTCATTT -s Anc0.Anc0refChr5 4313 8 - 87904 TCTCATTT -s Anc1.Anc1refChr7 4546 8 + 47259 TCTCATTT -s Anc2.Anc2refChr15 5639 8 - 86568 TCTCATTT -s mr.mrrefChr5 127478 8 + 294540 CTTCATTT -s simCow_chr6.simCow.chr6 339116 8 - 602619 TCTTGTTG -s simDog_chr6.simDog.chr6 339951 7 - 593897 TA-CATTT -s simHuman_chr6.simHuman.chr6 193376 8 + 601863 TCTCATTT -s simHuman_chr6.simHuman.chr6 255972 8 + 601863 TCTCATTT -s simRat_chr6.simRat.chr6 265114 8 + 647215 CTTCATTT - -a -s simMouse_chr6.simMouse.chr6 275905 30 + 636262 ACTCTCAGATAAACTACCGATGTTCCTATC -s Anc0.Anc0refChr5 4322 30 - 87904 ACTATCATATAATCTACTGAGGTTCTTATC -s Anc1.Anc1refChr7 4555 30 + 47259 ACTATCATATAATCTACTGAGGTTCTTATC -s Anc2.Anc2refChr15 5648 30 - 86568 ACTATCATATAATCTACTGAGGTTCTTATC -s mr.mrrefChr5 127486 30 + 294540 ACTCTCAGATAAACTACTGATGTTCTTATC -s simCow_chr6.simCow.chr6 339125 30 - 602619 ACGATCATATAGTCTACTGAGGTTCTTATC -s simDog_chr6.simDog.chr6 339959 30 - 593897 ACTATCATATAATCTACTAACGTGCTTACC -s simHuman_chr6.simHuman.chr6 193385 30 + 601863 ACTATCATATAATCTACTGAGGTTCTTGTC -s simHuman_chr6.simHuman.chr6 255981 30 + 601863 ACTATCATATAATCTACTGAGGTTCTTGTC -s simRat_chr6.simRat.chr6 265122 26 + 647215 GACG----ATAACCTACTGATGTTCTTATC - -a -s simMouse_chr6.simMouse.chr6 275935 13 + 636262 TTGATCATGAGCA -s Anc0.Anc0refChr5 4381 13 - 87904 TTGATCATGAGCA -s Anc1.Anc1refChr7 4614 13 + 47259 TTGATCATGAGCA -s Anc2.Anc2refChr15 5707 13 - 86568 TTGATCATGAGCA -s mr.mrrefChr5 127516 13 + 294540 TTGATCATGAGCA -s simCow_chr6.simCow.chr6 339184 13 - 602619 TTGATCATGAACA -s simDog_chr6.simDog.chr6 340018 13 - 593897 TTGATCATGGGTA -s simHuman_chr6.simHuman.chr6 193444 13 + 601863 TTGATCATGAGCA -s simHuman_chr6.simHuman.chr6 256040 13 + 601863 TTGATCATGAGCA -s simRat_chr6.simRat.chr6 265148 13 + 647215 TTGATCATGAGCA - -a -s simMouse_chr6.simMouse.chr6 275948 11 + 636262 CCCATCGGAAA -s Anc0.Anc0refChr5 4394 11 - 87904 ACCATTGCAAG -s Anc1.Anc1refChr7 4627 11 + 47259 ACCATTGCAAG -s Anc2.Anc2refChr15 5732 11 - 86568 GCCATTGCAAG -s mr.mrrefChr5 127529 11 + 294540 CCCATCGGAAA -s simCow_chr6.simCow.chr6 339209 11 - 602619 GCCGTTGTAAG -s simDog_chr6.simDog.chr6 340048 11 - 593897 GCCATTACAAG -s simHuman_chr6.simHuman.chr6 193457 11 + 601863 ATTATTGCAAG -s simHuman_chr6.simHuman.chr6 256053 1 + 601863 A---------- -s simRat_chr6.simRat.chr6 265161 11 + 647215 TCCATTTGAAA - -a -s simMouse_chr6.simMouse.chr6 275959 14 + 636262 GAGTTGTTTGACTA -s Anc0.Anc0refChr5 4415 14 - 87904 GAGTTGTCTGAACA -s Anc1.Anc1refChr7 4648 14 + 47259 GAGTTGTCTGAACA -s Anc2.Anc2refChr15 5753 14 - 86568 GAGTTGTCTGAACA -s mr.mrrefChr5 127540 14 + 294540 GAGTTGTTTGACTA -s simCow_chr6.simCow.chr6 339255 14 - 602619 GGGTTCTTTGAATA -s simDog_chr6.simDog.chr6 340069 13 - 593897 -AGTGGTCTGAACA -s simHuman_chr6.simHuman.chr6 193478 14 + 601863 GAGTTGTCTGAACA -s simHuman_chr6.simHuman.chr6 256057 14 + 601863 GAGTTGTCTGAACA -s simRat_chr6.simRat.chr6 265172 14 + 647215 GAGTTGTTTGACTA - -a -s simMouse_chr6.simMouse.chr6 275973 18 + 636262 GTGGTCATTTAAAACTTA -s Anc0.Anc0refChr5 4436 18 - 87904 ATGGTCATTCATAATATA -s Anc1.Anc1refChr7 4669 18 + 47259 ATGGTCATTCATAATATA -s Anc2.Anc2refChr15 5774 18 - 86568 ATGGTCATTCATAATATA -s mr.mrrefChr5 127554 18 + 294540 GTGGTCATTTAAAATATA -s simCow_chr6.simCow.chr6 339276 17 - 602619 ATGGTCAT-CATATTATA -s simDog_chr6.simDog.chr6 340089 18 - 593897 ATCATCATCCATAATATC -s simHuman_chr6.simHuman.chr6 193499 18 + 601863 ATGGCCATTCATAATATA -s simHuman_chr6.simHuman.chr6 256078 18 + 601863 ATGGCCATTCATAATATG -s simRat_chr6.simRat.chr6 265186 18 + 647215 GTGGTCATCTAAAATAAA - -a -s simMouse_chr6.simMouse.chr6 275991 24 + 636262 TTTTAAGAGAACTTGTCTATTGTT -s Anc0.Anc0refChr5 4461 24 - 87904 TTATAAGATGAATGGTCTATTGTT -s Anc1.Anc1refChr7 4694 24 + 47259 TTATAAGATGAATGGTCTATTGTT -s Anc2.Anc2refChr15 5799 24 - 86568 TTGTAAGATGAATGGTCTACTGCT -s mr.mrrefChr5 127572 24 + 294540 TTTTAAGAGAACTTGTCTATTGTT -s simCow_chr6.simCow.chr6 339300 24 - 602619 TTGTAAGATGAGTGGCTTATTTGT -s simDog_chr6.simDog.chr6 340114 24 - 593897 TTGTAAGATGAATGATCTACTGAT -s simHuman_chr6.simHuman.chr6 193524 23 + 601863 TTATAAGGTGAATGGTCTATT-TT -s simHuman_chr6.simHuman.chr6 256103 23 + 601863 TTATAAGGTGAATGGTCTTTG-TT -s simRat_chr6.simRat.chr6 265204 24 + 647215 TTTTAAGTGAACTTGGCTATTGTA - -a -s simMouse_chr6.simMouse.chr6 276015 7 + 636262 AAAGCTG -s Anc0.Anc0refChr5 4485 7 - 87904 AAAGCTG -s Anc1.Anc1refChr7 4718 7 + 47259 AAAGCTG -s Anc2.Anc2refChr15 5823 7 - 86568 AAGGTCA -s mr.mrrefChr5 127596 7 + 294540 AAAGCTG -s simCow_chr6.simCow.chr6 339326 7 - 602619 AAGGTCC -s simDog_chr6.simDog.chr6 340138 7 - 593897 AAGGTCA -s simHuman_chr6.simHuman.chr6 193547 7 + 601863 AGAGCTG -s simHuman_chr6.simHuman.chr6 256126 7 + 601863 GGAGCTG -s simRat_chr6.simRat.chr6 265228 7 + 647215 AAAACTG - -a -s simMouse_chr6.simMouse.chr6 276022 26 + 636262 AGGTCTGGACCACTATAGGCTCTCAG -s Anc0.Anc0refChr5 4493 22 - 87904 ----ATAGACCACTATAGACTCTCAG -s Anc1.Anc1refChr7 4728 26 + 47259 AAGTATAGACCACTATAGACTCTCAG -s Anc2.Anc2refChr15 5831 22 - 86568 ----ATAGACCACTATAGACTCTCAG -s mr.mrrefChr5 127603 26 + 294540 AGGTATGGACCACTATAGGCTCTCAG -s simCow_chr6.simCow.chr6 339334 22 - 602619 ----GTACACCACTATCGACACTCAG -s simDog_chr6.simDog.chr6 340146 22 - 593897 ----ATAAACCACCATAGACTCTAAG -s simHuman_chr6.simHuman.chr6 193557 26 + 601863 AAGTAGAGACCACTATAGACTCTCAG -s simHuman_chr6.simHuman.chr6 256136 26 + 601863 AAGTAGAGACCACTATAGACTCTCAG -s simRat_chr6.simRat.chr6 265235 26 + 647215 AGGTATGGACCACTATAGGCTCTCAA - -a -s simMouse_chr6.simMouse.chr6 276048 10 + 636262 CAGGAGAGAA -s Anc0.Anc0refChr5 4516 9 - 87904 -AGAAGAGAA -s Anc1.Anc1refChr7 4769 10 + 47259 CAGAAGAGAA -s Anc2.Anc2refChr15 5854 9 - 86568 -AGAAGAGAA -s mr.mrrefChr5 127629 10 + 294540 CAGAAGAGAA -s simCow_chr6.simCow.chr6 339357 9 - 602619 -AGATGAGAC -s simDog_chr6.simDog.chr6 340169 9 - 593897 -AGAAGAGAA -s simHuman_chr6.simHuman.chr6 193598 10 + 601863 CAGAAGAGAA -s simHuman_chr6.simHuman.chr6 256177 10 + 601863 CAGAAGAAAA -s simRat_chr6.simRat.chr6 265261 10 + 647215 CAGAAGAGAA - -a -s simMouse_chr6.simMouse.chr6 276058 29 + 636262 GGGATCAGAAAGGGCTAGATAGGATTAGG -s Anc0.Anc0refChr5 4531 29 - 87904 AGGATCAGTCCAGGCTAGGTGGAATTAAG -s Anc1.Anc1refChr7 4785 29 + 47259 AGGATCAGTCCAGGCTAGGTGGAATTAAG -s Anc2.Anc2refChr15 5869 29 - 86568 AGGCTCAGTCCACACTAGGTGGAATTAAG -s mr.mrrefChr5 127639 29 + 294540 GGGATCAGAAAGGGCTAGGTAGGATTAGG -s simCow_chr6.simCow.chr6 339372 29 - 602619 ATGCTCAATCCACACTAGGTAGCATTAAG -s simDog_chr6.simDog.chr6 340184 29 - 593897 ACGCTCAGTTCACACTAGGTTGACTTAAG -s simHuman_chr6.simHuman.chr6 193614 29 + 601863 AGGATCAGTCCAGGCTAAGTGGAATTAAG -s simHuman_chr6.simHuman.chr6 256193 29 + 601863 AGGATCAGTCCAGGCTAAGTGGAATTAAG -s simRat_chr6.simRat.chr6 265271 29 + 647215 GGGATAAGAAAGGGCTAGGCAGTTTTAGG - -a -s simMouse_chr6.simMouse.chr6 276087 11 + 636262 GATATCGCACC -s Anc0.Anc0refChr5 4560 11 - 87904 AATATCACACC -s Anc1.Anc1refChr7 4814 11 + 47259 AATATCACACC -s Anc2.Anc2refChr15 5898 11 - 86568 AATATCACACC -s mr.mrrefChr5 127668 11 + 294540 GATATCGCACC -s simCow_chr6.simCow.chr6 339428 11 - 602619 AAGGTCACACC -s simDog_chr6.simDog.chr6 340213 11 - 593897 GGAAACACAGC -s simHuman_chr6.simHuman.chr6 193643 11 + 601863 AATATCACACC -s simHuman_chr6.simHuman.chr6 256222 11 + 601863 AATATCACACC -s simRat_chr6.simRat.chr6 265300 11 + 647215 GGTATCGCACC - -a -s simMouse_chr6.simMouse.chr6 276098 15 + 636262 CTCTAAAGAGGTGGA -s Anc0.Anc0refChr5 4571 15 - 87904 ACGTAAAGGAGTAGA -s Anc1.Anc1refChr7 4825 15 + 47259 ACGTAAAGGAGTAGA -s Anc2.Anc2refChr15 5909 15 - 86568 ACGTAGAGGAGTAGA -s mr.mrrefChr5 127679 15 + 294540 CTCTAAAGAGGTGGA -s simCow_chr6.simCow.chr6 339443 15 - 602619 CCGCAGGGAATTAGA -s simDog_chr6.simDog.chr6 340224 15 - 593897 ATTTAGACCAATGGC -s simHuman_chr6.simHuman.chr6 193654 15 + 601863 ACGTAAAGGAGTAGA -s simHuman_chr6.simHuman.chr6 256233 15 + 601863 ACGTACAGGAGTAGA -s simRat_chr6.simRat.chr6 265311 15 + 647215 CTCTACAGAGGTGGA - -a -s simMouse_chr6.simMouse.chr6 276113 20 + 636262 TATCAATCTGAAACATGGAG -s Anc0.Anc0refChr5 4586 20 - 87904 CACCAAATTGAGATGTGGAG -s Anc1.Anc1refChr7 4840 20 + 47259 CACCAAATTGAGATGTGGAG -s Anc2.Anc2refChr15 5924 20 - 86568 CACCAAATTGAGATGTGGAG -s mr.mrrefChr5 127694 20 + 294540 TACCAATCTGAAACATGGAG -s simCow_chr6.simCow.chr6 339459 16 - 602619 TACTAAATT----TGTAGTG -s simDog_chr6.simDog.chr6 340239 20 - 593897 CATCCACTTCAAATCAGGAG -s simHuman_chr6.simHuman.chr6 193669 20 + 601863 CACCAAATTGAGATGTGGAG -s simHuman_chr6.simHuman.chr6 256248 20 + 601863 CACCAAATTGAGATGTGGAG -s simRat_chr6.simRat.chr6 265326 20 + 647215 TACTCACCTGAAACATGGAG - -a -s simMouse_chr6.simMouse.chr6 276133 2 + 636262 AT -s Anc0.Anc0refChr5 4606 2 - 87904 AT -s Anc1.Anc1refChr7 4860 2 + 47259 AT -s Anc2.Anc2refChr15 5944 2 - 86568 AT -s mr.mrrefChr5 127714 2 + 294540 AT -s simCow_chr6.simCow.chr6 339738 2 - 602619 AT -s simDog_chr6.simDog.chr6 340259 2 - 593897 AT -s simHuman_chr6.simHuman.chr6 193689 2 + 601863 AT -s simHuman_chr6.simHuman.chr6 256268 2 + 601863 AT -s simRat_chr6.simRat.chr6 265346 2 + 647215 AT - -a -s simMouse_chr6.simMouse.chr6 276135 2 + 636262 GA -s Anc0.Anc0refChr5 4608 2 - 87904 TG -s Anc1.Anc1refChr7 4862 2 + 47259 TG -s Anc2.Anc2refChr15 5946 2 - 86568 TG -s mr.mrrefChr5 127716 2 + 294540 GA -s simCow_chr6.simCow.chr6 63758 2 + 602619 CG -s simDog_chr6.simDog.chr6 340261 2 - 593897 TA -s simHuman_chr6.simHuman.chr6 193691 2 + 601863 TG -s simHuman_chr6.simHuman.chr6 256270 2 + 601863 TG -s simRat_chr6.simRat.chr6 265348 2 + 647215 CA - -a -s simMouse_chr6.simMouse.chr6 276137 9 + 636262 GTAATCCGG -s Anc0.Anc0refChr5 4612 9 - 87904 GTAAAACCA -s Anc1.Anc1refChr7 4866 9 + 47259 GTAAAACCA -s Anc2.Anc2refChr15 5950 9 - 86568 GTAAATCCA -s mr.mrrefChr5 127718 9 + 294540 GTAATCCGG -s simCow_chr6.simCow.chr6 63762 9 + 602619 GTAAATCCA -s simDog_chr6.simDog.chr6 340265 9 - 593897 GTTAATTTG -s simHuman_chr6.simHuman.chr6 193695 9 + 601863 GTAAAACCA -s simHuman_chr6.simHuman.chr6 256274 9 + 601863 GTAAAACCA -s simRat_chr6.simRat.chr6 265350 9 + 647215 GTAATCTGG - -a -s simMouse_chr6.simMouse.chr6 276146 12 + 636262 GCCAACATAGCA -s Anc0.Anc0refChr5 4621 11 - 87904 GCCACCATAGC- -s Anc1.Anc1refChr7 4875 11 + 47259 GCCACCATAGC- -s Anc2.Anc2refChr15 5959 11 - 86568 GCCACCATAGG- -s mr.mrrefChr5 127727 12 + 294540 GCCAACATAGCA -s simCow_chr6.simCow.chr6 63771 11 + 602619 GCCAACATAGG- -s simDog_chr6.simDog.chr6 340274 11 - 593897 GGCACCATAGG- -s simHuman_chr6.simHuman.chr6 256283 11 + 601863 GCCAGCATAGC- -s simRat_chr6.simRat.chr6 265359 12 + 647215 GCCAACATGGCA - -a -s simMouse_chr6.simMouse.chr6 276158 12 + 636262 CAACAGGTTCGT -s Anc0.Anc0refChr5 4632 12 - 87904 CAACGGGTTCGT -s Anc1.Anc1refChr7 4886 12 + 47259 CAACGGGTTCGT -s Anc2.Anc2refChr15 5970 12 - 86568 CAACGGGTTCAT -s mr.mrrefChr5 127739 12 + 294540 CAACGGGTTCGT -s simCow_chr6.simCow.chr6 63783 12 + 602619 CAACTGGTTCAC -s simDog_chr6.simDog.chr6 340285 12 - 593897 CAAAGTGTCTAT -s simHuman_chr6.simHuman.chr6 256294 12 + 601863 TAACGGGTTCGT -s simRat_chr6.simRat.chr6 265371 12 + 647215 CAACGGGTTCAT - -a -s simMouse_chr6.simMouse.chr6 276170 22 + 636262 CCTAGTTGCAGTGAGTGTCAGT -s Anc0.Anc0refChr5 4651 22 - 87904 CCTAGTTCCAGTGAGCATCAGA -s Anc1.Anc1refChr7 4905 22 + 47259 CCTAGTTCCAGTGAGCATCAGA -s Anc2.Anc2refChr15 5989 22 - 86568 TCTAGTTCCAGTGAACATCAGA -s mr.mrrefChr5 127751 22 + 294540 CCTAGTTGCAGTGAGCATCAGA -s simCow_chr6.simCow.chr6 63802 22 + 602619 TGTACTCGCTGTGAACATCAGA -s simDog_chr6.simDog.chr6 340302 22 - 593897 TCTAGTTCCAATGGACATCAGA -s simHuman_chr6.simHuman.chr6 256313 22 + 601863 CCTAGATCTAGTGAGCATCAAA -s simRat_chr6.simRat.chr6 265383 22 + 647215 CCTAGTTGCAGTGAGCATTAGA - -a -s simMouse_chr6.simMouse.chr6 276192 26 + 636262 GGGACACTTGCCACGAGCTCCATCAT -s Anc0.Anc0refChr5 4676 26 - 87904 AGGAGAATTGCCATGAGGTCCAACAT -s Anc1.Anc1refChr7 4930 26 + 47259 AGGAGAATTGCCATGAGGTCCAACAT -s Anc2.Anc2refChr15 6014 26 - 86568 AGGAGAATTGCCATGAGGTCCAACAT -s mr.mrrefChr5 127773 26 + 294540 GGGACACTTGCCACGAGCTCCATCAT -s simCow_chr6.simCow.chr6 63827 22 + 602619 AGAA----TGCCGTGAGGTCCAACAT -s simDog_chr6.simDog.chr6 340327 24 - 593897 AGGTGAATTGTAATGAGG--CAGCAT -s simHuman_chr6.simHuman.chr6 256338 25 + 601863 AGGAGAATGACCATGAGGTCCAACA- -s simRat_chr6.simRat.chr6 265405 26 + 647215 GGGACACTTGCCAGGAGCCCCATCAT - -a -s simMouse_chr6.simMouse.chr6 276218 39 + 636262 GGAACAAAAATCAAGGCTTCTTTCTGAGCCAGGACCATA -s Anc0.Anc0refChr5 4704 14 - 87904 -------------------------AAGCCAGAACCATG -s Anc1.Anc1refChr7 4963 39 + 47259 GAAATAGAAGATTGGGCACCTTCATAAGCCAGAACCATG -s Anc2.Anc2refChr15 6042 14 - 86568 -------------------------AAGCTACAACCATG -s mr.mrrefChr5 127807 39 + 294540 GGAACAAAAGTCAAGGCTTCTTTCTGAGCCAGGACCATA -s simCow_chr6.simCow.chr6 63851 14 + 602619 -------------------------AAACTACAACTACG -s simDog_chr6.simDog.chr6 340353 14 - 593897 -------------------------AAGGTACAACCATG -s simHuman_chr6.simHuman.chr6 256368 39 + 601863 GAAATAGAAGATTGGGCACCTTCATAAGCCAGATCCTTG -s simRat_chr6.simRat.chr6 265439 39 + 647215 GGAACAAAAGCCAAGGCCTCCTTGTGAGCCAGGACCATA - -a -s simMouse_chr6.simMouse.chr6 276257 7 + 636262 TGGCGGG -s Anc0.Anc0refChr5 4720 7 - 87904 TGGGAGG -s Anc1.Anc1refChr7 5004 7 + 47259 TGGGAGG -s Anc2.Anc2refChr15 6058 7 - 86568 TGGGAAG -s mr.mrrefChr5 127848 7 + 294540 TGGCAGG -s simCow_chr6.simCow.chr6 63866 7 + 602619 TGGGATG -s simDog_chr6.simDog.chr6 340369 7 - 593897 TGGGAAA -s simHuman_chr6.simHuman.chr6 256409 7 + 601863 TGGGAGG -s simRat_chr6.simRat.chr6 265480 7 + 647215 TGGCAGG - -a -s simMouse_chr6.simMouse.chr6 276264 7 + 636262 ACAAGAC -s Anc0.Anc0refChr5 4728 7 - 87904 AGAAGAT -s Anc1.Anc1refChr7 5012 7 + 47259 AGAAGAT -s Anc2.Anc2refChr15 6066 7 - 86568 AGAAGAT -s mr.mrrefChr5 127855 7 + 294540 ACAAGAC -s simCow_chr6.simCow.chr6 63873 5 + 602619 --AAGAG -s simDog_chr6.simDog.chr6 340377 7 - 593897 AGTATAT -s simHuman_chr6.simHuman.chr6 256417 7 + 601863 AAAAGAT -s simRat_chr6.simRat.chr6 265487 7 + 647215 ATAAGAC - -a -s simMouse_chr6.simMouse.chr6 276271 8 + 636262 TGCAGATC -s Anc0.Anc0refChr5 4737 8 - 87904 TGTTGATT -s Anc1.Anc1refChr7 5021 8 + 47259 TGTTGATT -s Anc2.Anc2refChr15 6075 8 - 86568 TGTTGATT -s mr.mrrefChr5 127864 8 + 294540 TGCAGATT -s simCow_chr6.simCow.chr6 63880 8 + 602619 TGTTGACT -s simDog_chr6.simDog.chr6 340386 8 - 593897 TATTCATT -s simHuman_chr6.simHuman.chr6 256426 8 + 601863 TGTTGATT -s simRat_chr6.simRat.chr6 265496 8 + 647215 TGCAGATT - -a -s simMouse_chr6.simMouse.chr6 276279 22 + 636262 GCCCTCAAACACCATTTTGGGT -s Anc0.Anc0refChr5 4745 22 - 87904 GCCTTCAAACACCATTTTGAGT -s Anc1.Anc1refChr7 5029 22 + 47259 GCCTTCAAACACCATTTTGAGT -s Anc2.Anc2refChr15 6083 22 - 86568 GTCTTCAAATACCATTTTGAGT -s mr.mrrefChr5 127872 22 + 294540 GCCCTCAAACACCATTTTGGGT -s simCow_chr6.simCow.chr6 63888 22 + 602619 TTCTTCAAATACTGTTTGGAGC -s simDog_chr6.simDog.chr6 340396 22 - 593897 GTTTTCAAATACCATTCTGAGT -s simHuman_chr6.simHuman.chr6 256434 22 + 601863 GCCTCGAAACACCATTTTGAGT -s simRat_chr6.simRat.chr6 265504 22 + 647215 GCCCTCAAAAACCATTTTGGGT - -a -s simMouse_chr6.simMouse.chr6 276301 41 + 636262 AACACATTACAGCTTAATTTCAAGTCGAACTTAGTATACGA -s Anc0.Anc0refChr5 4767 41 - 87904 AGCAATTCATAGCTTAGTTTCCAGTCAAATCCATTGTTCAA -s Anc1.Anc1refChr7 5051 41 + 47259 AGCAATTCATAGCTTAGTTTCCAGTCAAATCCATTGTTCAA -s Anc2.Anc2refChr15 6105 41 - 86568 AGCAATTCATAGCTTAGTTTCCAGTCAAATCCATTGTTCAA -s mr.mrrefChr5 127894 41 + 294540 AACAAATTATAGCTTAATTTCAAGTCAAACTTAGTATACAA -s simCow_chr6.simCow.chr6 63911 41 + 602619 AGCGATTTGTAGTTTAGTTCTAACTCAAATCCATGCTTCAA -s simDog_chr6.simDog.chr6 340418 41 - 593897 AGCAAGTCATAGCTTAGTTTCCAGTCAAATCCATTGTTCAA -s simHuman_chr6.simHuman.chr6 256456 41 + 601863 AGCAATTCATTGCCACGTTTCCAGTCAAATCCACTGTTCAG -s simRat_chr6.simRat.chr6 265526 41 + 647215 AACAAATTATAACTTAATTTCAAGTCAAACATAGCAAACAA - -a -s simMouse_chr6.simMouse.chr6 276342 222 + 636262 GGTAGTGGTGGGTTAATCATAAGGTAGGTACATACATTGTACGAAATGCATTTTATCCTCTGCAGATGTAACTTACTGCATCCTGATTCGGGTACCGTCCAATATATCAGTGTTTGGTAACTTCTGTGTCCAATATAACCATGGAAATATGTGCAAGGGGTACTACCTGATACGTTGGTGTTTGGTGACTTCTGTGTCCAATATAACCATGGAAATATGTGC -s Anc0.Anc0refChr5 4809 69 - 87904 TATAGTGGTGGGTTCATCATAA---------------------------------------------------------------------------------------------------------------------------------------------------------TGCTGTTTAGTGACCTAGGAATAGCATATGACTATGGAAATACATGC -s Anc1.Anc1refChr7 5093 69 + 47259 TATAGTGGTGGGTTCATCATAA---------------------------------------------------------------------------------------------------------------------------------------------------------TGCTGTTTAGTGACCTAGGAATAGCATATGACTATGGAAATACATGC -s Anc2.Anc2refChr15 6147 69 - 86568 TATAGTGGTGGGTTCATCATAA---------------------------------------------------------------------------------------------------------------------------------------------------------TGCTGTTTAGTGACCTAGGAATAGCATATGACTATGGAAATACATGC -s mr.mrrefChr5 127935 195 + 294540 GGTAGTGGTGGGTTAATCATAAGGTAGGTACATACATTGTAC---------------------------AACTTACTGCATCCTGATTCGGGTACCGTCCAATATATCAGTGTTTGGTAACTTCTGTGTCCAATATAACCATGGAAATATGTGCAAGGGGTACTACCTGATACGTTGGTGTTTGGTGACTTCTGTGTCCAATATAACCATGGAAATATGTGC -s simCow_chr6.simCow.chr6 63953 69 + 602619 TATAGTGGTGAGTTCATCATAA---------------------------------------------------------------------------------------------------------------------------------------------------------TGCTGTTTAGTGACCATGGAATAGCATATAACTATGGAAAAACATGC -s simDog_chr6.simDog.chr6 340460 69 - 593897 TGTAGCAGTGGTTTCATCATAA---------------------------------------------------------------------------------------------------------------------------------------------------------TGCTGTTCAGTGACCTAGGAATAGCATATGAGTAAGGAAATGCATGC -s simHuman_chr6.simHuman.chr6 256498 69 + 601863 TATGGTGGTGGGTTCACCGTCA---------------------------------------------------------------------------------------------------------------------------------------------------------TGCTGTTTAGTGTCCTAGGAATAGCGTAACACTATGGAAATACATGC -s simRat_chr6.simRat.chr6 265567 195 + 647215 GGTAGAGGTGGGTTGATCATGAGGTAGGTACATACATTGTGC---------------------------AACTTACCGCATCCTGATTGGGATGCTGTCCAATACATCAGCATTTGGTGACTTCTGCATCCAATATAACCATGGAAATATGCACAAGGGGTACCACCTGATACATCAGTGTTTGGTGATTTTTGTGTCCAATATAGCCAAGGAAATATGTGC - -a -s simMouse_chr6.simMouse.chr6 276564 1 + 636262 A -s Anc0.Anc0refChr5 4883 1 - 87904 A -s Anc1.Anc1refChr7 5167 1 + 47259 A -s Anc2.Anc2refChr15 6226 1 - 86568 A -s mr.mrrefChr5 128130 1 + 294540 A -s simCow_chr6.simCow.chr6 64032 1 + 602619 A -s simDog_chr6.simDog.chr6 340539 1 - 593897 A -s simHuman_chr6.simHuman.chr6 256572 1 + 601863 A -s simRat_chr6.simRat.chr6 265762 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 276565 10 + 636262 GTGCATTGAC -s Anc0.Anc0refChr5 4884 10 - 87904 AGCCATCCAC -s Anc1.Anc1refChr7 5168 10 + 47259 AGCCATCCAC -s Anc2.Anc2refChr15 6227 10 - 86568 AGCCATCCAC -s mr.mrrefChr5 128131 10 + 294540 GTGCATTGAC -s simCow_chr6.simCow.chr6 64033 10 + 602619 AGGCATCCAC -s simDog_chr6.simDog.chr6 340540 10 - 593897 AGCCTTCTCC -s simHuman_chr6.simHuman.chr6 256573 10 + 601863 AGCCATCCAC -s simRat_chr6.simRat.chr6 265779 10 + 647215 GTGCACTGAC - -a -s simMouse_chr6.simMouse.chr6 276575 4 + 636262 AATT -s Anc0.Anc0refChr5 4897 4 - 87904 AACT -s Anc1.Anc1refChr7 5181 4 + 47259 AACT -s Anc2.Anc2refChr15 6248 4 - 86568 AACT -s mr.mrrefChr5 128141 4 + 294540 AATT -s simCow_chr6.simCow.chr6 64065 4 + 602619 AACT -s simDog_chr6.simDog.chr6 340561 4 - 593897 AACT -s simHuman_chr6.simHuman.chr6 256586 4 + 601863 AACT -s simRat_chr6.simRat.chr6 265789 4 + 647215 AATT - -a -s simMouse_chr6.simMouse.chr6 276579 3 + 636262 TAG -s Anc0.Anc0refChr5 4901 3 - 87904 GAG -s Anc1.Anc1refChr7 5185 3 + 47259 GAG -s Anc2.Anc2refChr15 6253 3 - 86568 GAG -s mr.mrrefChr5 128145 3 + 294540 TAG -s simCow_chr6.simCow.chr6 64070 2 + 602619 GA- -s simDog_chr6.simDog.chr6 340566 3 - 593897 GAG -s simHuman_chr6.simHuman.chr6 256590 3 + 601863 CAG -s simRat_chr6.simRat.chr6 265793 3 + 647215 CAA - -a -s simMouse_chr6.simMouse.chr6 276582 3 + 636262 ATT -s Anc0.Anc0refChr5 4904 3 - 87904 ATT -s Anc1.Anc1refChr7 5188 3 + 47259 ATT -s Anc2.Anc2refChr15 6256 3 - 86568 ATT -s mr.mrrefChr5 128148 3 + 294540 ATT -s simCow_chr6.simCow.chr6 64072 1 + 602619 --T -s simDog_chr6.simDog.chr6 340569 3 - 593897 ATT -s simHuman_chr6.simHuman.chr6 256593 3 + 601863 ACT -s simRat_chr6.simRat.chr6 265804 3 + 647215 ATG - -a -s simMouse_chr6.simMouse.chr6 276585 4 + 636262 GAAC -s Anc0.Anc0refChr5 4907 4 - 87904 TTTC -s Anc1.Anc1refChr7 5191 4 + 47259 TTTC -s Anc2.Anc2refChr15 6263 4 - 86568 TTTA -s mr.mrrefChr5 128151 4 + 294540 GAAC -s simCow_chr6.simCow.chr6 64077 4 + 602619 TTTA -s simDog_chr6.simDog.chr6 340576 4 - 593897 TTTA -s simHuman_chr6.simHuman.chr6 256596 4 + 601863 TCTC -s simRat_chr6.simRat.chr6 265807 4 + 647215 GACC - -a -s simMouse_chr6.simMouse.chr6 276589 63 + 636262 TAGATATGTTTTACTCTTTAGACCCTGCAAATTATAGTGACTTGTCCACAATTAAGGGGCATT -s Anc0.Anc0refChr5 4911 53 - 87904 GAGAGAGGCT----------GACCATATGGTTTATAGTGACTAATCTACAAATAAGTGGCATT -s Anc1.Anc1refChr7 5195 53 + 47259 GAGAGAGGCT----------GACCATATGGTTTATAGTGACTAATCTACAAATAAGTGGCATT -s Anc2.Anc2refChr15 6267 53 - 86568 GAGAGAGGCT----------GACCATATGGTTTCTAGTGACTAATATACAAAGAAGTAGCATT -s mr.mrrefChr5 128155 63 + 294540 TAGATATGTTTTACTCTTTAGACCCTGCAAATTATAGTGACTTGTCCACAATTAAGGGGCATT -s simCow_chr6.simCow.chr6 64088 51 + 602619 AAGTCAGGAT----------GACCATAAAGTTTTTAGTGACTAGTGTGC--AAAAGCAGCATT -s simDog_chr6.simDog.chr6 340580 50 - 593897 GAGAGAAGCT----------GACCATATGGTTTCTAGTGGCTAATATACAAAGGTGTAGC--- -s simHuman_chr6.simHuman.chr6 256600 53 + 601863 CATAAAGACT----------GACAGTATGGTTTATAGCAACTAACCTATGAATAAGTGGCATT -s simRat_chr6.simRat.chr6 265811 63 + 647215 TAGATATGATTTGCTCTTTAGACTCTGCAAATTATAGTGACTTGTCCACAATTAAGGGGAATT - -a -s simMouse_chr6.simMouse.chr6 276652 7 + 636262 AACCATA -s Anc0.Anc0refChr5 4976 7 - 87904 AACCCTA -s Anc1.Anc1refChr7 5260 7 + 47259 AACCCTA -s Anc2.Anc2refChr15 6332 7 - 86568 AACCCTA -s mr.mrrefChr5 128218 7 + 294540 AACCATA -s simCow_chr6.simCow.chr6 64151 7 + 602619 AACACTA -s simDog_chr6.simDog.chr6 340642 7 - 593897 AACCCCA -s simHuman_chr6.simHuman.chr6 256665 7 + 601863 AACTGTA -s simRat_chr6.simRat.chr6 265874 7 + 647215 GACCAAA - -a -s simMouse_chr6.simMouse.chr6 276659 7 + 636262 TTGTTTT -s Anc0.Anc0refChr5 4983 7 - 87904 TTGTTTT -s Anc1.Anc1refChr7 5267 7 + 47259 TTGTTTT -s Anc2.Anc2refChr15 6339 7 - 86568 TTGTTTT -s mr.mrrefChr5 128225 7 + 294540 TTGTTTT -s simCow_chr6.simCow.chr6 64158 7 + 602619 TTGTTTT -s simDog_chr6.simDog.chr6 340660 7 - 593897 TTGTTTT -s simHuman_chr6.simHuman.chr6 256672 7 + 601863 TTGTTTT -s simRat_chr6.simRat.chr6 265881 7 + 647215 TCATTTT - -a -s simMouse_chr6.simMouse.chr6 276666 22 + 636262 GTAACATCCTCACAGGTATCAC -s Anc0.Anc0refChr5 4990 18 - 87904 GTTATATCCTCAC-GGTAT--- -s Anc1.Anc1refChr7 5274 22 + 47259 GTTATATCCTCACCGGTATGGC -s Anc2.Anc2refChr15 6346 18 - 86568 GTTGTATCCTCGT-GGTAT--- -s mr.mrrefChr5 128232 22 + 294540 GTAACATCCTCACAGGTATCAC -s simCow_chr6.simCow.chr6 64166 13 + 602619 GTTGCATACT------TAT--- -s simDog_chr6.simDog.chr6 340667 18 - 593897 GTTGTATCCTCGT-GGTAT--- -s simHuman_chr6.simHuman.chr6 256679 22 + 601863 GTTATATCCTCACCTTTTTGGC -s simRat_chr6.simRat.chr6 265888 22 + 647215 CTCATATCCTCACAGGTATCAC - -a -s simMouse_chr6.simMouse.chr6 276688 22 + 636262 AACTTGGAAATTGGGGAATCCC -s Anc0.Anc0refChr5 5012 22 - 87904 AACTTGGAGATTGAGGGATCTC -s Anc1.Anc1refChr7 5301 22 + 47259 AACTTGGAGATTGAGGGATCTC -s Anc2.Anc2refChr15 6368 22 - 86568 CACGTGGAGATTGAGGGATCTC -s mr.mrrefChr5 128254 22 + 294540 AACTTGGAAATTGGGGAATCCC -s simCow_chr6.simCow.chr6 64181 22 + 602619 GGCCTGGAAATTGGGGGATCTC -s simDog_chr6.simDog.chr6 340689 22 - 593897 CATGTGGAGATTGAAGGATATC -s simHuman_chr6.simHuman.chr6 256706 22 + 601863 AACTTGGAGGTTGAGGGATCTC -s simRat_chr6.simRat.chr6 265910 22 + 647215 AACATGGAGATTGGGGAATCCA - -a -s simMouse_chr6.simMouse.chr6 276710 14 + 636262 CGTAGATCAATCAG -s Anc0.Anc0refChr5 5035 14 - 87904 CATAGATCAATCAG -s Anc1.Anc1refChr7 5324 14 + 47259 CATAGATCAATCAG -s Anc2.Anc2refChr15 6391 14 - 86568 CACAAATCAATCAG -s mr.mrrefChr5 128276 14 + 294540 CGTAGATCAATCAG -s simCow_chr6.simCow.chr6 64204 14 + 602619 CACAATTCAATCAG -s simDog_chr6.simDog.chr6 340712 14 - 593897 CGCAAATCAGTCTG -s simHuman_chr6.simHuman.chr6 256729 14 + 601863 CATAGATCAATCAG -s simRat_chr6.simRat.chr6 265932 14 + 647215 CATAGATCAATTAG - -a -s simMouse_chr6.simMouse.chr6 276724 28 + 636262 TGTATTAATGTGAATATGCTTAGACTGT -s Anc0.Anc0refChr5 5050 28 - 87904 TGTATCAAGATGAATATGCCTAGAGTGG -s Anc1.Anc1refChr7 5339 28 + 47259 TGTATCAAGATGAATATGCCTAGAGTGG -s Anc2.Anc2refChr15 6406 28 - 86568 TGTAACAAGATGAATATGCCTAGAGTGG -s mr.mrrefChr5 128290 28 + 294540 TGTATTAATGTGAATATGCTTAGACTGT -s simCow_chr6.simCow.chr6 64219 28 + 602619 TGTAGCAAATTGAATGTGTGTCGAGTGA -s simDog_chr6.simDog.chr6 340727 28 - 593897 TGTAACAAGATGAATATGCCTAGAGTGG -s simHuman_chr6.simHuman.chr6 256744 28 + 601863 TGTTTCAAGATGAATATGCCTAGAGTGG -s simRat_chr6.simRat.chr6 265947 28 + 647215 CATATTAATGTGAACATGCTAGGACTAT - -a -s simMouse_chr6.simMouse.chr6 276752 5 + 636262 CATAA -s Anc0.Anc0refChr5 5078 5 - 87904 CAAAA -s Anc1.Anc1refChr7 5367 5 + 47259 CAAAA -s Anc2.Anc2refChr15 6434 5 - 86568 CGAAA -s mr.mrrefChr5 128318 5 + 294540 CATAA -s simCow_chr6.simCow.chr6 64247 5 + 602619 TGAAA -s simDog_chr6.simDog.chr6 340852 5 - 593897 CGATA -s simHuman_chr6.simHuman.chr6 256772 5 + 601863 CAAAA -s simRat_chr6.simRat.chr6 265975 5 + 647215 CATAA - -a -s simMouse_chr6.simMouse.chr6 276757 38 + 636262 TTGAGCACTACAAACTGGTGACAGGGCCTGTAAAAAAA -s Anc0.Anc0refChr5 5083 36 - 87904 CTGAGCA--ACAAGCTAGTGAGAGGGCCTGAAAAGAGA -s Anc1.Anc1refChr7 5372 36 + 47259 CTGAGCA--ACAAGCTAGTGAGAGGGCCTGAAAAGAGA -s Anc2.Anc2refChr15 6439 36 - 86568 CTGAGCA--ACAAGCCAGTGAGAGGGCCTGAAAAGAGA -s mr.mrrefChr5 128323 38 + 294540 TTGAGCACTACAAACTGGTGACAGGGCCTGTAAAAAAA -s simCow_chr6.simCow.chr6 64252 36 + 602619 CTGAGTA--ACACACCAGTGAGAGGGGCTCAGACGAGA -s simDog_chr6.simDog.chr6 340857 36 - 593897 CTGAGCA--ACAAGCCAGTGAGAGGGCCTGAAAAGCGA -s simHuman_chr6.simHuman.chr6 256777 27 + 601863 CTGAGCA--ACAAGCT---------GCCTGAAAGCAGA -s simRat_chr6.simRat.chr6 266033 38 + 647215 TTGAGCAGTCCAATCTGATGACAGTGCCTGTAAAAAGA - -a -s simMouse_chr6.simMouse.chr6 276795 16 + 636262 TTGTTACAACAAGCAT -s Anc0.Anc0refChr5 5119 16 - 87904 CTTTTGCAACATGGAT -s Anc1.Anc1refChr7 5408 16 + 47259 CTTTTGCAACATGGAT -s Anc2.Anc2refChr15 6475 16 - 86568 CTTTTGCAACATGGTT -s mr.mrrefChr5 128361 16 + 294540 TTGTTACAACAAGCAT -s simCow_chr6.simCow.chr6 64288 16 + 602619 CTTTTTCAACATGGCT -s simDog_chr6.simDog.chr6 340895 16 - 593897 CTACTGCAATACGGTT -s simHuman_chr6.simHuman.chr6 256804 16 + 601863 CTTTTGCAACATGGAT -s simRat_chr6.simRat.chr6 266071 16 + 647215 TTGTAACAACAAGCAT - -a -s simMouse_chr6.simMouse.chr6 276811 41 + 636262 CCTGACCGACTAGATAGATGGATTTGATCTTAACTGACATT -s Anc0.Anc0refChr5 5135 32 - 87904 CCTCACGGTT----TAGATGGATCCCATCCCAAC-----CT -s Anc1.Anc1refChr7 5424 37 + 47259 CCTCACGGTT----TAGATGGATCCCATCCCAACTGCTGCT -s Anc2.Anc2refChr15 6491 32 - 86568 CCTCATGGTT----TAAATGGATCCCATCCCAAC-----CT -s mr.mrrefChr5 128377 41 + 294540 CCTGACCGACTAGATAGATGGATTTGATCTTAACTGACATT -s simCow_chr6.simCow.chr6 64310 10 + 602619 CCTGGTGGTG------------------------------- -s simDog_chr6.simDog.chr6 340911 32 - 593897 TCTCATGGTT----TAAATGGATCCCATCCCAAC-----CT -s simHuman_chr6.simHuman.chr6 256820 37 + 601863 CCTCACTGTT----TAGACGGCTCCCATCCGGACTGCTGCT -s simRat_chr6.simRat.chr6 266087 41 + 647215 CCTGACAGATTAAATAAATGTATTTGATCCTATCTGACTTT - -a -s simMouse_chr6.simMouse.chr6 276852 44 + 636262 TTGTGATCTTCCCTTTTGATTTAGGAACACAGTTCATAATTCCA -s Anc0.Anc0refChr5 5193 36 - 87904 TT--------CACTTTTCTTGTCGGATGACATTTCTTAATTCAA -s Anc1.Anc1refChr7 5487 36 + 47259 TT--------CACTTTTCTTGTCGGATGACATTTCTTAATTCAA -s Anc2.Anc2refChr15 6549 36 - 86568 TT--------CACTTTTCTTGTCGGATGTCATTTCTTAATTAAA -s mr.mrrefChr5 128418 36 + 294540 TT--------CCCTTTTGATTTAGGAACACAGTTCATAATTCCA -s simCow_chr6.simCow.chr6 340216 18 - 602619 --------------------------TGTCATTTTCCAATGTAA -s simDog_chr6.simDog.chr6 340969 36 - 593897 TT--------CACTTTTCTTGTCGGAAGTCAATACTTAATTAAA -s simHuman_chr6.simHuman.chr6 256884 36 + 601863 TT--------CACTTTTATCCTTTGCTGACATTTCTTAATTCAA -s simRat_chr6.simRat.chr6 266128 36 + 647215 TT--------CAATTATGTTCTTGGCTCACAGTTCATAATTCAG - -a -s simMouse_chr6.simMouse.chr6 276896 4 + 636262 CATT -s Anc0.Anc0refChr5 5231 4 - 87904 CAAC -s Anc1.Anc1refChr7 5525 4 + 47259 CAAC -s Anc2.Anc2refChr15 6587 4 - 86568 CAAC -s mr.mrrefChr5 128454 4 + 294540 CATT -s simCow_chr6.simCow.chr6 340236 4 - 602619 CAAT -s simDog_chr6.simDog.chr6 341007 4 - 593897 CACC -s simHuman_chr6.simHuman.chr6 256922 4 + 601863 CAAC -s simRat_chr6.simRat.chr6 266164 4 + 647215 CATC - -a -s simMouse_chr6.simMouse.chr6 276900 67 + 636262 TTTAATTATATAAAAACAGTCCTACTGACTTGTGGGGACATTGTACTGGTTTGTGTACAACACTTAA -s Anc0.Anc0refChr5 5235 18 - 87904 TTTAGTTATATAA------TC-------------------------------------------ACT -s Anc1.Anc1refChr7 5529 18 + 47259 TTTAGTTATATAA------TC-------------------------------------------ACT -s Anc2.Anc2refChr15 6591 18 - 86568 TTTAGCTATTTAA------TC-------------------------------------------ACT -s mr.mrrefChr5 128458 24 + 294540 TTTAATTATATAAAAACAGTC-------------------------------------------TAA -s simCow_chr6.simCow.chr6 340253 18 - 602619 TCTAGCCAGCTAA------TC-------------------------------------------AGA -s simDog_chr6.simDog.chr6 341011 18 - 593897 TTTAGCTATTTAA------TC-------------------------------------------ACT -s simHuman_chr6.simHuman.chr6 256926 18 + 601863 ATTAGTTATATAA------TC-------------------------------------------ACT -s simRat_chr6.simRat.chr6 266168 24 + 647215 TCTAGTTATCTAAAAACAGTC-------------------------------------------TAA - -a -s simMouse_chr6.simMouse.chr6 276967 18 + 636262 CCTACTGACTTGTGGTGA -s Anc0.Anc0refChr5 5253 18 - 87904 CCCACCAAGTTGGAGAGG -s Anc1.Anc1refChr7 5547 18 + 47259 CCCACCAAGTTGGAGAGG -s Anc2.Anc2refChr15 6609 18 - 86568 CCCACCAAGATGGAGAGG -s mr.mrrefChr5 128482 18 + 294540 CCTACTGACTTGTGGTGA -s simCow_chr6.simCow.chr6 340271 12 - 602619 CCCTCCAAGGTG------ -s simDog_chr6.simDog.chr6 341029 18 - 593897 CCCACTAAGATGGAGAGG -s simHuman_chr6.simHuman.chr6 256944 18 + 601863 CACACCAAGTTGGATGGT -s simRat_chr6.simRat.chr6 266199 18 + 647215 CCCACCGAAGTGTAGGGA - -a -s simMouse_chr6.simMouse.chr6 276985 28 + 636262 CATTGTATTGGTTTGTGTACAACACTTA -s Anc0.Anc0refChr5 5271 23 - 87904 C-----ACTGGTCTATACACAACACTCA -s Anc1.Anc1refChr7 5565 23 + 47259 C-----ACTGGTCTATACACAACACTCA -s Anc2.Anc2refChr15 6627 23 - 86568 C-----ACTGTTCCATACACAACACTCA -s mr.mrrefChr5 128500 28 + 294540 CATTGTATTGGTTTGTGTACAACACTTA -s simCow_chr6.simCow.chr6 340283 10 - 602619 ------------------ATAACACTCA -s simDog_chr6.simDog.chr6 341049 23 - 593897 C-----ACTGTTCCATACACAACAGTCA -s simHuman_chr6.simHuman.chr6 256962 23 + 601863 C-----ACTGGTCTATACACAACACTCA -s simRat_chr6.simRat.chr6 266217 28 + 647215 CATTGTACTGGGTTGTATACAACACATA - -a -s simMouse_chr6.simMouse.chr6 277013 33 + 636262 AGTCGATGAATTCACGGCTACAGGCTTGCCTGT -s Anc0.Anc0refChr5 5302 32 - 87904 AGTCAGTGAATCCACAGCTGCAGA-TTGCATGC -s Anc1.Anc1refChr7 5596 32 + 47259 AGTCAGTGAATCCACAGCTGCAGA-TTGCATGC -s Anc2.Anc2refChr15 6658 32 - 86568 AGTCAGTGAATCCAGAGCTGCAAA-TTGCATGC -s mr.mrrefChr5 128528 33 + 294540 AGTCGATGAATTCACGGCTACAGGCTTGCCTGT -s simCow_chr6.simCow.chr6 340301 32 - 602619 AGTCAGTTAATCTATAGCTGCAAA-TTGCATGC -s simDog_chr6.simDog.chr6 341080 32 - 593897 AGTCAATGAGTCCAGAGCTGCAAA-TTGCGTGC -s simHuman_chr6.simHuman.chr6 256993 32 + 601863 AGTCAGTGAATCCACAGCTGCAGA-TTGCATGC -s simRat_chr6.simRat.chr6 266245 33 + 647215 AATCAGTGAATTGACAGCTACAAGCTTGCCTGT - -a -s simMouse_chr6.simMouse.chr6 277046 16 + 636262 GCAAAACAGATATTTA -s Anc0.Anc0refChr5 5339 11 - 87904 ACA-----GGCATTTA -s Anc1.Anc1refChr7 5633 11 + 47259 ACA-----GGCATTTA -s Anc2.Anc2refChr15 6695 11 - 86568 ACA-----AGCATTTA -s mr.mrrefChr5 128561 11 + 294540 GCA-----GATATTTA -s simCow_chr6.simCow.chr6 340337 8 - 602619 --------TGCATTTA -s simDog_chr6.simDog.chr6 341117 11 - 593897 ACA-----AGCATTTA -s simHuman_chr6.simHuman.chr6 257030 11 + 601863 ACA-----GGCAATTA -s simRat_chr6.simRat.chr6 266278 11 + 647215 GCA-----GATCTCTC - -a -s simMouse_chr6.simMouse.chr6 277062 4 + 636262 TTGT -s Anc0.Anc0refChr5 5350 4 - 87904 TTGT -s Anc1.Anc1refChr7 5644 4 + 47259 TTGT -s Anc2.Anc2refChr15 6706 4 - 86568 TCGT -s mr.mrrefChr5 128572 4 + 294540 TTGT -s simCow_chr6.simCow.chr6 340345 4 - 602619 TTGG -s simDog_chr6.simDog.chr6 341128 4 - 593897 TCAT -s simHuman_chr6.simHuman.chr6 257056 4 + 601863 TTGA -s simRat_chr6.simRat.chr6 266289 4 + 647215 TTGT - -a -s simMouse_chr6.simMouse.chr6 277066 68 + 636262 TCTGTGCCTTATTGGATCTGTAGCCAGTGCTGGCCAGCTTTTGGAGCACAAAAGGCCTCAGCCCTGGC -s Anc0.Anc0refChr5 5354 68 - 87904 TCTGTGCATTGTTGAATCCGTTGGCACCATAAGCCAGGTTTTGAATGATAAATAACCTCACCCAGAAG -s Anc1.Anc1refChr7 5648 68 + 47259 TCTGTGCATTGTTGAATCCGTTGGCACCATAAGCCAGGTTTTGAATGATAAATAACCTCACCCAGAAG -s Anc2.Anc2refChr15 6719 68 - 86568 TCTGTGCATTGTTGAATCCGTTGGTACCATAAGCTGGGTTTTGAATGATAAATAACCTTACCCAGAAG -s mr.mrrefChr5 128576 68 + 294540 TCTGTGCCTTATTGGATCTGTAGCCAGTGCTGGCCAGCTTTTGGAGCACAAAAGGCCTCAGCCCTGGC -s simCow_chr6.simCow.chr6 340357 60 - 602619 --------TCGTTGAATCCGTTGGTACCACAAGCTGGGTTTTGAATGATAAATAACCTGACCCAGAGG -s simDog_chr6.simDog.chr6 341141 50 - 593897 TCTGTGCACTG------------------TAAGCTGTGTTTTGGATGATAAATAACCTTACCCCTAAG -s simHuman_chr6.simHuman.chr6 257060 68 + 601863 CCTATGCATTGTTGACTCCGTGGGCACCAGAATCCAGGTTTCGAATGATAAAGAATCTCACCCAGAAG -s simRat_chr6.simRat.chr6 266293 68 + 647215 ACTATGCCTTGTTGGAACTGTGGGGAGTGCTAGCCAGCTTTTAGACCATAAAAGGCCTGACCCCTGGC - -a -s simMouse_chr6.simMouse.chr6 277134 80 + 636262 TGCGGCCATGAAGCAAGAATCACTGTCAATCCTGTCTCATGAGCAGCTTTTAAATTGTAAAAGACCTGACACCTGGCTTG -s Anc0.Anc0refChr5 5422 5 - 87904 TG---------------------------------------------------------------------------TTG -s Anc1.Anc1refChr7 5716 5 + 47259 TG---------------------------------------------------------------------------TTG -s Anc2.Anc2refChr15 6816 5 - 86568 TT---------------------------------------------------------------------------TTG -s mr.mrrefChr5 128644 76 + 294540 TGCGGCCATGAAGCAA---TCACTGTCAATCCTGTCTCATGAGCAGCTTTTAAATTGTAAAAGACCTGACAC-TGGCTTG -s simCow_chr6.simCow.chr6 340447 5 - 602619 CT---------------------------------------------------------------------------TCA -s simDog_chr6.simDog.chr6 341220 5 - 593897 TT---------------------------------------------------------------------------TTG -s simHuman_chr6.simHuman.chr6 257128 5 + 601863 TG---------------------------------------------------------------------------TAG -s simRat_chr6.simRat.chr6 266361 76 + 647215 TGCAGCCATAAAGCAA---TCACTGTCATTCCTGTATCTTGCCCAGCTTTTAAATCGTAAAAGACCTGACAT-TGGCTGG - -a -s simMouse_chr6.simMouse.chr6 277214 68 + 636262 CAATAAAGCAACTACCACTGTCACTGTCATCTCAGAATCATGCTGTATAAAGTTATGAAGATTAACGA -s Anc0.Anc0refChr5 5427 62 - 87904 CAATGAAGTAACAACCACTGTAATT------CAAGAAGCACACTGTGTGAAGCCACAAAGTTTAACAC -s Anc1.Anc1refChr7 5721 62 + 47259 CAATGAAGTAACAACCACTGTAATT------CAAGAAGCACACTGTGTGAAGCCACAAAGTTTAACAC -s Anc2.Anc2refChr15 6821 62 - 86568 CAATGAAGTAACAACCACTGTAATT------CAAGAAGTACACTGTGTGAGGCCACAAAGTTTAACAC -s mr.mrrefChr5 128720 62 + 294540 CAATAAAGCAACTACCACTGTCACT------TCAGAATCATGCTGTATAAAGTTATGAAGATTAACGA -s simCow_chr6.simCow.chr6 340452 62 - 602619 CAATGAAGTAACAACCACTGTAACT------CAGGAAGTACGTTGTATTGGGCCACAAGGTTTAACAC -s simDog_chr6.simDog.chr6 341225 62 - 593897 CAATGAAGCAACACCCACTGTGGTT------CAAGGAGTACACTGTGTGAGGCCAAGAAGTTGAACGC -s simHuman_chr6.simHuman.chr6 257133 62 + 601863 CAATGAAGTAACAACCACTGAAATT------CAAGAAGCAGACAGCGTCAAGCCACAAAGTTTAACAC -s simRat_chr6.simRat.chr6 266439 62 + 647215 CAACAAAGCAACTACCACTTCCGAT------TCTGAATCATGCTGTATAAAGCTGTAAAGATTAGCGA - -a -s simMouse_chr6.simMouse.chr6 277282 1 + 636262 A -s Anc0.Anc0refChr5 5490 1 - 87904 A -s Anc1.Anc1refChr7 5784 1 + 47259 A -s Anc2.Anc2refChr15 6884 1 - 86568 A -s mr.mrrefChr5 128782 1 + 294540 A -s simCow_chr6.simCow.chr6 340515 1 - 602619 A -s simDog_chr6.simDog.chr6 341288 1 - 593897 A -s simHuman_chr6.simHuman.chr6 257196 1 + 601863 A -s simRat_chr6.simRat.chr6 266501 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 277283 13 + 636262 GTACAGCATATGA -s Anc0.Anc0refChr5 5491 13 - 87904 GTTCAGCAAATGA -s Anc1.Anc1refChr7 5785 13 + 47259 GTTCAGCAAATGA -s Anc2.Anc2refChr15 6886 13 - 86568 GTTCAGCAAATGA -s mr.mrrefChr5 128783 13 + 294540 GTACAGCATATGA -s simCow_chr6.simCow.chr6 340517 13 - 602619 GCTCAGCAAGTGA -s simDog_chr6.simDog.chr6 341290 13 - 593897 GTTGAGCAAATGA -s simHuman_chr6.simHuman.chr6 257197 13 + 601863 GTGCAGCAAAGGA -s simRat_chr6.simRat.chr6 266502 13 + 647215 ATACAGCAAATGA - -a -s simMouse_chr6.simMouse.chr6 277296 25 + 636262 ATTATTGATGTCTTGATATACCATA -s Anc0.Anc0refChr5 5504 18 - 87904 ATTATCTATGTCT-------CAATA -s Anc1.Anc1refChr7 5798 18 + 47259 ATTATCTATGTCT-------CAATA -s Anc2.Anc2refChr15 6899 18 - 86568 ATTGTCTATGTTT-------TAACA -s mr.mrrefChr5 128796 18 + 294540 ATTATTGATGTCT-------CCATA -s simCow_chr6.simCow.chr6 340530 18 - 602619 ATTGTCTATGATT-------TAAAA -s simDog_chr6.simDog.chr6 341304 18 - 593897 ATTGTCTATGTTT-------TGGCA -s simHuman_chr6.simHuman.chr6 257210 18 + 601863 ATTATCTATGTCT-------CAATA -s simRat_chr6.simRat.chr6 266515 18 + 647215 ATTATTGATGTCT-------CCATC - -a -s simMouse_chr6.simMouse.chr6 277321 32 + 636262 AGTAGGGGGGGGTGCCTGTTAATTGTGCAATC -s Anc0.Anc0refChr5 5528 27 - 87904 -GTAAGTGGTGAAGTCTGTTTAATGTA----C -s Anc1.Anc1refChr7 5822 28 + 47259 AGTAAGTGGTGAAGTCTGTTTAATGTA----C -s Anc2.Anc2refChr15 6923 27 - 86568 -GTAAGTGGTGAAGTCTGTTTAATGTA----C -s mr.mrrefChr5 128814 32 + 294540 AGTAGGGGGGGGTGCCTGTTAATTGTGCAATC -s simCow_chr6.simCow.chr6 340554 22 - 602619 -AT-----GTGACGCCTGCTTTCTGTG----C -s simDog_chr6.simDog.chr6 341328 26 - 593897 -GTAAGTGGTAGA-TCTGTTCAATGTA----C -s simHuman_chr6.simHuman.chr6 257235 28 + 601863 AGTAAGAGGTGAAGTGTGTTTAATGGA----C -s simRat_chr6.simRat.chr6 266533 32 + 647215 AGTAGGGGGGGGTGCCTGTTAAGTGTACAATC - -a -s simMouse_chr6.simMouse.chr6 277353 48 + 636262 TAAATTACATACTGATGGATCACAGTTGTGCTCTTTAATATGTTCTGA -s Anc0.Anc0refChr5 5555 20 - 87904 T-------------------CACAGTTGTGATCCTGAA---------A -s Anc1.Anc1refChr7 5850 29 + 47259 TTAATAA--GA--------TCACAGTTGTGATCCTGAA---------A -s Anc2.Anc2refChr15 6950 20 - 86568 T-------------------CACAGTTGTGATCCTGAA---------A -s mr.mrrefChr5 128846 46 + 294540 TAAATTA--TACTGATGGATCACAGTTGTGCTCTTTAATATGTTCTGA -s simCow_chr6.simCow.chr6 340606 20 - 602619 T-------------------AACAGTTGAGATTCTGGA---------A -s simDog_chr6.simDog.chr6 341354 20 - 593897 C-------------------CACAGTTGTGATCCTGAA---------A -s simHuman_chr6.simHuman.chr6 257263 9 + 601863 TTAATAA--GA------------------------------------- -s simRat_chr6.simRat.chr6 266565 46 + 647215 TAAATTA--TACTGATGGATCATAGTAGTGTTCTTTAATATGTTCTGA - -a -s simMouse_chr6.simMouse.chr6 277401 24 + 636262 GACACATGTCATGAGCATCAGGTC -s Anc0.Anc0refChr5 5575 24 - 87904 GACATAAGCTATAACCACTAGTAC -s Anc1.Anc1refChr7 5879 24 + 47259 GACATAAGCTATAACCACTAGTAC -s Anc2.Anc2refChr15 6970 24 - 86568 GACATAAGCTATAACCACTAGTAC -s mr.mrrefChr5 128892 24 + 294540 GACACATGTCATGAGCATCAGGTC -s simCow_chr6.simCow.chr6 340626 24 - 602619 GATATATGCCATGACCACTAGGAC -s simDog_chr6.simDog.chr6 341375 24 - 593897 GACATAAGCTATAACCACTAGTAC -s simRat_chr6.simRat.chr6 266611 24 + 647215 CACACATTTCATGAGCATTAAGTC - -a -s simMouse_chr6.simMouse.chr6 277425 18 + 636262 ACAGTCAATTGTTCTAAC -s Anc0.Anc0refChr5 5599 13 - 87904 ATAGTCAATTATT----- -s Anc1.Anc1refChr7 5903 13 + 47259 ATAGTCAATTATT----- -s Anc2.Anc2refChr15 6995 13 - 86568 ATAGTTAGTTATT----- -s mr.mrrefChr5 128916 18 + 294540 ACAGTCAATTGTTCTAAC -s simCow_chr6.simCow.chr6 340651 13 - 602619 ATAGTTGTTCATC----- -s simDog_chr6.simDog.chr6 341400 13 - 593897 ATAGTTAGTTATT----- -s simHuman_chr6.simHuman.chr6 257272 9 + 601863 ----TCAAATATT----- -s simRat_chr6.simRat.chr6 266636 18 + 647215 ATAGTCAATTGTTGTAAC - -a -s simMouse_chr6.simMouse.chr6 277443 2 + 636262 TT -s Anc0.Anc0refChr5 5612 2 - 87904 GA -s Anc1.Anc1refChr7 5916 2 + 47259 GA -s Anc2.Anc2refChr15 7008 2 - 86568 GA -s mr.mrrefChr5 128934 2 + 294540 TT -s simCow_chr6.simCow.chr6 340664 2 - 602619 TA -s simDog_chr6.simDog.chr6 341413 2 - 593897 GA -s simHuman_chr6.simHuman.chr6 257281 2 + 601863 GA -s simRat_chr6.simRat.chr6 266666 2 + 647215 TT - -a -s simMouse_chr6.simMouse.chr6 277445 14 + 636262 TGTCACCTTTTAAA -s Anc0.Anc0refChr5 5614 14 - 87904 TGGCACCTGGGCAG -s Anc1.Anc1refChr7 5918 14 + 47259 TGGCACCTGGGCAG -s Anc2.Anc2refChr15 7035 14 - 86568 TGGGACCTGGGCAG -s mr.mrrefChr5 128936 14 + 294540 TGTCACCTTTTAAA -s simCow_chr6.simCow.chr6 340691 13 - 602619 AGGGAC-TGGCCAG -s simDog_chr6.simDog.chr6 341442 14 - 593897 TGGGACCTGAGCTC -s simHuman_chr6.simHuman.chr6 257283 14 + 601863 TGGCTCCTGGGCAG -s simRat_chr6.simRat.chr6 266668 14 + 647215 TGACACTATCTAAG - -a -s simMouse_chr6.simMouse.chr6 277459 51 + 636262 ATATATCTAAGGCTACTAAAGAGTTAAGCTGACCTCCTCATTATTATCTAC -s Anc0.Anc0refChr5 5630 30 - 87904 ATGTATCT-----TATGAGAGACTTTAACTGC----------------TAA -s Anc1.Anc1refChr7 5934 30 + 47259 ATGTATCT-----TATGAGAGACTTTAACTGC----------------TAA -s Anc2.Anc2refChr15 7051 30 - 86568 AGGTATCT-----TATGAGAGACTTTAACTGC----------------TAA -s mr.mrrefChr5 128950 51 + 294540 ATATATCTAAGGCTACTAAAGAGTTAAGCTGACCTCCTCATTATTATCTAC -s simCow_chr6.simCow.chr6 340706 30 - 602619 GGGTATCC-----TATTAGAGACCGTACCTGC----------------CAA -s simDog_chr6.simDog.chr6 341458 30 - 593897 AGGGATCT-----TATGAGAGACTTTGACTGC----------------TAG -s simHuman_chr6.simHuman.chr6 257299 30 + 601863 ATGTGTCT-----TATGAGAGGCTTTATCTGG----------------TGA -s simRat_chr6.simRat.chr6 266682 51 + 647215 ATAGAGCTAAGGCTATTAAAGAATGAAGTTGATCTCCTCTTTACTGTCTCC - -a -s simMouse_chr6.simMouse.chr6 277510 11 + 636262 TTTGCTCATTT -s Anc0.Anc0refChr5 5660 11 - 87904 TTTGCTCATCT -s Anc1.Anc1refChr7 5964 11 + 47259 TTTGCTCATCT -s Anc2.Anc2refChr15 7081 11 - 86568 TTCGCTCATCT -s mr.mrrefChr5 129001 11 + 294540 TTTGCTCATTT -s simCow_chr6.simCow.chr6 340747 11 - 602619 TTAGCTCATTT -s simDog_chr6.simDog.chr6 341488 11 - 593897 TTCGCTTTCCT -s simHuman_chr6.simHuman.chr6 257329 11 + 601863 TTTGGTCATCT -s simRat_chr6.simRat.chr6 266733 11 + 647215 TTTGCTCATTT - -a -s simMouse_chr6.simMouse.chr6 277521 4 + 636262 CCTT -s Anc0.Anc0refChr5 5671 4 - 87904 CCTA -s Anc1.Anc1refChr7 5975 4 + 47259 CCTA -s Anc2.Anc2refChr15 7092 4 - 86568 CCTA -s mr.mrrefChr5 129012 4 + 294540 CCTT -s simCow_chr6.simCow.chr6 340758 4 - 602619 CCTA -s simDog_chr6.simDog.chr6 341502 4 - 593897 CCTA -s simHuman_chr6.simHuman.chr6 257340 4 + 601863 TCTA -s simRat_chr6.simRat.chr6 266744 4 + 647215 CCTG - -a -s simMouse_chr6.simMouse.chr6 277525 25 + 636262 TAGGCCTGCACAGCCTGGTTATGAG -s Anc0.Anc0refChr5 5675 25 - 87904 TAGGCCTGCTTAGAGTGGTTATTAG -s Anc1.Anc1refChr7 5979 25 + 47259 TAGGCCTGCTTAGAGTGGTTATTAG -s Anc2.Anc2refChr15 7096 25 - 86568 TAGGCCTGCTTAGAGTGATTATTAG -s mr.mrrefChr5 129016 25 + 294540 TAGGCCTGCACAGCCTGGTTATGAG -s simCow_chr6.simCow.chr6 340762 23 - 602619 TAAGCCTGATTAG--TGTTTCTCAT -s simDog_chr6.simDog.chr6 341506 25 - 593897 TAGGCCTGCTAACAGTGATTATTAG -s simHuman_chr6.simHuman.chr6 257344 25 + 601863 TAGGCGTGCCTAGAGTGGTTACTAG -s simRat_chr6.simRat.chr6 266749 25 + 647215 TAGGCCTGCATAGCCTGGTTATCAG - -a -s simMouse_chr6.simMouse.chr6 277550 18 + 636262 GGAAGCAAAATAGCTGTG -s Anc0.Anc0refChr5 5700 18 - 87904 GGCATCAAAATGACAGCA -s Anc1.Anc1refChr7 6004 18 + 47259 GGCATCAAAATGACAGCA -s Anc2.Anc2refChr15 7121 18 - 86568 GCCATCAAAATGACAGCA -s mr.mrrefChr5 129041 18 + 294540 GGAAGCAAAATAGCTGTG -s simCow_chr6.simCow.chr6 340785 18 - 602619 GTCATCAAAATGATAGCA -s simDog_chr6.simDog.chr6 341560 18 - 593897 GCCATCAAAATGACAGCA -s simHuman_chr6.simHuman.chr6 257369 18 + 601863 GGCATCAAAATTACAGCA -s simRat_chr6.simRat.chr6 266774 18 + 647215 GCAAGCAAAATAACAGCA - -a -s simMouse_chr6.simMouse.chr6 277568 44 + 636262 TGTTTGTGCATGAATGTTTTGAATACTTAGAGTGCTAAAGAGAA -s Anc0.Anc0refChr5 5718 43 - 87904 CA-TTGTGCATGAACTATTTGAATACTTCATGTGCCAGAGATGA -s Anc1.Anc1refChr7 6022 43 + 47259 CA-TTGTGCATGAACTATTTGAATACTTCATGTGCCAGAGATGA -s Anc2.Anc2refChr15 7139 43 - 86568 CA-TAATACATGAGCTACTTGGATACTCCATGCGCCAGAGATGA -s mr.mrrefChr5 129059 44 + 294540 TGTTTGTGCATGAATGTTTTGAATACTTAGAGTGCTAAAGAGAA -s simCow_chr6.simCow.chr6 340804 43 - 602619 CA-AAATACATGAGCTACTTGGATACTCCATGCGCCAGAGATGA -s simDog_chr6.simDog.chr6 341578 3 - 593897 TA-T---------------------------------------- -s simHuman_chr6.simHuman.chr6 257387 43 + 601863 CA-TTGTGCATGAACTATTAAAATACATGATGTGCCAGAGAACA -s simRat_chr6.simRat.chr6 266792 44 + 647215 TGATTGTGCATGAACTTTTTGAATAGTTAGAGTGTTAAAGAGAA - -a -s simMouse_chr6.simMouse.chr6 277612 5 + 636262 TGGTC -s Anc0.Anc0refChr5 5766 5 - 87904 TGGTC -s Anc1.Anc1refChr7 6070 5 + 47259 TGGTC -s Anc2.Anc2refChr15 7187 5 - 86568 TGATC -s mr.mrrefChr5 129103 5 + 294540 TGGTC -s simCow_chr6.simCow.chr6 340852 5 - 602619 TGATC -s simHuman_chr6.simHuman.chr6 257435 5 + 601863 TTGTC -s simRat_chr6.simRat.chr6 266836 5 + 647215 TGGTT - -a -s simMouse_chr6.simMouse.chr6 277617 8 + 636262 TATGCCTC -s Anc0.Anc0refChr5 5771 8 - 87904 TTTGTTTT -s Anc1.Anc1refChr7 6075 8 + 47259 TTTGTTTT -s Anc2.Anc2refChr15 7192 8 - 86568 TTGGTTTT -s mr.mrrefChr5 129108 8 + 294540 TATGCCTC -s simCow_chr6.simCow.chr6 340862 8 - 602619 TTGGTTTT -s simHuman_chr6.simHuman.chr6 257440 8 + 601863 TTTGTTTT -s simRat_chr6.simRat.chr6 266841 8 + 647215 TGTGTCTC - -a -s simMouse_chr6.simMouse.chr6 277625 8 + 636262 TAGCTAGT -s Anc0.Anc0refChr5 5781 5 - 87904 T--CTAC- -s Anc1.Anc1refChr7 6085 6 + 47259 T--CTACT -s Anc2.Anc2refChr15 7202 5 - 86568 C--TTAC- -s mr.mrrefChr5 129116 6 + 294540 T--CTAGT -s simCow_chr6.simCow.chr6 340872 5 - 602619 C--TTAC- -s simHuman_chr6.simHuman.chr6 257450 6 + 601863 T--CTACT -s simRat_chr6.simRat.chr6 266849 6 + 647215 T--TTAGT - -a -s simMouse_chr6.simMouse.chr6 277633 1 + 636262 G -s Anc0.Anc0refChr5 5792 1 - 87904 G -s Anc1.Anc1refChr7 6097 1 + 47259 G -s Anc2.Anc2refChr15 7213 1 - 86568 G -s mr.mrrefChr5 129122 1 + 294540 G -s simCow_chr6.simCow.chr6 340883 1 - 602619 A -s simDog_chr6.simDog.chr6 341587 1 - 593897 G -s simHuman_chr6.simHuman.chr6 257466 1 + 601863 G -s simRat_chr6.simRat.chr6 266855 1 + 647215 G - -a -s simMouse_chr6.simMouse.chr6 277634 3 + 636262 GTT -s Anc0.Anc0refChr3 220729 3 - 222631 GCT -s Anc1.Anc1refChr5 2248 3 - 6477 GCT -s Anc2.Anc2refChr13 92427 3 - 96486 GCT -s mr.mrrefChr5 129123 3 + 294540 GTT -s simCow_chr6.simCow.chr6 243124 3 - 602619 GGT -s simDog_chr6.simDog.chr6 243765 3 - 593897 GCT -s simHuman_chr6.simHuman.chr6 353602 3 - 601863 ACT -s simRat_chr6.simRat.chr6 266856 3 + 647215 ATT - -a -s simMouse_chr6.simMouse.chr6 277637 6 + 636262 TAGATA -s Anc0.Anc0refChr3 220732 6 - 222631 TAGATA -s Anc1.Anc1refChr5 2251 6 - 6477 TAGATA -s Anc2.Anc2refChr13 92430 6 - 96486 TAATTA -s mr.mrrefChr5 129126 6 + 294540 TAGATA -s simCow_chr6.simCow.chr6 243130 6 - 602619 TATGCA -s simDog_chr6.simDog.chr6 243768 6 - 593897 TAATTA -s simHuman_chr6.simHuman.chr6 353605 6 - 601863 TAGATA -s simRat_chr6.simRat.chr6 266859 6 + 647215 TAGATA - -a -s simMouse_chr6.simMouse.chr6 277643 7 + 636262 GTGGTTT -s Anc0.Anc0refChr3 220742 7 - 222631 GTGGTAT -s Anc1.Anc1refChr5 2261 7 - 6477 GTGGTAT -s Anc2.Anc2refChr13 92451 7 - 96486 ATGGCAG -s mr.mrrefChr5 129132 7 + 294540 GTGGTTT -s simCow_chr6.simCow.chr6 243152 7 - 602619 GTAGCAG -s simDog_chr6.simDog.chr6 243789 7 - 593897 ATGGCAG -s simHuman_chr6.simHuman.chr6 353615 7 - 601863 GTGGTAT -s simRat_chr6.simRat.chr6 266865 7 + 647215 GTGGTTC - -a -s simMouse_chr6.simMouse.chr6 277650 12 + 636262 AGAAGAGATCCT -s Anc0.Anc0refChr3 220751 12 - 222631 AGGGGAGGTCCT -s Anc1.Anc1refChr5 2270 12 - 6477 AGGGGAGGTCCT -s Anc2.Anc2refChr13 92464 12 - 96486 AGGGGAGGTCCT -s mr.mrrefChr5 129139 12 + 294540 AGAAGAGATCCT -s simCow_chr6.simCow.chr6 243165 12 - 602619 AAGGGAGGTCTT -s simDog_chr6.simDog.chr6 243802 12 - 593897 AGGGAAAGTCCT -s simHuman_chr6.simHuman.chr6 353624 12 - 601863 AGGGGAGGTCCT -s simRat_chr6.simRat.chr6 266872 12 + 647215 ACGAGAGATCTT - -a -s simMouse_chr6.simMouse.chr6 277662 6 + 636262 GTCAAA -s Anc0.Anc0refChr3 220768 4 - 222631 GTCA-- -s Anc1.Anc1refChr5 2287 4 - 6477 GTCA-- -s Anc2.Anc2refChr13 92481 4 - 96486 GTCA-- -s mr.mrrefChr5 129151 4 + 294540 GTCA-- -s simCow_chr6.simCow.chr6 243182 4 - 602619 GTCA-- -s simDog_chr6.simDog.chr6 243819 4 - 593897 GTCA-- -s simHuman_chr6.simHuman.chr6 353641 4 - 601863 GTCA-- -s simRat_chr6.simRat.chr6 266884 4 + 647215 GTCA-- - -a -s simMouse_chr6.simMouse.chr6 277668 13 + 636262 TGTATATTTAATG -s Anc0.Anc0refChr3 220774 13 - 222631 TGTATATTTAGTG -s Anc1.Anc1refChr5 2293 13 - 6477 TGTATATTTAGTG -s Anc2.Anc2refChr13 92487 13 - 96486 TGTATATTTAGTG -s mr.mrrefChr5 129155 13 + 294540 TGTATATTTAATG -s simCow_chr6.simCow.chr6 243188 13 - 602619 TGTATATTAAGTG -s simDog_chr6.simDog.chr6 243825 13 - 593897 TGTATAGCTAGTG -s simHuman_chr6.simHuman.chr6 353647 13 - 601863 TATATATTTAGTG -s simRat_chr6.simRat.chr6 266888 13 + 647215 TCTAGTGTGAACA - -a -s simMouse_chr6.simMouse.chr6 277681 4 + 636262 GAAA -s Anc0.Anc0refChr3 220793 4 - 222631 GAAA -s Anc1.Anc1refChr5 2312 4 - 6477 GAAA -s Anc2.Anc2refChr13 92506 4 - 96486 AAAA -s mr.mrrefChr5 129168 4 + 294540 GAAA -s simCow_chr6.simCow.chr6 243207 4 - 602619 AAAA -s simDog_chr6.simDog.chr6 243844 4 - 593897 AAAA -s simHuman_chr6.simHuman.chr6 353666 4 - 601863 GAAA -s simRat_chr6.simRat.chr6 266901 4 + 647215 GATA - -a -s simMouse_chr6.simMouse.chr6 277685 10 + 636262 CTGACCGGTT -s Anc0.Anc0refChr3 220797 10 - 222631 CTAATCCTTT -s Anc1.Anc1refChr5 2316 10 - 6477 CTAATCCTTT -s Anc2.Anc2refChr13 92510 10 - 96486 CTAATCCTTT -s mr.mrrefChr5 129172 10 + 294540 CTGACCGGTT -s simCow_chr6.simCow.chr6 243211 10 - 602619 CTAACCTTTT -s simDog_chr6.simDog.chr6 243849 10 - 593897 CCAATCCTTT -s simHuman_chr6.simHuman.chr6 353670 10 - 601863 CTAATCCTTT -s simRat_chr6.simRat.chr6 266905 10 + 647215 CCGACCAGTT - -a -s simMouse_chr6.simMouse.chr6 277695 15 + 636262 AAGTCAGGTTGAGAT -s Anc0.Anc0refChr3 220807 15 - 222631 AAGCCAGGTTGGTGT -s Anc1.Anc1refChr5 2326 15 - 6477 AAGCCAGGTTGGTGT -s Anc2.Anc2refChr13 92520 15 - 96486 AAGCTGGGTTGGTGT -s mr.mrrefChr5 129182 15 + 294540 AAGTCAGGTTGAGAT -s simCow_chr6.simCow.chr6 243221 12 - 602619 AA---GGGTTGGTGG -s simDog_chr6.simDog.chr6 243859 12 - 593897 GAGCTGGGTAG---T -s simHuman_chr6.simHuman.chr6 353680 15 - 601863 AACCCAGGTTGGTGT -s simRat_chr6.simRat.chr6 266917 15 + 647215 AAATCAGCTTGAGAT - -a -s simMouse_chr6.simMouse.chr6 277710 17 + 636262 ACTGTGGGATCTACAAC -s Anc0.Anc0refChr3 220822 17 - 222631 ACCATGGGATCAATAAC -s Anc1.Anc1refChr5 2341 17 - 6477 ACCATGGGATCAATAAC -s Anc2.Anc2refChr13 92535 17 - 96486 ACCATGGGATCAATGAC -s mr.mrrefChr5 129197 17 + 294540 ACTGTGGGATCTACAAC -s simCow_chr6.simCow.chr6 243235 17 - 602619 ACCATTGGATCAATGAC -s simDog_chr6.simDog.chr6 243871 17 - 593897 ACCATGGGATCAATGCC -s simHuman_chr6.simHuman.chr6 353695 17 - 601863 ACCATGGGATTAATAAC -s simRat_chr6.simRat.chr6 266932 17 + 647215 ACTGTGGGATCTACAAC - -a -s simMouse_chr6.simMouse.chr6 277727 6 + 636262 TTGCTA -s Anc0.Anc0refChr3 220840 6 - 222631 TTGTTA -s Anc1.Anc1refChr5 2359 6 - 6477 TTGTTA -s Anc2.Anc2refChr13 92553 6 - 96486 TTGTTA -s mr.mrrefChr5 129214 6 + 294540 TTGCTA -s simCow_chr6.simCow.chr6 243253 6 - 602619 TTGTTC -s simDog_chr6.simDog.chr6 243889 6 - 593897 TTGTTA -s simHuman_chr6.simHuman.chr6 353713 6 - 601863 TTGTTA -s simRat_chr6.simRat.chr6 266949 6 + 647215 TTGTTG - -a -s simMouse_chr6.simMouse.chr6 277733 35 + 636262 CTGGCATTAGTGGGCACTACTGAGGTAGGTTGCTC -s Anc0.Anc0refChr3 220850 34 - 222631 CTGGCCTTTACAGGCACAATCTAG-TAGGCTGCTC -s Anc1.Anc1refChr5 2369 34 - 6477 CTGGCCTTTACAGGCACAATCTAG-TAGGCTGCTC -s Anc2.Anc2refChr13 92563 34 - 96486 CTGGCCTTTACAGGCACAATCTAG-TAGGCTGCTC -s mr.mrrefChr5 129220 34 + 294540 CTGGCATTAGTGGGCACTACTGAG-TAGGTTGCTC -s simCow_chr6.simCow.chr6 243263 34 - 602619 CTGGCCTCTACAGGCACAGTCTGG-TAGTCTTCTC -s simDog_chr6.simDog.chr6 243899 34 - 593897 CCCGCCTTTATGGGCACAATATAG-TAGGCTGCCC -s simHuman_chr6.simHuman.chr6 353723 34 - 601863 TTGGCCTTTACAGGCACAAGCTAG-TAGGCTGCTC -s simRat_chr6.simRat.chr6 266959 34 + 647215 CTGGCCTTATTGGGCACTACTAAG-TAGGTTGCTC - -a -s simMouse_chr6.simMouse.chr6 277768 21 + 636262 CACCTTTTAGTCTAAGTTGTT -s Anc0.Anc0refChr3 220886 21 - 222631 CACCTTTTGGCATTGGTCCTT -s Anc1.Anc1refChr5 2405 21 - 6477 CACCTTTTGGCATTGGTCCTT -s Anc2.Anc2refChr13 92599 21 - 96486 CATCTTTTGGCATTGATCCCT -s mr.mrrefChr5 129254 21 + 294540 CACCTTTTAGTCTAAGTTGTT -s simCow_chr6.simCow.chr6 243299 21 - 602619 CATCTTTTGGCATTGATTCCT -s simDog_chr6.simDog.chr6 243935 21 - 593897 TGTCTTTTAGCATCGATCCCC -s simHuman_chr6.simHuman.chr6 353759 21 - 601863 CACCTTTTGGCATTGGTCATT -s simRat_chr6.simRat.chr6 266993 21 + 647215 CACCTTTTAGTCAAAGCTGTT - -a -s simMouse_chr6.simMouse.chr6 277789 47 + 636262 TCTGACTTCTAGATAAAGTCTCCGCACTATTACGACTGGTACATCCA -s Anc0.Anc0refChr3 220907 47 - 222631 TTTGACTTTCATATGAAGTCCATGCACTATTACACATGGGACATCCA -s Anc1.Anc1refChr5 2426 47 - 6477 TTTGACTTTCATATGAAGTCCATGCACTATTACACATGGGACATCCA -s Anc2.Anc2refChr13 92621 47 - 96486 TTTGACTATCATATGAAGTCCATGCACTATAACACATGGGACACCCA -s mr.mrrefChr5 129275 47 + 294540 TCTGACTTCTAGATAAAGTCTCCGCACTATTACGACTGGTACATCCA -s simCow_chr6.simCow.chr6 243321 47 - 602619 TTTGATGCTCATATGAAGTCCACACACTATAGCACGTGGAACACCAG -s simDog_chr6.simDog.chr6 243957 47 - 593897 TCCAACTATCATATGAAGTCCATGCACTATAACACATGGGACACCCA -s simHuman_chr6.simHuman.chr6 353780 42 - 601863 TTTGACTTTCGTATGAAGTCCATGCACCTCT-----TGGGTTGTCCA -s simRat_chr6.simRat.chr6 267014 47 + 647215 TCTGACTTCTAGATAATATTTCTGCACCGTCACAACTGGTACATCCA - -a -s simMouse_chr6.simMouse.chr6 277836 20 + 636262 GTTAAAATGATGGGTCATAG -s Anc0.Anc0refChr3 220954 20 - 222631 CTTAATATGATGGATCACAG -s Anc1.Anc1refChr5 2473 20 - 6477 CTTAATATGATGGATCACAG -s Anc2.Anc2refChr13 92668 20 - 96486 CTTAATATGATGGATCACAG -s mr.mrrefChr5 129322 20 + 294540 GTTAAAATGATGGGTCATAG -s simCow_chr6.simCow.chr6 243368 20 - 602619 CTAAACATGATGGCTCCCAG -s simDog_chr6.simDog.chr6 244004 20 - 593897 CTTCATATGATGGATCACAG -s simHuman_chr6.simHuman.chr6 353828 20 - 601863 ATTAGTATGATGGATCACAG -s simRat_chr6.simRat.chr6 267061 20 + 647215 GTTATAATGATGGATTATAG - -a -s simMouse_chr6.simMouse.chr6 277856 7 + 636262 CCTCTCC -s mr.mrrefChr5 129342 7 + 294540 CCTCTCC -s simRat_chr6.simRat.chr6 267112 7 + 647215 CCATTCC - -a -s simMouse_chr6.simMouse.chr6 277863 69 + 636262 TGGTGGTATTGTAAGGAGATTATCTAGTACCAACATTTAGCTATAGAGAGACCCCTTACATATATAGTT -s Anc0.Anc0refChr3 220974 49 - 222631 -------------AGGGGATATGCT-------ATATTAAGCTATAGAGATACCCTTTACAGTTACAGTT -s Anc1.Anc1refChr5 2493 49 - 6477 -------------AGGGGATATGCT-------ATATTAAGCTATAGAGATACCCTTTACAGTTACAGTT -s Anc2.Anc2refChr13 92688 49 - 96486 -------------AGGGAATATGCT-------ATATTAAGCTATAGAGATACCCTTTACAGTTACAGTT -s mr.mrrefChr5 129349 69 + 294540 TGGTGGTATTGTAAGGAGATTATCTAGTACCAACATTTAGCTATAGAGAGACCCCTTACATATATAGTT -s simCow_chr6.simCow.chr6 243388 42 - 602619 -------------AGGGAATATGCT-------ATATTAAGCTATAGA-------TTTACATTCACAGTT -s simDog_chr6.simDog.chr6 244024 49 - 593897 -------------AGCAAATGTGCT-------ATATTAAGCTATAGAGATACCCTCTACAGTTACAGTC -s simHuman_chr6.simHuman.chr6 353848 49 - 601863 -------------AGGGGATACGCT-------ATATGAAGCTATAGAGATATCTATTGCAATAACAATT -s simRat_chr6.simRat.chr6 267123 69 + 647215 TGGTGGTATCGTATGGGGATCATCTAGTACCATCATTTATCTATAGAGCTACCTCTCACATGTATAGTT - -a -s simMouse_chr6.simMouse.chr6 277932 59 + 636262 AATTGCGTCTCACTGTTTGTGGAATTAATGCTTGGCTCTGTCAATCTCAAGCTTCACAT -s Anc0.Anc0refChr3 221023 57 - 222631 AATTTTGTCATATCATTTGTGGAATTAATATTTGGCTGTATGAATTATAAT-TTC-CAT -s Anc1.Anc1refChr5 2542 58 - 6477 AATTTTGTCATATCATTTGTGGAATTAATATTTGGCTGTATGAATTATAATCTTC-CAT -s Anc2.Anc2refChr13 92737 57 - 96486 AATTTTTTCATATCATTTATGCAAGTAATATTTGGCCGTATGATTTATAAT-TTC-CAT -s mr.mrrefChr5 129418 59 + 294540 AATTGCGTCTCACTGTTTGTGGAATTAATGCTTGGCTCTGTCAATCTCAAGCTTCACAT -s simCow_chr6.simCow.chr6 243431 31 - 602619 AATTTTTCTATATCATTT--------------------------TTATAAT-TTC-CAT -s simDog_chr6.simDog.chr6 244073 57 - 593897 AATTTTTTCATCTCATTTATGCAAGTAATATTTGGCCGTATGATTTATAAT-TTC-CCT -s simHuman_chr6.simHuman.chr6 353897 58 - 601863 AATTTTGTCAGATCATTTGTGGGATTAACATTTGGCTACATAAACTCTCTTCTTC-CAT -s simRat_chr6.simRat.chr6 267192 59 + 647215 AACTTCGTCACACCGTTTGTAGAATTAACGCTTTGCTCTGTCAATGTCAAGCTTCAAGA - -a -s simMouse_chr6.simMouse.chr6 277991 28 + 636262 TCAATGATCCCATTATTACATGGGTTTC -s Anc0.Anc0refChr3 221083 27 - 222631 TGAATGA-TCCATTATTACACTGGACTC -s Anc1.Anc1refChr5 2603 27 - 6477 TGAATGA-TCCATTATTACACTGGACTC -s Anc2.Anc2refChr13 92797 27 - 96486 TGAATGA-TCCATTACTACACTGGACTC -s mr.mrrefChr5 129477 27 + 294540 TCAATGA-CCCATTATTACATGGGTTTC -s simCow_chr6.simCow.chr6 243465 27 - 602619 TGAATGA-TCCATTACTACACTGGATTT -s simDog_chr6.simDog.chr6 244133 25 - 593897 TTAATG---CCATAACTACGCTGGACTC -s simHuman_chr6.simHuman.chr6 353958 27 - 601863 TGAATGA-ACCATTATCATACTGGGCTC -s simRat_chr6.simRat.chr6 267251 27 + 647215 TCAATGA-ACCATTATTATATGGGATTC - -a -s simMouse_chr6.simMouse.chr6 278019 12 + 636262 ATTAAGATTTTT -s Anc0.Anc0refChr3 221149 12 - 222631 ATTAGAATGTCT -s Anc1.Anc1refChr5 2669 12 - 6477 ATTAGAATGTCT -s Anc2.Anc2refChr13 92863 12 - 96486 ATTAGAATGTCT -s mr.mrrefChr5 129504 12 + 294540 ATTAAGATTTTT -s simCow_chr6.simCow.chr6 243530 12 - 602619 ATTAGAACGTCT -s simDog_chr6.simDog.chr6 244185 12 - 593897 TTAATAATGCCT -s simHuman_chr6.simHuman.chr6 354024 12 - 601863 ATTAGAATGTCT -s simRat_chr6.simRat.chr6 267278 12 + 647215 ATTTAGATTTTT - -a -s simMouse_chr6.simMouse.chr6 278031 16 + 636262 AATAGTAGGCCCACAA -s Anc0.Anc0refChr3 221161 16 - 222631 AACAGTAAGTCCATGA -s Anc1.Anc1refChr5 2681 16 - 6477 AACAGTAAGTCCATGA -s Anc2.Anc2refChr13 92875 16 - 96486 AACAGTAAATCCATGA -s mr.mrrefChr5 129516 16 + 294540 AATAGTAGGCCCACAA -s simCow_chr6.simCow.chr6 243542 16 - 602619 AACAGTAATTCCTTTA -s simDog_chr6.simDog.chr6 244198 16 - 593897 AACAGTAGATCCAAGA -s simHuman_chr6.simHuman.chr6 354036 16 - 601863 AACAGTAAGTCCATGA -s simRat_chr6.simRat.chr6 267290 16 + 647215 AATAGTAGACCCATAA - -a -s simMouse_chr6.simMouse.chr6 278047 26 + 636262 CTGCCTACTTGAAATGCTCTTCTGTC -s Anc0.Anc0refChr3 221181 18 - 222631 CTCCTCACAA--------CTTCTGAT -s Anc1.Anc1refChr5 2701 18 - 6477 CTCCTCACAA--------CTTCTGAT -s Anc2.Anc2refChr13 92895 18 - 96486 CTCCTCACAA--------CTTCTGAT -s mr.mrrefChr5 129532 18 + 294540 CTGCCTACTT--------CTTCTGTC -s simCow_chr6.simCow.chr6 243562 18 - 602619 CTCCTGACAA--------ATTCTGAT -s simDog_chr6.simDog.chr6 244218 18 - 593897 CTCCTCACAG--------CTTCTGAC -s simHuman_chr6.simHuman.chr6 354056 18 - 601863 CTCCTCACAA--------CTTCTGGT -s simRat_chr6.simRat.chr6 267306 18 + 647215 GTGCCTCCTT--------CTTCTGTC - -a -s simMouse_chr6.simMouse.chr6 278073 84 + 636262 TATGCTGGGAAGCAGAGCATTTGAGTTAAGTTTACCTGAAGAAATACGCTTGGCTTCACACCTTGTATCCGGGTTTACACCTAC -s Anc0.Anc0refChr3 221199 63 - 222631 AGGGCT---ACACAGGGCATTTGAGTTTAGTTTACCTGAGAAAATACAC------------------TCAGGTTCTCCACCAGC -s Anc1.Anc1refChr5 2719 64 - 6477 AGGGCT---ACACAGGGCATTTGAGTTTAGTTTACCTGAGAAAATACACT-----------------TCAGGTTCTCCACCAGC -s Anc2.Anc2refChr13 92918 63 - 96486 AGGGGT---ACACAGGGCATTTGAGTTTAGTTTACCTGAGAAAATACAC------------------TCAGGTTCTCCACCAGC -s mr.mrrefChr5 129550 83 + 294540 TATGCTGGGAAGCAGAGCATTTGAGTTAAGTTTACCTGAAGAAATACGCT-GGCTTCACACCTTGTATCCGGGTTTACACCTAC -s simCow_chr6.simCow.chr6 243585 63 - 602619 TGGGGT---ACACAGGGCACTTGAGTTTAATTTACCTGAGGAAATACAC------------------TTAGGTTCTGTGCCTCC -s simDog_chr6.simDog.chr6 244241 63 - 593897 AGGGGC---ATACAGGGCATTCGAGTTTGGTTGACATGAAAAAATACTC------------------CCAGGTTCTCCACCAGC -s simHuman_chr6.simHuman.chr6 354074 47 - 601863 AGGGCT---ACACAGGGCATTTGAATTTAGTTTACCTGAGAGAATACACT---------------------------------- -s simRat_chr6.simRat.chr6 267324 83 + 647215 TACGATGGGGAGCGGAGCATTTGAGTTTAGTTTACCTGAAGAAATACACT-GGCTTCATACCGTGTACCTGGGTTTACACCTAC - -a -s simMouse_chr6.simMouse.chr6 278157 46 + 636262 TATCTGGGTTTACACCGACTTGCTGCTTATTAGTTAGCACAAAAAG -s Anc0.Anc0refChr3 221262 23 - 222631 T-------------------TACTGCTCATCCATTAGTGTG----A -s Anc1.Anc1refChr5 2783 25 - 6477 T-------------------TACTGCTCATCCATTAGTGTGA--CA -s Anc2.Anc2refChr13 92984 23 - 96486 T-------------------TACTGCTCATCCATTAGTGTG----A -s mr.mrrefChr5 129633 27 + 294540 T-------------------TGCTGCTTATTAGTTAGCACAAAAAG -s simCow_chr6.simCow.chr6 243651 23 - 602619 T-------------------TGCTGCTGATTCATTAGCATG----A -s simDog_chr6.simDog.chr6 244307 23 - 593897 T-------------------TACTGCTCATCCATTAGTGTG----A -s simHuman_chr6.simHuman.chr6 354121 2 - 601863 --------------------------------------------CA -s simRat_chr6.simRat.chr6 267407 27 + 647215 T-------------------TGCTGCTTATTAGTTAGCACAAGAAG - -a -s simMouse_chr6.simMouse.chr6 278203 52 + 636262 TGTAGATTTTAGGATTGGCATTTAAGCTGAGATGGGACAAGTATCTCGTTTC -s Anc0.Anc0refChr3 221285 52 - 222631 TATAGATTTTAGGATTGGATTTTGAGCTGAGACTGAACAAGTAGCTTGTGCC -s Anc1.Anc1refChr5 2808 52 - 6477 TATAGATTTTAGGATTGGATTTTGAGCTGAGACTGAACAAGTAGCTTGTGCC -s Anc2.Anc2refChr13 93007 52 - 96486 TATAGATTTTAGGATTGGATTTTGAGTTGAGTCTGAACAAGTAGCTTGTGCC -s mr.mrrefChr5 129660 52 + 294540 TGTAGATTTTAGGATTGGCATTTAAGCTGAGATGGGACAAGTATCTCGTTTC -s simCow_chr6.simCow.chr6 243674 32 - 602619 --------------------TTTGAAGTGGGTCTGGATAAGTAGCTTGTGTC -s simDog_chr6.simDog.chr6 244335 52 - 593897 TATAGATTTTAGGATTGGATTCTAAGTTAAGTTTGAGCAAGTAGCTTGTGCC -s simHuman_chr6.simHuman.chr6 354123 52 - 601863 TATTGATCTTAGGATTGATTTTTGAGCTGAGACTGAACAAGTAGCTTGTGCC -s simRat_chr6.simRat.chr6 267434 52 + 647215 TGTAGCTTTTAGGATTGGCATTGAAGCTGGTATGGGCCAAATATCTTGTTTC - -a -s simMouse_chr6.simMouse.chr6 278255 21 + 636262 CATGCCCAATAACAGTCATGG -s Anc0.Anc0refChr3 221341 20 - 222631 TATGCCC-ATAATCGTCAGGG -s Anc1.Anc1refChr5 2864 20 - 6477 TATGCCC-ATAATCGTCAGGG -s Anc2.Anc2refChr13 93063 20 - 96486 TATGCCC-ATAATCATCAGGG -s mr.mrrefChr5 129712 21 + 294540 CATGCCCAATAACAGTCATGG -s simCow_chr6.simCow.chr6 243710 20 - 602619 TATGTCC-AGAATTATCAGAG -s simDog_chr6.simDog.chr6 244391 20 - 593897 TGTGCCC-TTAATCATCAGGG -s simHuman_chr6.simHuman.chr6 354179 20 - 601863 TATGCCC-ATAATGGTCAAGG -s simRat_chr6.simRat.chr6 267486 21 + 647215 CATGCCTAATAACAATCATGG - -a -s simMouse_chr6.simMouse.chr6 278276 6 + 636262 CCATCC -s Anc0.Anc0refChr3 221361 6 - 222631 CCCTCC -s Anc1.Anc1refChr5 2884 6 - 6477 CCCTCC -s Anc2.Anc2refChr13 93083 6 - 96486 CCCTCC -s mr.mrrefChr5 129733 6 + 294540 CCATCC -s simCow_chr6.simCow.chr6 243730 6 - 602619 CACTGC -s simDog_chr6.simDog.chr6 244412 6 - 593897 CCCCCC -s simHuman_chr6.simHuman.chr6 354199 6 - 601863 CCCTTC -s simRat_chr6.simRat.chr6 267507 6 + 647215 CCATCC - -a -s simMouse_chr6.simMouse.chr6 278282 9 + 636262 AAAAATGTA -s Anc0.Anc0refChr3 221376 9 - 222631 AACAATTTA -s Anc1.Anc1refChr5 2899 9 - 6477 AACAATTTA -s Anc2.Anc2refChr13 93098 9 - 96486 AACAATTTG -s mr.mrrefChr5 129739 9 + 294540 AAAAATGTA -s simCow_chr6.simCow.chr6 243743 5 - 602619 ----ATCTG -s simDog_chr6.simDog.chr6 244427 9 - 593897 AACAATTTG -s simHuman_chr6.simHuman.chr6 354214 9 - 601863 AACAATTTA -s simRat_chr6.simRat.chr6 267513 9 + 647215 AAAAATGTA - -a -s simMouse_chr6.simMouse.chr6 278291 26 + 636262 CTGGACTGACAATCCTGCCATCCTAG -s Anc0.Anc0refChr3 221386 26 - 222631 CCATACCAACAATTTGTCCATACTAG -s Anc1.Anc1refChr5 2909 26 - 6477 CCATACCAACAATTTGTCCATACTAG -s Anc2.Anc2refChr13 93108 26 - 96486 CCATACCAATAATTTGTCCATACTAA -s mr.mrrefChr5 129748 26 + 294540 CTGGACTGACAATCCTGCCATCCTAG -s simCow_chr6.simCow.chr6 243749 26 - 602619 CCATACTAATACTTGGTCCATGCTAC -s simDog_chr6.simDog.chr6 244437 26 - 593897 CCATACCTATAATTTGTCCATACTAA -s simHuman_chr6.simHuman.chr6 354224 26 - 601863 CCATACCAGCAATTTGTTCAAACTGG -s simRat_chr6.simRat.chr6 267522 26 + 647215 CTGGACTGACAATCTTGCCATTCTAG - -a -s simMouse_chr6.simMouse.chr6 278317 3 + 636262 TTC -s Anc0.Anc0refChr3 221413 3 - 222631 TTA -s Anc1.Anc1refChr5 2936 3 - 6477 TTA -s Anc2.Anc2refChr13 93135 3 - 96486 TCA -s mr.mrrefChr5 129774 3 + 294540 TTC -s simCow_chr6.simCow.chr6 243776 3 - 602619 TCA -s simDog_chr6.simDog.chr6 244464 3 - 593897 TCA -s simHuman_chr6.simHuman.chr6 354251 3 - 601863 TTA -s simRat_chr6.simRat.chr6 267548 3 + 647215 TTC - -a -s simMouse_chr6.simMouse.chr6 278320 2 + 636262 CA -s Anc0.Anc0refChr3 221416 2 - 222631 CA -s Anc1.Anc1refChr5 2939 2 - 6477 CA -s Anc2.Anc2refChr13 93138 2 - 96486 CA -s mr.mrrefChr5 129777 2 + 294540 CA -s simCow_chr6.simCow.chr6 243779 2 - 602619 CA -s simDog_chr6.simDog.chr6 244467 2 - 593897 CA -s simHuman_chr6.simHuman.chr6 354254 2 - 601863 CA -s simRat_chr6.simRat.chr6 267552 2 + 647215 CA - -a -s simMouse_chr6.simMouse.chr6 278322 4 + 636262 GGGT -s Anc0.Anc0refChr3 221420 4 - 222631 GGTG -s Anc1.Anc1refChr5 2943 4 - 6477 GGTG -s Anc2.Anc2refChr13 93142 4 - 96486 GGTG -s mr.mrrefChr5 129779 4 + 294540 GGGT -s simCow_chr6.simCow.chr6 243783 4 - 602619 TATG -s simDog_chr6.simDog.chr6 244471 4 - 593897 GGTG -s simHuman_chr6.simHuman.chr6 354258 4 - 601863 GGTG -s simRat_chr6.simRat.chr6 267554 4 + 647215 GGGT - -a -s simMouse_chr6.simMouse.chr6 278326 23 + 636262 TTCCCTTAAGAGGCTTGCTGCAT -s Anc0.Anc0refChr3 221424 23 - 222631 TTCCTTTAAGAGACTTATGGCAT -s Anc1.Anc1refChr5 2947 23 - 6477 TTCCTTTAAGAGACTTATGGCAT -s Anc2.Anc2refChr13 93146 23 - 96486 TTCCTTTAAGAGACTTATGGGCT -s mr.mrrefChr5 129783 23 + 294540 TTCCCTTAAGAGGCTTGCTGCAT -s simCow_chr6.simCow.chr6 243787 23 - 602619 TTCCTTTAAGGAACCTATGGGCT -s simDog_chr6.simDog.chr6 244475 20 - 593897 TTCCTTTAATAGACTGCTG---G -s simHuman_chr6.simHuman.chr6 354262 22 - 601863 TACTTTTAAGAGA-GTATGGCAT -s simRat_chr6.simRat.chr6 267559 23 + 647215 TTCCCTTAAGAGATTTGCTGCCT - -a -s simMouse_chr6.simMouse.chr6 278349 6 + 636262 AGAGTC -s Anc0.Anc0refChr3 221450 6 - 222631 GTGATT -s Anc1.Anc1refChr5 2973 6 - 6477 GTGATT -s Anc2.Anc2refChr13 93172 6 - 96486 GTGATT -s mr.mrrefChr5 129806 6 + 294540 AGAGTC -s simCow_chr6.simCow.chr6 243813 6 - 602619 GTGATT -s simDog_chr6.simDog.chr6 244498 6 - 593897 GTGATT -s simHuman_chr6.simHuman.chr6 354287 6 - 601863 GTGTCT -s simRat_chr6.simRat.chr6 267582 6 + 647215 CAAGTC - -a -s simMouse_chr6.simMouse.chr6 278355 9 + 636262 CTGTATTTT -s Anc0.Anc0refChr3 221456 9 - 222631 CTTTATCTT -s Anc1.Anc1refChr5 2979 9 - 6477 CTTTATCTT -s Anc2.Anc2refChr13 93178 9 - 96486 CTTTATCTT -s mr.mrrefChr5 129812 9 + 294540 CTGTATTTT -s mr.mrrefChr5 130035 9 + 294540 CGTCGGCGT -s simCow_chr6.simCow.chr6 243819 9 - 602619 TTTTATCTT -s simDog_chr6.simDog.chr6 244504 9 - 593897 CTTTATCTT -s simHuman_chr6.simHuman.chr6 354293 9 - 601863 CCTTATCTT -s simMouse_chr6.simMouse.chr6 278578 9 + 636262 CGTCGGCGT -s simRat_chr6.simRat.chr6 267588 9 + 647215 TGTGATTTT - -a -s simMouse_chr6.simMouse.chr6 278364 2 + 636262 GC -s Anc0.Anc0refChr3 221465 2 - 222631 GC -s Anc1.Anc1refChr5 2988 2 - 6477 GC -s Anc2.Anc2refChr13 93187 2 - 96486 GC -s mr.mrrefChr5 129821 2 + 294540 GC -s mr.mrrefChr5 130044 1 + 294540 G- -s simCow_chr6.simCow.chr6 243828 2 - 602619 GC -s simDog_chr6.simDog.chr6 244513 2 - 593897 GC -s simHuman_chr6.simHuman.chr6 354302 2 - 601863 GC -s simMouse_chr6.simMouse.chr6 278590 1 + 636262 G- -s simRat_chr6.simRat.chr6 267597 2 + 647215 AC - -a -s simMouse_chr6.simMouse.chr6 278366 1 + 636262 C -s Anc0.Anc0refChr3 221467 1 - 222631 C -s Anc1.Anc1refChr5 2990 1 - 6477 C -s Anc2.Anc2refChr13 93200 1 - 96486 C -s mr.mrrefChr5 129823 1 + 294540 C -s simCow_chr6.simCow.chr6 243841 1 - 602619 C -s simDog_chr6.simDog.chr6 244527 1 - 593897 T -s simHuman_chr6.simHuman.chr6 354304 1 - 601863 C -s simRat_chr6.simRat.chr6 267599 1 + 647215 C - -a -s simMouse_chr6.simMouse.chr6 278367 17 + 636262 CTTCTAGTTCTCTCTGC -s Anc0.Anc0refChr3 221469 17 - 222631 CATCTAGTCCTCTCTGC -s Anc1.Anc1refChr5 2992 17 - 6477 CATCTAGTCCTCTCTGC -s Anc2.Anc2refChr13 93202 17 - 96486 CATCTAGTCCTCTCTGC -s mr.mrrefChr5 129824 17 + 294540 CTTCTAGTTCTCTCTGC -s mr.mrrefChr5 130045 17 + 294540 CTGCAAGTTCTCTTTGC -s simCow_chr6.simCow.chr6 243843 17 - 602619 CATCTGGTCCTCTCTGT -s simDog_chr6.simDog.chr6 244529 17 - 593897 CATCTAGACCTCTCTGC -s simHuman_chr6.simHuman.chr6 354306 17 - 601863 CATTTAGTCCTCTCTGC -s simMouse_chr6.simMouse.chr6 278591 17 + 636262 CTGCAAGTTCTCTTTGC -s simRat_chr6.simRat.chr6 267600 17 + 647215 CTTCTAGTTCTCTCTGT - -a -s simMouse_chr6.simMouse.chr6 278384 21 + 636262 CCGAATGAACTATACAATACT -s Anc0.Anc0refChr3 221499 19 - 222631 TTG--TGAACTCTACAAAATT -s Anc1.Anc1refChr5 3022 21 - 6477 TTGAATGAACTCTACAAAATT -s Anc2.Anc2refChr13 93232 19 - 96486 TTG--TGAACTCTTGAAAATT -s mr.mrrefChr5 129841 21 + 294540 CCGAATGAACTATACAATACT -s mr.mrrefChr5 130075 21 + 294540 TTGAATGAACTATACCATACT -s simCow_chr6.simCow.chr6 243873 19 - 602619 TCG--TGAACTCTGGAAAAGT -s simDog_chr6.simDog.chr6 244559 19 - 593897 TTG--TTCACTCTTGAAAATT -s simHuman_chr6.simHuman.chr6 354336 21 - 601863 TTGAATGAACTCTCAATAATT -s simMouse_chr6.simMouse.chr6 278621 21 + 636262 TTGAATGAACTATACCATACT -s simRat_chr6.simRat.chr6 267617 21 + 647215 CGGAATGAACTATACAATACT - -a -s simMouse_chr6.simMouse.chr6 278405 4 + 636262 GCAG -s Anc0.Anc0refChr3 221518 4 - 222631 GCAG -s Anc1.Anc1refChr5 3043 4 - 6477 GCAG -s Anc2.Anc2refChr13 93251 4 - 96486 GCAG -s mr.mrrefChr5 129862 4 + 294540 GCAG -s mr.mrrefChr5 130096 4 + 294540 GCAG -s simCow_chr6.simCow.chr6 243892 4 - 602619 GCAG -s simDog_chr6.simDog.chr6 244579 4 - 593897 ACAA -s simHuman_chr6.simHuman.chr6 354357 4 - 601863 GCAG -s simMouse_chr6.simMouse.chr6 278642 4 + 636262 GCAG -s simRat_chr6.simRat.chr6 267638 4 + 647215 GCAG - -a -s simMouse_chr6.simMouse.chr6 278409 19 + 636262 GGGCATTTTGAATATCACT -s Anc0.Anc0refChr3 221522 19 - 222631 AGGGGTTTTGAATGTCATT -s Anc1.Anc1refChr5 3047 19 - 6477 AGGGGTTTTGAATGTCATT -s Anc2.Anc2refChr13 93255 19 - 96486 AGGGGTTTTGCATGTCATT -s mr.mrrefChr5 129866 19 + 294540 GGGCATTTTGAATATCACT -s mr.mrrefChr5 130100 19 + 294540 GGAAGCTTTGAATACTACT -s simCow_chr6.simCow.chr6 243900 19 - 602619 AGGGATTTTGAATGTCACT -s simDog_chr6.simDog.chr6 244583 19 - 593897 AGGTGTTTTGCATGTCATT -s simHuman_chr6.simHuman.chr6 354361 19 - 601863 ATGGGTTCTGGATGTTATT -s simMouse_chr6.simMouse.chr6 278646 19 + 636262 GGAAGCTTTGAATACTACT -s simRat_chr6.simRat.chr6 267642 19 + 647215 GGGTGATTTGAATATCATT - -a -s simMouse_chr6.simMouse.chr6 278428 21 + 636262 TGACCTGGACATCTGGCTATT -s Anc0.Anc0refChr3 221541 21 - 222631 TGACCAGGGCTTCTGGCTATT -s Anc1.Anc1refChr5 3066 21 - 6477 TGACCAGGGCTTCTGGCTATT -s Anc2.Anc2refChr13 93274 21 - 96486 TGACCAGGGCTTCTGGCTATT -s mr.mrrefChr5 129885 21 + 294540 TGACCTGGACATCTGGCTATT -s mr.mrrefChr5 130119 21 + 294540 AGACCCGGGCTTTTGGTTGTC -s simCow_chr6.simCow.chr6 243921 21 - 602619 TCACCAGGGCTCCTGGCTCAC -s simDog_chr6.simDog.chr6 244602 21 - 593897 TGACCAAGGCTTCTAGCTATT -s simHuman_chr6.simHuman.chr6 354380 16 - 601863 TGACCAGAGCTTCTGG----- -s simMouse_chr6.simMouse.chr6 278665 21 + 636262 AGACCCAGGCTTTTGGTTGTC -s simRat_chr6.simRat.chr6 267790 21 + 647215 AGACCCGGGCTTTTGGCTCTC -s simRat_chr6.simRat.chr6 267661 21 + 647215 TGACCCGGGCTTCTAGCTCTC - -a -s simMouse_chr6.simMouse.chr6 278449 8 + 636262 GCCATAAG -s Anc0.Anc0refChr3 221562 8 - 222631 GCCCTAAG -s Anc1.Anc1refChr5 3087 8 - 6477 GCCCTAAG -s Anc2.Anc2refChr13 93295 8 - 96486 GTACTAAG -s mr.mrrefChr5 129906 8 + 294540 GCCATAAG -s mr.mrrefChr5 130140 8 + 294540 ACCCTAAC -s simCow_chr6.simCow.chr6 243942 8 - 602619 GTACTAAG -s simDog_chr6.simDog.chr6 244624 8 - 593897 GTACTAAG -s simHuman_chr6.simHuman.chr6 354396 1 - 601863 -------A -s simMouse_chr6.simMouse.chr6 278686 8 + 636262 ACCCTAAC -s simRat_chr6.simRat.chr6 267811 8 + 647215 ACCCTAAG -s simRat_chr6.simRat.chr6 267682 8 + 647215 ACTATAAG - -a -s simMouse_chr6.simMouse.chr6 278457 5 + 636262 AATGG -s Anc0.Anc0refChr3 221570 5 - 222631 AATGG -s Anc1.Anc1refChr5 3095 5 - 6477 AATGG -s Anc2.Anc2refChr13 93304 5 - 96486 AATGG -s mr.mrrefChr5 129914 5 + 294540 AATGG -s mr.mrrefChr5 130148 5 + 294540 ACTGG -s simCow_chr6.simCow.chr6 243950 4 - 602619 -ATTG -s simDog_chr6.simDog.chr6 244648 5 - 593897 AGTGG -s simHuman_chr6.simHuman.chr6 354397 5 - 601863 AATGG -s simMouse_chr6.simMouse.chr6 278694 5 + 636262 ACTGG -s simRat_chr6.simRat.chr6 267819 5 + 647215 AATGG -s simRat_chr6.simRat.chr6 267690 5 + 647215 AATGG - -a -s simMouse_chr6.simMouse.chr6 278462 30 + 636262 ACTAGCAGAGGAGGTCTATATTACTGTAAG -s Anc0.Anc0refChr3 221575 30 - 222631 ACCATGAAGGGAACACTAGAATACTGCAAT -s Anc1.Anc1refChr5 3100 30 - 6477 ACCATGAAGGGAACACTAGAATACTGCAAT -s Anc2.Anc2refChr13 93309 30 - 96486 ACCATGAAGGGAACACTAGAATACTGCACT -s mr.mrrefChr5 129919 30 + 294540 ACTAGCAGAGGAGGTCTATATTACTGTAAG -s mr.mrrefChr5 130170 30 + 294540 ACCATGAGAGGAAGTCTAGAACACTGTAAG -s simCow_chr6.simCow.chr6 243954 30 - 602619 ACTATGAAGGGAACACTAGAATACTGCAGT -s simDog_chr6.simDog.chr6 244653 27 - 593897 ACCATGAAGGGAACACTACAATACT---CT -s simHuman_chr6.simHuman.chr6 354402 30 - 601863 ACCATGAAGGAAACACTAGAATACTGCAAT -s simMouse_chr6.simMouse.chr6 278716 30 + 636262 AGTGTGAGAGGAAGTCTGGCACACTGTAAG -s simRat_chr6.simRat.chr6 267841 30 + 647215 ACCATGAGAGGAAGTCTAGAACCCTGTAGG -s simRat_chr6.simRat.chr6 267695 30 + 647215 ACTAGGAGAGGATGTCTAGAATACTGTAGG - -a -s simMouse_chr6.simMouse.chr6 278492 1 + 636262 T -s mr.mrrefChr5 129949 1 + 294540 T -s simRat_chr6.simRat.chr6 267725 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 278493 5 + 636262 TGCTG -s Anc0.Anc0refChr3 221605 5 - 222631 TGCTG -s Anc1.Anc1refChr5 3130 5 - 6477 TGCTG -s Anc2.Anc2refChr13 93339 5 - 96486 TGCTG -s mr.mrrefChr5 129950 5 + 294540 TGCTG -s mr.mrrefChr5 130200 5 + 294540 TGCTG -s simCow_chr6.simCow.chr6 243984 5 - 602619 TCCGG -s simDog_chr6.simDog.chr6 244680 5 - 593897 TGCTG -s simHuman_chr6.simHuman.chr6 354432 5 - 601863 TGCTG -s simMouse_chr6.simMouse.chr6 278746 5 + 636262 TGCTG -s simRat_chr6.simRat.chr6 267871 5 + 647215 TGCTA -s simRat_chr6.simRat.chr6 267726 5 + 647215 TGTTA - -a -s simMouse_chr6.simMouse.chr6 278498 7 + 636262 CTCACAT -s Anc0.Anc0refChr3 221610 7 - 222631 GCCACGT -s Anc1.Anc1refChr5 3135 7 - 6477 GCCACGT -s Anc2.Anc2refChr13 93344 7 - 96486 GCCACGT -s mr.mrrefChr5 129955 7 + 294540 CTCACAT -s mr.mrrefChr5 130205 7 + 294540 AACACAT -s simCow_chr6.simCow.chr6 243989 7 - 602619 ACCACGT -s simDog_chr6.simDog.chr6 244685 7 - 593897 GCCACAT -s simHuman_chr6.simHuman.chr6 354437 7 - 601863 GCCACGT -s simMouse_chr6.simMouse.chr6 278751 7 + 636262 AACACAT -s simRat_chr6.simRat.chr6 267881 7 + 647215 AACACAT -s simRat_chr6.simRat.chr6 267731 7 + 647215 TTCACAT - -a -s simMouse_chr6.simMouse.chr6 278505 17 + 636262 GAAGCAATACCTTATTA -s Anc0.Anc0refChr3 221617 17 - 222631 GAAACAAAACTGTCTTA -s Anc1.Anc1refChr5 3142 17 - 6477 GAAACAAAACTGTCTTA -s Anc2.Anc2refChr13 93351 17 - 96486 GAAACAAAACTGTCTTA -s mr.mrrefChr5 129962 17 + 294540 GAAGCAATACCTTATTA -s mr.mrrefChr5 130212 17 + 294540 GGAACTATAATTTCTTA -s simCow_chr6.simCow.chr6 243996 17 - 602619 GAAACAAAACTGTCTTG -s simDog_chr6.simDog.chr6 244692 17 - 593897 GCAACAACACTGTCTGA -s simHuman_chr6.simHuman.chr6 354450 17 - 601863 AAAACAAAACTGTTTTA -s simMouse_chr6.simMouse.chr6 278758 17 + 636262 GGAACTATAATTTCTTG -s simRat_chr6.simRat.chr6 267888 17 + 647215 GGAACTATAATTTCTCA -s simRat_chr6.simRat.chr6 267738 17 + 647215 GAAACAATACTTTCTTA - -a -s simMouse_chr6.simMouse.chr6 278522 14 + 636262 TAACAAGCAGGCGG -s Anc0.Anc0refChr3 221634 14 - 222631 TAACAAGCAGGCAG -s Anc1.Anc1refChr5 3159 14 - 6477 TAACAAGCAGGCAG -s Anc2.Anc2refChr13 93368 14 - 96486 TAACAAGCAGGCAG -s mr.mrrefChr5 129979 14 + 294540 TAACAAGCAGGTGG -s mr.mrrefChr5 130229 14 + 294540 TAACAAGCAGGCAG -s simCow_chr6.simCow.chr6 244013 14 - 602619 TAATAAGCAGGCAG -s simDog_chr6.simDog.chr6 244715 10 - 593897 TGACAAATGG---- -s simHuman_chr6.simHuman.chr6 354467 14 - 601863 TAACAAGCAGGCAA -s simMouse_chr6.simMouse.chr6 278775 14 + 636262 TAACAAGCAAGTAG -s simRat_chr6.simRat.chr6 267905 14 + 647215 TACTACGCAGGCAG -s simRat_chr6.simRat.chr6 267755 14 + 647215 TAACAAGCAGGTGG - -a -s simMouse_chr6.simMouse.chr6 278536 2 + 636262 TC -s Anc0.Anc0refChr3 221648 2 - 222631 TC -s Anc1.Anc1refChr5 3173 2 - 6477 TC -s Anc2.Anc2refChr13 93382 2 - 96486 TG -s mr.mrrefChr5 129993 2 + 294540 TC -s mr.mrrefChr5 130243 2 + 294540 TC -s simCow_chr6.simCow.chr6 244027 2 - 602619 TG -s simHuman_chr6.simHuman.chr6 354483 2 - 601863 TC -s simMouse_chr6.simMouse.chr6 278789 2 + 636262 TC -s simRat_chr6.simRat.chr6 267919 2 + 647215 TC -s simRat_chr6.simRat.chr6 267769 2 + 647215 TC - -a -s simMouse_chr6.simMouse.chr6 278538 5 + 636262 TCTAT -s Anc0.Anc0refChr3 221650 5 - 222631 TATCA -s Anc1.Anc1refChr5 3175 5 - 6477 TATCA -s Anc2.Anc2refChr13 93384 5 - 96486 TCTCA -s mr.mrrefChr5 129995 5 + 294540 TATAT -s mr.mrrefChr5 130245 5 + 294540 CATAA -s simCow_chr6.simCow.chr6 244029 5 - 602619 TCTCA -s simHuman_chr6.simHuman.chr6 354485 5 - 601863 TAGCA -s simMouse_chr6.simMouse.chr6 278791 5 + 636262 CATAA -s simRat_chr6.simRat.chr6 267771 5 + 647215 TATAA - -a -s simMouse_chr6.simMouse.chr6 278543 23 + 636262 GGTACCCTACAATTCAAGATAGT -s Anc0.Anc0refChr3 221655 20 - 222631 TG-GCCCTAC--TGCTACATAAT -s Anc1.Anc1refChr5 3180 23 - 6477 TGTGCCCTACAATGCTACATAAT -s Anc2.Anc2refChr13 93389 20 - 96486 TA-GCCCTAC--TGCCAAATAAT -s mr.mrrefChr5 130000 23 + 294540 GGTACCCTACAATTCAAGATAGT -s mr.mrrefChr5 130250 23 + 294540 TGTGGCCTACAATCCTCCATACT -s simCow_chr6.simCow.chr6 244034 20 - 602619 TA-GCCCTAC--TGCCAAATAAT -s simHuman_chr6.simHuman.chr6 354490 22 - 601863 TG-ACCTTACAATGCTACATGAT -s simMouse_chr6.simMouse.chr6 278796 23 + 636262 TGTGGCCTACAATCCTCCATACC -s simRat_chr6.simRat.chr6 267921 23 + 647215 TGTGGTCTATGATCCACCATACT -s simRat_chr6.simRat.chr6 267776 14 + 647215 GGGACCCTACAATT--------- - -a -s simMouse_chr6.simMouse.chr6 278566 12 + 636262 CTCCAAGCATTT -s Anc0.Anc0refChr3 221675 6 - 222631 CTCCGA------ -s Anc1.Anc1refChr5 3203 6 - 6477 CTCCGA------ -s Anc2.Anc2refChr13 93409 6 - 96486 TTCCGA------ -s mr.mrrefChr5 130023 12 + 294540 CTCCAAGCATTT -s mr.mrrefChr5 130273 6 + 294540 CTCCAA------ -s simCow_chr6.simCow.chr6 244056 6 - 602619 TTCCGA------ -s simHuman_chr6.simHuman.chr6 354512 6 - 601863 CTCAGA------ -s simMouse_chr6.simMouse.chr6 278819 6 + 636262 CTCCAA------ -s simRat_chr6.simRat.chr6 267944 6 + 647215 CTCCAA------ - -a -s simMouse_chr6.simMouse.chr6 278587 3 + 636262 TAA - -a -s simMouse_chr6.simMouse.chr6 278608 13 + 636262 ATCCTTCTTGCCT -s Anc0.Anc0refChr3 221486 13 - 222631 CCACTTATTGTCT -s Anc1.Anc1refChr5 3009 13 - 6477 CCACTTATTGTCT -s Anc2.Anc2refChr13 93219 13 - 96486 CCACTTATTGTTT -s mr.mrrefChr5 130062 13 + 294540 ATCCTTCTTGCCT -s simCow_chr6.simCow.chr6 243860 13 - 602619 CCATTCCTTGTTT -s simDog_chr6.simDog.chr6 244546 13 - 593897 CGACTTATTGCTT -s simHuman_chr6.simHuman.chr6 354323 13 - 601863 CCTCTTTTCATCT - -a -s simMouse_chr6.simMouse.chr6 278699 17 + 636262 TCTGTGAGAGGAACTCT -s mr.mrrefChr5 130153 17 + 294540 TCTGTGAGAGGAACTCT -s simRat_chr6.simRat.chr6 267824 17 + 647215 TCTGGGAGAGGAAGTCA - -a -s simMouse_chr6.simMouse.chr6 278825 40 + 636262 TCATTTGGTTGGCATTAAGCGGCAACTGGATTCATTGTAC -s Anc1.Anc1refChr5 3209 39 - 6477 TTATCTGGATGGTGCTA-GCAGCAAATGTGTACATTGTAT -s mr.mrrefChr5 130279 40 + 294540 TCATTTGGTTGGCACTAAGCAGCAACTGGATTCATTGTAC -s simHuman_chr6.simHuman.chr6 354518 39 - 601863 TTATCTGGATGGTGCTA-GCAGCAAATGTGTACATTGTAT -s simRat_chr6.simRat.chr6 267950 40 + 647215 TCATTTGGTTGGCACTAAGCAGCAATTGAATTCATTATAC - -a -s simMouse_chr6.simMouse.chr6 278865 41 + 636262 CACAGGGGGGGTTATTGGAAGTAATGTTTCACCACAGCCTC -s Anc1.Anc1refChr5 3248 41 - 6477 CACAGTAGGAGGTATTGGAGTTGCTGTTTCCCTGCAGCCCT -s mr.mrrefChr5 130319 41 + 294540 CACAGTAGGGGTTATTGGAAGTGATGTTTCACCACAGCCTC -s simHuman_chr6.simHuman.chr6 354558 41 - 601863 CACAGTAGGAGGTATTGGAGTTGCTGTTTCCCTGCAGCCCT -s simRat_chr6.simRat.chr6 267990 41 + 647215 CAGAATAGGGGCTATTCGAAGTGATGTTTCACCACAGCCTC - -a -s simMouse_chr6.simMouse.chr6 278906 70 + 636262 AAAAGATCATCCATGCCTGCAGGTGGATGGTGTATATACCAAGCTGGTGCAAATATTTTTCAAGTAATCT -s Anc0.Anc0refChr3 221681 12 - 222631 ----------------------------------------------------------TTTAAATCATCC -s Anc1.Anc1refChr5 3289 69 - 6477 AAAAACCCATCCAAGCATCCAGATGACTGGGATATATATGCAGCTG-TCAAAATAGCTTTTAAATCATCC -s Anc2.Anc2refChr13 93415 12 - 96486 ----------------------------------------------------------TTTAAATTATCC -s mr.mrrefChr5 130360 70 + 294540 AAAAGATCATCCATGCCTCCAGGTGGATGGTATATATACCAAGCTGGTGAAAATATTTTTCAAGTCATCT -s simCow_chr6.simCow.chr6 244062 8 - 602619 ----------------------------------------------------------T----ATTATTC -s simDog_chr6.simDog.chr6 244725 11 - 593897 -----------------------------------------------------------TTAAGATATCT -s simHuman_chr6.simHuman.chr6 354607 69 - 601863 AAAAACCCATCCAAGCATCCAGATGACTGGGATATATATGCAGCTG-TCAAAATAGCTTTTAAATCACCC -s simRat_chr6.simRat.chr6 268031 70 + 647215 AAAAGATCATCCATGCCTCCAGGTGGATGATATATGTGCTAAGCCGGTGAAAATATTTCTCAAGCCAACT - -a -s simMouse_chr6.simMouse.chr6 278976 29 + 636262 GGTGTGGTTGCTCCTATAGCTTCATTTTT -s Anc0.Anc0refChr3 221693 28 - 222631 GTTGTGGTTGTTCTTATAGCCTC-TTCCT -s Anc1.Anc1refChr5 3358 28 - 6477 GTTGTGGTTGTTCTTATAGCCTC-TTCCT -s Anc2.Anc2refChr13 93427 28 - 96486 GTTGTGCTTGTTCTTATTGCCTC-TTCCT -s mr.mrrefChr5 130430 29 + 294540 GGTGTGGTTGCTCTTATAGCTTCATTCTT -s simCow_chr6.simCow.chr6 244077 28 - 602619 GTTGTGTTTGTTCTTACTACCTC-TTCTT -s simDog_chr6.simDog.chr6 244736 28 - 593897 GTTGTTCTTATTCTTGTTGCCTC-TCCCT -s simHuman_chr6.simHuman.chr6 354676 28 - 601863 GTTGTGGTTGTTCTCATAGCCTC-TTCCT -s simRat_chr6.simRat.chr6 268101 28 + 647215 GGTGT-GTTCCTCTTATAGCTTCATTCTC - -a -s simMouse_chr6.simMouse.chr6 279005 11 + 636262 AGTACGTTAAC -s Anc0.Anc0refChr3 221721 11 - 222631 GGTTTACTTAC -s Anc1.Anc1refChr5 3386 11 - 6477 GGTTTACTTAC -s Anc2.Anc2refChr13 93456 11 - 96486 GGTTTACTTAG -s mr.mrrefChr5 130459 11 + 294540 AGTATGTTAAC -s simCow_chr6.simCow.chr6 244106 11 - 602619 GCTTTTCTCAG -s simDog_chr6.simDog.chr6 244765 11 - 593897 GGTTTACTTGG -s simHuman_chr6.simHuman.chr6 354704 11 - 601863 GGTTTACTGAC -s simRat_chr6.simRat.chr6 268129 11 + 647215 AGTATGTTAAC - -a -s simMouse_chr6.simMouse.chr6 279016 287 + 636262 CCTGGGCCATCTTCTGGATCTGAGGTGGACTGGGGATCTACAATGTACGTGTGGAGATCAATTGACATTTCGTTTCGCAGGGCCGAGTCGTAGCCAAGCCCCGACCGTGTGTACATGACTGCAAGGGGCAGGCGTAGCCAAGCACTGACCGTATGTACGCGGCCGCCTGGGGAAGGGTCATAGCCAAGCACTAACTGTGTGTACATGGCAGCGTTGGCCTTTTTTTGGGGATTTGCACAAGGTGCTGTGCAAAGTCTAAGTAGCGTTAAAGGTTAACATATGAAGGA -s Anc0.Anc0refChr3 221738 43 - 222631 CCTGGGCCAACTTCTTGATCTAAGGT----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GGTTAACATATGTATGA -s Anc1.Anc1refChr5 3403 43 - 6477 CCTGGGCCAACTTCTTGATCTAAGGT----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GGTTAACATATGTATGA -s Anc2.Anc2refChr13 93473 43 - 96486 CCTGGGCCAATTTCTTGATCTAAGGT----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GGTCAACATATGTATGA -s mr.mrrefChr5 130470 43 + 294540 CCTGGGCCATCTTCTGGATCTGAGGT----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GGTTAACATATGTAGGA -s simCow_chr6.simCow.chr6 244123 43 - 602619 CCTGGGCCAATTTCTTGATCGATGGG----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GGTCAACATGTGTATTG -s simDog_chr6.simDog.chr6 244782 43 - 593897 CCTGGGCCAATTTCTTGATCTAAGGT----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GGTCATCACATGTATGA -s simHuman_chr6.simHuman.chr6 354721 43 - 601863 CCCGGGCTAACTTCTAGATCTAAGGT----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GGTTAACATATGTATGA -s simRat_chr6.simRat.chr6 268140 43 + 647215 CCTGGGCCATCTTCTGGTTCTGAGGT----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GGTCAACATATGTAGGA - -a -s simMouse_chr6.simMouse.chr6 279303 5 + 636262 CCTAA -s Anc0.Anc0refChr3 221781 5 - 222631 TTAAA -s Anc1.Anc1refChr5 3446 5 - 6477 TTAAA -s Anc2.Anc2refChr13 93516 5 - 96486 TTAAA -s mr.mrrefChr5 130513 5 + 294540 CCTAA -s simCow_chr6.simCow.chr6 244166 5 - 602619 TTAAA -s simDog_chr6.simDog.chr6 244830 5 - 593897 TTAAA -s simHuman_chr6.simHuman.chr6 354764 5 - 601863 TTAAA -s simRat_chr6.simRat.chr6 268183 5 + 647215 CCTAA - -a -s simMouse_chr6.simMouse.chr6 279308 4 + 636262 AATA -s Anc0.Anc0refChr3 221786 4 - 222631 AACA -s Anc1.Anc1refChr5 3451 4 - 6477 AACA -s Anc2.Anc2refChr13 93542 4 - 96486 AACA -s mr.mrrefChr5 130518 4 + 294540 AACA -s simCow_chr6.simCow.chr6 244201 4 - 602619 ACGA -s simDog_chr6.simDog.chr6 244856 4 - 593897 AACA -s simHuman_chr6.simHuman.chr6 354769 4 - 601863 AACA -s simRat_chr6.simRat.chr6 268188 4 + 647215 AACA - -a -s simMouse_chr6.simMouse.chr6 279312 2 + 636262 AT -s Anc0.Anc0refChr3 221790 2 - 222631 CT -s Anc1.Anc1refChr5 3455 2 - 6477 CT -s Anc2.Anc2refChr13 93548 2 - 96486 CT -s mr.mrrefChr5 130522 2 + 294540 CT -s simCow_chr6.simCow.chr6 244207 2 - 602619 CA -s simDog_chr6.simDog.chr6 244862 2 - 593897 CT -s simHuman_chr6.simHuman.chr6 354773 2 - 601863 CC -s simRat_chr6.simRat.chr6 268192 2 + 647215 CT - -a -s simMouse_chr6.simMouse.chr6 279314 21 + 636262 GAAAGCTAGCATGTCCAGCAA -s Anc0.Anc0refChr3 221792 21 - 222631 GCAAAGTAGCAAGTCTAGCAA -s Anc1.Anc1refChr5 3457 21 - 6477 GCAAAGTAGCAAGTCTAGCAA -s Anc2.Anc2refChr13 93550 21 - 96486 GCAAAATAGCAAGTCTAGCAA -s mr.mrrefChr5 130524 21 + 294540 GAAAAGTAGCAAGTCCAGCAA -s simCow_chr6.simCow.chr6 244209 21 - 602619 GCAAAATAACAAGTCTCTCTG -s simDog_chr6.simDog.chr6 244864 21 - 593897 GCAAGATAGCAAGTCTAGCAA -s simHuman_chr6.simHuman.chr6 354780 21 - 601863 GCAAAGTAGCAAGTCTAGCAA -s simRat_chr6.simRat.chr6 268194 21 + 647215 GAAAAGCAGCAAGATAAGCAG - -a -s simMouse_chr6.simMouse.chr6 279335 16 + 636262 GGGCCTGGGGCTCCTG -s Anc0.Anc0refChr3 221813 16 - 222631 GAGCTTGGGGATACTG -s Anc1.Anc1refChr5 3478 16 - 6477 GAGCTTGGGGATACTG -s Anc2.Anc2refChr13 93571 16 - 96486 GAGCTTGGGGATACTG -s mr.mrrefChr5 130545 16 + 294540 GGGCTTGGGGCTCCTG -s simCow_chr6.simCow.chr6 244230 16 - 602619 GAACTTGGTGCAAGTG -s simDog_chr6.simDog.chr6 244885 14 - 593897 GAGCTTGGGGATAC-- -s simHuman_chr6.simHuman.chr6 354801 16 - 601863 GTGCTTGGAGTTACTC -s simRat_chr6.simRat.chr6 268216 6 + 647215 AAGATC---------- - -a -s simMouse_chr6.simMouse.chr6 279351 32 + 636262 TAGTCCAGTGTCTCTCAAAGATGGAATAAACT -s Anc0.Anc0refChr3 221829 32 - 222631 TAGTCCAGTGTCTCACAAAGATGGAATAAGCT -s Anc1.Anc1refChr5 3494 32 - 6477 TAGTCCAGTGTCTCACAAAGATGGAATAAGCT -s Anc2.Anc2refChr13 93587 32 - 96486 TGGTCCAGTGTGTCACAAGGATGGAAATAGCC -s mr.mrrefChr5 130561 32 + 294540 TAGTCCAGTGTCTCTCAAAGATGGAATAAACT -s simCow_chr6.simCow.chr6 244253 32 - 602619 TGGTCCAGTGTGTCACAAGGATGGAAATAGCC -s simHuman_chr6.simHuman.chr6 354817 32 - 601863 TAATCCAGTGTCTCACAAAGATGGAATATGCT - -a -s simMouse_chr6.simMouse.chr6 279383 41 + 636262 ATGTACCAAGTCAATAGACTTGCCTGAGTTGGTAGGGTTCA -s Anc0.Anc0refChr3 221872 36 - 222631 ATGTAGCAAGTCAGGAGA-----TTGAGATCATGGGGTTCA -s Anc1.Anc1refChr5 3537 36 - 6477 ATGTAGCAAGTCAGGAGA-----TTGAGATCATGGGGTTCA -s Anc2.Anc2refChr13 93630 36 - 96486 ATCTAGCAAGTCAGGAGA-----TTAAGATCATGGGGTTCA -s mr.mrrefChr5 130593 36 + 294540 ATGTACCAAGTCAATAGA-----CTGAGTTGGTAGGGTTCA -s simCow_chr6.simCow.chr6 244296 36 - 602619 ATCTAGCAAGTTAGGAGA-----TTAAGATCATGGGGTTTA -s simDog_chr6.simDog.chr6 244899 32 - 593897 ----TGCAAGTCAGGAGA-----TTAAGATCATGGGGTTCA -s simHuman_chr6.simHuman.chr6 354860 36 - 601863 ATGTAGAAACTCAGGAGA-----TTGAGATCATGGGGTTCA -s simRat_chr6.simRat.chr6 268222 17 + 647215 ------------------------TGAGTTGGTAAGGTTCA - -a -s simMouse_chr6.simMouse.chr6 279424 11 + 636262 ATATCTCAATT -s Anc0.Anc0refChr3 221908 11 - 222631 ACATTTCCATG -s Anc1.Anc1refChr5 3573 11 - 6477 ACATTTCCATG -s Anc2.Anc2refChr13 93666 11 - 96486 ACATTTCCATG -s mr.mrrefChr5 130629 11 + 294540 ATATCTCAATT -s simCow_chr6.simCow.chr6 244332 11 - 602619 TCATTTCCATT -s simDog_chr6.simDog.chr6 244949 11 - 593897 ACATTTCCATG -s simHuman_chr6.simHuman.chr6 354896 11 - 601863 ACATTGCTATC -s simRat_chr6.simRat.chr6 268239 11 + 647215 ATGTCTCAATT - -a -s simMouse_chr6.simMouse.chr6 279435 12 + 636262 AAGCTCTGTGAC -s Anc0.Anc0refChr3 221926 12 - 222631 ATGCTTGCTGGC -s Anc1.Anc1refChr5 3591 12 - 6477 ATGCTTGCTGGC -s Anc2.Anc2refChr13 93684 12 - 96486 ATGCTTGCTGGC -s mr.mrrefChr5 130640 12 + 294540 ATGCTCTGTGAC -s simCow_chr6.simCow.chr6 244350 12 - 602619 ATGCTTGCTGGC -s simDog_chr6.simDog.chr6 244967 12 - 593897 ATGCTTGCTTGG -s simHuman_chr6.simHuman.chr6 354914 12 - 601863 ATACTTACTGGC -s simRat_chr6.simRat.chr6 268250 12 + 647215 ATGCTCTGTGAC - -a -s simMouse_chr6.simMouse.chr6 279447 57 + 636262 AAACAAAATTGTCTGCAGTGGGTTGTTCACATGGAGCCCTACCAAGTTGGAGCCCTA -s Anc0.Anc0refChr3 221954 41 - 222631 AAACAGAGTTGTCTGCATGGAGTTGTCTGCATGGAGCTCTA---------------- -s Anc1.Anc1refChr5 3619 41 - 6477 AAACAGAGTTGTCTGCATGGAGTTGTCTGCATGGAGCTCTA---------------- -s Anc2.Anc2refChr13 93712 41 - 96486 AAACAGGGTTGTCTGCATGGAGTTGTCTGCATAGAGCTCTA---------------- -s mr.mrrefChr5 130652 57 + 294540 AAACAAAATTGTCTGCATTGGGTTGTTCACATGGAGCCCTACCAAGTTGGAGCCCTA -s simCow_chr6.simCow.chr6 244377 37 - 602619 AAACA----TGTATGCATATAGTTGGCTGCACAGAGCTCTA---------------- -s simDog_chr6.simDog.chr6 244995 41 - 593897 AAACAGGGTTGTCTGCATGGAGTGGTCTGCATAGAGCTCGA---------------- -s simHuman_chr6.simHuman.chr6 354942 41 - 601863 AAACAGAGTTGTCTGCATGGTGTTGTCTGCAGGGAGCTCTA---------------- -s simRat_chr6.simRat.chr6 268262 57 + 647215 AAACAAAATTGCCTGGATTCGGTTGTTCACATGGAGCCCTACCAAGTTGGAGCCTCA - -a -s simMouse_chr6.simMouse.chr6 279504 175 + 636262 CAAGTGTATGACAAAAAACTTGAAGACAGGGTGACACACAGTGTATGCATGCGCATAGGTTCCTAAACATTCTACATCCTTCAACGTTTAGCAGTCGGTAAAAGTAACATCGAACAAGTTAAGGGACTTATGTCTAGCTGTCCAGGTCAGAACTAGTGGTATGGTCCAAATTACA -s Anc0.Anc0refChr3 221995 40 - 222631 ---------------------------------------------------------------------------------------------------------------------------------------AGCTGTTCAGATCAACACTGGTGGTGTAGTCCCAATTACA -s Anc1.Anc1refChr5 3660 40 - 6477 ---------------------------------------------------------------------------------------------------------------------------------------AGCTGTTCAGATCAACACTGGTGGTGTAGTCCCAATTACA -s Anc2.Anc2refChr13 93753 40 - 96486 ---------------------------------------------------------------------------------------------------------------------------------------AGCTGTTCAGTTCAACACAGGAAGTGTAGTCCCAATTACA -s mr.mrrefChr5 130709 80 + 294540 CAAGTGTATGACAAAAAACTTGAAGACAGGGTGACACA-----------------------------------------------------------------------------------------------CTAGCTGTCCAGATCAAAACTAGTGGTATGGTCCAAATTACA -s simCow_chr6.simCow.chr6 244414 40 - 602619 ---------------------------------------------------------------------------------------------------------------------------------------AGCTGTTCAGTTCAACACAGGAAGTGTCGGCCTAATTACA -s simDog_chr6.simDog.chr6 245036 18 - 593897 ---------------------------------------------------------------------------------------------------------------------------------------AG----------------------TGTAGTCCCAATTAGA -s simHuman_chr6.simHuman.chr6 354983 40 - 601863 ---------------------------------------------------------------------------------------------------------------------------------------AGCTGTTCAGATCAATGCTGGTGATGTAGCCCGAATTACA -s simRat_chr6.simRat.chr6 268320 80 + 647215 CAAGTGTATGACAAAAAACCTGTAGACAGGGTGACACA-----------------------------------------------------------------------------------------------CCAGCTGTCCAGATCAAAACTAGCGGTATGGTCCAAATTACA - -a -s simMouse_chr6.simMouse.chr6 279679 43 + 636262 TCTAGCCCAGGGCAGCATGGTGCAGACCAAGAGGACAGTATAA -s Anc0.Anc0refChr3 222036 42 - 222631 CCTGGCCCATGGCAGTATGGTGCAGGCCGACAGA-CAGGACAA -s Anc1.Anc1refChr5 3701 42 - 6477 CCTGGCCCATGGCAGTATGGTGCAGGCCGACAGA-CAGGACAA -s Anc2.Anc2refChr13 93794 42 - 96486 CCTGGCCCATGCCAGTATGGTGCAGGCCGACAGA-CAAGTCAG -s mr.mrrefChr5 130790 43 + 294540 TCTAGCCCAGGGCAGCATGGTGCAGACCAAGAGGACAGTATAA -s simCow_chr6.simCow.chr6 244455 42 - 602619 CCTGGCCCATGTCGACATGGTGTAGGCCAAGTGA-CGAGTCAG -s simDog_chr6.simDog.chr6 245055 41 - 593897 CTGGGGCCATGCCAGTATGAGGCATGCTGACAGG-CAAGTCA- -s simHuman_chr6.simHuman.chr6 355024 42 - 601863 CCTGGCCCACAGCAGTATGGTGCAGGCCCACAGA-CAGCACAA -s simRat_chr6.simRat.chr6 268401 43 + 647215 TCTATCCCATGGGAGCATAGTACAGACCAAGAGGACAGTATTA - -a -s simMouse_chr6.simMouse.chr6 279722 1 + 636262 T -s Anc0.Anc0refChr3 222080 1 - 222631 T -s Anc1.Anc1refChr5 3745 1 - 6477 T -s Anc2.Anc2refChr13 93838 1 - 96486 C -s mr.mrrefChr5 130833 1 + 294540 T -s simCow_chr6.simCow.chr6 244499 1 - 602619 C -s simHuman_chr6.simHuman.chr6 355068 1 - 601863 T -s simRat_chr6.simRat.chr6 268444 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 279723 25 + 636262 GAAGAAACCTAAAAGGTAGTGTAAC -s Anc0.Anc0refChr3 222082 25 - 222631 GTGGAAGCCCAAAAGGTAGTGGACC -s Anc1.Anc1refChr5 3747 25 - 6477 GTGGAAGCCCAAAAGGTAGTGGACC -s Anc2.Anc2refChr13 93840 25 - 96486 TTGGAAGCTCCAAAGGCAGAGGACC -s mr.mrrefChr5 130835 25 + 294540 GAGGAAGCCTAAAAGGTAGTGTAAC -s simCow_chr6.simCow.chr6 244503 25 - 602619 TTGGAAGCACCATAGGAAGAGGACC -s simDog_chr6.simDog.chr6 245096 19 - 593897 ----ACGTTCCAACAGCAGAAAA-- -s simHuman_chr6.simHuman.chr6 355070 25 - 601863 GTGGAAGCCCAACAGGTAGTGGATC -s simRat_chr6.simRat.chr6 268446 25 + 647215 GAGGAAGCCTAAGAGGTAGTGTAAC - -a -s simMouse_chr6.simMouse.chr6 279748 13 + 636262 AATCTGGTGGAAC -s Anc0.Anc0refChr3 222111 13 - 222631 ACATTTGTGGAAC -s Anc1.Anc1refChr5 3776 13 - 6477 ACATTTGTGGAAC -s Anc2.Anc2refChr13 93869 13 - 96486 ACATTTGTGGAGC -s mr.mrrefChr5 130860 13 + 294540 AATCTGGTGGAAC -s simCow_chr6.simCow.chr6 244532 13 - 602619 ACATTTGTGGAGC -s simDog_chr6.simDog.chr6 245115 1 - 593897 ------------G -s simHuman_chr6.simHuman.chr6 355099 13 - 601863 ACATTTAAGGAAC -s simRat_chr6.simRat.chr6 268471 13 + 647215 AATCTGGTGGAAC - -a -s simMouse_chr6.simMouse.chr6 279761 15 + 636262 TAAATGCCTAATGGA -s Anc0.Anc0refChr3 222124 15 - 222631 TACATACCTAAGTGA -s Anc1.Anc1refChr5 3789 15 - 6477 TACATACCTAAGTGA -s Anc2.Anc2refChr13 93882 15 - 96486 TACATACCTAAGTGA -s mr.mrrefChr5 130873 15 + 294540 TACATGCCTAATGGA -s simCow_chr6.simCow.chr6 244545 15 - 602619 TACACACCTAAGTGA -s simDog_chr6.simDog.chr6 245116 15 - 593897 TATATTCCTAAGTGG -s simHuman_chr6.simHuman.chr6 355112 15 - 601863 TACATACCTAAGCGA -s simRat_chr6.simRat.chr6 268485 15 + 647215 TACATGTCTAATGGA - -a -s simMouse_chr6.simMouse.chr6 279776 16 + 636262 GTTTAACTTGGAGTAC -s Anc0.Anc0refChr3 222139 16 - 222631 TTTCAACTTAGATTAC -s Anc1.Anc1refChr5 3804 16 - 6477 TTTCAACTTAGATTAC -s Anc2.Anc2refChr13 93897 16 - 96486 TTTCAACCTAGATAAC -s mr.mrrefChr5 130888 16 + 294540 GTTTAACTTGGAGTAC -s simCow_chr6.simCow.chr6 244568 16 - 602619 TTTTAACCTAGACCAC -s simDog_chr6.simDog.chr6 245131 16 - 593897 TTTCAACCTACATACA -s simHuman_chr6.simHuman.chr6 355127 16 - 601863 TTTCAACTTAGATTAC -s simRat_chr6.simRat.chr6 268500 16 + 647215 GTTTAACTTGAAATAC - -a -s simMouse_chr6.simMouse.chr6 279792 36 + 636262 TCACTATCAGTATCAAAGGTACTATGGATCCCAGTC -s Anc0.Anc0refChr3 222174 36 - 222631 TTATAATCTGTATCAAAGATACTATTAATTCTAGTC -s Anc1.Anc1refChr5 3839 36 - 6477 TTATAATCTGTATCAAAGATACTATTAATTCTAGTC -s Anc2.Anc2refChr13 93939 36 - 96486 TTATAATCTGTATCAAAGATACTATTAATTCTAGTC -s mr.mrrefChr5 130904 36 + 294540 TCATGGTCAGTATCAAAGATACTATTGATCCCAGTC -s simCow_chr6.simCow.chr6 244609 36 - 602619 TCATAATCTGTATCAAAGATACTATTAATTCTAGTC -s simDog_chr6.simDog.chr6 245177 36 - 593897 TTATAATAAGTATCAAAGTTACCATTAGTGCTAGTC -s simHuman_chr6.simHuman.chr6 355162 36 - 601863 TTATTAGCTGTATCAAGGATACTACTAATTTTGGTC -s simRat_chr6.simRat.chr6 268516 36 + 647215 TCATGGTCAGTATGAAAGATACTATTGATCCCAGTC - -a -s simMouse_chr6.simMouse.chr6 279828 9 + 636262 CCTCAGCTT -s Anc0.Anc0refChr3 222210 9 - 222631 CCTCAGCCT -s Anc1.Anc1refChr5 3875 9 - 6477 CCTCAGCCT -s Anc2.Anc2refChr13 93975 9 - 96486 CCTCCGCCC -s mr.mrrefChr5 130940 9 + 294540 CCTCAGCTT -s simCow_chr6.simCow.chr6 244649 9 - 602619 CCTCTGCGG -s simDog_chr6.simDog.chr6 245213 9 - 593897 CCTCCACCC -s simHuman_chr6.simHuman.chr6 355198 9 - 601863 CCTCAGCAT -s simRat_chr6.simRat.chr6 268552 9 + 647215 CCTCAGCTC - -a -s simMouse_chr6.simMouse.chr6 279837 23 + 636262 CAGGAGGCAGGTTAGCATAACAA -s Anc0.Anc0refChr3 222223 23 - 222631 TAGGAGGTAGGTGAGGCAAACAA -s Anc1.Anc1refChr5 3888 23 - 6477 TAGGAGGTAGGTGAGGCAAACAA -s Anc2.Anc2refChr13 93988 23 - 96486 TAGGAGGTAGGTGAGGCACACCA -s mr.mrrefChr5 130949 23 + 294540 CAGGAGGCAGGTTAGGATAACAA -s simCow_chr6.simCow.chr6 244662 23 - 602619 TAGCAGGTAGGTGAGACACAACA -s simDog_chr6.simDog.chr6 245226 23 - 593897 TAGGAGGTAGGCGAGGCACACCA -s simHuman_chr6.simHuman.chr6 355211 23 - 601863 TAGGAGGTAGGTGAGGCAAACAA -s simRat_chr6.simRat.chr6 268561 23 + 647215 CAGGATGCAGGTTAGGATAACAA - -a -s simMouse_chr6.simMouse.chr6 279860 2 + 636262 TG -s Anc0.Anc0refChr3 222246 2 - 222631 TG -s Anc1.Anc1refChr5 3911 2 - 6477 TG -s Anc2.Anc2refChr13 94011 2 - 96486 TG -s mr.mrrefChr5 130972 2 + 294540 TG -s simCow_chr6.simCow.chr6 244686 2 - 602619 AG -s simDog_chr6.simDog.chr6 245249 2 - 593897 TG -s simHuman_chr6.simHuman.chr6 355234 2 - 601863 TA -s simRat_chr6.simRat.chr6 268584 2 + 647215 TG - -a -s simMouse_chr6.simMouse.chr6 279862 2 + 636262 CA -s Anc0.Anc0refChr3 222251 2 - 222631 CA -s Anc1.Anc1refChr5 3916 2 - 6477 CA -s Anc2.Anc2refChr13 94016 2 - 96486 CA -s mr.mrrefChr5 130974 2 + 294540 CA -s simCow_chr6.simCow.chr6 244691 2 - 602619 CC -s simDog_chr6.simDog.chr6 245254 2 - 593897 CA -s simHuman_chr6.simHuman.chr6 355239 2 - 601863 CC -s simRat_chr6.simRat.chr6 268586 2 + 647215 CA - -a -s simMouse_chr6.simMouse.chr6 279864 17 + 636262 CTTTGTCAAAAATTTTC -s Anc0.Anc0refChr3 222253 17 - 222631 CTTTGTCAAAAGTTGTC -s Anc1.Anc1refChr5 3918 17 - 6477 CTTTGTCAAAAGTTGTC -s Anc2.Anc2refChr13 94022 17 - 96486 CTATTCCCAAGGTAGTC -s mr.mrrefChr5 130976 17 + 294540 CTTTGTCAAAAATTTTC -s simCow_chr6.simCow.chr6 244697 17 - 602619 CTAATCCTGAGGTAGTC -s simDog_chr6.simDog.chr6 245260 17 - 593897 CTATTCCCAAGGCAATG -s simHuman_chr6.simHuman.chr6 355241 17 - 601863 TTTTGTCAAAAGTTGTC -s simRat_chr6.simRat.chr6 268588 17 + 647215 CTTTGTCAGAAATTTTC - -a -s simMouse_chr6.simMouse.chr6 279881 114 + 636262 TTACAATTGTGTCATCAAAAAATGTGTCCCATTCCGCCTTCATCTTGAGCCAAAAAAACTATATCATTCTACTGTCATATACATAATGACTATTTGTTTGTGACCAAAACAGTC -s Anc0.Anc0refChr3 222270 69 - 222631 TTACAATT----------AGAAGGTGTTTCATTCTGCAT-----------------------------------TCATATACTTGATAATTATTTGCTTGTGACTAAAAGAATC -s Anc1.Anc1refChr5 3935 79 - 6477 TTACAATTATGTCAGCAGAGAAGGTGTTTCATTCTGCAT-----------------------------------TCATATACTTGATAATTATTTGCTTGTGACTAAAAGAATC -s Anc2.Anc2refChr13 94039 69 - 96486 TTACTGTT----------GGAAGGTCTTTCATTTTACAT-----------------------------------TAATATCCTTAATAATTCCTTGCCTGTGACTAAAAGAATC -s mr.mrrefChr5 130993 113 + 294540 TTACAATTATGTCATCAAAAAATGTGTTCCATTCCGCCTTCATCTTGAGCC-AAAAAACTATATCATTCTACTGTCATATACTTGATGACTATTTGTTTGTGACCAAAACAGTC -s simCow_chr6.simCow.chr6 244717 12 - 602619 TTGCTACT----------GAAA-------------------------------------------------------------------------------------------- -s simDog_chr6.simDog.chr6 245277 69 - 593897 TTACTGTT----------GGAAGGTCTTTCATTTTACAT-----------------------------------TAATATCCTTAATAATTCCTTGCCTGTGACTAAAAGAATC -s simHuman_chr6.simHuman.chr6 355258 79 - 601863 TTACAACTATGTCAGCAGATAACGTGTTTCATTCGGCTT-----------------------------------TCATATACTTGATAATTATTTGCTCAGTACTAAAAAAATC -s simRat_chr6.simRat.chr6 268605 113 + 647215 TTACAATTATGTCATCAAAAAATGTGTTCCATTCTGCCTTCATCTTAAACC-AAAAAATTTTATCATTCTGGTTTCATACACTTGATGACTATTTGTTGGTGAACAAAAGAGAC - -a -s simMouse_chr6.simMouse.chr6 279995 63 + 636262 AATTGACACACACGACAATGCGATTCTACTCCTAAGATAGTGAAACGTGATGTATGCTCTCAA -s Anc0.Anc0refChr3 222344 17 - 222631 AATCATTACCCATGTCA---------------------------------------------- -s Anc1.Anc1refChr5 4019 17 - 6477 AATCATTACCCATGTCA---------------------------------------------- -s Anc2.Anc2refChr13 94113 17 - 96486 AGTCGTTACCCATGTCA---------------------------------------------- -s mr.mrrefChr5 131106 17 + 294540 AATCAACACACATGACA---------------------------------------------- -s simCow_chr6.simCow.chr6 244732 17 - 602619 TGTCCTAATCTATGTCA---------------------------------------------- -s simDog_chr6.simDog.chr6 245351 16 - 593897 AGTCGATACCCA-GTCA---------------------------------------------- -s simHuman_chr6.simHuman.chr6 355342 17 - 601863 AATCATTACCCATGTCA---------------------------------------------- -s simRat_chr6.simRat.chr6 268718 17 + 647215 AATCAACACGCATGACA---------------------------------------------- - -a -s simMouse_chr6.simMouse.chr6 280058 15 + 636262 TCCCACCCATTATTG -s Anc0.Anc0refChr3 222361 15 - 222631 TTTCACCGTTTATTA -s Anc1.Anc1refChr5 4036 15 - 6477 TTTCACCGTTTATTA -s Anc2.Anc2refChr13 94132 15 - 96486 TTTCACTGTTTGTTA -s mr.mrrefChr5 131123 15 + 294540 TTCCACCCATTATTA -s simCow_chr6.simCow.chr6 244751 15 - 602619 AAAAAATGTGTGATA -s simDog_chr6.simDog.chr6 245369 15 - 593897 TTTCACTGTTTGTTA -s simHuman_chr6.simHuman.chr6 355359 15 - 601863 TTGCACCATTCATTA -s simRat_chr6.simRat.chr6 268735 15 + 647215 TTCCACGCCTTATTA - -a -s simMouse_chr6.simMouse.chr6 280073 12 + 636262 GTTGACTTCAGT -s Anc0.Anc0refChr3 222390 12 - 222631 TTTGACTTCAGT -s Anc1.Anc1refChr5 4065 12 - 6477 TTTGACTTCAGT -s Anc2.Anc2refChr13 94161 12 - 96486 TTTGACCTCAGT -s mr.mrrefChr5 131138 12 + 294540 GTTGACTTCAGT -s simCow_chr6.simCow.chr6 244780 9 - 602619 ATTAAT---AAT -s simDog_chr6.simDog.chr6 245398 12 - 593897 TTTGACCTCAGT -s simHuman_chr6.simHuman.chr6 355388 12 - 601863 CTTGACTTCAGT -s simRat_chr6.simRat.chr6 268750 3 + 647215 G---------AA - -a -s simMouse_chr6.simMouse.chr6 280085 21 + 636262 AGGTCTGTCTTGTAAACATAA -s Anc0.Anc0refChr3 222402 21 - 222631 AGGTTGATCCTGTAAACATAA -s Anc1.Anc1refChr5 4077 21 - 6477 AGGTTGATCCTGTAAACATAA -s Anc2.Anc2refChr13 94173 21 - 96486 ACGTTGATCCTGTAAGCATAA -s mr.mrrefChr5 131150 21 + 294540 AGGTCTGTCTTGTAAACATAA -s simCow_chr6.simCow.chr6 244789 19 - 602619 TCATTGA--CTGCAAGAATCA -s simDog_chr6.simDog.chr6 245410 21 - 593897 ACGTTAATCCTGTAAGCATAA -s simHuman_chr6.simHuman.chr6 355434 18 - 601863 AGGTTGCCCCTGGAGAC---A -s simRat_chr6.simRat.chr6 268753 21 + 647215 AGGTATGTCTTGTAAACATAG - -a -s simMouse_chr6.simMouse.chr6 280106 12 + 636262 AAGCATTTTGTT -s Anc0.Anc0refChr3 222423 12 - 222631 AAGCATTTTCTT -s Anc1.Anc1refChr5 4098 12 - 6477 AAGCATTTTCTT -s Anc2.Anc2refChr13 94194 12 - 96486 AAGCATTTTCTT -s mr.mrrefChr5 131171 12 + 294540 AAGCATTTTCTT -s simCow_chr6.simCow.chr6 244810 12 - 602619 AAGCATTTTCCT -s simDog_chr6.simDog.chr6 245431 12 - 593897 AAGCACATCTTT -s simHuman_chr6.simHuman.chr6 355452 12 - 601863 AAGTATTTTCTT -s simRat_chr6.simRat.chr6 268774 12 + 647215 GAGCAGTTTCTT - -a -s simMouse_chr6.simMouse.chr6 280118 14 + 636262 TTTCTCTCATGACA -s Anc0.Anc0refChr3 222436 14 - 222631 TGTTTCTCATGGTA -s Anc1.Anc1refChr5 4111 14 - 6477 TGTTTCTCATGGTA -s Anc2.Anc2refChr13 94207 14 - 96486 TGTTTCTCATGGTA -s mr.mrrefChr5 131183 14 + 294540 TTTCTCTCATGGTA -s simCow_chr6.simCow.chr6 244823 13 - 602619 TTTTT-TCCTGATA -s simDog_chr6.simDog.chr6 245444 14 - 593897 TGTTCCTCATGGTA -s simHuman_chr6.simHuman.chr6 355465 14 - 601863 AGATTCCCATGGTA -s simRat_chr6.simRat.chr6 268786 14 + 647215 TTTCTCTCATGGTA - -a -s simMouse_chr6.simMouse.chr6 280132 47 + 636262 ATGGTGGGAGATGGAAGTTCCAAACCATCTATATTTCTATACCACTG -s Anc0.Anc0refChr3 222453 44 - 222631 TTGGTAGAAAAAAGTA---ACACACTAAATATATTTTTACACCTCCA -s Anc1.Anc1refChr5 4128 44 - 6477 TTGGTAGAAAAAAGTA---ACACACTAAATATATTTTTACACCTCCA -s Anc2.Anc2refChr13 94224 44 - 96486 TTGGAAGACAAAAGTA---ACACACTAAATATATTTTCACACCTCTA -s mr.mrrefChr5 131197 47 + 294540 ATGGTGGAAGATAGAAGTTCCAAACCATCTATATTTCTATACCACCG -s simCow_chr6.simCow.chr6 244839 44 - 602619 TTGGAACACAAAAGTA---ACACACCCAATATATTTTGACACGTCTG -s simDog_chr6.simDog.chr6 245461 44 - 593897 TTGGAAGCCAAAAGTT---ACAGACTAAATCTATTTTCATACCTCTA -s simHuman_chr6.simHuman.chr6 355486 44 - 601863 TTGTTAGAAAAAAAGA---ACACACTAAATATATTTTTACACCCCCA -s simRat_chr6.simRat.chr6 268800 47 + 647215 ATGGTGGAGGATAGAAATTCCAAACCATTTATATTTCTAAACCTCCG - -a -s simMouse_chr6.simMouse.chr6 280179 42 + 636262 TCACCACAAATCATTAATTTACAGGCCAGCTTTTAGTATTGA -s Anc0.Anc0refChr3 222500 40 - 222631 TTT--ACACATCATTAATAGGAGGGCCAACTTTGGGTATTTA -s Anc1.Anc1refChr5 4175 42 - 6477 TTTACACACATCATTAATAGGAGGGCCAACTTTGGGTATTTA -s Anc2.Anc2refChr13 94271 40 - 96486 TTT--ACACATCATTAATAGGAGGGCCAACTTTGGGTATTTA -s mr.mrrefChr5 131244 42 + 294540 TCACCACACATCATTAATTTGCGGGCCAGCTTTTAGTATTGA -s simCow_chr6.simCow.chr6 244886 39 - 602619 TTG--ACG-ATTATTCGTCTAGCGGCCAATTTTGAATATTCA -s simDog_chr6.simDog.chr6 245508 40 - 593897 TTT--ACACATCATTAATAGGAGGGCCAACCTTGGGAATTTA -s simHuman_chr6.simHuman.chr6 355533 42 - 601863 TTTACACACATCATTATTAGGAGGGCCAACTCCGGGTATTTA -s simRat_chr6.simRat.chr6 268847 37 + 647215 TCACCAAACAT-----ATTTGTGTACCAGTTTTTTGTATTGA - -a -s simMouse_chr6.simMouse.chr6 280221 55 + 636262 GTTCTCCAATCCTAATTGTCCTAACATTCTCCTGCTGTCACTGTTCGGCCAGCTT -s Anc0.Anc0refChr3 222540 54 - 222631 GCTCTCCAATTCCAAGCAT-CAAATATTCTCCTGCTGTCACTCCTGGTCCAACAT -s Anc1.Anc1refChr5 4217 55 - 6477 GCTCTCCAATTCCAAGCATCCAAATATTCTCCTGCTGTCACTCCTGGTCCAACAT -s Anc2.Anc2refChr13 94312 54 - 96486 GCTCTCCAATTACAAGCAT-CAAATATTCTCCTGTTGTCATTCCTGGTCCAACAT -s mr.mrrefChr5 131286 55 + 294540 GTTCTCCAATTCTAATTGTCCAAACATTCTCCTGCTGTCACTGTTCGTCCAGCTT -s simCow_chr6.simCow.chr6 244926 51 - 602619 GCTCTTCAATTACAAGCAT-C---TTTTCTCCTGTTGTCATTACTGGTTCCACAT -s simDog_chr6.simDog.chr6 245549 51 - 593897 GCTCTCCAATTACAAGCAT-CAAATACTTTCCTGTT--CA-TCCTGGTCCAACAT -s simHuman_chr6.simHuman.chr6 355575 54 - 601863 CGT-TCCAATTCCTGGCATCCATATATTCTCCTGCTGTCACTCCTGGTCCAACAT -s simRat_chr6.simRat.chr6 268884 55 + 647215 GTTCTTCAATTCAAATTGTCCAAACTTTCTCCTGTTGTCACTGTTTGTCTGGGTT - -a -s simMouse_chr6.simMouse.chr6 280276 35 + 636262 GAGCCAAACTGCTATAATTTGGTCAGGGCATGGCA -s Anc0.Anc0refChr3 222596 35 - 222631 GAATCAGGCTAGTGTATATTAATCATAGCAATGTA -s Anc1.Anc1refChr5 4274 35 - 6477 GAATCAGGCTAGTGTATATTAATCATAGCAATGTA -s Anc2.Anc2refChr13 94368 35 - 96486 GAATCAGGCTAGTGTTTATTAATCATGACATTCAA -s mr.mrrefChr5 131343 35 + 294540 GAGCCAGACTGCTGTATTTTGGTCAGGGCATGGCA -s simCow_chr6.simCow.chr6 244979 35 - 602619 GAATCAGGCTAGCGTGTATTAATCATGACATTCAT -s simDog_chr6.simDog.chr6 245602 31 - 593897 ----TAAGGTAGTACTTATTAATCATGACATTCAA -s simHuman_chr6.simHuman.chr6 355631 35 - 601863 GACTCAGGCTTGTGTATCTTCATCATAGCAATGTA -s simRat_chr6.simRat.chr6 268941 35 + 647215 GAGCCAGACTGCTGTATTTTAGTCAGGGCATAGCA - -a -s simMouse_chr6.simMouse.chr6 280311 7 + 636262 AAGACAT -s Anc0.Anc0refChr8 3663 7 - 17196 GATATAA -s Anc1.Anc1refChr5 4309 7 - 6477 GATATAT -s Anc1.Anc1refChr8 47192 7 - 57822 GATATAA -s Anc2.Anc2refChr10 1327 7 - 1800 GATATAA -s mr.mrrefChr5 131378 7 + 294540 GAGACAT -s mr.mrrefChr5 143927 7 + 294540 GGTATAA -s simCow_chr6.simCow.chr6 332213 7 - 602619 GACATAA -s simDog_chr6.simDog.chr6 261625 7 + 593897 GTTATAA -s simHuman_chr6.simHuman.chr6 361894 7 - 601863 GATATAA -s simHuman_chr6.simHuman.chr6 355669 7 - 601863 GATATAT -s simMouse_chr6.simMouse.chr6 293002 7 + 636262 GGTATAA -s simRat_chr6.simRat.chr6 281792 7 + 647215 GGTATAA -s simRat_chr6.simRat.chr6 268976 7 + 647215 GAGACAT - -a -s simMouse_chr6.simMouse.chr6 280318 10 + 636262 GGCCCTCTGT -s Anc0.Anc0refChr8 3670 10 - 17196 CCCTCTCCAA -s Anc1.Anc1refChr5 4316 10 - 6477 AACTCTCCAC -s Anc1.Anc1refChr8 47199 10 - 57822 CCCTCTCCAA -s Anc2.Anc2refChr10 1334 10 - 1800 CCCTCTCCAA -s mr.mrrefChr5 131385 10 + 294540 GGCCCTCTGT -s mr.mrrefChr5 143934 10 + 294540 CCTTCTTCAA -s simCow_chr6.simCow.chr6 332220 10 - 602619 CTCTCTTCAA -s simDog_chr6.simDog.chr6 261632 10 + 593897 CCCTCTCCAA -s simHuman_chr6.simHuman.chr6 361901 10 - 601863 CCCTCTCCAA -s simHuman_chr6.simHuman.chr6 355676 10 - 601863 AACTCTCCAC -s simMouse_chr6.simMouse.chr6 293010 10 + 636262 CCTTCTTCAA -s simRat_chr6.simRat.chr6 281799 10 + 647215 CCTTCTACAA -s simRat_chr6.simRat.chr6 268983 10 + 647215 GGCCTGCTTT - -a -s simMouse_chr6.simMouse.chr6 280328 1 + 636262 G -s mr.mrrefChr5 131395 1 + 294540 G -s simRat_chr6.simRat.chr6 268993 1 + 647215 G - -a -s simMouse_chr6.simMouse.chr6 280329 4 + 636262 ATTG -s Anc0.Anc0refChr8 3680 4 - 17196 ACCA -s Anc1.Anc1refChr5 4326 4 - 6477 ATCA -s Anc1.Anc1refChr8 47209 4 - 57822 ACCA -s Anc2.Anc2refChr10 1344 4 - 1800 ACCA -s mr.mrrefChr5 131396 4 + 294540 ATTG -s mr.mrrefChr5 143944 4 + 294540 TACA -s simCow_chr6.simCow.chr6 332230 4 - 602619 TCCA -s simDog_chr6.simDog.chr6 261642 4 + 593897 ACCA -s simHuman_chr6.simHuman.chr6 361911 4 - 601863 CTCA -s simHuman_chr6.simHuman.chr6 355686 4 - 601863 ATCA -s simMouse_chr6.simMouse.chr6 293020 4 + 636262 CACA -s simRat_chr6.simRat.chr6 281809 4 + 647215 TACA -s simRat_chr6.simRat.chr6 268994 4 + 647215 ATTG - -a -s simMouse_chr6.simMouse.chr6 280333 4 + 636262 TCCA -s Anc0.Anc0refChr8 3684 4 - 17196 TCCC -s Anc1.Anc1refChr5 4330 4 - 6477 TTCC -s Anc1.Anc1refChr8 47213 4 - 57822 TCCC -s Anc2.Anc2refChr10 1348 4 - 1800 TCCC -s mr.mrrefChr5 131400 4 + 294540 TCCA -s simCow_chr6.simCow.chr6 332234 4 - 602619 TCCC -s simDog_chr6.simDog.chr6 261646 4 + 593897 CCCT -s simHuman_chr6.simHuman.chr6 361915 4 - 601863 TCCC -s simHuman_chr6.simHuman.chr6 355690 4 - 601863 TTCC -s simRat_chr6.simRat.chr6 269003 4 + 647215 TCCA - -a -s simMouse_chr6.simMouse.chr6 280337 14 + 636262 TCAATTCAATCTAG -s Anc0.Anc0refChr8 3688 14 - 17196 TTAATTCAACATAG -s Anc1.Anc1refChr5 4334 14 - 6477 TCAAATCAACATAG -s Anc1.Anc1refChr8 47217 14 - 57822 TTAATTCAACATAG -s Anc2.Anc2refChr10 1352 14 - 1800 TTAATTCAACATAG -s mr.mrrefChr5 131404 14 + 294540 TCAATTCAATCTAG -s mr.mrrefChr5 143948 14 + 294540 CTAAATTGGTGTAA -s simCow_chr6.simCow.chr6 332238 12 - 602619 TTAATT--ACATAG -s simDog_chr6.simDog.chr6 261650 14 + 593897 TTAGTTTAACATGG -s simHuman_chr6.simHuman.chr6 361919 14 - 601863 TGATCTCAACATAG -s simHuman_chr6.simHuman.chr6 355694 14 - 601863 TCAAATCAACATAG -s simMouse_chr6.simMouse.chr6 293024 14 + 636262 CTAAATTGGTGTAA -s simRat_chr6.simRat.chr6 281813 14 + 647215 CTAATTTCACGTAA -s simRat_chr6.simRat.chr6 269007 14 + 647215 TAAATTCGATCTAG - -a -s simMouse_chr6.simMouse.chr6 280351 2 + 636262 AC -s Anc0.Anc0refChr8 3702 2 - 17196 AG -s Anc1.Anc1refChr5 4348 2 - 6477 AG -s Anc1.Anc1refChr8 47231 2 - 57822 CG -s Anc2.Anc2refChr10 1366 2 - 1800 AG -s mr.mrrefChr5 131418 2 + 294540 AG -s mr.mrrefChr5 143962 2 + 294540 CC -s simCow_chr6.simCow.chr6 332250 2 - 602619 AG -s simDog_chr6.simDog.chr6 261664 2 + 593897 AG -s simHuman_chr6.simHuman.chr6 361942 2 - 601863 CG -s simHuman_chr6.simHuman.chr6 355708 2 - 601863 AG -s simMouse_chr6.simMouse.chr6 293038 2 + 636262 CC -s simRat_chr6.simRat.chr6 281827 2 + 647215 AC -s simRat_chr6.simRat.chr6 269021 2 + 647215 AG - -a -s simMouse_chr6.simMouse.chr6 280353 14 + 636262 ACAACAACAATTAC -s Anc0.Anc0refChr8 3707 14 - 17196 AGATCAAGGAGTGC -s Anc1.Anc1refChr5 4353 14 - 6477 GGATCAAGGAGTGC -s Anc1.Anc1refChr8 47236 14 - 57822 AGATCAAGGAGTGC -s Anc2.Anc2refChr10 1371 14 - 1800 AGATCAAGGAGTGC -s mr.mrrefChr5 131423 14 + 294540 AGAACAAGAATTAC -s mr.mrrefChr5 143967 14 + 294540 AGATCAAGAAGTGC -s simCow_chr6.simCow.chr6 332255 14 - 602619 AGCTCCAAGAGTGC -s simDog_chr6.simDog.chr6 261669 14 + 593897 AGAACTAGGATCAC -s simHuman_chr6.simHuman.chr6 361947 14 - 601863 AGATCAAGCAGTGC -s simHuman_chr6.simHuman.chr6 355713 14 - 601863 GGATCAAGGAGTGC -s simMouse_chr6.simMouse.chr6 293043 14 + 636262 AGATCAAGAAGTGC -s simRat_chr6.simRat.chr6 281832 14 + 647215 CGATCAAGAAGTGA -s simRat_chr6.simRat.chr6 269026 14 + 647215 AGAACAAGTATCAC - -a -s simMouse_chr6.simMouse.chr6 280367 20 + 636262 TTTGCCAAGGCGGCAAAGTT -s Anc0.Anc0refChr8 3723 20 - 17196 TGTGCTAAGGCAGCAAAATT -s Anc1.Anc1refChr5 4369 20 - 6477 TGTGCTAAGGCGGCAAAATT -s Anc1.Anc1refChr8 47252 20 - 57822 TGTGCTAAGGCAGCAAAGTT -s Anc2.Anc2refChr10 1387 20 - 1800 TGTGCCAAGGCAGCAAAATT -s mr.mrrefChr5 131439 20 + 294540 TTTGCCAAGGCGGCAAAGTT -s mr.mrrefChr5 143983 20 + 294540 TGTGATAAGGTAGCAAAGTT -s simCow_chr6.simCow.chr6 332271 20 - 602619 TGTGCCAAGGTGGCAAACTC -s simDog_chr6.simDog.chr6 261685 20 + 593897 TGTGTCAAGGGAGCAAAATT -s simHuman_chr6.simHuman.chr6 361963 20 - 601863 TGTGCTATTGCAACAAAGTT -s simHuman_chr6.simHuman.chr6 355729 20 - 601863 TGTGCTAAGGCGGCAAAATT -s simMouse_chr6.simMouse.chr6 293059 20 + 636262 TGTGATAAGGTAGCCAAGTT -s simRat_chr6.simRat.chr6 281848 20 + 647215 TGTGATATGGTAGCAAAGTT -s simRat_chr6.simRat.chr6 269042 20 + 647215 CTTGCCAAGGCAGCAAGGTT - -a -s simMouse_chr6.simMouse.chr6 280387 1 + 636262 G -s Anc0.Anc0refChr8 3743 1 - 17196 G -s Anc1.Anc1refChr5 4389 1 - 6477 G -s Anc1.Anc1refChr8 47272 1 - 57822 G -s Anc2.Anc2refChr10 1407 1 - 1800 G -s mr.mrrefChr5 131459 1 + 294540 G -s mr.mrrefChr5 144003 1 + 294540 G -s simCow_chr6.simCow.chr6 332291 1 - 602619 G -s simDog_chr6.simDog.chr6 261705 1 + 593897 G -s simHuman_chr6.simHuman.chr6 361983 1 - 601863 G -s simHuman_chr6.simHuman.chr6 355751 1 - 601863 G -s simMouse_chr6.simMouse.chr6 293079 1 + 636262 G -s simRat_chr6.simRat.chr6 281868 1 + 647215 G -s simRat_chr6.simRat.chr6 269062 1 + 647215 G - -a -s simMouse_chr6.simMouse.chr6 280388 6 + 636262 TATAGA -s Anc0.Anc0refChr8 3746 6 - 17196 GCGAGA -s Anc1.Anc1refChr5 4392 6 - 6477 CCGAGA -s Anc1.Anc1refChr8 47275 6 - 57822 GCCAGA -s Anc2.Anc2refChr10 1410 6 - 1800 GCGAGA -s mr.mrrefChr5 131462 6 + 294540 CATAGA -s mr.mrrefChr5 144006 6 + 294540 GCCAGA -s simCow_chr6.simCow.chr6 332294 6 - 602619 GTGAGA -s simDog_chr6.simDog.chr6 261708 6 + 593897 CCGAGA -s simHuman_chr6.simHuman.chr6 361986 6 - 601863 GCCAGA -s simHuman_chr6.simHuman.chr6 355754 6 - 601863 CCGAGA -s simMouse_chr6.simMouse.chr6 293082 6 + 636262 GCCAGA -s simRat_chr6.simRat.chr6 281871 6 + 647215 GCCAGA -s simRat_chr6.simRat.chr6 269065 6 + 647215 CACAGA - -a -s simMouse_chr6.simMouse.chr6 280394 3 + 636262 TTA -s Anc0.Anc0refChr8 3756 3 - 17196 TTA -s Anc1.Anc1refChr5 4398 3 - 6477 TTA -s Anc1.Anc1refChr8 47285 3 - 57822 TTA -s Anc2.Anc2refChr10 1420 3 - 1800 TTA -s mr.mrrefChr5 131468 3 + 294540 TTA -s mr.mrrefChr5 144016 3 + 294540 TTG -s simCow_chr6.simCow.chr6 332303 3 - 602619 TTA -s simDog_chr6.simDog.chr6 261718 3 + 593897 TTA -s simHuman_chr6.simHuman.chr6 361996 3 - 601863 TCA -s simHuman_chr6.simHuman.chr6 355762 3 - 601863 TTA -s simMouse_chr6.simMouse.chr6 293092 3 + 636262 TTG -s simRat_chr6.simRat.chr6 281881 3 + 647215 TTG -s simRat_chr6.simRat.chr6 269071 3 + 647215 TTA - -a -s simMouse_chr6.simMouse.chr6 280397 5 + 636262 ACCCT -s Anc0.Anc0refChr8 3759 5 - 17196 ACCTT -s Anc1.Anc1refChr5 4401 5 - 6477 ACCCT -s Anc1.Anc1refChr8 47288 5 - 57822 ACCTT -s Anc2.Anc2refChr10 1423 5 - 1800 ACCTT -s mr.mrrefChr5 131471 5 + 294540 ACCCT -s simCow_chr6.simCow.chr6 332306 5 - 602619 ACCTT -s simDog_chr6.simDog.chr6 261721 5 + 593897 ACCTC -s simHuman_chr6.simHuman.chr6 361999 5 - 601863 CCCCT -s simHuman_chr6.simHuman.chr6 355765 5 - 601863 ACCCT -s simRat_chr6.simRat.chr6 269074 5 + 647215 ACCCC - -a -s simMouse_chr6.simMouse.chr6 280402 6 + 636262 TCCACT -s Anc0.Anc0refChr8 3764 6 - 17196 CTGACC -s Anc1.Anc1refChr5 4406 6 - 6477 CCCACC -s Anc1.Anc1refChr8 47293 6 - 57822 CTGACC -s Anc2.Anc2refChr10 1428 6 - 1800 CTGACC -s mr.mrrefChr5 131476 6 + 294540 TCCACT -s simCow_chr6.simCow.chr6 332328 6 - 602619 CTGGGT -s simDog_chr6.simDog.chr6 261726 6 + 593897 CTGACC -s simHuman_chr6.simHuman.chr6 362004 6 - 601863 CCCACC -s simHuman_chr6.simHuman.chr6 355770 6 - 601863 CCCACC -s simRat_chr6.simRat.chr6 269079 6 + 647215 TCCACT - -a -s simMouse_chr6.simMouse.chr6 280408 1 + 636262 A -s Anc0.Anc0refChr8 3770 1 - 17196 A -s Anc1.Anc1refChr5 4412 1 - 6477 A -s Anc1.Anc1refChr8 47299 1 - 57822 A -s Anc2.Anc2refChr10 1434 1 - 1800 A -s mr.mrrefChr5 131482 1 + 294540 A -s mr.mrrefChr5 144019 1 + 294540 A -s simCow_chr6.simCow.chr6 332334 1 - 602619 A -s simDog_chr6.simDog.chr6 261732 1 + 593897 A -s simHuman_chr6.simHuman.chr6 362010 1 - 601863 A -s simHuman_chr6.simHuman.chr6 355776 1 - 601863 A -s simMouse_chr6.simMouse.chr6 293095 1 + 636262 A -s simRat_chr6.simRat.chr6 281884 1 + 647215 G -s simRat_chr6.simRat.chr6 269085 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 280409 6 + 636262 CTCCTG -s Anc0.Anc0refChr8 3771 6 - 17196 TCCATG -s Anc1.Anc1refChr5 4413 6 - 6477 TCCATG -s Anc1.Anc1refChr8 47300 6 - 57822 TCCATG -s Anc2.Anc2refChr10 1435 6 - 1800 TCCATG -s mr.mrrefChr5 131483 6 + 294540 CCCATG -s mr.mrrefChr5 144020 6 + 294540 TCCCTT -s simCow_chr6.simCow.chr6 332391 6 - 602619 TCTAGG -s simDog_chr6.simDog.chr6 261733 6 + 593897 CCCATG -s simHuman_chr6.simHuman.chr6 362011 6 - 601863 TCCATG -s simHuman_chr6.simHuman.chr6 355777 6 - 601863 TCCATG -s simMouse_chr6.simMouse.chr6 293096 6 + 636262 TCCCTT -s simRat_chr6.simRat.chr6 281895 6 + 647215 TCCCTT -s simRat_chr6.simRat.chr6 269086 4 + 647215 CCCA-- - -a -s simMouse_chr6.simMouse.chr6 280415 1 + 636262 G -s Anc0.Anc0refChr8 3789 1 - 17196 C -s Anc1.Anc1refChr5 4423 1 - 6477 G -s Anc1.Anc1refChr8 47318 1 - 57822 C -s Anc2.Anc2refChr10 1453 1 - 1800 C -s mr.mrrefChr5 131493 1 + 294540 G -s mr.mrrefChr5 144041 1 + 294540 C -s simCow_chr6.simCow.chr6 332408 1 - 602619 C -s simDog_chr6.simDog.chr6 261751 1 + 593897 C -s simHuman_chr6.simHuman.chr6 362029 1 - 601863 C -s simHuman_chr6.simHuman.chr6 355788 1 - 601863 G -s simMouse_chr6.simMouse.chr6 293117 1 + 636262 C -s simRat_chr6.simRat.chr6 281916 1 + 647215 A -s simRat_chr6.simRat.chr6 269094 1 + 647215 G - -a -s simMouse_chr6.simMouse.chr6 280416 6 + 636262 TAGGGG -s Anc0.Anc0refChr8 3790 6 - 17196 TTGGAG -s Anc1.Anc1refChr5 4424 6 - 6477 CTGGAG -s Anc1.Anc1refChr8 47319 6 - 57822 TTGGAG -s Anc2.Anc2refChr10 1454 6 - 1800 TTGGAG -s mr.mrrefChr5 131494 6 + 294540 CTGGGG -s mr.mrrefChr5 144042 6 + 294540 ATGGAC -s simCow_chr6.simCow.chr6 332409 6 - 602619 TTGGAG -s simDog_chr6.simDog.chr6 261752 6 + 593897 TCGGGG -s simHuman_chr6.simHuman.chr6 362030 6 - 601863 TTGAAG -s simHuman_chr6.simHuman.chr6 355789 6 - 601863 CTGGAG -s simMouse_chr6.simMouse.chr6 293118 6 + 636262 ATGGAC -s simRat_chr6.simRat.chr6 281917 6 + 647215 TTGGAC -s simRat_chr6.simRat.chr6 269101 6 + 647215 CTGGGG - -a -s simMouse_chr6.simMouse.chr6 280422 1 + 636262 A -s mr.mrrefChr5 131500 1 + 294540 A -s simRat_chr6.simRat.chr6 269107 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 280423 4 + 636262 CTTA -s Anc0.Anc0refChr8 3796 4 - 17196 TTTA -s Anc1.Anc1refChr5 4430 4 - 6477 TTTA -s Anc1.Anc1refChr8 47325 4 - 57822 TTTA -s Anc2.Anc2refChr10 1460 4 - 1800 TTTA -s mr.mrrefChr5 131501 4 + 294540 TTTA -s mr.mrrefChr5 144048 4 + 294540 TTCG -s simCow_chr6.simCow.chr6 332415 4 - 602619 TTTA -s simDog_chr6.simDog.chr6 261758 4 + 593897 TATA -s simHuman_chr6.simHuman.chr6 362036 4 - 601863 TTTA -s simHuman_chr6.simHuman.chr6 355795 4 - 601863 TTTA -s simMouse_chr6.simMouse.chr6 293124 4 + 636262 TTCG -s simRat_chr6.simRat.chr6 281923 4 + 647215 TCCA -s simRat_chr6.simRat.chr6 269108 4 + 647215 TTTA - -a -s simMouse_chr6.simMouse.chr6 280427 1 + 636262 T -s Anc0.Anc0refChr8 3800 1 - 17196 T -s Anc1.Anc1refChr5 4434 1 - 6477 T -s Anc1.Anc1refChr8 47329 1 - 57822 T -s Anc2.Anc2refChr10 1464 1 - 1800 T -s mr.mrrefChr5 131505 1 + 294540 T -s mr.mrrefChr5 144052 1 + 294540 T -s simCow_chr6.simCow.chr6 332419 1 - 602619 T -s simDog_chr6.simDog.chr6 261791 1 + 593897 T -s simHuman_chr6.simHuman.chr6 362040 1 - 601863 T -s simHuman_chr6.simHuman.chr6 355799 1 - 601863 T -s simMouse_chr6.simMouse.chr6 293128 1 + 636262 T -s simRat_chr6.simRat.chr6 281927 1 + 647215 A -s simRat_chr6.simRat.chr6 269112 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 280428 1 + 636262 A -s Anc0.Anc0refChr8 3801 1 - 17196 A -s Anc1.Anc1refChr5 4435 1 - 6477 T -s Anc1.Anc1refChr8 47330 1 - 57822 A -s Anc2.Anc2refChr10 1465 1 - 1800 A -s mr.mrrefChr5 131506 1 + 294540 A -s simCow_chr6.simCow.chr6 332420 1 - 602619 G -s simDog_chr6.simDog.chr6 261792 1 + 593897 A -s simHuman_chr6.simHuman.chr6 362041 1 - 601863 A -s simHuman_chr6.simHuman.chr6 355800 1 - 601863 T -s simRat_chr6.simRat.chr6 269113 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 280429 7 + 636262 TAGGTTA -s Anc0.Anc0refChr8 3802 7 - 17196 TAGGTTA -s Anc1.Anc1refChr5 4436 7 - 6477 TAGGTTA -s Anc1.Anc1refChr8 47331 7 - 57822 TAGGCTA -s Anc2.Anc2refChr10 1466 7 - 1800 TAGGTTA -s mr.mrrefChr5 131507 7 + 294540 TAGGTTA -s mr.mrrefChr5 144053 7 + 294540 TAGGCTA -s simCow_chr6.simCow.chr6 332421 7 - 602619 TAGACTA -s simDog_chr6.simDog.chr6 261793 7 + 593897 TAGGTTA -s simHuman_chr6.simHuman.chr6 362042 7 - 601863 TAGGCTA -s simHuman_chr6.simHuman.chr6 355801 7 - 601863 TAGGTTA -s simMouse_chr6.simMouse.chr6 293129 7 + 636262 TAGGCTA -s simRat_chr6.simRat.chr6 281928 7 + 647215 TAGGTTA -s simRat_chr6.simRat.chr6 269114 7 + 647215 TAGGTTA - -a -s simMouse_chr6.simMouse.chr6 280436 1 + 636262 A -s Anc0.Anc0refChr8 3809 1 - 17196 A -s Anc1.Anc1refChr5 4443 1 - 6477 A -s Anc1.Anc1refChr8 47338 1 - 57822 A -s Anc2.Anc2refChr10 1473 1 - 1800 A -s mr.mrrefChr5 131514 1 + 294540 A -s simCow_chr6.simCow.chr6 332428 1 - 602619 A -s simDog_chr6.simDog.chr6 261800 1 + 593897 A -s simHuman_chr6.simHuman.chr6 362049 1 - 601863 C -s simHuman_chr6.simHuman.chr6 355808 1 - 601863 A -s simRat_chr6.simRat.chr6 269121 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 280437 14 + 636262 AATTGCTCATTCAG -s Anc0.Anc0refChr8 3810 14 - 17196 AATTGTTCAGTTAG -s Anc1.Anc1refChr5 4444 14 - 6477 AAGTGTTTAATCAG -s Anc1.Anc1refChr8 47339 14 - 57822 ATTTGTTCAGTTAG -s Anc2.Anc2refChr10 1474 14 - 1800 AATTGTTCAGTTAG -s mr.mrrefChr5 131515 14 + 294540 AATTGCTCATTCAG -s mr.mrrefChr5 144060 14 + 294540 ATTTGGTCAGGTAG -s simCow_chr6.simCow.chr6 332429 14 - 602619 AATTGTTCAGTCAG -s simDog_chr6.simDog.chr6 261801 14 + 593897 AATTGTTCAGTTGG -s simHuman_chr6.simHuman.chr6 362050 14 - 601863 ATTTGTTCAATTAG -s simHuman_chr6.simHuman.chr6 355809 14 - 601863 AAGTGTTTAATCAG -s simMouse_chr6.simMouse.chr6 293136 14 + 636262 ATTTGGTCAGGTAG -s simRat_chr6.simRat.chr6 281935 14 + 647215 ACTTGGTCAGATAA -s simRat_chr6.simRat.chr6 269122 14 + 647215 AATTGCTCATTCAG - -a -s simMouse_chr6.simMouse.chr6 280451 2 + 636262 AA -s Anc0.Anc0refChr8 3824 2 - 17196 AA -s Anc1.Anc1refChr5 4458 2 - 6477 AA -s Anc1.Anc1refChr8 47353 2 - 57822 AA -s Anc2.Anc2refChr10 1488 2 - 1800 AA -s mr.mrrefChr5 131529 2 + 294540 AA -s mr.mrrefChr5 144195 2 + 294540 AA -s simCow_chr6.simCow.chr6 332443 2 - 602619 AA -s simDog_chr6.simDog.chr6 261815 2 + 593897 AA -s simHuman_chr6.simHuman.chr6 362064 2 - 601863 AA -s simHuman_chr6.simHuman.chr6 355823 2 - 601863 AA -s simMouse_chr6.simMouse.chr6 293272 2 + 636262 AC -s simRat_chr6.simRat.chr6 282070 2 + 647215 AA -s simRat_chr6.simRat.chr6 269136 2 + 647215 AA - -a -s simMouse_chr6.simMouse.chr6 280453 2 + 636262 TA -s Anc0.Anc0refChr8 3827 2 - 17196 CA -s Anc1.Anc1refChr5 4461 2 - 6477 CA -s Anc1.Anc1refChr8 47356 2 - 57822 GA -s Anc2.Anc2refChr10 1491 2 - 1800 CC -s mr.mrrefChr5 131532 2 + 294540 TA -s mr.mrrefChr5 144198 2 + 294540 GA -s simCow_chr6.simCow.chr6 332446 2 - 602619 CC -s simDog_chr6.simDog.chr6 261818 2 + 593897 CC -s simHuman_chr6.simHuman.chr6 362067 2 - 601863 GA -s simHuman_chr6.simHuman.chr6 355826 2 - 601863 CA -s simMouse_chr6.simMouse.chr6 293275 2 + 636262 GA -s simRat_chr6.simRat.chr6 282073 2 + 647215 AA -s simRat_chr6.simRat.chr6 269139 2 + 647215 TT - -a -s simMouse_chr6.simMouse.chr6 280455 1 + 636262 G -s Anc0.Anc0refChr8 3837 1 - 17196 A -s Anc1.Anc1refChr5 4463 1 - 6477 G -s Anc1.Anc1refChr8 47366 1 - 57822 A -s Anc2.Anc2refChr10 1501 1 - 1800 A -s mr.mrrefChr5 131534 1 + 294540 G -s mr.mrrefChr5 144208 1 + 294540 A -s simCow_chr6.simCow.chr6 332456 1 - 602619 A -s simDog_chr6.simDog.chr6 261828 1 + 593897 A -s simHuman_chr6.simHuman.chr6 362077 1 - 601863 A -s simHuman_chr6.simHuman.chr6 355828 1 - 601863 G -s simMouse_chr6.simMouse.chr6 293285 1 + 636262 A -s simRat_chr6.simRat.chr6 282083 1 + 647215 A -s simRat_chr6.simRat.chr6 269141 1 + 647215 G - -a -s simMouse_chr6.simMouse.chr6 280456 6 + 636262 CAACCT -s Anc0.Anc0refChr8 3838 6 - 17196 GAAAGT -s Anc1.Anc1refChr5 4464 6 - 6477 GAAAAT -s Anc1.Anc1refChr8 47367 6 - 57822 GAAAGT -s Anc2.Anc2refChr10 1502 6 - 1800 GAAAGT -s mr.mrrefChr5 131535 6 + 294540 GAACAT -s mr.mrrefChr5 144209 6 + 294540 GAAGGC -s simCow_chr6.simCow.chr6 332457 6 - 602619 GAAAGG -s simDog_chr6.simDog.chr6 261829 6 + 593897 GAAAGT -s simHuman_chr6.simHuman.chr6 362078 6 - 601863 AAAAGT -s simHuman_chr6.simHuman.chr6 355837 6 - 601863 GAAAAT -s simMouse_chr6.simMouse.chr6 293286 6 + 636262 GAAGGC -s simRat_chr6.simRat.chr6 282084 6 + 647215 GAAGGC -s simRat_chr6.simRat.chr6 269142 6 + 647215 GAGCAT - -a -s simMouse_chr6.simMouse.chr6 280462 2 + 636262 AA -s Anc0.Anc0refChr8 3844 2 - 17196 GT -s Anc1.Anc1refChr5 4470 2 - 6477 GT -s Anc1.Anc1refChr8 47373 2 - 57822 GT -s Anc2.Anc2refChr10 1508 2 - 1800 GT -s mr.mrrefChr5 131541 2 + 294540 GA -s simCow_chr6.simCow.chr6 332463 2 - 602619 GT -s simDog_chr6.simDog.chr6 261835 2 + 593897 GT -s simHuman_chr6.simHuman.chr6 362084 2 - 601863 GT -s simHuman_chr6.simHuman.chr6 355843 2 - 601863 GT -s simRat_chr6.simRat.chr6 269148 2 + 647215 GA - -a -s simMouse_chr6.simMouse.chr6 280464 14 + 636262 ATTGTAAAATTTGA -s Anc0.Anc0refChr8 3846 14 - 17196 ATTGAAAAATCTGA -s Anc1.Anc1refChr5 4472 14 - 6477 ATTGAAAAATCTGA -s Anc1.Anc1refChr8 47375 14 - 57822 ATTGAAAAATCTGA -s Anc2.Anc2refChr10 1510 14 - 1800 ATTGAAAAATCTGA -s mr.mrrefChr5 131543 14 + 294540 ATTGTAAAATTTGA -s mr.mrrefChr5 144215 14 + 294540 ATTGAAAAATCTGA -s simCow_chr6.simCow.chr6 332465 14 - 602619 ATTGAAAAATCTGA -s simDog_chr6.simDog.chr6 261837 14 + 593897 ATTGAAAAATCTGA -s simHuman_chr6.simHuman.chr6 362086 14 - 601863 ATCAAAAAATCTGA -s simHuman_chr6.simHuman.chr6 355845 14 - 601863 ATTGAAAAATCTGA -s simMouse_chr6.simMouse.chr6 293292 14 + 636262 ATTGAAAAATCTGA -s simRat_chr6.simRat.chr6 282090 14 + 647215 ATTGAAAAATCTGA -s simRat_chr6.simRat.chr6 269150 14 + 647215 ATAGGAAAATTTGA - -a -s simMouse_chr6.simMouse.chr6 280478 24 + 636262 CACTATTGGGTTCATGAGAACCCG -s Anc0.Anc0refChr8 3860 24 - 17196 CACCATTGTGTTCATGTACACCTA -s Anc1.Anc1refChr5 4486 24 - 6477 CACCACTGTGTTGATGTACACCCA -s Anc1.Anc1refChr8 47389 24 - 57822 CACCATTGTGTCCACGTACACCTA -s Anc2.Anc2refChr10 1524 24 - 1800 CACCATTGTGTTCATGTACACCTA -s mr.mrrefChr5 131557 24 + 294540 CACTATTGGGTTCATGAGCACCCG -s mr.mrrefChr5 144229 24 + 294540 CACTATTGTGTCGACGTATAACTA -s simCow_chr6.simCow.chr6 332479 24 - 602619 CACCATTTTGTTCATGGACGCCTA -s simDog_chr6.simDog.chr6 261851 24 + 593897 CACCATTGTGTTCATGCACACCTA -s simHuman_chr6.simHuman.chr6 362106 24 - 601863 CATCATTGTGTCCACGTACACCTA -s simHuman_chr6.simHuman.chr6 355859 24 - 601863 CACCACTGTGTTGATGTACACCCA -s simMouse_chr6.simMouse.chr6 293306 24 + 636262 CACTATAGTATTGACGTATAAGTA -s simRat_chr6.simRat.chr6 282104 24 + 647215 CACTATTGTGTCAATGTATAACTA -s simRat_chr6.simRat.chr6 269164 21 + 647215 CACTATTGAGTTCATGAGCAC--- - -a -s simMouse_chr6.simMouse.chr6 280502 3 + 636262 TCA -s Anc0.Anc0refChr8 3884 3 - 17196 CCT -s Anc1.Anc1refChr5 4510 3 - 6477 TCT -s Anc1.Anc1refChr8 47413 3 - 57822 CCT -s Anc2.Anc2refChr10 1548 3 - 1800 CCT -s mr.mrrefChr5 131581 3 + 294540 TCA -s mr.mrrefChr5 144253 3 + 294540 CCT -s simCow_chr6.simCow.chr6 332503 3 - 602619 CCT -s simDog_chr6.simDog.chr6 261875 3 + 593897 CAT -s simHuman_chr6.simHuman.chr6 362130 3 - 601863 CCT -s simHuman_chr6.simHuman.chr6 355885 3 - 601863 TCT -s simMouse_chr6.simMouse.chr6 293330 3 + 636262 CCT -s simRat_chr6.simRat.chr6 282128 3 + 647215 CCT - -a -s simMouse_chr6.simMouse.chr6 280505 1 + 636262 G -s Anc0.Anc0refChr8 3890 1 - 17196 A -s Anc1.Anc1refChr5 4513 1 - 6477 G -s Anc1.Anc1refChr8 47419 1 - 57822 A -s Anc2.Anc2refChr10 1554 1 - 1800 A -s mr.mrrefChr5 131584 1 + 294540 G -s mr.mrrefChr5 144259 1 + 294540 A -s simCow_chr6.simCow.chr6 332509 1 - 602619 A -s simDog_chr6.simDog.chr6 261881 1 + 593897 G -s simHuman_chr6.simHuman.chr6 362136 1 - 601863 A -s simHuman_chr6.simHuman.chr6 355888 1 - 601863 G -s simMouse_chr6.simMouse.chr6 293336 1 + 636262 A -s simRat_chr6.simRat.chr6 282134 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 280506 20 + 636262 ATGTGGTCCAAGAGTGCTAT -s Anc0.Anc0refChr8 3891 20 - 17196 ATGTGATGCAAGTGCACTAG -s Anc1.Anc1refChr5 4514 20 - 6477 ATGTGATGCAAGTGCACTAG -s Anc1.Anc1refChr8 47420 20 - 57822 ATATGATGCAAGTGCACTAG -s Anc2.Anc2refChr10 1555 20 - 1800 ATGTGATGCAAGTGCACTAG -s mr.mrrefChr5 131585 20 + 294540 ATGTGGTCCAAGAGTGCTAT -s mr.mrrefChr5 144260 20 + 294540 ACATGATGTAAGTGCACTAA -s simCow_chr6.simCow.chr6 332510 20 - 602619 ACGTGCTGTGAGTACACTAG -s simDog_chr6.simDog.chr6 261882 15 + 593897 ATGTGATGCAAGTG-----G -s simHuman_chr6.simHuman.chr6 362137 20 - 601863 ATATGAGACAAGTGCATTAG -s simHuman_chr6.simHuman.chr6 355890 20 - 601863 ATGTGATGCAAGTGCACTAG -s simMouse_chr6.simMouse.chr6 293337 20 + 636262 ACATGATGTAAGTGCACTAA -s simRat_chr6.simRat.chr6 282135 20 + 647215 ACAGGATGTAAGTGCACCAA - -a -s simMouse_chr6.simMouse.chr6 280526 43 + 636262 AACAATCAATTCAGTGGGGCGAGAGTTAGATCCCAGTAAGACT -s Anc0.Anc0refChr8 3912 42 - 17196 AGCAGCCATTTCGATGAGATGAGAGTTACATCCCTGT-ACACT -s Anc1.Anc1refChr5 4534 42 - 6477 AGCAGCCATTATGATGGGACAAGAATTACATCCCTGT-ATACT -s Anc1.Anc1refChr8 47441 42 - 57822 AGCAGCCATTTCAATGAGATGAGAGTTATATCCCTGT-ACACT -s Anc2.Anc2refChr10 1576 42 - 1800 AGCAGCCATTTCGATGAGATGAGAGTTACATCCCTGT-ACACT -s mr.mrrefChr5 131605 42 + 294540 AACAATCAATTCAGTGGGGCGAGAGTTAGATCCCAGT-AGACT -s mr.mrrefChr5 144281 42 + 294540 ACCACAAATTTGAATTTGACAAGAGCCATATCTCTGT-ACACT -s simCow_chr6.simCow.chr6 332531 41 - 602619 -GCAGCCAACTCAGTAAGATGAGAATTACATCTTAGT-ACACC -s simDog_chr6.simDog.chr6 261898 42 + 593897 AGCAGCCATATCGCTGACATGTGAGTTACATCCCTGT-ACACT -s simHuman_chr6.simHuman.chr6 362158 42 - 601863 GGCAGCCATTTCAATGGGATGAGAGTTATATTCATGT-ACACT -s simHuman_chr6.simHuman.chr6 355910 42 - 601863 AGCAGCCATTATGATGGGACAAGAATTACATCCCTGT-ACACT -s simMouse_chr6.simMouse.chr6 293358 23 + 636262 ACC-------------------GAGCCATGTCTCTGT-ACACT -s simRat_chr6.simRat.chr6 282156 42 + 647215 ACCACAAATTTGAATTTGACAAGAGCCATATCTCTGT-ACACT -s simRat_chr6.simRat.chr6 269185 12 + 647215 ------------------------------TCCCAGT-AGACT - -a -s simMouse_chr6.simMouse.chr6 280569 3 + 636262 GAC -s Anc0.Anc0refChr8 3954 3 - 17196 GAC -s Anc1.Anc1refChr5 4576 3 - 6477 GAC -s Anc1.Anc1refChr8 47483 3 - 57822 GGT -s Anc2.Anc2refChr10 1618 3 - 1800 GAC -s mr.mrrefChr5 131647 3 + 294540 GAC -s mr.mrrefChr5 144343 3 + 294540 GGT -s simCow_chr6.simCow.chr6 332572 3 - 602619 CAA -s simDog_chr6.simDog.chr6 261940 3 + 593897 GAC -s simHuman_chr6.simHuman.chr6 362200 3 - 601863 AGT -s simHuman_chr6.simHuman.chr6 355952 3 - 601863 CAC -s simMouse_chr6.simMouse.chr6 293401 2 + 636262 -GT -s simRat_chr6.simRat.chr6 282218 3 + 647215 GGT -s simRat_chr6.simRat.chr6 269197 3 + 647215 GAC - -a -s simMouse_chr6.simMouse.chr6 280572 1 + 636262 C -s Anc0.Anc0refChr8 3965 1 - 17196 G -s Anc1.Anc1refChr5 4579 1 - 6477 A -s Anc1.Anc1refChr8 47494 1 - 57822 G -s Anc2.Anc2refChr10 1629 1 - 1800 G -s mr.mrrefChr5 131650 1 + 294540 C -s mr.mrrefChr5 144354 1 + 294540 T -s simCow_chr6.simCow.chr6 332583 1 - 602619 A -s simDog_chr6.simDog.chr6 261951 1 + 593897 G -s simHuman_chr6.simHuman.chr6 362211 1 - 601863 G -s simHuman_chr6.simHuman.chr6 355955 1 - 601863 A -s simMouse_chr6.simMouse.chr6 293411 1 + 636262 T -s simRat_chr6.simRat.chr6 282229 1 + 647215 C -s simRat_chr6.simRat.chr6 269200 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 280573 1 + 636262 T -s Anc0.Anc0refChr8 3966 1 - 17196 T -s Anc1.Anc1refChr5 4580 1 - 6477 T -s Anc2.Anc2refChr10 1630 1 - 1800 T -s mr.mrrefChr5 131651 1 + 294540 T -s simCow_chr6.simCow.chr6 332584 1 - 602619 T -s simDog_chr6.simDog.chr6 261952 1 + 593897 T -s simHuman_chr6.simHuman.chr6 355956 1 - 601863 T -s simRat_chr6.simRat.chr6 269201 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 280574 1 + 636262 T -s Anc0.Anc0refChr8 3967 1 - 17196 T -s Anc1.Anc1refChr5 4581 1 - 6477 T -s Anc1.Anc1refChr8 47495 1 - 57822 C -s Anc2.Anc2refChr10 1631 1 - 1800 T -s mr.mrrefChr5 131652 1 + 294540 T -s mr.mrrefChr5 144355 1 + 294540 C -s simCow_chr6.simCow.chr6 332585 1 - 602619 A -s simDog_chr6.simDog.chr6 261953 1 + 593897 T -s simHuman_chr6.simHuman.chr6 362212 1 - 601863 C -s simHuman_chr6.simHuman.chr6 355957 1 - 601863 T -s simMouse_chr6.simMouse.chr6 293412 1 + 636262 C -s simRat_chr6.simRat.chr6 282230 1 + 647215 C -s simRat_chr6.simRat.chr6 269202 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 280575 2 + 636262 GA -s Anc0.Anc0refChr8 3968 2 - 17196 CC -s Anc1.Anc1refChr5 4582 2 - 6477 CA -s Anc1.Anc1refChr8 47496 2 - 57822 CC -s Anc2.Anc2refChr10 1632 2 - 1800 CC -s mr.mrrefChr5 131653 2 + 294540 GA -s mr.mrrefChr5 144356 2 + 294540 CA -s simCow_chr6.simCow.chr6 332586 2 - 602619 CG -s simDog_chr6.simDog.chr6 261954 2 + 593897 CC -s simHuman_chr6.simHuman.chr6 362213 2 - 601863 CC -s simHuman_chr6.simHuman.chr6 355958 2 - 601863 CA -s simMouse_chr6.simMouse.chr6 293413 2 + 636262 CA -s simRat_chr6.simRat.chr6 269203 2 + 647215 GA - -a -s simMouse_chr6.simMouse.chr6 280577 2 + 636262 AG -s Anc0.Anc0refChr8 3970 2 - 17196 AC -s Anc1.Anc1refChr5 4584 2 - 6477 AG -s Anc1.Anc1refChr8 47498 2 - 57822 AC -s Anc2.Anc2refChr10 1634 2 - 1800 AC -s mr.mrrefChr5 131655 2 + 294540 AG -s mr.mrrefChr5 144358 2 + 294540 TG -s simCow_chr6.simCow.chr6 332588 2 - 602619 AC -s simDog_chr6.simDog.chr6 261956 2 + 593897 AC -s simHuman_chr6.simHuman.chr6 362215 2 - 601863 AC -s simHuman_chr6.simHuman.chr6 355960 2 - 601863 AG -s simMouse_chr6.simMouse.chr6 293415 2 + 636262 TG -s simRat_chr6.simRat.chr6 282231 2 + 647215 TG -s simRat_chr6.simRat.chr6 269205 2 + 647215 AG - -a -s simMouse_chr6.simMouse.chr6 280579 1 + 636262 A -s Anc0.Anc0refChr6 0 1 - 1880 A -s Anc1.Anc1refChr5 4586 1 - 6477 A -s Anc2.Anc2refChr13 94404 1 - 96486 A -s mr.mrrefChr5 131657 1 + 294540 A -s simCow_chr6.simCow.chr6 245015 1 - 602619 A -s simDog_chr6.simDog.chr6 245634 1 - 593897 A -s simHuman_chr6.simHuman.chr6 355962 1 - 601863 A -s simRat_chr6.simRat.chr6 269207 1 + 647215 G - -a -s simMouse_chr6.simMouse.chr6 280580 21 + 636262 GGTCTCATGAAGTCAGACTGA -s Anc0.Anc0refChr6 8 21 - 1880 GGTCTCTTGTAGTCAGGCATA -s Anc1.Anc1refChr5 4594 21 - 6477 GGTCTCTTGTAGTCAGGCATA -s Anc2.Anc2refChr13 94412 21 - 96486 AGTCTCTTATAGTCAGGCATA -s mr.mrrefChr5 131665 21 + 294540 GGTCTCATGAAGTCAGACTGA -s simCow_chr6.simCow.chr6 245021 19 - 602619 AATCTCTC-TAGTCAGGGA-A -s simDog_chr6.simDog.chr6 245642 21 - 593897 AGCCTCTTATAGTCTGGCCTA -s simHuman_chr6.simHuman.chr6 355970 21 - 601863 GGTCTCCTGTAGTCAGGCAAA -s simRat_chr6.simRat.chr6 269215 21 + 647215 GGTCTCATGAATTCAGACTGA - -a -s simMouse_chr6.simMouse.chr6 280601 9 + 636262 GCATCGATT -s Anc0.Anc0refChr6 30 9 - 1880 GTCTCAATT -s Anc1.Anc1refChr5 4616 9 - 6477 GTCTCAATT -s Anc2.Anc2refChr13 94434 9 - 96486 GTCTCAATT -s mr.mrrefChr5 131686 9 + 294540 GCATCAATT -s simCow_chr6.simCow.chr6 245041 9 - 602619 GTCTCAATT -s simDog_chr6.simDog.chr6 245664 9 - 593897 AGCTCAATT -s simHuman_chr6.simHuman.chr6 355992 9 - 601863 GTCTCAATT -s simRat_chr6.simRat.chr6 269236 9 + 647215 GCATCAATT - -a -s simMouse_chr6.simMouse.chr6 280610 10 + 636262 CAGTGAGGGA -s Anc0.Anc0refChr6 40 10 - 1880 CAGTGAGGGA -s Anc1.Anc1refChr5 4626 10 - 6477 CAGTGAGGGA -s Anc2.Anc2refChr13 94444 10 - 96486 GAGTGAGGGA -s mr.mrrefChr5 131696 10 + 294540 CAGTGAGGGA -s simCow_chr6.simCow.chr6 245051 10 - 602619 GAGTGAGGGA -s simDog_chr6.simDog.chr6 245674 10 - 593897 GAGTGAGGAG -s simHuman_chr6.simHuman.chr6 356002 10 - 601863 CAGTAAGGGA -s simRat_chr6.simRat.chr6 269246 10 + 647215 TAGTGAGGGA - -a -s simMouse_chr6.simMouse.chr6 280620 57 + 636262 TACATACTGTTTACCACACCCCATGGAGGGAAGGAGCAAAGTATTATTAGTAGCAGG -s Anc0.Anc0refChr6 53 48 - 1880 -ACATACTGTTGGCCACACCCCAT-----GAGAGAGCAGAGTACTACT--TAGCA-G -s Anc1.Anc1refChr5 4639 49 - 6477 TACATACTGTTGGCCACACCCCAT-----GAGAGAGCAGAGTACTACT--TAGCA-G -s Anc2.Anc2refChr13 94457 48 - 96486 -ACATACTGTTGGCCACCCACAAT-----GAGAGAGCAGAGTACTACT--TAGCA-G -s mr.mrrefChr5 131706 57 + 294540 TACATACTGTTTACCACACCCCATGGAGGGAAGGAGCAAAGTATTATTAGTAGCAGG -s simCow_chr6.simCow.chr6 245064 48 - 602619 -ACGTACTGTTGGCCACCACCCAT-----GAGAGAGCAGAGTAGCACT--CAGCA-G -s simDog_chr6.simDog.chr6 245687 48 - 593897 -ACATATTGTTGGCCACCCACAAT-----GAGAGAGCAGAGTACTACT--TAGAA-G -s simHuman_chr6.simHuman.chr6 356024 40 - 601863 TGCATACTGTTGGCCACACCAC--------------CAGAGTACTACT--TAGCA-G -s simRat_chr6.simRat.chr6 269256 57 + 647215 TACATACTGTTTACCACATCCCATGAAGGGAAGGAGCAAAGTATTGTTAGGAGCAGG - -a -s simMouse_chr6.simMouse.chr6 280677 5 + 636262 TCTAT -s Anc0.Anc0refChr6 101 5 - 1880 TGTAT -s Anc1.Anc1refChr5 4688 5 - 6477 TGTAT -s Anc2.Anc2refChr13 94509 5 - 96486 TGTAT -s mr.mrrefChr5 131763 5 + 294540 TCTAT -s simCow_chr6.simCow.chr6 245116 5 - 602619 CATAT -s simDog_chr6.simDog.chr6 245739 5 - 593897 TGTAT -s simHuman_chr6.simHuman.chr6 356064 5 - 601863 TGTAT -s simRat_chr6.simRat.chr6 269313 5 + 647215 TCTAT - -a -s simMouse_chr6.simMouse.chr6 280682 20 + 636262 GTGTTCTGAAATGAGGAAGA -s Anc0.Anc0refChr6 106 20 - 1880 GTATACTGAAATGAGGAAGA -s Anc1.Anc1refChr5 4693 20 - 6477 GTATACTGAAATGAGGAAGA -s Anc2.Anc2refChr13 94514 20 - 96486 GTATACCAAAATGAGGAAGA -s mr.mrrefChr5 131768 20 + 294540 GTGTTCTGAAATGAGGAAGA -s simCow_chr6.simCow.chr6 245122 20 - 602619 GTATACCAAAATGGCAAAGA -s simDog_chr6.simDog.chr6 245744 20 - 593897 GTATATCAAAATGAGGAAGA -s simHuman_chr6.simHuman.chr6 356069 20 - 601863 GTATACTGAAATGAGGAAGA -s simRat_chr6.simRat.chr6 269318 20 + 647215 GTGTTCTGAAATGAGGAAGA - -a -s simMouse_chr6.simMouse.chr6 280702 11 + 636262 GAAAGATGGTG -s Anc0.Anc0refChr6 126 11 - 1880 AAAAGAAGGGG -s Anc1.Anc1refChr5 4713 11 - 6477 AAAAGAAGGGG -s Anc2.Anc2refChr13 94534 11 - 96486 AAAAGAAGGGG -s mr.mrrefChr5 131788 11 + 294540 GAAAGATGGTG -s simCow_chr6.simCow.chr6 245142 11 - 602619 TAGAGAAGGTG -s simDog_chr6.simDog.chr6 245764 11 - 593897 AAAAGAAGAGG -s simHuman_chr6.simHuman.chr6 356089 11 - 601863 AAAACAGGGGG -s simRat_chr6.simRat.chr6 269342 11 + 647215 GAAAGGTAGTG - -a -s simMouse_chr6.simMouse.chr6 280713 91 + 636262 GGTTGGGAAACCTTCACATGTATTATTGCATTATGTCAACATACACATAAGTCACAGTTGTACCAAAAGTCAGGAGTAGGGACTCCAGTTT -s Anc0.Anc0refChr6 143 91 - 1880 GATTGGAGAACACTCATGTATGTTAAGGTATTACCTCAATAACCACATCCATCTCAAATGGACTAAGTGTCTGGAATAGGGACTCCAGTTT -s Anc1.Anc1refChr5 4730 91 - 6477 GATTGGAGAACACTCATGTATGTTAAGGTATTACCTCAATAACCACATCCATCTCAAATGGACTAAGTGTCTGGAATAGGGACTCCAGTTT -s Anc2.Anc2refChr13 94551 91 - 96486 GATTGGAGACCACTCATGTATGTTAAGGTATCACCTCAATAACCACATCCATCTCAGATGGGCTAACTGTCAGGAATAGGCACTCCAGCTT -s mr.mrrefChr5 131805 91 + 294540 GATTGGGAAACATTCACATGTATTAAGGCATTATGTCAACATACACATCAGTCACAATTGTACTAAGAGTCTGGAATAGGGACTCCAGTTT -s simCow_chr6.simCow.chr6 245159 64 - 602619 TATTAGAGATCACTCATGGATGCCAAGGTATGACGTTAATAACCACATCCATTCTAGATGGCCT--------------------------- -s simDog_chr6.simDog.chr6 245787 91 - 593897 GAGTGGGGACCACTTGTGTATATTAAGGTATCACCTCAATAGCCACAATCACCTCAGAGAGGTTAACTGTCAGGAATAGGCACTCCAGCTT -s simHuman_chr6.simHuman.chr6 356106 91 - 601863 GATTGGAGAACACTCATGTATGTTAAGGTATTAATCACTAACCCACATCCATCTCAAATGCACTAAGTGTCTCAAATAGAGACTCCAGTTT -s simRat_chr6.simRat.chr6 269359 91 + 647215 AATTGGGAAACATTCACATGTATTAAGGCATTATGTCAACATACAAATCTGTTACAACTGTACTAAGAGTCTGGAACAGGGACTCTAGTTT - -a -s simMouse_chr6.simMouse.chr6 280804 3 + 636262 AAT -s Anc0.Anc0refChr6 234 3 - 1880 AAC -s Anc1.Anc1refChr5 4821 3 - 6477 AAC -s Anc2.Anc2refChr13 94642 3 - 96486 AAC -s mr.mrrefChr5 131896 3 + 294540 AAT -s simDog_chr6.simDog.chr6 245881 3 - 593897 AAC -s simHuman_chr6.simHuman.chr6 356197 3 - 601863 AAC -s simRat_chr6.simRat.chr6 269450 3 + 647215 CAT - -a -s simMouse_chr6.simMouse.chr6 280807 89 + 636262 ATCCGTATGAATCTACCCATGAAATGCACAACTAGGGCATAATAAGATGAGTGGCTGACCAATTAGGATGTTTGCCAGTAGAAATTCAA -s Anc0.Anc0refChr6 251 89 - 1880 ATCTGTAAAAATCTACTGGTGAAAACCCCAACCACAGCATGATGAAATTAGCTGCAGACTTATACAGATGTTTAACAATAGAAACTGAA -s Anc1.Anc1refChr5 4838 89 - 6477 ATCTGTAAAAATCTACTGGTGAAAACCCCAACCACAGCATGATGAAATTAGCTGCAGACTTATACAGATGTTTAACAATAGAAACTGAA -s Anc2.Anc2refChr13 94659 89 - 96486 ATCTGTAAAAATCTACTGGTGAAAACCCCAACCACAGCATGATGAAATTAGCTGCAGACTTATACATATGTTTAATAATTGAAGCTGAA -s mr.mrrefChr5 131899 89 + 294540 ATCTGTAAGAATCTACCCGTGAAAACCACAACTAGAGCATGATAAAATGAGTGGCTGACCAATTAGGATGTTTGCCAGTAGAAACTCAA -s simCow_chr6.simCow.chr6 245226 82 - 602619 CTCTGTAAAGATCATCTGGTGAAAACCCCCACCAC---ACGATGCAATAAG--GCAGACTTATACATATGTTCA--AAGTGGAGGCGAA -s simDog_chr6.simDog.chr6 245919 88 - 593897 ATCTGTAAGAATCTACTGGTGAAAATTCCAACCACAGCATGATGAAATTAGCTGT-GACTTATGCATATGTTTAATTATTGAAGCTGAA -s simHuman_chr6.simHuman.chr6 356214 89 - 601863 ATCTGTAAACATTTACTGGTGGAAACCTCAACCACAGCATGCTGTATTTAGCTACAGACTGATACAGATTTTTAACAATAGAAACTGAA -s simRat_chr6.simRat.chr6 269453 80 + 647215 ATCTGTAAGAATCTACCCGTGAAAACTCCAACTAGAGCATGATAAAA---------GGCCAACTAGGATGTTTGCCAGTAGAATCTCAA - -a -s simMouse_chr6.simMouse.chr6 280896 119 + 636262 AAGAGCAACAGAATGCTCATGTTTGCCAGTAGAAATTCAAAAGAGCAACAGAATGCTATCTATGCAAGATGAAAGTGGTAGCAGCACAATGCCTCCACCTGATGCTAGATAATCTGAGC -s Anc0.Anc0refChr6 347 77 - 1880 AAGTGTAAC----------------------------------------AGAAGGC--TCTACTTTAAATGAAAGTGACAACAGCACAACAGGTCAATTTCATGCTAAACAATCTGTGT -s Anc1.Anc1refChr5 4934 77 - 6477 AAGTGTAAC----------------------------------------AGAAGGC--TCTACTTTAAATGAAAGTGACAACAGCACAACAGGTCAATTTCATGCTAAACAATCTGTGT -s Anc2.Anc2refChr13 94755 77 - 96486 AAGTGTAAC----------------------------------------AGAAGGC--TCTACTCTAAATGGAAATGACAACAGCACAACAGGTCAATTTCATGCTAAACAATCTGTGT -s mr.mrrefChr5 131988 78 + 294540 AAGAGCAAC---------------------------------------CAGAGTGC--TCTATGTAAGATGAAAGTGGCAGCAGCACAACGCCTCCATCTGATGCTAAATAATCTGAGT -s simCow_chr6.simCow.chr6 245315 76 - 602619 AACTGTAAC----------------------------------------AGAAGGC--TCTACTCTAACTATAA-TAACAACACCACAACAGGTTAGCTTTATGCTAAACAATCTGTTT -s simDog_chr6.simDog.chr6 246015 76 - 593897 GAGTGTAAT----------------------------------------AGAAGGT--TATACTCTAAATGGAAAAGGCAACAGCACAACAGGTCAATT-CATGCTGAACTGTCTGTGT -s simHuman_chr6.simHuman.chr6 356310 77 - 601863 AAGTGTAAC----------------------------------------AGGAGAC--TCCACTTTAAATGAAAGTGACAACAGCACAGCAGATCAATTCCATACTAAACAATATGTGT -s simRat_chr6.simRat.chr6 269533 77 + 647215 AAGAACAAC---------------------------------------CAGAGTGC--TTTATGTAAGATGAAAGGAGCAGCAGTAC-ACGCCTCCATCTGATGGTAAATAATCCGAGT - -a -s simMouse_chr6.simMouse.chr6 281015 106 + 636262 GCTGTTGAACATTGAATTAGTGCACTACATTTGTTTAGGGGTCCACTGGTGGTACACGATTCTCTTATCATGATGTTTGTGCACACCTCGTGGTGTCCTACTTTAT -s Anc0.Anc0refChr6 424 104 - 1880 GCTGTATAACCTTAAATTGATGCACTACATTTGTTCAGGGGTTCACT-GCAGCACCAAGTTCTCTTGACCAAAAGTTTGTTCAC-CCCATCTGTGTCCTATCTCAT -s Anc1.Anc1refChr5 5011 104 - 6477 GCTGTATAACCTTAAATTGATGCACTACATTTGTTCAGGGGTTCACT-GCAGCACCAAGTTCTCTTGACCAAAAGTTTGTTCAC-CCCATCTGTGTCCTATCTCAT -s Anc2.Anc2refChr13 94832 104 - 96486 TCTGTATAACCTTAAATTGATGCACTGCACTTGTTCAGGGGTTTGCT-GCAGCACCAAGTTCTCCTGACCAAAAGTTTGTTCAC-CCCATCTGTGTCCTATCTCCT -s mr.mrrefChr5 132066 106 + 294540 GCTGTTTAACATTGAATTAATGCACTACATTTGTTCAGGGGTCCACTGGTGGTACAAGATTCTCTTATCATGATGTTTGTGCACACCTAGTGGTGTCCTACTTTAT -s simCow_chr6.simCow.chr6 245391 102 - 602619 ACAGTATACCCTTGAAGTGATGCACTGAGGTTGTACAGGGATTTGCT-GAAGCACCAAGT--CCCTGTCTGAATGTTTGTTCAC-CCCATCTATGTCCTATCTCCC -s simDog_chr6.simDog.chr6 246091 101 - 593897 TCTTA--GAACCTAAATTAATGCACTGCACTTGTTCAGCAGTTTGCT-GCAGCACCAAGTTCTCCTGA-CAAAAGTTTGTTCAT-CCCATCTGTGTCCTATCTCCT -s simHuman_chr6.simHuman.chr6 356387 104 - 601863 GTGGTATAACCTTAAATTGATGGACTACATTCATTCAGGGGTTCATT-GCAGCACCAAGTGCTCTTGACCAAACATTTGTTAAC-CTCATCTGTGTCCTAACTCAT -s simRat_chr6.simRat.chr6 269611 98 + 647215 ACTGTTTAACATTGAATTAATGCACTACATTTGTTCAGGGGTCCACTGGTGGTACAAGATTCTCTTATCATGATGTTTGTACACACCTAGTGGTGTCC-------- - -a -s simMouse_chr6.simMouse.chr6 281121 27 + 636262 TTTTTATAAAGGTAATCTAACATCTCA -s Anc0.Anc0refChr6 528 27 - 1880 TTTTTCCAGAGGTCATCTAGCATCTTT -s Anc1.Anc1refChr5 5115 27 - 6477 TTTTTCCAGAGGTCATCTAGCATCTTT -s Anc2.Anc2refChr13 94936 27 - 96486 TTTTTCCAGGGGTCAGCTAGCTTCCTT -s mr.mrrefChr5 132172 27 + 294540 TTTTTATAAAGGTAATCTAACATCTCA -s simCow_chr6.simCow.chr6 245496 21 - 602619 TTTTTCCTGGGGTCAGCTGGC------ -s simDog_chr6.simDog.chr6 246192 27 - 593897 TTTTTCCAGGGGTCAGCTAACTTCCTT -s simHuman_chr6.simHuman.chr6 356491 27 - 601863 TTTTTTCAGAAGTCATCTAGCATCTTT -s simRat_chr6.simRat.chr6 269709 25 + 647215 --TTTATAAAGGTAAGCTAACCTCTCA - -a -s simMouse_chr6.simMouse.chr6 281148 32 + 636262 TGACTCCCTCACACTTTATCTTAGTACTCTCC -s Anc0.Anc0refChr6 555 6 - 1880 GAACT--------------------------C -s Anc1.Anc1refChr5 5142 6 - 6477 GAACT--------------------------C -s Anc2.Anc2refChr13 94963 6 - 96486 GAACC--------------------------C -s mr.mrrefChr5 132199 29 + 294540 TGACTCCCT---ACTTTATCTTAGTACTCTCC -s simCow_chr6.simCow.chr6 245517 5 - 602619 -AACC--------------------------C -s simDog_chr6.simDog.chr6 246219 6 - 593897 GGACC--------------------------C -s simHuman_chr6.simHuman.chr6 356518 6 - 601863 GAACT--------------------------C -s simRat_chr6.simRat.chr6 269736 29 + 647215 TGACTCCTG---ACTTTATCTTAGTACTCGCC - -a -s simMouse_chr6.simMouse.chr6 281180 23 + 636262 CCCACTTTCCTTCATTTAAAGGC -s Anc0.Anc0refChr6 561 23 - 1880 CCCACTTTCCTTCATTTAAAGGC -s Anc1.Anc1refChr5 5148 23 - 6477 CCCACTTTCCTTCATTTAAAGGC -s Anc2.Anc2refChr13 94972 23 - 96486 CCCACTTTCTTTCATTTAAAGGC -s mr.mrrefChr5 132228 23 + 294540 CCCACTTTCCTTCATTTAAAGGC -s simCow_chr6.simCow.chr6 245525 23 - 602619 CCTACTTTCTTTCATTTAAGGGT -s simDog_chr6.simDog.chr6 246228 23 - 593897 CCCACTTTCTTTCACCCAAAGGC -s simHuman_chr6.simHuman.chr6 356524 23 - 601863 CCCACTTTCCTTCCTTTGAAGGC -s simRat_chr6.simRat.chr6 269765 23 + 647215 CCCACTTTCCTTCGTTTAAAGGC - -a -s simMouse_chr6.simMouse.chr6 281203 22 + 636262 TTGCTCATTGAATGGAATGCAG -s Anc0.Anc0refChr6 584 22 - 1880 TCACTGCTGAAATGGAATCCAG -s Anc1.Anc1refChr5 5171 22 - 6477 TCACTGCTGAAATGGAATCCAG -s Anc2.Anc2refChr13 94995 22 - 96486 TCACTGCTGAAGTGGGATCCAG -s mr.mrrefChr5 132251 22 + 294540 TTGCTGATGGAATGGAATGCAG -s simCow_chr6.simCow.chr6 245548 20 - 602619 TCACTGC--AAGAGGGATTTAG -s simDog_chr6.simDog.chr6 246362 22 - 593897 TCACTGCTGAAGTGGGATCCAG -s simHuman_chr6.simHuman.chr6 356547 22 - 601863 TCACTGCTGAAACGGAATCCAG -s simRat_chr6.simRat.chr6 269788 22 + 647215 TTGATGATGGAATGGAATGCAG - -a -s simMouse_chr6.simMouse.chr6 281225 13 + 636262 TACATCAAAGTAG -s Anc0.Anc0refChr6 638 13 - 1880 TCCATCAAAGTAG -s Anc1.Anc1refChr5 5225 13 - 6477 TCCATCAAAGTAG -s Anc2.Anc2refChr13 95049 13 - 96486 TCCATCAAAGTAG -s mr.mrrefChr5 132273 13 + 294540 TACATCAAAGTAG -s simCow_chr6.simCow.chr6 245605 13 - 602619 TTCATTAAAGTAG -s simDog_chr6.simDog.chr6 246416 13 - 593897 TCCTTCAAAGTAG -s simHuman_chr6.simHuman.chr6 356601 13 - 601863 TCCAGCAAAGTAG -s simRat_chr6.simRat.chr6 269810 13 + 647215 TTCATCAAATCAG - -a -s simMouse_chr6.simMouse.chr6 281238 11 + 636262 GTGTTTTATTA -s Anc0.Anc0refChr6 651 11 - 1880 ATGCTTTTTTA -s Anc1.Anc1refChr5 5238 11 - 6477 ATGCTTTTTTA -s Anc2.Anc2refChr13 95062 11 - 96486 ATGCTTTTTTA -s mr.mrrefChr5 132286 11 + 294540 GTGTTTTATTA -s simCow_chr6.simCow.chr6 245619 11 - 602619 ATGTTTTTTTA -s simDog_chr6.simDog.chr6 246429 9 - 593897 GTGC--TTTCT -s simHuman_chr6.simHuman.chr6 356614 11 - 601863 ACGCTTTTTTA -s simRat_chr6.simRat.chr6 269823 11 + 647215 GTGTTTTCTTA - -a -s simMouse_chr6.simMouse.chr6 281249 19 + 636262 TCCAACCAGTTCTGTTTGC -s Anc0.Anc0refChr6 674 19 - 1880 TCCTACCAGCTCTATTTCC -s Anc1.Anc1refChr5 5261 19 - 6477 TCCTACCAGCTCTATTTCC -s Anc2.Anc2refChr13 95086 19 - 96486 TCCTACCAGTTCTATTTCC -s mr.mrrefChr5 132297 19 + 294540 TCCAACCAGCTCTGTTTGC -s simCow_chr6.simCow.chr6 245643 19 - 602619 CCCAACCAATTCTATTTTC -s simDog_chr6.simDog.chr6 246451 19 - 593897 TCCTACCAGTTCGATTTCT -s simHuman_chr6.simHuman.chr6 356637 19 - 601863 TCCCACCAGCTCTATTTCC -s simRat_chr6.simRat.chr6 269834 11 + 647215 TCCAACCAGCT-------- - -a -s simMouse_chr6.simMouse.chr6 281268 63 + 636262 TTAAAGATAACTCACCTTGTTCATCCTCTCTCACTTTGGGGGTATAGAAGATGTTCATCATAT -s Anc0.Anc0refChr6 696 63 - 1880 TTAAAGGTAGCCCCCCTTATTCATTCTCTCTCACTTTGAGGGTATAAAAGATGTTCATCAGAT -s Anc1.Anc1refChr5 5283 63 - 6477 TTAAAGGTAGCCCCCCTTATTCATTCTCTCTCACTTTGAGGGTATAAAAGATGTTCATCAGAT -s Anc2.Anc2refChr13 95108 63 - 96486 TTAAAGGTAGCCCCGCTTATTTATTCTCTCTCACTTTGACGGTATAAAAGATGTTCATCATAT -s mr.mrrefChr5 132316 63 + 294540 TTAAAGATAACTCACCTTGTTCATCCTCTCTCACTTTGGGGGTATAGAAGATGTTCATCAGAT -s simCow_chr6.simCow.chr6 245665 62 - 602619 TTAAA-GTAGCCCCACTTATTGATTCTCTCTCACTTTGAGGGTATTAAGGACATTCAGCGCAT -s simDog_chr6.simDog.chr6 246473 62 - 593897 TTAGAGGTA-CCCAGCTTATTTATTCTGTCTGACTTTCACGGTAAAAGAGATGTTCATCATAT -s simHuman_chr6.simHuman.chr6 356659 62 - 601863 TTAAAGGTAGCCCCCCCTCTTCATTCTCTCTCACCCTGAGGG-ATAAAAGATGTTCATCAGAT -s simRat_chr6.simRat.chr6 269845 63 + 647215 TTAAAGATAACTCTCATTGTTCTTCCTCTCTCATTTTGGGGGTATAGAAGCTGTTTGTCAGAC - -a -s simMouse_chr6.simMouse.chr6 281331 29 + 636262 TCCTGAATACAAGAGGTGGGCAACTCATC -s Anc0.Anc0refChr6 759 16 - 1880 TCCTGTA-ACTAGAGAC------------ -s Anc1.Anc1refChr5 5346 16 - 6477 TCCTGTA-ACTAGAGAC------------ -s Anc2.Anc2refChr13 95173 16 - 96486 TTCTGTA-ACTAGAGAC------------ -s mr.mrrefChr5 132379 28 + 294540 TCCTGAA-ACAAGAGGCGGGCAACTCATC -s simCow_chr6.simCow.chr6 245729 16 - 602619 TTCTGTA-ACTATAGAC------------ -s simDog_chr6.simDog.chr6 246537 16 - 593897 TCCTGCA-ACTAGAGAC------------ -s simHuman_chr6.simHuman.chr6 356721 15 - 601863 TCTT-TA-CCTAGAGAC------------ -s simRat_chr6.simRat.chr6 269908 28 + 647215 TCCTGAA-ACAAGAGGCGAGCAACTCATC - -a -s simMouse_chr6.simMouse.chr6 281360 102 + 636262 CACCTAGAGCTGTCAGTTGTTCACTTCTCCCCATCAGCAGAGGGTGTCATCCATCATCCTTCTTAACAGTGGCGGCAGCAACAATCATGTCAGTAGAGGATC -s Anc0.Anc0refChr6 775 39 - 1880 ----------------------------------TAACAGAGGATGC----CAGCGTCGTTGG-------------------------GTCACTAGAAGACC -s Anc1.Anc1refChr5 5362 39 - 6477 ----------------------------------TAACAGAGGATGC----CAGCGTCGTTGG-------------------------GTCACTAGAAGACC -s Anc2.Anc2refChr13 95189 39 - 96486 ----------------------------------TAACAGAGGATGC----CAGCGGTGTTAG-------------------------ACCACTAGAAAACC -s mr.mrrefChr5 132407 102 + 294540 CACCTAGAGCTGTCAGTTGTTCACTTCTCCCCATCAGCAGAGGGTGTCATCCATCATCCTTGGTAACAGTGGCGGCAGCAACAATCATGTCACTAGAGGATC -s simCow_chr6.simCow.chr6 245745 39 - 602619 ----------------------------------TAACAAAGGATGC----CAGTGGTGTTTG-------------------------ACCACTAGAAAACC -s simDog_chr6.simDog.chr6 246553 39 - 593897 ----------------------------------TAACAGAAGACGC----CAGCAGTGTCAA-------------------------ACCACTAGAAAACC -s simHuman_chr6.simHuman.chr6 356736 39 - 601863 ----------------------------------TAACAGTGGATGG----CAGCGTCTTTGG-------------------------GTCACCAGAAGGCA -s simRat_chr6.simRat.chr6 269942 102 + 647215 CACCTCAAGCTGTCAGTTTTCAGGCTCTCACCTTCGGCAGAGGGTGCCATCCATCATCCTTGGTAATAGTGATGGCAGCAACAATCATGTCACTAGAGCATC - -a -s simMouse_chr6.simMouse.chr6 281462 1 + 636262 G -s Anc0.Anc0refChr6 814 1 - 1880 A -s Anc1.Anc1refChr5 5401 1 - 6477 A -s Anc2.Anc2refChr13 95228 1 - 96486 A -s mr.mrrefChr5 132509 1 + 294540 A -s simCow_chr6.simCow.chr6 245785 1 - 602619 A -s simDog_chr6.simDog.chr6 246592 1 - 593897 A -s simHuman_chr6.simHuman.chr6 356775 1 - 601863 A -s simRat_chr6.simRat.chr6 270044 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 281463 127 + 636262 TTTCCTTATTATCATATGACTCTAAAGTATTGGAGAGTTGTGGTAAGCAGTAAGCCCAGACTTCGGAATGAAGATATCAGAATTTGCAACTCAGGTTTTTCACAATCACAAACTGCCATTGAAAAGT -s Anc0.Anc0refChr6 815 111 - 1880 TTT-CTTATTATCATACTAGT-------------AAGTGGTCTTAAGAACTGTCCCCAGACTTTAGACTGAAGATATAAAAATTTGTGGCTCAGGTTTAT--CAATCACAAAGAGCCATCGACAAGT -s Anc1.Anc1refChr5 5402 113 - 6477 TTT-CTTATTATCATACTAGT-------------AAGTGGTCTTAAGAACTGTCCCCAGACTTTAGACTGAAGATATAAAAATTTGTGGCTCAGGTTTATCACAATCACAAAGAGCCATCGACAAGT -s Anc2.Anc2refChr13 95229 111 - 96486 CTT-CTTATTACCATGCTAGT-------------AAGTGGTCTAGAGAACTGTCCCCAGATTTTAGACTGAAGATATAAAAATTTGTGGCCCAGGTTGAT--CAATCACAAAGAGCCATCAACAATT -s mr.mrrefChr5 132510 114 + 294540 TTTCCTTATTATCATATGACT-------------GAGTTGTGGTAAGCACTAACCCCAGACTTCAGACTGAAGATATCAGAATTTGTAGCTCAGGTTTTTCACAATCACAAACTGCCATCGAAAAGT -s simCow_chr6.simCow.chr6 245786 110 - 602619 CTT-CTTACTACCATGCTAGT-------------AAGTGGTCTGGAGAATGATCCCCAGATTTCAGACTGAAGATCTAAAAATTTGTGGCCTAGGTTAAT--CAACAAC-AAGAGTCATCAACAATT -s simDog_chr6.simDog.chr6 246593 103 - 593897 --A-CTTATGGCCA-----GT-------------AAGTAGTCTAGAGAACTGTCCCCAGATTTTAGACTGAAAATATGGAAATTTGTAGCCCA-GTTGTT--CAATCACAAAGAGCCATCAACAATT -s simHuman_chr6.simHuman.chr6 356776 113 - 601863 TTT-CTTATTATCATACTGGT-------------AAGTGGTCTTAAGAACTGTCCCTAGGCTCTAGACTGAAGATATAAAAATTTGTGGCTCAGGTTTATCAATCTCACAAAGAGCCATCGACAAGT -s simRat_chr6.simRat.chr6 270052 114 + 647215 TTTCCTTATTATCATATGCCT-------------GATTTGTGACAAGCACTAACCCCAGACTTCAGACTGAAGATATCAGAATTTGTAGCTCAGGCTGTTCACGATCACAAACTGCCATCGAAAAGT - -a -s simMouse_chr6.simMouse.chr6 281590 18 + 636262 GGCATGGACTAAATTCAT -s Anc0.Anc0refChr6 926 14 - 1880 GG----CATCGTCATGAG -s Anc1.Anc1refChr5 5515 14 - 6477 GG----CATCGTCATGAG -s Anc2.Anc2refChr13 95340 14 - 96486 GG----CATCGTCATGAG -s mr.mrrefChr5 132624 14 + 294540 GG----GACTGAATTCAT -s simCow_chr6.simCow.chr6 245896 14 - 602619 GG----CATCATCCTGGG -s simDog_chr6.simDog.chr6 246717 14 - 593897 GG----CACTGTAATCAA -s simHuman_chr6.simHuman.chr6 356889 14 - 601863 GG----CATCGTCATGAG -s simRat_chr6.simRat.chr6 270166 14 + 647215 GG----GGCTGAATTAAT - -a -s simMouse_chr6.simMouse.chr6 281608 5 + 636262 GGTCC -s Anc0.Anc0refChr6 940 5 - 1880 GGCTT -s Anc1.Anc1refChr5 5529 5 - 6477 GGCTT -s Anc2.Anc2refChr13 95354 5 - 96486 GGCTT -s mr.mrrefChr5 132638 5 + 294540 GGTCC -s simCow_chr6.simCow.chr6 245910 5 - 602619 GACTG -s simDog_chr6.simDog.chr6 246734 5 - 593897 GGCTT -s simHuman_chr6.simHuman.chr6 356903 5 - 601863 GGCTT -s simRat_chr6.simRat.chr6 270180 5 + 647215 GGTCC - -a -s simMouse_chr6.simMouse.chr6 281613 21 + 636262 CTTACATTCACACACATGCTA -s Anc0.Anc0refChr6 945 6 - 1880 TCT---------------TAA -s Anc1.Anc1refChr5 5534 6 - 6477 TCT---------------TAA -s Anc2.Anc2refChr13 95359 6 - 96486 TCT---------------TAA -s mr.mrrefChr5 132643 6 + 294540 CTT---------------CAA -s simCow_chr6.simCow.chr6 245915 6 - 602619 CTT---------------CAA -s simDog_chr6.simDog.chr6 246743 6 - 593897 TCT---------------TGA -s simHuman_chr6.simHuman.chr6 356908 6 - 601863 TGT---------------TAA -s simRat_chr6.simRat.chr6 270185 6 + 647215 CTT---------------CAA - -a -s simMouse_chr6.simMouse.chr6 281634 1 + 636262 C -s Anc0.Anc0refChr6 954 1 - 1880 C -s Anc1.Anc1refChr5 5543 1 - 6477 C -s Anc2.Anc2refChr13 95368 1 - 96486 C -s mr.mrrefChr5 132649 1 + 294540 C -s simCow_chr6.simCow.chr6 245924 1 - 602619 C -s simDog_chr6.simDog.chr6 246752 1 - 593897 T -s simHuman_chr6.simHuman.chr6 356917 1 - 601863 C -s simRat_chr6.simRat.chr6 270191 1 + 647215 C - -a -s simMouse_chr6.simMouse.chr6 281635 36 + 636262 AGACAATACATATTATAAGGTCAGTGGCCCAAATAC -s Anc0.Anc0refChr6 955 36 - 1880 AGACATTATCTATCATAAAATGCATGGCTCAAATCA -s Anc1.Anc1refChr5 5544 36 - 6477 AGACATTATCTATCATAAAATGCATGGCTCAAATCA -s Anc2.Anc2refChr13 95369 36 - 96486 AGACATTATCTATCATAAAATGCATGGCTCAAATCA -s mr.mrrefChr5 132650 36 + 294540 AGACAATACATATTATAAGGTGAGTGGCCCAAATAA -s simCow_chr6.simCow.chr6 245925 33 - 602619 AGATGTT-TCTATCATAAAATGCA--ACTCGTGTCA -s simDog_chr6.simDog.chr6 246789 36 - 593897 AGACATTATCTATTGTAAAATGCATGGCACAAATCA -s simHuman_chr6.simHuman.chr6 356918 36 - 601863 AGACACTCTCCATCACAAAATGCATGGCTCAGATCA -s simRat_chr6.simRat.chr6 270192 36 + 647215 AAACAATACATATTATAAGGTGAGTGGCCCAAATGA - -a -s simMouse_chr6.simMouse.chr6 281671 23 + 636262 TTTGGTAAATGAGCAGCAAGAAC -s Anc0.Anc0refChr6 991 20 - 1880 TTTGGTAAAAGAGCAGC---AAC -s Anc1.Anc1refChr5 5580 23 - 6477 TTTGGTAAAAGAGCAGCATTAAC -s Anc2.Anc2refChr13 95405 20 - 96486 TTTGGTAAAAGAGCAGC---AAC -s mr.mrrefChr5 132686 23 + 294540 TTTGGTAAATGAGCAGCAAGAAC -s simCow_chr6.simCow.chr6 245959 20 - 602619 TTTGGTAAAAGAGCAGC---AAA -s simDog_chr6.simDog.chr6 246825 20 - 593897 TTTGGTAAAAGAGCAGC---AAC -s simHuman_chr6.simHuman.chr6 356954 23 - 601863 TTTTGCAAAAGAGCCATATTAAC -s simRat_chr6.simRat.chr6 270228 23 + 647215 TTTGGTAAATGAGCAGCTAGAAC - -a -s simMouse_chr6.simMouse.chr6 281694 30 + 636262 AGAAGCATAACCCATGGAGTATGTACTGTG -s Anc0.Anc0refChr6 1011 30 - 1880 AGAAGCATACCTGACGGCATATCTACAGTG -s Anc1.Anc1refChr5 5603 30 - 6477 AGAAGCATACCTGACGGCATATCTACAGTG -s Anc2.Anc2refChr13 95425 30 - 96486 AGAAGCACTCCTGACAGCATATCTACAGTG -s mr.mrrefChr5 132709 30 + 294540 AGAAGCATAACCCATGGAGTATGTACTGTG -s simCow_chr6.simCow.chr6 245979 15 - 602619 AGG---------------GCATCTAAAGTG -s simDog_chr6.simDog.chr6 246849 30 - 593897 GGAAGCACTCCTGACAGCATATCTACATTG -s simHuman_chr6.simHuman.chr6 356977 30 - 601863 AGAAGTTTACCTGGAGGCATATCTACAGCA -s simRat_chr6.simRat.chr6 270251 28 + 647215 AGAAGCATAATCAATGGAGTACAAAT--TG - -a -s simMouse_chr6.simMouse.chr6 281724 107 + 636262 TTGGTAATAAAGGACAAGAAGCAAATCATAATTTGCTGCTCCAGTATGATAGGGGATATAGAAGCGTTTAGGGGCCCCGGAGTCCTGTAATCAACATCTTATTTAAA -s Anc0.Anc0refChr6 1048 101 - 1880 TTAGTAATTAAGTAA---AAGCAAGTCATAATG---TGCTCCAGAATGATAGAGGATATAGAAATGTTTAAGGGTTCTGGAAACTTCAAATAATCATCTAACTTAAA -s Anc1.Anc1refChr5 5640 101 - 6477 TTAGTAATTAAGTAA---AAGCAAGTCATAATG---TGCTCCAGAATGATAGAGGATATAGAAATGTTTAAGGGTTCTGGAAACTTCAAATAATCATCTAACTTAAA -s Anc2.Anc2refChr13 95462 101 - 96486 TTAGTAATGAGGTAA---AAGCAAGTCATAATG---TGCTCCACACTGATAGAGGATATAGAAATGTTCAAGGCTTCTGGGAACTTCAAATAATCATCTTACTTAAA -s mr.mrrefChr5 132739 104 + 294540 TTGGTAATTAAGGAC---AAGCAAATCATAATTTGCTGCTCCAGTATGATAGGGGATATAGAAGTGTTTAAGGGCCCTGGAGTCCTGTAATCAACATCTAACTTAAA -s simCow_chr6.simCow.chr6 246001 85 - 602619 TTAGCAATCAGGTAA---AAGCAAGCCATAACG---TCCTCCACGCTAATAGAGG-------------CAGG---TCTAGAAAATTCTAATAACCATCTTACTTAGA -s simDog_chr6.simDog.chr6 246886 101 - 593897 TTAGTAATGAGGAAA---AAGCAGGTCATAGTG---TGCTCTACACTGATAGAGGATATAGAAATGTTCAAGGCTTCTGGGAACTTCAAATAATCATCTTACTTAAG -s simHuman_chr6.simHuman.chr6 357014 94 - 601863 TTAGTGATTAAGTAA---AAGCTAGTCACAATG---GGCTCCAGAATGATAGAGGATAGAGAACTGTTTGAGGGTTCTGGA-------AATGATCATCTAACTTAAA -s simRat_chr6.simRat.chr6 270279 104 + 647215 TTGGTAACTAAGGAC---AAGCAGCTCATAATTTGCTGGCCTAGTATGATAGGGGATATAGTAGTGCTTAAGGGCCCTGGAGGCCTCTAATCAACATCTAACCTAAA - -a -s simMouse_chr6.simMouse.chr6 281831 27 + 636262 AGTCCCTATAGCCCGATGTTATTGCTT -s Anc0.Anc0refChr6 1150 23 - 1880 AGTCCACATAGCGATA----AAAGCTT -s Anc1.Anc1refChr5 5742 23 - 6477 AGTCCACATAGCGATA----AAAGCTT -s Anc2.Anc2refChr13 95564 23 - 96486 AGTCCACATAGTGATA----AAAGCTT -s mr.mrrefChr5 132843 27 + 294540 AGTCCCTATAGCCCTATGTTATAGCTT -s simCow_chr6.simCow.chr6 246087 23 - 602619 AGACCACATGGTGGTA----AAAACTT -s simDog_chr6.simDog.chr6 246988 22 - 593897 AGTCTGCGTAGTGAT-----AAAGCTC -s simHuman_chr6.simHuman.chr6 357109 23 - 601863 ACTCCACATAGCAATA----AAAGCTT -s simRat_chr6.simRat.chr6 270383 27 + 647215 AGTCCCTATAGTCTTATGTTATAGCTT - -a -s simMouse_chr6.simMouse.chr6 281858 63 + 636262 TAGTACCCAACCCACTAAATACTCTTGGCATCTTGAAACATAGGTACTTCATAAGCTTATCAT -s Anc0.Anc0refChr6 1173 63 - 1880 TAGTCTACACACTATTATAGACTTTTGGTATCTCGAGAAATAAGTATTTCATAAGCTTATCAT -s Anc1.Anc1refChr5 5765 63 - 6477 TAGTCTACACACTATTATAGACTTTTGGTATCTCGAGAAATAAGTATTTCATAAGCTTATCAT -s Anc2.Anc2refChr13 95739 63 - 96486 TAGTCTACACAGTATTATAGATTTTTGGTATCTCGAGAAACAAGTATTTCATAAGCTTATCAT -s mr.mrrefChr5 132870 63 + 294540 TAGTACCCAACCCACTAAATACTCTTGGTATCTTGAAACATAAGTATTTCATAAGCTTATCAT -s simCow_chr6.simCow.chr6 246273 63 - 602619 TAGTCTAATCAGTATTATAGTTTTTTTTTATCTTCAGAGACACCTATTTCATCAGCTCATGAT -s simDog_chr6.simDog.chr6 247161 63 - 593897 TAGGCTGCACAGTATTATAGATTTTTGGTAGCTCGAGAAACAAGTAATTCGAAAGCGTAACAT -s simHuman_chr6.simHuman.chr6 357138 60 - 601863 TTATCTAGACACTATTATAGACTT---GTGTCTCAAGAAATGAGTATTTCATAAGCTTATCAT -s simRat_chr6.simRat.chr6 270410 63 + 647215 TAGTACCCAACCCATTAAATACTCTTGGTATCTTGAAACATTAGTATTTCATAAGCTTATCAT - -a -s simMouse_chr6.simMouse.chr6 281921 71 + 636262 CTCTGGGTCATAGCCCAAGTAAAGGTAATACCCTGTACTTCTATGATACACTTGAAGGAAAATAGTTCTTT -s Anc0.Anc0refChr6 1236 69 - 1880 CTTTGGGTCATATACTAAGTAGAGGTCATACCCAAAACC--TCTAATACACTTGAAGGTCAATAGTTCTGT -s Anc1.Anc1refChr5 5828 69 - 6477 CTTTGGGTCATATACTAAGTAGAGGTCATACCCAAAACC--TCTAATACACTTGAAGGTCAATAGTTCTGT -s Anc2.Anc2refChr13 95802 69 - 96486 CTTTGGGTCATATACTAAGTAGAGGTCATACACAAAACC--TCTAATACATTTGAAGGTCAATAGTTCTGT -s mr.mrrefChr5 132933 69 + 294540 CTTTGGGTCATAGCCCAAGTAAAGGTAATACCCTGTACT--TATGATACACTTGAAGGAAAATAGTTCTGT -s simCow_chr6.simCow.chr6 246336 67 - 602619 CTTCGGGTCATACACCAAGTAGAGGTTATACACAGGACC--TCTAATACATTT-AAGGTCAAT-GTTCTCT -s simDog_chr6.simDog.chr6 247224 60 - 593897 CTTTGGGACATATACTAAGTAGAGGTCATACACAAA-----------ACATTTGAAGGTTAATAGTTCTGC -s simHuman_chr6.simHuman.chr6 357204 64 - 601863 CCTTGGGTCATATACTAAGTAGTGGTCATACCCAAAACC-------TACACTTGAAGGTCAATAGATCTGT -s simRat_chr6.simRat.chr6 270473 69 + 647215 CTTTGGGTCATAGCCCAAGTAAAGATAATACTCTGTACT--TATGATAAACTTGAAGGAAAATAGTTCTGT - -a -s simMouse_chr6.simMouse.chr6 281992 74 + 636262 AATCATAAATTGCAGGAGACTGCCCAGGAATATTAGGGGAAGGAAGATCGAAGGAAGATCTTTATGAATGGTAG -s Anc0.Anc0refChr6 1305 63 - 1880 GTTCATAAATCGCACTTGCCTGCCCTGGAGTAATGAAGG-----------AAGGAACATGTTTTTTAATGGTAG -s Anc1.Anc1refChr5 5897 63 - 6477 GTTCATAAATCGCACTTGCCTGCCCTGGAGTAATGAAGG-----------AAGGAACATGTTTTTTAATGGTAG -s Anc2.Anc2refChr13 95871 63 - 96486 GTCTGTGAATCACACTTGCCTGCCCTGGAGTAATGAAGG-----------ATAGAACATGTTTTTTAATGGCAG -s mr.mrrefChr5 133002 63 + 294540 GATCATAAATTGCAGGAGACTGCCCAGGAATAATAGGGG-----------AAGGAAGATCTTTATGAATGGTAG -s simCow_chr6.simCow.chr6 246403 62 - 602619 GTCCATGATTCACAATTCTCTACCCTGGTGT-ATGAAGG-----------ATAGAATATATTTTGTAATTGCAG -s simDog_chr6.simDog.chr6 247284 63 - 593897 GTCTGTGAATCATGCTTACCTCTCCAGGAGGAATGAAGG-----------ATAGAACATGTTTTTTAATGTCAG -s simHuman_chr6.simHuman.chr6 357272 57 - 601863 GTTCAAAGATCGC------ATGCCCTGGGGTAATGAAGG-----------AAGGAACATGTCTCTCAACAGTAG -s simRat_chr6.simRat.chr6 270542 63 + 647215 GATCATAAATTGCAGTACACTGGCCAGGAAGAACAGGGG-----------AAGTAAGATCTTTATGTATGGTAG - -a -s simMouse_chr6.simMouse.chr6 282066 24 + 636262 GTATGCTTACATACCCAGATTGCC -s Anc0.Anc0refChr6 1368 22 - 1880 GTATACCTAGGTGTCCAAATTG-- -s Anc1.Anc1refChr5 5960 24 - 6477 GTATACCTAGGTGTCCAAATTGTC -s Anc2.Anc2refChr13 95951 22 - 96486 GTATACCTAGGTGTCCAAATTA-- -s mr.mrrefChr5 133065 24 + 294540 GTATGCTTACATACCCAGATTGCC -s simCow_chr6.simCow.chr6 246482 22 - 602619 GTAGGCATAGGTGTCCAAATTA-- -s simDog_chr6.simDog.chr6 247347 22 - 593897 GTATACCTAGGTGTCCAAGTTA-- -s simHuman_chr6.simHuman.chr6 357329 24 - 601863 GTCTACCTAGGTGTCCAAATGGTC -s simRat_chr6.simRat.chr6 270605 24 + 647215 GTATGCTTACATACCCGGATTGCC - -a -s simMouse_chr6.simMouse.chr6 282090 8 + 636262 CCCTTTCA -s Anc0.Anc0refChr6 1390 5 - 1880 ---ATACA -s Anc1.Anc1refChr5 5984 8 - 6477 CCTATACA -s Anc2.Anc2refChr13 95973 5 - 96486 ---ATATC -s mr.mrrefChr5 133089 8 + 294540 CCCATTCA -s simCow_chr6.simCow.chr6 246504 5 - 602619 ---ATGTC -s simDog_chr6.simDog.chr6 247369 5 - 593897 ---ATATC -s simHuman_chr6.simHuman.chr6 357359 8 - 601863 CCTATCCA -s simRat_chr6.simRat.chr6 270629 8 + 647215 CCCATTCA - -a -s simMouse_chr6.simMouse.chr6 282098 38 + 636262 CCCTCAGCATCTTGGGGATATGTACAATAAGGCTTGGA -s Anc0.Anc0refChr6 1395 38 - 1880 CCCTCAGCATCCTACGGATATGCACAATAAGGCTTGTT -s Anc1.Anc1refChr5 5992 38 - 6477 CCCTCAGCATCCTACGGATATGCACAATAAGGCTTGTT -s Anc2.Anc2refChr13 95978 38 - 96486 CCCCCACCATCCTACGGATATGCACAATAAGGCTTGTA -s mr.mrrefChr5 133097 38 + 294540 CCCTCAGCATCTTAGGGATATGCACAATAAGGCTTGTT -s simCow_chr6.simCow.chr6 246509 36 - 602619 TCCCCGCCATCCTATGG--ATGCAGAATAAGCATTGTT -s simDog_chr6.simDog.chr6 247374 23 - 593897 CCCCTACCATCCTACGGATATGT--------------- -s simHuman_chr6.simHuman.chr6 357381 38 - 601863 CCCTCAGCATCCTACGGATATGCACAATAAGGCTTTTT -s simRat_chr6.simRat.chr6 270637 38 + 647215 CCCTCAGCATCTTAGGGGTATGCACAATCAGGCTTGTT - -a -s simMouse_chr6.simMouse.chr6 282136 34 + 636262 GGAGTTCTTAACACAATAAGCTTTTCTGTTCTTG -s Anc0.Anc0refChr6 1433 34 - 1880 TAAGCTCTTAATGTGATAAGTTTTCCTATTTTTG -s Anc1.Anc1refChr5 6030 34 - 6477 TAAGCTCTTAATGTGATAAGTTTTCCTATTTTTG -s Anc2.Anc2refChr13 96016 34 - 96486 TAAGCTCTTAATGTGATAAGTTTTCCCATCTTTG -s mr.mrrefChr5 133135 34 + 294540 GGAGCTCTTAACACGATAAGCTTTCCTGTTCTTG -s simCow_chr6.simCow.chr6 246545 34 - 602619 TAAGCTCTGAATGTTATAAGTTTTCCCATCTTTT -s simDog_chr6.simDog.chr6 247397 33 - 593897 -GAAATTTTAACATGATAAGTTTTCCCATCTTTG -s simHuman_chr6.simHuman.chr6 357420 34 - 601863 TAAGCTCTTAATGTGATAAGTTTTCCTATTTTTG -s simRat_chr6.simRat.chr6 270675 34 + 647215 GGAGCTCTTAACACGATAAGCTTTCCTGTTCTTG - -a -s simMouse_chr6.simMouse.chr6 282170 4 + 636262 TCCA -s Anc0.Anc0refChr6 1467 4 - 1880 TCCA -s Anc1.Anc1refChr5 6064 4 - 6477 TCCA -s Anc2.Anc2refChr13 96050 4 - 96486 TCCC -s mr.mrrefChr5 133169 4 + 294540 TCCA -s simCow_chr6.simCow.chr6 246579 3 - 602619 TCC- -s simDog_chr6.simDog.chr6 247430 4 - 593897 TCCC -s simHuman_chr6.simHuman.chr6 357570 4 - 601863 TCTA -s simRat_chr6.simRat.chr6 270709 4 + 647215 TTCC - -a -s simMouse_chr6.simMouse.chr6 282174 3 + 636262 CCA -s Anc0.Anc0refChr6 1471 3 - 1880 ATG -s Anc1.Anc1refChr5 6068 3 - 6477 ATG -s Anc2.Anc2refChr13 96054 3 - 96486 ATG -s mr.mrrefChr5 133173 3 + 294540 CCA -s simCow_chr6.simCow.chr6 246582 3 - 602619 AGG -s simDog_chr6.simDog.chr6 247440 3 - 593897 ATG -s simHuman_chr6.simHuman.chr6 357574 3 - 601863 ATG -s simRat_chr6.simRat.chr6 270713 3 + 647215 CCA - -a -s simMouse_chr6.simMouse.chr6 282177 48 + 636262 GTTATAGGGTTACTAGTATAATCTTGTAATAGCAGGATGGGACCAGCC -s Anc0.Anc0refChr6 1474 48 - 1880 ATTATTGAGTAACTGTCACAGTGATGTGTAAGCAGGATGGAGCCAGCC -s Anc1.Anc1refChr5 6071 48 - 6477 ATTATTGAGTAACTGTCACAGTGATGTGTAAGCAGGATGGAGCCAGCC -s Anc2.Anc2refChr13 96058 48 - 96486 ATTATTGAGTAAATGTCACAGTGATGTGCAAGCAGGATGGAGCCAGAT -s mr.mrrefChr5 133176 48 + 294540 GTTATTGGGTAACTGTTACAATGATGTATTAGCAGGATGGGACCAGCC -s simCow_chr6.simCow.chr6 246586 48 - 602619 GTTATTGAGTAAATGTCACAGTGGCGTGCAAGCAAGATGGAGCCAGGT -s simDog_chr6.simDog.chr6 247444 48 - 593897 ATAATTGAGTAAACGTCACAGTCATGTGCAAGCAGGATGGAGCCAGAT -s simHuman_chr6.simHuman.chr6 357577 48 - 601863 TTTTATGAGTAACTGTCACAGTGATGTGTGAGCAGAATGAAGCCAGCC -s simRat_chr6.simRat.chr6 270716 48 + 647215 GTTATTGGGTAGATGTTACAATGATGTATTAGCAGGATGGGACCAGTT - -a -s simMouse_chr6.simMouse.chr6 282225 62 + 636262 TCTGGTGAAAGTATTAGGGCATTAATATTCATTTTTAAGCCTGTACCTTCCATGACTCACCT -s Anc0.Anc0refChr6 1523 62 - 1880 TCTGGTGAAAGTATTAGGGCATTAATACTTATTTTTTGTCCTATACCTTGCATAATTCACCT -s Anc1.Anc1refChr5 6120 62 - 6477 TCTGGTGAAAGTATTAGGGCATTAATACTTATTTTTTGTCCTATACCTTGCATAATTCACCT -s Anc2.Anc2refChr13 96107 62 - 96486 TCTGGTGAAAGTATTGTGGCATTAATACTTGTTTTTTGTCCTATACCTTGCATAATTCACCT -s mr.mrrefChr5 133224 62 + 294540 TCTGGTGAAAGTATTAGGGCATTAATATTCATTTTTAAGCCTGTACCTTCCATGACTCACCT -s simCow_chr6.simCow.chr6 246635 60 - 602619 CCTGGTGA--GTACGGTGGAATTAATACCTGTTTTTTGTCCTATACCTTGTATAATCTATCT -s simDog_chr6.simDog.chr6 247493 62 - 593897 TCTCGTGGAAGTATTGTGGCTTTAATACTTGTTTATTGTCCTATACCTTGCACAATTCACCT -s simHuman_chr6.simHuman.chr6 357626 62 - 601863 TCTGGTGAAAGTATCAGGGCATTAATACTTATTTTTTCTCCTATACCTTGCATAATGCACCT -s simRat_chr6.simRat.chr6 270764 2 + 647215 TC------------------------------------------------------------ - -a -s simMouse_chr6.simMouse.chr6 282287 4 + 636262 AAGT -s Anc0.Anc0refChr6 1587 4 - 1880 AAGT -s Anc1.Anc1refChr5 6184 4 - 6477 AAGT -s Anc2.Anc2refChr13 96171 4 - 96486 AAGT -s mr.mrrefChr5 133286 4 + 294540 AAGT -s simCow_chr6.simCow.chr6 246697 4 - 602619 AAGT -s simDog_chr6.simDog.chr6 247557 4 - 593897 TAGT -s simHuman_chr6.simHuman.chr6 357690 4 - 601863 AAGT - -a -s simMouse_chr6.simMouse.chr6 282291 14 + 636262 AGCTCTCCCATCAC -s Anc0.Anc0refChr6 1591 14 - 1880 AGCTCTTCAATCAC -s Anc1.Anc1refChr5 6188 14 - 6477 AGCTCTTCAATCAC -s Anc2.Anc2refChr13 96180 14 - 96486 ACCTCTTCAATCAC -s mr.mrrefChr5 133290 14 + 294540 AGCTCTCCCATCAC -s simCow_chr6.simCow.chr6 246706 14 - 602619 AACTCTTCAATCAC -s simDog_chr6.simDog.chr6 247566 14 - 593897 ACCTCTTCGGTCAC -s simHuman_chr6.simHuman.chr6 357694 14 - 601863 AGCTCTTCAATCGC - -a -s simMouse_chr6.simMouse.chr6 282305 20 + 636262 CTTTATGGCTAGATGGCCCT -s Anc0.Anc0refChr6 1606 20 - 1880 CTTCATAACTAGATGGCCCT -s Anc1.Anc1refChr5 6203 20 - 6477 CTTCATAACTAGATGGCCCT -s Anc2.Anc2refChr13 96195 20 - 96486 CTTCATAACCAGATGGCCAT -s mr.mrrefChr5 133304 20 + 294540 CTTTATGACTAGATGGCCCT -s simCow_chr6.simCow.chr6 246721 20 - 602619 CTTCAAAGCCACATAGCCAT -s simDog_chr6.simDog.chr6 247581 17 - 593897 TTTCATAATCAGATGGC--- -s simHuman_chr6.simHuman.chr6 357709 20 - 601863 CTTCATAACTATATGACCCT -s simRat_chr6.simRat.chr6 270766 16 + 647215 ----ATTACTAGACTGCCCT - -a -s simMouse_chr6.simMouse.chr6 282325 147 + 636262 ACGTCAACTCATATCTGCTGTTAGAGCCAATTAATAAGACCATGAAACAGCTAATGGTCAAGTTGGCCTGGCGAGTGATCCCAGAGAGTGAGCCAATGATACAACATGGAAAGGCTTTGCAAATCTTGCCCATCAAATTTATTCCTC -s Anc0.Anc0refChr6 1628 128 - 1880 ATGACAGCTTATATCTGGCATCAAATCCAAGTAATAACATCATGAAACAGCTAATGGTCAAATT-------------------GAGAGTCCGCCAATAAGAGAACATGGGAAGGTTTAGCCAATGTTGCAAGCCTAATATTTCCTTG -s Anc1.Anc1refChr5 6225 128 - 6477 ATGACAGCTTATATCTGGCATCAAATCCAAGTAATAACATCATGAAACAGCTAATGGTCAAATT-------------------GAGAGTCCGCCAATAAGAGAACATGGGAAGGTTTAGCCAATGTTGCAAGCCTAATATTTCCTTG -s Anc2.Anc2refChr13 96217 128 - 96486 ATAACAGCTTATATCTGGCACCAAAACCAAGTAATAACATCATGAGCCAGCTAATGGTCTAATG-------------------AAGAGTCCGCCAACAAGAGAACATGAGTAGGTTTAGCCAACGTTGCAAGCCTAATATTTCCTTG -s mr.mrrefChr5 133324 128 + 294540 ATGTCAGCTCATATCTGCCATTAGATCCAATTAATAAGACCATGAAACAGCTAATGGTCAAGTT-------------------GAGAGTGAGCCAATGATACAACATGGAAAGGCTTTGCAAATCTTGCCCGTCAAATTTATTCCTG -s simCow_chr6.simCow.chr6 246743 122 - 602619 ATCAAAGCTTATATCTGCCACCAAAACCAAGTAATAATATT-TGCTGTAGCTAATGGTCGAATG-------------------AAGAGTCAACCAGCAAGAGGACAAGAG-AGGTT----CAACATTGTACATCTAATATTACCTTG -s simDog_chr6.simDog.chr6 247598 126 - 593897 --AACTGCTTATATCTGGCACCAAAACCAAGTAATCACATCATAAGCCAGTTAATGGTATAATG-------------------AAGAGTCCGCCAACAAAAGAACATGAGTAGGTTTAGCCAACGTAGCAAGCCTAATATTTCCTCG -s simHuman_chr6.simHuman.chr6 357731 128 - 601863 ATGACAGCTTACATCTAGCATCAAATCCAAGTAATAACATCATGAAAAAGCTAATGGTCAAACT-------------------GAGAGTTGGCTGATAAGAGAACATAGGAAAGTGTAGCCATTGTTGCAAGCCTAATATTTCTGTG -s simRat_chr6.simRat.chr6 270782 99 + 647215 ATGTCAGCTCATATCTGCCATTAGATCCAATTAATAAAACC-----ACAGCTACTGGT-------------------------------------------CAACGTGGAAAGGCTTTGCAAATCTTGTGTGTCAAATGTATTCCTG - -a -s simMouse_chr6.simMouse.chr6 282472 41 + 636262 AGGCTGGAGTTTTACAGTAACACTCCTAAATAGTGCATGGA -s Anc0.Anc0refChr6 1756 40 - 1880 AGCTAGAGGTATAATGGTGACATT-GTCAATAGTACAAGGA -s Anc1.Anc1refChr5 6353 40 - 6477 AGCTAGAGGTATAATGGTGACATT-GTCAATAGTACAAGGA -s Anc2.Anc2refChr13 96346 40 - 96486 AGCTAGAGTTATAATGGTGACATT-GTCAATGATATAAGGA -s mr.mrrefChr5 133452 40 + 294540 AGGCTGAAGTTTAACAGTGACATT-CTAAATAGTGCATGGA -s simCow_chr6.simCow.chr6 246866 40 - 602619 GGCTACAGTTATCATGGTGATGTT-GTCAATTATATAAAGA -s simDog_chr6.simDog.chr6 247725 40 - 593897 AGTTAGAGTTATAATGGTGACATT-GTCAATGACATGAGGA -s simHuman_chr6.simHuman.chr6 357859 40 - 601863 AGCTAGAGGTGTAATGGTGACATT-GTCAATAGTACAACGA -s simRat_chr6.simRat.chr6 270881 30 + 647215 AGGCTAAAGTTGAACAATGATATT-----------CATGGA - -a -s simMouse_chr6.simMouse.chr6 282513 24 + 636262 GATTTCCTGTGCTGACTTATATGA -s Anc0.Anc0refChr5 80143 24 - 87904 GGTTTCCTGTACTGACTTATATGA -s Anc1.Anc1refChr8 36748 24 - 57822 GGTTTCCTGTACTGACTTATATGA -s Anc2.Anc2refChr15 85833 24 - 86568 GGTTTCCTGTACTAATTAATATGA -s mr.mrrefChr5 133560 24 + 294540 GATTTCCTGTGCTGACTTATATGA -s simCow_chr6.simCow.chr6 247075 24 - 602619 GATTTCCAGTACTAATCAATATGA -s simDog_chr6.simDog.chr6 247925 24 - 593897 GGTTTCCTGTACTAATTAACATGA -s simHuman_chr6.simHuman.chr6 414896 24 - 601863 GCTTTCAGGTCCTGACTTCTGTGA -s simRat_chr6.simRat.chr6 270986 24 + 647215 GACTTCCTGTGCTGCCTTATATGA - -a -s simMouse_chr6.simMouse.chr6 282537 8 + 636262 GTTGCTCT -s Anc0.Anc0refChr5 80167 8 - 87904 ATTGCACT -s Anc1.Anc1refChr8 36772 8 - 57822 ATTGCACT -s Anc2.Anc2refChr15 85857 8 - 86568 ATTGCACT -s mr.mrrefChr5 133584 8 + 294540 ATTGCTCT -s simCow_chr6.simCow.chr6 247099 8 - 602619 ATTTCCCT -s simDog_chr6.simDog.chr6 247949 8 - 593897 ATTGTACC -s simHuman_chr6.simHuman.chr6 414920 8 - 601863 ATTACACT -s simRat_chr6.simRat.chr6 271013 8 + 647215 ATTGCTCT - -a -s simMouse_chr6.simMouse.chr6 282545 12 + 636262 GCATTGTGACCT -s Anc0.Anc0refChr5 80175 10 - 87904 GCAAAATGA--T -s Anc1.Anc1refChr8 36780 10 - 57822 GCAAAATGA--T -s Anc2.Anc2refChr15 85865 10 - 86568 GCAAAATAA--T -s mr.mrrefChr5 133592 12 + 294540 GCATTGTGACCT -s simCow_chr6.simCow.chr6 247107 10 - 602619 GCAAAATAG--T -s simDog_chr6.simDog.chr6 247959 4 - 593897 GC------A--T -s simHuman_chr6.simHuman.chr6 414928 10 - 601863 GCAAGATGA--T -s simRat_chr6.simRat.chr6 271021 12 + 647215 GCATAGTGACCT - -a -s simMouse_chr6.simMouse.chr6 282557 5 + 636262 TACGC -s Anc0.Anc0refChr5 80191 5 - 87904 TGTTC -s Anc1.Anc1refChr8 36796 5 - 57822 TGTTC -s Anc2.Anc2refChr15 85881 5 - 86568 TGTTC -s mr.mrrefChr5 133610 5 + 294540 TGTGC -s simCow_chr6.simCow.chr6 247123 5 - 602619 TGTAC -s simDog_chr6.simDog.chr6 247969 4 - 593897 TATT- -s simHuman_chr6.simHuman.chr6 414944 5 - 601863 TGTTC -s simRat_chr6.simRat.chr6 271039 5 + 647215 TGTGC - -a -s simMouse_chr6.simMouse.chr6 282562 62 + 636262 CATGCACTGAGAATAGTTGGAGTACCAGTAACCTGAGAATCTATTCAAATCTTTGCAGCTAT -s Anc0.Anc0refChr5 80196 61 - 87904 CTTGCATTGAGAATAGTTGGAGTTCT-GTAACCTAAGTATCTATTCAGATTTTTGTAGCTAA -s Anc1.Anc1refChr8 36801 61 - 57822 CTTGCATTGAGAATAGTTGGAGTTCT-GTAACCTAAGTATCTATTCAGATTTTTGTAGCTAA -s Anc2.Anc2refChr15 85886 61 - 86568 CTTGCATTGAGAATAGTTCGAGTTCT-GTAACCTAAGTATCTATTCAGATTTTTGTAGCCAA -s mr.mrrefChr5 133615 62 + 294540 CATGCACTGAGAATAGTTGGAGTACCAGTAACCTGAGAATCTATTCAAATCTTTGCAGCTAA -s simCow_chr6.simCow.chr6 247128 61 - 602619 CTTGCATTGAGAATAGTCAGAGTACT-GCAACCTAAGCACCTATTCAGATTTCTTTAGCCAA -s simDog_chr6.simDog.chr6 247973 51 - 593897 -----ATTGAGAATAGTTCGAGTTCT-GTAACCTGAGTATCTTGTCAGATTTTAGTA----- -s simHuman_chr6.simHuman.chr6 414953 61 - 601863 CTTGCATTTAAAATAGTTGCAGTTCT-GTAACCTAAGTATCTATTCAGATTTTTGTAGCTAA -s simRat_chr6.simRat.chr6 271044 62 + 647215 GATGCACTGAGAATAGTTGGAGTACCAGTAACCTGAGAATCTATTCAAACCTTTGCAACTAA - -a -s simMouse_chr6.simMouse.chr6 282624 48 + 636262 ACCCACCTCTCAGTTTTTAGTGATCATGCTTTGAGCTATAAATACAGT -s Anc0.Anc0refChr5 80257 44 - 87904 ACCCACCTCTCAATCTTTATTGATT----TTTGAGCTAGAAATGGAGC -s Anc1.Anc1refChr8 36862 48 - 57822 ACCCACCTCTCAATCTTTATTGATTGTCCTTTGAGCTAGAAATGGAGC -s Anc2.Anc2refChr15 85947 44 - 86568 ACCCACCTCTCAATCCTTATGGATT----TTTGGGCTAGATAGGGAGC -s mr.mrrefChr5 133677 48 + 294540 ACCCACCTCTCAATTTTTAGTGATCGTGCTTTGAGCTAGAAATACAGT -s simCow_chr6.simCow.chr6 247189 44 - 602619 ACCCACCTTTCAATCCTTATGGATT----TTTGGGCTAGATAGGGAGC -s simDog_chr6.simDog.chr6 248024 9 - 593897 --CTACCACAC------------------------------------- -s simHuman_chr6.simHuman.chr6 415015 48 - 601863 ACCCTCCTCTCCATCTTTATTGATTGTCCATTGAACTAGAAATGTAGC -s simRat_chr6.simRat.chr6 271106 48 + 647215 ACCCACCTCTCAATTTTCAGTGATCGCACTTTGAGCTGGAAATACAGT - -a -s simMouse_chr6.simMouse.chr6 282672 26 + 636262 AATATGTCTCGGACAGGCACCTGTGT -s Anc0.Anc0refChr5 80301 18 - 87904 A-CA-TTTTTAGACAG----CTAG-- -s Anc1.Anc1refChr8 36910 19 - 57822 A-CATTTTTTAGACAG----CTAG-- -s Anc2.Anc2refChr15 85991 18 - 86568 A-CA-TTTTTAGACAG----CTAG-- -s mr.mrrefChr5 133725 22 + 294540 AATATTTCTTGGACAG----CTGGGT -s simCow_chr6.simCow.chr6 247236 17 - 602619 A-CA-TTTTT-GACAG----CTGG-- -s simDog_chr6.simDog.chr6 248033 10 - 593897 ----------AGACAG----CTAA-- -s simHuman_chr6.simHuman.chr6 415063 19 - 601863 A-CATTCTTTAGACAG----TTAG-- -s simRat_chr6.simRat.chr6 271154 22 + 647215 AATATTTCTTGGACAG----CCGGGC - -a -s simMouse_chr6.simMouse.chr6 282698 8 + 636262 TCTGGATA -s Anc0.Anc0refChr5 80319 8 - 87904 TGTGGAGA -s Anc1.Anc1refChr8 36929 8 - 57822 TGTGGAGA -s Anc2.Anc2refChr15 86009 8 - 86568 TGTGGAGA -s mr.mrrefChr5 133747 8 + 294540 TGTGGATA -s simCow_chr6.simCow.chr6 247253 8 - 602619 TGTGGAGA -s simDog_chr6.simDog.chr6 248061 8 - 593897 TGCATAGA -s simHuman_chr6.simHuman.chr6 415082 8 - 601863 TGTGGAGA -s simRat_chr6.simRat.chr6 271176 8 + 647215 TGTGGATA - -a -s simMouse_chr6.simMouse.chr6 282706 9 + 636262 GGATAGCAC -s Anc0.Anc0refChr5 80340 4 - 87904 G-----TGG -s Anc1.Anc1refChr8 36950 4 - 57822 G-----TGG -s Anc2.Anc2refChr15 86030 4 - 86568 G-----TGG -s mr.mrrefChr5 133755 4 + 294540 G-----TGC -s simCow_chr6.simCow.chr6 247275 4 - 602619 A-----TAG -s simDog_chr6.simDog.chr6 248082 4 - 593897 G-----TGG -s simHuman_chr6.simHuman.chr6 415103 4 - 601863 G-----TGG -s simRat_chr6.simRat.chr6 271184 4 + 647215 G-----TGC - -a -s simMouse_chr6.simMouse.chr6 282715 4 + 636262 CACT -s Anc0.Anc0refChr5 80344 4 - 87904 CACT -s Anc1.Anc1refChr8 36954 4 - 57822 CACT -s Anc2.Anc2refChr15 86035 4 - 86568 CATT -s mr.mrrefChr5 133759 4 + 294540 CACT -s simCow_chr6.simCow.chr6 247280 2 - 602619 CA-- -s simDog_chr6.simDog.chr6 248087 4 - 593897 CATT -s simHuman_chr6.simHuman.chr6 415107 4 - 601863 CACT -s simRat_chr6.simRat.chr6 271188 4 + 647215 CACT - -a -s simMouse_chr6.simMouse.chr6 282719 17 + 636262 AGCTCTAGTGTTATGAG -s Anc0.Anc0refChr5 80354 17 - 87904 AGCTTTAGTGTTATGAG -s Anc1.Anc1refChr8 36964 17 - 57822 AGCTTTAGTGTTATGAG -s Anc2.Anc2refChr15 86093 17 - 86568 GGCTTTAGTGTTTTGAG -s mr.mrrefChr5 133763 17 + 294540 AGCTCTAGTGTTATGAG -s simCow_chr6.simCow.chr6 247346 17 - 602619 GGCTTTAGTGTTTTGAG -s simDog_chr6.simDog.chr6 248146 8 - 593897 GGCTCTAG--------- -s simHuman_chr6.simHuman.chr6 415117 17 - 601863 AGCTTTAGTATCATGAG -s simRat_chr6.simRat.chr6 271192 17 + 647215 AGCTCTAATGTTATGAG - -a -s simMouse_chr6.simMouse.chr6 282736 11 + 636262 AGGCTGTATCA -s Anc0.Anc0refChr5 80371 11 - 87904 AACTGATGGTA -s Anc1.Anc1refChr8 36981 11 - 57822 AACTGATGGTA -s Anc2.Anc2refChr15 86110 11 - 86568 AACTGATGGTA -s mr.mrrefChr5 133780 11 + 294540 AGGTTGTAGCA -s simCow_chr6.simCow.chr6 247364 11 - 602619 AACTGACGGTA -s simDog_chr6.simDog.chr6 248154 8 - 593897 ---CGATGGTG -s simHuman_chr6.simHuman.chr6 415134 9 - 601863 AACTGATGG-- -s simRat_chr6.simRat.chr6 271209 11 + 647215 AGGTTGTAGAA - -a -s simMouse_chr6.simMouse.chr6 282747 19 + 636262 ATTAACATATATAGAATCT -s Anc0.Anc0refChr5 80382 19 - 87904 GTTGCCAGAGATAGAATCT -s Anc1.Anc1refChr8 36992 19 - 57822 GTTGCCAGAGATAGAATCT -s Anc2.Anc2refChr15 86124 19 - 86568 GTTGCCAGAGATGGAATCT -s mr.mrrefChr5 133791 19 + 294540 ATTAACATATATAGAATCT -s simCow_chr6.simCow.chr6 247378 19 - 602619 GTTGACACAGATGGAATCT -s simDog_chr6.simDog.chr6 248165 19 - 593897 GTTGCCAGAGATGGAATCT -s simHuman_chr6.simHuman.chr6 415143 8 - 601863 -----------TAGATCAT -s simRat_chr6.simRat.chr6 271220 19 + 647215 ATTAACATAGATAGAGTCC - -a -s simMouse_chr6.simMouse.chr6 282766 5 + 636262 TGATA -s Anc0.Anc0refChr5 80401 5 - 87904 TGATT -s Anc1.Anc1refChr8 37011 5 - 57822 TGATT -s Anc2.Anc2refChr15 86145 5 - 86568 TGGTT -s mr.mrrefChr5 133810 5 + 294540 TGATA -s simCow_chr6.simCow.chr6 247399 5 - 602619 TGGCT -s simDog_chr6.simDog.chr6 248186 5 - 593897 TGGTT -s simHuman_chr6.simHuman.chr6 415151 5 - 601863 TGATG -s simRat_chr6.simRat.chr6 271239 5 + 647215 TGATA - -a -s simMouse_chr6.simMouse.chr6 282771 3 + 636262 TGA -s Anc0.Anc0refChr5 80406 3 - 87904 TGA -s Anc1.Anc1refChr8 37016 3 - 57822 TGA -s Anc2.Anc2refChr15 86150 3 - 86568 TGA -s mr.mrrefChr5 133815 3 + 294540 TGA -s simCow_chr6.simCow.chr6 247404 3 - 602619 TGT -s simDog_chr6.simDog.chr6 248191 3 - 593897 TGA -s simHuman_chr6.simHuman.chr6 415156 3 - 601863 TTA -s simRat_chr6.simRat.chr6 271248 3 + 647215 TGG - -a -s simMouse_chr6.simMouse.chr6 282774 19 + 636262 ATATCATTGTTCTGCTAGC -s Anc0.Anc0refChr5 80409 19 - 87904 CTATCATTGTTTTGCTTGT -s Anc1.Anc1refChr8 37019 19 - 57822 CTATCATTGTTTTGCTTGT -s Anc2.Anc2refChr15 86154 19 - 86568 CCATCAATGTTTTGCTTGT -s mr.mrrefChr5 133818 19 + 294540 ATATCATTGTTCTGCTAGC -s simCow_chr6.simCow.chr6 247409 19 - 602619 CCATCAGTGTCTTGCTTGT -s simDog_chr6.simDog.chr6 248195 19 - 593897 CTATCAATGTTTTGCTTGT -s simHuman_chr6.simHuman.chr6 415159 8 - 601863 CTTGTATT----------- -s simRat_chr6.simRat.chr6 271251 19 + 647215 ATATCAATGTTTTGCTAAC - -a -s simMouse_chr6.simMouse.chr6 282793 10 + 636262 ATTGTGTAGC -s Anc0.Anc0refChr5 80428 10 - 87904 ATTGTGTAAC -s Anc1.Anc1refChr8 37038 10 - 57822 ATTGTGTAAC -s Anc2.Anc2refChr15 86174 10 - 86568 ATTGTGTGTC -s mr.mrrefChr5 133837 10 + 294540 ATTGTGTAAC -s simCow_chr6.simCow.chr6 247429 10 - 602619 CTTGTGTGTC -s simDog_chr6.simDog.chr6 248215 10 - 593897 ATTGTGTGTC -s simHuman_chr6.simHuman.chr6 415167 8 - 601863 --TGTGTAAC -s simRat_chr6.simRat.chr6 271270 10 + 647215 ATTGTGCAAC - -a -s simMouse_chr6.simMouse.chr6 282803 14 + 636262 CTCACTCTCTACCT -s Anc0.Anc0refChr5 80438 14 - 87904 TTTACTTTCTACTT -s Anc1.Anc1refChr8 37048 14 - 57822 TTTACTTTCTACTT -s Anc2.Anc2refChr15 86184 14 - 86568 TTTACTTTCTACTT -s mr.mrrefChr5 133847 14 + 294540 CTCACTCTCTACCT -s simCow_chr6.simCow.chr6 247439 14 - 602619 TTTACTTTATACTT -s simDog_chr6.simDog.chr6 248225 9 - 593897 TTTAATTTC----- -s simHuman_chr6.simHuman.chr6 415175 14 - 601863 TGTACTTTCTGCTT -s simRat_chr6.simRat.chr6 271283 14 + 647215 CCCACTCACTACCT - -a -s simMouse_chr6.simMouse.chr6 282817 5 + 636262 CACAA -s Anc0.Anc0refChr5 80452 5 - 87904 CGCAG -s Anc1.Anc1refChr8 37062 5 - 57822 CGCAG -s Anc2.Anc2refChr15 86198 5 - 86568 CACAG -s mr.mrrefChr5 133861 5 + 294540 CGCAA -s simCow_chr6.simCow.chr6 247453 5 - 602619 CACAG -s simHuman_chr6.simHuman.chr6 415197 4 - 601863 CG-AG -s simRat_chr6.simRat.chr6 271297 5 + 647215 CGCAA - -a -s simMouse_chr6.simMouse.chr6 282822 5 + 636262 TCATT -s Anc0.Anc0refChr5 80457 5 - 87904 TCATT -s Anc1.Anc1refChr8 37067 5 - 57822 TCATT -s Anc2.Anc2refChr15 86556 5 - 86568 TCACT -s mr.mrrefChr5 133866 5 + 294540 TCATT -s simCow_chr6.simCow.chr6 346447 5 + 602619 TCACC -s simDog_chr6.simDog.chr6 248805 5 - 593897 TCACT -s simHuman_chr6.simHuman.chr6 415201 5 - 601863 TCTTA -s simRat_chr6.simRat.chr6 271302 5 + 647215 TCATT - -a -s simMouse_chr6.simMouse.chr6 282827 10 + 636262 ATAATTACAT -s Anc0.Anc0refChr5 80462 10 - 87904 ATAATTATAC -s Anc1.Anc1refChr8 37072 10 - 57822 ATAATTATAC -s Anc2.Anc2refChr14 3 10 - 7748 ATACCTATAC -s mr.mrrefChr5 133871 10 + 294540 ATAATTATAT -s simCow_chr6.simCow.chr6 247463 10 - 602619 ATATCTATAC -s simDog_chr6.simDog.chr6 249532 10 - 593897 ATGCCTATAC -s simHuman_chr6.simHuman.chr6 415206 10 - 601863 ATAACAGTAC -s simRat_chr6.simRat.chr6 271307 10 + 647215 ATAATTATAT - -a -s simMouse_chr6.simMouse.chr6 282837 37 + 636262 CATTCCAAAGACTCATCTGAAACTCTGACTTGTACAG -s Anc0.Anc0refChr5 80472 31 - 87904 CATTCTCATGACTAATCTGAAACT------CAGACTT -s Anc1.Anc1refChr8 37082 31 - 57822 CATTCTCATGACTAATCTGAAACT------CAGACTT -s Anc2.Anc2refChr14 13 31 - 7748 CATTCTCATCAATAATCTAAAACT------CAGACTT -s mr.mrrefChr5 133881 31 + 294540 CATTCCAATGACTCATCTGAAACT------TGTACAG -s simCow_chr6.simCow.chr6 247473 29 - 602619 CTTTCTCTGCATTAATCTAAA--T------TAGACTC -s simDog_chr6.simDog.chr6 249544 31 - 593897 CATTCTCATCTATAATTTAAAACT------CAGACCT -s simHuman_chr6.simHuman.chr6 415216 31 - 601863 AATTCTCATGACTAATCTGAAACT------CAGACTT -s simRat_chr6.simRat.chr6 271317 31 + 647215 CATTCCAATGACTCATCTGAAACT------TGTGCAG - -a -s simMouse_chr6.simMouse.chr6 282874 3 + 636262 GCA -s Anc0.Anc0refChr5 80503 3 - 87904 GTA -s Anc1.Anc1refChr8 37113 3 - 57822 GTA -s Anc2.Anc2refChr14 46 3 - 7748 GCA -s mr.mrrefChr5 133912 3 + 294540 GTA -s simCow_chr6.simCow.chr6 247504 3 - 602619 GCA -s simDog_chr6.simDog.chr6 249577 3 - 593897 GCA -s simHuman_chr6.simHuman.chr6 415247 3 - 601863 GTA -s simRat_chr6.simRat.chr6 271348 3 + 647215 GTA - -a -s simMouse_chr6.simMouse.chr6 282877 13 + 636262 AACGTAAAGTAGA -s Anc0.Anc0refChr5 80506 12 - 87904 AGC-TAAAATAGT -s Anc1.Anc1refChr8 37116 12 - 57822 AGC-TAAAATAGT -s Anc2.Anc2refChr14 49 12 - 7748 AGC-TCAAATATT -s mr.mrrefChr5 133915 13 + 294540 AACCTAAAGTAGA -s simCow_chr6.simCow.chr6 247507 12 - 602619 AGC-TGTCATATC -s simDog_chr6.simDog.chr6 249580 12 - 593897 AGC-TCAAATATT -s simHuman_chr6.simHuman.chr6 415255 12 - 601863 AGC-TAAAACAGT -s simRat_chr6.simRat.chr6 271351 13 + 647215 AAACTAAGGTAGA - -a -s simMouse_chr6.simMouse.chr6 282890 36 + 636262 GTCAGGGAAGATGGAAAGAAGGCAGAGAGAAGATTT -s Anc0.Anc0refChr5 80518 22 - 87904 GTCAGGAAAG-----------GCAGATAGGTT---T -s Anc1.Anc1refChr8 37128 22 - 57822 GTCAGGAAAG-----------GCAGATAGGTT---T -s Anc2.Anc2refChr14 61 22 - 7748 GTCAGGAAAG-----------GCAGATAGGTT---T -s mr.mrrefChr5 133928 33 + 294540 GTCAGGGAAGATGGAAAGAAGGCAGAGAGGAG---T -s simCow_chr6.simCow.chr6 247519 22 - 602619 GTCAGGATAG-----------GCAGATAGTGT---T -s simDog_chr6.simDog.chr6 249592 22 - 593897 GTCAGGAAAG-----------GCAGATAGGTT---T -s simHuman_chr6.simHuman.chr6 415267 22 - 601863 ATCAGGAAAG-----------GCAGGTAGGTT---T -s simRat_chr6.simRat.chr6 271392 33 + 647215 GTGAGGGAACATGGAGATGAGGCAGAAAGGAA---T - -a -s simMouse_chr6.simMouse.chr6 282926 1 + 636262 C -s Anc0.Anc0refChr5 80541 1 - 87904 C -s Anc1.Anc1refChr8 37151 1 - 57822 C -s Anc2.Anc2refChr14 84 1 - 7748 C -s mr.mrrefChr5 133961 1 + 294540 C -s simCow_chr6.simCow.chr6 247542 1 - 602619 C -s simDog_chr6.simDog.chr6 249615 1 - 593897 C -s simHuman_chr6.simHuman.chr6 415290 1 - 601863 C -s simRat_chr6.simRat.chr6 271425 1 + 647215 C - -a -s simMouse_chr6.simMouse.chr6 282927 11 + 636262 CTGTCCAAAGA -s Anc0.Anc0refChr5 80542 11 - 87904 CTGCCCAACCA -s Anc1.Anc1refChr8 37152 11 - 57822 CTGCCCAACCA -s Anc2.Anc2refChr14 85 11 - 7748 ATGCCCAACCA -s mr.mrrefChr5 133962 11 + 294540 CTGTCTACCGA -s simCow_chr6.simCow.chr6 247545 11 - 602619 ATGCCCAACCT -s simDog_chr6.simDog.chr6 249616 11 - 593897 ATGTCCAACTA -s simHuman_chr6.simHuman.chr6 415291 11 - 601863 CTGCCCAACCA -s simRat_chr6.simRat.chr6 271426 11 + 647215 CTCTCTACCGA - -a -s simMouse_chr6.simMouse.chr6 282938 10 + 636262 TGCCAGGGAG -s Anc0.Anc0refChr5 80556 10 - 87904 TGCCAAGGAT -s Anc1.Anc1refChr8 37166 10 - 57822 TGCCAAGGAT -s Anc2.Anc2refChr14 99 10 - 7748 TGCCAAGGAT -s mr.mrrefChr5 133973 10 + 294540 TGCCAAGGAG -s simCow_chr6.simCow.chr6 247559 10 - 602619 TGCCAAGGAG -s simDog_chr6.simDog.chr6 249630 10 - 593897 CATCATGTAT -s simHuman_chr6.simHuman.chr6 415305 10 - 601863 TGCCAAGGAT -s simRat_chr6.simRat.chr6 271437 10 + 647215 TGCCAAAGAG - -a -s simMouse_chr6.simMouse.chr6 282948 22 + 636262 TGGTCATGATATCGGTGAAAGT -s Anc0.Anc0refChr5 80566 22 - 87904 CGGCCATGATATTAGTGAAAGC -s Anc1.Anc1refChr8 37176 22 - 57822 CGGCCATGATATTAGTGAAAGC -s Anc2.Anc2refChr14 109 22 - 7748 CGGCCATGATATTAGTGAAAGC -s mr.mrrefChr5 133983 22 + 294540 CGGTCATGATATCAGTGAAAGT -s simCow_chr6.simCow.chr6 247569 22 - 602619 GGGCCATGATATCTGTGAAAAC -s simDog_chr6.simDog.chr6 249643 22 - 593897 CCGCCATGATATTAGAGAAAGC -s simHuman_chr6.simHuman.chr6 415315 22 - 601863 CGTCCATGATACTAGTGAGAGC -s simRat_chr6.simRat.chr6 271447 22 + 647215 CGGTCATGATCTCAGTGAAAGT - -a -s simMouse_chr6.simMouse.chr6 282970 1 + 636262 T -s Anc0.Anc0refChr5 80588 1 - 87904 T -s Anc1.Anc1refChr8 37198 1 - 57822 T -s Anc2.Anc2refChr14 136 1 - 7748 T -s mr.mrrefChr5 134005 1 + 294540 T -s simCow_chr6.simCow.chr6 247596 1 - 602619 T -s simDog_chr6.simDog.chr6 249670 1 - 593897 T -s simHuman_chr6.simHuman.chr6 415337 1 - 601863 T -s simRat_chr6.simRat.chr6 271469 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 282971 13 + 636262 CACTCTGTGTCTG -s Anc0.Anc0refChr5 80600 13 - 87904 CCCACTGTATCCT -s Anc1.Anc1refChr8 37210 13 - 57822 CCCACTGTATCCT -s Anc2.Anc2refChr14 148 13 - 7748 CCCACTGTATCCT -s mr.mrrefChr5 134006 13 + 294540 CACTCTGTGTCTG -s simCow_chr6.simCow.chr6 247608 13 - 602619 TCCACCATATCTG -s simDog_chr6.simDog.chr6 249682 13 - 593897 CCCACTGCATCCT -s simHuman_chr6.simHuman.chr6 415349 13 - 601863 CCCGCTGTAACCT -s simRat_chr6.simRat.chr6 271470 13 + 647215 GGCTCTGTGTCTG - -a -s simMouse_chr6.simMouse.chr6 282984 32 + 636262 TTGAGTGGTGTTATAGAATGCCAATGAAGGTC -s Anc0.Anc0refChr5 80613 32 - 87904 TTGTGTAGTGTTGTGAAATGACAGTGAAAGCC -s Anc1.Anc1refChr8 37223 32 - 57822 TTGTGTAGTGTTGTGAAATGACAGTGAAAGCC -s Anc2.Anc2refChr14 161 32 - 7748 TTGTGTAATGTTGTGAAATGACAGTGAAAGCC -s mr.mrrefChr5 134019 32 + 294540 TTGAGTGGTGTTATAGAATGCCAGTGAAGGCC -s simCow_chr6.simCow.chr6 247621 32 - 602619 TTGTGTAATGTAGTGGAATGACAGTGAAAGCC -s simDog_chr6.simDog.chr6 249696 32 - 593897 TTGTGTAAACTTGTGAAATGACAGTGAGAGCT -s simHuman_chr6.simHuman.chr6 415362 32 - 601863 TTGTGTAGTGTTTTGAAATGTCAGTGAAAGCC -s simRat_chr6.simRat.chr6 271483 32 + 647215 TTCAGTGGTGTTGTAGCATGCCAGTGGAGGCC - -a -s simMouse_chr6.simMouse.chr6 283016 46 + 636262 AAACTCTTGCTTAACTCAAGGCAAGAAGGAAATCTAGACATAGACA -s Anc0.Anc0refChr5 80645 33 - 87904 AAACTCTTACTTA---CAGAGCA--------ATCAAAACAAGGA-- -s Anc1.Anc1refChr8 37255 33 - 57822 AAACTCTTACTTA---CAGAGCA--------ATCAAAACAAGGA-- -s Anc2.Anc2refChr14 193 33 - 7748 AAACTCTTACTTA---TCGAGTA--------ATCAAAACAAGGA-- -s mr.mrrefChr5 134051 46 + 294540 AAACTCTTGCTTAACTCAAGGCAAGAAGGAAATCTAGACATGGACA -s simCow_chr6.simCow.chr6 247653 33 - 602619 AAACTCTTAATTA---TGGTGTA--------AATGAAACAAGGA-- -s simDog_chr6.simDog.chr6 249729 33 - 593897 AAATCCTTACTTA---TCGAGTA--------ATCAAAACAAGGA-- -s simHuman_chr6.simHuman.chr6 415394 33 - 601863 AAACTCTTACATA---CACAGCG--------ATCAAAACAAGGA-- -s simRat_chr6.simRat.chr6 271515 46 + 647215 AAACTATTGTTTAACTCAAGGCAAGAAGAGAATCTGGACATGGGCA - -a -s simMouse_chr6.simMouse.chr6 283062 29 + 636262 ATAGAGTGGCTTCCAATTTACCTGTAGGA -s Anc0.Anc0refChr5 80678 14 - 87904 ---------------ATGAGCCGGTCTGG -s Anc1.Anc1refChr8 37288 14 - 57822 ---------------ATGAGCCGGTCTGG -s Anc2.Anc2refChr14 226 14 - 7748 ---------------ATGAGATGTTCTGG -s mr.mrrefChr5 134097 29 + 294540 ATAGAGCGGCTTCCAATGTACCTGTAGGA -s simCow_chr6.simCow.chr6 247686 14 - 602619 ---------------ATGAGATGTAGTGG -s simDog_chr6.simDog.chr6 249762 14 - 593897 ---------------ATGAGATGTTCTGG -s simHuman_chr6.simHuman.chr6 415427 14 - 601863 ---------------ATGCGCCAGTCAGG -s simRat_chr6.simRat.chr6 271563 29 + 647215 ATAGAGCAGCTTCCAATGTACCTGGAAGA - -a -s simMouse_chr6.simMouse.chr6 283091 20 + 636262 GAGTTTTGGATGAACTGCCC -s Anc0.Anc0refChr5 80694 20 - 87904 GCAATTAGTGTAAACTACCC -s Anc1.Anc1refChr8 37304 20 - 57822 GCAATTAGTGTAAACTACCC -s Anc2.Anc2refChr14 242 20 - 7748 ACAATTAGTGTAAACTACCC -s mr.mrrefChr5 134126 20 + 294540 GAGTTTTGGATGAACTACCC -s simCow_chr6.simCow.chr6 247702 20 - 602619 ACAATTAGTGTAAACTACCC -s simDog_chr6.simDog.chr6 249781 19 - 593897 ACAATTACTGCAAA-TACCC -s simHuman_chr6.simHuman.chr6 415443 20 - 601863 GCAATTAGTGTAAACTACCC -s simRat_chr6.simRat.chr6 271592 20 + 647215 GAGTTTTGGATGAACTACCC - -a -s simMouse_chr6.simMouse.chr6 283111 66 + 636262 TCTGTACCTCTATGCCAAGCAGGAAGCAATCAGTGCACACAGTACGGAGTGTTCCTGGGTTGGGAT -s Anc0.Anc0refChr5 80716 66 - 87904 TATATACCTCTGGCGCAAAAAGGAGGCATTCAGTTTACATAGTAAGGAGTGTTCCCTAGTGTAAAC -s Anc1.Anc1refChr8 37326 66 - 57822 TATATACCTCTGGCGCAAAAAGGAGGCATTCAGTTTACATAGTAAGGAGTGTTCCCTAGTGTAAAC -s Anc2.Anc2refChr14 264 66 - 7748 TATACACCTCTGGCGCAAAAAGGAGGCATTCAGTTTACATAGTAAGGAGTAGTCCCTAGTGTAAAC -s mr.mrrefChr5 134146 66 + 294540 TATATACCTCTATGCCAAGAAGGAGGCAATCAGTGCACACAGTACGGAGTGTTCCTGAGTTGGAAT -s simCow_chr6.simCow.chr6 247724 66 - 602619 TATACACCTCTTGCCCAAAAAGGATGCATCAGGTTTACCTAATAAGGGGCAGTCCCTAGTGTGAAC -s simDog_chr6.simDog.chr6 249802 60 - 593897 TCTACACCTGTGGCGCAAAAAGGAGGCATTCAGTATAAATAGTAAGGAGTAGT------TGAATAA -s simHuman_chr6.simHuman.chr6 415465 65 - 601863 TATATACCTCTGGATCAA-AAGGAGGTGTTCAGTTTACATAGTGGGGAGTGTTCCCTACTGTAAAC -s simRat_chr6.simRat.chr6 271612 66 + 647215 TATATACCTCTATGCCATGAAGGAGGCAATCAGTGCACACAGTAAGAAGTGTTCCTGAGTTGGAAT - -a -s simMouse_chr6.simMouse.chr6 283177 10 + 636262 AGCTTCATGG -s Anc0.Anc0refChr5 80782 9 - 87904 CACT-CATGG -s Anc1.Anc1refChr8 37392 10 - 57822 CACTACATGG -s Anc2.Anc2refChr14 330 9 - 7748 CCCT-CATGG -s mr.mrrefChr5 134212 10 + 294540 AACTTCATGG -s simCow_chr6.simCow.chr6 247792 9 - 602619 CCCT-CATGG -s simDog_chr6.simDog.chr6 249862 9 - 593897 CCCT-CATAG -s simHuman_chr6.simHuman.chr6 415530 10 - 601863 CACCACATGG -s simRat_chr6.simRat.chr6 271678 10 + 647215 AACTTCATGG - -a -s simMouse_chr6.simMouse.chr6 283187 8 + 636262 ACAAATGG -s Anc0.Anc0refChr5 80792 8 - 87904 GCAGAAGC -s Anc1.Anc1refChr8 37403 8 - 57822 GCAGAAGC -s Anc2.Anc2refChr14 340 8 - 7748 GCAGAAGC -s mr.mrrefChr5 134222 8 + 294540 ACAGATGG -s simCow_chr6.simCow.chr6 247802 8 - 602619 GCATAACA -s simDog_chr6.simDog.chr6 249872 8 - 593897 GCTGAAGC -s simHuman_chr6.simHuman.chr6 415541 8 - 601863 GCAGAAGC -s simRat_chr6.simRat.chr6 271688 8 + 647215 ACAGATGG - -a -s simMouse_chr6.simMouse.chr6 283195 53 + 636262 ATAAATTAAAAAGGGGAGAGAGTAGAGTCAACCAGTTCTCATTCTCCCGGAGA -s Anc0.Anc0refChr5 80800 52 - 87904 ATAAATTGGGA-GAGGAGAGAGGGGAGACAACCAGTTCTTTTTCTCCTGAAAA -s Anc1.Anc1refChr8 37411 52 - 57822 ATAAATTGGGA-GAGGAGAGAGGGGAGACAACCAGTTCTTTTTCTCCTGAAAA -s Anc2.Anc2refChr14 348 52 - 7748 ACAAATCGAGA-GAGGAGAGAGGGGAGTCAACCAGTTCTTTTTCTACTGAAAA -s mr.mrrefChr5 134230 53 + 294540 ATAAATTAGGAAGGGGAGAGAGTAGAGACAACCAGTTCTTATTCTCCTGAAGA -s simCow_chr6.simCow.chr6 247810 52 - 602619 ACAAATCGAGG-GAGGAGGGAGGGGTGCCAAACAGTTCCTTGTTAACTAAAAA -s simDog_chr6.simDog.chr6 249883 52 - 593897 GCAAACCAAGA-GAGAAGAGAGGGGAGTCAGCCAGCTCTTTTTCTACTGAATA -s simHuman_chr6.simHuman.chr6 415549 52 - 601863 ATAACTTGGGA-GAAGAGAGAGGGGAGACAACCAGTACTTTTGCTCCTGAAAA -s simRat_chr6.simRat.chr6 271696 53 + 647215 ATAAATTAGGAAGGGGAGAGAGTAAAGACAACCAGTTCCTATTCTCCTGAAGA - -a -s simMouse_chr6.simMouse.chr6 283248 7 + 636262 CAGAATG -s Anc0.Anc0refChr5 80853 7 - 87904 TGGAATG -s Anc1.Anc1refChr8 37464 7 - 57822 TGGAATG -s Anc2.Anc2refChr14 401 7 - 7748 TGGAATG -s mr.mrrefChr5 134283 7 + 294540 CAGAATG -s simCow_chr6.simCow.chr6 247863 7 - 602619 TGGAGTA -s simDog_chr6.simDog.chr6 249936 7 - 593897 TGGAATG -s simHuman_chr6.simHuman.chr6 415602 7 - 601863 TGGAATG -s simRat_chr6.simRat.chr6 271749 7 + 647215 CAGAATG - -a -s simMouse_chr6.simMouse.chr6 283255 33 + 636262 TAGGCTAGACATAGTACCAGGTTAGGCAGGCAG -s Anc0.Anc0refChr5 80860 29 - 87904 TAGTCCAGAATCAGTACCAGGT----CAGGTAT -s Anc1.Anc1refChr8 37471 29 - 57822 TAGTCCAGAATCAGTACCAGGT----CAGGTAT -s Anc2.Anc2refChr14 408 29 - 7748 TAGTCCAGGATCAGTACCAGGT----CAGGTAT -s mr.mrrefChr5 134290 33 + 294540 TAGGCCAGAAATAGTACCAGGTTAGGCAGGCAT -s simCow_chr6.simCow.chr6 247871 29 - 602619 TAGTCCAGGATTAGTACCAGGT----CATGTAT -s simDog_chr6.simDog.chr6 249943 29 - 593897 TAGTCCAAGGTCAGTACTAGGT----CAGGTAT -s simHuman_chr6.simHuman.chr6 415609 29 - 601863 TATTCCAGAATCAGTACCAGGT----CAGGTAT -s simRat_chr6.simRat.chr6 271756 33 + 647215 TGAGCCAGGAGTAATACCAGGTTAGGCAGGGAT - -a -s simMouse_chr6.simMouse.chr6 283288 43 + 636262 TAGCTCAACATATTGGATCCAATGATTGATGTAGTATTCCATA -s Anc0.Anc0refChr5 80889 40 - 87904 TAACTCTACATATGGCATC---TGATCTGCCAGTTGATGTACA -s Anc1.Anc1refChr8 37500 40 - 57822 TAACTCTACATATGGCATC---TGATCTGCCAGTTGATGTACA -s Anc2.Anc2refChr14 437 40 - 7748 TAACTCTACATATGGCATC---TGATGTACCAGTTGATGTACA -s mr.mrrefChr5 134323 43 + 294540 TAGCTCAACATATTGCATCCAATGATCGGTGTGGTATTGCATA -s simCow_chr6.simCow.chr6 247917 40 - 602619 TAACCCAATATATGGCATC---TGATGTACATGTTGATGTATA -s simDog_chr6.simDog.chr6 249972 39 - 593897 TAG-TCTACATATGGCATC---TGATGTAGCAGTTGATGTACA -s simHuman_chr6.simHuman.chr6 415638 40 - 601863 TAACTCGACATATGGCATC---TGATCTGCTGGTTGATGTACA -s simRat_chr6.simRat.chr6 271789 43 + 647215 GAGCTCAACACATTGCATCCAATGATCGGTGTGGTATTGCATG - -a -s simMouse_chr6.simMouse.chr6 283331 15 + 636262 GGCTGCCCATTTTTG -s Anc0.Anc0refChr5 80929 15 - 87904 GGCTGACTTTTTTTG -s Anc1.Anc1refChr8 37540 15 - 57822 GGCTGACTTTTTTTG -s Anc2.Anc2refChr14 484 15 - 7748 GGCTGACTTTTTTTG -s mr.mrrefChr5 134366 15 + 294540 GGCTGCCCATTTTTG -s simCow_chr6.simCow.chr6 247964 15 - 602619 GGCTGGCTGTTTCTG -s simDog_chr6.simDog.chr6 250018 15 - 593897 GGCTGACTTTTTTTG -s simHuman_chr6.simHuman.chr6 415678 1 - 601863 A-------------- -s simRat_chr6.simRat.chr6 271832 15 + 647215 GGCATCCCATTTTTG - -a -s simMouse_chr6.simMouse.chr6 283346 5 + 636262 TCTTA -s Anc0.Anc0refChr5 80944 5 - 87904 TCATA -s Anc1.Anc1refChr8 37555 5 - 57822 TCATA -s Anc2.Anc2refChr14 499 5 - 7748 TCATA -s mr.mrrefChr5 134381 5 + 294540 TCATA -s simCow_chr6.simCow.chr6 247979 5 - 602619 TCTTA -s simDog_chr6.simDog.chr6 250033 5 - 593897 TCATA -s simHuman_chr6.simHuman.chr6 415679 5 - 601863 TCATA -s simRat_chr6.simRat.chr6 271848 5 + 647215 TCATA - -a -s simMouse_chr6.simMouse.chr6 283351 11 + 636262 CTTTTGTACCC -s Anc0.Anc0refChr5 80949 11 - 87904 TTTTGCTAACC -s Anc1.Anc1refChr8 37560 11 - 57822 TTTTGCTAACC -s Anc2.Anc2refChr14 511 11 - 7748 TTTTGCTAACC -s mr.mrrefChr5 134386 11 + 294540 CTTTGGTACCC -s simCow_chr6.simCow.chr6 247991 10 - 602619 TTTTGGT-ACC -s simDog_chr6.simDog.chr6 250045 11 - 593897 TTTTGCTAACC -s simHuman_chr6.simHuman.chr6 415684 11 - 601863 GACTGTTAACC -s simRat_chr6.simRat.chr6 271853 11 + 647215 TCTTGGTACCT - -a -s simMouse_chr6.simMouse.chr6 283362 17 + 636262 AGCAGTCATTATGGTTG -s Anc0.Anc0refChr5 80960 17 - 87904 TGCAGTCTTTATGGTTG -s Anc1.Anc1refChr8 37571 17 - 57822 TGCAGTCTTTATGGTTG -s Anc2.Anc2refChr14 526 17 - 7748 TGCAGTCTTTATGGTTG -s mr.mrrefChr5 134397 17 + 294540 AGCAGTCTTTATGGTTG -s simCow_chr6.simCow.chr6 248005 17 - 602619 TGCAGTTTCTATCGTTG -s simDog_chr6.simDog.chr6 250060 17 - 593897 TGCAGTCTTCATGGTCG -s simHuman_chr6.simHuman.chr6 415695 17 - 601863 TGCAGTCTTTATGGTTG -s simRat_chr6.simRat.chr6 271864 17 + 647215 AGCAGTCTTTATGGTTG - -a -s simMouse_chr6.simMouse.chr6 283379 72 + 636262 TCATGGGTTACCTTATATAGGAATGCCTGCAAGTGCCTGTGAGGATAGAAATTGACTGGAATGTCCACTCAA -s Anc0.Anc0refChr5 80978 70 - 87904 TCATAGGTCAACTTATATAAAAATGCCTGAAAATGCCAG--AGGGTAGAAATAGACTGGTACCCCTATCCAC -s Anc1.Anc1refChr8 37589 70 - 57822 TCATAGGTCAACTTATATAAAAATGCCTGAAAATGCCAG--AGGGTAGAAATAGACTGGTACCCCTATCCAC -s Anc2.Anc2refChr14 544 70 - 7748 TCATAGGTCAACATATGTAAAAATGCCTGAAAATGCCAG--TGGGCAGAAATAGACTGGTACCCCTATCCAC -s mr.mrrefChr5 134414 70 + 294540 TCATAGGTTACCTTATATAGGAATGCCTGAAAGTGCCTG--AGGATAGAAATAGACTGGAATGTCCACTCAA -s simCow_chr6.simCow.chr6 248023 69 - 602619 T-ATAGGTCAACATATCTTAAACTCCCTGAAAATGCCAA--GGGGAAGAAATTGACTGGTACCCCTATCCAC -s simDog_chr6.simDog.chr6 250078 68 - 593897 TCATAGGTGAACATATGTAAAAATGCCTGAAAATGGCCG--TAGGCAGAAATAGA--GGTACCCCTACCCAC -s simHuman_chr6.simHuman.chr6 415713 70 - 601863 CCGTAAGTCAACTTATATAAAAATAACTAAAAATGCCAG--AGGGTAGAAATAGACTAGTACCCCTATCCAC -s simRat_chr6.simRat.chr6 271881 70 + 647215 TCATAGGTTACCCTCTCTAGGAATGCCTGAAAGTGCCTG--AGGATAGAAATAGACTGGATTGTCCACTCAA - -a -s simMouse_chr6.simMouse.chr6 283451 10 + 636262 TGGCTAATAA -s Anc0.Anc0refChr5 81054 10 - 87904 GGCACATTAA -s Anc1.Anc1refChr8 37665 10 - 57822 GGCACATTAA -s Anc2.Anc2refChr14 620 10 - 7748 GGCACATTAA -s mr.mrrefChr5 134490 10 + 294540 TGGCTAATAA -s simCow_chr6.simCow.chr6 248098 10 - 602619 GATGCACTAA -s simDog_chr6.simDog.chr6 250152 10 - 593897 AGCACTTTAA -s simHuman_chr6.simHuman.chr6 415789 10 - 601863 GGCACAGCAG -s simRat_chr6.simRat.chr6 271957 10 + 647215 TGGCTAATAA - -a -s simMouse_chr6.simMouse.chr6 283461 14 + 636262 TCATAAAAGTCTGT -s Anc0.Anc0refChr5 81064 14 - 87904 TCATCAATGTTTGT -s Anc1.Anc1refChr8 37675 14 - 57822 TCATCAATGTTTGT -s Anc2.Anc2refChr14 630 14 - 7748 TCATCAATGTTTGT -s mr.mrrefChr5 134500 14 + 294540 TCATAAAAGTTTGT -s simCow_chr6.simCow.chr6 248110 14 - 602619 TCATCAACCCTTGT -s simDog_chr6.simDog.chr6 250162 14 - 593897 TCATCAATGTTTGT -s simHuman_chr6.simHuman.chr6 415800 14 - 601863 TCATCAATGTTTGT -s simRat_chr6.simRat.chr6 271967 14 + 647215 TCATAAGCATTTGT - -a -s simMouse_chr6.simMouse.chr6 283475 7 + 636262 AGAATTT -s Anc0.Anc0refChr5 81079 7 - 87904 AAAATTG -s Anc1.Anc1refChr8 37690 7 - 57822 AAAATTG -s Anc2.Anc2refChr14 645 7 - 7748 AAAATTG -s mr.mrrefChr5 134514 7 + 294540 AGAATTT -s simCow_chr6.simCow.chr6 248125 7 - 602619 AAAATTG -s simDog_chr6.simDog.chr6 250177 7 - 593897 AAAATAG -s simHuman_chr6.simHuman.chr6 415815 7 - 601863 AAAATTG -s simRat_chr6.simRat.chr6 271981 7 + 647215 AGAATTT - -a -s simMouse_chr6.simMouse.chr6 283482 234 + 636262 TGGATGGTGTTAAGTTAAGAAGTGCGTAGATCATATACATCATAACTACCAGACAGACTTAGCTCCCTTTCCTGTGGGGCTTATCAAGAACCCAGGATTACTTAACATCATAAGCCCAGCCTTAATTTTAAAAGCAAAGGGTTGACGATGAAAGCTCATAGAGTTATTAGTACCACTCATCTATCCATGTAAACATGCTGAAGCTTCATACCCAAGTGCAGCCTAGCAAATACT -s Anc0.Anc0refChr5 81233 31 - 87904 GAGATAGTGTTAAGTCAAGA------TAAACCATA-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CC -s Anc1.Anc1refChr8 37844 31 - 57822 GAGATAGTGTTAAGTCAAGA------TAAACCATA-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CC -s Anc2.Anc2refChr14 799 31 - 7748 GAGATAGTGTTAAGTCAAGA------TAATCCTTA-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CC -s mr.mrrefChr5 134641 37 + 294540 TAGATGGTGTTAAGTTAAGAAGTGCGTAAATCATA-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CT -s simCow_chr6.simCow.chr6 248271 31 - 602619 GAGATAGTGTTAAGTTAATA------TAATCCTTA-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GG -s simDog_chr6.simDog.chr6 250314 30 - 593897 AAGA-AGTCTTAAAGCAAGA------CAATTCTTA-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CC -s simHuman_chr6.simHuman.chr6 415970 31 - 601863 GAGGTAGTGTTAAGTCTAGA------TAAACCATA-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CC -s simRat_chr6.simRat.chr6 272110 37 + 647215 TAAATGGTGTTAAGTTAAGAAGTTCATAAATCATA-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CT - -a -s simMouse_chr6.simMouse.chr6 283716 2 + 636262 AG -s Anc0.Anc0refChr5 81272 2 - 87904 AG -s Anc1.Anc1refChr8 37883 2 - 57822 AG -s Anc2.Anc2refChr14 838 2 - 7748 AG -s mr.mrrefChr5 134678 2 + 294540 AG -s simCow_chr6.simCow.chr6 248310 2 - 602619 AG -s simDog_chr6.simDog.chr6 250352 2 - 593897 AG -s simHuman_chr6.simHuman.chr6 416009 2 - 601863 AG -s simRat_chr6.simRat.chr6 272147 2 + 647215 AG - -a -s simMouse_chr6.simMouse.chr6 283718 73 + 636262 CAAACCAAACCACTACAAAGATGCCAGTCTCTAATTTGACAATAGATGACATCATTAGTTTGGCTAAACATGA -s Anc0.Anc0refChr5 81479 51 - 87904 CAAATCAGAGCA-----------------AACATGATAGCTGCCA-----GTTATAAATCTACTTACAGATCA -s Anc1.Anc1refChr8 38091 51 - 57822 CAAATCAGAGCA-----------------AACATGATAGCTGCCA-----GTTATAAATCTACTTACAGATCA -s Anc2.Anc2refChr14 1056 51 - 7748 CAAATCAGAGCA-----------------AACACCATAGGTGCCA-----GTTGTAAATCTACTTACAGATCA -s mr.mrrefChr5 134868 71 + 294540 CAAACCAGACCACTACAAA--TGCCAGTCACTATGTTGGCTACAGATGACGTTATTAATTTGGCTAAAGATGA -s simCow_chr6.simCow.chr6 248508 35 - 602619 --AATCAGGGCA-----------------GACACCATAGGTGCCA-----AT--------------CAGATCA -s simDog_chr6.simDog.chr6 250635 50 - 593897 CAAAT-AAAGAA-----------------AACACCATTGGTGCCA-----GTTGTAAATCTACTTACAGATCA -s simHuman_chr6.simHuman.chr6 416217 51 - 601863 CAAATCAGAGCA-----------------AACATGATAGCTCCCA-----GTTATAAATCTACATACGGCTCA -s simRat_chr6.simRat.chr6 272343 71 + 647215 CAAACCAGGCCACTCCAAA--TGCTGGTCACTATGTTGGCTACAGATGACGTTACTAATTTGGCTAGAGATGA - -a -s simMouse_chr6.simMouse.chr6 283791 20 + 636262 CCTTAGCCATGGTCTGAGGC -s Anc0.Anc0refChr5 81531 20 - 87904 CCTGAGTCATAATCCAGGCT -s Anc1.Anc1refChr8 38143 20 - 57822 CCTGAGTCATAATCCAGGCT -s Anc2.Anc2refChr14 1108 20 - 7748 CCTGAGTCATAATCCAGGCT -s mr.mrrefChr5 134939 20 + 294540 CCTTAGTCATGATCTGAGCC -s simCow_chr6.simCow.chr6 248544 20 - 602619 CCTTAGCCATAATGCAGGCT -s simDog_chr6.simDog.chr6 250686 20 - 593897 CCTGAATTATAACCCAGGAT -s simHuman_chr6.simHuman.chr6 416269 20 - 601863 CCCCAGTCATAATCCAGGCT -s simRat_chr6.simRat.chr6 272414 20 + 647215 CCATAGTCATCATCTGAGCC - -a -s simMouse_chr6.simMouse.chr6 283811 54 + 636262 CTGAGCAGCTGGAATTGTGGGTATTCTTCATCTGTCCTCAAAAAATGGAATATT -s Anc0.Anc0refChr5 81564 51 - 87904 CTCAACAGCTGGAAACACGGCTTTACTTGATCAGCATTCAGAGAAT---CTGAC -s Anc1.Anc1refChr8 38176 51 - 57822 CTCAACAGCTGGAAACACGGCTTTACTTGATCAGCATTCAGAGAAT---CTGAC -s Anc2.Anc2refChr14 1141 51 - 7748 TTCAACACCTGGAAACACGGCTTTACTTGATCAGCATTCAGAGAAT---CTGAC -s mr.mrrefChr5 134959 54 + 294540 CTGAACAGCTGGAAATGTGGGTATTCTTCATCTGTCCTCAAAGAATGGAATGTT -s simCow_chr6.simCow.chr6 248577 51 - 602619 TTCAACAACTGGAAATAGGGCTTTACTTCATTAGCATTCAGAGTAT---CTGAC -s simDog_chr6.simDog.chr6 250719 51 - 593897 TTCAACACCTGGAAACACGGCTCTACTTGATCAGCCTTCAGAGAAC---CTGGC -s simHuman_chr6.simHuman.chr6 416302 51 - 601863 CTCAACAGTTGGAAACAAGGCTTTACTTTATCATCATTCAGAGAAT---CTGAC -s simRat_chr6.simRat.chr6 272434 54 + 647215 CTGAACAACTGGAAAAGTGGATATTCTGCCTCCGTTCTCTAAGAATGGAATGTT - -a -s simMouse_chr6.simMouse.chr6 283865 29 + 636262 TTGATGGGTTTACCTGATTGCTGCATATT -s Anc0.Anc0refChr5 81615 29 - 87904 TTTAGGGATTCCTCTGACTGTTGCCTATT -s Anc1.Anc1refChr8 38227 29 - 57822 TTTAGGGATTCCTCTGACTGTTGCCTATT -s Anc2.Anc2refChr14 1193 29 - 7748 TTTAGGGATTCCTCTGACTGTTGCCTATT -s mr.mrrefChr5 135013 29 + 294540 TTTATGGGTTTACCTGATTGCTGCATATT -s simCow_chr6.simCow.chr6 248629 29 - 602619 TCTGGGGATTCCTACAATTGTTGCCTTTT -s simDog_chr6.simDog.chr6 250771 29 - 593897 TTTAGGCATTCATCTGACTGTTGCCTACT -s simHuman_chr6.simHuman.chr6 416353 29 - 601863 TTTAGGGATTCCTCTGACTGTTGCCTATT -s simRat_chr6.simRat.chr6 272488 29 + 647215 TTTGTGGGTTTACCTGATTGCTGCATATT - -a -s simMouse_chr6.simMouse.chr6 283894 11 + 636262 GGAGACTGACC -s Anc0.Anc0refChr5 81645 11 - 87904 GGAGGCTGTCC -s Anc1.Anc1refChr8 38257 11 - 57822 GGAGGCTGTCC -s Anc2.Anc2refChr14 1223 11 - 7748 GGAGGCTGTCC -s mr.mrrefChr5 135043 11 + 294540 GGAGACTGACC -s simCow_chr6.simCow.chr6 248659 11 - 602619 GGAGGTAGTCC -s simDog_chr6.simDog.chr6 250801 11 - 593897 GGAGACTGTCC -s simHuman_chr6.simHuman.chr6 416386 11 - 601863 GAAGGCTGTCC -s simRat_chr6.simRat.chr6 272518 11 + 647215 GGAGACTGACC - -a -s simMouse_chr6.simMouse.chr6 283905 4 + 636262 TCTA -s Anc0.Anc0refChr5 81656 4 - 87904 TCTT -s Anc1.Anc1refChr8 38268 4 - 57822 TCTT -s Anc2.Anc2refChr14 1235 4 - 7748 TCTT -s mr.mrrefChr5 135054 4 + 294540 TCTA -s simCow_chr6.simCow.chr6 248671 4 - 602619 ACCA -s simDog_chr6.simDog.chr6 250813 4 - 593897 TCTT -s simHuman_chr6.simHuman.chr6 416397 4 - 601863 TCTT -s simRat_chr6.simRat.chr6 272529 4 + 647215 TCCA - -a -s simMouse_chr6.simMouse.chr6 283909 7 + 636262 AACTCTT -s Anc0.Anc0refChr5 81661 7 - 87904 AACTCTT -s Anc1.Anc1refChr8 38273 7 - 57822 AACTCTT -s Anc2.Anc2refChr14 1240 7 - 7748 AACTCCT -s mr.mrrefChr5 135058 7 + 294540 AACTCTT -s simCow_chr6.simCow.chr6 248676 7 - 602619 AACTCCT -s simDog_chr6.simDog.chr6 250818 7 - 593897 AACTCCT -s simHuman_chr6.simHuman.chr6 416402 7 - 601863 AACTCTT -s simRat_chr6.simRat.chr6 272533 7 + 647215 AACACTA - -a -s simMouse_chr6.simMouse.chr6 283916 36 + 636262 GTCCATCTTTATGTCTTGATTCACAGCATCTAGGAA -s Anc0.Anc0refChr5 81668 27 - 87904 GTAAGTTGTTATATCTTGAATCACAGT--------- -s Anc1.Anc1refChr8 38280 27 - 57822 GTAAGTTGTTATATCTTGAATCACAGT--------- -s Anc2.Anc2refChr14 1247 27 - 7748 GTAAGTTGTTATATCTTGAAACACAGT--------- -s mr.mrrefChr5 135065 35 + 294540 GTCCATCTTTATGTCTTGATTCACAGCATCTAGGA- -s simCow_chr6.simCow.chr6 248683 26 - 602619 GTAAGTTGTTAT-TCTTGAACCACAGT--------- -s simDog_chr6.simDog.chr6 250827 27 - 593897 GTCGGTTGTTAGATCTTGAAACACAGT--------- -s simHuman_chr6.simHuman.chr6 416409 27 - 601863 GTAAGTTGTTATATCTTAAATCACAGT--------- -s simRat_chr6.simRat.chr6 272540 35 + 647215 GTCCATCTTTATGTCTTGATTCATAGCATCTAGGA- - -a -s simMouse_chr6.simMouse.chr6 283952 16 + 636262 GTCTTGTCCTAATACA -s Anc0.Anc0refChr5 5181 16 + 87904 GTCCTGTCTTAACTTA -s Anc1.Anc1refChr8 18484 16 + 57822 GTCCTGTCTTAACTTA -s Anc2.Anc2refChr14 5364 16 + 7748 GTCCTGTCTTAACTTG -s mr.mrrefChr5 135100 16 + 294540 GTCTTGTCCTAATACA -s simCow_chr6.simCow.chr6 352651 15 + 602619 GTCCTG-CTTAACTTG -s simDog_chr6.simDog.chr6 341851 16 + 593897 GTCCTGTTTTAGCTAG -s simHuman_chr6.simHuman.chr6 184311 16 + 601863 GTCCTGTCTTAACTTA -s simRat_chr6.simRat.chr6 272575 16 + 647215 GTCTTGTCCTAATACA - -a -s simMouse_chr6.simMouse.chr6 283968 4 + 636262 ACAG -s Anc0.Anc0refChr5 5198 4 + 87904 ACAG -s Anc1.Anc1refChr8 18501 4 + 57822 ACAG -s Anc2.Anc2refChr14 5381 4 + 7748 ACAG -s mr.mrrefChr5 135116 4 + 294540 ACAG -s simCow_chr6.simCow.chr6 352667 4 + 602619 ACAG -s simDog_chr6.simDog.chr6 341868 4 + 593897 ACAG -s simHuman_chr6.simHuman.chr6 184328 4 + 601863 ACAG -s simRat_chr6.simRat.chr6 272591 4 + 647215 ACAG - -a -s simMouse_chr6.simMouse.chr6 283972 83 + 636262 TGTGACATGCCAGACTCAAATAATGCCTGCACTCCATACCTGATGCCTACACAGGGGAAAGCTTGATACTACACACAGGCACA -s Anc0.Anc0refChr5 5202 64 + 87904 AGC------CCAGACTCAAATAAAGGTTTGCTTTCATAGTTGCTGCCTGCTCAGGTGAGAGTT-------------TGGCACA -s Anc1.Anc1refChr8 18505 64 + 57822 AGC------CCAGACTCAAATAAAGGTTTGCTTTCATAGTTGCTGCCTGCTCAGGTGAGAGTT-------------TGGCACA -s Anc2.Anc2refChr14 5390 64 + 7748 ATC------CCAGACCTGAATAAATGTTTGCTTTCATGGTTGCTGCCTGCTCAGGTGAGAGTC-------------TGGCACA -s mr.mrrefChr5 135120 70 + 294540 TGTGACATGCCAGACTCAAATAATGCCTGCATTTCATAGCTGATGCCTACACAGGGGAAAGCT-------------AGGCACA -s simCow_chr6.simCow.chr6 352677 64 + 602619 ATA------CCAGTCCTGAACAAATGTTTGCTTCCATGGTTGCTGCCCACACAGGTGAGAATC-------------TGGCACA -s simDog_chr6.simDog.chr6 341877 64 + 593897 ATC------CCAGATCTGAATAACTGTTTGTTTTCATGCTTGCTGCCTGCTCAGGTGAGAGTC-------------TGGCACA -s simHuman_chr6.simHuman.chr6 184332 64 + 601863 AGC------CCAGACTCAAATAGAGATGTGCTTTTATAGTTGCTGCCTCAGGTGGTGAGAGTT-------------GGGCACA -s simRat_chr6.simRat.chr6 272595 57 + 647215 TGTGACATGCAAGACTTAAATAATGCCTGCTTTTCACAGCTGATGCCTTCACAGGGG-------------------------- - -a -s simMouse_chr6.simMouse.chr6 284055 122 + 636262 GGAATAGATGAGGGCTGGGATCTTAGAAACAGGATGGCAATGAATCCAAGATAATAAACTGTTATGAGATTATAGAGTAGTAGTTGTAGGAGGCTATTCAGGAGAATGAATTCGAAACAATG -s Anc0.Anc0refChr5 5270 56 + 87904 GGAATAGATGATGGCTTGGAGCTTAGAACCAAGGTG------------------------------------------------------------------AAAAGGAATTTGAGACAATG -s Anc1.Anc1refChr8 18573 56 + 57822 GGAATAGATGATGGCTTGGAGCTTAGAACCAAGGTG------------------------------------------------------------------AAAAGGAATTTGAGACAATG -s Anc2.Anc2refChr14 5458 56 + 7748 GGAACAAATGATGGCTTGGAGCTTGGAACCAAGGTG------------------------------------------------------------------AAAAGGAATCTAAGACAATG -s mr.mrrefChr5 135190 56 + 294540 GGAATAGATGAGGGCTGGGATCTTAGAAACAGGATG------------------------------------------------------------------AGAATGAATTCGAAACAATG -s simCow_chr6.simCow.chr6 352745 56 + 602619 GGAACAAATGATGGCCTGAAGTTTGGAACTGGCATG------------------------------------------------------------------AAAAGGAATCTAAGACAATT -s simDog_chr6.simDog.chr6 341945 55 + 593897 GGGACA-ATGGTGGCTTGGGGCTTGGAACCAAGGTG------------------------------------------------------------------AAAGGGAATCTAAGACCATG -s simHuman_chr6.simHuman.chr6 184400 56 + 601863 GGAGTAGATGATGGCTTGGAGCTTAGAACCAAGGTG------------------------------------------------------------------AAAAGGCGTTTGAGACAATG - -a -s simMouse_chr6.simMouse.chr6 284177 32 + 636262 TAATGAGTTTAAGGAAGAATAGTCTCTTATCA -s Anc0.Anc0refChr5 5326 30 + 87904 AAA-GAATTTAGGGAAAAATAGTCTCTTC-CA -s Anc1.Anc1refChr8 18629 30 + 57822 AAA-GAATTTAGGGAAAAATAGTCTCTTC-CA -s Anc2.Anc2refChr14 5514 30 + 7748 AAA-GAATTTAGGGAAAAATAGTCTCTTC-CA -s mr.mrrefChr5 135246 30 + 294540 TAA-GAGTTTAAGGAAGAATAGTCTCTTA-CA -s simCow_chr6.simCow.chr6 352801 30 + 602619 CAA-GAATTTATGGAAAAATAGTCTCTTA-TA -s simDog_chr6.simDog.chr6 342001 30 + 593897 AAA-GACTTTAGGGAAAAATAGTCTCTTC-CA -s simHuman_chr6.simHuman.chr6 184456 30 + 601863 AAA-GAATTTAGGGAATAATAGTCTCTTG-CA - -a -s simMouse_chr6.simMouse.chr6 284209 28 + 636262 GTACCATTGTATCTGTGGTTCCTCTGTG -s Anc0.Anc0refChr5 5356 16 + 87904 GTACCCCTGCTTCT------------TG -s Anc1.Anc1refChr8 18659 16 + 57822 GTACCCCTGCTTCT------------TG -s Anc2.Anc2refChr14 5544 16 + 7748 GTACCCCTGCTTCT------------TT -s mr.mrrefChr5 135276 16 + 294540 GTACCATTGTATCT------------TG -s simCow_chr6.simCow.chr6 352832 15 + 602619 GTACCCCTGTTTCT------------T- -s simDog_chr6.simDog.chr6 342088 16 + 593897 GTAGCCCTGCTCCT------------TT -s simHuman_chr6.simHuman.chr6 184486 16 + 601863 GTACCTCTGCTTCT------------TG - -a -s simMouse_chr6.simMouse.chr6 284237 40 + 636262 TGGCTGAAGTAACTTGCACAGTTAATATGGTAAAGGATGC -s Anc0.Anc0refChr5 5372 39 + 87904 TGGGTGTAGTAACTTGCACAGTTA-CATAATAGAGTATGC -s Anc1.Anc1refChr8 18675 39 + 57822 TGGGTGTAGTAACTTGCACAGTTA-CATAATAGAGTATGC -s Anc2.Anc2refChr14 5573 39 + 7748 TGGGTGTAGTAACCTGCACAGTGA-CATAATAGAGTATGC -s mr.mrrefChr5 135292 40 + 294540 TGGCTGAAGTAACTTGCACAGTTAACATGGTAAAGGATGC -s simCow_chr6.simCow.chr6 352860 39 + 602619 TGGGTTTAGTAACCTGCACAGTGA-CATAATAGGGTATAC -s simDog_chr6.simDog.chr6 342149 38 + 593897 TGGGTGTAGTAACCTGCACG-TGA-CATGATAGAGTATGC -s simHuman_chr6.simHuman.chr6 184502 39 + 601863 TGGGTGTAGTAACTTGTACAATTA-CATAATACAGTATGC -s simRat_chr6.simRat.chr6 272652 18 + 647215 ----------------------CAACATGGTAAAGAATGC - -a -s simMouse_chr6.simMouse.chr6 284277 12 + 636262 CACCTACAGGCA -s Anc0.Anc0refChr5 5430 12 + 87904 CACCCCAAGACA -s Anc1.Anc1refChr8 18733 12 + 57822 CACCCCAAGACA -s Anc2.Anc2refChr14 5631 12 + 7748 CACCCCATGATG -s mr.mrrefChr5 135332 12 + 294540 CACCTACAGGCA -s simCow_chr6.simCow.chr6 352918 11 + 602619 CACTGTATGG-G -s simDog_chr6.simDog.chr6 342211 12 + 593897 CACCCCATGATG -s simHuman_chr6.simHuman.chr6 184560 12 + 601863 CGCCCCAAGACA -s simRat_chr6.simRat.chr6 272670 12 + 647215 CACCTACAGGCA - -a -s simMouse_chr6.simMouse.chr6 284289 120 + 636262 TTAAGCTAACCCTAACATCTGAGGCACTATCTGAGAATTGTGTAATGGAGGGAGAGTAATCATGTCAAATTGGAGATTGGTTGGAATATGCAAGAAGCTCTGTCTTCAGAGATTGGTTAG -s Anc0.Anc0refChr5 5442 84 + 87904 TTAACCTGGTGCTAGCATCTGAGGCACTACCCTAGAACTGTGTAAGAGAGGAAGGGCAATCATGTCAAGT------------------------------------CAGAGATTAGTTGG -s Anc1.Anc1refChr8 18745 84 + 57822 TTAACCTGGTGCTAGCATCTGAGGCACTACCCTAGAACTGTGTAAGAGAGGAAGGGCAATCATGTCAAGT------------------------------------CAGAGATTAGTTGG -s Anc2.Anc2refChr14 5646 84 + 7748 TTAACCTGGTGCTAGCATCTGAGGCACTACCCTAGAACTGTGTAAGAGAGGATGGGCAATCATGTCAAGT------------------------------------CAGAGATTAGTTGG -s mr.mrrefChr5 135344 120 + 294540 TTAAGCTAATCCTAACATCTGAGGCACTATCTGAGAACTGTGTAATGGAGGGAGAGTAATCATGTCAAGTTGGAGATTAGTTGGAATATACAAGAAGCTCTGTCTTCAGAGATTGGTTAG -s simCow_chr6.simCow.chr6 352932 84 + 602619 TTAACCTGCGGCTAGCATCTGGGGCACTACCCTAGAACTGTGTAAGAGAGGATGGGCAATCATGTCAAGT------------------------------------CAGAGATTAGCTGG -s simDog_chr6.simDog.chr6 342226 83 + 593897 TAAACCTGGTGATAGCATCTGAGGCATTACCCTAG-ACTTTGTAGGAGAGCATGAGCGATGATGTCAAGT------------------------------------CAGAGATTTGTTGG -s simHuman_chr6.simHuman.chr6 184572 83 + 601863 TTAACCTG-TGCTAGCATCTGAGGCACTACCCTAGGACTGTCTAAAAGAGGAAGGGCAATCATGTCAAGT------------------------------------CAGAGACTAGTTTG -s simRat_chr6.simRat.chr6 272682 120 + 647215 TTAAACTAATCATAATGTCTGAGGCACTATCTCAGAACTGTGTAATGGAGAGGGAGTAATCATGTCAAGTTGGAGGTTAGTTGGAATACACAAGAAGCTCTGTCTTCAGAGATTGGGTAA - -a -s simMouse_chr6.simMouse.chr6 284409 22 + 636262 TATATACAAGAATCTCTCTCTT -s Anc0.Anc0refChr5 5526 22 + 87904 TATGTACAGGGAACTCTCTCTT -s Anc1.Anc1refChr8 18829 22 + 57822 TATGTACAGGGAACTCTCTCTT -s Anc2.Anc2refChr14 5730 22 + 7748 TATGCACAGGGAACTCTTTCTT -s mr.mrrefChr5 135464 22 + 294540 TATATACAAGAATCTCTCTCTT -s simCow_chr6.simCow.chr6 353016 22 + 602619 TATGCACAGGGAACTCTTTGTT -s simDog_chr6.simDog.chr6 342312 22 + 593897 TGTGCACAGGGAATGCTTTCTT -s simHuman_chr6.simHuman.chr6 184655 22 + 601863 TATGTACAGGGAACTGTCTCTT -s simRat_chr6.simRat.chr6 272802 22 + 647215 TATATACAAGAATCCTTCTCTT - -a -s simMouse_chr6.simMouse.chr6 284431 46 + 636262 TTTCCGGTACATGTTGCTTGTGGAACCTTTGCCCCAACAGGAGTCA -s Anc0.Anc0refChr5 5552 46 + 87904 TTTCTGGTACATGTTGCTTACAATACCTTAGACCTGACAGGAGTCA -s Anc1.Anc1refChr8 18855 46 + 57822 TTTCTGGTACATGTTGCTTACAATACCTTAGACCTGACAGGAGTCA -s Anc2.Anc2refChr14 5756 46 + 7748 TTTCTGGTACATGTTGCTTGCAATACCTTAGACCTGACAGGTGTCA -s mr.mrrefChr5 135490 46 + 294540 TTTCTGGTACATGTTGCTTACAAAACCTTTGCCCTGACAGGAGTCA -s simCow_chr6.simCow.chr6 353042 46 + 602619 TTTCTGATATGTGTTGCTAGCGAAACCTTAAATCTGAGAAGTGTCA -s simDog_chr6.simDog.chr6 342338 46 + 593897 TTTCTGGTACATGTTGGTTGCAGTCCCTTAGACCTGACAGGTGTCA -s simHuman_chr6.simHuman.chr6 184681 46 + 601863 TTTCTGGTCCATGTTGCTCACAAGACCTTAGACCTGACAGGAGCCA -s simRat_chr6.simRat.chr6 272828 46 + 647215 TTTCTGGTACATGTTGCTTACAAAACCTTTGCCTTGACAGCAGTCT - -a -s simMouse_chr6.simMouse.chr6 284477 31 + 636262 AAAAAGGACCACTGGAGTACTACATGGTACT -s Anc0.Anc0refChr5 5598 29 + 87904 AAA--GGAGCACTAGAATCCTTCCCAAAAGG -s Anc1.Anc1refChr8 18901 29 + 57822 AAA--GGAGCACTAGAATCCTTCCCAAAAGG -s Anc2.Anc2refChr14 5802 29 + 7748 AAA--GGAGCACTAGAATCCTTCCCAAAAGG -s mr.mrrefChr5 135536 31 + 294540 AAAAAGGACCACTGGAATACTACATGGAAGT -s simCow_chr6.simCow.chr6 353133 29 + 602619 AAA--GGAGCACTAGGATCCTTCCCAAAAGG -s simDog_chr6.simDog.chr6 342384 29 + 593897 AAA--GGAGCACAAGAATCCCACCCAAAAGG -s simHuman_chr6.simHuman.chr6 184727 29 + 601863 AAA--GGAGCTCTAGAATCCTTCCCAAAAGG -s simRat_chr6.simRat.chr6 272874 31 + 647215 ATAAAGAACCACTGGAATATTACTTGGAAGT - -a -s simMouse_chr6.simMouse.chr6 284508 54 + 636262 TTTCAGGATTGCAATATACTACTATCAGACAGATGGGAAGAGTGGGGGTTTGAT -s Anc0.Anc0refChr5 5627 54 + 87904 TGTCAGGATTGCAACATACTGCCATCTGACAGATGTAAAGAATGGGGGTTTGAA -s Anc1.Anc1refChr8 18930 54 + 57822 TGTCAGGATTGCAACATACTGCCATCTGACAGATGTAAAGAATGGGGGTTTGAA -s Anc2.Anc2refChr14 5832 54 + 7748 TGTCAGGATTGCAACATACTGCCATCTGGCAGATGTAAAGAGTGGGGGTTTGAA -s mr.mrrefChr5 135567 54 + 294540 TTTCAGGATTGCAATATACTACTATCAGACAGATGGAAAGAATGGGGGTTTGAT -s simCow_chr6.simCow.chr6 353163 44 + 602619 TGTCAGGATTGCAACATACTACCATCTGGCAGATGTAAAGAGTG---------- -s simDog_chr6.simDog.chr6 342414 36 + 593897 TGTCAGGATTGCGACATACTG------------------GAGTGGGGGTTTGAA -s simHuman_chr6.simHuman.chr6 184756 54 + 601863 TGTCAGGATTGTAGAATACTGCCATTTGATAGATGTAGAGAATGGGGGTTTGAA -s simRat_chr6.simRat.chr6 272905 52 + 647215 TTTTAGAATTGCAATATATTACTACCAGAAAGATGGAAAGGAGGGG--TATGAT - -a -s simMouse_chr6.simMouse.chr6 284562 1 + 636262 G -s Anc0.Anc0refChr5 5741 1 + 87904 A -s Anc1.Anc1refChr8 19044 1 + 57822 A -s Anc2.Anc2refChr14 5947 1 + 7748 A -s mr.mrrefChr5 135621 1 + 294540 G -s simCow_chr6.simCow.chr6 353261 1 + 602619 A -s simDog_chr6.simDog.chr6 342515 1 + 593897 A -s simRat_chr6.simRat.chr6 272957 1 + 647215 G - -a -s simMouse_chr6.simMouse.chr6 284563 26 + 636262 CTTGGGTAATTTGCATGTGCTTTACC -s Anc0.Anc0refChr5 5742 26 + 87904 CTTGGGTACTTTGGGTATGTTTTGTA -s Anc1.Anc1refChr8 19045 26 + 57822 CTTGGGTACTTTGGGTATGTTTTGTA -s Anc2.Anc2refChr14 5959 26 + 7748 CTTGGGTACTTTGGGTATGTTTTGTA -s mr.mrrefChr5 135622 26 + 294540 CTTGGGTACTTTGCATGTGCTTTACC -s simCow_chr6.simCow.chr6 353273 26 + 602619 CTTTGGTACTGTGGATGTGTCTTGTA -s simDog_chr6.simDog.chr6 342527 26 + 593897 CTTAGGCTCTTTGGTTATGTTTCGTA -s simRat_chr6.simRat.chr6 272958 26 + 647215 CTAGGGTACTTTGTGTCTACTTTGCA - -a -s simMouse_chr6.simMouse.chr6 284589 9 + 636262 TGCCGCTGT -s Anc0.Anc0refChr5 5774 9 + 87904 TGTCGTTTC -s Anc1.Anc1refChr8 19077 9 + 57822 TGTCGTTTC -s Anc2.Anc2refChr14 5992 9 + 7748 TGTCATTTC -s mr.mrrefChr5 135648 9 + 294540 TGCCGCTGT -s simCow_chr6.simCow.chr6 353308 9 + 602619 TGTCATTTC -s simDog_chr6.simDog.chr6 342560 9 + 593897 TGTCATTTC -s simHuman_chr6.simHuman.chr6 184876 9 + 601863 TATGGAATC -s simRat_chr6.simRat.chr6 273000 9 + 647215 TGCCACTGT - -a -s simMouse_chr6.simMouse.chr6 284598 42 + 636262 AGTAGTCTTGCAAACTCAGTCACTGCAAGGTGAATCTCTGTG -s Anc0.Anc0refChr5 5783 42 + 87904 AGTAGACTGGCAACCTCAATCTCTGCAAGGACGATCTCCCTA -s Anc1.Anc1refChr8 19086 42 + 57822 AGTAGACTGGCAACCTCAATCTCTGCAAGGACGATCTCCCTA -s Anc2.Anc2refChr14 6001 42 + 7748 ATTAGACTGGCAACCTCAATCTCTGCAAGAACGATCTCCCTG -s mr.mrrefChr5 135657 42 + 294540 AGTAGTCTTGCAAACTCAGTCACTGCAAGGTGAATCTCTGTA -s simCow_chr6.simCow.chr6 353317 42 + 602619 ATTAGATTGCCAGCCTCAAGCTCTACAGGAATGATCACCCTG -s simDog_chr6.simDog.chr6 342569 42 + 593897 ATTAGACTGGCAACCTCAATCTGTGCAAGAACGATCTCTCTG -s simHuman_chr6.simHuman.chr6 185008 42 + 601863 AGTAGCCTGGTCACCTCAAACTTTGCAAGGACCATCTCCCTA -s simRat_chr6.simRat.chr6 273009 42 + 647215 ATTAGTCTTGCAAACTCAGTCGCTGCAAGGTGAATCTCTGTA - -a -s simMouse_chr6.simMouse.chr6 284640 11 + 636262 CCCTTTCCAGC -s Anc0.Anc0refChr5 5825 9 + 87904 TCTTCCCC--T -s Anc1.Anc1refChr8 19128 11 + 57822 TCTTCCCCAGT -s Anc2.Anc2refChr14 6043 9 + 7748 TCTTCCCC--T -s mr.mrrefChr5 135699 11 + 294540 CCCTTTCCAGC -s simCow_chr6.simCow.chr6 353359 9 + 602619 TCTTCCCC--T -s simDog_chr6.simDog.chr6 342611 9 + 593897 TCTTCACC--T -s simHuman_chr6.simHuman.chr6 185050 11 + 601863 TCTTCCCCAGT -s simRat_chr6.simRat.chr6 273052 11 + 647215 CCCTTTACAGC - -a -s simMouse_chr6.simMouse.chr6 284651 20 + 636262 CATGAGTACCATTGCTATTA -s Anc0.Anc0refChr5 5836 20 + 87904 CAGTAGTACCACTTGTATTT -s Anc1.Anc1refChr8 19141 20 + 57822 CAGTAGTACCACTTGTATTT -s Anc2.Anc2refChr14 6054 20 + 7748 CAGTAATACCACTTGTATTT -s mr.mrrefChr5 135710 20 + 294540 CATGAGTACCATTGCTATTA -s simCow_chr6.simCow.chr6 353373 20 + 602619 AAGTAATATCACTAGTACTT -s simDog_chr6.simDog.chr6 342622 19 + 593897 T-GTAATACAACTTGTTTTA -s simHuman_chr6.simHuman.chr6 185063 20 + 601863 CAGTAGTACCACCTGTATCT -s simRat_chr6.simRat.chr6 273063 20 + 647215 CATGAGTACTATTGCTATTA - -a -s simMouse_chr6.simMouse.chr6 284671 2 + 636262 TA -s Anc0.Anc0refChr5 5856 2 + 87904 TA -s Anc1.Anc1refChr8 19161 2 + 57822 TA -s Anc2.Anc2refChr14 6074 2 + 7748 TA -s mr.mrrefChr5 135730 2 + 294540 TA -s simCow_chr6.simCow.chr6 353393 2 + 602619 TA -s simDog_chr6.simDog.chr6 342656 2 + 593897 TA -s simHuman_chr6.simHuman.chr6 185083 2 + 601863 TA -s simRat_chr6.simRat.chr6 273083 2 + 647215 TA - -a -s simMouse_chr6.simMouse.chr6 284673 10 + 636262 GGGCTTGCTG -s Anc0.Anc0refChr5 5858 10 + 87904 GAATTTACTG -s Anc1.Anc1refChr8 19163 10 + 57822 GAATTTACTG -s Anc2.Anc2refChr14 6076 10 + 7748 GAATTTACTG -s mr.mrrefChr5 135732 10 + 294540 GGGCTTGCTG -s simCow_chr6.simCow.chr6 353402 10 + 602619 GAATTTACTG -s simDog_chr6.simDog.chr6 342658 10 + 593897 GAATTTGCTG -s simHuman_chr6.simHuman.chr6 185085 10 + 601863 GAATTTAATG -s simRat_chr6.simRat.chr6 273085 10 + 647215 GGGCTTGCTG - -a -s simMouse_chr6.simMouse.chr6 284683 13 + 636262 CTAACTCTGTACT -s Anc0.Anc0refChr5 5869 13 + 87904 CTAACTTTGTCCC -s Anc1.Anc1refChr8 19174 13 + 57822 CTAACTTTGTCCC -s Anc2.Anc2refChr14 6087 13 + 7748 CTAACTTTGTCCA -s mr.mrrefChr5 135742 13 + 294540 CTAACTCTGTACC -s simCow_chr6.simCow.chr6 353413 13 + 602619 CTAACTTTGTGCA -s simDog_chr6.simDog.chr6 342669 13 + 593897 CTAACCTTGTTCA -s simHuman_chr6.simHuman.chr6 185096 13 + 601863 CTAACTTTGTCCC -s simRat_chr6.simRat.chr6 273095 13 + 647215 CTAGCTCTGTACC - -a -s simMouse_chr6.simMouse.chr6 284696 33 + 636262 TACATACTTGAACAGAGCTCATTTTGCAGCTGT -s Anc0.Anc0refChr5 5882 33 + 87904 CACTTACCCAGCCAGAACTCATCTTGCAATTGT -s Anc1.Anc1refChr8 19187 33 + 57822 CACTTACCCAGCCAGAACTCATCTTGCAATTGT -s Anc2.Anc2refChr14 6100 33 + 7748 CACTTACCCAGCCAGAACTCATCTTGCAATTGT -s mr.mrrefChr5 135755 33 + 294540 TACTTACTCGAACAGAGCTCATTTTGCAACTGT -s simCow_chr6.simCow.chr6 353426 30 + 602619 CACCTATCCAGCTAG---TCGTCTTCCAATTGT -s simDog_chr6.simDog.chr6 342682 33 + 593897 CATTTACCCAGCCAAAACTCATCTTGGAATTGT -s simHuman_chr6.simHuman.chr6 185109 33 + 601863 CACTTACCCACCCAGAATTCATCTTGCAATTGA -s simRat_chr6.simRat.chr6 273109 33 + 647215 TACTTTCTCGAGCAGAGCTCATTTTGCAACTTT - -a -s simMouse_chr6.simMouse.chr6 284729 6 + 636262 ACTTGA -s Anc0.Anc0refChr5 5915 6 + 87904 GCTTGA -s Anc1.Anc1refChr8 19220 6 + 57822 GCTTGA -s Anc2.Anc2refChr14 6134 6 + 7748 GCTTTA -s mr.mrrefChr5 135788 6 + 294540 GCTTGA -s simCow_chr6.simCow.chr6 353457 6 + 602619 GCTGTA -s simDog_chr6.simDog.chr6 342716 6 + 593897 GCTTTA -s simHuman_chr6.simHuman.chr6 185142 6 + 601863 GCTTGA -s simRat_chr6.simRat.chr6 273142 6 + 647215 GCTTGA - -a -s simMouse_chr6.simMouse.chr6 284735 23 + 636262 TCGACCTAGGTAGCCAGAGCTAG -s Anc0.Anc0refChr5 5921 23 + 87904 TCAACCTAAGTGGCCAGAGTCAG -s Anc1.Anc1refChr8 19226 23 + 57822 TCAACCTAAGTGGCCAGAGTCAG -s Anc2.Anc2refChr14 6140 23 + 7748 TCAACCTATGTGGCCAGAGTCAG -s mr.mrrefChr5 135794 23 + 294540 TCAACCTAAGTAGCCAGAGTCAG -s simCow_chr6.simCow.chr6 353464 23 + 602619 TTACCCTATGTGGCCAGAGTCAG -s simDog_chr6.simDog.chr6 342722 23 + 593897 TCAACCTATGTGGCTAGGGTCAG -s simHuman_chr6.simHuman.chr6 185148 23 + 601863 TCAACCTAAGTGGCAAGAGTCAG -s simRat_chr6.simRat.chr6 273148 23 + 647215 TCAACCTAAGTAGCCAGAGTCAG - -a -s simMouse_chr6.simMouse.chr6 284758 21 + 636262 ACTTGGGGTTGTTATAAAGGA -s Anc0.Anc0refChr5 5959 21 + 87904 ACTTGGGGTTGCTACAAAGGA -s Anc1.Anc1refChr8 19264 21 + 57822 ACTTGGGGTTGCTACAAAGGA -s Anc2.Anc2refChr14 6184 21 + 7748 ACTTGGGGTTGCTACAAAGGA -s mr.mrrefChr5 135832 21 + 294540 ACTTGGGGTTGCTATAAAGGA -s simCow_chr6.simCow.chr6 353508 21 + 602619 ACTTGGGGTGGCTATAACAGA -s simDog_chr6.simDog.chr6 342752 21 + 593897 GCTTAGGGTTGCTACAAAGGA -s simHuman_chr6.simHuman.chr6 185186 21 + 601863 ACTTGGGGTTTCTCCAAGGGC -s simRat_chr6.simRat.chr6 273192 21 + 647215 ACTTGGGTTCACTATAAAGGA - -a -s simMouse_chr6.simMouse.chr6 284779 74 + 636262 AGATAGTGACAGATTTACTGATTCCAGGTCTTGGCTAATTGAAACCTTATGATTGTGGATGTAAGTGACGGAAG -s Anc0.Anc0refChr5 5980 73 + 87904 AAATAGTGACAGACTTATTGAATC-ATGCTTTGGATTGTATGAACCTTATGATTGTGGATGTGAATGAAGGAAG -s Anc1.Anc1refChr8 19285 74 + 57822 AAATAGTGACAGACTTATTGAATCCATGCTTTGGATTGTATGAACCTTATGATTGTGGATGTGAATGAAGGAAG -s Anc2.Anc2refChr14 6207 73 + 7748 AAATAGTGACAGACTTATTTAATC-AGGCTTTGGATTGTATGAACCTTATGATTGTGGATGTGAATGAAAGAAG -s mr.mrrefChr5 135853 74 + 294540 AAATAGTGACAGATTTATTGATTCCATGTCTTGGATAATTGGAACCTTATGATTGTGGATGTAAGTGACGGAAG -s simCow_chr6.simCow.chr6 353530 67 + 602619 ------TGACAAACCTGTTTAATC-AGACTTTGGATTGTATGAATGTTATGATTGTGGCTAGGAATGAAGCACA -s simDog_chr6.simDog.chr6 342776 73 + 593897 AAATAGTGACAGATATATTTAATC-AGGCTTTGGATTATATGAACCTTATGATTGCGGATGTGAATGAAAGAAG -s simHuman_chr6.simHuman.chr6 185207 68 + 601863 TAATAC------ACTTATTGAATCCATGCTTCCGATTGTATGAACCTTATGATTGTGGATGTGAATAAGGGATA -s simRat_chr6.simRat.chr6 273213 74 + 647215 AAATAGTGACAGATTTATTGAGTCCATGTCTTGGAAAATTGGAACCTTATGATTGTGGATGTAAGTGAAAGAAG - -a -s simMouse_chr6.simMouse.chr6 284853 29 + 636262 GCCATGAACATACCTCTTCAGCAGTGTTT -s Anc0.Anc0refChr5 6053 29 + 87904 ACAATAAACATACCTCACCAGCATTGTTT -s Anc1.Anc1refChr8 19359 29 + 57822 ACAATAAACATACCTCACCAGCATTGTTT -s Anc2.Anc2refChr14 6318 29 + 7748 ACAATAAACATACCTCACCAGCATTGTTT -s mr.mrrefChr5 135927 29 + 294540 GCCATGAACATACCTCTCCAGCATTGTTT -s simCow_chr6.simCow.chr6 353745 29 + 602619 ATGATAAATATACCTCACCAGCATCATTA -s simDog_chr6.simDog.chr6 342887 29 + 593897 ACAATATGCATACCGAAACAGCATTGTTT -s simHuman_chr6.simHuman.chr6 185275 29 + 601863 ACAAATAACTTACCTCACTAGCATTGTTT -s simRat_chr6.simRat.chr6 273287 29 + 647215 GCCATGAACATACCTCTCCAGCATTGTCT - -a -s simMouse_chr6.simMouse.chr6 284882 29 + 636262 CTGAACATTTTAGGTGGCCTAGGGCAGTA -s Anc0.Anc0refChr5 6083 29 + 87904 CTGAACATTATGAGTGGCCCCAGGCTGGT -s Anc1.Anc1refChr8 19389 29 + 57822 CTGAACATTATGAGTGGCCCCAGGCTGGT -s Anc2.Anc2refChr14 6348 29 + 7748 CTGAACATTATAAGTGCCACCAGGCTGGT -s mr.mrrefChr5 135956 29 + 294540 CTGAACATTTTGGGTGGCCCAGGGCAGTG -s simCow_chr6.simCow.chr6 353775 29 + 602619 ATGAACATTATAAGTGTCAAAAGACTGGT -s simDog_chr6.simDog.chr6 342917 29 + 593897 CTGAACATTATAATTGCCACCAGGCTGGA -s simHuman_chr6.simHuman.chr6 185305 25 + 601863 CTGAACATTATGAG--GTC--AGGCCAGT -s simRat_chr6.simRat.chr6 273316 29 + 647215 CTGAACACTTTGGGTGGCCCAGGGCAGTG - -a -s simMouse_chr6.simMouse.chr6 284911 4 + 636262 AGAA -s Anc0.Anc0refChr5 6113 4 + 87904 AGAA -s Anc1.Anc1refChr8 19419 4 + 57822 AGAA -s Anc2.Anc2refChr14 6378 4 + 7748 AGCA -s mr.mrrefChr5 135986 4 + 294540 AGAA -s simCow_chr6.simCow.chr6 353805 4 + 602619 TGTA -s simDog_chr6.simDog.chr6 342947 4 + 593897 AGCA -s simHuman_chr6.simHuman.chr6 185331 4 + 601863 GGAA -s simRat_chr6.simRat.chr6 273346 4 + 647215 AGAT - -a -s simMouse_chr6.simMouse.chr6 284915 1 + 636262 T -s Anc0.Anc0refChr5 6145 1 + 87904 T -s Anc1.Anc1refChr8 19451 1 + 57822 T -s Anc2.Anc2refChr14 6410 1 + 7748 T -s mr.mrrefChr5 135990 1 + 294540 T -s simCow_chr6.simCow.chr6 353837 1 + 602619 T -s simDog_chr6.simDog.chr6 342979 1 + 593897 G -s simHuman_chr6.simHuman.chr6 185363 1 + 601863 T -s simRat_chr6.simRat.chr6 273350 1 + 647215 C - -a -s simMouse_chr6.simMouse.chr6 284916 4 + 636262 GTGT -s Anc0.Anc0refChr5 6146 4 + 87904 GTGT -s Anc1.Anc1refChr8 19452 4 + 57822 GTGT -s Anc2.Anc2refChr14 6411 4 + 7748 GTGT -s mr.mrrefChr5 135991 4 + 294540 GTGT -s simCow_chr6.simCow.chr6 353847 4 + 602619 ATGA -s simDog_chr6.simDog.chr6 342980 4 + 593897 GTGT -s simHuman_chr6.simHuman.chr6 185364 4 + 601863 GTGT -s simRat_chr6.simRat.chr6 273351 4 + 647215 GTGT - -a -s simMouse_chr6.simMouse.chr6 284920 53 + 636262 GATCATATCTTGAGGAAGTGCTTCCATGTTAGTGGAAGAAGATAGCCAATTAT -s Anc0.Anc0refChr5 6156 53 + 87904 GATCCGATCTTGCGAAAGTGCTTCCATGGTAGTAGAAGGAGACATCCATACAT -s Anc1.Anc1refChr8 19462 53 + 57822 GATCCGATCTTGCGAAAGTGCTTCCATGGTAGTAGAAGGAGACATCCATACAT -s Anc2.Anc2refChr14 6421 53 + 7748 GATCCGATCTTGCAAAAGTGCTTCCTTGGTAGTAGAAGGAGACATTCATACAT -s mr.mrrefChr5 135995 53 + 294540 GATCATATCTTGAGGAAGTGCTTCCATGTTAGTAGAAGAAGATAGCCAATTAT -s simCow_chr6.simCow.chr6 353857 53 + 602619 GATCATGCCTTGCAGAGGTGCTTTCCTGGTAGTAGAAGGAGACATTCATGCAT -s simDog_chr6.simDog.chr6 342990 53 + 593897 GATCCGATCTTGCAAAAATAGATCCTTGGTAGTAAAAGGAGATGCTAATACAT -s simHuman_chr6.simHuman.chr6 185374 53 + 601863 GATCGCATCTGGTGAAAGTGCTTCCATGGTAGTAGAGGGAAACATCCATACAC -s simRat_chr6.simRat.chr6 273355 53 + 647215 GATCATATCTTACAGAAGTGCTCCCATGCTAGTAAAAGAAGATAGCTGATTAT - -a -s simMouse_chr6.simMouse.chr6 284973 45 + 636262 TGCCAAAAACATACGGTTCCAGCTCAGGTCCTCTTTTTAAACAGA -s Anc0.Anc0refChr5 82734 45 - 87904 AGCCAAAAACATGCTATTTCACTGCAGGTTCTCTCTTTAGGCCAA -s Anc1.Anc1refChr8 39349 45 - 57822 AGCCAAAAACATGCTATTTCACTGCAGGTTCTCTCTTTAGGCCAA -s Anc2.Anc2refChr14 2395 45 - 7748 AGCCAGAAACAGGCTATTTCACTGCAGGCTCTCTCTTTAGGCCAA -s mr.mrrefChr5 136048 45 + 294540 TGCCAAAAACATACGGTTCCAGTTCAGGTCCTCTTTTTAAGCAGA -s simCow_chr6.simCow.chr6 249980 44 - 602619 ACCCATACACAGACTATTTCACTGCAGTCTCTCTCCTTAGA-CAA -s simDog_chr6.simDog.chr6 252057 45 - 593897 GGCCGGTAACGGGTTATCTCACTCCAGGCTCTCTTTTTAGGCAGA -s simHuman_chr6.simHuman.chr6 417569 45 - 601863 AGCTAAAAACATGCTATTTCAATGCAGGTTCCATCTATAGGCCAA -s simRat_chr6.simRat.chr6 273408 45 + 647215 TGCCACAAACATACAGTTCCTGTTCAGGCCCTTTTTTTAAGCAGA - -a -s simMouse_chr6.simMouse.chr6 285018 44 + 636262 TGGGGGGTGCCATAAACCATAAGTTATGTCAGAATGACAGTAAG -s Anc0.Anc0refChr5 82805 43 - 87904 TGGGGGGTGCCATGAACTGTAGGGTAAGTCAGA-TGACATTAGG -s Anc1.Anc1refChr8 39420 43 - 57822 TGGGGGGTGCCATGAACTGTAGGGTAAGTCAGA-TGACATTAGG -s Anc2.Anc2refChr14 2466 43 - 7748 TGGGGGGTGCCGTGAACTGTAGGGTGACTCAGA-TGACATTAGG -s mr.mrrefChr5 136093 44 + 294540 TGGGGGGTGCCATAAACCATAAGTTATGTCAGAATGACATTAAG -s simCow_chr6.simCow.chr6 250050 42 - 602619 TGGTGGGGGCTCTGAACAGAAGTCAGA-TCAGA-CGACATTAGG -s simDog_chr6.simDog.chr6 252128 43 - 593897 TGGGAGGTGCCGTGAGCTGTAGGGTGACCCAGA-TGACATTAGG -s simHuman_chr6.simHuman.chr6 417640 43 - 601863 TGGGGCATGCCATGAACTGTAGGGTAAGTCAGG-TCACTTTAGG -s simRat_chr6.simRat.chr6 273453 44 + 647215 TGGGAGTTGCTATAAACCATAAGTTATGTCAGACTGACATTAAG - -a -s simMouse_chr6.simMouse.chr6 285062 61 + 636262 GGCCCTAGGTTGACCTTTATTCTCCTCTAGAGAAACATTGACTTTTATTCTACTCTAAAGA -s Anc0.Anc0refChr5 82850 43 - 87904 GGCCCTAGGTTGACTTTTACTCTACTCTAGAGGA-CAATGTC-----------------GA -s Anc1.Anc1refChr8 39465 43 - 57822 GGCCCTAGGTTGACTTTTACTCTACTCTAGAGGA-CAATGTC-----------------GA -s Anc2.Anc2refChr14 2511 43 - 7748 AGCCCTAGGTTGACTTTTACTCTACTCTAGAGGA-CAATGTC-----------------GA -s mr.mrrefChr5 136137 60 + 294540 GGCCCTAGGTTGACTTTTATTCTCCTCTAGAGAA-CATTGACTTTTATTCTACTCTAAAGA -s simCow_chr6.simCow.chr6 250094 43 - 602619 AGCCCTGGGTTGACTTTTACTCTACTCCAGAGGA-CAACGAC-----------------AA -s simDog_chr6.simDog.chr6 252173 43 - 593897 AGCCCTAAGTTTACTTTTACTTTACTCTAGAGGG-CACTGTT-----------------GA -s simHuman_chr6.simHuman.chr6 417685 43 - 601863 GGCCCTAGGTTGGCTCTTACTCTACTCTAGAGGA-CAATGTC-----------------GA -s simRat_chr6.simRat.chr6 273497 48 + 647215 GGCCCTAGGTTGACTTTTGTTCT-------------ATTCACTTTTATTCTACTCTACGGA - -a -s simMouse_chr6.simMouse.chr6 285123 24 + 636262 GCTTCTTCCAAGGGCCACTGCTAT -s Anc0.Anc0refChr5 82893 24 - 87904 ACTTCTTCTAAGTGCCACTGCTAT -s Anc1.Anc1refChr8 39508 24 - 57822 ACTTCTTCTAAGTGCCACTGCTAT -s Anc2.Anc2refChr14 2554 24 - 7748 ACTCCTTCTAAGTGCCACTGCTAA -s mr.mrrefChr5 136197 24 + 294540 ACTTCTTCCAAGTGCCACTGCTAT -s simCow_chr6.simCow.chr6 250137 24 - 602619 ACTCCTTCAAAGTGCCACGGCTAG -s simDog_chr6.simDog.chr6 252216 24 - 593897 ACTCCTTCTAAGTGGCACTGATAA -s simHuman_chr6.simHuman.chr6 417728 24 - 601863 ACTTCTTCTAACTGCCACTGCTAT -s simRat_chr6.simRat.chr6 273550 24 + 647215 ACTTCTTCCTAGTGCCACTGCAAT - -a -s simMouse_chr6.simMouse.chr6 285147 48 + 636262 TAGCTAGTGCCTTACCTTGAGATTGCCAGAACATCAGTCTACACTCAC -s Anc0.Anc0refChr5 82936 48 - 87904 CAGCAAGTGCCTTATCTTGTAATTGCTAGAACATCAGAGTACACTCAC -s Anc1.Anc1refChr8 39551 48 - 57822 CAGCAAGTGCCTTATCTTGTAATTGCTAGAACATCAGAGTACACTCAC -s Anc2.Anc2refChr14 2597 48 - 7748 CAGCAAGTGCCTTATCTTGTAGTTGCTAGAACATCAGAGTACACTCAC -s mr.mrrefChr5 136221 48 + 294540 CAGCTAGTGCCTTACCTTGTGATTGCCAGAACATCAGTCTACACTCAC -s simCow_chr6.simCow.chr6 250173 48 - 602619 CGACAAGTGCCTTATCTTGTGGGTGCTAGACCATCAGAACACAGTAAC -s simDog_chr6.simDog.chr6 252259 48 - 593897 CAGCAAGTGCCTTCACTTGTAGTTGCCAGAACATCAGTGTTCACCCAC -s simHuman_chr6.simHuman.chr6 417771 48 - 601863 CAGCAACGGTCTTATCTTGTAATTGCTAAAATATCAGAGTACACTTGT -s simRat_chr6.simRat.chr6 273574 45 + 647215 CAGCTAGTGCCTTACTTTGTGACTGCCAGAACATCTGTCT---CTCAC - -a -s simMouse_chr6.simMouse.chr6 285195 27 + 636262 AGAATGTCTCCTGTAGCCAAATTAACA -s Anc0.Anc0refChr5 82984 27 - 87904 AGAATGCCTCTTGCAAACAAATTAAGA -s Anc1.Anc1refChr8 39599 27 - 57822 AGAATGCCTCTTGCAAACAAATTAAGA -s Anc2.Anc2refChr14 2646 27 - 7748 AGGATGCCTATTGCAAACAAATTAAGA -s mr.mrrefChr5 136269 27 + 294540 AGAATGTCTCCTGTAACCAAATTAACA -s simCow_chr6.simCow.chr6 250222 24 - 602619 ATGATGTCT-TTGCGAACAAATTAA-- -s simDog_chr6.simDog.chr6 252308 27 - 593897 AGGATGCCCACTACAGACTAGTTAAGA -s simHuman_chr6.simHuman.chr6 417819 25 - 601863 CAA--GACTCTTGCAAACAAACTAAGA -s simRat_chr6.simRat.chr6 273619 27 + 647215 ACAATGTCTCCTGTAACTAAATTAACA - -a -s simMouse_chr6.simMouse.chr6 285222 1 + 636262 A -s Anc0.Anc0refChr5 83011 1 - 87904 A -s Anc1.Anc1refChr8 39626 1 - 57822 A -s Anc2.Anc2refChr14 2673 1 - 7748 C -s mr.mrrefChr5 136296 1 + 294540 A -s simDog_chr6.simDog.chr6 252335 1 - 593897 C -s simHuman_chr6.simHuman.chr6 417856 1 - 601863 A -s simRat_chr6.simRat.chr6 273646 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 285223 11 + 636262 AACTAACCTTA -s Anc0.Anc0refChr5 83012 10 - 87904 AGTTAACATT- -s Anc1.Anc1refChr8 39627 11 - 57822 AGTTAACATTA -s Anc2.Anc2refChr14 2675 10 - 7748 AGTCAACATT- -s mr.mrrefChr5 136297 11 + 294540 AATTAACCTTA -s simCow_chr6.simCow.chr6 250246 1 - 602619 ---------T- -s simDog_chr6.simDog.chr6 252337 10 - 593897 AGTCAACATT- -s simHuman_chr6.simHuman.chr6 417857 11 - 601863 AGTTGGCAATA -s simRat_chr6.simRat.chr6 273647 11 + 647215 AATTAACCTTA - -a -s simMouse_chr6.simMouse.chr6 285234 63 + 636262 CTGAAGGTCCTTGGTCTCTTTTATGTGTTTAACATGCAGGTAACAACTTGTAAGCTTACAACT -s Anc0.Anc0refChr5 83032 62 - 87904 CTGAGGGTAATTAACCTCTTCTATGTATTCAAGATACAATTA-TAACTAGTTAGACTTCAATT -s Anc1.Anc1refChr8 39653 63 - 57822 CTGAGGGTAATTAACCTCTTCTATGTATTCAAGATACAATTACTAACTAGTTAGACTTCAATT -s Anc2.Anc2refChr14 2695 62 - 7748 CTGAGGGTAATTAACCTCTCCTATGTATTCAAGATACAACTA-TAACTAATTGGACTTCAATC -s mr.mrrefChr5 136323 63 + 294540 CTGAAGGTCCTTAGTCTCTTTTATGTGTTTAACATGCAGTTAACAACTTGTTAGCTTACAATT -s simCow_chr6.simCow.chr6 250257 37 - 602619 CTGAGGGT-CCTAGCCTCTCCCATGTATGCAAGGTTCA------------------------- -s simDog_chr6.simDog.chr6 252357 62 - 593897 CTGAGAGGAATTAACCACTCCTATGTATTAAAAATATGACTA-TAACTAATTGGACTTCAATC -s simHuman_chr6.simHuman.chr6 417893 56 - 601863 CTGAGGGTAATTAACCTCTTGT-------CAAGATACATTTACAAACTGGTTAGACCTCAATT -s simRat_chr6.simRat.chr6 273673 61 + 647215 CTGAAGGTCCTTAGTCTGTTTTATGCGTTTAACATGCAATTAACAGCTTGTTA--TTACAATT - -a -s simMouse_chr6.simMouse.chr6 285297 68 + 636262 GTTGGATACAATGATATTGCCAATGTAACCCATTCAAGTCGTATAATTTGTTGTCTCATCAGCCAACT -s Anc0.Anc0refChr5 83094 68 - 87904 GTTGGACTCAATAATACCTCACGTAAAACCCTTTCAGGTCATATATCTTGTTTGGTCATCAGCCAGGT -s Anc1.Anc1refChr8 39716 68 - 57822 GTTGGACTCAATAATACCTCACGTAAAACCCTTTCAGGTCATATATCTTGTTTGGTCATCAGCCAGGT -s Anc2.Anc2refChr14 2757 68 - 7748 GCAGGTATAGAAAATACCTCACATAAAACCCTTTTAGGTCATATATCTTGTTTGGTTATCAGCCAGGT -s mr.mrrefChr5 136386 68 + 294540 GTTGGACACAATAATATTGCCAGTGTAACCCATTCAAGTCATATAATTTGTTGTCTCATCAGCCAACT -s simCow_chr6.simCow.chr6 250294 44 - 602619 ------------------------GAAACCCTCTTAGGTTATATAGTTTGTTTGGTTACCAGCCAGGT -s simDog_chr6.simDog.chr6 252420 68 - 593897 GCAGGTATAGAAAATACCTCACATAGAACCCTTTTATGTCGTATATCTTGTTTGGTTATCGGGCAGGT -s simHuman_chr6.simHuman.chr6 417949 68 - 601863 GTTGGACCCAATAATACCTTAGGTAAAGCCTTTTCAGGTCATATACATTGTTTGGTCATTAGCGAGGT -s simRat_chr6.simRat.chr6 273734 68 + 647215 GTTGGACACAACAATATTGCCAGTGTAACCCATTCAAGTCATATAGTTTGTTGTCTAATCAGCCAACT - -a -s simMouse_chr6.simMouse.chr6 285365 2 + 636262 AC -s Anc0.Anc0refChr5 83162 2 - 87904 AC -s Anc1.Anc1refChr8 39784 2 - 57822 AC -s Anc2.Anc2refChr14 2825 2 - 7748 AC -s mr.mrrefChr5 136454 2 + 294540 AC -s simCow_chr6.simCow.chr6 250338 2 - 602619 CA -s simDog_chr6.simDog.chr6 252488 2 - 593897 AC -s simHuman_chr6.simHuman.chr6 418017 2 - 601863 AT -s simRat_chr6.simRat.chr6 273803 2 + 647215 AC - -a -s simMouse_chr6.simMouse.chr6 285367 21 + 636262 TAGATGAACTGATGTAAGAAA -s Anc0.Anc0refChr5 83164 16 - 87904 TG-----ACTGGTATAAGAGA -s Anc1.Anc1refChr8 39786 16 - 57822 TG-----ACTGGTATAAGAGA -s Anc2.Anc2refChr14 2833 16 - 7748 TG-----ACTGGTATAAGAGA -s mr.mrrefChr5 136456 16 + 294540 TA-----ACTGATGTAAGAGA -s simCow_chr6.simCow.chr6 250346 16 - 602619 TG-----GCTGGTACACAAGA -s simDog_chr6.simDog.chr6 252498 16 - 593897 TG-----ACTGGTATAAGAGA -s simHuman_chr6.simHuman.chr6 418019 16 - 601863 GG-----ACTTGTATAAGAGA -s simRat_chr6.simRat.chr6 273805 16 + 647215 TA-----ACTGATGTAAGAGA - -a -s simMouse_chr6.simMouse.chr6 285388 41 + 636262 TTGACCATTCTGGCTAACTTGATGGTTTCAATCCGGGTAAG -s Anc0.Anc0refChr5 83180 41 - 87904 TTGACCATTCTAGCTAGCTCTATGGCTTCAATCTGAGTAGA -s Anc1.Anc1refChr8 39802 41 - 57822 TTGACCATTCTAGCTAGCTCTATGGCTTCAATCTGAGTAGA -s Anc2.Anc2refChr14 2849 41 - 7748 TTGACCATTTTAGCTAGCTCTATGGCTTGAATCTGAGTAGA -s mr.mrrefChr5 136472 41 + 294540 TTGACCATTCTAGCTAACTTGATGGTTTCAATCCGGGTAAG -s simCow_chr6.simCow.chr6 250362 41 - 602619 TTGACCATTTTTCCTAGCTCTATGGCTGAAATCTGAGCAGA -s simDog_chr6.simDog.chr6 252514 41 - 593897 TTGATCATTTTAGCTAAGTCTATGGCTTGAACCTGAGTAGA -s simHuman_chr6.simHuman.chr6 418035 41 - 601863 TTGACCACTCTAGCTAGCTCTACAGCTTCAGTCTGAATAGA -s simRat_chr6.simRat.chr6 273834 41 + 647215 CTGACCATTCTAGCTAACTTGATGGATTCAATCAGCGTAAG - -a -s simMouse_chr6.simMouse.chr6 285429 7 + 636262 GTAATAG -s Anc0.Anc0refChr5 83221 7 - 87904 GTCAAAG -s Anc1.Anc1refChr8 39843 7 - 57822 GTCAAAG -s Anc2.Anc2refChr14 2898 7 - 7748 GTCTAAG -s mr.mrrefChr5 136513 7 + 294540 GTCATAG -s simCow_chr6.simCow.chr6 250411 7 - 602619 GTCTAAG -s simDog_chr6.simDog.chr6 252563 7 - 593897 TTCTAAG -s simHuman_chr6.simHuman.chr6 418076 7 - 601863 GCCAGAG -s simRat_chr6.simRat.chr6 273875 7 + 647215 GTCATAG - -a -s simMouse_chr6.simMouse.chr6 285436 12 + 636262 GTCTACAGTAGT -s Anc0.Anc0refChr5 83228 12 - 87904 GTCAACAGTATT -s Anc1.Anc1refChr8 39850 12 - 57822 GTCAACAGTATT -s Anc2.Anc2refChr14 2928 12 - 7748 GTCAACAATATT -s mr.mrrefChr5 136520 12 + 294540 GTCAACAGTAGT -s simCow_chr6.simCow.chr6 250446 12 - 602619 GTCAACAATATT -s simDog_chr6.simDog.chr6 252594 12 - 593897 GTCAGCAATATT -s simHuman_chr6.simHuman.chr6 418083 12 - 601863 ATGAAGAGTATT -s simRat_chr6.simRat.chr6 273882 12 + 647215 GTCAACAGTACT - -a -s simMouse_chr6.simMouse.chr6 285448 75 + 636262 GGCTACAATGTATCTACTCCTCGTGATGGGAAATGCAGCTGAGAATGTTAGACGCAACCTAGCCCTAGAAATAAG -s Anc0.Anc0refChr5 83240 68 - 87904 GGCTACATAGTTTCTATTCCTCGTAGTGTGCAACACAAATGAGAA-GATGTACGCAACCTAG------AAATAAA -s Anc1.Anc1refChr8 39862 68 - 57822 GGCTACATAGTTTCTATTCCTCGTAGTGTGCAACACAAATGAGAA-GATGTACGCAACCTAG------AAATAAA -s Anc2.Anc2refChr14 2940 68 - 7748 GGCTACATAGTTTCTATTCCTTGTAGTGTGCCACACAAATGAGAA-CATGTATGCAACCTAG------GAATAAA -s mr.mrrefChr5 136532 75 + 294540 GGCTACAATGTATCTACTCCTCGTGGTGGGAAATGCAACTGAGAATGTTAGACGCAACCTAGCCCTAGAAATAAA -s simCow_chr6.simCow.chr6 250459 68 - 602619 GGCTACATAGTTTCTATCCCATATAGTGTGATACACAAATGCAAA-AATGTATGCAACCTAG------GTATAAA -s simDog_chr6.simDog.chr6 252606 68 - 593897 CGCTACATAGTTTCTATTCCTTGTAGTGTGCCACACAAATGAGAA-CAGGTATGCAACCTGA------GAATAAA -s simHuman_chr6.simHuman.chr6 418095 67 - 601863 GGCTACACAGTTCCTGTTCC-CGTAGTGTCTAACACAAATGAGAA-GATGTACACAATCTAG------AAATAAA -s simRat_chr6.simRat.chr6 273894 75 + 647215 AGCTACAATGTATCTACTCCTCGTGGTGGGAGATGCAACTGAGAATGTAAGATGCAACCTAGGCCTAAGAATAAA - -a -s simMouse_chr6.simMouse.chr6 285523 167 + 636262 TGGATGAATGAACGGGCAATCTAGAAGTTAACGGATGAACAAACGGACGAAATCATCTCACTATCACCAGGGGGAAACCAACATCCAAGTATCTGGAGTTTGGTAATTATGGAGACTTGCAGGGCCTTTTAGTAGTCTTACATCAAACTATTAGGAATAGTACAGGT -s Anc0.Anc0refChr5 83308 4 - 87904 TGAA------------------------------------------------------------------------------------------------------------------------------------------------------------------- -s Anc1.Anc1refChr8 39930 4 - 57822 TGAA------------------------------------------------------------------------------------------------------------------------------------------------------------------- -s Anc2.Anc2refChr14 3008 4 - 7748 TGAA------------------------------------------------------------------------------------------------------------------------------------------------------------------- -s mr.mrrefChr5 136607 164 + 294540 TGGATGAATGAACGGGCAATCTAGAAGTTAACGGATGAACAAACGGACGAAATCATCTCACTATCACCAGGGGG--ACCAACATCCAAGTATCTGGAGTTTGGTAATTATGGAGACTTGCAGGGCCTTTTAGTAGTCTTACATCAAACTATTAGGAAT-GTACAGGT -s simCow_chr6.simCow.chr6 250531 4 - 602619 TGAA------------------------------------------------------------------------------------------------------------------------------------------------------------------- -s simDog_chr6.simDog.chr6 252674 4 - 593897 TGTA------------------------------------------------------------------------------------------------------------------------------------------------------------------- -s simHuman_chr6.simHuman.chr6 418162 4 - 601863 TGAA------------------------------------------------------------------------------------------------------------------------------------------------------------------- -s simRat_chr6.simRat.chr6 273969 164 + 647215 TAGATGAGTAAACAGGCACTCTAGTAGTTAGTGGATGAACAAATGGACAAAATCTTCTGATGATGGACAGTGGG--ACCAACATTCAGGCATCTGGAGTATGGTAACTATGGACACTTGCAGGGCCTTTTAAATGTCCTATGTCGAGCTATTGGGAAT-GTACAGGT - -a -s simMouse_chr6.simMouse.chr6 285690 41 + 636262 ATCCAAAGGATGACAAGAGTAGACCAATACCTTTTAATTGT -s Anc0.Anc0refChr5 83312 13 - 87904 ----------------------------ACCTTCTGATGAT -s Anc1.Anc1refChr8 39934 13 - 57822 ----------------------------ACCTTCTGATGAT -s Anc2.Anc2refChr14 3012 13 - 7748 ----------------------------ACCTACTGATGAT -s mr.mrrefChr5 136771 41 + 294540 ATCCAAAGGATGACAAGAGTAGACCAATACCTTTTAATTGT -s simCow_chr6.simCow.chr6 250535 13 - 602619 ----------------------------ACCCACTGATGAT -s simDog_chr6.simDog.chr6 252678 10 - 593897 -------------------------------TACTAACAAT -s simHuman_chr6.simHuman.chr6 418166 13 - 601863 ----------------------------ACCTTCTGATGAT -s simRat_chr6.simRat.chr6 274144 41 + 647215 ATTCAAAGGATGGCAAGAGTAGACCAATACCTTTTAATCGT - -a -s simMouse_chr6.simMouse.chr6 285731 1 + 636262 C -s Anc0.Anc0refChr5 83415 1 - 87904 C -s Anc1.Anc1refChr8 40037 1 - 57822 C -s Anc2.Anc2refChr14 3178 1 - 7748 C -s mr.mrrefChr5 136812 1 + 294540 C -s simCow_chr6.simCow.chr6 250704 1 - 602619 G -s simDog_chr6.simDog.chr6 252841 1 - 593897 C -s simHuman_chr6.simHuman.chr6 418271 1 - 601863 T -s simRat_chr6.simRat.chr6 274185 1 + 647215 C - -a -s simMouse_chr6.simMouse.chr6 285732 71 + 636262 CTATGTCAAACTGTTGGGAATAGTACAGGTACAGTGCGCAGACCCAAAGGATGTCAAGAGTAGACCAATGC -s Anc0.Anc0refChr5 83416 34 - 87904 CTATGTCCGC-------------------------------------AGTATGACAAGAGTAAAAAAATGC -s Anc1.Anc1refChr8 40038 71 - 57822 CTATGTCCGCCGTTTCCAAATAACACATGCACATTACACAGATTCAAAGTATGACAAGAGTAAAAAAATGC -s Anc2.Anc2refChr14 3179 34 - 7748 CTATGTCCGC-------------------------------------AGTATGACAAGAGTAAAAAAATGC -s mr.mrrefChr5 136813 71 + 294540 CTATGTCAAACTGTTGGGAATAGTACAGGTACAGTGCGCAGACCCAAAGGATGTCAAGAGTAGACCAATGC -s simCow_chr6.simCow.chr6 250705 34 - 602619 ACAGGTCCAA-------------------------------------AGTATAACAATAGTAGAAAAATAC -s simDog_chr6.simDog.chr6 252842 34 - 593897 CTATGTCAGC-------------------------------------CTTATGACAAGAGTAAAAAAATGC -s simHuman_chr6.simHuman.chr6 418272 71 - 601863 CGATGTCCGCCGTTTCCAAATAACACATGCACATTACACAGATTCAAAGTATGATAAGAGCTAAAAAATGC -s simRat_chr6.simRat.chr6 274188 71 + 647215 CTATGTCAAACTGTTGGGAATAGTACAGGTACAATACACAGATCCAAAGGATAGTAAGAATAGACCAATGC - -a -s simMouse_chr6.simMouse.chr6 285803 13 + 636262 AATAGATTGCGTA -s Anc0.Anc0refChr5 83459 13 - 87904 GACAAACTATGCA -s Anc1.Anc1refChr8 40118 13 - 57822 GACAAACTATGCA -s Anc2.Anc2refChr14 3222 13 - 7748 GACAAACTATGCA -s mr.mrrefChr5 136884 13 + 294540 AATAGATTGCGTA -s simCow_chr6.simCow.chr6 250748 13 - 602619 GACAAACTATGCA -s simDog_chr6.simDog.chr6 252885 13 - 593897 GACGAACTATGCA -s simHuman_chr6.simHuman.chr6 418352 13 - 601863 GACAAACTATGCA -s simRat_chr6.simRat.chr6 274259 13 + 647215 AATAGACCACACA - -a -s simMouse_chr6.simMouse.chr6 285816 15 + 636262 GTTAGCAACAGGCAG -s Anc0.Anc0refChr5 83473 15 - 87904 GATGGCAGAAGGCAA -s Anc1.Anc1refChr8 40132 15 - 57822 GATGGCAGAAGGCAA -s Anc2.Anc2refChr14 3236 15 - 7748 GATGGCAGAAGGCTA -s mr.mrrefChr5 136897 15 + 294540 GTTAGCAACAGGCAG -s simCow_chr6.simCow.chr6 250762 14 - 602619 GATGGCAAAAGAC-A -s simDog_chr6.simDog.chr6 252899 15 - 593897 TAGAACAGAAGGCTA -s simHuman_chr6.simHuman.chr6 418366 15 - 601863 GATGGCAGAAAGCAA -s simRat_chr6.simRat.chr6 274272 15 + 647215 GATAGCAACTGGCAA - -a -s simMouse_chr6.simMouse.chr6 285831 5 + 636262 CTTGG -s Anc0.Anc0refChr5 83488 5 - 87904 CTTGA -s Anc1.Anc1refChr8 40147 5 - 57822 CTTGA -s Anc2.Anc2refChr14 3251 5 - 7748 TCTGA -s mr.mrrefChr5 136912 5 + 294540 CTTGG -s simCow_chr6.simCow.chr6 250776 5 - 602619 TCTGA -s simDog_chr6.simDog.chr6 252914 5 - 593897 TCTGA -s simHuman_chr6.simHuman.chr6 418930 5 - 601863 CTTGA -s simRat_chr6.simRat.chr6 274287 5 + 647215 CTTGG - -a -s simMouse_chr6.simMouse.chr6 285836 43 + 636262 GGCTAAGCTGCCCTGATGGATGGAAGGTTGTGTCATCCTGACC -s Anc0.Anc0refChr5 83493 38 - 87904 GGACATGA-----TGGTGATAGGAATATTGAGTCAGCCAGGAC -s Anc1.Anc1refChr8 40152 43 - 57822 GGACATGAGGCCCTGGTGATAGGAATATTGAGTCAGCCAGGAC -s Anc2.Anc2refChr14 3256 38 - 7748 GGACCTGA-----TAGTGATAGGTTTATTGAGCCAGCCAGGAC -s mr.mrrefChr5 136917 43 + 294540 GGCTAAGCTGCCCTGATGGATGGAAGGTTGTGTCATCCTGACC -s simCow_chr6.simCow.chr6 250781 38 - 602619 GGCCCTAA-----TGATATTAGAATTATTGAGCCAGCCAGTAC -s simDog_chr6.simDog.chr6 252919 38 - 593897 GGACCTGA-----TAGTGATAGGTTTATTGAGCCAGCCAGGAC -s simHuman_chr6.simHuman.chr6 418939 43 - 601863 GGTCATGAGGCCCTGGTGACAGGAACATTGAGTGCACCAGGAC -s simRat_chr6.simRat.chr6 274292 43 + 647215 GGCTAAGCTGCCCTGATGGATGGACTGTTACAGCAGCCTGACC - -a -s simMouse_chr6.simMouse.chr6 285879 13 + 636262 TTGTCTTCTGAAT -s Anc0.Anc0refChr5 83531 10 - 87904 TCCTCTGCTA--- -s Anc1.Anc1refChr8 40195 13 - 57822 TCCTCTGCTAAAT -s Anc2.Anc2refChr14 3294 10 - 7748 TCCACCGCTA--- -s mr.mrrefChr5 136960 13 + 294540 TTGTCTTCTGAAT -s simCow_chr6.simCow.chr6 250819 10 - 602619 TCAGCCACTA--- -s simDog_chr6.simDog.chr6 252957 10 - 593897 TCCACCGCTA--- -s simHuman_chr6.simHuman.chr6 418982 13 - 601863 ACATCTGCTCAAT -s simRat_chr6.simRat.chr6 274339 13 + 647215 TTGTCTTCTGAAT - -a -s simMouse_chr6.simMouse.chr6 285892 15 + 636262 CAGGCAATATATTAA -s Anc0.Anc0refChr5 83541 15 - 87904 CAGCCAAGATATTAA -s Anc1.Anc1refChr8 40208 15 - 57822 CAGCCAAGATATTAA -s Anc2.Anc2refChr14 3304 15 - 7748 CCGCCAAGGTATTGA -s mr.mrrefChr5 136973 15 + 294540 CAGGCAATATATTAA -s simCow_chr6.simCow.chr6 250832 15 - 602619 CTGCCAAGGTATAGA -s simDog_chr6.simDog.chr6 252967 15 - 593897 CCGCCAAGGTATTGA -s simHuman_chr6.simHuman.chr6 418995 15 - 601863 CAGCAAAGATATTAA -s simRat_chr6.simRat.chr6 274352 15 + 647215 CAGCCAATATATTAA - -a -s simMouse_chr6.simMouse.chr6 285907 24 + 636262 TTTTAATAGAAAGATTTTAAGGTC -s Anc0.Anc0refChr5 83562 24 - 87904 TTCAATTAGAAATGTTGTAAAGTT -s Anc1.Anc1refChr8 40229 24 - 57822 TTCAATTAGAAATGTTGTAAAGTT -s Anc2.Anc2refChr14 3325 24 - 7748 TTCAATTAGAAGTGTTGTAAAGTT -s mr.mrrefChr5 136988 24 + 294540 TTTTAATAGAAAGATTTTAAGGTC -s simCow_chr6.simCow.chr6 250853 24 - 602619 TTCCCCTAGAAGTGTTGTAAAGTT -s simDog_chr6.simDog.chr6 252988 24 - 593897 TTCAATTAGAAGTGTTGTAAAGTT -s simHuman_chr6.simHuman.chr6 419018 24 - 601863 TTCCCTTAGAAATGTTGTAAAGTT -s simRat_chr6.simRat.chr6 274367 24 + 647215 TATTCACAGAAAGATTATAAGGTC - -a -s simMouse_chr6.simMouse.chr6 285931 15 + 636262 AGGGGCATCTTATCT -s Anc0.Anc0refChr5 83586 15 - 87904 AGGAGTATTTTACTT -s Anc1.Anc1refChr8 40253 15 - 57822 AGGAGTATTTTACTT -s Anc2.Anc2refChr14 3349 15 - 7748 AAGAGTATTTTACTT -s mr.mrrefChr5 137012 15 + 294540 AGGGGCATCTTATCT -s simCow_chr6.simCow.chr6 250878 15 - 602619 AAGAGTAATTTCTGT -s simDog_chr6.simDog.chr6 253012 15 - 593897 AAGAGTATTTTACTT -s simHuman_chr6.simHuman.chr6 419042 12 - 601863 AG---TAATTTACTT -s simRat_chr6.simRat.chr6 274391 15 + 647215 AGGAGTATCTTACTT - -a -s simMouse_chr6.simMouse.chr6 285946 10 + 636262 TTGCCAAAAT -s Anc0.Anc0refChr5 83601 10 - 87904 TTGCAAAAGT -s Anc1.Anc1refChr8 40268 10 - 57822 TTGCAAAAGT -s Anc2.Anc2refChr14 3370 10 - 7748 TTGCAAAAGT -s mr.mrrefChr5 137027 10 + 294540 TTGCCAAAAT -s simCow_chr6.simCow.chr6 250899 10 - 602619 CTGCATAGAT -s simDog_chr6.simDog.chr6 253033 10 - 593897 TTGCAAAAGT -s simHuman_chr6.simHuman.chr6 419054 10 - 601863 TTGCAAAAGT -s simRat_chr6.simRat.chr6 274406 10 + 647215 TTGCCAAACT - -a -s simMouse_chr6.simMouse.chr6 285956 38 + 636262 GAAGGTTAATGATACATTACAATTTTCAAGTTGCTCAG -s Anc0.Anc0refChr5 83611 36 - 87904 GAACA--AACTGAAGATTACAATTTTCATGGTGCTCAG -s Anc1.Anc1refChr8 40278 38 - 57822 GAACACTAACTGAAGATTACAATTTTCATGGTGCTCAG -s Anc2.Anc2refChr14 3380 36 - 7748 GAACA--AACTGAAGACTACAATTTAAATGGTGCTCAG -s mr.mrrefChr5 137037 38 + 294540 GAAGGTTAATGATACATTACAATTTTCAAGTTGCTCAG -s simCow_chr6.simCow.chr6 250909 36 - 602619 GAAGA--CACTGAAAGTTACAATTTACATGGTGCTCAG -s simDog_chr6.simDog.chr6 253045 36 - 593897 GAACA--AACTGAAGACTACAATTTAAATGGTGCTCAG -s simHuman_chr6.simHuman.chr6 419064 38 - 601863 GCACACTCACTGAATATTACAATTTTCATGCCACCTAA -s simRat_chr6.simRat.chr6 274416 38 + 647215 GAAGATTTACTGAACATTACAAGTTACAAGGTGCTCAG - -a -s simMouse_chr6.simMouse.chr6 285994 19 + 636262 CTGAGAAGGTTAAGACCCT -s Anc0.Anc0refChr5 83647 19 - 87904 CTGAGAAGACTAAGACCCT -s Anc1.Anc1refChr8 40316 19 - 57822 CTGAGAAGACTAAGACCCT -s Anc2.Anc2refChr14 3420 19 - 7748 CTGAGAAGACCAAGACTCT -s mr.mrrefChr5 137075 19 + 294540 CTGAGAAGGTTAAGACCCT -s simCow_chr6.simCow.chr6 250949 19 - 602619 CTAAGAAGGACAGGACTCA -s simDog_chr6.simDog.chr6 253085 19 - 593897 CTGAGAAGACCAAGACTCT -s simHuman_chr6.simHuman.chr6 419102 16 - 601863 ---AGAAGACTCTTGCCTT -s simRat_chr6.simRat.chr6 274454 19 + 647215 CTGAGAAGGCTAAGACGCT - -a -s simMouse_chr6.simMouse.chr6 286013 39 + 636262 TAACCTTTTCAAGAATACCAAGTCCAGCACTTTATTTTG -s Anc0.Anc0refChr5 83666 22 - 87904 T-----------------CAAGCTCAAGATTGTCTTCTT -s Anc1.Anc1refChr8 40335 22 - 57822 T-----------------CAAGCTCAAGATTGTCTTCTT -s Anc2.Anc2refChr14 3455 22 - 7748 T-----------------CAAACTCAAGATTGTCTTCTT -s mr.mrrefChr5 137094 22 + 294540 T-----------------CAAGTCCAGCACTTTATTTTG -s simCow_chr6.simCow.chr6 250984 22 - 602619 T-----------------AATACTCAACCCTGCATCCTG -s simDog_chr6.simDog.chr6 253121 22 - 593897 T-----------------CAAACTCAAGATTGTCTTCTT -s simHuman_chr6.simHuman.chr6 419118 5 - 601863 A-----------------TAGG----------------- -s simRat_chr6.simRat.chr6 274473 22 + 647215 T-----------------CAAGCCTAGCATTTTGTTTCA - -a -s simMouse_chr6.simMouse.chr6 286052 30 + 636262 TTTAGGCACTGGACTCTTCATAGCCACTAG -s Anc0.Anc0refChr5 83688 30 - 87904 TTTAGGAGTTGGGGACATCTGGAGCACGAG -s Anc1.Anc1refChr8 40357 30 - 57822 TTTAGGAGTTGGGGACATCTGGAGCACGAG -s Anc2.Anc2refChr14 3477 30 - 7748 TTTAGGAGTTGGGGACATCTGGAGCACGAG -s mr.mrrefChr5 137116 30 + 294540 TTTAGGCACTGGACTCTTCATAGCCACTAG -s simCow_chr6.simCow.chr6 251015 30 - 602619 TATAGGTGTTGGGGTCATCTGAAGCACTGG -s simDog_chr6.simDog.chr6 253143 30 - 593897 TTTAGGAGTTGGGGACATCTGGAGCACGAG -s simRat_chr6.simRat.chr6 274495 30 + 647215 TTTGGGCAGTGGGCTCTTCATAGCCACCTG - -a -s simMouse_chr6.simMouse.chr6 286082 18 + 636262 AGCCTAAGGGTAAACCAA -s Anc0.Anc0refChr5 83718 16 - 87904 CTCTTTAGGGTGACCT-- -s Anc1.Anc1refChr8 40387 16 - 57822 CTCTTTAGGGTGACCT-- -s Anc2.Anc2refChr14 3508 16 - 7748 CTCTTTAGGGTGACCT-- -s mr.mrrefChr5 137146 18 + 294540 AGCCTAAGGGTAAACCAA -s simCow_chr6.simCow.chr6 251046 16 - 602619 ATCCCAAGAGTGAGCT-- -s simDog_chr6.simDog.chr6 253174 16 - 593897 CTCTTTAGGGTGACCT-- -s simRat_chr6.simRat.chr6 274525 18 + 647215 TGCCTAAGGGTAAACCAA - -a -s simMouse_chr6.simMouse.chr6 286100 41 + 636262 GTGTACAAACTCCTCCGCTATCAGTATCTTCATCTACAGGT -s Anc0.Anc0refChr5 83734 40 - 87904 GTATAAGAATGCCTCTGA-GTCAGAATGTCCATCTACAAGT -s Anc1.Anc1refChr8 40403 40 - 57822 GTATAAGAATGCCTCTGA-GTCAGAATGTCCATCTACAAGT -s Anc2.Anc2refChr14 3524 40 - 7748 GTATAAGAATGCCCCTGA-GCCAGAATGTCCATCTATAAGT -s mr.mrrefChr5 137164 41 + 294540 GTGTACAAACTCCTCCGCTATCAGTATCTTCATCTACAGGT -s simCow_chr6.simCow.chr6 251065 40 - 602619 GTGTAAGAGTGCCCCTGG-GCCAGGATGTCCATCTATAAGT -s simDog_chr6.simDog.chr6 253190 40 - 593897 GTATAAGAATGCCCCTGA-GCAAGAATGTCCATCTATAATT -s simHuman_chr6.simHuman.chr6 419123 33 - 601863 -------AATGCATCTGA-GTCACAATGTCCTTTTACAAGT -s simRat_chr6.simRat.chr6 274543 41 + 647215 GTGTACAAATTCCTGCTCTATCAGTATCTTCACCTACTGGA - -a -s simMouse_chr6.simMouse.chr6 286141 12 + 636262 CCAGTCCTTCAA -s Anc0.Anc0refChr5 83775 12 - 87904 CCAATCCCTCAA -s Anc1.Anc1refChr8 40444 12 - 57822 CCAATCCCTCAA -s Anc2.Anc2refChr14 3565 12 - 7748 CCAATCCCTCAA -s mr.mrrefChr5 137205 12 + 294540 CCAGTCCTTCAA -s simCow_chr6.simCow.chr6 251106 12 - 602619 ACAATCCCTCAA -s simDog_chr6.simDog.chr6 253231 12 - 593897 CTAAGTCCTCAA -s simHuman_chr6.simHuman.chr6 419157 12 - 601863 CCAATCCATTCA -s simRat_chr6.simRat.chr6 274584 12 + 647215 TCAGTCCTTGAA - -a -s simMouse_chr6.simMouse.chr6 286153 3 + 636262 TCG -s Anc0.Anc0refChr5 83787 3 - 87904 TCA -s Anc1.Anc1refChr8 40456 3 - 57822 TCA -s Anc2.Anc2refChr14 3577 3 - 7748 TCA -s mr.mrrefChr5 137217 3 + 294540 TCG -s simCow_chr6.simCow.chr6 251118 3 - 602619 GCC -s simDog_chr6.simDog.chr6 253243 3 - 593897 TCA -s simHuman_chr6.simHuman.chr6 419170 3 - 601863 TAA -s simRat_chr6.simRat.chr6 274596 3 + 647215 TTT - -a -s simMouse_chr6.simMouse.chr6 286156 5 + 636262 TCTTT -s Anc0.Anc0refChr5 83790 5 - 87904 TCTGT -s Anc1.Anc1refChr8 40459 5 - 57822 TCTGT -s Anc2.Anc2refChr14 3584 5 - 7748 TCTGT -s mr.mrrefChr5 137220 5 + 294540 TCTTT -s simCow_chr6.simCow.chr6 251125 5 - 602619 TCTGT -s simDog_chr6.simDog.chr6 253250 5 - 593897 TTTGT -s simHuman_chr6.simHuman.chr6 419173 5 - 601863 TCTGT -s simRat_chr6.simRat.chr6 274599 5 + 647215 TTTCT - -a -s simMouse_chr6.simMouse.chr6 286161 16 + 636262 CCATCAGGACCCTCAT -s Anc0.Anc0refChr5 83809 16 - 87904 CTAACGGCACCATATT -s Anc1.Anc1refChr8 40478 16 - 57822 CTAACGGCACCATATT -s Anc2.Anc2refChr14 3603 16 - 7748 CTCATGGCACTATATT -s mr.mrrefChr5 137225 16 + 294540 CCATCAGGACCCTCAT -s simCow_chr6.simCow.chr6 251144 16 - 602619 CTCATGGCACTATATT -s simDog_chr6.simDog.chr6 253322 16 - 593897 ATCATGACACTATAAT -s simHuman_chr6.simHuman.chr6 419192 16 - 601863 CGAACGGCACCATGTT -s simRat_chr6.simRat.chr6 274604 16 + 647215 CCATCAGGGCCCTCAT - -a -s simMouse_chr6.simMouse.chr6 286177 17 + 636262 TGTGGACACAGGCGCAG -s Anc0.Anc0refChr5 83826 17 - 87904 TGTGGACACGGGCCCAG -s Anc1.Anc1refChr8 40495 17 - 57822 TGTGGACACGGGCCCAG -s Anc2.Anc2refChr14 3620 17 - 7748 TGTGGACACGGGCCAGG -s mr.mrrefChr5 137241 17 + 294540 TGTGGACACAGGCGCAG -s simCow_chr6.simCow.chr6 251161 17 - 602619 TGTTGACATGGGCTAGG -s simDog_chr6.simDog.chr6 253339 17 - 593897 TGTGTACCCAGGGCAGA -s simHuman_chr6.simHuman.chr6 419209 17 - 601863 TGTGGACACGGGCCCAG -s simRat_chr6.simRat.chr6 274620 17 + 647215 TGTGGACTCAGGCCCAG - -a -s simMouse_chr6.simMouse.chr6 286194 14 + 636262 CTGCCCCCCTTAAA -s Anc0.Anc0refChr5 83845 11 - 87904 GTCCCCT---TAAA -s Anc1.Anc1refChr8 40514 11 - 57822 GTCCCCT---TAAA -s Anc2.Anc2refChr14 3639 11 - 7748 GTCCCCT---TAAA -s mr.mrrefChr5 137258 11 + 294540 ATTCCCC---TAAA -s simCow_chr6.simCow.chr6 251180 11 - 602619 GTCCCGT---TAAA -s simDog_chr6.simDog.chr6 253358 11 - 593897 GTCCCCT---TAAA -s simHuman_chr6.simHuman.chr6 419228 11 - 601863 GTCCCCT---TAAA -s simRat_chr6.simRat.chr6 274637 11 + 647215 AGTCCCC---TAAA - -a -s simMouse_chr6.simMouse.chr6 286208 64 + 636262 TTCCGGATGCTTAAGGATCAGGTCTGTAGAAATCCATGCTTAATCGTCAAGCTGTAGATATCTG -s Anc0.Anc0refChr5 83856 36 - 87904 TTTCTGCTGCTTGAGGCTCAGGT----------------------------CTGTAGAGATCTG -s Anc1.Anc1refChr8 40525 36 - 57822 TTTCTGCTGCTTGAGGCTCAGGT----------------------------CTGTAGAGATCTG -s Anc2.Anc2refChr14 3650 36 - 7748 GTTCTGCTGCTTGAGGCTCAGGT----------------------------CTGTAGAGATCTG -s mr.mrrefChr5 137269 36 + 294540 TTCCAGATGCTTAAGGATCAGGT----------------------------CTGTAGATATCTG -s simCow_chr6.simCow.chr6 251197 36 - 602619 GTTCTGCTGCCTGAGGCTCAAGC----------------------------CTGTAGAGATCTA -s simDog_chr6.simDog.chr6 253369 36 - 593897 GTTCTGCTAATTGAGGCCCAGGT----------------------------CTGCAGCGATCAG -s simHuman_chr6.simHuman.chr6 419239 36 - 601863 TTTGCACTGCTTGAGGCTCAGAT----------------------------CTGTAAAGATCTG -s simRat_chr6.simRat.chr6 274648 36 + 647215 TTCCAGATGCTTAAGGATCAGGT----------------------------CTGTAGAAATCCT - -a -s simMouse_chr6.simMouse.chr6 286272 4 + 636262 ATGC -s Anc0.Anc0refChr5 83895 4 - 87904 TTAC -s Anc1.Anc1refChr8 40564 4 - 57822 TTAC -s Anc2.Anc2refChr14 3689 4 - 7748 TTAC -s mr.mrrefChr5 137305 4 + 294540 ATGC -s simCow_chr6.simCow.chr6 251236 4 - 602619 ATAC -s simDog_chr6.simDog.chr6 253408 4 - 593897 TCAC -s simHuman_chr6.simHuman.chr6 419278 4 - 601863 CTTC - -a -s simMouse_chr6.simMouse.chr6 286276 16 + 636262 ACAATAATTTTCTATC -s Anc0.Anc0refChr5 83899 1 - 87904 T--------------- -s Anc1.Anc1refChr8 40568 16 - 57822 TGAATCATAAGGTGTC -s Anc2.Anc2refChr14 3693 1 - 7748 T--------------- -s mr.mrrefChr5 137309 16 + 294540 ACAATAATTTTCTATC -s simCow_chr6.simCow.chr6 251240 1 - 602619 T--------------- -s simDog_chr6.simDog.chr6 253416 1 - 593897 T--------------- -s simHuman_chr6.simHuman.chr6 419282 16 - 601863 TGAGTCATAAGGTGTC - -a -s simMouse_chr6.simMouse.chr6 286292 1 + 636262 A -s Anc0.Anc0refChr5 83931 1 - 87904 A -s Anc1.Anc1refChr8 40811 1 - 57822 A -s Anc2.Anc2refChr14 3731 1 - 7748 A -s mr.mrrefChr5 137325 1 + 294540 A -s simCow_chr6.simCow.chr6 251271 1 - 602619 A -s simDog_chr6.simDog.chr6 253456 1 - 593897 A -s simHuman_chr6.simHuman.chr6 419558 1 - 601863 A - -a -s simMouse_chr6.simMouse.chr6 286293 42 + 636262 ACCTAATTTCCTATCCACTGTCTCAATGATCTCTTTAGATCT -s Anc0.Anc0refChr5 83932 42 - 87904 CCCTAATCTTCTATCCACTAGCTCAATGATCTCTTTAGATCT -s Anc1.Anc1refChr8 40812 42 - 57822 CCCTAATCTTCTATCCACTAGCTCAATGATCTCTTTAGATCT -s Anc2.Anc2refChr14 3732 42 - 7748 CCATAATCTTCTATCCACTAGCTCAATGATCTCTTTAGATCT -s mr.mrrefChr5 137326 42 + 294540 ACCTAATTTCCTATCCACTGTCTCAATGATCTCTTTAGATCT -s simCow_chr6.simCow.chr6 251272 35 - 602619 CCATAATC-----TCCACTGGATCTAT--CCTCTTTAGATCT -s simDog_chr6.simDog.chr6 253460 42 - 593897 TCATAATCTTCTATCTACTAGCTCAATGATCTGTTTAGGTCT -s simHuman_chr6.simHuman.chr6 419559 42 - 601863 CCCTTATCTTCTATCCACTAGCCCAATGATCTCTTTAGATCT - -a -s simMouse_chr6.simMouse.chr6 286335 5 + 636262 GGATA -s Anc0.Anc0refChr5 83976 5 - 87904 GGATA -s Anc1.Anc1refChr8 40856 5 - 57822 GGATA -s Anc2.Anc2refChr14 3776 5 - 7748 GGATA -s mr.mrrefChr5 137368 5 + 294540 GGATA -s simCow_chr6.simCow.chr6 251309 5 - 602619 TGATA -s simDog_chr6.simDog.chr6 253504 5 - 593897 GGACC -s simHuman_chr6.simHuman.chr6 419603 5 - 601863 GGATA - -a -s simMouse_chr6.simMouse.chr6 286340 20 + 636262 TGTGGAATCTTAGTTACGAG -s Anc0.Anc0refChr5 83981 20 - 87904 TGTGAAATCTTAGTTACAAT -s Anc1.Anc1refChr8 40861 20 - 57822 TGTGAAATCTTAGTTACAAT -s Anc2.Anc2refChr14 3781 20 - 7748 TCTTAAATATTAATTACGAT -s mr.mrrefChr5 137373 20 + 294540 TGTGAAATCTTAGTTACAAG -s simCow_chr6.simCow.chr6 251317 20 - 602619 TCTTAATTACAAATGTCCAT -s simDog_chr6.simDog.chr6 253509 20 - 593897 TCTTAAATATTAACTACGAT -s simHuman_chr6.simHuman.chr6 419608 20 - 601863 TGTGAAGTCTTAGTTACAAT -s simRat_chr6.simRat.chr6 274684 20 + 647215 TGTGAAATCTTTGTTACAAC - -a -s simMouse_chr6.simMouse.chr6 286360 52 + 636262 GCCAAAGGGATCACTAATAGGTTACAGGATCACTAATAGGTTACTATCCTCC -s Anc0.Anc0refChr5 84008 32 - 87904 GC-AAGGGGATCACTAATAGGTTGC-------------------TATCCTCT -s Anc1.Anc1refChr8 40888 32 - 57822 GC-AAGGGGATCACTAATAGGTTGC-------------------TATCCTCT -s Anc2.Anc2refChr14 3808 32 - 7748 TC-ATGGGGATCACTAATAAGTTGC-------------------TATCTGCT -s mr.mrrefChr5 137393 32 + 294540 GC-AAAGGGATCACTAATAGGTTAC-------------------TATCCTCC -s simCow_chr6.simCow.chr6 251342 29 - 602619 AC-AT---GATCATTAATAAGTAGC-------------------TATTGGCT -s simDog_chr6.simDog.chr6 253536 32 - 593897 TT-ATGGGGATCACTAATAAGTTGC-------------------TATCTGCT -s simHuman_chr6.simHuman.chr6 419635 29 - 601863 GC-AAGGGAAGCACCAATAGGT----------------------TATCCTCT -s simRat_chr6.simRat.chr6 274704 21 + 647215 GT-AAAAGGATCACTAATAGGT------------------------------ - -a -s simMouse_chr6.simMouse.chr6 286412 18 + 636262 AAGTGACTGTATGGACTT -s Anc0.Anc0refChr5 84040 18 - 87904 ACACAATTGTATGAACTT -s Anc1.Anc1refChr8 40920 18 - 57822 ACACAATTGTATGAACTT -s Anc2.Anc2refChr14 3840 18 - 7748 ACACAATTGTACAAACAT -s mr.mrrefChr5 137425 18 + 294540 AAGTGACTGTATGGACTT -s simCow_chr6.simCow.chr6 251376 18 - 602619 ACACAATTGTACAAACAT -s simDog_chr6.simDog.chr6 253568 18 - 593897 ACACAATTGTTCAAACAT -s simHuman_chr6.simHuman.chr6 419664 18 - 601863 ACACCATCGTATGAACTT - -a -s simMouse_chr6.simMouse.chr6 286430 29 + 636262 CAAATAACCAATTAGCTAACAGGTCAAGT -s Anc0.Anc0refChr5 84058 29 - 87904 CAAATTACCAAATATTTTACGGGTCAAGT -s Anc1.Anc1refChr8 40938 29 - 57822 CAAATTACCAAATATTTTACGGGTCAAGT -s Anc2.Anc2refChr14 3858 29 - 7748 AAAATTACCAAATATTTTAAGGGTCAAGT -s mr.mrrefChr5 137443 29 + 294540 CAAATAACCAATTAGTTAACGGGTCAAGT -s simCow_chr6.simCow.chr6 251407 28 - 602619 AAAATTACC-AATATTTTATGGGCCAAAT -s simDog_chr6.simDog.chr6 253586 29 - 593897 AAAAGTACCAATTAGTTTAAGGGTCAAGT -s simHuman_chr6.simHuman.chr6 419682 29 - 601863 CCAATTACCAAATATTTTCCTGGTCAAGT -s simRat_chr6.simRat.chr6 274725 26 + 647215 ---ATAACCAATTAGTTAACGGGTCAAAT - -a -s simMouse_chr6.simMouse.chr6 286459 12 + 636262 GTTCAGAATTTT -s Anc0.Anc0refChr5 84087 12 - 87904 ATTCAAAACTTT -s Anc1.Anc1refChr8 40967 12 - 57822 ATTCAAAACTTT -s Anc2.Anc2refChr14 3887 12 - 7748 AACCAAAACTTT -s mr.mrrefChr5 137472 12 + 294540 GTTCAAAATTTT -s simCow_chr6.simCow.chr6 251436 12 - 602619 AGCCAAATCTTT -s simDog_chr6.simDog.chr6 253615 12 - 593897 AACCAAAACTCT -s simHuman_chr6.simHuman.chr6 419711 12 - 601863 ATTCAAAACTTT -s simRat_chr6.simRat.chr6 274751 12 + 647215 GTTCAAAGTTTA - -a -s simMouse_chr6.simMouse.chr6 286471 52 + 636262 CAGATTCCAACTGCCATGGCAATTCTGCTGGCAAACCTCCATGCACATTCAA -s Anc0.Anc0refChr5 84099 38 - 87904 CAGACTCCAACTTCCACAGTAATTCTGCCA--------------ACATTCGA -s Anc1.Anc1refChr8 40979 38 - 57822 CAGACTCCAACTTCCACAGTAATTCTGCCA--------------ACATTCGA -s Anc2.Anc2refChr14 3899 38 - 7748 CAGACTCCAACTTCCACAGTAATTCTGCCA--------------ACATTCGA -s mr.mrrefChr5 137484 52 + 294540 CAGACTCCAACTGCCATGGCAATTCTGCTGACATACCTCCATGCACATTCAA -s simCow_chr6.simCow.chr6 251455 38 - 602619 CAGATTGAAAACTCCACAGTAATTCTACCA--------------ACATTCGA -s simDog_chr6.simDog.chr6 253627 38 - 593897 CAGACTCCAACTTCCATATTAATTCTGCCA--------------ACATCCAA -s simHuman_chr6.simHuman.chr6 419723 38 - 601863 CAGACTCCAACTTCCACAGTAATCCTGCCA--------------ACATTTGA -s simRat_chr6.simRat.chr6 274763 52 + 647215 CAGACTCCCACTGCCATGCAAATTCCGCTGACATACCTCAATGCACACTGAA - -a -s simMouse_chr6.simMouse.chr6 286523 40 + 636262 AACTCAAGGCATCTGATCGCCATACATTTGAATCATGGCT -s Anc0.Anc0refChr5 84139 31 - 87904 AACTTAACGTGTCTGGTGGCCTTACAACTAA--------- -s Anc1.Anc1refChr8 41019 40 - 57822 AACTTAACGTGTCTGGTGGCCTTACAACTAAACCATGTCT -s Anc2.Anc2refChr14 3939 31 - 7748 AACTTAACGTATCTGGTGGCTTTACAACTGA--------- -s mr.mrrefChr5 137538 40 + 294540 AACTCAAGGCGTCTGATGGCCATACAATTAAATCATGGCT -s simCow_chr6.simCow.chr6 251495 20 - 602619 AAATCAATGTCTGTGATGAC-------------------- -s simDog_chr6.simDog.chr6 253667 31 - 593897 AACTTGACGCATCTGGTGGCTTTACAACTGA--------- -s simHuman_chr6.simHuman.chr6 419763 36 - 601863 AGCTTAACGTGTCTGGTGGCCTTAC----AAACCATGTCT -s simRat_chr6.simRat.chr6 274817 40 + 647215 AACTCAAGGCGTATGATGGCCATACAATTAAATCACGGCA - -a -s simMouse_chr6.simMouse.chr6 286563 89 + 636262 TGGAAAATTCTACTTCCTGCAACTTCAAGAAAGGCCTTGAACCCGATTAATAAGTATCCCACAAACCCACCTTTACTTGCCACTATCTT -s Anc0.Anc0refChr5 84232 81 - 87904 TGGAAAATTAAGCTCCCTGGCACTTCAGGAAAGGCTTGAAACCCGATT----AGTACCCCCTATACCCCCCTTGACTTGCCACTA---- -s Anc1.Anc1refChr8 41121 81 - 57822 TGGAAAATTAAGCTCCCTGGCACTTCAGGAAAGGCTTGAAACCCGATT----AGTACCCCCTATACCCCCCTTGACTTGCCACTA---- -s Anc2.Anc2refChr14 4032 81 - 7748 CAGAAAATTAAGCTCTCCTGCACTCTAGGAAAGGCTTGAAACCCAATT----AGTACCCCCTATACCCCTGTTGACTTGCTACTA---- -s mr.mrrefChr5 137578 89 + 294540 TGGAAAATTCTACTTCCTGCAACTTCAAGAAAGGCCTTGAACCCGATTAATAAGTACCCCACAAACCCACCTTTACTTGCCACTATCTT -s simCow_chr6.simCow.chr6 251568 80 - 602619 CAGAAAATTAAGCT-ACCTGCACTTTAGAAAAGGCCTTAGACCCAATT----ATTACCCCCTATACTCCAACTGACTTGCTACTA---- -s simDog_chr6.simDog.chr6 253760 72 - 593897 CAGAAAATTA-GTTCTACTGCACTCTATGGACGACTTGGAACCCAACT----AGTCCCCCCTATACCCCTGTTGACT------------ -s simHuman_chr6.simHuman.chr6 419930 80 - 601863 TGGAAAATTAAGCTCCCTGGCAC-TCAGGACAGGCTTCAAACCCGATT----GATACTGCCTATACCCCCCTTGATTATCCTCTA---- -s simRat_chr6.simRat.chr6 274857 89 + 647215 TGGAAAATTCTTCTTCCTGCAACAGCAAGAAAGGCCTTGAACCCATTTAGGAAATACCCCACAAACTCGCCTTTACTCACCACTATCTT - -a -s simMouse_chr6.simMouse.chr6 286652 18 + 636262 CCCTTGCTTGGTTCCCTT -s Anc0.Anc0refChr5 84313 13 - 87904 -----ACTTGGATCTCTT -s Anc1.Anc1refChr8 41202 13 - 57822 -----ACTTGGATCTCTT -s Anc2.Anc2refChr14 4113 13 - 7748 -----TCTTGGATCTCTT -s mr.mrrefChr5 137667 18 + 294540 CCCTTACTTGGTTCCCTT -s simCow_chr6.simCow.chr6 251648 13 - 602619 -----TCTAGGAGCTCTT -s simDog_chr6.simDog.chr6 253832 11 - 593897 -------TTGGATCACTT -s simHuman_chr6.simHuman.chr6 420010 13 - 601863 -----ACTTGGATCTCTT -s simRat_chr6.simRat.chr6 274950 18 + 647215 CCTTTACTTGGTTCCGTT - -a -s simMouse_chr6.simMouse.chr6 286670 29 + 636262 ACAATCACTCCTATGTAATGCAACCAATC -s Anc0.Anc0refChr5 84326 29 - 87904 ATAATCACCTCTATTTAATGCAATAAATT -s Anc1.Anc1refChr8 41215 29 - 57822 ATAATCACCTCTATTTAATGCAATAAATT -s Anc2.Anc2refChr14 4126 29 - 7748 ATAATCACCTCTATTTAATGCAATAAATT -s mr.mrrefChr5 137685 29 + 294540 ACAATCACCCCTATGTAATGCAATCAATC -s simCow_chr6.simCow.chr6 251676 29 - 602619 ATAATCACCTCTATTTAATGCAATAAATT -s simDog_chr6.simDog.chr6 253843 29 - 593897 GTAATCAACTCTATTTTAAGCAATAAATT -s simHuman_chr6.simHuman.chr6 420023 29 - 601863 ATGATCACCTCTATTTATTGGAATAAATT -s simRat_chr6.simRat.chr6 274968 27 + 647215 ACAATCACC--TATATAATGCAATCGATC - -a -s simMouse_chr6.simMouse.chr6 286699 31 + 636262 AAAGTGTAAATAGGGACATCACTGTTGTTTG -s Anc0.Anc0refChr5 84355 23 - 87904 AAAT-----A--AGCACATCACTGT-ATCTG -s Anc1.Anc1refChr8 41244 23 - 57822 AAAT-----A--AGCACATCACTGT-ATCTG -s Anc2.Anc2refChr14 4155 23 - 7748 AAAT-----A--AGCACATCACTGC-ATCTG -s mr.mrrefChr5 137714 28 + 294540 AAAGTGTAAA--GGGACATCACTGT-GTCTG -s simCow_chr6.simCow.chr6 251712 23 - 602619 AAAT-----A--GGCATGTCAGTGC-ATCTG -s simDog_chr6.simDog.chr6 253872 23 - 593897 AAAT-----A--AGCACATCACTGC-ATCTG -s simHuman_chr6.simHuman.chr6 420052 16 - 601863 A--------------ACATCACTGT-ATCTG -s simRat_chr6.simRat.chr6 274995 28 + 647215 AAGATGTGAA--GGGACATCACTGT-GTCTG - -a -s simMouse_chr6.simMouse.chr6 286730 8 + 636262 AGTTGAGC -s Anc0.Anc0refChr5 84378 8 - 87904 TGGTCAGT -s Anc1.Anc1refChr8 41267 8 - 57822 TGGTCAGT -s Anc2.Anc2refChr14 4180 8 - 7748 TGGGCAGT -s mr.mrrefChr5 137742 8 + 294540 AGTTGAGC -s simCow_chr6.simCow.chr6 251738 8 - 602619 TGGGCAGA -s simDog_chr6.simDog.chr6 253897 8 - 593897 TGGGCAGT -s simHuman_chr6.simHuman.chr6 420068 8 - 601863 TGGTCAAT -s simRat_chr6.simRat.chr6 275023 8 + 647215 AGTTGAGC - -a -s simMouse_chr6.simMouse.chr6 286738 9 + 636262 ATTGCAACT -s Anc0.Anc0refChr5 84386 4 - 87904 GATG----- -s Anc1.Anc1refChr8 41275 4 - 57822 GATG----- -s Anc2.Anc2refChr14 4192 4 - 7748 GATG----- -s mr.mrrefChr5 137750 9 + 294540 ATTGCAACT -s simCow_chr6.simCow.chr6 251750 4 - 602619 GATG----- -s simDog_chr6.simDog.chr6 253909 4 - 593897 GATG----- -s simHuman_chr6.simHuman.chr6 420076 4 - 601863 GATG----- -s simRat_chr6.simRat.chr6 275031 9 + 647215 ATTGCAACC - -a -s simMouse_chr6.simMouse.chr6 286747 5 + 636262 TGATA -s Anc0.Anc0refChr5 84390 5 - 87904 TGATG -s Anc1.Anc1refChr8 41279 5 - 57822 TGATG -s Anc2.Anc2refChr14 4196 5 - 7748 TGATG -s mr.mrrefChr5 137759 5 + 294540 TGATA -s simCow_chr6.simCow.chr6 251754 2 - 602619 TT--- -s simDog_chr6.simDog.chr6 253915 5 - 593897 TGATG -s simHuman_chr6.simHuman.chr6 420080 5 - 601863 TGATG -s simRat_chr6.simRat.chr6 275040 5 + 647215 TGATA - -a -s simMouse_chr6.simMouse.chr6 286752 4 + 636262 TAGA -s Anc0.Anc0refChr5 84437 4 - 87904 TAGT -s Anc1.Anc1refChr8 41326 4 - 57822 TAGT -s Anc2.Anc2refChr14 4243 4 - 7748 TAGT -s mr.mrrefChr5 137790 4 + 294540 TAGA -s simCow_chr6.simCow.chr6 251797 4 - 602619 TAGT -s simDog_chr6.simDog.chr6 253974 4 - 593897 TAGT -s simHuman_chr6.simHuman.chr6 420127 4 - 601863 TAGT -s simRat_chr6.simRat.chr6 275071 4 + 647215 TAGA - -a -s simMouse_chr6.simMouse.chr6 286756 170 + 636262 CACCAAACACAAGACAAGACTGCCACACACATTCACTATACAGTACCTGTTCTGCTCACAGAACAAGGGTTATGGTTACCAGACATTTTTATAAAAAATTGTCTTCTGGATCTGATATTTATGCCCTGCTCCACATACCTATTTACTAGATGGCACCAGGCTTCACCAGT -s Anc0.Anc0refChr5 84441 157 - 87904 CATCTACCATAAGAATAGACAGCCACACGCATGAACTATGCGGTCCTCATTCCACTCCCAAAAC------TAG------CAGAGGTTTTTATATCAAATTATCT-CTAAATTCTGAATTTGTGCCCTGATCAACGCACCTGTTTACCAGATGATCCCAGTCTTCACCAGT -s Anc1.Anc1refChr8 41330 164 - 57822 CATCTACCATAAGAATAGACAGCCACACGCATGAACTATGCGGTCCTCATTCCACTCCCAAAAC------TAGGGTCACCAGAGGTTTTTATATCAAATTATCTCCTAAATTCTGAATTTGTGCCCTGATCAACGCACCTGTTTACCAGATGATCCCAGTCTTCACCAGT -s Anc2.Anc2refChr14 4247 157 - 7748 CATCTACCATGAGAATAGACAGCCACACGTCTGAACTATGCGGCCCTCATCCCATTGCCAAAAA------TAG------CAGAGGTTTTTATCTCAATTTATCT-CTAAAATCTGAATTTGTGCCCTGATTAACGCAGCTGTTTACCAGATGATCCCAGTCTTCATCAGT -s mr.mrrefChr5 137794 170 + 294540 CATCAAACATAAGACAAGACTGCCACACACATTCACTATACAGTACCTGTTCTGCTCCCAAAACAAGGGTTATGGTTACCAGAGGTTTTTATAAAAAATTGTCTTCTGAATCTGGAATTTATGCCCTGCTCCACATACCTATTTACTAGATGGTACCAGGCTTCACCAGT -s simCow_chr6.simCow.chr6 251808 150 - 602619 CATCTATCATGAGAATAGACAG---CAAGTCTCAATGATGTGGCCCTCATCCTAAAACCAGGAT------TAC------CAGATGTTTCTAC----ATTAACTT-CGAAAATCTGAATTTGTGCCCTGATTAACACAGCTATTTACAAGATGATGCCAGTCTTCAGCAGT -s simDog_chr6.simDog.chr6 253978 150 - 593897 CATCTACTACGAGAATGAACATCCATAC----GAACTAGGCAGCCCTTATCCCATTGCCAAAAA------TAG------GAGAGG--TTTATCTCAATTTATCT-CTAAAATCTGAATCTGTGCCCTGATTAA-GCAGTTGTTTACCAGATGATCCCAGCCTTCATCAGT -s simHuman_chr6.simHuman.chr6 420131 164 - 601863 CATCTACCATAAGAATAGACAGCCACACGCATGAACTATGAGGTCCTCATTCCTCTCCCAAAAC------TGGGGTCACCAGAGGTTTTTATAGCAAATTATCTACTAAATTCTGAATTAGTGCCCTGATCAATGCGCCTTTTTACCAGATGATTCCTGTTTTCACCAGT -s simRat_chr6.simRat.chr6 275075 170 + 647215 CATCAAGCATAAGACCAGACTGCAACACAAGTTCACTAAACAGTACCTGTTCGGCTCCCAAAACAAGGGTGATGGATACTAGAGGTGTCCATAAAAAATTGTCTGCTGAATCTGGAATTTATGCCCTGCTCCACATCCCTATTTACTAGATGGTACCAGGCTTTGCCAGT - -a -s simMouse_chr6.simMouse.chr6 286926 15 + 636262 AATCCCTGTTGTAGG -s Anc0.Anc0refChr5 84598 15 - 87904 AAAACCTGTTATAGG -s Anc1.Anc1refChr8 41494 15 - 57822 AAAACCTGTTATAGG -s Anc2.Anc2refChr14 4404 15 - 7748 AAAACCTGTTATGGG -s mr.mrrefChr5 137964 15 + 294540 AATCCCTGTTGTAGG -s simCow_chr6.simCow.chr6 251959 15 - 602619 AAAAACTCTTATGGT -s simDog_chr6.simDog.chr6 254128 15 - 593897 AAAGCCTGTTATGGG -s simHuman_chr6.simHuman.chr6 420295 15 - 601863 AGAACCTGTTATAGG -s simRat_chr6.simRat.chr6 275245 15 + 647215 AATCTCTGTTGTAAG - -a -s simMouse_chr6.simMouse.chr6 286941 24 + 636262 TCCCAGTGAAATCCCTAGACTTGG -s Anc0.Anc0refChr5 84614 24 - 87904 TCCCATTGAAATATTTAGTCTTGG -s Anc1.Anc1refChr8 41510 24 - 57822 TCCCATTGAAATATTTAGTCTTGG -s Anc2.Anc2refChr14 4420 24 - 7748 TCCCATTGAAATATTTATTAGTGG -s mr.mrrefChr5 137980 24 + 294540 TCCCAGTGAAATATCTAGTCTTGG -s simCow_chr6.simCow.chr6 251975 24 - 602619 TCCCATTGAAATACTTATTAGTGG -s simDog_chr6.simDog.chr6 254144 19 - 593897 TTTCTTTGAAATATTTATC----- -s simHuman_chr6.simHuman.chr6 420311 24 - 601863 TCCTATTGAAATATTCAGTCTTGG -s simRat_chr6.simRat.chr6 275261 24 + 647215 TCCCACTGAAATATCTAGTCTTGG - -a -s simMouse_chr6.simMouse.chr6 286965 57 + 636262 TATTTTATAACCGTCTAATAAGGGATAATTTAACCCAGAGTCGCAGCTTATTACAGT -s Anc0.Anc0refChr5 84638 39 - 87904 TAAATTGTG------------------GATCAACCCAGGGTAGCAGCTTAGTATAGT -s Anc1.Anc1refChr8 41534 57 - 57822 TAAATTGTGGCTAATTAATAGAGGACAGATCAACCCAGGGTAGCAGCTTAGTATAGT -s Anc2.Anc2refChr14 4444 39 - 7748 TAAATTGTG------------------GACCAAGCCAGGGTAGCAGCTTAGTATAGT -s mr.mrrefChr5 138004 57 + 294540 TATTTTATAACTGTCTAATAAGGGATAGTTCAACCCAGAGTCGCAGCTTATTACAGT -s simCow_chr6.simCow.chr6 252007 39 - 602619 TAAATTGTG------------------GACCAAGCCTGGGTAGCAGCTTAGTACAGT -s simDog_chr6.simDog.chr6 254163 23 - 593897 ----------------------------------CCAGGGTCACAGCTTAGTATAGT -s simHuman_chr6.simHuman.chr6 420335 44 - 601863 TACATTGTGGCTAATTAATAGAGGACAGATCAACC-------------CAGAGTGGC -s simRat_chr6.simRat.chr6 275285 57 + 647215 TATTTTATCACTGTCAAATGAGGGATAGTTCAAACCAGAGTTGCAGCTTAGTACAGT - -a -s simMouse_chr6.simMouse.chr6 287022 4 + 636262 CATC -s Anc0.Anc0refChr5 84678 4 - 87904 TTTC -s Anc1.Anc1refChr8 41592 4 - 57822 TTTC -s Anc2.Anc2refChr14 4484 4 - 7748 TTTC -s mr.mrrefChr5 138061 4 + 294540 TATC -s simCow_chr6.simCow.chr6 252047 4 - 602619 TTTC -s simDog_chr6.simDog.chr6 254187 4 - 593897 TTTT -s simHuman_chr6.simHuman.chr6 420380 4 - 601863 TTTC -s simRat_chr6.simRat.chr6 275342 4 + 647215 TCTT - -a -s simMouse_chr6.simMouse.chr6 287026 27 + 636262 GAGAAGCAGTTCACAGGCAAATTCCAC -s Anc0.Anc0refChr5 84682 26 - 87904 CAGAAGTCATCTCTTGGTGTATTGTA- -s Anc1.Anc1refChr8 41596 26 - 57822 CAGAAGTCATCTCTTGGTGTATTGTA- -s Anc2.Anc2refChr14 4490 26 - 7748 CAGAAGTCATCTCTTGGTGTATTGTA- -s mr.mrrefChr5 138065 26 + 294540 GAGAAGCCATCCACTGGTAAATTCCA- -s simCow_chr6.simCow.chr6 252053 26 - 602619 CAGAAGTCACTTCCTGGTGTATTGTA- -s simDog_chr6.simDog.chr6 254193 26 - 593897 CAGAAGTCATCTATTCGTGTATTGCA- -s simHuman_chr6.simHuman.chr6 420384 26 - 601863 CAGACATCATCTCTTGGTGTATTATA- -s simRat_chr6.simRat.chr6 275348 26 + 647215 GAGAAGCCACCCACTGGTAAATTGCA- - -a -s simMouse_chr6.simMouse.chr6 287053 40 + 636262 TAGAATACTAAGCTCACAGACTTGAAGAAGTTCATAGTAC -s Anc0.Anc0refChr5 84710 38 - 87904 T-GAACACTAGGCTTACAGACCTTAGGAAGTT-ATAGTGC -s Anc1.Anc1refChr8 41624 39 - 57822 TAGAACACTAGGCTTACAGACCTTAGGAAGTT-ATAGTGC -s Anc2.Anc2refChr14 4518 38 - 7748 T-GAACACTAGGCTTACAGAACCTAGGAAGTT-CTAGTGC -s mr.mrrefChr5 138091 40 + 294540 TAGAATACTAAGCTCACAGACCTGAAGAAGTTCATAGTAC -s simCow_chr6.simCow.chr6 252081 35 - 602619 T-AGACACTAGGCTTACAGCAC-TGGGCAATT-T--GTGC -s simDog_chr6.simDog.chr6 254221 38 - 593897 T-GAACACTAGGCTTACATAAGCTAGGAAGCT-CTAGTGC -s simHuman_chr6.simHuman.chr6 420412 39 - 601863 TAGAACACTTGGCTTACAGACCTTAGGAAGTT-ATAGTGC -s simRat_chr6.simRat.chr6 275374 40 + 647215 TAGAATACTAAGCTCACAGACCTGAAGAGGTTAATAGTAC - -a -s simMouse_chr6.simMouse.chr6 287093 4 + 636262 TTGG -s Anc0.Anc0refChr5 84753 4 - 87904 TTGG -s Anc1.Anc1refChr8 41668 4 - 57822 TTGG -s Anc2.Anc2refChr14 4561 4 - 7748 TTGG -s mr.mrrefChr5 138131 4 + 294540 TTGG -s simCow_chr6.simCow.chr6 252121 4 - 602619 TTGG -s simDog_chr6.simDog.chr6 254264 4 - 593897 TTGG -s simHuman_chr6.simHuman.chr6 420456 4 - 601863 TTCA -s simRat_chr6.simRat.chr6 275414 4 + 647215 TTGG - -a -s simMouse_chr6.simMouse.chr6 287097 18 + 636262 TAGAGATAATAGGCTGCT -s Anc0.Anc0refChr5 84757 18 - 87904 TAAAGATAATAGGCTTCT -s Anc1.Anc1refChr8 41672 18 - 57822 TAAAGATAATAGGCTTCT -s Anc2.Anc2refChr14 4565 18 - 7748 TAAAGATAATAGGCTTCT -s mr.mrrefChr5 138135 18 + 294540 TAGAGATAATAGGCTGCT -s simCow_chr6.simCow.chr6 252126 17 - 602619 TGAAGATAATAAGCCTC- -s simDog_chr6.simDog.chr6 254268 18 - 593897 CAAAGATAATTGGCTTCT -s simHuman_chr6.simHuman.chr6 420460 18 - 601863 TAAAGATTATAGGCTTCT -s simRat_chr6.simRat.chr6 275418 18 + 647215 TAGAGATAATGGGCTACT - -a -s simMouse_chr6.simMouse.chr6 287115 2 + 636262 CT -s Anc0.Anc0refChr5 84776 2 - 87904 AA -s Anc1.Anc1refChr8 41691 2 - 57822 AA -s Anc2.Anc2refChr14 4584 2 - 7748 AA -s mr.mrrefChr5 138154 2 + 294540 CT -s simDog_chr6.simDog.chr6 254287 2 - 593897 AA -s simHuman_chr6.simHuman.chr6 420479 2 - 601863 AA -s simRat_chr6.simRat.chr6 275437 2 + 647215 CT - -a -s simMouse_chr6.simMouse.chr6 287117 4 + 636262 GTAA -s Anc0.Anc0refChr5 84778 4 - 87904 ACTA -s Anc1.Anc1refChr8 41693 4 - 57822 ACTA -s Anc2.Anc2refChr14 4586 4 - 7748 ACTA -s mr.mrrefChr5 138156 4 + 294540 ATAA -s simDog_chr6.simDog.chr6 254297 4 - 593897 ACTA -s simHuman_chr6.simHuman.chr6 420481 4 - 601863 ACTA -s simRat_chr6.simRat.chr6 275439 4 + 647215 ATAA - -a -s simMouse_chr6.simMouse.chr6 287121 18 + 636262 CTAGCACATAGCTTACAG -s Anc0.Anc0refChr5 84782 18 - 87904 CTAACATATATCTCATGA -s Anc1.Anc1refChr8 41697 18 - 57822 CTAACATATATCTCATGA -s Anc2.Anc2refChr14 4591 18 - 7748 CTCACATATATACCATTA -s mr.mrrefChr5 138160 18 + 294540 CTAACATATAGCTTACGG -s simCow_chr6.simCow.chr6 252144 18 - 602619 CTCACACATATACCAGTA -s simDog_chr6.simDog.chr6 254302 18 - 593897 CTCACATACACACCATTA -s simHuman_chr6.simHuman.chr6 420485 18 - 601863 TCAATATATCTCTCATGA -s simRat_chr6.simRat.chr6 275443 18 + 647215 CTAACATATAGCTTACGG - -a -s simMouse_chr6.simMouse.chr6 287139 6 + 636262 TTAGCA -s Anc0.Anc0refChr5 84817 6 - 87904 TTGGCA -s Anc1.Anc1refChr8 41732 6 - 57822 TTGGCA -s Anc2.Anc2refChr14 4626 6 - 7748 TTGGCA -s mr.mrrefChr5 138178 6 + 294540 TTAGCA -s simCow_chr6.simCow.chr6 252179 6 - 602619 TTGTCA -s simDog_chr6.simDog.chr6 254337 6 - 593897 TTGGTG -s simHuman_chr6.simHuman.chr6 420520 6 - 601863 TTGGCA -s simRat_chr6.simRat.chr6 275461 6 + 647215 TTAGCA - -a -s simMouse_chr6.simMouse.chr6 287145 133 + 636262 TACTAAAGGTATTCCTGATTCCTAGTAGGAAAGAAGTGGAATATGACATCCAAGTGATTTTATCTGTCAAGTGAGATGAGATCACTTGGATGTCATGTTCTACTTCTTTACTAAGACTGAGGGATACCCTTAG -s Anc0.Anc0refChr5 84823 65 - 87904 TACCAAGGGTACTCCCGGGTCTTAGTG---AAGGAACAAAATATGACATCCAACTGATCTTATCTGTT----------------------------------------------------------------- -s Anc1.Anc1refChr8 41738 65 - 57822 TACCAAGGGTACTCCCGGGTCTTAGTG---AAGGAACAAAATATGACATCCAACTGATCTTATCTGTT----------------------------------------------------------------- -s Anc2.Anc2refChr14 4632 65 - 7748 TAACAAGGGTACTCCCAGGTCTTAGTG---AAGGAACAAGATATGACATCCAACTGATTCTATCTGTT----------------------------------------------------------------- -s mr.mrrefChr5 138184 130 + 294540 TACCAAGGGTATTCCTGAGTCCTAGTA---AAGAAGTGGAATATGACATCCAACTGATCTTATCTGTCAAGTGAGATGAGATCACTTGGATGTCATGTTCTACTTCTTTACTAAGACTGAGGGATACCCTTAG -s simCow_chr6.simCow.chr6 252204 65 - 602619 TAACAAGGGTACTGCTTGGTCTTAGTA---AAGGAACAAGATATGGCATTCAACTGATTATATCTGTT----------------------------------------------------------------- -s simDog_chr6.simDog.chr6 254343 63 - 593897 TAACAAGGGTGCTCCCAGGTCTTAGTG---AAGGAATGGGGTA--ACATCCAATTGATTCTATCTGTT----------------------------------------------------------------- -s simHuman_chr6.simHuman.chr6 420526 65 - 601863 TACCACGGATACTCCCGGGTCTTAGTG---AAGGAACAAAATATGACATCCAACTGATCTTAACTGTT----------------------------------------------------------------- -s simRat_chr6.simRat.chr6 275467 130 + 647215 TACCAAGGGTATTCCTGAGTCCCAGTA---AAGAACTTGAATATGACATTCAACTGATCTTATCTGTCAAGTCAGATGAGATCACTTGGATGTTCTACTCTGCTTCTTTACTGAGACTCAGGAATACCCTTAG - -a -s simMouse_chr6.simMouse.chr6 287278 27 + 636262 ATGCTAAGGCTAAAAGCTTATGCCACA -s mr.mrrefChr5 138314 27 + 294540 ATGCTAAGGCTAAAAGCTTATGCCACA -s simRat_chr6.simRat.chr6 275598 27 + 647215 ATGCTAACTCTAGAAGCTCAACCCACG - -a -s simMouse_chr6.simMouse.chr6 287305 148 + 636262 CGCCAACCTCCCTAATGGAGGGGCTTGTGTTATTGTGGTGGCTCTGCACTGACTAAACATGAGCACAACTATGTGCCAGTTATAGAAGCCTATTATCTCTAACAAATGCTATTAACTTCCTCAGTCCTCGCTTTATAAGTTTCTACCA -s Anc0.Anc0refChr5 84888 9 - 87904 -----------------------------------------------------------------------------------------------------------------------------------------TGTTCTTA--A -s Anc1.Anc1refChr8 41803 11 - 57822 -----------------------------------------------------------------------------------------------------------------------------------------TGTTCTTATTA -s Anc2.Anc2refChr14 4697 9 - 7748 -----------------------------------------------------------------------------------------------------------------------------------------TGTTCTTA--A -s mr.mrrefChr5 138341 128 + 294540 CGCCAACCTCCCTAATGGAGGGGCTTGTGTTATTGTGGTGGCTCTGCACTGACTAAACATGAGCACAACTATGTGCCAGTTATAGAAGCCTATTATCTCTAACAAATGCTATTAAC--------------------AAGTTTCTACCA -s simCow_chr6.simCow.chr6 252269 9 - 602619 -----------------------------------------------------------------------------------------------------------------------------------------TGTTCTTG--A -s simDog_chr6.simDog.chr6 254406 9 - 593897 -----------------------------------------------------------------------------------------------------------------------------------------TGTTCTTA--A -s simHuman_chr6.simHuman.chr6 420591 11 - 601863 -----------------------------------------------------------------------------------------------------------------------------------------TGCCCTCATTA -s simRat_chr6.simRat.chr6 275629 128 + 647215 TGCCAAACTCCCAAATGGGGGGGCTTGTGTTATTGTGATGGCTCAGCACTGGCTAAACTTGAGCCCAGCTATGTGCCAGTTACAGAAGCCTCTTTTCTCTACCAAACGCTGTTAAC--------------------GAGTTTATACCA - -a -s simMouse_chr6.simMouse.chr6 287453 71 + 636262 GGACGTTATCGCGTCCCACAGCAACATGAGTATTATACCCAACATCTATCTGGGTGAGTTATGGTTAAGAA -s Anc0.Anc0refChr5 84900 58 - 87904 AG-------C-TGCCTATCAGGAA----AATTTCACACCCCACATCTATCTGCA-AAGCTATGGTGAAGAA -s Anc1.Anc1refChr8 41817 59 - 57822 AG-------C-TGCCTATCAGGAA----AATTTCACACCCCACATCTATCTGCAGAAGCTATGGTGAAGAA -s Anc2.Anc2refChr14 4709 58 - 7748 AG-------C-TGCCTATCAGGAA----AATTTCACACCCCACATCTATTTGCA-AAGCTATGGTGAAGAA -s mr.mrrefChr5 138469 64 + 294540 GG-------CGCGTCCCACAGCAACATGAGTATTATACCCAACATCTATCTGGGTGAGTTATGGTTAAGAA -s simCow_chr6.simCow.chr6 252281 58 - 602619 AG-------C-TGCCTATCAGGGA----AATGTCACATCCCAGATCTATTTGCA-AAGCTGTGGTAAAGAA -s simDog_chr6.simDog.chr6 254418 58 - 593897 CA-------T-TGCCTATCAGTAA----AATTTCCTACCCCACATCCATTTGCA-AAGCTATGGTGAATAA -s simHuman_chr6.simHuman.chr6 420605 59 - 601863 AG-------C-TGCCTATCAGGAA----AATTTCACACCCCATATCTATCTGCAGAAGCTATGGTGAAGAG -s simRat_chr6.simRat.chr6 275757 64 + 647215 AG-------CATGTTCCACAGCTATATGAGTATTACACACGACGCTTATTGGGGTGAGTTATGATAAAGAA - -a -s simMouse_chr6.simMouse.chr6 287524 24 + 636262 GGATTTGGAGTGTAAGTTTTCAGC -s Anc0.Anc0refChr5 84958 24 - 87904 GCATTTGGAGCGCAACTTCTTAGT -s Anc1.Anc1refChr8 41876 24 - 57822 GCATTTGGAGCGCAACTTCTTAGT -s Anc2.Anc2refChr14 4767 24 - 7748 GCATTTGGAGCACAACTTCTTAGT -s mr.mrrefChr5 138533 24 + 294540 GGATTTGGAGTGTAAGTTTTCAGC -s simCow_chr6.simCow.chr6 252339 21 - 602619 GCATCTGGAGCATAACATCTT--- -s simDog_chr6.simDog.chr6 254476 24 - 593897 GCATTTGGAGCACAACTTCTCAGT -s simHuman_chr6.simHuman.chr6 420664 21 - 601863 GTATTCAG---GCAACTTCTTAGT -s simRat_chr6.simRat.chr6 275823 24 + 647215 GCATTTGGAGTCTAGGTCTTCAGC - -a -s simMouse_chr6.simMouse.chr6 287548 18 + 636262 AACACAGACGACGTAGGC -s Anc0.Anc0refChr5 84983 18 - 87904 AACACAGTAGATGTAGGC -s Anc1.Anc1refChr8 41901 18 - 57822 AACACAGTAGATGTAGGC -s Anc2.Anc2refChr14 4792 18 - 7748 AGCACAGTAGATGTAGGC -s mr.mrrefChr5 138557 18 + 294540 AACACAGACGACGTAGGC -s simCow_chr6.simCow.chr6 252360 18 - 602619 ACCACAGGAGATGTAGGC -s simDog_chr6.simDog.chr6 254501 18 - 593897 AGCACAGTAGATGTGGGC -s simHuman_chr6.simHuman.chr6 420686 18 - 601863 AACACAGCAGATGTAGGC -s simRat_chr6.simRat.chr6 275847 18 + 647215 AACACAGGAGATGTAGGC - -a -s simMouse_chr6.simMouse.chr6 287566 25 + 636262 CTATTTCACTCATAATCAAGCAGTA -s Anc0.Anc0refChr5 85001 25 - 87904 ACCCATCTCTCACAATCAAACAGTA -s Anc1.Anc1refChr8 41919 25 - 57822 ACCCATCTCTCACAATCAAACAGTA -s Anc2.Anc2refChr14 4810 25 - 7748 ACCCATCTATCACAATCAAACAGTG -s mr.mrrefChr5 138575 25 + 294540 CTATTTCACTCATAATCAAGCAGTA -s simCow_chr6.simCow.chr6 252379 25 - 602619 CCCCATTGATCACCATCAAACAGTG -s simDog_chr6.simDog.chr6 254519 21 - 593897 AACCATCTATCACAGTCAAAC---- -s simHuman_chr6.simHuman.chr6 420704 25 - 601863 TCCCGTCTCTCACAATCAAACATTA -s simRat_chr6.simRat.chr6 275865 25 + 647215 TTATTTCACTTGTAATCAAGCAGTA - -a -s simMouse_chr6.simMouse.chr6 287591 13 + 636262 ATAATGTAGGTCG -s Anc0.Anc0refChr5 85026 13 - 87904 GTAAGGTAGTTCA -s Anc1.Anc1refChr8 41944 13 - 57822 GTAAGGTAGTTCA -s Anc2.Anc2refChr14 4835 13 - 7748 GTAAGGTAGTGCA -s mr.mrrefChr5 138600 13 + 294540 ATAATGTAGGTCG -s simCow_chr6.simCow.chr6 252404 13 - 602619 GTAATGTAGTCCA -s simDog_chr6.simDog.chr6 254540 10 - 593897 ---AGATCATGTA -s simHuman_chr6.simHuman.chr6 420729 13 - 601863 GTAAGGTAGCTCA -s simRat_chr6.simRat.chr6 275987 13 + 647215 ATAATGTAGGTTG - -a -s simMouse_chr6.simMouse.chr6 287604 7 + 636262 AAATCAT -s Anc0.Anc0refChr5 85044 7 - 87904 TAATCAA -s Anc1.Anc1refChr8 41962 7 - 57822 TAATCAA -s Anc2.Anc2refChr14 4853 7 - 7748 TAATCCA -s mr.mrrefChr5 138613 7 + 294540 AAATCAT -s simCow_chr6.simCow.chr6 252424 3 - 602619 TA----A -s simDog_chr6.simDog.chr6 254555 7 - 593897 AAATCCA -s simHuman_chr6.simHuman.chr6 420749 7 - 601863 TAATCAG -s simRat_chr6.simRat.chr6 276000 7 + 647215 AAATTAT - -a -s simMouse_chr6.simMouse.chr6 287611 1 + 636262 T -s Anc0.Anc0refChr5 85051 1 - 87904 G -s Anc1.Anc1refChr8 41969 1 - 57822 G -s Anc2.Anc2refChr14 4862 1 - 7748 G -s mr.mrrefChr5 138620 1 + 294540 T -s simCow_chr6.simCow.chr6 252429 1 - 602619 G -s simDog_chr6.simDog.chr6 254564 1 - 593897 G -s simHuman_chr6.simHuman.chr6 420756 1 - 601863 G -s simRat_chr6.simRat.chr6 276007 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 287612 13 + 636262 AGGACACAAAAAA -s Anc0.Anc0refChr5 85059 8 - 87904 AGGAC---AAG-- -s Anc1.Anc1refChr8 41977 8 - 57822 AGGAC---AAG-- -s Anc2.Anc2refChr14 4870 8 - 7748 AGGAC---AAG-- -s mr.mrrefChr5 138621 11 + 294540 AGGACACAAAA-- -s simCow_chr6.simCow.chr6 252437 8 - 602619 TGGCC---AAG-- -s simDog_chr6.simDog.chr6 254572 8 - 593897 AGGAC---AAG-- -s simHuman_chr6.simHuman.chr6 420764 8 - 601863 AGGAC---AGG-- -s simRat_chr6.simRat.chr6 276008 11 + 647215 AGAACACAAGA-- - -a -s simMouse_chr6.simMouse.chr6 287625 12 + 636262 TAGTCATATATA -s Anc0.Anc0refChr5 85067 12 - 87904 TAGTCATATATA -s Anc1.Anc1refChr8 41985 12 - 57822 TAGTCATATATA -s Anc2.Anc2refChr14 4878 12 - 7748 TAGTCATATATA -s mr.mrrefChr5 138632 12 + 294540 TAGTCATATATA -s simCow_chr6.simCow.chr6 252445 12 - 602619 TAGTCGTATATA -s simDog_chr6.simDog.chr6 254863 12 - 593897 TAGTCATATATA -s simHuman_chr6.simHuman.chr6 420772 12 - 601863 TAGTCATATACA -s simRat_chr6.simRat.chr6 276019 12 + 647215 TAGTTATACATA - -a -s simMouse_chr6.simMouse.chr6 287637 5 + 636262 TTTAG -s Anc0.Anc0refChr5 85079 5 - 87904 TTTAG -s Anc1.Anc1refChr8 41997 5 - 57822 TTTAG -s Anc2.Anc2refChr14 4890 5 - 7748 TTTAG -s mr.mrrefChr5 138644 5 + 294540 TTTAG -s simCow_chr6.simCow.chr6 252463 5 - 602619 TTAGG -s simDog_chr6.simDog.chr6 254875 5 - 593897 TTTAG -s simHuman_chr6.simHuman.chr6 420784 5 - 601863 TTTAG -s simRat_chr6.simRat.chr6 276031 5 + 647215 TCTAG - -a -s simMouse_chr6.simMouse.chr6 287642 33 + 636262 TACCATGAAAATATCCCCATGATGATGACCAAG -s Anc0.Anc0refChr5 85096 33 - 87904 TATAATGAAAGTTTCCCCAGAATGATGACCTAT -s Anc1.Anc1refChr8 42014 33 - 57822 TATAATGAAAGTTTCCCCAGAATGATGACCTAT -s Anc2.Anc2refChr14 4907 33 - 7748 TATAATTAAAGGTTCCCCAGAATGATGACCTAT -s mr.mrrefChr5 138649 33 + 294540 TACCATGAAAATATCCCCATGATGATGACCAAG -s simCow_chr6.simCow.chr6 252480 32 - 602619 GATAATAAAAGGTTCCCCAGAA-GGTGACCAGT -s simDog_chr6.simDog.chr6 254892 33 - 593897 TATAATTAAAGGCTCCCCAGAATGATGACCTAT -s simHuman_chr6.simHuman.chr6 420801 33 - 601863 TATAATGAAAGTTTCCCCAGAGTGATGACCTAT -s simRat_chr6.simRat.chr6 276036 33 + 647215 TACAATGAAAGTATCACCATGATGGTGACCGAG - -a -s simMouse_chr6.simMouse.chr6 287675 4 + 636262 CTTG -s Anc0.Anc0refChr5 85129 4 - 87904 CTTG -s Anc1.Anc1refChr8 42047 4 - 57822 CTTG -s Anc2.Anc2refChr14 4940 4 - 7748 CTTG -s mr.mrrefChr5 138682 4 + 294540 CTTG -s simCow_chr6.simCow.chr6 252513 4 - 602619 TTTG -s simDog_chr6.simDog.chr6 254925 4 - 593897 CTTC -s simHuman_chr6.simHuman.chr6 420834 4 - 601863 CTTG -s simRat_chr6.simRat.chr6 276069 4 + 647215 CCTG - -a -s simMouse_chr6.simMouse.chr6 287679 23 + 636262 TTTTTTATCTTGTCTTGTGGGGA -s Anc0.Anc0refChr5 85135 18 - 87904 CTTTTTACAGTGA-----GAGGA -s Anc1.Anc1refChr8 42053 18 - 57822 CTTTTTACAGTGA-----GAGGA -s Anc2.Anc2refChr14 4946 18 - 7748 CTTTTTGCAGTGA-----GAGAA -s mr.mrrefChr5 138686 18 + 294540 TTTTTTATCTTGT-----GGGGA -s simCow_chr6.simCow.chr6 252519 18 - 602619 TTTTTTGCAGTGA-----GAGAA -s simDog_chr6.simDog.chr6 254931 18 - 593897 CTTTTTGCAGTGA-----GAGAA -s simHuman_chr6.simHuman.chr6 420840 18 - 601863 CTCTTAACAATGA-----GAGGA -s simRat_chr6.simRat.chr6 276073 18 + 647215 GTTTTTATCTTGT-----GAAGA - -a -s simMouse_chr6.simMouse.chr6 287702 20 + 636262 GAATAATTAGCACATACTTG -s Anc0.Anc0refChr5 85171 20 - 87904 GAACAATCATTACAGTATTG -s Anc1.Anc1refChr8 42089 20 - 57822 GAACAATCATTACAGTATTG -s Anc2.Anc2refChr14 4982 20 - 7748 GAACAATCATTACAGTAATG -s mr.mrrefChr5 138704 20 + 294540 GAATAATTAGCACATACTTG -s simCow_chr6.simCow.chr6 252555 19 - 602619 AAACAATCATTACAGTACT- -s simDog_chr6.simDog.chr6 254967 20 - 593897 GAACAATCATTGCGGTAATG -s simHuman_chr6.simHuman.chr6 420876 20 - 601863 GAACAACCATTACAGTATTG -s simRat_chr6.simRat.chr6 276091 20 + 647215 GAATAATTAGCTCATACTCA - -a -s simMouse_chr6.simMouse.chr6 287722 56 + 636262 TGGACAATTAAGGTATGCCCTACCCATTATCGCATATTTTCTGGCTTGGGGTTGAA -s Anc0.Anc0refChr5 85268 45 - 87904 ----AGGT---TGTATACCCTAACCACAGTCTCATAGCTTCTG----GGGGACAGG -s Anc1.Anc1refChr8 42186 49 - 57822 TGGGAGGT---TGTATACCCTAACCACAGTCTCATAGCTTCTG----GGGGACAGG -s Anc2.Anc2refChr14 5079 45 - 7748 ----AGGT---TGAATACCCTAACCCCAGTTTCAGAGCTTCTT----GGGGACAGG -s mr.mrrefChr5 138724 56 + 294540 TGGACAATTAAGGTATGCCCTACCCATTATCGCATATTTTCTGGCTTGGGGATGGA -s simCow_chr6.simCow.chr6 252652 44 - 602619 ----AGGT---CAAATTCCCTAA-CTCAGTTTCACAGTTTCTT----GGGGACGGG -s simDog_chr6.simDog.chr6 255133 45 - 593897 ----AGGT---TGAATACCATCACCCCAGTTTCAGAGCTTCTT----GGGGCTATG -s simHuman_chr6.simHuman.chr6 421006 49 - 601863 TGGGAGGT---AGTATAGCCTAACCACAGTCTCATACCTTCTG----GGGGACAGG -s simRat_chr6.simRat.chr6 276111 56 + 647215 TGAACAATCAAGGTATGCCCCACCCATTATTGCATATTTTCTGGCTGGGAGATGGA - -a -s simMouse_chr6.simMouse.chr6 287778 10 + 636262 GACACTACTC -s Anc0.Anc0refChr5 85313 10 - 87904 GACTTTACTA -s Anc1.Anc1refChr8 42235 10 - 57822 GACTTTACTA -s Anc2.Anc2refChr14 5124 10 - 7748 GACCTGACAA -s mr.mrrefChr5 138780 10 + 294540 GACTCTACTC -s simCow_chr6.simCow.chr6 253291 10 - 602619 GATCTAACAT -s simDog_chr6.simDog.chr6 255178 10 - 593897 GACCTGACAA -s simHuman_chr6.simHuman.chr6 421055 9 - 601863 GACT-TCCTA -s simRat_chr6.simRat.chr6 276167 10 + 647215 GACTCTACGC - -a -s simMouse_chr6.simMouse.chr6 287788 8 + 636262 ATCTTATT -s Anc0.Anc0refChr5 85323 8 - 87904 ATCTTATT -s Anc1.Anc1refChr8 42245 8 - 57822 ATCTTATT -s Anc2.Anc2refChr14 5134 8 - 7748 GGCTTATG -s mr.mrrefChr5 138790 8 + 294540 ATCTTATT -s simCow_chr6.simCow.chr6 253302 8 - 602619 GACCTATG -s simDog_chr6.simDog.chr6 255188 8 - 593897 GGCTTATG -s simHuman_chr6.simHuman.chr6 421064 8 - 601863 ATCTTGTT -s simRat_chr6.simRat.chr6 276177 8 + 647215 ATCTTATT - -a -s simMouse_chr6.simMouse.chr6 287796 7 + 636262 CAACCTC -s Anc0.Anc0refChr5 85331 6 - 87904 CA-CCTC -s Anc1.Anc1refChr8 42253 7 - 57822 CATCCTC -s Anc2.Anc2refChr14 5142 6 - 7748 CA-CCTT -s mr.mrrefChr5 138798 7 + 294540 CATCCTC -s simCow_chr6.simCow.chr6 253314 6 - 602619 CA-TCTT -s simDog_chr6.simDog.chr6 255196 6 - 593897 CA-CCTT -s simHuman_chr6.simHuman.chr6 421072 7 - 601863 CATCCTC -s simRat_chr6.simRat.chr6 276185 7 + 647215 CATCCTC - -a -s simMouse_chr6.simMouse.chr6 287803 15 + 636262 TCTGTGACTCCCTCC -s Anc0.Anc0refChr5 85338 15 - 87904 TATGTGACTACCTGC -s Anc1.Anc1refChr8 42261 15 - 57822 TATGTGACTACCTGC -s Anc2.Anc2refChr14 5149 15 - 7748 TATGTGACTACCTGC -s mr.mrrefChr5 138805 15 + 294540 TCTGTGACTCCCTCC -s simCow_chr6.simCow.chr6 253321 15 - 602619 TATGTGACTACCTGC -s simDog_chr6.simDog.chr6 255203 15 - 593897 TATGTGACTACCTGC -s simHuman_chr6.simHuman.chr6 421080 15 - 601863 TATGTAACTACCAAC -s simRat_chr6.simRat.chr6 276192 15 + 647215 TTTATGACTCCCTCC - -a -s simMouse_chr6.simMouse.chr6 287818 118 + 636262 TTCATGATAGTTCCCATTACCTGACAGCTTTGCAGCATAGCAAGTTTAAAACATTCATGCTCTTTACCACCTCTACTAGCTCCATCCAGCATATTTTGAGAGCAGCAGATCATGGAGG -s Anc0.Anc0refChr5 85353 113 - 87904 TGCATGGCAGATCCCAGTACTTAACAGTTTTGCAGTATAGTCATCATAAAACTTTCAT--TCTTTGCCACCTTTACTAACACCCTCCAGGATATCAT--GGGCAGCAGATTATAGA-G -s Anc1.Anc1refChr8 42276 117 - 57822 TGCATGGCAGATCCCAGTACTTAACAGTTTTGCAGTATAGTCATCATAAAACTTTCATACTCTTTGCCACCTTTACTAACACCCTCCAGGATATCATAAGGGCAGCAGATTATAGA-G -s Anc2.Anc2refChr14 5164 113 - 7748 TGCATGGCAGATCACAGTACTCAACAGTTTTGCAGTATAGTCATCATAATACTTTCAT--TCTCTGCTACCTTTACTAACACCCTCCAGGATATCAT--GCATGGCAGATTACAGA-G -s mr.mrrefChr5 138820 118 + 294540 TTCATGATAGTTCCCATTACCTAACAGCTTTGCAGCATAGTAAGTTTAAAACTTTCATGCTCTTTACCACCTCTACTAGCTCCATCCAGCATATTTTGAGGGCAGCAGATCATGGAGG -s simCow_chr6.simCow.chr6 253336 110 - 602619 TCCATGGCAGA--ACAGTACTGGA-AGTTTTGCAGTCTAGTCATCATAATACTTACAA--TCCCTGCTCACTCGTCTTACACCCTCCAGGATATCAT--GCATGGCTGACTACAGG-G -s simDog_chr6.simDog.chr6 255218 83 - 593897 TGCATGCCAGATCACAGTACTCAACAGTTTTACAGTAT-------------CTTTCAT--TCTCTGCCACCTTTACTAATGCCCTTC------------------CAGGTTA-AGA-G -s simHuman_chr6.simHuman.chr6 421095 116 - 601863 TGCATGGCAGATCCCAGGACTTAACACTTTTGTATTATTGTCATAAGAAAACTTTCATACT-TTTCTCACCTTTACTAACACCCTCTAGACCATCATAAGGGCAGCAGATTATAGC-G -s simRat_chr6.simRat.chr6 276208 116 + 647215 TTCATGATAGTTCCCACTACCCAACAGCTTTGCAGCATAGTAAGTCTAAAACTTTCATTCTCTTAACCACCTCTACTAGCTCCATCCAGCATATTTTGAGGGC--CAGATCATGGAGG - -a -s simMouse_chr6.simMouse.chr6 287936 39 + 636262 GACAAGCTCATTAGGTGATCAAGCGGTGACTTCAAACAA -s Anc0.Anc0refChr5 85466 39 - 87904 CACCAGTAAAATAGGTGATTAAGTAGCAAGTTCAGATAA -s Anc1.Anc1refChr8 42393 39 - 57822 CACCAGTAAAATAGGTGATTAAGTAGCAAGTTCAGATAA -s Anc2.Anc2refChr14 5277 39 - 7748 CACCAGTAAAACAGGTGATTAAGTAACAAGTTCAGATAA -s mr.mrrefChr5 138938 39 + 294540 GACAAGTACATTAGGTGATCAAGTGGTGACTTCAAACAA -s simCow_chr6.simCow.chr6 253447 36 - 602619 CACAAGTAAAAGAGGTGATTAA---ACGAGTTCAGATAG -s simDog_chr6.simDog.chr6 255301 39 - 593897 CACCAGTAAAACAGGTGATTAAGTAACAAATACAGATAA -s simHuman_chr6.simHuman.chr6 421211 39 - 601863 CACTAGTAAAATAGGTGATTATGTAGCAAGTTCAGGTCA -s simRat_chr6.simRat.chr6 276324 39 + 647215 GATAAGTACATTAGGTGATCAAGTGGTGACTTCAAACAA - -a -s simMouse_chr6.simMouse.chr6 287975 31 + 636262 GATCAGTTGGGTTGGAAATTCTCTGAAGGCA -s Anc0.Anc0refChr5 85507 31 - 87904 GATCAGTTGGTTCTGAAAATTCCTGAGGGTA -s Anc1.Anc1refChr8 42434 31 - 57822 GATCAGTTGGTTCTGAAAATTCCTGAGGGTA -s Anc2.Anc2refChr14 5318 31 - 7748 GATTAGTTGGTTCTGAAAATTCCTGAGGGTA -s mr.mrrefChr5 138977 31 + 294540 GATCAGTTGGGTTGGAAATTTTCTGAGGGCA -s simCow_chr6.simCow.chr6 253485 29 - 602619 GACTAGTTGGTACTGAAAATTACTGAGTG-- -s simDog_chr6.simDog.chr6 255342 31 - 593897 GATTATTTGGTTCTGAAAATTCCTGAGGGTA -s simHuman_chr6.simHuman.chr6 421252 31 - 601863 AATCAGGTGTTTCTGAAAATTCCTGAGGGTA -s simRat_chr6.simRat.chr6 276363 31 + 647215 GATCTGCTGGGTTGGAAAGTTTCTGAGGGCA - -a -s simMouse_chr6.simMouse.chr6 288006 33 + 636262 AGGTGCTTCTGTCATCTGCACCCTAGTCCCTTG -s Anc0.Anc0refChr5 85538 33 - 87904 AGGTACACCTGTCATTTGCATTCTTGTTCCTTG -s Anc1.Anc1refChr8 42465 33 - 57822 AGGTACACCTGTCATTTGCATTCTTGTTCCTTG -s Anc2.Anc2refChr14 5354 33 - 7748 GGGTACACCTGCCATTTGCAATCTTGTTCCTTG -s mr.mrrefChr5 139008 33 + 294540 AGGTGCTTCTGTCATCTGCATCCTAGTCCCTTG -s simCow_chr6.simCow.chr6 253517 33 - 602619 GGGTACACCAGACATTTACAATCTTGTTCCTTG -s simDog_chr6.simDog.chr6 255378 33 - 593897 GGGTACACTTACCATCTGTGATCCTGTTCCTTG -s simHuman_chr6.simHuman.chr6 421283 33 - 601863 AGGAACCCCTGTCGTTTGCATTGTTGTTCCTTG -s simRat_chr6.simRat.chr6 276394 33 + 647215 TGGTGCTTCTGTCATCTGCATCATGCTCCCTTG - -a -s simMouse_chr6.simMouse.chr6 288039 21 + 636262 GCCCCACATGTGAGTAGGGTG -s Anc0.Anc0refChr5 85571 21 - 87904 ATCCTAGATTTGAGTAAGACT -s Anc1.Anc1refChr8 42498 21 - 57822 ATCCTAGATTTGAGTAAGACT -s Anc2.Anc2refChr14 5387 21 - 7748 ATCCTAGATTTGAGTAAGACT -s mr.mrrefChr5 139041 21 + 294540 GCCCCACATGTGAGTAAGGTG -s simCow_chr6.simCow.chr6 253550 21 - 602619 ATCCTAGATTTGAGTAAGACT -s simDog_chr6.simDog.chr6 255414 21 - 593897 ATCTTAGATTTGAGTAAGACT -s simHuman_chr6.simHuman.chr6 421316 21 - 601863 ATCCTAGATTCGCGTAAGTCT -s simRat_chr6.simRat.chr6 276427 21 + 647215 GCCCCATGTATGAGTAAGGTG - -a -s simMouse_chr6.simMouse.chr6 288060 89 + 636262 CCCACAATCATCTGATCTAGGAGTCTGTCTTTTGGATCTGAAGAGGTTAGCCTAAAGTATATCATAGAGAAAGGGTCACTGTGGAGGGG -s Anc0.Anc0refChr5 85596 89 - 87904 CCCGCAATCATCTGAATTAGGAGTCTGTCTTCTGGACCTGATGGGGATAGCCTAAAGTATATCATAGGGAAAGAGTCATTGTGGTGGGG -s Anc1.Anc1refChr8 42523 89 - 57822 CCCGCAATCATCTGAATTAGGAGTCTGTCTTCTGGACCTGATGGGGATAGCCTAAAGTATATCATAGGGAAAGAGTCATTGTGGTGGGG -s Anc2.Anc2refChr14 5412 89 - 7748 CTTGCAATCATCTGAATTAGGAGTCTGTCTTCTGGACCTGATGGGGATAGCCTAAAGTATATCATAGGGAAAGAGCCATTCTGGTGGGG -s mr.mrrefChr5 139062 89 + 294540 CCCACAATCATCTGATCTAGGAGTCTGTCTTCTGGATCTGAAGAGGATAGCCTAAAGTATATCATAGAGAAAGGGTCACTGTGGAGGGG -s simCow_chr6.simCow.chr6 253575 89 - 602619 GTTGCACTCATCCAAATTGCATGTATGGCTTCTGGGACTCACGAGGATAGCATAAAGTATACTATAGGGAAAGAGCCATTCTGGCGGGG -s simDog_chr6.simDog.chr6 255439 89 - 593897 CTTGCAATCATCTGAATTAGGAGTCTGTCTGTTGGACCTGATAGGAATAGCCTAAAGTATATCATAGGGAAAGAGCTGTTCCAGTGGGG -s simHuman_chr6.simHuman.chr6 421341 89 - 601863 CCCGCAATCATCTGAATTATGAGTTTGTCTTCTGGACCTGAGGGGGAAAGCCTAAACTATATCATAGGGGAAGAGTCATTGTGGTAGGG -s simRat_chr6.simRat.chr6 276448 89 + 647215 CCCACAATTATCTGATCTAGGAGTCTGTCTTCTGGATCTGAAAAAGATAGCCTACAGTATATCATAGAGAAACGGTCAATATGGAGGGG - -a -s simMouse_chr6.simMouse.chr6 288149 13 + 636262 AAATGTAAGCACT -s Anc0.Anc0refChr5 85685 12 - 87904 ATAC-TAAGTACT -s Anc1.Anc1refChr8 42612 12 - 57822 ATAC-TAAGTACT -s Anc2.Anc2refChr14 5501 12 - 7748 ATAC-TAAATACT -s mr.mrrefChr5 139151 13 + 294540 AAATGTAAGCACT -s simCow_chr6.simCow.chr6 253767 12 - 602619 ATAA-TAAATACC -s simDog_chr6.simDog.chr6 255528 12 - 593897 ATAC-TAAAAATT -s simHuman_chr6.simHuman.chr6 421430 12 - 601863 ATAC-TAAGTACT -s simRat_chr6.simRat.chr6 276537 13 + 647215 AAATATAAGCACT - -a -s simMouse_chr6.simMouse.chr6 288162 37 + 636262 TGTGGTTGCTGAAGATGATGTGGATAGGAACAGCAAA -s Anc0.Anc0refChr5 85697 25 - 87904 CCTGAAAGCTTCAGA------------GAGGTGCATA -s Anc1.Anc1refChr8 42624 35 - 57822 CCTGAAAGCTTCAGA--GTTGACATAGGAGGTGCATA -s Anc2.Anc2refChr14 5513 25 - 7748 CTTGAAAGCTTTAGA------------GAGGTGCATG -s mr.mrrefChr5 139164 37 + 294540 TCTGGTTGCTGCAGATGGTGTGCATAGGAACAGCAAA -s simCow_chr6.simCow.chr6 253779 25 - 602619 CTTGAAAGCTTTAGA------------GAGGTGCATG -s simDog_chr6.simDog.chr6 255540 21 - 593897 CTTGAAAGCTTTAGA------------GATGTG---- -s simHuman_chr6.simHuman.chr6 421452 35 - 601863 CCTGAGAACTTCAGA--GTTGACATAGGAGGTGCAGA -s simRat_chr6.simRat.chr6 276550 37 + 647215 TCTGGTGGCTGCAGATGGTGTGCATAGGAACAGCAAA - -a -s simMouse_chr6.simMouse.chr6 288199 35 + 636262 CTTCAATAATGCCCCTACTTTTTCTTTGCCATCTA -s Anc0.Anc0refChr5 85722 35 - 87904 CTACACCAGGGTTCTTGCCTTTTCCTTGTGATCTA -s Anc1.Anc1refChr8 42659 35 - 57822 CTACACCAGGGTTCTTGCCTTTTCCTTGTGATCTA -s Anc2.Anc2refChr14 5538 35 - 7748 CTACACCAGGGTTCTTGCCTTTTCCTTGTGATCTA -s mr.mrrefChr5 139201 35 + 294540 CTTCAATAATGCTCTTGCTTTTTCCTTGTCATCTA -s simCow_chr6.simCow.chr6 253818 34 - 602619 CTATGCTGGGGTTCTTGCCCTTTCCTTG-GATCTG -s simDog_chr6.simDog.chr6 255561 34 - 593897 -TACACCATGGATCTTGCCTTTTCCTTGTGATCCA -s simHuman_chr6.simHuman.chr6 421487 35 - 601863 CTACATCAGGGTTCTTGCCTTTTCCTTGTGATTTA -s simRat_chr6.simRat.chr6 276587 35 + 647215 CTTCAATAAAGCTCTTGCTTTTTCCTTGTCATCTA - -a -s simMouse_chr6.simMouse.chr6 288234 13 + 636262 TAAAGAAGATACA -s Anc0.Anc0refChr5 85772 5 - 87904 TAAA--------A -s Anc1.Anc1refChr8 42709 13 - 57822 TAAATATGATATA -s Anc2.Anc2refChr14 5588 5 - 7748 TAAG--------A -s mr.mrrefChr5 139236 13 + 294540 TAAAGAAGATACA -s simCow_chr6.simCow.chr6 253867 5 - 602619 TGAG--------A -s simDog_chr6.simDog.chr6 255610 3 - 593897 TAA---------- -s simHuman_chr6.simHuman.chr6 421537 13 - 601863 TAAATATGATATT -s simRat_chr6.simRat.chr6 276622 13 + 647215 AAAAGAAGATACA - -a -s simMouse_chr6.simMouse.chr6 288247 64 + 636262 GAAACATTTTATGTAGTTAAGGTAAGGCATGTCAGAGCCCCTTTGAAGGAATATCCTCTGCGAT -s Anc0.Anc0refChr5 85777 43 - 87904 GAGTCATTTT---------------GATCTGTAAACACCCC---TAAGGCATA---TCTTGGAC -s Anc1.Anc1refChr8 42722 43 - 57822 GAGTCATTTT---------------GATCTGTAAACACCCC---TAAGGCATA---TCTTGGAC -s Anc2.Anc2refChr14 5593 43 - 7748 TAGTCATGTG---------------AATCTGTAAACACCCC---TAAGGCTCA---TCTTGGAC -s mr.mrrefChr5 139249 64 + 294540 GAGACATTTTATGTAGTTAAGGTAAGGCATGTCAGAGCCCCTTTGAAGGAATATCCTCTGCGAT -s simCow_chr6.simCow.chr6 253872 43 - 602619 TAGTCATGTG---------------AATCTGTAAACACCCC---TAAGGCTCA---TCTTCGAC -s simDog_chr6.simDog.chr6 255613 13 - 593897 ------------------------------------------------GCTCA---TGCTGGCA -s simHuman_chr6.simHuman.chr6 421550 43 - 601863 GAGTCATTTT---------------GATCCATAAACATTCC---AAAGGCATG---TCTTTGAC -s simRat_chr6.simRat.chr6 276669 64 + 647215 GGGAGATTTTATGTAGCTAAGGTAAGGTATGTCAAAGCCTCTTCTGAGGAATATCTTCAGCAAT - -a -s simMouse_chr6.simMouse.chr6 288311 8 + 636262 TTATTTTC -s Anc0.Anc0refChr5 85820 8 - 87904 ATATAGTG -s Anc1.Anc1refChr8 42765 8 - 57822 ATATAGTG -s Anc2.Anc2refChr14 5636 8 - 7748 ATATAGTG -s mr.mrrefChr5 139313 8 + 294540 TTATTTTC -s simCow_chr6.simCow.chr6 253915 8 - 602619 AGATAGTG -s simDog_chr6.simDog.chr6 255628 8 - 593897 ATGTAGTT -s simHuman_chr6.simHuman.chr6 421593 8 - 601863 ATATAGTG -s simRat_chr6.simRat.chr6 276733 8 + 647215 TTATTGTC - -a -s simMouse_chr6.simMouse.chr6 288319 4 + 636262 ACTT -s Anc0.Anc0refChr5 85828 4 - 87904 AGTT -s Anc1.Anc1refChr8 42773 4 - 57822 AGTT -s Anc2.Anc2refChr14 5644 4 - 7748 AGTT -s mr.mrrefChr5 139321 4 + 294540 ACTT -s simCow_chr6.simCow.chr6 253923 4 - 602619 AGTT -s simDog_chr6.simDog.chr6 255637 4 - 593897 AATA -s simHuman_chr6.simHuman.chr6 421601 4 - 601863 AGTT -s simRat_chr6.simRat.chr6 276741 4 + 647215 ACTT - -a -s simMouse_chr6.simMouse.chr6 288323 8 + 636262 GTAGACCA -s Anc0.Anc0refChr5 85833 8 - 87904 GGAGACCA -s Anc1.Anc1refChr8 42778 8 - 57822 GGAGACCA -s Anc2.Anc2refChr14 5649 8 - 7748 GGAGACCA -s mr.mrrefChr5 139325 8 + 294540 GTAGACCA -s simCow_chr6.simCow.chr6 253933 8 - 602619 GAAGACCA -s simDog_chr6.simDog.chr6 255642 8 - 593897 GGAGACAA -s simHuman_chr6.simHuman.chr6 421606 8 - 601863 GGAGACCA -s simRat_chr6.simRat.chr6 276745 8 + 647215 GCAGTCCA - -a -s simMouse_chr6.simMouse.chr6 288331 7 + 636262 CCCATGT -s Anc0.Anc0refChr5 85845 7 - 87904 CAGAGGT -s Anc1.Anc1refChr8 42790 7 - 57822 CAGAGGT -s Anc2.Anc2refChr14 5661 7 - 7748 GAGAGGA -s mr.mrrefChr5 139333 7 + 294540 CCCATGT -s simCow_chr6.simCow.chr6 253945 7 - 602619 GAGAGGC -s simDog_chr6.simDog.chr6 255654 7 - 593897 GAGAGGA -s simHuman_chr6.simHuman.chr6 421618 7 - 601863 CAGAGGT -s simRat_chr6.simRat.chr6 276753 7 + 647215 CCCTTGT - -a -s simMouse_chr6.simMouse.chr6 288338 7 + 636262 TTAACTA -s Anc0.Anc0refChr5 85854 7 - 87904 TTAGCTA -s Anc1.Anc1refChr8 42799 7 - 57822 TTAGCTA -s Anc2.Anc2refChr14 5670 7 - 7748 TGGGTTA -s mr.mrrefChr5 139340 7 + 294540 TTAACTA -s simCow_chr6.simCow.chr6 253954 7 - 602619 TGGGGTA -s simDog_chr6.simDog.chr6 255663 7 - 593897 TGGGTTA -s simHuman_chr6.simHuman.chr6 421627 7 - 601863 TTAGCTA -s simRat_chr6.simRat.chr6 276760 7 + 647215 TTAATTA - -a -s simMouse_chr6.simMouse.chr6 288345 199 + 636262 TCACTTGTGGATCACTTATATAACAGTTTACAACTGGTTGTTTACATTGAAAGTGGGCCTTGTTACCAAGAGTGATTCCCAGCACCCTATACTATAGTGTTTGTTCTGTTGCATCTACCCTAGCCAAGTATATGTATTCAGAGCATGGAGAATACCTGCACCGCCAAGGTCAGCCATATCATTCATACATGGAACATAA -s Anc0.Anc0refChr5 85864 8 - 87904 TCATT--------------------------------------------T--------------------A-------------------------------------------------------------------------------------------------------------------------------A -s Anc1.Anc1refChr8 42809 8 - 57822 TCATT--------------------------------------------T--------------------A-------------------------------------------------------------------------------------------------------------------------------A -s Anc2.Anc2refChr14 5680 8 - 7748 TCATT--------------------------------------------T--------------------G-------------------------------------------------------------------------------------------------------------------------------A -s mr.mrrefChr5 139347 28 + 294540 TCACT--------------------------------------------AAAGTGGGCCTTGTTACCAAGA-------------------------------------------------------------------------------------------------------------------------------A -s simCow_chr6.simCow.chr6 253964 8 - 602619 TCATT--------------------------------------------T--------------------G-------------------------------------------------------------------------------------------------------------------------------A -s simDog_chr6.simDog.chr6 255673 8 - 593897 TCATT--------------------------------------------T--------------------G-------------------------------------------------------------------------------------------------------------------------------A -s simHuman_chr6.simHuman.chr6 421637 8 - 601863 TCATT--------------------------------------------T--------------------A-------------------------------------------------------------------------------------------------------------------------------A -s simRat_chr6.simRat.chr6 276767 27 + 647215 TCACT--------------------------------------------AAAGTGGGCCTTGTTTTCAAGG-------------------------------------------------------------------------------------------------------------------------------- - -a -s simMouse_chr6.simMouse.chr6 288544 14 + 636262 TTCCAGCATCATAA -s Anc0.Anc0refChr5 85872 14 - 87904 CTGCAGCCCCGGAA -s Anc1.Anc1refChr8 42817 14 - 57822 CTGCAGCCCCGGAA -s Anc2.Anc2refChr14 5688 14 - 7748 CTGCAGCCCAGGAA -s mr.mrrefChr5 139375 14 + 294540 TTCCAGCCTCGGAA -s simCow_chr6.simCow.chr6 253972 14 - 602619 CTGCAGCACAGTAA -s simDog_chr6.simDog.chr6 255681 14 - 593897 CTGTAGCCCAGGAA -s simHuman_chr6.simHuman.chr6 421645 13 - 601863 CTGCAGCC-CAGGA -s simRat_chr6.simRat.chr6 277062 14 + 647215 TTACAGCCTGGGAA - -a -s simMouse_chr6.simMouse.chr6 288558 2 + 636262 CG -s Anc0.Anc0refChr5 85989 2 - 87904 CC -s Anc1.Anc1refChr8 42934 2 - 57822 CC -s Anc2.Anc2refChr14 5805 2 - 7748 CC -s mr.mrrefChr5 139491 2 + 294540 CA -s simCow_chr6.simCow.chr6 254087 2 - 602619 CC -s simDog_chr6.simDog.chr6 255799 2 - 593897 CC -s simHuman_chr6.simHuman.chr6 421761 2 - 601863 CC -s simRat_chr6.simRat.chr6 277184 2 + 647215 CA - -a -s simMouse_chr6.simMouse.chr6 288560 14 + 636262 TTTCCCCCAATCAA -s Anc0.Anc0refChr5 86050 14 - 87904 TTTCCTCCAATTGA -s Anc1.Anc1refChr8 42995 14 - 57822 TTTCCTCCAATTGA -s Anc2.Anc2refChr14 5866 14 - 7748 TTTCCCCCAGTTGA -s mr.mrrefChr5 139493 14 + 294540 TTTCCTCCAATCAA -s simCow_chr6.simCow.chr6 254246 14 - 602619 TATCCCCTAGTTGA -s simDog_chr6.simDog.chr6 255942 14 - 593897 TTTCCCCCAGTGGA -s simHuman_chr6.simHuman.chr6 421825 14 - 601863 TTTCCTCCAATTGA -s simRat_chr6.simRat.chr6 277186 14 + 647215 TTTCCTCCAGTCAA - -a -s simMouse_chr6.simMouse.chr6 288574 13 + 636262 AATATGTTGTGTA -s Anc0.Anc0refChr5 86066 13 - 87904 AATATAATGAGTA -s Anc1.Anc1refChr8 43011 13 - 57822 AATATAATGAGTA -s Anc2.Anc2refChr14 5882 13 - 7748 AATATAATCAGTG -s mr.mrrefChr5 139509 13 + 294540 AATATATTGAGTA -s simCow_chr6.simCow.chr6 254262 13 - 602619 AATATAAAAAGTG -s simDog_chr6.simDog.chr6 255958 13 - 593897 AATATAATCAGTG -s simHuman_chr6.simHuman.chr6 421841 13 - 601863 AATATAATGAGTA -s simRat_chr6.simRat.chr6 277202 13 + 647215 AATATACTGAGTA - -a -s simMouse_chr6.simMouse.chr6 288587 29 + 636262 CTATGTGTTGTCAAGCGTGTCATAGTGCC -s Anc0.Anc0refChr8 6 29 - 17196 CCACAGTGTGTCAAGTGTGTCATAAGCCT -s Anc1.Anc1refChr8 43034 29 - 57822 CCACAGTGTGTCAAGTGTGTCATAAGCCT -s Anc2.Anc2refChr15 85342 29 + 86568 CCACAGTGTGTCAAGTGTGTCAGAAGCCT -s mr.mrrefChr5 139522 29 + 294540 CTATGTGTTGTCAAGCGTGTCATAGTGCC -s simCow_chr6.simCow.chr6 267795 29 + 602619 CCACGGTGTGTCACATGTGTCAGAAGTCC -s simDog_chr6.simDog.chr6 258411 29 + 593897 CCATAATGTGTCAAGTATATCAGAAGCCT -s simHuman_chr6.simHuman.chr6 421881 29 - 601863 CCACAGTGTGTCAAGTGTGTCATAAGCCT -s simRat_chr6.simRat.chr6 277215 29 + 647215 CTATGTGTTGTGAAGCGTGTCATAGCACA - -a -s simMouse_chr6.simMouse.chr6 288616 3 + 636262 GGC -s Anc0.Anc0refChr8 36 3 - 17196 GGC -s Anc1.Anc1refChr8 43064 3 - 57822 GGC -s Anc2.Anc2refChr15 85372 3 + 86568 GGC -s mr.mrrefChr5 139552 3 + 294540 GGC -s simCow_chr6.simCow.chr6 267825 3 + 602619 GGA -s simDog_chr6.simDog.chr6 258441 3 + 593897 GGC -s simHuman_chr6.simHuman.chr6 421911 3 - 601863 GGC -s simRat_chr6.simRat.chr6 277245 3 + 647215 GGC - -a -s simMouse_chr6.simMouse.chr6 288619 39 + 636262 CTTTCTGATTAATGCGATCCTCTTGACAAGAATACAAAG -s Anc0.Anc0refChr8 39 39 - 17196 CTTTCTGAGTACTGTGACTATTCTGGCAAGACTACAAAG -s Anc1.Anc1refChr8 43067 39 - 57822 CTTTCTGAGTACTGTGACTATTCTGGCAAGACTACAAAG -s Anc2.Anc2refChr15 85375 39 + 86568 CTTTCTGAGTACTGTGTCTATTCTGGCAAGACTACAATG -s mr.mrrefChr5 139555 39 + 294540 CTTTCTGATTAATGCGATTCTCTTGACAAGAATACAAAG -s simCow_chr6.simCow.chr6 267847 39 + 602619 TTTTCTGATTAGCACAACTATTCTGGCAAGACTCCAATG -s simDog_chr6.simDog.chr6 258444 39 + 593897 CTTTCTGAGTACTGTGTCTATTCTGGCTCGACTACAATG -s simHuman_chr6.simHuman.chr6 421914 35 - 601863 CTTCCCGACTAC----ACTATTCTGGCAAGACTATAGAG -s simRat_chr6.simRat.chr6 277248 39 + 647215 CTTTCTGATTAATGTAATTTTCTTGACAAGATCACAAAG - -a -s simMouse_chr6.simMouse.chr6 288658 1 + 636262 A -s Anc0.Anc0refChr8 81 1 - 17196 A -s Anc1.Anc1refChr8 43109 1 - 57822 A -s Anc2.Anc2refChr15 85417 1 + 86568 A -s mr.mrrefChr5 139594 1 + 294540 A -s simCow_chr6.simCow.chr6 267889 1 + 602619 A -s simDog_chr6.simDog.chr6 258486 1 + 593897 A -s simHuman_chr6.simHuman.chr6 421952 1 - 601863 A -s simRat_chr6.simRat.chr6 277287 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 288659 13 + 636262 AGTCTGAATCCTG -s Anc0.Anc0refChr8 82 13 - 17196 AGTCAGAGTCTTG -s Anc1.Anc1refChr8 43110 13 - 57822 AGTCAGAGTCTTG -s Anc2.Anc2refChr15 85418 13 + 86568 AGTCAGAGTCTTG -s mr.mrrefChr5 139595 13 + 294540 AGTCTGAATCCTG -s simCow_chr6.simCow.chr6 267890 13 + 602619 AGTCCAAGTCTTG -s simDog_chr6.simDog.chr6 258491 13 + 593897 AGTAAGACTCTTG -s simHuman_chr6.simHuman.chr6 421953 13 - 601863 AATCAGAGTCATG -s simRat_chr6.simRat.chr6 277288 13 + 647215 AGTCTAAATCCTG - -a -s simMouse_chr6.simMouse.chr6 288672 31 + 636262 ATACCAGGTGCTTGGTGACTATCAGATTTTA -s Anc0.Anc0refChr8 96 31 - 17196 ATAGCAAGTTCTTGGACACTTTTTGATTTTT -s Anc1.Anc1refChr8 43124 31 - 57822 ATAGCAAGTTCTTGGACACTTTTTGATTTTT -s Anc2.Anc2refChr15 85432 31 + 86568 ATAGCAAGTTCTTGGACACTTTTTCATTTTT -s mr.mrrefChr5 139609 31 + 294540 ATACCAGGTGCTTGGTGACTATCAGATTTTA -s simCow_chr6.simCow.chr6 267904 31 + 602619 GCAGCAAGTTCGTGAGCACTTTTTCATTTTT -s simDog_chr6.simDog.chr6 258505 31 + 593897 ATAGCAAGTGCTTGGATACTTTTTCATTTTT -s simHuman_chr6.simHuman.chr6 421967 31 - 601863 ATAGCAAGTTCTTGTACACTCTTTGATGTTT -s simRat_chr6.simRat.chr6 277302 31 + 647215 ATACCAGGTCCTTGGTGACTATGAGATTTTA - -a -s simMouse_chr6.simMouse.chr6 288703 12 + 636262 GCTGTCATGATT -s Anc0.Anc0refChr8 127 8 - 17196 CT----ACATTT -s Anc1.Anc1refChr8 43155 12 - 57822 CTGACCACATTT -s Anc2.Anc2refChr15 85463 8 + 86568 CT----ACGTGT -s mr.mrrefChr5 139640 12 + 294540 GCTGCCACAATT -s simCow_chr6.simCow.chr6 267935 8 + 602619 GT----TTGCAT -s simDog_chr6.simDog.chr6 258541 8 + 593897 CT----ACGTGT -s simHuman_chr6.simHuman.chr6 421998 11 - 601863 CTGACCACATT- -s simRat_chr6.simRat.chr6 277333 12 + 647215 GCTGCCACAATT - -a -s simMouse_chr6.simMouse.chr6 288715 4 + 636262 ACAG -s Anc0.Anc0refChr8 135 4 - 17196 ACAG -s Anc1.Anc1refChr8 43167 4 - 57822 ACAG -s Anc2.Anc2refChr15 85471 4 + 86568 ACAG -s mr.mrrefChr5 139652 4 + 294540 ACAG -s simCow_chr6.simCow.chr6 267946 4 + 602619 ACAG -s simDog_chr6.simDog.chr6 258549 4 + 593897 ACAG -s simRat_chr6.simRat.chr6 277345 4 + 647215 ACAG - -a -s simMouse_chr6.simMouse.chr6 288719 40 + 636262 GGGGGTGGAATTGGACAGGGGATCTACAATGTACATCGGG -s Anc0.Anc0refChr8 139 32 - 17196 TGGGGGGAA----GACTGGAGGT----GATGAAGTTAGGG -s Anc1.Anc1refChr8 43171 32 - 57822 TGGGGGGAA----GACTGGAGGT----GATGAAGTTAGGG -s Anc2.Anc2refChr15 85475 32 + 86568 TGGGGGGAA----GACTGGAGGT----GATGAAGTTAGGG -s mr.mrrefChr5 139656 40 + 294540 GGGGGTGGAATTGGACAGGGGATCTACAATGTACATCGGG -s simCow_chr6.simCow.chr6 267950 32 + 602619 TGGGGAGAA----GACTGGAGCT----GATAAAGGTAAAG -s simDog_chr6.simDog.chr6 258553 32 + 593897 TGGGGGGAA----GACTGGAGGT----GATGAAGTTAGGG -s simRat_chr6.simRat.chr6 277361 40 + 647215 GGGAGTGGAAACAGACAGGAGATCTATAATGGACATGGGG - -a -s simMouse_chr6.simMouse.chr6 288759 31 + 636262 GGTTCCGGTCACATCTCATCAAGTAGGGGTG -s Anc0.Anc0refChr8 171 27 - 17196 GATTCTGGTCACAT----TCTAATATCGGCT -s Anc1.Anc1refChr8 43203 27 - 57822 GATTCTGGTCACAT----TCTAATATCGGCT -s Anc2.Anc2refChr15 85520 27 + 86568 GATTCTGGTCACAT----TCTAATATCGGCT -s mr.mrrefChr5 139696 31 + 294540 GGTTCCGGTCACATCTCATCAAGTAGGGGTG -s simCow_chr6.simCow.chr6 267995 27 + 602619 GATTCTGGACACAT----TTTAATATTGGCT -s simDog_chr6.simDog.chr6 258598 27 + 593897 GATTCTGGTCACAT----TCTAATATCGGCT -s simRat_chr6.simRat.chr6 277401 31 + 647215 GGTCTCCTTGACATCATGTCAAGTCGGGGTG - -a -s simMouse_chr6.simMouse.chr6 288790 42 + 636262 AGGAAGAATGATAAACTAGGGGCCCTTTGTAGTGGGTTTTTT -s Anc0.Anc0refChr8 198 39 - 17196 GTCAAAAGAGAGAG---AGGAGTCTTCTGTAGTGAAATTCTG -s Anc1.Anc1refChr8 43230 39 - 57822 GTCAAAAGAGAGAG---AGGAGTCTTCTGTAGTGAAATTCTG -s Anc2.Anc2refChr15 85547 39 + 86568 GTCAAAAGAGAGAG---AGGAGTCTTCTGTAGTGAAATTCTG -s mr.mrrefChr5 139727 42 + 294540 AGGAAGAATGATAAACTAGGGGCCCTTTGTAGTGGGTTTTTT -s simCow_chr6.simCow.chr6 268023 39 + 602619 GTACAAGGAGAGGG---AGGAGTCTTCTGTAGTAAGATTCTG -s simDog_chr6.simDog.chr6 258625 39 + 593897 GTCAAAAGAGAGAG---AGGAGTCTTCTGTAGTGAAATTCTG -s simRat_chr6.simRat.chr6 277432 42 + 647215 AGGAAAAGTGATGAACTAAGAGCCTATTGTAGTGAGTTTTTT - -a -s simMouse_chr6.simMouse.chr6 288832 22 + 636262 CATAGAACCTGATACTTGTTAA -s Anc0.Anc0refChr8 237 22 - 17196 AACACATTCTGATATTGGCTGG -s Anc1.Anc1refChr8 43269 22 - 57822 AACACATTCTGATATTGGCTGG -s Anc2.Anc2refChr15 85586 22 + 86568 AACACATTCTAATATTGGCTGG -s mr.mrrefChr5 139769 22 + 294540 CATAGAACCTGATACTTGTTAG -s simCow_chr6.simCow.chr6 268094 22 + 602619 AGCACATTCCAACATTTGCTGA -s simDog_chr6.simDog.chr6 258664 22 + 593897 GACCCACTCTAATATTGGCCAG -s simHuman_chr6.simHuman.chr6 422009 14 - 601863 --------TTGATATTGGCTGG -s simRat_chr6.simRat.chr6 277474 22 + 647215 CACAGACCCTGATACTTGTTCG - -a -s simMouse_chr6.simMouse.chr6 288854 48 + 636262 GTATTCCATGAGAGTATCAAAGTGAATGGTTCAAACCCTGTAGAACTT -s Anc0.Anc0refChr8 260 48 - 17196 ATAATAAGAGGGAAGAGCAAGGTGAACAGTTAGAACCCCATATAACTT -s Anc1.Anc1refChr8 43292 48 - 57822 ATAATAAGAGGGAAGAGCAAGGTGAACAGTTAGAACCCCATATAACTT -s Anc2.Anc2refChr15 85609 48 + 86568 ATAATAAGAGGGAAGAGCAAGGTGAACAGTCAGAACCCCATATAACTT -s mr.mrrefChr5 139791 48 + 294540 GTATTCCGAGAGAGTAGCAAAGTGAATGGTTCAAACCCTGTAGAACTT -s simCow_chr6.simCow.chr6 268117 47 + 602619 ATAATAAGAGGGAGGAGCTAGGTGAAC-TTCAGAACCCCATATAACTT -s simDog_chr6.simDog.chr6 258687 48 + 593897 ATACTGAGAGAGAAGAGCAAGGTGAACAGTCAGACCCCCAAATAACAT -s simHuman_chr6.simHuman.chr6 422024 48 - 601863 ATAATAGGAGGGAAGAGCAAGGTGAACAGTTAGAACCCCATATTACTT -s simRat_chr6.simRat.chr6 277496 48 + 647215 GTATTCCGAGAGAGTAGCAAAGTGAATGGTTCAAACGCTGTAGAAGGT - -a -s simMouse_chr6.simMouse.chr6 288902 81 + 636262 TGTCACTTTACAAACATGGCCTGAGTAATCTTAAGATGTCAGTACACACCTTCATGTGGTTCATCATGTTCTATTGGGGAA -s Anc0.Anc0refChr8 339 78 - 17196 GGACATTTCACCAACATTGATCTAACCAATTTAACATGTCAGTGCACACCTACATTAGGTTCCTTGTGTTGTA---GGGAT -s Anc1.Anc1refChr8 43371 78 - 57822 GGACATTTCACCAACATTGATCTAACCAATTTAACATGTCAGTGCACACCTACATTAGGTTCCTTGTGTTGTA---GGGAT -s Anc2.Anc2refChr15 85688 78 + 86568 GGACATTTCACCAACATTGATCTAACCAAGTTAACATGCCAGTGCACACTCTCATTAGTTTTCTTGTATTGTA---TGGGT -s mr.mrrefChr5 139855 81 + 294540 TGTCACTTTACAAACATGGCCCGAGTAATTTTAACATGTCAGTACACACCTACATTTGGTTCATTATGTTCTATTGGGGAA -s simCow_chr6.simCow.chr6 268195 76 + 602619 GGACACTTAACAATCGTTGATCTACCCAAATTAATATGCCAGCATACACTCTCAATTGTTCACCTGCATTGTA---TGG-- -s simDog_chr6.simDog.chr6 258759 78 + 593897 GAACCTTTCACCAATATCGAGTTAACCATGTTAACATACCAGTGCACACTCTCATTAGTTTTGTTGTATTGTA---TAGGT -s simHuman_chr6.simHuman.chr6 422103 78 - 601863 GGACATTTCACCAACATTGATCTATCCAATTTAACATGTCAGTGGACACCTACATTGGGTTCCTTGTGTTGTA---GGGAC -s simRat_chr6.simRat.chr6 277560 81 + 647215 TGTCACTTTACAAACATGGCCCAAGTTATTCTGACATCTCAGTACACACCTACATTTGGTTCATTATGTTTTATTGGGGAA - -a -s simMouse_chr6.simMouse.chr6 288983 18 + 636262 CCCTTCTAAGGGACTCTC -s Anc0.Anc0refChr8 417 18 - 17196 TCCTTTTAAGGGATTTTC -s Anc1.Anc1refChr8 43449 18 - 57822 TCCTTTTAAGGGATTTTC -s Anc2.Anc2refChr15 85766 18 + 86568 TCCTTTCAAGGGATTTTC -s mr.mrrefChr5 139936 18 + 294540 CCCTTCTAAGGGACTCTC -s simCow_chr6.simCow.chr6 268271 18 + 602619 CCCTTTCAAGGGATTTTC -s simDog_chr6.simDog.chr6 258839 18 + 593897 TCCTTTCAAGGGATTTTC -s simHuman_chr6.simHuman.chr6 422181 15 - 601863 TGCAGTTAAAGGAAT--- -s simRat_chr6.simRat.chr6 277641 18 + 647215 CCCTTTCAAGGTAGTCTC - -a -s simMouse_chr6.simMouse.chr6 289001 42 + 636262 AGGGCCAGGGAAACAATTCAGGAAATATGTTCTAACCCCACC -s Anc0.Anc0refChr8 435 42 - 17196 TGGACCACTGAGACAAGTCAGGACAAGTGTTAAATATCCACC -s Anc1.Anc1refChr8 43467 42 - 57822 TGGACCACTGAGACAAGTCAGGACAAGTGTTAAATATCCACC -s Anc2.Anc2refChr15 85786 42 + 86568 TGGACCACTGAGACAAGTCAGGACAAGTGTTAAATATCCACC -s mr.mrrefChr5 139954 42 + 294540 AGGGCCAGGGAAACAATTCAGGAAATATGTTCTAACCCCACC -s simCow_chr6.simCow.chr6 268291 42 + 602619 GGGTTAGGTGAACCTAGTCAGCACATGTATGAAGAATCCACT -s simDog_chr6.simDog.chr6 258859 42 + 593897 TGGACCACTGAGACAAGTCAGGACAAGTGTTAAATATCCACC -s simRat_chr6.simRat.chr6 277659 42 + 647215 AGGACCAGGGAAACAAATCAAGGAATGTGCTCTAATCACACC - -a -s simMouse_chr6.simMouse.chr6 289043 24 + 636262 TCGATGCTCCGACATACCTACATA -s Anc0.Anc0refChr8 477 23 - 17196 TAAAGGAATCAATCTACTTG-ATA -s Anc1.Anc1refChr8 43509 23 - 57822 TAAAGGAATCAATCTACTTG-ATA -s Anc2.Anc2refChr15 85845 23 + 86568 TAAAGGAATCAATCTACTTG-ATA -s mr.mrrefChr5 139996 23 + 294540 TCGATGCTCCGACATACCTA-ATA -s simCow_chr6.simCow.chr6 268350 23 + 602619 TAAAGCAATTAATCTACTTG-ATC -s simDog_chr6.simDog.chr6 258919 23 + 593897 TAAAGGAATCAATCAAATTC-ATA -s simHuman_chr6.simHuman.chr6 422196 14 - 601863 ---------CAATCTACTTG-GTA -s simRat_chr6.simRat.chr6 277701 23 + 647215 TCAACGCGCTGCCACATCTA-ATA - -a -s simMouse_chr6.simMouse.chr6 289067 47 + 636262 TTCAACAAATCCCAACCAGAAAGGTGATGCCTGAAAGATACCCTCAT -s Anc0.Anc0refChr8 510 46 - 17196 TGTAACAAATTCCACCTGAAAA-ATGATGCCTGTAAGGAATTCTCCT -s Anc1.Anc1refChr8 43542 47 - 57822 TGTAACAAATTCCACCTGAAAAGATGATGCCTGTAAGGAATTCTCCT -s Anc2.Anc2refChr15 85878 46 + 86568 TGTAACAAATTCTGCCTGAAAA-ATGATGCCTGTAAAGAATTCTCCT -s mr.mrrefChr5 140019 47 + 294540 TTCAACAAATCCCAACCAGAAAGGTGATGCCTGAAAGATACCCTCAT -s simCow_chr6.simCow.chr6 268383 46 + 602619 TTTAACAAATTCTGCCTGAAAG-ATGATGCCTGGAAAGATTTCTCCC -s simDog_chr6.simDog.chr6 258952 46 + 593897 TGTAACAAATTCTGCCTGAAAA-ATGATGCCTGTAAAGAATTCTCCT -s simHuman_chr6.simHuman.chr6 422220 47 - 601863 TGTAACAAATTCCACCTGAAAAGTAAATGCCTATACGGAATTCTCCT -s simRat_chr6.simRat.chr6 277724 47 + 647215 TTCAATGAATCCCAGCTGGAAAGGTGATACCTGAAAAGACCCCTCAT - -a -s simMouse_chr6.simMouse.chr6 289114 2 + 636262 CC -s Anc0.Anc0refChr8 556 2 - 17196 CC -s Anc1.Anc1refChr8 43589 2 - 57822 CC -s Anc2.Anc2refChr15 85925 2 + 86568 CC -s mr.mrrefChr5 140066 2 + 294540 CC -s simCow_chr6.simCow.chr6 268430 2 + 602619 CC -s simDog_chr6.simDog.chr6 258999 2 + 593897 CC -s simHuman_chr6.simHuman.chr6 422267 2 - 601863 CT -s simRat_chr6.simRat.chr6 277771 2 + 647215 GC - -a -s simMouse_chr6.simMouse.chr6 289116 4 + 636262 TTTA -s Anc0.Anc0refChr8 558 4 - 17196 CGTG -s Anc1.Anc1refChr8 43591 4 - 57822 CGTG -s Anc2.Anc2refChr15 85927 4 + 86568 CGGG -s mr.mrrefChr5 140068 4 + 294540 TTTA -s simCow_chr6.simCow.chr6 268432 4 + 602619 TAAG -s simDog_chr6.simDog.chr6 259006 4 + 593897 CGGG -s simHuman_chr6.simHuman.chr6 422269 3 - 601863 GCT- -s simRat_chr6.simRat.chr6 277773 4 + 647215 TTTA - -a -s simMouse_chr6.simMouse.chr6 289120 39 + 636262 GATCACAGATGAACTCTCTATCAATCCAAGTCCATTTTC -s Anc0.Anc0refChr8 562 39 - 17196 GATGGCCAACAAACCCTTTATCAATCTGAATTTGTTTTC -s Anc1.Anc1refChr8 43595 39 - 57822 GATGGCCAACAAACCCTTTATCAATCTGAATTTGTTTTC -s Anc2.Anc2refChr15 85931 39 + 86568 GATGGCCAACAAGCCCCTTATCAATCCGAATTTGTTTTC -s mr.mrrefChr5 140072 39 + 294540 GATCACAGATGAACTCTCTATCAATCTAAGTCCATTTTC -s simCow_chr6.simCow.chr6 268436 39 + 602619 GATGGCCAATAAGCCCCCTATCAATCCAAATCTGTTTTC -s simDog_chr6.simDog.chr6 259010 39 + 593897 GATGGCCAACAAGCCCCTTACCAATCCGAATTTGTTTTC -s simHuman_chr6.simHuman.chr6 357988 39 - 601863 AACAGCCAGAAAAGACTGTATGTATATGAATGTGTTTTC -s simRat_chr6.simRat.chr6 277777 39 + 647215 GATCACAGATGAACTCTCTATCAATCTAAGTCCATTTTC - -a -s simMouse_chr6.simMouse.chr6 289159 16 + 636262 TAGTCAATGAAGATCT -s Anc0.Anc0refChr8 601 16 - 17196 TAATCAATGAATATCT -s Anc1.Anc1refChr8 43634 16 - 57822 TAATCAATGAATATCT -s Anc2.Anc2refChr15 85970 16 + 86568 TAGCCAATGAATATCT -s mr.mrrefChr5 140111 16 + 294540 TAATCAATGAAGATCT -s simCow_chr6.simCow.chr6 268476 16 + 602619 TAGCCAGTGATTATCT -s simDog_chr6.simDog.chr6 259049 16 + 593897 TGGCCAATAAATATTT -s simHuman_chr6.simHuman.chr6 358027 16 - 601863 TAATCAATGACTATCT -s simRat_chr6.simRat.chr6 277816 16 + 647215 TAATCAAAGAAGATTT - -a -s simMouse_chr6.simMouse.chr6 289175 107 + 636262 CAGGTCACAGAAGTGAGCATAGAATTGCCACTTTGCCCTCAAAAGTTGGTCTGGACCCTTAGATTCCTATTTCAATGCATAACGTCTATCAAGTGTCTCATCACAAT -s Anc0.Anc0refChr8 617 83 - 17196 CATGCCACAGAAGTG----TAGAATTGATA--------------------CTGGACCCTCAGATTCCTGTTTCACTACTTGGCATCTATCAAGTGTCTCAACACAAT -s Anc1.Anc1refChr8 43650 83 - 57822 CATGCCACAGAAGTG----TAGAATTGATA--------------------CTGGACCCTCAGATTCCTGTTTCACTACTTGGCATCTATCAAGTGTCTCAACACAAT -s Anc2.Anc2refChr15 85986 83 + 86568 CATGCCACAGAAGTA----TAGAATTGATA--------------------TCAGACCCTCAAATTCCTGTTTCACTACTTGGCATCTATCAAGTGTCTCAACACAAG -s mr.mrrefChr5 140127 107 + 294540 CAGGTCACAGAAGTGAGCATAGAATTGCTACTTTGCCCTCAAAAGTTGGTCTGGACCCTTAGATTCCTGTTTCAATACATAGCATCTATCAAGTGTCTCAACACAAT -s simCow_chr6.simCow.chr6 268492 81 + 602619 CATGCCAAATAAGTA----TAGAATTG--A--------------------TCAGACCCTCATATTCCTGTTTCATTACTTGGCATCCATCAACTGTTTCAACACAAC -s simDog_chr6.simDog.chr6 259104 77 + 593897 CAAGCCACAGAAGCA----TCAACTTAATA--------------------TCAGTCACTCAAA------TTTCACTGTTTGGCATCTACCAAGTGTCTCAACGCAAG -s simHuman_chr6.simHuman.chr6 358043 83 - 601863 AATGCCACAGAAGTG----TAGAATTGATA--------------------CTGAACCCTCAGATTCCTGTTTCACTACTTGGCATTTATCAAATGTCTCAACACAAT -s simRat_chr6.simRat.chr6 277832 107 + 647215 GTAGTCACAGAAGTGAGCATAGAATTGCTACTGTGCCCTCGTAAGTTGGTCTGGACCCTTAGATTCCTGTTTCAACACATAGCATCTATCAAGTGTCTCAACACAAT - -a -s simMouse_chr6.simMouse.chr6 289282 8 + 636262 TTGCCACC -s Anc0.Anc0refChr8 700 8 - 17196 TGTCTACA -s Anc1.Anc1refChr8 43733 8 - 57822 TGTCTACA -s Anc2.Anc2refChr15 86069 8 + 86568 TGTCTACA -s mr.mrrefChr5 140234 8 + 294540 TTGCCACC -s simCow_chr6.simCow.chr6 268579 8 + 602619 GGTGTACC -s simDog_chr6.simDog.chr6 259181 8 + 593897 TGCCTACA -s simHuman_chr6.simHuman.chr6 358126 8 - 601863 TGTCTACT -s simRat_chr6.simRat.chr6 277939 8 + 647215 TTGCCTCC - -a -s simMouse_chr6.simMouse.chr6 289290 19 + 636262 ATCGAATCCATCAACCAGG -s Anc0.Anc0refChr8 711 19 - 17196 ATCTAATCCATCAATCCTG -s Anc1.Anc1refChr8 43744 19 - 57822 ATCTAATCCATCAATCCTG -s Anc2.Anc2refChr15 86080 19 + 86568 ATCTAATTCATCAATCCTG -s mr.mrrefChr5 140242 19 + 294540 ATCGAATCCATCAACCAGG -s simCow_chr6.simCow.chr6 268590 19 + 602619 ATCTGATTCCTCAACCCTG -s simDog_chr6.simDog.chr6 259192 19 + 593897 ATCTAATTCATCAATCATG -s simHuman_chr6.simHuman.chr6 358137 19 - 601863 ATCTAATCCACCAATCCTG -s simRat_chr6.simRat.chr6 277947 19 + 647215 ATCAAATTCATCTACTAGG - -a -s simMouse_chr6.simMouse.chr6 289309 23 + 636262 CAACAACATTCTGAAGGTCACGA -s Anc0.Anc0refChr8 734 23 - 17196 CAACAACATTCTGAAGAAAAGAG -s Anc1.Anc1refChr8 43767 23 - 57822 CAACAACATTCTGAAGAAAAGAG -s Anc2.Anc2refChr15 86103 23 + 86568 CAACAGCACTCTGTAGAAAGGAG -s mr.mrrefChr5 140261 23 + 294540 CAACAACATTCTGAAGGTCACGA -s simCow_chr6.simCow.chr6 268613 13 + 602619 CAACGGCACTCTG---------- -s simDog_chr6.simDog.chr6 259215 23 + 593897 CAACAGTACACTGTAGAAAGGAG -s simHuman_chr6.simHuman.chr6 358160 23 - 601863 CAACAACATTCTAAAGAGAAGAG -s simRat_chr6.simRat.chr6 277966 23 + 647215 CAACAACACTCTGGAGGCCAAGA - -a -s simMouse_chr6.simMouse.chr6 289332 24 + 636262 CTAGTCATTGAACTCATCCACCCA -s Anc0.Anc0refChr8 757 24 - 17196 CTAGTCTTTAAAGTCATCCACCCT -s Anc1.Anc1refChr8 43790 24 - 57822 CTAGTCTTTAAAGTCATCCACCCT -s Anc2.Anc2refChr15 86126 24 + 86568 CTGGTCTTTAAAGTCATCCACCCT -s mr.mrrefChr5 140284 24 + 294540 CTAGTCTTTGAACTCATCCACCCA -s simCow_chr6.simCow.chr6 268626 19 + 602619 -----CTTTGAAGTCATCCACCCT -s simDog_chr6.simDog.chr6 259247 24 + 593897 CTGGTCTCTAAAGTCATTCACCCT -s simHuman_chr6.simHuman.chr6 358183 24 - 601863 ATAGTCTTCAAATTCATCCAACCT -s simRat_chr6.simRat.chr6 277989 24 + 647215 CTAGTCTTTGAACTCACCAACCCC - -a -s simMouse_chr6.simMouse.chr6 289356 39 + 636262 AGTGAGCACCCTACATTTCCACTGTCTTATGGCACCTGA -s Anc0.Anc0refChr8 781 39 - 17196 ATGGATCACCCTACATTTCCCCTGTCTCATGGTCCCTAA -s Anc1.Anc1refChr8 43814 39 - 57822 ATGGATCACCCTACATTTCCCCTGTCTCATGGTCCCTAA -s Anc2.Anc2refChr15 86150 39 + 86568 ATGGGTCACCCTACATTTCCCCTGTCTCGTGTTCCTAAA -s mr.mrrefChr5 140308 39 + 294540 AGGGAGCACCCTACATTTCCACTGTCTTATGGCACCTGA -s simCow_chr6.simCow.chr6 268646 35 + 602619 ATGGGTCACTTGACATTTCCCCTGTCATGCGATGC---- -s simDog_chr6.simDog.chr6 259271 36 + 593897 AT---TCACCCTGCATTTGCCCTGTCTCGTGTTCCTAAA -s simHuman_chr6.simHuman.chr6 358207 39 - 601863 ATGGATCACCCTACATCTCCCCTGTTTCATGGTCTCTAA -s simRat_chr6.simRat.chr6 278013 39 + 647215 AGGGAGCATCCTACATTTTCGCTGTCTTATGGCACTTGA - -a -s simMouse_chr6.simMouse.chr6 289395 9 + 636262 GCTCTGTTA -s Anc0.Anc0refChr8 877 9 - 17196 GTTCTGCTA -s Anc1.Anc1refChr8 43910 9 - 57822 GTTCTGCTA -s Anc2.Anc2refChr15 86255 9 + 86568 TTTTTGCAA -s mr.mrrefChr5 140386 9 + 294540 GCTCTGTTA -s simCow_chr6.simCow.chr6 268761 9 + 602619 CCTTTGTCA -s simDog_chr6.simDog.chr6 259364 9 + 593897 TTTTTTCAA -s simHuman_chr6.simHuman.chr6 358306 9 - 601863 GTTCTGCTA -s simRat_chr6.simRat.chr6 278091 9 + 647215 GCTCCATTA - -a -s simMouse_chr6.simMouse.chr6 289404 16 + 636262 AGTTGTGAATGAGATT -s Anc0.Anc0refChr8 886 15 - 17196 TGTCATGAATGAG-TT -s Anc1.Anc1refChr8 43919 16 - 57822 TGTCATGAATGAGCTT -s Anc2.Anc2refChr15 86264 15 + 86568 TGTCATGAATGAG-TT -s mr.mrrefChr5 140395 16 + 294540 AGTTGTGAATGAGATT -s simCow_chr6.simCow.chr6 268770 15 + 602619 TGTCATGAATGAG-TT -s simDog_chr6.simDog.chr6 53682 15 + 593897 TGTCCTGAATGAG-TT -s simHuman_chr6.simHuman.chr6 358315 14 - 601863 TGTCATGAAT--GCTT -s simRat_chr6.simRat.chr6 278100 16 + 647215 AGTTGAGAATGAGTTT - -a -s simMouse_chr6.simMouse.chr6 289420 10 + 636262 AAAGTAGTCT -s Anc0.Anc0refChr8 901 7 - 17196 CA---AGCCC -s Anc1.Anc1refChr8 43935 7 - 57822 CA---AGCCC -s Anc2.Anc2refChr15 86279 7 + 86568 CA---AGCCC -s mr.mrrefChr5 140411 10 + 294540 AAAGTAGTCT -s simCow_chr6.simCow.chr6 268786 7 + 602619 CA---AGCCA -s simDog_chr6.simDog.chr6 53697 7 + 593897 CA---AGCCC -s simHuman_chr6.simHuman.chr6 358329 7 - 601863 CA---AGCCC -s simRat_chr6.simRat.chr6 278116 10 + 647215 AAAGTAGTCT - -a -s simMouse_chr6.simMouse.chr6 289430 18 + 636262 TATCTGTATAACTTGGTT -s Anc0.Anc0refChr8 908 15 - 17196 TA---GTCCAATATGTTT -s Anc1.Anc1refChr8 43942 15 - 57822 TA---GTCCAATATGTTT -s Anc2.Anc2refChr15 86286 15 + 86568 AA---GTCCAATATGTTT -s mr.mrrefChr5 140421 18 + 294540 TATCTGTATAATTTGGTT -s simCow_chr6.simCow.chr6 268793 15 + 602619 AT---GTCAAATATGTTT -s simDog_chr6.simDog.chr6 53704 15 + 593897 AA---GTCCAATATGTTT -s simHuman_chr6.simHuman.chr6 358336 15 - 601863 TA---GTTCAATATGTTT -s simRat_chr6.simRat.chr6 278128 18 + 647215 GATCTGTATAATTTGGTT - -a -s simMouse_chr6.simMouse.chr6 289448 37 + 636262 AGATAGAATGGAGTAGGAAGTGTGTCAGATAAGTAAC -s Anc0.Anc0refChr8 923 36 - 17196 GAACAGAATGGAGTAGGAAGTGC-TCTGATAAGTAAC -s Anc1.Anc1refChr8 43957 37 - 57822 GAACAGAATGGAGTAGGAAGTGCGTCTGATAAGTAAC -s Anc2.Anc2refChr15 86303 36 + 86568 GAACAGAATGGAGTAAGGAATGC-TCTGATAAGTAAC -s mr.mrrefChr5 140439 37 + 294540 AGATAGAATGGAGTAGGAAGTGTGTCAGATAAGTAAC -s simCow_chr6.simCow.chr6 268810 25 + 602619 GAGCAGAATGGA------------TCTGATTGGTACC -s simDog_chr6.simDog.chr6 53721 35 + 593897 GAATGGATCGGAGTAAGGAATGC--TAGATAAGTAAC -s simHuman_chr6.simHuman.chr6 358351 37 - 601863 GAACAGAATGGCTTAGGACGTGCGTCTGATAAGTAAC -s simRat_chr6.simRat.chr6 278146 37 + 647215 AGAGGGAATGGAGTCGGAAATGTGTTGAATAAGTAAC - -a -s simMouse_chr6.simMouse.chr6 289485 196 + 636262 ATTGCCAGTTGTGCATATAAAATTCTGTCAAATAGGGTAGGCTCATTCAATCAAGTCCACAGGTTAATATCACTTGCCCACAGTTATCTTTTGGTTCTGCTAAACTCAACTGAAAACTAGTCTTCCGTGACCCTTTAAACCATCTCCTTTTCTGTGTACTTGAGGCTGTCGGTATAATTGAATTTCACTCTCGGTA -s Anc0.Anc0refChr8 961 50 - 17196 ATTTCCAGTTGTGTATGTAAAATTCTGTCAAATAGGGTAGTGCCTGCCA--------------------------------------------------------------------------------------------------------------------------------------------------C -s Anc1.Anc1refChr8 43996 50 - 57822 ATTTCCAGTTGTGTATGTAAAATTCTGTCAAATAGGGTAGTGCCTGCCA--------------------------------------------------------------------------------------------------------------------------------------------------C -s Anc2.Anc2refChr15 86341 50 + 86568 ATCTCCAGTTGGGTATGTAAAATTCTGTGAAATAGGGGAGTGCCTGCAA--------------------------------------------------------------------------------------------------------------------------------------------------C -s mr.mrrefChr5 140476 50 + 294540 ATTGCCAGTTGTGTATATAAAATTCTGTCAAATAGGGTAGGCTCATTCA--------------------------------------------------------------------------------------------------------------------------------------------------A -s simCow_chr6.simCow.chr6 268837 50 + 602619 CTCTCCAGTAGAGTTAGTAAAATTTAGTGAAATAAGGGAGTGCCTGCAA--------------------------------------------------------------------------------------------------------------------------------------------------C -s simDog_chr6.simDog.chr6 53758 50 + 593897 ATCTTCAGTTGGGTATGTAAGTTTCTATGAAATAGGGGAGTGCCTGCAG--------------------------------------------------------------------------------------------------------------------------------------------------C -s simHuman_chr6.simHuman.chr6 358390 50 - 601863 ATTTCTGGTTGTGTACGGAAAATTCTGTCAAATGGGGTAGAGCCTGCCA--------------------------------------------------------------------------------------------------------------------------------------------------C -s simRat_chr6.simRat.chr6 278183 50 + 647215 TTAGCCAGTTGTGTATATAAAATTCTATCAAATAGGGTAGGCTCATTCA--------------------------------------------------------------------------------------------------------------------------------------------------A - -a -s simMouse_chr6.simMouse.chr6 289681 30 + 636262 TAATTGAATTTCTGTTCCTGATTTGCAAGA -s Anc1.Anc1refChr8 44195 13 - 57822 TAGTTTAATT-----------------ATA -s mr.mrrefChr5 140526 30 + 294540 TAATTGAATTTCTGTTCCTGATTTGCAAGA -s simHuman_chr6.simHuman.chr6 358645 13 - 601863 TAGTTTAATT-----------------ATA -s simRat_chr6.simRat.chr6 278233 30 + 647215 TAATTAAATTTCTGTTCCCGATTTGCAAGA - -a -s simMouse_chr6.simMouse.chr6 289711 12 + 636262 GAGGAAATTTAA -s Anc0.Anc0refChr8 1160 8 - 17196 TAGG----TTAA -s Anc1.Anc1refChr8 44208 12 - 57822 TAGGAAGTTTAA -s Anc2.Anc2refChr5 6588 8 - 8386 TAGG----TGCA -s mr.mrrefChr5 140556 12 + 294540 GAGGAAGTTTAA -s simCow_chr6.simCow.chr6 329592 8 - 602619 TGAA----TTCA -s simDog_chr6.simDog.chr6 331790 8 - 593897 TAGG----TGCA -s simHuman_chr6.simHuman.chr6 358658 12 - 601863 TAGGAAGTTTAA -s simRat_chr6.simRat.chr6 278263 12 + 647215 AAAGAAGTTTAA - -a -s simMouse_chr6.simMouse.chr6 289723 3 + 636262 TAT -s Anc0.Anc0refChr8 1168 3 - 17196 AAG -s Anc1.Anc1refChr8 44220 3 - 57822 AAG -s Anc2.Anc2refChr5 6596 3 - 8386 AGG -s mr.mrrefChr5 140568 3 + 294540 TAT -s simCow_chr6.simCow.chr6 329606 3 - 602619 AAG -s simDog_chr6.simDog.chr6 54782 3 + 593897 AGG -s simHuman_chr6.simHuman.chr6 358670 3 - 601863 AAG -s simRat_chr6.simRat.chr6 278275 3 + 647215 TAT - -a -s simMouse_chr6.simMouse.chr6 289726 18 + 636262 CATCCCATACCTTGTTAG -s Anc0.Anc0refChr8 1174 18 - 17196 CATCCCATACACGGTTCA -s Anc1.Anc1refChr8 44226 18 - 57822 CATCCCATACACGGTTCA -s Anc2.Anc2refChr5 6602 18 - 8386 CATCCCTTGACTGACTCA -s mr.mrrefChr5 140571 18 + 294540 CATCCCATACACTGTTAG -s simCow_chr6.simCow.chr6 329612 18 - 602619 CGTGGGTTGAGTAATTCA -s simDog_chr6.simDog.chr6 54788 18 + 593897 CATCCCTTGACTGACTCA -s simHuman_chr6.simHuman.chr6 358676 18 - 601863 CTTTCCATACACGGTTGT -s simRat_chr6.simRat.chr6 278278 18 + 647215 CATCCCATACACTGTTAG - -a -s simMouse_chr6.simMouse.chr6 289744 98 + 636262 GAATCTCCCTAATAGGAGGATTCTGTACCTTTAGTGATTGATGTCATCCATGCTTTGTTTGCTTTTAGCTTGTATCCTTGTTGAAGATTGCTGATTGT -s Anc0.Anc0refChr8 1192 20 - 17196 GTATCTCCCTAAT------------------------------------------------------------------------------TGATCTT -s Anc1.Anc1refChr8 44244 90 - 57822 GTATCTCCCTAATAAATAGATGCTTTACATTTGTTGACGGCGCTTAGCCATGCTTTCTT-------AGATTGTAACCT-ATTGTAAGTCGCTGATCTT -s Anc2.Anc2refChr5 6620 20 - 8386 ATATCTCCATGAT------------------------------------------------------------------------------TGACCTT -s mr.mrrefChr5 140589 98 + 294540 GAATCTCCCTAATAGGAGGATGCTGTACCTTTATTGATTGATGTCATCCATGCTTTCTTTGCTTTTAGCTTGTATCCTTGTTGAAAATTGCTGATTGT -s simCow_chr6.simCow.chr6 329630 20 - 602619 ACATCTTCATGAT------------------------------------------------------------------------------TGATCTT -s simDog_chr6.simDog.chr6 54806 20 + 593897 ATATCTCCATGAT------------------------------------------------------------------------------TGACCTT -s simHuman_chr6.simHuman.chr6 358727 90 - 601863 GCCTCTCCCTAATAAATAGATGCTTTACATTTGTTGACGGCGCTTAGCCATGCTTTCTT-------AGATTGTAACCT-ATTGTAAGTCGCTGATGAT -s simRat_chr6.simRat.chr6 278296 96 + 647215 GAATTTCCCTAATGGCAGGATGCTGTACC--CATTGATCGATGTCATCCATGCTTTCATCGCTTTTAGTGTGTATCCTTGTTGAAAATTGCTGATTGT - -a -s simMouse_chr6.simMouse.chr6 289842 19 + 636262 TTATAGAACTCTCCTTTAT -s Anc0.Anc0refChr8 1212 19 - 17196 TTGTAATATTATCATTTAT -s Anc1.Anc1refChr8 44334 19 - 57822 TTGTAATATTATCATTTAT -s Anc2.Anc2refChr5 6640 19 - 8386 CTGTAATGTTAACATTCAT -s mr.mrrefChr5 140687 19 + 294540 TTATAGAACTCTCCTTTAT -s simCow_chr6.simCow.chr6 329650 19 - 602619 ATGTAATGTTAATACTGTT -s simDog_chr6.simDog.chr6 54826 19 + 593897 CTGTAATGTTAACATTCAT -s simHuman_chr6.simHuman.chr6 358820 19 - 601863 TTTTAATAATTTCATTTAA -s simRat_chr6.simRat.chr6 278392 19 + 647215 TCATAGAACTCTCCTTGAT - -a -s simMouse_chr6.simMouse.chr6 289861 24 + 636262 CAAGTCACCAGTAGCCACCAGAGG -s Anc0.Anc0refChr8 1231 21 - 17196 CAAG---CCTGTGGTCACCAGAAG -s Anc1.Anc1refChr8 44353 24 - 57822 CAAGGCACCTGTGGTCACCAGAAG -s Anc2.Anc2refChr5 6659 21 - 8386 AAAG---CCTGACATCTCCAGATG -s mr.mrrefChr5 140706 24 + 294540 CAAGTCACCAGTGGCCACCAGAAG -s simCow_chr6.simCow.chr6 329671 21 - 602619 AAAA---CCTGTTGTCTCCAGATG -s simDog_chr6.simDog.chr6 54845 21 + 593897 AAAG---CCTGACATCTCCAGATG -s simHuman_chr6.simHuman.chr6 358839 24 - 601863 CAAGGCACCTGTGGACATCGAAAA -s simRat_chr6.simRat.chr6 278411 24 + 647215 CAAATCACCAGTGGCCACTAGAAG - -a -s simMouse_chr6.simMouse.chr6 289885 18 + 636262 TCAACAGGTAAGCTATGA -s Anc0.Anc0refChr8 1252 18 - 17196 TTAACATGTACTCTATGA -s Anc1.Anc1refChr8 44377 18 - 57822 TTAACATGTACTCTATGA -s Anc2.Anc2refChr5 6683 18 - 8386 TTAACGTGTACTTATTGA -s mr.mrrefChr5 140730 18 + 294540 TTAACAGGTAAGCTATGA -s simCow_chr6.simCow.chr6 329695 18 - 602619 TCAACCTGTTCTTACAGA -s simDog_chr6.simDog.chr6 54869 18 + 593897 TTAACGTGTACTTATTGA -s simHuman_chr6.simHuman.chr6 358863 18 - 601863 GTTCTATACATTCTATCA -s simRat_chr6.simRat.chr6 278435 18 + 647215 TTAACAGGTAACCTATGA - -a -s simMouse_chr6.simMouse.chr6 289903 2 + 636262 GT -s Anc0.Anc0refChr8 1270 2 - 17196 GC -s Anc1.Anc1refChr8 44395 2 - 57822 GC -s Anc2.Anc2refChr5 6701 2 - 8386 GC -s mr.mrrefChr5 140748 2 + 294540 GT -s simCow_chr6.simCow.chr6 329713 2 - 602619 GA -s simDog_chr6.simDog.chr6 54888 2 + 593897 GC -s simHuman_chr6.simHuman.chr6 358881 2 - 601863 AC -s simRat_chr6.simRat.chr6 278453 2 + 647215 GT - -a -s simMouse_chr6.simMouse.chr6 289905 12 + 636262 GTCTGATTTTAG -s Anc0.Anc0refChr8 1272 12 - 17196 TTCTGATTTTAG -s Anc1.Anc1refChr8 44397 12 - 57822 TTCTGATTTTAG -s Anc2.Anc2refChr5 6703 12 - 8386 TACTTGTGATGA -s mr.mrrefChr5 140750 12 + 294540 GTCTGATTTTAG -s simCow_chr6.simCow.chr6 329715 12 - 602619 TAATTGTGTTGA -s simDog_chr6.simDog.chr6 54890 12 + 593897 TACTTGTGATGA -s simHuman_chr6.simHuman.chr6 358953 12 - 601863 ATTTGATTTGAG -s simRat_chr6.simRat.chr6 278455 12 + 647215 GACTCATTTTAG - -a -s simMouse_chr6.simMouse.chr6 289917 6 + 636262 TACCAT -s Anc0.Anc0refChr8 1284 6 - 17196 TACTAT -s Anc1.Anc1refChr8 44409 6 - 57822 TACTAT -s Anc2.Anc2refChr5 6715 6 - 8386 TACTCT -s mr.mrrefChr5 140762 6 + 294540 TACCAT -s simCow_chr6.simCow.chr6 329728 6 - 602619 TACTCT -s simDog_chr6.simDog.chr6 54902 6 + 593897 TACTCT -s simHuman_chr6.simHuman.chr6 358965 6 - 601863 TACTAC -s simRat_chr6.simRat.chr6 278467 6 + 647215 CGCCAT - -a -s simMouse_chr6.simMouse.chr6 289923 2 + 636262 AC -s Anc0.Anc0refChr8 1290 2 - 17196 AC -s Anc1.Anc1refChr8 44415 2 - 57822 AC -s Anc2.Anc2refChr5 6723 2 - 8386 AT -s mr.mrrefChr5 140768 2 + 294540 AC -s simCow_chr6.simCow.chr6 329736 2 - 602619 AT -s simDog_chr6.simDog.chr6 54910 2 + 593897 AT -s simHuman_chr6.simHuman.chr6 358971 2 - 601863 AC -s simRat_chr6.simRat.chr6 278473 2 + 647215 AC - -a -s simMouse_chr6.simMouse.chr6 289925 2 + 636262 TC -s Anc0.Anc0refChr8 1292 2 - 17196 CT -s Anc1.Anc1refChr8 44417 2 - 57822 CT -s Anc2.Anc2refChr5 6725 2 - 8386 CT -s mr.mrrefChr5 140770 2 + 294540 CC -s simCow_chr6.simCow.chr6 329738 2 - 602619 CT -s simDog_chr6.simDog.chr6 54913 2 + 593897 CT -s simHuman_chr6.simHuman.chr6 358973 2 - 601863 CT -s simRat_chr6.simRat.chr6 278475 2 + 647215 CC - -a -s simMouse_chr6.simMouse.chr6 289927 13 + 636262 CTCCTTTTTTTCT -s Anc0.Anc0refChr8 1294 12 - 17196 ATCCT-TCTATTG -s Anc1.Anc1refChr8 44419 12 - 57822 ATCCT-TCTATTG -s Anc2.Anc2refChr5 6729 12 - 8386 ATCTT-TCTGCTG -s mr.mrrefChr5 140772 12 + 294540 CTCCT-TTTATCT -s simCow_chr6.simCow.chr6 329742 12 - 602619 GTATG-TCTGCTG -s simDog_chr6.simDog.chr6 54917 12 + 593897 ATCTT-TCTGCTG -s simHuman_chr6.simHuman.chr6 358975 12 - 601863 ATTCT-CCTATTG -s simRat_chr6.simRat.chr6 278477 12 + 647215 TTCCT-TTTATCT - -a -s simMouse_chr6.simMouse.chr6 289940 18 + 636262 CTTTGTTGTGCAAGGAAG -s Anc0.Anc0refChr8 1306 17 - 17196 CGTCATTGT-TGCGGAAG -s Anc1.Anc1refChr8 44431 18 - 57822 CGTCATTGTGTGCGGAAG -s Anc2.Anc2refChr5 6741 17 - 8386 GGTCAGTGT-TCCGGGTG -s mr.mrrefChr5 140784 18 + 294540 CTTCGTTGTGTGAGGAAG -s simCow_chr6.simCow.chr6 329758 17 - 602619 AGTCAGTCT-CCCAGGTG -s simDog_chr6.simDog.chr6 54929 17 + 593897 GGTCAGTGT-TCCGGGTG -s simHuman_chr6.simHuman.chr6 358987 18 - 601863 CCTCCTAGTGTGCGTAAA -s simRat_chr6.simRat.chr6 278489 18 + 647215 CTTCATTGTGTGAGGAAG - -a -s simMouse_chr6.simMouse.chr6 289958 17 + 636262 ATCGGACCCCAATACTA -s Anc0.Anc0refChr8 1323 8 - 17196 ATTT---------ACTA -s Anc1.Anc1refChr8 44449 17 - 57822 ATTTGACCCCAATACTA -s Anc2.Anc2refChr5 6758 8 - 8386 ATTT---------ACTG -s mr.mrrefChr5 140802 17 + 294540 ATCTGACCCCAATACTA -s simCow_chr6.simCow.chr6 329775 8 - 602619 ACTT---------ACTG -s simDog_chr6.simDog.chr6 54949 8 + 593897 ATTT---------ACTG -s simHuman_chr6.simHuman.chr6 359005 14 - 601863 ---TGACCCCAATACTA -s simRat_chr6.simRat.chr6 278507 10 + 647215 ATTT-------AGACTA - -a -s simMouse_chr6.simMouse.chr6 289975 46 + 636262 ATATAGCAGAAAGGATATTGGAAAGCAATATAATGATCTGGTCCTG -s Anc0.Anc0refChr8 1331 38 - 17196 ATATAGCAATATGGAGATTGGACATC-AT-------TCTGGTTCAG -s Anc1.Anc1refChr8 44466 39 - 57822 ATATAGCAATATGGAGATTGGACATCTAT-------TCTGGTTCAG -s Anc2.Anc2refChr5 6766 38 - 8386 ATACATCAATATGGTGTTTGCACTTC-AT-------TATAGTTCAG -s mr.mrrefChr5 140819 46 + 294540 ATATAGCAAAAAGGATATTGGACAGCTATATAATGATCTGGTTCTG -s simCow_chr6.simCow.chr6 329783 38 - 602619 AATCATCACTATTGTATGCTAACTTC-AT-------AGTTATTCAG -s simDog_chr6.simDog.chr6 54957 38 + 593897 ATACATCAATATGGTGTTTGCACTTC-AT-------TATAGTTCAG -s simHuman_chr6.simHuman.chr6 359023 39 - 601863 AAATAGCAACAGGGACAGTGGACAACTGT-------TCTGGCTCCA -s simRat_chr6.simRat.chr6 278517 46 + 647215 ATATAGCCAAAAAGATATTGGACGGCTACATATTGGTCTGGTTTTG - -a -s simMouse_chr6.simMouse.chr6 290021 44 + 636262 CGTAATGGAGCACACTCTTAGTATGCACACAAGTGGAATTAGGG -s Anc0.Anc0refChr8 1369 6 - 17196 TTTAAT-------------------------------------- -s Anc1.Anc1refChr8 44505 43 - 57822 TTTAATGGCAT-CACTTATAGCATGCACATTACTAGATTGATGG -s Anc2.Anc2refChr5 6805 6 - 8386 TTTAAT-------------------------------------- -s mr.mrrefChr5 140865 44 + 294540 TTTAATGGAGCACACTTTTAGTATGCACACAAGTGGAATTAGGG -s simCow_chr6.simCow.chr6 329825 6 - 602619 TTGAAT-------------------------------------- -s simDog_chr6.simDog.chr6 54996 6 + 593897 TTTAAT-------------------------------------- -s simHuman_chr6.simHuman.chr6 359062 43 - 601863 TTTACTGGCAT-CACTTATAGCATGCACATTACTAGATTGATGG -s simRat_chr6.simRat.chr6 278563 44 + 647215 TTTAATGGGGCACACTTTTAGTATACACACAAGTGGAATTAGGG - -a -s simMouse_chr6.simMouse.chr6 290065 30 + 636262 TTATTAGATGATGCCAGGCCAACACTGGGG -s Anc1.Anc1refChr8 44549 30 - 57822 TCGTCAGATATTGCTAGGCCAACATTGGGG -s mr.mrrefChr5 140910 30 + 294540 TTATCAGATGATGCTAGGCCAACACTGGGG -s simHuman_chr6.simHuman.chr6 359110 30 - 601863 TCGTCAGATATTGCTAGGCCAACATTGGGG -s simRat_chr6.simRat.chr6 278608 30 + 647215 TTATCAGATGATGCTATGCCAGTACTCAGG - -a -s simMouse_chr6.simMouse.chr6 290095 14 + 636262 TAAATTCTTCCCAA -s Anc1.Anc1refChr8 44579 10 - 57822 TA--TTCTTT--GA -s mr.mrrefChr5 140940 14 + 294540 TAAATTCTTCCCAA -s simHuman_chr6.simHuman.chr6 359140 10 - 601863 TA--TTCTTT--GA -s simRat_chr6.simRat.chr6 278645 14 + 647215 TAAATTCTTCCCAA - -a -s simMouse_chr6.simMouse.chr6 290109 40 + 636262 CATAAAGGTCACCCCCATATGATGCTCTTCCCTTGCTTGG -s Anc1.Anc1refChr8 44598 40 - 57822 TATAAAGGTTTCCTCCATGTATGACTGTTCTCTTTCCTCA -s mr.mrrefChr5 140963 40 + 294540 CATAAAGGTCACCCCCATATAATGCTCTTCCCTTGCCTCG -s simHuman_chr6.simHuman.chr6 359159 40 - 601863 TATAAAGGTTTCCTCCATGTATGACTGTTCTCTTTCCTCA -s simRat_chr6.simRat.chr6 278668 40 + 647215 CATAGAGGTCCCCCCCATATAACGCTCTTCCCTTGTCCCG - -a -s simMouse_chr6.simMouse.chr6 290149 318 + 636262 GTGGGCTAATTGCACAAAGATATAGAATCATCTAGATTTCTCAGCTTTAAGTTTACTCAACCATCTGGACATTCACACTTAACAGCAAACTCATAGGTAATCCCCAGTCTCATTTAGATGCTTTAACTGATGAGTACTTCATCGGAACTATTCAACATATTATTCGGGTATGCATATTATTCAGTTATGAGTTACTTAAAGGTGGTATTGTTCTTGGGCTGAGGTGTTTATGCAGTTGCCCTTGCGTATGGATAAGTAAACCAATTTCTAAAGAGAGGAAGTTTGCCATGCTGCCCTCTTCTGTACCCTGAAGCACAA -s Anc1.Anc1refChr8 44638 32 - 57822 GTTGCTTAATCGTATTAAGACATGGAACCATC---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- -s mr.mrrefChr5 141003 296 + 294540 GTGGGCTAATTGCACAAAGATATAGAATCATCTAGATTTCTCAGCTTTAAGTTTACTCAACCATCTGGACATTCACACTTAACAGCAAACTCATAGGTAATCCCCAGTCTCATTTAGATGCTTTAACTGATGAGTA-TTCATCGGAACTATTCAACATATTAT-CGGGTATGCATATTATTCA----------ACTTAAAGGTGGTATTGTTCTTGGGCTGAGGTGTTTATGCAGTTGCCCTTGCGTATGGATAAGTAAACCAATTTCTAAAGAGAGGAAGTTTGCCAT------CTCTTCTGTAC----AAGCACAA -s simHuman_chr6.simHuman.chr6 359200 32 - 601863 GTTGCTTAATCGTATTAAGACATGGAACCATC---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- -s simRat_chr6.simRat.chr6 278708 296 + 647215 GTGGGCCAATTGCACAAAGATATAGAATCATCTAGATTTCCCAGTTCTAAGTCTACTCAACCACCTGGACATTGACACTCAACAGCCAACTCATGGTTAAACACCAATCTCTTTCAGATGCTTTAACTGGCAAGTA-TTCATTTGAGCTATTCAACATATTAT-CAGTTATGCTTATTATTCA----------ACTTAAAGGCAGTATTGTCCTTGAGGTGAGGTGTTTATGCAGTAGCCCTTGGGTATACATAAGTTGACCAATTTCTAAAGTGGGAAAATTTGTCAT------CCCTTCTGTAC----AAGAACAG - -a -s simMouse_chr6.simMouse.chr6 290467 41 + 636262 TAGAGAAATCAGGTTAATCCCTTGTTAAACCCGTTAAAGAT -s mr.mrrefChr5 141299 40 + 294540 TAGAGAAATCAGGTTAATCCCTTGTTAAACCC-TTAAAGAT -s simRat_chr6.simRat.chr6 279011 40 + 647215 TAGAGAATTCAGGTTAATCCCTTGCTAAATCC-TTAAAGAT - -a -s simMouse_chr6.simMouse.chr6 290508 24 + 636262 TGCCCTAAATTTACTATCTTCACA -s mr.mrrefChr5 141339 24 + 294540 TGCCCTAAATTTACTATCTTCACA -s simRat_chr6.simRat.chr6 279052 24 + 647215 TGCCCTAAATTTACCATCTTCACA - -a -s simMouse_chr6.simMouse.chr6 290532 14 + 636262 TGTCCCATTAGTTA -s mr.mrrefChr5 141363 14 + 294540 TGTCCCATTAGTTA -s simRat_chr6.simRat.chr6 279077 14 + 647215 TGTGCCATTGGTAA - -a -s simMouse_chr6.simMouse.chr6 290546 18 + 636262 TTAATTGAGAATAAAGAC -s mr.mrrefChr5 141377 18 + 294540 TTAATTGAGAATAAAGAC -s simRat_chr6.simRat.chr6 279177 18 + 647215 TTAACTGAGATTCAAGAC - -a -s simMouse_chr6.simMouse.chr6 290564 34 + 636262 TGATGGATTGTCTATTAAATGATGCCCATCCTGA -s mr.mrrefChr5 141395 34 + 294540 TGATGGATTGTCTATTAAATGATGCCCATCCTGA -s simRat_chr6.simRat.chr6 279198 34 + 647215 TGATGGATTGTCTATTAATTGACACTCTTACTGA - -a -s simMouse_chr6.simMouse.chr6 290598 56 + 636262 TTGAACTTTGGTAGTGTTAATAGGTCTGACCCTACAGTTCGCACCCTAATATTCAA -s mr.mrrefChr5 141429 55 + 294540 TTGAACTTTGGTAGTGTTAATAGGTCTGACCCTACAGTTCGCACCCTAATAT-CAA -s simRat_chr6.simRat.chr6 279237 55 + 647215 TTCGACTGTGGTAGTGTTAATAAGTCTGACCCTACAATTCACACCCTAATAT-CAA - -a -s simMouse_chr6.simMouse.chr6 290654 38 + 636262 ACTACAAGAGCTCTAGTCTAAGAGCTAAAGTGAATCCA -s mr.mrrefChr5 141484 38 + 294540 ACTACAAGAGCTCTAGTCTAAGAGCTAAAGTGAATCCA -s simRat_chr6.simRat.chr6 279317 38 + 647215 ACTAGAAGAGCTATAGTCTAAGAGCTAAAGTGAATCCA - -a -s simMouse_chr6.simMouse.chr6 290692 22 + 636262 TGGGCTAGATATTCTGGATTCA -s Anc0.Anc0refChr8 1375 4 - 17196 ------------------TTCA -s Anc1.Anc1refChr8 44670 5 - 57822 -----------------ATTCA -s Anc2.Anc2refChr5 6811 4 - 8386 ------------------TTTA -s mr.mrrefChr5 141522 22 + 294540 TGGGCTAGATATTCTGGATTCA -s simCow_chr6.simCow.chr6 329831 4 - 602619 ------------------TCTA -s simDog_chr6.simDog.chr6 55002 4 + 593897 ------------------TTCA -s simHuman_chr6.simHuman.chr6 359232 5 - 601863 -----------------Attca -s simRat_chr6.simRat.chr6 279356 22 + 647215 TGAGCTAGATATTCTGGATTCA - -a -s simMouse_chr6.simMouse.chr6 290714 144 + 636262 GTGGTTTTACCAAAGATTTAACCAAGAAATTAGTCTTTGCTTTTTCGATTTATAGTACTAGACCATTTGGCTAACCTGACATGAGGTAGACATCCTTATATAGGGTCAACCCAGGTGTGCATGGGGGACAGAGTAGTTCTCCTC -s Anc0.Anc0refChr8 1379 41 - 17196 GTGATTTTACCAAGAAATCAA-----------GTCTTTACTTT-------------------------------------------------------------------------------------------A-TGCACTTA -s Anc1.Anc1refChr8 44675 41 - 57822 GTGATTTTACCAAGAAATCAA-----------GTCTTTACTTT-------------------------------------------------------------------------------------------A-TGCACTTA -s Anc2.Anc2refChr5 6815 41 - 8386 GTGATTTTACCAAGAAATCAA-----------GTCTTTACTTT-------------------------------------------------------------------------------------------G-TGCACTTA -s mr.mrrefChr5 141544 139 + 294540 GTGGTTTTACCAAAGATTTAACCAA---ATTAGTCTTTGCTTTTTCGATTTATAGTACTAGACCATTTGGCTAACCTGACATGAGGTAGACATCCTTATATAGGGTCAACCCAGGTGTGCATGGGGG-CAGAGTA-TTCTCCTC -s simCow_chr6.simCow.chr6 329835 41 - 602619 GTTGTTTTACCAAGGAAACAA-----------GGCTTTACTTT-------------------------------------------------------------------------------------------G-TGCACTTA -s simDog_chr6.simDog.chr6 55006 24 + 593897 GTGATTTCACCAAGA--TCAA-----------GTCTC----------------------------------------------------------------------------------------------------------- -s simHuman_chr6.simHuman.chr6 359398 41 - 601863 GTGATTTTACCAAGAAATCAA-----------GTCTTTACCTT-------------------------------------------------------------------------------------------A-AGCCTTTA -s simRat_chr6.simRat.chr6 279378 139 + 647215 TTTATTTTACCAAGGATTCTACTAA---ATTAATCTTTCATTTGTCAATTTTTAGTACTAGACCATCTGGCCAACTTGACATGAGGTGCACAGCCATATATAGGATCAACCTATGAGTGTGTGAGGG-CAGAGTA-TCCCCCTC - -a -s simMouse_chr6.simMouse.chr6 290858 49 + 636262 AGATTTTAGCATCTACCACAAAGCTTGCATTTTATTAATCTCATGCTGT -s Anc0.Anc0refChr8 1420 34 - 17196 AGGTTTTAGCATCTTTCACATGGCATTCAATCT---------------C -s Anc1.Anc1refChr8 44716 45 - 57822 AGGTTTTAGCATCTTTCACATGGCATTCAATCTATCCATTTCA----AC -s Anc2.Anc2refChr5 6856 34 - 8386 AGGTTATACCATCCTTCACATGGGATTCAATCT---------------C -s mr.mrrefChr5 141683 49 + 294540 AGATTTTAGCATCTTCCACAAAGCTTGCATTTTATTAATTTCATGCTGT -s simCow_chr6.simCow.chr6 329878 34 - 602619 AGGTTATACCATCCTTCACATGGGATTCAATCT---------------C -s simHuman_chr6.simHuman.chr6 359439 43 - 601863 GTGTTTTAGTATCTTTCACACGGCATCCGGC--ATCCATTTCA----AC -s simRat_chr6.simRat.chr6 279517 45 + 647215 AGAGTTTGGGACCTTCC----AGCTTGCATTTTATTAATTTCATTATGT - -a -s simMouse_chr6.simMouse.chr6 290907 35 + 636262 TGGGAGAATGTGTAAGTACCTATCCTTGTGGTTTG -s Anc0.Anc0refChr8 1471 35 - 17196 TAGAAGAATGTGTATATACCTATCCTCGCCGTTTG -s Anc1.Anc1refChr8 44778 35 - 57822 TAGAAGAATGTGTATATACCTATCCTCGCCGTTTG -s Anc2.Anc2refChr5 6907 35 - 8386 TCAAAGAATGAATATATACCTGTTCTTGCCGTTTG -s mr.mrrefChr5 141749 35 + 294540 TAGGAGAATGTGTAAATACCTATCCTCGTGGTTTG -s simCow_chr6.simCow.chr6 329929 35 - 602619 TCAAAGAATGAATATATACCTGTTCTTGCCCTCTG -s simDog_chr6.simDog.chr6 55030 5 + 593897 ------------------------------GGTTG -s simHuman_chr6.simHuman.chr6 359499 35 - 601863 AAGAAGAATGTGTATATACCCATCGTCTCAGTTTG -s simRat_chr6.simRat.chr6 279583 35 + 647215 TAGGAGAATGTGTAAATACCTATTCTCATGGTTTG - -a -s simMouse_chr6.simMouse.chr6 290942 35 + 636262 GGCAATCCCTGCAACACGACCCAATTGGCTTTGCT -s Anc0.Anc0refChr8 1507 32 - 17196 G---ATCTCTGCAAGATGAATAGATTGTCTGTACT -s Anc1.Anc1refChr8 44814 35 - 57822 GGCAATCTCTGCAAGATGAATAGATTGTCTGTACT -s Anc2.Anc2refChr5 6943 32 - 8386 G---ATCTCTGCAAGATGAATAGATTGTCTGTACT -s mr.mrrefChr5 141784 35 + 294540 GGCAATCTCTGCAACATGACCCAATTGGCTTTGCT -s simCow_chr6.simCow.chr6 329965 32 - 602619 G---TGCTCAGCAAGATAAATAGATTGTCTGTCCT -s simDog_chr6.simDog.chr6 55036 32 + 593897 G---ATTTCTGCAAGATGAATAGACTGTCTGTACT -s simHuman_chr6.simHuman.chr6 359535 35 - 601863 GGCAGTCTCTGCAAGATGAATAGATTGTTTGTACT -s simRat_chr6.simRat.chr6 279618 35 + 647215 GGCAATCTCTGCAACATGACCCAATCGGCTTTGCT - -a -s simMouse_chr6.simMouse.chr6 290977 6 + 636262 GTGGCT -s Anc0.Anc0refChr8 1539 6 - 17196 GTCTGT -s Anc1.Anc1refChr8 44849 6 - 57822 GTCTGT -s Anc2.Anc2refChr5 6975 6 - 8386 GTCTGT -s mr.mrrefChr5 141819 6 + 294540 GTGGCT -s simCow_chr6.simCow.chr6 329997 3 - 602619 GTC--- -s simDog_chr6.simDog.chr6 55073 6 + 593897 GTCTGT -s simHuman_chr6.simHuman.chr6 359570 6 - 601863 GTATGT -s simRat_chr6.simRat.chr6 279653 6 + 647215 GTGGCT - -a -s simMouse_chr6.simMouse.chr6 290983 74 + 636262 GGTTATAGGCATGACTTGAATAGGTCTAACCAGACACGCCCAAATGGACCTGAGTATGATCTGAGGGCTTGGGT -s Anc0.Anc0refChr8 1545 53 - 17196 GTTTGTGGGCATTAGTTGTATAGC-------AGATGCAT------GGACTTAGGTCTGATCCA--------GAG -s Anc1.Anc1refChr8 44855 66 - 57822 GTTTGTGGGCATTAGTTGTATAGCTGCAGCTAGATGCATTCAAGTGGACTTAGGTCTGATCCA--------GAG -s Anc2.Anc2refChr5 6981 53 - 8386 GTTTGTGGGCATCAGTTATATATC-------AGATGCAT------GGATTTAGATCTGTTCCA--------TAG -s mr.mrrefChr5 141825 74 + 294540 GTTTATGGGCATTAGTTGAATAGGTCTAACTAGACACACCCAAATGGACCTGAGTATGATCTGAGGGCTGGGGT -s simDog_chr6.simDog.chr6 55080 53 + 593897 GTTTGTGGGCATCAGTTATATATC-------AGATGCAT------GGATTTAGATCTGTTCCA--------TAG -s simHuman_chr6.simHuman.chr6 359576 66 - 601863 GTTTGTGGGCATTTGTTGGATAGCTGCAGCTAAATGCATTCAAGTGAACTGTGGTGTGATCCA--------GAA -s simRat_chr6.simRat.chr6 279659 73 + 647215 GTTGATGGGCATTAGTTGAATAGGTCTAATTAGACACACCAAAATGGACCTGAATTTGT-CTGAGGGCTGGGGT - -a -s simMouse_chr6.simMouse.chr6 291057 4 + 636262 TGAT -s Anc0.Anc0refChr8 1598 4 - 17196 TGAT -s Anc1.Anc1refChr8 44921 4 - 57822 TGAT -s Anc2.Anc2refChr5 7034 4 - 8386 TTGT -s mr.mrrefChr5 141899 4 + 294540 TGAT -s simDog_chr6.simDog.chr6 55137 4 + 593897 TTGT -s simHuman_chr6.simHuman.chr6 359642 4 - 601863 TGAT -s simRat_chr6.simRat.chr6 279732 4 + 647215 TGAT - -a -s simMouse_chr6.simMouse.chr6 291061 1 + 636262 T -s Anc0.Anc0refChr8 1605 1 - 17196 T -s Anc1.Anc1refChr8 44928 1 - 57822 T -s Anc2.Anc2refChr5 7041 1 - 8386 T -s mr.mrrefChr5 141903 1 + 294540 T -s simDog_chr6.simDog.chr6 55144 1 + 593897 T -s simHuman_chr6.simHuman.chr6 359649 1 - 601863 T -s simRat_chr6.simRat.chr6 279736 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 291062 7 + 636262 TCGCATG -s Anc0.Anc0refChr8 1606 7 - 17196 TTTCATG -s Anc1.Anc1refChr8 44929 7 - 57822 TTTCATG -s Anc2.Anc2refChr5 7042 7 - 8386 TTTCATG -s mr.mrrefChr5 141904 7 + 294540 TCGCATG -s simDog_chr6.simDog.chr6 55146 7 + 593897 TTTCATG -s simHuman_chr6.simHuman.chr6 359650 7 - 601863 TTTGATG -s simRat_chr6.simRat.chr6 279737 7 + 647215 TCGTATG - -a -s simMouse_chr6.simMouse.chr6 291069 13 + 636262 TCCGCACATGCCG -s Anc0.Anc0refChr8 1613 13 - 17196 TCTGTCTATGCCG -s Anc1.Anc1refChr8 44936 13 - 57822 TCTGTCTATGCCG -s Anc2.Anc2refChr5 7049 13 - 8386 CCTGTCTATGACA -s mr.mrrefChr5 141911 13 + 294540 TCCGCATATGCCG -s simDog_chr6.simDog.chr6 55154 13 + 593897 CCTGTCTATGACA -s simHuman_chr6.simHuman.chr6 359657 13 - 601863 TCTGTCTATGCAG -s simRat_chr6.simRat.chr6 279744 13 + 647215 TCCACATATGCTG - -a -s simMouse_chr6.simMouse.chr6 291082 41 + 636262 TGTCAAATTGCCTCTTCATCTTTGGTTTTTTAATTCATTAT -s Anc0.Anc0refChr8 1627 26 - 17196 TGTCAAATTGGACCTTTAT-TTTGGTT-------------- -s Anc1.Anc1refChr8 44950 40 - 57822 TGTCAAATTGGACCTTTAT-TTTGGTTTTTCAATTTATAAT -s Anc2.Anc2refChr5 7063 26 - 8386 TGTCAAATTGGACCTTTGT-CTTGGTT-------------- -s mr.mrrefChr5 141924 41 + 294540 TGTCAAATTGCACCTTCATCTTTGGTTTTTTAATTTATTAT -s simDog_chr6.simDog.chr6 55168 26 + 593897 TGTCAAATTGGACCTTTGT-CTTGGTT-------------- -s simHuman_chr6.simHuman.chr6 359671 40 - 601863 TGTCAGATTAAACCTTTAT-TTGGGTTTTTCAATTTATAAT -s simRat_chr6.simRat.chr6 279757 41 + 647215 TGCCAAATTGCACCTTCATCTTTGGTTTTTTAATTTATTAT - -a -s simMouse_chr6.simMouse.chr6 291123 54 + 636262 GGACCCATTATTCCGCCTTGAGTCTTAAAATGCTAAAATGGAGTGTAATTAGCT -s Anc0.Anc0refChr8 1653 19 - 17196 -----------------------------------AAATGGAGTGTACTCAGCT -s Anc1.Anc1refChr8 44990 54 - 57822 GGAGTGAGTATTCTCCCTTTAGTTCTAAGATTCTAAAATGGAGTGTACTCAGCT -s Anc2.Anc2refChr5 7089 19 - 8386 -----------------------------------AAATGGAGTGTACTCAGCT -s mr.mrrefChr5 141965 54 + 294540 GGACCCATTATTCCGCCTTGAGTCTTAAAATGCTAAAATGGAGTGTACTTAGCT -s simDog_chr6.simDog.chr6 55194 19 + 593897 -----------------------------------AAATGGAGTGTACTCAGCT -s simHuman_chr6.simHuman.chr6 359717 54 - 601863 GGAGTGAGTATTCTCCCTTTAGTTCTAAGATTCTAGAATGGAGTGCACCCAGCT -s simRat_chr6.simRat.chr6 279798 54 + 647215 GGACCCATTATTCGACCTTGAGTCTTAAAATACTACAATGGAGTGTACTGAGCT - -a -s simMouse_chr6.simMouse.chr6 291177 46 + 636262 TTGTGACAGATTTGTGATGGCTCCAGTGGTTTTTTAAAATTATAAA -s Anc0.Anc0refChr8 1672 44 - 17196 TCATGAGTGATTTGTAATGTTACCTGTGCTTTTTTA-C-TTACAAA -s Anc1.Anc1refChr8 45044 45 - 57822 TCATGAGTGATTTGTAATGTTACCTGTGCTTTTTTAGC-TTACAAA -s Anc2.Anc2refChr5 7108 44 - 8386 TCAAAGGGGATTTGTAATGTTACCTGTGCTTTTTTA-C-TTACAGA -s mr.mrrefChr5 142019 46 + 294540 TTGTGACTGATTTGTGATGGCTCCTGTGGTTTTTTAAAATTATAAA -s simDog_chr6.simDog.chr6 55215 44 + 593897 TCAAAGGGGATTTGTAATGTTACCTGTGCTTTTTTA-C-TTACAGA -s simHuman_chr6.simHuman.chr6 359771 45 - 601863 TCATGAGTGATGTGTAATGATACCTATGCTTTTTTAGT-TTACAAA -s simRat_chr6.simRat.chr6 279852 46 + 647215 TTGTGACTGATTTGTGATGGCTCCTGTGATTTTTTAAAATTATAAA - -a -s simMouse_chr6.simMouse.chr6 291223 13 + 636262 GCAAGGCATCATT -s Anc0.Anc0refChr8 1716 13 - 17196 GGAAGGCATGATT -s Anc1.Anc1refChr8 45089 13 - 57822 GGAAGGCATGATT -s Anc2.Anc2refChr5 7152 13 - 8386 GGCAGGCATGATT -s mr.mrrefChr5 142065 13 + 294540 GGAAGGCATCATT -s simDog_chr6.simDog.chr6 55259 13 + 593897 GGCAGGCATGATT -s simHuman_chr6.simHuman.chr6 359818 13 - 601863 GGAAGGCTTGATT -s simRat_chr6.simRat.chr6 279898 13 + 647215 GGCAGGCATCATT - -a -s simMouse_chr6.simMouse.chr6 291236 15 + 636262 GTAACAACATGCCAT -s Anc0.Anc0refChr8 1730 15 - 17196 GTAACAACATGCCAC -s Anc1.Anc1refChr8 45103 15 - 57822 GTAACAACATGCCAC -s Anc2.Anc2refChr5 7166 15 - 8386 GTAACTATATGCCAC -s mr.mrrefChr5 142078 15 + 294540 GTAACAACATGCCAT -s simDog_chr6.simDog.chr6 55273 15 + 593897 GTAACTATATGCCAC -s simHuman_chr6.simHuman.chr6 359832 15 - 601863 GTAACAGCATGCCAC -s simRat_chr6.simRat.chr6 279911 15 + 647215 GCAACAACATGCGTG - -a -s simMouse_chr6.simMouse.chr6 291251 22 + 636262 GGCCTTAGGATGAAGATCCCGC -s Anc0.Anc0refChr8 1746 22 - 17196 AACCTTAGAATAAGAATGGTGC -s Anc1.Anc1refChr8 45119 22 - 57822 AACCTTAGAATAAGAATGGTGC -s Anc2.Anc2refChr5 7182 22 - 8386 AACGTTATGCTGAGAATGGTGC -s mr.mrrefChr5 142093 22 + 294540 GGCCTTAGAATAAGGATCCCGC -s simDog_chr6.simDog.chr6 55289 22 + 593897 AACGTTATGCTGAGAATGGTGC -s simHuman_chr6.simHuman.chr6 359848 22 - 601863 AACCTTAGAACAAGAATGATGC -s simRat_chr6.simRat.chr6 279926 22 + 647215 GGCCTTAGAATAAGGTTTGCCC - -a -s simMouse_chr6.simMouse.chr6 291273 10 + 636262 TGGTTATCAA -s Anc0.Anc0refChr8 1768 10 - 17196 AGGGTAACAA -s Anc1.Anc1refChr8 45141 10 - 57822 AGGGTAACAA -s Anc2.Anc2refChr5 7204 10 - 8386 AGGGTAACAA -s mr.mrrefChr5 142115 10 + 294540 TGGTTAACAA -s simDog_chr6.simDog.chr6 55311 10 + 593897 AGGGTAACAA -s simHuman_chr6.simHuman.chr6 359871 10 - 601863 GGGGTAACAA -s simRat_chr6.simRat.chr6 279948 10 + 647215 TGGTTAACAA - -a -s simMouse_chr6.simMouse.chr6 291283 59 + 636262 TCAGATCCTCTTTTGCTGCTCAAATGAAAAAATTAGCAACAGCAGAGGATCACATAAGC -s Anc0.Anc0refChr8 1786 49 - 17196 CCAGACCCTGATTTTCTGCTTAA-----TGGATTAGCATTGAAAGAATATCCCA----- -s Anc1.Anc1refChr8 45159 54 - 57822 CCAGACCCTGATTTTCTGCTTAAATGGATGGATTAGCATTGAAAGAATATCCCA----- -s Anc2.Anc2refChr5 7222 49 - 8386 CCAGGTCCTGATCTTATGCTTAG-----TGGATTAGCATTGAGTAAATATCCCA----- -s mr.mrrefChr5 142133 59 + 294540 CCAGACCCTCTTTTTCTGCTCAAATGAAAAAATTAGCATTAGAAGAGGATCACATAAGC -s simDog_chr6.simDog.chr6 55329 49 + 593897 CCAGGTCCTGATCTTATGCTTAG-----TGGATTAGCATTGAGTAAATATCCCA----- -s simHuman_chr6.simHuman.chr6 359889 54 - 601863 CCAGACCATTAATTTCTGCTGTAATGGAGGGGTTAGCATTGAAAGAACATCCCA----- -s simRat_chr6.simRat.chr6 279966 59 + 647215 CCAGACCCTCTTTTTCTGCTCAAATGAAAAAATTAGCATTAGAGGAGGATCACATAAGC - -a -s simMouse_chr6.simMouse.chr6 291342 21 + 636262 AAGCATCTGATTGAGTCTAAT -s Anc0.Anc0refChr8 1835 18 - 17196 AAATATGGGATTGAATGC--- -s Anc1.Anc1refChr8 45213 21 - 57822 AAATATGGGATTGAATGCAAC -s Anc2.Anc2refChr5 7271 18 - 8386 AAATATGGGGTTGCATGC--- -s mr.mrrefChr5 142192 21 + 294540 AAGCATCTGATTGAGTCTAAT -s simDog_chr6.simDog.chr6 55379 18 + 593897 AAATATGGGGTTGCATGC--- -s simHuman_chr6.simHuman.chr6 359943 21 - 601863 AACTATGGAATTAAATTCAAC -s simRat_chr6.simRat.chr6 280025 21 + 647215 AAGCATTTGATTGAGTCTAAT - -a -s simMouse_chr6.simMouse.chr6 291363 108 + 636262 TTTTTCATTTGCTTTGCATATCCTCTCTACTCTATGGTTTGCATCACCTTGGGGAATTTTTGTTAACTCAGGGCCTCATTAATATATGATACTCAGGACATCCTATGT -s Anc0.Anc0refChr8 1853 18 - 17196 ------------------------------------------------------------------------------------------CATCATGCCATCTGTTGC -s Anc1.Anc1refChr8 45235 82 - 57822 GTTAT-------TTTGCATACTCTATATTTTTTGTG-------------------ATTCTTGTAGTCTCAGGGCCCCACTAATATAAGCTCATCATGCCATCTGTTGC -s Anc2.Anc2refChr5 7289 18 - 8386 ------------------------------------------------------------------------------------------CATTATACCACATGTTGC -s mr.mrrefChr5 142214 108 + 294540 TTTTTCATTTGCTTTGCATATCCTCTCTTTTCTATGGTTTGCATCACCTTGGGGAATTTTTGTTAACTCAGGGCCTCATTAATATATGATACTCAGGACATCCTATGC -s simCow_chr6.simCow.chr6 330000 18 - 602619 ------------------------------------------------------------------------------------------CATTATACCACATGTTGC -s simHuman_chr6.simHuman.chr6 359965 82 - 601863 GTTAT-------TTTGCATACTCTATATTTTTTGTG-------------------ATTCTTGTAGTCTCAGGGCCCCACTAATATAAGCTCATCGTGCCATCTGTTGC -s simRat_chr6.simRat.chr6 280047 108 + 647215 TTTTTCATTTGCTTTGCGTATCCTCTCTTTTCTATGGTTTGCATTGACTTGGGAAATTTTTGTTAACTCAGGGCCTCATTAATATATAATACTAAGGACATCCAATGC - -a -s simMouse_chr6.simMouse.chr6 291471 30 + 636262 TTCTGCCATATTATGCCCTAATCTGCTTAC -s Anc0.Anc0refChr8 1910 29 - 17196 TTCTGCTGT-TGATGCCCTAATCAGCTGGC -s Anc1.Anc1refChr8 45356 29 - 57822 TTCTGCTGT-TGATGCCCTAATCAGCTGGC -s Anc2.Anc2refChr5 7346 29 - 8386 TTCCACTGC-TGATGCCCTAATCAATTGGC -s mr.mrrefChr5 142322 30 + 294540 TTCTGCCATATTATGCCCTAATCTGCTTAC -s simCow_chr6.simCow.chr6 330070 29 - 602619 TTCCACTGC-TGATGCCCTAATCAATTGGC -s simHuman_chr6.simHuman.chr6 360086 29 - 601863 TTCTGCTGT-TGATGCCCTAATCCGCTGTC -s simRat_chr6.simRat.chr6 280155 30 + 647215 TCTAACCATATTATGCCCTAATCTGATTAC - -a -s simMouse_chr6.simMouse.chr6 291501 10 + 636262 CATAATTGAA -s Anc0.Anc0refChr8 1939 9 - 17196 CATTATTG-A -s Anc1.Anc1refChr8 45385 9 - 57822 CATTATTG-A -s Anc2.Anc2refChr5 7375 9 - 8386 CATGCTTG-A -s mr.mrrefChr5 142352 9 + 294540 CATTATTG-A -s simCow_chr6.simCow.chr6 330099 9 - 602619 CATGCTTG-A -s simHuman_chr6.simHuman.chr6 360115 9 - 601863 TATTATTG-A -s simRat_chr6.simRat.chr6 280190 9 + 647215 CATTATTG-A - -a -s simMouse_chr6.simMouse.chr6 291511 9 + 636262 CAGTGATTT -s Anc0.Anc0refChr8 1948 9 - 17196 TCGACCTTT -s Anc1.Anc1refChr8 45394 9 - 57822 TCGACCTTT -s Anc2.Anc2refChr5 7385 9 - 8386 TCGACTTTT -s mr.mrrefChr5 142361 9 + 294540 CCGTCCTTT -s simCow_chr6.simCow.chr6 330109 9 - 602619 TCGACTTTT -s simHuman_chr6.simHuman.chr6 360124 9 - 601863 ACAACCTTT -s simRat_chr6.simRat.chr6 280199 9 + 647215 CCGTCCTTT - -a -s simMouse_chr6.simMouse.chr6 291520 6 + 636262 CTGTTG -s Anc0.Anc0refChr8 1957 5 - 17196 CTGTC- -s Anc1.Anc1refChr8 45403 6 - 57822 CTGTCG -s Anc2.Anc2refChr5 7394 5 - 8386 CTGCC- -s mr.mrrefChr5 142370 6 + 294540 CTGTTG -s simDog_chr6.simDog.chr6 55397 5 + 593897 CTGCC- -s simHuman_chr6.simHuman.chr6 360138 6 - 601863 CTGTCG -s simRat_chr6.simRat.chr6 280208 3 + 647215 C---TG - -a -s simMouse_chr6.simMouse.chr6 291526 4 + 636262 AAGA -s Anc0.Anc0refChr8 1962 4 - 17196 AACA -s Anc1.Anc1refChr8 45409 4 - 57822 AACA -s Anc2.Anc2refChr5 7725 4 - 8386 AACG -s mr.mrrefChr5 142376 4 + 294540 AAGA -s simCow_chr6.simCow.chr6 330595 4 - 602619 ATTG -s simDog_chr6.simDog.chr6 259630 4 + 593897 AACG -s simHuman_chr6.simHuman.chr6 360144 4 - 601863 AGCA -s simRat_chr6.simRat.chr6 280211 4 + 647215 AAGA - -a -s simMouse_chr6.simMouse.chr6 291530 11 + 636262 GTGTTTTCCAT -s Anc0.Anc0refChr8 1966 11 - 17196 GTCTTTTCCAT -s Anc1.Anc1refChr8 45413 11 - 57822 GTCTTTTCCAT -s Anc2.Anc2refChr5 7729 11 - 8386 GCCTTTTGCTT -s mr.mrrefChr5 142380 11 + 294540 GTGTTTTCCAT -s simCow_chr6.simCow.chr6 330599 11 - 602619 GCCTTCTCCAT -s simDog_chr6.simDog.chr6 259641 11 + 593897 GCCTTTTGCTT -s simHuman_chr6.simHuman.chr6 360148 11 - 601863 GTCTTTCCCAT -s simRat_chr6.simRat.chr6 280215 11 + 647215 GTGTTCTCCAT - -a -s simMouse_chr6.simMouse.chr6 291541 7 + 636262 CAGAATA -s Anc0.Anc0refChr8 1977 6 - 17196 CTGA-CA -s Anc1.Anc1refChr8 45424 7 - 57822 CTGAACA -s Anc2.Anc2refChr5 7740 6 - 8386 CTGA-CA -s Anc2.Anc2refChr5 7403 6 - 8386 CCGA-CA -s mr.mrrefChr5 142391 7 + 294540 CTGAATA -s simCow_chr6.simCow.chr6 330610 6 - 602619 CTAA-CA -s simDog_chr6.simDog.chr6 55406 6 + 593897 CCGA-CA -s simDog_chr6.simDog.chr6 259652 6 + 593897 CTGA-CA -s simHuman_chr6.simHuman.chr6 360159 7 - 601863 CTGTACA -s simRat_chr6.simRat.chr6 280226 7 + 647215 CTGAATA - -a -s simMouse_chr6.simMouse.chr6 291548 4 + 636262 TCAT -s Anc0.Anc0refChr8 1983 4 - 17196 GCCT -s Anc1.Anc1refChr8 45431 4 - 57822 GCCT -s Anc2.Anc2refChr5 7746 4 - 8386 GCAT -s mr.mrrefChr5 142398 4 + 294540 TCAT -s simCow_chr6.simCow.chr6 330616 4 - 602619 GCCT -s simDog_chr6.simDog.chr6 259658 4 + 593897 GCAT -s simHuman_chr6.simHuman.chr6 360166 4 - 601863 GCCG -s simRat_chr6.simRat.chr6 280233 4 + 647215 CCAT - -a -s simMouse_chr6.simMouse.chr6 291552 7 + 636262 TCTTGTT -s Anc0.Anc0refChr8 1987 7 - 17196 TCTTTGT -s Anc1.Anc1refChr8 45435 7 - 57822 TCTTTGT -s Anc2.Anc2refChr5 7750 7 - 8386 TCTTTGT -s Anc2.Anc2refChr5 7409 7 - 8386 TCTTCAT -s mr.mrrefChr5 142402 7 + 294540 TCTTGTT -s simCow_chr6.simCow.chr6 330620 7 - 602619 TCTTTGT -s simDog_chr6.simDog.chr6 55595 7 + 593897 TCTTCAT -s simDog_chr6.simDog.chr6 259662 7 + 593897 TCTTTGT -s simHuman_chr6.simHuman.chr6 360170 7 - 601863 TCTTTGT -s simRat_chr6.simRat.chr6 280237 7 + 647215 TCTCAAT - -a -s simMouse_chr6.simMouse.chr6 291559 1 + 636262 G -s Anc0.Anc0refChr8 1994 1 - 17196 C -s Anc1.Anc1refChr8 45442 1 - 57822 C -s Anc2.Anc2refChr5 7757 1 - 8386 C -s Anc2.Anc2refChr5 7416 1 - 8386 C -s mr.mrrefChr5 142409 1 + 294540 C -s simCow_chr6.simCow.chr6 330118 1 - 602619 C -s simCow_chr6.simCow.chr6 330627 1 - 602619 C -s simDog_chr6.simDog.chr6 55602 1 + 593897 T -s simDog_chr6.simDog.chr6 259669 1 + 593897 C -s simHuman_chr6.simHuman.chr6 360177 1 - 601863 C -s simRat_chr6.simRat.chr6 280244 1 + 647215 C - -a -s simMouse_chr6.simMouse.chr6 291560 13 + 636262 TGACCTGATGTCG -s Anc0.Anc0refChr8 1995 13 - 17196 TGATTTGATGTTG -s Anc1.Anc1refChr8 45443 13 - 57822 TGATTTGATGTTG -s Anc2.Anc2refChr5 7758 13 - 8386 TAACTTGATGTTG -s Anc2.Anc2refChr5 7417 13 - 8386 TGATTTCATGTTA -s mr.mrrefChr5 142410 13 + 294540 TGACTTGATGTCG -s simCow_chr6.simCow.chr6 330119 13 - 602619 TGACCGAATACCA -s simCow_chr6.simCow.chr6 330628 13 - 602619 TACCTTAATGTTG -s simDog_chr6.simDog.chr6 55603 13 + 593897 AGATTTCATGTTA -s simDog_chr6.simDog.chr6 259671 13 + 593897 TAACTTGATGTTG -s simHuman_chr6.simHuman.chr6 360178 13 - 601863 TGATTTGATGTTG -s simRat_chr6.simRat.chr6 280245 13 + 647215 TGACTTGATGTCG - -a -s simMouse_chr6.simMouse.chr6 291573 1 + 636262 T -s Anc0.Anc0refChr8 2008 1 - 17196 T -s Anc1.Anc1refChr8 45456 1 - 57822 T -s Anc2.Anc2refChr5 7771 1 - 8386 A -s Anc2.Anc2refChr5 7430 1 - 8386 T -s mr.mrrefChr5 142423 1 + 294540 T -s simCow_chr6.simCow.chr6 330641 1 - 602619 G -s simDog_chr6.simDog.chr6 55616 1 + 593897 T -s simDog_chr6.simDog.chr6 259684 1 + 593897 A -s simHuman_chr6.simHuman.chr6 360191 1 - 601863 G -s simRat_chr6.simRat.chr6 280258 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 291574 2 + 636262 TA -s Anc0.Anc0refChr8 2009 2 - 17196 CA -s Anc1.Anc1refChr8 45457 2 - 57822 TA -s Anc2.Anc2refChr5 7772 2 - 8386 CA -s Anc2.Anc2refChr5 7431 2 - 8386 CA -s mr.mrrefChr5 142424 2 + 294540 TA -s simCow_chr6.simCow.chr6 330132 2 - 602619 CA -s simCow_chr6.simCow.chr6 330642 2 - 602619 CT -s simDog_chr6.simDog.chr6 55617 2 + 593897 CA -s simDog_chr6.simDog.chr6 259685 2 + 593897 CA -s simHuman_chr6.simHuman.chr6 360192 2 - 601863 TG -s simRat_chr6.simRat.chr6 280259 2 + 647215 CA - -a -s simMouse_chr6.simMouse.chr6 291576 8 + 636262 CATCTTCG -s Anc0.Anc0refChr8 2016 8 - 17196 CAGCTTGT -s Anc1.Anc1refChr8 45464 8 - 57822 CAGCTTGT -s Anc2.Anc2refChr5 7779 8 - 8386 CAGCTTGT -s Anc2.Anc2refChr5 7438 8 - 8386 CAGCTTGT -s mr.mrrefChr5 142426 8 + 294540 CATCTTCT -s simCow_chr6.simCow.chr6 330139 8 - 602619 CAGCTTGT -s simCow_chr6.simCow.chr6 330649 8 - 602619 CAGCTTGT -s simDog_chr6.simDog.chr6 55624 8 + 593897 CAGCTTGT -s simDog_chr6.simDog.chr6 259692 8 + 593897 CAGCTTGT -s simHuman_chr6.simHuman.chr6 360199 8 - 601863 CAGCTTGT -s simRat_chr6.simRat.chr6 280261 8 + 647215 CATCTTCT - -a -s simMouse_chr6.simMouse.chr6 291584 17 + 636262 CAGACTCCACGAGGGCA -s Anc0.Anc0refChr8 2024 17 - 17196 CAGACACCAATAGGGCA -s Anc1.Anc1refChr8 45472 17 - 57822 CAGACACCAATAGGGCA -s Anc2.Anc2refChr5 7787 17 - 8386 CAGACACCATTGGGGCA -s Anc2.Anc2refChr5 7446 17 - 8386 CAGACACCAACAGGGCA -s mr.mrrefChr5 142434 17 + 294540 CAGACTCCACGAGGGCA -s simCow_chr6.simCow.chr6 330147 17 - 602619 CAGACGCTGGCAGGGCA -s simCow_chr6.simCow.chr6 330661 17 - 602619 CAGACACTAAGGGAGTA -s simDog_chr6.simDog.chr6 55632 17 + 593897 CAGGCACCAACAGGGCA -s simDog_chr6.simDog.chr6 259700 17 + 593897 CAGACACCATTGGGGCA -s simHuman_chr6.simHuman.chr6 360207 17 - 601863 CAGACACCAATCAGGTG -s simRat_chr6.simRat.chr6 280269 17 + 647215 CAAGCTCCACCAGAGCA - -a -s simMouse_chr6.simMouse.chr6 291601 2 + 636262 AT -s Anc0.Anc0refChr8 2041 2 - 17196 AT -s Anc1.Anc1refChr8 45489 2 - 57822 AT -s Anc2.Anc2refChr5 7804 2 - 8386 CT -s Anc2.Anc2refChr5 7463 2 - 8386 AT -s mr.mrrefChr5 142451 2 + 294540 AT -s simCow_chr6.simCow.chr6 330164 2 - 602619 GT -s simCow_chr6.simCow.chr6 330681 2 - 602619 CT -s simDog_chr6.simDog.chr6 55649 2 + 593897 AT -s simDog_chr6.simDog.chr6 259717 2 + 593897 CT -s simHuman_chr6.simHuman.chr6 360224 2 - 601863 AA -s simRat_chr6.simRat.chr6 280286 2 + 647215 AC - -a -s simMouse_chr6.simMouse.chr6 291603 5 + 636262 GCAAG -s Anc0.Anc0refChr8 2043 5 - 17196 GCTAG -s Anc1.Anc1refChr8 45491 5 - 57822 GCTAG -s Anc2.Anc2refChr5 7465 5 - 8386 GCTAG -s mr.mrrefChr5 142453 5 + 294540 GCTAG -s simCow_chr6.simCow.chr6 330166 5 - 602619 GCTAG -s simDog_chr6.simDog.chr6 55651 5 + 593897 GCTGG -s simHuman_chr6.simHuman.chr6 360226 5 - 601863 GCTAG -s simRat_chr6.simRat.chr6 280288 5 + 647215 GTTAG - -a -s simMouse_chr6.simMouse.chr6 291608 5 + 636262 AATTG -s Anc0.Anc0refChr8 2048 5 - 17196 AATCC -s Anc1.Anc1refChr8 45496 5 - 57822 AATCC -s Anc2.Anc2refChr5 7806 5 - 8386 AGTCC -s Anc2.Anc2refChr5 7470 5 - 8386 AATCC -s mr.mrrefChr5 142458 5 + 294540 AATTG -s simCow_chr6.simCow.chr6 330171 5 - 602619 GATCT -s simCow_chr6.simCow.chr6 330683 5 - 602619 AGAAC -s simDog_chr6.simDog.chr6 55656 5 + 593897 AATCC -s simDog_chr6.simDog.chr6 259719 5 + 593897 AGTCC -s simHuman_chr6.simHuman.chr6 360231 4 - 601863 AATC- -s simRat_chr6.simRat.chr6 280293 5 + 647215 AATAC - -a -s simMouse_chr6.simMouse.chr6 291613 15 + 636262 AACATCTCAGGTCCA -s Anc0.Anc0refChr8 2053 15 - 17196 AACTTGTCAGGGACA -s Anc1.Anc1refChr8 45501 15 - 57822 AACTTGTCAGGGACA -s Anc2.Anc2refChr5 7811 15 - 8386 AACTTGTCAGGGACA -s Anc2.Anc2refChr5 7475 15 - 8386 AACTTGTCAGGGACA -s mr.mrrefChr5 142463 15 + 294540 AACATCTCAGGTCCA -s simCow_chr6.simCow.chr6 330176 15 - 602619 AACTGGTTAGGCACA -s simCow_chr6.simCow.chr6 330690 15 - 602619 GACTTGTCAGGAATA -s simDog_chr6.simDog.chr6 55661 15 + 593897 AACCTGTCAAGGACA -s simDog_chr6.simDog.chr6 259724 15 + 593897 AACTTGTCAGGGACA -s simHuman_chr6.simHuman.chr6 360235 14 - 601863 -ACTTGTCAGGGACA -s simRat_chr6.simRat.chr6 280298 15 + 647215 AAGATATCAGGTCCA - -a -s simMouse_chr6.simMouse.chr6 291628 6 + 636262 CAAAAT -s Anc0.Anc0refChr8 2068 6 - 17196 CAGATG -s Anc1.Anc1refChr8 45516 6 - 57822 CAGATG -s Anc2.Anc2refChr5 7826 6 - 8386 CAGATG -s Anc2.Anc2refChr5 7490 6 - 8386 CAAATG -s mr.mrrefChr5 142478 6 + 294540 CAAAAG -s simCow_chr6.simCow.chr6 330191 6 - 602619 CAAATA -s simCow_chr6.simCow.chr6 330705 6 - 602619 CAGAGG -s simDog_chr6.simDog.chr6 55676 6 + 593897 CCAATG -s simDog_chr6.simDog.chr6 259739 6 + 593897 CAGATG -s simHuman_chr6.simHuman.chr6 360256 6 - 601863 CAGATG -s simRat_chr6.simRat.chr6 280313 6 + 647215 CAACAG - -a -s simMouse_chr6.simMouse.chr6 291634 15 + 636262 AAGTTGCAACCATCC -s Anc0.Anc0refChr8 2074 15 - 17196 AAGATGCTACCATCC -s Anc1.Anc1refChr8 45522 15 - 57822 AAGATGCTACCATCC -s Anc2.Anc2refChr5 7832 15 - 8386 AGGATGCTATCATCC -s Anc2.Anc2refChr5 7496 15 - 8386 AAGATGCTACCATCC -s mr.mrrefChr5 142484 15 + 294540 AAGTTGCAACCATCC -s simCow_chr6.simCow.chr6 330197 15 - 602619 AAGATGCTACCGTCC -s simCow_chr6.simCow.chr6 330712 15 - 602619 AAGATGCTACCATCC -s simDog_chr6.simDog.chr6 55682 15 + 593897 AAGATGATACCATTC -s simDog_chr6.simDog.chr6 259745 15 + 593897 AGGATGCTATCATCC -s simHuman_chr6.simHuman.chr6 360262 15 - 601863 AAGATGCTACCATCC -s simRat_chr6.simRat.chr6 280319 15 + 647215 CAGTTGGAACCATCC - -a -s simMouse_chr6.simMouse.chr6 291649 5 + 636262 TTTGC -s Anc0.Anc0refChr8 2089 5 - 17196 CTTGT -s Anc1.Anc1refChr8 45537 5 - 57822 TTTGT -s Anc2.Anc2refChr5 7850 5 - 8386 CTTGT -s Anc2.Anc2refChr5 7511 5 - 8386 CTTGT -s mr.mrrefChr5 142499 5 + 294540 TTTGT -s simCow_chr6.simCow.chr6 330212 5 - 602619 CTTTT -s simCow_chr6.simCow.chr6 330753 5 - 602619 GTATT -s simDog_chr6.simDog.chr6 55697 5 + 593897 CTTGT -s simDog_chr6.simDog.chr6 55739 5 + 593897 CTTGT -s simHuman_chr6.simHuman.chr6 360277 5 - 601863 TTTGT -s simRat_chr6.simRat.chr6 280334 5 + 647215 TTTGT - -a -s simMouse_chr6.simMouse.chr6 291654 29 + 636262 CTTACCTTCAACCCATTTGTGAGGTAGTG -s Anc0.Anc0refChr8 2094 27 - 17196 TTCACCTTCA--CCATTTGTCTGGGACTG -s Anc1.Anc1refChr8 45542 27 - 57822 TTCACCTTCA--CCATTTGTCTGGGACTG -s Anc2.Anc2refChr5 7516 27 - 8386 TTCACCTTCA--CCATTTGTCTGGGACTG -s mr.mrrefChr5 142504 29 + 294540 CTCACCTTCAACCCATTTGTGAGGTAGTG -s simCow_chr6.simCow.chr6 330217 25 - 602619 TTTACATTTA--TCATT--TCTGGTACGA -s simDog_chr6.simDog.chr6 55702 27 + 593897 TTCACCTTCA--CCATTTGTCTGGGACTG -s simHuman_chr6.simHuman.chr6 360282 19 - 601863 ATCACCTCCA--CCAC--------ACATG -s simRat_chr6.simRat.chr6 280339 29 + 647215 CTCATCTACAGCCCATTTATTGGGTAGTG - -a -s simMouse_chr6.simMouse.chr6 291683 8 + 636262 TTCTGGCC -s Anc0.Anc0refChr8 2121 8 - 17196 TTCTTGCC -s Anc1.Anc1refChr8 45569 8 - 57822 TTCTTGCC -s Anc2.Anc2refChr5 7543 8 - 8386 TTCTTGCC -s mr.mrrefChr5 142533 8 + 294540 TTCTTGCC -s simCow_chr6.simCow.chr6 330412 8 - 602619 TTGTGGGT -s simDog_chr6.simDog.chr6 55729 8 + 593897 TTCTTGCC -s simHuman_chr6.simHuman.chr6 360301 8 - 601863 TTTTTGCC -s simRat_chr6.simRat.chr6 280368 8 + 647215 TTCTTGCC - -a -s simMouse_chr6.simMouse.chr6 291691 2 + 636262 AG -s Anc0.Anc0refChr8 2129 2 - 17196 TG -s Anc1.Anc1refChr8 45577 2 - 57822 TG -s Anc2.Anc2refChr5 7551 2 - 8386 AG -s mr.mrrefChr5 142541 2 + 294540 TG -s simCow_chr6.simCow.chr6 330420 2 - 602619 TG -s simDog_chr6.simDog.chr6 259455 2 + 593897 AG -s simHuman_chr6.simHuman.chr6 360309 2 - 601863 TG -s simRat_chr6.simRat.chr6 280376 2 + 647215 TG - -a -s simMouse_chr6.simMouse.chr6 291693 5 + 636262 CCTAA -s Anc0.Anc0refChr8 2131 5 - 17196 CCTAT -s Anc1.Anc1refChr8 45579 5 - 57822 CCTAT -s Anc2.Anc2refChr5 7557 5 - 8386 TCTAG -s mr.mrrefChr5 142543 5 + 294540 CCTAA -s simCow_chr6.simCow.chr6 330426 5 - 602619 TCTAG -s simDog_chr6.simDog.chr6 259461 5 + 593897 TCTAG -s simHuman_chr6.simHuman.chr6 360311 5 - 601863 CCTAT -s simRat_chr6.simRat.chr6 280378 5 + 647215 CCTGA - -a -s simMouse_chr6.simMouse.chr6 291698 9 + 636262 TATTCTAGG -s Anc0.Anc0refChr8 2136 9 - 17196 TATCCTGGG -s Anc1.Anc1refChr8 45584 9 - 57822 TATCCTGGG -s Anc2.Anc2refChr5 7855 9 - 8386 TATCCTGGG -s Anc2.Anc2refChr5 7562 9 - 8386 TGTGCTGAG -s mr.mrrefChr5 142548 9 + 294540 TATTCTAGG -s simCow_chr6.simCow.chr6 330431 9 - 602619 TGTACTCAG -s simCow_chr6.simCow.chr6 330758 9 - 602619 TATCCTGGG -s simDog_chr6.simDog.chr6 259466 9 + 593897 TGTGCTGAG -s simDog_chr6.simDog.chr6 55744 9 + 593897 TATCCTGGG -s simHuman_chr6.simHuman.chr6 360316 9 - 601863 TATCCTGGG -s simRat_chr6.simRat.chr6 280383 9 + 647215 TATTCAAGG - -a -s simMouse_chr6.simMouse.chr6 291707 9 + 636262 TTAAATACT -s Anc0.Anc0refChr8 2145 8 - 17196 CTTG-TAGT -s Anc1.Anc1refChr8 45593 8 - 57822 CTTG-TAGT -s Anc2.Anc2refChr5 7864 8 - 8386 CCTG-TGGT -s mr.mrrefChr5 142557 9 + 294540 TTAAATACT -s simCow_chr6.simCow.chr6 330767 8 - 602619 CCTG-TGTT -s simDog_chr6.simDog.chr6 55753 8 + 593897 CCTG-TGGT -s simHuman_chr6.simHuman.chr6 360325 6 - 601863 CT---TATG -s simRat_chr6.simRat.chr6 280392 9 + 647215 TTAAATGAT - -a -s simMouse_chr6.simMouse.chr6 291716 50 + 636262 CTCCTGGTATGTCAGTGAGGGAGATAGCAGAGAGAGAGAATCAAAGGAGA -s Anc0.Anc0refChr8 2153 44 - 17196 ATCCTGGTATGTAAGTGAGGGAGATGGCAG----ACAGAATGGTAAGA-- -s Anc1.Anc1refChr8 45601 44 - 57822 ATCCTGGTATGTAAGTGAGGGAGATGGCAG----ACAGAATGGTAAGA-- -s Anc2.Anc2refChr5 7872 44 - 8386 ATCCTGGTATGTAAGTGAGGGAGATGGCAG----ACAGAATGGTAAGA-- -s mr.mrrefChr5 142566 46 + 294540 CTCCTGGTATGTCAGTGAGGGAGATGGCAG----AGAGAATCAAAAGAGA -s simCow_chr6.simCow.chr6 330782 44 - 602619 GTCCTGGAATGTAAGTGAAGGAGTTAGCGT----ACAGAATGGTAAGA-- -s simDog_chr6.simDog.chr6 55761 44 + 593897 ATCCTGGTATGTAAGTGAGGGAGATGGCAG----ACAGAATGGTAAGA-- -s simHuman_chr6.simHuman.chr6 360331 44 - 601863 GCCCTGGTGTGTGAGGGAGGGAGGTGGCAG----ATAGAATGGTAAGA-- -s simRat_chr6.simRat.chr6 280401 46 + 647215 CTCCAGGTATGTCAGTGAGTGAGATGGCAG----AGAGAATCACAAGAGA - -a -s simMouse_chr6.simMouse.chr6 291766 40 + 636262 GAATCATGTACATTATTTGTGGCTTTGCACTCGAGGAAAA -s Anc0.Anc0refChr8 2197 29 - 17196 -----------AGCATTAGTTGCTTAGCACTCAAGGAGAT -s Anc1.Anc1refChr8 45645 29 - 57822 -----------AGCATTAGTTGCTTAGCACTCAAGGAGAT -s Anc2.Anc2refChr5 7916 29 - 8386 -----------AGCATTAGTTCTTCAGCACTCAAGGAGGT -s mr.mrrefChr5 142612 40 + 294540 GAATCATGTACATTATTTGTTGCTTTGCACTCAAGGAGAA -s simCow_chr6.simCow.chr6 330826 26 - 602619 -----------ACCAGTTGTTCTTCAGCACTCAAGGA--- -s simDog_chr6.simDog.chr6 55805 23 + 593897 -----------AGTATTAGTC------CACTTAATGAGGT -s simHuman_chr6.simHuman.chr6 360375 29 - 601863 -----------AGCATTGGTTGCTTAGCACTCAAGGAGAT -s simRat_chr6.simRat.chr6 280456 40 + 647215 GAATCATGTACACTATTTGTTGCTTTGCACTCAAGGAGAA - -a -s simMouse_chr6.simMouse.chr6 291806 14 + 636262 GGACAGCATGTGGT -s Anc0.Anc0refChr8 2226 14 - 17196 GGAGGACATGTGGT -s Anc1.Anc1refChr8 45674 14 - 57822 GGAGGACATGTGGT -s Anc2.Anc2refChr5 7945 14 - 8386 GTGGAACATGTGGC -s mr.mrrefChr5 142652 14 + 294540 GGACGACATGTGGT -s simDog_chr6.simDog.chr6 55828 14 + 593897 GTGGAACATGTGGC -s simHuman_chr6.simHuman.chr6 360405 14 - 601863 GGAGGAAATGTGGT -s simRat_chr6.simRat.chr6 280496 14 + 647215 GGAAGACATGTGCC - -a -s simMouse_chr6.simMouse.chr6 291820 26 + 636262 CAAAGATATAATGACAATGGATCTGG -s Anc0.Anc0refChr8 2240 26 - 17196 CCAAGATAGAATGATGTTAAATCAGA -s Anc1.Anc1refChr8 45688 26 - 57822 CCAAGATAGAATGATGTTAAATCAGA -s Anc2.Anc2refChr5 7959 26 - 8386 CAAAGATAGCAGGATGTCAAATCAGA -s mr.mrrefChr5 142666 26 + 294540 CCAAGATATAATGATAATGAATCTGG -s simDog_chr6.simDog.chr6 55844 26 + 593897 CAAAGATAGCAGGATGTCAAATCAGA -s simHuman_chr6.simHuman.chr6 360419 26 - 601863 CCAAGATAGAATGATGTTAAGTCAGA -s simRat_chr6.simRat.chr6 280510 26 + 647215 CCAAGATATAATGATAATGAATCTGG - -a -s simMouse_chr6.simMouse.chr6 291846 3 + 636262 ACA -s Anc0.Anc0refChr8 2274 3 - 17196 GTA -s Anc1.Anc1refChr8 45722 3 - 57822 GTA -s Anc2.Anc2refChr5 7993 3 - 8386 TTA -s mr.mrrefChr5 142692 3 + 294540 GCA -s simDog_chr6.simDog.chr6 55878 3 + 593897 TTA -s simHuman_chr6.simHuman.chr6 360453 3 - 601863 GTA -s simRat_chr6.simRat.chr6 280536 3 + 647215 GCA - -a -s simMouse_chr6.simMouse.chr6 291849 48 + 636262 GATCATGACAGGTTGCATGTTTGTGTTGTGGTTAATTGCAGTAAAGTG -s Anc0.Anc0refChr8 2277 42 - 17196 AATCATGACAGTTTTCATATT------GTGATCATTCTCAGTAGATTG -s Anc1.Anc1refChr8 45725 42 - 57822 AATCATGACAGTTTTCATATT------GTGATCATTCTCAGTAGATTG -s Anc2.Anc2refChr5 7996 42 - 8386 AATCACAACAATTTTCACACT------GTGAGCATGCTCAGTAGATTG -s mr.mrrefChr5 142695 48 + 294540 AATCATGACAGGTTGCATGTTTGTGTTGTGGTTAATTGCAGTAGAGTG -s simDog_chr6.simDog.chr6 55897 42 + 593897 AATCACAACAATTTTCACACT------GTGAGCATGCTCAGTAGATTG -s simHuman_chr6.simHuman.chr6 360456 42 - 601863 AATCATGCCTGTTTTCATCTT------GTGATCGCTCTCAGTAGATCA -s simRat_chr6.simRat.chr6 280539 48 + 647215 AGTCATGATAGATTGCATGTTTGTGTTGTGGTTAATTGCAATAGAGTG - -a -s simMouse_chr6.simMouse.chr6 291897 6 + 636262 TCCAAA -s Anc0.Anc0refChr8 2319 6 - 17196 TATGGC -s Anc1.Anc1refChr8 45767 6 - 57822 TATGGC -s Anc2.Anc2refChr5 8038 6 - 8386 TATGGC -s mr.mrrefChr5 142743 6 + 294540 TCCAGC -s simDog_chr6.simDog.chr6 55939 6 + 593897 TATGGC -s simHuman_chr6.simHuman.chr6 360498 6 - 601863 TGTGGC -s simRat_chr6.simRat.chr6 280588 6 + 647215 TCCTGC - -a -s simMouse_chr6.simMouse.chr6 291903 20 + 636262 AACTATTGATCTATGAGGCT -s Anc0.Anc0refChr8 2325 16 - 17196 AACTATTGATCTGT----CT -s Anc1.Anc1refChr8 45773 16 - 57822 AACTATTGATCTGT----CT -s Anc2.Anc2refChr5 8044 16 - 8386 AGCTGTTGATCTGC----CT -s mr.mrrefChr5 142749 20 + 294540 AACTATTGATCTATGAGGCT -s simDog_chr6.simDog.chr6 55950 16 + 593897 AGCTGTTGATCTGC----CT -s simHuman_chr6.simHuman.chr6 360504 16 - 601863 AACTATTGATCTGT----CT -s simRat_chr6.simRat.chr6 280594 20 + 647215 AACTATTGATCTTTGAGGCT - -a -s simMouse_chr6.simMouse.chr6 291923 23 + 636262 CTTTGGTTCCTCTGGCAACTCTT -s Anc0.Anc0refChr8 2341 23 - 17196 CTGAGGTTCTTACAGTAGCTCTT -s Anc1.Anc1refChr8 45789 23 - 57822 CTGAGGTTCTTACAGTAGCTCTT -s Anc2.Anc2refChr5 8060 23 - 8386 TTGCAGCTCTTACACCAACATTT -s mr.mrrefChr5 142769 23 + 294540 CTTAGGTTCCTCTGGTAGCTCTT -s simDog_chr6.simDog.chr6 55966 23 + 593897 TTGCAGCTCTTACACCAACATTT -s simHuman_chr6.simHuman.chr6 360521 23 - 601863 CGCAGATTCTTACAGTAGCTCTT -s simRat_chr6.simRat.chr6 280614 23 + 647215 CTTAGGTTCCTCTGGTAGCTCTT - -a -s simMouse_chr6.simMouse.chr6 291951 8 + 636262 TGGCCTGA -s Anc0.Anc0refChr8 2370 8 - 17196 TGTCTTGA -s Anc1.Anc1refChr8 45818 8 - 57822 TGTCTTGA -s Anc2.Anc2refChr5 8089 8 - 8386 TGGCTCAA -s mr.mrrefChr5 142798 8 + 294540 TGTCCTGA -s simDog_chr6.simDog.chr6 55995 8 + 593897 TGGCTCAA -s simHuman_chr6.simHuman.chr6 360550 8 - 601863 TGTCGTGA -s simRat_chr6.simRat.chr6 280643 8 + 647215 TGTCCTGA - -a -s simMouse_chr6.simMouse.chr6 292374 40 + 636262 GTGAAATGATCCAACCATTTGAAGTGAAGAATCAGGTGAG -s Anc0.Anc0refChr8 2894 40 - 17196 GCACAATGATTTGACCATCTAGTGTGTGGAGTCAGATGAG -s Anc1.Anc1refChr8 46348 40 - 57822 GCACAATGATTTGACCATCTAGTGTGTGGAGTCAGATGAG -s Anc2.Anc2refChr5 7571 9 - 8386 -------------------------------CCAGATGAG -s Anc2.Anc2refChr10 558 40 - 1800 GCACAATGATTTGATCATCTAGTGTGTGGAGTCAGATGAG -s mr.mrrefChr5 143268 40 + 294540 GCAAAATGATCTGACCATCTAATGTGAAGAATCAGGTGAG -s simCow_chr6.simCow.chr6 331618 39 - 602619 A-ACAATGATTTGGTCTTTTACTGTGTGGAGCCAGATGAG -s simCow_chr6.simCow.chr6 330440 9 - 602619 -------------------------------TCAGACAAG -s simDog_chr6.simDog.chr6 260848 37 + 593897 GCACAAT---TTGATCATCTAGCATGTGGAATCAGATGTG -s simDog_chr6.simDog.chr6 259475 9 + 593897 -------------------------------CCAGATGAG -s simHuman_chr6.simHuman.chr6 360969 40 - 601863 GCACAATGATTTGACCATCTAGTGTGTGGAGGCACATGAG -s simRat_chr6.simRat.chr6 281095 40 + 647215 ACAAAATGATCTGACCATCTAATATGAAGAATCAGGTGAG - -a -s simMouse_chr6.simMouse.chr6 292414 22 + 636262 AAGAAGTTAGTAACCTCATTGT -s Anc0.Anc0refChr8 2934 22 - 17196 AAGTGGTTAGAAATCTCATTGT -s Anc1.Anc1refChr8 46388 22 - 57822 AAGTGGTTAGAAATCTCATTGT -s Anc2.Anc2refChr5 7580 21 - 8386 A-GTGGTTAGTAATCTCATTGT -s Anc2.Anc2refChr10 598 22 - 1800 AAGCGGTGAGAAATCTCATTGT -s mr.mrrefChr5 143308 22 + 294540 AAGAAGTTAGAAATCTCATTGT -s simCow_chr6.simCow.chr6 331657 22 - 602619 AAGGGGTCAGGAATCTCATTGT -s simCow_chr6.simCow.chr6 330449 21 - 602619 A-GTGATTAAAAATTTCATGGT -s simDog_chr6.simDog.chr6 260885 22 + 593897 AAGCACTGAGAAATCTCACTGT -s simDog_chr6.simDog.chr6 259485 21 + 593897 A-GTGGTTAGTAATCTCATTGT -s simHuman_chr6.simHuman.chr6 361009 22 - 601863 ACATGGTTAGACATCTTGTGGT -s simRat_chr6.simRat.chr6 281135 22 + 647215 AAGGAATTAGAAATCTCATAGT - -a -s simMouse_chr6.simMouse.chr6 292436 1 + 636262 A -s Anc0.Anc0refChr8 2956 1 - 17196 G -s Anc1.Anc1refChr8 46410 1 - 57822 G -s Anc2.Anc2refChr5 7601 1 - 8386 G -s Anc2.Anc2refChr10 620 1 - 1800 A -s mr.mrrefChr5 143330 1 + 294540 A -s simCow_chr6.simCow.chr6 331679 1 - 602619 A -s simCow_chr6.simCow.chr6 330470 1 - 602619 A -s simDog_chr6.simDog.chr6 259506 1 + 593897 G -s simHuman_chr6.simHuman.chr6 361031 1 - 601863 G -s simRat_chr6.simRat.chr6 281157 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 292437 12 + 636262 CATCTTAACCTA -s Anc0.Anc0refChr8 2957 12 - 17196 TATCTAATCTTG -s Anc1.Anc1refChr8 46411 12 - 57822 TATCTAATCTTG -s Anc2.Anc2refChr5 7602 12 - 8386 TATCCAATCTTG -s Anc2.Anc2refChr10 621 12 - 1800 TATCTAATCTTG -s mr.mrrefChr5 143331 12 + 294540 CATCTAAACCTA -s simCow_chr6.simCow.chr6 331680 12 - 602619 TATCTAATCTTG -s simCow_chr6.simCow.chr6 330471 12 - 602619 TATCTTAGCTTG -s simDog_chr6.simDog.chr6 260907 12 + 593897 TATCTAATCTTG -s simDog_chr6.simDog.chr6 259507 12 + 593897 TATCCAATCTTG -s simHuman_chr6.simHuman.chr6 361032 12 - 601863 TATCTAATCTTG -s simRat_chr6.simRat.chr6 281158 12 + 647215 CATCTAAACCTA - -a -s simMouse_chr6.simMouse.chr6 292449 3 + 636262 TGG -s Anc0.Anc0refChr8 2969 3 - 17196 GGG -s Anc1.Anc1refChr8 46423 3 - 57822 GGG -s Anc2.Anc2refChr5 7614 3 - 8386 TGT -s Anc2.Anc2refChr10 633 3 - 1800 GGG -s mr.mrrefChr5 143343 3 + 294540 TGG -s simCow_chr6.simCow.chr6 331693 3 - 602619 GGG -s simCow_chr6.simCow.chr6 330483 3 - 602619 TGG -s simDog_chr6.simDog.chr6 260919 3 + 593897 GGG -s simDog_chr6.simDog.chr6 259519 3 + 593897 TGT -s simHuman_chr6.simHuman.chr6 361044 3 - 601863 GGG -s simRat_chr6.simRat.chr6 281170 3 + 647215 TCA - -a -s simMouse_chr6.simMouse.chr6 292452 1 + 636262 G -s Anc0.Anc0refChr8 2972 1 - 17196 G -s Anc1.Anc1refChr8 46426 1 - 57822 G -s Anc2.Anc2refChr5 7617 1 - 8386 G -s mr.mrrefChr5 143346 1 + 294540 G -s simCow_chr6.simCow.chr6 330486 1 - 602619 G -s simDog_chr6.simDog.chr6 259522 1 + 593897 G -s simHuman_chr6.simHuman.chr6 361047 1 - 601863 G -s simRat_chr6.simRat.chr6 281173 1 + 647215 G - -a -s simMouse_chr6.simMouse.chr6 292453 10 + 636262 CAATCTACTA -s Anc0.Anc0refChr8 2973 9 - 17196 TTATTTGCT- -s Anc1.Anc1refChr8 46427 9 - 57822 TTATCTGCA- -s Anc2.Anc2refChr5 7618 9 - 8386 TTATTTGCT- -s Anc2.Anc2refChr10 636 9 - 1800 TTATTTACT- -s mr.mrrefChr5 143347 9 + 294540 CAATCTACT- -s simCow_chr6.simCow.chr6 331696 9 - 602619 TTATCTCCT- -s simCow_chr6.simCow.chr6 330487 9 - 602619 CTATGTACT- -s simDog_chr6.simDog.chr6 260922 9 + 593897 TTATTTACT- -s simDog_chr6.simDog.chr6 259523 9 + 593897 TTATTTGCT- -s simHuman_chr6.simHuman.chr6 361048 9 - 601863 TTATCTGAA- -s simRat_chr6.simRat.chr6 281174 9 + 647215 CAATCTACT- - -a -s simMouse_chr6.simMouse.chr6 292463 5 + 636262 CATGT -s Anc0.Anc0refChr8 2983 5 - 17196 GGAGT -s Anc1.Anc1refChr8 46436 5 - 57822 GGAGT -s Anc2.Anc2refChr5 7628 4 - 8386 GGAA- -s Anc2.Anc2refChr10 646 5 - 1800 GGAGT -s mr.mrrefChr5 143356 5 + 294540 CGTGT -s simCow_chr6.simCow.chr6 331706 5 - 602619 GGAGT -s simCow_chr6.simCow.chr6 330497 4 - 602619 GGAG- -s simDog_chr6.simDog.chr6 260932 5 + 593897 GGGAT -s simDog_chr6.simDog.chr6 259533 4 + 593897 GGAA- -s simHuman_chr6.simHuman.chr6 361057 5 - 601863 GGAGT -s simRat_chr6.simRat.chr6 281183 5 + 647215 CGTAT - -a -s simMouse_chr6.simMouse.chr6 292468 16 + 636262 GACCTGTGGCTATAGG -s Anc0.Anc0refChr8 2988 16 - 17196 GATCTGCTGCTACAAT -s Anc1.Anc1refChr8 46441 16 - 57822 GATCTGCTGCTACAAT -s Anc2.Anc2refChr5 7632 16 - 8386 AGTCTGTGGCTACAAT -s Anc2.Anc2refChr10 651 16 - 1800 GATCTGCTGCTAGAAT -s mr.mrrefChr5 143361 16 + 294540 GATCTGTGGCTATAGG -s simCow_chr6.simCow.chr6 331712 16 - 602619 GATCTGCTACTAGAAT -s simCow_chr6.simCow.chr6 330502 16 - 602619 AGGCTGCTTATACAGT -s simDog_chr6.simDog.chr6 260937 16 + 593897 GATTTGCTGCTAGAAT -s simDog_chr6.simDog.chr6 259537 16 + 593897 AGTCTGTGGCTACAAT -s simHuman_chr6.simHuman.chr6 361062 16 - 601863 GCTCTGCTGCTACAAT -s simRat_chr6.simRat.chr6 281188 16 + 647215 GATCTGTAGCTATGGG - -a -s simMouse_chr6.simMouse.chr6 292484 10 + 636262 GTGTTGTAGA -s Anc0.Anc0refChr8 3025 10 - 17196 GTGTTATCTG -s Anc1.Anc1refChr8 46478 10 - 57822 GTGTTATCTG -s Anc2.Anc2refChr5 7669 10 - 8386 GTGCTGTTTG -s Anc2.Anc2refChr10 688 10 - 1800 GTGTTTTCTG -s mr.mrrefChr5 143377 10 + 294540 GTGTTATAGA -s simCow_chr6.simCow.chr6 331771 10 - 602619 GCACTGTCTG -s simCow_chr6.simCow.chr6 330539 10 - 602619 GTGCTATCCA -s simDog_chr6.simDog.chr6 260974 10 + 593897 GTGTCTTTTA -s simDog_chr6.simDog.chr6 259574 10 + 593897 GTGCTGTTTG -s simHuman_chr6.simHuman.chr6 361099 10 - 601863 GTGTTATCTG -s simRat_chr6.simRat.chr6 281204 10 + 647215 GTGTTATACA - -a -s simMouse_chr6.simMouse.chr6 292494 4 + 636262 GAGC -s Anc0.Anc0refChr8 3035 4 - 17196 GGAC -s Anc1.Anc1refChr8 46488 4 - 57822 GGAC -s Anc2.Anc2refChr5 7679 4 - 8386 GAAC -s Anc2.Anc2refChr10 698 4 - 1800 GGAC -s mr.mrrefChr5 143387 4 + 294540 GAGC -s simCow_chr6.simCow.chr6 331781 4 - 602619 GGAT -s simCow_chr6.simCow.chr6 330549 4 - 602619 GGAT -s simDog_chr6.simDog.chr6 260987 4 + 593897 AGAC -s simDog_chr6.simDog.chr6 259584 4 + 593897 GAAC -s simHuman_chr6.simHuman.chr6 361109 4 - 601863 GGAC -s simRat_chr6.simRat.chr6 281214 4 + 647215 GAGC - -a -s simMouse_chr6.simMouse.chr6 292498 4 + 636262 CTGA -s Anc0.Anc0refChr8 3065 4 - 17196 CTGT -s Anc1.Anc1refChr8 46518 4 - 57822 CTGA -s Anc2.Anc2refChr5 7709 4 - 8386 TTAT -s Anc2.Anc2refChr10 728 4 - 1800 CTCT -s mr.mrrefChr5 143391 4 + 294540 CTGA -s simCow_chr6.simCow.chr6 331811 4 - 602619 ATTT -s simCow_chr6.simCow.chr6 330579 4 - 602619 TCAT -s simDog_chr6.simDog.chr6 261017 4 + 593897 CTCT -s simDog_chr6.simDog.chr6 259614 4 + 593897 TTAT -s simHuman_chr6.simHuman.chr6 361139 4 - 601863 CTGA -s simRat_chr6.simRat.chr6 281218 4 + 647215 CCTG - -a -s simMouse_chr6.simMouse.chr6 292502 6 + 636262 TTTTCT -s Anc0.Anc0refChr8 3069 6 - 17196 TATTAT -s Anc1.Anc1refChr8 46522 6 - 57822 TATTAT -s Anc2.Anc2refChr5 7717 6 - 8386 TGTTAT -s Anc2.Anc2refChr10 732 6 - 1800 TTTTAT -s mr.mrrefChr5 143395 6 + 294540 TATTCT -s simCow_chr6.simCow.chr6 331815 6 - 602619 TTTTGT -s simCow_chr6.simCow.chr6 330587 6 - 602619 CATTAT -s simDog_chr6.simDog.chr6 261021 6 + 593897 TTTTAA -s simDog_chr6.simDog.chr6 259622 6 + 593897 TGTTAT -s simHuman_chr6.simHuman.chr6 361143 6 - 601863 TAGTAT -s simRat_chr6.simRat.chr6 281222 6 + 647215 TATTCT - -a -s simMouse_chr6.simMouse.chr6 292508 4 + 636262 GGTC -s Anc0.Anc0refChr8 3075 4 - 17196 GGTC -s Anc1.Anc1refChr8 46528 4 - 57822 GGTC -s Anc2.Anc2refChr5 7723 2 - 8386 TG-- -s Anc2.Anc2refChr10 738 4 - 1800 GGTC -s mr.mrrefChr5 143401 4 + 294540 GGTC -s simCow_chr6.simCow.chr6 331822 4 - 602619 GGTC -s simCow_chr6.simCow.chr6 330593 2 - 602619 TG-- -s simDog_chr6.simDog.chr6 261027 4 + 593897 GGTC -s simDog_chr6.simDog.chr6 259628 2 + 593897 TG-- -s simHuman_chr6.simHuman.chr6 361149 4 - 601863 AGTC -s simRat_chr6.simRat.chr6 281228 4 + 647215 GGTC - -a -s simMouse_chr6.simMouse.chr6 292512 8 + 636262 AATGTACC -s Anc0.Anc0refChr8 3080 8 - 17196 AATGGACC -s Anc1.Anc1refChr8 46533 8 - 57822 AATGGACC -s Anc2.Anc2refChr10 743 8 - 1800 AATGGACC -s mr.mrrefChr5 143405 8 + 294540 AATGTACC -s simCow_chr6.simCow.chr6 331827 6 - 602619 ACTGGA-- -s simDog_chr6.simDog.chr6 261032 8 + 593897 AATGTACC -s simHuman_chr6.simHuman.chr6 361154 8 - 601863 AATGGACC -s simRat_chr6.simRat.chr6 281232 8 + 647215 AATGTACC - -a -s simMouse_chr6.simMouse.chr6 292520 16 + 636262 TGTTACTGTTGAATCC -s Anc0.Anc0refChr8 3096 16 - 17196 TGTTACAGCTAAATCC -s Anc1.Anc1refChr8 46549 16 - 57822 TGTTACAGCTAAATCC -s Anc2.Anc2refChr10 759 16 - 1800 CTTTACATCCAAATCT -s mr.mrrefChr5 143420 16 + 294540 TGTTACAGTTGAATCC -s simDog_chr6.simDog.chr6 261048 16 + 593897 CTTTACATCCAAATCT -s simHuman_chr6.simHuman.chr6 361170 16 - 601863 TGTTACAGCTAAATCC -s simRat_chr6.simRat.chr6 281247 16 + 647215 TGTTACAGTAGAATCC - -a -s simMouse_chr6.simMouse.chr6 292536 18 + 636262 CATAAAAAATTTGTCACT -s Anc0.Anc0refChr8 3112 11 - 17196 CACAAAAAATT------- -s Anc1.Anc1refChr8 46565 18 - 57822 CACAAAAAATTTGGCACT -s Anc2.Anc2refChr10 775 11 - 1800 TACGAAAAGTT------- -s mr.mrrefChr5 143436 18 + 294540 CATAAAAAATTTGTCACT -s simDog_chr6.simDog.chr6 261064 11 + 593897 TACGAAAAGTT------- -s simHuman_chr6.simHuman.chr6 361186 18 - 601863 CACAAAAAACTTGGCACT -s simRat_chr6.simRat.chr6 281264 18 + 647215 TATCAAAAGTTTGTCACT - -a -s simMouse_chr6.simMouse.chr6 292554 30 + 636262 AGGATATGAAGCCTTAACTGTGGACAAGGG -s Anc1.Anc1refChr8 46720 28 - 57822 AGTGTATGAAGCTTTATCTGT--ACATTAA -s mr.mrrefChr5 143454 30 + 294540 AGGATATGAAGCCTTAACTGTGGACAAGGG -s simHuman_chr6.simHuman.chr6 361385 28 - 601863 AGTGTATGAAGCTTTATCTGT--ACATTAA -s simRat_chr6.simRat.chr6 281282 30 + 647215 AGGATATGAAGCCTTAACTGTGGATAAGGG - -a -s simMouse_chr6.simMouse.chr6 292584 28 + 636262 GTAGCTGAGCGCTACCTAGCTTAGCAAG -s Anc1.Anc1refChr8 46748 28 - 57822 GAACCTGAACCGTACACAGCTTAGTAAG -s mr.mrrefChr5 143484 28 + 294540 GTAGCTGAGCGCTACCTAGCTTAGCAAG -s simHuman_chr6.simHuman.chr6 361413 28 - 601863 GAACCTGAACCGTACACAGCTTAGTAAG -s simRat_chr6.simRat.chr6 281348 28 + 647215 GGAGCTGAACACTTCCTAGCTTAGCAGG - -a -s simMouse_chr6.simMouse.chr6 292612 10 + 636262 AGAATGAGTC -s Anc0.Anc0refChr8 3260 1 - 17196 ---------C -s Anc1.Anc1refChr8 46776 10 - 57822 AGAGTGTGTC -s Anc2.Anc2refChr10 923 1 - 1800 ---------C -s mr.mrrefChr5 143512 10 + 294540 AGAATGAGTC -s simDog_chr6.simDog.chr6 261234 1 + 593897 ---------C -s simHuman_chr6.simHuman.chr6 361455 10 - 601863 AGAGTGTGTC -s simRat_chr6.simRat.chr6 281376 10 + 647215 TGAATGAATC - -a -s simMouse_chr6.simMouse.chr6 292622 16 + 636262 GTGTGCCAGATGAATG -s Anc0.Anc0refChr8 3262 16 - 17196 GTATGCCATGGGAAAG -s Anc1.Anc1refChr8 46787 16 - 57822 GTATGCCATGGGAAAG -s Anc2.Anc2refChr10 925 16 - 1800 GCACGTATTGGGGAAG -s mr.mrrefChr5 143522 16 + 294540 GTGTGCCAGATGAATG -s simCow_chr6.simCow.chr6 331833 5 - 602619 -----------GCTAA -s simDog_chr6.simDog.chr6 261236 16 + 593897 GCACGTATTGGTGAGG -s simHuman_chr6.simHuman.chr6 361466 16 - 601863 GTATGCCATGAGAAAG -s simRat_chr6.simRat.chr6 281387 16 + 647215 GTGTGCCAGATGAATG - -a -s simMouse_chr6.simMouse.chr6 292638 46 + 636262 TCCAACCACAGTCCCATTCCATTGTATAATAAACTATTTCATTTAG -s Anc0.Anc0refChr8 3278 46 - 17196 TCCAACTAGGGTCTCATTCCTTCTTATATTAGACCAGTATACCTGG -s Anc1.Anc1refChr8 46803 46 - 57822 TCCAACTAGGGTCTCATTCCTTCTTATATTAGACCAGTATACCTGG -s Anc2.Anc2refChr10 941 46 - 1800 TCCAACTAGGGTCTCATTTCTTCTTACATTAGACCAGTATACCTGG -s mr.mrrefChr5 143538 46 + 294540 TCCAACCACAGTCCCATTCCATTGTATAATAAACTATTTCATTTAG -s simCow_chr6.simCow.chr6 331838 46 - 602619 TCCAACAAGGGTCTCATTTCTTCTTAGATGAGACCGGTATTCTTAT -s simDog_chr6.simDog.chr6 261257 41 + 593897 TCCAGCTAGGGTCTC-----TTCTTACATTAGACCAGTATATCTGG -s simHuman_chr6.simHuman.chr6 361482 46 - 601863 TCCAACTAGGGCCTCCTCCCTTCTCATACTTGACCAGTATGCCTGG -s simRat_chr6.simRat.chr6 281403 46 + 647215 TCCAACCACAGTCCTATTCCATAATATACTAAACTATTTCATTTAG - -a -s simMouse_chr6.simMouse.chr6 292684 1 + 636262 T -s Anc0.Anc0refChr8 3324 1 - 17196 T -s Anc1.Anc1refChr8 46849 1 - 57822 T -s Anc2.Anc2refChr10 987 1 - 1800 T -s mr.mrrefChr5 143584 1 + 294540 T -s simCow_chr6.simCow.chr6 331884 1 - 602619 T -s simDog_chr6.simDog.chr6 261299 1 + 593897 T -s simHuman_chr6.simHuman.chr6 361528 1 - 601863 T -s simRat_chr6.simRat.chr6 281449 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 292685 50 + 636262 CAGAGCACAATTGTAATCTTACACACATCCAAGCAATCAGGGCTGTTATT -s Anc0.Anc0refChr8 3325 45 - 17196 CAGAGCGTAATAGTAAGTTTGAATACA-----GTAGATAGAGTTGTACAT -s Anc1.Anc1refChr8 46850 45 - 57822 CAGAGCGTAATAGTAAGTTTGAATACA-----GTAGATAGAGTTGTACAT -s Anc2.Anc2refChr10 988 45 - 1800 CTGAGGGTATCAGTAAGTGTGAATACA-----GTAGATGGAGTTGTACAT -s mr.mrrefChr5 143585 50 + 294540 CAGAGCACAATTGTAATCTTACACACATCCAAGCAATCAGGGCTGTTATT -s simCow_chr6.simCow.chr6 331890 29 - 602619 CTGTG----------------AACATG-----GTAGATGGAGTTGTAAGT -s simDog_chr6.simDog.chr6 261300 32 + 593897 CTGAGGGTATCAGTAAGTGTGAATACA-----GT-------------CAT -s simHuman_chr6.simHuman.chr6 361529 45 - 601863 CAGGGCGTTATAATACGTTTGAGTACA-----GTAGGAAGAGGTGTACAT -s simRat_chr6.simRat.chr6 281450 50 + 647215 CAGAGCACTATGGTAAGCTTGCACATAACCAAGCAATCAAAGCTGATATT - -a -s simMouse_chr6.simMouse.chr6 292735 42 + 636262 GCCATTGAAGTGAGGCAGATCCATTAGAAACAGCAGGTGTAT -s Anc0.Anc0refChr8 3370 41 - 17196 GCCACCTTAGTGAGACAGATC-ACTAGAAACACTAGATGTAC -s Anc1.Anc1refChr8 46895 41 - 57822 GCCACCTTAGTGAGACAGATC-ACTAGAAACACTAGATGTAC -s Anc2.Anc2refChr10 1033 41 - 1800 GCAACCTTAGTGAGACAGATC-ACTAGAAACACTGGATGTAC -s mr.mrrefChr5 143635 42 + 294540 GCCACTGTAGTAAGGCAGATCCATTAGAAACAGCAGGTGTAT -s simCow_chr6.simCow.chr6 331920 40 - 602619 GCTGCATTAGTAGGACAGATC-ACTA-AAACAGTGGAAGTAT -s simDog_chr6.simDog.chr6 261332 40 + 593897 -CAACCTTAGTGAGACGGATC-ACTAGAAACACTGGATATAC -s simHuman_chr6.simHuman.chr6 361574 41 - 601863 GCCATCTTAGTGCAACAGATC-ACTAGAAACAATAGATGCAC -s simRat_chr6.simRat.chr6 281500 42 + 647215 GCCACTGTAGTAAGGCAGATCCATTAGAAACAGCAAGTGTAA - -a -s simMouse_chr6.simMouse.chr6 292777 49 + 636262 CATATGGCTATGTGGGTCTTAATCCAGAAGAGTTCTACCTCACATCTGA -s Anc0.Anc0refChr8 3425 49 - 17196 CATATGGTTGTGTGTGTCTCAATCTAGACCAGGGCTGTCTCACATGTGT -s Anc1.Anc1refChr8 46950 49 - 57822 CATATGGTTGTGTGTGTCTCAATCTAGACCAGGGCTGTCTCACATGTGT -s Anc2.Anc2refChr10 1088 49 - 1800 CATATGGTTGTGTGTGACTCAATCTAGACCAGGGCTGTCTCACATGTGT -s mr.mrrefChr5 143685 49 + 294540 CATATGGCTATGTGGGTCTTAATCCAGAAGAGTTCTGCCTCACATGTGA -s simCow_chr6.simCow.chr6 331974 49 - 602619 CCTCTGGGTGGCTGTGCCTCAATCCAGACATAAGCTGTCTCATATGTGT -s simDog_chr6.simDog.chr6 261386 49 + 593897 CATATTGTTGTGTTTGAATCAATCTAGAACAGGGCTCTCTCACTTTTGT -s simHuman_chr6.simHuman.chr6 361629 49 - 601863 CATATGATTGTTTGTGTCTGAATCGAGACTAGGCTTGTGTCACATGTGC -s simRat_chr6.simRat.chr6 281550 49 + 647215 CATGTGTCTATGTGGGTCTTAATCCAGAACAGTTCTGCCTAACATGTGA - -a -s simMouse_chr6.simMouse.chr6 292826 41 + 636262 TAACAGGATAAACATTGAAAACCTCCTAGCTTTGCTCCTTC -s Anc0.Anc0refChr8 3475 41 - 17196 TCCCAGAATAAAGATTGAAAGCTTTTTAGCTCTGAGCCCTA -s Anc1.Anc1refChr8 47000 41 - 57822 TCCCAGAATAAAGATTGAAAGCTTTTTAGCTCTGAGCCCTA -s Anc2.Anc2refChr10 1138 41 - 1800 TCCCAGAATAAAGATTGAAAGCTTTTTAGCTCTGAGCCCTA -s mr.mrrefChr5 143734 41 + 294540 TAACAGAATAAACATTGAAAACCTTCTAGCTTTGCTCTCTC -s simCow_chr6.simCow.chr6 332024 41 - 602619 ACCCAGAGTAAAGATCCAAAGCCGTTTAGCTCTGAGCTCTA -s simDog_chr6.simDog.chr6 261436 41 + 593897 TCCCAAAATAAAGATTGGAAGCTTTTTAGCTCTGAGCCCGA -s simHuman_chr6.simHuman.chr6 361679 41 - 601863 TCTCAGAATAAAGATTGAAAGCTTTATAGTTCTTAGCCTTA -s simRat_chr6.simRat.chr6 281599 41 + 647215 TAGCAGAATACACATTGAAAATCTTCTAGCTTTGCACTCTC - -a -s simMouse_chr6.simMouse.chr6 292867 22 + 636262 CTGAATGTCATAGGTAAGAGAT -s Anc0.Anc0refChr8 3534 20 - 17196 --GAATGTCATAAGTAGGGAAT -s Anc1.Anc1refChr8 47059 20 - 57822 --GAATGTCATAAGTAGGGAAT -s Anc2.Anc2refChr10 1197 20 - 1800 --GAATTTCATAAATAGGGACT -s mr.mrrefChr5 143794 22 + 294540 CAGAATGTCATAAGTAAGAGAT -s simCow_chr6.simCow.chr6 332083 19 - 602619 --CAATTTCATAAA-AGGGAGT -s simDog_chr6.simDog.chr6 261495 20 + 593897 --GAATTTCATAAATAGGGTCT -s simHuman_chr6.simHuman.chr6 361738 20 - 601863 --GAATGTCATAAGCCGGGAAT -s simRat_chr6.simRat.chr6 281659 22 + 647215 CAGAATGTCATAAGTAAGATAT - -a -s simMouse_chr6.simMouse.chr6 292889 2 + 636262 AA -s Anc0.Anc0refChr8 3554 2 - 17196 AA -s Anc1.Anc1refChr8 47079 2 - 57822 AA -s Anc2.Anc2refChr10 1218 2 - 1800 AG -s mr.mrrefChr5 143816 2 + 294540 AA -s simCow_chr6.simCow.chr6 332103 2 - 602619 AG -s simDog_chr6.simDog.chr6 261516 2 + 593897 AG -s simHuman_chr6.simHuman.chr6 361758 2 - 601863 TA -s simRat_chr6.simRat.chr6 281681 2 + 647215 CA - -a -s simMouse_chr6.simMouse.chr6 292891 51 + 636262 TTGCCATTAGTTGGTGGTACTTTTACCGACACTTGTGCTGTGACCTCGGCA -s Anc0.Anc0refChr8 3556 51 - 17196 TTGTCATTAGTTGGTTATACTTTTACCAACATTTGCACTGTGACCTGGGCA -s Anc1.Anc1refChr8 47081 51 - 57822 TTGTCATTAGTTGGTTATACTTTTACCAACATTTGCACTGTGACCTGGGCA -s Anc2.Anc2refChr10 1220 51 - 1800 TTGTCATTAGTTGGTTATACTTTTACCAACATTTGCAGTGTGACCTGGGCA -s mr.mrrefChr5 143818 51 + 294540 TTGCCATTGGTTGGTTATACTTTTACCGACACTTGTGCCGTGACCTCGGCA -s simCow_chr6.simCow.chr6 332105 51 - 602619 TTGCCATTGGTTGGTTATACTTTCACCAACACTTGTGGCGGGCCCTGGGAA -s simDog_chr6.simDog.chr6 261518 51 + 593897 TTATCATTAGTTGGTTATATCTTTACCAATATCTGCAGTTTGACCTGGGCA -s simHuman_chr6.simHuman.chr6 361785 51 - 601863 CTGTCATTAGTTCGTTGTACTTTTACCAACATTTGCACTGTGATCAAGACA -s simRat_chr6.simRat.chr6 281683 51 + 647215 TTGTCATTGATTGGTTACACTTGTACCCACACCTGCGCCGTGACTTAGGCA - -a -s simMouse_chr6.simMouse.chr6 292942 3 + 636262 ATT -s Anc0.Anc0refChr8 3607 3 - 17196 ATC -s Anc1.Anc1refChr8 47132 3 - 57822 ATC -s Anc2.Anc2refChr10 1271 3 - 1800 ACC -s mr.mrrefChr5 143869 3 + 294540 ATT -s simCow_chr6.simCow.chr6 332156 3 - 602619 ACC -s simDog_chr6.simDog.chr6 261569 3 + 593897 ACT -s simHuman_chr6.simHuman.chr6 361840 3 - 601863 ATC -s simRat_chr6.simRat.chr6 281734 3 + 647215 ATT - -a -s simMouse_chr6.simMouse.chr6 292945 1 + 636262 G -s Anc0.Anc0refChr8 3610 1 - 17196 G -s Anc1.Anc1refChr8 47135 1 - 57822 G -s Anc2.Anc2refChr10 1274 1 - 1800 G -s mr.mrrefChr5 143872 1 + 294540 G -s simCow_chr6.simCow.chr6 332160 1 - 602619 G -s simDog_chr6.simDog.chr6 261572 1 + 593897 G -s simHuman_chr6.simHuman.chr6 361843 1 - 601863 G -s simRat_chr6.simRat.chr6 281737 1 + 647215 G - -a -s simMouse_chr6.simMouse.chr6 292946 11 + 636262 ATAACACCCAT -s Anc0.Anc0refChr8 3614 7 - 17196 ----TGCCCAT -s Anc1.Anc1refChr8 47139 11 - 57822 ATCATGCCCAT -s Anc2.Anc2refChr10 1278 7 - 1800 ----TGTTCAT -s mr.mrrefChr5 143873 11 + 294540 ATAATGCCCAT -s simCow_chr6.simCow.chr6 332164 7 - 602619 ----TGATTAT -s simDog_chr6.simDog.chr6 261576 7 + 593897 ----TGTTCAT -s simHuman_chr6.simHuman.chr6 361847 11 - 601863 ATCATGCCCAT -s simRat_chr6.simRat.chr6 281738 11 + 647215 ATAATGCCCAT - -a -s simMouse_chr6.simMouse.chr6 292957 45 + 636262 AATTATTCTATTGGCAGGGGGGATTGGCTTTGGGTCAGCGAGTCA -s Anc0.Anc0refChr8 3621 42 - 17196 AATTATTTTCCTGCTCAAGG--ATTGGCTTTGCATGA-TAAGTGA -s Anc1.Anc1refChr8 47150 42 - 57822 AATTATTTTCCTGCTCAAGG--ATTGGCTTTGCATGA-TAAGTGA -s Anc2.Anc2refChr10 1285 42 - 1800 CATCATTTTCCTGCTCAAGG--ATTGGCTTTGCATGG-TAAGTGA -s mr.mrrefChr5 143884 43 + 294540 AATTATTTTACTGGCAGGGG--ATTGGCTTTGGGTCAGCGAGTCA -s simCow_chr6.simCow.chr6 332171 42 - 602619 TATTATCTTGCTAGTCGAAG--ATTGGCTTTGCATAG-AAAGTGG -s simDog_chr6.simDog.chr6 261583 42 + 593897 CATCATTTTCCTGCTCAAGG--ATTGGCTCTGCATGG-TGAGTGA -s simHuman_chr6.simHuman.chr6 361869 25 - 601863 AATTATT-------------------GCTTTGAATGA-TAAGTGA -s simRat_chr6.simRat.chr6 281749 43 + 647215 AATTATTTTACTTGCAGGGG--ATTGGGTAAGGGTCAGCGAGTCA - -a -s simMouse_chr6.simMouse.chr6 293009 1 + 636262 A - -a -s simMouse_chr6.simMouse.chr6 293040 3 + 636262 CCA -s Anc0.Anc0refChr8 3704 3 - 17196 CGA -s Anc1.Anc1refChr5 4350 3 - 6477 CAA -s Anc1.Anc1refChr8 47233 3 - 57822 CGA -s Anc2.Anc2refChr10 1368 3 - 1800 TGA -s mr.mrrefChr5 143964 3 + 294540 CCA -s mr.mrrefChr5 131420 3 + 294540 CAC -s simCow_chr6.simCow.chr6 332252 3 - 602619 TGA -s simDog_chr6.simDog.chr6 261666 3 + 593897 TGA -s simHuman_chr6.simHuman.chr6 355710 3 - 601863 CAA -s simHuman_chr6.simHuman.chr6 361944 3 - 601863 CAA -s simRat_chr6.simRat.chr6 269023 3 + 647215 CAC -s simRat_chr6.simRat.chr6 281829 3 + 647215 CAA - -a -s simMouse_chr6.simMouse.chr6 293057 2 + 636262 AG -s Anc0.Anc0refChr8 3721 2 - 17196 AT -s Anc1.Anc1refChr5 4367 2 - 6477 AT -s Anc1.Anc1refChr8 47250 2 - 57822 AT -s Anc2.Anc2refChr10 1385 2 - 1800 AT -s mr.mrrefChr5 143981 2 + 294540 AG -s mr.mrrefChr5 131437 2 + 294540 AG -s simCow_chr6.simCow.chr6 332269 2 - 602619 AT -s simDog_chr6.simDog.chr6 261683 2 + 593897 AT -s simHuman_chr6.simHuman.chr6 355727 2 - 601863 AT -s simHuman_chr6.simHuman.chr6 361961 2 - 601863 AT -s simRat_chr6.simRat.chr6 269040 2 + 647215 AG -s simRat_chr6.simRat.chr6 281846 2 + 647215 AG - -a -s simMouse_chr6.simMouse.chr6 293080 2 + 636262 AG -s Anc0.Anc0refChr8 3744 2 - 17196 AG -s Anc1.Anc1refChr5 4390 2 - 6477 GC -s Anc1.Anc1refChr8 47273 2 - 57822 AG -s Anc2.Anc2refChr10 1408 2 - 1800 AG -s mr.mrrefChr5 144004 2 + 294540 AG -s mr.mrrefChr5 131460 2 + 294540 GT -s simCow_chr6.simCow.chr6 332292 2 - 602619 AG -s simDog_chr6.simDog.chr6 261706 2 + 593897 AG -s simHuman_chr6.simHuman.chr6 355752 2 - 601863 GC -s simHuman_chr6.simHuman.chr6 361984 2 - 601863 AC -s simRat_chr6.simRat.chr6 269063 2 + 647215 GT -s simRat_chr6.simRat.chr6 281869 2 + 647215 AG - -a -s simMouse_chr6.simMouse.chr6 293088 4 + 636262 GTTT -s Anc0.Anc0refChr8 3752 4 - 17196 GATT -s Anc1.Anc1refChr8 47281 4 - 57822 GATT -s Anc2.Anc2refChr10 1416 4 - 1800 GATT -s mr.mrrefChr5 144012 4 + 294540 GTTT -s simCow_chr6.simCow.chr6 332300 3 - 602619 GTT- -s simDog_chr6.simDog.chr6 261714 4 + 593897 GGTT -s simHuman_chr6.simHuman.chr6 361992 4 - 601863 GATT -s simRat_chr6.simRat.chr6 281877 4 + 647215 GATT - -a -s simMouse_chr6.simMouse.chr6 293102 3 + 636262 TCC -s Anc0.Anc0refChr8 3777 3 - 17196 TCC -s Anc1.Anc1refChr5 4419 3 - 6477 CCC -s Anc1.Anc1refChr8 47306 3 - 57822 TCC -s Anc2.Anc2refChr10 1441 3 - 1800 TGC -s mr.mrrefChr5 144026 3 + 294540 TCC -s mr.mrrefChr5 131489 3 + 294540 CCC -s simCow_chr6.simCow.chr6 332397 3 - 602619 TGC -s simDog_chr6.simDog.chr6 261739 3 + 593897 TGT -s simHuman_chr6.simHuman.chr6 355784 3 - 601863 CCC -s simHuman_chr6.simHuman.chr6 362017 3 - 601863 TCC -s simRat_chr6.simRat.chr6 269090 3 + 647215 CCC -s simRat_chr6.simRat.chr6 281901 3 + 647215 CCC - -a -s simMouse_chr6.simMouse.chr6 293105 11 + 636262 TGGATCTCATA -s Anc0.Anc0refChr8 3780 8 - 17196 C---TGGTATA -s Anc1.Anc1refChr8 47309 8 - 57822 C---TGGTATA -s Anc2.Anc2refChr10 1444 8 - 1800 C---TGGTATA -s mr.mrrefChr5 144029 11 + 294540 TGGATCTCATA -s simCow_chr6.simCow.chr6 332400 8 - 602619 C---TGAAACA -s simDog_chr6.simDog.chr6 261742 8 + 593897 C---TGGTCTA -s simHuman_chr6.simHuman.chr6 362020 8 - 601863 C---TTGTATA -s simRat_chr6.simRat.chr6 281904 11 + 647215 TGAATCTCAAA - -a -s simMouse_chr6.simMouse.chr6 293116 1 + 636262 T -s Anc0.Anc0refChr8 3788 1 - 17196 T -s Anc1.Anc1refChr5 4422 1 - 6477 T -s Anc1.Anc1refChr8 47317 1 - 57822 T -s Anc2.Anc2refChr10 1452 1 - 1800 T -s mr.mrrefChr5 144040 1 + 294540 T -s mr.mrrefChr5 131492 1 + 294540 T -s simDog_chr6.simDog.chr6 261750 1 + 593897 T -s simHuman_chr6.simHuman.chr6 355787 1 - 601863 T -s simHuman_chr6.simHuman.chr6 362028 1 - 601863 T -s simRat_chr6.simRat.chr6 269093 1 + 647215 T -s simRat_chr6.simRat.chr6 281915 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 293150 122 + 636262 CATCTATGTTGTTTCCTGATCCACACCTGTCGAGTTCATAGAGAAGATAGTTTTTGAGACAAAGGGAACTCCTCTGTACTAGTGGCATGGACTGAGTTGCAAAGTGGGACAATGTCAGCCAG -s mr.mrrefChr5 144074 121 + 294540 CATCTATGTTGTTTCCTGATCCACACCTGTCGAGTTCATAG-GAAGATAGTTTTTGAGACAAAGGGAACTCCTCTGTACTAGTGGCATGGACTGAGTTGCAAAGTGGGACAATGCCAGCCAG -s simRat_chr6.simRat.chr6 281949 121 + 647215 CATCTAGGTTGTTTCCTGACCCACACCTGTGGAGTTCACAG-GAGGGTAGTTTATAGTAGCAAGGGAACTCCTCCGCACTAGTGGCATGGACTGAGTTGCAAACTGGGACAATGCCAGCAAG - -a -s simMouse_chr6.simMouse.chr6 293274 1 + 636262 T -s Anc0.Anc0refChr8 3826 1 - 17196 A -s Anc1.Anc1refChr5 4460 1 - 6477 A -s Anc1.Anc1refChr8 47355 1 - 57822 T -s Anc2.Anc2refChr10 1490 1 - 1800 A -s mr.mrrefChr5 144197 1 + 294540 T -s mr.mrrefChr5 131531 1 + 294540 C -s simCow_chr6.simCow.chr6 332445 1 - 602619 A -s simDog_chr6.simDog.chr6 261817 1 + 593897 A -s simHuman_chr6.simHuman.chr6 355825 1 - 601863 A -s simHuman_chr6.simHuman.chr6 362066 1 - 601863 T -s simRat_chr6.simRat.chr6 269138 1 + 647215 C -s simRat_chr6.simRat.chr6 282072 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 293277 8 + 636262 AAAACCCT -s Anc0.Anc0refChr8 3829 8 - 17196 AAGACCCT -s Anc1.Anc1refChr8 47358 8 - 57822 AAGACCCT -s Anc2.Anc2refChr10 1493 8 - 1800 AAGACTCT -s mr.mrrefChr5 144200 8 + 294540 AAAACCCT -s simCow_chr6.simCow.chr6 332448 8 - 602619 AAGACCCT -s simDog_chr6.simDog.chr6 261820 8 + 593897 AAAACTCT -s simHuman_chr6.simHuman.chr6 362069 8 - 601863 AAGACCCT -s simRat_chr6.simRat.chr6 282075 8 + 647215 AAAACCCC - -a -s simMouse_chr6.simMouse.chr6 293333 3 + 636262 CCA -s Anc0.Anc0refChr8 3887 3 - 17196 CCA -s Anc1.Anc1refChr8 47416 3 - 57822 CCA -s Anc2.Anc2refChr10 1551 3 - 1800 CTG -s mr.mrrefChr5 144256 3 + 294540 CCA -s simCow_chr6.simCow.chr6 332506 3 - 602619 CCA -s simDog_chr6.simDog.chr6 261878 3 + 593897 CTG -s simHuman_chr6.simHuman.chr6 362133 3 - 601863 CCA -s simRat_chr6.simRat.chr6 282131 3 + 647215 CCA - -a -s simMouse_chr6.simMouse.chr6 293357 1 + 636262 A -s Anc0.Anc0refChr8 3911 1 - 17196 A -s Anc1.Anc1refChr8 47440 1 - 57822 A -s Anc2.Anc2refChr10 1575 1 - 1800 A -s mr.mrrefChr5 144280 1 + 294540 A -s simCow_chr6.simCow.chr6 332530 1 - 602619 A -s simDog_chr6.simDog.chr6 261897 1 + 593897 A -s simHuman_chr6.simHuman.chr6 362157 1 - 601863 A -s simRat_chr6.simRat.chr6 282155 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 293381 20 + 636262 CACTAACCCATATGTCAGCT -s mr.mrrefChr5 144323 20 + 294540 CACTAACCCATATGTCAGCT -s simRat_chr6.simRat.chr6 282198 20 + 647215 CACTAACCCATATGTCAGCT - -a -s simMouse_chr6.simMouse.chr6 293403 8 + 636262 GTGACTGT -s Anc0.Anc0refChr8 3957 8 - 17196 TGGACTCT -s Anc1.Anc1refChr8 47486 8 - 57822 TGGACTCT -s Anc2.Anc2refChr10 1621 8 - 1800 TGGACCTT -s mr.mrrefChr5 144346 8 + 294540 GTGACTCT -s simCow_chr6.simCow.chr6 332575 8 - 602619 TAGAACTC -s simDog_chr6.simDog.chr6 261943 8 + 593897 TGGCCCTT -s simHuman_chr6.simHuman.chr6 362203 8 - 601863 AGGACTCT -s simRat_chr6.simRat.chr6 282221 8 + 647215 GTGACTCT - -a -s simMouse_chr6.simMouse.chr6 293417 7 + 636262 GATTCAT -s Anc0.Anc0refChr8 3972 7 - 17196 CCTGCAG -s Anc1.Anc1refChr8 47500 7 - 57822 CCTGCAG -s Anc2.Anc2refChr10 1636 7 - 1800 CCTGTAG -s mr.mrrefChr5 144360 7 + 294540 GATTCAG -s simCow_chr6.simCow.chr6 332590 7 - 602619 CCTATAG -s simDog_chr6.simDog.chr6 261958 7 + 593897 CCTGTAG -s simHuman_chr6.simHuman.chr6 362217 7 - 601863 TCTCCAG -s simRat_chr6.simRat.chr6 282233 7 + 647215 GACTCAG - -a -s simMouse_chr6.simMouse.chr6 293424 3 + 636262 AAC -s Anc0.Anc0refChr8 3982 3 - 17196 AAC -s Anc1.Anc1refChr8 47510 3 - 57822 AAC -s Anc2.Anc2refChr10 1646 3 - 1800 GAC -s mr.mrrefChr5 144370 3 + 294540 AAC -s simCow_chr6.simCow.chr6 332600 3 - 602619 GAC -s simDog_chr6.simDog.chr6 261968 3 + 593897 GAG -s simHuman_chr6.simHuman.chr6 362227 3 - 601863 AAC -s simRat_chr6.simRat.chr6 282243 3 + 647215 AAC - -a -s simMouse_chr6.simMouse.chr6 293427 6 + 636262 ATGAGA -s Anc0.Anc0refChr8 3985 6 - 17196 AATAGA -s Anc1.Anc1refChr8 47513 6 - 57822 AATAGA -s Anc2.Anc2refChr10 1649 6 - 1800 AATAAG -s mr.mrrefChr5 144373 6 + 294540 ATGAGA -s simCow_chr6.simCow.chr6 332619 6 - 602619 GATAAG -s simDog_chr6.simDog.chr6 261971 1 + 593897 A----- -s simHuman_chr6.simHuman.chr6 362230 6 - 601863 AATAGA -s simRat_chr6.simRat.chr6 282246 6 + 647215 ATGAGA - -a -s simMouse_chr6.simMouse.chr6 293433 119 + 636262 GCTCTGCCAAGGACCTTTTTTAATGAATTGTATACTGTATATGTGTTTACTTAAATAGCAAAAAACATTATTGTTGTATACAGCTACATAAATACAGGATGGAGAAGAGTTGTACCAGT -s Anc0.Anc0refChr8 3992 114 - 17196 GCTCTGCC-AGG---CTTTTTATTGAATTATATACTGGCT-TATTTTTTTTTAATTAGCAATAAATCTTAATAATGTGTAATGTTACTTAAATATAAGACAAGGATGAGTTTTGCCAGT -s Anc1.Anc1refChr8 47520 117 - 57822 GCTCTGCC-AGGACACTTTTTATTGAATTATATACTGGCT-TATTTTTTTTTAATTAGCAATAAATCTTAATAATGTGTAATGTTACTTAAATATAAGACAAGGATGAGTTTTGCCAGT -s Anc2.Anc2refChr10 1656 114 - 1800 GCTCTGCC-AGG---CTTTTCATTGAATCATATACTGGCT-TATTTTTTTTTAATTAGCAATAAATCTTAATAACATGTAATGTTACTTAAGCATAAGACAAGGATGAGTTTTGCCAGT -s mr.mrrefChr5 144379 118 + 294540 GCTCTGCC-AGGACCTTTTTTAATGAATTGTATACTGTATATGTGTTTTCTTAAATAGCAAAAAACATTATTGTTGTGTACAGCTACATAAATACAAGACAGGGAAGAGTTGTACCAGT -s simCow_chr6.simCow.chr6 332626 111 - 602619 GCTCTGCC-AGG---CTTTTCAATGAATCATATACTGGCT-TATTTTTTATTAAT-AGCAATA--TCTTGATTACATGTAATATTACCTAAGAATCAGACAAGGATGGGTTTTGCCAGT -s simDog_chr6.simDog.chr6 261972 93 + 593897 -----------------------TGAATCATATACTGGCT-TATTTTTTT--AAGTAGCAATAAATCTTAATAACATATAATGTCACTTAAGCATAAGACAAGGATGAATTTTGCCAGT -s simHuman_chr6.simHuman.chr6 362237 117 - 601863 CCTCTGCC-AGGACACTCTGTATTGAATTATATACTGGCT-TAATTTTTTTTAATTAGCAATAAATCTTACCAATGTGTAGTGTTACTTAAATATAAGACAAGGGTGAGTTTTTCCAGT -s simRat_chr6.simRat.chr6 282252 118 + 647215 GCTCTGCC-AGGACCTTTTTTAATGAATTGTATACTGCATATGCGTTTTCTCAAATAGCAAGAAACATAATTGTTGTGTACAGCTATATAAATACAAGGCAGGGAAAAGGTATGCCAGT - -a -s simMouse_chr6.simMouse.chr6 293552 30 + 636262 TCCCAGGCTCTCGACACAAAGTATGCTCAT -s Anc0.Anc0refChr8 4113 22 - 17196 TTCAAGGCTATTGACGCCATGT-------- -s Anc1.Anc1refChr8 47644 30 - 57822 TTCAAGGCTATTGACGCCATGTCAGCAACT -s Anc2.Anc2refChr10 1777 22 - 1800 TTCAAGGCTATTGAAGCCTTGT-------- -s mr.mrrefChr5 144497 30 + 294540 TTCCAGGCTCTTGACACAAAGTAAGCTCAT -s simCow_chr6.simCow.chr6 332744 22 - 602619 TTCAAGGCTATTGATGCCCTGT-------- -s simDog_chr6.simDog.chr6 262076 22 + 593897 GTCAGGGCTAATAAAACCTTGT-------- -s simHuman_chr6.simHuman.chr6 362361 30 - 601863 TTCAAGGCTATTGGCGCCATGTCAGCAACT -s simRat_chr6.simRat.chr6 282370 30 + 647215 TTCCAGGCACTTGACACTAAGTGAGCTCAT - -a -s simMouse_chr6.simMouse.chr6 293582 10 + 636262 CAGGAGTTGT -s Anc0.Anc0refChr8 4135 10 - 17196 CAAAAATTGT -s Anc1.Anc1refChr8 47674 10 - 57822 CAAAAATTGT -s Anc2.Anc2refChr5 1798 10 + 8386 CAAAAATTGT -s mr.mrrefChr5 144527 10 + 294540 CAGGAGTTGT -s simCow_chr6.simCow.chr6 273027 10 + 602619 GATTAATTGT -s simDog_chr6.simDog.chr6 262107 10 + 593897 CAAAAGTTGT -s simHuman_chr6.simHuman.chr6 362392 10 - 601863 CAAAAATTGT -s simRat_chr6.simRat.chr6 282400 10 + 647215 CAGGAGTTGC - -a -s simMouse_chr6.simMouse.chr6 293592 7 + 636262 ACATTTG -s Anc0.Anc0refChr8 4145 7 - 17196 CTACATG -s Anc1.Anc1refChr8 47684 7 - 57822 CTACATG -s Anc2.Anc2refChr5 1808 7 + 8386 CTACATG -s mr.mrrefChr5 144537 7 + 294540 ACATTTG -s simCow_chr6.simCow.chr6 273037 7 + 602619 CTATAGA -s simDog_chr6.simDog.chr6 262119 7 + 593897 ATACATG -s simHuman_chr6.simHuman.chr6 362402 7 - 601863 CTAGCTG -s simRat_chr6.simRat.chr6 282410 7 + 647215 ACACTTG - -a -s simMouse_chr6.simMouse.chr6 293599 2 + 636262 GG -s Anc0.Anc0refChr8 4155 2 - 17196 GG -s Anc1.Anc1refChr8 47694 2 - 57822 GG -s Anc2.Anc2refChr5 1818 2 + 8386 GG -s mr.mrrefChr5 144544 2 + 294540 GG -s simCow_chr6.simCow.chr6 273047 2 + 602619 GT -s simDog_chr6.simDog.chr6 262129 2 + 593897 CG -s simHuman_chr6.simHuman.chr6 362412 2 - 601863 GG -s simRat_chr6.simRat.chr6 282417 2 + 647215 GG - -a -s simMouse_chr6.simMouse.chr6 293601 9 + 636262 CAGTAGAAC -s Anc0.Anc0refChr8 4157 9 - 17196 GGGTTGAAT -s Anc1.Anc1refChr8 47696 9 - 57822 GGGTTGAAT -s Anc2.Anc2refChr5 1820 9 + 8386 GGGTTGAAT -s mr.mrrefChr5 144546 9 + 294540 CAGTAGAAC -s simCow_chr6.simCow.chr6 273050 9 + 602619 GGGTCATAT -s simDog_chr6.simDog.chr6 262131 9 + 593897 GGGTTGAAT -s simHuman_chr6.simHuman.chr6 362414 9 - 601863 GGGTTGAAT -s simRat_chr6.simRat.chr6 282419 9 + 647215 CACTAGAAA - -a -s simMouse_chr6.simMouse.chr6 293610 1 + 636262 T -s Anc0.Anc0refChr8 4170 1 - 17196 T -s Anc1.Anc1refChr8 47709 1 - 57822 T -s Anc2.Anc2refChr5 1833 1 + 8386 T -s mr.mrrefChr5 144555 1 + 294540 T -s simCow_chr6.simCow.chr6 273063 1 + 602619 T -s simDog_chr6.simDog.chr6 262144 1 + 593897 T -s simHuman_chr6.simHuman.chr6 362427 1 - 601863 T -s simRat_chr6.simRat.chr6 282428 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 293611 21 + 636262 GTATCAGACGAGTTGCACCTA -s Anc0.Anc0refChr8 4171 21 - 17196 GTATCACATGAGTTCCACCTA -s Anc1.Anc1refChr8 47710 21 - 57822 GTATCACATGAGTTCCACCTA -s Anc2.Anc2refChr5 1834 21 + 8386 GTCTCACATGTGTTCCACCCA -s mr.mrrefChr5 144556 21 + 294540 GTATCAGATGAGTTCCACCTA -s simCow_chr6.simCow.chr6 273064 21 + 602619 GTCTCACATGTGATCCACCCA -s simDog_chr6.simDog.chr6 262145 21 + 593897 GTCTCATAGGTGTTCCACCCA -s simHuman_chr6.simHuman.chr6 362428 21 - 601863 GTATCACATGAGTTCCGCCTA -s simRat_chr6.simRat.chr6 282430 21 + 647215 GTCTCAGGTGAGTTCCACCTA - -a -s simMouse_chr6.simMouse.chr6 293632 17 + 636262 TTTGCAAAAAAAGATGG -s Anc0.Anc0refChr8 4192 17 - 17196 TTTGCAGATTGGGATGT -s Anc1.Anc1refChr8 47731 17 - 57822 TTTGCAGATTGGGATGT -s Anc2.Anc2refChr5 1855 17 + 8386 TTTGCAGATTGGGATGT -s mr.mrrefChr5 144577 17 + 294540 TTTGCAAAAAAAGATGG -s simCow_chr6.simCow.chr6 273085 14 + 602619 T--GCAGATTGG-ACAT -s simDog_chr6.simDog.chr6 262177 17 + 593897 TTTGCTGATAGGGGTGT -s simHuman_chr6.simHuman.chr6 362449 17 - 601863 TTTGCAGATTGGGATGT -s simRat_chr6.simRat.chr6 282451 17 + 647215 TTTGCATAAAAAGCTGG - -a -s simMouse_chr6.simMouse.chr6 293649 29 + 636262 TGGAGAATAACCCTATTTTTGCAGTCTAG -s Anc0.Anc0refChr8 4210 29 - 17196 TGAAGGTTAATTCTCTATTAGCAGTTTTG -s Anc1.Anc1refChr8 47749 29 - 57822 TGAAGGTTAATTCTCTATTAGCAGTTTTG -s Anc2.Anc2refChr5 1873 29 + 8386 TGAAGGTTAATTCTCTACTAGCAGTTTTA -s mr.mrrefChr5 144595 29 + 294540 TGAAGAATAACCCTCTATTTGCAGTTTAG -s simCow_chr6.simCow.chr6 273100 29 + 602619 CAAAGATTAATTCTCCACTAGCAGTCTTC -s simDog_chr6.simDog.chr6 262197 29 + 593897 TGGAGGTTAATTCTCTACTAGCACTTTTA -s simHuman_chr6.simHuman.chr6 362467 29 - 601863 TGAAACTAAATTCTCTATCAGCAGTTTTG -s simRat_chr6.simRat.chr6 282469 29 + 647215 TGAAGAACAACCCTCTATTTACAGTTTAG - -a -s simMouse_chr6.simMouse.chr6 293678 17 + 636262 ATCGCCAGGGAATCTCT -s Anc0.Anc0refChr8 4240 17 - 17196 ATCACTGGGGATTGTGT -s Anc1.Anc1refChr8 47779 17 - 57822 ATCACTGGGGATTGTGT -s Anc2.Anc2refChr5 1903 17 + 8386 ATCACTGGGGATTGTGT -s mr.mrrefChr5 144624 17 + 294540 ATCGCCAGGGATTCTCT -s simCow_chr6.simCow.chr6 273130 9 + 602619 ACCATTGGG-------- -s simDog_chr6.simDog.chr6 262227 17 + 593897 ATCACTGGGGATTGTGT -s simHuman_chr6.simHuman.chr6 362497 17 - 601863 ATCTCTCGGGATTGCAC -s simRat_chr6.simRat.chr6 282498 13 + 647215 ATCAT----GATTCTCT - -a -s simMouse_chr6.simMouse.chr6 293695 6 + 636262 AGGATT -s Anc0.Anc0refChr8 4257 6 - 17196 AGGCTT -s Anc1.Anc1refChr8 47796 6 - 57822 AGGCTT -s Anc2.Anc2refChr5 1920 6 + 8386 AGGCTT -s mr.mrrefChr5 144641 6 + 294540 AGGATT -s simDog_chr6.simDog.chr6 262247 6 + 593897 AGGCTT -s simHuman_chr6.simHuman.chr6 362514 6 - 601863 AGACTT -s simRat_chr6.simRat.chr6 282511 6 + 647215 AGGAGA - -a -s simMouse_chr6.simMouse.chr6 293701 7 + 636262 TAAAATC -s Anc0.Anc0refChr8 4263 7 - 17196 TAAAACC -s Anc1.Anc1refChr8 47802 7 - 57822 TAAAACC -s Anc2.Anc2refChr5 1926 7 + 8386 AAAAACC -s mr.mrrefChr5 144647 7 + 294540 TAAAATC -s simDog_chr6.simDog.chr6 262253 7 + 593897 AAAAACC -s simHuman_chr6.simHuman.chr6 362522 7 - 601863 TAAGACC -s simRat_chr6.simRat.chr6 282517 7 + 647215 TAAAATC - -a -s simMouse_chr6.simMouse.chr6 293708 44 + 636262 TTTATTGGTACCTGCAATAGAGTTTGATACATGGTGGCTGTAAC -s Anc0.Anc0refChr8 4276 37 - 17196 TCTTTTGGTTCTTGCAA-------TGCTCGAAGGTAGCTGTAAA -s Anc1.Anc1refChr8 47815 37 - 57822 TCTTTTGGTTCTTGCAA-------TGCTCGAAGGTAGCTGTAAA -s Anc2.Anc2refChr5 1939 37 + 8386 TCTATTGGGTTTTGCAA-------TGCCCGAAGGTACTCGTAAA -s mr.mrrefChr5 144654 44 + 294540 TTTTTTGGTACCTGCAATAGAGTTTGATACATGGTGGCTGTAAC -s simDog_chr6.simDog.chr6 262266 37 + 593897 TCTATTGGGTTTTGCAA-------TGCCCGAAGGTACTCGTAAA -s simHuman_chr6.simHuman.chr6 362535 32 - 601863 TCTTTTGGTCCTTGCAA-------TGCTCTACAGCAGCT----- -s simRat_chr6.simRat.chr6 282524 44 + 647215 TTTTTCGGTACCTGCAATAGAGTTTTATGCATGGAGGCTGTAAA - -a -s simMouse_chr6.simMouse.chr6 293752 13 + 636262 AGGTGTTACCTAT -s Anc0.Anc0refChr8 4313 13 - 17196 AGCTAATACCTTA -s Anc1.Anc1refChr8 47852 13 - 57822 AGCTAATACCTTA -s Anc2.Anc2refChr5 1985 13 + 8386 AGCTAATACCTTA -s mr.mrrefChr5 144698 13 + 294540 AGGTGTTACCTAT -s simCow_chr6.simCow.chr6 273148 13 + 602619 GCCTAATACCCTT -s simDog_chr6.simDog.chr6 262372 13 + 593897 AGCTAATACCTTA -s simHuman_chr6.simHuman.chr6 362567 4 - 601863 ---------CTCA -s simRat_chr6.simRat.chr6 282568 13 + 647215 AGGTGTTAGCGAT - -a -s simMouse_chr6.simMouse.chr6 293765 28 + 636262 TAAGGGTCCTGTTGCAAAGTCATTCTGA -s Anc0.Anc0refChr8 4326 28 - 17196 TAAGGGTCCCAGTGCAAAATCAGTCTGA -s Anc1.Anc1refChr8 47865 28 - 57822 TAAGGGTCCCAGTGCAAAATCAGTCTGA -s Anc2.Anc2refChr5 2003 28 + 8386 TAAGGGTCCCAGTGCAAAATCAGACTGA -s mr.mrrefChr5 144711 28 + 294540 TAAGGGTCCTATTGCAAAGTCATTCTGA -s simCow_chr6.simCow.chr6 273166 28 + 602619 TAAACATCCCAGTGTGAGATTAGACTAA -s simDog_chr6.simDog.chr6 262390 28 + 593897 TAAGGGTCCCAGTGCAAAATCAGACTGA -s simHuman_chr6.simHuman.chr6 362571 24 - 601863 TAAAGGTCCCACTACAAAA----TCTGA -s simRat_chr6.simRat.chr6 282581 24 + 647215 T----GTTCTATCTTGATGTCAGACTGA - -a -s simMouse_chr6.simMouse.chr6 293793 13 + 636262 TCAGTAGAGGTTA -s Anc0.Anc0refChr8 4354 13 - 17196 TCAATAGGTGTTG -s Anc1.Anc1refChr8 47893 13 - 57822 TCAATAGGTGTTG -s Anc2.Anc2refChr5 2031 13 + 8386 TCAATAGGGGTTG -s mr.mrrefChr5 144739 13 + 294540 TCAGTAGATGTTA -s simCow_chr6.simCow.chr6 273211 13 + 602619 TCGATAGAGGTTA -s simDog_chr6.simDog.chr6 262418 13 + 593897 TCAATAGGGGTTG -s simHuman_chr6.simHuman.chr6 362595 12 - 601863 TCAATAGGTGTT- -s simRat_chr6.simRat.chr6 282605 13 + 647215 TCAGTAGATGTTA - -a -s simMouse_chr6.simMouse.chr6 293806 12 + 636262 CTTTTGTGAATT -s Anc0.Anc0refChr8 4367 12 - 17196 CTTTATTGAATT -s Anc1.Anc1refChr8 47906 12 - 57822 CTTTATTGAATT -s Anc2.Anc2refChr5 2059 12 + 8386 CTTTATGCAATT -s mr.mrrefChr5 144752 12 + 294540 CTTTTGTGAATT -s simCow_chr6.simCow.chr6 273239 12 + 602619 CCCTATCCAATC -s simDog_chr6.simDog.chr6 262443 12 + 593897 CTTTAAGCAATT -s simHuman_chr6.simHuman.chr6 362607 11 - 601863 -TTTATTGAATT -s simRat_chr6.simRat.chr6 282618 12 + 647215 CTTTTGTGAATT - -a -s simMouse_chr6.simMouse.chr6 293818 13 + 636262 AGGTTGAATTAAG -s Anc0.Anc0refChr8 4380 13 - 17196 ATGTTTAAGTGAG -s Anc1.Anc1refChr8 47919 13 - 57822 ATGTTTAAGTGAG -s Anc2.Anc2refChr5 2072 13 + 8386 ATGTTTAGGTGAA -s mr.mrrefChr5 144764 13 + 294540 AGGTTGAATTAAG -s simCow_chr6.simCow.chr6 273252 13 + 602619 ACGTTTATGTGAA -s simDog_chr6.simDog.chr6 262456 13 + 593897 ATGTTTAGGTGAA -s simHuman_chr6.simHuman.chr6 362619 13 - 601863 ATGTTTAAGTGAG -s simRat_chr6.simRat.chr6 282630 13 + 647215 AGGTTAAATTAAA - -a -s simMouse_chr6.simMouse.chr6 293831 11 + 636262 ATTAACATGTG -s Anc0.Anc0refChr8 4412 11 - 17196 ATTACTTTCTG -s Anc1.Anc1refChr8 47951 11 - 57822 ATTACTTTCTG -s Anc2.Anc2refChr5 2104 11 + 8386 ATTGCTTTCTT -s mr.mrrefChr5 144777 11 + 294540 ATTAATATGTG -s simCow_chr6.simCow.chr6 273284 11 + 602619 ATTGCCTTCTA -s simDog_chr6.simDog.chr6 262485 11 + 593897 ATTGCTTTCTT -s simHuman_chr6.simHuman.chr6 362651 11 - 601863 ATTACTTTCTG -s simRat_chr6.simRat.chr6 282643 11 + 647215 TTTAATATGTG - -a -s simMouse_chr6.simMouse.chr6 293842 18 + 636262 GCTCTACCTTAATTCATC -s Anc0.Anc0refChr8 4467 18 - 17196 GCTCTTCATTCATTAGTC -s Anc1.Anc1refChr8 48006 18 - 57822 GCTCTTCATTCATTAGTC -s Anc2.Anc2refChr5 2159 18 + 8386 GCTTTTCATTCATTAGCC -s mr.mrrefChr5 144788 18 + 294540 GCTCTACCTTAATTCATC -s simCow_chr6.simCow.chr6 273340 18 + 602619 GCTGTTCATTCATTAGCA -s simDog_chr6.simDog.chr6 262540 18 + 593897 GCTTTTCATTCATTAGCC -s simHuman_chr6.simHuman.chr6 362706 18 - 601863 GCTCTTCAGTCATTAGTC -s simRat_chr6.simRat.chr6 282654 18 + 647215 GCTCTGCCTTAATTCATC - -a -s simMouse_chr6.simMouse.chr6 293860 38 + 636262 TTATAGCTGTATGTGTGTTTGGCTGCTGCCTCTTTTGA -s Anc0.Anc0refChr8 4491 38 - 17196 CTATAGCTGGATTTGGGTTGGGCTGCCGCCTCTCGGGA -s Anc1.Anc1refChr8 48030 38 - 57822 CTATAGCTGGATTTGGGTTGGGCTGCCGCCTCTCGGGA -s Anc2.Anc2refChr5 2183 38 + 8386 CTATAGTTGGAATTGGGTTAGGCTGCCGCCTCTCGGGA -s mr.mrrefChr5 144812 38 + 294540 TTATAGCTGTATGTGTGTTGGGCTGCTGCCTCTTTTGA -s simCow_chr6.simCow.chr6 273364 38 + 602619 CTATAGTTGGAATTGGGTCAGACTGCCACCTCTTGGGA -s simDog_chr6.simDog.chr6 262564 38 + 593897 CTAATGTTGGAATTGGGTTAGGCTACTGCCTCTCGGGA -s simHuman_chr6.simHuman.chr6 362730 37 - 601863 CTATAGCTGGATTCG-GGCGGGTGGCCGCCTCTCAGGA -s simRat_chr6.simRat.chr6 282680 38 + 647215 TTATAGCTGTATGTGTGTTGGTCTGCTGCCTCTTTTGA - -a -s simMouse_chr6.simMouse.chr6 293898 49 + 636262 CAGTTAACTCAGAAATGGAGTTCATTTATTGACTCTTACTCTCAAATCT -s Anc0.Anc0refChr8 4536 49 - 17196 CAGTTTACTCTTAAATGGAGTTCATCCATTGACGCTTGTTCTCATATCT -s Anc1.Anc1refChr8 48075 49 - 57822 CAGTTTACTCTTAAATGGAGTTCATCCATTGACGCTTGTTCTCATATCT -s Anc2.Anc2refChr5 2228 49 + 8386 CAGCTTACTCTTAAATAGAGTTCATCCATTGACGCTTGTTCCCATATCT -s mr.mrrefChr5 144850 49 + 294540 CAGTTAACTCAGAAATGGAGTTCATTTATTGACTCTTACTCTCAAATCT -s simCow_chr6.simCow.chr6 273409 49 + 602619 CGGCTGACTATGAAATAAAGTTCACCTAGTGGTGCTTATTCCCATATCT -s simDog_chr6.simDog.chr6 262609 48 + 593897 CAGCTTA-GCTTAAATAGAGTTCATCCATTGACGCTTGTTTCCATACCC -s simHuman_chr6.simHuman.chr6 362774 49 - 601863 CAGTTTACTCTCAAATGGATTTCCTCCATTGACGCTGGTTCTCATATCT -s simRat_chr6.simRat.chr6 282718 48 + 647215 CAGTAAACTCATAAATGGGGAGCATTTATTTACACTTAC-CTCAAATCT - -a -s simMouse_chr6.simMouse.chr6 293947 4 + 636262 AAGG -s Anc0.Anc0refChr8 4585 2 - 17196 AA-- -s Anc1.Anc1refChr8 48124 2 - 57822 AA-- -s Anc2.Anc2refChr5 2277 2 + 8386 AA-- -s mr.mrrefChr5 144899 4 + 294540 AAGG -s simCow_chr6.simCow.chr6 273458 2 + 602619 AA-- -s simDog_chr6.simDog.chr6 262658 2 + 593897 AA-- -s simHuman_chr6.simHuman.chr6 362823 2 - 601863 AA-- -s simRat_chr6.simRat.chr6 282766 4 + 647215 GAAG - -a -s simMouse_chr6.simMouse.chr6 293951 63 + 636262 TGTAGGTCAGTATAGGTAGGACGGATAACAACAGTCTTGTCCCCTGTGACCAGGCAGTGTTCT -s Anc0.Anc0refChr8 4587 38 - 17196 ------------------------ATAAC-AAAGTCTTGTCCCTTGTGACCAGGCAGAGTTTC -s Anc1.Anc1refChr8 48126 39 - 57822 ------------------------ATAACAAAAGTCTTGTCCCTTGTGACCAGGCAGAGTTTC -s Anc2.Anc2refChr5 2279 38 + 8386 ------------------------ATAAC-AAAGTCTTGTCCCTTGTGACCAAGCAGAGTTTC -s mr.mrrefChr5 144903 63 + 294540 TGTAGGTCAGTATAGGTAGGACGGATAACAACAGTCTTGTCCCCTGTGACCAGGCAGTGTTCT -s simCow_chr6.simCow.chr6 273460 38 + 602619 ------------------------ATAAC-AAAGTCTTGTCGCATGCAACCAAGAAGAGTTTC -s simDog_chr6.simDog.chr6 262660 34 + 593897 ------------------------CTAAC-AAG----TATCCCTTGTGACGGAGCAGAGTTTC -s simHuman_chr6.simHuman.chr6 362825 39 - 601863 ------------------------ATAACAAAGGTCTTGTCCCTGGTGACCAGGCAGAGTTTC -s simRat_chr6.simRat.chr6 282773 63 + 647215 TGTGGGACAGTATGTGTAGGGCAGATAACAACAGTCTTGTCCTCTGTAACCATGCAGTGTTCT - -a -s simMouse_chr6.simMouse.chr6 294014 20 + 636262 CATATCGTCATTTTAAAACT -s Anc0.Anc0refChr8 4625 13 - 17196 CATA--GTCTGATT-----T -s Anc1.Anc1refChr8 48165 18 - 57822 CATA--GTCTGATTATAAGT -s Anc2.Anc2refChr5 2317 13 + 8386 CATA--TTTTGATT-----T -s mr.mrrefChr5 144966 20 + 294540 CATATCGTCATTTTAAAACT -s simCow_chr6.simCow.chr6 273510 13 + 602619 CATA--TCTTCATT-----T -s simDog_chr6.simDog.chr6 262694 13 + 593897 TATA--TTTTGATT-----T -s simHuman_chr6.simHuman.chr6 362864 18 - 601863 CATG--GTCTGGTTATAAGC -s simRat_chr6.simRat.chr6 282836 20 + 647215 CATATTATCATTTTAAAACT - -a -s simMouse_chr6.simMouse.chr6 294034 23 + 636262 TCAGTACACAATATATTCCAATG -s Anc0.Anc0refChr8 4638 10 - 17196 TCAGTACACA------------- -s Anc1.Anc1refChr8 48183 22 - 57822 TCAGTACACAGT-TTCCCTAATT -s Anc2.Anc2refChr5 2330 10 + 8386 TCAGTATGCA------------- -s mr.mrrefChr5 144986 23 + 294540 TCAGTACACAATATATTCCAATG -s simCow_chr6.simCow.chr6 273528 10 + 602619 TCAGTAAACA------------- -s simDog_chr6.simDog.chr6 262707 10 + 593897 TCAGTATGCA------------- -s simHuman_chr6.simHuman.chr6 362882 22 - 601863 TCCAGGCAGAGT-TTCCCTAATT -s simRat_chr6.simRat.chr6 282856 23 + 647215 TCAGTACACTAGATATTCCAGGG - -a -s simMouse_chr6.simMouse.chr6 294057 16 + 636262 TGATAAGATATATAGG -s Anc0.Anc0refChr8 4648 10 - 17196 TGAT------TTTAAG -s Anc1.Anc1refChr8 48205 10 - 57822 TGAT------TTTAAG -s Anc2.Anc2refChr5 2340 10 + 8386 TGCT------CTGAAG -s mr.mrrefChr5 145009 12 + 294540 TGATA----ATATAAG -s simCow_chr6.simCow.chr6 273559 10 + 602619 TGGT------CTGAGT -s simDog_chr6.simDog.chr6 262717 10 + 593897 TGCT------CTGAAG -s simHuman_chr6.simHuman.chr6 362904 10 - 601863 TGAT------TTTAAG -s simRat_chr6.simRat.chr6 282879 12 + 647215 TGATA----ATAAAAG - -a -s simMouse_chr6.simMouse.chr6 294073 29 + 636262 CTCTAGGGAATCTGACCAGCATCCTTGGT -s Anc0.Anc0refChr8 4658 28 - 17196 CTCT-GGACATCTGCCCAGTGCCTTTGGT -s Anc1.Anc1refChr8 48215 28 - 57822 CTCT-GGACATCTGCCCAGTGCCTTTGGT -s Anc2.Anc2refChr5 2351 28 + 8386 CTCT-GGACATCTGCCCAGTGCCTTTGGT -s mr.mrrefChr5 145021 28 + 294540 CTCT-GGGAATCTGACCAGCATCCTTGGT -s simCow_chr6.simCow.chr6 273570 28 + 602619 CGCT-AGACGTCTGACCAGTCCCTTTAGT -s simDog_chr6.simDog.chr6 262728 28 + 593897 CTCT-GGAAATCTGCCCAGTGCCTTTGGT -s simHuman_chr6.simHuman.chr6 362914 5 - 601863 CTCA-G----------------------- -s simRat_chr6.simRat.chr6 282891 28 + 647215 CTCT-TGGAATCTGGCCAGTATCCATGGT - -a -s simMouse_chr6.simMouse.chr6 294102 38 + 636262 TAGCAATATGACTTTGGAGTGTGTACAGCTGATAACTA -s Anc0.Anc0refChr8 4686 2 - 17196 TA------------------------------------ -s Anc1.Anc1refChr8 48243 2 - 57822 TA------------------------------------ -s Anc2.Anc2refChr5 2379 2 + 8386 TA------------------------------------ -s mr.mrrefChr5 145049 38 + 294540 TAGCAATATGACTTTGGAGTGTGTACAGCTGATAACTA -s simCow_chr6.simCow.chr6 273606 2 + 602619 TA------------------------------------ -s simDog_chr6.simDog.chr6 262756 2 + 593897 TA------------------------------------ -s simRat_chr6.simRat.chr6 282919 38 + 647215 TAGCAATATGACATTGAAGTCTGTACAGCTTATAACTA - -a -s simMouse_chr6.simMouse.chr6 294140 25 + 636262 GAGATAAGTACTAGGTCAAGGCAAT -s Anc1.Anc1refChr8 48245 14 - 57822 -----------TACACAAACCCAAT -s mr.mrrefChr5 145087 25 + 294540 GAGATAAGTACTAGGCCAAGGCAAT -s simHuman_chr6.simHuman.chr6 362919 14 - 601863 -----------TACACAAACCCAAT -s simRat_chr6.simRat.chr6 282958 25 + 647215 GAGATAAGTACTAGGCCAAGGCGAT - -a -s simMouse_chr6.simMouse.chr6 294165 11 + 636262 TGGGCTGGCGA -s Anc0.Anc0refChr8 4712 11 - 17196 TGGGAAAGCAT -s Anc1.Anc1refChr8 48283 11 - 57822 TGGGAAAGCAT -s Anc2.Anc2refChr5 2406 11 + 8386 TGGCAAAGCAT -s mr.mrrefChr5 145133 11 + 294540 TGGGCTGGCAA -s simCow_chr6.simCow.chr6 273657 11 + 602619 TGGCATAGAAT -s simDog_chr6.simDog.chr6 262784 11 + 593897 TTGCAAGGCAT -s simHuman_chr6.simHuman.chr6 362961 11 - 601863 TGGGACAGTAT -s simRat_chr6.simRat.chr6 283004 11 + 647215 TAAGCTGGCAA - -a -s simMouse_chr6.simMouse.chr6 294176 34 + 636262 AACATAAGTACAGGTAAGGTTCACCCAAAAAGTA -s Anc0.Anc0refChr8 4723 11 - 17196 AACATG-----------------------AGGGA -s Anc1.Anc1refChr8 48294 11 - 57822 AACATG-----------------------AGGGA -s Anc2.Anc2refChr5 2417 11 + 8386 AACATG-----------------------AGGGA -s mr.mrrefChr5 145144 34 + 294540 AACATGAGTGCAGGTAAGGTTCACCCAAAAAGTA -s simCow_chr6.simCow.chr6 273679 11 + 602619 AATAAG-----------------------AGGGA -s simDog_chr6.simDog.chr6 262795 11 + 593897 AGCATG-----------------------AGGGA -s simHuman_chr6.simHuman.chr6 362972 11 - 601863 AACATG-----------------------AGAGA -s simRat_chr6.simRat.chr6 283015 34 + 647215 AACATGAGTGCAGATAAGAGACTCCCAAAAAGTA - -a -s simMouse_chr6.simMouse.chr6 294210 46 + 636262 TCTAAAACTGCTACCCTTATCATTATAGGAACAATAGTAGTGTCTG -s Anc0.Anc0refChr8 4734 28 - 17196 TC-----------------CCATTA-AGGAACAATTGTAGTGTCTG -s Anc1.Anc1refChr8 48305 29 - 57822 TC-----------------CCATTATAGGAACAATTGTAGTGTCTG -s Anc2.Anc2refChr5 2428 28 + 8386 TC-----------------CCATTA-AGGAACAATTGTAATGTCTG -s mr.mrrefChr5 145178 46 + 294540 TCTAAAACTGCTACCCTTATCATTATAGGAACAATAGTAGTGTCTG -s simCow_chr6.simCow.chr6 273690 28 + 602619 TC-----------------CCACTA-AGGAACAATTGTTCCCCTTG -s simDog_chr6.simDog.chr6 262808 28 + 593897 TC-----------------TGATTG-AGGAATAACTGTAATGTCTG -s simHuman_chr6.simHuman.chr6 362983 29 - 601863 TC-----------------CCATTATAGGAACAATGGTAGTGTCTG -s simRat_chr6.simRat.chr6 283049 46 + 647215 TCCAAAACTGCTACCCTTATCGTTATAGGGACGTTAGTAGTGTCTG - -a -s simMouse_chr6.simMouse.chr6 294256 7 + 636262 TCCCTGT -s Anc0.Anc0refChr8 4762 7 - 17196 TCCCTGT -s Anc1.Anc1refChr8 48334 7 - 57822 TCCCTGT -s Anc2.Anc2refChr5 2456 7 + 8386 GTGTTGT -s mr.mrrefChr5 145224 7 + 294540 TCCCTGT -s simCow_chr6.simCow.chr6 273718 7 + 602619 GGGTTGT -s simDog_chr6.simDog.chr6 262853 7 + 593897 GTGTTGT -s simHuman_chr6.simHuman.chr6 363012 7 - 601863 TCCCTGT -s simRat_chr6.simRat.chr6 283095 7 + 647215 TCCTTAT - -a -s simMouse_chr6.simMouse.chr6 294263 13 + 636262 CTGTGATCCAACC -s Anc0.Anc0refChr8 4769 13 - 17196 CTATTATCCCACA -s Anc1.Anc1refChr8 48341 13 - 57822 CTATTATCCCACA -s Anc2.Anc2refChr5 2464 13 + 8386 ATATTATCCCACA -s mr.mrrefChr5 145231 13 + 294540 CTGTGATCCAACC -s simCow_chr6.simCow.chr6 273726 7 + 602619 ATA-TATC----- -s simDog_chr6.simDog.chr6 262861 13 + 593897 ATCTTAAACCACA -s simHuman_chr6.simHuman.chr6 363019 13 - 601863 CTAGTATCCCGCG -s simRat_chr6.simRat.chr6 283102 13 + 647215 CTGTGATCCAACC - -a -s simMouse_chr6.simMouse.chr6 294276 57 + 636262 TGACATGCATCTTGTGTTGTCCTGTGTGAAGACTGTGATTAGCCAATATGGTCGCCC -s Anc0.Anc0refChr8 4782 30 - 17196 TGAC---------------------------ACTGTGATCTGGTGATATGGTAGCCC -s Anc1.Anc1refChr8 48354 30 - 57822 TGAC---------------------------ACTGTGATCTGGTGATATGGTAGCCC -s Anc2.Anc2refChr5 2477 30 + 8386 CGAC---------------------------CCTGTGATCTGGTGAAATGGTAGCCC -s mr.mrrefChr5 145244 57 + 294540 TGACATGCATCTTGTGTTGTCCTGTGTGAAGACTGTGATTAGGCAATATGGTAGCCC -s simCow_chr6.simCow.chr6 273733 29 + 602619 -AAC---------------------------CCTGTTATCTGGTGAAAAAGTAGCTC -s simDog_chr6.simDog.chr6 262883 30 + 593897 CGAC---------------------------CCTGTGATCTGGGGAAATGGTAGCCC -s simHuman_chr6.simHuman.chr6 363032 30 - 601863 TGCC---------------------------ACTGTGTTCTAGTGATATGGTAGGCC -s simRat_chr6.simRat.chr6 283115 57 + 647215 TGACTTACATCTTGTGTTGTCCTGTGTAATGACTGTGATTCGGCAATATGGTAGCCC - -a -s simMouse_chr6.simMouse.chr6 294333 47 + 636262 CCTCATAGACGTTGATTTTCCCAAAGGCAGACTCCAACCTAGGGTGC -s Anc0.Anc0refChr8 4812 33 - 17196 CTTAGCAGCCAT-GACCTCTTTGAAGATAGAGC-------------C -s Anc1.Anc1refChr8 48384 33 - 57822 CTTAGCAGCCAT-GACCTCTTTGAAGATAGAGC-------------C -s Anc2.Anc2refChr5 2522 33 + 8386 CTTAGCAGCCAT-TGCTTCTTTGCAGATGGAGC-------------C -s mr.mrrefChr5 145301 47 + 294540 CCTCATAGCCATTGACCTTTCCGAAGGCAGACTCCAACCTAGGGTGC -s simCow_chr6.simCow.chr6 273777 21 + 602619 CTTAGCA-----------TTTTACAGATCCGG--------------- -s simDog_chr6.simDog.chr6 262928 33 + 593897 CTTAGCAGCCAT-TGCTTCTTGGCAGAAGGAGC-------------C -s simHuman_chr6.simHuman.chr6 363062 33 - 601863 CTTAGCAGCCAT-GACCTATTTGAAGATAGAGC-------------C -s simRat_chr6.simRat.chr6 283172 47 + 647215 CCACATAGCCATTGACCTTTGAGAAGGCAGACTCCAACCTAGGGTGA - -a -s simMouse_chr6.simMouse.chr6 294380 7 + 636262 TGGTAGT -s Anc0.Anc0refChr8 4845 7 - 17196 TTGTAAT -s Anc1.Anc1refChr8 48417 7 - 57822 TTGTAAT -s Anc2.Anc2refChr5 2555 7 + 8386 TTGTGAT -s mr.mrrefChr5 145348 7 + 294540 TTGTAGT -s simCow_chr6.simCow.chr6 273798 7 + 602619 GTGTGAT -s simDog_chr6.simDog.chr6 262971 7 + 593897 TTGTGAT -s simHuman_chr6.simHuman.chr6 363095 7 - 601863 TTGCATT -s simRat_chr6.simRat.chr6 283219 7 + 647215 TTGTAGT - -a -s simMouse_chr6.simMouse.chr6 294387 17 + 636262 ATAACTAACAATATGAT -s Anc0.Anc0refChr8 4852 17 - 17196 CTCCCCAGCAATGTGAC -s Anc1.Anc1refChr8 48424 17 - 57822 CTCCCCAGCAATGTGAC -s Anc2.Anc2refChr5 2562 17 + 8386 CTCCCCTGCAATGTGAC -s mr.mrrefChr5 145355 17 + 294540 ATACCTAACAATGTGAC -s simCow_chr6.simCow.chr6 273805 17 + 602619 CTCCCCTGCAATGTGAC -s simDog_chr6.simDog.chr6 262978 17 + 593897 CTCCCCTGCAATGTGAG -s simHuman_chr6.simHuman.chr6 363105 17 - 601863 CCCCCCAGCAATGTGAC -s simRat_chr6.simRat.chr6 283226 17 + 647215 ATACCTAACAATGTGAC - -a -s simMouse_chr6.simMouse.chr6 294404 23 + 636262 TCTCTGTGCTAACATACTCTTAC -s Anc0.Anc0refChr8 4871 23 - 17196 TCTCTGTGCCAGCATGCCCTTAC -s Anc1.Anc1refChr8 48443 23 - 57822 TCTCTGTGCCAGCATGCCCTTAC -s Anc2.Anc2refChr5 2581 23 + 8386 TCTCTGTGTCAGCATGCCCTTGC -s mr.mrrefChr5 145372 23 + 294540 TCTCTGTGCTAGCATGCCCTTAC -s simCow_chr6.simCow.chr6 273824 21 + 602619 --CCTGAGTCAGCAGGCCCTTGC -s simDog_chr6.simDog.chr6 262997 23 + 593897 TCTCTGTGTCAGCATACCCTTGC -s simHuman_chr6.simHuman.chr6 363125 23 - 601863 TCAGCATGCCAGAATGCCCTTAC -s simRat_chr6.simRat.chr6 283243 23 + 647215 TCTCTGTGTTGGCATGCCCCTAC - -a -s simMouse_chr6.simMouse.chr6 294427 12 + 636262 ATAAGGCGCTGA -s Anc0.Anc0refChr8 4894 12 - 17196 AAAAGGTGCTGA -s Anc1.Anc1refChr8 48466 12 - 57822 AAAAGGTGCTGA -s Anc2.Anc2refChr5 2604 12 + 8386 TAAAGGTGCTGA -s mr.mrrefChr5 145395 12 + 294540 ATAAGGCGCTGA -s simCow_chr6.simCow.chr6 273845 8 + 602619 TAAAGCTG---- -s simDog_chr6.simDog.chr6 263020 12 + 593897 TAAAAGTGCTGA -s simHuman_chr6.simHuman.chr6 363151 12 - 601863 AGAAGGTGCTGA -s simRat_chr6.simRat.chr6 283266 12 + 647215 ATAAGGCGCTGA - -a -s simMouse_chr6.simMouse.chr6 294439 50 + 636262 ATGAGAGAAATATAGTGAAGAGTCATTGCCTTACGTCATTAAGTCCAAAA -s Anc0.Anc0refChr8 4906 48 - 17196 TAGAAAGGA--AGAGtcaagagtcattgccttaggtcattaagtccaaaa -s Anc1.Anc1refChr8 48478 48 - 57822 TAGAAAGGA--AGAGtcaagagtcattgccttaggtcattaagtccaaaa -s Anc2.Anc2refChr5 2616 48 + 8386 TAGAAAGGT--AGTGgcaagagtcattgccttagggcattgagtccaaaa -s mr.mrrefChr5 145407 50 + 294540 ATGAGAGAAATATAGTGAAGAGTCATTGCCTTACGTCATTAAGTCCAAAA -s simCow_chr6.simCow.chr6 273853 42 + 602619 -----AGGT--AGTAGCAAGAGTCAT-ACCCTGGGCTATTCAGTCCAAAA -s simDog_chr6.simDog.chr6 263036 47 + 593897 TAGAAGTGT--AGTGgcaagaggcattgccttagggcactg-gtccaaaa -s simHuman_chr6.simHuman.chr6 363163 48 - 601863 TGGAAAGGa--aaagtcaagagtcattgccttaggtcattacatccagaa -s simRat_chr6.simRat.chr6 283278 50 + 647215 ATGAGAGAAATAGAGCAAAGAGTCCTTGACTTATGTCATTTAGACCAAAA - -a -s simMouse_chr6.simMouse.chr6 294489 45 + 636262 TCATTAATACGGAAACAACTGACAACCTCCAGCTGAGCAATTTGA -s Anc0.Anc0refChr8 4963 45 - 17196 ttgttaatactgatacaattgacaagcgccagctgagcattataa -s Anc1.Anc1refChr8 48535 45 - 57822 ttgttaatactgatacaattgacaagcgccagctgagcatTATAA -s Anc2.Anc2refChr5 2673 45 + 8386 ttgttaatactgatacaattgacaagcgccagctgagcatcataa -s mr.mrrefChr5 145457 45 + 294540 TCGTTAATACGGAAACAACTGACAACCTCCAGCTGAGCATTTTGA -s simCow_chr6.simCow.chr6 273904 39 + 602619 ATCTTATTACTGATAAAACTGACAAGCACTAGCTGAGCA------ -s simDog_chr6.simDog.chr6 263092 43 + 593897 ttgttaatactgatacaattgataagcgcca--tgggcatcataa -s simHuman_chr6.simHuman.chr6 363220 40 - 601863 ctgctaatcc-----taattgacaggcgccaactgagcatTATAG -s simRat_chr6.simRat.chr6 283328 45 + 647215 TCGTTAATATGGATACAACTGACAACCTCCAGCTGAGCATTTTGA - -a -s simMouse_chr6.simMouse.chr6 294534 42 + 636262 TGCAAGAAAGTGAGAAGTACCATATCAATATGTTTTAAAAAC -s Anc0.Anc0refChr8 5008 34 - 17196 ttcaa-------acaagtacc-aatcaatatcaccaacctac -s Anc1.Anc1refChr8 48580 34 - 57822 ttcaa-------acaagtacc-aatcaatatcaccaacctac -s Anc2.Anc2refChr5 2718 34 + 8386 ttgaa-------acaagcacc-aagcggtatcaccaacctgc -s mr.mrrefChr5 145502 42 + 294540 TGCAAGAAAGTGAGAAGTACCATATCAATATGTTTTAACAAC -s simDog_chr6.simDog.chr6 263203 34 + 593897 ttgaa-------acaagcacc-aagcggtatcaccaacctgc -s simHuman_chr6.simHuman.chr6 363260 34 - 601863 ttcaa-------ataagtatc-catcaatatcaccaacctac -s simRat_chr6.simRat.chr6 283373 42 + 647215 TGCAAGAAAATGAGAGGTACGATATCAATATGTTGTAGCAAC - -a -s simMouse_chr6.simMouse.chr6 294576 41 + 636262 CATGGCAGTACATGCCACCTGGTTAGTGGATGCCAACTGGT -s Anc0.Anc0refChr8 5043 37 - 17196 catgaaaataaat-ccaac---ttagttgaaagcgactttt -s Anc1.Anc1refChr8 48615 37 - 57822 catgaaaataaat-ccaac---ttagttgaaagcgactttt -s Anc2.Anc2refChr5 2753 37 + 8386 catgacgagaaag-ctgac---ttcgttaaaagcgactttt -s mr.mrrefChr5 145544 41 + 294540 CATGGAAGTACATGCCAACTGGTTAGTGGATGCCAACTGGT -s simDog_chr6.simDog.chr6 263238 37 + 593897 catgacgagaaag-ctgac---ttcgttaaaagcgactttt -s simHuman_chr6.simHuman.chr6 363295 37 - 601863 catgcaaataaat-ccaac---ttagcagagatccactttt -s simRat_chr6.simRat.chr6 283415 41 + 647215 AATGGAAGGACATACTAACTCGTTAGTGGGTGCCAACTGGT - -a -s simMouse_chr6.simMouse.chr6 294617 32 + 636262 CTAGTGGATCCTCCAGCAAGTGTTAAATGATA -s Anc0.Anc0refChr8 5081 15 - 17196 ctatttttttgtccc----------------- -s Anc1.Anc1refChr8 48653 27 - 57822 ctatttttttgtcccac-----cctgatgtta -s Anc2.Anc2refChr5 2791 15 + 8386 ctatttttttgtccc----------------- -s mr.mrrefChr5 145585 32 + 294540 CTAGTGGATCCTCCAACAAGTGCTAAATGATA -s simDog_chr6.simDog.chr6 263276 15 + 593897 ctatttttttgtccc----------------- -s simHuman_chr6.simHuman.chr6 363333 27 - 601863 ctatttttctatcccac-----cctgatgtta -s simRat_chr6.simRat.chr6 283456 32 + 647215 GCCGTAGATCCTTCAACAAGTACAAAATGATA - -a -s simMouse_chr6.simMouse.chr6 294649 32 + 636262 CAATCTACACTTCCGGGCAAAGAATCCAACTT -s Anc1.Anc1refChr8 48680 29 - 57822 caacctaca---catgctaatgaatccaactt -s mr.mrrefChr5 145617 32 + 294540 CAATCTACACTTCATGGCAAAGAATCCAACTT -s simHuman_chr6.simHuman.chr6 363364 29 - 601863 caacctaca---catgctaatgaatccaactt -s simRat_chr6.simRat.chr6 283488 32 + 647215 CAATCTACACCGCATGTCAAAGAATCCTACTT - -a -s simMouse_chr6.simMouse.chr6 294681 14 + 636262 AAATGTTTGATCTC -s Anc1.Anc1refChr8 48709 14 - 57822 agaaattcactttc -s mr.mrrefChr5 145649 14 + 294540 AGATGTTTGATCTC -s simHuman_chr6.simHuman.chr6 363396 14 - 601863 agaaattcactttc -s simRat_chr6.simRat.chr6 283520 14 + 647215 AGATGTTGGATCTC - -a -s simMouse_chr6.simMouse.chr6 294695 18 + 636262 CTTTAACTTTCCATGACG -s Anc0.Anc0refChr8 5096 8 - 17196 ----------ccctgatg -s Anc1.Anc1refChr8 48723 18 - 57822 ttctgccccaccctgatg -s Anc2.Anc2refChr5 2806 8 + 8386 ----------ccctgatg -s mr.mrrefChr5 145663 18 + 294540 CTTTGACTTACCCTGACG -s simDog_chr6.simDog.chr6 263291 8 + 593897 ----------ccctgatg -s simHuman_chr6.simHuman.chr6 363417 18 - 601863 ttctgccccatcctgaag -s simRat_chr6.simRat.chr6 283534 18 + 647215 CTTTGACTTACACTGATG - -a -s simMouse_chr6.simMouse.chr6 294713 43 + 636262 TAACATTTAATATTATGCTAGCAAACCAGTTAGCCAGTTAGAT -s Anc0.Anc0refChr8 5104 30 - 17196 taacatttaat-gtaggcc----aaccaggtagc--------t -s Anc1.Anc1refChr8 48741 35 - 57822 taacatttaatagtaggccatcaaaccaggtagc--------t -s Anc2.Anc2refChr5 2814 30 + 8386 taatatttaat-gtaggcc----aacccagtagc--------c -s mr.mrrefChr5 145681 35 + 294540 TAAcatttaatattaggctagcaaaccagttagc--------t -s simDog_chr6.simDog.chr6 263299 30 + 593897 taatatttaat-gtaggcc----aacccagtagc--------c -s simHuman_chr6.simHuman.chr6 363436 35 - 601863 taacatttgttagtaggccatcaacataggttgc--------t -s simRat_chr6.simRat.chr6 283552 35 + 647215 TAAcatttaatattagaataacaaaccagttagc--------g - -a -s simMouse_chr6.simMouse.chr6 294756 74 + 636262 TATCTAACAGTGTGATTCTTTAAGGTGATGTAAATAGAAGTCGGTCTTATTCTGCTTAGACTACAATCTACTTA -s Anc0.Anc0refChr8 5134 53 - 17196 tctttaacagtgctattttataa-gtgatatagagagaag--ggtcccattct------------------tca -s Anc1.Anc1refChr8 48776 55 - 57822 tctttaacagtgctattttataa-gtgatatagagagaagttggtcccattct------------------tca -s Anc2.Anc2refChr5 2847 53 + 8386 tcttgaatggtgctactttataa-ataacatagagaggag--ggtcccattct------------------gca -s mr.mrrefChr5 145716 58 + 294540 tatttaacagtgtgattctttaaggtgatgtaaatagaagtcggtcttattctg----------------ctta -s simDog_chr6.simDog.chr6 263332 53 + 593897 tcttgaatggtgctactttataa-ataacatagagaggag--ggtcccattct------------------gca -s simHuman_chr6.simHuman.chr6 363471 55 - 601863 cgtttaacagtgacattttacaa-gtgatatggaaagacattggtcacactct------------------tca -s simRat_chr6.simRat.chr6 283587 58 + 647215 tatttaacagtgtgactctctaaggtgatgtaagtagtagtcagtcttatgctg----------------cttg - -a -s simMouse_chr6.simMouse.chr6 294830 8 + 636262 GACTACAA -s Anc0.Anc0refChr8 5187 8 - 17196 gactacaa -s Anc1.Anc1refChr8 48831 8 - 57822 gactacaa -s Anc2.Anc2refChr5 2900 8 + 8386 aacttaaa -s mr.mrrefChr5 145774 8 + 294540 gactacaa -s simDog_chr6.simDog.chr6 263393 8 + 593897 aacttaaa -s simHuman_chr6.simHuman.chr6 363526 8 - 601863 gactacaa -s simRat_chr6.simRat.chr6 283645 8 + 647215 gactgcaa - -a -s simMouse_chr6.simMouse.chr6 294838 146 + 636262 TCTATTGAAACTAAGAGAGTTGAAGGAGGCATTTCGCCAATTTGGAAAAAGCCTGTGTGTTGTACTGATTTCCAAAGCACGCCATAGGATAAAGTGATGGTTGTAACCAGGATCTGGTGGCCTAGAAAAGATGTCACGGGTGATTG -s Anc0.Anc0refChr8 5195 18 - 17196 tcgattgaaaatgaagga-------------------------------------------------------------------------------------------------------------------------------- -s Anc1.Anc1refChr8 48839 19 - 57822 tcgattgaaaatgaaggag------------------------------------------------------------------------------------------------------------------------------- -s Anc2.Anc2refChr5 2908 18 + 8386 tgggttgaaaatgaagga-------------------------------------------------------------------------------------------------------------------------------- -s mr.mrrefChr5 145782 145 + 294540 tctattgaaactgagggagttgaaggaggcatttcgccaatttggaaaaagc-tgtgtgttgtactgatttccaaaGCACGCCATAGGATAAAGTGATGGTTGTAACCAGGATCTGGTGGCCTAGAAAAGATGTCACGGGTGATTG -s simDog_chr6.simDog.chr6 263403 18 + 593897 tgggttgaaaatgaagga-------------------------------------------------------------------------------------------------------------------------------- -s simHuman_chr6.simHuman.chr6 363534 19 - 601863 tccattgaaattgaaggag------------------------------------------------------------------------------------------------------------------------------- -s simRat_chr6.simRat.chr6 283653 145 + 647215 tctattgaaactgagggagttgaagtagacatttcaccgatttggaacaagt-tgtgtgttgtgctgatttccaaaGCATGGCATACGACAAAGTGATGTAGGTAACCAGGATCTGGTGGCCTAGAAAAGACGACAAAGTTGATTA - -a -s simMouse_chr6.simMouse.chr6 294984 27 + 636262 TTGTGAATACAGCCTGACTTGTCCACT -s mr.mrrefChr5 145927 27 + 294540 TTGTGAATACAGCCTGACTTGTCCACT -s simRat_chr6.simRat.chr6 283803 27 + 647215 TCGTGAACCCAGCCTGAGTCGTTGGCT - -a -s simMouse_chr6.simMouse.chr6 295011 422 + 636262 TGCACCAAAATAGTGCCATTCAATAATGTCTCACAAAGCTtaaccactgacttgttctttttagatccacacaggctctttaacttgtgtacatccacacatgcttgttgattttgggtttaactgcagttgacttcggattcttcagcattgactttggcatcttcagcgtgtatgcttcttctgtgctaatgtctagaatggtgcttccaagattatcctgtaaacttttcctgctctttgggcgatgagaatctaaaactttattatactgaccttgtttcttcgaaactgcacctggtattaatggtattaggcattaagaaaggctcaagttttaacccttggcagattgataaccagttcctccaacatcacctacttattgagtagcgaatcgttggcccccttaaggcttcgct -s mr.mrrefChr5 145954 406 + 294540 TGCACCAAAATAGTGCCATTCAATAATGTCTCACAAAGCTtaaccactgacttgttctttttagatccacacaggctctttaacttgtgtacatccacacatgcttgttgattttgggtttaactgcagttgacttcggattcttcagcattgactttggcatcttcagcgtgtatgcttcttctgtgctaatgtctagaatggtgcttccaagattatcctgtaaacttttcctgctctttgggcgatgagaatctaaaactttattatactgaccttgtttcttcgaaactgcacctggtattaa----------------gaaaggctcaagttttaacccttggcagattgataaccagttcctccaacatcacctacttattgagtagcgaatcgttggcccccttaaggcttcgct -s simRat_chr6.simRat.chr6 283840 406 + 647215 TGCACCAAAATAGTTCTGTTCAATAATGTCTCATGAAGCTtagctactgactcgtattctttagatccacacgggctctttaacttgtgtaagtccacacatccttgttgattttgggttgaggtgcagttgactttggcatctccaacattgactttggagtcttcagcatgtacgcttcttctgtgcaaatacctagaatgatgttttcaagattatcctgtaaggttttcatgctctttgggggatgagaatttagaactttagtatactcacattgtttcttccaaactgcacctggtattaa----------------gaaaggcccaagttttaacccttggcggattgataaccagttcctcctacatcacctacttattgaatagtgaatccttggcccacttagggtttcact - -a -s simMouse_chr6.simMouse.chr6 295433 16 + 636262 acaaaacgtgatccag -s mr.mrrefChr5 146360 16 + 294540 acaaaacgtgatccag -s simRat_chr6.simRat.chr6 284247 16 + 647215 accaaatgtgacacag - -a -s simMouse_chr6.simMouse.chr6 295449 78 + 636262 tagtagatggatagttggacgatagaaccagccttagacagctccattttatttccacgtaaagtaatgattttcaga -s mr.mrrefChr5 146376 78 + 294540 tagtagatggatagttggacgatagaaccagccttagacagctccattttatttccacgtaaagtaatgattttcaga -s simRat_chr6.simRat.chr6 284264 78 + 647215 tagtaaatgggtagttggaggatagaaccaaccttagacggctccatttgatttctacataaagtaatgattttCAGA - -a -s simMouse_chr6.simMouse.chr6 295527 8 + 636262 taccagga -s mr.mrrefChr5 146454 8 + 294540 taccagga -s simRat_chr6.simRat.chr6 284776 8 + 647215 TACCAGGA - -a -s simMouse_chr6.simMouse.chr6 295535 114 + 636262 tactttcatcctagtgcacagcagtaaaaattgaaagcaggaagcatgatctggccgtcttgatttttttcatttagaatcaactttgacatgggccctcttttttgatttgtc -s mr.mrrefChr5 146462 100 + 294540 tactttc-------------gcagtaaaaattgaaagcaggaagcatgatctggccgtcttgatttttttcatttagaatcaactttgacatgggccctcttttt-gatttgtc -s simRat_chr6.simRat.chr6 284788 100 + 647215 TGCTTTT-------------gcagtaaagcttgacatgaagaagcatgatcctgccagctcaatttttttcatttagaatcaaatttgacacgggttcgctcttt-gatctgtc - -a -s simMouse_chr6.simMouse.chr6 295649 234 + 636262 accaacggtttttttacccaatggtttttttacaagcagtgaacaagcagggccatcgttgtcttgataggatgtcctgttaaatcaaatctgtataggagcttgtgtaagactaggtttctcagattcaaaatgttcacctgccaacccaagaagatttaataatcttgacattaatattggtttcccctattaaaatttcaagaaaaggtttgcaaatcctagtaggctctt -s mr.mrrefChr5 146562 201 + 294540 accaacggtttttttacccaatggtttttttacaagcagtgaacaagcagggccatcgttgtcttgataggatgtcct-----atcaaatctgta-------------aagactaggtttctcagattcaaaatgttcacct-----------aagatttaataat-ttgacattaatattggtttcccctattaa--tttcaagaaaaggtt-gcaaatcctagtaggctctt -s simRat_chr6.simRat.chr6 284889 201 + 647215 aaaaacggtttttttacccagtggtttttttacaagcagtgaacaagctgggccatcactgtcttgataggatgtcct-----atcaaatctgaa-------------aggactagatttctcagattcaaaacattcacct-----------aagatttgataat-ttggcatgaatattggtttcccctattaa--tttttagaaagggtt-gcaaatcctagtaggatcct - -a -s simMouse_chr6.simMouse.chr6 295883 15 + 636262 tgatgtcttgtacaa -s mr.mrrefChr5 146763 15 + 294540 tgatgtcttgtacaa -s simRat_chr6.simRat.chr6 285103 15 + 647215 tgatgtcttgtacaa - -a -s simMouse_chr6.simMouse.chr6 295898 6 + 636262 ttcact -s mr.mrrefChr5 146778 6 + 294540 ttcact -s simRat_chr6.simRat.chr6 285138 6 + 647215 ttcact - -a -s simMouse_chr6.simMouse.chr6 295904 11 + 636262 tgggttaatca -s mr.mrrefChr5 146784 11 + 294540 tgggttaatca -s simRat_chr6.simRat.chr6 285145 11 + 647215 cgggtcagtca - -a -s simMouse_chr6.simMouse.chr6 295915 19 + 636262 tcgagggcaattcactcat -s mr.mrrefChr5 146795 19 + 294540 tcgagggcaattcactcat -s simRat_chr6.simRat.chr6 285195 19 + 647215 ttgaaggccattcactcac - -a -s simMouse_chr6.simMouse.chr6 295934 104 + 636262 gctgtaaactacctgttggttattcttgtatatagaagtatgtgacttgggcacattaactttatcactggcaacttcactcagagtactagtagtttgagaag -s mr.mrrefChr5 146814 104 + 294540 gctgtaaactacctgttggttattcttgtatatagaagtatgtgacttgggcacattaactttatcactggcaacttcactcagagtactagtagtttgagaag -s simRat_chr6.simRat.chr6 285217 104 + 647215 actgtgaactgtctgttggatattcttgtatataaatgtatgtgactcgagcacattgactttatcaccagaaacatcactcagagtactagtagttctagaag - -a -s simMouse_chr6.simMouse.chr6 296038 98 + 636262 gttactgctcaacagtgtaggccttccttagtatacaatcatggaacctgcaaatacagaaagcataaccctctcctcgcccaattggcacactgcac -s mr.mrrefChr5 146918 95 + 294540 gttactgctcaacagtgtaggccttccttagtatacaatcatggaacctgcaaatacagaaagcataaccctctcctcgcccaat---cacactgcac -s simRat_chr6.simRat.chr6 285376 95 + 647215 gttactggtcaacagtgtcagcctccctaagtatacaaccatgtcatctgcaaatacagaaagtataaccttcacctcacccaat---cacacagccc - -a -s simMouse_chr6.simMouse.chr6 296136 331 + 636262 tcatctctcccctggcaatttttcatagtaatagctttagatcatagtgaacaaaagtggagaaatagaacagcccagctggtcatagtgagaatgttcatcaatttattataagtccccctgataatgttgaggtaattgtcctgtggctctggctgattgagaatggtcaacatgtaatcatttttgatttgcttaatcagttggacatatctaggaatggatatcatcatatgcttgttctgattgctgcggtttttgggttgtatcacatttataggcctgcgtgattttagctaacccagctctccagttgtgaaccaaacgattg -s mr.mrrefChr5 147013 210 + 294540 tcatctctcccctggca-------------------------------------------------------------------------------------------------------------------------ttgtcctgtggctctggctgattgagaatggtcaacatgtaatcatttttgatttgcttaatcagttggacatatctaggaatggatatcatcatatgcttgttctgattgctgcggtttttgggttgtatcacatttataggcctgcgtgattttagctaacccagctctccagttgtgaaccaaacgattg -s simRat_chr6.simRat.chr6 285475 210 + 647215 tcatctttcccctggca-------------------------------------------------------------------------------------------------------------------------ttgccctgcggttctggctgattgagaatgatcagcatgtaatcattgttgatttgcttaattagttggacatatctatgaatggatataatcatatggttgttctgatcgctacagtttttgagttgtatcacagttacaggcttgcgtgattttggctaccccagcactccagttgtggacaagacaatca - -a -s simMouse_chr6.simMouse.chr6 296467 15 + 636262 GTACCTAGTGCAGGG -s mr.mrrefChr5 147223 15 + 294540 gtacctagtgcaggg -s simRat_chr6.simRat.chr6 285981 15 + 647215 gtacttagttcaggg - -a -s simMouse_chr6.simMouse.chr6 296482 163 + 636262 GGACAAGAACATAGCAAATACATTGGATCagaaagtagcaaatatattggatcccaactagcttggaatccacagtgcgaggccgatgatgtttttgctttgtgatgatttaaacatcagctgggttggtggttatcaccccatttttcaaacctatataatt -s mr.mrrefChr5 147238 129 + 294540 ggacaagaacatagcaaatacattg----------------------------------agcttggaatccacagtgcgaggccgatgatgtttttgctttgtgatgatttaaacatcagctgggttggtggttatcaccccatttttcaaacctatataatt -s simRat_chr6.simRat.chr6 285997 129 + 647215 ggacaagataaaagcagataggttg----------------------------------agcttggaattcatagtttgatgccattgatgattttactctgtgatggtttacatgtcagctgggttggaagttatcaccccacttttcaagcctatatgatt - -a -s simMouse_chr6.simMouse.chr6 296645 151 + 636262 gtcactgttagcaaaggtctatctgttttgttaatttagtcaaaagacccgggctttcgactcgttgaccttactcaaagtctccagcattttagtgctctttaaattaaattttatcgtggccattttatgctatctgccctttaatgcg -s mr.mrrefChr5 147367 151 + 294540 gtcactgttagcaaaggtctatctgttttgttaatttagtcaaaagacccgggctttcgactcgttgaccttactcaaagtctccagcattttagtgctctttaaattaaattttatcgtggccattttatgctatctgccctttaatgcg -s simRat_chr6.simRat.chr6 286148 151 + 647215 gtcactgttagcaaaggcctatccattttgttagtttagtcacaaagccagggttttggactcattgaccttactccaggtctcccgcattctagtgccctttaaatcaaattttatcttagccattttctgctagctgctcataaaggta - -a -s simMouse_chr6.simMouse.chr6 296796 279 + 636262 aaactcctcagttctttcagtctgaacttctaaagtactatgtgtaatatccctcatcccgtctgcccggcatcacacaactgttccaacaccccccttaatccagtactaaatagctcccagatgttctgatatgtggggggttgtggttctcattacctttaagagacatcctgatctctggcttaatttcattatgaagccaatcttcTTAatattcttttttttccgctccgtattgtggttactcctgaaattggccccactatagtgagcaag -s mr.mrrefChr5 147518 266 + 294540 aaactcctcagttctttcagtctgaacttcta---tactatgtgtaatatccctcatcccgtctgcccggcatcacacaactgttccaacacccccct-aatccagtactaaatagctcccagatgttctgatatgtggggggttgtggttctcattacctttaagagacatcctgatctctggcttaatttcattatgaagc--------ttaatattcttttttttccgctccgtattgtggttactc-tgaaattggccccactatagtgagcaag -s simRat_chr6.simRat.chr6 286300 266 + 647215 aaactccgaagttctttccatcagaactacca---taccatgtgtaatgtccctcatcccttccgcatggcatcgcacaactgttctaacacccctcc-gatccagttctaaagagctcccagatgttctgatatgtgggcagtcgtggttctcattactctcaaaggacatcttgatctctggctaaatctcaGTATAAggc--------ttaatttccttttttttctgctctgtatcgtgcttactc-taccattggccccagggtagtgagcaag - -a -s simMouse_chr6.simMouse.chr6 297075 23 + 636262 catctacaaggagaaatgttcag -s mr.mrrefChr5 147784 23 + 294540 catctacaaggagaaatgttcag -s simRat_chr6.simRat.chr6 286570 23 + 647215 catctacaagtataaatgttcag - -a -s simMouse_chr6.simMouse.chr6 297098 65 + 636262 ttatcattgctaactgtttgttggaccatagtgaaataatcagcttaggtctggaacacaggtca -s mr.mrrefChr5 147807 65 + 294540 ttatcattgctaactgtttgttggaccatagtgaaataatcagcttaggtctggaacacaggtca -s simRat_chr6.simRat.chr6 286594 65 + 647215 ttatcatcaccaactgtatgctggaccagagtgaaataatcagcttaggtccggaaaggaggtca - -a -s simMouse_chr6.simMouse.chr6 297163 244 + 636262 ctgatagaaatcagggcaggacacttaccccgaataacctcacactgatggCTCTCCTAcagcctgaattggatgcaaagtctcgtgaatattaatctagtcaagtggacttggtcagaaggtgagttcaatcattgggtgttctcattCATGTTGTAGGTGGTGTACACCTGTCACATACTACCAGGTCTCATGCCTGTTGTTGCATGTTGGACTAACTTATCCAGAATTGTAACAGAATTAC -s mr.mrrefChr5 147872 235 + 294540 ctgatagaaatcagg-caggacacttaccccgaataacctcacactgatggctctcctacagcctgaattggatgcaaagtctcgtgaatattaatctagtcaagtggacttggtcagaaggtgagttcaatcattgggtgttctcattCATGT-GTAGGTGGTGTACACCTGTCACATACTACCAGGTCTCATGCCTGTTGTTGCA-------CTAACTTATCCAGAATTGTAACAGAATTAC -s simRat_chr6.simRat.chr6 286660 235 + 647215 cagctagaaaccagg-cagggcacttacgcagaataacctcgcgccagtagctctcctacaatcagcattggacgcaaagtctggtaaatattaacctagtcaagtggacttggtggggaagtcagtatgatcattgggtgttctcattTATGT-ATAGGTGGCGTACATCTGTCACACACTACTAGGTCTCATGCCAGTTGTCGCG-------CTACCTTATCCAGAGTTGTAACATAATTGC - -a -s simMouse_chr6.simMouse.chr6 297407 58 + 636262 AAAGAAAACCAGGATGCCAGTCATTACTTGACCATGAGTGCACCCATTGTCTCCAACT -s Anc0.Anc0refChr8 5213 6 - 17196 ----------------------------------------------------actact -s Anc1.Anc1refChr8 48858 7 - 57822 ---------------------------------------------------tactact -s Anc2.Anc2refChr5 2926 6 + 8386 ----------------------------------------------------actact -s mr.mrrefChr5 148107 58 + 294540 aaagaaaaccaggatgccagtcattacttgaccatgagtgcacccattgtctccaact -s simDog_chr6.simDog.chr6 263421 6 + 593897 ----------------------------------------------------actact -s simHuman_chr6.simHuman.chr6 363553 7 - 601863 ---------------------------------------------------tactact -s simRat_chr6.simRat.chr6 288277 58 + 647215 atagagaaccagtgggccagtcatcgcttgattgggagtggactgatcatctcaaact - -a -s simMouse_chr6.simMouse.chr6 297465 5 + 636262 TACAG -s Anc0.Anc0refChr8 5219 5 - 17196 tacag -s Anc1.Anc1refChr8 48865 5 - 57822 tacag -s Anc2.Anc2refChr5 2932 5 + 8386 tgctg -s mr.mrrefChr5 148165 5 + 294540 tacag -s simDog_chr6.simDog.chr6 263445 5 + 593897 tgctg -s simHuman_chr6.simHuman.chr6 363560 5 - 601863 tacag -s simRat_chr6.simRat.chr6 288335 5 + 647215 tacaa - -a -s simMouse_chr6.simMouse.chr6 297470 47 + 636262 CCATACATACATCAATGATAATCAAATTACATTCTTAGGAACAGTGT -s Anc1.Anc1refChr8 49350 39 - 57822 ctgtactt-------tctaa-taaaattatattcctaggaacattgc -s mr.mrrefChr5 148170 39 + 294540 ccatacat-------tgata-tcaaattacattcttaggaacaGTGT -s simHuman_chr6.simHuman.chr6 364327 39 - 601863 ctgtactt-------tctaa-taaaattatattcctaggaacattgc -s simRat_chr6.simRat.chr6 288340 39 + 647215 ccatacat-------tgcta-tcaaattaaataactaggaaccATAC - -a -s simMouse_chr6.simMouse.chr6 297517 8 + 636262 AAGAGTTA -s Anc1.Anc1refChr8 49389 8 - 57822 aagatcta -s mr.mrrefChr5 148209 8 + 294540 AAGAGTTA -s simHuman_chr6.simHuman.chr6 364382 8 - 601863 aagatcta -s simRat_chr6.simRat.chr6 288379 8 + 647215 AAGGCCTA - -a -s simMouse_chr6.simMouse.chr6 297525 1 + 636262 T -s Anc1.Anc1refChr8 49397 1 - 57822 g -s mr.mrrefChr5 148217 1 + 294540 T -s simHuman_chr6.simHuman.chr6 364392 1 - 601863 g -s simRat_chr6.simRat.chr6 288387 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 297526 136 + 636262 ACTTAAGTATGTGGTCCACCTGCTAAAATTAAAGATGGAAGCTACTTAAGAATCAGACAAATGTTTTATGGGTTGTCAGACTTAGTTGGAAAGACATGAAAGTACAAATTTACAACATACATCTAGCCTTAACAGG -s Anc1.Anc1refChr8 49398 121 - 57822 actagaatacacaatccacctactaaatt----aatggtagctagataataaactgacgaatattaaatg-----------ttaatgggaaaaacaagaaaatgccagtttacgcaaaaaaaacagctctaacaaa -s mr.mrrefChr5 148218 136 + 294540 ACTTAAGTATGTGGTCCACCTGCTAAAATTAAAGATGGAAGCTACTTAAGAATCAGACAAATGTTTTATGGGTTGTCAGACTTAGTTGGAAAGACATGAAAGTACAAATTTACAACATACATCTAGCCTTAACAGG -s simHuman_chr6.simHuman.chr6 364393 121 - 601863 actagaatacacaatccacctactaaatt----aatggtagctagataataaactgacgaatattaaatg-----------ttaatgggaaaaacaagaaaatgccagtttacgcaaaaaaaacagctctaacaaa -s simRat_chr6.simRat.chr6 288390 136 + 647215 ACTTAAGTACACAGTCCACCTGCTAAAATTAAAGATGGTAGCTACTTAAGAATCAAACACATGTTTTATAGGTTGTCAGACTTAGTTGGAAAGACATGAAAGTACTAATTTACACCAAACATCCAGCTATAACAGG - -a -s simMouse_chr6.simMouse.chr6 297662 32 + 636262 TAGATGAGAAGCCATCTGAGTCCGAACAGTTG -s Anc0.Anc0refChr8 5704 23 - 17196 ---------ttccttctgagtcagaaaatttg -s Anc1.Anc1refChr8 49519 32 - 57822 taggtgagattccttctgagtcagaaaatttg -s Anc2.Anc2refChr5 3417 23 + 8386 ---------ttccttgtgactcagaaagttca -s mr.mrrefChr5 148354 32 + 294540 TAGATGAGAAGCCATCTGAGTCCGAACAGTTG -s simDog_chr6.simDog.chr6 264026 23 + 593897 ---------TTCCTTGTgactcagaaagttca -s simHuman_chr6.simHuman.chr6 364623 32 - 601863 taggtgagatcctttcggagtcagaaaaattg -s simRat_chr6.simRat.chr6 288526 32 + 647215 TAGGTGAGAACCTGCCTGAGTCTGAAAAGTTG - -a -s simMouse_chr6.simMouse.chr6 297694 23 + 636262 GACAGTACTACTCCACCTAATTC -s Anc0.Anc0refChr8 5731 15 - 17196 gatggtattacaca--------t -s Anc1.Anc1refChr8 49555 23 - 57822 gatggtattacacaaccagattt -s Anc2.Anc2refChr5 3444 15 + 8386 aatggtattacaca--------t -s mr.mrrefChr5 148386 23 + 294540 GACAGTACTACTCCACCTAATTC -s simDog_chr6.simDog.chr6 264053 15 + 593897 aatggtattacaca--------t -s simHuman_chr6.simHuman.chr6 364659 23 - 601863 gatggtgttacactaccagatta -s simRat_chr6.simRat.chr6 288558 23 + 647215 GATGGTAATACACTACATAATTC - -a -s simMouse_chr6.simMouse.chr6 297717 1 + 636262 T -s Anc0.Anc0refChr8 5746 1 - 17196 t -s Anc1.Anc1refChr8 49578 1 - 57822 t -s Anc2.Anc2refChr5 3459 1 + 8386 t -s mr.mrrefChr5 148409 1 + 294540 T -s simDog_chr6.simDog.chr6 264068 1 + 593897 t -s simHuman_chr6.simHuman.chr6 364682 1 - 601863 t -s simRat_chr6.simRat.chr6 288587 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 297718 28 + 636262 TAGTACTAGAAGATAAGAAACATCAACA -s Anc0.Anc0refChr8 5784 28 - 17196 tagtaccagaagatcagaaacatggacc -s Anc1.Anc1refChr8 49616 28 - 57822 tagtaccagaagatcagaaacatggacc -s Anc2.Anc2refChr5 3497 28 + 8386 tagtaccaaaagaccagaaacatggacc -s mr.mrrefChr5 148410 28 + 294540 TAGTACTAGAAGATAAGAAACATCAACA -s simDog_chr6.simDog.chr6 264106 28 + 593897 tagtaccaaaagaccagaaacatggacc -s simHuman_chr6.simHuman.chr6 364720 28 - 601863 taggaccagaaggtccgaaccatagacc -s simRat_chr6.simRat.chr6 288588 28 + 647215 TAGTATAGCAAGATCAGAAACATAAATA - -a -s simMouse_chr6.simMouse.chr6 297746 6 + 636262 ATACCA -s Anc0.Anc0refChr8 5812 6 - 17196 agacaa -s Anc1.Anc1refChr8 49644 6 - 57822 agacaa -s Anc2.Anc2refChr5 3525 6 + 8386 tggcaa -s mr.mrrefChr5 148438 6 + 294540 ATACCA -s simDog_chr6.simDog.chr6 264135 6 + 593897 tggcaa -s simHuman_chr6.simHuman.chr6 364748 6 - 601863 agacaa -s simRat_chr6.simRat.chr6 288616 6 + 647215 ATACCA - -a -s simMouse_chr6.simMouse.chr6 297752 48 + 636262 GAATTTATTGAGAATAAGGTTTATCCCACAAAGAGTTTATCCCACAAT -s Anc0.Anc0refChr8 5824 31 - 17196 gaatttgttaaaaatgatgtttatccc-cat----------------t -s Anc1.Anc1refChr8 49656 32 - 57822 gaatttgttaaaaatgatgtttatccctcat----------------t -s Anc2.Anc2refChr5 3537 31 + 8386 gaatttgttaaaaatgatgtttgtccc-cat----------------t -s mr.mrrefChr5 148444 32 + 294540 GAATTTATTGAGAATAAGGTTTATCCCACAA----------------T -s simDog_chr6.simDog.chr6 264147 31 + 593897 gaatttgttaaaaatgatgtttgtccc-cat----------------t -s simHuman_chr6.simHuman.chr6 364774 32 - 601863 gaatttgtcaaaaatggtatttatccctcat----------------t -s simRat_chr6.simRat.chr6 288622 32 + 647215 AAATTTGTCAAGAGTAAGATTTATCCCACAA----------------T - -a -s simMouse_chr6.simMouse.chr6 297800 30 + 636262 GAAGCCAAACAGAAGGGCACTACATATTAG -s Anc1.Anc1refChr8 49799 26 - 57822 agagttaatcgaaggaacaccaaata---- -s mr.mrrefChr5 148476 30 + 294540 GAAGCCAAACAGAAGGGCACTACATATTAG -s simHuman_chr6.simHuman.chr6 365031 26 - 601863 agagttaatcgaaggaacaccaaata---- -s simRat_chr6.simRat.chr6 288654 30 + 647215 GACGCCAAACAGAAGGCAGCTACATATTAG - -a -s simMouse_chr6.simMouse.chr6 297830 13 + 636262 AACAGAAATAATA -s Anc1.Anc1refChr8 49825 12 - 57822 aattgagttaa-a -s mr.mrrefChr5 148506 13 + 294540 AACAGAAATAATA -s simHuman_chr6.simHuman.chr6 365139 12 - 601863 aattgagttaa-a -s simRat_chr6.simRat.chr6 288684 13 + 647215 AATAGAAAAAATA - -a -s simMouse_chr6.simMouse.chr6 297843 64 + 636262 AATGGAGGCCAAGAAGGCATAAGACTCCAAAAATCTGCCTCCACAGTCAACAAGGAGCTTAGGA -s Anc1.Anc1refChr8 49837 54 - 57822 aatggaggttgaaagggca----------aaagccagccactacggcctatcataagcctagaa -s mr.mrrefChr5 148519 64 + 294540 AATGGAGGCCAAGAAGGCATAAGACTCCAAAAATCTGCCTCCACAGTCAACAAGGAGCTTAGGA -s simHuman_chr6.simHuman.chr6 365151 54 - 601863 aatggaggttgaaagggca----------aaagccagccactacggcctatcataagcctagaa -s simRat_chr6.simRat.chr6 288699 64 + 647215 AGTGGAGGCCAAGAAGGCATAAGACTCCAGAAATCAGCCTCCACAGTCAACGAGGAGCTTAGGA - -a -s simMouse_chr6.simMouse.chr6 297907 12 + 636262 GTTAGGTCAAAA -s Anc0.Anc0refChr8 5965 12 - 17196 gttgggacaagg -s Anc1.Anc1refChr8 49891 12 - 57822 gttgggacaagg -s Anc2.Anc2refChr8 1 12 - 12804 attgggacaggg -s mr.mrrefChr5 148583 12 + 294540 GTTAGGTCAAAA -s simCow_chr6.simCow.chr6 310551 12 - 602619 attgggacaaga -s simDog_chr6.simDog.chr6 264291 12 + 593897 attgggacaggg -s simHuman_chr6.simHuman.chr6 365205 12 - 601863 gttgtgacaagg -s simRat_chr6.simRat.chr6 288763 12 + 647215 GTTACATCCAAG - -a -s simMouse_chr6.simMouse.chr6 297919 27 + 636262 CCAGCTGTTCACTCCTAAGAGGATTAG -s Anc0.Anc0refChr8 5983 27 - 17196 ccacctattcacccacaagaggattag -s Anc1.Anc1refChr8 49909 27 - 57822 ccacctattcacccacaagaggattag -s Anc2.Anc2refChr8 19 27 - 12804 ccacctattcacccactaaaggatgag -s mr.mrrefChr5 148595 27 + 294540 CCAGCTGTTCACTCCTAAGAGGATTAG -s simCow_chr6.simCow.chr6 310572 27 - 602619 ccagctatccatccacaagaggatgag -s simDog_chr6.simDog.chr6 264309 27 + 593897 ccacctattcacccactaaaggatgag -s simHuman_chr6.simHuman.chr6 365223 27 - 601863 ccacctattcatctgcaagaggactag -s simRat_chr6.simRat.chr6 288775 27 + 647215 CCAGTTGTCCACTCCTTAGAGGGTTAG - -a -s simMouse_chr6.simMouse.chr6 297946 4 + 636262 TCAC -s Anc0.Anc0refChr8 6010 3 - 17196 tca- -s Anc1.Anc1refChr8 49936 4 - 57822 tcac -s Anc2.Anc2refChr8 46 3 - 12804 gta- -s mr.mrrefChr5 148622 4 + 294540 TCAC -s simCow_chr6.simCow.chr6 310599 3 - 602619 tta- -s simDog_chr6.simDog.chr6 264336 3 + 593897 gta- -s simHuman_chr6.simHuman.chr6 365250 4 - 601863 tcac -s simRat_chr6.simRat.chr6 288804 4 + 647215 TCAC - -a -s simMouse_chr6.simMouse.chr6 297950 42 + 636262 CCAAGTCACCTAGGTCTATGATGCACCCTTGCACACATACCA -s Anc0.Anc0refChr8 6013 32 - 17196 cca---------gttccacaatggactcccacagatacacc- -s Anc1.Anc1refChr8 49940 33 - 57822 cca---------gttccacaatggactcccacagatacaccg -s Anc2.Anc2refChr8 49 32 - 12804 cca---------gttccacaacggactcccacagatacacc- -s mr.mrrefChr5 148626 42 + 294540 CCAAGTCACCTAGGTCTATGATGCACCCTTGCACACATACCA -s simCow_chr6.simCow.chr6 310602 32 - 602619 cat---------gtttcacaatggactcgcacagatattcc- -s simDog_chr6.simDog.chr6 264340 32 + 593897 cca---------gttccacaacggactcccacagatacacc- -s simHuman_chr6.simHuman.chr6 365254 33 - 601863 cca---------gttccaccatggactcacacagatacactg -s simRat_chr6.simRat.chr6 288808 42 + 647215 TCAAGTCACCTAGCTCTATGATGCACTCTTGTAGATAGAGCA - -a -s simMouse_chr6.simMouse.chr6 297992 17 + 636262 CAAGACGGCCAAAGATA -s Anc0.Anc0refChr8 6045 17 - 17196 agagaccaccgatgtaa -s Anc1.Anc1refChr8 49973 17 - 57822 agagaccaccgatgtaa -s Anc2.Anc2refChr8 81 17 - 12804 agagaccaccgatgtaa -s mr.mrrefChr5 148668 17 + 294540 CAAGACGGCCAAAGATA -s simCow_chr6.simCow.chr6 310635 17 - 602619 agaggcaaccaacaaaa -s simDog_chr6.simDog.chr6 264372 17 + 593897 agagaccaccgatgtaa -s simHuman_chr6.simHuman.chr6 365287 8 - 601863 agagagaa--------- -s simRat_chr6.simRat.chr6 288850 17 + 647215 CAAGACAGCCAAAGATG - -a -s simMouse_chr6.simMouse.chr6 298009 33 + 636262 GAAATAAAGTCTAAGCAAGAGGCATGAACAAAA -s Anc0.Anc0refChr8 6062 28 - 17196 cacaca----caagacaagttgga-gataagaa -s Anc1.Anc1refChr8 49990 28 - 57822 cacaca----caagacaagttgga-gataagaa -s Anc2.Anc2refChr8 98 28 - 12804 cacaca----caagacaagttgga-gataagaa -s mr.mrrefChr5 148685 29 + 294540 GAAATA----CTAAGCAAGAGGCATGAACAAAA -s simCow_chr6.simCow.chr6 310654 28 - 602619 cacaca----aaagacaagcaaga-ggcatgaa -s simDog_chr6.simDog.chr6 264389 28 + 593897 cacaca----caagacaagttgga-gataagaa -s simRat_chr6.simRat.chr6 288867 29 + 647215 GAAATA----CTAAACAAGAGGTATGAACAACA - -a -s simMouse_chr6.simMouse.chr6 298042 2 + 636262 CT -s Anc0.Anc0refChr8 6090 2 - 17196 tg -s Anc1.Anc1refChr8 50018 2 - 57822 tg -s Anc2.Anc2refChr8 126 2 - 12804 tg -s mr.mrrefChr5 148714 2 + 294540 CT -s simCow_chr6.simCow.chr6 310682 2 - 602619 ta -s simDog_chr6.simDog.chr6 264417 2 + 593897 tg -s simRat_chr6.simRat.chr6 288899 2 + 647215 CT - -a -s simMouse_chr6.simMouse.chr6 298044 12 + 636262 GCTACAAAGGCA -s Anc0.Anc0refChr8 6092 12 - 17196 gttgccagggaa -s Anc1.Anc1refChr8 50020 12 - 57822 gttgccagggaa -s Anc2.Anc2refChr8 128 12 - 12804 gttgccagggaa -s mr.mrrefChr5 148716 12 + 294540 GCTACAAAGGCA -s simCow_chr6.simCow.chr6 310689 12 - 602619 gctgctatggat -s simDog_chr6.simDog.chr6 264419 12 + 593897 gttgccagggaa -s simRat_chr6.simRat.chr6 288901 12 + 647215 GCTATATGGGCT - -a -s simMouse_chr6.simMouse.chr6 298056 17 + 636262 AAGATGTCCATGCCTCA -s Anc0.Anc0refChr8 6104 17 - 17196 gagatgtcaatgtctca -s Anc1.Anc1refChr8 50032 17 - 57822 gagatgtcaatgtctca -s Anc2.Anc2refChr8 159 17 - 12804 gagatgtcaatgtctca -s mr.mrrefChr5 148728 17 + 294540 AAGATGTCCATGCCTCA -s simCow_chr6.simCow.chr6 310720 17 - 602619 aagatgtccatgtttca -s simDog_chr6.simDog.chr6 264450 17 + 593897 gagatgtcaatgtctca -s simRat_chr6.simRat.chr6 288913 17 + 647215 AAGATGTCTGTGCCTCA - -a -s simMouse_chr6.simMouse.chr6 298073 3 + 636262 GAG -s Anc0.Anc0refChr8 6121 3 - 17196 gga -s Anc1.Anc1refChr8 50049 3 - 57822 gga -s Anc2.Anc2refChr8 176 3 - 12804 gga -s mr.mrrefChr5 148745 3 + 294540 GAG -s simCow_chr6.simCow.chr6 310738 3 - 602619 aga -s simDog_chr6.simDog.chr6 264467 3 + 593897 gga -s simRat_chr6.simRat.chr6 288930 3 + 647215 GAG - -a -s simMouse_chr6.simMouse.chr6 298076 43 + 636262 CTAAAACAGCATACATTTCCCTTCTTTATTTCAATAAGTTGAT -s Anc0.Anc0refChr8 6124 42 - 17196 ctagaagagtgcactttctcatcccccaagttaataagt-gat -s Anc1.Anc1refChr8 50052 42 - 57822 ctagaagagtgcactttctcatcccccaagttaataagt-gat -s Anc2.Anc2refChr8 184 42 - 12804 ctagaagagtgcactttctcatcccccaagttaataagt-gat -s mr.mrrefChr5 148748 43 + 294540 CTAAAACAGCATACATTTCCCTTCTTTATTTCAATAAGTTGAT -s simCow_chr6.simCow.chr6 310746 42 - 602619 cttgaactgtgtattttcttcacccccatttaaataagt-gag -s simDog_chr6.simDog.chr6 264475 42 + 593897 ctagaagagtgcactttctcatcccccaagttaaTAAGT-GAT -s simRat_chr6.simRat.chr6 288933 43 + 647215 CTAGAACAGGATACATTTTCCTTCCTTGTTTCAATAAGTTGAT - -a -s simMouse_chr6.simMouse.chr6 298119 12 + 636262 ATCTCCTCAACT -s Anc0.Anc0refChr8 6166 12 - 17196 atctccttacct -s Anc1.Anc1refChr8 50094 12 - 57822 atctccttacct -s Anc2.Anc2refChr8 231 12 - 12804 atctccttacct -s mr.mrrefChr5 148791 12 + 294540 ATCTCCTCAACT -s simCow_chr6.simCow.chr6 310793 12 - 602619 gcccccttacct -s simDog_chr6.simDog.chr6 264522 12 + 593897 ATCTCCTTACCT -s simRat_chr6.simRat.chr6 288976 12 + 647215 ATCTCCTTAACT - -a -s simMouse_chr6.simMouse.chr6 298131 3 + 636262 AAC -s Anc0.Anc0refChr8 6178 2 - 17196 AG- -s Anc1.Anc1refChr8 50106 2 - 57822 AG- -s Anc2.Anc2refChr8 243 2 - 12804 AG- -s mr.mrrefChr5 148803 3 + 294540 AAC -s simCow_chr6.simCow.chr6 310808 2 - 602619 AG- -s simDog_chr6.simDog.chr6 264534 2 + 593897 AG- -s simRat_chr6.simRat.chr6 288988 3 + 647215 AAA - -a -s simMouse_chr6.simMouse.chr6 298134 59 + 636262 CAGGAGGTCCTTATGGCTAGCAAGACTCTATAGTAGTGTTGACACATAAAGAGCCAGCT -s Anc0.Anc0refChr8 6180 9 - 17196 --------------------------------------------------GAGCAGACT -s Anc1.Anc1refChr8 50108 9 - 57822 --------------------------------------------------GAGCAGACT -s Anc2.Anc2refChr8 245 9 - 12804 --------------------------------------------------GAGCAGACT -s mr.mrrefChr5 148806 36 + 294540 CAGGAGGTCCTTATGGCTA-----------------------CACATAAAGAGCCAGCT -s simCow_chr6.simCow.chr6 310810 9 - 602619 --------------------------------------------------GAGGGGTCT -s simDog_chr6.simDog.chr6 264536 9 + 593897 --------------------------------------------------GAGCAGACT -s simRat_chr6.simRat.chr6 288992 36 + 647215 CAAGAGGCCCTTATGTCTA-----------------------CACGTAAAGAGCCAACT - -a -s simMouse_chr6.simMouse.chr6 298193 5 + 636262 CATAC -s Anc0.Anc0refChr8 6189 5 - 17196 TGTAA -s Anc1.Anc1refChr8 50117 5 - 57822 TGTAA -s Anc2.Anc2refChr8 254 5 - 12804 TGTAA -s mr.mrrefChr5 148842 5 + 294540 CATAC -s simCow_chr6.simCow.chr6 310822 5 - 602619 TGTAA -s simDog_chr6.simDog.chr6 264545 5 + 593897 TGTAA -s simRat_chr6.simRat.chr6 289028 5 + 647215 CATAC - -a -s simMouse_chr6.simMouse.chr6 298198 33 + 636262 TTCAGAACTTGGAGTGAAATGCATACTCATTTA -s Anc0.Anc0refChr8 6194 32 - 17196 TTAATAACTTGAAACGAAATGCATACTTAATT- -s Anc1.Anc1refChr8 50122 32 - 57822 TTAATAACTTGAAACGAAATGCATACTTAATT- -s Anc2.Anc2refChr8 259 32 - 12804 TTAATAACTTGAAACGAAATGCATACTTAATT- -s mr.mrrefChr5 148847 33 + 294540 TTCAGAACTTGGAGTGAAATGCATACTCATTTA -s simCow_chr6.simCow.chr6 310836 32 - 602619 TTAAGGTCCTAAAGTGAAACACATACTTGATT- -s simDog_chr6.simDog.chr6 264550 32 + 593897 TTAATAACTTGAAACGAAATGCATACTTAATT- -s simRat_chr6.simRat.chr6 289033 33 + 647215 TTCAGAACTTGGAGTAAAATGCATACTCATTTA - -a -s simMouse_chr6.simMouse.chr6 298231 10 + 636262 AGCATTCTGG -s Anc0.Anc0refChr8 6226 5 - 17196 -----TCTAG -s Anc1.Anc1refChr8 50154 5 - 57822 -----TCTAG -s Anc2.Anc2refChr8 291 5 - 12804 -----TCTAG -s mr.mrrefChr5 148880 10 + 294540 AGCATTCTGG -s simCow_chr6.simCow.chr6 310868 5 - 602619 -----TGTAG -s simDog_chr6.simDog.chr6 264582 5 + 593897 -----TCTAG -s simRat_chr6.simRat.chr6 289067 10 + 647215 GGCATTGCAG - -a -s simMouse_chr6.simMouse.chr6 298241 14 + 636262 GGGGCTTGACCTCA -s Anc0.Anc0refChr8 6231 14 - 17196 GAGGCTTGTACTTA -s Anc1.Anc1refChr8 50159 14 - 57822 GAGGCTTGTACTTA -s Anc2.Anc2refChr8 298 14 - 12804 GAGGCTTGTACTTA -s mr.mrrefChr5 148890 14 + 294540 GGGGCTTGACCTCA -s simCow_chr6.simCow.chr6 310875 14 - 602619 GAGGCTTGCACTTA -s simDog_chr6.simDog.chr6 264589 14 + 593897 GAGGCTTGTACTTA -s simRat_chr6.simRat.chr6 289077 14 + 647215 GGGGCTTAAGCTTA - -a -s simMouse_chr6.simMouse.chr6 298255 17 + 636262 AAAAATGAACACACTAA -s Anc0.Anc0refChr8 6245 5 - 17196 G------------TTGT -s Anc1.Anc1refChr8 50173 5 - 57822 G------------TTGT -s Anc2.Anc2refChr8 312 5 - 12804 G------------TTGT -s mr.mrrefChr5 148904 17 + 294540 AAAAATGAACACACTAA -s simCow_chr6.simCow.chr6 310896 5 - 602619 G------------ATGC -s simDog_chr6.simDog.chr6 264603 5 + 593897 G------------TTGT -s simRat_chr6.simRat.chr6 289091 17 + 647215 AAAAATGAACACATTAA - -a -s simMouse_chr6.simMouse.chr6 298272 16 + 636262 GTCCATTTTAAGCCTC -s Anc0.Anc0refChr8 6250 16 - 17196 GTCCAATTGAATCCTT -s Anc1.Anc1refChr8 50178 16 - 57822 GTCCAATTGAATCCTT -s Anc2.Anc2refChr8 317 16 - 12804 GTCCAATTGAATCCTT -s mr.mrrefChr5 148921 16 + 294540 GTCCATTTTAAGCCTC -s simCow_chr6.simCow.chr6 310906 16 - 602619 GTCCGTTTCAATCCTT -s simDog_chr6.simDog.chr6 264608 16 + 593897 GTCCAATTGAATCCTT -s simRat_chr6.simRat.chr6 289108 16 + 647215 GTCCATCCTAAGCCCC - -a -s simMouse_chr6.simMouse.chr6 298288 4 + 636262 ATAA -s Anc0.Anc0refChr8 6266 4 - 17196 ACAA -s Anc1.Anc1refChr8 50194 4 - 57822 ACAA -s Anc2.Anc2refChr8 333 4 - 12804 ACAA -s mr.mrrefChr5 148937 4 + 294540 ATAA -s simCow_chr6.simCow.chr6 310922 4 - 602619 ATAA -s simDog_chr6.simDog.chr6 264644 4 + 593897 ACAA -s simRat_chr6.simRat.chr6 289124 4 + 647215 ATAG - -a -s simMouse_chr6.simMouse.chr6 298292 2 + 636262 GA -s Anc0.Anc0refChr8 6270 2 - 17196 CA -s Anc1.Anc1refChr8 50198 2 - 57822 CA -s Anc2.Anc2refChr8 337 2 - 12804 CA -s mr.mrrefChr5 148941 2 + 294540 GA -s simCow_chr6.simCow.chr6 310926 2 - 602619 CC -s simDog_chr6.simDog.chr6 264648 2 + 593897 CA -s simRat_chr6.simRat.chr6 289165 2 + 647215 GA - -a -s simMouse_chr6.simMouse.chr6 298294 70 + 636262 ATGCATTAAGTCCATTTCCAACCTCATACCATGAGTGTAAAAAAGACTAGTTAGTGGTTCTGTGCTGCCT -s Anc0.Anc0refChr8 6272 12 - 17196 ATGAATGAAGGC---------------------------------------------------------- -s Anc1.Anc1refChr8 50200 12 - 57822 ATGAATGAAGGC---------------------------------------------------------- -s Anc2.Anc2refChr8 341 12 - 12804 ATGAATGAAGGC---------------------------------------------------------- -s mr.mrrefChr5 148943 70 + 294540 ATGCATTAAGTCCATTTCCAACCTCATACCATGAGTGTAAAAAAGACTAGTTAGTGGTTCTGTGCTGCCT -s simCow_chr6.simCow.chr6 310930 12 - 602619 GCAGTGGAAAGC---------------------------------------------------------- -s simDog_chr6.simDog.chr6 264652 12 + 593897 ATGAATGAAGGC---------------------------------------------------------- -s simRat_chr6.simRat.chr6 289167 70 + 647215 ATGCATTAATTCCATTGCAAACCTCATAGGATAAGAGTAAAAAAGGCCAGTTTGGGGTCCTGTGCTGCCC - -a -s simMouse_chr6.simMouse.chr6 298364 60 + 636262 TTCATGTGTGGTAACTTCCATTTAATGAGGGTGTGTCCTCTCAGGTCAACTGGGGATTAG -s mr.mrrefChr5 149013 44 + 294540 TTCATGTGTGGTAACTT----------------TGTCCTCTCAGGTCAACTGGGGATTAG -s simRat_chr6.simRat.chr6 289238 44 + 647215 TTCATGTGTGGTATCTT----------------TGTATGCTTAGGTCAACTGGGGATTAG - -a -s simMouse_chr6.simMouse.chr6 298424 10 + 636262 AAAATAGTCT -s mr.mrrefChr5 149057 10 + 294540 AAAATAGTCT -s simRat_chr6.simRat.chr6 289286 10 + 647215 AAAACAGTCT - -a -s simMouse_chr6.simMouse.chr6 298434 22 + 636262 ATTTGCACACGAAAGACTTAGA -s Anc0.Anc0refChr8 6284 10 - 17196 ------------AAGACTTAAA -s Anc1.Anc1refChr8 50212 10 - 57822 ------------AAGACTTAAA -s Anc2.Anc2refChr8 353 10 - 12804 ------------AAGACTTAAA -s mr.mrrefChr5 149067 22 + 294540 ATTTGCACACGAAAGACTTAGA -s simCow_chr6.simCow.chr6 310942 10 - 602619 ------------AAGACTTAAA -s simDog_chr6.simDog.chr6 264664 10 + 593897 ------------AAGACTTAAA -s simRat_chr6.simRat.chr6 289300 22 + 647215 ATTTGCACATGAAAGACTTAGA - -a -s simMouse_chr6.simMouse.chr6 298456 22 + 636262 GGAGAGGCTGACACTTAAAAAC -s Anc0.Anc0refChr8 6294 21 - 17196 G-ATTGTCTCACATTTAAAAAC -s Anc1.Anc1refChr8 50222 21 - 57822 G-ATTGTCTCACATTTAAAAAC -s Anc2.Anc2refChr8 363 21 - 12804 G-ATTGTCTCACATTTAAAAAC -s mr.mrrefChr5 149089 22 + 294540 GGAGAGGCTGACACTTAAAAAC -s simCow_chr6.simCow.chr6 310953 21 - 602619 G-CGAGGTTCACATTTAAAAAC -s simDog_chr6.simDog.chr6 264674 21 + 593897 G-ATTGTCTCACATTGAAGAAC -s simHuman_chr6.simHuman.chr6 365295 12 - 601863 ----------ccaTTTAAAAAT -s simRat_chr6.simRat.chr6 289322 22 + 647215 GGAGAGGCTGACACTTAAAAAC - -a -s simMouse_chr6.simMouse.chr6 298478 17 + 636262 CATTACTCTGTTCATGG -s Anc0.Anc0refChr8 6329 17 - 17196 CATTACATGAGTCATGT -s Anc1.Anc1refChr8 50257 17 - 57822 CATTACATGAGTCATGT -s Anc2.Anc2refChr8 399 17 - 12804 CACTACATGAGTAATGT -s mr.mrrefChr5 149125 17 + 294540 CATTACTCTATTCATGG -s simCow_chr6.simCow.chr6 310989 17 - 602619 CACTATACTAGTAATGT -s simDog_chr6.simDog.chr6 264710 10 + 593897 CACTACATG-------T -s simHuman_chr6.simHuman.chr6 365321 17 - 601863 CATTACCTAAATCACTT -s simRat_chr6.simRat.chr6 289359 17 + 647215 CATTACTCTATTCATGG - -a -s simMouse_chr6.simMouse.chr6 298495 10 + 636262 AATTAAAGGA -s Anc0.Anc0refChr8 6354 10 - 17196 AAGTTAAAGA -s Anc1.Anc1refChr8 50282 10 - 57822 AAGTTAAAGA -s Anc2.Anc2refChr8 424 10 - 12804 TAGTTAAAGA -s mr.mrrefChr5 149150 10 + 294540 AATTTAAGGA -s simCow_chr6.simCow.chr6 311074 8 - 602619 TTGTTTAA-- -s simDog_chr6.simDog.chr6 264727 9 + 593897 -AGTCAAAGA -s simHuman_chr6.simHuman.chr6 365346 10 - 601863 AAGTTACAGA -s simRat_chr6.simRat.chr6 289384 10 + 647215 AAATTAAGGA - -a -s simMouse_chr6.simMouse.chr6 298505 11 + 636262 GAGGGCGTACT -s Anc0.Anc0refChr8 6364 11 - 17196 AAGGGTCAACT -s Anc1.Anc1refChr8 50292 11 - 57822 AAGGGTCAACT -s Anc2.Anc2refChr8 434 11 - 12804 TAGGGTCAATT -s mr.mrrefChr5 149160 11 + 294540 AAGGGTGAACT -s simCow_chr6.simCow.chr6 311082 11 - 602619 TGGGGTCAATT -s simDog_chr6.simDog.chr6 264736 11 + 593897 CAGGGTCAATT -s simHuman_chr6.simHuman.chr6 365393 11 - 601863 AGTGATCAACT -s simRat_chr6.simRat.chr6 289394 11 + 647215 AAGGGTGAACT - -a -s simMouse_chr6.simMouse.chr6 298516 20 + 636262 GAGACATGAGACATGCATCG -s Anc0.Anc0refChr8 6375 19 - 17196 GAGAG-GGGGGCATGTATTG -s Anc1.Anc1refChr8 50303 20 - 57822 GAGAGGGGGGGCATGTATTG -s Anc2.Anc2refChr8 445 19 - 12804 GAGAG-GGGGGCATGTATTG -s mr.mrrefChr5 149171 20 + 294540 GAGACATGAGACATGCATCG -s simCow_chr6.simCow.chr6 311093 19 - 602619 GAGAG-GGGGGCGTGTATTG -s simDog_chr6.simDog.chr6 264747 19 + 593897 AAAAG-AGGGGCATGTATTG -s simHuman_chr6.simHuman.chr6 365404 20 - 601863 GAGAGGGGGGGCATGTATTG -s simRat_chr6.simRat.chr6 289408 20 + 647215 GAAATATGAGACATGCATCA - -a -s simMouse_chr6.simMouse.chr6 298536 2 + 636262 CC -s Anc0.Anc0refChr8 6394 2 - 17196 CT -s Anc1.Anc1refChr8 50323 2 - 57822 CT -s Anc2.Anc2refChr8 467 2 - 12804 CT -s mr.mrrefChr5 149191 2 + 294540 CC -s simCow_chr6.simCow.chr6 311115 2 - 602619 CC -s simDog_chr6.simDog.chr6 264769 2 + 593897 CT -s simHuman_chr6.simHuman.chr6 365424 2 - 601863 TT -s simRat_chr6.simRat.chr6 289428 2 + 647215 CC - -a -s simMouse_chr6.simMouse.chr6 298538 40 + 636262 ACCTGATTATCTCATAAGGCAACATAAAGTAGTTAAGAGT -s Anc0.Anc0refChr8 6400 40 - 17196 ACTGCATAAACTCATAAGGCAGCTTAAAAGAGTTAAAAGT -s Anc1.Anc1refChr8 50329 40 - 57822 ACTGCATAAACTCATAAGGCAGCTTAAAAGAGTTAAAAGT -s Anc2.Anc2refChr8 473 40 - 12804 ACTGCATAAACTCATAAGACAGCTTAAAAGAGTTAAAAGT -s mr.mrrefChr5 149193 40 + 294540 ACCTAATTATCTCATAAGGCAACATAAAATAGTTAAGAGT -s simCow_chr6.simCow.chr6 311121 40 - 602619 ACTGCTTAAACTTGTAAGACAGCTTAAAAGAGTTAGAGAT -s simDog_chr6.simDog.chr6 264775 40 + 593897 ACTTCATAAACTCATAAAACAGCTTCAAAGAGTTAAAAGT -s simHuman_chr6.simHuman.chr6 365430 40 - 601863 ACTGCATACACTCATGAGGCAGCTTAAAAGAGTTAAATGT -s simRat_chr6.simRat.chr6 289430 40 + 647215 ACCCAATTATCTCATAAGGCAACATAAAAAAGTTAAGAGT - -a -s simMouse_chr6.simMouse.chr6 298578 5 + 636262 ATTTG -s Anc0.Anc0refChr8 6446 5 - 17196 ATGTG -s Anc1.Anc1refChr8 50375 5 - 57822 ATGTG -s Anc2.Anc2refChr8 519 5 - 12804 ATGTG -s mr.mrrefChr5 149236 5 + 294540 ATGTG -s simCow_chr6.simCow.chr6 311167 5 - 602619 ATGTG -s simDog_chr6.simDog.chr6 264821 5 + 593897 ATGTG -s simHuman_chr6.simHuman.chr6 365476 5 - 601863 ATGTG -s simRat_chr6.simRat.chr6 289473 5 + 647215 ATGTG - -a -s simMouse_chr6.simMouse.chr6 298583 5 + 636262 TGGTG -s Anc0.Anc0refChr8 6451 5 - 17196 TGGTA -s Anc1.Anc1refChr8 50380 5 - 57822 TGGTA -s Anc2.Anc2refChr8 527 5 - 12804 TGGTA -s mr.mrrefChr5 149241 5 + 294540 TGGTG -s simCow_chr6.simCow.chr6 311175 5 - 602619 TGCTA -s simDog_chr6.simDog.chr6 264829 5 + 593897 TGGTA -s simHuman_chr6.simHuman.chr6 365481 5 - 601863 TGGTT -s simRat_chr6.simRat.chr6 289478 5 + 647215 TGGTG - -a -s simMouse_chr6.simMouse.chr6 298588 42 + 636262 ATGGCATAAGGATGCACTTTGAGAAAATCTAGAAACAGAGGG -s Anc0.Anc0refChr8 6456 42 - 17196 ATGTTATAAGGCTACATGTTGACAAAAGATTAAAACAGAGAG -s Anc1.Anc1refChr8 50385 42 - 57822 ATGTTATAAGGCTACATGTTGACAAAAGATTAAAACAGAGAG -s Anc2.Anc2refChr8 532 42 - 12804 ATGTTACAAGGCTAAATGTTGACAAAAGATTAAAACAGAGAG -s mr.mrrefChr5 149246 42 + 294540 ATGGCATAAGGCTGCACTTTGAGAAAATCTAAAAACAGAGAG -s simCow_chr6.simCow.chr6 311180 42 - 602619 ATGTTACAATGCTATATGTTGACAAAGGATTCAAACAGCAAG -s simDog_chr6.simDog.chr6 264900 41 + 593897 ATGTTACAAG-CTAAATGTTGATAAAAGATTAAAACAGAGAC -s simHuman_chr6.simHuman.chr6 365486 42 - 601863 ATGTTATGAGGCCACATGTTGGCAAAAGATCACAACAGAGAG -s simRat_chr6.simRat.chr6 289483 42 + 647215 ATGACATAAGGCTTCACTTTGAGATAATGTTAAAACAGAGAG - -a -s simMouse_chr6.simMouse.chr6 298630 12 + 636262 AACCTCTAGCCA -s Anc0.Anc0refChr8 6499 12 - 17196 AACCTCTAACCA -s Anc1.Anc1refChr8 50428 12 - 57822 AACCTCTAACCA -s Anc2.Anc2refChr8 575 12 - 12804 AACCTCTAACCA -s mr.mrrefChr5 149289 12 + 294540 AACCTCTAGCCA -s simCow_chr6.simCow.chr6 311223 12 - 602619 AACCTCTAACCA -s simDog_chr6.simDog.chr6 264942 12 + 593897 AAACACTAACTG -s simHuman_chr6.simHuman.chr6 365529 12 - 601863 GACCTCTAACCA -s simRat_chr6.simRat.chr6 289526 12 + 647215 TACCATTAGCCA - -a -s simMouse_chr6.simMouse.chr6 298642 103 + 636262 CGGCAATGTGCTCGCACAAGCAGTCTAACAGCACAGCAATGGGCTTGTTGAAAGCATGGAATAAGATACTCCCGAACGCCGTGTGAACTTGCAATAGGTAGGG -s Anc0.Anc0refChr8 6511 73 - 17196 CAGAAATG---------GGGGCGTGTAAAAGCACGGAGTCTGACCTCTTCAA---------TAACATA------------GTGTGAACTTGCCATAAGTAGAG -s Anc1.Anc1refChr8 50440 77 - 57822 CAGAAATGTA-----ATGGGGCGTGTAAAAGCACGGAGTCTGACCTCTTCAA---------TAACATA------------GTGTGAACTTGCCATAAGTAGAG -s Anc2.Anc2refChr8 587 73 - 12804 CAAACATG---------GGGGCTTGTAGAAGCATGGAGTCTGACCTCTTCCA---------TAACATA------------GTGTCAACTAACCATAAGCAAAG -s mr.mrrefChr5 149301 91 + 294540 CAGCAATGTGCTCGCACAAGCAGTCTAACAGCACAGCGATGGGCTTGTTCAAAGCATGGAATAAGATA------------GTGTGAACTTGCCATAAGTAGGG -s simCow_chr6.simCow.chr6 311236 73 - 602619 TGAACATG---------TAGGCTCACAGAAGCATGCAGTCTGACCTTTGCTA---------TAACATA------------GCGTAAACTAAACATAAGCAAAG -s simDog_chr6.simDog.chr6 264954 73 + 593897 CAAACATG---------GGGGCTTGTAGACGCATGGAGCCTGACCTCTTCCA---------TAACACG------------ATGTCAACTAACCATAAGCAAAG -s simHuman_chr6.simHuman.chr6 365541 77 - 601863 CAGAAATGTA-----ATGTGTGGTGTGAAAGCACCGAGTGTGACCTCTTCAC---------TAATATA------------GTGTGAGCTTGCCATAACTGGAG -s simRat_chr6.simRat.chr6 289538 86 + 647215 CAGCAATGCGCTTACACAAGCAGTCTAACACCACAGCGATGGGCTTGTACAAAGCATGGAATACCATA-----------------CACTTGCCATAAGAAAGG - -a -s simMouse_chr6.simMouse.chr6 298745 2 + 636262 TT -s Anc0.Anc0refChr8 6586 2 - 17196 TT -s Anc1.Anc1refChr8 50519 2 - 57822 TT -s Anc2.Anc2refChr8 662 2 - 12804 AT -s mr.mrrefChr5 149392 2 + 294540 TT -s simCow_chr6.simCow.chr6 311311 2 - 602619 CT -s simDog_chr6.simDog.chr6 265029 2 + 593897 AT -s simHuman_chr6.simHuman.chr6 365620 2 - 601863 TT -s simRat_chr6.simRat.chr6 289624 2 + 647215 TT - -a -s simMouse_chr6.simMouse.chr6 298747 6 + 636262 TTCACT -s Anc0.Anc0refChr8 6603 6 - 17196 TTCACC -s Anc1.Anc1refChr8 50536 6 - 57822 TTCACC -s Anc2.Anc2refChr8 680 6 - 12804 TTCACC -s mr.mrrefChr5 149394 6 + 294540 TTCACT -s simCow_chr6.simCow.chr6 311329 6 - 602619 TTCACC -s simDog_chr6.simDog.chr6 265047 6 + 593897 TTCACC -s simHuman_chr6.simHuman.chr6 365637 6 - 601863 TTCACC -s simRat_chr6.simRat.chr6 289626 6 + 647215 TTTACT - -a -s simMouse_chr6.simMouse.chr6 298753 4 + 636262 GACA -s Anc0.Anc0refChr8 6610 3 - 17196 -ACA -s Anc1.Anc1refChr8 50546 4 - 57822 GACA -s Anc2.Anc2refChr8 687 3 - 12804 -ACA -s mr.mrrefChr5 149404 4 + 294540 GACA -s simCow_chr6.simCow.chr6 311336 3 - 602619 -ACA -s simDog_chr6.simDog.chr6 265054 3 + 593897 -ATA -s simHuman_chr6.simHuman.chr6 365647 4 - 601863 GACA -s simRat_chr6.simRat.chr6 289636 4 + 647215 AACA - -a -s simMouse_chr6.simMouse.chr6 298757 23 + 636262 ACTCATCAGTAGCTGAATAATCC -s Anc0.Anc0refChr8 6633 22 - 17196 ACTCATCA-TAGCTGGATACTAT -s Anc1.Anc1refChr8 50570 22 - 57822 ACTCATCA-TAGCTGGATACTAT -s Anc2.Anc2refChr8 710 22 - 12804 ACTCATCA-TAGCTAGATACTAT -s mr.mrrefChr5 149408 23 + 294540 ACTCATCAGTAGCTGAATAATAC -s simCow_chr6.simCow.chr6 311358 22 - 602619 ACCCATCA-TAGCTAGATACTAT -s simDog_chr6.simDog.chr6 265077 22 + 593897 ACTCATCA-TAGCTAGATACTCT -s simHuman_chr6.simHuman.chr6 365671 22 - 601863 ACTCATCA-TAGCTGGGTAGCAT -s simRat_chr6.simRat.chr6 289640 23 + 647215 ACTCATCAGTAGCTGAATAATAC - -a -s simMouse_chr6.simMouse.chr6 298780 13 + 636262 CCCTAATAGGGGG -s Anc0.Anc0refChr8 6655 13 - 17196 CCTTAACAGGGGG -s Anc1.Anc1refChr8 50592 13 - 57822 CCTTAACAGGGGG -s Anc2.Anc2refChr8 732 13 - 12804 CCTTAACAGGGGG -s mr.mrrefChr5 149431 13 + 294540 CCCTAATAGGGGG -s simCow_chr6.simCow.chr6 311380 13 - 602619 CACCAATAGGGGG -s simDog_chr6.simDog.chr6 265099 13 + 593897 GCTTAACAGGGGG -s simHuman_chr6.simHuman.chr6 365693 13 - 601863 CTTTACAAGGGGG -s simRat_chr6.simRat.chr6 289670 13 + 647215 CCCTAATAGGAGG - -a -s simMouse_chr6.simMouse.chr6 298793 1 + 636262 T -s Anc0.Anc0refChr8 6701 1 - 17196 T -s Anc1.Anc1refChr8 50638 1 - 57822 T -s Anc2.Anc2refChr8 778 1 - 12804 T -s mr.mrrefChr5 149444 1 + 294540 T -s simCow_chr6.simCow.chr6 311426 1 - 602619 A -s simDog_chr6.simDog.chr6 265146 1 + 593897 T -s simHuman_chr6.simHuman.chr6 365739 1 - 601863 T -s simRat_chr6.simRat.chr6 289683 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 298794 50 + 636262 GCACACTAAAGGAACAACGCAACATATCCCTACCTTGTAAGCCTGAAGTC -s Anc0.Anc0refChr8 6702 50 - 17196 GCAACGTGAAGGAACAATCCAGCATAACCCTGTCTTCTGAGCCCCAACTT -s Anc1.Anc1refChr8 50639 50 - 57822 GCAACGTGAAGGAACAATCCAGCATAACCCTGTCTTCTGAGCCCCAACTT -s Anc2.Anc2refChr8 779 50 - 12804 ACAACGTGAAGGAACAATCCAGCATAACACTGTCTTCTGAGCCCCAACTT -s mr.mrrefChr5 149445 50 + 294540 GCACACTAAAGGAACAACGCAACATATCCCTACCTTGTGAGCCTGAGCTC -s simCow_chr6.simCow.chr6 311427 50 - 602619 ACAACATGAGGGAACAATCCAGCATAACTCTGTCGTCTCCACACCAATTT -s simDog_chr6.simDog.chr6 265150 50 + 593897 ACAACGTGAAGGAACAATCCAGCTTAACACTGTCTTATGAGACCCAACTT -s simHuman_chr6.simHuman.chr6 365740 50 - 601863 GCAGCGTGAAGGAGCGATCCAGCATACCCCTGTCTTCTGAGCCCCAACTT -s simRat_chr6.simRat.chr6 289684 50 + 647215 GCATGCTAAAGGAACAACACGACATATCCCTACCTTAAGAGCCTGAGCGC - -a -s simMouse_chr6.simMouse.chr6 298844 5 + 636262 ACCGT -s Anc0.Anc0refChr8 6756 5 - 17196 ACCAT -s Anc1.Anc1refChr8 50693 5 - 57822 ACCAT -s Anc2.Anc2refChr8 833 5 - 12804 TGCAT -s mr.mrrefChr5 149495 5 + 294540 ACCGT -s simCow_chr6.simCow.chr6 311481 5 - 602619 TGCAT -s simDog_chr6.simDog.chr6 265202 2 + 593897 ---AT -s simHuman_chr6.simHuman.chr6 365794 5 - 601863 ACCAC -s simRat_chr6.simRat.chr6 289734 5 + 647215 GCCTT - -a -s simMouse_chr6.simMouse.chr6 298849 27 + 636262 CCGCATTGTGAGTCTGTCTCACTTTGG -s Anc0.Anc0refChr8 6762 26 - 17196 CCACATTGTAAATAT-TGTCATTTTTG -s Anc1.Anc1refChr8 50699 26 - 57822 CCACATTGTAAATAT-TGTCATTTTTG -s Anc2.Anc2refChr8 839 26 - 12804 CCACATTGTAAATAT-TGTCATTTTTG -s mr.mrrefChr5 149500 26 + 294540 CCGCATTGTAAGTCT-TGTCACTTTGG -s simCow_chr6.simCow.chr6 311487 26 - 602619 CCACCTTGTAGAGAT-TGTGATCTTTG -s simDog_chr6.simDog.chr6 265205 26 + 593897 CCACACTTTGAATAT-TGTCAATTTAC -s simHuman_chr6.simHuman.chr6 365800 26 - 601863 CCACATTGTAAATAC-TGTCATTTTTG -s simRat_chr6.simRat.chr6 289739 26 + 647215 CTGCATTGTAGGTCT-TGTCACTTTAG - -a -s simMouse_chr6.simMouse.chr6 298876 40 + 636262 AAAAGCAGAATGGTGGTGGATCATTAGAAATACCAGTTTG -s Anc0.Anc0refChr8 6793 39 - 17196 GAAGGA-GATGGGCGATGGATCAGTAGAACCATCATTTTG -s Anc1.Anc1refChr8 50730 39 - 57822 GAAGGA-GATGGGCGATGGATCAGTAGAACCATCATTTTG -s Anc2.Anc2refChr8 870 39 - 12804 GAAGGT-GATGGGCGATGGATCAGTAGAACCATCATTTTG -s mr.mrrefChr5 149531 40 + 294540 AAAAGAAGAATGGTGGTGGATCATTAGAAATACCAGTTTG -s simCow_chr6.simCow.chr6 311518 39 - 602619 GAAGCT-GATGGGTGGTGGATCTGTAGAGCTAGCAGCATG -s simDog_chr6.simDog.chr6 265236 39 + 593897 GAAGGT-GATGGGCGATGGATCAGTAGAACCATCATTTTG -s simHuman_chr6.simHuman.chr6 365831 6 - 601863 GAATCA---------------------------------- -s simRat_chr6.simRat.chr6 289770 40 + 647215 AAAAGAGGGATGGTAGTGGATCATTAAAAATAACAGTTTG - -a -s simMouse_chr6.simMouse.chr6 298916 33 + 636262 GTTATAAGATTGTCTGTCTGGTTACAGAGGTCT -s Anc0.Anc0refChr8 6832 4 - 17196 ATT-----------------------G------ -s Anc1.Anc1refChr8 50769 4 - 57822 ATT-----------------------G------ -s Anc2.Anc2refChr8 909 4 - 12804 ATT-----------------------G------ -s mr.mrrefChr5 149571 10 + 294540 GTT-----------------------GAGGTCT -s simCow_chr6.simCow.chr6 311565 4 - 602619 AAT-----------------------G------ -s simDog_chr6.simDog.chr6 265275 4 + 593897 ATT-----------------------G------ -s simRat_chr6.simRat.chr6 289810 10 + 647215 GGT-----------------------GAAATCT - -a -s simMouse_chr6.simMouse.chr6 298949 10 + 636262 TCTGCCCTAC -s Anc0.Anc0refChr8 6836 10 - 17196 TCCGTCTTAT -s Anc1.Anc1refChr8 50773 10 - 57822 TCCGTCTTAT -s Anc2.Anc2refChr8 913 10 - 12804 TCCGTCTTAT -s mr.mrrefChr5 149581 10 + 294540 TCTGCCCTAC -s simCow_chr6.simCow.chr6 311569 10 - 602619 CCTGTCTGGT -s simDog_chr6.simDog.chr6 265279 10 + 593897 TCCGTCTTAT -s simRat_chr6.simRat.chr6 289821 10 + 647215 ACTGCTGTGT - -a -s simMouse_chr6.simMouse.chr6 298959 12 + 636262 AGCTCAATCCAG -s Anc0.Anc0refChr8 6846 12 - 17196 AACGTAATCAAA -s Anc1.Anc1refChr8 50783 12 - 57822 AACGTAATCAAA -s Anc2.Anc2refChr8 927 12 - 12804 AACGTAATCAAA -s mr.mrrefChr5 149591 12 + 294540 AGCTCAATCCAG -s simCow_chr6.simCow.chr6 311583 12 - 602619 ACAGTAGTCAAA -s simDog_chr6.simDog.chr6 265293 12 + 593897 AACCTAAACAAA -s simRat_chr6.simRat.chr6 289831 12 + 647215 AGCTCAATCCAG - -a -s simMouse_chr6.simMouse.chr6 298971 28 + 636262 GATCAAGTGGTGTAGCGAAAATCGGTAA -s Anc0.Anc0refChr8 6858 28 - 17196 GGGTAATCACAGGAATGAATATTGGTAA -s Anc1.Anc1refChr8 50795 28 - 57822 GGGTAATCACAGGAATGAATATTGGTAA -s Anc2.Anc2refChr8 948 28 - 12804 GGGTAATCACAGGAATGAATATTGGGAT -s mr.mrrefChr5 149603 28 + 294540 GATTAAGTGGTGTAGCGAAAAATGGTAA -s simCow_chr6.simCow.chr6 311604 28 - 602619 GATTAATCACAGGATTGGATACTGTGAT -s simDog_chr6.simDog.chr6 265314 28 + 593897 GGGTAATCACAGGAATGAATATTGGGAT -s simHuman_chr6.simHuman.chr6 365837 19 - 601863 ---------CAGGATTGAATGGTGATGA -s simRat_chr6.simRat.chr6 289843 28 + 647215 GATTAAGTGGTGTATCGAAAAATGGTGA - -a -s simMouse_chr6.simMouse.chr6 298999 84 + 636262 AAAATACTATGGTCCCATAGCATTGAAGATGTCTGCTTGCTACAGCAGCAAGTCCTAGGTCTTGGGGTTAGGTACTCCAACTGC -s Anc0.Anc0refChr8 6886 84 - 17196 AAACTAACATGGTCCCATGGCATAGTAGATGTCTGCTTACTAAACTGGCAACTCCTAGGTCATGGAAGTAAGTACTCCCACTGC -s Anc1.Anc1refChr8 50823 84 - 57822 AAACTAACATGGTCCCATGGCATAGTAGATGTCTGCTTACTAAACTGGCAACTCCTAGGTCATGGAAGTAAGTACTCCCACTGC -s Anc2.Anc2refChr8 976 84 - 12804 AAACTTACATGGTCCCATGGCATAGTGGATGTCTGCTTACTAAACTGGCAACCTCTAGGTCATGGAAGTAAATACTCCCAATGC -s mr.mrrefChr5 149631 84 + 294540 AAAATACTATGGTCCCATAGCATAGTAGATGTCTGCTTGCTACACCAGCAAGTCCTAGGTCTTGGGATTAGGTACTCCAACTGC -s simCow_chr6.simCow.chr6 311633 83 - 602619 AAACTTACATGGTCTCGTGGCA-AGTGGATGTTTGCTTAGTAGACTGGCAACATCTAGGTCATGAAAGTAAATACTCCCAGTGC -s simDog_chr6.simDog.chr6 265342 84 + 593897 AAACTTACATGGTCCTATGGCATAGCGGATGTCTGATTGCTAAACTGGCACCCTCTAGGTCATGGGGGTAAATACTCCCAATAC -s simHuman_chr6.simHuman.chr6 365856 83 - 601863 AAC-TATCACGGTTCCATGGCATAGTAGATGTATGCTCACTAAACTGGCAATTCCTAGGTCATGGAACTAAGGACACCCACTGC -s simRat_chr6.simRat.chr6 289871 84 + 647215 AAAAAACTATGGTCCCATAGCATAGTGGATGTCTGCTTGCTACACCAACAAGTCCTAGGTCTTGGGATCAGGTACTCCAACTGC - -a -s simMouse_chr6.simMouse.chr6 299083 5 + 636262 CAACT -s Anc0.Anc0refChr8 6970 5 - 17196 TGACT -s Anc1.Anc1refChr8 50907 5 - 57822 TGACT -s Anc2.Anc2refChr8 1060 5 - 12804 TAACT -s mr.mrrefChr5 149715 5 + 294540 CGACT -s simCow_chr6.simCow.chr6 311716 5 - 602619 TAACC -s simDog_chr6.simDog.chr6 265426 5 + 593897 TAACT -s simHuman_chr6.simHuman.chr6 365939 5 - 601863 TGACT -s simRat_chr6.simRat.chr6 289960 5 + 647215 CGACT - -a -s simMouse_chr6.simMouse.chr6 299088 20 + 636262 GGCCTGGAGGCTGTGTGGCA -s Anc0.Anc0refChr8 6975 16 - 17196 GG----GAGCCTGAGTGGCA -s Anc1.Anc1refChr8 50912 16 - 57822 GG----GAGCCTGAGTGGCA -s Anc2.Anc2refChr8 1065 16 - 12804 TG----GAACCTGAGTGGCA -s mr.mrrefChr5 149720 20 + 294540 GGCCTGGAGCCTGTGTGGCA -s simCow_chr6.simCow.chr6 311721 12 - 602619 --------ATTTGAGTGGCA -s simDog_chr6.simDog.chr6 265435 16 + 593897 TG----GAACCTGAGTGGCA -s simHuman_chr6.simHuman.chr6 365944 16 - 601863 GG----GAGCCTGACTGGCA -s simRat_chr6.simRat.chr6 289965 20 + 647215 GGCCTGGAGCCTGTGTGGCA - -a -s simMouse_chr6.simMouse.chr6 299108 4 + 636262 GGTT -s Anc0.Anc0refChr8 6991 4 - 17196 GGCT -s Anc1.Anc1refChr8 50928 4 - 57822 GGCT -s Anc2.Anc2refChr8 1083 4 - 12804 GGCT -s mr.mrrefChr5 149740 4 + 294540 GGTT -s simCow_chr6.simCow.chr6 311735 4 - 602619 GTCT -s simDog_chr6.simDog.chr6 265453 4 + 593897 GGCT -s simHuman_chr6.simHuman.chr6 365960 4 - 601863 AGAT -s simRat_chr6.simRat.chr6 289985 4 + 647215 GGTT - -a -s simMouse_chr6.simMouse.chr6 299112 13 + 636262 AGATCTAAAGTGG -s Anc0.Anc0refChr8 6997 13 - 17196 AGATCTAAAGTGG -s Anc1.Anc1refChr8 50934 13 - 57822 AGATCTAAAGTGG -s Anc2.Anc2refChr8 1089 13 - 12804 AGATCTAAAGTGG -s mr.mrrefChr5 149744 13 + 294540 AGATCTAAAGTGG -s simCow_chr6.simCow.chr6 311741 13 - 602619 CGACCTAAAGTGG -s simDog_chr6.simDog.chr6 265459 13 + 593897 AGATCTAAAGTGG -s simHuman_chr6.simHuman.chr6 365966 13 - 601863 AGGTCTAAAGTGG -s simRat_chr6.simRat.chr6 289989 13 + 647215 AAATCTAAAATGG - -a -s simMouse_chr6.simMouse.chr6 299125 35 + 636262 TATGTAACAGCCCCTTGATCAAATCTGTATCTTGT -s Anc0.Anc0refChr8 7019 35 - 17196 TACAAAATAGCCCTCTGATCAAATCTGTATCTTGC -s Anc1.Anc1refChr8 50956 35 - 57822 TACAAAATAGCCCTCTGATCAAATCTGTATCTTGC -s Anc2.Anc2refChr8 1111 35 - 12804 TACAAAATAGCCTTCTGATCATGTCTATATCTTGC -s mr.mrrefChr5 149757 35 + 294540 TACATAACAGCCCCCTGATCAAATCTGTATCTTGT -s simCow_chr6.simCow.chr6 311764 26 - 602619 T-CAAAACAGCCTTCTAAT--------TAACTTGC -s simDog_chr6.simDog.chr6 265481 35 + 593897 TACAAAATAGCCTTCTGACCATGTCTATATCTTGC -s simHuman_chr6.simHuman.chr6 365991 35 - 601863 TACAAAATAACACTCTGATCCAATCTGTATCTTGG -s simRat_chr6.simRat.chr6 290002 35 + 647215 TACATAACAGCCTCCTGATCAAGTCTGTATCTTGT - -a -s simMouse_chr6.simMouse.chr6 299160 15 + 636262 GATGGAGGTCTTCAT -s Anc0.Anc0refChr8 7056 15 - 17196 AATGGGTGCTGTCAT -s Anc1.Anc1refChr8 50993 15 - 57822 AATGGGTGCTGTCAT -s Anc2.Anc2refChr8 1148 15 - 12804 AATGGGTGCTGTCAT -s mr.mrrefChr5 149792 15 + 294540 GATGGAGGTTTTCAT -s simCow_chr6.simCow.chr6 311792 15 - 602619 AATGGGAGCTGTCAT -s simDog_chr6.simDog.chr6 265518 15 + 593897 AATCCATGCTGTCAT -s simHuman_chr6.simHuman.chr6 366028 15 - 601863 AATGGGTGCTGTCCT -s simRat_chr6.simRat.chr6 290037 15 + 647215 GATGGAGGTTCTCAT - -a -s simMouse_chr6.simMouse.chr6 299175 4 + 636262 GCCC -s Anc0.Anc0refChr8 7071 4 - 17196 TCCC -s Anc1.Anc1refChr8 51008 4 - 57822 TCCC -s Anc2.Anc2refChr8 1166 4 - 12804 TCCC -s mr.mrrefChr5 149807 4 + 294540 GCCC -s simCow_chr6.simCow.chr6 311810 4 - 602619 TCCC -s simDog_chr6.simDog.chr6 265536 4 + 593897 TCTC -s simHuman_chr6.simHuman.chr6 366043 4 - 601863 CCCC -s simRat_chr6.simRat.chr6 290052 4 + 647215 GCCC - -a -s simMouse_chr6.simMouse.chr6 299179 28 + 636262 AAAGATATAAGGGCTGAGACACCATCTA -s Anc0.Anc0refChr8 7075 28 - 17196 AAAGATAGAAGGACTAAGACTCCATCTA -s Anc1.Anc1refChr8 51012 28 - 57822 AAAGATAGAAGGACTAAGACTCCATCTA -s Anc2.Anc2refChr8 1170 28 - 12804 AAAGATAGAATGACTGATACTCCATCTA -s mr.mrrefChr5 149811 28 + 294540 AAAGATATAAGGACTAAGACACCATCTA -s simCow_chr6.simCow.chr6 311814 28 - 602619 AAAGATAGAAAGACTGATACTCCAACTA -s simDog_chr6.simDog.chr6 265540 28 + 593897 AAGGATAGTATTACTGATACTCCATCCA -s simHuman_chr6.simHuman.chr6 366048 28 - 601863 AAAGATAGAAGGACTAAGACTCCATCTA -s simRat_chr6.simRat.chr6 290056 28 + 647215 AAAGATATAAGGACTAAGACACCATCTA - -a -s simMouse_chr6.simMouse.chr6 299207 4 + 636262 CATC -s Anc0.Anc0refChr8 7106 4 - 17196 TATA -s Anc1.Anc1refChr8 51043 4 - 57822 TATA -s Anc2.Anc2refChr8 1201 4 - 12804 TATA -s mr.mrrefChr5 149839 4 + 294540 TATC -s simCow_chr6.simCow.chr6 311845 4 - 602619 TATC -s simDog_chr6.simDog.chr6 265572 4 + 593897 TATA -s simHuman_chr6.simHuman.chr6 366079 4 - 601863 TATA -s simRat_chr6.simRat.chr6 290084 4 + 647215 TATC - -a -s simMouse_chr6.simMouse.chr6 299211 1 + 636262 A -s Anc0.Anc0refChr8 7110 1 - 17196 A -s Anc1.Anc1refChr8 51047 1 - 57822 A -s Anc2.Anc2refChr8 1205 1 - 12804 A -s mr.mrrefChr5 149843 1 + 294540 A -s simCow_chr6.simCow.chr6 311849 1 - 602619 A -s simDog_chr6.simDog.chr6 321088 1 - 593897 A -s simHuman_chr6.simHuman.chr6 366083 1 - 601863 A -s simRat_chr6.simRat.chr6 290088 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 299212 3 + 636262 GTA -s Anc0.Anc0refChr8 7111 3 - 17196 GAA -s Anc1.Anc1refChr8 51048 3 - 57822 GAA -s Anc2.Anc2refChr8 1207 3 - 12804 AAA -s mr.mrrefChr5 149844 3 + 294540 GTA -s simCow_chr6.simCow.chr6 311851 3 - 602619 AAA -s simDog_chr6.simDog.chr6 321090 3 - 593897 AAA -s simHuman_chr6.simHuman.chr6 366084 3 - 601863 GAA -s simRat_chr6.simRat.chr6 290089 3 + 647215 GTA - -a -s simMouse_chr6.simMouse.chr6 299215 37 + 636262 CTGACAATCACATTCCATGCATCTCATTTTCACCAGA -s Anc0.Anc0refChr8 7161 31 - 17196 CTGGTGAGC-----CCATGCTTTT-ATCTTCACTAGA -s Anc1.Anc1refChr8 51098 37 - 57822 CTGGTGAGCACATTCCATGCTTTTCATCTTCACTAGA -s Anc2.Anc2refChr8 1257 31 - 12804 CTGGTGAGC-----CCATGATTTT-ATCTTCACTAGA -s mr.mrrefChr5 149847 37 + 294540 CTGACAATCACATTCCATGCATTTCATTTTCACTAGA -s simCow_chr6.simCow.chr6 311901 31 - 602619 CTGGCACGC-----TCATGATTGT-GTCTTCAGTGGA -s simDog_chr6.simDog.chr6 321139 31 - 593897 CTGGTGAGC-----CCATGATTTT-AGCTTCGCTAGA -s simHuman_chr6.simHuman.chr6 366136 37 - 601863 CTGGTGACCACATTCCATGCTTTTCATCTCCACTAGA -s simRat_chr6.simRat.chr6 290092 37 + 647215 CTGACAAGCACATTCCATGCATTTCATTTTCACTAGA - -a -s simMouse_chr6.simMouse.chr6 299252 14 + 636262 TCTACAGTCAACTG -s Anc0.Anc0refChr8 7195 14 - 17196 CCTATATTCCACTA -s Anc1.Anc1refChr8 51138 14 - 57822 CCTATATTCCACTA -s Anc2.Anc2refChr8 1291 14 - 12804 CCCATATAACACTA -s mr.mrrefChr5 149884 14 + 294540 CCTACAGTCAACTG -s simCow_chr6.simCow.chr6 311935 14 - 602619 CACATATCACATTA -s simDog_chr6.simDog.chr6 321173 14 - 593897 CCCAGATAACACTA -s simHuman_chr6.simHuman.chr6 366176 14 - 601863 CCTATATTCCACTA -s simRat_chr6.simRat.chr6 290129 14 + 647215 CCTGCAGTTGACTG - -a -s simMouse_chr6.simMouse.chr6 299266 39 + 636262 TCATTACATGGGACAGGCCACAGCCCATTCTGAGGCATT -s Anc0.Anc0refChr8 7213 39 - 17196 ATGTGATACAGGACAGGCCAAAGCCCTTCCTAAGGCATT -s Anc1.Anc1refChr8 51156 39 - 57822 ATGTGATACAGGACAGGCCAAAGCCCTTCCTAAGGCATT -s Anc2.Anc2refChr8 1309 39 - 12804 ATGTGATTTAGGACAGGCCAAAGCCCTTCCTAAAGCATT -s mr.mrrefChr5 149902 39 + 294540 ACATGACACAGGACAGGCCACAGCCCATTCTGAGGCATT -s simCow_chr6.simCow.chr6 311953 39 - 602619 ATGTGATTTAAGATATGCCTAAGTCCTTCCTGAAGCTTC -s simDog_chr6.simDog.chr6 321192 39 - 593897 ATGTGAGTTAGGCCAGGTCAAAGCCCTTCCTAAAGCATT -s simHuman_chr6.simHuman.chr6 366194 39 - 601863 ATGTGATACAGGACAGGCCAAAGCACTTGCTAAGTCATT -s simRat_chr6.simRat.chr6 290147 39 + 647215 ACATGACACAGGACAGGCCATAGTGCATTCTGAGGCATT - -a -s simMouse_chr6.simMouse.chr6 299305 8 + 636262 CAGAGCTT -s Anc0.Anc0refChr8 7258 8 - 17196 CAGTGCTT -s Anc1.Anc1refChr8 51201 8 - 57822 CAGTGCTT -s Anc2.Anc2refChr8 1354 8 - 12804 CAGTGCTG -s mr.mrrefChr5 149941 8 + 294540 CAGAGCTT -s simCow_chr6.simCow.chr6 311998 8 - 602619 CAGAGCTC -s simDog_chr6.simDog.chr6 321237 8 - 593897 TTGTGCTG -s simHuman_chr6.simHuman.chr6 366239 7 - 601863 CAG-GCCT -s simRat_chr6.simRat.chr6 290186 8 + 647215 CAGAGCTT - -a -s simMouse_chr6.simMouse.chr6 299313 20 + 636262 TAGTGGAGAAGTAGCCGAAG -s Anc0.Anc0refChr8 7266 20 - 17196 TAATGAAGAGATATCTGAAT -s Anc1.Anc1refChr8 51209 20 - 57822 TAATGAAGAGATATCTGAAT -s Anc2.Anc2refChr8 1362 20 - 12804 TAATGAAGAGATATTTGAAT -s mr.mrrefChr5 149949 20 + 294540 TAGTGAAGAAGTAGCTGAAG -s simCow_chr6.simCow.chr6 312010 20 - 602619 TAATGAAGGGATATATGAAT -s simDog_chr6.simDog.chr6 321245 20 - 593897 TAGTGAAGAGATATTTGAAT -s simHuman_chr6.simHuman.chr6 366246 20 - 601863 TAATGAAGACATACCTGAAT -s simRat_chr6.simRat.chr6 290194 20 + 647215 TAGTGAAGAAGTAGTTGAAG - -a -s simMouse_chr6.simMouse.chr6 299333 6 + 636262 TCCACT -s Anc0.Anc0refChr8 7295 6 - 17196 TCTACT -s Anc1.Anc1refChr8 51238 6 - 57822 TCTACT -s Anc2.Anc2refChr8 1391 6 - 12804 TCTACT -s mr.mrrefChr5 149969 6 + 294540 TCCACT -s simCow_chr6.simCow.chr6 312102 6 - 602619 TCTACT -s simDog_chr6.simDog.chr6 321274 6 - 593897 TCTACT -s simHuman_chr6.simHuman.chr6 366275 6 - 601863 TCTACT -s simRat_chr6.simRat.chr6 290214 6 + 647215 TTCACT - -a -s simMouse_chr6.simMouse.chr6 299339 22 + 636262 AGAAGGGCAGGTTGAAAACAGA -s Anc0.Anc0refChr8 7301 15 - 17196 AGA---G----TTAAGAACAGT -s Anc1.Anc1refChr8 51244 15 - 57822 AGA---G----TTAAGAACAGT -s Anc2.Anc2refChr8 1397 15 - 12804 AGA---G----GCAAGAGCAGT -s mr.mrrefChr5 149975 19 + 294540 AGA---GCAGGTTGAAAACAGA -s simCow_chr6.simCow.chr6 312108 15 - 602619 GGG---G----ACAATCGCAGC -s simDog_chr6.simDog.chr6 321281 15 - 593897 AAA---G----GCAAGAGCAGT -s simHuman_chr6.simHuman.chr6 366281 15 - 601863 AGA---G----TTAACAACATT -s simRat_chr6.simRat.chr6 290220 19 + 647215 AGA---GCGGGTTGAAAACAGA - -a -s simMouse_chr6.simMouse.chr6 299361 23 + 636262 GATCAATTCTATGAGTCCTGTCA -s Anc0.Anc0refChr8 7316 17 - 17196 CTTGAATATCATGTTGA------ -s Anc1.Anc1refChr8 51259 23 - 57822 CTTGAATATCATGTTGATTGTAA -s Anc2.Anc2refChr8 1415 17 - 12804 CTTGAATATCAAGTTGA------ -s mr.mrrefChr5 149994 23 + 294540 GATCAATTCTATGAGTCCTGTCA -s simCow_chr6.simCow.chr6 312126 17 - 602619 ATTGAATGTCAAGTTGA------ -s simDog_chr6.simDog.chr6 321299 17 - 593897 CTTGATTATCAAGTTGA------ -s simHuman_chr6.simHuman.chr6 366296 23 - 601863 CTTGAATATCATGCTGGTTGTAA -s simRat_chr6.simRat.chr6 290239 23 + 647215 GATCAATTCTAAGAGTCCTGTCA - -a -s simMouse_chr6.simMouse.chr6 299384 23 + 636262 AAGTGGTAGAAATTATGTTAGGC -s Anc0.Anc0refChr8 7333 17 - 17196 ------TTGTAATTATGTAAGAA -s Anc1.Anc1refChr8 51282 23 - 57822 ATATGGTTGTAATTATGTAAGAA -s Anc2.Anc2refChr8 1432 17 - 12804 ------TTGTAATTATGTAAGAA -s mr.mrrefChr5 150017 23 + 294540 AAGTGGTTGTAATTATGTTAGGC -s simCow_chr6.simCow.chr6 312143 17 - 602619 ------TTGAAATTATGTAAGTA -s simDog_chr6.simDog.chr6 321316 17 - 593897 ------TTGTAATTATGCAAGAA -s simHuman_chr6.simHuman.chr6 366323 23 - 601863 ATATGGTTGTAATTACATAAGAA -s simRat_chr6.simRat.chr6 290262 23 + 647215 ACGTGGTTGTAGTTATGTTAGGC - -a -s simMouse_chr6.simMouse.chr6 299407 3 + 636262 ACA -s Anc0.Anc0refChr8 7351 3 - 17196 ACA -s Anc1.Anc1refChr8 51306 3 - 57822 ACA -s Anc2.Anc2refChr8 1450 3 - 12804 GCA -s mr.mrrefChr5 150040 3 + 294540 ACA -s simCow_chr6.simCow.chr6 312161 3 - 602619 GCA -s simDog_chr6.simDog.chr6 321334 3 - 593897 GCA -s simHuman_chr6.simHuman.chr6 366347 3 - 601863 ACA -s simRat_chr6.simRat.chr6 290285 3 + 647215 ACA - -a -s simMouse_chr6.simMouse.chr6 299410 49 + 636262 TAGCAAGATGGCTGTACAGTTGGGATAATAACTCCTCCTTTGATACACG -s Anc0.Anc0refChr8 7355 48 - 17196 TAGCAAGATAGCCATACAGCTGGGA-GGCAATTCCTTGTGTGACAGGGG -s Anc1.Anc1refChr8 51310 49 - 57822 TAGCAAGATAGCCATACAGCTGGGATGGCAATTCCTTGTGTGACAGGGG -s Anc2.Anc2refChr8 1454 48 - 12804 TAGCAAGATAACCATACAGCTGGGA-GGCACTTCCTTGTGTGACAGGGG -s mr.mrrefChr5 150043 49 + 294540 TAGCAAGATGGCTGTACAGTTGGGATAATAATTCCTCCTTTGATACAGG -s simCow_chr6.simCow.chr6 312165 48 - 602619 TAGGAATGTAACCATATAGCCGGTA-AGCACTTCCTTGTGTGACAGGGG -s simDog_chr6.simDog.chr6 321338 48 - 593897 TAGCAAGATAACCGTACAGCTGGGA-GGTACTTCCTTGTGAGACAGGGG -s simHuman_chr6.simHuman.chr6 366351 49 - 601863 TAGCAACAAAGCGATAAAGCTGGGATGGCAATTCCTTGTATGACAAGGG -s simRat_chr6.simRat.chr6 290288 47 + 647215 TAGT--GATGGCTGTACAGTTGGGACAATAATTCCTCCTGTGATACAGG - -a -s simMouse_chr6.simMouse.chr6 299459 7 + 636262 CCCATCC -s Anc0.Anc0refChr8 7403 4 - 17196 CCC---C -s Anc1.Anc1refChr8 51359 4 - 57822 CCC---C -s Anc2.Anc2refChr8 1502 4 - 12804 CCC---C -s mr.mrrefChr5 150092 7 + 294540 CCCATCC -s simCow_chr6.simCow.chr6 312213 4 - 602619 CTC---C -s simDog_chr6.simDog.chr6 321386 4 - 593897 CCC---C -s simHuman_chr6.simHuman.chr6 366400 4 - 601863 CCC---C -s simRat_chr6.simRat.chr6 290397 7 + 647215 CTCATCC - -a -s simMouse_chr6.simMouse.chr6 299466 2 + 636262 AG -s Anc0.Anc0refChr8 7407 2 - 17196 AG -s Anc1.Anc1refChr8 51363 2 - 57822 AG -s Anc2.Anc2refChr8 1506 2 - 12804 AG -s mr.mrrefChr5 150099 2 + 294540 AG -s simCow_chr6.simCow.chr6 312219 2 - 602619 AG -s simDog_chr6.simDog.chr6 321390 2 - 593897 AG -s simHuman_chr6.simHuman.chr6 366404 2 - 601863 AG -s simRat_chr6.simRat.chr6 290404 2 + 647215 AG - -a -s simMouse_chr6.simMouse.chr6 299468 64 + 636262 AAATAGCAAATAATTCACAAACGTCTTCCCCTCATGAAGTACATTTACTACATCAAATGTTTGT -s Anc0.Anc0refChr8 7409 64 - 17196 AAACAGCAAATAATTCAGATTTGTACTCCCCTTATCAAGTAGGTGTACTACATGAAGTGTTTGT -s Anc1.Anc1refChr8 51365 64 - 57822 AAACAGCAAATAATTCAGATTTGTACTCCCCTTATCAAGTAGGTGTACTACATGAAGTGTTTGT -s Anc2.Anc2refChr8 1508 64 - 12804 AAACAGCAAATAACTCAGATTTATACTCCTCTTATCAAGTAGGTGTACTACATGAAGTGTTTGC -s mr.mrrefChr5 150101 64 + 294540 AAATAGCAAATAATTCACAATCGTATTCCCCTCATGAAGTACATTTACTACATCAAATGTTTGT -s simCow_chr6.simCow.chr6 312221 64 - 602619 AAACATCAAATAACTCAGCTTTTTACTCTTCTTATTGAGTAGCCATACTACATGAAGTGTTTGC -s simDog_chr6.simDog.chr6 321393 64 - 593897 AAACAGTAAATAACTCAGATTTATACTCCTCTCATCAAGTAGGTGTACTACATGGAGTGTGTGC -s simHuman_chr6.simHuman.chr6 366406 64 - 601863 AAACAGCAAGTAATTCAAATTAGTACTCCCCTTATCAAGTTGGTGTCCTACATGAAGTCTTTGT -s simRat_chr6.simRat.chr6 290406 64 + 647215 AAATATGAAATAACTCACCATTTTATTTGCTTCATGAAGTACATTTACTACATTAAATGTTTGC - -a -s simMouse_chr6.simMouse.chr6 299532 42 + 636262 AGTCCCCCTACTTCATGGAGTGGTTCATCTGGTTGCAATTCT -s Anc0.Anc0refChr8 7475 37 - 17196 AGTCCC-ATACTTCTTGGAGCAGTTT----GGTGGCACCTGT -s Anc1.Anc1refChr8 51431 38 - 57822 AGTCCC-ATACTTCTTGGAGCAGTTTG---GGTGGCACCTGT -s Anc2.Anc2refChr8 1574 37 - 12804 AGTCCC-AGACTTATTGGAGCACTTT----GTTGACACCTGT -s mr.mrrefChr5 150165 39 + 294540 AGTCCCCATACTTCATGGAGCGGTTCA---GGTGGCAATTCT -s simCow_chr6.simCow.chr6 312287 37 - 602619 AGTCCC-AGACTTAGGGGAGCAGTTT----GTTGAGACCTGT -s simDog_chr6.simDog.chr6 321459 37 - 593897 AGTCCC-AGACTTATTGAAGCACTTT----GTTGACACCTGT -s simHuman_chr6.simHuman.chr6 366472 38 - 601863 AGTCCC-ATACTTCTAGGAGCAGATTG---GGTGGCACCTGT -s simRat_chr6.simRat.chr6 290470 39 + 647215 GATCCCCAAACTTCATGGAGCGGGCCA---GGTGGCAATTAT - -a -s simMouse_chr6.simMouse.chr6 299574 63 + 636262 TCAGTGTAACATGAAGGAGGGCTGCATTTTACTGCCATTTAAATATCTTCCCAAGATATATGT -s Anc0.Anc0refChr8 7512 62 - 17196 ACGGTGTAACA-GGACGAGGGACATGTTTTTCTGCCATGCAAATATTTTTCCAAGATGAATAC -s Anc1.Anc1refChr8 51469 63 - 57822 ACGGTGTAACACGGACGAGGGACATGTTTTTCTGCCATGCAAATATTTTTCCAAGATGAATAC -s Anc2.Anc2refChr8 1611 62 - 12804 AAGGTGGAACA-GGACGAGGGACATGTTTTTCTGCCATGCAAATATTTTTCCAAGATGAATAC -s mr.mrrefChr5 150204 63 + 294540 TCAGTGTAACATGAAGGAGGGCTGCATTTTACTGCCATTCAAATATCTTCCCAAGATGTATGT -s simCow_chr6.simCow.chr6 312324 62 - 602619 AAGGAGGAATA-GGCAGAAGGACATGTTCTGCTGCCATCCTAATATTTTTCCAAGGTTAATAC -s simDog_chr6.simDog.chr6 321496 62 - 593897 AAGGTGGAACA-GGACGAGGGACATGTTTTTGTGCCATGCAAATATTTTTCTGGCATGAATAC -s simHuman_chr6.simHuman.chr6 366518 12 - 601863 CCTGTTTAACAC--------------------------------------------------- -s simRat_chr6.simRat.chr6 290509 63 + 647215 GCTGTCGAATATGAAGGAGGGCTGCCTTTTACTGCCATTCAAATATCTTCCCAAGATGTATGT - -a -s simMouse_chr6.simMouse.chr6 299637 19 + 636262 CCACTGACTCTTGTCTTAA -s Anc0.Anc0refChr8 7589 13 - 17196 ------ACCCTTCTCTTAA -s Anc1.Anc1refChr8 51547 13 - 57822 ------ACCCTTCTCTTAA -s Anc2.Anc2refChr8 1688 13 - 12804 ------ACCCTTCTCTTAA -s mr.mrrefChr5 150282 19 + 294540 CCACTGACTCTTGTCTTAA -s simCow_chr6.simCow.chr6 312400 13 - 602619 ------ACAGTACTCTTAA -s simDog_chr6.simDog.chr6 321573 13 - 593897 ------ACCCCTCTCTAAA -s simRat_chr6.simRat.chr6 290588 19 + 647215 CCACTAACTCTTGTCTTAA - -a -s simMouse_chr6.simMouse.chr6 299656 81 + 636262 TCTTTCTTATACGACTTTCTATAGAATCATTCATAGTCAGAATACAAAACCCCTGTCTGCAAGATGCACAGTCTGCGGATG -s Anc0.Anc0refChr8 7602 81 - 17196 TATCTCTTGCATGAATTTGTATAAATTCATCCAAAGTCCCCATACACAACCCCCTTCTGCAAGATCCCCATACAGCAGATG -s Anc1.Anc1refChr8 51560 81 - 57822 TATCTCTTGCATGAATTTGTATAAATTCATCCAAAGTCCCCATACACAACCCCCTTCTGCAAGATCCCCATACAGCAGATG -s Anc2.Anc2refChr8 1703 81 - 12804 TATCTCTTGCATGAATTTGTATAAATTCATCCAAAGTCCCCATACACAACCCCCTTCTGCAAGATCCCCATACAGCAGATG -s mr.mrrefChr5 150301 81 + 294540 TATTTCTTACATGACTTTGTATAAAATCATTCATAGTCAGAATACAAAACCCCCGTCTGCAAGATGCACAGTCTGCAGATG -s simCow_chr6.simCow.chr6 312416 48 - 602619 TACCTTTAGCAGGAATTTGTATAGATT---------------------------------AACATCCCCATCTAGCAGATG -s simDog_chr6.simDog.chr6 321588 81 - 593897 TATCTCCTGCATGGATTTGTATAAATTCATCCAAAGTCCCCATACACAACCCCCTTCTGCAAGATCCCCATACAGCAAATG -s simRat_chr6.simRat.chr6 290607 81 + 647215 TATTTCTTACATGACTTTGTATAAAATCATTCATAGTCATAATCCAAAATCCCCATCTGCAAGATGCACACTCCACAGATA - -a -s simMouse_chr6.simMouse.chr6 299737 27 + 636262 ATAGTCTCACTTGACTACTGGCCTATG -s Anc0.Anc0refChr8 7683 23 - 17196 ATAGTCTCACTCT----GAACTATTTG -s Anc1.Anc1refChr8 51641 23 - 57822 ATAGTCTCACTCT----GAACTATTTG -s Anc2.Anc2refChr8 1800 23 - 12804 ATAGTCTCACTCT----GAACTATTTG -s mr.mrrefChr5 150382 27 + 294540 ATAGTCTCACTCGACTAGTAGTCTATG -s simCow_chr6.simCow.chr6 312481 22 - 602619 ATACTCTCATGCC-----AATCATTTG -s simDog_chr6.simDog.chr6 321692 23 - 593897 ATAGGCCCACTCT----GAACTATTTG -s simRat_chr6.simRat.chr6 290688 27 + 647215 GTAGTCTCACTCAATTAGTAGTGTATG - -a -s simMouse_chr6.simMouse.chr6 299764 30 + 636262 TCCCCTGACACATCTTTAGTTGTTAATTTA -s Anc0.Anc0refChr8 7706 29 - 17196 TCTCTCCACCCATATATAGTTGCTAA-TTA -s Anc1.Anc1refChr8 51664 29 - 57822 TCTCTCCACCCATATATAGTTGCTAA-TTA -s Anc2.Anc2refChr8 1823 29 - 12804 TCTCTCCACCCATATATAGTTGCTAA-TTA -s mr.mrrefChr5 150409 30 + 294540 TCCCCTGACACATCTTTAGTTGTTAATTTA -s simCow_chr6.simCow.chr6 312503 24 - 602619 TCCATCCGCCCAT-TATAATAGCTA----- -s simDog_chr6.simDog.chr6 321896 29 - 593897 TCTCTCCACCCATATATAGTTGCAAA-TTA -s simDog_chr6.simDog.chr6 321715 29 - 593897 TCTCTCCACCCATATATAGTTGCTAA-TTA -s simRat_chr6.simRat.chr6 290715 30 + 647215 TCCCCTAACAAACCTTTAGTTGTTAAGATA - -a -s simMouse_chr6.simMouse.chr6 299794 10 + 636262 AATCCCCATC -s Anc0.Anc0refChr8 7735 10 - 17196 AAGCACGATC -s Anc1.Anc1refChr8 51693 10 - 57822 AAGCACGATC -s Anc2.Anc2refChr8 1852 10 - 12804 AAGCACGATC -s mr.mrrefChr5 150439 10 + 294540 AATCACCATC -s simDog_chr6.simDog.chr6 321927 10 - 593897 AAGCATAATC -s simDog_chr6.simDog.chr6 321744 10 - 593897 AAGCACGATC -s simRat_chr6.simRat.chr6 290745 10 + 647215 AACCACCATC - -a -s simMouse_chr6.simMouse.chr6 299804 8 + 636262 GACAATTG -s Anc0.Anc0refChr8 7745 7 - 17196 -ACAATGG -s Anc1.Anc1refChr8 51703 7 - 57822 -ACAATGG -s Anc2.Anc2refChr8 1862 7 - 12804 -ACAATGG -s mr.mrrefChr5 150449 8 + 294540 GACAATTG -s simDog_chr6.simDog.chr6 321937 7 - 593897 -ACAATGG -s simDog_chr6.simDog.chr6 321754 7 - 593897 -ACAATGG -s simRat_chr6.simRat.chr6 290762 8 + 647215 CACACTTG - -a -s simMouse_chr6.simMouse.chr6 299812 8 + 636262 TAATCAGA -s Anc0.Anc0refChr8 7773 8 - 17196 TTATCATG -s Anc1.Anc1refChr8 51731 8 - 57822 TTATCATG -s Anc2.Anc2refChr8 1892 8 - 12804 TTATCATG -s mr.mrrefChr5 150478 8 + 294540 TAATCAGA -s simCow_chr6.simCow.chr6 312551 8 - 602619 TCACCATA -s simDog_chr6.simDog.chr6 321967 8 - 593897 TTATCCTG -s simDog_chr6.simDog.chr6 321784 8 - 593897 TTATCATG -s simRat_chr6.simRat.chr6 290791 8 + 647215 CAATCAGA - -a -s simMouse_chr6.simMouse.chr6 299820 57 + 636262 TTGGGTTACACATCAGCCTGCCTGATGTACAGAACACTCCTTCCAAGCAAGTTGCTT -s Anc0.Anc0refChr8 7781 41 - 17196 TGG----ACCTATCTGATGTA--------GAGAAC---CATTTC-AACACAAAGCTT -s Anc1.Anc1refChr8 51739 41 - 57822 TGG----ACCTATCTGATGTA--------GAGAAC---CATTTC-AACACAAAGCTT -s Anc2.Anc2refChr8 1900 41 - 12804 TGG----ACCTATCTGATGTA--------GAGAAC---CATTTC-AACACAAAGCTT -s mr.mrrefChr5 150486 48 + 294540 TTGGGTTACACATCAGCCTGC--------CAGAACACTCCTTCC-AGCAAGTTGCTT -s simCow_chr6.simCow.chr6 312567 41 - 602619 TGG----ACCGTTCTGATATA--------CAGGTC---CATTTC-AAAACAAAGCTT -s simDog_chr6.simDog.chr6 321975 41 - 593897 CAG----ACCTGTCTGGTGTA--------GAGAGC---CATTTC-AACACAAAGTTT -s simDog_chr6.simDog.chr6 321792 41 - 593897 TGG----ATCTATCTCATGTA--------GAGAAC---CATTTC-AACACAAAGCTT -s simRat_chr6.simRat.chr6 290799 48 + 647215 TTGGGTTACAGATCAGTCTTC--------CAGTACGCTCCTTCT-AGCGAGTTGCTT - -a -s simMouse_chr6.simMouse.chr6 299877 4 + 636262 GTTT -s Anc0.Anc0refChr8 7822 4 - 17196 CTGT -s Anc1.Anc1refChr8 51780 4 - 57822 CTGT -s Anc2.Anc2refChr8 1941 4 - 12804 CTGT -s mr.mrrefChr5 150534 4 + 294540 GTTT -s simCow_chr6.simCow.chr6 312608 4 - 602619 TTGT -s simDog_chr6.simDog.chr6 322017 4 - 593897 CTGC -s simDog_chr6.simDog.chr6 321833 4 - 593897 CTGT -s simRat_chr6.simRat.chr6 290847 4 + 647215 GTTT - -a -s simMouse_chr6.simMouse.chr6 299881 59 + 636262 AGTCCCCACAGCTGTGGATGCCACAACAATTTGAAATACAAGCTGTCTGCTTGTGAACC -s Anc0.Anc0refChr8 7826 59 - 17196 AGTCTCAATAGTCTTGGATGGCCCAGAAATTAGAACTTCGATTCACCTGTGATTGACCC -s Anc1.Anc1refChr8 51784 59 - 57822 AGTCTCAATAGTCTTGGATGGCCCAGAAATTAGAACTTCGATTCACCTGTGATTGACCC -s Anc2.Anc2refChr8 1950 59 - 12804 AGTCTCAATAGTCTTGGATGGCCCAGAAATTAGAACTTCGATTCACCTGTGATTGACCC -s mr.mrrefChr5 150538 59 + 294540 AGTCCCCACAGCTGTGGATGCCACAACAATTTGAAATACAAGCTGTCTGCTTGTGAACC -s simCow_chr6.simCow.chr6 312617 59 - 602619 AGCCTCAATGGCTTAGGATGGCCCAGCAATTAGTACTTCAATCCACCTATCATTGATCT -s simDog_chr6.simDog.chr6 322026 59 - 593897 AGTCTCAATAGTATTGGATGGCCCAGAAATTAGAACTTTGATTCACCTGTGATTGACCC -s simDog_chr6.simDog.chr6 321842 54 - 593897 AGTCTCAATAGTCTTGGATGGCCCAGAAATTAGAACTTCGATTCACCTGATTTG----- -s simRat_chr6.simRat.chr6 290851 59 + 647215 AGTCCCCACAGCCATGGATACTACAACAATTCAAAATCCTAGCTGTCTGCTCGAGAACC - -a -s simMouse_chr6.simMouse.chr6 299940 9 + 636262 AGCACACAT -s Anc0.Anc0refChr8 7885 9 - 17196 AGGATATGG -s Anc1.Anc1refChr8 51843 9 - 57822 AGGATATGG -s Anc2.Anc2refChr8 2010 9 - 12804 AGGATATGG -s mr.mrrefChr5 150597 9 + 294540 AGCACACAT -s simCow_chr6.simCow.chr6 312677 9 - 602619 GGAGTATGG -s simDog_chr6.simDog.chr6 322086 9 - 593897 AGGATATGG -s simRat_chr6.simRat.chr6 290910 9 + 647215 AGCACACAT - -a -s simMouse_chr6.simMouse.chr6 299949 8 + 636262 GGCAAGGG -s Anc0.Anc0refChr8 7894 8 - 17196 TGAAAGCA -s Anc1.Anc1refChr8 51852 8 - 57822 TGAAAGCA -s Anc2.Anc2refChr8 2019 8 - 12804 TGAAAGCA -s mr.mrrefChr5 150606 8 + 294540 GGCAAGGG -s simCow_chr6.simCow.chr6 312686 8 - 602619 TGTAAGAA -s simDog_chr6.simDog.chr6 322095 8 - 593897 TGAAAGCA -s simRat_chr6.simRat.chr6 290954 8 + 647215 GACATGGA - -a -s simMouse_chr6.simMouse.chr6 299957 38 + 636262 ACCAATTTCAGAGCTCACATAGGCCGGTTACCAAGAGT -s Anc0.Anc0refChr8 7902 10 - 17196 TCTAATTTCA---------------------------- -s Anc1.Anc1refChr8 51860 10 - 57822 TCTAATTTCA---------------------------- -s Anc2.Anc2refChr8 2027 10 - 12804 TCTAATTTCA---------------------------- -s mr.mrrefChr5 150614 38 + 294540 ACCAATTTCAGAGCTCACATAGGCCGGTTACCAAGAGT -s simCow_chr6.simCow.chr6 312712 10 - 602619 TGCAATTTGA---------------------------- -s simDog_chr6.simDog.chr6 322103 10 - 593897 TCTAATTTCA---------------------------- -s simRat_chr6.simRat.chr6 290962 38 + 647215 ACCAATTTCAGAGTTCATATAGGCCTGTTACCAAGAGT - -a -s simMouse_chr6.simMouse.chr6 299995 33 + 636262 TGGGATAAGGGGATTCGTCATTCTTCGTGATTA -s Anc0.Anc0refChr8 7912 14 - 17196 -------------------AGTTCTCGTGATTA -s Anc1.Anc1refChr8 51870 14 - 57822 -------------------AGTTCTCGTGATTA -s Anc2.Anc2refChr8 2037 14 - 12804 -------------------AGTTCTCGTGATTA -s mr.mrrefChr5 150652 33 + 294540 TGGGATAAGGGGATTCGTCATTCTTCGTGATTA -s simCow_chr6.simCow.chr6 312722 14 - 602619 -------------------AGTTCATGTGATAA -s simDog_chr6.simDog.chr6 322113 14 - 593897 -------------------AGTTCTCGTGATTA -s simRat_chr6.simRat.chr6 291036 33 + 647215 TGGCATAAGGGGGTTTGTCATTTGTCATGATTA - -a -s simMouse_chr6.simMouse.chr6 300028 43 + 636262 CAACCAAGGTTCAATATATCTTCAGATGGATGATCTACATCTT -s Anc0.Anc0refChr8 7926 40 - 17196 CTACATAAATTCATTATATCTTGAATTGTATGATC--CCTCT- -s Anc1.Anc1refChr8 51884 40 - 57822 CTACATAAATTCATTATATCTTGAATTGTATGATC--CCTCT- -s Anc2.Anc2refChr8 2226 40 - 12804 CTACATAAATTCATTATATCTTGAATTGTATGATC--CCTCT- -s mr.mrrefChr5 150685 43 + 294540 CAACCAAGGTTCAATATATCTTCAGATGGATGATCTACATCTT -s simCow_chr6.simCow.chr6 312948 40 - 602619 CTATCGAAATTCACTGCATCTTGGTTTGCATGATC--TCTAC- -s simDog_chr6.simDog.chr6 322334 40 - 593897 CTACATAAATTCATTATATCTTGAATTGTATGATC--CCTCT- -s simRat_chr6.simRat.chr6 291069 43 + 647215 TTACCAAGGTTCATTATATCTTGAGATGGATGATCTACGGCTT - -a -s simMouse_chr6.simMouse.chr6 300071 58 + 636262 TTTGAGTACCAGGGTTGTTGAGTACCAAGGGTCCAGTATTTACTTACTTGGCTAATAG -s Anc0.Anc0refChr8 7966 1 - 17196 ---------------------------------------------------------G -s Anc1.Anc1refChr8 51924 1 - 57822 ---------------------------------------------------------G -s Anc2.Anc2refChr8 2266 1 - 12804 ---------------------------------------------------------G -s mr.mrrefChr5 150728 58 + 294540 TTTGAGTACCAGGGTTGTTGAGTACCAAGGGTCCAGTATTTACTTACTTGGCTAATAG -s simCow_chr6.simCow.chr6 312988 1 - 602619 ---------------------------------------------------------G -s simDog_chr6.simDog.chr6 322374 1 - 593897 ---------------------------------------------------------G -s simRat_chr6.simRat.chr6 291116 58 + 647215 TTTGAGTACCAGGGTTTTTGAGTACTAGGGGCTCAGTATTTGTTTACTTGGCTCATAG - -a -s simMouse_chr6.simMouse.chr6 300129 32 + 636262 GAGCCCAATACTCCTGAATGTGGGGGATGAGA -s Anc0.Anc0refChr8 7967 32 - 17196 GCGGCCAATACTGCTCAATGTGGTTGATGAGA -s Anc1.Anc1refChr8 51925 32 - 57822 GCGGCCAATACTGCTCAATGTGGTTGATGAGA -s Anc2.Anc2refChr8 2267 32 - 12804 GCGGCCAATACTGCTCAATGTGGTTGATGAGA -s mr.mrrefChr5 150786 32 + 294540 GAGCCCAATACTCCTGAATGTGGGGGATGAGA -s simCow_chr6.simCow.chr6 313004 32 - 602619 GGGGCTAACACTACATAATGTGGGTGGTGGAA -s simDog_chr6.simDog.chr6 322375 32 - 593897 GCGGCCAATACTGCTCAATGTGGTTGATGAGA -s simRat_chr6.simRat.chr6 291174 32 + 647215 GGACCCAGTACTGCTTAATGTGGGGGATGTGA - -a -s simMouse_chr6.simMouse.chr6 300161 5 + 636262 ATATT -s Anc0.Anc0refChr8 7999 5 - 17196 ATGTA -s Anc1.Anc1refChr8 51957 5 - 57822 ATGTA -s Anc2.Anc2refChr8 2300 5 - 12804 ATGTA -s mr.mrrefChr5 150818 5 + 294540 ATATT -s simCow_chr6.simCow.chr6 313037 5 - 602619 ATGCA -s simDog_chr6.simDog.chr6 322408 5 - 593897 ATGTA -s simRat_chr6.simRat.chr6 291209 5 + 647215 CTATT - -a -s simMouse_chr6.simMouse.chr6 300166 63 + 636262 TTTAGAACTTGTGGAAAGGACCCTTGGGTGTGGGTGTATACCATAATCTCTAGCAGGTACCTG -s Anc0.Anc0refChr8 8004 39 - 17196 CTAAAAACTTCTAGAACCAAACA---------------------AGTTTTTTGTTGGTAC--- -s Anc1.Anc1refChr8 51962 39 - 57822 CTAAAAACTTCTAGAACCAAACA---------------------AGTTTTTTGTTGGTAC--- -s Anc2.Anc2refChr8 2305 39 - 12804 CTAAAAACTTCTAGAACCAAACA---------------------AGTTTTTTGTTGGTAC--- -s mr.mrrefChr5 150823 63 + 294540 TTTAGAACTTGTGGAAAGGACCCTTGGGTGTGGGTGTATACCATAATCTCTAGCAGGTACCTG -s simCow_chr6.simCow.chr6 313042 39 - 602619 CTAAGAACTGCTTGAGATAACAG---------------------AGATTCTCTTTAGTAC--- -s simDog_chr6.simDog.chr6 322415 39 - 593897 CTAAAAACTTCTAGAACCAAACA---------------------AGTTTTTTGTTGGTAC--- -s simRat_chr6.simRat.chr6 291214 63 + 647215 TTTGAAACTTGTGGAAAGTACCCTTGGGTGTGGGTGTATTCTATAATCTTTAGTTCATACATG - -a -s simMouse_chr6.simMouse.chr6 300229 14 + 636262 GATCTTGGTTACCT -s Anc0.Anc0refChr8 8043 14 - 17196 GATCAAAATTACCT -s Anc1.Anc1refChr8 52001 14 - 57822 GATCAAAATTACCT -s Anc2.Anc2refChr8 2344 14 - 12804 GATCAAAATTACCT -s mr.mrrefChr5 150886 14 + 294540 GATCTTGGTTACCT -s simCow_chr6.simCow.chr6 313081 14 - 602619 AAACAAAATTACCT -s simDog_chr6.simDog.chr6 322458 14 - 593897 GATCAAAATTACCT -s simRat_chr6.simRat.chr6 291277 14 + 647215 GATCTAGGTTACCC - -a -s simMouse_chr6.simMouse.chr6 300243 115 + 636262 TTTGAATTGACTTTTGTAGATTTACGCCGGTATACTCCAAGTAAAGTAGGTGATATAGGATAGGTGACTCTTCTGCCACTTCACAGTTCAATACCCTCCACCCACCATCCACATG -s Anc0.Anc0refChr8 8057 3 - 17196 T----------------------------------------------------------------------------------------------------------------TG -s Anc1.Anc1refChr8 52015 3 - 57822 T----------------------------------------------------------------------------------------------------------------TG -s Anc2.Anc2refChr8 2358 3 - 12804 T----------------------------------------------------------------------------------------------------------------TG -s mr.mrrefChr5 150900 111 + 294540 TTTGAATTGACTTTTGTAGATTTACGCCGGTATACTCCAAGTAAAG-AGGTGATATAGGATAGGTGACTCTTCTGCCACTTCACAGTTCAATACCCT---CCCACCATCCACATG -s simCow_chr6.simCow.chr6 313095 3 - 602619 T----------------------------------------------------------------------------------------------------------------CC -s simDog_chr6.simDog.chr6 322472 3 - 593897 T----------------------------------------------------------------------------------------------------------------TG -s simRat_chr6.simRat.chr6 291325 111 + 647215 TTCGAATTGACTGTCATAGATTTGTGCCAGTACACTTTGAGAAAAG-AGGTGATACAGGATAGTTGACTCTTCTGCCACTTCACAGTTCACTACCCC---CCCACCATCCACATG - -a -s simMouse_chr6.simMouse.chr6 300358 5 + 636262 TCCAA -s Anc0.Anc0refChr8 8060 5 - 17196 TCTAA -s Anc1.Anc1refChr8 52018 5 - 57822 TCTAA -s Anc2.Anc2refChr8 2361 5 - 12804 TCTAA -s mr.mrrefChr5 151011 5 + 294540 TCCAA -s simCow_chr6.simCow.chr6 313105 5 - 602619 TCTAT -s simDog_chr6.simDog.chr6 322475 5 - 593897 TCTAA -s simRat_chr6.simRat.chr6 291436 5 + 647215 TCCAA - -a -s simMouse_chr6.simMouse.chr6 300363 5 + 636262 TATTT -s Anc0.Anc0refChr8 8065 5 - 17196 GATTT -s Anc1.Anc1refChr8 52023 5 - 57822 GATTT -s Anc2.Anc2refChr8 2371 5 - 12804 GATTT -s mr.mrrefChr5 151016 5 + 294540 TATTT -s simCow_chr6.simCow.chr6 313115 5 - 602619 GAGTT -s simDog_chr6.simDog.chr6 322485 5 - 593897 GATTT -s simRat_chr6.simRat.chr6 291441 5 + 647215 TATTC - -a -s simMouse_chr6.simMouse.chr6 300368 4 + 636262 CAAG -s Anc0.Anc0refChr8 8070 4 - 17196 CAAG -s Anc1.Anc1refChr8 52028 4 - 57822 CAAG -s Anc2.Anc2refChr8 2376 4 - 12804 CAAG -s mr.mrrefChr5 151021 4 + 294540 CAAG -s simCow_chr6.simCow.chr6 313139 4 - 602619 CAAG -s simDog_chr6.simDog.chr6 322490 4 - 593897 CAAG -s simRat_chr6.simRat.chr6 291446 4 + 647215 CAAG - -a -s simMouse_chr6.simMouse.chr6 300372 16 + 636262 GCCTTTGCGTAGGACT -s Anc0.Anc0refChr8 8074 15 - 17196 ACTTTTGTGAGGGAC- -s Anc1.Anc1refChr8 52032 15 - 57822 ACTTTTGTGAGGGAC- -s Anc2.Anc2refChr8 2395 15 - 12804 ACTTTTGTGAGGGAC- -s mr.mrrefChr5 151025 16 + 294540 GCCTTTGCGTAGGACT -s simCow_chr6.simCow.chr6 313162 15 - 602619 ACTTTCATGAGGAAT- -s simDog_chr6.simDog.chr6 322509 15 - 593897 ACTTTTGTGAGGGAC- -s simRat_chr6.simRat.chr6 291450 16 + 647215 CTTTTTGTGTAGGACT - -a -s simMouse_chr6.simMouse.chr6 300388 8 + 636262 TTGAACAT -s Anc0.Anc0refChr8 8089 8 - 17196 TTGCACAT -s Anc1.Anc1refChr8 52047 8 - 57822 TTGCACAT -s Anc2.Anc2refChr8 2410 8 - 12804 TTGCACAT -s mr.mrrefChr5 151041 8 + 294540 TTGAACAT -s simCow_chr6.simCow.chr6 313177 8 - 602619 TCGCATGT -s simDog_chr6.simDog.chr6 322525 8 - 593897 TTGCACAT -s simRat_chr6.simRat.chr6 291466 8 + 647215 TTGCACAT - -a -s simMouse_chr6.simMouse.chr6 300396 8 + 636262 AGTCAATG -s Anc0.Anc0refChr8 8097 8 - 17196 GGTTAATG -s Anc1.Anc1refChr8 52055 8 - 57822 GGTTAATG -s Anc2.Anc2refChr8 2418 8 - 12804 GGTTAATG -s mr.mrrefChr5 151049 8 + 294540 AGTCAATG -s simCow_chr6.simCow.chr6 313185 8 - 602619 GAAGAATG -s simDog_chr6.simDog.chr6 322534 8 - 593897 GGTTAATG -s simRat_chr6.simRat.chr6 291474 8 + 647215 AGTCAATG - -a -s simMouse_chr6.simMouse.chr6 300404 13 + 636262 TGAGTAACCTGAG -s Anc0.Anc0refChr8 8105 12 - 17196 TGT-TCACCTGAC -s Anc1.Anc1refChr8 52063 12 - 57822 TGT-TCACCTGAC -s Anc2.Anc2refChr8 2427 12 - 12804 TGT-TCACCTGAC -s mr.mrrefChr5 151057 12 + 294540 TGA-TAACCTGAG -s simCow_chr6.simCow.chr6 313194 12 - 602619 TGC-TCACCTGAT -s simDog_chr6.simDog.chr6 322543 12 - 593897 TGT-TCACCTGAC -s simRat_chr6.simRat.chr6 291482 12 + 647215 CCA-TAACCTGAG - -a -s simMouse_chr6.simMouse.chr6 300417 16 + 636262 TATCCTTGACACTGAA -s Anc0.Anc0refChr8 8117 10 - 17196 T-TTTTTTAT-----T -s Anc1.Anc1refChr8 52075 10 - 57822 T-TTTTTTAT-----T -s Anc2.Anc2refChr8 2439 10 - 12804 T-TTTTTTAT-----T -s mr.mrrefChr5 151069 15 + 294540 T-TCCTTGACACTGAA -s simCow_chr6.simCow.chr6 313206 10 - 602619 T-CTTTGTAT-----T -s simDog_chr6.simDog.chr6 322558 10 - 593897 T-TTTTTTAT-----T -s simRat_chr6.simRat.chr6 291494 15 + 647215 T-TTCTTGACACTGAA - -a -s simMouse_chr6.simMouse.chr6 300433 23 + 636262 TAATTAATTTCATGCTGAGAGCA -s Anc0.Anc0refChr8 8127 23 - 17196 TAATTAACCTCAAGTCGTATGCC -s Anc1.Anc1refChr8 52085 23 - 57822 TAATTAACCTCAAGTCGTATGCC -s Anc2.Anc2refChr8 2449 23 - 12804 TAATTAACCTCAAGTCGTATGCC -s mr.mrrefChr5 151084 23 + 294540 TAATTAATTTCATGCTGAGAGCA -s simCow_chr6.simCow.chr6 313216 23 - 602619 TAGATAACTCTAAGTTGTGTAGC -s simDog_chr6.simDog.chr6 322572 23 - 593897 TAATTAACCTCAAGTCGTATGCC -s simRat_chr6.simRat.chr6 291509 23 + 647215 TCATTAATTTCATGCTGAGGGCA - -a -s simMouse_chr6.simMouse.chr6 300456 22 + 636262 AATTACAACTACAATTAATGGT -s Anc0.Anc0refChr8 8150 22 - 17196 AATTTCAGTTGAGACTAATAAT -s Anc1.Anc1refChr8 52108 22 - 57822 AATTTCAGTTGAGACTAATAAT -s Anc2.Anc2refChr8 2479 22 - 12804 AATTTCAGTTGAGACTAATAAT -s mr.mrrefChr5 151107 22 + 294540 AATTACAACTACAATTAATGGT -s simCow_chr6.simCow.chr6 313246 22 - 602619 AATCGCAGTCAAAACTAATATT -s simDog_chr6.simDog.chr6 322602 22 - 593897 AATTTCAGTTGAGACTAATAAT -s simRat_chr6.simRat.chr6 291532 22 + 647215 AAATATAACTACAATTAATGGT - -a -s simMouse_chr6.simMouse.chr6 300478 11 + 636262 AAGTTTCCAAG -s Anc0.Anc0refChr8 8172 7 - 17196 GACTTTC---- -s Anc1.Anc1refChr8 52130 7 - 57822 GACTTTC---- -s Anc2.Anc2refChr8 2501 7 - 12804 GACTTTC---- -s mr.mrrefChr5 151129 11 + 294540 AAGTTTCCAAG -s simCow_chr6.simCow.chr6 313269 7 - 602619 GATATTC---- -s simDog_chr6.simDog.chr6 322624 7 - 593897 GACTTTC---- -s simRat_chr6.simRat.chr6 291554 11 + 647215 AAGTTTCCAAG - -a -s simMouse_chr6.simMouse.chr6 300489 11 + 636262 AAATACTATTG -s Anc0.Anc0refChr8 8179 11 - 17196 AATTCATATAG -s Anc1.Anc1refChr8 52137 11 - 57822 AATTCATATAG -s Anc2.Anc2refChr8 2508 11 - 12804 AATTCATATAG -s mr.mrrefChr5 151140 11 + 294540 AAATACTATTG -s simCow_chr6.simCow.chr6 313280 11 - 602619 AATTAGTACAA -s simDog_chr6.simDog.chr6 322631 11 - 593897 AATTCATATAG -s simRat_chr6.simRat.chr6 291565 11 + 647215 AAATACTATTG - -a -s simMouse_chr6.simMouse.chr6 300500 27 + 636262 TTCGAACAGCTATAAGTTTATTAAATG -s Anc0.Anc0refChr8 8190 26 - 17196 TATGAAATGTCCTAAGTTT-CTAAATG -s Anc1.Anc1refChr8 52148 26 - 57822 TATGAAATGTCCTAAGTTT-CTAAATG -s Anc2.Anc2refChr8 2519 26 - 12804 TATGAAATGTCCTAAGTTT-CTAAATG -s mr.mrrefChr5 151151 27 + 294540 TTCGAACAGCTATAAGTTTATTAAATG -s simCow_chr6.simCow.chr6 313297 26 - 602619 CATAAGAAGTCCTGCAGTC-CTGACCG -s simDog_chr6.simDog.chr6 322642 26 - 593897 TATGAAATGTCCTAAGTTT-CTAAATG -s simRat_chr6.simRat.chr6 291576 27 + 647215 TATGGATAGCTATAAATCTGCTAATTG - -a -s simMouse_chr6.simMouse.chr6 300527 15 + 636262 TTTTTCCTTTCAAAC -s Anc0.Anc0refChr8 8216 15 - 17196 TTGTTCCTTTAGAAC -s Anc1.Anc1refChr8 52174 15 - 57822 TTGTTCCTTTAGAAC -s Anc2.Anc2refChr8 2545 15 - 12804 TTGTTCCTTTAGAAC -s mr.mrrefChr5 151178 15 + 294540 TTTTTCCTTTCAAAC -s simCow_chr6.simCow.chr6 313323 15 - 602619 TTGTTCCTTTAGAAC -s simDog_chr6.simDog.chr6 322669 15 - 593897 TTGTTCCTTTAGAAC -s simRat_chr6.simRat.chr6 291603 15 + 647215 TGCTTCCTTTAAAAC - -a -s simMouse_chr6.simMouse.chr6 300542 7 + 636262 TAGATGT -s Anc0.Anc0refChr8 8231 7 - 17196 TATATAG -s Anc1.Anc1refChr8 52189 7 - 57822 TATATAG -s Anc2.Anc2refChr8 2560 7 - 12804 TATATAG -s mr.mrrefChr5 151193 7 + 294540 TAGATGT -s simCow_chr6.simCow.chr6 313342 7 - 602619 TATATCT -s simDog_chr6.simDog.chr6 322684 7 - 593897 TATATAG -s simRat_chr6.simRat.chr6 291618 7 + 647215 TAGATAT - -a -s simMouse_chr6.simMouse.chr6 300549 17 + 636262 GAATTCATGTGCCATAG -s Anc0.Anc0refChr8 8238 17 - 17196 AACTTTATGCAACATAG -s Anc1.Anc1refChr8 52196 17 - 57822 AACTTTATGCAACATAG -s Anc2.Anc2refChr8 2567 17 - 12804 AACTTTATGCAACATAG -s mr.mrrefChr5 151200 17 + 294540 GAATTCATGTGCCATAG -s simCow_chr6.simCow.chr6 313349 17 - 602619 AAATTTATGGAACATAC -s simDog_chr6.simDog.chr6 322691 17 - 593897 AACTTTATGCAACATAG -s simRat_chr6.simRat.chr6 291629 17 + 647215 GAATTTATGTGACATAG - -a -s simMouse_chr6.simMouse.chr6 300566 2 + 636262 GC -s Anc0.Anc0refChr8 8255 2 - 17196 AT -s Anc1.Anc1refChr8 52213 2 - 57822 AT -s Anc2.Anc2refChr8 2641 2 - 12804 AT -s mr.mrrefChr5 151217 2 + 294540 GC -s simCow_chr6.simCow.chr6 313425 2 - 602619 AT -s simDog_chr6.simDog.chr6 322765 2 - 593897 AT -s simRat_chr6.simRat.chr6 291646 2 + 647215 GT - -a -s simMouse_chr6.simMouse.chr6 300568 95 + 636262 TTCTCACGGGTCTAGTGGTAGTTGTTAAACACTTCATTGTGAACCCAATGAAGCTCAACATATGGTGTAATCTAATCAGCACTCTCGCGAGTGCC -s Anc0.Anc0refChr8 8257 14 - 17196 TTGTCG---------------------------------------------------------------------------------CTAGTGCC -s Anc1.Anc1refChr8 52215 14 - 57822 TTGTCG---------------------------------------------------------------------------------CTAGTGCC -s Anc2.Anc2refChr8 2643 14 - 12804 TTGTCG---------------------------------------------------------------------------------CTAGTGCC -s mr.mrrefChr5 151219 14 + 294540 TTCTCA---------------------------------------------------------------------------------CGAGTGCC -s simCow_chr6.simCow.chr6 313429 14 - 602619 TTATTG---------------------------------------------------------------------------------TTAGTGCC -s simDog_chr6.simDog.chr6 322767 14 - 593897 TTGTCG---------------------------------------------------------------------------------CTAGTGCC -s simRat_chr6.simRat.chr6 291648 14 + 647215 GTCTCA---------------------------------------------------------------------------------CAAGTGCC - -a -s simMouse_chr6.simMouse.chr6 300663 76 + 636262 CCTTTGACTCTTGGATACATGGAGTATGACTGACACTGTTTGAGCTAGCTTTTGGCTTCAGGGATGTACACAGCAA -s Anc0.Anc0refChr8 8271 5 - 17196 CCTTT----------------------------------------------------------------------- -s Anc1.Anc1refChr8 52229 5 - 57822 CCTTT----------------------------------------------------------------------- -s Anc2.Anc2refChr8 2659 5 - 12804 CCTTT----------------------------------------------------------------------- -s mr.mrrefChr5 151233 76 + 294540 CCTTTGACTCTTGGATACATGGAGTATGACTGACACTGTTTGAGCTAGCTTTTGGCTTCAGGGATGTACACAGCAA -s simCow_chr6.simCow.chr6 313445 5 - 602619 CCTTA----------------------------------------------------------------------- -s simDog_chr6.simDog.chr6 322783 5 - 593897 CCTTT----------------------------------------------------------------------- -s simRat_chr6.simRat.chr6 291662 76 + 647215 CCTTTGACTTTTGGATACATGAAGTATGACTGACACTGTTTGAGATGGCTATGGGCGTCAGAGATGTACACATCGA - -a -s simMouse_chr6.simMouse.chr6 300739 8 + 636262 TGCTACAG -s mr.mrrefChr5 151309 8 + 294540 TGCTACAG -s simRat_chr6.simRat.chr6 291739 8 + 647215 TATTACAG - -a -s simMouse_chr6.simMouse.chr6 300747 89 + 636262 TTGCTGCCAGCATCACAGCTGGAATGACAGATTGAATTGGCAATCAGTCTCTGGGAAAATATGGGTCCCCCTGCTACACTTTTTATTTT -s mr.mrrefChr5 151317 63 + 294540 TTGCTGCCAG---------------------TTGAATTGGCAATCAGTCTCTGGGAAAATATGGGTCCCCCTGCTACACTTTTT----- -s simRat_chr6.simRat.chr6 291748 63 + 647215 CTGGTGCCAG---------------------TTGAGTTGGCAATGAGTCTGTGGGAAAGTCTGTGTCCACCTCCTACCCTTTTT----- - -a -s simMouse_chr6.simMouse.chr6 300836 8 + 636262 AAGAAGTT -s Anc0.Anc0refChr8 8276 3 - 17196 -----ATT -s Anc1.Anc1refChr8 52234 3 - 57822 -----ATT -s Anc2.Anc2refChr8 2664 3 - 12804 -----ATT -s mr.mrrefChr5 151380 8 + 294540 AAGAAGTT -s simCow_chr6.simCow.chr6 313450 3 - 602619 -----ATT -s simDog_chr6.simDog.chr6 322788 3 - 593897 -----ATT -s simRat_chr6.simRat.chr6 291941 8 + 647215 AAGCAGTT - -a -s simMouse_chr6.simMouse.chr6 300844 52 + 636262 CATTCAAGAAGTGGTATCTACATCCCTACTTTAACAGACAATCTTACATGTC -s Anc0.Anc0refChr8 8279 47 - 17196 GATTTCATAACAGGCACCTGCATTCATCCAGTAACAAATAGGTTT-----CC -s Anc1.Anc1refChr8 52237 47 - 57822 GATTTCATAACAGGCACCTGCATTCATCCAGTAACAAATAGGTTT-----CC -s Anc2.Anc2refChr8 2667 47 - 12804 GATTTCATAACAGGCACCTGCATTCATCCAGTAACAAATAGGTTT-----CC -s mr.mrrefChr5 151388 52 + 294540 CATTCAAGAAGTGGTATCTACATCCCTACTTTAACAGACAATCTTACATGTC -s simCow_chr6.simCow.chr6 313470 47 - 602619 AATTTAATGACTGGTGCTTGCATACATCCACTAACAAATGGGTAC-----CT -s simDog_chr6.simDog.chr6 322791 47 - 593897 GATTTCATAACAGGCACCTGCATTCATCCAGTAACAAATAGGTTT-----CC -s simRat_chr6.simRat.chr6 291949 52 + 647215 CATTTAAGAAGTGGTATCTGCATCCTTACTTTACAAAACAATCTAACTTGCC - -a -s simMouse_chr6.simMouse.chr6 300896 20 + 636262 TACCACCCTCCTCAACAGCC -s Anc0.Anc0refChr8 8326 16 - 17196 TGGCTCCCTCATCGA----T -s Anc1.Anc1refChr8 52284 16 - 57822 TGGCTCCCTCATCGA----T -s Anc2.Anc2refChr8 2714 16 - 12804 TGGCTCCCTCATCGA----T -s mr.mrrefChr5 151440 20 + 294540 TACCACCCTCCTCAACAGCC -s simCow_chr6.simCow.chr6 313536 16 - 602619 TGGGTCTCCCATCCC----T -s simDog_chr6.simDog.chr6 322838 16 - 593897 TGGCTCCCTCATCGA----T -s simRat_chr6.simRat.chr6 292001 20 + 647215 TGCTGCCCTCCTCTACACCT - -a -s simMouse_chr6.simMouse.chr6 300916 5 + 636262 TGTGG -s Anc0.Anc0refChr8 8342 5 - 17196 TGTGG -s Anc1.Anc1refChr8 52300 5 - 57822 TGTGG -s Anc2.Anc2refChr8 2730 5 - 12804 TGTGG -s mr.mrrefChr5 151460 5 + 294540 TGTGG -s simCow_chr6.simCow.chr6 313585 5 - 602619 TGTTG -s simDog_chr6.simDog.chr6 322854 5 - 593897 TGTGG -s simRat_chr6.simRat.chr6 292021 5 + 647215 TGTGG - -a -s simMouse_chr6.simMouse.chr6 300921 15 + 636262 GGACCAAAGTTCTTG -s Anc0.Anc0refChr8 8347 15 - 17196 GGACCAAAATACCTA -s Anc1.Anc1refChr8 52305 15 - 57822 GGACCAAAATACCTA -s Anc2.Anc2refChr8 2736 15 - 12804 GGACCAAAATACCTA -s mr.mrrefChr5 151465 15 + 294540 GGACCAAAGTTCTTG -s simCow_chr6.simCow.chr6 313591 15 - 602619 TGGCCAGAATGCTTA -s simDog_chr6.simDog.chr6 322860 15 - 593897 GGACCAAAATACCTA -s simRat_chr6.simRat.chr6 292026 15 + 647215 AGACCAAAGTTCTTG - -a -s simMouse_chr6.simMouse.chr6 300936 7 + 636262 ATTCACT -s Anc0.Anc0refChr8 8362 7 - 17196 ACTCACT -s Anc1.Anc1refChr8 52320 7 - 57822 ACTCACT -s Anc2.Anc2refChr8 2751 7 - 12804 ACTCACT -s mr.mrrefChr5 151480 7 + 294540 ATTCACT -s simCow_chr6.simCow.chr6 313612 7 - 602619 ATTCCCT -s simDog_chr6.simDog.chr6 322875 7 - 593897 ACTCACT -s simRat_chr6.simRat.chr6 292041 7 + 647215 ATTCACT - -a -s simMouse_chr6.simMouse.chr6 300943 31 + 636262 TTGGGATTATCATTGGCTGGAGTCTACCTAA -s Anc0.Anc0refChr8 8369 24 - 17196 TTAAGGCCACCATCAGCGAAAGCC------- -s Anc1.Anc1refChr8 52327 24 - 57822 TTAAGGCCACCATCAGCGAAAGCC------- -s Anc2.Anc2refChr8 2758 24 - 12804 TTAAGGCCACCATCAGCGAAAGCC------- -s mr.mrrefChr5 151487 31 + 294540 TTGGGATTATCATTGGCTGGAGTCTACCTAA -s simCow_chr6.simCow.chr6 313619 24 - 602619 CCAAGGCTATCATTAGTGAAAGTC------- -s simDog_chr6.simDog.chr6 322882 24 - 593897 TTAAGGCCACCATCAGCGAAAGCC------- -s simRat_chr6.simRat.chr6 292056 31 + 647215 TCAGGATTATCATTGGTTGAAGTCTGCCTGA - -a -s simMouse_chr6.simMouse.chr6 300974 10 + 636262 CTTTTGGCTT -s Anc0.Anc0refChr8 8393 10 - 17196 CTGTGGGTTC -s Anc1.Anc1refChr8 52351 10 - 57822 CTGTGGGTTC -s Anc2.Anc2refChr8 2782 10 - 12804 CTGTGGGTTC -s mr.mrrefChr5 151518 10 + 294540 CTTTTGGCTT -s simCow_chr6.simCow.chr6 313643 10 - 602619 CCTTAGATTC -s simDog_chr6.simDog.chr6 322914 10 - 593897 CTGTGGGTTC -s simRat_chr6.simRat.chr6 292087 10 + 647215 CTTCTGGCTC - -a -s simMouse_chr6.simMouse.chr6 300984 3 + 636262 CAA -s Anc0.Anc0refChr8 8403 3 - 17196 CCA -s Anc1.Anc1refChr8 52361 3 - 57822 CCA -s Anc2.Anc2refChr8 2792 3 - 12804 CCA -s mr.mrrefChr5 151528 3 + 294540 CAA -s simCow_chr6.simCow.chr6 313656 3 - 602619 CCA -s simDog_chr6.simDog.chr6 322924 3 - 593897 CCA -s simRat_chr6.simRat.chr6 292097 3 + 647215 CAA - -a -s simMouse_chr6.simMouse.chr6 300987 17 + 636262 GTGATTGTTTTTACAAG -s Anc0.Anc0refChr8 8406 17 - 17196 TTTATTGTTTTCAGGGG -s Anc1.Anc1refChr8 52364 17 - 57822 TTTATTGTTTTCAGGGG -s Anc2.Anc2refChr8 2796 17 - 12804 TTTATTGTTTTCAGGGG -s mr.mrrefChr5 151531 17 + 294540 GTGATTGTTTTTACAAG -s simCow_chr6.simCow.chr6 313660 17 - 602619 CCTAATGTTTTTAGAGA -s simDog_chr6.simDog.chr6 322938 17 - 593897 TTTATTGTTTTCAGGGG -s simRat_chr6.simRat.chr6 292100 17 + 647215 GTAATTGTTCTTAGAAG - -a -s simMouse_chr6.simMouse.chr6 301004 12 + 636262 ATAGACCCAAGG -s Anc0.Anc0refChr8 8423 9 - 17196 ATATTC---ATG -s Anc1.Anc1refChr8 52381 9 - 57822 ATATTC---ATG -s Anc2.Anc2refChr8 2814 9 - 12804 ATATTC---ATG -s mr.mrrefChr5 151548 12 + 294540 ATAGACCCAAGG -s simCow_chr6.simCow.chr6 313678 9 - 602619 AGATCC---ACG -s simDog_chr6.simDog.chr6 322956 9 - 593897 ATATTC---ATG -s simRat_chr6.simRat.chr6 292117 12 + 647215 GTAGACTCAAGG - -a -s simMouse_chr6.simMouse.chr6 301016 23 + 636262 AATCTAAGATTGCTAACTTCTTC -s Anc0.Anc0refChr8 8432 23 - 17196 AACTTGAGGATGTTAACTCAACC -s Anc1.Anc1refChr8 52390 23 - 57822 AACTTGAGGATGTTAACTCAACC -s Anc2.Anc2refChr8 2823 23 - 12804 AACTTGAGGATGTTAACTCAACC -s mr.mrrefChr5 151560 23 + 294540 AATCTAAGATTGCTAACTTCTTC -s simCow_chr6.simCow.chr6 313687 23 - 602619 AACTCAAGAAAGTTAACTCTGCT -s simDog_chr6.simDog.chr6 322966 23 - 593897 AACTTGAGGATGTTAACTCAACC -s simRat_chr6.simRat.chr6 292129 23 + 647215 AATCTAAGATTGTTGACTTCTTC - -a -s simMouse_chr6.simMouse.chr6 301039 9 + 636262 CTCACTGGT -s Anc0.Anc0refChr8 8455 9 - 17196 CTCACTTGA -s Anc1.Anc1refChr8 52413 9 - 57822 CTCACTTGA -s Anc2.Anc2refChr8 2855 9 - 12804 CTCACTTGA -s mr.mrrefChr5 151583 9 + 294540 CTCACTGGT -s simCow_chr6.simCow.chr6 313719 9 - 602619 CTTGTGAGA -s simDog_chr6.simDog.chr6 322998 9 - 593897 CTCACTTGA -s simRat_chr6.simRat.chr6 292152 9 + 647215 CTCACTGGT - -a -s simMouse_chr6.simMouse.chr6 301048 11 + 636262 GACTTGGTAAA -s Anc0.Anc0refChr8 8464 11 - 17196 AGCCTGGGAAA -s Anc1.Anc1refChr8 52422 11 - 57822 AGCCTGGGAAA -s Anc2.Anc2refChr8 2864 11 - 12804 AGCCTGGGAAA -s mr.mrrefChr5 151592 11 + 294540 GACTTGGTAAA -s simCow_chr6.simCow.chr6 313728 11 - 602619 AACCTGAGATA -s simDog_chr6.simDog.chr6 323008 11 - 593897 AGCCTGGGAAA -s simRat_chr6.simRat.chr6 292161 11 + 647215 GACGTGATAAA - -a -s simMouse_chr6.simMouse.chr6 301059 1 + 636262 G -s Anc0.Anc0refChr8 8475 1 - 17196 T -s Anc1.Anc1refChr8 52433 1 - 57822 T -s Anc2.Anc2refChr8 2875 1 - 12804 T -s mr.mrrefChr5 151603 1 + 294540 G -s simCow_chr6.simCow.chr6 313739 1 - 602619 C -s simDog_chr6.simDog.chr6 323019 1 - 593897 T -s simRat_chr6.simRat.chr6 292301 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 301060 9 + 636262 ATGTATAGC -s Anc0.Anc0refChr8 8476 9 - 17196 AAGTGTAGC -s Anc1.Anc1refChr8 52434 9 - 57822 AAGTGTAGC -s Anc2.Anc2refChr8 2877 9 - 12804 AAGTGTAGC -s mr.mrrefChr5 151604 9 + 294540 ATGTATAGC -s simCow_chr6.simCow.chr6 313741 9 - 602619 AAGCACATC -s simDog_chr6.simDog.chr6 323025 9 - 593897 AAGTGTAGC -s simRat_chr6.simRat.chr6 292302 9 + 647215 TTAGATAGC - -a -s simMouse_chr6.simMouse.chr6 301069 3 + 636262 CAA -s Anc0.Anc0refChr8 8485 3 - 17196 CCA -s Anc1.Anc1refChr8 52443 3 - 57822 CCA -s Anc2.Anc2refChr8 2946 3 - 12804 CCA -s mr.mrrefChr5 151613 3 + 294540 CAA -s simCow_chr6.simCow.chr6 313875 3 - 602619 TGA -s simDog_chr6.simDog.chr6 323097 3 - 593897 CCA -s simRat_chr6.simRat.chr6 292311 3 + 647215 CAA - -a -s simMouse_chr6.simMouse.chr6 301072 56 + 636262 TCTCCCCCCTCATGTGCTTTATTGTGGATCAGTCCTACCCTGTACTACCTATTAAA -s Anc0.Anc0refChr8 8488 56 - 17196 CCCCCCCCCTGGTGGGCTTTAATGAAAATAATTCTGACCTTGAGCCATTTAGTACA -s Anc1.Anc1refChr8 52446 56 - 57822 CCCCCCCCCTGGTGGGCTTTAATGAAAATAATTCTGACCTTGAGCCATTTAGTACA -s Anc2.Anc2refChr8 2949 56 - 12804 CCCCCCCCCTGGTGGGCTTTAATGAAAATAATTCTGACCTTGAGCCATTTAGTACA -s mr.mrrefChr5 151616 56 + 294540 TCTCCCCCCTCATGTGCTTTATTGTGGATCAGTCCTACCCTGTACTACCTATTAAA -s simCow_chr6.simCow.chr6 313878 56 - 602619 CCTCCCCCCTGGTACGCTTTGATGACAATAATTCTGTCCTTCAGCTATTTATTAAA -s simDog_chr6.simDog.chr6 323101 56 - 593897 CCCCCCCCCTGGTGGGCTTTAATGAAAATAATTCTGACCTTGAGCCATTTAGTACA -s simRat_chr6.simRat.chr6 292314 56 + 647215 CCTCCCCCCTCCTGTGCTTTATTGAGGATCACTCCTACCCTGTGTTACCTATTAGA - -a -s simMouse_chr6.simMouse.chr6 301128 19 + 636262 GTGAAGTTGTGTTAGTCCA -s Anc0.Anc0refChr8 8544 17 - 17196 A--AAGTTGTGTTTGTTAA -s Anc1.Anc1refChr8 52502 17 - 57822 A--AAGTTGTGTTTGTTAA -s Anc2.Anc2refChr8 3007 17 - 12804 A--AAGTTGTGTTTGTTAA -s mr.mrrefChr5 151672 17 + 294540 G--AAGTTGTGTTAGTCCA -s simCow_chr6.simCow.chr6 313936 17 - 602619 A--AAGTTGTATTTGTTGA -s simDog_chr6.simDog.chr6 323159 17 - 593897 A--AAGTTGTGTTTGTTAA -s simRat_chr6.simRat.chr6 292370 17 + 647215 G--AAGGTGTGTTAAACCA - -a -s simMouse_chr6.simMouse.chr6 301147 4 + 636262 GTGT -s Anc0.Anc0refChr8 8561 4 - 17196 ATAT -s Anc1.Anc1refChr8 52519 4 - 57822 ATAT -s Anc2.Anc2refChr8 3024 4 - 12804 ATAT -s mr.mrrefChr5 151689 4 + 294540 GTGT -s simCow_chr6.simCow.chr6 313985 4 - 602619 ATAT -s simDog_chr6.simDog.chr6 323176 4 - 593897 ATAT -s simRat_chr6.simRat.chr6 292387 4 + 647215 GTAT - -a -s simMouse_chr6.simMouse.chr6 301151 3 + 636262 GTG -s Anc0.Anc0refChr8 8565 3 - 17196 AGA -s Anc1.Anc1refChr8 52523 3 - 57822 AGA -s Anc2.Anc2refChr8 3533 3 - 12804 AGA -s mr.mrrefChr5 151693 3 + 294540 GTG -s simCow_chr6.simCow.chr6 252826 3 - 602619 AGA -s simDog_chr6.simDog.chr6 323779 3 - 593897 AGA -s simRat_chr6.simRat.chr6 292391 3 + 647215 GTA - -a -s simMouse_chr6.simMouse.chr6 301154 6 + 636262 TAGGTG -s Anc0.Anc0refChr8 8568 6 - 17196 TAGTTG -s Anc1.Anc1refChr8 52526 6 - 57822 TAGTTG -s Anc2.Anc2refChr8 3536 6 - 12804 TAGTTG -s mr.mrrefChr5 151696 6 + 294540 TAGGTG -s simCow_chr6.simCow.chr6 252829 6 - 602619 TATTTG -s simDog_chr6.simDog.chr6 323794 6 - 593897 TAGTTG -s simRat_chr6.simRat.chr6 292394 6 + 647215 CAGGTG - -a -s simMouse_chr6.simMouse.chr6 301160 33 + 636262 TGCCCCCAATCCATAGATGAGGGTTTTCACTAT -s Anc0.Anc0refChr8 8574 14 - 17196 TGCCTCTTTGTCAC------------------- -s Anc1.Anc1refChr8 52532 14 - 57822 TGCCTCTTTGTCAC------------------- -s Anc2.Anc2refChr8 3542 14 - 12804 TGCCTCTTTGTCAC------------------- -s mr.mrrefChr5 151702 33 + 294540 TGCCCCCAATCCATAGATGAGGGTTTTCACTAT -s simCow_chr6.simCow.chr6 252835 11 - 602619 TTCCTCTC---AAC------------------- -s simDog_chr6.simDog.chr6 323812 14 - 593897 TGCCTCTTTGTCAT------------------- -s simRat_chr6.simRat.chr6 292400 33 + 647215 TGTCCCCAATCCATAGATGAGGGTTTTCATCAT - -a -s simMouse_chr6.simMouse.chr6 301193 160 + 636262 GCCATGATATACTATTAACTCTATCTACTACAAAGAGGTATGATCAGCAGTAGAGTGGTGGTTCAGGTAGAGTCATGGTTTAGTTGGTACCACTGATTAGTGTAAAGAATTTGATCTAAGTGTATCCTGAGCTTACCCCAGTTCCTTGCTTCAGCTATTT -s mr.mrrefChr5 151735 160 + 294540 GCCATGATATACTATTAACTCTATCTACTACAAAGAGGTATGATCAGCAGTAGAGTGGTGGTTCAGGTAGAGTCATGGTTTAGTTGGTACCACTGATTAGTGTAAAGAATTTGATCTAAGTGTATCCTGAGCTTACCCCAGTTCCTTGCTTCAGCTATTT -s simRat_chr6.simRat.chr6 292447 160 + 647215 GCCATGCTATACAGTTGACTCTTTCTACCACAAGGAGGTGTGATCAATAGTAGAGCAATGGTTTGGGTAGAGTCATGGTTTAGTTGGTTTCACCGATTAGCAAAAAGAATTCGATCTAAGTGCATCCTGAGTTTAATCCATTTCCTTGCTTTGGCTACCT - -a -s simMouse_chr6.simMouse.chr6 301353 23 + 636262 GCTCGAAGATTTGCTTTGCAAAT -s mr.mrrefChr5 151895 23 + 294540 GCTCGAAGATTTGCTTTGCAAAT -s simRat_chr6.simRat.chr6 292610 23 + 647215 GCTGTTAGACTTGCTTTGCAAAT - -a -s simMouse_chr6.simMouse.chr6 301376 97 + 636262 TAATGAGTGATGGCTTAATTACACCTAATCTTGTTGCTATTGTTACATTAGATGAACTACTCAGGTGTAATCCATTATTTCAATAGCTGTATCTAGG -s mr.mrrefChr5 151918 97 + 294540 TAATGAGTGATGGCTTAATTACACCTAATCTTGTTGCTATTGTTACATTAGATGAACTACTCAGGTGTAATCCATTATTTCAATAGCTGTATCTAGG -s simRat_chr6.simRat.chr6 292650 97 + 647215 TAATGAGCGATGGCTTGATTACACCTAATCTTGTTACTGTCCTTACATTAACTGAGCTACTCGGGAGTAATCTATTATTTCAAGAGCTGTATCTAGG - -a -s simMouse_chr6.simMouse.chr6 301473 87 + 636262 CACACAACAGATGGTTTTGACACCTTTTTGACATCTTATCTCAGAACCTTACCCCAGGACAAGCTATATCTCAGCACAATTTAAATT -s mr.mrrefChr5 152015 76 + 294540 CACACAACAGATGGTTTTGACACCTT-----------ATCTCAGAACCTTACCCCAGGACAAGCTATATCTCAGCACAATTTAAATT -s simRat_chr6.simRat.chr6 292748 76 + 647215 CACACAATAGATGGTTTCAACACCTT-----------ATCTCAGTATCTTACCCCAGGACAAGCTATATCCCAGCACAAATTAAATT - -a -s simMouse_chr6.simMouse.chr6 301560 104 + 636262 TATTTAATCATTTAATCTCATAAGCCCCGGTAACATATTCTTGCCAGAAACCACTTTCAATATTAGAGTTAGAGTTAGAGGCCTAAGCCACTGTCAGCCTAAAC -s Anc0.Anc0refChr8 8588 19 - 17196 -------------------------------------------------------------------------------------AGTCATTGTAAGCCTCAGG -s Anc1.Anc1refChr8 52546 19 - 57822 -------------------------------------------------------------------------------------AGTCATTGTAAGCCTCAGG -s Anc2.Anc2refChr8 3556 19 - 12804 -------------------------------------------------------------------------------------GGTCATTGTAGGCCTCAGG -s mr.mrrefChr5 152091 98 + 294540 TATTTAATCATTTAATCTCATAAGCCCCGGTAACATATTCTTGCCAGAAACCACTTTCAATATTAGA------GTTAGAGGCCTAAGCCACTGTCAGCCTAAAC -s simCow_chr6.simCow.chr6 252846 19 - 602619 -------------------------------------------------------------------------------------GGTTATTGCAGGCTTCAGG -s simDog_chr6.simDog.chr6 323826 19 - 593897 -------------------------------------------------------------------------------------GGTCATTGTAGGCCTCAGG -s simHuman_chr6.simHuman.chr6 366530 19 - 601863 -------------------------------------------------------------------------------------AGTCATTGTAAGCCTTAGG -s simRat_chr6.simRat.chr6 292831 98 + 647215 TATTTAATTATTTAATCTCATAAGCCCAGGTAAAATACTCTTGCCACAAACCAACAACAATATCAGA------GTTAAAGGCCTAAGCCACTGTTTGCTTAAAC - -a -s simMouse_chr6.simMouse.chr6 301664 68 + 636262 CATTGATTTCTAGACTCTTGACCATGTGCCCCCCTGTTTATCAATTTATATGAACTTGGCCCTCTCAG -s Anc0.Anc0refChr8 8607 21 - 17196 TATTTATTTTTGGAGGTGTAA----------------------------------------------- -s Anc1.Anc1refChr8 52565 21 - 57822 TATTTATTTTTGGAGGTGTAA----------------------------------------------- -s Anc2.Anc2refChr8 3576 21 - 12804 TATTTATTTTTGCAGGTGCAA----------------------------------------------- -s mr.mrrefChr5 152189 68 + 294540 CATTGATTTCTAGACTCTTGACCATGTGCCCCCCTGTTTATCAATTTATATGAACTTGGCCCTCTCAG -s simCow_chr6.simCow.chr6 252866 21 - 602619 GTCTATTTTTTGCAGGTGGAA----------------------------------------------- -s simDog_chr6.simDog.chr6 323846 21 - 593897 TATTTATTCCCACAGGTACAA----------------------------------------------- -s simHuman_chr6.simHuman.chr6 366549 21 - 601863 TATTTATGTTTGGAGGTGTAA----------------------------------------------- -s simRat_chr6.simRat.chr6 292929 68 + 647215 CATTGATTTCTGGACTCTCAACCATGTTCCCCCCTGTTTATCAGTATATATGAACTTGCCCTGCCCTG - -a -s simMouse_chr6.simMouse.chr6 301732 84 + 636262 CTTTCTCATGACTTGCTTGAGGTTTATTCAGGGCTATGTTGCAGTTCCTCAATACCTCTTCCAGATATTCCAGATTTCTAGATA -s mr.mrrefChr5 152257 84 + 294540 CTTTCTCATGACTTGCTTGAGGTTTATTCAGGGCTATGTTGCAGTTCCTCAATACCTCTTCCAGATATTCCAGATTTCTAGATA -s simRat_chr6.simRat.chr6 292998 84 + 647215 CTTTATCATGATTCGCTGGAGATTTATTCAGGGCTATGTTGCAATCCCTCAATGCCTCTTCCATGTGTACCAGTTTTCTAGATA - -a -s simMouse_chr6.simMouse.chr6 301816 23 + 636262 CCACAAAGTTTATGATCCCTGGA -s Anc0.Anc0refChr8 8628 21 - 17196 --ATAAGATTTATGCTCCCTAGA -s Anc1.Anc1refChr8 52586 21 - 57822 --ATAAGATTTATGCTCCCTAGA -s Anc2.Anc2refChr8 3597 21 - 12804 --GTAAGATTTATGCCCCCAAGA -s mr.mrrefChr5 152341 23 + 294540 CCACAAAGTTTATGATCCCTGGA -s simCow_chr6.simCow.chr6 252887 21 - 602619 --GTAAGATTTGTGCCCCCCCTC -s simDog_chr6.simDog.chr6 323867 21 - 593897 --GTAAGGTCTATGCCCCCAAGA -s simHuman_chr6.simHuman.chr6 366570 21 - 601863 --ATAGTATTTATGCTTCTTAGA -s simRat_chr6.simRat.chr6 293083 23 + 647215 CCACAAAGCCTATGATCCCTGGA - -a -s simMouse_chr6.simMouse.chr6 301839 81 + 636262 GTGGATATAAGTTGTTTTGCAATTGCTGGCGCCTTGGTTGGACACAGAGATGCACCATTATCGTGTGTTGCATAATAGGCA -s Anc0.Anc0refChr8 8649 43 - 17196 ATGGATCTGAGTTGTCTTACAGATGCTGATGCATTGGGTGGAT-------------------------------------- -s Anc1.Anc1refChr8 52607 43 - 57822 ATGGATCTGAGTTGTCTTACAGATGCTGATGCATTGGGTGGAT-------------------------------------- -s Anc2.Anc2refChr8 3618 43 - 12804 ATGGATCTGAGTTGTCATACCGATGCTGATGGATCAGGCCGAT-------------------------------------- -s mr.mrrefChr5 152364 70 + 294540 GTGGATATAAGTTGTTTTGCAATTGCTGGCGCCTTGGTTGGACACA-----------TTATCGTGTGTTGCATAATAGGCA -s simCow_chr6.simCow.chr6 252909 31 - 602619 GCTCACCTGGAGTGGAATGCTGATGCTG------------GAT-------------------------------------- -s simDog_chr6.simDog.chr6 323888 43 - 593897 ATGGATCTGAGTTGTCATACCAATGCTGATGGATCAGGCCGAT-------------------------------------- -s simHuman_chr6.simHuman.chr6 366591 43 - 601863 ATAGGTCTGAGTTGTCTTACAGATTCTGATGCATTGGATGGAT-------------------------------------- -s simRat_chr6.simRat.chr6 293106 70 + 647215 GTGGCTATGAGTTGTTTTGCAATTGCGGGTGCCTTAGTTGGGCACT-----------TTTTACTGTTTAGTGTCATGTGCA - -a -s simMouse_chr6.simMouse.chr6 301920 70 + 636262 GCAAGTGACTTCTTACTGTTAGTGTCATATGCATACTGTGCAAACTAGCACATATAAGGCTTGCTATGTC -s Anc0.Anc0refChr8 8692 39 - 17196 -------GCTTTTTACTGTTAGTGTCAAA------------------------ATAAGGTTTGCTATGTA -s Anc1.Anc1refChr8 52650 39 - 57822 -------GCTTTTTACTGTTAGTGTCAAA------------------------ATAAGGTTTGCTATGTA -s Anc2.Anc2refChr8 3661 39 - 12804 -------GCTTTTTACTGTTAGTGTCAAA------------------------ATAAAGTTTGCTATGTA -s mr.mrrefChr5 152434 70 + 294540 GCAAGTGACTTCTTACTGTTAGTGTCATATGCATACTGTGCAAACTAGCACATATAAGGCTTGCTATGTC -s simCow_chr6.simCow.chr6 252940 39 - 602619 -------GCATTTTACTGTCAGCATCAAA------------------------ATAAAGTTTGCTATGTA -s simDog_chr6.simDog.chr6 323931 39 - 593897 -------GTTTTTTGCTGTTAGTGTCAAA------------------------ATAAAGTTTGCTATGTA -s simHuman_chr6.simHuman.chr6 366634 39 - 601863 -------GCTTTTTACCACTAGTGTCACA------------------------ATAAGGTTTGCTATATA -s simRat_chr6.simRat.chr6 293222 70 + 647215 GTTGGGCACTTTTTAATGTTAGTGTCATACGCTTACTGTGGAAACTAGCAGATATAAAGCTTGCCATGTC - -a -s simMouse_chr6.simMouse.chr6 301990 18 + 636262 AAAAGCTCCAGAAAGCTA -s Anc0.Anc0refChr8 8731 18 - 17196 GAAACCTTCTGAAAGCAG -s Anc1.Anc1refChr8 52689 18 - 57822 GAAACCTTCTGAAAGCAG -s Anc2.Anc2refChr8 3700 18 - 12804 GAAACCTTCTGAAAGTAG -s mr.mrrefChr5 152504 18 + 294540 AAAAGCTCCAGAAAGCTA -s simCow_chr6.simCow.chr6 253001 18 - 602619 GAAACCTTCAGAAGGTAG -s simDog_chr6.simDog.chr6 323970 17 - 593897 -CCGTCTTCTCACAGTAG -s simHuman_chr6.simHuman.chr6 366673 18 - 601863 GAAACCTTCGGAAAGCAG -s simRat_chr6.simRat.chr6 293292 18 + 647215 AAAAGCTCCAGTAAGCTA - -a -s simMouse_chr6.simMouse.chr6 302008 32 + 636262 GGCAGAATCGATTAAGATGCTCTGAGAGGCAA -s Anc0.Anc0refChr8 8752 32 - 17196 GGCAAAATTGATCGTATGTTTCTGGGAGGCAA -s Anc1.Anc1refChr8 52710 32 - 57822 GGCAAAATTGATCGTATGTTTCTGGGAGGCAA -s Anc2.Anc2refChr8 3721 32 - 12804 GGCAAAATTGATCGTATGTTTCTGGGAGGCAA -s mr.mrrefChr5 152522 32 + 294540 GGCAGAATCGATTAAGATGCTCTGAGAGGCAA -s simCow_chr6.simCow.chr6 253022 32 - 602619 GTCAAAATTGATTGTATGTTTCTGGGGGGCAA -s simDog_chr6.simDog.chr6 323990 32 - 593897 GGATAAATTGATCGCATGATTTTGGGAGACAA -s simHuman_chr6.simHuman.chr6 366694 32 - 601863 GACAAAATTGATCGTATGTTTCTGGGAGGCGA -s simRat_chr6.simRat.chr6 293310 32 + 647215 GACAAAATTGATTAAAACAATCTGAGAGGCAA - -a -s simMouse_chr6.simMouse.chr6 302040 8 + 636262 CTGTTCCT -s Anc0.Anc0refChr8 8798 8 - 17196 CTGTTCCT -s Anc1.Anc1refChr8 52756 8 - 57822 CTGTTCCT -s Anc2.Anc2refChr8 3767 8 - 12804 CTGTTCCT -s mr.mrrefChr5 152554 8 + 294540 CTGTTCCT -s simCow_chr6.simCow.chr6 253067 8 - 602619 CTGTTTCT -s simDog_chr6.simDog.chr6 324031 5 - 593897 ---TTCCT -s simHuman_chr6.simHuman.chr6 366746 8 - 601863 CTGCTCCT -s simRat_chr6.simRat.chr6 293355 8 + 647215 CTGTTCCT - -a -s simMouse_chr6.simMouse.chr6 302048 6 + 636262 TTAAGG -s Anc0.Anc0refChr8 8806 6 - 17196 AAAATG -s Anc1.Anc1refChr8 52764 6 - 57822 AAAATG -s Anc2.Anc2refChr8 3849 6 - 12804 AAAATG -s mr.mrrefChr5 152562 6 + 294540 TTAAGG -s simCow_chr6.simCow.chr6 253176 6 - 602619 ATAATG -s simDog_chr6.simDog.chr6 324110 6 - 593897 AAAATA -s simHuman_chr6.simHuman.chr6 366754 6 - 601863 AAAATG -s simRat_chr6.simRat.chr6 293363 6 + 647215 TTCAGG - -a -s simMouse_chr6.simMouse.chr6 302054 39 + 636262 TTTAAAGTAGAAATAGGTATGGCTAGGATATGAATAGGA -s Anc0.Anc0refChr8 8819 26 - 17196 GTTGAACAGGAAATAT-----------GTAGG--TAGGA -s Anc1.Anc1refChr8 52777 28 - 57822 GTTGAACAGGAAATAT-----------GTAGGAATAGGA -s Anc2.Anc2refChr8 3862 26 - 12804 GTTGAACAGGAACTGT-----------GCAAG--TAACA -s mr.mrrefChr5 152568 28 + 294540 TTTAAAGTAGAAATAG-----------ATATGAATAGGA -s simCow_chr6.simCow.chr6 253189 5 - 602619 ----------------------------------TAACA -s simDog_chr6.simDog.chr6 324123 26 - 593897 GTTGAACAGGAACTGT-----------GCAAG--TAACA -s simHuman_chr6.simHuman.chr6 366767 28 - 601863 GTTGAACAGGAAATAT-----------GTGGGCACAGGA -s simRat_chr6.simRat.chr6 293369 28 + 647215 TTTAAAGTAGAAATAG-----------ATATGAATAGGA - -a -s simMouse_chr6.simMouse.chr6 302093 242 + 636262 TTTATGATACTTCTGTATCCCTGTACTCATTAGGAGAGCCTCACTTGAGAGAAATTTGGATGATGATAGTTGAATGGAATCTTCAACCATAGAGATAACTACGCAGGCTATATCTATTTGGGCGCACTAGAGCTTCCTGAAAATAATCTTGGAGTAAGTTTGAACACGCAGTACATGGGATATAAGGGGGTAAACCCATTCATAGCTGCATGTACAAGTCATCATGATTCAGGGCAGCGAAC -s Anc0.Anc0refChr8 8855 42 - 17196 TCATTTATATCTCAATATCCC---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AGTCATCTTGATCCAGGACAG----- -s Anc1.Anc1refChr8 52815 47 - 57822 TCATTTATATCTCAATATCCC---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AGTCATCTTGATCCAGGACAGAGAAC -s Anc2.Anc2refChr8 3898 42 - 12804 TCATTTATATCTCAATAACTC---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AGTCATCTTGATCCAGAACAG----- -s mr.mrrefChr5 152596 238 + 294540 TTTATGATACTTCTGTATCCCTGTACTCATTAGGAGAGCCTCACTTGAGAGAAAT--GGATGATGATAGTTGAATGGAATCTTCAACCATAGAGATA--TACGCAGGCTATATCTATTTGGGCGCACTAGAGCTTCCTGAAAATAATCTTGGAGTAAGTTTGAACACGCAGTACATGGGATATAAGGGGGTAAACCCATTCATAGCTGCATGTACAAGTCATCATGATTCAGGGCAGCGAAC -s simCow_chr6.simCow.chr6 253204 42 - 602619 TCATTTAAATCTCAATAAATC---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TGTCATCTTGATCTTGAACAG----- -s simDog_chr6.simDog.chr6 324159 41 - 593897 TCATT-ATATGTCACAAACTA---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AATCATCTTGATCCAGAACAG----- -s simHuman_chr6.simHuman.chr6 366805 47 - 601863 TCATTTATATCTCAATATTCC---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AGTTATCCTGATCCAGGAGAAAGAAC -s simRat_chr6.simRat.chr6 293397 238 + 647215 TTTGTGATATTTCTGGATCCCTGTACTCATCAGGAGAACATCATTCGAGACAAAT--GGATGATGATAGTTAAAAGGAATTGTCAACCATGGAGATA--TATTCAGGCTAGTTCTATTTGGGCCCACTAGAACTTCTTGAAAACAATCTTGGAGTATATTTGAATAGGAAATACATGGGCCATAAGGGGGTAAAGCCATACATAGCATCATATACCAGTCATTGTGATTCGGGGCAGGGAAC - -a -s simMouse_chr6.simMouse.chr6 302335 1 + 636262 A -s Anc0.Anc0refChr8 8897 1 - 17196 A -s Anc1.Anc1refChr8 52862 1 - 57822 A -s Anc2.Anc2refChr8 3940 1 - 12804 A -s mr.mrrefChr5 152834 1 + 294540 A -s simCow_chr6.simCow.chr6 253246 1 - 602619 A -s simDog_chr6.simDog.chr6 324200 1 - 593897 G -s simHuman_chr6.simHuman.chr6 366857 1 - 601863 A -s simRat_chr6.simRat.chr6 293635 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 302336 9 + 636262 ATCCGATAT -s Anc0.Anc0refChr8 8898 9 - 17196 ATTCAATAT -s Anc1.Anc1refChr8 52863 9 - 57822 ATTCAATAT -s Anc2.Anc2refChr8 3941 9 - 12804 ACTCAATAT -s mr.mrrefChr5 152835 9 + 294540 ATCCGATAT -s simCow_chr6.simCow.chr6 253247 9 - 602619 ACCCAATAT -s simDog_chr6.simDog.chr6 324201 9 - 593897 ACTCAGTAT -s simHuman_chr6.simHuman.chr6 366858 9 - 601863 ATTCAATAT -s simRat_chr6.simRat.chr6 293638 9 + 647215 ATCCAATAT - -a -s simMouse_chr6.simMouse.chr6 302345 36 + 636262 ATAGGAAGTTCATAGGATATGCTAGTGTTCACCTTT -s Anc0.Anc0refChr8 9412 35 - 17196 ACCAGTAGTTCATGA-ATTTGCTAGTGTCCACCTTT -s Anc1.Anc1refChr8 53377 35 - 57822 ACCAGTAGTTCATGA-ATTTGCTAGTGTCCACCTTT -s Anc2.Anc2refChr8 4457 35 - 12804 ACCAGTAGTTCATGA-AATTGCTTGTATCTACCTTT -s mr.mrrefChr5 152844 35 + 294540 ATAGGAAGTTCATAG-ATATGCTAGTGTTCACCTTT -s simCow_chr6.simCow.chr6 314924 35 - 602619 ACCAGTTGTTCATGA-AATTGCTTGTATCTACCTTC -s simDog_chr6.simDog.chr6 324676 14 - 593897 ACCAGTAGTTC----------------------TGT -s simHuman_chr6.simHuman.chr6 367395 35 - 601863 ACCAGCAATTCACGA-ATTTGCTAGTGCCCACTTTT -s simRat_chr6.simRat.chr6 293647 35 + 647215 ACAGGAAGTTCATAA-ATATGCTAGTGTTCACCTTG - -a -s simMouse_chr6.simMouse.chr6 302381 22 + 636262 TGGGGTGGCTTGAATTTTCTGT -s Anc0.Anc0refChr8 9448 18 - 17196 TGAGGTGGGATCAAT----TGC -s Anc1.Anc1refChr8 53413 18 - 57822 TGAGGTGGGATCAAT----TGC -s Anc2.Anc2refChr8 4493 18 - 12804 TGAGGTGAGATCAAT----TGC -s mr.mrrefChr5 152879 22 + 294540 TGGGGTGGCTTGAATTTTCTGT -s simCow_chr6.simCow.chr6 314960 18 - 602619 TCAGGTGAGATCAAT----TGT -s simDog_chr6.simDog.chr6 324691 18 - 593897 TGATGTGAGATCAAT----TGC -s simHuman_chr6.simHuman.chr6 367431 18 - 601863 TGAGGTGGGGTCAAT----TGC -s simRat_chr6.simRat.chr6 293682 22 + 647215 TGGGGCGGGTTGAATTTCTTGT - -a -s simMouse_chr6.simMouse.chr6 302403 127 + 636262 GGGGAGGACGATTGGGGCATGACCCTTGGGCATGACAACAATCTGACATACTCCCATTACAGTGGTGACTTATTAAACTTATATCTGTCATGCCCACTGGCTTCAGGAGTGAAGCCCATCTCTACTA -s Anc0.Anc0refChr8 9466 8 - 17196 GTGGAGGA----------------------------------------------------------------------------------------------------------------------- -s Anc1.Anc1refChr8 53431 8 - 57822 GTGGAGGA----------------------------------------------------------------------------------------------------------------------- -s Anc2.Anc2refChr8 4513 8 - 12804 GTGGAGGA----------------------------------------------------------------------------------------------------------------------- -s mr.mrrefChr5 152901 120 + 294540 GGGGAGGACGATTGGG-CATGACCCTTGGGCATGACAACAA------ATACTCCCATTACAGTGGTGACTTATTAAACTTATATCTGTCATGCCCACTGGCTTCAGGAGTGAAGCCCATCTCTACTA -s simCow_chr6.simCow.chr6 314980 8 - 602619 GTAGCAGA----------------------------------------------------------------------------------------------------------------------- -s simDog_chr6.simDog.chr6 324711 8 - 593897 GTGGAGGA----------------------------------------------------------------------------------------------------------------------- -s simHuman_chr6.simHuman.chr6 367449 8 - 601863 GTGGAGGA----------------------------------------------------------------------------------------------------------------------- -s simRat_chr6.simRat.chr6 293704 120 + 647215 AGAGAGACCAATTGGA-CATGACCATTGGGCATGACAACAG------ATACTCCCATCACAGTGGTGATTTATTATACTCATATTTATTCATCCCCATGGCTTCGGGAGTGAGGCCCATCTCTACTA - -a -s simMouse_chr6.simMouse.chr6 302530 6 + 636262 ACAGTT -s mr.mrrefChr5 153021 6 + 294540 ACAGTT -s simRat_chr6.simRat.chr6 293825 6 + 647215 ACAGTT - -a -s simMouse_chr6.simMouse.chr6 302536 43 + 636262 ACACATCACACCTCCCTCATCAGCATAAAAGGAGTTACTTTGC -s mr.mrrefChr5 153027 43 + 294540 ACACATCACACCTCCCTCATCAGCATAAAAGGAGTTACTTTGC -s simRat_chr6.simRat.chr6 293833 43 + 647215 ACACACCACACCCTCTTTGTCAGCATTAATGGAGTTACTTTGC - -a -s simMouse_chr6.simMouse.chr6 302579 22 + 636262 AGTTGTTCAGTTATGGTTGAAT -s mr.mrrefChr5 153070 22 + 294540 AGTTGTTCAGTTATGGTTGAAT -s simRat_chr6.simRat.chr6 293877 22 + 647215 AGTTGCTCAGTTATGCTTGAAT - -a -s simMouse_chr6.simMouse.chr6 302601 15 + 636262 AATTCCCTTATTGCC -s mr.mrrefChr5 153092 15 + 294540 AATTCCCTTATTGCC -s simRat_chr6.simRat.chr6 293903 15 + 647215 AGTTCCCTTATGGCC - -a -s simMouse_chr6.simMouse.chr6 302616 158 + 636262 AGGTGCTTCTTCATGCACTCACATTCATGACAACTGGGTCGTGATGCCAGTCCTTATACACAGACTCATTAACTTTTGACTGGGTGTGAGTAGCCAATCTTCTGAAGGTTGGAGACAACTCCACATCCTGCTGACAGAGTTGATCACCTTCATCCATT -s mr.mrrefChr5 153107 158 + 294540 AGGTGCTTCTTCATGCACTCACATTCATGACAACTGGGTCGTGATGCCAGTCCTTATACACAGACTCATTAACTTTTGACTGGGTGTGAGTAGCCAATCTTCTGAAGGTTGGAGACAACTCCACATCCTGCTGACAGAGTTGATCACCTTCATCCATT -s simRat_chr6.simRat.chr6 293921 158 + 647215 AGGTGCTTCCTCATGTGCTCACTTTCATAACACCTGGGTATTGATGCCAGTCCATCTACTCAGACTAATTAATTTTTGAGTGTGTGTGAACTGGCAGTCTTCTGAGGCTTGGAGACGACTTAAAATCCACCTGACAGAGGTGAGCACGTTCATCCGTT - -a -s simMouse_chr6.simMouse.chr6 302774 9 + 636262 ATATGTCTC -s mr.mrrefChr5 153265 9 + 294540 ATATGTCTC -s simRat_chr6.simRat.chr6 294080 9 + 647215 ATATGTCTC - -a -s simMouse_chr6.simMouse.chr6 302783 19 + 636262 TCTCTGAATAAATTAAGCT -s mr.mrrefChr5 153274 19 + 294540 TCTCTGAATAAATTAAGCT -s simRat_chr6.simRat.chr6 294356 19 + 647215 TCTGTCAATGAAGTCAACA - -a -s simMouse_chr6.simMouse.chr6 302802 41 + 636262 AGTAATGTCTCCAGTATATCTAACCTACAACCAGATACAAC -s mr.mrrefChr5 153293 41 + 294540 AGTAATGTCTCCAGTATATCTAACCTACAACCAGATACAAC -s simRat_chr6.simRat.chr6 294377 41 + 647215 AGTAATGCTTCCAGTATATCTGACCTACAGCCAGATACAAC - -a -s simMouse_chr6.simMouse.chr6 302843 10 + 636262 AATGGGTCAC -s mr.mrrefChr5 153334 10 + 294540 AACGGGTCAC -s simRat_chr6.simRat.chr6 294422 10 + 647215 GACGGGTCAT - -a -s simMouse_chr6.simMouse.chr6 302853 72 + 636262 CATTCTTTAGGTGACTTTATTATACTCGGTGCCTCTGTGCCATACACCAGGTACTCATTTTCCCTACTTACC -s Anc0.Anc0refChr8 6490 66 + 17196 CATTCTTTTGAGGGA------ATACGAGGTGCTTATGTGCCTTACACTTGTGACTTCTTCTCTCTATAGAGC -s Anc1.Anc1refChr8 3151 66 + 57822 CATTCTTTTGAGGGA------ATACGAGGTGCTTATGTGCCTTACACTTGTGACTTCTTCTCTCTATAGAGC -s Anc2.Anc2refChr8 6731 66 + 12804 CATTCTTTTGAGGGA------ATAGGAGGTGCTTATGTGCCTTACGAGTGTGAATTCTCCTCTCAATAAGGT -s mr.mrrefChr5 153380 72 + 294540 CATTCTTTAGATGGCTTTATTATACTAGGTGCCTCTGTGCCATACACTTGGGACTTATTTTCCCTACTGACC -s simCow_chr6.simCow.chr6 315803 62 - 602619 CTTTCTTTTTAGGGA------ATAGGAGGTCCTTTTGTGGCTTATGAATGCAAATTCTCCTCTCAATT---- -s simDog_chr6.simDog.chr6 267483 52 + 593897 CATTCATTTGAGGGA------ATAGGAGGTGCTTATCTGCCTTACGAGTGTGA--------------AAGGT -s simHuman_chr6.simHuman.chr6 233070 66 + 601863 CATTCTTTTAAGAGA------ATACAAGGTGCTTGTGTGCCTTAAACTTGAGACTTCTTCTCACTATCGAGC -s simRat_chr6.simRat.chr6 294468 72 + 647215 CATTCTTTAGATGGCCTTGTTATACTAGGTGCCTCTGTGGCATGCACTTGGGAATTGTTTTCCCAACTGACC - -a -s simMouse_chr6.simMouse.chr6 302925 18 + 636262 TCTCTATTGAGTGGAATT -s Anc0.Anc0refChr8 6560 11 + 17196 ACTCTTATGAG------- -s Anc1.Anc1refChr8 3221 11 + 57822 ACTCTTATGAG------- -s Anc2.Anc2refChr8 6801 11 + 12804 ACTCTTATGAG------- -s mr.mrrefChr5 153452 18 + 294540 ACTCTATTGAGTGGAATT -s simDog_chr6.simDog.chr6 267539 11 + 593897 ACTCTTATGAG------- -s simHuman_chr6.simHuman.chr6 233140 11 + 601863 ACTCTTCTGAG------- -s simRat_chr6.simRat.chr6 294540 18 + 647215 ACTCTATTGAGTGGAGAT - -a -s simMouse_chr6.simMouse.chr6 302943 9 + 636262 TGTTAAAGA -s Anc0.Anc0refChr8 6571 9 + 17196 AGTTATTTA -s Anc1.Anc1refChr8 3232 9 + 57822 AGTTATTTA -s Anc2.Anc2refChr8 6812 9 + 12804 AATTGTTTA -s mr.mrrefChr5 153470 9 + 294540 TGTTAAATA -s simDog_chr6.simDog.chr6 267554 9 + 593897 AATTGTTTA -s simHuman_chr6.simHuman.chr6 233151 9 + 601863 AGTTATGTA -s simRat_chr6.simRat.chr6 294558 9 + 647215 TGTAAAATA - -a -s simMouse_chr6.simMouse.chr6 302952 18 + 636262 GAAGGCGTAATGGGTGAA -s Anc0.Anc0refChr8 6580 18 + 17196 GAAGGAGTAAGAGGCAAG -s Anc1.Anc1refChr8 3241 18 + 57822 GAAGGAGTAAGAGGCAAG -s Anc2.Anc2refChr8 6821 18 + 12804 GATGGAAAAAGAGGCAAG -s mr.mrrefChr5 153479 18 + 294540 GAAGGAGTAATGGGCGAA -s simCow_chr6.simCow.chr6 315865 8 - 602619 ----------GAGGCAAG -s simDog_chr6.simDog.chr6 267565 18 + 593897 GATGGAAAAAGAGCAAAG -s simHuman_chr6.simHuman.chr6 233160 18 + 601863 GAAGGAGTTAGAGGCAAG -s simRat_chr6.simRat.chr6 294567 18 + 647215 AAAGGAGTAATGGGCGAA - -a -s simMouse_chr6.simMouse.chr6 302970 5 + 636262 AACTC -s Anc0.Anc0refChr8 6611 5 + 17196 AAGTC -s Anc1.Anc1refChr8 3272 5 + 57822 AAGTC -s Anc2.Anc2refChr8 6852 5 + 12804 AAGTC -s mr.mrrefChr5 153497 5 + 294540 AACTC -s simCow_chr6.simCow.chr6 315883 5 - 602619 AAGTC -s simDog_chr6.simDog.chr6 267596 5 + 593897 AAGTT -s simHuman_chr6.simHuman.chr6 233191 5 + 601863 AAGTC -s simRat_chr6.simRat.chr6 294585 5 + 647215 AGCTC - -a -s simMouse_chr6.simMouse.chr6 302975 5 + 636262 AAACT -s Anc0.Anc0refChr8 6616 5 + 17196 AAAAC -s Anc1.Anc1refChr8 3277 5 + 57822 AAAAC -s Anc2.Anc2refChr8 6858 5 + 12804 AAAGT -s mr.mrrefChr5 153502 5 + 294540 AAAAC -s simCow_chr6.simCow.chr6 315889 5 - 602619 AAAGT -s simDog_chr6.simDog.chr6 267602 5 + 593897 AAAGT -s simHuman_chr6.simHuman.chr6 233196 5 + 601863 TGAAC -s simRat_chr6.simRat.chr6 294590 5 + 647215 AAAAC - -a -s simMouse_chr6.simMouse.chr6 302980 23 + 636262 TTGGCCTACAACTCGAATAAACA -s Anc0.Anc0refChr8 6621 20 + 17196 TTGGAATACAACTTG---ACATA -s Anc1.Anc1refChr8 3282 20 + 57822 TTGGAATACAACTTG---ACATA -s Anc2.Anc2refChr8 6863 20 + 12804 TTGGAATACAACTTG---ATATA -s mr.mrrefChr5 153507 23 + 294540 TTGGCCTACAACTTGAATACACA -s simCow_chr6.simCow.chr6 315894 20 - 602619 TTGGAATACAACATG---AGATA -s simDog_chr6.simDog.chr6 267607 20 + 593897 TTGGAATACAGCTTG---ATATA -s simHuman_chr6.simHuman.chr6 233209 20 + 601863 TTGGAATATAACCTG---ACATG -s simRat_chr6.simRat.chr6 294595 23 + 647215 TTGGCGTACAACTTGAATGCACA - -a -s simMouse_chr6.simMouse.chr6 303003 22 + 636262 GAAGGCCTTAGATGGGAATGCC -s Anc0.Anc0refChr8 6641 22 + 17196 GAATTCCTTAAATGGGAATTTC -s Anc1.Anc1refChr8 3302 22 + 57822 GAATTCCTTAAATGGGAATTTC -s Anc2.Anc2refChr8 6888 22 + 12804 GAATTCCTTATATGGGAATTTC -s mr.mrrefChr5 153530 22 + 294540 GAAGGCCTTAAATGGGAATGCC -s simCow_chr6.simCow.chr6 315919 22 - 602619 GGGTTCTTTACATGGGAATTTC -s simDog_chr6.simDog.chr6 267633 22 + 593897 GAATTCCTTATATTGGGATTTC -s simHuman_chr6.simHuman.chr6 233229 22 + 601863 GAATTTCTTAAATGGGAATTTC -s simRat_chr6.simRat.chr6 294618 22 + 647215 AAAGGCCTTAAATGGGAAAGCC - -a -s simMouse_chr6.simMouse.chr6 303025 75 + 636262 TTAGACAAATAAACTACTTCAATGAATGGTCTGGTTACTACAAAAAGAAGTACAAGGATGTGAGCCACACTTCCC -s Anc0.Anc0refChr8 6663 74 + 17196 TCAAATGAATAAACCAATTTGATA-AGAGTCCTGTTACTATAACAAGAGGTACAAGAATGCAAGTCACTCATCCT -s Anc1.Anc1refChr8 3324 74 + 57822 TCAAATGAATAAACCAATTTGATA-AGAGTCCTGTTACTATAACAAGAGGTACAAGAATGCAAGTCACTCATCCT -s Anc2.Anc2refChr8 6910 74 + 12804 TCAAATGAATAAGCCAATTTGATA-AGATTGCTGTTACTATAACAAAACATACCAGAATGCAAGTCATTCATCCT -s mr.mrrefChr5 153552 74 + 294540 TTAGATGAATAAACTAATTCAATG-ATGGTCCGGTTACTATAACAAGAGGTACAAGAATGTGAGCCACACTTCCC -s simCow_chr6.simCow.chr6 315941 74 - 602619 TCAAACGAATGAGCCAATTTGATA-AGATTTCCGTTACTGTAACAAAACATACCAGAATGCATCTCAATTGACCT -s simDog_chr6.simDog.chr6 267656 54 + 593897 TTAGATGAATAAGCCAATTTGATA-AGATTGCTTTTGCCAT--------------------AAGTGATTCATCCT -s simHuman_chr6.simHuman.chr6 233251 74 + 601863 TCAAATGGATAAATCAATGTGATA-AGAGTCCTGTTACTATTACAAGCGGTGTAAGAATGCAAGTCACTCATCCT -s simRat_chr6.simRat.chr6 294640 74 + 647215 TTAGATGAATGAAATAATTCTATG-ATGGTCCAGTTATTATAACAAGAGGGACAAGAATGTGAGCCACACTTCCC - -a -s simMouse_chr6.simMouse.chr6 303100 31 + 636262 AAATCTTATAGGTCAGTACCTTAAGTATCAT -s Anc0.Anc0refChr8 6737 24 + 17196 AGGTATTGCAAGTCAGCA-------TCCTAA -s Anc1.Anc1refChr8 3398 24 + 57822 AGGTATTGCAAGTCAGCA-------TCCTAA -s Anc2.Anc2refChr8 6984 24 + 12804 GGGTATTGCAAGTCAGCA-------TCCTGA -s mr.mrrefChr5 153626 26 + 294540 AAATATTATAGGTCAGTAT-----GTACTAT -s simCow_chr6.simCow.chr6 316016 23 - 602619 GGGTATTGCAAGT-AGCA-------TCTTGA -s simDog_chr6.simDog.chr6 267710 22 + 593897 GAG-ATTG-GAGTCAGCA-------TCCAGA -s simHuman_chr6.simHuman.chr6 233325 24 + 601863 AGGTATTGCAAGCCAGCA-------TTCTAA -s simRat_chr6.simRat.chr6 294714 25 + 647215 -AATATTATAGGTCAGTAT-----GTACTGC - -a -s simMouse_chr6.simMouse.chr6 303131 1 + 636262 A -s Anc0.Anc0refChr8 6761 1 + 17196 C -s Anc1.Anc1refChr8 3422 1 + 57822 C -s Anc2.Anc2refChr8 7008 1 + 12804 C -s mr.mrrefChr5 153652 1 + 294540 A -s simCow_chr6.simCow.chr6 316046 1 - 602619 A -s simDog_chr6.simDog.chr6 267732 1 + 593897 C -s simHuman_chr6.simHuman.chr6 233349 1 + 601863 C -s simRat_chr6.simRat.chr6 294739 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 303132 17 + 636262 CAAAATATAATCCATTA -s Anc0.Anc0refChr8 6762 11 + 17196 CAAT------TCCATTC -s Anc1.Anc1refChr8 3423 11 + 57822 CAAT------TCCATTC -s Anc2.Anc2refChr8 7009 11 + 12804 CAAT------CCCATTC -s mr.mrrefChr5 153653 17 + 294540 CAATATATAATCCATTC -s simCow_chr6.simCow.chr6 316047 11 - 602619 CAAT------CCCACTC -s simDog_chr6.simDog.chr6 267772 11 + 593897 CAAT------CCCATTC -s simHuman_chr6.simHuman.chr6 233350 11 + 601863 CAAT------TCCATTC -s simRat_chr6.simRat.chr6 294740 17 + 647215 CAATATATAATCCATTC - -a -s simMouse_chr6.simMouse.chr6 303149 17 + 636262 TGACAACAGTTGAAGGG -s Anc0.Anc0refChr8 6777 17 + 17196 TGAAAACTGTGGAATGT -s Anc1.Anc1refChr8 3438 17 + 57822 TGAAAACTGTGGAATGT -s Anc2.Anc2refChr8 7024 17 + 12804 TGAAAACTGTGGAATGT -s mr.mrrefChr5 153670 17 + 294540 TGACAACAATTGAAGGG -s simCow_chr6.simCow.chr6 316062 17 - 602619 TGAACACTATTGAATGT -s simDog_chr6.simDog.chr6 267787 17 + 593897 TGAAAACTGTGGAGTGG -s simHuman_chr6.simHuman.chr6 233365 17 + 601863 CGGAAAGTGTGAAATGT -s simRat_chr6.simRat.chr6 294757 17 + 647215 TGACAACAATTATAGGA - -a -s simMouse_chr6.simMouse.chr6 303166 6 + 636262 GAGAAT -s Anc0.Anc0refChr8 6794 6 + 17196 AAAAAT -s Anc1.Anc1refChr8 3455 6 + 57822 AAAAAT -s Anc2.Anc2refChr8 7041 6 + 12804 AAAAAT -s mr.mrrefChr5 153687 6 + 294540 GAGAAT -s simCow_chr6.simCow.chr6 316079 4 - 602619 AGAA-- -s simDog_chr6.simDog.chr6 267810 6 + 593897 AAAAAT -s simHuman_chr6.simHuman.chr6 233382 6 + 601863 AAAAAT -s simRat_chr6.simRat.chr6 294774 6 + 647215 GTGTAT - -a -s simMouse_chr6.simMouse.chr6 303172 26 + 636262 AGTATTGGACTCTACCCACGGATTTT -s Anc0.Anc0refChr8 6801 26 + 17196 AGTATTAGACACTGCCCCTAGGCTTC -s Anc1.Anc1refChr8 3462 26 + 57822 AGTATTAGACACTGCCCCTAGGCTTC -s Anc2.Anc2refChr8 7048 26 + 12804 AGTGTTAGACACTGCCCTTAGGCTTC -s mr.mrrefChr5 153693 26 + 294540 AGTATTGGACTCTACCCCTGGATTTT -s simCow_chr6.simCow.chr6 316083 18 - 602619 ------AAACACTGCCCTTAGGCT-- -s simDog_chr6.simDog.chr6 267817 26 + 593897 AGTGTTAGACACTACCCTGTTGCTTC -s simHuman_chr6.simHuman.chr6 233389 26 + 601863 AGTATTAGACACTGCCCCTAGGCTTC -s simRat_chr6.simRat.chr6 294780 26 + 647215 AGTATTGGACTCTACCCCTGGATCTT - -a -s simMouse_chr6.simMouse.chr6 303198 106 + 636262 GAAAGGGCTTGATTTAACACTTAGCACACAGACAGCACATATGGATCAGTGTAACAGCACTTCATGAAAATAAGTTGGCTGATGAGGGATAGGGATGTAGGCTGAA -s Anc0.Anc0refChr8 6948 42 + 17196 GAAAGGGCTTAATTT------------------------------TCTGGGTGACAGGACT--ATGAAAATAAG-------------------------------- -s Anc1.Anc1refChr8 3609 42 + 57822 GAAAGGGCTTAATTT------------------------------TCTGGGTGACAGGACT--ATGAAAATAAG-------------------------------- -s Anc2.Anc2refChr8 7196 42 + 12804 AAAAGGCCTTAATTT------------------------------CCTGGGTGACAGGCCT--ATGAAAATAAG-------------------------------- -s mr.mrrefChr5 153719 106 + 294540 GAAAGGGCTTGATTTAACACTTAGCACACAGACAGCACATATGGATCAGTGTAACAGCACTTCATGAAAATAAGTTGGCTGATGAGGGATAGGGATGTAGGATGAA -s simCow_chr6.simCow.chr6 316212 3 - 602619 -----------------------------------------------------------------------AAG-------------------------------- -s simDog_chr6.simDog.chr6 267961 42 + 593897 AAAAGGCCTTAATTT------------------------------CCTGGGTGACAGGCCT--ATGAAAATAAA-------------------------------- -s simHuman_chr6.simHuman.chr6 233543 42 + 601863 GAAAAGGCTTAATTT------------------------------TCTGCTGGACAGGACT--ATCAATATAAG-------------------------------- -s simRat_chr6.simRat.chr6 294806 105 + 647215 GAAAGGGCTTGAATTACCAGTTAGCCCACAAACAGAACATATGGATTAGTATAACAGCACTTCATGAGAATAAATTGGCCGATGAGGGATAGGGATGTAGGAT-GA - -a -s simMouse_chr6.simMouse.chr6 303304 3 + 636262 TGA -s Anc0.Anc0refChr8 10783 3 - 17196 TGA -s Anc1.Anc1refChr8 54748 3 - 57822 TGA -s Anc2.Anc2refChr8 6157 3 - 12804 TAA -s mr.mrrefChr5 153825 3 + 294540 TGA -s simCow_chr6.simCow.chr6 286900 3 + 602619 TAC -s simDog_chr6.simDog.chr6 326498 3 - 593897 TAA -s simHuman_chr6.simHuman.chr6 368875 3 - 601863 TGA -s simRat_chr6.simRat.chr6 294911 3 + 647215 TGA - -a -s simMouse_chr6.simMouse.chr6 303307 5 + 636262 AGAAG -s Anc0.Anc0refChr8 10786 5 - 17196 AGAAG -s Anc1.Anc1refChr8 54751 5 - 57822 AGAAG -s Anc2.Anc2refChr8 6160 5 - 12804 AGAAG -s mr.mrrefChr5 153828 5 + 294540 AGAAG -s simCow_chr6.simCow.chr6 316566 5 - 602619 AGAAG -s simDog_chr6.simDog.chr6 326501 5 - 593897 TGGAG -s simHuman_chr6.simHuman.chr6 368878 5 - 601863 AGAAA -s simRat_chr6.simRat.chr6 294914 5 + 647215 AGAAG - -a -s simMouse_chr6.simMouse.chr6 303312 23 + 636262 TTCATAGAACAAAGTACTGTCAC -s Anc0.Anc0refChr8 10791 21 - 17196 T-CATAGAGTACA-CACCATCAC -s Anc1.Anc1refChr8 54756 21 - 57822 T-CATAGAGTACA-CACCATCAC -s Anc2.Anc2refChr8 6165 21 - 12804 T-CGTAGAGCACA-CACCATCAT -s mr.mrrefChr5 153833 23 + 294540 TTCATAGAATAAAGTACCGTCAC -s simCow_chr6.simCow.chr6 316572 17 - 602619 T-CCTAGAGCACA-CACCA---- -s simDog_chr6.simDog.chr6 326506 19 - 593897 ---GTGGAGCACA-CACCATCAT -s simHuman_chr6.simHuman.chr6 368883 21 - 601863 T-CATAGGCTCCA-CACCATCAC -s simRat_chr6.simRat.chr6 294919 23 + 647215 TTCATAAAATAAAGTACCGTCAC - -a -s simMouse_chr6.simMouse.chr6 303335 17 + 636262 CAGTTTTTCAGGAAGCC -s Anc0.Anc0refChr8 10812 13 - 17196 CAGTTTGTCAT----TC -s Anc1.Anc1refChr8 54777 13 - 57822 CAGTTTGTCAT----TC -s Anc2.Anc2refChr8 6187 13 - 12804 AAGTATATCAT----TA -s mr.mrrefChr5 153856 13 + 294540 CAGTTTGTCAG----CC -s simCow_chr6.simCow.chr6 316589 11 - 602619 --ATATATCAT----TG -s simDog_chr6.simDog.chr6 326526 13 - 593897 AAGTATATCAT----TA -s simHuman_chr6.simHuman.chr6 368904 13 - 601863 CAATTTGTTGT----TC -s simRat_chr6.simRat.chr6 294942 13 + 647215 CAGTTTGTCAG----CC - -a -s simMouse_chr6.simMouse.chr6 303352 35 + 636262 ACCTCTGTCTTCAATAGTTGTCATCCATTTCTTCG -s Anc0.Anc0refChr8 10831 35 - 17196 AGCTCTTTCTTCATTAGTTCTCACCCCTTTATTTG -s Anc1.Anc1refChr8 54796 35 - 57822 AGCTCTTTCTTCATTAGTTCTCACCCCTTTATTTG -s Anc2.Anc2refChr8 6206 35 - 12804 AGGCCTTTCTTCATTAGTTCTCACCCCTTTATTTG -s mr.mrrefChr5 153869 35 + 294540 ACCTCTGTCTTCAATAGTTGTCATCCATTTCTTTG -s simCow_chr6.simCow.chr6 316606 35 - 602619 AGGCCTCCCTTCACTAATTCTCACCCCTTCTTTTG -s simDog_chr6.simDog.chr6 326545 35 - 593897 AGGCCTTTCTTCATTTGTTCTCGGTCCTTTATTTT -s simHuman_chr6.simHuman.chr6 368923 35 - 601863 AGCTCTTTCTTTATTAGTTCTCACCCTTTTATCTG -s simRat_chr6.simRat.chr6 294955 35 + 647215 ACCTCTCTCTTCAATAGTTGTCATCTATTTCCTTG - -a -s simMouse_chr6.simMouse.chr6 303387 3 + 636262 CTA -s Anc0.Anc0refChr8 10866 3 - 17196 CTA -s Anc1.Anc1refChr8 54831 3 - 57822 CTA -s Anc2.Anc2refChr8 6241 3 - 12804 CTA -s mr.mrrefChr5 153904 3 + 294540 CTA -s simCow_chr6.simCow.chr6 316641 3 - 602619 TAA -s simDog_chr6.simDog.chr6 326590 3 - 593897 CTA -s simHuman_chr6.simHuman.chr6 368958 3 - 601863 CTA -s simRat_chr6.simRat.chr6 294990 3 + 647215 CTA - -a -s simMouse_chr6.simMouse.chr6 303390 38 + 636262 ATAGTATGTAGATCAATTCATCAGTTCGTCACTTTGAC -s Anc0.Anc0refChr8 10869 35 - 17196 ATAGTTTGTAGATCTATTTGTCACTCT--CAATTTC-C -s Anc1.Anc1refChr8 54834 36 - 57822 ATAGTTTGTAGATCTATTTGTCACTCT--CAATTTCTC -s Anc2.Anc2refChr8 6244 35 - 12804 ATAGTTTGTAGATCTATTTGTCACACT--CTATTAC-C -s mr.mrrefChr5 153907 38 + 294540 ATAGTATGTAGATCAATTCATCAGTTTGTCACTTTGTC -s simCow_chr6.simCow.chr6 316644 35 - 602619 ATAACTTGTGGATCTATTTGTCACACT--CTATAAC-C -s simDog_chr6.simDog.chr6 326593 35 - 593897 GTAGTTTGCAGATCTATTTGTCACACT--TTACTAC-C -s simHuman_chr6.simHuman.chr6 368961 36 - 601863 AGAGATCGTAGATCTATTTGACACTCT--CAATTTCTC -s simRat_chr6.simRat.chr6 294994 38 + 647215 ATAGTGTGTAGATCAATTCTTTAGTTTGTCACTTTGTC - -a -s simMouse_chr6.simMouse.chr6 303428 15 + 636262 CACCAAGCACATGCC -s Anc0.Anc0refChr8 10904 12 - 17196 C-CCATGAGC--GGT -s Anc1.Anc1refChr8 54870 12 - 57822 C-CCATGAGC--GGT -s Anc2.Anc2refChr8 6279 12 - 12804 C-CTATGAGC--GGG -s mr.mrrefChr5 153945 14 + 294540 C-CCAAGCACATGCT -s simCow_chr6.simCow.chr6 316679 12 - 602619 C-CTATCAGC--AGG -s simDog_chr6.simDog.chr6 326628 12 - 593897 C-CTATGAGT--GGG -s simHuman_chr6.simHuman.chr6 369010 12 - 601863 C-CCATGAGC--GGT -s simRat_chr6.simRat.chr6 295032 14 + 647215 C-CCAAGCACATGCT - -a -s simMouse_chr6.simMouse.chr6 303443 10 + 636262 ATGCCAATTG -s Anc0.Anc0refChr8 10918 10 - 17196 GTGCCTATTG -s Anc1.Anc1refChr8 54884 10 - 57822 GTGCCTATTG -s Anc2.Anc2refChr8 6293 10 - 12804 GTGTCTATTG -s mr.mrrefChr5 153961 10 + 294540 GTGCCAATTG -s simCow_chr6.simCow.chr6 316693 10 - 602619 ATGTCTATTG -s simDog_chr6.simDog.chr6 326642 10 - 593897 GTGTCTATTG -s simHuman_chr6.simHuman.chr6 369024 10 - 601863 GTGCCTATTG -s simRat_chr6.simRat.chr6 295048 10 + 647215 GGGCCAATTG - -a -s simMouse_chr6.simMouse.chr6 303453 12 + 636262 GTCGACCTTGGT -s Anc0.Anc0refChr8 10928 12 - 17196 ATCAGGTTTAGT -s Anc1.Anc1refChr8 54894 12 - 57822 ATCAGGTTTAGT -s Anc2.Anc2refChr8 6303 12 - 12804 AACAGGTTTAGT -s mr.mrrefChr5 153971 12 + 294540 GTCAACCTTGGT -s simCow_chr6.simCow.chr6 316703 12 - 602619 AGCAGGTCTAGT -s simDog_chr6.simDog.chr6 326654 12 - 593897 AACAGGTTTAAT -s simHuman_chr6.simHuman.chr6 369034 12 - 601863 ATTAGGTTTAGT -s simRat_chr6.simRat.chr6 295058 12 + 647215 GTCAACCTTGGT - -a -s simMouse_chr6.simMouse.chr6 303465 7 + 636262 GGTTAAA -s Anc0.Anc0refChr8 10940 7 - 17196 GGTTAAT -s Anc1.Anc1refChr8 54906 7 - 57822 GGTTAAT -s Anc2.Anc2refChr8 6322 7 - 12804 GGTTAAT -s mr.mrrefChr5 153983 7 + 294540 GGTTAAA -s simCow_chr6.simCow.chr6 316722 7 - 602619 GGGCAAT -s simDog_chr6.simDog.chr6 326678 7 - 593897 GGTTAAT -s simHuman_chr6.simHuman.chr6 369046 7 - 601863 GGTGAAT -s simRat_chr6.simRat.chr6 295070 7 + 647215 GGTTAAA - -a -s simMouse_chr6.simMouse.chr6 303472 24 + 636262 AGAGCTAAGGTTAACTCAGGAGGG -s Anc0.Anc0refChr8 10947 23 - 17196 AGAGCTAAAGTTAAC-CAGTAGTG -s Anc1.Anc1refChr8 54913 24 - 57822 AGAGCTAAAGTTAACTCAGTAGTG -s Anc2.Anc2refChr8 6329 23 - 12804 ATGGTGTAAGTTTGC-CGGTAGTC -s mr.mrrefChr5 153990 24 + 294540 AGAGCTAAGGTTAACTCAGGAGTG -s simCow_chr6.simCow.chr6 316829 23 - 602619 ATGCAGATAACTTGT-CAATAGTC -s simDog_chr6.simDog.chr6 326685 23 - 593897 ATGGTGTAAGTTTGC-CGGTAGTC -s simHuman_chr6.simHuman.chr6 369053 24 - 601863 AGAGCTAATGTTAACTCAGAAGTG -s simRat_chr6.simRat.chr6 295077 24 + 647215 AGAGCTAAGGCTAACTCAGGAGTG - -a -s simMouse_chr6.simMouse.chr6 303496 67 + 636262 CCAAAAACAACCAGAGGCAAATGTCGACAACTAACAACTTCCACTGGGAGAGTTATTCACATCTTTT -s Anc0.Anc0refChr8 11251 5 - 17196 CTTAC-------------------------------------------------------------- -s Anc1.Anc1refChr8 55224 5 - 57822 CTTAC-------------------------------------------------------------- -s Anc2.Anc2refChr8 6658 5 - 12804 CATAC-------------------------------------------------------------- -s mr.mrrefChr5 154014 5 + 294540 CTAAA-------------------------------------------------------------- -s simCow_chr6.simCow.chr6 317024 5 - 602619 CATTC-------------------------------------------------------------- -s simDog_chr6.simDog.chr6 326934 5 - 593897 CATAC-------------------------------------------------------------- -s simHuman_chr6.simHuman.chr6 369373 5 - 601863 CTTAC-------------------------------------------------------------- -s simRat_chr6.simRat.chr6 295104 5 + 647215 CTATT-------------------------------------------------------------- - -a -s simMouse_chr6.simMouse.chr6 303563 5 + 636262 TATGG -s Anc0.Anc0refChr8 11256 5 - 17196 TGTAG -s Anc1.Anc1refChr8 55229 5 - 57822 TGTAG -s Anc2.Anc2refChr8 6663 5 - 12804 TGTAG -s mr.mrrefChr5 154019 5 + 294540 TGTGG -s simCow_chr6.simCow.chr6 317029 5 - 602619 TCTAG -s simDog_chr6.simDog.chr6 326939 5 - 593897 TGTAG -s simHuman_chr6.simHuman.chr6 369378 5 - 601863 TGTAG -s simRat_chr6.simRat.chr6 295296 5 + 647215 TGGGG - -a -s simMouse_chr6.simMouse.chr6 303568 6 + 636262 AGCATT -s Anc0.Anc0refChr8 11262 2 - 17196 AG---- -s Anc1.Anc1refChr8 55235 2 - 57822 AG---- -s Anc2.Anc2refChr8 6669 2 - 12804 AG---- -s mr.mrrefChr5 154025 6 + 294540 AGCATT -s simCow_chr6.simCow.chr6 317035 2 - 602619 AT---- -s simDog_chr6.simDog.chr6 326945 2 - 593897 AG---- -s simHuman_chr6.simHuman.chr6 369384 2 - 601863 AG---- -s simRat_chr6.simRat.chr6 295302 6 + 647215 AGCCTT - -a -s simMouse_chr6.simMouse.chr6 303574 54 + 636262 CCTGCTATCTGATCTAGCGTGTGAATCAATCCTAGGCCCACAAATGTTGCTTTG -s Anc0.Anc0refChr8 11267 54 - 17196 CCTGCTAGCTGATCTAGCTTTTGAATTAATCACTGGCTCACATATGGTCTATGG -s Anc1.Anc1refChr8 55240 54 - 57822 CCTGCTAGCTGATCTAGCTTTTGAATTAATCACTGGCTCACATATGGTCTATGG -s Anc2.Anc2refChr8 6679 54 - 12804 CCTGCTAGCCAATCTTGCTTTTGAGTTAATCACTGGCTAGCATATGGTCTATGG -s mr.mrrefChr5 154034 54 + 294540 CCTGCTATCTGATCTAGCGTGTGAATCAATCCTAGGCCCACATATGTTGCTTGG -s simCow_chr6.simCow.chr6 317045 52 - 602619 CCTGATATCTGATCTTGCTTT--AGTTAATCACTGGCTTGCATATGGTCTATGG -s simDog_chr6.simDog.chr6 326955 54 - 593897 CATGCTAGCCAATCTTGCTTATGAGTTAGTGACTGGCTAGCATATGGTCTCTGG -s simHuman_chr6.simHuman.chr6 369389 46 - 601863 CCTGCT---TGATCTAGCTTTTGAATAAATCACTGGCTCACATCTA-----CGG -s simRat_chr6.simRat.chr6 295315 54 + 647215 CCTGCTACCTGATCTAGTGGGTGAATCAATCCTATGCCTGCATATGTTGCTTGG - -a -s simMouse_chr6.simMouse.chr6 303628 3 + 636262 ATA -s Anc0.Anc0refChr8 11321 3 - 17196 ATA -s Anc1.Anc1refChr8 55294 3 - 57822 ATA -s Anc2.Anc2refChr8 6733 3 - 12804 GTA -s mr.mrrefChr5 154088 3 + 294540 ATA -s simCow_chr6.simCow.chr6 317098 3 - 602619 TTA -s simDog_chr6.simDog.chr6 327009 3 - 593897 GTA -s simHuman_chr6.simHuman.chr6 369435 3 - 601863 ACA -s simRat_chr6.simRat.chr6 295369 3 + 647215 CAA - -a -s simMouse_chr6.simMouse.chr6 303631 23 + 636262 GCATGCGTTATGGGTGCTGTCAT -s Anc0.Anc0refChr8 11324 19 - 17196 ACATTAGTTA----TGTTGTCTT -s Anc1.Anc1refChr8 55297 19 - 57822 ACATTAGTTA----TGTTGTCTT -s Anc2.Anc2refChr8 6736 19 - 12804 ACATTAGTTA----TGGTGTCTT -s mr.mrrefChr5 154091 23 + 294540 GCATGAGTTATGGGTGTTGTCAT -s simCow_chr6.simCow.chr6 317101 19 - 602619 ACCTTTGTTA----TGGTGTTTT -s simDog_chr6.simDog.chr6 327299 19 - 593897 ACATTATGTA----TGGTGTCTT -s simHuman_chr6.simHuman.chr6 369438 19 - 601863 ACATTAGTTA----TGTTGTCTT -s simRat_chr6.simRat.chr6 295372 23 + 647215 GCATGAGTTATGGGTGTTGTTAC - -a -s simMouse_chr6.simMouse.chr6 303654 42 + 636262 TCAGCAATATAGAATTGACTGTCTAAAACTCATGAGTTATGG -s Anc0.Anc0refChr8 11346 27 - 17196 ACAGCAATATGGAGTTGATTGCTT--AAC------------- -s Anc1.Anc1refChr8 55319 29 - 57822 ACAGCAATATGGAGTTGATTGCTTAAAAC------------- -s Anc2.Anc2refChr8 6758 27 - 12804 ACAGCAATATGGAGTTGATTGCTT--AAC------------- -s mr.mrrefChr5 154117 42 + 294540 TCAGCAATATGGAATTGACTGCTTAAAACTCATGAGTTATGG -s simCow_chr6.simCow.chr6 317123 22 - 602619 ACAGCAATAA-----TGATTGCTT--GAC------------- -s simDog_chr6.simDog.chr6 327321 27 - 593897 ATAGCAATATGGAGTTGACTGCTC--AAC------------- -s simHuman_chr6.simHuman.chr6 369460 29 - 601863 ACAGGAACATGGATTTGATAGCTTAAAAC------------- -s simRat_chr6.simRat.chr6 295398 42 + 647215 TCAGCAATGTGGAATTGAATGCTTAATGCTCATGAGTTATGG - -a -s simMouse_chr6.simMouse.chr6 303696 83 + 636262 GTGCCATCGGTTGGCAATGGGGAATTAACTGCTTACAGCTAGGCATTGCTAGAACCCCTACTCAAAGTGCATCAAGATGCAAG -s Anc0.Anc0refChr8 11373 38 - 17196 ----------TGGGCAAT---------G----TT----------------AGAACTCCTGCCCACAGTAC------ATGCAAG -s Anc1.Anc1refChr8 55348 51 - 57822 ----------TGGGCAAT---------G----TTAAAACT---------CAGAACTCCTGCCCACAGTACTTGAAGATGCAAG -s Anc2.Anc2refChr8 6785 38 - 12804 ----------TGGGCAAT---------G----TT----------------ATAATTCCTGCCCACAGTAC------ATAGAAG -s mr.mrrefChr5 154159 74 + 294540 GTGCCATCGGTTGGCAAT---------ACTGCTTAAAACTAGGCATTGCTAGAACCCCTGCTCACAGTGCATCAAGATGCAAG -s simCow_chr6.simCow.chr6 317145 38 - 602619 ----------TGGGCTAT---------G----TT----------------ATAATTCCTGCCCAGAGTAC------ATAGAGG -s simDog_chr6.simDog.chr6 327348 38 - 593897 ----------TGGGCAAT---------G----GT----------------ATAATTCCCATCCACAGTAC------ATAGGAG -s simHuman_chr6.simHuman.chr6 369489 51 - 601863 ----------TGGGCAAT---------G----TTAAAACT---------CAGAACTCCTGCCCACAGTCATTGAAGGTGCAAG -s simRat_chr6.simRat.chr6 295441 74 + 647215 GTGTCATTCTTTGGCAAT---------ACTGCTTAAAACTAGGCACTGCTAAAACCCTTGCTCACAGTGGATCAAGATGCAAG - -a -s simMouse_chr6.simMouse.chr6 303779 31 + 636262 ATACATGAGAAAGGTGCAGATTCTAGCTGTG -s Anc0.Anc0refChr8 11411 31 - 17196 ACACCTGAGGAAGGTTTAAATTCTAGCTGCA -s Anc1.Anc1refChr8 55399 31 - 57822 ACACCTGAGGAAGGTTTAAATTCTAGCTGCA -s Anc2.Anc2refChr8 6823 31 - 12804 ACACCTGAGGGAGGTTTAAATTTTAGCTGCA -s mr.mrrefChr5 154233 31 + 294540 ATACATGAGAAAGGTGCAGATTCTAGCTGTG -s simCow_chr6.simCow.chr6 317194 25 - 602619 ATACCTGAGA---GTTTAAAT---AGCTGCC -s simDog_chr6.simDog.chr6 327386 29 - 593897 CCACC--AAGGAGGTCTAAATTTTAGCTGCA -s simHuman_chr6.simHuman.chr6 369540 31 - 601863 ACACCTGAGGAAGGTTTAAATTCTAGTTGCA -s simRat_chr6.simRat.chr6 295515 31 + 647215 ATACAGGAAAAAGGTGCTGATTCTAACTGTG - -a -s simMouse_chr6.simMouse.chr6 303810 99 + 636262 TGTGCCTCCCAGCTTTGGGTTCCAACTTTCACCCCACTGTTCACCAGAGACTCCAGGTATGGTCAAGATTAGGTTGATGTATATCTATGGGGTACACAT -s Anc0.Anc0refChr8 11443 84 - 17196 CACGTCTCCCAACTTTGACTT-------------CAGTGTTTACCAGC-ACTCCAGACATGG-TAAGATTAGATTTGCTTATATCAATAGAATTCCCAT -s Anc1.Anc1refChr8 55431 97 - 57822 CACGTCTCCCAACTTTGACTTCCAACTTTAACCCCAGTGTTTACCAGC-ACTCCAGACATGG-TAAGATTAGATTTGCTTATATCAATAGAATTCCCAT -s Anc2.Anc2refChr8 6855 84 - 12804 TACATATCCCAACTTTAACTT-------------TAAGGTTTACCAGC-ACTCCAGACATGG-TAAGATTAGATTTGCTTACATCAATAGAATTCCCAT -s mr.mrrefChr5 154264 98 + 294540 CATGCCTCCCAGCTTTGGGTTCCAACTTTAACCCCACTGTTCACCAGAGACTCCAGGTATGG-CAAGATTAGGTTGGTTTATATCTATGGGGTACACAT -s simCow_chr6.simCow.chr6 317220 84 - 602619 TGTATATCCAAACTTTAACCT-------------CAGGGTTTACCAGC-ACTCCAGATATGG-TAAGATTACATTTGCTTACATAAATTGAATTCCCAT -s simDog_chr6.simDog.chr6 327416 84 - 593897 TACATATCCCAACTTTAATTT-------------TAAGATTCACCAGC-ACCCCAGACATGG-TAGAATCAGATTTGCTTACTTCGATAGAATCCCCAT -s simHuman_chr6.simHuman.chr6 369572 92 - 601863 CACGTCTCCCAACTCTGTCTCCCAACTTTAACCCCAGTGTTTA------GCTACACACATGG-TAAGCTTAGAGTTGCTTATATCAATAGTATTCCCAT -s simRat_chr6.simRat.chr6 295546 98 + 647215 CATGCCTCCCAGCTATGGGTTCCAATCTTAAGCCCACTGTTCACCAGAGACTCCAGGTATGG-CAAGATTAAGTTGGTTTATATCTATGGGGTACACAT - -a -s simMouse_chr6.simMouse.chr6 303909 29 + 636262 ATGTGGCACACTGTCCCAGATTGAAACTT -s Anc0.Anc0refChr8 11528 28 - 17196 ATGTTGCACATTATCTCAGAT-AAAACCC -s Anc1.Anc1refChr8 55529 28 - 57822 ATGTTGCACATTATCTCAGAT-AAAACCC -s Anc2.Anc2refChr8 6940 28 - 12804 TTGTTGCACATTATCTCAGAT-AGAGCCC -s mr.mrrefChr5 154362 28 + 294540 ATGTGGCACATTGTCCCAGAT-GAAACCC -s simCow_chr6.simCow.chr6 317305 27 - 602619 TTGTGGCACATTATCT-AGAT-AGAGCCC -s simDog_chr6.simDog.chr6 327501 28 - 593897 TTGTTGCACATTGTCTCAGAT-AGAGCCC -s simHuman_chr6.simHuman.chr6 369665 28 - 601863 AGGTAGCACATTATCTCAGAT-AAAACCC -s simRat_chr6.simRat.chr6 295644 20 + 647215 ATGTGGCACATTGTCCC---------CCC - -a -s simMouse_chr6.simMouse.chr6 303938 119 + 636262 AAGCTTCACCAATGTAGTATTGACTATCTTGGACCTACAAGATCTTCCCCTAATAACTAGGGAAGGGCAGAATATTGATGAGTTGACTCTTGAGGTGCTAAAGTGCTAATATAAAGGGA -s Anc0.Anc0refChr8 11565 106 - 17196 AAGCTTCATAAATTTGTCTAGCACAACCTTGATTCTATAAGA----CCTCTATTAACTGGGAAAGGACAAATTATAGATGAATTCATTCTAGAGGTGCTAAAAT---------AATGAG -s Anc1.Anc1refChr8 55566 106 - 57822 AAGCTTCATAAATTTGTCTAGCACAACCTTGATTCTATAAGA----CCTCTATTAACTGGGAAAGGACAAATTATAGATGAATTCATTCTAGAGGTGCTAAAAT---------AATGAG -s Anc2.Anc2refChr8 6977 106 - 12804 CGGCTTCATAAATTTGTCTGGCACAACCTTGATTCTACAAGA----CCTCTATTAACTGGGAAAGGACAAATAATAGATGCATTCATTCTAGAGGTGCTAAAAT---------AAAGGG -s mr.mrrefChr5 154390 119 + 294540 AAGCTTCACCAATGTAGTAATGACTATCTTGGATCTATAAGATCTTCCTCTAATAACTGGGGAAGGGCAGAATATTGATGAGTTGACTCTAGAGGTGCTAAAATGCTAATATAAATGAA -s simCow_chr6.simCow.chr6 317334 97 - 602619 --------TAAATTTGTCTTTTACAACTTTGTATCTCAATGA----CCTTTATTGATTGAGAAAAAGCAAATAATGGGTGGATTCATTCTAGAGGTACTAAAAT---------AA-GGG -s simDog_chr6.simDog.chr6 327538 106 - 593897 CGGCTTCATCAATTTGTCTGGCACAACCTTGATCCTACAAGA----CCTCCATTAACTGGGAAAGGACAAATAATAGATGCATTCAATCTAGTGGCGCTAAAAT---------AAAGGG -s simHuman_chr6.simHuman.chr6 369702 106 - 601863 AAGCTTCATAAATTTGTCCACAACAACCTTTACTGTATAAGA----CCTCTATTATCTGTTAAACGTCGAATTCCAGATGAATTCATTCTAGAGGTGCTGAAAT---------AATGAG -s simRat_chr6.simRat.chr6 295664 119 + 647215 AAGCTTCACCAATGTAGTGATGACTATCTAGGGTCTATAAGATCTTCCTCTAATAACTGGGGAAGGGTAGAATATTTATGAGTTGACTCTAGAGGTGTTAAAATGCTAATATGAATGAA - -a -s simMouse_chr6.simMouse.chr6 304057 18 + 636262 TTGTGATACTGAGCCACA -s Anc0.Anc0refChr8 11671 18 - 17196 TCCTGATACTGAGCCACG -s Anc1.Anc1refChr8 55672 18 - 57822 TCCTGATACTGAGCCACG -s Anc2.Anc2refChr8 7083 18 - 12804 TCCTGATACTGAGCCACG -s mr.mrrefChr5 154509 18 + 294540 TTGTGATACTGAGCCACA -s simCow_chr6.simCow.chr6 317431 18 - 602619 CCCTGATACTTAGCCACG -s simDog_chr6.simDog.chr6 327645 18 - 593897 TCCTGTTACTGAGCCGCG -s simHuman_chr6.simHuman.chr6 369808 18 - 601863 TCCTGATACTGAGCCACG -s simRat_chr6.simRat.chr6 295783 18 + 647215 TTGCAATACTGAGTCACA - -a -s simMouse_chr6.simMouse.chr6 304075 70 + 636262 TGAGTAGTCAAACAAGGAGTGTGACCCAGTAGCCAACCTAATCTGTGTACTCAGGGCCCCAGAGCTAGCT -s Anc0.Anc0refChr8 11689 69 - 17196 TGAGTATTGAAGCAAGGAGCATGCCCCAGTAACCAA-CTAATTTGTGTACTCAGGACCCTTCAGCTAGTT -s Anc1.Anc1refChr8 55690 69 - 57822 TGAGTATTGAAGCAAGGAGCATGCCCCAGTAACCAA-CTAATTTGTGTACTCAGGACCCTTCAGCTAGTT -s Anc2.Anc2refChr8 7101 69 - 12804 TGAGTATTAAGGCAAGAAGCATGCCCCAGCAACCTA-CTAATTTATGTATTCAGAACCCTTCAGCTAGTT -s mr.mrrefChr5 154527 70 + 294540 TGAGTAGTGAAACAAGGAGTGTGACCCAGTAGCCAACCTAATCTGTGTACTCAGGGCCCCAGAGCTAGCT -s simCow_chr6.simCow.chr6 317449 69 - 602619 TGAGTATCAAGGCAGGAAGGACACCCCAGCAACCGA-CTAATTTATGTATTCAGAACTCTTCAGCCAATT -s simDog_chr6.simDog.chr6 327663 69 - 593897 TAAGTGCTAAGGCAAGAAGCATGCCTCGGCAACCTA-CTAAGTTAGGTATTCAGAACCCTTCAGCTAGTT -s simHuman_chr6.simHuman.chr6 369844 69 - 601863 TGAGTATTGAAGCAAAGGGCATGCCCCAGTAACCAA-GGAATTTGTGTACTCAGGACCCTGCTGCTAGTT -s simRat_chr6.simRat.chr6 295801 70 + 647215 TGAGTAGTGAACCCAGGAGTGTGACCCAGTAGCCAACCTAATCCGTGTACTCAGGGCCCCAGAGCTAGCT - -a -s simMouse_chr6.simMouse.chr6 304145 30 + 636262 CTAAGGCTGACAGACATATTTGAGTTTTTA -s Anc0.Anc0refChr8 11768 30 - 17196 CTAAGGTTGACAAGCATTCTTGAATTTTTG -s Anc1.Anc1refChr8 55769 30 - 57822 CTAAGGTTGACAAGCATTCTTGAATTTTTG -s Anc2.Anc2refChr8 7180 30 - 12804 CTAAGGTTGATGAGTGTTCTTGAATTTTTG -s mr.mrrefChr5 154607 30 + 294540 CTAAGGCTGACAGACATACTTGAGTTTTTA -s simCow_chr6.simCow.chr6 317528 30 - 602619 CTAAGGTTGATGAGTGTGCTTAAATTATTG -s simDog_chr6.simDog.chr6 327742 30 - 593897 CTAGAGTTTATGGGTGTTCTTGAATTTTTT -s simHuman_chr6.simHuman.chr6 369923 30 - 601863 CTAAGGTTGACAAGCATTCTTGAATTTTTG -s simRat_chr6.simRat.chr6 295881 30 + 647215 TTAAGACTGACAGACATACTTAAGCTCTTA - -a -s simMouse_chr6.simMouse.chr6 304175 51 + 636262 CTCCGATTATCATATGGCACTGCTTCATGTTTACTCACCAGATGTAACATA -s Anc0.Anc0refChr8 11801 51 - 17196 TTCCTATTATCATACGGCACTGCTTCATGTTTACTCACCAGATGCAACATA -s Anc1.Anc1refChr8 55802 51 - 57822 TTCCTATTATCATACGGCACTGCTTCATGTTTACTCACCAGATGCAACATA -s Anc2.Anc2refChr8 7213 51 - 12804 TTTCTATTATCATACAGCACTGCTTCATGCTAACTCACCAGATGCCACATA -s mr.mrrefChr5 154637 51 + 294540 CTCCGATTATCATATGGCACTGCTTCATGTTTACTCACCAGATGTAACATA -s simCow_chr6.simCow.chr6 317561 51 - 602619 ATTCAATCATCATACAGCACTGCGTCATGCTAACTCACCAGACACCACATA -s simDog_chr6.simDog.chr6 327775 45 - 593897 T--CTATTATCATACAGCACTGCTTCAT----ACTCACTAGATGCCACATA -s simHuman_chr6.simHuman.chr6 369956 51 - 601863 TTCCTATTATCTTAGGGCACTCCTTCATGTTTACTAACCAGCTGGAACATA -s simRat_chr6.simRat.chr6 295911 51 + 647215 CTCCCATTATCATATGGCACTGCTTCATGTTTACTCACCAGATGTAACACA - -a -s simMouse_chr6.simMouse.chr6 304226 11 + 636262 GGGGGAGATGT -s Anc0.Anc0refChr8 11852 11 - 17196 GGGGGGAGTGC -s Anc1.Anc1refChr8 55853 11 - 57822 GGGGGGAGTGC -s Anc2.Anc2refChr8 7264 11 - 12804 GGGGGGAGTGC -s mr.mrrefChr5 154688 11 + 294540 GGGGGAGGTGT -s simCow_chr6.simCow.chr6 317614 11 - 602619 GGGGAGAGTGC -s simDog_chr6.simDog.chr6 327820 11 - 593897 GGGGGGAGTGC -s simHuman_chr6.simHuman.chr6 370007 11 - 601863 TGGGGGAGTGC -s simRat_chr6.simRat.chr6 295962 11 + 647215 GGGGGAGGTGT - -a -s simMouse_chr6.simMouse.chr6 304237 14 + 636262 TAGTGGACAACCAC -s Anc0.Anc0refChr8 11863 14 - 17196 AAGAGAGCAATCAC -s Anc1.Anc1refChr8 55864 14 - 57822 AAGAGAGCAATCAC -s Anc2.Anc2refChr8 7275 14 - 12804 AAGAGAGCAATCAC -s mr.mrrefChr5 154699 14 + 294540 TAGTGAACAACCAC -s simCow_chr6.simCow.chr6 317625 14 - 602619 AAGAGTGCAATCAC -s simDog_chr6.simDog.chr6 327831 14 - 593897 AAAAGAGCAGTCAC -s simHuman_chr6.simHuman.chr6 370018 14 - 601863 AAGAGAGCAAATGC -s simRat_chr6.simRat.chr6 296021 14 + 647215 TAGTGAACAACCAC - -a -s simMouse_chr6.simMouse.chr6 304251 2 + 636262 TA -s Anc0.Anc0refChr8 11877 2 - 17196 TA -s Anc1.Anc1refChr8 55878 2 - 57822 TA -s Anc2.Anc2refChr8 7289 2 - 12804 TA -s mr.mrrefChr5 154713 2 + 294540 TA -s simCow_chr6.simCow.chr6 317639 2 - 602619 TT -s simDog_chr6.simDog.chr6 327845 2 - 593897 TA -s simHuman_chr6.simHuman.chr6 370032 2 - 601863 TA -s simRat_chr6.simRat.chr6 296038 2 + 647215 TA - -a -s simMouse_chr6.simMouse.chr6 304253 19 + 636262 TGGGATGACTCTGTGTGGT -s Anc0.Anc0refChr8 11879 19 - 17196 CCAGAGGACTATTTGTGGT -s Anc1.Anc1refChr8 55880 19 - 57822 CCAGAGGACTATTTGTGGT -s Anc2.Anc2refChr8 7291 19 - 12804 CCAGAGGATTATTTGTGGT -s mr.mrrefChr5 154715 19 + 294540 CGGGATGACTCTGTGTGGT -s simCow_chr6.simCow.chr6 317642 19 - 602619 CCAGAGGATTATTTGTGGT -s simDog_chr6.simDog.chr6 327847 19 - 593897 CCAGAGGCTTATTTGAGGT -s simHuman_chr6.simHuman.chr6 370034 19 - 601863 CCAGAGGACTATTTGTGGT -s simRat_chr6.simRat.chr6 296040 19 + 647215 CTGGATGACTCTCTGTGGT - -a -s simMouse_chr6.simMouse.chr6 304272 65 + 636262 TAGTTAATTAAGCACCCTTGTCCTAACTTGGATTCAGTCACGCTTCACATCTTACTGTTCAACAT -s Anc0.Anc0refChr8 11909 64 - 17196 CAGTTAATTAAGCACCCTTGCCCTTGGTTGGGCTAGGTGACTCTTCTTATC-TACTGTTTATTGT -s Anc1.Anc1refChr8 55910 64 - 57822 CAGTTAATTAAGCACCCTTGCCCTTGGTTGGGCTAGGTGACTCTTCTTATC-TACTGTTTATTGT -s Anc2.Anc2refChr8 7321 64 - 12804 CAGTTAATTAAGTGCCCTTGCCAATGGTTGGACTAGGTGACTCTTCTTATT-TACTGTTCATTGT -s mr.mrrefChr5 154734 65 + 294540 TAGTTAATTAAGCACCCTTGCCCTAACTTGGGTTCAGTCACGCTTCTCATCTTACTGTTTAACAT -s simCow_chr6.simCow.chr6 317666 57 - 602619 ---TTAATAA----ACCTTACCTATGTTTGGTCTAGATGACTCTTCTAATT-TGGTGTTGCTTGT -s simDog_chr6.simDog.chr6 327881 64 - 593897 CAGTTAATTAAGTGCCCTTGCCAATGGTTGGATTAGGTGACTCTTCTTGTT-CACTGTTCATTGT -s simHuman_chr6.simHuman.chr6 370064 64 - 601863 CAGCTAATTAAGCATCCTTGCCCTTGGTTGGGCCAGGTTACTCTTCTTATC-TACTGTCTTCTGT -s simRat_chr6.simRat.chr6 296059 65 + 647215 TAGGTAATTAAGCACCCTTGCCCTGACTTGGGTTCAGTCAAGCTTCTCATTTTACTGTTTAGCAT - -a -s simMouse_chr6.simMouse.chr6 304337 7 + 636262 CAGATCT -s Anc0.Anc0refChr8 11982 7 - 17196 CAGATCT -s Anc1.Anc1refChr8 55983 7 - 57822 CAGATCT -s Anc2.Anc2refChr8 7394 7 - 12804 CAGCTCT -s mr.mrrefChr5 154799 7 + 294540 CAGATCT -s simCow_chr6.simCow.chr6 317732 7 - 602619 CAGCTCT -s simDog_chr6.simDog.chr6 327954 7 - 593897 CAGCTCT -s simHuman_chr6.simHuman.chr6 370137 7 - 601863 CAGATCT -s simRat_chr6.simRat.chr6 296124 7 + 647215 CAGATCT - -a -s simMouse_chr6.simMouse.chr6 304344 4 + 636262 TTGA -s Anc0.Anc0refChr8 11990 4 - 17196 TTCT -s Anc1.Anc1refChr8 55991 4 - 57822 TTCT -s Anc2.Anc2refChr8 7402 4 - 12804 CTCT -s mr.mrrefChr5 154806 4 + 294540 TTGA -s simCow_chr6.simCow.chr6 317740 1 - 602619 C--- -s simDog_chr6.simDog.chr6 327962 4 - 593897 CTCT -s simHuman_chr6.simHuman.chr6 370145 4 - 601863 TTCT -s simRat_chr6.simRat.chr6 296131 4 + 647215 TTGA - -a -s simMouse_chr6.simMouse.chr6 304348 8 + 636262 AGCCATAT -s Anc0.Anc0refChr8 11994 8 - 17196 AGCCTTAT -s Anc1.Anc1refChr8 55995 8 - 57822 AGCCTTAT -s Anc2.Anc2refChr8 7455 8 - 12804 AGTCTGAC -s mr.mrrefChr5 154810 8 + 294540 AGCCATAT -s simCow_chr6.simCow.chr6 317793 8 - 602619 AGTCTGAC -s simDog_chr6.simDog.chr6 328048 8 - 593897 AGTCTGAC -s simHuman_chr6.simHuman.chr6 370149 8 - 601863 AACCTTAT -s simRat_chr6.simRat.chr6 296135 8 + 647215 AGCCACAT - -a -s simMouse_chr6.simMouse.chr6 304356 11 + 636262 CAAAGCTCCCC -s Anc0.Anc0refChr8 12010 11 - 17196 CATGGTTTCCC -s Anc1.Anc1refChr8 56011 11 - 57822 CATGGTTTCCC -s Anc2.Anc2refChr8 7471 11 - 12804 CATGGTTTCCT -s mr.mrrefChr5 154818 11 + 294540 CAAAGCTCCCC -s simCow_chr6.simCow.chr6 317809 11 - 602619 CACAGTTTCCT -s simDog_chr6.simDog.chr6 328064 11 - 593897 CATGGTTTACT -s simHuman_chr6.simHuman.chr6 370165 11 - 601863 CATGGTTTCCC -s simRat_chr6.simRat.chr6 296143 6 + 647215 CAAAGC----- - -a -s simMouse_chr6.simMouse.chr6 304367 23 + 636262 TATTGTATAACCCTCACAATAGC -s Anc0.Anc0refChr8 12062 22 - 17196 CATAGTGTGACATT-ATGACAGC -s Anc1.Anc1refChr8 56063 23 - 57822 CATAGTGTGACATTCATGACAGC -s Anc2.Anc2refChr8 7523 22 - 12804 CATAGTGTGACATT-ATGAGAGC -s mr.mrrefChr5 154829 23 + 294540 TATTGTATAACCCTCACAACAGC -s simCow_chr6.simCow.chr6 317861 20 - 602619 CATAGTGTGACA---ATGAGAGC -s simDog_chr6.simDog.chr6 328101 14 - 593897 CATAGTGTAACATT--------- -s simHuman_chr6.simHuman.chr6 370217 23 - 601863 CATAGTGTGACATTCGTGACAGC -s simRat_chr6.simRat.chr6 296149 9 + 647215 --------------CACAACAGC - -a -s simMouse_chr6.simMouse.chr6 304390 26 + 636262 TCAAGGAACATTTTGCATTCAATCAT -s Anc0.Anc0refChr8 12084 26 - 17196 TCAGGGAACATTTTGGCTTCTATCAT -s Anc1.Anc1refChr8 56086 26 - 57822 TCAGGGAACATTTTGGCTTCTATCAT -s Anc2.Anc2refChr8 7545 26 - 12804 TCAGGGAACATTTTGGCTTCTACCAC -s mr.mrrefChr5 154852 26 + 294540 TCAAGGAACATTTTGCATTCAATCAT -s simCow_chr6.simCow.chr6 317881 26 - 602619 TCAGGGAACATTTTGGCTTCTACCAC -s simHuman_chr6.simHuman.chr6 370241 26 - 601863 TCAGTGAATATTTTGGGTTCTATCAT -s simRat_chr6.simRat.chr6 296158 26 + 647215 TCAAGGAACATTTTACATTCAATCAC - -a -s simMouse_chr6.simMouse.chr6 304416 50 + 636262 GGAGGTGAGATTGCTGATGATTCATTTCTACCAACCTAGGATAACACAAG -s Anc0.Anc0refChr8 12116 47 - 17196 TGGGACAAAATTGCTA---ATTCATTTTTATCAGTCTAGGGGGCTACAAA -s Anc1.Anc1refChr8 56118 50 - 57822 TGGGACAAAATTGCTAATGATTCATTTTTATCAGTCTAGGGGGCTACAAA -s Anc2.Anc2refChr8 7577 47 - 12804 TGGGACAAAATTGCTA---ATTCATTTTTATCAGTCTAGGGGGCTGCAAA -s mr.mrrefChr5 154878 50 + 294540 GGAGGTGAGATTGCTGATGATTCATTTCTACCAGCCTAGGATACCACAAG -s simCow_chr6.simCow.chr6 317913 40 - 602619 TGGGACAGAATT-------ATGCATTCTTATCAGTCTAGGGGTCCGT--- -s simDog_chr6.simDog.chr6 328115 41 - 593897 ------AAAATTGCTA---ATTTTTTTTTATTAGTTCAGTGGGTTGCAAA -s simHuman_chr6.simHuman.chr6 370273 50 - 601863 TGGGACAAAATTGCTAATGACTCATTTTTAACAGTCTAGGGAGCAACAAA -s simRat_chr6.simRat.chr6 296184 50 + 647215 AGATGAGAGATGGCTGCTGATTCATTTCTACTGGCCAAGGATACCACAAT - -a -s simMouse_chr6.simMouse.chr6 304466 40 + 636262 ACCCATAGTGCTGAGTGGTTGTGTTAAGAACACACATTTA -s Anc0.Anc0refChr8 12199 40 - 17196 ACCCATGGTGATGAGCGTTTGTGTATTAGACACACATCCA -s Anc1.Anc1refChr8 56204 40 - 57822 ACCCATGGTGATGAGCGTTTGTGTATTAGACACACATCCA -s Anc2.Anc2refChr8 7676 40 - 12804 ACCAGTGGTGCTGAGCGTTTTTGTATTAGACACAGATCCA -s mr.mrrefChr5 154928 40 + 294540 ACCCATGGTGATGAGTGGTTGTGTTAAGGACACACATCTA -s simCow_chr6.simCow.chr6 318012 37 - 602619 AGCTGTGGTGCTGAGTGTTTTCTTAGTAGA---ATGTCTA -s simDog_chr6.simDog.chr6 328208 39 - 593897 ACCAGTGGTGCTGAGCGTTT-TGTATTAAACACTGATCCA -s simHuman_chr6.simHuman.chr6 370359 40 - 601863 ACCCATGGTGATGAGCGTTTGTGTGTTAGACACACATCCA -s simRat_chr6.simRat.chr6 296234 40 + 647215 ACCCATGGGGATGAGTGGTTGTGTCAAGGACACACATCTA - -a -s simMouse_chr6.simMouse.chr6 304506 64 + 636262 GGTATGATCAAGGCAACCAGGGGGCTATGTTTCCTGGAATATCCTAAGAAGTGATTGTAGACTG -s Anc0.Anc0refChr8 12239 56 - 17196 AGTGTGATCAAGGCACACTGGTTCCTGTGGTTCCTTGAATATCCCAAGAAGTAATT-------- -s Anc1.Anc1refChr8 56244 64 - 57822 AGTGTGATCAAGGCACACTGGTTCCTGTGGTTCCTTGAATATCCCAAGAAGTAATTATAGATCG -s Anc2.Anc2refChr8 7716 56 - 12804 AGTGCAATCAACACACACTGGTTCCGGGCATTCCTTGAATATCCCTAGAAGTAATT-------- -s mr.mrrefChr5 154968 64 + 294540 AGTGTGATCAAGGCACCCAGGGGCCTATGGTTCCTTGAATATCCTAAGAAGTAATTGTAGACTG -s simCow_chr6.simCow.chr6 318051 30 - 602619 AGTGCAATTGACTATTAATGGGTCCCCACA---------------------------------- -s simDog_chr6.simDog.chr6 328247 55 - 593897 GGTGCAATCAA-ACACACTGGTTCCGGGCATTCCTTGAATATCCCTAGAAGTAATT-------- -s simHuman_chr6.simHuman.chr6 370399 64 - 601863 AGTGTGATCAAGGCACACCGGTTCCTGTGGTTCCTTGAATATCCCAACAAGAAATTATAGATCG -s simRat_chr6.simRat.chr6 296274 64 + 647215 AGTGTGAACAAGGCACCCAGAGGCCTATAGTTCCTTGATTATCCTAAGAAGCAATTGCAGACTG - -a -s simMouse_chr6.simMouse.chr6 304570 12 + 636262 ATAAGACTGTGA -s Anc0.Anc0refChr8 12298 12 - 17196 CAAAGACTGAGA -s Anc1.Anc1refChr8 56313 12 - 57822 CAAAGACTGAGA -s Anc2.Anc2refChr8 7775 12 - 12804 CAAAAATCTAGT -s mr.mrrefChr5 155037 12 + 294540 ATAAGACTGTGA -s simDog_chr6.simDog.chr6 328305 12 - 593897 CAAAAATCTAGT -s simHuman_chr6.simHuman.chr6 370468 12 - 601863 TCAAGTCTGGTA -s simRat_chr6.simRat.chr6 296343 12 + 647215 GTAAGACTGTGA - -a -s simMouse_chr6.simMouse.chr6 304582 16 + 636262 TTTGCTTGCAATTTCG -s Anc0.Anc0refChr8 12310 16 - 17196 TGTGCTAGTATTTTAG -s Anc1.Anc1refChr8 56325 16 - 57822 TGTGCTAGTATTTTAG -s Anc2.Anc2refChr8 7787 16 - 12804 TGTACTAGTATTTTAG -s mr.mrrefChr5 155049 16 + 294540 TTTGCTTGCAATTTAG -s simDog_chr6.simDog.chr6 272809 16 + 593897 TGTACTAGTATTTTAG -s simHuman_chr6.simHuman.chr6 370480 16 - 601863 TGTGCTACTATTTGAG -s simRat_chr6.simRat.chr6 296355 13 + 647215 ---GCTTGCAATCTAG - -a -s simMouse_chr6.simMouse.chr6 304598 10 + 636262 TCAGTGTCAG -s Anc0.Anc0refChr8 12326 10 - 17196 CGAGTGTCAG -s Anc1.Anc1refChr8 56341 10 - 57822 CGAGTGTCAG -s Anc2.Anc2refChr8 7803 10 - 12804 CGCGCACCAG -s mr.mrrefChr5 155065 10 + 294540 TCAGTGTCAG -s simDog_chr6.simDog.chr6 272826 10 + 593897 CGCGCACCAG -s simHuman_chr6.simHuman.chr6 370496 10 - 601863 AGAGTGTCAG -s simRat_chr6.simRat.chr6 296368 10 + 647215 CCAGTGTCAG - -a -s simMouse_chr6.simMouse.chr6 304608 29 + 636262 TGACATCGTGAGTATACTAGGTTTGTGGT -s Anc0.Anc0refChr8 12352 29 - 17196 TAGTGCTGTGAGTAAGCTAAGTTTGAAGG -s Anc1.Anc1refChr8 56367 29 - 57822 TAGTGCTGTGAGTAAGCTAAGTTTGAAGG -s Anc2.Anc2refChr8 7829 29 - 12804 TAGTGCTGAGGGTAAGCTGAAGTTGAAGG -s mr.mrrefChr5 155090 29 + 294540 TAACACTGTGAGTATACTAGGTTTGTGGG -s simDog_chr6.simDog.chr6 272852 29 + 593897 TAGTGCTGAGGGTAAGCTGAAGTTGAAGG -s simHuman_chr6.simHuman.chr6 370522 29 - 601863 TAGTGCTGTAAGTAGGCTAAGTCTGCAGG -s simRat_chr6.simRat.chr6 296394 29 + 647215 TAACACTGTGAGTATACTAGGCTGGTGAG - -a -s simMouse_chr6.simMouse.chr6 304637 53 + 636262 AGTTATTATTTGGTCCTATCAACCCAATGGGGTTATGAAATGCCAACTCACAG -s Anc0.Anc0refChr8 12381 50 - 17196 AGTTATTATAGG-TGCTAGCAACCCAATGTGGTTATGAAATGCCAGCTCAT-- -s Anc1.Anc1refChr8 56396 50 - 57822 AGTTATTATAGG-TGCTAGCAACCCAATGTGGTTATGAAATGCCAGCTCAT-- -s Anc2.Anc2refChr8 7866 50 - 12804 GGTTATTATAGG-TGCTAGCAACCCAATGTGGTTATGAAATGCCAGCTCAT-- -s mr.mrrefChr5 155119 50 + 294540 AGTTATTATTTG-TCCTATCAACCCAATGGGGTTATGAAATGCCAACTCAC-- -s simCow_chr6.simCow.chr6 318089 50 - 602619 GGTTATTACATG-TGTTAGCAATGCAATTTGGTTATGAAATGCCAGTTAAT-- -s simDog_chr6.simDog.chr6 272964 50 + 593897 GGTTATTATAGG-TGCTAACAACCCAATGTGATTATGAAGTGCCAGCTCAT-- -s simHuman_chr6.simHuman.chr6 370551 50 - 601863 AGTTATTATACG-CGCTAGCAACCCAATGTGGTTATGAAATGCCAGCTCAT-- -s simRat_chr6.simRat.chr6 296423 49 + 647215 AGTTACTATTTG-TCCTATCAACCCAATGGGATTATGAAGTGTCAACTCA--- - -a -s simMouse_chr6.simMouse.chr6 304690 2 + 636262 TT -s Anc0.Anc0refChr8 12431 2 - 17196 TT -s Anc1.Anc1refChr8 56446 2 - 57822 TT -s Anc2.Anc2refChr8 7919 2 - 12804 TT -s mr.mrrefChr5 155169 2 + 294540 TT -s simCow_chr6.simCow.chr6 318142 2 - 602619 TT -s simDog_chr6.simDog.chr6 273017 2 + 593897 TT -s simHuman_chr6.simHuman.chr6 370601 2 - 601863 TT - -a -s simMouse_chr6.simMouse.chr6 304692 56 + 636262 TTCAGCAGCATTTTTTCAATGCGTATAGCATGAATTAGGTGTGCAGGGAGGACAAA -s Anc0.Anc0refChr8 12433 56 - 17196 TTCACCGGTGTTTGTAAAGAGAGTATAACATGGATTAGATGCACAGGGAGGACAAA -s Anc1.Anc1refChr8 56448 56 - 57822 TTCACCGGTGTTTGTAAAGAGAGTATAACATGGATTAGATGCACAGGGAGGACAAA -s Anc2.Anc2refChr8 7921 56 - 12804 CTCACCAGTGTTTGTAAAGAGAGTATAACATGGATTAAGTGCACATGGAGGACAAA -s mr.mrrefChr5 155171 56 + 294540 TTCAGCGGCATTTTTTCAGTGAGTATAGCATGAATTAGATGTACAGGGAGGACAAA -s simCow_chr6.simCow.chr6 318146 56 - 602619 CACACCAGCGCTTGTAAACAGAGTACAACATGGCTTAAGTGCACATGGAGGAAAAA -s simDog_chr6.simDog.chr6 273019 56 + 593897 CTCACCAGTGTTTGTAAAGAGAGGATAACATGGATTGAGTGTGCATGGAGTACAAA -s simHuman_chr6.simHuman.chr6 370603 56 - 601863 TGCACTGGTGTTTATAATGGGAGTATAACACAGGATAGATGCAAAGGGAGGTCAAA -s simRat_chr6.simRat.chr6 296472 55 + 647215 -TCAGCGGCATTTTTTCAGTGAGTATAGCATGAATTAGATGTACAAGGAGGACAAA - -a -s simMouse_chr6.simMouse.chr6 304748 17 + 636262 TTTAATGGCATACACTG -s Anc0.Anc0refChr8 12489 16 - 17196 TTTATTGGCATG-GCTG -s Anc1.Anc1refChr8 56504 16 - 57822 TTTATTGGCATG-GCTG -s Anc2.Anc2refChr8 7977 16 - 12804 TTTAGTGGCATG-GCTG -s mr.mrrefChr5 155227 17 + 294540 TTTATTGGCATACACTG -s simCow_chr6.simCow.chr6 318202 16 - 602619 TTTACTGGCATG-GCTG -s simDog_chr6.simDog.chr6 273075 8 + 593897 TTTAGTGG--------- -s simHuman_chr6.simHuman.chr6 370660 16 - 601863 TTTATTGGCATG-GCTG -s simRat_chr6.simRat.chr6 296527 17 + 647215 TTTATTGGCAAACACTG - -a -s simMouse_chr6.simMouse.chr6 304765 10 + 636262 ATAAAACTTA -s Anc0.Anc0refChr8 12513 10 - 17196 ATTAAATTTA -s Anc1.Anc1refChr8 56528 10 - 57822 ATTAAATTTA -s Anc2.Anc2refChr8 8001 10 - 12804 ATTAAATTTA -s mr.mrrefChr5 155244 10 + 294540 ATAAAACTTA -s simCow_chr6.simCow.chr6 318226 10 - 602619 TTTAAATTTA -s simDog_chr6.simDog.chr6 273090 10 + 593897 AGTAAGTTTA -s simHuman_chr6.simHuman.chr6 370684 10 - 601863 ATTAAATTTA -s simRat_chr6.simRat.chr6 296544 10 + 647215 ATAAAACTTA - -a -s simMouse_chr6.simMouse.chr6 304775 7 + 636262 GGGCAAT -s Anc0.Anc0refChr8 12523 7 - 17196 GACTAAT -s Anc1.Anc1refChr8 56538 7 - 57822 GACTAAT -s Anc2.Anc2refChr8 8011 7 - 12804 GACTAAT -s mr.mrrefChr5 155254 7 + 294540 GGGCAAT -s simCow_chr6.simCow.chr6 318236 7 - 602619 GACTAAT -s simDog_chr6.simDog.chr6 273101 7 + 593897 GAGTAAT -s simHuman_chr6.simHuman.chr6 370694 7 - 601863 GACTAAT -s simRat_chr6.simRat.chr6 296554 7 + 647215 GGGAAAT - -a -s simMouse_chr6.simMouse.chr6 304782 62 + 636262 TTGGGGCATGGGAACACTGCACTGTCAAGTCAAGCCTGATATTACAAGGCAACTGTTCATGC -s Anc0.Anc0refChr8 12530 59 - 17196 TTTAGTCAGGGGAGTTCTGCACTATGGAGTAGGTACTGATGGTACCAAGCAACTG-T--TTG -s Anc1.Anc1refChr8 56545 61 - 57822 TTTAGTCAGGGGAGTTCTGCACTATGGAGTAGGTACTGATGGTACCAAGCAACTG-TCATTG -s Anc2.Anc2refChr8 8018 59 - 12804 TTTAGTCAGGGGAGTTTTGCACTATGGAGTAGGTACTGATGGCACCAAGCAACTG-T--TTG -s mr.mrrefChr5 155261 62 + 294540 TTGGGGCATGGGAACACTGCACTGTCAAGTCAAGCCTGATGTTACAAGGCAACTGTTCATGC -s simCow_chr6.simCow.chr6 318250 59 - 602619 TTTGGTCAGGGGAGCATTGCACTCCATAGTAGATACTGATGGCACAAAATAACTT-T--TTG -s simDog_chr6.simDog.chr6 273108 59 + 593897 TCTAATCAAGGGCATTTTACGTTATGGAGTAGGTACTGAGGTCACCAAGCAATTG-T--TAG -s simHuman_chr6.simHuman.chr6 370701 61 - 601863 TTTAGTCAGGGGAGTTCTGTACTTTGGAGAGGGTACTGATGGTACCAAGCCACTG-TCATTG -s simRat_chr6.simRat.chr6 296561 62 + 647215 CTGGGGCATGGGAACACTGCACTGTCAAGTCAAGCCTGATGTCACAAGGCAACTGCACATGT - -a -s simMouse_chr6.simMouse.chr6 304844 15 + 636262 TCTGTTAGATTGTTT -s Anc0.Anc0refChr8 12589 15 - 17196 CCTGTTAGATTGCTT -s Anc1.Anc1refChr8 56606 15 - 57822 CCTGTTAGATTGCTT -s Anc2.Anc2refChr8 8077 15 - 12804 CCTGTTAGATTGCTT -s mr.mrrefChr5 155323 15 + 294540 CCTGTTAGATTGCTT -s simCow_chr6.simCow.chr6 318312 15 - 602619 CCTGTTAGATTGCTA -s simDog_chr6.simDog.chr6 273167 15 + 593897 CCTGTTAGATAGCTT -s simHuman_chr6.simHuman.chr6 370762 15 - 601863 CCTGTTAGATTGCTC -s simRat_chr6.simRat.chr6 296623 15 + 647215 CCTGTGAGATTACTT - -a -s simMouse_chr6.simMouse.chr6 304859 46 + 636262 TAACACACCATGATCATTCCTACTATTGCTACTGTATACTTGCCTC -s Anc0.Anc0refChr8 12604 46 - 17196 CAACACACTATGATAATTTCTCCTATTTCTGCTGTTTACTTGCCTT -s Anc1.Anc1refChr8 56621 46 - 57822 CAACACACTATGATAATTTCTCCTATTTCTGCTGTTTACTTGCCTT -s Anc2.Anc2refChr8 8092 46 - 12804 CAACACACTATGATAATTTCTCCTATTTCTGCTACTTACTTGCCTT -s mr.mrrefChr5 155338 46 + 294540 TAACACACCATGATCATTCCTACTATTGCTACTGTATACTTGCCTC -s simCow_chr6.simCow.chr6 318327 45 - 602619 TAGCACACTATGATA-CTTCTCCTATTTCTCCCTGTCCTTTCCCTT -s simDog_chr6.simDog.chr6 273186 46 + 593897 CAACACATTATGCTGATTTCTCCTATTTTTGCTACTTACTTGCTTT -s simHuman_chr6.simHuman.chr6 370777 43 - 601863 AAACATACTGTGATAAT---TCCTATATCTGCTGTTTTCTTGCCTT -s simRat_chr6.simRat.chr6 296638 44 + 647215 TAACACACAATGCTCATT--TACTATTGCTATTGTATACGTGCCTC - -a -s simMouse_chr6.simMouse.chr6 304905 4 + 636262 GGGC -s Anc0.Anc0refChr8 12650 4 - 17196 GGGC -s Anc1.Anc1refChr8 56667 4 - 57822 GGGC -s Anc2.Anc2refChr8 8138 4 - 12804 GGGC -s mr.mrrefChr5 155384 4 + 294540 GGGC -s simCow_chr6.simCow.chr6 318373 4 - 602619 GGGC -s simDog_chr6.simDog.chr6 273232 4 + 593897 GGGT -s simHuman_chr6.simHuman.chr6 370820 4 - 601863 AGGC -s simRat_chr6.simRat.chr6 296682 4 + 647215 GGGC - -a -s simMouse_chr6.simMouse.chr6 304909 5 + 636262 ATGTG -s Anc0.Anc0refChr8 12654 5 - 17196 ATGTG -s Anc1.Anc1refChr8 56671 5 - 57822 ATGTG -s Anc2.Anc2refChr8 8142 5 - 12804 ATCTG -s mr.mrrefChr5 155388 5 + 294540 ATGTG -s simCow_chr6.simCow.chr6 318377 5 - 602619 ATCTG -s simDog_chr6.simDog.chr6 273241 5 + 593897 ATCTC -s simHuman_chr6.simHuman.chr6 370824 5 - 601863 ATGTG -s simRat_chr6.simRat.chr6 296686 5 + 647215 ATGTG - -a -s simMouse_chr6.simMouse.chr6 304914 10 + 636262 GGCACGTGTG -s Anc0.Anc0refChr8 12662 10 - 17196 GACGCATGTG -s Anc1.Anc1refChr8 56679 10 - 57822 GACGCATGTG -s Anc2.Anc2refChr8 8150 10 - 12804 TACGCACGTG -s mr.mrrefChr5 155393 10 + 294540 GGCACATGTG -s simCow_chr6.simCow.chr6 318385 10 - 602619 TACACACGTG -s simDog_chr6.simDog.chr6 273248 7 + 593897 ---GCACGTG -s simHuman_chr6.simHuman.chr6 370832 10 - 601863 GATGCATGTG -s simRat_chr6.simRat.chr6 296691 10 + 647215 GGCTCATATG - -a -s simMouse_chr6.simMouse.chr6 304924 48 + 636262 TTTGGTATTAATATGCCATGAACTTGTTATTAATCCTCTAACAATGTG -s Anc0.Anc0refChr8 12672 48 - 17196 TTGGATATTAACATACCATGAACCTGCTGCCAATCACTTGACAATGCT -s Anc1.Anc1refChr8 56689 48 - 57822 TTGGATATTAACATACCATGAACCTGCTGCCAATCACTTGACAATGCT -s Anc2.Anc2refChr8 8160 48 - 12804 TTGGACATTAACATACTGTGATTCTGCTGCCAATCACTTGACAATGCT -s mr.mrrefChr5 155403 48 + 294540 TTTGGTATTAATATGCCATGAACCTGCTGTTAATCCTCTAACAATGCT -s simCow_chr6.simCow.chr6 318395 48 - 602619 AAGGACATTAACATACTGTGACACTGCTGCCAATCACTTGGCAATACT -s simDog_chr6.simDog.chr6 273255 30 + 593897 TT------------------ATTCTGCCGCCAATCACGTGACAATGCT -s simHuman_chr6.simHuman.chr6 370848 48 - 601863 TTGGATATCAACACACCATCAACCTTCTGCCAATGACTTGACAATGCT -s simRat_chr6.simRat.chr6 296701 38 + 647215 TTTGGTATTAATATGCCAGGAGCCTACTGTTAATC----------GCT - -a -s simMouse_chr6.simMouse.chr6 304972 5 + 636262 GTTTG -s Anc0.Anc0refChr8 12721 5 - 17196 GATTA -s Anc1.Anc1refChr8 56738 5 - 57822 GATTA -s Anc2.Anc2refChr8 8209 5 - 12804 GATTA -s mr.mrrefChr5 155451 5 + 294540 GATTA -s simCow_chr6.simCow.chr6 318444 5 - 602619 AATGA -s simDog_chr6.simDog.chr6 273286 5 + 593897 GATTA -s simHuman_chr6.simHuman.chr6 370897 5 - 601863 GATTA -s simRat_chr6.simRat.chr6 296739 5 + 647215 GATTA - -a -s simMouse_chr6.simMouse.chr6 304977 72 + 636262 CAATCTTCTTACGTAGGAAAACCAGATAGGCTAACCACGTTATTAGGACCTGCATTGGAGGTGTTTGTTTAC -s Anc0.Anc0refChr8 12726 32 - 17196 TATTCTTCTTATCTAGGAAAAGCAC----------------ATTAGG------------------------C -s Anc1.Anc1refChr8 56743 56 - 57822 TATTCTTCTTATCTAGGAAAAGCAC----------------ATTAGGATCTCTGCTGAAAGCCTTCCCTTAC -s Anc2.Anc2refChr8 8214 32 - 12804 TATTCCTATTATCTGGGCAGAGCAC----------------ATCAGG------------------------T -s mr.mrrefChr5 155456 72 + 294540 CAATCTTCTTACCTAGGAAAACCAGATAGGCTAACCACATTATTAGGACCTGTATTGGAGGTGTTCGTTTAC -s simCow_chr6.simCow.chr6 318449 32 - 602619 TACTCATATTATCTGGGTAGAGCAC----------------ATCAGG------------------------T -s simDog_chr6.simDog.chr6 273292 32 + 593897 TATACCCATCATCTGGGCAGAGCAC----------------ATCAGG------------------------T -s simHuman_chr6.simHuman.chr6 370902 56 - 601863 TATTCTTCCTTTCTAGGACACATAC----------------ATTAGGATCTCTGCTGAAAGCCTTCCCTTAC -s simRat_chr6.simRat.chr6 296744 72 + 647215 CAATATTCTTCCCTAGGGAAACCAGATAGGCCAACTACATTATTAGGACCTGTATTGGAGATGTTCTTTTAC - -a -s simMouse_chr6.simMouse.chr6 305049 9 + 636262 CCACGTCAT -s Anc0.Anc0refChr8 12758 9 - 17196 CCACTTCAT -s Anc1.Anc1refChr8 56799 9 - 57822 CCACTTCAT -s Anc2.Anc2refChr8 8246 9 - 12804 GCACTTCAT -s mr.mrrefChr5 155528 9 + 294540 CCACGTCAT -s simCow_chr6.simCow.chr6 318486 9 - 602619 GCACTTCAT -s simDog_chr6.simDog.chr6 273324 9 + 593897 GCACTTCAT -s simHuman_chr6.simHuman.chr6 370958 9 - 601863 CCACTTCAT -s simRat_chr6.simRat.chr6 296816 8 + 647215 CCACGTCA- - -a -s simMouse_chr6.simMouse.chr6 305058 2 + 636262 GC -s Anc0.Anc0refChr8 12768 2 - 17196 AC -s Anc1.Anc1refChr8 56809 2 - 57822 AC -s Anc2.Anc2refChr8 8256 2 - 12804 AG -s mr.mrrefChr5 155537 2 + 294540 GC -s simCow_chr6.simCow.chr6 318496 2 - 602619 AA -s simDog_chr6.simDog.chr6 273334 2 + 593897 AG -s simHuman_chr6.simHuman.chr6 370968 2 - 601863 AC -s simRat_chr6.simRat.chr6 296824 1 + 647215 -C - -a -s simMouse_chr6.simMouse.chr6 305060 31 + 636262 TCCCAAGAGTGATTCCTGGAAAACCCTTTGC -s Anc0.Anc0refChr8 12770 29 - 17196 TCCTGATTGGGATCTCCAGA--ACCCTTTGC -s Anc1.Anc1refChr8 56811 29 - 57822 TCCTGATTGGGATCTCCAGA--ACCCTTTGC -s Anc2.Anc2refChr8 8258 29 - 12804 TCCTGATTGGGGTCTCCAGA--ACCTTTTGC -s mr.mrrefChr5 155539 29 + 294540 TCCCAAGTGTGATCCCCAGA--ACCCTTTGC -s simCow_chr6.simCow.chr6 318500 28 - 602619 TCTCAATCAGGGTATCCAGG--ACC-GCTGC -s simDog_chr6.simDog.chr6 273336 29 + 593897 TCCTGCTTGGGGTCTCCAGA--GCCTTTTGC -s simHuman_chr6.simHuman.chr6 370970 29 - 601863 TCCAGACTGGGATCTTCAGA--ACCCTTTGC -s simRat_chr6.simRat.chr6 296825 29 + 647215 TCCCAATTGTGATCCCCAGA--ACCCTTTGC - -a -s simMouse_chr6.simMouse.chr6 305091 4 + 636262 ATTA -s Anc0.Anc0refChr8 12799 4 - 17196 CTGG -s Anc1.Anc1refChr8 56840 4 - 57822 CTGG -s Anc2.Anc2refChr8 8287 4 - 12804 CTGG -s mr.mrrefChr5 155568 4 + 294540 ATTA -s simCow_chr6.simCow.chr6 318528 4 - 602619 GTTG -s simDog_chr6.simDog.chr6 273366 4 + 593897 CTGA -s simHuman_chr6.simHuman.chr6 370999 4 - 601863 CTGG -s simRat_chr6.simRat.chr6 296854 4 + 647215 ATTA - -a -s simMouse_chr6.simMouse.chr6 305095 22 + 636262 GTCTCAAGGTTGTACATATTAG -s Anc0.Anc0refChr8 12803 21 - 17196 CTTTCAAGATTATACATGTTA- -s Anc1.Anc1refChr8 56844 22 - 57822 CTTTCAAGATTATACATGTTAG -s Anc2.Anc2refChr8 8291 21 - 12804 CTTATAAGACTATACATGTTA- -s mr.mrrefChr5 155572 22 + 294540 GTCTCAAGGTTATACATATTAG -s simCow_chr6.simCow.chr6 318532 21 - 602619 GTTGTGAGACTATACATGTTA- -s simDog_chr6.simDog.chr6 273372 21 + 593897 CTAATAAGACTATACATGTTA- -s simHuman_chr6.simHuman.chr6 371003 22 - 601863 CTTTCAAGATTATTCATGTTAG -s simRat_chr6.simRat.chr6 296858 22 + 647215 GCCTCAAGCTTATACATATTAG - -a -s simMouse_chr6.simMouse.chr6 305117 55 + 636262 GCTGGATCTCACGTTATCTGATTATATGTGTTGTTGCATCATCACTAAGCTTAAT -s Anc0.Anc0refChr8 12824 45 - 17196 ----GAGCTCATGCCATCTGTAC-CATCTA-----GTGACTTCAGTGAGCTCAAT -s Anc1.Anc1refChr8 56866 49 - 57822 GCTCGAGCTCATGCCATCTGTAC-CATCTA-----GTGACTTCAGTGAGCTCAAT -s Anc2.Anc2refChr8 8312 45 - 12804 ----GAGCTCATGCCATCTGTAC-CATCAA-----GTGACTTCAGTGAGCTCCAT -s mr.mrrefChr5 155594 55 + 294540 GCTGGATCTCATGTTATCTGAATACATCTGTAGTTGCATCATCACTAAGCTTAAT -s simCow_chr6.simCow.chr6 318553 45 - 602619 ----GAGCTCATGCCATCTGTAC-CATCAA-----GTAACATCAGTAACCACCAT -s simDog_chr6.simDog.chr6 273393 45 + 593897 ----GAAGTCGTGCCATCTGTAC-TATCAA-----GTGACTTCAGTGAGCTCCAT -s simHuman_chr6.simHuman.chr6 371026 49 - 601863 GCTCAAGCTCATGCCATCTGTAC-CATCTA-----GTGACTCCAGGGAGCCCAGT -s simRat_chr6.simRat.chr6 296880 55 + 647215 GCTGGATCTCATGTTATCTGGATACATCTGTAGTTGCATCATCGCTAAGCTTAAT - -a -s simMouse_chr6.simMouse.chr6 305172 20 + 636262 TTGTAATAGTCCATATTAAA -s Anc0.Anc0refChr8 12869 18 - 17196 TCTTAGTGGACC--TTTAAA -s Anc1.Anc1refChr8 56915 18 - 57822 TCTTAGTGGACC--TTTAAA -s Anc2.Anc2refChr8 8357 18 - 12804 TCTGAGTGGACC--TTTATA -s mr.mrrefChr5 155649 20 + 294540 TTGTAATAGTCCATTTTAAA -s simCow_chr6.simCow.chr6 318607 18 - 602619 TCTAAGTGGAGA--TCTGGA -s simDog_chr6.simDog.chr6 273438 17 + 593897 -CTGAAAGGACC--TTTATA -s simHuman_chr6.simHuman.chr6 371075 18 - 601863 TCCTAGTGGACC--TTTCAA -s simRat_chr6.simRat.chr6 296935 20 + 647215 TGGTAATAGTCCATTTTCAA - -a -s simMouse_chr6.simMouse.chr6 305192 32 + 636262 GTCCAATTGATTTTAAGTTCCTCACATCTCAT -s Anc0.Anc0refChr8 12903 32 - 17196 GTCCAATGATTTTTAAGTTGCTCACATCCCAT -s Anc1.Anc1refChr8 56949 32 - 57822 GTCCAATGATTTTTAAGTTGCTCACATCCCAT -s Anc2.Anc2refChr8 8398 32 - 12804 GTCAAATGATTTTTAAGTTGCTCACATCCCAT -s mr.mrrefChr5 155669 32 + 294540 GTCCAATTGATTTTAAGTTCCTCACATCTCAT -s simCow_chr6.simCow.chr6 318648 32 - 602619 GGCAAATGAGTATTAAGTTGCTAACAACCCAT -s simDog_chr6.simDog.chr6 273478 32 + 593897 GTCAAATGATATTTAAGTTGCTCATATCCCAT -s simHuman_chr6.simHuman.chr6 371109 32 - 601863 GTCCAACGATTTTTAAGATGCTCACATGCCAT -s simRat_chr6.simRat.chr6 296955 32 + 647215 GTCCAATTGATGTTGAGGTCCTCACATCTCAT - -a -s simMouse_chr6.simMouse.chr6 305224 3 + 636262 TTG -s Anc0.Anc0refChr8 12940 3 - 17196 TCA -s Anc1.Anc1refChr8 56986 3 - 57822 TCA -s Anc2.Anc2refChr8 8435 3 - 12804 TCA -s mr.mrrefChr5 155701 3 + 294540 TTG -s simCow_chr6.simCow.chr6 318686 3 - 602619 TCA -s simDog_chr6.simDog.chr6 273515 3 + 593897 TTT -s simHuman_chr6.simHuman.chr6 371146 3 - 601863 TCA -s simRat_chr6.simRat.chr6 296987 3 + 647215 TTG - -a -s simMouse_chr6.simMouse.chr6 305227 9 + 636262 GCTGGTGAC -s Anc0.Anc0refChr8 12943 9 - 17196 GCTGATGAG -s Anc1.Anc1refChr8 56989 9 - 57822 GCTGATGAG -s Anc2.Anc2refChr8 8438 9 - 12804 GCTGATGAG -s mr.mrrefChr5 155704 9 + 294540 GCTGGTGAG -s simCow_chr6.simCow.chr6 318696 9 - 602619 GCTGATGAG -s simDog_chr6.simDog.chr6 273518 9 + 593897 GCTGATGAG -s simHuman_chr6.simHuman.chr6 371149 9 - 601863 GTTGATGAG -s simRat_chr6.simRat.chr6 296990 9 + 647215 GCTGGTGAG - -a -s simMouse_chr6.simMouse.chr6 305236 9 + 636262 GCCTAAACT -s Anc0.Anc0refChr8 12964 9 - 17196 GCCTAAACT -s Anc1.Anc1refChr8 57010 9 - 57822 GCCTAAACT -s Anc2.Anc2refChr8 8459 9 - 12804 GCCTAAACT -s mr.mrrefChr5 155713 9 + 294540 GCCTAAACT -s simCow_chr6.simCow.chr6 318717 9 - 602619 GCCTATACT -s simDog_chr6.simDog.chr6 273539 9 + 593897 GCCTGAATT -s simHuman_chr6.simHuman.chr6 371170 9 - 601863 GCCCAAACA -s simRat_chr6.simRat.chr6 296999 9 + 647215 GCCTAAGCT - -a -s simMouse_chr6.simMouse.chr6 305245 7 + 636262 TTTCTTT -s Anc0.Anc0refChr8 13024 7 - 17196 TTTCTTT -s Anc1.Anc1refChr8 57075 7 - 57822 TTTCTTT -s Anc2.Anc2refChr8 8519 7 - 12804 TCTCTTT -s mr.mrrefChr5 155772 7 + 294540 TTTCTTT -s simDog_chr6.simDog.chr6 273598 7 + 593897 TCTCTTT -s simHuman_chr6.simHuman.chr6 371235 7 - 601863 ATTCTCT -s simRat_chr6.simRat.chr6 297058 7 + 647215 TTTCTTT - -a -s simMouse_chr6.simMouse.chr6 305252 15 + 636262 GATTGAGACGTGTAG -s Anc0.Anc0refChr8 13032 15 - 17196 GATGGAGATGCACAG -s Anc1.Anc1refChr8 57083 15 - 57822 GATGGAGATGCACAG -s Anc2.Anc2refChr8 8527 15 - 12804 GATAGAAAGGCACAA -s mr.mrrefChr5 155779 15 + 294540 GATGGAGATGTGTAG -s simDog_chr6.simDog.chr6 273606 15 + 593897 GATAGAAAGGCACAA -s simHuman_chr6.simHuman.chr6 371243 15 - 601863 GATGGAGGTGCACAG -s simRat_chr6.simRat.chr6 297065 15 + 647215 GATGGAGATGTGTAG - -a -s simMouse_chr6.simMouse.chr6 305267 81 + 636262 ACAGGGCTTTGATGAACTTATATATCAGCTAAATGACTAAATAAAAAAAATAATATTCCTCTGAGAGATGACGTACACCAT -s Anc0.Anc0refChr8 13048 77 - 17196 ACAATGCCTTG---AACTTAGGAAT-AACTAGATGACTATGCAAATACAGCAATTTTCCTTTGGATGAAAATGCACACTAT -s Anc1.Anc1refChr8 57099 77 - 57822 ACAATGCCTTG---AACTTAGGAAT-AACTAGATGACTATGCAAATACAGCAATTTTCCTTTGGATGAAAATGCACACTAT -s Anc2.Anc2refChr8 8543 77 - 12804 ACAATGCCTTA---AACTTAGGAAT-AATTGGATGACTATGCAAATACAGCAATTTTCCTTTGGATGAAAATGCATACTAT -s mr.mrrefChr5 155794 79 + 294540 ACAGGGCTTTGA--AACTTATATATCAGCTAAATGACTATGTAAAAAAAATAATATTCCTCTGAGAGATGACGTACACCAT -s simCow_chr6.simCow.chr6 318760 48 - 602619 ---------------------------------TGATTATGCAAATACAACAATTTTTCTTTGAAAACAAATGCAAAATGC -s simDog_chr6.simDog.chr6 273622 77 + 593897 ACAATGCCTTA---AACTTAGGAAT-AATTGGATGCCTATGCAAACACAGCGATTTTCCTTTGGGTGAAAGTGCATACTAT -s simHuman_chr6.simHuman.chr6 371259 77 - 601863 ACAATGTCTTG---AACTTACGAAT-AACTAGAGGACTATGCAAATACCGCAGTTTTCTTTTGGATGAAAATCCACACTAT -s simRat_chr6.simRat.chr6 297080 65 + 647215 ACAGG---------AACTTATAGATCACCTACATGACTATGTTAAAAAAATAAAAT-CCTCTGAGAGATGACGTA------ - -a -s simMouse_chr6.simMouse.chr6 305348 5 + 636262 ATATT -s Anc0.Anc0refChr8 13126 5 - 17196 ACATT -s Anc1.Anc1refChr8 57177 5 - 57822 ACATT -s Anc2.Anc2refChr8 8621 5 - 12804 ACATT -s mr.mrrefChr5 155873 5 + 294540 ATATT -s simCow_chr6.simCow.chr6 318809 5 - 602619 GTGCC -s simDog_chr6.simDog.chr6 273700 5 + 593897 ACATT -s simHuman_chr6.simHuman.chr6 371337 5 - 601863 ACATT - -a -s simMouse_chr6.simMouse.chr6 305353 17 + 636262 ACCCTAGGGGATGTAAC -s Anc0.Anc0refChr8 13131 17 - 17196 ACTCTAGGGGATGTAAT -s Anc1.Anc1refChr8 57182 17 - 57822 ACTCTAGGGGATGTAAT -s Anc2.Anc2refChr8 8626 17 - 12804 ACTCTAGGGGAACTAAT -s mr.mrrefChr5 155878 17 + 294540 ACCCTAGGGGATGTAAC -s simCow_chr6.simCow.chr6 318818 16 - 602619 ACTCAAGAATAAC-AAT -s simDog_chr6.simDog.chr6 273705 17 + 593897 ACTCTAGGGGAACTAAT -s simHuman_chr6.simHuman.chr6 371342 17 - 601863 ACTCTCGGGGATGTAAT - -a -s simMouse_chr6.simMouse.chr6 305370 25 + 636262 CTGTTGCATAACAGCCATGCCCCCA -s Anc0.Anc0refChr8 13150 24 - 17196 CT-TTGCATTACAGCCACACTGCTG -s Anc1.Anc1refChr8 57201 24 - 57822 CT-TTGCATTACAGCCACACTGCTG -s Anc2.Anc2refChr8 8645 24 - 12804 TT-TTGCATTACAGCTACACTGCTG -s mr.mrrefChr5 155895 24 + 294540 CT-TTGCATAACAGCCATGCCCCCA -s simCow_chr6.simCow.chr6 318836 23 - 602619 TT-TTGCATTACAGCAAC-TTGCTG -s simDog_chr6.simDog.chr6 273749 24 + 593897 TC-TTGCATTCCAGCTACACTGTTG -s simHuman_chr6.simHuman.chr6 371361 24 - 601863 CT-TTGCATTAGAGCCCCACTACTG -s simRat_chr6.simRat.chr6 297145 12 + 647215 -------------GCAATGCCCCCA - -a -s simMouse_chr6.simMouse.chr6 305395 24 + 636262 TAACCCAAGTCTTTGTTCCTAATC -s Anc0.Anc0refChr8 13174 24 - 17196 TAACCCAGGTCTTTGATTCTGATT -s Anc1.Anc1refChr8 57225 24 - 57822 TAACCCAGGTCTTTGATTCTGATT -s Anc2.Anc2refChr8 8669 24 - 12804 TAACCCAGGTCTTCAATTGTGATT -s mr.mrrefChr5 155919 24 + 294540 TAACCCAGGTCTTTGTTCCTAATC -s simCow_chr6.simCow.chr6 318859 24 - 602619 TAACCCGGGTCCTCAGATTTGATT -s simDog_chr6.simDog.chr6 273774 24 + 593897 TACCCCAGGTCTTCAATTGCGATT -s simHuman_chr6.simHuman.chr6 371385 24 - 601863 TAACCCAGATCTTTGATACTGATT -s simRat_chr6.simRat.chr6 297157 24 + 647215 TAACCCAGGTTTTTGTTTCAAAGC - -a -s simMouse_chr6.simMouse.chr6 305419 55 + 636262 TGTGTAACATCATTGGAGAGAACAACTGGCATCCAGGTCATCTACTCCTCCAAAG -s Anc0.Anc0refChr8 13200 55 - 17196 TTTCAGGCATCAGTTAAGAGAACAACTGGAATACAGGTTATATACACCTCCTAAG -s Anc1.Anc1refChr8 57251 55 - 57822 TTTCAGGCATCAGTTAAGAGAACAACTGGAATACAGGTTATATACACCTCCTAAG -s Anc2.Anc2refChr8 8695 55 - 12804 TTTCAAGCATCAGTTAAGAGAACAACTGGAATACAGGTTATATACACCTCCTAAG -s mr.mrrefChr5 155943 55 + 294540 TGTGTGACATCATTGGAGAGAACAACTGGCATCCAGGTCATCTACTCCTCCAAAG -s simCow_chr6.simCow.chr6 318885 55 - 602619 TTTCAAGCATCAGTTGAGAGAACAACTGGAATACAGGTTATATACATCTGCTAGA -s simDog_chr6.simDog.chr6 273800 42 + 593897 TT-------------AAGAGGACAACTCGAACACAGGTTATATACACCTCCTAAG -s simHuman_chr6.simHuman.chr6 371411 55 - 601863 CTTCAGGCATCACTCAAGAAAACTACTGGAATACAGGTTATATACACCTCCGAAG -s simRat_chr6.simRat.chr6 297181 55 + 647215 TGTGTGACATCATTGGGGAGAACAACTTCCATCTAGGTCATCTGCTCGTCCAAAG - -a -s simMouse_chr6.simMouse.chr6 305474 41 + 636262 CTATGGCATGAACTCTTAAGCTGTAGCTGGGAAGTGTTTCT -s Anc0.Anc0refChr8 13255 21 - 17196 TC-TGGAGTGCACTCTCAAGCT------------------- -s Anc1.Anc1refChr8 57306 21 - 57822 TC-TGGAGTGCACTCTCAAGCT------------------- -s Anc2.Anc2refChr8 8750 21 - 12804 TC-TGGAGTGCACTCTCAGGTG------------------- -s mr.mrrefChr5 155998 39 + 294540 TTATGGCATGAACTCTTAAGCTGTAGC--GGAAGTGTTTCT -s simCow_chr6.simCow.chr6 318940 9 - 602619 TC-T------------CAGATG------------------- -s simDog_chr6.simDog.chr6 273843 21 + 593897 TC-TGGAGTGCACTCTCAGGTG------------------- -s simHuman_chr6.simHuman.chr6 371466 21 - 601863 TC-TGGAGTGCACTCTCAAGCT------------------- -s simRat_chr6.simRat.chr6 297236 39 + 647215 TTGTGGCATGAGCTCTTAAACAGTAGT--GGAAGTGTTTAT - -a -s simMouse_chr6.simMouse.chr6 305515 47 + 636262 TGAAGCTATTATAGCTATAATAGCCTGGGAAGTTCATACAGCCTGTG -s Anc0.Anc0refChr8 13276 26 - 17196 -------------------ATAGACTGGGAAGTTCTTAAAG-CTCT- -s Anc1.Anc1refChr8 57327 27 - 57822 -------------------ATAGACTGGGAAGTTCTTAAAG-CTCTA -s Anc2.Anc2refChr8 8771 26 - 12804 -------------------ATAGACTGGGAAGTTCTTAAAG-CTGT- -s mr.mrrefChr5 156037 47 + 294540 TGAAGCTATTATAGCTATAATAGCCTGGGAAGTTCATACAGCCTCTG -s simCow_chr6.simCow.chr6 318949 26 - 602619 -------------------CTATACTGGGATGTTCTTACAA-CTTT- -s simDog_chr6.simDog.chr6 273864 26 + 593897 -------------------ATAGACTGGGAAGTTCCAAAGG-TTGT- -s simHuman_chr6.simHuman.chr6 371487 27 - 601863 -------------------ATAGACTGCCAAGTTCTTAGAG-CTCTA -s simRat_chr6.simRat.chr6 297277 47 + 647215 TGAAGCTGTAATTGCTATAATACCCTGGGAAGTTCATGCCTCTTCTG - -a -s simMouse_chr6.simMouse.chr6 305562 60 + 636262 CTCTATTACATTTATCTATAGAGACTAACGTTCCCCAAAAGTTCTGGTGCTTATCTCCTA -s Anc0.Anc0refChr8 13302 59 - 17196 CTCAATTACATTTAACTATGCAGACTGACGTTTACTTAAAGATATGG-ATCCAATCCCAA -s Anc1.Anc1refChr8 57354 60 - 57822 CTCAATTACATTTAACTATGCAGACTGACGTTTACTTAAAGATATGGAATCCAATCCCAA -s Anc2.Anc2refChr8 8797 59 - 12804 CTCAATTACATTTAACTATGCAAACTGACGTTTACTAAAAGATATGG-ATCCAATCTCAA -s mr.mrrefChr5 156084 60 + 294540 CTCTATTACATTTATCTATGGAGACTAACGTTCCCTTAAAGTTCTGGTGCTTATCCCCTA -s simCow_chr6.simCow.chr6 318977 57 - 602619 CTCAAT-ACATTCA-CTATGCAAACTGACTTTTACTAAAAGAAATGG-ATCTGAACTCAA -s simDog_chr6.simDog.chr6 273890 57 + 593897 CACAATTACATTTAACTGTGCAAACT-ATGTTTACT-AAAGATATGG-ATCCAGTCTCAA -s simHuman_chr6.simHuman.chr6 371514 60 - 601863 CTCAATTACATTTAATAATGCAGACTGACATTTACTTAAAGATAGGGAATCCAATCCCAA -s simRat_chr6.simRat.chr6 297324 60 + 647215 TTCTATTACATTTGTCTATGGAGACTAATGTACTCTTAATGTTCTGGTCCTTATCCCCGA - -a -s simMouse_chr6.simMouse.chr6 305622 3 + 636262 GGT -s Anc0.Anc0refChr8 13361 3 - 17196 GGT -s Anc1.Anc1refChr8 57414 3 - 57822 GGT -s Anc2.Anc2refChr8 8857 3 - 12804 GGT -s mr.mrrefChr5 156144 3 + 294540 GGT -s simCow_chr6.simCow.chr6 319035 3 - 602619 GGG -s simDog_chr6.simDog.chr6 273948 3 + 593897 GGT -s simHuman_chr6.simHuman.chr6 371574 3 - 601863 AGT -s simRat_chr6.simRat.chr6 297384 3 + 647215 GGT - -a -s simMouse_chr6.simMouse.chr6 305625 67 + 636262 ATAAGGTCCAAATCTTTAATCTGGACAGCTGGGTCATATAAGGACAATCTGTCTACTGGCATAACCT -s Anc0.Anc0refChr8 13364 60 - 17196 AT-------GAAGATTTACTCTGAACAGCTGGGTCATATAGGCCCAGTCTGTCCACTGCCAAAACCC -s Anc1.Anc1refChr8 57417 60 - 57822 AT-------GAAGATTTACTCTGAACAGCTGGGTCATATAGGCCCAGTCTGTCCACTGCCAAAACCC -s Anc2.Anc2refChr8 8860 60 - 12804 AT-------GAAGATTTACTCTGAACAGCTGGATCATGTAGGCCCAGTCTGTCCACTGCTGAAACCC -s mr.mrrefChr5 156147 67 + 294540 ATAAGGTCCAAATCTTTAATCTGAACAGCTGGGTCATATAAGGCCAATCTGTCTACTGCCATAACCT -s simCow_chr6.simCow.chr6 319038 60 - 602619 AT-------CAAAATTTACTTTGAACGGCTGGATCGTGTAGGCCCAGTCTGTACACCACTGTAACGT -s simDog_chr6.simDog.chr6 273951 60 + 593897 AT-------GAAGACTTACTCTGAACAGCTGGATCATGTAGGTCAAGTCTGTCCACTGCTGAAACCC -s simHuman_chr6.simHuman.chr6 371578 60 - 601863 AT-------GAAGTTTTACTCTGAACAACTGGGTCATATAGGCCCAGTCAGTCCATTGCCAGAACCC -s simRat_chr6.simRat.chr6 297387 67 + 647215 ATAAGGTCCAAATCTTTAATCTGAACAGCTGGGTCACATAAGGCCAATCTGTCTGCTGCCATAACTT - -a -s simMouse_chr6.simMouse.chr6 305692 27 + 636262 TGAAGCATACCTTTTGCTCATCTCCAC -s Anc0.Anc0refChr8 13424 27 - 17196 TGAAGCATACCCTTCACTCACCTCCAC -s Anc1.Anc1refChr8 57477 27 - 57822 TGAAGCATACCCTTCACTCACCTCCAC -s Anc2.Anc2refChr8 8922 27 - 12804 TAGATCATACCCTTCACTCACCTCCAC -s mr.mrrefChr5 156214 27 + 294540 TGAAGCATACCTTTTGCTCATCTCCAT -s simCow_chr6.simCow.chr6 319100 27 - 602619 TAGATCATACCCTTCACTCACCTCCAT -s simDog_chr6.simDog.chr6 274013 27 + 593897 TAGATCATACCCTTCACTCACCTCCAC -s simHuman_chr6.simHuman.chr6 371638 6 - 601863 TGAAGC--------------------- -s simRat_chr6.simRat.chr6 297454 27 + 647215 TGAAGCATACCTTTTGCCCATCTCCAT - -a -s simMouse_chr6.simMouse.chr6 305719 5 + 636262 GATAT -s Anc0.Anc0refChr8 13451 5 - 17196 GTTGT -s Anc1.Anc1refChr8 57504 5 - 57822 GTTGT -s Anc2.Anc2refChr8 8952 5 - 12804 GTTGT -s mr.mrrefChr5 156241 5 + 294540 GATAT -s simCow_chr6.simCow.chr6 319130 5 - 602619 GATAT -s simDog_chr6.simDog.chr6 274043 5 + 593897 GTTGT -s simRat_chr6.simRat.chr6 297481 5 + 647215 GATAT - -a -s simMouse_chr6.simMouse.chr6 305724 12 + 636262 AACTGAGCAGAG -s Anc0.Anc0refChr8 13456 12 - 17196 TCCTGTCCTTAG -s Anc1.Anc1refChr8 57509 12 - 57822 TCCTGTCCTTAG -s Anc2.Anc2refChr8 8957 12 - 12804 TCCTGTCCTTAG -s mr.mrrefChr5 156246 12 + 294540 AACTGAGCTGAG -s simCow_chr6.simCow.chr6 319136 12 - 602619 TCCATACTTTAG -s simDog_chr6.simDog.chr6 274048 12 + 593897 TCCTGTCCTTAG -s simRat_chr6.simRat.chr6 297486 12 + 647215 AACTGAGCTAAG - -a -s simMouse_chr6.simMouse.chr6 305736 33 + 636262 GTTTTTGAAAATAGAGGATTAAGGTTTAACATA -s Anc0.Anc0refChr8 13468 31 - 17196 CTTTTAGTAAATAAATGGCCAGAGTTTCACA-- -s Anc1.Anc1refChr8 57521 31 - 57822 CTTTTAGTAAATAAATGGCCAGAGTTTCACA-- -s Anc2.Anc2refChr8 8974 31 - 12804 CTTTTAGTAAATAAATGGCCAGAGTTTCACA-- -s mr.mrrefChr5 156258 31 + 294540 GTTTTTGAAAATAGAGGACTAAGGTTTAACA-- -s simCow_chr6.simCow.chr6 319153 31 - 602619 CTGCTAAGCAGCAGATGATCAAGGCTTCAGA-- -s simDog_chr6.simDog.chr6 274065 31 + 593897 CTTTTAGTAAATAAATGGCCAGAGTTTCACA-- -s simRat_chr6.simRat.chr6 297498 31 + 647215 GTTTTTTAAAATAGAGGACTAAGGTTTAACA-- - -a -s simMouse_chr6.simMouse.chr6 305769 8 + 636262 CCTGAAGC -s Anc0.Anc0refChr8 13499 8 - 17196 CCCGGAAC -s Anc1.Anc1refChr8 57552 8 - 57822 CCCGGAAC -s Anc2.Anc2refChr8 9006 8 - 12804 CCCGGAAC -s mr.mrrefChr5 156289 8 + 294540 CCTGAAGC -s simCow_chr6.simCow.chr6 319185 8 - 602619 CCCTGAAG -s simDog_chr6.simDog.chr6 274097 8 + 593897 CCCGGAAC -s simHuman_chr6.simHuman.chr6 371644 3 - 601863 -----AAC -s simRat_chr6.simRat.chr6 297529 8 + 647215 CCTGAAGC - -a -s simMouse_chr6.simMouse.chr6 305777 3 + 636262 AAT -s Anc0.Anc0refChr8 13507 3 - 17196 AGT -s Anc1.Anc1refChr8 57560 3 - 57822 AGT -s Anc2.Anc2refChr8 9017 3 - 12804 AGT -s mr.mrrefChr5 156297 3 + 294540 AAT -s simCow_chr6.simCow.chr6 319196 3 - 602619 AGT -s simDog_chr6.simDog.chr6 274108 3 + 593897 AGT -s simHuman_chr6.simHuman.chr6 371647 3 - 601863 ATT -s simRat_chr6.simRat.chr6 297537 3 + 647215 AAT - -a -s simMouse_chr6.simMouse.chr6 305780 12 + 636262 AGGTTTGCATAG -s Anc0.Anc0refChr8 13510 12 - 17196 AGGTTTACATAT -s Anc1.Anc1refChr8 57563 12 - 57822 AGGTTTACATAT -s Anc2.Anc2refChr8 9020 12 - 12804 AGGTTTACATAT -s mr.mrrefChr5 156300 12 + 294540 AGGTTTGCATAG -s simCow_chr6.simCow.chr6 319200 12 - 602619 AGGTCTACATAA -s simDog_chr6.simDog.chr6 274111 12 + 593897 GGGTTTACATAT -s simHuman_chr6.simHuman.chr6 371650 12 - 601863 AGGTTTACATAT -s simRat_chr6.simRat.chr6 297540 12 + 647215 GGGTTTGTGTAG - -a -s simMouse_chr6.simMouse.chr6 305792 16 + 636262 TGGGTAAGACTGGTTC -s Anc0.Anc0refChr8 13526 11 - 17196 TT-----GCCTTGTAC -s Anc1.Anc1refChr8 57579 11 - 57822 TT-----GCCTTGTAC -s Anc2.Anc2refChr8 9036 11 - 12804 TT-----GCATTGGAC -s mr.mrrefChr5 156316 16 + 294540 TGAGTAAGACTGGTTC -s simCow_chr6.simCow.chr6 319216 9 - 602619 TT-----TCG--GGAC -s simDog_chr6.simDog.chr6 274127 11 + 593897 TA-----GCATTGGAC -s simHuman_chr6.simHuman.chr6 371666 11 - 601863 TT-----GCCCTGTAC -s simRat_chr6.simRat.chr6 297556 16 + 647215 TGAGTGAGCCCGATTC - -a -s simMouse_chr6.simMouse.chr6 305808 3 + 636262 ACA -s Anc0.Anc0refChr8 13539 3 - 17196 ACA -s Anc1.Anc1refChr8 57592 3 - 57822 ACA -s Anc2.Anc2refChr8 9049 3 - 12804 ACA -s mr.mrrefChr5 156332 3 + 294540 ACA -s simCow_chr6.simCow.chr6 319227 3 - 602619 AAA -s simDog_chr6.simDog.chr6 274140 3 + 593897 ACA -s simHuman_chr6.simHuman.chr6 371679 3 - 601863 ACA -s simRat_chr6.simRat.chr6 297572 3 + 647215 ACA - -a -s simMouse_chr6.simMouse.chr6 305811 9 + 636262 TTGAGCTCT -s Anc0.Anc0refChr8 13543 9 - 17196 TTGAACTAT -s Anc1.Anc1refChr8 57596 9 - 57822 TTGAACTAT -s Anc2.Anc2refChr8 9053 9 - 12804 TTGAACTAT -s mr.mrrefChr5 156335 9 + 294540 TTGAGCTCT -s simCow_chr6.simCow.chr6 319231 9 - 602619 TTGAACTAT -s simDog_chr6.simDog.chr6 274144 9 + 593897 TTGAACCAT -s simHuman_chr6.simHuman.chr6 371683 9 - 601863 TTGAACTAT -s simRat_chr6.simRat.chr6 297575 9 + 647215 TTGAGCTCT - -a -s simMouse_chr6.simMouse.chr6 305820 1 + 636262 A -s Anc0.Anc0refChr8 13552 1 - 17196 A -s Anc1.Anc1refChr8 57605 1 - 57822 A -s Anc2.Anc2refChr8 9064 1 - 12804 A -s mr.mrrefChr5 156344 1 + 294540 A -s simCow_chr6.simCow.chr6 319242 1 - 602619 A -s simDog_chr6.simDog.chr6 274155 1 + 593897 C -s simHuman_chr6.simHuman.chr6 371692 1 - 601863 A -s simRat_chr6.simRat.chr6 297584 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 305821 2 + 636262 TC -s Anc0.Anc0refChr8 13557 2 - 17196 TC -s Anc1.Anc1refChr8 57610 2 - 57822 TC -s Anc2.Anc2refChr8 9069 2 - 12804 TC -s mr.mrrefChr5 156345 2 + 294540 TC -s simCow_chr6.simCow.chr6 319247 2 - 602619 TC -s simDog_chr6.simDog.chr6 274160 2 + 593897 TC -s simHuman_chr6.simHuman.chr6 371697 2 - 601863 TC -s simRat_chr6.simRat.chr6 297585 2 + 647215 TC - -a -s simMouse_chr6.simMouse.chr6 305823 111 + 636262 TAGACTGGGTGTATCCATATATGGAGTGAGTTCTGGGTGATTTTCCCAAGTTGTGTTTCTAATATTTCTGTCCCTGCATGGAATATTATCTAGGAGGTTAGCCTGCACATC -s Anc0.Anc0refChr8 13559 38 - 17196 TGAACAGCGTGTGC-------------------------------------------------------------------------ATTCAGGAGGTTAGCCTGCATATC -s Anc1.Anc1refChr8 57612 38 - 57822 TGAACAGCGTGTGC-------------------------------------------------------------------------ATTCAGGAGGTTAGCCTGCATATC -s Anc2.Anc2refChr8 9071 38 - 12804 TGAACAGCGCCTGC-------------------------------------------------------------------------ATTCAGGAGGTTAGCCTGTTTATC -s mr.mrrefChr5 156347 38 + 294540 TAGACAGGGTGTAC-------------------------------------------------------------------------ATTTAGGAGGTTAGCCTGCACATC -s simCow_chr6.simCow.chr6 319255 38 - 602619 GGAACAGCGTCTGC-------------------------------------------------------------------------ATCAAGGGGGTTGACCTGTTTATC -s simDog_chr6.simDog.chr6 274162 38 + 593897 TGAACAGCCCCTGC-------------------------------------------------------------------------ATTCAGGAGGTTAGCCTGTTTACC -s simHuman_chr6.simHuman.chr6 371699 36 - 601863 TGAACA--GTGCCT-------------------------------------------------------------------------GATCAGGAGGTGAGTCTGCATATA -s simRat_chr6.simRat.chr6 297587 38 + 647215 TGGACAGGATGTAC-------------------------------------------------------------------------ATTGAGGGGGTTAGCCTGCTCATC - -a -s simMouse_chr6.simMouse.chr6 305934 20 + 636262 AGCACTTACTAATCCACTGT -s Anc0.Anc0refChr8 13609 20 - 17196 AGCATTTACCTATTCACTGT -s Anc1.Anc1refChr8 57662 20 - 57822 AGCATTTACCTATTCACTGT -s Anc2.Anc2refChr8 9121 20 - 12804 GGCATTTACCTATTCATTGT -s mr.mrrefChr5 156385 20 + 294540 AGCACTTACTAATCCACTGT -s simCow_chr6.simCow.chr6 319305 20 - 602619 GGCATTTACCTATTCATTGT -s simDog_chr6.simDog.chr6 274212 20 + 593897 GGCATTTACCTATTCATTGT -s simHuman_chr6.simHuman.chr6 371747 20 - 601863 AGCGTTTAACTATTCACTGT -s simRat_chr6.simRat.chr6 297625 20 + 647215 AGCACTTACTAATCCGCCGT - -a -s simMouse_chr6.simMouse.chr6 305954 97 + 636262 ACCTAGAATAGCTGGCCAATTCATTCAAGTTTGCAGGAAACCTCATAGTTTAGCCCCCCATGTAGTGTTACCCCGAACAGTCTGGTGGTTGATGATT -s Anc0.Anc0refChr8 13629 40 - 17196 CATTAGACTGGCTAATCAAT---------------------------------------------------------CAGTCTCACTGTGGACAATT -s Anc1.Anc1refChr8 57682 40 - 57822 CATTAGACTGGCTAATCAAT---------------------------------------------------------CAGTCTCACTGTGGACAATT -s Anc2.Anc2refChr8 9141 40 - 12804 CATCAGACTGTCTAATCAAT---------------------------------------------------------CAGTCTCACTGTGGACAATT -s mr.mrrefChr5 156405 40 + 294540 ACTTAGAATGGCTAACCAAT---------------------------------------------------------CAGTCTGGTGGTTGATGATT -s simCow_chr6.simCow.chr6 319325 40 - 602619 CCTCAGACTGTCTAACTCAT---------------------------------------------------------CAGTACCACTGGGGACAATC -s simDog_chr6.simDog.chr6 274233 30 + 593897 CAT----------AATCAAT---------------------------------------------------------CAGTCTCACCCTGGACAATT -s simHuman_chr6.simHuman.chr6 371767 40 - 601863 CATTTGACTGGCTAATCAAT---------------------------------------------------------CAGTCACACTGTGGACTAAT -s simRat_chr6.simRat.chr6 297645 40 + 647215 ACTTAGAATGACTAACCAAT---------------------------------------------------------CAGTCTGGTGGTTGGTGATT - -a -s simMouse_chr6.simMouse.chr6 306051 16 + 636262 GAAAATTATAAGGTGT -s Anc0.Anc0refChr8 13669 16 - 17196 GACTATTAGAATGTGA -s Anc1.Anc1refChr8 57722 16 - 57822 GACTATTAGAATGTGA -s Anc2.Anc2refChr8 9181 16 - 12804 GACTATTAGAATGTGA -s mr.mrrefChr5 156445 16 + 294540 GAATATTATAAGGTGA -s simCow_chr6.simCow.chr6 319366 16 - 602619 AACTATCAGAACGTGA -s simDog_chr6.simDog.chr6 274263 16 + 593897 GACTATTAGAATGCCA -s simHuman_chr6.simHuman.chr6 371807 16 - 601863 GTCTATTAGAGTGTGA -s simRat_chr6.simRat.chr6 297685 16 + 647215 GAATATTATAAGGTGA - -a -s simMouse_chr6.simMouse.chr6 306067 9 + 636262 GTGTTCTAG -s Anc0.Anc0refChr8 13689 9 - 17196 TTAATAGTG -s Anc1.Anc1refChr8 57742 9 - 57822 TTAATAGTG -s Anc2.Anc2refChr8 9201 9 - 12804 TTACCAGTG -s mr.mrrefChr5 156461 9 + 294540 GTGATCTAG -s simCow_chr6.simCow.chr6 319386 9 - 602619 TGACCTGTG -s simDog_chr6.simDog.chr6 274283 9 + 593897 TTCCCAGTG -s simHuman_chr6.simHuman.chr6 371827 9 - 601863 TTAATAATG -s simRat_chr6.simRat.chr6 297701 9 + 647215 GTGATCTAG - -a -s simMouse_chr6.simMouse.chr6 306076 19 + 636262 TGGATTGGTGTTACAAGGT -s Anc0.Anc0refChr8 13698 16 - 17196 TGGCA--TTAC-ACTAGGT -s Anc1.Anc1refChr8 57751 19 - 57822 TGGCATGTTACTACTAGGT -s Anc2.Anc2refChr8 9210 16 - 12804 TGGCA--TTAC-ACTAGGT -s mr.mrrefChr5 156470 19 + 294540 TGGATTGGTATTACTAGGT -s simCow_chr6.simCow.chr6 319395 14 - 602619 CA-CA--TTAC-ACTAGG- -s simDog_chr6.simDog.chr6 274295 16 + 593897 TGGCA--TTAC-ACTAGGT -s simHuman_chr6.simHuman.chr6 371836 19 - 601863 TGGCGTGTTACTACTAGGT -s simRat_chr6.simRat.chr6 297710 14 + 647215 TGG-----TAGTACTAGGT - -a -s simMouse_chr6.simMouse.chr6 306095 6 + 636262 ACGCAT -s Anc0.Anc0refChr8 13714 5 - 17196 ACGCA- -s Anc1.Anc1refChr8 57770 5 - 57822 ACGCA- -s Anc2.Anc2refChr8 9227 5 - 12804 ACTTA- -s mr.mrrefChr5 156489 6 + 294540 ACGCAT -s simCow_chr6.simCow.chr6 319410 5 - 602619 ACATA- -s simDog_chr6.simDog.chr6 274312 5 + 593897 ACTTG- -s simHuman_chr6.simHuman.chr6 371855 5 - 601863 GTGCA- -s simRat_chr6.simRat.chr6 297724 6 + 647215 ACGCAT - -a -s simMouse_chr6.simMouse.chr6 306101 46 + 636262 GCAAGTGTTATGCCTTTATGTCTCTTTTATCCTAGGCATGCTTCCG -s Anc0.Anc0refChr8 13720 46 - 17196 ATAAGTGTTATGCCTTTGTGTTTATTGTGTATCAGGCATACTCTCG -s Anc1.Anc1refChr8 57776 46 - 57822 ATAAGTGTTATGCCTTTGTGTTTATTGTGTATCAGGCATACTCTCG -s Anc2.Anc2refChr8 9233 46 - 12804 ATAAGTGTTATGCCTTTGTGTTGATTGTGTATCGGGCATAATCTCG -s mr.mrrefChr5 156496 46 + 294540 GCATGTGTTATGCCTTTATGTTTCTTTTATCTTAGGCATACTTCCG -s simCow_chr6.simCow.chr6 319416 46 - 602619 ATATGTGTTATGCCTTTGTGTTCATCGTGTATTGGGAATAATCTTG -s simDog_chr6.simDog.chr6 274318 46 + 593897 ATAAGTGTTATGCCTTTGTATTGATTGGGTATCGGGCATAATCTCG -s simHuman_chr6.simHuman.chr6 371861 46 - 601863 ATGCATATTATGTCTTTGTGTTTGTTGTGTATCAGGCATACTCTCT -s simRat_chr6.simRat.chr6 297731 40 + 647215 GCATGTGTTATCC------GTTCCTTTTATCTTAGTCATACTTCTG - -a -s simMouse_chr6.simMouse.chr6 306147 7 + 636262 TCATAGA -s Anc0.Anc0refChr7 15623 7 + 16696 TTCTGAA -s Anc1.Anc1refChr4 16339 7 - 17549 TTCTGAA -s Anc2.Anc2refChr5 7273 7 + 8386 TTCGGAA -s mr.mrrefChr5 156542 7 + 294540 TCATAAA -s simCow_chr6.simCow.chr6 278104 7 + 602619 TTCCAAA -s simDog_chr6.simDog.chr6 314898 7 - 593897 TTCGGAG -s simHuman_chr6.simHuman.chr6 299502 7 - 601863 TTCTGAA -s simRat_chr6.simRat.chr6 297771 7 + 647215 TCATAAA - -a -s simMouse_chr6.simMouse.chr6 306154 17 + 636262 CAGAGTTTGATGTGATG -s Anc0.Anc0refChr7 15630 17 + 16696 CAGGGTTTAGTGTGATG -s Anc1.Anc1refChr4 16346 17 - 17549 CAGGGTTTAGTGTGATG -s Anc2.Anc2refChr5 7280 17 + 8386 CAGGGTATAGTGCGATG -s mr.mrrefChr5 156549 17 + 294540 CAGAGTTTGATGTGATG -s simCow_chr6.simCow.chr6 278111 17 + 602619 TGGGGTCTGGTGAGATG -s simDog_chr6.simDog.chr6 314911 17 - 593897 CAGGGTATAATGCGATG -s simHuman_chr6.simHuman.chr6 299509 17 - 601863 CAGGGTTCAGTGTGATG -s simRat_chr6.simRat.chr6 297778 17 + 647215 AAGATTTTGATGTGATG - -a -s simMouse_chr6.simMouse.chr6 306171 48 + 636262 TTGGGTGACCTCAACCTTATGCTTACACAAGTAAGAACTTAGGTATAG -s Anc0.Anc0refChr7 15650 37 + 16696 TTGGGTGACCTAATCTTTACG--------AT---TAACTTTGGTATAT -s Anc1.Anc1refChr4 16366 40 - 17549 TTGGGTGACCTAATCTTTACG--------ATTAATAACTTTGGTATAT -s Anc2.Anc2refChr5 7300 37 + 8386 TTGGGTAACCTAATCTTTACG--------AT---CAACTTTGGTATAT -s mr.mrrefChr5 156569 48 + 294540 TTGGGTGACCTCAACCTTATGCTTACACAAGTAAGAACTTAGGTATAG -s simCow_chr6.simCow.chr6 278131 37 + 602619 TTGGGTAACCTGATGTTTGCA--------At---caactctggtctat -s simDog_chr6.simDog.chr6 314931 37 - 593897 TTGGGCAACCTAATCTCTATG--------TT---CAACTTTGGCATAT -s simHuman_chr6.simHuman.chr6 299529 40 - 601863 TTGGGTGCCCTAATATTTACG--------ATTAATAACTTTGGTATAT -s simRat_chr6.simRat.chr6 297798 48 + 647215 TTGGGTGACCTTAACCTTATGCTTAGACAAGTGAGAACTTAAGTATAG - -a -s simMouse_chr6.simMouse.chr6 306219 19 + 636262 TGTGATAGTCCCATCCAGT -s Anc0.Anc0refChr7 15689 19 + 16696 TGTGATGACCAGGTCCAAT -s Anc1.Anc1refChr4 16408 19 - 17549 TGTGATGACCAGGTCCAAT -s Anc2.Anc2refChr5 7339 19 + 8386 TGTGATGACAAGGTCCAAT -s mr.mrrefChr5 156617 19 + 294540 TGTGATAGTCACATCCAAT -s simCow_chr6.simCow.chr6 278170 18 + 602619 tgtgac-acaagatctaat -s simDog_chr6.simDog.chr6 314970 19 - 593897 TGGGGTGACAAGGTCCAAT -s simHuman_chr6.simHuman.chr6 299571 19 - 601863 TGTGATGACCAGGTCCGAT -s simRat_chr6.simRat.chr6 297846 19 + 647215 TGTGATAGTCACATCCAAT - -a -s simMouse_chr6.simMouse.chr6 306238 11 + 636262 TTCAACTGCTC -s Anc0.Anc0refChr7 15708 11 + 16696 TTCAACTTCTT -s Anc1.Anc1refChr4 16427 11 - 17549 TTCAACTTCTT -s Anc2.Anc2refChr5 7358 11 + 8386 TTCAACTTCTT -s mr.mrrefChr5 156636 11 + 294540 TTCAACTGCTC -s simCow_chr6.simCow.chr6 278188 11 + 602619 ttcaaattctt -s simDog_chr6.simDog.chr6 315201 11 - 593897 TCCAACTCCTT -s simHuman_chr6.simHuman.chr6 299590 11 - 601863 TTTAACTTCTT -s simRat_chr6.simRat.chr6 297865 11 + 647215 TTCAACTGCTC - -a -s simMouse_chr6.simMouse.chr6 306249 41 + 636262 ATGTAGGAAAGACAGTCTTGTTAGCGCCATTTCTTGTACTG -s Anc0.Anc0refChr7 15734 36 + 16696 GTTT-----TGTCAGTTTTGTTATCACcattccttGCAGAG -s Anc1.Anc1refChr4 16453 41 - 17549 GTTTAGTTATGTCAGTTTTGTTATCACCATTCCTTGCAGAG -s Anc2.Anc2refChr5 7384 36 + 8386 GTTT-----TGTCAGTTTCGCTATCACcacttcctGCAGAG -s mr.mrrefChr5 156647 41 + 294540 ATGTAGGAAAGACAGTCTTGTTAGCACCATTCCTTGTACAG -s simCow_chr6.simCow.chr6 278213 28 + 602619 ------------cagttt-gctagcaccacttcctgcacag -s simDog_chr6.simDog.chr6 315227 28 - 593897 GTTT-----TGTCAGCATCGCTTTTAC--------ATAGAG -s simHuman_chr6.simHuman.chr6 299616 41 - 601863 GTTTAGTTATGCCAGTTTTGTTATCACCATTCCTTGCATAG -s simRat_chr6.simRat.chr6 297876 41 + 647215 ATGTAGGAAAGATAGTCTTGTTAGCACCACTCCTTATACAG - -a -s simMouse_chr6.simMouse.chr6 306290 45 + 636262 GAATCTCTGATTCGCCTTCACAATTCTGCACTACCTGATGAAAGT -s Anc0.Anc0refChr7 15771 43 + 16696 GGACCTTTGACCTGCATTTTCAGTTCTgcttta-c-gatggAAGA -s Anc1.Anc1refChr4 16495 44 - 17549 GGACCTTTGACCTGCATTTTCAGTTCTGCTTTA-CTGATGGAAGA -s Anc2.Anc2refChr5 7421 43 + 8386 GGACCTTTGACCTGCATTTTCAGTCCTgatttt-c-aatggAAGA -s mr.mrrefChr5 156688 45 + 294540 GAACCTCTGATTCGCATTCACAATTCTGCACTACCTGATGAAAGA -s simCow_chr6.simCow.chr6 278242 33 + 602619 gaacctttg----------tcagtccagatttt-c-aatggaggg -s simDog_chr6.simDog.chr6 315256 31 - 593897 GGACCTTTGACCTGCATTTTCAGTCCT--------------CAGA -s simHuman_chr6.simHuman.chr6 299658 44 - 601863 GCACCCTTGACCTGCATTTTCAGTTCTGCTTTA-CTGCTGGAAGA -s simRat_chr6.simRat.chr6 297917 45 + 647215 GAACCTCTGCTTCACATTCACAATTCTGCACTGCCTGATGAAAGA - -a -s simMouse_chr6.simMouse.chr6 306335 1 + 636262 A -s Anc0.Anc0refChr7 15837 1 + 16696 A -s Anc1.Anc1refChr4 16562 1 - 17549 A -s Anc2.Anc2refChr5 7487 1 + 8386 A -s mr.mrrefChr5 156733 1 + 294540 A -s simCow_chr6.simCow.chr6 278298 1 + 602619 a -s simDog_chr6.simDog.chr6 315310 1 - 593897 A -s simHuman_chr6.simHuman.chr6 299725 1 - 601863 G -s simRat_chr6.simRat.chr6 297962 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 306336 38 + 636262 GGTACTCACAAAACTAACACATGATTGCTTATGGTACA -s Anc0.Anc0refChr7 15838 36 + 16696 GATACGCGCAGAAC--ACACATAATTGCTTATGGAACA -s Anc1.Anc1refChr4 16563 38 - 17549 GATACGCGCAGAACTAACACATAATTGCTTATGGAACA -s Anc2.Anc2refChr5 7488 36 + 8386 GATATGTGGAGAAC--AAACATGATTGTTTATGGAACA -s mr.mrrefChr5 156734 38 + 294540 GGTACTCACAAAACTAACACATAATTGCTTATGGTACA -s simCow_chr6.simCow.chr6 278307 36 + 602619 GATATGTGGAGAAC--AAACATCATTGTTTATGGAAGA -s simDog_chr6.simDog.chr6 315311 23 - 593897 GA---------------AACATGATTGTTTATGGAACA -s simHuman_chr6.simHuman.chr6 299726 38 - 601863 GATACCCCCAGAACTAACACATAATCGCTTATGGAACA -s simRat_chr6.simRat.chr6 297963 38 + 647215 GGTACTCACAAAACGAACACATAATTGCTTATGGTACA - -a -s simMouse_chr6.simMouse.chr6 306374 2 + 636262 GA -s Anc0.Anc0refChr7 15874 2 + 16696 GA -s Anc1.Anc1refChr4 16601 2 - 17549 GA -s Anc2.Anc2refChr5 7524 2 + 8386 GA -s mr.mrrefChr5 156772 2 + 294540 GA -s simCow_chr6.simCow.chr6 278343 2 + 602619 AG -s simDog_chr6.simDog.chr6 315336 2 - 593897 GA -s simHuman_chr6.simHuman.chr6 299764 2 - 601863 GA -s simRat_chr6.simRat.chr6 298001 2 + 647215 GA - -a -s simMouse_chr6.simMouse.chr6 306376 45 + 636262 CTTATTCCAACCATATATCATACACAAGCTTTTCTCACAGCATGA -s Anc0.Anc0refChr7 15877 45 + 16696 CTTATTCCAACCATCTGTCATACATCGGTTCTCATGACAGCACAG -s Anc1.Anc1refChr4 16604 45 - 17549 CTTATTCCAACCATCTGTCATACATCGGTTCTCATGACAGCACAG -s Anc2.Anc2refChr5 7527 45 + 8386 CTTATTCCCACCATCTGTCATACATCGGTTCTCATGACAGCACAG -s mr.mrrefChr5 156774 45 + 294540 CTTATTCCAACCATCTATCATACACAAGCTTTTCTCACAGCATGG -s simCow_chr6.simCow.chr6 278346 44 + 602619 CTCATCCCC-CCATCTGTCATACACCGGTTTTCAAGACAGCACAG -s simDog_chr6.simDog.chr6 315339 35 - 593897 TTTATTCCCA-----TGTCATACAT-----CTCATGACAGCACAT -s simHuman_chr6.simHuman.chr6 299767 45 - 601863 CTTATTCCAGCCATCTGTCATACATTTTATCTCATGACAGCACAG -s simRat_chr6.simRat.chr6 298003 37 + 647215 CTTATTCCAACCATCTATCACGCAAAAGCT--------TGCATGG - -a -s simMouse_chr6.simMouse.chr6 306421 88 + 636262 GTGAGGTGTGGCATAGTGGCTTAATATTTTGGGCACTTTTTCTCTCTGAAAAGTTAGTTCAAAGAAGAACTACATCCAGCACCAAGGT -s Anc0.Anc0refChr7 15922 74 + 16696 GTG----GTGTTATGGTGGCTTAATGTTCTGGGCACTTTTTATC-CTAGAAAATCAATTAAAAGAAGAGCTACAT---------ATAT -s Anc1.Anc1refChr4 16649 74 - 17549 GTG----GTGTTATGGTGGCTTAATGTTCTGGGCACTTTTTATC-CTAGAAAATCAATTAAAAGAAGAGCTACAT---------ATAT -s Anc2.Anc2refChr5 7572 74 + 8386 GTG----GTGTTATGGTGGCGTAATGTTCTAAGCACTTTTCATC-ATAGAAAATCAAGTAAAAGAAGAGCTACAA---------ATAT -s mr.mrrefChr5 156819 87 + 294540 GTGAGGTGTGGTATAGTGGCTTAATATTTTGGGCACTTTTTCTCTCTGGAAAATCAGTTCAAAGAAGAGCTACATCCAGCACC-ATGT -s simCow_chr6.simCow.chr6 278394 74 + 602619 GTT----GTGGCATAGTGGCCTAATGTTCTAAGCACTTTTCATC-ATAAAAAATCAAGTAAAAAAAAAGATACAA---------ATAT -s simDog_chr6.simDog.chr6 315374 73 - 593897 GTG----G-GTTGTGGTATGGTAGTGGTGTAAGCACTTTTCAGC-ATAGAATGTCAAGCGAATGTAGAGCTAGAA---------ATAT -s simHuman_chr6.simHuman.chr6 299812 74 - 601863 GCG----GTGATATGGTGGCTTAATGTTCTGGGCACTTTTTGTC-CTAGACAATCAATTAGAAGAAGAGCTACAT---------GTAT -s simRat_chr6.simRat.chr6 298040 86 + 647215 GTGAGGTGTAGTATAGTGGCTTAGTATTTTGGGCACTTTTTCTCTGTGGAAAATCAG-TCAAAGAGGAGGTACATCCAGCACC-ATGT - -a -s simMouse_chr6.simMouse.chr6 306509 31 + 636262 AAGATGTCACCCTTGAGTGGCACGGGCAGTA -s Anc0.Anc0refChr7 15996 31 + 16696 AGATTGTCACCCCTGAGTGGCATAGGCAATG -s Anc1.Anc1refChr4 16723 31 - 17549 AGATTGTCACCCCTGAGTGGCATAGGCAATG -s Anc2.Anc2refChr5 7647 31 + 8386 AGATTGTCACACCTGAGTGGCACAGGCAATG -s mr.mrrefChr5 156906 31 + 294540 AGGATGTCACCCTTGAGTGGCATGGGCAGTG -s simCow_chr6.simCow.chr6 278469 31 + 602619 AGATCGTCACTCTTCAGTGGCTCAGGCAGCA -s simDog_chr6.simDog.chr6 315448 31 - 593897 AGTTTGTCACACCTGAGTGACACAGGCAATG -s simHuman_chr6.simHuman.chr6 299886 31 - 601863 AGATTGTCACCCCCAAGTAGCATATGCAATG -s simRat_chr6.simRat.chr6 298126 31 + 647215 AGGATGTAACCCTTGGGTGGCATGGGCAGTG - -a -s simMouse_chr6.simMouse.chr6 306540 28 + 636262 AAACAGCTGATTTATAAATGTACGACTT -s Anc0.Anc0refChr7 16032 28 + 16696 CAAAAGCTAGTTTATTAAGGTATAATTT -s Anc1.Anc1refChr4 16759 28 - 17549 CAAAAGCTAGTTTATTAAGGTATAATTT -s Anc2.Anc2refChr5 7683 28 + 8386 CAAAAGCTAGTTTACTAAGGTATAATTT -s mr.mrrefChr5 156937 28 + 294540 AAACAGCTGGTTTATTAATGTACAACTT -s simCow_chr6.simCow.chr6 278504 28 + 602619 CCAATGCTAGTTTCCCAAGGTATAATTT -s simDog_chr6.simDog.chr6 315484 28 - 593897 CAAAAGCTAGTTTACTAAGGCATAATAT -s simHuman_chr6.simHuman.chr6 299922 28 - 601863 CAAAAGCTAGTTTATTAAGATATAATTT -s simRat_chr6.simRat.chr6 298157 28 + 647215 AAACAGCTGGTTTATTAATGTACAACTT - -a -s simMouse_chr6.simMouse.chr6 306568 8 + 636262 CAAGCAGC -s Anc0.Anc0refChr7 16070 8 + 16696 CTAGGAGT -s Anc1.Anc1refChr4 16797 8 - 17549 CTAGGAGT -s Anc2.Anc2refChr5 7721 8 + 8386 CTAGGGGT -s mr.mrrefChr5 156965 8 + 294540 CAAGCAGT -s simCow_chr6.simCow.chr6 278542 8 + 602619 CTAGGGGT -s simDog_chr6.simDog.chr6 315522 8 - 593897 CCAGGGGT -s simHuman_chr6.simHuman.chr6 299960 8 - 601863 CTAAGAGT -s simRat_chr6.simRat.chr6 298185 8 + 647215 CGAGCAGT - -a -s simMouse_chr6.simMouse.chr6 306576 22 + 636262 GTCCCAATGGGTGTAGTCAACA -s Anc0.Anc0refChr7 16078 22 + 16696 GTCCAAATGGATGTAGTAAGCA -s Anc1.Anc1refChr4 16805 22 - 17549 GTCCAAATGGATGTAGTAAGCA -s Anc2.Anc2refChr5 7729 22 + 8386 GTCCAAATGGATTTAGTAAGCA -s mr.mrrefChr5 156973 22 + 294540 GTCCCAATGGGTGTAGTCAACA -s simCow_chr6.simCow.chr6 278550 20 + 602619 ATCCA--TGGTTATAGTAGGCA -s simDog_chr6.simDog.chr6 315561 22 - 593897 GCCCAAATGGATTTGGTAAGTA -s simHuman_chr6.simHuman.chr6 299968 22 - 601863 GTCCATCTAGATGTAGTAATCA -s simRat_chr6.simRat.chr6 298193 22 + 647215 GTCCTAATGCGTGTAGCCAATA - -a -s simMouse_chr6.simMouse.chr6 306598 25 + 636262 TATAATATCAGACCTTCACTACAGA -s Anc0.Anc0refChr7 16101 25 + 16696 TATAATATCACAACTTCACTTTAAA -s Anc1.Anc1refChr4 16828 25 - 17549 TATAATATCACAACTTCACTTTAAA -s Anc2.Anc2refChr5 7752 25 + 8386 TTTAACATCACAACTTCACTTTAAA -s mr.mrrefChr5 156995 25 + 294540 TATAATATCAGACCTTCACTACAGA -s simCow_chr6.simCow.chr6 278571 15 + 602619 ----------AAACTTCATTGTAAA -s simDog_chr6.simDog.chr6 315584 25 - 593897 TTTAACATCACAACTGAACTTTAAA -s simHuman_chr6.simHuman.chr6 299991 25 - 601863 TATAATATCACAAATTCACTCTAAA -s simRat_chr6.simRat.chr6 298215 25 + 647215 TATAATGTCAGACTTTCACTAGAGA - -a -s simMouse_chr6.simMouse.chr6 306623 106 + 636262 AGGCTCCATACAGAGGTTACACTCACATGCTCTGTCAATCAGAAAGACCCTACATCTATAGGCTCAGTCATCCATCACCAAGATTATGCACTTGCTGCTTGCTGAT -s Anc0.Anc0refChr7 16128 14 + 16696 AGGCTCCATGCTGA-------------------------------------------------------------------------------------------- -s Anc1.Anc1refChr4 16855 14 - 17549 AGGCTCCATGCTGA-------------------------------------------------------------------------------------------- -s Anc2.Anc2refChr5 7779 14 + 8386 AGGCTCCATGCTGA-------------------------------------------------------------------------------------------- -s mr.mrrefChr5 157020 99 + 294540 AGGCTCCATACAGAGGTTACACTCACATGCTCTGTCAATCAGAAAGACCCTACATCTATAGGCTCAGTCATCCATCACCAAGATTATGCA-------CTTGCTGAT -s simCow_chr6.simCow.chr6 278588 14 + 602619 AGGCTCCATGCTGA-------------------------------------------------------------------------------------------- -s simDog_chr6.simDog.chr6 315611 14 - 593897 AGGCTCCAGGGTGA-------------------------------------------------------------------------------------------- -s simHuman_chr6.simHuman.chr6 300018 14 - 601863 AGGCTCCATGCTGA-------------------------------------------------------------------------------------------- -s simRat_chr6.simRat.chr6 298240 99 + 647215 AGGCTCCATACGGAGATTACACTCGCATGCTGTGTCAATCAGAAAGACGCTACATCTATAAGCTCAGTCATCCATCACCAAGATTGAGCA-------CTTGCTGAT - -a -s simMouse_chr6.simMouse.chr6 306729 44 + 636262 AATTTTCCCGGAAAGTAAGGATCTGGGCTTGCTTACAATCATGT -s Anc0.Anc0refChr7 16142 44 + 16696 AATCTACATCGAAATTAAGAATCTGGGCTTGCTTTCAATCATCT -s Anc1.Anc1refChr4 16869 44 - 17549 AATCTACATCGAAATTAAGAATCTGGGCTTGCTTTCAATCATCT -s Anc2.Anc2refChr5 7794 44 + 8386 AATCTACACCAAAATTAAGAATCTGGGCTTGCTTTTGATCATCT -s mr.mrrefChr5 157119 44 + 294540 AATTTTCCTGGAAAGTAAGGATCTGGGCTTGCTTACAATCATGT -s simCow_chr6.simCow.chr6 278603 44 + 602619 AATCTGTTGCATAATTGATAATCTGGGCTTGCTTTTCAGCATCT -s simDog_chr6.simDog.chr6 315626 44 - 593897 AATCTACACCAAAATTAAGGATCTGGGCTTGCTTTTGATCATCC -s simHuman_chr6.simHuman.chr6 300032 44 - 601863 ACTCTACATTGAAATTAAGAATCTGGGCTTGCCTTCAATCATCT -s simRat_chr6.simRat.chr6 298339 44 + 647215 AATTTTTCTGGAAAGTAAGGATCTGGGCTTGCTCAAAATCACGT - -a -s simMouse_chr6.simMouse.chr6 306773 1 + 636262 A -s Anc0.Anc0refChr7 16186 1 + 16696 A -s Anc1.Anc1refChr4 16913 1 - 17549 A -s Anc2.Anc2refChr5 7838 1 + 8386 A -s mr.mrrefChr5 157163 1 + 294540 A -s simCow_chr6.simCow.chr6 278647 1 + 602619 A -s simDog_chr6.simDog.chr6 315724 1 - 593897 A -s simHuman_chr6.simHuman.chr6 300076 1 - 601863 A -s simRat_chr6.simRat.chr6 298383 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 306774 9 + 636262 ACAGTAGCT -s Anc0.Anc0refChr7 16187 9 + 16696 GCATTGGCT -s Anc1.Anc1refChr4 16914 9 - 17549 GCATTGGCT -s Anc2.Anc2refChr5 7839 9 + 8386 GCATTGGCT -s mr.mrrefChr5 157164 9 + 294540 ACAGTGGCT -s simCow_chr6.simCow.chr6 278649 9 + 602619 GCATTGGCC -s simDog_chr6.simDog.chr6 315725 9 - 593897 GCATTGGCT -s simHuman_chr6.simHuman.chr6 300077 9 - 601863 GCATTGGCT -s simRat_chr6.simRat.chr6 298384 9 + 647215 ACAGTGGCT - -a -s simMouse_chr6.simMouse.chr6 306783 70 + 636262 ACTTCAACTCCGTATGTGAAAGCCAATGCTAGTTGATGATAAAGGTATAATCCTATAGCATCTTAGGTGC -s Anc0.Anc0refChr7 16206 68 + 16696 ACTTCAATGCAATATTTGAAAGTCCATGCTAA-TGATGATAGAGGTACAATCCTG-AACTTCTTAGGTGC -s Anc1.Anc1refChr4 16933 68 - 17549 ACTTCAATGCAATATTTGAAAGTCCATGCTAA-TGATGATAGAGGTACAATCCTG-AACTTCTTAGGTGC -s Anc2.Anc2refChr5 7858 68 + 8386 ACTTCAATGCAATATTTGAAAGTTCATGCTAA-TGATGATAGAGGTGCAATCCTG-AACTTCTTAGGTGC -s mr.mrrefChr5 157173 70 + 294540 ACTTCAATTCCATATGTGAAAGCCAATGCTAGTTGATGATAAAGGTATAATCCTATAGCATCTTAGGTGC -s simCow_chr6.simCow.chr6 278668 68 + 602619 ACTTCAATGCAATATCCAAAGGTGCATGCTGC-TGATGATAGAGGTGCAATCCTG-CATTTCTTAGCTTC -s simDog_chr6.simDog.chr6 315744 68 - 593897 TCTTCAATGCAATAGTTGAAAGTTCATGCTAA-TGATGATTGACATGCAATCCTT-AACTTCTAAGGTGT -s simHuman_chr6.simHuman.chr6 300096 65 - 601863 ACTTCAATGCAATATTTTAAAGTCGATACCA----ATGATAGAGGTACAATCCTG-AACTTTTTAGGTGC -s simRat_chr6.simRat.chr6 298393 70 + 647215 ACTTCAATTCCATATATGAAAGCCAATGCTACTTGATAACAAAAGTGTAATCCTATAGCATCTTAGGTGC - -a -s simMouse_chr6.simMouse.chr6 306853 33 + 636262 ACTTCAAGTGGCAGACTTGTCGATGCACCAATA -s Anc0.Anc0refChr7 16274 33 + 16696 ACCTTAATTTCTAATCTGACTGATGCACCATTA -s Anc1.Anc1refChr4 17001 33 - 17549 ACCTTAATTTCTAATCTGACTGATGCACCATTA -s Anc2.Anc2refChr5 7926 33 + 8386 ACCTTAATTTCTGATCTGACTGAAACACCATTA -s mr.mrrefChr5 157243 33 + 294540 ACTTTAAGTGGCAGACTTGCTGATGCACCAATA -s simCow_chr6.simCow.chr6 278736 33 + 602619 ACCTTAATTTCTGATCTGAATAAATGACCATTA -s simDog_chr6.simDog.chr6 315819 33 - 593897 GTCATAATTTTGGATCTGACTGAAACACCATTA -s simHuman_chr6.simHuman.chr6 300161 33 - 601863 ACCTTAATTTCTAATCTGACTGATGCACCATTA -s simRat_chr6.simRat.chr6 298463 33 + 647215 ACTTTAAGTGGCAGACTTGCTGATGCACCAATA - -a -s simMouse_chr6.simMouse.chr6 306886 37 + 636262 AATTACACACATACTCTAGTCTACAGTTGTTGTGCTG -s Anc0.Anc0refChr7 16311 35 + 16696 AGTTACACACATACTTTAGTCTAAAGTTGT--TGCTG -s Anc1.Anc1refChr4 17038 35 - 17549 AGTTACACACATACTTTAGTCTAAAGTTGT--TGCTG -s Anc2.Anc2refChr5 7963 35 + 8386 AGTTACACACAGACTTTAGTCTAAAGTTGT--TGCTG -s mr.mrrefChr5 157276 35 + 294540 AGTTACACACATACTCTAGTCTACAGTTGT--TGCTG -s simCow_chr6.simCow.chr6 278773 34 + 602619 AGTAAATAACAGAGCTTA-TCTAAAGTTGT--TGCTG -s simDog_chr6.simDog.chr6 315856 35 - 593897 AGTTACACACAGACTTTAGCCTAAAGTTGT--TGCTG -s simHuman_chr6.simHuman.chr6 300198 35 - 601863 AGTTACACATGTACTTTAGTCTAAAGTTAT--TGCTG -s simRat_chr6.simRat.chr6 298496 35 + 647215 AGTTACACACATACTCTAGACTACAATTGT--TGCTG - -a -s simMouse_chr6.simMouse.chr6 306923 52 + 636262 TCTCATGACAGATAAAAGTGTCTAGGGTTATCCATGTAAACTTCTAGGAACC -s Anc0.Anc0refChr7 16347 52 + 16696 TGTCATGACAGGTGAAAGTGACTAGGGTTATTCATGTAAATTCCTAGGAATC -s Anc1.Anc1refChr4 17074 52 - 17549 TGTCATGACAGGTGAAAGTGACTAGGGTTATTCATGTAAATTCCTAGGAATC -s Anc2.Anc2refChr5 7999 52 + 8386 TGTCATGACAGGTGAAAGAGACTAGGGTTTTTCATGTACACTCCTAAGACTC -s mr.mrrefChr5 157312 52 + 294540 TCTCATGACAGGTAAAAGTGTCTAGGGTTATTCATGTAAATTTCTAGGAACC -s simCow_chr6.simCow.chr6 278808 52 + 602619 AGTCTTGATAGGTGAAAGAGTTTAGGGTTGTTTGTATACAGTCCCAAGATTC -s simDog_chr6.simDog.chr6 315892 50 - 593897 TGTCACGGCAGGCAAAAGAGACTAGGGCTTTTCATGTA--CTCCTAAGACTC -s simHuman_chr6.simHuman.chr6 300234 52 - 601863 TGTCATGACAGGTGAGATTGCCTAGGGTTATTCATGTAAGTTCCTAGGAAGC -s simRat_chr6.simRat.chr6 298532 52 + 647215 TTTCATGACAGGTAAAAGTGTCGAGGGTTATTCATGTAAATTTCTAGGAACC - -a -s simMouse_chr6.simMouse.chr6 306975 7 + 636262 AACAATT -s Anc0.Anc0refChr7 16399 7 + 16696 AACAATT -s Anc1.Anc1refChr4 17126 7 - 17549 AACAATT -s Anc2.Anc2refChr5 8051 7 + 8386 CACAATT -s mr.mrrefChr5 157364 7 + 294540 AACAATT -s simCow_chr6.simCow.chr6 279100 7 + 602619 CATAATC -s simDog_chr6.simDog.chr6 315942 7 - 593897 CACAATT -s simHuman_chr6.simHuman.chr6 300286 7 - 601863 AACAGTT -s simRat_chr6.simRat.chr6 298584 7 + 647215 CACAATT - -a -s simMouse_chr6.simMouse.chr6 306982 9 + 636262 AACCATGAC -s Anc0.Anc0refChr7 16412 9 + 16696 AACCATGAC -s Anc1.Anc1refChr4 17139 9 - 17549 AACCATGAC -s Anc2.Anc2refChr5 8064 9 + 8386 AACCATGAC -s mr.mrrefChr5 157371 9 + 294540 AACCATGAC -s simCow_chr6.simCow.chr6 279117 9 + 602619 AGCCATGAC -s simDog_chr6.simDog.chr6 315955 9 - 593897 GACCATGGC -s simHuman_chr6.simHuman.chr6 300299 9 - 601863 AACCATGAT -s simRat_chr6.simRat.chr6 298591 9 + 647215 AACCATGAC - -a -s simMouse_chr6.simMouse.chr6 306991 56 + 636262 TACAAAGAGCTTGGTTTTCACATGTTTCAACATTAAATATCGTCAATCCACATAAG -s Anc0.Anc0refChr7 16428 55 + 16696 TAGAAGGAGTTTGATCGTTGCATGTTTTAACATCAAATATCTCT-GTCCACATAAG -s Anc1.Anc1refChr4 17155 55 - 17549 TAGAAGGAGTTTGATCGTTGCATGTTTTAACATCAAATATCTCT-GTCCACATAAG -s Anc2.Anc2refChr5 8117 55 + 8386 TAGAAGGAGTTTGATCGTTGCATGTTTTGACATCAAGTATCTCT-GTTCACATGAG -s mr.mrrefChr5 157380 56 + 294540 TACAAGGAGCTTGATTTTCACATGTTTCAACATTAAATATCTTTAATCCACATAAG -s simCow_chr6.simCow.chr6 279171 54 + 602619 TAAGGAGAGTTTAATTGTTGCATGTTTGGACATGAACTGTCTCT-A-TCACATGAG -s simDog_chr6.simDog.chr6 316008 54 - 593897 TAGAAGGAGTCTGATCGTTGCATGTTTTGCCATCAGGTAGC-CT-GTTCATGTGAG -s simHuman_chr6.simHuman.chr6 300315 51 - 601863 TAGAAGGAGTTTGAT----GCATGCTTTAACATCCAATATCTCT-GTCCGCATAGG -s simRat_chr6.simRat.chr6 298600 56 + 647215 TACAAGGAGCTTGATTTTCACTTGTTTCAACACTTAATGTCTTTAATCCACACAAG - -a -s simMouse_chr6.simMouse.chr6 307047 52 + 636262 CTGCACCTCAAGACTAACCCTTCTACTATACGACCCTACGCATAGTCCATGC -s Anc0.Anc0refChr7 16695 1 + 16696 C--------------------------------------------------- -s Anc1.Anc1refChr4 17422 48 - 17549 CTTCACAGCAAAACT-ACTGCTCAACTATAGGCCCCTATGCATGCTCC---C -s Anc2.Anc2refChr5 8385 1 + 8386 C--------------------------------------------------- -s mr.mrrefChr5 157436 52 + 294540 CTGCACCTCAAGACTAACCCTTCTACTATACGACCCTACGCATAGTCCATGC -s simDog_chr6.simDog.chr6 316169 1 - 593897 C--------------------------------------------------- -s simHuman_chr6.simHuman.chr6 300624 48 - 601863 CTTCACAGCAAAACT-ACTGCTCAACTATAGGCCCCTATGCATGCTCC---C -s simRat_chr6.simRat.chr6 298656 52 + 647215 CTGTACCTCTAGACTAGCTCTCCTACTATATGACCCTATCCATAGTCAATGT - -a -s simMouse_chr6.simMouse.chr6 307099 15 + 636262 CATGGTCATCTCTAT -s Anc1.Anc1refChr4 17470 15 - 17549 CATATTAATTTCTGT -s mr.mrrefChr5 157488 15 + 294540 CATGGTCATCTCTAT -s simHuman_chr6.simHuman.chr6 300672 15 - 601863 CATATTAATTTCTGT -s simRat_chr6.simRat.chr6 298709 15 + 647215 CATGGTCGTCTGTAG - -a -s simMouse_chr6.simMouse.chr6 307114 71 + 636262 TTGTAACTTAGCCAGTGAATGGCTTCTTGTGGTGCCCTTGAAACACTAGTACCAGATGATGTGGATTCTCT -s Anc1.Anc1refChr4 17485 59 - 17549 CCATAACTTATTACGT-AATGCAATCTT------CCC---ATACTCTAAGA--AGATGCAATGGAATCTTT -s mr.mrrefChr5 157503 71 + 294540 TTGTAACTTAGCCAGTGAATGGCTTCTTGTGGTGCCCTTGAAACACTAGTACCAGATGATGTGGATTCTCT -s simHuman_chr6.simHuman.chr6 300688 59 - 601863 CCATAACTTATTACGT-AATGCAATCTT------CCC---ATACTCTAAGA--AGATGCAATGGAATCTTT -s simRat_chr6.simRat.chr6 298724 71 + 647215 TTGTAACTTAGTCAGTGAATGGCTTCCTGTGATACCCTTGGAACACCAGTACCAGATGATGTGGATTGTAT - -a -s simMouse_chr6.simMouse.chr6 307185 27 + 636262 ACACTGGTTAACAAGATGCTAATGCTT -s Anc1.Anc1refChr4 17544 5 - 17549 ACATA---------------------- -s mr.mrrefChr5 157574 27 + 294540 ACACTGGTTAACAAGATGCTAATGCTT -s simHuman_chr6.simHuman.chr6 300747 5 - 601863 ACATA---------------------- -s simRat_chr6.simRat.chr6 298799 27 + 647215 AAACTGGTTAACTAGATGCTAATGCCT - -a -s simMouse_chr6.simMouse.chr6 307212 2 + 636262 TC -s mr.mrrefChr5 157601 2 + 294540 TC -s simRat_chr6.simRat.chr6 298827 2 + 647215 TC - -a -s simMouse_chr6.simMouse.chr6 307214 4 + 636262 TCTT -s Anc0.Anc0refChr8 0 4 + 17196 TCTT -s Anc1.Anc1refChr3 0 4 + 3661 TCTT -s Anc2.Anc2refChr8 0 4 + 12804 TCTA -s mr.mrrefChr5 157603 4 + 294540 TCTT -s simCow_chr6.simCow.chr6 322878 4 - 602619 TCTA -s simDog_chr6.simDog.chr6 316247 4 - 593897 TCTA -s simRat_chr6.simRat.chr6 298829 4 + 647215 TCCT - -a -s simMouse_chr6.simMouse.chr6 307218 7 + 636262 CCTGCTC -s Anc0.Anc0refChr8 4 7 + 17196 CCAGATC -s Anc1.Anc1refChr3 4 7 + 3661 CCAGATC -s Anc2.Anc2refChr8 16 7 + 12804 CCAGATC -s mr.mrrefChr5 157607 7 + 294540 CCTGCTC -s simCow_chr6.simCow.chr6 322894 7 - 602619 CCAAATG -s simDog_chr6.simDog.chr6 316263 7 - 593897 CCAGGTC -s simHuman_chr6.simHuman.chr6 226357 3 + 601863 ----ATC -s simRat_chr6.simRat.chr6 298833 7 + 647215 CCCACTC - -a -s simMouse_chr6.simMouse.chr6 307225 2 + 636262 AA -s Anc0.Anc0refChr8 13 2 + 17196 AA -s Anc1.Anc1refChr3 13 2 + 3661 AA -s Anc2.Anc2refChr8 25 2 + 12804 AA -s mr.mrrefChr5 157616 2 + 294540 AA -s simCow_chr6.simCow.chr6 322903 2 - 602619 AA -s simDog_chr6.simDog.chr6 316272 1 - 593897 A- -s simHuman_chr6.simHuman.chr6 226362 2 + 601863 AA -s simRat_chr6.simRat.chr6 298842 2 + 647215 AC - -a -s simMouse_chr6.simMouse.chr6 307227 8 + 636262 ACTAAGGT -s Anc0.Anc0refChr8 16 8 + 17196 ATTAAGGT -s Anc1.Anc1refChr3 16 8 + 3661 ATTAAGGT -s Anc2.Anc2refChr8 28 8 + 12804 ATTAAGGT -s mr.mrrefChr5 157618 8 + 294540 ACTAAGGT -s simCow_chr6.simCow.chr6 322906 6 - 602619 ACTAGG-- -s simDog_chr6.simDog.chr6 316273 7 - 593897 -TTAAGGT -s simHuman_chr6.simHuman.chr6 226365 8 + 601863 GTTAAGGT -s simRat_chr6.simRat.chr6 298844 8 + 647215 ACTAAGGT - -a -s simMouse_chr6.simMouse.chr6 307235 18 + 636262 GAGGGTTTTGAGTTTCCT -s Anc0.Anc0refChr8 24 15 + 17196 GAA--TTTAGAGTGGC-T -s Anc1.Anc1refChr3 24 15 + 3661 GAA--TTTAGAGTGGC-T -s Anc2.Anc2refChr8 36 15 + 12804 GAT--TTTAGAGTCGC-T -s mr.mrrefChr5 157626 15 + 294540 GAG--TTTTGAGTTGC-T -s mr.mrrefChr5 160750 15 + 294540 GGA--TTGTGTCTGGC-T -s simCow_chr6.simCow.chr6 322912 15 - 602619 AAT--GTTTGAGTCTC-T -s simDog_chr6.simDog.chr6 316280 14 - 593897 GAT--TCTAGAGTCG--T -s simHuman_chr6.simHuman.chr6 226373 15 + 601863 GAA--TTTAGTGTGGC-T -s simMouse_chr6.simMouse.chr6 310367 15 + 636262 GGA--TTGTGTCTGGC-T -s simRat_chr6.simRat.chr6 302058 15 + 647215 AGA--TCATGCCTGGC-T -s simRat_chr6.simRat.chr6 298852 15 + 647215 GAG--TTTTGAGTTGC-T - -a -s simMouse_chr6.simMouse.chr6 307253 17 + 636262 ATTTGCTTGCTCATCTA -s Anc0.Anc0refChr8 39 17 + 17196 ATTTGCTTGCTCATCTC -s Anc1.Anc1refChr3 39 17 + 3661 ATTTGCTTGCTCATCTC -s Anc2.Anc2refChr8 51 17 + 12804 ATTTGCTTGCTCGTCTC -s mr.mrrefChr5 157641 17 + 294540 ATTTGCTTGCTCATCTA -s mr.mrrefChr5 160766 17 + 294540 AATTTCTTACCACCCTA -s simCow_chr6.simCow.chr6 322927 17 - 602619 ATTTGCTTGGTCCTCTC -s simDog_chr6.simDog.chr6 316294 17 - 593897 ATTTGCTTGCTTGTCTC -s simHuman_chr6.simHuman.chr6 226388 17 + 601863 ATTTGCTTGCTCATCCC -s simMouse_chr6.simMouse.chr6 310383 17 + 636262 AATTTCTTACCACCCTA -s simRat_chr6.simRat.chr6 302074 17 + 647215 AATTTCTTACTATTCTA -s simRat_chr6.simRat.chr6 298867 17 + 647215 ATTTGCTTGCTCATCTG - -a -s simMouse_chr6.simMouse.chr6 307270 3 + 636262 CTC -s Anc0.Anc0refChr8 56 3 + 17196 CTT -s Anc1.Anc1refChr3 56 3 + 3661 CTT -s Anc2.Anc2refChr8 68 3 + 12804 CTT -s mr.mrrefChr5 157658 3 + 294540 CTC -s simCow_chr6.simCow.chr6 322944 3 - 602619 CTC -s simDog_chr6.simDog.chr6 316311 3 - 593897 TTT -s simHuman_chr6.simHuman.chr6 226405 3 + 601863 CTT -s simRat_chr6.simRat.chr6 298884 3 + 647215 CTC - -a -s simMouse_chr6.simMouse.chr6 307273 14 + 636262 TTCCGCTGTGCTGT -s Anc0.Anc0refChr8 59 14 + 17196 TCCCCCTGTGCTGT -s Anc1.Anc1refChr3 59 14 + 3661 TCCCCCTGTGCTGT -s Anc2.Anc2refChr8 71 14 + 12804 TGCCCCTGTGCTGT -s mr.mrrefChr5 157661 14 + 294540 TTCCGCTGTGCTGT -s mr.mrrefChr5 160783 14 + 294540 TCCCCCTTTGCAGT -s simCow_chr6.simCow.chr6 322947 14 - 602619 CGCCCCTGTGCTGT -s simDog_chr6.simDog.chr6 316314 14 - 593897 TGCCTCTGTGCTGC -s simHuman_chr6.simHuman.chr6 226408 14 + 601863 TCCCCTTGTGCTGT -s simMouse_chr6.simMouse.chr6 310400 14 + 636262 TCCCCCTTTGCAGT -s simRat_chr6.simRat.chr6 302091 14 + 647215 TCCCCCTGTGCAGT -s simRat_chr6.simRat.chr6 298887 13 + 647215 TTCTG-TGTGCCAT - -a -s simMouse_chr6.simMouse.chr6 307287 1 + 636262 T -s mr.mrrefChr5 157675 1 + 294540 T -s simRat_chr6.simRat.chr6 298900 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 307288 2 + 636262 AA -s Anc0.Anc0refChr8 73 2 + 17196 AA -s Anc1.Anc1refChr3 73 2 + 3661 AA -s Anc2.Anc2refChr8 85 2 + 12804 AA -s mr.mrrefChr5 157676 2 + 294540 AA -s mr.mrrefChr5 160797 2 + 294540 AG -s simCow_chr6.simCow.chr6 322961 2 - 602619 AA -s simDog_chr6.simDog.chr6 316328 2 - 593897 AA -s simHuman_chr6.simHuman.chr6 226422 2 + 601863 AA -s simMouse_chr6.simMouse.chr6 310414 2 + 636262 AG -s simRat_chr6.simRat.chr6 302105 2 + 647215 AA -s simRat_chr6.simRat.chr6 298901 2 + 647215 AA - -a -s simMouse_chr6.simMouse.chr6 307290 31 + 636262 TCTTATTTTGGGTTAAGTCTATGATTGGTAT -s Anc0.Anc0refChr8 75 31 + 17196 CCTTATTTTGGGTTGAGTCTCTGATGGATAT -s Anc1.Anc1refChr3 75 31 + 3661 CCTTATTTTGGGTTGAGTCTCTGATGGATAT -s Anc2.Anc2refChr8 87 31 + 12804 CCTTATATTGGGTCCAGTCTCTGCTGGATAT -s mr.mrrefChr5 157678 31 + 294540 TCTTATTTTGGGTTGAGTCTATGATTGATAT -s mr.mrrefChr5 160799 31 + 294540 CCATACTTTGGGTTGGGCCTCTCATGGGTAT -s simCow_chr6.simCow.chr6 322965 31 - 602619 CTTTATCTTGGGTGCAGTCTCTGGTGGATAC -s simDog_chr6.simDog.chr6 316330 31 - 593897 CCTTACATTGGGTCCAGTCTCCGCTGAATAT -s simHuman_chr6.simHuman.chr6 226424 31 + 601863 CCTTATTTTGGGTTGAGTCTCTGATAGATAT -s simMouse_chr6.simMouse.chr6 310416 31 + 636262 CCATACTTTGGGTTGGGCCTCTCATGGGTAT -s simRat_chr6.simRat.chr6 302107 31 + 647215 CCATACTTTGAGTTAGGCCTTTTATGGATAT -s simRat_chr6.simRat.chr6 298903 31 + 647215 TCTTATTTTGGGTTGAATCTATGATTGATAT - -a -s simMouse_chr6.simMouse.chr6 307321 20 + 636262 GATGATAAGATTAGTAGGAT -s Anc0.Anc0refChr8 106 20 + 17196 AATGGTAATATTTGTAGGAT -s Anc1.Anc1refChr3 106 20 + 3661 AATGGTAATATTTGTAGGAT -s Anc2.Anc2refChr8 118 20 + 12804 AATGGTAATATTTGCAGGGT -s mr.mrrefChr5 157709 20 + 294540 AATGATAAGATTAGTAGGAT -s mr.mrrefChr5 160830 20 + 294540 AATGCCGAGATCTGTGAGAT -s simCow_chr6.simCow.chr6 322996 20 - 602619 AATGATAATATCTTAAGGGT -s simDog_chr6.simDog.chr6 316361 18 - 593897 ATTGGTAATATTTGCAGG-- -s simHuman_chr6.simHuman.chr6 226455 20 + 601863 AATGGTAATATTTGTAGGAT -s simMouse_chr6.simMouse.chr6 310461 20 + 636262 AATGCCGAGATCTGTGAGAT -s simRat_chr6.simRat.chr6 302138 20 + 647215 AATGGTGAGAACTGTGAGAT -s simRat_chr6.simRat.chr6 298934 20 + 647215 AATGATAAGATCAGTACGAT - -a -s simMouse_chr6.simMouse.chr6 307341 67 + 636262 GAATTGGGGGAAACAGATGCTGGCATGTAAAGACACTCCACTTTACAGTTTATGCCTTAGTCTAGTT -s Anc0.Anc0refChr8 126 62 + 17196 T---TGGGGGAAACCAACATTG--ACATAAAACCTCTCCACCTTTCAGTTGACTCCTTATTCTCCTT -s Anc1.Anc1refChr3 126 67 + 3661 TGATTGGGGGAAACCAACATTGGCACATAAAACCTCTCCACCTTTCAGTTGACTCCTTATTCTCCTT -s Anc2.Anc2refChr8 138 62 + 12804 T---TGGGGGAAACCTACAAAG--ACATAAAACCTGTCCACCTTTCAATTGACTCCATATTCTCCTT -s mr.mrrefChr5 157729 67 + 294540 GAATTGGGGGAAACAAACGCTGGCATGTAAAGACACTCCACCTTACAGTTGATTCCTTATTCTAGTT -s mr.mrrefChr5 160850 67 + 294540 TGAGTCAAGGCAAAAAACATTACCACATGAAACTGCACAATCTACTAGATGATTCATCATTCTTTTT -s simCow_chr6.simCow.chr6 323019 62 - 602619 T---TGGGGGAAACCTACAAAG--GTATAAAACCTTCCCACCCTTCAATGGGCTCCCTATTCACCTT -s simDog_chr6.simDog.chr6 316379 43 - 593897 ------------------------ACATGAAACCAGTCCACCTTTGAATTAACTCCATATTCTCCTT -s simHuman_chr6.simHuman.chr6 226475 64 + 601863 T---TGGGGGAAACCAGCGTTAGCACATAAAACCTCTCCACCTTTCAGTTGCCTCTTTATTCTCCTT -s simMouse_chr6.simMouse.chr6 310481 67 + 636262 TGAGTCAAGGCAAAAAACATTACCACATGAAACTGCACAATCTACTAGATGATTCATCATTCTTTTT -s simRat_chr6.simRat.chr6 302158 67 + 647215 TGAGTCAAAGTAAACAACACTGGCACATGAAACTGCACAACCTAAGGGATTATTCATCATTCTTCTT -s simRat_chr6.simRat.chr6 298954 67 + 647215 TAATTGGGGGAAACAAACACTGGTGTCTAGAGACACTCCACCTTACAGTTGATTCCTTATTCTAGTT - -a -s simMouse_chr6.simMouse.chr6 307408 1 + 636262 T -s Anc0.Anc0refChr8 188 1 + 17196 T -s Anc1.Anc1refChr3 193 1 + 3661 T -s Anc2.Anc2refChr8 200 1 + 12804 T -s mr.mrrefChr5 157796 1 + 294540 T -s mr.mrrefChr5 160923 1 + 294540 T -s simCow_chr6.simCow.chr6 323081 1 - 602619 T -s simDog_chr6.simDog.chr6 316422 1 - 593897 T -s simHuman_chr6.simHuman.chr6 226539 1 + 601863 T -s simMouse_chr6.simMouse.chr6 310554 1 + 636262 T -s simRat_chr6.simRat.chr6 302231 1 + 647215 T -s simRat_chr6.simRat.chr6 299021 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 307409 27 + 636262 GAATGGAATGTTCTTGCATAGTGGTGC -s Anc0.Anc0refChr8 190 27 + 17196 GAATGCAGAACTCTTCTTTTACTCTGT -s Anc1.Anc1refChr3 195 27 + 3661 GAATGCAGAACTCTTCTTTTACTCTGT -s Anc2.Anc2refChr8 202 27 + 12804 GAATGCATAACTATTCTTTTACTCTGT -s mr.mrrefChr5 157797 27 + 294540 GAATGGAATGTTCTTGTATAGTAGTGC -s mr.mrrefChr5 160924 27 + 294540 TAGTGTAGGACTGTTCTTTTTCTCTGC -s simCow_chr6.simCow.chr6 323083 27 - 602619 GGATGCAAAACTATGCTTTGTCTCTGT -s simDog_chr6.simDog.chr6 316424 27 - 593897 AAGTACATAGCTATTCTTTTACTTTGT -s simHuman_chr6.simHuman.chr6 226541 27 + 601863 GAATGCAGAACCCTTCGTTCACTCTGT -s simMouse_chr6.simMouse.chr6 310555 27 + 636262 TAGTGTAGGACTGTTCTTTTTCTCTGC -s simRat_chr6.simRat.chr6 302232 27 + 647215 TAGTGTAGAACTGTTCTTTTTCTCTAC -s simRat_chr6.simRat.chr6 299022 27 + 647215 GAATGGAATGTTCTTGTATAGTAGTGC - -a -s simMouse_chr6.simMouse.chr6 307436 4 + 636262 CATC -s Anc0.Anc0refChr8 217 4 + 17196 GGTG -s Anc1.Anc1refChr3 222 4 + 3661 GGTG -s Anc2.Anc2refChr8 229 4 + 12804 GGTG -s mr.mrrefChr5 157824 4 + 294540 CATT -s mr.mrrefChr5 160951 4 + 294540 CGTC -s simCow_chr6.simCow.chr6 279844 4 + 602619 GGTG -s simDog_chr6.simDog.chr6 316451 4 - 593897 GGTG -s simHuman_chr6.simHuman.chr6 226568 4 + 601863 GGTG -s simMouse_chr6.simMouse.chr6 310582 4 + 636262 CGTC -s simRat_chr6.simRat.chr6 302259 4 + 647215 AGTC -s simRat_chr6.simRat.chr6 299049 4 + 647215 CATT - -a -s simMouse_chr6.simMouse.chr6 307440 14 + 636262 AAGTGGTGTCTTTT -s Anc0.Anc0refChr8 235 14 + 17196 AAGTGATGTTTATC -s Anc1.Anc1refChr3 240 14 + 3661 AAGTGATGTTTATC -s Anc2.Anc2refChr8 248 14 + 12804 AAGTGATGTTTATC -s mr.mrrefChr5 157828 14 + 294540 AAGTGGTGTCTATT -s mr.mrrefChr5 160963 14 + 294540 AGGTGAAGTTTACC -s simCow_chr6.simCow.chr6 279873 14 + 602619 AAATGATTTTTATC -s simDog_chr6.simDog.chr6 316470 14 - 593897 AAGTGATGTTTATC -s simHuman_chr6.simHuman.chr6 226586 14 + 601863 AAGTGATGTTAATT -s simMouse_chr6.simMouse.chr6 310594 14 + 636262 AGGTGAAGTTTACC -s simRat_chr6.simRat.chr6 302271 14 + 647215 AGATGAAGTTTACC -s simRat_chr6.simRat.chr6 299053 14 + 647215 AAGTGGTGTCTATT - -a -s simMouse_chr6.simMouse.chr6 307454 1 + 636262 G -s Anc0.Anc0refChr8 249 1 + 17196 C -s Anc1.Anc1refChr3 254 1 + 3661 C -s Anc2.Anc2refChr8 262 1 + 12804 C -s mr.mrrefChr5 157842 1 + 294540 G -s simCow_chr6.simCow.chr6 279887 1 + 602619 C -s simDog_chr6.simDog.chr6 316484 1 - 593897 C -s simHuman_chr6.simHuman.chr6 226600 1 + 601863 C -s simRat_chr6.simRat.chr6 299067 1 + 647215 G - -a -s simMouse_chr6.simMouse.chr6 307455 20 + 636262 TCAGAGACAGGCCTCCATGA -s Anc0.Anc0refChr8 250 20 + 17196 TCAAAGATAGGCCTATATGT -s Anc1.Anc1refChr3 255 20 + 3661 TCAAAGATAGGCCTATATGT -s Anc2.Anc2refChr8 263 20 + 12804 TCACAGATAGGCCTATATGC -s mr.mrrefChr5 157843 20 + 294540 TCAAAGACAGGCCTCCATGA -s mr.mrrefChr5 160977 20 + 294540 TAAAAAATAGGCCTATTTCT -s simCow_chr6.simCow.chr6 279888 19 + 602619 TCACGG-TAGGTCTACATAC -s simDog_chr6.simDog.chr6 316485 20 - 593897 TCACAGATAGGCCTGTCTGC -s simHuman_chr6.simHuman.chr6 226601 20 + 601863 TTAAAGATAGGCCTATATGT -s simMouse_chr6.simMouse.chr6 310608 20 + 636262 TAAAAAATAGGCCTATTTCT -s simRat_chr6.simRat.chr6 302285 20 + 647215 TATGAAATAGGCCCATTTTT -s simRat_chr6.simRat.chr6 299068 20 + 647215 TCAAAGGCAGGCCTCCATGA - -a -s simMouse_chr6.simMouse.chr6 307475 3 + 636262 CTT -s Anc0.Anc0refChr8 270 3 + 17196 CTT -s Anc1.Anc1refChr3 275 3 + 3661 CTT -s Anc2.Anc2refChr8 283 3 + 12804 CTT -s mr.mrrefChr5 157863 3 + 294540 CTT -s simCow_chr6.simCow.chr6 279907 3 + 602619 CTA -s simDog_chr6.simDog.chr6 316505 3 - 593897 CTT -s simHuman_chr6.simHuman.chr6 226621 3 + 601863 GTT -s simRat_chr6.simRat.chr6 299088 3 + 647215 CTT - -a -s simMouse_chr6.simMouse.chr6 307478 9 + 636262 GCTACTTCA -s Anc0.Anc0refChr8 273 9 + 17196 ACCACTTCA -s Anc1.Anc1refChr3 278 9 + 3661 ACCACTTCA -s Anc2.Anc2refChr8 286 9 + 12804 ACCACTTCA -s mr.mrrefChr5 157866 9 + 294540 GCTACTTCA -s mr.mrrefChr5 160997 9 + 294540 GCCCATCCA -s simCow_chr6.simCow.chr6 279910 9 + 602619 ACCACTCCA -s simDog_chr6.simDog.chr6 316508 9 - 593897 ACCACTTCA -s simHuman_chr6.simHuman.chr6 226624 9 + 601863 AACATTTCA -s simMouse_chr6.simMouse.chr6 310628 9 + 636262 GCCCATCCA -s simRat_chr6.simRat.chr6 302305 9 + 647215 GCTAAACCA -s simRat_chr6.simRat.chr6 299091 9 + 647215 GCTACTTCA - -a -s simMouse_chr6.simMouse.chr6 307487 10 + 636262 GTTGAGACTT -s Anc0.Anc0refChr8 283 10 + 17196 GATGAGAAGT -s Anc1.Anc1refChr3 288 10 + 3661 GATGAGAAGT -s Anc2.Anc2refChr8 296 10 + 12804 GATGAGAAGT -s mr.mrrefChr5 157875 10 + 294540 GTTGAGACTT -s mr.mrrefChr5 161007 10 + 294540 ACTGAGAAAT -s simCow_chr6.simCow.chr6 279920 10 + 602619 GATGAGAGGT -s simDog_chr6.simDog.chr6 316518 10 - 593897 GATGAGAAGT -s simHuman_chr6.simHuman.chr6 226634 10 + 601863 GATGAAAAGT -s simMouse_chr6.simMouse.chr6 310638 10 + 636262 ACTGAGAAAT -s simRat_chr6.simRat.chr6 302315 10 + 647215 GCGGAGAAAT -s simRat_chr6.simRat.chr6 299100 10 + 647215 GTTGAGACTG - -a -s simMouse_chr6.simMouse.chr6 307497 22 + 636262 ACAGAAAGTTACCAGTCACTCT -s Anc0.Anc0refChr8 293 22 + 17196 ATGGAGAGTTACCAGTCTCTTT -s Anc1.Anc1refChr3 298 22 + 3661 ATGGAGAGTTACCAGTCTCTTT -s Anc2.Anc2refChr8 306 22 + 12804 ATGGAGAGTTCCCAGTCTCTTT -s mr.mrrefChr5 157885 22 + 294540 ACAGAAAGTTACCAGTCACTCT -s simCow_chr6.simCow.chr6 279930 21 + 602619 ATGA-GAATCCCCAGTTTCGTT -s simDog_chr6.simDog.chr6 316528 22 - 593897 AAGGAGAGTTCCCGCCCCATAT -s simHuman_chr6.simHuman.chr6 226644 22 + 601863 ATGGAGAGTTACTAGTCTCTTT -s simRat_chr6.simRat.chr6 299110 22 + 647215 ACAGAAAGTTACCAGTCACTCT - -a -s simMouse_chr6.simMouse.chr6 307519 82 + 636262 CAAGGCTTTTTTTGTTGCTGCTGCCCATAGGTTCCCAGCAAACCTAATTGATCTGAACATTGATTGGTCTGACACTCCAGGC -s Anc0.Anc0refChr8 331 81 + 17196 CAAGGTGTTTTCTGTTTCTGTTGCCCATAGATCCTCAGTCAGCCAAAA-GATCTGAAGCTTGATTGGTCTAACACCCCAGGT -s Anc1.Anc1refChr3 336 82 + 3661 CAAGGTGTTTTCTGTTTCTGTTGCCCATAGATCCTCAGTCAGCCAAAATGATCTGAAGCTTGATTGGTCTAACACCCCAGGT -s Anc2.Anc2refChr8 344 81 + 12804 CAAGGTGTTTTTTGTTTCTGTTGCCCATAGACCCTCAGTCAGGCAAAA-GATCTGGAGCTTGACTGGGCAAACACCCCAGGT -s mr.mrrefChr5 157907 82 + 294540 CAAGGTTTTTTCTGTTGCTGCTGCCCATAGGTTCCCAGTAAACCAAATTGATCTGAAGATTGATTGGTCTGACACTCCAGGC -s simCow_chr6.simCow.chr6 279962 33 + 602619 CAAGGTGTTTTTTGTCTCTGGTGC----------CCTCTCAGA--------------------------------------- -s simDog_chr6.simDog.chr6 316564 81 - 593897 AAAGGTGTATTTTGTTTCTGTTGCCCATAGACCCTAAGTGAGGCAAAA-GATCTGGAGCTTGACTGGGCAAACACCCCAGGT -s simHuman_chr6.simHuman.chr6 226682 82 + 601863 CCAGGTGTTTTCAGTTTCTTTTGCACATAGATACTCAATCAGCCAAACTGATCTGAAGCTTCATTAGTCTAACACCCCAAGT -s simRat_chr6.simRat.chr6 299132 82 + 647215 CAAGGTTTTTTCTGTTGCCACTGCCCGTACGTTCCCAGTAAACCAAATTGACCTGAAGATTAATTGCTCTGTCACTCCAGGC - -a -s simMouse_chr6.simMouse.chr6 307601 13 + 636262 ATGCAACTAGAAG -s Anc0.Anc0refChr8 413 13 + 17196 TTGCAGATGGAGG -s Anc1.Anc1refChr3 419 13 + 3661 TTGCAGATGGAGG -s Anc2.Anc2refChr8 426 13 + 12804 TTGCAGATGGAGG -s mr.mrrefChr5 157989 13 + 294540 ATGCAACTAGAAG -s simDog_chr6.simDog.chr6 316646 13 - 593897 TTGCAGATGGAGG -s simHuman_chr6.simHuman.chr6 226765 13 + 601863 GTGCAGGTGGAGG -s simRat_chr6.simRat.chr6 299214 10 + 647215 ATGC---TAGAAG - -a -s simMouse_chr6.simMouse.chr6 307614 82 + 636262 ATGTTTTTGCTAGATCTGTCGGAAATTGTACATTGCTGGAGCAGCAGCACCACACAACTGTATGAGCAGTAAAAAATTGAGG -s Anc0.Anc0refChr8 426 30 + 17196 AT----------------------------------------------------CAACCGTACAACAAGTGAAAAATTGAGG -s Anc1.Anc1refChr3 432 30 + 3661 AT----------------------------------------------------CAACCGTACAACAAGTGAAAAATTGAGG -s Anc2.Anc2refChr8 445 30 + 12804 AT----------------------------------------------------CAACTGTACAACAAGTGAAAAATTGAGG -s mr.mrrefChr5 158002 75 + 294540 ATGT-------AGATCTGTCGGAAATTGTACATTGCTGGAGCAGCAGCACCACACAACCGTATGAGCAGTAAAAAATTGAGG -s simCow_chr6.simCow.chr6 280001 30 + 602619 AT----------------------------------------------------CAAATGTACAACAAGTGAAAAATCAAGG -s simDog_chr6.simDog.chr6 316665 30 - 593897 AT----------------------------------------------------TAACTGTCCAACAAGTAAAAAAGTGAAG -s simHuman_chr6.simHuman.chr6 226778 30 + 601863 AT----------------------------------------------------CAACCGTACAGAAAGTGAAAAATTGAGA -s simRat_chr6.simRat.chr6 299224 75 + 647215 ATGT-------AGATCTGTCAAAAATTGTACATTGCTGGAGCAGCAGCACCACACAGCCATATGAGCAGTAAAAAATTGAGG - -a -s simMouse_chr6.simMouse.chr6 307696 7 + 636262 ATATCTG -s Anc0.Anc0refChr8 476 7 + 17196 ACACCTA -s Anc1.Anc1refChr3 482 7 + 3661 ACACCTA -s Anc2.Anc2refChr8 495 7 + 12804 ACATGTA -s mr.mrrefChr5 158077 7 + 294540 ATACCTG -s simCow_chr6.simCow.chr6 280051 7 + 602619 ACATTTA -s simDog_chr6.simDog.chr6 316715 7 - 593897 ACGTGTA -s simHuman_chr6.simHuman.chr6 226828 7 + 601863 ACACCTA -s simRat_chr6.simRat.chr6 299299 7 + 647215 ATACCTG - -a -s simMouse_chr6.simMouse.chr6 307703 7 + 636262 CTGGAGA -s Anc0.Anc0refChr8 491 7 + 17196 TTAAAAA -s Anc1.Anc1refChr3 497 7 + 3661 TTAAAAA -s Anc2.Anc2refChr8 510 7 + 12804 TTAAAAA -s mr.mrrefChr5 158084 7 + 294540 TTGAAGA -s simCow_chr6.simCow.chr6 280066 7 + 602619 TCAAAAA -s simDog_chr6.simDog.chr6 316730 7 - 593897 TTAAAAA -s simHuman_chr6.simHuman.chr6 226843 7 + 601863 TTAAATA -s simRat_chr6.simRat.chr6 299306 7 + 647215 TTGAAGA - -a -s simMouse_chr6.simMouse.chr6 307710 32 + 636262 GAAGTACACTTGGTTGGTGAGAACTATCTGAT -s Anc0.Anc0refChr8 499 29 + 17196 AAAGTACCCTCAACTGGTGAGTACTATC---T -s Anc1.Anc1refChr3 505 29 + 3661 AAAGTACCCTCAACTGGTGAGTACTATC---T -s Anc2.Anc2refChr8 518 29 + 12804 AAAGTGCCTTCAACTGGTGAGTACTATC---T -s mr.mrrefChr5 158092 32 + 294540 GAAGTACACTTAGTTGGTGAGAACTATCTGAT -s simCow_chr6.simCow.chr6 280074 29 + 602619 CAGGTGTTGTCAACTGATGAGTACTATC---T -s simDog_chr6.simDog.chr6 316738 29 - 593897 AAATGGCCTTCAACCAGGGAGTACTCTC---T -s simHuman_chr6.simHuman.chr6 226851 29 + 601863 TGTGTACCCTCAACTGGTAAGGACTATC---T -s simRat_chr6.simRat.chr6 299314 32 + 647215 GAAGTACACTTAGGTGGTGAGAAATATCTGAT - -a -s simMouse_chr6.simMouse.chr6 307742 4 + 636262 TGTA -s Anc0.Anc0refChr8 528 4 + 17196 CGCA -s Anc1.Anc1refChr3 534 4 + 3661 CGCA -s Anc2.Anc2refChr8 547 4 + 12804 CGCA -s mr.mrrefChr5 158124 4 + 294540 TGTA -s simCow_chr6.simCow.chr6 280103 4 + 602619 TGCC -s simDog_chr6.simDog.chr6 316768 4 - 593897 CACA -s simHuman_chr6.simHuman.chr6 226880 4 + 601863 CGCA -s simRat_chr6.simRat.chr6 299346 4 + 647215 TCTA - -a -s simMouse_chr6.simMouse.chr6 307746 4 + 636262 CCTT -s Anc0.Anc0refChr8 532 4 + 17196 CCTG -s Anc1.Anc1refChr3 538 4 + 3661 CCTG -s Anc2.Anc2refChr8 580 4 + 12804 CCTG -s mr.mrrefChr5 158128 4 + 294540 CCTG -s simCow_chr6.simCow.chr6 280143 4 + 602619 CCAG -s simDog_chr6.simDog.chr6 316800 3 - 593897 -CTG -s simHuman_chr6.simHuman.chr6 226884 4 + 601863 CCTG -s simRat_chr6.simRat.chr6 299350 4 + 647215 CCTG - -a -s simMouse_chr6.simMouse.chr6 307750 2 + 636262 AC -s Anc0.Anc0refChr8 537 2 + 17196 TT -s Anc1.Anc1refChr3 543 2 + 3661 TT -s Anc2.Anc2refChr8 585 2 + 12804 TC -s mr.mrrefChr5 158132 2 + 294540 AT -s simCow_chr6.simCow.chr6 280148 2 + 602619 TC -s simDog_chr6.simDog.chr6 316804 2 - 593897 TC -s simHuman_chr6.simHuman.chr6 226889 2 + 601863 TT -s simRat_chr6.simRat.chr6 299354 2 + 647215 AT - -a -s simMouse_chr6.simMouse.chr6 307752 29 + 636262 ATGTAATTAAGCCAGTTAAAAAAACATAC -s Anc0.Anc0refChr8 539 29 + 17196 ATGTACTTAAGCAAATTAAAAAAACATAC -s Anc1.Anc1refChr3 545 29 + 3661 ATGTACTTAAGCAAATTAAAAAAACATAC -s Anc2.Anc2refChr8 587 29 + 12804 ATGTACTTGAGCAAATTATAAAAACATAC -s mr.mrrefChr5 158134 29 + 294540 ATGTAATTAAGCCAGTTAAAAAAACATAC -s simCow_chr6.simCow.chr6 280153 28 + 602619 ATGTACTTCAGCAAATTATAAA-ACATAC -s simDog_chr6.simDog.chr6 316806 29 - 593897 ATGGACTTGAGCAAATTATAAGAGCATAC -s simHuman_chr6.simHuman.chr6 226891 29 + 601863 ATGTACTTAAGTAAATTAAAAAGACTTAC -s simRat_chr6.simRat.chr6 299356 29 + 647215 ATGTAATTAAGCCAGTTAGAAAAACATAC - -a -s simMouse_chr6.simMouse.chr6 307781 32 + 636262 TGAATTTTGGTAAGAGGAAGACATCCAGTGTC -s Anc0.Anc0refChr8 568 32 + 17196 TGAATTGTGGTAAGTGGAAACTAAGAAACATC -s Anc1.Anc1refChr3 574 32 + 3661 TGAATTGTGGTAAGTGGAAACTAAGAAACATC -s Anc2.Anc2refChr8 616 32 + 12804 TGAACCGTGGTAAGTGGAAACTTAGAAACATC -s mr.mrrefChr5 158163 32 + 294540 TGAATTTTGGTAAGAGGAAACTATCAAGTGTC -s simCow_chr6.simCow.chr6 280181 32 + 602619 CACACCGTGCTAAGTGGAAACTTAGTTACATC -s simDog_chr6.simDog.chr6 316835 28 - 593897 TGA----TGGTAAGTGGAAATTTAAAAATATC -s simHuman_chr6.simHuman.chr6 226920 32 + 601863 TTAATTGTGGTCAGTGGGAACTAAGAAACACT -s simRat_chr6.simRat.chr6 299386 32 + 647215 TAAATTTTGGTAAGAGGAAACTATCAAGTGTC - -a -s simMouse_chr6.simMouse.chr6 307813 14 + 636262 AGGGAATCCCACAA -s Anc0.Anc0refChr8 600 14 + 17196 AGGGTAGCCCACAA -s Anc1.Anc1refChr3 606 14 + 3661 AGGGTAGCCCACAA -s Anc2.Anc2refChr8 648 14 + 12804 AGGGTAGCCCACAC -s mr.mrrefChr5 158195 14 + 294540 AGGGAAGCCCACAA -s simCow_chr6.simCow.chr6 280224 14 + 602619 AGGACGACCCGCAC -s simDog_chr6.simDog.chr6 316863 14 - 593897 AGTGTAGCCCACAC -s simHuman_chr6.simHuman.chr6 226952 14 + 601863 AGGGGAGCCCATGA -s simRat_chr6.simRat.chr6 299418 14 + 647215 AGGGAAGCCCACAA - -a -s simMouse_chr6.simMouse.chr6 307827 8 + 636262 TCCGAATG -s Anc0.Anc0refChr8 614 8 + 17196 TCCAGATG -s Anc1.Anc1refChr3 620 8 + 3661 TCCAGATG -s Anc2.Anc2refChr8 662 8 + 12804 TCCAGATA -s mr.mrrefChr5 158209 8 + 294540 TCCGAATG -s simCow_chr6.simCow.chr6 280240 8 + 602619 TCCAGATA -s simDog_chr6.simDog.chr6 316877 8 - 593897 TCAAGATA -s simHuman_chr6.simHuman.chr6 226966 8 + 601863 TCCTGATG -s simRat_chr6.simRat.chr6 299432 8 + 647215 TGCCAATG - -a -s simMouse_chr6.simMouse.chr6 307835 17 + 636262 TGGTCAGAGAGTGTGTA -s Anc0.Anc0refChr8 631 16 + 17196 TAGGAAGGGAGAG-GTA -s Anc1.Anc1refChr3 637 17 + 3661 TAGGAAGGGAGAGTGTA -s Anc2.Anc2refChr8 679 16 + 12804 TAGGAAGGGAGAG-ATA -s mr.mrrefChr5 158217 17 + 294540 TAGTCAGAGAGTGTGTA -s simCow_chr6.simCow.chr6 280257 16 + 602619 TAGGACAGGAGAG-TTA -s simDog_chr6.simDog.chr6 316894 16 - 593897 TAAGAAGGGTGAG-ATA -s simHuman_chr6.simHuman.chr6 226983 17 + 601863 TAGGAAGGGAGAGTGTG -s simRat_chr6.simRat.chr6 299440 17 + 647215 TAATCAGAGAGTTTGTA - -a -s simMouse_chr6.simMouse.chr6 307852 60 + 636262 TTGGGAAGTGCCTATATAATCCCTTGCATGCCACTATGGGTTTGAGGGCCAGAGTCTATA -s Anc0.Anc0refChr8 648 60 + 17196 TAGGGGAGAGTCAATATGGCCATTCTGCTGTCTCTAAGGGATTTAGGACCAGATTCTATT -s Anc1.Anc1refChr3 655 60 + 3661 TAGGGGAGAGTCAATATGGCCATTCTGCTGTCTCTAAGGGATTTAGGACCAGATTCTATT -s Anc2.Anc2refChr8 696 60 + 12804 GAGGGGAGATTCAACATGGCCATTCTGCTGTCTCTAAGCGATTTAGGACCAGCTTCTATT -s mr.mrrefChr5 158234 60 + 294540 TTGGGAAGTGCCTATATGATCCCTCGCATGCCACTATGGGTTTGAGGGCCAGAGTCTATA -s simCow_chr6.simCow.chr6 280274 55 + 602619 GAGGGGAGAATCATCTTGGCCAATCTGCTGTCTCTTA---ATTCAGGCC--GTTTCTATT -s simDog_chr6.simDog.chr6 316911 60 - 593897 GAGGGGAGATTCAACATGGCCATTCTGCTGTCTCCATGCGATTTAGGATCAGCTTGTATC -s simHuman_chr6.simHuman.chr6 227001 59 + 601863 TAGGGGAGCGTCAATATGGCTGGTCCACTGTCTCTAAGGGATTTAGGACCAGATTCTAT- -s simRat_chr6.simRat.chr6 299457 60 + 647215 TTGGGAAGAAGCTATATGATCCCTCACATGCTACTATGGGTTTAAGGGCAAGAGTCTATA - -a -s simMouse_chr6.simMouse.chr6 307912 20 + 636262 TCTAAAGAAATCGACCAAAA -s Anc0.Anc0refChr8 708 20 + 17196 TCTAAAGAAAAAGAACAAGA -s Anc1.Anc1refChr3 715 20 + 3661 TCTAAAGAAAAAGAACAAGA -s Anc2.Anc2refChr8 756 20 + 12804 TCTATAGAAAAAGAACATGA -s mr.mrrefChr5 158294 20 + 294540 TCTAAAGAAATCGACCAAAA -s mr.mrrefChr5 161186 20 + 294540 TCCGAAAAAAAAGAAGAAGA -s simCow_chr6.simCow.chr6 280329 20 + 602619 TCCAAAGACAATGAACATGA -s simDog_chr6.simDog.chr6 316971 20 - 593897 TCTATTGAAAAAGAACATGA -s simHuman_chr6.simHuman.chr6 227060 12 + 601863 TTTAAGA--------CAAGA -s simMouse_chr6.simMouse.chr6 310896 20 + 636262 TCCGAAAAAAAAGAAGAAGA -s simRat_chr6.simRat.chr6 302537 20 + 647215 TCAGAAGCCAAAGGACACGA -s simRat_chr6.simRat.chr6 299517 20 + 647215 TCTAAAGAAAAGGACCAAAA - -a -s simMouse_chr6.simMouse.chr6 307932 13 + 636262 TAGCATAAGTTTC -s Anc0.Anc0refChr8 728 13 + 17196 AAGCATAGAGTTT -s Anc1.Anc1refChr3 735 13 + 3661 AAGCATAGAGTTT -s Anc2.Anc2refChr8 776 13 + 12804 AAGCATAGAGTTT -s mr.mrrefChr5 158314 13 + 294540 TAGCATAAAGTTC -s mr.mrrefChr5 161206 13 + 294540 TAGTCCATAGTTT -s simCow_chr6.simCow.chr6 280349 13 + 602619 GACCATAACCTAC -s simDog_chr6.simDog.chr6 316991 13 - 593897 AGGCATAGAGTTT -s simHuman_chr6.simHuman.chr6 227072 13 + 601863 AAGCATAGAGTTT -s simMouse_chr6.simMouse.chr6 310916 13 + 636262 TAGTCCATAGTTT -s simRat_chr6.simRat.chr6 302558 13 + 647215 CAGTATATAGTTT -s simRat_chr6.simRat.chr6 299537 13 + 647215 TAGCACAAAGTTG - -a -s simMouse_chr6.simMouse.chr6 307945 37 + 636262 CTTACTACTACTACAGCTATACTAAGTATTTGAGATG -s Anc0.Anc0refChr8 741 35 + 17196 CTT--TACTATAATAGCTATACGAAGTATTTCATATG -s Anc1.Anc1refChr3 748 35 + 3661 CTT--TACTATAATAGCTATACGAAGTATTTCATATG -s Anc2.Anc2refChr8 789 35 + 12804 CTT--TACTATAATAGCTTTACGAAGTATTTCATATG -s mr.mrrefChr5 158327 35 + 294540 CTT--TACTACTACAGCTATACTAAGTATTTGAGATG -s mr.mrrefChr5 161224 35 + 294540 CTT--TATAACTATAGGTATATGAAGTATTTCATATG -s simCow_chr6.simCow.chr6 280362 35 + 602619 TTT--TACTGTAATAGCTTCACGAAGTGTTTCATATG -s simDog_chr6.simDog.chr6 317004 35 - 593897 CTT--TACTATTATAGCTTTACGAAGTATTTCATGTG -s simHuman_chr6.simHuman.chr6 227085 35 + 601863 CTT--CATGATAATAGCTGTATGAAGTATTTCATATG -s simMouse_chr6.simMouse.chr6 310934 35 + 636262 CTT--TATAACTATAGGTATATGAAGTATTTCATATG -s simRat_chr6.simRat.chr6 302576 35 + 647215 TTT--TGTTACTACAGTTATATGAAGTATTTCATATG -s simRat_chr6.simRat.chr6 299550 35 + 647215 CTT--TACTACTGCAGCTATACTGAGTATTTGAGATG - -a -s simMouse_chr6.simMouse.chr6 307982 24 + 636262 GCCAATTGGAATTGCCTTTCATCT -s Anc0.Anc0refChr8 776 17 + 17196 A-------GGGCTGCCTTTCATTT -s Anc1.Anc1refChr3 783 24 + 3661 ACCAGTGGGGGCTGCCTTTCATTT -s Anc2.Anc2refChr8 824 17 + 12804 A-------GGGCTGCCTTTCATTT -s mr.mrrefChr5 158362 24 + 294540 GCCAATTGGAATTGCCTTTCATCT -s mr.mrrefChr5 161259 24 + 294540 ACTTGTGTGGATTGCTTTCATGTT -s simCow_chr6.simCow.chr6 280397 17 + 602619 A-------GGGTGGCCTTTCATTC -s simDog_chr6.simDog.chr6 317039 17 - 593897 A-------GGGCTGCCTTGCATAT -s simHuman_chr6.simHuman.chr6 227120 17 + 601863 -------GAAGCTGCTTTTCCTTT -s simMouse_chr6.simMouse.chr6 310969 24 + 636262 ACTTGTGTGGATTGCTTTCATGTT -s simRat_chr6.simRat.chr6 302612 24 + 647215 ACTCGTGTGAATTTCTTCCTTGTT -s simRat_chr6.simRat.chr6 299585 24 + 647215 GCCAATTGGAATTCCCTTTCATCT - -a -s simMouse_chr6.simMouse.chr6 308006 16 + 636262 TCGCAGTTTAAAAAAC -s Anc0.Anc0refChr8 795 16 + 17196 GGCAGTTTTTAAACAA -s Anc1.Anc1refChr3 809 16 + 3661 GGCAGTTTTTAAACAA -s Anc2.Anc2refChr8 843 16 + 12804 GGCAGTTTTTAAACAA -s mr.mrrefChr5 158386 16 + 294540 TCGCAGTTTAAAAAAC -s mr.mrrefChr5 161283 16 + 294540 GTAAGTATTCAGACTA -s simCow_chr6.simCow.chr6 280416 16 + 602619 GGCAGTTTTTAAGCAA -s simDog_chr6.simDog.chr6 317058 16 - 593897 GGCAGTTTTTAAACAA -s simHuman_chr6.simHuman.chr6 227139 16 + 601863 GGCAGTCTTTATACAA -s simMouse_chr6.simMouse.chr6 310993 16 + 636262 GTAAGTATTCAGACTA -s simRat_chr6.simRat.chr6 302636 16 + 647215 GTAAGTATTCAGGCTA -s simRat_chr6.simRat.chr6 299609 16 + 647215 TCACAGTTCAAAAATC - -a -s simMouse_chr6.simMouse.chr6 308022 9 + 636262 TGTGACCTT -s Anc0.Anc0refChr8 811 7 + 17196 TGTAACC-- -s Anc1.Anc1refChr3 825 9 + 3661 TGTAACCTT -s Anc2.Anc2refChr8 859 7 + 12804 TGTAACC-- -s mr.mrrefChr5 158402 9 + 294540 TGTGACCTT -s mr.mrrefChr5 161299 9 + 294540 TGTAACCTT -s simCow_chr6.simCow.chr6 280432 5 + 602619 T--CAAT-- -s simDog_chr6.simDog.chr6 317079 7 - 593897 TGTAACC-- -s simHuman_chr6.simHuman.chr6 227155 7 + 601863 TGTAACC-- -s simMouse_chr6.simMouse.chr6 311009 9 + 636262 TGTAACCTT -s simRat_chr6.simRat.chr6 302652 9 + 647215 TGTAACCCC -s simRat_chr6.simRat.chr6 299625 9 + 647215 TGTGACCTT - -a -s simMouse_chr6.simMouse.chr6 308031 3 + 636262 ACT -s Anc0.Anc0refChr8 1097 3 + 17196 ACT -s Anc1.Anc1refChr3 1122 3 + 3661 ACT -s Anc2.Anc2refChr8 1147 3 + 12804 ACT -s mr.mrrefChr5 158643 3 + 294540 ACT -s mr.mrrefChr5 161632 3 + 294540 ACT -s simCow_chr6.simCow.chr6 280691 3 + 602619 TCT -s simDog_chr6.simDog.chr6 317367 3 - 593897 ACA -s simHuman_chr6.simHuman.chr6 227427 3 + 601863 ACT -s simMouse_chr6.simMouse.chr6 311348 3 + 636262 ACT -s simRat_chr6.simRat.chr6 302998 3 + 647215 ACT -s simRat_chr6.simRat.chr6 299904 3 + 647215 ACT - -a -s simMouse_chr6.simMouse.chr6 308034 2 + 636262 TG -s Anc0.Anc0refChr8 1100 2 + 17196 TG -s Anc1.Anc1refChr3 1125 2 + 3661 TG -s Anc2.Anc2refChr8 1150 2 + 12804 TG -s mr.mrrefChr5 158646 2 + 294540 TG -s simCow_chr6.simCow.chr6 280694 2 + 602619 GG -s simDog_chr6.simDog.chr6 317370 2 - 593897 TG -s simHuman_chr6.simHuman.chr6 227430 2 + 601863 AG -s simRat_chr6.simRat.chr6 299907 2 + 647215 TG - -a -s simMouse_chr6.simMouse.chr6 308036 7 + 636262 GCACATA -s Anc0.Anc0refChr8 1102 7 + 17196 GTACATG -s Anc1.Anc1refChr3 1127 7 + 3661 GTACATG -s Anc2.Anc2refChr8 1152 7 + 12804 GTACATG -s mr.mrrefChr5 158648 7 + 294540 GCACATG -s simCow_chr6.simCow.chr6 280696 7 + 602619 GCACATG -s simDog_chr6.simDog.chr6 590004 6 - 593897 GT-CAGG -s simHuman_chr6.simHuman.chr6 227432 7 + 601863 GTGCATG -s simRat_chr6.simRat.chr6 299909 7 + 647215 GCTCATG - -a -s simMouse_chr6.simMouse.chr6 308043 3 + 636262 GTC -s Anc0.Anc0refChr8 1109 3 + 17196 ATC -s Anc1.Anc1refChr3 1134 3 + 3661 ATC -s Anc2.Anc2refChr8 1159 3 + 12804 ATT -s mr.mrrefChr5 158655 3 + 294540 ATC -s mr.mrrefChr5 161635 3 + 294540 AAA -s simCow_chr6.simCow.chr6 280703 3 + 602619 ATT -s simDog_chr6.simDog.chr6 590010 3 - 593897 ATT -s simHuman_chr6.simHuman.chr6 227439 3 + 601863 ATC -s simMouse_chr6.simMouse.chr6 311351 3 + 636262 AAA -s simRat_chr6.simRat.chr6 303001 3 + 647215 AAA -s simRat_chr6.simRat.chr6 299916 3 + 647215 ATC - -a -s simMouse_chr6.simMouse.chr6 308046 13 + 636262 ATCCTGCACTCTA -s Anc0.Anc0refChr8 1112 13 + 17196 ATCCTGTGCTCTA -s Anc1.Anc1refChr3 1137 13 + 3661 ATCCTGTGCTCTA -s Anc2.Anc2refChr8 1162 13 + 12804 ATCCTGTGCTCTA -s mr.mrrefChr5 158658 13 + 294540 ATCCTGCACTCTA -s mr.mrrefChr5 161638 13 + 294540 GTCCTGTGCCCCA -s simCow_chr6.simCow.chr6 280706 13 + 602619 ATCCTGTCCTGGA -s simDog_chr6.simDog.chr6 590013 13 - 593897 ATCTTGTGCCCTA -s simHuman_chr6.simHuman.chr6 227442 13 + 601863 ATCCTGGGCTCCT -s simMouse_chr6.simMouse.chr6 311370 13 + 636262 GTCCTGTGCCCCA -s simRat_chr6.simRat.chr6 303004 13 + 647215 GTCCTGTGCCCCA -s simRat_chr6.simRat.chr6 299919 13 + 647215 ATCCTGCATTCTA - -a -s simMouse_chr6.simMouse.chr6 308059 8 + 636262 ATTGTACC -s Anc0.Anc0refChr8 1125 8 + 17196 AGTGGACT -s Anc1.Anc1refChr3 1150 8 + 3661 AGTGGACT -s Anc2.Anc2refChr8 1175 8 + 12804 AGTGGACT -s mr.mrrefChr5 158671 8 + 294540 AGTGTACC -s mr.mrrefChr5 161651 8 + 294540 ATTTGAAT -s simCow_chr6.simCow.chr6 280719 8 + 602619 AGCTGACT -s simDog_chr6.simDog.chr6 590026 8 - 593897 AGTGAACT -s simHuman_chr6.simHuman.chr6 227455 8 + 601863 AGTGGACT -s simMouse_chr6.simMouse.chr6 311383 8 + 636262 ATTTGAAT -s simRat_chr6.simRat.chr6 303029 8 + 647215 ATTTGAAT -s simRat_chr6.simRat.chr6 299932 8 + 647215 AGTGTACA - -a -s simMouse_chr6.simMouse.chr6 308067 22 + 636262 CAGTATTGTTCAACCAGCAAAC -s Anc0.Anc0refChr8 1136 22 + 17196 CAGTATTCTTTAACTGGTGAAC -s Anc1.Anc1refChr3 1161 22 + 3661 CAGTATTCTTTAACTGGTGAAC -s Anc2.Anc2refChr8 1186 22 + 12804 CAGTATTCTTTAACAGGTGAAC -s mr.mrrefChr5 158679 22 + 294540 CAGTATTGTTCAACTAGCAAAC -s mr.mrrefChr5 161662 22 + 294540 CAATTTCCTTTAACTAATGAAC -s simCow_chr6.simCow.chr6 280730 22 + 602619 CAATATTCCTTAACAGGTGAAC -s simDog_chr6.simDog.chr6 590037 22 - 593897 CAGTATTCTTTAATAGGTGAAC -s simHuman_chr6.simHuman.chr6 227463 22 + 601863 GGGTATATTATAACTGGTAAAT -s simMouse_chr6.simMouse.chr6 311394 22 + 636262 CAATTTCCTTTAACTAATGAAC -s simRat_chr6.simRat.chr6 303040 22 + 647215 CAGTGTCCTTTAACTAATGAAC -s simRat_chr6.simRat.chr6 299940 22 + 647215 CAGTATTCTTCAACTTCCAAAC - -a -s simMouse_chr6.simMouse.chr6 308089 13 + 636262 CTCCCCCAGAGAG -s Anc0.Anc0refChr8 1163 13 + 17196 CTTCCCCAGAGAA -s Anc1.Anc1refChr3 1188 13 + 3661 CTTCCCCAGAGAA -s Anc2.Anc2refChr8 1213 13 + 12804 CCTCCCCAGAGAA -s mr.mrrefChr5 158701 13 + 294540 CTTCCCCAGAGAG -s mr.mrrefChr5 161689 13 + 294540 CTTTCCCAGAGTA -s simCow_chr6.simCow.chr6 280757 13 + 602619 CTTCCCCAGAGAA -s simDog_chr6.simDog.chr6 590064 13 - 593897 CCTCCCCAAAGAA -s simHuman_chr6.simHuman.chr6 227490 12 + 601863 CT-CTCCAGAGAA -s simMouse_chr6.simMouse.chr6 311421 13 + 636262 CTTTCCCAGAGTA -s simRat_chr6.simRat.chr6 303067 13 + 647215 CTTCCCCAGAATA -s simRat_chr6.simRat.chr6 299962 13 + 647215 CTTCCCCAGAGAG - -a -s simMouse_chr6.simMouse.chr6 308102 27 + 636262 GCAATGACATACAAGCCCAGTCTCTGT -s Anc0.Anc0refChr8 1176 27 + 17196 GCAATAACATACAAGCCCCTTCTTTAT -s Anc1.Anc1refChr3 1201 27 + 3661 GCAATAACATACAAGCCCCTTCTTTAT -s Anc2.Anc2refChr8 1226 27 + 12804 ACAATAACATAAATGCCCCTTCTTTAT -s mr.mrrefChr5 158714 27 + 294540 GCAATAACATACAAGCCCATTCTCTAT -s mr.mrrefChr5 161702 27 + 294540 GGAACAATATGTAGTCCCCTTCTCCAT -s simCow_chr6.simCow.chr6 280770 27 + 602619 ACAATAACCTGAAGGCCCTTCCTTTAT -s simDog_chr6.simDog.chr6 590077 26 - 593897 ATAATAACATAAATGCCCCTT-TTTAT -s simHuman_chr6.simHuman.chr6 227502 27 + 601863 GCAATAACATACAAGCCCGTTCTTTAT -s simMouse_chr6.simMouse.chr6 311439 27 + 636262 GGAACAATATGTAGTCCCCTTCTCCAT -s simRat_chr6.simRat.chr6 303080 27 + 647215 GGACTAATATGTAGTCCCCTTCTCCAT -s simRat_chr6.simRat.chr6 299975 27 + 647215 GCAATAACATACAAGCCCATGGTCTAT - -a -s simMouse_chr6.simMouse.chr6 308129 4 + 636262 AACA -s Anc0.Anc0refChr8 1203 2 + 17196 --TG -s Anc1.Anc1refChr3 1228 4 + 3661 AATG -s Anc2.Anc2refChr8 1253 2 + 12804 --TG -s mr.mrrefChr5 158741 4 + 294540 AACA -s mr.mrrefChr5 161729 4 + 294540 AATG -s simCow_chr6.simCow.chr6 280797 2 + 602619 --TG -s simDog_chr6.simDog.chr6 590103 2 - 593897 --TG -s simHuman_chr6.simHuman.chr6 227529 4 + 601863 AGTG -s simMouse_chr6.simMouse.chr6 311466 4 + 636262 AATG -s simRat_chr6.simRat.chr6 303107 4 + 647215 AATG -s simRat_chr6.simRat.chr6 608840 4 - 647215 AGCA -s simRat_chr6.simRat.chr6 300005 4 + 647215 ATCA - -a -s simMouse_chr6.simMouse.chr6 308133 50 + 636262 TACTAGCATAATACTAGAATTCCTAGCATGTGATCAAAGATGTATCCCTG -s mr.mrrefChr5 158745 50 + 294540 TACTAGCATACTACTAGAATTTCTAGTCTGTTATCAAAAATGTATCCCTG -s simRat_chr6.simRat.chr6 608844 50 - 647215 TACAAGCATACTACTAGAATTTCAAGTCTGTTATCTAAAATGTATGTCTG -s simRat_chr6.simRat.chr6 300009 50 + 647215 TACTAGCATACTACCAGAATTTCTATTCTTTTATCAAAAATGTATCCCGG - -a -s simMouse_chr6.simMouse.chr6 308183 6 + 636262 TATACA -s mr.mrrefChr5 158795 6 + 294540 TATACA -s simRat_chr6.simRat.chr6 300059 6 + 647215 TACACA - -a -s simMouse_chr6.simMouse.chr6 308189 5 + 636262 GAAGG -s mr.mrrefChr5 158801 5 + 294540 GAAGG -s simRat_chr6.simRat.chr6 608894 5 - 647215 GAAGG -s simRat_chr6.simRat.chr6 300065 5 + 647215 GAAGG - -a -s simMouse_chr6.simMouse.chr6 308194 3 + 636262 GGA -s Anc0.Anc0refChr8 1209 3 + 17196 GGA -s Anc1.Anc1refChr3 1238 3 + 3661 GGA -s Anc2.Anc2refChr8 1259 3 + 12804 GGA -s mr.mrrefChr5 158818 3 + 294540 GGA -s mr.mrrefChr5 161739 3 + 294540 TGA -s simCow_chr6.simCow.chr6 280803 3 + 602619 GGA -s simDog_chr6.simDog.chr6 590109 3 - 593897 GGA -s simHuman_chr6.simHuman.chr6 227537 3 + 601863 GAA -s simMouse_chr6.simMouse.chr6 311476 3 + 636262 TGA -s simRat_chr6.simRat.chr6 303117 3 + 647215 TGA -s simRat_chr6.simRat.chr6 608911 3 - 647215 GGC -s simRat_chr6.simRat.chr6 300082 3 + 647215 GAT - -a -s simMouse_chr6.simMouse.chr6 308197 6 + 636262 AATATC -s Anc0.Anc0refChr8 1212 6 + 17196 TTTCTA -s Anc1.Anc1refChr3 1241 6 + 3661 TTTCTA -s Anc2.Anc2refChr8 1268 6 + 12804 TTTCTA -s mr.mrrefChr5 158821 6 + 294540 GATGTC -s mr.mrrefChr5 161742 6 + 294540 GATCCC -s simCow_chr6.simCow.chr6 280812 6 + 602619 CTTCTA -s simDog_chr6.simDog.chr6 590118 6 - 593897 TTTCCA -s simHuman_chr6.simHuman.chr6 227540 6 + 601863 TTTTTA -s simMouse_chr6.simMouse.chr6 311479 6 + 636262 GATCCC -s simRat_chr6.simRat.chr6 303120 6 + 647215 AATTCC -s simRat_chr6.simRat.chr6 608914 6 - 647215 GATGTG -s simRat_chr6.simRat.chr6 300085 6 + 647215 GATGTC - -a -s simMouse_chr6.simMouse.chr6 308203 2 + 636262 AG -s Anc0.Anc0refChr8 1218 2 + 17196 TG -s Anc1.Anc1refChr3 1247 2 + 3661 TG -s Anc2.Anc2refChr8 1274 2 + 12804 TG -s mr.mrrefChr5 158827 2 + 294540 AT -s mr.mrrefChr5 161748 2 + 294540 GT -s simCow_chr6.simCow.chr6 280818 2 + 602619 TG -s simDog_chr6.simDog.chr6 590124 2 - 593897 TG -s simHuman_chr6.simHuman.chr6 227546 2 + 601863 TG -s simMouse_chr6.simMouse.chr6 311487 2 + 636262 GT -s simRat_chr6.simRat.chr6 303126 2 + 647215 AT -s simRat_chr6.simRat.chr6 608920 2 - 647215 AT -s simRat_chr6.simRat.chr6 300091 2 + 647215 GT - -a -s simMouse_chr6.simMouse.chr6 308205 13 + 636262 ACTTCAGCGTTTC -s mr.mrrefChr5 158829 13 + 294540 ACTTCAGCGCTTC -s simRat_chr6.simRat.chr6 608922 13 - 647215 ACTTCAGTGCTTC -s simRat_chr6.simRat.chr6 300093 13 + 647215 ACCTCAGCGCTTC - -a -s simMouse_chr6.simMouse.chr6 308218 25 + 636262 TTTGTGTATGCGATTTCAAAACAGC -s Anc0.Anc0refChr8 1220 25 + 17196 TTTGTGTACTCCATTTCAAAACATC -s Anc1.Anc1refChr3 1249 25 + 3661 TTTGTGTACTCCATTTCAAAACATC -s Anc2.Anc2refChr8 1276 25 + 12804 TTTGTGTACTCTATTTCAAAACATC -s mr.mrrefChr5 158842 25 + 294540 TATGTGTATGCCATTTCAAAACAGC -s mr.mrrefChr5 161750 25 + 294540 TTGGTGTACTCCATCTCAGGACAGT -s simCow_chr6.simCow.chr6 280820 25 + 602619 TTTGTGTACTCCATTTCAAAAGATC -s simDog_chr6.simDog.chr6 590126 25 - 593897 TTCATGTACTCTGTTTCAAAACATC -s simHuman_chr6.simHuman.chr6 227548 25 + 601863 TTTGTGTATTCAACTTCAGAACATT -s simMouse_chr6.simMouse.chr6 311489 25 + 636262 TTGGTGTACTCCATCTCAGGACAGT -s simRat_chr6.simRat.chr6 303128 25 + 647215 TTGGTGTACTTCAGCACAAGGTGGT -s simRat_chr6.simRat.chr6 608935 25 - 647215 TATGTGTGTGCCATTTCAACCCAAC -s simRat_chr6.simRat.chr6 300106 25 + 647215 TATGTGTATGCCATTTCAAAACAGC - -a -s simMouse_chr6.simMouse.chr6 308243 11 + 636262 ACTAAGGGCAT -s Anc0.Anc0refChr8 1245 11 + 17196 ACTTCAGGCTT -s Anc1.Anc1refChr3 1274 11 + 3661 ACTTCAGGCTT -s Anc2.Anc2refChr8 1301 11 + 12804 ACTTCAGGCTT -s mr.mrrefChr5 158867 11 + 294540 ACTAAGGGCAT -s simCow_chr6.simCow.chr6 280845 11 + 602619 GCTTCACGCTT -s simDog_chr6.simDog.chr6 590151 11 - 593897 ACTTCAGGCTT -s simHuman_chr6.simHuman.chr6 227573 11 + 601863 ACTTCAGGCCT -s simRat_chr6.simRat.chr6 608960 11 - 647215 ACCACGGGCAT -s simRat_chr6.simRat.chr6 300131 11 + 647215 ACTAAGGACAC - -a -s simMouse_chr6.simMouse.chr6 308254 1 + 636262 A -s Anc0.Anc0refChr8 1258 1 + 17196 A -s Anc1.Anc1refChr3 1287 1 + 3661 A -s Anc2.Anc2refChr8 1314 1 + 12804 A -s mr.mrrefChr5 158878 1 + 294540 A -s simCow_chr6.simCow.chr6 280858 1 + 602619 A -s simDog_chr6.simDog.chr6 590164 1 - 593897 A -s simHuman_chr6.simHuman.chr6 227586 1 + 601863 A -s simRat_chr6.simRat.chr6 608971 1 - 647215 A -s simRat_chr6.simRat.chr6 300142 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 308255 15 + 636262 TGATATGAACCTATC -s Anc0.Anc0refChr8 1259 15 + 17196 TGGCATAAACCTATC -s Anc1.Anc1refChr3 1288 15 + 3661 TGGCATAAACCTATC -s Anc2.Anc2refChr8 1315 15 + 12804 TGGCATAAACCAATC -s mr.mrrefChr5 158879 15 + 294540 TGATATGAACCTATC -s mr.mrrefChr5 161775 15 + 294540 TGACATAGACCTATA -s simCow_chr6.simCow.chr6 280859 15 + 602619 TGGCAAAAACCCATC -s simDog_chr6.simDog.chr6 590166 15 - 593897 TGGCATAAACCAATC -s simHuman_chr6.simHuman.chr6 227587 15 + 601863 CAGCATAAACCTATC -s simMouse_chr6.simMouse.chr6 311528 15 + 636262 TGACATAGACCTATA -s simRat_chr6.simRat.chr6 303153 15 + 647215 TGGCATAGACCTATA -s simRat_chr6.simRat.chr6 608972 15 - 647215 TGTTATGAATCTATC -s simRat_chr6.simRat.chr6 300143 15 + 647215 AGATATGAGCCTACC - -a -s simMouse_chr6.simMouse.chr6 308270 21 + 636262 AGGGAGTGGTTCATTATTCCA -s Anc0.Anc0refChr8 1274 21 + 17196 AGGCAGTGGGTTATTGTTTCT -s Anc1.Anc1refChr3 1303 21 + 3661 AGGCAGTGGGTTATTGTTTCT -s Anc2.Anc2refChr8 1330 21 + 12804 AAGCAATGGGTTATTGTTTCT -s mr.mrrefChr5 158894 21 + 294540 AGAGAGTGGTTCATTGTTCCA -s mr.mrrefChr5 161790 21 + 294540 AGATAGTTGGTTATTATTTCT -s simCow_chr6.simCow.chr6 280874 14 + 602619 A-------GGTTATCGTTTCT -s simDog_chr6.simDog.chr6 590181 21 - 593897 AAGCAATGGACTATTGTTTCT -s simHuman_chr6.simHuman.chr6 227602 19 + 601863 ATGCAGTGGGTTAGTGTTT-- -s simMouse_chr6.simMouse.chr6 311543 21 + 636262 AGATAGTTGGTTATTATTTCT -s simRat_chr6.simRat.chr6 303168 21 + 647215 AGGTAGTTGGTTATTATTTCT -s simRat_chr6.simRat.chr6 608990 21 - 647215 CAATAGTGGTTAACTGGCAAA -s simRat_chr6.simRat.chr6 300158 21 + 647215 AGAGCGTGGTTCATTGTTCCA - -a -s simMouse_chr6.simMouse.chr6 308291 7 + 636262 GGGTTTT -s Anc0.Anc0refChr8 1295 3 + 17196 GTC---- -s Anc1.Anc1refChr3 1324 7 + 3661 GTCTTTT -s Anc2.Anc2refChr8 1351 3 + 12804 GTC---- -s mr.mrrefChr5 158915 7 + 294540 GGGTTTT -s mr.mrrefChr5 161811 7 + 294540 GTCTTCT -s simCow_chr6.simCow.chr6 280888 1 + 602619 G------ -s simDog_chr6.simDog.chr6 590202 3 - 593897 GTC---- -s simHuman_chr6.simHuman.chr6 227621 2 + 601863 -----TT -s simMouse_chr6.simMouse.chr6 311564 7 + 636262 GTCTTCT -s simRat_chr6.simRat.chr6 303189 7 + 647215 GTCTTCT -s simRat_chr6.simRat.chr6 300179 7 + 647215 GTATTTT - -a -s simMouse_chr6.simMouse.chr6 308298 4 + 636262 GTCT -s Anc0.Anc0refChr8 1298 4 + 17196 GTCC -s Anc1.Anc1refChr3 1331 4 + 3661 GTCC -s Anc2.Anc2refChr8 1354 4 + 12804 GTCC -s mr.mrrefChr5 158922 4 + 294540 GTCC -s mr.mrrefChr5 161818 4 + 294540 GTCC -s simCow_chr6.simCow.chr6 280889 4 + 602619 GTGC -s simDog_chr6.simDog.chr6 590206 4 - 593897 GTCC -s simHuman_chr6.simHuman.chr6 227623 4 + 601863 GTCC -s simMouse_chr6.simMouse.chr6 311571 4 + 636262 GTCC -s simRat_chr6.simRat.chr6 303196 4 + 647215 GTCC -s simRat_chr6.simRat.chr6 300186 4 + 647215 ATCC - -a -s simMouse_chr6.simMouse.chr6 308302 6 + 636262 TTATCC -s Anc0.Anc0refChr8 1302 6 + 17196 TTGTTA -s Anc1.Anc1refChr3 1335 6 + 3661 TTGTTA -s Anc2.Anc2refChr8 1358 6 + 12804 TTGTTG -s mr.mrrefChr5 158926 6 + 294540 TTATCA -s simCow_chr6.simCow.chr6 280893 6 + 602619 TTGTTG -s simDog_chr6.simDog.chr6 590210 6 - 593897 TTATTG -s simHuman_chr6.simHuman.chr6 227627 6 + 601863 TTGTTA -s simRat_chr6.simRat.chr6 300190 6 + 647215 TTATCA - -a -s simMouse_chr6.simMouse.chr6 308308 3 + 636262 GAC -s Anc0.Anc0refChr8 1308 3 + 17196 GCC -s Anc1.Anc1refChr3 1341 3 + 3661 GCC -s Anc2.Anc2refChr8 1364 3 + 12804 GCC -s mr.mrrefChr5 158932 3 + 294540 GAC -s mr.mrrefChr5 161822 3 + 294540 TTT -s simCow_chr6.simCow.chr6 280899 3 + 602619 GCC -s simDog_chr6.simDog.chr6 590216 3 - 593897 CCC -s simHuman_chr6.simHuman.chr6 227633 3 + 601863 GCC -s simMouse_chr6.simMouse.chr6 311575 3 + 636262 TTT -s simRat_chr6.simRat.chr6 303200 3 + 647215 CTT -s simRat_chr6.simRat.chr6 300196 3 + 647215 GAC - -a -s simMouse_chr6.simMouse.chr6 308311 30 + 636262 ATGTAAGCATTGGTTGTTCTAGTGGTATTA -s Anc0.Anc0refChr8 1313 30 + 17196 ATATGAACAGCAGTTGTTCTAGTGATCTTA -s Anc1.Anc1refChr3 1346 30 + 3661 ATATGAACAGCAGTTGTTCTAGTGATCTTA -s Anc2.Anc2refChr8 1369 30 + 12804 ATAGGACCAGCAGTTGTTCTAGTGATCTTA -s mr.mrrefChr5 158937 30 + 294540 ATGTAAGCATTGGTTGTTCTAGTGGTATTA -s mr.mrrefChr5 161827 30 + 294540 ATATAAACAGCCATTGCTCTGGTTACCTGG -s simCow_chr6.simCow.chr6 280904 21 + 602619 AGAA---------TTGTTCTAGTGATCCTA -s simDog_chr6.simDog.chr6 590221 29 - 593897 TTAGGACCAGCAGTTGTTGTAGTGAGCT-A -s simHuman_chr6.simHuman.chr6 227638 30 + 601863 ATATGAACACCAGTTGCTCTAGTGGTTTTA -s simMouse_chr6.simMouse.chr6 311584 30 + 636262 ATATAAACAGCCATTGCTCTGGTTACCTGG -s simRat_chr6.simRat.chr6 303205 30 + 647215 ATATAGACAGGCATTGCTCCGGTTAATTGG -s simRat_chr6.simRat.chr6 300201 30 + 647215 ATGTAAGCATTGGATGTTCTGGTGATATTA - -a -s simMouse_chr6.simMouse.chr6 308341 11 + 636262 CGGCAGTCTTT -s Anc0.Anc0refChr8 1343 11 + 17196 CAGCAGTCTTT -s Anc1.Anc1refChr3 1376 11 + 3661 CAGCAGTCTTT -s Anc2.Anc2refChr8 1399 11 + 12804 CAGTAGTCTTT -s mr.mrrefChr5 158967 11 + 294540 CGGCAGTCTTT -s simCow_chr6.simCow.chr6 280925 11 + 602619 CAGTAGTCCTT -s simDog_chr6.simDog.chr6 590250 11 - 593897 CAGTAGTCTTT -s simHuman_chr6.simHuman.chr6 227668 11 + 601863 CAGCAGTCATT -s simRat_chr6.simRat.chr6 300231 11 + 647215 CGGCAGTCTTT - -a -s simMouse_chr6.simMouse.chr6 308352 5 + 636262 TCATA -s Anc0.Anc0refChr8 1354 5 + 17196 TCATA -s Anc1.Anc1refChr3 1387 5 + 3661 TCATA -s Anc2.Anc2refChr8 1410 5 + 12804 TCATA -s mr.mrrefChr5 158978 5 + 294540 TCATA -s mr.mrrefChr5 161857 5 + 294540 TTATA -s simCow_chr6.simCow.chr6 280936 5 + 602619 TCATA -s simDog_chr6.simDog.chr6 590261 5 - 593897 TCTTA -s simHuman_chr6.simHuman.chr6 227679 5 + 601863 CCATC -s simMouse_chr6.simMouse.chr6 311614 5 + 636262 TTATA -s simRat_chr6.simRat.chr6 303235 5 + 647215 TTATT -s simRat_chr6.simRat.chr6 300242 5 + 647215 TCATA - -a -s simMouse_chr6.simMouse.chr6 308357 3 + 636262 ACC -s Anc0.Anc0refChr8 1359 3 + 17196 ACC -s Anc1.Anc1refChr3 1392 3 + 3661 ACC -s Anc2.Anc2refChr8 1415 3 + 12804 ACC -s mr.mrrefChr5 158983 3 + 294540 ACC -s simCow_chr6.simCow.chr6 280941 3 + 602619 ACC -s simDog_chr6.simDog.chr6 590266 3 - 593897 ACC -s simHuman_chr6.simHuman.chr6 227684 3 + 601863 ACC -s simRat_chr6.simRat.chr6 300247 3 + 647215 ACC - -a -s simMouse_chr6.simMouse.chr6 308360 1 + 636262 C -s Anc0.Anc0refChr8 1362 1 + 17196 C -s Anc1.Anc1refChr3 1395 1 + 3661 C -s Anc2.Anc2refChr8 1418 1 + 12804 C -s mr.mrrefChr5 158986 1 + 294540 C -s mr.mrrefChr5 161862 1 + 294540 C -s simCow_chr6.simCow.chr6 280944 1 + 602619 C -s simDog_chr6.simDog.chr6 590269 1 - 593897 T -s simHuman_chr6.simHuman.chr6 227687 1 + 601863 C -s simMouse_chr6.simMouse.chr6 311619 1 + 636262 C -s simRat_chr6.simRat.chr6 303240 1 + 647215 C -s simRat_chr6.simRat.chr6 300250 1 + 647215 C - -a -s simMouse_chr6.simMouse.chr6 308361 2 + 636262 AA -s Anc0.Anc0refChr8 1363 2 + 17196 AA -s Anc1.Anc1refChr3 1397 2 + 3661 AA -s Anc2.Anc2refChr8 1419 2 + 12804 AA -s mr.mrrefChr5 158988 2 + 294540 AA -s mr.mrrefChr5 161864 2 + 294540 AA -s simCow_chr6.simCow.chr6 280945 2 + 602619 GA -s simDog_chr6.simDog.chr6 590270 2 - 593897 AA -s simHuman_chr6.simHuman.chr6 227691 2 + 601863 AA -s simMouse_chr6.simMouse.chr6 311621 2 + 636262 AA -s simRat_chr6.simRat.chr6 303242 2 + 647215 AA -s simRat_chr6.simRat.chr6 300252 2 + 647215 AA - -a -s simMouse_chr6.simMouse.chr6 308363 5 + 636262 TCATA -s Anc0.Anc0refChr8 1365 5 + 17196 TTGTC -s Anc1.Anc1refChr3 1399 5 + 3661 TTGTC -s Anc2.Anc2refChr8 1421 5 + 12804 TTGTC -s mr.mrrefChr5 158990 5 + 294540 TCATA -s simCow_chr6.simCow.chr6 280947 5 + 602619 TTGTC -s simDog_chr6.simDog.chr6 590272 5 - 593897 TTGTC -s simHuman_chr6.simHuman.chr6 227693 5 + 601863 TTGTC -s simRat_chr6.simRat.chr6 300254 5 + 647215 TCATA - -a -s simMouse_chr6.simMouse.chr6 308368 17 + 636262 AGTATATTTGTATCCGC -s Anc0.Anc0refChr8 1370 17 + 17196 AGTTGGGTTGTACCAGC -s Anc1.Anc1refChr3 1404 17 + 3661 AGTTGGGTTGTACCAGC -s Anc2.Anc2refChr8 1426 17 + 12804 AGTTTGGTTGTACCAGC -s mr.mrrefChr5 158995 17 + 294540 AGTAGATTTGTATCCGC -s mr.mrrefChr5 161866 17 + 294540 AGCTGGTTCATACCAGC -s simCow_chr6.simCow.chr6 280952 17 + 602619 AGTTTGGTTGTACCAGC -s simDog_chr6.simDog.chr6 590277 17 - 593897 AGATTGGTTGTACCAGC -s simHuman_chr6.simHuman.chr6 227698 17 + 601863 AGTTGGGTTGTAGCATC -s simMouse_chr6.simMouse.chr6 311623 17 + 636262 AGCTGGTTCATACCAGC -s simRat_chr6.simRat.chr6 303245 17 + 647215 AGCTGGTTCCTACAAGC -s simRat_chr6.simRat.chr6 300259 17 + 647215 AGTAGATTTGTGTCTGC - -a -s simMouse_chr6.simMouse.chr6 308385 6 + 636262 CTGATC -s Anc0.Anc0refChr8 1387 6 + 17196 CTTACC -s Anc1.Anc1refChr3 1421 6 + 3661 CTTACC -s Anc2.Anc2refChr8 1443 6 + 12804 CTTACG -s mr.mrrefChr5 159012 6 + 294540 CTGATC -s mr.mrrefChr5 161885 6 + 294540 CTTATC -s simCow_chr6.simCow.chr6 280971 6 + 602619 CTTACT -s simDog_chr6.simDog.chr6 590294 4 - 593897 C--ACG -s simHuman_chr6.simHuman.chr6 227715 6 + 601863 TTTACC -s simMouse_chr6.simMouse.chr6 311642 6 + 636262 CTTATC -s simRat_chr6.simRat.chr6 303264 6 + 647215 CTTACC -s simRat_chr6.simRat.chr6 300276 6 + 647215 CTGATC - -a -s simMouse_chr6.simMouse.chr6 308391 5 + 636262 TGTCT -s Anc0.Anc0refChr8 1393 1 + 17196 T---- -s Anc1.Anc1refChr3 1427 5 + 3661 TCCCT -s Anc2.Anc2refChr8 1449 1 + 12804 T---- -s mr.mrrefChr5 159018 5 + 294540 TGTCT -s simCow_chr6.simCow.chr6 280977 1 + 602619 T---- -s simDog_chr6.simDog.chr6 590298 1 - 593897 T---- -s simHuman_chr6.simHuman.chr6 227721 5 + 601863 TCCCT -s simRat_chr6.simRat.chr6 300282 5 + 647215 TATCT - -a -s simMouse_chr6.simMouse.chr6 308396 3 + 636262 ATG -s Anc1.Anc1refChr3 1432 3 + 3661 ATG -s mr.mrrefChr5 159023 3 + 294540 ATG -s simHuman_chr6.simHuman.chr6 227731 3 + 601863 ATG -s simRat_chr6.simRat.chr6 300287 3 + 647215 ATA - -a -s simMouse_chr6.simMouse.chr6 308399 13 + 636262 TTGAATGGCCTTG -s Anc0.Anc0refChr8 1394 3 + 17196 ----------TTC -s Anc1.Anc1refChr3 1435 13 + 3661 TTTAAATATATTC -s Anc2.Anc2refChr8 1450 3 + 12804 ----------TTC -s mr.mrrefChr5 159026 13 + 294540 TTGAATGGTATTG -s simCow_chr6.simCow.chr6 280978 3 + 602619 ----------TTC -s simDog_chr6.simDog.chr6 590299 3 - 593897 ----------TTC -s simHuman_chr6.simHuman.chr6 227736 13 + 601863 TTTAAATATATTC -s simRat_chr6.simRat.chr6 300290 13 + 647215 CTGAATGGTATTG - -a -s simMouse_chr6.simMouse.chr6 308412 9 + 636262 CATAATTTC -s Anc0.Anc0refChr8 1397 9 + 17196 TTCTCTCCC -s Anc1.Anc1refChr3 1448 9 + 3661 TTCTCTCCC -s Anc2.Anc2refChr8 1453 9 + 12804 TTCTCTCCC -s mr.mrrefChr5 159039 9 + 294540 CATCATTTC -s mr.mrrefChr5 161891 9 + 294540 CTCTCTTCC -s simCow_chr6.simCow.chr6 280981 9 + 602619 TTCTCTCCC -s simDog_chr6.simDog.chr6 590302 9 - 593897 TTCTCTCCC -s simHuman_chr6.simHuman.chr6 227749 9 + 601863 TTCCCTCCC -s simMouse_chr6.simMouse.chr6 311648 9 + 636262 CTCTCTTCC -s simRat_chr6.simRat.chr6 303270 9 + 647215 CTCTCTTCT -s simRat_chr6.simRat.chr6 300303 9 + 647215 CATCATTTC - -a -s simMouse_chr6.simMouse.chr6 308421 6 + 636262 AAAGGA -s mr.mrrefChr5 159048 6 + 294540 AAAGGA -s simRat_chr6.simRat.chr6 300312 6 + 647215 AAAGGA - -a -s simMouse_chr6.simMouse.chr6 308427 16 + 636262 CGATGCATTCATATGA -s Anc0.Anc0refChr8 1406 16 + 17196 TCATGGATTTAAATAT -s Anc1.Anc1refChr3 1457 16 + 3661 TCATGGATTTAAATAT -s Anc2.Anc2refChr8 1462 16 + 12804 TCATGGATTTAAATCT -s mr.mrrefChr5 159054 16 + 294540 CGATGCATTTAAATGA -s mr.mrrefChr5 161900 16 + 294540 TCCTGAACATAAGTAG -s simCow_chr6.simCow.chr6 280990 16 + 602619 TCATGGTTTTAAATCT -s simDog_chr6.simDog.chr6 590311 16 - 593897 TCATTGATTTAAACCT -s simHuman_chr6.simHuman.chr6 227758 16 + 601863 TCATGGATTTAAATAT -s simMouse_chr6.simMouse.chr6 311657 16 + 636262 TCCTGAACATAAGTAG -s simRat_chr6.simRat.chr6 303279 16 + 647215 TCTTGAACATAAGTAC -s simRat_chr6.simRat.chr6 300318 16 + 647215 CAATGCATTTAAATGA - -a -s simMouse_chr6.simMouse.chr6 308443 6 + 636262 CAATGC -s Anc1.Anc1refChr3 1473 6 + 3661 CAATAT -s mr.mrrefChr5 159070 6 + 294540 CAATGT -s simHuman_chr6.simHuman.chr6 227785 6 + 601863 CAATAT -s simRat_chr6.simRat.chr6 300334 6 + 647215 CAGTGT - -a -s simMouse_chr6.simMouse.chr6 308449 13 + 636262 ATATGATCATTCA -s Anc0.Anc0refChr8 1422 8 + 17196 ATTGGAT-----A -s Anc1.Anc1refChr3 1479 8 + 3661 ATTGGAT-----A -s Anc2.Anc2refChr8 1478 8 + 12804 ATTGAAT-----A -s mr.mrrefChr5 159076 8 + 294540 ATTGGAT-----A -s mr.mrrefChr5 161916 8 + 294540 ATTTGAT-----A -s simCow_chr6.simCow.chr6 281006 8 + 602619 ATTGAAT-----A -s simDog_chr6.simDog.chr6 590327 8 - 593897 GTTGAAT-----A -s simHuman_chr6.simHuman.chr6 227791 8 + 601863 ATTGTAT-----A -s simMouse_chr6.simMouse.chr6 311673 8 + 636262 ATTTGAT-----A -s simRat_chr6.simRat.chr6 303295 8 + 647215 ATTAGAC-----A -s simRat_chr6.simRat.chr6 300340 8 + 647215 ACTGCAT-----A - -a -s simMouse_chr6.simMouse.chr6 308462 3 + 636262 AAG -s mr.mrrefChr5 159084 3 + 294540 AAG -s simRat_chr6.simRat.chr6 300348 3 + 647215 TAG - -a -s simMouse_chr6.simMouse.chr6 308465 4 + 636262 GACA -s Anc0.Anc0refChr8 1430 3 + 17196 GCC- -s Anc1.Anc1refChr3 1487 4 + 3661 GCCC -s Anc2.Anc2refChr8 1486 3 + 12804 GCC- -s mr.mrrefChr5 159087 4 + 294540 GACA -s mr.mrrefChr5 161924 4 + 294540 GCCC -s simCow_chr6.simCow.chr6 281014 3 + 602619 GCC- -s simDog_chr6.simDog.chr6 590335 3 - 593897 GCC- -s simHuman_chr6.simHuman.chr6 227799 3 + 601863 GCC- -s simMouse_chr6.simMouse.chr6 311681 4 + 636262 GCCC -s simRat_chr6.simRat.chr6 303303 4 + 647215 GCCC -s simRat_chr6.simRat.chr6 300351 4 + 647215 GACA - -a -s simMouse_chr6.simMouse.chr6 308469 9 + 636262 ATGCATTCA -s Anc0.Anc0refChr8 1437 9 + 17196 ACCCTTTCA -s Anc1.Anc1refChr3 1495 9 + 3661 ACCCTTTCA -s Anc2.Anc2refChr8 1493 9 + 12804 ACCCTGTCA -s mr.mrrefChr5 159091 9 + 294540 ATGCATTCA -s mr.mrrefChr5 161933 9 + 294540 ACCTTTTCA -s simCow_chr6.simCow.chr6 281021 9 + 602619 ACCCCCTCA -s simDog_chr6.simDog.chr6 590342 9 - 593897 AGCCTGTCT -s simHuman_chr6.simHuman.chr6 227806 9 + 601863 ACCCTTTCA -s simMouse_chr6.simMouse.chr6 311690 9 + 636262 ACCTTTTCA -s simRat_chr6.simRat.chr6 303312 9 + 647215 ACCTTTCCA -s simRat_chr6.simRat.chr6 300355 9 + 647215 ATGAATTCA - -a -s simMouse_chr6.simMouse.chr6 308478 7 + 636262 GATGAGA -s Anc0.Anc0refChr8 1446 7 + 17196 GGTGTCA -s Anc1.Anc1refChr3 1504 7 + 3661 GGTGTCA -s Anc2.Anc2refChr8 1502 7 + 12804 ATTGTCA -s mr.mrrefChr5 159100 7 + 294540 GATGACA -s mr.mrrefChr5 161945 7 + 294540 GGTCACA -s simCow_chr6.simCow.chr6 281030 7 + 602619 AATGTCA -s simDog_chr6.simDog.chr6 590351 7 - 593897 ATTGTCA -s simHuman_chr6.simHuman.chr6 227815 7 + 601863 CGTATCA -s simMouse_chr6.simMouse.chr6 311702 7 + 636262 GGTCACA -s simRat_chr6.simRat.chr6 303324 7 + 647215 AGTCACA -s simRat_chr6.simRat.chr6 300364 7 + 647215 GATGACA - -a -s simMouse_chr6.simMouse.chr6 308485 16 + 636262 ATGCATGTGAAAAGAC -s Anc0.Anc0refChr8 1453 14 + 17196 AAGCATG--AAAAGAC -s Anc1.Anc1refChr3 1511 14 + 3661 AAGCATG--AAAAGAC -s Anc2.Anc2refChr8 1509 14 + 12804 AAGTGTG--AAAAGAC -s mr.mrrefChr5 159107 16 + 294540 ATGCATGTGAAAAGAC -s simCow_chr6.simCow.chr6 281037 14 + 602619 GAGTGCG--AAAAAAC -s simDog_chr6.simDog.chr6 590358 14 - 593897 ACGTGTG--AAAAGCC -s simHuman_chr6.simHuman.chr6 227822 14 + 601863 AAGCATG--AAAAGAC -s simRat_chr6.simRat.chr6 300371 16 + 647215 ATGCATGTGAAAAGAC - -a -s simMouse_chr6.simMouse.chr6 308501 28 + 636262 CTGAACTTAATTAATGTCTTGATAAAAT -s Anc0.Anc0refChr8 1467 28 + 17196 TTTAACCTGATCAATATTTTCCTGAAAT -s Anc1.Anc1refChr3 1525 28 + 3661 TTTAACCTGATCAATATTTTCCTGAAAT -s Anc2.Anc2refChr8 1523 28 + 12804 TTTAGCCTGATCAATAGTTTCCTGAATC -s mr.mrrefChr5 159123 28 + 294540 CTGAACTTGATCAATATCTTGATGAAAT -s simCow_chr6.simCow.chr6 281051 28 + 602619 CTTAGCCTGATCAGTGCCTTCACAATGC -s simDog_chr6.simDog.chr6 317394 28 - 593897 TAAAGCATGGCCCATAGTAGTCTGGATC -s simHuman_chr6.simHuman.chr6 227836 28 + 601863 GTTAACCTGATCAATATGTTCCTGACAT -s simRat_chr6.simRat.chr6 300387 28 + 647215 CTCAACATGATCAATATCTTGACGAAAT - -a -s simMouse_chr6.simMouse.chr6 308529 9 + 636262 TAGCCACAC -s Anc0.Anc0refChr8 1496 9 + 17196 CAGTCACAA -s Anc1.Anc1refChr3 1554 9 + 3661 CAGTCACAA -s Anc2.Anc2refChr8 1552 9 + 12804 CAGTCACAA -s mr.mrrefChr5 159151 9 + 294540 TAGCCACAC -s simCow_chr6.simCow.chr6 281080 9 + 602619 CAGGCACAC -s simDog_chr6.simDog.chr6 317423 9 - 593897 CAGTCGCAA -s simHuman_chr6.simHuman.chr6 227865 9 + 601863 CAGTCACAA -s simRat_chr6.simRat.chr6 300415 9 + 647215 AGGGCACAC - -a -s simMouse_chr6.simMouse.chr6 308538 28 + 636262 TGTCCCTATACATGGGAGACTGACTCTG -s Anc0.Anc0refChr8 1505 28 + 17196 TGACCTTATACCCCTGAGATTAGCTCTG -s Anc1.Anc1refChr3 1563 28 + 3661 TGACCTTATACCCCTGAGATTAGCTCTG -s Anc2.Anc2refChr8 1561 28 + 12804 TGACCTTATACCCCTGAGATTAGCTCTG -s mr.mrrefChr5 159160 28 + 294540 TGTCCCTATACCTCTGAGACTGGCTCTG -s mr.mrrefChr5 161952 28 + 294540 TGACCTTATACCCCTGAAAGTAGGTCTG -s simCow_chr6.simCow.chr6 281089 28 + 602619 TGAGGTAATAGCGCTCTGATTAGTTCTG -s simDog_chr6.simDog.chr6 317432 28 - 593897 TGACCCTATACTCCTGAGATTGGCTCTA -s simHuman_chr6.simHuman.chr6 227874 27 + 601863 T-ACCTTATACCCCTGAGTTTAGCTCTG -s simMouse_chr6.simMouse.chr6 311709 28 + 636262 TGACCTTATACCCCTGAAAGTAGGTCTG -s simRat_chr6.simRat.chr6 303331 28 + 647215 TGACCTTATACCCCTGAGATAAGGTCTA -s simRat_chr6.simRat.chr6 300424 28 + 647215 TGTCCCTATACCTCTGAGAATGGCTCTG - -a -s simMouse_chr6.simMouse.chr6 308566 2 + 636262 GC -s mr.mrrefChr5 159188 2 + 294540 GC -s simRat_chr6.simRat.chr6 300452 2 + 647215 GA - -a -s simMouse_chr6.simMouse.chr6 308568 43 + 636262 ACACTGGTAAGTACCACTGCACTTATGGTTGTGATGTTAGCAA -s Anc0.Anc0refChr8 1533 43 + 17196 ATACTGGTAAGTACCATGGCATGTATGATCATAGTAAAACCAA -s Anc1.Anc1refChr3 1591 43 + 3661 ATACTGGTAAGTACCATGGCATGTATGATCATAGTAAAACCAA -s Anc2.Anc2refChr8 1589 43 + 12804 ATACTAGTAGGTACCATGGCCTGCATGATCATACTAAAACTAA -s mr.mrrefChr5 159190 43 + 294540 ACACTGGTAAGTACCATGGCACTTATGGTTGTAGTATTAGCAA -s mr.mrrefChr5 161980 43 + 294540 ACACTGGTAAGTACAATGGCACATATGATCATGATAAAACAGA -s simCow_chr6.simCow.chr6 281117 43 + 602619 GTATTTGCAGTTACAAGGATGTGAATGATCACATAAAAACGAA -s simDog_chr6.simDog.chr6 317460 43 - 593897 ATACCAGTAGGTACCATGGCCTGCATGGCCATGCTAGAACTAA -s simHuman_chr6.simHuman.chr6 227901 43 + 601863 ATACTGGTCAGTATCATGGCATGTATGATAATAGTAAAACCAA -s simMouse_chr6.simMouse.chr6 311737 43 + 636262 ACACTGGTAAGTACAATGGCACATATGATCATGATAAAACAGA -s simRat_chr6.simRat.chr6 303359 43 + 647215 ATACTGGTGAGTACAATGGCACAAATGATCATGATAAAATGGA -s simRat_chr6.simRat.chr6 300454 36 + 647215 ACACAGTTGAGTACCATGGCA-------TTGCAGTACTAGCGA - -a -s simMouse_chr6.simMouse.chr6 308611 3 + 636262 GAG -s Anc0.Anc0refChr8 1578 3 + 17196 GAG -s Anc1.Anc1refChr3 1636 3 + 3661 GAG -s Anc2.Anc2refChr8 1634 3 + 12804 GAG -s mr.mrrefChr5 159233 3 + 294540 GAG -s mr.mrrefChr5 162025 3 + 294540 GGG -s simCow_chr6.simCow.chr6 281162 3 + 602619 GAG -s simDog_chr6.simDog.chr6 317505 3 - 593897 GAG -s simHuman_chr6.simHuman.chr6 227946 3 + 601863 GAG -s simMouse_chr6.simMouse.chr6 311782 3 + 636262 GGG -s simRat_chr6.simRat.chr6 303404 3 + 647215 GGG -s simRat_chr6.simRat.chr6 300490 3 + 647215 GAG - -a -s simMouse_chr6.simMouse.chr6 308614 2 + 636262 TT -s Anc0.Anc0refChr8 1583 2 + 17196 CT -s Anc1.Anc1refChr3 1641 2 + 3661 CT -s Anc2.Anc2refChr8 1639 2 + 12804 TT -s mr.mrrefChr5 159238 2 + 294540 CT -s mr.mrrefChr5 162030 2 + 294540 CT -s simCow_chr6.simCow.chr6 281167 2 + 602619 TT -s simDog_chr6.simDog.chr6 317510 2 - 593897 TT -s simHuman_chr6.simHuman.chr6 227951 2 + 601863 CC -s simMouse_chr6.simMouse.chr6 311787 2 + 636262 CT -s simRat_chr6.simRat.chr6 303409 2 + 647215 CT -s simRat_chr6.simRat.chr6 300495 2 + 647215 CT - -a -s simMouse_chr6.simMouse.chr6 308616 22 + 636262 AGAATAGGATCCGCTAGGCAGA -s Anc0.Anc0refChr8 1585 22 + 17196 AGGACAAGAACAGCTAAGAATA -s Anc1.Anc1refChr3 1643 22 + 3661 AGGACAAGAACAGCTAAGAATA -s Anc2.Anc2refChr8 1642 22 + 12804 AGGGCAAGAACAGCTAAGAATA -s mr.mrrefChr5 159240 22 + 294540 AGAACAGGATCCGCTAGGCAGA -s mr.mrrefChr5 162032 22 + 294540 AGGACAAGACCAGCTAAGTTGA -s simCow_chr6.simCow.chr6 281170 22 + 602619 AGCGCAAGAACAGTTAAGAATA -s simDog_chr6.simDog.chr6 317513 22 - 593897 AGGGCAAGAACAGCTAAGTATA -s simHuman_chr6.simHuman.chr6 227953 22 + 601863 AGGACAGTAGCTGCTGGGAATA -s simMouse_chr6.simMouse.chr6 311789 22 + 636262 AGGACAAGACCAGCTAAGTTGA -s simRat_chr6.simRat.chr6 303411 22 + 647215 AGGACAAGACCAGCTAAGTAGA -s simRat_chr6.simRat.chr6 300497 22 + 647215 AGAACAGGATGCCCTAGGCAGA - -a -s simMouse_chr6.simMouse.chr6 308638 1 + 636262 G -s Anc0.Anc0refChr8 1607 1 + 17196 G -s Anc1.Anc1refChr3 1665 1 + 3661 G -s Anc2.Anc2refChr8 1664 1 + 12804 G -s mr.mrrefChr5 159262 1 + 294540 G -s simCow_chr6.simCow.chr6 281192 1 + 602619 G -s simDog_chr6.simDog.chr6 317535 1 - 593897 G -s simHuman_chr6.simHuman.chr6 227975 1 + 601863 T -s simRat_chr6.simRat.chr6 300519 1 + 647215 G - -a -s simMouse_chr6.simMouse.chr6 308639 8 + 636262 CTGTAAAT -s Anc0.Anc0refChr8 1608 8 + 17196 CTATAAAG -s Anc1.Anc1refChr3 1666 8 + 3661 CTATAAAG -s Anc2.Anc2refChr8 1665 8 + 12804 CTAGGAAG -s mr.mrrefChr5 159263 8 + 294540 CTGTAAAG -s mr.mrrefChr5 162054 8 + 294540 TTGATAAG -s simCow_chr6.simCow.chr6 281193 8 + 602619 CTAAGTAG -s simDog_chr6.simDog.chr6 317536 8 - 593897 CTTGGAAG -s simHuman_chr6.simHuman.chr6 227976 8 + 601863 CTATAACG -s simMouse_chr6.simMouse.chr6 311811 8 + 636262 TTGATAAG -s simRat_chr6.simRat.chr6 303433 8 + 647215 TCTATAAG -s simRat_chr6.simRat.chr6 300520 8 + 647215 CTGTAAAG - -a -s simMouse_chr6.simMouse.chr6 308647 2 + 636262 CC -s Anc0.Anc0refChr8 1616 2 + 17196 CT -s Anc1.Anc1refChr3 1674 2 + 3661 CT -s Anc2.Anc2refChr8 1673 2 + 12804 CT -s mr.mrrefChr5 159271 2 + 294540 CC -s mr.mrrefChr5 162062 2 + 294540 CA -s simCow_chr6.simCow.chr6 281201 2 + 602619 TT -s simDog_chr6.simDog.chr6 317544 2 - 593897 CT -s simHuman_chr6.simHuman.chr6 227984 2 + 601863 CT -s simMouse_chr6.simMouse.chr6 311819 2 + 636262 CA -s simRat_chr6.simRat.chr6 303442 2 + 647215 CA -s simRat_chr6.simRat.chr6 300528 2 + 647215 TC - -a -s simMouse_chr6.simMouse.chr6 308649 1 + 636262 T -s mr.mrrefChr5 159273 1 + 294540 T -s simRat_chr6.simRat.chr6 300530 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 308650 21 + 636262 ATAAAGCTTAGGGTCAAAATT -s Anc0.Anc0refChr8 1618 21 + 17196 ATGAAGATTAGGGTCAAAATT -s Anc1.Anc1refChr3 1676 21 + 3661 ATGAAGATTAGGGTCAAAATT -s Anc2.Anc2refChr8 1675 21 + 12804 ATGAAGATAAGGGTCAAAATC -s mr.mrrefChr5 159274 21 + 294540 ATAAAGCTTAGGGTCAAAATT -s mr.mrrefChr5 162064 21 + 294540 ACCAGGATTAGGTCCAAAGCT -s simCow_chr6.simCow.chr6 281203 21 + 602619 ATGAAGATAAGGTTCAAAACT -s simDog_chr6.simDog.chr6 317546 20 - 593897 ATAAAGATAAGGGTCAAA-TC -s simHuman_chr6.simHuman.chr6 227986 21 + 601863 ATGAATATTAGGGTCAAAATG -s simMouse_chr6.simMouse.chr6 311821 21 + 636262 ACCAGGATTAGGTCCAAAGCT -s simRat_chr6.simRat.chr6 303444 21 + 647215 ACCAGTAATAGGTCCAGGGCT -s simRat_chr6.simRat.chr6 300531 21 + 647215 ATATAGCTTGGGGTCAAAAAT - -a -s simMouse_chr6.simMouse.chr6 308671 33 + 636262 CAATCAGGGTCAAAATTCAATCAATGTAGATTT -s Anc0.Anc0refChr8 1643 16 + 17196 CAATGA-----------------ATGTTTATCT -s Anc1.Anc1refChr3 1701 16 + 3661 CAATGA-----------------ATGTTTATCT -s Anc2.Anc2refChr8 1700 16 + 12804 CAATGT-----------------ATGTTTATCT -s mr.mrrefChr5 159295 16 + 294540 CAATCA-----------------ATGTAGATTT -s mr.mrrefChr5 162089 16 + 294540 TAAGGC-----------------ATGTCTAACT -s simCow_chr6.simCow.chr6 281228 16 + 602619 CAATAT-----------------ATGTTTATCT -s simDog_chr6.simDog.chr6 317570 16 - 593897 CAATGT-----------------ATGTTTCTCT -s simHuman_chr6.simHuman.chr6 228011 16 + 601863 TAATCA-----------------ATGTTTATTT -s simMouse_chr6.simMouse.chr6 311846 16 + 636262 TAAGGC-----------------ATGTCTAACT -s simRat_chr6.simRat.chr6 303469 16 + 647215 CAATGT-----------------TTGTCTAACT -s simRat_chr6.simRat.chr6 300552 16 + 647215 CAATCA-----------------ATGTACATAT - -a -s simMouse_chr6.simMouse.chr6 308704 2 + 636262 GT -s mr.mrrefChr5 159311 2 + 294540 GT -s simRat_chr6.simRat.chr6 300568 2 + 647215 GT - -a -s simMouse_chr6.simMouse.chr6 308706 1 + 636262 A -s Anc0.Anc0refChr8 1659 1 + 17196 A -s Anc1.Anc1refChr3 1717 1 + 3661 A -s Anc2.Anc2refChr8 1716 1 + 12804 A -s mr.mrrefChr5 159313 1 + 294540 A -s mr.mrrefChr5 162105 1 + 294540 A -s simCow_chr6.simCow.chr6 281244 1 + 602619 A -s simDog_chr6.simDog.chr6 317586 1 - 593897 G -s simHuman_chr6.simHuman.chr6 228027 1 + 601863 A -s simMouse_chr6.simMouse.chr6 311862 1 + 636262 A -s simRat_chr6.simRat.chr6 303485 1 + 647215 A -s simRat_chr6.simRat.chr6 300570 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 308707 8 + 636262 CATGAAAA -s Anc0.Anc0refChr8 1660 8 + 17196 CAGGGAAA -s Anc1.Anc1refChr3 1718 8 + 3661 CAGGGAAA -s Anc2.Anc2refChr8 1717 8 + 12804 CAGGGAAA -s mr.mrrefChr5 159314 8 + 294540 CATGAAAA -s mr.mrrefChr5 162106 8 + 294540 CTGGGCAA -s simCow_chr6.simCow.chr6 281246 8 + 602619 CAGGAAGA -s simDog_chr6.simDog.chr6 317587 8 - 593897 AAGGGAAA -s simHuman_chr6.simHuman.chr6 228028 8 + 601863 CAGGGCAA -s simMouse_chr6.simMouse.chr6 311863 8 + 636262 CTGGGCAA -s simRat_chr6.simRat.chr6 303486 8 + 647215 CTGGGCAA -s simRat_chr6.simRat.chr6 300571 8 + 647215 CATGAAAA - -a -s simMouse_chr6.simMouse.chr6 308715 4 + 636262 TACT -s Anc0.Anc0refChr8 1668 3 + 17196 AGA- -s Anc1.Anc1refChr3 1726 4 + 3661 AGAT -s Anc2.Anc2refChr8 1725 3 + 12804 AGA- -s mr.mrrefChr5 159322 4 + 294540 TGCT -s simCow_chr6.simCow.chr6 281254 3 + 602619 AGA- -s simDog_chr6.simDog.chr6 317595 3 - 593897 AAA- -s simHuman_chr6.simHuman.chr6 228036 4 + 601863 AGAT -s simRat_chr6.simRat.chr6 300579 4 + 647215 TGCT - -a -s simMouse_chr6.simMouse.chr6 308719 3 + 636262 GGT -s Anc1.Anc1refChr3 1730 3 + 3661 AGA -s mr.mrrefChr5 159326 3 + 294540 GGT -s mr.mrrefChr5 162114 3 + 294540 AAA -s simHuman_chr6.simHuman.chr6 228040 3 + 601863 AGT -s simMouse_chr6.simMouse.chr6 311871 3 + 636262 AAA -s simRat_chr6.simRat.chr6 303494 3 + 647215 AAA -s simRat_chr6.simRat.chr6 300583 3 + 647215 GGG - -a -s simMouse_chr6.simMouse.chr6 308722 8 + 636262 CAAGACAA -s Anc0.Anc0refChr8 1671 8 + 17196 CAAAACCA -s Anc1.Anc1refChr3 1733 8 + 3661 CAAAACCA -s Anc2.Anc2refChr8 1728 8 + 12804 AAAAACCA -s mr.mrrefChr5 159329 8 + 294540 CAAAACAA -s mr.mrrefChr5 162117 8 + 294540 CAAAACCA -s simCow_chr6.simCow.chr6 281257 8 + 602619 AGAAATCA -s simDog_chr6.simDog.chr6 317598 8 - 593897 AAAAACCA -s simHuman_chr6.simHuman.chr6 228043 8 + 601863 TAAAGCCA -s simMouse_chr6.simMouse.chr6 311874 8 + 636262 CAAAACCA -s simRat_chr6.simRat.chr6 303503 8 + 647215 CAAAACCA -s simRat_chr6.simRat.chr6 300586 8 + 647215 CACAACAA - -a -s simMouse_chr6.simMouse.chr6 308730 10 + 636262 ATATTATACC -s Anc0.Anc0refChr8 1687 10 + 17196 TTATTATGCT -s Anc1.Anc1refChr3 1749 10 + 3661 TTATTATGCT -s Anc2.Anc2refChr8 1744 10 + 12804 TTATTATGCT -s mr.mrrefChr5 159337 10 + 294540 ATATTATGCC -s mr.mrrefChr5 162125 10 + 294540 TTGTTTTATC -s simCow_chr6.simCow.chr6 281274 10 + 602619 TTATCATGCT -s simDog_chr6.simDog.chr6 317614 10 - 593897 TTATTATGCT -s simHuman_chr6.simHuman.chr6 228059 10 + 601863 TTATTATGCT -s simMouse_chr6.simMouse.chr6 311882 10 + 636262 TTGTTTTATC -s simRat_chr6.simRat.chr6 303511 10 + 647215 TCACGTTAGC -s simRat_chr6.simRat.chr6 300594 10 + 647215 ATATTATGAC - -a -s simMouse_chr6.simMouse.chr6 308740 10 + 636262 CTGTAAGAAG -s Anc0.Anc0refChr8 1697 10 + 17196 CCATAAGAAG -s Anc1.Anc1refChr3 1759 10 + 3661 CCATAAGAAG -s Anc2.Anc2refChr8 1754 10 + 12804 CCATAAGAGG -s mr.mrrefChr5 159347 10 + 294540 CTATAAGAAG -s simCow_chr6.simCow.chr6 281284 10 + 602619 CCATAGGAGG -s simDog_chr6.simDog.chr6 317624 10 - 593897 CCATAAGAGG -s simHuman_chr6.simHuman.chr6 228069 10 + 601863 CCATGAGCAG -s simRat_chr6.simRat.chr6 300604 10 + 647215 CTATAAGAAG - -a -s simMouse_chr6.simMouse.chr6 308750 2 + 636262 TG -s Anc0.Anc0refChr8 1707 2 + 17196 TG -s Anc1.Anc1refChr3 1769 2 + 3661 TG -s Anc2.Anc2refChr8 1764 2 + 12804 TG -s mr.mrrefChr5 159357 2 + 294540 TG -s mr.mrrefChr5 162135 2 + 294540 TA -s simCow_chr6.simCow.chr6 281294 2 + 602619 TG -s simDog_chr6.simDog.chr6 317634 2 - 593897 TG -s simHuman_chr6.simHuman.chr6 228079 2 + 601863 TA -s simMouse_chr6.simMouse.chr6 311892 2 + 636262 TA -s simRat_chr6.simRat.chr6 303521 2 + 647215 TA -s simRat_chr6.simRat.chr6 300614 2 + 647215 TG - -a -s simMouse_chr6.simMouse.chr6 308752 46 + 636262 AATGTTAGCTTTTCACTTTGGCACAAGGTGGCCAACAATTTGACAT -s Anc0.Anc0refChr8 1709 46 + 17196 GATGATAGCTTTACACATCAGTACAAGATGGCCAGCAATTTGGCAT -s Anc1.Anc1refChr3 1771 46 + 3661 GATGATAGCTTTACACATCAGTACAAGATGGCCAGCAATTTGGCAT -s Anc2.Anc2refChr8 1766 46 + 12804 GATGATAGGTCTACACATCAGTACAACATGGCCAGAAATTTGGCAC -s mr.mrrefChr5 159359 46 + 294540 AATGATAGCTTTTCACATTGGTACAAGGTGGCCAGCAATTTGACAT -s mr.mrrefChr5 162137 46 + 294540 GATAATAACTTTATAAATCAGCACAAAATGCTCAGCAACTTGGAAT -s simCow_chr6.simCow.chr6 281296 46 + 602619 GATGATAGATGTCTGCATCAGTGCAATGTGGACAGAAATCTGGCAG -s simDog_chr6.simDog.chr6 317636 46 - 593897 AATGAGAGGGCTACACATCAGTACTACATGGCCAGAAAATTGGCAC -s simHuman_chr6.simHuman.chr6 228081 46 + 601863 GATGATAGCTTTACACATCAGTACAAGATCGCAAGTAATTTGGCTT -s simMouse_chr6.simMouse.chr6 311895 46 + 636262 GATAATAACTTTATAAATCAGCACAAAATGCTCAGCAACTTGGAAT -s simRat_chr6.simRat.chr6 303523 46 + 647215 GACGCTAACTTTATAGATCAGCACAAAATGTCCAGCAATTTGGAAT -s simRat_chr6.simRat.chr6 300616 45 + 647215 AATCATAGCTTTCCACATTGATACAAGGTGGCCAGCA-TTTGACGT - -a -s simMouse_chr6.simMouse.chr6 308798 10 + 636262 GTTGTTTCAC -s Anc0.Anc0refChr8 1755 8 + 17196 ATTGTTTT-- -s Anc1.Anc1refChr3 1817 8 + 3661 ATTGTTTT-- -s Anc2.Anc2refChr8 1812 8 + 12804 ACTGTTTT-- -s mr.mrrefChr5 159405 8 + 294540 GTTGTTTC-- -s mr.mrrefChr5 162183 8 + 294540 CTCTTTCT-- -s simCow_chr6.simCow.chr6 281342 8 + 602619 ACTGTTTT-- -s simDog_chr6.simDog.chr6 317682 8 - 593897 ACCCTTTG-- -s simHuman_chr6.simHuman.chr6 228127 8 + 601863 ATTGTTTT-- -s simMouse_chr6.simMouse.chr6 311942 8 + 636262 CTCTTTCT-- -s simRat_chr6.simRat.chr6 303569 8 + 647215 CTCTTTTT-- -s simRat_chr6.simRat.chr6 300661 8 + 647215 GTTGTTTA-- - -a -s simMouse_chr6.simMouse.chr6 308808 17 + 636262 TCCTCTGACAAGATTTC -s Anc0.Anc0refChr8 1764 17 + 17196 TCCTCTGATGAGATTTT -s Anc1.Anc1refChr3 1826 17 + 3661 TCCTCTGATGAGATTTT -s Anc2.Anc2refChr8 1821 17 + 12804 TCCTTTGATGAGAGCAT -s mr.mrrefChr5 159413 17 + 294540 TCCTCTGATAAGATTTC -s mr.mrrefChr5 162191 17 + 294540 TCTACTGCCATGATTTT -s simCow_chr6.simCow.chr6 281351 17 + 602619 CCCTTAGATAAAACTGT -s simDog_chr6.simDog.chr6 317691 17 - 593897 TCCTTTGATGAGAGCAT -s simHuman_chr6.simHuman.chr6 228136 17 + 601863 TCCTCTGATGAGATTTC -s simMouse_chr6.simMouse.chr6 311950 17 + 636262 TCTACTGCCATGATTTT -s simRat_chr6.simRat.chr6 303577 17 + 647215 TCTACAGCCATGATTTT -s simRat_chr6.simRat.chr6 300669 17 + 647215 TTCCCTAATAAGATTTT - -a -s simMouse_chr6.simMouse.chr6 308825 1 + 636262 T -s Anc0.Anc0refChr8 1782 1 + 17196 T -s Anc1.Anc1refChr3 1844 1 + 3661 T -s Anc2.Anc2refChr8 1839 1 + 12804 T -s mr.mrrefChr5 159430 1 + 294540 T -s mr.mrrefChr5 162209 1 + 294540 T -s simCow_chr6.simCow.chr6 281369 1 + 602619 T -s simDog_chr6.simDog.chr6 317709 1 - 593897 T -s simMouse_chr6.simMouse.chr6 311968 1 + 636262 T -s simRat_chr6.simRat.chr6 303595 1 + 647215 T -s simRat_chr6.simRat.chr6 300686 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 308826 7 + 636262 CTTGCAC -s Anc0.Anc0refChr8 1783 7 + 17196 CTTGTAC -s Anc1.Anc1refChr3 1845 7 + 3661 CTTGTAC -s Anc2.Anc2refChr8 1840 7 + 12804 CTTCTAC -s mr.mrrefChr5 159431 7 + 294540 CTTGCAC -s mr.mrrefChr5 162210 7 + 294540 CTTGTAC -s simCow_chr6.simCow.chr6 281370 7 + 602619 CTCCCAC -s simDog_chr6.simDog.chr6 317752 7 - 593897 CTTCTAC -s simMouse_chr6.simMouse.chr6 311969 7 + 636262 CTTGTAC -s simRat_chr6.simRat.chr6 303596 7 + 647215 CTTGTAC -s simRat_chr6.simRat.chr6 300687 7 + 647215 CTTGCAC - -a -s simMouse_chr6.simMouse.chr6 308833 26 + 636262 TGCCTGATGTTCATCTAACTCTAGCC -s Anc0.Anc0refChr8 1793 25 + 17196 C-CCTGATATTCTTCCACCTCTAGCC -s Anc1.Anc1refChr3 1855 25 + 3661 C-CCTGATATTCTTCCACCTCTAGCC -s Anc2.Anc2refChr8 1850 25 + 12804 C-CCTGATATTCCTCCACCTCTAGCC -s mr.mrrefChr5 159438 25 + 294540 T-CCTGATGTTCTTCTACCTCTAGCC -s mr.mrrefChr5 162220 25 + 294540 C-CCTGGCACACTTTAACCTCTAGCC -s simCow_chr6.simCow.chr6 281380 23 + 602619 C-TCTGATATCCCTCTAC--CTAGCC -s simDog_chr6.simDog.chr6 317762 25 - 593897 C-CCGGATATTCCTACACCTCCAGCC -s simHuman_chr6.simHuman.chr6 228153 24 + 601863 --CCTGATGTTCTTCCACCTCTAGAC -s simMouse_chr6.simMouse.chr6 311979 25 + 636262 C-CCTGGCACACTTTAACCTCTAGCC -s simRat_chr6.simRat.chr6 303607 25 + 647215 C-CCTGACATCCTTTAACCTCTGGCC -s simRat_chr6.simRat.chr6 300694 25 + 647215 T-CCTGATGTTCTTCTACATCTAGCA - -a -s simMouse_chr6.simMouse.chr6 308859 4 + 636262 TGCG -s Anc0.Anc0refChr8 1818 4 + 17196 TGTG -s Anc1.Anc1refChr3 1880 4 + 3661 TGTG -s Anc2.Anc2refChr8 1875 4 + 12804 TGTG -s mr.mrrefChr5 159463 4 + 294540 TGTG -s mr.mrrefChr5 162246 4 + 294540 TGTA -s simCow_chr6.simCow.chr6 281403 4 + 602619 TGTC -s simDog_chr6.simDog.chr6 317787 4 - 593897 TGTG -s simHuman_chr6.simHuman.chr6 228177 4 + 601863 TGTA -s simMouse_chr6.simMouse.chr6 312005 4 + 636262 TGTA -s simRat_chr6.simRat.chr6 303633 4 + 647215 TGTA -s simRat_chr6.simRat.chr6 300719 4 + 647215 TATG - -a -s simMouse_chr6.simMouse.chr6 308863 3 + 636262 AAC -s Anc0.Anc0refChr8 1822 3 + 17196 TAT -s Anc1.Anc1refChr3 1884 3 + 3661 TAT -s Anc2.Anc2refChr8 1879 3 + 12804 TAT -s mr.mrrefChr5 159467 3 + 294540 AAC -s simCow_chr6.simCow.chr6 281407 3 + 602619 TAC -s simDog_chr6.simDog.chr6 317791 3 - 593897 CAT -s simHuman_chr6.simHuman.chr6 228181 3 + 601863 TAT -s simRat_chr6.simRat.chr6 300723 3 + 647215 AAC - -a -s simMouse_chr6.simMouse.chr6 308866 12 + 636262 TTAGAATAACAT -s Anc0.Anc0refChr8 1825 12 + 17196 TCAGAATAAAAT -s Anc1.Anc1refChr3 1887 12 + 3661 TCAGAATAAAAT -s Anc2.Anc2refChr8 1882 12 + 12804 TCAGAATAAAAT -s mr.mrrefChr5 159470 12 + 294540 TCAGAATAAAAT -s mr.mrrefChr5 162250 12 + 294540 TCAGAGTGAACT -s simCow_chr6.simCow.chr6 281410 12 + 602619 TCAGAATATAAT -s simDog_chr6.simDog.chr6 317794 12 - 593897 TCAGAGTAAAAT -s simHuman_chr6.simHuman.chr6 228184 12 + 601863 TCAGAATAAACT -s simMouse_chr6.simMouse.chr6 312009 12 + 636262 TCAGAGTGAACT -s simRat_chr6.simRat.chr6 303637 12 + 647215 TCAGAATAAAGT -s simRat_chr6.simRat.chr6 300726 12 + 647215 TCAGAATAAAAT - -a -s simMouse_chr6.simMouse.chr6 308878 1 + 636262 G -s Anc0.Anc0refChr8 1837 1 + 17196 G -s Anc1.Anc1refChr3 1899 1 + 3661 G -s Anc2.Anc2refChr8 1894 1 + 12804 G -s mr.mrrefChr5 159482 1 + 294540 G -s mr.mrrefChr5 162262 1 + 294540 A -s simCow_chr6.simCow.chr6 281422 1 + 602619 G -s simDog_chr6.simDog.chr6 317806 1 - 593897 G -s simHuman_chr6.simHuman.chr6 228196 1 + 601863 A -s simMouse_chr6.simMouse.chr6 312023 1 + 636262 A -s simRat_chr6.simRat.chr6 303649 1 + 647215 A -s simRat_chr6.simRat.chr6 300738 1 + 647215 G - -a -s simMouse_chr6.simMouse.chr6 308879 9 + 636262 AGGGTGGCC -s Anc0.Anc0refChr8 1840 5 + 17196 GTT----CC -s Anc1.Anc1refChr3 1902 9 + 3661 GTTTTTGCC -s Anc2.Anc2refChr8 1897 5 + 12804 GTT----CT -s mr.mrrefChr5 159483 9 + 294540 AGGGTGGCC -s mr.mrrefChr5 162263 9 + 294540 GCATTTGCC -s simCow_chr6.simCow.chr6 281425 5 + 602619 GTT----CT -s simDog_chr6.simDog.chr6 317809 5 - 593897 GAT----CT -s simHuman_chr6.simHuman.chr6 228199 9 + 601863 GTTTCTGCA -s simMouse_chr6.simMouse.chr6 312024 9 + 636262 GCATTTGCC -s simRat_chr6.simRat.chr6 303650 9 + 647215 GCATTTGCC -s simRat_chr6.simRat.chr6 300739 9 + 647215 AGGGTGGCC - -a -s simMouse_chr6.simMouse.chr6 308888 3 + 636262 CCT -s mr.mrrefChr5 159492 3 + 294540 CAT -s simRat_chr6.simRat.chr6 300748 3 + 647215 CAT - -a -s simMouse_chr6.simMouse.chr6 308891 2 + 636262 TG -s Anc0.Anc0refChr8 1845 2 + 17196 TT -s Anc1.Anc1refChr3 1911 2 + 3661 TT -s Anc2.Anc2refChr8 1902 2 + 12804 TT -s mr.mrrefChr5 159495 2 + 294540 TG -s mr.mrrefChr5 162272 2 + 294540 TG -s simCow_chr6.simCow.chr6 281430 2 + 602619 TT -s simDog_chr6.simDog.chr6 317814 2 - 593897 TT -s simHuman_chr6.simHuman.chr6 228208 2 + 601863 TT -s simMouse_chr6.simMouse.chr6 312033 2 + 636262 TG -s simRat_chr6.simRat.chr6 303659 2 + 647215 TT -s simRat_chr6.simRat.chr6 300751 2 + 647215 TG - -a -s simMouse_chr6.simMouse.chr6 308893 4 + 636262 CTTC -s Anc0.Anc0refChr8 1850 4 + 17196 CTTT -s Anc1.Anc1refChr3 1916 4 + 3661 CTTT -s Anc2.Anc2refChr8 1907 4 + 12804 CTTT -s mr.mrrefChr5 159500 4 + 294540 CTTT -s mr.mrrefChr5 162277 4 + 294540 GTTT -s simCow_chr6.simCow.chr6 281435 4 + 602619 CTTT -s simDog_chr6.simDog.chr6 317819 4 - 593897 CTTT -s simHuman_chr6.simHuman.chr6 228213 4 + 601863 CTCT -s simMouse_chr6.simMouse.chr6 312038 4 + 636262 GTTT -s simRat_chr6.simRat.chr6 303664 4 + 647215 GTTT -s simRat_chr6.simRat.chr6 300756 4 + 647215 CTTT - -a -s simMouse_chr6.simMouse.chr6 308897 5 + 636262 GTAAC -s Anc0.Anc0refChr8 1913 5 + 17196 GTAAT -s Anc1.Anc1refChr3 1980 5 + 3661 GTAAT -s Anc2.Anc2refChr8 1970 5 + 12804 TTCAC -s mr.mrrefChr5 159504 5 + 294540 GTAAT -s mr.mrrefChr5 162383 5 + 294540 GTAAT -s simCow_chr6.simCow.chr6 281496 5 + 602619 TACAC -s simDog_chr6.simDog.chr6 317881 5 - 593897 TTCAC -s simMouse_chr6.simMouse.chr6 312153 5 + 636262 GTAAT -s simRat_chr6.simRat.chr6 303776 5 + 647215 GTAAT -s simRat_chr6.simRat.chr6 300760 5 + 647215 GTAAT - -a -s simMouse_chr6.simMouse.chr6 308902 1 + 636262 C -s Anc0.Anc0refChr8 1918 1 + 17196 C -s Anc1.Anc1refChr3 1985 1 + 3661 C -s Anc2.Anc2refChr8 1975 1 + 12804 C -s mr.mrrefChr5 159509 1 + 294540 C -s mr.mrrefChr5 162396 1 + 294540 C -s simCow_chr6.simCow.chr6 281501 1 + 602619 C -s simDog_chr6.simDog.chr6 317886 1 - 593897 C -s simMouse_chr6.simMouse.chr6 312166 1 + 636262 C -s simRat_chr6.simRat.chr6 303789 1 + 647215 C -s simRat_chr6.simRat.chr6 300765 1 + 647215 C - -a -s simMouse_chr6.simMouse.chr6 308903 13 + 636262 ATGACATGTGACC -s Anc0.Anc0refChr8 1919 12 + 17196 ACGAGGT-TGTCC -s Anc1.Anc1refChr3 1986 12 + 3661 ACGAGGT-TGTCC -s Anc2.Anc2refChr8 1976 12 + 12804 TAGAGGG-TACAC -s mr.mrrefChr5 159510 12 + 294540 ATGACGT-TGTCC -s mr.mrrefChr5 162397 12 + 294540 ACTAGGT-ACTCC -s simCow_chr6.simCow.chr6 281502 12 + 602619 TTAAGGG-TACAC -s simDog_chr6.simDog.chr6 317891 12 - 593897 TAGAGGG-TACAC -s simMouse_chr6.simMouse.chr6 312167 12 + 636262 ACTAGGT-ACTCC -s simRat_chr6.simRat.chr6 303790 12 + 647215 ACTAGGT-ACTCC -s simRat_chr6.simRat.chr6 300766 10 + 647215 A--GCGT-TGTCC - -a -s simMouse_chr6.simMouse.chr6 308916 6 + 636262 TTATTT -s Anc0.Anc0refChr8 1931 6 + 17196 ATATTT -s Anc1.Anc1refChr3 1998 6 + 3661 ATATTT -s Anc2.Anc2refChr8 2016 6 + 12804 ATATTT -s mr.mrrefChr5 159522 6 + 294540 TTATTT -s mr.mrrefChr5 162409 6 + 294540 ATGTTT -s simCow_chr6.simCow.chr6 281542 4 + 602619 ATA--T -s simDog_chr6.simDog.chr6 317945 6 - 593897 TCATTT -s simHuman_chr6.simHuman.chr6 228276 6 + 601863 ATATTT -s simMouse_chr6.simMouse.chr6 312179 6 + 636262 ATGTTT -s simRat_chr6.simRat.chr6 303802 6 + 647215 ACATTT -s simRat_chr6.simRat.chr6 300776 6 + 647215 TTATTT - -a -s simMouse_chr6.simMouse.chr6 308922 27 + 636262 ACCTGTAGAACAAAGGTTTGACCTTGG -s Anc0.Anc0refChr8 1937 27 + 17196 ACTTGAAGGAAGAAGGTCTGACCTTGA -s Anc1.Anc1refChr3 2004 27 + 3661 ACTTGAAGGAAGAAGGTCTGACCTTGA -s Anc2.Anc2refChr8 2022 27 + 12804 ACTTGAAGGAAGAAGGTCTGACCTTGA -s mr.mrrefChr5 159528 27 + 294540 ACCTGTAGGACAAAGGTCTGACCTTGG -s mr.mrrefChr5 162417 27 + 294540 ACTTGAAGGAAAAAGGTCTGACCCCTA -s simCow_chr6.simCow.chr6 281546 27 + 602619 GCTTGAATGAAGAAGGTCTGACCTTGA -s simDog_chr6.simDog.chr6 317951 24 - 593897 ACTT---GAAAGAAGGTCTGACCTTGA -s simHuman_chr6.simHuman.chr6 228282 27 + 601863 ACTTAAAGGAAGAAGGTCTGGCCTCAA -s simMouse_chr6.simMouse.chr6 312187 27 + 636262 ACTTGAAGGAAAAAGGTCTGACCCCTA -s simRat_chr6.simRat.chr6 303810 27 + 647215 ACCTGAAGGAAAAAGGTCTAACCCCAA -s simRat_chr6.simRat.chr6 300782 27 + 647215 ACCTGTAGGACAAAAGTCTGACCTTGG - -a -s simMouse_chr6.simMouse.chr6 308949 18 + 636262 TTTCCACTGAATTCAGCC -s Anc0.Anc0refChr8 1964 18 + 17196 TTTCCACTTATATCAACT -s Anc1.Anc1refChr3 2031 18 + 3661 TTTCCACTTATATCAACT -s Anc2.Anc2refChr8 2049 18 + 12804 TTTGCACTTATATCAATT -s mr.mrrefChr5 159555 18 + 294540 TTTCCACTGAAATCAACT -s mr.mrrefChr5 162444 18 + 294540 CTCCCATTTATGTCAACT -s simCow_chr6.simCow.chr6 281574 18 + 602619 TTTCCACTTATATCACAT -s simDog_chr6.simDog.chr6 317975 18 - 593897 GTTGCATTTGTATCAATT -s simHuman_chr6.simHuman.chr6 228309 18 + 601863 TTTTAACTCATATCTACT -s simMouse_chr6.simMouse.chr6 312214 18 + 636262 CTCCCATTTATGTCAACT -s simRat_chr6.simRat.chr6 303837 18 + 647215 CTCCCATTTATGTCAGCA -s simRat_chr6.simRat.chr6 300809 18 + 647215 TTGCTGCCGAAATCAAct - -a -s simMouse_chr6.simMouse.chr6 308967 18 + 636262 AGTTTTAATATTGCTCTT -s Anc0.Anc0refChr8 1983 18 + 17196 agattcaatatcgctctt -s Anc1.Anc1refChr3 2050 18 + 3661 AGATtcaatatcgctctt -s Anc2.Anc2refChr8 2068 18 + 12804 ggatccaatatcgctctt -s mr.mrrefChr5 159573 18 + 294540 AGTTtcaatattgctctt -s mr.mrrefChr5 162463 18 + 294540 AGATTCAGTACCACTTTC -s simCow_chr6.simCow.chr6 281593 18 + 602619 ggatcaaataccgctcct -s simDog_chr6.simDog.chr6 317994 18 - 593897 ggatccaatattgctctt -s simHuman_chr6.simHuman.chr6 228328 18 + 601863 ACGCtcaatatcactctc -s simMouse_chr6.simMouse.chr6 312233 18 + 636262 AGATTCAGTACCACTTTC -s simRat_chr6.simRat.chr6 303856 18 + 647215 AGATTCTATATCACTTTC -s simRat_chr6.simRat.chr6 300827 17 + 647215 agtttcaatat-gttctt - -a -s simMouse_chr6.simMouse.chr6 308985 2 + 636262 GT -s Anc0.Anc0refChr8 2001 2 + 17196 ct -s Anc1.Anc1refChr3 2068 2 + 3661 ct -s Anc2.Anc2refChr8 2086 2 + 12804 ct -s mr.mrrefChr5 159591 2 + 294540 gt -s mr.mrrefChr5 162481 2 + 294540 CT -s simCow_chr6.simCow.chr6 281611 2 + 602619 ct -s simDog_chr6.simDog.chr6 318018 2 - 593897 ct -s simHuman_chr6.simHuman.chr6 228346 2 + 601863 ct -s simMouse_chr6.simMouse.chr6 312251 2 + 636262 CT -s simRat_chr6.simRat.chr6 303874 2 + 647215 CT -s simRat_chr6.simRat.chr6 300844 2 + 647215 gt - -a -s simMouse_chr6.simMouse.chr6 308987 1 + 636262 A -s Anc0.Anc0refChr8 2003 1 + 17196 a -s Anc1.Anc1refChr3 2070 1 + 3661 a -s Anc2.Anc2refChr8 2088 1 + 12804 a -s mr.mrrefChr5 159593 1 + 294540 a -s simCow_chr6.simCow.chr6 281613 1 + 602619 a -s simDog_chr6.simDog.chr6 318020 1 - 593897 a -s simHuman_chr6.simHuman.chr6 228348 1 + 601863 a -s simRat_chr6.simRat.chr6 300846 1 + 647215 a - -a -s simMouse_chr6.simMouse.chr6 308988 5 + 636262 GTTTG -s Anc0.Anc0refChr8 2004 5 + 17196 gtttg -s Anc1.Anc1refChr3 2071 5 + 3661 gtttg -s Anc2.Anc2refChr8 2089 5 + 12804 gttca -s mr.mrrefChr5 159594 5 + 294540 gtttg -s mr.mrrefChr5 162483 5 + 294540 GTCTG -s simCow_chr6.simCow.chr6 281614 5 + 602619 gttca -s simDog_chr6.simDog.chr6 318021 5 - 593897 gttca -s simHuman_chr6.simHuman.chr6 228349 5 + 601863 gtttg -s simMouse_chr6.simMouse.chr6 312253 5 + 636262 GTCTG -s simRat_chr6.simRat.chr6 303877 5 + 647215 GTTTA -s simRat_chr6.simRat.chr6 300847 5 + 647215 gtctg - -a -s simMouse_chr6.simMouse.chr6 308993 8 + 636262 TTCCTAAC -s Anc0.Anc0refChr8 2009 8 + 17196 gttatgtg -s Anc1.Anc1refChr3 2076 8 + 3661 gttatgtg -s Anc2.Anc2refChr8 2094 8 + 12804 gttatgtg -s mr.mrrefChr5 159599 8 + 294540 gtcctaac -s mr.mrrefChr5 162517 8 + 294540 GTCATGAC -s simCow_chr6.simCow.chr6 281619 8 + 602619 gttatgag -s simDog_chr6.simDog.chr6 318026 8 - 593897 gtcatgtg -s simHuman_chr6.simHuman.chr6 228354 8 + 601863 gttttatg -s simMouse_chr6.simMouse.chr6 312287 8 + 636262 GTCATGAC -s simRat_chr6.simRat.chr6 303911 8 + 647215 GTCATGGC -s simRat_chr6.simRat.chr6 300852 8 + 647215 gtcctaac - -a -s simMouse_chr6.simMouse.chr6 309001 1 + 636262 A -s Anc0.Anc0refChr8 2017 1 + 17196 a -s Anc1.Anc1refChr3 2084 1 + 3661 a -s Anc2.Anc2refChr8 2102 1 + 12804 a -s mr.mrrefChr5 159607 1 + 294540 a -s mr.mrrefChr5 162525 1 + 294540 A -s simCow_chr6.simCow.chr6 281663 1 + 602619 a -s simDog_chr6.simDog.chr6 318034 1 - 593897 g -s simHuman_chr6.simHuman.chr6 228362 1 + 601863 a -s simMouse_chr6.simMouse.chr6 312295 1 + 636262 A -s simRat_chr6.simRat.chr6 303919 1 + 647215 A -s simRat_chr6.simRat.chr6 300860 1 + 647215 a - -a -s simMouse_chr6.simMouse.chr6 309002 9 + 636262 Gtgcaacac -s Anc0.Anc0refChr8 2020 9 + 17196 gtgtgacac -s Anc1.Anc1refChr3 2087 9 + 3661 gtgtgacac -s Anc2.Anc2refChr8 2105 9 + 12804 gtgtgacac -s mr.mrrefChr5 159608 9 + 294540 gtgcaacac -s mr.mrrefChr5 162528 9 + 294540 GTGAGACAC -s simCow_chr6.simCow.chr6 281666 9 + 602619 ctgtgacac -s simDog_chr6.simDog.chr6 318038 9 - 593897 gtatgacat -s simHuman_chr6.simHuman.chr6 228365 9 + 601863 gtgtgatgc -s simMouse_chr6.simMouse.chr6 312298 9 + 636262 GTGAGACAC -s simRat_chr6.simRat.chr6 303922 9 + 647215 GTGAGATAC -s simRat_chr6.simRat.chr6 300861 9 + 647215 atgcaacac - -a -s simMouse_chr6.simMouse.chr6 309011 41 + 636262 agcttgagtggtcccactttcaaggcctccaggttgagaAT -s Anc0.Anc0refChr8 2029 41 + 17196 agcttgaggggtcccattttcaaaagtttcaggttgcaatt -s Anc1.Anc1refChr3 2096 41 + 3661 agcttgaggggtcccattttcaaaagtttcaggttgcaatt -s Anc2.Anc2refChr8 2114 41 + 12804 cgctaaaggggtcccagttttaaaagtttcaggttgcaatt -s mr.mrrefChr5 159617 41 + 294540 agcttgagtggtcccactttcaaggcctccaggttgagaat -s mr.mrrefChr5 162572 41 + 294540 agttgcaggagtcccatgttgacaggattctggttctgagt -s simCow_chr6.simCow.chr6 281675 41 + 602619 agcttgaggtgttcccactttgaaaatttcatgtagcagtt -s simDog_chr6.simDog.chr6 318047 37 - 593897 cgctaaaagggtcccagttttaaaggtt--aggatgcaa-- -s simHuman_chr6.simHuman.chr6 228374 37 + 601863 ----tgaggggcctcattctcaaaacttacaggttgcaatt -s simMouse_chr6.simMouse.chr6 312342 41 + 636262 AGTTGCAGGAGTCCCATGTTGACAGGATTCTGGTTCTGAGT -s simRat_chr6.simRat.chr6 304001 41 + 647215 agctgcaagggtcccattttgacaggattctggttctgatt -s simRat_chr6.simRat.chr6 300870 41 + 647215 agcttaagaggtcccactttcaaggcctccagtttgtgaat - -a -s simMouse_chr6.simMouse.chr6 309052 1 + 636262 T -s mr.mrrefChr5 159658 1 + 294540 t -s simRat_chr6.simRat.chr6 300911 1 + 647215 c - -a -s simMouse_chr6.simMouse.chr6 309053 13 + 636262 AAGATGTGATGCA -s Anc0.Anc0refChr8 2070 13 + 17196 aagatgtaataca -s Anc1.Anc1refChr3 2137 13 + 3661 aagatgtaataca -s Anc2.Anc2refChr8 2155 13 + 12804 aggagccaataca -s mr.mrrefChr5 159659 13 + 294540 aagatgtgctgca -s mr.mrrefChr5 162613 13 + 294540 atgatgtgataca -s simCow_chr6.simCow.chr6 281716 13 + 602619 aggagccaataca -s simDog_chr6.simDog.chr6 318084 4 - 593897 ---------gaca -s simHuman_chr6.simHuman.chr6 228411 13 + 601863 aaagtttactaca -s simMouse_chr6.simMouse.chr6 312383 13 + 636262 ATGATGTGATACA -s simRat_chr6.simRat.chr6 304042 13 + 647215 ataatgtgagaca -s simRat_chr6.simRat.chr6 300912 13 + 647215 aggatgtcctgca - -a -s simMouse_chr6.simMouse.chr6 309066 3 + 636262 CCA -s mr.mrrefChr5 159672 3 + 294540 gca -s simRat_chr6.simRat.chr6 300925 3 + 647215 gta - -a -s simMouse_chr6.simMouse.chr6 309069 12 + 636262 ACTAGAGGGTTC -s Anc0.Anc0refChr8 2083 12 + 17196 gcttgagggacc -s Anc1.Anc1refChr3 2150 12 + 3661 gcttgagggacc -s Anc2.Anc2refChr8 2168 12 + 12804 gcttgagggacc -s mr.mrrefChr5 159675 12 + 294540 actagagggttc -s mr.mrrefChr5 162626 12 + 294540 gcttaagagatc -s simCow_chr6.simCow.chr6 281729 12 + 602619 ccatgagggatc -s simDog_chr6.simDog.chr6 318088 12 - 593897 gcttgaggggcc -s simHuman_chr6.simHuman.chr6 228424 12 + 601863 gcttgagggacc -s simMouse_chr6.simMouse.chr6 312396 12 + 636262 GCTTAAGAGATC -s simRat_chr6.simRat.chr6 304055 12 + 647215 gcttaatggatt -s simRat_chr6.simRat.chr6 300928 12 + 647215 gttggagggttc - -a -s simMouse_chr6.simMouse.chr6 309081 6 + 636262 CCTGTT -s Anc0.Anc0refChr8 2095 6 + 17196 ccagtt -s Anc1.Anc1refChr3 2162 6 + 3661 ccagtt -s Anc2.Anc2refChr8 2180 6 + 12804 acagtt -s mr.mrrefChr5 159687 6 + 294540 ccagtt -s mr.mrrefChr5 162638 6 + 294540 gtacta -s simCow_chr6.simCow.chr6 281741 6 + 602619 atagtt -s simDog_chr6.simDog.chr6 318100 6 - 593897 acagtc -s simHuman_chr6.simHuman.chr6 228436 6 + 601863 ccagat -s simMouse_chr6.simMouse.chr6 312411 6 + 636262 GTACTA -s simRat_chr6.simRat.chr6 304067 6 + 647215 gtactt -s simRat_chr6.simRat.chr6 300940 6 + 647215 ccagtt - -a -s simMouse_chr6.simMouse.chr6 309087 3 + 636262 TTA -s Anc0.Anc0refChr8 2101 3 + 17196 aca -s Anc1.Anc1refChr3 2168 3 + 3661 aca -s Anc2.Anc2refChr8 2186 3 + 12804 aca -s mr.mrrefChr5 159693 3 + 294540 tta -s simCow_chr6.simCow.chr6 281747 3 + 602619 cta -s simDog_chr6.simDog.chr6 318106 3 - 593897 aca -s simRat_chr6.simRat.chr6 300946 3 + 647215 tta - -a -s simMouse_chr6.simMouse.chr6 309090 10 + 636262 GGACTTACAG -s Anc0.Anc0refChr8 2104 7 + 17196 agattt---t -s Anc1.Anc1refChr3 2171 10 + 3661 agatttccat -s Anc2.Anc2refChr8 2189 7 + 12804 agattt---t -s mr.mrrefChr5 159696 10 + 294540 ggacttacag -s mr.mrrefChr5 162644 10 + 294540 agatttccag -s simCow_chr6.simCow.chr6 281750 7 + 602619 agattt---t -s simDog_chr6.simDog.chr6 318109 7 - 593897 agattt---t -s simHuman_chr6.simHuman.chr6 228442 10 + 601863 tgaattctat -s simMouse_chr6.simMouse.chr6 312417 10 + 636262 AGATTTCCAG -s simRat_chr6.simRat.chr6 304073 10 + 647215 aggctgccag -s simRat_chr6.simRat.chr6 300949 10 + 647215 ggacttccag - -a -s simMouse_chr6.simMouse.chr6 309100 1 + 636262 T -s Anc0.Anc0refChr8 2122 1 + 17196 t -s Anc1.Anc1refChr3 2192 1 + 3661 t -s Anc2.Anc2refChr8 2207 1 + 12804 t -s mr.mrrefChr5 159706 1 + 294540 T -s mr.mrrefChr5 162664 1 + 294540 t -s simCow_chr6.simCow.chr6 281768 1 + 602619 t -s simDog_chr6.simDog.chr6 318127 1 - 593897 c -s simHuman_chr6.simHuman.chr6 228463 1 + 601863 t -s simMouse_chr6.simMouse.chr6 312437 1 + 636262 T -s simRat_chr6.simRat.chr6 304093 1 + 647215 c -s simRat_chr6.simRat.chr6 300959 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 309101 1 + 636262 C -s Anc0.Anc0refChr8 2124 1 + 17196 c -s Anc1.Anc1refChr3 2194 1 + 3661 c -s Anc2.Anc2refChr8 2209 1 + 12804 c -s mr.mrrefChr5 159707 1 + 294540 T -s mr.mrrefChr5 162665 1 + 294540 c -s simCow_chr6.simCow.chr6 281770 1 + 602619 c -s simDog_chr6.simDog.chr6 318129 1 - 593897 c -s simHuman_chr6.simHuman.chr6 228465 1 + 601863 c -s simMouse_chr6.simMouse.chr6 312439 1 + 636262 C -s simRat_chr6.simRat.chr6 304094 1 + 647215 c -s simRat_chr6.simRat.chr6 300960 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 309102 8 + 636262 TGGATGAT -s Anc0.Anc0refChr8 2125 8 + 17196 tggggggt -s Anc1.Anc1refChr3 2195 8 + 3661 tggggggt -s Anc2.Anc2refChr8 2210 8 + 12804 tggggggt -s mr.mrrefChr5 159708 8 + 294540 TGGATGAT -s mr.mrrefChr5 162666 8 + 294540 tggaggat -s simCow_chr6.simCow.chr6 281772 8 + 602619 tgaggggt -s simDog_chr6.simDog.chr6 318186 8 - 593897 tggggggt -s simHuman_chr6.simHuman.chr6 228466 8 + 601863 tggggggt -s simMouse_chr6.simMouse.chr6 312440 8 + 636262 TGGAGGAT -s simRat_chr6.simRat.chr6 304095 8 + 647215 tggaggat -s simRat_chr6.simRat.chr6 300961 8 + 647215 TGGATCAT - -a -s simMouse_chr6.simMouse.chr6 309110 10 + 636262 CAAATAGAGC -s Anc0.Anc0refChr8 2136 10 + 17196 caaataaatt -s Anc1.Anc1refChr3 2206 10 + 3661 caaataaatt -s Anc2.Anc2refChr8 2221 10 + 12804 cgaataaatt -s mr.mrrefChr5 159716 10 + 294540 CAAATAAAGC -s mr.mrrefChr5 162677 10 + 294540 caaacaTACC -s simCow_chr6.simCow.chr6 281783 10 + 602619 caattaaatt -s simDog_chr6.simDog.chr6 318197 10 - 593897 cgaatgaatt -s simHuman_chr6.simHuman.chr6 228477 10 + 601863 ttaataagtt -s simMouse_chr6.simMouse.chr6 312451 10 + 636262 CAAACATACC -s simRat_chr6.simRat.chr6 304106 10 + 647215 caaataTATC -s simRat_chr6.simRat.chr6 300969 10 + 647215 CAAATAAAAC - -a -s simMouse_chr6.simMouse.chr6 309120 12 + 636262 TGTGTGATGCAG -s Anc0.Anc0refChr8 2146 12 + 17196 taggatatgtac -s Anc1.Anc1refChr3 2216 12 + 3661 taggatatgtac -s Anc2.Anc2refChr8 2231 12 + 12804 taggatatgtac -s mr.mrrefChr5 159726 12 + 294540 TGGGTGATGTAG -s simCow_chr6.simCow.chr6 281793 10 + 602619 taag--gtggac -s simDog_chr6.simDog.chr6 318207 12 - 593897 taggatatttac -s simHuman_chr6.simHuman.chr6 228487 12 + 601863 taggctatgtac -s simRat_chr6.simRat.chr6 300979 12 + 647215 TGGGTGATGTAG - -a -s simMouse_chr6.simMouse.chr6 309132 3 + 636262 ACA -s Anc0.Anc0refChr8 2158 3 + 17196 aca -s Anc1.Anc1refChr3 2228 3 + 3661 aca -s Anc2.Anc2refChr8 2243 3 + 12804 aca -s mr.mrrefChr5 159738 3 + 294540 ACA -s mr.mrrefChr5 162687 3 + 294540 ACA -s simCow_chr6.simCow.chr6 281803 3 + 602619 aca -s simDog_chr6.simDog.chr6 318219 3 - 593897 aca -s simHuman_chr6.simHuman.chr6 228499 3 + 601863 aca -s simMouse_chr6.simMouse.chr6 312461 3 + 636262 ACA -s simRat_chr6.simRat.chr6 304116 3 + 647215 CCA -s simRat_chr6.simRat.chr6 300991 3 + 647215 ACA - -a -s simMouse_chr6.simMouse.chr6 309135 14 + 636262 TATGATGTACCAAG -s Anc0.Anc0refChr8 2161 14 + 17196 aatcaagtactatt -s Anc1.Anc1refChr3 2231 14 + 3661 aatcaagtactatt -s Anc2.Anc2refChr8 2246 14 + 12804 aatcaagtactatt -s mr.mrrefChr5 159741 14 + 294540 TATGATGTACCATT -s mr.mrrefChr5 162690 14 + 294540 AGTTGGGAGGGACT -s simCow_chr6.simCow.chr6 281806 14 + 602619 aatcatgtccaatt -s simDog_chr6.simDog.chr6 318222 14 - 593897 aaccaagcactaac -s simHuman_chr6.simHuman.chr6 228502 14 + 601863 aatcaagtgctatt -s simMouse_chr6.simMouse.chr6 312464 14 + 636262 AGTTGGGAGGGACT -s simRat_chr6.simRat.chr6 304202 14 + 647215 AGTTGGGAAGGACT -s simRat_chr6.simRat.chr6 300994 14 + 647215 TATGACATACAATT - -a -s simMouse_chr6.simMouse.chr6 309149 3 + 636262 TAG -s Anc0.Anc0refChr8 2175 3 + 17196 gag -s Anc1.Anc1refChr3 2245 3 + 3661 gag -s Anc2.Anc2refChr8 2260 3 + 12804 gaa -s mr.mrrefChr5 159755 3 + 294540 TAG -s simCow_chr6.simCow.chr6 281820 3 + 602619 gaa -s simDog_chr6.simDog.chr6 318236 3 - 593897 gaa -s simHuman_chr6.simHuman.chr6 228516 3 + 601863 gag -s simRat_chr6.simRat.chr6 301008 3 + 647215 CAG - -a -s simMouse_chr6.simMouse.chr6 309152 1 + 636262 G -s Anc0.Anc0refChr8 2178 1 + 17196 g -s Anc1.Anc1refChr3 2248 1 + 3661 g -s Anc2.Anc2refChr8 2263 1 + 12804 c -s mr.mrrefChr5 159758 1 + 294540 G -s mr.mrrefChr5 162704 1 + 294540 G -s simCow_chr6.simCow.chr6 281823 1 + 602619 c -s simDog_chr6.simDog.chr6 318239 1 - 593897 c -s simHuman_chr6.simHuman.chr6 228519 1 + 601863 g -s simMouse_chr6.simMouse.chr6 312478 1 + 636262 G -s simRat_chr6.simRat.chr6 304216 1 + 647215 G -s simRat_chr6.simRat.chr6 301011 1 + 647215 G - -a -s simMouse_chr6.simMouse.chr6 309153 2 + 636262 AT -s Anc0.Anc0refChr8 2214 2 + 17196 ac -s Anc1.Anc1refChr3 2284 2 + 3661 ac -s Anc2.Anc2refChr8 2299 2 + 12804 ac -s mr.mrrefChr5 159759 2 + 294540 AT -s mr.mrrefChr5 162705 2 + 294540 AT -s simCow_chr6.simCow.chr6 281859 2 + 602619 ac -s simDog_chr6.simDog.chr6 318275 2 - 593897 ac -s simHuman_chr6.simHuman.chr6 228569 2 + 601863 ac -s simMouse_chr6.simMouse.chr6 312479 2 + 636262 AT -s simRat_chr6.simRat.chr6 304217 2 + 647215 AA -s simRat_chr6.simRat.chr6 301012 2 + 647215 AT - -a -s simMouse_chr6.simMouse.chr6 309155 6 + 636262 TCTCTA -s Anc0.Anc0refChr8 2250 6 + 17196 tctcta -s Anc1.Anc1refChr3 2405 6 + 3661 TCTCTA -s Anc2.Anc2refChr8 2335 6 + 12804 tttctt -s mr.mrrefChr5 159761 6 + 294540 TCTCTA -s mr.mrrefChr5 162903 6 + 294540 TCTGTA -s simCow_chr6.simCow.chr6 281893 6 + 602619 tttctt -s simDog_chr6.simDog.chr6 318311 6 - 593897 tttcct -s simHuman_chr6.simHuman.chr6 228690 6 + 601863 tttctt -s simMouse_chr6.simMouse.chr6 312677 6 + 636262 TCTGTA -s simRat_chr6.simRat.chr6 304440 6 + 647215 TCTCTA -s simRat_chr6.simRat.chr6 301014 6 + 647215 TCACTA - -a -s simMouse_chr6.simMouse.chr6 309161 1 + 636262 A -s Anc1.Anc1refChr3 2411 1 + 3661 a -s mr.mrrefChr5 159767 1 + 294540 A -s simHuman_chr6.simHuman.chr6 228696 1 + 601863 a -s simRat_chr6.simRat.chr6 301020 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 309162 12 + 636262 CTTGCAAACACA -s Anc1.Anc1refChr3 2412 12 + 3661 CATGCCAAGACA -s mr.mrrefChr5 159768 12 + 294540 CTTGCAAACACA -s mr.mrrefChr5 162909 12 + 294540 CCTGCTAAGACA -s simHuman_chr6.simHuman.chr6 228697 12 + 601863 cagcccaagaca -s simMouse_chr6.simMouse.chr6 312683 12 + 636262 CCTGCTAACACA -s simRat_chr6.simRat.chr6 304446 12 + 647215 CTTGCTAAGACA -s simRat_chr6.simRat.chr6 301021 12 + 647215 CTAGGAAGCACA - -a -s simMouse_chr6.simMouse.chr6 309174 3 + 636262 CAG -s Anc1.Anc1refChr3 2427 3 + 3661 CAA -s mr.mrrefChr5 159780 3 + 294540 CAG -s mr.mrrefChr5 162924 3 + 294540 CAA -s simHuman_chr6.simHuman.chr6 228712 3 + 601863 caa -s simMouse_chr6.simMouse.chr6 312698 3 + 636262 CAA -s simRat_chr6.simRat.chr6 304461 3 + 647215 CAA -s simRat_chr6.simRat.chr6 301033 3 + 647215 CAG - -a -s simMouse_chr6.simMouse.chr6 309177 2 + 636262 TT -s Anc0.Anc0refChr8 2293 2 + 17196 ct -s Anc1.Anc1refChr3 2467 2 + 3661 ct -s Anc2.Anc2refChr8 2378 2 + 12804 ct -s mr.mrrefChr5 159783 2 + 294540 TT -s mr.mrrefChr5 162927 2 + 294540 CT -s simCow_chr6.simCow.chr6 281936 2 + 602619 ct -s simDog_chr6.simDog.chr6 318355 2 - 593897 ct -s simHuman_chr6.simHuman.chr6 228758 2 + 601863 ct -s simMouse_chr6.simMouse.chr6 312701 2 + 636262 CT -s simRat_chr6.simRat.chr6 304464 2 + 647215 TC -s simRat_chr6.simRat.chr6 301036 2 + 647215 TG - -a -s simMouse_chr6.simMouse.chr6 309179 6 + 636262 GAGGGG -s Anc0.Anc0refChr8 2295 6 + 17196 aacgtG -s Anc1.Anc1refChr3 2469 6 + 3661 aacgtG -s Anc2.Anc2refChr8 2380 6 + 12804 aacgtG -s mr.mrrefChr5 159785 6 + 294540 GAGGGG -s simCow_chr6.simCow.chr6 281938 5 + 602619 aG-GTG -s simDog_chr6.simDog.chr6 318357 6 - 593897 aacatA -s simHuman_chr6.simHuman.chr6 228760 6 + 601863 aatgtG -s simRat_chr6.simRat.chr6 301038 6 + 647215 GAGCGG - -a -s simMouse_chr6.simMouse.chr6 309185 1 + 636262 A -s Anc0.Anc0refChr8 2301 1 + 17196 A -s Anc1.Anc1refChr3 2475 1 + 3661 A -s Anc2.Anc2refChr8 2386 1 + 12804 A -s mr.mrrefChr5 159791 1 + 294540 A -s simCow_chr6.simCow.chr6 281943 1 + 602619 A -s simDog_chr6.simDog.chr6 318363 1 - 593897 A -s simHuman_chr6.simHuman.chr6 228766 1 + 601863 G -s simRat_chr6.simRat.chr6 301079 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 309186 30 + 636262 TCAGTACCTGCAGTTCTGTGACTGTCTTAT -s Anc0.Anc0refChr8 2302 30 + 17196 TCTGTGCCTGTAGTTCCTTGATTGTTGTAT -s Anc1.Anc1refChr3 2476 30 + 3661 TCTGTGCCTGTAGTTCCTTGATTGTTGTAT -s Anc2.Anc2refChr8 2387 30 + 12804 TCTGTGCCTGTAGTTCCTTGGTTGTTGTAT -s mr.mrrefChr5 159792 30 + 294540 TCAGTACCTGCAGTTCTGTGACTGTCTTAT -s mr.mrrefChr5 162929 30 + 294540 TCAGTGCCTGTAGCTCCTTGAGAATGATAC -s simCow_chr6.simCow.chr6 281944 29 + 602619 TCAG-GCCGGTAATTCCTTAGGTGTTGTAT -s simDog_chr6.simDog.chr6 318364 29 - 593897 GCTGTGCCTGTAGTTTCTTG-TTGTTGTAT -s simHuman_chr6.simHuman.chr6 228767 30 + 601863 TCTGTGGCCGTAGTTCTTTGATTGCTGTAG -s simMouse_chr6.simMouse.chr6 312703 30 + 636262 TCAGTGCCTGTAGCTCCTTGAGAATGATAC -s simRat_chr6.simRat.chr6 304466 30 + 647215 TCAGTGCCTGTAGGTCCTTGCGAATGATAC -s simRat_chr6.simRat.chr6 301080 30 + 647215 TCAGTACCTGCAGTTCCGTGGCCGTTTAAT - -a -s simMouse_chr6.simMouse.chr6 309216 12 + 636262 CAAACATTTTTT -s Anc0.Anc0refChr8 2334 10 + 17196 CCA--AGTTTTC -s Anc1.Anc1refChr3 2508 10 + 3661 CCA--AGTTTTC -s Anc2.Anc2refChr8 2419 10 + 12804 CCA--AGTTTTC -s mr.mrrefChr5 159822 10 + 294540 CAA--ATTTTTT -s mr.mrrefChr5 162961 10 + 294540 CAA--ATTTTTT -s simCow_chr6.simCow.chr6 281975 10 + 602619 CCC--AGCTTTC -s simDog_chr6.simDog.chr6 318395 6 - 593897 TCA--AGT---- -s simHuman_chr6.simHuman.chr6 228799 10 + 601863 CCA--AGTTTTC -s simMouse_chr6.simMouse.chr6 312735 10 + 636262 CAA--ATTTTTT -s simRat_chr6.simRat.chr6 304498 10 + 647215 CAA--GTTTTTT -s simRat_chr6.simRat.chr6 301110 10 + 647215 CAA--ATGTTTT - -a -s simMouse_chr6.simMouse.chr6 309228 1 + 636262 C -s mr.mrrefChr5 159832 1 + 294540 C -s simRat_chr6.simRat.chr6 301120 1 + 647215 C - -a -s simMouse_chr6.simMouse.chr6 309229 16 + 636262 ATAAACACTTGTCAAG -s Anc0.Anc0refChr8 2344 16 + 17196 ATAGACATTGGTGGAG -s Anc1.Anc1refChr3 2518 16 + 3661 ATAGACATTGGTGGAG -s Anc2.Anc2refChr8 2429 16 + 12804 ATAGACATTGGTGGAG -s mr.mrrefChr5 159833 16 + 294540 ATAAACACTTGTCAAG -s mr.mrrefChr5 162971 16 + 294540 ACTGACATCAGTGGAG -s simCow_chr6.simCow.chr6 281985 16 + 602619 ATAGACATTGGTGGAG -s simDog_chr6.simDog.chr6 318401 14 - 593897 --ACACATTGGGGGAG -s simHuman_chr6.simHuman.chr6 228809 16 + 601863 ATAGCGATTGGTGGAG -s simMouse_chr6.simMouse.chr6 312745 16 + 636262 GCTGACATCAGAGGAG -s simRat_chr6.simRat.chr6 304508 16 + 647215 ACTGACATCAGTGGTG -s simRat_chr6.simRat.chr6 301121 16 + 647215 ATAAGCACTGGTCAAG - -a -s simMouse_chr6.simMouse.chr6 309245 25 + 636262 CTTACTAGCGGCTCTCCTTGGCATT -s Anc0.Anc0refChr8 2368 25 + 17196 CTTGCAACTGGCTCTTCCTGACACT -s Anc1.Anc1refChr3 2542 25 + 3661 CTTGCAACTGGCTCTTCCTGACACT -s Anc2.Anc2refChr8 2453 25 + 12804 TTTGCAACTGGCTCTTCCTGACACT -s mr.mrrefChr5 159849 25 + 294540 CTTACTAGCGGCTCTCCTTGGCATT -s mr.mrrefChr5 162995 25 + 294540 CTTGCAGCTGGCCTTCCCTGACACT -s simCow_chr6.simCow.chr6 282009 25 + 602619 TTTGCAACTGGCCCTTCCTGACACT -s simDog_chr6.simDog.chr6 318423 25 - 593897 TCCGCAACTGGCTGTTACTGGCAAT -s simHuman_chr6.simHuman.chr6 228833 25 + 601863 ATTGCATCTGGCTCTTCCAGACACC -s simMouse_chr6.simMouse.chr6 312772 25 + 636262 CTTGCAGCTGGCCTTCCCTGACACT -s simRat_chr6.simRat.chr6 304532 25 + 647215 CTTGTAGTTGGCCTTCCCTGACACT -s simRat_chr6.simRat.chr6 301141 25 + 647215 CTTACCCGCTGCTCTCCTTGGCACT - -a -s simMouse_chr6.simMouse.chr6 309270 1 + 636262 T -s Anc0.Anc0refChr8 2393 1 + 17196 C -s Anc1.Anc1refChr3 2567 1 + 3661 C -s Anc2.Anc2refChr8 2478 1 + 12804 C -s mr.mrrefChr5 159874 1 + 294540 T -s simCow_chr6.simCow.chr6 282034 1 + 602619 C -s simDog_chr6.simDog.chr6 318448 1 - 593897 C -s simHuman_chr6.simHuman.chr6 228858 1 + 601863 C -s simRat_chr6.simRat.chr6 301166 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 309271 9 + 636262 AATATATTG -s Anc0.Anc0refChr8 2394 9 + 17196 AATGCATTG -s Anc1.Anc1refChr3 2568 9 + 3661 AATGCATTG -s Anc2.Anc2refChr8 2479 9 + 12804 AATGCATTG -s mr.mrrefChr5 159875 9 + 294540 AATATATTG -s mr.mrrefChr5 163020 9 + 294540 AATGCATCA -s simCow_chr6.simCow.chr6 282035 9 + 602619 AATGCATTG -s simDog_chr6.simDog.chr6 318449 9 - 593897 AATGCACTG -s simHuman_chr6.simHuman.chr6 228859 9 + 601863 GATGCATTA -s simMouse_chr6.simMouse.chr6 312797 9 + 636262 AATGCATCA -s simRat_chr6.simRat.chr6 304557 9 + 647215 AATGCATCA -s simRat_chr6.simRat.chr6 301167 9 + 647215 AATGCATTG - -a -s simMouse_chr6.simMouse.chr6 309280 28 + 636262 ACTTTGCCATTTCACTGGCAGCTACACA -s Anc0.Anc0refChr8 2403 21 + 17196 AGCACACCACATCACTGGCAA------- -s Anc1.Anc1refChr3 2577 28 + 3661 AGCACACCACATCACTGGCAACTAGAAA -s Anc2.Anc2refChr8 2488 21 + 12804 AGCACACCACGTCACTAGCAA------- -s mr.mrrefChr5 159884 28 + 294540 ACTTTGCCATTTCACTGGCAGCTACACA -s mr.mrrefChr5 163029 28 + 294540 AGCACACCTCATCACTGGCAACTAGAGA -s simCow_chr6.simCow.chr6 282044 21 + 602619 AGCACACCATCTCACTAGCAA------- -s simDog_chr6.simDog.chr6 318459 21 - 593897 GGCATACCACGTCACTAGCAA------- -s simHuman_chr6.simHuman.chr6 228868 28 + 601863 AGCACACCACAGCACTGGCAAGTAGAAA -s simMouse_chr6.simMouse.chr6 312806 28 + 636262 AGCACACCTCATCACTGGCAACTAGAGA -s simRat_chr6.simRat.chr6 304566 28 + 647215 AGCACACCTCATCACTGGCAGCTAGAGA -s simRat_chr6.simRat.chr6 301176 28 + 647215 ACTTCGTCATTTCACTGGCAGCTACACA - -a -s simMouse_chr6.simMouse.chr6 309308 32 + 636262 TGTTCTCACTGGCAGCTACATTCGTGATGAGC -s mr.mrrefChr5 159912 21 + 294540 TGTTCTCACTGGCAGCTA-----------AGC -s simRat_chr6.simRat.chr6 301204 21 + 647215 TGTCCCCACTGACAGCTA-----------AGC - -a -s simMouse_chr6.simMouse.chr6 309340 40 + 636262 AAATGTATCGGACACCTGCATGAAGTCTGGAGCTACAGTA -s mr.mrrefChr5 159933 40 + 294540 AAATGTATCGGACACCTGCATGAAGTCTGGAGCTACAGTA -s simRat_chr6.simRat.chr6 301227 40 + 647215 AAATGGATTGAACACATGTATAAAGTCTTCAGCTAAAGTA - -a -s simMouse_chr6.simMouse.chr6 309380 324 + 636262 CATGGTTAATGTATTGTACTAATGGAGTAAGTTATGTTGGACCATTAGGCAGTGCACCCACCAGGTTTATAATTGGATTCATATGGCTCTGGCCACTTCATGTATATGTCTGATGCACTTTTTCCCACCTGTAATAAAATAGAGATGGATTCAGGCCTTATAAAACAAACTAGCCCATAAGTTAGCACCCAGGTCTATTCAGGTTCTGATTAAATATCATATTTCCAGTCGCCCCATGAGAGATTCTCTAAGGAGCATGACTGACAAGTGATGAAAGGCCTCCTTGATGGTAATCTGCACATAAGTGGGGTGATCATACTAAAG -s mr.mrrefChr5 159973 136 + 294540 CATGGTTAATGTATTGTACTAATGGAGTAAG----GTTGGACCATTAGGCAGTGCACCCACCAGGTTTATAATTGGATTCATATGGCTCTGGCCACTTCATGTATATGTCTGATGCACTTTTTCCCAC----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ATCATACTAAAG -s simRat_chr6.simRat.chr6 345812 136 - 647215 CCTCATTTTAGGATTGTACTAATGGAGTAAG----ATTGGACCATTAAGCAGTGCACCCACCAGGTTTATAATGGGGTTCATATGGCTTTGGCTACTTCATGTATATGTCTGATGCACTTCTGCCCAC----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AACATTACCATG - -a -s simMouse_chr6.simMouse.chr6 309704 10 + 636262 GGCTTAATGG -s mr.mrrefChr5 160109 10 + 294540 GGCTTAATGG -s simRat_chr6.simRat.chr6 301403 10 + 647215 TGCCTAGAGG - -a -s simMouse_chr6.simMouse.chr6 309714 226 + 636262 ACTCGGCTGATGCAGGGTAGCCAGGGCTCATTATGTAAATCCTGATTAGTACTGGATTGGATTGGAGATTGAGGGTGTCTCAGGGGCATCAAGGAGGGTGTCGTACTTTAGAATCAGAGATTACCTCCTGGAGTTGGTTATCAAGATTTGTATCCAGGCAAACTTGATCGTGGGGACCACCTACCTATCACCACTGTGGTTAATATTGATTGGTCTTGCACATATT -s mr.mrrefChr5 160119 218 + 294540 ACTCGGCTGATGCAGGGTAGCCAGGGCTCATTATGTAAATCCTGATTAGTACTGGATTGGATTG------GAGGGTGTCTCAGGGGCA--AAGGAGGGTGTCGTACTTTAGAATCAGAGATTACCTCCTGGAGTTGGTTATCAAGATTTGTATCCAGGCAAACTTGATCGTGGGGACCACCTACCTATCACCACTGTGGTTAATATTGATTGGTCTTGCACATATT -s simRat_chr6.simRat.chr6 301414 218 + 647215 ACTCAGTTGATGCTGGGTAGCCAGGGCTCATCATGCTAATCCTGATTAGTGATGAATTGGATTG------GAGGGTGTCTCAGGGGCA--AAGGAGCATGTCGTACTGTAGAATCAGAGATGACCCCCTGAAATTGGTTCACAAGAATTCTATCCAGGCAGACTTGTTCATAGAGACTGCCTACATGCCACCGCTGTGATTAAAATTGATTGGTTATGCATATATT - -a -s simMouse_chr6.simMouse.chr6 309940 29 + 636262 GTGGGCTTAGGTGTAGTTGATGCACAGGG -s mr.mrrefChr5 160337 29 + 294540 GTGGGCTTAGGTGTAGTTGATGCACAGGG -s simRat_chr6.simRat.chr6 301643 29 + 647215 GTGGGCATAGGTGAGCTTGATGCACAGAG - -a -s simMouse_chr6.simMouse.chr6 309969 391 + 636262 CTCAGATTCGATCTAGCAAGAGATGTTATTAATGACACTATTCCAAGCAAAGTCTATAGGTGCAATGTGTGGGTAACTAAACTCAGCTTGGACAGGTGACAAAAACGTGTAGTCATTTGCATGGGGATACAGGTGTAGCTCAATTGTTGCGATGCCTTGGGATACATGCTGCTGCTGCCACTCCAGACAGAAGAGGACACTCGCAATCACTTCAGTCTTGTGTGGCCATAGACAGGTGTTCACAGCCTATCTACAGCCTCCCTGGGTCACGGCCAGTGGGCATTAAATATGTTGGACCATGCTTGACCAAGTCTTCTCACTGCTAATTGTGTGTATGAGTAGACTTGCTTGGATACCTACGGGTCACTGAGATGCTCCAAACCCTGCTAGC -s mr.mrrefChr5 160366 377 + 294540 CTCAGATTCGATCTAGCAAGAGATGTTATTAATGACACTAT---AAGCAAAGTCTATAGGTGCAATGTGTGGGTAACTAAACTCAGCTTGGACAGGTGACAAAAACGTGTAGTCATTTGCATGGGGATACAGGTGTAGCTCAATTGTTGCGATGCCTTGGGATACATGCTGCTGCTGCCACTCCAGACAGAAGAGGACACTCGCAATCACTTCAGTCTTGTGTGGCCATAGACAGGTGTTCACAGCCTATC-ACAGCCTCCCTGGGTCAC--CCAGTGGGCATTAAATATGTTGGACCATGCTTGACCAAGTCTTCTCACTGCTAATTGTGTGTATGAGTAGACTTGCTTG--------CGGGTCACTGAGATGCTCCAAACCCTGCTAGC -s simRat_chr6.simRat.chr6 301673 377 + 647215 CTCAGATTCTTTCTAACAAAAGATGTTATTAATTATGCCAT---AAGAAGGGTTTATAGGTGCTATGTGCGGCTAACTAAACTCAGCTTGGACAGGTGACATATACACATAGTTACATGCATGCAGATGCAGGTGCAGCTCAATTTTTGTGATGCCTCGGGATACATGCTGTTGCTGTCACTCCAGACAGAAGAGGGCACTTGCAATCACTTTGATTCTGTGCAGCCACAGACAGGTTTTCACAGCATTTC-ACGACCTCCCTGGATCAT--CCGTGGGGGACCAAATATGTTGGACCATGCATGACCAAGTCTTCTCAATGCTCATTGTGTGCATGAGCAGACTTGCTTG--------CTCGTCACTGAGATGCTCAGAACACTGCTAGC - -a -s simMouse_chr6.simMouse.chr6 310360 7 + 636262 TGCACCT -s mr.mrrefChr5 160743 7 + 294540 TGCACCT -s simRat_chr6.simRat.chr6 302051 7 + 647215 TGCACCT - -a -s simMouse_chr6.simMouse.chr6 310382 1 + 636262 G -s mr.mrrefChr5 160765 1 + 294540 G -s simRat_chr6.simRat.chr6 302073 1 + 647215 G - -a -s simMouse_chr6.simMouse.chr6 310447 14 + 636262 AATGCAGAGATCCT - -a -s simMouse_chr6.simMouse.chr6 310548 6 + 636262 CCCCTG -s mr.mrrefChr5 160917 6 + 294540 CCCCTG -s simRat_chr6.simRat.chr6 302225 6 + 647215 CCCCTG - -a -s simMouse_chr6.simMouse.chr6 310586 6 + 636262 TGCAGT -s Anc0.Anc0refChr8 221 6 + 17196 TGCAGT -s Anc1.Anc1refChr3 226 6 + 3661 TGCAGT -s Anc2.Anc2refChr8 233 6 + 12804 TACAGT -s mr.mrrefChr5 160955 6 + 294540 TGCAGT -s simCow_chr6.simCow.chr6 279848 6 + 602619 TACAGT -s simDog_chr6.simDog.chr6 316455 6 - 593897 TACAGT -s simHuman_chr6.simHuman.chr6 226572 6 + 601863 TGCAGT -s simRat_chr6.simRat.chr6 302263 6 + 647215 TGCAGT - -a -s simMouse_chr6.simMouse.chr6 310592 2 + 636262 TG -s Anc0.Anc0refChr8 233 2 + 17196 TG -s Anc1.Anc1refChr3 238 2 + 3661 TG -s Anc2.Anc2refChr8 246 2 + 12804 TG -s mr.mrrefChr5 160961 2 + 294540 TG -s simCow_chr6.simCow.chr6 279871 2 + 602619 TG -s simDog_chr6.simDog.chr6 316468 2 - 593897 TG -s simHuman_chr6.simHuman.chr6 226584 2 + 601863 TG -s simRat_chr6.simRat.chr6 302269 2 + 647215 TG - -a -s simMouse_chr6.simMouse.chr6 310637 1 + 636262 T -s Anc0.Anc0refChr8 282 1 + 17196 T -s Anc1.Anc1refChr3 287 1 + 3661 T -s Anc2.Anc2refChr8 295 1 + 12804 T -s mr.mrrefChr5 161006 1 + 294540 T -s simCow_chr6.simCow.chr6 279919 1 + 602619 T -s simDog_chr6.simDog.chr6 316517 1 - 593897 T -s simHuman_chr6.simHuman.chr6 226633 1 + 601863 C -s simRat_chr6.simRat.chr6 302314 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 310648 211 + 636262 GACAGTGAGTTACCAGTCTCTTTGTGAATATCCTGGTGTCTTCTGTTTGTGTTGTTGACAGGTTCTCAAGGAGTCACGATGATCTGATTCTCGACTGGTCTAAGCTACTGAGGTAAAGGATTGAATGTGTAACAAGTAGAAATCTATGGTTGTCCTCATCGCACTGGTCATATATATTTTGATCCTCAGGCAGCAAGTATCCTGAACTGGT -s mr.mrrefChr5 161017 132 + 294540 G---------------------------------------------TTGTGTTGTTGACAGGTTCTCAAGGAGTC----------------------------------GAGGTAAAGGATTGAATGTGTAACAAGTAGAAATCTATGGTTGTCCTCATCGCACTGGTCATATATATTTTGATCCTCAGGCAGCAAGTATCCTGAACTGGT -s simRat_chr6.simRat.chr6 302325 132 + 647215 A---------------------------------------------TTATGTTGCTGACAGGTTCTCAGGGAATC----------------------------------TGGGTAGAGGATTGAAGGTGCAATGAATAGGAAGTTAAGGTTGTCCTTGTTGCACGGGTCACATAAATTCTGATCCTCAGGAAGCACATACCCTGGACTGGC - -a -s simMouse_chr6.simMouse.chr6 310859 37 + 636262 GCAAATTAGAAATTTAATGAATAGGGAAAGCAGTTTT -s mr.mrrefChr5 161149 37 + 294540 GCAAATTAGAAATTTAATGAATAGGGAAAGCAGTTTT -s simRat_chr6.simRat.chr6 302500 37 + 647215 GCAGGTTAAAAATCTAATGAATTGGGTAAGTGGTTCT - -a -s simMouse_chr6.simMouse.chr6 310929 5 + 636262 GTTTT -s mr.mrrefChr5 161219 5 + 294540 GTTTT -s simRat_chr6.simRat.chr6 302571 5 + 647215 TTTTT - -a -s simMouse_chr6.simMouse.chr6 311018 15 + 636262 GTATCAGGCGTAGGC -s mr.mrrefChr5 161308 15 + 294540 GTATCAGGCGTAGGC -s simRat_chr6.simRat.chr6 302661 15 + 647215 ACATCAGACGTAGGC - -a -s simMouse_chr6.simMouse.chr6 311033 5 + 636262 ATATC -s Anc0.Anc0refChr8 818 5 + 17196 GCATC -s Anc1.Anc1refChr3 834 5 + 3661 GCATC -s Anc2.Anc2refChr8 866 5 + 12804 GCATA -s mr.mrrefChr5 161323 5 + 294540 ATATC -s mr.mrrefChr5 158411 5 + 294540 ACATC -s simCow_chr6.simCow.chr6 280437 5 + 602619 GTATA -s simDog_chr6.simDog.chr6 317086 5 - 593897 ACATA -s simHuman_chr6.simHuman.chr6 227162 5 + 601863 GCATT -s simRat_chr6.simRat.chr6 299634 5 + 647215 ACATC -s simRat_chr6.simRat.chr6 302676 5 + 647215 ATATC - -a -s simMouse_chr6.simMouse.chr6 311038 6 + 636262 AGGCAA -s Anc0.Anc0refChr8 823 6 + 17196 GGGCAA -s Anc1.Anc1refChr3 839 6 + 3661 GGGCAA -s Anc2.Anc2refChr8 871 6 + 12804 GGGCAA -s mr.mrrefChr5 161328 6 + 294540 AGGCAA -s mr.mrrefChr5 158416 6 + 294540 AGGCAA -s simCow_chr6.simCow.chr6 280442 6 + 602619 AGACTA -s simDog_chr6.simDog.chr6 317091 6 - 593897 GGGCAA -s simHuman_chr6.simHuman.chr6 227167 6 + 601863 GGGCAA -s simRat_chr6.simRat.chr6 299641 6 + 647215 AGGCAA -s simRat_chr6.simRat.chr6 302681 6 + 647215 AGGCAA - -a -s simMouse_chr6.simMouse.chr6 311044 8 + 636262 GGGTTACT -s Anc0.Anc0refChr8 829 6 + 17196 GGGT--TA -s Anc1.Anc1refChr3 845 6 + 3661 GGGT--TA -s Anc2.Anc2refChr8 877 6 + 12804 GGGT--TA -s mr.mrrefChr5 161334 6 + 294540 GGGT--CT -s mr.mrrefChr5 158422 6 + 294540 AAGT--CA -s simCow_chr6.simCow.chr6 280448 6 + 602619 GGGT--TG -s simDog_chr6.simDog.chr6 317097 6 - 593897 GGGT--TA -s simHuman_chr6.simHuman.chr6 227173 6 + 601863 AGGT--TA -s simRat_chr6.simRat.chr6 299654 6 + 647215 AAGT--CA -s simRat_chr6.simRat.chr6 302687 6 + 647215 GTGT--CG - -a -s simMouse_chr6.simMouse.chr6 311052 4 + 636262 TAGA -s Anc0.Anc0refChr8 841 4 + 17196 CAGA -s Anc1.Anc1refChr3 859 4 + 3661 CAGA -s Anc2.Anc2refChr8 889 4 + 12804 CTAA -s mr.mrrefChr5 161340 4 + 294540 TAGA -s mr.mrrefChr5 158435 4 + 294540 CAGA -s simCow_chr6.simCow.chr6 280460 4 + 602619 CTAA -s simDog_chr6.simDog.chr6 317109 4 - 593897 CTAT -s simHuman_chr6.simHuman.chr6 227187 4 + 601863 CAGA -s simRat_chr6.simRat.chr6 299667 4 + 647215 CAGA -s simRat_chr6.simRat.chr6 302693 4 + 647215 TAGA - -a -s simMouse_chr6.simMouse.chr6 311056 6 + 636262 CAGGGT -s Anc0.Anc0refChr8 845 6 + 17196 GAGGGT -s Anc1.Anc1refChr3 863 6 + 3661 GAGGGT -s Anc2.Anc2refChr8 893 6 + 12804 GAGGGT -s mr.mrrefChr5 161344 6 + 294540 CAGGGT -s mr.mrrefChr5 158439 6 + 294540 GAAGGT -s simCow_chr6.simCow.chr6 280464 5 + 602619 GAGA-T -s simDog_chr6.simDog.chr6 317113 6 - 593897 AAGGGT -s simHuman_chr6.simHuman.chr6 227191 6 + 601863 GAGGGT -s simRat_chr6.simRat.chr6 299676 6 + 647215 GAAGGT -s simRat_chr6.simRat.chr6 302697 6 + 647215 CAGGGT - -a -s simMouse_chr6.simMouse.chr6 311062 1 + 636262 T -s Anc0.Anc0refChr8 855 1 + 17196 T -s Anc1.Anc1refChr3 873 1 + 3661 T -s Anc2.Anc2refChr8 903 1 + 12804 T -s mr.mrrefChr5 161350 1 + 294540 T -s mr.mrrefChr5 158445 1 + 294540 T -s simCow_chr6.simCow.chr6 280473 1 + 602619 T -s simDog_chr6.simDog.chr6 317123 1 - 593897 T -s simHuman_chr6.simHuman.chr6 227201 1 + 601863 T -s simRat_chr6.simRat.chr6 299682 1 + 647215 T -s simRat_chr6.simRat.chr6 302703 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 311063 12 + 636262 GCAACCAGATTT -s mr.mrrefChr5 161351 10 + 294540 GCAACCAGA--T -s simRat_chr6.simRat.chr6 302704 10 + 647215 ACAATAAGA--T - -a -s simMouse_chr6.simMouse.chr6 311075 11 + 636262 TGTTCCTATTA -s Anc0.Anc0refChr8 856 11 + 17196 TGGTCCTTTTT -s Anc1.Anc1refChr3 874 11 + 3661 TGGTCCTTTTT -s Anc2.Anc2refChr8 904 11 + 12804 TAGTCCTTTTT -s mr.mrrefChr5 161361 11 + 294540 TGTTCCTATTA -s mr.mrrefChr5 158446 11 + 294540 TGGTATTTTGG -s simCow_chr6.simCow.chr6 280474 11 + 602619 TAGGCCTTTTT -s simDog_chr6.simDog.chr6 317124 11 - 593897 TAGTCCATTTT -s simHuman_chr6.simHuman.chr6 227202 11 + 601863 TTGTCCTTTTT -s simRat_chr6.simRat.chr6 299683 11 + 647215 TGGTATTTTGG -s simRat_chr6.simRat.chr6 302714 11 + 647215 TGGTCCTATTA - -a -s simMouse_chr6.simMouse.chr6 311086 5 + 636262 ATGCA -s Anc0.Anc0refChr8 867 5 + 17196 ATACG -s Anc1.Anc1refChr3 885 5 + 3661 ATACG -s Anc2.Anc2refChr8 915 5 + 12804 ATACG -s mr.mrrefChr5 161372 5 + 294540 ATGCA -s mr.mrrefChr5 158457 5 + 294540 GAACA -s simCow_chr6.simCow.chr6 280485 5 + 602619 ATATG -s simDog_chr6.simDog.chr6 317135 5 - 593897 ATGCG -s simHuman_chr6.simHuman.chr6 227213 5 + 601863 ATAAG -s simRat_chr6.simRat.chr6 299694 5 + 647215 GAACA -s simRat_chr6.simRat.chr6 302727 5 + 647215 ATGGG - -a -s simMouse_chr6.simMouse.chr6 311091 2 + 636262 CT -s Anc0.Anc0refChr8 874 2 + 17196 CT -s Anc1.Anc1refChr3 892 2 + 3661 CT -s Anc2.Anc2refChr8 922 2 + 12804 CT -s mr.mrrefChr5 161377 2 + 294540 CT -s mr.mrrefChr5 158464 2 + 294540 CT -s simCow_chr6.simCow.chr6 280492 2 + 602619 CT -s simDog_chr6.simDog.chr6 317142 2 - 593897 CT -s simHuman_chr6.simHuman.chr6 227220 2 + 601863 CT -s simRat_chr6.simRat.chr6 299701 2 + 647215 CT -s simRat_chr6.simRat.chr6 302732 2 + 647215 CT - -a -s simMouse_chr6.simMouse.chr6 311093 2 + 636262 GT -s Anc0.Anc0refChr8 876 2 + 17196 GT -s Anc1.Anc1refChr3 894 2 + 3661 GT -s Anc2.Anc2refChr8 924 2 + 12804 GG -s mr.mrrefChr5 161379 2 + 294540 GT -s mr.mrrefChr5 158466 2 + 294540 GT -s simCow_chr6.simCow.chr6 280494 2 + 602619 GG -s simDog_chr6.simDog.chr6 317144 2 - 593897 GG -s simHuman_chr6.simHuman.chr6 227222 2 + 601863 GT -s simRat_chr6.simRat.chr6 299704 2 + 647215 GT -s simRat_chr6.simRat.chr6 302734 2 + 647215 GG - -a -s simMouse_chr6.simMouse.chr6 311095 1 + 636262 T -s Anc0.Anc0refChr8 878 1 + 17196 T -s Anc1.Anc1refChr3 896 1 + 3661 T -s Anc2.Anc2refChr8 926 1 + 12804 T -s mr.mrrefChr5 161381 1 + 294540 T -s simCow_chr6.simCow.chr6 280496 1 + 602619 T -s simDog_chr6.simDog.chr6 317146 1 - 593897 T -s simRat_chr6.simRat.chr6 302736 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 311096 19 + 636262 ATCCTAAAGTTTAAGTTAG -s Anc0.Anc0refChr8 879 19 + 17196 GTCCTATAACTTAAGTTAG -s Anc1.Anc1refChr3 897 19 + 3661 GTCCTATAACTTAAGTTAG -s Anc2.Anc2refChr8 927 19 + 12804 GTCCTATAACTTAAGTTAG -s mr.mrrefChr5 161382 19 + 294540 ATCCTAAAGTTTAAGTTAG -s mr.mrrefChr5 158468 19 + 294540 ATCTTATAACTGAAGCCAG -s simCow_chr6.simCow.chr6 280497 19 + 602619 GTCCTATAATTTAAGTCAG -s simDog_chr6.simDog.chr6 317147 19 - 593897 GCCCTATAACTTAAGTTAG -s simHuman_chr6.simHuman.chr6 227224 19 + 601863 GTCCTGTACCTTAAGTTAA -s simRat_chr6.simRat.chr6 299706 19 + 647215 ATCTTATAACTGAAGCCAG -s simRat_chr6.simRat.chr6 302737 19 + 647215 ATCCTGGAAGTTAAGTTAG - -a -s simMouse_chr6.simMouse.chr6 311115 2 + 636262 TA -s Anc0.Anc0refChr8 898 2 + 17196 TT -s Anc1.Anc1refChr3 916 2 + 3661 TT -s Anc2.Anc2refChr8 946 2 + 12804 TT -s mr.mrrefChr5 161401 2 + 294540 TA -s mr.mrrefChr5 158487 2 + 294540 TC -s simCow_chr6.simCow.chr6 280516 2 + 602619 TT -s simDog_chr6.simDog.chr6 317166 2 - 593897 TT -s simHuman_chr6.simHuman.chr6 227243 2 + 601863 TT -s simRat_chr6.simRat.chr6 299725 2 + 647215 TC -s simRat_chr6.simRat.chr6 302757 2 + 647215 TA - -a -s simMouse_chr6.simMouse.chr6 311117 4 + 636262 ATTA -s Anc0.Anc0refChr8 901 4 + 17196 AACA -s Anc1.Anc1refChr3 919 4 + 3661 AACA -s Anc2.Anc2refChr8 949 4 + 12804 AACA -s mr.mrrefChr5 161403 4 + 294540 ATTA -s mr.mrrefChr5 158490 4 + 294540 ATCA -s simCow_chr6.simCow.chr6 280519 4 + 602619 ATCA -s simDog_chr6.simDog.chr6 317169 4 - 593897 CAAG -s simHuman_chr6.simHuman.chr6 227246 4 + 601863 AACA -s simRat_chr6.simRat.chr6 299728 4 + 647215 ATCA -s simRat_chr6.simRat.chr6 302759 4 + 647215 ATTA - -a -s simMouse_chr6.simMouse.chr6 311121 15 + 636262 AGCCAAAAAGAGTAT -s Anc0.Anc0refChr8 905 15 + 17196 AGACAGACAGGTTAT -s Anc1.Anc1refChr3 923 15 + 3661 AGACAGACAGGTTAT -s Anc2.Anc2refChr8 953 15 + 12804 AGACAGACAGGTTAT -s mr.mrrefChr5 161407 15 + 294540 AGCCAAAAAGAGTAT -s mr.mrrefChr5 158494 15 + 294540 AGACAGGCAGTGTAT -s simCow_chr6.simCow.chr6 280523 15 + 602619 AGACACCAAGGTTAT -s simDog_chr6.simDog.chr6 317175 15 - 593897 AGACAGACAGGGTAT -s simHuman_chr6.simHuman.chr6 227250 15 + 601863 AGACAGATAGGTTAT -s simRat_chr6.simRat.chr6 299732 15 + 647215 AGACAGGCAGTGTAT -s simRat_chr6.simRat.chr6 302763 15 + 647215 AGCGGAAGAGGGTAT - -a -s simMouse_chr6.simMouse.chr6 311136 6 + 636262 GGGTGT -s mr.mrrefChr5 161422 6 + 294540 GGGTGT -s simRat_chr6.simRat.chr6 302778 6 + 647215 GGGTAT - -a -s simMouse_chr6.simMouse.chr6 311142 9 + 636262 GATAGCATG -s Anc0.Anc0refChr8 920 9 + 17196 GATAGAGTT -s Anc1.Anc1refChr3 938 9 + 3661 GATAGAGTT -s Anc2.Anc2refChr8 968 9 + 12804 GATAGAGTT -s mr.mrrefChr5 161428 9 + 294540 GATAGCATG -s mr.mrrefChr5 158509 9 + 294540 TATAAGGTG -s simCow_chr6.simCow.chr6 280538 9 + 602619 GACTAAGTT -s simDog_chr6.simDog.chr6 317190 9 - 593897 GGTAGAGTT -s simHuman_chr6.simHuman.chr6 227265 9 + 601863 GATATAGTT -s simRat_chr6.simRat.chr6 299747 9 + 647215 TATAAGGTG -s simRat_chr6.simRat.chr6 302784 9 + 647215 GATAGCATG - -a -s simMouse_chr6.simMouse.chr6 311151 5 + 636262 CATTT -s Anc0.Anc0refChr8 929 5 + 17196 CATTT -s Anc1.Anc1refChr3 947 5 + 3661 CATTT -s Anc2.Anc2refChr8 977 5 + 12804 CTTTT -s mr.mrrefChr5 161437 5 + 294540 CATTT -s mr.mrrefChr5 158518 5 + 294540 TATGT -s simCow_chr6.simCow.chr6 280547 5 + 602619 CTTTT -s simDog_chr6.simDog.chr6 317199 5 - 593897 CTTTT -s simHuman_chr6.simHuman.chr6 227274 5 + 601863 TGTCT -s simRat_chr6.simRat.chr6 299777 5 + 647215 TATGT -s simRat_chr6.simRat.chr6 302793 5 + 647215 CTTTT - -a -s simMouse_chr6.simMouse.chr6 311156 21 + 636262 GCATGAAATTGGATTTTGCCT -s Anc0.Anc0refChr8 934 21 + 17196 ATGTAAAGTTAGAGTTTGTCT -s Anc1.Anc1refChr3 952 21 + 3661 ATGTAAAGTTAGAGTTTGTCT -s Anc2.Anc2refChr8 982 21 + 12804 ATGTAAAGTTAGAGTTTGTCT -s mr.mrrefChr5 161442 21 + 294540 GCATGAAATTGGATTTTGCCT -s simCow_chr6.simCow.chr6 280552 21 + 602619 ATGTAAAGTTAGAGTTGGTTT -s simDog_chr6.simDog.chr6 317204 21 - 593897 ATGTAAAGTTAGAGTTTGTCT -s simRat_chr6.simRat.chr6 302798 21 + 647215 GCATGAATTTAGACCTTGCCC - -a -s simMouse_chr6.simMouse.chr6 311177 6 + 636262 TTCTAT -s Anc0.Anc0refChr8 955 6 + 17196 TTAAAC -s Anc1.Anc1refChr3 973 6 + 3661 TTAAAC -s Anc2.Anc2refChr8 1003 6 + 12804 ATAAAC -s mr.mrrefChr5 161463 6 + 294540 TTCTAT -s mr.mrrefChr5 158523 6 + 294540 TTAAAC -s simCow_chr6.simCow.chr6 280573 6 + 602619 ATAAAC -s simDog_chr6.simDog.chr6 317225 6 - 593897 ATAAAA -s simHuman_chr6.simHuman.chr6 227279 6 + 601863 TTAAAC -s simRat_chr6.simRat.chr6 299782 6 + 647215 TTAAAC -s simRat_chr6.simRat.chr6 302819 6 + 647215 TTATAA - -a -s simMouse_chr6.simMouse.chr6 311183 2 + 636262 TG -s Anc0.Anc0refChr8 961 2 + 17196 TA -s Anc1.Anc1refChr3 979 2 + 3661 TA -s Anc2.Anc2refChr8 1009 2 + 12804 TA -s mr.mrrefChr5 161469 2 + 294540 TG -s mr.mrrefChr5 158529 2 + 294540 TG -s simCow_chr6.simCow.chr6 280583 2 + 602619 TA -s simDog_chr6.simDog.chr6 317231 2 - 593897 TA -s simHuman_chr6.simHuman.chr6 227285 2 + 601863 TA -s simRat_chr6.simRat.chr6 299788 2 + 647215 TG -s simRat_chr6.simRat.chr6 302825 2 + 647215 TG - -a -s simMouse_chr6.simMouse.chr6 311185 16 + 636262 GGCAAATAAATGTGCA -s mr.mrrefChr5 161471 15 + 294540 GGCAAA-AAATGTGCA -s simRat_chr6.simRat.chr6 302827 15 + 647215 GGCAAG-GAATAAGCT - -a -s simMouse_chr6.simMouse.chr6 311201 2 + 636262 TA -s Anc0.Anc0refChr8 963 2 + 17196 GG -s Anc1.Anc1refChr3 981 2 + 3661 GG -s Anc2.Anc2refChr8 1011 2 + 12804 GG -s mr.mrrefChr5 161486 2 + 294540 TA -s mr.mrrefChr5 158531 2 + 294540 TG -s simCow_chr6.simCow.chr6 280585 2 + 602619 GG -s simDog_chr6.simDog.chr6 317233 2 - 593897 GG -s simHuman_chr6.simHuman.chr6 227287 2 + 601863 GG -s simRat_chr6.simRat.chr6 299790 2 + 647215 TG -s simRat_chr6.simRat.chr6 302842 2 + 647215 GA - -a -s simMouse_chr6.simMouse.chr6 311203 2 + 636262 GG -s Anc0.Anc0refChr8 965 2 + 17196 GG -s Anc1.Anc1refChr3 983 2 + 3661 GG -s Anc2.Anc2refChr8 1015 2 + 12804 GG -s mr.mrrefChr5 161488 2 + 294540 GG -s mr.mrrefChr5 158533 2 + 294540 GG -s simCow_chr6.simCow.chr6 280589 2 + 602619 GG -s simDog_chr6.simDog.chr6 317237 2 - 593897 GT -s simHuman_chr6.simHuman.chr6 227289 2 + 601863 GG -s simRat_chr6.simRat.chr6 299794 2 + 647215 GG -s simRat_chr6.simRat.chr6 302844 2 + 647215 GG - -a -s simMouse_chr6.simMouse.chr6 311205 4 + 636262 GTAA -s Anc0.Anc0refChr8 967 4 + 17196 TTAA -s Anc1.Anc1refChr3 985 4 + 3661 TTAA -s Anc2.Anc2refChr8 1017 4 + 12804 TTAA -s mr.mrrefChr5 161490 4 + 294540 GTAA -s mr.mrrefChr5 158535 4 + 294540 TTAA -s simCow_chr6.simCow.chr6 280591 4 + 602619 TTAA -s simDog_chr6.simDog.chr6 317239 4 - 593897 TTAA -s simHuman_chr6.simHuman.chr6 227291 4 + 601863 TTAA -s simRat_chr6.simRat.chr6 299796 4 + 647215 TTAA -s simRat_chr6.simRat.chr6 302852 4 + 647215 AAAA - -a -s simMouse_chr6.simMouse.chr6 311209 10 + 636262 CATAGGATAG -s Anc0.Anc0refChr8 975 10 + 17196 CACAGGAAAG -s Anc1.Anc1refChr3 993 10 + 3661 CACAGGAAAG -s Anc2.Anc2refChr8 1025 10 + 12804 CACAGGAAAG -s mr.mrrefChr5 161494 10 + 294540 CATAGGATAG -s mr.mrrefChr5 158540 10 + 294540 AAAAGGAGAG -s simCow_chr6.simCow.chr6 280599 10 + 602619 CACAGGAACG -s simDog_chr6.simDog.chr6 317247 10 - 593897 CACAGGAAAG -s simHuman_chr6.simHuman.chr6 227299 10 + 601863 CACATGAAAG -s simRat_chr6.simRat.chr6 299801 10 + 647215 AAAAGGAGAG -s simRat_chr6.simRat.chr6 302856 10 + 647215 CATAGAATAG - -a -s simMouse_chr6.simMouse.chr6 311219 5 + 636262 CCTAT -s mr.mrrefChr5 161504 5 + 294540 CCTAT -s simRat_chr6.simRat.chr6 302866 5 + 647215 TCAAT - -a -s simMouse_chr6.simMouse.chr6 311224 12 + 636262 ATACCACTGAAC -s Anc0.Anc0refChr8 985 11 + 17196 GTATGATGGA-C -s Anc1.Anc1refChr3 1003 12 + 3661 GTATGATGGAAC -s Anc2.Anc2refChr8 1035 11 + 12804 GTATGATGGA-T -s mr.mrrefChr5 161509 12 + 294540 ATACCACTGAAC -s mr.mrrefChr5 158550 12 + 294540 GTATTACAGAAC -s simCow_chr6.simCow.chr6 280609 10 + 602619 GGATGATGGA-- -s simDog_chr6.simDog.chr6 317257 10 - 593897 -TATGGAGCT-T -s simHuman_chr6.simHuman.chr6 227309 11 + 601863 GTATGATGGAG- -s simRat_chr6.simRat.chr6 299811 12 + 647215 GTATTACAGAAC -s simRat_chr6.simRat.chr6 302871 12 + 647215 ATACCACTGAAC - -a -s simMouse_chr6.simMouse.chr6 311236 20 + 636262 TCAAATGTCTGCAGTTTTAT -s Anc0.Anc0refChr8 996 7 + 17196 -------------TTTTCAT -s Anc1.Anc1refChr3 1015 7 + 3661 -------------TTTTCAT -s Anc2.Anc2refChr8 1046 7 + 12804 -------------TTTTCAT -s mr.mrrefChr5 161521 20 + 294540 TCAAATGTCTGCAGTTTTAT -s simDog_chr6.simDog.chr6 317267 7 - 593897 -------------TTTTCAT -s simHuman_chr6.simHuman.chr6 227320 7 + 601863 -------------ATTTCAT -s simRat_chr6.simRat.chr6 302883 20 + 647215 TCAAATGTCTGCAGTTTTAT - -a -s simMouse_chr6.simMouse.chr6 311256 1 + 636262 G -s Anc0.Anc0refChr8 1003 1 + 17196 G -s Anc1.Anc1refChr3 1022 1 + 3661 G -s Anc2.Anc2refChr8 1053 1 + 12804 G -s mr.mrrefChr5 161541 1 + 294540 G -s mr.mrrefChr5 158562 1 + 294540 G -s simDog_chr6.simDog.chr6 317274 1 - 593897 G -s simHuman_chr6.simHuman.chr6 227327 1 + 601863 G -s simRat_chr6.simRat.chr6 299823 1 + 647215 G -s simRat_chr6.simRat.chr6 302903 1 + 647215 G - -a -s simMouse_chr6.simMouse.chr6 311257 19 + 636262 AAAAATGCAGATTACTTTT -s Anc0.Anc0refChr8 1004 18 + 17196 TAAAATAC-AGTTTACTTT -s Anc1.Anc1refChr3 1023 18 + 3661 TAAAATAC-AGTTTACTTT -s Anc2.Anc2refChr8 1054 18 + 12804 TAAAATAA-CCTTCACTTC -s mr.mrrefChr5 161542 18 + 294540 AAAAATGC-GATTACTTTT -s mr.mrrefChr5 158563 18 + 294540 TGAAACAC-AGATTATTTT -s simCow_chr6.simCow.chr6 280619 8 + 602619 --AAACAA-CC-------- -s simDog_chr6.simDog.chr6 317275 18 - 593897 TAACATGA-CCTTCACTTC -s simHuman_chr6.simHuman.chr6 227328 18 + 601863 TAAAATAG-AGATTACTTT -s simRat_chr6.simRat.chr6 299824 18 + 647215 TGAAACAC-AGATTATTTT -s simRat_chr6.simRat.chr6 302908 18 + 647215 AAAAATGC-GATTACTTTC - -a -s simMouse_chr6.simMouse.chr6 311276 31 + 636262 AAGGTGAGAAGCAATGCGTAATCATACATAG -s Anc0.Anc0refChr8 1023 25 + 17196 CAAGT----AACAATGCAGAATCATACA--A -s Anc1.Anc1refChr3 1042 31 + 3661 CAAGTGTCAAACAATGCAGAATCATACATGA -s Anc2.Anc2refChr8 1073 25 + 12804 CAAGC----AACAATGCAGAATCATACA--A -s mr.mrrefChr5 161560 31 + 294540 AAGGTGAGAAGCAATGCGTAATCATACATAG -s mr.mrrefChr5 158582 31 + 294540 CACATGCCAAATAATGCATAATCACAAATGA -s simCow_chr6.simCow.chr6 280627 15 + 602619 ----------ACAGTGCAAA----CGCA--G -s simDog_chr6.simDog.chr6 317294 25 - 593897 CAAGC----AACAATGTAGAATCATAAA--A -s simHuman_chr6.simHuman.chr6 227347 31 + 601863 CAAGTATCAAACAATTCAGAACTATACATGA -s simRat_chr6.simRat.chr6 299843 31 + 647215 CACATGCCAAATAATGCATAATCACAAATGA -s simRat_chr6.simRat.chr6 302926 31 + 647215 AAAGTGAGAAGCAATGCATAATCATACATAG - -a -s simMouse_chr6.simMouse.chr6 311307 8 + 636262 TGTTGATG -s Anc0.Anc0refChr8 1048 8 + 17196 TGATGATG -s Anc1.Anc1refChr3 1073 8 + 3661 TGATGATG -s Anc2.Anc2refChr8 1098 8 + 12804 TGATGATG -s mr.mrrefChr5 161591 8 + 294540 TGTTGATG -s simCow_chr6.simCow.chr6 280642 8 + 602619 CGATGATG -s simDog_chr6.simDog.chr6 317319 8 - 593897 TGATGGCT -s simHuman_chr6.simHuman.chr6 227378 8 + 601863 TGATGATG -s simRat_chr6.simRat.chr6 302957 8 + 647215 TGATGATG - -a -s simMouse_chr6.simMouse.chr6 311315 7 + 636262 ATTTGTA -s Anc0.Anc0refChr8 1056 7 + 17196 GTATTTA -s Anc1.Anc1refChr3 1081 7 + 3661 GTATTTA -s Anc2.Anc2refChr8 1106 7 + 12804 GTATTGA -s mr.mrrefChr5 161599 7 + 294540 ATTTGTA -s mr.mrrefChr5 158613 7 + 294540 ATGGGTA -s simCow_chr6.simCow.chr6 280650 7 + 602619 AGTTCCA -s simDog_chr6.simDog.chr6 317327 6 - 593897 GTA-TGG -s simHuman_chr6.simHuman.chr6 227386 7 + 601863 GTACTTA -s simRat_chr6.simRat.chr6 299874 7 + 647215 ATGGGTA -s simRat_chr6.simRat.chr6 302965 7 + 647215 GTATGTA - -a -s simMouse_chr6.simMouse.chr6 311322 3 + 636262 TAT -s Anc0.Anc0refChr8 1063 3 + 17196 TAT -s Anc1.Anc1refChr3 1088 3 + 3661 TAT -s Anc2.Anc2refChr8 1113 3 + 12804 TAT -s mr.mrrefChr5 161606 3 + 294540 TAT -s simCow_chr6.simCow.chr6 280657 3 + 602619 TAT -s simDog_chr6.simDog.chr6 317333 3 - 593897 TAT -s simHuman_chr6.simHuman.chr6 227393 3 + 601863 TAT -s simRat_chr6.simRat.chr6 302972 3 + 647215 TAT - -a -s simMouse_chr6.simMouse.chr6 311325 3 + 636262 ACA -s Anc0.Anc0refChr8 1066 3 + 17196 ACA -s Anc1.Anc1refChr3 1091 3 + 3661 ACA -s Anc2.Anc2refChr8 1116 3 + 12804 ACA -s mr.mrrefChr5 161609 3 + 294540 ACA -s mr.mrrefChr5 158620 3 + 294540 AAA -s simCow_chr6.simCow.chr6 280660 3 + 602619 ACA -s simDog_chr6.simDog.chr6 317336 3 - 593897 ATA -s simHuman_chr6.simHuman.chr6 227396 3 + 601863 ACA -s simRat_chr6.simRat.chr6 299881 3 + 647215 AAA -s simRat_chr6.simRat.chr6 302975 3 + 647215 ACA - -a -s simMouse_chr6.simMouse.chr6 311328 17 + 636262 TTGTGGTTAAACCCATT -s Anc0.Anc0refChr8 1070 17 + 17196 CCATGGATAAACCCATT -s Anc1.Anc1refChr3 1095 17 + 3661 CCATGGATAAACCCATT -s Anc2.Anc2refChr8 1120 17 + 12804 CCATGGGTAAACCCATT -s mr.mrrefChr5 161612 17 + 294540 TTGTGGTTAAACCCATT -s mr.mrrefChr5 158623 17 + 294540 CTATTAATAGTAACAAT -s simCow_chr6.simCow.chr6 280664 17 + 602619 TCATGGGTAGGCCTATT -s simDog_chr6.simDog.chr6 317340 17 - 593897 CCATGGGTAAACCCAGA -s simHuman_chr6.simHuman.chr6 227400 17 + 601863 CCATGAATAACCACATT -s simRat_chr6.simRat.chr6 299884 17 + 647215 CTATTAATAGTAACAAT -s simRat_chr6.simRat.chr6 302978 17 + 647215 TTGTGGGTAAACCCATT - -a -s simMouse_chr6.simMouse.chr6 311345 3 + 636262 TAT -s Anc0.Anc0refChr8 1094 3 + 17196 ACA -s Anc1.Anc1refChr3 1119 3 + 3661 ACA -s Anc2.Anc2refChr8 1144 3 + 12804 ACA -s mr.mrrefChr5 161629 3 + 294540 TAT -s mr.mrrefChr5 158640 3 + 294540 GCA -s simCow_chr6.simCow.chr6 280688 3 + 602619 ATA -s simDog_chr6.simDog.chr6 317364 3 - 593897 ACA -s simHuman_chr6.simHuman.chr6 227424 3 + 601863 ACA -s simRat_chr6.simRat.chr6 299901 3 + 647215 GCA -s simRat_chr6.simRat.chr6 302995 3 + 647215 TAC - -a -s simMouse_chr6.simMouse.chr6 311354 16 + 636262 AATTTGGCAGATAATT - -a -s simMouse_chr6.simMouse.chr6 311391 3 + 636262 GGG -s Anc0.Anc0refChr8 1133 3 + 17196 GTG -s Anc1.Anc1refChr3 1158 3 + 3661 GTG -s Anc2.Anc2refChr8 1183 3 + 12804 GTG -s mr.mrrefChr5 161659 3 + 294540 GGG -s simCow_chr6.simCow.chr6 280727 3 + 602619 GGG -s simDog_chr6.simDog.chr6 590034 3 - 593897 ATG -s simRat_chr6.simRat.chr6 303037 3 + 647215 GGG - -a -s simMouse_chr6.simMouse.chr6 311416 5 + 636262 TAGTC -s Anc0.Anc0refChr8 1158 5 + 17196 TAGAC -s Anc1.Anc1refChr3 1183 5 + 3661 TAGAC -s Anc2.Anc2refChr8 1208 5 + 12804 TAAAC -s mr.mrrefChr5 161684 5 + 294540 TAGTC -s simCow_chr6.simCow.chr6 280752 5 + 602619 TAAAC -s simDog_chr6.simDog.chr6 590059 5 - 593897 TAAAC -s simHuman_chr6.simHuman.chr6 227485 5 + 601863 TAGAC -s simRat_chr6.simRat.chr6 303062 5 + 647215 TACTT - -a -s simMouse_chr6.simMouse.chr6 311434 5 + 636262 GAGTG - -a -s simMouse_chr6.simMouse.chr6 311470 6 + 636262 CATCAA -s Anc0.Anc0refChr8 1205 4 + 17196 CAT--A -s Anc1.Anc1refChr3 1232 6 + 3661 CATCAA -s Anc2.Anc2refChr8 1255 4 + 12804 CAT--A -s mr.mrrefChr5 161733 6 + 294540 CATCAA -s mr.mrrefChr5 158812 6 + 294540 CAGCAA -s simCow_chr6.simCow.chr6 280799 4 + 602619 CAT--A -s simDog_chr6.simDog.chr6 590105 4 - 593897 CAT--A -s simHuman_chr6.simHuman.chr6 227533 4 + 601863 AAG--A -s simRat_chr6.simRat.chr6 608905 6 - 647215 CAGGAA -s simRat_chr6.simRat.chr6 300076 6 + 647215 CAGCAA -s simRat_chr6.simRat.chr6 303111 6 + 647215 CATCAT - -a -s simMouse_chr6.simMouse.chr6 311485 2 + 636262 TA - -a -s simMouse_chr6.simMouse.chr6 311514 14 + 636262 GTTTCAGGTCTGTA - -a -s simMouse_chr6.simMouse.chr6 311578 6 + 636262 GTAGCT -s Anc0.Anc0refChr8 1311 2 + 17196 T----C -s Anc1.Anc1refChr3 1344 2 + 3661 T----C -s Anc2.Anc2refChr8 1367 2 + 12804 T----C -s mr.mrrefChr5 161825 2 + 294540 G----T -s mr.mrrefChr5 158935 2 + 294540 C----G -s simCow_chr6.simCow.chr6 280902 2 + 602619 T----T -s simDog_chr6.simDog.chr6 590219 2 - 593897 T----C -s simHuman_chr6.simHuman.chr6 227636 2 + 601863 T----C -s simRat_chr6.simRat.chr6 300199 2 + 647215 C----G -s simRat_chr6.simRat.chr6 303203 2 + 647215 G----T - -a -s simMouse_chr6.simMouse.chr6 311620 1 + 636262 C -s Anc1.Anc1refChr3 1396 1 + 3661 C -s mr.mrrefChr5 161863 1 + 294540 C -s mr.mrrefChr5 158987 1 + 294540 C -s simHuman_chr6.simHuman.chr6 227690 1 + 601863 C -s simRat_chr6.simRat.chr6 300251 1 + 647215 C -s simRat_chr6.simRat.chr6 303241 1 + 647215 C - -a -s simMouse_chr6.simMouse.chr6 311640 2 + 636262 AA -s mr.mrrefChr5 161883 2 + 294540 AA -s simRat_chr6.simRat.chr6 303262 2 + 647215 AA - -a -s simMouse_chr6.simMouse.chr6 311685 5 + 636262 CTTGC -s Anc0.Anc0refChr8 1433 4 + 17196 -TTGC -s Anc1.Anc1refChr3 1491 4 + 3661 -TTGC -s Anc2.Anc2refChr8 1489 4 + 12804 -TTGC -s mr.mrrefChr5 161928 5 + 294540 CTTGC -s simCow_chr6.simCow.chr6 281017 4 + 602619 -TTGT -s simDog_chr6.simDog.chr6 590338 4 - 593897 -TTGC -s simHuman_chr6.simHuman.chr6 227802 4 + 601863 -TTCC -s simRat_chr6.simRat.chr6 303307 5 + 647215 CTTGC - -a -s simMouse_chr6.simMouse.chr6 311699 3 + 636262 TCA -s mr.mrrefChr5 161942 3 + 294540 TCA -s simRat_chr6.simRat.chr6 303321 3 + 647215 TCA - -a -s simMouse_chr6.simMouse.chr6 311780 2 + 636262 TT -s Anc0.Anc0refChr8 1576 2 + 17196 AA -s Anc1.Anc1refChr3 1634 2 + 3661 AA -s Anc2.Anc2refChr8 1632 2 + 12804 AA -s mr.mrrefChr5 162023 2 + 294540 TT -s simCow_chr6.simCow.chr6 281160 2 + 602619 AA -s simDog_chr6.simDog.chr6 317503 2 - 593897 AA -s simHuman_chr6.simHuman.chr6 227944 2 + 601863 AA -s simRat_chr6.simRat.chr6 303402 2 + 647215 AT - -a -s simMouse_chr6.simMouse.chr6 311785 2 + 636262 AC -s Anc0.Anc0refChr8 1581 2 + 17196 GA -s Anc1.Anc1refChr3 1639 2 + 3661 GA -s Anc2.Anc2refChr8 1637 2 + 12804 GA -s mr.mrrefChr5 162028 2 + 294540 AC -s mr.mrrefChr5 159236 2 + 294540 GA -s simCow_chr6.simCow.chr6 281165 2 + 602619 CA -s simDog_chr6.simDog.chr6 317508 2 - 593897 GA -s simHuman_chr6.simHuman.chr6 227949 2 + 601863 GA -s simRat_chr6.simRat.chr6 300493 2 + 647215 GA -s simRat_chr6.simRat.chr6 303407 2 + 647215 AA - -a -s simMouse_chr6.simMouse.chr6 311842 4 + 636262 GAAC -s Anc0.Anc0refChr8 1639 4 + 17196 GAAC -s Anc1.Anc1refChr3 1697 4 + 3661 GAAC -s Anc2.Anc2refChr8 1696 4 + 12804 GAAC -s mr.mrrefChr5 162085 4 + 294540 GAAC -s simCow_chr6.simCow.chr6 281224 4 + 602619 GATC -s simDog_chr6.simDog.chr6 317566 4 - 593897 AAAC -s simHuman_chr6.simHuman.chr6 228007 4 + 601863 GAAC -s simRat_chr6.simRat.chr6 303465 4 + 647215 GAAC - -a -s simMouse_chr6.simMouse.chr6 311894 1 + 636262 G - -a -s simMouse_chr6.simMouse.chr6 311941 1 + 636262 A - -a -s simMouse_chr6.simMouse.chr6 311967 1 + 636262 A -s Anc0.Anc0refChr8 1781 1 + 17196 A -s Anc1.Anc1refChr3 1843 1 + 3661 A -s Anc2.Anc2refChr8 1838 1 + 12804 A -s mr.mrrefChr5 162208 1 + 294540 A -s simCow_chr6.simCow.chr6 281368 1 + 602619 T -s simDog_chr6.simDog.chr6 317708 1 - 593897 A -s simRat_chr6.simRat.chr6 303594 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 311976 3 + 636262 ATC -s Anc0.Anc0refChr8 1790 3 + 17196 ACC -s Anc1.Anc1refChr3 1852 3 + 3661 ACC -s Anc2.Anc2refChr8 1847 3 + 12804 ACC -s mr.mrrefChr5 162217 3 + 294540 ATC -s simCow_chr6.simCow.chr6 281377 3 + 602619 ACC -s simDog_chr6.simDog.chr6 317759 3 - 593897 ACC -s simRat_chr6.simRat.chr6 303604 3 + 647215 ACC - -a -s simMouse_chr6.simMouse.chr6 312004 1 + 636262 C -s mr.mrrefChr5 162245 1 + 294540 C -s simRat_chr6.simRat.chr6 303632 1 + 647215 C - -a -s simMouse_chr6.simMouse.chr6 312021 2 + 636262 CC - -a -s simMouse_chr6.simMouse.chr6 312035 3 + 636262 GCT -s Anc0.Anc0refChr8 1847 3 + 17196 GCC -s Anc1.Anc1refChr3 1913 3 + 3661 GCC -s Anc2.Anc2refChr8 1904 3 + 12804 GCC -s mr.mrrefChr5 162274 3 + 294540 GCT -s mr.mrrefChr5 159497 3 + 294540 GCC -s simCow_chr6.simCow.chr6 281432 3 + 602619 GCC -s simDog_chr6.simDog.chr6 317816 3 - 593897 GCC -s simHuman_chr6.simHuman.chr6 228210 3 + 601863 TCC -s simRat_chr6.simRat.chr6 300753 3 + 647215 GCC -s simRat_chr6.simRat.chr6 303661 3 + 647215 GCT - -a -s simMouse_chr6.simMouse.chr6 312042 2 + 636262 CT -s Anc0.Anc0refChr8 1854 2 + 17196 CT -s Anc1.Anc1refChr3 1920 2 + 3661 CT -s Anc2.Anc2refChr8 1911 2 + 12804 CT -s mr.mrrefChr5 162281 2 + 294540 CT -s simCow_chr6.simCow.chr6 281439 2 + 602619 AT -s simDog_chr6.simDog.chr6 317823 2 - 593897 CT -s simHuman_chr6.simHuman.chr6 228217 2 + 601863 CT -s simRat_chr6.simRat.chr6 303668 2 + 647215 CT - -a -s simMouse_chr6.simMouse.chr6 312044 4 + 636262 TTCA -s Anc0.Anc0refChr8 1856 4 + 17196 TTGA -s Anc1.Anc1refChr3 1922 4 + 3661 TTGA -s Anc2.Anc2refChr8 1913 4 + 12804 TTGA -s mr.mrrefChr5 162283 4 + 294540 TTCA -s simCow_chr6.simCow.chr6 281441 4 + 602619 TTGA -s simDog_chr6.simDog.chr6 317825 4 - 593897 TTGA -s simHuman_chr6.simHuman.chr6 228219 4 + 601863 TTGA -s simRat_chr6.simRat.chr6 303674 4 + 647215 TTCA - -a -s simMouse_chr6.simMouse.chr6 312048 26 + 636262 AAAATATACTCGTAATAATCAAAACT -s Anc0.Anc0refChr8 1865 26 + 17196 AGGCCATACTCATAGTAATCAGAACT -s Anc1.Anc1refChr3 1931 26 + 3661 AGGCCATACTCATAGTAATCAGAACT -s Anc2.Anc2refChr8 1922 26 + 12804 AGGCCTTACTCATAGTGATCAGAACT -s mr.mrrefChr5 162287 26 + 294540 AAAATATACTCGTAATAATCAAAACT -s simCow_chr6.simCow.chr6 281450 25 + 602619 AAGG-TTACTCATTGTGATTGGAACT -s simDog_chr6.simDog.chr6 317834 26 - 593897 AGCCCTTACTCATAGTGATCAGAACT -s simHuman_chr6.simHuman.chr6 228228 25 + 601863 AGGTCATACTCA-AGTAATCAGAACT -s simRat_chr6.simRat.chr6 303678 26 + 647215 AAAATATAGTCATTATAATTAAAACT - -a -s simMouse_chr6.simMouse.chr6 312074 6 + 636262 TTTAAT -s Anc0.Anc0refChr8 1892 6 + 17196 TTTTGT -s Anc1.Anc1refChr3 1958 6 + 3661 TTTTGT -s Anc2.Anc2refChr8 1949 6 + 12804 TCTTGT -s mr.mrrefChr5 162313 6 + 294540 TTTAAT -s simCow_chr6.simCow.chr6 281476 5 + 602619 TCTTG- -s simDog_chr6.simDog.chr6 317861 5 - 593897 -CTTGT -s simHuman_chr6.simHuman.chr6 228254 6 + 601863 TTTTGT -s simRat_chr6.simRat.chr6 303704 6 + 647215 TCTTAT - -a -s simMouse_chr6.simMouse.chr6 312080 73 + 636262 TCTAGTTTGACTGCAGGAGGAACAACAATAGTTTATAGTTACTCACCCTACATGAGAAGTAATGCAGAGGGCG -s Anc0.Anc0refChr8 1898 15 + 17196 TCTAACTTGA-GACAG--------------------------------------------------------- -s Anc1.Anc1refChr3 1964 16 + 3661 TCTAACTTGAAGACAG--------------------------------------------------------- -s Anc2.Anc2refChr8 1955 15 + 12804 TCTTACTTTT-TCCAG--------------------------------------------------------- -s mr.mrrefChr5 162319 64 + 294540 TCTAGTTTGACTGCAGGAGGAACAACAATAGTTTATAGTTACTCACCCTA---------TAATGCAGAGGGCG -s simCow_chr6.simCow.chr6 281481 15 + 602619 TCCCAACTTT-TTAAG--------------------------------------------------------- -s simDog_chr6.simDog.chr6 317866 15 - 593897 TTTTTCTTTT-TCCAG--------------------------------------------------------- -s simHuman_chr6.simHuman.chr6 228260 16 + 601863 CCTAACTTGAAGCCAG--------------------------------------------------------- -s simRat_chr6.simRat.chr6 303712 64 + 647215 TCTGGCTTAAATGCAGTTTGAACAGCAATAATTTATAGTTACCCACCCTC---------TGATGTGGAGGCAG - -a -s simMouse_chr6.simMouse.chr6 312158 8 + 636262 GTGGACTG -s mr.mrrefChr5 162388 8 + 294540 GTGGACTG -s simRat_chr6.simRat.chr6 303781 8 + 647215 GTGGACTA - -a -s simMouse_chr6.simMouse.chr6 312185 2 + 636262 CT -s mr.mrrefChr5 162415 2 + 294540 CT -s simRat_chr6.simRat.chr6 303808 2 + 647215 CC - -a -s simMouse_chr6.simMouse.chr6 312232 1 + 636262 C -s Anc0.Anc0refChr8 1982 1 + 17196 t -s Anc1.Anc1refChr3 2049 1 + 3661 T -s Anc2.Anc2refChr8 2067 1 + 12804 t -s mr.mrrefChr5 162462 1 + 294540 C -s simCow_chr6.simCow.chr6 281592 1 + 602619 t -s simDog_chr6.simDog.chr6 317993 1 - 593897 t -s simHuman_chr6.simHuman.chr6 228327 1 + 601863 T -s simRat_chr6.simRat.chr6 303855 1 + 647215 C - -a -s simMouse_chr6.simMouse.chr6 312258 29 + 636262 TCATCTTAGTTCCTTATTCACAAGAGACA -s mr.mrrefChr5 162488 29 + 294540 TCATCTTAGTTCCTTATTCACAAGAGACA -s simRat_chr6.simRat.chr6 303882 29 + 647215 TCGTCTCCATTCCTATTATACAAGAGACA - -a -s simMouse_chr6.simMouse.chr6 312296 1 + 636262 G -s Anc0.Anc0refChr8 2018 1 + 17196 g -s Anc1.Anc1refChr3 2085 1 + 3661 g -s Anc2.Anc2refChr8 2103 1 + 12804 g -s mr.mrrefChr5 162526 1 + 294540 G -s simCow_chr6.simCow.chr6 281664 1 + 602619 g -s simDog_chr6.simDog.chr6 318035 1 - 593897 g -s simHuman_chr6.simHuman.chr6 228363 1 + 601863 g -s simRat_chr6.simRat.chr6 303920 1 + 647215 G - -a -s simMouse_chr6.simMouse.chr6 312297 1 + 636262 T -s Anc0.Anc0refChr8 2019 1 + 17196 a -s Anc1.Anc1refChr3 2086 1 + 3661 a -s Anc2.Anc2refChr8 2104 1 + 12804 a -s mr.mrrefChr5 162527 1 + 294540 T -s simCow_chr6.simCow.chr6 281665 1 + 602619 t -s simDog_chr6.simDog.chr6 318037 1 - 593897 a -s simHuman_chr6.simHuman.chr6 228364 1 + 601863 g -s simRat_chr6.simRat.chr6 303921 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 312307 11 + 636262 CTTATTTAAAA -s mr.mrrefChr5 162537 11 + 294540 CTTATTTAAAA -s simRat_chr6.simRat.chr6 303931 11 + 647215 CTTATCTAAAA - -a -s simMouse_chr6.simMouse.chr6 312318 24 + 636262 TGGGCAGTCATGACAGTGCAAGAT -s mr.mrrefChr5 162548 24 + 294540 TGGGcagtcatgacagtgcaagat -s simRat_chr6.simRat.chr6 303977 24 + 647215 CGGGcagtcatgacagtgcaagat - -a -s simMouse_chr6.simMouse.chr6 312408 3 + 636262 CCA - -a -s simMouse_chr6.simMouse.chr6 312427 10 + 636262 AGGTGGCAAG -s Anc0.Anc0refChr8 2112 10 + 17196 aggttgcaag -s Anc1.Anc1refChr3 2182 10 + 3661 aggttgcaag -s Anc2.Anc2refChr8 2197 10 + 12804 aggttgcaag -s mr.mrrefChr5 162654 10 + 294540 aggtggcaag -s simCow_chr6.simCow.chr6 281758 10 + 602619 atggtgcatg -s simDog_chr6.simDog.chr6 318117 10 - 593897 aggttgcaag -s simHuman_chr6.simHuman.chr6 228453 10 + 601863 aggtcagaag -s simRat_chr6.simRat.chr6 304083 10 + 647215 gggtggcaag - -a -s simMouse_chr6.simMouse.chr6 312438 1 + 636262 G - -a -s simMouse_chr6.simMouse.chr6 312448 3 + 636262 TAT -s Anc0.Anc0refChr8 2133 3 + 17196 tag -s Anc1.Anc1refChr3 2203 3 + 3661 tag -s Anc2.Anc2refChr8 2218 3 + 12804 tag -s mr.mrrefChr5 162674 3 + 294540 tat -s simCow_chr6.simCow.chr6 281780 3 + 602619 tag -s simDog_chr6.simDog.chr6 318194 3 - 593897 tag -s simHuman_chr6.simHuman.chr6 228474 3 + 601863 tag -s simRat_chr6.simRat.chr6 304103 3 + 647215 tgg - -a -s simMouse_chr6.simMouse.chr6 312481 6 + 636262 CGCAGT -s Anc0.Anc0refChr8 2216 6 + 17196 ctcagc -s Anc1.Anc1refChr3 2286 6 + 3661 ctcagc -s Anc2.Anc2refChr8 2301 6 + 12804 cttagc -s mr.mrrefChr5 162707 6 + 294540 CGCAGT -s simCow_chr6.simCow.chr6 281861 6 + 602619 cttagc -s simDog_chr6.simDog.chr6 318277 6 - 593897 cttagc -s simHuman_chr6.simHuman.chr6 228571 6 + 601863 ctcagc -s simRat_chr6.simRat.chr6 304219 6 + 647215 TGCAGT - -a -s simMouse_chr6.simMouse.chr6 312487 61 + 636262 ATGTAGCTCTAAGGCAGGAATGAAACTTCTAATTCTATAAGGAAGTGTGCCATCACTCCAA -s Anc0.Anc0refChr8 2223 7 + 17196 acacaac------------------------------------------------------ -s Anc1.Anc1refChr3 2293 45 + 3661 acacaaccttatggcagaaatgaaatttcttacagcccaagggag---------------- -s Anc2.Anc2refChr8 2308 7 + 12804 acacaac------------------------------------------------------ -s mr.mrrefChr5 162713 61 + 294540 ATGTAGCCCTAAGGCAGGAATGAAACTTCTAATTGTACAAGGAAGTGTGCCATCACTCCAA -s simCow_chr6.simCow.chr6 281868 7 + 602619 atgcaac------------------------------------------------------ -s simDog_chr6.simDog.chr6 318284 7 - 593897 acacaac------------------------------------------------------ -s simHuman_chr6.simHuman.chr6 228578 45 + 601863 acacaacctcatggcagaaatgcattttcttacagcccaagggag---------------- -s simRat_chr6.simRat.chr6 304225 61 + 647215 ATGTAGCCCTAAGGCAGGAACAAAACTTCTAATAGCACAACGAAGTGTGGCATCACTCCTA - -a -s simMouse_chr6.simMouse.chr6 312548 129 + 636262 CTGGAATGTATGCCATTTTTGACAGGTGAGTAAGCAGAGGTGGCTAGGGGTATTGTGCCTGTGAGTAAGGTTATCAACAAAGCACATTAAAGAGAGGCTAACATGGAATGTCACTTGTCTCACACCATG -s Anc0.Anc0refChr8 2230 20 + 17196 -------------------------------------------------------------------------------------gttgaggag---------tggaa---------------atgaaa -s Anc1.Anc1refChr3 2338 67 + 3661 -----------------------------------------------agggaatggaagagggaataatggtagcaacacagcacgttgaggagggactaacgtggaa---------------atgaaa -s Anc2.Anc2refChr8 2315 20 + 12804 -------------------------------------------------------------------------------------gttatagag---------tggaa---------------atgaaa -s mr.mrrefChr5 162774 129 + 294540 CTGGAATATATGCCATTTTTGACAGGTGAGTAAGCAGAGGTGGCTAGGGGTATTGTACCAGTGAGTAAGGTTATCAACAAAGCACATTAAAGAGAGGCTAACATGGAATGTCACTTGTCTCATACCATG -s simCow_chr6.simCow.chr6 281875 18 + 602619 -------------------------------------------------------------------------------------tt--ttaag---------tggaa---------------atgcaa -s simDog_chr6.simDog.chr6 318291 20 - 593897 -------------------------------------------------------------------------------------gttatagag---------cagaa---------------ctcaaa -s simHuman_chr6.simHuman.chr6 228623 67 + 601863 -----------------------------------------------agggaatggaagagggaataatggtagcaacacagcacgttgaggagggactaacgtggaa---------------atgaaa -s simRat_chr6.simRat.chr6 304311 129 + 647215 CTGGAATATGTGCCATTTTTGACAGGTGAGTAAGCAGAGGTGGCTAAGGGTATTGTACCAACGAGTAAGGTTAACAACAAAGCGCATCACAGATAGGCTAACATGGAATGTCACCAGTCTGATACGATG - -a -s simMouse_chr6.simMouse.chr6 312695 3 + 636262 AAT -s Anc1.Anc1refChr3 2424 3 + 3661 gcc -s mr.mrrefChr5 162921 3 + 294540 AAT -s simHuman_chr6.simHuman.chr6 228709 3 + 601863 gcc -s simRat_chr6.simRat.chr6 304458 3 + 647215 AGT - -a -s simMouse_chr6.simMouse.chr6 312733 2 + 636262 AG -s Anc0.Anc0refChr8 2332 2 + 17196 GG -s Anc1.Anc1refChr3 2506 2 + 3661 GG -s Anc2.Anc2refChr8 2417 2 + 12804 GG -s mr.mrrefChr5 162959 2 + 294540 AG -s simCow_chr6.simCow.chr6 281973 2 + 602619 GG -s simDog_chr6.simDog.chr6 318393 2 - 593897 AG -s simHuman_chr6.simHuman.chr6 228797 2 + 601863 GG -s simRat_chr6.simRat.chr6 304496 2 + 647215 AG - -a -s simMouse_chr6.simMouse.chr6 312761 11 + 636262 GCAAGACAATA -s Anc0.Anc0refChr8 2360 8 + 17196 TCAC---AAAC -s Anc1.Anc1refChr3 2534 8 + 3661 TCAC---AAAC -s Anc2.Anc2refChr8 2445 8 + 12804 TCAC---AAAC -s mr.mrrefChr5 162987 8 + 294540 GCAA---AATA -s simCow_chr6.simCow.chr6 282001 8 + 602619 GCAG---AGAC -s simDog_chr6.simDog.chr6 318415 8 - 593897 TCAC---AAAC -s simHuman_chr6.simHuman.chr6 228825 8 + 601863 CCCC---AAAT -s simRat_chr6.simRat.chr6 304524 8 + 647215 ACAA---AAGC - -a -s simMouse_chr6.simMouse.chr6 312834 12 + 636262 GACATTGGTGTG -s Anc0.Anc0refChr8 2424 1 + 17196 -----------T -s Anc1.Anc1refChr3 2605 12 + 3661 TATGATAATGTT -s Anc2.Anc2refChr8 2509 1 + 12804 -----------T -s mr.mrrefChr5 163057 12 + 294540 GATGTTGGTGTG -s simCow_chr6.simCow.chr6 282065 1 + 602619 -----------T -s simDog_chr6.simDog.chr6 318480 1 - 593897 -----------T -s simHuman_chr6.simHuman.chr6 228896 12 + 601863 TATGATAATGTT -s simRat_chr6.simRat.chr6 304594 12 + 647215 GATGTTGGTGTG - -a -s simMouse_chr6.simMouse.chr6 312846 79 + 636262 TGCACCAGAATGAATCGGGCACATGTATGAAATCCTCGCTCCATCATAGGCCAGGTGGACCCACCATTAAAAGATCAAA -s Anc0.Anc0refChr8 2426 64 + 17196 TGGGCAAGAATGAGTCAGACAC---CTTTAAATA--------ATA----ACCAACTAGGTGCACCAGTAAGAGGTCCAA -s Anc1.Anc1refChr3 2618 71 + 3661 TGGGCAAGAATGAGTCAGACACATGCTTTAAATA--------ATAGTAGACCAACTAGGTGCACCAGTAAGAGGTCCAA -s Anc2.Anc2refChr8 2511 64 + 12804 TGTGCATGAAATGGCCTGCTAC---CTCTCAATA--------TTA----ACCTACTAGGTGCACCAGTAAGAGGTCCAA -s mr.mrrefChr5 163070 79 + 294540 TGCGCCAGAATGAATCAGACACATGTATGAAATCCTCGCTCCATCATAGGCCAGGTGGACCCACCATTAAGAGGTCAAA -s simCow_chr6.simCow.chr6 282067 64 + 602619 TGTGCATGAAATGGCCTTGTAC---CTCATATCA--------CTG----ACCTACTCAGAGCACCAGTAAGAGGTCCAA -s simDog_chr6.simDog.chr6 318482 64 - 593897 TATGCATGAAATGGCCTGCTAT---CTCTCAATA--------TTA----ACCTAGTAGGTGTACCGGTAATAGTTTCAA -s simHuman_chr6.simHuman.chr6 228909 71 + 601863 TGGGCAAGGGTGAGTCAGACATATGCGTTAAATA--------ATAGTAGACCAACTAGGTGCACCAATAAGAGGTCCAA -s simRat_chr6.simRat.chr6 304607 67 + 647215 TGCGCCAGAATGAATCAGACACATGTATGAAATCCTTGCTCCATCATAGG------------AACATTTAGAGGTCAAA - -a -s simMouse_chr6.simMouse.chr6 312925 252 + 636262 TATAACTTTCTCATGCTTAACATTGCTTAGATTTTGCACAACAGTGCCTCGTGCCTCGTGCAAAGCTTCATTAAATGGCAAACATGGACACGTACAAGCGGTTAGTGCTTCACCCTGCCCTGCTTGATGTGATGTAAAACAGTCACAGGCACCTGTAGAGGGAGCCTGTTCACCTCACACAAGAGGTTTGACATGTTTCCCTTTCTCCATTATTATTAGCTAGTTGAAGACCTTTTATCTCTTTTAATAGCC -s Anc0.Anc0refChr8 2490 50 + 17196 TCTACCTTACTC---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CATTAGTCTTCTAAAGACTTTTCA-CTCTTTTAAAGACC -s Anc1.Anc1refChr3 2689 50 + 3661 TCTACCTTACTC---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CATTAGTCTTCTAAAGACTTTTCA-CTCTTTTAAAGACC -s Anc2.Anc2refChr8 2582 50 + 12804 TCTACCTTACTC---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CATTAGTCTTCTAAAGACTTTTCA-CTTTTCTAAAGACT -s mr.mrrefChr5 163149 226 + 294540 TATACCTTTCTCATGCTTAACAT-GCTTAGATTTTGCACA----------GTGCCTCGTGCAAAGCTTCATTAAATGGCAAACATGGACACGTACAAGCGGTTAGTGCTTCACCCTGCCCTGCTTGATGTGATGTAAAACAGTCACAGGCAC-TGTAGAGGGAGCCTGTTCACCTCACACAAGAGGTTTGACATGTTTC--------------TATTAGCTAGTTGAAGACCTTTTATCTCTTTTAAAAGCC -s simCow_chr6.simCow.chr6 282138 48 + 602619 GGGATCTTATTC---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CACT--TCTTCTAGAGACTCTTCA-CTAGTCTAAAGACT -s simDog_chr6.simDog.chr6 318561 48 - 593897 TCTACCTTACTC---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CATTAGTCTTCTGAAGACTTT--A-CTTTTCTAAAGACT -s simHuman_chr6.simHuman.chr6 228980 50 + 601863 TCTACCTTACTC---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CGTTAGTCTTCTAAAGACTTTTCA-CTCTTTTAAAGACC -s simRat_chr6.simRat.chr6 304674 204 + 647215 TATACCTTTCTCATATATAACGT-GCTTAGATTTCACACA----------GTGCCTCGTGCAAAGCTCCATTAAATGGCAAATGTGGCCATGTATATGCAGCTAGTGCTTCACCCTGCCTTGCTTGATGCAATGTTAAACAGCCACAGGCAC-TGCAAAGGGAGCCTGTTCACCTCACGCATGATGTTTGTCATGTTTC------------------------------------TATCTCTTTTAAAAGCC - -a -s simMouse_chr6.simMouse.chr6 313177 10 + 636262 AATCCTTGAA -s Anc0.Anc0refChr8 2546 10 + 17196 AATGCTAAAT -s Anc1.Anc1refChr3 2745 10 + 3661 AATGCTAAAT -s Anc2.Anc2refChr8 2638 10 + 12804 AATGCTAAAT -s mr.mrrefChr5 163375 10 + 294540 AATCCTAGAT -s simCow_chr6.simCow.chr6 282189 8 + 602619 --TGCCAATT -s simDog_chr6.simDog.chr6 318616 10 - 593897 AATCCTAAAT -s simHuman_chr6.simHuman.chr6 229036 10 + 601863 AATGCTACAT -s simRat_chr6.simRat.chr6 304878 10 + 647215 AATCCTAGAT - -a -s simMouse_chr6.simMouse.chr6 313187 19 + 636262 TAGAATGGGTTAAAACCTT -s Anc0.Anc0refChr8 2557 19 + 17196 AGAGATGGATCCAAACCTT -s Anc1.Anc1refChr3 2756 19 + 3661 AGAGATGGATCCAAACCTT -s Anc2.Anc2refChr8 2649 19 + 12804 AGAGATGGATCCAAGCCTT -s mr.mrrefChr5 163385 19 + 294540 AGAGATGGGTTAAAACCTT -s simCow_chr6.simCow.chr6 282198 19 + 602619 AGAGGTGGATTCATGCTAT -s simDog_chr6.simDog.chr6 318627 19 - 593897 AGAGATGGATCCAAGCCTT -s simHuman_chr6.simHuman.chr6 229047 19 + 601863 AGAGATGGATCCAGACCTT -s simRat_chr6.simRat.chr6 304888 19 + 647215 AGAGATGGGTTAAAACCTT - -a -s simMouse_chr6.simMouse.chr6 313206 5 + 636262 TTAAG -s Anc0.Anc0refChr8 2580 5 + 17196 TAAAG -s Anc1.Anc1refChr3 2779 5 + 3661 TAAAG -s Anc2.Anc2refChr8 2672 5 + 12804 TAAAC -s mr.mrrefChr5 163404 5 + 294540 TTAAG -s simCow_chr6.simCow.chr6 282221 3 + 602619 TGA-- -s simDog_chr6.simDog.chr6 318650 5 - 593897 TAAAC -s simHuman_chr6.simHuman.chr6 229070 5 + 601863 TAAAG -s simRat_chr6.simRat.chr6 304907 4 + 647215 ATG-G - -a -s simMouse_chr6.simMouse.chr6 313211 23 + 636262 TTCATTGGCTTAGTCAGGTTTTG -s Anc0.Anc0refChr8 2588 17 + 17196 TCCCCTGGCTTATTCAG------ -s Anc1.Anc1refChr3 2787 17 + 3661 TCCCCTGGCTTATTCAG------ -s Anc2.Anc2refChr8 2680 17 + 12804 CCCCCTGGCCTATTTAG------ -s mr.mrrefChr5 163409 23 + 294540 TTCACTGGCTTAGTCAGGTTTTG -s simCow_chr6.simCow.chr6 282226 17 + 602619 CCCCCTGGCCTATTTGG------ -s simDog_chr6.simDog.chr6 318658 17 - 593897 CCCCCAGGCCTATTTAG------ -s simHuman_chr6.simHuman.chr6 229078 17 + 601863 TCCCCTCGCTTATCCAG------ -s simRat_chr6.simRat.chr6 304911 23 + 647215 TTGACTGGCCTACTCAGGTTTTG - -a -s simMouse_chr6.simMouse.chr6 313234 4 + 636262 ATTA -s Anc0.Anc0refChr8 2605 4 + 17196 ATTA -s Anc1.Anc1refChr3 2804 4 + 3661 ATTA -s Anc2.Anc2refChr8 2697 4 + 12804 GTTG -s mr.mrrefChr5 163432 4 + 294540 ATTA -s simCow_chr6.simCow.chr6 282243 4 + 602619 GTTG -s simDog_chr6.simDog.chr6 318684 4 - 593897 GTTG -s simHuman_chr6.simHuman.chr6 229095 4 + 601863 ATTA -s simRat_chr6.simRat.chr6 304934 4 + 647215 ATCA - -a -s simMouse_chr6.simMouse.chr6 313238 109 + 636262 TTTCATTGGTTTGTAGCTGCACTTCGAAGGAAGCTATCCACTTAGCCCACTTAATCATTGGAGCATAAACTGACAAGTTTTAGAGCATAAACTGACAAGTTTTAAACAA -s Anc0.Anc0refChr8 2609 87 + 17196 CTGCTCTGACTTGGAGCTGCACTTTGAAAGAATCTCTTTTCTTATCTCTCTTAATCATTGGAGCATAAACTGAAAAGTTAAG----------------------AATAT -s Anc1.Anc1refChr3 2808 87 + 3661 CTGCTCTGACTTGGAGCTGCACTTTGAAAGAATCTCTTTTCTTATCTCTCTTAATCATTGGAGCATAAACTGAAAAGTTAAG----------------------AATAT -s Anc2.Anc2refChr8 2701 87 + 12804 CTGCTCTGACTTGGAGCTGCACTTTAAGAGAATCTCTCTTCTTATCTCTCTTGACCATTGGAGCATCAACCGAAAAGTTAAG----------------------TATAT -s mr.mrrefChr5 163436 87 + 294540 TTGCATTGGTTTGTAGCTGCACTTTGAAGGAAGCTATTCACTTAGCCCACTTAATCATTGGAGCATAAACTGACAAGTTTTA----------------------AACAA -s simCow_chr6.simCow.chr6 282259 87 + 602619 CTGCTCCAATTTTAGGCTGCACTTTAAGAGAAGCCCTCTTCTTATCTCTCATGACCATTGAAGCATGAACGGAAAAGTTGAG----------------------CATTT -s simDog_chr6.simDog.chr6 318688 79 - 593897 CAGCTTTGACTTGGAACTG-ACCTTAAGCTACTCTCTCTTCTTATCTCTCT-------AGGAGCATCAACCAAAAAGTTAAG----------------------TATAT -s simHuman_chr6.simHuman.chr6 229099 87 + 601863 CTGCTCTGACTTGCAGCTGCACTTTGAAAGAATCTCTTGTCTTATCTCTCTTAATCACTGGAACAAAAACTGAAATGCCAAC----------------------AATAT -s simRat_chr6.simRat.chr6 304938 87 + 647215 TTGCGTTGGTTCGTAGCTGTACTTTAGAGGAAGCTATTTACTTAGCCTGCTTCATCATTGAAGAATGAACTGACAGGTTTTA----------------------AACAG - -a -s simMouse_chr6.simMouse.chr6 313347 19 + 636262 CCTCCTCAATGATAAACTG -s Anc0.Anc0refChr8 2696 19 + 17196 CCTCCTCGATAATAAACTG -s Anc1.Anc1refChr3 2895 19 + 3661 CCTCCTCGATAATAAACTG -s Anc2.Anc2refChr8 2788 19 + 12804 CCTACTCGAGAATAAACTG -s mr.mrrefChr5 163523 19 + 294540 CCTCCTCAATAATAAACTG -s simCow_chr6.simCow.chr6 282347 19 + 602619 CCAACTCAAAAATAAACTG -s simDog_chr6.simDog.chr6 318767 19 - 593897 CCTAATCGAGAATAAACTG -s simHuman_chr6.simHuman.chr6 229186 19 + 601863 CCTCCCCTATAATAAACTG -s simRat_chr6.simRat.chr6 305025 19 + 647215 CTTCCTCAACAAGAAATTG - -a -s simMouse_chr6.simMouse.chr6 313366 12 + 636262 CTGCAAAAGTGA -s Anc0.Anc0refChr8 2715 9 + 17196 CC-CATAAGT-- -s Anc1.Anc1refChr3 2914 9 + 3661 CC-CATAAGT-- -s Anc2.Anc2refChr8 2807 9 + 12804 CC-CATAAGT-- -s mr.mrrefChr5 163542 12 + 294540 CTGCATAAGTGA -s simCow_chr6.simCow.chr6 282367 9 + 602619 CC-CATAAGT-- -s simDog_chr6.simDog.chr6 318786 9 - 593897 CC-CATAAGT-- -s simHuman_chr6.simHuman.chr6 229205 9 + 601863 CC-CTTAAGT-- -s simRat_chr6.simRat.chr6 305044 12 + 647215 TTGCATAAGTGA - -a -s simMouse_chr6.simMouse.chr6 313378 30 + 636262 ATGATGCATCCATACTAAACAACCAGGGAG -s Anc0.Anc0refChr8 2724 27 + 17196 --AGGGCAACCATGCTAAGAGGCCAGAG-G -s Anc1.Anc1refChr3 2923 27 + 3661 --AGGGCAACCATGCTAAGAGGCCAGAG-G -s Anc2.Anc2refChr8 2816 27 + 12804 --AGGGCAAACATGCTAAGAGGCCAGAG-G -s mr.mrrefChr5 163554 30 + 294540 ATGAGGCATCCATGCTAAACAGCCAGGGAG -s simCow_chr6.simCow.chr6 282376 27 + 602619 --AGGGCAATCATGCTAAGAGGCCATAA-G -s simDog_chr6.simDog.chr6 318795 23 - 593897 --GGGG---ACATG-TAAGAGGCCAGGG-G -s simHuman_chr6.simHuman.chr6 229214 27 + 601863 --AGGGCAACTATGCTAAGAGGACAGAG-G -s simRat_chr6.simRat.chr6 305059 30 + 647215 ATGAGGCATCCATGATAAACAGCCAGGGAG - -a -s simMouse_chr6.simMouse.chr6 313408 12 + 636262 ATCAAATTAAGA -s Anc0.Anc0refChr8 2751 12 + 17196 ACCAGGCTGAGG -s Anc1.Anc1refChr3 2950 12 + 3661 ACCAGGCTGAGG -s Anc2.Anc2refChr8 2843 12 + 12804 ACCATGCTGAGG -s mr.mrrefChr5 163584 12 + 294540 ATCAGATTGAGA -s simCow_chr6.simCow.chr6 282410 12 + 602619 ACGATGCTAAGA -s simDog_chr6.simDog.chr6 318818 12 - 593897 ACCATGCTGAGG -s simHuman_chr6.simHuman.chr6 229241 12 + 601863 ACCAGGCTGAGG -s simRat_chr6.simRat.chr6 305089 12 + 647215 ATCAGATTGAGA - -a -s simMouse_chr6.simMouse.chr6 313420 4 + 636262 CTGG -s Anc0.Anc0refChr8 2763 4 + 17196 CTGG -s Anc1.Anc1refChr3 2962 4 + 3661 CTGG -s Anc2.Anc2refChr8 2855 4 + 12804 CTGG -s mr.mrrefChr5 163596 4 + 294540 CTGG -s simCow_chr6.simCow.chr6 282505 4 + 602619 CTAG -s simDog_chr6.simDog.chr6 318830 4 - 593897 CTGG -s simHuman_chr6.simHuman.chr6 229253 4 + 601863 CTGG -s simRat_chr6.simRat.chr6 305101 4 + 647215 CAGG - -a -s simMouse_chr6.simMouse.chr6 313424 47 + 636262 AGTGCCAGAATTTAGCTCTTCTGTATTGATTAATGATCAAATCGACT -s Anc0.Anc0refChr8 2767 47 + 17196 ACAGCCAGAACTGAGCACTTCGCTCATGATTTGTGATGGAATGGACT -s Anc1.Anc1refChr3 2966 47 + 3661 ACAGCCAGAACTGAGCACTTCGCTCATGATTTGTGATGGAATGGACT -s Anc2.Anc2refChr8 2859 47 + 12804 GCAGCCAGGACTGAGCACCTAGCTCATGATTTGTGATGGCATGGACT -s mr.mrrefChr5 163600 47 + 294540 ACAGCCAGAACTTAGCTCTTCTGTATTGATTAATGATCAAATCGACT -s simCow_chr6.simCow.chr6 282509 29 + 602619 GCATCAAGGACAG------------------TGTGATGGCATGGACT -s simDog_chr6.simDog.chr6 318834 47 - 593897 GCAGCCAGGACTTAGCACCTAGCTCATGATTAACGATGACATGGACT -s simHuman_chr6.simHuman.chr6 229265 47 + 601863 ACAGCCAGAACTGAGCACTTCATTTCTGATTTGTGAAGGAACTGATT -s simRat_chr6.simRat.chr6 305105 47 + 647215 ACAGCCAGAACTTAACTCACCTGTTTTGATTAATAATCAAATCGGCT - -a -s simMouse_chr6.simMouse.chr6 313471 9 + 636262 GAAGTTTGT -s Anc0.Anc0refChr8 2814 7 + 17196 GGAG--GGC -s Anc1.Anc1refChr3 3013 9 + 3661 GGAGATGGC -s Anc2.Anc2refChr8 2906 7 + 12804 GGAG--GGC -s mr.mrrefChr5 163647 9 + 294540 GAAGTTTGT -s simCow_chr6.simCow.chr6 282538 7 + 602619 GGAG--AAT -s simDog_chr6.simDog.chr6 318881 7 - 593897 GCAG--GGC -s simHuman_chr6.simHuman.chr6 229312 9 + 601863 AGTGATGGA -s simRat_chr6.simRat.chr6 305157 9 + 647215 GAAGACTGT - -a -s simMouse_chr6.simMouse.chr6 313480 35 + 636262 TGGGACATCAAGAAGAGTGTCTTGCTGTAGGATCA -s Anc0.Anc0refChr8 2826 35 + 17196 CAAGAAATCAAGGACAGTGCCATATTTTAGAGTCA -s Anc1.Anc1refChr3 3027 35 + 3661 CAAGAAATCAAGGACAGTGCCATATTTTAGAGTCA -s Anc2.Anc2refChr8 2918 35 + 12804 CAAGAAATCAAGGACAGTGCCATATTTTAGAGTAA -s mr.mrrefChr5 163656 35 + 294540 TGGGACATCAAGAAGAGTGTCTTGCTGTAGGATCA -s simCow_chr6.simCow.chr6 282550 35 + 602619 TGAGACATCAAGGACAGCACCACATTTCAGAATAA -s simDog_chr6.simDog.chr6 318893 35 - 593897 CAAGCAATCAAGGACAGTGCCATATTTTAGAGTAA -s simHuman_chr6.simHuman.chr6 229326 35 + 601863 CTTGAGTTGGAGGACAGTGACATATTTTAGACTCA -s simRat_chr6.simRat.chr6 305166 35 + 647215 TGGGATATCAAGAATAGTGTCTTGCTGTAGGATCA - -a -s simMouse_chr6.simMouse.chr6 313515 13 + 636262 TTTAATCTGGTGA -s Anc0.Anc0refChr8 2872 13 + 17196 TCTACGCTGGTGC -s Anc1.Anc1refChr3 3073 13 + 3661 TCTACGCTGGTGC -s Anc2.Anc2refChr8 2964 13 + 12804 TCTACGCTGGTGC -s mr.mrrefChr5 163691 13 + 294540 TTTAATCTGGTGA -s simCow_chr6.simCow.chr6 282596 13 + 602619 TCTAAGCTGATAC -s simDog_chr6.simDog.chr6 318939 13 - 593897 TTTACACTGGTGC -s simHuman_chr6.simHuman.chr6 229372 13 + 601863 TCTACGCTGGTGC -s simRat_chr6.simRat.chr6 305201 13 + 647215 CTTAATCTGGTGG - -a -s simMouse_chr6.simMouse.chr6 313528 66 + 636262 TTAATTGTTATATCTAGGAACGTTTGTTCATATGAACCTATTAGAGGTTGCACTAAGCCTAACCGT -s Anc0.Anc0refChr8 2885 58 + 17196 TTGATAGTTATATCCAGGCAGATTGGTTAATATAAACGCTTTAGGAGCTGCACTA--------TAA -s Anc1.Anc1refChr3 3086 58 + 3661 TTGATAGTTATATCCAGGCAGATTGGTTAATATAAACGCTTTAGGAGCTGCACTA--------TAA -s Anc2.Anc2refChr8 2977 58 + 12804 TTGACAGTTGCATCCAGGCAGATTTCTTAATATAATCGCTTTAGGAGCTGCACTG--------TAA -s mr.mrrefChr5 163704 58 + 294540 TTAATTGTTATATCTAGGCAGATTGGTTAATATAAACCTATTAGAGGTTGCACTA--------CGT -s simCow_chr6.simCow.chr6 282609 47 + 602619 TTGACAGTTGTATTTGGGCAAGTTCC--AATTTA---------GGAACTGTACTG--------TAA -s simDog_chr6.simDog.chr6 318952 58 - 593897 TTAACAGGTGCATCCAGGCAGATTTCTTATAATTATCGCTTTAGGAGCTGCACTG--------TAA -s simHuman_chr6.simHuman.chr6 229385 53 + 601863 CTGATAGTTAT--CCAGGCAGATTGGTTAATATAGAGTCCTTAGGAGCCGGTCTA----------- -s simRat_chr6.simRat.chr6 305215 42 + 647215 TTAATTGTTATATTTAGGCAGATTGGTTAATGTAAATCT------------------------CAT - -a -s simMouse_chr6.simMouse.chr6 313594 9 + 636262 CTAACCCTC -s Anc0.Anc0refChr8 2943 9 + 17196 TCAACCTTC -s Anc1.Anc1refChr3 3144 9 + 3661 TCAACCTTC -s Anc2.Anc2refChr8 3035 9 + 12804 TCAACCTTC -s mr.mrrefChr5 163762 9 + 294540 TGAACCCTC -s simCow_chr6.simCow.chr6 282657 9 + 602619 TTAAGCTTA -s simDog_chr6.simDog.chr6 319010 9 - 593897 TCAACCTTC -s simHuman_chr6.simHuman.chr6 229438 5 + 601863 ----CTTTG -s simRat_chr6.simRat.chr6 305257 9 + 647215 TGAACCCTC - -a -s simMouse_chr6.simMouse.chr6 313603 37 + 636262 CTTGGGTAGCTGGCTTGATATGTGTATACTGGACACA -s Anc0.Anc0refChr8 2955 18 + 17196 CT-GGCTTGC-------ACAT---------AGA--TG -s Anc1.Anc1refChr3 3156 28 + 3661 CTTGGCTTGCTGGCATTACAT---------AGACATG -s Anc2.Anc2refChr8 3047 18 + 12804 CT-GGCTTGC-------ACAT---------GGA--TG -s mr.mrrefChr5 163771 37 + 294540 CTTGGGTAGCTGGCTTGATATGTGTATACTAGACATG -s simCow_chr6.simCow.chr6 282717 18 + 602619 CT-GGTTTGC-------AAAT---------GTA--TG -s simDog_chr6.simDog.chr6 319022 18 - 593897 CC-AGCCTGC-------ACAT---------GGA--TG -s simHuman_chr6.simHuman.chr6 229446 28 + 601863 CCTGGCTTGCTGGCATTACAT---------AGACATG -s simRat_chr6.simRat.chr6 305266 35 + 647215 CTTGGGCAGCTGGCTGGAT--TTGTAGACTAGACATG - -a -s simMouse_chr6.simMouse.chr6 313640 32 + 636262 ATGTGAAGCTGATGCAGTTACAGTCACATTGT -s Anc0.Anc0refChr8 2978 32 + 17196 AGGTGTAGCTGATGCAGGGACAGTGTCATTTT -s Anc1.Anc1refChr3 3189 32 + 3661 AGGTGTAGCTGATGCAGGGACAGTGTCATTTT -s Anc2.Anc2refChr8 3070 32 + 12804 AGGTGTAGCTAATGCAAGGACAGAGTCATGTT -s mr.mrrefChr5 163808 32 + 294540 ATGTGAAGCTGATGCAGTTACAGTCTCATTGT -s simCow_chr6.simCow.chr6 282740 32 + 602619 GAGTGCAGTTAATTTAAGGGCAGAGTCATATT -s simDog_chr6.simDog.chr6 319045 29 - 593897 AGGTGTAGCTAATGCAAGTACA---TCATGTT -s simHuman_chr6.simHuman.chr6 229479 32 + 601863 AGGTGTAGCTGATGCAGGGACAGTGTCATTTT -s simRat_chr6.simRat.chr6 305301 32 + 647215 ATGTGAAGCTGATGCAGTCACAGTCTCATTGT - -a -s simMouse_chr6.simMouse.chr6 313672 14 + 636262 GACAAGCCATTATT -s Anc0.Anc0refChr8 3018 14 + 17196 AACAAGATGTTATT -s Anc1.Anc1refChr3 3229 14 + 3661 AACAAGATGTTATT -s Anc2.Anc2refChr8 3110 14 + 12804 AACAAGATGTTATT -s mr.mrrefChr5 163840 14 + 294540 GACAAGCTATTATT -s simDog_chr6.simDog.chr6 319082 14 - 593897 AACAAGATGTTATT -s simHuman_chr6.simHuman.chr6 229519 14 + 601863 AACCAGATCTTATT -s simRat_chr6.simRat.chr6 305333 14 + 647215 GACAGACTGTTATT - -a -s simMouse_chr6.simMouse.chr6 313686 22 + 636262 AGCGTACTTGATTCAGGTATGT -s Anc0.Anc0refChr8 3032 15 + 17196 AGTGTAGTTATTCC-------G -s Anc1.Anc1refChr3 3243 22 + 3661 AGTGTAGTTATTCCAAGTGAAG -s Anc2.Anc2refChr8 3125 15 + 12804 ATTGTAGTGATTCC-------G -s mr.mrrefChr5 163854 22 + 294540 AGTGTACTTATTTCAGGTATGT -s simDog_chr6.simDog.chr6 319097 15 - 593897 ATTGTAGTGATTCC-------G -s simHuman_chr6.simHuman.chr6 229533 22 + 601863 AGTCCAGTTATTCCAAGTGAAG -s simRat_chr6.simRat.chr6 305347 22 + 647215 AGTGTACTTATTTCTGGTATCT - -a -s simMouse_chr6.simMouse.chr6 313708 8 + 636262 TTAGGTGC -s Anc0.Anc0refChr8 3047 8 + 17196 TTAGGTGC -s Anc1.Anc1refChr3 3265 8 + 3661 TTAGGTGC -s Anc2.Anc2refChr8 3140 8 + 12804 TAAGGTGC -s mr.mrrefChr5 163876 8 + 294540 TTAGGTGC -s simDog_chr6.simDog.chr6 319112 8 - 593897 TAAGGTGC -s simHuman_chr6.simHuman.chr6 229558 8 + 601863 TTAGGAGC -s simRat_chr6.simRat.chr6 305369 8 + 647215 GTAGGTGC - -a -s simMouse_chr6.simMouse.chr6 313716 17 + 636262 TATGTGTAGGTAGCTAA -s Anc0.Anc0refChr8 3055 12 + 17196 -----GTGAGTGACCAA -s Anc1.Anc1refChr3 3273 17 + 3661 TCTATGTGAGTGACCAA -s Anc2.Anc2refChr8 3148 12 + 12804 -----ATGATTGACCAA -s mr.mrrefChr5 163884 17 + 294540 TATATGTAGGTAGCCAA -s simCow_chr6.simCow.chr6 282777 11 + 602619 ------TGTTTTATCAA -s simDog_chr6.simDog.chr6 319120 12 - 593897 -----ATGATTGACCGA -s simHuman_chr6.simHuman.chr6 229567 17 + 601863 TCTATGTGAGTCACCAA -s simRat_chr6.simRat.chr6 305377 17 + 647215 TATATGAAGATAGCCAA - -a -s simMouse_chr6.simMouse.chr6 313733 10 + 636262 AGGCACAGAA -s Anc0.Anc0refChr8 3071 10 + 17196 AGCGTGAAAG -s Anc1.Anc1refChr3 3294 10 + 3661 AGCGTGAAAG -s Anc2.Anc2refChr8 3164 10 + 12804 ATCGTGAATG -s mr.mrrefChr5 163901 10 + 294540 AGCCACAGAA -s simCow_chr6.simCow.chr6 282792 10 + 602619 AAAATGGATG -s simDog_chr6.simDog.chr6 319136 10 - 593897 ATCGGGAATG -s simHuman_chr6.simHuman.chr6 229588 10 + 601863 AGCTTAAAAG -s simRat_chr6.simRat.chr6 305413 10 + 647215 ATCCACAGAA - -a -s simMouse_chr6.simMouse.chr6 313743 69 + 636262 ATGAATACATGTACATGTTAACAGGTGTGGCTCATCTTGATGTGATGCCTTGGAATGCACACTGCCATG -s Anc0.Anc0refChr8 3087 69 + 17196 TTGAACATGTGTTCATATGGACAGGTGTAGCTTGTATTGTTGTGATGCCTAGGGATACATGATGCTATC -s Anc1.Anc1refChr3 3310 69 + 3661 TTGAACATGTGTTCATATGGACAGGTGTAGCTTGTATTGTTGTGATGCCTAGGGATACATGATGCTATC -s Anc2.Anc2refChr8 3180 69 + 12804 TTGAACATGTGCTCATATGGACAGGTGTAGCTTGTATTGTTGTGATGCCTAGGGCTACATGATGCTATC -s mr.mrrefChr5 163911 69 + 294540 ATGAATATGTGTTCATGTTAACAGGTGTAGCTCATATTGATGTGATGCCTTGGGATGCATGCTGCCATG -s simCow_chr6.simCow.chr6 282808 69 + 602619 TTGAACATGTTGTCCTATAAACAGGTGTAGCTTATGTCGTTGTGATGTCTAGGGCTACATGATGCTATC -s simDog_chr6.simDog.chr6 319152 69 - 593897 TTGAACATGTGCTCATGTGGGCAGATGTAACTTGTATTGTTGTAATGCCTAGGGCTACATGATGCTATG -s simHuman_chr6.simHuman.chr6 229604 69 + 601863 TTCAACATGTGTTCATATGTAAAGGTGTAGCTTGTAATGTTGTGATACCTGTGGATACATGATGCTATC -s simRat_chr6.simRat.chr6 305423 56 + 647215 ATGAATATGTGTTC----------TTGTAGCTCATATTGATGTG---CCCTGGGATGCATGCTGCCATA - -a -s simMouse_chr6.simMouse.chr6 313812 42 + 636262 ACTCCAAATGCATGGCAGCTTTCTTTGTTTTGAAGATGGTGT -s Anc0.Anc0refChr8 3156 39 + 17196 GCCTCA--CACAGAAGAGCGG-CTTTGTTTTGAGGATGGTGG -s Anc1.Anc1refChr3 3379 39 + 3661 GCCTCA--CACAGAAGAGCGG-CTTTGTTTTGAGGATGGTGG -s Anc2.Anc2refChr8 3249 39 + 12804 GCCAAA--CACAGAAGAGTGG-CTTTGTTTTGAGGATGGTGG -s mr.mrrefChr5 163980 42 + 294540 ACTTCAAACGCATAGCAGCTTTCTTTGTTTTGAAGATGGTGT -s simCow_chr6.simCow.chr6 282878 39 + 602619 GCCCAA--AACAGAATAGAGG-CTTTGTTTTGAGGGTGGTTG -s simDog_chr6.simDog.chr6 319221 37 - 593897 AGCAAA--CAC--ATGAGTGG-CCTTATTTTGAGCATGGTGG -s simHuman_chr6.simHuman.chr6 229673 39 + 601863 GCCTCA--CACGGAAGAGCAG-CTTTGCTTTGAGGAAGGTGA -s simRat_chr6.simRat.chr6 305479 42 + 647215 ACTTCAAACACATAGTAGCTTTCTTTGTTTTGAAGGTGGTGT - -a -s simMouse_chr6.simMouse.chr6 313854 1 + 636262 A -s Anc0.Anc0refChr8 3195 1 + 17196 A -s Anc1.Anc1refChr3 3418 1 + 3661 A -s Anc2.Anc2refChr8 3288 1 + 12804 A -s mr.mrrefChr5 164022 1 + 294540 A -s simCow_chr6.simCow.chr6 282919 1 + 602619 A -s simDog_chr6.simDog.chr6 319258 1 - 593897 A -s simHuman_chr6.simHuman.chr6 229712 1 + 601863 A -s simRat_chr6.simRat.chr6 305521 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 313855 41 + 636262 TATATAAGTATGTATTCACCAGCTCTCTAGGTTCTGGCCAG -s Anc0.Anc0refChr8 3196 41 + 17196 CATATGAATACCTATTCACCAGCTCTCTGGGTTCTGGCCAG -s Anc1.Anc1refChr3 3419 41 + 3661 CATATGAATACCTATTCACCAGCTCTCTGGGTTCTGGCCAG -s Anc2.Anc2refChr8 3289 41 + 12804 CATATGAATACCTATTTACCAGCTCTCTGAGTTCTAGCCAG -s mr.mrrefChr5 164023 41 + 294540 TATATAAATATGTATTCACCAGCTCTCTAGGTTCTGGCCAG -s simCow_chr6.simCow.chr6 282920 41 + 602619 TATATGAGTACCTATTAACCAGCTCTCTGAGCTCTAGCCAG -s simDog_chr6.simDog.chr6 319335 41 - 593897 CGTATGAATACCTATTTGCCAGCTCTCTGAGTTCTACCCTG -s simHuman_chr6.simHuman.chr6 229713 41 + 601863 GATATTAATACCTATTCACCAGCTCCCTGGCTTCTGGCCAG -s simRat_chr6.simRat.chr6 305522 41 + 647215 TATATAGATGTGCATTCACTAGCTTTCTAAGTTCTGGCCAG - -a -s simMouse_chr6.simMouse.chr6 313896 13 + 636262 AGCCTTAAATATA -s Anc0.Anc0refChr8 3239 13 + 17196 AGCCTTAAATTTG -s Anc1.Anc1refChr3 3462 13 + 3661 AGCCTTAAATTTG -s Anc2.Anc2refChr8 3332 13 + 12804 AGCCTCAAATTTG -s mr.mrrefChr5 164064 13 + 294540 AGCCTTAAATATA -s simCow_chr6.simCow.chr6 282963 13 + 602619 AGCCTCAAGTTTA -s simDog_chr6.simDog.chr6 319376 7 - 593897 ------AAATTTG -s simHuman_chr6.simHuman.chr6 229756 13 + 601863 GGCTATAAAGTAG -s simRat_chr6.simRat.chr6 305563 13 + 647215 AGCCTTAAATATA - -a -s simMouse_chr6.simMouse.chr6 313909 2 + 636262 CC -s Anc0.Anc0refChr8 3257 2 + 17196 CC -s Anc1.Anc1refChr3 3480 2 + 3661 CC -s Anc2.Anc2refChr8 3350 2 + 12804 CC -s mr.mrrefChr5 164082 2 + 294540 CC -s simCow_chr6.simCow.chr6 282981 2 + 602619 CT -s simDog_chr6.simDog.chr6 319388 2 - 593897 CC -s simHuman_chr6.simHuman.chr6 229774 2 + 601863 CC -s simRat_chr6.simRat.chr6 305581 2 + 647215 CC - -a -s simMouse_chr6.simMouse.chr6 313911 39 + 636262 TTGCATGACCAATCAATTTTACTATTCAATGAGTATTGG -s Anc0.Anc0refChr8 3259 33 + 17196 T------ACCAATTAATCTCACTACTCATTGAGTGTTTA -s Anc1.Anc1refChr3 3482 39 + 3661 TTACGTTACCAATTAATCTCACTACTCATTGAGTGTTTA -s Anc2.Anc2refChr8 3352 33 + 12804 C------ACCAATTAATCTCACTGCTCATTGAGTGTTTA -s mr.mrrefChr5 164084 39 + 294540 TTGCATGACCAATTAATCTTACTACTCAATGAGTGTTGA -s simCow_chr6.simCow.chr6 282983 33 + 602619 G------ACCCATTAATCACACTGCTAATTGAGTGTCTA -s simDog_chr6.simDog.chr6 319390 33 - 593897 C------ACCAATTAATCTCACTGCTCATTGGGTGATTG -s simHuman_chr6.simHuman.chr6 229777 39 + 601863 TTACGTTACCAGTTCATCTAACTACTCATTGAGTGTTTA -s simRat_chr6.simRat.chr6 305583 39 + 647215 TTGCATGACCAATTGATCTCACTACTCAGTGAGTGTTGA - -a -s simMouse_chr6.simMouse.chr6 313950 5 + 636262 TGTGG -s Anc0.Anc0refChr8 3292 5 + 17196 ATTGG -s Anc1.Anc1refChr3 3521 5 + 3661 ATTGG -s Anc2.Anc2refChr8 3385 5 + 12804 ATTGG -s mr.mrrefChr5 164123 5 + 294540 TGTGG -s simCow_chr6.simCow.chr6 283021 5 + 602619 AGAGG -s simDog_chr6.simDog.chr6 319423 5 - 593897 ATTGG -s simHuman_chr6.simHuman.chr6 229816 5 + 601863 AATGG -s simRat_chr6.simRat.chr6 305622 5 + 647215 TGTAG - -a -s simMouse_chr6.simMouse.chr6 313955 11 + 636262 CATTGGGATGA -s Anc0.Anc0refChr8 3342 11 + 17196 CATTGAGATGA -s Anc1.Anc1refChr3 3571 11 + 3661 CATTGAGATGA -s Anc2.Anc2refChr8 3435 11 + 12804 CATTGAGATGA -s mr.mrrefChr5 164128 11 + 294540 CATTGGGATGA -s simCow_chr6.simCow.chr6 283067 11 + 602619 CATTGAGATGG -s simDog_chr6.simDog.chr6 319473 11 - 593897 CATCAAGGTGA -s simHuman_chr6.simHuman.chr6 229866 11 + 601863 CGTTGAGATGA -s simRat_chr6.simRat.chr6 305627 11 + 647215 CATTGGGATGA - -a -s simMouse_chr6.simMouse.chr6 313966 15 + 636262 ATGATTTTACTTTAT -s Anc0.Anc0refChr8 3358 15 + 17196 ATGATTTTAGCTTCT -s Anc1.Anc1refChr3 3587 15 + 3661 ATGATTTTAGCTTCT -s Anc2.Anc2refChr8 3451 15 + 12804 ATGACTTTAGCTTCT -s mr.mrrefChr5 164142 15 + 294540 ATGATTTTACTTTAT -s simCow_chr6.simCow.chr6 283083 15 + 602619 ATGTCTTTAGCTTCT -s simDog_chr6.simDog.chr6 319489 10 - 593897 ATGACTTCAG----- -s simHuman_chr6.simHuman.chr6 229882 15 + 601863 ATGATTTTAGCCTCT -s simRat_chr6.simRat.chr6 305641 15 + 647215 ATAATTTTACTTTAT - -a -s simMouse_chr6.simMouse.chr6 313981 25 + 636262 ACCTAGACCATGCCTAACTCAATTT -s Anc0.Anc0refChr8 3373 25 + 17196 ACCTAGATTGTGCCTGACTGAATTC -s Anc1.Anc1refChr3 3602 25 + 3661 ACCTAGATTGTGCCTGACTGAATTC -s Anc2.Anc2refChr8 3466 25 + 12804 ACCTATATTATGGCTTAGTGAATCC -s mr.mrrefChr5 164157 25 + 294540 ACCTAGACCGTGCCTGACTCAATTT -s simCow_chr6.simCow.chr6 283098 25 + 602619 ACCTATATTATGGCTTAGTGAATCC -s simHuman_chr6.simHuman.chr6 229897 25 + 601863 ACCTAGATAGTACCTGACTGATTTC -s simRat_chr6.simRat.chr6 305663 25 + 647215 ATCTAGACTGTGCCTGACTCAATTT - -a -s simMouse_chr6.simMouse.chr6 314006 25 + 636262 GGAGATAATGAGACTGAATCAGAAA -s Anc0.Anc0refChr8 3401 24 + 17196 TGAGATAATGGGAGTGAATTA-TAA -s Anc1.Anc1refChr3 3630 24 + 3661 TGAGATAATGGGAGTGAATTA-TAA -s Anc2.Anc2refChr8 3494 24 + 12804 TGAGATAATGGGAGTGAATTA-TAA -s mr.mrrefChr5 164185 24 + 294540 GGAGATAATGAGACTGAATCA-AAA -s simCow_chr6.simCow.chr6 283126 24 + 602619 GGAGGTAATGAAAATGAACTA-TAG -s simDog_chr6.simDog.chr6 319502 24 - 593897 TGAGATAATGGGGGTGAATTA-TAA -s simHuman_chr6.simHuman.chr6 229925 24 + 601863 TGAGATAATGGGAGTGAATAA-TGA -s simRat_chr6.simRat.chr6 305691 24 + 647215 GGAGATAATAAGACTGAACCA-AAA - -a -s simMouse_chr6.simMouse.chr6 314031 1 + 636262 C -s Anc1.Anc1refChr3 3660 1 + 3661 A -s mr.mrrefChr5 164209 1 + 294540 C -s simHuman_chr6.simHuman.chr6 229955 1 + 601863 T -s simRat_chr6.simRat.chr6 305715 1 + 647215 C - -a -s simMouse_chr6.simMouse.chr6 314032 28 + 636262 TGAAGTGCAGAAGCTCAGACTTGGATAA -s Anc0.Anc0refChr7 1075 27 - 16696 AAAAGTACAAAAGTTCAGGTC-GTATAA -s Anc1.Anc1refChr4 1212 28 + 17549 AAAAGTACAAAAGTTCAGGTCTGTATAA -s Anc2.Anc2refChr5 1115 27 - 8386 AAAAGTACAAAGGTTCAGGTC-ATATAA -s mr.mrrefChr5 164210 28 + 294540 TAAAGTGCAGAAGTTCAGATTTGGATAA -s simCow_chr6.simCow.chr6 324517 27 - 602619 TAAAGTATGAATGTTCAGGCC-TGATAG -s simDog_chr6.simDog.chr6 279001 27 + 593897 AAAAGTACAAAGGTTCAGGTC-ATATGA -s simHuman_chr6.simHuman.chr6 302363 28 + 601863 CAAAGTACAAAAGTCCCGCTCTGAATaa -s simRat_chr6.simRat.chr6 305716 28 + 647215 TAGAGTGCAGAAGTTCGGGTTTGGATAA - -a -s simMouse_chr6.simMouse.chr6 314060 30 + 636262 CTTGGTGGTAACATTCAGTGCCCCAGAATG -s Anc0.Anc0refChr7 1117 30 - 16696 cttggcaataccatttaggaccccaaaatg -s Anc1.Anc1refChr4 1255 30 + 17549 cttggcaataccatttaggaccccaaaatg -s Anc2.Anc2refChr5 1158 30 - 8386 cttggcaataccatttaggacctaaaaacc -s mr.mrrefChr5 164248 30 + 294540 CTTGGTGATAACATTCAGTACCCCAGAATG -s simCow_chr6.simCow.chr6 324560 30 - 602619 tttgagaataccatgcatgacctttaaaca -s simDog_chr6.simDog.chr6 279044 30 + 593897 CTTGGCGATACCATTTGGGATTTAAGATCC -s simHuman_chr6.simHuman.chr6 302406 30 + 601863 cttggaaataccattaaggaccccaaaatg -s simRat_chr6.simRat.chr6 305754 30 + 647215 ATTGATGACAACATCCAGTACCCCAGAATG - -a -s simMouse_chr6.simMouse.chr6 314090 10 + 636262 AAGCTTCATG -s Anc0.Anc0refChr7 1152 10 - 16696 aagtttcatg -s Anc1.Anc1refChr4 1290 10 + 17549 aagtttcatg -s Anc2.Anc2refChr5 1193 10 - 8386 aagtttcatg -s mr.mrrefChr5 164278 10 + 294540 AAGCTTCATG -s simCow_chr6.simCow.chr6 324595 10 - 602619 aaacttcatg -s simDog_chr6.simDog.chr6 279079 9 + 593897 AAGTCTCAT- -s simHuman_chr6.simHuman.chr6 302441 10 + 601863 aaggttcatg -s simRat_chr6.simRat.chr6 305784 10 + 647215 AAGCTTCACG - -a -s simMouse_chr6.simMouse.chr6 314100 7 + 636262 ACTAAAG -s Anc0.Anc0refChr7 1162 7 - 16696 tttaaag -s Anc1.Anc1refChr4 1300 7 + 17549 tttaaag -s Anc2.Anc2refChr5 1203 7 - 8386 tttaaag -s mr.mrrefChr5 164288 7 + 294540 ACTAAAG -s simCow_chr6.simCow.chr6 324607 7 - 602619 tttaaag -s simDog_chr6.simDog.chr6 279088 7 + 593897 TTCAAAG -s simHuman_chr6.simHuman.chr6 302451 7 + 601863 tttaaag -s simRat_chr6.simRat.chr6 305794 7 + 647215 ACTAAAG - -a -s simMouse_chr6.simMouse.chr6 314107 211 + 636262 TGCTTGTTACAGTGATAGATAAATCTAAGGTTGGAACACATGCATACCATTTTATAATATATCGAAGACTGTAGATATGACGACAGACCAAGTACTGCGAGTGTTGTTGTATGAGATCATATAAACGAGCATGAGTGAGCTCAAGAACAAGTTGATAGCCCCTGCAGCATAGTCATCAAATAGGGCCCATGTATCTATGGATTCAAGTGAG -s Anc0.Anc0refChr7 1169 190 - 16696 tgcctatgataatggtggataatactaagatctaagcaaaagaatacaatgtcat--tacatcagagactccaggtatgactgaagaccaggaatcacgagtgctggtgtat-------------------tggatgagcatatgaactagcaaaatatccttgcttcttattcatcagatagggctcttgtgtctagggtttcaaatgag -s Anc1.Anc1refChr4 1307 190 + 17549 tgcctatgataatggtggataatactaagatctaagcaaaagaatacaatgtcat--tacatcagagactccaggtatgactgaagaccaggaatcacgagtgctggtgtat-------------------tggatgagcatatgaactagcaaaatatccttgcttcttattcatcagatagggctcttgtgtctagggtttcaaatgag -s Anc2.Anc2refChr5 1210 190 - 8386 catctatgatgatggtggataatactaagatctaagcaaaagaatacaatgtcat--tacatcagagactccaggtacagctgaagaccagaagtaacgagtgctggtgaat-------------------tggaggagcatctgaattagcaaaatatccttgcttcttattcatcagataggtttcttgtgtctagggtttcaaatgag -s mr.mrrefChr5 164295 211 + 294540 TGCTTGTTACAGTGGTAGATAAAACTAAGGTTGAAACAAATGAATACCATTTTATAATATATCGAAGACTGTAGATATGACGACAGACCAAGTACCACGAGTGTTGGTGTATGAGATCATATAAACGAGCATGAATGAGCTCAAGAACAAGTTAATTGCCCCTGCAGCATAGTCATCAAATAGGGCTCTTGTATCTAGGGTTTCAAATGAG -s simCow_chr6.simCow.chr6 324614 188 - 602619 tacctatgatcatgatggataacactaagatcccagcaaatgaatacaatgttat--ttcatcagagactccaggtccagctgaagaccagaagtaacgagtgctggtgaat-------------------tggaggagcatctgaattagcaaaaaatccttacttcttattcatc--ataggtttcttgagtctagggtttcagatgag -s simDog_chr6.simDog.chr6 279095 134 + 593897 CATCTACGGTGATTGTGGATAATATTAAGATCTAAGCAAAAGAATGCAATGTCAT--TACATCAGGGACTCCAGGTA---------------------------------------------------------------------------AGAATGTCCATGCTTCTAATTCATCAGATAGGTTTCTCATGTATAGGGTTTCAAATGAG -s simHuman_chr6.simHuman.chr6 302459 190 + 601863 tgcatatgataatggtggataatactaagatataagcaaacaaatatgacatcat--tagatcagagactccaggtgtgattgaagaccaggaaacaccagtggtggtgtgt-------------------tggatgagcctacgaacttgcaaaatatcctggcttcttattcagcggatagggctcttgcttctagggttttaaatgag -s simRat_chr6.simRat.chr6 305801 211 + 647215 CACTTTTTACAGTGGCAGATAAAACTAAGTTTGAATCAAATGAATACCAAGTTACAATATATCGAAGACTGTAGATATGACAACAGACCAAGTACCACAAGTGTTGGTGTATGAAGCCATATAAGAGAGCATTCATGAGCTCAAGAAGAAGTTAATTGCCCCTGCAACATGGTCATCAAATAGGGCTCTTGTATCTAGGCTTTCAAATGAG - -a -s simMouse_chr6.simMouse.chr6 314318 18 + 636262 TCAATACAAACCCTTGCA -s Anc0.Anc0refChr7 1359 18 - 16696 ttgatacaagtccatgag -s Anc1.Anc1refChr4 1497 18 + 17549 ttgatacaagtccatgag -s Anc2.Anc2refChr5 1400 18 - 8386 ttgatacaagtccatggg -s mr.mrrefChr5 164506 18 + 294540 TCAATACAAACCCTTGAG -s simCow_chr6.simCow.chr6 324802 18 - 602619 ttgacacaagtccatggg -s simDog_chr6.simDog.chr6 279229 18 + 593897 TTGATACAAGTCCATGGG -s simHuman_chr6.simHuman.chr6 302651 18 + 601863 ttgatacaagtccatgag -s simRat_chr6.simRat.chr6 306012 18 + 647215 TCAATACAAACCCTTGAG - -a -s simMouse_chr6.simMouse.chr6 314336 1 + 636262 G -s Anc0.Anc0refChr7 1377 1 - 16696 a -s Anc1.Anc1refChr4 1515 1 + 17549 a -s Anc2.Anc2refChr5 1418 1 - 8386 a -s mr.mrrefChr5 164524 1 + 294540 G -s simCow_chr6.simCow.chr6 324821 1 - 602619 a -s simDog_chr6.simDog.chr6 279247 1 + 593897 A -s simHuman_chr6.simHuman.chr6 302669 1 + 601863 a -s simRat_chr6.simRat.chr6 306030 1 + 647215 G - -a -s simMouse_chr6.simMouse.chr6 314337 9 + 636262 AAAAGATTA -s Anc0.Anc0refChr7 1378 9 - 16696 aaaagATTA -s Anc1.Anc1refChr4 1516 9 + 17549 aaaagATTA -s Anc2.Anc2refChr5 1419 9 - 8386 aaaagATTA -s mr.mrrefChr5 164525 9 + 294540 AAAAGATTA -s simCow_chr6.simCow.chr6 324822 9 - 602619 aaaaaATTA -s simDog_chr6.simDog.chr6 279255 9 + 593897 GAAAGATTA -s simHuman_chr6.simHuman.chr6 302670 9 + 601863 aaaagatta -s simRat_chr6.simRat.chr6 306031 9 + 647215 AAAAGATTA - -a -s simMouse_chr6.simMouse.chr6 314346 7 + 636262 GTAACCC -s Anc0.Anc0refChr7 1387 7 - 16696 GTAACCC -s Anc1.Anc1refChr4 1525 7 + 17549 GTAACCC -s Anc2.Anc2refChr5 1428 7 - 8386 GTAACCC -s mr.mrrefChr5 164534 7 + 294540 GTAACCC -s simCow_chr6.simCow.chr6 324833 7 - 602619 GTAACCT -s simDog_chr6.simDog.chr6 279264 7 + 593897 GTAATCC -s simHuman_chr6.simHuman.chr6 302679 7 + 601863 gtaaccc -s simRat_chr6.simRat.chr6 306040 7 + 647215 GTAACTC - -a -s simMouse_chr6.simMouse.chr6 314353 26 + 636262 ATGAAATGGTAGGCCAAGGATAGCCA -s Anc0.Anc0refChr7 1395 24 - 16696 ATGAAAAGATAGGCCAA--AtAACCA -s Anc1.Anc1refChr4 1533 26 + 17549 ATGAAAAGATAGGCCAAggAtAACCA -s Anc2.Anc2refChr5 1436 24 - 8386 ATGAAAAGATTGGGCCA--AtAACCA -s mr.mrrefChr5 164541 26 + 294540 ATGAAATGGTAGGCCAAGGATAGCCA -s simCow_chr6.simCow.chr6 324841 23 - 602619 ATGAAAAGGTGGGACCA--A-AACCA -s simDog_chr6.simDog.chr6 279272 24 + 593897 ATGAATAGAATGGGCCA--ATAACCA -s simHuman_chr6.simHuman.chr6 302687 26 + 601863 atgaaaagataggccaaggataacca -s simRat_chr6.simRat.chr6 306047 26 + 647215 ATTAAGTGGTAGGCCAAGGATAGCCA - -a -s simMouse_chr6.simMouse.chr6 314379 128 + 636262 GTAAATCTTCCTTATCTCACCATTCATTCACACAGATGCTTCCTATAACACTTTGTCACCTTTGAACACATCTTGTGGACTCTAAACAGATGCTTCCAGGGACCTTTGTCACTTCTAAACATATCTTG -s Anc0.Anc0refChr7 1419 14 - 16696 CTAAGT------------------------------------------------------------------------------------------------------------------ATGCTTTG -s Anc1.Anc1refChr4 1559 14 + 17549 CTAAGT------------------------------------------------------------------------------------------------------------------ATGCTTTG -s Anc2.Anc2refChr5 1460 14 - 8386 CTAAGT------------------------------------------------------------------------------------------------------------------ATGCTTTG -s mr.mrrefChr5 164567 14 + 294540 GTAAAT------------------------------------------------------------------------------------------------------------------ATATCTTG -s simCow_chr6.simCow.chr6 324870 14 - 602619 CTAAGT------------------------------------------------------------------------------------------------------------------GTGCCTGG -s simDog_chr6.simDog.chr6 279296 14 + 593897 CTAAGT------------------------------------------------------------------------------------------------------------------ATGCTTTG -s simHuman_chr6.simHuman.chr6 302713 14 + 601863 ctaagt------------------------------------------------------------------------------------------------------------------atGCATTG -s simRat_chr6.simRat.chr6 306073 14 + 647215 GTAAAT------------------------------------------------------------------------------------------------------------------ACATTTTG - -a -s simMouse_chr6.simMouse.chr6 314507 109 + 636262 TAGACTCCCATCAAGATGTATGCCACACTTGTTATCCCTATCTATGGCCAGAGAGTGGATTAAATGATTTATTTTAGCTATGTGACCTTAGATTCACTGACTTTCTTAT -s Anc0.Anc0refChr7 1503 83 - 16696 TAGACT---AGGAAGGTAT----TCTGCTTAGCAGACTTCCATGTGGCAAAAAAGTGTATCAAAAGATTTATTTT-------------------GACTGCCTTCCCCTA -s Anc1.Anc1refChr4 1643 97 + 17549 TAGACT---AGGAAGGTAT----TCTGCTTAGCAGACTTCCATGTGGCAAAAAAGTGTATCAAAAGATTTATTTTAACTG-----ATTTGTTTTGACTGCCTTCCCCTA -s Anc2.Anc2refChr5 1544 83 - 8386 TAGACT---AGGAAGGTAT----TCTGCTTAACAGACTTCCATGAGGCAAAAAAGTGTATCAAAAGATTTATTTT-------------------GACTGCCTTCCCCTA -s mr.mrrefChr5 164648 102 + 294540 TAGACT---ATGAAGATAT----CACACTTGGTATCCCTATCTGTGGCAAGAGAGTGGATTAAATGATTTATTTTAGCTATATGACCTTAGATTCACTGCCTTTCCTAT -s simCow_chr6.simCow.chr6 324954 82 - 602619 TAGACT---AGAAGGATAC----TTTGCCTAACAGATATACATGA-GCAAAAAAGTTTACCAAAAGATTTATTTT-------------------GACTGCCCTGCCCAA -s simDog_chr6.simDog.chr6 279391 82 + 593897 TAGACT---TGG-AGGTAT----TCTGATTAATAGACTTCAGTGAGGAAAAAAAGTGTATCAAAAGATTTATTTT-------------------GACTGTCTTCCCCTA -s simHuman_chr6.simHuman.chr6 302797 97 + 601863 TAAACT---AGGAAGGTAT----TGTGCTTAGCCAACTTTCACGTGGCAAAAAGGTGTATCAAAGGATGTATTTTAACTG-----ATTTGTTTTGACTGCTATAGCCGG -s simRat_chr6.simRat.chr6 306209 90 + 647215 TAGACT---ACGAAGATAT----CACACTTGGGATCCCTATCTGTGGCAAGAGAGTGG------------ATTTTTGGTGCATGACCTTAGATTCATTGCCTTTCCTTT - -a -s simMouse_chr6.simMouse.chr6 314616 14 + 636262 GTTCAGAGGTTGTG -s Anc0.Anc0refChr7 1587 14 - 16696 ATACAGAGATTGTT -s Anc1.Anc1refChr4 1741 14 + 17549 ATACAGAGATTGTT -s Anc2.Anc2refChr5 1628 14 - 8386 ATACAGAGATTGTT -s mr.mrrefChr5 164751 14 + 294540 GTTCAGAGGTTGTG -s simCow_chr6.simCow.chr6 325037 14 - 602619 ATACATAGGTTGTT -s simDog_chr6.simDog.chr6 279474 14 + 593897 ATACAGAGATTGTT -s simHuman_chr6.simHuman.chr6 302895 14 + 601863 ATCCAGAGATTGTT -s simRat_chr6.simRat.chr6 306300 14 + 647215 GTTCGGAGGTTGTA - -a -s simMouse_chr6.simMouse.chr6 314630 7 + 636262 GACACAC -s Anc0.Anc0refChr7 1601 7 - 16696 GATACAT -s Anc1.Anc1refChr4 1755 7 + 17549 GATACAT -s Anc2.Anc2refChr5 1676 7 - 8386 GTTTCAT -s mr.mrrefChr5 164765 7 + 294540 GACACAC -s simCow_chr6.simCow.chr6 325604 7 - 602619 GTTTCAT -s simHuman_chr6.simHuman.chr6 302909 7 + 601863 GATACAT -s simRat_chr6.simRat.chr6 306314 7 + 647215 GACACAC - -a -s simMouse_chr6.simMouse.chr6 314637 8 + 636262 CACCACAT -s Anc0.Anc0refChr7 1608 8 - 16696 CAACATAT -s Anc1.Anc1refChr4 1762 8 + 17549 CAACATAT -s Anc2.Anc2refChr5 1683 8 - 8386 CAAGATAG -s mr.mrrefChr5 164772 8 + 294540 CACCACAT -s simCow_chr6.simCow.chr6 325626 8 - 602619 CAAGATAG -s simHuman_chr6.simHuman.chr6 302916 8 + 601863 CAACATAT -s simRat_chr6.simRat.chr6 306321 8 + 647215 CACCAAAT - -a -s simMouse_chr6.simMouse.chr6 314645 14 + 636262 ATATAGAACTGCCT -s Anc0.Anc0refChr7 1616 14 - 16696 ACAGACAACTGCCT -s Anc1.Anc1refChr4 1770 14 + 17549 ACAGACAACTGCCT -s Anc2.Anc2refChr5 1691 14 - 8386 ACAGACTCATGCCT -s mr.mrrefChr5 164780 14 + 294540 ATATAGAACTGCCT -s simCow_chr6.simCow.chr6 325636 14 - 602619 ACAGACTCATGCCT -s simHuman_chr6.simHuman.chr6 302924 14 + 601863 ACAAATAACTGCCT -s simRat_chr6.simRat.chr6 306329 14 + 647215 ATAGAGAACTGCCT - -a -s simMouse_chr6.simMouse.chr6 314659 2 + 636262 TG -s Anc0.Anc0refChr7 1630 2 - 16696 TG -s Anc1.Anc1refChr4 1784 2 + 17549 TG -s Anc2.Anc2refChr5 1705 2 - 8386 TG -s mr.mrrefChr5 164794 2 + 294540 TG -s simCow_chr6.simCow.chr6 325662 2 - 602619 TG -s simHuman_chr6.simHuman.chr6 302938 2 + 601863 TG -s simRat_chr6.simRat.chr6 306343 2 + 647215 TG - -a -s simMouse_chr6.simMouse.chr6 314661 23 + 636262 TCATGTTACAAGCACACATAGGT -s Anc0.Anc0refChr7 1632 23 - 16696 TTATGTTACTAGTAAACATAGTT -s Anc1.Anc1refChr4 1786 23 + 17549 TTATGTTACTAGTAAACATAGTT -s Anc2.Anc2refChr5 1707 23 - 8386 TTATGTTGCTAGTAAACATAATT -s mr.mrrefChr5 164796 23 + 294540 TCATGTTACAAGCACACATAGGT -s simCow_chr6.simCow.chr6 325665 23 - 602619 TTATGTGGCGAGCAAAGATACTT -s simDog_chr6.simDog.chr6 279827 19 + 593897 ----GTTGCTAATAAACATAATT -s simHuman_chr6.simHuman.chr6 302940 23 + 601863 TTATGTTACCAGTAAACATAGTT -s simRat_chr6.simRat.chr6 306345 23 + 647215 TCATGTTACAAGCCCACATAGGT - -a -s simMouse_chr6.simMouse.chr6 314684 19 + 636262 ACTTACAGGAATCTGATAA -s Anc0.Anc0refChr7 1656 14 - 16696 ACTTACAGGCATCT----- -s Anc1.Anc1refChr4 1810 19 + 17549 ACTTACAGGCATCTGGTCA -s Anc2.Anc2refChr5 1731 14 - 8386 ACTGACAGGCACCT----- -s mr.mrrefChr5 164820 19 + 294540 ACTTACAGGAATCTGATAA -s simCow_chr6.simCow.chr6 325689 14 - 602619 AATGACAAGCACCT----- -s simDog_chr6.simDog.chr6 279847 11 + 593897 AC---CAGGCACCT----- -s simHuman_chr6.simHuman.chr6 302964 19 + 601863 GCTTACAGGCATCTGGTCA -s simRat_chr6.simRat.chr6 306369 19 + 647215 ACTTTCTGGAATCTGATAA - -a -s simMouse_chr6.simMouse.chr6 314703 3 + 636262 CCA -s Anc1.Anc1refChr4 1829 3 + 17549 CCA -s mr.mrrefChr5 164839 3 + 294540 CCA -s simHuman_chr6.simHuman.chr6 302989 3 + 601863 CCA -s simRat_chr6.simRat.chr6 306388 3 + 647215 CCA - -a -s simMouse_chr6.simMouse.chr6 314706 3 + 636262 TTG -s Anc1.Anc1refChr4 1832 3 + 17549 ATG -s mr.mrrefChr5 164842 3 + 294540 TTG -s simHuman_chr6.simHuman.chr6 302992 3 + 601863 ATG -s simRat_chr6.simRat.chr6 306400 3 + 647215 TCG - -a -s simMouse_chr6.simMouse.chr6 314709 160 + 636262 CATAACTGACTGGGTTTCACACCTTCTTTCCCATCAGGACACTCTGTGCATGGAATCTGACAACATGGCTTCCCATATATGAAGAGCATCTCACTTGCTGTGAGAATTGGAGCCAGCAGATGTGGAAAATACCCTACTTGATAGTCTTATGTCTGGCAAG -s Anc0.Anc0refChr7 1690 100 - 16696 CATAACTTACAAGGATTTGACCCTTCTGTCCCATCACGACACTCTGTGAATTGAAACTGTAATCTAAGCTTCCCATATTTGAACAGCATGTCACTGGCTT------------------------------------------------------------ -s Anc1.Anc1refChr4 1855 100 + 17549 CATAACTTACAAGGATTTGACCCTTCTGTCCCATCACGACACTCTGTGAATTGAAACTGTAATCTAAGCTTCCCATATTTGAACAGCATGTCACTGGCTT------------------------------------------------------------ -s Anc2.Anc2refChr5 1765 100 - 8386 CATAACTTACAAGGATTTGACCCTTCTGTTCCATCACGACACTATGTGAATTGAAACTGTAATCTAAGCTTCCCCAATTTGAACAGCATGTAACTGGCTT------------------------------------------------------------ -s mr.mrrefChr5 164845 160 + 294540 CATAACTGACTGGGTTTCACACCTTCTTTCCCATCAGGACACTCTGTGCATGGAATCTGACAACATGGCTTCCCATATATGAAGAGCATCTCACTTGCTGTGAGAATTGGAGCCAGCAGATGTGGAAAATACCCTACTTGATAGTCTTATGTCTGGCAAG -s simCow_chr6.simCow.chr6 325723 98 - 602619 CATAACTCACAAGTGTTAGACCCTTC-ATTCCATCACGAC-CTTCATGAATTGAAACTGTAATTTTGGCTCCACTGATTCGAACAGCACGTGACTGGCTT------------------------------------------------------------ -s simDog_chr6.simDog.chr6 279875 100 + 593897 CATAACTTACAAGGATTTGGCTCTTGTGTTCCATCAGGACACTATGGGAAGTGAAACTGTCGTCTAAGCTTCCCCAATTTGAGCAGAGTGTAACTGACTT------------------------------------------------------------ -s simHuman_chr6.simHuman.chr6 303119 98 + 601863 CACAGCTTGCAAGGATTTGACCCTTCTGTCCCATCACGACACTCTGTGAATTGAAGCTGGAATCTCAGCT--CCATATTTGAACAGCATGTCACTGGCTT------------------------------------------------------------ -s simRat_chr6.simRat.chr6 306403 160 + 647215 CATTAATGACAAGGTTTGGCCCCTTCTTTTTCATCAGGACACTCTGTGCATTGAATCTCATAACATGGCTTCCTGTGTATGAAGAGAAGCTCACTTTCTGTGAGAATAGGAGCCAGTAGACGCCAAATATATCCCACTTGATAGCCTTATGTCTGGCAAG - -a -s simMouse_chr6.simMouse.chr6 314869 38 + 636262 TGGATTAAATGATTTATTTCGACTGCCTTACCTTAGAC -s mr.mrrefChr5 165005 38 + 294540 TGGATTAAATGATTTATTTCGACTGCCTTACCTTAGAC -s simRat_chr6.simRat.chr6 306567 38 + 647215 TGGAGTAAATGATTCAATTCAACTCCCTTACCTTAGAC - -a -s simMouse_chr6.simMouse.chr6 314907 130 + 636262 TCACTGGTCTACCTAATATTCAGAGATTATGCTGTGCATCAAAACTGGAAGATTGTCCCCCCATTATATGAACAGCATATCACTGGCCAAAAGTGTTAAATCACCCTCATAATCACAAGAGAACACTTCA -s Anc0.Anc0refChr7 1790 38 - 16696 --------------------------------------------------------------------------------------------GGGTTTCATCACCCTCATCTTCATTAGAGATAACTCTA -s Anc1.Anc1refChr4 1955 38 + 17549 --------------------------------------------------------------------------------------------GGGTTTCATCACCCTCATCTTCATTAGAGATAACTCTA -s Anc2.Anc2refChr5 1868 38 - 8386 --------------------------------------------------------------------------------------------GGGTTTCATTACCCTCATCTTCATTAAAGATAGCCCTA -s mr.mrrefChr5 165043 130 + 294540 TCACTGGTCTACCTAATATTCAGAGATTATGCTGTGCATCAAAACTGGAAGATTGTCCCCCCATTATATGAACAGCATATCACTGGCCAAAAGGGTTTGATCACCCTCATATTCACAAGAGATCACTCCA -s simCow_chr6.simCow.chr6 325824 38 - 602619 --------------------------------------------------------------------------------------------GAGTTTCATTACCCTCACCTTCATAAAAGATAGTCCTG -s simDog_chr6.simDog.chr6 279978 38 + 593897 --------------------------------------------------------------------------------------------GGGTTTGATTACCCTCATCTTTATTGAGGATAGCCCCA -s simHuman_chr6.simHuman.chr6 303217 36 + 601863 --------------------------------------------------------------------------------------------GGGTTTCAGCACCCTCATGTTCA--AGAGATAACTCTA -s simRat_chr6.simRat.chr6 306606 128 + 647215 TCTCTGACTTACCTAATAATCAGAGATTACGCTGTGCATTAAAACTGAAAGATTTACCCCCCAT-ATATGAACAGCACATGACTGGC-ATAGGGGTTTGATGACCCTCATATTCACAAGAGATCACTCCA - -a -s simMouse_chr6.simMouse.chr6 315037 86 + 636262 GTTCAGAGAACATCAGATTCTATTGACAAATTTCAACCCATTGAATAATCACCTGCTACCTGTTCAGGTGATAAAAATAGGGAATA -s Anc0.Anc0refChr7 1828 78 - 16696 GTGCAAAGAACAATAAATTCTATTTGCACATTT--------TGAATAATCACCTGTTAACTGATCGAGTGATATAAATAAGGATTA -s Anc1.Anc1refChr4 1993 78 + 17549 GTGCAAAGAACAATAAATTCTATTTGCACATTT--------TGAATAATCACCTGTTAACTGATCGAGTGATATAAATAAGGATTA -s Anc2.Anc2refChr5 1906 78 - 8386 GTGCAAAGAACAATAAATTCTATTTGCACATTT--------TGAATAATCACCTGTTAACTGATCGAGTGATATACATGAGGATTA -s mr.mrrefChr5 165173 86 + 294540 GTTCAGAGAGCATCAGATTCTATTTACACATTTCAACCCATTGAATAATCACCTGCTACCTGTTCAGGTGATAAAAATAGGGAATA -s simCow_chr6.simCow.chr6 325862 77 - 602619 ATGCAAAGAACAATAGATTCTATTTGCACAATT--------TGAATAATCACCTATTAACTGGT-GGGTGATATACATGGGGGTTA -s simDog_chr6.simDog.chr6 280016 78 + 593897 GTGCAAAGAGCATTAAATCCTATGTGCACATTT--------TGAATAATCACCTGCTAACTAATCGAGTGGTATACATGAGGATTA -s simHuman_chr6.simHuman.chr6 303254 78 + 601863 GCGTGAAGAACAATAAATTCTATTTGCACATTT--------TGAATAATCACCTGTCCACTGATTGAGTGATATCAATAAGGATCA -s simRat_chr6.simRat.chr6 306734 86 + 647215 GTTAAGAGAGCATCAGATTCTGCTTACACATTTCAACTCCTTGAATAATCACCTGTTACCTGTTCAGGTGATAAAAATAGGAAATA - -a -s simMouse_chr6.simMouse.chr6 315123 10 + 636262 TGGCATAGCA -s Anc0.Anc0refChr7 1906 10 - 16696 TGGCATACCT -s Anc1.Anc1refChr4 2071 10 + 17549 TGGCATACCT -s Anc2.Anc2refChr5 1984 10 - 8386 TGGCATACCT -s mr.mrrefChr5 165259 10 + 294540 TGGCATACCA -s simCow_chr6.simCow.chr6 325939 10 - 602619 TGGCATACTT -s simDog_chr6.simDog.chr6 280115 10 + 593897 TAGCACACCT -s simHuman_chr6.simHuman.chr6 303332 10 + 601863 TGGCATACCT -s simRat_chr6.simRat.chr6 306820 10 + 647215 TGGCATACCA - -a -s simMouse_chr6.simMouse.chr6 315133 66 + 636262 GTAACCATTAGCATTACATTTTTCCAACCTCATGTGCATCACTCAGCATTATTTTTTTCTGGCCTT -s Anc0.Anc0refChr7 1916 31 - 16696 GGTACCAT-----------------------------------CAGTATCTTTTTTTTTTGACCCT -s Anc1.Anc1refChr4 2081 31 + 17549 GGTACCAT-----------------------------------CAGTATCTTTTTTTTTTGACCCT -s Anc2.Anc2refChr5 1994 31 - 8386 GGTACCAG-----------------------------------CAGTATCTTTTTTTTTTGATCCT -s mr.mrrefChr5 165269 66 + 294540 GTAACCATTAGCATTATATTTTTCCAACCTCATGTGCATCACTCAGCATTATTTTTTTCTGACCTT -s simCow_chr6.simCow.chr6 325950 31 - 602619 GGTACCCG-----------------------------------CAGCATCTTTTTTTTTGAATCCT -s simDog_chr6.simDog.chr6 280127 31 + 593897 GGTGCCAG-----------------------------------CAGTATCTTTTTTTTTTGATCCT -s simHuman_chr6.simHuman.chr6 303342 31 + 601863 GGCAACAT-----------------------------------CAGTATGTTTTTCTCTTGGCCCT -s simRat_chr6.simRat.chr6 306830 66 + 647215 GGAACCATAAGCATCATATGCTTCCAACCTTTTGTGCATCATTAAGCATTGTTTTTTTCTGACCTT - -a -s simMouse_chr6.simMouse.chr6 315199 16 + 636262 GTGTGCCTCAGCGCTA -s Anc0.Anc0refChr7 1947 16 - 16696 GTGTGTCTCAGCCTTA -s Anc1.Anc1refChr4 2112 16 + 17549 GTGTGTCTCAGCCTTA -s Anc2.Anc2refChr5 2025 16 - 8386 GTATGTCTCAGCCTTA -s mr.mrrefChr5 165335 16 + 294540 GTGTGCCTCAGCCCTA -s simCow_chr6.simCow.chr6 325982 16 - 602619 GCATGGCTCAATCTTA -s simDog_chr6.simDog.chr6 280158 16 + 593897 GTATGTCTCAGCCTTA -s simHuman_chr6.simHuman.chr6 303373 13 + 601863 GTGTGTCTTTG---GG -s simRat_chr6.simRat.chr6 306896 16 + 647215 GTGTGCATCAGCCCTA - -a -s simMouse_chr6.simMouse.chr6 315215 38 + 636262 ACTCAGACCAGAAGTTAGACCCCCATTATGTTAGGGTG -s Anc0.Anc0refChr7 1963 37 - 16696 ACTCAGCCCATGAGTTAGACCAGC-TTGTATTagggtg -s Anc1.Anc1refChr4 2128 37 + 17549 ACTCAGCCCATGAGTTAGACCAGC-TTGTATTagggtg -s Anc2.Anc2refChr5 2044 37 - 8386 ACTCAGCCCATGAGTTAGACCAGC-TTGTATTacggtt -s mr.mrrefChr5 165351 38 + 294540 ACTCAGACCAGAAGTTAGACCCCCATTATGTTAGGGTG -s simCow_chr6.simCow.chr6 326001 37 - 602619 ACTTAGCCCATGAGTTAGACCAGC-TTATATTACggtt -s simDog_chr6.simDog.chr6 280177 28 + 593897 ATTCAGCCCATGAGTTTGA-CAGA-GTGCA-------- -s simHuman_chr6.simHuman.chr6 303386 37 + 601863 ACTCAGGCCATGAGTTAGACCAGC-TTGTATTaggttg -s simRat_chr6.simRat.chr6 306912 38 + 647215 ACTCTGTCCAGAAGCTAGATCCAGATTATGTTGGGGTT - -a -s simMouse_chr6.simMouse.chr6 315253 19 + 636262 GCTTCCATATTATTCTTCC -s Anc0.Anc0refChr7 2001 19 - 16696 gattccatattcctcttct -s Anc1.Anc1refChr4 2166 19 + 17549 gattccatattcctcttct -s Anc2.Anc2refChr5 2082 19 - 8386 gattccacgttcctgtttt -s mr.mrrefChr5 165389 19 + 294540 GCTTCCATATTATTCTTCC -s simCow_chr6.simCow.chr6 326039 19 - 602619 gattccacgttcctgtttt -s simHuman_chr6.simHuman.chr6 303424 19 + 601863 gattccatatcgctcttct -s simRat_chr6.simRat.chr6 306950 19 + 647215 GCTTCCATATTATTCTTCC - -a -s simMouse_chr6.simMouse.chr6 315272 14 + 636262 AATTTGATGGCACA -s Anc0.Anc0refChr7 2020 13 - 16696 g-tttgattgccca -s Anc1.Anc1refChr4 2185 13 + 17549 g-tttgattgccca -s Anc2.Anc2refChr5 2101 13 - 8386 g-ttcgattgtcca -s mr.mrrefChr5 165408 14 + 294540 AATTTGATGGCACA -s simCow_chr6.simCow.chr6 326059 13 - 602619 g-ttcgattgtcca -s simHuman_chr6.simHuman.chr6 303443 13 + 601863 g-tttgattactta -s simRat_chr6.simRat.chr6 306969 14 + 647215 AATTCAATAGCACT - -a -s simMouse_chr6.simMouse.chr6 315286 55 + 636262 CAATATAGCTCCCAGAGTTATCTTACCCCAAATGGTTCAATTTAAAGGTCCTGAG -s Anc0.Anc0refChr7 2037 43 - 16696 ttatatagctcaaggagttattttac------------gattttcaggtaatgag -s Anc1.Anc1refChr4 2202 43 + 17549 ttatatagctcaaggagttattttac------------gattttcaggtaatgag -s Anc2.Anc2refChr5 2118 43 - 8386 ttatataggtcaaggagttattttat------------gactttcagctaatcag -s mr.mrrefChr5 165422 43 + 294540 CAATATAGCTCCCAGAGTTATCTTAC------------AATTTAAAGGTCCTGAG -s simCow_chr6.simCow.chr6 326077 43 - 602619 ttatataggtcaaggagttattttat------------gactttcagCTAATCAG -s simHuman_chr6.simHuman.chr6 303460 43 + 601863 tgacaaagctcaaggagtcagtttac------------ggttctcaggttgtgag -s simRat_chr6.simRat.chr6 306983 43 + 647215 GAATATAGCTCCAAGAGTTATTTTAC------------GACTTTAAGGTCCTGAG - -a -s simMouse_chr6.simMouse.chr6 315341 110 + 636262 CTTGGGGGGTATTTAAACATTTCCAGGACACTAAAGTTATGTGTTTTACTACTTCTACTGCTGCCACATCAGAGACCCTAGAGGTCATATTGTGCAAGATGGTTCGGGCA -s Anc0.Anc0refChr7 2082 9 - 16696 ctggggggG----------------------------------------------------------------------------------------------------- -s Anc1.Anc1refChr4 2247 25 + 17549 ctggggggGtagctagtaaattgag------------------------------------------------------------------------------------- -s Anc2.Anc2refChr5 2163 9 - 8386 ctgtggagG----------------------------------------------------------------------------------------------------- -s mr.mrrefChr5 165465 81 + 294540 CTTGGGGGGTATTTAAACATTTCCAGGACACTAAA----TGTGTTTTA-----------------------GAGACCCTAGAGGTCATATTGTGCAAGATGGTTCGGG-- -s simCow_chr6.simCow.chr6 326122 9 - 602619 CTGTGGAGG----------------------------------------------------------------------------------------------------- -s simHuman_chr6.simHuman.chr6 303505 25 + 601863 ctggggggttagctagtaaattgag------------------------------------------------------------------------------------- -s simRat_chr6.simRat.chr6 307026 81 + 647215 CTTGGGGGGTATTTAATCATTTCCAGGACATAGAA----TCTGTTGTA-----------------------GAGACCCAGATGGTCATACTATGCGAGATGGTTCAGG-- - -a -s simMouse_chr6.simMouse.chr6 315451 115 + 636262 GTTTGGTGAAGTATTGATAGTGTTCTAAAACTAGAACTATCTCTTTCAGAGTCCCACTACCTAGGTGTCATTCATGAACCATTGTTCCTTTATTCAAAATGCAGGGAAGATGCAG -s Anc1.Anc1refChr4 2272 24 + 17549 ------------------------------------------------------------------------------------------tat-TAAAATACAGTGGAGATGGAA -s mr.mrrefChr5 165546 103 + 294540 GTTTG-----------ATAGTGTTCAAAAACTAGAACTATCTCTTTCAGAGTCCCACTACCTAGGTGTCATTCATGAACCATTGTTCCTTTAT-CAAAATGCAGGGGAGATGCAG -s simHuman_chr6.simHuman.chr6 303530 24 + 601863 ------------------------------------------------------------------------------------------tat-TAAAATACAGTGGAGATGGAA -s simRat_chr6.simRat.chr6 307108 103 + 647215 GTTTG-----------ATAGGGTTCAAAAACTGGACCTATCTCTTCCAGAGTCCCACTACCTAGGCGTCATTCATAGACCCTTGTTCCTTTAT-CATAATGCAGGGGAGATGCAT - -a -s simMouse_chr6.simMouse.chr6 315566 5 + 636262 TCATG -s Anc1.Anc1refChr4 2296 5 + 17549 CTATA -s mr.mrrefChr5 165649 5 + 294540 TTATG -s simHuman_chr6.simHuman.chr6 303554 5 + 601863 CTATA -s simRat_chr6.simRat.chr6 307213 5 + 647215 TTATG - -a -s simMouse_chr6.simMouse.chr6 315571 30 + 636262 TAGGTCTATGACTATTATCTGGTAGAGGAA -s Anc0.Anc0refChr7 2091 5 - 16696 -------------------------ATGAA -s Anc1.Anc1refChr4 2301 30 + 17549 CAGTTCTATAGCCATCCCCTGGCAGATGAA -s Anc2.Anc2refChr5 2172 5 - 8386 -------------------------ATGGA -s mr.mrrefChr5 165654 30 + 294540 CAGGTCTATGACTATTATCTGGTAGAGGAA -s simCow_chr6.simCow.chr6 326131 5 - 602619 -------------------------ATGGA -s simHuman_chr6.simHuman.chr6 303560 30 + 601863 CAGTTCTATAGCCATCCCCTGGCAGATGAA -s simRat_chr6.simRat.chr6 307218 20 + 647215 CAGGTCTATGTGTATTATTT---------- - -a -s simMouse_chr6.simMouse.chr6 315601 15 + 636262 TGGGGGATTGGGATT -s Anc0.Anc0refChr7 2096 15 - 16696 TCAGAGATAGGAATT -s Anc1.Anc1refChr4 2331 15 + 17549 TCAGAGATAGGAATT -s Anc2.Anc2refChr5 2177 15 - 8386 TCAAAGACAGGAGTT -s mr.mrrefChr5 165684 15 + 294540 TGGGGGATTGGGATT -s simCow_chr6.simCow.chr6 326141 15 - 602619 TCAAAGACAGGAGTT -s simHuman_chr6.simHuman.chr6 303590 15 + 601863 TAAGAAATAGGAATC - -a -s simMouse_chr6.simMouse.chr6 315616 20 + 636262 ACACATGATTATCCCCACTC -s Anc0.Anc0refChr7 2119 14 - 16696 ATACACCATTGTC------C -s Anc1.Anc1refChr4 2354 14 + 17549 ATACACCATTGTC------C -s Anc2.Anc2refChr5 2200 14 - 8386 ATACACCATGGTC------C -s mr.mrrefChr5 165699 14 + 294540 ACACATGATTATC------C -s simCow_chr6.simCow.chr6 326169 14 - 602619 GTACACCATGGTC------C -s simDog_chr6.simDog.chr6 280208 14 + 593897 ACACACCATGCTC------C -s simHuman_chr6.simHuman.chr6 303613 14 + 601863 ATACACCATTGTC------C - -a -s simMouse_chr6.simMouse.chr6 315636 20 + 636262 ATCCAGCACCAACCACCCTA -s Anc0.Anc0refChr7 2133 20 - 16696 ATCCAGCATTAACTCTCCTG -s Anc1.Anc1refChr4 2368 20 + 17549 ATCCAGCATTAACTCTCCTG -s Anc2.Anc2refChr5 2220 20 - 8386 ATCCAGTATTGACTCTCCTG -s mr.mrrefChr5 165713 20 + 294540 ATCCAGCACCAACCACCCTA -s simCow_chr6.simCow.chr6 326189 20 - 602619 ATCCAGGATAGATTTTCCTG -s simDog_chr6.simDog.chr6 280228 20 + 593897 ATCCAGTATTGACTCTCCTA -s simHuman_chr6.simHuman.chr6 303627 20 + 601863 ATCCAGCAATAGCTCTCGTG - -a -s simMouse_chr6.simMouse.chr6 315656 17 + 636262 ATGTTAGCTCCAAAATG -s Anc0.Anc0refChr7 2160 17 - 16696 ATGTTAGCTCCAAGATG -s Anc1.Anc1refChr4 2395 17 + 17549 ATGTTAGCTCCAAGATG -s Anc2.Anc2refChr5 2247 17 - 8386 ATGTTAGCTCCAAGACG -s mr.mrrefChr5 165733 17 + 294540 ATGTTAGCTCCAAAATG -s simCow_chr6.simCow.chr6 326216 17 - 602619 ATGTTAGCTCAAGGATG -s simDog_chr6.simDog.chr6 280255 17 + 593897 ATGTTAGCTCCAAGACG -s simDog_chr6.simDog.chr6 318094 17 + 593897 ATGTTAGCTCCAAGACG -s simHuman_chr6.simHuman.chr6 303654 17 + 601863 ATGTTAGCCTGAAGATG - -a -s simMouse_chr6.simMouse.chr6 315673 64 + 636262 ATGTGCCAGAACTCTAGATATGCGGAAAATTAGGTAAGCTTCATCTGACTGAGCTTTCAAATTT -s Anc0.Anc0refChr7 2177 64 - 16696 AAGTACCAGAACTCCAGCTATGTGGAAAGCTAGATTAGCTCTGCCTAACCCAGCTTTGGAAGCT -s Anc1.Anc1refChr4 2412 64 + 17549 AAGTACCAGAACTCCAGCTATGTGGAAAGCTAGATTAGCTCTGCCTAACCCAGCTTTGGAAGCT -s Anc2.Anc2refChr5 2264 64 - 8386 AAATACCAAGACCCCGGCTATATGTAAAGCTAGATTAGCCCTGCCTAACCCAGCTCTGGAAGCT -s mr.mrrefChr5 165750 64 + 294540 ATGTGCCAGAACTCCAGATATGTGGAAAATTAGGTAAGCTTCACCTGACCGAGCTTTGGAATTT -s simCow_chr6.simCow.chr6 326235 64 - 602619 ACACACCAAGACTTCAGTTATGTGAAAAGCTAGAGTAGACCAACCTAACCCAGCTTTCGAAGCC -s simDog_chr6.simDog.chr6 280272 58 + 593897 AAATAC------CCCGGCTATATGTAAAGCTAGATTAGCCCTGCCTAACCCAGCTCTGGAAGCT -s simDog_chr6.simDog.chr6 318111 58 + 593897 AAATAC------CCCGGCTATATGTAAAGCTAGATTAGCCCTGCCTAACCCAGCTCTGGAAGCT -s simHuman_chr6.simHuman.chr6 303671 52 + 601863 ACGCACCAGAATTCCAGCTCTGTGGA------------CTCTGCCTAACCCTGCTTTGGAAGCT -s simRat_chr6.simRat.chr6 307238 59 + 647215 -----CTAGAAATTCAGATATGTGGAAAATAAGGTAGGCTTCACCTGACCAAGCTTTGGAAATT - -a -s simMouse_chr6.simMouse.chr6 315737 24 + 636262 CAAGCCCTAGTATTAATCCTGACT -s Anc0.Anc0refChr7 2248 24 - 16696 TAAGCCCCAGTGTTAAGCCCAACT -s Anc1.Anc1refChr4 2483 24 + 17549 TAAGCCCCAGTGTTAAGCCCAACT -s Anc2.Anc2refChr5 2335 24 - 8386 CAAGCTTCAGTGTCAAGTCCACCT -s mr.mrrefChr5 165821 24 + 294540 TAAGCCCTAGTATTAATCCTGACT -s simCow_chr6.simCow.chr6 326306 24 - 602619 TAAGGCTCAGTGCTAAGCCCTCCT -s simDog_chr6.simDog.chr6 280337 24 + 593897 CAAGCTTCAGTGTCAAGTCCACCT -s simDog_chr6.simDog.chr6 318176 24 + 593897 CAAGCTTCAGTGTCAAGTCCACCT -s simHuman_chr6.simHuman.chr6 303730 24 + 601863 TAAGCCCCAGTCTTAAGCCCAACT -s simRat_chr6.simRat.chr6 307304 24 + 647215 TAAACCCTAGCATTAATCATGCCT - -a -s simMouse_chr6.simMouse.chr6 315761 21 + 636262 GGACAGCAACTGAAATAAGGT -s Anc0.Anc0refChr7 2272 21 - 16696 GGATAGTAACGGCCATAGTCT -s Anc1.Anc1refChr4 2507 21 + 17549 GGATAGTAACGGCCATAGTCT -s Anc2.Anc2refChr5 2360 21 - 8386 GGATAGTAAAGGCCAAAGTCT -s mr.mrrefChr5 165845 21 + 294540 GGATAGCAACTGAAATAAGCT -s simCow_chr6.simCow.chr6 326330 20 - 602619 AGATAGTAA-GGCTGTAGTCT -s simDog_chr6.simDog.chr6 280362 21 + 593897 GGATAGTAAAGGCCAAAGTCT -s simDog_chr6.simDog.chr6 318201 21 + 593897 GGATAGTAAAGGCCAAAGTCT -s simHuman_chr6.simHuman.chr6 303754 21 + 601863 GGATGGTAACAGCTGTAGTCT -s simRat_chr6.simRat.chr6 307328 21 + 647215 GTATAGGGACTAGAAATTGCT - -a -s simMouse_chr6.simMouse.chr6 315782 14 + 636262 ACATTTCACCCAGA -s Anc0.Anc0refChr7 2294 10 - 16696 ACATT----CCAGA -s Anc1.Anc1refChr4 2529 10 + 17549 ACATT----CCAGA -s Anc2.Anc2refChr5 2382 10 - 8386 ATATT----CCAGG -s mr.mrrefChr5 165866 14 + 294540 ACATTTCACCCAGA -s simCow_chr6.simCow.chr6 326351 10 - 602619 ATATT----CCAAT -s simDog_chr6.simDog.chr6 280384 10 + 593897 ATATT----CCAGG -s simDog_chr6.simDog.chr6 318223 10 + 593897 ATATT----CCAGG -s simHuman_chr6.simHuman.chr6 303776 10 + 601863 ACATT----CCAGA -s simRat_chr6.simRat.chr6 307349 14 + 647215 ACAATTCACCCAAA - -a -s simMouse_chr6.simMouse.chr6 315796 35 + 636262 TGAGTTTAGTGCTTATCAATCATGCAACCAGGAGG -s Anc0.Anc0refChr7 2304 34 - 16696 TGAGTTTGATGTT-GTCAACAGTGGGACCATGAAT -s Anc1.Anc1refChr4 2539 34 + 17549 TGAGTTTGATGTT-GTCAACAGTGGGACCATGAAT -s Anc2.Anc2refChr5 2392 34 - 8386 TGGGTTTGATGTT-GTCCACAGTTGGACCATGAAT -s mr.mrrefChr5 165880 35 + 294540 TGAGTTTAGTGTTTATCAATCATGCAACCAGGAAG -s simCow_chr6.simCow.chr6 326370 9 - 602619 TGGGTTTGA-------------------------- -s simDog_chr6.simDog.chr6 280394 34 + 593897 TGGGTTTGATGTT-GTCCACAGTTGGACCATGAAT -s simDog_chr6.simDog.chr6 318233 9 + 593897 TGGGTTTGA-------------------------- -s simHuman_chr6.simHuman.chr6 303786 34 + 601863 CTAGTTTGACGTT-GTCAACAGTGTTGGCATGAAT -s simRat_chr6.simRat.chr6 307363 35 + 647215 TGAGTTTAGTGTCTATCAATCATGCAACTAGGAAG - -a -s simMouse_chr6.simMouse.chr6 315831 9 + 636262 GGTTAATCT -s Anc0.Anc0refChr7 2338 9 - 16696 GGTTAAACT -s Anc1.Anc1refChr4 2573 9 + 17549 GGTTAAACT -s Anc2.Anc2refChr5 2426 9 - 8386 GGTTAAATT -s mr.mrrefChr5 165915 9 + 294540 GGTTAAACT -s simCow_chr6.simCow.chr6 326379 9 - 602619 GGTTAAATT -s simDog_chr6.simDog.chr6 280428 9 + 593897 GGTTAAACT -s simDog_chr6.simDog.chr6 318242 7 + 593897 TGTT--GTA -s simHuman_chr6.simHuman.chr6 303825 9 + 601863 GGTTAAACT -s simRat_chr6.simRat.chr6 307398 9 + 647215 GGTTAAACT - -a -s simMouse_chr6.simMouse.chr6 315840 1 + 636262 G -s Anc0.Anc0refChr7 2347 1 - 16696 G -s Anc1.Anc1refChr4 2582 1 + 17549 G -s Anc2.Anc2refChr5 2435 1 - 8386 G -s mr.mrrefChr5 165924 1 + 294540 G -s simCow_chr6.simCow.chr6 326388 1 - 602619 G -s simDog_chr6.simDog.chr6 318249 1 + 593897 A -s simHuman_chr6.simHuman.chr6 303834 1 + 601863 G -s simRat_chr6.simRat.chr6 307407 1 + 647215 G - -a -s simMouse_chr6.simMouse.chr6 315841 23 + 636262 GGGCAACCTGGACTTGTACAGCG -s Anc0.Anc0refChr7 2348 23 - 16696 GAGCAATCTGAACTTGCAATGTT -s Anc1.Anc1refChr4 2583 23 + 17549 GAGCAATCTGAACTTGCAATGTT -s Anc2.Anc2refChr5 2436 23 - 8386 GAGCAATCTGAACTTGCAATGTT -s mr.mrrefChr5 165925 23 + 294540 GGGCAATCTGGACTTGTACAGCT -s simCow_chr6.simCow.chr6 326389 23 - 602619 GGGCAATCTGGACTGACGATGTT -s simDog_chr6.simDog.chr6 280437 23 + 593897 GAGCAATCTGAGCTTGCAACGTT -s simDog_chr6.simDog.chr6 318250 4 + 593897 GAGC------------------- -s simHuman_chr6.simHuman.chr6 303835 23 + 601863 GAGCAATCTGAACCTGCAATGTT -s simRat_chr6.simRat.chr6 307408 23 + 647215 GGGCAATCTGGACTAGTACAGCT - -a -s simMouse_chr6.simMouse.chr6 315864 13 + 636262 ATATGAGTATCCC -s Anc0.Anc0refChr7 2371 13 - 16696 ATATTCATGTCCC -s Anc1.Anc1refChr4 2606 13 + 17549 ATATTCATGTCCC -s Anc2.Anc2refChr5 2459 13 - 8386 TTATTCATGTCCC -s mr.mrrefChr5 165948 13 + 294540 ATATGAGTATCCC -s simCow_chr6.simCow.chr6 326413 13 - 602619 TTATTCATTTCCT -s simDog_chr6.simDog.chr6 280460 13 + 593897 TTATTCATGGCCC -s simHuman_chr6.simHuman.chr6 303858 13 + 601863 ATGTTCATGTCCC -s simRat_chr6.simRat.chr6 307431 13 + 647215 ATATGAGTATCCC - -a -s simMouse_chr6.simMouse.chr6 315877 2 + 636262 AT -s Anc0.Anc0refChr7 2384 2 - 16696 AT -s Anc1.Anc1refChr4 2619 2 + 17549 AT -s Anc2.Anc2refChr5 2472 2 - 8386 AT -s mr.mrrefChr5 165961 2 + 294540 AT -s simCow_chr6.simCow.chr6 326426 2 - 602619 CT -s simDog_chr6.simDog.chr6 280473 2 + 593897 AT -s simHuman_chr6.simHuman.chr6 303871 2 + 601863 AT -s simRat_chr6.simRat.chr6 307445 2 + 647215 AT - -a -s simMouse_chr6.simMouse.chr6 315879 29 + 636262 CCTCCTCACCCCATGTACTGACAGGTATT -s Anc0.Anc0refChr7 2386 26 - 16696 CCCAGTCACCCCAGGCATTGACAGAC--- -s Anc1.Anc1refChr4 2621 29 + 17549 CCCAGTCACCCCAGGCATTGACAGACAAT -s Anc2.Anc2refChr5 2475 26 - 8386 CCCAGTCACTCCAGGCATTGACAGGC--- -s mr.mrrefChr5 165963 29 + 294540 CCTCCTCACCCCATGTACTGACAGACATT -s simCow_chr6.simCow.chr6 326429 26 - 602619 CCCAGTAACTCCAGGCGTTTACAGGC--- -s simDog_chr6.simDog.chr6 280476 26 + 593897 CCCAATCACTCCAGGCATTGACAGGC--- -s simHuman_chr6.simHuman.chr6 303873 29 + 601863 TCCAGTCAGCCCAGGCATTGACAGACAAT -s simRat_chr6.simRat.chr6 307447 29 + 647215 CCTCTTCATGCCATGTACTAACAGACATT - -a -s simMouse_chr6.simMouse.chr6 315908 21 + 636262 AGCAAATTCATGTATAGAGGC -s Anc0.Anc0refChr7 2412 21 - 16696 GGCAATCACATGTATAGAAGA -s Anc1.Anc1refChr4 2650 21 + 17549 GGCAATCACATGTATAGAAGA -s Anc2.Anc2refChr5 2501 21 - 8386 GGCAATCACATATATAGCAGA -s mr.mrrefChr5 165992 21 + 294540 AGCAATTACATGTATAGAAGA -s simCow_chr6.simCow.chr6 326458 20 - 602619 GGCAATCACATATAT-GTAGA -s simDog_chr6.simDog.chr6 280502 21 + 593897 GGCAGTCACATGTATAGCAGA -s simHuman_chr6.simHuman.chr6 303902 21 + 601863 GGGGATCACATGTATAGAAGA -s simRat_chr6.simRat.chr6 307476 21 + 647215 AGCAATTACATGTATAGAAGA - -a -s simMouse_chr6.simMouse.chr6 315929 38 + 636262 GCTTGGAATCTAAGCAAACACAGAATCATAATCATTTT -s Anc0.Anc0refChr7 2433 38 - 16696 GATGAGAATCTAAGTAAGCACAGAATCACGGTCAGATT -s Anc1.Anc1refChr4 2671 38 + 17549 GATGAGAATCTAAGTAAGCACAGAATCACGGTCAGATT -s Anc2.Anc2refChr5 2522 38 - 8386 GATGAGAATCTAAGTAAGTACAGAATCACGGTCTGATT -s mr.mrrefChr5 166013 38 + 294540 GCTTGGAATCTAAGCAAACACAGAATCATAATCATTTT -s simCow_chr6.simCow.chr6 326478 26 - 602619 GATGAGAATCTAAGTTAGTACAAATT------------ -s simDog_chr6.simDog.chr6 280523 38 + 593897 GATGAGAACCTAAGTAAGTACAGAAACACGGTCTGATT -s simHuman_chr6.simHuman.chr6 303966 38 + 601863 GATCATAATCTTAGTAAGCACAGAATCAGGGTCAGCTT -s simRat_chr6.simRat.chr6 307497 38 + 647215 GCTTGAAATTTAAGCAAACACAGATTCAAAATCATTTA - -a -s simMouse_chr6.simMouse.chr6 315967 22 + 636262 CAATCTACTAGCATTGTACTGT -s Anc0.Anc0refChr7 2488 22 - 16696 CAGATTATTAGAATTGTACTGT -s Anc1.Anc1refChr4 2726 22 + 17549 CAGATTATTAGAATTGTACTGT -s Anc2.Anc2refChr5 2577 22 - 8386 CTGATTGTTAGAATTGTACTGT -s mr.mrrefChr5 166051 22 + 294540 CAATTTACTAGCATTGTACTGT -s simDog_chr6.simDog.chr6 280578 22 + 593897 CTGATTGTTAGAATTGTACTGT -s simHuman_chr6.simHuman.chr6 304021 22 + 601863 CAGATTATTAGTACTGTAGAGT -s simRat_chr6.simRat.chr6 307535 22 + 647215 TAATTTACTAGAATTGTACTGT - -a -s simMouse_chr6.simMouse.chr6 315989 58 + 636262 CTCCCCTTACCCAAAGATATGCATCGCCAAATAACGGAAGACTGCCTAAAGTGATGGT -s Anc0.Anc0refChr7 2510 33 - 16696 CACCC------TGAAGAAATGACACTCCAAATAATGGAA------------------- -s Anc1.Anc1refChr4 2748 39 + 17549 CACCCCCTGCCTGAAGAAATGACACTCCAAATAATGGAA------------------- -s Anc2.Anc2refChr5 2599 33 - 8386 CACTG------TGAGAAAAAGACACTCCAAATAATGGAA------------------- -s mr.mrrefChr5 166073 58 + 294540 CTCCCCTTGCCCAAAGATATGCATCGCCAAATAACGGAAGACTGCCTAAAGTGATGGC -s simCow_chr6.simCow.chr6 326504 30 - 602619 ---TG------AAAGAAATAGACACTCCAAATAATGGGA------------------- -s simDog_chr6.simDog.chr6 280600 33 + 593897 CACTG------TGAGAGAAACACACTCCAAGTAATGGAA------------------- -s simHuman_chr6.simHuman.chr6 304050 39 + 601863 CGCCCCCTGCCTCAAGAAATGACACTCCGAATAATGGAA------------------- -s simRat_chr6.simRat.chr6 307557 58 + 647215 CTCCCCTTGCCCAAAGACATGCATCACCAAATAAGGGATAACTGCCTAAAGGGATCGC - -a -s simMouse_chr6.simMouse.chr6 316047 64 + 636262 ACTCTAGAAGAAAAGTCCTTAAAGTTCCATTACTTTTAAATTACGTCCCATAGACATTGTTGGG -s Anc0.Anc0refChr7 2543 54 - 16696 ---------AAGT-GTCCTTAAAATGATGGTACTTTTAAAATAGGTACGAAAGACATTGTTGAA -s Anc1.Anc1refChr4 2787 55 + 17549 ---------AAGTAGTCCTTAAAATGATGGTACTTTTAAAATAGGTACGAAAGACATTGTTGAA -s Anc2.Anc2refChr5 2632 54 - 8386 ---------AGGT-GACCTTAAAATGATGGTAATTTTATAATAGGTACGAAAGACATTGTTGAA -s mr.mrrefChr5 166131 64 + 294540 ACTCTAGAAAAAAAGTCCTTAAAGTGCCATTACTTTTAAATTACGTCCCAAAGACATTGTTGGG -s simCow_chr6.simCow.chr6 326534 54 - 602619 ---------AGTT-GACTTTAAAGTGATGGTAGGTTAAGAACAGGTGCTAAAGATATTGTTAGA -s simDog_chr6.simDog.chr6 280633 54 + 593897 ---------AGGT-GACCGTAAAATAATGGTAATTTTATACTAGGAATGAAAGACATTTTTGAA -s simHuman_chr6.simHuman.chr6 304089 55 + 601863 ---------AAGCAGTCCTTAAAATGATGGTACTTTGAAAATAGGTACAAAAGACATTGTTGAA -s simRat_chr6.simRat.chr6 307616 64 + 647215 ACTTTAAACAAAAAGTCCTTAGTGTGCCATTACTTTTAAATTACATCCCAAAGACATTGTTGGG - -a -s simMouse_chr6.simMouse.chr6 316111 334 + 636262 TGGTACCTGCTTGGTACTTGGTACCAGTGGCTTAATGTTGTCAAGATTTTGTACAGTACCTTGTGCAAAGTTCCAATAAAAGGCAAATGTAGCTGTGTGCATGTGGTTAGTAGTTGGCTGCTGAGCCCGCCTCACTTCATGAGCTGTCAAGCAGCTGCAGACACCAGGAGAAGAAGTCTGCCTGCCTCATGCACTGCCAAGTGATCACAGGGACATGTAGAAGGACCCAACACCCTCCACCCCATAAACTGCATGAGATGCTATTTATTGCACAATACTCATAACCAAGATTCTTTCCAGCTTCATGATGTTCACAACTCTTGGCTCTTGGGGG -s Anc0.Anc0refChr7 2597 24 - 16696 TGGTACCTCCTTGGCACAAGT----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GGG -s Anc1.Anc1refChr4 2842 24 + 17549 TGGTACCTCCTTGGCACAAGT----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GGG -s Anc2.Anc2refChr5 2686 24 - 8386 TGGCACCTCCTGGGCACAAGT----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GGG -s mr.mrrefChr5 166195 293 + 294540 TGGTACCTGCTTGGTACTTGGTACCAGTGGCTTAATG-----------------------TTGTGCAAAGTTCCAATAAAAGGCAAATGT-GCTGTGTGCATGTGGTTAGTAGTTGGCTGCTGAGC---------------AGCTGTCAAGCAGCTGCAGACACCAGGAGAAGAAGTCTGCCTGCCTCATGCACTGCCAAGTGATCACAGGGACATGTAGAAGGACCCAACACCCTCCACCCCATAAACT-CATGAGATGCTATTTATTGCACAATACTCATAACCAAGATTC-TTCCAGCTTCATGATGTTCACAACTCTTGGCTCTTGGGGG -s simCow_chr6.simCow.chr6 326600 24 - 602619 AGGCACCTCATGGGCATAAGT----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GGG -s simDog_chr6.simDog.chr6 280687 24 + 593897 TGGCACCCCCAGGACACAAGT----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GGG -s simHuman_chr6.simHuman.chr6 304144 24 + 601863 TGGTACCTCCTTAGCACAGGT----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GTA -s simRat_chr6.simRat.chr6 307680 293 + 647215 TGGCACCTGCTCGATACTTGGCACCAGTTGCTTAACG-----------------------TTGTGTAAAGTTCCAATAAAAGGCAAATGT-GCCATGTGCATGCGGCAAGCACTCGGCTGCAGAGC---------------AGCTATCCAGCAACTGCAGGCACCAGGTGAAGAAGCCTGCCTGCCTCATGCACTGTCATGTGATTGCAGACACCTGCGGAAGGACCCAACACCCTCCACGCCATAAACC-CGTAAGATGCTATTTATTGCACAATACTCATAATCAACATTC-TTCCGTCTTCATGGTGTTCATGACTCCTGGCTATTGGGGG - -a -s simMouse_chr6.simMouse.chr6 316445 12 + 636262 CAGGGGTCTGTA -s Anc0.Anc0refChr7 2621 12 - 16696 CAGGGATATGCC -s Anc1.Anc1refChr4 2866 12 + 17549 CAGGGATATGCC -s Anc2.Anc2refChr5 2710 12 - 8386 CAGAGATACGCC -s mr.mrrefChr5 166488 12 + 294540 CAGGGGTCTGCA -s simCow_chr6.simCow.chr6 326629 12 - 602619 CAGAGATACACA -s simDog_chr6.simDog.chr6 280711 12 + 593897 CAGAGGTACGCC -s simHuman_chr6.simHuman.chr6 304168 12 + 601863 CAGGGATGTGCC -s simRat_chr6.simRat.chr6 307973 12 + 647215 CTGGGGTCTGCG - -a -s simMouse_chr6.simMouse.chr6 316457 14 + 636262 AATACTGCCTCTGA -s Anc0.Anc0refChr7 2634 14 - 16696 AAAACTGCATCTCA -s Anc1.Anc1refChr4 2879 14 + 17549 AAAACTGCATCTCA -s Anc2.Anc2refChr5 2723 14 - 8386 AAAACTGCATCTCA -s mr.mrrefChr5 166500 14 + 294540 AATACTGCCTCTGA -s simCow_chr6.simCow.chr6 326642 14 - 602619 CATATTGCATCTCA -s simDog_chr6.simDog.chr6 280724 14 + 593897 AAAACTACATTTCA -s simHuman_chr6.simHuman.chr6 304181 14 + 601863 AAAACTGCATCTCA -s simRat_chr6.simRat.chr6 307985 13 + 647215 AACAATGCCTCTG- - -a -s simMouse_chr6.simMouse.chr6 316471 4 + 636262 CTAT -s Anc0.Anc0refChr7 2648 4 - 16696 CTAT -s Anc1.Anc1refChr4 2893 4 + 17549 CTAT -s Anc2.Anc2refChr5 2737 4 - 8386 CTAC -s mr.mrrefChr5 166514 4 + 294540 CTAT -s simCow_chr6.simCow.chr6 326659 4 - 602619 CTAC -s simDog_chr6.simDog.chr6 280738 4 + 593897 CTAC -s simHuman_chr6.simHuman.chr6 304195 4 + 601863 CTAT - -a -s simMouse_chr6.simMouse.chr6 316475 5 + 636262 CTCTT -s Anc0.Anc0refChr7 2653 5 - 16696 CTCTT -s Anc1.Anc1refChr4 2898 5 + 17549 CTCTT -s Anc2.Anc2refChr5 2742 5 - 8386 CTCTT -s mr.mrrefChr5 166518 5 + 294540 CTCTT -s simCow_chr6.simCow.chr6 326664 5 - 602619 CTCTT -s simDog_chr6.simDog.chr6 280743 5 + 593897 CTCTT -s simHuman_chr6.simHuman.chr6 304200 5 + 601863 CCCTT - -a -s simMouse_chr6.simMouse.chr6 316480 38 + 636262 GTAGCATTGAAGAAGTTTACGTATTTCATGCCTAACAT -s Anc0.Anc0refChr7 2658 38 - 16696 TAGGGAAATAAAAGATTGGTTCATTCCATGCTTAACAT -s Anc1.Anc1refChr4 2903 38 + 17549 TAGGGAAATAAAAGATTGGTTCATTCCATGCTTAACAT -s Anc2.Anc2refChr5 2747 38 - 8386 TAGGGAAATAAAAGATTGGTTCATTCCATGCTTAACAT -s mr.mrrefChr5 166523 38 + 294540 GTAGCATTGAAGAAGTTTATGTATTCCATGCCTAACAT -s simCow_chr6.simCow.chr6 326670 38 - 602619 TAGGGAAATAAAAGATTTAGGCATTCCATGCTTAACAT -s simDog_chr6.simDog.chr6 280748 34 + 593897 ----GCAGTATAAGGTTGGTTCATTCCATGCTTAATGT -s simHuman_chr6.simHuman.chr6 304205 38 + 601863 CCGGGAAATAAAAGATTGGTACATTCCATGCTTAACAT -s simRat_chr6.simRat.chr6 307998 25 + 647215 -------------AGATTATGTATTCCATGCCTAACAT - -a -s simMouse_chr6.simMouse.chr6 316518 69 + 636262 CCAAAACTTTAGTGACTCTTAAAGCAGAAGCACGCTGGCTTAACACTGAGGATTGCCTCTGTTCTGTCA -s Anc0.Anc0refChr7 2696 68 - 16696 CCAAACCCTT-GCTGTCCTAATAGCACCACCCCACTACCTTAAAAGTGAGGATTGCTCCTGAGCTGTCT -s Anc1.Anc1refChr4 2941 69 + 17549 CCAAACCCTTAGCTGTCCTAATAGCACCACCCCACTACCTTAAAAGTGAGGATTGCTCCTGAGCTGTCT -s Anc2.Anc2refChr5 2785 68 - 8386 CCAAACCCTT-GCTGTCCTAGTAGCACCACCCCAATACCTTAAAAGTGAGCATTGCTTCTGAGATGCCT -s mr.mrrefChr5 166561 69 + 294540 CCAAAACTTTAGTGGCTCTTAAAGCACAAGCACACTGCCTTAACACTGAGGATTGCCCCTGTTCTGTCA -s simCow_chr6.simCow.chr6 326709 54 - 602619 CTAAACCCTT-G-TGTCCCAGTAGCACCAGCTCAATACCTTAAAAGTGGCCATTGC------------- -s simDog_chr6.simDog.chr6 280782 59 + 593897 CC----------CTGTCCTAGTAGCACCACCCCAATACTTTAAAGGTGAGCTTTGCTTCTGAGATGCCT -s simHuman_chr6.simHuman.chr6 304243 69 + 601863 CCACACACTTAGCAGTCCTAATAGCACCATTCGACTACCTTAAAAGTGAGGATTGCTCATGACCTGTCT -s simRat_chr6.simRat.chr6 308023 69 + 647215 CAAAAACTTTAGTGGATTTTAAAGCACAAGCAAACTGCCTTAGCGCTGAGGAGTGCCCCTGTTCTGGCA - -a -s simMouse_chr6.simMouse.chr6 316587 6 + 636262 CACTAA -s Anc0.Anc0refChr7 2764 6 - 16696 CACTAA -s Anc1.Anc1refChr4 3010 6 + 17549 CACTAA -s Anc2.Anc2refChr5 2853 6 - 8386 AACTTA -s mr.mrrefChr5 166630 6 + 294540 CACTAA -s simDog_chr6.simDog.chr6 280849 6 + 593897 AACTTA -s simHuman_chr6.simHuman.chr6 304312 6 + 601863 CACTAA -s simRat_chr6.simRat.chr6 308092 6 + 647215 CAATAA - -a -s simMouse_chr6.simMouse.chr6 316593 16 + 636262 AGTATGTACAGTACAT -s Anc0.Anc0refChr7 2770 16 - 16696 AGTGTGTGCAGTACAT -s Anc1.Anc1refChr4 3016 16 + 17549 AGTGTGTGCAGTACAT -s Anc2.Anc2refChr5 2859 16 - 8386 AGTGTGTGCAGTACAT -s mr.mrrefChr5 166636 16 + 294540 AGTATGTGCAGTACAT -s simDog_chr6.simDog.chr6 280862 16 + 593897 AGTGTGTGCAGTACAT -s simHuman_chr6.simHuman.chr6 304318 16 + 601863 AGTGGGTGCAGTACAT -s simRat_chr6.simRat.chr6 308098 16 + 647215 AGTATGGGCAGTACAA - -a -s simMouse_chr6.simMouse.chr6 316609 6 + 636262 TATGCT -s Anc0.Anc0refChr7 2786 6 - 16696 CATGCT -s Anc1.Anc1refChr4 3032 6 + 17549 CATGCT -s Anc2.Anc2refChr5 2875 6 - 8386 CAGACT -s mr.mrrefChr5 166652 6 + 294540 TATGCT -s simDog_chr6.simDog.chr6 280885 6 + 593897 CAGACT -s simHuman_chr6.simHuman.chr6 304334 6 + 601863 CATGCT -s simRat_chr6.simRat.chr6 308114 6 + 647215 TATGTT - -a -s simMouse_chr6.simMouse.chr6 316615 9 + 636262 GCAGACACA -s Anc0.Anc0refChr7 3062 9 - 16696 GCAGAAGTA -s Anc1.Anc1refChr4 3308 9 + 17549 GCAGAAGTA -s Anc2.Anc2refChr5 3161 9 - 8386 GCAGAAGTA -s mr.mrrefChr5 166658 9 + 294540 GCAGACACA -s simDog_chr6.simDog.chr6 281197 9 + 593897 GCAGAAGTA -s simHuman_chr6.simHuman.chr6 304636 9 + 601863 GCAGAAGTA -s simRat_chr6.simRat.chr6 308120 9 + 647215 GCAGACACA - -a -s simMouse_chr6.simMouse.chr6 316624 7 + 636262 GAGGGAT -s Anc0.Anc0refChr7 3071 7 - 16696 TTGGGAT -s Anc1.Anc1refChr4 3317 7 + 17549 TTGGGAT -s Anc2.Anc2refChr5 3170 7 - 8386 TTGGGAT -s mr.mrrefChr5 166667 7 + 294540 GAGGGAT -s simCow_chr6.simCow.chr6 327027 4 - 602619 ---GGAT -s simDog_chr6.simDog.chr6 281207 7 + 593897 TTGGGAT -s simHuman_chr6.simHuman.chr6 304645 7 + 601863 TTAGGAT -s simRat_chr6.simRat.chr6 308129 7 + 647215 GTGGGAT - -a -s simMouse_chr6.simMouse.chr6 316631 5 + 636262 CAATA -s Anc0.Anc0refChr7 3079 5 - 16696 CAATA -s Anc1.Anc1refChr4 3325 5 + 17549 CAATA -s Anc2.Anc2refChr5 3178 5 - 8386 CAATA -s mr.mrrefChr5 166674 5 + 294540 CAATA -s simCow_chr6.simCow.chr6 327032 5 - 602619 CAATA -s simDog_chr6.simDog.chr6 281215 5 + 593897 CAATA -s simHuman_chr6.simHuman.chr6 304653 5 + 601863 CAGTA -s simRat_chr6.simRat.chr6 308136 5 + 647215 CAATA - -a -s simMouse_chr6.simMouse.chr6 316636 104 + 636262 AAATGAGTCGACGATAACACAACGTTAAAAATAGCTTTCTAGTCCCCTCTGGGGTTTGTTCGTTGGACAGGGCATCTATAATGTACTCGGGGAACTACACATGA -s Anc0.Anc0refChr7 3090 54 - 16696 CAATGAGTCGATAATAATACAACATTCAGAATAGCTTTCTAATCCCCTCTTGG--------------------------------------------------A -s Anc1.Anc1refChr4 3336 54 + 17549 CAATGAGTCGATAATAATACAACATTCAGAATAGCTTTCTAATCCCCTCTTGG--------------------------------------------------A -s Anc2.Anc2refChr5 3189 54 - 8386 CAATGAGTCAATAATAATACAACATTCAGAATAGCTTTCTAATCCCCTCTTGG--------------------------------------------------A -s mr.mrrefChr5 166679 102 + 294540 AAATGAGTCGACAATAATACAACATTAAGAATAGCTTTCTAGTCCCCTCTGGGGTTTGTTCGTTGGACAGGGCATCTATAATGTACTCGGGGAAC--CACATGA -s simCow_chr6.simCow.chr6 327043 54 - 602619 CAACGAGTCAATAATAATACAACATTCTGAATAGCTTTCTAATTCCCTCTAGG--------------------------------------------------A -s simDog_chr6.simDog.chr6 281226 54 + 593897 CTATGAGTCAATAATCATACAATATTCAGAATTACTTTCTAATCCCCTGTTTG--------------------------------------------------A -s simHuman_chr6.simHuman.chr6 304664 54 + 601863 CAAAGAGTTGATAATAATACACCATTTGGAATAGCTTTCCAATGCCCTCCTGG--------------------------------------------------A -s simRat_chr6.simRat.chr6 308141 102 + 647215 AAATGAGTCAACAATAATATAACATTCAGAAAATCTTTTTAGTCACCACTGGGGTTTTTTTGTAGGGCAGGGGATCTACAATGTATGCGGGGAAC--CACATGA - -a -s simMouse_chr6.simMouse.chr6 316740 63 + 636262 CAAGCCTCTTGTTAGAGGCACCACACTCACAAATTATGAGTTTATTTCTAGTGAGTGATTTGC -s Anc0.Anc0refChr7 3144 58 - 16696 GAAATCTTTTTTTAG-----CTATTCCCATGAGCCATAATTTTGTATCTAGTGAATAATTTGC -s Anc1.Anc1refChr4 3390 58 + 17549 GAAATCTTTTTTTAG-----CTATTCCCATGAGCCATAATTTTGTATCTAGTGAATAATTTGC -s Anc2.Anc2refChr5 3243 58 - 8386 GAAATCTTTTTTTAG-----CTGTTCCCATGAGCCATAATTTTGTATCTAGTGAATAATTTGC -s mr.mrrefChr5 166781 63 + 294540 CAAGCCTCTTGTTAGAGGCACCACACTCACAAATTATGAGTTTATTTCTAGTGAGTGATTTGC -s simCow_chr6.simCow.chr6 327097 58 - 602619 GAAGTCTGTTTTTAA-----CTGTTCCCATGAGTTATAAATTTGTCTCTAGCAAATATTTAGT -s simDog_chr6.simDog.chr6 281284 52 + 593897 GAAATCTTTTCTGTG-----------CCATGGGCCATAATTCTGTATCTAGTGAATAATTTGC -s simHuman_chr6.simHuman.chr6 304718 43 + 601863 GAAATCTTTTTTTAG-----CTATCCCCATGAGCCAAAATCTT---------------TTTGT -s simRat_chr6.simRat.chr6 308243 63 + 647215 CAAACCTCTTGCACGATGCGTTGCACTCATAAATTATGAATTTGTATCCAGTGAATGATTTGC - -a -s simMouse_chr6.simMouse.chr6 316803 6 + 636262 CTATGC -s Anc0.Anc0refChr7 3202 6 - 16696 GTGTGC -s Anc1.Anc1refChr4 3448 6 + 17549 GTGTGC -s Anc2.Anc2refChr5 3301 6 - 8386 GTGTGC -s mr.mrrefChr5 166844 6 + 294540 CTATGC -s simCow_chr6.simCow.chr6 327155 6 - 602619 GCATGT -s simDog_chr6.simDog.chr6 281338 6 + 593897 GTGTGC -s simHuman_chr6.simHuman.chr6 304761 6 + 601863 GCCTAA -s simRat_chr6.simRat.chr6 308306 6 + 647215 CTATGC - -a -s simMouse_chr6.simMouse.chr6 316809 4 + 636262 AACT -s Anc0.Anc0refChr7 3701 4 - 16696 AACC -s Anc1.Anc1refChr4 3947 4 + 17549 AACC -s Anc2.Anc2refChr5 3840 4 - 8386 GTGC -s mr.mrrefChr5 166850 4 + 294540 AACT -s simCow_chr6.simCow.chr6 327809 4 - 602619 GTGC -s simDog_chr6.simDog.chr6 281887 4 + 593897 GTGC -s simHuman_chr6.simHuman.chr6 305307 4 + 601863 AACC -s simRat_chr6.simRat.chr6 308312 4 + 647215 GTCT - -a -s simMouse_chr6.simMouse.chr6 316813 10 + 636262 CTTCTGGACT -s Anc0.Anc0refChr7 3705 2 - 16696 CT-------- -s Anc1.Anc1refChr4 3951 2 + 17549 CT-------- -s Anc2.Anc2refChr5 3844 2 - 8386 CT-------- -s mr.mrrefChr5 166854 10 + 294540 CTTCTGGACT -s simCow_chr6.simCow.chr6 327813 2 - 602619 TC-------- -s simDog_chr6.simDog.chr6 281891 2 + 593897 CT-------- -s simHuman_chr6.simHuman.chr6 305311 2 + 601863 CT-------- -s simRat_chr6.simRat.chr6 308373 10 + 647215 CTTTTGGATT - -a -s simMouse_chr6.simMouse.chr6 316823 70 + 636262 TGGAGTATTTACAAGTTGTGGGCCATCTCGTGTGCCATGCACAGACTATAAGTTCTCAACTGACTGAACC -s mr.mrrefChr5 166864 70 + 294540 TGGAGTATTTACAAGTTGTGGGCCATCTCGTGTGCCATGCACAGACTATAAGTTCTCAACTGACTGAACC -s simRat_chr6.simRat.chr6 308388 70 + 647215 TGGAGAATTTACAAGTTGTGGGCCAGCTCATGTGGCATGCACAGACTTCAAGTTCTGAACTGACTGGACC - -a -s simMouse_chr6.simMouse.chr6 316893 179 + 636262 AGATTAATGAAGAGGGGATGCGATCAAAAGGATGGGAAGCAGTGACCTAAAAAATGATTACTCTCTAGGCTATTGAGCAATGAATTCTTCTGGATCATCCCTACAAATATCATCAGATGTGGAAACTCAAGTGGACCTAACTAAAGTTCAGTTTTACACAATTTGCCAAGCTAATTTTA -s mr.mrrefChr5 166934 170 + 294540 AGATTAATGAAGAGGGGATGCGATCAAAAGGATGGGAAGCAGTGACCTAAAAAATGATTACTCTCTAGGCT------CAATGAATTCT---GGATCATCCCTACAAATATCATCAGATGTGGAAACTCAAGTGGACCTAACTAAAGTTCAGTTTTACACAATTTGCCAAGCTAATTTTA -s simRat_chr6.simRat.chr6 308459 170 + 647215 AGATTAGTGAAGAGCAAATACGATCAGAAGTATGGAAAGTAGTGACTCAAGATATGATTACTCTCTTAACC------CAATGAATTCT---GGATCATCCCTACAAATACCATCAGATGCGGAAACTCCAGTGGATCCGGCTAAAATTCAGTTTTACACAATTTGCCAAGCTAATTTAA - -a -s simMouse_chr6.simMouse.chr6 317072 3 + 636262 GAA -s mr.mrrefChr5 167104 3 + 294540 GAA -s simRat_chr6.simRat.chr6 308640 3 + 647215 GAA - -a -s simMouse_chr6.simMouse.chr6 317075 61 + 636262 ATTCTTTCTACACAGTTTATGAAGTTTGCCTCTTACTGGAGCTTTGCATGAGGCATTGTGT -s mr.mrrefChr5 167107 61 + 294540 ATTCTTTCTACACAGTTTATGAAGTTTGCCTCTTACTGGAGCTTTGCATGAGGCATTGTGT -s simRat_chr6.simRat.chr6 308646 61 + 647215 ATTCTGTCTACTCAGTTCATGAAGTTTGCCTCTTATTGAAGCTTTACATGATGCATTATGT - -a -s simMouse_chr6.simMouse.chr6 317136 39 + 636262 AAATATAATCCATGTTAAGGTGCAACTCAGATGTAGGAT -s mr.mrrefChr5 167168 39 + 294540 AAATATAATCCATGTTAAGGTGCAACTCAGATGTAGGAT -s simRat_chr6.simRat.chr6 308708 39 + 647215 AAATACAACCAATGTTAAGGTGCAACTCAGGTCGAGATT - -a -s simMouse_chr6.simMouse.chr6 317175 109 + 636262 GCCAATGCAGGTTCCCACAGATTTGGTCTGGCTTACTTCACAAGGTGCATTCCCAGCAAGAGGTTTCCTGTTCTAGCTGCTTTCCCAGCAAGAGGTATCCCAGGCTACA -s Anc0.Anc0refChr7 3707 24 - 16696 -------------------------------------------------------------------------------------CAGCAACAGGTGTCCCTTTCTACA -s Anc1.Anc1refChr4 3953 24 + 17549 -------------------------------------------------------------------------------------CAGCAACAGGTGTCCCTTTCTACA -s Anc2.Anc2refChr5 3846 24 - 8386 -------------------------------------------------------------------------------------CAGCTACAGGTGTCCCTTTCTACA -s mr.mrrefChr5 167207 104 + 294540 GCCAATGCAGGTTCCCACA---TTGGTCTGGCTTACTTCACAAGG--CATTCCCAGCAAGAGGTTTCCTGTTCTAGCTGCTTTCCCAGCAAGAGGTATCCCAGGCTACA -s simCow_chr6.simCow.chr6 327815 24 - 602619 -------------------------------------------------------------------------------------TAGCTCCAGGTGTCCCTTTCTACA -s simDog_chr6.simDog.chr6 281893 19 + 593897 -------------------------------------------------------------------------------------CAGCTACTGGCATCCC-----ACA -s simHuman_chr6.simHuman.chr6 305313 24 + 601863 -------------------------------------------------------------------------------------CAGCAACAGGTGTCCCTTTCTACC -s simRat_chr6.simRat.chr6 308750 104 + 647215 GCAAAATCAGGTTCCCAGA---TTGGCTTGGCCTACTTCACAGGG--CATTCCCAGCAAGAGGTTTCCTGTTCTAGCCAGATTCCCAGCAACAGGAATCATGTTCTACA - -a -s simMouse_chr6.simMouse.chr6 317284 4 + 636262 TGTC -s Anc0.Anc0refChr7 3731 4 - 16696 TGTC -s Anc1.Anc1refChr4 3977 4 + 17549 TGTC -s Anc2.Anc2refChr5 3870 4 - 8386 TGTC -s mr.mrrefChr5 167311 4 + 294540 TGTC -s simCow_chr6.simCow.chr6 327840 4 - 602619 CGTC -s simDog_chr6.simDog.chr6 281912 4 + 593897 TGTC -s simHuman_chr6.simHuman.chr6 305337 4 + 601863 TGTC -s simRat_chr6.simRat.chr6 308854 4 + 647215 TATC - -a -s simMouse_chr6.simMouse.chr6 317288 65 + 636262 AACTTCATGAGACTTCTCACAGAACCTAATCAGGCACTGCGGTACTGCACAATGTATGCATTTTC -s Anc0.Anc0refChr7 3735 6 - 16696 AAGTTC----------------------------------------------------------- -s Anc1.Anc1refChr4 3981 51 + 17549 AAGTTCATGAGGCAACTCCAAGGACTGGGTCA-----------CCTGCATTGGGTGT-CATGT-- -s Anc2.Anc2refChr5 3874 6 - 8386 AAGTTC----------------------------------------------------------- -s mr.mrrefChr5 167315 65 + 294540 AACTTCATGAGACTTCTCACAGAACCTAATCAGGCACTGCGGTACTGCACAATGTATGCATTTTC -s simCow_chr6.simCow.chr6 327860 6 - 602619 AACTTC----------------------------------------------------------- -s simDog_chr6.simDog.chr6 281916 6 + 593897 AAGTTC----------------------------------------------------------- -s simHuman_chr6.simHuman.chr6 305341 51 + 601863 AATTTCATGAGGCAACTCCAAGGACTGGGTCA-----------CCTGCATTGGGTGT-CATGT-- -s simRat_chr6.simRat.chr6 308858 65 + 647215 AACTTCAAGAGACACCTCACAGAACCTATTCAGGTTGTGGGGTGTTGTACAATGTATGCACTTCC - -a -s simMouse_chr6.simMouse.chr6 317353 78 + 636262 AAAATATCGTGCATTATATGCATTTCCAAACTTTTCTGGTATAACTCACCCTTCTACCTAAGAGCTTGTTGGATCGCT -s Anc0.Anc0refChr7 3741 42 - 16696 -----------------------------------CTGGTATGA-TCACCCTGATCCCCAAGAGGGTGTTGGATTGCT -s Anc1.Anc1refChr4 4032 74 + 17549 --GGTGTTGTGGAT-GTAGGCATTCTTAAACTCACCTGGTATGA-TCACCCTGATCCCCAAGAGGGTGTTGGATTGCT -s Anc2.Anc2refChr5 3880 42 - 8386 -----------------------------------CTTGTATGA-TAACCCTGATCCCCAAGAGGGTGTGGGATTCCT -s mr.mrrefChr5 167380 78 + 294540 AAAATATCGTGCATTATATGCATTTCCAAACTTTTCTGGTATAACTCACCCTTCTACCTAAGAGCTTGTTGGATCGCT -s simCow_chr6.simCow.chr6 327866 42 - 602619 -----------------------------------CTTGGTTGA-TAACCCTGATCCCCAAGAAGGTGTCGCATTCAT -s simDog_chr6.simDog.chr6 281922 42 + 593897 -----------------------------------CTTGTATGA-TACCCCTGATCCCCGAGAGAGTGTGTGATTCCT -s simHuman_chr6.simHuman.chr6 305392 74 + 601863 --GGTGTTGTGGAT-GTAGGCATTCTTAAACTCACCTGGTACGG-TCAACCTGATTCTCAAGAGGGTGTTGGACTGCT -s simRat_chr6.simRat.chr6 308924 78 + 647215 AAAAGATCGTGCATTATATGCATTTTCAAACTTTGCTTGTACAACTCGTCCTTCCACCTAAGAGCTTGTTGGATTGCT - -a -s simMouse_chr6.simMouse.chr6 317431 45 + 636262 TGAGTCCTTCTAGGATAAGACAACACTATGCACACTGAATTACTT -s Anc0.Anc0refChr7 3784 23 - 16696 TGAACCCCTCTAGGACAGTTCAA---------------------- -s Anc1.Anc1refChr4 4107 32 + 17549 TGAACCCCTCTAGGACAGTTCAA-AC------------ACCCCTC -s Anc2.Anc2refChr5 3923 23 - 8386 TGAACCCCTCCATAACAGTTCAA---------------------- -s mr.mrrefChr5 167458 44 + 294540 TGAGTCCTTCTAGGATAAGACAA-ACTATGCACACTGAATTACTT -s simCow_chr6.simCow.chr6 327909 22 - 602619 TGAAACCGTCCATAGCAATTAA----------------------- -s simDog_chr6.simDog.chr6 281965 23 + 593897 TGAACCCCTCCATAACAGTTCAA---------------------- -s simHuman_chr6.simHuman.chr6 305467 32 + 601863 CGAACCCCTCTGGGACAGTTCAG-AC------------ACCCCTC -s simRat_chr6.simRat.chr6 309002 44 + 647215 TGAATCCTTTTAGGATAAAACAA-ACTGTGTGCGCCAAACAACTT - -a -s simMouse_chr6.simMouse.chr6 317476 16 + 636262 AAGACTTGCATAACAG -s Anc1.Anc1refChr4 4139 8 + 17549 AGGA--------ACAG -s mr.mrrefChr5 167502 16 + 294540 AAGACTTGCATAACAG -s simHuman_chr6.simHuman.chr6 305499 8 + 601863 AGGA--------ACAG -s simRat_chr6.simRat.chr6 309047 16 + 647215 AAAACTTGCATAACAG - -a -s simMouse_chr6.simMouse.chr6 317492 52 + 636262 TCCAGACAATGATATTCTCATATCTGCTCAGGATGCCACTTGTGGTATTACT -s Anc0.Anc0refChr7 3807 14 - 16696 ----GACAACAATAT----------------------------------ACT -s Anc1.Anc1refChr4 4147 18 + 17549 TTCGGACAACAATAT----------------------------------ACT -s Anc2.Anc2refChr5 3946 14 - 8386 ----GACAGCAAGAT----------------------------------ATT -s mr.mrrefChr5 167518 18 + 294540 TCCAGACAATGATAT----------------------------------ACT -s simCow_chr6.simCow.chr6 327931 14 - 602619 ----GACAGCAAGAT----------------------------------ATT -s simHuman_chr6.simHuman.chr6 305507 18 + 601863 TTCGGACAACACTAT----------------------------------GCT -s simRat_chr6.simRat.chr6 309065 18 + 647215 TCCAGACAATGCTAT----------------------------------ATT - -a -s simMouse_chr6.simMouse.chr6 317544 37 + 636262 GGAATCGTACTGTATCATCCAAGTATGGCAAATAATA -s Anc0.Anc0refChr7 3859 22 - 16696 GGAATCATGCTGAATCAGCCAA--------------- -s Anc1.Anc1refChr4 4203 22 + 17549 GGAATCATGCTGAATCAGCCAA--------------- -s Anc2.Anc2refChr5 3998 22 - 8386 TGACTCATGATGAATCAGCCAA--------------- -s mr.mrrefChr5 167536 22 + 294540 GGAATCGTACTGTATCATCCAA--------------- -s simCow_chr6.simCow.chr6 327983 22 - 602619 TGACTCATGATGAATCAGCCAA--------------- -s simHuman_chr6.simHuman.chr6 305563 22 + 601863 GGAATCATGCTAAATCTGCCTA--------------- -s simRat_chr6.simRat.chr6 309083 22 + 647215 TGAATCATACTGTATCAGCCAA--------------- - -a -s simMouse_chr6.simMouse.chr6 317581 17 + 636262 CCCGACTCACAATGCTT -s Anc0.Anc0refChr7 3899 14 - 16696 CCA---TCAGCATGCTT -s Anc1.Anc1refChr4 4243 17 + 17549 CCAGACTCAGCATGCTT -s Anc2.Anc2refChr5 4038 14 - 8386 CCA---TGAGCATACTT -s mr.mrrefChr5 167558 17 + 294540 CCCGACTCACAATGCTT -s simCow_chr6.simCow.chr6 328023 14 - 602619 CCA---TGAGCATACTT -s simHuman_chr6.simHuman.chr6 305603 17 + 601863 TCAGACCCAATATGCTT -s simRat_chr6.simRat.chr6 309105 17 + 647215 CCTGACTCACAATGCTT - -a -s simMouse_chr6.simMouse.chr6 317598 7 + 636262 CTCTCAA -s Anc0.Anc0refChr7 4073 7 - 16696 CTCTGTA -s Anc1.Anc1refChr4 4420 7 + 17549 CTCTGTA -s Anc2.Anc2refChr5 4212 7 - 8386 CTTTGTC -s mr.mrrefChr5 167575 7 + 294540 CTCTCAA -s simCow_chr6.simCow.chr6 328197 7 - 602619 CTTCACC -s simDog_chr6.simDog.chr6 282109 7 + 593897 CTTTGTC -s simHuman_chr6.simHuman.chr6 305784 7 + 601863 CTCTGTA -s simRat_chr6.simRat.chr6 309122 7 + 647215 CTCTCAA - -a -s simMouse_chr6.simMouse.chr6 317605 16 + 636262 ACACATTACAAACTAA -s Anc0.Anc0refChr7 4080 9 - 16696 A----TAAC---ATAA -s Anc1.Anc1refChr4 4427 9 + 17549 A----TAAC---ATAA -s Anc2.Anc2refChr5 4220 9 - 8386 A----TAAC---ATAA -s mr.mrrefChr5 167582 12 + 294540 A----TTACAAACTAA -s simCow_chr6.simCow.chr6 328205 9 - 602619 A----TAAC---ATAA -s simDog_chr6.simDog.chr6 282117 9 + 593897 A----CAAC---ATGA -s simHuman_chr6.simHuman.chr6 305791 9 + 601863 A----TAAC---GTAA -s simRat_chr6.simRat.chr6 309129 12 + 647215 A----TTGCAAACTTA - -a -s simMouse_chr6.simMouse.chr6 317621 113 + 636262 TGGACAGTTCCATCCCTTTATCACTCATAAATTCCCAACTAACCTTGTTCAGCCCTTGAACAGACCATTGCATTCAATACATAGGCCATTTACCCTAGAACTATTCCAATTCC -s Anc0.Anc0refChr7 4089 107 - 16696 TGCACAATTGCACCCTTACACCATTCATATATTTCCCATCAACATTGTTCAGCTTTTGAAGAGACCATTGTGTTCCATAGATAGTCCATGGGCCCTTGTAATATTCC------ -s Anc1.Anc1refChr4 4436 107 + 17549 TGCACAATTGCACCCTTACACCATTCATATATTTCCCATCAACATTGTTCAGCTTTTGAAGAGACCATTGTGTTCCATAGATAGTCCATGGGCCCTTGTAATATTCC------ -s Anc2.Anc2refChr5 4229 107 - 8386 CTCACAAGTGCACCTTAACACCATTCATATATTTCCCATCAACATTGTCCAGCTTTTGAAGAGACCATTGTGTTTCATAGATAGTACATGGGCCCTTGTAATATTCC------ -s mr.mrrefChr5 167594 113 + 294540 TGGACAATTCCATCCCTATACCATTCATAAATTCCCAACTAACCTTGTTCAGCCTTTGAAGAGACCATTGCATTCAATACATAGGCCATTGGCCCTAGTACTATTCCAATTCC -s simCow_chr6.simCow.chr6 328214 100 - 602619 TGCACAAGCGCACCT---CACCATTCACAGATTTCCCATCAACATTGTCCAGCTTCTGAAGGGACCATTGTGTTTCATAAAAAGTGCATGGGCCC----AATATTCC------ -s simDog_chr6.simDog.chr6 282126 95 + 593897 CTCACAAGTGCATCTTAACACCATTCATATATTTCCCAT------------ACTTTTGAAGAGTCCATTGTGTTTCATAGATAGTACATGGGCCCTTGTAACATTCC------ -s simHuman_chr6.simHuman.chr6 305801 107 + 601863 TGTCCAATTACACCCATACCCCATTCAAATATGGTACATCAATTTTGATCAGCTTTTGAAGCGACCATTGTGTTCCATAGATAATCCATGGGCCCTTGTAATAATCC------ -s simRat_chr6.simRat.chr6 309141 113 + 647215 CGTACAAGTCCATCCCTATACCATGCATAGATTCCTGACTAACCTTGTTCAGCCTTTGAAGAGACCATTGCATTCAATACATAGGCCATTGGCCCTAGTACTATTTAAATTCC - -a -s simMouse_chr6.simMouse.chr6 317734 16 + 636262 ATTCCTACATTGCTTT -s Anc0.Anc0refChr7 4230 8 - 16696 CTTCCTAC-------- -s Anc1.Anc1refChr4 4577 8 + 17549 CTTCCTAC-------- -s Anc2.Anc2refChr5 4370 8 - 8386 CTTGTTAC-------- -s mr.mrrefChr5 167740 16 + 294540 ATTCCTACATTGCTTT -s simCow_chr6.simCow.chr6 328350 8 - 602619 CTGTATAC-------- -s simDog_chr6.simDog.chr6 282246 8 + 593897 TTTGTCAC-------- -s simHuman_chr6.simHuman.chr6 305942 8 + 601863 CTTCCTAC-------- -s simRat_chr6.simRat.chr6 309287 16 + 647215 ATGCCTACATTGCTAT - -a -s simMouse_chr6.simMouse.chr6 317750 4 + 636262 TTTG -s Anc0.Anc0refChr7 4238 4 - 16696 ATTG -s Anc1.Anc1refChr4 4585 4 + 17549 ATTG -s Anc2.Anc2refChr5 4378 4 - 8386 ATCA -s mr.mrrefChr5 167756 4 + 294540 TTTG -s simCow_chr6.simCow.chr6 328359 4 - 602619 ATCA -s simHuman_chr6.simHuman.chr6 305950 4 + 601863 CTTG -s simRat_chr6.simRat.chr6 309303 4 + 647215 TTTG - -a -s simMouse_chr6.simMouse.chr6 317754 10 + 636262 CCTTTGGCAT -s Anc0.Anc0refChr7 4242 10 - 16696 CTTTTGGCAT -s Anc1.Anc1refChr4 4589 10 + 17549 CTTTTGGCAT -s Anc2.Anc2refChr5 4382 10 - 8386 CTTTTGACAT -s mr.mrrefChr5 167760 10 + 294540 CTTTTGGCAT -s simCow_chr6.simCow.chr6 328363 10 - 602619 CTATTGAGAG -s simDog_chr6.simDog.chr6 282254 8 + 593897 --TGTGACAT -s simHuman_chr6.simHuman.chr6 305954 10 + 601863 TTTTTGGCAT -s simRat_chr6.simRat.chr6 309308 10 + 647215 CTTTTGGCAT - -a -s simMouse_chr6.simMouse.chr6 317764 24 + 636262 ATAATAGGTTGTTTATCCATGAGA -s Anc0.Anc0refChr7 4252 24 - 16696 ATAATAGGTTGTTTATCCATGAGC -s Anc1.Anc1refChr4 4599 24 + 17549 ATAATAGGTTGTTTATCCATGAGC -s Anc2.Anc2refChr5 4393 24 - 8386 ATAATAGATTGTTTATCCATGAGC -s mr.mrrefChr5 167770 24 + 294540 ATAATAGGTTGTTTATCCATGAGA -s simCow_chr6.simCow.chr6 328374 24 - 602619 ATCATAGATTGTATATCCATGAGC -s simDog_chr6.simDog.chr6 282263 24 + 593897 ATAACAGATTGTTTTTCCATGAGT -s simHuman_chr6.simHuman.chr6 305964 24 + 601863 ATAATGGGGTGCTTATCCATGAGC -s simRat_chr6.simRat.chr6 309318 24 + 647215 ATATTAGGTTATTTATCCATGAGG - -a -s simMouse_chr6.simMouse.chr6 317788 5 + 636262 TGTAT -s Anc0.Anc0refChr7 4280 5 - 16696 TGAAT -s Anc1.Anc1refChr4 4627 5 + 17549 TGAAT -s Anc2.Anc2refChr5 4421 5 - 8386 TGAAC -s mr.mrrefChr5 167794 5 + 294540 TGTAT -s simCow_chr6.simCow.chr6 328402 5 - 602619 TGAAC -s simDog_chr6.simDog.chr6 282291 5 + 593897 TGCAC -s simHuman_chr6.simHuman.chr6 305992 5 + 601863 TGAAT -s simRat_chr6.simRat.chr6 309342 5 + 647215 TATAT - -a -s simMouse_chr6.simMouse.chr6 317793 19 + 636262 AGGAAACTTATCTCACCCA -s Anc0.Anc0refChr7 4285 19 - 16696 AGGACACTTATCTGACCCA -s Anc1.Anc1refChr4 4632 19 + 17549 AGGACACTTATCTGACCCA -s Anc2.Anc2refChr5 4429 19 - 8386 CGGACACTTTCCTGACCTG -s mr.mrrefChr5 167799 19 + 294540 AGGAAACTTATCTCACCCA -s simCow_chr6.simCow.chr6 328410 19 - 602619 TGGACACTTTCCTGACCTG -s simDog_chr6.simDog.chr6 282299 19 + 593897 CGAACACTTTCTTGACCTG -s simHuman_chr6.simHuman.chr6 305997 19 + 601863 AGGACACTTATCCAACCCA -s simRat_chr6.simRat.chr6 309347 19 + 647215 AGGAAACTTATCTCACCGA - -a -s simMouse_chr6.simMouse.chr6 317812 28 + 636262 ATGAGTAAACAAAACTTATTATCTGGGT -s Anc0.Anc0refChr7 4305 27 - 16696 ATATACAAACAAAACTTGTT-TGTTGGT -s Anc1.Anc1refChr4 4652 27 + 17549 ATATACAAACAAAACTTGTT-TGTTGGT -s Anc2.Anc2refChr5 4449 27 - 8386 ATATACAAAAAAAACTTGTT-TGTTGGT -s mr.mrrefChr5 167818 28 + 294540 ATAAGTAAACAAAACTTATTATCTGGGT -s simCow_chr6.simCow.chr6 328430 27 - 602619 ATATGCAAAAAAAACTTGTT-TGTTGGT -s simDog_chr6.simDog.chr6 282319 27 + 593897 ATTTACAATAAAAAGTTGCT-TGTTGGT -s simHuman_chr6.simHuman.chr6 306017 27 + 601863 ATATACAAACAAAACTTGTT-TATTGGT -s simRat_chr6.simRat.chr6 309366 28 + 647215 ATAGGTAAACAAAACTTATTATCTGGGT - -a -s simMouse_chr6.simMouse.chr6 317840 46 + 636262 CACATTAGAGTGTTGTGGCCCAGTACAAGTGTGAGTTTGCTGTCCT -s Anc0.Anc0refChr7 4337 46 - 16696 CATACTAGAGTGCTGTGGTACAAAACAAATGTGAGTCTGCTACCCT -s Anc1.Anc1refChr4 4684 46 + 17549 CATACTAGAGTGCTGTGGTACAAAACAAATGTGAGTCTGCTACCCT -s Anc2.Anc2refChr5 4481 46 - 8386 CATACTAGAGTGCTGTGGTACAAAACAAATGTGCATCTGCCACCCT -s mr.mrrefChr5 167851 46 + 294540 CACATTAGAGTGCTGTGGCACAGTACAAGTGTGAGTTTGCTGCCCT -s simCow_chr6.simCow.chr6 328462 41 - 602619 CATGCTAGAGTGCTGTGGTACAAAACAGAGGTGCATCTGCC----- -s simDog_chr6.simDog.chr6 282351 46 + 593897 TGTACCAGAGTGCTATGGTATGGAACAATTGCGCATCTGCCACCCT -s simHuman_chr6.simHuman.chr6 306049 46 + 601863 CAAACTAGAGTGCTGTGGTACAAAACAAACGTGAGTCTCCTACACT -s simRat_chr6.simRat.chr6 309399 39 + 647215 CATAT-------CTGTGGCACAGTACAAGTGTGAGTTTGCTGCCCT - -a -s simMouse_chr6.simMouse.chr6 317886 65 + 636262 CATGCTCAGGAACCTGTCAGGCACTCAAACTGTACAAAATAGGACAGTCTACACACTCATGTGTG -s Anc0.Anc0refChr7 4385 65 - 16696 CAGTCTCAGGAACCAGGCAGGCTCCAAATCTGTACAAGATGTAGCAGTCTATACCCTCATGAGTG -s Anc1.Anc1refChr4 4732 65 + 17549 CAGTCTCAGGAACCAGGCAGGCTCCAAATCTGTACAAGATGTAGCAGTCTATACCCTCATGAGTG -s Anc2.Anc2refChr5 4529 65 - 8386 CAGTCTCAGAAACCAGGTGGGCTTCATATCTGTACTAGATGTAGCAGTCTATACCCTCATGAGTG -s mr.mrrefChr5 167897 65 + 294540 CATTCTCAGGAACCTGTCAGGCACTCAAACTGTACAAAATAGAACAGTCTACACACTCATGTGTG -s simCow_chr6.simCow.chr6 328503 46 - 602619 -------------------GACTTCACATCTGTAAGAGATGTGGCTGTCTATACCCTCATGGGTG -s simDog_chr6.simDog.chr6 282399 65 + 593897 CAGTCTCAGAAACCAGGTGGGCTTCATATCGGTACTAGATCTAGCAGTCTACACCCTCATCAGTG -s simHuman_chr6.simHuman.chr6 306097 65 + 601863 CAGTCTCAAGAACCAGGCAGGTCCCAAATTTGTACAAGATGTAGCAGTCCATACCCTCATGAGTG -s simRat_chr6.simRat.chr6 309438 65 + 647215 CATTCTCAGGGACCTGTCTGGCACTCAAAATGTACAAAATAGAACAGTCTACACACTAATGTGTG - -a -s simMouse_chr6.simMouse.chr6 317951 6 + 636262 GGATCC -s Anc0.Anc0refChr7 4451 6 - 16696 GGATGG -s Anc1.Anc1refChr4 4798 6 + 17549 GGATGG -s Anc2.Anc2refChr5 4595 6 - 8386 GGATGG -s mr.mrrefChr5 167962 6 + 294540 GGATCC -s simCow_chr6.simCow.chr6 328550 6 - 602619 GAGTGA -s simDog_chr6.simDog.chr6 282465 6 + 593897 GGATGG -s simHuman_chr6.simHuman.chr6 306163 6 + 601863 GGATGG -s simRat_chr6.simRat.chr6 309503 6 + 647215 GGGTCC - -a -s simMouse_chr6.simMouse.chr6 317957 4 + 636262 CGTC -s Anc0.Anc0refChr7 4457 4 - 16696 TGTC -s Anc1.Anc1refChr4 4804 4 + 17549 TGTC -s Anc2.Anc2refChr5 4601 4 - 8386 TGTC -s mr.mrrefChr5 167968 4 + 294540 TGTC -s simCow_chr6.simCow.chr6 328556 4 - 602619 TATC -s simDog_chr6.simDog.chr6 282472 4 + 593897 TGTC -s simHuman_chr6.simHuman.chr6 306169 4 + 601863 TGTC -s simRat_chr6.simRat.chr6 309509 4 + 647215 TGCA - -a -s simMouse_chr6.simMouse.chr6 317961 25 + 636262 AGATTTCATATTCTGACTCAAGTAT -s Anc0.Anc0refChr7 4461 25 - 16696 AGGTTCCATGTTCCAGTGGCAGTGC -s Anc1.Anc1refChr4 4808 25 + 17549 AGGTTCCATGTTCCAGTGGCAGTGC -s Anc2.Anc2refChr5 4605 25 - 8386 AGGTTCCATGTTTCAGTGGCAGTGC -s mr.mrrefChr5 167972 25 + 294540 AGATTTCATATTCTGACTGAAGTGT -s simCow_chr6.simCow.chr6 328560 25 - 602619 GAGGTCCATGTTGGAGTGGCAGTGC -s simDog_chr6.simDog.chr6 282477 25 + 593897 AGGTTTCATGTTTCAGTGGCAGTGC -s simHuman_chr6.simHuman.chr6 306173 25 + 601863 AGGTTCCATGTTCCAGTGGCAGTGC -s simRat_chr6.simRat.chr6 309513 25 + 647215 AGATTTCATATTCAGACTGAAGTGT - -a -s simMouse_chr6.simMouse.chr6 317986 12 + 636262 CTCAGGTGATTT -s Anc0.Anc0refChr7 4486 11 - 16696 CTCAGGTGA-TT -s Anc1.Anc1refChr4 4833 11 + 17549 CTCAGGTGA-TT -s Anc2.Anc2refChr5 4630 11 - 8386 CTTAGGTGA-TT -s mr.mrrefChr5 167997 11 + 294540 CTCAGGTGA-TT -s simCow_chr6.simCow.chr6 328585 11 - 602619 CTTAGGTGA-TA -s simDog_chr6.simDog.chr6 282502 11 + 593897 TTTAGGTGC-CT -s simHuman_chr6.simHuman.chr6 306198 11 + 601863 CTCAGGTGA-TG -s simRat_chr6.simRat.chr6 309606 11 + 647215 CTCAGGTGA-TT - -a -s simMouse_chr6.simMouse.chr6 317998 25 + 636262 GCTTGGATAGCTCTACCTCTGTTCC -s Anc0.Anc0refChr7 4499 25 - 16696 GCCGGTATTGCTCTACATCTGCTCT -s Anc1.Anc1refChr4 4846 25 + 17549 GCCGGTATTGCTCTACATCTGCTCT -s Anc2.Anc2refChr5 4643 25 - 8386 GCTGGTATTGCTCTACATCTGCTCT -s mr.mrrefChr5 168008 25 + 294540 GCCTGGATAGCTCTACCTCTGTTCC -s simCow_chr6.simCow.chr6 328598 25 - 602619 GTTTTTATTGCTCTACAGCTGCTGT -s simDog_chr6.simDog.chr6 282515 25 + 593897 GCTGGTATTGCTCTACATCTGCACT -s simHuman_chr6.simHuman.chr6 306211 25 + 601863 GCCGGTCTTGTTCCACATCTGCTCT -s simRat_chr6.simRat.chr6 309617 25 + 647215 GCCTGGATAGCTCTACCTCTGTCCC - -a -s simMouse_chr6.simMouse.chr6 318023 29 + 636262 AATTTATCCTTCTTGCTCCTGGGAATAGT -s Anc0.Anc0refChr7 4524 19 - 16696 GATTTGTCATCC----------GAATAGT -s Anc1.Anc1refChr4 4871 19 + 17549 GATTTGTCATCC----------GAATAGT -s Anc2.Anc2refChr5 4668 19 - 8386 GATTTGTCATCC----------AAATATT -s mr.mrrefChr5 168033 29 + 294540 AATTTGTCCTTCTTGCTCCTGGGAATAGT -s simCow_chr6.simCow.chr6 328634 19 - 602619 GATGTTTCCTCA----------AAATATT -s simDog_chr6.simDog.chr6 282540 12 + 593897 GATTTGACACCC----------------- -s simHuman_chr6.simHuman.chr6 306236 19 + 601863 GATTTGTCTTCC----------GAATAGT -s simRat_chr6.simRat.chr6 309642 29 + 647215 AATTTGTCCTTCTGTCCCCTGGGAATAGT - -a -s simMouse_chr6.simMouse.chr6 318052 15 + 636262 TTCTTGAGAATAGTC -s Anc0.Anc0refChr7 4543 5 - 16696 TT----------GTC -s Anc1.Anc1refChr4 4890 5 + 17549 TT----------GTC -s Anc2.Anc2refChr5 4687 5 - 8386 TT----------GTC -s mr.mrrefChr5 168062 15 + 294540 TTCTTGAGAATAGTC -s simCow_chr6.simCow.chr6 328657 5 - 602619 TA----------GTC -s simDog_chr6.simDog.chr6 282552 5 + 593897 TT----------GCC -s simHuman_chr6.simHuman.chr6 306255 5 + 601863 TT----------GTC -s simRat_chr6.simRat.chr6 309671 15 + 647215 TTCTTGAGAATGGTC - -a -s simMouse_chr6.simMouse.chr6 318067 25 + 636262 TCTTTTTGTAGCCCGAAACCCACAA -s Anc0.Anc0refChr7 4548 14 - 16696 TTTCTC-----------ACCCACAA -s Anc1.Anc1refChr4 4895 14 + 17549 TTTCTC-----------ACCCACAA -s Anc2.Anc2refChr5 4692 14 - 8386 TTTCTC-----------ACGCACAA -s mr.mrrefChr5 168077 25 + 294540 TCTTTTTGTAGCCCGAAACCCACAA -s simCow_chr6.simCow.chr6 328662 14 - 602619 CCTCTC-----------CCTTATGA -s simDog_chr6.simDog.chr6 282566 14 + 593897 TTTGTG-----------AGGCACAA -s simHuman_chr6.simHuman.chr6 306260 14 + 601863 TGTCTC-----------ACCCACAA -s simRat_chr6.simRat.chr6 309686 25 + 647215 TCTTTTTGTGGACCACAACCCAGAA - -a -s simMouse_chr6.simMouse.chr6 318092 2 + 636262 TG -s Anc0.Anc0refChr7 4562 2 - 16696 tt -s Anc1.Anc1refChr4 4909 2 + 17549 TT -s Anc2.Anc2refChr5 4706 2 - 8386 tt -s mr.mrrefChr5 168102 2 + 294540 TG -s simDog_chr6.simDog.chr6 329607 2 - 593897 tt -s simHuman_chr6.simHuman.chr6 306274 2 + 601863 AT -s simRat_chr6.simRat.chr6 309711 2 + 647215 CA - -a -s simMouse_chr6.simMouse.chr6 318094 31 + 636262 CTTGTTCCACTTAGTTCCATCCATTGCCACT -s Anc0.Anc0refChr7 4564 9 - 16696 CTTCTTTAA---------------------- -s Anc1.Anc1refChr4 4911 9 + 17549 CTTCTTTAA---------------------- -s Anc2.Anc2refChr7 2 9 + 32194 CTTATTTAA---------------------- -s mr.mrrefChr5 168104 31 + 294540 CTTGTTCCACTTAGTTCCATCCATTGCCACT -s simCow_chr6.simCow.chr6 295362 9 + 602619 CTTATTTAA---------------------- -s simDog_chr6.simDog.chr6 282582 9 + 593897 CTTACTTAA---------------------- -s simHuman_chr6.simHuman.chr6 306276 9 + 601863 CTTCTTTAA---------------------- -s simRat_chr6.simRat.chr6 309718 31 + 647215 CTTGTCCCACTGAGTTTCATCCATTGCCAAT - -a -s simMouse_chr6.simMouse.chr6 318125 90 + 636262 GTATCCTATTTTCTATATACTTGGTAAGCCTCTGATATGTGTTTCTTGCTCTTGAGAACAGTTTCTTTAGAATAGTCTTTTTTTGTGGGC -s mr.mrrefChr5 168135 90 + 294540 GTATCCTATTTTCTATATACTTGGTAAGCCTCTGATATGTGTTTCTTGCTCTTGAGAACAGTTTCTTTAGAATAGTCTTTTTTTGTGGGC -s simRat_chr6.simRat.chr6 309750 90 + 647215 GTATTCTATTTTCTATATACTTGGTAAGCCTCTGATTTTTCTCTCTCGCTCCTGGGAACATTTTCTTGAAAATAGTCTCTTTTTGTGGGC - -a -s simMouse_chr6.simMouse.chr6 318215 26 + 636262 CCATTTGGTTTAGTCCATTGCCAATT -s Anc0.Anc0refChr7 4573 22 - 16696 ----TTATTTTAGTCAATTGCCCATT -s Anc1.Anc1refChr4 4920 22 + 17549 ----TTATTTTAGTCAATTGCCCATT -s Anc2.Anc2refChr7 11 22 + 32194 ----TTATTTTAGTCAATTGCCAACC -s mr.mrrefChr5 168225 26 + 294540 CCATTTGGTTTAGTCCATTGCCAATT -s simCow_chr6.simCow.chr6 295371 22 + 602619 ----TTATTTTGGTCACTAGCCAACC -s simDog_chr6.simDog.chr6 282591 17 + 593897 ----TTATTCTAGTCAATTGC----- -s simHuman_chr6.simHuman.chr6 306285 22 + 601863 ----TTATTTTAGTCAATTGCCCATT -s simRat_chr6.simRat.chr6 309860 26 + 647215 CCACTTAGTTTAGTCCATTGCCAATT - -a -s simMouse_chr6.simMouse.chr6 318241 30 + 636262 GAATTCTATTTTCTATGTACTTGAAAAGCC -s Anc0.Anc0refChr7 4595 23 - 16696 TTATTCTGTGCTCTATATACTTG------- -s Anc1.Anc1refChr4 4942 23 + 17549 TTATTCTGTGCTCTATATACTTG------- -s Anc2.Anc2refChr7 33 23 + 32194 TTATTCTATACTCTCTATACTTG------- -s mr.mrrefChr5 168251 30 + 294540 GAATTCTATTTTCTATGTACTTGAAAAGCC -s simCow_chr6.simCow.chr6 295393 23 + 602619 TCATTCTATACTCTCTATACTTG------- -s simDog_chr6.simDog.chr6 282608 23 + 593897 TTATTCTATATTCCCTATACTCC------- -s simHuman_chr6.simHuman.chr6 306307 23 + 601863 TTATTCTGTGCTCTATATACTTG------- -s simRat_chr6.simRat.chr6 309887 30 + 647215 AAACTCGATTTTCTATGTATTTGGTAAGCC - -a -s simMouse_chr6.simMouse.chr6 318271 5 + 636262 TGCCT -s Anc0.Anc0refChr7 4635 5 - 16696 TGCCT -s Anc1.Anc1refChr4 4982 5 + 17549 TGCCT -s Anc2.Anc2refChr7 73 5 + 32194 TGCCT -s mr.mrrefChr5 168281 5 + 294540 TGCCT -s simCow_chr6.simCow.chr6 295432 5 + 602619 TGCCT -s simDog_chr6.simDog.chr6 282648 5 + 593897 TGCCT -s simHuman_chr6.simHuman.chr6 306347 5 + 601863 TGCTA -s simRat_chr6.simRat.chr6 309917 5 + 647215 TGCCT - -a -s simMouse_chr6.simMouse.chr6 318276 16 + 636262 AGGTGTACTCCTTTCC -s Anc0.Anc0refChr7 4640 16 - 16696 AGCTTTACTCCTGACC -s Anc1.Anc1refChr4 4987 16 + 17549 AGCTTTACTCCTGACC -s Anc2.Anc2refChr7 78 16 + 32194 GGCTTTACTCCTGACC -s mr.mrrefChr5 168286 16 + 294540 AGGTGTACTCCTTTCC -s simCow_chr6.simCow.chr6 295439 16 + 602619 GGGTCTACTCCTAACC -s simDog_chr6.simDog.chr6 282653 13 + 593897 GGCTTTGCCCCTG--- -s simHuman_chr6.simHuman.chr6 306352 16 + 601863 AGATTTACTCCTCGCC -s simRat_chr6.simRat.chr6 309922 16 + 647215 GGGTTTACACCTTTCC - -a -s simMouse_chr6.simMouse.chr6 318292 83 + 636262 TGAGTTAACAGCTCCAACTACAGACTTCATGAGCTGGGGCAGCCTAAACACCTAGTATTCATCATCAAGATGTTGGAAACTGG -s Anc0.Anc0refChr7 4664 76 - 16696 TGTGTTTCTAGCTCCAACTACAAACTTCATAGTCTGGGGCCATCTACACGGCTAACATTCCTCAGCAA---A----AAACTGG -s Anc1.Anc1refChr4 5011 76 + 17549 TGTGTTTCTAGCTCCAACTACAAACTTCATAGTCTGGGGCCATCTACACGGCTAACATTCCTCAGCAA---A----AAACTGG -s Anc2.Anc2refChr7 102 76 + 32194 TGTATCTCTAGCTCCAACTAGAAACTTGATAGTCTGGGGCCATCTACACGGCTAACATTCCACAGCAA---A----ATGTTGG -s mr.mrrefChr5 168302 80 + 294540 TGAGTTAACAGCTCCAACTACAGACTTCATGAGCTGGGGCAGCCTAAACACCTAGTATTCATCATCAA---GTTGGAAACTGG -s simCow_chr6.simCow.chr6 295463 76 + 602619 TGTATCTCTAGCTCCAACTAGAAACTTTGTGGTCTGGAGCCATCAACAGGGCTAATATTCACCAGCAA---A----ACGTTAG -s simDog_chr6.simDog.chr6 282666 68 + 593897 --------TAGCTCCAACTAGAAACTTGATAATCTGGGGTAAGCTACACAGCAGACATACCACAGCAA---A----ATGTTGA -s simHuman_chr6.simHuman.chr6 306376 75 + 601863 TGGGTTTCTAACTCCATCTACCAACTTCATAGTCGGGGGCCATCTACATGGCTAA-ATTCCTCAGCAA---C----AAACTAG -s simRat_chr6.simRat.chr6 309938 80 + 647215 TGAGTTGACAGCTACAACTATAAACTTTATGAGCTGGGGCAACCTAAACATCTAGGATTCATCAGCAA---ATTAAAAACTGG - -a -s simMouse_chr6.simMouse.chr6 318375 1 + 636262 C -s Anc0.Anc0refChr7 4740 1 - 16696 C -s Anc1.Anc1refChr4 5087 1 + 17549 C -s Anc2.Anc2refChr7 179 1 + 32194 C -s mr.mrrefChr5 168382 1 + 294540 C -s simCow_chr6.simCow.chr6 295540 1 + 602619 C -s simDog_chr6.simDog.chr6 282735 1 + 593897 C -s simHuman_chr6.simHuman.chr6 306451 1 + 601863 C -s simRat_chr6.simRat.chr6 310018 1 + 647215 C - -a -s simMouse_chr6.simMouse.chr6 318376 88 + 636262 CTCTCTCCCTTCATTGGTCAAAGCTCACGTCAGCCTTCTATAGTGACTATAAACAATGGCACTGCTCCACAGCACTGAGATACATGCT -s Anc0.Anc0refChr7 4741 86 - 16696 CTTAGTCCCTCAAATGGTCAGCACACACATAAGCTTCATATATCAGCTCCAAACGATGC--TGACTCTACAGCAATGACATAAAGGCT -s Anc1.Anc1refChr4 5088 86 + 17549 CTTAGTCCCTCAAATGGTCAGCACACACATAAGCTTCATATATCAGCTCCAAACGATGC--TGACTCTACAGCAATGACATAAAGGCT -s Anc2.Anc2refChr7 180 86 + 32194 CTTAGTTCCTCAAATGGTCAGCACACACATAACCTTCATATATCAGCTCCAAACGCTGC--TGACTCTACAGCAATGACATAAAGGCT -s mr.mrrefChr5 168383 86 + 294540 CTCTCTCCCTTCATTGGTCAAAGCTCACGTCAGCCTTCTATAGTGACTATAAACAATGG--CTGCTCCACAGCACTGAGATACATGCT -s simCow_chr6.simCow.chr6 295541 86 + 602619 CTTTGGTTCTCAAATGGTCAACACACACATAACCTTCATATGTCAGGTCTTAACACTGC--TTACTCTACAGCAATAATATACAGGCT -s simDog_chr6.simDog.chr6 282736 86 + 593897 TTTAATTCTTCAAATGGTCAGCACACACATAACCTTCATATATTAGCTCCAAACGCTGC--TGGCTCTACATCAATGACATAAAAGCT -s simHuman_chr6.simHuman.chr6 306476 86 + 601863 CTTGGCCCCTCACCTGGTCAGCACACGCATTAGCTTCATATATCAGCTCCAAATGATGT--TCACGTTACTGCAATGACCTATAGGCT -s simRat_chr6.simRat.chr6 310019 86 + 647215 CTCTCTCCCTTCTTTGGCTAGAACACACATCAGCTTCCTATAGTGACTGCAAACGATGG--CTGCTCCAAAGCAATGAGATACATGTT - -a -s simMouse_chr6.simMouse.chr6 318464 6 + 636262 AATGAT -s Anc0.Anc0refChr7 4834 6 - 16696 AGCAAC -s Anc1.Anc1refChr4 5181 6 + 17549 AGCAAC -s Anc2.Anc2refChr7 273 6 + 32194 AGCAAC -s mr.mrrefChr5 168469 6 + 294540 AATGAT -s simCow_chr6.simCow.chr6 295634 6 + 602619 AGCAAC -s simDog_chr6.simDog.chr6 282829 6 + 593897 AGCAAC -s simHuman_chr6.simHuman.chr6 306569 6 + 601863 AGCAAG -s simRat_chr6.simRat.chr6 310105 6 + 647215 AATGAT - -a -s simMouse_chr6.simMouse.chr6 318470 10 + 636262 ATCCAGGGTG -s Anc0.Anc0refChr7 4840 10 - 16696 TTGCTGAGTG -s Anc1.Anc1refChr4 5187 10 + 17549 TTGCTGAGTG -s Anc2.Anc2refChr7 279 10 + 32194 TTGCTGAGTG -s mr.mrrefChr5 168475 10 + 294540 ATCCAGGGTG -s simCow_chr6.simCow.chr6 295640 10 + 602619 TTGCTGAGAG -s simDog_chr6.simDog.chr6 282855 10 + 593897 TTGCTGAGTG -s simHuman_chr6.simHuman.chr6 306575 10 + 601863 CTGCTGATTG -s simRat_chr6.simRat.chr6 310111 10 + 647215 ATCCAGGGTG - -a -s simMouse_chr6.simMouse.chr6 318480 28 + 636262 AATTCATTTTCTCTCATAGGACAACCTC -s Anc0.Anc0refChr7 4850 28 - 16696 AAGTCATTTTCTTTTATAAGCCAACCTG -s Anc1.Anc1refChr4 5197 28 + 17549 AAGTCATTTTCTTTTATAAGCCAACCTG -s Anc2.Anc2refChr7 289 28 + 32194 GGGTTATTTTTGTTTATAAGCCAACCCG -s mr.mrrefChr5 168485 28 + 294540 AATTCATTTTCTCTCATAGGACAACCTC -s simCow_chr6.simCow.chr6 295650 28 + 602619 GGGTTATTTTTGATTATAAGCCAACCAG -s simDog_chr6.simDog.chr6 282865 28 + 593897 GGATTATTTTTGTTTACAAGCCAACCCG -s simHuman_chr6.simHuman.chr6 306585 28 + 601863 AAGCCATTTACTTAGATAAGCCAAATTG -s simRat_chr6.simRat.chr6 310137 28 + 647215 AATTCATTTTCTCTCATAGGTCAACCTC - -a -s simMouse_chr6.simMouse.chr6 318508 38 + 636262 TTCTTGTCTTAGAGGACAGACTTCTTGACTAGAAGCTT -s Anc0.Anc0refChr7 4878 38 - 16696 TTCTTGTGCGAGGCAGCAGATCTCTTGCTTGGAAGCAG -s Anc1.Anc1refChr4 5225 38 + 17549 TTCTTGTGCGAGGCAGCAGATCTCTTGCTTGGAAGCAG -s Anc2.Anc2refChr7 317 38 + 32194 TTCTTGTGCGAGGCAGCAGATCTCTTGCTTGGAAACAG -s mr.mrrefChr5 168513 38 + 294540 TTCTTGTCTTAGAGGACAGACTTCTTGACTAGAAGCTT -s simCow_chr6.simCow.chr6 295679 35 + 602619 GGCATGTG---GGCAGCAAATCTCTTGTCTGAAAACAG -s simDog_chr6.simDog.chr6 282893 38 + 593897 TTCTTATACGAGGCACCAGATTTCTTGCTCGGAAACAG -s simHuman_chr6.simHuman.chr6 306613 19 + 601863 TTCTTG-------------------TGTTAGGCGGCAG -s simRat_chr6.simRat.chr6 310165 38 + 647215 TTCTAGTCTTAGGGAGCAGACTCCTAGACCTGAAGCCC - -a -s simMouse_chr6.simMouse.chr6 318546 13 + 636262 TCCTGCATTGGTT -s Anc0.Anc0refChr7 4916 13 - 16696 TCTTGCGTTGGCT -s Anc1.Anc1refChr4 5263 13 + 17549 TCTTGCGTTGGCT -s Anc2.Anc2refChr7 355 13 + 32194 ACTTAGGTTGGCT -s mr.mrrefChr5 168551 13 + 294540 TCCTGCATTGGTT -s simCow_chr6.simCow.chr6 295714 13 + 602619 CCTTGGGTTGGCT -s simDog_chr6.simDog.chr6 282931 13 + 593897 ACTTAGGTTGGCT -s simHuman_chr6.simHuman.chr6 306635 10 + 601863 TCATGCTTGG--- -s simRat_chr6.simRat.chr6 310203 13 + 647215 TCCTGTATTGGTT - -a -s simMouse_chr6.simMouse.chr6 318559 5 + 636262 TATGG -s Anc0.Anc0refChr7 4929 5 - 16696 CAGTA -s Anc1.Anc1refChr4 5276 5 + 17549 CAGTA -s Anc2.Anc2refChr7 372 5 + 32194 CAGTA -s mr.mrrefChr5 168564 5 + 294540 TATGG -s simCow_chr6.simCow.chr6 295731 5 + 602619 CAGTA -s simDog_chr6.simDog.chr6 282947 2 + 593897 ---TT -s simRat_chr6.simRat.chr6 310216 5 + 647215 TATGG - -a -s simMouse_chr6.simMouse.chr6 318564 19 + 636262 ATGCGTTTACAGGACAGAA -s Anc0.Anc0refChr7 4934 19 - 16696 ATCCATTGACAGTGCAGAA -s Anc1.Anc1refChr4 5281 19 + 17549 ATCCATTGACAGTGCAGAA -s Anc2.Anc2refChr7 377 19 + 32194 ATCCATTGACAGTGCAGAA -s mr.mrrefChr5 168569 19 + 294540 ATGCGTTTACAGGACAGAA -s simCow_chr6.simCow.chr6 295743 19 + 602619 ACCCATTGACAGTGCAGAA -s simDog_chr6.simDog.chr6 282949 19 + 593897 ATCTATTAACAGTGCAGAA -s simRat_chr6.simRat.chr6 310221 19 + 647215 ATTTGTTGACAGGACAGAA - -a -s simMouse_chr6.simMouse.chr6 318583 20 + 636262 CTGACTACTTATATGTGTAG -s Anc0.Anc0refChr7 4953 20 - 16696 CTGGATGCTTATACATCTAG -s Anc1.Anc1refChr4 5300 20 + 17549 CTGGATGCTTATACATCTAG -s Anc2.Anc2refChr7 396 20 + 32194 CTGGATGCTTATACATCTAG -s mr.mrrefChr5 168588 20 + 294540 CTGACTACTTATATGTGTAG -s simCow_chr6.simCow.chr6 295762 20 + 602619 CTGAGTGCTTATACATTTAG -s simDog_chr6.simDog.chr6 282968 20 + 593897 CTGGATGCTTATACATCTAG -s simRat_chr6.simRat.chr6 310253 20 + 647215 CTAAACATTTATACGTGTAG - -a -s simMouse_chr6.simMouse.chr6 318603 56 + 636262 CATGTAAGTTTAATAGCTGCCATACATATTTCAAAGCTTATATAAAGTGAAACAGC -s Anc0.Anc0refChr7 4973 27 - 16696 CATGTAAGTAT--------------A---------------ACACattaagaaagt -s Anc1.Anc1refChr4 5320 27 + 17549 CATGTAAGTAT--------------A---------------ACACattaagaaagt -s Anc2.Anc2refChr7 417 27 + 32194 CATGTAAGTAT--------------A---------------ACACattaagaaagt -s mr.mrrefChr5 168608 42 + 294540 CATGTAAGTTT--------------ATATTTCAAAGCTTATATAAAGTGAAACAGC -s simCow_chr6.simCow.chr6 295783 27 + 602619 TGTGTGAATTT--------------A---------------ACAGattataaaatt -s simDog_chr6.simDog.chr6 282989 27 + 593897 CATGTAAGTAT--------------A---------------ACACATTAAGAAAGT -s simRat_chr6.simRat.chr6 310274 42 + 647215 CATATAAGTTT--------------ATATTTGGAAGTTTATACAAAGTGATAAAGT - -a -s simMouse_chr6.simMouse.chr6 318659 7 + 636262 AAATTAA -s Anc0.Anc0refChr7 5000 7 - 16696 aaattaa -s Anc1.Anc1refChr4 5347 7 + 17549 AAATTAA -s Anc2.Anc2refChr7 444 7 + 32194 agattaa -s mr.mrrefChr5 168650 7 + 294540 AAATTAA -s simCow_chr6.simCow.chr6 295822 7 + 602619 aaattaa -s simDog_chr6.simDog.chr6 283016 7 + 593897 AGATTAA -s simHuman_chr6.simHuman.chr6 306645 7 + 601863 AAAACAT -s simRat_chr6.simRat.chr6 310316 7 + 647215 AAATTAA - -a -s simMouse_chr6.simMouse.chr6 318666 25 + 636262 CTTACTGGACTGTTATGTGAGCCGT -s Anc0.Anc0refChr7 5007 23 - 16696 CTTATTGGACTCTTATAAGAGTC-- -s Anc1.Anc1refChr4 5354 23 + 17549 CTTATTGGACTCTTATAAGAGTC-- -s Anc2.Anc2refChr7 453 23 + 32194 TCTATTGAACTCTTCTAAGGGTC-- -s mr.mrrefChr5 168657 23 + 294540 CTTACTGGACTGTTATGTGAGCC-- -s simCow_chr6.simCow.chr6 295831 23 + 602619 GCTACTGGCCTCTTTTAACAGTC-- -s simDog_chr6.simDog.chr6 283025 23 + 593897 TCTATTGAACTCTTCTAAGGGTC-- -s simHuman_chr6.simHuman.chr6 306652 23 + 601863 CTTGGTTGGCTCCAACACTAATC-- -s simRat_chr6.simRat.chr6 310323 23 + 647215 CTGACTAGAGTGTTATGTGAGCC-- - -a -s simMouse_chr6.simMouse.chr6 318691 144 + 636262 AAAAGCGCAATCATGAACAATCTGCTGTTGGCGGCGAGTCTGCATTCATATCTGCCATATCTGCCTGTGTACCTGACCTGGATTGAATGGATTGAAATTACTGTGCAATAAACTGATTCTTGCCCATTGACCATATGGTCTAAT -s Anc0.Anc0refChr7 5030 133 - 16696 ACAAGGGCTATTATGAATAGTCTGCTATTTGCAGCTAGTCTGCATC-----------TGTCTTCCTGCCTGACTGACCTAGATTTTGTGGACTGATAATTTTATGCAATAAACTGTTTCTTGCTCATTGACAATATGCTCTTAT -s Anc1.Anc1refChr4 5377 133 + 17549 ACAAGGGCTATTATGAATAGTCTGCTATTTGCAGCTAGTCTGCATC-----------TGTCTTCCTGCCTGACTGACCTAGATTTTGTGGACTGATAATTTTATGCAATAAACTGTTTCTTGCTCATTGACAATATGCTCTTAT -s Anc2.Anc2refChr7 476 133 + 32194 ATAAGGGCTATTATGAATAGTCTGCTATTTGCAGCTAGTGTGCATC-----------TGTCTTCCTGCCTGACTGACCTAGATTTTGTGGACTGATAATTTTATGCCATAAACTGTTTCTTGCTCATTGACAATATGCTCTTCT -s mr.mrrefChr5 168680 135 + 294540 ACAAGCGCAATCATGAACAATCTGCTGTTGGCAGCGAGTCTGCATT---------CATATCTGCCTGTGTAACTGACCTAGATTTTATGGATTGAAATTATTGTGCAATAAACTGATTCTTGCCCATTGACCATATGGTCTAAT -s simCow_chr6.simCow.chr6 295854 132 + 602619 CTAAGGGCTATTATGAATAGTCTGTTATCCAGAGCTAATG-GCATC-----------TGTCTTCACGTCTGACCAACCTAGATTGTGTGGACTGATATCTTTATGCGATTGACTGTTTCTTCCTCATTGACAATATACTCTTCT -s simDog_chr6.simDog.chr6 283048 133 + 593897 ATAAGGGCAATTATGACTAATCTGCTATTTGCAGCTAGTGTGCTTC-----------TGTCTTTCTGCCTGACTGACCTAGATTTTCTGTCCTGACAATTTTATGGCATAAACTGCTTCTTGCTCACTGACAGTATGCTTTTCT -s simHuman_chr6.simHuman.chr6 306680 130 + 601863 ACAGGGGCTATTATAAATAGTCTGGTATTTGCA---AGACTGCATC-----------TGCCTACTTGCTTGACTGACCTAGCTTTTGTGGACTAATAATTTACTGCAATAAACTGTTTCTTGCTCATTGACAATGTGCTCTTAT -s simRat_chr6.simRat.chr6 310346 133 + 647215 ACAAGCGTAATCATGAACAATCTGCCTTTGGCAACTAATCTGCATT---------CATATCTGCCTGTGTAATTGACGTAGATTTTATGGATTGAAATCATTGTGCAATAAACTGCTTC-TGCCCATTGACCATA-GGTCTAAC - -a -s simMouse_chr6.simMouse.chr6 318835 50 + 636262 GATGTTTCTACACCACAGCTGGAAGAAAACTAGTGGTAATGCCAGCTGGC -s Anc0.Anc0refChr7 5164 33 - 16696 GATGTTT-----------------GAGAACTAGGGCTAATGCCAGCCTGG -s Anc1.Anc1refChr4 5511 33 + 17549 GATGTTT-----------------GAGAACTAGGGCTAATGCCAGCCTGG -s Anc2.Anc2refChr7 610 33 + 32194 AATGTTT-----------------GAGAACTAGGGCTAATGCCAGCCTGG -s mr.mrrefChr5 168815 50 + 294540 GATGTTTCTACACCACAGCTGGAAGAAAACTAGTGGTAATGCCAGCTGGC -s simCow_chr6.simCow.chr6 295987 33 + 602619 AATGTTT-----------------GAGAATTAGGTCTAACCCTGGCCTAG -s simDog_chr6.simDog.chr6 283182 32 + 593897 AA-GTTT-----------------GATAACTAGGGCTAATGCCAGCCTGG -s simHuman_chr6.simHuman.chr6 306811 33 + 601863 GATGTGT-----------------GAGAACTAGAGCCAAGGCCAGCCCGG -s simRat_chr6.simRat.chr6 310479 47 + 647215 AATGTTTCTACGCCACAACTGGAAG---ACTAGTGGTTATGCCAGTTGGC - -a -s simMouse_chr6.simMouse.chr6 318885 68 + 636262 TATTCTCAGCCAGTACCAGAAGCATTTGGCCAGATAATTAACCCTGCTATGAGCTTTGATATGAGGAT -s Anc0.Anc0refChr7 5197 67 - 16696 TGTGCTGGGCCAGTACCAAGATCTTTTGGTAAGGTAATTAACCTCACTATGAGATTTAATGCGAGTA- -s Anc1.Anc1refChr4 5544 67 + 17549 TGTGCTGGGCCAGTACCAAGATCTTTTGGTAAGGTAATTAACCTCACTATGAGATTTAATGCGAGTA- -s Anc2.Anc2refChr7 643 67 + 32194 TGTGCTGGGCCAGTACCAAGATCTTTTGGTAAGGTAATTAACCTCACTTTGAGATTTAGTACGAGTA- -s mr.mrrefChr5 168865 68 + 294540 TATTCTCAGCCAGTACCAGAAGCATTTGGCAAGATAATTAACCTCGCTATGAGCTTTGATGTGAGGAT -s simCow_chr6.simCow.chr6 296020 67 + 602619 TATGCTGGGCCAGCACCAAGATCTTTTGGTAAGGTAATTATCCTCACTTTGAGATCTACTACGAGCG- -s simDog_chr6.simDog.chr6 283214 67 + 593897 TGTACTGGGCCAGTGCCAAGATTTTTTGGTAATGTAATTAACCCCACTTTGGCATTTAGTATGAGTA- -s simHuman_chr6.simHuman.chr6 306844 67 + 601863 TGTGCTGGACCAGTACCAACATCTTTTGGTAAGGTAATTAACCTCACTATAAGATTTAATGCAGGAA- -s simRat_chr6.simRat.chr6 310539 68 + 647215 TATTCTCAGCCAGTACCAGAAGCATTTGGCAAGATAATTAACCTCGCTATGAGCTCTGACGTGAGGAT - -a -s simMouse_chr6.simMouse.chr6 318953 15 + 636262 AAAGTTATCAAGACA -s Anc0.Anc0refChr7 5266 14 - 16696 CAAG-TATAAAGGTA -s Anc1.Anc1refChr4 5613 15 + 17549 CAAGTTATAAAGGTA -s Anc2.Anc2refChr7 712 14 + 32194 CAAG-TATAAAGGTA -s mr.mrrefChr5 168935 15 + 294540 AAAGTTATAAAGACA -s simCow_chr6.simCow.chr6 296089 14 + 602619 CAAG-CATAAAGGTA -s simDog_chr6.simDog.chr6 283283 5 + 593897 CAAG-T--------- -s simHuman_chr6.simHuman.chr6 306913 15 + 601863 CAAGTTGTAAAGGTA -s simRat_chr6.simRat.chr6 310609 15 + 647215 AAAGTTATAAAGACA - -a -s simMouse_chr6.simMouse.chr6 318968 3 + 636262 TGG -s Anc0.Anc0refChr7 5280 3 - 16696 TAA -s Anc1.Anc1refChr4 5628 3 + 17549 TAA -s Anc2.Anc2refChr7 726 3 + 32194 GAA -s mr.mrrefChr5 168950 3 + 294540 TGG -s simCow_chr6.simCow.chr6 296104 3 + 602619 GAA -s simHuman_chr6.simHuman.chr6 306928 3 + 601863 TAA -s simRat_chr6.simRat.chr6 310624 3 + 647215 AGG - -a -s simMouse_chr6.simMouse.chr6 318971 32 + 636262 TCTACACTGTGGATTGCCACATTGGGGGGGTG -s Anc0.Anc0refChr7 5290 27 - 16696 TCTA-CCC-TGGATTGCCATATT---TGGGTG -s Anc1.Anc1refChr4 5638 28 + 17549 TCTACCCC-TGGATTGCCATATT---TGGGTG -s Anc2.Anc2refChr7 736 27 + 32194 TATA-TCC-TGAATTGCCATATT---TGGGTG -s mr.mrrefChr5 168953 29 + 294540 TCTACACTGTGGATTGCCACATT---TGGGTG -s simCow_chr6.simCow.chr6 296114 27 + 602619 TATA-TCC-TGAATTGCCAAATT---TGGGTC -s simDog_chr6.simDog.chr6 283288 14 + 593897 ---------------ACAATATT---TGGGTG -s simHuman_chr6.simHuman.chr6 306938 28 + 601863 TCTACCCC-TGGGTTGCCAGCTT---TGTGTG -s simRat_chr6.simRat.chr6 310627 29 + 647215 TTTATGCTGTGGATTGCCATGTT---TGGGTG - -a -s simMouse_chr6.simMouse.chr6 319003 8 + 636262 TGGTGAGA -s Anc0.Anc0refChr7 5318 8 - 16696 TGAACAGA -s Anc1.Anc1refChr4 5667 8 + 17549 TGAACAGA -s Anc2.Anc2refChr7 764 8 + 32194 CAAACAGA -s mr.mrrefChr5 168982 8 + 294540 TGGTGAGA -s simCow_chr6.simCow.chr6 296142 8 + 602619 CAAACAGG -s simDog_chr6.simDog.chr6 283303 8 + 593897 CAAACAGA -s simHuman_chr6.simHuman.chr6 306967 8 + 601863 TGAATAGA -s simRat_chr6.simRat.chr6 310656 8 + 647215 TGGTGAGA - -a -s simMouse_chr6.simMouse.chr6 319011 15 + 636262 ATATGGAATATGTGT -s Anc0.Anc0refChr7 5326 15 - 16696 ACATGGAATATGTGT -s Anc1.Anc1refChr4 5675 15 + 17549 ACATGGAATATGTGT -s Anc2.Anc2refChr7 772 15 + 32194 ACATGGAATATGTGT -s mr.mrrefChr5 168990 15 + 294540 ATATGGAATATGTGT -s simCow_chr6.simCow.chr6 296150 15 + 602619 ACATGGAATATGTGT -s simDog_chr6.simDog.chr6 283311 15 + 593897 ACATGGAATATGTGT -s simHuman_chr6.simHuman.chr6 306975 15 + 601863 ACATGGAATATGAGT -s simRat_chr6.simRat.chr6 310717 15 + 647215 ATATGGAATGTATGT - -a -s simMouse_chr6.simMouse.chr6 319026 36 + 636262 GATGCTCTGTTACTGCAAGATGGGTCAAGACTACAA -s Anc0.Anc0refChr7 5342 36 - 16696 AATTGCCTGCTACATCAAGAAGTGTCAAGACTTCAA -s Anc1.Anc1refChr4 5691 36 + 17549 AATTGCCTGCTACATCAAGAAGTGTCAAGACTTCAA -s Anc2.Anc2refChr7 788 36 + 32194 AATTGCCTGCTACATAGAGAAGTGTCAAGACTTCAA -s mr.mrrefChr5 169005 36 + 294540 GATTCTCTGTTACAGCAAGATGGGTCAAGACTACAA -s simCow_chr6.simCow.chr6 296166 32 + 602619 AATTGCCAGCCACATTCAAAA-TGTCAAGAATT--- -s simDog_chr6.simDog.chr6 283327 36 + 593897 AATCGTCTGCTACGTAGAGATGTGTCAAGACTTCAA -s simHuman_chr6.simHuman.chr6 306991 36 + 601863 AATTTCCTGCTACATCAAGAAGTGTCAAGACTTCAA -s simRat_chr6.simRat.chr6 310732 36 + 647215 GATTCTCCATTACAACAAGATGGATCAAGACTGCTA - -a -s simMouse_chr6.simMouse.chr6 319062 10 + 636262 GCTCAGTATG -s Anc0.Anc0refChr7 5392 10 - 16696 GCCCAGTATG -s Anc1.Anc1refChr4 5741 10 + 17549 GCCCAGTATG -s Anc2.Anc2refChr7 838 10 + 32194 TCCCAGTATG -s mr.mrrefChr5 169041 10 + 294540 GCTCAGTATG -s simCow_chr6.simCow.chr6 296207 10 + 602619 CACAAGCATG -s simDog_chr6.simDog.chr6 283378 10 + 593897 TCCCAGTCTG -s simHuman_chr6.simHuman.chr6 307041 10 + 601863 GCCCAGTATG -s simRat_chr6.simRat.chr6 310768 10 + 647215 GCTCAGTATG - -a -s simMouse_chr6.simMouse.chr6 319072 8 + 636262 TGTAGTTC -s Anc0.Anc0refChr7 5402 8 - 16696 TAGAATAC -s Anc1.Anc1refChr4 5751 8 + 17549 TAGAATAC -s Anc2.Anc2refChr7 848 8 + 32194 TAGAAAAC -s mr.mrrefChr5 169051 8 + 294540 TGTAATTC -s simCow_chr6.simCow.chr6 296220 8 + 602619 TAGAAAGC -s simDog_chr6.simDog.chr6 283388 8 + 593897 CGGAAAAC -s simHuman_chr6.simHuman.chr6 307051 8 + 601863 TAGAATAC -s simRat_chr6.simRat.chr6 310778 8 + 647215 TGTCATTC - -a -s simMouse_chr6.simMouse.chr6 319080 8 + 636262 CCATTAGG -s Anc0.Anc0refChr7 5418 8 - 16696 CCTAGGGG -s Anc1.Anc1refChr4 5767 8 + 17549 CCTAGGGG -s Anc2.Anc2refChr7 864 8 + 32194 CCTAGGGG -s mr.mrrefChr5 169059 8 + 294540 CCATTAGG -s simCow_chr6.simCow.chr6 296236 8 + 602619 CCTTGGGA -s simDog_chr6.simDog.chr6 283404 8 + 593897 CCTAAGGG -s simHuman_chr6.simHuman.chr6 307067 8 + 601863 CCCAGGGG -s simRat_chr6.simRat.chr6 310786 8 + 647215 CCATTAGG - -a -s simMouse_chr6.simMouse.chr6 319088 3 + 636262 TAA -s Anc0.Anc0refChr7 5444 3 - 16696 CAA -s Anc1.Anc1refChr4 5793 3 + 17549 CAA -s Anc2.Anc2refChr7 892 3 + 32194 CAA -s mr.mrrefChr5 169067 3 + 294540 TAA -s simCow_chr6.simCow.chr6 296264 3 + 602619 CAA -s simDog_chr6.simDog.chr6 283432 3 + 593897 CAA -s simHuman_chr6.simHuman.chr6 307093 3 + 601863 CAA -s simRat_chr6.simRat.chr6 310794 3 + 647215 TAA - -a -s simMouse_chr6.simMouse.chr6 319091 11 + 636262 TACCTTGATTT -s Anc0.Anc0refChr7 5447 1 - 16696 T---------- -s Anc1.Anc1refChr4 5796 11 + 17549 TACCTTGATTT -s Anc2.Anc2refChr7 895 1 + 32194 C---------- -s mr.mrrefChr5 169070 11 + 294540 TACCTTGATTT -s simCow_chr6.simCow.chr6 296269 1 + 602619 C---------- -s simDog_chr6.simDog.chr6 283435 1 + 593897 C---------- -s simHuman_chr6.simHuman.chr6 307096 11 + 601863 TACCTTGATTT -s simRat_chr6.simRat.chr6 310797 11 + 647215 TACCCTGATTT - -a -s simMouse_chr6.simMouse.chr6 319102 17 + 636262 TTAAGCCTACAAATGTC -s Anc0.Anc0refChr7 5448 2 - 16696 ---------------TC -s Anc1.Anc1refChr4 5807 17 + 17549 CTATGCCTACAAATGTC -s Anc2.Anc2refChr7 896 2 + 32194 ---------------TC -s mr.mrrefChr5 169081 17 + 294540 TTAAGCCTACAAATGTC -s simCow_chr6.simCow.chr6 296270 2 + 602619 ---------------CT -s simDog_chr6.simDog.chr6 283436 2 + 593897 ---------------TC -s simHuman_chr6.simHuman.chr6 307113 17 + 601863 CTATGCCTACAAATGTC -s simRat_chr6.simRat.chr6 310808 17 + 647215 TTGAGACTACAAATATC - -a -s simMouse_chr6.simMouse.chr6 319119 14 + 636262 CAAGTATCTGCACC -s Anc0.Anc0refChr7 5471 14 - 16696 CAAATGTCTGCACC -s Anc1.Anc1refChr4 5845 14 + 17549 CAAATGTCTGCACC -s Anc2.Anc2refChr7 919 14 + 32194 CAAATGTCTGCACC -s mr.mrrefChr5 169098 14 + 294540 CAAGTATCTGCACC -s simCow_chr6.simCow.chr6 296293 14 + 602619 CAATTGTCTGCACC -s simDog_chr6.simDog.chr6 283459 14 + 593897 CACATGCCTGCACC -s simHuman_chr6.simHuman.chr6 307151 14 + 601863 CAAATGTCTGCACT -s simRat_chr6.simRat.chr6 310825 14 + 647215 CAAGTATCTCCATC - -a -s simMouse_chr6.simMouse.chr6 319133 6 + 636262 ACTCTT -s Anc0.Anc0refChr7 5486 6 - 16696 AGTTCT -s Anc1.Anc1refChr4 5860 6 + 17549 AGTTCT -s Anc2.Anc2refChr7 934 6 + 32194 AGTTCT -s mr.mrrefChr5 169112 6 + 294540 ACTCTT -s simCow_chr6.simCow.chr6 296308 6 + 602619 AGTCCT -s simDog_chr6.simDog.chr6 283474 5 + 593897 ACAT-G -s simHuman_chr6.simHuman.chr6 307166 6 + 601863 AGTTCT -s simRat_chr6.simRat.chr6 310839 6 + 647215 GCTCTT - -a -s simMouse_chr6.simMouse.chr6 319139 20 + 636262 GGTATGCTTTAGAGGGCTGA -s Anc0.Anc0refChr7 5492 18 - 16696 GAGTTCATTGACAAGG--GA -s Anc1.Anc1refChr4 5866 18 + 17549 GAGTTCATTGACAAGG--GA -s Anc2.Anc2refChr7 940 18 + 32194 GAGTTCATTGACAAGG--GA -s mr.mrrefChr5 169118 20 + 294540 GGTATGCTTTACAGGGCTGA -s simCow_chr6.simCow.chr6 296316 18 + 602619 GAGTTCATTGACAAGG--GA -s simDog_chr6.simDog.chr6 283479 18 + 593897 GAGTTCATTGAAAAGG--GA -s simHuman_chr6.simHuman.chr6 307172 18 + 601863 GAGTTCATTGACAAGG--GA -s simRat_chr6.simRat.chr6 310845 20 + 647215 GGCATTCATTACAGGGGTGA - -a -s simMouse_chr6.simMouse.chr6 319159 6 + 636262 AAGTGT -s Anc0.Anc0refChr7 5510 6 - 16696 AATCAT -s Anc1.Anc1refChr4 5884 6 + 17549 AATCAT -s Anc2.Anc2refChr7 958 6 + 32194 AATCAT -s mr.mrrefChr5 169138 6 + 294540 AATCGT -s simCow_chr6.simCow.chr6 296337 6 + 602619 AAGAAT -s simDog_chr6.simDog.chr6 283497 6 + 593897 ACTCAC -s simHuman_chr6.simHuman.chr6 307190 6 + 601863 AATCAT -s simRat_chr6.simRat.chr6 310865 6 + 647215 AATCGT - -a -s simMouse_chr6.simMouse.chr6 319165 1 + 636262 G -s Anc0.Anc0refChr7 5517 1 - 16696 C -s Anc1.Anc1refChr4 5891 1 + 17549 C -s Anc2.Anc2refChr7 965 1 + 32194 C -s mr.mrrefChr5 169145 1 + 294540 G -s simCow_chr6.simCow.chr6 296344 1 + 602619 C -s simDog_chr6.simDog.chr6 283504 1 + 593897 C -s simHuman_chr6.simHuman.chr6 307197 1 + 601863 C -s simRat_chr6.simRat.chr6 310872 1 + 647215 G - -a -s simMouse_chr6.simMouse.chr6 319166 26 + 636262 CACAATTCATGAACATACAGGCTGGG -s Anc0.Anc0refChr7 5518 26 - 16696 CCCTGTTCATGAGCACACAGGGTGGG -s Anc1.Anc1refChr4 5892 26 + 17549 CCCTGTTCATGAGCACACAGGGTGGG -s Anc2.Anc2refChr7 966 26 + 32194 CCCTGTTGATGAGCACACAGAGTGGG -s mr.mrrefChr5 169146 26 + 294540 CCCAGTTCATGAACATACAGGCTGGG -s simCow_chr6.simCow.chr6 296395 26 + 602619 CCCTGTTGGTGAGCACACAGTGTGGG -s simDog_chr6.simDog.chr6 283505 26 + 593897 CCCTATTGATAAGCACATAGAGTGGG -s simHuman_chr6.simHuman.chr6 307198 26 + 601863 CCCTGTTCATGAGGACACAGGGTGGG -s simRat_chr6.simRat.chr6 310873 26 + 647215 CCCAGTTCATGAACATACAGGTAGGG - -a -s simMouse_chr6.simMouse.chr6 319192 7 + 636262 AGACTGG -s Anc0.Anc0refChr7 5544 7 - 16696 AGGATGG -s Anc1.Anc1refChr4 5918 7 + 17549 AGGATGG -s Anc2.Anc2refChr7 992 7 + 32194 TGGATGT -s mr.mrrefChr5 169172 7 + 294540 AGACTGG -s simCow_chr6.simCow.chr6 296421 7 + 602619 TGAATGG -s simDog_chr6.simDog.chr6 283531 7 + 593897 TGGATGT -s simHuman_chr6.simHuman.chr6 307226 7 + 601863 AGGGTGG -s simRat_chr6.simRat.chr6 310899 7 + 647215 AGACCGG - -a -s simMouse_chr6.simMouse.chr6 319199 19 + 636262 CCTCAAACCATGTCCATCA -s Anc0.Anc0refChr7 5551 19 - 16696 CCTCATACCATGGCTTTAA -s Anc1.Anc1refChr4 5925 19 + 17549 CCTCATACCATGGCTTTAA -s Anc2.Anc2refChr7 999 19 + 32194 CCTCATAACACTGCTTTAG -s mr.mrrefChr5 169179 19 + 294540 CCTCAAACCATGTCTATCA -s simCow_chr6.simCow.chr6 296428 19 + 602619 CTTCAAAACACTGCTTTAG -s simDog_chr6.simDog.chr6 283538 19 + 593897 CCTTATAACACTGCTTTAG -s simHuman_chr6.simHuman.chr6 307235 19 + 601863 CCTCACACCATGGCTTTAA -s simRat_chr6.simRat.chr6 310906 19 + 647215 CCTCAAACCATTAGTATCA - -a -s simMouse_chr6.simMouse.chr6 319218 2 + 636262 TT -s Anc0.Anc0refChr7 5573 2 - 16696 TT -s Anc1.Anc1refChr4 5947 2 + 17549 TT -s Anc2.Anc2refChr7 1021 2 + 32194 TT -s mr.mrrefChr5 169198 2 + 294540 TT -s simCow_chr6.simCow.chr6 296450 2 + 602619 TT -s simDog_chr6.simDog.chr6 283560 2 + 593897 TT -s simHuman_chr6.simHuman.chr6 307257 2 + 601863 TT -s simRat_chr6.simRat.chr6 310925 2 + 647215 TT - -a -s simMouse_chr6.simMouse.chr6 319220 16 + 636262 TTATTAAACTTTCTAA -s Anc0.Anc0refChr7 5575 14 - 16696 TAAGTG--CTTACTCA -s Anc1.Anc1refChr4 5949 14 + 17549 TAAGTG--CTTACTCA -s Anc2.Anc2refChr7 1023 14 + 32194 TAAGTG--CACACTCA -s mr.mrrefChr5 169200 16 + 294540 TTATTAAACTTTCTAA -s simCow_chr6.simCow.chr6 296454 14 + 602619 TAAGTG--CACACTCA -s simDog_chr6.simDog.chr6 283562 5 + 593897 -----------ATCCA -s simHuman_chr6.simHuman.chr6 307259 14 + 601863 TAAATG--CTTACTCT -s simRat_chr6.simRat.chr6 310927 16 + 647215 TTATTAAACTCTGTAA - -a -s simMouse_chr6.simMouse.chr6 319236 41 + 636262 CTCCAGCATTCTTAAAACCTAAGTCCTCTGACCCTAAAGTG -s Anc0.Anc0refChr7 5589 41 - 16696 GTCCAACATCCTTAAAACCTAGGACCTGTGACCCTAAGGTG -s Anc1.Anc1refChr4 5963 41 + 17549 GTCCAACATCCTTAAAACCTAGGACCTGTGACCCTAAGGTG -s Anc2.Anc2refChr7 1037 41 + 32194 GTCCAACATCTGTAGAACCTAGGACCTGTGACCCTAAGGTG -s mr.mrrefChr5 169216 41 + 294540 CTCCAGCATTCTTAAAACCTAAGTCCTCTGACCCTAAAGTG -s simCow_chr6.simCow.chr6 296482 41 + 602619 ATCCAACATCTGTAGAACCTATGACCCATGAACCTACAGTG -s simDog_chr6.simDog.chr6 283567 32 + 593897 GTGCAG---------AACCTAGGATCTGTGACCCCAAGGTA -s simHuman_chr6.simHuman.chr6 307273 41 + 601863 GTCCAACATCCTTAAAACCTAGGACCTGTGACCCTAAGATG -s simRat_chr6.simRat.chr6 310943 41 + 647215 CCCCAGCATTCTTAAATCCTAAGTCCTCTGACCTTACAGTG - -a -s simMouse_chr6.simMouse.chr6 319277 4 + 636262 TGAC -s Anc1.Anc1refChr4 6004 4 + 17549 TGAT -s mr.mrrefChr5 169257 4 + 294540 TGAC -s simHuman_chr6.simHuman.chr6 307316 4 + 601863 TGAT -s simRat_chr6.simRat.chr6 310984 4 + 647215 TGAC - -a -s simMouse_chr6.simMouse.chr6 319281 27 + 636262 TTTAAGTATCATTCGGGCTCCACTTTA -s Anc0.Anc0refChr7 5645 27 - 16696 TTTTAGTATCACTAAGGCTCTACTATA -s Anc1.Anc1refChr4 6023 27 + 17549 TTTTAGTATCACTAAGGCTCTACTATA -s Anc2.Anc2refChr7 1093 27 + 32194 TTTTAGTATCACTAAGGTTCTACTATA -s mr.mrrefChr5 169261 27 + 294540 TTTAAGTATCATTCGGGCTCCACTTTA -s simCow_chr6.simCow.chr6 296538 24 + 602619 TTTTGGTATTTCTGAGGTTCC---ATA -s simDog_chr6.simDog.chr6 283614 27 + 593897 TTTTAGTATCACTAAGGTTCTACTGTC -s simHuman_chr6.simHuman.chr6 307336 21 + 601863 TCTTAGTATCA------CCTTACTATA -s simRat_chr6.simRat.chr6 310988 27 + 647215 TTTAAGTATCATTCGGGCTCCACTTTA - -a -s simMouse_chr6.simMouse.chr6 319308 10 + 636262 GAATCACACA -s Anc0.Anc0refChr7 5712 3 - 16696 -------ACA -s Anc1.Anc1refChr4 6090 10 + 17549 AATTAACACA -s Anc2.Anc2refChr7 1160 3 + 32194 -------ACA -s mr.mrrefChr5 169288 10 + 294540 GAATCACACA -s simCow_chr6.simCow.chr6 296605 3 + 602619 -------TTA -s simDog_chr6.simDog.chr6 283790 3 + 593897 -------ACT -s simHuman_chr6.simHuman.chr6 307482 10 + 601863 AATTAACACA -s simRat_chr6.simRat.chr6 311015 10 + 647215 GACCCACGCA - -a -s simMouse_chr6.simMouse.chr6 319318 22 + 636262 GTTATTAATAACTTTGGTATCT -s Anc0.Anc0refChr7 5718 19 - 16696 GTTGTTAATAACTTTGGT---T -s Anc1.Anc1refChr4 6103 22 + 17549 GTTGTTAATAACTTTGGTGTCT -s Anc2.Anc2refChr7 1166 19 + 32194 GTGGTAAATAGCTTTGGT---T -s mr.mrrefChr5 169298 22 + 294540 GTTATTAATAACTTTGGTATCT -s simCow_chr6.simCow.chr6 296611 13 + 602619 GTGCAACAAAGCT--------- -s simDog_chr6.simDog.chr6 283796 19 + 593897 GTGGTAAATAGCTTTGGT---T -s simHuman_chr6.simHuman.chr6 307495 22 + 601863 GTTGTTAATAACTCTAGTGTCT -s simRat_chr6.simRat.chr6 311025 19 + 647215 G---TTAACAATTTTGGTATCT - -a -s simMouse_chr6.simMouse.chr6 319340 43 + 636262 TGACGGAATGTATGCAGGAAAAAACCATGAATTGAGTTCTCCT -s Anc0.Anc0refChr7 5739 39 - 16696 CACTGTAATATATGTAGGGAAAT----GAAATCATGTTCTGCT -s Anc1.Anc1refChr4 6127 43 + 17549 CACTGTAATATATGTAGGGAAATAATAGAAATCATGTTCTGCT -s Anc2.Anc2refChr7 1187 39 + 32194 CACTGTAATATATGTAGGGAAAT----GAAATCATGTTTTGCT -s mr.mrrefChr5 169320 43 + 294540 TGATGGAATGTATGCAGGAAAAAACCATGAATCAAGTTCTCCT -s simCow_chr6.simCow.chr6 296624 22 + 602619 -ACTGTGCCATATAGAGGAAAAC-------------------- -s simDog_chr6.simDog.chr6 283817 39 + 593897 CATTGTAATATATGTAGGGAAAT----GAAATCATGTTTTGCT -s simHuman_chr6.simHuman.chr6 307519 42 + 601863 CACTATAATATA-GTAGGGAAGTAATAGAAATCATGTTCTGCT -s simRat_chr6.simRat.chr6 311044 43 + 647215 TGATGAAATGTATGCCGGAAAAAACCATGAATCAAGTTCTCCT - -a -s simMouse_chr6.simMouse.chr6 319383 43 + 636262 TGAGGCATATATTGCCCCACACAATTGATTTTGAGGATAAAAT -s Anc0.Anc0refChr7 5779 43 - 16696 TTGGGCATGTATTACCCCACATAATTAATCATGAGGATAAAAT -s Anc1.Anc1refChr4 6171 43 + 17549 TTGGGCATGTATTACCCCACATAATTAATCATGAGGATAAAAT -s Anc2.Anc2refChr7 1227 43 + 32194 TTTGGCACGTATTACGCGACATAATTAATCATGAGTATAAGAT -s mr.mrrefChr5 169363 43 + 294540 TGGGGCATATATTGCCCCACACAATTAATTTTGAGGATAAAAT -s simDog_chr6.simDog.chr6 283857 43 + 593897 TTTGGCACGTATTACGCGACATAATTAATCATGAGTATAAGAT -s simHuman_chr6.simHuman.chr6 307562 43 + 601863 TAGGGTTTGTATTACCCCACATAATTAATCCTGAGGATAAAAT -s simRat_chr6.simRat.chr6 311087 43 + 647215 TGGGGCATATATCGCCCCACACAATTAATTTTGAGGATAAAAT - -a -s simMouse_chr6.simMouse.chr6 319426 16 + 636262 GGAAAGGACATAGACA -s Anc0.Anc0refChr7 5825 16 - 16696 AGAAATAACATAAGAA -s Anc1.Anc1refChr4 6217 16 + 17549 AGAAATAACATAAGAA -s Anc2.Anc2refChr7 1273 16 + 32194 AGAAATAACATAAGAA -s mr.mrrefChr5 169406 16 + 294540 AGAAAGGACATAGACA -s simDog_chr6.simDog.chr6 283903 16 + 593897 AGAAATAACATAAGAA -s simHuman_chr6.simHuman.chr6 307608 16 + 601863 AGAAATACTATAAGAA -s simRat_chr6.simRat.chr6 311130 16 + 647215 AGAAAGGACATAGACA - -a -s simMouse_chr6.simMouse.chr6 319442 10 + 636262 ATGTAGATAG -s Anc0.Anc0refChr7 5841 10 - 16696 ACATGGATAG -s Anc1.Anc1refChr4 6233 10 + 17549 ACATGGATAG -s Anc2.Anc2refChr7 1289 10 + 32194 ACACAGATAG -s mr.mrrefChr5 169422 10 + 294540 ATATGGATAG -s simDog_chr6.simDog.chr6 283919 10 + 593897 ACACAGATAG -s simHuman_chr6.simHuman.chr6 307624 10 + 601863 ACATGGATAG -s simRat_chr6.simRat.chr6 311183 10 + 647215 ATATGGATAG - -a -s simMouse_chr6.simMouse.chr6 319452 99 + 636262 ATCACCTTTGAGGATAACACAGTACGCTGGTTGCAAGTTGTTTCCTTCTACTATAGTACAGGGATTTTGTGAGGCATCATATCATAGAGGAGCACAGCA -s Anc0.Anc0refChr7 5851 35 - 16696 ACCACAC----------------------GTTGCAAGTTGTTT------------------------------------------GGAGAAGCACTGCA -s Anc1.Anc1refChr4 6243 35 + 17549 ACCACAC----------------------GTTGCAAGTTGTTT------------------------------------------GGAGAAGCACTGCA -s Anc2.Anc2refChr7 1299 35 + 32194 ACCAAAC----------------------GTTGCAAGGAGTTT------------------------------------------GATGAAACACTGCA -s mr.mrrefChr5 169432 91 + 294540 ATCACATTTGA--ATAACACAGTACGCTGGTTGCAAGTTGTTTCCTTCTACTATAGTACAGGGATTTTGTGAGGCAT------ATAGAGGAGCACAGCA -s simCow_chr6.simCow.chr6 296646 31 + 602619 ----AAC----------------------TTGGAATGGAGCTT------------------------------------------GATGACAAATTGCA -s simDog_chr6.simDog.chr6 283942 31 + 593897 ACCAAAT----------------------GGTACAAGGAGTTT----------------------------------------------AAACACTGCA -s simHuman_chr6.simHuman.chr6 307634 35 + 601863 ACCACAC----------------------GTTGCAAGTTCTTT------------------------------------------GGAGAAGCACTGCA -s simRat_chr6.simRat.chr6 311193 91 + 647215 ATCTCATTCGA--ATAGCATAGTACACTGGTTGCAAGTTGTTTCCTACTACTATAGCACATGAATTTTATGAGGCAT------ATAGAGGAGCACAGCA - -a -s simMouse_chr6.simMouse.chr6 319551 4 + 636262 TTGT -s Anc0.Anc0refChr7 5886 4 - 16696 TTGT -s Anc1.Anc1refChr4 6278 4 + 17549 TTGT -s Anc2.Anc2refChr7 1334 4 + 32194 TATT -s mr.mrrefChr5 169523 4 + 294540 TTGT -s simCow_chr6.simCow.chr6 296677 4 + 602619 CATT -s simDog_chr6.simDog.chr6 283994 4 + 593897 TATT -s simHuman_chr6.simHuman.chr6 307669 4 + 601863 TTGT -s simRat_chr6.simRat.chr6 311284 4 + 647215 TTGC - -a -s simMouse_chr6.simMouse.chr6 319555 15 + 636262 ATCTTTAGGGTGAAT -s Anc0.Anc0refChr7 5890 15 - 16696 AACTTTAGTGAACTT -s Anc1.Anc1refChr4 6282 15 + 17549 AACTTTAGTGAACTT -s Anc2.Anc2refChr7 1338 15 + 32194 AACTTTACTGAACTT -s mr.mrrefChr5 169527 15 + 294540 ATCTTTAGGGTGAAT -s simCow_chr6.simCow.chr6 296684 15 + 602619 AACTTTATTTAAATT -s simDog_chr6.simDog.chr6 283998 15 + 593897 AGTCTTACTGAACAC -s simHuman_chr6.simHuman.chr6 307673 15 + 601863 AACTTTAGTGGACTT -s simRat_chr6.simRat.chr6 311288 15 + 647215 ACCTTTAGCATGACT - -a -s simMouse_chr6.simMouse.chr6 319570 36 + 636262 TACTGCAGTATTGGGTTGCTCATAATTGGCCTACCA -s Anc0.Anc0refChr7 5907 33 - 16696 TTTTGCAGTGTTGGTTTGCTTGT---TGGCCAGGCA -s Anc1.Anc1refChr4 6299 33 + 17549 TTTTGCAGTGTTGGTTTGCTTGT---TGGCCAGGCA -s Anc2.Anc2refChr7 1355 33 + 32194 TTTTACAGTGTTGGTCTGCTTGT---TGTCAAGGCA -s mr.mrrefChr5 169544 36 + 294540 TATTGCAGTATTGGTTTGCTCATAATTGGCCCACCA -s simCow_chr6.simCow.chr6 296701 33 + 602619 TTTTATAGTGTTAGTCTGCTTGT---CGTTTCAGCT -s simDog_chr6.simDog.chr6 284033 33 + 593897 TTTTACCGTGTTGGTCTGCTTCT---TGTCAAGGCA -s simHuman_chr6.simHuman.chr6 307690 33 + 601863 TCTTGCAGTGTTGGTTTGCTTGT---TGGCCAGGCA -s simRat_chr6.simRat.chr6 311305 36 + 647215 TGTTGCAGTATTGGTTTGCTCATAATTGTCCCACCA - -a -s simMouse_chr6.simMouse.chr6 319606 14 + 636262 GAGGCTTGTTGAGG -s Anc0.Anc0refChr7 5952 14 - 16696 GAGCACTATTGAGG -s Anc1.Anc1refChr4 6344 14 + 17549 GAGCACTATTGAGG -s Anc2.Anc2refChr7 1400 14 + 32194 GAGCACTATTGAGG -s mr.mrrefChr5 169580 14 + 294540 AAGGATTGTTGAGG -s simCow_chr6.simCow.chr6 296751 13 + 602619 GAGCATTATT-AGG -s simDog_chr6.simDog.chr6 284078 14 + 593897 GAGTACTATTGAGA -s simHuman_chr6.simHuman.chr6 307755 14 + 601863 GAGCACTAATGAGG -s simRat_chr6.simRat.chr6 311341 14 + 647215 ACGTATTGTTGAGG - -a -s simMouse_chr6.simMouse.chr6 319620 121 + 636262 ACCCCACACCCACAGGCCTCCCATCCAGCATAGCTATTTCAATTGTATGAAGGGCGACTAGGCAACAATGGCTGCAGTCTAGGCAGTTGAAACATTTTTTACTTTGGTACCTGCATATATT -s Anc0.Anc0refChr7 5973 120 - 16696 ACACTGTGCCTCCAGACACCTCATCCAGTCCAGACACCTGAATTGTATGATGGGTGAC-ATCCATCAACGGCAGCAGTCTGAGTAGTTATAACATTTGTAACTTAGGCACCTGCATATATT -s Anc1.Anc1refChr4 6365 121 + 17549 ACACTGTGCCTCCAGACACCTCATCCAGTCCAGACACCTGAATTGTATGATGGGTGACTATCCATCAACGGCAGCAGTCTGAGTAGTTATAACATTTGTAACTTAGGCACCTGCATATATT -s Anc2.Anc2refChr7 1421 120 + 32194 ACACTGTGCCTCCAGACACCTCATCCAGTCCGGACACCTGAATTGTATATAAGGTGAC-ATCCATCAACGGCAGAGGTCTGAGTAGTAATAACATCTGTAACTTAGGCACCTGCATATATA -s mr.mrrefChr5 169601 121 + 294540 ACCCCACACCTCCAGGCCTCCCATCCAGTACAGCTATTTCAATTGTATGATGGGCGACTAGGCAACAATGGCTGCAGTCTAGGCAGTTGAAACATTTTTTACTTTGGTACCTGCATATATT -s simCow_chr6.simCow.chr6 296771 118 + 602619 ACACTGTGCCTCCAGACAAA--ATCCAGTCCACATCCCTGAATTGTATAGAGGGTGAC-ATCCATCAATTGCAGAGGTCTGAGTAGCAATAATATCTGTAACTTAAGCACCTGCATATATA -s simDog_chr6.simDog.chr6 284099 120 + 593897 CCACTGTGCTTCCAGACACCTCATCTAGTCTGGACACCTGAATTGTATATAAGGTGAC-ATCCTTCAACGGCAGAGTTCTGAGTAATAAAGACATCTGTAACTTAGGCACCTGCAAATACA -s simHuman_chr6.simHuman.chr6 307776 101 + 601863 ACACTGTGCCTCCAGTTTCCTTGTCCAGTCCAA------------GGTGATGTGTATCTAA--------GGCAGCAGTCTTAGTAGATATAACAATTGTAACTTAGGCACCTGCATATCTT -s simRat_chr6.simRat.chr6 311362 119 + 647215 ACCCCACATTTCCAGAGCTCCCATCCAGTGCAGCCATCTCAATTGTATGATGGGAGACTCGGCAGTGATGGCTGCAGTCTAGGCAG--GAAATATTTTGTACTTGGGTACCTGCATATATT - -a -s simMouse_chr6.simMouse.chr6 319741 70 + 636262 CTCTGGTTATTGATTCAGTTGCATGGTGAACTTTGCTCTAAACTCCAAAATGCTTACGGAGTGGTCCCAG -s Anc0.Anc0refChr7 6093 34 - 16696 CTGTTGCTATCAATTTGGTTGCATGCTGTACTG-----------------------------------A- -s Anc1.Anc1refChr4 6486 34 + 17549 CTGTTGCTATCAATTTGGTTGCATGCTGTACTG-----------------------------------A- -s Anc2.Anc2refChr7 1541 34 + 32194 CTGTTGCTATCAACTTGTTTACATGCTGTACTG-----------------------------------A- -s mr.mrrefChr5 169722 35 + 294540 CTCTGGCTATTAATTCGGTTGCATGGTGTACTT-----------------------------------AG -s simCow_chr6.simCow.chr6 296889 29 + 602619 CTATTGCTACCACCATGAT-----GCTGTTCTG-----------------------------------A- -s simDog_chr6.simDog.chr6 284219 34 + 593897 CTGTTGCGATCAACTTGTTTACATGCTGTACTG-----------------------------------A- -s simHuman_chr6.simHuman.chr6 307878 31 + 601863 CTGTTGCTATCAATGTGGTTGCATGCTGTAC--------------------------------------- -s simRat_chr6.simRat.chr6 311481 35 + 647215 CCCTGGCTATTAATTCGGTTGCATGGTGTACTT-----------------------------------GG - -a -s simMouse_chr6.simMouse.chr6 319811 18 + 636262 CTACTCTCCTTATTCGTC -s Anc0.Anc0refChr7 6127 18 - 16696 CTAATGTCCTTATTCATC -s Anc1.Anc1refChr4 6520 18 + 17549 CTAATGTCCTTATTCATC -s Anc2.Anc2refChr7 1575 18 + 32194 CTAATGTCCTTATTCATC -s mr.mrrefChr5 169757 18 + 294540 CTACTCTCCTTATTCGTC -s simCow_chr6.simCow.chr6 296919 18 + 602619 CTACTCTCCTGATTCCTT -s simDog_chr6.simDog.chr6 284253 18 + 593897 CTAATGTCCTTATTGATC -s simHuman_chr6.simHuman.chr6 307909 11 + 601863 -------CTTTACTCTTC -s simRat_chr6.simRat.chr6 311516 17 + 647215 CTACT-TCCTCATATATC - -a -s simMouse_chr6.simMouse.chr6 319829 19 + 636262 AGGAGGGTGCGAAGGTGTT -s Anc0.Anc0refChr7 6145 18 - 16696 AAAGGGATGGTGGGGTGT- -s Anc1.Anc1refChr4 6538 19 + 17549 AAAGGGATGGTGGGGTGTC -s Anc2.Anc2refChr7 1593 18 + 32194 AAAGGAATGGTGGGGTGT- -s mr.mrrefChr5 169775 19 + 294540 AGGAGGGTGCGAAGGTGTT -s simCow_chr6.simCow.chr6 296937 18 + 602619 AAAGGAATGGTGGGGTGT- -s simDog_chr6.simDog.chr6 284271 18 + 593897 AGAGGAATGGTGGGCGGT- -s simHuman_chr6.simHuman.chr6 307922 19 + 601863 ACTGGGACAGTGGGGTATC -s simRat_chr6.simRat.chr6 311533 19 + 647215 AGAAGGGTGAGAAGGTGTT - -a -s simMouse_chr6.simMouse.chr6 319848 28 + 636262 TCTGGATAGATCTTGTGGTCTACAAACA -s Anc0.Anc0refChr7 6163 28 - 16696 CATGGATCAATGATGTGGTGTTCACACA -s Anc1.Anc1refChr4 6557 28 + 17549 CATGGATCAATGATGTGGTGTTCACACA -s Anc2.Anc2refChr7 1611 28 + 32194 CATGGATCAATGATGTGGTGTTCACACA -s mr.mrrefChr5 169794 28 + 294540 TATGGATAGATCATGTGGTCTACACACA -s simCow_chr6.simCow.chr6 296955 27 + 602619 TATGGAT-AATGATGTAATTTTTACACA -s simDog_chr6.simDog.chr6 284289 28 + 593897 CATGGATCAGTGACGTGGTGTTCACACA -s simHuman_chr6.simHuman.chr6 307942 27 + 601863 CATGGATGAATGATGTG-TTTCCACACA -s simRat_chr6.simRat.chr6 311552 27 + 647215 TATGGATAGGTCATGTGGTCTACACG-A - -a -s simMouse_chr6.simMouse.chr6 319876 5 + 636262 TCTTG -s Anc0.Anc0refChr7 6191 5 - 16696 TCACG -s Anc1.Anc1refChr4 6585 5 + 17549 TCACG -s Anc2.Anc2refChr7 1639 5 + 32194 TCACG -s mr.mrrefChr5 169822 5 + 294540 TCTTG -s simCow_chr6.simCow.chr6 297246 5 + 602619 TCACG -s simDog_chr6.simDog.chr6 284317 5 + 593897 TAATC -s simHuman_chr6.simHuman.chr6 307969 5 + 601863 TCACG -s simRat_chr6.simRat.chr6 311579 5 + 647215 TCTTG - -a -s simMouse_chr6.simMouse.chr6 319881 4 + 636262 TATT -s Anc0.Anc0refChr7 6197 4 - 16696 TAGT -s Anc1.Anc1refChr4 6591 4 + 17549 TAGT -s Anc2.Anc2refChr7 1645 4 + 32194 CAGT -s mr.mrrefChr5 169827 4 + 294540 TATT -s simCow_chr6.simCow.chr6 297252 3 + 602619 GA-T -s simDog_chr6.simDog.chr6 284323 4 + 593897 CAGT -s simHuman_chr6.simHuman.chr6 307975 4 + 601863 TAGT -s simRat_chr6.simRat.chr6 311584 4 + 647215 TAAT - -a -s simMouse_chr6.simMouse.chr6 319885 53 + 636262 CACAGAATTCTGAAATTAAAACATTTGGTCTTCCCAAATCAACTTATGATATG -s Anc0.Anc0refChr7 6207 53 - 16696 CAACGATCACAGTAGTAAAAACATTTAGCCTCCCCAAACATGCTTTTGGTTTG -s Anc1.Anc1refChr4 6601 53 + 17549 CAACGATCACAGTAGTAAAAACATTTAGCCTCCCCAAACATGCTTTTGGTTTG -s Anc2.Anc2refChr7 1655 53 + 32194 TGACAGTCACAGTAGTAAAAACATTTAGCCTCCACAAACATGTGGTTAGTTTG -s mr.mrrefChr5 169831 53 + 294540 CACAGAATTCTGAAATTAAAACATTTAGTCTTCCCAAATCTACTTATGATATG -s simDog_chr6.simDog.chr6 284333 53 + 593897 TGACAGTCACAGTAGTAAAAACATTTAGCCTCCACAAACATGTGGTTAGTTTG -s simHuman_chr6.simHuman.chr6 307985 53 + 601863 CAACGATCACAGTAGTGAAAACAATTAACTTCCCCAAACTTGCTTGCGGTTTG -s simRat_chr6.simRat.chr6 311588 53 + 647215 CACAGAATTTTGAAATTAGAACATTTAGTCTTGCTAAATCTACTTCTGACATG - -a -s simMouse_chr6.simMouse.chr6 319938 27 + 636262 TGCTGTTCAAGATTGAGTGGTGCTTGT -s Anc0.Anc0refChr7 6260 27 - 16696 TACCGTTCGAGAGCAGGTGATATTTGT -s Anc1.Anc1refChr4 6654 27 + 17549 TACCGTTCGAGAGCAGGTGATATTTGT -s Anc2.Anc2refChr7 1708 27 + 32194 TGTTGTGTGAGAGCAGTTGATATTTGC -s mr.mrrefChr5 169884 27 + 294540 TACCGTTCAAGATTGAGTGGTGCTTGT -s simDog_chr6.simDog.chr6 284386 27 + 593897 TGTTGTGTGAGAGCAGTTGATATTTGC -s simHuman_chr6.simHuman.chr6 308038 27 + 601863 TACCATTCGAGAGCAGGTTATTACTGT -s simRat_chr6.simRat.chr6 311695 27 + 647215 TACCGGTCAAGATTGAGTGGTGGTTGT - -a -s simMouse_chr6.simMouse.chr6 319965 53 + 636262 CCCCAACCAAGATAGAAAAAATGCTTTACTTTCTCTGGGGAAGTAATATTCAG -s Anc0.Anc0refChr7 6287 52 - 16696 ACCCGGCCAAGATAGCAAAAATACTTTACCTTCTC-AGAGAAGTAATATCTAG -s Anc1.Anc1refChr4 6681 52 + 17549 ACCCGGCCAAGATAGCAAAAATACTTTACCTTCTC-AGAGAAGTAATATCTAG -s Anc2.Anc2refChr7 1735 52 + 32194 ACCAGGTTACGATAGCAAAAATACTTTACCTTCTC-AGAGAAGTAATATCTAG -s mr.mrrefChr5 169911 53 + 294540 CCCCAACCAAGATAGAAAAAATACTTTACCTTCTCCAGGGAAGTAATATTCAG -s simCow_chr6.simCow.chr6 297257 37 + 602619 ---------------CAAAAATACTTTACCTTCTC-AAAGAAGGAATATTTAA -s simDog_chr6.simDog.chr6 284414 52 + 593897 ACCAGGTTACGATAGCAAAAATACTTTGCCTTCTC-TGCGTAGTAATATCCAG -s simHuman_chr6.simHuman.chr6 308065 52 + 601863 ACCCTGCCAAAAAACCAAAAATACTTTACCTTCTC-AGAGAAGTAATATCTAG -s simRat_chr6.simRat.chr6 311722 53 + 647215 CCCCAACCAAGATAGAAGAAATACTTTACCTTCTACAGGGAAGTAATATTCAG - -a -s simMouse_chr6.simMouse.chr6 320018 116 + 636262 CTGAGTAGCAAGACTAAACACACCAGCAGCCTCGTGTTAAATAGATCCCCCATGGTGCTCAGGTTCAAAAAGGAGAAGGAAGAGTTTACAAAACTAGATCAGAAGTTTGATATTCA -s Anc0.Anc0refChr7 6339 113 - 16696 AAGAGCATTAAGACT--ACACACCATAAACCCTATGTTAAACAATTACCTCATGGTGCTCAGCTTCAGAAA-GAGAGATAAAAGTTTCCAAAACTAGAGGAGAAGTTTATTATTCA -s Anc1.Anc1refChr4 6733 114 + 17549 AAGAGCATTAAGACT--ACACACCATAAACCCTATGTTAAACAATTACCTCATGGTGCTCAGCTTCAGAAAGGAGAGATAAAAGTTTCCAAAACTAGAGGAGAAGTTTATTATTCA -s Anc2.Anc2refChr7 1787 113 + 32194 AAGAGCATTACGACT--ACACACCATAAACCCTATGTTAAACAATTACCTCATGGTGCACAGCTTCAGAAA-GAGAGATGAAAGTTCCCAAAACTAGAGGGAAAGTTTATTATTTA -s mr.mrrefChr5 169964 114 + 294540 CTGAGTAGTAAGACT--ACACACCAGCAGCCTCATGTTAAATAGATCCCCCATGGTGCTCAGGTTCAAAAAGGAGAGGGAAGAGTTTACAAAACTAGATCAGAAGTTTGATATTCA -s simCow_chr6.simCow.chr6 297294 108 + 602619 AAGAGCA----GACT--ACAGACCATAAACCCTATGTTATACAACTACCTCATGGCGAACAGCTTC-GACA-GAGAGATGAAAATTCCCAAAACCAGAGGGAAAGTTTAATCTTGA -s simDog_chr6.simDog.chr6 284466 113 + 593897 AAGCACATTACCACT--ACACACCAAAAAGCCTGTGTTAAACAATTATCTCATATTGCACAGCTTCAAAAA-GAGAGATGGAAGTTCCCAGAACTAGAGAGAAAGTTTATTATTTA -s simHuman_chr6.simHuman.chr6 308119 107 + 601863 TGGAGCACTAAGACT--ACACATCATTACCCCTATGTTAAACG----CGTCATGGTGCTCAGCTTCAGAAACGAAAGAAAAAAGTTTCCAA---TAGGGGAGACATTTATTATTCA -s simRat_chr6.simRat.chr6 311775 110 + 647215 CCAAGTTGTAAGG------ACCCCAGCAGACTCATGTTAAATAGATCCCCCATGGTGCTCAGGTTCAAAAAAGAGAGGGAAGAGTTTACAAAACTAGATCAGATGTTTGATATTTG - -a -s simMouse_chr6.simMouse.chr6 320134 52 + 636262 AACGGTTGGGTTGGACAAGGTTGTTATTAGAATTCTATAGCATACCCCTAGT -s Anc0.Anc0refChr7 6452 50 - 16696 AAAGATTGGGTCGGA--GGGTTGCCATTAGGACTACATATCATAAACCTCAT -s Anc1.Anc1refChr4 6847 52 + 17549 AAAGATTGGGTCGGATTGGGTTGCCATTAGGACTACATATCATAAACCTCAT -s Anc2.Anc2refChr7 1900 50 + 32194 AAAGATTGGGTTGGA--GGGTTGCCATTAGGACTACATATCATAAACCTCAT -s mr.mrrefChr5 170078 52 + 294540 AAAGGTTGGGTCGGACAAGGTTGCTATTAGGATTCTATAGCATACCCCTAGT -s simCow_chr6.simCow.chr6 297402 50 + 602619 AAAGCTTGGGTTCGA--GTGTTATCATAAGAACTACATTCTGTAAACCTCAT -s simDog_chr6.simDog.chr6 284584 50 + 593897 AAAGATTGGGTTGGA--GGGTTGCCGTTAGGACTACATATCATAAATTCCAC -s simHuman_chr6.simHuman.chr6 308226 52 + 601863 AAAGATTAGGTCGGATTGGGTTCCCATTAGGAGAAAATATCATAAACCTCAT -s simRat_chr6.simRat.chr6 311885 48 + 647215 AAAAGTTGGGTCAGACAAGGTTGCTATAAGGATTCTATAGCACACCCC---- - -a -s simMouse_chr6.simMouse.chr6 320186 14 + 636262 CAGTCTCCTGACAG -s Anc0.Anc0refChr7 6508 14 - 16696 CAGTTTCCTCACAG -s Anc1.Anc1refChr4 6905 14 + 17549 CAGTTTCCTCACAG -s Anc2.Anc2refChr7 1956 14 + 32194 CAGTTTCCTCACAG -s mr.mrrefChr5 170130 14 + 294540 CAGTCTCCTGACAG -s simCow_chr6.simCow.chr6 297458 14 + 602619 CAGTTTCCTCACTT -s simDog_chr6.simDog.chr6 284640 14 + 593897 CACTTTTCTCACAG -s simHuman_chr6.simHuman.chr6 308284 14 + 601863 CAGTGTCCTCATGG - -a -s simMouse_chr6.simMouse.chr6 320200 32 + 636262 GAACACAGTCTCTAGAAAATAGGTAGCAACCA -s Anc0.Anc0refChr7 6522 25 - 16696 GAACAC-------AAAAAGCAGATAGCAAGGG -s Anc1.Anc1refChr4 6919 25 + 17549 GAACAC-------AAAAAGCAGATAGCAAGGG -s Anc2.Anc2refChr7 1971 25 + 32194 GAACAC-------AAAAAGCAGATAGCAAGGG -s mr.mrrefChr5 170144 25 + 294540 GAACAC-------AGAAAATAGGTAGCAACCA -s simCow_chr6.simCow.chr6 297473 23 + 602619 GAAAAC-------AAAAAGCAGGTAACAA--G -s simDog_chr6.simDog.chr6 284655 24 + 593897 GGACAC-------AAAAA-CAGATAGCAAGGA -s simHuman_chr6.simHuman.chr6 308298 25 + 601863 GAATAC-------AAAAAGCAGACAGCTAATG - -a -s simMouse_chr6.simMouse.chr6 320232 114 + 636262 CCAGTCAATGCAGGAGGGCTCTGAAATTGCAAACAAAGCATTTGTGAGGCAATAGCATACCCGAGTGCTCAAATGGCACAAACCAAGGTATATCCCAGAATAGCTATCATACCC -s Anc0.Anc0refChr7 6548 13 - 16696 TAAGTAAATGCCG----------------------------------------------------------------------------------------------------- -s Anc1.Anc1refChr4 6945 13 + 17549 TAAGTAAATGCCG----------------------------------------------------------------------------------------------------- -s Anc2.Anc2refChr7 1997 13 + 32194 TAAGTATGTGCCG----------------------------------------------------------------------------------------------------- -s mr.mrrefChr5 170169 20 + 294540 CCAGTCAATGCAGGAG----------------------------------------------------------------------------------------------ACCC -s simCow_chr6.simCow.chr6 297497 10 + 602619 TAAGT---TGCTG----------------------------------------------------------------------------------------------------- -s simDog_chr6.simDog.chr6 284679 11 + 593897 --AGCATGTGCCG----------------------------------------------------------------------------------------------------- -s simHuman_chr6.simHuman.chr6 308324 13 + 601863 TGAGTAAATGCCG----------------------------------------------------------------------------------------------------- -s simRat_chr6.simRat.chr6 311933 4 + 647215 --------------------------------------------------------------------------------------------------------------ACCC - -a -s simMouse_chr6.simMouse.chr6 320346 57 + 636262 AGACCAGACCTTATCAAGGAGTGTGGGTCCACCCATTACCCATTACGATGTAGCACT -s mr.mrrefChr5 170189 50 + 294540 AGACCAGACCTTATCAAGGAGTGTGGGTCC-------ACCCATTACGATGTAGCACT -s simRat_chr6.simRat.chr6 311939 50 + 647215 GGACCAGACCTTATCAAGGACTGTGGTCCC-------ACCCATTACGATGTAGCACT - -a -s simMouse_chr6.simMouse.chr6 320403 70 + 636262 TGACGCGTGTCATACCTGGACCAGATTTATTAATGACTATGGGTCCACCTACCTCAATGTAGGTCTCACT -s Anc0.Anc0refChr7 6561 4 - 16696 ------------------------------------------------------------------TAGT -s Anc1.Anc1refChr4 6958 4 + 17549 ------------------------------------------------------------------TAGT -s Anc2.Anc2refChr7 2010 4 + 32194 ------------------------------------------------------------------TAGT -s mr.mrrefChr5 170239 70 + 294540 TGACGCGTGTCATACCTGGACCAGATTTATTAATGACTATGGGTCCACCTACCTCAATGTAGGTCTCACT -s simCow_chr6.simCow.chr6 297507 4 + 602619 ------------------------------------------------------------------TAGT -s simDog_chr6.simDog.chr6 284690 4 + 593897 ------------------------------------------------------------------TAGT -s simHuman_chr6.simHuman.chr6 308337 4 + 601863 ------------------------------------------------------------------TAGT -s simRat_chr6.simRat.chr6 311999 70 + 647215 TAATGACTGGCATACTTGGACCAGACTTATTAATGACTGTGGGTCCACCCATCTCAGTGTAGCACTCATT - -a -s simMouse_chr6.simMouse.chr6 320473 18 + 636262 GGGGAAATGAATTTCACT -s Anc0.Anc0refChr7 6566 18 - 16696 GGGGAAATCAATTCTACT -s Anc1.Anc1refChr4 6963 18 + 17549 GGGGAAATCAATTCTACT -s Anc2.Anc2refChr7 2015 18 + 32194 GGGGGAACCAATTCTGCT -s mr.mrrefChr5 170310 18 + 294540 GGGGAAATGAATTTCACT -s simCow_chr6.simCow.chr6 297512 18 + 602619 GGGGTAACCAATTCTGCT -s simDog_chr6.simDog.chr6 284695 17 + 593897 GGGGGTACCA-TTCTGCT -s simHuman_chr6.simHuman.chr6 308342 18 + 601863 AGGAAAATCAATTCTACT -s simRat_chr6.simRat.chr6 312070 18 + 647215 GGGGAAATGAATTTCACA - -a -s simMouse_chr6.simMouse.chr6 320491 12 + 636262 TCTACAGCAGGC -s Anc0.Anc0refChr7 6584 12 - 16696 CCTACAGCAGGC -s Anc1.Anc1refChr4 6981 12 + 17549 CCTACAGCAGGC -s Anc2.Anc2refChr7 2033 12 + 32194 CATACAGCAGGC -s mr.mrrefChr5 170328 12 + 294540 TCTACAGCAGGC -s simCow_chr6.simCow.chr6 297535 12 + 602619 CAGACAGCAGGC -s simDog_chr6.simDog.chr6 284712 12 + 593897 CATACAGCAGGC -s simHuman_chr6.simHuman.chr6 308360 12 + 601863 CCTACTGCAGGC -s simRat_chr6.simRat.chr6 312088 12 + 647215 TCTACAGCAGGC - -a -s simMouse_chr6.simMouse.chr6 320503 1 + 636262 A -s Anc0.Anc0refChr7 6596 1 - 16696 C -s Anc1.Anc1refChr4 6993 1 + 17549 C -s Anc2.Anc2refChr7 2045 1 + 32194 C -s mr.mrrefChr5 170340 1 + 294540 A -s simCow_chr6.simCow.chr6 297552 1 + 602619 C -s simDog_chr6.simDog.chr6 284724 1 + 593897 C -s simHuman_chr6.simHuman.chr6 308372 1 + 601863 C -s simRat_chr6.simRat.chr6 312100 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 320504 21 + 636262 AGGTCAGATTGCTTATCATCA -s Anc0.Anc0refChr7 6597 21 - 16696 AGCTCAGATTGCTTATGATCA -s Anc1.Anc1refChr4 6994 21 + 17549 AGCTCAGATTGCTTATGATCA -s Anc2.Anc2refChr7 2046 21 + 32194 AGCTCAGATTGCTTATGATCA -s mr.mrrefChr5 170341 21 + 294540 AGGTCAGATTGCTTATCATCA -s simCow_chr6.simCow.chr6 297553 21 + 602619 AGCTTAGATTGCTTGTGGTCA -s simDog_chr6.simDog.chr6 284725 21 + 593897 AGTTCAGATTGCTTATGAACA -s simHuman_chr6.simHuman.chr6 308373 21 + 601863 AGCTCAAATTGCTTATGATCA -s simRat_chr6.simRat.chr6 312106 21 + 647215 AGGTCAGATTGCTTATTATCA - -a -s simMouse_chr6.simMouse.chr6 320525 2 + 636262 AT -s Anc0.Anc0refChr7 6618 2 - 16696 AT -s Anc1.Anc1refChr4 7015 2 + 17549 AT -s Anc2.Anc2refChr7 2067 2 + 32194 AT -s mr.mrrefChr5 170362 2 + 294540 AT -s simCow_chr6.simCow.chr6 297574 2 + 602619 AT -s simDog_chr6.simDog.chr6 284746 2 + 593897 AT -s simHuman_chr6.simHuman.chr6 308394 2 + 601863 AG -s simRat_chr6.simRat.chr6 312135 2 + 647215 AT - -a -s simMouse_chr6.simMouse.chr6 320527 5 + 636262 TGCCC -s Anc0.Anc0refChr7 6620 5 - 16696 GGCAC -s Anc1.Anc1refChr4 7017 5 + 17549 GGCAC -s Anc2.Anc2refChr7 2069 5 + 32194 GGCAC -s mr.mrrefChr5 170364 5 + 294540 TGCAC -s simCow_chr6.simCow.chr6 297576 5 + 602619 GGCAC -s simDog_chr6.simDog.chr6 284763 5 + 593897 GGAAC -s simHuman_chr6.simHuman.chr6 308396 5 + 601863 GGCAC -s simRat_chr6.simRat.chr6 312137 5 + 647215 TGCAC - -a -s simMouse_chr6.simMouse.chr6 320532 11 + 636262 TTGTCACACAA -s Anc0.Anc0refChr7 6646 11 - 16696 TTGTCACCCTA -s Anc1.Anc1refChr4 7043 11 + 17549 TTGTCACCCTA -s Anc2.Anc2refChr7 2095 11 + 32194 TTGTCACCCTT -s mr.mrrefChr5 170369 11 + 294540 TTGTCACACTA -s simCow_chr6.simCow.chr6 297614 11 + 602619 TTGTTGCCCTG -s simDog_chr6.simDog.chr6 284789 11 + 593897 TTGTCATCCAT -s simHuman_chr6.simHuman.chr6 308422 11 + 601863 TCGTCACCCTA -s simRat_chr6.simRat.chr6 312142 6 + 647215 TTG-----CTA - -a -s simMouse_chr6.simMouse.chr6 320543 20 + 636262 TCTCCGCTATATATGGGGTT -s Anc0.Anc0refChr7 6658 20 - 16696 TCTCAGCTATATATAATGTT -s Anc1.Anc1refChr4 7055 20 + 17549 TCTCAGCTATATATAATGTT -s Anc2.Anc2refChr7 2107 20 + 32194 TCTCACCTATAAATAATGTT -s mr.mrrefChr5 170380 20 + 294540 TCTCCGCTATATATGGGGTT -s simCow_chr6.simCow.chr6 297626 20 + 602619 TCTCACCTATACATAATGTT -s simDog_chr6.simDog.chr6 284801 20 + 593897 TCTCACCCATAAACAATGTT -s simHuman_chr6.simHuman.chr6 308434 20 + 601863 TCTCAGCTATATATAATGTT -s simRat_chr6.simRat.chr6 312148 19 + 647215 TCT-TGCTATATATGGGGTT - -a -s simMouse_chr6.simMouse.chr6 320563 10 + 636262 TGATCAATGA -s Anc0.Anc0refChr7 6678 10 - 16696 TGATCCACTA -s Anc1.Anc1refChr4 7075 10 + 17549 TGATCCACTA -s Anc2.Anc2refChr7 2127 10 + 32194 TGATCCACTG -s mr.mrrefChr5 170400 10 + 294540 TGATCAATGA -s simCow_chr6.simCow.chr6 297661 10 + 602619 TGATCCACTG -s simDog_chr6.simDog.chr6 284821 10 + 593897 TGATCCAGTG -s simHuman_chr6.simHuman.chr6 308454 10 + 601863 TGATCCCCCA -s simRat_chr6.simRat.chr6 312167 10 + 647215 TAATCAATGA - -a -s simMouse_chr6.simMouse.chr6 320573 42 + 636262 AGATTCAACTTTCCATGAGTCCTTTTTGTTCATATTGGTAAA -s Anc0.Anc0refChr7 6689 42 - 16696 GGATCAAGGTTTCCATGAGTTTTTTTAGTCTGTGTTATTAAA -s Anc1.Anc1refChr4 7086 42 + 17549 GGATCAAGGTTTCCATGAGTTTTTTTAGTCTGTGTTATTAAA -s Anc2.Anc2refChr7 2138 42 + 32194 GGATCAAGGTTTCCATGAGTTTTTTTAGTCTGTGTTATTAAA -s mr.mrrefChr5 170410 42 + 294540 AGATTCAACTTTCCATGAGTCCTTTTTGTTTATATTGTTAAA -s simCow_chr6.simCow.chr6 297672 42 + 602619 GGATCCAGGGTTCCATAGGTTTTTTTAGTTTGTGTTTTTAAA -s simDog_chr6.simDog.chr6 284832 42 + 593897 GGAGGAAGATTTGCATGAGTTTTTTTGTTCTGTGTTATTAAA -s simHuman_chr6.simHuman.chr6 308465 42 + 601863 GGATCAAGGTCTCCATGAGTTTTTTTAGCCTGTGTTATTAAG -s simRat_chr6.simRat.chr6 312177 42 + 647215 ACATGCAACTTTCCATGAGGCCTTTTTGTGTATCTTGTTAAA - -a -s simMouse_chr6.simMouse.chr6 320615 3 + 636262 TCA -s Anc0.Anc0refChr7 6731 3 - 16696 TCC -s Anc1.Anc1refChr4 7128 3 + 17549 TCC -s Anc2.Anc2refChr7 2181 3 + 32194 TCC -s mr.mrrefChr5 170452 3 + 294540 TCA -s simCow_chr6.simCow.chr6 297715 3 + 602619 CCC -s simDog_chr6.simDog.chr6 284876 3 + 593897 TGC -s simHuman_chr6.simHuman.chr6 308507 3 + 601863 GCC -s simRat_chr6.simRat.chr6 312219 3 + 647215 TCA - -a -s simMouse_chr6.simMouse.chr6 320618 102 + 636262 CCGTGATATCCTAACAAATTTCCTTAATGAGGCAGAACAGCAACAACTATCTGGGGAGTTGGGAATGGTACTATGCATGAGGCAGAACAGCAACCACTATCT -s Anc0.Anc0refChr7 6735 50 - 16696 ATGCAATATCCCATGCAATGACATAG--------------------------------------------------ATGAG--CACACAGCAGCCACTGTTT -s Anc1.Anc1refChr4 7132 50 + 17549 ATGCAATATCCCATGCAATGACATAG--------------------------------------------------ATGAG--CACACAGCAGCCACTGTTT -s Anc2.Anc2refChr7 2185 50 + 32194 ATGCAATATCTCATGCAATGACATAG--------------------------------------------------GTGTG--CACACAGCTGCCGTTGTTC -s mr.mrrefChr5 170456 52 + 294540 CCGTGATATCCTAGCAAATTTCCTTA--------------------------------------------------ATGAGGCAGAACAGCAACCACTATCT -s simCow_chr6.simCow.chr6 297719 46 + 602619 ATGCAATATCTCATGCGATGAGATAG--------------------------------------------------GTGGG--CACTCAACTG----TGTTC -s simDog_chr6.simDog.chr6 284880 48 + 593897 ATGTGAAATCTCATGCAATGACACAG--------------------------------------------------GTGTG--AACACAGCTGCCGTGGT-- -s simHuman_chr6.simHuman.chr6 308511 50 + 601863 ATGCAATATCCCAAGCAAAGATGTGG--------------------------------------------------ATCAG--CACACAGCAGCTACTGTTT -s simRat_chr6.simRat.chr6 312223 52 + 647215 CCGTGATATCCTAGCAAGTTTCCTTA--------------------------------------------------ATGAGGCAGAACAGAAACCACTATCT - -a -s simMouse_chr6.simMouse.chr6 320720 4 + 636262 GGGG -s Anc0.Anc0refChr7 6794 4 - 16696 GAAG -s Anc1.Anc1refChr4 7191 4 + 17549 GAAG -s Anc2.Anc2refChr7 2244 4 + 32194 GAAG -s mr.mrrefChr5 170508 4 + 294540 GAAG -s simCow_chr6.simCow.chr6 297774 4 + 602619 CAAG -s simDog_chr6.simDog.chr6 284936 4 + 593897 GAAA -s simHuman_chr6.simHuman.chr6 308570 4 + 601863 GAAG -s simRat_chr6.simRat.chr6 312275 4 + 647215 GAAG - -a -s simMouse_chr6.simMouse.chr6 320724 8 + 636262 AGTTGGGA -s Anc0.Anc0refChr7 6816 8 - 16696 AGCTGGGA -s Anc1.Anc1refChr4 7213 8 + 17549 AGCTGGGA -s Anc2.Anc2refChr7 2268 8 + 32194 AGCTGAGG -s mr.mrrefChr5 170512 8 + 294540 AGTTGGGA -s simCow_chr6.simCow.chr6 297804 8 + 602619 AGCTGAGG -s simDog_chr6.simDog.chr6 284960 8 + 593897 GGCTGAGG -s simHuman_chr6.simHuman.chr6 308592 8 + 601863 AGCTGGGA -s simRat_chr6.simRat.chr6 312279 8 + 647215 ATTTGGTA - -a -s simMouse_chr6.simMouse.chr6 320732 26 + 636262 ATGGTACTATGCATAAGTGAATTCGC -s Anc0.Anc0refChr7 6824 26 - 16696 GTAATACTGTATAAAAATAAGTCTGT -s Anc1.Anc1refChr4 7221 26 + 17549 GTAATACTGTATAAAAATAAGTCTGT -s Anc2.Anc2refChr7 2278 26 + 32194 GTAATACTGTATAAAAATAAGTCTGT -s mr.mrrefChr5 170520 26 + 294540 ATGGTACTATGCATAAGTAAATCCGC -s simCow_chr6.simCow.chr6 297814 26 + 602619 GTAATACTATACAGAAATAAGTCTGT -s simDog_chr6.simDog.chr6 284970 26 + 593897 GTAATACTGTATAAAAGTAAGTTTGT -s simHuman_chr6.simHuman.chr6 308600 26 + 601863 GTAATATTCCAAAAAGATAAGTCTGT -s simRat_chr6.simRat.chr6 312287 26 + 647215 ATTGTACTGTGCATATGTAAATCAGC - -a -s simMouse_chr6.simMouse.chr6 320758 23 + 636262 ATGTAAACCAACTCAAAAACTGC -s Anc0.Anc0refChr7 6853 22 - 16696 ACGAAAACCAAGTCAAGT-CTGT -s Anc1.Anc1refChr4 7250 22 + 17549 ACGAAAACCAAGTCAAGT-CTGT -s Anc2.Anc2refChr7 2307 22 + 32194 ACGAAAATCAAGTCAAGT-CTGT -s mr.mrrefChr5 170549 23 + 294540 ATGAAAACCAACTCAAAAACTGC -s simCow_chr6.simCow.chr6 297843 22 + 602619 ATGAAATTCGAGTCAAGT-CACT -s simDog_chr6.simDog.chr6 284999 22 + 593897 ACCAAAATCAAGTCAAGT-CTGT -s simHuman_chr6.simHuman.chr6 308629 22 + 601863 AAGAAAACCCAGTCATCT-CTGT -s simRat_chr6.simRat.chr6 312316 23 + 647215 ATGAAAACCAACTCCAAAACAGC - -a -s simMouse_chr6.simMouse.chr6 320781 14 + 636262 TGCTCTAAACACCC -s Anc0.Anc0refChr7 6904 14 - 16696 TGCTCTGAAAATCA -s Anc1.Anc1refChr4 7301 14 + 17549 TGCTCTGAAAATCA -s Anc2.Anc2refChr7 2358 14 + 32194 TGATCTGAAAATCA -s mr.mrrefChr5 170595 14 + 294540 TGCTCTAAACACCC -s simCow_chr6.simCow.chr6 297891 14 + 602619 TGATCTGAAAATCA -s simHuman_chr6.simHuman.chr6 308680 14 + 601863 TGCTCTGTCACTGA -s simRat_chr6.simRat.chr6 312362 14 + 647215 TGCTCTAAACACTC - -a -s simMouse_chr6.simMouse.chr6 320795 18 + 636262 AAGTATTTAGAGGCTTCT -s Anc0.Anc0refChr7 6920 18 - 16696 ACCTATTCAGAGGTTTGT -s Anc1.Anc1refChr4 7317 18 + 17549 ACCTATTCAGAGGTTTGT -s Anc2.Anc2refChr7 2374 18 + 32194 TCCTATTCAGTGGTTTGT -s mr.mrrefChr5 170609 18 + 294540 AAGTATTTGGAGGCTTCT -s simCow_chr6.simCow.chr6 297907 18 + 602619 TCCTATTCAGTGGTTTGT -s simHuman_chr6.simHuman.chr6 308696 18 + 601863 ACTTATTCAGAAGATTGT -s simRat_chr6.simRat.chr6 312376 18 + 647215 AAGTATATGGAGGCTTCT - -a -s simMouse_chr6.simMouse.chr6 320813 3 + 636262 AGA -s Anc0.Anc0refChr7 6938 1 - 16696 A-- -s Anc1.Anc1refChr4 7335 1 + 17549 A-- -s Anc2.Anc2refChr7 2392 1 + 32194 G-- -s mr.mrrefChr5 170627 3 + 294540 AGA -s simCow_chr6.simCow.chr6 297936 1 + 602619 G-- -s simHuman_chr6.simHuman.chr6 308714 1 + 601863 A-- -s simRat_chr6.simRat.chr6 312394 3 + 647215 GGA - -a -s simMouse_chr6.simMouse.chr6 320816 90 + 636262 TGATGTATTGATCCTCAGTCAATGGCTTTTCTCTCCTACTGCTCTTTGACATGTCCCATATCATTAGACACAAACTTACTTTATGTTTAC -s Anc0.Anc0refChr7 6939 67 - 16696 --ATGTATGGATCCTCAGTCATTTGTCTACAGGTTATCTAGTTTT---------------------GAAATAAATTTACTGTATTTTTAT -s Anc1.Anc1refChr4 7336 67 + 17549 --ATGTATGGATCCTCAGTCATTTGTCTACAGGTTATCTAGTTTT---------------------GAAATAAATTTACTGTATTTTTAT -s Anc2.Anc2refChr7 2393 67 + 32194 --ATGTAGAGATTCTCAGTCATATGTCTACAGGGTATCTAGTTTA---------------------GAAATAAATTCACTGTATTTTTAT -s mr.mrrefChr5 170630 90 + 294540 TGATGTATGGATCCTCAGTCAATGGCTTTCCTCTCCTACAGCTCTTTGAAATACCCCATATCATTAGAAACAAACTTACTTTATGTTTAC -s simCow_chr6.simCow.chr6 297937 61 + 602619 --ATGTAGAGATGCTCAGTTGTGTCTCTACAGGGTATCTAGTTTA---------------------GAAACAATTTCCCCGAAT------ -s simDog_chr6.simDog.chr6 285050 50 + 593897 --------AGATTCTCAGTCACATGTCT-----------AGTTTA---------------------GGAATAAATTCACTGTATTTTTAT -s simHuman_chr6.simHuman.chr6 308715 67 + 601863 --ATGGATGGATCCTCAATCATTTGTCTGCAGGTTATCTAGTTTT---------------------GAAATAAATTTACTCCATTTTTAT -s simRat_chr6.simRat.chr6 312420 90 + 647215 TGCTGTATGGATCCTCAGTCAATGGCTTTCCTATCCTACAGCCCTTTGAAATACCCCATATCATTAGAAACAAACTCACTATATGTTGAT - -a -s simMouse_chr6.simMouse.chr6 320906 28 + 636262 TTTGCTAACCTTCTTGGCTTTAAAATCC -s Anc0.Anc0refChr7 7018 28 - 16696 CTCGCTAACCCCCCAGTGCTTATGACCT -s Anc1.Anc1refChr4 7415 28 + 17549 CTCGCTAACCCCCCAGTGCTTATGACCT -s Anc2.Anc2refChr7 2472 28 + 32194 CTCGCTAACCCCCCAGTGTTTGTGACCT -s mr.mrrefChr5 170720 28 + 294540 TTTGCTAACCTTCCAGGCCTTATGACCT -s simCow_chr6.simCow.chr6 298010 28 + 602619 GTTGCTAACCCCCTGGTGATTGGGACCT -s simDog_chr6.simDog.chr6 285112 28 + 593897 CTCGCGAACCCCCCAGTGTTTGTTACCT -s simHuman_chr6.simHuman.chr6 308794 28 + 601863 CTCGCTAACCCCCCAGCACGCATGACCT -s simRat_chr6.simRat.chr6 312510 28 + 647215 TATAGTGGCCTTCCAGTGCTTGTGGCTT - -a -s simMouse_chr6.simMouse.chr6 320934 39 + 636262 TAATGCTCTTAACATTATTTCGGAAGATGTAATACCTCA -s Anc0.Anc0refChr7 7046 19 - 16696 GAAG--TCTTACCATTA-----GA-------------CA -s Anc1.Anc1refChr4 7443 19 + 17549 GAAG--TCTTACCATTA-----GA-------------CA -s Anc2.Anc2refChr7 2500 19 + 32194 GAAG--TCTTACCATTA-----GA-------------CA -s mr.mrrefChr5 170748 37 + 294540 TAAT--TCTTAACATTATTTCGGAAGATGTAATACCTCA -s simCow_chr6.simCow.chr6 298038 19 + 602619 AAGG--TCTTGCAATTA-----GG-------------CA -s simDog_chr6.simDog.chr6 285144 17 + 593897 GAAG--TCTTACCATTG-----AA--------------- -s simHuman_chr6.simHuman.chr6 308822 19 + 601863 GAAA--GTCCTCCATTA-----GA-------------CA -s simRat_chr6.simRat.chr6 312538 37 + 647215 CAAT--CCTTAACATTATTTCGCAAGATATAATACCTCA - -a -s simMouse_chr6.simMouse.chr6 320973 88 + 636262 ACTCAATATGTATGATGTCAAATGACACCAGAGATAGCTATGCCTACTGCACTAACCTAGCAAGTCTTATAATTATAGTCAATTAGAG -s Anc0.Anc0refChr7 7065 82 - 16696 ATTCAATATCTATAATACTAAATGTCATCACACATGGCTATCCCTACCTCAGTAACTTAGTGGGTCTTATGATTACAGTTAA------ -s Anc1.Anc1refChr4 7462 82 + 17549 ATTCAATATCTATAATACTAAATGTCATCACACATGGCTATCCCTACCTCAGTAACTTAGTGGGTCTTATGATTACAGTTAA------ -s Anc2.Anc2refChr7 2519 82 + 32194 ATTCAATATCCATAATACTAAATGTCATCACACATGGCTATCCCTGCCTCAGCAACTTGGTGGGTCTTATGATTACAGTTAA------ -s mr.mrrefChr5 170785 88 + 294540 ACTCAATATGTATGATATTAAATGACATCAGAGATGGCTATGCCTACTGCACTAACCTAGTAGGTCTTATGATTATAGTCAATTAGAG -s simCow_chr6.simCow.chr6 298067 77 + 602619 ATTCAATAGCAATAGGACTAAATGTTATCACAC-----TATACCTGCTGCAGGAACGTGGTGGGTCTTATCATTACAGTCAA------ -s simDog_chr6.simDog.chr6 285161 77 + 593897 -----ACATCCATCATACTAAATGTCAATACACATGGCTAACCCTGCCTCAGCAATTAGGTGGGTCTTATGATTACAATTAA------ -s simHuman_chr6.simHuman.chr6 308841 79 + 601863 ATTCAATATCTATACTACTAAACGTCATCA---ATGGCTATCCTTACCCCAGTAACTTAGTGGGTCTTATGAATACAGTAAA------ -s simRat_chr6.simRat.chr6 312575 88 + 647215 ACCCAATATGTATGATATTAAATGACATCAGATGCGGCTATGCCTGTTGCACTAACCTAGTAGGTCTTGTGATTATGGTCAATTAGGG - -a -s simMouse_chr6.simMouse.chr6 321061 75 + 636262 CATAACATATGTCTGCCTGAAGAGTGCGTCCTTTCTGTGTATATAACAGGTTCAATGGTCACATTATGCAAGGGC -s Anc0.Anc0refChr7 7147 69 - 16696 CAT------TGACTTCCTGGCTAGTTAGTTCTCTCTTTGTACATCACAGGTCCAATGGTCACATTATGCCAGGTC -s Anc1.Anc1refChr4 7544 69 + 17549 CAT------TGACTTCCTGGCTAGTTAGTTCTCTCTTTGTACATCACAGGTCCAATGGTCACATTATGCCAGGTC -s Anc2.Anc2refChr7 2601 69 + 32194 CAT------TGAGTTGCTGGCTAGTTAGTTATCTCTTTGTACATCACAGGTCCAATGGTCACCTTATGCCAGGTC -s mr.mrrefChr5 170873 75 + 294540 CATAACATATGTCTGCCTGAAGAGTGCGTCCTTTCTGTGTACATAACAGGTCCAATGGTCACATTATGCAAGGTC -s simCow_chr6.simCow.chr6 298157 69 + 602619 CAT------TGAGTTGCTGACTTGTTAGTTTTTTCTTTGCACAAGACACGTCCAATGCTCATCTTATTCCAGGTT -s simDog_chr6.simDog.chr6 285238 59 + 593897 T---------------TTGGGTA-TGGCATATCTTTTTTTGCGTCACAGGTCCAATGGTCACCTTATGCAAGATC -s simHuman_chr6.simHuman.chr6 308920 69 + 601863 CAT------TGCCTTCCTGGCTAGTTAGTTCCCTCTCTGTACATCTCAGGTCCAATGGTCACATTATGCCAGGTC -s simRat_chr6.simRat.chr6 312663 75 + 647215 CATAGCTTATGTCTGCCTGAAGAGTGCATCCTTTCTGTGTACATAAGAGGTCTGATGGTCACATTATGCAAGGTC - -a -s simMouse_chr6.simMouse.chr6 321136 89 + 636262 AATGTATTGCAATCATCACAATGTCAATTAATGCCCACCCCAGGCTGCTCCTAACTTTACACTTTCAACCATGTTAAGTACAATAATAG -s Anc0.Anc0refChr7 7216 89 - 16696 AGTGTCTTACTATAGCCAAATTGTCGATTATGGCCCAGCTCAGGCCAAGCATTAACTAACACTGATAAACATGATAAGTACAATGACAG -s Anc1.Anc1refChr4 7613 89 + 17549 AGTGTCTTACTATAGCCAAATTGTCGATTATGGCCCAGCTCAGGCCAAGCATTAACTAACACTGATAAACATGATAAGTACAATGACAG -s Anc2.Anc2refChr7 2670 89 + 32194 AGTGTCTTACTATAGCCAAATTGTCGGTTGTGGCCTAGCTCAGGCCAAGCATTAACTAACATTGATAAACATGATAAGTACAATGACAG -s mr.mrrefChr5 170948 89 + 294540 AATGTATTACAATCATCACAATGTCAATTAATGCCCACCCCAGGCTGCTCCTAACTTAACACTTTTAACCATGATAAGTACAATAATAG -s simCow_chr6.simCow.chr6 298226 89 + 602619 AGTGTCTTAGTATAGCCAAGTTGTCAGTTGTAGCCTGGCTCAAGGCAAGCACTAACTAACATTGATAAACATTGTAACTAAATTGATAT -s simDog_chr6.simDog.chr6 285297 89 + 593897 AGTGTCTCACTATGGCTGAATTGTTGGTTGTGGCCTAGCTCGGGCCAAGTATTAACTAAACTTGATGCATATGATCAGTACAATGACAG -s simHuman_chr6.simHuman.chr6 308989 89 + 601863 AGTGTCTTACTATAGCCAGATTGTCCATTAGGGCCCAGCTTAGGTCAGGCATTAAATAACACTAATAAACATGATAAGTGCAATGACAG -s simRat_chr6.simRat.chr6 312740 89 + 647215 ATTGTATGACAATCATCAAAATGTCAATTGAAGCCCACCCCAGGCTGATCCTAACTTAACACTTTTAACCATGAGAAGAACAATCATAT - -a -s simMouse_chr6.simMouse.chr6 321225 30 + 636262 CCCAGATGTTTAGGGGACCTGGTAGCGGGG -s Anc0.Anc0refChr7 7309 27 - 16696 CTCAGATATTCAAGGGA-CTAG--GTGGGG -s Anc1.Anc1refChr4 7706 28 + 17549 CTCAGATATTCAAGGGACCTAG--GTGGGG -s Anc2.Anc2refChr7 2763 27 + 32194 CTCAGATATTCAAGGGA-CTAG--GTGGGG -s mr.mrrefChr5 171037 30 + 294540 CCCAGATATTTAGGGGACCTGGTAGTGGGG -s simCow_chr6.simCow.chr6 298319 23 + 602619 TTATGATATTCAAGGGA-CTTG--GT---- -s simDog_chr6.simDog.chr6 285390 26 + 593897 C-CAGATATTCAGGGGA-CTAG--GTGGGG -s simHuman_chr6.simHuman.chr6 309082 28 + 601863 CTCAGATATTCAAGGGATCTCG--GTGATG -s simRat_chr6.simRat.chr6 312829 30 + 647215 TACAGACATGTAGGGAACCTGAGAGTGGGG - -a -s simMouse_chr6.simMouse.chr6 321255 13 + 636262 AACACCTGAAAAT -s Anc0.Anc0refChr7 7336 13 - 16696 GACACCTGAAATC -s Anc1.Anc1refChr4 7734 13 + 17549 GACACCTGAAATC -s Anc2.Anc2refChr7 2790 13 + 32194 GTCGCCTGAAATC -s mr.mrrefChr5 171067 13 + 294540 AACACCTGAAAAT -s simCow_chr6.simCow.chr6 298342 9 + 602619 ----CCTGAAACC -s simDog_chr6.simDog.chr6 285419 13 + 593897 GTCGCCTGAAATC -s simHuman_chr6.simHuman.chr6 309110 13 + 601863 GACACCAGAAATC -s simRat_chr6.simRat.chr6 312859 13 + 647215 AACACCTGAAAGT - -a -s simMouse_chr6.simMouse.chr6 321268 11 + 636262 GTCAGCCCATG -s Anc0.Anc0refChr7 7349 10 - 16696 CCAAGCC-ATA -s Anc1.Anc1refChr4 7747 10 + 17549 CCAAGCC-ATA -s Anc2.Anc2refChr7 2803 10 + 32194 CCAAGTC-ATA -s mr.mrrefChr5 171080 11 + 294540 GCAAGCCCATA -s simCow_chr6.simCow.chr6 298351 10 + 602619 GCAAGTC-ATA -s simDog_chr6.simDog.chr6 285436 10 + 593897 CCAAGTC-ATA -s simHuman_chr6.simHuman.chr6 309123 10 + 601863 TCAAGCC-ATA -s simRat_chr6.simRat.chr6 312872 11 + 647215 GCAAGTCCATA - -a -s simMouse_chr6.simMouse.chr6 321279 24 + 636262 CTAATATGATCCCATGATATCAGC -s Anc0.Anc0refChr7 7437 24 - 16696 TTAATGTGGCCCCACACAATCAGC -s Anc1.Anc1refChr4 7836 24 + 17549 TTAATGTGGCCCCACACAATCAGC -s Anc2.Anc2refChr7 2891 24 + 32194 TTAATGTGGCCCCACACAATCAGC -s mr.mrrefChr5 171091 24 + 294540 CTAATATGATCCCACACTATCAGC -s simCow_chr6.simCow.chr6 298436 24 + 602619 TTAGTTTGGCCCCACACAATCAGC -s simDog_chr6.simDog.chr6 285528 24 + 593897 TTAATGTTGCCCCACATAATCAGC -s simHuman_chr6.simHuman.chr6 309228 24 + 601863 TTAATGTGGCCACGCACAATCAGC -s simRat_chr6.simRat.chr6 312883 24 + 647215 CTAATATGATTCCACACCATCAGC - -a -s simMouse_chr6.simMouse.chr6 321303 17 + 636262 AGGCAAAGGGATGTGGC -s Anc0.Anc0refChr7 7461 17 - 16696 AGGGAAAGAGATGTGAC -s Anc1.Anc1refChr4 7860 17 + 17549 AGGGAAAGAGATGTGAC -s Anc2.Anc2refChr7 2915 17 + 32194 AGGGAAAGAGATGAGAC -s mr.mrrefChr5 171115 17 + 294540 AGGCAAAGAGATGTGGC -s simCow_chr6.simCow.chr6 298460 17 + 602619 AGAGAAAGAATTGAGAC -s simDog_chr6.simDog.chr6 285552 17 + 593897 AGGAAAAGGGATGAGAC -s simHuman_chr6.simHuman.chr6 309252 17 + 601863 AGGGAAACAGATGTTAC -s simRat_chr6.simRat.chr6 312946 17 + 647215 AGGAAAAGAGATGTGGC - -a -s simMouse_chr6.simMouse.chr6 321320 1 + 636262 A -s Anc0.Anc0refChr7 7478 1 - 16696 A -s Anc1.Anc1refChr4 7877 1 + 17549 A -s Anc2.Anc2refChr7 2932 1 + 32194 A -s mr.mrrefChr5 171132 1 + 294540 A -s simCow_chr6.simCow.chr6 298794 1 + 602619 G -s simDog_chr6.simDog.chr6 307407 1 - 593897 A -s simHuman_chr6.simHuman.chr6 309269 1 + 601863 T -s simRat_chr6.simRat.chr6 312963 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 321321 6 + 636262 CATGTG -s Anc0.Anc0refChr7 7479 6 - 16696 CAGTTA -s Anc1.Anc1refChr4 7878 6 + 17549 CAGTTA -s Anc2.Anc2refChr7 2933 6 + 32194 CAGATA -s mr.mrrefChr5 171133 6 + 294540 CATTTG -s simCow_chr6.simCow.chr6 298803 6 + 602619 CGCCAC -s simDog_chr6.simDog.chr6 307408 6 - 593897 CAGATA -s simHuman_chr6.simHuman.chr6 309270 6 + 601863 CAATCA -s simRat_chr6.simRat.chr6 312964 6 + 647215 CCTTTG - -a -s simMouse_chr6.simMouse.chr6 321327 9 + 636262 ACAACAAGA -s Anc0.Anc0refChr7 7485 9 - 16696 AGAAGAACA -s Anc1.Anc1refChr4 7884 9 + 17549 AGAAGAACA -s Anc2.Anc2refChr7 2941 9 + 32194 AGAAGAACA -s mr.mrrefChr5 171139 9 + 294540 ACAACAAGA -s simCow_chr6.simCow.chr6 298821 9 + 602619 AGAAGAACA -s simHuman_chr6.simHuman.chr6 309276 9 + 601863 AGAAGAACA -s simRat_chr6.simRat.chr6 312970 9 + 647215 ACAACAAGA - -a -s simMouse_chr6.simMouse.chr6 321336 13 + 636262 TGCATCAAAATGC -s Anc0.Anc0refChr7 7494 13 - 16696 TGGAAAAAAATGC -s Anc1.Anc1refChr4 7893 13 + 17549 TGGAAAAAAATGC -s Anc2.Anc2refChr7 2950 13 + 32194 TGGGAAAAAGTGC -s mr.mrrefChr5 171148 13 + 294540 TGCATCAAAATGC -s simCow_chr6.simCow.chr6 298830 13 + 602619 TGGGAAAAAGTGC -s simCow_chr6.simCow.chr6 299593 13 + 602619 TGGGAAAAAGTGC -s simHuman_chr6.simHuman.chr6 309285 13 + 601863 TGAAAAACAATGC -s simRat_chr6.simRat.chr6 312979 13 + 647215 TGCATCAACATGC - -a -s simMouse_chr6.simMouse.chr6 321349 23 + 636262 CTCATGTCTCTGGAAGTTCCACT -s Anc0.Anc0refChr7 7507 23 - 16696 CTCATGACTAGGGCAGTCCCACT -s Anc1.Anc1refChr4 7906 23 + 17549 CTCATGACTAGGGCAGTCCCACT -s Anc2.Anc2refChr7 2963 23 + 32194 CTCTTGACTAGGACTGGTCCACT -s mr.mrrefChr5 171161 23 + 294540 CTCATGTCTCGGGAAGTCCCACT -s simCow_chr6.simCow.chr6 298849 23 + 602619 CTCTTGACTAGGACTGGTTTACT -s simCow_chr6.simCow.chr6 299606 23 + 602619 CTCTTAACTGTGACTGGTCCACT -s simHuman_chr6.simHuman.chr6 309298 23 + 601863 CTCATGACTAGGGCAGTCCCACT -s simRat_chr6.simRat.chr6 312992 23 + 647215 CTCATGTCTTGAAGAGTCCCCCT - -a -s simMouse_chr6.simMouse.chr6 321372 17 + 636262 TTATGATTAAGGTCCAG -s Anc0.Anc0refChr7 7530 17 - 16696 CCACGACTAAGGTTCAG -s Anc1.Anc1refChr4 7929 17 + 17549 CCACGACTAAGGTTCAG -s Anc2.Anc2refChr7 2986 17 + 32194 CCACTACAAAGGTTCAG -s mr.mrrefChr5 171184 17 + 294540 TCATGATTAAGGTCCAG -s simCow_chr6.simCow.chr6 298873 17 + 602619 CCACTACATAGGCTCAG -s simCow_chr6.simCow.chr6 299629 17 + 602619 CCACTCCAAAGGCTCAG -s simDog_chr6.simDog.chr6 307416 11 - 593897 ------TAAAGGTTCAA -s simHuman_chr6.simHuman.chr6 309321 17 + 601863 CCAGGACTAAGGTTCAG -s simRat_chr6.simRat.chr6 313015 17 + 647215 TCATGATTAAGGTCCAG - -a -s simMouse_chr6.simMouse.chr6 321389 77 + 636262 GGGGCAAGGTCACAAGAAAACAGGCTGCTGTGCTTGGGCACCCCTCCATGTCGGGATTATAACCCCTGTCTATGTCT -s Anc0.Anc0refChr7 7550 77 - 16696 GAAGCAAGGTCTCAAGAAAATAGGCTGTGATATCTGAGCACCCCTCCATGTGGGAATTAACACCCTTGTCTATAGTC -s Anc1.Anc1refChr4 7949 77 + 17549 GAAGCAAGGTCTCAAGAAAATAGGCTGTGATATCTGAGCACCCCTCCATGTGGGAATTAACACCCTTGTCTATAGTC -s Anc2.Anc2refChr7 3006 77 + 32194 GAAGCAAGGTCTAAAGAAAATAGGCTGTGATATCTGAGCACCCCTCCATGTGGGAATTAACACCCTTGTCTATAGTC -s mr.mrrefChr5 171201 77 + 294540 GAGGCAAGGTCTCAAGAAAACAGGCTGCTGTGCTTGAGCACCCCTCCATGTGGGGATTATAACCCTTGTCTATGTCC -s simCow_chr6.simCow.chr6 298893 71 + 602619 GAAGCAAGATCCAAAGATAATAGG-TGTGATATCTGAGCACTGCTCCGTGTGGG-----TCACCCTTGTCTATAGTT -s simCow_chr6.simCow.chr6 299649 57 + 602619 GAAGCAAGGTCCAATGATAATG---------------GCATCACTCCATGTGGG-----CCACCCTTGTCTATAGTC -s simDog_chr6.simDog.chr6 307430 71 - 593897 GAAGCAAGGTCTGGAGAAAATAAGCTGTGATATTTGCGCACCCGTCCATGTAGGAATTAACACCCTTGTCT------ -s simHuman_chr6.simHuman.chr6 309341 77 + 601863 GAAGCGAGGTCTCAAGTAAATAGGCAGTGATATCTGAGGACCCCTCCATGTGGGAATTAACACTCTTGTCTATAGTC -s simRat_chr6.simRat.chr6 313032 76 + 647215 AAGGCAAGGTCTTAAGAAAAAAGGCTGATGGGCTTGAGCACCCCTCCATGTGGGGATTATAACACTTGTCTATG-CC - -a -s simMouse_chr6.simMouse.chr6 321466 10 + 636262 AGACAAGTCT -s Anc0.Anc0refChr7 7627 9 - 16696 AGA-ATAATG -s Anc1.Anc1refChr4 8026 9 + 17549 AGA-ATAATG -s Anc2.Anc2refChr7 3090 9 + 32194 AGA-ATAATG -s mr.mrrefChr5 171278 9 + 294540 AGA-ATGTCG -s simCow_chr6.simCow.chr6 298971 9 + 602619 AGA-ATAATG -s simCow_chr6.simCow.chr6 299713 9 + 602619 AGA-ATAATG -s simDog_chr6.simDog.chr6 307507 9 - 593897 AGA-ATAATG -s simHuman_chr6.simHuman.chr6 309418 9 + 601863 AGG-ATAATG -s simRat_chr6.simRat.chr6 313108 9 + 647215 AGA-ATGTAG - -a -s simMouse_chr6.simMouse.chr6 321476 2 + 636262 AG -s Anc0.Anc0refChr7 7636 2 - 16696 AG -s Anc1.Anc1refChr4 8035 2 + 17549 AG -s Anc2.Anc2refChr7 3100 2 + 32194 AG -s mr.mrrefChr5 171287 2 + 294540 AG -s simCow_chr6.simCow.chr6 298981 2 + 602619 TA -s simCow_chr6.simCow.chr6 299723 2 + 602619 AA -s simDog_chr6.simDog.chr6 307517 2 - 593897 AG -s simHuman_chr6.simHuman.chr6 309427 2 + 601863 AG -s simRat_chr6.simRat.chr6 313117 2 + 647215 AA - -a -s simMouse_chr6.simMouse.chr6 321478 48 + 636262 ACAAAACCTGGCCAATGTCAATGTCCTGAAAGACCATACAGCCTCATG -s Anc0.Anc0refChr7 7643 48 - 16696 ACTAAGCCTGGCCAATGTCACCATCCAAAAAGGCAGTATAGCCTTAGG -s Anc1.Anc1refChr4 8042 48 + 17549 ACTAAGCCTGGCCAATGTCACCATCCAAAAAGGCAGTATAGCCTTAGG -s Anc2.Anc2refChr7 3107 48 + 32194 ACTAAGCCTGGCCAATGACACCATCCAAAACAGCAGTATAGCCTTAGG -s mr.mrrefChr5 171289 48 + 294540 ACAAAACCTGGCCAATGTCAATGTCCTGAAAGACCATACAGCCTCATG -s simCow_chr6.simCow.chr6 298988 48 + 602619 ACTAAGCCTGGCTAATTACACTATCCAAAACAGCATTATAGCTTTAGG -s simCow_chr6.simCow.chr6 299730 42 + 602619 ACTAAGCCTGGCTGTT------ATCCAAAACGGCAGTATAGCGTTAGG -s simDog_chr6.simDog.chr6 307524 48 - 593897 ACTAAACCTGGCCAATGACACCATCCAAAACAGCCATATAGGCTCAAG -s simHuman_chr6.simHuman.chr6 309434 48 + 601863 ACTAAGCCTGGCCGGTGTCACCATCCAAAAAGCCTGCATGGCCTTAGG -s simRat_chr6.simRat.chr6 313119 48 + 647215 ACAAAACCTGGCCAATGTCAATGTCCTGAAAAACCCTACTGCCTCATG - -a -s simMouse_chr6.simMouse.chr6 321526 26 + 636262 TGAGGTATCACTGGCATGATGAGGTT -s Anc0.Anc0refChr7 7725 26 - 16696 TGAGTTCTCACTTGAAAGATAAGATT -s Anc1.Anc1refChr4 8124 26 + 17549 TGAGTTCTCACTTGAAAGATAAGATT -s Anc2.Anc2refChr7 3198 26 + 32194 TGAGTTCCCACTTGAAAGAGAAGATT -s mr.mrrefChr5 171338 26 + 294540 TGAGGTATCACTGGCAAGATGAGGTT -s simCow_chr6.simCow.chr6 299067 26 + 602619 TGAGCTCCCACTTGAAGCAAAAGATT -s simCow_chr6.simCow.chr6 299939 26 + 602619 TGAGTTCCCACTTGAAAGAGAAGATT -s simDog_chr6.simDog.chr6 307614 20 - 593897 TGAGTTCC------AAAAAGCAGATT -s simHuman_chr6.simHuman.chr6 309516 26 + 601863 TGACTTCTCACCTGTAAGATAAGATT -s simRat_chr6.simRat.chr6 313168 26 + 647215 TGAGATATCACTAGCAAGATGAGGTC - -a -s simMouse_chr6.simMouse.chr6 321552 32 + 636262 GGCAATCTTCACTTTGGACTGTGATTGGGTAC -s Anc0.Anc0refChr7 7752 32 - 16696 GGCAGTACTCGCTTTGCACTGTGGTTGGGCCT -s Anc1.Anc1refChr4 8151 32 + 17549 GGCAGTACTCGCTTTGCACTGTGGTTGGGCCT -s Anc2.Anc2refChr7 3225 32 + 32194 GGCAGTACTTGCTTTGTACTGTGGTTGGGCCT -s mr.mrrefChr5 171365 32 + 294540 GGCAATCTTCACTTTGCACTGTGGTTGGGTAT -s simCow_chr6.simCow.chr6 299094 32 + 602619 GGCAGTACTTACTTTGTACTGTGGTTGGGCCT -s simCow_chr6.simCow.chr6 299966 30 + 602619 GTCAGTACTTGCTTCGTAATGTGGCTGTGC-- -s simDog_chr6.simDog.chr6 307635 32 - 593897 GGCAGTACTTGCCTTGTACTATGGTTGGGCCT -s simHuman_chr6.simHuman.chr6 309543 31 + 601863 GGCAGTACTCGCAT-ACACTGTGGATGGGCCT -s simRat_chr6.simRat.chr6 313195 32 + 647215 GGCAATCTTCACTGTGCACTGTGGTTACGTAT - -a -s simMouse_chr6.simMouse.chr6 321584 1 + 636262 C -s Anc0.Anc0refChr7 7784 1 - 16696 C -s Anc1.Anc1refChr4 8183 1 + 17549 C -s Anc2.Anc2refChr7 3257 1 + 32194 C -s mr.mrrefChr5 171397 1 + 294540 C -s simCow_chr6.simCow.chr6 299996 1 + 602619 C -s simDog_chr6.simDog.chr6 307667 1 - 593897 C -s simHuman_chr6.simHuman.chr6 309574 1 + 601863 C -s simRat_chr6.simRat.chr6 313227 1 + 647215 G - -a -s simMouse_chr6.simMouse.chr6 321585 20 + 636262 TTTTTATGACTTAGCCCTCA -s Anc0.Anc0refChr7 7785 20 - 16696 TGTTTATGACTTAGCCCTCA -s Anc1.Anc1refChr4 8184 20 + 17549 TGTTTATGACTTAGCCCTCA -s Anc2.Anc2refChr7 3258 20 + 32194 TGTTTATGACTTAGCCCTCA -s mr.mrrefChr5 171398 20 + 294540 TTTTTATGACTTAGCCCTCA -s simCow_chr6.simCow.chr6 299126 20 + 602619 TGTTTATGACTTAGCCCTCA -s simCow_chr6.simCow.chr6 299997 20 + 602619 CATTTATGACTTAGCCTTTA -s simDog_chr6.simDog.chr6 307668 20 - 593897 TGTTTATGTCTTAGCCCTCA -s simHuman_chr6.simHuman.chr6 309575 20 + 601863 TGTTTATGACTTAGCCCTCA -s simRat_chr6.simRat.chr6 313228 20 + 647215 TCTTTATGACCTAACCCTCA - -a -s simMouse_chr6.simMouse.chr6 321605 1 + 636262 A -s Anc0.Anc0refChr7 7805 1 - 16696 A -s Anc1.Anc1refChr4 8204 1 + 17549 A -s Anc2.Anc2refChr7 3278 1 + 32194 A -s mr.mrrefChr5 171418 1 + 294540 A -s simCow_chr6.simCow.chr6 299158 1 + 602619 A -s simCow_chr6.simCow.chr6 300017 1 + 602619 A -s simDog_chr6.simDog.chr6 307688 1 - 593897 A -s simHuman_chr6.simHuman.chr6 309595 1 + 601863 A -s simRat_chr6.simRat.chr6 313248 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 321606 1 + 636262 T -s Anc0.Anc0refChr7 7806 1 - 16696 T -s Anc1.Anc1refChr4 8205 1 + 17549 T -s Anc2.Anc2refChr7 3279 1 + 32194 T -s mr.mrrefChr5 171419 1 + 294540 T -s simCow_chr6.simCow.chr6 299159 1 + 602619 T -s simCow_chr6.simCow.chr6 300025 1 + 602619 T -s simDog_chr6.simDog.chr6 307689 1 - 593897 T -s simHuman_chr6.simHuman.chr6 309596 1 + 601863 T -s simRat_chr6.simRat.chr6 313249 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 321607 18 + 636262 CTTGACAACCCTAGTCAC -s Anc0.Anc0refChr7 7815 18 - 16696 CTTGACAACCCTATTTCC -s Anc1.Anc1refChr4 8214 18 + 17549 CTTGACAACCCTATTTCC -s Anc2.Anc2refChr7 3288 18 + 32194 CTTGACAACCCTATTTCC -s mr.mrrefChr5 171420 18 + 294540 CTTGACAACCCTAGTTAC -s simCow_chr6.simCow.chr6 299168 18 + 602619 ATTTACAATCTTGTTTAC -s simCow_chr6.simCow.chr6 300034 10 + 602619 CTTGACAACC-------- -s simDog_chr6.simDog.chr6 307698 18 - 593897 CTTGACAACCCCATTTCC -s simHuman_chr6.simHuman.chr6 309605 18 + 601863 CTTGACAACCGTATTTTC -s simRat_chr6.simRat.chr6 313250 18 + 647215 CTTTACAACCCTAGTTAC - -a -s simMouse_chr6.simMouse.chr6 321625 26 + 636262 TGCACTGCCTTAACTATAACCCTTTA -s Anc0.Anc0refChr7 7833 26 - 16696 TGCTCCATCTTGACTATAATCCTCTA -s Anc1.Anc1refChr4 8232 26 + 17549 TGCTCCATCTTGACTATAATCCTCTA -s Anc2.Anc2refChr7 3306 26 + 32194 TCTTCCATCTTGACTATAATCCTCAA -s mr.mrrefChr5 171438 26 + 294540 TGCACCACCTTAACTATAATCCTTTA -s simCow_chr6.simCow.chr6 299186 26 + 602619 TATTCCAACTTGACTATAATGCTACA -s simDog_chr6.simDog.chr6 307716 26 - 593897 TCTTCTATCTCAACTATAATCCTCAA -s simHuman_chr6.simHuman.chr6 309623 24 + 601863 TGCTCCAA--TGACAATAATTCTCTA -s simRat_chr6.simRat.chr6 313279 26 + 647215 TGCCCCACCCTAACTAGAATGCTTTA - -a -s simMouse_chr6.simMouse.chr6 321651 5 + 636262 CCCCG -s Anc0.Anc0refChr7 7870 5 - 16696 TCCAG -s Anc1.Anc1refChr4 8269 5 + 17549 TCCAG -s Anc2.Anc2refChr7 3343 5 + 32194 GCCAG -s mr.mrrefChr5 171464 5 + 294540 TCCCG -s simCow_chr6.simCow.chr6 299223 5 + 602619 GCCAG -s simDog_chr6.simDog.chr6 307753 5 - 593897 GCTGG -s simHuman_chr6.simHuman.chr6 309658 5 + 601863 TCCAG -s simRat_chr6.simRat.chr6 313305 3 + 647215 TCC-- - -a -s simMouse_chr6.simMouse.chr6 321656 15 + 636262 CTAGGATTGCATTAA -s Anc0.Anc0refChr7 7884 14 - 16696 CTATAGT-GCCATAC -s Anc1.Anc1refChr4 8283 14 + 17549 CTATAGT-GCCATAC -s Anc2.Anc2refChr7 3357 14 + 32194 CTATAGT-ACCATAC -s mr.mrrefChr5 171469 15 + 294540 CTATGATTGCATTAA -s simCow_chr6.simCow.chr6 299237 14 + 602619 TTATGGT-ACCATAC -s simDog_chr6.simDog.chr6 307767 14 - 593897 CTATAAT-ACCACAC -s simHuman_chr6.simHuman.chr6 309672 14 + 601863 CTACAGT-GCCCTAC -s simRat_chr6.simRat.chr6 313308 14 + 647215 CTATGATTGCA-TAA - -a -s simMouse_chr6.simMouse.chr6 321671 15 + 636262 AGCTGAACCCTTCAG -s Anc0.Anc0refChr7 7900 15 - 16696 AGCTGGCCCCTTCCA -s Anc1.Anc1refChr4 8299 15 + 17549 AGCTGGCCCCTTCCA -s Anc2.Anc2refChr7 3373 15 + 32194 AGCTGGCACCTTCCA -s mr.mrrefChr5 171484 15 + 294540 AGCTGAACCCTTCAG -s simCow_chr6.simCow.chr6 299253 15 + 602619 AGCTGGTGCCATACA -s simDog_chr6.simDog.chr6 307783 15 - 593897 AACTGGCACTTTCCA -s simHuman_chr6.simHuman.chr6 309688 15 + 601863 AGCTGGCCCCTTCCA -s simRat_chr6.simRat.chr6 313322 14 + 647215 AACTGAA-CCTTCAG - -a -s simMouse_chr6.simMouse.chr6 321686 3 + 636262 ACC -s Anc0.Anc0refChr7 7917 3 - 16696 GCC -s Anc1.Anc1refChr4 8316 3 + 17549 GCC -s Anc2.Anc2refChr7 3390 3 + 32194 GCA -s mr.mrrefChr5 171501 3 + 294540 ACC -s simCow_chr6.simCow.chr6 299270 3 + 602619 TCA -s simDog_chr6.simDog.chr6 307800 3 - 593897 GCA -s simHuman_chr6.simHuman.chr6 309705 3 + 601863 CCC -s simRat_chr6.simRat.chr6 313339 3 + 647215 ACC - -a -s simMouse_chr6.simMouse.chr6 321689 7 + 636262 CAATATG -s Anc0.Anc0refChr7 7922 7 - 16696 CATTCTG -s Anc1.Anc1refChr4 8321 7 + 17549 CATTCTG -s Anc2.Anc2refChr7 3395 7 + 32194 TATTCTG -s mr.mrrefChr5 171504 7 + 294540 CAATATG -s simCow_chr6.simCow.chr6 299275 7 + 602619 TATTCTG -s simDog_chr6.simDog.chr6 307805 1 - 593897 T------ -s simHuman_chr6.simHuman.chr6 309710 7 + 601863 CATTTTG -s simRat_chr6.simRat.chr6 313342 7 + 647215 CAACATG - -a -s simMouse_chr6.simMouse.chr6 321696 85 + 636262 TAACAGCCCTCACCTTGATTTGGCAAGGAGAGTGCATATAAGCCCTTAGTACCATGATTCTCCAATGAATGGGAGAGTAATAAGT -s Anc0.Anc0refChr7 7930 85 - 16696 TACTATCCCCCACCTTGATCTGACAGCAAGCATGTATAAAAGCTCTCTGTCCCATGATTCTCCAATGAATAGAAGAGTAATAACA -s Anc1.Anc1refChr4 8329 85 + 17549 TACTATCCCCCACCTTGATCTGACAGCAAGCATGTATAAAAGCTCTCTGTCCCATGATTCTCCAATGAATAGAAGAGTAATAACA -s Anc2.Anc2refChr7 3403 85 + 32194 TACTATCCCCCACCTTGATCTGACAGCAAGCATGTATGAAAGCTCTCTATCCCATTATTCTCCGATGAATAAAAGAGGCATAACA -s mr.mrrefChr5 171511 85 + 294540 TAGTAGCCCTCACCTTGATTTGGCAAGGAGAATGCATATAAGCCCTTAGTACCATGATTCTCCAATGAATAGGAGAGTAATAAGT -s simCow_chr6.simCow.chr6 299283 79 + 602619 TACTATCTCACACCTTGATCTCATGGTAAGCACGTATGAAAGCTCTCTATCTCATTATCCTCCAATGAATAAA------ATAGTG -s simCow_chr6.simCow.chr6 299411 76 + 602619 ---TATCTCCCGCTTTGATCTGACAGCAAGCAAGTATGCAAGCTCTAAATCCCATTATTCTCCGAAGAATGAA------ATAAGG -s simDog_chr6.simDog.chr6 307807 85 - 593897 CAATATTCTCCACCTTGATCAGACAGCAAGCATGTATGAAAGCTCTCTATCCCATTATTCTCTGATGAACTAAAGAGGCATAACA -s simHuman_chr6.simHuman.chr6 309718 85 + 601863 TGCTACCCCCTACCTGGATCTGACAGTAAGCATGTATAAAAGGTCTCTGTCCCATGATTCTCCAATGAATAGAAGAGTAATAAAA -s simRat_chr6.simRat.chr6 313349 84 + 647215 TAGTAAAACTCACCTTGACTTGGC-AGTAGAATGCATATAATCCCTTAGTGCCATGATTCTCCAATGAATAGGACAGTAATAAGT - -a -s simMouse_chr6.simMouse.chr6 321781 8 + 636262 CAAGAACC -s Anc0.Anc0refChr7 8015 8 - 16696 CAAGTGCC -s Anc1.Anc1refChr4 8414 8 + 17549 CAAGTGCC -s Anc2.Anc2refChr7 3488 8 + 32194 CAAGTGCC -s mr.mrrefChr5 171596 8 + 294540 CAAGAACC -s simCow_chr6.simCow.chr6 299487 8 + 602619 CAAGTATC -s simDog_chr6.simDog.chr6 307892 8 - 593897 CAGGTGCC -s simHuman_chr6.simHuman.chr6 309803 8 + 601863 CAAATGCC -s simRat_chr6.simRat.chr6 313433 8 + 647215 CAGGAACC - -a -s simMouse_chr6.simMouse.chr6 321789 10 + 636262 TGAAGATTCA -s Anc0.Anc0refChr7 8026 10 - 16696 TGAACATTTT -s Anc1.Anc1refChr4 8425 10 + 17549 TGAACATTTT -s Anc2.Anc2refChr7 3499 10 + 32194 CAAACATTTT -s mr.mrrefChr5 171604 10 + 294540 TGAACATTCA -s simCow_chr6.simCow.chr6 299498 10 + 602619 CAAACATTTA -s simDog_chr6.simDog.chr6 307903 10 - 593897 CAAACATTTT -s simHuman_chr6.simHuman.chr6 309814 9 + 601863 TGGACATT-G -s simRat_chr6.simRat.chr6 313441 10 + 647215 TGAACATTCA - -a -s simMouse_chr6.simMouse.chr6 321799 27 + 636262 TATATGGCTTTTGGGAACTCCAGGGTC -s Anc0.Anc0refChr7 8036 27 - 16696 TAAATGGCTTGTGTGACCCCCGGGGTC -s Anc1.Anc1refChr4 8435 27 + 17549 TAAATGGCTTGTGTGACCCCCGGGGTC -s Anc2.Anc2refChr7 3509 27 + 32194 TAAATGGCTTGTGTGACCCCCGGGGTC -s mr.mrrefChr5 171614 27 + 294540 TATATGGCTTTTGGGAACCCCAGGGTC -s simCow_chr6.simCow.chr6 299508 27 + 602619 TAAATGGCTTTCATGACCACTGGGGAC -s simDog_chr6.simDog.chr6 307913 27 - 593897 TAAATGGCTTGTGTGACCCCCAGGGTG -s simHuman_chr6.simHuman.chr6 309823 23 + 601863 TAAATGGC----GAGGTCCCCGGGTTC -s simRat_chr6.simRat.chr6 313463 27 + 647215 TATATGGCTTTCGTGAACCCCAGGGTC - -a -s simMouse_chr6.simMouse.chr6 321826 10 + 636262 TAAGCTCATC -s Anc0.Anc0refChr7 8063 10 - 16696 TGGATTCATT -s Anc1.Anc1refChr4 8462 10 + 17549 TGGATTCATT -s Anc2.Anc2refChr7 3536 10 + 32194 TGGATTCAAT -s mr.mrrefChr5 171641 10 + 294540 TAAGTTCATT -s simCow_chr6.simCow.chr6 299535 8 + 602619 GGGATTGA-- -s simCow_chr6.simCow.chr6 300044 8 + 602619 CTGTTTCC-- -s simDog_chr6.simDog.chr6 307940 10 - 593897 TGAATTCAAT -s simHuman_chr6.simHuman.chr6 309847 10 + 601863 TCGATTCCTT -s simRat_chr6.simRat.chr6 313490 10 + 647215 TAAGTTCATT - -a -s simMouse_chr6.simMouse.chr6 321836 3 + 636262 GAG -s Anc0.Anc0refChr7 8073 3 - 16696 GAG -s Anc1.Anc1refChr4 8472 3 + 17549 GAG -s Anc2.Anc2refChr7 3546 3 + 32194 GAG -s mr.mrrefChr5 171651 3 + 294540 GAG -s simCow_chr6.simCow.chr6 300052 3 + 602619 AAG -s simDog_chr6.simDog.chr6 307950 3 - 593897 GAG -s simHuman_chr6.simHuman.chr6 309857 3 + 601863 GAG -s simRat_chr6.simRat.chr6 313500 3 + 647215 AAG - -a -s simMouse_chr6.simMouse.chr6 321839 18 + 636262 TTACAGGATCACAATAGA -s Anc0.Anc0refChr7 8076 18 - 16696 CTGCAGGGTAACAATAGA -s Anc1.Anc1refChr4 8475 18 + 17549 CTGCAGGGTAACAATAGA -s Anc2.Anc2refChr7 3549 18 + 32194 CTGCAGGGTAACAATAGA -s mr.mrrefChr5 171654 18 + 294540 CTACAGGGTCACAATAGA -s simCow_chr6.simCow.chr6 299543 18 + 602619 CTGTAGGGTAACAGCAGA -s simCow_chr6.simCow.chr6 300055 18 + 602619 CTGGAGGGTAACAATGGA -s simDog_chr6.simDog.chr6 307953 18 - 593897 CTGCAGGACAGCAATAGA -s simHuman_chr6.simHuman.chr6 309860 18 + 601863 CAGCAGGGTAACAATAGA -s simRat_chr6.simRat.chr6 313503 18 + 647215 CTACAGGGTCACAATAGA - -a -s simMouse_chr6.simMouse.chr6 321857 4 + 636262 GGAT -s Anc0.Anc0refChr7 8094 4 - 16696 TACT -s Anc1.Anc1refChr4 8493 4 + 17549 TACT -s Anc2.Anc2refChr7 3567 4 + 32194 TACT -s mr.mrrefChr5 171672 4 + 294540 GACT -s simCow_chr6.simCow.chr6 300073 4 + 602619 TATT -s simDog_chr6.simDog.chr6 307971 4 - 593897 TACT -s simHuman_chr6.simHuman.chr6 309878 4 + 601863 TACG -s simRat_chr6.simRat.chr6 313521 4 + 647215 GACT - -a -s simMouse_chr6.simMouse.chr6 321861 7 + 636262 ATTGAGT -s Anc0.Anc0refChr7 8098 7 - 16696 ATTGGGT -s Anc1.Anc1refChr4 8497 7 + 17549 ATTGGGT -s Anc2.Anc2refChr7 3571 7 + 32194 ATTGGGT -s mr.mrrefChr5 171676 7 + 294540 ATTGAGT -s simCow_chr6.simCow.chr6 299561 5 + 602619 AATAG-- -s simCow_chr6.simCow.chr6 300077 5 + 602619 AGTAG-- -s simDog_chr6.simDog.chr6 307975 7 - 593897 GTTGAGT -s simHuman_chr6.simHuman.chr6 309882 7 + 601863 ATTGGGT -s simRat_chr6.simRat.chr6 313525 7 + 647215 ATTGAGT - -a -s simMouse_chr6.simMouse.chr6 321868 29 + 636262 CCTCACAAAGTACCATGGTTTGTTGTAAA -s Anc0.Anc0refChr7 8108 12 - 16696 CTTCAGAAGGT-----------------C -s Anc1.Anc1refChr4 8507 12 + 17549 CTTCAGAAGGT-----------------C -s Anc2.Anc2refChr7 3581 12 + 32194 CTTCAGAAGGT-----------------C -s mr.mrrefChr5 171683 12 + 294540 CCTCAGAAAGT-----------------A -s simCow_chr6.simCow.chr6 299566 7 + 602619 ---TATA--GT-----------------C -s simCow_chr6.simCow.chr6 300082 7 + 602619 ---TAGA--GT-----------------C -s simDog_chr6.simDog.chr6 308010 12 - 593897 CTTCAGAAGGT-----------------A -s simHuman_chr6.simHuman.chr6 309892 12 + 601863 CTTCAGAATGT-----------------G -s simRat_chr6.simRat.chr6 313532 12 + 647215 CCTCAGAAGTT-----------------A - -a -s simMouse_chr6.simMouse.chr6 321897 21 + 636262 GTGCCCTGTTGGAAATATTCC -s Anc0.Anc0refChr7 8121 19 - 16696 ATACCCTGCG--AACTATAGA -s Anc1.Anc1refChr4 8520 19 + 17549 ATACCCTGCG--AACTATAGA -s Anc2.Anc2refChr7 3594 19 + 32194 ACACCCTGCG--TTCTATAGA -s mr.mrrefChr5 171695 21 + 294540 GTGCCCTGCTGGAAATATTCC -s simCow_chr6.simCow.chr6 299574 19 + 602619 ACAGTATGCA--CTCTATGGA -s simCow_chr6.simCow.chr6 300090 19 + 602619 ACAGCATACA--TGCTATAGA -s simDog_chr6.simDog.chr6 308023 10 - 593897 AAACCCTGTG----------- -s simHuman_chr6.simHuman.chr6 309905 19 + 601863 ATACCCTACG--AACATTAAA -s simRat_chr6.simRat.chr6 313544 21 + 647215 GTGCCCTGCTGGAAATGTTCC - -a -s simMouse_chr6.simMouse.chr6 321918 12 + 636262 TATTTGCAGTAA -s Anc0.Anc0refChr7 8140 12 - 16696 CATTTGCAACAA -s Anc1.Anc1refChr4 8539 12 + 17549 CATTTGCAACAA -s Anc2.Anc2refChr7 3613 12 + 32194 CATTTGCAACAA -s mr.mrrefChr5 171716 12 + 294540 TATTTGCAATAA -s simCow_chr6.simCow.chr6 300109 12 + 602619 TTTTTGCAACAA -s simDog_chr6.simDog.chr6 308033 12 - 593897 CATTTGCGGGAA -s simHuman_chr6.simHuman.chr6 309924 12 + 601863 CATTTACAACAA -s simRat_chr6.simRat.chr6 313565 12 + 647215 TATTAGCAATAA - -a -s simMouse_chr6.simMouse.chr6 321930 35 + 636262 TGTTACCAGAGTAACTGATCACACAAGTTATTTTG -s mr.mrrefChr5 232848 35 + 294540 CGTTGCCAAAGTAACTGATTACACAAGCTATTTTG -s simMouse_chr6.simMouse.chr6 379414 35 + 636262 CGTTGCCGAAGTAACTGATTGCACAAGCTATATAG - -a -s simMouse_chr6.simMouse.chr6 321965 4 + 636262 TACA -s Anc1.Anc1refChr6 31417 4 - 197743 TTCA -s mr.mrrefChr3 108429 4 - 181027 TTCA -s mr.mrrefChr5 232947 4 + 294540 TTCA -s simMouse_chr6.simMouse.chr6 116019 4 - 636262 TTCA -s simMouse_chr6.simMouse.chr6 379549 4 + 636262 TTCA -s simRat_chr6.simRat.chr6 115541 4 - 647215 TTCA -s simRat_chr6.simRat.chr6 378743 4 + 647215 TTCA -s simRat_chr6.simRat.chr6 194006 4 - 647215 TTCA - -a -s simMouse_chr6.simMouse.chr6 321969 1 + 636262 T -s Anc1.Anc1refChr6 31421 1 - 197743 T -s mr.mrrefChr3 108433 1 - 181027 T -s mr.mrrefChr5 232951 1 + 294540 T -s simMouse_chr6.simMouse.chr6 116023 1 - 636262 T -s simMouse_chr6.simMouse.chr6 379553 1 + 636262 T -s simRat_chr6.simRat.chr6 115545 1 - 647215 T -s simRat_chr6.simRat.chr6 378747 1 + 647215 T -s simRat_chr6.simRat.chr6 194017 1 - 647215 T - -a -s simMouse_chr6.simMouse.chr6 321970 5 + 636262 AGGCT -s mr.mrrefChr5 232952 5 + 294540 AGGCA -s simMouse_chr6.simMouse.chr6 379554 5 + 636262 AGGCA -s simRat_chr6.simRat.chr6 378748 5 + 647215 ATGCA -s simRat_chr6.simRat.chr6 194018 5 - 647215 AGGAC - -a -s simMouse_chr6.simMouse.chr6 321975 7 + 636262 CCTCCCA -s Anc1.Anc1refChr6 31422 7 - 197743 CTAGCCC -s mr.mrrefChr3 108434 7 - 181027 CTAGTCT -s mr.mrrefChr5 232957 7 + 294540 CCTGCCC -s simMouse_chr6.simMouse.chr6 116024 7 - 636262 CTAGTCT -s simMouse_chr6.simMouse.chr6 379559 7 + 636262 CCTGCCC -s simRat_chr6.simRat.chr6 115549 7 - 647215 CTACTCC -s simRat_chr6.simRat.chr6 378753 7 + 647215 CCTGCCC -s simRat_chr6.simRat.chr6 194023 7 - 647215 TCTGACT - -a -s simMouse_chr6.simMouse.chr6 321982 3 + 636262 CTA -s Anc1.Anc1refChr6 31429 3 - 197743 CTA -s mr.mrrefChr3 108443 3 - 181027 CTA -s mr.mrrefChr5 232964 3 + 294540 CTA -s simMouse_chr6.simMouse.chr6 116033 3 - 636262 CTA -s simMouse_chr6.simMouse.chr6 379566 3 + 636262 CTA -s simRat_chr6.simRat.chr6 115558 3 - 647215 CTA -s simRat_chr6.simRat.chr6 378760 3 + 647215 CTA -s simRat_chr6.simRat.chr6 194030 3 - 647215 CTA - -a -s simMouse_chr6.simMouse.chr6 321985 49 + 636262 TAATACAATTTCTTTTGTGTGCTCCTTCACACTGTATGAGGTTTACTTG -s Anc1.Anc1refChr6 31432 49 - 197743 TAATACAATCTATCTCTTATGCTCCTTCACACCGGATGAGGTTTGCTTG -s mr.mrrefChr3 108446 49 - 181027 TAATACAATCTATCTCTTATGCTCCTTTATACCAGATGAGGTTTGCTTG -s mr.mrrefChr5 232967 49 + 294540 TAATACAATCTGTTTCGTATGCTCCTTCACACTGTATGAGGTTTACCTG -s simMouse_chr6.simMouse.chr6 116036 49 - 636262 TAATACAATCTATCTCTTATGCTCCTTTATACCAGATGAGGTTTGCTTG -s simMouse_chr6.simMouse.chr6 379569 49 + 636262 TAATACAACCTGTTTCGTATGCTCCTTCAAACTGTGTGAGGTTCACCTG -s simRat_chr6.simRat.chr6 115564 49 - 647215 TAATACAATCTATTTCTTATGCTCCTTCATACCGAATGAGGTTTACTTG -s simRat_chr6.simRat.chr6 378763 49 + 647215 TAATACAATCTGTTCCGTATGCTCCTTCCCACTGTATGAGGTTTACCTG -s simRat_chr6.simRat.chr6 194033 45 - 647215 --ATACAATCAATTTCTTACGCTCCTTCATACCGA--GAGGTTTACCTG - -a -s simMouse_chr6.simMouse.chr6 322034 10 + 636262 ACTGATTTCT -s mr.mrrefChr5 233016 10 + 294540 ACTAATTTCT -s simMouse_chr6.simMouse.chr6 379618 7 + 636262 ---AATTTCT -s simRat_chr6.simRat.chr6 378812 10 + 647215 ACTAACTTCT -s simRat_chr6.simRat.chr6 194078 10 - 647215 GCCGGTTTTT - -a -s simMouse_chr6.simMouse.chr6 322044 2 + 636262 TC -s mr.mrrefChr5 233026 2 + 294540 TC -s simMouse_chr6.simMouse.chr6 379625 2 + 636262 TC -s simRat_chr6.simRat.chr6 378822 2 + 647215 TC -s simRat_chr6.simRat.chr6 194095 2 - 647215 TC - -a -s simMouse_chr6.simMouse.chr6 322046 35 + 636262 CTTTTACGTGAATGTTCTTGTCCTCAGTACATACC -s Anc1.Anc1refChr6 31481 31 - 197743 CTTTTACTTGCATGTTCCTGTCCTT----CATGCC -s mr.mrrefChr3 108495 31 - 181027 CTTTTACCTGCATTCTCCTGTCCAT----CATGCC -s mr.mrrefChr5 233028 31 + 294540 CTTTTACTTGAATGTTCCTGTCCTT----CATACC -s simMouse_chr6.simMouse.chr6 116085 31 - 636262 CTTTTACCTGCATTCTCCTGTCCAT----CATGCC -s simMouse_chr6.simMouse.chr6 379627 31 + 636262 CTCTTACTTGAATGTTCCTGTCCTT----CATGCC -s simRat_chr6.simRat.chr6 115626 31 - 647215 TTCTTACTTGAATGCTCTTGTCCAT----CATGCT -s simRat_chr6.simRat.chr6 378824 31 + 647215 CTTTTATTTGAATGTTCCAGTCCTT----CAACCG -s simRat_chr6.simRat.chr6 194097 31 - 647215 CTTTTACTCAAATGTCCCTGTGCTT----CAAACA - -a -s simMouse_chr6.simMouse.chr6 322081 1 + 636262 A -s Anc1.Anc1refChr6 31512 1 - 197743 A -s mr.mrrefChr3 108526 1 - 181027 A -s mr.mrrefChr5 233059 1 + 294540 A -s simMouse_chr6.simMouse.chr6 116116 1 - 636262 A -s simMouse_chr6.simMouse.chr6 379658 1 + 636262 A -s simRat_chr6.simRat.chr6 115657 1 - 647215 A -s simRat_chr6.simRat.chr6 194128 1 - 647215 A - -a -s simMouse_chr6.simMouse.chr6 322082 35 + 636262 TATGAGATTTACTGGACTGTTTTTATTCCCTCACC -s Anc1.Anc1refChr6 31513 35 - 197743 TGTGAGGTTTACTTGACTGTTTTTGTTCCCTCACC -s mr.mrrefChr3 108527 35 - 181027 TGTGAGGATTACTTGACTGTTTTTGTTCCCTCACC -s mr.mrrefChr5 233060 35 + 294540 TATAAGGTTTACTTGACTGTTTTTGTTCCCTCACC -s simMouse_chr6.simMouse.chr6 116117 35 - 636262 TGTGAGGATTACTTGACTGTTTTTGTTCCCTCACC -s simMouse_chr6.simMouse.chr6 379659 35 + 636262 TACAAGGTTTACTTGACTGTTTTTGTTCCCTCACC -s simRat_chr6.simRat.chr6 115658 35 - 647215 TGAGAGGTTTACTAGACTCTTTTTGTTCACTCACT -s simRat_chr6.simRat.chr6 378855 35 + 647215 TACAAGGTTTACTTGACTGTTTTTGTTCCCTCACC -s simRat_chr6.simRat.chr6 194129 35 - 647215 TATAAGGTTTACTTGACTGTTTTTGTTCCATCACC - -a -s simMouse_chr6.simMouse.chr6 322117 8 + 636262 ATCTTAGG -s Anc1.Anc1refChr6 31548 8 - 197743 ATATTAGG -s mr.mrrefChr3 108562 8 - 181027 ATATTAGG -s mr.mrrefChr5 233095 8 + 294540 ATATTAGG -s simMouse_chr6.simMouse.chr6 116152 8 - 636262 ATATTAGG -s simMouse_chr6.simMouse.chr6 379694 8 + 636262 ATATTAGG -s simRat_chr6.simRat.chr6 115693 8 - 647215 ATATTAGG -s simRat_chr6.simRat.chr6 378890 8 + 647215 ATATTAGG -s simRat_chr6.simRat.chr6 194237 8 - 647215 ATATTAGG - -a -s simMouse_chr6.simMouse.chr6 322125 7 + 636262 TGTATTT -s Anc1.Anc1refChr6 31556 7 - 197743 TGTATTT -s mr.mrrefChr3 108570 7 - 181027 TGTACTT -s mr.mrrefChr5 233103 7 + 294540 TGTATTT -s simMouse_chr6.simMouse.chr6 116160 7 - 636262 TGTACTT -s simRat_chr6.simRat.chr6 115701 7 - 647215 TGTACTT -s simRat_chr6.simRat.chr6 194245 7 - 647215 TGTACTT - -a -s simMouse_chr6.simMouse.chr6 322132 27 + 636262 GACTGTCGCACTTCTGATTATTTCCAT -s Anc1.Anc1refChr6 31563 27 - 197743 GGAGGTGGCACTTCTGACTATGACCAT -s mr.mrrefChr3 108577 27 - 181027 GGAGATGGCACTTATGACCATGACCGC -s mr.mrrefChr5 233110 27 + 294540 GAAGGTGGCACTTCTGAGTATGGCCAT -s simMouse_chr6.simMouse.chr6 116167 27 - 636262 GGAGATGGCACTTATGACCATGACCGC -s simMouse_chr6.simMouse.chr6 379702 27 + 636262 GAAGGTGGCACTTCTGAGTATGGCCAT -s simRat_chr6.simRat.chr6 115708 27 - 647215 GAAGGTGGCACTTTTGAGTATGGCCGT -s simRat_chr6.simRat.chr6 378898 27 + 647215 GAGGGTGGCACTTCTGAGTATGGCCAT -s simRat_chr6.simRat.chr6 194252 27 - 647215 GAAGGTGGCACTTTTGAGTATGGCCGT - -a -s simMouse_chr6.simMouse.chr6 322159 5 + 636262 ATTCT -s mr.mrrefChr5 233143 5 + 294540 ATGCT -s simMouse_chr6.simMouse.chr6 379735 5 + 636262 ATGCT -s simRat_chr6.simRat.chr6 378931 5 + 647215 ATGCT -s simRat_chr6.simRat.chr6 194285 5 - 647215 GTGCT - -a -s simMouse_chr6.simMouse.chr6 322164 39 + 636262 TCTCCACAATATTAGATTTCTTGGTTATTAGCCATCTTG -s Anc1.Anc1refChr6 31594 23 - 197743 TCTCCACTATATTATATTTCTTG---------------- -s mr.mrrefChr3 108608 23 - 181027 TCTCCACTATATTGTGTTTCTTG---------------- -s mr.mrrefChr5 233148 23 + 294540 TCTCCACAATATTAGATTTCTTG---------------- -s simMouse_chr6.simMouse.chr6 116205 23 - 636262 TCTCCACTATATTGTGTTTCTTG---------------- -s simMouse_chr6.simMouse.chr6 379740 23 + 636262 TCTCCACGACATTAGATTTTTTG---------------- -s simRat_chr6.simRat.chr6 115739 23 - 647215 TCCCCAATATATGATTGTCCTTG---------------- -s simRat_chr6.simRat.chr6 378936 23 + 647215 TCTCCACAATATTAGATTTGCTG---------------- -s simRat_chr6.simRat.chr6 194290 10 - 647215 TCCCCACTAT----------------------------- - -a -s simMouse_chr6.simMouse.chr6 322203 27 + 636262 ATTGTGTGTCTTATGTCTCCTCAGAGT -s Anc1.Anc1refChr6 31617 27 - 197743 ATTGTCTGTCTTATGGCTCTTCAGAGT -s mr.mrrefChr3 108631 27 - 181027 ATTGTCCACGTTATGGCTCTTCAGAGT -s mr.mrrefChr5 233171 27 + 294540 ATTGTCTGTCTTATGGCTCTTCAGAGT -s simMouse_chr6.simMouse.chr6 116228 27 - 636262 ATTGTCCACGTTATGGCTCTTCAGAGT -s simMouse_chr6.simMouse.chr6 379763 17 + 636262 ACTT----------GGCTCACCAGAGT -s simRat_chr6.simRat.chr6 115805 27 - 647215 ATTGTCCGTGTTATGACTCTTCAGAGT -s simRat_chr6.simRat.chr6 378959 27 + 647215 ATTTTCCATCTTATGGCTCTTCAGAAT -s simRat_chr6.simRat.chr6 194300 24 - 647215 -TCGTCTGTGTTATGGCTTTTCAGA-- - -a -s simMouse_chr6.simMouse.chr6 322230 14 + 636262 ATCACCGCCGGCTC -s mr.mrrefChr5 233198 14 + 294540 ATCACTGCTGGCTC -s simMouse_chr6.simMouse.chr6 379780 14 + 636262 ATCACTACTGGACC -s simRat_chr6.simRat.chr6 378986 14 + 647215 ATCAGTGCTGGCTC -s simRat_chr6.simRat.chr6 194324 2 - 647215 ------------CC - -a -s simMouse_chr6.simMouse.chr6 322244 3 + 636262 TTT -s Anc1.Anc1refChr6 31644 3 - 197743 TTT -s mr.mrrefChr3 108658 3 - 181027 TTG -s mr.mrrefChr5 233212 3 + 294540 TTT -s simMouse_chr6.simMouse.chr6 116255 3 - 636262 TTG -s simMouse_chr6.simMouse.chr6 379794 3 + 636262 TTT -s simRat_chr6.simRat.chr6 115832 3 - 647215 TTC -s simRat_chr6.simRat.chr6 379000 3 + 647215 TTT -s simRat_chr6.simRat.chr6 194326 3 - 647215 TTT - -a -s simMouse_chr6.simMouse.chr6 322247 19 + 636262 CCGTATGCTTCTCCACTGT -s Anc1.Anc1refChr6 31661 19 - 197743 TCATGTGCTTTTCCACTAT -s mr.mrrefChr3 108675 19 - 181027 TCATGTGCTTTTCCACTAT -s mr.mrrefChr5 233229 19 + 294540 TCGTATGCTTCTCCACTAT -s simMouse_chr6.simMouse.chr6 116272 19 - 636262 TCATGTGCTTTTCCACTAT -s simMouse_chr6.simMouse.chr6 379811 18 + 636262 TCGTACACTTATCCAGTA- -s simRat_chr6.simRat.chr6 115849 19 - 647215 TCGTGTGCTTCTCCACTGC -s simRat_chr6.simRat.chr6 379017 19 + 647215 ACATACGTTTCTCCGGTTT -s simRat_chr6.simRat.chr6 194343 19 - 647215 TCGTGTGCTTTTCCCCTAT - -a -s simMouse_chr6.simMouse.chr6 322266 1 + 636262 A -s Anc1.Anc1refChr6 31680 1 - 197743 A -s mr.mrrefChr3 108723 1 - 181027 A -s mr.mrrefChr5 233248 1 + 294540 A -s simMouse_chr6.simMouse.chr6 116320 1 - 636262 A -s simRat_chr6.simRat.chr6 115897 1 - 647215 C -s simRat_chr6.simRat.chr6 379036 1 + 647215 A -s simRat_chr6.simRat.chr6 194362 1 - 647215 A - -a -s simMouse_chr6.simMouse.chr6 322267 5 + 636262 ACCAC -s Anc1.Anc1refChr6 31753 5 - 197743 ATCCA -s mr.mrrefChr3 108832 5 - 181027 CACCA -s mr.mrrefChr5 233323 5 + 294540 ATCCA -s simMouse_chr6.simMouse.chr6 116429 5 - 636262 CACCA -s simMouse_chr6.simMouse.chr6 379901 5 + 636262 CTCCA -s simRat_chr6.simRat.chr6 116007 5 - 647215 CTCCA -s simRat_chr6.simRat.chr6 379111 5 + 647215 CTCCA -s simRat_chr6.simRat.chr6 194406 5 - 647215 ATCCC - -a -s simMouse_chr6.simMouse.chr6 322272 2 + 636262 TT -s mr.mrrefChr5 233328 2 + 294540 TT -s simMouse_chr6.simMouse.chr6 379906 2 + 636262 TT -s simRat_chr6.simRat.chr6 379116 2 + 647215 TT -s simRat_chr6.simRat.chr6 194411 2 - 647215 TT - -a -s simMouse_chr6.simMouse.chr6 322274 4 + 636262 AAAC -s Anc1.Anc1refChr6 31758 4 - 197743 ACGT -s mr.mrrefChr3 108837 4 - 181027 ACGC -s mr.mrrefChr5 233330 4 + 294540 ACAT -s simMouse_chr6.simMouse.chr6 116456 4 - 636262 ACGC -s simMouse_chr6.simMouse.chr6 379908 4 + 636262 GCAT -s simRat_chr6.simRat.chr6 116012 4 - 647215 ACGT -s simRat_chr6.simRat.chr6 379118 4 + 647215 ACAT -s simRat_chr6.simRat.chr6 194413 4 - 647215 GCAC - -a -s simMouse_chr6.simMouse.chr6 322278 9 + 636262 ACCCATCCC -s mr.mrrefChr5 233339 9 + 294540 ACCCATCCC -s simMouse_chr6.simMouse.chr6 379917 9 + 636262 ACCCATCCC -s simRat_chr6.simRat.chr6 379127 9 + 647215 GCCCATCCC -s simRat_chr6.simRat.chr6 194422 1 - 647215 --------T - -a -s simMouse_chr6.simMouse.chr6 322287 9 + 636262 CCCCTAAaa -s Anc1.Anc1refChr6 31766 9 - 197743 CCCTTACaa -s mr.mrrefChr3 108845 9 - 181027 CCCTTACAA -s mr.mrrefChr5 233348 9 + 294540 CCCCTACaa -s simMouse_chr6.simMouse.chr6 116464 9 - 636262 CCCTTACAA -s simMouse_chr6.simMouse.chr6 379926 9 + 636262 CCCCTAcaa -s simRat_chr6.simRat.chr6 116020 9 - 647215 CCCTTACAA -s simRat_chr6.simRat.chr6 379136 9 + 647215 CCCCTACTA -s simRat_chr6.simRat.chr6 194423 9 - 647215 CCCTTACAA - -a -s simMouse_chr6.simMouse.chr6 322296 17 + 636262 tcttattggaatgagct -s Anc1.Anc1refChr6 31775 17 - 197743 gcttattgggacgagtt -s mr.mrrefChr3 108854 17 - 181027 GCTTCAtgagacgagtt -s mr.mrrefChr5 233357 17 + 294540 tcttattgggacgagct -s simMouse_chr6.simMouse.chr6 116473 17 - 636262 GCTTCAtgagacgagtt -s simMouse_chr6.simMouse.chr6 379935 17 + 636262 tcttattgggacaagct -s simRat_chr6.simRat.chr6 116029 17 - 647215 TCCTCATGGgacgggtt -s simRat_chr6.simRat.chr6 379145 17 + 647215 Tcttattgggacgagct -s simRat_chr6.simRat.chr6 194433 17 - 647215 TCTCAAGAGGACAGGTA - -a -s simMouse_chr6.simMouse.chr6 322313 2 + 636262 ac -s Anc1.Anc1refChr6 31792 2 - 197743 ga -s mr.mrrefChr3 108875 2 - 181027 ga -s mr.mrrefChr5 233374 2 + 294540 ga -s simMouse_chr6.simMouse.chr6 116494 2 - 636262 ga -s simMouse_chr6.simMouse.chr6 379952 2 + 636262 ga -s simRat_chr6.simRat.chr6 116050 2 - 647215 gc -s simRat_chr6.simRat.chr6 379162 2 + 647215 ga -s simRat_chr6.simRat.chr6 194450 2 - 647215 Ga - -a -s simMouse_chr6.simMouse.chr6 322315 1 + 636262 a -s Anc1.Anc1refChr6 31794 1 - 197743 a -s mr.mrrefChr3 108877 1 - 181027 a -s mr.mrrefChr5 233376 1 + 294540 a -s simMouse_chr6.simMouse.chr6 116496 1 - 636262 a -s simMouse_chr6.simMouse.chr6 379954 1 + 636262 a -s simRat_chr6.simRat.chr6 116052 1 - 647215 a -s simRat_chr6.simRat.chr6 379164 1 + 647215 a -s simRat_chr6.simRat.chr6 194467 1 - 647215 a - -a -s simMouse_chr6.simMouse.chr6 322316 23 + 636262 aaacacttttgtaaatgcttctt -s Anc1.Anc1refChr6 31796 23 - 197743 gtacacttttgtaaatgcttctt -s mr.mrrefChr3 108879 23 - 181027 gtacacttttgtaaatgcttctt -s mr.mrrefChr5 233378 23 + 294540 gtacacttttgtaaatgcttctt -s simMouse_chr6.simMouse.chr6 116498 23 - 636262 gtacacttttgtaaatgcttctt -s simMouse_chr6.simMouse.chr6 379956 23 + 636262 gtatacttttgtaagtgcttctt -s simRat_chr6.simRat.chr6 116054 23 - 647215 gtacacttttgtagatgcttctt -s simRat_chr6.simRat.chr6 379166 23 + 647215 ggatacttttgtaaatgcttctt -s simRat_chr6.simRat.chr6 194469 23 - 647215 gtacacttttgtaaatgcttctt - -a -s simMouse_chr6.simMouse.chr6 322339 1 + 636262 t -s Anc1.Anc1refChr6 31819 1 - 197743 t -s mr.mrrefChr3 108902 1 - 181027 t -s mr.mrrefChr5 233401 1 + 294540 t -s simMouse_chr6.simMouse.chr6 116521 1 - 636262 t -s simMouse_chr6.simMouse.chr6 379979 1 + 636262 t -s simRat_chr6.simRat.chr6 116077 1 - 647215 t -s simRat_chr6.simRat.chr6 194492 1 - 647215 t - -a -s simMouse_chr6.simMouse.chr6 322340 10 + 636262 ggagtgtaga -s Anc1.Anc1refChr6 31820 10 - 197743 gaaacgtaga -s mr.mrrefChr3 108903 10 - 181027 ggagcgtgga -s mr.mrrefChr5 233402 10 + 294540 gaaatgtaga -s simMouse_chr6.simMouse.chr6 116522 10 - 636262 ggagcgtgga -s simMouse_chr6.simMouse.chr6 379980 10 + 636262 gaaatgtaga -s simRat_chr6.simRat.chr6 116078 10 - 647215 ggagcgtaga -s simRat_chr6.simRat.chr6 379189 10 + 647215 aaaatgtaga -s simRat_chr6.simRat.chr6 194493 10 - 647215 ggagcgtaaa - -a -s simMouse_chr6.simMouse.chr6 322350 22 + 636262 cttcttctccagcaagagaatg -s Anc1.Anc1refChr6 31830 22 - 197743 cttcttgtctagtaagcaaatg -s mr.mrrefChr3 108913 22 - 181027 cttcttctctaacagccaaatg -s mr.mrrefChr5 233412 22 + 294540 cttcttgtgtagtaagagaatg -s simMouse_chr6.simMouse.chr6 116532 22 - 636262 cttcttctctaacagccaaatg -s simMouse_chr6.simMouse.chr6 379990 22 + 636262 cttcttgtgtagtaagaggatg -s simRat_chr6.simRat.chr6 116103 22 - 647215 CTTCTTCTTTGGCAAGTGAGTG -s simRat_chr6.simRat.chr6 379199 22 + 647215 cttcttgtgtagtgagagaacg -s simRat_chr6.simRat.chr6 194503 19 - 647215 cttctcttgca---agggaatg - -a -s simMouse_chr6.simMouse.chr6 322372 4 + 636262 ccta -s mr.mrrefChr5 233434 4 + 294540 tcta -s simMouse_chr6.simMouse.chr6 380012 4 + 636262 tcta -s simRat_chr6.simRat.chr6 379221 4 + 647215 tcta -s simRat_chr6.simRat.chr6 194522 4 - 647215 tcta - -a -s simMouse_chr6.simMouse.chr6 322376 10 + 636262 tccatgactc -s Anc0.Anc0refChr3 12691 10 + 222631 tctaggtTGC -s Anc1.Anc1refChr6 45596 10 + 197743 tctaggtTGC -s Anc2.Anc2refChr13 15429 10 + 96486 TCTAGGTTGT -s mr.mrrefChr5 233438 10 + 294540 tttatgtctc -s simCow_chr6.simCow.chr6 371446 10 + 602619 TCTAGGTTGT -s simDog_chr6.simDog.chr6 361495 10 + 593897 TCTAGGTTGT -s simHuman_chr6.simHuman.chr6 369792 3 + 601863 -------GGC -s simMouse_chr6.simMouse.chr6 380016 10 + 636262 tttatgtctc -s simRat_chr6.simRat.chr6 379225 10 + 647215 tttgtgtctc -s simRat_chr6.simRat.chr6 194526 10 - 647215 ttcatgtctc - -a -s simMouse_chr6.simMouse.chr6 322386 17 + 636262 gtctcttaatggtgttg -s Anc0.Anc0refChr3 12707 6 + 222631 AACTTT----------- -s Anc1.Anc1refChr6 45612 6 + 197743 AACTTT----------- -s Anc2.Anc2refChr13 15446 6 + 96486 AACCTT----------- -s mr.mrrefChr5 233454 17 + 294540 atcttttaatggtgtcg -s simCow_chr6.simCow.chr6 371463 6 + 602619 AACCCT----------- -s simDog_chr6.simDog.chr6 361512 6 + 593897 AACCTT----------- -s simHuman_chr6.simHuman.chr6 369801 6 + 601863 AGCTTT----------- -s simMouse_chr6.simMouse.chr6 380032 17 + 636262 atcttttattgttgtcg -s simRat_chr6.simRat.chr6 379241 17 + 647215 atcttattatgttgtca -s simRat_chr6.simRat.chr6 194542 17 - 647215 atctcttaatagtgttg - -a -s simMouse_chr6.simMouse.chr6 322403 4 + 636262 tttt -s mr.mrrefChr5 233471 2 + 294540 tt-- -s simRat_chr6.simRat.chr6 194559 2 - 647215 tt-- - -a -s simMouse_chr6.simMouse.chr6 322407 13 + 636262 ggtgactgttttg -s mr.mrrefChr5 233473 13 + 294540 ggttttcgttttg -s simMouse_chr6.simMouse.chr6 380049 13 + 636262 gtttttcatgttg -s simRat_chr6.simRat.chr6 379258 13 + 647215 aattataattttg -s simRat_chr6.simRat.chr6 194561 13 - 647215 ggttttcgttttg - -a -s simMouse_chr6.simMouse.chr6 322420 26 + 636262 tgtatatctgttaaggaacagggcct -s mr.mrrefChr5 233493 18 + 294540 tgtaattctgttatgga--------c -s simMouse_chr6.simMouse.chr6 380069 18 + 636262 tgtaattctgttataga--------c -s simRat_chr6.simRat.chr6 379278 18 + 647215 tgtgattctattatgga--------c -s simRat_chr6.simRat.chr6 194582 18 - 647215 tgtaagtatgttatgga--------c - -a -s simMouse_chr6.simMouse.chr6 322446 43 + 636262 gtgataccaggctcctctcaaatgagtaagtggcaaaATTTAT -s mr.mrrefChr5 233605 43 + 294540 gtgaaaccaggcccctcttagatgaataagtggcagaattttt -s simMouse_chr6.simMouse.chr6 380209 43 + 636262 gtggaaccaggcccctcttagacgattaagtggcagaatcttt -s simRat_chr6.simRat.chr6 379390 43 + 647215 gagaaaccaggcacctcttacatgaataagtggcagaatcttt -s simRat_chr6.simRat.chr6 194600 43 - 647215 gtgaaaccaggcccctctcagatgaataagtggcaaaattttt - -a -s simMouse_chr6.simMouse.chr6 322489 25 + 636262 CAATGTCAAACATCAAGGCCCTTTC -s mr.mrrefChr5 233773 25 + 294540 gagtgttaagcatcaagggttcttc -s simMouse_chr6.simMouse.chr6 380377 22 + 636262 gagtg---ggcatcaagggttcttc -s simRat_chr6.simRat.chr6 379556 25 + 647215 gtgtgttgagcattataggttcttc -s simRat_chr6.simRat.chr6 194808 25 - 647215 gcatgttaagcataaaaggctcttc - -a -s simMouse_chr6.simMouse.chr6 322514 10 + 636262 CATGTAACTC -s mr.mrrefChr5 233802 10 + 294540 gctatatctt -s simMouse_chr6.simMouse.chr6 380403 10 + 636262 gctatatctt -s simRat_chr6.simRat.chr6 379585 10 + 647215 gctatatctt -s simRat_chr6.simRat.chr6 194837 10 - 647215 cctatatctt - -a -s simMouse_chr6.simMouse.chr6 322524 2 + 636262 TG -s mr.mrrefChr5 233815 2 + 294540 tg -s simMouse_chr6.simMouse.chr6 380416 1 + 636262 t- -s simRat_chr6.simRat.chr6 379595 2 + 647215 tg -s simRat_chr6.simRat.chr6 194850 2 - 647215 ta - -a -s simMouse_chr6.simMouse.chr6 322526 42 + 636262 ctaatctgtcctctaaaatcttaacgtcccttggcggctgag -s mr.mrrefChr5 233827 42 + 294540 ctaagttgtcctctataatcttaacgctccttggcagctgag -s simRat_chr6.simRat.chr6 379607 42 + 647215 ctcagttgtccgctattatcttaacgctctttagcagctgag -s simRat_chr6.simRat.chr6 194862 42 - 647215 ctaagttgtcctctatgatcttaacactccttggcagctgac - -a -s simMouse_chr6.simMouse.chr6 322568 97 + 636262 ctttcctgatgtatggaagatggagcaattagaaagttgaaggatgaacttgaatttcagcaagaccatcttattgccatggcatatgggccaaatc -s mr.mrrefChr5 233995 97 + 294540 tcttcctgatgtatggaagatagagcaattggaaagttgagggatgaacttgattttcagcaagtccatcttactgccatgggctatgggccgaatc -s simMouse_chr6.simMouse.chr6 380475 90 + 636262 tcttcctgatgtatggaagatagagcaatggggaag--gagggatagccagga-----ggggtagccatcttactgccaagggctatgggccgaatc -s simRat_chr6.simRat.chr6 379792 97 + 647215 tcttcctgatgtatggaagatagagcaatgggaaagtttagggatgaacttgattttcaacaagtccatcttaccgccatgagctaagggctgaatc -s simRat_chr6.simRat.chr6 195030 92 - 647215 tcttcctgacgtgtggaagatagagcaattggaaagttgagggatgaacttgatttttgacaagtccatcttattgccatggtcta-----tgattc - -a -s simMouse_chr6.simMouse.chr6 322665 34 + 636262 ttgtagtatcagaatggtgttgttccagtgagtg -s mr.mrrefChr5 234092 34 + 294540 ttgtggtaccagaatagtgttgttttactgagag -s simMouse_chr6.simMouse.chr6 380565 34 + 636262 tcgtggcaccagtatagtgctgttttgctaagag -s simRat_chr6.simRat.chr6 379889 34 + 647215 tcgtggtaccagtatagtgtagttttactgagag -s simRat_chr6.simRat.chr6 195123 34 - 647215 ttgtgggaccagaatggtgttgttttaatgagag - -a -s simMouse_chr6.simMouse.chr6 322699 7 + 636262 ttgctta -s mr.mrrefChr5 234126 7 + 294540 tcactca -s simMouse_chr6.simMouse.chr6 380599 7 + 636262 tcactca -s simRat_chr6.simRat.chr6 379929 7 + 647215 tcactca -s simRat_chr6.simRat.chr6 195157 7 - 647215 tcgctcg - -a -s simMouse_chr6.simMouse.chr6 322706 18 + 636262 atagtagaatttgtgatc -s mr.mrrefChr5 234133 18 + 294540 atagtagaatttgtgata -s simMouse_chr6.simMouse.chr6 380628 18 + 636262 atggcaaagtccattcca -s simRat_chr6.simRat.chr6 379936 18 + 647215 atagtagaatttgttata -s simRat_chr6.simRat.chr6 195164 18 - 647215 atagtggaatttgtggtc - -a -s simMouse_chr6.simMouse.chr6 322724 186 + 636262 tgggaggattatgccaccggcccgatgcttctggcttggattctggcttggaacagacttcgctgtgatctattttcccccaggagtgcatgttagtggctcgctttttcggttccaagtaaacctaactcttgtctctttatactcagggaacagggccatagggcttttaatagtagtcctatt -s mr.mrrefChr5 234151 142 + 294540 tgggaggattatgccgccggcttgattc------------ttctggcttggaacggactttgcca--------------------------------ggctcgcttttctggttccaattaaacttaacgattgtttttttacactcagtaaacagggccacagggcttttgatagtagtcctatt -s simMouse_chr6.simMouse.chr6 380649 105 + 636262 cagaagaatcaagcaggcagcataaccc------------tcctggatcacaa----------------------------------------------------gttcta---ctatttgaacttgacaat--tttttttacactcagtaaacagggccacagggcttttgat------------ -s simRat_chr6.simRat.chr6 379954 142 + 647215 cgggagggttatgctgccagctcaattc------------ttttggcctggaatggactttgcca--------------------------------ggctcccttttttggttccaattaaacctgacgattttttttttacactcagtaaacagggccacagttcttttaatagtagttctttt -s simRat_chr6.simRat.chr6 195182 136 - 647215 tgggagggttatgccgctggcttgattc------------ttctggcttggaacggactttgcca--------------------------------------cttttctggttccaagtaaacttaatgatggtttttttacattcagtgaacagggccatcagacttttgatcgtagtcctgtt - -a -s simMouse_chr6.simMouse.chr6 322910 23 + 636262 agacctacagttgagattggata -s mr.mrrefChr5 234293 23 + 294540 agacctacaggtgagtttgtgta -s simRat_chr6.simRat.chr6 380111 23 + 647215 agacttataggtgagtttgtgta -s simRat_chr6.simRat.chr6 195318 23 - 647215 agctctacaggtaagtttgtgta - -a -s simMouse_chr6.simMouse.chr6 322933 42 + 636262 aacatcttcgagttcacattaagttgatcgactcatgagcat -s mr.mrrefChr5 234318 42 + 294540 aacatcttcaagttcacgttaagtcgatcgactcacgagcat -s simRat_chr6.simRat.chr6 380136 42 + 647215 aacatctctaagttcatgttaagccagtcaacccacaagcat -s simRat_chr6.simRat.chr6 195346 42 - 647215 aacatcttcaagttcacgttcagtcgatcgactcacgagcat - -a -s simMouse_chr6.simMouse.chr6 322975 10 + 636262 tcaatactct -s mr.mrrefChr5 234360 10 + 294540 tcaatattct -s simRat_chr6.simRat.chr6 380178 10 + 647215 tcaatattct -s simRat_chr6.simRat.chr6 195402 10 - 647215 ttaatattct - -a -s simMouse_chr6.simMouse.chr6 322985 50 + 636262 tgggattaattatcgtttctctgattagctttaatagtgggttttatatt -s mr.mrrefChr5 234370 50 + 294540 tgggattaattatcgtttctctgattagctttaatagtgggttttatatt -s simRat_chr6.simRat.chr6 195412 50 - 647215 ttggattatttattgtttctctgataagcttttatagtggattatgtatt - -a -s simMouse_chr6.simMouse.chr6 323035 6 + 636262 taataa -s mr.mrrefChr5 234420 6 + 294540 taataa -s simRat_chr6.simRat.chr6 195463 6 - 647215 taataa - -a -s simMouse_chr6.simMouse.chr6 323041 17 + 636262 gcagatcctttatgtct -s mr.mrrefChr5 234426 17 + 294540 gcagatcctttatgtct -s simRat_chr6.simRat.chr6 380188 17 + 647215 gcagatcatttatgtct -s simRat_chr6.simRat.chr6 195469 17 - 647215 gcagatcctttatgtct - -a -s simMouse_chr6.simMouse.chr6 323058 2 + 636262 tg -s mr.mrrefChr5 234443 2 + 294540 tg -s simRat_chr6.simRat.chr6 195486 2 - 647215 tg - -a -s simMouse_chr6.simMouse.chr6 323060 22 + 636262 agtcaactgtgtctctataaat -s mr.mrrefChr5 234445 22 + 294540 aatcaactgtgtctctagaaat -s simRat_chr6.simRat.chr6 380205 22 + 647215 aatcaactgggtctttagaaat -s simRat_chr6.simRat.chr6 195488 22 - 647215 aatcaactgcgttcctagaaat - -a -s simMouse_chr6.simMouse.chr6 323082 14 + 636262 tttcagattttaat -s mr.mrrefChr5 234543 14 + 294540 tctcagattttaat -s simMouse_chr6.simMouse.chr6 380793 14 + 636262 tctcagattttaat -s simRat_chr6.simRat.chr6 380303 14 + 647215 tctcagattttaat -s simRat_chr6.simRat.chr6 195606 14 - 647215 tttcacattttaat - -a -s simMouse_chr6.simMouse.chr6 323096 1 + 636262 a -s mr.mrrefChr5 234557 1 + 294540 a -s simRat_chr6.simRat.chr6 195620 1 - 647215 a - -a -s simMouse_chr6.simMouse.chr6 323097 32 + 636262 cattaattatgtaatcagagacttcagttaaa -s mr.mrrefChr5 234558 32 + 294540 ccttaattttgtaaccagagacttcagctaaa -s simMouse_chr6.simMouse.chr6 380807 32 + 636262 ccttaattttgtaactagagacttcagctata -s simRat_chr6.simRat.chr6 380317 32 + 647215 ccttaattttgtaactggggactccagctaaa -s simRat_chr6.simRat.chr6 195621 32 - 647215 cattaattttgtagccggaaacttcagctaaa - -a -s simMouse_chr6.simMouse.chr6 323129 45 + 636262 ttgtttatcagcttaagcaagtctacagctcctgccattggatta -s mr.mrrefChr5 234590 45 + 294540 ttgcttatcagcttaagtaagtttccagctgccgccattggatta -s simMouse_chr6.simMouse.chr6 380839 45 + 636262 tcgcttatcagcttatgtaagtttccagctgccgccatcagatta -s simRat_chr6.simRat.chr6 380349 45 + 647215 ttgcttatcagcttaagtaaggttccagcagccaccattgaatga -s simRat_chr6.simRat.chr6 195679 45 - 647215 ttgcttatcagcttaagcaagtttccagctactgccattgggtta - -a -s simMouse_chr6.simMouse.chr6 323174 150 + 636262 ctgaggtaaacagacatatcatccctgaatatcgaatgttttattttttctagttagtgtaaactgcatccaaatggctatcccatttatctggatcctgtcaggttgtccgcaccatattgaaagctttacttcttcttcatccaattg -s mr.mrrefChr5 234635 62 + 294540 ctgaggtatactatcatatcatccgcaa----------------------------------------------------------------------------------------atattgaaagctttatttcttcttcatccaattg -s simMouse_chr6.simMouse.chr6 380884 61 + 636262 c-gaggtatactatcatatcatctgcaa----------------------------------------------------------------------------------------atattgaaggttttatttcttcttcatccaattg -s simRat_chr6.simRat.chr6 380394 62 + 647215 ctgaggtgtactatcgtaccatcagcaa----------------------------------------------------------------------------------------atattgaaggctctatttcttcttcatccaattt -s simRat_chr6.simRat.chr6 195725 61 - 647215 cctgggtatact-tcatatcgtccacaa----------------------------------------------------------------------------------------atattgaaagtttcatctccccttcttccaatag - -a -s simMouse_chr6.simMouse.chr6 323324 100 + 636262 cctgcttatcttgatcctgttgggttgtctgcaccaatagctccaggattttgttgaagagcagtggtgatatggaacagccctgcctcctttttgtgcc -s mr.mrrefChr5 234702 100 + 294540 cctgtttatctttatcctgtcgggttgtctgcgccaatagttccaggattttgttaaacagcagtgatgatatggaacagccctgctgccttttcgtgcc -s simMouse_chr6.simMouse.chr6 380950 100 + 636262 accgtttatctttatcctgtctggttgtctgtgccaatagttccaggactttgttaaacagcagcgatgatatggaacagccctgctggcttttcgtgtc -s simRat_chr6.simRat.chr6 380461 100 + 647215 attgtttatctttaacctgtctggttgtctgcgccaatagttccaggactttgttaaacagcagtaatgatatagaacaaccctgctggcttttcacacc -s simRat_chr6.simRat.chr6 195791 100 - 647215 cctatttatctttatcctgtcgggctgtccacaccaatagttccaggattctgttgaacagcagcggtgatatggaaccgccctgccaccttgtcatgcc - -a -s simMouse_chr6.simMouse.chr6 323424 73 + 636262 ctttaaaagaaagacttcaatcctgcacccatttactattagattgcaagccggtttatcgtaaattgccctc -s mr.mrrefChr5 234802 73 + 294540 ctttaaagggaagacttcaagcctgcatccatttactattagattgcaaatcggtttatcgtaaattgcccta -s simMouse_chr6.simMouse.chr6 381050 72 + 636262 ctttaaagggaagac-tcaagcctgcatccatttattattagattgcaaatcagtttgtagtaaattactcta -s simRat_chr6.simRat.chr6 380561 73 + 647215 ctttaaagggaaggcttcaagcctgcatacatttactctgagatcgcagatcagttaattgtatattgctcta -s simRat_chr6.simRat.chr6 195903 73 - 647215 ttttaaagggaagacttcaagcctgcatccatttactattagattgcacgtgggtttatcgtaaattgcccta - -a -s simMouse_chr6.simMouse.chr6 323497 18 + 636262 acaacattgacgtagttg -s mr.mrrefChr5 234875 18 + 294540 acaacattgacgtagttg -s simRat_chr6.simRat.chr6 195976 18 - 647215 acaacattgatgtagttg - -a -s simMouse_chr6.simMouse.chr6 323515 32 + 636262 ccctcgacacacaactcattgaggatcattag -s mr.mrrefChr5 234893 32 + 294540 ccctcgatgcacaactcattgaggatcattag -s simMouse_chr6.simMouse.chr6 381122 32 + 636262 cccttgatgcaccatgcattgaggatcgttgg -s simRat_chr6.simRat.chr6 380634 32 + 647215 ccctcaatgcacaactcattgaggatcattag -s simRat_chr6.simRat.chr6 195994 32 - 647215 cccttgatgcataactcattaagaatccttag - -a -s simMouse_chr6.simMouse.chr6 323547 27 + 636262 catgtgatcctgctctgcctgtacggc -s mr.mrrefChr5 234925 27 + 294540 catgcaatcctgctcagtctgttcgat -s simMouse_chr6.simMouse.chr6 381155 27 + 636262 catgcaatcctgcttagtctgtttgat -s simRat_chr6.simRat.chr6 380666 27 + 647215 catgcagtcctgtttagtctgtttgat -s simRat_chr6.simRat.chr6 196026 27 - 647215 catgtaatcctgctccacctgttcgat - -a -s simMouse_chr6.simMouse.chr6 323574 2 + 636262 cg -s mr.mrrefChr5 234952 2 + 294540 tg -s simMouse_chr6.simMouse.chr6 381182 2 + 636262 tg -s simRat_chr6.simRat.chr6 196053 2 - 647215 gg - -a -s simMouse_chr6.simMouse.chr6 323576 14 + 636262 gcccgtcatctctt -s mr.mrrefChr5 234954 14 + 294540 gcccgtcctctctt -s simMouse_chr6.simMouse.chr6 381184 14 + 636262 gcctgacctctctt -s simRat_chr6.simRat.chr6 380693 14 + 647215 gtcaaacctctctt -s simRat_chr6.simRat.chr6 196055 14 - 647215 gcccattatctctt - -a -s simMouse_chr6.simMouse.chr6 323590 34 + 636262 atgtgattcttctgattggcccggttaataggtt -s mr.mrrefChr5 234983 34 + 294540 atgtgattctcctgattggcccggttaaccgttt -s simMouse_chr6.simMouse.chr6 381213 34 + 636262 ctgtgattctcctgattggccaggttatctgttt -s simRat_chr6.simRat.chr6 380722 34 + 647215 ctgtgattctcctgattgccccagttagccattt -s simRat_chr6.simRat.chr6 196084 34 - 647215 atgtgcttctcccgattagcccagttaaccagtt - -a -s simMouse_chr6.simMouse.chr6 323624 6 + 636262 gtatta -s mr.mrrefChr5 235017 6 + 294540 gtatta -s simRat_chr6.simRat.chr6 196118 6 - 647215 gtatta - -a -s simMouse_chr6.simMouse.chr6 323630 4 + 636262 tgct -s mr.mrrefChr5 235023 4 + 294540 catt -s simMouse_chr6.simMouse.chr6 381247 4 + 636262 cata -s simRat_chr6.simRat.chr6 380756 4 + 647215 catt -s simRat_chr6.simRat.chr6 196124 4 - 647215 catt - -a -s simMouse_chr6.simMouse.chr6 323634 14 + 636262 agcaggttttcata -s mr.mrrefChr5 235027 14 + 294540 agcaggttttcata -s simRat_chr6.simRat.chr6 196128 14 - 647215 aataggtatttgta - -a -s simMouse_chr6.simMouse.chr6 323648 3 + 636262 tct -s mr.mrrefChr5 235041 3 + 294540 tct -s simMouse_chr6.simMouse.chr6 381251 3 + 636262 tcc -s simRat_chr6.simRat.chr6 380760 3 + 647215 tct -s simRat_chr6.simRat.chr6 196142 3 - 647215 tct - -a -s simMouse_chr6.simMouse.chr6 323651 5 + 636262 Gttac -s mr.mrrefChr5 236044 5 + 294540 gtttc -s simMouse_chr6.simMouse.chr6 382010 4 + 636262 tttt- -s simRat_chr6.simRat.chr6 382002 5 + 647215 gtttt - -a -s simMouse_chr6.simMouse.chr6 323656 463 + 636262 cctcgacaaacaactcatagaggattgttagcatgtgatcctgctctgcctgctcgatcggcccgtcatctcttaggtgattctcttgatcagcccagttaataggttgtattatgctaataggttttcatatcggttaataggtcttcatatcttgcacactcctgggatccctggggtgagttgcaagtgattgtaatgtattggctttccgaccatttgctggtagtttcggttggcaagtatctggttcaagttcctgtcttgcaagatcaaaaccacaggtctaactctctgtcctctcactatggctttacttggtttggataccagtatgatgcatgacttgtgcaaatagtttggtagtattccccttaatttcaatggactgtggatcaagaaCTTTAGCAGCTGTGTGGAATGCCCTGGAACCATAGCATAGGTAGTCAAAACCAAAAATGTG -s Anc0.Anc0refChr7 8152 56 - 16696 C-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CAGCTGTGTGGTCTAACCTGCAACGATAGCATAGGTAGTTGTAACCAAAAATGTT -s Anc1.Anc1refChr4 8551 61 + 17549 C------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TAAAACAGCTGTGTGGTCTAACCTGCAACGATAGCATAGGTAGTTGTAACCAAAAATGTT -s Anc2.Anc2refChr7 3625 56 + 32194 C-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CAGCTGTGTGGTCTAACCTGCAATGATAGCATAGGTAGTTGTAACCAAAAATTTT -s mr.mrrefChr5 171728 443 + 294540 cctcgacaaacaactcatagaggattgttagcatgtgatcctgctctgcctgctcgatcggcccgtcatctcttaggtgattctcttgatcagcccagttaataggttgtattatgctaata-------------------aggtcttcatatcttgcacactcctgggatccctggggtgagttgcaagtgattgtaatgtattggctttccgaccatttgctggtagtttcggttggcaagtatctggttcaagttcctgtcttgcaagatcaaaaccacaggtctaactctctgtcctctcactatggctttacttggtttggataccagtatgatgcatgacttgtgcaaatagtttggtagtat-ccccttaatttcaatggactgtggatcaagaaCTTTAGCAGCTGTGTGGAATGACCTGGAACCATAGCATAGGTAGTCAAAACCAAAAATGTT -s simCow_chr6.simCow.chr6 300121 56 + 602619 C-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CAGCTGTATGTACTAACATGAGATGATAGCACAGGTAATTGCAGCAAAAAATTTT -s simDog_chr6.simDog.chr6 308045 56 - 593897 C-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CATCTGTGTGGTCTAACCTGCAATGATAACATAGGTAGTTGTAACCAAAAATTTC -s simHuman_chr6.simHuman.chr6 309936 61 + 601863 C------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TAAAACAGCTGTGTCAGCTAACCTGCCACAATGGCATAGATGGTTGTAACCAAAAATGTT -s simRat_chr6.simRat.chr6 315210 443 + 647215 cctctatacacaactcattgaggatcattagcatgtgattgtgctctgttggttcaatcagcccatcatctcttatgtgattctcctgattggccttgttaatgggttgtatagtgttaata-------------------atgtcttcatttcttgcaccatcctggcattcctggggcgaattctgagtggttgtaatgaattaactgtctggccatttgctggtagtttcgcttggcaagtgtctgggtcaggttcccatctttcaagatcaaaaacaaaggtctaactctctgttctctcactgtggctttactcgatttggatatcagtatgatgcatgacttgtgcaaatagtttggtagtat-ccccttgctttcaatgaattgtggctcgggAACTTTACCAGCTGTGTGGAATGACCTGTAACCATAGTGTGGGTAGACAAAATCAAAAATGTT - -a -s simMouse_chr6.simMouse.chr6 324119 16 + 636262 CAATCACACCTTCAAA -s Anc0.Anc0refChr7 8208 16 - 16696 CAAGGTTGTCTTCTAC -s Anc1.Anc1refChr4 8612 16 + 17549 CAAGGTTGTCTTCTAC -s Anc2.Anc2refChr7 3681 16 + 32194 CAAGGCTGACTTCTAC -s mr.mrrefChr5 172171 16 + 294540 CAAGCTTGTCTTCAAA -s simCow_chr6.simCow.chr6 300177 16 + 602619 CAAGGCTGCCCTCTAC -s simDog_chr6.simDog.chr6 308101 16 - 593897 CAAGGCTGACTTCTAC -s simHuman_chr6.simHuman.chr6 309997 16 + 601863 CAAGGTTGTCTTCTAC -s simRat_chr6.simRat.chr6 315654 16 + 647215 CAAGATTGTCTTCCAT - -a -s simMouse_chr6.simMouse.chr6 324135 1 + 636262 T -s Anc0.Anc0refChr7 8225 1 - 16696 T -s Anc1.Anc1refChr4 8629 1 + 17549 T -s Anc2.Anc2refChr7 3698 1 + 32194 T -s mr.mrrefChr5 172187 1 + 294540 T -s simCow_chr6.simCow.chr6 300194 1 + 602619 T -s simDog_chr6.simDog.chr6 308118 1 - 593897 G -s simHuman_chr6.simHuman.chr6 310014 1 + 601863 T -s simRat_chr6.simRat.chr6 315670 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 324136 61 + 636262 CATGCACATAGATCTGGGTAGGATGATCCTTGCCTCTTTGCAGAAAATAATCATGTTCCCT -s Anc0.Anc0refChr7 8228 48 - 16696 CATTAAGTCACACCTTGACGTCATG-------CACATGCATGGGTAGCA------TTGCCC -s Anc1.Anc1refChr4 8632 48 + 17549 CATTAAGTCACACCTTGACGTCATG-------CACATGCATGGGTAGCA------TTGCCC -s Anc2.Anc2refChr7 3701 48 + 32194 CACTAAGGCACACTTTGACCTCATG-------CACATGCATGGGTAGCA------TAGCCC -s mr.mrrefChr5 172190 61 + 294540 CATGAAGTCACACCTTGATGGCATGATCCTTGCCTCTTTGTAGAAAACAATCATGTTCCCT -s simCow_chr6.simCow.chr6 300197 34 + 602619 CACTAAGGCAC----CGACATTATA-------CA-GTGCCTGGGAC--------------- -s simDog_chr6.simDog.chr6 308121 48 - 593897 CACCAAGGAGCACTTTGACCTCATG-------CACAAGCATGGGTAGCA------TAGCCC -s simHuman_chr6.simHuman.chr6 310017 48 + 601863 CATTAAGTCACGCCTTGACGTCAAG-------CACATGCATGGGGAGCA------TTTCCC -s simRat_chr6.simRat.chr6 315673 61 + 647215 CATGAAGTCACACCTTCAAGGCATGATCCCTGCTTCCCTGTAGAAAACAGTTGTGTGCCCT - -a -s simMouse_chr6.simMouse.chr6 324197 22 + 636262 GCTTCTTAGAAGTAAACAGTGG -s Anc0.Anc0refChr7 8276 19 - 16696 GCTTGTTTGAG---AACAGTGG -s Anc1.Anc1refChr4 8680 19 + 17549 GCTTGTTTGAG---AACAGTGG -s Anc2.Anc2refChr7 3749 19 + 32194 GCTTGGTTGAG---AACAGTGG -s mr.mrrefChr5 172251 22 + 294540 GCTTCTTAGAAGTAAACAGTGG -s simCow_chr6.simCow.chr6 300231 18 + 602619 -CTTGCTGGAG---GTCAATGG -s simDog_chr6.simDog.chr6 308189 19 - 593897 GTTTAGTTGAG---AACAGTGG -s simHuman_chr6.simHuman.chr6 310065 19 + 601863 GCTTGTTTGAG---AATAGGGG -s simRat_chr6.simRat.chr6 315734 22 + 647215 GCTTCCTAGAAGAAAACAGTTG - -a -s simMouse_chr6.simMouse.chr6 324219 6 + 636262 CACTAT -s Anc0.Anc0refChr7 8295 6 - 16696 TACTCT -s Anc1.Anc1refChr4 8699 6 + 17549 TACTCT -s Anc2.Anc2refChr7 3768 6 + 32194 TAACCT -s mr.mrrefChr5 172273 6 + 294540 CACTAT -s simCow_chr6.simCow.chr6 300249 6 + 602619 TTACCT -s simDog_chr6.simDog.chr6 308208 5 - 593897 TAA-CT -s simHuman_chr6.simHuman.chr6 310084 6 + 601863 TACTCT -s simRat_chr6.simRat.chr6 315758 6 + 647215 CACTAT - -a -s simMouse_chr6.simMouse.chr6 324225 52 + 636262 GATTTTGGAGAATCCTCAGGGATAAGATCACTTACACTTTTACATCCCATAT -s Anc0.Anc0refChr7 8305 44 - 16696 GACTTTTGAGGATTCTTGTGTGTAGGACCACTTACA--------CCCCATAC -s Anc1.Anc1refChr4 8709 44 + 17549 GACTTTTGAGGATTCTTGTGTGTAGGACCACTTACA--------CCCCATAC -s Anc2.Anc2refChr7 3778 44 + 32194 GACTTTTGAGGATTCTTGTGTGTAGGCCCACTTACA--------CCTCAGAC -s mr.mrrefChr5 172279 52 + 294540 GATTCTGTGGAATTCTCAGAGATAAGATCACTTACACTCTTACATCCCATAT -s simCow_chr6.simCow.chr6 300259 44 + 602619 GATTCTTGACAATTCTTGTGCAAAAGCCCACTTACA--------CCTCAGAC -s simDog_chr6.simDog.chr6 308217 34 - 593897 GACTTTTAAGG--TCTTGTGTGTAGGCCCATTTACA---------------- -s simHuman_chr6.simHuman.chr6 310094 36 + 601863 GAAATTTGAGGATTCTT--------GACCACTTACA--------CCCCATAC -s simRat_chr6.simRat.chr6 315764 52 + 647215 GATTCTGTGGAATTGTCAGAAATAAGATGACTTACATTCTTGCATGTCATCT - -a -s simMouse_chr6.simMouse.chr6 324277 2 + 636262 GT -s Anc0.Anc0refChr7 8349 1 - 16696 A- -s Anc1.Anc1refChr4 8753 1 + 17549 A- -s Anc2.Anc2refChr7 3822 1 + 32194 A- -s mr.mrrefChr5 172331 2 + 294540 AT -s simCow_chr6.simCow.chr6 300317 1 + 602619 A- -s simHuman_chr6.simHuman.chr6 310130 1 + 601863 A- -s simRat_chr6.simRat.chr6 315816 2 + 647215 AT - -a -s simMouse_chr6.simMouse.chr6 324279 90 + 636262 ACGTTTATAATATCCTCAAGTGGTTATTATGGTCATGGTATCAGACCAGTCCGCAGGTAGATTGGTAGATCTAGGATAGTGTGAATTGGC -s Anc0.Anc0refChr7 8350 82 - 16696 ATGTGTATAGTATCCTCCAGTAGTGATTATGGTCATGACATCAAACCATCCAGCAAGAGGAGC--------TGGGATAGTGGGAGTTGGC -s Anc1.Anc1refChr4 8754 82 + 17549 ATGTGTATAGTATCCTCCAGTAGTGATTATGGTCATGACATCAAACCATCCAGCAAGAGGAGC--------TGGGATAGTGGGAGTTGGC -s Anc2.Anc2refChr7 3823 82 + 32194 ATATGTATAGTATGCCCCAGTAGTGCTTATGGTTATAACATCAAACCATCCAGCAAGAGGAGC--------TGGGATAGTGGGAGTTGGC -s mr.mrrefChr5 172333 90 + 294540 ATGTTTATAGTATCCTCAAGTGGTTATTATGGTCATGGCATCAAACCAGTCCGCAAGTAGATCGGTAGATCTAGGATAGTGTGAACTGGC -s simCow_chr6.simCow.chr6 300319 73 + 602619 ATATGTATAGTA---------GGTGCTTATGGTTATAATATCAAACCATCCAACGTGAGGAGC--------TGGGATAGTGGGAATTGAC -s simDog_chr6.simDog.chr6 286490 76 + 593897 ------ATAGAGTGCCCCAGTAGTGCTTAAGGTTATAACATCAAACCATCCTGCAAGAGGACC--------CGGGTTAGTGGAAGTTGGC -s simHuman_chr6.simHuman.chr6 310131 82 + 601863 ATGTGTATAGTATCCTCCAATAGTGATTGTTGTCATGACATCAAACCACCCAGTAAAAGGAGC--------TGGGATACTTGGAGATGGC -s simRat_chr6.simRat.chr6 315818 87 + 647215 ATGTTTATAGTATCCTCAAGTGGTTGTTATGTTCACGGCACCAAATCAGTTGGCAAGTAGATCGGTAGATCTAGGATAGTGAGAACT--- - -a -s simMouse_chr6.simMouse.chr6 324369 60 + 636262 TGCACGGTACTTGAATGATAATAGTAGGTTAAGAGCTCAATAATTTGCCAGAGATCTTGA -s Anc0.Anc0refChr7 8440 35 - 16696 TCTAC----TTTATACAGTAAAAC--AGTTAAATGGTCAAT------------------- -s Anc1.Anc1refChr4 8844 35 + 17549 TCTAC----TTTATACAGTAAAAC--AGTTAAATGGTCAAT------------------- -s Anc2.Anc2refChr7 3913 35 + 32194 TCTAC----TTGATGCAGTAAAAC--AGTGAAATAGTCTGC------------------- -s mr.mrrefChr5 172423 56 + 294540 TGCAC----CTTGAATGATAATAGTAAGTTAAGAGGTCAATAATTTGCCAGAGATCTTGA -s simCow_chr6.simCow.chr6 300399 28 + 602619 TCCAT----ATGATGCAGTAAAAC--AGTGAGGT-------------------------- -s simDog_chr6.simDog.chr6 286570 31 + 593897 CCTAC----TTGATGCAATAA------GCGAAATAGTCTGC------------------- -s simHuman_chr6.simHuman.chr6 310221 35 + 601863 TCTAC----TTTATACAGTAAAAT--AGTTAAATGGTCAAT------------------- -s simRat_chr6.simRat.chr6 315905 49 + 647215 ---------CTGGAATGCTAATAATAAGCCAAGAGGTCAATAA--TGCCAGAGACCTTGA - -a -s simMouse_chr6.simMouse.chr6 324429 98 + 636262 CAGAACATGACCAAATTATAACAGCCAGCAAATCCCAGCTTGCGTCTGCATGCTGAACCCCGCTTAGAGAACCCCTGCCTGGTAGTCTTCGTTTTTTA -s Anc0.Anc0refChr7 8475 44 - 16696 -----------------------------AATTCCCAGCATA-------------------GTTTAGAGAACCTTCA----GTAGTGGTTATTTTT-- -s Anc1.Anc1refChr4 8879 44 + 17549 -----------------------------AATTCCCAGCATA-------------------GTTTAGAGAACCTTCA----GTAGTGGTTATTTTT-- -s Anc2.Anc2refChr7 3948 44 + 32194 -----------------------------AATTTCCAGCAGA-------------------GTTTAGGGAACCTTCA----TTAGTGGTTATTTTT-- -s mr.mrrefChr5 172479 97 + 294540 CAGAACATGACCAAATTATAACAGCCAGCAAATCCCAGCTTGCGTCTGCATGCTG-ACCCCGCTTAGAGAACCCCTGCCTGGTAGTCGTTGTTTTTTA -s simCow_chr6.simCow.chr6 300427 37 + 602619 -----------------------------------CAGCAGA-------------------GTTTAGTGGACCTTCA----ATAGTAGTCATTTT--- -s simDog_chr6.simDog.chr6 286601 44 + 593897 -----------------------------AATTTCCATCAGA-------------------ATTTAGGGAACCTTCA----TTAGTGGCTATTTTT-- -s simHuman_chr6.simHuman.chr6 310256 44 + 601863 -----------------------------AATCCGCAGCATA-------------------GTTTAGAGAACCTTCA----GTAGTGGTTATTTTT-- -s simRat_chr6.simRat.chr6 315956 93 + 647215 CAGAACATAGCCAAATTACAACAGCCAGGTAATCCCAGTTTGTGTCTGCCCGTTG-ACCCCACCTAGAAAAC----GCCTGGTAGTTGTTGTTTTTTA - -a -s simMouse_chr6.simMouse.chr6 324527 7 + 636262 GGGCATA -s Anc0.Anc0refChr7 8519 7 - 16696 GTGCATG -s Anc1.Anc1refChr4 8923 7 + 17549 GTGCATG -s Anc2.Anc2refChr7 3992 7 + 32194 GTGCATG -s mr.mrrefChr5 172576 7 + 294540 GGGCATA -s simCow_chr6.simCow.chr6 300464 5 + 602619 --GCCTG -s simDog_chr6.simDog.chr6 286647 7 + 593897 GTGCATA -s simHuman_chr6.simHuman.chr6 310300 7 + 601863 GTGCAGG -s simRat_chr6.simRat.chr6 316049 7 + 647215 GGGTGTA - -a -s simMouse_chr6.simMouse.chr6 324534 32 + 636262 CTTTGTTACTGTTTGGGTGACTTTCTCGCTTC -s Anc0.Anc0refChr7 8526 32 - 16696 CTTTGTTACTGTTTGGATGAGTGTCTCTCACC -s Anc1.Anc1refChr4 8930 32 + 17549 CTTTGTTACTGTTTGGATGAGTGTCTCTCACC -s Anc2.Anc2refChr7 4000 32 + 32194 TTTTGTTACTGTTTGGATGAGTGTCTCTCACC -s mr.mrrefChr5 172583 32 + 294540 CTTTGTTACTGTTTGCGTGACTTTCACTCTCC -s simCow_chr6.simCow.chr6 300470 32 + 602619 TTTTTTTGCTGTTTTGATGAGTGTCCCTCACC -s simDog_chr6.simDog.chr6 286655 32 + 593897 TTTTGTTACAGTTTGGGTGAGTGGCTCTCACC -s simHuman_chr6.simHuman.chr6 310307 24 + 601863 CTCT--------TTGGATGAGTCTCTCTCATC -s simRat_chr6.simRat.chr6 316056 32 + 647215 CTTTGTTACTGTTTCCGCGACTTTCACTCACC - -a -s simMouse_chr6.simMouse.chr6 324566 30 + 636262 CAGAGATTAGGTTGTTGGACCCCAGAAGGG -s Anc0.Anc0refChr7 8558 30 - 16696 CAGACATTAGATTGTTGGACCCTAGAGGGT -s Anc1.Anc1refChr4 8962 30 + 17549 CAGACATTAGATTGTTGGACCCTAGAGGGT -s Anc2.Anc2refChr7 4032 30 + 32194 TGCACATTAGATTGTTGGACCCTAGAGGGT -s mr.mrrefChr5 172615 30 + 294540 CAGAGATTAGGTTGTTGGACTCCAGAAGGG -s simCow_chr6.simCow.chr6 300503 30 + 602619 TGCACTTTGGATTGCTAGGCCCAAGATGGC -s simDog_chr6.simDog.chr6 286687 30 + 593897 TGCACATGAGAGTGTCGGACCCTAGAGTGT -s simHuman_chr6.simHuman.chr6 310331 30 + 601863 CAGACATTAGTTTGTTGGACCCTAGAGGAT -s simRat_chr6.simRat.chr6 316088 26 + 647215 CAGAGTTTAGGTTGTTGGACTCCAGA---- - -a -s simMouse_chr6.simMouse.chr6 324596 34 + 636262 ACAGAGCTAAAGAGCGGCTTGATGTGATGGTCTG -s Anc0.Anc0refChr7 8589 33 - 16696 ACAGAGCCAATAAGCAGCTTAGT-TGTTGATTTG -s Anc1.Anc1refChr4 8993 33 + 17549 ACAGAGCCAATAAGCAGCTTAGT-TGTTGATTTG -s Anc2.Anc2refChr7 4063 33 + 32194 ACAGAGCCAATAAGCAGCTTAGT-TGTTGACTTG -s mr.mrrefChr5 172645 33 + 294540 ACAGAGCTAAAGAGCGGCTTGAT-TGATGGTCTG -s simCow_chr6.simCow.chr6 300534 33 + 602619 ACAGAGACAATGAGCAGGTTAGT-AGTCGCCTTG -s simDog_chr6.simDog.chr6 286718 33 + 593897 ACAGAGCCAATAAGCCACCTGGT-TGTTGACTTG -s simHuman_chr6.simHuman.chr6 310362 33 + 601863 AGAGATCCAGTAAGCAGCTCAGT-TGTTCATTTG - -a -s simMouse_chr6.simMouse.chr6 324630 66 + 636262 TCATGGTATTCATTAGTGTACATGAGCTTAGCAAAACAATCTCGTATGCTTAAATGCTGCCTGTAT -s Anc0.Anc0refChr7 8622 66 - 16696 TCATGGTTTTCAACACTCTACGTGAGCTTAGCAAAACGATCTGGAGTGCCCAAAGCCTCCCGATAT -s Anc1.Anc1refChr4 9026 66 + 17549 TCATGGTTTTCAACACTCTACGTGAGCTTAGCAAAACGATCTGGAGTGCCCAAAGCCTCCCGATAT -s Anc2.Anc2refChr7 4097 66 + 32194 TCAAGGTTTTCAACACTCTACGTGGGCTTAGCAGAACGATCTGGAGTAACCAAAGCCCCCTGATAT -s mr.mrrefChr5 172678 66 + 294540 TCATGGTATTCATTAGTGTACATGAGCTTAGCAAAACAATCTCGTATGCCCAAATGCTGCCTGTAT -s simCow_chr6.simCow.chr6 300568 63 + 602619 TCAAGGGTTTCAA---TCTACATGCGCTTAGCATAACGATCTGGGGTAGCCAAAGCCCCCTGATAT -s simDog_chr6.simDog.chr6 286752 65 + 593897 TCAAGGTTTGCAACACTTTTTGTGGGATTAGCAGATCAATCTGGAGTAACCAAAGCTCCCT-GCAT -s simHuman_chr6.simHuman.chr6 310395 66 + 601863 TCATGGCTTTCAACACTCTACTTGAGCTTAGCAAAACGATCTGGAGTGCCCAAAGTCTCCCCATAT -s simRat_chr6.simRat.chr6 316114 19 + 647215 ------------------------------------------CATATGCCCAAACGCTGCC----- - -a -s simMouse_chr6.simMouse.chr6 324696 43 + 636262 TTGCTTTGCTTGTGTAGGGTGATGCAAACGAAAAATCTGGATA -s Anc0.Anc0refChr7 8689 43 - 16696 TTGCTCTGCTTGTGTAGAGTGATGTCAATGTAAAATCTGGATA -s Anc1.Anc1refChr4 9093 43 + 17549 TTGCTCTGCTTGTGTAGAGTGATGTCAATGTAAAATCTGGATA -s Anc2.Anc2refChr7 4164 43 + 32194 TTACACTGCTTGTGTAGAGTGATATCAATGTAAAATCTGGATA -s mr.mrrefChr5 172745 43 + 294540 TTGCTTTGCTTGTGTAGAGTGATGTAAACGAAAAATCTGGATA -s simCow_chr6.simCow.chr6 300631 41 + 602619 --ACACTGCTTGTGTCGAGTGATATCAAGGTAAATTCTGGATA -s simDog_chr6.simDog.chr6 286818 43 + 593897 TTACACTGCATGTGTAGAGTGATATCAATGAAAAATCTGGATA -s simHuman_chr6.simHuman.chr6 310462 43 + 601863 TTGCTATGCTTGTGTAGAGTGAAGTCAATGTATAATCTGTATA -s simRat_chr6.simRat.chr6 316134 43 + 647215 TTGCTTTGTTTGTGTAGAGTGATGTAAACGAAAAATCTGGATA - -a -s simMouse_chr6.simMouse.chr6 324739 13 + 636262 TTACACTCAAAAA -s Anc0.Anc0refChr7 8732 13 - 16696 TTACTGTCAAAAA -s Anc1.Anc1refChr4 9136 13 + 17549 TTACTGTCAAAAA -s Anc2.Anc2refChr7 4207 13 + 32194 TTACTGTCAAGAA -s mr.mrrefChr5 172788 13 + 294540 TTACACTCAAAAA -s simCow_chr6.simCow.chr6 300673 13 + 602619 TTAATGTCAAGGA -s simDog_chr6.simDog.chr6 286861 13 + 593897 TCACTGCCAAGAA -s simHuman_chr6.simHuman.chr6 310505 13 + 601863 TTACTATCGAAAA -s simRat_chr6.simRat.chr6 316177 13 + 647215 TTACACTCAAAAA - -a -s simMouse_chr6.simMouse.chr6 324752 4 + 636262 TTCA -s Anc0.Anc0refChr7 8746 4 - 16696 TTCA -s Anc1.Anc1refChr4 9150 4 + 17549 TTCA -s Anc2.Anc2refChr7 4221 4 + 32194 TTCA -s mr.mrrefChr5 172802 4 + 294540 TTCA -s simCow_chr6.simCow.chr6 300687 4 + 602619 TTCA -s simDog_chr6.simDog.chr6 286875 2 + 593897 T--A -s simHuman_chr6.simHuman.chr6 310519 4 + 601863 TTCA -s simRat_chr6.simRat.chr6 316191 4 + 647215 TACA - -a -s simMouse_chr6.simMouse.chr6 324756 33 + 636262 TTAAGGCAGTCCTCCCATTTCTGATCTGTAAGT -s Anc0.Anc0refChr7 8751 33 - 16696 TGCAGGGACTCCTGCATATTCTGATCCCTAAGT -s Anc1.Anc1refChr4 9155 33 + 17549 TGCAGGGACTCCTGCATATTCTGATCCCTAAGT -s Anc2.Anc2refChr7 4226 33 + 32194 TGCAAAGGCTCCCGCATGTTCTGATCTCTAACG -s mr.mrrefChr5 172806 33 + 294540 TTAAGGCAGTCCTCCCAATTCTGATCCGTAAGT -s simCow_chr6.simCow.chr6 300692 30 + 602619 T---AAGGCACCCGCATCTTCTGATCTCTAAGG -s simDog_chr6.simDog.chr6 286878 29 + 593897 TGCA----CTTCCACATGTTCTGATGTCTAACG -s simHuman_chr6.simHuman.chr6 310524 33 + 601863 TCCAGGGACTCCTGCATAGTTTGAGCCACATGT -s simRat_chr6.simRat.chr6 316195 32 + 647215 TTAAGGCAGTCCTCCTAATTCTGACACGTAAG- - -a -s simMouse_chr6.simMouse.chr6 324789 17 + 636262 AACCCACTTACTAACTC -s Anc0.Anc0refChr7 8784 9 - 16696 AACCCA--GA------G -s Anc1.Anc1refChr4 9188 9 + 17549 AACCCA--GA------G -s Anc2.Anc2refChr7 4259 9 + 32194 AGCCCA--GA------G -s mr.mrrefChr5 172839 15 + 294540 AACCCA--TACTAACTT -s simCow_chr6.simCow.chr6 300722 9 + 602619 AGCCCA--GA------C -s simDog_chr6.simDog.chr6 286907 9 + 593897 AGCCCA--GA------G -s simHuman_chr6.simHuman.chr6 310564 9 + 601863 TATCTT--CA------G -s simRat_chr6.simRat.chr6 316227 6 + 647215 -----------TAACTT - -a -s simMouse_chr6.simMouse.chr6 324806 29 + 636262 ACTTACTATTTAAAAAGCGGTCAAGCTTG -s Anc0.Anc0refChr7 8793 29 - 16696 ATCCATTATTGAACCTGGACTGAGGAATG -s Anc1.Anc1refChr4 9197 29 + 17549 ATCCATTATTGAACCTGGACTGAGGAATG -s Anc2.Anc2refChr7 4271 29 + 32194 ATCCATTATTGAGCCTGGACTGAGGAATG -s mr.mrrefChr5 172854 29 + 294540 ACTCATTATTTAAACAGCGGTCAGGATTG -s simCow_chr6.simCow.chr6 300734 29 + 602619 ATTCATTCTTTACACTGGACTGAGGAATG -s simDog_chr6.simDog.chr6 286919 29 + 593897 ATCCATTATTGAGCCTGGACTCAGTAATA -s simHuman_chr6.simHuman.chr6 310573 29 + 601863 ATCTATGACTAGACTGGTAATGAGGTATG -s simRat_chr6.simRat.chr6 316233 28 + 647215 ACTCATTATCTAAGCACCGGTC-GGATTG - -a -s simMouse_chr6.simMouse.chr6 324835 1 + 636262 C -s Anc0.Anc0refChr7 8822 1 - 16696 T -s Anc1.Anc1refChr4 9226 1 + 17549 T -s Anc2.Anc2refChr7 4300 1 + 32194 T -s mr.mrrefChr5 172883 1 + 294540 T -s simCow_chr6.simCow.chr6 300763 1 + 602619 T -s simDog_chr6.simDog.chr6 286948 1 + 593897 T -s simHuman_chr6.simHuman.chr6 310663 1 + 601863 T -s simRat_chr6.simRat.chr6 316261 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 324836 9 + 636262 AGTCTTATT -s Anc0.Anc0refChr7 8823 9 - 16696 GGTCTTACT -s Anc1.Anc1refChr4 9227 9 + 17549 GGTCTTACT -s Anc2.Anc2refChr7 4304 9 + 32194 GGTCTAACT -s mr.mrrefChr5 172884 9 + 294540 GGTCTTATT -s simCow_chr6.simCow.chr6 300767 9 + 602619 GGTCTAACC -s simDog_chr6.simDog.chr6 286952 9 + 593897 GGTCTTATT -s simHuman_chr6.simHuman.chr6 310664 9 + 601863 GTGGTTACT -s simRat_chr6.simRat.chr6 316262 9 + 647215 GGTCTTATT - -a -s simMouse_chr6.simMouse.chr6 324845 26 + 636262 GGTTTGAGCTTCATGTATAGGCATGT -s Anc0.Anc0refChr7 8832 26 - 16696 AGTTTGAGCCACATATATCAGTATGT -s Anc1.Anc1refChr4 9236 26 + 17549 AGTTTGAGCCACATATATCAGTATGT -s Anc2.Anc2refChr7 4338 26 + 32194 AGTTTGAGCCACATATATCAATATGT -s mr.mrrefChr5 172893 26 + 294540 AGTTTGAGCTTCATGTATAGGCATGT -s simCow_chr6.simCow.chr6 300798 22 + 602619 ----TGAGCCACATATACAAATATAT -s simDog_chr6.simDog.chr6 286986 26 + 593897 AGTTTGAGCCACATATATCAACATGC -s simHuman_chr6.simHuman.chr6 310673 19 + 601863 AGCC-------CAGATATGTGTATTT -s simRat_chr6.simRat.chr6 316271 26 + 647215 AGGTTGAGCTTCATGTCCAGGTACGT - -a -s simMouse_chr6.simMouse.chr6 324871 13 + 636262 GAAGCTGTGCGCC -s Anc0.Anc0refChr7 8858 10 - 16696 TAAG-GAT--ACC -s Anc1.Anc1refChr4 9262 12 + 17549 TAAG-GATCCACC -s Anc2.Anc2refChr7 4364 10 + 32194 TAAG-GAT--ACC -s mr.mrrefChr5 172919 13 + 294540 GAAGCTGTCCGCC -s simCow_chr6.simCow.chr6 300824 10 + 602619 TATG-AAT--GTC -s simDog_chr6.simDog.chr6 287012 10 + 593897 CAAG-GCC--ACC -s simHuman_chr6.simHuman.chr6 310692 12 + 601863 TCAG-GATCCTCA -s simRat_chr6.simRat.chr6 316297 13 + 647215 GAAGTTGTCTGCC - -a -s simMouse_chr6.simMouse.chr6 324884 7 + 636262 CTGTATT -s Anc0.Anc0refChr7 8868 7 - 16696 CTGTATT -s Anc1.Anc1refChr4 9274 7 + 17549 CTGTATT -s Anc2.Anc2refChr7 4374 7 + 32194 CAGCATC -s mr.mrrefChr5 172932 7 + 294540 CTGTATT -s simCow_chr6.simCow.chr6 300834 7 + 602619 CACCCTC -s simDog_chr6.simDog.chr6 287022 7 + 593897 CAGCATC -s simHuman_chr6.simHuman.chr6 310710 7 + 601863 TTGTGTT -s simRat_chr6.simRat.chr6 316310 7 + 647215 CTGTATG - -a -s simMouse_chr6.simMouse.chr6 324891 28 + 636262 TAACACACTCTCCTTTGTATTCCCCCCA -s Anc0.Anc0refChr7 8875 24 - 16696 TA----CCCCTCCTTTGTATTTCCCTCA -s Anc1.Anc1refChr4 9281 26 + 17549 TAAG--CCCCTCCTTTGTATTTCCCTCA -s Anc2.Anc2refChr7 4381 24 + 32194 CA----CCCCTCGTTTGTGTTTCCCTTA -s mr.mrrefChr5 172939 28 + 294540 TAACACCCTCTCCTTTGTATTCCCCCCA -s simCow_chr6.simCow.chr6 300841 24 + 602619 CA----CCCCTGCTTTGTGCTTCCCCTA -s simDog_chr6.simDog.chr6 287032 24 + 593897 CA----CCCCTCGTTTGTGTTTCCCTTC -s simHuman_chr6.simHuman.chr6 310717 22 + 601863 TGAG------TCCTATATATTTCCCTCA -s simRat_chr6.simRat.chr6 316317 28 + 647215 TAACACCCTTTCCTTTGTTTTCCCCCCA - -a -s simMouse_chr6.simMouse.chr6 324919 72 + 636262 GGTCTGCTTCCCTCAGCGGCATTTCCGCACGGATCTTCTGCAGGTGAGGCTGTTCTATTTTGAATTGCTGGT -s Anc0.Anc0refChr7 8901 43 - 16696 GGTGTGCTTCCCACAGAGGCTCTTCTGCACTGAGCTTCTGGAG----------------------------- -s Anc1.Anc1refChr4 9309 72 + 17549 GGTGTGCTTCCCACAGAGGCTCTTCTGCACTGAGCTTCTGGAGGTGTGGCTATTCGGTACAGTGCTCCTGGC -s Anc2.Anc2refChr7 4407 43 + 32194 GGTGTGCTTCCCACAGAGGCTCTTCTGCAATGAGCTTCTGGAG----------------------------- -s mr.mrrefChr5 172967 72 + 294540 GGTCTGCTTCCCTCAGAGGCTTTTCTGCACGGATCTTCTGCAGGTGAGGCTGTTCTATTTTGAATTGCTGGT -s simCow_chr6.simCow.chr6 300867 41 + 602619 GGTGCGCTTCCCGTAGAGGTTATT--GCATTAAGCTTCTGGTC----------------------------- -s simDog_chr6.simDog.chr6 287058 43 + 593897 GGTGTGCTTTCCACAGAGGCTCTTCTACAATGAGCTTCTGGAG----------------------------- -s simHuman_chr6.simHuman.chr6 310741 72 + 601863 GGTGTGCTTCCCACATAAGCTCACCTGCACTGAGTGTCAGGAGGTGTGGCTATTCGGTACAGTGCTCCTGGC -s simRat_chr6.simRat.chr6 316345 72 + 647215 AGTCAGTTGCGCTCAGAAGCTTTTCTGCACGGATGTTCTGAAGCTGAGGCTGTTCTACATGGAATTGCTGGT - -a -s simMouse_chr6.simMouse.chr6 324991 19 + 636262 CAAATCAAGACTCAATTAC -s Anc0.Anc0refChr7 8950 19 - 16696 CACTGGAATAATCACTCAC -s Anc1.Anc1refChr4 9387 19 + 17549 CACTGGAATAATCACTCAC -s Anc2.Anc2refChr7 4456 19 + 32194 CACTGGAGTCATCACTCAC -s mr.mrrefChr5 173039 19 + 294540 CAAATCAAGACTCAATTAC -s simCow_chr6.simCow.chr6 300914 19 + 602619 CAGTGTAGTCATGATTCAA -s simDog_chr6.simDog.chr6 287107 19 + 593897 CACAGGAGTCATCACTCAC -s simHuman_chr6.simHuman.chr6 310820 19 + 601863 CATTGGAATAATTACTCAT -s simRat_chr6.simRat.chr6 316417 19 + 647215 CAAACAAAGACTCAATCAC - -a -s simMouse_chr6.simMouse.chr6 325010 12 + 636262 AGTGGATAAGTA -s Anc0.Anc0refChr7 8969 12 - 16696 GATGCAGGAGTA -s Anc1.Anc1refChr4 9406 12 + 17549 GATGCAGGAGTA -s Anc2.Anc2refChr7 4475 12 + 32194 GATTCTGGAGGA -s mr.mrrefChr5 173058 12 + 294540 AGTGGATAAGTA -s simCow_chr6.simCow.chr6 300933 12 + 602619 GACACTGCAGCA -s simDog_chr6.simDog.chr6 287130 11 + 593897 GATTCTCGAAG- -s simHuman_chr6.simHuman.chr6 310839 12 + 601863 GATGCAGGAGTG -s simRat_chr6.simRat.chr6 316436 12 + 647215 AGTGGATAAGTA - -a -s simMouse_chr6.simMouse.chr6 325022 46 + 636262 ATCAACTGAAAACAATCTGCTCCTTCTGGTCCTCTGCTCCTGAATC -s Anc0.Anc0refChr7 8982 33 - 16696 ATCATATGGTATGA-------------GGTCTATTGCTTGTAGAAG -s Anc1.Anc1refChr4 9419 33 + 17549 ATCATATGGTATGA-------------GGTCTATTGCTTGTAGAAG -s Anc2.Anc2refChr7 4488 33 + 32194 ACAATACAGTGTGA-------------GGTCTATTGCTTGTAGAAG -s mr.mrrefChr5 173070 46 + 294540 ATCAACTGAAAACAATCTGCTCCTTCTGGTCCTCTGCTCCTGAATC -s simCow_chr6.simCow.chr6 300946 29 + 602619 ACAAT----TGTGA-------------CATCTATTGCTTGTAGAAG -s simDog_chr6.simDog.chr6 287141 24 + 593897 ---ATACAGTGTGA-------------GGTCCGTT-----TATAA- -s simHuman_chr6.simHuman.chr6 310852 33 + 601863 ATCATGTGGTATGA-------------GGTCTATGAATTGTAGAAG -s simRat_chr6.simRat.chr6 316448 46 + 647215 ATAGACTTAAAACAATCGGCTCCTTCTGGTGCTCCGCTTTTGAATC - -a -s simMouse_chr6.simMouse.chr6 325068 22 + 636262 TTGAGTGATGACTAATGTACCA -s Anc0.Anc0refChr7 9021 22 - 16696 TTGGGTGTTTCTTTGACCACCA -s Anc1.Anc1refChr4 9458 22 + 17549 TTGGGTGTTTCTTTGACCACCA -s Anc2.Anc2refChr7 4527 22 + 32194 TTGGTGCTGTCTTTGACCACCA -s mr.mrrefChr5 173116 22 + 294540 TTGAGTGATGACTAATGTACCA -s simCow_chr6.simCow.chr6 300981 22 + 602619 TTGGTGCTATCTTTGACCACCA -s simDog_chr6.simDog.chr6 287170 17 + 593897 TTG-----GTCTTTGACCACCA -s simHuman_chr6.simHuman.chr6 310891 22 + 601863 TTGGGTGTTTCTTGGACCAGCA -s simRat_chr6.simRat.chr6 316494 22 + 647215 TTGAGTGATGACTGATGTACCA - -a -s simMouse_chr6.simMouse.chr6 325090 22 + 636262 CCACACCTCCATCAGCGCACAA -s Anc0.Anc0refChr7 9043 6 - 16696 A---ATCCC------------- -s Anc1.Anc1refChr4 9480 6 + 17549 A---ATCCC------------- -s Anc2.Anc2refChr7 4549 6 + 32194 A---TTCCC------------- -s mr.mrrefChr5 173138 6 + 294540 C---ACCTC------------- -s simCow_chr6.simCow.chr6 301003 6 + 602619 A---TGACC------------- -s simDog_chr6.simDog.chr6 287190 6 + 593897 A---TTCCC------------- -s simHuman_chr6.simHuman.chr6 310913 6 + 601863 A---ATCCC------------- -s simRat_chr6.simRat.chr6 316516 6 + 647215 C---ACCTC------------- - -a -s simMouse_chr6.simMouse.chr6 325112 72 + 636262 TGAACTCCTGCAATCCATACAAGTCCAATGTATAGTTTTTGACCCTTCATATCGAATTGTTGTGACAGGTCC -s Anc0.Anc0refChr7 9051 69 - 16696 TGAAATCCTGCAAATCCTGCTAGACCATGTTCTAGTTCTCAACCCTTCAAATGGAATTGTTGT---AGTTCT -s Anc1.Anc1refChr4 9488 69 + 17549 TGAAATCCTGCAAATCCTGCTAGACCATGTTCTAGTTCTCAACCCTTCAAATGGAATTGTTGT---AGTTCT -s Anc2.Anc2refChr7 4557 69 + 32194 TAAAATCCTGCAAATCCTGCTAGATCATGTTCTAGTTCTCAACCCTTCAAATGGAATTGTTGT---AGTTCT -s mr.mrrefChr5 173144 72 + 294540 TGAACTCCTGCAATCCATACAAGTCCAATGTATAGTTTTTGACCCTTCATATCGAATTGTTGTGACAGGTCC -s simCow_chr6.simCow.chr6 301011 69 + 602619 TAAAATCCTGCAAATCCTGCTTGATCATGTTATATTTTTCAAACCTTCGGATTGTAGTGTTAT---AGTGCT -s simDog_chr6.simDog.chr6 287198 69 + 593897 CAAAATCCCGCGAACCCCGCTAGATCACATTCTAGGTCTCAACCCTTCAAATGGAATTGTTGT---AGTTCT -s simHuman_chr6.simHuman.chr6 310921 55 + 601863 TGAAATCCTGCAAATTCTCCCAGACCATGTTGTAGTTCTCATCCCTTCAAATGAA----------------- -s simRat_chr6.simRat.chr6 316522 72 + 647215 TGAAGTCCTGCAATCTGTACAAGTTCAATGGATAGTTTTCTACCCTCCATATCGAATTGTTATGACAGGCCA - -a -s simMouse_chr6.simMouse.chr6 325184 5 + 636262 TAAAC -s Anc0.Anc0refChr7 9120 5 - 16696 TACTC -s Anc1.Anc1refChr4 9557 5 + 17549 TACTC -s Anc2.Anc2refChr7 4626 5 + 32194 TACTC -s mr.mrrefChr5 173216 5 + 294540 TAAAC -s simCow_chr6.simCow.chr6 301080 5 + 602619 TAATC -s simDog_chr6.simDog.chr6 287268 5 + 593897 TACTC -s simRat_chr6.simRat.chr6 316594 5 + 647215 TAGAC - -a -s simMouse_chr6.simMouse.chr6 325189 13 + 636262 TTAGTTTTAGGAC -s Anc0.Anc0refChr7 9125 12 - 16696 TTA-TTGTCACAC -s Anc1.Anc1refChr4 9562 12 + 17549 TTA-TTGTCACAC -s Anc2.Anc2refChr7 4631 12 + 32194 TTG-ATGTCACAC -s mr.mrrefChr5 173221 12 + 294540 TTA-TTTTAAGAC -s simDog_chr6.simDog.chr6 287284 12 + 593897 TTG-ATGTCACAC -s simHuman_chr6.simHuman.chr6 310976 12 + 601863 TCA-TTGTCACGG -s simRat_chr6.simRat.chr6 316599 12 + 647215 TTA-CTTTAAGAC - -a -s simMouse_chr6.simMouse.chr6 325202 36 + 636262 AACCTCAAACAACACGAGGTACAGCCCTGTAATGAT -s Anc0.Anc0refChr7 9161 13 - 16696 -----------------------CCCCTGTAATGAT -s Anc1.Anc1refChr4 9598 36 + 17549 ATCCTCAAACAATATGAGATAAGCCCCTGTAATGAT -s Anc2.Anc2refChr7 4667 13 + 32194 -----------------------CCTCTTTAATCAT -s mr.mrrefChr5 173233 36 + 294540 AACCTCAAACAACATGAGGTAAGGCCCTGTAATGAT -s simDog_chr6.simDog.chr6 287320 13 + 593897 -----------------------CCTCTTTAATCAT -s simHuman_chr6.simHuman.chr6 311196 36 + 601863 ATCCTCAAACAATATGAGATAAGACCCTGTAATGAT -s simRat_chr6.simRat.chr6 316611 36 + 647215 AACCTCAGACAGCATGAGTTAAGGCCATGTATTGAC - -a -s simMouse_chr6.simMouse.chr6 325238 45 + 636262 AACATTTGCTGTCATGGCAACTTGCGGGAAAAGACATACAGTTTG -s Anc0.Anc0refChr7 9174 44 - 16696 -ATATTTACTGTCATGTTGACTTATGGGCACAGAGATAGATCGTG -s Anc1.Anc1refChr4 9634 45 + 17549 AATATTTACTGTCATGTTGACTTATGGGCACAGAGATAGATCGTG -s Anc2.Anc2refChr7 4680 44 + 32194 -ATATTTACTGCCATGTTGAGTTATAAGCACAGAGATAGATCGTG -s mr.mrrefChr5 173269 45 + 294540 AATATTTGCTGTCATGGCAACTTGTGGGAAAAGACATACAGCTTG -s simDog_chr6.simDog.chr6 287333 44 + 593897 -ATATTTACTGCCATGTTGAGTTATAAGCACAGAGATAGATCGTG -s simHuman_chr6.simHuman.chr6 311235 45 + 601863 AATATTTCCTGTCATGATGACTTATGGGCACAGAAATAAGTTCTG -s simRat_chr6.simRat.chr6 316647 45 + 647215 AATATTTGTGGTTATGGCAACTTGTGAGAAAAGAGATACAGCTTG - -a -s simMouse_chr6.simMouse.chr6 325283 4 + 636262 TATA -s Anc0.Anc0refChr7 9242 4 - 16696 TGTA -s Anc1.Anc1refChr4 9703 4 + 17549 TGTA -s Anc2.Anc2refChr7 4748 4 + 32194 TGTA -s mr.mrrefChr5 173314 4 + 294540 TGTA -s simDog_chr6.simDog.chr6 287401 4 + 593897 TGTA -s simHuman_chr6.simHuman.chr6 311304 4 + 601863 TGTA -s simRat_chr6.simRat.chr6 316692 4 + 647215 TGTA - -a -s simMouse_chr6.simMouse.chr6 325287 10 + 636262 TGAGCTTGAA -s Anc0.Anc0refChr7 9246 10 - 16696 TGAGTTTGAA -s Anc1.Anc1refChr4 9707 10 + 17549 TGAGTTTGAA -s Anc2.Anc2refChr7 4752 10 + 32194 TGAGTTTGAA -s mr.mrrefChr5 173318 10 + 294540 TGAGCTTGAA -s simDog_chr6.simDog.chr6 287423 10 + 593897 TGAGTTTGAA -s simHuman_chr6.simHuman.chr6 311308 10 + 601863 TGGGTTTGAA -s simRat_chr6.simRat.chr6 316696 1 + 647215 T--------- - -a -s simMouse_chr6.simMouse.chr6 325297 5 + 636262 TGCTA -s Anc0.Anc0refChr7 9258 5 - 16696 TGCTA -s Anc1.Anc1refChr4 9719 5 + 17549 TGCTA -s Anc2.Anc2refChr7 4764 5 + 32194 TGTTA -s mr.mrrefChr5 173328 5 + 294540 TGCTA -s simCow_chr6.simCow.chr6 301087 5 + 602619 TGTTA -s simDog_chr6.simDog.chr6 287435 5 + 593897 CGTTA -s simHuman_chr6.simHuman.chr6 311320 5 + 601863 TGCTA -s simRat_chr6.simRat.chr6 316697 3 + 647215 --TTA - -a -s simMouse_chr6.simMouse.chr6 325302 5 + 636262 ATTAT -s Anc0.Anc0refChr7 9263 5 - 16696 CTTAT -s Anc1.Anc1refChr4 9724 5 + 17549 CTTAT -s Anc2.Anc2refChr7 4769 5 + 32194 CTTGT -s mr.mrrefChr5 173333 5 + 294540 ATTAT -s simCow_chr6.simCow.chr6 301092 5 + 602619 CTTGA -s simDog_chr6.simDog.chr6 287441 5 + 593897 CTTGT -s simHuman_chr6.simHuman.chr6 311325 5 + 601863 CTTAT -s simRat_chr6.simRat.chr6 316700 5 + 647215 ATTAT - -a -s simMouse_chr6.simMouse.chr6 325307 3 + 636262 GAA -s Anc0.Anc0refChr7 9268 3 - 16696 AAA -s Anc1.Anc1refChr4 9729 3 + 17549 AAA -s Anc2.Anc2refChr7 4774 3 + 32194 AAA -s mr.mrrefChr5 173338 3 + 294540 GAA -s simCow_chr6.simCow.chr6 301098 3 + 602619 CAA -s simDog_chr6.simDog.chr6 287446 3 + 593897 AAA -s simHuman_chr6.simHuman.chr6 311330 3 + 601863 AAT -s simRat_chr6.simRat.chr6 316705 3 + 647215 GAA - -a -s simMouse_chr6.simMouse.chr6 325310 16 + 636262 TAAATTGGCATCTAAT -s Anc0.Anc0refChr7 9271 16 - 16696 TCAATCTGCATTTAAT -s Anc1.Anc1refChr4 9732 16 + 17549 TCAATCTGCATTTAAT -s Anc2.Anc2refChr7 4777 16 + 32194 TCAATCTGCAGTTGAT -s mr.mrrefChr5 173341 16 + 294540 TCAATTGGCATCTAAT -s simCow_chr6.simCow.chr6 301101 16 + 602619 TCAATATGTGGACAAT -s simDog_chr6.simDog.chr6 287449 16 + 593897 TCAGACTGCAGTTGAT -s simHuman_chr6.simHuman.chr6 311333 16 + 601863 TCCATCTCCATTCACT -s simRat_chr6.simRat.chr6 316709 16 + 647215 TCAATTGGCATCTAAT - -a -s simMouse_chr6.simMouse.chr6 325326 3 + 636262 ACT -s Anc0.Anc0refChr7 9287 3 - 16696 TTT -s Anc1.Anc1refChr4 9748 3 + 17549 TTT -s Anc2.Anc2refChr7 4798 3 + 32194 TTT -s mr.mrrefChr5 173357 3 + 294540 ACT -s simCow_chr6.simCow.chr6 301122 3 + 602619 TTT -s simDog_chr6.simDog.chr6 287470 3 + 593897 TTC -s simHuman_chr6.simHuman.chr6 311349 3 + 601863 TTT -s simRat_chr6.simRat.chr6 316725 3 + 647215 ACT - -a -s simMouse_chr6.simMouse.chr6 325329 14 + 636262 ATAATCAATCTGTA -s Anc0.Anc0refChr7 9291 14 - 16696 CTACTCAGTATGAG -s Anc1.Anc1refChr4 9752 14 + 17549 CTACTCAGTATGAG -s Anc2.Anc2refChr7 4802 14 + 32194 CTGCTTAGTATGAG -s mr.mrrefChr5 173360 14 + 294540 ATAATCAATCTGTA -s simCow_chr6.simCow.chr6 301126 14 + 602619 TCTCTTAGTATGAG -s simDog_chr6.simDog.chr6 287474 14 + 593897 CTGCTTAGTATTGG -s simHuman_chr6.simHuman.chr6 311353 14 + 601863 CTACTCAGTATGAT -s simRat_chr6.simRat.chr6 316728 14 + 647215 AAAACCAATCTGTA - -a -s simMouse_chr6.simMouse.chr6 325343 19 + 636262 TTTAATGCTACTTATTGCA -s Anc0.Anc0refChr7 9305 19 - 16696 TTCAGACTTATCACTTACA -s Anc1.Anc1refChr4 9766 19 + 17549 TTCAGACTTATCACTTACA -s Anc2.Anc2refChr7 4816 19 + 32194 TTCAGACTTATCACTTACA -s mr.mrrefChr5 173374 19 + 294540 TTCAATGCTACTTATTGCA -s simCow_chr6.simCow.chr6 301146 19 + 602619 TTCAGACTTATTACTTATA -s simDog_chr6.simDog.chr6 287488 19 + 593897 TTCAGACCAATCACTTACA -s simHuman_chr6.simHuman.chr6 311367 19 + 601863 TTCAGACTTATCACTCACA -s simRat_chr6.simRat.chr6 316742 19 + 647215 TTCAATGCTACTTTTTCAA - -a -s simMouse_chr6.simMouse.chr6 325362 27 + 636262 CTAAGTTCTGCGGGCACACTTTCAAAA -s Anc0.Anc0refChr7 9328 27 - 16696 CTGCATCTAGCGCGTACCCTTCCAAAT -s Anc1.Anc1refChr4 9789 27 + 17549 CTGCATCTAGCGCGTACCCTTCCAAAT -s Anc2.Anc2refChr7 4839 27 + 32194 CTGCATCTAGTGCATACCCTTCTAAAT -s mr.mrrefChr5 173393 27 + 294540 CTAAGTTCTGCGGGCACACTTCCAAAA -s simCow_chr6.simCow.chr6 301169 27 + 602619 CTGCAACTAGTGCATAGCTTTCTATAA -s simDog_chr6.simDog.chr6 287511 27 + 593897 CTGCATCTAGTGCATGCCCTTTTAAAT -s simHuman_chr6.simHuman.chr6 311390 27 + 601863 CTGCATCTAGCGTGTACTCTTCCAAAT -s simRat_chr6.simRat.chr6 316761 27 + 647215 CTTAGTTCTAGGGACACACTTCCAAAA - -a -s simMouse_chr6.simMouse.chr6 325389 29 + 636262 AATGGAAGTAATTGTCCCTCTTCCCTATC -s Anc0.Anc0refChr7 9355 26 - 16696 TGTGA--GTCATTTTCCTTCTTCCC-ATC -s Anc1.Anc1refChr4 9816 26 + 17549 TGTGA--GTCATTTTCCTTCTTCCC-ATC -s Anc2.Anc2refChr7 4867 26 + 32194 TGTGA--GTCATTTTCCTTCTTCCC-ATC -s mr.mrrefChr5 173420 27 + 294540 AATGG--GTCATTGTCCTTCTTCCCTATC -s simCow_chr6.simCow.chr6 301197 26 + 602619 TGATA--GTCATTTTCCTTCTTCCC-ATC -s simDog_chr6.simDog.chr6 287539 26 + 593897 TTTGA--TTCATTTTCCTTTTTTCC-ACC -s simHuman_chr6.simHuman.chr6 311417 26 + 601863 TGTGA--GTCACTTTCCTCCTTCCC-ATC -s simRat_chr6.simRat.chr6 316788 23 + 647215 AATGG--ATC----TCTTTCTTCCTTATT - -a -s simMouse_chr6.simMouse.chr6 325418 3 + 636262 CAA -s Anc0.Anc0refChr7 9381 3 - 16696 CAA -s Anc1.Anc1refChr4 9842 3 + 17549 CAA -s Anc2.Anc2refChr7 4898 3 + 32194 CAG -s mr.mrrefChr5 173447 3 + 294540 CAA -s simCow_chr6.simCow.chr6 301228 3 + 602619 CAG -s simDog_chr6.simDog.chr6 287570 3 + 593897 CAG -s simHuman_chr6.simHuman.chr6 311443 3 + 601863 AGA -s simRat_chr6.simRat.chr6 316811 1 + 647215 --A - -a -s simMouse_chr6.simMouse.chr6 325421 28 + 636262 TAATGAACTCACAACAACTCTCTAGACG -s Anc0.Anc0refChr7 9394 28 - 16696 TAAGGAAATTAAAAAGGCTCTCATGGTG -s Anc1.Anc1refChr4 9855 28 + 17549 TAAGGAAATTAAAAAGGCTCTCATGGTG -s Anc2.Anc2refChr7 4913 28 + 32194 TAGGGACATTAAAAAGGCTCTCATGGTG -s mr.mrrefChr5 173450 28 + 294540 TAATGAACTCACAACAACTCTCTTGATG -s simCow_chr6.simCow.chr6 301243 28 + 602619 TAGGAGTATTCAAAAGGCTCTCATGGTT -s simDog_chr6.simDog.chr6 287585 28 + 593897 TAGGGACATTAAACAGGCTCTCATGGTG -s simHuman_chr6.simHuman.chr6 311456 28 + 601863 TAAGGAAATTAAAAAGGCTCTTGTGCTG -s simRat_chr6.simRat.chr6 316812 28 + 647215 TAATGAACTCACAACAACTCCCATCGTG - -a -s simMouse_chr6.simMouse.chr6 325449 8 + 636262 TGGGGTTG -s Anc0.Anc0refChr7 9427 8 - 16696 TGGGGTAA -s Anc1.Anc1refChr4 9888 8 + 17549 TGGGGTAA -s Anc2.Anc2refChr7 4946 8 + 32194 TGGGGTAA -s mr.mrrefChr5 173483 8 + 294540 TGGGGTTA -s simCow_chr6.simCow.chr6 301271 5 + 602619 ---GGTAA -s simDog_chr6.simDog.chr6 287618 8 + 593897 TGGGGTAA -s simHuman_chr6.simHuman.chr6 311489 8 + 601863 TGGGGTAA -s simRat_chr6.simRat.chr6 316845 8 + 647215 TGGGGTTA - -a -s simMouse_chr6.simMouse.chr6 325457 21 + 636262 AGGTTCAAACACTTGGGTGTT -s Anc0.Anc0refChr7 9435 21 - 16696 AGGTTCAACTACATGGGTACT -s Anc1.Anc1refChr4 9896 21 + 17549 AGGTTCAACTACATGGGTACT -s Anc2.Anc2refChr7 4956 21 + 32194 ATGTTCAACTGCATGGGTACT -s mr.mrrefChr5 173491 21 + 294540 AGGTTCAAACACTTGGGTGTT -s simCow_chr6.simCow.chr6 301278 21 + 602619 ACATTCAACTGCATGGGTACT -s simDog_chr6.simDog.chr6 287628 21 + 593897 ATGTTAGACTGTGAGGGCACT -s simHuman_chr6.simHuman.chr6 311546 21 + 601863 AGGTTCAACTACATGGGTAGT -s simRat_chr6.simRat.chr6 316853 21 + 647215 AGGCTCACACACCTGGGTGCT - -a -s simMouse_chr6.simMouse.chr6 325478 27 + 636262 TCTTAGTGCTTGGGGATCTAGGCTTTG -s Anc0.Anc0refChr7 9465 24 - 16696 TCTTA---CTCATGGTTCTGAATCTTA -s Anc1.Anc1refChr4 9926 27 + 17549 TCTTAATGCTCATGGTTCTGAATCTTA -s Anc2.Anc2refChr7 4986 24 + 32194 TTTTA---TTCATGGTTCTGAATTTTA -s mr.mrrefChr5 173512 27 + 294540 TCTTAGTGCTTGGGGATCTAGGCCTTG -s simCow_chr6.simCow.chr6 301308 24 + 602619 TTTTA---TTCAAGGTTCTCAATTTTA -s simDog_chr6.simDog.chr6 287658 24 + 593897 CTTTA---TTCATGGTTCTGGATTGTA -s simHuman_chr6.simHuman.chr6 311576 27 + 601863 TCTTAATGCTCATGGTTCTGAATCTTA -s simRat_chr6.simRat.chr6 316874 27 + 647215 TCTTGGTGCTTGAGGCTCTAGTCCTTG - -a -s simMouse_chr6.simMouse.chr6 325505 28 + 636262 CCAGAGGCCTCATTGATTACACGTTGTA -s Anc0.Anc0refChr7 9492 28 - 16696 CCAGAGGCCTCACTAACTACCCATTGTG -s Anc1.Anc1refChr4 9956 28 + 17549 CCAGAGGCCTCACTAACTACCCATTGTG -s Anc2.Anc2refChr7 5013 28 + 32194 CCAGAGGCCTCACTAACTACCCATTGTG -s mr.mrrefChr5 173542 28 + 294540 CCAGAGGCCTCACTGATTACACATTGTG -s simCow_chr6.simCow.chr6 301335 28 + 602619 CCAGAGCCCTCTCTTACTACCCACTTTT -s simDog_chr6.simDog.chr6 287685 28 + 593897 CCAGATGGCTCACTAGCTATGCATTGTG -s simHuman_chr6.simHuman.chr6 311606 28 + 601863 CCAGAGACCTCACTAACAACCCAGTGTG -s simRat_chr6.simRat.chr6 316904 28 + 647215 CCAGAAGTCTCACTGATTACACATTGTG - -a -s simMouse_chr6.simMouse.chr6 325533 63 + 636262 GTAAGTCACCCAGGTTTTGTAAGGTTGACGTCAGATGTCATAATAGTGATTCTTTAGTTTAAT -s Anc0.Anc0refChr7 9527 31 - 16696 CTAAGACACCCAAGATATTTG-----------------TA---------------AGATTAAT -s Anc1.Anc1refChr4 9991 31 + 17549 CTAAGACACCCAAGATATTTG-----------------TA---------------AGATTAAT -s Anc2.Anc2refChr7 5048 31 + 32194 CTAAGACACCCAAGATATTTG-----------------TA---------------AGATTAAT -s mr.mrrefChr5 173570 46 + 294540 GTAAGTCACCCAGGTTTTGTA-----------------CATAATAGTGATTCTTTAGTTTAAT -s simCow_chr6.simCow.chr6 301370 31 + 602619 CTACAATAACCAAGATATTTG-----------------TA---------------AGAGCAAC -s simDog_chr6.simDog.chr6 287718 29 + 593897 --AAGACACCCAATATGTTTG-----------------TA---------------AAGTTGAT -s simHuman_chr6.simHuman.chr6 311641 31 + 601863 ATAAGAAACTCAAGATATTTG-----------------TA---------------AGATTAAT -s simRat_chr6.simRat.chr6 316932 46 + 647215 GTAAGTCACGCAGGTTTTGTA-----------------CATAATGGTGATTCTTGAGTTTAAC - -a -s simMouse_chr6.simMouse.chr6 325596 14 + 636262 GTCTGCTTTATGGC -s Anc0.Anc0refChr7 9559 14 - 16696 CTAAGCATTATGGT -s Anc1.Anc1refChr4 10023 14 + 17549 CTAAGCATTATGGT -s Anc2.Anc2refChr7 5080 14 + 32194 CTAAGCATTGTAGT -s mr.mrrefChr5 173616 14 + 294540 CTCTGCTTTATGGC -s simCow_chr6.simCow.chr6 301402 14 + 602619 GTAAACATTGTAGT -s simDog_chr6.simDog.chr6 287748 14 + 593897 CAAAGCATAGTAGT -s simHuman_chr6.simHuman.chr6 311673 14 + 601863 CTAAGTGTTATGGT -s simRat_chr6.simRat.chr6 316978 14 + 647215 CTCTGCTTTATGGC - -a -s simMouse_chr6.simMouse.chr6 325610 70 + 636262 TGTCATAACTGTGAGTGTAGACAATATGGACGCTAAAGGATCATGGCCCTGCTTGCACATACATTTTATC -s Anc0.Anc0refChr7 9573 35 - 16696 AGTCATCTTCACAA-----------------------------------TACTTGCACTCACAGTTTATC -s Anc1.Anc1refChr4 10037 37 + 17549 AGTCATCTTCACAAG---------------------------------CTACTTGCACTCACAGTTTATC -s Anc2.Anc2refChr7 5173 35 + 32194 ACTCACCTTCACAA-----------------------------------TGCTTGCACACACAGTATATT -s mr.mrrefChr5 173630 70 + 294540 TGTCATAACTGTGAGTGTAGACAATATGGACGCTAAAGGATCATGGCCCTACTTGCACTTACATTTTATC -s simDog_chr6.simDog.chr6 287884 35 + 593897 ACTCACCTTCACAA-----------------------------------TGCTTGCACACACAGTATATT -s simHuman_chr6.simHuman.chr6 311687 37 + 601863 AGTAATGTTCACAAG---------------------------------CTACTTGCACTCGCACTTTACC -s simRat_chr6.simRat.chr6 316992 70 + 647215 TGCCATAACTGAGAGTGTAGACAATGTGGATACTAAAGGCCCATGGCCCTACTTGCACTTACATTTTATC - -a -s simMouse_chr6.simMouse.chr6 325680 3 + 636262 TAA -s Anc0.Anc0refChr7 9608 3 - 16696 TGA -s Anc1.Anc1refChr4 10074 3 + 17549 TGA -s Anc2.Anc2refChr7 5208 3 + 32194 GGG -s mr.mrrefChr5 173700 3 + 294540 TGA -s simCow_chr6.simCow.chr6 301515 3 + 602619 GAG -s simDog_chr6.simDog.chr6 287927 3 + 593897 GGG -s simHuman_chr6.simHuman.chr6 311724 3 + 601863 TGA -s simRat_chr6.simRat.chr6 317062 3 + 647215 TGA - -a -s simMouse_chr6.simMouse.chr6 325683 4 + 636262 AGCG -s Anc0.Anc0refChr7 9611 4 - 16696 AGCC -s Anc1.Anc1refChr4 10077 4 + 17549 AGCC -s Anc2.Anc2refChr7 5214 4 + 32194 ATCC -s mr.mrrefChr5 173703 4 + 294540 AGCG -s simCow_chr6.simCow.chr6 301521 4 + 602619 ATCC -s simDog_chr6.simDog.chr6 287933 4 + 593897 ATCC -s simHuman_chr6.simHuman.chr6 311727 4 + 601863 AGCT -s simRat_chr6.simRat.chr6 317065 4 + 647215 AGCG - -a -s simMouse_chr6.simMouse.chr6 325687 29 + 636262 TGTGATCTATTGCAGTACTTGGTGATAAA -s Anc0.Anc0refChr7 9637 29 - 16696 TGTGACTTATCTCAGTACTTGGGGATCAG -s Anc1.Anc1refChr4 10103 29 + 17549 TGTGACTTATCTCAGTACTTGGGGATCAG -s Anc2.Anc2refChr7 5245 29 + 32194 TGTGACTTATCTCAGTACTTGGGGACCAG -s mr.mrrefChr5 173707 29 + 294540 TGTGATCTATTGCAGTACTTGGTGATAAA -s simCow_chr6.simCow.chr6 301552 26 + 602619 TGTGACTTATC--AGTACTTGGGGA-CTG -s simDog_chr6.simDog.chr6 287964 29 + 593897 TGTGACATATCTCAGCACCTGGGGACAAG -s simHuman_chr6.simHuman.chr6 311753 29 + 601863 TGTGACTTATCTCAGTATTCGGAGATCAG -s simRat_chr6.simRat.chr6 317069 27 + 647215 TG--ATCTCTTGCAGTACTTGGTGATAAA - -a -s simMouse_chr6.simMouse.chr6 325716 2 + 636262 CT -s Anc0.Anc0refChr7 9666 2 - 16696 CT -s Anc1.Anc1refChr4 10132 2 + 17549 CT -s Anc2.Anc2refChr7 5275 2 + 32194 TT -s mr.mrrefChr5 173736 2 + 294540 CT -s simCow_chr6.simCow.chr6 301579 2 + 602619 GT -s simDog_chr6.simDog.chr6 287994 2 + 593897 TT -s simHuman_chr6.simHuman.chr6 311782 2 + 601863 CT -s simRat_chr6.simRat.chr6 317096 2 + 647215 TT - -a -s simMouse_chr6.simMouse.chr6 325718 36 + 636262 CAACTAAAAACAGTGCTTTTATTAATAGGCTGTTGT -s Anc0.Anc0refChr7 9668 36 - 16696 CATCTAACAAGGATGCTACCAGCATCACTCTATTTT -s Anc1.Anc1refChr4 10134 36 + 17549 CATCTAACAAGGATGCTACCAGCATCACTCTATTTT -s Anc2.Anc2refChr7 5277 36 + 32194 CATCTAACAAGGGTGCTACCACCATCACTCTATTTT -s mr.mrrefChr5 173738 36 + 294540 CAACTAAAAACAATGCTTCTAGTAATAGTCTGTTTT -s simCow_chr6.simCow.chr6 301581 36 + 602619 CATCTAACAAGGGTTCTCCCACCATCAATCTATTTT -s simDog_chr6.simDog.chr6 287996 36 + 593897 CATCTAACTAGGGTGCTACCACCATCACTCTATATT -s simHuman_chr6.simHuman.chr6 311799 36 + 601863 CATCTAACATGGATGCTGCCAGCACAATTCTATTTT -s simRat_chr6.simRat.chr6 317098 36 + 647215 GACCTGAAAACAATACTTCTAGTAATACTCTGTTTT - -a -s simMouse_chr6.simMouse.chr6 325754 7 + 636262 ACAGGTC -s Anc0.Anc0refChr7 9704 7 - 16696 CCAGGTC -s Anc1.Anc1refChr4 10170 7 + 17549 CCAGGTC -s Anc2.Anc2refChr7 5313 7 + 32194 CCAGGTC -s mr.mrrefChr5 173774 7 + 294540 ACAGGTC -s simCow_chr6.simCow.chr6 301617 7 + 602619 CTAGGTC -s simDog_chr6.simDog.chr6 288032 7 + 593897 CCAGGTC -s simHuman_chr6.simHuman.chr6 311835 7 + 601863 CCATGTC -s simRat_chr6.simRat.chr6 317135 7 + 647215 ACAGGGC - -a -s simMouse_chr6.simMouse.chr6 325761 12 + 636262 TCAAATGAGATG -s Anc0.Anc0refChr7 9720 12 - 16696 TAGATTGGGATG -s Anc1.Anc1refChr4 10186 12 + 17549 TAGATTGGGATG -s Anc2.Anc2refChr7 5329 12 + 32194 TAGATCAGGATG -s mr.mrrefChr5 173790 12 + 294540 TCAATTGAGATG -s simCow_chr6.simCow.chr6 301633 12 + 602619 TAGATCAGGATG -s simDog_chr6.simDog.chr6 288048 12 + 593897 TAGATCAGCAAG -s simHuman_chr6.simHuman.chr6 311851 12 + 601863 TAGATTGGGATG -s simRat_chr6.simRat.chr6 317151 12 + 647215 TCCATTAAGATC - -a -s simMouse_chr6.simMouse.chr6 325773 14 + 636262 GCTACCAACTTTTT -s Anc0.Anc0refChr7 9732 14 - 16696 GCTATCAGATTTTT -s Anc1.Anc1refChr4 10198 14 + 17549 GCTATCAGATTTTT -s Anc2.Anc2refChr7 5341 14 + 32194 TTTATCAGATTTTT -s mr.mrrefChr5 173802 14 + 294540 GCTACCAACTTTTT -s simCow_chr6.simCow.chr6 301645 14 + 602619 CTGATCAGACTTTT -s simDog_chr6.simDog.chr6 288060 14 + 593897 TTTATCAGATATTT -s simHuman_chr6.simHuman.chr6 311864 14 + 601863 GCATTCAGATTTTT -s simRat_chr6.simRat.chr6 317163 14 + 647215 GCTAGCAACTTTTT - -a -s simMouse_chr6.simMouse.chr6 325787 8 + 636262 TAGTCAAA -s Anc0.Anc0refChr7 9746 6 - 16696 TA--CAAA -s Anc1.Anc1refChr4 10212 6 + 17549 TA--CAAA -s Anc2.Anc2refChr7 5356 6 + 32194 GA--CAAA -s mr.mrrefChr5 173816 6 + 294540 TA--CAAA -s simCow_chr6.simCow.chr6 301660 6 + 602619 AA--GAAA -s simDog_chr6.simDog.chr6 288075 6 + 593897 GA--CAAA -s simHuman_chr6.simHuman.chr6 311878 6 + 601863 TT--CAAA -s simRat_chr6.simRat.chr6 317177 6 + 647215 TA--GAAG - -a -s simMouse_chr6.simMouse.chr6 325795 7 + 636262 AGCTTCA -s Anc0.Anc0refChr7 9752 7 - 16696 AGATCCA -s Anc1.Anc1refChr4 10218 7 + 17549 AGATCCA -s Anc2.Anc2refChr7 5362 7 + 32194 AGATCCA -s mr.mrrefChr5 173822 7 + 294540 AGCTTCA -s simCow_chr6.simCow.chr6 301666 7 + 602619 AGATTCA -s simDog_chr6.simDog.chr6 288081 7 + 593897 AGACCCA -s simHuman_chr6.simHuman.chr6 311886 7 + 601863 AGGTCCA -s simRat_chr6.simRat.chr6 317183 7 + 647215 AGCTTCA - -a -s simMouse_chr6.simMouse.chr6 325802 50 + 636262 AATTTGTTGACAATGTCTAACTCCTAGTATTGATAGCATTAATCTGCTCT -s Anc0.Anc0refChr7 9759 50 - 16696 AATTTGTTGACAGTATCTAACTCTTATTATTGATTGCATTAACCTGCTAT -s Anc1.Anc1refChr4 10225 50 + 17549 AATTTGTTGACAGTATCTAACTCTTATTATTGATTGCATTAACCTGCTAT -s Anc2.Anc2refChr7 5375 50 + 32194 AATTTGTTGTCAGTATCTAACTTTTATTGTTCATAGCATTAACCTGCTAA -s mr.mrrefChr5 173829 50 + 294540 AATTTGTTGACAATGTCTAACTCCTAGTATTGATTGCATTAATCTGCTCT -s simCow_chr6.simCow.chr6 301679 50 + 602619 AATTTGTTGTCAGTATCCGACTTTTGCTGCCTATCTCAGTAACCTGCTCA -s simDog_chr6.simDog.chr6 288094 50 + 593897 AATTTGTTGTTAGTAGCTAACTTCTATTGTTCATAGCATTAACCTGCGAA -s simHuman_chr6.simHuman.chr6 311893 50 + 601863 AATTTGTTGACAGTATCTAGCTCTTATCATTGATTATATTAACCTGCTTT -s simRat_chr6.simRat.chr6 317190 50 + 647215 AATTTGTTGACAATGTCTAACTCCTGGTATCCACTGCATTAATCTGCCCT - -a -s simMouse_chr6.simMouse.chr6 325852 71 + 636262 GTTAACCTATCCTGGTGTTTATACACCTTGATTGATGGGCTGAACCCAAATAGGCGTGATATGAATAGAAT -s Anc0.Anc0refChr7 9817 47 - 16696 ------------------TTACACACCTTGAG----GATCTGAGCCTAAATATGCGTG--AGGGCCTAAAT -s Anc1.Anc1refChr4 10283 66 + 17549 GC-GGTCCAGCTTGATGTTTACACACCTTGAG----GATCTGAGCCTAAATATGCGTGATAGGGCCTAAAT -s Anc2.Anc2refChr7 5433 47 + 32194 ------------------TTACACACCTTGAT----GATCTGGGCCTAAATATGCATG--AGGGCCTAAAT -s mr.mrrefChr5 173879 70 + 294540 GT-AACCTAGCCTGGTGTTTATACACCTTGAGTGATGGTCTGAACCTAAATAGGCGTGATATGACTAGAAT -s simCow_chr6.simCow.chr6 301737 42 + 602619 ------------------TTACGCACCTTGAT----GATCTGGGCCTAACTAGGCATG--ATGGC-----T -s simDog_chr6.simDog.chr6 288152 47 + 593897 ------------------TTACACACTTTGAT----GATCTGGCCCTAGAAATGTATG--GGGGCCTAAAT -s simHuman_chr6.simHuman.chr6 311958 66 + 601863 GC-GGTCCAGCTTGATGTCTCCACACCTTGAG----GATATCAGCTTAAATATGCGTGATAGGGCCTAAAT -s simRat_chr6.simRat.chr6 317240 69 + 647215 GT-AACCTAGCCTG-TGTTTATACACCTTGAGTGATGGTCTGAACCTGAGTTGACACGACATGTCTAGAAT - -a -s simMouse_chr6.simMouse.chr6 325923 3 + 636262 GCA -s Anc0.Anc0refChr7 9866 3 - 16696 GCA -s Anc1.Anc1refChr4 10351 3 + 17549 GCA -s Anc2.Anc2refChr7 5482 3 + 32194 TTA -s mr.mrrefChr5 173949 3 + 294540 GCA -s simCow_chr6.simCow.chr6 301781 3 + 602619 TTA -s simDog_chr6.simDog.chr6 288201 3 + 593897 TTA -s simHuman_chr6.simHuman.chr6 312026 3 + 601863 GCA -s simRat_chr6.simRat.chr6 317309 3 + 647215 GCA - -a -s simMouse_chr6.simMouse.chr6 325926 107 + 636262 TGATATCACTACAATCATCTGCATCTCAAAGACACCTAATTGATGGGCTTGTATTATTTCCCTCAGTTGGAGACAGTGTATGCCCATGTAGGGACAATACCCATTTC -s Anc0.Anc0refChr7 9873 106 - 16696 CAGTCTGACACCAATTAATGTGGCCTCAACCACAACTAATTGTTGGGCTA-CATGATGTCCCTCAGTGTGGCACAGTGTATGCCCATGTAGTAACAATACCCATTTT -s Anc1.Anc1refChr4 10358 106 + 17549 CAGTCTGACACCAATTAATGTGGCCTCAACCACAACTAATTGTTGGGCTA-CATGATGTCCCTCAGTGTGGCACAGTGTATGCCCATGTAGTAACAATACCCATTTT -s Anc2.Anc2refChr7 5489 106 + 32194 CAGTCTGACACCAATTAATGTGGCCTCAACCAGAACTGATTGTTAGGCTA-CATGATGTCCCTCAGTGTGGCACAGTGTATGCCCATGCAGTAACAATACCCATTGT -s mr.mrrefChr5 173952 106 + 294540 TGATATCACTGCAATCATTTACATCTCAAAGACACCTAATTGATGGGCTT-TATGATTTCCCTCAGTTTGAGACAGTGTATGCCCATGTAGGGACAATACCCACTTT -s simCow_chr6.simCow.chr6 301788 101 + 602619 CAGTCTAACATCTATTAATGTGGCCTCAACGAGAA-----TATTAGGCTA-CATGATGTCCCTCAGAGTGGTGCAGTGTATGCCCATGCAGAAACAGTACCTATTGT -s simDog_chr6.simDog.chr6 288208 103 + 593897 CAGTCTGACACCAATTAATGTGGCCTCAACCAGCACTGATTGCTAGTCTA-CATCATGTCCCTCAGTATGGCACAGTGTATGCCCATGCAATAGCAATGCCCAT--- -s simHuman_chr6.simHuman.chr6 312033 106 + 601863 AAGTTTGACACCATTTAATGTGGCCTCAACAACAACTAATTGTTGGGCTA-AATGATGTCCCTCAGTGTGGCACAGTGCATGCCCATGTAGCAACAACACCACTTTT -s simRat_chr6.simRat.chr6 317312 106 + 647215 TGATATCACTGCAATAAATTACATCTCAAAGACACCTAATTGAGGGGCTT-TATGATTTCCCTCAGTCTGAGACAGTGTATGCCCATGCAGGGACAATGCACACTTT - -a -s simMouse_chr6.simMouse.chr6 326033 41 + 636262 TAATATCAAAAAATACGGACTATCAGTCAATAAAGGTCTGT -s Anc0.Anc0refChr7 9980 37 - 16696 ATATTTCAAAAAATACGGACTGTCAGTCAACAAA----TGT -s Anc1.Anc1refChr4 10465 40 + 17549 ATATTTCAAAAAATACGGACTGTCAGTCAACAAAGGT-TGT -s Anc2.Anc2refChr7 5596 37 + 32194 ATATTTTAAAAAATACAGACTGTCAGTCAACAAA----TGT -s mr.mrrefChr5 174058 41 + 294540 TTATATCAAAAAATACGGACTATCAGTCAATAAAGGTCTGT -s simCow_chr6.simCow.chr6 301890 37 + 602619 ATATTTTAAAAAACACAAACTGTCAGTTAATTAA----TGG -s simDog_chr6.simDog.chr6 288311 26 + 593897 -----------AGTACAGACTGTCAGCCAACAAA----TGT -s simHuman_chr6.simHuman.chr6 312140 32 + 601863 CTATTTCTAAAGATACGGATTGTCTGTCA-----GGT---- -s simRat_chr6.simRat.chr6 317418 36 + 647215 TTTCAATACAAAA-----ACTATCCTTCAATAAAGGTCTGT - -a -s simMouse_chr6.simMouse.chr6 326074 27 + 636262 ACTGAGAATACCGCATCTAATTACCAA -s Anc0.Anc0refChr7 10017 27 - 16696 GTTGGGAAGAGTGCATCTAATTACCAC -s Anc1.Anc1refChr4 10505 27 + 17549 GTTGGGAAGAGTGCATCTAATTACCAC -s Anc2.Anc2refChr7 5633 27 + 32194 GTTGGGAAGAGTGCATCTAATTACCAC -s mr.mrrefChr5 174099 27 + 294540 ACTGAGAATACTGCATCTAATTACCAA -s simCow_chr6.simCow.chr6 301927 27 + 602619 GTTGGGAAGAGTACATCTAATTACCAC -s simDog_chr6.simDog.chr6 288341 23 + 593897 GATGGGGAGAGTGCATCAAATTA---- -s simHuman_chr6.simHuman.chr6 312172 24 + 601863 --TGGGAAGA-TGCATCTAATTATTAC -s simRat_chr6.simRat.chr6 317454 23 + 647215 ACTGAGAATAGTGCATCTAATTA---- - -a -s simMouse_chr6.simMouse.chr6 326101 38 + 636262 CACTATGAAGTTTAGTTGACTCCTGCTATCCTTTGTCA -s Anc0.Anc0refChr7 10058 37 - 16696 CACCATC-AACTTTGATCAAGACTGCAATCGTTCAAGA -s Anc1.Anc1refChr4 10546 38 + 17549 CACCATCAAACTTTGATCAAGACTGCAATCGTTCAAGA -s Anc2.Anc2refChr7 5674 37 + 32194 CACCATC-AACATTGATCAAGACTGCAATCGTTCAAGA -s mr.mrrefChr5 174126 38 + 294540 CACTATGAAGTTTAGTTGACTCCTGCTATCCTTTGTGA -s simCow_chr6.simCow.chr6 301971 37 + 602619 GACCACT-ATCATTGATCAAGACCACAGTCGTTCAAGA -s simDog_chr6.simDog.chr6 288371 37 + 593897 CACCCTC-AACATTGACCAAGGCTGCAATCTTTTGAGA -s simHuman_chr6.simHuman.chr6 312210 38 + 601863 CACCAGCTAACTTTGATCAAGACTGCAATTGTTCAAGA -s simRat_chr6.simRat.chr6 317477 30 + 647215 --------AGTTTAATGGACTGGTGCTATCCTTTGTGA - -a -s simMouse_chr6.simMouse.chr6 326139 13 + 636262 TATGGCCATGGCC -s Anc0.Anc0refChr7 10095 13 - 16696 CACAGCCATGGTC -s Anc1.Anc1refChr4 10584 13 + 17549 CACAGCCATGGTC -s Anc2.Anc2refChr7 5711 13 + 32194 CACAGCCATGGTC -s mr.mrrefChr5 174164 13 + 294540 TATGGCCATGGCC -s simCow_chr6.simCow.chr6 302008 13 + 602619 CACAGTGATTGTC -s simDog_chr6.simDog.chr6 288408 13 + 593897 CAGAGCCATGGTC -s simHuman_chr6.simHuman.chr6 312248 13 + 601863 CACATCCATCATC -s simRat_chr6.simRat.chr6 317509 13 + 647215 TATGGCCACGGCC - -a -s simMouse_chr6.simMouse.chr6 326152 47 + 636262 AGGGTGATATGGAGTATCCATATCACACCTTATGTCAAACACTTGAA -s Anc0.Anc0refChr7 10108 45 - 16696 AGGGCCATGTG-AGCATCCACACCACACCTGATATTGTA-AGTTAAA -s Anc1.Anc1refChr4 10597 45 + 17549 AGGGCCATGTG-AGCATCCACACCACACCTGATATTGTA-AGTTAAA -s Anc2.Anc2refChr7 5724 45 + 32194 AGGGCCATGGG-AGCATCCACACCACACCTGGAATTGTA-AGTTAAA -s mr.mrrefChr5 174177 47 + 294540 AGGGTGATATGGAGTATCCATATCACACCTTATGTCAAACACTTGAA -s simCow_chr6.simCow.chr6 302021 45 + 602619 AAGGTCTTGGG-TGCATCAATAACACAGCTAGAATGATA-AGTTGAG -s simDog_chr6.simDog.chr6 288430 45 + 593897 AGGCCCATGGG-AGCATCCACTCGGCACCTGGAATTGTA-GGTCAAA -s simHuman_chr6.simHuman.chr6 312261 45 + 601863 AGGGCCATGTG-AGAATCCAGACCACACCTCATATTGTA-AGTTAAA -s simRat_chr6.simRat.chr6 317522 47 + 647215 AGGGTGATACGGAGTATCCATGTCACACCTTATGTCAAACACTTGGA - -a -s simMouse_chr6.simMouse.chr6 326199 18 + 636262 ACCTGGTTAGGTTTAGCA -s Anc0.Anc0refChr7 10153 17 - 16696 ATCTGGT-GAATTCTTCA -s Anc1.Anc1refChr4 10642 18 + 17549 ATCTGGTAGAATTCTTCA -s Anc2.Anc2refChr7 5769 17 + 32194 ATCTGGT-GAATTCTTCC -s mr.mrrefChr5 174224 18 + 294540 ATCTGGTTAGGTTCAGCA -s simCow_chr6.simCow.chr6 302066 17 + 602619 ATCTGGG-GAATCCTTCC -s simDog_chr6.simDog.chr6 288475 17 + 593897 ACCTGGT-GAATTCTTCC -s simHuman_chr6.simHuman.chr6 312306 18 + 601863 GTATGGTAGAATTCGTCA -s simRat_chr6.simRat.chr6 317572 18 + 647215 ATCTGGTTAGGTTCAGCA - -a -s simMouse_chr6.simMouse.chr6 326217 26 + 636262 TCAACAATGAGTAGATATCCTCTCCC -s Anc0.Anc0refChr7 10186 26 - 16696 TCAACAATAAGCAGATATTTTATCTT -s Anc1.Anc1refChr4 10676 26 + 17549 TCAACAATAAGCAGATATTTTATCTT -s Anc2.Anc2refChr7 5802 26 + 32194 TCAACAATAACCAGATATTTTTTCTT -s mr.mrrefChr5 174242 26 + 294540 TCAACAATGAGTAGATATTCTATCCC -s simCow_chr6.simCow.chr6 302099 26 + 602619 TCAACAATGACCAGATATTTTTTCTT -s simDog_chr6.simDog.chr6 288508 26 + 593897 TCGGCAACAACCAGACAGTTTTTCTT -s simHuman_chr6.simHuman.chr6 312340 26 + 601863 TCAACACTCAGCAAATATTTTATCTT -s simRat_chr6.simRat.chr6 317590 26 + 647215 TTGACAATGAGTAGAAATTCTATCCC - -a -s simMouse_chr6.simMouse.chr6 326243 7 + 636262 ATGTGTC -s Anc0.Anc0refChr7 10212 7 - 16696 ATGTGTC -s Anc1.Anc1refChr4 10702 7 + 17549 ATGTGTC -s Anc2.Anc2refChr7 5828 7 + 32194 ATGTATC -s mr.mrrefChr5 174268 7 + 294540 ATGTGTC -s simCow_chr6.simCow.chr6 302125 7 + 602619 CTGTATC -s simDog_chr6.simDog.chr6 288534 7 + 593897 ATGTATA -s simHuman_chr6.simHuman.chr6 312367 7 + 601863 GTGTGTC -s simRat_chr6.simRat.chr6 317616 7 + 647215 ATGTGTC - -a -s simMouse_chr6.simMouse.chr6 326250 40 + 636262 ACTCGCATAGTTGCATGTTATCATGTTGTCCATGCCACAC -s Anc0.Anc0refChr7 10221 40 - 16696 ACTACCATAGTTGCATGATATTTTGGTGCCCTAGACACAC -s Anc1.Anc1refChr4 10711 40 + 17549 ACTACCATAGTTGCATGATATTTTGGTGCCCTAGACACAC -s Anc2.Anc2refChr7 5837 40 + 32194 ACTACCATAGTTGCATGTTATTTTGGTGCCCTAGAAACCC -s mr.mrrefChr5 174277 40 + 294540 ACTACCATAGTTGCATGATATTTTGTTGTCCATGCCACAC -s simCow_chr6.simCow.chr6 302134 40 + 602619 ACTAACTTAGTTGCGTGTTATTCTAGTGCCCAAGAAACCC -s simDog_chr6.simDog.chr6 288543 39 + 593897 A-TACTATAGTTCCATGTTATTTTGAGGCCCTAGAAACCC -s simHuman_chr6.simHuman.chr6 312376 40 + 601863 ACTACCATAGTTGCATGATATTTTGGTACCCCAGTCAAAC -s simRat_chr6.simRat.chr6 317625 40 + 647215 ACTACTATAGTTGCATGACATTTCGTTGTCCATGCCCCAC - -a -s simMouse_chr6.simMouse.chr6 326290 21 + 636262 CCAACCTCCTTTTGTCAATTG -s Anc0.Anc0refChr7 10261 21 - 16696 CTAACCCCCTTTTGTCAATTG -s Anc1.Anc1refChr4 10751 21 + 17549 CTAACCCCCTTTTGTCAATTG -s Anc2.Anc2refChr7 5877 21 + 32194 TTAACCCCCTTTTGTCAAATG -s mr.mrrefChr5 174317 21 + 294540 CCAACCTCCTTTTGTCAATTG -s simCow_chr6.simCow.chr6 302174 21 + 602619 TTGACCCCCCTTTGTTAAACG -s simDog_chr6.simDog.chr6 288582 21 + 593897 TTAACCACCTTTTGTCAAATG -s simHuman_chr6.simHuman.chr6 312418 21 + 601863 CTAACCCCCTTTAGTCAATTG -s simRat_chr6.simRat.chr6 317665 21 + 647215 CCAACCTCCTTTTGTCAATTG - -a -s simMouse_chr6.simMouse.chr6 326311 30 + 636262 TATTCTGACTGTTCATGATAACAATATTTA -s Anc0.Anc0refChr7 10283 30 - 16696 TGCCATGACTGTACATTATAACCATCTTTA -s Anc1.Anc1refChr4 10773 30 + 17549 TGCCATGACTGTACATTATAACCATCTTTA -s Anc2.Anc2refChr7 5899 30 + 32194 TGCCATGACTGTATATTATAACCATCTATA -s mr.mrrefChr5 174339 30 + 294540 TATCCTGACTGTTCATTATAACAATATTTA -s simCow_chr6.simCow.chr6 302196 30 + 602619 TTTCATGCCTGTAAATTATAACAAATGTTT -s simDog_chr6.simDog.chr6 288604 30 + 593897 TGCTGTGACCGTATATTATAACCATCTATA -s simHuman_chr6.simHuman.chr6 312440 30 + 601863 TGCCATAACTGTACATTATAACGATGTTAA -s simRat_chr6.simRat.chr6 317687 30 + 647215 TATCCTGACTCTCCATTATAACAATATTTA - -a -s simMouse_chr6.simMouse.chr6 326341 12 + 636262 GTCTTTAAAGCT -s Anc0.Anc0refChr7 10313 12 - 16696 GTCGTTATAGCT -s Anc1.Anc1refChr4 10803 12 + 17549 GTCGTTATAGCT -s Anc2.Anc2refChr7 5931 12 + 32194 GTAGTTATAGCT -s mr.mrrefChr5 174369 12 + 294540 GTCTTTAAAGCT -s simCow_chr6.simCow.chr6 302228 12 + 602619 CAAATTATAGCT -s simDog_chr6.simDog.chr6 288636 12 + 593897 GTAGTTATAGTT -s simHuman_chr6.simHuman.chr6 312470 4 + 601863 GTC--------T -s simRat_chr6.simRat.chr6 317717 12 + 647215 GTCTTTAAAGCT - -a -s simMouse_chr6.simMouse.chr6 326353 52 + 636262 CACAATAATGGTTTCATTGTGTAAACATGGCGCCTTCAACCATTCAACCTCC -s Anc0.Anc0refChr7 10326 52 - 16696 CACGATAGTGATATCAATGCATAAATGTGGCATCCTCAACAATTCATCCTCA -s Anc1.Anc1refChr4 10816 52 + 17549 CACGATAGTGATATCAATGCATAAATGTGGCATCCTCAACAATTCATCCTCA -s Anc2.Anc2refChr7 5944 52 + 32194 CATGATTGTGATATCAATGCATAAATGTGGCATCCTCAACAATTCATCCTCA -s mr.mrrefChr5 174382 52 + 294540 CACAATAGTGGTTTCATTGTGTAAATGTGGCACCTTCAACAATTCAACCTCA -s simCow_chr6.simCow.chr6 302241 52 + 602619 CATGATTATGATATCAATGCAAAAATGTGGCATCCTCAATAATTCATCTTTT -s simDog_chr6.simDog.chr6 288649 52 + 593897 CATGAATGGGAGATCAATGCATAAATGTGGCATCCTCAACAATTCATCCACA -s simHuman_chr6.simHuman.chr6 312475 52 + 601863 CACGATAGTGATATCAATGCATGAATGTGGCATCCTCAGGAATTCATCCTCA -s simRat_chr6.simRat.chr6 317730 52 + 647215 CACAATAGTGGTTTCAGTGTGTAAGTGTGGCACCTTCAACAATTCAACCCCA - -a -s simMouse_chr6.simMouse.chr6 326405 74 + 636262 GAAATGCTAGTGTAATACAATCAGGGATCTGCTGAGACTCAGTTGCAATATGTCTAGGGCTTCAAAACCTTAGT -s Anc0.Anc0refChr7 10378 51 - 16696 GGAATTCTCTTGGAAATAGATCA-----------------------ATTGTATTTAGAGCTTCAAAACCTTTGT -s Anc1.Anc1refChr4 10868 51 + 17549 GGAATTCTCTTGGAAATAGATCA-----------------------ATTGTATTTAGAGCTTCAAAACCTTTGT -s Anc2.Anc2refChr7 5996 51 + 32194 GGAATTCTCTTGGAAATAGGCCA-----------------------ATGGTATTTAGAGCTTCAAAACCTTTGT -s mr.mrrefChr5 174434 74 + 294540 GGAATTCTCTTGTAATACAATCAGGGATCTGCTGAGACTCAGTTGCAATATGTCTAGGGCTTCAAAACCTTAGT -s simCow_chr6.simCow.chr6 302293 49 + 602619 AAAATTCTCTCGGATATAA--TA-----------------------ATGGTATTTAGAGCTTCAAAACCTATAT -s simDog_chr6.simDog.chr6 288701 51 + 593897 GGAATTCTTTTGGAAATAGGCCA-----------------------ATGGTATTCAGGGCTTCAGGACCTTTGT -s simHuman_chr6.simHuman.chr6 312527 51 + 601863 GGAATTCTCTTAGAAATGCATCA-----------------------ATTGTATGTAGACCTCCAAAACTGTTGT -s simRat_chr6.simRat.chr6 317784 55 + 647215 AGAATTCTCTTGTGGTATGATCAGGGATCTGCTGAGACTCAGTTGCAATGTGCTT------------------- - -a -s simMouse_chr6.simMouse.chr6 326479 111 + 636262 ACAATGTAGGATGAAAAGTGATTACAGCGGCTCCCAACCAGAACAGACTACTATCCCCCAACTAATTAGCATGTTTAGCATGTTGGAATTGGGCTTGGACCGTTTACCCAC -s Anc0.Anc0refChr7 10429 105 - 16696 AGGATGTAGTACAAAA-GGGATTACACCGGGTCC-TACCAGATTAGACTACTATCACCCAACAAATAAGTATGTTGGAGATGT-GGGGTTGGGA---GACAGTTTCCCCAC -s Anc1.Anc1refChr4 10919 105 + 17549 AGGATGTAGTACAAAA-GGGATTACACCGGGTCC-TACCAGATTAGACTACTATCACCCAACAAATAAGTATGTTGGAGATGT-GGGGTTGGGA---GACAGTTTCCCCAC -s Anc2.Anc2refChr7 6047 105 + 32194 AGGATGTAGTACAAAA-TGGATTACACCGGGTCC-TGCCAGATTAGACTACTATCACCCGGCAAGTAAGTATGTTGGAGATGT-GGGGTTGGGA---GACAGTTTCCCCAC -s mr.mrrefChr5 174508 107 + 294540 ACAATGTAGGATGAAAAGTGATTACAGCGGGTCC-AACCAGAACAGACTACTATCACCCAACAAATTAGCATGTTTAGCATGTTGGAATTGGGC---GACAGTTTCCCCAC -s simCow_chr6.simCow.chr6 302346 95 + 602619 AGTACATAGTACAAAA-CAGATTGCACCGGGTCC-TGCCAGATTAGACTACGATCA----------GTGTATGTAGGAGAGAC-AGGGTTGGGA---GACAGTTTCCCCAC -s simDog_chr6.simDog.chr6 288752 95 + 593897 AGGATGTAGTACAAAA-TGGATCACACCAGGT-----------TAGACTACTATGACCCGGCAAGTAAGTATGTTGGAGATGT-GGGGTTTGGA---GATAGGGGCCCCAC -s simHuman_chr6.simHuman.chr6 312578 105 + 601863 AGGAAGTAGTACAAAA-GGGATTACACCGGGTCC-TACCAGATTAGACTAGTATCACCCAACAAATAAGTATCTTGGAGGTGT-GGGGCTGGGA---AACAGTTTCCCTGT -s simRat_chr6.simRat.chr6 317839 105 + 647215 -CAATGTAGGATGAAAAGCAATTACAGCAGGTCC-AACCAGAACAGACTACTATCACCCAACAAATTAGCATGTTTCGCATGTTGGAATTGGGC---GACAGTTTCCAC-C - -a -s simMouse_chr6.simMouse.chr6 326590 20 + 636262 TATCCTTACCTTAAGCAAAG -s Anc0.Anc0refChr7 10534 20 - 16696 TAGTCTTGCATTAAGCACTG -s Anc1.Anc1refChr4 11024 20 + 17549 TAGTCTTGCATTAAGCACTG -s Anc2.Anc2refChr7 6152 20 + 32194 TAGCCTTGCATTAAGCACTG -s mr.mrrefChr5 174615 20 + 294540 TATTCTTACATTAAGCACAG -s simCow_chr6.simCow.chr6 302441 19 + 602619 TAGCCTT-CATTAAGCACTA -s simDog_chr6.simDog.chr6 288848 20 + 593897 TAGCCTTGCATTAAGCACTG -s simHuman_chr6.simHuman.chr6 312683 20 + 601863 TAATTTTTCATTAAGTACTG -s simRat_chr6.simRat.chr6 317944 20 + 647215 TGTTCTGACATTAAGCACAG - -a -s simMouse_chr6.simMouse.chr6 326610 14 + 636262 CTTCCCTCTGTGCT -s Anc0.Anc0refChr7 10554 14 - 16696 CTTGTCTCCTGGCT -s Anc1.Anc1refChr4 11044 14 + 17549 CTTGTCTCCTGGCT -s Anc2.Anc2refChr7 6172 14 + 32194 CTTGCCTCCTGGAC -s mr.mrrefChr5 174635 14 + 294540 CTTCTCTCTTTGCT -s simCow_chr6.simCow.chr6 302460 14 + 602619 CTAGCCACCCGGAC -s simDog_chr6.simDog.chr6 288868 14 + 593897 CTTGCCTCGTGGAC -s simHuman_chr6.simHuman.chr6 312703 14 + 601863 CTTGTCTCCTGGCT -s simRat_chr6.simRat.chr6 318000 14 + 647215 CTTCTGTCTTCACT - -a -s simMouse_chr6.simMouse.chr6 326624 67 + 636262 TCAGGAGTGGGCATGCAGTCATATTGTTCTGGAGCCTCAGAGTATTACTGATGGTATGCGTATTCAG -s Anc0.Anc0refChr7 10568 67 - 16696 TCAAGACTGGGCACACAGTCATAGTGTTTTGCAAACTCAGTGTAGTACTGGTGGTATTCAGATGAAG -s Anc1.Anc1refChr4 11058 67 + 17549 TCAAGACTGGGCACACAGTCATAGTGTTTTGCAAACTCAGTGTAGTACTGGTGGTATTCAGATGAAG -s Anc2.Anc2refChr7 6190 67 + 32194 TCAAGACTGGGCACATAGTCATAGATGTTGGCAAACTCAGTGTAGTACTGGTGGTGATCAGATGAAG -s mr.mrrefChr5 174649 67 + 294540 TCAGGAGTGGGCATGCAGTCATATTGTTCTGGAGCCTCAGAGTATTACTGATGGTATGCATATGCAG -s simCow_chr6.simCow.chr6 302478 66 + 602619 TCAAGATGTGGCACAGAGTCATAGATGT-AGCAAACCCAGTGTTATACTGGAGGAGATTGTATGAAG -s simDog_chr6.simDog.chr6 288886 64 + 593897 TCAAGACTGGGCACTTATTCATAGATGTTGGCAAACTCAGGGTAGTACTGGTGGTGATCAGATA--- -s simHuman_chr6.simHuman.chr6 312717 67 + 601863 TAAAGACTGGGCACACAGTCATAATGTTGTGCGAACTCAGTGTAGTACTGCTGGCATTCACATGAAG -s simRat_chr6.simRat.chr6 318014 67 + 647215 TCAGGAGTGAGCTTGCAGTCATATTGTTCTGGAGCCTGAGAGTATTACTGATGGTATGCATATGCAG - -a -s simMouse_chr6.simMouse.chr6 326691 4 + 636262 CCCA -s Anc0.Anc0refChr7 10635 4 - 16696 GCCA -s Anc1.Anc1refChr4 11125 4 + 17549 GCCA -s Anc2.Anc2refChr7 6257 4 + 32194 GACA -s mr.mrrefChr5 174716 4 + 294540 CCCA -s simCow_chr6.simCow.chr6 302545 4 + 602619 GATA -s simDog_chr6.simDog.chr6 288950 2 + 593897 --CA -s simHuman_chr6.simHuman.chr6 312784 4 + 601863 GCCA -s simRat_chr6.simRat.chr6 318081 4 + 647215 CCCA - -a -s simMouse_chr6.simMouse.chr6 326695 37 + 636262 GGAAATTGGCCATTGCCCATACTGGCTCCCCAAAATA -s Anc0.Anc0refChr7 10639 37 - 16696 CACTATAGGCTATAGCTCATACTAGCTCCTTAGAATA -s Anc1.Anc1refChr4 11129 37 + 17549 CACTATAGGCTATAGCTCATACTAGCTCCTTAGAATA -s Anc2.Anc2refChr7 6261 37 + 32194 CACTATAGGCTATAGCTGATAATGCCCCCTTAGAATA -s mr.mrrefChr5 174720 37 + 294540 GGAAATTGGCCATTGCCCATACTAGCTCCCCAAAATA -s simCow_chr6.simCow.chr6 302549 37 + 602619 GATAACATGCTACAGCCAATAATGCCCTGTTGCAATA -s simDog_chr6.simDog.chr6 288952 37 + 593897 CACTATAGGATGTAGCTGATAATGCCCCCTTAGAATA -s simHuman_chr6.simHuman.chr6 312788 37 + 601863 AACTGTAGGCTATGGCACATTCTAGCTCAGTAGAGTT -s simRat_chr6.simRat.chr6 318086 37 + 647215 GGAAATTGGCCATTGCCCATACTAGCTCCCCCAAATA - -a -s simMouse_chr6.simMouse.chr6 326732 39 + 636262 CATAGGTAGACTCGTTGGTCCGTGTATGGGGCCAAGTTC -s Anc0.Anc0refChr7 10676 20 - 16696 CAGATGCAGA------AGTGCC-------------ACTC -s Anc1.Anc1refChr4 11166 20 + 17549 CAGATGCAGA------AGTGCC-------------ACTC -s Anc2.Anc2refChr7 6300 20 + 32194 AAGATGCAGA------AGTGCC-------------ACTC -s mr.mrrefChr5 174757 26 + 294540 CATAGGTAGACTCATTGGTCCG-------------GTTC -s simCow_chr6.simCow.chr6 302588 15 + 602619 -----GCAGA------AGTGCA-------------ACAC -s simDog_chr6.simDog.chr6 288991 15 + 593897 AAGATGCACA-----------C-------------ACTT -s simHuman_chr6.simHuman.chr6 312825 20 + 601863 CAGATGCAGA------AGTACT-------------ACTC -s simRat_chr6.simRat.chr6 318123 26 + 647215 CATAAGTAGATTCATCCATCTT-------------GTTC - -a -s simMouse_chr6.simMouse.chr6 326771 1 + 636262 C -s Anc0.Anc0refChr7 10696 1 - 16696 C -s Anc1.Anc1refChr4 11186 1 + 17549 C -s Anc2.Anc2refChr7 6320 1 + 32194 C -s mr.mrrefChr5 174783 1 + 294540 C -s simCow_chr6.simCow.chr6 302604 1 + 602619 T -s simDog_chr6.simDog.chr6 289006 1 + 593897 C -s simHuman_chr6.simHuman.chr6 312845 1 + 601863 C -s simRat_chr6.simRat.chr6 318149 1 + 647215 C - -a -s simMouse_chr6.simMouse.chr6 326772 123 + 636262 AGATTGCACCCACTTAACCAGCTTTTCCTCCAGTAGTATCTTCTTTATACATTTTTCAACCTTAGTTTATTCTTCATAAATTTTTCAATGTAAGTTTACGGGCAGGTCTTTAGAGCGTTTGGG -s Anc0.Anc0refChr7 10699 96 - 16696 AGCTTACAACTACTTAACCAGATTTTCCTCCAGTA---TCTTCTTTATACATCTCTCAAACT-AAATT---------------------GTGGGTATGTAGCCA--TCTTTAGAGTGTGGGGG -s Anc1.Anc1refChr4 11189 97 + 17549 AGCTTACAACTACTTAACCAGATTTTCCTCCAGTA---TCTTCTTTATACATCTCTCAAACTAAAATT---------------------GTGGGTATGTAGCCA--TCTTTAGAGTGTGGGGG -s Anc2.Anc2refChr7 6323 96 + 32194 AGCTTACAACTACTTAACCAGATTTTCCTCCAGTA---TCTTCTTCATACATCTCTCAAACC-AAATT---------------------GTGGGTATGTAGCCA--TCTTTAGAGTGTGGGGG -s mr.mrrefChr5 174784 123 + 294540 AGATTGCACCCACTTAACCAGCTTTTCCTCCAGTAGTATCTTCTTTATACATTTTTCAAACTTAGTTTATTCTTCATAAATTTTTCAATGTAAGTTTATGGGCAGGTCTTTAGAGTGTTTGGG -s simCow_chr6.simCow.chr6 302607 93 + 602619 AGCCTACAACTACTTAACCAGATTTTCCTCCAGTA---TTTTCCTCACACATCTCTCAAACC-A---T---------------------GTAGGTATGTAGCCA--TTTTTTGAGCGTGGGAG -s simDog_chr6.simDog.chr6 289009 73 + 593897 TCCTTA----------------------TCCAGTA---TCTTCTTCATACATCTTGCAAACC-AAATT---------------------TTGGATGTGTAGACA--TCTTTAGAGTATGTGG- -s simHuman_chr6.simHuman.chr6 312848 97 + 601863 AGCTTACGTTTGCTTAACCAGATTGTCCTCCAGGA---TCTTCTTTATACATCTCTCAAACTAAAATT---------------------GTGGGTATGTTGCCA--TCTTTAGAGTGTGGGGG -s simRat_chr6.simRat.chr6 318150 116 + 647215 AG-------CGACTTAACTAGCCTTCCCTCCAGTAGTATCTTCTTTATAAATTTTTCTAACTTAGTCTATTCCTTATACATTTTTCAAAGTAAGTTTATAGGCAGGTCTTTAGAGTGTTCAGG - -a -s simMouse_chr6.simMouse.chr6 326895 173 + 636262 GTACCTGTATGCTTTACCTGTATGCTTTGAGTGAAACGCCTTGCTTGAACAGCAATTTAATTTTGCATAAGTGAAATGCTTTGCTTGAATAGCAGTTTAATTGATTTACCAGGATATCACAAGTGTTCAATATGACTGGCAATAAACACCCAAGTTGAACTCTCAGAATTTCA -s Anc0.Anc0refChr7 10797 136 - 16696 GTGCCTGAGTGTTT---GTGCATA-----ATCAAAATGCCTTGCT-----GGCTATTTAATCTT------------------------ATAGCAGTTTAATTTATTTACCATGAGATAGCTAGAACTTACTACAATTGGCAATAAACAGCTGGATTTAGCTCCAAGGATTTGA -s Anc1.Anc1refChr4 11288 136 + 17549 GTGCCTGAGTGTTT---GTGCATA-----ATCAAAATGCCTTGCT-----GGCTATTTAATCTT------------------------ATAGCAGTTTAATTTATTTACCATGAGATAGCTAGAACTTACTACAATTGGCAATAAACAGCTGGATTTAGCTCCAAGGATTTGA -s Anc2.Anc2refChr7 6421 136 + 32194 GTGCCTGAGTGTTT---GTGCATG-----GTCAAAATGTCTTGCT-----GGCTATTTAATCCT------------------------ATAGCAGTTTTATTTAATTACCATGAGATAGCTAGAACTTACTACAATTGGCAATAAACAGCTGGATTTAGCTTCAGGGATTTGA -s mr.mrrefChr5 174907 165 + 294540 GTACCTGAATGCTT---CTGCATA-----AGTGAAATGCCTTGCTTGAACAGCAATTTAATTTTGCATAAGTGAAATGCTTTGCTTGAATAGCAGTTTAATTGATTTACCAGGAGATAGCAAGTGTTCAATATGACTGGCAATAAACACCCAAGTTGAACTCCCAGAATTTCA -s simCow_chr6.simCow.chr6 302702 136 + 602619 GTGCCTGAGTGTTT---GTGCATG-----GTTGAAATGTGTTGTA-----GACTCTATGATCCT------------------------ATAGCAGTTTTTCTTAACTACCATGGGAGAGCTAGAACTTACTACAATTGGCAATAAACAACTAGATTTAGCTTCAAGGATTTCA -s simDog_chr6.simDog.chr6 289084 136 + 593897 GGACCTTGGTGTTT---GTGCATG-----GTCAAAACATCTTGCT-----GGCCATTTAATCCT------------------------ATAGCAGTTTTATTTAATTACTATGAAATAGCTAGCAATCACCACAATCAGCAATAAGCAGCTGGATTTGGGTTTAGGGATTTGA -s simHuman_chr6.simHuman.chr6 312947 133 + 601863 GTGCCTGAGTGTTG---GTGCATA-----AT---GATGCCTTGCT-----GGCTGTTTAATCTT------------------------ATAGCAGTTCAATTTATTTACCATGAGCTAGCTAGAACTTGCTACATTTGCCAATCAACAGCTCGATCTAGCTCCAAGGATTTGA -s simRat_chr6.simRat.chr6 318266 164 + 647215 GTACCTGAATGCTT---CTGCATA-----AGTGAAATGCCTTGCTCGAATAGCGACTTAATTTTGCATAAGTTAAATGCCTTGCTTGACTAGCAGTTTAATTAATTTACCAGGAGATAGTGAGTGGTCAATATGACGGG-AATAAACACCCATGTTGAACTCCCAGAATTTCA - -a -s simMouse_chr6.simMouse.chr6 327068 3 + 636262 GCA -s Anc0.Anc0refChr7 10933 3 - 16696 GCG -s Anc1.Anc1refChr4 11424 3 + 17549 GCG -s Anc2.Anc2refChr7 6558 3 + 32194 GCT -s mr.mrrefChr5 175072 3 + 294540 GCG -s simCow_chr6.simCow.chr6 302839 3 + 602619 GCT -s simDog_chr6.simDog.chr6 289221 3 + 593897 GCT -s simHuman_chr6.simHuman.chr6 313080 3 + 601863 GGG -s simRat_chr6.simRat.chr6 318430 3 + 647215 GTG - -a -s simMouse_chr6.simMouse.chr6 327071 21 + 636262 TGTGACTCGTAAATCATGAGT -s Anc0.Anc0refChr7 10936 21 - 16696 TGTGACTAATTAATGATAAGT -s Anc1.Anc1refChr4 11427 21 + 17549 TGTGACTAATTAATGATAAGT -s Anc2.Anc2refChr7 6561 21 + 32194 TGTGACTAATTAGTGATAAGT -s mr.mrrefChr5 175075 21 + 294540 TGTGACTCGTAAATCATGAGT -s simCow_chr6.simCow.chr6 302842 21 + 602619 TGTGACTAACTAGTGATAAGT -s simDog_chr6.simDog.chr6 289224 21 + 593897 TGTTACTAATTAGTGACGAAT -s simHuman_chr6.simHuman.chr6 313104 21 + 601863 TATGACTAATTAATGATAAGT -s simRat_chr6.simRat.chr6 318433 21 + 647215 TGTAACTTGTAAACAATGAGT - -a -s simMouse_chr6.simMouse.chr6 327092 27 + 636262 ACGTTAGCACCTATTAACAATTGGATG -s Anc0.Anc0refChr7 10957 26 - 16696 ACCTTAGCACCCATTAGCAAATAGAT- -s Anc1.Anc1refChr4 11448 27 + 17549 ACCTTAGCACCCATTAGCAAATAGATG -s Anc2.Anc2refChr7 6584 26 + 32194 ACCTTAGCACGCATTAGCAAATAGAT- -s mr.mrrefChr5 175096 27 + 294540 ACGTTAGCACCTATTAACAATTGGATG -s simCow_chr6.simCow.chr6 302865 25 + 602619 ACAT-AGCACACATTAGCAACTACAT- -s simDog_chr6.simDog.chr6 289247 24 + 593897 ACCTTAACAAGCA--AGCAAATAGGT- -s simHuman_chr6.simHuman.chr6 313125 27 + 601863 ACCTTAGCACCCACTATCAAGTAGATG -s simRat_chr6.simRat.chr6 318454 27 + 647215 ATGTTAGGACGTATTAACAACTGGATG - -a -s simMouse_chr6.simMouse.chr6 327119 24 + 636262 TTCCATCCTTTTTAGTTTAATCTT -s Anc0.Anc0refChr7 10986 24 - 16696 CTCCATCCCTTTTAATTTGACTAT -s Anc1.Anc1refChr4 11478 24 + 17549 CTCCATCCCTTTTAATTTGACTAT -s Anc2.Anc2refChr7 6613 24 + 32194 CTCTATCCCCTTTAATTTGACTAT -s mr.mrrefChr5 175123 24 + 294540 TTCCATCCTTTTTAATTTAACCTT -s simCow_chr6.simCow.chr6 302893 24 + 602619 CTCTATACTGTTTAATATGACTCT -s simDog_chr6.simDog.chr6 289274 23 + 593897 CTCTCTCCCCTTTCATTTGCTTA- -s simHuman_chr6.simHuman.chr6 313157 24 + 601863 CTCCATCCCTTTTAATTTGACTAT -s simRat_chr6.simRat.chr6 318481 21 + 647215 TTACATCCTT---AATTTAACCTT - -a -s simMouse_chr6.simMouse.chr6 327143 69 + 636262 TTCCCTTTTTGTTATGCTGTGTATCTCACATTGTGCTTTCTTAATCTCCCATTTCCAAGTGAGTGGCAA -s Anc0.Anc0refChr7 11011 64 - 16696 TTCCCTTTTGGTTGTGTTGGATGTCTCACACTGTGTCTTCTTAATCTCCA-----TATGTGGGTCGCAA -s Anc1.Anc1refChr4 11503 64 + 17549 TTCCCTTTTGGTTGTGTTGGATGTCTCACACTGTGTCTTCTTAATCTCCA-----TATGTGGGTCGCAA -s Anc2.Anc2refChr7 6638 64 + 32194 TTCCCTTTTGGTTGTGTTGGATGTCTCACACAGTGTCTTCTCAATCTCCA-----TATGTGGGTCGCAA -s mr.mrrefChr5 175147 69 + 294540 TTCCCTTTTTGTTATGCTGGATATCTCACATTGTGCTTTCTTAATCTCCAATTTCCAAGTGAGTGGCAA -s simCow_chr6.simCow.chr6 302918 64 + 602619 TTCCCTTTTTATTGTGTTGGATGTCTCATGCAGTGCCCTCTCAATCTCCA-----TATGTGGGTGGCAA -s simDog_chr6.simDog.chr6 289298 64 + 593897 TCCTCGTTTGGCTCAGTTGGATGTCTCACACAGTGTCTTCTCAATTTCCA-----TAAGTGAGTCGCAA -s simHuman_chr6.simHuman.chr6 313182 64 + 601863 TTCCCTTTTCGTTGTGTTGGATGTCTCACACTGTGTCTTCTTGATCCCCA-----TATGTGGGTCGCAA -s simRat_chr6.simRat.chr6 318502 66 + 647215 TTCCCTTTTTGTTATA---GATCTCTCACATTGTGCTGTCTTAATCTCCAATTTCCAAGTGTGTGGCAA - -a -s simMouse_chr6.simMouse.chr6 327212 3 + 636262 CAA -s Anc0.Anc0refChr7 11075 3 - 16696 CAC -s Anc1.Anc1refChr4 11567 3 + 17549 CAC -s Anc2.Anc2refChr7 6702 3 + 32194 CAC -s mr.mrrefChr5 175216 3 + 294540 CAA -s simCow_chr6.simCow.chr6 302983 3 + 602619 TGC -s simDog_chr6.simDog.chr6 289362 3 + 593897 CAC -s simHuman_chr6.simHuman.chr6 313246 3 + 601863 CAC -s simRat_chr6.simRat.chr6 318568 3 + 647215 CAA - -a -s simMouse_chr6.simMouse.chr6 327215 26 + 636262 CCTTCCTGTTCTCTACAGGCTGCCTC -s Anc0.Anc0refChr7 11080 26 - 16696 CCTGCCTGTTCTCTCCAGGCTCCCTC -s Anc1.Anc1refChr4 11572 26 + 17549 CCTGCCTGTTCTCTCCAGGCTCCCTC -s Anc2.Anc2refChr7 6707 26 + 32194 TCTGCCTGTTCTCTCTAGGCTCCCTC -s mr.mrrefChr5 175219 26 + 294540 CCTTCCTGTTCTCTCCAGGCTCCCTC -s simCow_chr6.simCow.chr6 302988 26 + 602619 TCTGCCTGCTTTCTCAAGGCTCCCTC -s simDog_chr6.simDog.chr6 289367 26 + 593897 TCTGCTTGTTCTCTCTCGACTCCCTC -s simHuman_chr6.simHuman.chr6 313251 26 + 601863 CCTGCCTGTTCTCTCCAGGCTCCCTC -s simRat_chr6.simRat.chr6 318571 26 + 647215 CCTTCCTGTTCTCTCCAGGCTCCCTC - -a -s simMouse_chr6.simMouse.chr6 327241 58 + 636262 GTAGCCCAATTGACTGGGAGCCCCTATCCTTGAGGTTTATCCTACTTAGGGGTGGTAG -s Anc0.Anc0refChr7 11106 53 - 16696 ACAGCCAAGTTCACAGGGAACCACTAATCTTGATGTCTACACCACTCAGGCAT----- -s Anc1.Anc1refChr4 11598 53 + 17549 ACAGCCAAGTTCACAGGGAACCACTAATCTTGATGTCTACACCACTCAGGCAT----- -s Anc2.Anc2refChr7 6733 53 + 32194 ACAGCTAAGTTCACAGGGAACCACTAATCTTGATGTCCACACCCCTCAGGCAT----- -s mr.mrrefChr5 175245 58 + 294540 GTAGCCCAATTGACTGGGAGCCCCTATCCTTGAGGTCTATCCTACTTAGGGGTGGTAG -s simCow_chr6.simCow.chr6 303014 53 + 602619 ACAGCTAAGTTGACAGGAAACCACTAATCTTGATGTCCACACCCCTCAGGAAT----- -s simDog_chr6.simDog.chr6 289394 40 + 593897 ATAGCTAAATTCACAGGGAACCACTAACCTTGATGT-------------GCAC----- -s simHuman_chr6.simHuman.chr6 313277 53 + 601863 ACAGCCAAGTTCACAGGGAAACACTAATCTTGGTGTCTAAGTCAGTCAGGCTT----- -s simRat_chr6.simRat.chr6 318597 57 + 647215 GTAGCCCAATTGACTGGGGGCCCCTACCCTTGAGGTCTATCC-ACTTAGGGGCAGTAG - -a -s simMouse_chr6.simMouse.chr6 327299 27 + 636262 CTGGCTTGTAAGATTGACTGCAACCAA -s Anc0.Anc0refChr7 11159 27 - 16696 CTACCTTGTAAGATCCACTGTGACAAA -s Anc1.Anc1refChr4 11651 27 + 17549 CTACCTTGTAAGATCCACTGTGACAAA -s Anc2.Anc2refChr7 6786 27 + 32194 CTACCTTGTAAGATCCACTGTGACAAA -s mr.mrrefChr5 175303 27 + 294540 CTGGCTTGTAAGATTGACTGCAACCAA -s simCow_chr6.simCow.chr6 303070 27 + 602619 CCACCTTGTAAGAGCCACTGTGACAAA -s simDog_chr6.simDog.chr6 289434 27 + 593897 CTGCCCTGTAAGATCCACTCTGACAAA -s simHuman_chr6.simHuman.chr6 313330 27 + 601863 GTATCTTGTAAGATCCACTGTGACAAA -s simRat_chr6.simRat.chr6 318654 27 + 647215 CTGGCTTGTAAGATGGACCGCAACCAA - -a -s simMouse_chr6.simMouse.chr6 327326 49 + 636262 TTATTATAGACTAGCCAAACCAGACATCTTTGCATGTTGGTTCAACACA -s Anc0.Anc0refChr7 11186 49 - 16696 TTGTCATAGAAAGGCCTATCCAGACATCTTTGTGTGTTGGCTCCACACT -s Anc1.Anc1refChr4 11678 49 + 17549 TTGTCATAGAAAGGCCTATCCAGACATCTTTGTGTGTTGGCTCCACACT -s Anc2.Anc2refChr7 6813 49 + 32194 TTGTCATAGAAACGCCTATCCAGACATCTTTGTGTGTTGGCTCCACACT -s mr.mrrefChr5 175330 49 + 294540 TTATTATAGACTGGCCAAACCAGACATCTTTGCATGTTGGTTCAACACA -s simCow_chr6.simCow.chr6 303109 48 + 602619 CTATTGTAGAAACGCCTATCAAGACA-CTCTGTGTGTTGGCTCCATGCT -s simDog_chr6.simDog.chr6 289461 49 + 593897 TTGTCATAGAAGCGCTTAACCAGACATCTTCGCATGTTGGCTCCACACT -s simHuman_chr6.simHuman.chr6 313357 47 + 601863 TTGTAAGAAA--GTCCTATCCAGATATCTTTGTGTTTTAGATCCACACT -s simRat_chr6.simRat.chr6 318681 49 + 647215 TTATTATAGAATGGCCAAATGAGAAGTCTTTGCATGTTGGTTCAACACA - -a -s simMouse_chr6.simMouse.chr6 327375 16 + 636262 CAGCACATTATATCAA -s Anc0.Anc0refChr7 11235 12 - 16696 CCACACATCA----CA -s Anc1.Anc1refChr4 11727 12 + 17549 CCACACATCA----CA -s Anc2.Anc2refChr7 6862 12 + 32194 CCACACATCA----CA -s mr.mrrefChr5 175379 16 + 294540 CAGCACATCATATCAA -s simCow_chr6.simCow.chr6 303157 1 + 602619 C--------------- -s simDog_chr6.simDog.chr6 289510 12 + 593897 CCACACATCA----CA -s simHuman_chr6.simHuman.chr6 313404 12 + 601863 GCACACATCA----GA -s simRat_chr6.simRat.chr6 318733 16 + 647215 CAGAACATCATCTCAA - -a -s simMouse_chr6.simMouse.chr6 327391 10 + 636262 TTGGTAAGCA -s Anc0.Anc0refChr7 11247 10 - 16696 TTGGTAAGCT -s Anc1.Anc1refChr4 11739 10 + 17549 TTGGTAAGCT -s Anc2.Anc2refChr7 6874 10 + 32194 CTGGGAAGCT -s mr.mrrefChr5 175395 10 + 294540 TTGGTAAGCA -s simDog_chr6.simDog.chr6 289530 10 + 593897 CTGGGAAGCT -s simHuman_chr6.simHuman.chr6 313416 10 + 601863 TTGGTGAGCT -s simRat_chr6.simRat.chr6 318749 10 + 647215 TTGGAAAGGC - -a -s simMouse_chr6.simMouse.chr6 327401 94 + 636262 ATCAAAGATGTATCCTGCCACAAATGCCCTAGATTCTGAAGTGCTGATGTTCGTGTTATTACATGCCTTTTAGTTCATATGTATACTGTGGATG -s Anc0.Anc0refChr7 11259 60 - 16696 ATAAAAG-TGTAATCTGTAACAAATGCTCCAAATCCTGAAGTGC----------------------TTCTATGT-CTGATG----------ATG -s Anc1.Anc1refChr4 11751 60 + 17549 ATAAAAG-TGTAATCTGTAACAAATGCTCCAAATCCTGAAGTGC----------------------TTCTATGT-CTGATG----------ATG -s Anc2.Anc2refChr7 6886 60 + 32194 ATAAAGA-TATAATTGATATGAAATGCTTCAACTCCTGACATGC----------------------TTCTATGT-CTGATG----------TTG -s mr.mrrefChr5 175405 91 + 294540 ATCAAAG-TGTATTCTGCCACAAATGCCCTAGATTCTGAAGTGCTGATGTTCGTGTTGATACATGCCTTTTAGT-CATATGTA-ACTGTGGATG -s simDog_chr6.simDog.chr6 289542 60 + 593897 ATAAAGA-TATAATTGATATGAAATGCTTCAACTCCTGACATGC----------------------TTCTATGT-CTGATG----------TTG -s simHuman_chr6.simHuman.chr6 313428 60 + 601863 ATAAAAG-TGTACTCTGGGACAAATGCTCCAAATCCTGGAGTAC----------------------TCAGATGT-TTGATA----------ATG -s simRat_chr6.simRat.chr6 318759 91 + 647215 AACAAAG-AATATTCTGCCACAAATGCCCTAGATTCTGAAGTGCTGAAGTTCGCATTGATACATGCCTTTTAGT-CATATGTA-ACTGTGGAGG - -a -s simMouse_chr6.simMouse.chr6 327495 23 + 636262 AAAAGAACCTCTGACTAATAGTC -s Anc0.Anc0refChr7 11319 23 - 16696 GAAGAAACTGCTGACTGTTTGTC -s Anc1.Anc1refChr4 11811 23 + 17549 GAAGAAACTGCTGACTGTTTGTC -s Anc2.Anc2refChr7 6946 23 + 32194 GAAGTAACTGCTGACTGTTTGTC -s mr.mrrefChr5 175496 23 + 294540 AAAAAAACCTCTGACTGATAGTC -s simDog_chr6.simDog.chr6 289605 23 + 593897 GAAGTAACTGCTGACTGTTTGTC -s simHuman_chr6.simHuman.chr6 313488 23 + 601863 GAAGAAACTGCTGACTGTTTGGC -s simRat_chr6.simRat.chr6 318850 23 + 647215 AAGTAAACCTCTGACTGATAGTT - -a -s simMouse_chr6.simMouse.chr6 327518 7 + 636262 TGGATGT -s Anc0.Anc0refChr7 11342 7 - 16696 TAGATGC -s Anc1.Anc1refChr4 11834 7 + 17549 TAGATGC -s Anc2.Anc2refChr7 6969 7 + 32194 TGGATAC -s mr.mrrefChr5 175519 7 + 294540 TAGATGT -s simDog_chr6.simDog.chr6 289642 7 + 593897 TGGATAC -s simHuman_chr6.simHuman.chr6 313511 7 + 601863 TAGATGC -s simRat_chr6.simRat.chr6 318873 7 + 647215 AAGAGGT - -a -s simMouse_chr6.simMouse.chr6 327525 41 + 636262 CACAAAATTCTGGAGGAAAATGAAGAATCTGTCAATAAATC -s Anc0.Anc0refChr7 11406 30 - 16696 AGCAGGATCCTTGGTGAAAATGAC-----------TAAACT -s Anc1.Anc1refChr4 11898 30 + 17549 AGCAGGATCCTTGGTGAAAATGAC-----------TAAACT -s Anc2.Anc2refChr7 7033 30 + 32194 AGTGGGATCCTTAGTAAAAATGAC-----------TAAACT -s mr.mrrefChr5 175582 38 + 294540 AACAAGATTCTGGAGGAAAATGAAGAATC---CAATAAATT -s simCow_chr6.simCow.chr6 303201 30 + 602619 AGTGGGATCCTTAGTAAAAATGAC-----------TAAACT -s simHuman_chr6.simHuman.chr6 313575 30 + 601863 AGCAGGATCCTTGCTGAAAATGAC-----------TAAACT -s simRat_chr6.simRat.chr6 318936 38 + 647215 AACAAGATTCTGGGGGAAAATGAAGAATA---CAATAAATT - -a -s simMouse_chr6.simMouse.chr6 327566 30 + 636262 TGTTCAGGATTGGCATAAACATAATCTGGA -s Anc0.Anc0refChr7 11440 30 - 16696 TGTTTAAGATTGACAAGAGCATAGTCTGGA -s Anc1.Anc1refChr4 11932 30 + 17549 TGTTTAAGATTGACAAGAGCATAGTCTGGA -s Anc2.Anc2refChr7 7067 30 + 32194 TGTCTAAGATTGACAAAAGCATAGTTGGGA -s mr.mrrefChr5 175624 30 + 294540 TGTTCAGGATTGGCAAGAACATAATCTGGA -s simCow_chr6.simCow.chr6 303235 30 + 602619 TGTCTGAGATTGACAAAAGCATAGTTGGGA -s simDog_chr6.simDog.chr6 289706 28 + 593897 --TCTAAGCTTGACAAAAGCATAGTTGGGA -s simHuman_chr6.simHuman.chr6 313609 30 + 601863 TGTTTAAGACTGACAAGAGCATAGCCTGGA -s simRat_chr6.simRat.chr6 318978 30 + 647215 TGTTGAGGATTGTCAAGAACATAATCTGGA - -a -s simMouse_chr6.simMouse.chr6 327596 38 + 636262 GTCCAGTCTGCAGCGTCACCCTTATAGGAGGACAAGCG -s Anc0.Anc0refChr7 11470 38 - 16696 ATCTAGTCTGCAGCCTCACACTTATAGAAGAACAAGGT -s Anc1.Anc1refChr4 11962 38 + 17549 ATCTAGTCTGCAGCCTCACACTTATAGAAGAACAAGGT -s Anc2.Anc2refChr7 7097 38 + 32194 ATCTAGTCTGCTGCCTCACACTTATAGAAGAACAAGGT -s mr.mrrefChr5 175654 38 + 294540 GTCCAGTCTGCAGCCTCACCCTTATAGAAGGACAAGGG -s simCow_chr6.simCow.chr6 303265 38 + 602619 ATCTAGTCTGCAGCCTCACATGTGTAGAAGAACAAGGT -s simDog_chr6.simDog.chr6 289734 38 + 593897 ATTCAGTCTGCTGCCTCACACTTATTGAAGAACAAGGT -s simHuman_chr6.simHuman.chr6 313639 37 + 601863 ATCTAGTCTGCA-CCTCACACTTAAAGAAGAAATGGGT -s simRat_chr6.simRat.chr6 319020 38 + 647215 GTCCAGTCTGCAGCCTCACGCTTGTGAAAGGACAAGGG - -a -s simMouse_chr6.simMouse.chr6 327634 22 + 636262 ATTCACGAAAGCGATTCACGAG -s Anc0.Anc0refChr7 11508 9 - 16696 ATTCAGAA-------------G -s Anc1.Anc1refChr4 12000 9 + 17549 ATTCAGAA-------------G -s Anc2.Anc2refChr7 7135 9 + 32194 ATTCAGAA-------------G -s mr.mrrefChr5 175692 9 + 294540 ATTCAGGA-------------G -s simCow_chr6.simCow.chr6 303304 9 + 602619 ATGCAGAA-------------G -s simDog_chr6.simDog.chr6 289772 9 + 593897 ATTCAGAA-------------G -s simHuman_chr6.simHuman.chr6 313676 8 + 601863 AAGCAG-A-------------G -s simRat_chr6.simRat.chr6 319058 9 + 647215 ATTCAGGA-------------G - -a -s simMouse_chr6.simMouse.chr6 327656 14 + 636262 GGGTTGGGACACTT -s Anc0.Anc0refChr7 11517 14 - 16696 GGGCTGGGACACAT -s Anc1.Anc1refChr4 12009 14 + 17549 GGGCTGGGACACAT -s Anc2.Anc2refChr7 7150 14 + 32194 GGACTGGGACATAT -s mr.mrrefChr5 175701 14 + 294540 GGGTTGGGACACTT -s simCow_chr6.simCow.chr6 303319 13 + 602619 GGACTGGTATA-AT -s simDog_chr6.simDog.chr6 289787 14 + 593897 CGACTGGGACGTGT -s simHuman_chr6.simHuman.chr6 313684 14 + 601863 GGGCTGGGACACAA -s simRat_chr6.simRat.chr6 319067 14 + 647215 GGGTTGGGACACTT - -a -s simMouse_chr6.simMouse.chr6 327670 18 + 636262 TGAGTGATACTTTTGGCA -s Anc1.Anc1refChr4 12062 18 + 17549 TGACGGATATTTTAGGCA -s mr.mrrefChr5 175715 18 + 294540 TGAGTGATACTTTTGGCA -s simHuman_chr6.simHuman.chr6 314059 18 + 601863 TGACGGATATTTTAGGCA -s simRat_chr6.simRat.chr6 319081 18 + 647215 TGAGTGACGCTTATGGCA - -a -s simMouse_chr6.simMouse.chr6 327688 47 + 636262 ACTGATAAAAAAGCAATTGGCAACACACATAGCCTAATCCAGGAATA -s Anc1.Anc1refChr4 12080 47 + 17549 GGTGTTGAAAAAGAAACTAGCAACAAACTTAGCCCACACCAAGAATA -s mr.mrrefChr5 175733 47 + 294540 ACTGATAAAAAAGCAACTGGCAACACACATAGCCTAAACCAGGAATA -s simHuman_chr6.simHuman.chr6 314077 47 + 601863 GGTGTTGAAAAAGAAACTAGCAACAAACTTAGCCCACACCAAGAATA -s simRat_chr6.simRat.chr6 319105 47 + 647215 ACTGATAAAAAAACAACTGAAAACTGGTATAGCCAAAATTGGGAATA - -a -s simMouse_chr6.simMouse.chr6 327735 7 + 636262 AGTTCCA -s Anc0.Anc0refChr7 11570 6 - 16696 -GTTCCA -s Anc1.Anc1refChr4 12127 7 + 17549 AGTTCCA -s Anc2.Anc2refChr7 7203 6 + 32194 -GTTCCA -s mr.mrrefChr5 175780 7 + 294540 AGTTCCA -s simCow_chr6.simCow.chr6 303376 6 + 602619 -TTTGCA -s simDog_chr6.simDog.chr6 289840 6 + 593897 -GTTCAA -s simHuman_chr6.simHuman.chr6 314148 7 + 601863 AGTTCCA -s simRat_chr6.simRat.chr6 319152 7 + 647215 AGTTCCA - -a -s simMouse_chr6.simMouse.chr6 327742 4 + 636262 AATA -s Anc0.Anc0refChr7 11577 4 - 16696 GAGT -s Anc1.Anc1refChr4 12135 4 + 17549 GAGT -s Anc2.Anc2refChr7 7210 4 + 32194 GAGT -s mr.mrrefChr5 175788 4 + 294540 AAGA -s simCow_chr6.simCow.chr6 303383 4 + 602619 GAGT -s simDog_chr6.simDog.chr6 289847 4 + 593897 GAGT -s simHuman_chr6.simHuman.chr6 314156 4 + 601863 GAGT -s simRat_chr6.simRat.chr6 319160 4 + 647215 AAGA - -a -s simMouse_chr6.simMouse.chr6 327746 9 + 636262 GATAGCCAA -s Anc0.Anc0refChr7 11581 9 - 16696 GATAGCCAA -s Anc1.Anc1refChr4 12139 9 + 17549 GATAGCCAA -s Anc2.Anc2refChr7 7214 9 + 32194 GATGGCCAA -s mr.mrrefChr5 175792 9 + 294540 GATAGCCAA -s simCow_chr6.simCow.chr6 303394 9 + 602619 GATGGCTAA -s simDog_chr6.simDog.chr6 289851 9 + 593897 GACGGTCAA -s simHuman_chr6.simHuman.chr6 314160 9 + 601863 GATAGCCAA -s simRat_chr6.simRat.chr6 319164 9 + 647215 GATAGCCAA - -a -s simMouse_chr6.simMouse.chr6 327755 8 + 636262 TTGCCATG -s Anc0.Anc0refChr7 11592 8 - 16696 TTACCATG -s Anc1.Anc1refChr4 12150 8 + 17549 TTACCATG -s Anc2.Anc2refChr7 7225 8 + 32194 TCACCATG -s mr.mrrefChr5 175801 8 + 294540 TTGCCATG -s simCow_chr6.simCow.chr6 303405 8 + 602619 TCACCATG -s simDog_chr6.simDog.chr6 289862 8 + 593897 TCACTGTG -s simHuman_chr6.simHuman.chr6 314171 8 + 601863 TTACCATG -s simRat_chr6.simRat.chr6 319173 8 + 647215 TTGCTATG - -a -s simMouse_chr6.simMouse.chr6 327763 3 + 636262 GTA -s Anc0.Anc0refChr7 11601 3 - 16696 GTA -s Anc1.Anc1refChr4 12159 3 + 17549 GTA -s Anc2.Anc2refChr7 7234 3 + 32194 GTA -s mr.mrrefChr5 175810 3 + 294540 GTA -s simCow_chr6.simCow.chr6 303414 3 + 602619 GTA -s simDog_chr6.simDog.chr6 289871 2 + 593897 -TA -s simHuman_chr6.simHuman.chr6 314180 3 + 601863 GTA -s simRat_chr6.simRat.chr6 319182 3 + 647215 GTA - -a -s simMouse_chr6.simMouse.chr6 327766 16 + 636262 TTTGATGAAGTTACAA -s Anc0.Anc0refChr7 11604 13 - 16696 ATTAA---AATTACAA -s Anc1.Anc1refChr4 12162 13 + 17549 ATTAA---AATTACAA -s Anc2.Anc2refChr7 7237 13 + 32194 AATAA---AATTATGA -s mr.mrrefChr5 175813 16 + 294540 TTTGATGAAGTTACAA -s simCow_chr6.simCow.chr6 303420 13 + 602619 AATGA---GATAATGA -s simDog_chr6.simDog.chr6 289873 13 + 593897 AACAA---AACTATGA -s simHuman_chr6.simHuman.chr6 314183 13 + 601863 ATTAA---AATTACAA -s simRat_chr6.simRat.chr6 319185 16 + 647215 TTTTATGAGGCTACAA - -a -s simMouse_chr6.simMouse.chr6 327782 54 + 636262 CACTGGAAGACCAACTTTTGGCAGAGGTTGCTATAATGTTTGAAAAATTTACAT -s Anc0.Anc0refChr7 11617 18 - 16696 TACA------------------------------------TGGAAGATTTACTC -s Anc1.Anc1refChr4 12175 18 + 17549 TACA------------------------------------TGGAAGATTTACTC -s Anc2.Anc2refChr7 7250 18 + 32194 TACA------------------------------------TGGAAGATTTTCTC -s mr.mrrefChr5 175829 54 + 294540 CACTGGAAGACCAACTTTTGGCAGAGGTTGCTATAATGTTTGAAAAATTTACAT -s simCow_chr6.simCow.chr6 303435 18 + 602619 CACA------------------------------------TGAAAGATTTACTC -s simDog_chr6.simDog.chr6 289886 18 + 593897 TAAT------------------------------------TGGGAGATATTATT -s simHuman_chr6.simHuman.chr6 314196 18 + 601863 TACA------------------------------------TGCAAGATTTACCC -s simRat_chr6.simRat.chr6 319201 52 + 647215 CACTGGGAAACTAATTTTTGGGAGAGGTTGCCATAATGTTTGAAAAATCTAC-- - -a -s simMouse_chr6.simMouse.chr6 327836 27 + 636262 TTTGCACAAGTTGTTTTCTTACAGGGC -s Anc0.Anc0refChr7 11635 27 - 16696 TTGGCAAAGGTTGTTTTCTTATGAGAC -s Anc1.Anc1refChr4 12193 27 + 17549 TTGGCAAAGGTTGTTTTCTTATGAGAC -s Anc2.Anc2refChr7 7268 27 + 32194 TTGGCAAAGGTTGTTTTCTTATGAGAT -s mr.mrrefChr5 175883 27 + 294540 TTTGCACAAGTTGTTTTCTTACAGGGC -s simCow_chr6.simCow.chr6 303453 26 + 602619 TTGGCAAGGGT-GTCTTCTCCCTAGAA -s simDog_chr6.simDog.chr6 289904 27 + 593897 TTGGCAAAGCTTGTTTCCTTATGAGAT -s simHuman_chr6.simHuman.chr6 314216 27 + 601863 TTGGCAAAGGTTGTTTTCTTATGATAC -s simRat_chr6.simRat.chr6 319253 14 + 647215 -------------TATTATTACAGGGC - -a -s simMouse_chr6.simMouse.chr6 327863 21 + 636262 AGTGTTGTGTGCTCTTATCAA -s Anc0.Anc0refChr7 11662 21 - 16696 AGTGCTGTGTGCACTTATCAT -s Anc1.Anc1refChr4 12220 21 + 17549 AGTGCTGTGTGCACTTATCAT -s Anc2.Anc2refChr7 7295 21 + 32194 AGTGTTATGTGCACTTATCAT -s mr.mrrefChr5 175910 21 + 294540 AGTGCTGTGTGCTCTTATCAA -s simCow_chr6.simCow.chr6 303479 21 + 602619 AGTGTTATGTGCACTTATTAT -s simDog_chr6.simDog.chr6 290007 21 + 593897 AGTGTTATATGCACTGATCAT -s simHuman_chr6.simHuman.chr6 314243 21 + 601863 AGTGCTGTGTGCACTTATCAT -s simRat_chr6.simRat.chr6 319267 21 + 647215 AATGCTGTGTGCTCTTATCAA - -a -s simMouse_chr6.simMouse.chr6 327884 18 + 636262 CATAACTTTTACAGTGTT -s Anc0.Anc0refChr7 11713 16 - 16696 AACAACTCTGA--GTGCT -s Anc1.Anc1refChr4 12271 17 + 17549 AACAACTCTGAT-GTGCT -s Anc2.Anc2refChr7 7346 16 + 32194 AACATCTCTGG--GTGCT -s mr.mrrefChr5 175952 18 + 294540 CATAACTTTGACAGTGCT -s simCow_chr6.simCow.chr6 303526 16 + 602619 AAAATCTCTGG--GTGCG -s simDog_chr6.simDog.chr6 290058 16 + 593897 AACATCTCTGG--GCACT -s simHuman_chr6.simHuman.chr6 314294 17 + 601863 AACCACTCTGAT-GTGCT -s simRat_chr6.simRat.chr6 319309 18 + 647215 CATAACTTTGACAGTGCT - -a -s simMouse_chr6.simMouse.chr6 327902 151 + 636262 TCTGTATATTATAATACTGAAATTACCCTACCTGTGTTATCCTCCTCTGCTTAACAAAAAAGTGAATTAAGTATCCCAATTTTAGAGTATAAGCTTTCACAAGTCACCATATGAAACTCACCATATGATTAGACTAAACTGTCTATTGGGA -s Anc0.Anc0refChr7 11733 136 - 16696 TCAAGATATTTTGATACCAAAATTACCCTACTAGTTCCATCTCCCTCTGCTTGACAAAAAAGTGGATTAAGTATCCCAATTTTAGAGGAGAATCTT-CATAA--------------CTCAACAAATGATTAGACTGACCTATCTATTGGAA -s Anc1.Anc1refChr4 12292 136 + 17549 TCAAGATATTTTGATACCAAAATTACCCTACTAGTTCCATCTCCCTCTGCTTGACAAAAAAGTGGATTAAGTATCCCAATTTTAGAGGAGAATCTT-CATAA--------------CTCAACAAATGATTAGACTGACCTATCTATTGGAA -s Anc2.Anc2refChr7 7366 136 + 32194 TGAAGATATCTTGATACCAGAATCACCCTACTAGTTCCATCCCCCTCTGCATGACAAAAAAGTGGATTAAGTATCCCAATTTTAGAGGAGAATCTT-CATAA--------------CTAGACAAATGATTAGACTGACCTATCTGTTGGAA -s mr.mrrefChr5 175970 137 + 294540 TCTGTATATTATAATACCAAAATTACCCTACCAGTGTTATCTTCCTCTGCTTGACAAAAAAGTGAATTAAGTATCCCAATTTTAGAGTATAAGCTTTCATAA--------------CTCAACATATGATTAGACTAAACTGTCTATTGGAA -s simCow_chr6.simCow.chr6 303546 136 + 602619 TTAAGATATCTTGATACCAGAATCACCCTACTGGTTCCATCCCCCTCTGCATGACCAAAAAGTGGATTTATTATGCCAATTTTAGAAGAGAACATT-CACAG--------------CTTGACAAATGATTAGACTGACACATCTGTTGAAA -s simDog_chr6.simDog.chr6 290078 107 + 593897 TGAAGATAT--------------------ACTAGTTCCATCCTCC---------CAAAAGAGTGGATCAAGTATCCCAATTTTAGAGGATAATCTC-CATAA--------------CTAGACAAATTATTAGACTGACCTGTCTGTTTGTA -s simHuman_chr6.simHuman.chr6 314315 136 + 601863 TCAAGATATTCTTATACCAAAATTACCCTGCTAGTTCCATCTCCCTCTGCTTGACAAAAAAGTGGATTGAGTGTCCCAATTTTAGAGGAGAATCTT-CATAA--------------CCCAACAAATGATTAGACTGACCTACTTATTGGAA -s simRat_chr6.simRat.chr6 319327 137 + 647215 TCTGTATAGTATAATACCAAAATTACCCTACCAGTGTTATCTTCCTCTACTTGACAGAAAAGTGAATTAAGTATCCCACTTTTAGAGTATAAGCTTTCATGA--------------TTAAACATATGGTCAAACTAAACGGTCTGTTGGAA - -a -s simMouse_chr6.simMouse.chr6 328053 37 + 636262 TACAAGCCTCCTCACTAGATGTAACTAACAATGAACT -s Anc0.Anc0refChr7 11870 37 - 16696 TGCAAGTCTCATCACTAGATCCAACTTCCAATGAGGT -s Anc1.Anc1refChr4 12429 37 + 17549 TGCAAGTCTCATCACTAGATCCAACTTCCAATGAGGT -s Anc2.Anc2refChr7 7503 37 + 32194 TGCAAGTCTCATCACTAGACCCAACTTCCAATGAGGT -s mr.mrrefChr5 176107 37 + 294540 TGCAAGTCTCCTCACTAGATGCAACTTACAATGAACT -s simCow_chr6.simCow.chr6 303683 29 + 602619 TGCAAGTCTCATCA--------GACTTTTGATGAGGT -s simDog_chr6.simDog.chr6 290186 32 + 593897 -----CTCTTACCACTAGACCCAGCTTCCAATGAGCT -s simHuman_chr6.simHuman.chr6 314452 37 + 601863 TGTGGGTCTCATCACTAGATACAACTTCCAATGAGGT -s simRat_chr6.simRat.chr6 319464 37 + 647215 TGCAAGTCTCCTCTCTAGATGCGACTTTCAATGAACC - -a -s simMouse_chr6.simMouse.chr6 328090 11 + 636262 ATGCTGCACTG -s Anc0.Anc0refChr7 11907 11 - 16696 GTGTGGCACTT -s Anc1.Anc1refChr4 12466 11 + 17549 GTGTGGCACTT -s Anc2.Anc2refChr7 7540 11 + 32194 GTGTGGCACAT -s mr.mrrefChr5 176144 11 + 294540 GTGCTGCACTG -s simCow_chr6.simCow.chr6 303714 11 + 602619 GTGTGGCACCT -s simDog_chr6.simDog.chr6 290218 11 + 593897 ATGTGGCACAT -s simHuman_chr6.simHuman.chr6 314489 11 + 601863 GTGTCGCACTT -s simRat_chr6.simRat.chr6 319501 11 + 647215 GTGCTCCACTG - -a -s simMouse_chr6.simMouse.chr6 328101 25 + 636262 AAAGCTACCCTGAGAGGGTTTCCAC -s Anc0.Anc0refChr7 11921 25 - 16696 AAAGTTATCCCAAGGGAGTGGTCCC -s Anc1.Anc1refChr4 12480 25 + 17549 AAAGTTATCCCAAGGGAGTGGTCCC -s Anc2.Anc2refChr7 7554 25 + 32194 AAAGTGATTCCAAGGGAGTGGTCCC -s mr.mrrefChr5 176155 25 + 294540 AAAGCTACCCTGAGAGGGTTTCCCC -s simCow_chr6.simCow.chr6 303728 25 + 602619 AAAGTCATTCCATGGGAGTGGTCCC -s simDog_chr6.simDog.chr6 290232 25 + 593897 AAAGTGATTCCGAGGGAATGGTCCC -s simHuman_chr6.simHuman.chr6 314503 25 + 601863 AAAGATATCCGACGGAAGTAGTCCC -s simRat_chr6.simRat.chr6 319512 25 + 647215 AAGGCTAGCCTGAGAGGATGTCCCC - -a -s simMouse_chr6.simMouse.chr6 328126 86 + 636262 CTCCCAACCTTAATGTAACTGTCTCTGTGCCAATCTCCACAAGTCCCAGTTCCGTCCACTAGTGGAACAACATCCCATTAACTCCA -s Anc0.Anc0refChr7 11946 64 - 16696 AGCCAAGCCTCGCT---ACCGTAGCTGTGGCAATCTTCACAGATT--AGTTC-----------------ACATCCCCTTAATTTTA -s Anc1.Anc1refChr4 12505 83 + 17549 AGCCAAGCCTCGCT---ACCGTAGCTGTGGCAATCTTCACAGATTCCAGTTCCCCCAACCAGGGGCACAACATCCCCTTAATTTTA -s Anc2.Anc2refChr7 7580 64 + 32194 AGCCAAGCCTCGCT---ACCGTAGCTGTGGCAATCTTCCCAGGTG--AGTTC-----------------AGAACTCCTTAATTTTA -s mr.mrrefChr5 176180 86 + 294540 ATCCAAACCTTAATGTAACTGTCTCTGCGCCAATCTCCACAGATTCCAGTTCCGTCCACTAGTGGAACAACATCCCATTAACTCCA -s simCow_chr6.simCow.chr6 303754 39 + 602619 ATCCAGGCCTGGCT---GCTGTAGCTGTGA-AATCTTCC-------------------------------------------TTTA -s simDog_chr6.simDog.chr6 290258 64 + 593897 AGCTAAGCCCCACT---ACCATAGCTGTGGCAATCTTCTCAGGTG--AGTTC-----------------AGAACTCCTTAATTTTA -s simHuman_chr6.simHuman.chr6 314528 73 + 601863 AACCAATCTTCGCT---ACCG----------ATTCTTCATGGACTCCAGTTCCCCCAACCAGGGGCACACCATCCCCTTAATTTTA -s simRat_chr6.simRat.chr6 319537 79 + 647215 ATCCAAGCCTTAACATAACTGTCTCTGCGCCAATCTCCACAGATTCCAGTTC-------TAGTGGAACAACATCCTGTTCACTCCA - -a -s simMouse_chr6.simMouse.chr6 328212 1 + 636262 A -s Anc0.Anc0refChr7 12010 1 - 16696 A -s Anc1.Anc1refChr4 12588 1 + 17549 A -s Anc2.Anc2refChr7 7649 1 + 32194 A -s mr.mrrefChr5 176266 1 + 294540 A -s simCow_chr6.simCow.chr6 303798 1 + 602619 A -s simDog_chr6.simDog.chr6 290327 1 + 593897 A -s simHuman_chr6.simHuman.chr6 314601 1 + 601863 A -s simRat_chr6.simRat.chr6 319616 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 328213 53 + 636262 ATTACTATCTGTATTGCGCAGAAACTAACTCTCCAGTTTTTTCCTCTAGCCGG -s Anc0.Anc0refChr7 12011 53 - 16696 ATTTTTATCTATGTTGAGCAGAAATTAATGCTCTGCCTCATTCCTCTGACCAT -s Anc1.Anc1refChr4 12589 53 + 17549 ATTTTTATCTATGTTGAGCAGAAATTAATGCTCTGCCTCATTCCTCTGACCAT -s Anc2.Anc2refChr7 7650 53 + 32194 ATGTTTATCTATGTCGAGTAGATATTGATGCTCTGCCTCACTCCTCTGACTTT -s mr.mrrefChr5 176267 53 + 294540 ATTACTATCTGTATTGCGCAGAAATTAATTCTCCAGTTTATTCCTCTGACCAG -s simCow_chr6.simCow.chr6 303799 34 + 602619 A--CCAATCTCTGTCCTATGGTTATTGTTGCTAGAC----------------- -s simDog_chr6.simDog.chr6 290328 53 + 593897 ATGTTTATCTATATCGAGTATATATTGATGCTCTGGCTCACTCCTCTGACTTT -s simHuman_chr6.simHuman.chr6 314608 53 + 601863 AGTTTTATCCATGTTGGGCAGAAATTAATGCTCTGCCTCATTTCTTTGACCAA -s simRat_chr6.simRat.chr6 319617 53 + 647215 CTTACTATCTGTATTGTACAGAAATTAATTCTCGAGTTTATTCCTCTGACCAG - -a -s simMouse_chr6.simMouse.chr6 328266 35 + 636262 AATACTATTCAGTGTCCCCTACTTATTCCAAATCA -s Anc0.Anc0refChr7 12064 23 - 16696 AAT-----------TCATGTGCTTATTGCTA-TCA -s Anc1.Anc1refChr4 12642 34 + 17549 AATACTATTCTGTGTCATGTGCTTATTGCTA-TCA -s Anc2.Anc2refChr7 7703 23 + 32194 AAT-----------TCATGTGATTCTGGCTC-TTA -s mr.mrrefChr5 176320 34 + 294540 AATACTATTCAGTGTCCCCTACTTATTCCTA-TCA -s simDog_chr6.simDog.chr6 290381 23 + 593897 AAT-----------TCATGTGATTCTGGCTC-TTA -s simHuman_chr6.simHuman.chr6 314676 34 + 601863 CATACTATTCTGTGTCATATGCTTAGTGCTA-CCT -s simRat_chr6.simRat.chr6 319670 34 + 647215 AATACTATTCGGTGTCCCCTACTTATTCCTA-TCA - -a -s simMouse_chr6.simMouse.chr6 328301 15 + 636262 TGCATAAGGTAGGAC -s Anc0.Anc0refChr7 12087 14 - 16696 TGCATAA-ATAGGAC -s Anc1.Anc1refChr4 12676 14 + 17549 TGCATAA-ATAGGAC -s Anc2.Anc2refChr7 7728 14 + 32194 TGCATAG-GCAGGAC -s mr.mrrefChr5 176354 15 + 294540 TGCATAAGATAGGAC -s simCow_chr6.simCow.chr6 303833 14 + 602619 TGCATAG-GCAGGAC -s simHuman_chr6.simHuman.chr6 314710 14 + 601863 TGCATAA-ATAGGAC -s simRat_chr6.simRat.chr6 319704 15 + 647215 TGCGCAAGATAGGAC - -a -s simMouse_chr6.simMouse.chr6 328316 4 + 636262 ATAC -s Anc0.Anc0refChr7 12101 4 - 16696 ATAC -s Anc1.Anc1refChr4 12690 4 + 17549 ATAC -s Anc2.Anc2refChr7 7742 4 + 32194 ATAA -s mr.mrrefChr5 176369 4 + 294540 ATAC -s simCow_chr6.simCow.chr6 303848 4 + 602619 ATAA -s simHuman_chr6.simHuman.chr6 314724 4 + 601863 ATAC -s simRat_chr6.simRat.chr6 319719 4 + 647215 ATAC - -a -s simMouse_chr6.simMouse.chr6 328320 1 + 636262 G -s Anc0.Anc0refChr7 12107 1 - 16696 G -s Anc1.Anc1refChr4 12696 1 + 17549 G -s Anc2.Anc2refChr7 7748 1 + 32194 G -s mr.mrrefChr5 176373 1 + 294540 G -s simCow_chr6.simCow.chr6 303854 1 + 602619 G -s simHuman_chr6.simHuman.chr6 314730 1 + 601863 G -s simRat_chr6.simRat.chr6 319723 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 328321 12 + 636262 TTTGGCTTAGAC -s Anc0.Anc0refChr7 12108 12 - 16696 CTTGGCTCATAC -s Anc1.Anc1refChr4 12697 12 + 17549 CTTGGCTCATAC -s Anc2.Anc2refChr7 7749 12 + 32194 CTTGGCTCATAC -s mr.mrrefChr5 176374 12 + 294540 TTTGGCTCAGAC -s simCow_chr6.simCow.chr6 303859 12 + 602619 CTTGGCTCATAC -s simDog_chr6.simDog.chr6 290406 8 + 593897 ----GCTCATAC -s simHuman_chr6.simHuman.chr6 314731 12 + 601863 ATTGGCTCATAC -s simRat_chr6.simRat.chr6 319724 12 + 647215 TTTGGTTCAGAC - -a -s simMouse_chr6.simMouse.chr6 328333 64 + 636262 CATAGACACTATAGATTGCAGATCTTTCAGCAGTATGTCTTCAACATGGACTTATAGTGAATGG -s Anc0.Anc0refChr7 12121 64 - 16696 CATAGTCAACACAGCTTGCGTATCTTTCAACAGTTTGTCATTAAGATGTACTCATAATGGATGG -s Anc1.Anc1refChr4 12710 64 + 17549 CATAGTCAACACAGCTTGCGTATCTTTCAACAGTTTGTCATTAAGATGTACTCATAATGGATGG -s Anc2.Anc2refChr7 7762 64 + 32194 CATAGTCAACACAGCTTATGTATCTTCCAACAGTTTGTCATTAAGATGTACTCATCATGGATGG -s mr.mrrefChr5 176386 64 + 294540 CATAGACACTATAGATTGCAGATCTTTCAGCAGTATGTCTTCAACATGGACTTATAATGAATGG -s simCow_chr6.simCow.chr6 303872 64 + 602619 CATAGTCAATACAGTTTAAGTATCTTTCAACAGTTTGTCATTAAGATGTACTCAGCATAAATGA -s simDog_chr6.simDog.chr6 290415 53 + 593897 TATAGTAGACACAGCTTATGTATCTTCCAACAGTT-----------TTTACTGATCACGGATGG -s simHuman_chr6.simHuman.chr6 314744 54 + 601863 CATAGCCAAGACA---TGC-------TCAACAGTTGGTCATTGAGATGCACTCATAATGTATGG -s simRat_chr6.simRat.chr6 319736 64 + 647215 CATAGACACTATAGATTGTGGATCTTTCAGTAGTATGTTTTCAACATGGACTTATAATGAATGA - -a -s simMouse_chr6.simMouse.chr6 328397 15 + 636262 GACCTCTGGCCAAGG -s Anc0.Anc0refChr3 85153 14 - 222631 GACTTCTA-CCAGTG -s Anc1.Anc1refChr6 25029 15 - 197743 GACTTCTAGCCAGTG -s Anc2.Anc2refChr1 92182 14 - 142988 GACTTCTA-CCAGTG -s mr.mrrefChr3 101993 15 - 181027 GACTTCTAGCCAGTG -s mr.mrrefChr5 176450 15 + 294540 GACCTCTGGCCAAGG -s simCow_chr6.simCow.chr6 94689 14 - 602619 TAATTCTA-CCAGTT -s simDog_chr6.simDog.chr6 96706 14 - 593897 GACTTCTG-CTAGTG -s simHuman_chr6.simHuman.chr6 97280 14 - 601863 GACTTCTA-CCAGGG -s simMouse_chr6.simMouse.chr6 109056 15 - 636262 GACTTCTAGCCAGTG -s simRat_chr6.simRat.chr6 108974 15 - 647215 GACTTCTGGCCGGCA -s simRat_chr6.simRat.chr6 319800 15 + 647215 GACCTCTGGCCGGCG - -a -s simMouse_chr6.simMouse.chr6 328412 20 + 636262 CGCATCATTGACTTAAACTA -s Anc0.Anc0refChr3 85167 17 - 222631 GGCATCATTGACTTAAA--- -s Anc1.Anc1refChr6 25044 20 - 197743 GGCATCATTGACTTAAACTA -s Anc2.Anc2refChr1 92196 17 - 142988 GGCATCATTGGCTTAAA--- -s mr.mrrefChr3 102008 20 - 181027 GGCATCATTGACTTAAACTA -s mr.mrrefChr5 176465 20 + 294540 CGCATCATTGACTTAAACTA -s simCow_chr6.simCow.chr6 94724 17 - 602619 GGCATTATTGCCTTAAA--- -s simDog_chr6.simDog.chr6 96720 17 - 593897 AGCATCATTGGCTTAAA--- -s simHuman_chr6.simHuman.chr6 97294 20 - 601863 GGTATCATTGACCTAAATGA -s simMouse_chr6.simMouse.chr6 109071 20 - 636262 GGCATCATTGACTTAAACTA -s simRat_chr6.simRat.chr6 108989 20 - 647215 GACATCATTGACTTAAACTA -s simRat_chr6.simRat.chr6 319815 20 + 647215 GACATCATTGATTTAAACTA - -a -s simMouse_chr6.simMouse.chr6 328432 3 + 636262 TTG -s Anc0.Anc0refChr3 85184 1 - 222631 --G -s Anc1.Anc1refChr6 25064 3 - 197743 CTG -s Anc2.Anc2refChr1 92213 1 - 142988 --G -s mr.mrrefChr3 102028 3 - 181027 CGG -s mr.mrrefChr5 176485 3 + 294540 TTG -s simCow_chr6.simCow.chr6 94741 1 - 602619 --T -s simDog_chr6.simDog.chr6 96737 1 - 593897 --G -s simHuman_chr6.simHuman.chr6 97314 3 - 601863 CTG -s simMouse_chr6.simMouse.chr6 109091 3 - 636262 CGG -s simRat_chr6.simRat.chr6 319835 3 + 647215 CTG - -a -s simMouse_chr6.simMouse.chr6 328435 6 + 636262 GCCAGC -s Anc0.Anc0refChr3 85188 6 - 222631 GTCTTC -s Anc1.Anc1refChr6 25070 6 - 197743 GTCTTC -s Anc2.Anc2refChr1 92217 6 - 142988 GTTTTC -s mr.mrrefChr3 102031 6 - 181027 GCCGTC -s mr.mrrefChr5 176488 6 + 294540 GCCAGC -s simCow_chr6.simCow.chr6 94745 5 - 602619 GT-TTC -s simDog_chr6.simDog.chr6 96741 6 - 593897 GTTTTC -s simHuman_chr6.simHuman.chr6 97320 6 - 601863 GTCTTC -s simMouse_chr6.simMouse.chr6 109094 6 - 636262 GCCGTC -s simRat_chr6.simRat.chr6 319838 6 + 647215 GCCATC - -a -s simMouse_chr6.simMouse.chr6 328441 4 + 636262 TGCT -s Anc0.Anc0refChr3 85194 4 - 222631 TCCT -s Anc1.Anc1refChr6 25076 4 - 197743 TCCT -s Anc2.Anc2refChr1 92223 4 - 142988 TCCT -s mr.mrrefChr3 102037 4 - 181027 AGCT -s mr.mrrefChr5 176494 4 + 294540 TGCT -s simCow_chr6.simCow.chr6 94750 4 - 602619 TCTT -s simDog_chr6.simDog.chr6 96749 4 - 593897 CCCT -s simHuman_chr6.simHuman.chr6 97326 4 - 601863 TCCT -s simMouse_chr6.simMouse.chr6 109100 4 - 636262 AGCT -s simRat_chr6.simRat.chr6 319844 4 + 647215 TGCT - -a -s simMouse_chr6.simMouse.chr6 328445 5 + 636262 ACCAT -s Anc0.Anc0refChr3 85198 5 - 222631 ATTAT -s Anc1.Anc1refChr6 25080 5 - 197743 ATTAT -s Anc2.Anc2refChr1 92227 5 - 142988 ATTAT -s mr.mrrefChr3 102041 5 - 181027 ACTAT -s mr.mrrefChr5 176498 5 + 294540 ACCAT -s simCow_chr6.simCow.chr6 94754 5 - 602619 ATTAG -s simDog_chr6.simDog.chr6 96753 5 - 593897 ATTAT -s simHuman_chr6.simHuman.chr6 97330 5 - 601863 ATTAT -s simMouse_chr6.simMouse.chr6 109104 5 - 636262 ACTAG -s simRat_chr6.simRat.chr6 109009 5 - 647215 ACAAT -s simRat_chr6.simRat.chr6 319848 5 + 647215 ATTAT - -a -s simMouse_chr6.simMouse.chr6 328450 3 + 636262 TAT -s Anc0.Anc0refChr3 85207 3 - 222631 TAC -s Anc1.Anc1refChr6 25089 3 - 197743 TAC -s Anc2.Anc2refChr1 92236 3 - 142988 TAC -s mr.mrrefChr3 102046 3 - 181027 TAT -s mr.mrrefChr5 176503 3 + 294540 TAT -s simCow_chr6.simCow.chr6 94763 3 - 602619 TAC -s simDog_chr6.simDog.chr6 96762 3 - 593897 TAC -s simHuman_chr6.simHuman.chr6 97339 3 - 601863 TAC -s simMouse_chr6.simMouse.chr6 109109 3 - 636262 TAT -s simRat_chr6.simRat.chr6 109014 3 - 647215 TAT -s simRat_chr6.simRat.chr6 319853 3 + 647215 TTT - -a -s simMouse_chr6.simMouse.chr6 328453 10 + 636262 TTTGATACCC -s Anc0.Anc0refChr3 85210 10 - 222631 TCTTATACCA -s Anc1.Anc1refChr6 25092 10 - 197743 TCTTATACCA -s Anc2.Anc2refChr1 92239 10 - 142988 TCTTATACCT -s mr.mrrefChr3 102049 10 - 181027 TTTAATATCA -s mr.mrrefChr5 176506 10 + 294540 TTTGATACCC -s simCow_chr6.simCow.chr6 94766 10 - 602619 TCTTATACCA -s simDog_chr6.simDog.chr6 96765 10 - 593897 CCCTATACCT -s simHuman_chr6.simHuman.chr6 97342 10 - 601863 TCTTACACCA -s simMouse_chr6.simMouse.chr6 109112 10 - 636262 TTTAATATCA -s simRat_chr6.simRat.chr6 109017 10 - 647215 TTTTATACCA -s simRat_chr6.simRat.chr6 319902 10 + 647215 TTTAATACCA - -a -s simMouse_chr6.simMouse.chr6 328463 30 + 636262 CCCTATCAGCACACAATCATGTTAGAGCTC -s Anc0.Anc0refChr3 85220 25 - 222631 CTCTATC----CACAATGTTGAT-GATCTC -s Anc1.Anc1refChr6 25102 30 - 197743 CTCTATCAGCACACAATGTTGATAGATCTC -s Anc2.Anc2refChr1 92249 25 - 142988 CTCTATC----CACGATGTTGAT-GATTTT -s mr.mrrefChr3 102059 30 - 181027 CTCTATCAACATCCAATCATGTTAGAGCTC -s mr.mrrefChr5 176516 30 + 294540 CCCTATCAGCACACAATCATGTTAGAGCTC -s simCow_chr6.simCow.chr6 94776 24 - 602619 CTCTATA----CATGAGGTTG-T-GGTTTA -s simDog_chr6.simDog.chr6 96775 25 - 593897 CCCTGTC----CACGGTGTTGAT-GATTCT -s simHuman_chr6.simHuman.chr6 97353 26 - 601863 TTTTATC----CACAATGTTAATGGATCTC -s simMouse_chr6.simMouse.chr6 109122 30 - 636262 CTCTATCAACACACAATCATGTTAGAGGTC -s simRat_chr6.simRat.chr6 109027 30 - 647215 CTCTATCAGCATCCAATCATGTTACAACTC -s simRat_chr6.simRat.chr6 319912 30 + 647215 CTCCATAAGCACACAATCATGTTAGAGCTT - -a -s simMouse_chr6.simMouse.chr6 328493 7 + 636262 CTATCTG -s Anc0.Anc0refChr3 85245 7 - 222631 CTAACTG -s Anc1.Anc1refChr6 25132 7 - 197743 CTAACTG -s Anc2.Anc2refChr1 92274 7 - 142988 CTTACCC -s mr.mrrefChr3 102089 7 - 181027 CTATCTG -s mr.mrrefChr5 176546 7 + 294540 CTATCTG -s simCow_chr6.simCow.chr6 94800 7 - 602619 CTTACCC -s simDog_chr6.simDog.chr6 96800 7 - 593897 CTTAACC -s simHuman_chr6.simHuman.chr6 97379 7 - 601863 CTAACTG -s simMouse_chr6.simMouse.chr6 109152 7 - 636262 CTATCTG -s simRat_chr6.simRat.chr6 109059 7 - 647215 CTATCTG -s simRat_chr6.simRat.chr6 319942 7 + 647215 CTAATTG - -a -s simMouse_chr6.simMouse.chr6 328500 16 + 636262 ATGAGACATATGAACA -s Anc0.Anc0refChr3 85252 16 - 222631 ATGAGACTTGTGAACA -s Anc1.Anc1refChr6 25139 16 - 197743 ATGAGACTTGTGAACA -s Anc2.Anc2refChr1 92281 16 - 142988 ATGAGACTTGTGAACA -s mr.mrrefChr3 102096 16 - 181027 ATGAGACATATGAACA -s mr.mrrefChr5 176553 16 + 294540 ATGAGACATATGAACA -s simCow_chr6.simCow.chr6 94807 16 - 602619 ATGAGACTGGTGATCA -s simDog_chr6.simDog.chr6 96808 16 - 593897 ATCAGACCTGTGGACA -s simHuman_chr6.simHuman.chr6 97386 16 - 601863 ATGAGACTTGTGAACA -s simMouse_chr6.simMouse.chr6 109159 16 - 636262 ATGAGGCATATGAACA -s simRat_chr6.simRat.chr6 109066 16 - 647215 ATGAGACATCTGAACA -s simRat_chr6.simRat.chr6 319949 16 + 647215 ATGAGACATATGGACA - -a -s simMouse_chr6.simMouse.chr6 328516 4 + 636262 GGTA -s Anc0.Anc0refChr3 85268 4 - 222631 GGTA -s Anc1.Anc1refChr6 25155 4 - 197743 GGTA -s Anc2.Anc2refChr1 92297 4 - 142988 GACA -s mr.mrrefChr3 102112 4 - 181027 GGTA -s mr.mrrefChr5 176569 4 + 294540 GGTA -s simCow_chr6.simCow.chr6 94823 4 - 602619 CACA -s simDog_chr6.simDog.chr6 96824 4 - 593897 GACA -s simHuman_chr6.simHuman.chr6 97402 4 - 601863 GGTA -s simMouse_chr6.simMouse.chr6 109175 4 - 636262 GGTA -s simRat_chr6.simRat.chr6 319965 4 + 647215 GGTA - -a -s simMouse_chr6.simMouse.chr6 328520 2 + 636262 AT -s Anc0.Anc0refChr3 85272 2 - 222631 AT -s Anc1.Anc1refChr6 25159 2 - 197743 AT -s Anc2.Anc2refChr1 92301 2 - 142988 GT -s mr.mrrefChr3 102116 2 - 181027 AT -s mr.mrrefChr5 176573 2 + 294540 AT -s simCow_chr6.simCow.chr6 94827 2 - 602619 GT -s simDog_chr6.simDog.chr6 96828 2 - 593897 GT -s simHuman_chr6.simHuman.chr6 97406 2 - 601863 AT -s simMouse_chr6.simMouse.chr6 109179 2 - 636262 AT -s simRat_chr6.simRat.chr6 109082 2 - 647215 AT -s simRat_chr6.simRat.chr6 319969 2 + 647215 AT - -a -s simMouse_chr6.simMouse.chr6 328522 16 + 636262 TATAAGGAACTAGCTC -s Anc0.Anc0refChr3 85274 16 - 222631 AACAAGGAACTAGCTT -s Anc1.Anc1refChr6 25161 16 - 197743 AACAAGGAACTAGCTT -s Anc2.Anc2refChr1 92303 16 - 142988 AACAAGGAACTAGCTT -s mr.mrrefChr3 102118 16 - 181027 CATAAGGAACTAGCTC -s mr.mrrefChr5 176575 16 + 294540 TATAAGGAACTAGCTC -s simCow_chr6.simCow.chr6 94829 16 - 602619 CACAAGGAACTAGCTT -s simDog_chr6.simDog.chr6 96831 16 - 593897 AACAAGGACATAGCTT -s simHuman_chr6.simHuman.chr6 97408 16 - 601863 AACAAAGAACTAGCTT -s simMouse_chr6.simMouse.chr6 109181 16 - 636262 CATAAGGAAAGAGCTC -s simRat_chr6.simRat.chr6 109084 16 - 647215 CATAAGGAACTGGCTC -s simRat_chr6.simRat.chr6 319971 16 + 647215 TACAAAGAACTAGCTC - -a -s simMouse_chr6.simMouse.chr6 328538 21 + 636262 ATGAAAGGCAGACACTTTATC -s Anc0.Anc0refChr3 85291 20 - 222631 G-GTAAGACAGACTCTTTATC -s Anc1.Anc1refChr6 25178 20 - 197743 G-GTAAGACAGACTCTTTATC -s Anc2.Anc2refChr1 92320 20 - 142988 G-ATAAGACAGACTCTTGATC -s mr.mrrefChr3 102135 20 - 181027 G-GAAAGGCAGACACTTTGTC -s mr.mrrefChr5 176591 20 + 294540 A-GAAAGGCAGACACTTTATC -s simCow_chr6.simCow.chr6 94846 19 - 602619 G-A-AAGACAGAGCCTGGATA -s simDog_chr6.simDog.chr6 96848 20 - 593897 G-ATAAGGCTGACTCTTGATC -s simHuman_chr6.simHuman.chr6 97425 20 - 601863 G-GTAAGACAGACTCCAAATT -s simMouse_chr6.simMouse.chr6 109198 20 - 636262 G-GAAAGGCAGACACTTTGTC -s simRat_chr6.simRat.chr6 109101 20 - 647215 G-GAAAGGCAGAAACTTTGTC -s simRat_chr6.simRat.chr6 319987 20 + 647215 A-GGTAGGCGGACACTTTATC - -a -s simMouse_chr6.simMouse.chr6 328559 4 + 636262 TCCA -s Anc0.Anc0refChr3 85311 4 - 222631 TCTA -s Anc1.Anc1refChr6 25198 4 - 197743 TCTA -s Anc2.Anc2refChr1 92340 4 - 142988 TCTA -s mr.mrrefChr3 102155 4 - 181027 ACCA -s mr.mrrefChr5 176611 4 + 294540 TCCA -s simCow_chr6.simCow.chr6 94865 4 - 602619 TCTA -s simDog_chr6.simDog.chr6 96868 4 - 593897 TGTA -s simHuman_chr6.simHuman.chr6 97445 4 - 601863 TCTA -s simMouse_chr6.simMouse.chr6 109218 4 - 636262 ACCA -s simRat_chr6.simRat.chr6 320007 4 + 647215 TCCA - -a -s simMouse_chr6.simMouse.chr6 328563 12 + 636262 GGAAAGAAGTAG -s Anc0.Anc0refChr3 85315 4 - 222631 GGGA-------- -s Anc1.Anc1refChr6 25202 12 - 197743 GGGAAGAGGTAG -s Anc2.Anc2refChr1 92344 4 - 142988 GGGA-------- -s mr.mrrefChr3 102159 12 - 181027 GGAAAGAGGTAG -s mr.mrrefChr5 176615 12 + 294540 GGAAAGAAGTAG -s simCow_chr6.simCow.chr6 94869 4 - 602619 GGGA-------- -s simDog_chr6.simDog.chr6 96872 4 - 593897 GGGA-------- -s simHuman_chr6.simHuman.chr6 97449 12 - 601863 GGGAAAGGGTAG -s simMouse_chr6.simMouse.chr6 109222 12 - 636262 GGAAAGAGGTAG -s simRat_chr6.simRat.chr6 109121 12 - 647215 TGAAAGAGCGGG -s simRat_chr6.simRat.chr6 320011 12 + 647215 GGAAAGAGGTAG - -a -s simMouse_chr6.simMouse.chr6 328575 53 + 636262 CGGCTCATAGTGGATGGGATAGGTTTGAGTCACTGGGTTGGTTCAGTGTCTCC -s Anc0.Anc0refChr7 12186 35 - 16696 -----------------GGTAGTTTCTAGTCACTGGACCAGCTCAGAGGCTC- -s Anc1.Anc1refChr4 12775 35 + 17549 -----------------GGTAGTTTCTAGTCACTGGACCAGCTCAGAGGCTC- -s Anc2.Anc2refChr7 7827 35 + 32194 -----------------GGCAGTTTCTAGTCACCTGACCAGCTCAGAGGCTC- -s mr.mrrefChr5 176627 52 + 294540 CGGCTCATAGTGGATGGGATAGGTTCGAGTCACTGGGCTAGTTCAGTGTCTC- -s simCow_chr6.simCow.chr6 303937 35 + 602619 -----------------GCCAGCTTCTAGACACCAAACCAACTCAGAGGCTC- -s simDog_chr6.simDog.chr6 290469 34 + 593897 -----------------GGCAGTTTCTAGTCACCTGACCAGCACAGAGGCT-- -s simHuman_chr6.simHuman.chr6 314799 35 + 601863 -----------------TGTAGTTTCTAGCCACTGGACCAGCTCAGAGGCTC- -s simRat_chr6.simRat.chr6 320023 52 + 647215 CAGCTCATAGTGAATGGGATAGGTTCGAGTCACTGGGCTAGATCAGTGTCTC- - -a -s simMouse_chr6.simMouse.chr6 328628 33 + 636262 ACCCAGATGTTAGATTGTCCTGCTTTAGAATTG -s Anc0.Anc0refChr7 12225 33 - 16696 GTCTAGGTGTTGTGTTGTGCACATTCTAAATTG -s Anc1.Anc1refChr4 12814 33 + 17549 GTCTAGGTGTTGTGTTGTGCACATTCTAAATTG -s Anc2.Anc2refChr7 7866 33 + 32194 GTCTAGGTGGTGTGTTGTGCACATTCTAAATTG -s mr.mrrefChr5 176679 33 + 294540 ACCCAGATGTTATATTGTCCTGCTTTAAATTTG -s simCow_chr6.simCow.chr6 303976 28 + 602619 T-----GTGGCATGGTGTGCACATTCAAAATCA -s simDog_chr6.simDog.chr6 290504 33 + 593897 GTCTAGGTGGTGTGTTGCGCGTATTCTAAATTG -s simHuman_chr6.simHuman.chr6 314838 33 + 601863 CTCTAAGTGTTTTGATGTTCACATTCCAAGTTG -s simRat_chr6.simRat.chr6 320075 27 + 647215 ACCCAGATGTTATCTTGT------TTAAATTTG - -a -s simMouse_chr6.simMouse.chr6 328661 80 + 636262 AAGGTGTTTGAAGTCCAGGGGGGCAATGGTATATGACGCAGATAGGTTGGCAAACATTGTAACGTGGGGCTAAGAACCGT -s Anc0.Anc0refChr7 12261 76 - 16696 AAAGTGTTCTAA-TCCAAGGGAGGATTGGTACGCAAGACAGATAGGTCAGCAAA---TATAGCATGGGGTTGAAACCCAG -s Anc1.Anc1refChr4 12850 76 + 17549 AAAGTGTTCTAA-TCCAAGGGAGGATTGGTACGCAAGACAGATAGGTCAGCAAA---TATAGCATGGGGTTGAAACCCAG -s Anc2.Anc2refChr7 7902 76 + 32194 AAAGTGTTCTAA-TCCAAGGGAGGATTGGCACGCAAGACAGAAAGGTCAGCAAC---TATAGCATGGGGTTGAAACCCAG -s mr.mrrefChr5 176712 80 + 294540 AAGGTGTTTGAAGTCCAGGGGGGGAATGGTATATGACACAGATAGGTTGGCAAACATTGTAGCATGGGGCTAAGAACCAG -s simCow_chr6.simCow.chr6 304007 76 + 602619 AAAGTGCTGTAA-TCCAAGGGAAAATTGGAATGCAAGATGGAAAGATAAGCAAG---TACAGCATGGGGTTGAAACCCAG -s simDog_chr6.simDog.chr6 290540 73 + 593897 AAAGTCTTCTAA-TCCAAGGGTGGATTGGCACACAAGACACA---GTCAGCAAC---TATAGCATGGGGTTGGAACCCAG -s simHuman_chr6.simHuman.chr6 314874 75 + 601863 AAAGTGTTCTAA--TCAAAGGAGGATTGGTCCGCAAGAGAGATAGGTCAGCAAA---TATAGCATGAGCTCCAAACCCAG -s simRat_chr6.simRat.chr6 320102 80 + 647215 AAGGTGTTTGAAGTTCAGGGGGGGAATGGTAGATGACACAGATAGGTTGGCAAATCTTGTAGCATGGGGCTAAGAACCAG - -a -s simMouse_chr6.simMouse.chr6 328741 49 + 636262 TCAGGTCAAATGGATAGGTCAGTATGTGTAGCATAGGATCAAAAACTAG -s Anc0.Anc0refChr7 12337 14 - 16696 GCCAATC-AATGGAC---------------------------------- -s Anc1.Anc1refChr4 12926 14 + 17549 GCCAATC-AATGGAC---------------------------------- -s Anc2.Anc2refChr7 7978 14 + 32194 GCCAATC-AATGGAC---------------------------------- -s mr.mrrefChr5 176792 49 + 294540 TCAGGTCAAATGGATAGGTCAGTATGTGTAGCATAGGATCAAAAACTAG -s simCow_chr6.simCow.chr6 304083 14 + 602619 CTCAATC-AATGGAC---------------------------------- -s simDog_chr6.simDog.chr6 290615 2 + 593897 GC----------------------------------------------- -s simHuman_chr6.simHuman.chr6 314949 14 + 601863 GCCAATC-AATGGAC---------------------------------- -s simRat_chr6.simRat.chr6 320182 49 + 647215 CCAGATCAAATGGATAGGTCAGTATGTGTAACATGAGGTCACAAACCAG - -a -s simMouse_chr6.simMouse.chr6 328790 14 + 636262 CTTTATAGCCTATA -s Anc0.Anc0refChr7 12351 12 - 16696 CTTGA--GCTTATA -s Anc1.Anc1refChr4 12940 12 + 17549 CTTGA--GCTTATA -s Anc2.Anc2refChr7 7992 12 + 32194 CAGGA--GTTTATA -s mr.mrrefChr5 176841 14 + 294540 CTTTATGGCCTATA -s simCow_chr6.simCow.chr6 304098 12 + 602619 CAGGA--GTTTGTA -s simDog_chr6.simDog.chr6 290617 3 + 593897 -----------ATA -s simHuman_chr6.simHuman.chr6 314963 12 + 601863 CTTGA--GCTTATA -s simRat_chr6.simRat.chr6 320231 14 + 647215 CTCTATGGTCTATA - -a -s simMouse_chr6.simMouse.chr6 328804 38 + 636262 AGAGGAGCCCAACATCTTTTAAAGCCACCATTCTGTCA -s Anc0.Anc0refChr7 12364 38 - 16696 AGAAGCGCTCAACATCTTTTAAACCTACCATACTGTTC -s Anc1.Anc1refChr4 12953 38 + 17549 AGAAGCGCTCAACATCTTTTAAACCTACCATACTGTTC -s Anc2.Anc2refChr7 8005 38 + 32194 AGAAGCGCTCAACATCTTTTAAACCTACCATACTGTTC -s mr.mrrefChr5 176855 38 + 294540 AGAGGAGCTCAACATCTTTTAAAGCTACCATTCTGTCC -s simCow_chr6.simCow.chr6 304111 38 + 602619 AGAAGCGCTGAGCATCTTTTAAACCCGCCACACTGTCC -s simDog_chr6.simDog.chr6 290621 38 + 593897 AGAAGCCCTCAACATCTTTTGAATCTACCATACTGCTC -s simHuman_chr6.simHuman.chr6 314976 38 + 601863 ATAAGTGTCCAACATTCTTTAAACCTACCATGCTGTTC -s simRat_chr6.simRat.chr6 320245 38 + 647215 AGATGAGTTCAACATCTTTTAAAACTACCATTCTGTCC - -a -s simMouse_chr6.simMouse.chr6 328842 8 + 636262 TTATTTAC -s Anc0.Anc0refChr7 12402 8 - 16696 TAATTTAC -s Anc1.Anc1refChr4 12991 8 + 17549 TAATTTAC -s Anc2.Anc2refChr7 8043 8 + 32194 TAATTTAC -s mr.mrrefChr5 176893 8 + 294540 TAATTTAC -s simCow_chr6.simCow.chr6 304149 7 + 602619 -AACATGC -s simDog_chr6.simDog.chr6 290659 8 + 593897 TATTTTAC -s simHuman_chr6.simHuman.chr6 315019 8 + 601863 TAATTTAC -s simRat_chr6.simRat.chr6 320283 8 + 647215 TAATTTAC - -a -s simMouse_chr6.simMouse.chr6 328850 8 + 636262 ATAAGGTA -s Anc0.Anc0refChr7 12410 8 - 16696 ACAACGAA -s Anc1.Anc1refChr4 12999 8 + 17549 ACAACGAA -s Anc2.Anc2refChr7 8051 8 + 32194 ACAACGAA -s mr.mrrefChr5 176901 8 + 294540 ATAAGGTA -s simCow_chr6.simCow.chr6 304156 8 + 602619 ACAAGGAA -s simDog_chr6.simDog.chr6 290667 8 + 593897 ACAACGAT -s simHuman_chr6.simHuman.chr6 315027 8 + 601863 ACAAAGAA -s simRat_chr6.simRat.chr6 320298 8 + 647215 ATAAGGTA - -a -s simMouse_chr6.simMouse.chr6 328858 11 + 636262 GAGGAGGGACA -s Anc0.Anc0refChr7 12418 11 - 16696 GAGGAGTGACC -s Anc1.Anc1refChr4 13007 11 + 17549 GAGGAGTGACC -s Anc2.Anc2refChr7 8059 11 + 32194 GAGGAGTGACC -s mr.mrrefChr5 176909 11 + 294540 GAGGAGTGACC -s simCow_chr6.simCow.chr6 304165 11 + 602619 GAGGAGTGACC -s simDog_chr6.simDog.chr6 290675 11 + 593897 GAGGAGTGACC -s simHuman_chr6.simHuman.chr6 315035 11 + 601863 GAGAACTACCT -s simRat_chr6.simRat.chr6 320306 11 + 647215 GAAGAGTGACC - -a -s simMouse_chr6.simMouse.chr6 328869 101 + 636262 AGGATTAGAACTCTAGAGACCCATATGTTCCAAGAGTTCGCTGAAGCCCATATGTGCACAGAGTTTGCTTTTGAACAATTATATGGGATCCTGGACAGTGA -s Anc0.Anc0refChr7 12429 79 - 16696 AGGAGGCAAGCTCTAAAGTCCCATACGTTCCTAAAGT----------------------AGAGACTGCATTTAAACAGTTGTCTGGGCTCACACACAGGTA -s Anc1.Anc1refChr4 13018 79 + 17549 AGGAGGCAAGCTCTAAAGTCCCATACGTTCCTAAAGT----------------------AGAGACTGCATTTAAACAGTTGTCTGGGCTCACACACAGGTA -s Anc2.Anc2refChr7 8070 79 + 32194 AGAAGGCAAGCTCTAAAGTCCCATACGTTCCTAAAGT----------------------AGAGACTGCATTTACACAGTTGTCTGGGCTCACACACAGGTA -s mr.mrrefChr5 176920 101 + 294540 AGGATTAGAACTCTAGAGACCCATATGTTCCAAGAGTTCGCTGAAGCCCATATGTGCACAGAGTTTGCTTTTGAACAATTATACGGGCTCACAGACAGTGA -s simCow_chr6.simCow.chr6 304176 79 + 602619 ATGATCCAAGCTCTAAAGGTCCATATGTTCTTAAAGC----------------------AGAGACTGCGTGTACACGGTTGTCTGGGATCCAACACAGGTA -s simDog_chr6.simDog.chr6 290686 79 + 593897 AGAAGGCAAGCTCTAAAGTCCCATACGTTCCTAAAGT----------------------AGGGACTGCATTTACACAGTTGTCCGGGCTCACAAACAGGCA -s simHuman_chr6.simHuman.chr6 315048 45 + 601863 AGG--------------------------------------------------------AGAGACTGCATCTAAACATTTGTCTGGGCTCAGACTCAGGTA -s simRat_chr6.simRat.chr6 320317 101 + 647215 AGGATCAGAACTCTAGAAACCCATATGTTCTCAGAGTTTGCTGAAGCCCACCTGTACCCAGAGCTTGCTTTTGAACAATTATACGGGCTCACAGACAGCGA - -a -s simMouse_chr6.simMouse.chr6 328970 20 + 636262 TTTAACTATTATGCATCCTG -s Anc0.Anc0refChr7 12508 16 - 16696 TCTAAATGTTAGGTA----G -s Anc1.Anc1refChr4 13097 16 + 17549 TCTAAATGTTAGGTA----G -s Anc2.Anc2refChr7 8149 16 + 32194 TCTAAATGTTAGGTG----A -s mr.mrrefChr5 177021 20 + 294540 TTTAAATATTATGCATCCTG -s simCow_chr6.simCow.chr6 304255 16 + 602619 ACTATATGTTCAGTG----A -s simDog_chr6.simDog.chr6 290765 16 + 593897 TTCAAATGTTAGGTG----A -s simHuman_chr6.simHuman.chr6 315093 16 + 601863 TCTAAATGTTACGTA----G -s simRat_chr6.simRat.chr6 320424 19 + 647215 TTTAAAT-TTATGGATCGTG - -a -s simMouse_chr6.simMouse.chr6 328990 45 + 636262 ACCTTGACCTTTAGCTCCCTGCTCTGAAACAACAATCCATTAGTC -s Anc0.Anc0refChr7 12524 42 - 16696 AGCATGACC-CTACCTCTATGCTGTGGAACACTCCTACATT--TC -s Anc1.Anc1refChr4 13113 44 + 17549 AGCATGACC-CTACCTCTATGCTGTGGAACACTCCTACATTAGTC -s Anc2.Anc2refChr7 8165 42 + 32194 AGCATGACC-CTACCTCTATGTTGTGGAGCACTCCTACATT--CT -s mr.mrrefChr5 177041 45 + 294540 ACCTTGACCTTTAGCTCCCTGCTCTGAAACAACAATACATTAGTC -s simCow_chr6.simCow.chr6 304273 28 + 602619 AGCATGACC-CTACCTCTGGGTTA----------CTACA------ -s simDog_chr6.simDog.chr6 290781 42 + 593897 AGCATGACC-CTTGCTCCATGTTGTGGAGCACTCCTACATT--CT -s simHuman_chr6.simHuman.chr6 315109 44 + 601863 ATCACGACC-CCACCTGTATGCTGTGGAACACTCTTACATTAGTC -s simRat_chr6.simRat.chr6 320443 45 + 647215 ACCTTGACCTTTACCTCCCTGCTCTGAAACAACGACACATTAGTT - -a -s simMouse_chr6.simMouse.chr6 329035 1 + 636262 T -s Anc0.Anc0refChr7 12574 1 - 16696 T -s Anc1.Anc1refChr4 13165 1 + 17549 T -s Anc2.Anc2refChr7 8215 1 + 32194 T -s mr.mrrefChr5 177086 1 + 294540 T -s simCow_chr6.simCow.chr6 304306 1 + 602619 C -s simDog_chr6.simDog.chr6 290831 1 + 593897 T -s simHuman_chr6.simHuman.chr6 315161 1 + 601863 T -s simRat_chr6.simRat.chr6 320488 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 329036 40 + 636262 GCTTACTACTCAGATAATGCTCAATTATTCATAGGAGCTA -s Anc0.Anc0refChr7 12575 40 - 16696 GGTTATTACACAGATGATGTTTAATTATTCATAGGAGCTA -s Anc1.Anc1refChr4 13166 40 + 17549 GGTTATTACACAGATGATGTTTAATTATTCATAGGAGCTA -s Anc2.Anc2refChr7 8216 40 + 32194 AGTTGTCACAGAGATGATGTTTAAGTATTCATAGGAACTA -s mr.mrrefChr5 177087 40 + 294540 GCTTACTACTCAGATAATGCTCAATTATTCATAGGAGCTA -s simCow_chr6.simCow.chr6 304307 40 + 602619 ATGTTTAACAAAGGTGATGTTTAAGTATTCACAGGTGCTA -s simDog_chr6.simDog.chr6 290832 40 + 593897 AGTTGCCACAGAGACAATGTTCACGTATTCATTGGAACTG -s simHuman_chr6.simHuman.chr6 315162 38 + 601863 GGTTATTAAACAGATGATGTTTAATTATTTGTAG--GCTA -s simRat_chr6.simRat.chr6 320490 40 + 647215 GATTACTCCTCAGATAATGCTGAATTATTCATGGTAGCTA - -a -s simMouse_chr6.simMouse.chr6 329076 20 + 636262 CTGCTCAGTTGAAATCATGA -s Anc0.Anc0refChr7 12618 14 - 16696 CAAGCTAATTGAA------A -s Anc1.Anc1refChr4 13209 14 + 17549 CAAGCTAATTGAA------A -s Anc2.Anc2refChr7 8259 14 + 32194 CAAGCTAATTGAA------A -s mr.mrrefChr5 177130 20 + 294540 CAACTCAGTTGAAATCATGA -s simCow_chr6.simCow.chr6 304350 14 + 602619 CAAGCTAGCTGAA------A -s simDog_chr6.simDog.chr6 290875 14 + 593897 CAAACTAATTGAA------A -s simHuman_chr6.simHuman.chr6 315203 14 + 601863 CAAGCTACTTGAA------A -s simRat_chr6.simRat.chr6 320534 20 + 647215 CAATTCAGTTGAAATCATGA - -a -s simMouse_chr6.simMouse.chr6 329096 16 + 636262 AAGAAAGAAAAGCATT -s Anc0.Anc0refChr7 12632 16 - 16696 AAGAAAGACAGGTATT -s Anc1.Anc1refChr4 13223 16 + 17549 AAGAAAGACAGGTATT -s Anc2.Anc2refChr7 8273 16 + 32194 AAAAAAGACAGGTATT -s mr.mrrefChr5 177150 16 + 294540 AAGAAAGAAAGGCATT -s simCow_chr6.simCow.chr6 304364 10 + 602619 ------GACAGATATT -s simDog_chr6.simDog.chr6 290895 16 + 593897 AAAAAAGACAGGTATT -s simHuman_chr6.simHuman.chr6 315217 16 + 601863 AAGAAAGCCAAGTTTT -s simRat_chr6.simRat.chr6 320554 16 + 647215 AAGAAAGAGAGGCATT - -a -s simMouse_chr6.simMouse.chr6 329112 1 + 636262 A -s Anc0.Anc0refChr7 12653 1 - 16696 A -s Anc1.Anc1refChr4 13244 1 + 17549 A -s Anc2.Anc2refChr7 8294 1 + 32194 G -s mr.mrrefChr5 177166 1 + 294540 A -s simCow_chr6.simCow.chr6 304384 1 + 602619 G -s simDog_chr6.simDog.chr6 290916 1 + 593897 G -s simHuman_chr6.simHuman.chr6 315238 1 + 601863 A -s simRat_chr6.simRat.chr6 320570 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 329113 48 + 636262 CTTTAAATCCAGCTGATGATTCCAACCACCTGCGCACAAGGGATGGGT -s Anc0.Anc0refChr7 12654 46 - 16696 TATAAGATTCAGCTG--TATTCCAACCACCTGCACATATAGGATGGAT -s Anc1.Anc1refChr4 13245 46 + 17549 TATAAGATTCAGCTG--TATTCCAACCACCTGCACATATAGGATGGAT -s Anc2.Anc2refChr7 8295 46 + 32194 TATAAGATTCAGATG--TATTCCAACCACCAGCACATATAGGATGGAC -s mr.mrrefChr5 177167 48 + 294540 CTTTAAATCCAGCTGATGATTCCAACCACCTGCACACAAGGGATGGGT -s simCow_chr6.simCow.chr6 304385 46 + 602619 TATATGATTAAGATG--TATTCCAAACACCAGCGCATATAGGATGGAC -s simDog_chr6.simDog.chr6 290917 46 + 593897 TACAAAAATCAGATA--TATTCCAACCACTAGCACATATAGGATGGAC -s simHuman_chr6.simHuman.chr6 315239 46 + 601863 TGTAAGGTTCAGCGG--TAGTCCAACCACCTGCTCATAGAGGATAGAT -s simRat_chr6.simRat.chr6 320581 48 + 647215 CTTCAAATCCAGCTGAGGATTCCAACCACCTGCACACAGGGGATGGGT - -a -s simMouse_chr6.simMouse.chr6 329161 31 + 636262 ACTATTGAAACTCTGGGACCCATGCACACCC -s Anc0.Anc0refChr7 12700 31 - 16696 ACTATTAAAATGCTGGGACCAGTACATACCC -s Anc1.Anc1refChr4 13291 31 + 17549 ACTATTAAAATGCTGGGACCAGTACATACCC -s Anc2.Anc2refChr7 8341 31 + 32194 ACTATTAAAATGATGGAACTAGTACATACCT -s mr.mrrefChr5 177215 31 + 294540 ACTATTGAAACTCTGGGACCCATACACACCC -s simCow_chr6.simCow.chr6 304431 31 + 602619 ACTATTAAAATGATATAATTTGTACAAATTT -s simDog_chr6.simDog.chr6 290963 31 + 593897 ACTATTAAAATAATGGGACTAGTACCTACCT -s simHuman_chr6.simHuman.chr6 315287 30 + 601863 ACTACTAAAATGCTG-GATCTGTAGATACCC -s simRat_chr6.simRat.chr6 320629 30 + 647215 ACTACTGAAA-TCTGCGACCCATACGCGCCC - -a -s simMouse_chr6.simMouse.chr6 329192 44 + 636262 TTTTCCTTGGCTGGGTAGGCTTATGCAGATTTACACACCCTTAG -s Anc0.Anc0refChr7 12731 36 - 16696 TTTTCCTTATTTAGTTATGCATATGAAG------AAACACTT-- -s Anc1.Anc1refChr4 13322 38 + 17549 TTTTCCTTATTTAGTTATGCATATGAAG----GCAAACACTT-- -s Anc2.Anc2refChr7 8372 36 + 32194 TTTTCCTTATTTAGTTATGCATATGAAG------AAACACTT-- -s mr.mrrefChr5 177246 44 + 294540 TTTTCCTTGGTTGGGTAGGCTTATGCAGATTTACACACCCTTAG -s simCow_chr6.simCow.chr6 304524 36 + 602619 ttatacaaatttatatatGTTTATGAAG------GAACAGTT-- -s simDog_chr6.simDog.chr6 290994 36 + 593897 TTTTCTTTGTTTAGTTATGCACATGAAG------ATGCACTT-- -s simHuman_chr6.simHuman.chr6 315317 38 + 601863 TTTTCCCCATTTAACTGTGAATATGAAG----GCAAACACTT-- -s simRat_chr6.simRat.chr6 320659 44 + 647215 TTTTCCTTGGTTGAAGAGGCTTATGCATATTCACAGACTCCTAG - -a -s simMouse_chr6.simMouse.chr6 329236 7 + 636262 CAGGGCT -s Anc0.Anc0refChr7 12767 6 - 16696 -AGGGTT -s Anc1.Anc1refChr4 13360 6 + 17549 -AGGGTT -s Anc2.Anc2refChr7 8408 6 + 32194 -ATGGTT -s mr.mrrefChr5 177290 7 + 294540 CAGGGTT -s simCow_chr6.simCow.chr6 304560 6 + 602619 -ATGGTT -s simDog_chr6.simDog.chr6 291030 6 + 593897 -ATGGTT -s simHuman_chr6.simHuman.chr6 315355 6 + 601863 -AGGGTT -s simRat_chr6.simRat.chr6 320709 7 + 647215 CAGGGTT - -a -s simMouse_chr6.simMouse.chr6 329243 31 + 636262 CACCTCTTAGCTAAGACTGCTCTTGATTGGC -s Anc0.Anc0refChr7 12775 31 - 16696 CACTTATTCACTTAGACTGCTCTCCAGTGGC -s Anc1.Anc1refChr4 13368 31 + 17549 CACTTATTCACTTAGACTGCTCTCCAGTGGC -s Anc2.Anc2refChr7 8416 31 + 32194 CACTTATTCACTTAGACTGCTCTCCAGTGGC -s mr.mrrefChr5 177299 31 + 294540 CACCTATTAGCTAAGACTGCTCTCGATTGGC -s simCow_chr6.simCow.chr6 304568 31 + 602619 GACCCATTCACTCAGACTGCTCTCCAGTGGG -s simDog_chr6.simDog.chr6 291038 31 + 593897 CACTTATTAACTTAGATTGCTCTCCAATAGC -s simHuman_chr6.simHuman.chr6 315363 30 + 601863 -AATTATTCACTTCGACTGCTCTCAAGCGGC -s simRat_chr6.simRat.chr6 320718 31 + 647215 CACCCATTGCCTAAGACTACTTTCGATTGGC - -a -s simMouse_chr6.simMouse.chr6 329274 12 + 636262 ATCCAAATATTT -s Anc0.Anc0refChr7 12806 12 - 16696 ATCCTGATATGT -s Anc1.Anc1refChr4 13399 12 + 17549 ATCCTGATATGT -s Anc2.Anc2refChr7 8447 12 + 32194 ATCCTGATATGT -s mr.mrrefChr5 177330 12 + 294540 ATCCAAATATGT -s simCow_chr6.simCow.chr6 304599 12 + 602619 ATCTTGGTATGT -s simDog_chr6.simDog.chr6 291070 12 + 593897 ATCCTGATATGT -s simHuman_chr6.simHuman.chr6 315393 12 + 601863 ATCCTGATATGT -s simRat_chr6.simRat.chr6 320749 12 + 647215 ATCCAAATATGT - -a -s simMouse_chr6.simMouse.chr6 329286 31 + 636262 CTCACACCCTTCCATACTCTTTCACTCTAAT -s Anc0.Anc0refChr7 12826 31 - 16696 CTAACACCCTTCCATACCCTCTCACTATGAT -s Anc1.Anc1refChr4 13419 31 + 17549 CTAACACCCTTCCATACCCTCTCACTATGAT -s Anc2.Anc2refChr7 8467 31 + 32194 CCAACACTCTTCCACAACCTCTCACTATGAT -s mr.mrrefChr5 177350 31 + 294540 CTAACACCCTTCCATACCCTTTCACTCTAAT -s simCow_chr6.simCow.chr6 304619 31 + 602619 CCAACACTCTTCCACATCCTCTCATCATGAT -s simDog_chr6.simDog.chr6 291090 30 + 593897 CCAACACT-TGCCACAACCCCTCACTATGAT -s simHuman_chr6.simHuman.chr6 315413 31 + 601863 GTGACACCCTTCCTTACTCTCTCACAATGAT -s simRat_chr6.simRat.chr6 320769 31 + 647215 CTAGCACCCTTCCATACCCTTTCACTCTCAT - -a -s simMouse_chr6.simMouse.chr6 329317 15 + 636262 TTGTTTGTGTTATAA -s Anc0.Anc0refChr7 12857 15 - 16696 TCGTTTGCATTATAA -s Anc1.Anc1refChr4 13450 15 + 17549 TCGTTTGCATTATAA -s Anc2.Anc2refChr7 8498 15 + 32194 TCGTTTGCATTATAA -s mr.mrrefChr5 177381 15 + 294540 TTGTTTGTGTTATAA -s simCow_chr6.simCow.chr6 304650 15 + 602619 TCGTTTATATAATAA -s simDog_chr6.simDog.chr6 291121 15 + 593897 TTGTTTGCATTATAA -s simHuman_chr6.simHuman.chr6 315444 15 + 601863 TCCTTTTCAATACAA -s simRat_chr6.simRat.chr6 320800 15 + 647215 TTGTTCTTGTTATAA - -a -s simMouse_chr6.simMouse.chr6 329332 27 + 636262 GTGTCTACCTCCTTATCTTGCTTACAA -s Anc0.Anc0refChr7 12874 26 - 16696 -TGTATACCTCCCTAGCTTACTAACAA -s Anc1.Anc1refChr4 13467 27 + 17549 GTGTATACCTCCCTAGCTTACTAACAA -s Anc2.Anc2refChr7 8515 26 + 32194 -TATACACCTCCCTAGCTTACTAACAA -s mr.mrrefChr5 177396 27 + 294540 GTGTCTACCTCCTTATCTTGCTTACAA -s simCow_chr6.simCow.chr6 304667 26 + 602619 -GATACACCTCCCTAGCCTGCTAACGA -s simDog_chr6.simDog.chr6 291138 26 + 593897 -TATCCACCCCCCTAACTTATTAACAA -s simHuman_chr6.simHuman.chr6 315461 27 + 601863 GTGTATACCTTCCTAGCTTACTAATCA -s simRat_chr6.simRat.chr6 320815 25 + 647215 GGGTCTACCTCCTTATATTGCT--CAA - -a -s simMouse_chr6.simMouse.chr6 329359 205 + 636262 TAGTTGTCATCACCAATGGCCCGTTTCCCTCGGTATGCAATAGCTTTCCACTGCTAAGTGTTGCTTCCACGTATGAAGGACCGACACTAATGGTTATCTGATCCCTGCAAGGATCATAGGGTGGACATTGCGCTGTGTATTGGGTTTTGACAATCTTTTTTCTGATCATGCCTCCATATCCAAACTTTATGACTTGGGGAGACAT -s Anc0.Anc0refChr7 12911 102 - 16696 AATTTACCATCACTAATTGCTCAATTCCCTCATAAGGC---AG----------------------------------------------------------------------------------------------------GTTTAGACAGGTTCCCTCTTGGAGCTGCCTGCATGTTCATACCTTATGGTTTGGAGAGACAC -s Anc1.Anc1refChr4 13505 102 + 17549 AATTTACCATCACTAATTGCTCAATTCCCTCATAAGGC---AG----------------------------------------------------------------------------------------------------GTTTAGACAGGTTCCCTCTTGGAGCTGCCTGCATGTTCATACCTTATGGTTTGGAGAGACAC -s Anc2.Anc2refChr7 8552 102 + 32194 AATTCACCATCACTCATTGCTCAATTCCCTCATAAGGC---AG----------------------------------------------------------------------------------------------------GTTTAGACAGGTTCCCTCTTGGAGCTGCCTGCATGTTCATATCTTATGGTTTGGAGACACAC -s mr.mrrefChr5 177423 105 + 294540 TAGTTGTCATCACCAATGGCCCAATTCCCTCGTTATGCAATAG----------------------------------------------------------------------------------------------------GTTTTGACAAGCTTTTTCCTGGTCATGCCTGCATATCCAAACCTTATGACTTGGGGAGACAT -s simCow_chr6.simCow.chr6 304704 97 + 602619 TCTCCACCAT-CCTCACTGCTCAATTTCCTCAAAATGC----------------------------------------------------------------------------------------------------------TCTTGACAGGTTCCCTTGTAAAGTCACTTGCATGTTCATAACTTAGTGTT-GGAGAAACAC -s simDog_chr6.simDog.chr6 291175 101 + 593897 AATTCAC-ATCACGCATCGCTCAACTCCCTCATAAGGC---AG----------------------------------------------------------------------------------------------------GTTTAGACAGGTTCCCTCTTGGAGCTGTCTGCATGTACATATCCTATGATCTGCAGACACAC -s simHuman_chr6.simHuman.chr6 315499 102 + 601863 AATTTCCCATCACTAATTGCTCAATTCCCTCAGAGGGC---AG----------------------------------------------------------------------------------------------------ATTTCGATAGGTCCCCTCTTGGAAGTGCCTGCATGTTCATACTTTACGGTTCAGAAAGAAAC -s simRat_chr6.simRat.chr6 320840 105 + 647215 TAGTTGTCATCACCAGTGGCCCAATTCCTTGGTTATTCAATAG----------------------------------------------------------------------------------------------------GTTTTGACAAGCTTTTTCCTGGTTGTTCCTGCATATCCAAAACTTATGACTTGGGGAGACAT - -a -s simMouse_chr6.simMouse.chr6 329564 1 + 636262 T -s Anc0.Anc0refChr7 13022 1 - 16696 A -s Anc1.Anc1refChr4 13616 1 + 17549 A -s Anc2.Anc2refChr7 8663 1 + 32194 A -s mr.mrrefChr5 177537 1 + 294540 T -s simCow_chr6.simCow.chr6 304810 1 + 602619 A -s simDog_chr6.simDog.chr6 291285 1 + 593897 A -s simHuman_chr6.simHuman.chr6 315610 1 + 601863 A -s simRat_chr6.simRat.chr6 320954 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 329565 1 + 636262 G -s Anc0.Anc0refChr7 13023 1 - 16696 G -s Anc1.Anc1refChr4 13617 1 + 17549 G -s Anc2.Anc2refChr7 8664 1 + 32194 G -s mr.mrrefChr5 177538 1 + 294540 G -s simCow_chr6.simCow.chr6 304826 1 + 602619 G -s simDog_chr6.simDog.chr6 291286 1 + 593897 G -s simHuman_chr6.simHuman.chr6 315611 1 + 601863 G -s simRat_chr6.simRat.chr6 320955 1 + 647215 G - -a -s simMouse_chr6.simMouse.chr6 329566 58 + 636262 TCAGACATGTAATGTTATGCCAATTTCAGAGTTTCAATAAGACACCAGATGTCTCTGA -s Anc0.Anc0refChr7 13043 57 - 16696 TCAGACATTTAATGTTATGCCGATTTCAAACTTTCAATAACACTCCAAATTTCTTTT- -s Anc1.Anc1refChr4 13637 57 + 17549 TCAGACATTTAATGTTATGCCGATTTCAAACTTTCAATAACACTCCAAATTTCTTTT- -s Anc2.Anc2refChr7 8690 57 + 32194 TCAGACATTTAATCTTATGCGGATTTCAAACTTTCAATAACACTCCAAATTTCTTTT- -s mr.mrrefChr5 177539 58 + 294540 TCAGACATGTATTGTTATGCCAATTTCAGAGTTTCAATAACACACCAGATGTCTTTGA -s simCow_chr6.simCow.chr6 304852 47 + 602619 TCAGACATGTAATCTTATGCTGATTTTAACCTTTCAATAACACTCCA----------- -s simDog_chr6.simDog.chr6 291312 54 + 593897 TCAGACAGTTA---TCATGTGGATTTCGAACTTTCATTTACACTGCTAATTTCTTTT- -s simHuman_chr6.simHuman.chr6 315631 57 + 601863 TTAGATATCTAATGTTATGCCCATTTCAATCTTTCAATAACACTCCAAGATTCTTTT- -s simRat_chr6.simRat.chr6 320956 58 + 647215 TCAGACATGTATTGTTATGCCAACTTCAGAGTTTCAATAACACACCAGATGTCTTTGA - -a -s simMouse_chr6.simMouse.chr6 329624 51 + 636262 CACAAGTAAACTGCAAAAAAGAAATCAGAATAAACATCATCAAAAAAAAAT -s Anc0.Anc0refChr7 13100 23 - 16696 CACCAGTAAACTGCAAAAAA----------------------------GAT -s Anc1.Anc1refChr4 13694 23 + 17549 CACCAGTAAACTGCAAAAAA----------------------------GAT -s Anc2.Anc2refChr7 8747 23 + 32194 CTCCAGTAAACTGCAAAAAT----------------------------GAA -s mr.mrrefChr5 177597 23 + 294540 CACAAGTAAACTGCAAAAGA----------------------------AAT -s simCow_chr6.simCow.chr6 304899 18 + 602619 -----ATAAACTGCAAAGAT----------------------------GAA -s simDog_chr6.simDog.chr6 291367 23 + 593897 CTCCAGTAAGATGGAAAAAT----------------------------GAA -s simHuman_chr6.simHuman.chr6 315688 23 + 601863 CACCAGTACACTGCAAAAAA----------------------------GAT -s simRat_chr6.simRat.chr6 321014 23 + 647215 CACAAGTAAACTGCAAAAGA----------------------------AAT - -a -s simMouse_chr6.simMouse.chr6 329675 32 + 636262 CAGAATAAACATCTTCTTCCACATCTATCTGT -s Anc0.Anc0refChr7 13125 32 - 16696 AACACTAATCATCATCTTCCGCATCTGCCTAT -s Anc1.Anc1refChr4 13719 32 + 17549 AACACTAATCATCATCTTCCGCATCTGCCTAT -s Anc2.Anc2refChr7 8772 32 + 32194 AACACTAATCATCATCTTCCGCATCTGCCTAT -s mr.mrrefChr5 177620 32 + 294540 CAGAATAAACATCATCTTCCACATCTATCTAT -s simCow_chr6.simCow.chr6 304919 32 + 602619 GACACCTATCATCATCTTCTGCTACTGACTAT -s simDog_chr6.simDog.chr6 291392 32 + 593897 AACATTAATCATCATCTCCCGCATCTACCTAT -s simHuman_chr6.simHuman.chr6 315713 32 + 601863 AACACTAATACTGACCTTCCGCATCTGCTAAT -s simRat_chr6.simRat.chr6 321037 32 + 647215 CAGAATAAACATCATCTTCCACACCTATCTAT - -a -s simMouse_chr6.simMouse.chr6 329707 24 + 636262 GAGAGTGATCTTGCAGGAAACACA -s Anc0.Anc0refChr7 13157 24 - 16696 GGTGGTGACATTACAGGGTTTATG -s Anc1.Anc1refChr4 13751 24 + 17549 GGTGGTGACATTACAGGGTTTATG -s Anc2.Anc2refChr7 8804 24 + 32194 AGTGGTGACATTACAGAGTTTATG -s mr.mrrefChr5 177652 24 + 294540 GAGAGTGATCTTGCAGGAATCACA -s simCow_chr6.simCow.chr6 304952 24 + 602619 AGTGGTGACATTACAGAGTCTATG -s simDog_chr6.simDog.chr6 291424 24 + 593897 AATAGTGCCATTATGGAGTTTACA -s simHuman_chr6.simHuman.chr6 315745 24 + 601863 GGAGGTGACATTACAGGGTTTATG -s simRat_chr6.simRat.chr6 321069 24 + 647215 GAGGCTGATCTTGCAGGAATCACA - -a -s simMouse_chr6.simMouse.chr6 329731 1 + 636262 T -s Anc0.Anc0refChr7 13182 1 - 16696 T -s Anc1.Anc1refChr4 13776 1 + 17549 T -s Anc2.Anc2refChr7 8829 1 + 32194 T -s mr.mrrefChr5 177677 1 + 294540 T -s simCow_chr6.simCow.chr6 304977 1 + 602619 A -s simDog_chr6.simDog.chr6 291449 1 + 593897 T -s simHuman_chr6.simHuman.chr6 315770 1 + 601863 T -s simRat_chr6.simRat.chr6 321094 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 329732 54 + 636262 CAGCTGGGCTTTCTCAGGCAGGAATCCAGCCTACTCTCTTTCTCGGGCAGGAAT -s Anc0.Anc0refChr7 13183 25 - 16696 CAGTTGG-----------------------------GCTTTCTTAGGCATGGAT -s Anc1.Anc1refChr4 13777 25 + 17549 CAGTTGG-----------------------------GCTTTCTTAGGCATGGAT -s Anc2.Anc2refChr7 8830 25 + 32194 CAGTTGG-----------------------------GCTTTCTTAGGCATGGAT -s mr.mrrefChr5 177678 25 + 294540 CAGCTGG-----------------------------TCTTTCTCAGGCAAGAAT -s simCow_chr6.simCow.chr6 304983 25 + 602619 CAGTTGG-----------------------------GCTTCCTTAGGCATGGAT -s simDog_chr6.simDog.chr6 291450 25 + 593897 TAGTTAG-----------------------------CCTTTCTTAAGCAAGGAT -s simHuman_chr6.simHuman.chr6 315771 25 + 601863 CAGTTGG-----------------------------GCTTTCTTAGCCATGGAT -s simRat_chr6.simRat.chr6 321095 25 + 647215 CAGCTGG-----------------------------TCTTTCTCAGACAAGAAT - -a -s simMouse_chr6.simMouse.chr6 329786 2 + 636262 CC -s Anc0.Anc0refChr7 13208 2 - 16696 CC -s Anc1.Anc1refChr4 13802 2 + 17549 CC -s Anc2.Anc2refChr7 8855 2 + 32194 TT -s mr.mrrefChr5 177703 2 + 294540 CC -s simCow_chr6.simCow.chr6 305013 2 + 602619 TT -s simDog_chr6.simDog.chr6 291475 2 + 593897 TT -s simHuman_chr6.simHuman.chr6 315796 2 + 601863 CC -s simRat_chr6.simRat.chr6 321120 2 + 647215 CC - -a -s simMouse_chr6.simMouse.chr6 329788 12 + 636262 AGCCTACTCTAG -s Anc0.Anc0refChr7 13210 5 - 16696 AGCCT------- -s Anc1.Anc1refChr4 13804 12 + 17549 AGCCTGATCCAG -s Anc2.Anc2refChr7 8857 5 + 32194 GCCCT------- -s mr.mrrefChr5 177705 12 + 294540 AGCCTACTCTAG -s simCow_chr6.simCow.chr6 305015 5 + 602619 GCCCT------- -s simDog_chr6.simDog.chr6 291477 5 + 593897 GCCCT------- -s simHuman_chr6.simHuman.chr6 315815 12 + 601863 AGCCAGATCCAG -s simRat_chr6.simRat.chr6 321122 12 + 647215 AGCCTGCTCTAG - -a -s simMouse_chr6.simMouse.chr6 329800 31 + 636262 TGCACTTAACCAGATCTGTGCCAAGGTTCAG -s Anc0.Anc0refChr7 13218 31 - 16696 TGCACTTAATCTGACTTCCCCCAAGGATTAG -s Anc1.Anc1refChr4 13819 31 + 17549 TGCACTTAATCTGACTTCCCCCAAGGATTAG -s Anc2.Anc2refChr7 8865 31 + 32194 TTCAGTTAATCTGCCTTCCCCCAAGGATTAG -s mr.mrrefChr5 177717 31 + 294540 TGCACTTAACCAGATCTGTGCCAAGGTTCAG -s simCow_chr6.simCow.chr6 305023 31 + 602619 TGCACTCCATCTGCCTTGCTCCGAGGTTTAG -s simDog_chr6.simDog.chr6 291485 28 + 593897 TTCAGTTAATC---CTCCCCCAAAGGATTAG -s simHuman_chr6.simHuman.chr6 315836 31 + 601863 TGCACTTAATCTGACTTTCACCAAAGCTTGG -s simRat_chr6.simRat.chr6 321134 31 + 647215 TGCACTTAACCAGATCTGTGCCAAGGTACAG - -a -s simMouse_chr6.simMouse.chr6 329831 10 + 636262 TTGTCCTTAA -s Anc0.Anc0refChr7 13249 10 - 16696 TTGTCCCTAA -s Anc1.Anc1refChr4 13850 10 + 17549 TTGTCCCTAA -s Anc2.Anc2refChr7 8896 10 + 32194 TTATCCCTAA -s mr.mrrefChr5 177748 10 + 294540 TTGTCCTTAA -s simCow_chr6.simCow.chr6 305054 10 + 602619 GCATCCCTAA -s simDog_chr6.simDog.chr6 291513 10 + 593897 TTATCCTTAA -s simHuman_chr6.simHuman.chr6 315867 10 + 601863 CTGTCACAAA -s simRat_chr6.simRat.chr6 321171 10 + 647215 TTGTCCTTAA - -a -s simMouse_chr6.simMouse.chr6 329841 18 + 636262 GAGTTCAAGTTTGAATTG -s Anc0.Anc0refChr7 13259 16 - 16696 CAGG--GAGTTTGAATTA -s Anc1.Anc1refChr4 13860 16 + 17549 CAGG--GAGTTTGAATTA -s Anc2.Anc2refChr7 8906 16 + 32194 CAGG--GAGTTTGAATTA -s mr.mrrefChr5 177758 18 + 294540 GAGTTCAAGTTTGAATTG -s simCow_chr6.simCow.chr6 305064 5 + 602619 CA-------------TTA -s simDog_chr6.simDog.chr6 291527 16 + 593897 TAGG--GAGTTTGAATCA -s simHuman_chr6.simHuman.chr6 315877 16 + 601863 CAGG--GAATTCGAATTA -s simRat_chr6.simRat.chr6 321181 18 + 647215 GAATTCAACTTTGAATTG - -a -s simMouse_chr6.simMouse.chr6 329859 59 + 636262 GACCATACAACGCAAATAATACCATAAGGAATCAGATATTAATGTATTGACAAGACACA -s Anc0.Anc0refChr7 13275 42 - 16696 AA--------------GGACACCAAAAGCATTTTG---ACAGTGTAATGATAAGACAGA -s Anc1.Anc1refChr4 13876 42 + 17549 AA--------------GGACACCAAAAGCATTTTG---ACAGTGTAATGATAAGACAGA -s Anc2.Anc2refChr7 8922 42 + 32194 CA--------------GGACACCAAAAGCATTTTG---ACAGCATAATGATAAGAAAGA -s mr.mrrefChr5 177776 59 + 294540 AACCATTTAACGCAGGTAACACCATAAGCAAGCAGATAATAATGTATTGATAAGGCACA -s simCow_chr6.simCow.chr6 305069 42 + 602619 CA--------------TGACACCAAAAGCACTTTG---ACAGCATAATGATAACAAAGA -s simDog_chr6.simDog.chr6 291616 42 + 593897 CT--------------GGACACCAAAAGCATTTTG---ACAGCATAATGATAAGGAAGA -s simHuman_chr6.simHuman.chr6 315893 41 + 601863 AA--------------GGACATGACAAGCATCTTG---ACAGTGTAGCAATAAGACA-A -s simRat_chr6.simRat.chr6 321199 59 + 647215 AAGCATTTAACGCAGGTAACACCCTAAGCAAGCAGATAATAATTTATCGATAAGGTACA - -a -s simMouse_chr6.simMouse.chr6 329918 11 + 636262 ACCAGTTTGGT -s Anc0.Anc0refChr7 13317 11 - 16696 ACCAGTTTAGA -s Anc1.Anc1refChr4 13918 11 + 17549 ACCAGTTTAGA -s Anc2.Anc2refChr7 8964 11 + 32194 ACCAGTTTAGA -s mr.mrrefChr5 177835 11 + 294540 ACCAGTTTAGT -s simCow_chr6.simCow.chr6 305113 11 + 602619 ACCAGTTTAAA -s simDog_chr6.simDog.chr6 291658 11 + 593897 ACCAGTTTAGA -s simHuman_chr6.simHuman.chr6 315934 11 + 601863 ACCAGTTTAGA -s simRat_chr6.simRat.chr6 321258 11 + 647215 ACCAGTTTAGT - -a -s simMouse_chr6.simMouse.chr6 329929 7 + 636262 AACTTGT -s Anc0.Anc0refChr7 13328 7 - 16696 TACTTAT -s Anc1.Anc1refChr4 13929 7 + 17549 TACTTAT -s Anc2.Anc2refChr7 8988 7 + 32194 TACTTAT -s mr.mrrefChr5 177846 7 + 294540 AACTTGT -s simCow_chr6.simCow.chr6 305137 7 + 602619 AACTTAT -s simDog_chr6.simDog.chr6 291682 7 + 593897 TGCTTAT -s simHuman_chr6.simHuman.chr6 315945 7 + 601863 TACTTAT -s simRat_chr6.simRat.chr6 321269 7 + 647215 AACTTGT - -a -s simMouse_chr6.simMouse.chr6 329936 12 + 636262 ATGGGGATGTGT -s Anc0.Anc0refChr7 13335 12 - 16696 GTGGGTATGTGT -s Anc1.Anc1refChr4 13936 12 + 17549 GTGGGTATGTGT -s Anc2.Anc2refChr7 8995 12 + 32194 GTGGGTATGTGT -s mr.mrrefChr5 177853 12 + 294540 ATGGGGATGTGT -s simCow_chr6.simCow.chr6 305145 12 + 602619 ATGGGTATGTGT -s simDog_chr6.simDog.chr6 291689 12 + 593897 GTGGGTATGTGT -s simHuman_chr6.simHuman.chr6 315952 12 + 601863 GTGGGCCTGTGT -s simRat_chr6.simRat.chr6 321276 12 + 647215 ATGGGGATGTGT - -a -s simMouse_chr6.simMouse.chr6 329948 2 + 636262 AA -s Anc0.Anc0refChr7 13347 2 - 16696 AT -s Anc1.Anc1refChr4 13948 2 + 17549 AT -s Anc2.Anc2refChr7 9007 2 + 32194 AT -s mr.mrrefChr5 177865 2 + 294540 AA -s simCow_chr6.simCow.chr6 305163 2 + 602619 AT -s simDog_chr6.simDog.chr6 291701 2 + 593897 AT -s simHuman_chr6.simHuman.chr6 315964 2 + 601863 AT -s simRat_chr6.simRat.chr6 321288 2 + 647215 AA - -a -s simMouse_chr6.simMouse.chr6 329950 13 + 636262 TGGTTGGCAACCC -s Anc0.Anc0refChr7 13349 13 - 16696 TGGTTGATACTCC -s Anc1.Anc1refChr4 13950 13 + 17549 TGGTTGATACTCC -s Anc2.Anc2refChr7 9009 13 + 32194 TGGTCGATACTCC -s mr.mrrefChr5 177867 13 + 294540 TGGTTGGCAACCC -s simCow_chr6.simCow.chr6 305170 13 + 602619 TGGTAGATATTCC -s simDog_chr6.simDog.chr6 291703 13 + 593897 TGGTCAATACTCC -s simHuman_chr6.simHuman.chr6 315966 13 + 601863 CAGCTGATGCTCC -s simRat_chr6.simRat.chr6 321290 13 + 647215 TGGCTGGCAACGC - -a -s simMouse_chr6.simMouse.chr6 329963 51 + 636262 ATCCTGTTAGTTATCCCATAGATGCCATGATATTCTTGACATACTGCGCCA -s Anc0.Anc0refChr7 13363 51 - 16696 ATAGTGTTAGTTAACTCATAGACACCATGATACTCTTGATCCATGTTGCCC -s Anc1.Anc1refChr4 13964 51 + 17549 ATAGTGTTAGTTAACTCATAGACACCATGATACTCTTGATCCATGTTGCCC -s Anc2.Anc2refChr7 9023 51 + 32194 ATAGTGCTAGTTAACTCATAGACACCATGATGCTCTTGATCCATGTTGCCC -s mr.mrrefChr5 177880 51 + 294540 ATCCTGTTAGTTATCCCATAGATGCCATGATATTCTTGACATACTGTGCCA -s simCow_chr6.simCow.chr6 305184 49 + 602619 ATAGT-CTTGTTAACT-ATAGACACCATGATGCTCTTGATCCATGTGGTCC -s simDog_chr6.simDog.chr6 291717 47 + 593897 GTAGTGCTA---AACTCATAGACAC-ATGATGCTCTCAATCCTTGTTGCCG -s simHuman_chr6.simHuman.chr6 315980 51 + 601863 ATAATGTTAGTTACCTCATAGACACCATGATACTATTGATCCATGTTGCCC -s simRat_chr6.simRat.chr6 321303 51 + 647215 ACCCTGTTAGTTATTCCATAGATGCCATGATATTCTTGACATACTGTGCCA - -a -s simMouse_chr6.simMouse.chr6 330014 4 + 636262 CAGG -s Anc0.Anc0refChr7 13416 4 - 16696 CAAG -s Anc1.Anc1refChr4 14017 4 + 17549 CAAG -s Anc2.Anc2refChr7 9076 4 + 32194 CAAG -s mr.mrrefChr5 177931 4 + 294540 CGGG -s simCow_chr6.simCow.chr6 305235 4 + 602619 CAGA -s simDog_chr6.simDog.chr6 291766 4 + 593897 CAAG -s simHuman_chr6.simHuman.chr6 316033 4 + 601863 CAAG -s simRat_chr6.simRat.chr6 321354 4 + 647215 CGAG - -a -s simMouse_chr6.simMouse.chr6 330018 5 + 636262 AACTC -s Anc0.Anc0refChr7 13420 5 - 16696 TACTT -s Anc1.Anc1refChr4 14021 5 + 17549 TACTT -s Anc2.Anc2refChr7 9091 5 + 32194 TACTT -s mr.mrrefChr5 177935 5 + 294540 AACTC -s simCow_chr6.simCow.chr6 305250 5 + 602619 TGATC -s simDog_chr6.simDog.chr6 291781 5 + 593897 TACTT -s simHuman_chr6.simHuman.chr6 316037 5 + 601863 TACTT -s simRat_chr6.simRat.chr6 321358 5 + 647215 AACTC - -a -s simMouse_chr6.simMouse.chr6 330023 59 + 636262 CCCATTTTGTAGTGGGTCCTTAGTTGTCACATGATCACACTCTACCTTCAGAAGTCACT -s Anc0.Anc0refChr7 13425 56 - 16696 CCAAGTTCGTGGCAGGTCTTCAGTAGT--CATGA-TACATTCCGCCTTCAGTGAGAATC -s Anc1.Anc1refChr4 14026 56 + 17549 CCAAGTTCGTGGCAGGTCTTCAGTAGT--CATGA-TACATTCCGCCTTCAGTGAGAATC -s Anc2.Anc2refChr7 9096 56 + 32194 CCAAGTTCATGGCAGGTCTTCACTAGT--CACAA-TACATTGCGCCTTCAGTGAGAATC -s mr.mrrefChr5 177940 59 + 294540 CCCATTTTGTAGTGGGTCCTTAGTTGTCACATGATTACACTCTGCCTTCAGAGGTCACC -s simCow_chr6.simCow.chr6 305256 33 + 602619 CCAAGTTCATGGCAGGTCTTCATTAGT--TGCAA-T----------------------- -s simDog_chr6.simDog.chr6 291786 56 + 593897 CCAAGGTCATAGCAGGTCTCTACTAGC--CACAA-TACATTGCGCCTTCAGTGAGAATC -s simHuman_chr6.simHuman.chr6 316042 56 + 601863 CCAAGTTCGTGCCTGGTTTTCAGTAGT--CATGA-CATATCCCGCCTCCAGTGAGAATT -s simRat_chr6.simRat.chr6 321363 59 + 647215 CCCATTCTGCAGTGGGTCCTTAGTTGTCACATGATTGCACTCTGCCTTCAGAGGTCACC - -a -s simMouse_chr6.simMouse.chr6 330082 30 + 636262 TTCCCTGAGTGGATATTTGGATGGGGCACC -s Anc0.Anc0refChr7 13527 29 - 16696 TC-CCAGAGTGGAGATTTGGATGGGACCAC -s Anc1.Anc1refChr4 14128 29 + 17549 TC-CCAGAGTGGAGATTTGGATGGGACCAC -s Anc2.Anc2refChr7 9198 29 + 32194 TC-CCAGAATGGAGTGATGGATGTGACCAC -s mr.mrrefChr5 177999 29 + 294540 TT-CCTGAGTGGATATTTGGATGGGGCACC -s simDog_chr6.simDog.chr6 291890 29 + 593897 TC-CCAGAATGGAGTGATGGATGTGACCAC -s simHuman_chr6.simHuman.chr6 316144 29 + 601863 TC-CCAGAGTGGAAATTTGGATTGGACTGT -s simRat_chr6.simRat.chr6 321422 29 + 647215 TT-CCTGAGTGGATATTCGGATAGGGCATT - -a -s simMouse_chr6.simMouse.chr6 330112 8 + 636262 TAAGATCA -s Anc0.Anc0refChr7 13556 7 - 16696 CAAGATC- -s Anc1.Anc1refChr4 14157 7 + 17549 CAAGATC- -s Anc2.Anc2refChr7 9227 7 + 32194 CAAAATC- -s mr.mrrefChr5 178028 8 + 294540 TAAGATCA -s simDog_chr6.simDog.chr6 295806 7 + 593897 CAAAATC- -s simHuman_chr6.simHuman.chr6 316173 7 + 601863 CAGGATC- -s simRat_chr6.simRat.chr6 321451 8 + 647215 TAAGATCA - -a -s simMouse_chr6.simMouse.chr6 330120 120 + 636262 GTACTCAAAATCCATTACCTGAACCATTCTGGAGAGCTGAACCGTACTGCCTGGAGACAATTGGCCCTATCCAAACGCGTTGAAAGTGGTGGTGAACCATGACAGATTATTTTCTAGAGC -s mr.mrrefChr5 178036 119 + 294540 GTACTCAAAATCCATTACCTGAACCATTCTGGAGA-CTGAACCGTACTGCCTGGAGACAATTGGCCCTATCCAAACGCGTTGAAAGTGGTGGTGAACCATGACAGATTATTTTCTAGAGC -s simRat_chr6.simRat.chr6 321464 119 + 647215 GTAATCAAAATCTATTGCCTGAACCATTCTGGAAA-CTGAACCCCACCGCCTGGAGACAATTGCCCTTATCAAAATATGTTGCAAATGGTGTTGACCCATGCCAGATTATTTTTTAGAAC - -a -s simMouse_chr6.simMouse.chr6 330240 116 + 636262 AACTAACATGGCATAAGACCTCCAATCACTAAGTTTGGATACTTCATATCTTAATTTTTGGCAGGTCATCCTGTTAGCTACTCAGCCTCTCCTTAGTGACACACCTGGTGTCCCTG -s mr.mrrefChr5 178155 116 + 294540 AACTAACATGGCATAAGACCTCCAATCACTAAGTTTGGATACTTCATATCTTAATTTTTGGCAGGTCATCCTGTTAGCTACTCAGCCTCTCCTTAGTGACACACCTGGTGTCCCTG -s simRat_chr6.simRat.chr6 321584 116 + 647215 AACTAGCACAGCATAAGACCTCCAGGTATGTATTTTAGATACTCCATATCTTATTTTTTGGCAGGTTGTCCTGTTAGCTAGCAAGCTTCTCCTTAGTGACAAACCTGGTGTTCGTG - -a -s simMouse_chr6.simMouse.chr6 330356 103 + 636262 ATTTCTCCATCTCAAAGTTCACACTGTTTTACAGTCAGGTTCTCTTCAACTCAATTGGGATGTGAAGTTCATATAACAGGGATTGGTGAGCTGACTTGATAGC -s Anc0.Anc0refChr7 13563 10 - 16696 ---------------------------------------------------------------------------------------------ACTTAGTAAC -s Anc1.Anc1refChr4 14164 10 + 17549 ---------------------------------------------------------------------------------------------ACTTAGTAAC -s Anc2.Anc2refChr7 9234 10 + 32194 ---------------------------------------------------------------------------------------------ACTCAGTAAT -s mr.mrrefChr5 178271 103 + 294540 ATTTCTCCATCTCAAAGTTCACACTGTTTTACAGTCAGGTTCTCTTCAACTCAATTGGGATGTGAAGTTCATATAACAGGGATTGGTGAGCTGACTTGATAGC -s simDog_chr6.simDog.chr6 295813 10 + 593897 ---------------------------------------------------------------------------------------------ACTCAGTAAT -s simHuman_chr6.simHuman.chr6 316180 10 + 601863 ---------------------------------------------------------------------------------------------ACTTTGTAAC -s simRat_chr6.simRat.chr6 321703 103 + 647215 ATTTCTTCATTTAACAGTTCACATTATTTTACAGTCAGGTACTCTTCAACTCAATTAGGATGAGAAGTTAATATAACAAGGATTGGTGAGCTGACCAGATAAG - -a -s simMouse_chr6.simMouse.chr6 330459 44 + 636262 CTGTTAATATTGTCACAGAATAAAACTGGGACTATATGATTGAA -s Anc0.Anc0refChr7 13747 44 - 16696 CTGTTCAAATTGCCATGAAGTAAATAAGGGACTATCTGATTGAA -s Anc1.Anc1refChr4 14348 44 + 17549 CTGTTCAAATTGCCATGAAGTAAATAAGGGACTATCTGATTGAA -s Anc2.Anc2refChr7 9467 44 + 32194 CTGTTCAAATTGCCATGAAGTAATTAAGGGACTATCTGATTGAA -s mr.mrrefChr5 178374 44 + 294540 CTGTTAATATTGTCACAGAATAAAACTGGGACTATATGATTGAA -s simCow_chr6.simCow.chr6 305422 44 + 602619 CTGTTCCAACTGTCATTAAGTAAGTAAGGGACAATCTGATTGAA -s simDog_chr6.simDog.chr6 296295 44 + 593897 CTGTTCAAATTGCCATGAAGTAATTGAGGAACTCTATGATTGGA -s simHuman_chr6.simHuman.chr6 316429 44 + 601863 CTGTTCAGGTTGGCATGAAGTAAACAAGTGACTATCTAATTGAA -s simRat_chr6.simRat.chr6 321806 44 + 647215 CTGTTAATGTAGTCACAGAGTAAAACTGGGACTATATGATTGAA - -a -s simMouse_chr6.simMouse.chr6 330503 3 + 636262 CAG -s Anc0.Anc0refChr7 13791 3 - 16696 TAG -s Anc1.Anc1refChr4 14392 3 + 17549 TAG -s Anc2.Anc2refChr7 9511 3 + 32194 TAG -s mr.mrrefChr5 178418 3 + 294540 CAG -s simCow_chr6.simCow.chr6 305466 3 + 602619 TAG -s simDog_chr6.simDog.chr6 296339 3 + 593897 CAG -s simHuman_chr6.simHuman.chr6 316473 3 + 601863 TAG -s simRat_chr6.simRat.chr6 321852 3 + 647215 CAG - -a -s simMouse_chr6.simMouse.chr6 330506 3 + 636262 GTT -s Anc0.Anc0refChr7 13796 3 - 16696 ATG -s Anc1.Anc1refChr4 14397 3 + 17549 ATG -s Anc2.Anc2refChr7 9516 3 + 32194 ATG -s mr.mrrefChr5 178421 3 + 294540 GTT -s simCow_chr6.simCow.chr6 305471 3 + 602619 ATG -s simDog_chr6.simDog.chr6 296344 3 + 593897 ATG -s simHuman_chr6.simHuman.chr6 316478 3 + 601863 ATG -s simRat_chr6.simRat.chr6 321855 3 + 647215 GTT - -a -s simMouse_chr6.simMouse.chr6 330509 6 + 636262 CATTAG -s Anc0.Anc0refChr7 13799 6 - 16696 CATTGG -s Anc1.Anc1refChr4 14400 6 + 17549 CATTGG -s Anc2.Anc2refChr7 9519 6 + 32194 CATTGT -s mr.mrrefChr5 178424 6 + 294540 CATTAG -s simCow_chr6.simCow.chr6 305474 6 + 602619 CATCGT -s simDog_chr6.simDog.chr6 296347 6 + 593897 CATTGT -s simHuman_chr6.simHuman.chr6 316481 6 + 601863 CATTGG -s simRat_chr6.simRat.chr6 321865 6 + 647215 TATTTA - -a -s simMouse_chr6.simMouse.chr6 330515 26 + 636262 ATTGTGTGGAACATCTAGTTCATGGT -s Anc0.Anc0refChr7 13807 13 - 16696 ATTGTGTGGA-------------AGT -s Anc1.Anc1refChr4 14408 13 + 17549 ATTGTGTGGA-------------AGT -s Anc2.Anc2refChr7 9527 13 + 32194 ATTGGGTGGA-------------AGT -s mr.mrrefChr5 178430 14 + 294540 ATTGTGTGGA------------TGGT -s simCow_chr6.simCow.chr6 305482 11 + 602619 ATTGGGTGAA-------------A-- -s simDog_chr6.simDog.chr6 296355 13 + 593897 ATTGGGTGGA-------------AGT -s simHuman_chr6.simHuman.chr6 316489 13 + 601863 ATTGTGTTGA-------------AGT -s simRat_chr6.simRat.chr6 321871 14 + 647215 ATGGTGTAGA------------TGGT - -a -s simMouse_chr6.simMouse.chr6 330541 6 + 636262 GTAGTT -s Anc0.Anc0refChr7 13820 6 - 16696 ATAGTT -s Anc1.Anc1refChr4 14421 6 + 17549 ATAGTT -s Anc2.Anc2refChr7 9540 6 + 32194 ATATTT -s mr.mrrefChr5 178444 6 + 294540 GTAGTT -s simDog_chr6.simDog.chr6 296369 6 + 593897 ATATTT -s simHuman_chr6.simHuman.chr6 316502 6 + 601863 ATAGTT -s simRat_chr6.simRat.chr6 321885 6 + 647215 GTAGTT - -a -s simMouse_chr6.simMouse.chr6 330547 4 + 636262 TGAG -s Anc0.Anc0refChr7 13833 4 - 16696 TAAG -s Anc1.Anc1refChr4 14434 4 + 17549 TAAG -s Anc2.Anc2refChr7 9553 4 + 32194 TAGG -s mr.mrrefChr5 178450 4 + 294540 TGAG -s simCow_chr6.simCow.chr6 305499 3 + 602619 TA-G -s simDog_chr6.simDog.chr6 296382 4 + 593897 GAGG -s simHuman_chr6.simHuman.chr6 316515 4 + 601863 TAAG -s simRat_chr6.simRat.chr6 321891 4 + 647215 CGAG - -a -s simMouse_chr6.simMouse.chr6 330551 77 + 636262 CATCACTGTGAGGATTAATTGGATGTTTCGGAATCCCAGATGTTTCGGGAATCCCGGCAGCTATCCTGAGGTAACCG -s Anc0.Anc0refChr7 13837 61 - 16696 CATTATTGTGAGGACTAGTAGGATGTTTCGG---------------GG-AATCCCTGCAGCTAGCCTGAGGTAACTG -s Anc1.Anc1refChr4 14438 61 + 17549 CATTATTGTGAGGACTAGTAGGATGTTTCGG---------------GG-AATCCCTGCAGCTAGCCTGAGGTAACTG -s Anc2.Anc2refChr7 9563 61 + 32194 CACTATTGTGGGTACTAGTAGGATGTTTCGG---------------GG-AATCCCTGCAGCTAGCATGAGGTAACTG -s mr.mrrefChr5 178454 76 + 294540 CATCACTGTGAGGATTAATTGGATGTTTCGGAATCCCAGATGTTTCGG-AATCCCGGCAGCTATCCTGAGGTAACCG -s simCow_chr6.simCow.chr6 305508 59 + 602619 CACTATTGTGTGTACTAGT--GATGTTTCGG---------------GG-AATTCCGGTCTCTAGCGTGAGGCGACTG -s simDog_chr6.simDog.chr6 296392 61 + 593897 CACTATCGTGGGTACTAGCAGAATGTTTCGA---------------GG-AATCCCTGCAGCTAGCATGAGGTAACTG -s simHuman_chr6.simHuman.chr6 316519 58 + 601863 CAT---TGTGAGGACTAGTCGGAACTTTCGG---------------GG-AATCCCCGCAGCTAGCCTGAGGTAACTG -s simRat_chr6.simRat.chr6 321895 76 + 647215 CATCACTGTGAGAACTAATTGGATGTTTCGGAATCTCAGATGTTTCGG-AATCCCAGCAGCTAACGTGAGGTAACCG - -a -s simMouse_chr6.simMouse.chr6 330628 7 + 636262 ACCTTAC -s Anc0.Anc0refChr7 13898 7 - 16696 ACCTCGT -s Anc1.Anc1refChr4 14499 7 + 17549 ACCTCGT -s Anc2.Anc2refChr7 9625 7 + 32194 ACCTCGT -s mr.mrrefChr5 178530 7 + 294540 ACCTTAC -s simCow_chr6.simCow.chr6 305568 7 + 602619 ACTCTGT -s simDog_chr6.simDog.chr6 296454 7 + 593897 ACCTCGT -s simHuman_chr6.simHuman.chr6 316577 7 + 601863 ATCTCGT -s simRat_chr6.simRat.chr6 321971 7 + 647215 ACCTCTG - -a -s simMouse_chr6.simMouse.chr6 330635 24 + 636262 TCGGGCTCAATTGGAATCGTTCCG -s Anc0.Anc0refChr7 13906 24 - 16696 TCGAGCTCCATGGGAAGCGTTCCG -s Anc1.Anc1refChr4 14507 24 + 17549 TCGAGCTCCATGGGAAGCGTTCCG -s Anc2.Anc2refChr7 9633 24 + 32194 TTGAGCTTCATGGGAAGCGTTCCG -s mr.mrrefChr5 178537 24 + 294540 TCGGGCTCAATTGGAATCGTTCCG -s simCow_chr6.simCow.chr6 305576 24 + 602619 TTGAGCTTTAGGGGAAGCGTTCCG -s simDog_chr6.simDog.chr6 296462 24 + 593897 TTTAGCTTCATGGGAAGCGTTCCG -s simHuman_chr6.simHuman.chr6 316585 24 + 601863 TCGAGCTCCATGGGAAGCGTTCCG -s simRat_chr6.simRat.chr6 321978 24 + 647215 TTGGGCTACATTGGAATCGTTCCG - -a -s simMouse_chr6.simMouse.chr6 330659 2 + 636262 AG -s Anc0.Anc0refChr7 13936 2 - 16696 AG -s Anc1.Anc1refChr4 14537 2 + 17549 AG -s Anc2.Anc2refChr7 9669 2 + 32194 CG -s mr.mrrefChr5 178561 2 + 294540 AG -s simCow_chr6.simCow.chr6 305613 2 + 602619 CG -s simDog_chr6.simDog.chr6 296498 2 + 593897 CG -s simHuman_chr6.simHuman.chr6 316615 2 + 601863 AG -s simRat_chr6.simRat.chr6 322002 2 + 647215 GG - -a -s simMouse_chr6.simMouse.chr6 330661 76 + 636262 TAAACACATTGGGCAGGCTCATTCTAGATGCCAAACAAGTGCCGGTCATTGCTTGACAGTGTATGAATCAGACAGG -s Anc0.Anc0refChr7 13938 8 - 16696 TCAACATA-------------------------------------------------------------------- -s Anc1.Anc1refChr4 14539 8 + 17549 TCAACATA-------------------------------------------------------------------- -s Anc2.Anc2refChr7 9671 8 + 32194 TCAACATA-------------------------------------------------------------------- -s mr.mrrefChr5 178563 74 + 294540 TAAACACATTGGGCAGGCTCATTCTAGATGCCAAA--AGTGCCGGTCATTGCTTGACAGTGTTTGAATCGGACAGG -s simCow_chr6.simCow.chr6 305615 8 + 602619 CCAACATA-------------------------------------------------------------------- -s simDog_chr6.simDog.chr6 296500 8 + 593897 TCGACATG-------------------------------------------------------------------- -s simHuman_chr6.simHuman.chr6 316617 8 + 601863 TCAACATA-------------------------------------------------------------------- -s simRat_chr6.simRat.chr6 322016 74 + 647215 TAAACATATCAGGCAGGCTCATTCTAGATGCGAAA--GGTGCCTGTCATCTCTCAACAGTGGTTGAATCGGACAGG - -a -s simMouse_chr6.simMouse.chr6 330737 591 + 636262 ATCTACAATGTACACAGGGGCCTGTCATTGCTTGACAGTGCATGAATCGGACAGGGGATCTACAATGTATGTGAGGAGATCATTTGATGTCTCTGGTATCCTGTCCTGTCACTTATAGTCGATAGAGAAGAAAATCTACTCCGACATTTATGATTCCCAAATGGTTCGAACCTCAATGGAAGACTATATAGTAGTGTTGACGGGTCGAGACGTGGAGTCCAAAGGTAGGGTTCCGAGGGTAGGGTTAAATGGTTCGAACTCTCATCGCAAGACTATATAGTAGTGTTGACGGGTCGAGATGTGGATTCCGGGGTTAGGACCATGCTGTCAATGGGTTCCATAGGAATTGTGCTACCTCCCAATTTCACTATTGCTCTAGACTCAAAAATGCTTACGGAGCGGTCCCTCATCAAGCGGAGCAGGCTTGTAGCCAAGTACTGAGCGTGTGTACATGGCTGTGCAGGGCAGGCTCATAGCCAAGCACTGACTGTGTGTACCATGGCTGGATTTGCTTTTTTTTGAAGATTTGCATGAGGCACTGTGCGAAGTCTAACCCAGGGCTAAGAGCCGGTCGCTGACGTGCCCAACTAG -s Anc0.Anc0refChr7 13946 26 - 16696 ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TA---GCCCGCCGCTGACCTGCCC-GCTAG -s Anc1.Anc1refChr4 14547 26 + 17549 ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TA---GCCCGCCGCTGACCTGCCC-GCTAG -s Anc2.Anc2refChr7 9679 26 + 32194 ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TG---GCCCGCCGCTGACCTGCCC-GATAG -s mr.mrrefChr5 178639 271 + 294540 ATCTACAATGTACACAGGGGCCTGTCATTGCTTGACAGTGCATGAATCGGACAGGGGATCTACAATGTATGTGAGGAGATCATTTGATGTCTC---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ATCAAGCGGAGCAGGCTTGTAGCCAAGTACTGAGCGTGTGTACATGGCTGTGCAGGGCAGGCTCATAGCCAAGCACTGACTGTGTGTAC-ATGGCTGGATTTGCTTTTTTTTGAAGATTTGCATGAGGCACTGTGCGAAGTCTAACC-AGTGTTA---GCCGGTCGCTGACGTGCCCAACTAG -s simCow_chr6.simCow.chr6 305623 26 + 602619 ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TG---GCCCGCCGCTAGCCTACCC-GATAG -s simDog_chr6.simDog.chr6 296508 26 + 593897 ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TG---GCCCGCCCCCGATCTGCCC-GATAA -s simHuman_chr6.simHuman.chr6 316625 26 + 601863 ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TA---GCCCGCCGCTGACCTGCCC-GCTAG -s simRat_chr6.simRat.chr6 322092 271 + 647215 ATCTACAATGTACACAGGTGCCCGTCTTTCCTTGACAGTGCACGAATCAGACAAGGGATCTACAATATATGCAGGAAGATCCATTGACATCTC---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ATCAAGCAGGGCAGGCTCGTAGCCAAGCACCAACCATGTGTACATGGCCGCGTGGGGCAGGCTCATAGCCAAGCACTAACCGTGTGTAC-ATGGCTGCATTTGCCTTTTTTTGGAAATTTGCACGAGGCACTGTGCAAAGTCTAACC-AGTGTTA---GCCGGTCGCTGACGTGCCCAACTGG - -a -s simMouse_chr6.simMouse.chr6 331328 10 + 636262 TTCGGATAGA -s Anc0.Anc0refChr7 13972 10 - 16696 CTAGGAGAGA -s Anc1.Anc1refChr4 14573 10 + 17549 CTAGGAGAGA -s Anc2.Anc2refChr7 9705 10 + 32194 CTAGGAGAGA -s mr.mrrefChr5 178910 10 + 294540 TTAGGATAGA -s simCow_chr6.simCow.chr6 305662 10 + 602619 CTAAGAAAGA -s simDog_chr6.simDog.chr6 296534 10 + 593897 CTAGGCGAGA -s simHuman_chr6.simHuman.chr6 316651 10 + 601863 CCAGGAGAGG -s simRat_chr6.simRat.chr6 322363 10 + 647215 TTAGGATAGA - -a -s simMouse_chr6.simMouse.chr6 331338 18 + 636262 CAGGAGCAGCACGCGTTG -s Anc0.Anc0refChr7 13983 18 - 16696 CGGGAGCAGCACGCGTAA -s Anc1.Anc1refChr4 14584 18 + 17549 CGGGAGCAGCACGCGTAA -s Anc2.Anc2refChr7 9716 18 + 32194 AGGAAGAAGCACGCGTAA -s mr.mrrefChr5 178920 18 + 294540 CAGGAGCAGCACGCGTTG -s simCow_chr6.simCow.chr6 305673 18 + 602619 AGGAAGAAACACGCATAA -s simDog_chr6.simDog.chr6 296545 18 + 593897 AGGACGAAGTACGCGTAA -s simHuman_chr6.simHuman.chr6 316662 18 + 601863 CGGGAGCAGCACGTGTAA -s simRat_chr6.simRat.chr6 322373 18 + 647215 CAGGAGCAACACGCGTTG - -a -s simMouse_chr6.simMouse.chr6 331356 10 + 636262 GGGAGAAACC -s Anc0.Anc0refChr7 14001 4 - 16696 AG------CC -s Anc1.Anc1refChr4 14602 4 + 17549 AG------CC -s Anc2.Anc2refChr7 9735 4 + 32194 AG------CG -s mr.mrrefChr5 178938 4 + 294540 GG------CC -s simCow_chr6.simCow.chr6 305692 4 + 602619 AG------CG -s simDog_chr6.simDog.chr6 296564 4 + 593897 AG------CG -s simHuman_chr6.simHuman.chr6 316680 4 + 601863 AG------GC -s simRat_chr6.simRat.chr6 322391 4 + 647215 GG------CC - -a -s simMouse_chr6.simMouse.chr6 331366 26 + 636262 TAATTGTGTTACTTCTATGCCCAAGT -s Anc0.Anc0refChr7 14005 21 - 16696 TAATTTTGTTACTTTT-----GGGAT -s Anc1.Anc1refChr4 14606 21 + 17549 TAATTTTGTTACTTTT-----GGGAT -s Anc2.Anc2refChr7 9739 21 + 32194 TAATTTTGTTACCTTT-----GGGAC -s mr.mrrefChr5 178942 21 + 294540 TAATTGTGTTACTTTT-----CAGAT -s simCow_chr6.simCow.chr6 305696 16 + 602619 -----CTGTTACCTTG-----GGGCA -s simDog_chr6.simDog.chr6 296573 19 + 593897 TAATTTTGT--ACTCT-----GGGAC -s simHuman_chr6.simHuman.chr6 316684 21 + 601863 TAATTATGTTACTTTT-----AGGAT -s simRat_chr6.simRat.chr6 322395 21 + 647215 TAATCGCGTTACTTTT-----CAGAG - -a -s simMouse_chr6.simMouse.chr6 331392 3 + 636262 AAC -s Anc0.Anc0refChr7 14026 3 - 16696 AAA -s Anc1.Anc1refChr4 14627 3 + 17549 AAA -s Anc2.Anc2refChr7 9771 3 + 32194 AAA -s mr.mrrefChr5 178963 3 + 294540 AAC -s simCow_chr6.simCow.chr6 305723 3 + 602619 TTA -s simDog_chr6.simDog.chr6 296603 3 + 593897 AAA -s simHuman_chr6.simHuman.chr6 316705 3 + 601863 AAA -s simRat_chr6.simRat.chr6 322416 3 + 647215 AAC - -a -s simMouse_chr6.simMouse.chr6 331395 47 + 636262 AAAGCAAAAAGTCTTGGAAATTGGATGAGGCTGTTTCCAAGCTTTTA -s Anc0.Anc0refChr7 14029 45 - 16696 AAATAAGAAAGTC-TAGGAAATTGATGCAGCTGTTTCCAAACCAGT- -s Anc1.Anc1refChr4 14630 45 + 17549 AAATAAGAAAGTC-TAGGAAATTGATGCAGCTGTTTCCAAACCAGT- -s Anc2.Anc2refChr7 9774 45 + 32194 AAATAAGAAAGTC-CAGGAAATTGATGCAGCTGTTTCCAAACCAGT- -s mr.mrrefChr5 178966 46 + 294540 AAAGCAAAAAGTCTTGGAAATTGGATGCGGCTGTTTCCAAACTTTT- -s simCow_chr6.simCow.chr6 305732 45 + 602619 GACCTAAAAAGTC-AAAATGTTTGATGCAGCTGTTTCCAAATCAGT- -s simDog_chr6.simDog.chr6 296606 45 + 593897 AAATAAGAAAGTC-CAGGAAATTGGTGCGGCTGTTTGCAAACCCAT- -s simHuman_chr6.simHuman.chr6 316708 34 + 601863 GA------------TAGGAACTTGATGCAGCTGTTCCCGAACCAGT- -s simRat_chr6.simRat.chr6 322419 46 + 647215 AAAACAAAAAGTTTTGGAAATTGAACGCGGCTGTTTCCAAACTTTT- - -a -s simMouse_chr6.simMouse.chr6 331442 4 + 636262 ACCA -s Anc0.Anc0refChr7 14075 3 - 16696 ACC- -s Anc1.Anc1refChr4 14676 4 + 17549 ACCA -s Anc2.Anc2refChr7 9820 3 + 32194 ACC- -s mr.mrrefChr5 179012 4 + 294540 ACCA -s simCow_chr6.simCow.chr6 305778 3 + 602619 ATC- -s simDog_chr6.simDog.chr6 296652 3 + 593897 CCC- -s simHuman_chr6.simHuman.chr6 316743 4 + 601863 ACCA -s simRat_chr6.simRat.chr6 322465 4 + 647215 ACCA - -a -s simMouse_chr6.simMouse.chr6 331446 35 + 636262 TCCTCATTAATTCCAGTTACCAGTTGAATTGTCAG -s Anc0.Anc0refChr7 14078 35 - 16696 TCCTGATGAATCCCAGTTACTATTTGAACTGTCGG -s Anc1.Anc1refChr4 14680 35 + 17549 TCCTGATGAATCCCAGTTACTATTTGAACTGTCGG -s Anc2.Anc2refChr7 9823 35 + 32194 TCCTGATGAATCCCAGTTACTATTTGAACTGTCGG -s mr.mrrefChr5 179016 35 + 294540 TCCTCATTAATTCCAGTTACTAGTTGAATTGTCAG -s simCow_chr6.simCow.chr6 305781 30 + 602619 TCCTGATCAATCCCAGTTAGTCTATGAAAT----- -s simDog_chr6.simDog.chr6 296655 35 + 593897 TCCTGATGAATCCCGGTTACTATTTGAACTGTCGG -s simHuman_chr6.simHuman.chr6 316753 35 + 601863 TATAGATGAGTCCCAGTTACTATTTGAAGTGTCTG -s simRat_chr6.simRat.chr6 322469 35 + 647215 TCCTCATTAATTCCAGTTACTAGTCAAATTGTCAG - -a -s simMouse_chr6.simMouse.chr6 331481 32 + 636262 TCCAGTATGATAATCCAACCTAAACTATGGAG -s Anc0.Anc0refChr7 14123 31 - 16696 TCCATGATCATAATCCAACCT-ACCTATGGGG -s Anc1.Anc1refChr4 14725 31 + 17549 TCCATGATCATAATCCAACCT-ACCTATGGGG -s Anc2.Anc2refChr7 9868 31 + 32194 TTCTTGATCCTAATCTAACTT-ACCTATGGGT -s mr.mrrefChr5 179061 31 + 294540 TCCAGTATGATAATCCAACCT-AACTATGGAG -s simCow_chr6.simCow.chr6 305820 31 + 602619 ATCTTGATCCTAATCTGACTG-ACCTATGGGG -s simDog_chr6.simDog.chr6 296700 27 + 593897 TTCTCGATCCCCGTCTAACTT-A----TGGGT -s simHuman_chr6.simHuman.chr6 316798 31 + 601863 TCCATGATCATAATCCAACCT-ACCTTTGGGG -s simRat_chr6.simRat.chr6 322514 31 + 647215 TCCAATATAATAATCTGACCT-ATCTATGGTG - -a -s simMouse_chr6.simMouse.chr6 331513 19 + 636262 TATCCAAACAACTTTTAAG -s Anc0.Anc0refChr7 14154 19 - 16696 TATCAGAACAACTTTTAAG -s Anc1.Anc1refChr4 14756 19 + 17549 TATCAGAACAACTTTTAAG -s Anc2.Anc2refChr7 9899 19 + 32194 TATCAGAAAAATTCTTAAG -s mr.mrrefChr5 179092 19 + 294540 TATCCAAACAACTTTTAAG -s simCow_chr6.simCow.chr6 305851 19 + 602619 TACTAGAAAAATTCTTAAG -s simDog_chr6.simDog.chr6 296727 15 + 593897 TATCAGAGAA----TTAGG -s simHuman_chr6.simHuman.chr6 316832 19 + 601863 TATCTGTACAACTTTTAAG -s simRat_chr6.simRat.chr6 322545 19 + 647215 TATCCAAACAACTTTTAAA - -a -s simMouse_chr6.simMouse.chr6 331532 5 + 636262 TCATT -s Anc0.Anc0refChr7 14173 5 - 16696 CCTTT -s Anc1.Anc1refChr4 14775 5 + 17549 CCTTT -s Anc2.Anc2refChr7 9918 5 + 32194 CCATT -s mr.mrrefChr5 179111 5 + 294540 TCTTT -s simCow_chr6.simCow.chr6 305874 5 + 602619 TCATT -s simDog_chr6.simDog.chr6 296742 5 + 593897 CCATT -s simHuman_chr6.simHuman.chr6 316851 5 + 601863 CCTTT -s simRat_chr6.simRat.chr6 322564 5 + 647215 TCTTT - -a -s simMouse_chr6.simMouse.chr6 331537 47 + 636262 CTGCTAAGTTAAGAAATGACACTACGTCTCAAGAGAAACCACTGTTT -s Anc0.Anc0refChr7 14178 40 - 16696 TTGTTAAGCTAAGAGATGACTCTACTGACCTAGAA-------TCCCT -s Anc1.Anc1refChr4 14780 40 + 17549 TTGTTAAGCTAAGAGATGACTCTACTGACCTAGAA-------TCCCT -s Anc2.Anc2refChr7 9923 40 + 32194 TTGTTAAGCTAATAGATGACTGTACTGACCTAGAA-------TCCCT -s mr.mrrefChr5 179116 47 + 294540 TTGCTAAGTTAAGAAATGACACTACGTCTCAAGAGAAACCACTCTCT -s simCow_chr6.simCow.chr6 305879 40 + 602619 ATGTCAAGCTAATAGATGACTGTACTAACATAGAA-------TTCCT -s simDog_chr6.simDog.chr6 296748 39 + 593897 TTGTTAAGCTAA-AGATAACTGTACTGATCTAGAA-------TCCCT -s simHuman_chr6.simHuman.chr6 316856 40 + 601863 TTGTTAAGCTAAGATATGACTCTACTGACCCAGAA-------CCGCT -s simRat_chr6.simRat.chr6 322569 47 + 647215 TTGCTAAGTTATGAAATGACCCTACATCTCAAGAGGATACACTCTCT - -a -s simMouse_chr6.simMouse.chr6 331584 14 + 636262 CTTTGACATAAGGG -s Anc0.Anc0refChr7 14218 14 - 16696 CTTTGATAAAAGCA -s Anc1.Anc1refChr4 14820 14 + 17549 CTTTGATAAAAGCA -s Anc2.Anc2refChr7 9964 14 + 32194 CTTTGATAAAAGCA -s mr.mrrefChr5 179163 14 + 294540 CTTTGACATAAGGG -s simCow_chr6.simCow.chr6 305920 13 + 602619 CTTTGACAA-AGCA -s simDog_chr6.simDog.chr6 296788 14 + 593897 CTTTGATGAAAGCA -s simHuman_chr6.simHuman.chr6 316896 14 + 601863 CTTTGATAATAGCA -s simRat_chr6.simRat.chr6 322616 12 + 647215 CTTTGACATAAG-- - -a -s simMouse_chr6.simMouse.chr6 331598 49 + 636262 TTAGACTCCCTCGACTAGTTCCACAATGCACAGCTCACAGAAAGACAAC -s Anc0.Anc0refChr7 14234 49 - 16696 TTTCATTCCCTCAATTAGCTCCACTACACACAGCTCTCAGAGTGCCCAC -s Anc1.Anc1refChr4 14836 49 + 17549 TTTCATTCCCTCAATTAGCTCCACTACACACAGCTCTCAGAGTGCCCAC -s Anc2.Anc2refChr7 9980 49 + 32194 TTTCATTCCCTCAATTAGCTCCACTACAAACAGCTTTCAGACTGCCCAC -s mr.mrrefChr5 179177 49 + 294540 TTAGACTCCCTCGACTAGTTCCACAATGCACAGCTCTCAGAGAGCCCAC -s simCow_chr6.simCow.chr6 305935 49 + 602619 TCTCATTCCCTCAACCAGCTCCACTACGAACAGCTTTCAGACTTCCCAC -s simDog_chr6.simDog.chr6 296804 49 + 593897 TTTCATTTCCCCAATTGGCTCCACTGCAAACACCTTTCAGTCTGTGCAC -s simHuman_chr6.simHuman.chr6 316912 49 + 601863 TTTCATTCCCTCAATTAGCTCCACTACACACAGCTCTCAGAGTGCCCAT -s simRat_chr6.simRat.chr6 322628 28 + 647215 -----------------GGTCCACAATGCACAGCTCT----GAGCCCAC - -a -s simMouse_chr6.simMouse.chr6 331647 77 + 636262 CACAGTGAGTTCTCAGACCAGGATAATACCTAATAAGGAGCATGCTCCAGTGATGTCAGGCACATGTTTGGGGTAGT -s Anc0.Anc0refChr7 14283 74 - 16696 CACATCCAGCTCTCAGACCAGC---ATGCCTTATAAGAACCATGCCCCAGTGATGTTAAGCATGTCTTTGGGGTTGT -s Anc1.Anc1refChr4 14885 74 + 17549 CACATCCAGCTCTCAGACCAGC---ATGCCTTATAAGAACCATGCCCCAGTGATGTTAAGCATGTCTTTGGGGTTGT -s Anc2.Anc2refChr7 10029 74 + 32194 CACATCCAGCTCTCAGACCAGC---ACGCCTCATAAGAACCATGCCCCAGTGATGTTAAGCATGTCTTTGGGGTTGT -s mr.mrrefChr5 179226 74 + 294540 CACAGCCAGTTCTCAGACCAGG---ATACCTTATAAGGAGCATGCTCCAGTGATGTCAGGCACATGTTTGGGGTAGT -s simCow_chr6.simCow.chr6 305984 68 + 602619 CACACCCAGTGCTTGGACGAAC---------CATAAGAACCATGCTCCAGTGATGTTAAGCACATCTTTGGGGTAGT -s simDog_chr6.simDog.chr6 296853 72 + 593897 CAGATCCAGCTCTCAGACCAGC---ACGCCTCATAGGTACCATCTCCAGTTGATGTACAGCATGTCTTT--GGATGT -s simHuman_chr6.simHuman.chr6 316977 74 + 601863 CACATCCAGCCTTAAGACCAGC---ATGCCTTGAAAGAGCCATGCGCCAGTGATGTTAAGCATGCCTTTAGGGTTGT -s simRat_chr6.simRat.chr6 322656 74 + 647215 CACAGCCAGTTCTCAGTCCAGG---ATACCTTATATGGAGCATGCTCCAGTGATGTCAGGCACATGTTTGGGGTAGC - -a -s simMouse_chr6.simMouse.chr6 331724 15 + 636262 CTGTCTCAATGTTCA -s Anc0.Anc0refChr7 14358 15 - 16696 CTGTCTTAATTTTCA -s Anc1.Anc1refChr4 14960 15 + 17549 CTGTCTTAATTTTCA -s Anc2.Anc2refChr7 10104 15 + 32194 CTGTCATAATTTTCA -s mr.mrrefChr5 179300 15 + 294540 CTGTCTCAATGTTCA -s simCow_chr6.simCow.chr6 306053 15 + 602619 CTGATATAGTTTTCA -s simDog_chr6.simDog.chr6 296926 15 + 593897 CTGTCATGATTTTCA -s simHuman_chr6.simHuman.chr6 317052 15 + 601863 CTTTCTTAACCTTCA -s simRat_chr6.simRat.chr6 322730 15 + 647215 CTGTCTCAATGCTCA - -a -s simMouse_chr6.simMouse.chr6 331739 3 + 636262 GAC -s Anc0.Anc0refChr7 14373 3 - 16696 GGC -s Anc1.Anc1refChr4 14975 3 + 17549 GGC -s Anc2.Anc2refChr7 10119 3 + 32194 GGC -s mr.mrrefChr5 179315 3 + 294540 GAC -s simCow_chr6.simCow.chr6 306068 3 + 602619 AGC -s simDog_chr6.simDog.chr6 296957 3 + 593897 GGC -s simHuman_chr6.simHuman.chr6 317067 3 + 601863 GCC -s simRat_chr6.simRat.chr6 322745 3 + 647215 GAC - -a -s simMouse_chr6.simMouse.chr6 331742 11 + 636262 AAGAACTAGCC -s Anc0.Anc0refChr7 14376 11 - 16696 TTGAATCTGCT -s Anc1.Anc1refChr4 14978 11 + 17549 TTGAATCTGCT -s Anc2.Anc2refChr7 10122 11 + 32194 TTGAGTCTGCT -s mr.mrrefChr5 179318 11 + 294540 AAGAACTAGCC -s simCow_chr6.simCow.chr6 306072 11 + 602619 TTGAGTCTGCT -s simDog_chr6.simDog.chr6 296960 11 + 593897 TTGTGTCTGCT -s simHuman_chr6.simHuman.chr6 317070 11 + 601863 TTAAATCTGCT -s simRat_chr6.simRat.chr6 322748 11 + 647215 AAGAACTAGCC - -a -s simMouse_chr6.simMouse.chr6 331753 46 + 636262 CAACACTGGGATGGCGGAGGGGAGCCCTGTTCAACCTTCCAGGACA -s Anc0.Anc0refChr7 14387 28 - 16696 CAGCC----------------AAGAGCTACACAA--TGCTAGGACT -s Anc1.Anc1refChr4 14989 28 + 17549 CAGCC----------------AAGAGCTACACAA--TGCTAGGACT -s Anc2.Anc2refChr7 10133 28 + 32194 CAGCC----------------AAGAGCTACACAA--TGCTGGGATT -s mr.mrrefChr5 179329 46 + 294540 CAACACTGGGATGGCGGAAGGGAGCCCTACTCAACCTTCCAGGACA -s simCow_chr6.simCow.chr6 306084 28 + 602619 CAGCT----------------GAGAACTACACAT--TACCGGGAGT -s simDog_chr6.simDog.chr6 296971 28 + 593897 ACAGC----------------AAGAGCGACACAA--TGCTGGGATT -s simHuman_chr6.simHuman.chr6 317081 28 + 601863 CAGCC----------------AAGATCTACACAA--TGCAAGGACT -s simRat_chr6.simRat.chr6 322759 33 + 647215 CA-------------GGTAGGGAGCCCTACTCAACCCTCCAGGCCA - -a -s simMouse_chr6.simMouse.chr6 331799 37 + 636262 GCAAAATGAAGCCTGCCCTGCTCAACCTTTCAGATAA -s Anc0.Anc0refChr7 14415 33 - 16696 GCAGAATTGA----GTCCTGCTCAGCCTTTCAGATAA -s Anc1.Anc1refChr4 15017 33 + 17549 GCAGAATTGA----GTCCTGCTCAGCCTTTCAGATAA -s Anc2.Anc2refChr7 10161 33 + 32194 GCAGAATTGA----GTCCTGGTCAGCCTTCCAGATAA -s mr.mrrefChr5 179375 33 + 294540 GCAAAATGAA----GCCCTGCTCAACCTTTCAGATAA -s simCow_chr6.simCow.chr6 306112 33 + 602619 GCAGAATGGT----GCCCTAGCAACCCTTCCAGATAA -s simDog_chr6.simDog.chr6 297017 33 + 593897 GCAGAATTGA----GTCCTGGTCAGTCTACCAGATAA -s simHuman_chr6.simHuman.chr6 317109 24 + 601863 GCAGAAT-------------CTCAGCTTTTCAGATAA -s simRat_chr6.simRat.chr6 322792 33 + 647215 GCAAACTGAA----TCCCTACCCAACCTTTCAGATAA - -a -s simMouse_chr6.simMouse.chr6 331836 2 + 636262 GA -s Anc0.Anc0refChr7 14448 2 - 16696 GA -s Anc1.Anc1refChr4 15050 2 + 17549 GA -s Anc2.Anc2refChr7 10194 2 + 32194 GA -s mr.mrrefChr5 179408 2 + 294540 GA -s simCow_chr6.simCow.chr6 306158 2 + 602619 GA -s simDog_chr6.simDog.chr6 297050 2 + 593897 GA -s simHuman_chr6.simHuman.chr6 317133 2 + 601863 GA -s simRat_chr6.simRat.chr6 322825 2 + 647215 GA - -a -s simMouse_chr6.simMouse.chr6 331838 14 + 636262 ATCACCAACTAAGG -s Anc0.Anc0refChr7 14454 14 - 16696 TCCACCAACCTAGG -s Anc1.Anc1refChr4 15056 14 + 17549 TCCACCAACCTAGG -s Anc2.Anc2refChr7 10200 14 + 32194 TCCAACAACCTAGG -s mr.mrrefChr5 179414 14 + 294540 ATCACCAACTAAGG -s simCow_chr6.simCow.chr6 306164 14 + 602619 TCCAACAACCAAGG -s simDog_chr6.simDog.chr6 297056 14 + 593897 TCCAACAACCTAAG -s simHuman_chr6.simHuman.chr6 317139 14 + 601863 TCCACTGACCTAGG -s simRat_chr6.simRat.chr6 322831 14 + 647215 ATCACCAACTAAGG - -a -s simMouse_chr6.simMouse.chr6 331852 48 + 636262 TTTATTTTACTTGTACAAGTGTAAAGCATCGAAAACAACTCCTGAACA -s Anc0.Anc0refChr7 14468 47 - 16696 TTAGTTCTACCTGCTAGAGCATAAAGAATC-AAAACAAGTCCTGATCA -s Anc1.Anc1refChr4 15070 48 + 17549 TTAGTTCTACCTGCTAGAGCATAAAGAATCAAAAACAAGTCCTGATCA -s Anc2.Anc2refChr7 10214 47 + 32194 TTAGTACTACCTGCTAGAGCATAAAGAATC-AAAACAAGTCCTGATGA -s mr.mrrefChr5 179428 48 + 294540 TTTGTTCTACCTGTACGAGTATAAAGCATCAAAAACAACTCCTGAACA -s simCow_chr6.simCow.chr6 306178 43 + 602619 TTTA----ACCTGATAGCACCTAAAGAAAC-AAAACAAATCCTGATGA -s simDog_chr6.simDog.chr6 297070 47 + 593897 TCAGTACTACCTGCTAGAGTATAAAACTTC-AAAACAAGTCCTGCTGG -s simHuman_chr6.simHuman.chr6 317153 48 + 601863 TTAGTTCTACCTGCTAGAGCAGAAAGAATCAAACACAAGTCCTGATCA -s simRat_chr6.simRat.chr6 322851 48 + 647215 CTGGTTCTACCTGTACGAGTATAAAGCAACAAGAACAACTCCTGAGCA - -a -s simMouse_chr6.simMouse.chr6 331900 83 + 636262 CCCACTTCTATCCAATTGCACTATGCTCCCCTCCTGACCACCCACTCCAATCCACTTGAGTTATGCGCCCGCAACTCGCTCAT -s Anc0.Anc0refChr7 14518 42 - 16696 ----------------------------------------CCGCCTCC-ATCCAATCAAGCTACGTGCCCATGATTTGCTCCT -s Anc1.Anc1refChr4 15121 42 + 17549 ----------------------------------------CCGCCTCC-ATCCAATCAAGCTACGTGCCCATGATTTGCTCCT -s Anc2.Anc2refChr7 10264 42 + 32194 ----------------------------------------ACGCCTCC-AGCCAATCAAGCTACGCACCCATGATTTGCTCCT -s mr.mrrefChr5 179481 83 + 294540 CCCACTCCAATCCAATTGCACTATGCTCCCCTCCTGAGCACCGACTCCAATCCAATTGAGCTATGTGCCCACAATTCGCTCAT -s simCow_chr6.simCow.chr6 306224 39 + 602619 ----------------------------------------AC---TCC-AGTCTATCAAGATACCCACCTGTGATTTGCCCCT -s simDog_chr6.simDog.chr6 297120 40 + 593897 ------------------------------------------GCCTCA-AGCCAATCAAGCTAAGCACCCATGATTTGCTCCT -s simHuman_chr6.simHuman.chr6 317204 42 + 601863 ----------------------------------------CCACTTCC-ATGCCATCAAGCTACATGCCCATGATTTGCTCCT -s simRat_chr6.simRat.chr6 322906 83 + 647215 CCCACTCCAATCCAATTAATCTATGTGCCCCTCCTGAGCACGGACTCCAATCCAATTGAGCTATGTGCCCACAATTCGCTCAT - -a -s simMouse_chr6.simMouse.chr6 331983 18 + 636262 AGACACCAACAATCCCTT -s Anc0.Anc0refChr7 14560 18 - 16696 AGCCACAAAAAGCATCTT -s Anc1.Anc1refChr4 15163 18 + 17549 AGCCACAAAAAGCATCTT -s Anc2.Anc2refChr7 10306 18 + 32194 AACCACAAGAAGCATCTT -s mr.mrrefChr5 179564 18 + 294540 AGACACCAACAATCTCTT -s simCow_chr6.simCow.chr6 306274 18 + 602619 AATCCCAGTAAGCATTTT -s simDog_chr6.simDog.chr6 297160 18 + 593897 AACCAGAAGAAGCATCTT -s simHuman_chr6.simHuman.chr6 317246 17 + 601863 -GCCACAAAGAGCATCTT -s simRat_chr6.simRat.chr6 322989 18 + 647215 AGACACCAACAATCTCTT - -a -s simMouse_chr6.simMouse.chr6 332001 14 + 636262 TTTAGATAAAAAGC -s Anc0.Anc0refChr7 14578 14 - 16696 TTTAGATAAACGGC -s Anc1.Anc1refChr4 15181 14 + 17549 TTTAGATAAACGGC -s Anc2.Anc2refChr7 10324 14 + 32194 TCTAGATAAATGGC -s mr.mrrefChr5 179582 14 + 294540 TTTAGATAAACAGC -s simCow_chr6.simCow.chr6 306307 14 + 602619 TCTAGGTAAATGGT -s simDog_chr6.simDog.chr6 297178 14 + 593897 TCTAAATAAATCGC -s simHuman_chr6.simHuman.chr6 317263 14 + 601863 TTTAGATAGACGGC -s simRat_chr6.simRat.chr6 323007 14 + 647215 TTTAGATGAACAGC - -a -s simMouse_chr6.simMouse.chr6 332015 19 + 636262 CGGGTGTTTCAAATTAGTC -s Anc0.Anc0refChr7 14592 19 - 16696 TGGGTGCTTCAAATTACTC -s Anc1.Anc1refChr4 15195 19 + 17549 TGGGTGCTTCAAATTACTC -s Anc2.Anc2refChr7 10338 19 + 32194 TGGGTGCTTCAAATTACTC -s mr.mrrefChr5 179596 19 + 294540 TGGGTGCTTCAAATTACTC -s simCow_chr6.simCow.chr6 306321 19 + 602619 TGGGTGCCACAAATTACTC -s simDog_chr6.simDog.chr6 297192 19 + 593897 TGGGTGCTTCAAATTACTC -s simHuman_chr6.simHuman.chr6 317279 19 + 601863 TGCGTGCTTCAAATTACTC -s simRat_chr6.simRat.chr6 323021 19 + 647215 TGGGTGCTTCAAATTACTC - -a -s simMouse_chr6.simMouse.chr6 332034 2 + 636262 TT -s Anc0.Anc0refChr7 14619 2 - 16696 TA -s Anc1.Anc1refChr4 15222 2 + 17549 TA -s Anc2.Anc2refChr7 10365 2 + 32194 GG -s mr.mrrefChr5 179615 2 + 294540 TA -s simDog_chr6.simDog.chr6 297214 2 + 593897 GG -s simHuman_chr6.simHuman.chr6 317309 2 + 601863 TA -s simRat_chr6.simRat.chr6 323040 2 + 647215 TA - -a -s simMouse_chr6.simMouse.chr6 332036 23 + 636262 GGTGATATCAGATTTTGGTAATA -s Anc0.Anc0refChr7 14622 23 - 16696 GCTGATATGAGAATTTGGTCATG -s Anc1.Anc1refChr4 15225 23 + 17549 GCTGATATGAGAATTTGGTCATG -s Anc2.Anc2refChr7 10368 23 + 32194 GCTGATAAGAGCATTCGGTCATG -s mr.mrrefChr5 179617 23 + 294540 GGTGATATCAGATTTTGGTAATA -s simCow_chr6.simCow.chr6 306347 15 + 602619 --------GAACATTCGCTCATA -s simDog_chr6.simDog.chr6 297217 23 + 593897 GCTGATAAGAGCATTCGGTCATG -s simHuman_chr6.simHuman.chr6 317312 23 + 601863 GAGGATATGGGAATTTGGTCATG -s simRat_chr6.simRat.chr6 323042 23 + 647215 GGTGATATCAGATTTTGGCAATA - -a -s simMouse_chr6.simMouse.chr6 332059 46 + 636262 CACCAGACTGTTTTGAATCTGATACAAATGTTTCCTTCCACGGTAT -s Anc0.Anc0refChr7 14646 45 - 16696 -ACCAAACCGGGCTGAATCTGAAGGGATGTTTTTCTCACACAGTAT -s Anc1.Anc1refChr4 15249 45 + 17549 -ACCAAACCGGGCTGAATCTGAAGGGATGTTTTTCTCACACAGTAT -s Anc2.Anc2refChr7 10392 45 + 32194 -ACCAAAACGGGCTGAATCTGAGGGGACCTTTTTCTCACACAGCAT -s mr.mrrefChr5 179643 46 + 294540 CACCAGACTGTTTTGAATCTGAAACAATGGTTTCCTTCCACAGTAT -s simCow_chr6.simCow.chr6 306363 45 + 602619 -ACCAAAAGTGACTTAATATGAGCGGACTTTTTTCTCACACAACAC -s simDog_chr6.simDog.chr6 297241 45 + 593897 -ACCAAAACGGGCTGAAGCTGAGGGGTCCTTTTTCTTGTACAGCCT -s simHuman_chr6.simHuman.chr6 317336 45 + 601863 -ACTAAACCAGGCGGAATGTGAAGGGATGTTTTTCTCACACAGTAA -s simRat_chr6.simRat.chr6 323068 46 + 647215 CACCAGACTGTTTTGAATCTGAAACAATGGTTTCCTTTCACAATAT - -a -s simMouse_chr6.simMouse.chr6 332105 7 + 636262 ATGTAAT -s Anc0.Anc0refChr7 14691 7 - 16696 ATGTAAT -s Anc1.Anc1refChr4 15294 7 + 17549 ATGTAAT -s Anc2.Anc2refChr7 10438 7 + 32194 ATGTAAT -s mr.mrrefChr5 179689 7 + 294540 ATGTAAT -s simCow_chr6.simCow.chr6 306409 7 + 602619 ATGTAAT -s simDog_chr6.simDog.chr6 297287 7 + 593897 ATGCAAT -s simHuman_chr6.simHuman.chr6 317381 7 + 601863 ATGTAAT -s simRat_chr6.simRat.chr6 323114 7 + 647215 ATGTAAT - -a -s simMouse_chr6.simMouse.chr6 332112 8 + 636262 CTGTTCCT -s Anc0.Anc0refChr7 14698 8 - 16696 CCATTTTT -s Anc1.Anc1refChr4 15301 8 + 17549 CCATTTTT -s Anc2.Anc2refChr7 10445 8 + 32194 CCATTTTT -s mr.mrrefChr5 179696 8 + 294540 CCATTTTT -s simCow_chr6.simCow.chr6 306418 8 + 602619 CCATATTT -s simDog_chr6.simDog.chr6 297294 8 + 593897 CCATTCTT -s simHuman_chr6.simHuman.chr6 317388 8 + 601863 CCATTTTT -s simRat_chr6.simRat.chr6 323121 8 + 647215 CCATTTTT - -a -s simMouse_chr6.simMouse.chr6 332120 51 + 636262 AATATCTGAAGATGATCGTTCCAAGCAATGTCCTATCAGGGCCCATAACCA -s Anc0.Anc0refChr7 14706 5 - 16696 AATAT---------------------------------------------- -s Anc1.Anc1refChr4 15309 5 + 17549 AATAT---------------------------------------------- -s Anc2.Anc2refChr7 10453 5 + 32194 AATAT---------------------------------------------- -s mr.mrrefChr5 179704 5 + 294540 AATAT---------------------------------------------- -s simCow_chr6.simCow.chr6 306426 5 + 602619 AATAT---------------------------------------------- -s simDog_chr6.simDog.chr6 297302 5 + 593897 ACTAT---------------------------------------------- -s simHuman_chr6.simHuman.chr6 317396 5 + 601863 TATAT---------------------------------------------- -s simRat_chr6.simRat.chr6 323135 5 + 647215 CATGT---------------------------------------------- - -a -s simMouse_chr6.simMouse.chr6 332171 20 + 636262 TCCATTCACAGTAGGGCAAT -s Anc0.Anc0refChr7 14711 9 - 16696 TACGATCAC----------- -s Anc1.Anc1refChr4 15314 9 + 17549 TACGATCAC----------- -s Anc2.Anc2refChr7 10463 9 + 32194 TATGATCAC----------- -s mr.mrrefChr5 179709 20 + 294540 TCCATTCACAGTAGGGCAAT -s simCow_chr6.simCow.chr6 306436 9 + 602619 TATGATCAC----------- -s simDog_chr6.simDog.chr6 297312 9 + 593897 TGTGATCAC----------- -s simHuman_chr6.simHuman.chr6 317401 9 + 601863 TACGATCAC----------- -s simRat_chr6.simRat.chr6 323140 20 + 647215 TCCATTCACAACAGGACAAT - -a -s simMouse_chr6.simMouse.chr6 332191 98 + 636262 TATGCCAGATTATTGGCTGATAGTTCATGAGGATTAAAGGATTTAGTGACACTAGGCTAAATAAAACTTCTTGCAAACCACTCAGTCTCAATCCCCAA -s Anc0.Anc0refChr7 14720 12 - 16696 --------------------------------------------------------------------------------------TTCAATTGATAA -s Anc1.Anc1refChr4 15323 12 + 17549 --------------------------------------------------------------------------------------TTCAATTGATAA -s Anc2.Anc2refChr7 10472 12 + 32194 --------------------------------------------------------------------------------------TCCAATTGATAT -s mr.mrrefChr5 179729 98 + 294540 TATGCCAGATTATTGGCTGATAGTTCATGAGGATTAAAGGATTTAGTGACACTAGGCTAAATAAAACTTCTTGCAAACCACTCAGTCTCAATCCCCAA -s simCow_chr6.simCow.chr6 306445 12 + 602619 --------------------------------------------------------------------------------------CCCAACTGATAT -s simDog_chr6.simDog.chr6 297321 12 + 593897 --------------------------------------------------------------------------------------TCCAATTGATAT -s simHuman_chr6.simHuman.chr6 317410 12 + 601863 --------------------------------------------------------------------------------------TTCAATTGATGA -s simRat_chr6.simRat.chr6 323161 98 + 647215 TATACCAGATTATTGGCAGATAGCTCACAGGGCTTAAAGGACTGAATAACATTAGACTAAGTGAAACTTCTTGCAGACCACTCAGTCTCAATCCAGAA - -a -s simMouse_chr6.simMouse.chr6 332289 20 + 636262 GATGCTAGCTTCCATTTCCT -s Anc0.Anc0refChr7 14735 20 - 16696 GCTGCTAGCTTCCATTTGCT -s Anc1.Anc1refChr4 15338 20 + 17549 GCTGCTAGCTTCCATTTGCT -s Anc2.Anc2refChr7 10487 20 + 32194 GCTGTTAGCTTCCATTTGCT -s mr.mrrefChr5 179827 20 + 294540 GATGCTAGCTTCCATTTCCT -s simCow_chr6.simCow.chr6 306460 20 + 602619 GTTGTTGGCTACCATCTGGT -s simDog_chr6.simDog.chr6 297336 20 + 593897 ACTCTGAGCTTCGATTATCT -s simHuman_chr6.simHuman.chr6 317425 20 + 601863 GCTGCTAGCTTCCATTTGCT -s simRat_chr6.simRat.chr6 323259 20 + 647215 ACTACTAGCTTCCATTTCCT - -a -s simMouse_chr6.simMouse.chr6 332309 12 + 636262 ACATTATGATGT -s Anc0.Anc0refChr7 14757 10 - 16696 A--TCATGATGT -s Anc1.Anc1refChr4 15360 10 + 17549 A--TCATGATGT -s Anc2.Anc2refChr7 10509 10 + 32194 A--TCATAATGT -s mr.mrrefChr5 179847 10 + 294540 A--TTATGATGT -s simCow_chr6.simCow.chr6 306482 10 + 602619 A--TCATAATGT -s simDog_chr6.simDog.chr6 297358 10 + 593897 A--TTATAATGT -s simHuman_chr6.simHuman.chr6 317447 10 + 601863 A--TCTTGATGC -s simRat_chr6.simRat.chr6 323279 10 + 647215 A--TTGTGATGT - -a -s simMouse_chr6.simMouse.chr6 332321 37 + 636262 GTGTAGGTGGTAAGCCTAAAGATCTAAAGGGGTGTAC -s Anc0.Anc0refChr7 14772 36 - 16696 ATGTGGGCCATAAG-CCATAGATCTAAAGGGGGGTTC -s Anc1.Anc1refChr4 15375 37 + 17549 ATGTGGGCCATAAGCCCATAGATCTAAAGGGGGGTTC -s Anc2.Anc2refChr7 10524 36 + 32194 AGGTGGGCCATAAG-CCATAAATCTAAAGGGGGGTTC -s mr.mrrefChr5 179857 37 + 294540 GTGTAGGTGGTAAGCCTAAAGATCTAAAGGGGTGTAC -s simCow_chr6.simCow.chr6 306497 36 + 602619 GGGTGGTCCAGACA-CCATAAATCTAAAGGGGAGTTC -s simDog_chr6.simDog.chr6 297374 31 + 593897 AGGTGGGCCATAAG------AATCTGAAGGGGGGTCC -s simHuman_chr6.simHuman.chr6 317462 37 + 601863 ATGTGGGCCATAAGCCCATAGGTCTAAAGGGGCGTTC -s simRat_chr6.simRat.chr6 323289 37 + 647215 GTGTAGGTGGTAAGCCTAAAGATTTAAAGGGGTGTAC - -a -s simMouse_chr6.simMouse.chr6 332358 18 + 636262 TCATGTCAAACACCCACA -s Anc0.Anc0refChr7 14808 11 - 16696 CC------TACCCC-ACA -s Anc1.Anc1refChr4 15412 11 + 17549 CC------TACCCC-ACA -s Anc2.Anc2refChr7 10561 11 + 32194 CC------TATCCC-ACA -s mr.mrrefChr5 179894 17 + 294540 TCATGTCAAACACC-ACA -s simCow_chr6.simCow.chr6 306534 11 + 602619 CC------TCTCCC-ACA -s simDog_chr6.simDog.chr6 297406 11 + 593897 CC------TATCCC-ACC -s simHuman_chr6.simHuman.chr6 317499 11 + 601863 CC------CACTCC-ACA -s simRat_chr6.simRat.chr6 323326 17 + 647215 CCCACTCAAATACC-ACA - -a -s simMouse_chr6.simMouse.chr6 332376 17 + 636262 AAGGGATCAATTTACAG -s Anc0.Anc0refChr7 14823 17 - 16696 AAGGTATCAATTCACTG -s Anc1.Anc1refChr4 15427 17 + 17549 AAGGTATCAATTCACTG -s Anc2.Anc2refChr7 10576 17 + 32194 AAGGTATCAATTCACTG -s mr.mrrefChr5 179911 17 + 294540 AAGGGATCAATTTACAG -s simCow_chr6.simCow.chr6 306549 17 + 602619 CGGGTATATATTTACTG -s simDog_chr6.simDog.chr6 297421 17 + 593897 AAGGAATCAATTCACTG -s simHuman_chr6.simHuman.chr6 317514 17 + 601863 AAGGTAGCAATTGACTG -s simRat_chr6.simRat.chr6 323343 17 + 647215 AAGGGATCAATTTACAG - -a -s simMouse_chr6.simMouse.chr6 332393 8 + 636262 GCCCTAAA -s Anc0.Anc0refChr7 14842 8 - 16696 GTTCTAGA -s Anc1.Anc1refChr4 15446 8 + 17549 GTTCTAGA -s Anc2.Anc2refChr7 10595 8 + 32194 GTTCTAGA -s mr.mrrefChr5 179928 8 + 294540 GCCCTAAA -s simCow_chr6.simCow.chr6 306568 8 + 602619 GTTCTAGA -s simDog_chr6.simDog.chr6 297440 8 + 593897 GTTTTTGA -s simHuman_chr6.simHuman.chr6 317533 8 + 601863 GTTCTAGT -s simRat_chr6.simRat.chr6 323360 8 + 647215 GCCCTAGA - -a -s simMouse_chr6.simMouse.chr6 332401 3 + 636262 TTT -s Anc0.Anc0refChr7 14850 3 - 16696 TTT -s Anc1.Anc1refChr4 15454 3 + 17549 TTT -s Anc2.Anc2refChr7 10603 3 + 32194 TTT -s mr.mrrefChr5 179936 3 + 294540 TTT -s simCow_chr6.simCow.chr6 306578 3 + 602619 TTT -s simDog_chr6.simDog.chr6 297448 3 + 593897 TTT -s simHuman_chr6.simHuman.chr6 317541 3 + 601863 TTT -s simRat_chr6.simRat.chr6 323368 3 + 647215 TTT - -a -s simMouse_chr6.simMouse.chr6 332404 9 + 636262 CCGGACAGT -s Anc0.Anc0refChr7 14853 8 - 16696 CCAGAT-GT -s Anc1.Anc1refChr4 15457 8 + 17549 CCAGAT-GT -s Anc2.Anc2refChr7 10606 8 + 32194 CTAGAT-GT -s mr.mrrefChr5 179939 9 + 294540 CCGGACAGT -s simCow_chr6.simCow.chr6 306581 8 + 602619 CTAGAT-GT -s simDog_chr6.simDog.chr6 297451 8 + 593897 CTAGAC-GT -s simHuman_chr6.simHuman.chr6 317544 8 + 601863 CCAGAT-GT -s simRat_chr6.simRat.chr6 323383 9 + 647215 CCTTACTGC - -a -s simMouse_chr6.simMouse.chr6 332413 3 + 636262 GAG -s Anc0.Anc0refChr7 14861 3 - 16696 GAG -s Anc1.Anc1refChr4 15465 3 + 17549 GAG -s Anc2.Anc2refChr7 10614 3 + 32194 GAG -s mr.mrrefChr5 179948 3 + 294540 GAG -s simCow_chr6.simCow.chr6 306589 3 + 602619 ATG -s simDog_chr6.simDog.chr6 297459 3 + 593897 GAG -s simHuman_chr6.simHuman.chr6 317552 3 + 601863 GGG -s simRat_chr6.simRat.chr6 323399 3 + 647215 GGG - -a -s simMouse_chr6.simMouse.chr6 332416 10 + 636262 TAGCTTGCTG -s Anc0.Anc0refChr7 14890 10 - 16696 TACCACACTG -s Anc1.Anc1refChr4 15494 10 + 17549 TACCACACTG -s Anc2.Anc2refChr7 10643 10 + 32194 CACCACACTG -s mr.mrrefChr5 179951 10 + 294540 TAGCTTGCTG -s simCow_chr6.simCow.chr6 306618 9 + 602619 CACCA-GCTG -s simDog_chr6.simDog.chr6 297488 10 + 593897 CACCACACTG -s simHuman_chr6.simHuman.chr6 317582 10 + 601863 TACCACACTG -s simRat_chr6.simRat.chr6 323402 10 + 647215 AAGTCATCTG - -a -s simMouse_chr6.simMouse.chr6 332426 10 + 636262 AGTGAGGAGA -s Anc0.Anc0refChr7 14902 10 - 16696 AGTGAGGAGG -s Anc1.Anc1refChr4 15506 10 + 17549 AGTGAGGAGG -s Anc2.Anc2refChr7 10655 10 + 32194 AGCGAGGAGG -s mr.mrrefChr5 179961 10 + 294540 AGTGAGGAGA -s simCow_chr6.simCow.chr6 306629 10 + 602619 CACGAGGAGG -s simDog_chr6.simDog.chr6 297500 10 + 593897 AGCAAGGAGG -s simHuman_chr6.simHuman.chr6 317594 10 + 601863 AGTGAGGAGG -s simRat_chr6.simRat.chr6 323412 10 + 647215 AGTGGGGAGT - -a -s simMouse_chr6.simMouse.chr6 332436 40 + 636262 TAGCTGTAGGCCCGGAGTCCTCTTAGAAGAGAGCCAGGAA -s Anc0.Anc0refChr7 14918 37 - 16696 TAGCTGCAGGACCTGAGTCCTCTCAGGA---AGCTTGGTA -s Anc1.Anc1refChr4 15522 37 + 17549 TAGCTGCAGGACCTGAGTCCTCTCAGGA---AGCTTGGTA -s Anc2.Anc2refChr7 10671 37 + 32194 TAGCTGCAGGACCTGAGTCCTCTCAGGA---AGCTTGGTA -s mr.mrrefChr5 179971 40 + 294540 TAGCTGTAGGCCCGGAGTCCTCTTAGAAGAGAGCCAGGAA -s simCow_chr6.simCow.chr6 306645 37 + 602619 TAACTCCATGACCTGGGTCCTCTCAGTG---CTCTCAGGA -s simDog_chr6.simDog.chr6 297516 37 + 593897 TAGCTGTAGGACCTGAGTCCTCTCAGGA---AGCCTGGTA -s simHuman_chr6.simHuman.chr6 317610 37 + 601863 TGCCTGCAAGAATTGAGTCATCTCCAGA---AGCTTGGTA -s simRat_chr6.simRat.chr6 323422 40 + 647215 TAGTTGTAGGTCCTGAGTCCTCTTAGAAGAAAGCCTGGAA - -a -s simMouse_chr6.simMouse.chr6 332476 43 + 636262 TGCTAGCCAAGAATCTATGTCAGATTGCTCACTTAGGTCATGC -s Anc0.Anc0refChr7 14955 38 - 16696 TCCCAGCTAAAAATTTGTGGCAGA-----CAATTAGCTTAGAC -s Anc1.Anc1refChr4 15559 42 + 17549 TCCCAGCTAAAAATTTGTGGCAGACAG-TCAATTAGCTTAGAC -s Anc2.Anc2refChr7 10708 38 + 32194 TCCCAGCTAAAAATTTGTGGCAGA-----CAACTGTCTTAGAC -s mr.mrrefChr5 180011 43 + 294540 TGCTAGCCAAGAATCTATGTCAGATTGCTCACTTAGGTCATGC -s simCow_chr6.simCow.chr6 306684 38 + 602619 TTCCAGCCAAAAATTTTTATCAGC-----CAACTCATTTAGGC -s simDog_chr6.simDog.chr6 297553 38 + 593897 CCCCAGCTAAAAATTTGTGGCGGA-----CACCTGTCTAAGAC -s simHuman_chr6.simHuman.chr6 317647 42 + 601863 TCCCAGCTAATAGTTTGTGGCAGGCAG-TCAATTAGCTTAGAC -s simRat_chr6.simRat.chr6 323462 43 + 647215 TGCTAGCCAAGAATTCAAGTCAGATTCCTCACTTAAGTCACAC - -a -s simMouse_chr6.simMouse.chr6 332519 35 + 636262 AAGGATGGTTGACCAGATACCTTTCAAAATATACC -s Anc0.Anc0refChr7 14998 33 - 16696 AAGTATGG-TGCCCAGCTGTTTC-CCATACCTACC -s Anc1.Anc1refChr4 15606 33 + 17549 AAGTATGG-TGCCCAGCTGTTTC-CCATACCTACC -s Anc2.Anc2refChr7 10751 33 + 32194 AAGTATGG-TGCCAAGCTGTTTC-CCATACCTACC -s mr.mrrefChr5 180054 34 + 294540 AAGGATGGTTGACCAGATACCTT-CAAAATATACC -s simCow_chr6.simCow.chr6 306727 25 + 602619 AAGCATGG-TCGCTGGCTGT---------CCTACC -s simDog_chr6.simDog.chr6 297596 33 + 593897 AAGTATGA-TGCAAAGCTGTTTC-CCATACCTACC -s simHuman_chr6.simHuman.chr6 317694 33 + 601863 AAGTGTGG-TGCCCAGCTGTTTC-CTATAGCTACT -s simRat_chr6.simRat.chr6 323505 34 + 647215 AAGAAGGGTGGACCAGCTACCTT-CTAAATATACC - -a -s simMouse_chr6.simMouse.chr6 332554 38 + 636262 AGGTACATGTGATGGCTTCTCTTCTGCCACACTATTGA -s Anc0.Anc0refChr7 15031 35 - 16696 AGGTGCATGTGAT---TCCCCTTCTGCCACACTATTGA -s Anc1.Anc1refChr4 15639 35 + 17549 AGGTGCATGTGAT---TCCCCTTCTGCCACACTATTGA -s Anc2.Anc2refChr7 10784 35 + 32194 AGGTGCTATTGAT---TCCCCTTCCACCACACTATTGA -s mr.mrrefChr5 180088 38 + 294540 AGGTACATGTGATGGCTTCTCTTCTGCCACACTATTGA -s simCow_chr6.simCow.chr6 306752 35 + 602619 TGGTACGAACGAT---TCCCATTCCACCACACTATTGA -s simDog_chr6.simDog.chr6 297629 35 + 593897 AGGTGCTATTGAC---TTCCCTTCCACCACACAATAGA -s simHuman_chr6.simHuman.chr6 317728 35 + 601863 AGGTGCATGTGAT---TCCCCTTCTGCCGCACTGTTGA -s simRat_chr6.simRat.chr6 323539 38 + 647215 AGCTACATGTGATGGCTTCCCTTCTACCATACTATTAT - -a -s simMouse_chr6.simMouse.chr6 332592 73 + 636262 TACTCTCATTTTTTTGTTATCTGCTACAGGCAAACCGAACCATTGGTTCACAACGCAGTATTTATGATGTGAT -s Anc0.Anc0refChr7 15069 66 - 16696 T-------TTTATTTACTTGCTACTACAGGCATACAGAACCTTTGGCTCCTAAGTCAATCCTCACGGTGTTTT -s Anc1.Anc1refChr4 15677 66 + 17549 T-------TTTATTTACTTGCTACTACAGGCATACAGAACCTTTGGCTCCTAAGTCAATCCTCACGGTGTTTT -s Anc2.Anc2refChr7 10822 66 + 32194 T-------TTTATTTACTTGCTACTACAGGCATATAATGCTTTTGGCTTCTGAGTCAATCCTCACGGTGTTTG -s mr.mrrefChr5 180126 66 + 294540 T-------TTTTTTTGTTATCTGCTACAGGCAAACCGAACCATTGGTTCACAACGCAGTATTTATGATGTGAT -s simCow_chr6.simCow.chr6 306790 65 + 602619 T-------GTTCTTTACTTGCTACTACAGGCATATAATGGTTTTGGCTTCTGGGTCAATACTCTTGGTGTTT- -s simDog_chr6.simDog.chr6 297667 66 + 593897 T-------TTTATTTACTTGCCACCACAGGTATATAATGCTTTTGGTTTCCGAGTTGATCCTCACGATGTTTG -s simHuman_chr6.simHuman.chr6 317766 66 + 601863 T-------TTTATTTACTTGCTACTACAGGCATACAGAACCCCTGGCTCTTAAGTCAATGCTCGAGGTGTTTT -s simRat_chr6.simRat.chr6 323577 66 + 647215 T-------TTTTTTTGCTTTCTGCTACAGGCTCAAAAAACAATTGGTCCACAAAGCAGTATTTATAATCTGCT - -a -s simMouse_chr6.simMouse.chr6 332665 12 + 636262 ACTAAATGACAT -s Anc0.Anc0refChr7 15136 12 - 16696 GCTAGATGATAT -s Anc1.Anc1refChr4 15744 12 + 17549 GCTAGATGATAT -s Anc2.Anc2refChr7 10889 12 + 32194 GCTAGATGATAA -s mr.mrrefChr5 180192 12 + 294540 ACTAAATGACAT -s simCow_chr6.simCow.chr6 306856 12 + 602619 GTTAGATGATGG -s simDog_chr6.simDog.chr6 297734 12 + 593897 GCTAGATGGAAA -s simHuman_chr6.simHuman.chr6 317833 12 + 601863 GCTGGATGATAT -s simRat_chr6.simRat.chr6 323643 12 + 647215 ACTAAATTACAT - -a -s simMouse_chr6.simMouse.chr6 332677 16 + 636262 GGAGATTGTTGCACAG -s Anc0.Anc0refChr7 15175 16 - 16696 GGAAAGGGTTACACAG -s Anc1.Anc1refChr4 15783 16 + 17549 GGAAAGGGTTACACAG -s Anc2.Anc2refChr7 10928 16 + 32194 GGAAAGGATTACACAG -s mr.mrrefChr5 180204 16 + 294540 GGAGATTGTTGCACAG -s simCow_chr6.simCow.chr6 306895 15 + 602619 GTAAAGG-TTATACAG -s simDog_chr6.simDog.chr6 297773 16 + 593897 GGAAACAATTACACAA -s simHuman_chr6.simHuman.chr6 317872 16 + 601863 GGAAAGGGTTACACAG -s simRat_chr6.simRat.chr6 323655 16 + 647215 GGAAATTGTTGCAAAG - -a -s simMouse_chr6.simMouse.chr6 332693 152 + 636262 AGAAGTGTCCATATGAGGGGGCACCACCCAACCATTTTTTGACATGTCATAGCGTTAACCTACATTGAAAAACAATGAATATTGAGTATGATTCCAGAAAACACAGAAGTTTGTCTCTGTGTCATTTTAAAAATGTAGATACAGCTCCCAGC -s Anc0.Anc0refChr7 15192 32 - 16696 AG---TTTCCATATGATGGCGCACC---TAGCCTTTTT------------------------------------------------------------------------------------------------------------------ -s Anc1.Anc1refChr4 15800 32 + 17549 AG---TTTCCATATGATGGCGCACC---TAGCCTTTTT------------------------------------------------------------------------------------------------------------------ -s Anc2.Anc2refChr7 10945 32 + 32194 AG---TTTCCATATGATGGCACACT---TAGCCTTTTT------------------------------------------------------------------------------------------------------------------ -s mr.mrrefChr5 180220 139 + 294540 AG---TGTCCATATGAGGGGGCACC---CAACCATTTTTTGACATG-CATAGCGTTAACCTACATTGAAAAACAATGAATATTGAGTATGATTCCAGAAAACACA------TGTCTCTGTGTCATTTTAAAAATGTAGATACAGCTCCCAGC -s simCow_chr6.simCow.chr6 306911 31 + 602619 AG---TTTCCATAT-ATGGCCCACT---TAGCCTTTTT------------------------------------------------------------------------------------------------------------------ -s simDog_chr6.simDog.chr6 297790 32 + 593897 AA---TTTCCATCTGATGGCACACT---TGGCCTTTTT------------------------------------------------------------------------------------------------------------------ -s simHuman_chr6.simHuman.chr6 317889 32 + 601863 AG---TTTCCATATGATGGTGAACC---TAGCCTTTTT------------------------------------------------------------------------------------------------------------------ -s simRat_chr6.simRat.chr6 323671 139 + 647215 AG---TGTCCATATGAGGGTGCTCC---CAACCATACTTTGACATG-CATATCATTGACCTACTTTAAACAACAATGGATATTGAGTGTGATTTCAGAAAACACA------TGTCTCTGTTTCATTTTAAAAAAGTAGATCCAGCTCCCAAC - -a -s simMouse_chr6.simMouse.chr6 332845 53 + 636262 ATCACTTTGACTAACTGCATTGTTATGGCCCCAGTGTGTTGGACTCCAAACCA -s Anc0.Anc0refChr7 15224 52 - 16696 AGCACTTTGCCTAAGTGCTTCACCATGGCCACAGTGTGTT-GACCGCTTACCA -s Anc1.Anc1refChr4 15832 53 + 17549 AGCACTTTGCCTAAGTGCTTCACCATGGCCACAGTGTGTTAGACCGCTTACCA -s Anc2.Anc2refChr7 10977 52 + 32194 AGCACTTGACTCACGGGCTTCACCATAGCCGCAATGTGTT-TACTGCTTACCA -s mr.mrrefChr5 180359 53 + 294540 ATCACTTTGACTAACTGCATTGCTATGGCCACAGTGTGTTAGACCCCAAACCA -s simDog_chr6.simDog.chr6 297943 52 + 593897 AGCACTTGACTCACGGGCTTCACCATAGCCGCAATGTGTT-TACTGCTTACCA -s simHuman_chr6.simHuman.chr6 317921 53 + 601863 AGTACTCTGCCTAAATGCTTCACCATGGCCACAGTGTGTTAGACCGCTTACCA -s simRat_chr6.simRat.chr6 323810 53 + 647215 ATCACTTTGACTAACTGCACTGCTGTGGCTACAGTGGGTTAGACCCTGAACCA - -a -s simMouse_chr6.simMouse.chr6 332898 5 + 636262 TGTAC -s Anc0.Anc0refChr7 15276 3 - 16696 CGT-- -s Anc1.Anc1refChr4 15885 5 + 17549 CGTGC -s Anc2.Anc2refChr7 11029 3 + 32194 CGT-- -s mr.mrrefChr5 180412 5 + 294540 TGTAC -s simDog_chr6.simDog.chr6 297995 3 + 593897 CGT-- -s simHuman_chr6.simHuman.chr6 317974 5 + 601863 CATGC -s simRat_chr6.simRat.chr6 323878 5 + 647215 TGAAC - -a -s simMouse_chr6.simMouse.chr6 332903 4 + 636262 GCTC -s Anc0.Anc0refChr7 15279 3 - 16696 -CTC -s Anc1.Anc1refChr4 15890 4 + 17549 CCTC -s Anc2.Anc2refChr7 11032 3 + 32194 -CCC -s mr.mrrefChr5 180417 4 + 294540 GCTC -s simDog_chr6.simDog.chr6 297998 3 + 593897 -CCC -s simHuman_chr6.simHuman.chr6 317979 4 + 601863 CCTC -s simRat_chr6.simRat.chr6 323889 4 + 647215 ACTC - -a -s simMouse_chr6.simMouse.chr6 332907 80 + 636262 CCACACGTGACTATTTGTTAGCACAGCACAGAACCCATCATAACTACGGATAGCAGCTGTAGTAGCAGTCAGTGAGTGGG -s Anc0.Anc0refChr7 15282 74 - 16696 TGATATGAGACTATTTG-----ATAGCACAAACTCCATTGCAACTAAAGGTAGTCACTGAGGTAAC-ATTAGTGAGTGGA -s Anc1.Anc1refChr4 15894 75 + 17549 TGATATGAGACTATTTG-----ATAGCACAAACTCCATTGCAACTAAAGGTAGTCACTGAGGTAACAATTAGTGAGTGGA -s Anc2.Anc2refChr7 11035 74 + 32194 TGATATGAGACTATCGG-----ATGGCACAAATTCCATTTCAACTAAAGGTAGTCACAGAGGTAAT-ATTAGTGAGAGGA -s mr.mrrefChr5 180421 75 + 294540 CCACACGTGACTATTTG-----ATAGCACAGACTCCATTGTAACTACAGATAGCAGCTGAAGTAGCAGTTAGTGAGTGGG -s simCow_chr6.simCow.chr6 306942 59 + 602619 ----GTCACACTATAAG-----AT-----------TAACACAGCTAAAGGTGGCCACAGAGGTAAT-ATTAGTGAGAGGA -s simDog_chr6.simDog.chr6 286411 74 - 593897 TGATATGAGACTATCGG-----ATGGCACAAATTCCATTTCAACTAAAGGTAGTCTCAGAGTTAAT-GTTTGTAAGATGA -s simHuman_chr6.simHuman.chr6 317983 75 + 601863 TGATCAGAGACTATTTG-----ATAGCACGAACTCCGTTGCCACTAGAGGTTGTCACTGAGGTAACAAATAGTGAGTGGA -s simRat_chr6.simRat.chr6 323893 74 + 647215 CAACACTTGACTATTTG-----ATGGCACTGACTCCATTGTAACTATAAATAGCAGCTGAAGTAGCAGTT-GTGAGTGGG - -a -s simMouse_chr6.simMouse.chr6 332987 41 + 636262 GCTGAGTAGTAGAACTTTTATAAGATCTGTTTCATCTATAC -s Anc0.Anc0refChr7 15357 30 - 16696 ----------ATAACTTTGAT-GAATCTGTTTCACATATGC -s Anc1.Anc1refChr4 15978 40 + 17549 GCGGAGCAGTATAACTTTGAT-GAATCTGTTTCACATATGC -s Anc2.Anc2refChr7 11110 30 + 32194 ----------ATAACTTTGAT-GATTCTGTTTCACATCTGC -s mr.mrrefChr5 180505 41 + 294540 GCTGAGCAGTATAACTTTTATAAAATCTGTTTCATCTATAC -s simCow_chr6.simCow.chr6 307002 30 + 602619 ----------ACCACTTTGAT-GATTCTGTTTCACATTTGT -s simDog_chr6.simDog.chr6 286486 30 - 593897 ----------ATAACTTTGAT-CATTCTGTGTCACATCTGC -s simHuman_chr6.simHuman.chr6 318067 40 + 601863 GCGGAGCAGTATAATTTTGAT-GCATCAGTTTCACATATGA -s simRat_chr6.simRat.chr6 323976 41 + 647215 GCTTAGCAGTATAACTTTTATAAAATCTGGTTCATCTCTAC - -a -s simMouse_chr6.simMouse.chr6 333028 45 + 636262 TGCTAAGTATAGATGATGTCGTGTACATAAATGTGGACTGGTATA -s Anc0.Anc0refChr7 15387 45 - 16696 TGGTGAGTATAGATGATGTCATGTACACAAATGTGGTCTTGTATA -s Anc1.Anc1refChr4 16018 45 + 17549 TGGTGAGTATAGATGATGTCATGTACACAAATGTGGTCTTGTATA -s Anc2.Anc2refChr7 11143 45 + 32194 TGGTGAGTATAGATGATGTCATGTACACATATGTGGTCTTGTATA -s mr.mrrefChr5 180546 45 + 294540 TGGTAAGTATAGATGATGTCGTGTACACAAATGTGGACTGGTATA -s simCow_chr6.simCow.chr6 307036 45 + 602619 TGGTGAGTACACATGATGTCATGTACACACATGATGTCTTGTACA -s simDog_chr6.simDog.chr6 286519 44 - 593897 TGGTGAGTATAGATGATGTCATGTACACATATGTGGTCCT-TGTA -s simHuman_chr6.simHuman.chr6 318107 45 + 601863 TGGAGATTATAGCTGATGTCATATACACAAATATGGTCTTGTATA -s simRat_chr6.simRat.chr6 324017 45 + 647215 TGGTAAGTATTGATGATGTTGTGTACACAAATGTGGACTGGTATA - -a -s simMouse_chr6.simMouse.chr6 333073 38 + 636262 ACGACCAAGGGATGAAGACAAGGCTAGAGATGTTTAAA -s Anc0.Anc0refChr7 15439 37 - 16696 ACAACCCAGTGATAGAGAAAATGCTAAAAATATT-CAA -s Anc1.Anc1refChr4 16070 37 + 17549 ACAACCCAGTGATAGAGAAAATGCTAAAAATATT-CAA -s Anc2.Anc2refChr7 11195 37 + 32194 ACTACCCAGTGATAGAGAAAATGCTAAAAATATT-CAT -s mr.mrrefChr5 180591 37 + 294540 ACAACCAAGGGATGAAGACAAGGCTAGAGATGTT-AAA -s simCow_chr6.simCow.chr6 307088 35 + 602619 ATGAGCCAACATTAGAAAAAAGGCTAAAAAAATT---T -s simDog_chr6.simDog.chr6 286567 37 - 593897 ACTACCCAGTGATCGAGAAAATGCTAAAAATATT-CAT -s simHuman_chr6.simHuman.chr6 318159 37 + 601863 ACAACCTAGTGATAGAGAAGATGCTAAAAATATT-GTA -s simRat_chr6.simRat.chr6 324062 37 + 647215 ACAACCAAGGGATGAAGAGAAGGTTAGAGATGTT-AAA - -a -s simMouse_chr6.simMouse.chr6 333111 11 + 636262 ATTGTACTGGT -s Anc0.Anc0refChr7 15505 11 - 16696 ACCCCACTGGT -s Anc1.Anc1refChr4 16136 11 + 17549 ACCCCACTGGT -s Anc2.Anc2refChr7 11261 11 + 32194 ACCCCACTGGC -s mr.mrrefChr5 180628 11 + 294540 ATTGGACTGGT -s simCow_chr6.simCow.chr6 307151 9 + 602619 --CTTGCTGGA -s simDog_chr6.simDog.chr6 286633 11 - 593897 ACCCCACTGTC -s simHuman_chr6.simHuman.chr6 318225 11 + 601863 AACCCACTGGT -s simRat_chr6.simRat.chr6 324099 11 + 647215 ATTGGACTGGT - -a -s simMouse_chr6.simMouse.chr6 333122 78 + 636262 TCCAGTGGTCTGGGCCTTTGCCCCACAGGGGGCAGTCATGGTCCATGGCACAACAGAATGTGTAAGCAGACTCGGATG -s Anc0.Anc0refChr7 15516 78 - 16696 CCCGGTCGTCTGGGCCTTAGCCGCACAGGTTGTAGGCATAGTACATGACACAACAGAGTGTGTAAGCAGACTTAGAAG -s Anc1.Anc1refChr4 16147 78 + 17549 CCCGGTCGTCTGGGCCTTAGCCGCACAGGTTGTAGGCATAGTACATGACACAACAGAGTGTGTAAGCAGACTTAGAAG -s Anc2.Anc2refChr7 11272 78 + 32194 CCGGTTCGTCTAGGCCTTAGCTGCACAGGTTGTAGGCATAGTACATGACACGACAGAGTGTGGGAGCAGAGTTAGAAA -s mr.mrrefChr5 180639 78 + 294540 GCCAGTGGTCTGGGCCTTTGCCCCACAGGGGGCAGTCATGGTCCATGACACAACAGAATGTGTAAGCAGACTCGGAAG -s simCow_chr6.simCow.chr6 307161 35 + 602619 CCAGTTGGACTAGGACTTA-------------------------------------------GGATCAGAATTATACA -s simDog_chr6.simDog.chr6 286644 78 - 593897 CCGGTTCATCCAGGCATTAGCTGCACAGGTTGTAGGCATAGTACATGACACGACAGAGTGTGGGAGCAGAGTTAGAAG -s simHuman_chr6.simHuman.chr6 318236 76 + 601863 CCCTGTCGCCTGGGCCTTAACCTTATAGGTAGTAGGCTTACTTTGTAACACAGCAGT--GTGTAAGCAGACTTAGAAG -s simRat_chr6.simRat.chr6 324110 78 + 647215 GCCAGTGGTCTAGGCCTTTGCCCCACAGGGGGCAGTCATGGACCATGACACAACAGAATGTGTGAGCAGGCTCGGAAG - -a -s simMouse_chr6.simMouse.chr6 333200 4 + 636262 TATA -s Anc0.Anc0refChr7 15594 3 - 16696 TAT- -s Anc1.Anc1refChr4 16225 3 + 17549 TAT- -s Anc2.Anc2refChr7 11350 3 + 32194 TAT- -s mr.mrrefChr5 180717 4 + 294540 TATA -s simCow_chr6.simCow.chr6 307196 1 + 602619 T--- -s simDog_chr6.simDog.chr6 286722 3 - 593897 TAT- -s simHuman_chr6.simHuman.chr6 318321 3 + 601863 TAT- -s simRat_chr6.simRat.chr6 324188 4 + 647215 TATA - -a -s simMouse_chr6.simMouse.chr6 333204 23 + 636262 TGTCTTTTCCTTTTTGGGCCCAC -s Anc0.Anc0refChr7 15597 23 - 16696 TGTCTTTTCCTTTTTAGGTACAC -s Anc1.Anc1refChr4 16228 23 + 17549 TGTCTTTTCCTTTTTAGGTACAC -s Anc2.Anc2refChr7 11353 23 + 32194 TGTTTTTTCCTTTTTAGGTACTC -s mr.mrrefChr5 180721 23 + 294540 TGTCTTTTCCTTTTTGAGCCCAC -s simCow_chr6.simCow.chr6 307197 14 + 602619 ---------CTTTTTTAGTACTT -s simDog_chr6.simDog.chr6 286726 23 - 593897 TGTTTTTTCTTTTTTAGGCACTC -s simHuman_chr6.simHuman.chr6 318324 23 + 601863 TGTCTTTTCCTTCTAAGGTGCAC -s simRat_chr6.simRat.chr6 324192 23 + 647215 TGTCTTTTCCTTTTCCAGTCCAC - -a -s simMouse_chr6.simMouse.chr6 333227 22 + 636262 TTTCTATTAGGAATCTCATCTA -s Anc0.Anc0refChr7 15676 22 - 16696 TGTCTATTAGGTGTTTTGTCTA -s Anc1.Anc1refChr4 16307 22 + 17549 TGTCTATTAGGTGTTTTGTCTA -s Anc2.Anc2refChr7 11432 22 + 32194 TGTCTATTAATTGTTTTGTCTA -s mr.mrrefChr5 180744 22 + 294540 TTTCTATTAGGAATCTCATCTA -s simCow_chr6.simCow.chr6 307229 16 + 602619 ------TTAATGTTTTTGTCTC -s simDog_chr6.simDog.chr6 286805 22 - 593897 TGTCTATTAATTGTTTTGTCTA -s simHuman_chr6.simHuman.chr6 318424 22 + 601863 TGCCAATTAGGTGTTTTGTCGA -s simRat_chr6.simRat.chr6 324215 22 + 647215 TTTCTATTTGGAATCTCATCGA - -a -s simMouse_chr6.simMouse.chr6 333249 307 + 636262 TATTCTTTTAAAACACATAAACAATCGTCAAATCAGGATTTGATATTATAGAAACCACCAGGTGTTGTAATATGCAATaaagtcttgtagctgtgattcttcaagtctattttgtgtacataaagccttgCGTCTGCCACATCTTAAATACTGAATGGATATTACATTTAATGGGCGGCTATCATACCATAAGAGGCTTCCTTAGAGGAGCAAGGACAGGATGCAGCATAGGTATGAATTGTGATTTGCAAGCTATTGAAATATTGCAGCAATTTTGAGCTGTCAGTAGGGAAGAATAAAATTGAAA -s Anc0.Anc0refChr7 15698 42 - 16696 TATTCTTTTAAAATACATGAGCAATTGATAGATTAGGAATTG------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- -s Anc1.Anc1refChr4 16329 42 + 17549 TATTCTTTTAAAATACATGAGCAATTGATAGATTAGGAATTG------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- -s Anc2.Anc2refChr7 11469 42 + 32194 TAGTTTTTTAAAATACATGAGCAATTTATAGATTAGGAATCA------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- -s mr.mrrefChr5 180766 307 + 294540 TATTCTTTTAAAACACATGAACAATCGTCAAATTAGGATTTGATACTATAGAAACCACCAGGTGTTGTGATATGCAATaaagtcttgtagctgtgattcttcaagtctattttgcgtacataaagtcttgCGTCTGCCACATTTGAAATAATGAATGGATATTGCATATAATGGGCGACTATCATACCATAAGATGCTTTCTTAGCGGAGCCAGGACAGGATGCAGCATAGGTATGAATTGCGGTTTGCAAGTTATTGAAATATTGCAGCAATTCTGAGCTGTCAGTAGGGATGAATAAAATTGAAA -s simCow_chr6.simCow.chr6 307260 42 + 602619 TTTCCATATAAAATATATGAGCTCTTTTTTGATTGGGATTCA------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- -s simDog_chr6.simDog.chr6 286843 42 - 593897 TAGTTTTTTAAAATACATGAACAATTTATAGACTAGGAATCA------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- -s simHuman_chr6.simHuman.chr6 318446 42 + 601863 TGTACCTTACAAATGCGTGAGCAATTGATAGATCTGGACTTG------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- -s simRat_chr6.simRat.chr6 324237 307 + 647215 TATTCTTTTAAAACACATGAGGAATCATCAAATTGAGATTTGATACTATAGAAACCGCCAGGTGTTATGATATGCAATaaagtcttgtagttgtgattcttcaagtctattttgcgcatataaagtcttgtatctgCCACATTTGACATAATGAATGGATCTTGCATATAATGGGTGACTATCATACTATAAGATGCTTTCTTAGCGGAGCCAGGACAGGCTGCAGCATAGGTATGAATTGCTGTTTGCAAGTTATTGAAATATTGATGCAACTCTGAGCTGTTAGTAGGGATGAATAAAATTGAAA - -a -s simMouse_chr6.simMouse.chr6 333556 65 + 636262 TTAGAATACATGAGGACGACCTAATTGTCATAGACAACCTATAGTAGACATGTTAAATCACAATG -s mr.mrrefChr5 181074 65 + 294540 TTAGAATACATGAGGACAACCTAATTGTCATAAACAAACCATAGTAGACATGTTAAATCACAATG -s simRat_chr6.simRat.chr6 324545 65 + 647215 TTAGCATACATGAGGACAACCTAATTGGGATAAACAAACCATAGCAGACATGTTAGGTCATAATG - -a -s simMouse_chr6.simMouse.chr6 333621 90 + 636262 GGCTTATGTGGTAATATAGCATGATTGGTATGGGTAGGCCATAAACAGGCCATAAAAGAGACCCCAACTATACTACTCATACTGAGTTAC -s mr.mrrefChr5 181145 90 + 294540 AGCTTATGTGGTAATATAGCATGATTGGTATGGATAGGCCATAAACAGGCCATAAAAAAAACTCTGACTGTATTACTCATACTGAGTTAC -s simRat_chr6.simRat.chr6 324616 90 + 647215 AGCTTCTGTGTTAATCTATCAAGATTGGAAAGGATAGGCCATAAACAGGCCATAAAAAAAACTCTGACTGTATCACTCATACTGAATTAC - -a -s simMouse_chr6.simMouse.chr6 333711 38 + 636262 ACAGTACCAGAGGCTGTCTCACAAGAGAGTAGACTTTT -s mr.mrrefChr5 181235 38 + 294540 ACAGTACCAGAGGCTGTCTCACAAGAGAGTAGACTTTT -s simRat_chr6.simRat.chr6 324774 38 + 647215 ACAGTACAAGAGGTTTTCTCACAAGAGTGTAGACTTTT - -a -s simMouse_chr6.simMouse.chr6 333752 34 + 636262 TAATATTTATTGTTCTTTTCAGTGTGGGTAGGAG -s Anc1.Anc1refChr4 3 33 - 17549 TAATGTTTGCTCTTGATCTCAA-GTGGATAAGAA -s mr.mrrefChr5 181276 34 + 294540 TAATATTTGTTCTTCTTTTCAGTGTGGGTAAGAA -s simHuman_chr6.simHuman.chr6 282168 33 - 601863 TAATGTTTGCTCTTGATCTCAA-GTGGATAAGAA -s simRat_chr6.simRat.chr6 324815 34 + 647215 TAGTATTTGTTCTTTTTTTCGGTGTGGGTAAAAA - -a -s simMouse_chr6.simMouse.chr6 333786 33 + 636262 ACTTGTGTGGGCTGAGCATCACACCAATAAATC -s Anc1.Anc1refChr4 37 31 - 17549 ACT--TATAGACCAAGCCTCACACCCATTAATC -s mr.mrrefChr5 181311 33 + 294540 ACTTGTATGGGCTGAGCATCACACCAATAAATC -s simHuman_chr6.simHuman.chr6 282202 31 - 601863 ACT--TATAGACCAAGCCTCACACCCATTAATC -s simRat_chr6.simRat.chr6 324850 33 + 647215 ACTTGTATGGGCTGAGCATCACACCAATAAATC - -a -s simMouse_chr6.simMouse.chr6 333819 1 + 636262 C -s Anc1.Anc1refChr4 75 1 - 17549 T -s mr.mrrefChr5 181351 1 + 294540 C -s simHuman_chr6.simHuman.chr6 282240 1 - 601863 T -s simRat_chr6.simRat.chr6 324890 1 + 647215 C - -a -s simMouse_chr6.simMouse.chr6 333820 6 + 636262 ATGTCA -s Anc1.Anc1refChr4 76 6 - 17549 AGGTTA -s mr.mrrefChr5 181352 6 + 294540 ATGTCA -s simHuman_chr6.simHuman.chr6 282242 6 - 601863 AGGTTA -s simRat_chr6.simRat.chr6 324891 6 + 647215 ATGTCA - -a -s simMouse_chr6.simMouse.chr6 333826 12 + 636262 AATACATGCTAG -s Anc1.Anc1refChr4 83 12 - 17549 AACCAATGCCCG -s mr.mrrefChr5 181359 12 + 294540 AATACATGCTAG -s simHuman_chr6.simHuman.chr6 282249 12 - 601863 AACCAATGCCCG -s simRat_chr6.simRat.chr6 324898 12 + 647215 AATTTACACTAG - -a -s simMouse_chr6.simMouse.chr6 333838 10 + 636262 TCAAACATGT -s Anc1.Anc1refChr4 95 10 - 17549 TTAAGCACCA -s mr.mrrefChr5 181371 10 + 294540 TTAAGCATGA -s simHuman_chr6.simHuman.chr6 282262 10 - 601863 TTAAGCACCA -s simRat_chr6.simRat.chr6 324910 10 + 647215 TTAAGCATGA - -a -s simMouse_chr6.simMouse.chr6 333848 8 + 636262 AGGAGTGA -s Anc0.Anc0refChr4 13850 8 + 45765 ATCCATGA -s Anc1.Anc1refChr4 105 8 - 17549 ATCCATGA -s Anc2.Anc2refChr2 27070 8 - 27695 ATCCATGA -s mr.mrrefChr5 181381 8 + 294540 AGGAATGA -s simDog_chr6.simDog.chr6 287680 8 - 593897 ATCCATGA -s simHuman_chr6.simHuman.chr6 282272 8 - 601863 ATCTATAA -s simRat_chr6.simRat.chr6 324920 8 + 647215 AGGAATGA - -a -s simMouse_chr6.simMouse.chr6 333856 10 + 636262 GTGCCTCAAT -s Anc0.Anc0refChr4 13858 10 + 45765 GTGACTCAAG -s Anc1.Anc1refChr4 113 10 - 17549 GTGACTCAAG -s Anc2.Anc2refChr2 27078 10 - 27695 GTGACTCAAG -s mr.mrrefChr5 181389 10 + 294540 GTGCCTCAAT -s simDog_chr6.simDog.chr6 287699 10 - 593897 GTGACTCAAG -s simHuman_chr6.simHuman.chr6 282280 10 - 601863 GTGGCTCAAG -s simRat_chr6.simRat.chr6 324928 10 + 647215 GTGCCTCAGC - -a -s simMouse_chr6.simMouse.chr6 333894 3 + 636262 TCT -s Anc0.Anc0refChr4 13897 3 + 45765 TCT -s Anc1.Anc1refChr2 80754 3 - 144309 TCT -s Anc1.Anc1refChr4 151 3 - 17549 TCT -s Anc2.Anc2refChr2 27116 3 - 27695 TCT -s Anc2.Anc2refChr7 32 3 - 32194 TCT -s mr.mrrefChr0 44965 3 - 130230 TCT -s mr.mrrefChr5 181427 3 + 294540 TCT -s simDog_chr6.simDog.chr6 402266 3 - 593897 TCT -s simDog_chr6.simDog.chr6 287737 3 - 593897 TCT -s simHuman_chr6.simHuman.chr6 517333 3 - 601863 TCT -s simHuman_chr6.simHuman.chr6 282319 3 - 601863 TCT -s simRat_chr6.simRat.chr6 564882 3 - 647215 TCT -s simRat_chr6.simRat.chr6 324966 3 + 647215 TCT - -a -s simMouse_chr6.simMouse.chr6 333899 56 + 636262 CTTTTAGGGTATGCTAGTTTTCAGATAGAGTCTTATACACGTTTAGGGCGTTGGCT -s Anc0.Anc0refChr7 0 52 + 16696 GTCCCTGGG----ATAGTTATCAGATAGAGACTTGCACACTTTGCACACATCAGTT -s Anc1.Anc1refChr4 156 56 - 17549 GTCCCTGGGTAAGATAGTTATCAGATAGAGACTTGCACACTTTGCACACATCAGTT -s Anc2.Anc2refChr2 27121 52 - 27695 GTCCCTGGG----ATAGTTATAAGATAGAGATTTGCACACCTTGCACACACCAGGA -s mr.mrrefChr5 181432 56 + 294540 CTTTTAGGGTATGCTAGTTTTCAGATAGAGTCTTGTACACTTTTAAGGCATTGGTT -s simDog_chr6.simDog.chr6 287742 52 - 593897 GTCCCTGGG----ATAGTTATAAGATAGAGATTTGCACACCTTGCACACACCAGGA -s simHuman_chr6.simHuman.chr6 282324 56 - 601863 TCCCCTGGGTAAGATAGCCCTCAGATAGGTCCTTGCACACTCTGCACACATCACTT -s simRat_chr6.simRat.chr6 324971 56 + 647215 CTTTTGGAGTATGCTTGTTTTCAGATAGAATATTGTACATTTTTAAGGCATTGGTT - -a -s simMouse_chr6.simMouse.chr6 333955 2 + 636262 CT -s Anc0.Anc0refChr7 58 2 + 16696 CT -s Anc1.Anc1refChr4 218 2 - 17549 CT -s Anc2.Anc2refChr2 27179 2 - 27695 CT -s mr.mrrefChr5 181494 2 + 294540 CT -s simDog_chr6.simDog.chr6 287800 2 - 593897 CT -s simHuman_chr6.simHuman.chr6 282386 2 - 601863 CT -s simRat_chr6.simRat.chr6 325033 2 + 647215 CT - -a -s simMouse_chr6.simMouse.chr6 333957 22 + 636262 GACTTTGGATGGCTACTGATAT -s Anc0.Anc0refChr7 60 22 + 16696 CAGTCTGGACGGCCACTGACAT -s Anc1.Anc1refChr4 220 22 - 17549 CAGTCTGGACGGCCACTGACAT -s Anc2.Anc2refChr2 27181 22 - 27695 CAGGCTGGACAGCCACTGACTT -s mr.mrrefChr5 181496 22 + 294540 GACTTTGGATGGCTACTGATAT -s simDog_chr6.simDog.chr6 287804 22 - 593897 CAGGCTGGACAGCCACTGACTT -s simHuman_chr6.simHuman.chr6 282388 22 - 601863 CAATCTGGACGGCAACTAGAAC -s simRat_chr6.simRat.chr6 325035 22 + 647215 GACTTTGGATGGCTACTGAGTT - -a -s simMouse_chr6.simMouse.chr6 333979 41 + 636262 CACTAGGGCACCACAAACCATAAGCATAAGTGTGAAATTGT -s Anc0.Anc0refChr7 83 35 + 16696 CACAAGAGCACCACAATCCCTGAGCACATGT------TTGT -s Anc1.Anc1refChr4 243 41 - 17549 CACAAGAGCACCACAATCCCTGAGCACATGTGTGGAATTGT -s Anc2.Anc2refChr2 27204 35 - 27695 TGGAAGAGCACCACAATCCCTGAGCACATGC------CTGT -s mr.mrrefChr5 181519 41 + 294540 CACTAGAGCACCACAAACCCTAAGCATAAGTGTGAAATTGT -s simCow_chr6.simCow.chr6 307955 2 + 602619 ---------------------------------------GT -s simDog_chr6.simDog.chr6 287827 33 - 593897 TGGAAGAGCACCACAATCCCTGAGCACATGC------CT-- -s simHuman_chr6.simHuman.chr6 282411 41 - 601863 CACAAGAGCACCATAATTCCTGAGCACATGTGTGGAATTGC -s simRat_chr6.simRat.chr6 325058 41 + 647215 CACTAGAGTACCACAAACTCCAAGCATAAGTGTGAAATTGT - -a -s simMouse_chr6.simMouse.chr6 334020 18 + 636262 AACAAGTTAATTCTGAAG -s Anc0.Anc0refChr7 118 18 + 16696 AATACCACAATTCCCAAG -s Anc1.Anc1refChr4 284 18 - 17549 AATACCACAATTCCCAAG -s Anc2.Anc2refChr2 27239 18 - 27695 AATACCACAACTCCAGAG -s mr.mrrefChr5 181560 18 + 294540 AACAAGTTAATTCCCAAG -s simCow_chr6.simCow.chr6 307957 18 + 602619 AATACCACAACTCCAGAG -s simHuman_chr6.simHuman.chr6 282457 18 - 601863 AATACCACAATTCCCAAG -s simRat_chr6.simRat.chr6 325099 18 + 647215 AACAAGTTAATTCCCAAG - -a -s simMouse_chr6.simMouse.chr6 334038 60 + 636262 CTTCTGCCCAAGAAGACAGCATTTCTACGTTAAACAGCCTACACCACTTAATCCCTACAC -s Anc0.Anc0refChr7 138 59 + 16696 CA-GTGCTAGTGATGACAACTTTGCTATGTAAAACAGTCTCCACCTATAAATCTCCTCAC -s Anc1.Anc1refChr4 304 60 - 17549 CATGTGCTAGTGATGACAACTTTGCTATGTAAAACAGTCTCCACCTATAAATCTCCTCAC -s Anc2.Anc2refChr2 27259 59 - 27695 CA-GTGCTAGTGATGATAACTTCATTATGTTAAACAGTCTCCACTTAGAAATCACCGCAA -s mr.mrrefChr5 181580 60 + 294540 CTTGTGCCCAAGAAGACAGCATTGCTACGTAAAACAGCCTACACCACTTAATCTCTTCAC -s simCow_chr6.simCow.chr6 307977 59 + 602619 CA-GTGCTAGTGATGATAACTTCATTATGTTAAACAGTCTCCACTTAGAAATCACCGCAA -s simHuman_chr6.simHuman.chr6 282477 60 - 601863 CATGTACTAGTGAGGACGATCTTGCTGTATAAAACAGTCTCCACCTGTCTATCTCCTCAC -s simRat_chr6.simRat.chr6 325119 60 + 647215 CCTGTGCCTAAGAAGACAGCATTGCTACGTAAAACAGCCTACACCATTTGATCTCTTCAA - -a -s simMouse_chr6.simMouse.chr6 334098 8 + 636262 GTATTTAG -s Anc0.Anc0refChr7 215 8 + 16696 GTATTTAG -s Anc1.Anc1refChr4 382 8 - 17549 GTATTTAG -s Anc2.Anc2refChr2 27336 8 - 27695 GTATTTAG -s mr.mrrefChr5 181640 8 + 294540 GTATTTAG -s simCow_chr6.simCow.chr6 308054 8 + 602619 GTATTTAG -s simHuman_chr6.simHuman.chr6 282555 8 - 601863 TTATTCAG -s simRat_chr6.simRat.chr6 325179 8 + 647215 GGATTTAG - -a -s simMouse_chr6.simMouse.chr6 334106 14 + 636262 TGTAGCAAATTTGC -s Anc0.Anc0refChr7 223 12 + 16696 TGTAGCAAATTT-- -s Anc1.Anc1refChr4 390 14 - 17549 TGTAGCAAATTTTC -s Anc2.Anc2refChr2 27344 12 - 27695 TGTAGCAAATTT-- -s mr.mrrefChr5 181648 14 + 294540 TGTAGCAAATTTGC -s simCow_chr6.simCow.chr6 308063 12 + 602619 TGTAGCAAATTT-- -s simHuman_chr6.simHuman.chr6 282563 14 - 601863 TGTTGTAAATCTTC -s simRat_chr6.simRat.chr6 325187 14 + 647215 TGTAGCAAATTTGC - -a -s simMouse_chr6.simMouse.chr6 334120 13 + 636262 TAAGTTGTTGGAT -s Anc0.Anc0refChr7 235 12 + 16696 -GGGTTTTGGGAT -s Anc1.Anc1refChr4 404 13 - 17549 TGGGTTTTGGGAT -s Anc2.Anc2refChr2 27356 12 - 27695 -GGATCGTGGGCT -s mr.mrrefChr5 181662 13 + 294540 TAAGTTTTTGGAT -s simCow_chr6.simCow.chr6 308075 12 + 602619 -GGATCGTGGGCT -s simHuman_chr6.simHuman.chr6 282580 13 - 601863 TGGGTTTTGGGAT -s simRat_chr6.simRat.chr6 325201 13 + 647215 TAAATTTTTGGAT - -a -s simMouse_chr6.simMouse.chr6 334133 58 + 636262 GGAGCTTCAGTGCAGAGTTGTCAGCATCTAACCTTGTCACTATAGGGGACATGTTACT -s Anc0.Anc0refChr7 247 10 + 16696 GGTCCTTTGG------------------------------------------------ -s Anc1.Anc1refChr4 417 33 - 17549 GGTCCTTTGGTGTACAGCT-TCA----CCAACTGTGGC-------------------- -s Anc2.Anc2refChr2 27368 10 - 27695 GGCCCTTTGG------------------------------------------------ -s mr.mrrefChr5 181675 58 + 294540 GGTGCTTCAGTGCATAGTTGTCAGCATCTAACCTTGTCACTATAGGGGACATGTTACT -s simCow_chr6.simCow.chr6 308087 10 + 602619 GGCCCTTTGG------------------------------------------------ -s simHuman_chr6.simHuman.chr6 282601 33 - 601863 GGTCCTTTGGTGTACAGCT-TCA----CCAACTGTGGC-------------------- -s simRat_chr6.simRat.chr6 325214 58 + 647215 GGTGCTTCAATACATGGTCGTCAGCACTTAACCTTCTCACTATAGGGGACATGTCACT - -a -s simMouse_chr6.simMouse.chr6 334191 146 + 636262 ACTTCTCACATGGACCTGAGCACACAGGGTTGGTTGTGGACGAAACTCTATGCTAATAAACCATTGTATGGAAAGCTTTTGGGCTCCGAGACTACCAGCTGATTTGGAGATCTTAACTTTGGAATGTCATTAACAAGCCCAGCTGC -s Anc0.Anc0refChr7 257 50 + 16696 ----------------------------------------------------------------------GTATACTT--------------AACCATGTGATTGTGAGA--------GTGGAATGTGATTAAGGAACCCAG---- -s Anc1.Anc1refChr4 450 65 - 17549 -------------------------------------------------------AGAATCCTTTCCATGGTATACTT--------------AACCATGTGATTGTGAGA--------GTGGAATGTGATTAAGGAACCCAG---- -s Anc2.Anc2refChr2 27378 50 - 27695 ----------------------------------------------------------------------GTATACTT--------------AAAGTTGTGATTGTGGGA--------GTCAAATGTGACTAAGGAACCATG---- -s mr.mrrefChr5 181737 117 + 294540 ACTTCTCACATGAACCTGAG-----------------------------ATGCTAATAAACCATTGCATGGAAAGCTTTTGGGCTCCGAGACAACCAGCTGATTTGGAGATCTTAACTTTGGAATGTCATTAACAAGCCCAGCTGC -s simCow_chr6.simCow.chr6 308097 49 + 602619 ----------------------------------------------------------------------GTATACTT--------------AAAGTTGTGGCTGTAG-A--------GTCAAATGTATCTAAGGAACCTGG---- -s simDog_chr6.simDog.chr6 287860 48 - 593897 -----------------------------------------------------------------------CAGTCCT--------------AAAGTTTTGATTGTGGGA--------GT-AAATGAGACTAAGGAACCATG---- -s simHuman_chr6.simHuman.chr6 282634 65 - 601863 -------------------------------------------------------AGAATCCTTTCCATGGTATACTT--------------AACCATGTGATGGTGAGA--------GTGGAATGTTGTTAAGGAACCCAG---- -s simRat_chr6.simRat.chr6 325276 117 + 647215 ACTTTTTACATGAACCTAGG-----------------------------ATGTTATTAAATGGTGACATAGAAAGCTTTAGGGCTCTGAGACAGCCAGCTGATTTGGAGGTCTTGCCTTTGGAATGTCATTAACAAGCCCAGCTAC - -a -s simMouse_chr6.simMouse.chr6 334337 36 + 636262 AGGGCTTGCCCTAGCAAGGTCACTTTGGGTTCTGCC -s Anc0.Anc0refChr7 307 35 + 16696 AGC-CTTGCCCTAGCAAGGTAACTTCAGATCTCACT -s Anc1.Anc1refChr4 515 35 - 17549 AGC-CTTGCCCTAGCAAGGTAACTTCAGATCTCACT -s Anc2.Anc2refChr2 27428 35 - 27695 AGC-CTTACCCTAGCAAGGTAACTTCAGATCTCACT -s mr.mrrefChr5 181854 35 + 294540 AGG-CTTGCCCTAGCAAGGTCACTTTGGATCCTGCC -s simCow_chr6.simCow.chr6 308150 35 + 602619 AGC-CTTACCCTAGCAAGGCAACTACAGATTTCACC -s simDog_chr6.simDog.chr6 287908 32 - 593897 ----TTCACCCTAGCATAGTAACTTCAGATCTCACT -s simHuman_chr6.simHuman.chr6 282699 35 - 601863 AGC-CTTGCCCTAGCAAGGTAGCTTCAGATCTCACT -s simRat_chr6.simRat.chr6 325393 35 + 647215 AGG-CTTGCTCTAGCAAGGTCACTTTGGATCCTGCC - -a -s simMouse_chr6.simMouse.chr6 334373 15 + 636262 GGTGTATGCCTGAAT -s Anc0.Anc0refChr7 342 14 + 16696 AGTGGA-GCCCTAAT -s Anc1.Anc1refChr4 550 14 - 17549 AGTGGA-GCCCTAAT -s Anc2.Anc2refChr2 27463 14 - 27695 AGTGGA-CCCCTGAA -s mr.mrrefChr5 181889 15 + 294540 AGTGTATGCCTGAAT -s simCow_chr6.simCow.chr6 308185 14 + 602619 AGTGGA-TCCGTGAA -s simDog_chr6.simDog.chr6 287944 14 - 593897 AGTGGA-CCCCTGAA -s simHuman_chr6.simHuman.chr6 282734 14 - 601863 AGTGGA-GCCCAAGT -s simRat_chr6.simRat.chr6 325428 15 + 647215 AGTGTATGCCTGAAT - -a -s simMouse_chr6.simMouse.chr6 334388 22 + 636262 TGCACCAGCCGTTTTTTGGGAG -s Anc0.Anc0refChr7 356 16 + 16696 CTCAAGCCCTG------GGGTT -s Anc1.Anc1refChr4 564 16 - 17549 CTCAAGCCCTG------GGGTT -s Anc2.Anc2refChr2 27477 16 - 27695 CTCAAGCCCTG------AGGTT -s mr.mrrefChr5 181904 19 + 294540 TGCACCCGCCGTTT---GGGAG -s simCow_chr6.simCow.chr6 308201 14 + 602619 TCCAAGCCCTG--------GTT -s simDog_chr6.simDog.chr6 287958 16 - 593897 CTGAAGGGCTG------AGGTT -s simHuman_chr6.simHuman.chr6 282748 16 - 601863 AACAAGCCCTG------GGGGT -s simRat_chr6.simRat.chr6 325443 19 + 647215 TGCCCCCACCATCT---AGGAG - -a -s simMouse_chr6.simMouse.chr6 334410 9 + 636262 GAATTGAGC -s Anc0.Anc0refChr7 372 9 + 16696 GACTCAAGC -s Anc1.Anc1refChr4 580 9 - 17549 GACTCAAGC -s Anc2.Anc2refChr2 27493 9 - 27695 GACTTCAGC -s mr.mrrefChr5 181923 9 + 294540 GACTCAAGC -s simCow_chr6.simCow.chr6 308215 9 + 602619 GACTTGAGC -s simDog_chr6.simDog.chr6 287979 9 - 593897 GACTTCAGC -s simHuman_chr6.simHuman.chr6 282764 9 - 601863 GACTCAAAC -s simRat_chr6.simRat.chr6 325462 9 + 647215 GGCTCAAGC - -a -s simMouse_chr6.simMouse.chr6 334419 4 + 636262 TTGG -s Anc0.Anc0refChr7 381 4 + 16696 TGGG -s Anc1.Anc1refChr4 589 4 - 17549 TGGG -s Anc2.Anc2refChr2 27502 4 - 27695 TGGG -s mr.mrrefChr5 181932 4 + 294540 TTGG -s simCow_chr6.simCow.chr6 308225 4 + 602619 TGAG -s simDog_chr6.simDog.chr6 287988 4 - 593897 TGGG -s simHuman_chr6.simHuman.chr6 282773 4 - 601863 TGGG -s simRat_chr6.simRat.chr6 325471 4 + 647215 TTTG - -a -s simMouse_chr6.simMouse.chr6 334423 51 + 636262 GGGGCCGCACAAAGTAAATTTTTGTAGAATTATCCTCGGACTAATTCTATG -s Anc0.Anc0refChr7 483 36 + 16696 CAGACAGCA---------------TACAATCAGTCTGGGGATGATTCCGTA -s Anc1.Anc1refChr4 691 36 - 17549 CAGACAGCA---------------TACAATCAGTCTGGGGATGATTCCGTA -s Anc2.Anc2refChr2 27638 36 - 27695 CAGACAGCA---------------TACAATCAGTGTGGGGATGATTCCGTA -s mr.mrrefChr5 182026 36 + 294540 GAGGCCGCA---------------TAGAATTAGTCTGGGGATAATTCCATA -s simCow_chr6.simCow.chr6 308356 36 + 602619 AGGACTACA---------------TAGAATCAGTTTGAGGATGATTCCATA -s simDog_chr6.simDog.chr6 288127 36 - 593897 CAGATAGCA---------------CACAATCAGTGTGGGGATGATTCTGTT -s simHuman_chr6.simHuman.chr6 282875 36 - 601863 CAGACAGCA---------------TACAATCAGTCTGGGGATGATTCCTTA -s simRat_chr6.simRat.chr6 325607 36 + 647215 GAGGCGGCA---------------TAGAATTAGTCTGAGGATAATTCCATA - -a -s simMouse_chr6.simMouse.chr6 334474 2 + 636262 CT -s Anc0.Anc0refChr7 524 2 + 16696 CT -s Anc1.Anc1refChr4 732 2 - 17549 CT -s Anc2.Anc2refChr2 27679 2 - 27695 CT -s Anc2.Anc2refChr7 20243 2 - 32194 ct -s mr.mrrefChr5 182067 2 + 294540 CT -s simCow_chr6.simCow.chr6 308397 2 + 602619 CT -s simDog_chr6.simDog.chr6 288377 2 - 593897 CT -s simDog_chr6.simDog.chr6 473594 2 + 593897 ca -s simDog_chr6.simDog.chr6 288168 1 - 593897 T- -s simHuman_chr6.simHuman.chr6 282916 2 - 601863 CT -s simRat_chr6.simRat.chr6 325648 2 + 647215 CT - -a -s simMouse_chr6.simMouse.chr6 334476 135 + 636262 GCCTGAGATTACAAGAGTCTAATGAATTGTAATCACTGGTGACATACAGAGGTACTGTTGAGGTTGATGGTGTGCAAGTGCATATGCACCCACCTTTATTCGGACAGACCTAAGTGGCCTGCCAACAGCGAAAGA -s Anc0.Anc0refChr7 526 12 + 16696 CTTTGGGA---------------------------------------------------------------------------------------------------------------------------AAGA -s Anc1.Anc1refChr4 734 12 - 17549 GTTTGGGA---------------------------------------------------------------------------------------------------------------------------AAGA -s Anc2.Anc2refChr2 27681 12 - 27695 CCCAGGAA---------------------------------------------------------------------------------------------------------------------------AAGA -s Anc2.Anc2refChr7 20245 12 - 32194 CTTTTATA---------------------------------------------------------------------------------------------------------------------------AAGA -s mr.mrrefChr5 182069 12 + 294540 GCTTGAGA---------------------------------------------------------------------------------------------------------------------------AAGA -s simCow_chr6.simCow.chr6 308413 12 + 602619 CTTTTATA---------------------------------------------------------------------------------------------------------------------------AAGA -s simCow_chr6.simCow.chr6 308399 12 + 602619 CCCAGGAT---------------------------------------------------------------------------------------------------------------------------AAGA -s simDog_chr6.simDog.chr6 348838 11 - 593897 -TTTTATG---------------------------------------------------------------------------------------------------------------------------AAGA -s simDog_chr6.simDog.chr6 288169 7 - 593897 -----GAA---------------------------------------------------------------------------------------------------------------------------AAGA -s simHuman_chr6.simHuman.chr6 282918 12 - 601863 GTTTGGGA---------------------------------------------------------------------------------------------------------------------------AAGA -s simRat_chr6.simRat.chr6 325650 12 + 647215 ACTTCAGA---------------------------------------------------------------------------------------------------------------------------AAGA - -a -s simMouse_chr6.simMouse.chr6 334611 53 + 636262 ACCCTTAACAAAGACTCACACCTCTTGTTACCTCTTGTTTTTTTTATACCCAC -s Anc0.Anc0refChr7 538 41 + 16696 AGATTCCCCATAAGATAACATTTCTTGTT----------TCTGCTAA--CTTA -s Anc1.Anc1refChr4 746 41 - 17549 AGATTCCCCATAAGATAACATTTCTTGTT----------TCTGCTAA--CTTA -s Anc2.Anc2refChr7 20257 41 - 32194 GGATTCCCAATAAGATATCATTTCTGGTT----------TCTGCCTA--CTTA -s mr.mrrefChr5 182081 43 + 294540 ACCCTTAACATAGAATCACACCTCTTGTT----------TTTTTTATACCTAC -s simCow_chr6.simCow.chr6 308425 38 + 602619 GGATTA---ATTAGATATAATTTCTGGTT----------TCTGCTAG--ATTA -s simDog_chr6.simDog.chr6 348849 38 - 593897 GGCTCCCCATCA-GATATCGTTTTTGGC------------CTTCCTA--CGTT -s simDog_chr6.simDog.chr6 288379 16 - 593897 -----------------------CTGGT------------CTGCCTA--CATA -s simHuman_chr6.simHuman.chr6 282939 37 - 601863 AGATTCCCCATAAGATAACA----TTGTT----------CCTGCTAG--CTGA -s simRat_chr6.simRat.chr6 325662 43 + 647215 ACCCTTAACGTAGAATCACACTTCTTGAT----------TTTTTTATATTTAC - -a -s simMouse_chr6.simMouse.chr6 334664 8 + 636262 CCATTGAT -s Anc0.Anc0refChr7 579 8 + 16696 CCCTTGAT -s Anc1.Anc1refChr4 787 8 - 17549 CCCTTGAT -s Anc2.Anc2refChr7 20298 8 - 32194 CCCATGGT -s mr.mrrefChr5 182124 8 + 294540 CCATTGAT -s simCow_chr6.simCow.chr6 308465 6 + 602619 CCCATG-- -s simDog_chr6.simDog.chr6 348887 8 - 593897 CTCACAGG -s simDog_chr6.simDog.chr6 288395 6 - 593897 C--ATGGT -s simHuman_chr6.simHuman.chr6 282976 8 - 601863 CCCTTTAT -s simRat_chr6.simRat.chr6 325705 8 + 647215 CCATTCCT - -a -s simMouse_chr6.simMouse.chr6 334672 5 + 636262 ATCTC -s Anc0.Anc0refChr7 587 5 + 16696 TCTCA -s Anc1.Anc1refChr4 795 5 - 17549 TCTCA -s Anc2.Anc2refChr7 20312 5 - 32194 TCTCA -s mr.mrrefChr5 182132 5 + 294540 TTCTA -s simCow_chr6.simCow.chr6 308474 5 + 602619 TATCA -s simDog_chr6.simDog.chr6 348901 5 - 593897 TCGCA -s simDog_chr6.simDog.chr6 288407 5 - 593897 TCTCA -s simHuman_chr6.simHuman.chr6 282984 5 - 601863 TCTCA -s simRat_chr6.simRat.chr6 325713 5 + 647215 TTCTA - -a -s simMouse_chr6.simMouse.chr6 334677 9 + 636262 AGTGTGGAT -s Anc0.Anc0refChr7 592 9 + 16696 GGTGTGGAT -s Anc1.Anc1refChr4 800 9 - 17549 GGTGTGGAT -s Anc2.Anc2refChr7 20317 9 - 32194 GCTGTGGAT -s mr.mrrefChr5 182137 9 + 294540 AGTGTGGAT -s simCow_chr6.simCow.chr6 308479 9 + 602619 GCTATGGAT -s simDog_chr6.simDog.chr6 288412 9 - 593897 GCTGTGGAT -s simHuman_chr6.simHuman.chr6 282989 9 - 601863 GGCCTGGAT -s simRat_chr6.simRat.chr6 325718 9 + 647215 AGGGTGGAT - -a -s simMouse_chr6.simMouse.chr6 334686 48 + 636262 AGCCATAAGTCATCTTTGTTGTTGGATTTGCAGTTTTAGTAGTAGCTT -s Anc0.Anc0refChr7 601 38 + 16696 TGCCATTAATCATATTTGTTGTTGGAT----------AGTAGTTTCTT -s Anc1.Anc1refChr4 809 48 - 17549 TGCCATTAATCATATTTGTTGTTGGATTCACTGAGATAGTAGTTTCTT -s Anc2.Anc2refChr7 20326 38 - 32194 TGCCATTAATCATATTTATTGCTGTAT----------AGTAGTTTCTT -s mr.mrrefChr5 182146 48 + 294540 AGCCATAAGTCATCTTTGTTGTTGGATTTGCAGTTTTAGTAGTTGCTT -s simCow_chr6.simCow.chr6 308488 38 + 602619 TGCCATTACTCATGATTATAGCTGTTT----------AGCAGCTTCTT -s simDog_chr6.simDog.chr6 348906 38 - 593897 TGCCATTAATCATATTTATTGCTGTAT----------AGTAGTTTCTT -s simDog_chr6.simDog.chr6 288421 38 - 593897 TGTCATTAATCATATTTATTGCTGTAT----------AGTAGTTTCTT -s simHuman_chr6.simHuman.chr6 282998 48 - 601863 TGCAATCAATCATGTTTGTTGTTGGATTCACTGAGATAGTAGTTTCTT -s simRat_chr6.simRat.chr6 325727 48 + 647215 AGCTATAAGTCATCTTTGTCGGTGGATTTGCAGTTTTAGTAGTTGCTT - -a -s simMouse_chr6.simMouse.chr6 334734 15 + 636262 GTAGTCAATCTGCTA -s Anc0.Anc0refChr7 640 14 + 16696 ATGTTAT-GCTAATA -s Anc1.Anc1refChr4 858 14 - 17549 ATGTTAT-GCTAATA -s Anc2.Anc2refChr7 20365 14 - 32194 ATGTTAT-GCTAAAA -s mr.mrrefChr5 182195 14 + 294540 GTAGTCT-TCTGCTA -s simCow_chr6.simCow.chr6 308527 14 + 602619 TCAATGT-GTTAATC -s simDog_chr6.simDog.chr6 348945 14 - 593897 ATGTTAT-GCTAAAA -s simDog_chr6.simDog.chr6 288460 14 - 593897 ATGTTAT-GCTAAAA -s simHuman_chr6.simHuman.chr6 283047 14 - 601863 ATGTTAT-CCTAATA -s simRat_chr6.simRat.chr6 325776 14 + 647215 GTAGTCT-TCTGCTA - -a -s simMouse_chr6.simMouse.chr6 334749 21 + 636262 AACAGGGCTATCCTCTCTCAC -s Anc0.Anc0refChr7 670 21 + 16696 AATGGAGTTATTACCTATCAC -s Anc1.Anc1refChr4 888 21 - 17549 AATGGAGTTATTACCTATCAC -s Anc2.Anc2refChr7 20397 21 - 32194 AATGAAGTTATGACCTATCAC -s mr.mrrefChr5 182209 21 + 294540 AACAGAGCTATTATCTCTCAC -s simCow_chr6.simCow.chr6 308557 21 + 602619 AAGGGAGTTACCAACTATCCC -s simDog_chr6.simDog.chr6 348977 20 - 593897 AATGAAGTTATGACCT-TCAC -s simDog_chr6.simDog.chr6 288492 20 - 593897 AATTAAGTTATGACCT-TCAC -s simHuman_chr6.simHuman.chr6 283077 21 - 601863 AAAGGAGTTACTACCTATAAC -s simRat_chr6.simRat.chr6 325790 21 + 647215 AATAGAGACATTATCTCTCAC - -a -s simMouse_chr6.simMouse.chr6 334770 5 + 636262 CCATT -s Anc0.Anc0refChr7 724 5 + 16696 CCATT -s Anc1.Anc1refChr4 942 5 - 17549 CCATT -s Anc2.Anc2refChr7 20451 5 - 32194 CCATC -s mr.mrrefChr5 182250 5 + 294540 CCATT -s simCow_chr6.simCow.chr6 308617 5 + 602619 CCATC -s simDog_chr6.simDog.chr6 349020 5 - 593897 GCAGC -s simDog_chr6.simDog.chr6 288535 5 - 593897 CCATG -s simHuman_chr6.simHuman.chr6 283134 5 - 601863 CCATT -s simRat_chr6.simRat.chr6 325831 5 + 647215 CCATT - -a -s simMouse_chr6.simMouse.chr6 334775 15 + 636262 TTGATCATAATAGTG -s Anc0.Anc0refChr7 729 15 + 16696 CTGGTCATAATAGTG -s Anc1.Anc1refChr4 947 15 - 17549 CTGGTCATAATAGTG -s Anc2.Anc2refChr7 20456 15 - 32194 CCTGTCAGAATAGTG -s mr.mrrefChr5 182255 15 + 294540 CTGATCATAATAGTG -s simCow_chr6.simCow.chr6 308622 15 + 602619 CCTGTCAAAATAGTG -s simDog_chr6.simDog.chr6 288540 15 - 593897 ACTGTCAGAATTGTG -s simHuman_chr6.simHuman.chr6 283139 15 - 601863 CTGGTCATAATAGTG -s simRat_chr6.simRat.chr6 325836 15 + 647215 CTGCTCATAATAGTG - -a -s simMouse_chr6.simMouse.chr6 334790 13 + 636262 GTTGTGCTGAGAT -s Anc0.Anc0refChr7 745 13 + 16696 GTTGTCCTGAGAC -s Anc1.Anc1refChr4 963 13 - 17549 GTTGTCCTGAGAC -s Anc2.Anc2refChr7 20472 13 - 32194 GTTGTCCTGAGAC -s mr.mrrefChr5 182270 13 + 294540 GTTGTGCTGAGAT -s simCow_chr6.simCow.chr6 308638 12 + 602619 GTTGTTCTGAGA- -s simDog_chr6.simDog.chr6 288556 13 - 593897 GTTGTCCTGAGAC -s simHuman_chr6.simHuman.chr6 283155 13 - 601863 GTTGTCCTGAAAC -s simRat_chr6.simRat.chr6 325851 13 + 647215 GTTGTGCTAAGAT - -a -s simMouse_chr6.simMouse.chr6 334803 50 + 636262 GTGGTCATTTCTCACTGTTCTATACATAGAAGATTGTAGGCATTCTAGGG -s Anc0.Anc0refChr7 759 46 + 16696 GTGGTC----TTCAATGTTATATACATAGAGGATTGTAGACATTGTAAGA -s Anc1.Anc1refChr4 977 50 - 17549 GTGGTCACCTTTCAATGTTATATACATAGAGGATTGTAGACATTGTAAGA -s Anc2.Anc2refChr7 20486 46 - 32194 GTGGTC----TTCAATGTTATATACATAGAGGATTGTAGACATTGTAAGA -s mr.mrrefChr5 182283 50 + 294540 GTGGTCACTTCTCACTGTTCTATACATAGAAGATTGTAGGCATTCTAGGG -s simCow_chr6.simCow.chr6 308650 38 + 602619 ----------TTCAATGTTATATA--TAAAGTATTGTAGACATTGTAACA -s simDog_chr6.simDog.chr6 288570 46 - 593897 GTGGTC----TTCAATGTTGTATACAGGGAGGATTTCAGACATTGTAAGA -s simHuman_chr6.simHuman.chr6 283174 50 - 601863 GTGGTCACCTTTCTATGTTATATACATAGACGATTGTACACATTGTACGA -s simRat_chr6.simRat.chr6 325864 29 + 647215 GAGGTCACTTCTCACTGTTTTATACATTG--------------------- - -a -s simMouse_chr6.simMouse.chr6 334853 62 + 636262 GCTTGGCCCCATCACTAGTCCTGCAAGTCTAGAACGACACTTATGTCATCCAGTAAAGAGTT -s Anc0.Anc0refChr7 808 62 + 16696 ACCATACCCCTACACTGGCCTAGCAAGGCTGGAAGTAAACTTATTTGGTCCAGTGAAGAGTC -s Anc1.Anc1refChr4 1030 62 - 17549 ACCATACCCCTACACTGGCCTAGCAAGGCTGGAAGTAAACTTATTTGGTCCAGTGAAGAGTC -s Anc2.Anc2refChr7 20535 62 - 32194 ACCATACCCCTACACTGGCCTAGCGAGGCTGGAAGTAAACTTGTTTGGTCCAGTGAGGAGTC -s mr.mrrefChr5 182333 62 + 294540 GCTTGGCCCCATCACTAGTCTTGCAAGGCTAGAACGACACTTATGTGATCCAGTAAAGAGTC -s simCow_chr6.simCow.chr6 308691 62 + 602619 ACAACACCTCTACACTGGCTTAGCCAGGCTGGAAGTAAACTTGTTTGGTCCAGCGAGGAGTT -s simDog_chr6.simDog.chr6 288619 60 - 593897 ACCTTACCC--ACACTGGGCTAGCGAGGCTGGAGATAGACTTGTTTGGTCCAGTGAGAAGGC -s simHuman_chr6.simHuman.chr6 283227 62 - 601863 ACCATACCCCTACACCGGCCTAGCAAGGCTGAAAGTAAACTTATTTGGTTCAGTGAAGAGTC -s simRat_chr6.simRat.chr6 325893 42 + 647215 --------------------TTGCAAGGCTAGAAAGAGACTTATATGATCCAGTAAAGAGTC - -a -s simMouse_chr6.simMouse.chr6 334915 12 + 636262 ATGCATGCTCCC -s Anc0.Anc0refChr7 871 12 + 16696 ATGCACACTCCC -s Anc1.Anc1refChr4 1093 12 - 17549 ATGCACACTCCC -s Anc2.Anc2refChr7 20598 12 - 32194 ATGCACACTTCC -s mr.mrrefChr5 182395 12 + 294540 ATGCATGCTCCC -s simCow_chr6.simCow.chr6 308754 12 + 602619 ATGCACACTTCC -s simDog_chr6.simDog.chr6 288680 12 - 593897 ATGGGCACATCC -s simHuman_chr6.simHuman.chr6 283290 12 - 601863 ATGCACACTCCC -s simRat_chr6.simRat.chr6 325935 12 + 647215 ATGCATGCTCCC - -a -s simMouse_chr6.simMouse.chr6 334927 35 + 636262 AAAATGCATAGGTTCATGTGCATTCTGGACACTGC -s Anc0.Anc0refChr7 883 35 + 16696 AAAGTGCATATGTCCATGTGCACCCAGGACACCGC -s Anc1.Anc1refChr4 1105 35 - 17549 AAAGTGCATATGTCCATGTGCACCCAGGACACCGC -s Anc2.Anc2refChr7 20610 35 - 32194 AAGGTGCATATGTCCATGTGCAGCCAGGACACCCC -s mr.mrrefChr5 182407 35 + 294540 AAAGTGCATAGGTTCATGTGCACTCAGGACACTGC -s simCow_chr6.simCow.chr6 308766 32 + 602619 AATGTGCATATGTCC---TGCTGCCAGGACACCTC -s simDog_chr6.simDog.chr6 288692 33 - 593897 ATGCTGCATATA--CATGTGGAGCCCAGACACCCC -s simHuman_chr6.simHuman.chr6 283302 35 - 601863 AAAGTGGATATGTCCATGTGCACCCAGACCATAGT -s simRat_chr6.simRat.chr6 325948 35 + 647215 AAAGTGCTCAGGTTCATGTACACTCAGGACACTGC - -a -s simMouse_chr6.simMouse.chr6 334962 22 + 636262 TTTGAACTTTTCATTCTCTCAC -s Anc0.Anc0refChr7 918 22 + 16696 TTTGATCTTTTCCTTTATTCAC -s Anc1.Anc1refChr4 1140 22 - 17549 TTTGATCTTTTCCTTTATTCAC -s Anc2.Anc2refChr7 20645 22 - 32194 CTTGATCTTTTCCTTTATTCAC -s mr.mrrefChr5 182442 22 + 294540 TTTGAACTTTTCATTCTCTCAC -s simCow_chr6.simCow.chr6 308814 22 + 602619 CCATATCCTCTCCTTTATTCAC -s simDog_chr6.simDog.chr6 288725 22 - 593897 CTTGATCTTTTCCTTTATTCAC -s simHuman_chr6.simHuman.chr6 283337 22 - 601863 TTTGACCTTTTCTTATATTGCC -s simRat_chr6.simRat.chr6 325983 22 + 647215 TTTGAACTTCTCATTCTCACAC - -a -s simMouse_chr6.simMouse.chr6 334984 6 + 636262 ATATTC -s Anc0.Anc0refChr0 0 6 + 26507 aaactc -s Anc1.Anc1refChr6 0 6 + 197743 AAACTC -s Anc2.Anc2refChr6 0 6 + 7137 cacctc -s mr.mrrefChr5 182464 6 + 294540 ATATTC -s simCow_chr6.simCow.chr6 294939 6 - 602619 cacctc -s simHuman_chr6.simHuman.chr6 319698 6 + 601863 AAAAGC -s simRat_chr6.simRat.chr6 326005 6 + 647215 ATACTC - -a -s simMouse_chr6.simMouse.chr6 334990 1 + 636262 G -s Anc0.Anc0refChr0 6 1 + 26507 g -s Anc1.Anc1refChr6 6 1 + 197743 g -s Anc2.Anc2refChr6 6 1 + 7137 g -s mr.mrrefChr5 182470 1 + 294540 G -s simCow_chr6.simCow.chr6 294945 1 - 602619 g -s simRat_chr6.simRat.chr6 326014 1 + 647215 G - -a -s simMouse_chr6.simMouse.chr6 334991 11 + 636262 CAATGCTAGGT -s Anc0.Anc0refChr0 7 11 + 26507 cattagtagtt -s Anc1.Anc1refChr6 7 11 + 197743 cattagtAGTT -s Anc2.Anc2refChr6 8 11 + 7137 cattagtagta -s mr.mrrefChr5 182471 11 + 294540 CAATGTTAGGT -s simCow_chr6.simCow.chr6 294947 11 - 602619 catgagtagta -s simDog_chr6.simDog.chr6 306561 10 + 593897 -attagtagta -s simHuman_chr6.simHuman.chr6 319704 4 + 601863 -------AGTT -s simRat_chr6.simRat.chr6 326015 11 + 647215 CAATGTTAATT - -a -s simMouse_chr6.simMouse.chr6 335002 2 + 636262 AG -s Anc0.Anc0refChr0 18 2 + 26507 ag -s Anc1.Anc1refChr6 18 2 + 197743 AG -s Anc2.Anc2refChr6 19 2 + 7137 gg -s mr.mrrefChr5 182482 2 + 294540 AG -s simCow_chr6.simCow.chr6 294963 2 - 602619 gg -s simDog_chr6.simDog.chr6 306571 2 + 593897 gg -s simHuman_chr6.simHuman.chr6 319708 2 + 601863 AG -s simRat_chr6.simRat.chr6 326026 2 + 647215 TG - -a -s simMouse_chr6.simMouse.chr6 335004 3 + 636262 CTC -s Anc0.Anc0refChr0 23 3 + 26507 ctc -s Anc1.Anc1refChr6 23 3 + 197743 CTC -s Anc2.Anc2refChr6 24 3 + 7137 atc -s mr.mrrefChr5 182484 3 + 294540 CTC -s simCow_chr6.simCow.chr6 294968 3 - 602619 atc -s simDog_chr6.simDog.chr6 306576 3 + 593897 aac -s simHuman_chr6.simHuman.chr6 319713 3 + 601863 CTC -s simRat_chr6.simRat.chr6 326028 3 + 647215 CTC - -a -s simMouse_chr6.simMouse.chr6 335007 2 + 636262 CT -s Anc0.Anc0refChr0 26 2 + 26507 Ct -s Anc1.Anc1refChr6 26 2 + 197743 CT -s Anc2.Anc2refChr6 109 2 + 7137 Ct -s mr.mrrefChr5 182487 2 + 294540 CT -s simCow_chr6.simCow.chr6 295062 1 - 602619 C- -s simDog_chr6.simDog.chr6 306661 2 + 593897 ct -s simHuman_chr6.simHuman.chr6 319716 2 + 601863 CT -s simRat_chr6.simRat.chr6 326031 2 + 647215 TT - -a -s simMouse_chr6.simMouse.chr6 335009 1 + 636262 A -s Anc0.Anc0refChr0 33 1 + 26507 a -s Anc1.Anc1refChr6 33 1 + 197743 A -s Anc2.Anc2refChr6 116 1 + 7137 a -s mr.mrrefChr5 182489 1 + 294540 A -s simDog_chr6.simDog.chr6 306668 1 + 593897 a -s simHuman_chr6.simHuman.chr6 319723 1 + 601863 A -s simRat_chr6.simRat.chr6 326033 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 335010 61 + 636262 CCTGCAAAACTGTGCAACAGCACTAGCACTTCACCATGTCACCACTTATGAGTCTGAACCC -s Anc0.Anc0refChr0 34 48 + 26507 CCTCCTGATATCAAAAGGAGTATTAGGTTTTCCTCATGT-------------TCTAACCCC -s Anc1.Anc1refChr6 34 48 + 197743 CCTCCTGATATCAAAAGGAGTATTAGGTTTTCCTCATGT-------------TCTAACCCC -s Anc2.Anc2refChr6 117 48 + 7137 CATCCTGATATCAAAAGGAGTATTAGGTTTTCCTCATGT-------------AGTAACTTC -s mr.mrrefChr5 182490 61 + 294540 CCTGCAAAACTGTGCAACAGCACTAGCACTTCACCATGTCACCACTTATGAGTCTGAACCC -s simCow_chr6.simCow.chr6 295063 47 - 602619 CATCCTGACATCAAGTGGAGTATTAGTTTTACCTCCCAT-------------GGTAA-TTC -s simDog_chr6.simDog.chr6 306680 48 + 593897 catcctgttatcaaaaggtctattaGGTTTTCCTCATGT-------------AGTAACTTC -s simHuman_chr6.simHuman.chr6 319724 48 + 601863 CCTCCTGATTTTAAAAGGAGTATTATATTTTCCTCATGT-------------TCTAACCCC -s simRat_chr6.simRat.chr6 326034 61 + 647215 CCTGCAAGTCTGTGTAACAGCACTAGCATTTGATCATGTTATCATTTAGAAGTCTCAACTC - -a -s simMouse_chr6.simMouse.chr6 335071 3 + 636262 CCC -s Anc0.Anc0refChr0 82 3 + 26507 TGC -s Anc1.Anc1refChr6 82 3 + 197743 TGC -s Anc2.Anc2refChr6 165 3 + 7137 TAC -s mr.mrrefChr5 182551 3 + 294540 CGC -s simCow_chr6.simCow.chr6 295110 3 - 602619 ATC -s simDog_chr6.simDog.chr6 306728 3 + 593897 TAC -s simHuman_chr6.simHuman.chr6 319772 3 + 601863 TGC -s simRat_chr6.simRat.chr6 219561 3 + 647215 CGC -s simRat_chr6.simRat.chr6 326095 3 + 647215 CGC - -a -s simMouse_chr6.simMouse.chr6 335074 9 + 636262 TACTCATTT -s Anc0.Anc0refChr0 88 9 + 26507 TACTCATTT -s Anc1.Anc1refChr6 88 9 + 197743 TACTCATTT -s Anc2.Anc2refChr6 171 9 + 7137 TATGCATCC -s mr.mrrefChr5 182554 9 + 294540 TACTCACTT -s simCow_chr6.simCow.chr6 295116 3 - 602619 TAT------ -s simDog_chr6.simDog.chr6 306734 9 + 593897 TATGCATCC -s simHuman_chr6.simHuman.chr6 319778 9 + 601863 TACTCATTT -s simRat_chr6.simRat.chr6 219564 9 + 647215 TACTCACTT -s simRat_chr6.simRat.chr6 326098 9 + 647215 TACTCACTT - -a -s simMouse_chr6.simMouse.chr6 335083 108 + 636262 GTGTGTGTGCGTTTGTGTTGGTCAATACAGATTCATGGTGATAAGAGAGGCAAACTCAATTAAAAAATAAACTTTAGTGGCAACACAAAAACAAACTTCAGTGACAGT -s Anc0.Anc0refChr0 280 91 + 26507 GTGT-----CTCTTGG-CTGGTCAATACTGACTCA---TAGTAACAGAGGCAAAG----T---AAAATAAACTTCAATGGCAACAC-AAAATAAACTTCAGTGGCAAT -s Anc1.Anc1refChr6 280 97 + 197743 GTGT-----CTCTTGG-CTGGTCAATACTGACTCATAGTAGTAACAGAGGCAAAG----TTGAAAAATAAACTTCAATGGCAACAC-AAAATAAACTTCAGTGGCAAT -s Anc2.Anc2refChr6 363 91 + 7137 GTGT-----ATCTTGG-CTGGTCAATACTGACTCA---TAGTAACAGAGTCAAAG----T---GCCATTAACTCCAATGGCAGCAC-CAAATAACCTTCAATGGCAAT -s mr.mrrefChr5 182563 108 + 294540 GTGTGTGTGCTATTGTTCTGGTCAATACTGATTCATGGTGGTAAGAGAGGCAAAGTCAATTAAAAAATAATCTTCAGTGGCAACACAAAAACAAACTTCAGTGACAAT -s simCow_chr6.simCow.chr6 308962 31 + 602619 ------------------TGGTCAGTACTCACTGA---TGGTAACAGAATAA-------------------------------------------------------- -s simDog_chr6.simDog.chr6 288881 91 - 593897 GTGT-----ATCTTGG-CTAGTCAATACTGATTCA---TAGTAACAGAGTCAAAG----T---GCCATTAACTCCAATGGCAGCAC-CAAATAACCTTCAATGGCAAT -s simHuman_chr6.simHuman.chr6 320057 97 + 601863 GTGT-----CTCTTGC-CTGGTGAAAACTGACTCATAGTAGTAGCAGAGGTAAAG----TTGAAAAATAAACTTTAATGGCAACAT-AAAATAAACTATAGTGGCAAC -s simRat_chr6.simRat.chr6 219573 108 + 647215 GTGTGTGTGCTATTGTTCTGGTCAATACTGATTCATGCTGGTAAGAGAGGCAAGGTCAATTAAAAGATAATCTTCAGTAGCAACACAAAAACAAACCTCAATGACAAT -s simRat_chr6.simRat.chr6 326107 108 + 647215 GTGTGTGTGCTATTGTTCTGGTCAATACTGATTCATGGTGGTACGAGAGGCAAAGTCAATTAAAAAATAATCTTCAGTGCCAACACAAAAACAAACTTCAGTGACAAT - -a -s simMouse_chr6.simMouse.chr6 335191 44 + 636262 GCATTGTATGACAGTGTTATTGCATGTGCATGAAATTATCTCCC -s Anc0.Anc0refChr0 377 30 + 26507 CTATTTTATGGCAATATCC-TTCCTATACA-------------C -s Anc1.Anc1refChr6 383 30 + 197743 CTATTTTATGGCAATATCC-TTCCTATACA-------------C -s Anc2.Anc2refChr6 460 30 + 7137 CTTTTTCAAGGCAATATCC-TTCCTATACA-------------C -s mr.mrrefChr5 182671 43 + 294540 CCATTGTATGACAGTGTTA-CACCTGTGCATGAAATGGTCCCCC -s simDog_chr6.simDog.chr6 288978 30 - 593897 CTTTTTCAAGGCAATATCC-TTCCTATACA-------------C -s simHuman_chr6.simHuman.chr6 320160 30 + 601863 CTATTCTATGGCAATACCC-TTACTATACA-------------C -s simRat_chr6.simRat.chr6 219681 43 + 647215 CCATTGTATGAAAGTGTTA-CACCTGTGCATGAAATGGTCCCCC -s simRat_chr6.simRat.chr6 326215 41 + 647215 CCAT--TATGACAGTGTTA-CACCTGTGCATGAGATGGTCCCCC - -a -s simMouse_chr6.simMouse.chr6 335235 47 + 636262 CCTATTCTGCACCAAAGCTAGCAAGGGGTATATGAAAGTTATTCCAT -s Anc0.Anc0refChr0 407 44 + 26507 CCTGGGTAG---CAAATTGAGTGCTGATCATGGGATAACTATTACAT -s Anc1.Anc1refChr6 413 44 + 197743 CCTGGGTAG---CAAATTGAGTGCTGATCATGGGATAACTATTACAT -s Anc2.Anc2refChr6 490 44 + 7137 CCTGGGTAG---CAGCTTGTGTGCTGATCATGGGATAACTATGTCAT -s mr.mrrefChr5 182714 47 + 294540 CCTGTTCTGCACCAAAGCTAGCAAGGGGTATAGGAAAGTTATTACAT -s simCow_chr6.simCow.chr6 308993 19 + 602619 ----------------------------CTTGGGATAGTGATCTCAT -s simDog_chr6.simDog.chr6 289022 44 - 593897 CCTGGGTAG---CAGCTTGTGTGCTGATCATGAGATAACTATGTCAT -s simHuman_chr6.simHuman.chr6 320190 44 + 601863 CCTTGGAAG---CAAATTGAGTGCTGATCGTGGGATAAGCCTTACAT -s simRat_chr6.simRat.chr6 219724 47 + 647215 CCTGTTCTGCACCAAAGCTAGCAAGGGGTATAGGAAGGTTATTACAT -s simRat_chr6.simRat.chr6 326256 47 + 647215 CCTGTTCTGCACCAAAGCTAGCAAGGGGTATAGGAAAGTTATTACAT - -a -s simMouse_chr6.simMouse.chr6 335282 9 + 636262 TGAAGTAAT -s Anc0.Anc0refChr0 457 9 + 26507 TGTGGCCAT -s Anc1.Anc1refChr6 463 9 + 197743 TGTGGCCAT -s Anc2.Anc2refChr6 540 9 + 7137 TGTGGCCAT -s mr.mrrefChr5 182761 9 + 294540 TGAAGTAAT -s simCow_chr6.simCow.chr6 309018 9 + 602619 TGTGGCCAT -s simDog_chr6.simDog.chr6 289072 9 - 593897 TGTGGCCAT -s simHuman_chr6.simHuman.chr6 320240 9 + 601863 TGTGGCCAT -s simRat_chr6.simRat.chr6 219771 9 + 647215 TGAAATCCA -s simRat_chr6.simRat.chr6 326303 9 + 647215 TGAAGTAAT - -a -s simMouse_chr6.simMouse.chr6 335291 2 + 636262 AT -s Anc0.Anc0refChr0 466 2 + 26507 AC -s Anc1.Anc1refChr6 472 2 + 197743 AC -s Anc2.Anc2refChr6 549 2 + 7137 AC -s mr.mrrefChr5 182770 2 + 294540 AT -s simCow_chr6.simCow.chr6 309027 2 + 602619 AC -s simDog_chr6.simDog.chr6 289088 2 - 593897 AC -s simHuman_chr6.simHuman.chr6 320249 2 + 601863 AC -s simRat_chr6.simRat.chr6 219780 2 + 647215 AG -s simRat_chr6.simRat.chr6 326312 2 + 647215 AT - -a -s simMouse_chr6.simMouse.chr6 335293 41 + 636262 CCCATGATCCAAGCACAACAAGCAAGAGTGGCACCTATCAT -s Anc0.Anc0refChr0 470 41 + 26507 CCAAGGACCTATGGAAAGCAACTATGGGTGGCACCTGTCAT -s Anc1.Anc1refChr6 476 41 + 197743 CCAAGGACCTATGGAAAGCAACTATGGGTGGCACCTGTCAT -s Anc2.Anc2refChr6 553 41 + 7137 CCAAGGACCTTTGGAAAGCAACTATGGGTGGCACCTGTCAT -s mr.mrrefChr5 182772 41 + 294540 CCCACGACCCAAGCACAACTAGTAAGAGTGGCACCTATCAT -s simCow_chr6.simCow.chr6 309031 40 + 602619 TCAAGGACCCCTGGTAAACAACTATGGGCGGCATCTG-CAT -s simDog_chr6.simDog.chr6 289092 41 - 593897 CCCAGGACCTTTGAAAAGCAACTATGTGTGGCACCTGTCAT -s simHuman_chr6.simHuman.chr6 320253 40 + 601863 ACAATGACCTACGGAAAGCAACTATTGATGGCACTTGCCA- -s simRat_chr6.simRat.chr6 193715 41 + 647215 CCCACAACCCAAGCACAACTAGTGAGAGTGGCACCTATCAT -s simRat_chr6.simRat.chr6 326314 41 + 647215 CCCACGACCCAAGCACAACTAGTTAGGGTGGAACCTATCAT - -a -s simMouse_chr6.simMouse.chr6 335334 21 + 636262 CCCATCATCTGCTTAAACAGA -s Anc0.Anc0refChr0 511 10 + 26507 C-----------TGGAACAGG -s Anc1.Anc1refChr6 517 10 + 197743 C-----------TGGAACAGG -s Anc2.Anc2refChr6 597 10 + 7137 C-----------TGGAATAGG -s mr.mrrefChr5 182813 10 + 294540 C-----------TTAAACAGA -s simCow_chr6.simCow.chr6 309074 10 + 602619 C-----------TGGGAGAGG -s simDog_chr6.simDog.chr6 289136 10 - 593897 C-----------TGGAATAGG -s simHuman_chr6.simHuman.chr6 320293 7 + 601863 --------------GAACAGT -s simRat_chr6.simRat.chr6 193756 10 + 647215 C-----------TTAAACAGA -s simRat_chr6.simRat.chr6 326355 10 + 647215 C-----------TTAAATAGA - -a -s simMouse_chr6.simMouse.chr6 335355 1 + 636262 A -s Anc0.Anc0refChr0 521 1 + 26507 A -s Anc1.Anc1refChr6 527 1 + 197743 A -s Anc2.Anc2refChr6 607 1 + 7137 A -s mr.mrrefChr5 182823 1 + 294540 A -s simCow_chr6.simCow.chr6 309084 1 + 602619 A -s simDog_chr6.simDog.chr6 289146 1 - 593897 G -s simHuman_chr6.simHuman.chr6 320300 1 + 601863 A -s simRat_chr6.simRat.chr6 326365 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 335356 6 + 636262 TTTTGT -s Anc0.Anc0refChr0 522 6 + 26507 TTTTTT -s Anc1.Anc1refChr6 528 6 + 197743 TTTTTT -s Anc2.Anc2refChr6 608 6 + 7137 TTTTTT -s mr.mrrefChr5 182824 6 + 294540 TTTTTT -s simCow_chr6.simCow.chr6 309085 6 + 602619 TTTCTT -s simDog_chr6.simDog.chr6 289147 6 - 593897 TTCTTT -s simHuman_chr6.simHuman.chr6 320301 6 + 601863 TGTTTT -s simRat_chr6.simRat.chr6 193766 6 + 647215 TTTTTT -s simRat_chr6.simRat.chr6 326366 6 + 647215 TTTTTT - -a -s simMouse_chr6.simMouse.chr6 335362 15 + 636262 ATTAGGAAGGTAAGT -s Anc0.Anc0refChr0 607 15 + 26507 ATTTTGGAGGTGGGT -s Anc1.Anc1refChr6 613 15 + 197743 ATTTTGGAGGTGGGT -s Anc2.Anc2refChr6 693 15 + 7137 ATTTTGGAGGTGGGT -s mr.mrrefChr5 182830 15 + 294540 ATTAGGAAGGTGAGT -s simCow_chr6.simCow.chr6 309149 12 + 602619 ATTTTGG---TTGGT -s simDog_chr6.simDog.chr6 289234 15 - 593897 ATTTGGGAGGTGGCT -s simHuman_chr6.simHuman.chr6 320386 15 + 601863 ATTCTGGAAGTGGGT -s simRat_chr6.simRat.chr6 193772 15 + 647215 ATTAGGAAGGTGAGT -s simRat_chr6.simRat.chr6 326372 15 + 647215 ATTAGGAAGGTGAGT - -a -s simMouse_chr6.simMouse.chr6 335377 16 + 636262 TCATGGACTAACCAAT -s Anc0.Anc0refChr0 622 12 + 26507 TTGTGG----ATTTGC -s Anc1.Anc1refChr6 628 12 + 197743 TTGTGG----ATTTGC -s Anc2.Anc2refChr6 708 12 + 7137 TTGTGG----ATTTGC -s mr.mrrefChr5 182845 12 + 294540 TCATGG----ACCAAT -s simCow_chr6.simCow.chr6 309161 9 + 602619 TTG-GG----TTTT-- -s simDog_chr6.simDog.chr6 289249 12 - 593897 TCATGG----ATATGC -s simHuman_chr6.simHuman.chr6 320401 12 + 601863 TTGTGA----GTTTGC -s simRat_chr6.simRat.chr6 326387 12 + 647215 CCATGC----ACCAAT - -a -s simMouse_chr6.simMouse.chr6 335393 2 + 636262 CG -s Anc0.Anc0refChr0 634 2 + 26507 CG -s Anc1.Anc1refChr6 640 2 + 197743 CG -s Anc2.Anc2refChr6 720 2 + 7137 CG -s mr.mrrefChr5 182857 2 + 294540 CG -s simDog_chr6.simDog.chr6 289262 2 - 593897 CG -s simHuman_chr6.simHuman.chr6 320413 2 + 601863 CG -s simRat_chr6.simRat.chr6 326399 2 + 647215 CC - -a -s simMouse_chr6.simMouse.chr6 335395 30 + 636262 CTCTACACCAAGGGACTGCCTTAAGAAGAT -s Anc0.Anc0refChr0 660 30 + 26507 CTCTCTGCCAAGAGACTGCCTTAAGAAGAT -s Anc1.Anc1refChr6 666 30 + 197743 CTCTCTGCCAAGAGACTGCCTTAAGAAGAT -s Anc2.Anc2refChr6 746 30 + 7137 CTCTCTGCCAAGAGACTGCCCTAAGAAGAT -s mr.mrrefChr5 182859 30 + 294540 CTCTACACCAAGGGACTGCCTTAAGAAGAT -s simCow_chr6.simCow.chr6 309191 30 + 602619 TTCTGTGTCAAGATACTGTTCCAAGGAGCT -s simDog_chr6.simDog.chr6 289293 30 - 593897 CTCTCTGCCAAGAGACTGCCCTAAGAAGAT -s simHuman_chr6.simHuman.chr6 320439 30 + 601863 CTCTCTGCCAAGAGACTGCCTTAAGAAGAT -s simRat_chr6.simRat.chr6 326401 30 + 647215 CTCTACACCAAGGGATTGCCTTAAGAAGAC - -a -s simMouse_chr6.simMouse.chr6 335425 23 + 636262 AGCCCTTGTATCCAGATCATCTA -s Anc0.Anc0refChr0 691 23 + 26507 AGTCTTCGCACTCAGGTTCTTTA -s Anc1.Anc1refChr6 697 23 + 197743 AGTCTTCGCACTCAGGTTCTTTA -s Anc2.Anc2refChr6 777 23 + 7137 AGTCTCCACACTCAGGTTCTTTA -s mr.mrrefChr5 182889 23 + 294540 AGCCCTTGTACCCAGATCATCTA -s simCow_chr6.simCow.chr6 309222 23 + 602619 AGTCTCCATACCCAGGTTCTTTA -s simDog_chr6.simDog.chr6 289324 23 - 593897 AGTCTCCACACTTAGGTTCTTTA -s simHuman_chr6.simHuman.chr6 320470 23 + 601863 AGTCTTCGCACTCAGGTTCTTGG -s simRat_chr6.simRat.chr6 326431 23 + 647215 AGCCCTTGTACCTAGATCATCTA - -a -s simMouse_chr6.simMouse.chr6 335448 45 + 636262 AGAGCCACTTGAAGTAGGGCACAGTATTAACCTTTCCAGGTACGT -s Anc0.Anc0refChr0 714 45 + 26507 GAAACAATTAGAATTAGGGTGCAGTACTACCCTTCTCAGGCAAAT -s Anc1.Anc1refChr6 720 45 + 197743 GAAACAATTAGAATTAGGGTGCAGTACTACCCTTCTCAGGCAAAT -s Anc2.Anc2refChr6 800 45 + 7137 GAAACAATTAGAATCAGGGTGCAGTACTACCCTTCTCAAGCAAAT -s mr.mrrefChr5 182912 45 + 294540 AGAGCCACTAGAAGTAGGGCACAGTATTAACCTTTCCAGGCACAT -s simCow_chr6.simCow.chr6 309254 44 + 602619 GAAGCAACTAGAAGCAGGGTGCATT-CTACCCTACTCAAGCAATT -s simDog_chr6.simDog.chr6 289347 39 - 593897 GAAACAATTAGAATCAG------GTACAACCCCTCTTGAGCAGAT -s simHuman_chr6.simHuman.chr6 320493 45 + 601863 GAACCAATTAGTAATGGAGAGCAGTACTACCCTTCTCAGGCCAGT -s simRat_chr6.simRat.chr6 326454 45 + 647215 AGAGCCACTAGAAGTAGGGTCTAGTATTAACCTTTCCAGGCACAC - -a -s simMouse_chr6.simMouse.chr6 335493 104 + 636262 GTAGGTAATGTGCCATATTGAGAAACCTACTATATTAATTGATGAAAAAGCTGTGTCAATAGCACATTTGCCCTAATAAGATGGGCTTCCAGCCCTGGCCTCAA -s Anc0.Anc0refChr0 769 103 + 26507 GGTGGTACTGTGTTATGTTGAGATGCTTGCTTAATTAATTAATGATGTGCCCCTGCCAGTAGGACATTTG-CTTAAAAATATGGGCTCCCAACCCTGCCCTCAA -s Anc1.Anc1refChr6 775 104 + 197743 GGTGGTACTGTGTTATGTTGAGATGCTTGCTTAATTAATTAATGATGTGCCCCTGCCAGTAGGACATTTGCCTTAAAAATATGGGCTCCCAACCCTGCCCTCAA -s Anc2.Anc2refChr6 855 103 + 7137 GGTGGTACCATTTTATGTTGAGATGCTTGCTTAATTAATTACTGATGTGCCCCTGCCAGTTGGACATTTA-CTTAAAAATATGGGCTCCCAACCCTGGCCTCAA -s mr.mrrefChr5 182957 104 + 294540 GGAGGGAATGTGTCATATTGAGATACCTGCTATATTAATTAATGAAGAGGCCGTGTCAGTAGCACATTTGCCTTAATAATATGGGCTTCCAGCCCTGCCCTCAA -s simCow_chr6.simCow.chr6 309308 102 + 602619 AGTGGTGCCACTCAATATTGAGATGCTTGCTTAATCACTTGCTGAT-TGCCCCCACCATTTGGATGTTTA-CTTAAAGATATAAGCTCCCAACCCTGACCTCAA -s simDog_chr6.simDog.chr6 289396 97 - 593897 GGTGGTATCATTTTATGCTGAGATGCGTGCTTAATTAATTACTGATGTGCCCCTGCCAGTTGGACATT-------AAAATATGGGCTCCAAACCCTGGCCTCAA -s simHuman_chr6.simHuman.chr6 320548 104 + 601863 GGTGGTACTGTGTTATGTTGAGATGCTTGCTTGAATAATTAATGATGTGCCCCTGCCAGAAGGACATTTGCCTTAAAAGTGTGGGCTCCCAATCCTGCCCTCAA -s simRat_chr6.simRat.chr6 326499 103 + 647215 GGAGGGAACGTGTCAT-TTGAGATACCTGCTATATTAATTAATGAAGAGGTCGAGTCAGTAGAACATTTGCCTTAAGAATATGGGCTTCCAGCCCTGCCCTCGA - -a -s simMouse_chr6.simMouse.chr6 335597 40 + 636262 TTCTCTTAGGTACTATACATGTCCATGAGGCTATGTGTTA -s Anc0.Anc0refChr0 872 33 + 26507 CTATCTTATGTTCTAGACATATCCATAAGCC-------TA -s Anc1.Anc1refChr6 879 33 + 197743 CTATCTTATGTTCTAGACATATCCATAAGCC-------TA -s Anc2.Anc2refChr6 958 33 + 7137 CTATCTTATATTCTAGACATATCCACAAGCC-------TA -s mr.mrrefChr5 183061 40 + 294540 TTCTCTTATGTTCTAGACATATCCATGAGGCTATGTGTTA -s simCow_chr6.simCow.chr6 309410 33 + 602619 CCATCTTATGTTTTAGACCCATCCATAAGGC-------TA -s simDog_chr6.simDog.chr6 289493 33 - 593897 TTATCTTATATTCTAGACATATCCACAAGCC-------TA -s simDog_chr6.simDog.chr6 139918 27 - 593897 C------AGATTCTAGACATATCCACAAGCC-------TA -s simHuman_chr6.simHuman.chr6 320652 33 + 601863 CTGTCACATGTTCTAGACATATCCATAAAAC-------TA -s simRat_chr6.simRat.chr6 326602 40 + 647215 TTCTCTTATGTTCTAGATATATCCATGAGGCTATAGTTTA - -a -s simMouse_chr6.simMouse.chr6 335637 4 + 636262 TCCC -s Anc0.Anc0refChr0 929 4 + 26507 TCCC -s Anc1.Anc1refChr6 936 4 + 197743 TCCC -s Anc2.Anc2refChr6 1017 4 + 7137 TCCC -s mr.mrrefChr5 183125 4 + 294540 TCCC -s simCow_chr6.simCow.chr6 309464 4 + 602619 TTCC -s simDog_chr6.simDog.chr6 289552 4 - 593897 TCCC -s simDog_chr6.simDog.chr6 139971 4 - 593897 TCCC -s simHuman_chr6.simHuman.chr6 320709 4 + 601863 CCCC -s simRat_chr6.simRat.chr6 326750 4 + 647215 TCCC - -a -s simMouse_chr6.simMouse.chr6 335641 53 + 636262 TTTGGCGTCATATCCACCCCCAGCCTCGGCACGACTAAGACAGTGGATACCTA -s Anc0.Anc0refChr0 934 53 + 26507 TTCAGAGCCATGTCCACCCCCATCTTAGACACCACTAACACACTAGATACCTA -s Anc1.Anc1refChr6 941 53 + 197743 TTCAGAGCCATGTCCACCCCCATCTTAGACACCACTAACACACTAGATACCTA -s Anc2.Anc2refChr6 1022 53 + 7137 CTCAGAGCCATGTCCACCCCCATTTTAGGCACCACTAACACACTAGATACCTA -s mr.mrrefChr5 183129 53 + 294540 TTTAGAGTCATATCCACCCCCAGCTTCGACACGACTAAGACAGTGGATACCTA -s simCow_chr6.simCow.chr6 309469 53 + 602619 TTCAAAGCCATGTCCAGCCTCAATTTGGGCACCCTTAACGCACCAGTTACCTA -s simDog_chr6.simDog.chr6 289557 53 - 593897 CTCAGAGCCATGTCCACCCCCATTTTAGGCACCACTAACACACTAGATACCTA -s simDog_chr6.simDog.chr6 139976 53 - 593897 CTCAGAGCCATGTCCACCCCCATTTTAGGCACCACTAACACACTAGATACATT -s simHuman_chr6.simHuman.chr6 320714 53 + 601863 TTCAGAGCCATGTCACCTCTCACCTCAGACACCACTAACACATAAGAGACCTA -s simRat_chr6.simRat.chr6 326754 53 + 647215 TTTAGAGTCATATACGCCCCCGGCTTGGACGCTGCTAAGACACTGGATACCTA - -a -s simMouse_chr6.simMouse.chr6 335694 12 + 636262 AGATGGGCCTGC -s Anc0.Anc0refChr0 987 12 + 26507 AGCTACACAAGC -s Anc1.Anc1refChr6 994 12 + 197743 AGCTACACAAGC -s Anc2.Anc2refChr6 1075 12 + 7137 AGCTACACAAGC -s mr.mrrefChr5 183182 12 + 294540 AGCTGGGCCTGC -s simCow_chr6.simCow.chr6 309522 12 + 602619 AGCTACACAAGC -s simDog_chr6.simDog.chr6 289616 12 - 593897 AGCTACACAGAT -s simHuman_chr6.simHuman.chr6 320767 12 + 601863 AGCTACACAAGC -s simRat_chr6.simRat.chr6 326807 12 + 647215 AGCTGGGCCTGC - -a -s simMouse_chr6.simMouse.chr6 335706 23 + 636262 ATACAGTGGTCGGTAGCACCTAT -s Anc0.Anc0refChr0 1000 23 + 26507 ACATAGTGGTGGGTGGCATCCAC -s Anc1.Anc1refChr6 1007 23 + 197743 ACATAGTGGTGGGTGGCATCCAC -s Anc2.Anc2refChr6 1088 23 + 7137 ACATATTGGTGGGTGGCATCCAC -s mr.mrrefChr5 183195 23 + 294540 ATACAGTGGTCGGTAGCACCTAT -s simCow_chr6.simCow.chr6 309535 23 + 602619 ATGTACTGGTGGGTGGTATCCAC -s simDog_chr6.simDog.chr6 289629 23 - 593897 CCATATTGGTGGGTGGCATCCAC -s simHuman_chr6.simHuman.chr6 320780 23 + 601863 ACAGAGCGGTGGGTGGCATCCAC -s simRat_chr6.simRat.chr6 326820 23 + 647215 GTACTGTGGTCAGTAGCACCAAT - -a -s simMouse_chr6.simMouse.chr6 335729 12 + 636262 TTTACATTTATG -s Anc0.Anc0refChr0 1029 12 + 26507 TTGACATTTATA -s Anc1.Anc1refChr6 1036 12 + 197743 TTGACATTTATA -s Anc2.Anc2refChr6 1117 12 + 7137 CTACTACTTATA -s mr.mrrefChr5 183218 12 + 294540 TTGACATTTATA -s simCow_chr6.simCow.chr6 309564 12 + 602619 CTTCTAGTGATA -s simDog_chr6.simDog.chr6 289663 12 - 593897 CTACTACTTAGG -s simHuman_chr6.simHuman.chr6 320809 12 + 601863 TTGACTTTCATA -s simRat_chr6.simRat.chr6 326843 12 + 647215 TTGACATTTATA - -a -s simMouse_chr6.simMouse.chr6 335741 38 + 636262 TTGAAAGGGATAGGATACATGTGGCCATTGCAGAAGAG -s Anc0.Anc0refChr0 1041 38 + 26507 TTGAATGAAATGTCATGAATATGGCCATTGCAGGTGAG -s Anc1.Anc1refChr6 1048 38 + 197743 TTGAATGAAATGTCATGAATATGGCCATTGCAGGTGAG -s Anc2.Anc2refChr6 1129 38 + 7137 TTAAATGAAATGTCATGAATATGGCCATTGTAGGTGAG -s mr.mrrefChr5 183230 38 + 294540 TTGAAAGGGATAGCATACATATGGCCATTGCAGGAGAG -s simCow_chr6.simCow.chr6 309576 38 + 602619 CTAAATGCAATTACATCAATACAGCCATTGTAGGTGAG -s simDog_chr6.simDog.chr6 289675 38 - 593897 TCAAATGAAATGTCCTGAATATGTCCATTCTAGTTGAG -s simHuman_chr6.simHuman.chr6 320821 38 + 601863 TTGAATTAAATGCCATGAATATGGCAATTGCAGGTGGG -s simRat_chr6.simRat.chr6 326900 38 + 647215 TTGAAAGGGATAGCATACATATGGCCAGTGCAGGAGAG - -a -s simMouse_chr6.simMouse.chr6 335779 46 + 636262 TCTTAGTGCCCATATAGTCTTACACTCACTTGATGACAGACAGGAG -s Anc0.Anc0refChr0 1081 44 + 26507 CCTTAGTATCC--ATAATCTTAGACTCACTTGGTGACAGACATCAT -s Anc1.Anc1refChr6 1088 46 + 197743 CCTTAGTATCCATATAATCTTAGACTCACTTGGTGACAGACATCAT -s Anc2.Anc2refChr6 1169 44 + 7137 CGTCAGGATCC--ATAACTTTAGACTCACTTGGTGACAGACATCAT -s mr.mrrefChr5 183270 46 + 294540 TCTTAGTGCCCATATAGTCTTACACTCACTTGGTGACAGACAGGAT -s simCow_chr6.simCow.chr6 309616 41 + 602619 CATCAGACTCC--ATGGCCTTAGACTCACTTGGCGACAGACAT--- -s simDog_chr6.simDog.chr6 289715 44 - 593897 CGTCAGGATCC--ATAACTTTAGACTCACCTGGTTACAAACAGCAT -s simHuman_chr6.simHuman.chr6 320861 43 + 601863 CCTTAGTTTCCAT---TTCTTAGACTCACTTGGTGACAGACATCAT -s simRat_chr6.simRat.chr6 326940 46 + 647215 TCTCAGTGCCCATACAGTCTTAACCCCACTTGGTGACAGATAGGAT - -a -s simMouse_chr6.simMouse.chr6 335825 4 + 636262 GCAG -s Anc0.Anc0refChr0 1125 4 + 26507 GCAA -s Anc1.Anc1refChr6 1134 4 + 197743 GCAA -s Anc2.Anc2refChr6 1213 4 + 7137 GCAA -s mr.mrrefChr5 183316 4 + 294540 GCAG -s simDog_chr6.simDog.chr6 289763 4 - 593897 GCAA -s simHuman_chr6.simHuman.chr6 320904 4 + 601863 GCAA -s simRat_chr6.simRat.chr6 326986 4 + 647215 GCAG - -a -s simMouse_chr6.simMouse.chr6 335829 4 + 636262 TAGA -s Anc0.Anc0refChr0 1146 4 + 26507 TAGA -s Anc1.Anc1refChr6 1155 4 + 197743 TAGA -s Anc2.Anc2refChr6 1234 4 + 7137 TAGA -s mr.mrrefChr5 183320 4 + 294540 TAGA -s simCow_chr6.simCow.chr6 309668 4 + 602619 CAGA -s simDog_chr6.simDog.chr6 289784 4 - 593897 TAGA -s simHuman_chr6.simHuman.chr6 320925 4 + 601863 TAGA -s simRat_chr6.simRat.chr6 326990 4 + 647215 CAGA - -a -s simMouse_chr6.simMouse.chr6 335833 30 + 636262 ATAAATCATAACCAATAACTAAAAAATTGA -s Anc0.Anc0refChr0 1150 27 + 26507 GTG---CATCACCAATAACTAAGAAGTTGA -s Anc1.Anc1refChr6 1159 30 + 197743 GTGCATCATCACCAATAACTAAGAAGTTGA -s Anc2.Anc2refChr6 1238 27 + 7137 GTG---CATCACCAATAACTAAGAAGGTGA -s mr.mrrefChr5 183324 30 + 294540 ATAAATCATAACCAATAACTAAAAAATTGA -s simCow_chr6.simCow.chr6 309672 27 + 602619 GTG---AATCACCAATAACTAAGAAGGTGA -s simDog_chr6.simDog.chr6 289788 27 - 593897 GTA---CATCCCCAATAACTGAGGAAGTGA -s simHuman_chr6.simHuman.chr6 320929 30 + 601863 GTGCATGATCACCAATAGATAAGAAGTTGT -s simRat_chr6.simRat.chr6 326998 30 + 647215 ATAAATCATAACCAATAACTAAAAACTTGA - -a -s simMouse_chr6.simMouse.chr6 335863 29 + 636262 TGGAGACATCAACCCTGTGGTATGCAGAC -s Anc0.Anc0refChr0 1177 28 + 26507 TAGGGACATCAATTCTGAGGTGGGCAAA- -s Anc1.Anc1refChr6 1189 28 + 197743 TAGGGACATCAATTCTGAGGTGGGCAAA- -s Anc2.Anc2refChr6 1269 28 + 7137 TAGGGACATCAATTCTGAGTTGGGCAAA- -s mr.mrrefChr5 183354 29 + 294540 TGGAGACATCAATCCTGTGGTGTGCAGAC -s simCow_chr6.simCow.chr6 309703 22 + 602619 TAGGGACATCAATTCTGAGCTG------- -s simDog_chr6.simDog.chr6 289819 27 - 593897 TTGGGACACCAATCTTG-GTTGGGCAAA- -s simHuman_chr6.simHuman.chr6 320959 28 + 601863 TAGGGACATCAATTCTGAGGTGGGCAAA- -s simRat_chr6.simRat.chr6 327028 29 + 647215 TGGAGGCATCAATCCTGTGGTGTGCAGAG - -a -s simMouse_chr6.simMouse.chr6 335892 85 + 636262 TGTAATGACCACAGGACACATGACTGACATGACCACAGGACACACATTGTTCGGGGTACACAATGCATCACAAGGCTTGTAGGAA -s Anc0.Anc0refChr0 1205 60 + 26507 TGAGATGGCTACATG-CCTAC------------------------ATTGCAAGAAAGAGTTAGAGATTCACAAGGCATGTAACAG -s Anc1.Anc1refChr6 1217 60 + 197743 TGAGATGGCTACATG-CCTAC------------------------ATTGCAAGAAAGAGTTAGAGATTCACAAGGCATGTAACAG -s Anc2.Anc2refChr6 1297 60 + 7137 TGAGATGGCTACAGT-CCTAC------------------------ATCACAATAAAGAGTTAGAGATTCACAACGCATGTAGCAG -s mr.mrrefChr5 183383 61 + 294540 TGTGATGACCACATGACACAT------------------------ATTGTTCGGGGTACACAAAGCATCACAAGGCATGTAAGAA -s simCow_chr6.simCow.chr6 309725 58 + 602619 TGTGATTACAACAAT-CCCAC------------------------ATCACAATTAAGAGTTAGAGATTCACAAA--ATGTTGCAG -s simDog_chr6.simDog.chr6 289847 60 - 593897 TGAGATGGCTACAGT-CCTAC------------------------ATCACAATAAGGAGTCAGAGATTCACATCGCATGCAGCAA -s simHuman_chr6.simHuman.chr6 320987 60 + 601863 TGAGATGGCTAGGTG-CTGAC------------------------ATTGCAGGAAAGAGTTAGAGATACACAAGGGATGTAATAG -s simRat_chr6.simRat.chr6 327057 61 + 647215 TGGGATGACCACATGAGCCAT------------------------ATTGTTTGGGGCACACTAAGCATCACAGGGCATGTAAGAA - -a -s simMouse_chr6.simMouse.chr6 335977 48 + 636262 TTTTGCTGAAGTTATTCCATGTTGCGGGTCTATGGCAATTAGCTTGCT -s Anc0.Anc0refChr0 1265 47 + 26507 ATTT-CTGAGGTTATGTCATGTTGGGGGCCTATGGCAACTAGCTTGCT -s Anc1.Anc1refChr6 1277 47 + 197743 ATTT-CTGAGGTTATGTCATGTTGGGGGCCTATGGCAACTAGCTTGCT -s Anc2.Anc2refChr6 1357 47 + 7137 ATTT-CTGAGGTCATGTCATGTTGGGGACCTAGGGCAACTAGCTTGCT -s mr.mrrefChr5 183444 48 + 294540 TTTTGCTGAAGTTATTTCATGTTGCGGGCCTATGGCAATTAGCTTGCT -s simCow_chr6.simCow.chr6 309783 46 + 602619 -TTT-CTAAGGTAATGTCTTGTTGGGGACCTAGGGCAACAAGCTTGTT -s simDog_chr6.simDog.chr6 289907 47 - 593897 AATC-CTGAGGTCATCTCATGTTGGGGACCTAGGGCAACTAGCTTGCC -s simHuman_chr6.simHuman.chr6 321047 47 + 601863 ATTT-CTGAGGTTATGTCATGTAGGGGGCCTATGACAACTAGCTTGCT -s simRat_chr6.simRat.chr6 327131 48 + 647215 TTTTGTTGAAGTTATTTCATGTTGCGGACCTGGGGGAATTGGCTTGCT - -a -s simMouse_chr6.simMouse.chr6 336025 11 + 636262 GAAAGCTTTCA -s Anc0.Anc0refChr0 1314 11 + 26507 GCAATGTTTCA -s Anc1.Anc1refChr6 1326 11 + 197743 GCAATGTTTCA -s Anc2.Anc2refChr6 1406 11 + 7137 GCAATGTTTCA -s mr.mrrefChr5 183492 11 + 294540 GAAAGCTTTCA -s simCow_chr6.simCow.chr6 309831 11 + 602619 GCAATGTTTCA -s simDog_chr6.simDog.chr6 289956 11 - 593897 GCAATGATTCA -s simHuman_chr6.simHuman.chr6 321096 11 + 601863 GCAGTATTTCA -s simRat_chr6.simRat.chr6 327179 11 + 647215 AAATGCTTTCA - -a -s simMouse_chr6.simMouse.chr6 336036 9 + 636262 GGAGTTTGG -s Anc0.Anc0refChr0 1325 8 + 26507 -CAGTTTGG -s Anc1.Anc1refChr6 1337 8 + 197743 -CAGTTTGG -s Anc2.Anc2refChr6 1417 8 + 7137 -CAGTTTGG -s mr.mrrefChr5 183503 9 + 294540 GCAGTTTGG -s simCow_chr6.simCow.chr6 309842 8 + 602619 -CAGTTTGG -s simDog_chr6.simDog.chr6 289967 8 - 593897 -CGGTGTGG -s simHuman_chr6.simHuman.chr6 321107 8 + 601863 -CAGTTTGG -s simRat_chr6.simRat.chr6 327192 9 + 647215 GCAGTTTGG - -a -s simMouse_chr6.simMouse.chr6 336045 3 + 636262 AAT -s Anc0.Anc0refChr0 1333 3 + 26507 AGT -s Anc1.Anc1refChr6 1345 3 + 197743 AGT -s Anc2.Anc2refChr6 1425 3 + 7137 AGT -s mr.mrrefChr5 183512 3 + 294540 AAT -s simCow_chr6.simCow.chr6 309851 3 + 602619 AGT -s simDog_chr6.simDog.chr6 289975 3 - 593897 AGT -s simHuman_chr6.simHuman.chr6 321115 3 + 601863 TGT -s simRat_chr6.simRat.chr6 327201 3 + 647215 AAT - -a -s simMouse_chr6.simMouse.chr6 336048 19 + 636262 TTAGGAGTCAATGCACCAG -s Anc0.Anc0refChr0 1337 19 + 26507 TTAGGGGATAAAGTGACAA -s Anc1.Anc1refChr6 1349 19 + 197743 TTAGGGGATAAAGTGACAA -s Anc2.Anc2refChr6 1429 19 + 7137 TTAGGGGATAAAGTGACAA -s mr.mrrefChr5 183515 19 + 294540 TTAGGAGACAATGCAACAA -s simCow_chr6.simCow.chr6 309855 18 + 602619 TTGGGGTATAAAG-GACAA -s simDog_chr6.simDog.chr6 289979 19 - 593897 TTAAGGGGCGAAGTGACAA -s simHuman_chr6.simHuman.chr6 321119 19 + 601863 TTAGAGGATAAAAAGACAA -s simRat_chr6.simRat.chr6 327204 19 + 647215 TTAGGAGACGGTGCAACAA - -a -s simMouse_chr6.simMouse.chr6 336067 83 + 636262 AGACTTGGAGAATAACAGTATCTAAGTGTCCACACCAATCAGAGACATTACACACAGTCAAGAGGCCAGTGAATTCTCTGGTA -s Anc0.Anc0refChr0 1356 81 + 26507 AGAATAGGAGAACATCAGTATTAAATGGTGCACACTAA--GTGCACACTAAATACAATCAAGGGGCTTGTAAGTTCGCTGGTG -s Anc1.Anc1refChr6 1368 81 + 197743 AGAATAGGAGAACATCAGTATTAAATGGTGCACACTAA--GTGCACACTAAATACAATCAAGGGGCTTGTAAGTTCGCTGGTG -s Anc2.Anc2refChr6 1448 81 + 7137 AGAATAGGAGATCATCAGTATTAAATGGTGCACACTAA--GTGCACACTAAATACAACCAAGGGGCTTGTAAGTTTGCTGGTG -s mr.mrrefChr5 183534 83 + 294540 AGACTTGGAGAATAACAGTATCTAAGTGTGCACACCAATCGGGGACATTACACACAGTCAAGAGGCCAGTAAATTCTCTGGTA -s simCow_chr6.simCow.chr6 309898 80 + 602619 ACAATAGGGGATCACCAGTATTAAATGG-ATGCACTAA--GTGCCCGTGAAATACAGCCTAGGGGCTGGTAGGTTTGTTGGTG -s simDog_chr6.simDog.chr6 289998 81 - 593897 AGAATAGGAGATCCTCAGTATAAAGTGGTGCACACCGA--GTGCACACTGAGTACAACCAAGGGGCTTGTAAGTTTGCTGGTG -s simHuman_chr6.simHuman.chr6 321138 81 + 601863 GGAATAGGAGGACATCAGTATTAAATGGTGCACACTAA--GTGCACACTAAATGCACTCAAGGTGCTTGTAAGTTCAATGGTT -s simRat_chr6.simRat.chr6 327223 82 + 647215 AGTCTTGGAGA-TAAAAATATATAAGTGTGCACATCAATTGGGGACATTTCACATAATCAAGAGGCAGGTAAATTCTCTGGTC - -a -s simMouse_chr6.simMouse.chr6 336150 4 + 636262 CTTC -s Anc0.Anc0refChr0 1437 4 + 26507 CTTG -s Anc1.Anc1refChr6 1449 4 + 197743 CTTG -s Anc2.Anc2refChr6 1529 4 + 7137 CTTG -s mr.mrrefChr5 183617 4 + 294540 CTTC -s simCow_chr6.simCow.chr6 309979 4 + 602619 CTTG -s simDog_chr6.simDog.chr6 290079 4 - 593897 CTTG -s simHuman_chr6.simHuman.chr6 321219 4 + 601863 CTTG -s simRat_chr6.simRat.chr6 327305 4 + 647215 CATC - -a -s simMouse_chr6.simMouse.chr6 336154 37 + 636262 CACCATCAAAAACATGCTTCACATCAGCTCTCTCTAT -s Anc0.Anc0refChr0 1441 30 + 26507 CATTAT--AAAACATGCTTCACACCAGC-----TGCT -s Anc1.Anc1refChr6 1453 35 + 197743 CATTAT--AAAACATGCTTCACACCAGCTCTATTGCT -s Anc2.Anc2refChr6 1533 30 + 7137 CTTTAA--AAAACATGCTTCACACTAGC-----TGCT -s mr.mrrefChr5 183621 37 + 294540 CACCATCAAAAACATGCTTCACATCAGCTCTCTCTCT -s simCow_chr6.simCow.chr6 309983 30 + 602619 CTCTTA--GAAACATGCTCCACACTAGC-----TGAC -s simDog_chr6.simDog.chr6 290084 25 - 593897 TTTTAA--AAAACATGCTTCACACT----------CT -s simHuman_chr6.simHuman.chr6 321223 35 + 601863 CATTAT--CGAAAATGCGTCACACCAGCTCTATTGCT -s simRat_chr6.simRat.chr6 327309 37 + 647215 CACCAGCAAAATCATGCTTAAAATTAGCTTTCTCTCT - -a -s simMouse_chr6.simMouse.chr6 336191 56 + 636262 AGTTAATAGTTATCATTTAGATCACAGCCTTGTTCCATTAGCATCGGTCATATATT -s Anc0.Anc0refChr0 1497 56 + 26507 GGGCAGTAGCCACCACTTACATTGTCATCTTCATCTATTGGCATTAGCCAAATATT -s Anc1.Anc1refChr6 1514 56 + 197743 GGGCAGTAGCCACCACTTACATTGTCATCTTCATCTATTGGCATTAGCCAAATATT -s Anc2.Anc2refChr6 1589 56 + 7137 GGGCAGTAGCCACCACTTACGTTGTCATCTTCATCTATTGGCATTAGCCAAATTTT -s mr.mrrefChr5 183682 56 + 294540 AGGTAATAGTCACCATTTAGATCACAGCCTTGTTCCATTGGCATCGGTCATATATT -s simCow_chr6.simCow.chr6 310038 56 + 602619 GGGCAGTAACCACCACTTTCGTTGAATTCTTCATCTATCGGCATTAGCCATATGTT -s simDog_chr6.simDog.chr6 290135 55 - 593897 GGGCAGAAGCCACTACTTACGTTATCATCCACATCTGTTGGCATTAGC-AAACTTA -s simHuman_chr6.simHuman.chr6 321284 56 + 601863 GGGCAGTATCCACCACTTACATTGTTATCTTTGTCTATTGGCATTAGCTACATATT -s simRat_chr6.simRat.chr6 327370 56 + 647215 AGGTAATAGTCACCATTTAGGTCTCAGCCTTGTTCCATTGGCATCGGTCATATATT - -a -s simMouse_chr6.simMouse.chr6 336247 35 + 636262 AAGACACAAGATGATAAGATAATCGTTATTCAATG -s Anc0.Anc0refChr0 1558 34 + 26507 AACAGACAAGACAATAAGACAATCTTTTGTCAA-T -s Anc1.Anc1refChr6 1575 34 + 197743 AACAGACAAGACAATAAGACAATCTTTTGTCAA-T -s Anc2.Anc2refChr6 1650 34 + 7137 AACAGAGAAGACAATAAGACAATCAGTTGCAAA-T -s mr.mrrefChr5 183738 35 + 294540 AAGACACAAGATAATAAGATAATCTTTATTCAATG -s simCow_chr6.simCow.chr6 310099 34 + 602619 AACAGATAAGACAATAAGACAATCAGTTGCACA-T -s simDog_chr6.simDog.chr6 290194 15 - 593897 CACAGAGAAGAC-------------------AA-T -s simHuman_chr6.simHuman.chr6 321345 34 + 601863 AACAGACAAGAAACTAAGACAATATTTTGTCAA-T -s simRat_chr6.simRat.chr6 327426 35 + 647215 AAGACACAAAAGAATAAAATAATCTTTGTTCAATG - -a -s simMouse_chr6.simMouse.chr6 336282 1 + 636262 C -s Anc0.Anc0refChr0 1592 1 + 26507 T -s Anc1.Anc1refChr6 1609 1 + 197743 T -s Anc2.Anc2refChr6 1684 1 + 7137 T -s mr.mrrefChr5 183773 1 + 294540 C -s simCow_chr6.simCow.chr6 310133 1 + 602619 T -s simDog_chr6.simDog.chr6 290209 1 - 593897 C -s simHuman_chr6.simHuman.chr6 321379 1 + 601863 T -s simRat_chr6.simRat.chr6 327466 1 + 647215 C - -a -s simMouse_chr6.simMouse.chr6 336283 9 + 636262 AGGCGAAGA -s Anc0.Anc0refChr0 1594 9 + 26507 GGGATAAGA -s Anc1.Anc1refChr6 1611 9 + 197743 GGGATAAGA -s Anc2.Anc2refChr6 1686 9 + 7137 GGCATAAGA -s mr.mrrefChr5 183774 9 + 294540 AGGCGAAGA -s simCow_chr6.simCow.chr6 310135 9 + 602619 GGCAGAAGA -s simDog_chr6.simDog.chr6 290211 9 - 593897 GACATAAGA -s simHuman_chr6.simHuman.chr6 321381 9 + 601863 GGGATAAGA -s simRat_chr6.simRat.chr6 327467 9 + 647215 AGTTCAAGA - -a -s simMouse_chr6.simMouse.chr6 336292 4 + 636262 GCTA -s Anc0.Anc0refChr0 1603 4 + 26507 GCTA -s Anc1.Anc1refChr6 1620 4 + 197743 GCTA -s Anc2.Anc2refChr6 1695 4 + 7137 GCTA -s mr.mrrefChr5 183783 4 + 294540 GCTA -s simCow_chr6.simCow.chr6 310144 4 + 602619 GTTA -s simDog_chr6.simDog.chr6 290220 4 - 593897 GCTA -s simHuman_chr6.simHuman.chr6 321390 4 + 601863 GCTA -s simRat_chr6.simRat.chr6 327478 4 + 647215 GTTA - -a -s simMouse_chr6.simMouse.chr6 336296 17 + 636262 GACTAATGTGATGCATT -s Anc0.Anc0refChr0 1615 17 + 26507 GACTCATGTGATGAGTA -s Anc1.Anc1refChr6 1632 17 + 197743 GACTCATGTGATGAGTA -s Anc2.Anc2refChr6 1707 17 + 7137 GACTCATGTAATGAGTA -s mr.mrrefChr5 183787 17 + 294540 GACTAATGTGATGAATT -s simCow_chr6.simCow.chr6 310156 11 + 602619 AACT------ATGAATG -s simDog_chr6.simDog.chr6 290232 17 - 593897 GCCTCATGTAATGAGTA -s simHuman_chr6.simHuman.chr6 321402 17 + 601863 GACTCACATGATTACAA -s simRat_chr6.simRat.chr6 327482 17 + 647215 GACTAATGCGATGAATT - -a -s simMouse_chr6.simMouse.chr6 336313 20 + 636262 TCCCAACAGTGGGCTAACTT -s Anc0.Anc0refChr0 1633 20 + 26507 ACTCAACATTAAGCTAAGTT -s Anc1.Anc1refChr6 1650 20 + 197743 ACTCAACATTAAGCTAAGTT -s Anc2.Anc2refChr6 1725 20 + 7137 ACTTAACATTAAGCTAAGTT -s mr.mrrefChr5 183805 20 + 294540 TCCCAACAGTGGGCTAACTT -s simCow_chr6.simCow.chr6 310168 20 + 602619 AGTGAACATTAAGCCAAGTT -s simDog_chr6.simDog.chr6 290250 20 - 593897 ACCTAACATTAAGCTAAGTT -s simHuman_chr6.simHuman.chr6 321420 20 + 601863 ACTCAACATTACGCTAAGCT -s simRat_chr6.simRat.chr6 327500 20 + 647215 TCCCAGCACTGGGTTAACTT - -a -s simMouse_chr6.simMouse.chr6 336333 81 + 636262 TGTAAACTCTGACTGATTCCACTTCTTTACCATTCTACGGATATACGGCTAAGACCTACCCTGAGTTTCAGCTGATGATGG -s Anc0.Anc0refChr0 1653 68 + 26507 AGCAAATACTGACTGATCCAAACGAATTAACATGCTT-------------AGGACCTACCTGCAGCCCCAGCTTAAGGTGT -s Anc1.Anc1refChr6 1670 68 + 197743 AGCAAATACTGACTGATCCAAACGAATTAACATGCTT-------------AGGACCTACCTGCAGCCCCAGCTTAAGGTGT -s Anc2.Anc2refChr6 1745 68 + 7137 AGCAAATACTAACTGATCCAAATGAATTAATATGCTT-------------AGGACCTACCTGCAGCCCCAGCTTAAGGTGT -s mr.mrrefChr5 183825 81 + 294540 TGTAAATTCTGACTGATCCCACCTATTTAACATTCTACGGATATACGGGTAAGACCTACCCTGAGTTTCAGCTGATGATGG -s simCow_chr6.simCow.chr6 310191 61 + 602619 GGCAAATACTAACTGATCCAAATGAATTAATATGCTT-------------AAGACCTAGCTGCTGCCCCAGCTT------- -s simDog_chr6.simDog.chr6 290270 68 - 593897 AGCAAAGACTAAGTGATCCAAATGAATTAATGTGCTT-------------AGGACCTGCCTGCAGCCCTAACTCAAGGTGT -s simHuman_chr6.simHuman.chr6 321440 68 + 601863 AGCAAGTACTGACTGATCCAATCGAAGTAACATGCTT-------------ACGATTTACCAGCAGCCCCAGCTTGAGGTGT -s simRat_chr6.simRat.chr6 327520 81 + 647215 TGTAAATTCTGATTGACCCCACCCATTTAACATTCTATGGATATATGGGTAAGACCTACTCTGAGTTCCAGCTGATGATGC - -a -s simMouse_chr6.simMouse.chr6 336414 8 + 636262 GTCCTTGG -s Anc0.Anc0refChr0 1721 7 + 26507 AT-ATTGG -s Anc1.Anc1refChr6 1738 7 + 197743 AT-ATTGG -s Anc2.Anc2refChr6 1813 7 + 7137 AC-ATTGG -s mr.mrrefChr5 183906 8 + 294540 GTCCTTGG -s simCow_chr6.simCow.chr6 310252 5 + 602619 ---ATTGG -s simDog_chr6.simDog.chr6 290338 7 - 593897 AC-ATTGG -s simHuman_chr6.simHuman.chr6 321508 7 + 601863 AT-ATTGG -s simRat_chr6.simRat.chr6 327602 8 + 647215 ATCCTTGG - -a -s simMouse_chr6.simMouse.chr6 336422 25 + 636262 TGTCAGCTTGATTACAAATGTAGCA -s Anc0.Anc0refChr0 1728 25 + 26507 TGTCAGCTGGCTTACAAATGTAGCA -s Anc1.Anc1refChr6 1745 25 + 197743 TGTCAGCTGGCTTACAAATGTAGCA -s Anc2.Anc2refChr6 1821 25 + 7137 TGCCAGCTGGCTTACAAATGTAGCA -s mr.mrrefChr5 183914 25 + 294540 TGTCAGCTTGATTACAAATGTAGCA -s simCow_chr6.simCow.chr6 310258 25 + 602619 TGCCAGCTGGCTTGCACATGTCGCA -s simDog_chr6.simDog.chr6 290346 25 - 593897 TGCTAGCTGGCTAAAAAATGTAGCA -s simHuman_chr6.simHuman.chr6 321515 25 + 601863 TGTCAGCTGGCTTACAAATGTAGCA -s simRat_chr6.simRat.chr6 327610 25 + 647215 TGTCTTCTTGATTACAAATGTAGCA - -a -s simMouse_chr6.simMouse.chr6 336447 8 + 636262 TGTACCCC -s Anc0.Anc0refChr0 1753 8 + 26507 TGTGCCCT -s Anc1.Anc1refChr6 1770 8 + 197743 TGTGCCCT -s Anc2.Anc2refChr6 1847 8 + 7137 TGTGCCCT -s mr.mrrefChr5 183939 8 + 294540 TGTACCCC -s simCow_chr6.simCow.chr6 310284 8 + 602619 GGTGCCCT -s simDog_chr6.simDog.chr6 290372 8 - 593897 TGTGGCCT -s simHuman_chr6.simHuman.chr6 321580 8 + 601863 TGTGCCCT -s simRat_chr6.simRat.chr6 327635 8 + 647215 TGTACCCC - -a -s simMouse_chr6.simMouse.chr6 336455 13 + 636262 ATTCTTGACAGTG -s Anc0.Anc0refChr0 1763 9 + 26507 ----TCCACAGTG -s Anc1.Anc1refChr6 1780 13 + 197743 GTTTTCCACAGTG -s Anc2.Anc2refChr6 1857 9 + 7137 ----TCCACAGTG -s mr.mrrefChr5 183947 13 + 294540 GTTTTTGACAGTG -s simCow_chr6.simCow.chr6 310294 9 + 602619 ----TCTACATTG -s simDog_chr6.simDog.chr6 290382 9 - 593897 ----TCCATTGCT -s simHuman_chr6.simHuman.chr6 321592 13 + 601863 GTTTTCCGCAGTG -s simRat_chr6.simRat.chr6 327643 13 + 647215 GTTTTTTACAATG - -a -s simMouse_chr6.simMouse.chr6 336468 30 + 636262 CCTAGCTAGCCAAAACCTACAATCTGTAAG -s Anc0.Anc0refChr0 1788 29 + 26507 CTGGGCTAAAC-ATACCTGCAGCCGGTAAG -s Anc1.Anc1refChr6 1809 29 + 197743 CTGGGCTAAAC-ATACCTGCAGCCGGTAAG -s Anc2.Anc2refChr6 1883 29 + 7137 CTGGGCTAAAC-ATAGCTGCAGCCGGTAGG -s mr.mrrefChr5 183960 30 + 294540 CCTAGCTAACCAAAACCTACAATCTGTAAG -s simCow_chr6.simCow.chr6 310318 26 + 602619 ---GGCTAGGT-ATAGCTGCAGCCTGTAGG -s simDog_chr6.simDog.chr6 290408 29 - 593897 CTGGGCTAAAC-ATAGTTGCAGCCGGTAGG -s simHuman_chr6.simHuman.chr6 321621 29 + 601863 CTGGGCTAAAC-ATACCTGCAGCCCGTAAG -s simRat_chr6.simRat.chr6 327656 30 + 647215 CTTAGCTAAGCAAAGCCTACAATCAGTAAA - -a -s simMouse_chr6.simMouse.chr6 336498 21 + 636262 GTTAGTGATCTAATGGGATCA -s Anc0.Anc0refChr0 1819 21 + 26507 GTTAGTGAACTATTGGGGTAG -s Anc1.Anc1refChr6 1840 21 + 197743 GTTAGTGAACTATTGGGGTAG -s Anc2.Anc2refChr6 1914 21 + 7137 GTTAGTGTACTATTGGAGTAG -s mr.mrrefChr5 183990 21 + 294540 GTTAGTGAACTAATGGGATCA -s simCow_chr6.simCow.chr6 310346 21 + 602619 GCTTGTGTACTCTTCAAGTAG -s simDog_chr6.simDog.chr6 290439 21 - 593897 ATTAGTATACCATTGGAATAG -s simHuman_chr6.simHuman.chr6 321652 21 + 601863 GTTAGTGAACTGCTGGGGTAG -s simRat_chr6.simRat.chr6 327686 21 + 647215 GTTAGTGAACTAATGGGATGA - -a -s simMouse_chr6.simMouse.chr6 336519 33 + 636262 ACCCTCTATCGTGACCAGTCTTGGAGGACATTG -s Anc0.Anc0refChr0 1840 33 + 26507 ACCCTCTATCCTCACCAGTCCCCTAGGACGTTG -s Anc1.Anc1refChr6 1861 33 + 197743 ACCCTCTATCCTCACCAGTCCCCTAGGACGTTG -s Anc2.Anc2refChr6 1935 33 + 7137 ACCCTCCATCCTCACCAGTCCCCTAGGACGTTG -s mr.mrrefChr5 184011 33 + 294540 ACCCTCTATCGTGACCAGTCCCGGAGGACATTG -s simCow_chr6.simCow.chr6 310368 33 + 602619 ACCCTTCATCCTCATTGGTCCCCTAGGACATTG -s simDog_chr6.simDog.chr6 290460 33 - 593897 ACCCTCCATCCTCACCAATCCACTAGGACGTTG -s simHuman_chr6.simHuman.chr6 321673 33 + 601863 ACCCTCTATGTTCACCAGTACCCTAGGACGTTG -s simRat_chr6.simRat.chr6 327707 28 + 647215 ACCCTCTATAGTGACCAGGCCCGGAAGC----- - -a -s simMouse_chr6.simMouse.chr6 336552 1 + 636262 G -s Anc0.Anc0refChr0 1873 1 + 26507 T -s Anc1.Anc1refChr6 1894 1 + 197743 T -s Anc2.Anc2refChr6 1969 1 + 7137 T -s mr.mrrefChr5 184044 1 + 294540 G -s simCow_chr6.simCow.chr6 310402 1 + 602619 T -s simDog_chr6.simDog.chr6 290494 1 - 593897 T -s simHuman_chr6.simHuman.chr6 321706 1 + 601863 T - -a -s simMouse_chr6.simMouse.chr6 336553 9 + 636262 CACTCTTGC -s Anc0.Anc0refChr0 1876 9 + 26507 TAATCTTGT -s Anc1.Anc1refChr6 1897 9 + 197743 TAATCTTGT -s Anc2.Anc2refChr6 1972 9 + 7137 TAATTTTGT -s mr.mrrefChr5 184045 9 + 294540 CACTCTTGC -s simCow_chr6.simCow.chr6 310405 9 + 602619 TAATTCTGT -s simDog_chr6.simDog.chr6 290497 9 - 593897 TAATTTTAT -s simHuman_chr6.simHuman.chr6 321709 9 + 601863 TAATCTTGT - -a -s simMouse_chr6.simMouse.chr6 336562 36 + 636262 TATTGAATGTCCTAAGACAGGCAATAAATTAGATCA -s Anc0.Anc0refChr0 1887 36 + 26507 CCTTGAATATCCCAAGTCAGCAGACAAGTCAGATCA -s Anc1.Anc1refChr6 1908 36 + 197743 CCTTGAATATCCCAAGTCAGCAGACAAGTCAGATCA -s Anc2.Anc2refChr6 1983 36 + 7137 CCTTGAATATCCCAAGTAAGCAGACAAGCCGGATCA -s mr.mrrefChr5 184054 36 + 294540 TATTGAATATCCTAAGTCAGGCAATAAATTAGATCA -s simCow_chr6.simCow.chr6 310416 36 + 602619 CCTTGAATATCCGGAGAAGGCAGACATGCCTGATCT -s simDog_chr6.simDog.chr6 290507 32 - 593897 ----CAATATCCCAAGTAAGCAGACAAGCCGGATCA -s simHuman_chr6.simHuman.chr6 321720 36 + 601863 CGTTGAACAGCCCAAGTCAGAAGACAAGTCAGATTG -s simRat_chr6.simRat.chr6 327735 26 + 647215 ------ATATCTTAAGTCAGGCAATAAAATG----A - -a -s simMouse_chr6.simMouse.chr6 336598 82 + 636262 TTGCTCCATACCTCGAGTCTCAACTAGGTACCCAGGTACCACACGGCAAACAATCTTAATAGATTGACTTCCCTACTAACTA -s Anc0.Anc0refChr0 1923 73 + 26507 TCTCTCTGTAGTTTAGATTCTGA---------TAGGTACCACACAGCAATGAATCATAATAGGTTGACTTCCCTATTAACAA -s Anc1.Anc1refChr6 1944 73 + 197743 TCTCTCTGTAGTTTAGATTCTGA---------TAGGTACCACACAGCAATGAATCATAATAGGTTGACTTCCCTATTAACAA -s Anc2.Anc2refChr6 2019 73 + 7137 TCTCTCTGTAGTTTAGATTCTGA---------CAGGTGCCATACAGCAATGAATCATAATAAGTTGACTTCCCTATTAACAA -s mr.mrrefChr5 184090 82 + 294540 TTGCTCTGTACCTCGAGTCTCAACTAGGTAGCTAGGTACCACACAGCAATCAATCATAATAGATTGACTTCCCTACTAACTA -s simCow_chr6.simCow.chr6 310452 73 + 602619 TATCTATATAGTTTAGATTCTGA---------CAGATGCTATGGAACAGCGAATCATCTTAAGTTGACTACCCTAATTACAA -s simDog_chr6.simDog.chr6 290542 73 - 593897 TCTTTCTGTAGTTTAGATTCTGA---------CAGGTGCCATACAGCAATGAATCATAATAAATTGATTTCCCTATTAACAA -s simHuman_chr6.simHuman.chr6 321756 68 + 601863 TCTCTCTGTA-----GATTCTGA---------TAAGTACCCCACAGCAATGAATCATAATAGGTTGACTTCCCTATGAAAAA -s simRat_chr6.simRat.chr6 327761 82 + 647215 CTGCTCTGTATCTCAAGTCTCAACTAGTTAGCTAGGTACCACACAGCAATCAATCATAGTAGATTGACTTCCCTACTAACTA - -a -s simMouse_chr6.simMouse.chr6 336680 31 + 636262 GATCTAGGAATTCATATTTAGATCCAATAAT -s Anc0.Anc0refChr0 1997 28 + 26507 AACCTAGGAATTCATTTGTAGTACC---CTT -s Anc1.Anc1refChr6 2018 28 + 197743 AACCTAGGAATTCATTTGTAGTACC---CTT -s Anc2.Anc2refChr6 2093 28 + 7137 AGCATAGGAACTCATTTGTAGTACC---CTT -s mr.mrrefChr5 184172 31 + 294540 AATCTAGGAATTCATTTTTAGATCCAATAAT -s simCow_chr6.simCow.chr6 310526 28 + 602619 ATCATAGGAACTCTTTTGTAGTACC---CCT -s simDog_chr6.simDog.chr6 290616 27 - 593897 TGCATAGGAACTCATTTGTAGTATC---CT- -s simHuman_chr6.simHuman.chr6 321825 28 + 601863 AACCGAGGAATTCATTTGTAGTACC---CTT -s simRat_chr6.simRat.chr6 327843 31 + 647215 AATCTATGAGGTCATTTTCTGATCCAATAAT - -a -s simMouse_chr6.simMouse.chr6 336711 7 + 636262 CTCTATG -s Anc0.Anc0refChr0 2025 7 + 26507 GTCTGGG -s Anc1.Anc1refChr6 2046 7 + 197743 GTCTGGG -s Anc2.Anc2refChr6 2121 7 + 7137 GTCTGGG -s mr.mrrefChr5 184203 7 + 294540 ATCTATG -s simCow_chr6.simCow.chr6 310565 7 + 602619 GTCTGGG -s simDog_chr6.simDog.chr6 290643 4 - 593897 ---TGGG -s simHuman_chr6.simHuman.chr6 321853 7 + 601863 GTCTGGG -s simRat_chr6.simRat.chr6 327874 7 + 647215 ATCCGCC - -a -s simMouse_chr6.simMouse.chr6 336718 24 + 636262 CCGTTAACTAAAGCATTAAGGGTC -s Anc0.Anc0refChr0 2036 21 + 26507 ATGTTAGCTGAAGAAT---TGATC -s Anc1.Anc1refChr6 2057 24 + 197743 ATGTTAGCTGAAGAATTGATGATC -s Anc2.Anc2refChr6 2132 21 + 7137 ATGTTCGCTGAAGAAT---TGATC -s mr.mrrefChr5 184210 24 + 294540 CTGTTAACTAAAGCATTAAGGGTC -s simCow_chr6.simCow.chr6 310576 20 + 602619 CTGTTTGCTAACGTAG---T-ATC -s simDog_chr6.simDog.chr6 290651 18 - 593897 AGGTTCTCGGAAAACT---TG--- -s simHuman_chr6.simHuman.chr6 321864 24 + 601863 TTATTAGCTGAGGAATTGATGATC -s simRat_chr6.simRat.chr6 327881 24 + 647215 CTCTGTACTAAAGCATTAAGGGTC - -a -s simMouse_chr6.simMouse.chr6 336742 1 + 636262 T -s Anc0.Anc0refChr0 2063 1 + 26507 T -s Anc1.Anc1refChr6 2087 1 + 197743 T -s Anc2.Anc2refChr6 2159 1 + 7137 C -s mr.mrrefChr5 184234 1 + 294540 T -s simCow_chr6.simCow.chr6 310602 1 + 602619 C -s simDog_chr6.simDog.chr6 290674 1 - 593897 C -s simHuman_chr6.simHuman.chr6 321894 1 + 601863 T -s simRat_chr6.simRat.chr6 327905 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 336743 22 + 636262 GGGGGGGTGAGTTTCTAGGGGA -s Anc0.Anc0refChr0 2065 22 + 26507 GGTGGGGACTGCTTCTTGAGAA -s Anc1.Anc1refChr6 2089 22 + 197743 GGTGGGGACTGCTTCTTGAGAA -s Anc2.Anc2refChr6 2161 22 + 7137 GGTGGGAACTGCTTCTTGAGAA -s mr.mrrefChr5 184236 22 + 294540 GGGGGGGTGAGTTTCTAGGGGA -s simCow_chr6.simCow.chr6 310604 22 + 602619 GGTAGGAACTGATTCATTAAAA -s simDog_chr6.simDog.chr6 290676 22 - 593897 AGTGGGACCTGCTTCTTGAGAA -s simHuman_chr6.simHuman.chr6 321896 22 + 601863 GGTGGGGACTGGTTCTGGAGAA -s simRat_chr6.simRat.chr6 327907 22 + 647215 GGGGGGGTGAGTCTCGTGGGGA - -a -s simMouse_chr6.simMouse.chr6 336765 102 + 636262 TGGGTTTTGGACGTAGCCAATGAGATGATGGGCAATGAGAAATGACAGTGACCAACATATGGTGAGGCAATGAGGAATGACAGTGACCAACATATGGCAAGC -s Anc0.Anc0refChr0 2087 64 + 26507 CAGGTTATGCAAGTAGCCCATGAGAG--------------------------------------GGAGAATGTGAAATGAGAGTGGACAAGATAGGGCGAGC -s Anc1.Anc1refChr6 2111 64 + 197743 CAGGTTATGCAAGTAGCCCATGAGAG--------------------------------------GGAGAATGTGAAATGAGAGTGGACAAGATAGGGCGAGC -s Anc2.Anc2refChr6 2183 64 + 7137 CAGGTTATACATGTTGCCCATGAGAG--------------------------------------GGAGAGTGTGAGATAAGAGTGGACAAGATAGGGTGATC -s mr.mrrefChr5 184258 64 + 294540 TGGGTTTTGGAAGTAGCCAATGAGAT--------------------------------------AGGCAATGAGAAATGACAGTGACCAACATATGGCAAGC -s simCow_chr6.simCow.chr6 310626 64 + 602619 CAGGTTATACAGGTTGCCCATAAGGG--------------------------------------GGAGGGTGTGAGAGAAGAGTGAACAACATAGGGAAATT -s simDog_chr6.simDog.chr6 290698 63 - 593897 CAGGTTATACATGTTGTGCATGGGAG--------------------------------------GGC-AGTATGAGATAAGAGTGGATAAGATAGTGTGATC -s simHuman_chr6.simHuman.chr6 321919 64 + 601863 CAAGCTATGCAAGTAGCCCATGAGTG--------------------------------------GGAGAATGTGAAATGAGAGTGGACAAGAATGGGCGAGC -s simRat_chr6.simRat.chr6 327929 64 + 647215 TGGGTTTTGGAAGTAGACAATGAGAT--------------------------------------AGGCAATGAGATATGACAGTGACCAACATATGGTAGGC - -a -s simMouse_chr6.simMouse.chr6 336867 55 + 636262 CCTGCACAGACCTATTGTGATAGATGAACCCTCACATATTGCTTCCATTGATTGT -s Anc0.Anc0refChr0 2151 55 + 26507 CACATGGAGACCTATTGCAATAGAGAAACTTTCAAATATCATTTCCATTGCTAGT -s Anc1.Anc1refChr6 2175 55 + 197743 CACATGGAGACCTATTGCAATAGAGAAACTTTCAAATATCATTTCCATTGCTAGT -s Anc2.Anc2refChr6 2247 55 + 7137 CACATGGAGACCTATTGCAATAGAGAAACTTTCAAATATCATTTCCATTGCTAGT -s mr.mrrefChr5 184322 55 + 294540 CCTGTGGAGACCTATTGTGATAGAGGAACCCTCACATATTGTTTCCATTGCTTGT -s simCow_chr6.simCow.chr6 310690 55 + 602619 TATATGGAGACCTATTACAATAGAGAAACTTTCAAGTATCATTCCCATTGCTAGT -s simDog_chr6.simDog.chr6 290763 52 - 593897 CACATGAAGACCTATTGCAATAGAGAAACTTCCAAAAATCATTTCCATTGC---A -s simHuman_chr6.simHuman.chr6 321983 55 + 601863 CACATGGAGAACTATATCAATAGAGAAACTTTTATCTATCATTTTCATTGCTAGT -s simRat_chr6.simRat.chr6 327993 54 + 647215 CCTGTGGAGACTTTTTGTGATGGAGGAGCCCTC-CATATTGTTTCCATTGCTTGT - -a -s simMouse_chr6.simMouse.chr6 336922 22 + 636262 AGAGGGCAATGGGTAGTGGGAT -s Anc0.Anc0refChr0 2206 19 + 26507 ATACAGCA---GGTAAGGGGAT -s Anc1.Anc1refChr6 2230 19 + 197743 ATACAGCA---GGTAAGGGGAT -s Anc2.Anc2refChr6 2302 19 + 7137 ATGCAGCT---GGTAAGAGGAT -s mr.mrrefChr5 184377 22 + 294540 AGAGGGCAATGGGTAATGGGAT -s simCow_chr6.simCow.chr6 310756 19 + 602619 ATGCAGCT---GGGAGGAGGAG -s simDog_chr6.simDog.chr6 290815 19 - 593897 ATGCAGTT---GGTAAGAGAAT -s simHuman_chr6.simHuman.chr6 322038 19 + 601863 ATACTGCA---GTTAAGGGGAT -s simRat_chr6.simRat.chr6 328047 22 + 647215 AGAGGGCAATGGGTAATAGGGA - -a -s simMouse_chr6.simMouse.chr6 336944 25 + 636262 AAGTACTTATATAACCGCACTCCCC -s Anc0.Anc0refChr0 2225 25 + 26507 GAATACTTATATACCCATAGTCCCA -s Anc1.Anc1refChr6 2249 25 + 197743 GAATACTTATATACCCATAGTCCCA -s Anc2.Anc2refChr6 2321 25 + 7137 GAATGCTTATATACCCATAGTCCCA -s mr.mrrefChr5 184399 25 + 294540 AAGTACTTATATAACCACACTCCCC -s simCow_chr6.simCow.chr6 310775 25 + 602619 GAATGCTTATATACCCACAGTCCCA -s simDog_chr6.simDog.chr6 290834 25 - 593897 TATTGCTTATATACCCATAGTCCCA -s simHuman_chr6.simHuman.chr6 322057 25 + 601863 GAAGACTTATATACCCGTAGTCCCA -s simMouse_chr6.simMouse.chr6 489949 25 + 636262 AAGTACTTATATAACCACACTCCCC -s simRat_chr6.simRat.chr6 328069 25 + 647215 AAGTCCTTATCTAACCATACTCCAA - -a -s simMouse_chr6.simMouse.chr6 336969 36 + 636262 AGACTTACATTTAGGACATAGTTATTAAGCTTATAG -s Anc0.Anc0refChr0 2257 36 + 26507 AGACTTATGTTTAGGACATAGTTATAAGTCTCATAG -s Anc1.Anc1refChr6 2281 36 + 197743 AGACTTATGTTTAGGACATAGTTATAAGTCTCATAG -s Anc2.Anc2refChr6 2353 36 + 7137 AGACTTATGTTTAGGAAATAGTTACAAGTCTCATAG -s mr.mrrefChr5 184424 36 + 294540 AGACTTACATTTAGGACATAGTTATTAAGCTTATAG -s simCow_chr6.simCow.chr6 310807 33 + 602619 GGACTTATAT---GGAAATAGTTGCAAGTCTCATAG -s simDog_chr6.simDog.chr6 290866 36 - 593897 AGACTTATGTTTAGGAAATAGTCACAAGTCTCATAG -s simHuman_chr6.simHuman.chr6 322089 36 + 601863 TGACTTATGTTTTGGACATAGTTATAATTCTCATAG -s simMouse_chr6.simMouse.chr6 489974 36 + 636262 AGACTTACATTTAGGACATAGTTATTAAGCTTATAG -s simRat_chr6.simRat.chr6 328094 33 + 647215 AGACTTACATTTAGGACATAGTTA---GGCTCATAT - -a -s simMouse_chr6.simMouse.chr6 337005 25 + 636262 CTTTACCAATAACTCCCTCCTAATG -s Anc0.Anc0refChr0 2294 25 + 26507 CTTGTCCAATAGCTCCCTCCTAATG -s Anc1.Anc1refChr6 2318 25 + 197743 CTTGTCCAATAGCTCCCTCCTAATG -s Anc2.Anc2refChr6 2390 25 + 7137 CTTGTCCAATTGCTCACTGCTAATG -s mr.mrrefChr5 184460 25 + 294540 CTTTACCAATAACTCCCTCCTAATG -s simCow_chr6.simCow.chr6 310841 25 + 602619 CTTGTCCTATTACTCGCTTCTAAAG -s simDog_chr6.simDog.chr6 290903 25 - 593897 CTTGTTCAAGTGCTCACGGGTTATG -s simHuman_chr6.simHuman.chr6 322126 25 + 601863 CTTGTCCCATAGCTCCCTCCTAATG -s simMouse_chr6.simMouse.chr6 490010 25 + 636262 CTTTTCCAATAACTCCCTCCTTATG -s simRat_chr6.simRat.chr6 328127 25 + 647215 ACTTACCCATGAGTCCCACCTAATG - -a -s simMouse_chr6.simMouse.chr6 337030 23 + 636262 AGATGTATGACCTCACTGGCTTG -s Anc0.Anc0refChr0 2319 23 + 26507 AGGTGCATGCCCTCACTTGCTTG -s Anc1.Anc1refChr6 2343 23 + 197743 AGGTGCATGCCCTCACTTGCTTG -s Anc2.Anc2refChr6 2415 23 + 7137 AGGTGCATGCCCTCACTTGCTTA -s mr.mrrefChr5 184485 23 + 294540 AGATGTATGACCTCAATGGCTTG -s simCow_chr6.simCow.chr6 310880 23 + 602619 AGGTACATGGCCTCACTTGCTTT -s simDog_chr6.simDog.chr6 290928 23 - 593897 GGGTGCATGCTCGCACTTACTTA -s simHuman_chr6.simHuman.chr6 322151 23 + 601863 AGGTGCATGCCCTCACTTGATTG -s simMouse_chr6.simMouse.chr6 490035 23 + 636262 AGATGTATGACCTCAATGGCTTG -s simRat_chr6.simRat.chr6 328152 23 + 647215 AGATGTATGAACTCAATCGCTTA - -a -s simMouse_chr6.simMouse.chr6 337053 7 + 636262 TATTTAC -s Anc0.Anc0refChr0 2342 7 + 26507 TATTTAC -s Anc1.Anc1refChr6 2366 7 + 197743 TATTTAC -s Anc2.Anc2refChr6 2438 7 + 7137 AATTTAC -s mr.mrrefChr5 184508 7 + 294540 TATTTAC -s simCow_chr6.simCow.chr6 310903 7 + 602619 AACTTAC -s simDog_chr6.simDog.chr6 291084 7 - 593897 AATTTAC -s simDog_chr6.simDog.chr6 290951 7 - 593897 AATTTAC -s simHuman_chr6.simHuman.chr6 322174 7 + 601863 TATTTAT -s simMouse_chr6.simMouse.chr6 490058 7 + 636262 TATTTAT -s simRat_chr6.simRat.chr6 328175 7 + 647215 TATTTAC - -a -s simMouse_chr6.simMouse.chr6 337060 44 + 636262 CCCTACACCACAGATGTAGTGTCTAATCATACAGGCAAGTTGGG -s Anc0.Anc0refChr0 2349 36 + 26507 CCCTACAGCATAGATTTAGTGGCTAA--------GCAAGACAGG -s Anc1.Anc1refChr6 2373 36 + 197743 CCCTACAGCATAGATTTAGTGGCTAA--------GCAAGACAGG -s Anc2.Anc2refChr6 2445 36 + 7137 ACCCAGGGCATAGATTTAGTGGCTAA--------ACAAAACAGG -s mr.mrrefChr5 184515 44 + 294540 CCCTACACCACAGATGTAGTGTCTAATCATACAGGCAAGTTGGG -s simCow_chr6.simCow.chr6 310924 35 + 602619 CCACCAGGCATAG-TTCAATGGCTAA--------GCAAAACAGG -s simDog_chr6.simDog.chr6 291091 36 - 593897 ACCCAGGGCGTAGATTTAGTGGCTAT--------ACAAGACAGG -s simDog_chr6.simDog.chr6 290958 33 - 593897 ACCCAGGGCATAGATTTGGTGGCTAC--------ATAAAAC--- -s simHuman_chr6.simHuman.chr6 322181 30 + 601863 CCTTGCAGCA------TAGTGGCTAA--------GGGAGACACA -s simRat_chr6.simRat.chr6 328182 44 + 647215 CCCTACACCACAGATTTAGCATCTAATAATACAGGCAAGTTGTG - -a -s simMouse_chr6.simMouse.chr6 337104 11 + 636262 CAAGTGATTGC -s Anc0.Anc0refChr0 2385 11 + 26507 CAAGTGATTGC -s Anc1.Anc1refChr6 2409 11 + 197743 CAAGTGATTGC -s Anc2.Anc2refChr6 2481 11 + 7137 CAAGTGATTGC -s mr.mrrefChr5 184559 11 + 294540 CAAGTGATTGC -s simCow_chr6.simCow.chr6 310959 11 + 602619 CATGTTATTCT -s simDog_chr6.simDog.chr6 291128 11 - 593897 CAAGTGATTGC -s simDog_chr6.simDog.chr6 290991 9 - 593897 --AGTGATTAC -s simHuman_chr6.simHuman.chr6 322211 11 + 601863 CAAACAATTGC -s simRat_chr6.simRat.chr6 328226 11 + 647215 CAAGTGATCGC - -a -s simMouse_chr6.simMouse.chr6 337115 46 + 636262 TAAGATGAGATTTTTAACTAAAAAGGGGAGTAGTGGAAGGCATAGC -s Anc0.Anc0refChr0 2398 46 + 26507 TAATATGAGAGTTATAACAAAGAAAGAAAATAGTGGCAAACATATT -s Anc1.Anc1refChr6 2422 46 + 197743 TAATATGAGAGTTATAACAAAGAAAGAAAATAGTGGCAAACATATT -s Anc2.Anc2refChr6 2494 46 + 7137 TAATATGAAGGTTATAATAAAGAAAGAAACTAGTGGCCAACATGTT -s mr.mrrefChr5 184570 46 + 294540 TAAGATGAGATTTTTAACTAAGAAGGGGAATAGTGGCAGACATAGT -s simCow_chr6.simCow.chr6 310972 45 + 602619 TAACATGAAGGTTTTGATAAATAAAGAAACTAGTGG-CAACATAAG -s simDog_chr6.simDog.chr6 291141 46 - 593897 TAATATGAAGGCTATAATAAAGAAAGAAACTAGTGGCAAGCATGTT -s simDog_chr6.simDog.chr6 291002 46 - 593897 TAATATGAAGGTTAGAAACAAGAAAGAAACTAGTAGCCAACATGTT -s simHuman_chr6.simHuman.chr6 322224 46 + 601863 TAATATGTGAGTTATAACAAAGGAATAAAATGGTGGCAAATATATT -s simRat_chr6.simRat.chr6 328237 46 + 647215 TAGGCTGAGATTGTTAACTATGAAGGGGAATAGTGGCAGACATAGT - -a -s simMouse_chr6.simMouse.chr6 337161 31 + 636262 GCCCAAATAGCAAAATACACACATACCAGCC -s Anc0.Anc0refChr0 2444 29 + 26507 GCCCAGATTACAAA--ACACATAAGCAAGCC -s Anc1.Anc1refChr6 2468 29 + 197743 GCCCAGATTACAAA--ACACATAAGCAAGCC -s Anc2.Anc2refChr6 2540 29 + 7137 GCCCAGATTACACT--ACACATAAGCAAGCA -s mr.mrrefChr5 184616 29 + 294540 GCCCAAATAGCAAA--ACACACATACCAGCC -s simCow_chr6.simCow.chr6 311017 27 + 602619 GCCCAG--TACAAA--ACACATAAACAATCA -s simDog_chr6.simDog.chr6 291198 29 - 593897 GCCCAGATTACACT--ATGCATAAGCAAGCA -s simDog_chr6.simDog.chr6 291048 29 - 593897 GCCCACATTACACT--ACACACAAGCAAGCA -s simHuman_chr6.simHuman.chr6 322270 29 + 601863 GCCCAGATTATGAA--ACACATAAGCAAGCC -s simRat_chr6.simRat.chr6 328283 13 + 647215 GCCCAAAT------------ACATA------ - -a -s simMouse_chr6.simMouse.chr6 337192 6 + 636262 AGTGAT -s Anc0.Anc0refChr0 2473 6 + 26507 AGTGAT -s Anc1.Anc1refChr6 2497 6 + 197743 AGTGAT -s Anc2.Anc2refChr6 2569 6 + 7137 AGTGAT -s mr.mrrefChr5 184645 6 + 294540 AGTGAT -s simCow_chr6.simCow.chr6 311044 6 + 602619 AGTGAT -s simDog_chr6.simDog.chr6 291227 6 - 593897 GGTGTA -s simHuman_chr6.simHuman.chr6 322300 6 + 601863 AGTGAT - -a -s simMouse_chr6.simMouse.chr6 337198 12 + 636262 CTCTCAAGGGTG -s Anc0.Anc0refChr0 2484 12 + 26507 CTCTCGAGGATG -s Anc1.Anc1refChr6 2508 12 + 197743 CTCTCGAGGATG -s Anc2.Anc2refChr6 2580 12 + 7137 CTCTTGGGGATG -s mr.mrrefChr5 184651 12 + 294540 CTCTCAAGGGTG -s simCow_chr6.simCow.chr6 311055 12 + 602619 CTCTTGGGGCTG -s simDog_chr6.simDog.chr6 291238 11 - 593897 CTCCTAGGGAT- -s simHuman_chr6.simHuman.chr6 322311 12 + 601863 CTCTCGAGGATG -s simRat_chr6.simRat.chr6 328296 11 + 647215 -TCTAAAGGGTG - -a -s simMouse_chr6.simMouse.chr6 337210 58 + 636262 ATAGCATTATTCAAGGCATGGACTGTGACTTGGTATTAAATCATACTGCCCCAGTTGT -s Anc0.Anc0refChr0 2496 49 + 26507 ATAGAATTATTT-G----TGG-CA--ACC-TGGACTCAAATGATACTGCCCCAGCTGT -s Anc1.Anc1refChr6 2520 55 + 197743 ATAGAATTATTT-GGACATGG-CAGTACC-TGGACTCAAATGATACTGCCCCAGCTGT -s Anc2.Anc2refChr6 2592 49 + 7137 AAAGAATTATTT-G----TAG-CA--ACC-TGGACTCTAATGATACTGGCCCAGCTGT -s mr.mrrefChr5 184663 58 + 294540 ATAGCATTATTCAAGGCATGGACAGTGCCTTGGTCTCAAATCATACTGCCCCAGTTGT -s simCow_chr6.simCow.chr6 311069 20 + 602619 AAAGAATTATTT-G-------------------------------------CAGCTTG -s simDog_chr6.simDog.chr6 291249 36 - 593897 ------------------TAG-CA--ACC-TGGACTCTAATGATACTGGCCCAGTTGT -s simHuman_chr6.simHuman.chr6 322323 55 + 601863 ATAGAATTATTT-GGACATGG-CAGTACC-TAGACTCAAATGGTACTGCCCCAGCTGT -s simRat_chr6.simRat.chr6 328307 58 + 647215 ATAGTGATATTCAAGGCATGGGTACTGCCTTGGTCTCAAATCATACTGCCCCAGTTGT - -a -s simMouse_chr6.simMouse.chr6 337268 44 + 636262 AACCATTATTCTTCTGAGAGGGTCATACCATTGATGGTTTGTCT -s Anc0.Anc0refChr0 2545 40 + 26507 GACCATTATTCATTTGAGAAGTTCATACAATACAAG----GTCT -s Anc1.Anc1refChr6 2575 40 + 197743 GACCATTATTCATTTGAGAAGTTCATACAATACAAG----GTCT -s Anc2.Anc2refChr6 2647 40 + 7137 GACAATTATTCATTTGAAAAGTTCATACAATACAAG----GTCT -s mr.mrrefChr5 184721 44 + 294540 AACCATTATTCTTCTGAGAGGGTCATACCATTGATGGTTTGTCT -s simCow_chr6.simCow.chr6 311095 40 + 602619 GACAATTGCTCATTTGAAAAGTTCGTAAAATACAAG----GTCA -s simDog_chr6.simDog.chr6 291291 40 - 593897 GACAATTATTCATTTGGAAAATTCATACACTACAAG----GTCT -s simHuman_chr6.simHuman.chr6 322378 39 + 601863 GA-CATTATTCACTTGAGAAGTTATTACAATACAAG----GTCT -s simRat_chr6.simRat.chr6 328365 44 + 647215 AACCATTATTCTTCTGAGAGGGCCATACCATTGATGGTTTGTCT - -a -s simMouse_chr6.simMouse.chr6 337312 2 + 636262 CT -s Anc0.Anc0refChr0 2585 2 + 26507 CT -s Anc1.Anc1refChr6 2615 2 + 197743 CT -s Anc2.Anc2refChr6 2689 2 + 7137 CT -s mr.mrrefChr5 184765 2 + 294540 CT -s simCow_chr6.simCow.chr6 311137 2 + 602619 CT -s simDog_chr6.simDog.chr6 291333 2 - 593897 CT -s simHuman_chr6.simHuman.chr6 322417 2 + 601863 CT -s simRat_chr6.simRat.chr6 328409 2 + 647215 CT - -a -s simMouse_chr6.simMouse.chr6 337314 45 + 636262 GTTTGCCTATTTATGTCCAGTTATATATAGCCATCTATATTCATG -s Anc0.Anc0refChr0 2587 45 + 26507 GTTCTCTTATTTACATCCAATTATTTACATCCATTTATATTCATG -s Anc1.Anc1refChr6 2617 45 + 197743 GTTCTCTTATTTACATCCAATTATTTACATCCATTTATATTCATG -s Anc2.Anc2refChr6 2691 45 + 7137 GTTCTCTTATTTACATCCAATTGTTTACATCCAATTATATTTATG -s mr.mrrefChr5 184767 45 + 294540 GTTTGCCTATTTATGTCCAGTTATATATATCCATCTATATTCATG -s simCow_chr6.simCow.chr6 311141 43 + 602619 GTTCTTTTATGAACATCCAATTCTTTACTTCCAATTATACTGA-- -s simDog_chr6.simDog.chr6 291335 45 - 593897 TTATTCATATTTACATCCAATTGTTTACATCCAACTATATTTATG -s simHuman_chr6.simHuman.chr6 322419 45 + 601863 GTTCTCTTATTTACATCCAATTATTTACATCCATTAATATACATG -s simRat_chr6.simRat.chr6 328411 45 + 647215 GTTTGCCTATTTATGTCCAGTTATATATATCCATCTATATTCATG - -a -s simMouse_chr6.simMouse.chr6 337359 26 + 636262 TGGTACATATGCGCTTAGCCGTTGAC -s Anc0.Anc0refChr0 2632 13 + 26507 TACTTT-------------GTTTAAC -s Anc1.Anc1refChr6 2662 26 + 197743 TACTTTACTCGAGATTGGAGTTTAAC -s Anc2.Anc2refChr6 2736 13 + 7137 TACTTT-------------GTTTAAC -s mr.mrrefChr5 184812 26 + 294540 TGGTATACTTGAGATTAGACGTTGAC -s simCow_chr6.simCow.chr6 311184 8 + 602619 -----T-------------GCTGATT -s simDog_chr6.simDog.chr6 291588 13 - 593897 TACTTT-------------GTGTCAC -s simHuman_chr6.simHuman.chr6 322464 26 + 601863 TACTTTACTCGAGATTGGAGTTTAGC -s simRat_chr6.simRat.chr6 328456 26 + 647215 TGGTATACTGGAGATCAGATGTTGCC - -a -s simMouse_chr6.simMouse.chr6 337385 2 + 636262 TG -s Anc0.Anc0refChr0 2645 2 + 26507 TG -s Anc1.Anc1refChr6 2688 2 + 197743 TG -s Anc2.Anc2refChr6 2749 2 + 7137 TG -s mr.mrrefChr5 184838 2 + 294540 TG -s simCow_chr6.simCow.chr6 311192 2 + 602619 TG -s simDog_chr6.simDog.chr6 291601 2 - 593897 TG -s simHuman_chr6.simHuman.chr6 322490 2 + 601863 TG -s simRat_chr6.simRat.chr6 328491 2 + 647215 TG - -a -s simMouse_chr6.simMouse.chr6 337387 25 + 636262 TTGTACCGTGTGACTATTAAATGTG -s Anc0.Anc0refChr0 2648 25 + 26507 TTGTACAGCCTGGCTATCAAATGAG -s Anc1.Anc1refChr6 2691 25 + 197743 TTGTACAGCCTGGCTATCAAATGAG -s Anc2.Anc2refChr6 2752 25 + 7137 TTGTACAGCCTGGCTATCAAATTAG -s mr.mrrefChr5 184840 25 + 294540 TTGTACCGTGTGACTATTAAATGTG -s simCow_chr6.simCow.chr6 311195 25 + 602619 TTGTACAGCCTGGCTATCATACTAG -s simDog_chr6.simDog.chr6 291604 24 - 593897 ATCT-CGACCGGGCTATCAAATTAG -s simHuman_chr6.simHuman.chr6 322493 25 + 601863 TTGTACAGCCTAGCTATCAAATGAG -s simRat_chr6.simRat.chr6 328493 25 + 647215 TTATATCATGGGACTATTAAGAGTG - -a -s simMouse_chr6.simMouse.chr6 337412 7 + 636262 AGGTGAT -s Anc0.Anc0refChr0 2675 7 + 26507 AGGTGAC -s Anc1.Anc1refChr6 2718 7 + 197743 AGGTGAC -s Anc2.Anc2refChr6 2779 7 + 7137 AGGTGAC -s mr.mrrefChr5 184865 7 + 294540 AGGTGAC -s simCow_chr6.simCow.chr6 311222 7 + 602619 AGGTGAC -s simDog_chr6.simDog.chr6 291630 7 - 593897 AGGTGAC -s simHuman_chr6.simHuman.chr6 322520 7 + 601863 AGGTGAC -s simRat_chr6.simRat.chr6 328518 7 + 647215 AGGTGAC - -a -s simMouse_chr6.simMouse.chr6 337419 44 + 636262 TCCTAGAGAACCTAAAGAATTCATAAGGTCACTTTGCAATGATA -s Anc0.Anc0refChr0 2708 44 + 26507 TCATAGGGTACATCAAGAATGTACAAGGTGATTTTATAATGATA -s Anc1.Anc1refChr6 2751 44 + 197743 TCATAGGGTACATCAAGAATGTACAAGGTGATTTTATAATGATA -s Anc2.Anc2refChr6 2812 44 + 7137 TCATAGGGTACATCAAGAATGTACAAGGTGATTGTATAATGATA -s mr.mrrefChr5 184872 44 + 294540 TCATAGAGAACATAAAGAATTCATAAGGTCACTTTATAATGATA -s simCow_chr6.simCow.chr6 311255 38 + 602619 ACATAGGGTACATGACGAAC------GGTGGCTGTATAGTGATA -s simDog_chr6.simDog.chr6 291663 44 - 593897 TCATAGGGTACATCAAGAATGTACAATGTGATTGTATAATGATA -s simHuman_chr6.simHuman.chr6 322553 44 + 601863 TCATAGGGGACATTAAGAATGTACAAGGTGATTTTATAATGATA -s simRat_chr6.simRat.chr6 328525 44 + 647215 TCATAGAGAACATCTAGCTTTCATAAGGTCACTTTATAATGATA - -a -s simMouse_chr6.simMouse.chr6 337463 11 + 636262 CTCACATTATT -s Anc0.Anc0refChr0 2752 11 + 26507 GTCATCCCATT -s Anc1.Anc1refChr6 2795 11 + 197743 GTCATCCCATT -s Anc2.Anc2refChr6 2856 11 + 7137 GTCATCCCATT -s mr.mrrefChr5 184916 11 + 294540 CTCACATTATT -s simCow_chr6.simCow.chr6 311293 11 + 602619 GTCATCAGATT -s simDog_chr6.simDog.chr6 291707 11 - 593897 GTCATCCCATT -s simHuman_chr6.simHuman.chr6 322597 4 + 601863 GTCA------- -s simRat_chr6.simRat.chr6 328572 11 + 647215 CTCACCTTGTT - -a -s simMouse_chr6.simMouse.chr6 337474 16 + 636262 AATGTGCCAATCTAGT -s Anc0.Anc0refChr0 2763 16 + 26507 AATTTGCCTAGCTAGT -s Anc1.Anc1refChr6 2806 16 + 197743 AATTTGCCTAGCTAGT -s Anc2.Anc2refChr6 2871 16 + 7137 AATTTGCCTAGATAGT -s mr.mrrefChr5 184927 16 + 294540 AATTTGCCAAGCTAGT -s simCow_chr6.simCow.chr6 311308 16 + 602619 ATTTTCCCAAAACGGT -s simDog_chr6.simDog.chr6 291722 16 - 593897 AATTTGCCTAGATAGT -s simHuman_chr6.simHuman.chr6 322601 13 + 601863 ---TTGCGTGGCTGGT -s simRat_chr6.simRat.chr6 328584 16 + 647215 AATTTGCCCAGATAGT - -a -s simMouse_chr6.simMouse.chr6 337490 195 + 636262 ACCAGCTCATTTGCAAACCAAAAAATCTCAGCATAAATATTTAATGATGTTTAGATTTTTGCACAGTGCCTCATGCAAAGCTCCAATAAAACACAAACGTGGCCAAGTATATGCAGTAAATGATTGGCTGTGAGCCTGCCCCACATGGCCAAGTACATACAGTTAGTACATGGCTATGAGTAATATCAAGCCCAT -s Anc0.Anc0refChr0 2779 54 + 26507 CCATTCATATTTGCAAAATTAGAAATCCCAGTGTAAATA---------------------------------------------------------------------------------------------------------------------------------------------TAATAACAAGCCCAC -s Anc1.Anc1refChr6 2822 54 + 197743 CCATTCATATTTGCAAAATTAGAAATCCCAGTGTAAATA---------------------------------------------------------------------------------------------------------------------------------------------TAATAACAAGCCCAC -s Anc2.Anc2refChr6 2889 54 + 7137 CCACTCATATTTGCAAAATTAAAAATCCCAGTGTAAATA---------------------------------------------------------------------------------------------------------------------------------------------TAATAACAGGCCCAC -s mr.mrrefChr5 184943 194 + 294540 ACCTGCTCATTTGCAAACCAAGAAATCCCAGCATAAATATTTAATGATGTTTAGA-TTTTGCACAGTGCCTCATGCAAAGCTCCAATAAAACACAAACGTGGCCAAGTATATGCAGTAAATGATTGGCTGTGAGCCTGCCCCACATGGCCAAGTACATACAGTTAGTACATGGCTATGAGTAATATCAAGCCCAT -s simCow_chr6.simCow.chr6 311326 54 + 602619 CCACTCATGTTTGCAAAATGGAAAATCCCAGGGTAAATA---------------------------------------------------------------------------------------------------------------------------------------------TAATATCAGGCCCAC -s simDog_chr6.simDog.chr6 291740 53 - 593897 CCACTTACATTTGCAAAATTAAAAATCCCAATGTAAATA---------------------------------------------------------------------------------------------------------------------------------------------TTGT-ATAGGCCCGC -s simHuman_chr6.simHuman.chr6 322614 54 + 601863 CCATCCATATTTACAAAAATAGAAAGCCCAGTGTTGATA---------------------------------------------------------------------------------------------------------------------------------------------TAATGGCAAACCCAG -s simRat_chr6.simRat.chr6 328600 194 + 647215 GCCTGCTCATTTCCAAACCAAGAAATCCCAGCATAAATACTTAATATTGTTTGGA-TTTCACTCAGTGCCTCATGCAAAGCTCCAATAAAATGCAAACGTGGCCATGTACGAACAGTTAATGATTGTCTTTGAGCCTGCCCTGCGCAGCTGCATACATACAGTTAATGCTTGACTATATGTAATAACAAGCCCAT - -a -s simMouse_chr6.simMouse.chr6 337685 7 + 636262 TACTGCA -s Anc0.Anc0refChr0 2833 7 + 26507 TACTGCA -s Anc1.Anc1refChr6 2876 7 + 197743 TACTGCA -s Anc2.Anc2refChr6 2943 7 + 7137 TGCTGCA -s mr.mrrefChr5 185137 7 + 294540 TACTGCA -s simCow_chr6.simCow.chr6 311380 7 + 602619 TGCTGCA -s simDog_chr6.simDog.chr6 291793 7 - 593897 TGCCACA -s simHuman_chr6.simHuman.chr6 322668 7 + 601863 TACTGCC -s simRat_chr6.simRat.chr6 328795 7 + 647215 TACTGCA - -a -s simMouse_chr6.simMouse.chr6 337692 36 + 636262 GACACTAGACATTGCATGGAATGTACACCTGCAGGT -s Anc0.Anc0refChr0 2840 36 + 26507 GCAACTAGTCATTACATGGAATGTACACCTGTAGGT -s Anc1.Anc1refChr6 2883 36 + 197743 GCAACTAGTCATTACATGGAATGTACACCTGTAGGT -s Anc2.Anc2refChr6 2950 36 + 7137 GCAACTAGTCATTACATGGAATGTGCACCTGTAGGT -s mr.mrrefChr5 185144 36 + 294540 GACACTAGACATTGCATGGAATGTACACCTGTAGGT -s simCow_chr6.simCow.chr6 311387 36 + 602619 GGAACTAGTCCTTATATGGAATGTTCTCCTCTAAGT -s simDog_chr6.simDog.chr6 291800 36 - 593897 ACAACTAGTCATTACATGGAATGGGCACCTGCAGGT -s simHuman_chr6.simHuman.chr6 322675 36 + 601863 GCAACTAGGCATTACATGAAATGTACACCTATAGGT -s simRat_chr6.simRat.chr6 328803 36 + 647215 GACACTAGATATTGCATGGAATGTACATCTGTAGGT - -a -s simMouse_chr6.simMouse.chr6 337728 27 + 636262 GCAGACTTCCGATTCATCATCAATATA -s Anc0.Anc0refChr0 2876 23 + 26507 GTAGATTCACACTTCATAATGA--G-- -s Anc1.Anc1refChr6 2919 25 + 197743 GTAGATTCACACTTCATAATGACTG-- -s Anc2.Anc2refChr6 2986 23 + 7137 GTAGATTCACACTTCATAATGA--G-- -s mr.mrrefChr5 185180 27 + 294540 GCAGACTTCAGATTCATCATCAATATA -s simCow_chr6.simCow.chr6 311423 15 + 602619 ATGGGTTGGTACTTC------------ -s simDog_chr6.simDog.chr6 291836 23 - 593897 GCAGATTCACACTTCATAATGA--G-- -s simHuman_chr6.simHuman.chr6 322711 19 + 601863 GTAGA------CTTGATTATGACTG-- -s simRat_chr6.simRat.chr6 328863 27 + 647215 ACGGACTTCAACTTCATCATTAATATA - -a -s simMouse_chr6.simMouse.chr6 337755 31 + 636262 TAGATTTAAGGCTAGCGTGGAGGTGGGGAGA -s Anc0.Anc0refChr0 2899 13 + 26507 ------------------GGGAGTTGTCAAA -s Anc1.Anc1refChr6 2944 13 + 197743 ------------------GGGAGTTGTCAAA -s Anc2.Anc2refChr6 3009 13 + 7137 ------------------AGTAGTTGTCAAA -s mr.mrrefChr5 185207 31 + 294540 TAGATTTAAGGCTAGCGTGGGGGTGGGGAGA -s simDog_chr6.simDog.chr6 291859 13 - 593897 ------------------AGTAGTTGTCAAA -s simHuman_chr6.simHuman.chr6 322730 13 + 601863 ------------------GGGAGTTGACAAA -s simRat_chr6.simRat.chr6 328891 31 + 647215 TGGATTCAAGGCTAGCATGGGGGTGGGGAGA - -a -s simMouse_chr6.simMouse.chr6 337786 25 + 636262 GTATGAGAGGGAGGACAACATTAGA -s Anc0.Anc0refChr0 2912 17 + 26507 AGATGGGAGGGAGGATT-------- -s Anc1.Anc1refChr6 2957 25 + 197743 AGATGGGAGGGAGGATTATATTTGA -s Anc2.Anc2refChr6 3022 17 + 7137 ACATGGCGTAGAGGGTT-------- -s mr.mrrefChr5 185238 25 + 294540 GGATGAGAGGGAGGACAATATTAGA -s simDog_chr6.simDog.chr6 291872 17 - 593897 ACATGGCGTAGAGGGTT-------- -s simHuman_chr6.simHuman.chr6 322748 25 + 601863 TGATGGGAGGGGGTATGATATTTGA -s simRat_chr6.simRat.chr6 328922 25 + 647215 GGATTAGAAGGAGAAAAATATTAGA - -a -s simMouse_chr6.simMouse.chr6 337811 87 + 636262 AAACAAGCGTTCATGCTGGTATGCTTGCAGACATACGACATCCAGACAATGAGGTGAGCTTACAGTTCAGAGGATCACTCAATTGAC -s Anc0.Anc0refChr0 2929 64 + 26507 -----------------------ATTGGGGATATAGAAAGCCCAGACAATGAGGTGAGCTTACTGTTTAGAAGATTGCTCAATTGGT -s Anc1.Anc1refChr6 2982 87 + 197743 AAGTGAATGTGCAGCCTGATATGATTGGGGATATAGAAAGCCCAGACAATGAGGTGAGCTTACTGTTTAGAAGATTGCTCAATTGGT -s Anc2.Anc2refChr6 3039 64 + 7137 -----------------------ATTAGGGAGCTAGAAAGCCCAGGGAAAGAGGTAATCTTACTGCTTAGAAGATTGTTCACTTGGT -s mr.mrrefChr5 185263 87 + 294540 AAATAAGTGTTCATCCTGGTATGCTTGCAGATATACGACATCCAGACAATGAGGTGAGCTTACTGTTCAGAGGATCACTCAATTGAC -s simCow_chr6.simCow.chr6 311438 60 + 602619 ---------------------------TGCAGTTAGAACGCCCAGGGAAAAAGGTAACCTTACTGCTTAGATGTTTGTCTACTTGGT -s simDog_chr6.simDog.chr6 291889 64 - 593897 -----------------------ATTAGGGAGCTAGAAAGCCTAGGGACAGAGATAATATTACTGCTTTGTAGATTGTTCCCTTGGT -s simHuman_chr6.simHuman.chr6 322776 87 + 601863 AAGTGAATGTGCAGCCTGATATGACTGGGGATATAGAAAGCCCAAACAATGAGGTGGGCTTACTGTTTAAAAGATTGCTCAATCAGA -s simRat_chr6.simRat.chr6 328947 70 + 647215 AAATAAGTATTCATCCTGGTATGCTTGCAGATATATCACATCCAGACAATGATGAGAGTTTACTGTTCAG----------------- - -a -s simMouse_chr6.simMouse.chr6 337898 17 + 636262 TTTCCTAGACCAAAAGG -s Anc0.Anc0refChr0 2995 17 + 26507 TTTTCAACATCTCAAGG -s Anc1.Anc1refChr6 3071 17 + 197743 TTTTCAACATCTCAAGG -s Anc2.Anc2refChr6 3105 17 + 7137 TTTTTAACATCTCAGTG -s mr.mrrefChr5 185350 17 + 294540 TTTCCTAGACCAAAAGG -s simCow_chr6.simCow.chr6 311500 17 + 602619 TTTTTGATATCTCACAG -s simDog_chr6.simDog.chr6 291955 17 - 593897 TTATTAACATCTCAGTG -s simHuman_chr6.simHuman.chr6 322865 17 + 601863 TTTACAACATTTCAAGG -s simRat_chr6.simRat.chr6 329017 10 + 647215 -------GACCAAAAGG - -a -s simMouse_chr6.simMouse.chr6 337915 22 + 636262 CTTGTACAAAATCATTGAATCA -s Anc0.Anc0refChr0 3015 15 + 26507 CTTG-------TCATTGAATCC -s Anc1.Anc1refChr6 3091 15 + 197743 CTTG-------TCATTGAATCC -s Anc2.Anc2refChr6 3125 15 + 7137 CTTG-------CCATTGAGTCC -s mr.mrrefChr5 185367 22 + 294540 CTTGTACAAAATCATTGAATCA -s simCow_chr6.simCow.chr6 311520 15 + 602619 CTAA-------CATTTGAGTTC -s simDog_chr6.simDog.chr6 291975 15 - 593897 CTTG-------CCATTGAGCCC -s simHuman_chr6.simHuman.chr6 322885 15 + 601863 CTTG-------TCATTGAATCC -s simRat_chr6.simRat.chr6 329027 22 + 647215 CTTGCACAAAATCATTGAATCA - -a -s simMouse_chr6.simMouse.chr6 337937 32 + 636262 ACAACTTGTTTTTCCATCTCAATAAATTGACA -s Anc0.Anc0refChr0 3030 13 + 26507 GGCCCTGGCTATC------------------- -s Anc1.Anc1refChr6 3106 13 + 197743 GGCCCTGGCTATC------------------- -s Anc2.Anc2refChr6 3141 13 + 7137 GGCCCTGACTATC------------------- -s mr.mrrefChr5 185389 32 + 294540 ACAACTTGTTTTTCCATCTCAATAAATTGACA -s simCow_chr6.simCow.chr6 311536 13 + 602619 GGCCCTGACTATC------------------- -s simDog_chr6.simDog.chr6 291991 13 - 593897 GACCCTTATTCCA------------------- -s simHuman_chr6.simHuman.chr6 322900 13 + 601863 GGCCCTGGCTATC------------------- -s simRat_chr6.simRat.chr6 329049 32 + 647215 ATAACTTGTTCTTCCATCTCAATTAATTGACA - -a -s simMouse_chr6.simMouse.chr6 337969 10 + 636262 TTCAACCAAA -s Anc0.Anc0refChr0 3043 2 + 26507 --------GA -s Anc1.Anc1refChr6 3119 2 + 197743 --------GA -s Anc2.Anc2refChr6 3154 2 + 7137 --------GA -s mr.mrrefChr5 185421 10 + 294540 TTCAACCAAA -s simCow_chr6.simCow.chr6 311549 2 + 602619 --------GA -s simDog_chr6.simDog.chr6 292004 2 - 593897 --------GA -s simHuman_chr6.simHuman.chr6 322913 2 + 601863 --------GA -s simRat_chr6.simRat.chr6 329082 10 + 647215 TTCAATCTAA - -a -s simMouse_chr6.simMouse.chr6 337979 53 + 636262 GGGGACCAGATTTAGGCTTCAAAGAGAAAAGAAAAACTGTCTAGAACAAGATA -s Anc0.Anc0refChr0 3045 49 + 26507 GGTGGCAAGATTTAGTTTCCAAAGAGAAAAG-AAAACTGTCTAGCAC---AAT -s Anc1.Anc1refChr6 3121 52 + 197743 GGTGGCAAGATTTAGTTTCCAAAGAGAAAAG-AAAACTGTCTAGCACAAGAAT -s Anc2.Anc2refChr6 3156 49 + 7137 GGTGGCAAGGTTTAGTTTCCAAAGAGAGCAG-AAAATTGTCTAGCAC---TAT -s mr.mrrefChr5 185431 53 + 294540 GGGGGCCAGATTTAGGTTTCAAAGAGAAAAGAAAAACTGTCTAGAACAAGATA -s simCow_chr6.simCow.chr6 311551 2 + 602619 ---------------------------------------------------AT -s simDog_chr6.simDog.chr6 292010 49 - 593897 GGTGGCAAGGTTTAGTTTCCAAAGAGAGCAG-AAAATTGTCTAGCAC---TAT -s simHuman_chr6.simHuman.chr6 322915 52 + 601863 GGTGGCAACATTTAGTTTCCGAAGAGAAAAG-AGAACTGTCTTGCAAAAGAAT -s simRat_chr6.simRat.chr6 329092 53 + 647215 GGGGGGCAGATTTAGGTTTCAAAGAGAAAAGAAAAACTGTCTAGAACAATATA - -a -s simMouse_chr6.simMouse.chr6 338032 21 + 636262 ACATTTGGCCACTAATTGATT -s Anc0.Anc0refChr0 3094 21 + 26507 AAATCTGCAACCAATTTGATT -s Anc1.Anc1refChr6 3173 21 + 197743 AAATCTGCAACCAATTTGATT -s Anc2.Anc2refChr6 3205 21 + 7137 AAATTTGCAACCATTTTGAAG -s mr.mrrefChr5 185484 21 + 294540 ACATCTGGCCACAAATTGATT -s simCow_chr6.simCow.chr6 311553 21 + 602619 AAAGTTGGATCCAATTTGATC -s simDog_chr6.simDog.chr6 292059 21 - 593897 AAATTTGCAAACATTTTGAAG -s simHuman_chr6.simHuman.chr6 322967 19 + 601863 AAACCTG--TGCAACTAGATT -s simRat_chr6.simRat.chr6 329191 21 + 647215 ACATCCGGCCACAAATTGATT - -a -s simMouse_chr6.simMouse.chr6 338053 45 + 636262 TGGTGCATGGAGAAGCATGGGGGGACCAAATAGTAGGTCCAATAA -s Anc0.Anc0refChr0 3115 20 + 26507 TGGTGGATGGACTGGCATGG------------------------- -s Anc1.Anc1refChr6 3194 20 + 197743 TGGTGGATGGACTGGCATGG------------------------- -s Anc2.Anc2refChr6 3226 20 + 7137 TGGTGGATGGACTGGCATGG------------------------- -s mr.mrrefChr5 185505 45 + 294540 TGGTGCATGGAGAAGCATGGGGGGACCAAATAGTAggtccaataa -s simCow_chr6.simCow.chr6 311574 20 + 602619 TCGTGGCTAGACAAGCATGT------------------------- -s simDog_chr6.simDog.chr6 292080 20 - 593897 TGATGGATGGACTGGCATGG------------------------- -s simHuman_chr6.simHuman.chr6 322988 20 + 601863 TGGAGGATGGACGGGCATGG------------------------- -s simRat_chr6.simRat.chr6 329212 45 + 647215 TGGTGCATGGAGAAGCATGGGGGGACCAGATAGTAggttcaatga - -a -s simMouse_chr6.simMouse.chr6 338098 75 + 636262 tggaagaaactgtgtcccagcatggcagggtttatgatccaccctaagaaggaaaccttgatagaggtggtggac -s mr.mrrefChr5 185550 75 + 294540 tggaagaaactgtgtcccagcatggcagggtttatgatccaccctaagaaggaaaccttgatagaggtggtggac -s simRat_chr6.simRat.chr6 329265 75 + 647215 tggaagaaactgtgtcccagcatggcagggtttatgatccagcctaagaaggaaaccttaatagagctggtggac - -a -s simMouse_chr6.simMouse.chr6 338173 58 + 636262 tctaagaaatcagaggagagggctttcatggattggattcaggccaggttcaaggaat -s mr.mrrefChr5 185625 58 + 294540 tctaagaaatcagaggagagggctttcatggattggattcaggccaggttcaaggaat -s simRat_chr6.simRat.chr6 329344 58 + 647215 tcaaactaatcataggagagggctctcagggattgaattcaggccaggttcaagcaat - -a -s simMouse_chr6.simMouse.chr6 338231 97 + 636262 aattgacacaacacttaacactttaatgcaagtatttatgagtattggcttagaccgtgcaatcatcttcctcctgacgatgatggataatggatca -s mr.mrrefChr5 185683 97 + 294540 aattgacacaacacttaacactttaatgcaagtatttatgagtattggcttagaccgtgcaatcatcttcctcctgacgatgatggataatggatca -s simRat_chr6.simRat.chr6 329403 97 + 647215 aatggatacaacacttaacattttagtgcaggtattggtgagtattggcttagatcgtacatctatcttccttccgatgatgatggatgatggattg - -a -s simMouse_chr6.simMouse.chr6 338328 242 + 636262 ccttcagtaccgagcaagtggttgcaatgaatgtgactgggtatttgtaggggcattatgatgtttgatgtacttaacttgcccaggcctgcccacttccaacttttcagaagtttacctgccttttgtgagatggatcataccatgattagtttagtctgattgacccctattgatgaagtgctctatggaaatatcttaagagaaatgaatacataagaaaaatcaccaagtattgtctg -s mr.mrrefChr5 185780 241 + 294540 ccttcagtaccgagcaagtggttgcaatgaatgtgactgggtatttgtaggggcattatgatgtttgatgtacttaacttgcccaggcctgcccacttcc-acttttcagaagtttacctgccttttgtgagatggatcataccatgattagtttagtctgattgacccctattgatgaagtgctctatggaaatatcttaagagaaatgaatacataagaaaaatcaccaagtattgtctg -s simRat_chr6.simRat.chr6 329501 241 + 647215 ccttcagtactgagcaagtggttgtgatgaatatgatggtgcatttgtaggggtgtaacgatgttcaatgtacttaattcgtccaggcctgcccattttc-actattcaggattttccctgctttttgtcagatggatcaaaccatggttagtgtagtctgattgaaactaattgatgaagtgccctatgaaactatcttgagagaaatgaaaactttaggaagatcaccaagtgttgtttg - -a -s simMouse_chr6.simMouse.chr6 338570 35 + 636262 aggcccgcatcagcccaactagctgtgcagggact -s mr.mrrefChr5 186021 35 + 294540 aggcccgcatcagcccaactagctgtgcagggact -s simRat_chr6.simRat.chr6 329743 35 + 647215 aggcccctgtcagcccagctacctctgcggggatt - -a -s simMouse_chr6.simMouse.chr6 338605 54 + 636262 tcactggttgctgccagtacacctggtgcaagctccattcctactcctctccta -s mr.mrrefChr5 186056 54 + 294540 tcactggttgctgccagtacacctggtgcaagctccattcctactcctctccta -s simRat_chr6.simRat.chr6 329787 54 + 647215 tcacctgctgttgcccgtacacctgatacaagctccattccaactcctcttcaa - -a -s simMouse_chr6.simMouse.chr6 338659 151 + 636262 tgctaagttgtcaagatgagtcatggcatactcccctcttatgtactctgctaaacgccctgatggtggagtgccatgatgatccactagtgcctgactaccagtaagtactaatcttatccctctgatgtaTTTCTGGTGATCCAGTTGC -s mr.mrrefChr5 186110 151 + 294540 tgctaagttgtcaagatgagtcatggcatactcccctcttatgtactctgctaaacgccctgatggtggagtgccatgatgatccactagtgcctgactaccagtaagtactaatcttatccctctgatgtaTTTCTGGTGATCCAGTTGC -s simRat_chr6.simRat.chr6 329848 151 + 647215 tactaagttgtcaagatgagatatgacttgctcccctcttatgtagtctgctgaatcccctgatggaggactgctaggatgattcactaccacctgattaccagtaagtacTAATCTTATCCCTATGATTGATGTCTGCGGAACCAGTTGC - -a -s simMouse_chr6.simMouse.chr6 338810 52 + 636262 TGATTAACAGTTGGTATCCATCTGCGTCGTCTTGTGTCTTTGTCTCAGGAAA -s mr.mrrefChr5 186261 52 + 294540 TGATTAACAGTTGGTATCCATCTGCGTCGTCTTGTGTCTTTGTCTCAGGAAA -s simRat_chr6.simRat.chr6 330002 52 + 647215 TGATTAACAGTTGGTATCCATCTTCGTTGTCTTCTGTTGGTGTCTCAGGAAC - -a -s simMouse_chr6.simMouse.chr6 338862 29 + 636262 CACTAAAGCACACCCAACCATACTAACAT -s mr.mrrefChr5 186313 29 + 294540 CACTAAAGCACACCCAACCATACTAACAT -s simRat_chr6.simRat.chr6 330055 29 + 647215 TACTAAAGCACACCCAACCAGACCATCAG - -a -s simMouse_chr6.simMouse.chr6 338891 8 + 636262 ATGCTAGT -s mr.mrrefChr5 186342 8 + 294540 ATGCTAGT -s simRat_chr6.simRat.chr6 330085 8 + 647215 ATGCTAGT - -a -s simMouse_chr6.simMouse.chr6 338899 58 + 636262 AGTTGGAAATTAACACCAACCATTTTCTTATCTCAGTAGCATATTTTACTACAAGTAT -s mr.mrrefChr5 186350 53 + 294540 AGTTGGAAATTAAC----ACCATTTTCTTATCTCAGTAGCATATTTTACTAC-AGTAT -s simRat_chr6.simRat.chr6 330141 53 + 647215 AGTTGAAAATTAGC----ACCATTCTCTTCTCTAAGTAGCATATTGTACTAC-AGTAT - -a -s simMouse_chr6.simMouse.chr6 338957 214 + 636262 GCATCTGCGAGGTTCTGAAAGTGTCATCTTCTTATGTTgaacctagaagcatacaaagttgtttcccagtcccacacctgcacaatatctacacacctgatcgctctttctcagtatttaatgactgtgttggagggtgcTTGGTACACCAGTAAGTACATCGCTGTCTTATCTGCACTTGATTTACGGTATGCTCAGGTGGAATGTTAATTTG -s Anc0.Anc0refChr0 3135 12 + 26507 -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GGTAGATTGGCA----- -s Anc1.Anc1refChr6 3214 12 + 197743 -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GGTAGATTGGCA----- -s Anc2.Anc2refChr6 3246 12 + 7137 -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GGTAGATGGGCA----- -s mr.mrrefChr5 186403 209 + 294540 GCATCTGCGAGGTTCTGAAAGTGTCATCttcttatgttgaacctagaagcatacaaagttgtttcccagtcccacacctgcacaatatctacacacctgatcgctctttctcagtatttaatgactgtgttggagggtgcTTGGTACACCAGTAAGTACATCGCTGTCTTATCTGCACTTGATTTACGGTATGCTCAGGTGGAATGTTA----- -s simCow_chr6.simCow.chr6 311594 12 + 602619 -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GGTAAATGGGCA----- -s simDog_chr6.simDog.chr6 292100 12 - 593897 -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GGTAGATGGGCA----- -s simHuman_chr6.simHuman.chr6 323008 12 + 601863 -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GATAGCTTAGCG----- -s simRat_chr6.simRat.chr6 330195 209 + 647215 GAATCTGTTTTGTGTTGAAAGTGCCATCttcttgtcttgagccttgaagcatacaatgttgtttaccagtcccacatctgcacagtatctacacacatgattggtctttctcagtttttaatgactgtgttagagggTTCTTTGTGCACCAGTAAGTGCATCACTGTCTTATCTGCACTTGATTTAGGGTATGCTCAGGTAGAATGTTA----- - -a -s simMouse_chr6.simMouse.chr6 339171 16 + 636262 GAATTAAGTTAGACTT -s Anc0.Anc0refChr0 3147 16 + 26507 GAATTGAGTTGGACCG -s Anc1.Anc1refChr6 3226 16 + 197743 GAATTGAGTTGGACCG -s Anc2.Anc2refChr6 3279 16 + 7137 GAACTGAGTTGGACCG -s mr.mrrefChr5 186612 16 + 294540 GAATTAAGTTAGACTT -s simCow_chr6.simCow.chr6 311628 16 + 602619 GAAGTGAGATGAACCT -s simDog_chr6.simDog.chr6 292133 16 - 593897 GAACTGAGTTGGACTG -s simHuman_chr6.simHuman.chr6 323020 16 + 601863 GAGTAGAGTTGGACCA -s simRat_chr6.simRat.chr6 330404 16 + 647215 GAATCATGTTAGACTT - -a -s simMouse_chr6.simMouse.chr6 339187 21 + 636262 GCTCTGAGACTTGCTATGAGA -s Anc0.Anc0refChr0 3163 10 + 26507 TCCATGAGAC----------- -s Anc1.Anc1refChr6 3242 10 + 197743 TCCATGAGAC----------- -s Anc2.Anc2refChr6 3295 10 + 7137 TCCACCAGAC----------- -s mr.mrrefChr5 186628 21 + 294540 GCTCTGAGACTTGCTATGAGA -s simCow_chr6.simCow.chr6 311649 10 + 602619 TCTACCAGAC----------- -s simDog_chr6.simDog.chr6 292149 10 - 593897 TCCACCAGAT----------- -s simHuman_chr6.simHuman.chr6 323036 10 + 601863 TCCATGAAAC----------- -s simRat_chr6.simRat.chr6 330420 21 + 647215 GCTATGAGATTGGCTATGAGA - -a -s simMouse_chr6.simMouse.chr6 339208 10 + 636262 CCTGTCAGGC -s Anc0.Anc0refChr0 3173 5 + 26507 -----CCGTC -s Anc1.Anc1refChr6 3252 5 + 197743 -----CCGTC -s Anc2.Anc2refChr6 3305 5 + 7137 -----CCGTC -s mr.mrrefChr5 186649 10 + 294540 CCTGTCAGGC -s simCow_chr6.simCow.chr6 311659 5 + 602619 -----CCATC -s simDog_chr6.simDog.chr6 292159 5 - 593897 -----ACGTC -s simRat_chr6.simRat.chr6 330472 10 + 647215 TTTGTCAGGC - -a -s simMouse_chr6.simMouse.chr6 339218 35 + 636262 CTGATCTAGTTTCTTTTAACAATATCTGGTATGCA -s Anc0.Anc0refChr0 3178 35 + 26507 CTGATCATGTTTCTATTAACAGCATATGGTATGCA -s Anc1.Anc1refChr6 3257 35 + 197743 CTGATCATGTTTCTATTAACAGCATATGGTATGCA -s Anc2.Anc2refChr6 3310 35 + 7137 CTGATGATGTTTCTATTAACAGCACATGGTATGCA -s mr.mrrefChr5 186659 35 + 294540 CTGATCTTGTTTCTTTTAACAACATCTGGTATGCA -s simCow_chr6.simCow.chr6 311669 35 + 602619 CTGATGATGTTTCTATTAACAACACATGGTATGCA -s simDog_chr6.simDog.chr6 292164 35 - 593897 CTGATGGTGTTTCTGTTAACAGCCCATGATCTGCA -s simHuman_chr6.simHuman.chr6 323046 31 + 601863 ----CCATGTTTGTATTGACAGCATGCGGTATACA -s simRat_chr6.simRat.chr6 330482 35 + 647215 CTGATATTGTTTCTTTTAACAACATTGGATATGCA - -a -s simMouse_chr6.simMouse.chr6 339253 20 + 636262 TAAACTTAAATTAAAAATGG -s Anc0.Anc0refChr0 3223 14 + 26507 TGGACTTAAATTA------T -s Anc1.Anc1refChr6 3302 20 + 197743 TGGACTTAAATTAAAAGTGT -s Anc2.Anc2refChr6 3355 14 + 7137 TGGACTTAAATTA------T -s mr.mrrefChr5 186704 20 + 294540 TAAACTTAAATTAAAAATGG -s simCow_chr6.simCow.chr6 311714 14 + 602619 TGGACCTAAATTA------C -s simDog_chr6.simDog.chr6 292209 14 - 593897 TGGACTTAAATTA------T -s simHuman_chr6.simHuman.chr6 323082 20 + 601863 TGGACTTAAATTGAAAGTGT -s simRat_chr6.simRat.chr6 330527 20 + 647215 TAAACTTAAATTAAAAATGG - -a -s simMouse_chr6.simMouse.chr6 339273 11 + 636262 TTAGACTTACT -s Anc0.Anc0refChr0 3237 11 + 26507 TTAGGCTTATT -s Anc1.Anc1refChr6 3322 11 + 197743 TTAGGCTTATT -s Anc2.Anc2refChr6 3369 11 + 7137 TTAGGCTTATT -s mr.mrrefChr5 186724 11 + 294540 TTAGACTTACT -s simCow_chr6.simCow.chr6 311730 11 + 602619 TTAGGTTCATT -s simDog_chr6.simDog.chr6 292223 11 - 593897 ACAGACTTATT -s simHuman_chr6.simHuman.chr6 323102 11 + 601863 TTAGGCTTATT -s simRat_chr6.simRat.chr6 330547 11 + 647215 TTAGACTTACT - -a -s simMouse_chr6.simMouse.chr6 339284 58 + 636262 TTTTTTTATCACTGTCATACTTGATTGACCTAGTGGTGATGGAGGTGCCACTAAGGAG -s Anc0.Anc0refChr0 3252 57 + 26507 GTGTTTTATCCTTGTCCAAGTTGATTGAACTAGTGGTGGTGGTGGT-CTACTGAATAC -s Anc1.Anc1refChr6 3337 57 + 197743 GTGTTTTATCCTTGTCCAAGTTGATTGAACTAGTGGTGGTGGTGGT-CTACTGAATAC -s Anc2.Anc2refChr6 3384 57 + 7137 GTGTTTTATCCTTGTCCAAGTTGATTGAACTAGTGGTGGTGGTGGT-CTACTGAATAC -s mr.mrrefChr5 186735 58 + 294540 TTTTTTTATCACTGTCATACTTGATTGACCTAGTGGTGATGGAGGTGCCACTAAGGAG -s simCow_chr6.simCow.chr6 311745 57 + 602619 GTGTTTTATCCTTGTCCTAGTTGATTGAACTAGTGGTGGTGGTGGG-CTCCTGGACAC -s simDog_chr6.simDog.chr6 292238 53 - 593897 GTGTCTGACCCTCATACA--TTGATTGAACTAGC-GTGGTGGTGGT-CTAT-GAATAC -s simHuman_chr6.simHuman.chr6 323117 57 + 601863 GTCTTTTATCGTTGTCCAAGTTGATTGAACTACTGGCGCTAGTGGC-CTACAGAAAAC -s simRat_chr6.simRat.chr6 330558 58 + 647215 TTTTTGTAGCACTGTCATGTTTGACTGACCTAGTGGCGATGGAGGTGCCACTAAGGAG - -a -s simMouse_chr6.simMouse.chr6 339342 3 + 636262 CAG -s Anc0.Anc0refChr0 3309 3 + 26507 CAC -s Anc1.Anc1refChr6 3394 3 + 197743 CAC -s Anc2.Anc2refChr6 3441 3 + 7137 CAC -s mr.mrrefChr5 186793 3 + 294540 CAG -s simCow_chr6.simCow.chr6 311847 3 + 602619 AAC -s simDog_chr6.simDog.chr6 292291 2 - 593897 CA- -s simHuman_chr6.simHuman.chr6 323174 3 + 601863 CAA -s simRat_chr6.simRat.chr6 330616 3 + 647215 TAG - -a -s simMouse_chr6.simMouse.chr6 339345 32 + 636262 TGAAACAATTGCTACAAATTAAACTATAGCTC -s Anc0.Anc0refChr0 3318 32 + 26507 CGCAACAATCGCGACAAACTGAACTTTAGCTC -s Anc1.Anc1refChr6 3403 32 + 197743 CGCAACAATCGCGACAAACTGAACTTTAGCTC -s Anc2.Anc2refChr6 3450 32 + 7137 CGCAACAAACGCGGCAAACTGAGGTTTAGCTC -s mr.mrrefChr5 186796 32 + 294540 TGAAACAATTGCTACAAATTAAACTATAGCTC -s simCow_chr6.simCow.chr6 311856 32 + 602619 CACAATAAACGCGGCAAACTGAGTTTTAGCTC -s simDog_chr6.simDog.chr6 292293 31 - 593897 -GTAACAAATGCAGCAGAATAAGGTTTAGCTC -s simHuman_chr6.simHuman.chr6 323183 32 + 601863 GGCAACAATCGTGACAAACTGAACTGTAGCTC -s simRat_chr6.simRat.chr6 330619 31 + 647215 TG-AACAACTGCTACAAGTTAAACTATAGCTT - -a -s simMouse_chr6.simMouse.chr6 339377 23 + 636262 TGTTATACTAGGTATGACTGGGA -s Anc0.Anc0refChr0 3350 22 + 26507 TATCTTCTT-GGCATGACTGGGG -s Anc1.Anc1refChr6 3435 22 + 197743 TATCTTCTT-GGCATGACTGGGG -s Anc2.Anc2refChr6 3482 22 + 7137 TATCTTCTT-GGCATGACTGGGG -s mr.mrrefChr5 186828 23 + 294540 TGTTATCCTAGGTATGACTGGGA -s simCow_chr6.simCow.chr6 311889 21 + 602619 TGTCTCCTT-GGTATGTCTGGG- -s simDog_chr6.simDog.chr6 292324 22 - 593897 TATCTTCTT-GGCATGACTGGGG -s simHuman_chr6.simHuman.chr6 323215 22 + 601863 TATCGTGTT-GGCATGATTGGGG -s simRat_chr6.simRat.chr6 330650 23 + 647215 TGTTATCCTGGGTATAACTGGGT - -a -s simMouse_chr6.simMouse.chr6 339400 17 + 636262 CACTAAATCATGTGCTG -s Anc0.Anc0refChr0 3373 17 + 26507 GATTTAGCCATGTCCTG -s Anc1.Anc1refChr6 3458 17 + 197743 GATTTAGCCATGTCCTG -s Anc2.Anc2refChr6 3505 17 + 7137 GATTTAGCCATGTCCTG -s mr.mrrefChr5 186851 17 + 294540 GACTAAATCATGTGCTG -s simCow_chr6.simCow.chr6 311910 17 + 602619 GATTATGCCATATCCTG -s simDog_chr6.simDog.chr6 292347 17 - 593897 GATTTAGCCATGCCCTG -s simHuman_chr6.simHuman.chr6 323238 17 + 601863 GATCCAGCCATGTCCTG -s simRat_chr6.simRat.chr6 330673 17 + 647215 GACTAAATCATGTGCCG - -a -s simMouse_chr6.simMouse.chr6 339417 92 + 636262 CAAATTAATAATCTAGAAAATAAAAAAGCTCTGCAAGCACCGTCAACAGACTTTTTGGTTAAGGAGATGATTATTAACAAAAAATTGTGACC -s Anc0.Anc0refChr0 3391 90 + 26507 CTAAATAGTGGTCTACAAAATAAAAAAGCTTTGCAAGCACCATTAATAAAC--TTTGCCTAAGGAGATTAGTATTATCAAAAAATAGAGCAG -s Anc1.Anc1refChr6 3476 90 + 197743 CTAAATAGTGGTCTACAAAATAAAAAAGCTTTGCAAGCACCATTAATAAAC--TTTGCCTAAGGAGATTAGTATTATCAAAAAATAGAGCAG -s Anc2.Anc2refChr6 3523 90 + 7137 GTAAATAGTGGTCTACAAAATAAAAAAGCTTTGCAAACGCCATTAATAAGC--TGTGCCTAAGGAGATTAGCATTGTCAAAAAAAAGAGCAG -s mr.mrrefChr5 186868 92 + 294540 CAAATTAATAGTCTACAAAATAAAAAAGCTTTGCAAGCACCGTCAACAAACTTTTTGGCTAAGGAGATGAGTATTAACAAAAAATTGTGAAC -s simCow_chr6.simCow.chr6 311928 81 + 602619 GGAAATAGTAGTCCGCAAAATAAAAAAACTTTGCGAAA---------AGGC--TGTGCCTCAGGAGATTAGCATTTTCCAAAACAAGGGAAG -s simDog_chr6.simDog.chr6 292365 90 - 593897 GTAGTTAGGGATGTATAAAATAAGAATGCTTTGCAAACGCCATTAATCAGC--TGGGCCTAAGGAGGTTAGCATTGACACAAAAAAGAGCAG -s simHuman_chr6.simHuman.chr6 323256 90 + 601863 CTAAATAGTGGTCTACACAATACAAGAGCTTTGCTAGCACCATTAATAAAC--ATTGCTTGCATAAATTATTGTTATCAAAAAATAGAGCAG -s simRat_chr6.simRat.chr6 330690 89 + 647215 CAGGGTACTAGTTTACAAAATAAAAAAGCTTTGCAAGCACCATCAACAAACTATTTGACTAATGAGATGAGTAC---CGAAAAGGGGTGAAC - -a -s simMouse_chr6.simMouse.chr6 339509 27 + 636262 TCGGAAGATGGGCCTACATATTTGCAG -s Anc0.Anc0refChr0 3481 27 + 26507 ATGGAAGATGGCCCTACAAACTTGCTG -s Anc1.Anc1refChr6 3566 27 + 197743 ATGGAAGATGGCCCTACAAACTTGCTG -s Anc2.Anc2refChr6 3613 27 + 7137 ATAGAAGATGGCCCTACAAACTGGCTG -s mr.mrrefChr5 186960 27 + 294540 TTGGAAGATGGGCCTACATATTTGCTG -s simCow_chr6.simCow.chr6 312009 27 + 602619 ATCCAAGAGGGCCCTCCATACTGGCTG -s simDog_chr6.simDog.chr6 292455 27 - 593897 GTAGAAGATGGCCCTACAAACCGGCTG -s simHuman_chr6.simHuman.chr6 323353 27 + 601863 ATGGTAGATGGCCCTGCACACTTCCTG -s simRat_chr6.simRat.chr6 330779 27 + 647215 TTAGAAGATGGGCCTACATATTTGCTG - -a -s simMouse_chr6.simMouse.chr6 339536 36 + 636262 ATCTGCTTCTTGAGCCCAGGTGACCAGCCTGCAGAG -s Anc0.Anc0refChr0 3515 36 + 26507 ATCATCTACTTTAACCCAGGTGACCAGCCTCCACAA -s Anc1.Anc1refChr6 3600 36 + 197743 ATCATCTACTTTAACCCAGGTGACCAGCCTCCACAA -s Anc2.Anc2refChr6 3647 36 + 7137 ATCATCGACTTTAACCCAGGTCACCAGCCTCCACAA -s mr.mrrefChr5 186994 36 + 294540 ATCTGCTTCTTGAACCGAGGTGACCAGCCTGCAAAA -s simCow_chr6.simCow.chr6 312043 36 + 602619 ATTTTCCACTTTAACCGAGGCAACCCGCCTCAACAA -s simDog_chr6.simDog.chr6 292487 35 - 593897 -TCATTGACTTTAGCCCAGGTCACCAGCCTCCACAA -s simHuman_chr6.simHuman.chr6 323387 36 + 601863 GTCCTCTACTTTAACTCAGGTGACTAGCCCACACAA -s simRat_chr6.simRat.chr6 330813 36 + 647215 ATCTGCTTCTTGAACCGAGGTGACTAGGCTGCAAAA - -a -s simMouse_chr6.simMouse.chr6 339572 13 + 636262 GTCCACCCCGGTC -s Anc0.Anc0refChr0 3572 13 + 26507 GCCCACCCTGGCC -s Anc1.Anc1refChr6 3657 13 + 197743 GCCCACCCTGGCC -s Anc2.Anc2refChr6 3704 13 + 7137 GCTCACCCTGGCC -s mr.mrrefChr5 187030 13 + 294540 GTCCACCCTGGTC -s simCow_chr6.simCow.chr6 312097 13 + 602619 GCTCACCTTGGCC -s simDog_chr6.simDog.chr6 292543 13 - 593897 GCTCCCCCTGGCC -s simHuman_chr6.simHuman.chr6 323572 13 + 601863 GCCCACCCTGACC -s simRat_chr6.simRat.chr6 330849 13 + 647215 GACTACCCTGGTC - -a -s simMouse_chr6.simMouse.chr6 339585 53 + 636262 TACTTGCCCATTTCATTGCATTTGCCTGTGAATTTTACTTAGCTACGAGCCTG -s Anc0.Anc0refChr0 3585 8 + 26507 TACTTGTC--------------------------------------------- -s Anc1.Anc1refChr6 3670 8 + 197743 TACTTGTC--------------------------------------------- -s Anc2.Anc2refChr6 3717 8 + 7137 TACTTGTC--------------------------------------------- -s mr.mrrefChr5 187043 53 + 294540 TACTTGCCCATTTCATTGCATTTGCCTGTGAAGTTTACTTGGCCACGAGCCTG -s simCow_chr6.simCow.chr6 312110 8 + 602619 TATTTGTC--------------------------------------------- -s simDog_chr6.simDog.chr6 292557 8 - 593897 GGCTTGTC--------------------------------------------- -s simHuman_chr6.simHuman.chr6 323585 8 + 601863 TACTTGTC--------------------------------------------- -s simRat_chr6.simRat.chr6 330862 53 + 647215 TACTTGCCCATTTCATTGTATTTGCCTGCCGAGTCTACTTGACCATGAGCCTG - -a -s simMouse_chr6.simMouse.chr6 339638 49 + 636262 CCCGCTTGATGAGATGTCAAGCAATCTCCCCGTGTACATTGTAGATCCC -s mr.mrrefChr5 187096 49 + 294540 CCCGCTTGATGAGATGTCAAGCAATCTCCCCGTGTACATTGTAGATCCC -s simRat_chr6.simRat.chr6 330916 49 + 647215 CCTGCTTGGTGAGATGTCAGGTGCTCTCCCCACGTACATTGTAGATCCC - -a -s simMouse_chr6.simMouse.chr6 339687 213 + 636262 TGTCCGATTTATGCACTATCAAGCGATGACAGGCCCTCTTGTACATTGAAGAGCCCCTGTCTGATTCACGGACTGTCAAGCGATGTTGTATTCAACACACCCTTGGTCTACTTGCGCCTTCTGTTGTATTTAACATGAGTTGCATTCAACACGCCCTTGGTCTACTTGCGCCTTCTGTTGTATTTAACATCTACTCTTTAATAAGTTAGGGTG -s Anc0.Anc0refChr0 3593 43 + 26507 --------------------------------------------------------------------------------------------------------------------------------------------------------------------------CCTTCTGTTGTATTCAACAGCTGCTCTCTGACAAGTTAAGGCT -s Anc1.Anc1refChr6 3678 43 + 197743 --------------------------------------------------------------------------------------------------------------------------------------------------------------------------CCTTCTGTTGTATTCAACAGCTGCTCTCTGACAAGTTAAGGCT -s Anc2.Anc2refChr6 3725 43 + 7137 --------------------------------------------------------------------------------------------------------------------------------------------------------------------------CCTTCTGTTGTATTCAACAGCTGCTCTCTGACAAGCTAAAGCT -s mr.mrrefChr5 187145 158 + 294540 TGTCCGATTTATGCACTATCAAGCGATGACAGGCCCTCTTGTACATTGAAGA-CCCCTGTCTGATTCACGGACTGTCAAGCGATGTTGTATTCAACAC------------------------------------------------------GCCCTTGGTCTACTTGCGCCTTCTGTTGTATTTAACATCTACTCTTTAACAAGTTAGGGTG -s simCow_chr6.simCow.chr6 312118 35 + 602619 --------------------------------------------------------------------------------------------------------------------------------------------------------------------------CCTTT--TTGCATTCAACACCTGCTCTCTGACATGCT------ -s simDog_chr6.simDog.chr6 292565 43 - 593897 --------------------------------------------------------------------------------------------------------------------------------------------------------------------------TCTTCTGTTGTATTTGACTGCTGCTCTCTGACAAGCTAAAGCT -s simHuman_chr6.simHuman.chr6 323593 43 + 601863 --------------------------------------------------------------------------------------------------------------------------------------------------------------------------CCTTCTGTTGTATTCAACAACATCTTTCAGACAAGTTAAGGCT -s simRat_chr6.simRat.chr6 330966 158 + 647215 TACCCAATTCACGCACTATCAAGCAATGACAAGCCCTCACATACATTGCAGA-TCCCTGTCTGATTCATGCGCTGGCAAGTGATGTTGTATTGAACAT------------------------------------------------------GCCCTTGGTCTACTTGCACCTTCTGTTCTATTTAACATCTACTCTGTAGCAAGTTAGGGTG - -a -s simMouse_chr6.simMouse.chr6 339900 4 + 636262 AGCA -s Anc0.Anc0refChr0 3636 4 + 26507 GGCA -s Anc1.Anc1refChr6 3721 4 + 197743 GGCA -s Anc2.Anc2refChr6 3768 4 + 7137 GGCA -s mr.mrrefChr5 187303 4 + 294540 AGCA -s simCow_chr6.simCow.chr6 312153 4 + 602619 GGCA -s simDog_chr6.simDog.chr6 292610 4 - 593897 GGCA -s simHuman_chr6.simHuman.chr6 323636 4 + 601863 GGTG -s simRat_chr6.simRat.chr6 331124 4 + 647215 AGCA - -a -s simMouse_chr6.simMouse.chr6 339904 55 + 636262 CACAGTTGTTACTGCTCTAGCATCTCATTAAGATCCTCTGTAAGAAATTTATAAA -s Anc0.Anc0refChr0 3640 48 + 26507 GACAGTTGTAACTG--CTAACTGGTAATCTAAATCCT--T-AAGAAATTAAT--A -s Anc1.Anc1refChr6 3725 50 + 197743 GACAGTTGTAACTG--CTAACTGGTAATCTAAATCCTCAT-AAGAAATTAAT--A -s Anc2.Anc2refChr6 3775 48 + 7137 GACAGTTGTAACTG--CTAACTGGTAGTCTAAATCTT--T-AAGAAATTAAT--A -s mr.mrrefChr5 187307 50 + 294540 CACAGTTGTAACTG--CTAGCAGCTCATCTAGATCCTCTG-AAGAAATTTAT--A -s simCow_chr6.simCow.chr6 312160 48 + 602619 GACAGTAAGAACTG--CTAACTGGTAGACTAAATCTT--G-AAGAAATTCAT--A -s simDog_chr6.simDog.chr6 292617 48 - 593897 GACATTTGTAACTG--CTAACTGGTAGTCTAAATCTT--T-AAGAAATTAAT--A -s simHuman_chr6.simHuman.chr6 323640 50 + 601863 AACAGCTGTAACTG--CTGACGGGTAATCTAAAACCTCAT-AAGGAATTAAC--A -s simRat_chr6.simRat.chr6 331128 50 + 647215 CACATTTGTACCTG--CTAGCAGCCCATCTAGATCCTCTG-AAGAAATTTAT--A - -a -s simMouse_chr6.simMouse.chr6 339959 14 + 636262 AATAGAATGTTATG -s Anc0.Anc0refChr0 3689 14 + 26507 GATAGAATGTTATG -s Anc1.Anc1refChr6 3776 14 + 197743 GATAGAATGTTATG -s Anc2.Anc2refChr6 3824 14 + 7137 GATAGAATGTTATG -s mr.mrrefChr5 187357 14 + 294540 AATAGAATGTTATG -s simCow_chr6.simCow.chr6 312209 14 + 602619 CATAGTATGTTATG -s simDog_chr6.simDog.chr6 292666 14 - 593897 GGTAGAATGTCATG -s simHuman_chr6.simHuman.chr6 323691 14 + 601863 GAGAGAATGTTATG -s simRat_chr6.simRat.chr6 331178 14 + 647215 AATAGAATATTAAG - -a -s simMouse_chr6.simMouse.chr6 339973 3 + 636262 GTG -s Anc0.Anc0refChr0 3718 3 + 26507 GTG -s Anc1.Anc1refChr6 3805 3 + 197743 GTG -s Anc2.Anc2refChr6 3853 3 + 7137 GTG -s mr.mrrefChr5 187371 3 + 294540 GTG -s simCow_chr6.simCow.chr6 312238 3 + 602619 GTG -s simDog_chr6.simDog.chr6 292707 3 - 593897 GTG -s simHuman_chr6.simHuman.chr6 323720 3 + 601863 GTG -s simRat_chr6.simRat.chr6 331192 3 + 647215 GTG - -a -s simMouse_chr6.simMouse.chr6 339976 49 + 636262 CACATCATTTTGAAAGCATAATTTCTAATTTCATACAAGGAAGATATGA -s Anc0.Anc0refChr0 3721 19 + 26507 TGCATTGATTTGAAAGCAC------------------------------ -s Anc1.Anc1refChr6 3808 19 + 197743 TGCATTGATTTGAAAGCAC------------------------------ -s Anc2.Anc2refChr6 3856 19 + 7137 TGCATTGATTTGAAATCAC------------------------------ -s mr.mrrefChr5 187374 49 + 294540 TGCATCAATTTGAAAGCATAATTTCTAATTTCATACAAGGAAGATATGA -s simCow_chr6.simCow.chr6 312241 17 + 602619 TG--TGGGTTCGAAAACAC------------------------------ -s simDog_chr6.simDog.chr6 292718 19 - 593897 TGCATTTATTTGAATTCAT------------------------------ -s simHuman_chr6.simHuman.chr6 323723 19 + 601863 TGCATTGATTTGAAAGCAC------------------------------ -s simRat_chr6.simRat.chr6 331195 49 + 647215 TGCATCAATTTGAAAGCATGATTTCTAATCTCATACAAAGAAGATATGA - -a -s simMouse_chr6.simMouse.chr6 340025 17 + 636262 AGGTAGTTGACCACACT -s Anc0.Anc0refChr0 4027 17 + 26507 AGGCTGTTGACCTCACC -s Anc1.Anc1refChr6 4116 17 + 197743 AGGCTGTTGACCTCACC -s Anc2.Anc2refChr6 4190 17 + 7137 GAGCTGTTGACCTCACC -s mr.mrrefChr5 187687 17 + 294540 AGGCTGTTGACCACACT -s simCow_chr6.simCow.chr6 312485 17 + 602619 GAGGTGTTGACCTCACA -s simDog_chr6.simDog.chr6 293048 17 - 593897 GAGCAATTGGCCTCACC -s simHuman_chr6.simHuman.chr6 324137 17 + 601863 AGGCTGTTGACCTCACC -s simRat_chr6.simRat.chr6 331746 17 + 647215 AGACTGTTGACCACACT - -a -s simMouse_chr6.simMouse.chr6 340042 20 + 636262 AACTAAAAGTCTCATTGGTG -s Anc0.Anc0refChr0 4044 19 + 26507 AGCTAAAGCTCTCATTGGT- -s Anc1.Anc1refChr6 4133 20 + 197743 AGCTAAAGCTCTCATTGGTA -s Anc2.Anc2refChr6 4207 19 + 7137 AGGAAAAGCTCTCAATGGT- -s mr.mrrefChr5 187704 20 + 294540 AACTAAAGCTCTCATTGGTG -s simCow_chr6.simCow.chr6 312502 19 + 602619 AGCACCAGCTCTCAATGGT- -s simDog_chr6.simDog.chr6 293065 19 - 593897 AGGAAAAACTATCAATGGT- -s simHuman_chr6.simHuman.chr6 324156 20 + 601863 AGCTAAGGCTCTCATTGGTA -s simRat_chr6.simRat.chr6 331763 20 + 647215 GACCAAAGCTCTCATTGGTG - -a -s simMouse_chr6.simMouse.chr6 340062 4 + 636262 TTCA -s Anc0.Anc0refChr0 4131 4 + 26507 TTCA -s Anc1.Anc1refChr6 4221 4 + 197743 TTCA -s Anc2.Anc2refChr6 4294 4 + 7137 TACA -s mr.mrrefChr5 187724 4 + 294540 TTCA -s simCow_chr6.simCow.chr6 312591 4 + 602619 TACA -s simDog_chr6.simDog.chr6 293152 4 - 593897 TACA -s simHuman_chr6.simHuman.chr6 324262 4 + 601863 TTCA -s simRat_chr6.simRat.chr6 331783 4 + 647215 TTCA - -a -s simMouse_chr6.simMouse.chr6 340066 94 + 636262 ACCAGGTAAGTATATTAGTGCTGGATTGGTTGACACAGTTATATTTTCTGTGTTAAGACAGACAGGAGTGATTGCCTTGGAGCTGTGTGGTACA -s Anc0.Anc0refChr0 4144 93 + 26507 ACCAGCTAAGTATATTAATGCTGGTTGCAGTC-CACAGTTCTACTTTCTGTGTTAAGATAGATAAGAAGGAAAACCTTGGAGCTGGGAGGTACA -s Anc1.Anc1refChr6 4234 93 + 197743 ACCAGCTAAGTATATTAATGCTGGTTGCAGTC-CACAGTTCTACTTTCTGTGTTAAGATAGATAAGAAGGAAAACCTTGGAGCTGGGAGGTACA -s Anc2.Anc2refChr6 4307 93 + 7137 ACCAGCTAAGTATATTAATGCTGGTTGCAGTC-CACAGTTCTACTTTCCATGCTAAGATAGATAAGAAGGAAAAGCTAAGAGCTGGGAGGTACA -s mr.mrrefChr5 187728 93 + 294540 ACCAGGTAAGTATATTAATGCTGGATTGATTG-CACAGTTATATTTTCTGTGTTAAGACAGACAAGAGTGATTGCCTTGGAGCTGTGTGGTACA -s simCow_chr6.simCow.chr6 312604 93 + 602619 ACCAGTTAAGCAGACTAGTGCTGATTGCAATC-CACAGTTCTATATTCCATCCTACTATATATAAAAAAGAACAGCTAAGAGCTGGGAGGTACA -s simDog_chr6.simDog.chr6 293165 74 - 593897 ACCAGCGAAGTCTATTAA---CGGTTGCAGTC-TACAGCTCTGCTTTCCATGCTAAGATAGATAAGGAGGAAAAGC----------------CA -s simHuman_chr6.simHuman.chr6 324275 93 + 601863 ACCAGCTAAGTATATTAATGCTGTTTGCAGTT-CACAGTTCTACTTTCTGTGTTTAGATAGATGAGAAGGAAAACCTTGGAGCTGGGAGGTGCA -s simRat_chr6.simRat.chr6 331787 91 + 647215 ACTAGGTAAGGATATTCATGCAGGATTGAATG-CACAGT--TCTTTTTGGCGTTAAGACAGGCAAGAGTGATTGCTTTGAAGCTGTGTGGTACA - -a -s simMouse_chr6.simMouse.chr6 340160 8 + 636262 TGGGACAA -s Anc0.Anc0refChr0 4250 8 + 26507 AGGAACAA -s Anc1.Anc1refChr6 4340 8 + 197743 AGGAACAA -s Anc2.Anc2refChr6 4413 8 + 7137 AGGAACAA -s mr.mrrefChr5 187821 8 + 294540 TGGTACAA -s simCow_chr6.simCow.chr6 312710 8 + 602619 AGGAACAA -s simDog_chr6.simDog.chr6 293252 8 - 593897 AGGAACAA -s simHuman_chr6.simHuman.chr6 324381 8 + 601863 AGGAACGG -s simRat_chr6.simRat.chr6 331878 8 + 647215 TGGTACAA - -a -s simMouse_chr6.simMouse.chr6 340168 11 + 636262 GTCAGCCCTTC -s Anc0.Anc0refChr0 4271 3 + 26507 --------TTC -s Anc1.Anc1refChr6 4361 11 + 197743 GCCAGCACTTC -s Anc2.Anc2refChr6 4434 3 + 7137 --------TTC -s mr.mrrefChr5 187829 11 + 294540 GTCAGCCCTTC -s simCow_chr6.simCow.chr6 312731 3 + 602619 --------TTC -s simDog_chr6.simDog.chr6 293273 3 - 593897 --------TTC -s simHuman_chr6.simHuman.chr6 324414 11 + 601863 GCCAGCACTAC -s simRat_chr6.simRat.chr6 331886 11 + 647215 GTCAGCCCTTA - -a -s simMouse_chr6.simMouse.chr6 340179 15 + 636262 CACAAAGCAGGCAGT -s Anc0.Anc0refChr0 4274 15 + 26507 CAATAAGCAGACAGC -s Anc1.Anc1refChr6 4372 15 + 197743 CAATAAGCAGACAGC -s Anc2.Anc2refChr6 4437 15 + 7137 CAATAAGAAGACAGC -s mr.mrrefChr5 187840 15 + 294540 CAAAAAGCAGGCAGC -s simCow_chr6.simCow.chr6 312734 15 + 602619 CAGTAAGAAGACAGC -s simDog_chr6.simDog.chr6 293276 15 - 593897 TGAGAAGAAGACGGC -s simHuman_chr6.simHuman.chr6 324430 15 + 601863 CAATAAGCAGACAGC -s simRat_chr6.simRat.chr6 331897 15 + 647215 GAAAAAACAGGCAGC - -a -s simMouse_chr6.simMouse.chr6 340194 143 + 636262 CTGTTCAACAACAGGAGTTCTTATGTCACAAGAGAAGTACAGATGGGTAGCTGTTATTGGGATTTGGATATGTTGCATAATAACTGTTCATGAAAGTTATGGTCAAGGGTAATGAAATAGTCTGTGGACCATTTTACTATATA -s Anc0.Anc0refChr0 4295 141 + 26507 CTGTTCCAAGACAGCAGTGCTT-TGTTCCAAGAAAACTGCACATGGGTATCTGTTATAAGAAATTAGTTATATTGTACAA-GACTACTTGCAAACACTATGGCACAGGGTAGTAAGATTATGCTCGGAGTGTTTTACTTTATA -s Anc1.Anc1refChr6 4393 141 + 197743 CTGTTCCAAGACAGCAGTGCTT-TGTTCCAAGAAAACTGCACATGGGTATCTGTTATAAGAAATTAGTTATATTGTACAA-GACTACTTGCAAACACTATGGCACAGGGTAGTAAGATTATGCTCGGAGTGTTTTACTTTATA -s Anc2.Anc2refChr6 4458 141 + 7137 CTGTTCCAAGACACCAGTGGTC-TGTTCCAAGAAAACCGCACATGGGTATCTGTTATAAGAAATTAGTTATATTGTACGA-GAGTACTTGCAAACACTATGGCATAGGGTAGTAAGATTATGCTCGGAGTGTTTTACTTTATA -s mr.mrrefChr5 187855 142 + 294540 CTGTTCAACAACAGGAGTTCTTATGTCACAAGAGAAGTACAGATGGGTAGCTGTTATTGGGATTTGGATATGTTGCATAA-AACTGTTCATGAAAGTTATGGTCCAGGGTAGTGAAATAGTCTGTGGACCATTTTACTATATA -s simCow_chr6.simCow.chr6 312755 134 + 602619 TTGTTCCAAGACAACAGTGGTC-TGTTCCAGGAAAAGAGCACATGGATATCTGTTATAAGA------TAATATTGTACGA-GAGTACTTGCAAACACTATGACATAGGATAGTAAGATTATGCTTGGAGTGTTTTACCTT-TA -s simDog_chr6.simDog.chr6 293297 120 - 593897 CTGTTCCAACACACCAGTGGTC-TGTTCCAAGAAAACCACACATGGGTATCTGTTATTAGGAATTAGTTATATTG----------------------TATGGCATAGGGTAGTAAGATCATGTTCAGAGTGTTTTACTTTATA -s simHuman_chr6.simHuman.chr6 324451 141 + 601863 CTATCCTAAGACAGCAGTGCTT-TGTTTGAAGAAAACTGCACATGAGTACCTGCAATAAGAAATTAATTATTTTGTACAA-GACTACATGCAAATACCACCGCACAGGGTAGTAAGATTATGCTAGGAGTGTTTTACTTTATC -s simRat_chr6.simRat.chr6 331912 86 + 647215 CTGGTCAACAACAGGAGTTCTTATGTCACGAGGG---------------------------------------------------GTTCATGCAA------GTCCAGGATAGTGAAATAGTCGGTGGACCATTCCACTATATA - -a -s simMouse_chr6.simMouse.chr6 340337 2 + 636262 AT -s Anc0.Anc0refChr0 4445 2 + 26507 AT -s Anc1.Anc1refChr6 4543 2 + 197743 AT -s Anc2.Anc2refChr6 4608 2 + 7137 AT -s mr.mrrefChr5 187997 2 + 294540 AT -s simCow_chr6.simCow.chr6 312898 2 + 602619 GT -s simDog_chr6.simDog.chr6 293426 2 - 593897 AT -s simHuman_chr6.simHuman.chr6 324601 2 + 601863 AT -s simRat_chr6.simRat.chr6 331998 2 + 647215 AT - -a -s simMouse_chr6.simMouse.chr6 340339 29 + 636262 TACTTCCAGGGTATTGGAAGCTAGTGATG -s Anc0.Anc0refChr0 4469 29 + 26507 TACTTTCAGGATAGGGGAAGCTGGTAAGG -s Anc1.Anc1refChr6 4567 29 + 197743 TACTTTCAGGATAGGGGAAGCTGGTAAGG -s Anc2.Anc2refChr6 4632 29 + 7137 TACCTTCAGGATAGGGGAAACTGGTAAGA -s mr.mrrefChr5 188016 29 + 294540 TACTTCCAGGGTATTGGAAGCTAGTGATG -s simCow_chr6.simCow.chr6 312916 29 + 602619 TACATTCAGGATGCTAGAAACTGGTGAGA -s simDog_chr6.simDog.chr6 293450 29 - 593897 TATCTTCAGGATAGGGAAAAATTGTAAAA -s simHuman_chr6.simHuman.chr6 324625 29 + 601863 TACTTTCAGGATAGGGGAAGCTGATTAGG -s simRat_chr6.simRat.chr6 332017 29 + 647215 TACTTCCAGGGTATTGGAAACTAGTGATG - -a -s simMouse_chr6.simMouse.chr6 340368 3 + 636262 GCA -s Anc0.Anc0refChr0 4498 3 + 26507 GGG -s Anc1.Anc1refChr6 4596 3 + 197743 GGG -s Anc2.Anc2refChr6 4661 3 + 7137 GGG -s mr.mrrefChr5 188045 3 + 294540 GCA -s simCow_chr6.simCow.chr6 312959 3 + 602619 GGA -s simDog_chr6.simDog.chr6 293479 3 - 593897 GGG -s simHuman_chr6.simHuman.chr6 324654 3 + 601863 GGG -s simRat_chr6.simRat.chr6 332046 3 + 647215 GCA - -a -s simMouse_chr6.simMouse.chr6 340371 4 + 636262 CCTC -s Anc0.Anc0refChr0 4502 4 + 26507 CTAC -s Anc1.Anc1refChr6 4600 4 + 197743 CTAC -s Anc2.Anc2refChr6 4665 4 + 7137 CTAC -s mr.mrrefChr5 188048 4 + 294540 CCTC -s simCow_chr6.simCow.chr6 312963 4 + 602619 TTAC -s simDog_chr6.simDog.chr6 293483 4 - 593897 CTAC -s simHuman_chr6.simHuman.chr6 324658 4 + 601863 CTAC -s simRat_chr6.simRat.chr6 332049 4 + 647215 CCTC - -a -s simMouse_chr6.simMouse.chr6 340375 31 + 636262 ATCAGGACAAAGACTTGTCACGTTAACGTTA -s Anc0.Anc0refChr0 4506 25 + 26507 ATCATGATGCATATTTGTCA------TGTGA -s Anc1.Anc1refChr6 4604 25 + 197743 ATCATGATGCATATTTGTCA------TGTGA -s Anc2.Anc2refChr6 4669 25 + 7137 ATCATGATGCATATTTGTCA------TGTGA -s mr.mrrefChr5 188052 25 + 294540 ATCAGGACACAGACTTGTCA------CGTTA -s simCow_chr6.simCow.chr6 312971 18 + 602619 ATTGTGATACATACTTAT------------- -s simDog_chr6.simDog.chr6 293487 25 - 593897 ATCATGATGCAAATTTGTCA------TGTGA -s simHuman_chr6.simHuman.chr6 324662 25 + 601863 ATCATGATGCATATTTGTCA------GGTGA -s simRat_chr6.simRat.chr6 332053 22 + 647215 ATCAGAACACA---TTGTCA------TGTTA - -a -s simMouse_chr6.simMouse.chr6 340406 20 + 636262 ACTACAGTCTGTCCCATGCC -s Anc0.Anc0refChr0 4534 18 + 26507 --CACAGTCTGTGCTACGCT -s Anc1.Anc1refChr6 4632 20 + 197743 ATCACAGTCTGTGCTACGCT -s Anc2.Anc2refChr6 4697 18 + 7137 --CAAAGTCTGTGCTACGCT -s mr.mrrefChr5 188077 20 + 294540 ACTACAGTCTGTCCCATGCC -s simCow_chr6.simCow.chr6 312989 7 + 602619 -------------CTATGCC -s simDog_chr6.simDog.chr6 293515 18 - 593897 --CAAAGTCTGTGCTACGCT -s simHuman_chr6.simHuman.chr6 324693 20 + 601863 ATAACAGTCCATATAAAACT -s simRat_chr6.simRat.chr6 332075 20 + 647215 ACCAAAGTCTGTCTTATGTC - -a -s simMouse_chr6.simMouse.chr6 340426 18 + 636262 CACTATAAGTCCATATAA -s Anc0.Anc0refChr0 4552 18 + 26507 CAATACCAGTCCATATAA -s Anc1.Anc1refChr6 4652 18 + 197743 CAATACCAGTCCATATAA -s Anc2.Anc2refChr6 4715 18 + 7137 CAATACCAGTCCATATAA -s mr.mrrefChr5 188097 18 + 294540 CACTATCAGTCCATATAA -s simCow_chr6.simCow.chr6 312996 18 + 602619 CAATACCAGTCCAAATAA -s simDog_chr6.simDog.chr6 293533 18 - 593897 CAATACCATTCCATACAA -s simHuman_chr6.simHuman.chr6 324716 18 + 601863 CATTGCTTGTGCACATAA -s simRat_chr6.simRat.chr6 332095 18 + 647215 CTCTATCATTCCATAACA - -a -s simMouse_chr6.simMouse.chr6 340444 20 + 636262 AACATTTTGAAATCAGAAAA -s Anc0.Anc0refChr0 4570 20 + 26507 GACATCTAGAAATTGGAAAA -s Anc1.Anc1refChr6 4670 20 + 197743 GACATCTAGAAATTGGAAAA -s Anc2.Anc2refChr6 4733 20 + 7137 GACATCTAGAGATTGGGAAA -s mr.mrrefChr5 188115 20 + 294540 AACATCTTGAAATCAGAAAA -s simCow_chr6.simCow.chr6 313014 20 + 602619 GATATCTCAAGATTGGGAAA -s simDog_chr6.simDog.chr6 293551 20 - 593897 AACATCTAGAGATTGGGAAA -s simHuman_chr6.simHuman.chr6 324747 20 + 601863 GACCTCAAGAACCTGGAAAA -s simRat_chr6.simRat.chr6 332113 20 + 647215 AATATCTTGGAATCGGAAAA - -a -s simMouse_chr6.simMouse.chr6 340464 84 + 636262 AATGAGCTCTAGTAACTCAAGACTGGACACAAGGCACCAACCCCCGGTAACTCGCTGTACATTAGGGATACGCCACTTACGATG -s Anc0.Anc0refChr0 4590 20 + 26507 AAGATGCTTTAGTGAAT----ACT------------------------------------------------------------ -s Anc1.Anc1refChr6 4690 20 + 197743 AAGATGCTTTAGTGAAT----ACT------------------------------------------------------------ -s Anc2.Anc2refChr6 4753 20 + 7137 AAGATGCTTTAGTGAAT----AGT------------------------------------------------------------ -s mr.mrrefChr5 188135 24 + 294540 AATGAGCTCTAGTAACTCAAGACT------------------------------------------------------------ -s simCow_chr6.simCow.chr6 313048 20 + 602619 AAGATGCTTTATTAACT----AGT------------------------------------------------------------ -s simDog_chr6.simDog.chr6 293571 18 - 593897 C--ATGCTTTAGTGAAT----GGA------------------------------------------------------------ -s simHuman_chr6.simHuman.chr6 324767 20 + 601863 AAGATGTTTTAGTGAAC----ACT------------------------------------------------------------ -s simRat_chr6.simRat.chr6 332133 21 + 647215 AACAAGCTCTGGTAAC---AAGCT------------------------------------------------------------ - -a -s simMouse_chr6.simMouse.chr6 340548 20 + 636262 GTAGAGTAATTGATGAAAAT -s Anc0.Anc0refChr0 4611 20 + 26507 ATATGATAATTGGAGATAAA -s Anc1.Anc1refChr6 4711 20 + 197743 ATATGATAATTGGAGATAAA -s Anc2.Anc2refChr6 4774 20 + 7137 ATATGATAATTGGAGATAAA -s mr.mrrefChr5 188159 20 + 294540 GTAGAATAATTGGAGAAAAT -s simCow_chr6.simCow.chr6 313069 20 + 602619 ATAGGATAATTGGAGAAAGT -s simDog_chr6.simDog.chr6 293590 20 - 593897 ATTTGATCATTGGAGATAAA -s simHuman_chr6.simHuman.chr6 324788 20 + 601863 ATATGATAATTGGAGATAAG -s simRat_chr6.simRat.chr6 332154 20 + 647215 GTAGAATAATTGGAGAGAGT - -a -s simMouse_chr6.simMouse.chr6 340568 7 + 636262 AAGTGCA -s Anc0.Anc0refChr0 4631 7 + 26507 AAGTGCA -s Anc1.Anc1refChr6 4731 7 + 197743 AAGTGCA -s Anc2.Anc2refChr6 4794 7 + 7137 AAGTGCA -s mr.mrrefChr5 188179 7 + 294540 AAGTGCA -s simCow_chr6.simCow.chr6 313089 7 + 602619 AAGTGCA -s simDog_chr6.simDog.chr6 293611 7 - 593897 AAGCACA -s simHuman_chr6.simHuman.chr6 324808 7 + 601863 AAGTGCA -s simRat_chr6.simRat.chr6 332174 7 + 647215 AAGTGCA - -a -s simMouse_chr6.simMouse.chr6 340575 25 + 636262 CTGTGCAGACAAATATCAATGTGTA -s Anc0.Anc0refChr0 4638 25 + 26507 TAGTGCAAACAAACATCAATGTGTA -s Anc1.Anc1refChr6 4738 25 + 197743 TAGTGCAAACAAACATCAATGTGTA -s Anc2.Anc2refChr6 4802 25 + 7137 TAGTGCAAACAAACATCAATGTGTA -s mr.mrrefChr5 188186 25 + 294540 CTGTGCAAACAAATATCAATGTGTA -s simCow_chr6.simCow.chr6 313097 25 + 602619 TAGTGCAGTGAAACATCACTCAGTT -s simDog_chr6.simDog.chr6 293619 25 - 593897 TAATGCAAACACATATCAATGTGTA -s simHuman_chr6.simHuman.chr6 324815 25 + 601863 TAGTGCAAACAAACATCAATGTGTA -s simRat_chr6.simRat.chr6 332181 21 + 647215 CTGTGCAAAC----CTCGATGTGTA - -a -s simMouse_chr6.simMouse.chr6 340600 8 + 636262 TGATCTCA -s Anc0.Anc0refChr0 4663 8 + 26507 TGGTATTA -s Anc1.Anc1refChr6 4763 8 + 197743 TGGTATTA -s Anc2.Anc2refChr6 4827 8 + 7137 TGGTATTA -s mr.mrrefChr5 188211 8 + 294540 TGGTCTCA -s simCow_chr6.simCow.chr6 313122 8 + 602619 TGGCATTA -s simDog_chr6.simDog.chr6 293646 8 - 593897 TCGTATCC -s simHuman_chr6.simHuman.chr6 324840 8 + 601863 TGGTATTA -s simRat_chr6.simRat.chr6 332202 8 + 647215 TGGTCTAA - -a -s simMouse_chr6.simMouse.chr6 340608 20 + 636262 AAGGTGGGCCCTAGAACAGT -s Anc0.Anc0refChr0 4671 20 + 26507 AAGCTGGGCCTAAGGAAAGG -s Anc1.Anc1refChr6 4771 20 + 197743 AAGCTGGGCCTAAGGAAAGG -s Anc2.Anc2refChr6 4835 20 + 7137 AAGCCCGGCCTAAGGAAAGG -s mr.mrrefChr5 188219 20 + 294540 AAGGTGGGCCCTAGAAAAGT -s simCow_chr6.simCow.chr6 313131 20 + 602619 AAACCAGGCCTCAGGAATGT -s simDog_chr6.simDog.chr6 293654 20 - 593897 AAGCCCAACCCAAGGAAAGG -s simHuman_chr6.simHuman.chr6 324848 20 + 601863 ATGATGGGCCTAAAGAAAGA -s simRat_chr6.simRat.chr6 332210 20 + 647215 AAGGTGGGCCCTAGAAAAGT - -a -s simMouse_chr6.simMouse.chr6 340628 23 + 636262 CCATGGATCATCATAGAGCTAAT -s Anc0.Anc0refChr0 4698 23 + 26507 CTATAGATCATCATTGAGCTAAT -s Anc1.Anc1refChr6 4798 23 + 197743 CTATAGATCATCATTGAGCTAAT -s Anc2.Anc2refChr6 4891 23 + 7137 CTATAGATCATCATTGTACTAAG -s mr.mrrefChr5 188239 23 + 294540 CCATGGATCATCATAGAGCTAAT -s simCow_chr6.simCow.chr6 313187 10 + 602619 CTATTGATCA------------- -s simDog_chr6.simDog.chr6 293710 23 - 593897 CAATAGATTATCATTGTACTAAG -s simHuman_chr6.simHuman.chr6 324875 23 + 601863 CTATAGATCATTATCTAGCTAAT -s simRat_chr6.simRat.chr6 332230 23 + 647215 CCATGGACCATCTTAGATCTAAT - -a -s simMouse_chr6.simMouse.chr6 340651 16 + 636262 GGATGTAACTATCCTA -s Anc0.Anc0refChr0 4721 16 + 26507 GGATGTGACTACCCTA -s Anc1.Anc1refChr6 4821 16 + 197743 GGATGTGACTACCCTA -s Anc2.Anc2refChr6 4914 16 + 7137 AGATGTGACGACCCTA -s mr.mrrefChr5 188262 16 + 294540 GGATGTAACTATCCTA -s simCow_chr6.simCow.chr6 313197 3 + 602619 -------------CTA -s simDog_chr6.simDog.chr6 293733 16 - 593897 AGATGTGACGACCCTA -s simHuman_chr6.simHuman.chr6 324898 16 + 601863 GGATGTGACTACTCTA -s simRat_chr6.simRat.chr6 332257 16 + 647215 GGATGTAACTATCCTA - -a -s simMouse_chr6.simMouse.chr6 340667 83 + 636262 ATAGGAACTTGATTGTGGATCATGTGCCTATAGCCCATTACCAATTCAAATGTATGTAGGTCATGTCTTATGTAGGTCTTGTC -s Anc0.Anc0refChr0 4738 60 + 26507 AAGGGAACATGAGCGTAGA--A-----CCATAGCTCTTGACCACTTCCAGTG----------------AATTTTGGTCTTGTC -s Anc1.Anc1refChr6 4838 62 + 197743 AAGGGAACATGAGCGTAGAACA-----CCATAGCTCTTGACCACTTCCAGTG----------------AATTTTGGTCTTGTC -s Anc2.Anc2refChr6 4931 60 + 7137 AAGGAAACATGAGCATAGG--A-----CCATAGCTCTTGACCACTTCCAGTG----------------AATTATTGTCTTGTC -s mr.mrrefChr5 188279 67 + 294540 ATAGGAACTTGATTGTGGATCATGTGCCTATAGCCCATTACCAATTCAAATG----------------TATGTAGGTCTTGTC -s simCow_chr6.simCow.chr6 313201 48 + 602619 AAGGAAACATAAGCAT-GG--A-----TCATAGCTCTTTACCACTTTGAGTG----------------AATT----------- -s simDog_chr6.simDog.chr6 293750 60 - 593897 AAGGAAACATGAGCATAGG--A-----CCATAGCTCTTGACCACTTCCAGTG----------------AATTATTGTCTTGTC -s simHuman_chr6.simHuman.chr6 324915 36 + 601863 AAGGGAACAGGAGCGCAGAACA-----------------------------------------------ACTTCGGTCATGTC -s simRat_chr6.simRat.chr6 332274 67 + 647215 ACAGGAACTTGCTTGTGGACCATGTGCCTATAGCCCATTACCAGTTTAAATG----------------TATGTAGGTCTTGTT - -a -s simMouse_chr6.simMouse.chr6 340750 51 + 636262 TAGGAACAGCTCTTATTATATGAGTGCAGGGGATCAATGGCTACAGTTGGG -s Anc0.Anc0refChr0 4800 40 + 26507 TAGTGGCAGCTCTTATGA-----------GGGAGCAAGGGCCACAGTCGGG -s Anc1.Anc1refChr6 4902 51 + 197743 TAGTGGCAGCTCTTATGATATTAGTGCAGGGGAGCAAGGGCCACAGTCGGG -s Anc2.Anc2refChr6 4993 40 + 7137 GAGTGGCAGCTCTTATGA-----------GGGAGCAAGGGCCACAGTCGGA -s mr.mrrefChr5 188346 51 + 294540 TAGGAGCAGCTCTTATTATATGAGTGCAGGGGATCAATGGCTACAGTTGGG -s simCow_chr6.simCow.chr6 313249 39 + 602619 GAGT-GCAGCTCTTATGA-----------GGGAGCAAGGGCCAGAGTCGGA -s simDog_chr6.simDog.chr6 293812 40 - 593897 GGGTGGCAGCTCTTATGA-----------GGGAGCCAGAGCCACAGTCAGA -s simHuman_chr6.simHuman.chr6 324953 51 + 601863 TAGTGGCAACTCTTAGGATATTAGTGCAGGGGCGCAAGGGCCACAGTCGGG -s simRat_chr6.simRat.chr6 332341 50 + 647215 TAGAAGCAGCTCTTATAATATGAAAGCAGGGGATCAAT-GCTATAGCTGGG - -a -s simMouse_chr6.simMouse.chr6 340801 9 + 636262 AGTCAACAA -s Anc0.Anc0refChr0 4842 9 + 26507 AGATATCAA -s Anc1.Anc1refChr6 4955 9 + 197743 AGATATCAA -s Anc2.Anc2refChr6 5042 9 + 7137 AGATATCAA -s mr.mrrefChr5 188397 9 + 294540 AGTCAACAA -s simCow_chr6.simCow.chr6 313297 6 + 602619 AGATAT--- -s simDog_chr6.simDog.chr6 293861 9 - 593897 AACTATCAA -s simHuman_chr6.simHuman.chr6 325006 9 + 601863 AGATATCAA -s simRat_chr6.simRat.chr6 332391 9 + 647215 AACCAACAA - -a -s simMouse_chr6.simMouse.chr6 340810 11 + 636262 TACACGTTCTA -s Anc0.Anc0refChr0 4875 11 + 26507 TACATATTCTT -s Anc1.Anc1refChr6 4988 11 + 197743 TACATATTCTT -s Anc2.Anc2refChr6 5075 11 + 7137 TACACATTCTT -s mr.mrrefChr5 188411 11 + 294540 TACATGTTCTA -s simCow_chr6.simCow.chr6 313316 11 + 602619 TACACATTTTT -s simDog_chr6.simDog.chr6 293892 11 - 593897 TATACATTCTT -s simHuman_chr6.simHuman.chr6 325039 11 + 601863 TACATATTCTC -s simRat_chr6.simRat.chr6 332405 11 + 647215 TACATGTTTTA - -a -s simMouse_chr6.simMouse.chr6 340821 71 + 636262 GATAATCAAGGCATCTCTGTTCAGTAAATTTCTAGGTAGGCAGTGTTTTTGTCTCTTGGATGCAAAGATGA -s Anc0.Anc0refChr0 4886 71 + 26507 TCCAATAGTGGTATTGCTGCCTGTTAACCTTCTGGGTAGATACTGTTTTTCCTCTTTGAACCCAAAGATAG -s Anc1.Anc1refChr6 4999 71 + 197743 TCCAATAGTGGTATTGCTGCCTGTTAACCTTCTGGGTAGATACTGTTTTTCCTCTTTGAACCCAAAGATAG -s Anc2.Anc2refChr6 5086 71 + 7137 TCCAATAGTGGTATTGCTGCCTGTTAACCTTCTGGGTAGATACTGTTTTTCCTCTTTGAGCCCAAAGATAA -s mr.mrrefChr5 188422 71 + 294540 TATAATCATGGCATCTCTGTTCAGTAAATTTCTAGGTAGGTACTGTTTTTGTCTTTTGGATCCAAAGATGG -s simCow_chr6.simCow.chr6 313395 71 + 602619 TCCAATAGTTGTACTGCTTTCCATTAACCTTCTGGGTAGATACTGTTATTCCTCTTAGAGCCCAAAGGTAA -s simDog_chr6.simDog.chr6 293903 71 - 593897 TCCTATAGTGGTATTACTGCCTGTAAACCTTCTGGGTCGATATGGTTTTTCCTTCTTGAGCCCAAAGATAA -s simHuman_chr6.simHuman.chr6 325050 71 + 601863 TCCAATAGTGGTATTGCTACCTGATAACCTTCTGGGCATATACTGCTTTTCCTCTTTGAACCAAAGGATAG -s simRat_chr6.simRat.chr6 332416 71 + 647215 TATAATCATGGCATCTCTGTTCAGTAATTTTCTAGGTAGGTACTGTCTTTGTCTTTTGGATCCAAAGATGG - -a -s simMouse_chr6.simMouse.chr6 340892 16 + 636262 AATAACAAGCAAGGGC -s Anc0.Anc0refChr0 4957 16 + 26507 AGTAACAATCAAAGAC -s Anc1.Anc1refChr6 5070 16 + 197743 AGTAACAATCAAAGAC -s Anc2.Anc2refChr6 5157 16 + 7137 AGTAACAATTAAAAAC -s mr.mrrefChr5 188493 16 + 294540 AATAACAAGCAAGGGC -s simCow_chr6.simCow.chr6 313467 16 + 602619 AGTAACAATTGGACAA -s simDog_chr6.simDog.chr6 293974 16 - 593897 AGTAACAACTAAAAAC -s simHuman_chr6.simHuman.chr6 325121 16 + 601863 AGTAACAATCAAAGAC -s simRat_chr6.simRat.chr6 332487 16 + 647215 AATAATAAGCAAGAGC - -a -s simMouse_chr6.simMouse.chr6 340908 145 + 636262 AGGTTATTGGAACTAACTTCACTAGATATATACAAGGAAATCAATAATTGGTTGGAAGGTGAAAGATTGAAAAGGTGGTCTACCACCTCTACTTATAGTCGTGGTGGGAAAAGACTGAGAAGGCTGCACACTGCTCTACTAGCTT -s Anc0.Anc0refChr0 4973 96 + 26507 AGGTTATTGGAACTAATCTCACTAGATATATAAAAGCAAAACAACAAAATCTTGG-AGCTAAAAGACTGAAAAGGCTGCATAGTACCTCTACTAA------------------------------------------------TC -s Anc1.Anc1refChr6 5086 97 + 197743 AGGTTATTGGAACTAATCTCACTAGATATATAAAAGCAAAACAACAAAATCTTGGAAGCTAAAAGACTGAAAAGGCTGCATAGTACCTCTACTAA------------------------------------------------TC -s Anc2.Anc2refChr6 5173 96 + 7137 AGTTTATTTGAACTAATCTCACTAGATATATATAAGCAAAACAACAAAATCTTGG-AGCTAAAAGACTGAAAAGGCTGCATGGTACCACTTCTAA------------------------------------------------TC -s mr.mrrefChr5 188509 145 + 294540 AGGTTATTGGAACTAACTTCACTAGATATATAAAAGGAAAACAATAATTGGTTGGAAGGTGAAAGACTGAAAAGGCGGTCTACCACCTCTACTAATAGTCGTGGTGGGAAAAGACTGAGAAGGCTGCACACTGCTCTACTAGCTT -s simCow_chr6.simCow.chr6 313483 96 + 602619 AGCTTATTTGAACTAATCTCGCTAGATATATGCAAGCAAAACGACACAATCTTGG-AGCTAAAAGACTGAAAAGGCTGCATGGTAGCACTCCTAG------------------------------------------------TC -s simDog_chr6.simDog.chr6 293990 92 - 593897 AGTCTAATTGAACTGATCTCATAAGAGGTATATGAACAAAACAACAAAATCTTGG-AGCCAAAAGGCTGAAAAGGCTGCATGGTAC----TCTCA------------------------------------------------TC -s simHuman_chr6.simHuman.chr6 325137 91 + 601863 AGGTTATTGGAACTAATCTCACTAGATATATAAAGGCAGAACAAAA------TAGAAGCTAAAGGACTGAAAAGGCCTCACAATACCTCTACCAA------------------------------------------------TC -s simRat_chr6.simRat.chr6 332504 145 + 647215 AGGTTATTGGAACTACCTTCACTGGATATAGGAAAGGAAAACAATAATAGTCTTGAAGGTGAAAAACTGGGAAGGCAGTCTACCACCTCTACTAATAGTCTTGGTGGTCAAAGATTGAGAAGGCTGCACAATGCTCTACGAGCTT - -a -s simMouse_chr6.simMouse.chr6 341053 1 + 636262 A -s Anc0.Anc0refChr0 5069 1 + 26507 A -s Anc1.Anc1refChr6 5183 1 + 197743 A -s Anc2.Anc2refChr6 5272 1 + 7137 A -s mr.mrrefChr5 188654 1 + 294540 A -s simCow_chr6.simCow.chr6 313582 1 + 602619 A -s simDog_chr6.simDog.chr6 294085 1 - 593897 A -s simHuman_chr6.simHuman.chr6 325228 1 + 601863 A -s simRat_chr6.simRat.chr6 332649 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 341054 4 + 636262 CCTC -s Anc0.Anc0refChr0 5070 4 + 26507 ACTC -s Anc1.Anc1refChr6 5184 4 + 197743 ACTC -s Anc2.Anc2refChr6 5273 4 + 7137 ACTC -s mr.mrrefChr5 188655 4 + 294540 CCTC -s simCow_chr6.simCow.chr6 313583 4 + 602619 ACTC -s simDog_chr6.simDog.chr6 294086 4 - 593897 ACTC -s simHuman_chr6.simHuman.chr6 325229 4 + 601863 ACTC -s simRat_chr6.simRat.chr6 332652 4 + 647215 CCTC - -a -s simMouse_chr6.simMouse.chr6 341058 88 + 636262 TGTAATTCTGCTAACTTTCCACAAAAAGACAAGACAAGAGAAGGCAAGACCTTTATAGCAATAAGAGAAGACAATGATGGTAAGTAGC -s Anc0.Anc0refChr0 5074 83 + 26507 TGCA--TCTGCTCAATATCCATAAAAAAACAAGATGAAAAAAG--AAGACAGTTT-AGGTAATGGAGAAGGTGATGATGCACAGTGGT -s Anc1.Anc1refChr6 5188 83 + 197743 TGCA--TCTGCTCAATATCCATAAAAAAACAAGATGAAAAAAG--AAGACAGTTT-AGGTAATGGAGAAGGTGATGATGCACAGTGGT -s Anc2.Anc2refChr6 5280 83 + 7137 TGCC--TCTGCTCATTACCCATAAAAAAAAAAGATGAAGAAAG--AAGTGAGATT-AGGTAATGGAGAAGGTGATGATGCACAGTGGT -s mr.mrrefChr5 188659 88 + 294540 TGTAATTCTGCTAAATTTCCACAAAAAGACAAGACAAGAGAAGGCAAGACCTTTATAGCAATAAGAGAAGACAATGATGGAAAGTAGC -s simCow_chr6.simCow.chr6 313590 53 + 602619 AGCC--------------CGAAAAAGAAAACTGGTTAAGGTA---------------------GGAGAAGGCGAAGATGCAAAGTCAT -s simDog_chr6.simDog.chr6 294093 79 - 593897 TGCC--TCTGCTCATTACCCATAAAAAAAAAAGATGAAGAAAG--AAGTGAGATT-AGGTAATAG----GGTGATGATGGACAGTGGT -s simHuman_chr6.simHuman.chr6 325233 82 + 601863 TGCA--TCTGCTGAATATCCATAAAGA-ACAGGATGAAAAAAA--AAGACAATCC-AGGTCATGGAGAAGGTGATGCTGCAGAGTGGT -s simRat_chr6.simRat.chr6 332656 88 + 647215 TGTAATTTCGCTAAATGTCCACAAAAAGACAAGTCAAGAGACGGCAAAACCTTTATAGCAATAAGAGAAGACAATGATGGAAAGTAAA - -a -s simMouse_chr6.simMouse.chr6 341146 3 + 636262 TTG -s Anc0.Anc0refChr0 5157 3 + 26507 ATG -s Anc1.Anc1refChr6 5271 3 + 197743 ATG -s Anc2.Anc2refChr6 5363 3 + 7137 ATG -s mr.mrrefChr5 188747 3 + 294540 TTG -s simCow_chr6.simCow.chr6 313643 3 + 602619 GCC -s simDog_chr6.simDog.chr6 294177 3 - 593897 ATG -s simHuman_chr6.simHuman.chr6 325315 3 + 601863 ATG -s simRat_chr6.simRat.chr6 332744 3 + 647215 TCG - -a -s simMouse_chr6.simMouse.chr6 341149 10 + 636262 AATCTGTCAG -s Anc0.Anc0refChr0 5160 10 + 26507 AATCCTTCAG -s Anc1.Anc1refChr6 5274 10 + 197743 AATCCTTCAG -s Anc2.Anc2refChr6 5366 10 + 7137 AATCCTAGGG -s mr.mrrefChr5 188750 10 + 294540 AATCCGTCAG -s simCow_chr6.simCow.chr6 313646 10 + 602619 CATGCTAAGG -s simDog_chr6.simDog.chr6 294183 10 - 593897 AACCCTAGGA -s simHuman_chr6.simHuman.chr6 325318 10 + 601863 AATCCTTCAG -s simRat_chr6.simRat.chr6 332747 10 + 647215 AATCCATCAG - -a -s simMouse_chr6.simMouse.chr6 341159 6 + 636262 TACAGG -s Anc0.Anc0refChr0 5171 6 + 26507 AGTTGG -s Anc1.Anc1refChr6 5285 6 + 197743 AGTTGG -s Anc2.Anc2refChr6 5377 6 + 7137 AGTTGG -s mr.mrrefChr5 188761 6 + 294540 TACAGG -s simCow_chr6.simCow.chr6 313657 6 + 602619 AGTTGG -s simDog_chr6.simDog.chr6 294194 6 - 593897 AGTTGG -s simHuman_chr6.simHuman.chr6 325329 6 + 601863 AGTTGG -s simRat_chr6.simRat.chr6 332763 6 + 647215 CGCAGG - -a -s simMouse_chr6.simMouse.chr6 341165 7 + 636262 GATAAAA -s Anc0.Anc0refChr0 5210 1 + 26507 ------G -s Anc1.Anc1refChr6 5324 7 + 197743 GATAGAG -s Anc2.Anc2refChr6 5416 1 + 7137 ------G -s mr.mrrefChr5 188767 7 + 294540 GATAAAA -s simCow_chr6.simCow.chr6 313696 1 + 602619 ------G -s simHuman_chr6.simHuman.chr6 325403 7 + 601863 GATAGAG -s simRat_chr6.simRat.chr6 332769 7 + 647215 GATAAAG - -a -s simMouse_chr6.simMouse.chr6 341172 26 + 636262 GGACCCACTCGTGCTCTCTTAAAAAT -s Anc0.Anc0refChr0 5211 21 + 26507 GGACCCACTCCTGCCCT----AAAA- -s Anc1.Anc1refChr6 5331 22 + 197743 GGACCCACTCCTGCCCT----AAAAT -s Anc2.Anc2refChr6 5417 21 + 7137 GGACCGACTCCTGCCAT----AAAA- -s mr.mrrefChr5 188774 26 + 294540 GGACCCACTCGTGCTCTCTTAAAAAT -s simCow_chr6.simCow.chr6 313697 11 + 602619 ----------CAGCCTC----AGAA- -s simDog_chr6.simDog.chr6 294212 21 - 593897 GGACCGACTCGTGCTAT----AAAA- -s simHuman_chr6.simHuman.chr6 325411 22 + 601863 GGACCCACGCCTGCCCT----AAAAT -s simRat_chr6.simRat.chr6 332776 26 + 647215 GGACCCACTCCTGATATGTTATAAAT - -a -s simMouse_chr6.simMouse.chr6 341198 4 + 636262 GTGG -s Anc0.Anc0refChr0 5239 4 + 26507 GAGG -s Anc1.Anc1refChr6 5360 4 + 197743 GAGG -s Anc2.Anc2refChr6 5445 4 + 7137 CAGG -s mr.mrrefChr5 188800 4 + 294540 GTGG -s simCow_chr6.simCow.chr6 313715 4 + 602619 AAGG -s simDog_chr6.simDog.chr6 294240 4 - 593897 CAGG -s simHuman_chr6.simHuman.chr6 325440 4 + 601863 GCGG -s simRat_chr6.simRat.chr6 332802 4 + 647215 GTGT - -a -s simMouse_chr6.simMouse.chr6 341202 29 + 636262 GACAACTTTGGTTAACCAATCTGATAATG -s Anc0.Anc0refChr0 5252 29 + 26507 GATGCTTAAAGTTGGCCTGTCTGGTAATG -s Anc1.Anc1refChr6 5373 29 + 197743 GATGCTTAAAGTTGGCCTGTCTGGTAATG -s Anc2.Anc2refChr6 5458 29 + 7137 GATGCTTAAAGTTGGCCTGTCTGGTAATA -s mr.mrrefChr5 188804 29 + 294540 GACAACTTTGGTTAACCAATCTGATAATG -s simCow_chr6.simCow.chr6 313728 29 + 602619 GAGGCTCAAAGTTGGCCTGTCTGATGATA -s simDog_chr6.simDog.chr6 294252 29 - 593897 GATGCCTGAAGTTGCCCTGTCTAGCAATA -s simHuman_chr6.simHuman.chr6 325453 29 + 601863 GTTGGTTACAGTCGGCCTGTCTGGTAATG -s simRat_chr6.simRat.chr6 332806 29 + 647215 GATAACTGTGGTTAATCAGTGTGATATTG - -a -s simMouse_chr6.simMouse.chr6 341231 6 + 636262 TAGCCT -s Anc0.Anc0refChr0 5281 5 + 26507 T-GCTA -s Anc1.Anc1refChr6 5402 5 + 197743 T-GCTA -s Anc2.Anc2refChr6 5487 5 + 7137 T-GCTA -s mr.mrrefChr5 188833 6 + 294540 TAGCCT -s simCow_chr6.simCow.chr6 313781 5 + 602619 T-GCAA -s simDog_chr6.simDog.chr6 294281 5 - 593897 T-GCTA -s simHuman_chr6.simHuman.chr6 325482 5 + 601863 T-GCTA -s simRat_chr6.simRat.chr6 332835 6 + 647215 TAGCCT - -a -s simMouse_chr6.simMouse.chr6 341237 36 + 636262 TGGGCGTATGTAGTAATTGGAACAAAGCATTCATGT -s Anc0.Anc0refChr0 5286 19 + 26507 TAAG-----------------ATAGATTATCCATGT -s Anc1.Anc1refChr6 5407 19 + 197743 TAAG-----------------ATAGATTATCCATGT -s Anc2.Anc2refChr6 5500 19 + 7137 TAAG-----------------ATAGATTATCCATGT -s mr.mrrefChr5 188839 35 + 294540 TGGGCGTATGTAG-AATTGGAACAAAGCATTCATGT -s simCow_chr6.simCow.chr6 313794 18 + 602619 TAAG-----------------ATAGTATGTCCA-GT -s simDog_chr6.simDog.chr6 294294 19 - 593897 TAAG-----------------GTAGATTACCCATGA -s simHuman_chr6.simHuman.chr6 325487 19 + 601863 TAAG-----------------ATAGATTTTCCATGT -s simRat_chr6.simRat.chr6 332841 35 + 647215 TGGGTGTATGTAA-AATTGCAACTAAGCATTTATTT - -a -s simMouse_chr6.simMouse.chr6 341273 6 + 636262 TGTTTA -s Anc0.Anc0refChr0 5335 6 + 26507 GGCTTA -s Anc1.Anc1refChr6 5456 6 + 197743 GGCTTA -s Anc2.Anc2refChr6 5549 6 + 7137 GGCTTA -s mr.mrrefChr5 188874 6 + 294540 TGTTTA -s simCow_chr6.simCow.chr6 313842 6 + 602619 GGCTTA -s simDog_chr6.simDog.chr6 294338 6 - 593897 GGCCTA -s simHuman_chr6.simHuman.chr6 325536 6 + 601863 GGCTTG -s simRat_chr6.simRat.chr6 332876 6 + 647215 TGTTTA - -a -s simMouse_chr6.simMouse.chr6 341279 2 + 636262 GG -s Anc0.Anc0refChr0 5343 2 + 26507 GG -s Anc1.Anc1refChr6 5464 2 + 197743 GG -s Anc2.Anc2refChr6 5557 2 + 7137 GG -s mr.mrrefChr5 188880 2 + 294540 GG -s simCow_chr6.simCow.chr6 313852 2 + 602619 GG -s simDog_chr6.simDog.chr6 294346 2 - 593897 TG -s simHuman_chr6.simHuman.chr6 325544 2 + 601863 GG -s simRat_chr6.simRat.chr6 332882 2 + 647215 GG - -a -s simMouse_chr6.simMouse.chr6 341281 4 + 636262 TGTT -s Anc0.Anc0refChr0 5345 4 + 26507 TACT -s Anc1.Anc1refChr6 5466 4 + 197743 TACT -s Anc2.Anc2refChr6 5559 4 + 7137 TACA -s mr.mrrefChr5 188882 4 + 294540 TGTT -s simCow_chr6.simCow.chr6 313854 4 + 602619 TACA -s simDog_chr6.simDog.chr6 294350 4 - 593897 TACA -s simHuman_chr6.simHuman.chr6 325546 4 + 601863 TACT -s simRat_chr6.simRat.chr6 332884 4 + 647215 TGTT - -a -s simMouse_chr6.simMouse.chr6 341285 11 + 636262 GATTTCAACAG -s Anc0.Anc0refChr0 5350 11 + 26507 GAGTGCAGCAG -s Anc1.Anc1refChr6 5471 11 + 197743 GAGTGCAGCAG -s Anc2.Anc2refChr6 5564 11 + 7137 GAGTGCAGCAG -s mr.mrrefChr5 188886 11 + 294540 GATTTCAACAG -s simCow_chr6.simCow.chr6 313859 11 + 602619 GAGTGCAACAA -s simDog_chr6.simDog.chr6 294355 11 - 593897 TAGTGCAGCAG -s simHuman_chr6.simHuman.chr6 325551 11 + 601863 GAGTGCAGTAG -s simRat_chr6.simRat.chr6 332888 11 + 647215 GATATCCACAC - -a -s simMouse_chr6.simMouse.chr6 341296 62 + 636262 AAGATTGTGCACTCTGGGCATTAAAAAAGGCAGTAAGTTAAGCTGGCACATCGGTAAGTTCA -s Anc0.Anc0refChr0 5374 62 + 26507 AAAATTGTCCACTCCAGGTGTTAAAAAAAGGGACGAATGGAGCAGCCAGACCAATAAGCTAG -s Anc1.Anc1refChr6 5495 62 + 197743 AAAATTGTCCACTCCAGGTGTTAAAAAAAGGGACGAATGGAGCAGCCAGACCAATAAGCTAG -s Anc2.Anc2refChr6 5588 62 + 7137 AAAATTGGCCACTCCAGGTGTTAAAAAAAGGGACGAATGGAGCAGCCAGACCAATGCGCTAG -s mr.mrrefChr5 188897 62 + 294540 AAGATTGTGCACTCTGGGCATTAAAAAAGGCAGTAAGTTAAGCTGGCACATCGGTAAGTTCA -s simCow_chr6.simCow.chr6 313883 60 + 602619 AAAATTGGCTACTCCACTTGTGAAAAAAAGGAATG--TGAAGCAGGCAGGTCTTTgctaagg -s simDog_chr6.simDog.chr6 294379 62 - 593897 TAAATTGGCCACTCCAGGTGTTAAAAAAAAGGACAAATGGAGCAGCCAGACCAATGCGCTAG -s simHuman_chr6.simHuman.chr6 325575 62 + 601863 AAAATTGTTCACTCCAGGTGTTAAAAAAAGAGACGAATAGAGCAACCGGAGCAATAAGCTAG -s simRat_chr6.simRat.chr6 332899 62 + 647215 AAGCCTGTCCACTCCAGTCATTAAAAAAGGCAGTAATTTGAGCTGGCACATCGATAAGTTCA - -a -s simMouse_chr6.simMouse.chr6 341358 9 + 636262 AAGTTTGCC -s Anc0.Anc0refChr0 5446 9 + 26507 AATCTAGCC -s Anc1.Anc1refChr6 5567 9 + 197743 AATCTAGCC -s Anc2.Anc2refChr6 5660 9 + 7137 AATCTAGCC -s mr.mrrefChr5 188959 9 + 294540 AAGTTTGCC -s simCow_chr6.simCow.chr6 314010 9 + 602619 AATCTAGCC -s simDog_chr6.simDog.chr6 294451 9 - 593897 TATATAGAC -s simHuman_chr6.simHuman.chr6 325647 9 + 601863 AATCTAGCC -s simRat_chr6.simRat.chr6 332961 9 + 647215 AAATTAGCC - -a -s simMouse_chr6.simMouse.chr6 341367 40 + 636262 ACCTTTCCCAATGCAAGATGCAGAGCATCTGAGCCTACCC -s Anc0.Anc0refChr0 5456 32 + 26507 ATCTTTCACAAAGCCAGGTGCA--------CAACCAATCC -s Anc1.Anc1refChr6 5577 32 + 197743 ATCTTTCACAAAGCCAGGTGCA--------CAACCAATCC -s Anc2.Anc2refChr6 5670 32 + 7137 ATCTTTCACAAAGCCAGGTTCA--------CAACCAATCC -s mr.mrrefChr5 188968 40 + 294540 ACCTTTCCCAATGCAAGATGCAGAGCATCTGAGCCTACCC -s simCow_chr6.simCow.chr6 314020 32 + 602619 GTTTTTCACAAAGCCAGGAACA--------CAATCAATCC -s simDog_chr6.simDog.chr6 294461 32 - 593897 ACCTTTCACAAAAGCAGGTTCA--------CAACCAATCC -s simHuman_chr6.simHuman.chr6 325657 32 + 601863 ATCTTTCATTAAGCTAGGTGCA--------CAACCAATCC -s simRat_chr6.simRat.chr6 332970 40 + 647215 ATCTTGCACTATGCAAGATGCATAACATCTCAACCTATCC - -a -s simMouse_chr6.simMouse.chr6 341407 37 + 636262 CCTTCTCTATGTATAATTGTCATGTGGGAGTTAAATA -s Anc0.Anc0refChr0 5488 36 + 26507 CATTATCAGTATACAATGGTGATGTGGGTGTTGAAT- -s Anc1.Anc1refChr6 5609 36 + 197743 CATTATCAGTATACAATGGTGATGTGGGTGTTGAAT- -s Anc2.Anc2refChr6 5702 36 + 7137 CATTATTAGTATACAATGGTGATGTGGGTGTTGAAT- -s mr.mrrefChr5 189008 36 + 294540 CCTTCTCTATGTATAATTGTCATGTGGGAGTTAAAT- -s simCow_chr6.simCow.chr6 314052 29 + 602619 CATT-TGAGTATACAATTGT------GATGTTGAAT- -s simDog_chr6.simDog.chr6 294498 35 - 593897 CCTTATTAGCATATAATGG-GATGTGGGTGTTGAAT- -s simHuman_chr6.simHuman.chr6 325689 36 + 601863 CATTATCAGTATACAGTAGTAATAACAGGGTTGGAT- -s simRat_chr6.simRat.chr6 333010 36 + 647215 CCTTACCTATGTACAATTGTGGTGTGGGGGTCAAAT- - -a -s simMouse_chr6.simMouse.chr6 341444 28 + 636262 CAAAGTTGTTACTCATATTTTCAGACAC -s Anc0.Anc0refChr0 5525 28 + 26507 CTAAGTTGTAATTTACATCTTCAGAAAC -s Anc1.Anc1refChr6 5646 28 + 197743 CTAAGTTGTAATTTACATCTTCAGAAAC -s Anc2.Anc2refChr6 5739 28 + 7137 CTAAGTTGTATTTTACATCTTCAGGATC -s mr.mrrefChr5 189044 28 + 294540 CAAAGTTGTTACTCATATTTTCAGACAC -s simCow_chr6.simCow.chr6 314082 28 + 602619 TTAAGTTGTAGCTCTCATCATCAGGATC -s simDog_chr6.simDog.chr6 294534 28 - 593897 CTGAGTTGTTTTTTACACCTTCAGGATC -s simHuman_chr6.simHuman.chr6 325726 28 + 601863 CTAAGTTGTAATTTACATCTTCAGAAAC -s simRat_chr6.simRat.chr6 333046 28 + 647215 CAAAGTTGTTGCTCATATTTTCAGACAC - -a -s simMouse_chr6.simMouse.chr6 341472 120 + 636262 AATTTATGCCTGGAGTCCTCAATAACCATGGCATAAACAGCAGCTGGAAGGAGGCCTTAGCCCCATTGTGCAGTGAACTGGAGGGGCAAATTGGACTTCAGTGAACAAGCTGGGGGGGGC -s Anc0.Anc0refChr0 5559 34 + 26507 AA-----CCATGGAGCCC----------------------------------------------------------------------------ACTACAGT-----AGCGGGGTGGGGC -s Anc1.Anc1refChr6 5680 34 + 197743 AA-----CCATGGAGCCC----------------------------------------------------------------------------ACTACAGT-----AGCGGGGTGGGGC -s Anc2.Anc2refChr6 5773 34 + 7137 AA-----CCATGGAGCCC----------------------------------------------------------------------------AATACAGT-----GGTGGGTTGGGGC -s mr.mrrefChr5 189072 115 + 294540 AA-----GCCTGGAGTCCTCAATAACCATGGCATAAACAGCAGCTGGAAGGAGGCCTTAGCCCCATTGTGCAGTGAACTGGAGGGGCAAATTGGACTTCAGTGAACAAGCTGGGGGGGGC -s simCow_chr6.simCow.chr6 314117 34 + 602619 AA-----CTGCTGAGCAC----------------------------------------------------------------------------AATCCAGA-----GGTGGGTTGGCGG -s simDog_chr6.simDog.chr6 294568 34 - 593897 GA-----CCATGAAGTCC----------------------------------------------------------------------------AATACATT-----GGTGAATCAGGGC -s simHuman_chr6.simHuman.chr6 325760 34 + 601863 AA-----CCTTAGAGCCC----------------------------------------------------------------------------ACTACGGT-----AGCGGGGTGGGGC -s simRat_chr6.simRat.chr6 333074 115 + 647215 AA-----GTATGGAGTCCTCTATATCCGTGGCATGAGCCGCAGCTGCAAGGAATCCCTAGCCCCATTGTTCAGCTAACTGGAGTAGCAAATTGGATTTCAGTGAACAAGCTGGGGGGAGC - -a -s simMouse_chr6.simMouse.chr6 341592 61 + 636262 TTGGCCACCTCTAAGGACCCATCACAAATAGCCACTTGGGGACCGCCTGAATTCCACCCAT -s Anc0.Anc0refChr0 5593 46 + 26507 TGGGCCAGCTGTA----------ACAAATAA-----TGGGGACTGCCTTAATTGCAGCCAT -s Anc1.Anc1refChr6 5714 46 + 197743 TGGGCCAGCTGTA----------ACAAATAA-----TGGGGACTGCCTTAATTGCAGCCAT -s Anc2.Anc2refChr6 5807 46 + 7137 TGGGCCAGTTGTA----------ACAAATCA-----TGTGGACTGCCTTAATTGCCGCTAT -s mr.mrrefChr5 189187 61 + 294540 TTGGCCACCTCTAAGGACCCATCACAAATAGCCACTTGGGGACCGCCTGAATTCCACCCAT -s simCow_chr6.simCow.chr6 314151 46 + 602619 TAGGCCAGTTATA----------CTCACTGG-----TGTGGACTCCCTTAATTGCTGCTAT -s simDog_chr6.simDog.chr6 294602 46 - 593897 TGGACCAGTTGTA----------ACAAATCA-----TGTGGACTGCCTTAATTTCCTATAT -s simHuman_chr6.simHuman.chr6 325852 46 + 601863 TGGGCCAGCTGTA----------ACAAATAA-----TGGGGATTGCCTTAACTGCAGCCAT -s simRat_chr6.simRat.chr6 333189 61 + 647215 TAGGCTGCCTCTAAGAACACATTGTTAATGACCACTAGGTACCACCCTGAATTGCATCCAT - -a -s simMouse_chr6.simMouse.chr6 341653 17 + 636262 CACTACTCAATGTCTGC -s Anc0.Anc0refChr0 5639 17 + 26507 TGCTACTCAATGTCTGC -s Anc1.Anc1refChr6 5760 17 + 197743 TGCTACTCAATGTCTGC -s Anc2.Anc2refChr6 5856 17 + 7137 TGCTACTTAATGTCTGC -s mr.mrrefChr5 189248 17 + 294540 CACTACTCAATGTCTGC -s simCow_chr6.simCow.chr6 314200 17 + 602619 TGCTACTTTACATCTAC -s simDog_chr6.simDog.chr6 294651 17 - 593897 TGCTACTTAATGTCTGC -s simHuman_chr6.simHuman.chr6 325898 17 + 601863 TGCTACTCAATGTCTGG -s simRat_chr6.simRat.chr6 333250 17 + 647215 TACTATTCAATGTCTGT - -a -s simMouse_chr6.simMouse.chr6 341670 28 + 636262 ACCGAACAAATTTCTCCAGTTCAGTATG -s Anc0.Anc0refChr0 5657 25 + 26507 ACCATACCAATTTCACTGGCTCAGT--- -s Anc1.Anc1refChr6 5778 28 + 197743 ACCATACCAATTTCACTGGCTCAGTATA -s Anc2.Anc2refChr6 5874 25 + 7137 CCCATACCAATTTCACTGGCTCAGT--- -s mr.mrrefChr5 189265 28 + 294540 ACCGAACAAATTTCTCCAGTTCAGTATG -s simCow_chr6.simCow.chr6 314218 25 + 602619 CCTATAACAATTTCACTAGCTCAGT--- -s simDog_chr6.simDog.chr6 294669 23 - 593897 --CCTACCAATCTCACTGGCTCAGT--- -s simHuman_chr6.simHuman.chr6 325916 28 + 601863 ACCATACCAGTTTCATTGACTCAGTATA -s simRat_chr6.simRat.chr6 333267 28 + 647215 ACCACACCAATTTCTCCAGTTCAGTATG - -a -s simMouse_chr6.simMouse.chr6 341698 38 + 636262 TTTATTTCTCCTTCTATGATTCAACTGTGCGTGTAGTT -s Anc0.Anc0refChr0 5682 34 + 26507 ----TTTCTCTTTGCATATTTTGAATGTGCATGTAGTT -s Anc1.Anc1refChr6 5806 38 + 197743 TTTATTTCTCTTTGCATATTTTGAATGTGCATGTAGTT -s Anc2.Anc2refChr6 5899 34 + 7137 ----TTTATCTTCGCATATTTTGAATGTGCATGTAGTT -s mr.mrrefChr5 189293 38 + 294540 TTTATTTCTCCTTCTATGATTCAACTGTGCGTGTAGTT -s simCow_chr6.simCow.chr6 314243 34 + 602619 ----TTTATCTTCACACATTTTGAAAGTGCAAGTAGTT -s simDog_chr6.simDog.chr6 294692 34 - 593897 ----TTTAGCTTCGCATAATGTGAATGTGCATGTAGTT -s simHuman_chr6.simHuman.chr6 325945 38 + 601863 TTTATTTCTCTTTGCATATTTTGAATATGCATGTAATT -s simRat_chr6.simRat.chr6 333295 38 + 647215 TTTATTTCTATTTGCATGATTCCACTGTGCATGTAGTT - -a -s simMouse_chr6.simMouse.chr6 341736 5 + 636262 TGATT -s Anc0.Anc0refChr0 5716 5 + 26507 TGATT -s Anc1.Anc1refChr6 5844 5 + 197743 TGATT -s Anc2.Anc2refChr6 5933 5 + 7137 TGATT -s mr.mrrefChr5 189331 5 + 294540 TGATT -s simCow_chr6.simCow.chr6 314277 5 + 602619 TCATT -s simDog_chr6.simDog.chr6 294726 5 - 593897 TGATT -s simHuman_chr6.simHuman.chr6 325984 5 + 601863 TGAAT -s simRat_chr6.simRat.chr6 333333 5 + 647215 TGATG - -a -s simMouse_chr6.simMouse.chr6 341741 57 + 636262 GTGGTTTCCTGTCGAGGTGGACCCTACATATAAGACTTGGACTCACCTAGGGTCTTT -s Anc0.Anc0refChr0 5721 37 + 26507 GGGC-TTGGGGTG----TGAACCCTACAAACAAGGTTTATAC--------------- -s Anc1.Anc1refChr6 5849 37 + 197743 GGGC-TTGGGGTG----TGAACCCTACAAACAAGGTTTATAC--------------- -s Anc2.Anc2refChr6 5942 37 + 7137 GGGC-TTGGGATG----TGAACCCTGCAAACAGGGTTTATAC--------------- -s mr.mrrefChr5 189336 56 + 294540 GTGG-TTCCTGTCGAGGTGGACCCTACATATAAGACTTGGACTCACCTAGGGTCTTT -s simCow_chr6.simCow.chr6 314286 37 + 602619 GGGC-CTGAGAGG----TGAGCCCTACAAACAGGGTTTATAC--------------- -s simDog_chr6.simDog.chr6 294735 37 - 593897 TGGC-TTGGGATG----TGAACCCTGCAAACAGGGTTTATAC--------------- -s simHuman_chr6.simHuman.chr6 325989 33 + 601863 GGGC-ATGTAGTT----TGATTCCAAC----AAGGTTCATAC--------------- -s simRat_chr6.simRat.chr6 333338 56 + 647215 GTGG-TTCCTGTAGTTGAGGACCCTATAAATAAGACCTGGACCCACCCAGGGTCTTT - -a -s simMouse_chr6.simMouse.chr6 341798 72 + 636262 ATTGCCCTGTTATATGGACTGTCTGTTTTAAAGTGGATGGTTATGACCAGGGATCTTACTAGACACTCAGGT -s Anc0.Anc0refChr0 5758 53 + 26507 ------------------CTATCTATTTCAAAGCGGATGGTTACAGCCC-AAATTTTATTAGATCCTCAAGT -s Anc1.Anc1refChr6 5886 53 + 197743 ------------------CTATCTATTTCAAAGCGGATGGTTACAGCCC-AAATTTTATTAGATCCTCAAGT -s Anc2.Anc2refChr6 5979 53 + 7137 ------------------CTATCTATTTCAGAGCGGATGGTTACAGCCC-AAATTTTATTAGATCCTCAAGT -s mr.mrrefChr5 189392 72 + 294540 ATTGCCCTGTTATATGGACTGTCTGTTTTAAAGTGGATGGTTATGACCAGGGATCTTACTAGACACTCAGGT -s simCow_chr6.simCow.chr6 314323 53 + 602619 ------------------CAGTCTGTTTCAGAGCGGATGATTACAGCCC-GAACCTTATTAGATCATCCAGT -s simDog_chr6.simDog.chr6 294772 52 - 593897 ------------------CTATATATTTCAGGGTGGATGGTTACAGCCA-AGATTTAATTAG-TCCTCAAGT -s simHuman_chr6.simHuman.chr6 326022 53 + 601863 ------------------CTAACGATTTCAAAGCAGATGGTTACAGTCC-AAATTTTATCAGATCCTCTAGT -s simRat_chr6.simRat.chr6 333395 72 + 647215 ATTTCCCCGTTATATGGAATGTCTGTTTTAAAGTGGATGATTATGACCAGGGATCGTAATAGACACTCAAGT - -a -s simMouse_chr6.simMouse.chr6 341870 11 + 636262 AAGAATTATAT -s Anc0.Anc0refChr0 5811 11 + 26507 AACAGTTATAT -s Anc1.Anc1refChr6 5939 11 + 197743 AACAGTTATAT -s Anc2.Anc2refChr6 6032 11 + 7137 AACAGATACAT -s mr.mrrefChr5 189464 11 + 294540 AAGAATTATAT -s simCow_chr6.simCow.chr6 314376 11 + 602619 AACAGATACAT -s simDog_chr6.simDog.chr6 294824 11 - 593897 AACAGATACAT -s simHuman_chr6.simHuman.chr6 326077 11 + 601863 AATAGTTATGT -s simRat_chr6.simRat.chr6 333467 11 + 647215 AAGAATTATAT - -a -s simMouse_chr6.simMouse.chr6 341881 26 + 636262 GAGAATAAATTGTGGCATTGCTGTTC -s Anc0.Anc0refChr0 5824 14 + 26507 GAGAATAAATGATT------------ -s Anc1.Anc1refChr6 5952 14 + 197743 GAGAATAAATGATT------------ -s Anc2.Anc2refChr6 6045 14 + 7137 GAGAATAAATGATT------------ -s mr.mrrefChr5 189475 26 + 294540 GAGAATAAATTGTGGCATTGCTGTTC -s simCow_chr6.simCow.chr6 314389 13 + 602619 GAAAATAAATGA-T------------ -s simDog_chr6.simDog.chr6 294837 14 - 593897 GGGAATAAATGATT------------ -s simHuman_chr6.simHuman.chr6 326090 14 + 601863 GAGAATAAGTGATT------------ -s simRat_chr6.simRat.chr6 333478 26 + 647215 GAGAATCAATTGTGGTGTTGCTGCTA - -a -s simMouse_chr6.simMouse.chr6 341907 58 + 636262 CTGCCTATGCCATTTTTGACAGATATAGCTACAACTGTTTTAACAGGCTAGGGAGTAA -s mr.mrrefChr5 189501 58 + 294540 CTGCCTATGCCATTTTTGACAGATATAGCTACAACTGTTTTAACAGGCTAGGGAGTAA -s simRat_chr6.simRat.chr6 333525 58 + 647215 CTCCAAATGCCATTTTTGAAAGATATAGCTCCAACTGTTTTAACAGGCAAGGGAGTAA - -a -s simMouse_chr6.simMouse.chr6 341965 55 + 636262 CAGAATTATGCAGAAAGGATTATTGGTTTGCCAGGTGCAGAAAATTGATAACATA -s Anc0.Anc0refChr0 5838 37 + 26507 ------------------ATTATTGGTTCACCAGGTGCAAAAAATTGATAATGTA -s Anc1.Anc1refChr6 5966 37 + 197743 ------------------ATTATTGGTTCACCAGGTGCAAAAAATTGATAATGTA -s Anc2.Anc2refChr6 6059 37 + 7137 ------------------ATTATTGGTTCACCAGGTGCCAAAAATTGATAATGCA -s mr.mrrefChr5 189559 55 + 294540 CAGAATTATGCAGAAAGAATTATTGGTTTGCCAGGTGCAGAAAATTGATAACATA -s simCow_chr6.simCow.chr6 314402 37 + 602619 ------------------ATTATTCATTCACCAGGTGGGGAAAATTGGTAATGCA -s simDog_chr6.simDog.chr6 294851 37 - 593897 ------------------GTCATTGGTTGACCCAGTGCCAAAAATTGATAATGCA -s simHuman_chr6.simHuman.chr6 326104 37 + 601863 ------------------ACTATTGGTTCACTAGATGCAAAAAAGTGATAAAGTA -s simRat_chr6.simRat.chr6 333584 55 + 647215 GAGCATTATGCAGAAAGAATTGTTGGTTTGCCAGGTGCAGAAAATTGATAACATA - -a -s simMouse_chr6.simMouse.chr6 342020 5 + 636262 TTGAA -s Anc0.Anc0refChr0 5875 5 + 26507 TTTGA -s Anc1.Anc1refChr6 6003 5 + 197743 TTTGA -s Anc2.Anc2refChr6 6096 5 + 7137 TTTGA -s mr.mrrefChr5 189614 5 + 294540 TTGAA -s simCow_chr6.simCow.chr6 314439 5 + 602619 TTTTC -s simDog_chr6.simDog.chr6 294888 5 - 593897 TTTGA -s simHuman_chr6.simHuman.chr6 326141 5 + 601863 TTTGA -s simRat_chr6.simRat.chr6 333640 5 + 647215 TTAAA - -a -s simMouse_chr6.simMouse.chr6 342025 15 + 636262 TAGTATCGTCCAGAG -s Anc0.Anc0refChr0 5881 15 + 26507 TGCTATGCTACTGGA -s Anc1.Anc1refChr6 6009 15 + 197743 TGCTATGCTACTGGA -s Anc2.Anc2refChr6 6102 15 + 7137 CGCTATGCTACTGGA -s mr.mrrefChr5 189619 15 + 294540 TAGTATGGTCCAGAG -s simCow_chr6.simCow.chr6 314445 15 + 602619 CAGTATGCTACTGGA -s simDog_chr6.simDog.chr6 294894 15 - 593897 CGCTATGCTACTGAA -s simHuman_chr6.simHuman.chr6 326147 15 + 601863 TCATTTACTACTGGA -s simRat_chr6.simRat.chr6 333645 11 + 647215 TAATATGGTCC---- - -a -s simMouse_chr6.simMouse.chr6 342040 29 + 636262 GCAGATAGTGATCCATAACCTTCATGCCT -s Anc0.Anc0refChr0 5896 29 + 26507 ATAGATAAAGATTCATAACTGTCATGCTT -s Anc1.Anc1refChr6 6024 29 + 197743 ATAGATAAAGATTCATAACTGTCATGCTT -s Anc2.Anc2refChr6 6117 29 + 7137 ATAGATAAAGATTAAGAACTGTCATGCTA -s mr.mrrefChr5 189634 29 + 294540 GCAGATAGTGATTCATAACCTTCATGCCT -s simCow_chr6.simCow.chr6 314460 18 + 602619 ATTGATTAAGCCTAGGTA----------- -s simDog_chr6.simDog.chr6 294910 29 - 593897 ATAGATAAAGATTAAGAACTGTCATGCTA -s simHuman_chr6.simHuman.chr6 326162 29 + 601863 AGAGATAAAGGACCATAACTGTCATGCTT -s simRat_chr6.simRat.chr6 333656 28 + 647215 -CACATAGTGATTCATTACCTTCATGCCT - -a -s simMouse_chr6.simMouse.chr6 342069 40 + 636262 GCCTTTCTCAGGGTCCCCAATGCCCCACACCACACAAGGT -s Anc0.Anc0refChr0 5926 30 + 26507 GCCTTTCTGAGCATCC----TATCCC---CCAGG---GGT -s Anc1.Anc1refChr6 6054 33 + 197743 GCCTTTCTGAGCATCC----TATCCC---CCAGGCATGGT -s Anc2.Anc2refChr6 6147 30 + 7137 TCCCTTCTGAGCATCC----CATCTC---CTAGG---GGT -s mr.mrrefChr5 189663 40 + 294540 GCCTTTCTCAGCATCCCCAATCTCCCACACCACACAAGGT -s simCow_chr6.simCow.chr6 314478 4 + 602619 ---------------------------------G---GGT -s simDog_chr6.simDog.chr6 294940 30 - 593897 TCCCTTCTGAGCATCC----CATCTC---CTAGG---GGT -s simHuman_chr6.simHuman.chr6 326192 33 + 601863 GCTTTTCAGAGCATCT----TATCCC---CCAGGCATGGT -s simRat_chr6.simRat.chr6 333684 40 + 647215 GCCTTTCCCAGCACTCCCAATCTCACACACCACACAAAGT - -a -s simMouse_chr6.simMouse.chr6 342109 18 + 636262 ATATAATACTAGTAAACA -s Anc0.Anc0refChr0 5956 18 + 26507 GTATCATTTTTGTAATCT -s Anc1.Anc1refChr6 6087 18 + 197743 GTATCATTTTTGTAATCT -s Anc2.Anc2refChr6 6177 18 + 7137 GTCTCATTTTTGTAATCT -s mr.mrrefChr5 189703 18 + 294540 ATATAATACTTGTAAACA -s simCow_chr6.simCow.chr6 314482 18 + 602619 GTTTCATCTTTGTAATCT -s simDog_chr6.simDog.chr6 294970 18 - 593897 ATCTCATTTTTGTAATCC -s simHuman_chr6.simHuman.chr6 326231 18 + 601863 TTATCATTATTTTAATCT -s simRat_chr6.simRat.chr6 333724 18 + 647215 ATATAATGCTTGTAACCA - -a -s simMouse_chr6.simMouse.chr6 342127 16 + 636262 CTTCTCTGAGTTGTCT -s Anc0.Anc0refChr0 5974 16 + 26507 TTTCTCTAGGTGGTTT -s Anc1.Anc1refChr6 6105 16 + 197743 TTTCTCTAGGTGGTTT -s Anc2.Anc2refChr6 6195 16 + 7137 TTTCTCTAGGTGGTTT -s mr.mrrefChr5 189721 16 + 294540 CTTCTCTGGGTTGTCT -s simCow_chr6.simCow.chr6 314512 16 + 602619 TCTCTCCGGGTCATCC -s simDog_chr6.simDog.chr6 294988 16 - 593897 GTTCTCTAGATGGTTT -s simHuman_chr6.simHuman.chr6 326249 16 + 601863 TTTCTCTAGGTGGTTT -s simRat_chr6.simRat.chr6 333742 16 + 647215 CTTCTCTGGGGTGTCT - -a -s simMouse_chr6.simMouse.chr6 342143 1 + 636262 T -s Anc0.Anc0refChr0 5994 1 + 26507 A -s Anc1.Anc1refChr6 6125 1 + 197743 A -s Anc2.Anc2refChr6 6215 1 + 7137 A -s mr.mrrefChr5 189737 1 + 294540 T -s simCow_chr6.simCow.chr6 314532 1 + 602619 A -s simDog_chr6.simDog.chr6 295008 1 - 593897 A -s simHuman_chr6.simHuman.chr6 326269 1 + 601863 A -s simRat_chr6.simRat.chr6 333758 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 342144 43 + 636262 TCAAGGCACAACAGGTAAGTATGAGTGACCAACTTTGCTGAAA -s Anc0.Anc0refChr0 5995 43 + 26507 TCTAAGCGCAACTGATAAATGTGATTTTTTCACTTTAATGAAA -s Anc1.Anc1refChr6 6126 43 + 197743 TCTAAGCGCAACTGATAAATGTGATTTTTTCACTTTAATGAAA -s Anc2.Anc2refChr6 6216 43 + 7137 TCTCAGTGTAATTGATGAATGTGATTTTTTCACATTAATGAAG -s mr.mrrefChr5 189738 43 + 294540 TCAAGGCACAACAGGTAAGTATGAGTGACCAACTTTGCTGAAA -s simCow_chr6.simCow.chr6 314533 43 + 602619 TCTGGGTGTAATTGATGAATGTGGGTGTTTCATATTAATGAAG -s simDog_chr6.simDog.chr6 295009 23 - 593897 TATCATTGT----------CGTAATCTTTTCTC---------- -s simHuman_chr6.simHuman.chr6 326270 43 + 601863 TCTATGCGCGACTGAGAAATGTGATTATTTCACTTTAAACAAA -s simRat_chr6.simRat.chr6 333764 43 + 647215 TCAAGGCATAACAGATAAGTATGAGTGACCAACTTTGCTGAAA - -a -s simMouse_chr6.simMouse.chr6 342187 4 + 636262 TTCT -s Anc0.Anc0refChr0 6046 4 + 26507 TTCA -s Anc1.Anc1refChr6 6177 4 + 197743 TTCA -s Anc2.Anc2refChr6 6267 4 + 7137 TTCA -s mr.mrrefChr5 189781 4 + 294540 TTCT -s simCow_chr6.simCow.chr6 314584 4 + 602619 TCCA -s simDog_chr6.simDog.chr6 295032 3 - 593897 -TAG -s simHuman_chr6.simHuman.chr6 326322 4 + 601863 TTCA -s simRat_chr6.simRat.chr6 333815 4 + 647215 TTCA - -a -s simMouse_chr6.simMouse.chr6 342191 34 + 636262 TTGTTTTACAGTCCAGTTATTAGAGCTGGAGTTA -s Anc0.Anc0refChr0 6050 10 + 26507 ATGTTTTA------------------------GC -s Anc1.Anc1refChr6 6181 10 + 197743 ATGTTTTA------------------------GC -s Anc2.Anc2refChr6 6271 10 + 7137 ATGGTCTA------------------------GC -s mr.mrrefChr5 189785 19 + 294540 TTGTTTTACAGTCC---------------AGTTG -s simCow_chr6.simCow.chr6 314594 9 + 602619 ATAGTCGA------------------------G- -s simDog_chr6.simDog.chr6 295035 10 - 593897 ATGGTCTA------------------------AC -s simHuman_chr6.simHuman.chr6 326326 10 + 601863 ATGTTTTA------------------------GC -s simRat_chr6.simRat.chr6 333819 19 + 647215 TGGTTTTACAGTCC---------------AGTTG - -a -s simMouse_chr6.simMouse.chr6 342225 60 + 636262 TTAAAGCTGGTCTATGATTGTCCAACCTCCAAAATAACAATATAAGGTAACCCCCAAAAA -s Anc0.Anc0refChr0 6060 43 + 26507 TTAAAGGTGGTTAATGCTTGATCAATTCCCAAATAAACACCAT----------------- -s Anc1.Anc1refChr6 6191 43 + 197743 TTAAAGGTGGTTAATGCTTGATCAATTCCCAAATAAACACCAT----------------- -s Anc2.Anc2refChr6 6284 43 + 7137 TTAAAGGTGGTTAATGCTTGATCAATTCCCAAATAAACACCAG----------------- -s mr.mrrefChr5 189804 60 + 294540 TTAAAGGTGGTCTATGATTGTCCAACCCCCAAAATAACAATATAAGGTAACCCCCAAAAA -s simCow_chr6.simCow.chr6 314606 43 + 602619 TCAGGGGTGGTCGATGATGGATCAACTCCCAAATCAACACTAG----------------- -s simDog_chr6.simDog.chr6 295048 43 - 593897 TTAAAGGTGGTTAATGCATGATCAATTCCCAAATAAACACCAG----------------- -s simHuman_chr6.simHuman.chr6 326336 43 + 601863 TTAAAGGTGCTTAATGTTTCCTTGATTCCCAAATAAACACCAT----------------- -s simRat_chr6.simRat.chr6 333838 60 + 647215 TTAAAAGTGGTCTATGTCTATCCAACCCCCAAAATAACACTAATAGGTAACCCCCAAAAA - -a -s simMouse_chr6.simMouse.chr6 342285 36 + 636262 AATACCAATGGTGTCAGTGACAAAACATTCTCCTCC -s Anc0.Anc0refChr0 6103 23 + 26507 A-----------GTCATTGTCAAAA--CTCACCCTC -s Anc1.Anc1refChr6 6234 25 + 197743 A-----------GTCATTGTCAAAACCCTCACCCTC -s Anc2.Anc2refChr6 6331 23 + 7137 A-----------GTTATTGTCACAA--CTCACCCTC -s mr.mrrefChr5 189864 25 + 294540 A-----------GTCAGTGACAAAACATTCACCTCC -s simCow_chr6.simCow.chr6 314653 23 + 602619 G-----------GTTATTGTCATTA--CCCACCCTC -s simDog_chr6.simDog.chr6 295095 23 - 593897 A-----------GTTATTGTCACAA--TTCACCCTC -s simHuman_chr6.simHuman.chr6 326379 22 + 601863 A-----------GTCACTGTCCA---CCTCACCGTC -s simRat_chr6.simRat.chr6 333898 25 + 647215 G-----------GTCACTGACAAGACATTCACTTCT - -a -s simMouse_chr6.simMouse.chr6 342321 38 + 636262 ACTTGGACTAGTAGTGCTTTACTTCCACTGTGAGTGAC -s Anc0.Anc0refChr0 6126 38 + 26507 TTTTGGAGTAGGTGAGCTTCACTTACACTGTGGTTGAC -s Anc1.Anc1refChr6 6259 38 + 197743 TTTTGGAGTAGGTGAGCTTCACTTACACTGTGGTTGAC -s Anc2.Anc2refChr6 6354 38 + 7137 TTTTAGAGTAAGTGAGCTTCACTTACACTGTGGTCGAT -s mr.mrrefChr5 189889 38 + 294540 ACTTGGAGTAGTAGTGCTTTACTTCCACTGTGAGTGAC -s simCow_chr6.simCow.chr6 314676 38 + 602619 ACTTAGATGAAGTAAACTTCACTTACACTGTAGTCGAT -s simDog_chr6.simDog.chr6 295118 38 - 593897 TTTTAGAGTAAATGTGCCTCACCTACGCTGTGGTCAAT -s simHuman_chr6.simHuman.chr6 326401 38 + 601863 TTTTGGAGTAGGCGAGCTTCAGTTAGACTGTGGTTGAC -s simRat_chr6.simRat.chr6 333924 38 + 647215 GCTTGGAGTAGTCATGCTTTACTTTCACTGTGAATGAC - -a -s simMouse_chr6.simMouse.chr6 342359 1 + 636262 T -s Anc0.Anc0refChr0 6164 1 + 26507 T -s Anc1.Anc1refChr6 6297 1 + 197743 T -s Anc2.Anc2refChr6 6392 1 + 7137 A -s mr.mrrefChr5 189927 1 + 294540 T -s simCow_chr6.simCow.chr6 314714 1 + 602619 A -s simHuman_chr6.simHuman.chr6 326439 1 + 601863 T -s simRat_chr6.simRat.chr6 333969 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 342360 34 + 636262 AATGAAGCCACCCCATGGCATATTGACAACCAGG -s Anc0.Anc0refChr0 6172 34 + 26507 AATGAGGCTCCCGTATAATCTATGAACAGCCAAG -s Anc1.Anc1refChr6 6305 34 + 197743 AATGAGGCTCCCGTATAATCTATGAACAGCCAAG -s Anc2.Anc2refChr6 6400 34 + 7137 GAGGAGTCTCCCGTATAATCTATGAACAGCCAAG -s mr.mrrefChr5 189928 34 + 294540 AATGAAGCCCCCCCATGGCATATTAACAACCAGG -s simCow_chr6.simCow.chr6 314722 34 + 602619 GAGGAGACTGCCCCATGATTCATTATCTGTCAAG -s simDog_chr6.simDog.chr6 295156 30 - 593897 ----GGTCTCCCGTATAATCTATGAACAGCCAAG -s simHuman_chr6.simHuman.chr6 326447 16 + 601863 AATGAGGCTCCCTTAT------------------ -s simRat_chr6.simRat.chr6 333970 34 + 647215 AATGAAGCCCCCCCATGGCATAATAACAACCGGG - -a -s simMouse_chr6.simMouse.chr6 342394 32 + 636262 AAGTGTCATGTACAATATAATCCCTGCAATCT -s Anc0.Anc0refChr0 6206 32 + 26507 AGGTGTCATGTACAAGGTAATCCCAGTAATCT -s Anc1.Anc1refChr6 6339 32 + 197743 AGGTGTCATGTACAAGGTAATCCCAGTAATCT -s Anc2.Anc2refChr6 6435 32 + 7137 AGGTGTCATGTACAAGGTAATTCTAGTAATCT -s mr.mrrefChr5 189962 32 + 294540 AAGTGTCATGTACAATATAATCCCTGCAATCT -s simCow_chr6.simCow.chr6 314757 32 + 602619 AGGTGTCATGTACAAGGTAATTCTAGTAATCC -s simDog_chr6.simDog.chr6 295187 32 - 593897 AGGTGCCATGGATAACGTAATTCTAGGAATCT -s simHuman_chr6.simHuman.chr6 326463 30 + 601863 --GTGTCATGTACAGGGTAATCCCAGTAACTT -s simRat_chr6.simRat.chr6 334004 20 + 647215 AAGTGTCATGCACAAT------------ACCT - -a -s simMouse_chr6.simMouse.chr6 342426 40 + 636262 ACTGAGGTATGAGTCTAATGTTGAAGGATCTCTTCATGAA -s Anc0.Anc0refChr0 6238 31 + 26507 AATGAGGT-TTAGTCTGATGACAAAAA--------ATCAA -s Anc1.Anc1refChr6 6371 39 + 197743 AATGAGGT-TTAGTCTGATGACAAAAATTCAATTGATCAA -s Anc2.Anc2refChr6 6467 31 + 7137 AATGAGGT-GTAGGCTGAAGACAATAA--------ATCAG -s mr.mrrefChr5 189994 40 + 294540 ACTGAGGTGTGAGTCTAATGTTGAAGGATCTCTTCATAAA -s simCow_chr6.simCow.chr6 314789 29 + 602619 ATTAAGGT-GTGGG--GAACACAATTG--------ATCTG -s simDog_chr6.simDog.chr6 295223 31 - 593897 GATGTGGG-GAATGCTGAAGATGATAA--------ACCAG -s simHuman_chr6.simHuman.chr6 326493 39 + 601863 AGTGAGGT-TTAGTCCGATGACAAAAATTCAATTGGCTAA -s simRat_chr6.simRat.chr6 334024 40 + 647215 ACTGAGGTGTGAGTCTAATGATGAAGGATCTCTTCATAAA - -a -s simMouse_chr6.simMouse.chr6 342466 8 + 636262 AATAACTT -s Anc0.Anc0refChr0 6269 8 + 26507 GATAGCTT -s Anc1.Anc1refChr6 6410 8 + 197743 GATAGCTT -s Anc2.Anc2refChr6 6498 8 + 7137 GATAGCTT -s mr.mrrefChr5 190034 8 + 294540 GATAACTT -s simCow_chr6.simCow.chr6 314818 8 + 602619 GATTGCTT -s simDog_chr6.simDog.chr6 295254 8 - 593897 GATACTTT -s simHuman_chr6.simHuman.chr6 326534 8 + 601863 GATAGCAT -s simRat_chr6.simRat.chr6 334064 8 + 647215 GATAACTT - -a -s simMouse_chr6.simMouse.chr6 342474 97 + 636262 TTACACTGTCAATTGTCTCTATTAAAGGAGATTCTATTAAAGGAGATTCCCTTGTGACCATAGACATTGGACTAATGAAGCTGAAAAAAGGCCAAAT -s Anc0.Anc0refChr0 6277 81 + 26507 CC-TACTGTAAATTGTCTCTAGCAAAA------CAA------GAGC---CCTCGTGGCCATAGAAATTGGACTAATGAAGTTGAAAAAAATCAAGAT -s Anc1.Anc1refChr6 6418 81 + 197743 CC-TACTGTAAATTGTCTCTAGCAAAA------CAA------GAGC---CCTCGTGGCCATAGAAATTGGACTAATGAAGTTGAAAAAAATCAAGAT -s Anc2.Anc2refChr6 6507 81 + 7137 CC-TACTGTAAATAGTCTCTAGCAAAA------CAA------GAGC---CCTCGTGGCCATAGAAATTGGACTAATGAAGTAGAAAAAAATCAAGAT -s mr.mrrefChr5 190042 85 + 294540 TTACACTGTAAATTGTCTCTATTAAAGGA---TCTA------GAGA---CCTTGTGACCATAGACATTGGACTAATGAAGCTGAAAAAAGGCCAAAT -s simCow_chr6.simCow.chr6 314827 80 + 602619 CA-TGC-GTAAATCATCTGTAGCAAAA------CAA------GAGC---CCTCATGACCATAGAAATTAGACTAATGAAGTAGAAAAAGATTTAGAT -s simDog_chr6.simDog.chr6 295263 81 - 593897 CC-TACTGTAAATAGTCTCTAGCAAAT------CTA------GAGA---CCTTGTGGCCATAGAAATTGAACCAATGAAGTAGAAAAAAATCAAGAT -s simHuman_chr6.simHuman.chr6 326542 80 + 601863 CC-TACAGT-AACTGTCTCTAGCAAAA------CAA------GAAC---CCTCGTGGCCATAGAATGTGGACTAGTGAAGTTGAGAAAAACCAAGAT -s simRat_chr6.simRat.chr6 334072 58 + 647215 TTACGCTGTAAATTGTCTCTATTAAAGAA---------------------------------------GGACTAAGGAAGCTGAAAAAAGGCCAAGT - -a -s simMouse_chr6.simMouse.chr6 342571 21 + 636262 AATCAAGCAAGTAAAAGAGGT -s Anc0.Anc0refChr0 6368 21 + 26507 AATCAAGTAGGTAATAGAGGT -s Anc1.Anc1refChr6 6509 21 + 197743 AATCAAGTAGGTAATAGAGGT -s Anc2.Anc2refChr6 6598 21 + 7137 AATCAAGTAGGTAATAGAGGT -s mr.mrrefChr5 190128 21 + 294540 AATCAAGCAAGTAAAAGAGGT -s simCow_chr6.simCow.chr6 314917 21 + 602619 AACCAAATATGTAATAGAAGC -s simDog_chr6.simDog.chr6 295354 21 - 593897 GATCAAGTAGGTAATAAAGGT -s simHuman_chr6.simHuman.chr6 326632 21 + 601863 AATCAAGTAGGTAGTAGAGGT -s simRat_chr6.simRat.chr6 334131 21 + 647215 AATCACGCAAGTGACAGAGGT - -a -s simMouse_chr6.simMouse.chr6 342592 12 + 636262 TCCTAGTAATAG -s Anc0.Anc0refChr0 6389 10 + 26507 TGCTAATCAT-- -s Anc1.Anc1refChr6 6530 12 + 197743 TGCTAATCATAA -s Anc2.Anc2refChr6 6619 10 + 7137 TGCTAATCAT-- -s mr.mrrefChr5 190149 12 + 294540 TCCTAGTAATAG -s simCow_chr6.simCow.chr6 314938 10 + 602619 TGTCAATCCT-- -s simDog_chr6.simDog.chr6 295375 10 - 593897 TGCTAATTAT-- -s simHuman_chr6.simHuman.chr6 326654 12 + 601863 TACTAATCATAA -s simRat_chr6.simRat.chr6 334152 12 + 647215 CCCGAGTAATAT - -a -s simMouse_chr6.simMouse.chr6 342604 4 + 636262 TCCA -s Anc0.Anc0refChr0 6401 4 + 26507 CTTT -s Anc1.Anc1refChr6 6544 4 + 197743 CTTT -s Anc2.Anc2refChr6 6631 4 + 7137 CTTT -s mr.mrrefChr5 190161 4 + 294540 TCCA -s simCow_chr6.simCow.chr6 314950 4 + 602619 CTTT -s simDog_chr6.simDog.chr6 295387 4 - 593897 CTTT -s simHuman_chr6.simHuman.chr6 326671 4 + 601863 CTTT -s simRat_chr6.simRat.chr6 334164 4 + 647215 TCCA - -a -s simMouse_chr6.simMouse.chr6 342608 22 + 636262 CTATAAATAGAAAAATCATAGT -s Anc0.Anc0refChr0 6405 22 + 26507 CTATAAATGGGACCATCGTAGT -s Anc1.Anc1refChr6 6548 22 + 197743 CTATAAATGGGACCATCGTAGT -s Anc2.Anc2refChr6 6635 22 + 7137 CCATAAATGGGACCATAGTAGT -s mr.mrrefChr5 190165 22 + 294540 CTATAAATAGAAAAATCATAGT -s simCow_chr6.simCow.chr6 314954 22 + 602619 GCACAAATGGTAACATTAGAGT -s simDog_chr6.simDog.chr6 295391 22 - 593897 CCATAAATGGGACCATAGTAGT -s simHuman_chr6.simHuman.chr6 326675 17 + 601863 CTGTAAATGGGACCATC----- -s simRat_chr6.simRat.chr6 334173 22 + 647215 CTATAAATAGAAAAATCATAGT - -a -s simMouse_chr6.simMouse.chr6 342630 25 + 636262 TAACAGGATACAGCAGATGTCAATT -s Anc0.Anc0refChr0 6427 25 + 26507 TGGTAGGATACAGTAGATATTAATT -s Anc1.Anc1refChr6 6570 25 + 197743 TGGTAGGATACAGTAGATATTAATT -s Anc2.Anc2refChr6 6657 25 + 7137 TGGTAGGATACATTAGATATTAATT -s mr.mrrefChr5 190187 25 + 294540 TGACAGGATACAGTAGATGTCAATT -s simCow_chr6.simCow.chr6 314976 24 + 602619 TGGTAGGATACAATAGATATTAAT- -s simDog_chr6.simDog.chr6 295413 25 - 593897 TGGCAGGATACATTAGATATTTATT -s simHuman_chr6.simHuman.chr6 274937 25 - 601863 TGTTAGGATGCGGTAAACATTAATT -s simRat_chr6.simRat.chr6 334195 25 + 647215 TGACAGAATACAATAGATGTCAATT - -a -s simMouse_chr6.simMouse.chr6 342655 20 + 636262 CATATTATATGCTGTATCTG -s Anc0.Anc0refChr0 6452 14 + 26507 CA------ATGTTGTGTCTG -s Anc1.Anc1refChr6 6595 14 + 197743 CA------ATGTTGTGTCTG -s Anc2.Anc2refChr6 6682 14 + 7137 CT------ATGTTGTGTCTG -s mr.mrrefChr5 190212 20 + 294540 GATATTATATGCTGTATCTG -s simCow_chr6.simCow.chr6 315000 10 + 602619 ----------GTTGTGTCAG -s simDog_chr6.simDog.chr6 295442 14 - 593897 CT------ATGTTGTGTCTG -s simHuman_chr6.simHuman.chr6 274962 13 - 601863 CA------ATGATCTGCCT- -s simRat_chr6.simRat.chr6 334220 20 + 647215 GATATTACATTCTGTATCTG - -a -s simMouse_chr6.simMouse.chr6 342675 12 + 636262 TAGACTTTCGTT -s Anc0.Anc0refChr0 6471 8 + 26507 TTGCCTTT---- -s Anc1.Anc1refChr6 6614 8 + 197743 TTGCCTTT---- -s Anc2.Anc2refChr6 6701 8 + 7137 GTGCATTT---- -s mr.mrrefChr5 190237 12 + 294540 TAGACTTTCGTT -s simCow_chr6.simCow.chr6 315015 8 + 602619 CTGCCTTT---- -s simDog_chr6.simDog.chr6 295461 8 - 593897 GTGCATCT---- -s simHuman_chr6.simHuman.chr6 274977 8 - 601863 TGGCCTCT---- -s simRat_chr6.simRat.chr6 334246 8 + 647215 TAAACTTT---- - -a -s simMouse_chr6.simMouse.chr6 342687 19 + 636262 GATCACAAGGGGTTTGTAT -s Anc0.Anc0refChr0 6479 10 + 26507 AATCTTAAGG--------- -s Anc1.Anc1refChr6 6622 10 + 197743 AATCTTAAGG--------- -s Anc2.Anc2refChr6 6718 10 + 7137 AATCTTAAGG--------- -s mr.mrrefChr5 190249 10 + 294540 GATCACAAGG--------- -s simCow_chr6.simCow.chr6 315032 10 + 602619 AATCTTGAGT--------- -s simDog_chr6.simDog.chr6 295478 10 - 593897 GACCTCAAGG--------- -s simHuman_chr6.simHuman.chr6 274985 10 - 601863 AATCTTAAGG--------- - -a -s simMouse_chr6.simMouse.chr6 342706 3 + 636262 TGG -s Anc0.Anc0refChr0 6497 3 + 26507 TGG -s Anc1.Anc1refChr6 6640 3 + 197743 TGG -s Anc2.Anc2refChr6 6736 3 + 7137 TGG -s mr.mrrefChr5 190259 3 + 294540 TGG -s simCow_chr6.simCow.chr6 315050 3 + 602619 TAG -s simDog_chr6.simDog.chr6 295488 3 - 593897 TGG -s simHuman_chr6.simHuman.chr6 275003 3 - 601863 TGG - -a -s simMouse_chr6.simMouse.chr6 342709 17 + 636262 GGCCATGGCCTGAAAGC -s Anc0.Anc0refChr0 6500 17 + 26507 AGCCATGGTCTGACAGT -s Anc1.Anc1refChr6 6643 17 + 197743 AGCCATGGTCTGACAGT -s Anc2.Anc2refChr6 6739 17 + 7137 AGCTATAGTCTGACAGT -s mr.mrrefChr5 190262 17 + 294540 GGCCATGGTCTGAAAGC -s simCow_chr6.simCow.chr6 315056 17 + 602619 ATCGGTAATCTGGCAGT -s simDog_chr6.simDog.chr6 295491 17 - 593897 AGCTAAAGTCTGACAGC -s simHuman_chr6.simHuman.chr6 275006 10 - 601863 AGCCATGA-------AT -s simRat_chr6.simRat.chr6 334254 15 + 647215 --CCATGGTCTGCGAGC - -a -s simMouse_chr6.simMouse.chr6 342726 6 + 636262 TGGCCT -s Anc0.Anc0refChr0 6524 6 + 26507 TGGCCT -s Anc1.Anc1refChr6 6667 6 + 197743 TGGCCT -s Anc2.Anc2refChr6 6763 6 + 7137 GGGCCC -s mr.mrrefChr5 190279 6 + 294540 TGGCCT -s simCow_chr6.simCow.chr6 315080 6 + 602619 GGACCC -s simDog_chr6.simDog.chr6 295515 6 - 593897 GGGCTC -s simHuman_chr6.simHuman.chr6 275023 6 - 601863 TTGCCT -s simRat_chr6.simRat.chr6 334269 6 + 647215 TGGCCT - -a -s simMouse_chr6.simMouse.chr6 342732 103 + 636262 CCCCCAGATATTGTATACAACTAGTCAGAGTGATCACTACAGGACATTATCTTTGAGCCAAAGCAGTCCTCTGATGTTAGGCCATTGTGACTTGAGCTGCATT -s Anc0.Anc0refChr0 6546 99 + 26507 TCCACAGATACTGTATGCA-CTAATGAGAGTGATCACTACAGGAAATTTGTTTTGATTCAAACCAGTCCTCTGATGTGAGGCAGTTATGTCTTGAGCTG---T -s Anc1.Anc1refChr6 6691 102 + 197743 TCCACAGATACTGTATGCA-CTAATGAGAGTGATCACTACAGGAAATTTGTTTTGATTCAAACCAGTCCTCTGATGTGAGGCAGTTATGTCTTGAGCTGTATT -s Anc2.Anc2refChr6 6785 99 + 7137 TCCACAGCTGCTGTATGCA-CTAATGAGTGTGATCACTACATGAAATTTGTTTTGATTCAAACAAGTCCTTTGATGTGAGACAGCTATTTCTTGAGCTG---T -s mr.mrrefChr5 190299 103 + 294540 CCCCCAGATATTGTATACAACTAATCAGAGTGATCACTACAGGACATTAGCTTTGAGTCAAAGCAGTCCTCTGATGTTAGGCCATTGTGACTTGAGCTGCATT -s simCow_chr6.simCow.chr6 315088 94 + 602619 TCCACAGCTGCTGTATGCA-GCAGTGAGGGTGATCACTGCATGATATTTGTTGTGATTCAAATAAGT-----AATGTGAGACAAATGCTGCTTGTGCTG---T -s simDog_chr6.simDog.chr6 295537 99 - 593897 TCCACAGCTGCTGTATGCA-CTAATGAGTGTGATTGCTACATGAAATCTGCTTTGATTCAAACAAGTCCTTTGACGTGATACTGCTATTTCTTGAGTTG---T -s simHuman_chr6.simHuman.chr6 275047 102 - 601863 TCCATAGATACTGTATGCA-CTAATGAGAGCGATCACTTTGGGAAATTTGTTTAGATTTAAACCACTCCCCTGATGTGAGGCAGTTATGTCTTGGGCTAGATT -s simRat_chr6.simRat.chr6 334289 87 + 647215 CCCCAAGATATTGTATACAATTAACCAGAGTGATCACTACAGGATATTAGTTTTGAGTCAAAGCAATGCCCTT-TGCTAGCAGAT---------------ATT - -a -s simMouse_chr6.simMouse.chr6 342835 5 + 636262 ACATT -s Anc0.Anc0refChr0 6645 5 + 26507 ATGTT -s Anc1.Anc1refChr6 6793 5 + 197743 ATGTT -s Anc2.Anc2refChr6 6884 5 + 7137 ATGCT -s mr.mrrefChr5 190402 5 + 294540 ACATT -s simCow_chr6.simCow.chr6 315182 5 + 602619 ATGTT -s simDog_chr6.simDog.chr6 295636 5 - 593897 ATGCT -s simHuman_chr6.simHuman.chr6 326948 5 + 601863 ATGTT -s simRat_chr6.simRat.chr6 334376 5 + 647215 TCATT - -a -s simMouse_chr6.simMouse.chr6 342840 19 + 636262 CATCTCATTAAATCATGGG -s Anc0.Anc0refChr0 6653 19 + 26507 CATTTCATTAAGTCCTGGG -s Anc1.Anc1refChr6 6801 19 + 197743 CATTTCATTAAGTCCTGGG -s Anc2.Anc2refChr6 6892 19 + 7137 CATTTCATTAAGTCCTAGG -s mr.mrrefChr5 190407 19 + 294540 CATCTCATTAAATCATGGG -s simCow_chr6.simCow.chr6 315190 19 + 602619 CAACTCATTAAGTCTAAGG -s simDog_chr6.simDog.chr6 295644 19 - 593897 CATTTCAATAAGTCCTAGA -s simHuman_chr6.simHuman.chr6 326956 19 + 601863 CGTTTCATTAAGTCCTGGG -s simRat_chr6.simRat.chr6 334381 18 + 647215 CATCTCATT-AATCATGGG - -a -s simMouse_chr6.simMouse.chr6 342859 25 + 636262 GTTCTGACACTTGTTATTGTTGACA -s Anc0.Anc0refChr0 6672 25 + 26507 GGCCTGACACTTCTTATTGTTGACA -s Anc1.Anc1refChr6 6820 25 + 197743 GGCCTGACACTTCTTATTGTTGACA -s Anc2.Anc2refChr6 6911 25 + 7137 AGCCTGACACTTCTTATTGTTGACA -s mr.mrrefChr5 190426 25 + 294540 GTTCTGACACTTGTTATTGTTGACA -s simCow_chr6.simCow.chr6 315209 21 + 602619 TGGCTGACACATC----CGTTGACA -s simDog_chr6.simDog.chr6 295663 25 - 593897 AGCCCTACACTCCTTATTGTTGAGA -s simHuman_chr6.simHuman.chr6 326979 25 + 601863 GGACTGACACTTCTTATTGTTAACA -s simRat_chr6.simRat.chr6 334399 25 + 647215 GTGCTGACACTTGTTATTGTTGACA - -a -s simMouse_chr6.simMouse.chr6 342884 136 + 636262 CATTATTTaaactctatgcacatgcaatacacctcaaagggtgaaagtctcaggaatttaaggtgttcagagcaagggtggtagcgaaataaatttgggatatgtacaccaaccagcctatcgagctctttaTGAA -s Anc0.Anc0refChr0 7350 18 + 26507 CTTGATTTATATTCT----------------------------------------------------------------------------------------------------------------------GAA -s Anc1.Anc1refChr6 7498 18 + 197743 CTTGATTTATATTCT----------------------------------------------------------------------------------------------------------------------GAA -s Anc2.Anc2refChr17 459 18 + 28526 CTTGATTTATATTTT----------------------------------------------------------------------------------------------------------------------GAA -s mr.mrrefChr5 190451 131 + 294540 CATTATTTaaactctatgcacatgcaatacacctcaaagggtgaaagtctcaggaatttaaggtgttcagagcaa----ggtagcgaaataaatttgggatatgtacaccaacca-cctatcgagctctttatgaa -s simCow_chr6.simCow.chr6 315830 17 + 602619 CTTGATTTATATTT-----------------------------------------------------------------------------------------------------------------------GAA -s simDog_chr6.simDog.chr6 307953 18 + 593897 TTGAATCTGCATTTT----------------------------------------------------------------------------------------------------------------------GAA -s simHuman_chr6.simHuman.chr6 327683 18 + 601863 CTTGATTTATATTCA----------------------------------------------------------------------------------------------------------------------GAA -s simRat_chr6.simRat.chr6 334424 131 + 647215 CATTATTTaaactccatgctcatgcaatacacctaagggggtgtaaatttcaggaattttaggtgatctgagcag----cgtaggaaaatgattttgggatatgtacaccaacca-cttatcgagctctttatgta - -a -s simMouse_chr6.simMouse.chr6 343020 18 + 636262 GGATCGAACCAACATGTG -s Anc0.Anc0refChr0 7368 18 + 26507 GTAGAGAACCTTGGTGTT -s Anc1.Anc1refChr6 7516 18 + 197743 GTAGAGAACCTTGGTGTT -s Anc2.Anc2refChr17 479 18 + 28526 GTAGAGAGCCTTGGTCTT -s mr.mrrefChr5 190582 18 + 294540 ggATCGAACCAACATGTG -s simCow_chr6.simCow.chr6 315849 18 + 602619 GTGGAGAGCTTTGGTGTA -s simDog_chr6.simDog.chr6 307973 18 + 593897 GTAGAGAGGCTTGGTCTT -s simHuman_chr6.simHuman.chr6 327701 18 + 601863 GTAAAGAACCTTGGTGTT -s simRat_chr6.simRat.chr6 334555 18 + 647215 gaATCAGGCCAGCATGTG - -a -s simMouse_chr6.simMouse.chr6 343038 23 + 636262 ACCCAAATTTAGTAATTCACCTT -s Anc0.Anc0refChr0 7386 23 + 26507 ACCCAAACTTAGTAATTCACATT -s Anc1.Anc1refChr6 7534 23 + 197743 ACCCAAACTTAGTAATTCACATT -s Anc2.Anc2refChr17 497 23 + 28526 ACCCAAACTTACTAATTCACATT -s mr.mrrefChr5 190600 23 + 294540 ACCCAAACTTAGTAATTCACCTT -s simCow_chr6.simCow.chr6 315867 23 + 602619 ACTCACTCTCATTAATGCATATT -s simDog_chr6.simDog.chr6 307991 23 + 593897 ACCCAAACTTACTAATTCACATT -s simHuman_chr6.simHuman.chr6 327720 23 + 601863 ACCCTAACTTGGTAATTCGCATC -s simRat_chr6.simRat.chr6 334573 23 + 647215 ACCCAAACTTAGTAATCCACCTT - -a -s simMouse_chr6.simMouse.chr6 343061 1 + 636262 A -s Anc0.Anc0refChr0 7416 1 + 26507 G -s Anc1.Anc1refChr6 7564 1 + 197743 G -s Anc2.Anc2refChr17 527 1 + 28526 G -s mr.mrrefChr5 190630 1 + 294540 A -s simCow_chr6.simCow.chr6 315897 1 + 602619 A -s simDog_chr6.simDog.chr6 308021 1 + 593897 G -s simHuman_chr6.simHuman.chr6 327750 1 + 601863 G -s simRat_chr6.simRat.chr6 334603 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 343062 6 + 636262 CTAGAT -s Anc0.Anc0refChr0 7419 6 + 26507 CTAAAT -s Anc1.Anc1refChr6 7567 6 + 197743 CTAAAT -s Anc2.Anc2refChr17 530 6 + 28526 CTAAAC -s mr.mrrefChr5 190631 6 + 294540 CTAGAT -s simCow_chr6.simCow.chr6 315900 6 + 602619 CCAGAG -s simDog_chr6.simDog.chr6 308024 6 + 593897 CTAAAC -s simHuman_chr6.simHuman.chr6 327753 6 + 601863 CTAAAT -s simRat_chr6.simRat.chr6 334604 6 + 647215 CTTGAT - -a -s simMouse_chr6.simMouse.chr6 343068 2 + 636262 AT -s Anc0.Anc0refChr0 7430 2 + 26507 AT -s Anc1.Anc1refChr6 7578 2 + 197743 AT -s Anc2.Anc2refChr17 541 2 + 28526 AT -s mr.mrrefChr5 190637 2 + 294540 AT -s simCow_chr6.simCow.chr6 315911 2 + 602619 AT -s simDog_chr6.simDog.chr6 308035 2 + 593897 GT -s simHuman_chr6.simHuman.chr6 327764 2 + 601863 AT -s simRat_chr6.simRat.chr6 334610 2 + 647215 AT - -a -s simMouse_chr6.simMouse.chr6 343070 35 + 636262 CTAAAATGAAGTTATCCCTACCAAGCCCACTCGTG -s Anc0.Anc0refChr0 7457 33 + 26507 ATGCAGCAG-AACATAAC-AGCAAGCCTGCACCTG -s Anc1.Anc1refChr6 7605 33 + 197743 ATGCAGCAG-AACATAAC-AGCAAGCCTGCACCTG -s Anc2.Anc2refChr17 568 33 + 28526 ATGCAGCAG-AACATAAC-AGCAAGCCTGCACCTG -s mr.mrrefChr5 190664 34 + 294540 CTAAAATGA-GTTATCCCTACCAAGCCTGCACGTG -s simCow_chr6.simCow.chr6 315938 33 + 602619 ATGCAACAG-AACATAAC-TGCAAGCCTGCACCTG -s simDog_chr6.simDog.chr6 308062 33 + 593897 ATGCAGCAG-AACCCAAT-AGCAAGCCCGCGCTTG -s simHuman_chr6.simHuman.chr6 327791 33 + 601863 ATGCAGCAG-AACATAAC-AGGAAACCTGCACCTG -s simRat_chr6.simRat.chr6 334637 34 + 647215 CTAAAATGA-GTTATCCCTACCAAGCCTGCACATG - -a -s simMouse_chr6.simMouse.chr6 343105 27 + 636262 GCCGGCCACTGATGACATTGGCAAGGT -s Anc0.Anc0refChr0 7491 15 + 26507 GCTGGCAACTGATGA------------ -s Anc1.Anc1refChr6 7639 27 + 197743 GCTGGCAACTGATGACAGTGGCAACTC -s Anc2.Anc2refChr17 602 15 + 28526 GCTGGCAACTGATGA------------ -s mr.mrrefChr5 190699 27 + 294540 GCCGGCCACTGATGACATTGGCAAGGT -s simCow_chr6.simCow.chr6 315972 15 + 602619 GCTGGCAACTGATGA------------ -s simDog_chr6.simDog.chr6 308096 15 + 593897 ACTGGCAACTGATGA------------ -s simHuman_chr6.simHuman.chr6 327825 27 + 601863 GCTGGAGACAGATGACAGTGGCAACTC -s simRat_chr6.simRat.chr6 334672 27 + 647215 GCCGGCCACTGATGACATTGGCAAGGT - -a -s simMouse_chr6.simMouse.chr6 343132 26 + 636262 CAGGTGTTTAAGTAAGGACACTTACT -s Anc0.Anc0refChr0 7507 20 + 26507 ------TTGAAGCAGGGACGACCACT -s Anc1.Anc1refChr6 7667 20 + 197743 ------TTGAAGCAGGGACGACCACT -s Anc2.Anc2refChr17 618 20 + 28526 ------TTGGAACAGAGACGACCCCT -s mr.mrrefChr5 190727 26 + 294540 CAGGTGTTTAAGCAAGGACGATCACT -s simCow_chr6.simCow.chr6 315991 20 + 602619 ------TTGGAACAGAGACAGCCCCT -s simDog_chr6.simDog.chr6 308112 20 + 593897 ------TTGGAACTGAGACGACCCCT -s simHuman_chr6.simHuman.chr6 327853 20 + 601863 ------TTCAAGCAGGGACGTCCACT -s simRat_chr6.simRat.chr6 334705 26 + 647215 CAGGTGTTTGAGCAAGGAGGATCACT - -a -s simMouse_chr6.simMouse.chr6 343158 8 + 636262 CTCAATTA -s Anc0.Anc0refChr0 7535 8 + 26507 CACAAGTA -s Anc1.Anc1refChr6 7695 8 + 197743 CACAAGTA -s Anc2.Anc2refChr17 646 8 + 28526 CATATGTT -s mr.mrrefChr5 190753 8 + 294540 CTCAATTA -s simCow_chr6.simCow.chr6 316019 8 + 602619 CACAAGGT -s simCow_chr6.simCow.chr6 35490 8 - 602619 CATGTGAT -s simDog_chr6.simDog.chr6 308140 8 + 593897 CATATGTT -s simHuman_chr6.simHuman.chr6 327881 8 + 601863 CACAAGTA -s simRat_chr6.simRat.chr6 334731 8 + 647215 CTCAATTA - -a -s simMouse_chr6.simMouse.chr6 343166 14 + 636262 TGAGACCAAAAGTT -s Anc0.Anc0refChr0 7543 2 + 26507 A------------T -s Anc1.Anc1refChr6 7703 14 + 197743 AAAGACCACAAGTT -s Anc2.Anc2refChr17 654 2 + 28526 A------------T -s mr.mrrefChr5 190761 14 + 294540 TGAGACCAAAAGTT -s simCow_chr6.simCow.chr6 35498 2 - 602619 A------------T -s simHuman_chr6.simHuman.chr6 327889 14 + 601863 AAAGACCACAAGTG -s simRat_chr6.simRat.chr6 334739 14 + 647215 TGAGACCAAAAGTT - -a -s simMouse_chr6.simMouse.chr6 343180 12 + 636262 GGGTCTTAATTT -s Anc0.Anc0refChr0 7545 10 + 26507 GAG--TGAATTT -s Anc1.Anc1refChr6 7717 10 + 197743 GAG--TGAATTT -s Anc2.Anc2refChr17 656 10 + 28526 GAG--TGAATTT -s mr.mrrefChr5 190775 12 + 294540 GAGTCTTAATTT -s simCow_chr6.simCow.chr6 316027 10 + 602619 GAG--TGAATTT -s simCow_chr6.simCow.chr6 35500 10 - 602619 GAG--TGAATTT -s simDog_chr6.simDog.chr6 308148 10 + 593897 GAG--TGACTTT -s simHuman_chr6.simHuman.chr6 327903 10 + 601863 GAG--TGAATTT -s simRat_chr6.simRat.chr6 334753 12 + 647215 AAGGCTCAATTT - -a -s simMouse_chr6.simMouse.chr6 343192 13 + 636262 TTGTGGAGGGAGA -s Anc0.Anc0refChr0 7583 13 + 26507 TTGTGGACAGAGA -s Anc1.Anc1refChr6 7755 13 + 197743 TTGTGGACAGAGA -s Anc2.Anc2refChr17 694 13 + 28526 TTATGGACAGAGG -s mr.mrrefChr5 190787 13 + 294540 TTGTGGAGGGAGA -s simCow_chr6.simCow.chr6 316063 13 + 602619 TTATGGACAGAGG -s simCow_chr6.simCow.chr6 35536 13 - 602619 TTATGAACAGAGG -s simDog_chr6.simDog.chr6 308183 10 + 593897 ---TGGACAGAGG -s simHuman_chr6.simHuman.chr6 327949 13 + 601863 CTGTGGACAGACA -s simRat_chr6.simRat.chr6 334765 13 + 647215 TTGTGGAGGGAGA - -a -s simMouse_chr6.simMouse.chr6 343205 10 + 636262 TTCAGCCATA -s Anc0.Anc0refChr0 7596 10 + 26507 TACAGCCCTC -s Anc1.Anc1refChr6 7768 10 + 197743 TACAGCCCTC -s Anc2.Anc2refChr17 707 10 + 28526 TACAGCCCTT -s mr.mrrefChr5 190800 10 + 294540 TTCAGCCATC -s simCow_chr6.simCow.chr6 316079 10 + 602619 CACAGCCCTG -s simCow_chr6.simCow.chr6 35549 10 - 602619 CACAGCCCTG -s simDog_chr6.simDog.chr6 308193 10 + 593897 TGTAGCTCTT -s simHuman_chr6.simHuman.chr6 327962 10 + 601863 TCCAGCCCTC -s simRat_chr6.simRat.chr6 334778 10 + 647215 TTAAGCTATC - -a -s simMouse_chr6.simMouse.chr6 343215 108 + 636262 TCTGAAATGAAAAGAGGTCTCACACTACTGATAACAACCTTAGAGTAGTGTAATGCCCAGGTGAATGCTTATTTTGAACATTCTGGTTTATATCTAAAAGTGGTGTAA -s Anc0.Anc0refChr0 7606 108 + 26507 TCTGGAATCAAAAGAGGTCCTGTCCCCCAGATTGCCACCTTAGATTATTGCAATGCCCAGGTGTAGGCTTAGTTTAAACACTCTGCTTTATATCAGAAAGCAATCCAA -s Anc1.Anc1refChr6 7778 108 + 197743 TCTGGAATCAAAAGAGGTCCTGTCCCCCAGATTGCCACCTTAGATTATTGCAATGCCCAGGTGTAGGCTTAGTTTAAACACTCTGCTTTATATCAGAAAGCAATCCAA -s Anc2.Anc2refChr17 717 108 + 28526 TCTGGAATCAAAAGAGGTCCTGTCCCCCAGGTTGCCATCTTAGATTATTGCAATGCCCAGGTGTAGGCTTAGTTTACACACTCTGCTTTATATCAGAAAGCAATCCAA -s mr.mrrefChr5 190810 108 + 294540 TCTGAAATGAAAAGAGGTCTCACACTACTGATTACAACCTTAGAGTAGTGTAATGCCCAGGTGAATGCTTAGTTTAAACACTCTGGTTTATATCAAAAAGCGGTGCAA -s simCow_chr6.simCow.chr6 316089 108 + 602619 TCTGGACTCAAAAGATGTCGTATCCTGCAGGTTGCCATCTCAGATTATTGCAATGCCCAAGTGTACGCTTAGTTTACACGCTCTGCTCTATATTTGAAAGCAATCCAA -s simCow_chr6.simCow.chr6 35559 108 - 602619 TCTGGACTCAAAAGATGTCGTGTCGTCCAGATTGCCACCTCGGATTATTGCAATGCCCAAGTGTAGGCTTAGTTTACACACTCTGCTTTATATCCAAAAGCAATCCAA -s simDog_chr6.simDog.chr6 308203 108 + 593897 GCTGGAATGAAATGGGGTCCTGTCCCCCAGGTTGCCATGTTAGATGATTGCAATGCCCAGGTGTATGGTTAGTTTACAGTCTCTGCTTTATATCAGAAAGCAATCCAA -s simHuman_chr6.simHuman.chr6 327975 108 + 601863 TCTGGAATCAAGAGAGGTCCTGTCCCCCGGATTGCCACCTTAAATCATTGCAATGCCCAGGTATAGGTTTAGTTTAATCACTCTGCTTTGTATCAGATAACATTCCAA -s simRat_chr6.simRat.chr6 334788 108 + 647215 TCTGAAATGAAAAGAAGCCTCACACTTCTGATTACACCCTTAGACTACTGTAATGCCCAGGTGAGTGAGTAGTTTAAGCACTCTGGTTTATAACAAAAAGCGGTGCAA - -a -s simMouse_chr6.simMouse.chr6 343323 208 + 636262 GTGGCACTGTGAATTGATAAACATACACTACTCACAGAATGGGTTAATTAACCTCATATATACCACTCACAGACTGGGTTAATCAGGTCAATCAACCTCATATTCATTGTCATTTCTTACTTGCCAATTAAGGTTGACACTTGGTGGCACACTGCAAGTAAGGATACCAACCTTAGAAGCCAAAACCAACCTACAAGTACCAGAGTAT -s Anc0.Anc0refChr0 7715 9 + 26507 GTGTCAGTG------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- -s Anc1.Anc1refChr6 7887 9 + 197743 GTGTCAGTG------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- -s Anc2.Anc2refChr17 826 9 + 28526 ATGTCAGTG------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- -s mr.mrrefChr5 190918 157 + 294540 GTGGCACTGTAAGTCAATAAACATACACTA-------AATGGGTT--------------------------------------------AATCAACCTCATATTCATTGTCATTTCTTACTTGCCAATTAAGGTTGACACTTGGTGGCACACTGCAAGTAAGGATACCAACCTTAGAAGCCAAAACCAACCTACAAGTACCAGAGTAT -s simCow_chr6.simCow.chr6 316198 9 + 602619 ATGTCAGTG------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- -s simCow_chr6.simCow.chr6 35668 9 - 602619 GTGTCTGTG------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- -s simDog_chr6.simDog.chr6 308312 9 + 593897 ATGTCAGGG------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- -s simHuman_chr6.simHuman.chr6 328084 9 + 601863 GTGTCAGTG------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- -s simRat_chr6.simRat.chr6 334896 157 + 647215 ATGGCACTGCAAGTCAATAAACATATACCA-------AATGGGTT--------------------------------------------AATCAACCTCATATTCACTGTCATTACTTACTGGTCAATTAAGGCTGACAATTGGTGGCACACTGCAAGCAAAGATATCAACCTTAGAGGCCAAAACTGACTTACAAGTACCAGAGTAT - -a -s simMouse_chr6.simMouse.chr6 343531 6 + 636262 GTAAAA -s Anc0.Anc0refChr0 7724 2 + 26507 ----AA -s Anc1.Anc1refChr6 7896 2 + 197743 ----AA -s Anc2.Anc2refChr17 835 2 + 28526 ----AA -s mr.mrrefChr5 191075 6 + 294540 GTAAAA -s simCow_chr6.simCow.chr6 316207 2 + 602619 ----AA -s simCow_chr6.simCow.chr6 35677 2 - 602619 ----GA -s simDog_chr6.simDog.chr6 308321 2 + 593897 ----AA -s simHuman_chr6.simHuman.chr6 328093 2 + 601863 ----AA -s simRat_chr6.simRat.chr6 335055 6 + 647215 GTAAAA - -a -s simMouse_chr6.simMouse.chr6 343537 16 + 636262 GAACTGTTACAGTGGC -s Anc0.Anc0refChr0 7726 16 + 26507 AAGCTGTTACAGTGGC -s Anc1.Anc1refChr6 7898 16 + 197743 AAGCTGTTACAGTGGC -s Anc2.Anc2refChr17 847 16 + 28526 AAGCTGTTACAGTAGC -s mr.mrrefChr5 191081 16 + 294540 GAACTGTTACAGTGGC -s simCow_chr6.simCow.chr6 316219 16 + 602619 AAGCTGTTACAATGGG -s simCow_chr6.simCow.chr6 35689 16 - 602619 AAGCTGTTACAGTAGC -s simDog_chr6.simDog.chr6 308333 16 + 593897 AACCTGCTACAGTAGT -s simHuman_chr6.simHuman.chr6 328095 15 + 601863 AGGCCGTT-CAGTGGC -s simRat_chr6.simRat.chr6 335061 16 + 647215 GACCTGTTACAGCAGC - -a -s simMouse_chr6.simMouse.chr6 343553 19 + 636262 TTAATATTTTTTTAGATGG -s Anc0.Anc0refChr0 7742 19 + 26507 TTAACACTTCTTTACATGG -s Anc1.Anc1refChr6 7914 19 + 197743 TTAACACTTCTTTACATGG -s Anc2.Anc2refChr17 874 19 + 28526 TTAACACTTCTTTACATGG -s mr.mrrefChr5 191097 19 + 294540 TTAATACTTTTTTAGATGG -s simCow_chr6.simCow.chr6 316246 19 + 602619 TTAACACTTGTTCACATAG -s simCow_chr6.simCow.chr6 35716 19 - 602619 TTAACACTTCTTCACATGC -s simDog_chr6.simDog.chr6 308349 19 + 593897 TTAACACTTCTTTACATGG -s simHuman_chr6.simHuman.chr6 328110 19 + 601863 ATGACACTCCTTTACATGG -s simRat_chr6.simRat.chr6 335077 19 + 647215 TTAATACTTTTTTATATGG - -a -s simMouse_chr6.simMouse.chr6 343572 30 + 636262 TTATTTTACATATGGCATTATCTTCTGTGG -s Anc0.Anc0refChr0 7762 30 + 26507 TTATTTTATGCATGGCAGTACCTACCTTGG -s Anc1.Anc1refChr6 7934 30 + 197743 TTATTTTATGCATGGCAGTACCTACCTTGG -s Anc2.Anc2refChr17 894 30 + 28526 TTATATTATGCATGGCAGTACCTACCTTGG -s mr.mrrefChr5 191116 30 + 294540 TTATTTTACATATGGCATTATCTACCGTGG -s simCow_chr6.simCow.chr6 316266 27 + 602619 TTA---TATGCATGGGAGCACCTACCTTGG -s simCow_chr6.simCow.chr6 35736 27 - 602619 TTA---TATGCATGGTTGCACCTATTTTGG -s simDog_chr6.simDog.chr6 308369 30 + 593897 TTGTATTATGTATGGCAGTAGCTAACTTGG -s simHuman_chr6.simHuman.chr6 328130 30 + 601863 TTATTTTATGGATAGCAATACTTACCTTGG -s simRat_chr6.simRat.chr6 335096 24 + 647215 TTATTTTACATA------TAACTACCGTGG - -a -s simMouse_chr6.simMouse.chr6 343602 34 + 636262 TGGACTAGATTCTCCAAGAAACATTTTGGTTACG -s Anc0.Anc0refChr0 7792 23 + 26507 TATGCTAGTTT-----------ATATTAGATATA -s Anc1.Anc1refChr6 7964 23 + 197743 TATGCTAGTTT-----------ATATTAGATATA -s Anc2.Anc2refChr17 924 23 + 28526 TATGCCAGTTT-----------CTATTAGATATA -s mr.mrrefChr5 191146 34 + 294540 TGGACTAGTTTCTCCAAGAAACATTTTAGTTATA -s simCow_chr6.simCow.chr6 316293 23 + 602619 TATGCCGGTTT-----------CTACGAAATGCT -s simCow_chr6.simCow.chr6 35771 23 - 602619 TATGCCAGTTT-----------CTACTAAATACT -s simDog_chr6.simDog.chr6 308399 23 + 593897 TATGCGAGTTT-----------GTATTAGATATA -s simHuman_chr6.simHuman.chr6 328160 23 + 601863 TATGCTTGTTT-----------ATATTAGATATA -s simRat_chr6.simRat.chr6 335120 34 + 647215 TGGTCTAGTTTCTCCATGGAACGTTTTAGTTATA - -a -s simMouse_chr6.simMouse.chr6 343636 25 + 636262 ATCTGGTCAAGCTACAATTAAACTC -s Anc0.Anc0refChr0 7815 23 + 26507 ATTCAGCGAAGCTACAGTCAAA--C -s Anc1.Anc1refChr6 7987 25 + 197743 ATTCAGCGAAGCTACAGTCAAACTC -s Anc2.Anc2refChr17 947 23 + 28526 ATTCAGCGAAGCTCCAGTCAAA--C -s mr.mrrefChr5 191180 25 + 294540 ATCTAGTCAAGCTACAATTAAACTC -s simCow_chr6.simCow.chr6 316317 23 + 602619 ATTCGGCACAGCTCCAATCAAA--C -s simCow_chr6.simCow.chr6 35794 23 - 602619 ATTCGGCAAAGCTCCAATCAAA--C -s simDog_chr6.simDog.chr6 308422 23 + 593897 ATTCAGTGGAGCTCCAGCCAAA--C -s simHuman_chr6.simHuman.chr6 328183 25 + 601863 ATTCAGCGAAGCTACAGTCGAACTC -s simRat_chr6.simRat.chr6 335154 25 + 647215 ATCTAGTCAAGCTACAATTAAACTA - -a -s simMouse_chr6.simMouse.chr6 343661 28 + 636262 ATTGGTGTAAAAAAGCCTTTACTAATGA -s Anc0.Anc0refChr0 7847 28 + 26507 AATGAAGTAAAAAGAATTGTTGTAGTGA -s Anc1.Anc1refChr6 8021 28 + 197743 AATGAAGTAAAAAGAATTGTTGTAGTGA -s Anc2.Anc2refChr17 979 28 + 28526 AACAAAGTAAGAAGAATTGTTGTTGAGG -s mr.mrrefChr5 191205 28 + 294540 AATGGTGTAAAAAAGCCTTTACTAATGA -s simCow_chr6.simCow.chr6 316349 28 + 602619 AACAGAGTAAGAAGAATTGTTGTTGAGG -s simDog_chr6.simDog.chr6 308454 23 + 593897 AACAAAGTAGGAAA-----TTGTTGAGG -s simHuman_chr6.simHuman.chr6 328217 28 + 601863 AATGAAGTAAAAAGAATTGTTGTAGTGA -s simRat_chr6.simRat.chr6 335179 28 + 647215 TACAGTGTAAAAAACCATTTACTAACGA - -a -s simMouse_chr6.simMouse.chr6 343689 14 + 636262 AGTAAGCCCTGGAC -s Anc0.Anc0refChr0 7885 14 + 26507 ACTGAAAGCTACCT -s Anc1.Anc1refChr6 8059 14 + 197743 ACTGAAAGCTACCT -s Anc2.Anc2refChr17 1017 14 + 28526 TCAGAAAGATACCT -s mr.mrrefChr5 191233 14 + 294540 ACTAAACCCTAGAC -s simCow_chr6.simCow.chr6 316387 14 + 602619 GCAGAAATATACCC -s simDog_chr6.simDog.chr6 308487 14 + 593897 TTAGGGTGATGCTT -s simHuman_chr6.simHuman.chr6 328255 14 + 601863 ACTGAAAGCTACCT -s simRat_chr6.simRat.chr6 335207 14 + 647215 ACTAAACCCTAAAC - -a -s simMouse_chr6.simMouse.chr6 343703 11 + 636262 AGGTTTCGTTA -s Anc0.Anc0refChr0 7899 11 + 26507 GGGTAGTATCA -s Anc1.Anc1refChr6 8073 11 + 197743 GGGTAGTATCA -s Anc2.Anc2refChr17 1031 11 + 28526 GGGCAGTATCA -s mr.mrrefChr5 191247 11 + 294540 AGGTTTCATTA -s simCow_chr6.simCow.chr6 316401 11 + 602619 GGGCAGTATTA -s simDog_chr6.simDog.chr6 308502 11 + 593897 GGGCAGTTCCA -s simHuman_chr6.simHuman.chr6 328269 11 + 601863 GGGTAGTATGG -s simRat_chr6.simRat.chr6 335221 11 + 647215 AGGTTTCATAA - -a -s simMouse_chr6.simMouse.chr6 343714 86 + 636262 CATGAGGTAGTGGACATGCTGGCCACTCAGATTATGGAGATTGAAGTGGGTAATAATGAATCACTAGATTGACTTTCTCCTGGACA -s Anc0.Anc0refChr0 7910 86 + 26507 CATGAGGTGGTGTACAAACCTGCCTCTCAGATTATGAAGATTAGAATGATTGACAACAATTTGCTAGGTGGGCATTCTCCTGGATA -s Anc1.Anc1refChr6 8084 86 + 197743 CATGAGGTGGTGTACAAACCTGCCTCTCAGATTATGAAGATTAGAATGATTGACAACAATTTGCTAGGTGGGCATTCTCCTGGATA -s Anc2.Anc2refChr17 1046 86 + 28526 CATGAGGTGGTCTACAAACTTGCCTTGCAGATTATGAAGATTAGAATGATTGACAACAATTTGCTTGGGGGGCATTCTCCTGGGTA -s mr.mrrefChr5 191258 86 + 294540 CATGAGGTGGTGGACATACCGGCCACTCAGATTATGGAGATTAAAATGGGTAACAACAAATCGCTAGATTGACTTTCTCCTGGACA -s simCow_chr6.simCow.chr6 316416 84 + 602619 AATGAGGCGGTATGCAGACTTGTCT--CAGAGTATGAAGATTAGAATGATTGACAACAAGTTACTGGAGGGGCATTCTCCTTGGTA -s simDog_chr6.simDog.chr6 308517 86 + 593897 CATGAGGTGGTCTACAAACTTGCCTTGCAGATTATGAGGATTAGAATGATTGAGAACAATTTGCTTCGGGGGCGTTCTCTTGGGAA -s simHuman_chr6.simHuman.chr6 328280 84 + 601863 ATAAAGGTGGTGTACAAACCCGCCTCTTAGGCTATGAAGATTAGAAT--TTGACAACAATTAGCTAGGTGGGCATTCTCCTGGATA -s simRat_chr6.simRat.chr6 335232 86 + 647215 CATGAGGTGGAGGACATACCAGCCCCTCAGAATATGGACAATAAGATGACTAACAACAAATTGCTAGATTGACTTTCTCCTGGTCA - -a -s simMouse_chr6.simMouse.chr6 343800 33 + 636262 CAAAGTACTTATGTTGATTTTCCAGGCTAAAGT -s Anc0.Anc0refChr0 8001 33 + 26507 CAAGGTGATCATGTTAATTTCCCAGACCCTTAT -s Anc1.Anc1refChr6 8175 33 + 197743 CAAGGTGATCATGTTAATTTCCCAGACCCTTAT -s Anc2.Anc2refChr17 1137 33 + 28526 CAGGTTGATCATATTAATTTCCCAGACCCTTAT -s mr.mrrefChr5 191344 33 + 294540 CAAAGTACTTATGTTAATTTCCCAGGCTCAAAT -s simCow_chr6.simCow.chr6 316505 33 + 602619 CAGGTTGATCATATTATTTTCCCAGACCCTTTT -s simDog_chr6.simDog.chr6 308608 33 + 593897 CAGATTTATCATATTAATTGCCCAGACCCTTAT -s simHuman_chr6.simHuman.chr6 328369 33 + 601863 CAAGGTGATCATGTTAGTTTCCCAGACCCTTAC -s simRat_chr6.simRat.chr6 335318 30 + 647215 CAAACTACTTATGTTAATTTCCC---CTCCAAT - -a -s simMouse_chr6.simMouse.chr6 343833 16 + 636262 ACTAAGGTCCCTCTTT -s Anc0.Anc0refChr0 8038 16 + 26507 GCTAAGGTCCCTCTTT -s Anc1.Anc1refChr6 8212 16 + 197743 GCTAAGGTCCCTCTTT -s Anc2.Anc2refChr17 1174 16 + 28526 GCTAAGGTCCCTCTTT -s mr.mrrefChr5 191377 16 + 294540 GCTAAGGTCCCTCTTT -s simCow_chr6.simCow.chr6 316542 16 + 602619 GCTATGGTCCCTCTTT -s simDog_chr6.simDog.chr6 308645 16 + 593897 GCTTAAGTCCCTTTTT -s simHuman_chr6.simHuman.chr6 328406 16 + 601863 GCCAAGGTCCTCCTTT -s simRat_chr6.simRat.chr6 335348 16 + 647215 GCTAAGGTCCCTCTTT - -a -s simMouse_chr6.simMouse.chr6 343849 35 + 636262 GTAGATCTGACATGGATTTTTAAGGTAGGGTGCTG -s Anc0.Anc0refChr0 8054 33 + 26507 GTAGATCTTATATG--TTCTTAAGCCAAAGTACAT -s Anc1.Anc1refChr6 8228 33 + 197743 GTAGATCTTATATG--TTCTTAAGCCAAAGTACAT -s Anc2.Anc2refChr17 1190 33 + 28526 GTAGATCCTATATG--TCCCTAAGCCAAAGCACAT -s mr.mrrefChr5 191393 35 + 294540 GTAGATCTGACATGGATTTTTAAGGCAGGGTGCTG -s simCow_chr6.simCow.chr6 316558 33 + 602619 GTAGATCCTAGATG--TCCCTAAGCCAAAGAGGAT -s simDog_chr6.simDog.chr6 308661 29 + 593897 GTATATACTATATG--TC---AAGCCAAAGCAC-T -s simHuman_chr6.simHuman.chr6 328424 33 + 601863 GTAGACCTAATATG--TTCTTAAGCCAAAGTACAT -s simRat_chr6.simRat.chr6 335364 35 + 647215 GTAGATCTGACCTGAATTTTTAAGACAGGCTGCTG - -a -s simMouse_chr6.simMouse.chr6 343884 31 + 636262 GTTATTCAGGGTTTAATATTGTCAATACTGA -s Anc0.Anc0refChr0 8087 31 + 26507 GGTACCCATAGTTTAATATTGTTCATACTGG -s Anc1.Anc1refChr6 8261 31 + 197743 GGTACCCATAGTTTAATATTGTTCATACTGG -s Anc2.Anc2refChr17 1223 31 + 28526 GGTGCCCATAGTTTAATATTGTTCATACTGG -s mr.mrrefChr5 191428 31 + 294540 GGTATTCAGGGTTTAATATTGTTAATACTGG -s simCow_chr6.simCow.chr6 316592 31 + 602619 GGTGCCCATAGTTTAATATTGTTCATACTGG -s simDog_chr6.simDog.chr6 308690 31 + 593897 TGTGCCCATAGTTTAATATTGTTCATACCGG -s simHuman_chr6.simHuman.chr6 328457 31 + 601863 GGTACCTGTAGTGTGATATTGTTCATGCTGG -s simRat_chr6.simRat.chr6 335399 31 + 647215 GGTATTCAGGATTTAATATTGTTGATATTGG - -a -s simMouse_chr6.simMouse.chr6 343915 69 + 636262 TGGGACCTGTATGTACATTAAAGCCTAATGTGGCGGGGTCCTTGTACTAAGGCTGTTAGGTCTCGTACT -s Anc0.Anc0refChr0 8123 68 + 26507 TAGGGCCTCTTTGTGCATTAGAG-GTAATGTGGTGAGTTACCTGTACTAAGGCGGTTAGATCTCATACT -s Anc1.Anc1refChr6 8297 68 + 197743 TAGGGCCTCTTTGTGCATTAGAG-GTAATGTGGTGAGTTACCTGTACTAAGGCGGTTAGATCTCATACT -s Anc2.Anc2refChr17 1259 68 + 28526 TAGAGCCTCTTTGTGCATTAGAG-GTAATGTGGTGAGTTACCTGTACTAAGGTGGTTAGATCTGACACT -s mr.mrrefChr5 191459 68 + 294540 TGGGGCCTGTATGTGCATTAAAG-CTAATGTGGCGGGGTCCTTGTACTAAGGCTGTTAGGTCTCATACT -s simCow_chr6.simCow.chr6 316628 68 + 602619 TAAAGCATGTTTGTGCACACGGG-GCAATGTTGTGAGTTACCTGTACTAAGGTGTACAGTTCTGACACT -s simDog_chr6.simDog.chr6 308726 68 + 593897 TAGAACCTCTTTCTGCATTAGAG-GTAATGTGGTGAGCTGACTGTACTAAGGTAGTTAGATCTGACACT -s simHuman_chr6.simHuman.chr6 328493 68 + 601863 TAGGGCCAATTTGTGCATTAGAG-GTAATGTGGTGAGTTACCTGTACTAAAGCGGTTAGATCTCATACT -s simRat_chr6.simRat.chr6 335430 47 + 647215 TGGGGCCTGTATGTGCAT----------------------CTTGTACTATGGCCATTAGGTCTCATACT - -a -s simMouse_chr6.simMouse.chr6 343984 48 + 636262 GTAACGGCTAAAATTGGCCAGATTTTCTATTATAAAGCTAATGCTGTA -s Anc0.Anc0refChr0 8191 48 + 26507 GTAATAGTCAAGAGTGGATGTATTTCCTATAATAAAGCCGATGCTGAA -s Anc1.Anc1refChr6 8365 48 + 197743 GTAATAGTCAAGAGTGGATGTATTTCCTATAATAAAGCCGATGCTGAA -s Anc2.Anc2refChr17 1327 48 + 28526 GTAATAGTCAAGAGTGGATGTATTTCCTATAATAAAGCCGATGCTCAA -s mr.mrrefChr5 191527 48 + 294540 GTAACAGCTAAAATTGGCCAGATTTTCTATTATAAAGCTAATGCTGTA -s simCow_chr6.simCow.chr6 316717 46 + 602619 GTACTAATCAAGAGTGGCTTTATTT--TATAATAAAGCCAATGTGCAA -s simDog_chr6.simDog.chr6 308794 47 + 593897 GTAATAGTCAAGAGTGGATGTATTTCCTACCATAA-GCCGATGCTCAA -s simHuman_chr6.simHuman.chr6 328561 48 + 601863 GTAATAGTCAATGGTGGGTGTAGATCCTGTAATAAAGCCGATGCCGAT -s simRat_chr6.simRat.chr6 335477 48 + 647215 GTAACAGCTAAAATTGGCCAGATTTTTTATTATAAAGCTAATGTTTTA - -a -s simMouse_chr6.simMouse.chr6 344032 8 + 636262 ACTTCATG -s Anc0.Anc0refChr0 8239 8 + 26507 ATTCCATA -s Anc1.Anc1refChr6 8413 8 + 197743 ATTCCATA -s Anc2.Anc2refChr17 1375 8 + 28526 ATTCCATA -s mr.mrrefChr5 191575 8 + 294540 ACTTCATG -s simCow_chr6.simCow.chr6 316763 8 + 602619 ATTCCATA -s simDog_chr6.simDog.chr6 308841 8 + 593897 ATTCCATA -s simHuman_chr6.simHuman.chr6 328609 8 + 601863 GTTCCATA -s simRat_chr6.simRat.chr6 335530 8 + 647215 ACTTCATG - -a -s simMouse_chr6.simMouse.chr6 344040 39 + 636262 GTGTGTCCCTGCAATGAAACATACTGTGGCCCTTGATAA -s Anc0.Anc0refChr0 8247 39 + 26507 GTGTGTCCCTGCAACAAAATACACTGTGGCCGTTCATGA -s Anc1.Anc1refChr6 8421 39 + 197743 GTGTGTCCCTGCAACAAAATACACTGTGGCCGTTCATGA -s Anc2.Anc2refChr17 1388 39 + 28526 GTGTGTCCCTGCAACAAAATACACTGTGGCCGTTCATGA -s mr.mrrefChr5 191583 39 + 294540 GTGTGTCCCTGCAATGAAACATACTGTGGCCCTTGATAA -s simCow_chr6.simCow.chr6 316776 39 + 602619 GTGTGTTCCTGCAACAGACTACATTGTGGCCCTTCATGA -s simDog_chr6.simDog.chr6 308854 39 + 593897 GTGTGTCTCTGCAGCAAAATACACTGTGGTAGTTTGTGA -s simHuman_chr6.simHuman.chr6 328617 39 + 601863 CGCTGCCCCTGCAACAAAATACACTGTGGCCTTTCATGA -s simRat_chr6.simRat.chr6 335538 39 + 647215 GTGTGTCCCTGCAATGAAACATACCGTGGCGCTTGATAA - -a -s simMouse_chr6.simMouse.chr6 344079 23 + 636262 TTCTGTGGTAAATGGGATAATAC -s Anc0.Anc0refChr0 8286 23 + 26507 TTATGTGGTAGATGCCATAATGC -s Anc1.Anc1refChr6 8460 23 + 197743 TTATGTGGTAGATGCCATAATGC -s Anc2.Anc2refChr17 1428 23 + 28526 TTTTGTGGTAGATGCCATAATGC -s mr.mrrefChr5 191622 23 + 294540 TTATGTGGTAAATGGGATAATAC -s simCow_chr6.simCow.chr6 316816 23 + 602619 TCTTGCGGTGGATGCCATGGTGC -s simDog_chr6.simDog.chr6 308894 23 + 593897 TTTTGTGGTAGATGCCATAATGC -s simHuman_chr6.simHuman.chr6 328656 23 + 601863 TTATGTGGTAGATGCCATAATGT -s simRat_chr6.simRat.chr6 335577 23 + 647215 CTATGTGGTAAATGTGATAATAC - -a -s simMouse_chr6.simMouse.chr6 344102 11 + 636262 AGGTTAAGATG -s Anc0.Anc0refChr0 8313 11 + 26507 AGGCTAAGATG -s Anc1.Anc1refChr6 8487 11 + 197743 AGGCTAAGATG -s Anc2.Anc2refChr17 1455 11 + 28526 AGGCTAAGCTA -s mr.mrrefChr5 191645 11 + 294540 AGGTTAAGATG -s simCow_chr6.simCow.chr6 316843 5 + 602619 GGTTT------ -s simDog_chr6.simDog.chr6 308921 11 + 593897 AGGCTAAGCTA -s simHuman_chr6.simHuman.chr6 328683 11 + 601863 AGGCTAAGATG -s simRat_chr6.simRat.chr6 335600 11 + 647215 AGGTTAAGATG - -a -s simMouse_chr6.simMouse.chr6 344113 2 + 636262 CA -s Anc0.Anc0refChr0 8329 2 + 26507 CA -s Anc1.Anc1refChr6 8503 2 + 197743 CA -s Anc2.Anc2refChr17 1471 2 + 28526 CA -s mr.mrrefChr5 191656 2 + 294540 CA -s simDog_chr6.simDog.chr6 308939 2 + 593897 CA -s simHuman_chr6.simHuman.chr6 328699 2 + 601863 CA -s simRat_chr6.simRat.chr6 335611 2 + 647215 CA - -a -s simMouse_chr6.simMouse.chr6 344115 45 + 636262 GTAGTGATCTGAGCTACGAATACTAAACCAGAATGTTTTGTTCCA -s Anc0.Anc0refChr0 8345 36 + 26507 GTAGTGACCAG-------AATACTAAACCA-AATTTTTTGAT-CT -s Anc1.Anc1refChr6 8519 42 + 197743 GTAGTGACCAGAGAT-TAAATACTAAACCA-AATTTTTTGAT-CT -s Anc2.Anc2refChr17 1487 36 + 28526 GTAATGACCAG-------AATACTAAACCA-AACTCTTCCAA-CT -s mr.mrrefChr5 191665 44 + 294540 GTAGTGATCAGAGCTACAAATACTAAACCAGAATTTTTTGAT-CA -s simDog_chr6.simDog.chr6 308955 36 + 593897 GTAATGACCAG-------AATACTAAACCA-AACTCTTCCAA-CT -s simHuman_chr6.simHuman.chr6 328715 42 + 601863 GTAGGAACCAGAGAT-TAGATACTGAACCA-AATTTTGTGAT-CT -s simRat_chr6.simRat.chr6 335620 44 + 647215 GTAGTGATCAGAGCTACAAATACTAAACCAGAATTTTTTGAT-TA - -a -s simMouse_chr6.simMouse.chr6 344160 17 + 636262 TTTGTTTCCTGCTACCT -s Anc0.Anc0refChr0 8381 17 + 26507 GATGTTTCCTGCTACTT -s Anc1.Anc1refChr6 8561 17 + 197743 GATGTTTCCTGCTACTT -s Anc2.Anc2refChr17 1554 17 + 28526 GATGTTTCCTGCTACTT -s mr.mrrefChr5 191709 17 + 294540 TTTGTTTCCTGCTACCT -s simCow_chr6.simCow.chr6 316880 17 + 602619 GATGATTCCTGCCACTT -s simDog_chr6.simDog.chr6 309029 17 + 593897 AATGTTTCCTGCTGCCT -s simHuman_chr6.simHuman.chr6 328757 17 + 601863 GATGTGTCCTGCTACTT -s simRat_chr6.simRat.chr6 335664 17 + 647215 TTTGTTTCCTGGTACCT - -a -s simMouse_chr6.simMouse.chr6 344177 28 + 636262 ACCATTAGTGCATATCAGCAGCCCTCAA -s Anc0.Anc0refChr0 8398 28 + 26507 ACCACTGATACCTATCAGCAGCTGTTAA -s Anc1.Anc1refChr6 8578 28 + 197743 ACCACTGATACCTATCAGCAGCTGTTAA -s Anc2.Anc2refChr17 1572 28 + 28526 ACCACTGATACCTATTAGCAGCTGTTAA -s mr.mrrefChr5 191726 28 + 294540 ACCATTAGTGCATATCAGCAGCCCTCAA -s simCow_chr6.simCow.chr6 316898 28 + 602619 ACCCCTAATACCTATGAGCAGCTGTTCA -s simDog_chr6.simDog.chr6 309047 28 + 593897 ACCACTGATACCTATTGGCAGCTGTTAA -s simHuman_chr6.simHuman.chr6 328774 23 + 601863 ACCAC-----CCTATCAGCTGCTGTTAA -s simRat_chr6.simRat.chr6 335681 22 + 647215 ACTATTAGTGCATATCGG------TCAA - -a -s simMouse_chr6.simMouse.chr6 344205 44 + 636262 ACTACCGTGACCTTTGTGTATCGCACAGTCAACCCTTTGGCTTC -s Anc0.Anc0refChr0 8426 28 + 26507 AC---------CTTTGTGTCTCTCATGG-------TTTGATATC -s Anc1.Anc1refChr6 8606 37 + 197743 ACTACTCTGATCTTTGTGTCTCTCATGG-------TTTGATATC -s Anc2.Anc2refChr17 1600 28 + 28526 AC---------CTTTGTGTCTGTTATGG-------TTCTATATC -s mr.mrrefChr5 191754 44 + 294540 ACTACCCTGACCTTTGTGTATCGCACAGTCAACCCTTTGGCTTC -s simCow_chr6.simCow.chr6 316930 24 + 602619 AC---------CTTTGAGATTA----GG-------TTAAATATC -s simDog_chr6.simDog.chr6 309075 28 + 593897 GC---------CTTTGTGTCTGTTATAC-------TACTATGTC -s simHuman_chr6.simHuman.chr6 328797 37 + 601863 ACTACTCTGATCTTTGTGTCTCCCATGG-------TTTGATATC -s simRat_chr6.simRat.chr6 335703 44 + 647215 ACTACCCTGACCTTTATGTACCACACAGTCAACCCTTCGGACTC - -a -s simMouse_chr6.simMouse.chr6 344249 17 + 636262 TTTCTATAGCAATTTCA -s Anc0.Anc0refChr0 8457 17 + 26507 TACCTTTACCTTCTTCT -s Anc1.Anc1refChr6 8646 17 + 197743 TACCTTTACCTTCTTCT -s Anc2.Anc2refChr17 1631 17 + 28526 TACCTTTACCTTCTTCT -s mr.mrrefChr5 191798 17 + 294540 TTTCTATAGCAATTTCA -s simCow_chr6.simCow.chr6 316957 17 + 602619 TACTTTTACCTTCTTCC -s simDog_chr6.simDog.chr6 309106 17 + 593897 TACCTTGACCTTCTTCT -s simHuman_chr6.simHuman.chr6 328837 17 + 601863 TACCTGTACCCTCTTCT -s simRat_chr6.simRat.chr6 335747 17 + 647215 TTTCTAGAACAATTTCA - -a -s simMouse_chr6.simMouse.chr6 344266 9 + 636262 GAAAGTGTT -s Anc0.Anc0refChr0 8474 9 + 26507 GAAAAGGTT -s Anc1.Anc1refChr6 8663 9 + 197743 GAAAAGGTT -s Anc2.Anc2refChr17 1648 9 + 28526 TAAAAGCTT -s mr.mrrefChr5 191815 9 + 294540 GAAAGTGTT -s simCow_chr6.simCow.chr6 316974 9 + 602619 TACAAGCTT -s simDog_chr6.simDog.chr6 309133 9 + 593897 TAAATGCTT -s simHuman_chr6.simHuman.chr6 328854 8 + 601863 GAGAAGGT- -s simRat_chr6.simRat.chr6 335764 9 + 647215 GAAATAGTT - -a -s simMouse_chr6.simMouse.chr6 344275 17 + 636262 ATTCAATGTACTGATCC -s Anc0.Anc0refChr0 8483 17 + 26507 ATTCAGTATACTAACCC -s Anc1.Anc1refChr6 8672 17 + 197743 ATTCAGTATACTAACCC -s Anc2.Anc2refChr17 1658 17 + 28526 ATTCAGTATAGCAGCCC -s mr.mrrefChr5 191824 17 + 294540 ATTCAATGTACTAATCC -s simCow_chr6.simCow.chr6 316984 17 + 602619 ATACAATATACTAGCCC -s simDog_chr6.simDog.chr6 309143 17 + 593897 ATTCAGTATAGCAGCCT -s simHuman_chr6.simHuman.chr6 328862 7 + 601863 ----------CTAACCC -s simRat_chr6.simRat.chr6 335773 17 + 647215 ATTCAATGTACTAATCC - -a -s simMouse_chr6.simMouse.chr6 344292 83 + 636262 TCGCATGGTTGCTGTAAGTACCCATTCTGTGGGTTCACTGGCGGTCACTTTCTTGACACATCACATCCCAGGCAGCATGAATT -s Anc0.Anc0refChr0 8505 21 + 26507 T--------------------------------------------------------------TATTTGGGGTGTCATGGATT -s Anc1.Anc1refChr6 8694 21 + 197743 T--------------------------------------------------------------TATTTGGGGTGTCATGGATT -s Anc2.Anc2refChr17 1680 21 + 28526 T--------------------------------------------------------------TATTTGGGGTGTCATGGATT -s mr.mrrefChr5 191841 21 + 294540 T--------------------------------------------------------------CATCTCAGGCAGCATGAATT -s simCow_chr6.simCow.chr6 317007 21 + 602619 T--------------------------------------------------------------TTTTTGGGGTGTCATGGATT -s simDog_chr6.simDog.chr6 309166 21 + 593897 T--------------------------------------------------------------TATTTGGGGTGTCATGGATG -s simHuman_chr6.simHuman.chr6 328874 21 + 601863 T--------------------------------------------------------------TCTTTGGGGTGTCATGGATT -s simRat_chr6.simRat.chr6 335790 21 + 647215 T--------------------------------------------------------------CATCTCAGGCAACACGAATT - -a -s simMouse_chr6.simMouse.chr6 344375 49 + 636262 CTCCAGTCACTCTTGGTTACAATGTTTTATACTGATTTTGGTGTGTAAC -s Anc0.Anc0refChr0 8526 45 + 26507 C----TTTACTCTTGGTTTTAATTTTCGTGACCAGAATTAGAGTGTAAG -s Anc1.Anc1refChr6 8715 45 + 197743 C----TTTACTCTTGGTTTTAATTTTCGTGACCAGAATTAGAGTGTAAG -s Anc2.Anc2refChr17 1715 45 + 28526 T----TTTACTTTTGGTTTTAGTTTTCGTGCCCAGAATTAGAGTGTAAG -s mr.mrrefChr5 191862 45 + 294540 C----GTCACTCTTGGTTACAATGTTTTATACTGATTTTAGTGTGTAAC -s simCow_chr6.simCow.chr6 317044 45 + 602619 T----TTTACTTTTGCTATAATGTTTCTCATCCAGATTTATAGTGTGAG -s simDog_chr6.simDog.chr6 309201 37 + 593897 T----TT--------GTTTTAGTGTTCGTGCACAAAATTAGAACATAAG -s simHuman_chr6.simHuman.chr6 328895 45 + 601863 C----TTTGCTCTCGATTGTAACTCTCATGACAAGGATTAAGGTGTAAG -s simRat_chr6.simRat.chr6 335811 45 + 647215 C----GCCACTCTTGGTTACAATGTTTCATGCTCATTTTAGTGTGTAAT - -a -s simMouse_chr6.simMouse.chr6 344424 12 + 636262 ATGTTAGATCAT -s Anc0.Anc0refChr0 8571 12 + 26507 ATCTTAGCTTAT -s Anc1.Anc1refChr6 8760 12 + 197743 ATCTTAGCTTAT -s Anc2.Anc2refChr17 1760 12 + 28526 ATCTTAGCTTAT -s mr.mrrefChr5 191907 12 + 294540 ATGTTAGATCAT -s simCow_chr6.simCow.chr6 317089 12 + 602619 ATCTTATCTTAG -s simDog_chr6.simDog.chr6 309238 12 + 593897 ATCTTAGGTTAT -s simHuman_chr6.simHuman.chr6 328940 12 + 601863 ATCATGGCTTAT -s simRat_chr6.simRat.chr6 335861 12 + 647215 ACATCAATTCAT - -a -s simMouse_chr6.simMouse.chr6 344436 40 + 636262 ACTCTTAACAAACTTCCCCATGACCTGTGTGTTGTGTGAG -s Anc0.Anc0refChr0 8583 40 + 26507 ACTCTTAACAAGCTTTTTAGTGACTTGTGTGTCGTGTCTT -s Anc1.Anc1refChr6 8772 40 + 197743 ACTCTTAACAAGCTTTTTAGTGACTTGTGTGTCGTGTCTT -s Anc2.Anc2refChr17 1772 40 + 28526 ACTCTTAACAAGCTTTTTAGTGACTTGTGTGTCGTGTCTT -s mr.mrrefChr5 191919 40 + 294540 ACTCTTAACAAGCTTTCCCATGACTTGTGTGTTGTGTGAT -s simCow_chr6.simCow.chr6 317106 39 + 602619 ACTCTTGACAAGCTTTTTAGTGA-TTGTGTGTTGTGTCTT -s simDog_chr6.simDog.chr6 309250 40 + 593897 ACTCTTAAAAAGTTTTTTAGTGACCTGTGTGTCGTGTCTT -s simHuman_chr6.simHuman.chr6 328952 40 + 601863 ACTTTTAACAAGCTTTTTAGCGACTTGTGTGTCGTGTCCT -s simRat_chr6.simRat.chr6 335873 40 + 647215 ACTCTTAACAAGCTTTCCCATGACTTGTGTGTTGTGTGAT - -a -s simMouse_chr6.simMouse.chr6 344476 7 + 636262 GCGCCCC -s Anc0.Anc0refChr0 8623 7 + 26507 ATGCCCC -s Anc1.Anc1refChr6 8812 7 + 197743 ATGCCCC -s Anc2.Anc2refChr17 1812 7 + 28526 ATGCCCC -s mr.mrrefChr5 191959 7 + 294540 ATGCCCC -s simCow_chr6.simCow.chr6 317145 7 + 602619 TTGCCCC -s simDog_chr6.simDog.chr6 309301 7 + 593897 ACACCCC -s simHuman_chr6.simHuman.chr6 328992 7 + 601863 ATGCCCC -s simRat_chr6.simRat.chr6 335913 7 + 647215 ATGCCCC - -a -s simMouse_chr6.simMouse.chr6 344483 10 + 636262 ATGTATGGAG -s Anc0.Anc0refChr0 8630 10 + 26507 ATCTAAGGTC -s Anc1.Anc1refChr6 8819 10 + 197743 ATCTAAGGTC -s Anc2.Anc2refChr17 1819 10 + 28526 ATCTAAGGTC -s mr.mrrefChr5 191966 10 + 294540 ATCTATGGTC -s simCow_chr6.simCow.chr6 317153 10 + 602619 GTTGAAGGTC -s simDog_chr6.simDog.chr6 309308 10 + 593897 ATCTGACGAC -s simHuman_chr6.simHuman.chr6 328999 10 + 601863 ATCCAAGGTC -s simRat_chr6.simRat.chr6 335920 10 + 647215 ATCTATGGTC - -a -s simMouse_chr6.simMouse.chr6 344493 14 + 636262 AAATTCAAGCAATC -s Anc0.Anc0refChr0 8641 14 + 26507 AAGTTCATGCAAGG -s Anc1.Anc1refChr6 8830 14 + 197743 AAGTTCATGCAAGG -s Anc2.Anc2refChr17 1830 14 + 28526 CAGTTCATGCAAGG -s mr.mrrefChr5 191976 14 + 294540 AAGTTCAAGCAAGC -s simCow_chr6.simCow.chr6 317164 14 + 602619 TAGTCCAGGCAAGA -s simDog_chr6.simDog.chr6 309319 14 + 593897 CATTTCATGCAAGG -s simHuman_chr6.simHuman.chr6 329010 14 + 601863 AAGCGCACGCAAGG -s simRat_chr6.simRat.chr6 335930 14 + 647215 AAGACCAAGCAAGC - -a -s simMouse_chr6.simMouse.chr6 344507 34 + 636262 TGCCTATGGGATCTATACCAAGCATTGCCACCGT -s Anc0.Anc0refChr0 8655 34 + 26507 TCCCTGGAGGAACTATACCATGCAGAGCCACCGC -s Anc1.Anc1refChr6 8844 34 + 197743 TCCCTGGAGGAACTATACCATGCAGAGCCACCGC -s Anc2.Anc2refChr17 1844 34 + 28526 TCCCTGGAGGGACTATACCATGCAGAGCCACTGC -s mr.mrrefChr5 191990 34 + 294540 TGCCTGTGGGATCTATACCAAGCATTGCCACCGT -s simCow_chr6.simCow.chr6 317181 34 + 602619 TCTCTGGAGGGACTAAGCCATGCAGAGCCACAGA -s simDog_chr6.simDog.chr6 309333 34 + 593897 TCCCTGGAGGGACTATACTGTGCAGAGCTGCTGC -s simHuman_chr6.simHuman.chr6 329024 34 + 601863 TCCCTGGAGGAACTATAACATGCAGAGCCACCAC -s simRat_chr6.simRat.chr6 335944 34 + 647215 TGCCTGTGGGATCTATACCAAGCACTGCTGCCGT - -a -s simMouse_chr6.simMouse.chr6 344541 41 + 636262 GGGTCTCTATATGCATTTTGCATGTGCAACATAACATGGCA -s Anc0.Anc0refChr0 8695 41 + 26507 AGGTCTTTGTAGGCCTCTTGCGCCTGCTTCATAACATAGGA -s Anc1.Anc1refChr6 8884 41 + 197743 AGGTCTTTGTAGGCCTCTTGCGCCTGCTTCATAACATAGGA -s Anc2.Anc2refChr17 1884 41 + 28526 AGGTCTTTGTAGGGCTCTTGTGCCTACTTCATAACATAGGA -s mr.mrrefChr5 192024 41 + 294540 GGGTCTCTATATGCATCTTGCATGTGCAACATAACATGGGA -s simCow_chr6.simCow.chr6 317221 39 + 602619 AGGTACTGTT--TGCTCTTGAGCCTACTTCATACCACAGAA -s simDog_chr6.simDog.chr6 309373 41 + 593897 AGGTCTATGTAGGGCTCTCGTGCCTATTGAATAACTTAGGA -s simHuman_chr6.simHuman.chr6 329064 41 + 601863 AGGTCTTTGTAGGCCTCTTGCGCTGGCTTCGTAACATAGGA -s simRat_chr6.simRat.chr6 335978 41 + 647215 GGGTCTCTATACACATCTTGCATGTGCACCATAACATGGGA - -a -s simMouse_chr6.simMouse.chr6 344582 58 + 636262 CCATATACAAGTACGTAAAATTGCTATCTCTGAGGTATTCCATGCAGGCACTCACTGG -s Anc0.Anc0refChr0 8737 57 + 26507 TTCTGTACAGATACATAAAATTGGTGACTCTGAGGTACTACAGGTAAT-CCCCCTTGG -s Anc1.Anc1refChr6 8926 57 + 197743 TTCTGTACAGATACATAAAATTGGTGACTCTGAGGTACTACAGGTAAT-CCCCCTTGG -s Anc2.Anc2refChr17 1926 57 + 28526 TCTTGTACAGATACATGAAATTGGTGACTCTGAGGTACTACAGGTAAT-CCCCCTTCT -s mr.mrrefChr5 192065 57 + 294540 CTCTATACAAGTACATAAAATTGGTATCTCTGAGGTATTCCATGCAGG-ACTCACTGG -s simCow_chr6.simCow.chr6 317261 57 + 602619 TCTTGTACAGATACATGAAATTGCTGACTCTGTTGTACTATACATATT-GCTTCTACT -s simDog_chr6.simDog.chr6 309415 57 + 593897 TCTTATACAGAGACTTGAAATTTGTGACTCTGAGGTACTACAGGTAAT-CCCCCTTCT -s simHuman_chr6.simHuman.chr6 329106 34 + 601863 TTCTGGACAGATGCATAAAATTGGTGACTCTG------------------------GG -s simRat_chr6.simRat.chr6 336019 57 + 647215 CTCCATACAAGTACATAAAATTGGTATCTCTGAGGTATTACAGGTAGG-ACTTTCTGG - -a -s simMouse_chr6.simMouse.chr6 344640 25 + 636262 ATTTAAAGACCAAAGGAACCAGGAA -s Anc0.Anc0refChr0 8794 25 + 26507 AGTCGAAGACCAGAGGAGCCAGGAA -s Anc1.Anc1refChr6 8983 25 + 197743 AGTCGAAGACCAGAGGAGCCAGGAA -s Anc2.Anc2refChr17 1983 25 + 28526 AGTCGAAGACCAGAGGAGCCAGGAA -s mr.mrrefChr5 192122 25 + 294540 AGTTAAAGACCAAAGGAGCCAGGAA -s simCow_chr6.simCow.chr6 317318 22 + 602619 ---CAAAGACAGGAGGAGCCAGAAT -s simDog_chr6.simDog.chr6 309474 25 + 593897 AGTCGAAGACCAGAGGAACCAGGCA -s simHuman_chr6.simHuman.chr6 329140 24 + 601863 AGTC-AAGATCAGAGGAGCTAGGAA -s simRat_chr6.simRat.chr6 336076 25 + 647215 AGTTAAAAACCAAATGAGCAAGGAA - -a -s simMouse_chr6.simMouse.chr6 344665 42 + 636262 TAGCACACTCTAGCTTTCTATACAGTACTGGATTATTGTTCA -s Anc0.Anc0refChr0 8819 40 + 26507 TGGTACT--CTAACTTTTCATACTCTATTTGATTATTGTCCT -s Anc1.Anc1refChr6 9008 40 + 197743 TGGTACT--CTAACTTTTCATACTCTATTTGATTATTGTCCT -s Anc2.Anc2refChr17 2009 40 + 28526 TGGTACT--CTAACTTTTTGTGCTCTATTTGATTATTGTCCT -s mr.mrrefChr5 192147 40 + 294540 TGGCACA--CTAGCTTTCCATACACTACTGGATTATTGTTCA -s simCow_chr6.simCow.chr6 317341 40 + 602619 TGGCACT--CTAACTTTATGCTCTGTACTTGATTATTCTCCT -s simDog_chr6.simDog.chr6 309500 38 + 593897 TGGTACT--CTGACTTTTTGTGCCCTATTTGATTATTGTT-- -s simHuman_chr6.simHuman.chr6 329164 40 + 601863 TGGTACT--CTAACTTTTCATACTCTATTTGATTATTTTCCT -s simRat_chr6.simRat.chr6 336101 40 + 647215 TGGCACG--CTAGCCTTCCATACACTACTAGGCTATTGTTCA - -a -s simMouse_chr6.simMouse.chr6 344707 10 + 636262 GGAAGCAGGG -s Anc0.Anc0refChr0 8859 10 + 26507 AAAAGAAGTG -s Anc1.Anc1refChr6 9048 10 + 197743 AAAAGAAGTG -s Anc2.Anc2refChr17 2049 10 + 28526 AAAAGAAGTG -s mr.mrrefChr5 192187 10 + 294540 GAAAGCAGGG -s simCow_chr6.simCow.chr6 317404 10 + 602619 AACAGGAGTG -s simDog_chr6.simDog.chr6 309538 8 + 593897 --AAGAAGCA -s simHuman_chr6.simHuman.chr6 329204 10 + 601863 AAAAGAAGTG -s simRat_chr6.simRat.chr6 336141 10 + 647215 GAAAACAGGG - -a -s simMouse_chr6.simMouse.chr6 344717 60 + 636262 TATCTCAAGGGAAACCTAGTAGCACACCTTTTCTACGCATTGACCAAATATGAACAAATC -s Anc0.Anc0refChr0 8870 60 + 26507 TATTGCAATGAAAACATAGTGGCACACCTTTTCTATGTGTTCACCAAATGTGAATGGATG -s Anc1.Anc1refChr6 9059 60 + 197743 TATTGCAATGAAAACATAGTGGCACACCTTTTCTATGTGTTCACCAAATGTGAATGGATG -s Anc2.Anc2refChr17 2060 60 + 28526 TACTGCAATGAAAACATAGTGGCACACCTTTTCTATGTGTTCACCAAATGTGAGTGGATG -s mr.mrrefChr5 192197 60 + 294540 TATCTCAAGGAAAACCTAGTAGCACACCTTTTCTATGTGTTCACCAAATGTGAATAGATC -s simCow_chr6.simCow.chr6 317415 60 + 602619 TACCACAAGGGAAACATAGTGGCACACTTTTTGTGTGTGTTGACCAAATGTGAGTGGATG -s simDog_chr6.simDog.chr6 309547 60 + 593897 TACTGCAATGAAAACATAGTAGCACACCTTTTCTATGGGTTCACCAAATGTGAGTGGATG -s simHuman_chr6.simHuman.chr6 329215 58 + 601863 TATGGCAATGATATCGTAGTGGCACACCTTTTCCCTGTGTTCACTAGATGT--ATGGATG -s simRat_chr6.simRat.chr6 336151 60 + 647215 TATCTCGAGGAAAACCTCGTAGTACAACTTTTCTATGTGCTCACCAAATGTGGATAGATC - -a -s simMouse_chr6.simMouse.chr6 344777 29 + 636262 ATGGCATTCAGAAGTCAAAGTGTATGGGC -s Anc0.Anc0refChr0 8930 29 + 26507 ATGGCAATCAGAAGTCACAAGTTATGGAC -s Anc1.Anc1refChr6 9119 29 + 197743 ATGGCAATCAGAAGTCACAAGTTATGGAC -s Anc2.Anc2refChr17 2120 29 + 28526 ATGGCAATCAGAAGTCACAAGTTATGGAC -s mr.mrrefChr5 192257 29 + 294540 ATGGCAATCAGAAGTCAAAATGTATGGAC -s simCow_chr6.simCow.chr6 317476 29 + 602619 ATGGCACTCAGAGGTCACAAGTTATGGAC -s simDog_chr6.simDog.chr6 309607 29 + 593897 ATGGCAATCAGAAGTCACAAGTTATGGAC -s simHuman_chr6.simHuman.chr6 329273 29 + 601863 ATGGCAATCAGAAGTCACAAGTTATGGAC -s simRat_chr6.simRat.chr6 336211 29 + 647215 ATGGCAATCAGAAGTCGAAATGTATGGAT - -a -s simMouse_chr6.simMouse.chr6 344806 1 + 636262 C -s Anc0.Anc0refChr0 8959 1 + 26507 C -s Anc1.Anc1refChr6 9148 1 + 197743 C -s Anc2.Anc2refChr17 2149 1 + 28526 C -s mr.mrrefChr5 192286 1 + 294540 C -s simCow_chr6.simCow.chr6 317505 1 + 602619 C -s simDog_chr6.simDog.chr6 309645 1 + 593897 C -s simHuman_chr6.simHuman.chr6 329302 1 + 601863 C -s simRat_chr6.simRat.chr6 336240 1 + 647215 C - -a -s simMouse_chr6.simMouse.chr6 344807 19 + 636262 AGTTCTTGACACATGACCA -s Anc0.Anc0refChr0 8962 19 + 26507 AATTCCTGACACATGACTA -s Anc1.Anc1refChr6 9151 19 + 197743 AATTCCTGACACATGACTA -s Anc2.Anc2refChr17 2152 19 + 28526 TATTCCTGACACATGACTA -s mr.mrrefChr5 192287 19 + 294540 AGTTCTTGACACATGACCA -s simCow_chr6.simCow.chr6 317508 19 + 602619 TTTTCTGGACACAGGACTA -s simDog_chr6.simDog.chr6 309648 19 + 593897 TATCCCTGACACATGACTA -s simHuman_chr6.simHuman.chr6 329305 19 + 601863 AATTCCTGACACATGACTA -s simRat_chr6.simRat.chr6 336241 19 + 647215 AGTTCTTGACACATGGCCA - -a -s simMouse_chr6.simMouse.chr6 344826 6 + 636262 GGGATA -s Anc0.Anc0refChr0 8983 6 + 26507 GGGATA -s Anc1.Anc1refChr6 9172 6 + 197743 GGGATA -s Anc2.Anc2refChr17 2173 6 + 28526 GGGATA -s mr.mrrefChr5 192306 6 + 294540 GGGATA -s simCow_chr6.simCow.chr6 317529 6 + 602619 GGGATA -s simDog_chr6.simDog.chr6 309669 6 + 593897 GGGATA -s simHuman_chr6.simHuman.chr6 329326 6 + 601863 GGGATA -s simRat_chr6.simRat.chr6 336260 6 + 647215 GGGATA - -a -s simMouse_chr6.simMouse.chr6 344832 72 + 636262 CACTCATTCTGCGTGCAGAAGATCTGGTGAGCTAAAGGCCTCATGTATGAACGGTCCTTTGCTGGTTAGGAT -s Anc0.Anc0refChr0 8991 69 + 26507 TGATCA-TCTGCATGCAGGACATCTGGTGACCTAAGATCCTCCT-TATTGAC-ACCCTTTGCTGATTAGGAT -s Anc1.Anc1refChr6 9180 70 + 197743 TGATCA-TCTGCATGCAGGACATCTGGTGACCTAAGATCCTCCTGTATTGAC-ACCCTTTGCTGATTAGGAT -s Anc2.Anc2refChr17 2181 69 + 28526 TGCTCA-TCTGCAAGCAGGACATCTGGTGACCTAAAATCCTTCT-TATTGAT-GCCGTTTGCCAATTAGGAC -s mr.mrrefChr5 192312 72 + 294540 CAATCATTCTGCATGCAGAACATCTGGTGAGCTAAGGGCCTCCTGTATGAACGATCCTTTGCTGGTTAGGAT -s simCow_chr6.simCow.chr6 317537 67 + 602619 TGCTTA-TCTGCACGTAGGACAT--GGTGACCTAAAATCCTTCT-TATTAGT-GCCGTTTGCCAATTAGGAC -s simDog_chr6.simDog.chr6 309677 48 + 593897 TGCTCA-CCTGTGAGCAGGACATCTGCTGACCTAAAATCCTTCT--ATTGA--------------------- -s simHuman_chr6.simHuman.chr6 329334 70 + 601863 TGATCA-TCAGCATGCAGGACATGTGGTGACCTAAGATTGTCCTGTATTGAC-ACCCTTTGCTGATTAAGAT -s simRat_chr6.simRat.chr6 336266 72 + 647215 CAATCATTCTGCATGCAGAACATCTGGTGAGCTAAGGGCCTCCTGTATGAACAATCCTTTGCTGGTTAGGAC - -a -s simMouse_chr6.simMouse.chr6 344904 33 + 636262 AGCATGGTTCACTCCTATATTAGGACATGCCAG -s Anc0.Anc0refChr0 9060 32 + 26507 AGCCTGGTTCATTCCCATATGAGGACATCT-AG -s Anc1.Anc1refChr6 9250 33 + 197743 AGCCTGGTTCATTCCCATATGAGGACATCTCAG -s Anc2.Anc2refChr17 2250 32 + 28526 AGCCTGGTTCATTCCCACATAAGGACATCT-AG -s mr.mrrefChr5 192384 33 + 294540 AGCATGGTTCACTCCCATATGAGGACATGCCAG -s simCow_chr6.simCow.chr6 317605 32 + 602619 AGCCTGGTTCATTCCCACATAAGGACATCT-AG -s simHuman_chr6.simHuman.chr6 329404 33 + 601863 GGCCTCGTTTGTTCCCATATGAGGATGTCTCAG -s simRat_chr6.simRat.chr6 336338 33 + 647215 AGCATGGTTCACTCCCATATGAGGACATACCAG - -a -s simMouse_chr6.simMouse.chr6 344937 12 + 636262 GATTCATCAAGG -s Anc0.Anc0refChr0 9094 12 + 26507 GATTCATGAAAG -s Anc1.Anc1refChr6 9285 12 + 197743 GATTCATGAAAG -s Anc2.Anc2refChr17 2284 12 + 28526 GATTCATGAAAA -s mr.mrrefChr5 192417 12 + 294540 GATTCATCAAAG -s simCow_chr6.simCow.chr6 317639 12 + 602619 GATTCATGAAAA -s simHuman_chr6.simHuman.chr6 329439 12 + 601863 GGTTCATGAAAG -s simRat_chr6.simRat.chr6 336371 12 + 647215 GATTCATCACAG - -a -s simMouse_chr6.simMouse.chr6 344949 38 + 636262 ATCCTAAGGAACTTTTATAATGCCAATTTAATTCAACC -s Anc0.Anc0refChr0 9106 37 + 26507 ATCCTACGGCACTATTATAATGTTAATCTAAATCAA-C -s Anc1.Anc1refChr6 9297 37 + 197743 ATCCTACGGCACTATTATAATGTTAATCTAAATCAA-C -s Anc2.Anc2refChr17 2296 37 + 28526 ATTCTACAGCACTATAATAATGTTAATCTAAACGAA-C -s mr.mrrefChr5 192429 38 + 294540 ATCCTAAGGAACTTTTATAATGCCAATTTAATTCAACC -s simCow_chr6.simCow.chr6 317651 37 + 602619 ATTCTACAGCACTATAATAATGTTAATCTAAACGAA-C -s simHuman_chr6.simHuman.chr6 329451 37 + 601863 ATCCTAGGGTACTACTATAACGTTAATCTTAATCAA-C -s simRat_chr6.simRat.chr6 336390 38 + 647215 ATCCTAAGGAACTCTCATATTGCCAATATAGTCCAACC - -a -s simMouse_chr6.simMouse.chr6 344987 156 + 636262 AGTTCCAGATGTAATTGTGCCCCATGGGTGTTTTGGGCCAGTCTGGGGCCAGAATATATCAAACCTGTCTGAGTTCTATAACACTTCTATCATATCATGTGCTGGAGTATGGGGATAATAATTGGACCTAGTTGGATAGAGTATGCTTATGTTGCT -s Anc0.Anc0refChr0 9143 139 + 26507 GGTTACATATGCAATCATGCCCCATGCAGGCTTTGGATCAGTCTGATGCCAGA--ATACCTGCCCAGTCTAGGTTCTTAAACACTTCCAT---------------AGTAGATAATTAATGGGGAGGTCCAGTTGGACAGAGGATGCTTATATTAAG -s Anc1.Anc1refChr6 9334 139 + 197743 GGTTACATATGCAATCATGCCCCATGCAGGCTTTGGATCAGTCTGATGCCAGA--ATACCTGCCCAGTCTAGGTTCTTAAACACTTCCAT---------------AGTAGATAATTAATGGGGAGGTCCAGTTGGACAGAGGATGCTTATATTAAG -s Anc2.Anc2refChr17 2333 139 + 28526 GGTTACATGTGCAATCATGCCACAAGCAGGCTTTGCATTAGTCTGATGCCAGG--ATACCTGCTCAGTATAAGTTCCTAAACACTTCCAT---------------AGCAGATAATTAATGGGAAGGTTCAGTTGGGCAGAGGATGCTTATATTAAG -s mr.mrrefChr5 192467 151 + 294540 AGTTCCAGATGCAATCATGCCCCATGGGTGTTTTGGGTCAGTCTGAGGCCAGAATATATCAAACCTGTCTGGGTTCTATAACACTTCCATCATA-----TGCTGGAGTATGGGAATAATAATGGGATCTAGTTGGATAGAGTATGCTTATATTACT -s simCow_chr6.simCow.chr6 317689 139 + 602619 GGTTACATGTGCAATCATGCCACAAGCAGGCTTTGCATTAGTCTGATGCCAGG--ATACCTGCTCAGTATAAGTTCCTAAACACTTCCAT---------------AGCAGATAATTGATGGGAAAGTTGAGTTGGGAATAAGATGCTTATATTAAG -s simDog_chr6.simDog.chr6 309725 42 + 593897 -----------------------------------------------------------------------------------------------------------------ATTAATGGAAAGGTTCAGTTCG-CAGAGGATGCATGAACTAAG -s simHuman_chr6.simHuman.chr6 329488 139 + 601863 TGTTAAATATGCAATCAGGCCCCATGCAGGCTTTGGATCAATCTGATGCCAGA--CGAGCTGCCCAGTCTAGGTTTTTAAACCCTTCCAT---------------AGTGCACAACTAATGGGGAGGTCCAGTTGGACAGAGGATGCTTATATTAAG -s simRat_chr6.simRat.chr6 336428 151 + 647215 AGTTCTAAATGCAATCATGCCCCATGGGCATTTTGGGTCAGTGTGAGGCCAGAATATATCAATCCCATGTGGATCCTAGAACACTTCCCTCGCA-----TGTTGGAGAATGGGAATAATAATGGGATCTAGTTGGATAGTGTGTGCTTATATTACT - -a -s simMouse_chr6.simMouse.chr6 345143 21 + 636262 TTTGGGTCCTGCACTAGTTTA -s Anc0.Anc0refChr0 9283 21 + 26507 GTTGGGTCCTGCATTAGTTAA -s Anc1.Anc1refChr6 9474 21 + 197743 GTTGGGTCCTGCATTAGTTAA -s Anc2.Anc2refChr17 2473 21 + 28526 GTTGGGTCCTACATTAGTTAA -s mr.mrrefChr5 192619 21 + 294540 TTTGGGTCCTGCATTAGTTTA -s simCow_chr6.simCow.chr6 317829 21 + 602619 GCTGGGTCCTACATTAGTTAA -s simDog_chr6.simDog.chr6 309768 21 + 593897 TTTGGGTCCCACATTAGTTAA -s simHuman_chr6.simHuman.chr6 329628 21 + 601863 GTTGGGTACTGCATTAGTTAA -s simRat_chr6.simRat.chr6 336580 21 + 647215 TTTGGGTCCTGCATTAGTTTA - -a -s simMouse_chr6.simMouse.chr6 345164 10 + 636262 CCACCACCAT -s Anc0.Anc0refChr0 9305 10 + 26507 TCACTACCAA -s Anc1.Anc1refChr6 9496 10 + 197743 TCACTACCAA -s Anc2.Anc2refChr17 2495 10 + 28526 TTACTACAAA -s mr.mrrefChr5 192641 10 + 294540 CCACCACCAT -s simCow_chr6.simCow.chr6 317851 10 + 602619 TTACTACAAA -s simDog_chr6.simDog.chr6 309790 10 + 593897 TTACTACAAA -s simHuman_chr6.simHuman.chr6 329650 10 + 601863 TCACTGCCAG -s simRat_chr6.simRat.chr6 336602 10 + 647215 CCGCCACAAT - -a -s simMouse_chr6.simMouse.chr6 345174 17 + 636262 GAATGATAAGTGGTGGT -s Anc0.Anc0refChr0 9315 16 + 26507 AAATGAAAAATAAT-TT -s Anc1.Anc1refChr6 9506 17 + 197743 AAATGAAAAATAATATT -s Anc2.Anc2refChr17 2505 16 + 28526 AAATGAAAAATAAT-TT -s mr.mrrefChr5 192651 17 + 294540 GAATGATAAGTAGTGGT -s simCow_chr6.simCow.chr6 317863 13 + 602619 AAACCAAAACCAG---- -s simDog_chr6.simDog.chr6 309800 16 + 593897 AAATGAGAAATAAT-TT -s simHuman_chr6.simHuman.chr6 329660 15 + 601863 AAATGAAAATGAATA-- -s simRat_chr6.simRat.chr6 336612 17 + 647215 TATTGATAAACATTGAT - -a -s simMouse_chr6.simMouse.chr6 345191 13 + 636262 GGACCCAGGGACT -s Anc0.Anc0refChr0 9331 13 + 26507 GAGGCCAGGGACT -s Anc1.Anc1refChr6 9523 13 + 197743 GAGGCCAGGGACT -s Anc2.Anc2refChr17 2521 13 + 28526 GAGGCCAGGGACC -s mr.mrrefChr5 192668 13 + 294540 GGACCCAGGGACT -s simCow_chr6.simCow.chr6 317876 13 + 602619 GAGGTTAGGGACC -s simDog_chr6.simDog.chr6 309817 13 + 593897 GAGGCCAGGGATC -s simHuman_chr6.simHuman.chr6 329675 9 + 601863 ----TCAGGGACT -s simRat_chr6.simRat.chr6 336629 13 + 647215 GGACCCGGGGACT - -a -s simMouse_chr6.simMouse.chr6 345204 43 + 636262 TCTGTGGCTGACAGGCCCAGTGTAAAGTGCCTATGCCTAGGAT -s Anc0.Anc0refChr0 9347 31 + 26507 TCTGTGACTTGGAGGCCAAGTGTAAATTG------------AT -s Anc1.Anc1refChr6 9539 31 + 197743 TCTGTGACTTGGAGGCCAAGTGTAAATTG------------AT -s Anc2.Anc2refChr17 2537 31 + 28526 TCCATGACTTGGAGGCCAAGTGTACATTG------------GC -s mr.mrrefChr5 192681 43 + 294540 TCTGTGGCTGGCAGGCCCAGTGTAAAGTGCCTATGCCTAGGAT -s simCow_chr6.simCow.chr6 317892 31 + 602619 TCCATGGCTTAGAGGACTAATGTACATTG------------GC -s simDog_chr6.simDog.chr6 309833 24 + 593897 TCCATGAGTTGGAGGCCAAGTGTA------------------- -s simHuman_chr6.simHuman.chr6 329687 31 + 601863 TCTGTGCCTTGGAGGCTAAGTGTAAATTG------------AT -s simRat_chr6.simRat.chr6 336642 43 + 647215 TCTGTGGCTGGTAGGCCCAGTGCAAAGTGCCTATGTCTGAGAT - -a -s simMouse_chr6.simMouse.chr6 345247 49 + 636262 CCACTACCAAAGGCTCGTAAGTACCTCAAATGTACTAGTTCTTTCTCTG -s Anc0.Anc0refChr0 9378 46 + 26507 CAGGTCCCCAAGACTAGCAAGTCCCTAGAATGC---AGTtctttgactg -s Anc1.Anc1refChr6 9570 49 + 197743 CAGGTCCCCAAGACTAGCAAGTCCCTAGAATGCCCTAGTTCTTTGACTG -s Anc2.Anc2refChr17 2568 46 + 28526 CAAGTTCCCATGATTAGCAAGTCCCTAGAGTGC---AGTtatttgactg -s mr.mrrefChr5 192724 49 + 294540 CCGCTCCCAAAGGCTCGCAAGTACCTCAAATGTACTAGTTCTTTCTCTG -s simCow_chr6.simCow.chr6 317934 46 + 602619 CAAGTTCCCATGATTAGCAAGTCCCTAGAGTGC---AGTtatttgactg -s simHuman_chr6.simHuman.chr6 329718 49 + 601863 CAGTTCCCCAAGACCAGCAAGTCCCTAGGATGCCCTAGTTCCTTAACTG -s simRat_chr6.simRat.chr6 336685 49 + 647215 CTGCTCCCTGAGGCTCGCAAGTACCTTAAATGTACTGGTTCTTTCTCTG - -a -s simMouse_chr6.simMouse.chr6 345296 65 + 636262 TTCAACATGGACAACATGGAGATATCCCCTTATACTTATACAATTTTTCGGTGCATCAGATGTCC -s Anc0.Anc0refChr0 9424 38 + 26507 -----------------------aCCACCCTACATGGAAAAAAGTCTAGTGAACCCCAGAT---- -s Anc1.Anc1refChr6 9619 60 + 197743 TTCACGATGGGAAAAGTGGACA-ACCACCCTACATGGAAAAAAGTCTAGTGAACCCCAGAT---- -s Anc2.Anc2refChr17 2614 38 + 28526 -----------------------aCTACCCTGCATGGAAAAATGTCTAGTAAACCCCATAT---- -s mr.mrrefChr5 192773 64 + 294540 TTCAACATGGACAACATGGACATATCCCCTTACACTTATACAATTTTTCGGTGCATCAGAT-TCC -s simCow_chr6.simCow.chr6 317980 12 + 602619 -----------------------a--------------------------aaaccccccaa---- -s simDog_chr6.simDog.chr6 309857 37 + 593897 ------------------------CTACCCTGCATGGAAAAATGTCTAGTAAACCAAATAT---- -s simHuman_chr6.simHuman.chr6 329807 60 + 601863 TTCACGATGGGAAAAGTGGACA-ACCACCACACATGGAAAGAACTGTAGTGAACCCCAGAT---- -s simRat_chr6.simRat.chr6 336734 60 + 647215 TTCAACATGGACAACATGGACACATCCCTTTACACTTACAAAATTTTTTGGTGTATC-----TCC - -a -s simMouse_chr6.simMouse.chr6 345361 8 + 636262 TAAAATCC -s Anc0.Anc0refChr0 9462 8 + 26507 TAAAATCC -s Anc1.Anc1refChr6 9679 8 + 197743 TAAAATCC -s Anc2.Anc2refChr17 2652 8 + 28526 TGAGAAGC -s mr.mrrefChr5 192837 8 + 294540 TAAAATCC -s simCow_chr6.simCow.chr6 317992 8 + 602619 tgagaaac -s simDog_chr6.simDog.chr6 309895 8 + 593897 TGAGAAGC -s simHuman_chr6.simHuman.chr6 329867 8 + 601863 TAAAATCC -s simRat_chr6.simRat.chr6 336794 8 + 647215 TAGAATCC - -a -s simMouse_chr6.simMouse.chr6 345369 34 + 636262 ATTGATTCTCAGACATTGTGGAGATCGAATTCAG -s Anc0.Anc0refChr0 9470 34 + 26507 ATAGATTCTCAAATCTGATGGATATGGAGCTCAA -s Anc1.Anc1refChr6 9687 34 + 197743 ATAGATTCTCAAATCTGATGGATATGGAGCTCAA -s Anc2.Anc2refChr17 2660 34 + 28526 ATAGATTCTTGAATCTGATGGATATGGAGCTCAA -s mr.mrrefChr5 192845 34 + 294540 ATTGATTCTCAGACATGGTGGATATGGAGCTCAG -s simCow_chr6.simCow.chr6 318077 34 + 602619 ATAGATTCTTGAATCTGATGGATCTGGAGCTCAA -s simDog_chr6.simDog.chr6 309903 34 + 593897 ATAGGTTCTTGAATCTGATGGATATGGAGCTCAG -s simHuman_chr6.simHuman.chr6 329875 34 + 601863 ATAAATTCTCAACTCTGATGGGTATGGAGCTCAA -s simRat_chr6.simRat.chr6 336802 34 + 647215 ATTGATTCTCAGACATGGTGTATATGGAGCTCAG - -a -s simMouse_chr6.simMouse.chr6 345403 19 + 636262 TTAGAGGCCTGACTGGAGG -s Anc0.Anc0refChr0 9508 19 + 26507 TTAAAGTCCTGGTTGGAGG -s Anc1.Anc1refChr6 9725 19 + 197743 TTAAAGTCCTGGTTGGAGG -s Anc2.Anc2refChr17 2698 19 + 28526 TTAAAGTCCTGGTTGGAGG -s mr.mrrefChr5 192883 19 + 294540 TTAGAGGCCTGACTGGAGG -s simCow_chr6.simCow.chr6 318115 19 + 602619 CTAAGGTCCTGGTTGGAAA -s simDog_chr6.simDog.chr6 309941 19 + 593897 TCAAATTCCTGACTAGAGG -s simHuman_chr6.simHuman.chr6 329913 19 + 601863 ATAAAGTCCTGGTTGCAGG -s simRat_chr6.simRat.chr6 336840 19 + 647215 TTAGAGGCCTGACTGGAGG - -a -s simMouse_chr6.simMouse.chr6 345422 12 + 636262 TGACAGGTTCAT -s Anc0.Anc0refChr0 9527 12 + 26507 TGAGGCCCTCAT -s Anc1.Anc1refChr6 9744 12 + 197743 TGAGGCCCTCAT -s Anc2.Anc2refChr17 2717 12 + 28526 TGAGGCCCTCAT -s mr.mrrefChr5 192902 12 + 294540 TGACAGCTTCAT -s simCow_chr6.simCow.chr6 318134 12 + 602619 TGAGGTCTTCAT -s simDog_chr6.simDog.chr6 310004 12 + 593897 CAAGGCCCACAA -s simHuman_chr6.simHuman.chr6 329932 12 + 601863 TGAAGCCCTCAT -s simRat_chr6.simRat.chr6 336859 12 + 647215 CAACAGCTGCAT - -a -s simMouse_chr6.simMouse.chr6 345434 3 + 636262 AAT -s Anc0.Anc0refChr0 9539 3 + 26507 ACT -s Anc1.Anc1refChr6 9756 3 + 197743 ACT -s Anc2.Anc2refChr17 2729 3 + 28526 ACT -s mr.mrrefChr5 192914 3 + 294540 AAT -s simCow_chr6.simCow.chr6 318146 3 + 602619 ACT -s simDog_chr6.simDog.chr6 310020 3 + 593897 ACA -s simHuman_chr6.simHuman.chr6 329944 3 + 601863 ACT -s simRat_chr6.simRat.chr6 336871 3 + 647215 AAT - -a -s simMouse_chr6.simMouse.chr6 345437 48 + 636262 GTAAAGAAGTCTGAGGCATAATGGCAGATCCCTGTATTTTTATTAGAA -s Anc0.Anc0refChr0 9544 26 + 26507 GTGGGCATGTCTGATGTA------------CCCAT----------GAT -s Anc1.Anc1refChr6 9761 47 + 197743 GTGGGCATGTCTGATGTATTATGGCAGACCCCCATAATCTC-TTAGAT -s Anc2.Anc2refChr17 2734 26 + 28526 GAGGGCATGTCTGATGTA------------ACCAT----------GAT -s mr.mrrefChr5 192917 48 + 294540 GTGAAGAAGTCTGAGGCATAATGGCAGATCCCTGTATTTTTATTAGAA -s simCow_chr6.simCow.chr6 318151 24 + 602619 GAGGGCATGTCTGATCT--------------CTAT----------GAT -s simDog_chr6.simDog.chr6 310025 26 + 593897 CAGGGCTAGTTTGGTGTA------------ACCAT----------GCT -s simHuman_chr6.simHuman.chr6 329949 47 + 601863 GTGTTCATGTCTGATGTGTTATGGCAGACCCCCATAATCTC-TTAGAT -s simRat_chr6.simRat.chr6 336874 46 + 647215 GTGAAGGAGTCTGAGACAT--TGGCAGATCCCTGTATTTTTGTTAAAA - -a -s simMouse_chr6.simMouse.chr6 345485 4 + 636262 AAAA -s Anc0.Anc0refChr0 9570 4 + 26507 AATG -s Anc1.Anc1refChr6 9808 4 + 197743 AATG -s Anc2.Anc2refChr17 2760 4 + 28526 AATG -s mr.mrrefChr5 192965 4 + 294540 AAAA -s simCow_chr6.simCow.chr6 318175 4 + 602619 AGTG -s simDog_chr6.simDog.chr6 310063 4 + 593897 GATG -s simHuman_chr6.simHuman.chr6 329996 4 + 601863 AATT -s simRat_chr6.simRat.chr6 336920 4 + 647215 AAAA - -a -s simMouse_chr6.simMouse.chr6 345489 49 + 636262 TGGAAATGACGCTAACGAAAGAACAGGGCTAACTTCGCTCTAGGCATAC -s Anc0.Anc0refChr0 9574 19 + 26507 TGGAAACAAG---CACGACA---------------------------AC -s Anc1.Anc1refChr6 9812 22 + 197743 TGGAAACAAGGCCCACGACA---------------------------AC -s Anc2.Anc2refChr17 2764 19 + 28526 CGGACACAAA---CAGGACA---------------------------CT -s mr.mrrefChr5 192969 49 + 294540 TGGAAACAAGGCTCACGAAAGAACAGGGCTAACTTCGCTCTAGGCATAC -s simCow_chr6.simCow.chr6 318182 19 + 602619 CAATGACAGA---CCAAACA---------------------------CT -s simDog_chr6.simDog.chr6 310067 19 + 593897 CGGACACTAA---AAGGAAA---------------------------CT -s simHuman_chr6.simHuman.chr6 330000 22 + 601863 TGGCAACAAGGCCCACGGCA---------------------------AC -s simRat_chr6.simRat.chr6 336924 49 + 647215 TGGAATCAAGGCTCACAAAAGAACAGGGCTAACTTGGCTGTAGGCATAC - -a -s simMouse_chr6.simMouse.chr6 345538 30 + 636262 GAGGCTAACTTGGCTGTAGGCGTACTTTCA -s Anc0.Anc0refChr0 9593 30 + 26507 GAGGCAGACTTGGCTGTAATTATACTTTCA -s Anc1.Anc1refChr6 9834 30 + 197743 GAGGCAGACTTGGCTGTAATTATACTTTCA -s Anc2.Anc2refChr17 2783 30 + 28526 GACACAGATTGGGCCTTTATTATGCTAATG -s mr.mrrefChr5 193018 30 + 294540 GAGGCTAACTTGGCTGTAGTCATACTTTCA -s simCow_chr6.simCow.chr6 318201 30 + 602619 GATTTTGAGTGGGCATCTATTATGCTAAAG -s simDog_chr6.simDog.chr6 310086 30 + 593897 GACACAAGTGGTGCCTTTATTGTGTCAATG -s simHuman_chr6.simHuman.chr6 330022 30 + 601863 AAGGCCGACTTGGCTGTAATTACACTTTCA -s simRat_chr6.simRat.chr6 336978 30 + 647215 TAGGCTAACTTGGATGTAGTCATACTTTCA - -a -s simMouse_chr6.simMouse.chr6 345568 5 + 636262 TAGAT -s Anc0.Anc0refChr0 9623 5 + 26507 GACAT -s Anc1.Anc1refChr6 9864 5 + 197743 GACAT -s Anc2.Anc2refChr17 2813 5 + 28526 GACAT -s mr.mrrefChr5 193048 5 + 294540 TAGAT -s simCow_chr6.simCow.chr6 318231 5 + 602619 ACCGT -s simDog_chr6.simDog.chr6 310123 5 + 593897 GACAT -s simHuman_chr6.simHuman.chr6 330052 5 + 601863 GTCAT -s simRat_chr6.simRat.chr6 337008 5 + 647215 TAGAT - -a -s simMouse_chr6.simMouse.chr6 345573 3 + 636262 CAG -s Anc0.Anc0refChr0 9630 3 + 26507 CAG -s Anc1.Anc1refChr6 9871 3 + 197743 CAG -s Anc2.Anc2refChr17 2820 3 + 28526 CAG -s mr.mrrefChr5 193053 3 + 294540 CAG -s simCow_chr6.simCow.chr6 318238 3 + 602619 CCT -s simDog_chr6.simDog.chr6 310130 3 + 593897 AAG -s simHuman_chr6.simHuman.chr6 330059 3 + 601863 CAG -s simRat_chr6.simRat.chr6 337013 3 + 647215 CAG - -a -s simMouse_chr6.simMouse.chr6 345576 82 + 636262 ACATAGAGATCAAGTGGAAACTGATGCTTGAGGGCCCTTACTCCAGGAGCTGGATGGTAGAGAGGATAAGGCCACCTTTGTT -s Anc0.Anc0refChr0 9633 28 + 26507 ACGCACACATTCAATGGA------------------------------------------------------CAATTAGGGT -s Anc1.Anc1refChr6 9874 28 + 197743 ACGCACACATTCAATGGA------------------------------------------------------CAATTAGGGT -s Anc2.Anc2refChr17 2825 28 + 28526 ATGCACACTTTCAACTCA------------------------------------------------------CAATAAGAGT -s mr.mrrefChr5 193056 82 + 294540 ACATAGACATCAAGTGGAAACTGATGCTTGAGGGCCCTTACTGCAGGAGCTGGATGGTAGAGAGGATAAGGCCACCTTTGTT -s simCow_chr6.simCow.chr6 318243 28 + 602619 ATGTGCACTTTCAACTTA------------------------------------------------------CAAAGAGAGA -s simDog_chr6.simDog.chr6 310135 28 + 593897 ATGCACAATTCCAACTCA------------------------------------------------------AAATAAGAGT -s simHuman_chr6.simHuman.chr6 330062 28 + 601863 ACGCAAACATTGAATGGA------------------------------------------------------CATGTGGGGT -s simRat_chr6.simRat.chr6 337016 82 + 647215 ACAGTGACATCAACTTGAAACTTATGCTTGGGAGCCCTTACTGCAGGAGCTGGATGGTAGAGAGGATAATGCCATCCTTGTT - -a -s simMouse_chr6.simMouse.chr6 345658 30 + 636262 ATGATTTTTCACTGGGGTCATTTGTAACAT -s Anc0.Anc0refChr0 9661 27 + 26507 T---TTTTGACTAAGGGGCATTAGCAATAT -s Anc1.Anc1refChr6 9902 30 + 197743 TTGGTTTTGACTAAGGGGCATTAGCAATAT -s Anc2.Anc2refChr17 2853 27 + 28526 T---TTTTGACTAAGGGGCATTAGCAATAT -s mr.mrrefChr5 193138 30 + 294540 ATGATTTTTCACTGGGGTCATTTGTAACAT -s simCow_chr6.simCow.chr6 318272 27 + 602619 T---TCTTGAGCAGAGGTCACTAGAAATCT -s simDog_chr6.simDog.chr6 310163 27 + 593897 T---TTTTGACTGAGGGGCATTAGCAATAC -s simHuman_chr6.simHuman.chr6 330090 30 + 601863 CTGGTTCTGACTAAGGGCCATTGGCAATAT -s simRat_chr6.simRat.chr6 337098 30 + 647215 ATGATTTTTCACTGGGGTCACTTGTAACAT - -a -s simMouse_chr6.simMouse.chr6 345688 10 + 636262 TGAACAGCAG -s Anc0.Anc0refChr0 9688 10 + 26507 TAAACAGCCC -s Anc1.Anc1refChr6 9932 10 + 197743 TAAACAGCCC -s Anc2.Anc2refChr17 2880 10 + 28526 TAGAGAGCCC -s mr.mrrefChr5 193168 10 + 294540 TGAACAGCCG -s simCow_chr6.simCow.chr6 318299 10 + 602619 TATATAACCC -s simDog_chr6.simDog.chr6 310190 10 + 593897 TAGAGAGCCC -s simHuman_chr6.simHuman.chr6 330120 10 + 601863 TTAACAGCCT -s simRat_chr6.simRat.chr6 337137 10 + 647215 TGAAAAGACA - -a -s simMouse_chr6.simMouse.chr6 345698 6 + 636262 ATGAAT -s Anc0.Anc0refChr0 9698 6 + 26507 TTGACA -s Anc1.Anc1refChr6 9942 6 + 197743 TTGACA -s Anc2.Anc2refChr17 2890 6 + 28526 TTGACA -s mr.mrrefChr5 193178 6 + 294540 ATGAAT -s simCow_chr6.simCow.chr6 318309 5 + 602619 TTT-CT -s simDog_chr6.simDog.chr6 310200 6 + 593897 TTGACA -s simHuman_chr6.simHuman.chr6 330130 6 + 601863 TTGACA -s simRat_chr6.simRat.chr6 337149 6 + 647215 ATGAAT - -a -s simMouse_chr6.simMouse.chr6 345704 38 + 636262 CCTGGAAAGGCTAATGATGCTGGATAGTATATGCTTGG -s Anc0.Anc0refChr0 9704 38 + 26507 CCTGGAAAGGCTAATTATGCTGGATAGTGTAAGCCTGA -s Anc1.Anc1refChr6 9948 38 + 197743 CCTGGAAAGGCTAATTATGCTGGATAGTGTAAGCCTGA -s Anc2.Anc2refChr17 2899 38 + 28526 CCTGGAAAGGCTAATTATGCCAGATAGTGTAAGCCTGA -s mr.mrrefChr5 193184 38 + 294540 CCTGGAAAGGCTAATGATGCTGGATAGTGTATGCTTGG -s simCow_chr6.simCow.chr6 318317 31 + 602619 CTTGGAAAGGCTAATTATGC-------TGTAAGTGTGA -s simDog_chr6.simDog.chr6 310209 35 + 593897 CCTGGAAAG---AATTATGCCAGATAGTCTAAGCCCGA -s simHuman_chr6.simHuman.chr6 330136 37 + 601863 GATGGAAAGGCTAAGTATGCTGGATAGTGTA-GCCTGA -s simRat_chr6.simRat.chr6 337155 38 + 647215 CCTGGAAAGGTTAATGATGCTGGATAGTGTATGCTTTG - -a -s simMouse_chr6.simMouse.chr6 345742 50 + 636262 ATTTGGTTGTGAATGTCTGCCATGCTTCAACATAAGTCTTTCCACTTTTG -s Anc0.Anc0refChr0 9745 42 + 26507 ATTTGATGGAGAGTGTCTA--AC------ACTTGAGTCTTTCCCCTTGTG -s Anc1.Anc1refChr6 9989 44 + 197743 ATTTGATGGAGAGTGTCTACCAC------ACTTGAGTCTTTCCCCTTGTG -s Anc2.Anc2refChr17 2940 42 + 28526 ATTTGATGGAGAGTGTCTA--AC------ACTTGAGTCTTTCTCCTTGTG -s mr.mrrefChr5 193222 50 + 294540 ATTTGGTTGTGAATGTCTGCCATGCTTCAACATGAGTCTTTCCACTTTTG -s simCow_chr6.simCow.chr6 318351 42 + 602619 ATTTGATGGAGTGGGTCTA--AC------ACTTGAGCCTTTCGCCTTGTG -s simDog_chr6.simDog.chr6 310247 42 + 593897 GTTTGATGAAGACTGTCTA--AC------TCTTAAGTCGTTCTCCTTGTG -s simHuman_chr6.simHuman.chr6 330176 44 + 601863 ATTTGATGGCGAGTGTCTACCAC------ACCTGAGTATTTCCTCCCATG -s simRat_chr6.simRat.chr6 337193 50 + 647215 ATTTGGTTGTGCATTTCTGCCTTGCTTCAACATGAGTCTTTTCGGTTTTG - -a -s simMouse_chr6.simMouse.chr6 345792 3 + 636262 ATT -s Anc0.Anc0refChr0 9788 3 + 26507 ATT -s Anc1.Anc1refChr6 10034 3 + 197743 ATT -s Anc2.Anc2refChr17 2983 3 + 28526 ATC -s mr.mrrefChr5 193273 3 + 294540 ATT -s simCow_chr6.simCow.chr6 318394 2 + 602619 AT- -s simDog_chr6.simDog.chr6 310290 3 + 593897 ATC -s simHuman_chr6.simHuman.chr6 330221 3 + 601863 ATT -s simRat_chr6.simRat.chr6 337244 3 + 647215 ATT - -a -s simMouse_chr6.simMouse.chr6 345795 48 + 636262 GGTAAAGATAATAAGTTTTAATACAAAACTCATTGAAGATGTAATCTG -s Anc0.Anc0refChr0 9791 18 + 26507 TGCATCGGTGATAACTTT------------------------------ -s Anc1.Anc1refChr6 10037 18 + 197743 TGCATCGGTGATAACTTT------------------------------ -s Anc2.Anc2refChr17 2986 18 + 28526 TGCATCAGTGATAACTCT------------------------------ -s mr.mrrefChr5 193276 48 + 294540 GGTAAAGATAATAAGTTTTAATACAAAACTCATTGAAGATGTAATCTG -s simCow_chr6.simCow.chr6 318396 13 + 602619 -----CAGTAATAACTCA------------------------------ -s simDog_chr6.simDog.chr6 310375 18 + 593897 TGCATCAGTGATAACTCT------------------------------ -s simHuman_chr6.simHuman.chr6 330224 18 + 601863 TGCATTGCTGATAACTTT------------------------------ -s simRat_chr6.simRat.chr6 337247 48 + 647215 AGTGAAGGTAATAAGTTTTAATATAGAACTCATTGAGGGTATAATCGG - -a -s simMouse_chr6.simMouse.chr6 345843 29 + 636262 TGTCACAAGGTTAGGTGAAGCTTAGTAAC -s mr.mrrefChr5 193324 29 + 294540 TGTCACAAGGTTAGGTGAAGCTTAGTAAC -s simRat_chr6.simRat.chr6 337296 29 + 647215 TGTCACAAGATTAGGCAAAGCCTAGTAAC - -a -s simMouse_chr6.simMouse.chr6 345872 18 + 636262 ACTTCCCCCTAAAACTCT -s mr.mrrefChr5 193353 18 + 294540 ACTTCCCCCTAAAACTCT -s simRat_chr6.simRat.chr6 337332 18 + 647215 ACTTCCCTGCAAGACTGT - -a -s simMouse_chr6.simMouse.chr6 345890 25 + 636262 GATGTGCTAACCCATTGGTGGCTAG -s Anc0.Anc0refChr0 9809 21 + 26507 ----TATTAGCCCATTGGCTGCTAG -s Anc1.Anc1refChr6 10055 21 + 197743 ----TATTAGCCCATTGGCTGCTAG -s Anc2.Anc2refChr17 3004 21 + 28526 ----TATTGGCCGATTGACTGTTAG -s mr.mrrefChr5 193371 25 + 294540 GATGTACTAACCCATTGGTGGCTAG -s simCow_chr6.simCow.chr6 318409 21 + 602619 ----TATTGGCCAATTGACTGTTAT -s simDog_chr6.simDog.chr6 310393 21 + 593897 ----TATTGACCGATCGACTTTTAG -s simHuman_chr6.simHuman.chr6 330242 21 + 601863 ----TATTAGCCCATTGGCTGCTAG -s simRat_chr6.simRat.chr6 337356 25 + 647215 AATACACTGACCCATTGGTGGCTAG - -a -s simMouse_chr6.simMouse.chr6 345915 17 + 636262 ACTCCACAACATAGAGA -s Anc0.Anc0refChr0 9831 17 + 26507 CTTCTATAGACCAGAGA -s Anc1.Anc1refChr6 10077 17 + 197743 CTTCTATAGACCAGAGA -s Anc2.Anc2refChr17 3026 17 + 28526 CTTATGTAGACCAGAGA -s mr.mrrefChr5 193396 17 + 294540 ATTCCACAACATAGAGA -s simCow_chr6.simCow.chr6 318431 17 + 602619 CTGTGGTATACCAGATA -s simDog_chr6.simDog.chr6 310415 17 + 593897 CTTATGTGGACTATAGA -s simHuman_chr6.simHuman.chr6 330264 17 + 601863 GTTCTATAGACCAGAGA -s simRat_chr6.simRat.chr6 337381 17 + 647215 ATTTCACAACAGAGAGA - -a -s simMouse_chr6.simMouse.chr6 345932 12 + 636262 CGCTGCAATCAT -s Anc0.Anc0refChr0 9849 12 + 26507 CTCTACAATTGT -s Anc1.Anc1refChr6 10095 12 + 197743 CTCTACAATTGT -s Anc2.Anc2refChr17 3044 12 + 28526 CTCTACAATTGT -s mr.mrrefChr5 193413 12 + 294540 CGCTACAATTGT -s simCow_chr6.simCow.chr6 318449 10 + 602619 C--TACAATTGT -s simDog_chr6.simDog.chr6 310433 12 + 593897 CTCTATAACTGT -s simHuman_chr6.simHuman.chr6 330282 12 + 601863 CTCTACAATTGT -s simRat_chr6.simRat.chr6 337398 12 + 647215 CACTACAGTTGT - -a -s simMouse_chr6.simMouse.chr6 345944 50 + 636262 GTTATGGACAAACATCAGGCAGGTCGGCTGTGCACTTGAGAGTTTTCATG -s Anc0.Anc0refChr0 9870 40 + 26507 CTTATAGACAAAC------CAGGTCT----TAGACATGAGAGTTATTATG -s Anc1.Anc1refChr6 10116 44 + 197743 CTTATAGACAAAC------CAGGTCTGCTGTAGACATGAGAGTTATTATG -s Anc2.Anc2refChr17 3065 40 + 28526 CTTATATACAAAC------CAGGTCT----TAGACATGAGTGTTATTATG -s mr.mrrefChr5 193425 50 + 294540 GTTATGGACAAACATCAGGCAGGTCGGCTGTGCACTTGAGAGTTTTCATG -s simCow_chr6.simCow.chr6 318465 39 + 602619 -TTACATACCAAC------CAGGTGT----TACACATGAGTGCTTACATG -s simDog_chr6.simDog.chr6 310476 40 + 593897 CTTATGTACAACC------CAGGTCT----TAGACTCTAATGTTATTGTC -s simHuman_chr6.simHuman.chr6 330303 44 + 601863 ATTATAGAAAAAC------CAGGTCTGCTGTAGACATGAGAGTTGTGATG -s simRat_chr6.simRat.chr6 337410 20 + 647215 CTTATGGACACACATCAGGC------------------------------ - -a -s simMouse_chr6.simMouse.chr6 345994 13 + 636262 TTTAATTGCTTCA -s Anc0.Anc0refChr0 9910 12 + 26507 CCCAGTTGC-TTA -s Anc1.Anc1refChr6 10160 13 + 197743 CCCAGTTGCTTTA -s Anc2.Anc2refChr17 3105 12 + 28526 CCCAGTTGC-TTA -s mr.mrrefChr5 193475 13 + 294540 TTTAATTGCTTCA -s simCow_chr6.simCow.chr6 318504 12 + 602619 CCCAGCTGC-TTA -s simDog_chr6.simDog.chr6 310516 12 + 593897 CCCAGTTGC-TTA -s simHuman_chr6.simHuman.chr6 330348 13 + 601863 CCCACTCGCTTTA - -a -s simMouse_chr6.simMouse.chr6 346007 16 + 636262 ATTTTGGAATTTTGTT -s Anc0.Anc0refChr0 9922 16 + 26507 TTTATGGACTTCTGTT -s Anc1.Anc1refChr6 10173 16 + 197743 TTTATGGACTTCTGTT -s Anc2.Anc2refChr17 3117 16 + 28526 TTTACTTGCTTCTGTC -s mr.mrrefChr5 193488 16 + 294540 ATTTTGGAATTTTGTT -s simCow_chr6.simCow.chr6 318516 10 + 602619 TTTA------GCTGTC -s simDog_chr6.simDog.chr6 310528 16 + 593897 TTTACTTGCTTCTGTC -s simHuman_chr6.simHuman.chr6 330362 16 + 601863 GTTATGGACTTCGGTT -s simRat_chr6.simRat.chr6 337430 8 + 647215 --------ATTTTGTT - -a -s simMouse_chr6.simMouse.chr6 346023 77 + 636262 TTCCTGATAACTTTCAAGGCACAAATACCAACCCAGCCAAAGAAAATAGCGTTTGGTGGTTCAAGTTGTTTCTGATT -s Anc0.Anc0refChr0 9938 68 + 26507 TCCCTGGTAACTTTCATGGTTCAAATACCAAC----CGAACGATAATAGTATTCA---GTTCAACTTGTT--TGATT -s Anc1.Anc1refChr6 10189 69 + 197743 TCCCTGGTAACTTTCATGGTTCAAATACCAAC----CGAACGATAATAGTATTCAG--GTTCAACTTGTT--TGATT -s Anc2.Anc2refChr17 3133 68 + 28526 TCCCTGGTAACTTTCATGGTTCAAATACCAGC----CGAACGGTAATGATATTCA---GTTCAACTTGTT--TGATT -s mr.mrrefChr5 193504 75 + 294540 TTCCTGATAACTTTCAAGGCACAAATACCAACCCAGCCAAAGATAATAGCGTTTGGTGGTTCAACTTGTT--TGATT -s simCow_chr6.simCow.chr6 318526 68 + 602619 TCACTGGCAACTTTCATGGTTCAATGACAAGC----TGAATGGTAATGATATTCA---GTGCGACTCGCT--ATATT -s simDog_chr6.simDog.chr6 310544 68 + 593897 TCCCTGGTAACTTTCATGGTTCAAATATCCGC----CGAACGGTTATGATATTTG---GTTCAACTTGTT--TGACT -s simHuman_chr6.simHuman.chr6 330390 67 + 601863 TCCCTGGTAACTTTCATGATTCAAATACCAAC----CAAAGGATAATAGTATTCAG----TCAACTAGTT--TGATT -s simRat_chr6.simRat.chr6 337438 70 + 647215 TTCCTGATAACTTTCAAGGAACAAATACCAACCCAGACAAAGATGATAGCGTTTGGTGGTTCAACTTGTT------- - -a -s simMouse_chr6.simMouse.chr6 346100 25 + 636262 CTGTTCACCTGCATACTTGATATTA -s Anc0.Anc0refChr0 10011 25 + 26507 CTGTTTGATTGCATACATATTAGTA -s Anc1.Anc1refChr6 10263 25 + 197743 CTGTTTGATTGCATACATATTAGTA -s Anc2.Anc2refChr17 3206 25 + 28526 CCATTTGATTGCATGCACATTAGTA -s mr.mrrefChr5 193584 25 + 294540 CTGTTCACCTGCATACTTGATATTA -s simCow_chr6.simCow.chr6 318599 25 + 602619 CCATTTGATTGCATGCACATTAGTA -s simDog_chr6.simDog.chr6 310617 7 + 593897 CCATTTG------------------ -s simHuman_chr6.simHuman.chr6 330462 25 + 601863 CTGTTTGATTGCATACATATTACTA -s simRat_chr6.simRat.chr6 337616 25 + 647215 CTGTTCACCTGCATACTTGATATTA - -a -s simMouse_chr6.simMouse.chr6 346125 38 + 636262 CAGTTTTACATGTGCCATCTGAAGAGGGATGGAATTTT -s Anc0.Anc0refChr0 10036 36 + 26507 CAGTTTTACCTG--TGTTCTGAAGAGGGAGAGAGTTAC -s Anc1.Anc1refChr6 10288 36 + 197743 CAGTTTTACCTG--TGTTCTGAAGAGGGAGAGAGTTAC -s Anc2.Anc2refChr17 3231 36 + 28526 GAGTTCTACCTG--TGTTCTGGACAGGGAGAGAGTTAC -s mr.mrrefChr5 193609 36 + 294540 CAGTTTTACATG--CCATCTGAAGAGGGATGGAATTAT -s simCow_chr6.simCow.chr6 318624 36 + 602619 GAGTTCTACCTG--TGTCCTTGAAAGGGAAAAAGTTAC -s simDog_chr6.simDog.chr6 310624 27 + 593897 ---------TTG--TGTTCTGGACAGGGAGAGAGTTAT -s simHuman_chr6.simHuman.chr6 330490 36 + 601863 CACTCTTACCTG--TGTTTTGAAGGGGGAGAGAGTTAC -s simRat_chr6.simRat.chr6 337641 36 + 647215 CAGTTTTACATG--CTGTCTGGAGAGGGGTGGAATTAT - -a -s simMouse_chr6.simMouse.chr6 346163 47 + 636262 GCACACCATCTTAGCTGGGGAGTGTCATAAGGTTCTGAAACGCAGAT -s Anc0.Anc0refChr0 10072 47 + 26507 ACACACCATTTTAGCTGAGGAGTGTCACAAGGTTTTGAAAGGCAGAC -s Anc1.Anc1refChr6 10324 47 + 197743 ACACACCATTTTAGCTGAGGAGTGTCACAAGGTTTTGAAAGGCAGAC -s Anc2.Anc2refChr17 3267 47 + 28526 ACACACCATTTTAGCTGAGGAGTGTCACAAGGTTTTGAAAGGCAGAC -s mr.mrrefChr5 193645 47 + 294540 ACACACCATCTTAGCTGGGGAGTGTCATAAGGTTCTGAAAGGCAGAT -s simCow_chr6.simCow.chr6 318661 47 + 602619 ACACACCATTTGCTCTGAGGAGTGTCATGAGATTTTGAAGAGCAATT -s simDog_chr6.simDog.chr6 310651 47 + 593897 GCACATCATTTTAGCTGAGGAGAGTCACAGGGTTTTGAAAGGTAGAC -s simHuman_chr6.simHuman.chr6 330526 47 + 601863 ACACGCCATATTAGCTGAGGACTGTCACAAGGTTTTGAAAGGCAGAC -s simRat_chr6.simRat.chr6 337677 41 + 647215 ACACACCATCTTAGCT------TGTCATAAGGTTCTGAAGGGCAGAA - -a -s simMouse_chr6.simMouse.chr6 346210 30 + 636262 GTTCCTGCACTCAAAGGAAGTGCAGAAGCC -s Anc0.Anc0refChr0 10119 29 + 26507 ATTCCTACACTCAAA-GAAGCACAAAAACT -s Anc1.Anc1refChr6 10371 29 + 197743 ATTCCTACACTCAAA-GAAGCACAAAAACT -s Anc2.Anc2refChr17 3314 29 + 28526 ATTCCTACACTCAAA-CAGGCACAAAAACT -s mr.mrrefChr5 193692 30 + 294540 GTTCCTACACTCAAAGGAAGTGCAGAAGCT -s simCow_chr6.simCow.chr6 318708 29 + 602619 ATTCCTACACTCAAA-TAGGCACAAAAACT -s simDog_chr6.simDog.chr6 310705 29 + 593897 ACTACTATGCTCAAA-CAGGCAAAAAAACT -s simHuman_chr6.simHuman.chr6 330573 29 + 601863 ATTCTTACACTCAAA-GAAGCACGAAAACT -s simRat_chr6.simRat.chr6 337718 30 + 647215 GCCCCTACGCTCAAAAGAAGTGCAGAAGAT - -a -s simMouse_chr6.simMouse.chr6 346240 4 + 636262 ATTA -s Anc0.Anc0refChr0 10148 4 + 26507 ATTA -s Anc1.Anc1refChr6 10400 4 + 197743 ATTA -s Anc2.Anc2refChr17 3343 4 + 28526 ATTC -s mr.mrrefChr5 193722 4 + 294540 ATTA -s simCow_chr6.simCow.chr6 318737 4 + 602619 GTAC -s simDog_chr6.simDog.chr6 310734 4 + 593897 ATTC -s simHuman_chr6.simHuman.chr6 330602 4 + 601863 ATTA -s simRat_chr6.simRat.chr6 337751 4 + 647215 ACTA - -a -s simMouse_chr6.simMouse.chr6 346244 14 + 636262 TCAAGGGCCATAAA -s Anc0.Anc0refChr0 10154 14 + 26507 TCAAGGAGCTCAAA -s Anc1.Anc1refChr6 10406 14 + 197743 TCAAGGAGCTCAAA -s Anc2.Anc2refChr17 3349 14 + 28526 TCAAGGAGCTCAAA -s mr.mrrefChr5 193726 14 + 294540 TCAAGGGCCATAAA -s simCow_chr6.simCow.chr6 318743 14 + 602619 TCAAGGAGCTCAAT -s simDog_chr6.simDog.chr6 310740 14 + 593897 TCAAGGAGCTCAAA -s simHuman_chr6.simHuman.chr6 330608 14 + 601863 TCAAGGAGCTCGAA -s simRat_chr6.simRat.chr6 337755 14 + 647215 TCAAGGGACAAAAA - -a -s simMouse_chr6.simMouse.chr6 346258 19 + 636262 TTTGCCTACATTCTAATAG -s Anc0.Anc0refChr0 10173 19 + 26507 TTTGCATATGTTTTAGTAA -s Anc1.Anc1refChr6 10425 19 + 197743 TTTGCATATGTTTTAGTAA -s Anc2.Anc2refChr17 3368 19 + 28526 TTTGCATATGTTTTAGTAA -s mr.mrrefChr5 193740 19 + 294540 TTTGCCTACATTCTAGTAG -s simCow_chr6.simCow.chr6 318762 19 + 602619 TTTACATATGTCTTAGTAA -s simDog_chr6.simDog.chr6 310759 19 + 593897 TTTGTAGACGTTTTAGTGA -s simHuman_chr6.simHuman.chr6 330627 19 + 601863 TATGCATATGTTTTAGTAA -s simRat_chr6.simRat.chr6 337769 19 + 647215 TTTGTCTACATTCTCGTAG - -a -s simMouse_chr6.simMouse.chr6 346277 15 + 636262 TGAAGCCCATATGGT -s Anc0.Anc0refChr0 10192 15 + 26507 TGAACCCCTTGTGAT -s Anc1.Anc1refChr6 10444 15 + 197743 TGAACCCCTTGTGAT -s Anc2.Anc2refChr17 3397 15 + 28526 TAAACCCCTTGTGAT -s mr.mrrefChr5 193759 15 + 294540 TGAAGCCCATATGGT -s simCow_chr6.simCow.chr6 318791 15 + 602619 TGAAGCCCCAGTGAT -s simDog_chr6.simDog.chr6 310788 15 + 593897 TAAACCCCTTGTGAT -s simHuman_chr6.simHuman.chr6 330646 2 + 601863 TG------------- -s simRat_chr6.simRat.chr6 337788 14 + 647215 T-AAGCCCATGTGGT - -a -s simMouse_chr6.simMouse.chr6 346292 127 + 636262 AATCTAATGTAGGGCTATATTACCTGGATCTATCCCAACTTTTATCATGCTTCAAAATTTCAGAGCTACATTTATGGACACCCTATGGGATGCGTCAATCAATTAAAGACACAAAAGTAAGATGCAG -s Anc0.Anc0refChr0 10207 127 + 26507 GATTCAACATAGGGGTAAAGTACCAAGATGTATGTTAATTTTTATCACGCATCAAAATTTCAGGGCCACATTTATGGACATTCTATGGGATGCATCAATAGCTTAAAGAAACAACCACAAAATGCAG -s Anc1.Anc1refChr6 10459 127 + 197743 GATTCAACATAGGGGTAAAGTACCAAGATGTATGTTAATTTTTATCACGCATCAAAATTTCAGGGCCACATTTATGGACATTCTATGGGATGCATCAATAGCTTAAAGAAACAACCACAAAATGCAG -s Anc2.Anc2refChr17 3412 127 + 28526 GATTCAACATAGGGGTAAAGTACCAAGATGTATGTTAATTTGTATCACCCATCAAAATTTCAGGGCCACATTTTTGGATATTCTATGGGATGCATCAATAGCTTAAAGAAACCACCACAAAATGCAA -s mr.mrrefChr5 193774 127 + 294540 AATCTAATGTAGGGCTATATTACCTGGATCTATCCCAACTTTTATCATGCTTCAAAATTTCAGAGCTACATTTATGGACACCCTATGGGATGCATCAATCAATTAAAGACACAAAAGTAAGATGCAG -s simCow_chr6.simCow.chr6 318807 127 + 602619 GACTCAACATAGGTGTAGAGTACCAGGGACTATGTTAATTTGTATTATGTATAAAAATTTAAGGGCCACATTTTTGGATATTCTCTGGGATGCATCAATAGCTCAAAGAAACGACCACAATATGCAA -s simDog_chr6.simDog.chr6 310803 127 + 593897 GATTCAACATAGGGGTAAAGTACCAAGATGTATGTTAATTTGTATCACCCATCAAAAATTCAGGGCCACATTTTTGGATATTTTATAGGATGCATCAATAGCTTAAAAAAACCACTACAAAATGAAA -s simHuman_chr6.simHuman.chr6 330648 82 + 601863 -----------------------------------------TTTTCAGG----AAAATTTCAGGGCCATAATTATGGACATTCTATGGGATGCATCAATAGCTTAAAGAAACAACCACAACATACAG -s simRat_chr6.simRat.chr6 337802 127 + 647215 AATCTAATATAGAGGTAGACTACCGGGCTCTATCCCAACTTGTATCACGCTTCAAAATTCCAGAGCTACATTGATTGACACCCTATGGGATGTATCGATCAATTAAAGACGCGAAAGTAAGATGCGG - -a -s simMouse_chr6.simMouse.chr6 346419 93 + 636262 ATCTAGTGAGTTATGTTGCCAATCAAGCATATTGAAATAGCATCAGTAATAACAGATATCAATCTGCATCTATTAACAGGGGTTGTAACTAAA -s Anc0.Anc0refChr0 10334 92 + 26507 AGGGAGTGAGTTATAATGGTAATTTAGCA-ATATATGAAGTAGCAGTTAGAACAGGTGTCAATACACATCAACTAACAGGAGTTATAGCTACA -s Anc1.Anc1refChr6 10586 92 + 197743 AGGGAGTGAGTTATAATGGTAATTTAGCA-ATATATGAAGTAGCAGTTAGAACAGGTGTCAATACACATCAACTAACAGGAGTTATAGCTACA -s Anc2.Anc2refChr17 3539 92 + 28526 AGGGAGTGTGTTATAATGGTAATTTAGGA-ATATATAAAGTAGCAGTTAGAACAGGTGTCAATACACATCAGCTAACAGGAGTTATAGCTACA -s mr.mrrefChr5 193901 93 + 294540 ATCTAGTGAGTTATGTTGCCAATTAAGCATATTGAAGTAGCATCAGTAATAACAGGTGTCAATCTGCATCTATTAACAGGGGTTGTAACTAAA -s simCow_chr6.simCow.chr6 318934 90 + 602619 AGGGAATGGGTTACAATGGTAATCTAAAA-ATACTTAAAGTAGCAGCAAGAGCAGGTGTCAATACAGATCAGCTAACAGGATTTTTAGCTA-- -s simDog_chr6.simDog.chr6 310930 91 + 593897 AGGGAGTGTGTTATGATGGTAATTTAGGA-AAATATAAAGTAGC-ATTAGAACAGGTGTCAATACACATCAGTGAACAGGAGTTATAATTACA -s simHuman_chr6.simHuman.chr6 330730 92 + 601863 AGGACGTGAACTATAATGGTAATTCAGCA-ATGTACGAATTAGCTGTTAGAACAGGTGTAGATACACATCAACTAATGGGAGTCCTAGCTATG -s simRat_chr6.simRat.chr6 337931 81 + 647215 ATTTAGTGAGTTATGTTGCCAGTTGAGCATATTAAAGTAGCATCA----TGACAGGTGT------GGATCTATCAACAGGGGTT--CACTAGA - -a -s simMouse_chr6.simMouse.chr6 346512 5 + 636262 AATTG -s Anc0.Anc0refChr0 10426 5 + 26507 ATTTG -s Anc1.Anc1refChr6 10678 5 + 197743 ATTTG -s Anc2.Anc2refChr17 3631 5 + 28526 ATTTG -s mr.mrrefChr5 193994 5 + 294540 AATTG -s simCow_chr6.simCow.chr6 319024 5 + 602619 ATTTG -s simDog_chr6.simDog.chr6 311021 5 + 593897 ATTTG -s simHuman_chr6.simHuman.chr6 330822 5 + 601863 ATGTG -s simRat_chr6.simRat.chr6 338023 5 + 647215 AATTG - -a -s simMouse_chr6.simMouse.chr6 346517 1 + 636262 A -s Anc0.Anc0refChr0 10438 1 + 26507 G -s Anc1.Anc1refChr6 10690 1 + 197743 G -s Anc2.Anc2refChr17 3643 1 + 28526 G -s mr.mrrefChr5 193999 1 + 294540 A -s simCow_chr6.simCow.chr6 319036 1 + 602619 A -s simDog_chr6.simDog.chr6 311033 1 + 593897 G -s simHuman_chr6.simHuman.chr6 330834 1 + 601863 G -s simRat_chr6.simRat.chr6 338028 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 346518 16 + 636262 ACGGAAGTGGAAGATT -s Anc0.Anc0refChr0 10439 16 + 26507 ACTGAAGCTAAAGATT -s Anc1.Anc1refChr6 10691 16 + 197743 ACTGAAGCTAAAGATT -s Anc2.Anc2refChr17 3648 16 + 28526 TCTGAAGCTAAAGATC -s mr.mrrefChr5 194000 16 + 294540 ACGGAAGTGGAAGATT -s simCow_chr6.simCow.chr6 319041 16 + 602619 ACTAAGCTTAAAGGTC -s simDog_chr6.simDog.chr6 311038 16 + 593897 TCTGAAGCCAAAGATT -s simHuman_chr6.simHuman.chr6 330835 16 + 601863 AGAGAAGCCCTCGATT -s simRat_chr6.simRat.chr6 338029 16 + 647215 ACTGAACTGGAAGATT - -a -s simMouse_chr6.simMouse.chr6 346534 16 + 636262 TCGGAAATGTAATGAA -s Anc0.Anc0refChr0 10455 13 + 26507 ---AAAAAATAATGAA -s Anc1.Anc1refChr6 10707 16 + 197743 CCGAAAAAATAATGAA -s Anc2.Anc2refChr17 3664 13 + 28526 ---AAAAAATATAAGG -s mr.mrrefChr5 194016 16 + 294540 TCGGAAATGTAATGAA -s simCow_chr6.simCow.chr6 319057 13 + 602619 ---AAAAAATATTAGG -s simDog_chr6.simDog.chr6 311054 13 + 593897 ---AAAAAGTATAAGG -s simHuman_chr6.simHuman.chr6 330876 16 + 601863 CCGAACAAATAATGAA -s simRat_chr6.simRat.chr6 338045 15 + 647215 -CAGAAATGTAATGAA - -a -s simMouse_chr6.simMouse.chr6 346550 22 + 636262 CATATTACTGACCATCAAAAAC -s Anc0.Anc0refChr0 10468 22 + 26507 CACATGGAAGACTACCTAAACT -s Anc1.Anc1refChr6 10723 22 + 197743 CACATGGAAGACTACCTAAACT -s Anc2.Anc2refChr17 3677 22 + 28526 GACATGGAACATTACCTAAACT -s mr.mrrefChr5 194032 22 + 294540 CATATTACTGACCATCAAAACC -s simCow_chr6.simCow.chr6 319070 22 + 602619 AATATGGAGTGTCAGCTTGATC -s simDog_chr6.simDog.chr6 311067 22 + 593897 GACATCAAACATTGCTTAAACT -s simHuman_chr6.simHuman.chr6 330899 22 + 601863 CACATGGAAGACTACCTAAACT -s simRat_chr6.simRat.chr6 338060 22 + 647215 CATATCACTGACCATCAAAACC - -a -s simMouse_chr6.simMouse.chr6 346572 1 + 636262 C -s Anc0.Anc0refChr0 10490 1 + 26507 C -s Anc1.Anc1refChr6 10745 1 + 197743 C -s Anc2.Anc2refChr17 3699 1 + 28526 C -s mr.mrrefChr5 194054 1 + 294540 C -s simCow_chr6.simCow.chr6 319095 1 + 602619 T -s simDog_chr6.simDog.chr6 311089 1 + 593897 C -s simHuman_chr6.simHuman.chr6 330921 1 + 601863 C -s simRat_chr6.simRat.chr6 338082 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 346573 23 + 636262 AGCTTTCTGAAGACATTGATAAA -s Anc0.Anc0refChr0 10508 22 + 26507 -GTTTTTTGTCAAGATTGATAAA -s Anc1.Anc1refChr6 10763 23 + 197743 AGTTTTTTGTCAAGATTGATAAA -s Anc2.Anc2refChr17 3717 22 + 28526 -GTTTTTTGTCAAGATTTATGAA -s mr.mrrefChr5 194055 23 + 294540 AGCTTTCTGAAGACATTGATAAA -s simCow_chr6.simCow.chr6 319113 16 + 602619 -G------GACAGGAATAATGAA -s simDog_chr6.simDog.chr6 311107 22 + 593897 -GTTTTTTGTTAAGATTTATGAA -s simHuman_chr6.simHuman.chr6 330939 23 + 601863 ATTTTTTTGGCAAGATTGATAAA -s simRat_chr6.simRat.chr6 338083 21 + 647215 AGCTTTC--AAGACATTGATATA - -a -s simMouse_chr6.simMouse.chr6 346596 10 + 636262 CTTCTAGTTA -s Anc0.Anc0refChr0 10530 10 + 26507 CCCCCAATTC -s Anc1.Anc1refChr6 10786 10 + 197743 CCCCCAATTC -s Anc2.Anc2refChr17 3739 10 + 28526 GCCCCAATCC -s mr.mrrefChr5 194078 10 + 294540 CTTCTAGTTA -s simCow_chr6.simCow.chr6 319141 10 + 602619 GCTGGGATAT -s simDog_chr6.simDog.chr6 311129 10 + 593897 GCCCCACCCC -s simHuman_chr6.simHuman.chr6 330962 10 + 601863 CCCCCAATTC -s simRat_chr6.simRat.chr6 338104 10 + 647215 CTTCTAGTTA - -a -s simMouse_chr6.simMouse.chr6 346606 13 + 636262 AACCTTGTAAGAA -s Anc0.Anc0refChr0 10540 13 + 26507 AAGCCAGTAATAA -s Anc1.Anc1refChr6 10796 13 + 197743 AAGCCAGTAATAA -s Anc2.Anc2refChr17 3749 13 + 28526 AAGACAGAAATAA -s mr.mrrefChr5 194088 13 + 294540 AAGCTTGTAAGAA -s simCow_chr6.simCow.chr6 319151 13 + 602619 AATACATAAATAA -s simDog_chr6.simDog.chr6 311164 13 + 593897 AAGACAGAAATAA -s simHuman_chr6.simHuman.chr6 330972 13 + 601863 AGGCCAGTGATAG -s simRat_chr6.simRat.chr6 338114 13 + 647215 CAGCTTATAAAAA - -a -s simMouse_chr6.simMouse.chr6 346619 16 + 636262 GGCAAAGACATGTGAT -s Anc0.Anc0refChr0 10556 16 + 26507 GGGAAAGACACATGAC -s Anc1.Anc1refChr6 10812 16 + 197743 GGGAAAGACACATGAC -s Anc2.Anc2refChr17 3765 16 + 28526 GGGGAAGACATAAGAC -s mr.mrrefChr5 194104 16 + 294540 GGCAAAGACACATGAT -s simCow_chr6.simCow.chr6 319167 16 + 602619 GGGGACGACCTGAGAC -s simDog_chr6.simDog.chr6 311180 16 + 593897 GGGGAAGACATAAGAC -s simHuman_chr6.simHuman.chr6 330988 16 + 601863 GGGATAGACACATGAC -s simRat_chr6.simRat.chr6 338130 16 + 647215 AGCAAAGACACATGAT - -a -s simMouse_chr6.simMouse.chr6 346635 58 + 636262 TGTTAAAATATTACATGTGATATCAGAAATTAGGTTAGATCCAAAATACTTGAGAAAA -s Anc0.Anc0refChr0 10572 44 + 26507 TATTCAAATATTACATATAACATCAGAAATTTGACTA--------------GAGATGA -s Anc1.Anc1refChr6 10828 44 + 197743 TATTCAAATATTACATATAACATCAGAAATTTGACTA--------------GAGATGA -s Anc2.Anc2refChr17 3782 44 + 28526 TATTCAAATATTACATATATCATCAGAAATTTGATTA--------------GAGATGA -s mr.mrrefChr5 194120 58 + 294540 TGTTAAAATATTACATGTAACATCAGAAATTAGACTAGATCCAAAATACTTGAGAAAA -s simCow_chr6.simCow.chr6 319184 44 + 602619 CATTCAGATACTGCATAAAGCATCAGAAATTTGATTA--------------GAGATCA -s simDog_chr6.simDog.chr6 311197 44 + 593897 TGTTCAATTATTACATCTTTCATCAGAAATCTGATTG--------------GAGATGA -s simHuman_chr6.simHuman.chr6 331004 44 + 601863 TATTCAAATATTACATATAACATCAGAAATTTGACTA--------------GAGATGA -s simRat_chr6.simRat.chr6 338146 58 + 647215 TGTCAAAATATCACATGTAACATCAGAAATTAGACTAGATCCAATATACTCGAGAAAA - -a -s simMouse_chr6.simMouse.chr6 346693 1 + 636262 G -s Anc0.Anc0refChr0 10616 1 + 26507 G -s Anc1.Anc1refChr6 10872 1 + 197743 G -s Anc2.Anc2refChr17 3826 1 + 28526 G -s mr.mrrefChr5 194178 1 + 294540 G -s simCow_chr6.simCow.chr6 319228 1 + 602619 G -s simDog_chr6.simDog.chr6 311272 1 + 593897 G -s simHuman_chr6.simHuman.chr6 331048 1 + 601863 G -s simRat_chr6.simRat.chr6 338204 1 + 647215 G - -a -s simMouse_chr6.simMouse.chr6 346694 40 + 636262 GATGTAGTATACCTCATCAAGTCTCATGTTTTATATGATG -s Anc0.Anc0refChr0 10617 40 + 26507 GATGTAGTATACCTCCCCAAGTTTCACATTTTGTTTCATG -s Anc1.Anc1refChr6 10873 40 + 197743 GATGTAGTATACCTCCCCAAGTTTCACATTTTGTTTCATG -s Anc2.Anc2refChr17 3827 40 + 28526 GATGTAGTATACCTCCCCAACTTTGACATTTTGTTTCATG -s mr.mrrefChr5 194179 40 + 294540 GATGTAGTATACCTCACCAAGTCTCATGTTTTATATGATG -s simCow_chr6.simCow.chr6 319245 40 + 602619 GATGTAATATACCTTCCCACATTTAACATTTTGTGTCATG -s simDog_chr6.simDog.chr6 311273 40 + 593897 GATGTAGTATCCCTCCCCAACGTTGACATTTTGTTTCATG -s simHuman_chr6.simHuman.chr6 331049 40 + 601863 GATGTTGTGTACCTCCCCAAGTGTCACATTTTGTTTCATG -s simRat_chr6.simRat.chr6 338205 40 + 647215 GATGTAGTATACCTCACCAATCCTCATGTTTTACATAATG - -a -s simMouse_chr6.simMouse.chr6 346734 2 + 636262 AG -s Anc0.Anc0refChr0 10662 2 + 26507 GC -s Anc1.Anc1refChr6 10918 2 + 197743 GC -s Anc2.Anc2refChr17 3872 2 + 28526 GC -s mr.mrrefChr5 194224 2 + 294540 AC -s simCow_chr6.simCow.chr6 319290 2 + 602619 GC -s simDog_chr6.simDog.chr6 311318 2 + 593897 GC -s simRat_chr6.simRat.chr6 338250 2 + 647215 AC - -a -s simMouse_chr6.simMouse.chr6 346736 10 + 636262 ATCAAGGTGA -s Anc0.Anc0refChr0 10664 10 + 26507 ATCAAGGCCA -s Anc1.Anc1refChr6 10920 10 + 197743 ATCAAGGCCA -s Anc2.Anc2refChr17 3877 10 + 28526 ATCAAGGCCT -s mr.mrrefChr5 194226 10 + 294540 ATCAAGGTGA -s simCow_chr6.simCow.chr6 319295 10 + 602619 ATCAAGGCCT -s simDog_chr6.simDog.chr6 311323 10 + 593897 ATCAAGGCCT -s simHuman_chr6.simHuman.chr6 197524 2 - 601863 --------AA -s simRat_chr6.simRat.chr6 338252 10 + 647215 ATCAAGGCGA - -a -s simMouse_chr6.simMouse.chr6 346746 96 + 636262 TAACAGAAGCAGCAAGCCCAAGTCATTTGCTTAGCTGGTTTAGGTCAAGGCAGGGCTCTTGAATAATACTTAACTCACTGACCAAAAACAAAAAAC -s Anc0.Anc0refChr0 10674 71 + 26507 TAAGGGGTGCAGCAAGCCTCAAACATTTGATTATCTTGCCTGAGA-----CTAGGTCCTTGATCAATACTCCATCC-------------------- -s Anc1.Anc1refChr6 10930 71 + 197743 TAAGGGGTGCAGCAAGCCTCAAACATTTGATTATCTTGCCTGAGA-----CTAGGTCCTTGATCAATACTCCATCC-------------------- -s Anc2.Anc2refChr17 3887 71 + 28526 TAAGGGGTGCAGCAAGGCTCAAACATTTGATTATCATGCCTGAGA-----CTAGGTCCTTGATCAATACTCCATCC-------------------- -s mr.mrrefChr5 194236 91 + 294540 TAACAGAAGCAGCAAGCCCAAGTCATTTGCTTAGCTGGTTTAGGT-----CAGGGCTCTTGAATAATACTTAACTCACTGACCAAAAACAAAAAAC -s simCow_chr6.simCow.chr6 319305 70 + 602619 TAAGGGGTGTAG-AAATCTCAGACATTTGATTATTGTCCATGGGA-----CTAGGTCTTGGCTCAATACTTCATCC-------------------- -s simDog_chr6.simDog.chr6 311335 71 + 593897 TAAGGGAAGCAGCAAGGATTAAACATTCGATTAGCATGCCTGAGA-----CTAGGTTCTTGATCAATACTCCACCC-------------------- -s simHuman_chr6.simHuman.chr6 197526 71 - 601863 TAAGGGGTGCAGCAAGCCTCAAATATTTTATTATCTAGCCTGAGA-----CCAGGTCCTTGATCAAGACTCGATCC-------------------- -s simRat_chr6.simRat.chr6 338262 91 + 647215 TAACAGCGACAGCGAGTCCAAGTTATTTGCTTAACTGACTTGAGT-----CATGACTCTTGATTAATACTTAACTCACTGACCCATTAAAAATATC - -a -s simMouse_chr6.simMouse.chr6 346842 46 + 636262 AATCCAGGCAGCACACATACACTGTTCGCAGAGTCCCCGTACCCAG -s mr.mrrefChr5 194327 41 + 294540 AATCCAGGCAGCACACATACACTGTT----GAGT-CCCGTACCCAG -s simRat_chr6.simRat.chr6 338369 41 + 647215 CATGCAGAGAGTATACACATAATCTT----GAGT-TTCGTATCGAG - -a -s simMouse_chr6.simMouse.chr6 346888 49 + 636262 GGACTCACATGTAGGATTCATATGCGCAACATAATGAATATAGGGCCAT -s Anc0.Anc0refChr0 10745 9 + 26507 --------------------------------------CAGA--TCCAT -s Anc1.Anc1refChr6 11001 9 + 197743 --------------------------------------CAGA--TCCAT -s Anc2.Anc2refChr17 3984 9 + 28526 --------------------------------------CAGA--TCCAT -s mr.mrrefChr5 194368 43 + 294540 GGACTCACAT----GATTCATATGCGCAACATAATGAATATA--GCCAT -s simCow_chr6.simCow.chr6 319401 9 + 602619 --------------------------------------CATA--TCCAT -s simDog_chr6.simDog.chr6 311432 9 + 593897 --------------------------------------CAGA--TCCAT -s simHuman_chr6.simHuman.chr6 197597 9 - 601863 --------------------------------------CACA--TCCAT -s simRat_chr6.simRat.chr6 338411 43 + 647215 AGACCCTGAT----AACTCAAATAGTCCAGGTAACACACATA--ACCAT - -a -s simMouse_chr6.simMouse.chr6 346937 5 + 636262 GGTGG -s Anc0.Anc0refChr0 10754 5 + 26507 GATGG -s Anc1.Anc1refChr6 11010 5 + 197743 GATGG -s Anc2.Anc2refChr17 3993 5 + 28526 GATGG -s mr.mrrefChr5 194411 5 + 294540 GGTGG -s simCow_chr6.simCow.chr6 319410 5 + 602619 GATCA -s simDog_chr6.simDog.chr6 311442 5 + 593897 GGGGG -s simHuman_chr6.simHuman.chr6 197606 5 - 601863 GATTG -s simRat_chr6.simRat.chr6 338454 5 + 647215 GGTGG - -a -s simMouse_chr6.simMouse.chr6 346942 18 + 636262 CCCTATAAAAATGGTCTA -s Anc0.Anc0refChr0 10759 18 + 26507 CCCTATACAAAGGGTATA -s Anc1.Anc1refChr6 11015 18 + 197743 CCCTATACAAAGGGTATA -s Anc2.Anc2refChr17 3998 18 + 28526 CCCTATACAAAGGGTATA -s mr.mrrefChr5 194416 18 + 294540 CCCTATAAAAATGGTCTA -s simCow_chr6.simCow.chr6 319417 18 + 602619 CCCTATATAAAGGATATA -s simDog_chr6.simDog.chr6 311447 18 + 593897 CCCTATACAAAGGGTATA -s simHuman_chr6.simHuman.chr6 197611 18 - 601863 CCCTACTCAAAGGGTATA -s simRat_chr6.simRat.chr6 338459 18 + 647215 CCCTATAAAAGGGGGTCC - -a -s simMouse_chr6.simMouse.chr6 346960 4 + 636262 AAGT -s Anc0.Anc0refChr0 10777 4 + 26507 AAGT -s Anc1.Anc1refChr6 11033 4 + 197743 AAGT -s Anc2.Anc2refChr17 4016 4 + 28526 AAGT -s mr.mrrefChr5 194434 4 + 294540 AAGT -s simCow_chr6.simCow.chr6 319435 2 + 602619 AA-- -s simDog_chr6.simDog.chr6 311465 4 + 593897 GAGT -s simHuman_chr6.simHuman.chr6 331101 4 + 601863 AAAT -s simRat_chr6.simRat.chr6 338477 4 + 647215 AAGT - -a -s simMouse_chr6.simMouse.chr6 346964 2 + 636262 GA -s Anc0.Anc0refChr0 10781 2 + 26507 GA -s Anc1.Anc1refChr6 11037 2 + 197743 GA -s Anc2.Anc2refChr17 4020 2 + 28526 AA -s mr.mrrefChr5 194438 2 + 294540 GA -s simDog_chr6.simDog.chr6 311473 2 + 593897 AA -s simHuman_chr6.simHuman.chr6 331105 2 + 601863 GC -s simRat_chr6.simRat.chr6 338481 2 + 647215 GA - -a -s simMouse_chr6.simMouse.chr6 346966 5 + 636262 AGTTC -s Anc0.Anc0refChr0 10783 5 + 26507 TTATT -s Anc1.Anc1refChr6 11039 5 + 197743 TTATT -s Anc2.Anc2refChr17 4022 5 + 28526 TTACT -s mr.mrrefChr5 194440 5 + 294540 AGTTC -s simCow_chr6.simCow.chr6 319437 5 + 602619 CTAGT -s simDog_chr6.simDog.chr6 311478 5 + 593897 TGACT -s simHuman_chr6.simHuman.chr6 331107 5 + 601863 TTATG -s simRat_chr6.simRat.chr6 338483 5 + 647215 AGTTC - -a -s simMouse_chr6.simMouse.chr6 346971 206 + 636262 AACCCCTTTGACCTGAACAATGTTTGCTTACTGACAATCAGGTCATGCCACAGTCCAAATCGTGGATTCTCAGAGTTACAGGATTGATGGTATGAAGCTTTCCTAGACACTGATATTTTTAGAGGTGGCTGCAATGAGGCTTCCATACCTTATTCCCATAGGTAGAAGAAGCTGCTGGGTTATTTATGGGGGACAAGACCCTGGTG -s Anc0.Anc0refChr0 10788 44 + 26507 GACTCCATCA------------------------------------------------------------------------------------------------------------------------------------------------------------------TGTCAGGCCATTTGTGGGGTACATGACACTTGTG -s Anc1.Anc1refChr6 11044 44 + 197743 GACTCCATCA------------------------------------------------------------------------------------------------------------------------------------------------------------------TGTCAGGCCATTTGTGGGGTACATGACACTTGTG -s Anc2.Anc2refChr17 4027 44 + 28526 GACTCCATCA------------------------------------------------------------------------------------------------------------------------------------------------------------------TGTCAGGCCACTTGAGGGGTACATGACACTTGGG -s mr.mrrefChr5 194445 44 + 294540 AACCCCTTTG------------------------------------------------------------------------------------------------------------------------------------------------------------------TGCTGGGTTATTTATGGGGGACAAGACCCTGGTG -s simCow_chr6.simCow.chr6 319442 34 + 602619 AACTCC-TCA------------------------------------------------------------------------------------------------------------------------------------------------------------------TGTCAGGCCATACGGGGTGTAAATG--------- -s simDog_chr6.simDog.chr6 311483 44 + 593897 GACGCCACCA------------------------------------------------------------------------------------------------------------------------------------------------------------------TCTCAGGCCACTTGAGGGGTACATGACACTTGGG -s simHuman_chr6.simHuman.chr6 331112 41 + 601863 GACTCTATGT------------------------------------------------------------------------------------------------------------------------------------------------------------------GGTCAG---CTATGTGGGGTATAGGACACTCGTG -s simRat_chr6.simRat.chr6 338490 44 + 647215 AAACCCATTG------------------------------------------------------------------------------------------------------------------------------------------------------------------TGCTGCGTTATTTATGGGGAACAAGACGCTTGTA - -a -s simMouse_chr6.simMouse.chr6 347177 2 + 636262 TG -s Anc0.Anc0refChr0 10832 2 + 26507 TA -s Anc1.Anc1refChr6 11088 2 + 197743 TA -s Anc2.Anc2refChr17 4074 2 + 28526 TA -s mr.mrrefChr5 194489 2 + 294540 TG -s simDog_chr6.simDog.chr6 311530 2 + 593897 TA -s simHuman_chr6.simHuman.chr6 331153 2 + 601863 GC -s simRat_chr6.simRat.chr6 338534 2 + 647215 GG - -a -s simMouse_chr6.simMouse.chr6 347179 2 + 636262 TA -s Anc0.Anc0refChr0 10834 2 + 26507 TA -s Anc1.Anc1refChr6 11090 2 + 197743 TA -s Anc2.Anc2refChr17 4076 2 + 28526 TT -s mr.mrrefChr5 194491 2 + 294540 TA -s simDog_chr6.simDog.chr6 311532 2 + 593897 TT -s simHuman_chr6.simHuman.chr6 331155 2 + 601863 TA -s simRat_chr6.simRat.chr6 338541 2 + 647215 CA - -a -s simMouse_chr6.simMouse.chr6 347181 4 + 636262 GAAA -s Anc0.Anc0refChr0 10836 4 + 26507 GAAA -s Anc1.Anc1refChr6 11092 4 + 197743 GAAA -s Anc2.Anc2refChr17 4078 4 + 28526 GGGG -s mr.mrrefChr5 194493 4 + 294540 GAAA -s simDog_chr6.simDog.chr6 311534 4 + 593897 GGGG -s simHuman_chr6.simHuman.chr6 331170 4 + 601863 GAAA -s simRat_chr6.simRat.chr6 338543 4 + 647215 GAAA - -a -s simMouse_chr6.simMouse.chr6 347185 37 + 636262 ACATTGAAATAACCGCATTGATCACTGCCAAACTCCA -s Anc0.Anc0refChr0 10852 34 + 26507 TCATAGAACGAACCATATTGATCAGCCCCAAACT--- -s Anc1.Anc1refChr6 11108 34 + 197743 TCATAGAACGAACCATATTGATCAGCCCCAAACT--- -s Anc2.Anc2refChr17 4094 34 + 28526 TCATAGAACGAACCATGTCAACCCGCCCCGAGCT--- -s mr.mrrefChr5 194497 37 + 294540 ACATTGAAATAACCGCATTGATCACTGCCAAACTCCA -s simDog_chr6.simDog.chr6 311551 34 + 593897 TCATAGAACGAACCATGTCAACCCGCCCCGAGCT--- -s simHuman_chr6.simHuman.chr6 331186 34 + 601863 TCACAGTACCAAACATATTGGTCAACCCCAAACT--- -s simRat_chr6.simRat.chr6 338547 37 + 647215 ACATTGAAATAACCACATTGACCAATACCAAACTCCA - -a -s simMouse_chr6.simMouse.chr6 347222 36 + 636262 TTTCAAAGGGCTATTGGAAAACCGTTCAATCGGAAA -s Anc0.Anc0refChr0 10886 23 + 26507 TTT--------GATAGGGAAGCTGTT-----GGAAC -s Anc1.Anc1refChr6 11142 23 + 197743 TTT--------GATAGGGAAGCTGTT-----GGAAC -s Anc2.Anc2refChr17 4128 23 + 28526 TTT--------GATAGGGAAGCTGTC-----GGGAC -s mr.mrrefChr5 194534 36 + 294540 TTTCAAAGGGCTATTGGAAAACCGTTCAATCGGAAA -s simDog_chr6.simDog.chr6 311588 23 + 593897 TTT--------GATAGGGAAGCTGTC-----GGGAC -s simHuman_chr6.simHuman.chr6 331220 23 + 601863 TTT--------GATGGGGAAGCTGTT-----GGAAC -s simRat_chr6.simRat.chr6 338584 36 + 647215 TTTCGAGGGGCTATTGGAAAACTGTTAGATCAGAAA - -a -s simMouse_chr6.simMouse.chr6 347258 46 + 636262 AGGTGGTTTTAAGTAATGGTGATGCAGGATTACTGGGATGAATCCA -s Anc0.Anc0refChr0 10909 37 + 26507 CAGT-GTTCTAAGT-ATGGAGATGTTGGATATGT-------ATGGA -s Anc1.Anc1refChr6 11165 44 + 197743 CAGT-GTTCTAAGT-ATGGAGATGTTGGATATGTTGGATGAATGGA -s Anc2.Anc2refChr17 4151 37 + 28526 CAAT-GTTCTAAGT-ACGGAGATGTTGGATATGC-------ATGGG -s mr.mrrefChr5 194570 46 + 294540 AGGTGGTTTTAAGTAATGGTGATGCAGGATTACTGGGATGAATCCA -s simDog_chr6.simDog.chr6 311612 37 + 593897 CAAT-GTTCTAAGT-ACGGAGATGTTGGATATGC-------ATGGG -s simHuman_chr6.simHuman.chr6 331243 44 + 601863 CAGT-GTTATAAGT-ATGAAGATAGTGGAAATGTTGGATAAATGGA -s simRat_chr6.simRat.chr6 338620 46 + 647215 AGGATATTTTTAGTAATGGAGATGTAGGATCACTGAGATGAATCCA - -a -s simMouse_chr6.simMouse.chr6 347304 50 + 636262 GGTGCTGGGCAGTAGAAAAGTCACTATCTTTAAAAAATAGTAAAAACAGG -s Anc0.Anc0refChr0 10955 49 + 26507 TATGTTAAGTAA-ATGCAAGCCTTTATCTGTAACAAATAATGACAATGGG -s Anc1.Anc1refChr6 11218 49 + 197743 TATGTTAAGTAA-ATGCAAGCCTTTATCTGTAACAAATAATGACAATGGG -s Anc2.Anc2refChr17 4197 49 + 28526 TATGTTAAGTAA-GTGCAAGCCTTTAGCTGTAACAGATAATGACAATGGA -s mr.mrrefChr5 194616 50 + 294540 GGTGCTGGGCAGTAGAAAAGTCACTATCTTTAAAAAATAGTAAAAACAGG -s simDog_chr6.simDog.chr6 311658 49 + 593897 TATGTTAAGTAA-GTGCAAGCCTTTAGCTGTAACAGATAATGACAATGGA -s simHuman_chr6.simHuman.chr6 331296 49 + 601863 TTTGTCAAATAA-ATGGAAGCCTTAATCCGTAGCAAATAATGACAATGGG -s simRat_chr6.simRat.chr6 338666 50 + 647215 GCTGCAAGGCAGTAAAAAAGCCACTATCTTTGAAAAATAGTAAAAATGGG - -a -s simMouse_chr6.simMouse.chr6 347354 22 + 636262 AATAGTCTTCCAGAAAGTCACT -s Anc0.Anc0refChr0 11005 18 + 26507 CA----CTTCCAAGGAGTGATT -s Anc1.Anc1refChr6 11268 18 + 197743 CA----CTTCCAAGGAGTGATT -s Anc2.Anc2refChr17 4247 18 + 28526 CA----TTTCCAAGGAGTGATT -s mr.mrrefChr5 194666 18 + 294540 AA----CTTCCAGAAAGTCACT -s simDog_chr6.simDog.chr6 311708 18 + 593897 CA----TTTCCAAGGAGTGATT -s simHuman_chr6.simHuman.chr6 331346 18 + 601863 GA----CTTCCAAGGAGTTATC -s simRat_chr6.simRat.chr6 338716 18 + 647215 TG----CTTCCAGAAAGTCATT - -a -s simMouse_chr6.simMouse.chr6 347376 2 + 636262 GG -s Anc0.Anc0refChr0 11023 2 + 26507 GG -s Anc1.Anc1refChr6 11286 2 + 197743 GG -s Anc2.Anc2refChr17 4265 2 + 28526 TG -s mr.mrrefChr5 194684 2 + 294540 GG -s simDog_chr6.simDog.chr6 311726 2 + 593897 TG -s simHuman_chr6.simHuman.chr6 331377 2 + 601863 GG -s simRat_chr6.simRat.chr6 338734 2 + 647215 GG - -a -s simMouse_chr6.simMouse.chr6 347378 36 + 636262 CTGATAACTTGGGAAACATCTTTGCCATGTACTGGG -s Anc0.Anc0refChr0 11025 34 + 26507 CTGACAACTGGGGAAACATCTTTGCTATCTACT--T -s Anc1.Anc1refChr6 11288 34 + 197743 CTGACAACTGGGGAAACATCTTTGCTATCTACT--T -s Anc2.Anc2refChr17 4271 34 + 28526 CTGACAACTGGGGAAACATCTTTGCTATCTACT--T -s mr.mrrefChr5 194686 36 + 294540 CTGATAACTTGGGAAACATCTTTGCCATGTACTGGG -s simCow_chr6.simCow.chr6 319476 24 + 602619 ----------GGGGAACATCTTTGCTATCTACT--T -s simDog_chr6.simDog.chr6 311732 33 + 593897 CTGACAACTGGGGACACAATTCTGCTATCTACT--- -s simHuman_chr6.simHuman.chr6 331379 34 + 601863 CTGACAACTGGGGAAACATCTTTGCTATTTACT--C -s simRat_chr6.simRat.chr6 338736 36 + 647215 TTGATGACTGGGGAAACATCTTTGCCAAGTACTGGG - -a -s simMouse_chr6.simMouse.chr6 347414 20 + 636262 CCATTAGGTCGGGCTCATTC -s Anc0.Anc0refChr0 11059 20 + 26507 CCATTAGATGGCTTTCATGC -s Anc1.Anc1refChr6 11322 20 + 197743 CCATTAGATGGCTTTCATGC -s Anc2.Anc2refChr17 4305 20 + 28526 CCATCAGATGGCTTTTATGC -s mr.mrrefChr5 194722 20 + 294540 CCATTAGGTCGGGCTCATTC -s simCow_chr6.simCow.chr6 319502 20 + 602619 CCATCAGATGGCTTTTATTC -s simDog_chr6.simDog.chr6 311765 3 + 593897 -----------------TGG -s simHuman_chr6.simHuman.chr6 331413 20 + 601863 CCATTAGATGATTTTCATAC -s simRat_chr6.simRat.chr6 338772 20 + 647215 CCATTAGATTGCGCTCATCC - -a -s simMouse_chr6.simMouse.chr6 347434 8 + 636262 ACAAGCAC -s Anc0.Anc0refChr0 11088 8 + 26507 ACAGGCAC -s Anc1.Anc1refChr6 11351 8 + 197743 ACAGGCAC -s Anc2.Anc2refChr17 4334 8 + 28526 ACAGGCAC -s mr.mrrefChr5 194742 8 + 294540 ACAAGCAC -s simCow_chr6.simCow.chr6 319531 8 + 602619 ACAGGCAT -s simDog_chr6.simDog.chr6 311777 8 + 593897 ATAGGCAC -s simHuman_chr6.simHuman.chr6 331442 8 + 601863 ACAGACAG -s simRat_chr6.simRat.chr6 338792 8 + 647215 ACAAGCAC - -a -s simMouse_chr6.simMouse.chr6 347442 1 + 636262 A -s Anc0.Anc0refChr0 11096 1 + 26507 A -s Anc1.Anc1refChr6 11359 1 + 197743 A -s Anc2.Anc2refChr17 4342 1 + 28526 A -s mr.mrrefChr5 194750 1 + 294540 A -s simCow_chr6.simCow.chr6 319539 1 + 602619 G -s simDog_chr6.simDog.chr6 311785 1 + 593897 A -s simHuman_chr6.simHuman.chr6 331450 1 + 601863 A -s simRat_chr6.simRat.chr6 338825 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 347443 23 + 636262 TTAAAAAAATTCCTAGTCAGAGT -s Anc0.Anc0refChr0 11102 15 + 26507 ATAGAAAAATACCTA-------- -s Anc1.Anc1refChr6 11365 23 + 197743 ATAGAAAAATACCTAGCAACACC -s Anc2.Anc2refChr17 4348 15 + 28526 ATAGAAAAATACCTA-------- -s mr.mrrefChr5 194751 23 + 294540 TTAAAAAAATTCCTAGTCAGAGT -s simCow_chr6.simCow.chr6 319545 11 + 602619 ATA----AATACCTA-------- -s simDog_chr6.simDog.chr6 311791 15 + 593897 ATAGAAAAATACCTA-------- -s simHuman_chr6.simHuman.chr6 331456 23 + 601863 GTAGAAAAACACCTAGCAACACC -s simRat_chr6.simRat.chr6 338826 23 + 647215 TTAAAAAAATTCCTAGTCATACT - -a -s simMouse_chr6.simMouse.chr6 347466 13 + 636262 ACTAAATTAAGAT -s Anc0.Anc0refChr0 11117 13 + 26507 GCTAAACCAATAA -s Anc1.Anc1refChr6 11388 13 + 197743 GCTAAACCAATAA -s Anc2.Anc2refChr17 4363 13 + 28526 GCTAAGCCAATAA -s mr.mrrefChr5 194774 13 + 294540 ACTAAATTAAGAT -s simCow_chr6.simCow.chr6 319556 13 + 602619 GCTCCGTCTCTAG -s simDog_chr6.simDog.chr6 311806 13 + 593897 GCTAAGCAAATGA -s simHuman_chr6.simHuman.chr6 331481 13 + 601863 GCTATACCATTAA -s simRat_chr6.simRat.chr6 338849 13 + 647215 ACTAAATTAAGAT - -a -s simMouse_chr6.simMouse.chr6 347479 56 + 636262 GAGAATTATAATGCGGTGTCCTGCTTGTAGGTCGTCTAAGAGTATAGCTAACAATG -s Anc0.Anc0refChr0 11130 53 + 26507 GAAATATGAAGTGCGGTGT--T-TTAAAAGGTTGTGTAGCAGCATAACTAGAGATG -s Anc1.Anc1refChr6 11401 54 + 197743 GAAATATGAAGTGCGGTGT--TGTTAAAAGGTTGTGTAGCAGCATAACTAGAGATG -s Anc2.Anc2refChr17 4376 53 + 28526 GAAATATGAGGTGCGGTGT--T-TTAAAAGGTTGTGTAGCAGCATAACTAGAGATG -s mr.mrrefChr5 194787 56 + 294540 GAGAATTATAATGCGGTGTCCTGCTTGTAGGTCGTCTAAGAGTATAGCTAACAATG -s simCow_chr6.simCow.chr6 319569 46 + 602619 GAAAT-------GTGGTGT--A-TAAAAAGGTTGTGTAGCAGCATAACTAAAGATG -s simDog_chr6.simDog.chr6 311819 53 + 593897 GAATTATGAGGTGCTGTGT--T-TTAGACAGTTGTGTGGCAGCATAAATAGAGATG -s simHuman_chr6.simHuman.chr6 331494 54 + 601863 AAAATGCGAATTACGGGAT--TGTTAAAAGGTTGGGTAGCAGCATAACTAGAGTTG -s simRat_chr6.simRat.chr6 338883 56 + 647215 AAGAACTATAACGTGGTGGCCTGTTAGTAGGTTGTTTAAGAGCACAGCTAAAGATG - -a -s simMouse_chr6.simMouse.chr6 347535 5 + 636262 TTCTA -s Anc0.Anc0refChr0 11364 5 + 26507 TTCTA -s Anc1.Anc1refChr6 11636 5 + 197743 TTCTA -s Anc2.Anc2refChr17 4641 5 + 28526 TCCTA -s mr.mrrefChr5 194843 5 + 294540 TTCTA -s simCow_chr6.simCow.chr6 319930 5 + 602619 TCCTA -s simDog_chr6.simDog.chr6 312083 1 + 593897 ----A -s simHuman_chr6.simHuman.chr6 331730 5 + 601863 TTCTA -s simRat_chr6.simRat.chr6 338939 5 + 647215 TTCTA - -a -s simMouse_chr6.simMouse.chr6 347540 2 + 636262 TT -s Anc0.Anc0refChr0 11372 2 + 26507 TT -s Anc1.Anc1refChr6 11644 2 + 197743 TT -s Anc2.Anc2refChr17 4649 2 + 28526 TT -s mr.mrrefChr5 194848 2 + 294540 TT -s simCow_chr6.simCow.chr6 319938 2 + 602619 TT -s simDog_chr6.simDog.chr6 312087 2 + 593897 TT -s simHuman_chr6.simHuman.chr6 331738 2 + 601863 TT -s simRat_chr6.simRat.chr6 338944 2 + 647215 CT - -a -s simMouse_chr6.simMouse.chr6 347542 13 + 636262 GTGGTTGGGTTTT -s Anc0.Anc0refChr0 11374 13 + 26507 GTGGTCAGGTTTT -s Anc1.Anc1refChr6 11646 13 + 197743 GTGGTCAGGTTTT -s Anc2.Anc2refChr17 4651 13 + 28526 GTAGTCAGATTTT -s mr.mrrefChr5 194850 13 + 294540 GTGGTTGGGTTTT -s simCow_chr6.simCow.chr6 319940 13 + 602619 GTAGTTAGTTTTT -s simDog_chr6.simDog.chr6 312089 13 + 593897 GTAGTCAGATTTT -s simHuman_chr6.simHuman.chr6 331740 13 + 601863 GAGGTCCGGTTTT -s simRat_chr6.simRat.chr6 338954 13 + 647215 GTGGTTGAGTTTT - -a -s simMouse_chr6.simMouse.chr6 347555 2 + 636262 CC -s Anc0.Anc0refChr0 11388 2 + 26507 TC -s Anc1.Anc1refChr6 11660 2 + 197743 TC -s Anc2.Anc2refChr17 4665 2 + 28526 TC -s mr.mrrefChr5 194864 2 + 294540 CC -s simCow_chr6.simCow.chr6 319954 2 + 602619 CC -s simDog_chr6.simDog.chr6 312103 1 + 593897 T- -s simHuman_chr6.simHuman.chr6 331754 2 + 601863 TC -s simRat_chr6.simRat.chr6 338968 2 + 647215 CC - -a -s simMouse_chr6.simMouse.chr6 347557 28 + 636262 TGAAGCATACTACTAGCACGAACCCAAT -s Anc0.Anc0refChr0 11392 25 + 26507 ACAACTATACCACTAGAGTCAACT---T -s Anc1.Anc1refChr6 11664 25 + 197743 ACAACTATACCACTAGAGTCAACT---T -s Anc2.Anc2refChr17 4669 25 + 28526 ATAACTATATCACTAGAGTCAACT---T -s mr.mrrefChr5 194866 28 + 294540 TCAAGCATACCACTAGCATGAACTCAAT -s simCow_chr6.simCow.chr6 319958 25 + 602619 GTGAGCATATCACTTGAGTCAACT---T -s simDog_chr6.simDog.chr6 312106 16 + 593897 ATAACTTCATTATGAG------------ -s simHuman_chr6.simHuman.chr6 331758 25 + 601863 ACAAATATGCCACTAAAGTCGACC---T -s simRat_chr6.simRat.chr6 338970 28 + 647215 TCAAACATACCACTAGCATTAACTCATT - -a -s simMouse_chr6.simMouse.chr6 347585 7 + 636262 TGCGGAT -s Anc0.Anc0refChr0 11417 7 + 26507 CTTGGAT -s Anc1.Anc1refChr6 11689 7 + 197743 CTTGGAT -s Anc2.Anc2refChr17 4694 7 + 28526 CTTGGAT -s mr.mrrefChr5 194894 7 + 294540 TTTGGAT -s simCow_chr6.simCow.chr6 319986 7 + 602619 CTTGGAT -s simDog_chr6.simDog.chr6 312122 5 + 593897 --TGGAT -s simHuman_chr6.simHuman.chr6 331783 7 + 601863 CTTGGAT -s simRat_chr6.simRat.chr6 338998 7 + 647215 TTTGGGT - -a -s simMouse_chr6.simMouse.chr6 347592 4 + 636262 ACCA -s Anc0.Anc0refChr0 11429 4 + 26507 ACAA -s Anc1.Anc1refChr6 11701 4 + 197743 ACAA -s Anc2.Anc2refChr17 4706 4 + 28526 AGAA -s mr.mrrefChr5 194901 4 + 294540 ACCA -s simCow_chr6.simCow.chr6 319998 4 + 602619 AGAA -s simDog_chr6.simDog.chr6 312132 4 + 593897 AGAA -s simHuman_chr6.simHuman.chr6 331795 4 + 601863 ACAA -s simRat_chr6.simRat.chr6 339005 4 + 647215 ACCA - -a -s simMouse_chr6.simMouse.chr6 347596 11 + 636262 AAATTATTCCA -s Anc0.Anc0refChr0 11434 11 + 26507 AAATTATTCAC -s Anc1.Anc1refChr6 11706 11 + 197743 AAATTATTCAC -s Anc2.Anc2refChr17 4711 11 + 28526 AAATTATTTAC -s mr.mrrefChr5 194905 11 + 294540 AAATTATTCCA -s simCow_chr6.simCow.chr6 320003 11 + 602619 AGATTATTTCC -s simDog_chr6.simDog.chr6 312137 11 + 593897 AAATTGTTTAC -s simHuman_chr6.simHuman.chr6 331800 11 + 601863 AAATAATTCTC -s simRat_chr6.simRat.chr6 339009 11 + 647215 AAATCATTCCA - -a -s simMouse_chr6.simMouse.chr6 347607 14 + 636262 AGGTCCTTTCTAGC -s Anc0.Anc0refChr0 11446 14 + 26507 AGGCTCTTTCTACC -s Anc1.Anc1refChr6 11718 14 + 197743 AGGCTCTTTCTACC -s Anc2.Anc2refChr17 4723 14 + 28526 AAACTCTTTCTACC -s mr.mrrefChr5 194916 14 + 294540 AGGTCCTTTCTAGC -s simCow_chr6.simCow.chr6 320015 14 + 602619 AAACTCTTTCTATC -s simDog_chr6.simDog.chr6 312149 14 + 593897 AAAGTTTTTCTACC -s simHuman_chr6.simHuman.chr6 331815 14 + 601863 AGGCTCCTTCCCCC -s simRat_chr6.simRat.chr6 339020 14 + 647215 AGGTCCTTTCTAGC - -a -s simMouse_chr6.simMouse.chr6 347621 2 + 636262 AA -s Anc0.Anc0refChr0 11460 2 + 26507 AA -s Anc1.Anc1refChr6 11732 2 + 197743 AA -s Anc2.Anc2refChr17 4737 2 + 28526 AA -s mr.mrrefChr5 194930 2 + 294540 AA -s simCow_chr6.simCow.chr6 320029 2 + 602619 AA -s simDog_chr6.simDog.chr6 312163 2 + 593897 AA -s simHuman_chr6.simHuman.chr6 331829 2 + 601863 AA -s simRat_chr6.simRat.chr6 339035 2 + 647215 AA - -a -s simMouse_chr6.simMouse.chr6 347623 14 + 636262 GCTTAAACTATTGT -s Anc0.Anc0refChr0 11470 14 + 26507 GTTTCAACCATTGG -s Anc1.Anc1refChr6 11742 14 + 197743 GTTTCAACCATTGG -s Anc2.Anc2refChr17 4747 14 + 28526 ATTTCAACCATTGG -s mr.mrrefChr5 194932 14 + 294540 GCTTCAACCATTGT -s simCow_chr6.simCow.chr6 320039 14 + 602619 CCTTCAACCATTTG -s simDog_chr6.simDog.chr6 312173 14 + 593897 ATCCCAATCATAGT -s simHuman_chr6.simHuman.chr6 331839 14 + 601863 GTTTCAACCATTGG -s simRat_chr6.simRat.chr6 339037 14 + 647215 GCTTCAACCATTGT - -a -s simMouse_chr6.simMouse.chr6 347637 5 + 636262 CTCAC -s Anc0.Anc0refChr0 11484 5 + 26507 CCTAC -s Anc1.Anc1refChr6 11756 5 + 197743 CCTAC -s Anc2.Anc2refChr17 4761 5 + 28526 CCTAC -s mr.mrrefChr5 194946 5 + 294540 CTCAC -s mr.mrrefChr5 195411 5 + 294540 CCTGG -s simCow_chr6.simCow.chr6 320053 5 + 602619 TCTAC -s simDog_chr6.simDog.chr6 312187 5 + 593897 CCTAT -s simHuman_chr6.simHuman.chr6 331853 5 + 601863 CCCAC -s simMouse_chr6.simMouse.chr6 348101 5 + 636262 CCTGG -s simRat_chr6.simRat.chr6 339528 5 + 647215 TCTGG -s simRat_chr6.simRat.chr6 339051 5 + 647215 CTCAC - -a -s simMouse_chr6.simMouse.chr6 347642 8 + 636262 TACCTTTG -s Anc0.Anc0refChr0 11491 8 + 26507 TACCTTCA -s Anc1.Anc1refChr6 11763 8 + 197743 TACCTTCA -s Anc2.Anc2refChr17 4768 8 + 28526 TACCTTCA -s mr.mrrefChr5 194951 8 + 294540 TACCTTTG -s mr.mrrefChr5 195416 8 + 294540 TGCCTTTG -s simCow_chr6.simCow.chr6 320060 8 + 602619 TACCTTCA -s simDog_chr6.simDog.chr6 312194 8 + 593897 TACCTTTG -s simHuman_chr6.simHuman.chr6 331860 8 + 601863 TTCCTTCA -s simMouse_chr6.simMouse.chr6 348106 8 + 636262 TGCCTTTG -s simRat_chr6.simRat.chr6 339533 8 + 647215 TGCCTTTT -s simRat_chr6.simRat.chr6 339056 8 + 647215 CACCTTTG - -a -s simMouse_chr6.simMouse.chr6 347650 15 + 636262 TACTTAGGGACAAAC -s Anc0.Anc0refChr0 11500 15 + 26507 TGCTGATGGACAAAC -s Anc1.Anc1refChr6 11772 15 + 197743 TGCTGATGGACAAAC -s Anc2.Anc2refChr17 4777 15 + 28526 TGCTGATGGACAAAC -s mr.mrrefChr5 194959 15 + 294540 TACTTAGGGACAAAC -s mr.mrrefChr5 195425 15 + 294540 TACTGATGGACAAAC -s simCow_chr6.simCow.chr6 320069 15 + 602619 TACTCATGGACAATA -s simDog_chr6.simDog.chr6 312203 15 + 593897 TGCTGATGGTCAAAC -s simHuman_chr6.simHuman.chr6 331869 15 + 601863 TGCTGATGGACAAAC -s simMouse_chr6.simMouse.chr6 348115 15 + 636262 TACTGATGGACAAAC -s simRat_chr6.simRat.chr6 339542 15 + 647215 TACTGATGGACAAAC -s simRat_chr6.simRat.chr6 339064 15 + 647215 TACTTAGGGACAAAT - -a -s simMouse_chr6.simMouse.chr6 347665 15 + 636262 TTGATGTGACTTCTG -s Anc0.Anc0refChr0 11515 15 + 26507 TTGGCACAACTTCCA -s Anc1.Anc1refChr6 11787 15 + 197743 TTGGCACAACTTCCA -s Anc2.Anc2refChr17 4792 15 + 28526 TCGGCACAACTTCCA -s mr.mrrefChr5 194974 15 + 294540 TTGGTGTAACTTCTG -s mr.mrrefChr5 195451 15 + 294540 CTGGTGCACCTACTA -s simCow_chr6.simCow.chr6 320084 15 + 602619 TCGGCATAGCTTCTA -s simDog_chr6.simDog.chr6 312218 15 + 593897 TCAGCACAACTTCCA -s simHuman_chr6.simHuman.chr6 331884 15 + 601863 TTGGCACAACTTCCA -s simMouse_chr6.simMouse.chr6 348141 15 + 636262 CTGGTGCACTTACTG -s simRat_chr6.simRat.chr6 339568 15 + 647215 CTGGGGCACCTACTA -s simRat_chr6.simRat.chr6 339079 15 + 647215 TTGGTGCAACTTCTG - -a -s simMouse_chr6.simMouse.chr6 347680 12 + 636262 GTGCAACTTCAT -s mr.mrrefChr5 194989 12 + 294540 GTGCAACTTCAT -s simRat_chr6.simRat.chr6 339094 12 + 647215 ATGCAACTTCAC - -a -s simMouse_chr6.simMouse.chr6 347692 12 + 636262 CAGTGAAGTTCC -s Anc0.Anc0refChr0 11530 12 + 26507 TGGTGAATTTTT -s Anc1.Anc1refChr6 11802 12 + 197743 TGGTGAATTTTT -s Anc2.Anc2refChr17 4807 12 + 28526 TGGTGAATTTTT -s mr.mrrefChr5 195001 12 + 294540 TGGTGAAGTTTC -s mr.mrrefChr5 195466 12 + 294540 TGGTAATCATTT -s simCow_chr6.simCow.chr6 320099 12 + 602619 TGGTGAATTTTT -s simDog_chr6.simDog.chr6 312233 12 + 593897 TGGGGATTTTTC -s simHuman_chr6.simHuman.chr6 331899 12 + 601863 TGATAAATTTTT -s simMouse_chr6.simMouse.chr6 348156 12 + 636262 TGGTAATCATTT -s simRat_chr6.simRat.chr6 339583 12 + 647215 TGGTAATCCTTT -s simRat_chr6.simRat.chr6 339106 12 + 647215 TGGTGAGGTTTC - -a -s simMouse_chr6.simMouse.chr6 347704 7 + 636262 TCATATT -s Anc0.Anc0refChr0 11542 7 + 26507 TGATATT -s Anc1.Anc1refChr6 11814 7 + 197743 TGATATT -s Anc2.Anc2refChr17 4819 7 + 28526 TGATCTT -s mr.mrrefChr5 195013 7 + 294540 TCATATT -s mr.mrrefChr5 195478 6 + 294540 T-GTGTT -s simCow_chr6.simCow.chr6 320111 7 + 602619 TGGTCTT -s simDog_chr6.simDog.chr6 312245 7 + 593897 TGAACTC -s simHuman_chr6.simHuman.chr6 331911 7 + 601863 AGTTACT -s simMouse_chr6.simMouse.chr6 348168 6 + 636262 T-GTGTT -s simRat_chr6.simRat.chr6 339118 7 + 647215 TTATATT - -a -s simMouse_chr6.simMouse.chr6 347711 16 + 636262 CCTGTGTGTGTAACCA -s Anc0.Anc0refChr0 11549 16 + 26507 GCTGTCAGTAGAAGCA -s Anc1.Anc1refChr6 11821 16 + 197743 GCTGTCAGTAGAAGCA -s Anc2.Anc2refChr17 4826 16 + 28526 TCTGTCAGTAGAAGCA -s mr.mrrefChr5 195020 16 + 294540 CCTGTGTGTGTAACCA -s mr.mrrefChr5 195484 16 + 294540 GCTTTCAGTATAACGA -s simCow_chr6.simCow.chr6 320118 16 + 602619 CCTGTTAGTGGAAGCA -s simDog_chr6.simDog.chr6 312252 16 + 593897 TTTGTCAATAGAAGCA -s simHuman_chr6.simHuman.chr6 331918 16 + 601863 GCTGTCAGCAGGAGCA -s simMouse_chr6.simMouse.chr6 348174 16 + 636262 GCTTTCAGTATAACGA -s simRat_chr6.simRat.chr6 339595 16 + 647215 GTTATCAGTATAAATA -s simRat_chr6.simRat.chr6 339125 16 + 647215 CCGTTATGTGTAACCA - -a -s simMouse_chr6.simMouse.chr6 347727 18 + 636262 CATATTTAAAATCAAACT -s Anc0.Anc0refChr0 11565 18 + 26507 TGTTGTAGAAGTCGAACT -s Anc1.Anc1refChr6 11837 18 + 197743 TGTTGTAGAAGTCGAACT -s Anc2.Anc2refChr17 4842 18 + 28526 TGTTGTAGAAGTTGAACT -s mr.mrrefChr5 195036 18 + 294540 CATATTTAAAATCAAACT -s simCow_chr6.simCow.chr6 320134 13 + 602619 T-----AAAAGTTGAACT -s simDog_chr6.simDog.chr6 312268 18 + 593897 TGTTGTTGAAGTTGAACT -s simHuman_chr6.simHuman.chr6 331934 18 + 601863 TGTTGCAGAAGTCGAACT -s simRat_chr6.simRat.chr6 339141 18 + 647215 CACATCTAAAATCAAACT - -a -s simMouse_chr6.simMouse.chr6 347745 1 + 636262 A -s Anc0.Anc0refChr0 11583 1 + 26507 A -s Anc1.Anc1refChr6 11855 1 + 197743 A -s Anc2.Anc2refChr17 4860 1 + 28526 A -s mr.mrrefChr5 195054 1 + 294540 A -s simCow_chr6.simCow.chr6 320147 1 + 602619 A -s simDog_chr6.simDog.chr6 312287 1 + 593897 A -s simHuman_chr6.simHuman.chr6 331952 1 + 601863 A -s simRat_chr6.simRat.chr6 339159 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 347746 46 + 636262 TAAAGAAACAGCTCTACATTCACCCTCTTCCAGGGTAGTTTAGTTA -s Anc0.Anc0refChr0 11584 46 + 26507 GAAAGACGCAGCTCTATGTTCAGGTTCCTTGGTGGTAATTTGGTCA -s Anc1.Anc1refChr6 11856 46 + 197743 GAAAGACGCAGCTCTATGTTCAGGTTCCTTGGTGGTAATTTGGTCA -s Anc2.Anc2refChr17 4861 46 + 28526 GAAAGACGCAGGCCCATGTTCAGGTTCCTTGGTGGTAATTTGGTGA -s mr.mrrefChr5 195055 46 + 294540 TAAAGAAACAGCTCTACATTCACGCTCTTCCGTGGTAGATTAGTTA -s mr.mrrefChr5 195500 46 + 294540 TGATGACACAACTCTCAGTTCAGGTTCCTTGGTGGTAGTTTAGTCA -s simCow_chr6.simCow.chr6 320148 46 + 602619 ACAAGACACAGGCCCATGTTCAGGTTCCTTAGTGGTAAATTGGTGG -s simDog_chr6.simDog.chr6 312288 42 + 593897 GAAAGAGG----CTCACGTGCAGGTACATTGGTGGTAGTTTGATGA -s simHuman_chr6.simHuman.chr6 331953 46 + 601863 GTAAGACGCATCTCTATGTTTAGGTTCCTTGGTGGTAATTTGGTCA -s simMouse_chr6.simMouse.chr6 348190 46 + 636262 TGATAACATAACTCTCAGTTCCAGTTCCTTCGTGGTAGTCTAGTCT -s simRat_chr6.simRat.chr6 339611 46 + 647215 TGATGACACAACTCTGAGTTCAGGTCCCTTGGTGGTAGCTTAGTCA -s simRat_chr6.simRat.chr6 339160 46 + 647215 TGAAAAAACAGCACTACATGCATGCTCATCTGTGTTAGATTAATTA - -a -s simMouse_chr6.simMouse.chr6 347792 6 + 636262 ACTAGC -s Anc0.Anc0refChr0 11630 6 + 26507 ACTAAC -s Anc1.Anc1refChr6 11902 6 + 197743 ACTAAC -s Anc2.Anc2refChr17 4907 6 + 28526 ACTAAC -s mr.mrrefChr5 195101 6 + 294540 ACTAGC -s mr.mrrefChr5 195546 6 + 294540 ACTAAC -s simCow_chr6.simCow.chr6 320194 6 + 602619 ACTAAC -s simDog_chr6.simDog.chr6 312331 6 + 593897 ACTAAC -s simHuman_chr6.simHuman.chr6 331999 6 + 601863 ACTAAC -s simMouse_chr6.simMouse.chr6 348236 6 + 636262 ACTAAC -s simRat_chr6.simRat.chr6 339657 6 + 647215 ACTAAC -s simRat_chr6.simRat.chr6 339206 6 + 647215 ACTAGC - -a -s simMouse_chr6.simMouse.chr6 347798 6 + 636262 TGTCAC -s Anc0.Anc0refChr0 11636 6 + 26507 TGTCAC -s Anc1.Anc1refChr6 11910 6 + 197743 TGTCAC -s Anc2.Anc2refChr17 4913 6 + 28526 TGTCTC -s mr.mrrefChr5 195107 6 + 294540 TGTCAC -s mr.mrrefChr5 195554 6 + 294540 TGTTAT -s simCow_chr6.simCow.chr6 320200 6 + 602619 TGCGTT -s simDog_chr6.simDog.chr6 312337 6 + 593897 TGTCTC -s simHuman_chr6.simHuman.chr6 332007 6 + 601863 TTTTGT -s simMouse_chr6.simMouse.chr6 348244 6 + 636262 GGTTAT -s simRat_chr6.simRat.chr6 339665 6 + 647215 TGTTAT -s simRat_chr6.simRat.chr6 339212 6 + 647215 TGTCAC - -a -s simMouse_chr6.simMouse.chr6 347804 1 + 636262 C -s Anc0.Anc0refChr0 11642 1 + 26507 C -s Anc1.Anc1refChr6 11916 1 + 197743 C -s Anc2.Anc2refChr17 4919 1 + 28526 C -s mr.mrrefChr5 195113 1 + 294540 C -s mr.mrrefChr5 195561 1 + 294540 C -s simCow_chr6.simCow.chr6 320206 1 + 602619 C -s simDog_chr6.simDog.chr6 312343 1 + 593897 C -s simHuman_chr6.simHuman.chr6 332013 1 + 601863 C -s simMouse_chr6.simMouse.chr6 348251 1 + 636262 C -s simRat_chr6.simRat.chr6 339218 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 347805 6 + 636262 AGTAAT -s Anc0.Anc0refChr0 11643 6 + 26507 AACTAT -s Anc1.Anc1refChr6 11917 6 + 197743 AACTAT -s Anc2.Anc2refChr17 4933 6 + 28526 AACTTT -s mr.mrrefChr5 195114 6 + 294540 AGTAAT -s mr.mrrefChr5 195562 6 + 294540 ACCAAT -s simDog_chr6.simDog.chr6 312376 6 + 593897 AACTTT -s simHuman_chr6.simHuman.chr6 332014 6 + 601863 AACTAT -s simMouse_chr6.simMouse.chr6 348252 6 + 636262 ACCAAT -s simRat_chr6.simRat.chr6 339219 6 + 647215 AGTAAT - -a -s simMouse_chr6.simMouse.chr6 347811 2 + 636262 TA -s Anc0.Anc0refChr0 11657 2 + 26507 TG -s Anc1.Anc1refChr6 11931 2 + 197743 TG -s Anc2.Anc2refChr17 4947 2 + 28526 TG -s mr.mrrefChr5 195120 2 + 294540 TA -s mr.mrrefChr5 195568 2 + 294540 TG -s simDog_chr6.simDog.chr6 312390 2 + 593897 TG -s simHuman_chr6.simHuman.chr6 332028 2 + 601863 TG -s simMouse_chr6.simMouse.chr6 348258 2 + 636262 TG -s simRat_chr6.simRat.chr6 339225 2 + 647215 TA - -a -s simMouse_chr6.simMouse.chr6 347813 8 + 636262 ATTTTAAA -s Anc0.Anc0refChr0 11659 8 + 26507 ATTTATTT -s Anc1.Anc1refChr6 11933 8 + 197743 ATTTATTT -s Anc2.Anc2refChr17 4949 8 + 28526 ACTAATTT -s mr.mrrefChr5 195122 8 + 294540 ATTTTAAA -s mr.mrrefChr5 195570 8 + 294540 ATGTATAA -s simCow_chr6.simCow.chr6 320211 8 + 602619 AGTAATTT -s simDog_chr6.simDog.chr6 312395 8 + 593897 ACTAATTT -s simHuman_chr6.simHuman.chr6 332030 8 + 601863 CTATATTT -s simMouse_chr6.simMouse.chr6 348260 8 + 636262 ATGTATAA -s simRat_chr6.simRat.chr6 339672 8 + 647215 ATGTATAT -s simRat_chr6.simRat.chr6 339227 8 + 647215 ATTTTAAA - -a -s simMouse_chr6.simMouse.chr6 347821 2 + 636262 CT -s Anc0.Anc0refChr0 11672 1 + 26507 -T -s Anc1.Anc1refChr6 11946 2 + 197743 CT -s Anc2.Anc2refChr17 4962 1 + 28526 -T -s mr.mrrefChr5 195130 2 + 294540 CT -s mr.mrrefChr5 195583 2 + 294540 CA -s simCow_chr6.simCow.chr6 320224 1 + 602619 -T -s simDog_chr6.simDog.chr6 312408 1 + 593897 -T -s simHuman_chr6.simHuman.chr6 332043 1 + 601863 -T -s simMouse_chr6.simMouse.chr6 348273 2 + 636262 CA -s simRat_chr6.simRat.chr6 339685 2 + 647215 GA -s simRat_chr6.simRat.chr6 339235 2 + 647215 CT - -a -s simMouse_chr6.simMouse.chr6 347823 4 + 636262 AGAA -s Anc0.Anc0refChr0 11673 4 + 26507 ATAA -s Anc1.Anc1refChr6 11948 4 + 197743 ATAA -s Anc2.Anc2refChr17 4963 4 + 28526 ATAA -s mr.mrrefChr5 195132 4 + 294540 AGAA -s mr.mrrefChr5 195585 4 + 294540 AGAA -s simCow_chr6.simCow.chr6 320225 4 + 602619 ATAA -s simDog_chr6.simDog.chr6 312409 4 + 593897 ATAA -s simHuman_chr6.simHuman.chr6 332044 4 + 601863 ATAA -s simMouse_chr6.simMouse.chr6 348275 4 + 636262 AGAA -s simRat_chr6.simRat.chr6 339687 4 + 647215 AAAA -s simRat_chr6.simRat.chr6 339245 4 + 647215 AGAA - -a -s simMouse_chr6.simMouse.chr6 347827 7 + 636262 TCTAATA -s Anc0.Anc0refChr0 11677 7 + 26507 TCTAATA -s Anc1.Anc1refChr6 11952 7 + 197743 TCTAATA -s Anc2.Anc2refChr17 4967 7 + 28526 TTCAATA -s mr.mrrefChr5 195136 7 + 294540 TCTAATA -s mr.mrrefChr5 195595 7 + 294540 TGTAATG -s simCow_chr6.simCow.chr6 320229 7 + 602619 TGCAATA -s simDog_chr6.simDog.chr6 312413 7 + 593897 TTCAATC -s simHuman_chr6.simHuman.chr6 332048 6 + 601863 TC-AATA -s simMouse_chr6.simMouse.chr6 348285 7 + 636262 TGTAATG -s simRat_chr6.simRat.chr6 339697 7 + 647215 TGTAGTG -s simRat_chr6.simRat.chr6 339249 7 + 647215 TTTAATA - -a -s simMouse_chr6.simMouse.chr6 347834 18 + 636262 ATTCAAGAGAGCTAGGAA -s Anc0.Anc0refChr0 11684 18 + 26507 ATTCAAGAGAGCTGAGAG -s Anc1.Anc1refChr6 11959 18 + 197743 ATTCAAGAGAGCTGAGAG -s Anc2.Anc2refChr17 4974 18 + 28526 ATTCAAGAGAGCTGAGAG -s mr.mrrefChr5 195143 18 + 294540 ATTCAAGAGAGCTAGGAA -s mr.mrrefChr5 195618 18 + 294540 ATACAAGAGAGCTGAGAG -s simCow_chr6.simCow.chr6 320236 18 + 602619 ATTCAGGAGAGCTGAAAG -s simDog_chr6.simDog.chr6 312420 17 + 593897 ATT-AAGAGAGCTGAGAG -s simHuman_chr6.simHuman.chr6 332054 18 + 601863 ATTCAAGAGAGCTGACGG -s simMouse_chr6.simMouse.chr6 348308 18 + 636262 ATACAAGAGAGCTGAGAG -s simRat_chr6.simRat.chr6 339720 18 + 647215 ATACAAGAGAGCTGAGAG -s simRat_chr6.simRat.chr6 339256 16 + 647215 ATTCA--AGAGCCAGGAA - -a -s simMouse_chr6.simMouse.chr6 347852 3 + 636262 GTC -s Anc0.Anc0refChr0 11702 3 + 26507 GTC -s Anc1.Anc1refChr6 11977 3 + 197743 GTC -s Anc2.Anc2refChr17 4992 3 + 28526 GAC -s mr.mrrefChr5 195161 3 + 294540 GTC -s mr.mrrefChr5 195636 3 + 294540 GTT -s simCow_chr6.simCow.chr6 320254 3 + 602619 GCC -s simDog_chr6.simDog.chr6 312437 3 + 593897 GAC -s simHuman_chr6.simHuman.chr6 332072 3 + 601863 ATC -s simMouse_chr6.simMouse.chr6 348326 3 + 636262 GTT -s simRat_chr6.simRat.chr6 339742 3 + 647215 GTT -s simRat_chr6.simRat.chr6 339272 3 + 647215 GTC - -a -s simMouse_chr6.simMouse.chr6 347855 16 + 636262 TAATGTTTAGTTGCAT -s Anc0.Anc0refChr0 11706 16 + 26507 TAATGCTTAGACACAT -s Anc1.Anc1refChr6 11981 16 + 197743 TAATGCTTAGACACAT -s Anc2.Anc2refChr17 4996 16 + 28526 TAATGCTTTGACACAT -s mr.mrrefChr5 195165 16 + 294540 TAATGTTTAGTTGCAT -s mr.mrrefChr5 195640 16 + 294540 TAATGCTAATGCCCAG -s simCow_chr6.simCow.chr6 320258 16 + 602619 TAATGCTTTGACACAT -s simDog_chr6.simDog.chr6 312441 15 + 593897 TAATGCTT-GAGACAT -s simHuman_chr6.simHuman.chr6 332076 14 + 601863 --ATGCTTAGACACAT -s simMouse_chr6.simMouse.chr6 348330 16 + 636262 TAATGCTAATGCCCAG -s simRat_chr6.simRat.chr6 339746 16 + 647215 TAACACTAATGCTCAC -s simRat_chr6.simRat.chr6 339276 16 + 647215 TAATGTTTAGTGGGAT - -a -s simMouse_chr6.simMouse.chr6 347871 16 + 636262 ATAGATCGTAACGTTC -s Anc0.Anc0refChr0 11722 9 + 26507 ACA-------ACATCT -s Anc1.Anc1refChr6 11997 9 + 197743 ACA-------ACATCT -s Anc2.Anc2refChr17 5012 9 + 28526 ACA-------GTATCT -s mr.mrrefChr5 195181 16 + 294540 ATAGATCGTAACATTC -s simCow_chr6.simCow.chr6 320274 4 + 602619 A------------TCC -s simDog_chr6.simDog.chr6 312456 9 + 593897 ACA-------GTATCT -s simHuman_chr6.simHuman.chr6 332090 9 + 601863 ACA-------ACATCA -s simRat_chr6.simRat.chr6 339292 16 + 647215 ATAGATCATAACATTT - -a -s simMouse_chr6.simMouse.chr6 347887 18 + 636262 TGGTTTACTCTTTAGATG -s Anc0.Anc0refChr0 11731 18 + 26507 TGGTGTATCCTTAAGATG -s Anc1.Anc1refChr6 12006 18 + 197743 TGGTGTATCCTTAAGATG -s Anc2.Anc2refChr17 5021 18 + 28526 TGATGTATCCTTAAGATG -s mr.mrrefChr5 195197 18 + 294540 TGGTTTACTCTTTAGATG -s mr.mrrefChr5 195656 18 + 294540 TGGTGTTTCCCTAAGACA -s simCow_chr6.simCow.chr6 320278 12 + 602619 TGATGCTTCCTT------ -s simDog_chr6.simDog.chr6 312465 18 + 593897 TGATGTATCCACAAGATG -s simHuman_chr6.simHuman.chr6 332099 18 + 601863 TGGTGTATCCTTAAGCTG -s simMouse_chr6.simMouse.chr6 348346 18 + 636262 TGGTGTTTCCCTAAGACA -s simRat_chr6.simRat.chr6 339762 18 + 647215 TGGTGTTTCCCTAAGGCA -s simRat_chr6.simRat.chr6 339308 18 + 647215 TGGTTTACTCTTTAGATG - -a -s simMouse_chr6.simMouse.chr6 347905 1 + 636262 G -s Anc0.Anc0refChr0 11749 1 + 26507 G -s Anc1.Anc1refChr6 12024 1 + 197743 G -s Anc2.Anc2refChr17 5039 1 + 28526 G -s mr.mrrefChr5 195215 1 + 294540 G -s simCow_chr6.simCow.chr6 320290 1 + 602619 G -s simDog_chr6.simDog.chr6 312483 1 + 593897 G -s simHuman_chr6.simHuman.chr6 332117 1 + 601863 G -s simRat_chr6.simRat.chr6 339326 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 347906 7 + 636262 CTGGAAC -s Anc0.Anc0refChr0 11750 6 + 26507 CTGG-AC -s Anc1.Anc1refChr6 12025 7 + 197743 CTGGCAC -s Anc2.Anc2refChr17 5040 6 + 28526 CTAG-AC -s mr.mrrefChr5 195216 7 + 294540 CTGGAAC -s mr.mrrefChr5 195674 7 + 294540 CTGGCAC -s simCow_chr6.simCow.chr6 320291 6 + 602619 CAAC-AC -s simDog_chr6.simDog.chr6 312484 6 + 593897 CTAG-AC -s simHuman_chr6.simHuman.chr6 332118 6 + 601863 CTGG-AC -s simMouse_chr6.simMouse.chr6 348364 7 + 636262 CTGGCAC -s simRat_chr6.simRat.chr6 339780 7 + 647215 TTGCTAA -s simRat_chr6.simRat.chr6 339327 7 + 647215 CTGGAAC - -a -s simMouse_chr6.simMouse.chr6 347913 26 + 636262 TGTTTTTTGTTGGTATATTTCAGGTA -s Anc0.Anc0refChr0 11756 24 + 26507 TGTTTTCTGCTGTTTTATG--TGGTA -s Anc1.Anc1refChr6 12032 26 + 197743 TGTTTTCTGCTGTTTTATGCCTGGTA -s Anc2.Anc2refChr17 5046 24 + 28526 TGTTTTCTGCTGTTTTTTG--GGGTA -s mr.mrrefChr5 195223 26 + 294540 TGTTTTTTGCTGGTATATTTCAGGTA -s mr.mrrefChr5 195697 26 + 294540 TGTTTTTTGCTGTTCTATTCCTGGTA -s simCow_chr6.simCow.chr6 320297 24 + 602619 TGTTTTCTGCTGTTATTTT--CAGTA -s simDog_chr6.simDog.chr6 312490 24 + 593897 TGTTATCTGCCGTTTTTTG--GGGTA -s simHuman_chr6.simHuman.chr6 332124 26 + 601863 TGTTTCCCGCTGTCTTATGCCTGGTA -s simMouse_chr6.simMouse.chr6 348389 26 + 636262 TGTTTTTTGCTGTTCTATTCCCGTTA -s simRat_chr6.simRat.chr6 339803 26 + 647215 TGTTTTTTGCTGTTCTATTCCTGGTA -s simRat_chr6.simRat.chr6 339334 26 + 647215 TGTTTTTTGCTGGTTAAGTTCAGGTA - -a -s simMouse_chr6.simMouse.chr6 347939 37 + 636262 CATATGGTATACCAGCCATTTGTGTATTGGGTATAAC -s Anc0.Anc0refChr0 11780 37 + 26507 CCTAAGATCTCTTGACCATTTGTCCATTGGAAGCACC -s Anc1.Anc1refChr6 12058 37 + 197743 CCTAAGATCTCTTGACCATTTGTCCATTGGAAGCACC -s Anc2.Anc2refChr17 5070 37 + 28526 CCTAAGATCTCTTGACCATTTGTCCATCAGAAGCACC -s mr.mrrefChr5 195249 37 + 294540 CATATGGTATACCAGCCATTTGTGTATTGGGTATAAC -s mr.mrrefChr5 195723 37 + 294540 TCGGACACCTATTGGCCTTTGGTCCATTGGAAGTACC -s simCow_chr6.simCow.chr6 320321 37 + 602619 TCTAAGATCTCTTGCCAGATTGTTCATCAGAAGTACC -s simDog_chr6.simDog.chr6 312514 37 + 593897 CCTAAGATCTCTTGACCATTTGTCCATCAGAAGCACC -s simHuman_chr6.simHuman.chr6 332150 28 + 601863 CCTAAGACCACTCAACCATTTGT---------ACACC -s simMouse_chr6.simMouse.chr6 348415 37 + 636262 TCGGACACCTATTGGCCTTTGGTCCATTGCAAGTACC -s simRat_chr6.simRat.chr6 339833 37 + 647215 TTGGACATTCATTGGTGTTTGATCCATTGGAATTACC -s simRat_chr6.simRat.chr6 339360 37 + 647215 CATATGCTATACCAACCATTTGTGTATTGGTTATAAC - -a -s simMouse_chr6.simMouse.chr6 347976 10 + 636262 AGACATCAAG -s Anc0.Anc0refChr0 11817 10 + 26507 AGAAGTCAAA -s Anc1.Anc1refChr6 12095 10 + 197743 AGAAGTCAAA -s Anc2.Anc2refChr17 5107 10 + 28526 AGAAGTCAAA -s mr.mrrefChr5 195286 10 + 294540 AGACATCAAG -s mr.mrrefChr5 195760 10 + 294540 ACAAGTCAAG -s simCow_chr6.simCow.chr6 320367 10 + 602619 AGAAGTCAAC -s simDog_chr6.simDog.chr6 312551 10 + 593897 AGAAGTCAGA -s simHuman_chr6.simHuman.chr6 332178 10 + 601863 AGAAGTTAAA -s simMouse_chr6.simMouse.chr6 348452 10 + 636262 ACAAGTCAAG -s simRat_chr6.simRat.chr6 339870 10 + 647215 ACAAGTCGAG -s simRat_chr6.simRat.chr6 339397 10 + 647215 AGACATCAAG - -a -s simMouse_chr6.simMouse.chr6 347986 1 + 636262 G -s Anc0.Anc0refChr0 11827 1 + 26507 G -s Anc1.Anc1refChr6 12105 1 + 197743 G -s Anc2.Anc2refChr17 5117 1 + 28526 A -s mr.mrrefChr5 195296 1 + 294540 G -s simCow_chr6.simCow.chr6 320377 1 + 602619 A -s simDog_chr6.simDog.chr6 312561 1 + 593897 A -s simHuman_chr6.simHuman.chr6 332188 1 + 601863 G -s simRat_chr6.simRat.chr6 339407 1 + 647215 G - -a -s simMouse_chr6.simMouse.chr6 347987 7 + 636262 GCATGGT -s Anc0.Anc0refChr0 11828 7 + 26507 ATACAGG -s Anc1.Anc1refChr6 12106 7 + 197743 ATACAGG -s Anc2.Anc2refChr17 5118 7 + 28526 ATACAGG -s mr.mrrefChr5 195297 7 + 294540 GCATGGT -s mr.mrrefChr5 195770 7 + 294540 GTATAGG -s simCow_chr6.simCow.chr6 320378 7 + 602619 ATACAGG -s simDog_chr6.simDog.chr6 312562 7 + 593897 ATGCAGG -s simHuman_chr6.simHuman.chr6 332189 7 + 601863 ATACCGG -s simMouse_chr6.simMouse.chr6 348462 7 + 636262 ACATACA -s simRat_chr6.simRat.chr6 339880 7 + 647215 GTATGGG -s simRat_chr6.simRat.chr6 339408 7 + 647215 GCATAGT - -a -s simMouse_chr6.simMouse.chr6 347994 21 + 636262 GTTAGGATCAACTGGACATTA -s Anc0.Anc0refChr0 11848 21 + 26507 GTTTGGATCAACTAGGCATTA -s Anc1.Anc1refChr6 12126 21 + 197743 GTTTGGATCAACTAGGCATTA -s Anc2.Anc2refChr17 5138 21 + 28526 GTGTGGATCAACTAGGCATTA -s mr.mrrefChr5 195304 21 + 294540 GTTAGGATCAACTGGACATTA -s mr.mrrefChr5 195784 21 + 294540 GTTAGGATCAACTGGGCATTA -s simCow_chr6.simCow.chr6 320401 21 + 602619 GTGTGAATCAACTAGGCATTA -s simDog_chr6.simDog.chr6 312582 20 + 593897 GTGTGGATTAACTGAGCAAT- -s simHuman_chr6.simHuman.chr6 332209 21 + 601863 GTTTGGGTCAATTAGACATTA -s simMouse_chr6.simMouse.chr6 348476 21 + 636262 GTTAGGATCAACTGGGCATTA -s simRat_chr6.simRat.chr6 339894 21 + 647215 GTTGGGATCAACTGGGTATTA -s simRat_chr6.simRat.chr6 339415 20 + 647215 GTTAGGA-CAACTGGACATTA - -a -s simMouse_chr6.simMouse.chr6 348015 9 + 636262 TAAATTCTA -s Anc0.Anc0refChr0 11869 7 + 26507 T--ACTCCA -s Anc1.Anc1refChr6 12147 9 + 197743 TAGACTCCA -s Anc2.Anc2refChr17 5159 7 + 28526 T--ACTCCA -s mr.mrrefChr5 195325 9 + 294540 TAAATTCTA -s mr.mrrefChr5 195805 9 + 294540 AAGATAACA -s simCow_chr6.simCow.chr6 320424 7 + 602619 T--ACTCCA -s simDog_chr6.simDog.chr6 312602 2 + 593897 -------TA -s simHuman_chr6.simHuman.chr6 332230 7 + 601863 GAGGC--CA -s simMouse_chr6.simMouse.chr6 348497 9 + 636262 AAGATAACA -s simRat_chr6.simRat.chr6 339915 9 + 647215 CAGATTACA -s simRat_chr6.simRat.chr6 339435 9 + 647215 TAGATTCTA - -a -s simMouse_chr6.simMouse.chr6 348024 6 + 636262 TCAGGG -s Anc0.Anc0refChr0 11876 6 + 26507 CCAGGG -s Anc1.Anc1refChr6 12156 6 + 197743 CCAGGG -s Anc2.Anc2refChr17 5166 6 + 28526 CCTTGG -s mr.mrrefChr5 195334 6 + 294540 TCAGGG -s mr.mrrefChr5 195814 6 + 294540 TTGGGG -s simCow_chr6.simCow.chr6 320453 6 + 602619 CCTCAG -s simDog_chr6.simDog.chr6 312604 6 + 593897 CCTTGG -s simHuman_chr6.simHuman.chr6 332237 6 + 601863 CCAGGG -s simMouse_chr6.simMouse.chr6 348506 6 + 636262 TTGGGG -s simRat_chr6.simRat.chr6 339924 6 + 647215 TTGGGG -s simRat_chr6.simRat.chr6 339444 6 + 647215 TACGGG - -a -s simMouse_chr6.simMouse.chr6 348030 1 + 636262 C -s Anc0.Anc0refChr0 11882 1 + 26507 C -s Anc1.Anc1refChr6 12162 1 + 197743 C -s Anc2.Anc2refChr17 5178 1 + 28526 C -s mr.mrrefChr5 195340 1 + 294540 C -s mr.mrrefChr5 195820 1 + 294540 C -s simCow_chr6.simCow.chr6 320465 1 + 602619 C -s simDog_chr6.simDog.chr6 312616 1 + 593897 C -s simHuman_chr6.simHuman.chr6 332243 1 + 601863 T -s simMouse_chr6.simMouse.chr6 348512 1 + 636262 C -s simRat_chr6.simRat.chr6 339930 1 + 647215 C -s simRat_chr6.simRat.chr6 339450 1 + 647215 C - -a -s simMouse_chr6.simMouse.chr6 348031 30 + 636262 ACAGCAGCGTTTACAACTGGTCTGGGCCTG -s Anc0.Anc0refChr0 11884 30 + 26507 ACAGCAATGTGGACTACAGGTCTGGACCTG -s Anc1.Anc1refChr6 12164 30 + 197743 ACAGCAATGTGGACTACAGGTCTGGACCTG -s Anc2.Anc2refChr17 5180 30 + 28526 ACACCAATGTGGACTACAGGTCTGGACCTG -s mr.mrrefChr5 195341 30 + 294540 ACAGCAGCGTTTACAACTGGTCTGGGCCTG -s mr.mrrefChr5 195822 30 + 294540 GCAACAGTGTGAACAGTTGGTCTGGACCTG -s simCow_chr6.simCow.chr6 320467 30 + 602619 ATACCAATATGGACTGCAGATTTGGATCCG -s simDog_chr6.simDog.chr6 312618 30 + 593897 ACACCTATGTGGTTTACAGGTCTAGACCTT -s simHuman_chr6.simHuman.chr6 332245 30 + 601863 ACAGCAATGTGGACTATAGGTCTGGACCTG -s simMouse_chr6.simMouse.chr6 348514 30 + 636262 GCAACAGTGTGAACAGATGCTCTGGCCCTG -s simRat_chr6.simRat.chr6 339932 30 + 647215 GCAACAGTGTGAACACTGTGTCTGGACCTG -s simRat_chr6.simRat.chr6 339451 30 + 647215 ATTACAATGTGTACAACAGGTCTGGGCCTG - -a -s simMouse_chr6.simMouse.chr6 348061 2 + 636262 CG -s mr.mrrefChr5 195371 2 + 294540 CG -s simRat_chr6.simRat.chr6 339481 2 + 647215 CT - -a -s simMouse_chr6.simMouse.chr6 348063 6 + 636262 CAGCAT -s mr.mrrefChr5 195373 6 + 294540 CAGCAT -s simRat_chr6.simRat.chr6 339490 6 + 647215 CAGCAT - -a -s simMouse_chr6.simMouse.chr6 348069 7 + 636262 TACCAAT -s Anc0.Anc0refChr0 11914 6 + 26507 TA-CATT -s Anc1.Anc1refChr6 12194 7 + 197743 TACCATT -s Anc2.Anc2refChr17 5210 6 + 28526 TA-CATT -s mr.mrrefChr5 195379 7 + 294540 TACCAAT -s mr.mrrefChr5 195852 7 + 294540 TACCATT -s simCow_chr6.simCow.chr6 320497 6 + 602619 TA-CATT -s simDog_chr6.simDog.chr6 312648 6 + 593897 TA-CATT -s simHuman_chr6.simHuman.chr6 332275 6 + 601863 T-CCATT -s simMouse_chr6.simMouse.chr6 348544 7 + 636262 TACCATT -s simRat_chr6.simRat.chr6 339962 7 + 647215 TACCATT -s simRat_chr6.simRat.chr6 339496 7 + 647215 TACCAGT - -a -s simMouse_chr6.simMouse.chr6 348076 18 + 636262 GTTATGATAATAACTCAG -s mr.mrrefChr5 195386 18 + 294540 GTTATGATAATAACTCAG -s simRat_chr6.simRat.chr6 339503 18 + 647215 GTTATGATAAGAACCCAG - -a -s simMouse_chr6.simMouse.chr6 348094 7 + 636262 GATTGAG -s Anc0.Anc0refChr0 11920 7 + 26507 GGCTGTA -s Anc1.Anc1refChr6 12201 7 + 197743 GGCTGTA -s Anc2.Anc2refChr17 5216 7 + 28526 GGCTGTA -s mr.mrrefChr5 195404 7 + 294540 GATTGAG -s mr.mrrefChr5 195859 7 + 294540 TACTGCA -s simCow_chr6.simCow.chr6 320503 6 + 602619 G-CTGTA -s simDog_chr6.simDog.chr6 312659 7 + 593897 GGCTGTG -s simHuman_chr6.simHuman.chr6 332281 7 + 601863 GGCTGTA -s simMouse_chr6.simMouse.chr6 348551 7 + 636262 TACTGCA -s simRat_chr6.simRat.chr6 339969 7 + 647215 CACTGCA -s simRat_chr6.simRat.chr6 339521 7 + 647215 GATTAAG - -a -s simMouse_chr6.simMouse.chr6 348114 1 + 636262 C -s Anc0.Anc0refChr0 11499 1 + 26507 C -s Anc1.Anc1refChr6 11771 1 + 197743 C -s Anc2.Anc2refChr17 4776 1 + 28526 C -s mr.mrrefChr5 195424 1 + 294540 C -s simCow_chr6.simCow.chr6 320068 1 + 602619 C -s simDog_chr6.simDog.chr6 312202 1 + 593897 C -s simHuman_chr6.simHuman.chr6 331868 1 + 601863 C -s simRat_chr6.simRat.chr6 339541 1 + 647215 C - -a -s simMouse_chr6.simMouse.chr6 348130 11 + 636262 AGGTGCGACTT -s mr.mrrefChr5 195440 11 + 294540 AGGTGCGACTT -s simRat_chr6.simRat.chr6 339557 11 + 647215 ACGTGCAACTT - -a -s simMouse_chr6.simMouse.chr6 348242 2 + 636262 CC -s Anc1.Anc1refChr6 11908 2 + 197743 GA -s mr.mrrefChr5 195552 2 + 294540 CC -s simHuman_chr6.simHuman.chr6 332005 2 + 601863 GA -s simRat_chr6.simRat.chr6 339663 2 + 647215 CC - -a -s simMouse_chr6.simMouse.chr6 348250 1 + 636262 T -s mr.mrrefChr5 195560 1 + 294540 T -s simRat_chr6.simRat.chr6 339671 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 348268 5 + 636262 TGATG -s Anc0.Anc0refChr0 11667 5 + 26507 TGATG -s Anc1.Anc1refChr6 11941 5 + 197743 TGATG -s Anc2.Anc2refChr17 4957 5 + 28526 TGATG -s mr.mrrefChr5 195578 5 + 294540 TGATG -s simCow_chr6.simCow.chr6 320219 5 + 602619 CGATG -s simDog_chr6.simDog.chr6 312403 5 + 593897 TGATG -s simHuman_chr6.simHuman.chr6 332038 5 + 601863 TGATG -s simRat_chr6.simRat.chr6 339680 5 + 647215 CGATG - -a -s simMouse_chr6.simMouse.chr6 348279 6 + 636262 AGTGGT -s mr.mrrefChr5 195589 6 + 294540 AGTGGT -s simRat_chr6.simRat.chr6 339691 6 + 647215 AGAAGT - -a -s simMouse_chr6.simMouse.chr6 348292 16 + 636262 CTCAGGCATTGCTGGG -s mr.mrrefChr5 195602 16 + 294540 CTCAGGCATTGCTAGG -s simRat_chr6.simRat.chr6 339704 16 + 647215 CTCAGGCGTTGCTAGG - -a -s simMouse_chr6.simMouse.chr6 348329 1 + 636262 A -s Anc0.Anc0refChr0 11705 1 + 26507 A -s Anc1.Anc1refChr6 11980 1 + 197743 A -s Anc2.Anc2refChr17 4995 1 + 28526 A -s mr.mrrefChr5 195639 1 + 294540 A -s mr.mrrefChr5 195164 1 + 294540 A -s simCow_chr6.simCow.chr6 320257 1 + 602619 A -s simDog_chr6.simDog.chr6 312440 1 + 593897 A -s simHuman_chr6.simHuman.chr6 332075 1 + 601863 A -s simRat_chr6.simRat.chr6 339275 1 + 647215 A -s simRat_chr6.simRat.chr6 339745 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 348371 18 + 636262 AGCCTGCAATGTCCAGAT -s mr.mrrefChr5 195681 16 + 294540 AGCCTGCAAT--CCAGAT -s simRat_chr6.simRat.chr6 339787 16 + 647215 TGCCTACAAA--TCAGAT - -a -s simMouse_chr6.simMouse.chr6 348469 4 + 636262 ATAA -s Anc0.Anc0refChr0 11835 4 + 26507 ATAA -s Anc1.Anc1refChr6 12113 4 + 197743 ATAA -s Anc2.Anc2refChr17 5125 4 + 28526 ATAA -s mr.mrrefChr5 195777 4 + 294540 ATAA -s simCow_chr6.simCow.chr6 320385 4 + 602619 ATGA -s simDog_chr6.simDog.chr6 312569 4 + 593897 AGAT -s simHuman_chr6.simHuman.chr6 332196 4 + 601863 ATAA -s simRat_chr6.simRat.chr6 339887 4 + 647215 ACAG - -a -s simMouse_chr6.simMouse.chr6 348473 3 + 636262 AGG -s Anc0.Anc0refChr0 11845 3 + 26507 AGA -s Anc1.Anc1refChr6 12123 3 + 197743 AGA -s Anc2.Anc2refChr17 5135 3 + 28526 AGA -s mr.mrrefChr5 195781 3 + 294540 AGA -s simCow_chr6.simCow.chr6 320398 3 + 602619 AGA -s simDog_chr6.simDog.chr6 312579 3 + 593897 AGA -s simHuman_chr6.simHuman.chr6 332206 3 + 601863 AGA -s simRat_chr6.simRat.chr6 339891 3 + 647215 AGA - -a -s simMouse_chr6.simMouse.chr6 348513 1 + 636262 T -s Anc0.Anc0refChr0 11883 1 + 26507 T -s Anc1.Anc1refChr6 12163 1 + 197743 T -s Anc2.Anc2refChr17 5179 1 + 28526 T -s mr.mrrefChr5 195821 1 + 294540 T -s simCow_chr6.simCow.chr6 320466 1 + 602619 T -s simDog_chr6.simDog.chr6 312617 1 + 593897 T -s simHuman_chr6.simHuman.chr6 332244 1 + 601863 T -s simRat_chr6.simRat.chr6 339931 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 348558 3 + 636262 CCA -s Anc0.Anc0refChr0 11927 3 + 26507 CCA -s Anc1.Anc1refChr6 12208 3 + 197743 CCA -s Anc2.Anc2refChr17 5223 3 + 28526 CCA -s mr.mrrefChr5 195866 3 + 294540 CCA -s simCow_chr6.simCow.chr6 320509 3 + 602619 CCG -s simDog_chr6.simDog.chr6 312666 3 + 593897 CAA -s simHuman_chr6.simHuman.chr6 332288 3 + 601863 CCA -s simRat_chr6.simRat.chr6 339976 3 + 647215 CCA - -a -s simMouse_chr6.simMouse.chr6 348561 139 + 636262 GATTGCAGATGTTGCAATAACACCAGAGGTGTGTTATTTACTGCACCAGATTGCAGATGTTGCAATAACACCAGAGGTGTGTTAGGTGGCTCAGAGGTATCAGGTGTAGAGAGGAGCTCATGAAATTGGGATTAGTGTA -s Anc0.Anc0refChr0 11950 52 + 26507 G---------------------------------------------------------------------------GTGTG--AGGTGTCACAGTGCAT----------AGGGGAGATAATTCATTTGGGACTAATTTA -s Anc1.Anc1refChr6 12231 59 + 197743 G---------------------------------------------------------------------------GTGTG--AGGTGTCACAGTGCATGCATG---AGAGGGGAGATAATTCATTTGGGACTAATTTA -s Anc2.Anc2refChr17 5255 52 + 28526 G---------------------------------------------------------------------------ATGTC--AGGTGTCACAGTGCAT----------AAGAGAAACAGTTCATTTAGGACTAATTTA -s mr.mrrefChr5 195869 61 + 294540 G---------------------------------------------------------------------------GTGTGTTAGGTGTCTCAGAGGTATCAGG---AGAGAGGAGCTCATGAAATTGGGATTAGTGTA -s simCow_chr6.simCow.chr6 320541 51 + 602619 G---------------------------------------------------------------------------ATGTT--AGGTGTCACAGTTCAT----------AAGAGAAGGAGTTCATTTAGGACTATTT-A -s simDog_chr6.simDog.chr6 312698 52 + 593897 T---------------------------------------------------------------------------ATTAC--AAGTGTTACAGTGTAT----------AAGAGAAACAGTTCATTTAGGACTAATTTA -s simHuman_chr6.simHuman.chr6 332311 59 + 601863 G---------------------------------------------------------------------------GTGTG--GGGTGTCCCAGTGCATGCATG---AGAGGGGAGTTTATTCATCTGGGACTAATTCA -s simRat_chr6.simRat.chr6 339979 20 + 647215 G---------------------------------------------------------------------------GTGTGTTAGGTATC------------------------------------T--------TGTA - -a -s simMouse_chr6.simMouse.chr6 348700 83 + 636262 AAAGTGAAACAGTTAACTTTGAAATAATGGCTACACACATGAACCATCTTCTTGTCCCATCCCAACATTATCCTCAATATCAT -s Anc0.Anc0refChr0 12002 70 + 26507 AAAGTGAATCAATTCAGTGGGGAGTAATGGTTCCACATGTGAACTAACTTTTCCTGCCATA-------------TAATATCAT -s Anc1.Anc1refChr6 12290 70 + 197743 AAAGTGAATCAATTCAGTGGGGAGTAATGGTTCCACATGTGAACTAACTTTTCCTGCCATA-------------TAATATCAT -s Anc2.Anc2refChr17 5307 70 + 28526 AAAGTGAATCAATTCAGTGGGCAGTAATAGTTCCACATGTGAACTAACTTTTCCTGCCCAA-------------TAATATCAT -s mr.mrrefChr5 195930 83 + 294540 AAAGTGAAACAGTTAACTGGGGAATAATGGCTACACATGTGAACCATCTTCTTGTCCCATCCCAACATTATCCTCAATATCAT -s simCow_chr6.simCow.chr6 320592 70 + 602619 AAGGTGAAACAATTCAGTGAACGGTGATAGTTCCAAATGTGGACTAAGTTTTCCTCTGGCA-------------TAATACCAT -s simDog_chr6.simDog.chr6 312750 67 + 593897 GAAGAGA-TCAATCCTGTGGGCAGTA--AGGTCAACATGTGACCTAACTCTTCCCGCCCAA-------------TAATATCAT -s simHuman_chr6.simHuman.chr6 332370 70 + 601863 AAAGTGATGCAATTCAGTGGGGAGTACTGGTTCCACATGTGCACTAACTTTGCCTGCCATA-------------TAATATCAT -s simRat_chr6.simRat.chr6 340005 83 + 647215 AAAGCAAAACAGTTAACTGGGGAATAATAACTACACATGTGAACCATCTTCTTGCCATATCCCATCATTGCCCTAAATATCAT - -a -s simMouse_chr6.simMouse.chr6 348783 2 + 636262 CA -s Anc0.Anc0refChr0 12072 2 + 26507 CA -s Anc1.Anc1refChr6 12360 2 + 197743 CA -s Anc2.Anc2refChr17 5377 2 + 28526 CA -s mr.mrrefChr5 196013 2 + 294540 CA -s simCow_chr6.simCow.chr6 320662 2 + 602619 CA -s simDog_chr6.simDog.chr6 312826 2 + 593897 CA -s simHuman_chr6.simHuman.chr6 332440 2 + 601863 CA -s simRat_chr6.simRat.chr6 340088 2 + 647215 CA - -a -s simMouse_chr6.simMouse.chr6 348785 3 + 636262 GAG -s Anc0.Anc0refChr0 12074 3 + 26507 TTG -s Anc1.Anc1refChr6 12362 3 + 197743 TTG -s Anc2.Anc2refChr17 5379 3 + 28526 TTG -s mr.mrrefChr5 196015 3 + 294540 GAG -s simCow_chr6.simCow.chr6 320664 3 + 602619 TTG -s simDog_chr6.simDog.chr6 312828 3 + 593897 TTG -s simHuman_chr6.simHuman.chr6 332442 3 + 601863 ATG -s simRat_chr6.simRat.chr6 340091 3 + 647215 GAG - -a -s simMouse_chr6.simMouse.chr6 348788 36 + 636262 AATTACCAAAGTAAGGCTTCACTAGACTACACCTGA -s Anc0.Anc0refChr0 12077 36 + 26507 AATTATAAAAGTAAGGCTTCAATGTCCTACATCTGA -s Anc1.Anc1refChr6 12365 36 + 197743 AATTATAAAAGTAAGGCTTCAATGTCCTACATCTGA -s Anc2.Anc2refChr17 5382 36 + 28526 AATTATAAAAGCAAGACTTCAATGTCCTACATCTGA -s mr.mrrefChr5 196018 36 + 294540 AATTACAAAAGTAAGGCTTCACTAGACTACACCTGA -s simCow_chr6.simCow.chr6 320667 30 + 602619 AATTACAAGTGCAAGA--TCAA----CTACTTCTGA -s simDog_chr6.simDog.chr6 312832 36 + 593897 AATTATGAAAGCACAACTTCAATGTCCTCCATTTGG -s simHuman_chr6.simHuman.chr6 332445 36 + 601863 AATTATAAAAGTAAGGCTTCAGTGTTCTACATCTGA -s simRat_chr6.simRat.chr6 340094 36 + 647215 AATTACAAAAGCAAGGCTTCACTAGACTACACCTGA - -a -s simMouse_chr6.simMouse.chr6 348824 47 + 636262 TAAATGTGGAATCATTGTTCATGCACATTGAAAAGCTGATGTTGTGT -s Anc0.Anc0refChr0 12114 44 + 26507 CTTATGTGGAATGGTCAGTCAGGTACAGAGAATAACAGGT---GTGC -s Anc1.Anc1refChr6 12402 44 + 197743 CTTATGTGGAATGGTCAGTCAGGTACAGAGAATAACAGGT---GTGC -s Anc2.Anc2refChr17 5419 44 + 28526 CTTATCTGGAATGGTCAGTCAGGTACAGAGAATAACAGGT---TCCC -s mr.mrrefChr5 196055 47 + 294540 CAAATGTGGAATCATCGGTCAGGCACATTGAAAAACTGATGTTGTGT -s simCow_chr6.simCow.chr6 320698 44 + 602619 CCCATCTGGAATGGTCAGTCAGATACGGGGAGTAACAGGT---TCCC -s simDog_chr6.simDog.chr6 312869 36 + 593897 GTTACCTGGAATGGGTGGTCAGGTATAGAGAATAAC----------- -s simHuman_chr6.simHuman.chr6 332482 44 + 601863 CTTATGTGGAATGGTCAGTCAGGTCCAGCGAATAACAGGA---GTGG -s simRat_chr6.simRat.chr6 340131 46 + 647215 CAAGTCTGGAATCATCGGTCAGGCACATTGAAAAA-TGATATTGTGC - -a -s simMouse_chr6.simMouse.chr6 348871 31 + 636262 TCAAGGTTGACCTACTCTTATTCTTGTTCCT -s Anc0.Anc0refChr0 12158 28 + 26507 ACACGGCACACATACTATTA-TCTTAC--CA -s Anc1.Anc1refChr6 12446 30 + 197743 ACACGGCACACATACTATTA-TCTTACTTCA -s Anc2.Anc2refChr17 5463 28 + 28526 ACACAGCTCACATACTACTA-TCTTAC--CA -s mr.mrrefChr5 196102 31 + 294540 TCAAGGCAGACCTACTATTATTCTTGTTTCT -s simCow_chr6.simCow.chr6 320743 28 + 602619 ACACAGCTCACATACTGCTA-TCTTGC--CA -s simDog_chr6.simDog.chr6 312905 20 + 593897 --------CACAAATTACTA-TTGGAC--CA -s simHuman_chr6.simHuman.chr6 332526 30 + 601863 ACAGGGCACACATACCATTA-TCTTACTTCA -s simRat_chr6.simRat.chr6 340177 31 + 647215 TCAAGGCAGACTTACTATTATTCTTGTTTCT - -a -s simMouse_chr6.simMouse.chr6 348902 24 + 636262 CTTAAAATATCACCTTTAACCAAC -s Anc0.Anc0refChr0 12186 24 + 26507 GTTAAAATATCACCTTTAACCAAC -s Anc1.Anc1refChr6 12476 24 + 197743 GTTAAAATATCACCTTTAACCAAC -s Anc2.Anc2refChr17 5491 24 + 28526 GTTGAAATATCACCTTTAACCAAC -s mr.mrrefChr5 196133 24 + 294540 CTTAAAATATCACCTTTAACCAAC -s simCow_chr6.simCow.chr6 320772 24 + 602619 GTTGGAATATCACCTCTAACCAAC -s simDog_chr6.simDog.chr6 312925 24 + 593897 GTTGAAATATAACTTTTAACCAAC -s simHuman_chr6.simHuman.chr6 332556 24 + 601863 GTTAAAATATCGCCTTTAACCAAC -s simRat_chr6.simRat.chr6 340208 24 + 647215 CTTAAAATATCACCTTCAACCATC - -a -s simMouse_chr6.simMouse.chr6 348926 24 + 636262 CTCTCAGGAAAACCATCAAATGTC -s Anc0.Anc0refChr0 12211 24 + 26507 ATGTGAAGAAAACCATCAATTGAT -s Anc1.Anc1refChr6 12501 24 + 197743 ATGTGAAGAAAACCATCAATTGAT -s Anc2.Anc2refChr17 5516 24 + 28526 ATGTGAAGAAAACCATCAATTGAT -s mr.mrrefChr5 196157 24 + 294540 CTCTCAAGAAAACCATCAAATGTC -s simCow_chr6.simCow.chr6 320799 24 + 602619 ATGTGAAGAAGACCATGAATCGAT -s simDog_chr6.simDog.chr6 312950 24 + 593897 ATGATAAGAAAACCATCAATTGGT -s simHuman_chr6.simHuman.chr6 332581 24 + 601863 ATGTGAAGAAAACCATCAATTGAT -s simRat_chr6.simRat.chr6 340232 24 + 647215 CTCTCAAGAAAAACATAAACTGTC - -a -s simMouse_chr6.simMouse.chr6 348950 69 + 636262 AAAAAATTCTGACTTTAAGGACCCTGTGTGCCAGTAATCACCCTACTCTGTCTCACTGCCACCAAGAAT -s Anc0.Anc0refChr0 12242 64 + 26507 AAAAATTTTTGACTTT-----CACCCTGTGCTGATAATCACCCCATCCTGCCCTATTGCCACCAAGAAT -s Anc1.Anc1refChr6 12532 64 + 197743 AAAAATTTTTGACTTT-----CACCCTGTGCTGATAATCACCCCATCCTGCCCTATTGCCACCAAGAAT -s Anc2.Anc2refChr17 5547 64 + 28526 GAAAATTTTTGACTTG-----CACACTGTGCTGATAATCACCCCATCCTGCTCTATTGCCACCAAGAAT -s mr.mrrefChr5 196181 64 + 294540 AAAAAATTCTGACTTT-----CCCCGTGTGCCAGTAATCACCCTACTCTGTCTCACTGCCACCAAGAAT -s simCow_chr6.simCow.chr6 320830 64 + 602619 GAAAATTTTTGGCCTG-----CACGCTTGGCTAATAATCACCCCATCCTGCTCTACTGCCACCAAGAAT -s simDog_chr6.simDog.chr6 312981 64 + 593897 GAAAATTTTTGACTTG-----CACACTGTGCTGATAATCACCCCATCCCGCTCCATTGCCACCAAGAAT -s simHuman_chr6.simHuman.chr6 332612 64 + 601863 AAAAATTTTCGACTCT-----CACCCTGTGCTGAGAACCACCCCATCCTGCCCTATTGCCACCTAGAAT -s simRat_chr6.simRat.chr6 340256 64 + 647215 AAAAAGCCCTGACTTT-----CTCCTCATACCAGTAATCACCTTACTCTGTCTCACTGCCACCAAGAAT - -a -s simMouse_chr6.simMouse.chr6 349019 10 + 636262 GTATACAACC -s Anc0.Anc0refChr0 12310 10 + 26507 GTTTACAACC -s Anc1.Anc1refChr6 12600 10 + 197743 GTTTACAACC -s Anc2.Anc2refChr17 5615 10 + 28526 GTTTACAACC -s mr.mrrefChr5 196245 10 + 294540 GTATACAACC -s simCow_chr6.simCow.chr6 320898 10 + 602619 GTTTAAAGCC -s simDog_chr6.simDog.chr6 313049 10 + 593897 GTTTACAACC -s simHuman_chr6.simHuman.chr6 332680 10 + 601863 GTGTACAACC -s simRat_chr6.simRat.chr6 340320 10 + 647215 GTCTACAACC - -a -s simMouse_chr6.simMouse.chr6 349029 2 + 636262 GC -s Anc0.Anc0refChr0 12322 2 + 26507 GC -s Anc1.Anc1refChr6 12612 2 + 197743 GC -s Anc2.Anc2refChr17 5627 2 + 28526 GC -s mr.mrrefChr5 196257 2 + 294540 GC -s simCow_chr6.simCow.chr6 320910 2 + 602619 GT -s simDog_chr6.simDog.chr6 313061 2 + 593897 GC -s simHuman_chr6.simHuman.chr6 332692 2 + 601863 GC -s simRat_chr6.simRat.chr6 340332 2 + 647215 GC - -a -s simMouse_chr6.simMouse.chr6 349031 9 + 636262 GGAAGTCAC -s Anc0.Anc0refChr0 12324 7 + 26507 GGA--TCAC -s Anc1.Anc1refChr6 12614 9 + 197743 GGATGTCAC -s Anc2.Anc2refChr17 5629 7 + 28526 TGA--TCCC -s mr.mrrefChr5 196259 9 + 294540 GGATGTCAC -s simCow_chr6.simCow.chr6 320912 7 + 602619 TGA--CCCC -s simDog_chr6.simDog.chr6 313063 7 + 593897 CGA--TCCC -s simHuman_chr6.simHuman.chr6 332704 9 + 601863 GGATGTTAC -s simRat_chr6.simRat.chr6 340334 9 + 647215 AGATGGCAC - -a -s simMouse_chr6.simMouse.chr6 349040 21 + 636262 ACAATAAAACTGCTTCTTATT -s Anc0.Anc0refChr0 12331 21 + 26507 CCCAAACAACTGTTTCTTATT -s Anc1.Anc1refChr6 12623 21 + 197743 CCCAAACAACTGTTTCTTATT -s Anc2.Anc2refChr17 5636 21 + 28526 CCCAAACAACTGTTTTTTATT -s mr.mrrefChr5 196268 21 + 294540 ACAATAAAACTGCTTCTTATT -s simCow_chr6.simCow.chr6 320920 17 + 602619 CCCAAAC----GTTTTATATC -s simDog_chr6.simDog.chr6 313070 21 + 593897 TCCAAGGAACTGCCTTTTGTT -s simHuman_chr6.simHuman.chr6 332713 21 + 601863 CCGAAACAACTGTTTCTTATT -s simRat_chr6.simRat.chr6 340343 21 + 647215 ACAATAAAACTGCTTCTTGTG - -a -s simMouse_chr6.simMouse.chr6 349061 8 + 636262 CTCTTGGG -s Anc0.Anc0refChr0 12353 8 + 26507 CTCTTGCA -s Anc1.Anc1refChr6 12645 8 + 197743 CTCTTGCA -s Anc2.Anc2refChr17 5658 8 + 28526 CTCTTGCA -s mr.mrrefChr5 196289 8 + 294540 CTCTTGGG -s simCow_chr6.simCow.chr6 320938 8 + 602619 CTATACTA -s simDog_chr6.simDog.chr6 313092 8 + 593897 CTCTTGCA -s simHuman_chr6.simHuman.chr6 332735 8 + 601863 CTCTTACA -s simRat_chr6.simRat.chr6 340364 8 + 647215 CTCTTGGG - -a -s simMouse_chr6.simMouse.chr6 349069 17 + 636262 CAATTCTCAACTTTAGT -s Anc0.Anc0refChr0 12361 17 + 26507 AAACTCTCCTTTTTAGT -s Anc1.Anc1refChr6 12653 17 + 197743 AAACTCTCCTTTTTAGT -s Anc2.Anc2refChr17 5666 17 + 28526 ATCCTCTGCTTTTTAGT -s mr.mrrefChr5 196297 17 + 294540 CAATTCTCAATTTTAGT -s simCow_chr6.simCow.chr6 320947 14 + 602619 ATCCTC---TGTTTAGT -s simDog_chr6.simDog.chr6 313100 17 + 593897 ATCCTCTGCTTTTTAGT -s simHuman_chr6.simHuman.chr6 332743 17 + 601863 GAACTCTCTTTTTTAGT -s simRat_chr6.simRat.chr6 340372 17 + 647215 CAATTCTCAATTTTAGT - -a -s simMouse_chr6.simMouse.chr6 349086 16 + 636262 ACTTATATTGCCATAC -s Anc0.Anc0refChr0 12378 14 + 26507 ACT--TATTGGCATTC -s Anc1.Anc1refChr6 12670 14 + 197743 ACT--TATTGGCATTC -s Anc2.Anc2refChr17 5683 14 + 28526 AGT--TATTGGCATTC -s mr.mrrefChr5 196314 16 + 294540 ACTTATATTGCCATTC -s simCow_chr6.simCow.chr6 320961 14 + 602619 AGC--TATTGGCATTC -s simDog_chr6.simDog.chr6 313121 14 + 593897 GGT--TGCTGGTGTTC -s simHuman_chr6.simHuman.chr6 332760 14 + 601863 ACT--TATTGGCATTC -s simRat_chr6.simRat.chr6 340389 16 + 647215 GCTTATATTTCCATTC - -a -s simMouse_chr6.simMouse.chr6 349102 43 + 636262 TGAACCGTCTGAATATGATCCATTTGACTAGTCGATGTGTCAA -s Anc0.Anc0refChr0 12392 42 + 26507 T-TCTCATCTGAATATGATCCATGTAAATGGTAAATGTGTCAA -s Anc1.Anc1refChr6 12684 42 + 197743 T-TCTCATCTGAATATGATCCATGTAAATGGTAAATGTGTCAA -s Anc2.Anc2refChr17 5705 42 + 28526 T-CCTCATCTGATTATGATCCATGTAAATGGCAAATCTGTCAA -s mr.mrrefChr5 196330 43 + 294540 TGTACCGTCTGAATATGATCCATTTGACTAGTAGATGTGTCAA -s simCow_chr6.simCow.chr6 321003 42 + 602619 T-TTTCATCTGATTATGACTCATCTAAATGGCAAATCTGTCAA -s simDog_chr6.simDog.chr6 313143 26 + 593897 T-CCTCATCTGATCATGATCCATGTAA---------------- -s simHuman_chr6.simHuman.chr6 332774 42 + 601863 T-TCTCATCTGAATATGAGCCTTGTAAATGGTAAATGTGTCTA -s simRat_chr6.simRat.chr6 340405 40 + 647215 TGTA---TCTGAATACGATCCATTTGACTAGTAGATGTATCAA - -a -s simMouse_chr6.simMouse.chr6 349145 4 + 636262 CTAC -s Anc0.Anc0refChr0 12434 4 + 26507 CTGC -s Anc1.Anc1refChr6 12726 4 + 197743 CTGC -s Anc2.Anc2refChr17 5750 4 + 28526 CTGC -s mr.mrrefChr5 196373 4 + 294540 CTAC -s simCow_chr6.simCow.chr6 321048 4 + 602619 CTGC -s simDog_chr6.simDog.chr6 313169 1 + 593897 ---C -s simHuman_chr6.simHuman.chr6 332816 4 + 601863 CTGC -s simRat_chr6.simRat.chr6 340445 4 + 647215 CTAT - -a -s simMouse_chr6.simMouse.chr6 349149 19 + 636262 ATTATTACTCTGGATGCTT -s Anc0.Anc0refChr0 12438 19 + 26507 ATTATCACTCCAGATGTTT -s Anc1.Anc1refChr6 12730 19 + 197743 ATTATCACTCCAGATGTTT -s Anc2.Anc2refChr17 5754 19 + 28526 ATTATCGCTCCAGATGTTT -s mr.mrrefChr5 196377 19 + 294540 ATTATTACTCTGGATGCTT -s simCow_chr6.simCow.chr6 321052 19 + 602619 TTTATCCCTCCAGATGTTT -s simDog_chr6.simDog.chr6 313170 19 + 593897 ATTATTGTACCAGATGCTT -s simHuman_chr6.simHuman.chr6 332836 19 + 601863 ATTATCACTCCAGATGTTT -s simRat_chr6.simRat.chr6 340449 19 + 647215 ATTATTACTCTGGTTGCTT - -a -s simMouse_chr6.simMouse.chr6 349168 1 + 636262 C -s Anc0.Anc0refChr0 12457 1 + 26507 C -s Anc1.Anc1refChr6 12749 1 + 197743 C -s Anc2.Anc2refChr17 5773 1 + 28526 C -s mr.mrrefChr5 196396 1 + 294540 C -s simCow_chr6.simCow.chr6 321071 1 + 602619 C -s simDog_chr6.simDog.chr6 313189 1 + 593897 C -s simHuman_chr6.simHuman.chr6 332862 1 + 601863 C -s simRat_chr6.simRat.chr6 340468 1 + 647215 C - -a -s simMouse_chr6.simMouse.chr6 349169 27 + 636262 TAAGTGAGTGTCTTACAGACAGACATC -s Anc0.Anc0refChr0 12458 25 + 26507 AAATGGAGTAG--CTCAGGCTCACACC -s Anc1.Anc1refChr6 12750 27 + 197743 AAATGGAGTAGCTCTCAGGCTCACACC -s Anc2.Anc2refChr17 5775 25 + 28526 AAATGGTGTAG--CTCAAGATCACACT -s mr.mrrefChr5 196397 27 + 294540 AAAGTGAGTATCTTACAGACTCACATC -s simCow_chr6.simCow.chr6 321073 25 + 602619 AAATGGTGTAT--CACAAGATCACACT -s simDog_chr6.simDog.chr6 313191 13 + 593897 GAACGGTGTAG--TT------------ -s simHuman_chr6.simHuman.chr6 332863 27 + 601863 AAATGCAGTACCTATCAGGCTCGCACC -s simRat_chr6.simRat.chr6 340469 27 + 647215 AAAGTGAGTATCTTACAAACTCATGTC - -a -s simMouse_chr6.simMouse.chr6 349196 47 + 636262 TATTGAGCTCGTTAAAGGTGCAAACGTTCCCATGGGAGAGGTGGTAG -s Anc0.Anc0refChr0 12490 43 + 26507 TATCCAGTT----AATTGTCCAAAGGTTCTCACAGGAGAGGTGGTAT -s Anc1.Anc1refChr6 12784 47 + 197743 TATCCAGTTAGTCAATTGTCCAAAGGTTCTCACAGGAGAGGTGGTAT -s Anc2.Anc2refChr17 5807 43 + 28526 TATCCATTT----TATTGTCTGAAGCTTTTCACAGGAGAAGTGGCAT -s mr.mrrefChr5 196424 47 + 294540 TATTGAGCTTGTTAAAGGTGCAAAGGTTCCCATGGGAGAGGTGGTAG -s simCow_chr6.simCow.chr6 321105 43 + 602619 TATCCATTT----TATTGTCTGAAGCTTTTCACAGGAGAAGTGGCAT -s simHuman_chr6.simHuman.chr6 332899 47 + 601863 TATCCAGATAGTCAATTGTTCAAAGGTTCTCACAGGAGTGGTGGTGT -s simRat_chr6.simRat.chr6 340496 47 + 647215 TATTGAGCTTGTTATAGCTGTGAAGGTTCCCATGGGAGAGGTGGTAG - -a -s simMouse_chr6.simMouse.chr6 349243 4 + 636262 AATG -s Anc0.Anc0refChr0 12535 4 + 26507 AATG -s Anc1.Anc1refChr6 12833 4 + 197743 AATG -s Anc2.Anc2refChr17 5852 4 + 28526 CATT -s mr.mrrefChr5 196471 4 + 294540 AATG -s simCow_chr6.simCow.chr6 321150 4 + 602619 CATT -s simHuman_chr6.simHuman.chr6 332948 4 + 601863 AATG -s simRat_chr6.simRat.chr6 340543 4 + 647215 AATG - -a -s simMouse_chr6.simMouse.chr6 349247 2 + 636262 TA -s Anc0.Anc0refChr0 12578 2 + 26507 TA -s Anc1.Anc1refChr6 12876 2 + 197743 TA -s Anc2.Anc2refChr17 5896 2 + 28526 TG -s mr.mrrefChr5 196475 2 + 294540 TA -s simCow_chr6.simCow.chr6 321193 2 + 602619 TG -s simDog_chr6.simDog.chr6 313232 2 + 593897 TG -s simHuman_chr6.simHuman.chr6 333017 2 + 601863 TA -s simRat_chr6.simRat.chr6 340547 2 + 647215 TA - -a -s simMouse_chr6.simMouse.chr6 349249 36 + 636262 GATCCCACTCCTAGCAGTATCGTCAATAGTCTAGGG -s Anc0.Anc0refChr0 12580 36 + 26507 GCTCTCTCTCCTATTAGTGCCATTAATAGTCTAGAT -s Anc1.Anc1refChr6 12878 36 + 197743 GCTCTCTCTCCTATTAGTGCCATTAATAGTCTAGAT -s Anc2.Anc2refChr17 5898 36 + 28526 GCTCTCTCTCCTATTAGTGGCATTACTAGTCTAGAT -s mr.mrrefChr5 196477 36 + 294540 GATCTCACTCCTAGCAGTACCGTCAATAGTCTAGGG -s simCow_chr6.simCow.chr6 321195 36 + 602619 GCTCTCTCTCCCATTAGTGTCATTACTAGCCTTGAT -s simDog_chr6.simDog.chr6 313234 36 + 593897 GCTCTCCCTCCTATCAGTGGCATTACTAGTCTATAT -s simHuman_chr6.simHuman.chr6 333019 36 + 601863 GTTCTCTCTCCTATTAGTGCCATTAATAGTGTAGAT -s simRat_chr6.simRat.chr6 340550 36 + 647215 GATCTCACTCCTAGCATCACTGTCAATAGTCTAGGG - -a -s simMouse_chr6.simMouse.chr6 349285 13 + 636262 TGCTGTCCCATAT -s Anc0.Anc0refChr0 12617 13 + 26507 TGCTGTTCTGTTT -s Anc1.Anc1refChr6 12915 13 + 197743 TGCTGTTCTGTTT -s Anc2.Anc2refChr17 5935 13 + 28526 TGCTGTTTTGTTT -s mr.mrrefChr5 196513 13 + 294540 TGCTGTCCCATAT -s simCow_chr6.simCow.chr6 321232 13 + 602619 TGCTTTCGTGTTT -s simDog_chr6.simDog.chr6 313271 13 + 593897 TTTTGTTTTGTTT -s simHuman_chr6.simHuman.chr6 333056 10 + 601863 CGCTGTTCTG--- -s simRat_chr6.simRat.chr6 340586 13 + 647215 TGCTGTCGCATAC - -a -s simMouse_chr6.simMouse.chr6 349298 63 + 636262 ATACATTTTTAACCCATCAGGACTCTGTCTGTTCTAACCTGGTGACATCTGGGATGACTCTCA -s Anc0.Anc0refChr0 12630 58 + 26507 GTGCATTCCTGTCTCCTCGGTAGTCTTTGGATTATTCCCTGGTGAT-----GTCTGCCCCTCA -s Anc1.Anc1refChr6 12928 63 + 197743 GTGCATTCCTGTCTCCTCGGTAGTCTTTGGATTATTCCCTGGTGATGTCTGGTCTGCCCCTCA -s Anc2.Anc2refChr17 5948 58 + 28526 GTGCATTCCTATCTCCTTGGTGGTCTTTGGATTACTCCCTGGTGAT-----GTCTGCCCCTCA -s mr.mrrefChr5 196526 63 + 294540 ATACATTTTTGACCCATCGGGACTCTGTCTGTTATAACCTGGTGACATCTGGGATGACTCTCA -s simCow_chr6.simCow.chr6 321245 26 + 602619 GTGCATTCCTATCTCCAT---------------------------T-----GTCTGC-----A -s simDog_chr6.simDog.chr6 313285 58 + 593897 GTGCATTTCTATCTCCTTGGTGGTCTTTGGATTACTCCCTGGTGAT-----GTCTGCCCCTCA -s simHuman_chr6.simHuman.chr6 333066 63 + 601863 GTTCATTCCAGTTTCCTCGGTAGTCTTTGAATTATCTCCTGGTGATGTCTGGTCTGCCCCTCA -s simRat_chr6.simRat.chr6 340599 54 + 647215 ATACATTTTTGACCCATCGGGACTCTCCCTGCTATAACCTGGTGACAACTAGGA--------- - -a -s simMouse_chr6.simMouse.chr6 349361 44 + 636262 GTCACCAATCCTGGATCCATACATGTTCATCAATCATTAAGGAC -s Anc0.Anc0refChr0 12688 41 + 26507 GTCACCAATCCTGGAGCAGTACTTGTTCCTCGATCAGTAAG--- -s Anc1.Anc1refChr6 12991 41 + 197743 GTCACCAATCCTGGAGCAGTACTTGTTCCTCGATCAGTAAG--- -s Anc2.Anc2refChr17 6006 41 + 28526 GTCACCAATCCTGGAGCAGTACTTGTTCCTGGATCAGTAAA--- -s mr.mrrefChr5 196589 44 + 294540 GTCACCAATCCTGGATCCATACATGTTCATCGATCATTAAGGAC -s simCow_chr6.simCow.chr6 321271 41 + 602619 GTTACCAATCCTCAAGCAGTACTGGTTCCTGGATCAGTAAA--- -s simDog_chr6.simDog.chr6 313343 41 + 593897 GTCACCAATCCTGGAGCAGTACTTGTTCCTGGATCAGTAAA--- -s simHuman_chr6.simHuman.chr6 333152 41 + 601863 GTCACCAATCCTGGAGCAGTACTTATCCCCCGATAAGTAGG--- -s simRat_chr6.simRat.chr6 340653 39 + 647215 -----CCATCCTGGATCCACATAGGTTCATGGATCATTAAAAAC - -a -s simMouse_chr6.simMouse.chr6 349405 9 + 636262 CACCAGATT -s Anc0.Anc0refChr0 12729 9 + 26507 TACTGGATT -s Anc1.Anc1refChr6 13032 9 + 197743 TACTGGATT -s Anc2.Anc2refChr17 6047 9 + 28526 TACTGAATT -s mr.mrrefChr5 196633 9 + 294540 CACTAGATT -s simCow_chr6.simCow.chr6 321313 9 + 602619 CACTGTATT -s simDog_chr6.simDog.chr6 313384 9 + 593897 TCCTCAGTG -s simHuman_chr6.simHuman.chr6 333193 9 + 601863 TACTGGATT -s simRat_chr6.simRat.chr6 340692 9 + 647215 CACTAGATT - -a -s simMouse_chr6.simMouse.chr6 349414 1 + 636262 G -s Anc0.Anc0refChr0 12738 1 + 26507 G -s Anc1.Anc1refChr6 13041 1 + 197743 G -s Anc2.Anc2refChr17 6056 1 + 28526 G -s mr.mrrefChr5 196642 1 + 294540 G -s simCow_chr6.simCow.chr6 321333 1 + 602619 G -s simDog_chr6.simDog.chr6 313393 1 + 593897 G -s simHuman_chr6.simHuman.chr6 333202 1 + 601863 G -s simRat_chr6.simRat.chr6 340701 1 + 647215 G - -a -s simMouse_chr6.simMouse.chr6 349415 5 + 636262 CTAAA -s Anc0.Anc0refChr0 12739 5 + 26507 CTAAG -s Anc1.Anc1refChr6 13042 5 + 197743 CTAAG -s Anc2.Anc2refChr17 6057 5 + 28526 CTCAG -s mr.mrrefChr5 196643 5 + 294540 CTAAG -s simCow_chr6.simCow.chr6 321334 5 + 602619 CTCAG -s simDog_chr6.simDog.chr6 313446 5 + 593897 CTCAG -s simHuman_chr6.simHuman.chr6 333203 5 + 601863 CTAAG -s simRat_chr6.simRat.chr6 340702 5 + 647215 CTAAG - -a -s simMouse_chr6.simMouse.chr6 349420 3 + 636262 CAA -s Anc0.Anc0refChr0 12747 3 + 26507 CTG -s Anc1.Anc1refChr6 13050 3 + 197743 CTG -s Anc2.Anc2refChr17 6065 3 + 28526 CTG -s mr.mrrefChr5 196648 3 + 294540 CAG -s simCow_chr6.simCow.chr6 321342 3 + 602619 TAG -s simDog_chr6.simDog.chr6 313454 3 + 593897 CTG -s simHuman_chr6.simHuman.chr6 333211 3 + 601863 CTG -s simRat_chr6.simRat.chr6 340707 3 + 647215 CAG - -a -s simMouse_chr6.simMouse.chr6 349423 21 + 636262 ATGCAACTCACACATTTTTCT -s Anc0.Anc0refChr0 12750 18 + 26507 TTGTAGCCCATAC---CTTCT -s Anc1.Anc1refChr6 13053 18 + 197743 TTGTAGCCCATAC---CTTCT -s Anc2.Anc2refChr17 6068 18 + 28526 TTGTAGCCCATAC---CCTCT -s mr.mrrefChr5 196651 18 + 294540 ATGTAACTCACAC---CTTCT -s simCow_chr6.simCow.chr6 321345 18 + 602619 TTTTAGCCCACAT---CCTCT -s simDog_chr6.simDog.chr6 313471 18 + 593897 TAGAAGCACATAC---CCTCT -s simHuman_chr6.simHuman.chr6 333214 18 + 601863 TTGTAGCCCATGC---CTTCT -s simRat_chr6.simRat.chr6 340710 18 + 647215 ATGTAACTCACAC---CTCAT - -a -s simMouse_chr6.simMouse.chr6 349444 18 + 636262 TCTTGTTGGGGATGAGGA -s Anc0.Anc0refChr0 12768 18 + 26507 TGTCCTTGGGGATTAGGC -s Anc1.Anc1refChr6 13071 18 + 197743 TGTCCTTGGGGATTAGGC -s Anc2.Anc2refChr17 6086 18 + 28526 TGTCCTTGGGGATTAGGC -s mr.mrrefChr5 196669 18 + 294540 TCTTGTTGGGGATGAGGA -s simCow_chr6.simCow.chr6 321365 18 + 602619 GGCCCTTGGGGATTAGGC -s simDog_chr6.simDog.chr6 313489 18 + 593897 TGTCCTTGGGGACTAGGA -s simHuman_chr6.simHuman.chr6 333232 18 + 601863 TGTCATTGGTGATTAGGC -s simRat_chr6.simRat.chr6 340728 18 + 647215 TATTGTTGGGGATGAAGA - -a -s simMouse_chr6.simMouse.chr6 349462 59 + 636262 GTCTGTGCCCTATGTTGCTGGATTCCAAATTCTTTTTTCCCTTCTTGTCAACCCTCTGG -s Anc0.Anc0refChr0 12786 44 + 26507 GCCCCTACCTTATGTTACTGGATCCCAAATTCTTCTGTCCCTTC--------------- -s Anc1.Anc1refChr6 13089 57 + 197743 GCCCCTACCTTATGTTACTGGATCCCAAATTCTTCTGTCCCTTCCTGTCCACCTGCT-- -s Anc2.Anc2refChr17 6104 44 + 28526 GCCCCTACCTTATGTCACTGGATCCCAAATTCTTCTGTCCCTTC--------------- -s mr.mrrefChr5 196687 59 + 294540 GTCCGTGCCCTATGTTGCTGGATTCCAAATTCTTTTTTCCCTTCTTGTCAACCCTCTGG -s simCow_chr6.simCow.chr6 321384 44 + 602619 GCCCTCACCTTATGTCACTGGATCCTAAACTCTCCTGTCCCTTC--------------- -s simDog_chr6.simDog.chr6 313507 44 + 593897 GCCCCTGCCTTATTTCACTGGCTCCCAAATTCTTCCATCCCTTT--------------- -s simHuman_chr6.simHuman.chr6 333250 57 + 601863 GCCCCTACCTTCTGTTACTGGATCCCAAATCCTTCTGTCCCTTCCTGTCCACCTGCT-- -s simRat_chr6.simRat.chr6 340746 59 + 647215 TTCCATGCCCTATGTTGCTGGATTTAAAATTCTTTTTTCCCTTCTTGTCAACCCTCTTG - -a -s simMouse_chr6.simMouse.chr6 349521 45 + 636262 GTCCAGCTAATGTAGACGTATACTGGTCCCAGTGTCTGGAGACAG -s Anc0.Anc0refChr0 12830 7 + 26507 ------CTAATTT-------------------------------- -s Anc1.Anc1refChr6 13146 13 + 197743 CCCCAGCTAATTT-------------------------------- -s Anc2.Anc2refChr17 6148 7 + 28526 ------CTAATTC-------------------------------- -s mr.mrrefChr5 196746 45 + 294540 GCCCAGCTAATGTAGACATATACTGGTCCCAGTGTCTGGAGACAG -s simCow_chr6.simCow.chr6 321428 1 + 602619 ------T-------------------------------------- -s simDog_chr6.simDog.chr6 313551 7 + 593897 ------CTAATTC-------------------------------- -s simHuman_chr6.simHuman.chr6 333307 13 + 601863 CCCCAGCTGATTT-------------------------------- -s simRat_chr6.simRat.chr6 340815 45 + 647215 GCCCAGCTAATGTGGAGATACGCTGGTCCCTGTGTCTGGAGACAG - -a -s simMouse_chr6.simMouse.chr6 349566 23 + 636262 GCAACCCTAGCCATTAGGTGCAG -s Anc0.Anc0refChr0 12837 2 + 26507 ---------------------AC -s Anc1.Anc1refChr6 13159 2 + 197743 ---------------------AC -s Anc2.Anc2refChr17 6155 2 + 28526 ---------------------AC -s mr.mrrefChr5 196791 23 + 294540 GCAACCCTAGCCATTAGGTGCAG -s simDog_chr6.simDog.chr6 313558 2 + 593897 ---------------------AC -s simHuman_chr6.simHuman.chr6 333320 2 + 601863 ---------------------AC -s simRat_chr6.simRat.chr6 340866 23 + 647215 GTAACCCTAGTCATTAGGTGCAG - -a -s simMouse_chr6.simMouse.chr6 349589 16 + 636262 ACCTTCATTGGAACCT -s Anc0.Anc0refChr0 12839 16 + 26507 ACGTTCACTAGAACCC -s Anc1.Anc1refChr6 13161 16 + 197743 ACGTTCACTAGAACCC -s Anc2.Anc2refChr17 6157 16 + 28526 ACGTTCACTAGAACCC -s mr.mrrefChr5 196814 16 + 294540 ACCTTCATTGGAACCT -s simCow_chr6.simCow.chr6 321429 16 + 602619 GCGTTAAACAAAACCC -s simDog_chr6.simDog.chr6 313560 16 + 593897 ATGTTCACTAGAACCC -s simHuman_chr6.simHuman.chr6 333322 16 + 601863 ACATTCACTAGAACCC -s simRat_chr6.simRat.chr6 340899 16 + 647215 ACCTTCGTTGAAACCT - -a -s simMouse_chr6.simMouse.chr6 349605 35 + 636262 TTTCCTTAAACTTGACTCACATCTTTGTAAAGATT -s Anc0.Anc0refChr0 12855 35 + 26507 CTTCCTTATAGTTGGCTTATATCTGTATAAAGTTG -s Anc1.Anc1refChr6 13177 35 + 197743 CTTCCTTATAGTTGGCTTATATCTGTATAAAGTTG -s Anc2.Anc2refChr17 6173 35 + 28526 CTTCCTTATAGTTTGCTTATATCTGTATAAAGTTG -s mr.mrrefChr5 196830 35 + 294540 TTTCCTTAAACTTGACTCATATCTTTGTAAAGATT -s simCow_chr6.simCow.chr6 321778 34 + 602619 CTGCGTTATAGTTTGCT-ATATCTGTGTAAATTTG -s simDog_chr6.simDog.chr6 313576 35 + 593897 CTTCCTTAAAGTTTGCTTATATCTGTATAAAGTTG -s simHuman_chr6.simHuman.chr6 333338 35 + 601863 CTTCCTTCTAGTTGGTTTATAGCTGTATCAAGTTG -s simRat_chr6.simRat.chr6 340915 35 + 647215 TTTTCTTACATTTGACTCATATCTTAGAAAAGCTT - -a -s simMouse_chr6.simMouse.chr6 349640 1 + 636262 A -s Anc0.Anc0refChr0 12895 1 + 26507 A -s Anc1.Anc1refChr6 13217 1 + 197743 A -s Anc2.Anc2refChr17 6213 1 + 28526 A -s mr.mrrefChr5 196865 1 + 294540 A -s simCow_chr6.simCow.chr6 321817 1 + 602619 A -s simDog_chr6.simDog.chr6 313616 1 + 593897 A -s simHuman_chr6.simHuman.chr6 333378 1 + 601863 A -s simRat_chr6.simRat.chr6 340950 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 349641 7 + 636262 CCTGACA -s Anc0.Anc0refChr0 12896 7 + 26507 ATTGACA -s Anc1.Anc1refChr6 13218 7 + 197743 ATTGACA -s Anc2.Anc2refChr17 6215 7 + 28526 ATTGACA -s mr.mrrefChr5 196866 7 + 294540 CCTGACA -s simCow_chr6.simCow.chr6 321819 7 + 602619 ATTGACA -s simDog_chr6.simDog.chr6 313618 7 + 593897 ATTGACA -s simHuman_chr6.simHuman.chr6 333379 7 + 601863 ATTGATA -s simRat_chr6.simRat.chr6 340951 7 + 647215 CCTGACA - -a -s simMouse_chr6.simMouse.chr6 349648 2 + 636262 CA -s Anc0.Anc0refChr0 12903 2 + 26507 TA -s Anc1.Anc1refChr6 13225 2 + 197743 TA -s Anc2.Anc2refChr17 6222 2 + 28526 TA -s mr.mrrefChr5 196873 2 + 294540 CA -s simCow_chr6.simCow.chr6 321826 2 + 602619 CA -s simDog_chr6.simDog.chr6 313625 2 + 593897 TA -s simHuman_chr6.simHuman.chr6 333388 2 + 601863 TG -s simRat_chr6.simRat.chr6 340958 2 + 647215 CA - -a -s simMouse_chr6.simMouse.chr6 349650 20 + 636262 CAGGCAGACCAGACCTGCAG -s Anc0.Anc0refChr0 12905 11 + 26507 CAGTG---------CTACAA -s Anc1.Anc1refChr6 13227 11 + 197743 CAGTG---------CTACAA -s Anc2.Anc2refChr17 6229 11 + 28526 CAGTG---------CTACGA -s mr.mrrefChr5 196875 11 + 294540 CAGGC---------CTGCAG -s simCow_chr6.simCow.chr6 321833 11 + 602619 CAGTG---------CTACGA -s simDog_chr6.simDog.chr6 313632 11 + 593897 CAGTG---------CTACGA -s simHuman_chr6.simHuman.chr6 333390 11 + 601863 CAGTA---------CTACAA -s simRat_chr6.simRat.chr6 340960 11 + 647215 TGGGC---------CTCGAG - -a -s simMouse_chr6.simMouse.chr6 349670 35 + 636262 ACTCAGATGAAATACCGACGTAATGTACAATACTA -s Anc0.Anc0refChr0 12916 33 + 26507 CTCTAAGCATCATACAGGTGCAA--CATAAGGGTA -s Anc1.Anc1refChr6 13238 33 + 197743 CTCTAAGCATCATACAGGTGCAA--CATAAGGGTA -s Anc2.Anc2refChr17 6240 33 + 28526 CTCTAAGCATCACATATGTACAA--CATAAGGGTA -s mr.mrrefChr5 196886 35 + 294540 ACTCAGATAAAATACCGACGTAATGTACAATACTA -s simCow_chr6.simCow.chr6 321845 33 + 602619 CTCTAAGCATCACATATATATGA--CATTAGGGTA -s simDog_chr6.simDog.chr6 313643 27 + 593897 ------GCATCACATATGAACAA--CATAATGGTA -s simHuman_chr6.simHuman.chr6 333401 33 + 601863 TACTAAGCATCATACAGTTGCAA--CATAAGGGTA -s simRat_chr6.simRat.chr6 340971 35 + 647215 ACTCAGATAAGATACCGACGTAATGTACAATACTA - -a -s simMouse_chr6.simMouse.chr6 349705 11 + 636262 CTAGCTCTGAA -s Anc0.Anc0refChr0 12956 11 + 26507 CAAGGTTTGAA -s Anc1.Anc1refChr6 13278 11 + 197743 CAAGGTTTGAA -s Anc2.Anc2refChr17 6284 11 + 28526 CAAGGTTTGAA -s mr.mrrefChr5 196921 11 + 294540 CTAGTTCTGAA -s simCow_chr6.simCow.chr6 321889 11 + 602619 CAAGCTTTGAC -s simDog_chr6.simDog.chr6 313681 11 + 593897 CAAGGATTAAA -s simHuman_chr6.simHuman.chr6 333441 11 + 601863 CAAGATTTGAG -s simRat_chr6.simRat.chr6 341006 11 + 647215 CTAGTTCTGAA - -a -s simMouse_chr6.simMouse.chr6 349716 10 + 636262 GCATCCCTGT -s Anc0.Anc0refChr0 12979 10 + 26507 GCATTACATA -s Anc1.Anc1refChr6 13301 10 + 197743 GCATTACATA -s Anc2.Anc2refChr17 6307 10 + 28526 GCATTACATA -s mr.mrrefChr5 196932 10 + 294540 GCATCCCTGT -s simCow_chr6.simCow.chr6 321913 8 + 602619 GCAT--CATT -s simDog_chr6.simDog.chr6 313702 8 + 593897 --ATTACATA -s simHuman_chr6.simHuman.chr6 333464 10 + 601863 GCATTACATG -s simRat_chr6.simRat.chr6 341017 10 + 647215 GCATCCCTGT - -a -s simMouse_chr6.simMouse.chr6 349726 27 + 636262 GGGAGGCATGGGAAGTGGAGTGGGATT -s Anc0.Anc0refChr0 12989 27 + 26507 GTGAGACATGGGAAGAAGAGCAGGCTA -s Anc1.Anc1refChr6 13311 27 + 197743 GTGAGACATGGGAAGAAGAGCAGGCTA -s Anc2.Anc2refChr17 6317 27 + 28526 GTAAGATGTGGGACAAAGAGCAGGCTA -s mr.mrrefChr5 196942 27 + 294540 GGGAGGCATGGGAAGTAGAGTAGGATT -s simCow_chr6.simCow.chr6 321921 27 + 602619 GTAAGGTGTGGTAGTTAGTGCAGGCTA -s simDog_chr6.simDog.chr6 313716 27 + 593897 GTAAGATGTGAGACAAAGAGCAGGCTA -s simHuman_chr6.simHuman.chr6 333474 27 + 601863 GTGAGACATGGGAAGAAGAGAAGGCCA -s simRat_chr6.simRat.chr6 341027 27 + 647215 GGGAGGGATGGGAAACAGAGTAGGATT - -a -s simMouse_chr6.simMouse.chr6 349753 37 + 636262 ATGTAGCTTGGTTCCTACTCAGACTGACACCCACACA -s Anc0.Anc0refChr0 13016 37 + 26507 GTGCAACTTGATTTTTACCCGGACTGACACCCATACA -s Anc1.Anc1refChr6 13338 37 + 197743 GTGCAACTTGATTTTTACCCGGACTGACACCCATACA -s Anc2.Anc2refChr17 6347 37 + 28526 GTGCAACTTGATTTTTACCCGAACTGACACCCATACA -s mr.mrrefChr5 196969 37 + 294540 ATGTAACTTGGTTCCTACCCAGACTGACACCCACACA -s simCow_chr6.simCow.chr6 321951 37 + 602619 GTGAAACTTTTTTTTTACCCATACTGACACCCATACA -s simDog_chr6.simDog.chr6 313746 36 + 593897 GTGCAGCTTGATTCTTACCCGA-CTGACATCCATACA -s simHuman_chr6.simHuman.chr6 333501 36 + 601863 GTGCAACTTGATTTTTACCCGGTCTGATACCCATAC- -s simRat_chr6.simRat.chr6 341054 37 + 647215 ATGTAACTTAGTTCCTACCCAGACTGACACCCTCACA - -a -s simMouse_chr6.simMouse.chr6 349790 21 + 636262 AAGTCCAGGCCCTGAGTGAAA -s Anc0.Anc0refChr0 13053 21 + 26507 TGGTGCAACCACTGAGGCAAA -s Anc1.Anc1refChr6 13375 21 + 197743 TGGTGCAACCACTGAGGCAAA -s Anc2.Anc2refChr17 6388 21 + 28526 TGGTGCAACCACTGAGGCAAA -s mr.mrrefChr5 197006 21 + 294540 TAGTCCAGGCCCTGAGTGAAA -s simCow_chr6.simCow.chr6 321992 4 + 602619 -----------------CCAA -s simDog_chr6.simDog.chr6 313796 21 + 593897 TGGTGCAACCACTGAGGCAGA -s simHuman_chr6.simHuman.chr6 333537 21 + 601863 TGGTGCAACTACTAACACAAA -s simRat_chr6.simRat.chr6 341091 21 + 647215 TAGTCCAGGCCCCGAGCAAAA - -a -s simMouse_chr6.simMouse.chr6 349811 1 + 636262 G -s Anc0.Anc0refChr0 13074 1 + 26507 G -s Anc1.Anc1refChr6 13396 1 + 197743 G -s Anc2.Anc2refChr17 6409 1 + 28526 G -s mr.mrrefChr3 69024 1 + 181027 G -s mr.mrrefChr5 197027 1 + 294540 G -s simCow_chr6.simCow.chr6 321996 1 + 602619 G -s simDog_chr6.simDog.chr6 313817 1 + 593897 G -s simHuman_chr6.simHuman.chr6 333558 1 + 601863 G -s simMouse_chr6.simMouse.chr6 516405 1 + 636262 G -s simRat_chr6.simRat.chr6 527970 1 + 647215 G -s simRat_chr6.simRat.chr6 341112 1 + 647215 G - -a -s simMouse_chr6.simMouse.chr6 349812 3 + 636262 ATA -s Anc0.Anc0refChr0 13075 3 + 26507 ATA -s Anc1.Anc1refChr6 13397 3 + 197743 ATA -s Anc2.Anc2refChr17 6410 3 + 28526 ATA -s mr.mrrefChr3 69025 3 + 181027 ATA -s mr.mrrefChr5 197028 3 + 294540 ATA -s simCow_chr6.simCow.chr6 321997 3 + 602619 GTT -s simDog_chr6.simDog.chr6 313818 3 + 593897 ATA -s simHuman_chr6.simHuman.chr6 333559 3 + 601863 ATA -s simMouse_chr6.simMouse.chr6 516406 3 + 636262 AAA -s simRat_chr6.simRat.chr6 527971 3 + 647215 ATA -s simRat_chr6.simRat.chr6 341116 3 + 647215 ATA - -a -s simMouse_chr6.simMouse.chr6 349815 9 + 636262 GTCAATTGC -s Anc0.Anc0refChr0 13078 9 + 26507 GGCCACCCC -s Anc1.Anc1refChr6 13400 9 + 197743 GGCCACCCC -s Anc2.Anc2refChr17 6413 9 + 28526 GGCCACCCT -s mr.mrrefChr3 69028 9 + 181027 AGCCATCAC -s mr.mrrefChr5 197031 9 + 294540 GTCCATTGC -s simCow_chr6.simCow.chr6 322000 9 + 602619 GGCCACCTT -s simDog_chr6.simDog.chr6 313827 9 + 593897 TGCCACCCT -s simHuman_chr6.simHuman.chr6 333562 9 + 601863 GGCCACTCC -s simMouse_chr6.simMouse.chr6 516409 9 + 636262 AGTAATCAC -s simRat_chr6.simRat.chr6 527974 9 + 647215 GGCCATCAC -s simRat_chr6.simRat.chr6 341119 9 + 647215 GTACATTGC - -a -s simMouse_chr6.simMouse.chr6 349824 17 + 636262 TTAGCTTAGTTCACTTC -s Anc0.Anc0refChr0 13087 16 + 26507 CTTGCCTAGTTCACTT- -s Anc1.Anc1refChr6 13409 17 + 197743 CTTGCCTAGTTCACTTC -s Anc2.Anc2refChr17 6422 16 + 28526 CTTGCCTAGTTCACTT- -s mr.mrrefChr3 69037 17 + 181027 CCAGCCTAGTTCACTTG -s mr.mrrefChr5 197040 17 + 294540 CTAGCCTAGTTCACTTC -s simCow_chr6.simCow.chr6 322009 8 + 602619 CT--------TCACTT- -s simDog_chr6.simDog.chr6 313836 16 + 593897 CTTGCCTAGTTCTCTG- -s simHuman_chr6.simHuman.chr6 333571 17 + 601863 CTTGCCTTGTTCACATC -s simMouse_chr6.simMouse.chr6 516493 15 + 636262 CCA--TTGGCCCACATG -s simRat_chr6.simRat.chr6 527983 17 + 647215 CCAGCCTAGTTCACTCG -s simRat_chr6.simRat.chr6 341128 17 + 647215 CTAGCCTAGTGTACTTC - -a -s simMouse_chr6.simMouse.chr6 349841 1 + 636262 C -s Anc0.Anc0refChr0 13103 1 + 26507 C -s Anc1.Anc1refChr6 13426 1 + 197743 C -s Anc2.Anc2refChr17 6438 1 + 28526 C -s mr.mrrefChr3 69054 1 + 181027 C -s mr.mrrefChr5 197057 1 + 294540 C -s simCow_chr6.simCow.chr6 322017 1 + 602619 C -s simDog_chr6.simDog.chr6 313852 1 + 593897 C -s simMouse_chr6.simMouse.chr6 516508 1 + 636262 C -s simRat_chr6.simRat.chr6 341145 1 + 647215 C - -a -s simMouse_chr6.simMouse.chr6 349842 3 + 636262 ATC -s Anc0.Anc0refChr0 13104 3 + 26507 ACT -s Anc1.Anc1refChr6 13427 3 + 197743 ACT -s Anc2.Anc2refChr17 6439 3 + 28526 ACT -s mr.mrrefChr3 69055 3 + 181027 ATT -s mr.mrrefChr5 197058 3 + 294540 ATC -s simCow_chr6.simCow.chr6 322018 3 + 602619 ACT -s simDog_chr6.simDog.chr6 313853 3 + 593897 AAT -s simHuman_chr6.simHuman.chr6 333588 3 + 601863 ACG -s simMouse_chr6.simMouse.chr6 516509 3 + 636262 ATT -s simRat_chr6.simRat.chr6 528000 3 + 647215 ATT -s simRat_chr6.simRat.chr6 341146 3 + 647215 TTC - -a -s simMouse_chr6.simMouse.chr6 349845 12 + 636262 AAGGATCACTTT -s Anc0.Anc0refChr0 13108 12 + 26507 AAGGGTTATTTT -s Anc1.Anc1refChr6 13431 12 + 197743 AAGGGTTATTTT -s Anc2.Anc2refChr17 6443 12 + 28526 AAGGGTTATTTT -s mr.mrrefChr3 69059 12 + 181027 ATGGCTCATTGT -s mr.mrrefChr5 197061 12 + 294540 AAGGATCACTTT -s simCow_chr6.simCow.chr6 322022 12 + 602619 AAGTGTTATTTT -s simDog_chr6.simDog.chr6 313857 12 + 593897 AAGGGCTTTTTT -s simHuman_chr6.simHuman.chr6 333592 12 + 601863 AAGGGTTATTTT -s simMouse_chr6.simMouse.chr6 516513 12 + 636262 CTGTCTCATTGG -s simRat_chr6.simRat.chr6 528004 12 + 647215 ATGGGTCATTCT -s simRat_chr6.simRat.chr6 341149 12 + 647215 AAGGATCACTTT - -a -s simMouse_chr6.simMouse.chr6 349857 4 + 636262 CAAG -s Anc0.Anc0refChr0 13120 4 + 26507 TGGG -s Anc1.Anc1refChr6 13443 4 + 197743 TGGG -s Anc2.Anc2refChr17 6455 4 + 28526 TGGG -s mr.mrrefChr5 197073 4 + 294540 CAAG -s simCow_chr6.simCow.chr6 322034 4 + 602619 TGGG -s simDog_chr6.simDog.chr6 313869 4 + 593897 TGGG -s simHuman_chr6.simHuman.chr6 333604 4 + 601863 TGGG -s simRat_chr6.simRat.chr6 341163 4 + 647215 CAAG - -a -s simMouse_chr6.simMouse.chr6 349861 3 + 636262 GTA -s Anc0.Anc0refChr0 13126 3 + 26507 GTA -s Anc1.Anc1refChr6 13449 3 + 197743 GTA -s Anc2.Anc2refChr17 6461 3 + 28526 ATA -s mr.mrrefChr5 197077 3 + 294540 GTA -s simCow_chr6.simCow.chr6 322040 3 + 602619 ATC -s simDog_chr6.simDog.chr6 313875 3 + 593897 ATA -s simHuman_chr6.simHuman.chr6 333610 3 + 601863 GTG -s simRat_chr6.simRat.chr6 341167 3 + 647215 GCA - -a -s simMouse_chr6.simMouse.chr6 349864 10 + 636262 TAGTTCTTGA -s Anc0.Anc0refChr0 13129 10 + 26507 TAGTTTTTGA -s Anc1.Anc1refChr6 13452 10 + 197743 TAGTTTTTGA -s Anc2.Anc2refChr17 6464 10 + 28526 TAGTTTTTGA -s mr.mrrefChr3 69071 10 + 181027 TAGTCTTTGA -s mr.mrrefChr5 197080 10 + 294540 TAGTTCTTGA -s simCow_chr6.simCow.chr6 322043 10 + 602619 CAGTTTTTAA -s simDog_chr6.simDog.chr6 313878 10 + 593897 TTGTTTTTGA -s simHuman_chr6.simHuman.chr6 333613 10 + 601863 TAGTTTTTCA -s simMouse_chr6.simMouse.chr6 516525 10 + 636262 TAGTCTTTGA -s simRat_chr6.simRat.chr6 528016 10 + 647215 TAGGACGTAA -s simRat_chr6.simRat.chr6 341170 10 + 647215 GAGCTCTTGA - -a -s simMouse_chr6.simMouse.chr6 349874 10 + 636262 CTTGTCCATC -s Anc0.Anc0refChr0 13139 10 + 26507 CTCAACTGCC -s Anc1.Anc1refChr6 13462 10 + 197743 CTCAACTGCC -s Anc2.Anc2refChr17 6474 10 + 28526 GTCAACTGCC -s mr.mrrefChr3 69081 8 + 181027 --GAGCTGCC -s mr.mrrefChr5 197090 10 + 294540 CTCATCTGTC -s simCow_chr6.simCow.chr6 322053 10 + 602619 TTGAATAGTC -s simDog_chr6.simDog.chr6 313888 10 + 593897 GTCAACTGCC -s simHuman_chr6.simHuman.chr6 333623 10 + 601863 CTCAACTGTT -s simMouse_chr6.simMouse.chr6 516535 8 + 636262 --GAGCTGCC -s simRat_chr6.simRat.chr6 341180 10 + 647215 CTCATCTGTC - -a -s simMouse_chr6.simMouse.chr6 349884 4 + 636262 GATT -s Anc0.Anc0refChr0 13149 4 + 26507 ACTT -s Anc1.Anc1refChr6 13472 4 + 197743 ACTT -s Anc2.Anc2refChr17 6484 4 + 28526 ACTT -s mr.mrrefChr3 69089 4 + 181027 ACTT -s mr.mrrefChr5 197100 4 + 294540 GATT -s simCow_chr6.simCow.chr6 322063 4 + 602619 ACTT -s simDog_chr6.simDog.chr6 313898 4 + 593897 ACTT -s simHuman_chr6.simHuman.chr6 333633 4 + 601863 GATT -s simMouse_chr6.simMouse.chr6 516543 4 + 636262 ACTT -s simRat_chr6.simRat.chr6 528026 4 + 647215 AGTT -s simRat_chr6.simRat.chr6 341190 4 + 647215 AATT - -a -s simMouse_chr6.simMouse.chr6 349888 1 + 636262 T -s Anc0.Anc0refChr0 13153 1 + 26507 T -s Anc1.Anc1refChr6 13476 1 + 197743 T -s Anc2.Anc2refChr17 6489 1 + 28526 T -s mr.mrrefChr3 69093 1 + 181027 T -s mr.mrrefChr5 197104 1 + 294540 T -s simCow_chr6.simCow.chr6 322068 1 + 602619 T -s simDog_chr6.simDog.chr6 313903 1 + 593897 T -s simHuman_chr6.simHuman.chr6 333637 1 + 601863 T -s simMouse_chr6.simMouse.chr6 516547 1 + 636262 T -s simRat_chr6.simRat.chr6 528030 1 + 647215 T -s simRat_chr6.simRat.chr6 341194 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 349889 3 + 636262 CTT -s Anc0.Anc0refChr0 13156 3 + 26507 CTT -s Anc1.Anc1refChr6 13479 3 + 197743 CTT -s Anc2.Anc2refChr17 6492 3 + 28526 CTT -s mr.mrrefChr3 69096 3 + 181027 CTT -s mr.mrrefChr5 197105 3 + 294540 CTT -s simCow_chr6.simCow.chr6 322071 3 + 602619 CCT -s simDog_chr6.simDog.chr6 313906 3 + 593897 CTT -s simHuman_chr6.simHuman.chr6 333638 3 + 601863 CTG -s simMouse_chr6.simMouse.chr6 516550 3 + 636262 CTT -s simRat_chr6.simRat.chr6 528033 3 + 647215 CTT -s simRat_chr6.simRat.chr6 341195 3 + 647215 CTT - -a -s simMouse_chr6.simMouse.chr6 349892 8 + 636262 AGTGGAAC -s Anc0.Anc0refChr0 13159 8 + 26507 TCTTAATG -s Anc1.Anc1refChr6 13482 8 + 197743 TCTTAATG -s Anc2.Anc2refChr17 6499 8 + 28526 TCTTAATG -s mr.mrrefChr3 69099 8 + 181027 TTAGAAAG -s mr.mrrefChr5 197108 8 + 294540 AGTGAAAC -s simCow_chr6.simCow.chr6 322090 8 + 602619 CCTTAATG -s simDog_chr6.simDog.chr6 313913 8 + 593897 TTTTAATA -s simHuman_chr6.simHuman.chr6 333641 8 + 601863 GCTTAATG -s simMouse_chr6.simMouse.chr6 516553 8 + 636262 TTAGGAAG -s simRat_chr6.simRat.chr6 528036 8 + 647215 TTAGAAAG -s simRat_chr6.simRat.chr6 341198 8 + 647215 AGTGAACC - -a -s simMouse_chr6.simMouse.chr6 349900 9 + 636262 TCTCCTCTT -s Anc0.Anc0refChr0 13168 9 + 26507 AGCTTTCTT -s Anc1.Anc1refChr6 13491 9 + 197743 AGCTTTCTT -s Anc2.Anc2refChr17 6508 9 + 28526 AGCTTTCTT -s mr.mrrefChr3 69108 9 + 181027 AGATTTTTT -s mr.mrrefChr5 197117 9 + 294540 TCTTCTCTT -s simCow_chr6.simCow.chr6 322099 9 + 602619 AACTTTCTT -s simDog_chr6.simDog.chr6 313922 9 + 593897 AGTTTTCTT -s simHuman_chr6.simHuman.chr6 333650 9 + 601863 ACCTTTCTT -s simMouse_chr6.simMouse.chr6 516562 9 + 636262 ATAGTTTTT -s simRat_chr6.simRat.chr6 528045 9 + 647215 AGATTTTTT -s simRat_chr6.simRat.chr6 341207 9 + 647215 TCTTCTCTT - -a -s simMouse_chr6.simMouse.chr6 349909 13 + 636262 TGGAAGTTTAAAG -s Anc0.Anc0refChr0 13177 13 + 26507 TGGAAGTTTAAAG -s Anc1.Anc1refChr6 13500 13 + 197743 TGGAAGTTTAAAG -s Anc2.Anc2refChr17 6517 13 + 28526 TGGAAGTTTGAAG -s mr.mrrefChr3 69136 13 + 181027 TTGGGGCTTAGTG -s mr.mrrefChr5 197126 13 + 294540 TGGAAGTTTAAAG -s simCow_chr6.simCow.chr6 322108 13 + 602619 TGGAAGTGTGAGG -s simDog_chr6.simDog.chr6 313931 13 + 593897 TAGAAGTTTGAAG -s simHuman_chr6.simHuman.chr6 333659 13 + 601863 TGGAAGTACAAAG -s simMouse_chr6.simMouse.chr6 516590 13 + 636262 TTGGGGCTTAATG -s simRat_chr6.simRat.chr6 528073 13 + 647215 CTGGGGCTTAGTG -s simRat_chr6.simRat.chr6 341216 13 + 647215 TGGAGATTTAAAG - -a -s simMouse_chr6.simMouse.chr6 349922 1 + 636262 G -s Anc0.Anc0refChr0 13195 1 + 26507 G -s Anc1.Anc1refChr6 13518 1 + 197743 G -s Anc2.Anc2refChr17 6535 1 + 28526 G -s mr.mrrefChr3 69149 1 + 181027 G -s mr.mrrefChr5 197139 1 + 294540 G -s simCow_chr6.simCow.chr6 322126 1 + 602619 G -s simDog_chr6.simDog.chr6 313949 1 + 593897 A -s simHuman_chr6.simHuman.chr6 333677 1 + 601863 G -s simMouse_chr6.simMouse.chr6 516603 1 + 636262 G -s simRat_chr6.simRat.chr6 528086 1 + 647215 G -s simRat_chr6.simRat.chr6 341229 1 + 647215 G - -a -s simMouse_chr6.simMouse.chr6 349923 1 + 636262 A -s Anc0.Anc0refChr0 13196 1 + 26507 A -s Anc1.Anc1refChr6 13519 1 + 197743 A -s Anc2.Anc2refChr17 6536 1 + 28526 A -s mr.mrrefChr5 197140 1 + 294540 A -s simCow_chr6.simCow.chr6 322127 1 + 602619 A -s simDog_chr6.simDog.chr6 313950 1 + 593897 A -s simHuman_chr6.simHuman.chr6 333678 1 + 601863 A -s simRat_chr6.simRat.chr6 341230 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 349924 26 + 636262 AACCTTGTCCTGGGTCCTTTGCTCGG -s Anc0.Anc0refChr0 13197 26 + 26507 AGTCTTGTGCTGAGTCCTTTGCTTGG -s Anc1.Anc1refChr6 13520 26 + 197743 AGTCTTGTGCTGAGTCCTTTGCTTGG -s Anc2.Anc2refChr17 6537 26 + 28526 AGTCTTGTGCTGAGTCCTTTGCTTGG -s mr.mrrefChr3 69150 26 + 181027 AACCCTCCTCCCTTTCCTGTGCTTGG -s mr.mrrefChr5 197141 26 + 294540 AACCTTGTCATGGGTCCTTTGCTCGG -s simCow_chr6.simCow.chr6 322128 26 + 602619 AGTCTTGTGGTGGATCCTTTCCTTAG -s simDog_chr6.simDog.chr6 313951 26 + 593897 AGTCCTCTGCTGAGTCCTGTGCTTGG -s simHuman_chr6.simHuman.chr6 333679 26 + 601863 AGTCTTGTAATGAGTCCTTTGCTTGG -s simMouse_chr6.simMouse.chr6 516604 15 + 636262 GACCCTCCTCCCTTT----------- -s simRat_chr6.simRat.chr6 528087 26 + 647215 AACTCTCCTCCCTTTCCTGTGCTTGG -s simRat_chr6.simRat.chr6 341231 26 + 647215 AACCTTGTCATGGGTCCTTTGCTCAG - -a -s simMouse_chr6.simMouse.chr6 349950 4 + 636262 TGGC -s Anc0.Anc0refChr0 13224 4 + 26507 TGGT -s Anc1.Anc1refChr6 13547 4 + 197743 TGGT -s Anc2.Anc2refChr17 6564 4 + 28526 AGGT -s mr.mrrefChr3 69177 4 + 181027 TGGT -s mr.mrrefChr5 197167 4 + 294540 TGGT -s simCow_chr6.simCow.chr6 322155 4 + 602619 AGGT -s simDog_chr6.simDog.chr6 313978 4 + 593897 AGGT -s simHuman_chr6.simHuman.chr6 333706 4 + 601863 TGGT -s simRat_chr6.simRat.chr6 528114 4 + 647215 TGGT -s simRat_chr6.simRat.chr6 341257 4 + 647215 TGGT - -a -s simMouse_chr6.simMouse.chr6 349954 10 + 636262 AACCAGATAT -s Anc0.Anc0refChr0 13228 10 + 26507 AATTAGAGAG -s Anc1.Anc1refChr6 13551 10 + 197743 AATTAGAGAG -s Anc2.Anc2refChr17 6568 10 + 28526 AATTCGAGAA -s mr.mrrefChr3 69181 10 + 181027 AATTTGAGAG -s mr.mrrefChr5 197171 10 + 294540 AACCAGATAG -s simCow_chr6.simCow.chr6 322159 10 + 602619 CATTGGAGAA -s simDog_chr6.simDog.chr6 313989 10 + 593897 AATTCGAGAA -s simHuman_chr6.simHuman.chr6 333710 10 + 601863 AATCAGAGAT -s simRat_chr6.simRat.chr6 528118 10 + 647215 AATTTGAGAG -s simRat_chr6.simRat.chr6 341261 8 + 647215 AACCA--TAG - -a -s simMouse_chr6.simMouse.chr6 349964 10 + 636262 AAGGATCCTA -s Anc0.Anc0refChr0 13239 10 + 26507 AGGGAGTCTA -s Anc1.Anc1refChr6 13562 10 + 197743 AGGGAGTCTA -s Anc2.Anc2refChr17 6579 10 + 28526 AGAAAGTCTA -s mr.mrrefChr3 69192 10 + 181027 AGGGAAGCTG -s mr.mrrefChr5 197181 10 + 294540 AGGGATCCTA -s simCow_chr6.simCow.chr6 322170 10 + 602619 AGATAGCATA -s simDog_chr6.simDog.chr6 314000 10 + 593897 AGAAGGTCTT -s simHuman_chr6.simHuman.chr6 333721 10 + 601863 AGGGAGTCTA -s simRat_chr6.simRat.chr6 528129 10 + 647215 AGGGAAGCTG -s simRat_chr6.simRat.chr6 341269 10 + 647215 AGGCATCCTA - -a -s simMouse_chr6.simMouse.chr6 349974 53 + 636262 GCCGTATGTGCACTATGCTTGAGGTGTACTTGAAGATACGCTCACTACTATCA -s Anc0.Anc0refChr0 13249 53 + 26507 GTTGTGGGTGTACCTTGCTTGGGGAGTATTTGAAGAAAAGACCGCTACCACTG -s Anc1.Anc1refChr6 13572 53 + 197743 GTTGTGGGTGTACCTTGCTTGGGGAGTATTTGAAGAAAAGACCGCTACCACTG -s Anc2.Anc2refChr17 6589 53 + 28526 GTAGTGGGGGTACCTTACTTGGGAAGTATTTGAAAAAAAGACCGCTAACACTG -s mr.mrrefChr3 69202 53 + 181027 GTTGTAGATGTAGCTTGCTTGGGGTGCAATTGAAGAGAAGCATGTCACCACTG -s mr.mrrefChr5 197191 53 + 294540 GCCGTATGTACACTATGCTTGGGGTGTACTTGAAGATAAGCTCACTACCATCA -s simCow_chr6.simCow.chr6 322180 45 + 602619 GTAGTTGGGGTATTTTCCTTGACGAGTGTTTGAAAAAAAGACCGC-------- -s simDog_chr6.simDog.chr6 314010 53 + 593897 GTACTGGGGGTACCTTAATTGGGAAGTATTTGAAAAAGAGACCGCTAACACTG -s simHuman_chr6.simHuman.chr6 333731 53 + 601863 GCTGTGGGTATACCTTGCATGGGTAGTATTTGAGGAAAAAACCGTAACCATTG -s simRat_chr6.simRat.chr6 528140 53 + 647215 GTTGTAGATGTAGCTTGCTTGGGGTGCAATTGAAGAGAAGCATGTCACCACTG -s simRat_chr6.simRat.chr6 341279 52 + 647215 GCCACATGTACACGAG-CTCAGGGTATACTTGAAGATAAGCTCACTACCATCA - -a -s simMouse_chr6.simMouse.chr6 350027 5 + 636262 TAAAC -s Anc0.Anc0refChr0 13302 5 + 26507 TAAAC -s Anc1.Anc1refChr6 13625 5 + 197743 TAAAC -s Anc2.Anc2refChr17 6644 5 + 28526 TAACC -s mr.mrrefChr3 69255 5 + 181027 TAAAT -s mr.mrrefChr5 197244 5 + 294540 TAAAC -s simDog_chr6.simDog.chr6 314065 5 + 593897 TAACC -s simHuman_chr6.simHuman.chr6 333784 5 + 601863 CTAAC -s simRat_chr6.simRat.chr6 528193 5 + 647215 TAAAT -s simRat_chr6.simRat.chr6 341331 5 + 647215 TAAAC - -a -s simMouse_chr6.simMouse.chr6 350032 15 + 636262 ATCTCTTGTCTGATA -s Anc0.Anc0refChr0 13307 15 + 26507 ATCTTTTGCCTGAGA -s Anc1.Anc1refChr6 13630 15 + 197743 ATCTTTTGCCTGAGA -s Anc2.Anc2refChr17 6649 15 + 28526 ATCTTTTGCCCAAGA -s mr.mrrefChr3 69263 15 + 181027 GTCTATTGCATGAGG -s mr.mrrefChr5 197249 15 + 294540 ATCTCTTGTCTGAGA -s simDog_chr6.simDog.chr6 314070 15 + 593897 ATCTTTTGCCCAAGA -s simHuman_chr6.simHuman.chr6 333817 15 + 601863 ACTTTTTGCCTGAGA -s simRat_chr6.simRat.chr6 528201 15 + 647215 GTCTATTGCATGAGG -s simRat_chr6.simRat.chr6 341337 15 + 647215 ATCTATTGTCTGAGA - -a -s simMouse_chr6.simMouse.chr6 350047 6 + 636262 TGCACT -s Anc0.Anc0refChr0 13322 6 + 26507 TGGCCT -s Anc1.Anc1refChr6 13645 6 + 197743 TGGCCT -s Anc2.Anc2refChr17 6664 6 + 28526 TTGCCC -s mr.mrrefChr5 197264 6 + 294540 TGCACT -s simDog_chr6.simDog.chr6 314085 6 + 593897 TTGCCC -s simHuman_chr6.simHuman.chr6 333832 6 + 601863 AGGCCT -s simRat_chr6.simRat.chr6 341352 6 + 647215 TGCACT - -a -s simMouse_chr6.simMouse.chr6 350053 8 + 636262 CAAAAGGG -s Anc0.Anc0refChr0 13328 8 + 26507 AAAAAGAG -s Anc1.Anc1refChr6 13651 8 + 197743 AAAAAGAG -s Anc2.Anc2refChr17 6670 8 + 28526 AAAAAGAG -s mr.mrrefChr3 69278 8 + 181027 AAGAACAG -s mr.mrrefChr5 197270 8 + 294540 CAAAAGGG -s simCow_chr6.simCow.chr6 322225 1 + 602619 -------A -s simDog_chr6.simDog.chr6 314092 8 + 593897 AAAAAGAG -s simHuman_chr6.simHuman.chr6 333838 8 + 601863 GAAAAGAG -s simRat_chr6.simRat.chr6 528216 8 + 647215 AAGAACAG -s simRat_chr6.simRat.chr6 341358 8 + 647215 CAAAAGGG - -a -s simMouse_chr6.simMouse.chr6 350061 9 + 636262 GAGCCTACA -s Anc0.Anc0refChr0 13339 9 + 26507 AAACCTATG -s Anc1.Anc1refChr6 13662 9 + 197743 AAACCTATG -s Anc2.Anc2refChr17 6681 9 + 28526 AAACCTATG -s mr.mrrefChr3 69286 9 + 181027 GGATCTGCA -s mr.mrrefChr5 197278 9 + 294540 GAGCCTATG -s simCow_chr6.simCow.chr6 322229 9 + 602619 GAACCTATG -s simDog_chr6.simDog.chr6 314103 9 + 593897 AAGCCTACA -s simHuman_chr6.simHuman.chr6 333849 9 + 601863 AAACCTATG -s simRat_chr6.simRat.chr6 528224 9 + 647215 GGATCTGCA -s simRat_chr6.simRat.chr6 341366 9 + 647215 GAGCCTATG - -a -s simMouse_chr6.simMouse.chr6 350070 2 + 636262 GA -s Anc0.Anc0refChr0 13348 1 + 26507 G- -s Anc1.Anc1refChr6 13671 2 + 197743 GA -s Anc2.Anc2refChr17 6690 1 + 28526 G- -s mr.mrrefChr5 197287 2 + 294540 GA -s simCow_chr6.simCow.chr6 322238 1 + 602619 G- -s simDog_chr6.simDog.chr6 314112 1 + 593897 G- -s simHuman_chr6.simHuman.chr6 333858 2 + 601863 GA -s simRat_chr6.simRat.chr6 341375 2 + 647215 GA - -a -s simMouse_chr6.simMouse.chr6 350072 2 + 636262 AC -s Anc1.Anc1refChr6 13673 2 + 197743 AG -s mr.mrrefChr5 197289 2 + 294540 AC -s simHuman_chr6.simHuman.chr6 333861 2 + 601863 AG -s simRat_chr6.simRat.chr6 341377 2 + 647215 AC - -a -s simMouse_chr6.simMouse.chr6 350074 8 + 636262 AATAACAA -s Anc0.Anc0refChr0 13349 7 + 26507 -ATAACAG -s Anc1.Anc1refChr6 13675 8 + 197743 CATAACAG -s Anc2.Anc2refChr17 6691 7 + 28526 -ATAGCAG -s mr.mrrefChr3 69295 8 + 181027 TATAACAG -s mr.mrrefChr5 197291 8 + 294540 CATAACAA -s simCow_chr6.simCow.chr6 322239 7 + 602619 -ATAACAG -s simDog_chr6.simDog.chr6 314113 7 + 593897 -ATGGCAG -s simHuman_chr6.simHuman.chr6 333863 8 + 601863 CATACCTA -s simRat_chr6.simRat.chr6 528238 8 + 647215 TATAACAG -s simRat_chr6.simRat.chr6 341379 8 + 647215 CATAACAG - -a -s simMouse_chr6.simMouse.chr6 350082 16 + 636262 AGGTATTTTTGGTATG -s Anc0.Anc0refChr0 13357 16 + 26507 GGGTGTTTAGGGTATG -s Anc1.Anc1refChr6 13684 16 + 197743 GGGTGTTTAGGGTATG -s Anc2.Anc2refChr17 6699 16 + 28526 GGGTGTTTAGGGTATG -s mr.mrrefChr3 69304 16 + 181027 AAGCATACAAGGTATG -s mr.mrrefChr5 197299 16 + 294540 AGGTATTTTTGGTATG -s simCow_chr6.simCow.chr6 322247 16 + 602619 GGGTGTGTAAGGTATG -s simDog_chr6.simDog.chr6 314121 16 + 593897 GGGTGTTTAGGGTATG -s simHuman_chr6.simHuman.chr6 333872 16 + 601863 GGGTGTTTAGGGTATG -s simRat_chr6.simRat.chr6 528247 16 + 647215 AAGCATACAAGGTATG -s simRat_chr6.simRat.chr6 341387 16 + 647215 AGGTAGTTTTGGTATG - -a -s simMouse_chr6.simMouse.chr6 350098 8 + 636262 GCAGGGCT -s Anc0.Anc0refChr0 13373 8 + 26507 GCAAGTTT -s Anc1.Anc1refChr6 13700 8 + 197743 GCAAGTTT -s Anc2.Anc2refChr17 6715 8 + 28526 GCAAGTTT -s mr.mrrefChr3 69320 8 + 181027 GAAAGTTT -s mr.mrrefChr5 197315 8 + 294540 GCAGGTTT -s simCow_chr6.simCow.chr6 322263 8 + 602619 GCAAGTTC -s simDog_chr6.simDog.chr6 314137 8 + 593897 GTAAGTTT -s simHuman_chr6.simHuman.chr6 333888 8 + 601863 GCAAGTTT -s simMouse_chr6.simMouse.chr6 516619 8 + 636262 GAAAGTTT -s simRat_chr6.simRat.chr6 528263 8 + 647215 GCAAGTTG -s simRat_chr6.simRat.chr6 341403 8 + 647215 CCAGGTTT - -a -s simMouse_chr6.simMouse.chr6 350106 1 + 636262 G -s Anc0.Anc0refChr0 13381 1 + 26507 G -s Anc1.Anc1refChr6 13708 1 + 197743 G -s Anc2.Anc2refChr17 6723 1 + 28526 G -s mr.mrrefChr5 197323 1 + 294540 G -s simCow_chr6.simCow.chr6 322271 1 + 602619 A -s simDog_chr6.simDog.chr6 314145 1 + 593897 G -s simHuman_chr6.simHuman.chr6 333896 1 + 601863 G -s simRat_chr6.simRat.chr6 341411 1 + 647215 G - -a -s simMouse_chr6.simMouse.chr6 350107 2 + 636262 AG -s Anc0.Anc0refChr0 13382 2 + 26507 AG -s Anc1.Anc1refChr6 13709 2 + 197743 AG -s Anc2.Anc2refChr17 6724 2 + 28526 AG -s mr.mrrefChr3 69328 2 + 181027 AA -s mr.mrrefChr5 197324 2 + 294540 AG -s simCow_chr6.simCow.chr6 322272 2 + 602619 CG -s simDog_chr6.simDog.chr6 314146 2 + 593897 AA -s simHuman_chr6.simHuman.chr6 333897 2 + 601863 AG -s simMouse_chr6.simMouse.chr6 516627 2 + 636262 AA -s simRat_chr6.simRat.chr6 528271 2 + 647215 GG -s simRat_chr6.simRat.chr6 341412 2 + 647215 AG - -a -s simMouse_chr6.simMouse.chr6 350109 17 + 636262 CTACATACCATACCTAC -s Anc0.Anc0refChr0 13384 12 + 26507 CT-----CAATACCTTC -s Anc1.Anc1refChr6 13711 12 + 197743 CT-----CAATACCTTC -s Anc2.Anc2refChr17 6726 12 + 28526 GT-----CAAAACCGTC -s mr.mrrefChr3 69330 12 + 181027 CT-----AAATTCTTAC -s mr.mrrefChr5 197326 12 + 294540 CT-----CCATACCTAC -s simCow_chr6.simCow.chr6 322274 12 + 602619 AT-----TAAAACCATC -s simDog_chr6.simDog.chr6 314148 12 + 593897 GT-----CAAAAGCGTT -s simHuman_chr6.simHuman.chr6 333899 12 + 601863 CT-----CAATACCTTC -s simMouse_chr6.simMouse.chr6 516703 11 + 636262 CT-----AAATTCTTT- -s simRat_chr6.simRat.chr6 528273 12 + 647215 CT-----AAATTCTTAC -s simRat_chr6.simRat.chr6 341414 12 + 647215 CT-----CCCTACCTAC - -a -s simMouse_chr6.simMouse.chr6 350126 17 + 636262 TTCACACCAAAAGAATT -s Anc0.Anc0refChr0 13396 17 + 26507 TTCACATGAAAAGAAGT -s Anc1.Anc1refChr6 13723 17 + 197743 TTCACATGAAAAGAAGT -s Anc2.Anc2refChr17 6738 17 + 28526 TTCACATGAAAAGAAGT -s mr.mrrefChr3 69345 17 + 181027 TTCACATGAAATGAAGT -s mr.mrrefChr5 197338 17 + 294540 TTCACACCAAAAGAAGT -s simCow_chr6.simCow.chr6 322286 17 + 602619 TTCACATGAAAAGAGGT -s simDog_chr6.simDog.chr6 314160 17 + 593897 TTCACATGAAATGAAAT -s simHuman_chr6.simHuman.chr6 333911 17 + 601863 TTTCCATCAAAAGACGT -s simMouse_chr6.simMouse.chr6 516715 17 + 636262 TTCACATGAAACAAAGT -s simRat_chr6.simRat.chr6 528288 17 + 647215 TTCCCATTAAATGAGGT -s simRat_chr6.simRat.chr6 341426 17 + 647215 TTCACAGCAAAAGAAGT - -a -s simMouse_chr6.simMouse.chr6 350143 14 + 636262 CAGGCATCCCACAA -s Anc0.Anc0refChr0 13413 14 + 26507 CAGGCATCCCACAA -s Anc1.Anc1refChr6 13740 14 + 197743 CAGGCATCCCACAA -s Anc2.Anc2refChr17 6755 14 + 28526 CAGGCATCCCACAA -s mr.mrrefChr3 69362 14 + 181027 CATGCAGCCCACAA -s mr.mrrefChr5 197355 14 + 294540 CAGGCATCCCACAA -s simCow_chr6.simCow.chr6 322312 14 + 602619 CCGGCATCCCATTA -s simDog_chr6.simDog.chr6 314177 14 + 593897 CAGGCATCCCACAA -s simHuman_chr6.simHuman.chr6 333928 14 + 601863 CACACATCCCACAA -s simMouse_chr6.simMouse.chr6 516732 14 + 636262 CATGCAGCCCGCAA -s simRat_chr6.simRat.chr6 528305 14 + 647215 CATGCAGCCCACAA -s simRat_chr6.simRat.chr6 341443 14 + 647215 TAGGCTGCCCACAA - -a -s simMouse_chr6.simMouse.chr6 350157 51 + 636262 TGAAAAATTGTAACAACTCTGGTCTGCCCATAAGAATCTCAGTGTACTGCA -s Anc0.Anc0refChr0 13427 51 + 26507 AAAATAACTGCAATAACTCTGATTTGCACATAAGAATCTCAGATTACTGCA -s Anc1.Anc1refChr6 13754 51 + 197743 AAAATAACTGCAATAACTCTGATTTGCACATAAGAATCTCAGATTACTGCA -s Anc2.Anc2refChr17 6769 51 + 28526 AAAATAACTGCAATAACTCTGATTTGCACACCAGAATTTCAGACTACTGCA -s mr.mrrefChr3 69376 51 + 181027 AAAATAACTGTAATAACCCTGGTCTGCACATAGGGCTGTCAGAGTACTGCA -s mr.mrrefChr5 197369 51 + 294540 TGAAAAATTGTAACAACTCTGGTCTGCCCATAAGAATCTCAGATTACTGCA -s simCow_chr6.simCow.chr6 322326 48 + 602619 AAGATAA---CTATAGCTCTGTTTTCCACACCAGTATTACAGACTACTACA -s simDog_chr6.simDog.chr6 314191 51 + 593897 AAAATAACTGTAATAACCCTGACCTGCACACCAGAATTTCAGACAACTGCA -s simHuman_chr6.simHuman.chr6 333955 51 + 601863 AAAAAAATTACAATAACTCTAATTGGCACATGAGATTCCCAGATTACTGCA -s simMouse_chr6.simMouse.chr6 516746 50 + 636262 AAAATA-CTGCAATAACCCTGGTCTGCTCATAGAGCAGTCAGAGTACTGCA -s simRat_chr6.simRat.chr6 528319 51 + 647215 AAAATAACTGTAACAACCCTGGTCTGCACATGGGGCTCTCAGAGTACTGCA -s simRat_chr6.simRat.chr6 341457 51 + 647215 TGAAAAATTGTAACAACTCTGGTCAGCCCATAAGAATCTCAGATTATTGCA - -a -s simMouse_chr6.simMouse.chr6 350208 39 + 636262 CAGAAGCTGCCACTGGTTTGATCTCTGGTCCAAGGTAGT -s Anc0.Anc0refChr0 9556 29 - 26507 -AAAAGGGGCAACTG---------TTGGTCCAAGGTGGA -s Anc1.Anc1refChr6 180239 29 - 197743 -AAAAGGGGCAACTG---------TTGGTCCAAGGTGGA -s Anc2.Anc2refChr17 18022 29 - 28526 -GAGAGGGGCAACTG---------TCAGTCCAAGGTGAA -s mr.mrrefChr5 197420 39 + 294540 CAGAAGCTGCCACTGGCTTAATTTCTGGTCCAAGGTAGT -s simCow_chr6.simCow.chr6 276382 29 - 602619 -GATGAAGGCAATTG---------TCAGTCCAAGGTAAA -s simDog_chr6.simDog.chr6 275912 29 - 593897 -GAGAGGAGCAACTT---------TCAATCCAAGGTGAA -s simHuman_chr6.simHuman.chr6 263884 29 - 601863 -AAAAGGGGCACCTG---------TTGGTCCAAGGGGGA -s simRat_chr6.simRat.chr6 341508 39 + 647215 CAGAAGCTGCTACTGGCTTAATTTCTGGTCCAAGATAGT - -a -s simMouse_chr6.simMouse.chr6 350247 23 + 636262 TGGATTTCATAAGATCACTGGTC -s Anc0.Anc0refChr0 9585 23 - 26507 TGGGTTTCATGAGATCAGTGGTC -s Anc1.Anc1refChr6 180268 23 - 197743 TGGGTTTCATGAGATCAGTGGTC -s Anc2.Anc2refChr17 18051 23 - 28526 TGGGTTCCATGAGATCAGTAGTC -s mr.mrrefChr5 197459 23 + 294540 TGGATTTCATAAGATCACTGGTC -s simCow_chr6.simCow.chr6 276411 23 - 602619 TGGGTTCCTTGAAATCAGTAGTC -s simDog_chr6.simDog.chr6 275941 23 - 593897 TGGGTTCCATGAGATGAGTAGTC -s simHuman_chr6.simHuman.chr6 263913 23 - 601863 TTGGGTTCATGAGATCAATGGTT -s simRat_chr6.simRat.chr6 341548 23 + 647215 TGGATTTCCTAAGATCAGTGGTC - -a -s simMouse_chr6.simMouse.chr6 350270 1 + 636262 T -s Anc0.Anc0refChr0 9612 1 - 26507 T -s Anc1.Anc1refChr6 180295 1 - 197743 T -s Anc2.Anc2refChr17 18078 1 - 28526 T -s mr.mrrefChr5 197482 1 + 294540 T -s simCow_chr6.simCow.chr6 276438 1 - 602619 C -s simDog_chr6.simDog.chr6 275968 1 - 593897 T -s simHuman_chr6.simHuman.chr6 263941 1 - 601863 T -s simRat_chr6.simRat.chr6 341571 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 350271 4 + 636262 GTGT -s Anc0.Anc0refChr0 9613 4 - 26507 TTGC -s Anc1.Anc1refChr6 180296 4 - 197743 TTGC -s Anc2.Anc2refChr17 18079 4 - 28526 TTCC -s mr.mrrefChr5 197483 4 + 294540 GTGT -s simCow_chr6.simCow.chr6 276439 2 - 602619 T--C -s simDog_chr6.simDog.chr6 275969 4 - 593897 TTCC -s simHuman_chr6.simHuman.chr6 263942 4 - 601863 TTGC -s simRat_chr6.simRat.chr6 341577 4 + 647215 ATGT - -a -s simMouse_chr6.simMouse.chr6 350275 27 + 636262 ATTCAAACGAGATTAGTGGCCTGCTAG -s Anc0.Anc0refChr0 9617 17 - 26507 TTTCAAACAAGATTGGT---------- -s Anc1.Anc1refChr6 180300 17 - 197743 TTTCAAACAAGATTGGT---------- -s Anc2.Anc2refChr17 18083 17 - 28526 TTTCAAACAAGACTGGT---------- -s mr.mrrefChr5 197487 17 + 294540 ATTCAAACGAGATTAGT---------- -s simCow_chr6.simCow.chr6 276441 14 - 602619 TGTTGAACAAA---TGT---------- -s simDog_chr6.simDog.chr6 275975 17 - 593897 TTTCAAACAAGACTGAT---------- -s simHuman_chr6.simHuman.chr6 263946 17 - 601863 CCTCAAGCAAGATTGGT---------- -s simRat_chr6.simRat.chr6 341581 17 + 647215 CTGCAAACAAGATCGGT---------- - -a -s simMouse_chr6.simMouse.chr6 350302 12 + 636262 TTCTTGCAAACA -s Anc0.Anc0refChr0 9646 12 - 26507 TTCTGGTACACA -s Anc1.Anc1refChr6 180329 12 - 197743 TTCTGGTACACA -s Anc2.Anc2refChr17 18112 12 - 28526 TTCTGGTACACA -s mr.mrrefChr5 197504 12 + 294540 TTCTTGCAAACA -s simCow_chr6.simCow.chr6 276467 12 - 602619 TTCTGGTACACA -s simDog_chr6.simDog.chr6 276004 12 - 593897 TTCTGCTCCACA -s simHuman_chr6.simHuman.chr6 263975 12 - 601863 TTCTGGTACACA -s simRat_chr6.simRat.chr6 341598 12 + 647215 TTCTAGCACACA - -a -s simMouse_chr6.simMouse.chr6 350314 34 + 636262 TAACAACCCACCATGGCATGTAGATGGTGTACTA -s Anc0.Anc0refChr0 9658 34 - 26507 TAATAGCCCCCAAAGGTATGTAGATGGTGTACTA -s Anc1.Anc1refChr6 180341 34 - 197743 TAATAGCCCCCAAAGGTATGTAGATGGTGTACTA -s Anc2.Anc2refChr17 18124 34 - 28526 TAATAGCCCCCAAAGGTATGTTGATGGTGTACTA -s mr.mrrefChr5 197516 34 + 294540 TAACAACCCACCATGGCATGTAGATGGTGTACTA -s simCow_chr6.simCow.chr6 276566 34 - 602619 TTATAGCCCTCGAAGGTATCTGGATGGTGTGCTA -s simDog_chr6.simDog.chr6 276016 34 - 593897 TAATAGCCCCCAAGGGTATGTTGATGGCGTACAA -s simHuman_chr6.simHuman.chr6 263987 34 - 601863 TAATATAGCCCAAAGGTAAGTAAATGGTGCACTA -s simRat_chr6.simRat.chr6 341610 34 + 647215 AAATAACTCACCATGGTATGTAGATGGTGTTCTA - -a -s simMouse_chr6.simMouse.chr6 350348 6 + 636262 TTTGTT -s Anc0.Anc0refChr0 9705 6 - 26507 TTTGTT -s Anc1.Anc1refChr6 180388 6 - 197743 TTTGTT -s Anc2.Anc2refChr17 18171 6 - 28526 TGGCTT -s mr.mrrefChr5 197550 6 + 294540 TTTGTT -s simCow_chr6.simCow.chr6 276613 6 - 602619 TGACTT -s simDog_chr6.simDog.chr6 276063 6 - 593897 TGGCTT -s simHuman_chr6.simHuman.chr6 264034 6 - 601863 TTTGTT -s simRat_chr6.simRat.chr6 341644 6 + 647215 TTTGTC - -a -s simMouse_chr6.simMouse.chr6 350354 134 + 636262 TCCAATGTCTTGAGAATGGGGGATGCACTTATCTTAAGTGTAGGTTAGCCTGTTGTGTATTACCTTAAAACACTCTGCACTATAACAAGATCTACACGTCAGATCACTTACCTGAATTACCGCACTTACTTTGG -s Anc0.Anc0refChr0 9711 50 - 26507 TC------------------------------------------------------------------------------------AAGACACATACCTTAGATCAGTTGCCAGAATTACCGTACTTATTTTGG -s Anc1.Anc1refChr6 180394 50 - 197743 TC------------------------------------------------------------------------------------AAGACACATACCTTAGATCAGTTGCCAGAATTACCGTACTTATTTTGG -s Anc2.Anc2refChr17 18234 50 - 28526 TC------------------------------------------------------------------------------------AAGACACATACCTTAGATCAGTTGCCAGAATTACCCTACTTATTTTTG -s mr.mrrefChr5 197556 133 + 294540 TCCAATGTCTTGAGAATGGGGGATGCACTTATCTTAAGTGTAGGTTAGCCTGTTGTGTATTACCTTAAA-CACTCTGCACTATAACAAGATCTACACGTCAGATCACTTACCTGAATTACCGCACTTACTTTGG -s simCow_chr6.simCow.chr6 276700 50 - 602619 TC------------------------------------------------------------------------------------AAGACACATACCTTCGATCAGTTGCCATCATTAGTCCCCTTGTTTATT -s simDog_chr6.simDog.chr6 276129 50 - 593897 TC------------------------------------------------------------------------------------AAGACACATACCTTAGACCAGTTGCCAGAATTACCCTACTTATTTTTG -s simHuman_chr6.simHuman.chr6 264040 50 - 601863 TC------------------------------------------------------------------------------------AAGACACATTCCTTGAATCATTTGCCACAATTACAGGACCTATTCTGG -s simRat_chr6.simRat.chr6 341650 133 + 647215 TCCAATGTCTTGACCACTGGGGATGCACTTATCTTAAGTGTAGGTCAACCTGCTGTGTATTATCTTAAT-CACTCCACACTATTATAAAATGCACACCTCAGATCGCTTGCTTGAATTACCCCACCTATTTTGG - -a -s simMouse_chr6.simMouse.chr6 350488 21 + 636262 CATGACAGTGTAGGAACAAAC -s Anc0.Anc0refChr0 9762 6 - 26507 CATGAC--------------- -s Anc1.Anc1refChr6 180445 9 - 197743 CATGACAGC------------ -s Anc2.Anc2refChr17 18285 6 - 28526 CATGAC--------------- -s mr.mrrefChr5 197689 21 + 294540 CATGACAGTGTAGGAACAAAC -s simCow_chr6.simCow.chr6 276751 6 - 602619 CATGAC--------------- -s simDog_chr6.simDog.chr6 276180 6 - 593897 CCAGAC--------------- -s simHuman_chr6.simHuman.chr6 264091 9 - 601863 CATGACAGC------------ -s simRat_chr6.simRat.chr6 341783 21 + 647215 CATGACAGTGGAGGAACAAAC - -a -s simMouse_chr6.simMouse.chr6 350509 4 + 636262 TGTA -s Anc0.Anc0refChr0 9768 4 - 26507 TGCA -s Anc1.Anc1refChr6 180454 4 - 197743 TGCA -s Anc2.Anc2refChr17 18291 4 - 28526 TGCA -s mr.mrrefChr5 197710 4 + 294540 TGTA -s simCow_chr6.simCow.chr6 276759 4 - 602619 TGTA -s simDog_chr6.simDog.chr6 276186 4 - 593897 TGCA -s simRat_chr6.simRat.chr6 341804 4 + 647215 TGTA - -a -s simMouse_chr6.simMouse.chr6 350513 19 + 636262 GGATTGAGACGGATAGACT -s Anc0.Anc0refChr0 9772 19 - 26507 AAAATATGAAGGGCAGACT -s Anc1.Anc1refChr6 180458 19 - 197743 AAAATATGAAGGGCAGACT -s Anc2.Anc2refChr17 18295 19 - 28526 AAAATATGAAGGGCAGACT -s mr.mrrefChr5 197714 19 + 294540 GGATTGAGACGGATAGACT -s simCow_chr6.simCow.chr6 276771 19 - 602619 AGAATGTGAAGGGTAGCCT -s simDog_chr6.simDog.chr6 276190 19 - 593897 AAAATATGAAGGGCAGACT -s simRat_chr6.simRat.chr6 341808 19 + 647215 GGATTGAGAGGGACAGACT - -a -s simMouse_chr6.simMouse.chr6 350532 9 + 636262 GAGTGCAGA -s Anc0.Anc0refChr0 9791 6 - 26507 G---GCTAG -s Anc1.Anc1refChr6 180477 6 - 197743 G---GCTAG -s Anc2.Anc2refChr17 18314 6 - 28526 G---GCTAG -s mr.mrrefChr5 197733 9 + 294540 GAGTGCAGA -s simCow_chr6.simCow.chr6 276792 6 - 602619 G---GCCAG -s simDog_chr6.simDog.chr6 276209 6 - 593897 G---GCTAG -s simRat_chr6.simRat.chr6 341827 9 + 647215 GTGCACAGA - -a -s simMouse_chr6.simMouse.chr6 350541 13 + 636262 TATTTGGCACTCT -s Anc0.Anc0refChr0 9797 13 - 26507 TATTTTGTCCTCT -s Anc1.Anc1refChr6 180483 13 - 197743 TATTTTGTCCTCT -s Anc2.Anc2refChr17 18320 13 - 28526 TATTTTGTCCTCT -s mr.mrrefChr5 197742 13 + 294540 TATTTGGCACTCT -s simCow_chr6.simCow.chr6 276799 13 - 602619 TTTTTTGACCTCT -s simDog_chr6.simDog.chr6 276215 13 - 593897 TATTTTGTCCTCT -s simRat_chr6.simRat.chr6 341836 13 + 647215 TATTTCATACTCT - -a -s simMouse_chr6.simMouse.chr6 350554 30 + 636262 AAAGTATCTTTTGGTAGCCTAATCAACAGA -s Anc0.Anc0refChr0 9810 30 - 26507 AAAGCATCCTTTAGTAGCCTAATCAATGGG -s Anc1.Anc1refChr6 180496 30 - 197743 AAAGCATCCTTTAGTAGCCTAATCAATGGG -s Anc2.Anc2refChr17 18333 30 - 28526 AAAGCATCCTTTAGTCACTTATTCAATGGG -s mr.mrrefChr5 197755 30 + 294540 AAAGTATCTTTTGGTAGCCTAATCAACAGA -s simCow_chr6.simCow.chr6 276818 29 - 602619 TAAGCATCCTTTGATCACTTAGTCAA-GGG -s simDog_chr6.simDog.chr6 276228 30 - 593897 AAAGCATCCTTTAGTCAGTTATTCAATGGG -s simHuman_chr6.simHuman.chr6 264100 25 - 601863 -----ACCCTTTAGTAGCCTAACCAATGGG -s simRat_chr6.simRat.chr6 341849 30 + 647215 AAAGCATCCTTTGGTACCCTAATCAACAGA - -a -s simMouse_chr6.simMouse.chr6 350584 4 + 636262 CAAT -s Anc0.Anc0refChr0 9840 4 - 26507 CAAT -s Anc1.Anc1refChr6 180526 4 - 197743 CAAT -s Anc2.Anc2refChr17 18364 4 - 28526 CAAT -s mr.mrrefChr5 197785 4 + 294540 CAAT -s simCow_chr6.simCow.chr6 276848 4 - 602619 CAAT -s simDog_chr6.simDog.chr6 276259 4 - 593897 CAAT -s simHuman_chr6.simHuman.chr6 264125 4 - 601863 CAAT -s simRat_chr6.simRat.chr6 341879 4 + 647215 TAAT - -a -s simMouse_chr6.simMouse.chr6 350588 29 + 636262 GGGCTCTCAGAGGAGTGCTTGTTTGTGCC -s Anc0.Anc0refChr0 9844 22 - 26507 GCCCTCTTAAAAGGGTGCTTGT------- -s Anc1.Anc1refChr6 180530 29 - 197743 GCCCTCTTAAAAGGGTGCTTGTTTGTTCC -s Anc2.Anc2refChr17 18368 22 - 28526 GCCCTCCTTAAATGGTACCTGT------- -s mr.mrrefChr5 197789 29 + 294540 GGGCTCTCAGAGGAGTGCTTGTTTGTGCC -s simCow_chr6.simCow.chr6 276852 20 - 602619 GCC--TCTTAAATGGTAGCTGT------- -s simDog_chr6.simDog.chr6 276263 22 - 593897 GCCCTCCTTAAATGGTGCCTGT------- -s simHuman_chr6.simHuman.chr6 264161 29 - 601863 GACCTTTTAAATGGGTGCTTTGTTGTTCC -s simRat_chr6.simRat.chr6 341883 29 + 647215 GGGCTTTCAGGTGAGTGCTTGTTTGTGCC - -a -s simMouse_chr6.simMouse.chr6 350617 22 + 636262 AGTTAGGCTGTACTCCTTTCCT -s Anc0.Anc0refChr0 9866 5 - 26507 -GTTAG---------------- -s Anc1.Anc1refChr6 180559 22 - 197743 AGTTAGATTTTAGACCTTGTGT -s Anc2.Anc2refChr17 18390 5 - 28526 -GTTAG---------------- -s mr.mrrefChr5 197818 22 + 294540 AGTTAGGCTGTACTCCTTTCCT -s simCow_chr6.simCow.chr6 276872 5 - 602619 -TTTGG---------------- -s simDog_chr6.simDog.chr6 276285 5 - 593897 -GTTAG---------------- -s simHuman_chr6.simHuman.chr6 264194 22 - 601863 ACTTAAATTTTAGACCTTGTGT -s simRat_chr6.simRat.chr6 341912 22 + 647215 AGTTAGACTGTACTCTTTCCCT - -a -s simMouse_chr6.simMouse.chr6 350639 20 + 636262 TTGGTAAGCCTATAGATAAG -s Anc0.Anc0refChr0 9910 20 - 26507 TTGGTGAGCCTATACTAGAG -s Anc1.Anc1refChr6 180620 20 - 197743 TTGGTGAGCCTATACTAGAG -s Anc2.Anc2refChr17 18434 20 - 28526 CTGGTGAGCCTATGCTAGAG -s mr.mrrefChr5 197840 20 + 294540 TTGGTAAGCCTATAGATAAG -s simCow_chr6.simCow.chr6 276912 20 - 602619 CTAGCGAGCCTATGCTTGAG -s simDog_chr6.simDog.chr6 276313 20 - 593897 CCGGTGAGCTGATGCTAAAC -s simHuman_chr6.simHuman.chr6 264260 20 - 601863 TTGGTGACCCTATACTAGAG -s simRat_chr6.simRat.chr6 341934 20 + 647215 TTGGTAAGCCTATAGATAGG - -a -s simMouse_chr6.simMouse.chr6 350659 1 + 636262 T -s Anc0.Anc0refChr0 9930 1 - 26507 T -s Anc1.Anc1refChr6 180640 1 - 197743 T -s Anc2.Anc2refChr17 18457 1 - 28526 T -s mr.mrrefChr5 197860 1 + 294540 T -s simCow_chr6.simCow.chr6 276935 1 - 602619 T -s simDog_chr6.simDog.chr6 276336 1 - 593897 T -s simHuman_chr6.simHuman.chr6 264280 1 - 601863 G -s simRat_chr6.simRat.chr6 341954 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 350660 57 + 636262 TTGGCTTAGGAGCGTCATAAACCTATCCAATATATCGATATATTTGTTCTCACTCAA -s Anc0.Anc0refChr0 9931 45 - 26507 TTGACTCCACAACGTCATAAACCTACCCAGTATAT-------TTTTT-----CTTAA -s Anc1.Anc1refChr6 180641 45 - 197743 TTGACTCCACAACGTCATAAACCTACCCAGTATAT-------TTTTT-----CTTAA -s Anc2.Anc2refChr17 18458 45 - 28526 TTGACTCCACAACGTCACAAAGCTACCCAGTATAT-------TTATC-----CTTAA -s mr.mrrefChr5 197861 52 + 294540 TTGGCTTAGGAGCGTCATAAACCTATCCAATATATCGATATATTTGT-----CTCAA -s simCow_chr6.simCow.chr6 276936 38 - 602619 T--ATCCCAGAAC-----AGAGCTACCCAGAATAT-------TTATG-----GATAA -s simDog_chr6.simDog.chr6 276337 45 - 593897 TTGACTCCACAGCGTCACTAAGCAGCCCAATATAT-------TTATC-----CTTAA -s simHuman_chr6.simHuman.chr6 264283 45 - 601863 TTGACTCCATAATGTCATAAACCTACCCAGTATAT-------TTTTT-----CTTAA -s simRat_chr6.simRat.chr6 341955 52 + 647215 TTGGCTTAGTAGCATCATAAACCTATCCAATATATCAATATATGTGT-----CTCAA - -a -s simMouse_chr6.simMouse.chr6 350717 6 + 636262 ATCACA -s Anc0.Anc0refChr0 9978 6 - 26507 ACCACA -s Anc1.Anc1refChr6 180688 6 - 197743 ACCACA -s Anc2.Anc2refChr17 18505 6 - 28526 ACCACA -s mr.mrrefChr5 197913 6 + 294540 ATCACA -s simCow_chr6.simCow.chr6 276976 6 - 602619 ACAACA -s simDog_chr6.simDog.chr6 276383 6 - 593897 ACCACA -s simHuman_chr6.simHuman.chr6 264330 6 - 601863 ACCACA -s simRat_chr6.simRat.chr6 342007 6 + 647215 ACCACA - -a -s simMouse_chr6.simMouse.chr6 350723 85 + 636262 ATCAGTTTCTGTATTTCTCCATATCCTGATTCACAAGTTAGGCTAGTCCCTTACTGTGATTGTAATTTCATGACTCCTATACTAT -s Anc0.Anc0refChr0 9990 36 - 26507 ATCACTA---GCATTCCTCAACACCC--ATTCTGAAATTGG-------------------------------------------- -s Anc1.Anc1refChr6 180700 36 - 197743 ATCACTA---GCATTCCTCAACACCC--ATTCTGAAATTGG-------------------------------------------- -s Anc2.Anc2refChr17 18517 36 - 28526 GTCACTA---GCATTCCTCAACCCCC--ATTCTGAAACTGT-------------------------------------------- -s mr.mrrefChr5 197919 85 + 294540 ATCAGTTTCTGTATTTCTCCATATCCTGATTCACAAGTTAGGCTAGTCCCTTACTGTGATTGTAATTTCATGACTCCTATACTAT -s simCow_chr6.simCow.chr6 276988 36 - 602619 GTAACTA---GCAGTCCTCAACCCTC--ATTCTGAGGCTGT-------------------------------------------- -s simDog_chr6.simDog.chr6 276395 36 - 593897 GTCACTA---GCATTCTTCAACCCCC--AGTCTGAAACTGT-------------------------------------------- -s simHuman_chr6.simHuman.chr6 264342 36 - 601863 ATCACTA---GCATTCCTCAACAACC--ATTCTGAATTTGG-------------------------------------------- -s simRat_chr6.simRat.chr6 342013 85 + 647215 ATCAGTTTCTATATCTCTCCATATCTTGATCCATTGGTCAGGCTAATCCTTTACTGAGATTGTAATTGCATGACTGCTATAGTAT - -a -s simMouse_chr6.simMouse.chr6 350808 10 + 636262 GCCTCTTGCA -s mr.mrrefChr5 198004 10 + 294540 GCCTCTTGCA -s simRat_chr6.simRat.chr6 342101 10 + 647215 GCATCTTGCA - -a -s simMouse_chr6.simMouse.chr6 350818 259 + 636262 CCTGAGGCACTTGTTTTTGTTTTGTTAACAGAGTTCACATATGGATATGTTGTGACAGTGCATTCTCACTTATCTGTTAAAGCAGTTTTGGCTGGATTGGTTTAAACATGGCGCAAACTGCAAATGCAGTGACTCCACCAGTGTCCCCTCAACTCGCAGTCTTAATCTGTCACAACATCCACACTGATAAGCCTAAATTTGATGAATCAGAGAACAATGGCCCTCAGGCAAAAGTTTGATCCCAGAATGGATCACAGAC -s mr.mrrefChr5 198014 249 + 294540 CCTGAGGCACTT---------TTGTTAACAGAGTTCACATATGGATATGTTGTGACAGTGCATTCTCACTTATCTGTTAAAGCAGTTTTGGCTGGATTGGTTTAAACATGGCGCAAACTGCAAATGCAGTGACTCCACCAGTGTCCCCTCA-CTCGCAGTCTTAATCTGTCACAACATCCACACTGATAAGCCTAAATTTGATGAATCAGAGAACAATGGCCCTCAGGCAAAAGTTTGATCCCAGAATGGATCACAGAC -s simRat_chr6.simRat.chr6 342154 249 + 647215 CCTTAGTCACTT---------TTGTTAACAGACATTGCATATGGTTATGTTGTAATAGTGCACTCTCACTTACCTGTTAAAACAGTTTTAGCTAGATTGGTCGAAATGTGGCGCACAGTCCAAGCACAATGACTCACCAAGCATTCCCTCA-CACACAGTCTAAGACTGTCACAATATCCAACCTGATAAGGCTAAACTTGACGAATCAGACAACAACAGTCCACGGTCAAAAGTTGGATCCCAGAATGGATCCTAGAC - -a -s simMouse_chr6.simMouse.chr6 351077 35 + 636262 AGGGGTTTTCATCACATCTAGGTTGTACTTTACCT -s Anc0.Anc0refChr0 10026 26 - 26507 ---------CACAACTTCTAGGTTGGACTGTGGAT -s Anc1.Anc1refChr6 180736 26 - 197743 ---------CACAACTTCTAGGTTGGACTGTGGAT -s Anc2.Anc2refChr17 18553 26 - 28526 ---------CACAACTTCTAGATTGGACTGGGGAT -s mr.mrrefChr5 198263 35 + 294540 AGGGGTTTTCATCACATCTAGGTTGTACTTTACCT -s simCow_chr6.simCow.chr6 277024 26 - 602619 ---------CACACTTTCTACATTGGAATAGGCAT -s simDog_chr6.simDog.chr6 276431 26 - 593897 ---------TATGACTTCTAGACTGTCCTGGGGCT -s simHuman_chr6.simHuman.chr6 264378 26 - 601863 ---------CACAACTTCTAGGTTGGACTGTGGAT -s simRat_chr6.simRat.chr6 342404 35 + 647215 AGGGATGTTCATCAAACCTAGGTTGTACTCAACCT - -a -s simMouse_chr6.simMouse.chr6 351112 2 + 636262 TT -s Anc0.Anc0refChr0 10052 2 - 26507 TT -s Anc1.Anc1refChr6 180762 2 - 197743 TT -s Anc2.Anc2refChr17 18579 2 - 28526 TC -s mr.mrrefChr5 198298 2 + 294540 TT -s simCow_chr6.simCow.chr6 277050 2 - 602619 CC -s simDog_chr6.simDog.chr6 276457 2 - 593897 TC -s simHuman_chr6.simHuman.chr6 264404 2 - 601863 TT -s simRat_chr6.simRat.chr6 342462 2 + 647215 TT - -a -s simMouse_chr6.simMouse.chr6 351114 183 + 636262 AAATGAGTTGATCCACAAGGTTTGTCCCTGTGGTGGAATCATAGACTTTATGGAATCAAGGTGTGGTGAAAACAGTCACTATCATCATTTTGGTTGACTGCACATGGATATGATTTGCCTTTGATAAGCGGCAAGCATAAAGGGCCATTAAGTATCCTTATTGTAGAGACTGTTTCTCAGATC -s Anc0.Anc0refChr0 10061 41 - 26507 AAGTCAAACAC-----AAGGTTATTACTTATAAATGA-TCAA---CTTGA------------------------------------------------------------------------------------------------------------------------------------- -s Anc1.Anc1refChr6 180771 44 - 197743 AAGTCAAACAC-----AAGGTTATTACTTATAAATGA-TCAAAGACTTGA------------------------------------------------------------------------------------------------------------------------------------- -s Anc2.Anc2refChr17 18588 41 - 28526 AAGTCAAACAC-----AAGGTCATTATTTACAAATGA-TCAA---CTTGA------------------------------------------------------------------------------------------------------------------------------------- -s mr.mrrefChr5 198300 173 + 294540 AAATGAGTTGA-----AAGGTTTGTCCCTGTGGTGGAATCATAGACTTTATGGAATCAAGGTGTGGTGAAAACAGTCACTATCATCATTTTGGTTGACTGCACATGGATATGATTTGCCTTTGATAAGCGGCAAG--TAAAGGGCCATTAAGTATCCTTATTGTAGAGACT---TCTCAGATC -s simCow_chr6.simCow.chr6 277070 41 - 602619 AAGTCAAACGC-----AAGGTCATTATTTACAAGTGA-TCAA---CTAGA------------------------------------------------------------------------------------------------------------------------------------- -s simDog_chr6.simDog.chr6 276465 28 - 593897 AACTCAAGTAA-----AGCG-------------ATGA-TCAT---CTTGG------------------------------------------------------------------------------------------------------------------------------------- -s simHuman_chr6.simHuman.chr6 264413 44 - 601863 AAGTCATACAC-----AAGGTTATTACTCATTACTGA-TCAAAGACTTGA------------------------------------------------------------------------------------------------------------------------------------- -s simRat_chr6.simRat.chr6 342464 173 + 647215 CAATGGGTTGG-----AAGGTTTGTCCCTGTGGTGGAATCATAGACTTTATGGAACCAGGAAGTGGAGGAAACAGTTATTGTCATCATTTTGGTTAACTGCACTTGGGTATGGTTGATTTTTGATAATTGGCAAG--TAAAGGACCACTAAGTATCCTTATCGTAGAGACT---TCTAAGGAC - -a -s simMouse_chr6.simMouse.chr6 351297 32 + 636262 TGTGTGAGCCTCTGTGTAGAGACTGTTTCTCA -s mr.mrrefChr5 198473 31 + 294540 TGTGT-AGCCTCTGTGTAGAGACTGTTTCTCA -s simRat_chr6.simRat.chr6 342640 31 + 647215 TAAGT-ATCCTTATTGTAGAGACTTCTTCTCA - -a -s simMouse_chr6.simMouse.chr6 351329 51 + 636262 GATCTGTGTGAGCCTCTGCGTTAATGTTTGAGGGGGATGCTTAGAGGGTTG -s Anc0.Anc0refChr0 10102 21 - 26507 ------------------------------ATGGGGATGTGCACAAGGTTT -s Anc1.Anc1refChr6 180815 21 - 197743 ------------------------------ATGGGGATGTGCACAAGGTTT -s Anc2.Anc2refChr17 18629 21 - 28526 ------------------------------ATGGGGATGTGCACAAGGTTT -s mr.mrrefChr5 198504 51 + 294540 GATCTGTGTGAGCCTCTGCGTTAATGTCTGAGGGGGATGCTCAGAGGGTTG -s simCow_chr6.simCow.chr6 277111 19 - 602619 ------------------------------ATGTGGATGTG--CAAGATTT -s simDog_chr6.simDog.chr6 276493 21 - 593897 ------------------------------GTTGGGATGTGCACAAGGTTT -s simHuman_chr6.simHuman.chr6 264457 21 - 601863 ------------------------------ATGGGGATGTGCACAAGGTTT -s simRat_chr6.simRat.chr6 342673 46 + 647215 GATCTGTGTGAGCCCCTGGGTTAGTGTCTCAGGGGGATGCTCAGAG----- - -a -s simMouse_chr6.simMouse.chr6 351380 13 + 636262 GGGATGCTTAGAG -s Anc0.Anc0refChr0 10123 10 - 26507 G---TCCCTGTAG -s Anc1.Anc1refChr6 180836 10 - 197743 G---TCCCTGTAG -s Anc2.Anc2refChr17 18650 10 - 28526 C---TCCCTGTAG -s mr.mrrefChr5 198555 10 + 294540 G---TGCTTAGAG -s simCow_chr6.simCow.chr6 277130 10 - 602619 C---TCACTGTAG -s simDog_chr6.simDog.chr6 276571 10 - 593897 C---TCCCTGTAG -s simHuman_chr6.simHuman.chr6 264478 10 - 601863 G---TCCCTGTAG - -a -s simMouse_chr6.simMouse.chr6 351393 12 + 636262 GGTTGGGGGTGT -s Anc0.Anc0refChr0 10133 12 - 26507 GATCTCAGGTCT -s Anc1.Anc1refChr6 180846 12 - 197743 GATCTCAGGTCT -s Anc2.Anc2refChr17 18663 12 - 28526 AATCTCAGGTCT -s mr.mrrefChr5 198565 12 + 294540 GGTTGGGGGTGT -s simCow_chr6.simCow.chr6 277143 12 - 602619 AATCTTAAGTCT -s simDog_chr6.simDog.chr6 276584 12 - 593897 ACCCTCAGGTCT -s simHuman_chr6.simHuman.chr6 264488 12 - 601863 GATCTCAGCTTT -s simRat_chr6.simRat.chr6 342719 12 + 647215 GGATGGGGGTCT - -a -s simMouse_chr6.simMouse.chr6 351405 12 + 636262 TGTATGTGACAT -s Anc0.Anc0refChr0 10147 12 - 26507 TGTATATCACTT -s Anc1.Anc1refChr6 180860 12 - 197743 TGTATATCACTT -s Anc2.Anc2refChr17 18677 12 - 28526 TGGATATCACTT -s mr.mrrefChr5 198577 12 + 294540 TGTATGTGACAT -s simCow_chr6.simCow.chr6 277157 10 - 602619 TGGATATCA--T -s simDog_chr6.simDog.chr6 276598 12 - 593897 TGGATACCACTT -s simHuman_chr6.simHuman.chr6 264502 12 - 601863 TGTATATCACCT -s simRat_chr6.simRat.chr6 342731 12 + 647215 TGTATGTGACAT - -a -s simMouse_chr6.simMouse.chr6 351417 2 + 636262 AT -s Anc0.Anc0refChr0 10159 2 - 26507 CT -s Anc1.Anc1refChr6 180872 2 - 197743 CT -s Anc2.Anc2refChr17 18689 2 - 28526 CC -s mr.mrrefChr5 198589 2 + 294540 AT -s simCow_chr6.simCow.chr6 277167 2 - 602619 CC -s simDog_chr6.simDog.chr6 276610 2 - 593897 CC -s simHuman_chr6.simHuman.chr6 264514 2 - 601863 CT -s simRat_chr6.simRat.chr6 342749 2 + 647215 AT - -a -s simMouse_chr6.simMouse.chr6 351419 14 + 636262 CACCTAACTCAGTT -s Anc0.Anc0refChr0 10161 14 - 26507 CATCTAATTGGATT -s Anc1.Anc1refChr6 180874 14 - 197743 CATCTAATTGGATT -s Anc2.Anc2refChr17 18691 14 - 28526 CATGTAATTGGATT -s mr.mrrefChr5 198591 14 + 294540 CACCTAACTCAATT -s simCow_chr6.simCow.chr6 277169 13 - 602619 CAT-TAATTGGATG -s simDog_chr6.simDog.chr6 276612 14 - 593897 CATGTAGTTGGATT -s simHuman_chr6.simHuman.chr6 264516 14 - 601863 CATCTAATTTGATT -s simRat_chr6.simRat.chr6 342753 14 + 647215 CACTTAACTCAATC - -a -s simMouse_chr6.simMouse.chr6 351433 24 + 636262 GCTACAAGAGGATAGAATGCTCAA -s Anc0.Anc0refChr0 10187 24 - 26507 GCCATAACAGGACAGAGCACTTAA -s Anc1.Anc1refChr6 180900 24 - 197743 GCCATAACAGGACAGAGCACTTAA -s Anc2.Anc2refChr17 18717 24 - 28526 GCCATAGCAGGACAGAGCACTTAA -s mr.mrrefChr5 198605 24 + 294540 GCTACAAGAGGATAGAATGCTTAA -s simCow_chr6.simCow.chr6 277194 23 - 602619 CCTA-AGCAGGATAGAGCACTTAA -s simDog_chr6.simDog.chr6 276638 24 - 593897 GCCATAGTAGGACAGAACACCTAA -s simHuman_chr6.simHuman.chr6 264542 24 - 601863 GCCATAACAGGACAGAGCATTTAA -s simRat_chr6.simRat.chr6 342767 24 + 647215 GCTACAAGAGAATAGAATGCTTAA - -a -s simMouse_chr6.simMouse.chr6 351457 48 + 636262 TGACCCTATTATGACTAGCTATGGAAACTGTATCTTGCTCACATGTGC -s Anc0.Anc0refChr0 10212 47 - 26507 GGAACCTATTATGTATAGCCATCACAACTGTGTCTTATGCATATGAG- -s Anc1.Anc1refChr6 180925 47 - 197743 GGAACCTATTATGTATAGCCATCACAACTGTGTCTTATGCATATGAG- -s Anc2.Anc2refChr17 18742 47 - 28526 GGAACCTATTATGTATGGCCATCACAACTGTGCTCTATGCATTTGAA- -s mr.mrrefChr5 198630 48 + 294540 TGACCCTATTATGAATAGCTATGGCAACTGTATCTTACTCACATGAGC -s simCow_chr6.simCow.chr6 277218 42 - 602619 GGAACCTATTATGTATTGCCAT---AACTGTGCTCTATGCATTGG--- -s simDog_chr6.simDog.chr6 276663 42 - 593897 GACACCCGTTATGTATGGCCATCACAACTG-----TATATATTTGAA- -s simHuman_chr6.simHuman.chr6 264567 47 - 601863 AGAACCTATTATACATAGCCATCACAAGTGTGTCTTATGCATATGAG- -s simRat_chr6.simRat.chr6 342792 48 + 647215 TGACCCTACTATGGATAGCTATGGCAACTGTATCTTACTCACATGAGC - -a -s simMouse_chr6.simMouse.chr6 351505 46 + 636262 TCAAACTCCCATTCTCACTTTTATGCGTAACCAACAATGGGTATAG -s Anc0.Anc0refChr0 10259 46 - 26507 TCTACTCTCAACTGACAATTTTATATCTGAGAGCCAGTGGGTATTC -s Anc1.Anc1refChr6 180972 46 - 197743 TCTACTCTCAACTGACAATTTTATATCTGAGAGCCAGTGGGTATTC -s Anc2.Anc2refChr17 18789 46 - 28526 TTTACTCTCAACCGACAATTTTATATCTGAGAGCCAGTGGGTGTTC -s mr.mrrefChr5 198678 46 + 294540 TCAAATTCCCATTCTCAATTTTATGCCTAACCAACAATGGGTATAC -s simCow_chr6.simCow.chr6 277260 39 - 602619 -------TCATCCGACAACTGTATGTTTAAGAGTCAATGGGTGTAC -s simDog_chr6.simDog.chr6 276706 46 - 593897 TTTACTCTCAACCGACAGTTTTATATCTGAGAGCCAGTGGGTGTTC -s simHuman_chr6.simHuman.chr6 264614 46 - 601863 TCTACTCTTAACTAGCAATGTTGTATCTGAGAGCCAGTGACTACTC -s simRat_chr6.simRat.chr6 342840 46 + 647215 TCAAATTCCCATTGTCAATTTTATGCCTAACCAAAGATGGGTATAC - -a -s simMouse_chr6.simMouse.chr6 351551 42 + 636262 TGCAGAATACCATGGAATTTCAGAATGTTACCCTAAAACTTG -s Anc0.Anc0refChr0 10305 41 - 26507 C-CAAAGTACCATTGGATATCAGATTGTTGGCATAAAGGTTG -s Anc1.Anc1refChr6 181018 41 - 197743 C-CAAAGTACCATTGGATATCAGATTGTTGGCATAAAGGTTG -s Anc2.Anc2refChr17 18837 41 - 28526 C-CAAAGTGCCATTGGATATCAGATTGTTGGCATAAAGGTTG -s mr.mrrefChr5 198724 42 + 294540 TGCAGAATACCATGGAATTTCAGATTGTTGCCCTAAAGGTTG -s simCow_chr6.simCow.chr6 277301 41 - 602619 C-CAGAGTGCCACTGGATTTCAGATTGTTGGCATAAAGGTTG -s simDog_chr6.simDog.chr6 276754 40 - 593897 C-CAAAGTGCCATTAGGTATTAGATTGTTGGTATAAGAGTT- -s simHuman_chr6.simHuman.chr6 264660 41 - 601863 C-CATAGTACAATTGGATGTCAGATTGTTGGCATGAAGGTTT -s simRat_chr6.simRat.chr6 342886 42 + 647215 TGCGGAATACCATAGAAGCTCAGATTGTTGTCCCAAAGGTTG - -a -s simMouse_chr6.simMouse.chr6 351593 6 + 636262 TGCATG -s Anc0.Anc0refChr0 10348 6 - 26507 TAGCAG -s Anc1.Anc1refChr6 181061 6 - 197743 TAGCAG -s Anc2.Anc2refChr17 18880 6 - 28526 TAGCAG -s mr.mrrefChr5 198768 6 + 294540 TGCAAG -s simCow_chr6.simCow.chr6 277344 6 - 602619 TAGCAG -s simHuman_chr6.simHuman.chr6 264703 6 - 601863 TAACAG -s simRat_chr6.simRat.chr6 342930 6 + 647215 TGGAAA - -a -s simMouse_chr6.simMouse.chr6 351599 14 + 636262 GCTAGTCAATCAGA -s Anc0.Anc0refChr0 10354 14 - 26507 GCTGTTCACTTATA -s Anc1.Anc1refChr6 181067 14 - 197743 GCTGTTCACTTATA -s Anc2.Anc2refChr17 18886 14 - 28526 GCAGTCAACTTATA -s mr.mrrefChr5 198774 14 + 294540 GCTAGTCAATCAGA -s simCow_chr6.simCow.chr6 277391 14 - 602619 GCAGTCAACTTATA -s simHuman_chr6.simHuman.chr6 264709 14 - 601863 GCTGATCACTTACA -s simRat_chr6.simRat.chr6 342936 14 + 647215 ACTAGTCAATCAGA - -a -s simMouse_chr6.simMouse.chr6 351613 43 + 636262 TTCAAAGTATAATAACATACAGCATCCATGTTGCAGATGGTCC -s Anc0.Anc0refChr0 10368 32 - 26507 TTTAAAATATAAGAGCAT------TA-ATGTTG---GTGGTA- -s Anc1.Anc1refChr6 181081 33 - 197743 TTTAAAATATAAGAGCAT------TA-ATGTTG---GTGGTAC -s Anc2.Anc2refChr17 18900 32 - 28526 TTTAAAATATAAGAGCAT------TT-ATGTTG---GTGGTA- -s mr.mrrefChr5 198788 42 + 294540 TTCAAAGTATAAGAACATACAGCATA-ATGTTGCAGATGGTCC -s simCow_chr6.simCow.chr6 277414 31 - 602619 TTTAAAATATAAGAGGAT------AT-ATGTTG---GATGT-- -s simDog_chr6.simDog.chr6 276794 18 - 593897 --------------GCCT------TT-GGATTG---TTGGTA- -s simHuman_chr6.simHuman.chr6 264723 33 - 601863 TGTAAAATATAAGAGCAT------TA-ATGTTG---GTGGCTC -s simRat_chr6.simRat.chr6 342950 42 + 647215 GTCAATGTATAAGAACATACAGTGTA-ATGTTGTAGATGGTCC - -a -s simMouse_chr6.simMouse.chr6 351656 11 + 636262 CTTTAGACTCA -s Anc0.Anc0refChr0 10400 9 - 26507 --TTAGAGTCA -s Anc1.Anc1refChr6 181114 11 - 197743 TTTTAGAGTCA -s Anc2.Anc2refChr17 18932 9 - 28526 --TAAGAGTCA -s mr.mrrefChr5 198830 11 + 294540 CTTTAGAGTCA -s simCow_chr6.simCow.chr6 277445 9 - 602619 --TAACGCTCA -s simDog_chr6.simDog.chr6 276812 9 - 593897 --TAAGAGTTG -s simHuman_chr6.simHuman.chr6 264759 11 - 601863 TTTTAAAGTCA -s simRat_chr6.simRat.chr6 342992 11 + 647215 CTTGAGAGTCA - -a -s simMouse_chr6.simMouse.chr6 351667 13 + 636262 TCCAGGGTAACTT -s Anc0.Anc0refChr0 10409 13 - 26507 TCTAGGTGAGTTT -s Anc1.Anc1refChr6 181125 13 - 197743 TCTAGGTGAGTTT -s Anc2.Anc2refChr17 18941 13 - 28526 TCTAGATGAGTTT -s mr.mrrefChr5 198841 13 + 294540 TCCAGGGTAACTT -s simCow_chr6.simCow.chr6 277496 13 - 602619 TCTTGATGAGTTT -s simDog_chr6.simDog.chr6 276821 11 - 593897 CCTAG--CAGACC -s simHuman_chr6.simHuman.chr6 264770 13 - 601863 TCTAGGTGAGTTT -s simRat_chr6.simRat.chr6 343003 5 + 647215 TCCAA-------- - -a -s simMouse_chr6.simMouse.chr6 351680 14 + 636262 GAGTCAGCGTTGTA -s Anc0.Anc0refChr0 10429 14 - 26507 GAGTCAAAGTTAAA -s Anc1.Anc1refChr6 181145 14 - 197743 GAGTCAAAGTTAAA -s Anc2.Anc2refChr17 18961 14 - 28526 GCGTAAAATTTAAA -s mr.mrrefChr5 198854 14 + 294540 GAGTCAGCGTTGTA -s simCow_chr6.simCow.chr6 277516 14 - 602619 GGGATAATATCAAA -s simDog_chr6.simDog.chr6 276839 14 - 593897 ACATAAAATATAAA -s simHuman_chr6.simHuman.chr6 264790 14 - 601863 GAGTCAAAGTTAAA - -a -s simMouse_chr6.simMouse.chr6 351694 28 + 636262 TAATCTCAAACCTTGAATCCAAGTGCTC -s Anc0.Anc0refChr0 10443 24 - 26507 TA-TTTCAACCCTTGG---CAAATATTC -s Anc1.Anc1refChr6 181159 24 - 197743 TA-TTTCAACCCTTGG---CAAATATTC -s Anc2.Anc2refChr17 18975 24 - 28526 TA-TTCCCACCTTTGG---GTAATATTG -s mr.mrrefChr5 198868 24 + 294540 TA-TCTCAAACCTTGA---CAAGTGCTC -s simCow_chr6.simCow.chr6 277530 23 - 602619 TG-ATCTC-CCTTTGG---TTAATAGTA -s simDog_chr6.simDog.chr6 276861 24 - 593897 TA-TTCCCACTTATCA---GTGAACTTG -s simHuman_chr6.simHuman.chr6 264804 24 - 601863 TA-TTTCAACCCTTGG---CAAATATTC - -a -s simMouse_chr6.simMouse.chr6 351722 98 + 636262 TTTCACAGGTATCAGGTATAGGTGGGATTCAAAACCCCAAAGTTATAAACAAACAAATTACATTTTGCAAGGCTGTGTGCTACAACCATAATTGCACT -s Anc0.Anc0refChr0 10467 98 - 26507 TTTTGCAAGTATCATGTATCAGTGCAATTCCACACTCCAAATTTATAATTAACAAAGTTACATTTCACAAAGGTGTGCGCTAGGACCTTAATAAAGTT -s Anc1.Anc1refChr6 181183 98 - 197743 TTTTGCAAGTATCATGTATCAGTGCAATTCCACACTCCAAATTTATAATTAACAAAGTTACATTTCACAAAGGTGTGCGCTAGGACCTTAATAAAGTT -s Anc2.Anc2refChr17 18999 98 - 28526 ATTTGCAAGTGTCATGTATCAGTGCAATTCCACACTCCAAATTTATAATTTACAAAGTTACATTTCACAAAGGTGTGCGCTAGGGCCTTAATAAAGTT -s mr.mrrefChr5 198892 98 + 294540 TTTCACAGGTATCAGGTATAGGTGGGATTCAACACCCCAAAGTTATAAACAAAAAAGTTACATTTTACAAAGGTGTGTGCTACAACCATAATTGAGCT -s simCow_chr6.simCow.chr6 277555 85 - 602619 ATTTGCAAATGTCATGTATTGGTGCAATTTCACACTCTCAATTAATCATT-----------ATTTCATAAAGGTATGTGCTAGGTCATTAATAAAC-- -s simDog_chr6.simDog.chr6 276885 98 - 593897 ATTTGCAAGTGTCAAATATCAGCACAATGCCACACTCCAAATGTATAATTTACAAAGTTACATTTGACAAAGGTGTGCACTTGGGTCTTAATATAGTT -s simHuman_chr6.simHuman.chr6 264828 98 - 601863 TTGTGCAAGTATCATGTATGAGTGCAATTCCACACTCCAAATTTAAAATTAACAAAGTTACATTTCACAAAGGTGTAAGCTAGGACCTTAGTAAAGTT -s simRat_chr6.simRat.chr6 343008 93 + 647215 ----ACAGGTATCAG-TATAGCTGGGATTCAACACCCAAAAGTTATAAGCAAAAAAGTTCCATTTTACAAAGGTGTGGGCTACAGCCATAATTGAGCT - -a -s simMouse_chr6.simMouse.chr6 351820 56 + 636262 TATAGAGAGCCAAGCTTCTCAAAGATTAACTCATATGGGAATACAACCCTTATATA -s Anc0.Anc0refChr0 10571 56 - 26507 TATTTTAAGTGAAACTTCCCAAAGGTTTACTCAATTGGTAATACAAGCCTTAGTTA -s Anc1.Anc1refChr6 181287 56 - 197743 TATTTTAAGTGAAACTTCCCAAAGGTTTACTCAATTGGTAATACAAGCCTTAGTTA -s Anc2.Anc2refChr17 19103 56 - 28526 TGTTTTAAGTGAAACTTCCCAAAGGTTTGCCCAATTGGTAGTACAAGCCTTAGTTA -s mr.mrrefChr5 198990 56 + 294540 TATAGTAAGCCAAGCTTCTCAAAGGTTAACTCATTTGGGAATACAACCCTTATATA -s simCow_chr6.simCow.chr6 277640 33 - 602619 ----TTAAGTGATACTTCCCAAAGA-------------------AAGCATTAGCTA -s simDog_chr6.simDog.chr6 276989 47 - 593897 TGTT-------AAACTTCTCAAAGGTTTGCCCAATTGGTAGTACAAGCCT--TTTA -s simHuman_chr6.simHuman.chr6 264935 56 - 601863 TATTTTAAGTTAAACTTACCAAAGGTTTACTCAGTTGGTAATACAAGTCTAAGTTA -s simRat_chr6.simRat.chr6 343101 55 + 647215 TATGGTATGC-AAGGTTCTCAAAGGTAAACTCATTTGGGAATACAACCTTTCAATG - -a -s simMouse_chr6.simMouse.chr6 351876 27 + 636262 TCTATGGAGCTGACAGAATGGTCCTAA -s Anc0.Anc0refChr0 10627 27 - 26507 TCCATGTGGATAGAGGAACAGTCCTAA -s Anc1.Anc1refChr6 181343 27 - 197743 TCCATGTGGATAGAGGAACAGTCCTAA -s Anc2.Anc2refChr17 19159 27 - 28526 TCCATGTGGATAGAGGAACAGTCCTAA -s mr.mrrefChr5 199046 27 + 294540 TCCATGGGGATGACAGAACAGTCCTAA -s simCow_chr6.simCow.chr6 277674 27 - 602619 CCCAGATGGATAGGGGAAAAGTCCTAA -s simDog_chr6.simDog.chr6 277036 27 - 593897 TCCATGTGGACAGAGGAACACTCCTAA -s simHuman_chr6.simHuman.chr6 264991 27 - 601863 TCCATGTGGATAGAGGAACAGCCCTAA -s simRat_chr6.simRat.chr6 343156 27 + 647215 CCCATGGGGATGACAGAACAGTCCTGA - -a -s simMouse_chr6.simMouse.chr6 351903 12 + 636262 ATGTGGACACTC -s Anc0.Anc0refChr0 10654 12 - 26507 TTGTGAACATTC -s Anc1.Anc1refChr6 181370 12 - 197743 TTGTGAACATTC -s Anc2.Anc2refChr17 19186 12 - 28526 TTGTGAACATTA -s mr.mrrefChr5 199073 12 + 294540 ATGTGGACACTC -s simCow_chr6.simCow.chr6 277702 12 - 602619 TTGTAAACATTT -s simDog_chr6.simDog.chr6 277063 12 - 593897 TTGTGAACATAA -s simHuman_chr6.simHuman.chr6 265018 12 - 601863 TTGTGAACAGTC -s simRat_chr6.simRat.chr6 343183 12 + 647215 ATGTGGACACTC - -a -s simMouse_chr6.simMouse.chr6 351915 6 + 636262 TAACTA -s Anc0.Anc0refChr0 10667 6 - 26507 TAACTG -s Anc1.Anc1refChr6 181383 6 - 197743 TAACTG -s Anc2.Anc2refChr17 19199 6 - 28526 TAACTG -s mr.mrrefChr5 199086 6 + 294540 TAACTA -s simCow_chr6.simCow.chr6 277715 6 - 602619 TAACTG -s simDog_chr6.simDog.chr6 277076 6 - 593897 TAACTG -s simHuman_chr6.simHuman.chr6 265031 6 - 601863 TAACTG -s simRat_chr6.simRat.chr6 343196 6 + 647215 TAGCTA - -a -s simMouse_chr6.simMouse.chr6 351921 19 + 636262 GCTCATTCCTAGTTATTGG -s Anc0.Anc0refChr0 10674 19 - 26507 GCCCATTTCCACTTCTTCA -s Anc1.Anc1refChr6 181390 19 - 197743 GCCCATTTCCACTTCTTCA -s Anc2.Anc2refChr17 19206 19 - 28526 GCCCATTTCCACTTCTTCA -s mr.mrrefChr5 199092 19 + 294540 GCCCATTCCTAGTTATTGA -s simCow_chr6.simCow.chr6 277722 19 - 602619 GCCCATTTCCACTTCTTCA -s simDog_chr6.simDog.chr6 277083 19 - 593897 GTCCATTTCCACTTCTTCA -s simHuman_chr6.simHuman.chr6 265038 19 - 601863 GCCCATTTCCATTTCTTCA -s simRat_chr6.simRat.chr6 343202 19 + 647215 CCCCATTCCTAGTTATTAA - -a -s simMouse_chr6.simMouse.chr6 351940 10 + 636262 GGCCACACTT -s Anc0.Anc0refChr0 10694 10 - 26507 GGTTAAACCC -s Anc1.Anc1refChr6 181410 10 - 197743 GGTTAAACCC -s Anc2.Anc2refChr17 19226 10 - 28526 GGTTAAACCC -s mr.mrrefChr5 199111 10 + 294540 GGCCACACTT -s simCow_chr6.simCow.chr6 277742 10 - 602619 GGTTGAATCT -s simDog_chr6.simDog.chr6 277103 10 - 593897 GCTTAAACTC -s simHuman_chr6.simHuman.chr6 265058 10 - 601863 GGTTAAACCC -s simRat_chr6.simRat.chr6 343221 10 + 647215 GGCCACATTT - -a -s simMouse_chr6.simMouse.chr6 351950 86 + 636262 GTGCTTGCGTCCTTGAAAACCTCTAACAGAGCACCACACTGTGAGTATGAGTGGGGTGCGGCCACTGGCAGTGTTCTGTAGGAGTT -s Anc0.Anc0refChr0 10704 84 - 26507 TGGCCTGTCTCCTTAACAACCTCATACAGTGCATCTTACTGTGACTATGAGTGGGGAGTCTGTATTGGCAAGGTTGTGTAGGAA-- -s Anc1.Anc1refChr6 181420 84 - 197743 TGGCCTGTCTCCTTAACAACCTCATACAGTGCATCTTACTGTGACTATGAGTGGGGAGTCTGTATTGGCAAGGTTGTGTAGGAA-- -s Anc2.Anc2refChr17 19236 84 - 28526 TGGCCTGTCTCCTTAACAACCTCATACAGTGCATCTTACTGTGATTATGAGGGGGGAGTCTGTGTAGGCAAGGTTGTGCAGGTA-- -s mr.mrrefChr5 199121 86 + 294540 GTGCTTGTCTCCTTGAAAACCTCTAACAGAGCACCACACTGTGACTATGAGTGGGGTGCGGCCATTGGCAAGGTTCTGTAGGAGTT -s simCow_chr6.simCow.chr6 277753 81 - 602619 GGGCCTGTCTCCTTAACAACCTCATACAGTGCATCTTAATAAGATTATGAGGGGGGTGTCTGTGT---CAAGGTCCTGCAGGTA-- -s simDog_chr6.simDog.chr6 277113 83 - 593897 TGGCCTGTCTCCTT-ACATCCTCATACAGCACATCTTGCTGTTCTCATGATGGGTGAGTCTGTGTAGGCAAGGTTGTACAGGTA-- -s simHuman_chr6.simHuman.chr6 265068 84 - 601863 CGGCCTGTCTCCTTAACAACCTCATACAGTGCATCTTACTGTGACTATGAGTGGGGCGTTCATATTGACTAGGTTGTGTGGGAA-- -s simRat_chr6.simRat.chr6 343231 86 + 647215 GCGCTTGTCTCCTTGAAAACCTCTAACAGAGCACCACACTGTGACTATGAGTGGGGTGAGGGCATTGGCAAGGTTCTATAGGAGTT - -a -s simMouse_chr6.simMouse.chr6 352036 24 + 636262 GCTGTGGGGTTTGAATGGCCACCC -s Anc0.Anc0refChr0 10788 24 - 26507 ACCATGAGTCTTGAGGTGCAACTC -s Anc1.Anc1refChr6 181504 24 - 197743 ACCATGAGTCTTGAGGTGCAACTC -s Anc2.Anc2refChr17 19320 24 - 28526 ACCATGAATCTTGAGGTGCAACTC -s mr.mrrefChr5 199207 24 + 294540 GCTGTGAGGTTTGAATGGCCACCC -s simCow_chr6.simCow.chr6 277834 22 - 602619 --CGAGAAGCTTGAGACGCAACCC -s simDog_chr6.simDog.chr6 277199 24 - 593897 ACCATGAATCTAGAGGTGCAACTG -s simHuman_chr6.simHuman.chr6 265152 24 - 601863 ACCATGAGCCTTGATGTGCAACTC -s simRat_chr6.simRat.chr6 343317 20 + 647215 GCTGTGAGG----AATGGACACCC - -a -s simMouse_chr6.simMouse.chr6 352060 6 + 636262 TATTCT -s Anc0.Anc0refChr0 10818 6 - 26507 TAGTTT -s Anc1.Anc1refChr6 181534 6 - 197743 TAGTTT -s Anc2.Anc2refChr17 19352 6 - 28526 TAGTTT -s mr.mrrefChr5 199231 6 + 294540 TATTTT -s simCow_chr6.simCow.chr6 277864 6 - 602619 CCATTT -s simDog_chr6.simDog.chr6 277231 6 - 593897 TAGTTT -s simHuman_chr6.simHuman.chr6 265182 6 - 601863 TGGTTT -s simRat_chr6.simRat.chr6 343337 6 + 647215 AATTTT - -a -s simMouse_chr6.simMouse.chr6 352066 59 + 636262 ATGAAGCTTGAAACTATGGGGTCAATGTTTTTTTCTGTGTTGATGCTATCCAAGCCTAT -s Anc0.Anc0refChr0 10824 45 - 26507 GTGAAGCTTGAATCTAAGGGGTCAGTGTTTTTTTAT------ATTATATCC-------- -s Anc1.Anc1refChr6 181540 45 - 197743 GTGAAGCTTGAATCTAAGGGGTCAGTGTTTTTTTAT------ATTATATCC-------- -s Anc2.Anc2refChr17 19358 45 - 28526 GTGAAGCTTGAGTCTAAGAGGTCAGTGTTTTTTTAC------ATTATATCT-------- -s mr.mrrefChr5 199237 59 + 294540 ATGAAGCTTGAAACTAAGGGGTCAATGTTTTTTTCTGTGTTGATGCTATCCAAGCCTAT -s simCow_chr6.simCow.chr6 277870 45 - 602619 GTGAAGCTTGAGTCTAAGAGGTCAGCCTTTTTTTAC------ATTGTATCT-------- -s simDog_chr6.simDog.chr6 277238 45 - 593897 GTGAAGTTTGAGTCTAAGAGGTCACTGTTTTTTTAC------ATCACATCT-------- -s simHuman_chr6.simHuman.chr6 265188 45 - 601863 GTGAAGCTTGAATCTGAGGGGTCAGTGCTTTTTTAT------ATTATATCC-------- -s simRat_chr6.simRat.chr6 343343 59 + 647215 ATGAAACTTGAAACTAAGGGGCCAATGTTTTTTTCCTTCTTGATGCTATCCAAGCCTAT - -a -s simMouse_chr6.simMouse.chr6 352125 70 + 636262 AGACAGAGAACCAAATGAATAGTGCTACAGTGCCTGGTGGAGGAAGCTTCTTGTTGCATATTTCTGGCAC -s Anc0.Anc0refChr0 10869 50 - 26507 --------------------TACACTACCTTATGTTGTAGGAGAAGGTTTTAGTTTCATATTTCTGACAG -s Anc1.Anc1refChr6 181585 50 - 197743 --------------------TACACTACCTTATGTTGTAGGAGAAGGTTTTAGTTTCATATTTCTGACAG -s Anc2.Anc2refChr17 19403 50 - 28526 --------------------GACACTACCTAATGTTGTAGGAGACGGATTCAGTTTCATATTTCTGACAG -s mr.mrrefChr5 199296 70 + 294540 AGACAGAGAACCAAATGAATTGTGCTACAGTGCCTGGTGGAGGAAGCTTCTTGTTGCATATTTCTGGCAC -s simCow_chr6.simCow.chr6 277915 50 - 602619 --------------------GGCACTACCTAATGTTGTAGGAGATGGCTTCAGTTTTAAATTTCAGGCAC -s simDog_chr6.simDog.chr6 277283 50 - 593897 --------------------GACACTACCTAATATTGTAGGAGACGGATTCAGCTTCATACTTCTGACTG -s simHuman_chr6.simHuman.chr6 265233 50 - 601863 --------------------TACACTACCTTATGTTATAGGAGAAGATTTTAGTTCCATATTTCTGTCAG -s simRat_chr6.simRat.chr6 343434 69 + 647215 AGACAGATAACCAAATGAATTGTGCTACAGTGGCGGGTGAAG-AAGGTTCTTGTTGCATAATTCTGGCAC - -a -s simMouse_chr6.simMouse.chr6 352195 16 + 636262 TCATTACAAAGTGGTT -s Anc0.Anc0refChr0 10919 16 - 26507 TCATTATAAAATGGTC -s Anc1.Anc1refChr6 181635 16 - 197743 TCATTATAAAATGGTC -s Anc2.Anc2refChr17 19453 16 - 28526 TCATTATAAAACGGTC -s mr.mrrefChr5 199366 16 + 294540 TCATTATAAAGTGGTC -s simCow_chr6.simCow.chr6 277965 16 - 602619 ACATTATATCACAGTC -s simDog_chr6.simDog.chr6 277337 16 - 593897 TCATTATAAAACGACC -s simHuman_chr6.simHuman.chr6 265283 16 - 601863 TCATTATAAAATGGTC -s simRat_chr6.simRat.chr6 343503 16 + 647215 TCATTATAAAGCGGCC - -a -s simMouse_chr6.simMouse.chr6 352211 20 + 636262 AGTGTCTCCAGCCAACCATG -s Anc0.Anc0refChr0 10942 20 - 26507 GGTATCACCAGTAACCTATG -s Anc1.Anc1refChr6 181658 20 - 197743 GGTATCACCAGTAACCTATG -s Anc2.Anc2refChr17 19476 20 - 28526 GGTATCACCAGTAACCTATG -s mr.mrrefChr5 199382 20 + 294540 AGTGTCTCCAGCCAACCATG -s simCow_chr6.simCow.chr6 277988 20 - 602619 GGCATCACCAGTCACCTATT -s simDog_chr6.simDog.chr6 277360 20 - 593897 CGTATCACTGGTAACCTATG -s simHuman_chr6.simHuman.chr6 265306 20 - 601863 GGTATCACCAGTTTCCTGCG -s simRat_chr6.simRat.chr6 343519 13 + 647215 AGTGTC-------AACCATT - -a -s simMouse_chr6.simMouse.chr6 352231 1 + 636262 C -s Anc0.Anc0refChr0 10962 1 - 26507 A -s Anc1.Anc1refChr6 181678 1 - 197743 A -s Anc2.Anc2refChr17 19501 1 - 28526 A -s mr.mrrefChr5 199402 1 + 294540 C -s simCow_chr6.simCow.chr6 278013 1 - 602619 A -s simDog_chr6.simDog.chr6 277385 1 - 593897 A -s simHuman_chr6.simHuman.chr6 265326 1 - 601863 A -s simRat_chr6.simRat.chr6 343532 1 + 647215 C - -a -s simMouse_chr6.simMouse.chr6 352232 41 + 636262 TCAACGGGCTTTAATATTCCAGGACCCAGATCTAACACATA -s Anc0.Anc0refChr0 10964 40 - 26507 CCAACAGGCTTTGATGAGC-AGGGCCCAACTTTAACACATA -s Anc1.Anc1refChr6 181680 40 - 197743 CCAACAGGCTTTGATGAGC-AGGGCCCAACTTTAACACATA -s Anc2.Anc2refChr17 19503 40 - 28526 CCAACAGGCTTTGATGAGC-AGGATCCCACTTTGACATGTA -s mr.mrrefChr5 199403 40 + 294540 TCAACAGGCTTTAATGTTC-AGGGCCCAGATCTAACACATA -s simCow_chr6.simCow.chr6 278015 34 - 602619 CCAACAGGCTT------GC-AGGATCCCACTTTGATATGCA -s simDog_chr6.simDog.chr6 277387 40 - 593897 TCAACAGGCTTTGATGAGC-AGGATCGCACTTTGACATGTA -s simHuman_chr6.simHuman.chr6 265328 40 - 601863 CCAACAGGCTTTCATGGGC-AGAGCCCAACTTTAACACATA -s simRat_chr6.simRat.chr6 343533 40 + 647215 TCAACAGGCTTTAATGTTC-AGGGTCCAGAACTAACACATA - -a -s simMouse_chr6.simMouse.chr6 352273 24 + 636262 TGAACCCAATTTTTTGTAGGTAGG -s Anc0.Anc0refChr0 11005 21 - 26507 TGAACCCAATTCTTTGTCGG---G -s Anc1.Anc1refChr6 181721 21 - 197743 TGAACCCAATTCTTTGTCGG---G -s Anc2.Anc2refChr17 19544 21 - 28526 TGAACCCCATTTTTTATCAG---G -s mr.mrrefChr5 199444 24 + 294540 TGAACCCAATTCTTTGTAGGTAGG -s simCow_chr6.simCow.chr6 278050 21 - 602619 TGAACCCCATTTTTTATCAG---G -s simHuman_chr6.simHuman.chr6 265369 21 - 601863 TGAAGCCAATTCTTTGTCGG---G -s simRat_chr6.simRat.chr6 343574 24 + 647215 TGAAACCCGTTCTTTGTAGGGAGG - -a -s simMouse_chr6.simMouse.chr6 352297 86 + 636262 TTCAGGAACAACAAGTTACTGTGTATAAACTTTTTTTACCAGTAGTCATGCCTTAGGTCCCCGCCAAACAAGCTACTGTTCTATCC -s Anc0.Anc0refChr0 11030 71 - 26507 TTGTGGAACAACTAGGTATTGTGTGTGAAATGA-------GGTTTAGATGC----ACTCCC-TACAAGCAGGCTTGTTTTCTA--- -s Anc1.Anc1refChr6 181746 82 - 197743 TTGTGGAACAACTAGGTATTGTGTGTGAAATGAAATTCATGGTTTAGATGC----ACTCCCCTACAAGCAGGCTTGTTTTCTATCT -s Anc2.Anc2refChr17 19569 71 - 28526 TTGTGGAACAACTAGGTATTGTGTGTGGAAAAA-------GGGTTAGATGC----AATTCC-TACAAGCAGGCTTGTTTTCCA--- -s mr.mrrefChr5 199472 86 + 294540 TTGTGGAACAACAAGTTACTGTGTATAAACTGTTTTTACCAGTTTTGATGCCTTAGCTCCCCGACAAGCAAGCTACTGTTCTATCT -s simCow_chr6.simCow.chr6 278075 71 - 602619 TCATGGAACAACTAGGTATTGTGTGTGGAAAAA-------GGGTTAGATGC----AATTCC-TACAAGCAGGCTTGTTTTCCA--- -s simDog_chr6.simDog.chr6 277428 10 - 593897 -TGTGGAACAA--------------------------------------------------------------------------- -s simHuman_chr6.simHuman.chr6 265394 82 - 601863 TTGTGGAACAACGAAGTGATAACTGTGAAATGAAATTCATGGTTTAGATGC----ACTCCCCTACTAGGATGCCTGTTTTCTATCT -s simRat_chr6.simRat.chr6 343602 86 + 647215 TTGTGGAAGAACAAGTTAGTGCGTATAAACCGTGTTTACCAGTTTTGATGTCTTAGCTCCCCAACAAGAAAGCTACTGTTCTGTCT - -a -s simMouse_chr6.simMouse.chr6 352383 35 + 636262 GTATTATGTTAGTAGCAGAGAGCATAATAATTCAG -s Anc0.Anc0refChr0 11113 35 - 26507 GTATTATCTTTGTAGCAAGGAGCATAATAATTCAA -s Anc1.Anc1refChr6 181840 35 - 197743 GTATTATCTTTGTAGCAAGGAGCATAATAATTCAA -s Anc2.Anc2refChr17 19652 35 - 28526 GTATTACCTTTGTAGCAAGGATCTTAATAATTCAA -s mr.mrrefChr5 199558 35 + 294540 GTATTATGTTAGTAGCAAAGAGCATAATAATTCAG -s simCow_chr6.simCow.chr6 278154 35 - 602619 TTATTACCTTTGTAGCTAGGTTCTTAATAGTTCAA -s simDog_chr6.simDog.chr6 277450 29 - 593897 GTACTACCTT------AAGGATCTTAATAATTCAA -s simHuman_chr6.simHuman.chr6 265505 35 - 601863 GTATTATCTTTGTGGCAAGGAGGATAATAATTCAA -s simRat_chr6.simRat.chr6 343688 35 + 647215 GTATTATACTGGTAGCAAAGAACCCAATAATTCAG - -a -s simMouse_chr6.simMouse.chr6 352418 25 + 636262 TGGGCAACATTTGGCTGATCTATCT -s Anc0.Anc0refChr0 11176 25 - 26507 GGGGCAACTTTTCGTGAATCTATCT -s Anc1.Anc1refChr6 181903 25 - 197743 GGGGCAACTTTTCGTGAATCTATCT -s Anc2.Anc2refChr17 19720 25 - 28526 GGGGCAACTTTTCATGAATCTATTT -s mr.mrrefChr5 199593 25 + 294540 TGGGCAACATTTGGCTGATCTATCT -s simCow_chr6.simCow.chr6 278222 22 - 602619 GGGGCAACCTTTCATGAAGATA--- -s simDog_chr6.simDog.chr6 277512 25 - 593897 GGTGCAACTTTTCAGAAATCTATTT -s simHuman_chr6.simHuman.chr6 265568 25 - 601863 GGGGCAACTTTTTGTGAATCTATCT -s simRat_chr6.simRat.chr6 343723 25 + 647215 TCAGCAACATTTGGCTGATCTATCT - -a -s simMouse_chr6.simMouse.chr6 352443 24 + 636262 TTTATTGCTATCTGATTATCTGAA -s Anc0.Anc0refChr0 11201 24 - 26507 TCTGTCATCAACAAATAATCTGAA -s Anc1.Anc1refChr6 181928 24 - 197743 TCTGTCATCAACAAATAATCTGAA -s Anc2.Anc2refChr17 19745 24 - 28526 TCTGTCATCAACAAATAATCTGAA -s mr.mrrefChr5 199618 24 + 294540 TTTATTGCTAACTGATTATCTGAA -s simCow_chr6.simCow.chr6 278244 24 - 602619 TCTGTCATCAATATATAATCTGAA -s simDog_chr6.simDog.chr6 277538 23 - 593897 TCTGTTTTCAACTAATAATCC-AG -s simHuman_chr6.simHuman.chr6 265593 24 - 601863 TGTGTCATCAAGAAATAATCTGAA -s simRat_chr6.simRat.chr6 343748 24 + 647215 TTTATTGCTAACTGATTATCTGAA - -a -s simMouse_chr6.simMouse.chr6 352467 8 + 636262 GGGTACCT -s Anc0.Anc0refChr0 11226 8 - 26507 GGGCATCT -s Anc1.Anc1refChr6 181953 8 - 197743 GGGCATCT -s Anc2.Anc2refChr17 19770 8 - 28526 GGGCATCT -s mr.mrrefChr5 199642 8 + 294540 GGGCACCT -s simCow_chr6.simCow.chr6 278268 7 - 602619 -GGCATCT -s simDog_chr6.simDog.chr6 277562 8 - 593897 GGGCATCT -s simHuman_chr6.simHuman.chr6 265618 8 - 601863 GGGCATCT -s simRat_chr6.simRat.chr6 343772 8 + 647215 GGGCACCT - -a -s simMouse_chr6.simMouse.chr6 352475 11 + 636262 AGAAGTTCTTT -s Anc0.Anc0refChr0 11234 11 - 26507 AGAAGTGCTTC -s Anc1.Anc1refChr6 181961 11 - 197743 AGAAGTGCTTC -s Anc2.Anc2refChr17 19778 11 - 28526 AGAAGTGCTTC -s mr.mrrefChr5 199650 11 + 294540 AGAAGTGCTTT -s simCow_chr6.simCow.chr6 278275 11 - 602619 AGATGTACTTC -s simDog_chr6.simDog.chr6 277571 11 - 593897 AGCAGTGCTTC -s simHuman_chr6.simHuman.chr6 265626 11 - 601863 GGAAGTGATTA -s simRat_chr6.simRat.chr6 343780 11 + 647215 AGAAGTGCTTT - -a -s simMouse_chr6.simMouse.chr6 352486 64 + 636262 GTGGTATTACCATTAATCTAAGTGCACTCCCTGGCTTTCACGGCCCTGTACTGGCATCCAAATA -s Anc0.Anc0refChr0 11245 54 - 26507 TTGCCATCA----------ATGTACACTAGTTGGATTTCACTTGCCCGTGCAAACATCCAAATA -s Anc1.Anc1refChr6 181972 54 - 197743 TTGCCATCA----------ATGTACACTAGTTGGATTTCACTTGCCCGTGCAAACATCCAAATA -s Anc2.Anc2refChr17 19789 54 - 28526 TTGCCATCA----------ATGTACACCAGTTGGATTTCACTTGCCTGTGGAAACATCCAAATG -s mr.mrrefChr5 199661 64 + 294540 GTGCCATCACCATTAATCTATGTGCACTAGTTGGCTTTCACGTCCCCGTACTGGCATCCAAATA -s simCow_chr6.simCow.chr6 278287 53 - 602619 TTGTCATCA----------ATGCACAACGGCTGAATCTCACTACCCTGTGGAAACATCCAAAT- -s simDog_chr6.simDog.chr6 277582 53 - 593897 TTGCTGTCA----------ATGTACACCAGTTGGATTTCAC-TGCCTGGGGAAACATCCATATG -s simHuman_chr6.simHuman.chr6 265637 54 - 601863 TTGCCATCA----------ATGTACACTAGTTGCATTTCACTTGTCCATGCAAACATCCAAATA -s simRat_chr6.simRat.chr6 343791 63 + 647215 GTGCCCTCACCTTTAATGTATGTGCACTAGTTGGCTTTCACCTCCCCGT-CTGGCATCCAAATA - -a -s simMouse_chr6.simMouse.chr6 352550 4 + 636262 TTGA -s Anc0.Anc0refChr0 11299 4 - 26507 GTAC -s Anc1.Anc1refChr6 182026 4 - 197743 GTAC -s Anc2.Anc2refChr17 19843 4 - 28526 GTAC -s mr.mrrefChr5 199725 4 + 294540 GTGA -s simDog_chr6.simDog.chr6 277709 4 - 593897 GTAC -s simHuman_chr6.simHuman.chr6 265691 4 - 601863 GTAC -s simRat_chr6.simRat.chr6 343854 4 + 647215 GTGA - -a -s simMouse_chr6.simMouse.chr6 352554 2 + 636262 AC -s Anc0.Anc0refChr0 11303 2 - 26507 GT -s Anc1.Anc1refChr6 182030 2 - 197743 GT -s Anc2.Anc2refChr17 19847 2 - 28526 GT -s mr.mrrefChr5 199729 2 + 294540 AC -s simCow_chr6.simCow.chr6 278340 2 - 602619 TT -s simDog_chr6.simDog.chr6 277714 2 - 593897 GT -s simHuman_chr6.simHuman.chr6 265695 2 - 601863 GT -s simRat_chr6.simRat.chr6 343858 2 + 647215 CC - -a -s simMouse_chr6.simMouse.chr6 352556 26 + 636262 AAGGCCTGCTGGACACTCTGTAAATA -s Anc0.Anc0refChr0 11305 26 - 26507 AAGGTCTGCTGGACACTTTGTAAAAA -s Anc1.Anc1refChr6 182032 26 - 197743 AAGGTCTGCTGGACACTTTGTAAAAA -s Anc2.Anc2refChr17 19854 26 - 28526 AAGGTCTTCCGGATACTTTGTAAAAG -s mr.mrrefChr5 199731 26 + 294540 AAGGCCTGCTGGACACTCTGTAAATA -s simCow_chr6.simCow.chr6 278347 26 - 602619 AAAGTCTACCCGATACTTTGTAAATG -s simDog_chr6.simDog.chr6 277721 26 - 593897 AAGGCCTTCCGAATACTTTGTAAAAG -s simHuman_chr6.simHuman.chr6 265697 26 - 601863 AAGGTCTGTTGGACACTTTGTAAACA -s simRat_chr6.simRat.chr6 343860 26 + 647215 AAGGCCTGCTAGACACTCTGTAAAAA - -a -s simMouse_chr6.simMouse.chr6 352582 96 + 636262 GGGGCTAACCTGTGGTGCCAAAGAGATGAACTCTACAATAACCCCTTGACAGCCTTAAGAGAGAGCATGTGAAAATTACCTCATGTTTAGGCCAAA -s Anc0.Anc0refChr0 11331 83 - 26507 GGAACTGTCCTATG---CTCAAGATATGCAATCCACAACAATTTAGTGATAACCCCAAGACAGAGCATGTGAAAATCACCTC----------CAAA -s Anc1.Anc1refChr6 182058 83 - 197743 GGAACTGTCCTATG---CTCAAGATATGCAATCCACAACAATTTAGTGATAACCCCAAGACAGAGCATGTGAAAATCACCTC----------CAAA -s Anc2.Anc2refChr17 19882 83 - 28526 GGAACAGTCCTGTG---CTCAAGATATACAATCCGCAACAATTTAGTGATAATCCCTAAACAGAGCATGTAAAAATCACCTC----------CAAA -s mr.mrrefChr5 199757 93 + 294540 GGAACTAACCTATG---CCAAAGAGATGCACTCTACAATAACCCCTTGATAACCTTAAGAGAGAGCATGTGAAAATTACCTCATGTTTAGGCCAAA -s simCow_chr6.simCow.chr6 278375 81 - 602619 GGAACAGTCCCCTT---CTCAAGATACTCAAGC--CAACAATTTAGTGATAAACCCTGAATAGAGCATGTAACAACCACCTC----------TAAA -s simDog_chr6.simDog.chr6 277749 80 - 593897 GGAACAGTCCTGTG---CTTAAGAT-TAGAGTCCGCAACAATTTAGTGATAGT--CTAAACAGAGCGTGTAAAAATTGCCTC----------CAAA -s simHuman_chr6.simHuman.chr6 265723 83 - 601863 GGAACTCTCCTATG---CTCAAGATATGCAATTCACAACAATTTAGGGATAACCACAAGACAAAGTATGTGAAAATCACCTC----------CAAA -s simRat_chr6.simRat.chr6 343886 92 + 647215 AGAACTAACCCATG---CCAAGGAGATGCATTCAACAATAACCCCCT-ATAACCTTAAGAGAGAGCATGTGAAAATTACCTCATGTTTAGGCCACA - -a -s simMouse_chr6.simMouse.chr6 352678 61 + 636262 ATAACCCTTAGGTCCACGTAACTTACGGCAATTGTTGCCAGGGAGATAGGAAGTTCATTTG -s Anc0.Anc0refChr0 11414 57 - 26507 AGA----TTAAGTCAATGTAAGCCAGACCAATTGTTCACAAAAAAGATGGGGGATGAATTG -s Anc1.Anc1refChr6 182141 57 - 197743 AGA----TTAAGTCAATGTAAGCCAGACCAATTGTTCACAAAAAAGATGGGGGATGAATTG -s Anc2.Anc2refChr17 19965 57 - 28526 TGT----TTAAGTCAACATAAGCCAGACCAATTGTTCAGAAAAAAGATGAGGGATGAATTG -s mr.mrrefChr5 199850 61 + 294540 ATAACCCTTAGGTCCATGTAACTCAGGGCAATTGTTGCCAGAGAGATAGGAAGTTGATTTG -s simCow_chr6.simCow.chr6 278456 57 - 602619 CAT----TTAAGTCAACATAACCCAGATCAAGTGTTGAGAAGAAAGATGAGGGATGAATTG -s simDog_chr6.simDog.chr6 277829 57 - 593897 TGT----TTAAGTCAACATGAGCCAGACCAATTGTTCAGAAACAAGATGAGGGATGAATTG -s simHuman_chr6.simHuman.chr6 265806 57 - 601863 AGA----TTAAGTCAATGTAATCCAGACTAATTGTTCACAAAAAAGACAGGGGATGCGTTG -s simRat_chr6.simRat.chr6 344010 61 + 647215 ATAACCTCAAGGGCCATGTAACTCAGGACAATTATTGCCGGACAGATAGGAAGCTGATTTG - -a -s simMouse_chr6.simMouse.chr6 352739 7 + 636262 AACTTCA -s Anc0.Anc0refChr0 11473 7 - 26507 AGCTATA -s Anc1.Anc1refChr6 182200 7 - 197743 AGCTATA -s Anc2.Anc2refChr17 20024 7 - 28526 AGCTATT -s mr.mrrefChr5 199911 7 + 294540 AACTTCA -s simCow_chr6.simCow.chr6 278515 7 - 602619 AGCTATT -s simDog_chr6.simDog.chr6 277888 7 - 593897 AGCTATT -s simHuman_chr6.simHuman.chr6 265865 5 - 601863 GCCT--A -s simRat_chr6.simRat.chr6 344071 7 + 647215 AACTTCA - -a -s simMouse_chr6.simMouse.chr6 352746 29 + 636262 CCTCATTCAATAAGTTCCTTCTGTTCCAG -s Anc0.Anc0refChr0 11492 27 - 26507 --TGATTGAATAAGTTCATTCTTTTCCAG -s Anc1.Anc1refChr6 182219 27 - 197743 --TGATTGAATAAGTTCATTCTTTTCCAG -s Anc2.Anc2refChr17 20043 27 - 28526 --TGATTGAATAAGTTCATTTTTTTCCAC -s mr.mrrefChr5 199930 29 + 294540 CCTCATTCAATAAGTTCCTTCTGTTCCAG -s simCow_chr6.simCow.chr6 278534 27 - 602619 --TCATTAAAAAAGTTCATAATCTTCCAC -s simDog_chr6.simDog.chr6 277907 27 - 593897 --TGTCTGAATAAGTTCATTTGTTTCCAC -s simHuman_chr6.simHuman.chr6 265882 27 - 601863 --TTATTGAATAAGTTCATTCTTTTCCAG -s simRat_chr6.simRat.chr6 344090 29 + 647215 CCTCATTCAATAAGTTCCTTCCATTCCAG - -a -s simMouse_chr6.simMouse.chr6 352775 7 + 636262 GTACCAG -s Anc0.Anc0refChr0 11520 7 - 26507 GTACAAG -s Anc1.Anc1refChr6 182247 7 - 197743 GTACAAG -s Anc2.Anc2refChr17 20071 7 - 28526 TTACAAG -s mr.mrrefChr5 199959 7 + 294540 GTACCAG -s simCow_chr6.simCow.chr6 278562 5 - 602619 TTACA-- -s simDog_chr6.simDog.chr6 277935 7 - 593897 TTCCAAG -s simHuman_chr6.simHuman.chr6 265910 7 - 601863 GTATGAG -s simRat_chr6.simRat.chr6 344119 7 + 647215 GTGCCAG - -a -s simMouse_chr6.simMouse.chr6 352782 3 + 636262 TAA -s Anc0.Anc0refChr0 11529 3 - 26507 CCA -s Anc1.Anc1refChr6 182256 3 - 197743 CCA -s Anc2.Anc2refChr17 20080 3 - 28526 CCA -s mr.mrrefChr5 199966 3 + 294540 TAA -s simCow_chr6.simCow.chr6 278567 3 - 602619 CTG -s simDog_chr6.simDog.chr6 277944 3 - 593897 TCA -s simHuman_chr6.simHuman.chr6 265919 3 - 601863 CCA -s simRat_chr6.simRat.chr6 344126 3 + 647215 TAA - -a -s simMouse_chr6.simMouse.chr6 352785 1 + 636262 T -s Anc0.Anc0refChr0 11532 1 - 26507 T -s Anc1.Anc1refChr6 182259 1 - 197743 T -s Anc2.Anc2refChr17 20088 1 - 28526 T -s mr.mrrefChr5 199969 1 + 294540 T -s simCow_chr6.simCow.chr6 278575 1 - 602619 T -s simDog_chr6.simDog.chr6 277952 1 - 593897 T -s simHuman_chr6.simHuman.chr6 265922 1 - 601863 C -s simRat_chr6.simRat.chr6 344129 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 352786 8 + 636262 TGTCAAAA -s Anc0.Anc0refChr0 11533 8 - 26507 TTTCAGAA -s Anc1.Anc1refChr6 182260 8 - 197743 TTTCAGAA -s Anc2.Anc2refChr17 20089 8 - 28526 TTTCAGGA -s mr.mrrefChr5 199970 8 + 294540 TTTCAGAA -s simCow_chr6.simCow.chr6 278576 8 - 602619 TTCCAGTA -s simDog_chr6.simDog.chr6 277953 8 - 593897 TTTCAGGG -s simHuman_chr6.simHuman.chr6 265923 8 - 601863 TTTCAGAA -s simRat_chr6.simRat.chr6 344138 8 + 647215 TTTCAGGA - -a -s simMouse_chr6.simMouse.chr6 352794 6 + 636262 TGTAGC -s Anc0.Anc0refChr0 11541 6 - 26507 TGTAGC -s Anc1.Anc1refChr6 182268 6 - 197743 TGTAGC -s Anc2.Anc2refChr17 20105 6 - 28526 TGTAGC -s mr.mrrefChr5 199978 6 + 294540 TGTAGC -s simCow_chr6.simCow.chr6 278592 6 - 602619 AGTGGC -s simDog_chr6.simDog.chr6 277969 6 - 593897 TGTAGC -s simHuman_chr6.simHuman.chr6 265931 3 - 601863 ---AAC -s simRat_chr6.simRat.chr6 344154 6 + 647215 TGTACC - -a -s simMouse_chr6.simMouse.chr6 352800 28 + 636262 ATTTGAGACTAAGCTCCAATGTTGCCTC -s Anc0.Anc0refChr0 11550 28 - 26507 GTTTGAGACCAAACTCCAATGATGGTTG -s Anc1.Anc1refChr6 182277 28 - 197743 GTTTGAGACCAAACTCCAATGATGGTTG -s Anc2.Anc2refChr17 20114 28 - 28526 GTTTGATAGCAAACTCCAATGATGGTTG -s mr.mrrefChr5 199987 28 + 294540 GTTTGAGACTAAGCTCCAATGTTGCCTC -s simCow_chr6.simCow.chr6 278601 28 - 602619 ATTTAATAGCAAACTCCAATGATGTCTG -s simDog_chr6.simDog.chr6 277978 16 - 593897 GTTTG------------AATGATGGTAA -s simHuman_chr6.simHuman.chr6 265937 28 - 601863 GTTTGAGACCAAACTCCAATGATGGATG -s simRat_chr6.simRat.chr6 344163 28 + 647215 GTTTGAGACTAAGCTCCAAAGCTGTCTT - -a -s simMouse_chr6.simMouse.chr6 352828 70 + 636262 TCCTCATGAGAGCTCTGTAGCGATGTAGTAAGCAGGTTATTTTCGCTCATATTCTAGCTCAAGAACAGGC -s Anc0.Anc0refChr0 11578 7 - 26507 TCTT---------------------------------------------------------------GGC -s Anc1.Anc1refChr6 182305 7 - 197743 TCTT---------------------------------------------------------------GGC -s Anc2.Anc2refChr17 20142 7 - 28526 TCTT---------------------------------------------------------------GGC -s mr.mrrefChr5 200015 70 + 294540 TCCTCATGAGAGCTCTGTAGCGATGTAGTAAGCAGGTTATTTTCGCTCATATTCTAGCTCAAGAACAGGC -s simCow_chr6.simCow.chr6 278630 7 - 602619 TTTT---------------------------------------------------------------GGA -s simDog_chr6.simDog.chr6 277994 5 - 593897 TCT-----------------------------------------------------------------GC -s simHuman_chr6.simHuman.chr6 265965 7 - 601863 TCTC---------------------------------------------------------------GGC -s simRat_chr6.simRat.chr6 344191 70 + 647215 TCCTCAGGAGAGCTCTGTAGCGATGTAGTGAACGGACTATTTTCACTCATATTCTAGCTCAATAACTGGA - -a -s simMouse_chr6.simMouse.chr6 352898 27 + 636262 TCTAAGAGAATCAAAGTCCAGGGAGGC -s Anc0.Anc0refChr0 11585 26 - 26507 ACTACGGGAACCAAAG-TTAAGGAAGC -s Anc1.Anc1refChr6 182312 26 - 197743 ACTACGGGAACCAAAG-TTAAGGAAGC -s Anc2.Anc2refChr17 20149 26 - 28526 ATTACAGAAACCAAAG-TTAAGGAAGC -s mr.mrrefChr5 200085 26 + 294540 TCTAAGAGAATCAAAG-CCAGGGAGGC -s simCow_chr6.simCow.chr6 278637 26 - 602619 ATAACAGAAACCAAAC-TTAAGGAAGC -s simDog_chr6.simDog.chr6 278003 26 - 593897 ATTCCAGAAACCAAAG-TTGAGGAAGC -s simHuman_chr6.simHuman.chr6 265972 26 - 601863 ACTACGGGAACCAAAG-TTAAGGAAGC -s simRat_chr6.simRat.chr6 344261 26 + 647215 TCTATGGGAATCAAAA-CCAGAAAGGC - -a -s simMouse_chr6.simMouse.chr6 352925 22 + 636262 AGTAGTGTAAAACAGATAGCGG -s Anc0.Anc0refChr0 11615 19 - 26507 GGTTATGAAATAGAGA-ACA-- -s Anc1.Anc1refChr6 182342 20 - 197743 GGTTATGAAATAGAGATACA-- -s Anc2.Anc2refChr17 20179 19 - 28526 GGTTATTATATAGAGA-ACA-- -s mr.mrrefChr5 200111 20 + 294540 AGTAGTGTAAAACAGATAGC-- -s simCow_chr6.simCow.chr6 278667 17 - 602619 GGTTACAATATAGAT---TA-- -s simDog_chr6.simDog.chr6 278033 19 - 593897 GGTTATTATATAGAGA-ACA-- -s simHuman_chr6.simHuman.chr6 266002 20 - 601863 GGTTAAGAAATAAAGATAAA-- -s simRat_chr6.simRat.chr6 344287 20 + 647215 AGGAGTGTAAAACAGATAGT-- - -a -s simMouse_chr6.simMouse.chr6 352947 94 + 636262 ACCGCTGACAATAGTGGGAGTCAACTAGAGTTCCTCAGTGGCAAGAATATTTGAAACAGGAGCATGGGTACGTCAGGTTTACTCCTTTTGACAT -s Anc0.Anc0refChr0 11822 16 - 26507 ------------------------------------------------------------------------------TTACTATTTCTGACAT -s Anc1.Anc1refChr6 182550 16 - 197743 ------------------------------------------------------------------------------TTACTATTTCTGACAT -s Anc2.Anc2refChr17 20482 16 - 28526 ------------------------------------------------------------------------------TTACTATCTCTGACAT -s mr.mrrefChr5 200447 94 + 294540 ACCGCTGACAATAGTGGGAGTCAACTAGAGTTCCTCAGTGGCAAGAATATTTGAAACAGGAGCATGGGTACGTCAGGTTTACTCCTTTTGACAT -s simCow_chr6.simCow.chr6 278960 16 - 602619 ------------------------------------------------------------------------------CTACTCTCCCTGGCAT -s simDog_chr6.simDog.chr6 278478 16 - 593897 ------------------------------------------------------------------------------TTACTATCTCTGACAT -s simHuman_chr6.simHuman.chr6 266345 16 - 601863 ------------------------------------------------------------------------------TTATTATTTCTGACTT -s simRat_chr6.simRat.chr6 344708 94 + 647215 GCAGGTAACAATGACAGGAGTCAACTAGAGTTCCTCTCTGGCAAGAATGTATGAAACATGAGGATGTGTACATTAGGTTTATTCCTTTTGACAT - -a -s simMouse_chr6.simMouse.chr6 353041 4 + 636262 ATTA -s Anc0.Anc0refChr0 11842 4 - 26507 ATTA -s Anc1.Anc1refChr6 182570 4 - 197743 ATTA -s Anc2.Anc2refChr17 20502 4 - 28526 ATTA -s mr.mrrefChr5 200541 4 + 294540 ATTA -s simCow_chr6.simCow.chr6 278980 4 - 602619 ATTA -s simHuman_chr6.simHuman.chr6 266427 4 - 601863 ATTA -s simRat_chr6.simRat.chr6 344802 4 + 647215 ATTA - -a -s simMouse_chr6.simMouse.chr6 353045 72 + 636262 TTGCTAGCACTGACAGGTCATTGATCACACACCCTGAAGTAAACAACTTCATGTATACATCACATGCTGCTT -s Anc0.Anc0refChr0 11846 68 - 26507 T--CTGGCATTGACAGTTCATTCAC--AACACTCTGCAGTAAACAACTTCATGTATACATCACATGCTAATT -s Anc1.Anc1refChr6 182574 68 - 197743 T--CTGGCATTGACAGTTCATTCAC--AACACTCTGCAGTAAACAACTTCATGTATACATCACATGCTAATT -s Anc2.Anc2refChr17 20506 68 - 28526 T--TTGGCATTGATAGTTCATTCAC--AACACTCTGCAGTAAACAACTTCATGTATACATCACATGCTAATT -s mr.mrrefChr5 200545 70 + 294540 TTGCTAGCACTGACAGGTCATTGAT--CACACCCTGAAGTAAACAACTTCATGTATACATCACATGCTGCTT -s simCow_chr6.simCow.chr6 278986 68 - 602619 T--TTGGCATTGATAGTTCATTTGC--AACACTCTGCAGTAAACAACTTCATGTATACATCACATGCTAATT -s simDog_chr6.simDog.chr6 278496 49 - 593897 --------------------TTCAT--GACACTCT-CAGGACACAACTTCATGTATACATCACACGCTAATT -s simHuman_chr6.simHuman.chr6 266431 68 - 601863 T--CTGACAGTGACAGTTTATTCAC--ATCACTTTGCAGTGAATGTATTCATGTCTACATCACTTGCTAAAC -s simRat_chr6.simRat.chr6 344806 70 + 647215 TTGCTAGCAATGACAGGTCATTGAT--CACACCATGAAGTAAACAACTTCATGTATACATCACACGCTGGTT - -a -s simMouse_chr6.simMouse.chr6 353117 9 + 636262 CACGTGTAC -s Anc0.Anc0refChr0 11917 9 - 26507 TAAGTGTAA -s Anc1.Anc1refChr6 182645 9 - 197743 TAAGTGTAA -s Anc2.Anc2refChr17 20577 9 - 28526 TAAGCGTAA -s mr.mrrefChr5 200615 9 + 294540 CACGTGTAC -s simCow_chr6.simCow.chr6 279057 9 - 602619 TAAGCACAA -s simDog_chr6.simDog.chr6 278548 9 - 593897 TAAGCGTAA -s simHuman_chr6.simHuman.chr6 266502 9 - 601863 TATGTGGGA -s simRat_chr6.simRat.chr6 344876 9 + 647215 CACCTTTAC - -a -s simMouse_chr6.simMouse.chr6 353126 5 + 636262 TGCTG -s Anc0.Anc0refChr0 11926 5 - 26507 CACTT -s Anc1.Anc1refChr6 182654 5 - 197743 CACTT -s Anc2.Anc2refChr17 20586 5 - 28526 CACTT -s mr.mrrefChr5 200624 5 + 294540 TGCTG -s simCow_chr6.simCow.chr6 279071 5 - 602619 CACTG -s simDog_chr6.simDog.chr6 278557 5 - 593897 CACTT -s simHuman_chr6.simHuman.chr6 266511 5 - 601863 CACTA -s simRat_chr6.simRat.chr6 344885 5 + 647215 TGCTG - -a -s simMouse_chr6.simMouse.chr6 353131 46 + 636262 CGTCCTCTCAGTGAGACTCATCTTATGGCCATTGGGTATTTGCCCA -s Anc0.Anc0refChr0 11936 45 - 26507 CTTCTCCTCAGTCAGTCTCATCCCATGGCCCTAAGG-ATTTGCCCA -s Anc1.Anc1refChr6 182664 46 - 197743 CTTCTCCTCAGTCAGTCTCATCCCATGGCCCTAAGGTATTTGCCCA -s Anc2.Anc2refChr17 20596 45 - 28526 CTTCTCCTCAGTCAGTCTCATCCCATGGGCCTAAGG-GTCTGCCCA -s mr.mrrefChr5 200629 46 + 294540 CGTCCTCTCAGTGAGACTCATCTCATGGCCATTGGGTATTTGCCCA -s simCow_chr6.simCow.chr6 279081 45 - 602619 GTTTTCATCAGTGGGTCTCATCCCATGGGCCTAAGG-GTGCACCCA -s simDog_chr6.simDog.chr6 278567 24 - 593897 CTTCTCCTCAGTCAGT----------------------TCTGCACA -s simHuman_chr6.simHuman.chr6 266521 46 - 601863 CTCCTCCTCAGTAAGGCTCATCCCATGTCCCTAAAGTATTTGCCCA -s simRat_chr6.simRat.chr6 344890 46 + 647215 CATCCTCTCAGGGAGATTCTCCTCATGGCCATTGGGTATCTGCCCA - -a -s simMouse_chr6.simMouse.chr6 353177 31 + 636262 TAAGCTGGTATATTCCCAAGTATGTAGGCCA -s Anc0.Anc0refChr0 11982 29 - 26507 TAGGTTGTCATTTTCCCAAG-ATGTA-GCAA -s Anc1.Anc1refChr6 182711 29 - 197743 TAGGTTGTCATTTTCCCAAG-ATGTA-GCAA -s Anc2.Anc2refChr17 20642 29 - 28526 TAGGTTGTCATTTTCAAAGA-ATGTA-GCAA -s mr.mrrefChr5 200675 30 + 294540 TAAGCTGGCATATTCCCAAGTATGTA-GCCA -s simCow_chr6.simCow.chr6 279127 29 - 602619 TAGGTTGTCATTTTCTAAGA-ATGTA-GCAA -s simDog_chr6.simDog.chr6 278592 29 - 593897 CAGGTTATTGTCTTCAAAGA-ATGCA-GCAA -s simHuman_chr6.simHuman.chr6 266568 29 - 601863 TAGGTTGCCATTTTCCCAAG-AAGTA-GCAA -s simRat_chr6.simRat.chr6 344936 30 + 647215 TAAGCTGGCATATTCCCAGGTATGTA-GCCA - -a -s simMouse_chr6.simMouse.chr6 353208 50 + 636262 CTGGTACAGCCCTTGAGAAGTGACCAGAATCAAACTGGTTTAGACATTTT -s Anc0.Anc0refChr0 12013 48 - 26507 CAGGAATAGCCCTTGAAAAGTGACC--AATCAAACTGACTCACACATATC -s Anc1.Anc1refChr6 182742 48 - 197743 CAGGAATAGCCCTTGAAAAGTGACC--AATCAAACTGACTCACACATATC -s Anc2.Anc2refChr17 20673 48 - 28526 CAGGAATAGCCCTTGAAAAGTGACC--AATCCAACTGACTCACACATATC -s mr.mrrefChr5 200707 48 + 294540 CTGGTATAGCCCTTGAGAAGTGACC--AATCAAACTGGTTTAGACATTTT -s simCow_chr6.simCow.chr6 279158 48 - 602619 CAGAAATAGCCCTTGAATAGGGACC--AATTGCACTAACTCACATATATC -s simDog_chr6.simDog.chr6 278623 43 - 593897 CAGGAATAGCCTTTGAAAAGTAACC--AATCCAACTGACTTACAC----- -s simHuman_chr6.simHuman.chr6 266599 48 - 601863 CAGGAGTAGCCCTCGAAAAGTGACC--AATCAAACTGACTCACACATATC -s simRat_chr6.simRat.chr6 344968 48 + 647215 CTGGTATAGCCCTTGAGAAGTGACC--AATCAAGCTGGTCTATACATTTT - -a -s simMouse_chr6.simMouse.chr6 353258 96 + 636262 GATGGATCTAACGGGTTCTTAAGATTGCGACATAATAGGGCTCTTATTTAGttctaattagatgaacttcatgtaattcttctagttcaggtacaa -s Anc0.Anc0refChr0 12062 17 - 26507 GATGACTCCAGTGGACA------------------------------------------------------------------------------- -s Anc1.Anc1refChr6 182791 63 - 197743 GATGACTCCAGTGGACA---------------------------------ctcctaggtcagtagattccatacaaagcttctagtccagatatga -s Anc2.Anc2refChr17 20722 17 - 28526 GCTGACTCCAGTGGACA------------------------------------------------------------------------------- -s mr.mrrefChr5 200756 95 + 294540 GATGAATCTAACGGGTTCTTAAGATTGCGACATAATAGGGC-CTTATTTAGttctaattagatgaacttcatgtaattcttctagttcaggtacaa -s simCow_chr6.simCow.chr6 279207 17 - 602619 GCTGACTCCAGTGGACA------------------------------------------------------------------------------- -s simHuman_chr6.simHuman.chr6 266648 60 - 601863 GATGAGTCCAGTGt------------------------------------ctcctaggtcagtagattccatacaaagcttctagtccagatatga -s simRat_chr6.simRat.chr6 345017 95 + 647215 GATGAATCTTTCAGGTTTTTAAGATTGCAACATAATAGGGC-CTTATTTAGttccaattggatgatcttcatataattcttctagtttaggtacta - -a -s simMouse_chr6.simMouse.chr6 353354 17 + 636262 taactttagagtgtgta -s Anc1.Anc1refChr6 182869 17 - 197743 taactttagaacatgta -s mr.mrrefChr5 200866 17 + 294540 taactttagagtgtgta -s simHuman_chr6.simHuman.chr6 266743 17 - 601863 taactttagaacatgta -s simRat_chr6.simRat.chr6 345127 17 + 647215 tgctgctggagattggt - -a -s simMouse_chr6.simMouse.chr6 353371 18 + 636262 tgcaaaatatacctcaag -s Anc1.Anc1refChr6 182886 18 - 197743 cacaaaatagccctcaag -s mr.mrrefChr5 200883 18 + 294540 tgcaaaatatacctcaag -s simHuman_chr6.simHuman.chr6 266761 18 - 601863 cacaaaatagccctcaag -s simRat_chr6.simRat.chr6 345144 17 + 647215 tggttaata-acttcaga - -a -s simMouse_chr6.simMouse.chr6 353389 35 + 636262 gggtcccaactttgagattctcctgtttcaagtac -s Anc1.Anc1refChr6 182904 35 - 197743 gggtcccagcttcaagactatcgggttgcaagcgc -s mr.mrrefChr5 200901 35 + 294540 gggtcccaactttaagactctcctgtttcaagtgc -s simHuman_chr6.simHuman.chr6 266779 35 - 601863 gggtcccagcttcaagactatcgggttgcaagcgc -s simRat_chr6.simRat.chr6 345163 35 + 647215 GGGTCCTAACTCTAAGACTCTACTGTCTCAAGTGC - -a -s simMouse_chr6.simMouse.chr6 353424 26 + 636262 taggTATCAGGTGACACTGAATGGGG -s Anc0.Anc0refChr0 12079 5 - 26507 ----------------TTTAA----- -s Anc1.Anc1refChr6 182939 21 - 197743 gagttagcaaatTACATTTAA----- -s Anc2.Anc2refChr17 20739 5 - 28526 ----------------TCTAA----- -s mr.mrrefChr5 200936 26 + 294540 tagtTATCAAGTGACATTGAATGGGG -s simCow_chr6.simCow.chr6 279224 5 - 602619 ----------------TCTAA----- -s simHuman_chr6.simHuman.chr6 266818 21 - 601863 gagttagcaaatTACATTTAA----- -s simRat_chr6.simRat.chr6 345198 26 + 647215 TAGTTATCAAGTGACATTATTTGGGG - -a -s simMouse_chr6.simMouse.chr6 353450 25 + 636262 TCTGGGACAAGTCTCAGCTGAATGC -s Anc0.Anc0refChr0 12084 15 - 26507 ---CGGACATGGC-------AAAGC -s Anc1.Anc1refChr6 182960 15 - 197743 ---CGGACATGGC-------AAAGC -s Anc2.Anc2refChr17 20744 15 - 28526 ---CAGACATGGC-------AAATC -s mr.mrrefChr5 200962 25 + 294540 TCTGGGACAAGTCTCAGCTGAATGC -s simCow_chr6.simCow.chr6 279229 15 - 602619 ---CAGGCATGGC-------AAATC -s simDog_chr6.simDog.chr6 278666 12 - 593897 ------ACATATC-------AAATC -s simHuman_chr6.simHuman.chr6 266839 15 - 601863 ---AGGACGTGGC-------AAAGC -s simRat_chr6.simRat.chr6 345232 25 + 647215 TCTGATACAAGTCTCACCTGAGTGC - -a -s simMouse_chr6.simMouse.chr6 353475 5 + 636262 AAACA -s Anc0.Anc0refChr0 12099 5 - 26507 AGACA -s Anc1.Anc1refChr6 182975 5 - 197743 AGACA -s Anc2.Anc2refChr17 20759 5 - 28526 TGAAA -s mr.mrrefChr5 200987 5 + 294540 AAACA -s simCow_chr6.simCow.chr6 279245 5 - 602619 TGAAA -s simDog_chr6.simDog.chr6 278678 5 - 593897 TGAAA -s simHuman_chr6.simHuman.chr6 266854 5 - 601863 AGGCA -s simRat_chr6.simRat.chr6 345257 5 + 647215 AAACA - -a -s simMouse_chr6.simMouse.chr6 353480 14 + 636262 AGTCTCACCTCAGT -s Anc0.Anc0refChr0 12106 14 - 26507 AGTCTCACCTAATG -s Anc1.Anc1refChr6 182982 14 - 197743 AGTCTCACCTAATG -s Anc2.Anc2refChr17 20766 14 - 28526 AGTCTCACGTAATG -s mr.mrrefChr5 200992 14 + 294540 AGTCTCACCTCAGT -s simCow_chr6.simCow.chr6 279252 12 - 602619 --TTGCACATAATG -s simDog_chr6.simDog.chr6 278685 14 - 593897 AGTCTCATGTAATG -s simHuman_chr6.simHuman.chr6 266861 14 - 601863 GGTCACACCTAATG -s simRat_chr6.simRat.chr6 345262 14 + 647215 AGTCTCACCTTAAT - -a -s simMouse_chr6.simMouse.chr6 353494 78 + 636262 GTAAACTATTGCTGCAAACTGGACTAATAGTGCACAGTGTAACAGAAAGAGGTGGTATAAATAGTGGACTTAGTTAGC -s Anc0.Anc0refChr0 12120 76 - 26507 GCAAGCTATTGCTGCAA-CCTGATTAAGTGTACAAGGTATAC-AGTAAGAGCTGGTAGAAATAGTGTATTTGGTTAGC -s Anc1.Anc1refChr6 182996 77 - 197743 GCAAGCTATTGCTGCAAACCTGATTAAGTGTACAAGGTATAC-AGTAAGAGCTGGTAGAAATAGTGTATTTGGTTAGC -s Anc2.Anc2refChr17 20782 76 - 28526 GCAAGCTACAGCTGTAA-CCTGATTAAGTGCACCAGGTATAC-AGTAAGAGCTGGTAGGACTGGTGTATTTGGTCAGT -s mr.mrrefChr5 201006 77 + 294540 GTAAACTATTGCTGCAAACTGGACTAATAGTGCACAGTGTAC-AGAAAGAGGTGGTATAAATAGTGGATTTAGTTAGC -s simCow_chr6.simCow.chr6 279266 76 - 602619 GTAAGCTACAGCTGAGA-CCAGATTAAGCACACCAGGTGGAC-AGAGGGAAATGATAGGACTGGTGTATTTGGTCAGC -s simDog_chr6.simDog.chr6 278701 71 - 593897 GCAAGCGACAGCTGTAG-CCTGATTAAGTG-----GGTATAA-AGTAAGAGCTGGTAGGACTGTTTTATCTAGTCAGT -s simHuman_chr6.simHuman.chr6 266875 65 - 601863 GCAATCTATTGCTGCTAACCTGATTGAGGGTTCATGGTATAC-A------------AGAAATAGTGTATTTGGTTAGC -s simRat_chr6.simRat.chr6 345276 70 + 647215 GTAAATTATTGCCGCAAACTGAACTAATAATGCACAGTGTAC-AGAAAGAGGTAAGATA-------GATTTAGTTAGC - -a -s simMouse_chr6.simMouse.chr6 353572 2 + 636262 TC -s Anc0.Anc0refChr0 12196 2 - 26507 CC -s Anc1.Anc1refChr6 183073 2 - 197743 CC -s Anc2.Anc2refChr17 20859 2 - 28526 CC -s mr.mrrefChr5 201083 2 + 294540 TC -s simCow_chr6.simCow.chr6 279343 2 - 602619 AC -s simDog_chr6.simDog.chr6 278773 2 - 593897 CC -s simHuman_chr6.simHuman.chr6 266940 2 - 601863 CC -s simRat_chr6.simRat.chr6 345346 2 + 647215 TC - -a -s simMouse_chr6.simMouse.chr6 353574 5 + 636262 TCATA -s Anc0.Anc0refChr0 12207 5 - 26507 TCACA -s Anc1.Anc1refChr6 183084 5 - 197743 TCACA -s Anc2.Anc2refChr17 20870 5 - 28526 TTACA -s mr.mrrefChr5 201085 5 + 294540 TCATA -s simCow_chr6.simCow.chr6 279354 5 - 602619 TTACA -s simDog_chr6.simDog.chr6 278784 5 - 593897 TTTCG -s simHuman_chr6.simHuman.chr6 266951 5 - 601863 TCACA -s simRat_chr6.simRat.chr6 345348 5 + 647215 TCATA - -a -s simMouse_chr6.simMouse.chr6 353579 88 + 636262 GTAGGCAGCATAATCCTCACCAATGTTGTTAAAAGGGCACTGACAGCGCAATTCCTATGCATAATCATTTGAACAAACCATTGTCAGC -s Anc0.Anc0refChr0 12216 49 - 26507 GTAGGCAGCAGAATCATCACTAATGTC------------------------------TGGTTGA---------CAAGAGATTGTCAGC -s Anc1.Anc1refChr6 183093 58 - 197743 GTAGGCAGCAGAATCATCACTAATGTC------------------------------TGGTTGAACAAGTGAACAAGAGATTGTCAGC -s Anc2.Anc2refChr17 20879 49 - 28526 GCAGGCACCAGAATCATCACTAATGTC------------------------------TAGTTGA---------CAAGGGGTTGTCAGC -s mr.mrrefChr5 201090 88 + 294540 GTAGGCAGCATAATCCTCACCAATGTTGTTAAAAGGGCACTGACAGCGCAATTCCTATGCATAATCATTTGAACAAGACATTGTCAGC -s simCow_chr6.simCow.chr6 279363 49 - 602619 GCAGGCACCAGAATAAGCCTTAATATC------------------------------TTGTGGA---------CAAGGGGTAGCCTGC -s simDog_chr6.simDog.chr6 278793 49 - 593897 GCAGGCACCAGAACCATCACTAATGTC------------------------------AAGTTGC---------CAAGGGGTTTTCAAC -s simHuman_chr6.simHuman.chr6 266960 58 - 601863 GTGGGCAGCAAAGTCATCACTAATGTC------------------------------TGGTTGAACAAGTGAACAAGAGATTGTCAGC -s simRat_chr6.simRat.chr6 345353 87 + 647215 GTAGGCAGCATAATCCTCTCCAATG-TGTTAAAAAGGCATTAACATCCCAATTCCTAGACATAATCATTTGAACAAGACACAGCAGAC - -a -s simMouse_chr6.simMouse.chr6 353667 15 + 636262 CTGATTCCCATACAG -s Anc0.Anc0refChr0 12265 13 - 26507 CTGGTTCC--TACAG -s Anc1.Anc1refChr6 183151 13 - 197743 CTGGTTCC--TACAG -s Anc2.Anc2refChr17 20928 13 - 28526 CTGGTTCC--TAGAT -s mr.mrrefChr5 201178 13 + 294540 CTGATTCC--TACAG -s simCow_chr6.simCow.chr6 279412 13 - 602619 CTGGTTCC--TAAAA -s simDog_chr6.simDog.chr6 278842 13 - 593897 CTCGTTCC--TAGAT -s simHuman_chr6.simHuman.chr6 267018 13 - 601863 CTGGTTCC--TGCAG -s simRat_chr6.simRat.chr6 345458 13 + 647215 CTGATTCA--TACAG - -a -s simMouse_chr6.simMouse.chr6 353682 1 + 636262 C -s Anc0.Anc0refChr0 12280 1 - 26507 C -s Anc1.Anc1refChr6 183166 1 - 197743 C -s Anc2.Anc2refChr17 20943 1 - 28526 C -s mr.mrrefChr5 201191 1 + 294540 C -s simCow_chr6.simCow.chr6 279427 1 - 602619 C -s simDog_chr6.simDog.chr6 278857 1 - 593897 C -s simHuman_chr6.simHuman.chr6 267033 1 - 601863 C -s simRat_chr6.simRat.chr6 345471 1 + 647215 C - -a -s simMouse_chr6.simMouse.chr6 353683 9 + 636262 TCCTTCATT -s Anc0.Anc0refChr0 12302 9 - 26507 TTCTTCGTT -s Anc1.Anc1refChr6 183188 9 - 197743 TTCTTCGTT -s Anc2.Anc2refChr17 20965 9 - 28526 TTCTTTGCT -s mr.mrrefChr5 201213 9 + 294540 TCCTTCATT -s simCow_chr6.simCow.chr6 279449 8 - 602619 TTCTT-GCT -s simDog_chr6.simDog.chr6 278876 9 - 593897 TTCCTTGCT -s simHuman_chr6.simHuman.chr6 267055 9 - 601863 TTCTTCGTT -s simRat_chr6.simRat.chr6 345493 9 + 647215 TCCTTCATT - -a -s simMouse_chr6.simMouse.chr6 353692 64 + 636262 CTCGAAAGGGGTATATGCCCCTTAAACCAGTATATGCCTTAAACCACTAAGCTGGCCAAGGGGT -s Anc0.Anc0refChr0 12312 47 - 26507 CTTGAATAAGGGATACA--C---------------ACCTCAAAATACTAAACAGACCTAGGGGT -s Anc1.Anc1refChr6 183198 47 - 197743 CTTGAATAAGGGATACA--C---------------ACCTCAAAATACTAAACAGACCTAGGGGT -s Anc2.Anc2refChr17 20985 47 - 28526 CCTGAATAAGGGATACA--C---------------ACCTCAAAATACTAAACAGACCTAGTGGT -s mr.mrrefChr5 201222 62 + 294540 CTCGAAAGGGGTATATG--CCTTAAACCAGTATATGCCTTAAACCACTAAACTGGCCAAGGGGT -s simCow_chr6.simCow.chr6 279468 47 - 602619 CCCGAATAAGAGATACA--C---------------ACCTCAAAATACCAAATAGACTTAGTGGT -s simDog_chr6.simDog.chr6 278896 47 - 593897 CCTGGATAAGGGATGCA--C---------------ATCTCAAGATACTAAACAGACCTAGTGGT -s simHuman_chr6.simHuman.chr6 267065 47 - 601863 CTTGAAGAAGGGATACA--C---------------ACCTCAAAAAACTAAACAGTCCGTGGGGT -s simRat_chr6.simRat.chr6 345502 56 + 647215 CTC------GGTATATG--CCTTAAACCAGTATATGCCTTAAACCATTAAACTGGCCAAGGAAT - -a -s simMouse_chr6.simMouse.chr6 353756 27 + 636262 TGCTTAACAACTAAGACATGTGGTGTG -s Anc0.Anc0refChr0 12360 27 - 26507 TACTAAACAGCTAAGGGGTGTAGTGTG -s Anc1.Anc1refChr6 183246 27 - 197743 TACTAAACAGCTAAGGGGTGTAGTGTG -s Anc2.Anc2refChr17 21033 27 - 28526 TACTAAACAGCCAAGGGGTGTAGAGTG -s mr.mrrefChr5 201284 27 + 294540 TGCTTAACAGCTAAGACATGTGGTGTG -s simCow_chr6.simCow.chr6 279516 27 - 602619 AACTAAGGAGTCAAGAGGTGCAGAGCA -s simDog_chr6.simDog.chr6 278944 27 - 593897 TACTAAACAACCAAGGGGAGTAGAGTG -s simHuman_chr6.simHuman.chr6 267113 27 - 601863 TACTAAACAGCTAAGGGGTGTAGTGTG -s simRat_chr6.simRat.chr6 345558 27 + 647215 TGTTTAACAGCTAAGACATGTGGTGTG - -a -s simMouse_chr6.simMouse.chr6 353783 9 + 636262 TCATATCAC -s Anc0.Anc0refChr0 12387 5 - 26507 TCATC---- -s Anc1.Anc1refChr6 183273 5 - 197743 TCATC---- -s Anc2.Anc2refChr17 21060 5 - 28526 CCATC---- -s mr.mrrefChr5 201311 9 + 294540 TCATATCAC -s simCow_chr6.simCow.chr6 279543 5 - 602619 CTATC---- -s simDog_chr6.simDog.chr6 278972 5 - 593897 CCATC---- -s simHuman_chr6.simHuman.chr6 267140 5 - 601863 TCATC---- -s simRat_chr6.simRat.chr6 345585 9 + 647215 TCACATCAC - -a -s simMouse_chr6.simMouse.chr6 353792 62 + 636262 ATGCCAGCTTAGAGTACGTTAGAATCTTGCAATATAGACTCTCGTTACAGACATGACAGATG -s Anc0.Anc0refChr0 12392 16 - 26507 ----------------------------------------------ACAGACATGACAAGAT -s Anc1.Anc1refChr6 183278 16 - 197743 ----------------------------------------------ACAGACATGACAAGAT -s Anc2.Anc2refChr17 21065 16 - 28526 ----------------------------------------------ACAGACATGACAAGAT -s mr.mrrefChr5 201320 62 + 294540 ATGCCAGCTTAGAGTACGTTAGAATCTTGCAATATAGACTCTCGTTACAGACATGACAGATT -s simCow_chr6.simCow.chr6 279548 15 - 602619 ----------------------------------------------ACAGACATGGGGCGA- -s simDog_chr6.simDog.chr6 278977 16 - 593897 ----------------------------------------------ACAGACATGACAAGAT -s simHuman_chr6.simHuman.chr6 267145 16 - 601863 ----------------------------------------------ACAAGTGTGACAAGCT -s simRat_chr6.simRat.chr6 345596 62 + 647215 ATGACTGCTTAGAGTTCATAAGGATCTTACAATATAGACTCTCTTCACAGACATGACAGAAT - -a -s simMouse_chr6.simMouse.chr6 353854 19 + 636262 GATATGGAATCAAGTTACT -s Anc0.Anc0refChr0 12410 19 - 26507 GAGATGGTATCAAGTTACT -s Anc1.Anc1refChr6 183296 19 - 197743 GAGATGGTATCAAGTTACT -s Anc2.Anc2refChr17 21083 19 - 28526 GTGATGGTATCAAGTTACT -s mr.mrrefChr5 201382 19 + 294540 GATATGGAATCAAGTTACT -s simCow_chr6.simCow.chr6 279565 19 - 602619 GTGATGGTATCAAGTTACT -s simDog_chr6.simDog.chr6 278995 19 - 593897 GTAATTTTATCATGCTACT -s simHuman_chr6.simHuman.chr6 267163 19 - 601863 GAGATGGCATCAAGTTACT -s simRat_chr6.simRat.chr6 345658 19 + 647215 GATATGGAATCAAGTTACT - -a -s simMouse_chr6.simMouse.chr6 353873 1 + 636262 A -s Anc0.Anc0refChr0 12429 1 - 26507 A -s Anc1.Anc1refChr6 183315 1 - 197743 A -s Anc2.Anc2refChr17 21102 1 - 28526 A -s mr.mrrefChr5 201401 1 + 294540 A -s simCow_chr6.simCow.chr6 279593 1 - 602619 A -s simDog_chr6.simDog.chr6 279014 1 - 593897 A -s simHuman_chr6.simHuman.chr6 267182 1 - 601863 A -s simRat_chr6.simRat.chr6 345677 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 353874 3 + 636262 CTA -s Anc0.Anc0refChr0 12430 3 - 26507 GGA -s Anc1.Anc1refChr6 183316 3 - 197743 GGA -s Anc2.Anc2refChr17 21105 3 - 28526 GGA -s mr.mrrefChr5 201402 3 + 294540 CTA -s simCow_chr6.simCow.chr6 279596 3 - 602619 GTA -s simDog_chr6.simDog.chr6 279017 3 - 593897 GGG -s simHuman_chr6.simHuman.chr6 267183 3 - 601863 GGA -s simRat_chr6.simRat.chr6 345678 3 + 647215 CAA - -a -s simMouse_chr6.simMouse.chr6 353877 135 + 636262 TGACAATTTAGACTGTATTTGCTTTGGTGCAAGGTGTGTCTTCCACCCTCAGGCTGTCTGATCGGACCCGTTGAGACCCCCACAGAAGCGTATATCACAGTCTATAGCTCTGAGAGGAGGCCATGGGTGGGGGTA -s Anc0.Anc0refChr0 12433 129 - 26507 TG-----TAAGACTCCATTTGCTT-GCTGCAAGGTGTGTGTTCCAGCCTCAGGCTGTTTAATCCGGCCAGTTGAGACCCCTACAGAATCATATACCACAGATAATGGCACTGAGGGTGGGCCATGGGTGTGGGCA -s Anc1.Anc1refChr6 183319 129 - 197743 TG-----TAAGACTCCATTTGCTT-GCTGCAAGGTGTGTGTTCCAGCCTCAGGCTGTTTAATCCGGCCAGTTGAGACCCCTACAGAATCATATACCACAGATAATGGCACTGAGGGTGGGCCATGGGTGTGGGCA -s Anc2.Anc2refChr17 21108 129 - 28526 TG-----GACGACTCCATTTGCTT-GCTGCAAGGTGTGTGTTCCAGCCTCAGGCTGTTTAACCCGGCCAGTTGAGATCCCTGCAGAATCATATACCACAGATAATGGCAGTGAGGGTGGGCCATGGGTGTGGGCA -s mr.mrrefChr5 201405 135 + 294540 TGACAATTTAGACTGTATTTGCTTTGCTGCAAGGTGTGTCTTCCACCCTCAGGCTGTCTGATCGGACCAGTTGAGACCCCCACAGAAGCGTATATCACAGTCTATAGCACTGAGAGGAGGCCATGGGTGGGGGTA -s simCow_chr6.simCow.chr6 279614 113 - 602619 TG-----CAGGACTCCATCT-----GCTGCAAAGTATGTGTTACAGCCTCAGGCTGTTTAACCGGCCCAGTTGACATCCCTGCAGTGTTCCATACCACAGGTAATGGCATTGAGGGT------------TGGGCA -s simDog_chr6.simDog.chr6 279020 129 - 593897 TG-----GGCGACTCCATTTGCTT-ACTACAAGGTGTGTGTTCCAGCCTCAGTCTCCTTATCCCAGCCAGATGAGATCCCTGCAGAACCATATATTACAGATAATGGCAGTGAAGGTGGGCCATGGGTGTTGCCA -s simHuman_chr6.simHuman.chr6 267186 129 - 601863 TG-----TAAGACTCCATTTGCTG-GCTGCTGGGTGTGTGTACCGGCCTCAGGCTGTTTAATCAGGCCAGTCAAGACCACTACAGAATCTTATACCAGAGATAATGGCACTGCGCGTGGGACATAGGTGTGGGCA -s simRat_chr6.simRat.chr6 345681 135 + 647215 TGAGAATTTAGACTGTATCTGCTATGCTGCAAGGTGTGTCTTCCACCCTCAGGCTGTCTGATTGGACCAGTTGAGACCCCCACAGAAGCCTATATCACATTCTACAGCACTGAGAGCAGGCCATGGGTAGGGGTA - -a -s simMouse_chr6.simMouse.chr6 354012 14 + 636262 CAGACATGTTGCTG -s Anc0.Anc0refChr0 12568 14 - 26507 TAGACGTGATGCCG -s Anc1.Anc1refChr6 183454 14 - 197743 TAGACGTGATGCCG -s Anc2.Anc2refChr17 21243 14 - 28526 TAGATGAGATGTCG -s mr.mrrefChr5 201545 14 + 294540 CAGACATGTTGCTG -s simCow_chr6.simCow.chr6 279733 12 - 602619 TAAGTGACA--TCG -s simDog_chr6.simDog.chr6 279155 14 - 593897 TAGATGAGATGTCA -s simHuman_chr6.simHuman.chr6 267321 14 - 601863 TAGACCTGATGCAG -s simRat_chr6.simRat.chr6 345821 14 + 647215 CAGACATGTTGCTG - -a -s simMouse_chr6.simMouse.chr6 354026 8 + 636262 ACACAGTC -s Anc0.Anc0refChr0 12584 8 - 26507 GAACAGTC -s Anc1.Anc1refChr6 183470 8 - 197743 GAACAGTC -s Anc2.Anc2refChr17 21259 8 - 28526 GAACAGTC -s mr.mrrefChr5 201561 8 + 294540 ACACAGTC -s simCow_chr6.simCow.chr6 279747 8 - 602619 GAACAGTC -s simDog_chr6.simDog.chr6 279171 8 - 593897 AGACAGTC -s simHuman_chr6.simHuman.chr6 267337 8 - 601863 GAACAGTC -s simRat_chr6.simRat.chr6 345837 8 + 647215 ACACAGCC - -a -s simMouse_chr6.simMouse.chr6 354034 20 + 636262 AAAGGGGGTCAGACTACAGA -s Anc0.Anc0refChr0 12592 13 - 26507 CATTGGAG-------GCAGA -s Anc1.Anc1refChr6 183478 13 - 197743 CATTGGAG-------GCAGA -s Anc2.Anc2refChr17 21267 13 - 28526 CAATGGAG-------GCAGA -s mr.mrrefChr5 201569 20 + 294540 AATGGGAGTCAGACTACAGA -s simCow_chr6.simCow.chr6 279755 13 - 602619 CAGTGGAG-------GCAGA -s simDog_chr6.simDog.chr6 279212 13 - 593897 CAATGGAG-------GCAGA -s simHuman_chr6.simHuman.chr6 267345 13 - 601863 CATTGGAG-------GCAGA -s simRat_chr6.simRat.chr6 345845 20 + 647215 AATGGGAGTCAAACTTCAGA - -a -s simMouse_chr6.simMouse.chr6 354054 86 + 636262 CTCTATAATCCTGTACTAGGACTCAACACAAGAGCAAGACGCAATTTTTCTTGGACCCATTTCCTTTTCTTATTAAGAATTAGACC -s Anc0.Anc0refChr0 12605 86 - 26507 CTCCATAACTCTGTACTTGGACTTAGCACGATAGCAAGACAGAACATTTCATGAACCCACTTCCTGGTCCTTATGAGAATTAGAAC -s Anc1.Anc1refChr6 183491 86 - 197743 CTCCATAACTCTGTACTTGGACTTAGCACGATAGCAAGACAGAACATTTCATGAACCCACTTCCTGGTCCTTATGAGAATTAGAAC -s Anc2.Anc2refChr17 21280 86 - 28526 CTCCATAACTCTGTACTTGGACTTAGCATGATACCAAGACAGAACATTTCATGAACCCACCTCTTGGTCCTTATGAGAATTAGAAC -s mr.mrrefChr5 201589 86 + 294540 CTCCATAACCCTGTACTAGGACTCAACACAAGAGCAAGACGCAATTTTTCTTGGACCCATTTCCTTTTCCTATTAAGAATTAGAAC -s simCow_chr6.simCow.chr6 279769 82 - 602619 CTCCATAACCTTGCACTTGGACTCAGCATGATACCACGACAGAACAT----TGAAGCCACCTCTGGGTCTTTATCAAAATCAGAAT -s simDog_chr6.simDog.chr6 279225 86 - 593897 CTCCATAACTCTATACTTGGACTTAGCATAATACCAAGACAGAACATTTCATGAACTCACCCTTTGGTGCTTGTGGGACTTAAAAC -s simHuman_chr6.simHuman.chr6 267358 86 - 601863 CTTCATCACTCGGTAATTGGACTTCGTACGATAGCAAGACTGAACATTTTATGAACCATCTTCCTGGGCCTCATGAGAATTAGAAC -s simRat_chr6.simRat.chr6 345865 86 + 647215 CTCCATAACCCTGTGCTAGGACTCAACACAAGAGCAAGACACAATTTTTCTTGGACCCATTTCTTTTTCCTATTAAGAATTAGAAC - -a -s simMouse_chr6.simMouse.chr6 354140 6 + 636262 AGGAAG -s Anc0.Anc0refChr0 12691 6 - 26507 AGGTAA -s Anc1.Anc1refChr6 183577 6 - 197743 AGGTAA -s Anc2.Anc2refChr17 21366 6 - 28526 AGGTAA -s mr.mrrefChr5 201675 6 + 294540 AGGAAG -s simCow_chr6.simCow.chr6 279852 6 - 602619 AGATAA -s simDog_chr6.simDog.chr6 279311 6 - 593897 AGGTAA -s simHuman_chr6.simHuman.chr6 267444 6 - 601863 AGGTAT -s simRat_chr6.simRat.chr6 345951 6 + 647215 AGCAAG - -a -s simMouse_chr6.simMouse.chr6 354146 14 + 636262 GGGAGGGGGGTTGC -s Anc0.Anc0refChr0 12697 14 - 26507 GAAAGGGAGCTTCC -s Anc1.Anc1refChr6 183583 14 - 197743 GAAAGGGAGCTTCC -s Anc2.Anc2refChr17 21372 14 - 28526 GAAAGGGAGCTTCC -s mr.mrrefChr5 201681 14 + 294540 GGAAGGGGGGTTGC -s simCow_chr6.simCow.chr6 279863 14 - 602619 GAAAAGGGGCTGCC -s simDog_chr6.simDog.chr6 279317 14 - 593897 GTAAGGGACATTCC -s simHuman_chr6.simHuman.chr6 267450 14 - 601863 GAAAGCGAGCCTCT -s simRat_chr6.simRat.chr6 345957 14 + 647215 GGAAAGGGCGTTGC - -a -s simMouse_chr6.simMouse.chr6 354160 94 + 636262 CAGTAGGGGAGAAAATATAGTGAAAAGAGTATTTACAAGTGATCTGTAGACATAATCACACAGGAGGATGTAGCCTCTAGAGCAAGGCTTGCAA -s Anc0.Anc0refChr0 12715 94 - 26507 CAGTACAAGAGAATACATAGCGCAAAGAGCAATCATAAGCAATCTGTAAGCAGAATCACACAGGATGGTGCTGCCTCTATAGCAAGGCATGCAT -s Anc1.Anc1refChr6 183601 94 - 197743 CAGTACAAGAGAATACATAGCGCAAAGAGCAATCATAAGCAATCTGTAAGCAGAATCACACAGGATGGTGCTGCCTCTATAGCAAGGCATGCAT -s Anc2.Anc2refChr17 21390 94 - 28526 CAGTACAAGAGAATACATAGCGCAAAGAGCAATCATGAGCAATCTGTAAGCAGAACCACACAGGATGGTGCTGCCATTATAGCCAGAAATACAT -s mr.mrrefChr5 201695 94 + 294540 CAGTAGGGGAGAAAATATAGTGAAAAGAGTAATCATAAGTGATCTGTAGACATAATCACACAGGAGGATGTAGCCTCTAGAGCAAGGCTTGCAA -s simCow_chr6.simCow.chr6 279881 74 - 602619 CTTTAAAAGAGAAAACATAGTGAAAAGAGCAATCATGAGCAGTCTGTAAGCAGGACCACATAGTATTGTGCTG--------------------T -s simDog_chr6.simDog.chr6 279335 88 - 593897 CAGTACAGGAGCATACATAGCACACAGAACAAGC------AATCTGCAAGCGGAGCCACACTGGATGGTGTTGCCATTATAGCCAGAAATACAT -s simHuman_chr6.simHuman.chr6 267468 94 - 601863 CAGTATAAGAGAAGGCATAGCGTAAAGAGCAATCATATGGAATCTGTAAGCAGAATCACACAAGATGGTGCTGCCTCTATTGCAAGGCATGCAT -s simRat_chr6.simRat.chr6 345971 94 + 647215 CAGTAGGGAAGAAAATATGGTGAAAAGAGTAATCATAAGTGATCTGTAGACATAACCTCACAGGAGGATATAGCCTCTAAAGCGAGGCTTGCAA - -a -s simMouse_chr6.simMouse.chr6 354254 50 + 636262 CGGCTTTCCGTCATTGGCGCATCACAAAGGCTATGTGGTGGCACACAGTA -s Anc0.Anc0refChr0 12809 49 - 26507 CAGATCTCCCACATTGGG-CTTCATGGAGGCTACTTGGTGTCACATGATA -s Anc1.Anc1refChr6 183695 49 - 197743 CAGATCTCCCACATTGGG-CTTCATGGAGGCTACTTGGTGTCACATGATA -s Anc2.Anc2refChr17 21484 49 - 28526 CAGATCTCCCACATTGGG-CTTCCTGGAGGCTACTTGGTGTCACATGATA -s mr.mrrefChr5 201789 50 + 294540 CAGCTTTCCGTCATTGGGGCTTCACAAAGGCTACGTGGTGGCACACAGTA -s simCow_chr6.simCow.chr6 279955 47 - 602619 CAGAACT-CCTCATTGGG-C-TCGTGGAAGCTACATGGTGACACATGAGA -s simDog_chr6.simDog.chr6 279423 49 - 593897 CAGATCTCCCACATTTGG-CTTCCTGGAGGATACTTGGTGTCACACGATG -s simHuman_chr6.simHuman.chr6 267564 49 - 601863 CAGATCTCCCCCATTGGG-CTTCATGGAGGCTACTTCATGCCACATGATA -s simRat_chr6.simRat.chr6 346065 50 + 647215 CAGCTTTCCATCATTGGGACTTCACACAGGCTACATTGTGGCACAGAGTA - -a -s simMouse_chr6.simMouse.chr6 354304 13 + 636262 TGATATCATGATG -s Anc0.Anc0refChr0 12861 13 - 26507 TGATATCAAGATG -s Anc1.Anc1refChr6 183747 13 - 197743 TGATATCAAGATG -s Anc2.Anc2refChr17 21536 13 - 28526 TGATATCAAGCTG -s mr.mrrefChr5 201839 13 + 294540 TGATATCATGATG -s simCow_chr6.simCow.chr6 280095 13 - 602619 CCATATCAAGGTG -s simDog_chr6.simDog.chr6 279475 13 - 593897 TGATACCAAGCTG -s simHuman_chr6.simHuman.chr6 267616 13 - 601863 TGATATGAAGATG -s simRat_chr6.simRat.chr6 346115 13 + 647215 TGATATCATGATT - -a -s simMouse_chr6.simMouse.chr6 354317 68 + 636262 TAATGTGTTGGGAAGGTTTGGTGGACTCACCTTGATCCACAAATTGAGGCTAAGCTGTAAGGTAGTCT -s Anc0.Anc0refChr0 12874 44 - 26507 TGATGT------------------------CTCAACCCACATATTGAGGCTAAGTTGTAAGATAGTGG -s Anc1.Anc1refChr6 183760 67 - 197743 TGATGTGATGGGATGGATTGG-AGAGCTACCTCAACCCACATATTGAGGCTAAGTTGTAAGATAGTGG -s Anc2.Anc2refChr17 21550 44 - 28526 TTATCT------------------------CTCAACCCACATATTGAGGCTAAGTTGCAAGATAGTGG -s mr.mrrefChr5 201852 68 + 294540 TAATGTGTTGGGAAGGATTGGTGGACCTACCTTGATCCACAAATTGAGGCTAAGCTGTAAGGTAGTCT -s simCow_chr6.simCow.chr6 280109 44 - 602619 TTACCT------------------------TTCAACCCACATATTAAGGCTAAGCTGCAAGATAGTGA -s simDog_chr6.simDog.chr6 279489 44 - 593897 TTATCT------------------------CTCAACCCACATATTGAGGCTAAGTTGCATGATAGAGG -s simHuman_chr6.simHuman.chr6 267629 66 - 601863 TGATGTGATGGGATGGATTGG-AGAGCTACCTCAACTCACCTATCGAAGA-AAGTTGTAAGATAGTGG -s simRat_chr6.simRat.chr6 346128 67 + 647215 CAATGTGTTGGTAAGGATTGGTTGACCTACCTTGATCCAC-AATTGAGGCTAAGCTGTAAGGCAGTCT - -a -s simMouse_chr6.simMouse.chr6 354385 16 + 636262 TTTATCCCCCTGGCCT -s Anc0.Anc0refChr0 12919 14 - 26507 CTTAACTCCATT--CC -s Anc1.Anc1refChr6 183828 14 - 197743 CTTAACTCCATT--CC -s Anc2.Anc2refChr17 21595 14 - 28526 CTTAATTCCATA--CC -s mr.mrrefChr5 201920 16 + 294540 TTTATCCCCCTTGCCT -s simCow_chr6.simCow.chr6 280154 14 - 602619 CTTAATTTCCTA--CC -s simDog_chr6.simDog.chr6 279534 14 - 593897 CCTAATTCCATA--CC -s simHuman_chr6.simHuman.chr6 267696 14 - 601863 CTTAACTCCATT--CA -s simRat_chr6.simRat.chr6 346195 16 + 647215 TTTACCCCCCTTGCTT - -a -s simMouse_chr6.simMouse.chr6 354401 44 + 636262 CAAACTTTCTTAGGGCCAGGTATGGACCACTGAAATCACTAAAA -s Anc0.Anc0refChr0 12933 44 - 26507 CAAAAGGTGTTAGGGCCCTGTATGACCTAGTGAAATCATAAGGA -s Anc1.Anc1refChr6 183842 44 - 197743 CAAAAGGTGTTAGGGCCCTGTATGACCTAGTGAAATCATAAGGA -s Anc2.Anc2refChr17 21609 44 - 28526 TGGAAGGTGGTAGGGCCCTGTATGACCTAGTAATATCATAAGGA -s mr.mrrefChr5 201936 44 + 294540 CAAACTTTCTTAGGGCCAGGTATGGACCACTGAAATCACTAAAA -s simCow_chr6.simCow.chr6 280168 40 - 602619 TCCAAGGTGGTAGGGCCCCGTATGACCCAGTAAGATCATG---- -s simDog_chr6.simDog.chr6 279558 44 - 593897 TGGACAGAGGTGGGGTCCTGTATGACCTAGTAATATCACAAGGA -s simHuman_chr6.simHuman.chr6 267710 44 - 601863 CAAAAGGTGTTAGGGCCCTTTATGAGCTGGTGAAATCATAAGGA -s simRat_chr6.simRat.chr6 346211 44 + 647215 CAAACTTTCATAGGGCCAGGTATGGACCACTAATATCACTAAAG - -a -s simMouse_chr6.simMouse.chr6 354445 40 + 636262 GAAAATCAGGCCTATATATTTTCTAACTGATAGTTGATCC -s Anc0.Anc0refChr0 12977 10 - 26507 GAAATTAGGG------------------------------ -s Anc1.Anc1refChr6 183886 10 - 197743 GAAATTAGGG------------------------------ -s Anc2.Anc2refChr17 21653 10 - 28526 GAATTTAGGG------------------------------ -s mr.mrrefChr5 201980 40 + 294540 GAAAATCAGGCCTATATATTTTCTAACTGATAGTTGATCC -s simDog_chr6.simDog.chr6 279602 10 - 593897 GAATTTAGGG------------------------------ -s simHuman_chr6.simHuman.chr6 267805 10 - 601863 AAAATTAGTG------------------------------ -s simRat_chr6.simRat.chr6 346255 40 + 647215 GAAAGTGAGGCCAATATACTATATACATGATAGTTGATCC - -a -s simMouse_chr6.simMouse.chr6 354485 18 + 636262 ATTGCTAAATTGAAGTAG -s Anc0.Anc0refChr0 16951 18 + 26507 ATTGCTAAGTTGAGGTGG -s Anc1.Anc1refChr6 17504 18 + 197743 ATTGCTAAGTTGAGGTGG -s Anc2.Anc2refChr17 10504 18 + 28526 ATTGCTAAGTTGGGGTGG -s mr.mrrefChr5 202020 18 + 294540 ATTGCTAAATTGAAGTAG -s simCow_chr6.simCow.chr6 326237 18 + 602619 ATTGCTAAGTTGGACTGG -s simDog_chr6.simDog.chr6 317985 18 + 593897 ATTGCTGAGTTGGGGTGG -s simHuman_chr6.simHuman.chr6 337979 18 + 601863 ATTGCTAAGCGGAGGTGG -s simRat_chr6.simRat.chr6 346299 18 + 647215 ATTGCCAAATTGGAGTAG - -a -s simMouse_chr6.simMouse.chr6 354503 8 + 636262 CATAGGAT -s Anc0.Anc0refChr0 16969 8 + 26507 CATAAGAT -s Anc1.Anc1refChr6 17522 8 + 197743 CATAAGAT -s Anc2.Anc2refChr17 10529 8 + 28526 CATAAGCT -s mr.mrrefChr5 202038 8 + 294540 CATAGGAT -s simCow_chr6.simCow.chr6 326262 8 + 602619 GATAAGGT -s simDog_chr6.simDog.chr6 318010 8 + 593897 CATAGGCT -s simHuman_chr6.simHuman.chr6 337997 7 + 601863 -GTAAGAT -s simRat_chr6.simRat.chr6 346317 8 + 647215 CATAGGGT - -a -s simMouse_chr6.simMouse.chr6 354511 6 + 636262 GCAATA -s Anc0.Anc0refChr0 16979 6 + 26507 GCAATA -s Anc1.Anc1refChr6 17532 6 + 197743 GCAATA -s Anc2.Anc2refChr17 10539 6 + 28526 GCAATA -s mr.mrrefChr5 202046 6 + 294540 GCAATA -s simCow_chr6.simCow.chr6 326272 6 + 602619 GTAATA -s simDog_chr6.simDog.chr6 318020 6 + 593897 CCAATA -s simHuman_chr6.simHuman.chr6 338006 6 + 601863 GCAATA -s simRat_chr6.simRat.chr6 346325 6 + 647215 GCAGTA - -a -s simMouse_chr6.simMouse.chr6 354517 42 + 636262 CTTCATCCTAAAGGATCACCCTGATCAAAGTCTGCTTAGTCA -s Anc0.Anc0refChr0 16986 42 + 26507 CTACATTTTAAAGCATCACCCAGATCAAACCCTTCCTAGCCA -s Anc1.Anc1refChr6 17539 42 + 197743 CTACATTTTAAAGCATCACCCAGATCAAACCCTTCCTAGCCA -s Anc2.Anc2refChr17 10546 42 + 28526 CTACATTTTAAAACATCACCCAGATCACACCCTTTCTAGCCA -s mr.mrrefChr5 202052 42 + 294540 CTTCATCCTAAAGGATCACCCTGATCAAAGTCTGCTTAGTCA -s simCow_chr6.simCow.chr6 326279 40 + 602619 CTACAACTTAAAACATCAGATAGGTCAG--CCTTTCTAGTCA -s simDog_chr6.simDog.chr6 318027 42 + 593897 CTGCATTTTAAGACATCACCCAGATCACACCCTTTCGAGCCA -s simHuman_chr6.simHuman.chr6 338013 42 + 601863 CTACATTTTAGAGCATCACCCAGATAAAACCCTTCCTAGCCA -s simRat_chr6.simRat.chr6 346332 42 + 647215 CTTCACCCTAAAGGATCACCCTGATTAAAGTCTGCTTAGTGA - -a -s simMouse_chr6.simMouse.chr6 354559 1 + 636262 T -s Anc0.Anc0refChr0 17028 1 + 26507 T -s Anc1.Anc1refChr6 17581 1 + 197743 T -s Anc2.Anc2refChr17 10588 1 + 28526 T -s mr.mrrefChr5 202094 1 + 294540 T -s simCow_chr6.simCow.chr6 326319 1 + 602619 T -s simDog_chr6.simDog.chr6 318069 1 + 593897 T -s simHuman_chr6.simHuman.chr6 338056 1 + 601863 T -s simRat_chr6.simRat.chr6 346374 1 + 647215 C - -a -s simMouse_chr6.simMouse.chr6 354560 25 + 636262 GGATGTGTAGATCAGTCTGAACAAG -s Anc0.Anc0refChr0 17029 25 + 26507 CGAGGTGTGGATCAGGGTAGACAAG -s Anc1.Anc1refChr6 17582 25 + 197743 CGAGGTGTGGATCAGGGTAGACAAG -s Anc2.Anc2refChr17 10591 25 + 28526 CATGGTGTGGATCAGGGTAGGCAAG -s mr.mrrefChr5 202095 25 + 294540 GGATGTGTAGATCAGTCTGAACAAG -s simCow_chr6.simCow.chr6 326322 22 + 602619 ---AGTGTGTATGAGGGTAGGCAAG -s simDog_chr6.simDog.chr6 318072 17 + 593897 CATGGTGTAGATCACGG-------- -s simHuman_chr6.simHuman.chr6 338057 25 + 601863 CGAGGACTGGACCAGAGCAGACAAG -s simRat_chr6.simRat.chr6 346375 25 + 647215 AGATGTGTAGATCAGTCTGAACAAG - -a -s simMouse_chr6.simMouse.chr6 354585 33 + 636262 AACATGTCACAAAAAGAGATTCAATTGGTCTTG -s Anc0.Anc0refChr0 17065 13 + 26507 AAAA-----------GAGATCGGC--------- -s Anc1.Anc1refChr6 17618 22 + 197743 AAAA-----------GAGATCGGCTTTTCCCAG -s Anc2.Anc2refChr17 10627 13 + 28526 AAAA-----------GAGATCGGC--------- -s mr.mrrefChr5 202120 22 + 294540 AACA-----------GAGATTCAATTGGTCTTG -s simCow_chr6.simCow.chr6 326355 13 + 602619 AAGA-----------AAGATCAGC--------- -s simDog_chr6.simDog.chr6 318262 13 + 593897 AAAA-----------GAGATTGGC--------- -s simHuman_chr6.simHuman.chr6 338093 22 + 601863 AAAA-----------GAGATCTGCTTTTCCCAG -s simRat_chr6.simRat.chr6 346400 22 + 647215 CGCA-----------GAGATTCAATGGGCCTTT - -a -s simMouse_chr6.simMouse.chr6 354618 1 + 636262 T -s Anc1.Anc1refChr6 17640 1 + 197743 t -s mr.mrrefChr5 202142 1 + 294540 t -s simHuman_chr6.simHuman.chr6 338115 1 + 601863 T -s simRat_chr6.simRat.chr6 346427 1 + 647215 t - -a -s simMouse_chr6.simMouse.chr6 354619 5 + 636262 CAGGA -s Anc1.Anc1refChr6 17641 5 + 197743 caaaa -s mr.mrrefChr5 202143 5 + 294540 cagga -s simHuman_chr6.simHuman.chr6 338131 5 + 601863 CAAAA -s simRat_chr6.simRat.chr6 346428 5 + 647215 aagga - -a -s simMouse_chr6.simMouse.chr6 354624 91 + 636262 CAGaagaaaagaagtttgtggatatagggcaccaaaagcttaggccttgggacaaattcttcaatacttatttggctgaaaaggtacaggc -s Anc0.Anc0refChr0 17078 3 + 26507 ----AGA------------------------------------------------------------------------------------ -s Anc1.Anc1refChr6 17646 7 + 197743 cagaAGA------------------------------------------------------------------------------------ -s Anc2.Anc2refChr17 10640 3 + 28526 ----AGA------------------------------------------------------------------------------------ -s mr.mrrefChr5 202148 91 + 294540 cagaagaaaagaagtttgtggatatagggcaccaaaagcttaggccttgggacaaattcttcaatacttatttggctgaaaaggtacaggc -s simCow_chr6.simCow.chr6 326368 3 + 602619 ----AGA------------------------------------------------------------------------------------ -s simDog_chr6.simDog.chr6 318275 3 + 593897 ----AGA------------------------------------------------------------------------------------ -s simHuman_chr6.simHuman.chr6 338136 7 + 601863 CAGAAGA------------------------------------------------------------------------------------ -s simRat_chr6.simRat.chr6 346434 91 + 647215 caaaagaaaagaagtttgtggatatagtgaactaccagcttaggacttggaacaaatttttcaacacttatttggctgaaaagggacaggc - -a -s simMouse_chr6.simMouse.chr6 354715 307 + 636262 tgggttaagaaacaaaaaggagtacagatgaccttttcagaacaagcgtacaatacacaaaaagaaaacgaataacatgattaaaaaatgaactagacatcaacatgcacccaattgcaagggaggctgttgtgtcaaacaagcacgagaagaactgtgtttattcatggtcAGCCTATTGCACTCGTCTAGACCAGGGAACTTTAAACTTTACCTTTTCCTGATTGGTCCATCATACAAATATGCTCCACTCCTGTGTGATAATACGGTGTAGAGAACAAGGTGTTATGGTTCCATGTAACACCTA -s Anc0.Anc0refChr0 17081 61 + 26507 -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TGTGCTCCA-----GTGTGGTAATACAGAGCAGAGAACAAGGTGTTATGATTTCACATAACACCTA -s Anc1.Anc1refChr6 17653 61 + 197743 -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TGTGCTCCA-----GTGTGGTAATACAGAGCAGAGAACAAGGTGTTATGATTTCACATAACACCTA -s Anc2.Anc2refChr17 10643 61 + 28526 -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TGTGCTACA-----GTGTGGTAATACAGAGCAGAGGACAAGGTTTTATAATATCACATAACACCTA -s mr.mrrefChr5 202239 288 + 294540 tgggttaagaaacaaaaaggagtacagatgaccttttcagaacaagcgtacaatacacaaaaaga----gaataacatgattaaaaaatgaactagacatcaa---gcacccaattgcaagggaggctgttgtgtcaaacaagcacgagaagaactgtgtttattcatggtcagcctattgcactcgtctagaccagggaactt-------taccttttcctGATTGGTCCATCATACAAATATGCTCCA-----GTGTGATAATACAGTGTAGAGAACAAGGTGTTATGGTTCCATGTAACACCTA -s simCow_chr6.simCow.chr6 326371 56 + 602619 -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TGTGCTTCA-----GTGTCGTAATACAGA-CAGGGGACACAGTTCTAT----TCACATAAAACCTA -s simDog_chr6.simDog.chr6 318278 61 + 593897 -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TGTGCTACA-----GTGTGGTAGTACTGAGCAGAGGACAAGGTTTGATAATATCACATAACACCTA -s simHuman_chr6.simHuman.chr6 338143 61 + 601863 -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TGTGCTCCA-----ATGTGGCAACACAGAGCAGAGACCAAGGTGTTAAGATTTCACATAATACATA -s simRat_chr6.simRat.chr6 346529 287 + 647215 tggcttaagaactgagatggattacgaatggcctgttcacaacaagtgcgcaatacacaaaaaca----gaatggcatgattaaaaattgaagtacaaaccag---gcacccaatggcaagggaggctgttgtgtcaaacaagcacaagagtaagtttgttgagtcatgatcggcctattgcaccagtaagcatcagggaactt-------taccttttcctGATTAGTCCAGCATACAAATGTGCTTCA-----GTGTGATAA-ACAGTGTGTAGGACAAGCTGCTATGGTTCCATGAATCACCCA - -a -s simMouse_chr6.simMouse.chr6 355022 37 + 636262 TCTAATGGTCCTATAACGAGATTGAAGTGACAAAAGA -s Anc0.Anc0refChr0 17159 37 + 26507 TCTAATAGTCTTATAACAAGGTGAAAAGGACAAAAAA -s Anc1.Anc1refChr6 17731 37 + 197743 TCTAATAGTCTTATAACAAGGTGAAAAGGACAAAAAA -s Anc2.Anc2refChr17 10721 37 + 28526 TCTAATAGTCTTATAATGAGGTGAAAAGGACAAAAAG -s mr.mrrefChr5 202527 37 + 294540 TCTAATAGTCCTATAACAAGATTGAAGGGACAAAAGA -s simCow_chr6.simCow.chr6 326454 37 + 602619 TCCGATAGTCTGATAATGAGGTGAAAAGGACAGACAG -s simDog_chr6.simDog.chr6 318356 37 + 593897 TTTAATAGTCTTATAATGAGGTGAAAAGGCCAATAAG -s simHuman_chr6.simHuman.chr6 338221 37 + 601863 TCTAATAGTCTTATAACAAGGGGAAAAGGACAAAAAA -s simRat_chr6.simRat.chr6 346816 37 + 647215 TCTAATAGTCCTGTAACAAGATTGAAGGGACAAAAGA - -a -s simMouse_chr6.simMouse.chr6 355059 12 + 636262 ATAAATAAAATA -s Anc0.Anc0refChr0 17196 12 + 26507 ATTAATAAAGAA -s Anc1.Anc1refChr6 17768 12 + 197743 ATTAATAAAGAA -s Anc2.Anc2refChr17 10758 12 + 28526 ATTAATAAAGAA -s mr.mrrefChr5 202564 12 + 294540 ATAAATAAAATA -s simCow_chr6.simCow.chr6 326495 12 + 602619 ATTAGTAAAGAA -s simDog_chr6.simDog.chr6 318393 12 + 593897 ATTAATTGGGGG -s simHuman_chr6.simHuman.chr6 338258 12 + 601863 ATTAATAAAGAA -s simRat_chr6.simRat.chr6 346853 12 + 647215 ATAAATGAAAGA - -a -s simMouse_chr6.simMouse.chr6 355071 9 + 636262 CAAAAGGAT -s Anc0.Anc0refChr0 17211 5 + 26507 C----AGAC -s Anc1.Anc1refChr6 17783 9 + 197743 CAAGGAGAC -s Anc2.Anc2refChr17 10773 5 + 28526 C----AGAC -s mr.mrrefChr5 202576 9 + 294540 CAAGAGGAT -s simCow_chr6.simCow.chr6 326573 5 + 602619 C----AGAC -s simDog_chr6.simDog.chr6 318408 5 + 593897 C----ATAC -s simHuman_chr6.simHuman.chr6 338273 9 + 601863 CAAGGAGAC -s simRat_chr6.simRat.chr6 346865 9 + 647215 CAAGAGGGT - -a -s simMouse_chr6.simMouse.chr6 355080 10 + 636262 ACTGTCATCT -s Anc0.Anc0refChr0 17216 10 + 26507 ATTGTCATTC -s Anc1.Anc1refChr6 17792 10 + 197743 ATTGTCATTC -s Anc2.Anc2refChr17 10778 10 + 28526 ATTGTCTCCC -s mr.mrrefChr5 202585 10 + 294540 ACTGTCATTT -s simCow_chr6.simCow.chr6 326579 10 + 602619 AATGATTAGT -s simDog_chr6.simDog.chr6 318413 10 + 593897 ATTGTCTCCC -s simHuman_chr6.simHuman.chr6 338282 10 + 601863 ATTGCCATTC -s simRat_chr6.simRat.chr6 346874 10 + 647215 ACTGGCACTT - -a -s simMouse_chr6.simMouse.chr6 355090 30 + 636262 CATATTTAGTTAGGTAGAGAATACTGTCAT -s Anc0.Anc0refChr0 17235 19 + 26507 CTAATCTGGTAAGGTAGT-----------T -s Anc1.Anc1refChr6 17811 19 + 197743 CTAATCTGGTAAGGTAGT-----------T -s Anc2.Anc2refChr17 10797 19 + 28526 CTAATCTGATAAGGTAAT-----------T -s mr.mrrefChr5 202595 19 + 294540 CAAATTTAGTTAGGTAGG-----------T -s simCow_chr6.simCow.chr6 326598 19 + 602619 ATCATCTGATAAGGTAAT-----------T -s simDog_chr6.simDog.chr6 318430 5 + 593897 CTAAT------------------------- -s simHuman_chr6.simHuman.chr6 338301 19 + 601863 CCATTCTGGTATGGTAGT-----------T -s simRat_chr6.simRat.chr6 346884 17 + 647215 CAAATTTAGT--GGTGGG-----------T - -a -s simMouse_chr6.simMouse.chr6 355120 31 + 636262 CTCATATTTAGTTAGACAATCAATGAGCAGT -s Anc0.Anc0refChr0 17257 31 + 26507 TTGTTAGAAATTTAGACAAATAATTAGTTCT -s Anc1.Anc1refChr6 17833 31 + 197743 TTGTTAGAAATTTAGACAAATAATTAGTTCT -s Anc2.Anc2refChr17 10819 31 + 28526 TTGTGAGAAATTTAGACAAATCATTAGTTCT -s mr.mrrefChr5 202614 31 + 294540 TTGATATTTGGTTAGACAATTAATGAGCAGT -s simCow_chr6.simCow.chr6 326620 31 + 602619 TTGTGAGGAGCTCAGACAAATGATTAGTACC -s simDog_chr6.simDog.chr6 318435 25 + 593897 ------AAAATGTACGTATATCATCAGTTCT -s simHuman_chr6.simHuman.chr6 338323 31 + 601863 CTGTTAGAAATTTGGACAAACAATTAGTGCT -s simRat_chr6.simRat.chr6 346901 31 + 647215 TTGTGAGATGTTTAGGCAAATAATGAGCAGT - -a -s simMouse_chr6.simMouse.chr6 355151 88 + 636262 TAAGCAGTGAATCAACCCCACCCTACCATCCTAGGTAGAGGTGTCGGATGTGATTGGGTTTGTGGTAGATGAGTGGCTAGTACCATTC -s Anc0.Anc0refChr0 17302 43 + 26507 TAAGCATTGGACCATTTGCCCCTTAC-------------------------------------------TGAGAGGATCATAC--TTT -s Anc1.Anc1refChr6 17878 43 + 197743 TAAGCATTGGACCATTTGCCCCTTAC-------------------------------------------TGAGAGGATCATAC--TTT -s Anc2.Anc2refChr17 10864 43 + 28526 TAAGAATTGGACTATTTGCCCCTTAC-------------------------------------------TGGGAGGATCATAC--TTT -s mr.mrrefChr5 202645 85 + 294540 TAAGCAGTGAATCAACCCCACCCTACCATCCTAGGTAGAGGTGT---ATGTGATTGGGTTTGTGGTAGATGAGTGGCTAGTACCATTC -s simCow_chr6.simCow.chr6 326665 43 + 602619 TAAATTTTTGACTAATTGCCCCTTGC-------------------------------------------TGGGAGGATCATAC--TTT -s simDog_chr6.simDog.chr6 318476 24 + 593897 TCAGAATTGG----TTTCTCCGATAT-------------------------------------------TG----------------- -s simHuman_chr6.simHuman.chr6 338369 43 + 601863 TAAGCCTTGGACCATTTGCCCCTTAC-------------------------------------------TGAGAGGATCATAC--TTT -s simRat_chr6.simRat.chr6 346932 85 + 647215 TACGTAGCGAATGAACCCTACCCTACCATCCCAAGTAAAGGTGT---ATGTGATTAGCTTTGTGGTAGCTGAGCGGCTAGTGCTATTC - -a -s simMouse_chr6.simMouse.chr6 355239 80 + 636262 TTAGACCATAATGAAAAGTGACTAAATAATCAGTCCTAGGAATAATTACTCAGATATTGTTATGTTGCATGTATATAACT -s Anc0.Anc0refChr0 17345 37 + 26507 GTAGC---TCCTGAATCCTAATGAAAT-----GTCCTA----------------------------GCAAATA------- -s Anc1.Anc1refChr6 17921 70 + 197743 GTAGC---TCCTGAATCCTAATGAAATAATCGGTCCTAAAATCAGTTTCTCAAATCTGGTCACTTTGCAAATA------- -s Anc2.Anc2refChr17 10907 37 + 28526 GTAGC---CCCTGATTCCTAATGAAAT-----GTCCTA----------------------------GCAAATA------- -s mr.mrrefChr5 202730 80 + 294540 TTAGACCATAATGAAAAGTAACTAAATAATCAGTCCTAGGAATAATTACTCAAATATTGTTATGTTGCATATATATAACT -s simCow_chr6.simCow.chr6 326708 25 + 602619 GTAGC---CCCTGATTCCTAATGAAAT-----G----------------------------------------------- -s simDog_chr6.simDog.chr6 318500 12 + 593897 ---------------------------------TCCTA----------------------------GCAAATA------- -s simHuman_chr6.simHuman.chr6 338412 66 + 601863 GTCCC---TGTTGAATCCCAATGAAATAATCGGC----AAATCAGTTTCTCAAATCTGGTCACTTTGCAAATA------- -s simRat_chr6.simRat.chr6 347063 80 + 647215 TTGGACCGTAATGAAAAGGAAATACATCCTCAGTCCTGGGAATAATTACTCAAATGTTGTTATGTTGCTTATATATAACT - -a -s simMouse_chr6.simMouse.chr6 355319 6 + 636262 ATCCAA -s Anc0.Anc0refChr0 17382 6 + 26507 ATCCCA -s Anc1.Anc1refChr6 17991 6 + 197743 ATCCCA -s Anc2.Anc2refChr17 10944 6 + 28526 ATCCCA -s mr.mrrefChr5 202810 6 + 294540 ATCCAA -s simCow_chr6.simCow.chr6 326733 2 + 602619 ----TG -s simDog_chr6.simDog.chr6 318519 6 + 593897 ATCCCA -s simHuman_chr6.simHuman.chr6 338478 6 + 601863 ATCCGA -s simRat_chr6.simRat.chr6 347143 6 + 647215 ATCCAA - -a -s simMouse_chr6.simMouse.chr6 355325 34 + 636262 TGACAGATCCAGATTCCTGCTTGTATATTATAGA -s Anc0.Anc0refChr0 17389 34 + 26507 CCACAAATCCATGTGGCTGCTTGTGTATTATAGA -s Anc1.Anc1refChr6 17998 34 + 197743 CCACAAATCCATGTGGCTGCTTGTGTATTATAGA -s Anc2.Anc2refChr17 10951 34 + 28526 CCACAAATCCATGTGGATGCATGGGTATGATAGA -s mr.mrrefChr5 202816 34 + 294540 TGACAGATCCATATTCCTGCTTGTATATTATAGA -s simCow_chr6.simCow.chr6 326736 34 + 602619 CTAAAAATCCATATGGTTGCATGGGTATGGTAGA -s simDog_chr6.simDog.chr6 318526 34 + 593897 CCACAAATCCATGTGGATGTATAGATATGATAGA -s simHuman_chr6.simHuman.chr6 338485 34 + 601863 CCACCAATCCATGTCGCTGCTTGTGTATTATAGA -s simRat_chr6.simRat.chr6 347149 34 + 647215 TGACAGATTCATATTACTACTCGTATATTATAGA - -a -s simMouse_chr6.simMouse.chr6 355359 58 + 636262 CACCATAGGCATAAAGGCAGTGTGTGCTTGTAGTTCCCCTAAATTAGTAATGAAATTG -s Anc0.Anc0refChr0 17430 46 + 26507 -----TAAGCATAAAGGCA------TCTTGTTATCCCCCAG-ACTAGTAATGAAATTG -s Anc1.Anc1refChr6 18039 52 + 197743 TACTGTAAGCATAAAGGCA------TCTTGTTATCCCCCAGAACTAGTAATGAAATTG -s Anc2.Anc2refChr17 10992 46 + 28526 -----TAAGCACAGAGGCA------TCTTGTTATCCCCCAG-ACTAGTAATGAAATTG -s mr.mrrefChr5 202850 58 + 294540 TACCGTAAGCATAAAGGCAGTGTGTGCTTGTAGTTCCCCTGAATTAGTAATGAAATTG -s simCow_chr6.simCow.chr6 326777 46 + 602619 -----TAAGCACATAGGCA------TTTTGTAATCCTCCAG-ACTAGTAATGAGATCA -s simDog_chr6.simDog.chr6 318567 46 + 593897 -----TAGGCACAGAGGCA------TCTTGTTTTCCCCCAG-ACTAGTAAAAAAATTG -s simHuman_chr6.simHuman.chr6 338527 47 + 601863 TACTGTAAGCATGAGGGCA------TCATGTTATCCCCCAGA-----TAATGAAATTG -s simRat_chr6.simRat.chr6 347183 58 + 647215 TACCGTAAGCATAAAGGCAGTGTGTGCTTGCAGTTCCCCTGAATTAGTAATCGAATTG - -a -s simMouse_chr6.simMouse.chr6 355417 14 + 636262 TAGCAACCTGCAGC -s Anc0.Anc0refChr0 17476 14 + 26507 TAGCAGCCTACTGC -s Anc1.Anc1refChr6 18091 14 + 197743 TAGCAGCCTACTGC -s Anc2.Anc2refChr17 11038 14 + 28526 TAAGAGCCTACTGC -s mr.mrrefChr5 202908 14 + 294540 TAGCAACCTGCAGC -s simCow_chr6.simCow.chr6 326823 14 + 602619 TAATAGCCTACTAT -s simDog_chr6.simDog.chr6 318613 14 + 593897 TAAGAGCCTACTGC -s simHuman_chr6.simHuman.chr6 338578 9 + 601863 TAGCAGCCC----- -s simRat_chr6.simRat.chr6 347241 14 + 647215 TAACAACCTGCAGC - -a -s simMouse_chr6.simMouse.chr6 355431 20 + 636262 TGGTCTCATCCACATTGTAA -s Anc0.Anc0refChr0 17490 20 + 26507 AGGTCGGACCTATTTTGTGA -s Anc1.Anc1refChr6 18105 20 + 197743 AGGTCGGACCTATTTTGTGA -s Anc2.Anc2refChr17 11056 20 + 28526 AGGTCGGACCTATTTTGTGA -s mr.mrrefChr5 202922 20 + 294540 TGGTCTCATCCACATTGTAA -s simCow_chr6.simCow.chr6 326841 20 + 602619 TGATCTGACCTACATTGAAG -s simDog_chr6.simDog.chr6 318631 20 + 593897 AGGTCGGACCTATTTTGTGA -s simRat_chr6.simRat.chr6 347255 20 + 647215 TGGTCTAATCCACATTGTGA - -a -s simMouse_chr6.simMouse.chr6 355451 7 + 636262 GGACATG -s Anc0.Anc0refChr0 17510 7 + 26507 GACAATA -s Anc1.Anc1refChr6 18125 7 + 197743 GACAATA -s Anc2.Anc2refChr17 11076 7 + 28526 GACAATA -s mr.mrrefChr5 202942 7 + 294540 GGACATG -s simDog_chr6.simDog.chr6 318652 7 + 593897 GACAATA -s simRat_chr6.simRat.chr6 347275 7 + 647215 GGACATG - -a -s simMouse_chr6.simMouse.chr6 355458 16 + 636262 TGTTGGGGCTAGTATG -s Anc0.Anc0refChr0 17517 16 + 26507 TGTGGGGGTAAGTAGG -s Anc1.Anc1refChr6 18132 16 + 197743 TGTGGGGGTAAGTAGG -s Anc2.Anc2refChr17 11090 16 + 28526 CGTGGGGGTAAGTAGG -s mr.mrrefChr5 202949 16 + 294540 TGTTGGGGCTAGTATG -s simCow_chr6.simCow.chr6 326861 15 + 602619 -GTAGCCCTACGTGGC -s simDog_chr6.simDog.chr6 318666 16 + 593897 CGTGTGGGTAAGTAGG -s simHuman_chr6.simHuman.chr6 338587 16 + 601863 TGTGGGAATAGGTCAA -s simRat_chr6.simRat.chr6 347282 14 + 647215 AGT--AGTCCAGTATG - -a -s simMouse_chr6.simMouse.chr6 355474 24 + 636262 AGTAGAGATGGAGTACACTGGATG -s Anc0.Anc0refChr0 17533 9 + 26507 A---------------AATGTACA -s Anc1.Anc1refChr6 18148 9 + 197743 A---------------AATGTACA -s Anc2.Anc2refChr17 11106 9 + 28526 A---------------AATGTACA -s mr.mrrefChr5 202965 24 + 294540 AGTAGAGATGGAGTACACTGGATA -s simCow_chr6.simCow.chr6 326876 9 + 602619 A---------------GAAGTAGA -s simDog_chr6.simDog.chr6 318682 9 + 593897 T---------------AATGCACA -s simHuman_chr6.simHuman.chr6 338603 9 + 601863 A---------------AAGGTACA -s simRat_chr6.simRat.chr6 347296 24 + 647215 AGTAGAGATAGAGCACACTGGATA -s simRat_chr6.simRat.chr6 347416 3 + 647215 CAT--------------------- - -a -s simMouse_chr6.simMouse.chr6 355498 74 + 636262 AGAGTACTGGACCACGCTAGGCAACAACGACTGTCTTGAGACTCAAATATGAGCAGAGTCAAGGATAGTGCTAC -s Anc0.Anc0refChr0 17542 72 + 26507 AAAGCACAAAGCTATTCTGAGCAACAACAACTGTCTTGTCACTCGCATCCTAGCAGGGT-AAGGA-GGAGTTAA -s Anc1.Anc1refChr6 18157 74 + 197743 AAAGCACAAAGCTATTCTGAGCAACAACAACTGTCTTGTCACTCGCATCCTAGCAGGGTCAAGGACGGAGTTAA -s Anc2.Anc2refChr17 11115 72 + 28526 AAAGCACAAAGCTGTTCTGAGCAACAACAAGTGTCTCGTCACTTGCATCCAAGCAGGGT-AAGGA-GGAGTTAA -s mr.mrrefChr5 202989 74 + 294540 AGAGTACTAGTCCACGCTAAGCAACAACACCTGTCTTGAGACTCAAATATTAGCAGAGTCAAGGATGGTGTTAC -s simCow_chr6.simCow.chr6 326886 60 + 602619 AAAGCACAAAGCTGTTCTGAGCAACAACAATTGTCTCGTCATATGAATCCCAGCAGGGT-G------------- -s simDog_chr6.simDog.chr6 318691 71 + 593897 AAAGCACTAAGCAGCTC-GAACAACAACAAGTGTCTCATCACTTGCATCCAGGCAGAGT-AAGGA-GGAGTTAA -s simHuman_chr6.simHuman.chr6 338612 69 + 601863 AAAGCACAAAGCTATTCTGAGCAATGACAACTGTTTTGCCACTC-----CTAGCAGGGTCAAGGTCAGATTTAA -s simRat_chr6.simRat.chr6 347320 74 + 647215 AGAGTGCTAGTCCACGCTTAGCAACATCACCTGTCTTGAGACTGAAATATTAGCAGAGTCAAGGATGGTGTTAC -s simRat_chr6.simRat.chr6 347419 72 + 647215 -GTGTACTAGTCCACGCTAAGCAACAACACCTGTCTTG-GACTCAAATATTAGCAGAGTCAAAGATGGTGTCAC - -a -s simMouse_chr6.simMouse.chr6 355572 5 + 636262 GTATA -s Anc0.Anc0refChr0 17615 5 + 26507 CTGTA -s Anc1.Anc1refChr6 18232 5 + 197743 CTGTA -s Anc2.Anc2refChr17 11188 5 + 28526 CTGTA -s mr.mrrefChr5 203064 5 + 294540 GTGTA -s simCow_chr6.simCow.chr6 326946 5 + 602619 CTGTA -s simDog_chr6.simDog.chr6 318763 5 + 593897 CTGTA -s simHuman_chr6.simHuman.chr6 338682 5 + 601863 CTATA -s simRat_chr6.simRat.chr6 347395 5 + 647215 GAGTA -s simRat_chr6.simRat.chr6 347492 5 + 647215 GGGTA - -a -s simMouse_chr6.simMouse.chr6 355577 16 + 636262 TGATAGTCCATCATGG -s Anc0.Anc0refChr0 17621 16 + 26507 TGATGATCCAGCATGA -s Anc1.Anc1refChr6 18238 16 + 197743 TGATGATCCAGCATGA -s Anc2.Anc2refChr17 11194 16 + 28526 CTATGATCCCGCATGA -s mr.mrrefChr5 203069 16 + 294540 TGATAGTCCATCATGG -s simCow_chr6.simCow.chr6 326952 16 + 602619 CTATGATCCTGCATGA -s simDog_chr6.simDog.chr6 318769 16 + 593897 CTATGATCCCGTATTT -s simHuman_chr6.simHuman.chr6 338688 16 + 601863 TGATGATCCAGCATGA -s simRat_chr6.simRat.chr6 347400 16 + 647215 TGATAGTCCATCATGG -s simRat_chr6.simRat.chr6 347497 16 + 647215 TGATAGTCCATCATGG - -a -s simMouse_chr6.simMouse.chr6 355593 2 + 636262 CA -s Anc0.Anc0refChr0 17637 2 + 26507 GA -s Anc1.Anc1refChr6 18254 2 + 197743 GA -s Anc2.Anc2refChr17 11210 2 + 28526 GA -s mr.mrrefChr5 203085 2 + 294540 CA -s simCow_chr6.simCow.chr6 326979 2 + 602619 GA -s simDog_chr6.simDog.chr6 318785 2 + 593897 GA -s simHuman_chr6.simHuman.chr6 338704 2 + 601863 GA -s simRat_chr6.simRat.chr6 347513 2 + 647215 CA - -a -s simMouse_chr6.simMouse.chr6 355595 6 + 636262 TGTCAT -s Anc0.Anc0refChr0 17639 6 + 26507 TGTCAT -s Anc1.Anc1refChr6 18256 6 + 197743 TGTCAT -s Anc2.Anc2refChr17 11224 6 + 28526 TGTCCT -s mr.mrrefChr5 203087 6 + 294540 TGTCAT -s simCow_chr6.simCow.chr6 326993 6 + 602619 TGTACT -s simDog_chr6.simDog.chr6 318799 6 + 593897 TTTCCT -s simHuman_chr6.simHuman.chr6 338706 6 + 601863 TGTCAT -s simRat_chr6.simRat.chr6 347515 6 + 647215 TGTCAT - -a -s simMouse_chr6.simMouse.chr6 355601 32 + 636262 CTTGACCACAATTCGACCAATGCAGATAATAG -s Anc0.Anc0refChr0 17647 31 + 26507 CATACTAACAATTTGACCTTT-ACGATGACTC -s Anc1.Anc1refChr6 18264 32 + 197743 CATACTAACAATTTGACCTTTAACGATGACTC -s Anc2.Anc2refChr17 11241 31 + 28526 CATACTATCAGTTTGACTTTT-ACAGTGATTC -s mr.mrrefChr5 203093 32 + 294540 CTTGACCACAATTTGACCAATGCAGATAACAC -s simCow_chr6.simCow.chr6 327010 29 + 602619 CTTGCTA--AGTGAGTCATTT-ACATGGATTC -s simDog_chr6.simDog.chr6 318816 31 + 593897 CATACTATCAGTTTGACTTTT-ACAGTGATTG -s simHuman_chr6.simHuman.chr6 338714 32 + 601863 CATAGTAAAGATTTGATCTGTAATGATGACTC -s simRat_chr6.simRat.chr6 347521 32 + 647215 CTTGACCATAATTTGACCAATCCAGATAACAC - -a -s simMouse_chr6.simMouse.chr6 355633 3 + 636262 GAT -s Anc0.Anc0refChr0 17678 3 + 26507 GAT -s Anc1.Anc1refChr6 18296 3 + 197743 GAT -s Anc2.Anc2refChr17 11272 3 + 28526 AAT -s mr.mrrefChr5 203125 3 + 294540 GAT -s simCow_chr6.simCow.chr6 327039 3 + 602619 CAT -s simDog_chr6.simDog.chr6 318847 3 + 593897 AAT -s simHuman_chr6.simHuman.chr6 338766 3 + 601863 GTT -s simRat_chr6.simRat.chr6 347553 3 + 647215 CAG - -a -s simMouse_chr6.simMouse.chr6 355636 4 + 636262 TGTA -s Anc0.Anc0refChr0 17681 4 + 26507 TGTA -s Anc1.Anc1refChr6 18299 4 + 197743 TGTA -s Anc2.Anc2refChr17 11282 4 + 28526 TGTA -s mr.mrrefChr5 203128 4 + 294540 TGTA -s simCow_chr6.simCow.chr6 327049 4 + 602619 TGTA -s simDog_chr6.simDog.chr6 318857 4 + 593897 TGTA -s simHuman_chr6.simHuman.chr6 338769 4 + 601863 TGTA -s simRat_chr6.simRat.chr6 347556 4 + 647215 CATA - -a -s simMouse_chr6.simMouse.chr6 355640 74 + 636262 ATGTTGGGTCCATGTTGCAAGCAGCTCAAGGTTAGGATGATGTTTATATCTGATCACAGTGCAAAGTTGTGCAA -s Anc0.Anc0refChr0 17685 67 + 26507 ATGTT-GGTCCCTGTTGCAAGCAACTGAGGGTTAGGATGGTG------TCTGATTGTAGTGCAGAGTTGTGCAA -s Anc1.Anc1refChr6 18303 67 + 197743 ATGTT-GGTCCCTGTTGCAAGCAACTGAGGGTTAGGATGGTG------TCTGATTGTAGTGCAGAGTTGTGCAA -s Anc2.Anc2refChr17 11289 67 + 28526 ATGTT-GGTCCCTGTTGCAAGCAACTGAGGGTTTGGATGGTG------TCTGATTGTGGTACAGTGTTGTGCAA -s mr.mrrefChr5 203132 74 + 294540 ATGTTGGGTCCCTGTTGCAAGCAGCTCAAGGTTAGGATGATGTTTATATCTGATCACAGTGCAAAGTTGTGCAA -s simCow_chr6.simCow.chr6 327057 52 + 602619 ATATT-GGTCCCTGTTGCAAGCAACTGAGGGTTCAGATGG---------------------CAGTTCTGTGCAA -s simDog_chr6.simDog.chr6 318864 67 + 593897 ATGTT-GATTTCTGTTGCAAGCAACTGCAGGTTTGGATGGTG------TCTGATTGTGGTACAGTGTTGTACAA -s simHuman_chr6.simHuman.chr6 338773 67 + 601863 ATGTT-GGTCCCTGTTGCAAGCAACTGAGGTTCAGGATGCTG------CCTGACTGTAGTGTAGAGTTATGCTA -s simRat_chr6.simRat.chr6 347560 73 + 647215 -TGTTGGGTGTCGGTTGCAACCAGTTTAATGCTAGGATGGTGTTTATATCTGATGACGATGCAAAGTTGTGCAA - -a -s simMouse_chr6.simMouse.chr6 355714 9 + 636262 TGTGGCCTT -s Anc0.Anc0refChr0 17756 9 + 26507 TGTGGCACT -s Anc1.Anc1refChr6 18374 9 + 197743 TGTGGCACT -s Anc2.Anc2refChr17 11360 9 + 28526 TGTGGCACT -s mr.mrrefChr5 203210 9 + 294540 TGTGGCCTT -s simCow_chr6.simCow.chr6 327113 9 + 602619 TGTGAGACT -s simDog_chr6.simDog.chr6 318935 9 + 593897 TGTGGCATT -s simHuman_chr6.simHuman.chr6 338844 9 + 601863 TGTGGCACT -s simRat_chr6.simRat.chr6 347637 9 + 647215 TGTGGCCTT - -a -s simMouse_chr6.simMouse.chr6 355723 12 + 636262 TAACTTCTACAT -s Anc0.Anc0refChr0 17765 10 + 26507 TAAAATTTAT-- -s Anc1.Anc1refChr6 18383 12 + 197743 TAAAATTTATAC -s Anc2.Anc2refChr17 11369 10 + 28526 TGAAATTTAT-- -s mr.mrrefChr5 203219 12 + 294540 TAACTTTTACAT -s simCow_chr6.simCow.chr6 327130 10 + 602619 TGAAATTTAT-- -s simDog_chr6.simDog.chr6 318944 10 + 593897 TGAAATTTAT-- -s simHuman_chr6.simHuman.chr6 338853 12 + 601863 TAAAATTTATAC -s simRat_chr6.simRat.chr6 347646 12 + 647215 TTACTTTTACAT - -a -s simMouse_chr6.simMouse.chr6 355735 99 + 636262 GAGTGCTGGTAGTGTACCAAAACACCGGAGTTTCTAAAGTGTAGGGAACTCAGTATTGTGGAAGATAGAAGTTATGCATGGTGACTTTTGAATATAATA -s Anc0.Anc0refChr0 17775 88 + 26507 -----------GAGTATCAAGATGCAAGGAGGCCAAAAGTGCAGGAAACTCAGTATTGACGAACATGGGCACAATAAGAGGTGACTTATGAATAGGAAA -s Anc1.Anc1refChr6 18395 99 + 197743 GGCTGCTAGTAGAGTATCAAGATGCAAGGAGGCCAAAAGTGCAGGAAACTCAGTATTGACGAACATGGGCACAATAAGAGGTGACTTATGAATAGGAAA -s Anc2.Anc2refChr17 11379 88 + 28526 -----------TAGTACCAAGATGCAAGGAGGCCAAAGGTGCAGGAAACTCAGTATTGACAAACATGGACACAATAAGAGGTGACTTATGAATAAGAAA -s mr.mrrefChr5 203231 99 + 294540 GAGTGCTGGTAGTGTATCAAGACACCGGAATTTCTAAAGTGCAGGGAACTCAGTATTGTGGAACATGGGAGTTATGCATGGTGACTTTTGAATAGGATA -s simCow_chr6.simCow.chr6 327140 85 + 602619 -----------TAATAATAAGATGCAAGAAGGCCAAAGGTGCAGTAAACTCCATATTAACAATCATGGACACAATAAGGGTT---TTTTGATTATTAAC -s simDog_chr6.simDog.chr6 318954 87 + 593897 -----------TAGGACCAAGATGCAAAGAGACCAAAGGTGCA-GAAACTCAGTATTGACAGACATGGAAACAATAAGAGGTGACTTACAAATCAGAAA -s simHuman_chr6.simHuman.chr6 338878 91 + 601863 GGCTGCTAGTAGAGTATCGAGGTGTAAGGAGGCCAAGAGAGCAGGAAACTCAGTATTGATGAACATGAGCACC--------TGACTTCTGACTAGGAAG -s simRat_chr6.simRat.chr6 347658 99 + 647215 GATTGCTGGTAGTGTATCAAGACACGTGAATTTCTAAAGTGCAGGGAACTCAGCATTGTGGAACATGGGAGTGATCTGTGGTGAGTCTTGAATAGGATA - -a -s simMouse_chr6.simMouse.chr6 355834 1 + 636262 T -s Anc0.Anc0refChr0 17863 1 + 26507 T -s Anc1.Anc1refChr6 18494 1 + 197743 T -s Anc2.Anc2refChr17 11467 1 + 28526 T -s mr.mrrefChr5 203330 1 + 294540 T -s simCow_chr6.simCow.chr6 327225 1 + 602619 T -s simDog_chr6.simDog.chr6 319048 1 + 593897 T -s simHuman_chr6.simHuman.chr6 338969 1 + 601863 C -s simRat_chr6.simRat.chr6 347757 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 355835 54 + 636262 TAAAAGTGGGTAAGGTTGATTACATATAGTCAAATAATTTCAGATCCTCTTATC -s Anc0.Anc0refChr0 17866 49 + 26507 TAAAAATTGGTAAAGTTG-TTACAT---GTCAAACAATTG-AGATGCTTCTACG -s Anc1.Anc1refChr6 18497 51 + 197743 TAAAAATTGGTAAAGTTGATTACAT---GTCAAACAATTGCAGATGCTTCTACG -s Anc2.Anc2refChr17 11470 49 + 28526 TAAAAATCAGTAGAGTTG-TTACAT---GCCAAACAATCG-AGATGCTTCTACG -s mr.mrrefChr5 203331 54 + 294540 TAAAAGTTGGTAAGGTTGATTACATATAGTCAAATAATTTCAGATCCTCCTATC -s simCow_chr6.simCow.chr6 327228 43 + 602619 TGACGATCAGTCCA-------ACAT---GGCCAACTACCC-AGATGCTTCTACA -s simDog_chr6.simDog.chr6 319051 49 + 593897 AAAAAATCAGTAGGGTTG-TTACAC---ACCAAACATTCG-AGATACTTCTATG -s simHuman_chr6.simHuman.chr6 338972 51 + 601863 TAAAAATTGGTAAAGTTGATTACAT---GTTAAACAATTGCAGTTGCTTCTACG -s simRat_chr6.simRat.chr6 347758 54 + 647215 TAAAAGTTGGTAAGGTTGATTACATATAGTCAAGTAATTTCAAATCCTCCTAGA - -a -s simMouse_chr6.simMouse.chr6 355889 19 + 636262 GTCCCTCTGAGGCTGCTTT -s Anc0.Anc0refChr0 17916 16 + 26507 GTTCC---AGGGCGGCTTT -s Anc1.Anc1refChr6 18549 19 + 197743 GTTCCGGTAGGGCGGCTTT -s Anc2.Anc2refChr17 11520 16 + 28526 GTTCC---AGGGCGGCTTT -s mr.mrrefChr5 203386 19 + 294540 GTTCCTGTGAGGCTGCTTT -s simCow_chr6.simCow.chr6 327272 16 + 602619 GTTCC---AGGGCGGCTTT -s simDog_chr6.simDog.chr6 319101 8 + 593897 ATTC-----------CTCT -s simHuman_chr6.simHuman.chr6 339024 19 + 601863 GTTCTGGTAGGGACGCTTT -s simRat_chr6.simRat.chr6 347813 19 + 647215 GTTCCTGTGAGGCTGCCTT - -a -s simMouse_chr6.simMouse.chr6 355908 99 + 636262 GGAATCCATGTGACACATACCAACCAAGTGGATGCTCCTAGTTGATCATTTTACTGTCTAGTTCCTATGTATTACCATGCCTTCTGTGAGTTTCCCCTC -s Anc0.Anc0refChr0 18015 99 + 26507 TGAATCCATGTGTCATATACCAACCTTGTGGACACTACTTGTCAGACATTTTACTGTCTACTTCCTATATATTATTATTTCTTCTGTGAGTTTCCCTCC -s Anc1.Anc1refChr6 18651 99 + 197743 TGAATCCATGTGTCATATACCAACCTTGTGGACACTACTTGTCAGACATTTTACTGTCTACTTCCTATATATTATTATTTCTTCTGTGAGTTTCCCTCC -s Anc2.Anc2refChr17 11619 99 + 28526 TGAATTCATGTGTCATATACCAACCTTGTGGACACTACTTGGCAGACACTTTACTGTCTGCTGCCTATATACTATTATTTCTTCTTCGAATTTCCCTCC -s mr.mrrefChr5 203405 99 + 294540 GGAATCCATGTGACACATACCAACCAAGTGGACACTCCTTGTTGATCATTTTACTGTCTAGTTCCTATGTATTATTATGCCTTCTGTGAGTTTCCCTTC -s simCow_chr6.simCow.chr6 327358 94 + 602619 TGAATTCATGTGTCATATGCCAACCTTGGGGATACTATTT--CAAAC---TTATTGTCTGCTGCCTATATACTATTATTTCTTGTAAGATTTTCTCTCC -s simDog_chr6.simDog.chr6 319198 99 + 593897 CTAATTCATGTATCATATACCAACCTTGTGGACGGTACTTGGCAGTCACTTTACTGTCTGCTGCCTATATACTTTTATTTCTTCTTCAAATTTCCCTCC -s simHuman_chr6.simHuman.chr6 339126 98 + 601863 TGGATCCATGTGTCATATACCAACC-TGTGGACACTACTTGTCAGACATTATACTGCCTATTTTGTATATATTATTAGTTCTTCTGTGAGTTTCCCTCC -s simRat_chr6.simRat.chr6 347832 83 + 647215 GGAATCCATGTGACACATACCAACCAAGTGGACACTTGTTGATGATCATTTTAC----------------ATTATTATGCCTTCTGTGAGTTTCCCTTC - -a -s simMouse_chr6.simMouse.chr6 356007 3 + 636262 CAC -s Anc0.Anc0refChr0 18119 3 + 26507 GGC -s Anc1.Anc1refChr6 18755 3 + 197743 GGC -s Anc2.Anc2refChr17 11723 3 + 28526 GGC -s mr.mrrefChr5 203509 3 + 294540 CAC -s simCow_chr6.simCow.chr6 327457 3 + 602619 GGA -s simDog_chr6.simDog.chr6 319302 3 + 593897 GGC -s simHuman_chr6.simHuman.chr6 339229 3 + 601863 TGC -s simRat_chr6.simRat.chr6 347920 3 + 647215 CAC - -a -s simMouse_chr6.simMouse.chr6 356010 18 + 636262 TATAACAGTTTGGATGCT -s Anc0.Anc0refChr0 18122 14 + 26507 TGTAGCAGTTTGGG---- -s Anc1.Anc1refChr6 18758 14 + 197743 TGTAGCAGTTTGGG---- -s Anc2.Anc2refChr17 11726 14 + 28526 TGTAGGAGTTTGGG---- -s mr.mrrefChr5 203512 18 + 294540 TATAACAGTTTGGATGCT -s simCow_chr6.simCow.chr6 327460 11 + 602619 TGT---AATTTAGG---- -s simDog_chr6.simDog.chr6 319305 14 + 593897 TGTAGGAGTTTGGG---- -s simHuman_chr6.simHuman.chr6 339237 14 + 601863 TGTAGCAGTTTGGG---- -s simRat_chr6.simRat.chr6 347923 18 + 647215 TATAACAGTTTGGATGTT - -a -s simMouse_chr6.simMouse.chr6 356028 11 + 636262 GCAGAGGGACT -s Anc0.Anc0refChr0 18136 11 + 26507 ACTAAGTGACT -s Anc1.Anc1refChr6 18772 11 + 197743 ACTAAGTGACT -s Anc2.Anc2refChr17 11743 11 + 28526 ACTAAGTGACC -s mr.mrrefChr5 203530 11 + 294540 GCAGAGGGACT -s simCow_chr6.simCow.chr6 327474 11 + 602619 AAAAAGTGACC -s simDog_chr6.simDog.chr6 319322 11 + 593897 ACTAAGTGACC -s simHuman_chr6.simHuman.chr6 339251 11 + 601863 ACCCAGTGACT -s simRat_chr6.simRat.chr6 347941 11 + 647215 GCAGAGGGACT - -a -s simMouse_chr6.simMouse.chr6 356039 15 + 636262 GGACAAACATGAATG -s Anc0.Anc0refChr0 18147 15 + 26507 GGATTAGCATGAATG -s Anc1.Anc1refChr6 18783 15 + 197743 GGATTAGCATGAATG -s Anc2.Anc2refChr17 11754 15 + 28526 GGATTAGCATGAATG -s mr.mrrefChr5 203541 15 + 294540 GGATAAACATGAATG -s simCow_chr6.simCow.chr6 327485 15 + 602619 CAATTAGCAAGAATG -s simDog_chr6.simDog.chr6 319336 15 + 593897 GGATCAGCATGGATG -s simHuman_chr6.simHuman.chr6 339262 15 + 601863 GGATTAGCGTGAATG -s simRat_chr6.simRat.chr6 347952 15 + 647215 GGATAGACATGAATG - -a -s simMouse_chr6.simMouse.chr6 356054 77 + 636262 AACGTGAATTCTATTATTGCATCAGATCACTGGATAAACACATCATTAGAGCCTCTAATGATTACCACACTGTTTAT -s Anc0.Anc0refChr0 18181 61 + 26507 AAGGTGAATTCAATCATTGCATAAA--------GTAAACATATGGT--GACCCTCTAATCCTGATAAC------TAT -s Anc1.Anc1refChr6 18817 61 + 197743 AAGGTGAATTCAATCATTGCATAAA--------GTAAACATATGGT--GACCCTCTAATCCTGATAAC------TAT -s Anc2.Anc2refChr17 11788 61 + 28526 AAGGGGAATTCAATCATTGCATAAG--------GTAAACATATGGT--GACCCTGTGATCCTGGTAAT------TAT -s mr.mrrefChr5 203556 77 + 294540 AACGTGAATTCTATTATTGCATCAAATCACTGGATAAACACATCATTAGACCCTCTAATGATTATCACACTGTTTAT -s simCow_chr6.simCow.chr6 327515 57 + 602619 AAGGGGAGTTCAATCATTGCATAGG--------GTAAACATGTGGT--GTCCCTGTGATCCTGGTAA---------- -s simDog_chr6.simDog.chr6 319370 61 + 593897 AAAGGGAACTCAATCATCGCATAAG--------TAAAACATATGGT--GACCCTGTGATGCTGGTCAT------TAT -s simHuman_chr6.simHuman.chr6 339296 61 + 601863 AAGGTGAATTCAATCATTGCATTAA--------GTAAACATATGGT--GACCCGCTAATCCGGATAGC------TAT -s simRat_chr6.simRat.chr6 347967 76 + 647215 AACATGAATTCTATTATTGCATCAAATCATTTGATAAACAC-TCATTGGACCCTCTAATGATTATCTCACTGTTTCT - -a -s simMouse_chr6.simMouse.chr6 356131 7 + 636262 AGCTCAA -s Anc0.Anc0refChr0 18242 7 + 26507 GGCTCCA -s Anc1.Anc1refChr6 18878 7 + 197743 GGCTCCA -s Anc2.Anc2refChr17 11849 7 + 28526 GGCTCCA -s mr.mrrefChr5 203633 7 + 294540 AGCTCAA -s simCow_chr6.simCow.chr6 327572 7 + 602619 GTCTACA -s simDog_chr6.simDog.chr6 319436 7 + 593897 GGCTCCA -s simHuman_chr6.simHuman.chr6 339357 7 + 601863 GGCTCCA -s simRat_chr6.simRat.chr6 348043 7 + 647215 AGCTCAA - -a -s simMouse_chr6.simMouse.chr6 356138 8 + 636262 GTCATTAT -s Anc0.Anc0refChr0 18249 8 + 26507 GTTATTAA -s Anc1.Anc1refChr6 18885 8 + 197743 GTTATTAA -s Anc2.Anc2refChr17 11856 8 + 28526 GTTATTAA -s mr.mrrefChr5 203640 8 + 294540 GTCATTAT -s simCow_chr6.simCow.chr6 327579 8 + 602619 GTAATTAA -s simDog_chr6.simDog.chr6 319443 8 + 593897 GTTGCTAA -s simHuman_chr6.simHuman.chr6 339364 8 + 601863 GTTATTAA -s simRat_chr6.simRat.chr6 348053 8 + 647215 GTCATTAT - -a -s simMouse_chr6.simMouse.chr6 356146 15 + 636262 GATAAAATCTAGGAT -s Anc0.Anc0refChr0 18257 15 + 26507 GGAAAGATCTAGGAT -s Anc1.Anc1refChr6 18893 15 + 197743 GGAAAGATCTAGGAT -s Anc2.Anc2refChr17 11864 15 + 28526 GGAAAGATCTAGGAT -s mr.mrrefChr5 203648 15 + 294540 GAAAAAATCTAGGAT -s simCow_chr6.simCow.chr6 327587 15 + 602619 GGAAAGATCTAGGAT -s simDog_chr6.simDog.chr6 319452 15 + 593897 GGAAAGATCTGGGAT -s simHuman_chr6.simHuman.chr6 339372 15 + 601863 GGAAAGTTGCAGGAT -s simRat_chr6.simRat.chr6 348061 14 + 647215 GAAAAAATCTATGA- - -a -s simMouse_chr6.simMouse.chr6 356161 20 + 636262 GATATGGGAAAGGACAGACT -s Anc0.Anc0refChr0 18272 14 + 26507 GATA------AAGGCAGGTT -s Anc1.Anc1refChr6 18908 14 + 197743 GATA------AAGGCAGGTT -s Anc2.Anc2refChr17 11884 14 + 28526 GGTA------AAGGCAGGTT -s mr.mrrefChr5 203663 14 + 294540 GATA------AGGGCAGACT -s simCow_chr6.simCow.chr6 327607 14 + 602619 GGAA------AGGGCAGCTT -s simDog_chr6.simDog.chr6 319472 14 + 593897 GGTA------AAGACAGGCT -s simHuman_chr6.simHuman.chr6 339387 14 + 601863 AATA------GATGTAGGTT -s simRat_chr6.simRat.chr6 348075 9 + 647215 -----------GGGCAGACT - -a -s simMouse_chr6.simMouse.chr6 356181 17 + 636262 GGTAAGTCTTGCCATTG -s Anc0.Anc0refChr0 18288 17 + 26507 GGAGGGTCTTGCCATTG -s Anc1.Anc1refChr6 18924 17 + 197743 GGAGGGTCTTGCCATTG -s Anc2.Anc2refChr17 11900 17 + 28526 GGAGGGTCTTGCCATTG -s mr.mrrefChr5 203679 17 + 294540 GGTGAGTCTTGCCATTG -s simCow_chr6.simCow.chr6 327623 17 + 602619 GGATGGTTTTGCCATTT -s simDog_chr6.simDog.chr6 319488 17 + 593897 GGAGGCTCTTGCCATTG -s simHuman_chr6.simHuman.chr6 339403 17 + 601863 GGAGGGCCTTGCCAATG -s simRat_chr6.simRat.chr6 348086 17 + 647215 GGTGTGTCTTGCCACTG - -a -s simMouse_chr6.simMouse.chr6 356198 45 + 636262 TCCCACTAAATACTGATTGCAAGGCATCCTCAGAGCTGGTCAAAC -s Anc0.Anc0refChr0 18313 45 + 26507 TCCCACCAAGTACTGACTGCAAGTCAGCCTCAGAGCAGACCAGAC -s Anc1.Anc1refChr6 18949 45 + 197743 TCCCACCAAGTACTGACTGCAAGTCAGCCTCAGAGCAGACCAGAC -s Anc2.Anc2refChr17 11925 45 + 28526 TACCACCAAATACTGACTGCAAGTCAGCTTCAGAGCAGACCAGAT -s mr.mrrefChr5 203702 45 + 294540 TCCCACTAAGTACTGATTGCAAGGCATCCTCAGAGCTGGTCAAAC -s simCow_chr6.simCow.chr6 327648 41 + 602619 T----CAAAATACTGACTGCAAACCAGCTTCAGAGGATGCGAAAT -s simDog_chr6.simDog.chr6 319513 45 + 593897 TACCACCAAATACTCACTGCAAGTCAGCTTGAGAGCAGACCAGAT -s simHuman_chr6.simHuman.chr6 339428 44 + 601863 TCTAATCAAGCACTGACTG-GAGACAGCCTCAAAGTACACCAGAC -s simRat_chr6.simRat.chr6 348109 45 + 647215 TCACAGTAAGTACTAGTTGTAAGGCATCCACAGAGCTGGTCAAAC - -a -s simMouse_chr6.simMouse.chr6 356243 6 + 636262 ATACAT -s Anc0.Anc0refChr0 18358 6 + 26507 ACTCAT -s Anc1.Anc1refChr6 18994 6 + 197743 ACTCAT -s Anc2.Anc2refChr17 11970 6 + 28526 CCTCAT -s mr.mrrefChr5 203747 6 + 294540 ACACAT -s simCow_chr6.simCow.chr6 327697 6 + 602619 CCTCAT -s simDog_chr6.simDog.chr6 319558 6 + 593897 CCACAT -s simHuman_chr6.simHuman.chr6 339472 6 + 601863 ACTCAT -s simRat_chr6.simRat.chr6 348154 6 + 647215 CCACAT - -a -s simMouse_chr6.simMouse.chr6 356249 59 + 636262 CACAGACTGTAGCGACATATTATTAACTTGATTCATTCAGTTGTACAATTGTTAAATTC -s Anc0.Anc0refChr0 18377 59 + 26507 ACTAAATAATAGTGACATATTGCTAAGTTGTTTCACTTAGTCATACAGTTCTTAAGTTC -s Anc1.Anc1refChr6 19015 59 + 197743 ACTAAATAATAGTGACATATTGCTAAGTTGTTTCACTTAGTCATACAGTTCTTAAGTTC -s Anc2.Anc2refChr17 11989 59 + 28526 ACTAAACAATAGTGACATATTGTTAAGTTGTTTCACTTGCTCATACAGTCCATAAGCTC -s mr.mrrefChr5 203761 59 + 294540 CACAGATTGTAGTGACATATTACTAACTTGATTCACTCAGTTGTACAATTGTTAAATTC -s simCow_chr6.simCow.chr6 327716 59 + 602619 ACTAAACGATAGTGACATATTATTGAGTTGTTCGACTTGATTAGACAGTCCATAAGCTC -s simDog_chr6.simDog.chr6 319577 58 + 593897 GCAAAACAGTAGTAAC-TATTGTCAAGTTGTTTCACTTGCTCATACAGTCCATAAGCTC -s simHuman_chr6.simHuman.chr6 339493 58 + 601863 ACTAAATAATAGTGACATACTGCTAAGTTGTTTCACCTAGTGATACAGTT-TTAAGTTC -s simRat_chr6.simRat.chr6 348168 59 + 647215 TACAGATTGAAGTGACATATTACTAACTTGATTCACTCAGTTGTACAATTGTTACATTC - -a -s simMouse_chr6.simMouse.chr6 356308 5 + 636262 TACAA -s Anc0.Anc0refChr0 18436 5 + 26507 TACAA -s Anc1.Anc1refChr6 19074 5 + 197743 TACAA -s Anc2.Anc2refChr17 12048 5 + 28526 CACAA -s mr.mrrefChr5 203820 5 + 294540 TACAA -s simCow_chr6.simCow.chr6 327780 5 + 602619 CATGA -s simDog_chr6.simDog.chr6 319635 5 + 593897 CACAA -s simHuman_chr6.simHuman.chr6 339551 5 + 601863 TACAA -s simRat_chr6.simRat.chr6 348227 5 + 647215 TACAA - -a -s simMouse_chr6.simMouse.chr6 356313 67 + 636262 AGGAGGTGAATAAAGTTTGTTGTGCCAGATTTACTGGTCATGATGCATACTGAACAAGAATCATGAT -s Anc0.Anc0refChr0 18441 66 + 26507 AAGAGGTGCACAAAGTCTGTTGTGCCAGACATTCAGGTAGATACACATAGTGAATGCCAATCATGA- -s Anc1.Anc1refChr6 19079 67 + 197743 AAGAGGTGCACAAAGTCTGTTGTGCCAGACATTCAGGTAGATACACATAGTGAATGCCAATCATGAT -s Anc2.Anc2refChr17 12056 66 + 28526 AAGAGGAACACAAAGTCTGTTGTGCCAGACATTCAGGTAGATTCACATAGTGAATGCCAATTGTGA- -s mr.mrrefChr5 203825 67 + 294540 AGGAGGTGAATAAAGTCTGTTGTGCCAGATTTACTGGTCATGACGCATACTGAATGAGAATCATGAT -s simCow_chr6.simCow.chr6 327790 62 + 602619 AAGTCGAACATAAAGTCTGTCATGCCAGATATTCAGGTGGAAGTACATAGTGAATGC----TGGGA- -s simDog_chr6.simDog.chr6 319643 64 + 593897 AGGAGAAACACAAAGTCAGTTGTGCCAGACATACA--TAGATTCACATGGCAAATGCCAATTGTGA- -s simHuman_chr6.simHuman.chr6 339556 67 + 601863 AAGAGGTGCACTAAGTCTGTTGTGCTGGACATTCAGGTAGATACATATAGTGACTGCCAATCATGAT -s simRat_chr6.simRat.chr6 348232 65 + 647215 A--AGGTGAATAAAGTCCGTTGTCCCACATCCACTGATCACGACGCATACTGAATGAGAATGACGAT - -a -s simMouse_chr6.simMouse.chr6 356380 6 + 636262 TCAATT -s Anc0.Anc0refChr0 18515 4 + 26507 C--ATT -s Anc1.Anc1refChr6 19154 6 + 197743 CCAATT -s Anc2.Anc2refChr17 12130 4 + 28526 C--ATT -s mr.mrrefChr5 203892 6 + 294540 TCAATT -s simDog_chr6.simDog.chr6 319715 4 + 593897 C--ATT -s simHuman_chr6.simHuman.chr6 339631 6 + 601863 CCAATC -s simRat_chr6.simRat.chr6 348297 6 + 647215 TCAATT - -a -s simMouse_chr6.simMouse.chr6 356386 2 + 636262 AT -s Anc0.Anc0refChr0 18519 2 + 26507 GT -s Anc1.Anc1refChr6 19160 2 + 197743 GT -s Anc2.Anc2refChr17 12134 2 + 28526 GT -s mr.mrrefChr5 203898 2 + 294540 GT -s simDog_chr6.simDog.chr6 319719 2 + 593897 GT -s simHuman_chr6.simHuman.chr6 339648 2 + 601863 GC -s simRat_chr6.simRat.chr6 348303 2 + 647215 GT - -a -s simMouse_chr6.simMouse.chr6 356388 27 + 636262 GTTAATAAGGTCATGCCCTGTGCTTTT -s Anc0.Anc0refChr0 18521 27 + 26507 GTTGAAAACGTCATTCCCTCAGCCTCT -s Anc1.Anc1refChr6 19162 27 + 197743 GTTGAAAACGTCATTCCCTCAGCCTCT -s Anc2.Anc2refChr17 12143 27 + 28526 GTTGTAAACACCATTCCCTCAGCCTCT -s mr.mrrefChr5 203900 27 + 294540 GTTAATAAGGTCATGCCCTGTGCTTTT -s simCow_chr6.simCow.chr6 327852 17 + 602619 ----------CCATCCATTGAGCCTCT -s simDog_chr6.simDog.chr6 319728 27 + 593897 GTTGTAAACACAGTTCCCCCAGCCTCT -s simHuman_chr6.simHuman.chr6 339650 27 + 601863 ATTGAAAATGTCATACCCTTAGCCTCT -s simRat_chr6.simRat.chr6 348305 27 + 647215 GTTAATAAGGTCGTGACCTGCGCTTTT - -a -s simMouse_chr6.simMouse.chr6 356415 2 + 636262 GG -s Anc0.Anc0refChr0 18548 2 + 26507 TG -s Anc1.Anc1refChr6 19189 2 + 197743 TG -s Anc2.Anc2refChr17 12170 2 + 28526 TG -s mr.mrrefChr5 203927 2 + 294540 GG -s simCow_chr6.simCow.chr6 327869 2 + 602619 TG -s simDog_chr6.simDog.chr6 413885 2 + 593897 TG -s simHuman_chr6.simHuman.chr6 339677 2 + 601863 TG -s simRat_chr6.simRat.chr6 348332 2 + 647215 GG - -a -s simMouse_chr6.simMouse.chr6 356417 52 + 636262 TAGGAAGACAGTAGCAAGCTAAGTTGCTGTACCACCAGATGCGGCAGTCAAT -s Anc0.Anc0refChr0 18551 52 + 26507 AAAAAAGACAGTTGCAAGCTAACTTGCTGCACCACCAAATGTGCCAGTCTAT -s Anc1.Anc1refChr6 19192 52 + 197743 AAAAAAGACAGTTGCAAGCTAACTTGCTGCACCACCAAATGTGCCAGTCTAT -s Anc2.Anc2refChr17 12173 52 + 28526 AAAAAAGACAGTTGCAAGCTAACCTGCTGCACCACCAACTGTGCCAGTCTAT -s mr.mrrefChr5 203930 52 + 294540 TAAGAAGACAGTAGCAAGCTAAGTTGCTGTACCACCAGATGTGGCAGTCAAT -s simCow_chr6.simCow.chr6 327872 52 + 602619 GTAAAAAACAGATGTAAGCTAACCTGCTGCACTACCAACTGTGGCAGCCTAT -s simDog_chr6.simDog.chr6 413888 52 + 593897 AAAAAAGGCAGTTGCAAGCTAACCTGCTGTACCACCAACTGTGCTAGTTTAT -s simHuman_chr6.simHuman.chr6 339680 49 + 601863 AAAACAGACAGTTGCAAGCC---TTGCTGCACCACCAAATGTTCCAGTCTAT -s simRat_chr6.simRat.chr6 348335 52 + 647215 CCAGAAGACTATAGCAAGTTATGTTACTGTACCGCCAGATGTGGCAGTCAAT - -a -s simMouse_chr6.simMouse.chr6 356469 42 + 636262 TTTTGTCCTCACCACAGGGGATCCTGTGTGATACACAGCACA -s Anc0.Anc0refChr0 18607 42 + 26507 TTTTTTCCTAGGCATGGGGTATTTTGTTAGACACATAGCACA -s Anc1.Anc1refChr6 19248 42 + 197743 TTTTTTCCTAGGCATGGGGTATTTTGTTAGACACATAGCACA -s Anc2.Anc2refChr17 12229 42 + 28526 TCTTTTCCTAGGCATGGGGTATTTTGTTAGACACATAGCACA -s mr.mrrefChr5 203982 42 + 294540 TTTTGTCCTCACCATAGGGGATCTTGTGTGATACATAGCACA -s simCow_chr6.simCow.chr6 327928 42 + 602619 ACTTTTCCTAGGCAAGGGGCATTTTTTTGGACCCACATCACA -s simDog_chr6.simDog.chr6 413944 42 + 593897 TCTTTTTCTAGGCATGGGGTATTTTGTTAGACATATAGCAGG -s simHuman_chr6.simHuman.chr6 339733 42 + 601863 TTTTTTCCTAGGCATGGGATATTTTGTCAAACACATGGCACA -s simRat_chr6.simRat.chr6 348387 42 + 647215 TCTTGTCCTCCCCATAGGGGATCTTGTTTGATGCTTAGCACA - -a -s simMouse_chr6.simMouse.chr6 356511 30 + 636262 TATAAATTCACAGCTGCACTCTATTTACAA -s Anc0.Anc0refChr0 18653 22 + 26507 TAT-AATTTAAAA-------TCATTTATGA -s Anc1.Anc1refChr6 19294 23 + 197743 TATAAATTTAAAA-------TCATTTATGA -s Anc2.Anc2refChr17 12275 22 + 28526 TAT-AATTTAAAA-------TCATTTATGA -s mr.mrrefChr5 204024 30 + 294540 TATAAATTCACAGCTGCACTTTATTTACAA -s simCow_chr6.simCow.chr6 327974 22 + 602619 TAT-TGTTTTAAA-------TCATTATGGC -s simDog_chr6.simDog.chr6 413990 22 + 593897 TAT-AATTTAAAA-------TGATTTATGA -s simHuman_chr6.simHuman.chr6 339779 23 + 601863 TATAAGTCTAAAA-------TCACTTCTGA -s simRat_chr6.simRat.chr6 348429 25 + 647215 TATACATTCA-----GCATTTTATTTTAAA - -a -s simMouse_chr6.simMouse.chr6 356541 19 + 636262 TAATACGGTTCCCCAAGGC -s Anc0.Anc0refChr0 18676 16 + 26507 TT-TAC--TTCCTCATGGT -s Anc1.Anc1refChr6 19318 16 + 197743 TT-TAC--TTCCTCATGGT -s Anc2.Anc2refChr17 12298 16 + 28526 TT-TAC--TTCCTCATTGT -s mr.mrrefChr5 204054 18 + 294540 TA-TACGGTTCCCCAAGGC -s simCow_chr6.simCow.chr6 327997 16 + 602619 TT-TAC--TTCCTCATTGT -s simDog_chr6.simDog.chr6 414014 5 + 593897 TT-TGC------------- -s simHuman_chr6.simHuman.chr6 339803 14 + 601863 TT-TAC--TTCCTTTGG-- -s simRat_chr6.simRat.chr6 348454 18 + 647215 TA-TACAGTTCCCCAAAGC - -a -s simMouse_chr6.simMouse.chr6 356560 2 + 636262 AG -s Anc0.Anc0refChr0 18692 2 + 26507 AG -s Anc1.Anc1refChr6 19334 2 + 197743 AG -s Anc2.Anc2refChr17 12314 2 + 28526 AG -s mr.mrrefChr5 204072 2 + 294540 AG -s simCow_chr6.simCow.chr6 328019 2 + 602619 AG -s simHuman_chr6.simHuman.chr6 339817 2 + 601863 AT -s simRat_chr6.simRat.chr6 348472 2 + 647215 TG - -a -s simMouse_chr6.simMouse.chr6 356562 1 + 636262 C -s Anc0.Anc0refChr0 18694 1 + 26507 C -s Anc1.Anc1refChr6 19336 1 + 197743 C -s Anc2.Anc2refChr17 12318 1 + 28526 C -s mr.mrrefChr5 204074 1 + 294540 C -s simCow_chr6.simCow.chr6 328023 1 + 602619 C -s simHuman_chr6.simHuman.chr6 339819 1 + 601863 T -s simRat_chr6.simRat.chr6 348474 1 + 647215 C - -a -s simMouse_chr6.simMouse.chr6 356563 6 + 636262 CTATAT -s Anc0.Anc0refChr0 18695 6 + 26507 CTATAT -s Anc1.Anc1refChr6 19337 6 + 197743 CTATAT -s Anc2.Anc2refChr17 12319 6 + 28526 TTCTAT -s mr.mrrefChr5 204075 6 + 294540 CTATAT -s simCow_chr6.simCow.chr6 328035 6 + 602619 CTCTAG -s simDog_chr6.simDog.chr6 319755 6 + 593897 TTCTAT -s simHuman_chr6.simHuman.chr6 339820 6 + 601863 CTACTT -s simRat_chr6.simRat.chr6 348475 6 + 647215 CTATAT - -a -s simMouse_chr6.simMouse.chr6 356569 12 + 636262 CAAACTACAGAA -s Anc0.Anc0refChr0 18701 12 + 26507 CAAACAAAAGCA -s Anc1.Anc1refChr6 19343 12 + 197743 CAAACAAAAGCA -s Anc2.Anc2refChr17 12325 12 + 28526 CAAATAAAAGCA -s mr.mrrefChr5 204081 12 + 294540 CAAACTACAGAA -s simCow_chr6.simCow.chr6 328041 12 + 602619 CAAATAAAAGCA -s simDog_chr6.simDog.chr6 319761 12 + 593897 CAAATAAAAGCA -s simHuman_chr6.simHuman.chr6 339828 12 + 601863 CATACAAAAGCA -s simRat_chr6.simRat.chr6 348481 12 + 647215 CTAACTACAGAA - -a -s simMouse_chr6.simMouse.chr6 356581 19 + 636262 AGTATGTCAGCTTAGATTG -s Anc0.Anc0refChr0 18727 19 + 26507 AACATGTCAGCTTAGACTG -s Anc1.Anc1refChr6 19369 19 + 197743 AACATGTCAGCTTAGACTG -s Anc2.Anc2refChr17 12351 19 + 28526 AACATGTCAGCTTAGCTTG -s mr.mrrefChr5 204093 19 + 294540 AGTATGTCAGCTTAGACTG -s simCow_chr6.simCow.chr6 328068 19 + 602619 CACATGCTGGTTTAGCTCG -s simDog_chr6.simDog.chr6 319787 19 + 593897 AACATGTCAGCTTGGCTTG -s simHuman_chr6.simHuman.chr6 339854 19 + 601863 AACATGTCAGCTTAGACTG -s simRat_chr6.simRat.chr6 348493 19 + 647215 AGAATGCCAACTTAGACTG - -a -s simMouse_chr6.simMouse.chr6 356600 21 + 636262 GTTAATTGAAACTAAACCAAC -s Anc0.Anc0refChr0 18754 21 + 26507 GTTAATGGAAAGTAAACCAAC -s Anc1.Anc1refChr6 19396 21 + 197743 GTTAATGGAAAGTAAACCAAC -s Anc2.Anc2refChr17 12378 21 + 28526 GTTAATGGACAGTAAGCCAAC -s mr.mrrefChr5 204112 21 + 294540 GTTAATTGAAACTAAACCAAC -s simCow_chr6.simCow.chr6 328095 21 + 602619 GTTAGTAGACACTAACCCCAC -s simDog_chr6.simDog.chr6 319814 21 + 593897 GCTAATGGACGGTAAGCCAGC -s simHuman_chr6.simHuman.chr6 339881 21 + 601863 GTTAATGGAAATTAAACCAAC -s simRat_chr6.simRat.chr6 348512 21 + 647215 GTTAATTGAGACTAAGCCAAC - -a -s simMouse_chr6.simMouse.chr6 356621 29 + 636262 ATATTAAGTCGATCTGGCAGCCCATCAGA -s Anc0.Anc0refChr0 18775 29 + 26507 ATTTCTAGCCGATCCCGCATCCCTTCGAA -s Anc1.Anc1refChr6 19417 29 + 197743 ATTTCTAGCCGATCCCGCATCCCTTCGAA -s Anc2.Anc2refChr17 12399 29 + 28526 ATTCCTAGCCGATCCCTCGTCCCTTCGAA -s mr.mrrefChr5 204133 29 + 294540 ATATTAAGTCGATCTGGCAGCCCTTCGAA -s simCow_chr6.simCow.chr6 328117 23 + 602619 ATTCCTGGCCGAACACTC------TCGAA -s simDog_chr6.simDog.chr6 319835 29 + 593897 ATTCCTACCCGATCCGTCGTCCCTTTGAA -s simHuman_chr6.simHuman.chr6 339902 29 + 601863 ATTTCTAGCAGATCCCGCATCCCTCCGAA -s simRat_chr6.simRat.chr6 348533 29 + 647215 ATACTAAGACGATCTGGCAGCCCTTCGAA - -a -s simMouse_chr6.simMouse.chr6 356650 122 + 636262 AAGAATTCCCTAGCACGGACTGCAGTCCACCAGCGGTTTCATGGCCCGCTGGTCCGCGATAATAACGGAGATCAAGGTGAAAAAAAAGACGTACGAAGTTCATTGTTGGATCATGTCCGACC -s Anc0.Anc0refChr0 18804 101 + 26507 GGGACTCGCTTACCACGGATTTCAGTCCGCCAGT-CTTTTATGGCCCGCTGGTCCGCGACAACAACGGAGCTGATGGTGGAAAAGAAGTCGTACGAACTTCG-------------------- -s Anc1.Anc1refChr6 19446 121 + 197743 GGGACTCGCTTACCACGGATTTCAGTCCGCCAGT-CTTTTATGGCCCGCTGGTCCGCGACAACAACGGAGCTGATGGTGGAAAAGAAGTCGTACGAACTTCGTGAATGGATCATGTCCCATC -s Anc2.Anc2refChr17 12429 101 + 28526 GGGACTTGCTTACTACGGATTTCAGTTCGCTAGT-GTTTTATGGCCCGCTGGTCCGCGACAACAACGGAGCTGGTGGTGGAAAAGAAGTCGTACGTGCTTCG-------------------- -s mr.mrrefChr5 204162 122 + 294540 AGGAATCCCTTAGCACGGACTTCAGTCCACCAGCGCTTTTATGGCCCGCTGGTCCGCGACAATAACGGAGATGAAGGTGAAAAAAAAGACGTACGAAGTTCGTGGTTGGATCATGTCCGACC -s simCow_chr6.simCow.chr6 328141 95 + 602619 AAAGCTGGCTTACTACAGATTTCGGGTCACGAGT-GTTTCGCGGCCCGCTGGTCTGCGACATTAACGGAGCTGGTGGCGGAAAAGAAGTCGTAAGT-------------------------- -s simDog_chr6.simDog.chr6 319865 101 + 593897 GGGACCTGCTTACTGCGGATTTCAGTTCGCTAGT-GTTTTATGGCTCGCTGGTCCGTGACAACAACGGGGATGGGAGTGGAAAAGGAGTCGTACGTGCTTCG-------------------- -s simHuman_chr6.simHuman.chr6 339931 121 + 601863 GGGACTCGCTTACCACGGATTTCTGTCCTCCTGT-CTTTTATGGCCCGCTGGTCCGCGACAGCAGCGGAGCTGATGGTGGAAAAGAGGTCGCACGAACTTCGTGAATGAATTATGTCCCATC -s simRat_chr6.simRat.chr6 348562 109 + 647215 AGAAATCTCTTAGCACGGACTTCAGTCTACCAGCGCTATTATGGCCTCCAGGTCCGCGACAATAACGGAAATGAAGGTGA-------------CGGAGTTCGTGGTTGGATCATGTTCGACC - -a -s simMouse_chr6.simMouse.chr6 356772 4 + 636262 CTGA -s Anc0.Anc0refChr0 18909 4 + 26507 TCGA -s Anc1.Anc1refChr6 19571 4 + 197743 TCGA -s Anc2.Anc2refChr17 12534 4 + 28526 TGTC -s mr.mrrefChr5 204288 4 + 294540 CCGA -s simCow_chr6.simCow.chr6 328241 4 + 602619 TGTA -s simDog_chr6.simDog.chr6 320207 3 + 593897 -GTC -s simHuman_chr6.simHuman.chr6 340056 4 + 601863 TCGA -s simRat_chr6.simRat.chr6 348675 4 + 647215 CCGA - -a -s simMouse_chr6.simMouse.chr6 356776 277 + 636262 AGAACCTAACTGGCCTACTGCACTCATCAATCACAGAACTTTCTTTCAGTATCATGCTGGTCTATCCATAGATATGCCACATCATAGAGACCCTATGGTTATCCACCACCATTTATTGCTAAGACAAGATTTAGCTATCTTAATATATGGCTCTATTTAGACATACCTGTGTCCTACCATATTGCCCGTTTACTGGCACTTAAAGGTGTACTGTCCTTGACCTCAGAGAACTCCTGGATAAAGTATCAACACTAAAGAGTGAACTGTCATTGCCTAT -s Anc0.Anc0refChr0 18913 201 + 26507 AGAACCTAACTGGCCTACTGCACTCATCAATCACAATCCTTTCTCTTAGTATCATTCTAGTCTGTCCATTCATATGCTGCATCATGGAGAGCCTATGGTTAT---TCACCTTGTATTTGTGAGACAACATTTAGCTATCTTA-------------------------------------------------------------------------ACTGACCTCAGAGTACTCTTGGATACAGTACCAACACCCAAGAGTGAACTGTCACTGACCAT -s Anc1.Anc1refChr6 19575 273 + 197743 AGAACCTAACTGGCCTACTGCACTCATCAATCACAATCCTTTCTCTTAGTATCATTCTAGTCTGTCCATTCATATGCTGCATCATGGAGAGCCTATGGTTAT---TCACCTTGTATTTGTGAGACAACATTTAGCTATCTTAACATGTGGTCCTGTTGAGCCATATGTATGTCCTGACATACTGCT-GGCTGTTGGCACTTAAGAAAGGACTGGCACTGACCTCAGAGTACTCTTGGATACAGTACCAACACCCAAGAGTGAACTGTCACTGACCAT -s Anc2.Anc2refChr17 12538 201 + 28526 AGAACCTAACTGGCCTACTGCACTCATCAATAACAATCCTTTCTCTTAGTATCAGTCTAGTCTGTCCATTCATTTCCTGCATCATGGAGAGCCTATAGTTAT---TCACCTTGTGTTTGCAAAACAACATTTAGCTAACTTA-------------------------------------------------------------------------ACTGACCTCAGAGTATTCTTGGCTACAGTACCAACACCCAAGAGTGAATTCTCACTGACCAT -s mr.mrrefChr5 204292 276 + 294540 AGAACCTAACTGGCCTACTGCACTCATCAATCACAGAACTTTCTTTCAGTATCATGCTGGTCTATCCATAGATATGCCACATCATAGAGACCCTATGGTTATCC-CCACCATTTATTGCTGAGACAAGATTTAGCTATCTTAATATATGGCTCTATTTAGACATACCTATGTCCTACCATATTGCCCGTTTACTGGCACTTAAAGGTGTACTGTCCTTGACCTCAGAGAACTCCTGGATAAAGTATCAACACTAAAGAGTGAACTGTCATTGCCTAT -s simCow_chr6.simCow.chr6 328246 182 + 602619 AGAACCT--CTGGCCTA-TGCACTCATCAACAATAGTCCTTTCTCTCAGCAGCAGTGTAGTCTGCCCATTCATCTCCTGTATCATGGGGATCATATAGT--C---TCACCTTGCGTTTGCAAAACAACTATTAGATACCTTA-------------------------------------------------------------------------ACTGACCTCAGAGTTTTGTTGGTTAAAGTACCAACACCCAGG--------------GATCTT -s simDog_chr6.simDog.chr6 320210 191 + 593897 AGATCCTAACTGGCCTACTGTATTTATCAATAACAATTCTTTCTCTTAATATCAGTCTAGTATCTCCATTGATTTCCCACATCATGGAGAGCCCATAGTTAT---TTACCGGATGTTT----------ATTTGGCTAACTTA-------------------------------------------------------------------------ACTGACCTCAGAATATTCTTGGCTACAGTACCCACTACCAAGAGTGAATTCTCACTGACTAC -s simHuman_chr6.simHuman.chr6 340060 267 + 601863 AGAACCTAACTGGCTTACTGCACTCATCACTCACAATCCTTTCTCTTAGTATTGTTCTAGCCTGTCCATTCATATGCTGCATCATCG-----CTATGGGTAT---TCACCTTGTAATTGTGAGACAACATTTAACTATTTTAACATGTGGTCCTGTTGAGCCATATGTATGTCCTGACATACTGCT-GGCTGTTGGCACTTAAGAAAGGACTGGCACTGACCTCAGAGTACTCTTGGATAGAGT-CCAACACCCAAGAGTGAACTGTCACGAACCCT -s simRat_chr6.simRat.chr6 348679 250 + 647215 AGAACCTAACTGGCATATTGCACTCATCAACCACAGAACTTTCTTTCAATATCATGCTGGTCTATCCATAGATGTGCCACATCATAGAGAGCCTATGATTATCC-CCACCATATATTGCTGAGACAA-------------------------CCCTTTAGACATACCTA-GTGCTACCATATTGCCCATTTACTGGCACTTAAAGGTGTACTATTGTTGACCTCAGAGAACACCTGGGTAAAGTATCAACTCAAAAGAGTGAACTGTCATCGCCTAT - -a -s simMouse_chr6.simMouse.chr6 357053 1 + 636262 G -s Anc0.Anc0refChr0 19117 1 + 26507 G -s Anc1.Anc1refChr6 19851 1 + 197743 G -s Anc2.Anc2refChr17 12742 1 + 28526 G -s mr.mrrefChr5 204568 1 + 294540 G -s simCow_chr6.simCow.chr6 328431 1 + 602619 G -s simDog_chr6.simDog.chr6 320404 1 + 593897 G -s simHuman_chr6.simHuman.chr6 340330 1 + 601863 G -s simRat_chr6.simRat.chr6 348929 1 + 647215 G - -a -s simMouse_chr6.simMouse.chr6 357054 4 + 636262 CATG -s Anc0.Anc0refChr0 19118 4 + 26507 CATG -s Anc1.Anc1refChr6 19852 4 + 197743 CATG -s Anc2.Anc2refChr17 12743 4 + 28526 TATG -s mr.mrrefChr5 204569 4 + 294540 CATG -s simCow_chr6.simCow.chr6 328432 4 + 602619 TTTG -s simDog_chr6.simDog.chr6 320405 4 + 593897 TATG -s simHuman_chr6.simHuman.chr6 340331 4 + 601863 CATG -s simRat_chr6.simRat.chr6 348932 4 + 647215 TGTG - -a -s simMouse_chr6.simMouse.chr6 357058 76 + 636262 TGACCTTTTCATTGATCCAGCCCTTAGGCTGCTCTTTGCAAGCTAAGTTAGTTGCAATGTGTTGAATCAAATACGC -s Anc0.Anc0refChr0 19143 75 + 26507 TGCCCCTTTTATTAATTCAGCCCGTTGGCTGCTCTTTACAATCCTGGTTA-TAGCATTGTGTTGGATCAAATATAG -s Anc1.Anc1refChr6 19877 75 + 197743 TGCCCCTTTTATTAATTCAGCCCGTTGGCTGCTCTTTACAATCCTGGTTA-TAGCATTGTGTTGGATCAAATATAG -s Anc2.Anc2refChr17 12768 75 + 28526 TGCCCCTTTTATTAGTTTGGCCTGTTGGCTGCTCTTTTCCATCCTGGTTA-TAGCATTGTGTTGGATCAAATATAG -s mr.mrrefChr5 204573 76 + 294540 TGCCCTTTTCATTGATCCAGCCCTTTGGCTGCTCTTTACAAGCTAGGTTATTTGCAATGTGTTGGATCAAATATGC -s simCow_chr6.simCow.chr6 328457 75 + 602619 TGCCCCTTTTATTGGTTTGGCCTGTTGGCTGCTCCTCTTTATGTTGGTTA-CAGCATTGTGTTGAATCAAATATAG -s simDog_chr6.simDog.chr6 320430 75 + 593897 TGCCCCTTTCATTAGTTTGGCCTGTTGGCTGCTCTTTTCCATCCTGGCTT-TAGCATTGTATTGGATCAAATGCAA -s simHuman_chr6.simHuman.chr6 340356 75 + 601863 TGCCCCTTTTATTCAATCAGTCCGTTGGCTGCTCTTTACAATCCTGGTTA-TGGCATTGTGTTGGATCAAATATAG -s simRat_chr6.simRat.chr6 348936 76 + 647215 TGCGCATTTCATTGATCCAGCCCATTGGCTGCTCTTCACGAGCTAGGTTATTTGTAATGTGTTAGATTGAATATTC - -a -s simMouse_chr6.simMouse.chr6 357134 11 + 636262 GTCAATTGGTA -s Anc0.Anc0refChr0 19218 11 + 26507 GTCTATCCGTA -s Anc1.Anc1refChr6 19952 11 + 197743 GTCTATCCGTA -s Anc2.Anc2refChr17 12843 11 + 28526 GTCTATCCATA -s mr.mrrefChr5 204649 11 + 294540 GTCAATTGGTA -s simCow_chr6.simCow.chr6 328532 10 + 602619 GTCTATCC-CA -s simDog_chr6.simDog.chr6 320505 11 + 593897 GTCTATCCATA -s simHuman_chr6.simHuman.chr6 340431 11 + 601863 GTCTATATGTG -s simRat_chr6.simRat.chr6 349097 11 + 647215 ATCAATTGGTA - -a -s simMouse_chr6.simMouse.chr6 357145 3 + 636262 GTG -s Anc0.Anc0refChr0 19229 3 + 26507 GTG -s Anc1.Anc1refChr6 19963 3 + 197743 GTG -s Anc2.Anc2refChr17 12854 3 + 28526 GTG -s mr.mrrefChr5 204660 3 + 294540 GTG -s simCow_chr6.simCow.chr6 328542 3 + 602619 GTG -s simDog_chr6.simDog.chr6 320517 3 + 593897 GTG -s simHuman_chr6.simHuman.chr6 340442 3 + 601863 GCG -s simRat_chr6.simRat.chr6 349108 3 + 647215 GTG - -a -s simMouse_chr6.simMouse.chr6 357148 58 + 636262 CAGAGGCATCTACAGCTAGGTTACTTGCAATGTGTTGGATCAAATATGCATCAATTGG -s Anc0.Anc0refChr0 19232 10 + 26507 CTGA------------------------------------------------AATGGG -s Anc1.Anc1refChr6 19966 10 + 197743 CTGA------------------------------------------------AATGGG -s Anc2.Anc2refChr17 12857 10 + 28526 CTTA------------------------------------------------GCCGGA -s mr.mrrefChr5 204663 58 + 294540 CTGAGGCATCTACAGCTAGGTTACTTGCAATGTGTTGGATCAAATATGCATCAATTGG -s simCow_chr6.simCow.chr6 328545 10 + 602619 CCAA------------------------------------------------GCCGGA -s simDog_chr6.simDog.chr6 320520 10 + 593897 CTTA------------------------------------------------GCCAGA -s simHuman_chr6.simHuman.chr6 340445 10 + 601863 CTGA------------------------------------------------AATGGG -s simRat_chr6.simRat.chr6 349117 58 + 647215 CTGATACATCTGCAGCTAGGTCATTTGCAATGTGTTGGATCAAATATGCGTCAATTGG - -a -s simMouse_chr6.simMouse.chr6 357206 8 + 636262 TTGGTAGT -s Anc0.Anc0refChr0 19248 4 + 26507 T----ACA -s Anc1.Anc1refChr6 19982 4 + 197743 T----ACA -s Anc2.Anc2refChr17 12873 4 + 28526 T----ACA -s mr.mrrefChr5 204721 4 + 294540 T----AGT -s simCow_chr6.simCow.chr6 328561 4 + 602619 T----ACA -s simDog_chr6.simDog.chr6 320536 4 + 593897 T----ATA -s simHuman_chr6.simHuman.chr6 340461 4 + 601863 T----ACA -s simRat_chr6.simRat.chr6 349175 4 + 647215 T----AGT - -a -s simMouse_chr6.simMouse.chr6 357214 12 + 636262 ACAGAGCCCGAG -s Anc0.Anc0refChr0 19252 12 + 26507 ACAGTGCCTGGG -s Anc1.Anc1refChr6 19986 12 + 197743 ACAGTGCCTGGG -s Anc2.Anc2refChr17 12879 12 + 28526 ACAGTGCCTGGG -s mr.mrrefChr5 204725 12 + 294540 ACAGAGCCCGAG -s simCow_chr6.simCow.chr6 328567 12 + 602619 ACAGTACCTGGG -s simDog_chr6.simDog.chr6 320542 12 + 593897 ACAGTGCCTGGG -s simHuman_chr6.simHuman.chr6 340465 12 + 601863 ACAGTGCCTGGG -s simRat_chr6.simRat.chr6 349179 12 + 647215 GTAGAGTCAGAG - -a -s simMouse_chr6.simMouse.chr6 357226 7 + 636262 GCATCTA -s Anc0.Anc0refChr0 19270 7 + 26507 GTACTTA -s Anc1.Anc1refChr6 20004 7 + 197743 GTACTTA -s Anc2.Anc2refChr17 12897 7 + 28526 GTGCTTA -s mr.mrrefChr5 204737 7 + 294540 GCATCTA -s simCow_chr6.simCow.chr6 328585 7 + 602619 GTGCTAA -s simDog_chr6.simDog.chr6 320560 7 + 593897 CTGCTTA -s simHuman_chr6.simHuman.chr6 340483 7 + 601863 GTACTTA -s simRat_chr6.simRat.chr6 349191 7 + 647215 ACATCTA - -a -s simMouse_chr6.simMouse.chr6 357233 40 + 636262 CAGCCCTATCTTGCCCCAGCTAGTACTTGGTCAGCAGACG -s Anc0.Anc0refChr0 19278 40 + 26507 CAGGCCTAACATGCCATGGCTGGTACTTGATCAACAGAGG -s Anc1.Anc1refChr6 20012 40 + 197743 CAGGCCTAACATGCCATGGCTGGTACTTGATCAACAGAGG -s Anc2.Anc2refChr17 12905 40 + 28526 CAGGCTTAATATGCCATGACTGGTACTTGATCAATGGAAG -s mr.mrrefChr5 204744 40 + 294540 CAGCCCTATCTTGCCCCAGCTAGTACTTGATCAGCAGAGG -s simCow_chr6.simCow.chr6 328593 40 + 602619 CAAGCACAATATGACTTGACTGGTACTTGACCAATGGAAG -s simDog_chr6.simDog.chr6 320568 40 + 593897 CAGGTTTGATATGCCATGACTGGTACTTGATCAATGGAAG -s simHuman_chr6.simHuman.chr6 340491 40 + 601863 CGGGCCTAACCTGCCGTGGCTGGTGCTTGATTGACAGAGG -s simRat_chr6.simRat.chr6 349198 39 + 647215 CAGCCTTATCTGGCCC-AGCTAGTACTCAATCAGCAGAGG - -a -s simMouse_chr6.simMouse.chr6 357273 26 + 636262 GAGTCCCTGTACAAAGTCCCTTTACT -s Anc0.Anc0refChr0 19318 26 + 26507 AAGTCTCTGTGTTACATTGCTCTTCT -s Anc1.Anc1refChr6 20052 26 + 197743 AAGTCTCTGTGTTACATTGCTCTTCT -s Anc2.Anc2refChr17 12945 26 + 28526 AAGTCTCTGTGTTACATTGCTCTTCT -s mr.mrrefChr5 204784 26 + 294540 GAGTCCCTGTACAAAGTCCCTTTACT -s simCow_chr6.simCow.chr6 328633 26 + 602619 TAGTCTCTGTGTTAAATTGCTCTCGT -s simDog_chr6.simDog.chr6 320633 26 + 593897 AAGTCTCTGTGTTACATTGCTCTTCT -s simHuman_chr6.simHuman.chr6 340531 26 + 601863 AAGTCTCCGTGGTACATTGCTCTTCT -s simRat_chr6.simRat.chr6 349237 26 + 647215 GAGTCCCTGTACAAAGTCCCTTTACT - -a -s simMouse_chr6.simMouse.chr6 357299 47 + 636262 AGATTTCCTCTATTGGACACTAGTGAATTGTGCACTCAAATTCAATA -s Anc0.Anc0refChr0 19350 37 + 26507 ATATTTTC-CTATGAGAC---------TTGTGCTCTCTAGTTCAGTA -s Anc1.Anc1refChr6 20084 37 + 197743 ATATTTTC-CTATGAGAC---------TTGTGCTCTCTAGTTCAGTA -s Anc2.Anc2refChr17 12977 37 + 28526 ATATTTTC-CTATGAGAG---------TTGTGCTATATTGTTCAGTA -s mr.mrrefChr5 204810 47 + 294540 ATATTTCCTCTATTGGACACTAGTGAATTGTGCACTCAAATTCAATA -s simCow_chr6.simCow.chr6 328665 37 + 602619 ATATTCTT-CTATGAGAG---------TTGTGCATTACTGTTTGATA -s simDog_chr6.simDog.chr6 320665 36 + 593897 ATATTTTC-CTATGAGAG---------TTGTGCTATAT-GTTCAGTA -s simHuman_chr6.simHuman.chr6 340563 37 + 601863 ATATTTTC-CTATGAGCC---------TTGAGCGCTCTAGTTCAGGA -s simRat_chr6.simRat.chr6 349263 47 + 647215 ATATTTCCTCTTTTGGACACTAGTGGATTGTGCACTGAAATTCAATA - -a -s simMouse_chr6.simMouse.chr6 357346 16 + 636262 TGACCAAACGTACAAG -s Anc0.Anc0refChr0 19393 16 + 26507 TCTCCAAACATTAAAG -s Anc1.Anc1refChr6 20127 16 + 197743 TCTCCAAACATTAAAG -s Anc2.Anc2refChr17 13020 16 + 28526 CCTCCAAACATTAAAG -s mr.mrrefChr5 204857 16 + 294540 TGACCAAACGTACAAG -s simCow_chr6.simCow.chr6 328708 16 + 602619 CCTCCAAACATTAAAG -s simDog_chr6.simDog.chr6 320707 16 + 593897 CCTCCAAACACTAAAT -s simHuman_chr6.simHuman.chr6 340606 16 + 601863 TCTCCAAACATTAGAG -s simRat_chr6.simRat.chr6 349310 16 + 647215 TGACCAAACGGACAAG - -a -s simMouse_chr6.simMouse.chr6 357362 24 + 636262 ATGTCCATTCTATGCCTCCTCTAA -s Anc0.Anc0refChr0 19409 24 + 26507 AGGTATATTCTACATTTCCCCTGA -s Anc1.Anc1refChr6 20143 24 + 197743 AGGTATATTCTACATTTCCCCTGA -s Anc2.Anc2refChr17 13036 24 + 28526 GAGTATATTCTACATTTCCCCTGA -s mr.mrrefChr5 204873 24 + 294540 AGGTACATTCTACGCCTCCTCTAA -s simCow_chr6.simCow.chr6 328724 24 + 602619 GTGTACATCCTACATTTCCCCTGA -s simDog_chr6.simDog.chr6 320723 24 + 593897 GAGTATAGTCTCTATTTTCCCAGA -s simHuman_chr6.simHuman.chr6 340628 24 + 601863 AGGTAAATTCTACCTTTCCCCTGA -s simRat_chr6.simRat.chr6 349326 14 + 647215 AGGTACATTCTACG---------- - -a -s simMouse_chr6.simMouse.chr6 357386 28 + 636262 GAATTCGAGTCTAGACTTGACATGGTTT -s Anc0.Anc0refChr0 19433 22 + 26507 GA------GGGTAGATTTAACATGGTTC -s Anc1.Anc1refChr6 20167 22 + 197743 GA------GGGTAGATTTAACATGGTTC -s Anc2.Anc2refChr17 13060 22 + 28526 GA------GGGTAGATCTAACATGGCTC -s mr.mrrefChr5 204897 22 + 294540 GA------GTCTAGACTTGACATGGTTT -s simCow_chr6.simCow.chr6 328751 22 + 602619 GA------AGACAGGCCTGACATGGGTG -s simDog_chr6.simDog.chr6 320747 22 + 593897 GA------GGGTAGATCCAACACGGCTC -s simHuman_chr6.simHuman.chr6 340652 22 + 601863 GA------GGGTAGATTTAACATGGTTC -s simRat_chr6.simRat.chr6 349340 11 + 647215 -----------------TGACATGGTCT - -a -s simMouse_chr6.simMouse.chr6 357414 3 + 636262 AAT -s Anc0.Anc0refChr0 19455 3 + 26507 AAT -s Anc1.Anc1refChr6 20189 3 + 197743 AAT -s Anc2.Anc2refChr17 13087 3 + 28526 GAT -s mr.mrrefChr5 204919 3 + 294540 AAT -s simCow_chr6.simCow.chr6 328778 3 + 602619 GCT -s simDog_chr6.simDog.chr6 320774 3 + 593897 GAT -s simHuman_chr6.simHuman.chr6 340674 3 + 601863 AAT -s simRat_chr6.simRat.chr6 349351 3 + 647215 AAT - -a -s simMouse_chr6.simMouse.chr6 357417 7 + 636262 AAAATTA -s Anc0.Anc0refChr0 19465 3 + 26507 AAT---- -s Anc1.Anc1refChr6 20199 7 + 197743 AATACTG -s Anc2.Anc2refChr17 13097 3 + 28526 AAT---- -s mr.mrrefChr5 204922 7 + 294540 AAAATTA -s simCow_chr6.simCow.chr6 328788 3 + 602619 GAT---- -s simDog_chr6.simDog.chr6 320784 3 + 593897 AAT---- -s simHuman_chr6.simHuman.chr6 340684 7 + 601863 AACACTG -s simRat_chr6.simRat.chr6 349354 7 + 647215 AAGATTA - -a -s simMouse_chr6.simMouse.chr6 357424 6 + 636262 TACAGG -s Anc0.Anc0refChr0 19468 6 + 26507 GTTAGG -s Anc1.Anc1refChr6 20206 6 + 197743 GTTAGG -s Anc2.Anc2refChr17 13100 6 + 28526 GTTAGG -s mr.mrrefChr5 204929 6 + 294540 TACAGG -s simCow_chr6.simCow.chr6 328796 6 + 602619 GTTAGG -s simDog_chr6.simDog.chr6 320787 6 + 593897 GTTATG -s simHuman_chr6.simHuman.chr6 340691 6 + 601863 GTTAGG -s simRat_chr6.simRat.chr6 349361 6 + 647215 TACAGG - -a -s simMouse_chr6.simMouse.chr6 357430 88 + 636262 AAAAGATGAAGTGATGTGACTGAGCCAATTGATAAAGCAGTTTCCCTAACTACATGTCTAGCATTTGGTGCTACAAAAGGGTACCGGC -s Anc0.Anc0refChr0 19479 88 + 26507 AAAAGATGAAGTGACATGACTGAGTCATTTAGTAAATCCCTTCACCTAACTATGTATCTAGCATTTGGTGCTACTAAAAGGTACAAGT -s Anc1.Anc1refChr6 20217 88 + 197743 AAAAGATGAAGTGACATGACTGAGTCATTTAGTAAATCCCTTCACCTAACTATGTATCTAGCATTTGGTGCTACTAAAAGGTACAAGT -s Anc2.Anc2refChr17 13111 88 + 28526 AGCAGATGAAGTGACATGACTGAGTCATTTAGTAAATCCCTTCATCTAACTATGTATCTAGCATTTGGTGCTACTGAAAGGTACAAGT -s mr.mrrefChr5 204935 88 + 294540 AAAAGATGAAGTGATGTGACTGAGCCAATTGATAAATCAGTTTCCCTAACTATATGTCTAGCATTTGGTGCTACAAAAGGGTACCGGC -s simCow_chr6.simCow.chr6 328807 88 + 602619 AGCAGATGAAGTGACACGATCAAGTCAATCAATAAATCAATTCCTCTAACTATGTATCAAGCACTTGGTGCTACTGAAAGGTACAAGT -s simDog_chr6.simDog.chr6 320798 88 + 593897 AGCAAATGAAGTGACATGGCTGAGCTTTTTAGTAAATCCCTTTATCTAACTATGTGTCTAGCATTTGGTGCTACTGAAAGGTACAAGT -s simHuman_chr6.simHuman.chr6 340702 88 + 601863 AAAAGATGAGGTAACATGACTGAGTCACTTAGTAAATCCCTTCTCCTAACTATGCATCTAGTATTTGGTGCTACTAATAGGTACAAGT -s simRat_chr6.simRat.chr6 349367 76 + 647215 AAA-GATGAAGTGATGTGACT-----------TAAATCAGTTTCCATAACTATATGTCTAGCACTTGGTGCTACAAAATGGTACTGGC - -a -s simMouse_chr6.simMouse.chr6 357518 1 + 636262 C -s Anc0.Anc0refChr0 19567 1 + 26507 C -s Anc1.Anc1refChr6 20305 1 + 197743 C -s Anc2.Anc2refChr17 13199 1 + 28526 C -s mr.mrrefChr5 205023 1 + 294540 C -s simCow_chr6.simCow.chr6 328895 1 + 602619 C -s simDog_chr6.simDog.chr6 320886 1 + 593897 C -s simHuman_chr6.simHuman.chr6 340791 1 + 601863 T -s simRat_chr6.simRat.chr6 349443 1 + 647215 C - -a -s simMouse_chr6.simMouse.chr6 357519 4 + 636262 TTTC -s Anc0.Anc0refChr0 19586 4 + 26507 TTTT -s Anc1.Anc1refChr6 20325 4 + 197743 TTTT -s Anc2.Anc2refChr17 13218 4 + 28526 TTTT -s mr.mrrefChr5 205037 4 + 294540 TTTC -s simCow_chr6.simCow.chr6 328914 4 + 602619 TCCC -s simDog_chr6.simDog.chr6 320905 4 + 593897 TTTT -s simHuman_chr6.simHuman.chr6 340811 4 + 601863 TTTT -s simRat_chr6.simRat.chr6 349457 4 + 647215 TTTC - -a -s simMouse_chr6.simMouse.chr6 357523 26 + 636262 AAAAAACTGCATCTCCTGTATGATAT -s Anc0.Anc0refChr0 19590 26 + 26507 TGAGGATGATGTCCCTTGTTTGTTTC -s Anc1.Anc1refChr6 20329 26 + 197743 TGAGGATGATGTCCCTTGTTTGTTTC -s Anc2.Anc2refChr17 13222 26 + 28526 TGAGGATGATGTCCCTTGTTTGCCTC -s mr.mrrefChr5 205041 26 + 294540 AAAAGATTGCATCTCCTGTATGTTAT -s simCow_chr6.simCow.chr6 328918 22 + 602619 TGGGGATGACTGCTATTGT----CTC -s simDog_chr6.simDog.chr6 320913 26 + 593897 TGAGGATGATGTCCCCTGTTTGCCTC -s simHuman_chr6.simHuman.chr6 340815 26 + 601863 TGAGGATAATGTCCCTTGTTTGTTTC -s simRat_chr6.simRat.chr6 349461 26 + 647215 AAATGATTGCATCTCCTATATGTTAT - -a -s simMouse_chr6.simMouse.chr6 357549 77 + 636262 TTACAAAGCTATGTGCAGTGGTAAGTCTGCACAGCTTTATAGACATGTGGTTTATAGAGGAATATAGAGGAAACCTA -s Anc0.Anc0refChr0 19619 66 + 26507 TTACAAATCTATGTGCAGTGCTAAGTCTGCACAGCTTTGTAGGCTTGCAATTTACAAAGT-A----------ACCTT -s Anc1.Anc1refChr6 20358 66 + 197743 TTACAAATCTATGTGCAGTGCTAAGTCTGCACAGCTTTGTAGGCTTGCAATTTACAAAGT-A----------ACCTT -s Anc2.Anc2refChr17 13252 66 + 28526 TTACAAATCGATGTGCAGTGCTAAGTCTGTACAGCTTTGTATGCTTACAATTCACAAAGT-A----------ACCTT -s mr.mrrefChr5 205067 67 + 294540 TTACAAAGCTATGTGCAGTGGTAAGTCTGCACAGCTTTATAGGCATGCAGTTTATAGAGGAA----------ACCTA -s simCow_chr6.simCow.chr6 328944 66 + 602619 TTACAGATTGACGTGCAGTGCTAAGTTTGTACAGTTTTATATGCTTACTATTCACAGAGT-A----------AACTT -s simDog_chr6.simDog.chr6 320943 66 + 593897 TTACAAATCGATGTGCAGTACTAAGTCTGTACAGCTTTGTATGTTTATAATTCACAAAGT-A----------ACCCT -s simHuman_chr6.simHuman.chr6 340844 59 + 601863 TTACTAATCTATGTGTGGCGCTAAGTCTGCACAGCATTCTAGGCTTGCAATTT--------T----------GCCTT -s simRat_chr6.simRat.chr6 349487 67 + 647215 TTACAAAGCTATGTGCAGTGGTCAGTCTGCACAGCTTTATAGGCATGCAGTTGATAGAGGAA----------ACCTA - -a -s simMouse_chr6.simMouse.chr6 357626 7 + 636262 TGATATA -s Anc0.Anc0refChr0 19685 7 + 26507 TAGCATA -s Anc1.Anc1refChr6 20424 7 + 197743 TAGCATA -s Anc2.Anc2refChr17 13318 7 + 28526 TAGCATA -s mr.mrrefChr5 205134 7 + 294540 TGATATA -s simCow_chr6.simCow.chr6 329025 7 + 602619 TAAGATA -s simDog_chr6.simDog.chr6 321009 7 + 593897 ATGCATG -s simHuman_chr6.simHuman.chr6 340903 7 + 601863 TAGCATA -s simRat_chr6.simRat.chr6 349554 7 + 647215 TGATATA - -a -s simMouse_chr6.simMouse.chr6 357633 58 + 636262 ACCTGCAAAGCTTCATTGTAAAGCTACAGCTAGTTAAGCTTGTTTTGATACTCTTGTC -s Anc0.Anc0refChr0 19694 58 + 26507 ACCCGCAGAGATTCATTGTAAAGCTTCAGCTAGTTGACTTTGGGTTGATACTTTTGTC -s Anc1.Anc1refChr6 20433 58 + 197743 ACCCGCAGAGATTCATTGTAAAGCTTCAGCTAGTTGACTTTGGGTTGATACTTTTGTC -s Anc2.Anc2refChr17 13327 58 + 28526 ACCCGCAGAGATTCATTGCAAAGCTTCAGCTAGTTGACTTTGGGTCGATACTTTTAAC -s mr.mrrefChr5 205141 58 + 294540 ACCTGCAAAGCTTCATTGTAAAGCTACAGCTAGTTAACCTTGTTTTGATACTCTTGTC -s simCow_chr6.simCow.chr6 329038 58 + 602619 ACCTGCTAAGATTGATTGAAAAGCTCCAGCTAGTTGACTTTGGGTCGATACTTTTAAC -s simDog_chr6.simDog.chr6 321018 37 + 593897 ACTCGCAGAGATTCATTGCAAAGTTTAAGCTAGTTGA--------------------- -s simHuman_chr6.simHuman.chr6 340912 58 + 601863 ACCCGCATAGATCCATTGTTAGGCTTCAGCTAGTTGACTCTGGGTTGATACTTTTGTC -s simRat_chr6.simRat.chr6 349561 58 + 647215 ACCTGCAAAGCTTCATTGTAAAGCTCCAGCTAGTTAGCCTTGTATTGATACTCTTGTC - -a -s simMouse_chr6.simMouse.chr6 357691 28 + 636262 TAGAGTTAGTCTTTGATACCTAGTTAAA -s Anc0.Anc0refChr0 19752 25 + 26507 TA---TTATAGTTTGACACCTAGCTAAG -s Anc1.Anc1refChr6 20491 28 + 197743 TAGAGTTATAGTTTGACACCTAGCTAAG -s Anc2.Anc2refChr17 13385 25 + 28526 CA---CGATAGTTTGACACCTAACTAAG -s mr.mrrefChr5 205199 28 + 294540 TAGAGTTATTGTTTGATACCTAGTTAAA -s simCow_chr6.simCow.chr6 329096 25 + 602619 CA---CGATAGTTTGACACCTAACCGAG -s simDog_chr6.simDog.chr6 321055 9 + 593897 -------------------CTAACTAAG -s simHuman_chr6.simHuman.chr6 340971 28 + 601863 TAGAGTTGTGGCTTGACACCTGGCTAAG -s simRat_chr6.simRat.chr6 349619 28 + 647215 TAGAGTTATTGTTTCATACCTAATTAAA - -a -s simMouse_chr6.simMouse.chr6 357719 20 + 636262 CAAAAAACGGAGTAGTGTAT -s Anc0.Anc0refChr0 19786 20 + 26507 CAGACAAGCCAGTGATAAGT -s Anc1.Anc1refChr6 20528 20 + 197743 CAGACAAGCCAGTGATAAGT -s Anc2.Anc2refChr17 13419 20 + 28526 CAGACAGGCCAGTGACAAGT -s mr.mrrefChr5 205227 20 + 294540 CAAAAAACGGAGTAATGTAT -s simCow_chr6.simCow.chr6 329130 20 + 602619 CAGATAGGCAAGTGACAGGT -s simDog_chr6.simDog.chr6 321073 19 + 593897 TAGACAGG-CAGTGACGAGT -s simHuman_chr6.simHuman.chr6 341008 20 + 601863 CAGAGAAGCCAGTGATAAGT -s simRat_chr6.simRat.chr6 349647 20 + 647215 TGAAAAACAGAGTCATGTAT - -a -s simMouse_chr6.simMouse.chr6 357739 26 + 636262 TACTCTGCAGATGTTTACTTGAGGTC -s Anc0.Anc0refChr0 19807 26 + 26507 TACTCTGCAGTTGTTTACTTGAGGTC -s Anc1.Anc1refChr6 20549 26 + 197743 TACTCTGCAGTTGTTTACTTGAGGTC -s Anc2.Anc2refChr17 13440 26 + 28526 TCCTCTGCAGTTGTTTACTTGAGGTC -s mr.mrrefChr5 205248 26 + 294540 TACTCTGCAGATGTTTACTTGAGGTC -s simCow_chr6.simCow.chr6 329151 26 + 602619 TCCTCTGCCATTTTTTTCTAGAGGTC -s simDog_chr6.simDog.chr6 321093 26 + 593897 TCCTATGCAGTTGTTTACTTGAGGTT -s simHuman_chr6.simHuman.chr6 341029 26 + 601863 TACTCTGGGGTAGTTTACTTAAGGTC -s simRat_chr6.simRat.chr6 349668 26 + 647215 TACTTTGCAGATGTTTACTTGAGGTC - -a -s simMouse_chr6.simMouse.chr6 357765 12 + 636262 TTTGTTTGTGGA -s Anc0.Anc0refChr0 19833 12 + 26507 TTTGATTTTGGA -s Anc1.Anc1refChr6 20575 12 + 197743 TTTGATTTTGGA -s Anc2.Anc2refChr17 13466 12 + 28526 TTTGATTTTGGA -s mr.mrrefChr5 205274 12 + 294540 TTTGTTTGTGGA -s simCow_chr6.simCow.chr6 329177 12 + 602619 TTTAATCTTAGA -s simDog_chr6.simDog.chr6 321119 12 + 593897 TTTGATTTTGGA -s simHuman_chr6.simHuman.chr6 341056 12 + 601863 TTTGATTTTGAA -s simRat_chr6.simRat.chr6 349694 12 + 647215 TTTGTTTGCAGA - -a -s simMouse_chr6.simMouse.chr6 357777 19 + 636262 GCAGATCTCATAGACAGAA -s Anc0.Anc0refChr0 19845 19 + 26507 ACATTCCTCATAGACCAAC -s Anc1.Anc1refChr6 20587 19 + 197743 ACATTCCTCATAGACCAAC -s Anc2.Anc2refChr17 13478 19 + 28526 GCATTCCTCATAGACCAAC -s mr.mrrefChr5 205286 19 + 294540 ACAGTTCTCATAGACAAAA -s simCow_chr6.simCow.chr6 329190 19 + 602619 GCATTCCTCAGAGGCATCC -s simDog_chr6.simDog.chr6 321131 19 + 593897 GCATTCCTCATAGACCAAC -s simHuman_chr6.simHuman.chr6 341075 19 + 601863 ACAATCCTCATAGACCAAC -s simRat_chr6.simRat.chr6 349706 19 + 647215 ACAGTTCTCATAGACAAAA - -a -s simMouse_chr6.simMouse.chr6 357796 35 + 636262 TGTCATTTCTTGTTGAAGATAGTAGTACAAGAATC -s Anc0.Anc0refChr0 19866 35 + 26507 TGCCATTTATTGATGAAGATAGAAATAAGAAAATC -s Anc1.Anc1refChr6 20608 35 + 197743 TGCCATTTATTGATGAAGATAGAAATAAGAAAATC -s Anc2.Anc2refChr17 13499 35 + 28526 TGCCATTTGTTGATGAAAATAGAAATAAGAAAATC -s mr.mrrefChr5 205307 35 + 294540 TGTCATTTATTGTTGAAGATAGTAGTACAAGAATC -s simCow_chr6.simCow.chr6 329211 32 + 602619 TT---TGTGTTGATGAAAATAGAGGTACGATACTC -s simDog_chr6.simDog.chr6 321152 35 + 593897 TGCCATTTGTTGATGAAAATAGAAATAAGAAAATC -s simHuman_chr6.simHuman.chr6 341096 35 + 601863 TGCCGTTTATTGATGAAGATAGAACTAAGGAAATC -s simRat_chr6.simRat.chr6 349727 34 + 647215 GGTCACTTATTAT-GAAAATAGTAATACAAGAATT - -a -s simMouse_chr6.simMouse.chr6 357831 23 + 636262 CATTCTCAATTTATCCCCTATGC -s Anc0.Anc0refChr0 19969 21 + 26507 TATTGTTAATTTATCTCCTC--C -s Anc1.Anc1refChr6 20711 21 + 197743 TATTGTTAATTTATCTCCTC--C -s Anc2.Anc2refChr17 13602 21 + 28526 TATTGTTAATTTATCTCCCC--C -s mr.mrrefChr5 205342 23 + 294540 CATTCTCAATTTATCCCCTATGC -s simCow_chr6.simCow.chr6 329311 21 + 602619 CATCATTAATTTACCTCCCC--C -s simDog_chr6.simDog.chr6 321252 21 + 593897 TATTGGCAGATTATCTCGCC--T -s simHuman_chr6.simHuman.chr6 341199 21 + 601863 TATTGTTAATATATCTCCTC--C -s simRat_chr6.simRat.chr6 349761 23 + 647215 CATTCTCCATCTATCCCCTATGC - -a -s simMouse_chr6.simMouse.chr6 357854 10 + 636262 ATCATTTGTC -s Anc0.Anc0refChr0 19990 10 + 26507 CCCATCTTTC -s Anc1.Anc1refChr6 20732 10 + 197743 CCCATCTTTC -s Anc2.Anc2refChr17 13623 10 + 28526 CCCATCTTTA -s mr.mrrefChr5 205365 10 + 294540 ATCATTTGTC -s simCow_chr6.simCow.chr6 329338 10 + 602619 CTCATCTTTT -s simDog_chr6.simDog.chr6 321273 10 + 593897 CCCATCTTTA -s simHuman_chr6.simHuman.chr6 341220 10 + 601863 CCCACCTTTC -s simRat_chr6.simRat.chr6 349784 10 + 647215 ATTATTTATC - -a -s simMouse_chr6.simMouse.chr6 357864 38 + 636262 TTTCTTTGTTCTCATGCCAAAGTGCCCTGGGTGTGGTC -s Anc0.Anc0refChr0 20000 38 + 26507 TTTCTTGACATTCAGGCCAAAGTGTCTTCAGCTTGGTC -s Anc1.Anc1refChr6 20742 38 + 197743 TTTCTTGACATTCAGGCCAAAGTGTCTTCAGCTTGGTC -s Anc2.Anc2refChr17 13633 38 + 28526 TTTCTTGACATTCAGACCAAAGTGTTTTCAGCTTGGTC -s mr.mrrefChr5 205375 38 + 294540 TTTCTTTGTTCTCATGCCAAAGTGCCCTGGGTGTGGTC -s simCow_chr6.simCow.chr6 329348 38 + 602619 GTTCTTGACATCCAGACCAGAGTGTTCTCAGCTTGGTC -s simDog_chr6.simDog.chr6 321283 38 + 593897 TTTCTCCACTTTCAGACCAAAGTGCTTTCAGCCTGGTC -s simHuman_chr6.simHuman.chr6 341230 38 + 601863 TTTCTTGAGAATTGGGTCAAAAAGTCTTCAGCTTGGTC -s simRat_chr6.simRat.chr6 349817 38 + 647215 TTCCTCCGTTCTCGTGCCAAAGTGCCCTGGGCTTGGAC - -a -s simMouse_chr6.simMouse.chr6 357902 2 + 636262 CG -s Anc0.Anc0refChr0 20038 2 + 26507 CA -s Anc1.Anc1refChr6 20780 2 + 197743 CA -s Anc2.Anc2refChr17 13671 2 + 28526 TA -s mr.mrrefChr5 205413 2 + 294540 CG -s simCow_chr6.simCow.chr6 329386 2 + 602619 TA -s simDog_chr6.simDog.chr6 321321 2 + 593897 TG -s simHuman_chr6.simHuman.chr6 341558 2 + 601863 CA -s simRat_chr6.simRat.chr6 349855 2 + 647215 CA - -a -s simMouse_chr6.simMouse.chr6 357904 13 + 636262 TTTATAGTTTAAC -s Anc0.Anc0refChr0 20040 11 + 26507 TTCTT--TTTAAC -s Anc1.Anc1refChr6 20782 13 + 197743 TTCTTAATTTAAC -s Anc2.Anc2refChr17 14089 11 + 28526 TTCTT--TTTATT -s mr.mrrefChr5 205415 13 + 294540 TTTATAGTTTAAC -s simCow_chr6.simCow.chr6 329826 11 + 602619 TTCTA--TTTATG -s simDog_chr6.simDog.chr6 321759 11 + 593897 TTCTT--GTGACT -s simHuman_chr6.simHuman.chr6 341560 13 + 601863 TTCTTAATTTGAC -s simRat_chr6.simRat.chr6 349857 13 + 647215 TCTATAATCTAAC - -a -s simMouse_chr6.simMouse.chr6 357917 2 + 636262 TT -s Anc0.Anc0refChr0 20051 2 + 26507 TT -s Anc1.Anc1refChr6 20795 2 + 197743 TT -s Anc2.Anc2refChr17 14100 2 + 28526 AT -s mr.mrrefChr5 205428 2 + 294540 TT -s simCow_chr6.simCow.chr6 329837 2 + 602619 AT -s simDog_chr6.simDog.chr6 321770 2 + 593897 AA -s simHuman_chr6.simHuman.chr6 341573 2 + 601863 AT -s simRat_chr6.simRat.chr6 349880 2 + 647215 TT - -a -s simMouse_chr6.simMouse.chr6 357919 3 + 636262 CAC -s Anc0.Anc0refChr0 20053 3 + 26507 CAC -s Anc1.Anc1refChr6 20797 3 + 197743 CAC -s Anc2.Anc2refChr17 14102 3 + 28526 CAC -s mr.mrrefChr5 205430 3 + 294540 CAC -s simCow_chr6.simCow.chr6 329839 3 + 602619 CAC -s simDog_chr6.simDog.chr6 321777 3 + 593897 CTG -s simHuman_chr6.simHuman.chr6 341575 3 + 601863 AAC -s simRat_chr6.simRat.chr6 349882 3 + 647215 CAC - -a -s simMouse_chr6.simMouse.chr6 357922 2 + 636262 AA -s Anc1.Anc1refChr6 23049 2 + 197743 aa -s mr.mrrefChr5 205433 2 + 294540 AA -s simHuman_chr6.simHuman.chr6 344723 2 + 601863 aa -s simRat_chr6.simRat.chr6 349885 2 + 647215 AA - -a -s simMouse_chr6.simMouse.chr6 357924 20 + 636262 TTCCAACCAATGAGTACCAC -s Anc0.Anc0refChr0 22305 18 + 26507 taccagccaatgg--tccac -s Anc1.Anc1refChr6 23051 20 + 197743 taccagccaatggattccac -s Anc2.Anc2refChr17 16965 18 + 28526 TCCCTCCCAGTAG--CCCAT -s mr.mrrefChr5 205435 20 + 294540 TTCCAACCAATGAGTACCAC -s simCow_chr6.simCow.chr6 332703 18 + 602619 TCCCTCCCAGTAG--TGCAT -s simDog_chr6.simDog.chr6 324993 18 + 593897 TCCCTCCCAGTAG--CCCAT -s simHuman_chr6.simHuman.chr6 344727 20 + 601863 taccagccaatggattccac -s simRat_chr6.simRat.chr6 349887 20 + 647215 TTCTTACCAATCAGTACCAC - -a -s simMouse_chr6.simMouse.chr6 357944 4 + 636262 ATTT -s Anc0.Anc0refChr0 22323 1 + 26507 A--- -s Anc1.Anc1refChr6 23071 1 + 197743 A--- -s Anc2.Anc2refChr17 16983 1 + 28526 A--- -s mr.mrrefChr5 205455 1 + 294540 A--- -s simCow_chr6.simCow.chr6 332721 1 + 602619 A--- -s simDog_chr6.simDog.chr6 325011 1 + 593897 A--- -s simHuman_chr6.simHuman.chr6 346090 1 + 601863 A--- -s simRat_chr6.simRat.chr6 349907 1 + 647215 A--- - -a -s simMouse_chr6.simMouse.chr6 357948 148 + 636262 ACATGAAACTCTCTAATCTTTAAAGGCTAACATTCTATTGCAACCTAGTACGGCTCCAACAGGATTATTTCCATTATTGTAACAGTCCAAGGAAAGGATGGTGAGAAGAATAAGATGACCAGGGGGTCACGGGCTCTGTTTCAAAATT -s Anc0.Anc0refChr0 22324 23 + 26507 ACATAAACCTATGAACTCT----AGGT------------------------------------------------------------------------------------------------------------------------- -s Anc1.Anc1refChr6 23072 23 + 197743 ACATAAACCTATGAACTCT----AGGT------------------------------------------------------------------------------------------------------------------------- -s Anc2.Anc2refChr17 16990 23 + 28526 ACATCAACCTATGCTCTCC----GGGT------------------------------------------------------------------------------------------------------------------------- -s mr.mrrefChr5 205456 148 + 294540 ACATGAAACTCTCTAATCTTTAAAGGCTAACATTCTATTGCAACCTAGTACGGCTCCAACAGGATTATTTCCATTATTGTAACAGTCCAAGGAAAGGATGGTGAGAAGAATAAGATGACCAGGGGGTCACGGGCTCTGTTTCAAAATT -s simCow_chr6.simCow.chr6 332728 23 + 602619 ACAACAGCCAATGTTCTCC----TGGT------------------------------------------------------------------------------------------------------------------------- -s simDog_chr6.simDog.chr6 325018 23 + 593897 ACATCAACCTATGCTCTCC----GGGT------------------------------------------------------------------------------------------------------------------------- -s simHuman_chr6.simHuman.chr6 346091 23 + 601863 ACATAAACCTATGAACTCT----AGGT------------------------------------------------------------------------------------------------------------------------- -s simRat_chr6.simRat.chr6 349908 148 + 647215 GCATGAAACCCTTTAGTCTTTAAAGGCCAACATTATATTGAAACTTATTAAGGCTCGAAAAGGATTCTTTCCATCATTGTTACATTCCAAGGAGAGAGAGATGAGAAGGTTAAGGTGACCAGCGGGTCACAGGCTCAGTTTCAAAGTT - -a -s simMouse_chr6.simMouse.chr6 358096 123 + 636262 AGCCCTCCTAGCAGACTGGTTTATCTCTGAACTCAATGCATCCCAGTGGAGTCCTAGTTGGTAGCGACAAGATTTGCAGAGAGGGTCAGAGGAATCAGTAGGGAATCTTTATTGAAATAGGCA -s mr.mrrefChr5 205604 123 + 294540 AGCCCTCCTAGCAGACTGGTTTATCTCTGAACTCAATGCATCCCAGTGGAGTCCTAGTTGGTAGTGACAGGATTTGCAGAGAGAGTCAGAGGCATCAGTAGGGAATTTTTATTGAAATAGGCA -s simRat_chr6.simRat.chr6 350073 123 + 647215 AGCCCCCTTGGCAGGCTGGTAGATCTCTGAGCTCAATGCATCCCAGTGGAGTCCTAGTTGGTAGTAACAGGATTTGCAGAGAGAGTCAGAGGCATCAGTAGGGAATTTTTATTGAAATAGGCA - -a -s simMouse_chr6.simMouse.chr6 358219 128 + 636262 CGTCTTGTTTTATGCACTGATGTAATTATTTAGATCATCATGCAGTTATATACTTAATTTGAGCTTAAGATCAGAACAGGGTGACCGTATGATGGTGCTTCATGACAACTATCTCTTTATTATCATTA -s mr.mrrefChr5 205728 110 + 294540 TGTCTTGTTTTATGCACTGATGTAATTATTTAGATCA------------------AATTTGAGCTTAAGATCAGAACAGGGTGACCGTATGATGGTGCTTCATGACAACTATCTCTTTATTATCATTA -s simRat_chr6.simRat.chr6 350197 110 + 647215 TGTCTTGTTTTATGCCCTGGTGTATTCATTTAGATCA------------------AATTTGAGATTAAGATCAGAACAGAGTGACTATATGGTAATGCATCATGACAACTATCTCTTTATTATCACTG - -a -s simMouse_chr6.simMouse.chr6 358347 130 + 636262 GCAGCTCTTAGAGTGACTTCACTTTGGCTCCTGAGGGGATGAGCATGCAATCAGGGATCACTTCTTTGTTTCACCATTAATTCCCTTTCATTTCTTGGATTGCAATTAGTTAATGCCATTTTTTCACCTC -s mr.mrrefChr5 205838 128 + 294540 gcagctcTT-GAGTGACTTCA-TTTGGCTCCTGAGGGGATGAGCATGCAATCAGGgatcacttctttgtttcaccattaattccctttcatttcttggattgcaattagttaatgccattttttcacctc -s simRat_chr6.simRat.chr6 350497 128 + 647215 gcagcccTT-GAGTGGCTTCA-TTTGGCTCCTGGGGGGATAAGTATGCAATCAGGgcttccatctttgtttcactgttaattccctttcatttcttggattgcaattagttaatgacctcatctcacctc - -a -s simMouse_chr6.simMouse.chr6 358477 76 + 636262 CTCCTTGTGACACAAGTCTCACTATACAGACCCCTAACTTCAGTTCAATCTCAAGTGGACCTTAAGCACTTCAGTC -s mr.mrrefChr5 205966 65 + 294540 ctccttgtgacacaagtctcactatacagacccctaacttcagttcaatctcaagtg-----------cttcagtc -s simRat_chr6.simRat.chr6 350626 65 + 647215 ctccttgtaacactatactcactacatagacccctgacttcatatcaatctcaagtt-----------ctttggtc - -a -s simMouse_chr6.simMouse.chr6 358553 198 + 636262 CATTCTTCAAGGCACTTATGTTCTTAACTTCTTCTGTGCTTGTGCCTTATCTGCCTGTCAGTTTAGTTTCATGTGATGGAGGAACAAGTTCCGGTACGTCAGAATTTGCACCTTGTCACTAGGTCCTCAGAGGCAGGATCCTAGCTACACGTGAACCCCAAGGGTGCATGTTTAATTGGTACCCCATTGACTCAACCT -s mr.mrrefChr5 206031 178 + 294540 cattcttcaaggcacttatgttcttaacttcttctgtgcttgtgccttatctgcctgtcagtttagtttcatgtgatggaggaacaagttccggt---------------ccttgtcactaggt-----gaggcaggatcctagctacacgtgaaccccaagggtgcatgtttaattggtaccccattgactcaacct -s simRat_chr6.simRat.chr6 350693 178 + 647215 caatcttcaaggcacttatgtatttaactacttctgtccttgtgcgttatctgactgttagcttagttccaggtgatgggggaaaaaattacagt---------------tctggtcaatcagc-----aaggtagcatcctacccacacgtgaaccccatgggtgtgtttttaattggcatcccactgttacaactt - -a -s simMouse_chr6.simMouse.chr6 358751 6 + 636262 GTTATT -s mr.mrrefChr5 206209 6 + 294540 gttatt -s simRat_chr6.simRat.chr6 350872 6 + 647215 gtcacc - -a -s simMouse_chr6.simMouse.chr6 358757 62 + 636262 GGTACCATGTCAAGGCCAGCCTACCACACACATATTTCGTTGTCTCTACCAGCTGCCTGCAC -s mr.mrrefChr5 206215 61 + 294540 ggtaccatgtcaaggccagcctaccacacacatatttcgttgtctct-ccagctgcctgcac -s simRat_chr6.simRat.chr6 350879 61 + 647215 agtactatgttaaggtcagcctaccacccacatatttcgttgtctct-ccagctgtctgccc - -a -s simMouse_chr6.simMouse.chr6 358819 179 + 636262 TCTATGAGAAGGCCCTTAAAGCTCATGTATTCGTTTAGATACATGCATCCTGCTCATTCAGCCTGAATCCTCATTCTAGTGCCGTTGTCACCATTACTACCGATGTATATATTGTGGTcccttgtagtggcttgataacctttatgatgggaggtgctgtgaagtgtgcatgtacagca -s mr.mrrefChr5 206276 178 + 294540 tctatgagaaggcccttaaagctcatgtattcgTTTAGATACATGCATC-TGCTCATTCAGCCTGAATCCTCATTCTAGTGCCGTTGTCACCATTACTACCGATGTATAtattgtggtcccttgtagtggcttgataacctttatgatgggaggtgctgtgaagtgtgcatgtacagca -s simRat_chr6.simRat.chr6 350942 178 + 647215 tctgtataaaggcccttaaagcccatgtattcaTTTAGATATGTACATC-TGCTGATTCTGCTTGAATCCTCATCCTAGCTCCATTGTCACCATTGCTACTGCTGTATAcattgtaagcccttgcaatgccttgataacctttatagtaggaggtgctgtggagtgtgcatgtatagca - -a -s simMouse_chr6.simMouse.chr6 358998 154 + 636262 aaccatctgtacctcgcactgtctatctcatgtgaggttgtggtcagaccaagccctactgttacattgcaggagcagtgatgccacactcacactgtgtaacttgtgattatcaaattctttccattcccattaattcattatgactatagcc -s mr.mrrefChr5 206454 136 + 294540 aaccatctgtacctcgcactgtctatctcatgtgag------------------cctactgttacattgcaggagcagtgatgccacactcacactgtgtaacttgtgattatcaaattctttccattcccattaattcattatgactatagcc -s simRat_chr6.simRat.chr6 351121 136 + 647215 gaccatctgtacctcccactgtctatctcatatgag------------------cctattgttacattgcaggcagagtgatgccatactcacactgtatgacttgtgattatcaaattcgttccatttgcattaattcatcatgaatatagct - -a -s simMouse_chr6.simMouse.chr6 359152 98 + 636262 gaaagtcagtaccaattacaatatctgtagtcgaATCCCTGTAAGCAAATCCAGCCCTTTTAGGGTAGCTAGGGATTCCAGGCCATTCATTTTCAATA -s mr.mrrefChr5 206590 87 + 294540 gaaagtcagtaccaat----------gtagtcgaatcc-tgtaagcaaatccagcccTTTTAGGGTAGCTAGGGATTCCAGGCCATTCATTTTCAATA -s simRat_chr6.simRat.chr6 351258 87 + 647215 gaaggtcaatactaat----------gtaatcgagtcc-tgtaatcaaatccaccccTTTTAGGGTAGCTAGGGATTCCAGGCCCTTCATTTTCAATG - -a -s simMouse_chr6.simMouse.chr6 359250 84 + 636262 ATTACATTTATATTCTTCCAGTTCAGTTAAGAAGAGTGTGCCTGACTGATATGAGTAcatccatgcagagtaggtcatatcaga -s mr.mrrefChr5 206677 84 + 294540 ATTACATTTATATTCTTCCAGTTCAGTTAAGAAGAGTGTGCCTGACTGATATGAGTAcatccatgcagagtaggtcatatcaga -s simRat_chr6.simRat.chr6 351346 84 + 647215 ATTACATATATGTTCTTCCAGTTCAGTTAAGAAGAGTGCAACTGGCTGATGTGAGGCCACCCATGCAATGTGGGTCATAACAGA - -a -s simMouse_chr6.simMouse.chr6 359334 134 + 636262 catctgtttgtgtgctataaatttttttggtattgtgtgtcagatatattagggtcggggacctagtgaagtccttgtggttggggcaaacatgtgtgttAATTGTAGATACTTGTGCAGGGAAGATCAAGTGC -s mr.mrrefChr5 206761 112 + 294540 catctgtttgtgtgctataaatttttttggtattgtgtg----------------------cctagtgaagtccttgtggttggggcaaacatgtgtgttAATTGTAGATACTTGTGCAGGGAAGATCAAGTGC -s simRat_chr6.simRat.chr6 351433 112 + 647215 CAGCTGTTTGGGTGTTATGAATTTATTCGGTATGGTTTG----------------------CCTAGCAAAGTGCTTGTGGTTGTGGCAAACTTGTGTGTTCATTGTAGATACTGGTGCGGGGGAGATCAAGTGC - -a -s simMouse_chr6.simMouse.chr6 359468 10 + 636262 TAAGTATTTA -s mr.mrrefChr5 206873 10 + 294540 TAAGTATTTA -s simRat_chr6.simRat.chr6 351546 10 + 647215 TAAGTATTAA - -a -s simMouse_chr6.simMouse.chr6 359478 118 + 636262 TAACTGGCTGAGTCCCCACTCACAATTATAATTGTAATGTGAGCATGAGCCAAGACCTGATTGACTGACAGAATCCCCAAATCTGCATAGAGCTAAGACCTGATTGAGAGATTTACCa -s mr.mrrefChr5 206883 114 + 294540 TAACTGGCTGAGTCCCCACTCACAATTATAATTGTAATGTGAGCATGAGCCAAGACCTGAT----TGACAGAATCCCCAAATCTGCATAGagctaagacctgattgagagatttacca -s simRat_chr6.simRat.chr6 351557 114 + 647215 TAACTAGCTGCGTCCCCACTCTCAATTGTAATTATAATGTGAGCACAAGCCAAGACTTGAT----TAGCAGAATCACCAAATCAGCAAGGagccaggatttgattgacagacttacta - -a -s simMouse_chr6.simMouse.chr6 359596 11 + 636262 caggatgtatg -s Anc0.Anc0refChr0 20996 2 + 26507 ---------tg -s Anc1.Anc1refChr6 21740 2 + 197743 ---------tg -s Anc2.Anc2refChr17 15523 2 + 28526 ---------tg -s mr.mrrefChr5 206997 11 + 294540 caggatgtatg -s simCow_chr6.simCow.chr6 331565 2 + 602619 ---------tg -s simDog_chr6.simDog.chr6 323639 2 + 593897 ---------tg -s simRat_chr6.simRat.chr6 351695 11 + 647215 cagagtgtatg - -a -s simMouse_chr6.simMouse.chr6 359607 32 + 636262 gttcatagtaccagtaccaaaggtggagatag -s Anc0.Anc0refChr0 20998 32 + 26507 attcatattaccagtatagtaggtggggatag -s Anc1.Anc1refChr6 21742 32 + 197743 attcatattaccagtatagtaggtggggatag -s Anc2.Anc2refChr17 15525 32 + 28526 attcatattaccagtatagtaggtggggatag -s mr.mrrefChr5 207008 32 + 294540 gttcatagtaccagtaccaaaggtggagatag -s simCow_chr6.simCow.chr6 331569 32 + 602619 attcatatcactagtaaaggaattggggctaa -s simDog_chr6.simDog.chr6 323641 32 + 593897 attcatattaccagtatagtaggtggggatag -s simRat_chr6.simRat.chr6 351706 32 + 647215 attcatattaccagtatagaaggtggtgataa - -a -s simMouse_chr6.simMouse.chr6 359639 3 + 636262 atc -s Anc0.Anc0refChr0 21030 3 + 26507 acg -s Anc1.Anc1refChr6 21774 3 + 197743 acg -s Anc2.Anc2refChr17 15561 3 + 28526 acg -s mr.mrrefChr5 207040 3 + 294540 atc -s simCow_chr6.simCow.chr6 331605 3 + 602619 aag -s simDog_chr6.simDog.chr6 323678 3 + 593897 acg -s simRat_chr6.simRat.chr6 351738 3 + 647215 ctc - -a -s simMouse_chr6.simMouse.chr6 359642 59 + 636262 tgtttttcctgtgctgcaggggatgaaagtgtgaggctttcataagtttcattgcccca -s Anc0.Anc0refChr0 21033 52 + 26507 cgtgaccactggagtgcaggataagagagt-------cttcacatgtcccattgcccca -s Anc1.Anc1refChr6 21777 52 + 197743 cgtgaccactggagtgcaggataagagagt-------cttcacatgtcccattgcccca -s Anc2.Anc2refChr17 15564 52 + 28526 cgtgaccactggagtgcaggataagagagt-------cttcacatgtcccattgcccca -s mr.mrrefChr5 207043 59 + 294540 tgtttttcctgtgctgcaggggatgaaagtgtgaggctttcataagtttcattgcccca -s simCow_chr6.simCow.chr6 331608 22 + 602619 tgtgattgctgatgctgaggat------------------------------------- -s simDog_chr6.simDog.chr6 323681 52 + 593897 cgtgaccactggagtgcaggataagagagt-------cttcacatgtcccattgcccca -s simRat_chr6.simRat.chr6 351742 59 + 647215 tgtttttgctgtgctggaggggatgaaggtgataggccttcatatgtttcattactcaa - -a -s simMouse_chr6.simMouse.chr6 359701 20 + 636262 gTGCACAGTTGGTGCCAAAT -s Anc0.Anc0refChr0 21085 20 + 26507 gtgcacagccagcatgtagt -s Anc1.Anc1refChr6 21829 20 + 197743 gtgcacagccagcatgtagt -s Anc2.Anc2refChr17 15631 20 + 28526 gtgcacagccagcatgtagt -s mr.mrrefChr5 207102 20 + 294540 gTGCACAGTTGGTGCCAAAT -s simCow_chr6.simCow.chr6 331640 20 + 602619 gtgcacagctaatgtgtagt -s simDog_chr6.simDog.chr6 323747 11 + 593897 ---------ctgcatgaagt -s simRat_chr6.simRat.chr6 351801 20 + 647215 gTGCACAGTCAGTGCCAAAT - -a -s simMouse_chr6.simMouse.chr6 359721 10 + 636262 TAACCCTAGA -s Anc0.Anc0refChr0 21105 10 + 26507 tacccctggc -s Anc1.Anc1refChr6 21849 10 + 197743 tacccctggc -s Anc2.Anc2refChr17 15654 10 + 28526 tacccctggc -s mr.mrrefChr5 207122 10 + 294540 TAACCCTAGA -s simCow_chr6.simCow.chr6 331663 9 + 602619 tacctctgg- -s simDog_chr6.simDog.chr6 323761 10 + 593897 tacccctggc -s simRat_chr6.simRat.chr6 351821 10 + 647215 TAACCCTCGA - -a -s simMouse_chr6.simMouse.chr6 359731 11 + 636262 AGCTAAGGCCT -s Anc0.Anc0refChr0 21115 11 + 26507 cacttgagcct -s Anc1.Anc1refChr6 21859 11 + 197743 cacttgagcct -s Anc2.Anc2refChr17 15664 11 + 28526 cacttgagcct -s mr.mrrefChr5 207132 11 + 294540 AGCTAAGGCCT -s simCow_chr6.simCow.chr6 331672 5 + 602619 ------agcct -s simDog_chr6.simDog.chr6 323799 11 + 593897 cacttgaacct -s simRat_chr6.simRat.chr6 351831 11 + 647215 GGCTAAGGCCT - -a -s simMouse_chr6.simMouse.chr6 359742 62 + 636262 ACTGCACTTGGAACATGTTGATCAGACTAGacaacccttttggggcccaggcagttgcatag -s Anc0.Anc0refChr0 21126 56 + 26507 actga---gtggacgtgagtatgaacctagaagcctttttttgg-tccatgcatttgcac-- -s Anc1.Anc1refChr6 21870 56 + 197743 actga---gtggacgtgagtatgaacctagaagcctttttttgg-tccatgcatttgcac-- -s Anc2.Anc2refChr17 15701 56 + 28526 actga---gtggacgtgagtatgaacctagaagcctttttttgg-tccatgcatttgcac-- -s mr.mrrefChr5 207143 58 + 294540 ACTGC---TGGAACATGTTGATCAGACTAGacaacccttttggg-cccaggcagttgcatag -s simCow_chr6.simCow.chr6 331683 39 + 602619 --------------------atgaacctagaagcctttttttgg-tccatgcatttgcac-- -s simDog_chr6.simDog.chr6 323836 17 + 593897 ACTGA---GTGGACGTGAGT------------------------------------------ -s simRat_chr6.simRat.chr6 351842 58 + 647215 ACTGC---TGGAACATGGTAACCAGGCTAGacaacctttttggt-cccaggcatttgcatag - -a -s simMouse_chr6.simMouse.chr6 359804 36 + 636262 gaagtgaaactgatcttacttaggtgctcctctatg -s Anc0.Anc0refChr0 21182 34 + 26507 taactgtaactgagcttgcctc--tggcactctatg -s Anc1.Anc1refChr6 21926 34 + 197743 taactgtaactgagcttgcctc--tggcactctatg -s Anc2.Anc2refChr17 15757 34 + 28526 taactgtaactgagcttgcctc--tggcactctatg -s mr.mrrefChr5 207201 36 + 294540 gaagtgaaactgatcttacttaggtgctcctctatg -s simCow_chr6.simCow.chr6 331728 34 + 602619 taactgtaactgagcttgcctc--tggcactctatg -s simRat_chr6.simRat.chr6 351900 36 + 647215 gaagtgtaaccgatcttacccaggtgctcctctatg - -a -s simMouse_chr6.simMouse.chr6 359840 21 + 636262 tacctcaattatctctgcttt -s Anc0.Anc0refChr0 21216 21 + 26507 tttctcaattgtttttgctct -s Anc1.Anc1refChr6 21960 21 + 197743 tttctcaattgtttttgctct -s Anc2.Anc2refChr17 15792 21 + 28526 tttctcaattgtttttgctct -s mr.mrrefChr5 207237 21 + 294540 tacctcaattatctctgcttt -s simCow_chr6.simCow.chr6 331842 21 + 602619 tttctcaattgtttttgctct -s simRat_chr6.simRat.chr6 351936 21 + 647215 tacctcaattatctctactct - -a -s simMouse_chr6.simMouse.chr6 359861 8 + 636262 ttcttgtt -s Anc0.Anc0refChr0 21237 8 + 26507 gcttgggt -s Anc1.Anc1refChr6 21981 8 + 197743 gcttgggt -s Anc2.Anc2refChr17 15813 8 + 28526 gcttgggt -s mr.mrrefChr5 207258 8 + 294540 ttcttgtt -s simCow_chr6.simCow.chr6 331863 8 + 602619 gcttgggt -s simRat_chr6.simRat.chr6 351958 8 + 647215 ttctggtt - -a -s simMouse_chr6.simMouse.chr6 359869 29 + 636262 gcagttttgtggacagaagtgcttgattg -s Anc0.Anc0refChr0 21245 29 + 26507 gctgtaggacagacagaattgtatatttg -s Anc1.Anc1refChr6 21989 29 + 197743 gctgtaggacagacagaattgtatatttg -s Anc2.Anc2refChr17 15822 29 + 28526 gctgtaggacagacagaattgtatatttg -s mr.mrrefChr5 207266 29 + 294540 gcagttttgtggacagaagtgcttgattg -s simCow_chr6.simCow.chr6 331872 29 + 602619 gctgtaggacagacagaattgtatatttg -s simRat_chr6.simRat.chr6 351966 29 + 647215 gtagttaggtagactgaagtgcttgttcg - -a -s simMouse_chr6.simMouse.chr6 359898 10 + 636262 gtaattgaat -s Anc0.Anc0refChr0 21274 3 + 26507 a-------at -s Anc1.Anc1refChr6 22018 3 + 197743 a-------at -s Anc2.Anc2refChr17 15851 3 + 28526 a-------at -s mr.mrrefChr5 207295 3 + 294540 g-------at -s simCow_chr6.simCow.chr6 331902 3 + 602619 a-------at -s simRat_chr6.simRat.chr6 351995 3 + 647215 g-------at - -a -s simMouse_chr6.simMouse.chr6 359908 20 + 636262 tggatgtggttgtcctggga -s Anc0.Anc0refChr0 21277 20 + 26507 tggtcatgattgtcctggga -s Anc1.Anc1refChr6 22021 20 + 197743 tggtcatgattgtcctggga -s Anc2.Anc2refChr17 15856 20 + 28526 tggtcatgattgtcctggga -s mr.mrrefChr5 207298 20 + 294540 tggatgtggttgtcctggga -s simCow_chr6.simCow.chr6 331907 18 + 602619 tggtcatgattgtcctgg-- -s simDog_chr6.simDog.chr6 323853 2 + 593897 ------------------GA -s simRat_chr6.simRat.chr6 351998 20 + 647215 tggatatggttgtcctgggg - -a -s simMouse_chr6.simMouse.chr6 359928 59 + 636262 gttgcaagatgcagtttcagaccgactccagaataaaccagtaaattgcaaccccgcct -s Anc0.Anc0refChr0 21297 8 + 26507 gtcac---------------------------------------------------tct -s Anc1.Anc1refChr6 22041 8 + 197743 gtcac---------------------------------------------------tct -s Anc2.Anc2refChr17 15877 8 + 28526 gtcac---------------------------------------------------tct -s mr.mrrefChr5 207318 57 + 294540 gttgcaagatgcagtttcagaccgactccagaataaaccagtaaatt--aaccccgcct -s simDog_chr6.simDog.chr6 323856 8 + 593897 GTCAC---------------------------------------------------TCT -s simRat_chr6.simRat.chr6 352018 57 + 647215 gttacaaaatgcagtgccagagctacttcagaacaaaccagtagatg--aaccctgcct - -a -s simMouse_chr6.simMouse.chr6 359987 6 + 636262 gtgacc -s Anc0.Anc0refChr0 21305 6 + 26507 gtgatg -s Anc1.Anc1refChr6 22049 6 + 197743 gtgatg -s Anc2.Anc2refChr17 15885 6 + 28526 gtgatg -s mr.mrrefChr5 207375 6 + 294540 gtgacc -s simDog_chr6.simDog.chr6 323871 6 + 593897 gtgatg -s simRat_chr6.simRat.chr6 352075 6 + 647215 gtgacc - -a -s simMouse_chr6.simMouse.chr6 359993 15 + 636262 tcagcccccagtcta -s Anc0.Anc0refChr0 21311 6 + 26507 tcactc--------- -s Anc1.Anc1refChr6 22055 6 + 197743 tcactc--------- -s Anc2.Anc2refChr17 15891 6 + 28526 tcactc--------- -s mr.mrrefChr5 207381 6 + 294540 tcagcc--------- -s simDog_chr6.simDog.chr6 323877 6 + 593897 tcactc--------- -s simRat_chr6.simRat.chr6 352083 6 + 647215 ccagcc--------- - -a -s simMouse_chr6.simMouse.chr6 360008 26 + 636262 taaactgaagtcacaattgattttcc -s Anc0.Anc0refChr0 21317 26 + 26507 tgtactgaagccaccttggattttcc -s Anc1.Anc1refChr6 22061 26 + 197743 tgtactgaagccaccttggattttcc -s Anc2.Anc2refChr17 15909 26 + 28526 tgtactgaagccaccttggattttcc -s mr.mrrefChr5 207387 26 + 294540 taaactgaagtcacaattgattttcc -s simCow_chr6.simCow.chr6 331932 26 + 602619 tgaacagtagccaacttggatttccc -s simDog_chr6.simDog.chr6 323895 26 + 593897 agtgctgaagccaccctggattttcc -s simRat_chr6.simRat.chr6 352089 26 + 647215 taaactgaagtcacaattgattttcc - -a -s simMouse_chr6.simMouse.chr6 360034 24 + 636262 aatgagtacaaaagggttatctcc -s Anc0.Anc0refChr0 21343 24 + 26507 attgagaacagcaggattgtctct -s Anc1.Anc1refChr6 22087 24 + 197743 attgagaacagcaggattgtctct -s Anc2.Anc2refChr17 15935 24 + 28526 attgagaacagcaggattgtctct -s mr.mrrefChr5 207413 24 + 294540 aatgagtacaaaagggttatctcc -s simCow_chr6.simCow.chr6 331960 24 + 602619 gttgggaacagcaggattgtctct -s simDog_chr6.simDog.chr6 323921 24 + 593897 attgagaacagcaggattgtctcc -s simRat_chr6.simRat.chr6 352115 24 + 647215 aatgagtacaagagggttatctcc - -a -s simMouse_chr6.simMouse.chr6 360058 50 + 636262 ctttataatggaatggtagggttgcattccagattctggcagttaatcag -s Anc0.Anc0refChr0 21367 45 + 26507 tgttgtaatga-----ttaggctacacaccagactttgacatttattggg -s Anc1.Anc1refChr6 22111 45 + 197743 tgttgtaatga-----ttaggctacacaccagactttgacatttattggg -s Anc2.Anc2refChr17 15959 45 + 28526 tgttgtaatga-----ttaggctacacaccagactttgacatttattggg -s mr.mrrefChr5 207437 50 + 294540 ctttataatggaatggtagggttgcattccagattctggcagttaatcag -s simCow_chr6.simCow.chr6 331986 44 + 602619 tgctgtaatga-----tcag-ctacataccagagttcgatgtttagtggg -s simDog_chr6.simDog.chr6 323945 45 + 593897 tgttgtaatga-----ttaggctacacaccagactttgacatttattggg -s simRat_chr6.simRat.chr6 352139 50 + 647215 ctttataatagaatcagatggttgcataccagattttgacagttgattgg - -a -s simMouse_chr6.simMouse.chr6 360108 12 + 636262 gttgtgattttt -s Anc0.Anc0refChr0 21412 12 + 26507 tttggtgttttg -s Anc1.Anc1refChr6 22156 12 + 197743 tttggtgttttg -s Anc2.Anc2refChr17 16013 12 + 28526 tttggtgttttg -s mr.mrrefChr5 207487 12 + 294540 gttgtgattttt -s simCow_chr6.simCow.chr6 332039 12 + 602619 tttggcattcgg -s simDog_chr6.simDog.chr6 323999 12 + 593897 TTtggtgtttta -s simRat_chr6.simRat.chr6 352189 12 + 647215 gttgtgatcttt - -a -s simMouse_chr6.simMouse.chr6 360120 25 + 636262 ggctgaggtgcctcgattcttgagc -s Anc0.Anc0refChr0 21424 24 + 26507 ggctgatgtagcttg-ctcttgagt -s Anc1.Anc1refChr6 22168 24 + 197743 ggctgatgtagcttg-ctcttgagt -s Anc2.Anc2refChr17 16025 24 + 28526 ggctgatgtagcttg-ctcttgagt -s mr.mrrefChr5 207499 25 + 294540 ggctgaggtgcctcgattcttgagc -s simCow_chr6.simCow.chr6 332051 24 + 602619 gcttgatggacctac-atcttaagt -s simDog_chr6.simDog.chr6 324011 24 + 593897 ggctgatgtagtttg-ctcctgagt -s simRat_chr6.simRat.chr6 352203 25 + 647215 ggctgaggtgcattgcttctcaagc - -a -s simMouse_chr6.simMouse.chr6 360145 64 + 636262 ttgtgtggccccaggtgtacacccctagtgtgaagtaacctatctcatattgaccctccaaccc -s Anc0.Anc0refChr0 21448 42 + 26507 ct--------ccaggtg--------------gatgtaacccatcccatgttcactatttgtccc -s Anc1.Anc1refChr6 22192 42 + 197743 ct--------ccaggtg--------------gatgtaacccatcccatgttcactatttgtccc -s Anc2.Anc2refChr17 16052 42 + 28526 ct--------ccaggtg--------------gatgtaacccatcccatgttcactatttgtccc -s mr.mrrefChr5 207524 53 + 294540 tt--------ccaggtgtacacccct---gtgaagtaacctatctcatattgaccctccaaccc -s simCow_chr6.simCow.chr6 332078 42 + 602619 ct--------ccaggtg--------------gatgtagcccatccgatggtcactgtttgtccc -s simDog_chr6.simDog.chr6 324038 42 + 593897 tt--------ccaggta--------------gatgtaacccagcccatgttcactattggtcac -s simRat_chr6.simRat.chr6 352228 53 + 647215 tt--------cccagtgaacacttct---gtgaaattacctatctcatgttgacccttataccc - -a -s simMouse_chr6.simMouse.chr6 360209 18 + 636262 tcagtctgtgatgtccac -s Anc0.Anc0refChr0 21490 14 + 26507 tc----tgtgatgtccac -s Anc1.Anc1refChr6 22234 14 + 197743 tc----tgtgatgtccac -s Anc2.Anc2refChr17 16098 14 + 28526 tc----tgtgatgtccac -s mr.mrrefChr5 207577 14 + 294540 tc----tgtgatgtccac -s simCow_chr6.simCow.chr6 332124 14 + 602619 tc----tgtgatgcccac -s simDog_chr6.simDog.chr6 324084 14 + 593897 tc----tgtgatgtccac -s simRat_chr6.simRat.chr6 352281 14 + 647215 tc----tgtgatgtccct - -a -s simMouse_chr6.simMouse.chr6 360227 10 + 636262 cgtgtatcat -s Anc0.Anc0refChr0 21504 3 + 26507 cat------- -s Anc1.Anc1refChr6 22248 3 + 197743 cat------- -s Anc2.Anc2refChr17 16119 3 + 28526 cat------- -s mr.mrrefChr5 207591 3 + 294540 cgt------- -s simCow_chr6.simCow.chr6 332145 3 + 602619 cat------- -s simDog_chr6.simDog.chr6 324105 3 + 593897 cat------- -s simRat_chr6.simRat.chr6 352295 3 + 647215 cat------- - -a -s simMouse_chr6.simMouse.chr6 360237 14 + 636262 cccaactagtgcat -s Anc0.Anc0refChr0 21507 14 + 26507 cccagctagggcat -s Anc1.Anc1refChr6 22251 14 + 197743 cccagctagggcat -s Anc2.Anc2refChr17 16122 14 + 28526 cccagctagggcat -s mr.mrrefChr5 207594 14 + 294540 cccaactagtgcat -s simCow_chr6.simCow.chr6 332148 8 + 602619 cccagcta------ -s simDog_chr6.simDog.chr6 324108 14 + 593897 ccccgctagggcat -s simRat_chr6.simRat.chr6 508881 14 + 647215 CCCAACTAGTGCAC - -a -s simMouse_chr6.simMouse.chr6 360251 380 + 636262 cctgggagtatttgctgctgATTTCTCGAGGATTTCCATGAGGAGTCTCTTTGCTAGTATTGGTCTCTATTATTTGTGCCCCTACCACTTTACAAGCATTACGATGAGGGTGGCAAAGGGTGTCATGCAATGCAGCTGTATGCTCAGTAGAATCCACACTACTCCTGCAATGAGTGGACTAGGAACTCCATGTGGCCCCTGGCTCATGATTCCCTCAGAGTGATAtcccatgccacatcccgcctgcctcacacctccctgagctgttgttaaacactaccatatgattcataaatgtgccctgaacatctggcactataagtcttaaaATTTCAAAGGAGTAAGCATGTGTAATCCTTGAAGTTATTGAGGAACAGGCT -s Anc0.Anc0refChr0 21521 95 + 26507 ccagggagaact-gccacagatttcc--aaaatcttcatgcagaagcacatgacaagttttgaacttctctctctgtgctactattgttttaaaagta------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ -s Anc1.Anc1refChr6 22265 95 + 197743 ccagggagaact-gccacagatttcc--aaaatcttcatgcagaagcacatgacaagttttgaacttctctctctgtgctactattgttttaaaagta------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ -s Anc2.Anc2refChr17 16181 95 + 28526 ccagggagaact-gccacagatttcc--aaaatcttcatgcagaagcacatgacaagttttgaacttctctctctgtgctactattgttttaaaagta------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ -s mr.mrrefChr5 207608 182 + 294540 cctgggagtatttgctgctgATTTCTCGAGGATTTCCATGAGGAGTCTCTTTGCTAGTATTGGTCTCTATTATTTGTGCCCCTACCACTTTACAAGCATTACGATGAGGGTGGCAAAGGGTGTCATGCAATGCAGCTGTATGCTCAGTAGAATCCACACTACTCCTGCAATG-----------------------------------------------------------------------------------------------------------ccatatgatt------------------------------------------------------------------------------------------- -s simCow_chr6.simCow.chr6 332190 95 + 602619 ccagggagaact-gccacagatttcc--aaaatcttcatgcagaagcacatgacaagttttgaacttctctctctgtgctactattgttttaaaagta------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ -s simRat_chr6.simRat.chr6 508895 182 + 647215 CCTGGGAGAATTTGTTGCTGATATCTCCAGCATTTTCATAGGGAGTCTCTTTACTAGTATTGGTCTCTATTATTTGTGCCCCTACCACTTTGCAAGCATTGTAATAAGGGTGGCAAAGGATGTCATGCGACGAAGTTCTGTATTCAGTAGGATCCACCCTATTCTTGCAGTG-----------------------------------------------------------------------------------------------------------CCATCGGATT------------------------------------------------------------------------------------------- - -a -s simMouse_chr6.simMouse.chr6 360631 65 + 636262 TGTTTGTATGGGCTAACTGTGCAGGATGGTGAAGCATTCCCAATGTCTTCAAGCCTCTCATTACT -s mr.mrrefChr5 207790 65 + 294540 TGTTTGTATGGGCTAACTGTGCAGGATGGTGAAGCATTCCCAATGTCTTCAAGCCTCTCATTACT -s simRat_chr6.simRat.chr6 352298 65 + 647215 TGGTACTATAAGTCAACCATGCATGATGGTGAAGCACTCCCAATGTCTTCAAGCCTCTCGTTACT - -a -s simMouse_chr6.simMouse.chr6 360696 44 + 636262 GAACCAGAGGAGTTATATGGCATCTCAAGTATatctaatgtctc -s mr.mrrefChr5 207855 44 + 294540 GAACCAGAGGAGTTATATGGCATCTCAAGTATatctaatgtctc -s simRat_chr6.simRat.chr6 352368 44 + 647215 GAACCAGAACAGTTATATGGCATCTCAAGTATATCTAATGTCTC - -a -s simMouse_chr6.simMouse.chr6 360740 151 + 636262 ccccttgttgctgaaccagggaagttatatggcatccggtaaactagaGTCTAATGTCTCCAAGCCTCTTGTTGCTAAACCAGGGAAGTTATATGGCTTCCAGTAAACTGGAAGAATCCAAGTGTTGACTGACCTGTTTATCAaatcagtt -s Anc0.Anc0refChr0 21616 20 + 26507 -----------------------------------------------------------------------------------------------------------------------------------atctttgtcccctgccagtt -s Anc1.Anc1refChr6 22360 20 + 197743 -----------------------------------------------------------------------------------------------------------------------------------atctttgtcccctgccagtt -s Anc2.Anc2refChr17 16276 20 + 28526 -----------------------------------------------------------------------------------------------------------------------------------atctttgtcccctgccagtt -s mr.mrrefChr5 207899 100 + 294540 ccccttgttgctgaaccagggaagttatatggcatccggt-----------------------------------TAAACCAGGGAAGTTATATG----------------AAGAATCCAAGTGTTGACTGACCTGTTTATCAaatcagtt -s simCow_chr6.simCow.chr6 332285 20 + 602619 -----------------------------------------------------------------------------------------------------------------------------------atctttgtcccctgccagtt -s simRat_chr6.simRat.chr6 352416 100 + 647215 TCTCTTGTTGCTTAACCAGGGAAGTTACATGGCATCCCGT-----------------------------------TAAACTAGAAGAATCATATG----------------AAGAGTCCAAGCATTAACTGCTTTGTTTATCAaatcagtt - -a -s simMouse_chr6.simMouse.chr6 360891 40 + 636262 ggccagaattagtattacagttaggagtactttgtttttt -s Anc0.Anc0refChr0 21636 39 + 26507 ggccagaactggtgttataattaggtgagttttgtcttt- -s Anc1.Anc1refChr6 22380 39 + 197743 ggccagaactggtgttataattaggtgagttttgtcttt- -s Anc2.Anc2refChr17 16332 39 + 28526 ggccagaactggtgttataattaggtgagttttgtcttt- -s mr.mrrefChr5 207999 39 + 294540 ggccagaattagtattacagttaggagtactttgttttt- -s simCow_chr6.simCow.chr6 332341 1 + 602619 g--------------------------------------- -s simDog_chr6.simDog.chr6 324137 38 + 593897 -gccagaactggtgttataattaggtgagttttgtcttt- -s simRat_chr6.simRat.chr6 352516 39 + 647215 ggccagaattagtgttacagcaaggagtactttgctttt- - -a -s simMouse_chr6.simMouse.chr6 360931 8 + 636262 gcctctaa -s Anc0.Anc0refChr0 21675 8 + 26507 acctccca -s Anc1.Anc1refChr6 22419 8 + 197743 acctccca -s Anc2.Anc2refChr17 16372 8 + 28526 acctccca -s mr.mrrefChr5 208038 8 + 294540 gcctctaa -s simCow_chr6.simCow.chr6 332342 8 + 602619 acctgcca -s simDog_chr6.simDog.chr6 324176 8 + 593897 acccctaa -s simRat_chr6.simRat.chr6 352555 8 + 647215 gcctctaa - -a -s simMouse_chr6.simMouse.chr6 360939 30 + 636262 tgcactcctactaaccaccctattttgatg -s Anc0.Anc0refChr0 21683 12 + 26507 aacacccatact------------------ -s Anc1.Anc1refChr6 22427 12 + 197743 aacacccatact------------------ -s Anc2.Anc2refChr17 16380 12 + 28526 aacacccatact------------------ -s mr.mrrefChr5 208046 14 + 294540 tgcactcctactaa---------------- -s simCow_chr6.simCow.chr6 332354 12 + 602619 agcagccatatt------------------ -s simDog_chr6.simDog.chr6 324184 12 + 593897 aaccctcatact------------------ -s simRat_chr6.simRat.chr6 352563 14 + 647215 tgcacccctactaa---------------- - -a -s simMouse_chr6.simMouse.chr6 360969 256 + 636262 atatgattatgtgtgtgctgaactccctatataactgatgttataagggcccagtccctgctggtgatgattccattaatgcagtgcctttaggtactataattagcctctacattgggctgactctcccccagtcccaccatgacccctatcggatacttTGACCCCTATCTGATACTTCAGGTAGAGATCTCTCACTGTTCATTTCATAATACACCACTGATCTCTCCACTGAACTACGGTCTTCAATCTGAAC -s mr.mrrefChr5 208060 237 + 294540 atatgattatgtgtgtgctgaactccctatataactgatgttataagggcccagtccctgctggtgatgattccattaatgcagtgcctttaggtactataattagcctctacattgggctgactctcccccagtcccaccatgaccc-------------------ctatctgatacttcaggtagagatctctcactgttcatttcataatacaccactgatctctccactgaactacggtcttcaatctgaac -s simRat_chr6.simRat.chr6 353215 237 + 647215 ATATAATTACGTGTGTGCCGAACTCCGTATAAAACTGAGGctataaggacccagctcctgctggtgatggttccatcaatgcggtgcttttaagtactatgattagtctccacattgggctgactctcccccagtcccaccatgactc-------------------ccatctggtacttcaggtagagatatctgaccgttgatttcttagtacaaccctagtctttactctgaactactgtgtttaatgggaaa - -a -s simMouse_chr6.simMouse.chr6 361225 25 + 636262 TACTGTGTCCAATGGGATATTGTGA -s mr.mrrefChr5 208297 23 + 294540 tactgtgt--aatgggatattgtga -s simRat_chr6.simRat.chr6 353454 23 + 647215 tactgagt--aatgtagtattttga - -a -s simMouse_chr6.simMouse.chr6 361250 19 + 636262 TCCCTCAATACATTGTTCG -s mr.mrrefChr5 208320 19 + 294540 tccctcaatacattgttcg -s simRat_chr6.simRat.chr6 353501 19 + 647215 tccctccatacactgttca - -a -s simMouse_chr6.simMouse.chr6 361269 118 + 636262 TTCAGAGCATGATGTGGTAGTTGGTAGAAACTTACTCATAGAGTGACTCAGTTCAAAAGTCACTCAGTTTAAACAACGATGGGTTGGTTTTAAGCACAACAGGCCCCATCATACTTCT -s mr.mrrefChr5 208339 118 + 294540 ttcagAGCATGATGTGGTAGTTGGTAGAAACTTACTCATAGAGTGACTCAGTTCAAAAGTCACTCAGTTTAAACAACGATGGGTTGGTTTTAAGCACAACAGGCCCCATCATACTTCT -s simRat_chr6.simRat.chr6 353529 118 + 647215 gtgggAGCATAATGTGGTAGTTGGTAGAAATTTACTCATAGAGTGATTCAGCTCAAGACTCACCCAGTTTATACAATGATGGGTTGGTTTTAAGCACAACAGGCCCCATCATACTTCT - -a -s simMouse_chr6.simMouse.chr6 361387 56 + 636262 AGAAGCCGTCATTTCCAGCAAGACAGCAATGGGGTAAAACTTGAGGACCACCCCCT -s Anc0.Anc0refChr0 21695 5 + 26507 ---------------------------------------------------cccct -s Anc1.Anc1refChr6 22439 5 + 197743 ---------------------------------------------------cccct -s Anc2.Anc2refChr17 16392 5 + 28526 ---------------------------------------------------cccct -s mr.mrrefChr5 208457 56 + 294540 AGAAGCCGTCATTTCCAGCAAGACAGCAATGGGGTAAAACTTGAGGACCACCCCCT -s simCow_chr6.simCow.chr6 332366 5 + 602619 ---------------------------------------------------ccacc -s simDog_chr6.simDog.chr6 324196 5 + 593897 ---------------------------------------------------cacct -s simRat_chr6.simRat.chr6 353648 56 + 647215 AGAGGTCTTCATCTCCAACAAAACAGCAATGGGGTAAAACTTGATGTCCACCCCCT - -a -s simMouse_chr6.simMouse.chr6 361443 1 + 636262 A -s Anc0.Anc0refChr0 21700 1 + 26507 g -s Anc1.Anc1refChr6 22444 1 + 197743 g -s Anc2.Anc2refChr17 16714 1 + 28526 g -s mr.mrrefChr5 208513 1 + 294540 A -s simDog_chr6.simDog.chr6 324740 1 + 593897 g -s simRat_chr6.simRat.chr6 353704 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 361444 12 + 636262 TTGTTCTTATAG -s Anc0.Anc0refChr0 21701 11 + 26507 ttgcccttcta- -s Anc1.Anc1refChr6 22445 11 + 197743 ttgcccttcta- -s Anc2.Anc2refChr17 16715 11 + 28526 ttgcccttcta- -s mr.mrrefChr5 208514 12 + 294540 TTGTTCTTATAG -s simDog_chr6.simDog.chr6 324742 11 + 593897 ttgcccttcta- -s simRat_chr6.simRat.chr6 353705 12 + 647215 TTGTTCTTATAG - -a -s simMouse_chr6.simMouse.chr6 361456 14 + 636262 TTTGGTCACAAGAA -s Anc0.Anc0refChr0 21712 14 + 26507 ttcaatcgttagga -s Anc1.Anc1refChr6 22456 14 + 197743 ttcaatcgttagga -s Anc2.Anc2refChr17 16726 14 + 28526 ttcaatcgttagga -s mr.mrrefChr5 208526 14 + 294540 TTTGGTCACAAGAA -s simDog_chr6.simDog.chr6 324754 14 + 593897 ttcaatcgttagga -s simRat_chr6.simRat.chr6 353717 14 + 647215 TTTGGTCACAGGAT - -a -s simMouse_chr6.simMouse.chr6 361470 39 + 636262 TACAGCTTGAGGGGGGCCCGAGATTTAAGATCATGGCAC -s Anc0.Anc0refChr0 21726 36 + 26507 tgcagcttgagggggcctc-agttttaagaccatgg--c -s Anc1.Anc1refChr6 22470 36 + 197743 tgcagcttgagggggcctc-agttttaagaccatgg--c -s Anc2.Anc2refChr17 16745 36 + 28526 tgcagcttgagggggcctc-agttttaagaccatgg--c -s mr.mrrefChr5 208540 37 + 294540 TACAGCTTGAGGGGGGCCCGAGATTTAAGATCATGG--C -s simDog_chr6.simDog.chr6 324773 36 + 593897 tgcagcttgagggggcctc-agttttaagaccatgg--c -s simRat_chr6.simRat.chr6 353731 37 + 647215 TACAGCTTGAGGGGGGCCCCAGATTTAAGATCATGG--C - -a -s simMouse_chr6.simMouse.chr6 361509 21 + 636262 CATGATTCTAATGCATGTCAA -s Anc0.Anc0refChr0 21762 21 + 26507 agtgattttgaagcacgccta -s Anc1.Anc1refChr6 22506 21 + 197743 agtgattttgaagcacgccta -s Anc2.Anc2refChr17 16783 21 + 28526 agtgattttgaagcacgccta -s mr.mrrefChr5 208577 21 + 294540 CATGATTCTAATGCATGTCAA -s simDog_chr6.simDog.chr6 324811 21 + 593897 agtgattttgaagcacgccta -s simRat_chr6.simRat.chr6 353768 21 + 647215 CATGAATCTAATGCATGTCAA - -a -s simMouse_chr6.simMouse.chr6 361530 27 + 636262 CACTAGCCCCTTGGCACTTAATTCAAT -s Anc0.Anc0refChr0 21783 24 + 26507 cacT---TTCTTAGCACTCAAGTAAAT -s Anc1.Anc1refChr6 22527 24 + 197743 cacT---TTCTTAGCACTCAAGTAAAT -s Anc2.Anc2refChr17 16855 24 + 28526 cacT---TTCTTAGCACTCAAGTAAAT -s mr.mrrefChr5 208598 27 + 294540 CACTAGCCCCTTGGCACTTAATTCAAT -s simCow_chr6.simCow.chr6 332602 18 + 602619 ---------CTTAGCACTCAGGTAAAT -s simDog_chr6.simDog.chr6 324883 24 + 593897 CACT---TTGCTAGCCCTTAAGTAAAT -s simRat_chr6.simRat.chr6 353789 27 + 647215 TACTAGCCCCTTAGCACTCAATTCAAT - -a -s simMouse_chr6.simMouse.chr6 361557 31 + 636262 GATAAATACCTAATCTAAGGGTTCATGATGA -s Anc0.Anc0refChr0 21807 27 + 26507 G----ACATCTGATTCAAGATTTCATGATGA -s Anc1.Anc1refChr6 22551 27 + 197743 G----ACATCTGATTCAAGATTTCATGATGA -s Anc2.Anc2refChr17 16883 27 + 28526 G----ACATCTGATTCAAGATTTCATGATGA -s mr.mrrefChr5 208625 27 + 294540 G----ATACCTAATCTAAGGGTTCATGATGA -s simCow_chr6.simCow.chr6 332624 27 + 602619 C----ACATCTGATTCAGGATTTCATGATGA -s simDog_chr6.simDog.chr6 324911 27 + 593897 G----ACATCAAATTTAAGATTTCATGATGA -s simRat_chr6.simRat.chr6 353816 27 + 647215 G----ATACCTAAACCAAGGTATCTTGATGC - -a -s simMouse_chr6.simMouse.chr6 361588 9 + 636262 CTCAAGACA -s Anc0.Anc0refChr0 21834 9 + 26507 CACAGTACA -s Anc1.Anc1refChr6 22578 9 + 197743 CACAGTACA -s Anc2.Anc2refChr17 16923 9 + 28526 CACAGTACA -s mr.mrrefChr5 208652 9 + 294540 CTCAAGACA -s simCow_chr6.simCow.chr6 332664 7 + 602619 CACAGTA-- -s simDog_chr6.simDog.chr6 324951 9 + 593897 CACAGTACA -s simRat_chr6.simRat.chr6 353843 9 + 647215 CTCAATACA - -a -s simMouse_chr6.simMouse.chr6 361597 14 + 636262 GGTTCTAATCATGA -s Anc0.Anc0refChr0 21843 14 + 26507 GGTTTTAATCATGA -s Anc1.Anc1refChr6 22587 14 + 197743 GGTTTTAATCATGA -s Anc2.Anc2refChr17 16934 14 + 28526 GGTTTTAATCATGA -s mr.mrrefChr5 208661 14 + 294540 GGTTCTAATCATGA -s simCow_chr6.simCow.chr6 332672 14 + 602619 GGTTTTAATTACGA -s simDog_chr6.simDog.chr6 324962 14 + 593897 TGTTTTAGCCATGA -s simRat_chr6.simRat.chr6 353852 14 + 647215 GGTTCTAATGATGA - -a -s simMouse_chr6.simMouse.chr6 361611 5 + 636262 GAGTT -s Anc0.Anc0refChr0 21857 5 + 26507 AAGTT -s Anc1.Anc1refChr6 22601 5 + 197743 AAGTT -s Anc2.Anc2refChr17 16949 5 + 28526 AAGTT -s mr.mrrefChr5 208675 5 + 294540 GAGTT -s simCow_chr6.simCow.chr6 332687 5 + 602619 AAGAT -s simDog_chr6.simDog.chr6 324977 5 + 593897 AAGTT -s simRat_chr6.simRat.chr6 353866 5 + 647215 TAGGT - -a -s simMouse_chr6.simMouse.chr6 361616 15 + 636262 GATTGGACCCATGCT -s Anc0.Anc0refChr0 21862 15 + 26507 GCATGAACCTATGCT -s Anc1.Anc1refChr6 22606 15 + 197743 GCATGAACCTATGCT -s Anc2.Anc2refChr12 0 15 + 554 ACATAATTCTCTGCC -s mr.mrrefChr5 208680 15 + 294540 GATTGGACCCATGCT -s simCow_chr6.simCow.chr6 149223 15 - 602619 TTAACTTCCTCTGCC -s simDog_chr6.simDog.chr6 449248 15 + 593897 ACATAATTCTCTGCC -s simRat_chr6.simRat.chr6 353871 15 + 647215 TATTGGATGCATGCT - -a -s simMouse_chr6.simMouse.chr6 361631 1 + 636262 A -s Anc0.Anc0refChr0 21877 1 + 26507 C -s Anc1.Anc1refChr6 22621 1 + 197743 C -s Anc2.Anc2refChr12 52 1 + 554 T -s mr.mrrefChr5 208695 1 + 294540 A -s simCow_chr6.simCow.chr6 149274 1 - 602619 T -s simDog_chr6.simDog.chr6 449300 1 + 593897 T -s simRat_chr6.simRat.chr6 353886 1 + 647215 G - -a -s simMouse_chr6.simMouse.chr6 361632 49 + 636262 AGCCCATATAGCAGCTCTTAATAATAGCCACAATGGAAATGGAATGAAT -s Anc0.Anc0refChr0 22347 45 + 26507 AGCTCCTATGGCAGCTCTCATTAA-AGGTAAAATTGAA--GAAATG-GT -s Anc1.Anc1refChr6 23095 45 + 197743 AGCTCCTATGGCAGCTCTCATTAA-AGGTAAAATTGAA--GAAATG-GT -s Anc2.Anc2refChr17 17013 45 + 28526 AGCTCCTATGGCAGCTCTCATTAA-AGGTAAGAATGGG--GAAATG-GA -s mr.mrrefChr5 208696 48 + 294540 AGCCCATATAGCAGCTCTTAATAATAGCCACAATGGAAATGGAATG-AT -s simCow_chr6.simCow.chr6 332751 29 + 602619 AGCTCCTATGGCAGC-CCCATTAA-AGGTGA------------------ -s simDog_chr6.simDog.chr6 325041 45 + 593897 AGCTCCTATGGGAGCTCTTAATAC-AGGCAAGAATGGG--GAAATG-GA -s simHuman_chr6.simHuman.chr6 346114 45 + 601863 AGCGAGTATTGCAGCTCTCATTTA-AGGTAAAATTGAA--GAAATG-GT -s simRat_chr6.simRat.chr6 353887 48 + 647215 AGCCCCTATAGCAGCTCTTATAGATAGCAACAATGGAAACGGAATG-AT - -a -s simMouse_chr6.simMouse.chr6 361681 14 + 636262 CCTGGGAATTAGTG -s Anc0.Anc0refChr0 22393 14 + 26507 CCTGGAAATCAGTG -s Anc1.Anc1refChr6 23141 14 + 197743 CCTGGAAATCAGTG -s Anc2.Anc2refChr17 17059 14 + 28526 GTTGGAAATCAGCA -s mr.mrrefChr5 208744 14 + 294540 CCTGGGAATTAGTG -s simCow_chr6.simCow.chr6 332780 8 + 602619 ------AATCGGCC -s simDog_chr6.simDog.chr6 325087 14 + 593897 GTTGGAAATCAGCA -s simHuman_chr6.simHuman.chr6 346160 14 + 601863 CCTGGCAATCAGTG -s simRat_chr6.simRat.chr6 353935 14 + 647215 CCTGGGAACTAGTG - -a -s simMouse_chr6.simMouse.chr6 361695 26 + 636262 AAAAGCATTGATCTTCTAACCCGGTG -s Anc0.Anc0refChr0 22407 10 + 26507 AAAAGAGC----------------tg -s Anc1.Anc1refChr6 23155 26 + 197743 AAAAGAGCTgctcttctagttgggtg -s Anc2.Anc2refChr17 17073 10 + 28526 AAAAGAGC----------------TA -s mr.mrrefChr5 208758 26 + 294540 AAAAGCattgatcttctaacccggtg -s simCow_chr6.simCow.chr6 332788 10 + 602619 AAAAGAGC----------------TT -s simDog_chr6.simDog.chr6 325101 10 + 593897 AAAAGAGC----------------TA -s simHuman_chr6.simHuman.chr6 346176 26 + 601863 AGAAGAGCTgctcttctagttgggtg -s simRat_chr6.simRat.chr6 353949 26 + 647215 AAAAGCattgatcttctaacctagtg - -a -s simMouse_chr6.simMouse.chr6 361721 7 + 636262 GTTAAAA -s Anc0.Anc0refChr0 22454 7 + 26507 GTTTAAA -s Anc1.Anc1refChr6 23218 7 + 197743 GTTTAAA -s Anc2.Anc2refChr17 17120 7 + 28526 GGTTAAA -s mr.mrrefChr5 208784 7 + 294540 gttaaaa -s simCow_chr6.simCow.chr6 332842 7 + 602619 GGTAAAA -s simDog_chr6.simDog.chr6 325149 5 + 593897 --TTAAA -s simHuman_chr6.simHuman.chr6 346292 7 + 601863 GTTGAAA -s simRat_chr6.simRat.chr6 353975 7 + 647215 gatacca - -a -s simMouse_chr6.simMouse.chr6 361728 18 + 636262 CTTGTGAGAGACCCACTA -s Anc0.Anc0refChr0 22461 2 + 26507 CT---------------- -s Anc1.Anc1refChr6 23225 2 + 197743 CT---------------- -s Anc2.Anc2refChr17 17127 2 + 28526 CT---------------- -s mr.mrrefChr5 208791 18 + 294540 CTTGTGAGAGACCCACTA -s simCow_chr6.simCow.chr6 332849 2 + 602619 CT---------------- -s simDog_chr6.simDog.chr6 325154 2 + 593897 CT---------------- -s simHuman_chr6.simHuman.chr6 346299 2 + 601863 CT---------------- -s simRat_chr6.simRat.chr6 354042 18 + 647215 CTTCTGATTGCCTCAGTA - -a -s simMouse_chr6.simMouse.chr6 361746 279 + 636262 GGAATCCTTGCAGCTCCTTGTTTAGAGGCTCCATGGGAAGCTGTGGCAAGCAATCCCAAGTGACTCCCTGTTTGATGGTAGATTCAATCCTACTCCACTAGTTCCCCCACAAGTTCTACTAACGATGCCCATATGCCCCCCAGAGTGGTAACCAACCCAAAAGCCAGCTGTATGACTCTATGTGTGCCATATAGATTGAAGGGCCGCAGCTTCCAGATGGTATGCCGACAATCTCCAGAGGTGTTAAAACTTTCTGGATGTGAGGGATCAATAATCATG -s mr.mrrefChr5 208809 275 + 294540 GGAATCCTTGCAGCTCCTTGTTTAGAGGCTCCATGGGAAGCTGTGGCAAGCAATCCCAAGTGACTCCCTGTT---TGGTAGATTCAATCCTACTCCACTAGTTCCCCCACAAGTTCTACTAACGATGCCCATATGCCCCCCAGAGTGGTAACCAACCCAAAAGCCAGCTGTATGACTCTATGTGTGCCATATAGATTGAAGGGCCGCAGCTTCCAGATGGTATGCCGACAATCTCCAGAGGTGTTAAAACTTTCTGGATGTGAGGGAT-AATAATCATG -s simRat_chr6.simRat.chr6 354068 275 + 647215 GAGATCCTCACAGCTACTTGTTTAGGGGTTCCACGGGAAGCTGGATCCAGGAATGCCAAGTGACTCCCTGTT---TGGTAGATTCGGTCCTACTCCACTAGCTCCTCCACTAGTTCAATTAATAATGCCACTATGCCCCCCAGAGTGGTAGCCAACTCAAAAGCCAGCTGCGTCACCTTATGTATGCAATATAGGTTGAAGGGCTGCAGCTTCTAGATGGTATGCCAACAGTCTGCAGGGGTGTTATAACTTTCTGGTTGTGTGGGAT-AATAATTGTA - -a -s simMouse_chr6.simMouse.chr6 362025 82 + 636262 CAGAATTTGCACACCAACCAGGTACTCAAATAGGATTTGCCCATTGACTAAGTGCTATCAGGCCAGTATGGTTAACATTATA -s Anc0.Anc0refChr0 22463 3 + 26507 -------------------------------------------------------------------------------GTG -s Anc1.Anc1refChr6 23227 3 + 197743 -------------------------------------------------------------------------------GTG -s Anc2.Anc2refChr17 17129 3 + 28526 -------------------------------------------------------------------------------GTG -s mr.mrrefChr5 209084 82 + 294540 CAGAATTTGCACACCAACCAGGTACTCAAATAGGATTTGCCCATTGACTAAGTGCTATCAGGCCAGTATGGTTAACATTATA -s simCow_chr6.simCow.chr6 332851 3 + 602619 -------------------------------------------------------------------------------GTG -s simDog_chr6.simDog.chr6 325156 3 + 593897 -------------------------------------------------------------------------------GCA -s simHuman_chr6.simHuman.chr6 346301 3 + 601863 -------------------------------------------------------------------------------GTG -s simRat_chr6.simRat.chr6 354359 82 + 647215 TAGAATTTGCACACCATCCAGGCACTCAAATAGGATGTGCCCATTAACCAAATGCTATCAGACCGGTTTGATTAAAATTATA - -a -s simMouse_chr6.simMouse.chr6 362107 32 + 636262 ATATTTGAGCCAATGGTGATCACTCTGTTTCT -s Anc0.Anc0refChr0 22466 32 + 26507 AAAATTGAGCCAACAATGATGACTCTGGTGAT -s Anc1.Anc1refChr6 23230 32 + 197743 AAAATTGAGCCAACAATGATGACTCTGGTGAT -s Anc2.Anc2refChr17 17132 32 + 28526 AAAATTGAGCCAACAATTATGACTCTAGTGAT -s mr.mrrefChr5 209166 32 + 294540 ATATTTGAGCCAATGGTGATCACTCTGTTTCT -s simCow_chr6.simCow.chr6 332856 32 + 602619 ATAATTGAGCCCACAAGTATGACTCTAGTGAC -s simDog_chr6.simDog.chr6 325159 26 + 593897 CAAGTTGATCCAACAATTATGACTC------T -s simHuman_chr6.simHuman.chr6 346304 32 + 601863 ACAATTGAGCCAACAATGATGACTCTGGTGAT -s simRat_chr6.simRat.chr6 354441 32 + 647215 ACATTCGAGCCATTAGTGATGTCTCTGCTGCT - -a -s simMouse_chr6.simMouse.chr6 362139 3 + 636262 AAT -s Anc0.Anc0refChr0 22498 3 + 26507 AAT -s Anc1.Anc1refChr6 23262 3 + 197743 AAT -s Anc2.Anc2refChr17 17164 3 + 28526 AAT -s mr.mrrefChr5 209198 3 + 294540 AAT -s simCow_chr6.simCow.chr6 332890 3 + 602619 AAT -s simDog_chr6.simDog.chr6 325185 3 + 593897 AAT -s simHuman_chr6.simHuman.chr6 346336 3 + 601863 AAT -s simRat_chr6.simRat.chr6 354473 3 + 647215 AAT - -a -s simMouse_chr6.simMouse.chr6 362142 105 + 636262 TATAAATGCACCAGGTAACCCAGATTACTCGCTTTCTTCTTAGTACATTCCTTGGGGTTTCCTTTTAGAAGGCAACTGTTCATGCAGCACCTGACAGGTAGAGGC -s Anc0.Anc0refChr0 22603 105 + 26507 AGTATATGCACTAAATAACACAAAATTCTCATTACTTTCTTAGCATATTTCTTGGGGTTTCCTTATAAAAAACAATTATTGATGCAGGACCTGACAAGTAGAGGG -s Anc1.Anc1refChr6 23367 105 + 197743 AGTATATGCACTAAATAACACAAAATTCTCATTACTTTCTTAGCATATTTCTTGGGGTTTCCTTATAAAAAACAATTATTGATGCAGGACCTGACAAGTAGAGGG -s Anc2.Anc2refChr17 17269 105 + 28526 AGTATATCCACTGAATAACACAAAATTGTCATCACTGTCTTAGCATATTTCCTGGGGTTTCCTCATAAAAAACAATTATTGGTACAGGACCTGACAAGTAGAAGG -s mr.mrrefChr5 209201 105 + 294540 CATAAATGCACCAGGTAACCCAGATTACTCGTTTCCTTCTTAGTACATTTCTTGGGGTTTCCTTATAGAAGGCAACTGTTCATGCAGCACCTGACAAGTAGAGGC -s simCow_chr6.simCow.chr6 332926 103 + 602619 AGTATAACCACTGAGTGAGACAAAATTGTTATCACCACCTTATCATACTTCCTGGGGTTTTGTCATAAAGAATAATTGTTGGTACAGCACCTAACAAGT--AAGG -s simDog_chr6.simDog.chr6 325292 105 + 593897 AGTATATCTGTTGAATAACACAAAATAGTCATCACTGTCTTAGCATGTCTCCTGGGGTTTCCTCACAAAACACAATAATTGGTACAGGACCTGACAAGTAGAAGG -s simHuman_chr6.simHuman.chr6 346441 105 + 601863 TCTATATGCACTAAATAACACGAAATTCTCATTACATTCTTAGCATATTTCTTGGGGTTTCCTTATAAAAAACAATTTTTGATGCAGTGTCTGACAAGTAGCGGT -s simRat_chr6.simRat.chr6 354476 105 + 647215 CATAAATGCACCACGTAACCCAGATTACTCGTTTCCTTCTTAGTACATTTCTTGAGGTTTCCTCATAGAAGGCAACTGTTCATACAGCACCTGACAAGTAGAGGC - -a -s simMouse_chr6.simMouse.chr6 362247 20 + 636262 ATTCTCAATTCACCCCTGTG -s Anc0.Anc0refChr0 22709 20 + 26507 ACTCTCCTGTCACCCTTGAG -s Anc1.Anc1refChr6 23473 20 + 197743 ACTCTCCTGTCACCCTTGAG -s Anc2.Anc2refChr17 17375 20 + 28526 ACTCTCCTGTCACCCTTGAG -s mr.mrrefChr5 209306 20 + 294540 ATTCTCAATTCACCCCTGTG -s simCow_chr6.simCow.chr6 333030 20 + 602619 AATCTACTGTCACCCTTGAG -s simDog_chr6.simDog.chr6 325398 20 + 593897 ACTCTCCTGTCACCCTTCAG -s simHuman_chr6.simHuman.chr6 346547 20 + 601863 ACTCTCCTGTCACCCTTGAG -s simRat_chr6.simRat.chr6 354581 20 + 647215 CATCTCAATTCACCCCCGTG - -a -s simMouse_chr6.simMouse.chr6 362267 40 + 636262 TACCTCTTATGTGACCGGGAATTCAACATGCAAGCTATAC -s Anc0.Anc0refChr0 22730 40 + 26507 TAACTGCTTTGTGACACTCAAATCAGCATGCAAGCTATAC -s Anc1.Anc1refChr6 23494 40 + 197743 TAACTGCTTTGTGACACTCAAATCAGCATGCAAGCTATAC -s Anc2.Anc2refChr17 17396 40 + 28526 TAACCGCTTTGTGACACTCAAATCAGCATGCAAGCTATAC -s mr.mrrefChr5 209326 40 + 294540 TACCTCTTATGTGACCGGGAATTCAACATGCAAGCTATAC -s simCow_chr6.simCow.chr6 333051 39 + 602619 TAACCG-TTTGTGACACTCAAATTAGCATGTAAGCTATAC -s simDog_chr6.simDog.chr6 325419 40 + 593897 TAATCCCTTTGTAACACTCAAATCAGCATGCAACCCATAC -s simHuman_chr6.simHuman.chr6 346568 40 + 601863 TAACTGCTCCATGACACTCAAAGCAGCCTGGAAGGTATTC -s simRat_chr6.simRat.chr6 354601 36 + 647215 TACGCCTAATGTAACCTGGAA-TCAACATGCAAGCTG--- - -a -s simMouse_chr6.simMouse.chr6 362307 24 + 636262 AAATAATTTGACCAGAGGAACACT -s Anc0.Anc0refChr0 22771 24 + 26507 AAATAAATTGGTCAGAGAAATACT -s Anc1.Anc1refChr6 23535 24 + 197743 AAATAAATTGGTCAGAGAAATACT -s Anc2.Anc2refChr17 17437 24 + 28526 AGATAAATTTGTCAGAGAAATATT -s mr.mrrefChr5 209366 24 + 294540 AAATAATTTGACCAGAGAAACACT -s simCow_chr6.simCow.chr6 333091 19 + 602619 AGAT-AATTTATCAGAGAAA---- -s simDog_chr6.simDog.chr6 325460 24 + 593897 AGGTAAATTTGTCAGAGAAATATT -s simHuman_chr6.simHuman.chr6 346609 24 + 601863 AAATAAATTGGTCAGAAACAGGCG -s simRat_chr6.simRat.chr6 354637 24 + 647215 AAATAATACGACCGGGGAAACACT - -a -s simMouse_chr6.simMouse.chr6 362331 16 + 636262 AGTTCATTACACTAGG -s Anc0.Anc0refChr0 22795 11 + 26507 AGCTAGATAAA----- -s Anc1.Anc1refChr6 23559 11 + 197743 AGCTAGATAAA----- -s Anc2.Anc2refChr17 17461 11 + 28526 AGCTAGACAAT----- -s mr.mrrefChr5 209390 16 + 294540 AGTTCATTACACTAGG -s simCow_chr6.simCow.chr6 333110 8 + 602619 ---TAGCCATT----- -s simDog_chr6.simDog.chr6 325485 11 + 593897 AGCTAGACAAT----- -s simHuman_chr6.simHuman.chr6 346633 11 + 601863 AGCTAGATGAA----- -s simRat_chr6.simRat.chr6 354661 16 + 647215 AGTTTATTACACTAGC - -a -s simMouse_chr6.simMouse.chr6 362347 46 + 636262 TTGATTGCTTGTTCAGTATCTTCATTTTCCCAGCGTGGCTCTCCAG -s Anc0.Anc0refChr0 22806 40 + 26507 TCGATGGCTTGCTCACTGTTCTCATTTCACTGGC------CTCTAG -s Anc1.Anc1refChr6 23570 40 + 197743 TCGATGGCTTGCTCACTGTTCTCATTTCACTGGC------CTCTAG -s Anc2.Anc2refChr17 17472 40 + 28526 TCAATGGCTTGCCCACTGTTCTCATTTCACTGGC------CTCTAG -s mr.mrrefChr5 209406 46 + 294540 TTGATTGCTTGTTCAGTATCTTCATTTTCCCAGCGTGGCTCTCCAG -s simCow_chr6.simCow.chr6 333118 40 + 602619 TCAATGGCTTGCCCACTGTTTCCATTTTAGTGGC------CTATAG -s simDog_chr6.simDog.chr6 325501 40 + 593897 TCAATGGCTTGCCCACTCTTCTCATTTCACTGAC------CTCTAG -s simHuman_chr6.simHuman.chr6 346644 40 + 601863 TAGATGGCTTGCTGACTGATCTCATTTAACTGGC------CTCGAG -s simRat_chr6.simRat.chr6 354677 44 + 647215 TTGATTGCT--TTCAATATCTTCATTTTCACAGCATGTTTCACCAG - -a -s simMouse_chr6.simMouse.chr6 362393 30 + 636262 GCTCCAGCAGGTACGTATAACAAAGGCCTG -s Anc0.Anc0refChr0 22846 16 + 26507 GC--------------ATAACAGAGTACTG -s Anc1.Anc1refChr6 23610 16 + 197743 GC--------------ATAACAGAGTACTG -s Anc2.Anc2refChr17 17514 16 + 28526 GC--------------ATAACAGAATACTG -s mr.mrrefChr5 209452 30 + 294540 GCTCCAGCAGGTACGTATAACAAAGGCCTG -s simCow_chr6.simCow.chr6 333164 16 + 602619 GC--------------ATAACAGAATACTG -s simDog_chr6.simDog.chr6 325543 16 + 593897 GC--------------CTAAGAGAATACTG -s simHuman_chr6.simHuman.chr6 346684 16 + 601863 AC--------------ATAACAGAGTACTG -s simRat_chr6.simRat.chr6 354721 30 + 647215 GCTCCAGCAGGTAGGTATAACAAGAGCCAG - -a -s simMouse_chr6.simMouse.chr6 362423 1 + 636262 T -s Anc0.Anc0refChr0 22862 1 + 26507 T -s Anc1.Anc1refChr6 23626 1 + 197743 T -s Anc2.Anc2refChr17 17530 1 + 28526 T -s mr.mrrefChr5 209482 1 + 294540 T -s simCow_chr6.simCow.chr6 333180 1 + 602619 T -s simDog_chr6.simDog.chr6 325559 1 + 593897 T -s simHuman_chr6.simHuman.chr6 346700 1 + 601863 T -s simRat_chr6.simRat.chr6 354752 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 362424 6 + 636262 ACTCAA -s Anc0.Anc0refChr0 22864 3 + 26507 ACT--- -s Anc1.Anc1refChr6 23628 3 + 197743 ACT--- -s Anc2.Anc2refChr17 17532 3 + 28526 TCT--- -s mr.mrrefChr5 209483 6 + 294540 ACTCAA -s simCow_chr6.simCow.chr6 333182 3 + 602619 CCT--- -s simDog_chr6.simDog.chr6 325561 3 + 593897 TCT--- -s simHuman_chr6.simHuman.chr6 346702 3 + 601863 ACT--- -s simRat_chr6.simRat.chr6 354753 6 + 647215 ACTCAA - -a -s simMouse_chr6.simMouse.chr6 362430 19 + 636262 GAGCGAAGCCCTCACCACT -s Anc0.Anc0refChr0 22867 13 + 26507 ------AGCTCTTTCCAAT -s Anc1.Anc1refChr6 23631 13 + 197743 ------AGCTCTTTCCAAT -s Anc2.Anc2refChr17 17535 13 + 28526 ------AGCTTTTTCCAAT -s mr.mrrefChr5 209489 19 + 294540 GAGCGAAGCCCTCACCACT -s simCow_chr6.simCow.chr6 333185 13 + 602619 ------AGCTTTTTCCCAT -s simDog_chr6.simDog.chr6 325564 13 + 593897 ------TGCTTTTTGCAAC -s simHuman_chr6.simHuman.chr6 346705 13 + 601863 ------AGCTCTTCCCAAT -s simRat_chr6.simRat.chr6 354762 19 + 647215 GGGAGAAGCCCTCACCACT - -a -s simMouse_chr6.simMouse.chr6 362449 18 + 636262 TGGAGGAACTCCTGTGCA -s Anc0.Anc0refChr0 22880 15 + 26507 T---TATACTTCTCCCCC -s Anc1.Anc1refChr6 23644 15 + 197743 T---TATACTTCTCCCCC -s Anc2.Anc2refChr17 17548 15 + 28526 T---TATACTTCTCCCCC -s mr.mrrefChr5 209508 18 + 294540 TGGAGGAACTCCTGTGCC -s simCow_chr6.simCow.chr6 333202 15 + 602619 T---TGTACGCCCCCCCC -s simDog_chr6.simDog.chr6 325577 15 + 593897 T---CACACTTCTGCCCC -s simHuman_chr6.simHuman.chr6 346718 15 + 601863 T---TATACTTCTCCCCC -s simRat_chr6.simRat.chr6 354781 18 + 647215 TGGGGGAACCACTGTGCC - -a -s simMouse_chr6.simMouse.chr6 362467 2 + 636262 AT -s Anc0.Anc0refChr0 22896 2 + 26507 GC -s Anc1.Anc1refChr6 23660 2 + 197743 GC -s Anc2.Anc2refChr17 17564 2 + 28526 GC -s mr.mrrefChr5 209527 2 + 294540 AT -s simCow_chr6.simCow.chr6 333218 2 + 602619 GT -s simDog_chr6.simDog.chr6 325593 2 + 593897 GC -s simHuman_chr6.simHuman.chr6 346734 2 + 601863 GC -s simRat_chr6.simRat.chr6 354800 2 + 647215 AT - -a -s simMouse_chr6.simMouse.chr6 362469 2 + 636262 AC -s Anc0.Anc0refChr0 22898 2 + 26507 AC -s Anc1.Anc1refChr6 23662 2 + 197743 AC -s Anc2.Anc2refChr17 17566 2 + 28526 AC -s mr.mrrefChr5 209529 2 + 294540 AC -s simCow_chr6.simCow.chr6 333220 2 + 602619 AC -s simDog_chr6.simDog.chr6 325596 2 + 593897 AC -s simHuman_chr6.simHuman.chr6 346736 2 + 601863 AC -s simRat_chr6.simRat.chr6 354802 2 + 647215 AT - -a -s simMouse_chr6.simMouse.chr6 362471 1 + 636262 C -s Anc0.Anc0refChr0 22900 1 + 26507 A -s Anc1.Anc1refChr6 23664 1 + 197743 A -s Anc2.Anc2refChr17 17568 1 + 28526 A -s mr.mrrefChr5 209531 1 + 294540 C -s simCow_chr6.simCow.chr6 333222 1 + 602619 A -s simDog_chr6.simDog.chr6 325598 1 + 593897 A -s simHuman_chr6.simHuman.chr6 346738 1 + 601863 T -s simRat_chr6.simRat.chr6 354808 1 + 647215 C - -a -s simMouse_chr6.simMouse.chr6 362472 7 + 636262 AGTATTA -s Anc0.Anc0refChr0 23157 7 + 26507 AATACTT -s Anc1.Anc1refChr6 23921 7 + 197743 AATACTT -s Anc2.Anc2refChr17 17825 7 + 28526 AATACAT -s mr.mrrefChr5 209532 7 + 294540 AGTATTA -s simCow_chr6.simCow.chr6 333522 7 + 602619 CCTACAA -s simDog_chr6.simDog.chr6 325864 7 + 593897 AATGCAT -s simHuman_chr6.simHuman.chr6 347015 7 + 601863 AATACTC -s simRat_chr6.simRat.chr6 354809 7 + 647215 AAAATTA - -a -s simMouse_chr6.simMouse.chr6 362479 9 + 636262 TAACCTCCT -s Anc0.Anc0refChr0 23164 9 + 26507 TAACTTACT -s Anc1.Anc1refChr6 23928 9 + 197743 TAACTTACT -s Anc2.Anc2refChr17 17832 9 + 28526 TAACTTACT -s mr.mrrefChr5 209539 9 + 294540 TAACTTCCT -s simCow_chr6.simCow.chr6 333529 9 + 602619 TAACTTAGT -s simDog_chr6.simDog.chr6 325873 9 + 593897 CAACCTACT -s simHuman_chr6.simHuman.chr6 347022 9 + 601863 TAACTTACT -s simRat_chr6.simRat.chr6 354816 9 + 647215 CAACTTCCT - -a -s simMouse_chr6.simMouse.chr6 362488 34 + 636262 AACTATGGTAGTGTATGGTAGCGATTTCTTGCCC -s Anc0.Anc0refChr0 23173 23 + 26507 AA-----------TATAGTAATGATTTCTAATCC -s Anc1.Anc1refChr6 23937 23 + 197743 AA-----------TATAGTAATGATTTCTAATCC -s Anc2.Anc2refChr17 17841 23 + 28526 AA-----------TATAACAATGATTTCTGATCC -s mr.mrrefChr5 209548 34 + 294540 AACTATGGTAGTGTATAGTAGTGATTTCTAGCCC -s simCow_chr6.simCow.chr6 333539 23 + 602619 AA-----------TATAACAATGATTTCTGATCC -s simDog_chr6.simDog.chr6 325882 22 + 593897 -A-----------TATAACAATGAATTCTGATCC -s simHuman_chr6.simHuman.chr6 347031 23 + 601863 AA-----------TATAGTAATGATTTTTAATCC -s simRat_chr6.simRat.chr6 354825 34 + 647215 AAGTATAGTAGCGTATAGTAGTGATTTCTAGCCC - -a -s simMouse_chr6.simMouse.chr6 362522 19 + 636262 TATTAGCGTGTGACAGACT -s Anc0.Anc0refChr0 23205 19 + 26507 TGTTGAAATGGGAAAAACT -s Anc1.Anc1refChr6 23969 19 + 197743 TGTTGAAATGGGAAAAACT -s Anc2.Anc2refChr17 17873 19 + 28526 TGTTGAAGTGGGGAAAACT -s mr.mrrefChr5 209582 19 + 294540 TATTAGCATGTGACAGACT -s simCow_chr6.simCow.chr6 333571 18 + 602619 TGATCATGTGTGGTA-ATG -s simDog_chr6.simDog.chr6 325910 19 + 593897 TGTTGAAGTGGGGAAACCT -s simHuman_chr6.simHuman.chr6 347063 19 + 601863 TGTTGAAATGGGAAACACT -s simRat_chr6.simRat.chr6 354859 19 + 647215 AATTAGCATGTGACAGATT - -a -s simMouse_chr6.simMouse.chr6 362541 1 + 636262 G -s Anc0.Anc0refChr0 23229 1 + 26507 G -s Anc1.Anc1refChr6 23993 1 + 197743 G -s Anc2.Anc2refChr17 17897 1 + 28526 G -s mr.mrrefChr5 209601 1 + 294540 G -s simCow_chr6.simCow.chr6 333594 1 + 602619 G -s simDog_chr6.simDog.chr6 325934 1 + 593897 G -s simHuman_chr6.simHuman.chr6 347087 1 + 601863 G -s simRat_chr6.simRat.chr6 354878 1 + 647215 G - -a -s simMouse_chr6.simMouse.chr6 362542 10 + 636262 TCCTTATCCT -s Anc0.Anc0refChr0 23230 10 + 26507 TCCATACCCA -s Anc1.Anc1refChr6 23994 10 + 197743 TCCATACCCA -s Anc2.Anc2refChr17 17902 10 + 28526 TCCATACCCA -s mr.mrrefChr5 209602 10 + 294540 TCCTTATCCT -s simCow_chr6.simCow.chr6 333599 10 + 602619 TCCATACCCA -s simDog_chr6.simDog.chr6 325939 10 + 593897 TCCATACCCA -s simHuman_chr6.simHuman.chr6 347088 10 + 601863 ATGATACCCA -s simRat_chr6.simRat.chr6 354879 10 + 647215 TCCTTATCCT - -a -s simMouse_chr6.simMouse.chr6 362552 46 + 636262 CTAGCCTCTGGTACCCATATCACAGGCCTGTGGGTCTGTACCAAAA -s Anc0.Anc0refChr0 23240 39 + 26507 CCAGCCTCTGTTCTTCATGTTCCAGGCCTGTAAGCCTGT------- -s Anc1.Anc1refChr6 24004 39 + 197743 CCAGCCTCTGTTCTTCATGTTCCAGGCCTGTAAGCCTGT------- -s Anc2.Anc2refChr17 17918 39 + 28526 CCATCCTCCGTTCTTAATGTTCCAGGCCTGTAAGCCCGT------- -s mr.mrrefChr5 209612 46 + 294540 CTAGCCTCTGTTATCCATGTCACAGGCCTGTGGGTCTGTACCAAAA -s simCow_chr6.simCow.chr6 333615 35 + 602619 ----CCTTAGTGCTTAAGGTTCCAGGGCTGTAAGCCCGT------- -s simDog_chr6.simDog.chr6 325957 33 + 593897 CCATTCTCCATTCTAAATGTTCCAGGCCTGTGA------------- -s simHuman_chr6.simHuman.chr6 347098 39 + 601863 CCAGCCTCTGTTCTTCATGTTCAAGGCCTTTAAGCCTGC------- -s simRat_chr6.simRat.chr6 354889 46 + 647215 CTTGCCTCTGTTATCCACGTCACAGGCCTGTGGGTCTGTGCCGAAA - -a -s simMouse_chr6.simMouse.chr6 362598 55 + 636262 CTAGTAACAAGTGTGGAACTCTGTTCCTATATTGTTTGTACTGAAGTCTGTCTGA -s Anc0.Anc0refChr0 23279 45 + 26507 CTAG-AACAAGTGTAGCACTCTGTTCCTATGGTGTTT---------TCTGAGTGA -s Anc1.Anc1refChr6 24043 54 + 197743 CTAG-AACAAGTGTAGCACTCTGTTCCTATGGTGTTTGTATTGAGCTCTGAGTGA -s Anc2.Anc2refChr17 17957 45 + 28526 CCAA-CACAAGTGTAGCTTTCCGTTCCTAGGGGGTTT---------TCTGAGTGA -s mr.mrrefChr5 209658 55 + 294540 CTAGTAACAAGTGTGGAACTCTGTTCCTATATTGTTTGTACTGAAGTCTGTCTGA -s simCow_chr6.simCow.chr6 333651 45 + 602619 CCAA-CACAAGTGTAGCTTTCCGTTCCTAGGGGGTTT---------TCTGAGTGA -s simHuman_chr6.simHuman.chr6 347137 54 + 601863 CTAG-AACAAGTGGACTACTCTATTCCTATGGTGCTTGTATTGAGCTCTGAGTGG -s simRat_chr6.simRat.chr6 354935 54 + 647215 CAAGTAACAACTGTGGAACCGTGTTCCGATATTATTTGTACTG-AGACTGTCTGA - -a -s simMouse_chr6.simMouse.chr6 362653 1 + 636262 T -s Anc0.Anc0refChr0 23324 1 + 26507 T -s Anc1.Anc1refChr6 24097 1 + 197743 T -s Anc2.Anc2refChr17 18002 1 + 28526 T -s mr.mrrefChr5 209713 1 + 294540 T -s simCow_chr6.simCow.chr6 333696 1 + 602619 T -s simHuman_chr6.simHuman.chr6 347199 1 + 601863 T -s simRat_chr6.simRat.chr6 354989 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 362654 9 + 636262 TGTTGCTTC -s Anc0.Anc0refChr0 23325 9 + 26507 TGTTGCTTC -s Anc1.Anc1refChr6 24098 9 + 197743 TGTTGCTTC -s Anc2.Anc2refChr17 18004 9 + 28526 TTTTGCTTC -s mr.mrrefChr5 209714 9 + 294540 TGTTGCTTC -s simCow_chr6.simCow.chr6 333698 9 + 602619 TTTTGCTTC -s simHuman_chr6.simHuman.chr6 347200 9 + 601863 TGCATATTA -s simRat_chr6.simRat.chr6 354990 9 + 647215 TCTTGTATC - -a -s simMouse_chr6.simMouse.chr6 362663 18 + 636262 AACTGGAAGTCATCATCA -s Anc0.Anc0refChr0 23334 18 + 26507 AGCTGGAAGTCATCAGAA -s Anc1.Anc1refChr6 24107 18 + 197743 AGCTGGAAGTCATCAGAA -s Anc2.Anc2refChr17 18017 18 + 28526 AGTTGGAAGTCATCAGAA -s mr.mrrefChr5 209723 18 + 294540 AACTGGAAGTCATCATCA -s simCow_chr6.simCow.chr6 333711 18 + 602619 AGTTGGGAATCACCAGAA -s simDog_chr6.simDog.chr6 325990 13 + 593897 -----GAAGTTATCAGAG -s simHuman_chr6.simHuman.chr6 347209 18 + 601863 AGCTGGATGTCATCAGAA -s simRat_chr6.simRat.chr6 354999 15 + 647215 AAT---GAGTCATCATCA - -a -s simMouse_chr6.simMouse.chr6 362681 26 + 636262 GCAACCTACTGCTTTATCACCTGCGT -s Anc0.Anc0refChr0 23360 25 + 26507 GAAGCCTACTGCTTTGTCACCTG-GT -s Anc1.Anc1refChr6 24133 25 + 197743 GAAGCCTACTGCTTTGTCACCTG-GT -s Anc2.Anc2refChr17 18043 25 + 28526 GAAGCCTACTTGTTTGTCACCTG-GA -s mr.mrrefChr5 209741 26 + 294540 GCAACCTACTGCTTTATCACCTGCGT -s simCow_chr6.simCow.chr6 333737 25 + 602619 GAATCCTACTTGTTTATCACCTT-GA -s simDog_chr6.simDog.chr6 326011 25 + 593897 AAAGCCTACTTGTTTGTCACCAG-GA -s simHuman_chr6.simHuman.chr6 347235 25 + 601863 GAAGCCTACTGCTTTCTCACCTG-GT -s simRat_chr6.simRat.chr6 355014 26 + 647215 GCAACCTCCTGTTTTATCACCTGCGT - -a -s simMouse_chr6.simMouse.chr6 362707 47 + 636262 GACTTTTTAGAGGTCTTAACCTATTAACTTGACACAATCTGGAGATC -s Anc0.Anc0refChr0 23387 20 + 26507 CACTTTTCAGAGGTCTTAAC--------------------------- -s Anc1.Anc1refChr6 24160 20 + 197743 CACTTTTCAGAGGTCTTAAC--------------------------- -s Anc2.Anc2refChr17 18070 20 + 28526 CAGTCTCCAGAGGTCTTAAC--------------------------- -s mr.mrrefChr5 209767 47 + 294540 CACTTTTTAGAGGTCTTAACCTATTAACTTGACACAATCTGGAGATC -s simCow_chr6.simCow.chr6 333764 20 + 602619 CAGTCTCCAGAGGCCTTAAC--------------------------- -s simDog_chr6.simDog.chr6 326038 20 + 593897 CAGTCTCCATTGGTCTTAAC--------------------------- -s simHuman_chr6.simHuman.chr6 347262 20 + 601863 CACTTCTCAGAGGGCTTAAC--------------------------- -s simRat_chr6.simRat.chr6 355040 47 + 647215 CACTTTTTGGTGGTCTTAGCGCACTAGCTTAGCAAAGTCTAGAGATC - -a -s simMouse_chr6.simMouse.chr6 362754 56 + 636262 TCAGGAGGCCATGGGTTGGGGATGGCCCTGTTATACAACTCATAATCACTTGCATC -s Anc0.Anc0refChr0 23414 56 + 26507 TCAGAAGGCCACGGGTTGGGGATAGCCCAGTTGAACAGCTTGCAAACACCTGAGTC -s Anc1.Anc1refChr6 24187 56 + 197743 TCAGAAGGCCACGGGTTGGGGATAGCCCAGTTGAACAGCTTGCAAACACCTGAGTC -s Anc2.Anc2refChr17 18097 56 + 28526 TCAGAAGGCCACCGGTTGGGGATAACTCAGTTGAACAGCTTGCAAACACCTGAGTC -s mr.mrrefChr5 209824 56 + 294540 TCAGGAGGCCATGGGTTGGGGATGGCCCTGTTATACAACTTGTAATCACTTGCATC -s simCow_chr6.simCow.chr6 333790 56 + 602619 TCAGAAGGCCACTGGTTGGAGATCACTAAGTTAAACACCTTGCAAACACCTGATTC -s simDog_chr6.simDog.chr6 326065 56 + 593897 TCAGAAGGCCAACAGTTGGGGATAATTCAGTTGGACAGCATACAAGCGCATGAGTC -s simHuman_chr6.simHuman.chr6 347289 56 + 601863 TCAGAATGCCACGGGTTGGGGATTGCCCAGTGGAGTGGCTTGCAAACACCTGAGTC -s simRat_chr6.simRat.chr6 355099 56 + 647215 TCAGGAGGTCATGCGTTGGGGACAGCCCCATTACACAACTTGTAACCACTTGCATC - -a -s simMouse_chr6.simMouse.chr6 362810 7 + 636262 AATGACC -s Anc0.Anc0refChr0 23480 7 + 26507 AACAACA -s Anc1.Anc1refChr6 24253 7 + 197743 AACAACA -s Anc2.Anc2refChr17 18163 7 + 28526 AACAACA -s mr.mrrefChr5 209880 7 + 294540 AATGACC -s simCow_chr6.simCow.chr6 333856 7 + 602619 AACAACA -s simDog_chr6.simDog.chr6 326132 7 + 593897 AACAACA -s simHuman_chr6.simHuman.chr6 347355 7 + 601863 AACAACA -s simRat_chr6.simRat.chr6 355155 7 + 647215 AATGACC - -a -s simMouse_chr6.simMouse.chr6 362817 10 + 636262 TACTGAATGG -s Anc0.Anc0refChr0 23487 10 + 26507 CACTGAATGG -s Anc1.Anc1refChr6 24260 10 + 197743 CACTGAATGG -s Anc2.Anc2refChr17 18170 10 + 28526 CCCTGACTGA -s mr.mrrefChr5 209887 10 + 294540 TACTGAATGG -s simCow_chr6.simCow.chr6 333864 10 + 602619 CCCTGACTGA -s simDog_chr6.simDog.chr6 326139 3 + 593897 CCC------- -s simHuman_chr6.simHuman.chr6 347362 10 + 601863 CACTGGATGG -s simRat_chr6.simRat.chr6 355162 10 + 647215 TACTGAATGG - -a -s simMouse_chr6.simMouse.chr6 362827 11 + 636262 ATGAAAAATAT -s Anc0.Anc0refChr0 23497 11 + 26507 ATAAAAATTAT -s Anc1.Anc1refChr6 24270 11 + 197743 ATAAAAATTAT -s Anc2.Anc2refChr17 18180 11 + 28526 ATAAAAATTAT -s mr.mrrefChr5 209897 11 + 294540 ATGAAAAATAT -s simCow_chr6.simCow.chr6 333874 11 + 602619 ATAAAAATCAT -s simDog_chr6.simDog.chr6 326142 9 + 593897 --AAAAATTAC -s simHuman_chr6.simHuman.chr6 347372 11 + 601863 ATAAAAATTAT -s simRat_chr6.simRat.chr6 355173 11 + 647215 ATCAATGACCT - -a -s simMouse_chr6.simMouse.chr6 362838 5 + 636262 TTGAT -s Anc0.Anc0refChr0 23508 4 + 26507 TTGA- -s Anc1.Anc1refChr6 24281 5 + 197743 TTGAC -s Anc2.Anc2refChr17 18191 4 + 28526 TTGA- -s mr.mrrefChr5 209908 5 + 294540 TTGAT -s simCow_chr6.simCow.chr6 333885 4 + 602619 TCGA- -s simDog_chr6.simDog.chr6 326151 4 + 593897 CTGA- -s simHuman_chr6.simHuman.chr6 347383 5 + 601863 TTGAC -s simRat_chr6.simRat.chr6 355190 5 + 647215 CGGAT - -a -s simMouse_chr6.simMouse.chr6 362843 6 + 636262 GAAAAC -s Anc0.Anc0refChr0 23512 6 + 26507 GACAAC -s Anc1.Anc1refChr6 24286 6 + 197743 GACAAC -s Anc2.Anc2refChr17 18195 6 + 28526 ACCAAC -s mr.mrrefChr5 209913 6 + 294540 GAAAAC -s simCow_chr6.simCow.chr6 333890 6 + 602619 ACAAAC -s simDog_chr6.simDog.chr6 326155 6 + 593897 ACCAAC -s simHuman_chr6.simHuman.chr6 347469 6 + 601863 GAGAAC -s simRat_chr6.simRat.chr6 355195 6 + 647215 GAAAAC - -a -s simMouse_chr6.simMouse.chr6 362849 32 + 636262 TAGTCAGTCTCATAATCGCATGTGTCAGAGAA -s Anc0.Anc0refChr0 23518 13 + 26507 TAGCCAG-------------------AGAAAA -s Anc1.Anc1refChr6 24292 13 + 197743 TAGCCAG-------------------AGAAAA -s Anc2.Anc2refChr17 18201 13 + 28526 TAGCCAG-------------------AGAAAA -s mr.mrrefChr5 209919 32 + 294540 TAGTCAGTCTTATAATCGCATGTGTCAGAGAA -s simCow_chr6.simCow.chr6 333896 10 + 602619 AAGCCAT-------------------AGA--- -s simDog_chr6.simDog.chr6 326161 12 + 593897 TAGC-AG-------------------AAAAAA -s simHuman_chr6.simHuman.chr6 347475 13 + 601863 CAGCCAG-------------------AGATAA -s simRat_chr6.simRat.chr6 355203 32 + 647215 TATCTAGTTTTATAATCACATGTGTCGCAGAC - -a -s simMouse_chr6.simMouse.chr6 362881 24 + 636262 TACAGCAGTACCTCTCATATCCTG -s Anc0.Anc0refChr0 23533 24 + 26507 TGTTTCAATTCATATCACACCCTG -s Anc1.Anc1refChr6 24307 24 + 197743 TGTTTCAATTCATATCACACCCTG -s Anc2.Anc2refChr17 18216 24 + 28526 TGTTTCAATTCATATCACACCCTG -s mr.mrrefChr5 209951 24 + 294540 TGCAGCAGTACCTCTCATATCCTG -s simCow_chr6.simCow.chr6 333906 23 + 602619 -GTTTCAATTCATATCACCCACTG -s simDog_chr6.simDog.chr6 326175 22 + 593897 TGTTTCAATTC--ATCATACCCTG -s simHuman_chr6.simHuman.chr6 347490 24 + 601863 TGTTTCACTTCATATCACACCGTG -s simRat_chr6.simRat.chr6 355235 24 + 647215 TGCAGCAGTACCTCTCATATACTA - -a -s simMouse_chr6.simMouse.chr6 362905 8 + 636262 GACGATCT -s Anc0.Anc0refChr0 23562 8 + 26507 GAAAACCC -s Anc1.Anc1refChr6 24336 8 + 197743 GAAAACCC -s Anc2.Anc2refChr17 18245 8 + 28526 GAAAACCC -s mr.mrrefChr5 209975 8 + 294540 GACAACCT -s simCow_chr6.simCow.chr6 333934 8 + 602619 GAAAACCC -s simDog_chr6.simDog.chr6 326202 8 + 593897 GAAAACCC -s simHuman_chr6.simHuman.chr6 347519 8 + 601863 GAAAACCC -s simRat_chr6.simRat.chr6 355259 8 + 647215 GGCAACCT - -a -s simMouse_chr6.simMouse.chr6 362913 15 + 636262 CTCTAAAACATGAGG -s Anc0.Anc0refChr0 23573 15 + 26507 TGTTACAACATAAGG -s Anc1.Anc1refChr6 24347 15 + 197743 TGTTACAACATAAGG -s Anc2.Anc2refChr17 18256 15 + 28526 TGTTGCAACATAAGG -s mr.mrrefChr5 209983 15 + 294540 CTCTAAAACATGAGG -s simCow_chr6.simCow.chr6 333945 15 + 602619 TGTCGCAACATAGAG -s simDog_chr6.simDog.chr6 326213 12 + 593897 TGTT---GAATAAGG -s simHuman_chr6.simHuman.chr6 347530 15 + 601863 TGTTACAACATAAGG -s simRat_chr6.simRat.chr6 355267 15 + 647215 CTCTAAAACATTGGG - -a -s simMouse_chr6.simMouse.chr6 362928 3 + 636262 TAT -s Anc0.Anc0refChr0 23592 3 + 26507 TAG -s Anc1.Anc1refChr6 24366 3 + 197743 TAG -s Anc2.Anc2refChr17 18275 3 + 28526 TAG -s mr.mrrefChr5 209998 3 + 294540 TAT -s simCow_chr6.simCow.chr6 333964 3 + 602619 TAA -s simDog_chr6.simDog.chr6 326229 3 + 593897 TAG -s simHuman_chr6.simHuman.chr6 347549 3 + 601863 TAG -s simRat_chr6.simRat.chr6 355282 3 + 647215 TTT - -a -s simMouse_chr6.simMouse.chr6 362931 3 + 636262 ACT -s Anc0.Anc0refChr0 23595 3 + 26507 ACT -s Anc1.Anc1refChr6 24370 3 + 197743 ACT -s Anc2.Anc2refChr17 18278 3 + 28526 ACT -s mr.mrrefChr5 210002 3 + 294540 ACT -s simCow_chr6.simCow.chr6 333967 3 + 602619 ACT -s simDog_chr6.simDog.chr6 326232 3 + 593897 ACT -s simHuman_chr6.simHuman.chr6 347553 3 + 601863 CCT -s simRat_chr6.simRat.chr6 355286 3 + 647215 ACC - -a -s simMouse_chr6.simMouse.chr6 362934 26 + 636262 ACCATTTAAAGTTGAATTACATGGAT -s Anc0.Anc0refChr0 23598 26 + 26507 ACCATTTAAATTTGAATCTCATGAAT -s Anc1.Anc1refChr6 24373 26 + 197743 ACCATTTAAATTTGAATCTCATGAAT -s Anc2.Anc2refChr17 18281 26 + 28526 ACCATTTAAATTTGAATCTCATGAAT -s mr.mrrefChr5 210005 26 + 294540 ACCATTTAAAGTTGAATTACATGGAT -s simCow_chr6.simCow.chr6 333970 21 + 602619 ACCATTTAAATCTGAATTTCA----- -s simDog_chr6.simDog.chr6 326235 26 + 593897 ACCATTTAAGTTTGAATCTCGTGAAT -s simHuman_chr6.simHuman.chr6 347563 26 + 601863 ACCATGTCAAATTGAAACTCATGAAT -s simRat_chr6.simRat.chr6 355289 26 + 647215 ACCATTTAAAGTTGAATTGCATAGAT - -a -s simMouse_chr6.simMouse.chr6 362960 12 + 636262 TAGCTTGATGTT -s Anc0.Anc0refChr0 23624 12 + 26507 TAGTATGACTTC -s Anc1.Anc1refChr6 24399 12 + 197743 TAGTATGACTTC -s Anc2.Anc2refChr17 18307 12 + 28526 TAGTACGACTTC -s mr.mrrefChr5 210031 12 + 294540 TAGCTTGATGTC -s simCow_chr6.simCow.chr6 333991 12 + 602619 TAACAGAATTTC -s simDog_chr6.simDog.chr6 326261 12 + 593897 TAGTACGGCTTC -s simHuman_chr6.simHuman.chr6 347589 12 + 601863 TAGTATGAAATC -s simRat_chr6.simRat.chr6 355338 12 + 647215 TAGCTTGATGTC - -a -s simMouse_chr6.simMouse.chr6 362972 30 + 636262 GTATTCTGCAGACTTCAAGCCACTGAGCCC -s Anc0.Anc0refChr0 23637 30 + 26507 CTCTGCTACAGTTTTGAGGCACTTAGAACC -s Anc1.Anc1refChr6 24412 30 + 197743 CTCTGCTACAGTTTTGAGGCACTTAGAACC -s Anc2.Anc2refChr17 18320 30 + 28526 CCCTGCTACAGTTTTGAGGGACTTAGAACC -s mr.mrrefChr5 210043 30 + 294540 CTATTCTGCAGACTTCAAGCCACTGAGCCC -s simCow_chr6.simCow.chr6 334004 30 + 602619 CCTTGCTACAGTTTTGAGGGACTTAGAACC -s simDog_chr6.simDog.chr6 326274 21 + 593897 CCCTGC--CGATATTGAGGGACT------- -s simHuman_chr6.simHuman.chr6 347602 30 + 601863 CTGTGCTTCAGCTTTGAGGCATTTAGAACC -s simRat_chr6.simRat.chr6 355350 30 + 647215 CTATTCTATGGACTTCCAGTCACTCAGCCC - -a -s simMouse_chr6.simMouse.chr6 363002 151 + 636262 AACGTGGCATCACCTAATGGGATCAGTGTTGTCTTTTGGTGACAATTTATAACCATCACTGATAAATGATTGACTTGCATAGATGTTAGAACTTGGTCACATGCCTACGATAGCCATATCCTGCCCTGTGCCATCCTTCTGTGTTTGGGTT -s Anc0.Anc0refChr0 23667 151 + 26507 AACCCAGCATCAGCCCATGGAATCAGTGTTGGCTTAAATTGGCAATTGGGAATCAACACTAATAAATGGTCAGCTTGCATTTATATTAGATTTTGGTGGCATTCCTAGGATAGCCACATCCTGCCCTGTGCGATCCTTTTGGGTTTGGTCC -s Anc1.Anc1refChr6 24442 151 + 197743 AACCCAGCATCAGCCCATGGAATCAGTGTTGGCTTAAATTGGCAATTGGGAATCAACACTAATAAATGGTCAGCTTGCATTTATATTAGATTTTGGTGGCATTCCTAGGATAGCCACATCCTGCCCTGTGCGATCCTTTTGGGTTTGGTCC -s Anc2.Anc2refChr17 18350 151 + 28526 AACCCAGCGTCAGCCCATTGAATCAGTGTTGGCTCAAATTGGCAATTGGGGATCAACACTAATAGATGGTCAGCTTGCATTTATATTAGATTTTGGTGGCATTCCTTGGATAACCACATCCTGCCCTGTGTGATCCTTTCAGGTTTGGTCT -s mr.mrrefChr5 210073 151 + 294540 AACGTAGCATCACCTAATGGGATCAGTGTTGTCTTTTGGTGACAATTTATAACCATCACTGATAAATGGTTGGCTTGCATAGATGTTAGAACTTGGTCACATGCCTACGATAGCCATATCCTGCCCTGTGCCATCCTTCTGGGTTTGGGTC -s simCow_chr6.simCow.chr6 334040 137 + 602619 AACCCAACTTAAGCCCGTTGAATCAGTGTTGGCTCGAGTTAGCAATTGGGCATCAACACTAATATATGGTCAACTTGCACTTATATTAGATTTTGATGGCATGC--------------ACCTGCCCTGTGTGCTCCTTTCAGGTCGGGTCT -s simDog_chr6.simDog.chr6 326295 145 + 593897 ------GTGGCAGCCCATTGAATCAGTGTTGGCTCAAATTGACAATTGAGGATCAACACAGATAGATGGTTGGCTTGCATTTATGTTAGCATTTGGTGGCATTCCTTGGATAACCACATCCTGCCCTGTGTGATCCTTTCAGGTTTGGTCT -s simHuman_chr6.simHuman.chr6 347632 146 + 601863 TACTCAGCATTGTCCCAGGGAGTCAGT---GGCTTCAATTGGCAATCGGGAATC--CACTAATAAATCGTCAGTTTGTGTTTATATTAGATGTTGGTGGCATTCCTAATATAGCCACAGCCTGCCCTGTGCGATCCTTTTGGGTTTGGCCC -s simRat_chr6.simRat.chr6 355380 150 + 647215 AACGTAGGATCACCAAGTGGGATCAGTGTTGTCTTCTGGTAACAATTTACAACCATCACTGATATATGGCTGGC-TGCATAGAAGTTAGCACTTGGTCACATGCCAAGGATAGCCATGTCCTCCAATGTGCCATCCTTCTGGGTTTGGGTC - -a -s simMouse_chr6.simMouse.chr6 363153 76 + 636262 TGGGTTTGAAGCAAGCCTCATGACCCTGCTAGTCACCATCACTGTTGATGAAAGTTATTAATTAATGGAAACTCTG -s Anc0.Anc0refChr0 23824 74 + 26507 TTAGTCTGAAGATAGTCTCATGACGCTGTTACTTACCGTCCCCTTTGGTGAAGATTAATAATTAGTTGAAGTTC-- -s Anc1.Anc1refChr6 24599 76 + 197743 TTAGTCTGAAGATAGTCTCATGACGCTGTTACTTACCGTCCCCTTTGGTGAAGATTAATAATTAGTTGAAGTTCTG -s Anc2.Anc2refChr17 18507 74 + 28526 TTAGTCTGAAGATAGTCTCATGACCCTGTTACTTACTGTCCCCTGTGGTGGAGATTGATAATTAATTGAAGTTT-- -s mr.mrrefChr5 210224 76 + 294540 TGGGTTTGAAGCAAGCCTCATGACGCTGTTAGTCACCATCACTGTTGATGAAAGTTATTAATTAGTGGAAACTCTG -s simCow_chr6.simCow.chr6 334183 73 + 602619 TTGGTCTGAAGATAGTCTAATGGCCCTGTTACTTACTGTCTTCACTGATACAGATTGAT-ATTAATCAAAGTTT-- -s simDog_chr6.simDog.chr6 326446 74 + 593897 TTAGTCTGAAGATAGACTCATGACCCTGTTACTTAGTGTCCCCTGTGGTGGAAATTGATAATTAATTGAAGTTT-- -s simHuman_chr6.simHuman.chr6 347784 68 + 601863 TTAGTCTGAAGATAGTCTCATGACGCTGTTATTGACCGTCCCCCTTGGTCAAGATTAATAATTAG--------CTG -s simRat_chr6.simRat.chr6 355530 76 + 647215 TGGGTTTGAAGCAAGCCTTATGACGCTGTTAGTTACCATCTTTGTTAATGAAAGTTATTAATTAGTTGAAACTCTG - -a -s simMouse_chr6.simMouse.chr6 363229 5 + 636262 TGGTA -s Anc0.Anc0refChr0 23898 5 + 26507 TGGTA -s Anc1.Anc1refChr6 24675 5 + 197743 TGGTA -s Anc2.Anc2refChr17 18581 5 + 28526 TGGTA -s mr.mrrefChr5 210300 5 + 294540 TGGTA -s simDog_chr6.simDog.chr6 326522 5 + 593897 TGGTA -s simHuman_chr6.simHuman.chr6 347852 5 + 601863 TGGTA -s simRat_chr6.simRat.chr6 355606 5 + 647215 TGGTA - -a -s simMouse_chr6.simMouse.chr6 363234 38 + 636262 GGCCCATAACAGCAAAAGGTCTAATTTCATCCTAATAC -s Anc0.Anc0refChr0 23903 38 + 26507 GATAGTTAACAGCAGAAGGTCTAACTGATCTCTAATCC -s Anc1.Anc1refChr6 24680 38 + 197743 GATAGTTAACAGCAGAAGGTCTAACTGATCTCTAATCC -s Anc2.Anc2refChr17 18586 38 + 28526 GATAGTTAACAGCGGAAGGCCTAACTGATCTCTAATCC -s mr.mrrefChr5 210305 38 + 294540 GGTACATAACAGCAAAAGGTCTAATTTCATCCTAATCC -s simCow_chr6.simCow.chr6 334256 31 + 602619 -GCAGTATACATCCGAAAG------TGGTCTCCATTCC -s simDog_chr6.simDog.chr6 326532 37 + 593897 GATA-CTAATAGCGGAAGGCCTAACTGATCTCTAATCC -s simHuman_chr6.simHuman.chr6 347857 38 + 601863 AATAGTTAACAGCAGAAGGTCTATCTGATCTCTAATCT -s simRat_chr6.simRat.chr6 355611 36 + 647215 GTTACATA--AGCAAAAGGTCTAATCTCATCCTAACCC - -a -s simMouse_chr6.simMouse.chr6 363272 1 + 636262 T -s Anc0.Anc0refChr0 23941 1 + 26507 T -s Anc1.Anc1refChr6 24718 1 + 197743 T -s Anc2.Anc2refChr17 18625 1 + 28526 T -s mr.mrrefChr5 210343 1 + 294540 T -s simDog_chr6.simDog.chr6 326571 1 + 593897 T -s simHuman_chr6.simHuman.chr6 347895 1 + 601863 T -s simRat_chr6.simRat.chr6 355647 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 363273 28 + 636262 ATCTTATCCTAATCCTATCTTTTGCCAC -s Anc0.Anc0refChr0 23943 21 + 26507 ATATTTTGAT-------CGAACTGCCAC -s Anc1.Anc1refChr6 24720 21 + 197743 ATATTTTGAT-------CGAACTGCCAC -s Anc2.Anc2refChr17 18627 21 + 28526 ATATTTTGAT-------CGAACTGCCAC -s mr.mrrefChr5 210344 21 + 294540 ATCTTTTGAT-------TGTTCTGCCAC -s simCow_chr6.simCow.chr6 334288 21 + 602619 ATATTTTGAT-------TGAACTTCTAC -s simDog_chr6.simDog.chr6 326573 21 + 593897 ATATCATTAA-------CAAACTGCCAC -s simHuman_chr6.simHuman.chr6 347897 21 + 601863 ATATTTTGAT-------CGAACTGCCAC -s simRat_chr6.simRat.chr6 355648 21 + 647215 ATCTTTTGAT-------TGTGCTGCCAC - -a -s simMouse_chr6.simMouse.chr6 363301 26 + 636262 TTGGATGTTTTGTAATTTGATAATAG -s Anc0.Anc0refChr0 23964 26 + 26507 TTGGATGTTTTCTAATTTGATAATAG -s Anc1.Anc1refChr6 24741 26 + 197743 TTGGATGTTTTCTAATTTGATAATAG -s Anc2.Anc2refChr17 18648 26 + 28526 TTGGATGTTTTCTAATTTGATAATAG -s mr.mrrefChr5 210365 26 + 294540 TTGGATGTTTTGTAATTTGATAATAG -s simCow_chr6.simCow.chr6 334309 26 + 602619 TTGGATATTTTGTAATTTGATAATAG -s simDog_chr6.simDog.chr6 326594 26 + 593897 TTGGATGCTCTCTAATTTGATAGTAG -s simHuman_chr6.simHuman.chr6 347923 26 + 601863 TTAGATGTTTTATAATTTTACAATAG -s simRat_chr6.simRat.chr6 355669 25 + 647215 -TGGATTTTCTGTAACTTGATAATAG - -a -s simMouse_chr6.simMouse.chr6 363327 11 + 636262 GGGGAGAGTGT -s Anc0.Anc0refChr0 23990 11 + 26507 GAAGAAAGCAG -s Anc1.Anc1refChr6 24767 11 + 197743 GAAGAAAGCAG -s Anc2.Anc2refChr17 18674 11 + 28526 GAAGAAAGCAG -s mr.mrrefChr5 210391 11 + 294540 GGGGAAAGTGT -s simCow_chr6.simCow.chr6 334335 11 + 602619 AAAGGAAGGAG -s simDog_chr6.simDog.chr6 326623 9 + 593897 GAAGAAAGC-- -s simHuman_chr6.simHuman.chr6 347949 11 + 601863 GAAGAAAGCAG -s simRat_chr6.simRat.chr6 355694 11 + 647215 GGGGAATGTGT - -a -s simMouse_chr6.simMouse.chr6 363338 15 + 636262 TACTATTACTGGAGC -s Anc0.Anc0refChr0 24001 13 + 26507 TACT--TGTTAGTGT -s Anc1.Anc1refChr6 24778 14 + 197743 TACTA-TGTTAGTGT -s Anc2.Anc2refChr17 18685 13 + 28526 TACT--TGTTAGTGT -s mr.mrrefChr5 210402 15 + 294540 TACTATTACTGGAGC -s simCow_chr6.simCow.chr6 334346 13 + 602619 TACT--TGTTAGTGT -s simDog_chr6.simDog.chr6 326632 1 + 593897 --------------C -s simHuman_chr6.simHuman.chr6 347960 14 + 601863 TACTA-AGTTAGTGT -s simRat_chr6.simRat.chr6 355717 15 + 647215 TACTCTTACTGGAGC - -a -s simMouse_chr6.simMouse.chr6 363353 5 + 636262 ATTAT -s Anc0.Anc0refChr0 24014 5 + 26507 ACTAG -s Anc1.Anc1refChr6 24792 5 + 197743 ACTAG -s Anc2.Anc2refChr17 18698 5 + 28526 ACCAG -s mr.mrrefChr5 210417 5 + 294540 ATTAT -s simCow_chr6.simCow.chr6 334366 5 + 602619 ACCAG -s simDog_chr6.simDog.chr6 326633 5 + 593897 ACCAG -s simHuman_chr6.simHuman.chr6 347974 5 + 601863 ACTAG -s simRat_chr6.simRat.chr6 355732 5 + 647215 ATAAT - -a -s simMouse_chr6.simMouse.chr6 363358 12 + 636262 CCTGAGATCTGT -s Anc0.Anc0refChr0 24019 12 + 26507 CTAGAGATCCAT -s Anc1.Anc1refChr6 24797 12 + 197743 CTAGAGATCCAT -s Anc2.Anc2refChr17 18703 12 + 28526 GTAGAGATCCAT -s mr.mrrefChr5 210422 12 + 294540 CTTGAGATCTGT -s simCow_chr6.simCow.chr6 334374 12 + 602619 GTAGAAATCCAT -s simDog_chr6.simDog.chr6 326638 12 + 593897 GTAGAGATCCTT -s simHuman_chr6.simHuman.chr6 347979 12 + 601863 CTACAGATCCAT -s simRat_chr6.simRat.chr6 355737 12 + 647215 CTTGAGGTCTGT - -a -s simMouse_chr6.simMouse.chr6 363370 29 + 636262 AGCCTGCCACTGGTGTAAGAGGGTTGAGG -s Anc0.Anc0refChr0 24031 29 + 26507 GGCCTGCCACTGACATAAGAGGGTTAAGT -s Anc1.Anc1refChr6 24809 29 + 197743 GGCCTGCCACTGACATAAGAGGGTTAAGT -s Anc2.Anc2refChr17 18715 29 + 28526 GGCCTGCCACTGACATAAGAGGGTTAAGT -s mr.mrrefChr5 210434 29 + 294540 AGCCTGCCACTGGTGTAAGAGGGTTGAGG -s simCow_chr6.simCow.chr6 334386 29 + 602619 GGCCTGCCACTGACGTAAGAGGATTAAAT -s simDog_chr6.simDog.chr6 326650 29 + 593897 GGCCTGCCACAGACATAAATGGGTTGAGT -s simHuman_chr6.simHuman.chr6 347991 29 + 601863 CTCCTGCCACTGACATAAGAAGGTTAAGC -s simRat_chr6.simRat.chr6 355750 29 + 647215 AGCATGCCACTGGTGTAACAGGATTGAGG - -a -s simMouse_chr6.simMouse.chr6 363399 12 + 636262 TTCTACTTATGC -s Anc0.Anc0refChr0 24089 8 + 26507 TTCTAGC----T -s Anc1.Anc1refChr6 24867 12 + 197743 TTCTAGCTACAT -s Anc2.Anc2refChr17 18773 8 + 28526 TACTAGT----T -s mr.mrrefChr5 210492 12 + 294540 TTCTACTTACAT -s simCow_chr6.simCow.chr6 334440 8 + 602619 TAGTAGT----T -s simDog_chr6.simDog.chr6 326714 8 + 593897 TACTAGT----T -s simHuman_chr6.simHuman.chr6 348049 12 + 601863 TTCTAACTACAT -s simRat_chr6.simRat.chr6 355815 12 + 647215 TACTAGTTACAT - -a -s simMouse_chr6.simMouse.chr6 363411 28 + 636262 GCACTAAGAGTTGTAAATTCCTATATCG -s Anc0.Anc0refChr0 24097 28 + 26507 GCACTAAATGCAGCAAATCCTTATATAG -s Anc1.Anc1refChr6 24879 28 + 197743 GCACTAAATGCAGCAAATCCTTATATAG -s Anc2.Anc2refChr17 18781 28 + 28526 GCACTAAATGCAGCAGATCCTTATATAG -s mr.mrrefChr5 210504 28 + 294540 GCACTAAGAGTTGTAAATTCCTATATAG -s simCow_chr6.simCow.chr6 334453 28 + 602619 GCACTAAATGTGGCATATTGTTATATAG -s simDog_chr6.simDog.chr6 326722 28 + 593897 GTCCTATATGCAGCAGAACCCTATATAG -s simHuman_chr6.simHuman.chr6 348061 28 + 601863 GCACTAACTGCAGCAAATCTTTATACAG -s simRat_chr6.simRat.chr6 355827 27 + 647215 GCACTAAACAATG-AAATTCCTATATAG - -a -s simMouse_chr6.simMouse.chr6 363439 20 + 636262 AAGCTCTAACTGAGTCAATC -s Anc0.Anc0refChr0 24125 20 + 26507 AAGCTTTAACAGATTCAGTC -s Anc1.Anc1refChr6 24907 20 + 197743 AAGCTTTAACAGATTCAGTC -s Anc2.Anc2refChr17 18809 20 + 28526 AAGCTTTAGCAGATTCAGTC -s mr.mrrefChr5 210532 20 + 294540 AAGCTCTAACTGAGTCAGTC -s simCow_chr6.simCow.chr6 334527 20 + 602619 AAGCTTTAGCAGATGCAGTC -s simDog_chr6.simDog.chr6 326750 20 + 593897 AAGCTTTAGGAGATTCAGTG -s simHuman_chr6.simHuman.chr6 348093 20 + 601863 AAGCTATAACAGATTTAGCC -s simRat_chr6.simRat.chr6 355854 20 + 647215 AAGCTCTAACTGAGTCAGTC - -a -s simMouse_chr6.simMouse.chr6 363459 5 + 636262 CATAA -s Anc0.Anc0refChr0 24148 5 + 26507 TATAA -s Anc1.Anc1refChr6 24930 5 + 197743 TATAA -s Anc2.Anc2refChr17 18832 5 + 28526 TATAA -s mr.mrrefChr5 210552 5 + 294540 CATAA -s simCow_chr6.simCow.chr6 334550 5 + 602619 TATAA -s simDog_chr6.simDog.chr6 326773 5 + 593897 TATAA -s simHuman_chr6.simHuman.chr6 348116 5 + 601863 TAGAA -s simRat_chr6.simRat.chr6 355874 5 + 647215 CATAA - -a -s simMouse_chr6.simMouse.chr6 363464 46 + 636262 CTATGGTCAATTCTTTGAGAGGCGGTGGGGAACAATGTCATTGTCA -s Anc0.Anc0refChr0 24153 44 + 26507 CAACCCACAATTCTATCAGAGGGCATTGGGAAC-ATGTTGTTGCC- -s Anc1.Anc1refChr6 24935 44 + 197743 CAACCCACAATTCTATCAGAGGGCATTGGGAAC-ATGTTGTTGCC- -s Anc2.Anc2refChr17 18837 44 + 28526 CAACCCACTATTCTATCAGAGGGCATTGGGAAC-ATGTTGTTGCC- -s mr.mrrefChr5 210557 46 + 294540 CTATGGTCAATTCTTTGAGAGGTGGTGGGGAACAATGTCATTGTCA -s simCow_chr6.simCow.chr6 334555 40 + 602619 CAACAC----TTCTATCAGAAGGTTTTGGGAAC-AAGATGTTGCC- -s simDog_chr6.simDog.chr6 326778 44 + 593897 CAACCCACTATTCCATCAGAGGGCATTGGGAAC-ATGTTGTTGCC- -s simHuman_chr6.simHuman.chr6 348121 21 + 601863 CGACCCACAATTCTATCAGA------------------------C- -s simRat_chr6.simRat.chr6 355880 46 + 647215 CTATGGTCCATTCCTTGGGCGGTGGTTGGGAACAATGTTGTTGTCA - -a -s simMouse_chr6.simMouse.chr6 363510 9 + 636262 GCATCTGTC -s Anc0.Anc0refChr0 24197 9 + 26507 GTGACTGTC -s Anc1.Anc1refChr6 24979 9 + 197743 GTGACTGTC -s Anc2.Anc2refChr17 18881 9 + 28526 GTGACTGTC -s mr.mrrefChr5 210603 9 + 294540 GCATCTGTC -s simCow_chr6.simCow.chr6 334596 9 + 602619 GTGGATGTC -s simDog_chr6.simDog.chr6 326822 9 + 593897 GGTACTGTT -s simHuman_chr6.simHuman.chr6 348142 9 + 601863 GTGACTGTC -s simRat_chr6.simRat.chr6 355926 9 + 647215 GCATCTGTC - -a -s simMouse_chr6.simMouse.chr6 363519 26 + 636262 ACTCAGGTTGGTGAGTGGATCCACAA -s Anc0.Anc0refChr0 24208 26 + 26507 ATCCAAGTTGAATAACAGACCAAAAG -s Anc1.Anc1refChr6 24990 26 + 197743 ATCCAAGTTGAATAACAGACCAAAAG -s Anc2.Anc2refChr17 18892 26 + 28526 ATTCAAGTTGAATAACAGACCAAAAG -s mr.mrrefChr5 210614 26 + 294540 ATCCAGGTTGGAGAGCTGATTCACAA -s simCow_chr6.simCow.chr6 334607 26 + 602619 GTTCAAGTAGAATAATGGACAAGAAC -s simDog_chr6.simDog.chr6 326833 26 + 593897 ATTCAAATTGAATAACAGACCAACAG -s simHuman_chr6.simHuman.chr6 348153 26 + 601863 ATCCAAGTTGAATAACAGACCAAAGG -s simRat_chr6.simRat.chr6 355937 26 + 647215 ATCCAGGTTGGAAAGCTGATTTGAAA - -a -s simMouse_chr6.simMouse.chr6 363545 5 + 636262 TGAGA -s Anc0.Anc0refChr0 24234 5 + 26507 TGATA -s Anc1.Anc1refChr6 25016 5 + 197743 TGATA -s Anc2.Anc2refChr17 18918 5 + 28526 TGATA -s mr.mrrefChr5 210640 5 + 294540 TGAGA -s simCow_chr6.simCow.chr6 334633 5 + 602619 TGAGG -s simDog_chr6.simDog.chr6 326859 5 + 593897 AGATA -s simHuman_chr6.simHuman.chr6 348246 5 + 601863 TGATA -s simRat_chr6.simRat.chr6 355963 5 + 647215 TGAGA - -a -s simMouse_chr6.simMouse.chr6 363550 165 + 636262 GCTCAACGGCTGCCTGGTTGATTGATACATAAATTAGAATCCGCGTGGGCATGATTTCTGGGTGACACCAGGACACAGCCAAAACTGATTGAGAGGTGCTACAATCTTTGAATTATACATGTAGAATCAGATTCTGGTTGATTCTAGAGATAGACTCTATGTTTG -s Anc0.Anc0refChr0 24239 146 + 26507 GCTCAATGTCCACCTGGTTGATTG---CAAAAGTTAGATT----------------ACTGACTGGAACACAGACAGAGCTGAAACTGATACAGAAGTTGTACAATGTTTGAGTTACCCATGTAACATCATAATTTGGTTGGATCATGACAAAGAATCTATGTTTG -s Anc1.Anc1refChr6 25021 164 + 197743 GCTCAATGTCCACCTGGTTGATTGGGACAAAAGTTAGATTACTGACACTACTGA-CACTGACTGGAACACAGACAGAGCTGAAACTGATACAGAAGTTGTACAATGTTTGAGTTACCCATGTAACATCATAATTTGGTTGGATCATGACAAAGAATCTATGTTTG -s Anc2.Anc2refChr17 18923 146 + 28526 GCTCAATGTCCACCTGGTTGATTG---CAAAAGTCAGATT----------------AGTGACTGGAGCACAGACAGAGCTGAAACTGATACAGAGGTTGTACAATGTTTGAGTTACCCATGCAACATCATAATTTCGTTGGATCATGACAAAGAATCTATATTTG -s mr.mrrefChr5 210645 165 + 294540 GCTCAATGGCTGCCTGGTTGATTGATACATAAATTAGAATCCGGGTGGGCATGATTTCTGGGTGACACCAGGACACAGCTGAAACTGATTGAGAAGTGCTACAATCTTTGAATTATACATGTAGAATCAGATTCTGGTTGATTCTAGACATAGACTCTATGTTTG -s simCow_chr6.simCow.chr6 334638 123 + 602619 GCTCAATGTCCACCTGGTC-----------------------------------------ACTGGAGCACAGACAGAGCTGAAACAGATACAGATGTTGTATAGTGTTTAGGTCGCCCATGC-ACATCATAGTTTTAGTGAGTCATGATAAAGGCTTGATATTTG -s simDog_chr6.simDog.chr6 326864 145 + 593897 GCTCAATGTCCACCTGGTTGATTG---CAAAAGTCAGATT----------------AGTGTCTAGAGCACGGACAGAGTT-AAACTGAAACATAGGTAGTACCATGTTTGAGTTACTAATGCACCATCATAATTTCGTTTGATCATGACGAGGAAGCTATATTTG -s simHuman_chr6.simHuman.chr6 348251 164 + 601863 ACTTGATGTCCACTTGGTTGATTGGGATAAAAGTTAGACTACTGACACTACTGA-CACTGACTGGAATGCAGACAGAACTGAAACTGATACAGAAGTTGTACAATTTATGAGTTACCCATGTAACATCATACTTTGGTTGGATCATGACAAAGAGTCTATGTTTA -s simRat_chr6.simRat.chr6 355971 164 + 647215 GCTCAATGGCTGCCTGGTTGATTGACACAT-AATTAGATTCTGGCTGGGCATGATTCCCGGGCAATACCAGGACACAGCTGAGACTGATCAAGAAGTGCTAAAATCTTTGAATTATACATGTACAATCAGATTGTGGTTGATTCTAGACGTAGACTCTATGGTTG - -a -s simMouse_chr6.simMouse.chr6 363715 4 + 636262 GCAC -s Anc0.Anc0refChr0 24385 4 + 26507 GCAC -s Anc1.Anc1refChr6 25185 4 + 197743 GCAC -s Anc2.Anc2refChr17 19071 4 + 28526 GCAC -s mr.mrrefChr5 210810 4 + 294540 GCAC -s simCow_chr6.simCow.chr6 334763 1 + 602619 ---C -s simDog_chr6.simDog.chr6 327011 4 + 593897 GCAC -s simHuman_chr6.simHuman.chr6 348415 4 + 601863 GCAC -s simRat_chr6.simRat.chr6 356135 4 + 647215 GCAT - -a -s simMouse_chr6.simMouse.chr6 363719 20 + 636262 CCCGTTGAGACAGAGTAAGT -s Anc0.Anc0refChr0 24390 20 + 26507 GCCAATGACAGAGGAGAATT -s Anc1.Anc1refChr6 25190 20 + 197743 GCCAATGACAGAGGAGAATT -s Anc2.Anc2refChr17 19076 20 + 28526 GACAATGACAGAAGAGAATT -s mr.mrrefChr5 210814 20 + 294540 CCCGTTGAGACAGAGTAAGT -s simCow_chr6.simCow.chr6 334765 20 + 602619 GAAAATGACTGAAAAGAATT -s simDog_chr6.simDog.chr6 327016 19 + 593897 GACAAGCACAGA-GAGAATT -s simHuman_chr6.simHuman.chr6 348420 20 + 601863 TCCAATGACAGAGGAGAATT -s simRat_chr6.simRat.chr6 356139 20 + 647215 CTAGTAGAGACAGAGTAAGT - -a -s simMouse_chr6.simMouse.chr6 363739 24 + 636262 ACTGGGTCATCCTACTGTTCTGGG -s Anc0.Anc0refChr0 24411 23 + 26507 ACTAATTCTTCCCACTGATC-GGG -s Anc1.Anc1refChr6 25211 24 + 197743 ACTAATTCTTCCCACTGATCTGGG -s Anc2.Anc2refChr17 19097 23 + 28526 ACTAATTCTTCCCACTGATC-AGT -s mr.mrrefChr5 210834 24 + 294540 ACTGGGTCTTCCTACTGTTCTGGG -s simCow_chr6.simCow.chr6 334786 23 + 602619 ACTAAGTCTTCCCACCGATC-AGT -s simDog_chr6.simDog.chr6 327036 18 + 593897 ACTAATTCTTCCCACTGA------ -s simHuman_chr6.simHuman.chr6 348441 24 + 601863 ACTAATTCTTCCCACTAATCTGGG -s simRat_chr6.simRat.chr6 356159 24 + 647215 ACCTGGTCTTCCTACTGTTCTAGG - -a -s simMouse_chr6.simMouse.chr6 363763 2 + 636262 AT -s Anc0.Anc0refChr0 24434 2 + 26507 AT -s Anc1.Anc1refChr6 25235 2 + 197743 AT -s Anc2.Anc2refChr17 19120 2 + 28526 AT -s mr.mrrefChr5 210858 2 + 294540 AT -s simCow_chr6.simCow.chr6 334809 2 + 602619 AT -s simHuman_chr6.simHuman.chr6 348465 2 + 601863 AT -s simRat_chr6.simRat.chr6 356187 2 + 647215 AT - -a -s simMouse_chr6.simMouse.chr6 363765 23 + 636262 GCCCCTGTACACTAGGATACATT -s Anc0.Anc0refChr0 24449 23 + 26507 GCCCCTATACCCTAGGGTGTATT -s Anc1.Anc1refChr6 25250 23 + 197743 GCCCCTATACCCTAGGGTGTATT -s Anc2.Anc2refChr17 19135 23 + 28526 GTCCCTATACCCCAGAGCGTATT -s mr.mrrefChr5 210860 23 + 294540 GCCCCTGTACCCTAGGATATATT -s simCow_chr6.simCow.chr6 334824 22 + 602619 GTCCCTATATGTAAGAGCGTAT- -s simDog_chr6.simDog.chr6 327054 11 + 593897 --------ACCCCAGAG----CT -s simHuman_chr6.simHuman.chr6 348480 23 + 601863 ACCCCTATACCCTAGGGTGTATT -s simRat_chr6.simRat.chr6 356189 23 + 647215 GCCCCTGTACCCTAAAATATATC - -a -s simMouse_chr6.simMouse.chr6 363788 1 + 636262 C -s Anc0.Anc0refChr0 24472 1 + 26507 T -s Anc1.Anc1refChr6 25273 1 + 197743 T -s Anc2.Anc2refChr17 19160 1 + 28526 T -s mr.mrrefChr5 210883 1 + 294540 C -s simCow_chr6.simCow.chr6 334846 1 + 602619 A -s simDog_chr6.simDog.chr6 327067 1 + 593897 T -s simHuman_chr6.simHuman.chr6 348503 1 + 601863 T -s simRat_chr6.simRat.chr6 356212 1 + 647215 C - -a -s simMouse_chr6.simMouse.chr6 363789 8 + 636262 TCTCTGCC -s Anc0.Anc0refChr0 24474 8 + 26507 TCTTTGCC -s Anc1.Anc1refChr6 25275 8 + 197743 TCTTTGCC -s Anc2.Anc2refChr17 19162 8 + 28526 TCTTTACT -s mr.mrrefChr5 210884 8 + 294540 TCTCTGCC -s simCow_chr6.simCow.chr6 334848 8 + 602619 TCTTCACT -s simDog_chr6.simDog.chr6 327069 8 + 593897 TCTTTACT -s simHuman_chr6.simHuman.chr6 348505 8 + 601863 TATTTGTC -s simRat_chr6.simRat.chr6 356213 8 + 647215 TGTCTGCC - -a -s simMouse_chr6.simMouse.chr6 363797 172 + 636262 CTTGGTAAAGTGTTGAAGCAGTTTTCCGTACAGAGTAATACACTGTAACCAAGATCACCTACGTTTCACCTAAGTAGGTACTCGTAACTAAAAGATCACTTACATTTCACCTAAGTGCTCAGAAGTACAGTCCATACTTAAGTTCAATGGACCTTTTAACCTGGCCATGAGC -s Anc0.Anc0refChr0 24482 11 + 26507 CATAGTACAGT----------------------------------------------------------------------------------------------------------------------------------------------------------------- -s Anc1.Anc1refChr6 25283 11 + 197743 CATAGTACAGT----------------------------------------------------------------------------------------------------------------------------------------------------------------- -s Anc2.Anc2refChr17 19170 11 + 28526 CATAGTACAAT----------------------------------------------------------------------------------------------------------------------------------------------------------------- -s mr.mrrefChr5 210892 170 + 294540 CATGGTAAAGTGTTGAAACAGTTTCCCGTACAGAGTAGTACACTGTAACTAAGATCACTTACATTTCACCTAAGTAGGTACTCGTATCT--AAGATCACTTACATTTCACCTAAGTACTCAGAAGGGCAGTCCATACTTAAGTTCAATGGACCTTTTAACCTGGCCATGAGT -s simCow_chr6.simCow.chr6 334856 11 + 602619 TGTAGTACAAT----------------------------------------------------------------------------------------------------------------------------------------------------------------- -s simDog_chr6.simDog.chr6 327077 11 + 593897 CATAGTACAAT----------------------------------------------------------------------------------------------------------------------------------------------------------------- -s simHuman_chr6.simHuman.chr6 348516 11 + 601863 CATAGTACCGT----------------------------------------------------------------------------------------------------------------------------------------------------------------- -s simRat_chr6.simRat.chr6 356221 168 + 647215 CATGGTAAAGTGTTGCAACATTTTCTAGTACAGAGTAGTACACTGTAACTAAGATCACTTACATTCCACCTAAGTATGTATTGGTATCT--GAGATCACTTACACTCCACCTAAGTACTTAGA--GGTAGCCCACAAGTAACTTCAATGGATCTTTTAACTTGGCCATGAGT - -a -s simMouse_chr6.simMouse.chr6 363969 30 + 636262 CATCCAAAATTATGTGTATCCATACATCCA -s Anc0.Anc0refChr0 24893 30 + 26507 CATCCAAAATGTGGTGTATCCCTACACTTA -s Anc1.Anc1refChr6 25713 30 + 197743 CATCCAAAATGTGGTGTATCCCTACACTTA -s Anc2.Anc2refChr17 19633 30 + 28526 CATCCAAAATGTGGTGAATCCCTACATTTA -s mr.mrrefChr5 211062 30 + 294540 CATCCAAAATTATGTGTATCCATACACCCA -s simCow_chr6.simCow.chr6 337319 30 + 602619 CATCCAAAATGTAGTGAAACCCTACATTTA -s simDog_chr6.simDog.chr6 327538 30 + 593897 CATCCAAAATGTGGTGAATCCCTACAGTTA -s simHuman_chr6.simHuman.chr6 349428 26 + 601863 CATCCAAAAT----TATCACTCTACGCTTA -s simRat_chr6.simRat.chr6 356389 30 + 647215 CATCCAAAATTATGTGTATCCATACACCCA - -a -s simMouse_chr6.simMouse.chr6 363999 35 + 636262 CACACTTGTTAAGGTGCTTCTGATGCTGCATTGCT -s Anc0.Anc0refChr0 24924 31 + 26507 CTTGTTGTAAAA-G---TTTTGAGGCTGCATTGCC -s Anc1.Anc1refChr6 25744 34 + 197743 CTTGTTGTAAAA-GCAATTTTGAGGCTGCATTGCC -s Anc2.Anc2refChr17 19664 31 + 28526 CTTGTTGTAAAA-G---TTTTGAGACTGCATTGCC -s mr.mrrefChr5 211092 34 + 294540 CACATTTTTTAA-GTAGTTTTGAGGCTGCATTGCT -s simCow_chr6.simCow.chr6 337350 31 + 602619 CTTGTTGTAAAA-G---TTTTGGGTCTGCATTGCT -s simDog_chr6.simDog.chr6 327569 31 + 593897 CTTGTTGTAAAA-G---TTATGAGACTCTATCACC -s simHuman_chr6.simHuman.chr6 349455 34 + 601863 CTTGTTGTGAAA-GCAATTTTGAGGCTGCATTGCC -s simRat_chr6.simRat.chr6 356419 34 + 647215 CACATTTTTTAA-GTAGTTTTGTGGCTGCATTGCT - -a -s simMouse_chr6.simMouse.chr6 364034 49 + 636262 TCCCTAATGTTTGAGTCCAGCAATAAACTTGTACATCACAATTATGGCA -s Anc0.Anc0refChr0 24959 48 + 26507 ATTATAATGTTTAAGTCCAGCCATAGACTTGTGCATTACAATTTTGGC- -s Anc1.Anc1refChr6 25782 49 + 197743 ATTATAATGTTTAAGTCCAGCCATAGACTTGTGCATTACAATTTTGGCA -s Anc2.Anc2refChr17 19699 48 + 28526 ATTATAATGTTTAATTGCAGCCATAGACTTCTGCATTATTGTTTTGGC- -s mr.mrrefChr5 211130 49 + 294540 TTCATAATGTTTGAGTCCAGCAATAAACTTGTACATCACAATTATGGCA -s simCow_chr6.simCow.chr6 337385 48 + 602619 ATTCTAATGTTTAATTGTTGCCATGGATTTCTCCATTATCGTTTTGCC- -s simDog_chr6.simDog.chr6 327604 48 + 593897 ATTATAATGTTTAATTGCAGTCATAGACTTCTGCATTATTGTTTTGGC- -s simHuman_chr6.simHuman.chr6 349493 49 + 601863 ATTATAATCTCTAAGTCCGGCTATACACTTGTTATTTACAATTGTAGTA -s simRat_chr6.simRat.chr6 356457 49 + 647215 GTCACAATGTTTGAGTCCAGCAATAAACTTGTACATCACAATTATGGCA - -a -s simMouse_chr6.simMouse.chr6 364083 13 + 636262 TTAAGCCCACCGC -s Anc1.Anc1refChr6 25831 8 + 197743 ttaagcc-----C -s mr.mrrefChr5 211179 13 + 294540 TTAAGCCCACCGC -s simHuman_chr6.simHuman.chr6 349586 8 + 601863 ttaagcc-----C -s simRat_chr6.simRat.chr6 356506 13 + 647215 TTAAGCCCACCTC - -a -s simMouse_chr6.simMouse.chr6 364096 13 + 636262 CTGTTCCCAGATT -s Anc0.Anc0refChr0 25008 13 + 26507 TAGAAACCATATC -s Anc1.Anc1refChr6 25842 13 + 197743 TAGAAACCATATC -s Anc2.Anc2refChr17 19748 13 + 28526 TAGAAACCATATC -s mr.mrrefChr5 211195 13 + 294540 CTGTACCCATATC -s simCow_chr6.simCow.chr6 337434 13 + 602619 TAGTACCCATGTC -s simDog_chr6.simDog.chr6 327653 13 + 593897 CAGAGACCACATC -s simHuman_chr6.simHuman.chr6 349597 13 + 601863 TGGAATCTATATC -s simRat_chr6.simRat.chr6 356522 13 + 647215 CTGTACCCTTGTC - -a -s simMouse_chr6.simMouse.chr6 364109 58 + 636262 CAACCCTAAACTAGGCATGCATTACGCCTTTTCATGATAAACCCAATAAAATCATTGA -s Anc0.Anc0refChr0 25021 57 + 26507 C-ACCCCAATCTAGATACACCCCACACCTTTTGATGAGGAACCCAATAAACTCACTAA -s Anc1.Anc1refChr6 25855 57 + 197743 C-ACCCCAATCTAGATACACCCCACACCTTTTGATGAGGAACCCAATAAACTCACTAA -s Anc2.Anc2refChr17 19761 57 + 28526 C-ACTCCAATCTGGATACACCCCATACCTTTTGATGAGGAACCCAATAAACTCACTAA -s mr.mrrefChr5 211208 57 + 294540 C-ACCCTAAACTAGGCATGCATTACACCTTTTGATGATGAACCCAATAAAACCATTGA -s simCow_chr6.simCow.chr6 337447 57 + 602619 C-CCTTGAATCTTGCTACATCTCAAACCTTTTGATGAGGAACCCAATAAACCCACTAA -s simDog_chr6.simDog.chr6 327666 57 + 593897 C-ACTCCAATCTGGATACACCCCATCCCTATTGATGAAGAACCCAATAAACTCACTAA -s simHuman_chr6.simHuman.chr6 349610 53 + 601863 C-ACCCCAACCCAGATACACCACACACCTTTTGATGAG----CCAATAAATGCACTAA -s simRat_chr6.simRat.chr6 356539 57 + 647215 C-ACCCTAAGCTATGCATGCATAACACCTTTTGATGATGAACCCAATGAAACCATTGA - -a -s simMouse_chr6.simMouse.chr6 364167 75 + 636262 AACAAAAGGAAAAATAAAACTGGATGCATTAGCATTCCATGTCCAATGACACACACCACCACTGTGTAGGTCCTT -s Anc0.Anc0refChr0 25078 75 + 26507 AATAACTGAAAAACTAAAATTGGATGGACTGGGTTTCCAGGCCCAATAATACCCACAACCACTCTGTAAGTCCAT -s Anc1.Anc1refChr6 25912 75 + 197743 AATAACTGAAAAACTAAAATTGGATGGACTGGGTTTCCAGGCCCAATAATACCCACAACCACTCTGTAAGTCCAT -s Anc2.Anc2refChr17 19818 75 + 28526 AATTGCTGAAAAACTAAAATTGGATGGACTGGGTTTCCAGGCCCAATAATACCCACAACCACTCTTTAAGTCCAT -s mr.mrrefChr5 211265 75 + 294540 AACAACTGAAAAAATAAAATTGGATGCATTGGCATTCCATGCCCAATGACACACACAACCACTGTGTAGGTCCAT -s simCow_chr6.simCow.chr6 337504 75 + 602619 AATGCTTGAGGAACCAAGATTGAATGGACTGTGATTCTAGGCCCAATCATACCCACAACCACTCTATAAGATCAT -s simDog_chr6.simDog.chr6 327724 73 + 593897 AACTGCCAAAAAACTAAAATTGGATGGACTGGATTTCCAGGCCTAATAATACCCACAACCA--CTTTAAGTCCAT -s simHuman_chr6.simHuman.chr6 349663 75 + 601863 AATAACTGAAAAACTGGAATTGGATGGACTGGGCTCCCAGGCCCAATAATACCCACAACTGTTCTGTAAGTCCAT -s simRat_chr6.simRat.chr6 356596 75 + 647215 AACAACTGAAAACATAAAATTGGATGCATTGGCAGTTCATACCCAATGACACACACAACCACTGTGAAGGTCGAT - -a -s simMouse_chr6.simMouse.chr6 364242 22 + 636262 ATAAAGGCAAAATTATTAACAT -s Anc0.Anc0refChr0 25153 22 + 26507 CTAAAGGCAAGATTGTTGATAT -s Anc1.Anc1refChr6 25987 22 + 197743 CTAAAGGCAAGATTGTTGATAT -s Anc2.Anc2refChr17 19893 22 + 28526 CTAAAGGCAAGATTGTTGATAT -s mr.mrrefChr5 211340 22 + 294540 ATAAAGGCAAAATTATTAACAT -s simCow_chr6.simCow.chr6 337579 22 + 602619 CTCAAAGTAAGATGGTTGATAT -s simDog_chr6.simDog.chr6 327797 22 + 593897 ATATAGACAAGATTGTTGATAT -s simHuman_chr6.simHuman.chr6 349738 22 + 601863 CTAAAGGCAAGGTTGTTGTTAT -s simRat_chr6.simRat.chr6 356703 22 + 647215 ATAAAGGCAAAATTATTAAGAT - -a -s simMouse_chr6.simMouse.chr6 364264 49 + 636262 TAAAGTCTAAGCCAACCATGTTGTCAGTCAGCTTAAGATTAAGAGGAGT -s Anc0.Anc0refChr0 25175 31 + 26507 TAAAGTCTAGGTCAACCATGTTGACAG----CTT--------------C -s Anc1.Anc1refChr6 26009 45 + 197743 TAAAGTCTAGGTCAACCATGTTGACAG----CTTAATATTATAAGGCAC -s Anc2.Anc2refChr17 19915 31 + 28526 TAGAGTCTATGTCCACCATGTGGACTG----GTT--------------C -s mr.mrrefChr5 211362 45 + 294540 TAAAGTCTAGGTCAACCATGTTGTCAG----CTTAAGATTAAGAGGAGT -s simCow_chr6.simCow.chr6 337601 31 + 602619 AAGAGTCTATGTCCACTATGTGGATTG----CCT--------------T -s simDog_chr6.simDog.chr6 327819 31 + 593897 TAGAGTCTATGTCCACCATGTGGACTG----GTT--------------C -s simHuman_chr6.simHuman.chr6 349763 41 + 601863 GAAATTCTTGCTCAAA---GTTCACA-----CCTAATATTATAAGGCAC -s simRat_chr6.simRat.chr6 356725 42 + 647215 TAAAGTCTGGATCCAC---ATTGCCAG----CTTAAGATCAAGATGAGT - -a -s simMouse_chr6.simMouse.chr6 364313 6 + 636262 GAGTAG -s Anc0.Anc0refChr0 25206 6 + 26507 GAGTAG -s Anc1.Anc1refChr6 26054 6 + 197743 GAGTAG -s Anc2.Anc2refChr17 19946 6 + 28526 GTGCAG -s mr.mrrefChr5 211407 6 + 294540 GAGTAG -s simCow_chr6.simCow.chr6 337632 6 + 602619 TTTCAC -s simDog_chr6.simDog.chr6 327851 6 + 593897 GTGCAG -s simHuman_chr6.simHuman.chr6 349804 6 + 601863 GACTGG -s simRat_chr6.simRat.chr6 356767 6 + 647215 GAGTGG - -a -s simMouse_chr6.simMouse.chr6 364319 5 + 636262 CCTAC -s Anc0.Anc0refChr0 25212 5 + 26507 CCTAC -s Anc1.Anc1refChr6 26060 5 + 197743 CCTAC -s Anc2.Anc2refChr17 19952 5 + 28526 ACAAC -s mr.mrrefChr5 211413 5 + 294540 CCTAC -s simCow_chr6.simCow.chr6 337638 5 + 602619 ACAAT -s simDog_chr6.simDog.chr6 327857 5 + 593897 ACAAC -s simHuman_chr6.simHuman.chr6 349821 5 + 601863 CCTAC -s simRat_chr6.simRat.chr6 356773 5 + 647215 CTCAC - -a -s simMouse_chr6.simMouse.chr6 364324 21 + 636262 AGTACAATTTTATGCATTTGG -s Anc0.Anc0refChr0 25217 14 + 26507 T--ACGATTTTATGCA----- -s Anc1.Anc1refChr6 26065 21 + 197743 TAAACGATTTTATGCATTTGG -s Anc2.Anc2refChr17 19957 14 + 28526 T--ATGATTTTATACA----- -s mr.mrrefChr5 211418 21 + 294540 AGTACAATTTTATGCATTTGG -s simCow_chr6.simCow.chr6 337905 14 + 602619 T--ATGGTTTCTGACT----- -s simDog_chr6.simDog.chr6 327862 14 + 593897 T--ATGATTTTATACA----- -s simHuman_chr6.simHuman.chr6 349826 15 + 601863 TAAAC------CTGCATTTGG -s simRat_chr6.simRat.chr6 356778 21 + 647215 AGCACAATTTTATGCATTTTG - -a -s simMouse_chr6.simMouse.chr6 364345 7 + 636262 CAATCCC -s Anc1.Anc1refChr6 26086 6 + 197743 CA-TACC -s mr.mrrefChr5 211439 6 + 294540 CA-TCCC -s simHuman_chr6.simHuman.chr6 349849 6 + 601863 CA-TACC -s simRat_chr6.simRat.chr6 356799 6 + 647215 CA-CCCC - -a -s simMouse_chr6.simMouse.chr6 364352 21 + 636262 AAGCGACCCTAGGTGTCCTCA -s Anc1.Anc1refChr6 26092 21 + 197743 AAGCAATCGAAGGCACATTTA -s mr.mrrefChr5 211445 21 + 294540 AAGCGACCCTAGGTGTCCTCA -s simHuman_chr6.simHuman.chr6 349857 21 + 601863 AAGCAATCGAAGGCACATTTA -s simRat_chr6.simRat.chr6 356805 21 + 647215 AAGCAACCTTAGGTGTCTTCA - -a -s simMouse_chr6.simMouse.chr6 364373 5 + 636262 TTGCC -s Anc1.Anc1refChr6 26113 5 + 197743 TTGCT -s mr.mrrefChr5 211466 5 + 294540 TTGCC -s simHuman_chr6.simHuman.chr6 349880 5 + 601863 TTGCT -s simRat_chr6.simRat.chr6 356826 5 + 647215 TTGCT - -a -s simMouse_chr6.simMouse.chr6 364378 36 + 636262 TAGTTTATGAGAGTGTTGGCCAAACACAGCTTTGGT -s Anc0.Anc0refChr0 25231 15 + 26507 ---------------------AAATACAAGTCTAGT -s Anc1.Anc1refChr6 26118 30 + 197743 TCGCTTATGA------TTGCCAAATACAAGTCTAGT -s Anc2.Anc2refChr17 19971 15 + 28526 ---------------------ACATACAAGTCTAGT -s mr.mrrefChr5 211471 36 + 294540 TAGTTTATGAGAGTGTTGGCCAAACACAGCTTTGGT -s simCow_chr6.simCow.chr6 337919 15 + 602619 ---------------------CCATACAAGTTTACT -s simDog_chr6.simDog.chr6 327876 15 + 593897 ---------------------ACATACAAGTCTAGT -s simHuman_chr6.simHuman.chr6 349891 26 + 601863 TCGCTTATGA------TTGCCAAGTGCA----TAGA -s simRat_chr6.simRat.chr6 356831 36 + 647215 TAGTTTATGAGAGTGTTGTCCAAACACAGGTTTAGT - -a -s simMouse_chr6.simMouse.chr6 364414 3 + 636262 GAT -s Anc0.Anc0refChr0 25246 3 + 26507 GTT -s Anc1.Anc1refChr6 26148 3 + 197743 GTT -s Anc2.Anc2refChr17 19986 3 + 28526 GTT -s mr.mrrefChr5 211507 3 + 294540 GAT -s simCow_chr6.simCow.chr6 337934 3 + 602619 GTT -s simDog_chr6.simDog.chr6 327892 3 + 593897 GTT -s simHuman_chr6.simHuman.chr6 349917 3 + 601863 GTC -s simRat_chr6.simRat.chr6 356867 3 + 647215 GAT - -a -s simMouse_chr6.simMouse.chr6 364417 18 + 636262 GGGATTTTCACTAGCGGT -s Anc0.Anc0refChr0 25249 18 + 26507 GGGTAATCCACTAGCAGT -s Anc1.Anc1refChr6 26151 18 + 197743 GGGTAATCCACTAGCAGT -s Anc2.Anc2refChr17 19990 18 + 28526 GGGTAATCCACTAGTAGT -s mr.mrrefChr5 211510 18 + 294540 GGGATTTTCACTAGCGGT -s simCow_chr6.simCow.chr6 337938 18 + 602619 GAGTATTCCGTGATTTGC -s simDog_chr6.simDog.chr6 327896 18 + 593897 GGGTAATCCACTAGTAGT -s simHuman_chr6.simHuman.chr6 349920 18 + 601863 GGACAATATGCTACCCTT -s simRat_chr6.simRat.chr6 356870 18 + 647215 GGGATTTTCACTGGTGGT - -a -s simMouse_chr6.simMouse.chr6 364435 15 + 636262 TAAGAATACATCTGT -s Anc0.Anc0refChr0 25267 5 + 26507 ----------ACTTT -s Anc1.Anc1refChr6 26169 5 + 197743 ----------ACTTT -s Anc2.Anc2refChr17 20008 5 + 28526 ----------ACCTT -s mr.mrrefChr5 211528 15 + 294540 TAAGAATACATCTGT -s simCow_chr6.simCow.chr6 337956 5 + 602619 ----------ACTTA -s simDog_chr6.simDog.chr6 327914 5 + 593897 ----------ACCTT -s simHuman_chr6.simHuman.chr6 349938 5 + 601863 ----------CCTCC -s simRat_chr6.simRat.chr6 356894 15 + 647215 TAAAAAGAAGTCTGT - -a -s simMouse_chr6.simMouse.chr6 364450 26 + 636262 ATTTTAAACAAGAATTTGGGTGCTCA -s Anc0.Anc0refChr0 25272 26 + 26507 ATTGTAAACAAGAATTTCGGTGCTCA -s Anc1.Anc1refChr6 26174 26 + 197743 ATTGTAAACAAGAATTTCGGTGCTCA -s Anc2.Anc2refChr17 20026 26 + 28526 ATTGTGCACAAGAATTTCTGTGCCCA -s mr.mrrefChr5 211543 26 + 294540 ATTTTAAACAAGAATTTGGGTGCTCA -s simCow_chr6.simCow.chr6 337974 26 + 602619 AATGTAAGCAAGGATTCTTGCCCCCA -s simDog_chr6.simDog.chr6 327932 26 + 593897 ATTGTGCACAAGAATTTCTGTGCCCA -s simHuman_chr6.simHuman.chr6 349943 23 + 601863 ACTATAAACTAAGGC---GATGCTAC -s simRat_chr6.simRat.chr6 356909 26 + 647215 ATCTTTAGCGAAAATTTGGGTGCTCA - -a -s simMouse_chr6.simMouse.chr6 364476 16 + 636262 AGGCTGACTCTGCTAG -s Anc0.Anc0refChr0 25298 14 + 26507 G--CTATCTCTCCTAA -s Anc1.Anc1refChr6 26200 14 + 197743 G--CTATCTCTCCTAA -s Anc2.Anc2refChr17 20054 14 + 28526 G--TTATCTGTCCCAA -s mr.mrrefChr5 211569 14 + 294540 A--CTGACTCTGCTAG -s simCow_chr6.simCow.chr6 338002 14 + 602619 G--GTATCTTTGCAAA -s simDog_chr6.simDog.chr6 327960 14 + 593897 G--TTATCTGTCCCAA -s simHuman_chr6.simHuman.chr6 349966 14 + 601863 C--CTTCCTCCACTAT -s simRat_chr6.simRat.chr6 356935 14 + 647215 A--TTGACTCTACCAG - -a -s simMouse_chr6.simMouse.chr6 364492 12 + 636262 TGGTGACAGTCC -s Anc1.Anc1refChr6 26214 11 + 197743 TAAGGC-AGTCC -s mr.mrrefChr5 211583 11 + 294540 TGGTGA-AGTCC -s simHuman_chr6.simHuman.chr6 349984 11 + 601863 TAAGGC-AGTCC -s simRat_chr6.simRat.chr6 356949 11 + 647215 TGGTAA-AGTCT - -a -s simMouse_chr6.simMouse.chr6 364504 17 + 636262 AGTAGGTTTGGCATTTT -s Anc0.Anc0refChr0 25312 1 + 26507 ----------------T -s Anc1.Anc1refChr6 26225 17 + 197743 AGCGGATACAGACTCTT -s Anc2.Anc2refChr17 20068 1 + 28526 ----------------T -s mr.mrrefChr5 211594 17 + 294540 AGTAGGTTTGGCATTTT -s simCow_chr6.simCow.chr6 338016 1 + 602619 ----------------T -s simDog_chr6.simDog.chr6 327974 1 + 593897 ----------------T -s simHuman_chr6.simHuman.chr6 349999 17 + 601863 AGCGGATACAGACTCTT -s simRat_chr6.simRat.chr6 356960 17 + 647215 GGTTGGTTTAGTATTTT - -a -s simMouse_chr6.simMouse.chr6 364521 2 + 636262 TA -s Anc0.Anc0refChr0 25321 2 + 26507 TC -s Anc1.Anc1refChr6 26250 2 + 197743 TC -s Anc2.Anc2refChr17 20077 2 + 28526 TC -s mr.mrrefChr5 211611 2 + 294540 TA -s simCow_chr6.simCow.chr6 338026 2 + 602619 TC -s simDog_chr6.simDog.chr6 327983 2 + 593897 TT -s simHuman_chr6.simHuman.chr6 350024 2 + 601863 TC -s simRat_chr6.simRat.chr6 356977 2 + 647215 TC - -a -s simMouse_chr6.simMouse.chr6 364523 19 + 636262 GGTCACAAGGTGATATTAT -s Anc0.Anc0refChr0 25323 19 + 26507 AGTTAATAGCTAATAATCT -s Anc1.Anc1refChr6 26252 19 + 197743 AGTTAATAGCTAATAATCT -s Anc2.Anc2refChr17 20079 19 + 28526 AGTTAATAGCTAATAATCT -s mr.mrrefChr5 211613 19 + 294540 GGTCACAAGGTGATATTAT -s simCow_chr6.simCow.chr6 338028 19 + 602619 AGTTTGTTGGTTGTACCCT -s simDog_chr6.simDog.chr6 327992 19 + 593897 AGTCAATATCTAATAATCT -s simHuman_chr6.simHuman.chr6 350026 19 + 601863 AGTTAATAGTTACGAATTC -s simRat_chr6.simRat.chr6 356979 19 + 647215 GGTCAGAAGGTGATATTAT - -a -s simMouse_chr6.simMouse.chr6 364542 22 + 636262 TAGTACATGCCAAGTATATTAC -s Anc0.Anc0refChr0 25342 14 + 26507 T--------CAAGGTATATTAA -s Anc1.Anc1refChr6 26271 14 + 197743 T--------CAAGGTATATTAA -s Anc2.Anc2refChr17 20098 14 + 28526 T--------CAAGGTATATTAA -s mr.mrrefChr5 211632 22 + 294540 TAGTACATGCCAAGTATATTAC -s simCow_chr6.simCow.chr6 338181 14 + 602619 T--------TGAGGTATATTAA -s simDog_chr6.simDog.chr6 328011 14 + 593897 T--------CAAGGTATATTAA -s simHuman_chr6.simHuman.chr6 350045 14 + 601863 T--------CAAGGTATATGAA -s simRat_chr6.simRat.chr6 356998 22 + 647215 TATTACATGCGAAGTATGTTAC - -a -s simMouse_chr6.simMouse.chr6 364564 58 + 636262 TATCAGAGTTTGAGAGGGGGAATTAGGCTAATTTACTTTGAAGTGGCTTTACTGTGCA -s Anc0.Anc0refChr0 25356 52 + 26507 AGTCAGAATCAAAGAGGGGAGATTG------TTAACCTTCAAGTTTCTTTATTGTGCC -s Anc1.Anc1refChr6 26285 58 + 197743 AGTCAGAATCAAAGAGGGGAGATTGGGCTAATTAACCTTCAAGTTTCTTTATTGTGCC -s Anc2.Anc2refChr17 20112 52 + 28526 AGTCAGAATCAAAGAGGGGAGATTG------TTAGTCTTCAGGTTTCTTTTTTGTGCC -s mr.mrrefChr5 211654 58 + 294540 TATCAGAGTCTGAGAGGGGGAATTGGGCTAATTTACCTTGAAGTGGCTTTACTGTGCA -s simCow_chr6.simCow.chr6 338254 51 + 602619 AGTCAAAGTCAAAGAGGGGAAATT-------TTAGTCTTCAGGTTTCTTTTTTGTGCC -s simDog_chr6.simDog.chr6 328025 31 + 593897 AGTCAGAATCAAAGAGGGGAGATTG---------------------------TATGCC -s simHuman_chr6.simHuman.chr6 350059 58 + 601863 AGTCAGAATCAACGAGGGGAGATTGGGCTAATTAACCTTCAAGTTTCTTTATTGTACC -s simRat_chr6.simRat.chr6 357020 58 + 647215 CATCAGAGCCTGAGAGGTGGAATTGGGTTAATTTACCTTGAAGTGGCTTTTCTTTGCT - -a -s simMouse_chr6.simMouse.chr6 364622 22 + 636262 TATTGTATGGTCCCATTACAAA -s Anc0.Anc0refChr0 25408 22 + 26507 AATTGTATGGTCTCATTCCAAA -s Anc1.Anc1refChr6 26343 22 + 197743 AATTGTATGGTCTCATTCCAAA -s Anc2.Anc2refChr17 20165 22 + 28526 AATTGTATGGTCTCATTCCGAA -s mr.mrrefChr5 211712 22 + 294540 AATTGTATGGTCCCATTACAAA -s simCow_chr6.simCow.chr6 338306 22 + 602619 AATTGGATGGTCTGATTCCGAA -s simDog_chr6.simDog.chr6 328057 22 + 593897 AATCGTATGGTACCATTCTGAT -s simHuman_chr6.simHuman.chr6 350117 22 + 601863 AATTGCGTGTTCTCATTCCATA -s simRat_chr6.simRat.chr6 357078 22 + 647215 AGTTGTATGGTCCCATTACAAA - -a -s simMouse_chr6.simMouse.chr6 364644 54 + 636262 TCTTCATTGCATCCTTTATTGAACCTGGCCTGTCCCAAAAAGAAGGGATTTTCA -s Anc0.Anc0refChr0 25430 44 + 26507 TCTTTGTT----------TTGGACCTGGCCTGTTCCAGAAAGATGGAATTCTGG -s Anc1.Anc1refChr6 26365 54 + 197743 TCTTTGTTCCGTTCTTTATTGGACCTGGCCTGTTCCAGAAAGATGGAATTCTGG -s Anc2.Anc2refChr17 20187 44 + 28526 TCTTTGTT----------TTGGACCTGGCCTGTTCCAGAAAGATGGAATTCTGG -s mr.mrrefChr5 211734 54 + 294540 TCTTTGTTGCATTCTTTATTGAACCTGGCCTGTCCCAGAAAGAAGGGATTTTCA -s simCow_chr6.simCow.chr6 338339 42 + 602619 TCTTTGTT----------TTTGACCTG--CTGTTCAAAAGAAATGGAATTCTGG -s simDog_chr6.simDog.chr6 328079 44 + 593897 TGTTTGTT----------TTGGACTTGGCCTGTTCCAGGAAGATGGAATTCTGG -s simHuman_chr6.simHuman.chr6 350139 54 + 601863 TCTTTGCTCCGTTCTTTATTGTACCTGGCCTGTGCCAGAAAGATGGAATTCTGG -s simRat_chr6.simRat.chr6 357100 54 + 647215 TCTTTGTTGCATTCTTGTTTGGGCCTGGCCTGTTTCAGAAAGAAGGTATTTTCA - -a -s simMouse_chr6.simMouse.chr6 364698 5 + 636262 TCCCT -s Anc0.Anc0refChr0 25474 5 + 26507 CTTTG -s Anc1.Anc1refChr6 26419 5 + 197743 CTTTG -s Anc2.Anc2refChr17 20240 5 + 28526 CTTTG -s mr.mrrefChr5 211788 5 + 294540 TCCCT -s simCow_chr6.simCow.chr6 338390 5 + 602619 CAGTG -s simDog_chr6.simDog.chr6 328132 5 + 593897 CTTTG -s simHuman_chr6.simHuman.chr6 350193 5 + 601863 CTTTG -s simRat_chr6.simRat.chr6 357154 5 + 647215 TCCCT - -a -s simMouse_chr6.simMouse.chr6 364703 42 + 636262 TTTCATCACTTTTGTAAGAAGTTAAACAGAAAACAAGTATCA -s Anc0.Anc0refChr0 25479 42 + 26507 ATTTATCACTTTTTGAAGAAGTTAAAAGGAAGACAAGTATCA -s Anc1.Anc1refChr6 26424 42 + 197743 ATTTATCACTTTTTGAAGAAGTTAAAAGGAAGACAAGTATCA -s Anc2.Anc2refChr17 20245 42 + 28526 ATTTATCCCTTTTTGAAGAGGTTAAAAGGAAGACAAGTATCA -s mr.mrrefChr5 211793 42 + 294540 ATTCATCACTTTTGGAAGAAGTTAAACAGAAAACAAGTATCA -s simCow_chr6.simCow.chr6 338395 35 + 602619 TTTGGT-------TGAAGAGGTTAAAAGGGAGACACGTATCA -s simDog_chr6.simDog.chr6 328137 42 + 593897 ATTTATCCCTTTTTGAAGAGGTTAAAAGGAAAATGAGTATCA -s simHuman_chr6.simHuman.chr6 350198 42 + 601863 ATTTATCACTTTTTGAAGAAGTTAAATGGATGACAAGTAGCA -s simRat_chr6.simRat.chr6 357161 42 + 647215 ATTCATAACTTTTGGAAGAAGTTAAACAGAAAATGAGCGTTA - -a -s simMouse_chr6.simMouse.chr6 364745 33 + 636262 TCCTCCAGTGTTGAGTTATCTGTGTCCAATAAA -s Anc0.Anc0refChr0 25521 33 + 26507 ATTCCAACTGCTGAACTATTTTTGTCCAATAAA -s Anc1.Anc1refChr6 26466 33 + 197743 ATTCCAACTGCTGAACTATTTTTGTCCAATAAA -s Anc2.Anc2refChr17 20287 33 + 28526 ATTCCAACTGCTGAACTATTTTTTTCCAATGAA -s mr.mrrefChr5 211835 33 + 294540 TTCCCCAGTGTTGAGCTATTTGTGTCCAATAAA -s simCow_chr6.simCow.chr6 338432 33 + 602619 ATTCCAACTGCTGAACTATTTTTCTCCAATGAA -s simDog_chr6.simDog.chr6 328179 33 + 593897 ATCCAAACTCCTGAACTATTTTTTTTCAATGAA -s simHuman_chr6.simHuman.chr6 350240 33 + 601863 ATTCCAACTGCTGAACTCTTTTTGTCCAATAGA -s simRat_chr6.simRat.chr6 357203 33 + 647215 GTCCACAATGTTGAGCTATTTGTGTCCAATAAA - -a -s simMouse_chr6.simMouse.chr6 364778 57 + 636262 CTTTATTTCTAACACTACTTTATTCCTAACACTTCTGAAACTAAATGTAGTTAATGT -s Anc0.Anc0refChr0 25557 39 + 26507 CTTTAT-----------------TTTTAGCAATTTTG-AACTAAGTGCACTAAATGT -s Anc1.Anc1refChr6 26502 39 + 197743 CTTTAT-----------------TTTTAGCAATTTTG-AACTAAGTGCACTAAATGT -s Anc2.Anc2refChr17 20323 39 + 28526 GACATT-----------------TTTTAGCAATTTTC-AACTAAGGGCACTAAATGT -s mr.mrrefChr5 211868 40 + 294540 CTTTAT-----------------TCCTAACACTTTTGAAACTAAATGTACTAAATGT -s simCow_chr6.simCow.chr6 338468 38 + 602619 -CCACC-----------------TTTTCACAATTTTT-AACTAAGGGTACTACATAC -s simDog_chr6.simDog.chr6 328215 30 + 593897 GACATT-----------------TTTTAGCAATTTTC----------CACTAAATGT -s simHuman_chr6.simHuman.chr6 350276 39 + 601863 CTTTAT-----------------TTTTAGCAGTTTTG-AACTTATTGCACTAAATGT -s simRat_chr6.simRat.chr6 357236 40 + 647215 CTTTAT-----------------TACTAACACCTTTGAAACTGAATGTACTAAATGT - -a -s simMouse_chr6.simMouse.chr6 364835 75 + 636262 AGCAAGGCTGGAATAATTGTGATATTTCCTAAGGTACGTCTGTTCCACCCAGCGTTATGTGGTCTAGATTGTACT -s Anc0.Anc0refChr0 25596 74 + 26507 AGTAAGACTGGAATAGTTGTGGTATTTCTTAAGGCATATCTGTTCCACCCAGCATCAAGTGCTCTACATGAGGC- -s Anc1.Anc1refChr6 26541 74 + 197743 AGTAAGACTGGAATAGTTGTGGTATTTCTTAAGGCATATCTGTTCCACCCAGCATCAAGTGCTCTACATGAGGC- -s Anc2.Anc2refChr17 20362 74 + 28526 AGTAAGACTGGAATAGTTGTGGTATTTCTTAAGGCATATCCATTCTACCCAGCATTAAGAGCTCTACATGAGGC- -s mr.mrrefChr5 211908 75 + 294540 AGCAAGGCTGGAATAATTGTGATATTTCCTAAGGTATGTCTGTTCCACCCAGCGTCATGTGGTCTAGATTATGCT -s simCow_chr6.simCow.chr6 338506 74 + 602619 AGTAAACCTTGAATAGTTGTTATATCTCCTAAGGCAGATCCAGTCTACCCAGCATAAATGGCTCTACATGAGGC- -s simDog_chr6.simDog.chr6 328247 74 + 593897 GGTAAGACTGGAATAGTCATGGTACTTCTTAAGGCATACCCATTTTATGCAGCATTAAGAGCCCTTCATGAGGC- -s simHuman_chr6.simHuman.chr6 350315 74 + 601863 AGTAGGAATGGAATAGTTGTGGTATTTCTTAAGGGATATCTGTTCCTCCCAGCATCAAGTGCTCTACATGACGC- -s simRat_chr6.simRat.chr6 357276 71 + 647215 AGCCAGGCTGGAATAATTATGATATTTCCTGGGGTATGTCCATCCCACTCGGCGTCAGG----CTAGATCATGCT - -a -s simMouse_chr6.simMouse.chr6 364910 18 + 636262 ATGGAGAGTGCTACATCA -s Anc0.Anc0refChr0 25670 18 + 26507 ATGGAGAATGCACTATCA -s Anc1.Anc1refChr6 26615 18 + 197743 ATGGAGAATGCACTATCA -s Anc2.Anc2refChr17 20436 18 + 28526 ATTGAGAATGCACTATCA -s mr.mrrefChr5 211983 18 + 294540 ATGGAGAGTGCTACATCA -s simCow_chr6.simCow.chr6 338580 12 + 602619 TC------TACACCATCA -s simDog_chr6.simDog.chr6 328340 18 + 593897 ATTGAGAATGTACTATCG -s simHuman_chr6.simHuman.chr6 350389 18 + 601863 ATGCAGAATGCAGTTTTA -s simRat_chr6.simRat.chr6 357347 18 + 647215 ACGGAGACTGCTACATCA - -a -s simMouse_chr6.simMouse.chr6 364928 7 + 636262 CACTTTA -s Anc0.Anc0refChr0 25688 7 + 26507 CCATTTA -s Anc1.Anc1refChr6 26633 7 + 197743 CCATTTA -s Anc2.Anc2refChr17 20455 7 + 28526 CCATTTA -s mr.mrrefChr5 212001 7 + 294540 CACTTTA -s simCow_chr6.simCow.chr6 338593 7 + 602619 CAATTTA -s simDog_chr6.simDog.chr6 328359 7 + 593897 CCACTTA -s simHuman_chr6.simHuman.chr6 350407 7 + 601863 CCATGTA -s simRat_chr6.simRat.chr6 357365 7 + 647215 CACTCTA - -a -s simMouse_chr6.simMouse.chr6 364935 8 + 636262 AGAGAATA -s Anc0.Anc0refChr0 25699 8 + 26507 AGAGAATA -s Anc1.Anc1refChr6 26644 8 + 197743 AGAGAATA -s Anc2.Anc2refChr17 20466 8 + 28526 ATAGAATA -s mr.mrrefChr5 212012 8 + 294540 AGAGAATA -s simCow_chr6.simCow.chr6 338603 8 + 602619 ACAGAATA -s simDog_chr6.simDog.chr6 328370 8 + 593897 ATAGACTG -s simHuman_chr6.simHuman.chr6 350418 8 + 601863 AGAGAATA -s simRat_chr6.simRat.chr6 357376 8 + 647215 AGAGAGTA - -a -s simMouse_chr6.simMouse.chr6 364943 24 + 636262 AGCATAGTCATCCAGGGCAGGCCT -s Anc0.Anc0refChr0 25707 24 + 26507 AGTCTAGACATCCATGTCAGGTCT -s Anc1.Anc1refChr6 26652 24 + 197743 AGTCTAGACATCCATGTCAGGTCT -s Anc2.Anc2refChr17 20481 24 + 28526 AGTCTAGACATCCATGTCAGGTCT -s mr.mrrefChr5 212020 24 + 294540 AGCATAGTCATCCATGGCAGGCCT -s simCow_chr6.simCow.chr6 338618 23 + 602619 AGTTTAGACATCCACATCAGGTC- -s simDog_chr6.simDog.chr6 328385 24 + 593897 AGTCTAGAAATTCATGTCAGGTCT -s simHuman_chr6.simHuman.chr6 350426 24 + 601863 AATCTAGACATCCATGTTAGATCC -s simRat_chr6.simRat.chr6 357384 22 + 647215 AGCATAGTCATCTATGGCAGG--T - -a -s simMouse_chr6.simMouse.chr6 364967 12 + 636262 TGCCTCTTTAGC -s Anc0.Anc0refChr0 25732 12 + 26507 TGCATTTTTACT -s Anc1.Anc1refChr6 26677 12 + 197743 TGCATTTTTACT -s Anc2.Anc2refChr17 20506 12 + 28526 TCCATTTTTACT -s mr.mrrefChr5 212044 12 + 294540 TGCCTCTTTAGC -s simCow_chr6.simCow.chr6 338641 12 + 602619 TCGATTTTCATT -s simDog_chr6.simDog.chr6 328410 12 + 593897 TCCACTTTTACT -s simHuman_chr6.simHuman.chr6 350451 12 + 601863 TGCATATTTACT -s simRat_chr6.simRat.chr6 357406 12 + 647215 TGCCTCTTTAGC - -a -s simMouse_chr6.simMouse.chr6 364979 28 + 636262 CATGCTGGTGCCTACTATGTATGGAAAA -s Anc0.Anc0refChr0 25744 24 + 26507 CACACTCTTACCCAT----TATGGAGAA -s Anc1.Anc1refChr6 26689 24 + 197743 CACACTCTTACCCAT----TATGGAGAA -s Anc2.Anc2refChr17 20518 24 + 28526 CACACTCTTACCCAT----TACGGAGAA -s mr.mrrefChr5 212056 28 + 294540 CATACTGGTACCTACTATGTATGGAAAA -s simCow_chr6.simCow.chr6 338654 24 + 602619 CACCCTCTTACCCAT----TAGGGGGAA -s simDog_chr6.simDog.chr6 328422 24 + 593897 CACACTTCTATGCAT----AACCGAGAG -s simHuman_chr6.simHuman.chr6 350463 24 + 601863 CACACTCTTACCCAT----TATGGAGAA -s simRat_chr6.simRat.chr6 357418 28 + 647215 CATACTGGTACCTAACATGTATGGATAA - -a -s simMouse_chr6.simMouse.chr6 365007 1 + 636262 T -s Anc0.Anc0refChr0 25768 1 + 26507 T -s Anc1.Anc1refChr6 26713 1 + 197743 T -s Anc2.Anc2refChr17 20542 1 + 28526 T -s mr.mrrefChr5 212084 1 + 294540 T -s simCow_chr6.simCow.chr6 338707 1 + 602619 T -s simDog_chr6.simDog.chr6 328446 1 + 593897 T -s simHuman_chr6.simHuman.chr6 350487 1 + 601863 T -s simRat_chr6.simRat.chr6 357446 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 365008 8 + 636262 TTTTGTGC -s Anc0.Anc0refChr0 25769 8 + 26507 TTCCGTGC -s Anc1.Anc1refChr6 26714 8 + 197743 TTCCGTGC -s Anc2.Anc2refChr17 20543 8 + 28526 TTCCATGC -s mr.mrrefChr5 212085 8 + 294540 TTTTGTGC -s simCow_chr6.simCow.chr6 338708 8 + 602619 TTCCATGG -s simDog_chr6.simDog.chr6 328448 8 + 593897 TTCCATGC -s simHuman_chr6.simHuman.chr6 350488 8 + 601863 TTCCGTGT -s simRat_chr6.simRat.chr6 357447 8 + 647215 TTTTGTGC - -a -s simMouse_chr6.simMouse.chr6 365016 50 + 636262 TAGACCAGTATTTAGCCTTTCCCATCCCAACTTGAAATTGTCCTTCTGTT -s Anc0.Anc0refChr0 25777 50 + 26507 TAAATGAGTATGTAGCCTTTCTCATATTAACTTGAAATTGTCCTTCTATC -s Anc1.Anc1refChr6 26722 50 + 197743 TAAATGAGTATGTAGCCTTTCTCATATTAACTTGAAATTGTCCTTCTATC -s Anc2.Anc2refChr17 20551 50 + 28526 CTAATGAGTATGTAATCTTTCTCATATTAACTTGAAATTGTCCTTCTACC -s mr.mrrefChr5 212093 50 + 294540 TAGACCAGTATTTAGCCTTTCCCATCCCAACTTGAAATTGTCCTTCTGTT -s simCow_chr6.simCow.chr6 338716 50 + 602619 CTAACCAGTATGTAATCTTTCTCATATTAACTTGAAATTGCCCTCCTACC -s simDog_chr6.simDog.chr6 328456 50 + 593897 CTAGTGAAAATGATATTGTTCTAATACTGACTTGAAATTGTCCTTCTGCC -s simHuman_chr6.simHuman.chr6 350497 50 + 601863 TAATTTAGTATGTAGCCTTTCTCATTTTAACTTGCAGTTGTTCTTCTATC -s simRat_chr6.simRat.chr6 357455 50 + 647215 TGGACCAGTATTTAGCCTTTCCCATCCCGACTTGACATTGTCCTACTGTT - -a -s simMouse_chr6.simMouse.chr6 365066 28 + 636262 TGAACAACCTCGATTCTCCCAATGCTCT -s Anc0.Anc0refChr0 25835 28 + 26507 TGAACAACCCCCATTCCCCCAATGACCT -s Anc1.Anc1refChr6 26780 28 + 197743 TGAACAACCCCCATTCCCCCAATGACCT -s Anc2.Anc2refChr17 20609 28 + 28526 TGAACAACCCCCATTCCCCCAATGACCT -s mr.mrrefChr5 212143 28 + 294540 TGAACAACCTCCATTCTCCCAATGCTCT -s simCow_chr6.simCow.chr6 338774 22 + 602619 TGAACAA------TTCCCCAAATGGTCT -s simDog_chr6.simDog.chr6 328514 28 + 593897 TTAACACCCCCCATTCTCCCAATGACCT -s simHuman_chr6.simHuman.chr6 350555 28 + 601863 TGAACAACACCCATTCCAACACTGAGCT -s simRat_chr6.simRat.chr6 357505 28 + 647215 TGTACAACCTCCATTCTCTTGATGCTCT - -a -s simMouse_chr6.simMouse.chr6 365094 3 + 636262 GGG -s Anc0.Anc0refChr0 25868 3 + 26507 GGG -s Anc1.Anc1refChr6 26813 3 + 197743 GGG -s Anc2.Anc2refChr17 20642 3 + 28526 GGG -s mr.mrrefChr5 212176 3 + 294540 GGG -s simCow_chr6.simCow.chr6 338801 3 + 602619 CGG -s simDog_chr6.simDog.chr6 328547 3 + 593897 GGG -s simRat_chr6.simRat.chr6 357539 3 + 647215 GGG - -a -s simMouse_chr6.simMouse.chr6 365097 22 + 636262 GTCCCCTTAATTGTATTTAATG -s Anc0.Anc0refChr0 25871 22 + 26507 ACCCTCTTAATTTTATTTAATT -s Anc1.Anc1refChr6 26816 22 + 197743 ACCCTCTTAATTTTATTTAATT -s Anc2.Anc2refChr17 20646 22 + 28526 ACCCTCTTTATTTTATTTAATT -s mr.mrrefChr5 212179 22 + 294540 GTCCCCTTAATTTTATTTAATG -s simCow_chr6.simCow.chr6 338805 22 + 602619 GGCTTCTTTACTTTATTTTACT -s simDog_chr6.simDog.chr6 328551 22 + 593897 ACCCTCTTTATTTTATTCAATA -s simHuman_chr6.simHuman.chr6 350588 20 + 601863 --CCTCTCAATTTTGGTTAATT -s simRat_chr6.simRat.chr6 357542 22 + 647215 GCCTCCTTAATTTTATTTAATG - -a -s simMouse_chr6.simMouse.chr6 365119 7 + 636262 GAATTGG -s Anc0.Anc0refChr0 25893 7 + 26507 GACTTGG -s Anc1.Anc1refChr6 26838 7 + 197743 GACTTGG -s Anc2.Anc2refChr17 20668 7 + 28526 GACCTGG -s mr.mrrefChr5 212201 7 + 294540 GAATTGG -s simCow_chr6.simCow.chr6 338828 7 + 602619 AACCTGG -s simDog_chr6.simDog.chr6 328573 7 + 593897 GACCTGG -s simHuman_chr6.simHuman.chr6 350608 7 + 601863 GACTTGG -s simRat_chr6.simRat.chr6 357564 7 + 647215 GAATTGG - -a -s simMouse_chr6.simMouse.chr6 365126 14 + 636262 ATGCAAACAATGTT -s Anc0.Anc0refChr0 25900 14 + 26507 GTCCAAATAATGGA -s Anc1.Anc1refChr6 26845 14 + 197743 GTCCAAATAATGGA -s Anc2.Anc2refChr17 20675 14 + 28526 GCCCAAATAATGGA -s mr.mrrefChr5 212208 14 + 294540 ATGCAAACAATGTT -s simCow_chr6.simCow.chr6 338836 14 + 602619 GCCCAAATATTGGC -s simDog_chr6.simDog.chr6 328580 14 + 593897 ACCCAAGTAATGGA -s simHuman_chr6.simHuman.chr6 350615 6 + 601863 GTCCAA-------- -s simRat_chr6.simRat.chr6 357571 14 + 647215 ACATAAACAATGTT - -a -s simMouse_chr6.simMouse.chr6 365140 13 + 636262 TGATTATTGACAA -s Anc0.Anc0refChr0 25914 13 + 26507 TGACTATTAACAC -s Anc1.Anc1refChr6 26859 13 + 197743 TGACTATTAACAC -s Anc2.Anc2refChr17 20689 13 + 28526 TGACTGCTAACAC -s mr.mrrefChr5 212222 13 + 294540 TGATTATTGACAA -s simCow_chr6.simCow.chr6 338850 13 + 602619 TAGTTACTTACAC -s simDog_chr6.simDog.chr6 328595 13 + 593897 TGACTGCTAACAC -s simHuman_chr6.simHuman.chr6 350621 8 + 601863 -----ATTAACAC -s simRat_chr6.simRat.chr6 357585 13 + 647215 TGATTACTGACAA - -a -s simMouse_chr6.simMouse.chr6 365153 3 + 636262 TCA -s Anc0.Anc0refChr0 25927 3 + 26507 ACT -s Anc1.Anc1refChr6 26872 3 + 197743 ACT -s Anc2.Anc2refChr17 20702 3 + 28526 ACT -s mr.mrrefChr5 212235 3 + 294540 TCA -s mr.mrrefChr5 81905 3 - 294540 ACC -s simCow_chr6.simCow.chr6 338863 3 + 602619 AAT -s simDog_chr6.simDog.chr6 328608 3 + 593897 ACT -s simHuman_chr6.simHuman.chr6 350629 3 + 601863 ACT -s simMouse_chr6.simMouse.chr6 270703 3 - 636262 ACC -s simRat_chr6.simRat.chr6 289210 3 - 647215 ACC -s simRat_chr6.simRat.chr6 357598 3 + 647215 TCA - -a -s simMouse_chr6.simMouse.chr6 365156 39 + 636262 GGCCATGAGACATTCCAAATCGTGGATTCTCAGAGTTAC -s Anc0.Anc0refChr0 25930 39 + 26507 GGCCATGCCACATTCTGAATTATGGGTTCTCAAAGTTAC -s Anc1.Anc1refChr6 26875 39 + 197743 GGCCATGCCACATTCTGAATTATGGGTTCTCAAAGTTAC -s Anc2.Anc2refChr17 20705 39 + 28526 GGCCATGCCACATTCTGAATTATGGGTTCTCAAAGTTAC -s mr.mrrefChr5 212238 39 + 294540 GGCCATGACACATTCCAAATTGTGGATTCTCAAAGTTAC -s mr.mrrefChr5 81911 39 - 294540 GCCACTGACATGCTTTGAATTACATGTTTTCAAAGCAAC -s simCow_chr6.simCow.chr6 338866 39 + 602619 GGCCATGCCACACTGTGAATTATGGGTTCTCAAAGTTAC -s simDog_chr6.simDog.chr6 328611 29 + 593897 GGCCATGTCACATCCTGGAATATTGGT----------AC -s simHuman_chr6.simHuman.chr6 350632 39 + 601863 GTCCATGCCAGAATCTGAATTGTGAGTTCTCAAAGTTAA -s simMouse_chr6.simMouse.chr6 270709 39 - 636262 GCCACTGACATGCTTTGAATTACATGTTTTCAAAGCAAC -s simRat_chr6.simRat.chr6 289216 39 - 647215 GCCACTGACATGCTTTGAATTATAGGTTTTCAAAGCAAC -s simRat_chr6.simRat.chr6 357601 38 + 647215 GGC-ATGACACACTCCAAATTGTGGATGTTCAAACTTAC - -a -s simMouse_chr6.simMouse.chr6 365195 2 + 636262 AG -s Anc0.Anc0refChr0 25969 2 + 26507 AG -s Anc1.Anc1refChr6 26914 2 + 197743 AG -s Anc2.Anc2refChr17 20745 2 + 28526 GG -s mr.mrrefChr5 212277 2 + 294540 AA -s mr.mrrefChr5 81950 2 - 294540 AG -s simCow_chr6.simCow.chr6 338906 2 + 602619 GG -s simDog_chr6.simDog.chr6 328641 2 + 593897 GG -s simHuman_chr6.simHuman.chr6 350671 2 + 601863 AA -s simMouse_chr6.simMouse.chr6 270748 2 - 636262 AG -s simRat_chr6.simRat.chr6 289255 2 - 647215 AG -s simRat_chr6.simRat.chr6 357639 2 + 647215 AA - -a -s simMouse_chr6.simMouse.chr6 365197 2 + 636262 AA -s Anc0.Anc0refChr0 25971 2 + 26507 AA -s Anc1.Anc1refChr6 26916 2 + 197743 AA -s Anc2.Anc2refChr17 20747 2 + 28526 GG -s mr.mrrefChr5 212279 2 + 294540 AA -s mr.mrrefChr5 81952 2 - 294540 AA -s simCow_chr6.simCow.chr6 338908 2 + 602619 GG -s simDog_chr6.simDog.chr6 328643 2 + 593897 GG -s simHuman_chr6.simHuman.chr6 350673 2 + 601863 AA -s simMouse_chr6.simMouse.chr6 270750 2 - 636262 AA -s simRat_chr6.simRat.chr6 289264 2 - 647215 AA -s simRat_chr6.simRat.chr6 357641 2 + 647215 AA - -a -s simMouse_chr6.simMouse.chr6 365199 7 + 636262 GTAATGG -s mr.mrrefChr5 212281 7 + 294540 GTAATGG -s simRat_chr6.simRat.chr6 357643 7 + 647215 GTAATGG - -a -s simMouse_chr6.simMouse.chr6 365206 10 + 636262 TGTGAAGCTT -s Anc0.Anc0refChr0 25981 10 + 26507 TATAGAGCTA -s Anc1.Anc1refChr6 26926 10 + 197743 TATAGAGCTA -s Anc2.Anc2refChr17 20757 10 + 28526 TATAGAGCTG -s mr.mrrefChr5 212288 10 + 294540 TATGAAGCTT -s mr.mrrefChr5 81954 10 - 294540 TACATAGCTA -s simCow_chr6.simCow.chr6 338915 10 + 602619 CATAAAGCTG -s simDog_chr6.simDog.chr6 328653 10 + 593897 TATAGAGTTG -s simHuman_chr6.simHuman.chr6 350683 10 + 601863 TATAGGGCTA -s simMouse_chr6.simMouse.chr6 270752 10 - 636262 TACATAGCTA -s simRat_chr6.simRat.chr6 289266 10 - 647215 TATATGGCTA -s simRat_chr6.simRat.chr6 357650 10 + 647215 TATGAAGCGC - -a -s simMouse_chr6.simMouse.chr6 365216 3 + 636262 TTT -s Anc0.Anc0refChr0 25991 3 + 26507 TTT -s Anc1.Anc1refChr6 26936 3 + 197743 TTT -s Anc2.Anc2refChr17 20767 3 + 28526 TTT -s mr.mrrefChr5 212298 3 + 294540 TTT -s mr.mrrefChr5 81964 3 - 294540 TTG -s simCow_chr6.simCow.chr6 338925 3 + 602619 TTT -s simDog_chr6.simDog.chr6 328663 3 + 593897 TTT -s simHuman_chr6.simHuman.chr6 350693 3 + 601863 TTT -s simMouse_chr6.simMouse.chr6 270762 3 - 636262 TTG -s simRat_chr6.simRat.chr6 289277 3 - 647215 TTG -s simRat_chr6.simRat.chr6 357660 3 + 647215 TGC - -a -s simMouse_chr6.simMouse.chr6 365219 1 + 636262 T -s Anc0.Anc0refChr0 25994 1 + 26507 T -s Anc1.Anc1refChr6 26939 1 + 197743 T -s Anc2.Anc2refChr17 20770 1 + 28526 T -s mr.mrrefChr5 212301 1 + 294540 T -s simCow_chr6.simCow.chr6 338928 1 + 602619 T -s simDog_chr6.simDog.chr6 328666 1 + 593897 T -s simHuman_chr6.simHuman.chr6 350696 1 + 601863 T -s simRat_chr6.simRat.chr6 357663 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 365220 18 + 636262 AAACATTGATACTGTTAG -s Anc0.Anc0refChr0 25995 18 + 26507 AGACACCTATATTTTTAG -s Anc1.Anc1refChr6 26940 18 + 197743 AGACACCTATATTTTTAG -s Anc2.Anc2refChr17 20771 18 + 28526 AGACCCCTGTATTTTTAT -s mr.mrrefChr5 212302 18 + 294540 AGACACTGATATTTTTAG -s mr.mrrefChr5 81967 18 - 294540 AGACATGTATATTTTTAG -s simCow_chr6.simCow.chr6 338929 11 + 602619 AGAACCCT-------TAT -s simDog_chr6.simDog.chr6 328667 18 + 593897 AGACCCCTGTATTTTTAT -s simHuman_chr6.simHuman.chr6 350697 17 + 601863 AGACACCTACATTTTT-T -s simMouse_chr6.simMouse.chr6 270765 18 - 636262 AGACATGTATATTTTTAG -s simRat_chr6.simRat.chr6 289280 18 - 647215 AGACACATATATTCTTAG -s simRat_chr6.simRat.chr6 357664 18 + 647215 AGACACTGATATTTTTAG - -a -s simMouse_chr6.simMouse.chr6 365238 15 + 636262 AGGTTGCTGCAATGA -s Anc0.Anc0refChr0 26013 14 + 26507 -GGTAGCTGCACTGA -s Anc1.Anc1refChr6 26958 15 + 197743 AGGTAGCTGCACTGA -s Anc2.Anc2refChr17 20789 14 + 28526 -GGTAGCAGCACCAA -s mr.mrrefChr5 212320 15 + 294540 AGGTTGCTGCAATGA -s simCow_chr6.simCow.chr6 338940 14 + 602619 -AGTAGCAACACCAA -s simDog_chr6.simDog.chr6 328685 14 + 593897 -GGTACCAGCACCAA -s simHuman_chr6.simHuman.chr6 350714 15 + 601863 AGGTGGCTGCACTGA -s simRat_chr6.simRat.chr6 357682 15 + 647215 AGGTAGCTGCAACAG - -a -s simMouse_chr6.simMouse.chr6 365253 1 + 636262 C -s Anc0.Anc0refChr0 26032 1 + 26507 T -s Anc1.Anc1refChr6 26978 1 + 197743 T -s Anc2.Anc2refChr17 20808 1 + 28526 T -s mr.mrrefChr5 212335 1 + 294540 C -s simCow_chr6.simCow.chr6 338959 1 + 602619 T -s simDog_chr6.simDog.chr6 328704 1 + 593897 T -s simHuman_chr6.simHuman.chr6 350734 1 + 601863 T -s simRat_chr6.simRat.chr6 357697 1 + 647215 G - -a -s simMouse_chr6.simMouse.chr6 365254 11 + 636262 GCTTCCACGCC -s Anc0.Anc0refChr0 26033 11 + 26507 GCTTCCCCACC -s Anc1.Anc1refChr6 26979 11 + 197743 GCTTCCCCACC -s Anc2.Anc2refChr17 20809 11 + 28526 GCTCCCCCACC -s mr.mrrefChr5 212336 11 + 294540 GCTTCCACACC -s mr.mrrefChr5 81985 11 - 294540 GCAGCCACACC -s simCow_chr6.simCow.chr6 338960 11 + 602619 GCTCACCCACC -s simDog_chr6.simDog.chr6 328705 11 + 593897 GCTCCCCCACC -s simHuman_chr6.simHuman.chr6 350735 11 + 601863 GCTTCCCCATC -s simMouse_chr6.simMouse.chr6 270783 11 - 636262 GCAGCCACACC -s simRat_chr6.simRat.chr6 289298 11 - 647215 GCAGCCACACC -s simRat_chr6.simRat.chr6 357698 11 + 647215 GCTTCCACACC - -a -s simMouse_chr6.simMouse.chr6 365265 19 + 636262 TTATGCCCGCAGGTAGAAG -s Anc0.Anc0refChr0 26045 18 + 26507 TTATTCCCCCAA-TGGATG -s Anc1.Anc1refChr6 26992 19 + 197743 TTATTCCCCCAAGTGGATG -s Anc2.Anc2refChr17 20821 18 + 28526 CTAGTCCCTCAA-TGGATG -s mr.mrrefChr5 212347 19 + 294540 TTATTCCCGCAGGTAGATG -s mr.mrrefChr5 82001 19 - 294540 TGATAACCCCAAGTAGGTG -s simCow_chr6.simCow.chr6 338972 17 + 602619 TTAGTCCAT-GA-CGGATG -s simDog_chr6.simDog.chr6 328717 18 + 593897 CTAGTCCCTCAA-TGTATG -s simHuman_chr6.simHuman.chr6 350748 18 + 601863 -TATTCCCCCAAGTGGATG -s simMouse_chr6.simMouse.chr6 270799 19 - 636262 TGATAACCCCAAGTAGGTG -s simRat_chr6.simRat.chr6 289314 19 - 647215 TTACTACCTGAAGCAGGTG -s simRat_chr6.simRat.chr6 357709 19 + 647215 TTATTCCCGTAGGTAGATG - -a -s simMouse_chr6.simMouse.chr6 365284 11 + 636262 AGATTTCAATT -s Anc0.Anc0refChr0 26064 11 + 26507 AAGTCTCAATT -s Anc1.Anc1refChr6 27012 11 + 197743 AAGTCTCAATT -s Anc2.Anc2refChr17 20840 11 + 28526 AAGTCTGGATT -s mr.mrrefChr5 212366 11 + 294540 AAGTTTCAATT -s mr.mrrefChr5 82021 11 - 294540 AAGTCCCAATC -s simCow_chr6.simCow.chr6 338990 11 + 602619 AAGTCTTTATT -s simDog_chr6.simDog.chr6 328736 11 + 593897 AAGTCTGGATC -s simHuman_chr6.simHuman.chr6 350767 11 + 601863 AAGTCTCACTT -s simMouse_chr6.simMouse.chr6 270819 11 - 636262 AAGTCCCAATC -s simRat_chr6.simRat.chr6 289334 11 - 647215 AAGTCTCAATT -s simRat_chr6.simRat.chr6 357728 11 + 647215 AAGCTTCAATT - -a -s simMouse_chr6.simMouse.chr6 365295 1 + 636262 C -s Anc0.Anc0refChr0 26075 1 + 26507 C -s Anc1.Anc1refChr6 27023 1 + 197743 C -s Anc2.Anc2refChr17 20851 1 + 28526 C -s mr.mrrefChr5 212377 1 + 294540 C -s simCow_chr6.simCow.chr6 339001 1 + 602619 C -s simDog_chr6.simDog.chr6 328747 1 + 593897 C -s simHuman_chr6.simHuman.chr6 350778 1 + 601863 T -s simRat_chr6.simRat.chr6 357739 1 + 647215 C - -a -s simMouse_chr6.simMouse.chr6 365296 6 + 636262 CCTTGG -s Anc0.Anc0refChr0 26081 3 + 26507 CG-T-- -s Anc1.Anc1refChr6 27029 4 + 197743 CGTT-- -s Anc2.Anc2refChr17 20857 3 + 28526 CG-A-- -s mr.mrrefChr5 212378 6 + 294540 CCTTGG -s simCow_chr6.simCow.chr6 339009 3 + 602619 CT-A-- -s simDog_chr6.simDog.chr6 328750 3 + 593897 CG-A-- -s simHuman_chr6.simHuman.chr6 350784 4 + 601863 CATT-- -s simRat_chr6.simRat.chr6 357740 6 + 647215 CCTTGG - -a -s simMouse_chr6.simMouse.chr6 365302 16 + 636262 GTCTTGGCCTACTGGA -s Anc0.Anc0refChr0 26084 16 + 26507 GTTTTTTTAAATTGGT -s Anc1.Anc1refChr6 27033 16 + 197743 GTTTTTTTAAATTGGT -s Anc2.Anc2refChr17 20860 16 + 28526 GATTTTTTAAATTGGC -s mr.mrrefChr5 212384 16 + 294540 GTTTTGTCCGACTGGT -s mr.mrrefChr5 82032 16 - 294540 GGCTTCCTTAATTGGT -s simCow_chr6.simCow.chr6 339012 16 + 602619 GGTGTTTTAAATTGGC -s simDog_chr6.simDog.chr6 328753 16 + 593897 GATTCTTTAAATTGGC -s simHuman_chr6.simHuman.chr6 350788 15 + 601863 -TTTTTTTAGATTGGT -s simMouse_chr6.simMouse.chr6 270836 16 - 636262 GGCTTCCTTAATTGGT -s simRat_chr6.simRat.chr6 289345 16 - 647215 GGTTTCCTAAGCTGGT -s simRat_chr6.simRat.chr6 357746 16 + 647215 GTTTTGTCCGACTGGT - -a -s simMouse_chr6.simMouse.chr6 365318 31 + 636262 AGAGCACAGTTAACTAGGGGAGTCATCCTAC -s Anc0.Anc0refChr0 26102 31 + 26507 AGAGCACAGTGAACTAGGGGAGTTATCATTT -s Anc1.Anc1refChr6 27051 31 + 197743 AGAGCACAGTGAACTAGGGGAGTTATCATTT -s Anc2.Anc2refChr17 20878 31 + 28526 AGAGCTCAGTGGACTAGGGGAGTTATCATTT -s mr.mrrefChr5 212400 31 + 294540 AGAGCACAGTTAACTAGGGGAGTCATCCTAC -s mr.mrrefChr5 82050 31 - 294540 AGAGTGCAGTGAACCAGGGGAGTCACCATAT -s simCow_chr6.simCow.chr6 339030 31 + 602619 AGAGAGCAGTGGACTAGGTGAGATATAATTC -s simDog_chr6.simDog.chr6 328771 31 + 593897 AAAGCTCAGTGGCCCAGGGGCGTCACCATTT -s simHuman_chr6.simHuman.chr6 350805 31 + 601863 AGATCACAATGAACTAGGGGATTTATCGTTT -s simMouse_chr6.simMouse.chr6 270854 31 - 636262 AGAGTGCAGTGAACCAGGGGAGTCACCATAT -s simRat_chr6.simRat.chr6 289363 31 - 647215 AGAGTGCAGTGAGCCAGGGGAGTCACCATAT -s simRat_chr6.simRat.chr6 357762 31 + 647215 AGAGCACAGTTAACTAGGGAAGTCATCCTAC - -a -s simMouse_chr6.simMouse.chr6 365349 13 + 636262 ACTGCCAACAGAG -s Anc0.Anc0refChr0 26133 13 + 26507 AGTGCCAACAGTG -s Anc1.Anc1refChr6 27082 13 + 197743 AGTGCCAACAGTG -s Anc2.Anc2refChr17 20909 13 + 28526 AGTGCCAACAGTG -s mr.mrrefChr5 212431 13 + 294540 ACTGCCAACAGAG -s mr.mrrefChr5 82081 13 - 294540 ACGGCCAACAGTG -s simCow_chr6.simCow.chr6 339061 13 + 602619 TGTGCCAACAGTG -s simDog_chr6.simDog.chr6 328803 13 + 593897 AGTGCCAACAGTG -s simHuman_chr6.simHuman.chr6 350836 13 + 601863 AGTGCCAACAGTG -s simMouse_chr6.simMouse.chr6 270885 13 - 636262 ACGGCCAACAGTG -s simRat_chr6.simRat.chr6 289394 13 - 647215 AAGGCCAACAGTG -s simRat_chr6.simRat.chr6 357793 13 + 647215 ACTGCCAACAGAG - -a -s simMouse_chr6.simMouse.chr6 365362 2 + 636262 CT -s Anc0.Anc0refChr0 26146 2 + 26507 GT -s Anc1.Anc1refChr6 27095 2 + 197743 GT -s Anc2.Anc2refChr17 20922 2 + 28526 GT -s mr.mrrefChr5 212444 2 + 294540 GT -s simCow_chr6.simCow.chr6 339074 2 + 602619 GT -s simDog_chr6.simDog.chr6 328816 2 + 593897 GT -s simHuman_chr6.simHuman.chr6 350849 2 + 601863 GT -s simRat_chr6.simRat.chr6 357806 2 + 647215 GT - -a -s simMouse_chr6.simMouse.chr6 365408 2 + 636262 TG -s Anc0.Anc0refChr0 405 2 - 26507 TG -s Anc1.Anc1refChr6 170692 2 - 197743 TG -s Anc2.Anc2refChr17 7648 2 - 28526 TG -s mr.mrrefChr5 212490 2 + 294540 TG -s simCow_chr6.simCow.chr6 263589 2 - 602619 TG -s simDog_chr6.simDog.chr6 265126 2 - 593897 TG -s simHuman_chr6.simHuman.chr6 251058 2 - 601863 TA -s simRat_chr6.simRat.chr6 357852 2 + 647215 TG - -a -s simMouse_chr6.simMouse.chr6 365426 6 + 636262 TATTAC - -a -s simMouse_chr6.simMouse.chr6 365443 1 + 636262 A -s Anc0.Anc0refChr0 443 1 - 26507 G -s Anc1.Anc1refChr6 170731 1 - 197743 G -s Anc2.Anc2refChr17 7686 1 - 28526 G -s mr.mrrefChr5 212519 1 + 294540 A -s simCow_chr6.simCow.chr6 263629 1 - 602619 A -s simDog_chr6.simDog.chr6 265161 1 - 593897 G -s simHuman_chr6.simHuman.chr6 251096 1 - 601863 G -s simRat_chr6.simRat.chr6 357881 1 + 647215 G - -a -s simMouse_chr6.simMouse.chr6 365463 5 + 636262 TAGTG -s Anc0.Anc0refChr0 462 1 - 26507 ----G -s Anc1.Anc1refChr6 170751 2 - 197743 ---TG -s Anc2.Anc2refChr17 7705 1 - 28526 ----G -s mr.mrrefChr5 212539 5 + 294540 TAGTG -s simCow_chr6.simCow.chr6 263647 1 - 602619 ----G -s simDog_chr6.simDog.chr6 265180 1 - 593897 ----G -s simHuman_chr6.simHuman.chr6 251115 2 - 601863 ---TG -s simRat_chr6.simRat.chr6 357901 5 + 647215 TAGTG - -a -s simMouse_chr6.simMouse.chr6 365553 3 + 636262 ATT -s mr.mrrefChr5 212629 3 + 294540 ATT -s simRat_chr6.simRat.chr6 357999 3 + 647215 ATT - -a -s simMouse_chr6.simMouse.chr6 365559 71 + 636262 CTCACAAATAATTCCACTGCATAGCTGGAGTATGAGCAATGAGCATCATTGACATCCTCGCTGACTTCCAC -s Anc0.Anc0refChr0 26148 66 + 26507 CTTACAGTTAATTCCACTGCACAGCAGGAGAATGACTAATGAGTATCATTCACATCCCCATTGACT----- -s Anc1.Anc1refChr6 27097 66 + 197743 CTTACAGTTAATTCCACTGCACAGCAGGAGAATGACTAATGAGTATCATTCACATCCCCATTGACT----- -s Anc2.Anc2refChr17 20924 66 + 28526 CTTCCAGTTAATTTCACCATACAGTAGGAAAATGACTAATGAGTATCATTCACACCCCCATTGACT----- -s mr.mrrefChr5 212635 71 + 294540 CTCACAAATAATTCCACTGCACAGCAGGAGTATGAGCAATGAGCATCATTGACATCCTCGTTGACTTCCAC -s simCow_chr6.simCow.chr6 339076 48 + 602619 CTTCCAATAAATTTCACCA--CAATAG----------------TATCATTCACACCCCTGTTGACT----- -s simDog_chr6.simDog.chr6 328818 66 + 593897 TTTCCAGCTAACTTCACCATACAGTAGGAAAATGACTAATGAGCATCATCCACACTCCCATTGGTT----- -s simHuman_chr6.simHuman.chr6 350851 65 + 601863 CATACAG-TAATTCCGCTGCGCAGCAGGAGCATCACTAATAAGTAACATTTATTTCCCCATTGACT----- -s simRat_chr6.simRat.chr6 358005 71 + 647215 CTAACAAATAATTCCACTGCACAGCAGGAATATGAGCAATGAGCATCATTGACATCCTCTTTAACTTCCAC - -a -s simMouse_chr6.simMouse.chr6 365630 35 + 636262 TTGGTTTAGTCTTATAATTATTTACAACCAGTATG -s Anc0.Anc0refChr0 26214 35 + 26507 CTGGTCTAGTCCTATAATTGTTTACAACCCATTTG -s Anc1.Anc1refChr6 27163 35 + 197743 CTGGTCTAGTCCTATAATTGTTTACAACCCATTTG -s Anc2.Anc2refChr17 20990 35 + 28526 CTGGTCTAGTCCTATAATTGTTTACAACACATTTG -s mr.mrrefChr5 212706 35 + 294540 TTGGTTTAGTCTTATAATTGTTTACAACCAATTTG -s simCow_chr6.simCow.chr6 339125 35 + 602619 CTGGTTTAGTCCTCAAATTGTTTACAACACATTTG -s simDog_chr6.simDog.chr6 328884 35 + 593897 CTGGTCTAGTCCTATCATTGTTTCCAATACATTTG -s simHuman_chr6.simHuman.chr6 350916 35 + 601863 CTGGTCTAGTCCTATAAATGGATACAACCTACTTA -s simRat_chr6.simRat.chr6 358076 35 + 647215 TTAGTTTAGTCTTATAGTAGTTTACAACTAATTTG - -a -s simMouse_chr6.simMouse.chr6 365665 59 + 636262 TGCAGTGTATATTATTTAGGTGGCACCTGCCCACAACACTCTCTGTCAGATGGTAAAAA -s Anc0.Anc0refChr0 26249 22 + 26507 TGCAGGGTATATTATTTCTCTG------------------------------------- -s Anc1.Anc1refChr6 27198 22 + 197743 TGCAGGGTATATTATTTCTCTG------------------------------------- -s Anc2.Anc2refChr17 21034 22 + 28526 TGCAGGGTATATCATTTCTCTG------------------------------------- -s mr.mrrefChr5 212741 59 + 294540 TGCAGTGTATATTATTTAGGTGGCACCTGCCCACAACACTCTCTGTCAGATGGTAAAAA -s simCow_chr6.simCow.chr6 339169 22 + 602619 TGCAGGGTATATCATTTCTCTG------------------------------------- -s simDog_chr6.simDog.chr6 328928 22 + 593897 AGCAGGGTCTATCATTACTCTG------------------------------------- -s simHuman_chr6.simHuman.chr6 350951 22 + 601863 TCCAAGGTATGTTATTTCTCTG------------------------------------- -s simRat_chr6.simRat.chr6 358111 59 + 647215 TGCAGTGTATATCATGTAGGTGGCACCTGCCCGTGACCCACTTGGTCAGATGGCAAAGA - -a -s simMouse_chr6.simMouse.chr6 365724 24 + 636262 CCGTGCTAAGCAATGTGCTTTGTA -s Anc0.Anc0refChr0 26271 10 + 26507 --------------GTGCCTGGTG -s Anc1.Anc1refChr6 27220 10 + 197743 --------------GTGCCTGGTG -s Anc2.Anc2refChr17 21056 10 + 28526 --------------GTGCCTGGTG -s mr.mrrefChr5 212800 24 + 294540 CCGTGCTAAGCAATGTGCTTTGTA -s simCow_chr6.simCow.chr6 339191 10 + 602619 --------------GAGCCTACGG -s simDog_chr6.simDog.chr6 328950 10 + 593897 --------------GTGACTGGTG -s simHuman_chr6.simHuman.chr6 350973 10 + 601863 --------------GTGCCTGGTG -s simRat_chr6.simRat.chr6 358176 24 + 647215 CCATGTTAAGCGATGTGCTTTTTA - -a -s simMouse_chr6.simMouse.chr6 365748 11 + 636262 GAGTGCTTAAC -s Anc0.Anc0refChr0 26281 10 + 26507 TGGGG-TTGAC -s Anc1.Anc1refChr6 27230 10 + 197743 TGGGG-TTGAC -s Anc2.Anc2refChr17 21066 10 + 28526 TGTGG-TTGAC -s mr.mrrefChr5 212824 11 + 294540 GAGTGCTTAAC -s simCow_chr6.simCow.chr6 339201 10 + 602619 TGTGG-TTGAC -s simDog_chr6.simDog.chr6 328960 10 + 593897 TGTGA-CTGAC -s simHuman_chr6.simHuman.chr6 350983 10 + 601863 TGGGG-TTGAC -s simRat_chr6.simRat.chr6 358201 11 + 647215 GAGTGCTTAAC - -a -s simMouse_chr6.simMouse.chr6 365759 2 + 636262 AG -s Anc0.Anc0refChr0 26292 2 + 26507 AC -s Anc1.Anc1refChr6 27241 2 + 197743 AC -s Anc2.Anc2refChr17 21077 2 + 28526 AC -s mr.mrrefChr5 212835 2 + 294540 AG -s simCow_chr6.simCow.chr6 339212 2 + 602619 AC -s simDog_chr6.simDog.chr6 328971 2 + 593897 AC -s simHuman_chr6.simHuman.chr6 350994 2 + 601863 AT -s simRat_chr6.simRat.chr6 358212 2 + 647215 AG - -a -s simMouse_chr6.simMouse.chr6 365761 43 + 636262 CAAGATGTCCTCATACAGGGGATTCACATTGGAGGCATCAGCA -s Anc0.Anc0refChr0 26294 43 + 26507 TGAGAAGTCTTAGTACAGGGGACCCAATTTGGAGGCATTAAGA -s Anc1.Anc1refChr6 27243 43 + 197743 TGAGAAGTCTTAGTACAGGGGACCCAATTTGGAGGCATTAAGA -s Anc2.Anc2refChr17 21079 43 + 28526 TTAGAAGTCTTAGTACAGGGGACCCAATTTGGAGGCATTAAGA -s mr.mrrefChr5 212837 43 + 294540 TGAGATGTCCTCATACAGGGGATTCACATTGGAGGCATCAGCA -s simCow_chr6.simCow.chr6 339214 43 + 602619 TAAGAAGTCTTGGTACAGGGGACTCAATAGGTAGGCTTTAAGA -s simDog_chr6.simDog.chr6 328973 43 + 593897 TTAGAAGGCTTAGAACAGGGGACCCAATTTGGAGGCATTAGGA -s simHuman_chr6.simHuman.chr6 350996 22 + 601863 TGAGAAATCTTACTACA---------------------TAAGA -s simRat_chr6.simRat.chr6 358215 43 + 647215 TGTGATGTCCTCATACAGGGGATTCACATTGGAGGCATCAGCG - -a -s simMouse_chr6.simMouse.chr6 365804 13 + 636262 AATCGACCTGCCA -s Anc0.Anc0refChr0 26340 13 + 26507 TGATGATCTCCCA -s Anc1.Anc1refChr6 27289 13 + 197743 TGATGATCTCCCA -s Anc2.Anc2refChr17 21125 13 + 28526 TGATGATCTCCCA -s mr.mrrefChr5 212883 13 + 294540 AATTGACCTGCCA -s simCow_chr6.simCow.chr6 339260 13 + 602619 TGATGATTTTCTC -s simDog_chr6.simDog.chr6 329019 13 + 593897 TAATGAGCTCCCA -s simHuman_chr6.simHuman.chr6 351021 13 + 601863 TGATGATCTCCCA -s simRat_chr6.simRat.chr6 358263 13 + 647215 AATTGACCGTGCA - -a -s simMouse_chr6.simMouse.chr6 365817 65 + 636262 CTCCCGTTTGGCTGGGTGATTTTGTTGGCACCTAAGAAAACCATGCTGCATGAGACCCAAAGACT -s Anc0.Anc0refChr0 26353 64 + 26507 CTCCTGTTTGGTTGGGTTGTTTGGTTGGCACCTAAGAAG-CCTTACTGCAGGAGGCCTAAAGGCT -s Anc1.Anc1refChr6 27302 64 + 197743 CTCCTGTTTGGTTGGGTTGTTTGGTTGGCACCTAAGAAG-CCTTACTGCAGGAGGCCTAAAGGCT -s Anc2.Anc2refChr17 21138 64 + 28526 CTCCTGTTTGGTTGGGTTGTTTGGTTGTCACCTTAGAAA-CCTTACTGCAGGAAGCTTAAATGCT -s mr.mrrefChr5 212896 65 + 294540 CTCCCGTTTGGCTGGGTGATTTTGTTGGCACCTAAGAAGACCATGCTGCAGGAGACCCAAAGACT -s simCow_chr6.simCow.chr6 339275 64 + 602619 CTCCGGTTTGGTTGGGTTGTTATGTTGCCTTATTAAAAA-CCTTACTGCAGGCAAGTTAAATAAT -s simDog_chr6.simDog.chr6 329032 64 + 593897 CTCCTGATTGGTTGGGTTGTTTGATTGTCACCTTAGAAA-TCCTACTGCAGAAAGCTTTAATGCT -s simHuman_chr6.simHuman.chr6 351034 64 + 601863 CTCCTGTTTGGTTGGGTTTATTGGCTTGCACCTAGGATG-CCTTACTGCAGGAGGCCTAAAGGCT -s simRat_chr6.simRat.chr6 358276 64 + 647215 CTCCCATCTGGCTAGGTGATTTTGTTG-CACCTAAGCAGATCATGCTGCAGGAGACCCAAAAACT - -a -s simMouse_chr6.simMouse.chr6 365882 95 + 636262 GGGGCAGCATACTCTTCATCCGATTGTAGCATATTACCTGGTCATATGGTCCTCCTTTCTGCCTGATGAATGGCTCCTGGACAAGTGTGAGCATA -s Anc0.Anc0refChr0 26417 90 + 26507 GAGCTAAA--ACTCCTAATCTGATCGCAGCTCATTATCTGTCCATATAGTCCTCCTTTGTGCCTGGTGAACTGCT-CTGGACAA--GTGAGCATA -s Anc1.Anc1refChr6 27366 90 + 197743 GAGCTAAA--ACTCCTAATCTGATCGCAGCTCATTATCTGTCCATATAGTCCTCCTTTGTGCCTGGTGAACTGCT-CTGGACAA--GTGAGCATA -s Anc2.Anc2refChr17 21216 90 + 28526 GAGCTAAT--ACTCCCAATCTGGTCGCAGCTCATTATTTGTCCATATAGTTCTCCCTTGTGCCTGGTGAACTGCT-CTGGACAG--GTGAACATA -s mr.mrrefChr5 212961 95 + 294540 GAGGCAGAATACTCTTCATCCGATTGCAGCATATTACCTGGTCATATGGTCCTCCTTTCTGCCTGATGAATGGCTCCTGGACAAGTGTGAGCATA -s simCow_chr6.simCow.chr6 339353 90 + 602619 GAGCTAAC--ATTCCCAATCTGGTTGCAGTCTATAATTTGTCTATATAACTCTCCATTGTGCCTGGTGAACTGCT-TTGTACAG--GTGAACATA -s simDog_chr6.simDog.chr6 329110 84 + 593897 GAGCTAAT--ACTCCCAATCTGGTCGCAGCTCCTT----GTCCATATAGTTACCCCTTGTGCCTGTCGAACTTCT-CTAGTCAG--GTGAACA-- -s simHuman_chr6.simHuman.chr6 351098 88 + 601863 GAGCTAAA--ACTCCTGATCTGATAGCACCTCATTATCTGTCCATATTGTCCTCTTTTGTGC--AGTGAACTGCT-CTGGACAA--GTGAGCATA -s simRat_chr6.simRat.chr6 358340 95 + 647215 GAGGCGGAATACTCATCATCCAATTGCAGCATATTACCTGGTACTATGGTCCTACTTTCTGCCTGATGAATGGTTCCTGGACAAGTGTGAGCATA - -a -s simMouse_chr6.simMouse.chr6 365985 5 + 636262 GATCT -s Anc1.Anc1refChr6 27465 5 + 197743 TATCT -s mr.mrrefChr5 213064 5 + 294540 TATCT -s simHuman_chr6.simHuman.chr6 351195 5 + 601863 TATCT -s simRat_chr6.simRat.chr6 358443 5 + 647215 TATCA - -a -s simMouse_chr6.simMouse.chr6 366000 2 + 636262 CA -s Anc0.Anc0refChr1 12836 2 + 62388 CA -s Anc1.Anc1refChr6 27480 2 + 197743 CA -s Anc2.Anc2refChr17 21321 2 + 28526 CA -s mr.mrrefChr5 213079 2 + 294540 CA -s simCow_chr6.simCow.chr6 339457 2 + 602619 CA -s simDog_chr6.simDog.chr6 329207 2 + 593897 CA -s simHuman_chr6.simHuman.chr6 351210 2 + 601863 CA -s simRat_chr6.simRat.chr6 358458 2 + 647215 CA - -a -s simMouse_chr6.simMouse.chr6 366002 2 + 636262 CA -s Anc0.Anc0refChr1 12838 2 + 62388 CA -s Anc1.Anc1refChr6 27482 2 + 197743 CA -s Anc2.Anc2refChr17 21323 2 + 28526 CA -s mr.mrrefChr5 213081 2 + 294540 CA -s simCow_chr6.simCow.chr6 339459 2 + 602619 TG -s simDog_chr6.simDog.chr6 329209 2 + 593897 CA -s simHuman_chr6.simHuman.chr6 351213 2 + 601863 CA -s simRat_chr6.simRat.chr6 358460 2 + 647215 CA - -a -s simMouse_chr6.simMouse.chr6 366011 2 + 636262 TT -s Anc0.Anc0refChr1 12847 2 + 62388 TT -s Anc1.Anc1refChr6 27491 2 + 197743 TT -s Anc2.Anc2refChr3 14029 2 - 53186 TG -s Anc2.Anc2refChr17 21332 2 + 28526 TT -s mr.mrrefChr5 213090 2 + 294540 TT -s simCow_chr6.simCow.chr6 339468 2 + 602619 TT -s simCow_chr6.simCow.chr6 435015 2 - 602619 TG -s simDog_chr6.simDog.chr6 329218 2 + 593897 TT -s simDog_chr6.simDog.chr6 143161 2 + 593897 TG -s simHuman_chr6.simHuman.chr6 351221 1 + 601863 -C -s simRat_chr6.simRat.chr6 358469 2 + 647215 TT - -a -s simMouse_chr6.simMouse.chr6 366015 1 + 636262 A -s Anc1.Anc1refChr6 27495 1 + 197743 A -s mr.mrrefChr5 213094 1 + 294540 A -s simHuman_chr6.simHuman.chr6 351224 1 + 601863 A -s simRat_chr6.simRat.chr6 358473 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 366025 2 + 636262 GT - -a -s simMouse_chr6.simMouse.chr6 366044 6 + 636262 AATGAA -s Anc0.Anc0refChr1 12878 6 + 62388 AATGAA -s Anc1.Anc1refChr2 13678 6 - 144309 AATGAA -s Anc1.Anc1refChr6 27523 6 + 197743 AATGAA -s Anc2.Anc2refChr3 14060 6 - 53186 AATGAA -s Anc2.Anc2refChr17 21363 6 + 28526 AATGAA -s mr.mrrefChr5 213121 6 + 294540 AATGAA -s simCow_chr6.simCow.chr6 339499 6 + 602619 AATGAA -s simCow_chr6.simCow.chr6 435047 6 - 602619 TATGAA -s simDog_chr6.simDog.chr6 329249 6 + 593897 AATGAA -s simDog_chr6.simDog.chr6 143192 6 + 593897 AATGAT -s simHuman_chr6.simHuman.chr6 436398 6 - 601863 AATTAA -s simHuman_chr6.simHuman.chr6 351252 5 + 601863 GAT-AA -s simRat_chr6.simRat.chr6 358500 6 + 647215 AGTGAA - -a -s simMouse_chr6.simMouse.chr6 366081 1 + 636262 A -s Anc0.Anc0refChr1 12915 1 + 62388 A -s Anc1.Anc1refChr6 27560 1 + 197743 A -s Anc2.Anc2refChr17 21400 1 + 28526 A -s mr.mrrefChr5 213158 1 + 294540 A -s simCow_chr6.simCow.chr6 262914 1 - 602619 T -s simDog_chr6.simDog.chr6 329286 1 + 593897 A -s simHuman_chr6.simHuman.chr6 351288 1 + 601863 A -s simRat_chr6.simRat.chr6 358535 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 366118 1 + 636262 C -s Anc0.Anc0refChr1 12953 1 + 62388 C -s Anc1.Anc1refChr2 13752 1 - 144309 C -s Anc1.Anc1refChr6 27598 1 + 197743 C -s Anc2.Anc2refChr3 14133 1 - 53186 C -s Anc2.Anc2refChr17 21444 1 + 28526 C -s mr.mrrefChr5 213195 1 + 294540 C -s simCow_chr6.simCow.chr6 262977 1 - 602619 C -s simCow_chr6.simCow.chr6 435128 1 - 602619 C -s simDog_chr6.simDog.chr6 329330 1 + 593897 C -s simDog_chr6.simDog.chr6 143247 1 + 593897 C -s simHuman_chr6.simHuman.chr6 436472 1 - 601863 C -s simHuman_chr6.simHuman.chr6 351326 1 + 601863 C -s simRat_chr6.simRat.chr6 358572 1 + 647215 C - -a -s simMouse_chr6.simMouse.chr6 366125 2 + 636262 GA -s Anc0.Anc0refChr1 12960 2 + 62388 GA -s Anc1.Anc1refChr6 27605 2 + 197743 GA -s Anc2.Anc2refChr17 21451 2 + 28526 GA -s mr.mrrefChr5 213202 2 + 294540 GA -s simCow_chr6.simCow.chr6 262984 2 - 602619 GA -s simDog_chr6.simDog.chr6 329337 2 + 593897 GA -s simHuman_chr6.simHuman.chr6 351333 2 + 601863 GA -s simRat_chr6.simRat.chr6 358579 2 + 647215 AG - -a -s simMouse_chr6.simMouse.chr6 366149 4 + 636262 CTCT -s Anc0.Anc0refChr2 0 1 + 17989 G--- -s Anc1.Anc1refChr6 27629 4 + 197743 GTCT -s Anc2.Anc2refChr17 21475 1 + 28526 G--- -s mr.mrrefChr5 213226 4 + 294540 CTCT -s simCow_chr6.simCow.chr6 263008 1 - 602619 G--- -s simDog_chr6.simDog.chr6 329361 1 + 593897 G--- -s simHuman_chr6.simHuman.chr6 351366 4 + 601863 GTCT -s simRat_chr6.simRat.chr6 358603 4 + 647215 CACT - -a -s simMouse_chr6.simMouse.chr6 366153 48 + 636262 AGAACATACAAATAAGCTCTCCAAAGCAACCGATGACAGGTGTGCTTA -s Anc0.Anc0refChr2 1 8 + 17989 -GAACATAC--------------------------------------- -s Anc1.Anc1refChr6 27633 9 + 197743 AGAACATAC--------------------------------------- -s Anc2.Anc2refChr17 21476 8 + 28526 -GGACAGAC--------------------------------------- -s mr.mrrefChr5 213230 48 + 294540 AGAACATACAAATAAGCTCTCCAAAGCAACCGATGACAGGTGTGCTTA -s simCow_chr6.simCow.chr6 263009 8 - 602619 -GAATGAAC--------------------------------------- -s simDog_chr6.simDog.chr6 329362 8 + 593897 -GGACAGAC--------------------------------------- -s simHuman_chr6.simHuman.chr6 351382 7 + 601863 AGAGCAT----------------------------------------- -s simRat_chr6.simRat.chr6 358607 48 + 647215 AGAACATACAAATAAGCTCCCTGAAGCAACCAATCACGGGTGTGCTTA - -a -s simMouse_chr6.simMouse.chr6 366201 4 + 636262 TGCA -s Anc0.Anc0refChr2 9 4 + 17989 TACA -s Anc1.Anc1refChr6 27642 4 + 197743 TACA -s Anc2.Anc2refChr17 21484 4 + 28526 TACA -s mr.mrrefChr5 213278 4 + 294540 TGCA -s simCow_chr6.simCow.chr6 263035 4 - 602619 AACA -s simDog_chr6.simDog.chr6 329370 4 + 593897 TACA -s simRat_chr6.simRat.chr6 358655 4 + 647215 TGCA - -a -s simMouse_chr6.simMouse.chr6 366205 45 + 636262 ACAGCTAATGGGACTGCAACTTCATGGTCACTCAAGCTCTACACC -s Anc0.Anc0refChr2 13 44 + 17989 ACAATGAATGGGTGTGC-ATTTCATTGACACACAAGTCTAAGAAT -s Anc1.Anc1refChr6 27646 44 + 197743 ACAATGAATGGGTGTGC-ATTTCATTGACACACAAGTCTAAGAAT -s Anc2.Anc2refChr17 21489 44 + 28526 ACAATGAATGGGTGTGC-ATTTCATTGACACACAAGTCTAAGAAT -s mr.mrrefChr5 213282 45 + 294540 ACAGCTAATGGGACTGCAACTTCATGGTCACTCAAGCTCTACACC -s simCow_chr6.simCow.chr6 263040 44 - 602619 ATAGTGTCTGGTTGTGC-AATTCGTGGCCACACAAGTCTCAGAAT -s simDog_chr6.simDog.chr6 329375 44 + 593897 ACAATGAATGGGTGTGC-ATTTCATTGACACACAAGTCTAAGAAT -s simRat_chr6.simRat.chr6 358659 45 + 647215 ACAGCCGATGGGTCTTCGACTTCATGGTCGCTCAAGCCCTACACC - -a -s simMouse_chr6.simMouse.chr6 366250 5 + 636262 TAATG -s Anc0.Anc0refChr2 57 5 + 17989 AAATG -s Anc1.Anc1refChr6 27690 5 + 197743 AAATG -s Anc2.Anc2refChr17 21533 5 + 28526 AAATG -s mr.mrrefChr5 213327 5 + 294540 TAATG -s simCow_chr6.simCow.chr6 263084 5 - 602619 AAGTC -s simDog_chr6.simDog.chr6 329420 5 + 593897 AAATG -s simRat_chr6.simRat.chr6 358704 5 + 647215 TGATG - -a -s simMouse_chr6.simMouse.chr6 366255 2 + 636262 TA -s Anc0.Anc0refChr2 62 2 + 17989 TA -s Anc1.Anc1refChr6 27695 2 + 197743 TA -s Anc2.Anc2refChr17 21548 2 + 28526 TA -s mr.mrrefChr5 213332 2 + 294540 TA -s simCow_chr6.simCow.chr6 263099 2 - 602619 TA -s simDog_chr6.simDog.chr6 329435 2 + 593897 TA -s simRat_chr6.simRat.chr6 358709 2 + 647215 TA - -a -s simMouse_chr6.simMouse.chr6 366257 16 + 636262 GTGTTCAAATGGTATA -s Anc0.Anc0refChr2 64 16 + 17989 TTTCTTAAGTAATGTA -s Anc1.Anc1refChr6 27697 16 + 197743 TTTCTTAAGTAATGTA -s Anc2.Anc2refChr17 21550 16 + 28526 TTTCTTAAGTAATGTA -s mr.mrrefChr5 213334 16 + 294540 GTGTTCAAATGGTATA -s simCow_chr6.simCow.chr6 339723 16 + 602619 TTTCTTGGATAGTGTA -s simDog_chr6.simDog.chr6 329437 16 + 593897 TTTCTTAAGTAATGTA -s simRat_chr6.simRat.chr6 358711 16 + 647215 GTGTTCAAATCGCCTG - -a -s simMouse_chr6.simMouse.chr6 366273 13 + 636262 CACTCCAGCGATT -s Anc0.Anc0refChr2 80 11 + 17989 AA--TCAATGGGT -s Anc1.Anc1refChr6 27713 11 + 197743 AA--TCAATGGGT -s Anc2.Anc2refChr17 21566 11 + 28526 AA--TCAATGGGT -s mr.mrrefChr5 213350 13 + 294540 CACTCCAGCGATT -s simCow_chr6.simCow.chr6 339740 11 + 602619 AG--TCAATTGGT -s simDog_chr6.simDog.chr6 329453 11 + 593897 AA--TCAATGGGT -s simRat_chr6.simRat.chr6 358727 13 + 647215 CATTCCAGCCATT - -a -s simMouse_chr6.simMouse.chr6 366286 8 + 636262 GCTAAGCC -s Anc0.Anc0refChr2 91 8 + 17989 TCCATGGA -s Anc1.Anc1refChr6 27724 8 + 197743 TCCATGGA -s Anc2.Anc2refChr17 21577 8 + 28526 TCCATGGA -s mr.mrrefChr5 213363 8 + 294540 GCTAAGCC -s simCow_chr6.simCow.chr6 339779 8 + 602619 CCCGAGGA -s simDog_chr6.simDog.chr6 329464 8 + 593897 TCCATGGA -s simRat_chr6.simRat.chr6 358740 8 + 647215 GCAAAGCC - -a -s simMouse_chr6.simMouse.chr6 366294 63 + 636262 ACCATTAAGTAGGAACAATTTAAGGTTAATCATTGTTCATTGATAGCAGCACTAATAAGAACT -s Anc0.Anc0refChr2 99 63 + 17989 AGCATTAAGTAGGAGCAATCTAAGATTAATTGTTATTAGCTGATAGCAGCAATAAGACAGACT -s Anc1.Anc1refChr6 27732 63 + 197743 AGCATTAAGTAGGAGCAATCTAAGATTAATTGTTATTAGCTGATAGCAGCAATAAGACAGACT -s Anc2.Anc2refChr17 21585 63 + 28526 AGCATTAAGTAGGAGCAATCTAAGATTAATTGTTATTAGCTGATAGCAGCAATAAGACAGACT -s mr.mrrefChr5 213371 63 + 294540 ACCATTAAGTAGGAGCAATTTAAGATTAATCATTGTTCGTTGATAGCAGCACTAAGAAGAACT -s simCow_chr6.simCow.chr6 339790 63 + 602619 GGTAGTAAGTAGGAGTAATCTAACATTAATCCTTATTAGGTGATAGCAGCATTATGATTGACT -s simDog_chr6.simDog.chr6 329472 63 + 593897 AGCATTAAGCAGGAGCAATCTAAGGTCAATTGTAATTAGCTGATAGCAACAATAAGGCAGACT -s simRat_chr6.simRat.chr6 358748 63 + 647215 ATCATTAAGTATGAGCAATTTAAGATTAATTATTGTTCGTTGATAGCAGCACTAAGAAGAACT - -a -s simMouse_chr6.simMouse.chr6 366357 32 + 636262 TCATGCATGACTTATATCTATAGGAGGTCTCA -s Anc0.Anc0refChr2 162 20 + 17989 TAATGGATGCCTAATAT------------TAA -s Anc1.Anc1refChr6 27795 24 + 197743 TAATGGATGCCTAATAT--------GACCTAA -s Anc2.Anc2refChr17 21648 20 + 28526 TAATGGATGCCTAATAT------------TAA -s mr.mrrefChr5 213434 32 + 294540 TCATGCATGACTTATATCTATAGGAGGTCTCA -s simCow_chr6.simCow.chr6 339853 20 + 602619 TGATGGATGCCTAATAG------------TAA -s simDog_chr6.simDog.chr6 329538 20 + 593897 TAACAGATACCTAATAT------------TAA -s simHuman_chr6.simHuman.chr6 351389 7 + 601863 -------------------------GACCTAA -s simRat_chr6.simRat.chr6 358811 32 + 647215 TCATGCATGACTGATATCTATAGGAGGTCTCA - -a -s simMouse_chr6.simMouse.chr6 366389 44 + 636262 AAGCATCAAGGCCAGATGCCTCTGCTATTGTGCCAACCTTAGTA -s Anc0.Anc0refChr2 182 42 + 17989 GAGCACAAGATCCAAAGGCCT--GACATTGTGCCAACCTTAGTC -s Anc1.Anc1refChr6 27819 42 + 197743 GAGCACAAGATCCAAAGGCCT--GACATTGTGCCAACCTTAGTC -s Anc2.Anc2refChr17 21668 42 + 28526 GAGCACAAGATCCAAAGGCCT--GACATTGTGCCAACCTTAGTC -s mr.mrrefChr5 213466 42 + 294540 AAGCACCAAAGCCAAAGGCCT--GACATTGTGCCAACCTTAGTA -s simCow_chr6.simCow.chr6 339873 42 + 602619 GAGCTGAAAATCCAAAGGCCT--GACATTGTGCTAACCTTAGTC -s simDog_chr6.simDog.chr6 329572 40 + 593897 GAGCACAAGGTCCAAAGGCCT--GTCATTGTGCCAACGTTAG-- -s simHuman_chr6.simHuman.chr6 351396 42 + 601863 GAGCACAAGATTCAAGGGCCT--GACGTTGTGCCAACCTTAGCC -s simRat_chr6.simRat.chr6 358843 41 + 647215 AAGCACCAAAACCAAAG-CCT--GACATTGTGTGAACCTTAATA - -a -s simMouse_chr6.simMouse.chr6 366433 11 + 636262 AGTTTTGAGTG -s Anc0.Anc0refChr2 224 11 + 17989 AGATTTGAATG -s Anc1.Anc1refChr6 27861 11 + 197743 AGATTTGAATG -s Anc2.Anc2refChr17 21710 11 + 28526 AGATTTGGGTG -s mr.mrrefChr5 213508 11 + 294540 AGTTTTGAATG -s simCow_chr6.simCow.chr6 339941 11 + 602619 AGATTTGGGTG -s simDog_chr6.simDog.chr6 329612 9 + 593897 --ATTTGGGTG -s simHuman_chr6.simHuman.chr6 351438 11 + 601863 AGATTTGAATA -s simRat_chr6.simRat.chr6 358884 11 + 647215 GGTTTTGAACG - -a -s simMouse_chr6.simMouse.chr6 366444 5 + 636262 AGTCC -s Anc0.Anc0refChr2 235 5 + 17989 AGTGC -s Anc1.Anc1refChr6 27872 5 + 197743 AGTGC -s Anc2.Anc2refChr17 21721 5 + 28526 AGTGC -s mr.mrrefChr5 213519 5 + 294540 AGTCC -s simCow_chr6.simCow.chr6 339952 5 + 602619 GGTAC -s simDog_chr6.simDog.chr6 329621 5 + 593897 AGTGT -s simHuman_chr6.simHuman.chr6 351449 5 + 601863 AGTGC -s simRat_chr6.simRat.chr6 358896 5 + 647215 AGTCC - -a -s simMouse_chr6.simMouse.chr6 366449 16 + 636262 TCATGGCCTGTTTATT -s Anc0.Anc0refChr2 247 16 + 17989 TGTTGGCCTATTAATT -s Anc1.Anc1refChr6 27884 16 + 197743 TGTTGGCCTATTAATT -s Anc2.Anc2refChr17 21733 16 + 28526 TGTTGGTTTGTTAATT -s mr.mrrefChr5 213524 16 + 294540 TCATGGCCTATTTATT -s simCow_chr6.simCow.chr6 339964 16 + 602619 TGTTCATTTGTTAATT -s simDog_chr6.simDog.chr6 329633 16 + 593897 TCTTGGTTTGTTAATT -s simHuman_chr6.simHuman.chr6 351461 16 + 601863 TGTTGGCCCATTAATT -s simRat_chr6.simRat.chr6 358901 16 + 647215 TCATGGCCTAATTGTT - -a -s simMouse_chr6.simMouse.chr6 366465 1 + 636262 G -s Anc0.Anc0refChr2 263 1 + 17989 G -s Anc1.Anc1refChr6 27900 1 + 197743 G -s Anc2.Anc2refChr17 21829 1 + 28526 A -s mr.mrrefChr5 213540 1 + 294540 G -s simCow_chr6.simCow.chr6 340065 1 + 602619 A -s simDog_chr6.simDog.chr6 329734 1 + 593897 A -s simHuman_chr6.simHuman.chr6 351477 1 + 601863 G -s simRat_chr6.simRat.chr6 358917 1 + 647215 G - -a -s simMouse_chr6.simMouse.chr6 366466 15 + 636262 AACCTGGAGATCAGA -s Anc0.Anc0refChr2 275 12 + 17989 AACCTGTA---CAGC -s Anc1.Anc1refChr6 27912 12 + 197743 AACCTGTA---CAGC -s Anc2.Anc2refChr17 21841 12 + 28526 AACCTGTA---CAGC -s mr.mrrefChr5 213541 15 + 294540 AACCTGGAGATCAGA -s simCow_chr6.simCow.chr6 340077 12 + 602619 AACCTGTA---CAGC -s simDog_chr6.simDog.chr6 329746 12 + 593897 AATCTATA---CAGC -s simHuman_chr6.simHuman.chr6 351489 12 + 601863 AACCTGTA---CAGC -s simRat_chr6.simRat.chr6 358918 13 + 647215 AATCCGCAGATCA-- - -a -s simMouse_chr6.simMouse.chr6 366481 12 + 636262 TGATTAGAATTT -s Anc0.Anc0refChr2 287 12 + 17989 TGTCCAGGAATC -s Anc1.Anc1refChr6 27924 12 + 197743 TGTCCAGGAATC -s Anc2.Anc2refChr17 21853 12 + 28526 TTTCCAGGAAAC -s mr.mrrefChr5 213556 12 + 294540 TGATTAGAATTT -s simCow_chr6.simCow.chr6 340089 12 + 602619 TTGCCACGAAAC -s simDog_chr6.simDog.chr6 329759 12 + 593897 TTTCCAGGAAAC -s simHuman_chr6.simHuman.chr6 351501 12 + 601863 TGTCCAGGAATC -s simRat_chr6.simRat.chr6 358931 5 + 647215 -------AATTT - -a -s simMouse_chr6.simMouse.chr6 366493 35 + 636262 ATTATATAGTGATTCCCAAAAGCCTGACTGAATGA -s Anc0.Anc0refChr2 314 34 + 17989 ACTTTAGAGGGTTTCTT-AAGGCATGACTCAATGA -s Anc1.Anc1refChr6 27951 35 + 197743 ACTTTAGAGGGTTTCTTAAAGGCATGACTCAATGA -s Anc2.Anc2refChr17 21880 34 + 28526 ACTTTAGAGTGTTTCTT-AAGGCATGGCTCAATGA -s mr.mrrefChr5 213568 35 + 294540 ATTATATAGGGATTCTCAAAAGCCTGACTCAATGA -s simCow_chr6.simCow.chr6 340116 34 + 602619 ACTTTAGAGTGTTTCTT-AAGGCATGGCTCAATGA -s simHuman_chr6.simHuman.chr6 351528 35 + 601863 ACTCTAGAGGGTTGTTTAAAGGCATTACTCAAAGA -s simRat_chr6.simRat.chr6 358936 35 + 647215 ATTATATAGGGATTCTCAAGAGCCTGACTCAATGA - -a -s simMouse_chr6.simMouse.chr6 366528 45 + 636262 ATTAGAAATATGAGAGGGAAGCAAGTTTGCATACTTTATGCAGAC -s Anc0.Anc0refChr2 348 41 + 17989 ATT---AAGATGA-GGAGACTCATATTTGAATTCTTTATGCAGAT -s Anc1.Anc1refChr6 27986 41 + 197743 ATT---AAGATGA-GGAGACTCATATTTGAATTCTTTATGCAGAT -s Anc2.Anc2refChr17 21914 41 + 28526 AAA---AAGATGG-AGAGACTCATATCTGAATTCTTTGTGCAGAT -s mr.mrrefChr5 213603 45 + 294540 ATTAGAAATATGAGGGGGAAGCAAGTTTGCATACTTTATGCAGAT -s simCow_chr6.simCow.chr6 340153 41 + 602619 AAA---AAGATGG-AGAGACTCATATCTGAGCTCTTTGTGCAGTT -s simDog_chr6.simDog.chr6 329777 22 + 593897 -----------------------TGACTCAATTCTTTGTGCAGAT -s simHuman_chr6.simHuman.chr6 351563 41 + 601863 ATT---AAGATGA-GGAGACCCACATTTGAATTCTTTATGCAGAT -s simRat_chr6.simRat.chr6 358971 45 + 647215 ATTAGAAATATGAGGGGGAAGCAAGTTTGCATACTTTATGCAGAT - -a -s simMouse_chr6.simMouse.chr6 366573 16 + 636262 ACTGGGAGATAGAAGT -s Anc0.Anc0refChr2 397 16 + 17989 GCCAGGATGTAAAAAT -s Anc1.Anc1refChr6 28035 16 + 197743 GCCAGGATGTAAAAAT -s Anc2.Anc2refChr17 21963 16 + 28526 GACAGGATGTAAAAAT -s mr.mrrefChr5 213648 16 + 294540 ACTGGGAGATAGAAGT -s simCow_chr6.simCow.chr6 340202 16 + 602619 GGCAGGATGTAAAAAT -s simDog_chr6.simDog.chr6 329807 16 + 593897 GACAGGATGTAAAAAT -s simHuman_chr6.simHuman.chr6 351612 16 + 601863 GCCAGGATGTAAAAAT -s simRat_chr6.simRat.chr6 359016 16 + 647215 ACTGGGAGATAGAAGT - -a -s simMouse_chr6.simMouse.chr6 366589 36 + 636262 AACACTATGAGTTAGGAGATTACCCAAAACCCGCAC -s Anc0.Anc0refChr2 416 24 + 17989 AACCCCACCGGAAAGTATATCA------------AT -s Anc1.Anc1refChr6 28054 24 + 197743 AACCCCACCGGAAAGTATATCA------------AT -s Anc2.Anc2refChr17 21982 24 + 28526 AACCCCACTGGAAAGTATACCA------------AT -s mr.mrrefChr5 213664 36 + 294540 AACACTATCAGTTAGGAGATTACCCAAAACCCGCAC -s simCow_chr6.simCow.chr6 340221 20 + 602619 A----CAATAGAAAGTATACTA------------CT -s simDog_chr6.simDog.chr6 329826 24 + 593897 AACCCCACTGTAAAGCTTACCA------------AG -s simHuman_chr6.simHuman.chr6 351631 24 + 601863 AACCCCACCGGAGAGTATATCA------------AT -s simRat_chr6.simRat.chr6 359032 36 + 647215 AATGCTGTCAGGTAGGAGATAACCCAAAACCACTAC - -a -s simMouse_chr6.simMouse.chr6 366625 36 + 636262 TGGAAAAGTGCTGCTCGTCAAGAGTATTAGAATAGT -s Anc0.Anc0refChr2 440 34 + 17989 TGTAAAAATACTGCTGGT--TAAGCATTAGAATGGT -s Anc1.Anc1refChr6 28078 34 + 197743 TGTAAAAATACTGCTGGT--TAAGCATTAGAATGGT -s Anc2.Anc2refChr17 22006 34 + 28526 TGTCAAAATACTGCTGGG--CAAGCATTAGGATGGT -s mr.mrrefChr5 213700 36 + 294540 TGGAAAAATACTGCTCGTCATGAGTATTAGAATGGT -s simCow_chr6.simCow.chr6 340245 34 + 602619 TGTCAAAATATTGCTGGT--CAAGCATTGGGCTGTT -s simDog_chr6.simDog.chr6 329850 34 + 593897 TGTCAAAATACTGATGGG--CAAGCAATAGGATGGT -s simHuman_chr6.simHuman.chr6 351655 33 + 601863 TGTAAAAATACTGCT-GT--TAAGCATTAGAATGGT -s simRat_chr6.simRat.chr6 359068 31 + 647215 AAGAAAAACACTGCTCGTCATGAG---TAGAATG-- - -a -s simMouse_chr6.simMouse.chr6 366661 4 + 636262 GTCA -s Anc0.Anc0refChr2 474 4 + 17989 ATTA -s Anc1.Anc1refChr6 28112 4 + 197743 ATTA -s Anc2.Anc2refChr17 22044 4 + 28526 ATTA -s mr.mrrefChr5 213736 4 + 294540 GTCA -s simCow_chr6.simCow.chr6 340286 4 + 602619 ATTA -s simDog_chr6.simDog.chr6 329888 4 + 593897 ATTA -s simHuman_chr6.simHuman.chr6 351688 4 + 601863 ATTA -s simRat_chr6.simRat.chr6 359099 4 + 647215 GTCA - -a -s simMouse_chr6.simMouse.chr6 366665 6 + 636262 CTGATC -s Anc0.Anc0refChr2 478 6 + 17989 TAGGTA -s Anc1.Anc1refChr6 28116 6 + 197743 TAGGTA -s Anc2.Anc2refChr17 22048 6 + 28526 TACGTC -s mr.mrrefChr5 213740 6 + 294540 CTGATA -s simCow_chr6.simCow.chr6 340290 6 + 602619 TTTGTC -s simDog_chr6.simDog.chr6 329895 6 + 593897 TACATC -s simHuman_chr6.simHuman.chr6 351692 6 + 601863 TAGGTA -s simRat_chr6.simRat.chr6 359103 6 + 647215 CTGATA - -a -s simMouse_chr6.simMouse.chr6 366671 32 + 636262 AATGTTATTGAAGGGCCATGTCCTACAATTCA -s Anc0.Anc0refChr2 484 23 + 17989 A--------T-AGGGCCATGTCCATAAATTCA -s Anc1.Anc1refChr6 28122 24 + 197743 A--------TAAGGGCCATGTCCATAAATTCA -s Anc2.Anc2refChr17 22054 23 + 28526 A--------T-AGGGCCATGTCCATAAATACA -s mr.mrrefChr5 213746 32 + 294540 AATGTTATTGAAGGGCCATGTCCTACAATTCA -s simCow_chr6.simCow.chr6 340301 23 + 602619 A--------T-AGGGCCATATCCATGCATATG -s simDog_chr6.simDog.chr6 329901 23 + 593897 A--------C-AGGGCCATGTCCACAAATACA -s simHuman_chr6.simHuman.chr6 351698 22 + 601863 A--------TAAGG--CATTTCCATAAGTTCA -s simRat_chr6.simRat.chr6 359109 32 + 647215 AGTGTTATTGAAGGGCCAGGTCCTACAATCCA - -a -s simMouse_chr6.simMouse.chr6 366703 32 + 636262 TCCTACACTTCAAAATCTTGTCCACTTACATA -s Anc0.Anc0refChr2 512 32 + 17989 TCCTAAGCTTAATGATCCTATCCACTTACACA -s Anc1.Anc1refChr6 28151 32 + 197743 TCCTAAGCTTAATGATCCTATCCACTTACACA -s Anc2.Anc2refChr17 22082 32 + 28526 TCCTAAGCTTAATGATCCTATCCCCTTACACA -s mr.mrrefChr5 213778 32 + 294540 TCCTACACTTAAAAATCTTGTCCACTTACATA -s simCow_chr6.simCow.chr6 340329 29 + 602619 TCCTAAGCATGATGATCCTAACCCCTTAC--- -s simDog_chr6.simDog.chr6 329929 32 + 593897 TCCTAAGCTTAATGATCCTATCCCCATACACA -s simHuman_chr6.simHuman.chr6 351725 32 + 601863 TCCTGAGTTTAATTACCCTATCCACTTACACA -s simRat_chr6.simRat.chr6 359141 22 + 647215 TCCTACACGTAAACATCTTGTC---------- - -a -s simMouse_chr6.simMouse.chr6 366735 91 + 636262 CCAATCCACTTACAGGTGTTGTTGAGTGGTGAAAGTGACCACATAAGGCTGGCAACAGATCTCATGGGAAGCGCTTCCTTGTTTGGTGGAG -s Anc0.Anc0refChr2 545 59 + 17989 CCAATCCACTGACAGGGGTAGGTGAGTTGCAGAAGCAAACATGT------------ATATCTTATGCTAAG-------------------- -s Anc1.Anc1refChr6 28184 75 + 197743 CCAATCCACTGACAGGGGTAGGTGAGTTGCAGAAGCAAACATGT------------ATATCTTATGCTAAG----TCATCGCATGGTGTAA -s Anc2.Anc2refChr17 22115 59 + 28526 ACAATCCACTGACAGGGGTAAGAAACTTGCAGGATCAAATGGGT------------ATATCTTATGCTAAG-------------------- -s mr.mrrefChr5 213810 91 + 294540 CCAATCCACTTACAGGTGTTGTTGAGTGGTAAAAGTGACCATGTAAGGCTGGCAACAGATCTCATGGGAAGCGCTTCCTTGTTTGGTGGAG -s simCow_chr6.simCow.chr6 340358 59 + 602619 TCAATCCACTGATAGGGGTAAGAAACTTGCAGGATCAAATGGGT------------ATATCTTACACAAAG-------------------- -s simDog_chr6.simDog.chr6 329962 29 + 593897 ACAACCCAGTGACAGTGG------------------------------------------CTTATGCTAAG-------------------- -s simHuman_chr6.simHuman.chr6 351758 74 + 601863 CCAATCCACTGACAGGGGTGGATGGGTTGCAGAAGCAAACATGT------------ATACCTTATGCTAA-----TCATCGCATGGTGTAA -s simRat_chr6.simRat.chr6 359163 87 + 647215 ---ATCCACTTAGAGGTGTCGTAGAGTGGTACAAGTGACCATGAAAGGCTGGCAACAGATCTCATGGGATGCGCTTCCTTGTTTGGTGG-G - -a -s simMouse_chr6.simMouse.chr6 366826 86 + 636262 TCCATCTCAGTCCTCCAGTTCAATTAACAGAGGACTTGAATGGATAAGGGTGTGATCCAATTGCATACCATTAGTCACCAATGTGT -s Anc0.Anc0refChr2 604 7 + 17989 -------------------------------------------------------------------------------GATCAGT -s Anc1.Anc1refChr6 28259 69 + 197743 TGCATATTAAGCTTACAAACAAAC--ATGTAAAACTTAAGCAAACA---------------TGTATATCTTATGCTACCGATCAGT -s Anc2.Anc2refChr17 22174 7 + 28526 -------------------------------------------------------------------------------GATCAAT -s mr.mrrefChr5 213901 86 + 294540 TCCATCTCAGTCCTCCAGTTCAATTAATAGAGGACTTGAATGAATAAGGGTGTGATCCAATTGCATACCATTAGTCACCAATGTGT -s simCow_chr6.simCow.chr6 340417 7 + 602619 -------------------------------------------------------------------------------GATCAAT -s simDog_chr6.simDog.chr6 329991 7 + 593897 -------------------------------------------------------------------------------GATCAAT -s simHuman_chr6.simHuman.chr6 351845 69 + 601863 TGCATATTAAGCTTACAAACAAAC--ATGTAAAACTTAAGCAAACA---------------TGTATATCTTATGCTACCGATCAGT -s simRat_chr6.simRat.chr6 359250 86 + 647215 TCGATCTCAGTCCTCCAGTTCAATTAATAGAGGGGTTCAATGAATAAGAGTGTGATGAGGTTGCATAACATTAGTCACCAATGGGT - -a -s simMouse_chr6.simMouse.chr6 366912 1 + 636262 G -s Anc0.Anc0refChr2 611 1 + 17989 G -s Anc1.Anc1refChr6 28328 1 + 197743 G -s Anc2.Anc2refChr17 22181 1 + 28526 G -s mr.mrrefChr5 213987 1 + 294540 G -s simCow_chr6.simCow.chr6 340424 1 + 602619 G -s simDog_chr6.simDog.chr6 329998 1 + 593897 G -s simHuman_chr6.simHuman.chr6 351914 1 + 601863 G -s simRat_chr6.simRat.chr6 359421 1 + 647215 G - -a -s simMouse_chr6.simMouse.chr6 366913 4 + 636262 ATAG -s Anc0.Anc0refChr2 613 4 + 17989 ATGG -s Anc1.Anc1refChr6 28330 4 + 197743 ATGG -s Anc2.Anc2refChr17 22183 4 + 28526 TTGG -s mr.mrrefChr5 213988 4 + 294540 ATGG -s simCow_chr6.simCow.chr6 340426 4 + 602619 TTGA -s simDog_chr6.simDog.chr6 330000 4 + 593897 TTGG -s simHuman_chr6.simHuman.chr6 351916 4 + 601863 ATGG -s simRat_chr6.simRat.chr6 359422 4 + 647215 ATGG - -a -s simMouse_chr6.simMouse.chr6 366917 98 + 636262 AAAAAGGAGCACCTTCAGCATTAAGCTTACACCTGCACATAAACGTGGCACTGACACATAAACATGCTAAAGTTGCAAGCTAAAGTGACAAACAGACT -s Anc0.Anc0refChr2 621 60 + 17989 AACAAAGAACACCTTGCATATTAAACCT-------------------------ACAAACAAACATGTTAAACTTA-------------CAAACAGACT -s Anc1.Anc1refChr6 28338 60 + 197743 AACAAAGAACACCTTGCATATTAAACCT-------------------------ACAAACAAACATGTTAAACTTA-------------CAAACAGACT -s Anc2.Anc2refChr17 22191 60 + 28526 AACAAAGAACACCTTGCATGTTAAACCT-------------------------ACAAACAAACATGTTAAGCTTA-------------CAAACAAACT -s mr.mrrefChr5 213992 85 + 294540 AAAAAGGAACACCTTCAACATTAAGCTTACACCTGCACATAAACGTGGCACTGACACATAAACATGCTAAAGTTG-------------CAAACAGACT -s simCow_chr6.simCow.chr6 340434 60 + 602619 AGCAAAGATCATCTTGCATGGTAAACTT-------------------------ATAAACAAACATATTAACTTTG-------------CAAATAAACT -s simDog_chr6.simDog.chr6 330008 60 + 593897 AATAAAGAACACTTTGTATGTTGTACCT-------------------------ACAAGCAAACATGTTAAGCTTA-------------CCAACAAATT -s simHuman_chr6.simHuman.chr6 351924 60 + 601863 AACAAAAAACCCCTTGCATACTAAACCT-------------------------ACAAACAAACATCTTAAACTTA-------------CAAACAGACT -s simRat_chr6.simRat.chr6 359426 85 + 647215 AAAAAGGAACACCTTCAACATTAAGCTTACATGTACACATAGACATGACACCTAGGCATAAACATGCTACAGTTG-------------CAAACAGACT - -a -s simMouse_chr6.simMouse.chr6 367015 7 + 636262 GCTTGAC -s Anc0.Anc0refChr2 681 4 + 17989 GTTA--- -s Anc1.Anc1refChr6 28398 4 + 197743 GTTA--- -s Anc2.Anc2refChr17 22251 4 + 28526 GTCA--- -s mr.mrrefChr5 214077 7 + 294540 GCTAGAC -s simCow_chr6.simCow.chr6 340495 4 + 602619 GTCA--- -s simDog_chr6.simDog.chr6 330068 4 + 593897 GTCA--- -s simHuman_chr6.simHuman.chr6 351984 4 + 601863 GGTA--- -s simRat_chr6.simRat.chr6 359511 7 + 647215 GCCATAC - -a -s simMouse_chr6.simMouse.chr6 367022 11 + 636262 CGTATGGCTCA -s Anc0.Anc0refChr2 685 11 + 17989 CATATTTCTCA -s Anc1.Anc1refChr6 28402 11 + 197743 CATATTTCTCA -s Anc2.Anc2refChr17 22260 11 + 28526 CATATTTCTCA -s mr.mrrefChr5 214084 11 + 294540 CGTATGTCTCA -s simCow_chr6.simCow.chr6 340504 11 + 602619 TATATTTCTCA -s simDog_chr6.simDog.chr6 330077 11 + 593897 CATATTTCTTA -s simHuman_chr6.simHuman.chr6 351988 11 + 601863 CATATTTCCCA -s simRat_chr6.simRat.chr6 359518 11 + 647215 CTTATGTCTCA - -a -s simMouse_chr6.simMouse.chr6 367033 41 + 636262 CCCTGATTGATACATGTACCCAAGCAGAACTTTGAGGGGCC -s Anc0.Anc0refChr2 697 38 + 17989 CTTAGAGTGATA-ATGTGCCTAGGCTTAACTTTGAAGA--T -s Anc1.Anc1refChr6 28414 38 + 197743 CTTAGAGTGATA-ATGTGCCTAGGCTTAACTTTGAAGA--T -s Anc2.Anc2refChr17 22272 38 + 28526 CTTAAAGTCATA-ATGTGCATAGGCTTAACTTTAAAGA--T -s mr.mrrefChr5 214096 41 + 294540 CCCAGATTGATACATGTACCCAAGCAGAACTTTGAGGGGCC -s simCow_chr6.simCow.chr6 340516 38 + 602619 CTCAAAGTAATA-ATACACATAGGCTTAACTTTTAAGG--T -s simDog_chr6.simDog.chr6 330089 37 + 593897 CTTAAA-TCATA-ATGTGCATAGGCTTAACTTTAATGA--T -s simHuman_chr6.simHuman.chr6 352000 30 + 601863 CTAAGAGTGATA---GTGCCT------AACTTTGAAGA--T -s simRat_chr6.simRat.chr6 359530 41 + 647215 CCCAAATTGATACATGTATCCAGGCAAAACTTTGAGGGGCC - -a -s simMouse_chr6.simMouse.chr6 367074 5 + 636262 ACTGC -s Anc0.Anc0refChr2 735 5 + 17989 ACTGT -s Anc1.Anc1refChr6 28452 5 + 197743 ACTGT -s Anc2.Anc2refChr17 22313 5 + 28526 ACTGT -s mr.mrrefChr5 214137 5 + 294540 ACTGC -s simCow_chr6.simCow.chr6 340557 5 + 602619 AGTGT -s simDog_chr6.simDog.chr6 330129 5 + 593897 ACTGT -s simHuman_chr6.simHuman.chr6 352030 5 + 601863 AAAGT -s simRat_chr6.simRat.chr6 359571 5 + 647215 ACTGC - -a -s simMouse_chr6.simMouse.chr6 367079 49 + 636262 CCTACAACGTCATTGTATACAATGGAAAAAAAGAATAGTTAGCTGGCAA -s Anc0.Anc0refChr2 740 47 + 17989 TTTACAACATCACTGTGTACAACAAAACAAAAGAATAGTTCGCTGG--A -s Anc1.Anc1refChr6 28457 48 + 197743 TTTACAACATCACTGTGTACAACAAAACAAAAGAATAGTTCGCTGG-CA -s Anc2.Anc2refChr17 22320 47 + 28526 TTTACAACATTGCTATGCACAACAAAACAAAAGAATAGTTCGCTGG--A -s mr.mrrefChr5 214142 49 + 294540 CCTACAACGTCATTGTATACAATGGAAAAAAAGAATAGTTAGCTGGCCA -s simCow_chr6.simCow.chr6 340562 40 + 602619 -------CATTGCTATGCATAACAGAACAAAAGAATAGTTCGCTTG--C -s simDog_chr6.simDog.chr6 330142 47 + 593897 TTTACAACACTGCTATGCACAACAAAACAAAAGAATAGTTCGCTGG--A -s simHuman_chr6.simHuman.chr6 352035 37 + 601863 TTTACAACATCAATGTGTACAACATTACAAGAGAA------------CA -s simRat_chr6.simRat.chr6 359576 45 + 647215 CCTACAACGTC----TATACAATGGAAAAAAAGAATAGTTCGCTGGCCA - -a -s simMouse_chr6.simMouse.chr6 367128 10 + 636262 GAAATCCTAG -s Anc0.Anc0refChr2 787 10 + 17989 GAAATCCCAG -s Anc1.Anc1refChr6 28505 10 + 197743 GAAATCCCAG -s Anc2.Anc2refChr17 22367 10 + 28526 GAGCTCCCAG -s mr.mrrefChr5 214191 10 + 294540 GAAATCCTAG -s simCow_chr6.simCow.chr6 340602 10 + 602619 GAGCGCCCAG -s simDog_chr6.simDog.chr6 330192 10 + 593897 GAGCTTCCAG -s simHuman_chr6.simHuman.chr6 352072 10 + 601863 GCAATCCCAG -s simRat_chr6.simRat.chr6 359621 10 + 647215 GAAATCCTAG - -a -s simMouse_chr6.simMouse.chr6 367138 97 + 636262 CTCTGAAAGATGAAGAAAGTGGCCTTCCCGGTATGATGGGAGACACTGTTATACTTTTAAAGCAATTAGCCAATGCAATGCAAATCCCAAATCCCAC -s Anc0.Anc0refChr2 797 90 + 17989 CCTAGAAAGACCAAAAAAGTGGACTTCGTGGAATGGTGGACAACACTGTTATACTTTTACAGGAATAAGTCAATTTAATGCAAA-------TCCCTC -s Anc1.Anc1refChr6 28515 90 + 197743 CCTAGAAAGACCAAAAAAGTGGACTTCGTGGAATGGTGGACAACACTGTTATACTTTTACAGGAATAAGTCAATTTAATGCAAA-------TCCCTC -s Anc2.Anc2refChr17 22377 90 + 28526 CCTAGAAAGACCAAAAAGGTGGACTTTGTGTAATGGTGGACAACACTGTTATACTTTTACAAGAATAAGCCAATGTAATGTAAA-------TCCCTC -s mr.mrrefChr5 214201 97 + 294540 CTCTGAAAGATGAAGAAAGTGGCCTTCCTGGTATGATGGAAGACACTGTTATACTTTTAAAGCAATTAGTCAATTCAATGCAAATCCCAAATCCCAC -s simCow_chr6.simCow.chr6 340612 90 + 602619 CATAGAAAGACCAAAAGGTTGGACTTTGTGTAATGGTGGACAACACCATTATACTTTTACAAGCATGAGCCAGTGTGATGTAAA-------ACCCTC -s simDog_chr6.simDog.chr6 330208 90 + 593897 CCTAGAAAAACCAAAAAGGAGGTCTTTGTGTAATGGTGGACAGCACTGTTATACTTCTCCAAGAATAAGCCAATGTAAAGTAAA-------TTCCTC -s simHuman_chr6.simHuman.chr6 352082 90 + 601863 CCTAGCAAGACCAAAAAAGTGCACTTCATGGAATGGTGGACTACACTGTTACACTTTTACAGGAATAAGTCAATTTAATGCAAA-------TCCCTC -s simRat_chr6.simRat.chr6 359631 94 + 647215 CT---AAAAGTGAAGAAAGTGGCCTTCTTGGTATGATGGAGGACACTATTATACTTTTAGAACAATTAGTCAATTCAATGCAAATCCCAAATCCCAC - -a -s simMouse_chr6.simMouse.chr6 367235 10 + 636262 AGAGGCTACA -s Anc0.Anc0refChr2 888 10 + 17989 AAAGGCTATA -s Anc1.Anc1refChr6 28606 10 + 197743 AAAGGCTATA -s Anc2.Anc2refChr17 22468 10 + 28526 AAGGGCTATA -s mr.mrrefChr5 214299 10 + 294540 AAAGGCTACA -s simCow_chr6.simCow.chr6 340703 10 + 602619 AAGGGCTATG -s simDog_chr6.simDog.chr6 330299 10 + 593897 AAGGGCTATA -s simHuman_chr6.simHuman.chr6 352173 10 + 601863 AAAGGCCAAG -s simRat_chr6.simRat.chr6 359726 10 + 647215 AAAGGCTACA - -a -s simMouse_chr6.simMouse.chr6 367245 2 + 636262 AT -s Anc0.Anc0refChr2 898 2 + 17989 CT -s Anc1.Anc1refChr6 28616 2 + 197743 CT -s Anc2.Anc2refChr17 22479 2 + 28526 CT -s mr.mrrefChr5 214309 2 + 294540 AT -s simCow_chr6.simCow.chr6 340714 2 + 602619 AT -s simDog_chr6.simDog.chr6 330310 2 + 593897 CT -s simHuman_chr6.simHuman.chr6 352183 2 + 601863 CT -s simRat_chr6.simRat.chr6 359736 2 + 647215 AT - -a -s simMouse_chr6.simMouse.chr6 367247 5 + 636262 CTTTA -s Anc0.Anc0refChr2 900 5 + 17989 TTTAA -s Anc1.Anc1refChr6 28618 5 + 197743 TTTAA -s Anc2.Anc2refChr17 22481 5 + 28526 TTTAA -s mr.mrrefChr5 214311 5 + 294540 CTTTA -s simCow_chr6.simCow.chr6 340720 5 + 602619 TTTAA -s simDog_chr6.simDog.chr6 330312 5 + 593897 TTTAA -s simHuman_chr6.simHuman.chr6 352185 5 + 601863 TTTAA -s simRat_chr6.simRat.chr6 359738 5 + 647215 CTTTA - -a -s simMouse_chr6.simMouse.chr6 367252 3 + 636262 CTC -s Anc0.Anc0refChr2 905 3 + 17989 CCT -s Anc1.Anc1refChr6 28623 3 + 197743 CCT -s Anc2.Anc2refChr17 22526 3 + 28526 CCT -s mr.mrrefChr5 214316 3 + 294540 CTC -s simDog_chr6.simDog.chr6 330366 3 + 593897 CCT -s simHuman_chr6.simHuman.chr6 352190 3 + 601863 CCT -s simRat_chr6.simRat.chr6 359743 3 + 647215 CTC - -a -s simMouse_chr6.simMouse.chr6 367255 9 + 636262 AGGCCACAA -s Anc0.Anc0refChr2 908 9 + 17989 AGGCAGCAA -s Anc1.Anc1refChr6 28626 9 + 197743 AGGCAGCAA -s Anc2.Anc2refChr17 22529 9 + 28526 AGGCAGCAG -s mr.mrrefChr5 214319 9 + 294540 AGGCCACAA -s simDog_chr6.simDog.chr6 330369 9 + 593897 AGGCAGCAG -s simHuman_chr6.simHuman.chr6 352193 9 + 601863 AGACACCAA -s simRat_chr6.simRat.chr6 359752 9 + 647215 AGGCCACAA - -a -s simMouse_chr6.simMouse.chr6 367264 52 + 636262 GGAAGACTAATATGACTGTTCTTTGATATTAATTTCTGCAATCTGGAGGGAG -s Anc0.Anc0refChr2 917 52 + 17989 AAAAGACTAATATGTCTGTTCTCTTAGATGAAGCCCTCCTATCTGGAGGAGA -s Anc1.Anc1refChr6 28635 52 + 197743 AAAAGACTAATATGTCTGTTCTCTTAGATGAAGCCCTCCTATCTGGAGGAGA -s Anc2.Anc2refChr17 22538 52 + 28526 AAAAGACTAACATTTCAGTTGTCTTAGCTGCAGTCCTCCTATCTGGAGGAGA -s mr.mrrefChr5 214328 52 + 294540 GGAAGACTAATATGACTGTTCTTTGATATGAATCTCTCCAATCTGGAGGAAG -s simCow_chr6.simCow.chr6 340765 25 + 602619 -------------------------AACTAC--TCCTCCTACCTGGAGAAGA -s simDog_chr6.simDog.chr6 330389 51 + 593897 AAAAGACTAACATTTCAGTTGTCTTAGCTGCAGTCCTCCCATCT-GAGGAAA -s simHuman_chr6.simHuman.chr6 352202 52 + 601863 CAAAGACGGATATGTCTGTTCTCTTAGATGAAGCCCTCCTATCTTGAGGAGA -s simRat_chr6.simRat.chr6 359761 52 + 647215 GGAAGGCTAATATGGCTGTTCTTTGATATGAAACTCTCCAATCTGGAGGAAG - -a -s simMouse_chr6.simMouse.chr6 367316 24 + 636262 GCGCATGCTCTAGAACTGCATTGG -s Anc0.Anc0refChr2 969 20 + 17989 GC----TCTCCAGAAATGCATTGG -s Anc1.Anc1refChr6 28687 20 + 197743 GC----TCTCCAGAAATGCATTGG -s Anc2.Anc2refChr17 22595 20 + 28526 GT----TCCCCAGAAACACATTGG -s mr.mrrefChr5 214380 24 + 294540 GCGCATGCTCTAGAACTGCATTGG -s simCow_chr6.simCow.chr6 340795 20 + 602619 AA----GACCCACAAGAAAATTGG -s simDog_chr6.simDog.chr6 330445 20 + 593897 GT----TCCCCAGAAACACATTGG -s simHuman_chr6.simHuman.chr6 352254 20 + 601863 GC----TCTCCAGAAATGCATTGG -s simRat_chr6.simRat.chr6 359813 24 + 647215 GCATATGCCCTAGAACTGCATTGG - -a -s simMouse_chr6.simMouse.chr6 367340 39 + 636262 CAAACTGGGTATAAAAAAGAAAGGTTTTCAGGTGTTACA -s Anc0.Anc0refChr2 989 39 + 17989 CAAGTTGGGTCCAAAGAAGAGAAGACTTCTAGTGTTAGG -s Anc1.Anc1refChr6 28707 39 + 197743 CAAGTTGGGTCCAAAGAAGAGAAGACTTCTAGTGTTAGG -s Anc2.Anc2refChr17 22615 39 + 28526 CCAGTTGGGTCCAAAGAAGAGAAGACTTCTAGTATTAGG -s mr.mrrefChr5 214404 39 + 294540 CAAACTGGGTATAAAAAAGAGAGGATTTCAAGTGTTACA -s simCow_chr6.simCow.chr6 340815 39 + 602619 TCAGTTGGGTGCTTTGAAGAGAAAACTTCTGGTATTAGG -s simDog_chr6.simDog.chr6 330465 39 + 593897 CCAGTTCAGTCCAAAGAAGAGAAGACGTCTAGTATTAGT -s simHuman_chr6.simHuman.chr6 352275 39 + 601863 CAGGTTGGGTCGAAAGAAGAGAAGACTTCTAGTGTTGGG -s simRat_chr6.simRat.chr6 359837 37 + 647215 CAAACTGG--ACAAAAAAGGGACGATTTCAAGTGTTACA - -a -s simMouse_chr6.simMouse.chr6 367379 10 + 636262 GCAGTAGGTA -s Anc0.Anc0refChr2 1029 10 + 17989 GCAGTAGGTA -s Anc1.Anc1refChr6 28747 10 + 197743 GCAGTAGGTA -s Anc2.Anc2refChr17 22655 10 + 28526 GCAGTAGGTA -s mr.mrrefChr5 214444 10 + 294540 GCAGTAGGTA -s simCow_chr6.simCow.chr6 340855 8 + 602619 GCAGTAGG-- -s simDog_chr6.simDog.chr6 330505 10 + 593897 ACAGTAGGTA -s simHuman_chr6.simHuman.chr6 352315 10 + 601863 GCAGTGGACA -s simRat_chr6.simRat.chr6 359875 10 + 647215 GCAGTAGGTA - -a -s simMouse_chr6.simMouse.chr6 367389 31 + 636262 ACACCCCTCTATTTACCTTCTCTATTGATTT -s Anc0.Anc0refChr2 1039 24 + 17989 ACCCCTCTTTATTTAGTATCTTTA------- -s Anc1.Anc1refChr6 28757 24 + 197743 ACCCCTCTTTATTTAGTATCTTTA------- -s Anc2.Anc2refChr17 22704 24 + 28526 ATCCCTTTTTATTTAGTATCTTCA------- -s mr.mrrefChr5 214454 29 + 294540 ACACCCCTTTATTTACCTTCTCTA--GATTT -s simCow_chr6.simCow.chr6 340902 24 + 602619 TGCCCTTTTTATGTAGAAGCTTCA------- -s simDog_chr6.simDog.chr6 330566 24 + 593897 ATCCATTATTGTTTAGTATCATCA------- -s simHuman_chr6.simHuman.chr6 352325 24 + 601863 ACTCCTCTTGATTAAGTATCTTTA------- -s simRat_chr6.simRat.chr6 359885 25 + 647215 ACACCCCTTTATTTACCTTC------AATTT - -a -s simMouse_chr6.simMouse.chr6 367420 11 + 636262 TTTCAGCAAAT -s Anc0.Anc0refChr2 1063 11 + 17989 CTTCAGGTACT -s Anc1.Anc1refChr6 28781 11 + 197743 CTTCAGGTACT -s Anc2.Anc2refChr17 22735 11 + 28526 CCTCAGGTACT -s mr.mrrefChr5 214483 11 + 294540 TTTCAGCTAAT -s simCow_chr6.simCow.chr6 340933 11 + 602619 CCTCAACTACT -s simDog_chr6.simDog.chr6 330597 11 + 593897 CCTCAGGTACT -s simHuman_chr6.simHuman.chr6 352349 11 + 601863 CTTCAGGTCCT -s simRat_chr6.simRat.chr6 359910 11 + 647215 TTTCAGCTAAT - -a -s simMouse_chr6.simMouse.chr6 367431 47 + 636262 CTGACTATCTGGTGGTAGCCATCTTTTGCAGAGGTTGGCTCATGCCA -s Anc0.Anc0refChr2 1076 37 + 17989 CTGAACATCTGGTGATAGTTT-CTTATT-----GTTGGCTCAT---- -s Anc1.Anc1refChr6 28794 46 + 197743 CTGAACATCTGGTGATAGTTT-CTTATTTTGAGGTTGGCTCATGCCA -s Anc2.Anc2refChr17 22748 37 + 28526 CTGAACACCTGGTGATAGTTT-CTTATT-----ATTGGCTCAT---- -s mr.mrrefChr5 214494 47 + 294540 CTGACTATCTGGTGGTAGCCATCTTTTGCAGAGGTTGGCTCATGCCA -s simCow_chr6.simCow.chr6 340946 30 + 602619 CTGAATACTCAGCAATAATTT-TTTA------------CTCAT---- -s simDog_chr6.simDog.chr6 330610 37 + 593897 CTGAACACCTGGTGATAGACT-CTTATT-----ATTGGCTCAC---- -s simHuman_chr6.simHuman.chr6 352362 46 + 601863 CTGAACATCTGGTGATAGTTT-CTTATTTTGAGGCTGGTTGATGCCA -s simRat_chr6.simRat.chr6 359921 26 + 647215 CTGACTACCTGGTGGCAGCAATTTTT--------------------- - -a -s simMouse_chr6.simMouse.chr6 367478 33 + 636262 GGACTCATTAAATAGAGATTGAAGCAGGGTACA -s Anc0.Anc0refChr2 1113 27 + 17989 ----CCA--AAATAGAGAATGGTGTGGTGTACA -s Anc1.Anc1refChr6 28840 33 + 197743 TAGCCCATCAAATAGAGAATGGTGTGGTGTACA -s Anc2.Anc2refChr17 22785 27 + 28526 ----CCA--AAATAGGGAACGGTCTGGTGTACA -s mr.mrrefChr5 214541 33 + 294540 GGACTCATTAAATAGAGATTGAAGCAGGGTACA -s simCow_chr6.simCow.chr6 340976 27 + 602619 ----CTA--ATATAGGGAACGGCATTCTGTACA -s simDog_chr6.simDog.chr6 330650 21 + 593897 ----CCA--AAATAGG------TCTGGAGTTCA -s simHuman_chr6.simHuman.chr6 352411 33 + 601863 TAGCCCATCAAATAGAGTATGGTGTGGTGTACA - -a -s simMouse_chr6.simMouse.chr6 367511 90 + 636262 GGAAATGACTATTCCACCAATTATAACAGGACTTCCACATCTGGGCAGATTAGGAAAGTGTGATTTGCCTGACTAATGGTCTGTATGAGA -s Anc0.Anc0refChr2 1149 90 + 17989 AGAGACAATTAGACTACCAACCATAGCAAGATGCCTGCATGTTGGAAGATTAGAAAAGGGTGATGTGTGTCAATAATGACCTGCATGAAT -s Anc1.Anc1refChr6 28882 90 + 197743 AGAGACAATTAGACTACCAACCATAGCAAGATGCCTGCATGTTGGAAGATTAGAAAAGGGTGATGTGTGTCAATAATGACCTGCATGAAT -s Anc2.Anc2refChr17 22821 90 + 28526 AGAGACAATAAGACTACCAACCTTAGCAAGGTGCCTGCATGTTGGAAGATTAGAAAAGGATGATGTGTGTCAATTATGACCTGCATGAAT -s mr.mrrefChr5 214574 90 + 294540 GGAAATGACTATTCCACCAATTATAACAGGACTTCCACATCTGGGCAGATTAGGAAAGTGTGATTTGCCTGACTAATGGTCTGTATGAGA -s simCow_chr6.simCow.chr6 341012 77 + 602619 AGAGACAA--AGACTACCAACCTTAGCAGGGTGCCCGAATGTTGGAGGA-------AGGCTGAGATGTGTCATTTATGAC-TATATG--- -s simDog_chr6.simDog.chr6 330680 90 + 593897 AGAGACAATAGGATTACTAACCTTAACAAGGTGCCTGCATGTTGGAAAATTAGAAACGGATGATGTGTGTCAATTATGCCCTGCATGAAT -s simHuman_chr6.simHuman.chr6 352453 90 + 601863 AGAGACAATTAGACTATCAACCATAGCAAAATGCCTGCACATTGGAAGATTAGAGAAGGGTGACGTGTGTTAATAATGACGTGCACGAAT -s simRat_chr6.simRat.chr6 359947 32 + 647215 ----------------------------------------------------------TGTGATTTGCCTGATTAATGGTCAGTATGCGA - -a -s simMouse_chr6.simMouse.chr6 367601 38 + 636262 CAGTCTGAGTTGTGGCTACTGTGTTCCTGGACCCAGCA -s Anc0.Anc0refChr2 1239 28 + 17989 CA----------TGGCTGTAGTGGTTCTGGATCTGGCA -s Anc1.Anc1refChr6 28972 28 + 197743 CA----------TGGCTGTAGTGGTTCTGGATCTGGCA -s Anc2.Anc2refChr17 22911 28 + 28526 CA----------TCGTTGTAGTGGTTCTGGATCTGGCA -s mr.mrrefChr5 214664 38 + 294540 CAGTCTGAGTTGTGGCTACAGTGTTTCTGGACCCAGCA -s simCow_chr6.simCow.chr6 341089 24 + 602619 --------------GTTGTAGCGGTTCTGGATTTGGCA -s simDog_chr6.simDog.chr6 330773 28 + 593897 CA----------TCATAATAGTAGTTCTGGATCTGTCA -s simHuman_chr6.simHuman.chr6 352543 28 + 601863 CA----------TGGCTGTAGTGGCTCTAGATCTTGCA -s simRat_chr6.simRat.chr6 359979 38 + 647215 CAGTCTGCGTTGTGGCTACAGTGTTTCTGGACCCAGCA - -a -s simMouse_chr6.simMouse.chr6 367639 8 + 636262 TCACAGAG -s Anc0.Anc0refChr2 1267 8 + 17989 TTGCAGAG -s Anc1.Anc1refChr6 29000 8 + 197743 TTGCAGAG -s Anc2.Anc2refChr17 22939 8 + 28526 TTACAGAG -s mr.mrrefChr5 214702 8 + 294540 TCGCAGAG -s simCow_chr6.simCow.chr6 341117 8 + 602619 TTACAGAG -s simHuman_chr6.simHuman.chr6 352571 8 + 601863 TTGCAGAG -s simRat_chr6.simRat.chr6 360017 8 + 647215 TCGCAGAG - -a -s simMouse_chr6.simMouse.chr6 367647 18 + 636262 CGCCCCCAGACCTAGGAT -s Anc0.Anc0refChr2 1275 11 + 17989 C-------TCCCTAGGAT -s Anc1.Anc1refChr6 29008 11 + 197743 C-------TCCCTAGGAT -s Anc2.Anc2refChr17 22947 11 + 28526 C-------TCTCTAGGAT -s mr.mrrefChr5 214710 18 + 294540 CACCCCCAGACCTAGGAT -s simCow_chr6.simCow.chr6 341125 11 + 602619 C-------TCTCTAGGAT -s simHuman_chr6.simHuman.chr6 352580 11 + 601863 A-------TGCCTAGGAT -s simRat_chr6.simRat.chr6 360025 18 + 647215 CACCCCCACACCTATGAT - -a -s simMouse_chr6.simMouse.chr6 367665 1 + 636262 T -s Anc0.Anc0refChr2 1286 1 + 17989 T -s Anc1.Anc1refChr6 29019 1 + 197743 T -s Anc2.Anc2refChr17 22958 1 + 28526 T -s mr.mrrefChr5 214728 1 + 294540 T -s simCow_chr6.simCow.chr6 341136 1 + 602619 T -s simHuman_chr6.simHuman.chr6 352656 1 + 601863 C -s simRat_chr6.simRat.chr6 360043 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 367666 3 + 636262 CTG -s Anc0.Anc0refChr2 1288 3 + 17989 CTA -s Anc1.Anc1refChr6 29021 3 + 197743 CTA -s Anc2.Anc2refChr17 22960 3 + 28526 CTA -s mr.mrrefChr5 214730 3 + 294540 CTG -s simCow_chr6.simCow.chr6 341138 3 + 602619 CTA -s simHuman_chr6.simHuman.chr6 352658 3 + 601863 CCA -s simRat_chr6.simRat.chr6 360045 3 + 647215 CTG - -a -s simMouse_chr6.simMouse.chr6 367669 15 + 636262 ATAGGAGCATGTAAT -s Anc0.Anc0refChr2 1298 13 + 17989 ATATGAGCATGT-A- -s Anc1.Anc1refChr6 29031 14 + 197743 ATATGAGCATGT-AT -s Anc2.Anc2refChr17 22970 13 + 28526 AAAGGGGCACCT-A- -s mr.mrrefChr5 214733 14 + 294540 ATATGAGCATGT-AT -s simCow_chr6.simCow.chr6 341149 13 + 602619 AAAGGGGCACCT-A- -s simHuman_chr6.simHuman.chr6 352668 14 + 601863 ATATCAGCATGC-AT -s simRat_chr6.simRat.chr6 360048 14 + 647215 ACATGAGCATGT-AT - -a -s simMouse_chr6.simMouse.chr6 367684 6 + 636262 GAGTAG -s Anc1.Anc1refChr6 29045 6 + 197743 AAGAGG -s mr.mrrefChr5 214747 6 + 294540 GAGAAG -s simHuman_chr6.simHuman.chr6 352689 6 + 601863 AAGAGG -s simRat_chr6.simRat.chr6 360062 6 + 647215 GAGAAG - -a -s simMouse_chr6.simMouse.chr6 367690 22 + 636262 AAATCCTATTACATAGGAACAC -s Anc0.Anc0refChr2 1311 12 + 17989 ----------ACATAGAAACAC -s Anc1.Anc1refChr6 29051 22 + 197743 CAGTGGTATCACATAGAAACAC -s Anc2.Anc2refChr17 22983 12 + 28526 ----------ACGTAGAAACAT -s mr.mrrefChr5 214753 22 + 294540 AAATGCTATTACATAGAAACAC -s simCow_chr6.simCow.chr6 341162 12 + 602619 ----------ACGTAGAAACAT -s simHuman_chr6.simHuman.chr6 352702 22 + 601863 CAGTGGTATCATATAGAAACAC -s simRat_chr6.simRat.chr6 360068 22 + 647215 GAATGCTATTACATAGAATCAC - -a -s simMouse_chr6.simMouse.chr6 367712 23 + 636262 AAAGATGGGACTAATGAGAGACA -s Anc0.Anc0refChr2 1328 23 + 17989 ACAAATCACTCTAAAGTGAGACA -s Anc1.Anc1refChr6 29078 23 + 197743 ACAAATCACTCTAAAGTGAGACA -s Anc2.Anc2refChr17 23000 23 + 28526 ACAAAACACTTTAAACTGAGACT -s mr.mrrefChr5 214775 23 + 294540 AAAGATGGGACTAATGAGAGACA -s simCow_chr6.simCow.chr6 341179 23 + 602619 ACAATGCACTTGAAACTGAGATG -s simDog_chr6.simDog.chr6 330801 21 + 593897 --AAAACACTTTAAACTGAGACT -s simHuman_chr6.simHuman.chr6 352729 23 + 601863 ACAAATCATTCTAAAGTAAGACA -s simRat_chr6.simRat.chr6 360090 20 + 647215 AAAGATGGGACTAATGAGA---C - -a -s simMouse_chr6.simMouse.chr6 367735 12 + 636262 AAAACAAACTCC -s Anc0.Anc0refChr2 1360 12 + 17989 AAAACAAACTTC -s Anc1.Anc1refChr6 29110 12 + 197743 AAAACAAACTTC -s Anc2.Anc2refChr17 23032 12 + 28526 AAAACAAACTTC -s mr.mrrefChr5 214798 12 + 294540 AAAACAAACTTC -s simCow_chr6.simCow.chr6 341216 12 + 602619 AAACAAAACTTC -s simDog_chr6.simDog.chr6 330831 12 + 593897 AAAACAAACTAC -s simHuman_chr6.simHuman.chr6 352761 12 + 601863 AAAACAAAGTTC -s simRat_chr6.simRat.chr6 360110 12 + 647215 AAAACAAACTTC - -a -s simMouse_chr6.simMouse.chr6 367747 41 + 636262 ACTAGGAACCAGGAGGAGAAGTCATGGAATAAACACTGAAA -s Anc0.Anc0refChr2 1382 41 + 17989 GCTGGGAACCTGGGAGACAAGCTATAGAATAAACACTTAAA -s Anc1.Anc1refChr6 29132 41 + 197743 GCTGGGAACCTGGGAGACAAGCTATAGAATAAACACTTAAA -s Anc2.Anc2refChr17 23054 41 + 28526 GCTGGGAACCTGGGAGACAAGCTATAGAATAAACACTTAAA -s mr.mrrefChr5 214820 41 + 294540 ACTGGGAACCAGGAGGACAAGTTATAGAATAAACACTGAAA -s simCow_chr6.simCow.chr6 341238 41 + 602619 GCTGGGAACCTGTGAGACAAGCTATGGAATAAACACTTAAA -s simDog_chr6.simDog.chr6 330853 41 + 593897 GCTGGGTACCTGGGAGACAAGCTACAGTATAAACACTTAAA -s simHuman_chr6.simHuman.chr6 352783 41 + 601863 TCGGGGAACCTGGGAGACAAGCTATAGACTAAACACTTAAA -s simRat_chr6.simRat.chr6 360132 41 + 647215 ACTGGGAACCAGGAGGCCAAGTTATACAATAAACACTGAAG - -a -s simMouse_chr6.simMouse.chr6 367788 3 + 636262 ATG -s Anc0.Anc0refChr2 1426 3 + 17989 ATG -s Anc1.Anc1refChr6 29176 3 + 197743 ATG -s Anc2.Anc2refChr17 23098 3 + 28526 CTG -s mr.mrrefChr5 214864 3 + 294540 ATG -s simCow_chr6.simCow.chr6 341282 3 + 602619 CTG -s simDog_chr6.simDog.chr6 330897 3 + 593897 CTG -s simHuman_chr6.simHuman.chr6 352827 3 + 601863 ATG -s simRat_chr6.simRat.chr6 360176 3 + 647215 ATG - -a -s simMouse_chr6.simMouse.chr6 367791 9 + 636262 AACTCATTA -s Anc0.Anc0refChr2 1430 9 + 17989 AACTTATTG -s Anc1.Anc1refChr6 29180 9 + 197743 AACTTATTG -s Anc2.Anc2refChr17 23102 9 + 28526 AACCTATTG -s mr.mrrefChr5 214867 9 + 294540 AACTCATTG -s simCow_chr6.simCow.chr6 341286 9 + 602619 ATCCTTCTG -s simDog_chr6.simDog.chr6 330901 9 + 593897 AACCTATTG -s simHuman_chr6.simHuman.chr6 352831 9 + 601863 AACTTATTG -s simRat_chr6.simRat.chr6 360179 9 + 647215 AACTCAATG - -a -s simMouse_chr6.simMouse.chr6 367800 7 + 636262 GCTGGGA -s Anc0.Anc0refChr2 1440 7 + 17989 GCAACGA -s Anc1.Anc1refChr6 29190 7 + 197743 GCAACGA -s Anc2.Anc2refChr17 23112 7 + 28526 ACATCGA -s mr.mrrefChr5 214876 7 + 294540 GCTAGGA -s simCow_chr6.simCow.chr6 341296 7 + 602619 ACAGCAA -s simDog_chr6.simDog.chr6 330911 7 + 593897 AGGTCGA -s simHuman_chr6.simHuman.chr6 352841 7 + 601863 GCAACGA -s simRat_chr6.simRat.chr6 360188 7 + 647215 GCTAGGC - -a -s simMouse_chr6.simMouse.chr6 367807 20 + 636262 GGGACAGGAACAGTAACTTG -s Anc0.Anc0refChr2 1447 19 + 17989 GAGACA-GAACAGTAACTTG -s Anc1.Anc1refChr6 29197 19 + 197743 GAGACA-GAACAGTAACTTG -s Anc2.Anc2refChr17 23119 19 + 28526 GAGACC-GAACAGTAACCTG -s mr.mrrefChr5 214883 20 + 294540 GGGACAGGAACAGTAACTTG -s simCow_chr6.simCow.chr6 341304 19 + 602619 GAGACC-AAACATTAACCTG -s simDog_chr6.simDog.chr6 330918 18 + 593897 AGGTC--GAACAGCAACCTG -s simHuman_chr6.simHuman.chr6 352848 19 + 601863 GAGACA-GAACAATAACTTG -s simRat_chr6.simRat.chr6 360195 20 + 647215 GGGACAGGAACGTTAACTTG - -a -s simMouse_chr6.simMouse.chr6 367827 2 + 636262 AG -s Anc0.Anc0refChr2 1496 2 + 17989 AG -s Anc1.Anc1refChr6 29246 2 + 197743 AG -s Anc2.Anc2refChr17 23168 2 + 28526 AT -s mr.mrrefChr5 214903 2 + 294540 AG -s simCow_chr6.simCow.chr6 341355 2 + 602619 AC -s simDog_chr6.simDog.chr6 330966 2 + 593897 AT -s simHuman_chr6.simHuman.chr6 352897 2 + 601863 GG -s simRat_chr6.simRat.chr6 360215 2 + 647215 CG - -a -s simMouse_chr6.simMouse.chr6 367829 23 + 636262 CCTTCATGGAAAACACGCTTCAA -s Anc0.Anc0refChr2 1498 23 + 17989 CCCTCATTGAAAACACCCTATAT -s Anc1.Anc1refChr6 29248 23 + 197743 CCCTCATTGAAAACACCCTATAT -s Anc2.Anc2refChr17 23170 23 + 28526 CCCTCATTGAAACCACCCTATAT -s mr.mrrefChr5 214905 23 + 294540 CCTTCATGGAAAACACGCTTTAA -s simCow_chr6.simCow.chr6 341357 23 + 602619 TCCTCATTGAAACCACCCTACAC -s simDog_chr6.simDog.chr6 330971 23 + 593897 CCCTCATTGAAACCACCCTATAT -s simHuman_chr6.simHuman.chr6 352899 23 + 601863 CCCTCATTGAAAACACCCTATAT -s simRat_chr6.simRat.chr6 360217 23 + 647215 CCTTCATGAAAAACACACTTTAA - -a -s simMouse_chr6.simMouse.chr6 367852 4 + 636262 GTAC -s Anc0.Anc0refChr2 1521 4 + 17989 GTAT -s Anc1.Anc1refChr6 29271 4 + 197743 GTAT -s Anc2.Anc2refChr17 23193 4 + 28526 GTAT -s mr.mrrefChr5 214928 4 + 294540 GTAC -s simCow_chr6.simCow.chr6 341507 4 + 602619 GTAT -s simDog_chr6.simDog.chr6 330994 4 + 593897 GTAT -s simHuman_chr6.simHuman.chr6 352922 4 + 601863 GTAT -s simRat_chr6.simRat.chr6 360240 4 + 647215 GTAC - -a -s simMouse_chr6.simMouse.chr6 367856 44 + 636262 AACAGGAGTATAGACAGAATGGGGACGCATAACTGGTGGCCCAG -s Anc0.Anc0refChr2 1525 44 + 17989 ATCAGGAGTATAGTAGGAATGGGGATACTTACCTGCTAGTACAT -s Anc1.Anc1refChr6 29275 44 + 197743 ATCAGGAGTATAGTAGGAATGGGGATACTTACCTGCTAGTACAT -s Anc2.Anc2refChr17 23197 44 + 28526 ATCAGGAGTAGATTAGGAATTGGAATACTTACCTGCTATTACAT -s mr.mrrefChr5 214932 44 + 294540 AACAGGAGTATAGTAGGAATGGGGACACTTAACTGCTAGCCCAG -s simCow_chr6.simCow.chr6 341511 43 + 602619 ATCATGAGTTGATTAGGATTTGGAACACTTCCCTGCTA-TACAT -s simDog_chr6.simDog.chr6 330999 44 + 593897 ATCAGGGGTAGATTAGGAATTGGAATACTTAACTTCTATCACAT -s simHuman_chr6.simHuman.chr6 352926 44 + 601863 ATCAGGAGTATAGTAGTAATGGGGATACTTACCCGCTAGTACAT -s simRat_chr6.simRat.chr6 360244 44 + 647215 AACAAGAATATAGTAGGAATGGGGACACTTAACTGCTATCTCAG - -a -s simMouse_chr6.simMouse.chr6 367900 16 + 636262 TGACCCCTTGATACTA -s Anc0.Anc0refChr2 1570 16 + 17989 TGACCTTTTGATACTA -s Anc1.Anc1refChr6 29320 16 + 197743 TGACCTTTTGATACTA -s Anc2.Anc2refChr17 23242 16 + 28526 TGATCTTTTGATACTG -s mr.mrrefChr5 214977 16 + 294540 TGACCCCTTGATACTA -s simCow_chr6.simCow.chr6 341555 16 + 602619 CTATCTCTTGGTACTG -s simDog_chr6.simDog.chr6 331044 16 + 593897 TGATGTTTTGATACTG -s simHuman_chr6.simHuman.chr6 352971 16 + 601863 TGACCGTATTAAACTA -s simRat_chr6.simRat.chr6 360289 16 + 647215 TGACCCCTCAATACCA - -a -s simMouse_chr6.simMouse.chr6 367916 11 + 636262 ACTATGCTATG -s Anc0.Anc0refChr2 1588 11 + 17989 ACTCAACTCTG -s Anc1.Anc1refChr6 29338 11 + 197743 ACTCAACTCTG -s Anc2.Anc2refChr17 23260 11 + 28526 TCTCAACTCTG -s mr.mrrefChr5 214993 11 + 294540 ACTATGCTATG -s simCow_chr6.simCow.chr6 341571 10 + 602619 -ATCTATGCTA -s simDog_chr6.simDog.chr6 331062 11 + 593897 TCTTAACTCTG -s simHuman_chr6.simHuman.chr6 352989 11 + 601863 ACTCAACTCTG -s simRat_chr6.simRat.chr6 360305 11 + 647215 ATTATGTTATG - -a -s simMouse_chr6.simMouse.chr6 367927 2 + 636262 GC -s Anc0.Anc0refChr2 1599 2 + 17989 TG -s Anc1.Anc1refChr6 29349 2 + 197743 TG -s Anc2.Anc2refChr17 23271 2 + 28526 TG -s mr.mrrefChr5 215004 2 + 294540 GC -s simCow_chr6.simCow.chr6 341581 2 + 602619 TG -s simDog_chr6.simDog.chr6 331078 2 + 593897 TG -s simHuman_chr6.simHuman.chr6 353000 2 + 601863 TG -s simRat_chr6.simRat.chr6 360316 2 + 647215 GA - -a -s simMouse_chr6.simMouse.chr6 367929 23 + 636262 TAAACCTCAGGTGATCATTATTA -s Anc0.Anc0refChr2 1601 23 + 17989 TACAGCTAAGGCAGCCGTTATAA -s Anc1.Anc1refChr6 29351 23 + 197743 TACAGCTAAGGCAGCCGTTATAA -s Anc2.Anc2refChr17 23277 23 + 28526 TACAGCAAAGGCAGCCGTTATAA -s mr.mrrefChr5 215006 23 + 294540 TAAACCTCAGGTAACCATTATTA -s simCow_chr6.simCow.chr6 341587 23 + 602619 TGCCGCAAGGGCAGCAGTTATAT -s simDog_chr6.simDog.chr6 331084 23 + 593897 TACAGTAAAGGCAGCCGTTATAA -s simHuman_chr6.simHuman.chr6 353002 23 + 601863 TACAGCTAAGGCAGCTTTTATAA -s simRat_chr6.simRat.chr6 360318 22 + 647215 TAAACCT-GGGTAACCATTATTA - -a -s simMouse_chr6.simMouse.chr6 367952 11 + 636262 TCTAGGGCATC -s Anc0.Anc0refChr2 1625 11 + 17989 TCTAGGTCATC -s Anc1.Anc1refChr6 29375 11 + 197743 TCTAGGTCATC -s Anc2.Anc2refChr17 23301 11 + 28526 TCTAGATCATC -s mr.mrrefChr5 215029 11 + 294540 TCTAGGTCATC -s simCow_chr6.simCow.chr6 341611 11 + 602619 TCTAGATCATC -s simDog_chr6.simDog.chr6 331108 11 + 593897 TCTAGATAATA -s simHuman_chr6.simHuman.chr6 353026 11 + 601863 TCTAGGTCACC -s simRat_chr6.simRat.chr6 360340 11 + 647215 TCTAGGTCATC - -a -s simMouse_chr6.simMouse.chr6 367963 34 + 636262 AAGAGTCATGCTTATACCAACTACTCTGTAAGGC -s Anc0.Anc0refChr2 1650 34 + 17989 AAGATTCATGCATCAATCAACTACTCTCAAAGAC -s Anc1.Anc1refChr6 29401 34 + 197743 AAGATTCATGCATCAATCAACTACTCTCAAAGAC -s Anc2.Anc2refChr17 23326 34 + 28526 AAGATCCATGCATCAATCAACCACACTCAAAGAA -s mr.mrrefChr5 215055 34 + 294540 AAGAGTCATGCTTATACCAACTACTCTGTAAGGC -s simCow_chr6.simCow.chr6 341636 26 + 602619 AAGATCCATGCATGAATCAACCACCT-------- -s simDog_chr6.simDog.chr6 331133 34 + 593897 AAGATCTATGCATCAATTAACCACACTCAAAGAA -s simHuman_chr6.simHuman.chr6 353052 34 + 601863 AGAATTCAAGCATCAAGCAACTACTCTAAAAGAC -s simRat_chr6.simRat.chr6 360366 34 + 647215 AAGAGTCATGCTTATATCAACCACTCAGTAAGGC - -a -s simMouse_chr6.simMouse.chr6 367997 11 + 636262 ACCCTGGATAT -s Anc0.Anc0refChr2 1688 11 + 17989 ACTCTGGACAT -s Anc1.Anc1refChr6 29439 11 + 197743 ACTCTGGACAT -s Anc2.Anc2refChr17 23364 11 + 28526 AATCTGAGCAT -s mr.mrrefChr5 215089 11 + 294540 ACCCTGGATAT -s simCow_chr6.simCow.chr6 341664 11 + 602619 AATCTGAGCAT -s simDog_chr6.simDog.chr6 331171 11 + 593897 GATCTGAGCGT -s simHuman_chr6.simHuman.chr6 353091 11 + 601863 ACTCTGGACAT -s simRat_chr6.simRat.chr6 360400 11 + 647215 TCCCCCAATAT - -a -s simMouse_chr6.simMouse.chr6 368008 37 + 636262 TATGTGCCTAGTCATCCAGCCAGACAGTTGGATGGGA -s Anc0.Anc0refChr2 1700 33 + 17989 TAAGTGGCTATTTATCCAAACATACAGCAGGA----G -s Anc1.Anc1refChr6 29451 33 + 197743 TAAGTGGCTATTTATCCAAACATACAGCAGGA----G -s Anc2.Anc2refChr17 23376 33 + 28526 TAAGGCGCTATTTATCCAAACATACAGCAGGA----G -s mr.mrrefChr5 215100 33 + 294540 TATGTGCCTAGTCATCCAACCAGACAGTTGGA----G -s simCow_chr6.simCow.chr6 341676 33 + 602619 CCAGCAGCTATCTATCCCAACATACAGTGGGA----T -s simDog_chr6.simDog.chr6 331183 33 + 593897 TAAGGCCCTAATCATCCATACATGCTGCAGGT----G -s simHuman_chr6.simHuman.chr6 353103 33 + 601863 TAAGTGGCCATTTATCCAAACTTACAGCAGGA----G -s simRat_chr6.simRat.chr6 360411 33 + 647215 TATTTGACTAGTGATCCAACCAGACAGTGGGA----G - -a -s simMouse_chr6.simMouse.chr6 368045 41 + 636262 GATACTTTGATTGTATAAACCCTTTCCTGAACTAGACAAAT -s Anc0.Anc0refChr2 1784 40 + 17989 AGAATTACCGCTGTATATACTC-TTCTTGAATCAGATAAAT -s Anc1.Anc1refChr6 29535 40 + 197743 AGAATTACCGCTGTATATACTC-TTCTTGAATCAGATAAAT -s Anc2.Anc2refChr17 23460 40 + 28526 AGAATTACCTCTGTATATACTC-TTCTTGAATCAGATAAAT -s mr.mrrefChr5 215133 40 + 294540 AATACTTTGGTTGTATAAACTC-TTCCTGAATTAGACAAAT -s simCow_chr6.simCow.chr6 341789 40 + 602619 AGTACTACCTCTGTATATACTC-TTCTTGAGCCAAATAATT -s simDog_chr6.simDog.chr6 331253 37 + 593897 AGAATTACCTCTGTATATCCTC-TTC---AATCAGATAAAT -s simHuman_chr6.simHuman.chr6 353205 40 + 601863 AGAATTAACGCTGTATATACTC-TTCTTAAATCAGATAAAT -s simRat_chr6.simRat.chr6 360444 40 + 647215 AATACTCTGGTTGTATAAATTC-TTCCTGCATTAGACGAAT - -a -s simMouse_chr6.simMouse.chr6 368086 24 + 636262 GAAGGCTTTGAGCTGAGGGTCATT -s Anc0.Anc0refChr2 1824 24 + 17989 GAAGGGGTTGAGTTGATAGTCATC -s Anc1.Anc1refChr6 29575 24 + 197743 GAAGGGGTTGAGTTGATAGTCATC -s Anc2.Anc2refChr17 23500 24 + 28526 GAAGGGGTTGAGTTGATATTCATC -s mr.mrrefChr5 215173 24 + 294540 GAAGGCTTTGAGCTGAGGGTCATT -s simCow_chr6.simCow.chr6 341829 23 + 602619 GATTGGGTTGGGTTGATACTC-TC -s simDog_chr6.simDog.chr6 331290 24 + 593897 GAAGGGGTTGAGTTGATATTCATG -s simHuman_chr6.simHuman.chr6 353245 24 + 601863 GAAGGGGTTAAGTTAATAGCCATC -s simRat_chr6.simRat.chr6 360500 24 + 647215 GAGGGTTTTGAGCTGAGGGTCATT - -a -s simMouse_chr6.simMouse.chr6 368110 73 + 636262 TAACACCTTATTAGTACCAGGTACAGTGCCTGAGACCCACTAGTCTTTCTATGTCCGACATCTCATATAATAG -s Anc0.Anc0refChr2 1858 65 + 17989 T-AAATTTTCTTAATATTATGTGCAGTACCTTAGAC-------TCTTTCTGTGTCTGACATACCTTATGAGAT -s Anc1.Anc1refChr6 29609 73 + 197743 TAAAATTTTCTTAATATTATGTGCAGTACCTTAGACTCACAAATCTTTCTGTGTCTGACATACCTTATGAGAT -s Anc2.Anc2refChr17 23534 65 + 28526 T-AAATTTTCTTAATATTATCAGCAGTACCTTAGAC-------TCTTTCGGTGTCTGACATACCTTATGAGAT -s mr.mrrefChr5 215197 73 + 294540 TAACATCTTATTAGTACTAGGTGCAGTGCCTGAGACCCACTAGTCTTTCTATGTCTGACATCCCATATAATAG -s simCow_chr6.simCow.chr6 341862 61 + 602619 T-AAATTGTCTTGGTAT----GGCAATACTTTAAAC-------CCCTTCGGTGTCTGACATACCTTATGAGAT -s simDog_chr6.simDog.chr6 331324 64 + 593897 T-AAATTTTCTTAAAATTATCAGCAGTACCTTAGGC-------TCTTTTGGTGTCTGACATAC-TTATGACAT -s simHuman_chr6.simHuman.chr6 353279 73 + 601863 TGAAATTTTCTTATTATTATGTGCATCACCTTAGAGTCACAAATCTTTCTGCACCTAACATACCTTATGAGAT -s simRat_chr6.simRat.chr6 360524 73 + 647215 TAAGATCCTATTAGTACTGGGTGCAGTGCCTGATACCAACTGGTCCTTCCATGTATGATGTTCCATATAATAG - -a -s simMouse_chr6.simMouse.chr6 368183 19 + 636262 AAGAAGTTCTCACTAATTA -s Anc0.Anc0refChr2 1923 9 + 17989 AAGAAG----------CTT -s Anc1.Anc1refChr6 29682 19 + 197743 AAGAAGTTCTCACTTACTT -s Anc2.Anc2refChr17 23599 9 + 28526 GAGAAG----------AAT -s mr.mrrefChr5 215270 19 + 294540 AAGAAGTTCTCACTAACTA -s simCow_chr6.simCow.chr6 341923 9 + 602619 GAAAAG----------AGT -s simDog_chr6.simDog.chr6 331388 9 + 593897 GAGAAG----------AAT -s simHuman_chr6.simHuman.chr6 353355 19 + 601863 AAGAAGTTCTCACTTACTT -s simRat_chr6.simRat.chr6 360597 19 + 647215 AAGAAGTTCTCGCTAACTA - -a -s simMouse_chr6.simMouse.chr6 368202 3 + 636262 TTG -s Anc0.Anc0refChr2 1932 3 + 17989 TTG -s Anc1.Anc1refChr6 29701 3 + 197743 TTG -s Anc2.Anc2refChr17 23608 3 + 28526 CTG -s mr.mrrefChr5 215289 3 + 294540 TTG -s simCow_chr6.simCow.chr6 341933 3 + 602619 CCG -s simDog_chr6.simDog.chr6 331397 3 + 593897 CTG -s simHuman_chr6.simHuman.chr6 353374 3 + 601863 TTG -s simRat_chr6.simRat.chr6 360616 3 + 647215 TTG - -a -s simMouse_chr6.simMouse.chr6 368205 13 + 636262 TCAAAAGTTCTAG -s Anc0.Anc0refChr2 1940 13 + 17989 TCGAGAGTCCATA -s Anc1.Anc1refChr6 29709 13 + 197743 TCGAGAGTCCATA -s Anc2.Anc2refChr17 23616 13 + 28526 CCGAGAGTCTATA -s mr.mrrefChr5 215292 13 + 294540 TCAAAAGTTCTTG -s simCow_chr6.simCow.chr6 341941 8 + 602619 --GAGAGT---TG -s simDog_chr6.simDog.chr6 331405 13 + 593897 CCGGGAGCCTATA -s simHuman_chr6.simHuman.chr6 353382 13 + 601863 TCGACAGTCCCTA -s simRat_chr6.simRat.chr6 360619 13 + 647215 TCAAGAGTTCTTG - -a -s simMouse_chr6.simMouse.chr6 368218 3 + 636262 CTG -s Anc0.Anc0refChr2 1953 3 + 17989 TTG -s Anc1.Anc1refChr6 29722 3 + 197743 TTG -s Anc2.Anc2refChr17 23640 3 + 28526 TTT -s mr.mrrefChr5 215305 3 + 294540 CTG -s simCow_chr6.simCow.chr6 341960 3 + 602619 TTT -s simDog_chr6.simDog.chr6 331429 3 + 593897 TTT -s simHuman_chr6.simHuman.chr6 353395 3 + 601863 TCG -s simRat_chr6.simRat.chr6 360632 3 + 647215 CCA - -a -s simMouse_chr6.simMouse.chr6 368221 26 + 636262 ATTATTGTCAAGGCACCCATCTTAAA -s Anc0.Anc0refChr2 1957 26 + 17989 ATTAAATCAACAGTCCCTATCGTAAG -s Anc1.Anc1refChr6 29726 26 + 197743 ATTAAATCAACAGTCCCTATCGTAAG -s Anc2.Anc2refChr17 23644 26 + 28526 GTTAAATCAACAGTCCCTATCGTAAA -s mr.mrrefChr5 215308 26 + 294540 ATTATTGTCAAGGCACCCATCTTAAG -s simCow_chr6.simCow.chr6 341964 26 + 602619 GTTAAATGAACAATCCCTATAGCAAA -s simDog_chr6.simDog.chr6 331433 26 + 593897 GTTAAATCAACAGTCCATATCATAAA -s simHuman_chr6.simHuman.chr6 353399 26 + 601863 AATAAATCGACAGTCCCTATCGTAAG -s simRat_chr6.simRat.chr6 360635 26 + 647215 ATTAGTGTTAATGCGCCCATCTTGAG - -a -s simMouse_chr6.simMouse.chr6 368247 15 + 636262 GACATATCGCCCTTC -s Anc0.Anc0refChr2 1983 13 + 17989 --CTTATTGTCTTTC -s Anc1.Anc1refChr6 29752 13 + 197743 --CTTATTGTCTTTC -s Anc2.Anc2refChr17 23670 13 + 28526 --CTTATTGTCTTTC -s mr.mrrefChr5 215334 15 + 294540 GACATATCGCCCTTC -s simCow_chr6.simCow.chr6 341990 13 + 602619 --CTTATTGTCTTTC -s simDog_chr6.simDog.chr6 331459 13 + 593897 --CTCATTGTCAATC -s simHuman_chr6.simHuman.chr6 353425 13 + 601863 --CTTATTGTCTTTC -s simRat_chr6.simRat.chr6 360665 15 + 647215 GACATATCGCTCTTC - -a -s simMouse_chr6.simMouse.chr6 368262 4 + 636262 AAGA -s Anc0.Anc0refChr2 1996 4 + 17989 ATGA -s Anc1.Anc1refChr6 29765 4 + 197743 ATGA -s Anc2.Anc2refChr17 23683 4 + 28526 ATGA -s mr.mrrefChr5 215349 4 + 294540 ATGA -s simCow_chr6.simCow.chr6 342003 4 + 602619 ACAA -s simDog_chr6.simDog.chr6 331474 4 + 593897 ATGG -s simHuman_chr6.simHuman.chr6 353438 4 + 601863 ATGA -s simRat_chr6.simRat.chr6 360680 4 + 647215 ATGA - -a -s simMouse_chr6.simMouse.chr6 368266 26 + 636262 CAGGCCCTGGAATCCTTAGTCCCATA -s Anc0.Anc0refChr2 2002 25 + 17989 CAGTCCCTGGATTCC-TAAACCCATA -s Anc1.Anc1refChr6 29771 25 + 197743 CAGTCCCTGGATTCC-TAAACCCATA -s Anc2.Anc2refChr17 23689 25 + 28526 CAGTCTCTAGATTCC-TAAACCAATA -s mr.mrrefChr5 215353 25 + 294540 CAGGCCCTGGAATCC-TAGACCCATA -s simCow_chr6.simCow.chr6 342009 25 + 602619 CAGTCTCTAGATTCC-TAAACCAATA -s simHuman_chr6.simHuman.chr6 353444 25 + 601863 CAGTCCTTGGAGTCC-TAAACTCATA -s simRat_chr6.simRat.chr6 360684 25 + 647215 CAGGCTCTGGAATCC-AAGACCCATA - -a -s simMouse_chr6.simMouse.chr6 368292 53 + 636262 TCTCTGAAGGCAACAGATCTTTTCGTAGCATAAGCACAGACATGCTGAAGTAC -s Anc0.Anc0refChr2 2027 52 + 17989 TTTTTAAAGGCAACAGAT-TTTTTGTAGTATCAGCACAGACATGTTGAATTTT -s Anc1.Anc1refChr6 29796 52 + 197743 TTTTTAAAGGCAACAGAT-TTTTTGTAGTATCAGCACAGACATGTTGAATTTT -s Anc2.Anc2refChr17 23714 52 + 28526 CTTATAAAAGCAACAGAT-ATTTTTTAGTATCAACCCAGATGTGCTGAATTTT -s mr.mrrefChr5 215378 52 + 294540 TCTTTGAAGGCAACAGAT-TTTTTGTAGTATCAGCACAGACATGTTGAAGTAC -s simCow_chr6.simCow.chr6 342038 52 + 602619 CTTATAAAAGCAACAGAT-ATTTTTTAGTATCAACCCAGATGTGCTGAATTTT -s simDog_chr6.simDog.chr6 331479 6 + 593897 -----------------------------------------------AAGGTT -s simHuman_chr6.simHuman.chr6 353469 52 + 601863 TTTTTAAAGGCAACAGAG-TTTTTGTAATACCAGCACAGACATGTTGAATTTT -s simRat_chr6.simRat.chr6 360709 43 + 647215 TCTTTCAAGG----------TTTTGTAGTATCAGCAAAGATATGTTAGAGTAA - -a -s simMouse_chr6.simMouse.chr6 368345 68 + 636262 CATGACCCAGGTCTGGTAGGCATGGTTCAGGTCCCGGTGAGAGAAGAAAGATTACAATGTCTGAACAC -s Anc0.Anc0refChr2 2079 41 + 17989 CAT--------------------------GGCCAAGTTAAAAGAAG-AAAATTAAAATGCCAAAACAC -s Anc1.Anc1refChr6 29848 41 + 197743 CAT--------------------------GGCCAAGTTAAAAGAAG-AAAATTAAAATGCCAAAACAC -s Anc2.Anc2refChr17 23766 41 + 28526 CAG--------------------------GTCCAAGTTAAACAAAG-AAAATTAAAATGCCAAAATGC -s mr.mrrefChr5 215430 68 + 294540 CATGACCCAGGTCTGGTAGGCATGGTTCAGGTCAAGGTGAGAGAAGAAAGATTACAATGCCTGAACAC -s simCow_chr6.simCow.chr6 342101 41 + 602619 CAG--------------------------GTCGAAGTTGAAGAAGG-AAAATTAAAATGGCAAAATGC -s simDog_chr6.simDog.chr6 331485 41 + 593897 CAG--------------------------GTCCAAGTTAAACAAAG-GAAATTAAAATGCCAAAATGC -s simHuman_chr6.simHuman.chr6 353521 41 + 601863 TAT--------------------------GGCCAAATTAAAAGAAG-AAAATTAAAATGCCAAAACAC -s simRat_chr6.simRat.chr6 360752 68 + 647215 CATGACCCAGTTCTGGTCAGCATGATTCAGGTTAAGGTGAGAGAAGAGAGATTACAATCCCTGAACAC - -a -s simMouse_chr6.simMouse.chr6 368413 44 + 636262 CCACTTTAGTGACTTCTATAGGGTATTCTTAATGTGAATCTGAC -s Anc0.Anc0refChr2 2120 44 + 17989 CCACCTAAATGACCCCTGTGGAGCATTCTTAATGTGAATCTATC -s Anc1.Anc1refChr6 29889 44 + 197743 CCACCTAAATGACCCCTGTGGAGCATTCTTAATGTGAATCTATC -s Anc2.Anc2refChr17 23807 44 + 28526 CCACCTAAATGACCCCTGTGGAGCATTATTAATGTGAATCTATC -s mr.mrrefChr5 215498 44 + 294540 CCACTTTAGTGACTTCTATAGGGTATTCTTAATGTGAATCTGAC -s simCow_chr6.simCow.chr6 342142 44 + 602619 CCACCTGGGTGACCCCTGTGCAGCATTTGTAATGTGGATCTGTC -s simDog_chr6.simDog.chr6 331526 44 + 593897 CCGTGTAAATGACCCCTGTGGAGAATTATTAATGTGAATCTATC -s simHuman_chr6.simHuman.chr6 353562 44 + 601863 CCACCTAAATGACCCCTGTTGAGCATTCTTAATGTGAATCTATC -s simRat_chr6.simRat.chr6 360824 44 + 647215 CCAATTTAGTGCCTTCTATATGTTACTCTTAATGTGAATCTGAC - -a -s simMouse_chr6.simMouse.chr6 368457 6 + 636262 AAGCCT -s Anc0.Anc0refChr2 2164 6 + 17989 AAGCCT -s Anc1.Anc1refChr6 29933 6 + 197743 AAGCCT -s Anc2.Anc2refChr17 23851 6 + 28526 AAGCCT -s mr.mrrefChr5 215542 6 + 294540 AAGCCT -s simCow_chr6.simCow.chr6 342186 6 + 602619 AAGCAT -s simDog_chr6.simDog.chr6 331580 6 + 593897 AAGCCT -s simHuman_chr6.simHuman.chr6 353606 6 + 601863 AAGCCT -s simRat_chr6.simRat.chr6 360868 6 + 647215 AAGCCT - -a -s simMouse_chr6.simMouse.chr6 368463 86 + 636262 GCACATCAGTGTATTTGGTATTCCTGGTACCATAGTTCTAAAATCGCTATTCAACTAAGCATTATGGATGCACTGCAATTATTCTC -s Anc0.Anc0refChr2 2171 71 + 17989 GCGCATGAGTGTATCCTGTATTCCTGCAGCGCCAGTTCTGAAATCAC---------------TTTGGATGCACTGCAATTATTCCC -s Anc1.Anc1refChr6 29940 71 + 197743 GCGCATGAGTGTATCCTGTATTCCTGCAGCGCCAGTTCTGAAATCAC---------------TTTGGATGCACTGCAATTATTCCC -s Anc2.Anc2refChr17 23858 71 + 28526 GCGCATGAGTATATCCTGTATTCCTGCAGAGCCAGTTCTGAAATGAC---------------TGTGGATGCACTGCAAATATTCCC -s mr.mrrefChr5 215548 71 + 294540 GCACATCAGTGTATTCTGTATTCCTGGTACCATAGTTCTAAAATCGC---------------TTTGGATGCACTGCAATTATTCTC -s simCow_chr6.simCow.chr6 342193 71 + 602619 GCACATGACTATATCCTGTACTCCTGCAGTGCCAGTACTGAGATAGC---------------TCAGGATGCACTGCAAGTATTCCC -s simDog_chr6.simDog.chr6 331587 66 + 593897 GTGCATGAG-----CCTGTATTCCTGCCGAGCCAATTCTGAAATGAC---------------TGTAGTTACATTACAAATGTTCCC -s simHuman_chr6.simHuman.chr6 353613 71 + 601863 ACGCTGGAGTGTTTCCTGTATTCCTGCAGCTCGAGTCCTGAAATCAT---------------TTCGGATGCACTGCTATTATACCC -s simRat_chr6.simRat.chr6 360874 71 + 647215 GCACATCAGTGTATTCTGTATTCCTGGGACCATAGTTCTTAACATGC---------------TTTGGATGCACTGCCATTATTCAC - -a -s simMouse_chr6.simMouse.chr6 368549 10 + 636262 AGGCATATCT -s Anc0.Anc0refChr2 2242 10 + 17989 AGGGATATTC -s Anc1.Anc1refChr6 30011 10 + 197743 AGGGATATTC -s Anc2.Anc2refChr17 23931 10 + 28526 AGGGAAATTA -s mr.mrrefChr5 215619 10 + 294540 AGGCATATCC -s simCow_chr6.simCow.chr6 342266 10 + 602619 CATTAAATTT -s simDog_chr6.simDog.chr6 331655 10 + 593897 AGGGAAATTA -s simHuman_chr6.simHuman.chr6 353684 9 + 601863 AGGTATAT-C -s simRat_chr6.simRat.chr6 360945 10 + 647215 AGGCATATCC - -a -s simMouse_chr6.simMouse.chr6 368559 6 + 636262 GTAAAT -s Anc0.Anc0refChr2 2256 6 + 17989 ATAAAT -s Anc1.Anc1refChr6 30025 6 + 197743 ATAAAT -s Anc2.Anc2refChr17 23945 6 + 28526 ATCAGT -s mr.mrrefChr5 215629 6 + 294540 GTAAAT -s simCow_chr6.simCow.chr6 342280 6 + 602619 ATCAGT -s simDog_chr6.simDog.chr6 331669 6 + 593897 ACCAGT -s simHuman_chr6.simHuman.chr6 353697 6 + 601863 ATAAAT -s simRat_chr6.simRat.chr6 360955 6 + 647215 GTAAAT - -a -s simMouse_chr6.simMouse.chr6 368565 1 + 636262 A -s Anc0.Anc0refChr2 2262 1 + 17989 A -s Anc1.Anc1refChr6 30031 1 + 197743 A -s Anc2.Anc2refChr17 23951 1 + 28526 A -s mr.mrrefChr5 215635 1 + 294540 A -s simCow_chr6.simCow.chr6 342298 1 + 602619 A -s simDog_chr6.simDog.chr6 331675 1 + 593897 A -s simHuman_chr6.simHuman.chr6 353703 1 + 601863 A -s simRat_chr6.simRat.chr6 360961 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 368566 7 + 636262 AAGTATT -s Anc0.Anc0refChr2 2263 7 + 17989 AATTATT -s Anc1.Anc1refChr6 30032 7 + 197743 AATTATT -s Anc2.Anc2refChr17 23952 7 + 28526 AATTATT -s mr.mrrefChr5 215636 7 + 294540 AAGTATT -s simCow_chr6.simCow.chr6 342299 7 + 602619 AATTTTG -s simDog_chr6.simDog.chr6 331677 7 + 593897 AATTATT -s simHuman_chr6.simHuman.chr6 353704 7 + 601863 AATTATT -s simRat_chr6.simRat.chr6 360962 7 + 647215 AAGTATT - -a -s simMouse_chr6.simMouse.chr6 368573 14 + 636262 AATCAGTGTATGTA -s Anc0.Anc0refChr2 2271 14 + 17989 AATCAGTGTCAGTA -s Anc1.Anc1refChr6 30040 14 + 197743 AATCAGTGTCAGTA -s Anc2.Anc2refChr17 23960 14 + 28526 AATCAGTGTCAAAA -s mr.mrrefChr5 215644 14 + 294540 AATCAGTGTCTGTA -s simCow_chr6.simCow.chr6 342307 14 + 602619 AATCAGCGTCAAAA -s simDog_chr6.simDog.chr6 331685 14 + 593897 AACCAGTGTGAAAA -s simHuman_chr6.simHuman.chr6 353712 14 + 601863 AATCAGTGCCAGTA -s simRat_chr6.simRat.chr6 360970 14 + 647215 AATCAGTGTCTGTT - -a -s simMouse_chr6.simMouse.chr6 368587 30 + 636262 CCTTCCTGTATTAAAAGGTATCTATTTGCT -s Anc0.Anc0refChr2 2285 30 + 17989 CTGTTCTTTGCTAACTTGTGTCTAATTGTT -s Anc1.Anc1refChr6 30054 30 + 197743 CTGTTCTTTGCTAACTTGTGTCTAATTGTT -s Anc2.Anc2refChr17 23974 30 + 28526 CTGTTCTTTGCTAGCTTGTGTCTAATTGTT -s mr.mrrefChr5 215658 30 + 294540 CTTTTCTGTATTAAAAGGTGTCTAATTGCT -s simCow_chr6.simCow.chr6 342322 29 + 602619 TTTTTCTGTACTAGCT-TCGTAAAATTGTT -s simDog_chr6.simDog.chr6 331699 30 + 593897 CTGTTCTTTGCTAGCTTGTGTCTAGTTGTT -s simHuman_chr6.simHuman.chr6 353726 29 + 601863 CTGTTAT-TGCCAATTTGGGTCCAATTGTT -s simRat_chr6.simRat.chr6 360984 30 + 647215 CTTTTCTGGATTAAAAGGTGTCTAATTGCC - -a -s simMouse_chr6.simMouse.chr6 368617 25 + 636262 GTATCCGCTCAATGCCCACTTATCC -s Anc0.Anc0refChr2 2345 25 + 17989 GCATTCGCCCAATGCTAACTTATCT -s Anc1.Anc1refChr6 30114 25 + 197743 GCATTCGCCCAATGCTAACTTATCT -s Anc2.Anc2refChr17 24035 25 + 28526 GCATTCACCCAGTGCTAACTTGTCT -s mr.mrrefChr5 215718 25 + 294540 GTATCCGCTCAATGCCCACTTATCC -s simCow_chr6.simCow.chr6 342383 25 + 602619 GCATTCTCCCTGTGCAAACTTGTCT -s simDog_chr6.simDog.chr6 331760 25 + 593897 GTGTCTACCCAGTGCTAACTTGTCT -s simHuman_chr6.simHuman.chr6 353785 25 + 601863 GCATTCGCCCGATGCTAACTTATCG -s simRat_chr6.simRat.chr6 361045 25 + 647215 GTAACTGCTCAATGTCCACTTATCC - -a -s simMouse_chr6.simMouse.chr6 368642 32 + 636262 CCCTTTTGGAAAGTAAATATTCAATCAACTCT -s Anc0.Anc0refChr2 2370 32 + 17989 CTATTTTGGAAAGTGAAAATTCAATCAACCAT -s Anc1.Anc1refChr6 30139 32 + 197743 CTATTTTGGAAAGTGAAAATTCAATCAACCAT -s Anc2.Anc2refChr17 24060 32 + 28526 CTATTTTGAAAAGTGAAAATTCAATGAACCAT -s mr.mrrefChr5 215743 32 + 294540 CCCTTTTGGAAAGGAAATATTCAATCAACTCT -s simCow_chr6.simCow.chr6 342427 32 + 602619 CTATTTAGCAAAGTGAAAATTAAATCAACCAT -s simDog_chr6.simDog.chr6 331785 32 + 593897 CCATGTTGAAAAGTGAGGATTCAATGAACCAT -s simHuman_chr6.simHuman.chr6 353810 30 + 601863 CTATTTTGGAAAATTGAAATTCA--CAACCAT -s simRat_chr6.simRat.chr6 361070 25 + 647215 AC-------AAAGGAAATATTCAATCAACTCT - -a -s simMouse_chr6.simMouse.chr6 368674 6 + 636262 TAGGAG -s Anc0.Anc0refChr2 2405 6 + 17989 TAGGAG -s Anc1.Anc1refChr6 30174 6 + 197743 TAGGAG -s Anc2.Anc2refChr17 24096 6 + 28526 TAGGAA -s mr.mrrefChr5 215775 6 + 294540 TAGGAG -s simCow_chr6.simCow.chr6 342463 6 + 602619 TAGGAA -s simDog_chr6.simDog.chr6 331821 6 + 593897 TAGGAA -s simHuman_chr6.simHuman.chr6 353843 6 + 601863 TAGGAG -s simRat_chr6.simRat.chr6 361095 6 + 647215 TAGGAG - -a -s simMouse_chr6.simMouse.chr6 368680 9 + 636262 TAATTGTCA -s Anc0.Anc0refChr2 2417 9 + 17989 TAAAAGGCA -s Anc1.Anc1refChr6 30186 9 + 197743 TAAAAGGCA -s Anc2.Anc2refChr17 24108 9 + 28526 TATAAGGCT -s mr.mrrefChr5 215781 9 + 294540 TAATTGTCA -s simCow_chr6.simCow.chr6 342475 9 + 602619 TATAAGCCT -s simDog_chr6.simDog.chr6 331833 9 + 593897 GATGAGGCT -s simHuman_chr6.simHuman.chr6 353855 9 + 601863 TAAAAAGCA -s simRat_chr6.simRat.chr6 361101 9 + 647215 TCATTGTCA - -a -s simMouse_chr6.simMouse.chr6 368689 5 + 636262 GATGG -s Anc0.Anc0refChr2 2431 5 + 17989 TATGC -s Anc1.Anc1refChr6 30200 5 + 197743 TATGC -s Anc2.Anc2refChr17 24122 5 + 28526 TTGGC -s mr.mrrefChr5 215795 5 + 294540 TATGG -s simCow_chr6.simCow.chr6 342489 5 + 602619 TTGTC -s simDog_chr6.simDog.chr6 331847 5 + 593897 TTGGC -s simHuman_chr6.simHuman.chr6 353869 5 + 601863 TATGC -s simRat_chr6.simRat.chr6 361115 5 + 647215 TATGG - -a -s simMouse_chr6.simMouse.chr6 368694 46 + 636262 TACTGGACCCCAAGCCTCTCTGATTTCATACACTGAGTCTCTTAAG -s Anc0.Anc0refChr2 2436 33 + 17989 TACAAGACCCGGAGG--CTGCATTTTCATTCATT-----------G -s Anc1.Anc1refChr6 30205 33 + 197743 TACAAGACCCGGAGG--CTGCATTTTCATTCATT-----------G -s Anc2.Anc2refChr17 24127 33 + 28526 TACAAGGCCCGGAGG--CTGCATTTTCATTCTTT-----------G -s mr.mrrefChr5 215800 44 + 294540 TACAGGACCCCAAGC--CTCTGATTTCATACACTGAGTCTCTTAAG -s simCow_chr6.simCow.chr6 342505 33 + 602619 TACAAAGCCCAGAGG--CTGCAATTTCATTCTTT-----------G -s simDog_chr6.simDog.chr6 331852 24 + 593897 ---AAG----GTAGG--CT--ATTTTCATTCTTT-----------G -s simHuman_chr6.simHuman.chr6 353874 33 + 601863 TACAAGAACCGGAGA--CTTCATTTTGATTCATT-----------G -s simRat_chr6.simRat.chr6 361120 43 + 647215 TACAGGTCCCCAAGC--CTCTGATTTTA-ACACTGAGTCTCTTTAG - -a -s simMouse_chr6.simMouse.chr6 368740 34 + 636262 CACACAGTCTTAAAGAATCTGTTGGGATAAACCA -s Anc0.Anc0refChr2 2477 34 + 17989 TGCACTGGTTGAGGGAATCTGTGAGGGTAAGTTG -s Anc1.Anc1refChr6 30246 34 + 197743 TGCACTGGTTGAGGGAATCTGTGAGGGTAAGTTG -s Anc2.Anc2refChr17 24168 34 + 28526 TGCACTGGTTGAGGGAATTTGTGAGGGTAAGTTG -s mr.mrrefChr5 215852 34 + 294540 CACACAGTCTTAAAGAATCTGTTGGGATAAACCA -s simCow_chr6.simCow.chr6 342546 34 + 602619 CACACTGGTTGAGGGAATTGGTAAGGGTAAGATG -s simDog_chr6.simDog.chr6 331884 34 + 593897 TGCAGTGGTTCAAGAAATTTATGAGGGTAAGTTG -s simHuman_chr6.simHuman.chr6 353915 34 + 601863 TGCACTGGTTGAGGGAATCTGTGAGGGTAAGTTG -s simRat_chr6.simRat.chr6 361173 32 + 647215 CACACAGTCTTAAAGAATCTGTT--GATAAACCA - -a -s simMouse_chr6.simMouse.chr6 368774 4 + 636262 GAAA -s Anc0.Anc0refChr2 2511 4 + 17989 AAAA -s Anc1.Anc1refChr6 30280 4 + 197743 AAAA -s Anc2.Anc2refChr17 24202 4 + 28526 AAAA -s mr.mrrefChr5 215886 4 + 294540 GAAA -s simCow_chr6.simCow.chr6 342580 4 + 602619 AAAA -s simDog_chr6.simDog.chr6 331921 4 + 593897 AAAA -s simHuman_chr6.simHuman.chr6 353949 4 + 601863 AAAA -s simRat_chr6.simRat.chr6 361205 4 + 647215 GAAA - -a -s simMouse_chr6.simMouse.chr6 368778 2 + 636262 AA -s Anc0.Anc0refChr2 2516 2 + 17989 AA -s Anc1.Anc1refChr6 30285 2 + 197743 AA -s Anc2.Anc2refChr17 24207 2 + 28526 AA -s mr.mrrefChr5 215891 2 + 294540 AA -s simDog_chr6.simDog.chr6 331926 2 + 593897 AA -s simHuman_chr6.simHuman.chr6 353954 2 + 601863 AC -s simRat_chr6.simRat.chr6 361210 2 + 647215 AA - -a -s simMouse_chr6.simMouse.chr6 368780 23 + 636262 AGAAATCATCAGGTTTGCCTCAA -s Anc0.Anc0refChr2 2518 6 + 17989 AGA-----------------AGA -s Anc1.Anc1refChr6 30287 6 + 197743 AGA-----------------AGA -s Anc2.Anc2refChr17 24209 6 + 28526 AGA-----------------AGC -s mr.mrrefChr5 215893 22 + 294540 AGAAATCATC-GGTTTGCCTCAA -s simCow_chr6.simCow.chr6 342584 6 + 602619 AGA-----------------AGC -s simDog_chr6.simDog.chr6 331943 6 + 593897 AGA-----------------AGC -s simHuman_chr6.simHuman.chr6 353956 6 + 601863 ACA-----------------TGA -s simRat_chr6.simRat.chr6 361212 22 + 647215 AAAAATCAGC-GGATTACCTCAA - -a -s simMouse_chr6.simMouse.chr6 368803 30 + 636262 CATCAGGTAAGCGTGGTCCCAACTGTTATT -s Anc0.Anc0refChr2 2524 13 + 17989 TATCAGG-----------------GTGATC -s Anc1.Anc1refChr6 30293 13 + 197743 TATCAGG-----------------GTGATC -s Anc2.Anc2refChr17 24215 13 + 28526 TATCATG-----------------GTGATC -s mr.mrrefChr5 215915 30 + 294540 CATCAGGTAAGCGTGGTCCCAACTGTTATT -s simCow_chr6.simCow.chr6 342592 13 + 602619 TACTATG-----------------GCGATC -s simDog_chr6.simDog.chr6 331949 13 + 593897 TATCATA-----------------GTGATC -s simHuman_chr6.simHuman.chr6 353962 13 + 601863 TATCAGG-----------------GTGATC -s simRat_chr6.simRat.chr6 361234 30 + 647215 CATCAGGTAAGAGTGATCCCTATTCTTATT - -a -s simMouse_chr6.simMouse.chr6 368833 17 + 636262 ACAGGGCATTGGCCTGC -s Anc0.Anc0refChr2 2537 17 + 17989 ACAGGGCATTGGCCTGC -s Anc1.Anc1refChr6 30306 17 + 197743 ACAGGGCATTGGCCTGC -s Anc2.Anc2refChr17 24234 17 + 28526 ACAGGGCATTGGCTTGC -s mr.mrrefChr5 215945 17 + 294540 ACAGGGCATTGGCCTGC -s simCow_chr6.simCow.chr6 342616 17 + 602619 TCAGGGCATTGGCATGC -s simDog_chr6.simDog.chr6 331968 17 + 593897 ACAGGGCATTGGTTGGA -s simHuman_chr6.simHuman.chr6 353975 17 + 601863 ACAGGCAATTGGCCTGC -s simRat_chr6.simRat.chr6 361264 17 + 647215 ACAGGGGATTGGCCTGT - -a -s simMouse_chr6.simMouse.chr6 368850 19 + 636262 GTGAATGGGTGATACATTG -s Anc0.Anc0refChr2 2564 19 + 17989 GAAAATGGATGATTCATTT -s Anc1.Anc1refChr6 30333 19 + 197743 GAAAATGGATGATTCATTT -s Anc2.Anc2refChr17 24261 19 + 28526 GAAAATGGATGATTCATTT -s mr.mrrefChr5 215962 19 + 294540 GTGAATGGGTGATACATTG -s simCow_chr6.simCow.chr6 342643 19 + 602619 GTAAATGGATGATTCATTT -s simDog_chr6.simDog.chr6 331995 4 + 593897 AAA---------------T -s simHuman_chr6.simHuman.chr6 354002 19 + 601863 GCAAATGGATGATTCATTT -s simRat_chr6.simRat.chr6 361281 19 + 647215 GTGAATGCGTAATACGTTG - -a -s simMouse_chr6.simMouse.chr6 368869 8 + 636262 ATGACACG -s Anc0.Anc0refChr2 2588 8 + 17989 ATGACAAG -s Anc1.Anc1refChr6 30357 8 + 197743 ATGACAAG -s Anc2.Anc2refChr17 24285 8 + 28526 AGGACAAG -s mr.mrrefChr5 215981 8 + 294540 ATGACACG -s simCow_chr6.simCow.chr6 342667 8 + 602619 AGGACAAG -s simDog_chr6.simDog.chr6 332004 8 + 593897 GGAACAAG -s simHuman_chr6.simHuman.chr6 354026 8 + 601863 ATGATGAG -s simRat_chr6.simRat.chr6 361300 8 + 647215 GTGACAGG - -a -s simMouse_chr6.simMouse.chr6 368877 15 + 636262 AAACTGTGATCACCC -s Anc0.Anc0refChr2 2600 15 + 17989 AAATTGTGATCACCC -s Anc1.Anc1refChr6 30369 15 + 197743 AAATTGTGATCACCC -s Anc2.Anc2refChr17 24297 15 + 28526 AAGTTGTGATCACCC -s mr.mrrefChr5 215989 15 + 294540 AAACTGTGATCACCC -s simCow_chr6.simCow.chr6 342679 15 + 602619 AAGCAGTGTTCACCC -s simDog_chr6.simDog.chr6 332016 15 + 593897 AAGTTGTGATCACCC -s simHuman_chr6.simHuman.chr6 354038 15 + 601863 GAATTGTGATCACCC -s simRat_chr6.simRat.chr6 361308 15 + 647215 AAGCTGTGATCACCC - -a -s simMouse_chr6.simMouse.chr6 368892 8 + 636262 AAATTATG -s Anc1.Anc1refChr6 30412 8 + 197743 GAATTGTG -s mr.mrrefChr5 216004 8 + 294540 AAATTATG -s simHuman_chr6.simHuman.chr6 354137 8 + 601863 GAATTGTG -s simRat_chr6.simRat.chr6 361323 8 + 647215 AAATTTTG - -a -s simMouse_chr6.simMouse.chr6 368900 68 + 636262 TCACCCTTGGCAGCCTATACAGTAGCTATGGATTTATTGACACCTATATTGCAGCTGTTCATTTATGG -s Anc0.Anc0refChr2 2643 4 + 17989 ----------------------------------------------------------------ATGG -s Anc1.Anc1refChr6 30420 68 + 197743 TCACCCTAGACAGCTTATACAGCCGCTGCTGATTTATGGAGCTCTATACAGCCACTGTTGAGTGATGG -s Anc2.Anc2refChr17 24340 4 + 28526 ----------------------------------------------------------------ATGG -s mr.mrrefChr5 216012 68 + 294540 TCACCCTTGGCAGCCTATACAGTAGCTATGGATTTATGGACACCTATATTGCAGCTGTTCATTTATGG -s simCow_chr6.simCow.chr6 342723 4 + 602619 ----------------------------------------------------------------ATGG -s simDog_chr6.simDog.chr6 332059 4 + 593897 ----------------------------------------------------------------ATGG -s simHuman_chr6.simHuman.chr6 354146 68 + 601863 TCACCCTAGACAGCTTATACAGCCGCTGCTGATTTATGGAGCTCTATACAGCCACTGTTGAGTGGTGG -s simRat_chr6.simRat.chr6 361331 59 + 647215 TCACCCTTGGTTGCCTAGACAGTAGCTATGGATTTGTGGATGCCTTTATTGCAGCTGT---------G - -a -s simMouse_chr6.simMouse.chr6 368968 29 + 636262 AGGAGCCTATCCGGCAGCCAGTGTGTTAC -s Anc0.Anc0refChr2 2653 29 + 17989 AGTAGCCCATACAGCAGCTATCATGTTAT -s Anc1.Anc1refChr6 30494 29 + 197743 AGTAGCCCATACAGCAGCTATCATGTTAT -s Anc2.Anc2refChr17 24350 29 + 28526 AGTAGCCCATACAGCAGCTATCACATTAT -s mr.mrrefChr5 216080 29 + 294540 AGGAGCCTATCCGGCAGCTATTGTGTTAC -s simCow_chr6.simCow.chr6 342733 29 + 602619 AGTAGCCCATACAGCAGTTGTCACATTAT -s simDog_chr6.simDog.chr6 332069 29 + 593897 AGTAGCTCATCCAGCAGCTATCACATTAT -s simHuman_chr6.simHuman.chr6 354220 29 + 601863 AGTAGCCCATACAGGAGCTATCATGCTAT -s simRat_chr6.simRat.chr6 361390 29 + 647215 AGGAGCTTATCCGGCAGCTATTGTGTTAC - -a -s simMouse_chr6.simMouse.chr6 368997 63 + 636262 CAATGTAACACCAGTATACATCAGATATTAAGGAGCTGTATCATGCTATTGAGGTATCACCAT -s Anc0.Anc0refChr2 2682 50 + 17989 CAATGTAACACCACTATACAGC-------------CGGTATCATACTATTGATGGAACACCAT -s Anc1.Anc1refChr6 30523 50 + 197743 CAATGTAACACCACTATACAGC-------------CGGTATCATACTATTGATGGAACACCAT -s Anc2.Anc2refChr17 24379 50 + 28526 CAACGCCACACCACTATACAGC-------------CGTTATCACACTATTGATGGAACACCAT -s mr.mrrefChr5 216109 63 + 294540 CAATGTAACACCAGTATACATCAGATATTAAGGAGCTGTATCATACTATTGAGGGATCACCAT -s simCow_chr6.simCow.chr6 342762 50 + 602619 GAAAGAGACACCATTATACAGC-------------TGTTTCCACACTAGTGACGGGACACCAT -s simDog_chr6.simDog.chr6 332098 48 + 593897 CAACACCAAGCCACTATACAGC-------------C--TATCACACTCTTGATCAAACCTCAT -s simHuman_chr6.simHuman.chr6 354249 50 + 601863 CAATGTAGCACCAATATACAGC-------------CGGTATCATAGTATTGATGGAACACCAT -s simRat_chr6.simRat.chr6 361424 63 + 647215 GAATGTAACATTTGTAGACACCAGCTAGCATGGTGCCGTATCATACCATTGAGGGATCACCAT - -a -s simMouse_chr6.simMouse.chr6 369060 6 + 636262 CTGCTA -s Anc0.Anc0refChr2 2733 6 + 17989 CTGCTA -s Anc1.Anc1refChr6 30574 6 + 197743 CTGCTA -s Anc2.Anc2refChr17 24432 6 + 28526 CCGCTA -s mr.mrrefChr5 216173 6 + 294540 CTGCTA -s simCow_chr6.simCow.chr6 342815 2 + 602619 AC---- -s simDog_chr6.simDog.chr6 332149 6 + 593897 CTGCTA -s simHuman_chr6.simHuman.chr6 354300 6 + 601863 ATGCCG -s simRat_chr6.simRat.chr6 361488 6 + 647215 CTGCTA - -a -s simMouse_chr6.simMouse.chr6 369066 2 + 636262 TT -s Anc0.Anc0refChr2 2739 2 + 17989 TT -s Anc1.Anc1refChr6 30580 2 + 197743 TT -s Anc2.Anc2refChr17 24444 2 + 28526 TG -s mr.mrrefChr5 216179 2 + 294540 TT -s simCow_chr6.simCow.chr6 342823 2 + 602619 TG -s simDog_chr6.simDog.chr6 332161 2 + 593897 TG -s simHuman_chr6.simHuman.chr6 354306 2 + 601863 CT -s simRat_chr6.simRat.chr6 361494 2 + 647215 TT - -a -s simMouse_chr6.simMouse.chr6 369068 7 + 636262 GACTACC -s Anc0.Anc0refChr2 2762 7 + 17989 AATTATC -s Anc1.Anc1refChr6 30603 7 + 197743 AATTATC -s Anc2.Anc2refChr17 24467 7 + 28526 AATTATC -s mr.mrrefChr5 216181 7 + 294540 AACTACC -s simCow_chr6.simCow.chr6 342846 7 + 602619 AATAATT -s simDog_chr6.simDog.chr6 332184 7 + 593897 AAATATC -s simHuman_chr6.simHuman.chr6 354329 7 + 601863 AATTATC -s simRat_chr6.simRat.chr6 361496 7 + 647215 AACCACC - -a -s simMouse_chr6.simMouse.chr6 369075 9 + 636262 ATTAATGAG -s Anc0.Anc0refChr2 2769 9 + 17989 ATTATAGAA -s Anc1.Anc1refChr6 30610 9 + 197743 ATTATAGAA -s Anc2.Anc2refChr17 24485 9 + 28526 ATTATAGAA -s mr.mrrefChr5 216188 9 + 294540 ATTAAAGAG -s simCow_chr6.simCow.chr6 342864 9 + 602619 ATTATGGGG -s simDog_chr6.simDog.chr6 332204 9 + 593897 ATTATAGAA -s simHuman_chr6.simHuman.chr6 354336 9 + 601863 ATTATAGAA -s simRat_chr6.simRat.chr6 361503 9 + 647215 ATTGAAGAG - -a -s simMouse_chr6.simMouse.chr6 369084 37 + 636262 AGGTCTGGTCTTCCTGCAGTGGCTGACAATATTTAAC -s Anc0.Anc0refChr2 2782 30 + 17989 AAATTCACAGCTC--TCA-TTGCTTAGAG----AAAC -s Anc1.Anc1refChr6 30623 36 + 197743 AAATTCACAGCTCCATCA-TTGCTTAGAGAATCAAAC -s Anc2.Anc2refChr17 24498 30 + 28526 AAATTCCCAGCTT--TCA-TTGACTAGAG----AAAC -s mr.mrrefChr5 216197 37 + 294540 AGGTCCAGTCTTCCTGCAGTGGCTGACAAAATTAAAC -s simCow_chr6.simCow.chr6 342877 30 + 602619 AAATGTCCATCAT--TCA-ATGGCTAATG----AACC -s simDog_chr6.simDog.chr6 332217 30 + 593897 AAATTCCCAGCTT--TCA-TTGACTAGAG----AAAC -s simHuman_chr6.simHuman.chr6 354349 36 + 601863 AAATTCAAAACTCCATCA-TTGCTTAGGTAATCAAAC -s simRat_chr6.simRat.chr6 361512 37 + 647215 ATGTCCAGTCTTCCTACAGTGGCTAACAAAATTAAAC - -a -s simMouse_chr6.simMouse.chr6 369121 9 + 636262 CTTTCAAAA -s Anc0.Anc0refChr2 2814 9 + 17989 TTTCCAAAG -s Anc1.Anc1refChr6 30661 9 + 197743 TTTCCAAAG -s Anc2.Anc2refChr17 24530 9 + 28526 TTTCCAAAG -s mr.mrrefChr5 216234 9 + 294540 CTTTCAAAA -s simCow_chr6.simCow.chr6 342909 9 + 602619 TTTCCAAAA -s simDog_chr6.simDog.chr6 332249 9 + 593897 TTTCAAAAG -s simHuman_chr6.simHuman.chr6 354388 9 + 601863 TTTCCAAAG -s simRat_chr6.simRat.chr6 361549 9 + 647215 CTTTCAAAA - -a -s simMouse_chr6.simMouse.chr6 369130 9 + 636262 TAACTCAGC -s Anc0.Anc0refChr2 2825 9 + 17989 TATCTCAGC -s Anc1.Anc1refChr6 30672 9 + 197743 TATCTCAGC -s Anc2.Anc2refChr17 24541 9 + 28526 TGTCTCAGC -s mr.mrrefChr5 216245 9 + 294540 TAACTCAGC -s simCow_chr6.simCow.chr6 342920 9 + 602619 CCTATCAGC -s simDog_chr6.simDog.chr6 332260 9 + 593897 TGTCTCAGC -s simHuman_chr6.simHuman.chr6 354399 9 + 601863 TATCTCAGC -s simRat_chr6.simRat.chr6 361560 9 + 647215 TAACTCAGC - -a -s simMouse_chr6.simMouse.chr6 369139 39 + 636262 CTGTAGCCTACAAATTGGTGTGTGTTGGATACTTGTTAT -s Anc0.Anc0refChr2 2835 27 + 17989 CTATAACCTACAA------------TTGTTATTTGTTAT -s Anc1.Anc1refChr6 30682 27 + 197743 CTATAACCTACAA------------TTGTTATTTGTTAT -s Anc2.Anc2refChr17 24551 27 + 28526 CTATAACCTACAA------------TTGTTATTTGTTAT -s mr.mrrefChr5 216254 39 + 294540 CTGTAGCCTACAAATTGGTGTGTGTTGGATACTTGTTAT -s simCow_chr6.simCow.chr6 342930 27 + 602619 CTATAACCTACAA------------TTATTCTTTGCTAT -s simDog_chr6.simDog.chr6 332270 27 + 593897 CTATAACCTACAA------------CTGTTATTTGTTGT -s simHuman_chr6.simHuman.chr6 354409 27 + 601863 CAATAACCTACAA------------TTGTTATTTGTTAT -s simRat_chr6.simRat.chr6 361569 39 + 647215 CTGTAGCCTATGAATTGGTGTGTGTTGGATCCTTGTTAT - -a -s simMouse_chr6.simMouse.chr6 369178 5 + 636262 GCCAC -s Anc0.Anc0refChr2 2872 5 + 17989 GTCAC -s Anc1.Anc1refChr6 30719 5 + 197743 GTCAC -s Anc2.Anc2refChr17 24588 5 + 28526 GTCAC -s mr.mrrefChr5 216303 5 + 294540 GCCAC -s simCow_chr6.simCow.chr6 342967 5 + 602619 CTCAC -s simDog_chr6.simDog.chr6 332307 5 + 593897 GGCAC -s simHuman_chr6.simHuman.chr6 354446 5 + 601863 GTCAC -s simRat_chr6.simRat.chr6 361618 5 + 647215 GCCAC - -a -s simMouse_chr6.simMouse.chr6 369183 10 + 636262 CCTGTGATTA -s Anc0.Anc0refChr2 2877 10 + 17989 CCTGATCTCA -s Anc1.Anc1refChr6 30724 10 + 197743 CCTGATCTCA -s Anc2.Anc2refChr17 24593 10 + 28526 CCTGATCTCA -s mr.mrrefChr5 216308 10 + 294540 CCTGTGATTA -s simCow_chr6.simCow.chr6 342972 10 + 602619 ACTAACCTGG -s simDog_chr6.simDog.chr6 332312 10 + 593897 CCTGATCTCA -s simHuman_chr6.simHuman.chr6 354451 1 + 601863 C--------- -s simRat_chr6.simRat.chr6 361628 10 + 647215 CCTGCAAATA - -a -s simMouse_chr6.simMouse.chr6 369193 67 + 636262 AGAAAGAGGCAATTGCTTGTGTCCAGTGCCTGTTCTAATCCTATTTGGCTCGGATAAATTAGTAAAA -s Anc0.Anc0refChr2 2887 59 + 17989 AATGAGGTCCAATTTAATATGTCCAGTGCCTGTTC--------TTTGGCTTGGACAAATAAACATTA -s Anc1.Anc1refChr6 30734 59 + 197743 AATGAGGTCCAATTTAATATGTCCAGTGCCTGTTC--------TTTGGCTTGGACAAATAAACATTA -s Anc2.Anc2refChr17 24610 59 + 28526 AATGAGGTCCAATTTAATATGTCCAGTGCCTGTTT--------TTTGCCGTTGACAAATAAACATTA -s mr.mrrefChr5 216318 67 + 294540 AGTGAGAGGCAATTGCATGTGTCCAGTGCCTGTTCTAATCCTATTTGGCTCGGACAAATTAGTATAA -s simCow_chr6.simCow.chr6 342989 59 + 602619 AGTGAGGCTCAATTTAATATGTCCAGTGCCTGTTT--------TTTGTGACTGACAACTAAATATTA -s simDog_chr6.simDog.chr6 332329 59 + 593897 AATGAGGTCAAATTTAATGTGTCCAGTGCCTGTCT--------TTTGCCGTTGGCAAACAAACATGA -s simHuman_chr6.simHuman.chr6 354452 57 + 601863 --TGAGGTCCAATTTAATACGTCCAGTGCCTGTTC--------TCTGGCTTGGACAAATGGACATTA -s simRat_chr6.simRat.chr6 361638 67 + 647215 AGTGAGAGGCAATTGCATGTGTCCGGTGCCTGTTCTAACCCTACTTGGCTCGGACAAATTAGTATAA - -a -s simMouse_chr6.simMouse.chr6 369260 39 + 636262 CTCATTAACTAATGGCTTTCAGCGATTTCGACATTCGTG -s Anc0.Anc0refChr2 2959 39 + 17989 ACCGTTAACTAATGGCCCTGGGCCATTTCTACATTAGCA -s Anc1.Anc1refChr6 30806 39 + 197743 ACCGTTAACTAATGGCCCTGGGCCATTTCTACATTAGCA -s Anc2.Anc2refChr17 24682 39 + 28526 ACTGTTAACTAATGACCCTGGGCCATTTATGCATTAGCA -s mr.mrrefChr5 216385 39 + 294540 ATCATTAACTAATGGCTTTGAGCGATTTCGACATTCGTA -s simCow_chr6.simCow.chr6 343061 38 + 602619 ACTGT-AACTCATGACCCTTGGCAATTTGTGCCTTGGCA -s simDog_chr6.simDog.chr6 332401 39 + 593897 ACTGTTGACTAATGACCCTGGGCCATTTATGCATTAGCA -s simHuman_chr6.simHuman.chr6 354522 39 + 601863 ACCGTTAACTAATGGCCCTGGGCTGACTCCACACTAGCA -s simRat_chr6.simRat.chr6 361705 39 + 647215 ATCATTAACTAATGGCTTTGAGTGATTTCTACATTCATA - -a -s simMouse_chr6.simMouse.chr6 369299 5 + 636262 AGCAC -s Anc0.Anc0refChr2 3024 5 + 17989 AGAAC -s Anc1.Anc1refChr6 30871 5 + 197743 AGAAC -s Anc2.Anc2refChr17 24747 5 + 28526 AGAAC -s mr.mrrefChr5 216432 5 + 294540 AGCAC -s simCow_chr6.simCow.chr6 343119 5 + 602619 AGAAC -s simDog_chr6.simDog.chr6 332466 5 + 593897 AGAAC -s simHuman_chr6.simHuman.chr6 354587 5 + 601863 AGAAT -s simRat_chr6.simRat.chr6 361752 5 + 647215 AGCAC - -a -s simMouse_chr6.simMouse.chr6 369304 21 + 636262 CGGCCTGATCTCTTCCTTCTC -s Anc0.Anc0refChr2 3029 21 + 17989 CGGCCGGATCTCTTCCTTCTC -s Anc1.Anc1refChr6 30876 21 + 197743 CGGCCGGATCTCTTCCTTCTC -s Anc2.Anc2refChr17 24752 21 + 28526 CGGCCGGGTCTCCTCCTTCTC -s mr.mrrefChr5 216437 21 + 294540 CGGCCTGATCTCTTCCTTCTC -s simCow_chr6.simCow.chr6 343124 18 + 602619 TGCTCGGGACTTCCCCTT--- -s simDog_chr6.simDog.chr6 332471 21 + 593897 CGGCAGGGTCTCCTCCTCCTC -s simHuman_chr6.simHuman.chr6 354592 21 + 601863 CGGCCGGATTTCTTCCTTCTC -s simRat_chr6.simRat.chr6 361760 21 + 647215 CGGCCTGGTCTCTTCCTGCTC - -a -s simMouse_chr6.simMouse.chr6 369325 116 + 636262 CTTGGGCGGCAATCTACAACATGCATCTGTCATGAATAACTTGTCAAAAGACCCACTGGGGCACACATTTGTAGTGCCACTTCGAGTAACTTTGAGATGAGTGAATGACTTCTTCT -s Anc0.Anc0refChr2 3051 43 + 17989 CTTGGGCTG------------------------------------------------------------------ACTACTCTGAGGAATTCTGACCTGAATGAATT-------CT -s Anc1.Anc1refChr6 30898 43 + 197743 CTTGGGCTG------------------------------------------------------------------ACTACTCTGAGGAATTCTGACCTGAATGAATT-------CT -s Anc2.Anc2refChr17 24774 43 + 28526 CTAGGGCTG------------------------------------------------------------------ACTACTCTGAGGAATCCTGACCTGAATGAATT-------CT -s mr.mrrefChr5 216458 113 + 294540 CTTGGGCGGCAATCT---ACATGCATCTGTCATGAATAACTTGTCAAAAGACCCACTGGGGCACACATTTGTAGTGCCACTCCGAGTAACTTTGAGATGAGTGAATGACTTCTTCT -s simCow_chr6.simCow.chr6 343142 21 + 602619 ----------------------------------------------------------------------------------------ATCGTGACCTGAAAGAAGT-------CT -s simDog_chr6.simDog.chr6 332493 39 + 593897 CTAGGGCTG------------------------------------------------------------------ACTACTCTGAGGAAACCTGAC----ATAAATT-------CT -s simHuman_chr6.simHuman.chr6 354614 43 + 601863 CTTGGGCTG------------------------------------------------------------------ACTACTCAGAGCAATTCTAACCTGGATGAATA-------CT -s simRat_chr6.simRat.chr6 361781 108 + 647215 CTTGGGCGGCAATCT---ACACGCATCGGTCGTGAATAACTTGTCAAAAGACTGACGGGGGCACACACTTGTAGTGACCCTCCGAGTAACT-----ATGACTGAATGACTTCTGCT - -a -s simMouse_chr6.simMouse.chr6 369441 19 + 636262 ATAGGTAGGCCTTGCGGCC -s Anc0.Anc0refChr2 3094 19 + 17989 AGGGGTGCGCCTTGGGTCC -s Anc1.Anc1refChr6 30941 19 + 197743 AGGGGTGCGCCTTGGGTCC -s Anc2.Anc2refChr17 24817 19 + 28526 AGGGGTGCGCCTTGGGTCC -s mr.mrrefChr5 216571 19 + 294540 ATAGGTAGGCCTTGCGGCC -s simCow_chr6.simCow.chr6 343163 19 + 602619 AGGGCTCCGCCTTGGGTCC -s simDog_chr6.simDog.chr6 332532 19 + 593897 AGGGGTGCGACATGGGTCC -s simHuman_chr6.simHuman.chr6 354657 19 + 601863 AGGGGTTCGCCTTGGGTCC -s simRat_chr6.simRat.chr6 361925 19 + 647215 ATAGGTCGGCCTTGTGGCC - -a -s simMouse_chr6.simMouse.chr6 369460 9 + 636262 AGGTACTTT -s Anc0.Anc0refChr2 3113 9 + 17989 AGGTACCTC -s Anc1.Anc1refChr6 30960 9 + 197743 AGGTACCTC -s Anc2.Anc2refChr17 24836 9 + 28526 AGGTACCTC -s mr.mrrefChr5 216590 9 + 294540 AGGTACTTT -s simCow_chr6.simCow.chr6 343183 9 + 602619 AGGTACCTC -s simDog_chr6.simDog.chr6 332551 9 + 593897 AGGTACCTC -s simHuman_chr6.simHuman.chr6 354676 9 + 601863 AGGTATCTC -s simRat_chr6.simRat.chr6 361944 9 + 647215 AGGTACTTA - -a -s simMouse_chr6.simMouse.chr6 369469 28 + 636262 TCCAAAAAGATCAAACCTGGGTTCAGGA -s Anc0.Anc0refChr2 3126 28 + 17989 TCGAGAGCGGTCCAACAAGGCTTCAGGA -s Anc1.Anc1refChr6 30973 28 + 197743 TCGAGAGCGGTCCAACAAGGCTTCAGGA -s Anc2.Anc2refChr17 24849 28 + 28526 TCGAGAACGGTCCGACAAGGCTTCAGGC -s mr.mrrefChr5 216599 28 + 294540 TCCAAAGCGATCAAACCTGGGTTCAGGA -s simCow_chr6.simCow.chr6 343196 28 + 602619 TCGAGAACGGTCAGACAAGGCTTCAGGC -s simDog_chr6.simDog.chr6 332564 28 + 593897 ACGAGAACGGTACGATAGTGCTTCAGGC -s simHuman_chr6.simHuman.chr6 354689 28 + 601863 TCGAGAGCGGTCCAACAAGGCTTCGGGA -s simRat_chr6.simRat.chr6 361953 28 + 647215 TCCAAAGCGATCAAACCTGGGTTCAGGA - -a -s simMouse_chr6.simMouse.chr6 369497 5 + 636262 CACCA -s Anc0.Anc0refChr2 3154 3 + 17989 CA--T -s Anc1.Anc1refChr6 31001 3 + 197743 CA--T -s Anc2.Anc2refChr17 24877 3 + 28526 CA--T -s mr.mrrefChr5 216627 5 + 294540 CACCT -s simCow_chr6.simCow.chr6 343224 3 + 602619 CA--T -s simDog_chr6.simDog.chr6 332592 2 + 593897 C---T -s simHuman_chr6.simHuman.chr6 354717 3 + 601863 CG--T -s simRat_chr6.simRat.chr6 361986 5 + 647215 CACCT - -a -s simMouse_chr6.simMouse.chr6 369502 21 + 636262 GGTCTGGCGCATTGACCTTCA -s Anc0.Anc0refChr2 3157 19 + 17989 GGCCT--GGCATTCACTTTCA -s Anc1.Anc1refChr6 31004 19 + 197743 GGCCT--GGCATTCACTTTCA -s Anc2.Anc2refChr17 24880 19 + 28526 GGCCT--GGCATTCACTTTCA -s mr.mrrefChr5 216632 21 + 294540 GGTCTGGCGCATTGACCTTCA -s simCow_chr6.simCow.chr6 343229 19 + 602619 GGCCT--GGCATTCGCTTTCA -s simDog_chr6.simDog.chr6 332594 19 + 593897 GGCCT--GGCATTCACTTTGA -s simHuman_chr6.simHuman.chr6 354720 19 + 601863 GGCCT--TACATTCACGTTCA -s simRat_chr6.simRat.chr6 361991 21 + 647215 GGTCACGCGCATTGACCTTCA - -a -s simMouse_chr6.simMouse.chr6 369523 5 + 636262 ATCTC -s Anc0.Anc0refChr2 3176 5 + 17989 CTCTC -s Anc1.Anc1refChr6 31023 5 + 197743 CTCTC -s Anc2.Anc2refChr17 24899 5 + 28526 CTCTC -s mr.mrrefChr5 216653 5 + 294540 ATCTC -s simCow_chr6.simCow.chr6 343248 5 + 602619 CACTC -s simDog_chr6.simDog.chr6 332615 5 + 593897 CTCTC -s simHuman_chr6.simHuman.chr6 354739 5 + 601863 CTCTC -s simRat_chr6.simRat.chr6 362012 5 + 647215 ATCTC - -a -s simMouse_chr6.simMouse.chr6 369528 23 + 636262 ATTGGCGATCATGCATCCTAGAG -s Anc0.Anc0refChr2 3183 18 + 17989 -----GGATTAAGCATCCACGAG -s Anc1.Anc1refChr6 31032 23 + 197743 ATTAAGGATTAAGCATCCACGAG -s Anc2.Anc2refChr17 24906 18 + 28526 -----GGATTAAGCATCCACGAG -s mr.mrrefChr5 216658 23 + 294540 ATTGGCGATCATGCATCCTCGAG -s simCow_chr6.simCow.chr6 343255 18 + 602619 -----GAATCAGGAATCCTCGAG -s simDog_chr6.simDog.chr6 332622 18 + 593897 -----GGCTTAAGCATCCACGAG -s simHuman_chr6.simHuman.chr6 354748 23 + 601863 ATTAAGGATTAAGCATCCGCGAG -s simRat_chr6.simRat.chr6 362017 23 + 647215 ATTGGCGATCATCCATCCTCGAG - -a -s simMouse_chr6.simMouse.chr6 369551 2 + 636262 GT -s Anc0.Anc0refChr2 3201 2 + 17989 GT -s Anc1.Anc1refChr6 31055 2 + 197743 GT -s Anc2.Anc2refChr17 24924 2 + 28526 CG -s mr.mrrefChr5 216681 2 + 294540 GT -s simCow_chr6.simCow.chr6 343273 2 + 602619 CG -s simDog_chr6.simDog.chr6 332640 2 + 593897 TG -s simHuman_chr6.simHuman.chr6 354773 2 + 601863 GT -s simRat_chr6.simRat.chr6 362040 2 + 647215 GT - -a -s simMouse_chr6.simMouse.chr6 369553 81 + 636262 GTCTGGGGACGTTAAGGGTCTACAATGAGCGCCACGTACCTAGGGCATATAGTGGTTCGAAAATGGTGAAAGGTGAAAAGA -s Anc0.Anc0refChr2 3203 77 + 17989 GTCTGAGAACGTTAATGATCTGCAATCAGCGCCACGTATCGTGGGCCTATAGTAGTCCGAAAACGGCTAG----GAGACGT -s Anc1.Anc1refChr6 31057 77 + 197743 GTCTGAGAACGTTAATGATCTGCAATCAGCGCCACGTATCGTGGGCCTATAGTAGTCCGAAAACGGCTAG----GAGACGT -s Anc2.Anc2refChr17 24926 77 + 28526 GGCTGAGAACGTTAACGATCTGCAATCAGCGCCACGTATCGTGGGCCTATAGTAGTCCGATAACGGCTAG----GAGACGT -s mr.mrrefChr5 216683 81 + 294540 GTCTGGGAACGTTAATGGTCTGCAATGAGCGCCACGTATCTTGGGCCTATAGTGGTCCGAAAATGGTGAAAGGTGAGAAGA -s simCow_chr6.simCow.chr6 343275 76 + 602619 GCCTGGGTACGTTAACGATCTGCATTCAGCACCATTTATAGTGGCCCTGTAGTACTCCGATCACCGCCAG----GAGCCG- -s simDog_chr6.simDog.chr6 332642 77 + 593897 GGCTGAGAACGTTACCGATCTGCAATCAGCGACACGCATCGTCGGCCTATAGTAGCCCGATAACGGCTAG----GAGACGT -s simHuman_chr6.simHuman.chr6 354777 77 + 601863 GTCTGAGAACGTTAATGATTTGCGATCAGCGCTACATATCGTGGGCCTATAGTAGTCCGGAAACGCCTAG----GAGATGG -s simRat_chr6.simRat.chr6 362042 81 + 647215 GTCTGGGAACGTTAATGGTCTGCAATGAGCGCCACGTATCTTGGGCCTATAGTGACCCAAAGATGGTGAAAAATGAGAAGA - -a -s simMouse_chr6.simMouse.chr6 369634 33 + 636262 AAAGCACCTATGACGTGTGTGCCACTTGATAAC -s Anc0.Anc0refChr2 3287 21 + 17989 CAAGCATTTATGGT------------GGACCTC -s Anc1.Anc1refChr6 31141 21 + 197743 CAAGCATTTATGGT------------GGACCTC -s Anc2.Anc2refChr17 25010 21 + 28526 TAAGCATTTATGGT------------GGATATG -s mr.mrrefChr5 216764 21 + 294540 CAAGCATTTATGGC------------TGACCAC -s simCow_chr6.simCow.chr6 343351 20 + 602619 -AAGCATTTGTGAT------------GGATATG -s simDog_chr6.simDog.chr6 332726 21 + 593897 TGAGCATTTATGGT------------GGATATG -s simHuman_chr6.simHuman.chr6 354861 21 + 601863 CAAGCATTTATGGT------------GGACCCC -s simRat_chr6.simRat.chr6 362123 21 + 647215 CAAGCATTTATGGC------------TGACCCC - -a -s simMouse_chr6.simMouse.chr6 369667 6 + 636262 CATCCT -s Anc0.Anc0refChr2 3314 6 + 17989 CTTCCC -s Anc1.Anc1refChr6 31168 6 + 197743 CTTCCC -s Anc2.Anc2refChr17 25037 6 + 28526 CTCCTC -s mr.mrrefChr5 216785 6 + 294540 CTTCCT -s simCow_chr6.simCow.chr6 343377 6 + 602619 CTCATC -s simDog_chr6.simDog.chr6 332753 6 + 593897 CTCCTC -s simHuman_chr6.simHuman.chr6 354888 6 + 601863 CTTGCC -s simRat_chr6.simRat.chr6 362144 5 + 647215 CTTCC- - -a -s simMouse_chr6.simMouse.chr6 369673 53 + 636262 GGTGTTAGGCAGTAGGTTTACAGCGGTGGACAAGGGGAGTAGTCTAATCCCAC -s Anc0.Anc0refChr2 3320 40 + 17989 AGTAGTAGCCAAAGGGGTTGCAGCT-------------TCAGTCCAATCTTAA -s Anc1.Anc1refChr6 31174 40 + 197743 AGTAGTAGCCAAAGGGGTTGCAGCT-------------TCAGTCCAATCTTAA -s Anc2.Anc2refChr17 25060 40 + 28526 AGTAGTAGCCGAAGGGGTTGCAGCT-------------TCAGTCCAATCTTAA -s mr.mrrefChr5 216791 40 + 294540 GGTGTTAGGCAGTAGGTTTACAGCG-------------GTAGTCTAATCTCAA -s simCow_chr6.simCow.chr6 343400 40 + 602619 AGGAGTAGCCGAAGGGGTTACAGCT-------------TCAGTCCAATCTTAA -s simDog_chr6.simDog.chr6 332780 23 + 593897 AGTAGTAGC-GAAGGGGCTGCAAC----------------------------- -s simHuman_chr6.simHuman.chr6 354894 40 + 601863 AGTAGTAGCCAAAGGGGTTGCAGCT-------------TCAGCACAATCTTAA -s simRat_chr6.simRat.chr6 362149 12 + 647215 -----------------------------------------GTGGAGTATCAA - -a -s simMouse_chr6.simMouse.chr6 369726 54 + 636262 ATAGTCATGGTAAGCTCGCCTTATATAGTGACGCCTCCCCCAATCACCCTCTCT -s Anc0.Anc0refChr2 3360 37 + 17989 ACG-----AGTTAAGCCGCCTCAAATGGTG-CG-G----------TCCCACTTT -s Anc1.Anc1refChr6 31214 48 + 197743 ACGGTTACAGTTAAGCCGCCTCAAATGGTGACG-GT-----GACATCCCACTTT -s Anc2.Anc2refChr17 25100 37 + 28526 ACG-----AGTTGAGTCGCTCCAATTGGTT-CG-G----------TCCTACTTC -s mr.mrrefChr5 216831 53 + 294540 ATAGTCATGGTAAACCCGCCTTATATAGTGACG-CTCCCCCAATCACCCTCTCT -s simCow_chr6.simCow.chr6 343444 37 + 602619 ACG-----AGTTGAGTCGCTCCAATTGGTT-CG-G----------TCCTACTTC -s simHuman_chr6.simHuman.chr6 354934 48 + 601863 ACGGTTACAGTCAAACCGCCTCAAATGGTGATG-GT-----GACATCCCACGTT -s simRat_chr6.simRat.chr6 362161 43 + 647215 ATAATCATGGTAAACCCGCCTTA-----------CTCCCCCAATCATCTTCCTT - -a -s simMouse_chr6.simMouse.chr6 369780 1 + 636262 A -s Anc0.Anc0refChr2 3397 1 + 17989 A -s Anc1.Anc1refChr6 31262 1 + 197743 A -s Anc2.Anc2refChr17 25137 1 + 28526 A -s mr.mrrefChr5 216884 1 + 294540 A -s simCow_chr6.simCow.chr6 343481 1 + 602619 A -s simHuman_chr6.simHuman.chr6 354982 1 + 601863 A -s simRat_chr6.simRat.chr6 362205 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 369781 46 + 636262 TACACACTTCCTTATGTAGCCCTGCTACATTAGCATCTCATGTCTG -s Anc0.Anc0refChr2 3398 6 + 17989 TA----------------------------------------TGTG -s Anc1.Anc1refChr6 31263 6 + 197743 TA----------------------------------------TGTG -s Anc2.Anc2refChr17 25138 6 + 28526 TA----------------------------------------TGTG -s mr.mrrefChr5 216885 46 + 294540 TACACACTTCCTTATGTAGCCCTGCTACATTAGCATCTCATGTATG -s simCow_chr6.simCow.chr6 343493 6 + 602619 TA----------------------------------------TGTG -s simHuman_chr6.simHuman.chr6 354983 6 + 601863 TA----------------------------------------TGTG -s simRat_chr6.simRat.chr6 362206 46 + 647215 TACACACTTTCCTTTGTAGCCCTACTACATTAGCATCGCATGTATG - -a -s simMouse_chr6.simMouse.chr6 369827 83 + 636262 TATAACCCATTGCAAGCCAAATACCTGAGCCCTAGGGCGGAAAGAGTCAGACAGGCCCATGGTTACTATATGCTAGAAGAGTA -s Anc0.Anc0refChr2 3404 31 + 17989 T------------------------------------------GACT---------CCAGAGTC-CTATATACTAGAGGAGTA -s Anc1.Anc1refChr6 31269 31 + 197743 T------------------------------------------GACT---------CCAGAGTC-CTATATACTAGAGGAGTA -s Anc2.Anc2refChr17 25144 31 + 28526 T------------------------------------------GACT---------ATAGAGTC-CTATATACTAGAGCAGTA -s mr.mrrefChr5 216931 41 + 294540 T------------------------------------------GAGTCAGACAGGCCCATGGTTACTATATGCTAGAAGAGTA -s simCow_chr6.simCow.chr6 343500 31 + 602619 T------------------------------------------GACT---------ATAGTCTC-CTGTATACTAGAGCAGTT -s simDog_chr6.simDog.chr6 332803 24 + 593897 ----------------------------------------------------------AGAGTC-CTATATTCTAGAACAGTA -s simHuman_chr6.simHuman.chr6 354989 29 + 601863 T------------------------------------------AACT---------CCAGAGTC-CTATATACTAGAGGTG-- -s simRat_chr6.simRat.chr6 362252 41 + 647215 T------------------------------------------GAGACAGACAGGCCCATGGTTACTATATTCTAGAAGCATA - -a -s simMouse_chr6.simMouse.chr6 369910 34 + 636262 ATCTATCTGGTATCACCTGTGTATTCTCATGGTT -s Anc0.Anc0refChr2 3435 34 + 17989 CTGTATCTGGCACTACCTGCATACTTTCATGGCT -s Anc1.Anc1refChr6 31300 34 + 197743 CTGTATCTGGCACTACCTGCATACTTTCATGGCT -s Anc2.Anc2refChr17 25175 34 + 28526 CTGTATCTGGCACTATGTGCATACTTTCATGACT -s mr.mrrefChr5 216972 34 + 294540 ATCTATCTGGTATCACCTGTGTATTCTCATGGCT -s simCow_chr6.simCow.chr6 343531 34 + 602619 CTGAATTTGGCACTATGTGCATATTCTCGTGACT -s simDog_chr6.simDog.chr6 332827 30 + 593897 CTGTATCTGG----ATGTGCATACTTTCAGGATT -s simHuman_chr6.simHuman.chr6 355018 31 + 601863 ---TATCTGGCTCTACCTGCATAATTTCATGGCT -s simRat_chr6.simRat.chr6 362317 34 + 647215 ATCTATCTGGTATCACCTGTGTATTCTCATGGCG - -a -s simMouse_chr6.simMouse.chr6 369944 2 + 636262 TA -s Anc0.Anc0refChr2 3472 2 + 17989 TA -s Anc1.Anc1refChr6 31337 2 + 197743 TA -s Anc2.Anc2refChr17 25212 2 + 28526 TA -s mr.mrrefChr5 217009 2 + 294540 TA -s simCow_chr6.simCow.chr6 343568 2 + 602619 TA -s simDog_chr6.simDog.chr6 332860 2 + 593897 AA -s simHuman_chr6.simHuman.chr6 355052 2 + 601863 TA -s simRat_chr6.simRat.chr6 362354 2 + 647215 TA - -a -s simMouse_chr6.simMouse.chr6 369946 52 + 636262 GACAAGAGGTTGCAAACAATGCATATCAATCTTCATAATTTCCAAAATAGAG -s Anc0.Anc0refChr2 3475 47 + 17989 TACAAGAGGTTCTGAATGATATTTATCACTTCCCAAAGT-----AGGCAGAG -s Anc1.Anc1refChr6 31340 47 + 197743 TACAAGAGGTTCTGAATGATATTTATCACTTCCCAAAGT-----AGGCAGAG -s Anc2.Anc2refChr17 25215 47 + 28526 TACAAGAGGTTCTGAATGATATTTATCACTTCCCAAAGT-----AGGCAGGG -s mr.mrrefChr5 217011 52 + 294540 GACAAGAGGTTGCAAACAATGCATATCAATTTCCAAAATTTCCAAAATAGAG -s simCow_chr6.simCow.chr6 343571 47 + 602619 TGCAAGGGGTTCCAAATGCTATTTATCAGTTCCCAAAAT-----AGGCAGGG -s simDog_chr6.simDog.chr6 332863 47 + 593897 TACAATAGGTTCTGAATGATATTTATTGCTTCCCAAAGT-----AGGCAGGG -s simHuman_chr6.simHuman.chr6 355055 47 + 601863 TACAAGAGGTTCTGAATGATATGTATCACTTCCCAAAGT-----AGGCAGAG -s simRat_chr6.simRat.chr6 362356 52 + 647215 GATGAGGGGTTGCAAACAATGCATATCAGTTTCCAAAATTTCCAAAATAGAC - -a -s simMouse_chr6.simMouse.chr6 369998 7 + 636262 ACAAATT -s Anc0.Anc0refChr2 3522 7 + 17989 ATAACTT -s Anc1.Anc1refChr6 31387 7 + 197743 ATAACTT -s Anc2.Anc2refChr17 25262 7 + 28526 ATAACTT -s mr.mrrefChr5 217063 7 + 294540 ACAAATT -s simCow_chr6.simCow.chr6 343618 7 + 602619 AGAACTT -s simDog_chr6.simDog.chr6 332911 7 + 593897 ATAAGTC -s simHuman_chr6.simHuman.chr6 355102 7 + 601863 ATAACTT -s simRat_chr6.simRat.chr6 362408 7 + 647215 ACAAATT - -a -s simMouse_chr6.simMouse.chr6 370005 3 + 636262 TGA -s Anc0.Anc0refChr2 3531 3 + 17989 CGA -s Anc1.Anc1refChr6 31396 3 + 197743 CGA -s Anc2.Anc2refChr17 25271 3 + 28526 CGA -s mr.mrrefChr5 217070 3 + 294540 TGA -s simCow_chr6.simCow.chr6 343625 3 + 602619 TGA -s simDog_chr6.simDog.chr6 332920 3 + 593897 CGA -s simHuman_chr6.simHuman.chr6 355111 3 + 601863 AGA -s simRat_chr6.simRat.chr6 362415 3 + 647215 TGA - -a -s simMouse_chr6.simMouse.chr6 370008 50 + 636262 GGACCTCATAGGATGTAGGAATAATGCAATCTTTCAAAGTGTTTGGCTGT -s Anc0.Anc0refChr2 3534 50 + 17989 GGACTTCACAGGATGTGGGATCCATGAAATCTTTCAACATGTTAAGCCGT -s Anc1.Anc1refChr6 31399 50 + 197743 GGACTTCACAGGATGTGGGATCCATGAAATCTTTCAACATGTTAAGCCGT -s Anc2.Anc2refChr17 25274 50 + 28526 GTATTTCACAGGATGTGGTTTCCATCAAGTCTTTCAACATGGTAATACTG -s mr.mrrefChr5 217073 50 + 294540 GGACTTCATAGGATGTAGGAACAATGAAATCTTTCAAAGTGTTTGGCTGT -s simCow_chr6.simCow.chr6 343628 50 + 602619 GTATCTCAAAGCATGTTCAGCACATTAACTCTTATAACATGGTAATACTG -s simDog_chr6.simDog.chr6 332932 50 + 593897 GTATTTCACGGGATGCGGTTTCCATCAAGTCTTTCAACATGGTAATACTG -s simHuman_chr6.simHuman.chr6 355114 50 + 601863 GGGCTTCACAGGATGTGGGATCCATGAGATCTTTAAACACGTTGTGCCGT -s simRat_chr6.simRat.chr6 362418 50 + 647215 GGAGTTCATAGGATGTTGTAACAATGAAATCTTTCAAAGTGTTTGACTGT - -a -s simMouse_chr6.simMouse.chr6 370058 15 + 636262 CTGTAGTTCTCCCAG -s Anc0.Anc0refChr2 3584 15 + 17989 GTGTGGAACACTCAG -s Anc1.Anc1refChr6 31449 15 + 197743 GTGTGGAACACTCAG -s Anc2.Anc2refChr17 25324 15 + 28526 GTCAGGAGCACTCAC -s mr.mrrefChr5 217123 15 + 294540 CTGTAGTACTCCCAG -s simCow_chr6.simCow.chr6 343678 15 + 602619 TTCAGGACATCTAAT -s simDog_chr6.simDog.chr6 332982 15 + 593897 GTCAAGAGCACTCCC -s simHuman_chr6.simHuman.chr6 355221 15 + 601863 atgtggaacgttcag -s simRat_chr6.simRat.chr6 362468 15 + 647215 CTGTAGTACTCCCAG - -a -s simMouse_chr6.simMouse.chr6 370073 30 + 636262 TGTTTGTGGTTCTATGTCATTTTAATTTGG -s Anc0.Anc0refChr2 3602 30 + 17989 TGTTTGCGACTCTATGTCACTGGAATTCAT -s Anc1.Anc1refChr6 31467 30 + 197743 TGTTTGCGACTCTATGTCACTGGAATTCAT -s Anc2.Anc2refChr17 25342 30 + 28526 TGTTTGCGACTCTATGTCACTGGAATTCAT -s mr.mrrefChr5 217138 30 + 294540 TGTTTGTGGCTCTATGTCATTTTAATTTGG -s simCow_chr6.simCow.chr6 343711 30 + 602619 TGTCTGCTCCTCTATGTCACTGGAATCCAT -s simDog_chr6.simDog.chr6 333000 30 + 593897 GTTTTGGGACCCCATGTCATCAGAGTTCAT -s simHuman_chr6.simHuman.chr6 355239 30 + 601863 TGTTTGCGACTCTATGTCACTGGAATTGAT -s simRat_chr6.simRat.chr6 362483 30 + 647215 TGTTTGTGGCACTACGTTATTTTAATTTGG - -a -s simMouse_chr6.simMouse.chr6 370103 34 + 636262 GAAGTTGTAGGAGATGAGACCACTAGGACCTAAT -s Anc0.Anc0refChr2 3632 34 + 17989 GTAGTTGCAGGAGATGATGCCGCTAGGATCCAAT -s Anc1.Anc1refChr6 31497 34 + 197743 GTAGTTGCAGGAGATGATGCCGCTAGGATCCAAT -s Anc2.Anc2refChr17 25373 34 + 28526 GTAGTTGCAGAAGATGATGCTGTTAGGATCCAAT -s mr.mrrefChr5 217168 34 + 294540 GAAGTTGCAGGAGATGAGACCACTAGGACCCAAT -s simCow_chr6.simCow.chr6 343742 33 + 602619 G-AGTTGCAGAAGACAATACTGTTAGGATTCAAT -s simDog_chr6.simDog.chr6 333031 34 + 593897 GTAGTTGCAGAAAATGATGCTGTTAGGGTCCAAT -s simHuman_chr6.simHuman.chr6 355269 34 + 601863 AGTCATGCAAGAGATTATGCCGCTAGGATCCAAT -s simRat_chr6.simRat.chr6 362513 34 + 647215 GAAATTGCAGGAGATGAGACTACTAGGACCCAAT - -a -s simMouse_chr6.simMouse.chr6 370137 6 + 636262 CCTAAT -s Anc0.Anc0refChr2 3667 6 + 17989 CCTAAT -s Anc1.Anc1refChr6 31532 6 + 197743 CCTAAT -s Anc2.Anc2refChr17 25408 6 + 28526 CCTTAT -s mr.mrrefChr5 217202 6 + 294540 CCTAAT -s simCow_chr6.simCow.chr6 343776 6 + 602619 CCTTCT -s simDog_chr6.simDog.chr6 333066 6 + 593897 CCTTAT -s simHuman_chr6.simHuman.chr6 355304 6 + 601863 CATAAT -s simRat_chr6.simRat.chr6 362547 6 + 647215 CCTAAT - -a -s simMouse_chr6.simMouse.chr6 370143 47 + 636262 TGGTGTCAAGATCCATGATTCAACTAATTCTATAATCCCATTGCCTT -s Anc0.Anc0refChr2 3782 47 + 17989 TTGTGTCAGGGTCCATGATTCAGCTAACTCTATAATGCCCTTGCCTT -s Anc1.Anc1refChr6 31647 47 + 197743 TTGTGTCAGGGTCCATGATTCAGCTAACTCTATAATGCCCTTGCCTT -s Anc2.Anc2refChr17 25524 47 + 28526 TTGCGTCAGGATCCATGCTTCAGCCAACCCAACAGTTACCTTGCCCT -s mr.mrrefChr5 217208 47 + 294540 TTGTGTCAAGGTCCATGATTCAGCTAATTCTATAATGCCATTGCCTT -s simDog_chr6.simDog.chr6 333252 47 + 593897 TTGCGTCAGGATCCATGCTTCAGCCAACCCAACAGTTACCTTGCCCT -s simHuman_chr6.simHuman.chr6 355421 47 + 601863 TTGTGTCAGCGTCAATGATTCAGCTAACTCTATAAGGCCCTTACCTT -s simRat_chr6.simRat.chr6 362553 47 + 647215 TTGTGTCGAGGGCCACGGTTCAGCTAATTCAATAATGCCATTGCCTT - -a -s simMouse_chr6.simMouse.chr6 370190 4 + 636262 AAAG -s Anc0.Anc0refChr2 3834 4 + 17989 AAAG -s Anc1.Anc1refChr6 31699 4 + 197743 AAAG -s Anc2.Anc2refChr17 25576 4 + 28526 AGTG -s mr.mrrefChr5 217255 4 + 294540 AAAG -s simDog_chr6.simDog.chr6 333304 4 + 593897 AGTG -s simHuman_chr6.simHuman.chr6 355473 4 + 601863 AAAG -s simRat_chr6.simRat.chr6 362600 4 + 647215 AAAC - -a -s simMouse_chr6.simMouse.chr6 370194 22 + 636262 ACATCTGTTACTTGACACAAGA -s Anc0.Anc0refChr2 3838 19 + 17989 -TATCTGTCACTAA--ACATAA -s Anc1.Anc1refChr6 31703 22 + 197743 ATATCTGTCACTAAATACATAA -s Anc2.Anc2refChr17 25580 19 + 28526 -TAACTGTGACTAA--AAATAA -s mr.mrrefChr5 217259 22 + 294540 ACATCTGTCACTTAATACAAGA -s simDog_chr6.simDog.chr6 333308 19 + 593897 -TAACTGTGACTAA--AAATAA -s simHuman_chr6.simHuman.chr6 355545 22 + 601863 ATATCTGTCGCTAAATACACAA -s simRat_chr6.simRat.chr6 362604 22 + 647215 ACATCTGTCACTTAATACAAGA - -a -s simMouse_chr6.simMouse.chr6 370216 23 + 636262 GCTTCTTATCTTAATCAGGGGAC -s Anc0.Anc0refChr2 3857 20 + 17989 GGTGC---TCTTAATCAGGGGGT -s Anc1.Anc1refChr6 31725 20 + 197743 GGTGC---TCTTAATCAGGGGGT -s Anc2.Anc2refChr17 25599 20 + 28526 GGTGC---TTTTAATCAGGGGGT -s mr.mrrefChr5 217281 23 + 294540 GCTTCTTATCTTAATCAGGGGGT -s simDog_chr6.simDog.chr6 333327 20 + 593897 GGTGC---TTTTAATCAGGGGGT -s simHuman_chr6.simHuman.chr6 355567 20 + 601863 GATGT---TCCTGATCAGGGGGT -s simRat_chr6.simRat.chr6 362630 23 + 647215 CCTTCTTATCTTAATCAGGGGGT - -a -s simMouse_chr6.simMouse.chr6 370239 39 + 636262 CATCATCTAGTCAAAGCAATCCTGCCCTTGGGGGGGTCA -s Anc0.Anc0refChr2 3878 31 + 17989 TCTTATCTGGTCAGAGTG-------CCTTGGGGGTGTT- -s Anc1.Anc1refChr6 31746 38 + 197743 TCTTATCTGGTCAGAGTGATCCTCCCCTTGGGGGTGTT- -s Anc2.Anc2refChr17 25620 31 + 28526 TCTTGCTAGGTAGGAGTG-------CCTTGGTGGTGTT- -s mr.mrrefChr5 217304 39 + 294540 CATTATCTAGTCAAAGCAATCCTGCCCTTGGGGGTGTTA -s simDog_chr6.simDog.chr6 333348 31 + 593897 TCTTGCTAGGTAGGAGTG-------CCTTGGTGGTGTT- -s simHuman_chr6.simHuman.chr6 355588 34 + 601863 TCTTATCTGGTCAGA--CATCCTCCCC--GGGGGTGTT- -s simRat_chr6.simRat.chr6 362653 39 + 647215 CATTATCTAGTTAATGTGATCCCGCCCTTGGGGGTGTTA - -a -s simMouse_chr6.simMouse.chr6 370278 10 + 636262 TGTGTGCCAA -s Anc0.Anc0refChr2 3909 2 + 17989 --------AA -s Anc1.Anc1refChr6 31784 2 + 197743 --------AA -s Anc2.Anc2refChr17 25651 2 + 28526 --------AA -s mr.mrrefChr5 217343 10 + 294540 TGTGTGCCAA -s simDog_chr6.simDog.chr6 333379 2 + 593897 --------AA -s simHuman_chr6.simHuman.chr6 355622 2 + 601863 --------AA -s simRat_chr6.simRat.chr6 362702 10 + 647215 TGTGTGCCAA - -a -s simMouse_chr6.simMouse.chr6 370288 11 + 636262 CCCAGCTGTCC -s Anc0.Anc0refChr2 3911 11 + 17989 CCCAAGTATCC -s Anc1.Anc1refChr6 31786 11 + 197743 CCCAAGTATCC -s Anc2.Anc2refChr17 25653 11 + 28526 TCCAAGTACTC -s mr.mrrefChr5 217353 11 + 294540 CCCAACTGTCC -s simDog_chr6.simDog.chr6 333381 11 + 593897 TCCAAGTACTC -s simHuman_chr6.simHuman.chr6 355624 11 + 601863 CCCAAGTATCC -s simRat_chr6.simRat.chr6 362714 11 + 647215 CCCAACGGCCC - -a -s simMouse_chr6.simMouse.chr6 370299 30 + 636262 CCGGATGATGCAGTGGCACTTGAGAGTGGG -s Anc0.Anc0refChr2 3923 29 + 17989 TCAGATGTTGTAATGGTAATTGAGGA-GGG -s Anc1.Anc1refChr6 31798 30 + 197743 TCAGATGTTGTAATGGTAATTGAGGAGGGG -s Anc2.Anc2refChr17 25665 29 + 28526 TCAGATGTTATGATAGTCATTGAGCA-GGG -s mr.mrrefChr5 217364 30 + 294540 CCAGATGATGTAGTGGCAATTGAGGGTGGG -s simDog_chr6.simDog.chr6 333393 29 + 593897 TCAGATGTTATGATAGTCATTGAGCA-GGG -s simHuman_chr6.simHuman.chr6 355636 30 + 601863 TCAGATGTTGTAATGGTAATTGAAGAGGGG -s simRat_chr6.simRat.chr6 362725 30 + 647215 CAAAATAATGTGGTGGCAATTGATGGTGGG - -a -s simMouse_chr6.simMouse.chr6 370329 13 + 636262 TTAGGCTGATGGG -s Anc0.Anc0refChr2 3970 13 + 17989 TTAGGGTGATGTG -s Anc1.Anc1refChr6 31846 13 + 197743 TTAGGGTGATGTG -s Anc2.Anc2refChr17 25712 13 + 28526 TTAGGGTGATGTG -s mr.mrrefChr5 217394 13 + 294540 TTAGGCTGATGGG -s simDog_chr6.simDog.chr6 333440 13 + 593897 TTAGGGTGATGTG -s simHuman_chr6.simHuman.chr6 355694 13 + 601863 TTAGGGTGATGAG -s simRat_chr6.simRat.chr6 362755 13 + 647215 TTAGAACAATGGG - -a -s simMouse_chr6.simMouse.chr6 370342 9 + 636262 GGTGAGTTC -s Anc0.Anc0refChr2 3989 9 + 17989 GGTGACTTC -s Anc1.Anc1refChr6 31865 9 + 197743 GGTGACTTC -s Anc2.Anc2refChr17 25731 9 + 28526 GATGACTTG -s mr.mrrefChr5 217407 9 + 294540 GGTGAGTTC -s simDog_chr6.simDog.chr6 333459 9 + 593897 GATGACTTG -s simHuman_chr6.simHuman.chr6 355713 9 + 601863 GGTAACCTC -s simRat_chr6.simRat.chr6 362768 9 + 647215 GGCTAGTTC - -a -s simMouse_chr6.simMouse.chr6 370351 66 + 636262 AAACAAGACTTCAGTAAATGCCTTTGAAAAGGCACATAGCCATTCTTTTCCCATAAAAGTGATAGA -s Anc0.Anc0refChr2 3998 64 + 17989 AAAAAAGGGTTCAGT--ATGTCCTGACAAAAGCATATATATGTTCTTCTTCCATAAAAGTGATGGA -s Anc1.Anc1refChr6 31874 66 + 197743 AAAAAAGGGTTCAGTGAATGTCCTGACAAAAGCATATATATGTTCTTCTTCCATAAAAGTGATGGA -s Anc2.Anc2refChr17 25740 64 + 28526 AAAAAAGGGTTCAGC--ATCTCCTGACAAAAGCATATATATGTTGGCCTTCCATAAAAGTGATGGA -s mr.mrrefChr5 217416 66 + 294540 AAACAAGACTTCAGTAAATGCCCTGGCAAAAGCATATAGCCATTCTTTTTCCATAAAAGTGATGGA -s simCow_chr6.simCow.chr6 343833 57 + 602619 ------GGGGTCACC--CTCCCAGGATCCATG-ATATATATGTGAGGCTTCCATAAAAGTGATGTA -s simDog_chr6.simDog.chr6 333470 64 + 593897 AAAAAAGGGTTCAGC--ATCTTCTGGCAAAACCACATATATGTTGGCCTTCCATAAAAGTGACAGA -s simHuman_chr6.simHuman.chr6 355722 64 + 601863 AAAAAGGGGTTCAATGAATGTCCTGACAGAAGCATATAT--GTACTTCTTCGGTAAAAGTGATGTG -s simRat_chr6.simRat.chr6 362777 55 + 647215 AAACAAGACTT----------CCTGGCAAAAGTATGTACCCATTCTTTTTCCATAAAAGTGCTGG- - -a -s simMouse_chr6.simMouse.chr6 370417 15 + 636262 ATAGGTAGACAACAA -s Anc0.Anc0refChr2 4062 12 + 17989 AT---CAAAGGAGAA -s Anc1.Anc1refChr6 31940 12 + 197743 AT---CAAAGGAGAA -s Anc2.Anc2refChr17 25807 12 + 28526 AT---CAAAGGAGAA -s mr.mrrefChr5 217482 12 + 294540 AT---TAGACAACAA -s simCow_chr6.simCow.chr6 343893 12 + 602619 AT---CAAAGGACAG -s simDog_chr6.simDog.chr6 333537 12 + 593897 TT---CAAAGGAGAA -s simHuman_chr6.simHuman.chr6 355786 12 + 601863 AT---CAAAGGAGAA - -a -s simMouse_chr6.simMouse.chr6 370432 59 + 636262 GACTTATATACCAATCAAGCCAGCACAGCACAGCTCACTTGAAATTGTCAATCTGACAG -s Anc0.Anc0refChr2 4074 59 + 17989 GACCTATGTCACCACCAAGCCAGCACAATGCAGCTCACTTGACATTGTAAATCTTACAA -s Anc1.Anc1refChr6 31952 59 + 197743 GACCTATGTCACCACCAAGCCAGCACAATGCAGCTCACTTGACATTGTAAATCTTACAA -s Anc2.Anc2refChr17 25819 59 + 28526 GACCTATGTCACCACCAAGCCAGCACAATGCAGCTCACTTAACATTGTAAATCCTAAAA -s mr.mrrefChr5 217494 59 + 294540 GACTTATATACCAATCAAGCCAGCACAGCACAGCTCACTTGAAATTGTCAATCTGACAG -s simCow_chr6.simCow.chr6 343905 59 + 602619 GACCTATGTCAGCACCAAGCAAGCACAGTGCAGCTCACTTAACATTGGAAATGCCAAAG -s simDog_chr6.simDog.chr6 333551 59 + 593897 GCCTTATATCACCACTGAGCCGGCACAACACAGCCCACTTAACATTGTAAATCCTGAAA -s simHuman_chr6.simHuman.chr6 355798 59 + 601863 GACCAGTGCCACCACCAAGCCAGCATGATGGAGCTCACTTGACATTGTAAATCTTACAA - -a -s simMouse_chr6.simMouse.chr6 370491 47 + 636262 ACAGTTCAACAGTATACTAAACTCATGTCAAAACTATTCAGCATTGA -s Anc0.Anc0refChr2 4133 47 + 17989 CCAGTTCCACAGTGAATCAAACTCATGTCAAGACTATTCAGAATTCA -s Anc1.Anc1refChr6 32011 47 + 197743 CCAGTTCCACAGTGAATCAAACTCATGTCAAGACTATTCAGAATTCA -s Anc2.Anc2refChr17 25878 47 + 28526 CTATTCCCACAGTGAATCAAACTCATGTGAAGACTATTCGGAATTCA -s mr.mrrefChr5 217553 47 + 294540 ACAGTTCAACAGTATACTAAACTCATGTCAAAACTATTCAGCATTGA -s simCow_chr6.simCow.chr6 343964 33 + 602619 ATA--CCCATGGCAAATCAAACTCATGTGAAGA------------CA -s simDog_chr6.simDog.chr6 333628 46 + 593897 CTCTTCCCACAGTGAAT-AAACTCATGTGAATACTATTCGGAATTCA -s simHuman_chr6.simHuman.chr6 355857 47 + 601863 CCAGTTCCACAGTGAATCAAACTCATGCCCAGACTGGTCAGAATTCA - -a -s simMouse_chr6.simMouse.chr6 370538 6 + 636262 CCAACC -s Anc0.Anc0refChr2 4185 6 + 17989 CCAAGA -s Anc1.Anc1refChr6 32063 6 + 197743 CCAAGA -s Anc2.Anc2refChr17 25930 6 + 28526 CCTAGA -s mr.mrrefChr5 217600 6 + 294540 CCAACC -s simCow_chr6.simCow.chr6 344002 6 + 602619 CCTAGA -s simDog_chr6.simDog.chr6 333679 6 + 593897 CCTAGA -s simHuman_chr6.simHuman.chr6 355909 6 + 601863 CCAAAA - -a -s simMouse_chr6.simMouse.chr6 370544 6 + 636262 CTGCCG -s Anc0.Anc0refChr2 4191 6 + 17989 ATGAAT -s Anc1.Anc1refChr6 32069 6 + 197743 ATGAAT -s Anc2.Anc2refChr17 25943 6 + 28526 ATGAAT -s mr.mrrefChr5 217606 6 + 294540 CTGCCG -s simCow_chr6.simCow.chr6 344017 6 + 602619 ATGAAT -s simDog_chr6.simDog.chr6 333692 6 + 593897 ATGAAT -s simHuman_chr6.simHuman.chr6 355915 6 + 601863 ATGGGT - -a -s simMouse_chr6.simMouse.chr6 370550 36 + 636262 GCATTAAAGGATCTAGATGAGCTCAGTTCCATGTCA -s Anc0.Anc0refChr2 4197 23 + 17989 TCATT---GGATCACTATGAT----------TGTTA -s Anc1.Anc1refChr6 32075 32 + 197743 TCATT---GGATCACTATGATTTCAATT-CATGTTA -s Anc2.Anc2refChr17 25949 23 + 28526 TCATT---GCAGCACTATGTT----------GGATG -s mr.mrrefChr5 217612 32 + 294540 GCATT---GGATCTAGATGAGCTCAGTT-CATGTCA -s simCow_chr6.simCow.chr6 344028 23 + 602619 TCATT---CCAGCACCGTGCT----------GGGTT -s simDog_chr6.simDog.chr6 333698 23 + 593897 TCATT---GCAGCACTATGTT----------GGATG -s simHuman_chr6.simHuman.chr6 355921 32 + 601863 TCATT---GGGTCACAATGATTTCAATT-CATGTTA - -a -s simMouse_chr6.simMouse.chr6 370586 49 + 636262 CGGTCTCTCAGGTTCTCAGGTGGGTATGCTTGGAGCGCTCTAGTATGTG -s Anc0.Anc0refChr2 4223 31 + 17989 C-TTCTCTCAGCTAC-----------------TACTGCGCTTATATGTG -s Anc1.Anc1refChr6 32110 32 + 197743 CGTTCTCTCAGCTAC-----------------TACTGCGCTTATATGTG -s Anc2.Anc2refChr17 25975 31 + 28526 C-TCCTCTCTGCTAC-----------------TACTGAGCCTATAAGTG -s mr.mrrefChr5 217644 32 + 294540 CGGTCTCTCAGGTTC-----------------GAGCGCTCTAGTATGTG -s simCow_chr6.simCow.chr6 344054 25 + 602619 C-TCCCATCTGTTAC-----------------TACTGTGTGTA------ -s simDog_chr6.simDog.chr6 333724 30 + 593897 C-TC-TCTCTACTAA-----------------TACTGAACCTTTAAGTG -s simHuman_chr6.simHuman.chr6 355956 32 + 601863 CGTTCTCTAAGAGAC-----------------AACTGCGCTTATATGTG - -a -s simMouse_chr6.simMouse.chr6 370635 36 + 636262 GATACAAATTATCCTGGGTTTTGCATCATGTGTGTG -s Anc0.Anc0refChr2 4254 27 + 17989 GCCACAAA--ATACTGGG-TATGCATC------GCA -s Anc1.Anc1refChr6 32142 28 + 197743 GCCACAAA--ATACTGGGTTATGCATC------GCA -s Anc2.Anc2refChr17 26006 27 + 28526 GCCACACA--TGACTCAG-CATGCATA------GCA -s mr.mrrefChr5 217676 28 + 294540 GATACAAA--ATCCTGGGTTTTGCATC------GTG -s simCow_chr6.simCow.chr6 344079 23 + 602619 ----CACA--TGACTCAG-CATGCTTG------GAA -s simDog_chr6.simDog.chr6 333755 27 + 593897 GCCACACA--TGACTCAG-CATGCACA------GCA -s simHuman_chr6.simHuman.chr6 355988 28 + 601863 GCCACAAG--ATGCTGGGTTATGTATC------GCA - -a -s simMouse_chr6.simMouse.chr6 370671 9 + 636262 TACTTTCAG -s Anc0.Anc0refChr2 4281 9 + 17989 CACTTACAG -s Anc1.Anc1refChr6 32170 9 + 197743 CACTTACAG -s Anc2.Anc2refChr17 26033 9 + 28526 CACATACAG -s mr.mrrefChr5 217704 9 + 294540 TACTTTCAG -s simCow_chr6.simCow.chr6 344102 5 + 602619 TTTAT---- -s simDog_chr6.simDog.chr6 333783 9 + 593897 CACATACAG -s simHuman_chr6.simHuman.chr6 356016 9 + 601863 CACTTAGAG - -a -s simMouse_chr6.simMouse.chr6 370680 83 + 636262 GTAGCATTGCTCCAACGTATAGCCCCAGGTTATCTTTGATGCTGCATCAGGTGTGGTATATCTAGAGGGGCTGTATTACCTAA -s Anc0.Anc0refChr2 4290 26 + 17989 GGAGCATT-----AACCGATGAACC--AGTTGT-------------------------------------------------- -s Anc1.Anc1refChr6 32179 26 + 197743 GGAGCATT-----AACCGATGAACC--AGTTGT-------------------------------------------------- -s Anc2.Anc2refChr17 26042 26 + 28526 AGTGCATT-----TGTCGTTGAACC--AGTTGT-------------------------------------------------- -s mr.mrrefChr5 217713 76 + 294540 GTAGCATT-----AACGTATAGCCC--GGTTATCTTTGATGCTGCATCAGGTGTGGTATATCTAGAGGGGCTGTATTACCTAA -s simCow_chr6.simCow.chr6 344107 18 + 602619 -GTGCATG-----TGTCGCTGA---------GT-------------------------------------------------- -s simDog_chr6.simDog.chr6 333793 26 + 593897 AGTGCACT-----TGTCTTTGAACC--AGTTGT-------------------------------------------------- -s simHuman_chr6.simHuman.chr6 356025 26 + 601863 GGAGTGTT-----AACAGATGATGC--AGTTGT-------------------------------------------------- -s simRat_chr6.simRat.chr6 362832 35 + 647215 ------------------------------------------------AGGTGTGGTAGACCTAGAGGTGCAGTATTACGTGA - -a -s simMouse_chr6.simMouse.chr6 370763 9 + 636262 AAAGGCATT -s Anc0.Anc0refChr2 4316 1 + 17989 --------T -s Anc1.Anc1refChr6 32205 1 + 197743 --------T -s Anc2.Anc2refChr17 26068 1 + 28526 --------C -s mr.mrrefChr5 217789 9 + 294540 AAAGGCATT -s simCow_chr6.simCow.chr6 344125 1 + 602619 --------C -s simDog_chr6.simDog.chr6 333819 1 + 593897 --------C -s simHuman_chr6.simHuman.chr6 356051 1 + 601863 --------T -s simRat_chr6.simRat.chr6 362871 9 + 647215 GAAGCCATC - -a -s simMouse_chr6.simMouse.chr6 370772 31 + 636262 TGTGGCTATTATCTGTAATGGCGATTATCAC -s Anc0.Anc0refChr2 4317 31 + 17989 TGTGGCTATTATTTGATAAGGCCACCATCAT -s Anc1.Anc1refChr6 32206 31 + 197743 TGTGGCTATTATTTGATAAGGCCACCATCAT -s Anc2.Anc2refChr17 26069 31 + 28526 TGTGGCTATTACTTGATAATGCCACCATCAT -s mr.mrrefChr5 217798 31 + 294540 TGTGGCTATTATCTGTAATGGCGATTATCAC -s simCow_chr6.simCow.chr6 344126 31 + 602619 TGTGGCTATTAGTTGATGAAGCCACTATCAT -s simDog_chr6.simDog.chr6 333827 31 + 593897 TCTGGCTACTACTTGATAATGCCATCATCAT -s simHuman_chr6.simHuman.chr6 356052 31 + 601863 TGTGTCTATTATTTGAGAAGGCCACCCTCAT -s simRat_chr6.simRat.chr6 362880 31 + 647215 TGTGGGGTATTTCTGAATTGGTGATTATCAC - -a -s simMouse_chr6.simMouse.chr6 370803 7 + 636262 CATCTTA -s Anc0.Anc0refChr2 4348 7 + 17989 GATCTTG -s Anc1.Anc1refChr6 32237 7 + 197743 GATCTTG -s Anc2.Anc2refChr17 26100 7 + 28526 GAGCTTG -s mr.mrrefChr5 217829 7 + 294540 CATCTTA -s simCow_chr6.simCow.chr6 344157 7 + 602619 GAGCTCG -s simDog_chr6.simDog.chr6 333858 7 + 593897 GGGCTTG -s simDog_chr6.simDog.chr6 157057 7 - 593897 AATGTTG -s simHuman_chr6.simHuman.chr6 356083 7 + 601863 AATCGTG -s simRat_chr6.simRat.chr6 362911 7 + 647215 TATCTTA - -a -s simMouse_chr6.simMouse.chr6 370810 15 + 636262 CGTTGACTCCATCTA -s Anc0.Anc0refChr2 4656 15 + 17989 CTTTTAATTTATCTA -s Anc1.Anc1refChr6 32545 15 + 197743 CTTTTAATTTATCTA -s Anc2.Anc2refChr17 26517 15 + 28526 CTTTTAATTTATATG -s mr.mrrefChr5 217836 15 + 294540 CGTTGACTCCATCTA -s simDog_chr6.simDog.chr6 334268 15 + 593897 CTTTTAATTTATATG -s simHuman_chr6.simHuman.chr6 356423 15 + 601863 CTTTTAATTGACCTA -s simRat_chr6.simRat.chr6 362918 15 + 647215 CACTGTCTCCATCTA - -a -s simMouse_chr6.simMouse.chr6 370825 37 + 636262 GGCTTAGAGATGATGTCTAGTTAGCTAATGAGTGTCA -s Anc0.Anc0refChr2 4672 27 + 17989 GGCATTGAG------ACTTGTCAT----TGATTGTCA -s Anc1.Anc1refChr6 32561 31 + 197743 GGCATTGAG------ACTTGTCATACGATGATTGTCA -s Anc2.Anc2refChr17 26533 27 + 28526 GGCATTGAG------ACTTCTCAT----TGATTTTCA -s mr.mrrefChr5 217851 31 + 294540 GGCTTAGAG------TCTAGTTAGCTAATGAGTGTCA -s simDog_chr6.simDog.chr6 334284 27 + 593897 GGCATTGAG------ACTTCTCAT----TGATTTTCA -s simHuman_chr6.simHuman.chr6 356439 31 + 601863 GGCATTGAG------ACTTGTCATACGATAAATGGCA -s simRat_chr6.simRat.chr6 362933 31 + 647215 GGCTTAGAG------TCCAGTTGGCTAAAGAGTGTCA - -a -s simMouse_chr6.simMouse.chr6 370862 5 + 636262 CAATT -s Anc0.Anc0refChr2 4699 5 + 17989 TAATT -s Anc1.Anc1refChr6 32592 5 + 197743 TAATT -s Anc2.Anc2refChr17 26560 5 + 28526 TTTAC -s mr.mrrefChr5 217882 5 + 294540 CAATT -s simDog_chr6.simDog.chr6 334311 5 + 593897 TTTAC -s simHuman_chr6.simHuman.chr6 356486 5 + 601863 TAATT -s simRat_chr6.simRat.chr6 362964 5 + 647215 CAAAT - -a -s simMouse_chr6.simMouse.chr6 370867 4 + 636262 TGTT -s Anc0.Anc0refChr2 4704 4 + 17989 TACT -s Anc1.Anc1refChr6 32597 4 + 197743 TACT -s Anc2.Anc2refChr17 26565 4 + 28526 TACT -s mr.mrrefChr5 217887 4 + 294540 TGTT -s simDog_chr6.simDog.chr6 334316 4 + 593897 TACT -s simHuman_chr6.simHuman.chr6 356491 4 + 601863 TACT -s simRat_chr6.simRat.chr6 363214 4 + 647215 TGTT - -a -s simMouse_chr6.simMouse.chr6 370871 135 + 636262 TGATAAATTTCACTGTACCATCCTGTTCACTAAACCATTGTCCTCTAACAATGCTCCAGCTGTATGTCCAGAGTTGGCGGAAGGGGCTGCGGGCTAGTCAAGATCTCTCAGTGACAAGTAAATCTGGAGATTGGC -s Anc0.Anc0refChr2 4708 50 + 17989 TGAATAATTGCACTAAACTATCCT------------------------------------------------------------------------------------TAATTA-ATGTACATCTGGGGATGGAC -s Anc1.Anc1refChr6 32601 51 + 197743 TGAATAATTGCACTAAACTATCCT------------------------------------------------------------------------------------TAATTATATGTACATCTGGGGATGGAC -s Anc2.Anc2refChr17 26569 50 + 28526 TAAATAATTGCAGTAAACTATCCT------------------------------------------------------------------------------------TAATTA-GTGTGCATCTGAGGAGGGAC -s mr.mrrefChr5 217891 51 + 294540 TGATAAATTTCACTGTACCATCCT------------------------------------------------------------------------------------CAGTGACAAGTAAATCTGGAGATTGGC -s simDog_chr6.simDog.chr6 334320 50 + 593897 TAAATAATTGCAGTAAACTATCCT------------------------------------------------------------------------------------TAATTA-GTGTGCATCTGAGGAGGGAC -s simHuman_chr6.simHuman.chr6 356499 51 + 601863 TGAATAATTGCACTAGACTATCCT------------------------------------------------------------------------------------GAATTATATATATATCTGGGGATGGAA -s simRat_chr6.simRat.chr6 363218 51 + 647215 TGATAAATTGCACTAAACCATCCT------------------------------------------------------------------------------------CAGTAACAAGTAAATTTGGAGATTGGC - -a -s simMouse_chr6.simMouse.chr6 371006 4 + 636262 TGCA -s Anc0.Anc0refChr2 4758 4 + 17989 TGTA -s Anc1.Anc1refChr6 32652 4 + 197743 TGTA -s Anc2.Anc2refChr17 26619 4 + 28526 TATA -s mr.mrrefChr5 217942 4 + 294540 TGCA -s simDog_chr6.simDog.chr6 334570 4 + 593897 TATA -s simHuman_chr6.simHuman.chr6 356550 4 + 601863 TGTA -s simRat_chr6.simRat.chr6 363269 4 + 647215 TCTA - -a -s simMouse_chr6.simMouse.chr6 371010 16 + 636262 GCACTTGATAGATGGT -s Anc1.Anc1refChr6 32676 14 + 197743 GTGGGTAACAGAT--T -s mr.mrrefChr5 217946 16 + 294540 GCACTTGATAGATGGT -s simHuman_chr6.simHuman.chr6 356699 14 + 601863 GTGGGTAACAGAT--T -s simRat_chr6.simRat.chr6 363273 16 + 647215 ATGCTGGATAGATTGT - -a -s simMouse_chr6.simMouse.chr6 371026 39 + 636262 AGGAGCTAGTTTAAGAAAAGCAACAACTAGTTTGAGGAC -s Anc1.Anc1refChr6 32690 39 + 197743 TGCTGCTTCATTCTTAGAAGTGCCAACTAGGATAAGGCC -s mr.mrrefChr5 217962 39 + 294540 AGGAGCTAGTTTAAGAAAAGTAACAACTAGTTTGAGGAC -s simHuman_chr6.simHuman.chr6 356713 39 + 601863 TGCTGCTTCATTCTTAGAAGTGCCAACTAGGATAAGGCC -s simRat_chr6.simRat.chr6 363290 39 + 647215 AGGAGTTAGGCTAATAAAAATAGCAACTAGTTTGAGGAC - -a -s simMouse_chr6.simMouse.chr6 371065 14 + 636262 CATTTATGCCTTTG -s Anc1.Anc1refChr6 32729 14 + 197743 CATTTTCATCTTAG -s mr.mrrefChr5 218001 14 + 294540 CATTTATGCCTTTG -s simHuman_chr6.simHuman.chr6 356753 14 + 601863 CATTTTCATCTTAG -s simRat_chr6.simRat.chr6 363329 14 + 647215 CATGTATGCCTATG - -a -s simMouse_chr6.simMouse.chr6 371079 111 + 636262 TGCCCCTGGAACTCATTTGTTTTTGCTTGCTTGTGATATACAGAGTGCGGTGGTATACAGAATGCCATGCATGGCAGCAATGCCACGCATGGCAGCAGGAAGCATCAGTCC -s Anc0.Anc0refChr2 4782 3 + 17989 ------------------------------------------------------------------------------------------------------------CCA -s Anc1.Anc1refChr6 32743 76 + 197743 AACACTTGATGCTCACTTTTTTTCACTTGCTAGTGGTATATAGAGTACA-----------------AC------------------ACAGTGCAGTTGGAAGGGTTAACCA -s Anc2.Anc2refChr17 26643 3 + 28526 ------------------------------------------------------------------------------------------------------------TCA -s mr.mrrefChr5 218015 93 + 294540 TGCCCCTGGAACTCATTTGTTTTTGCTTGCTTGTGGTATACAGAGTGCGGTGGTATACAGAATGCCAT------------------GCATGGCAGCAGGAAGCATCAGCCC -s simDog_chr6.simDog.chr6 334595 3 + 593897 ------------------------------------------------------------------------------------------------------------TCA -s simHuman_chr6.simHuman.chr6 356767 76 + 601863 AACACTTGATGCTCACTTTTTTTCACTTGCTAGTGGTATATAGAGTACA-----------------AC------------------ACAGTGCAGTTGGAAGGGTTAACCA -s simRat_chr6.simRat.chr6 363432 93 + 647215 TGCCCCTGGAACTCATTTGTTTTTGCTTGCTGGTGGTTTACAGAGTGCTGTGGTGTACAGAATCCCAT------------------GCATGACAGCAGGAAGCATCAGCCC - -a -s simMouse_chr6.simMouse.chr6 371190 9 + 636262 TGGGATAGA -s Anc0.Anc0refChr2 4786 9 + 17989 TGGGATAGA -s Anc1.Anc1refChr6 32820 9 + 197743 TGGGATAGA -s Anc2.Anc2refChr17 26647 9 + 28526 TGGGGTAGA -s mr.mrrefChr5 218108 9 + 294540 TGGGATAGA -s simDog_chr6.simDog.chr6 334599 9 + 593897 TGGGGTAGA -s simHuman_chr6.simHuman.chr6 356844 9 + 601863 TGAGATAGA -s simRat_chr6.simRat.chr6 363525 9 + 647215 TGGGATAGA - -a -s simMouse_chr6.simMouse.chr6 371199 36 + 636262 ATGCTGTGTTGGTGTTCACTGCCATCACAAGGGGAG -s Anc0.Anc0refChr2 4805 36 + 17989 GTACTGTGCTGGCATTCACTGCAGTCAGGTAGGGAA -s Anc1.Anc1refChr6 32839 36 + 197743 GTACTGTGCTGGCATTCACTGCAGTCAGGTAGGGAA -s Anc2.Anc2refChr17 26666 36 + 28526 GGATACTTCTGGCATTCACAGCAGTCAGTTAGGGAA -s mr.mrrefChr5 218117 36 + 294540 ATGCTGTGTTGGTGTTCACTGCCATCAGGAGGGGAG -s simDog_chr6.simDog.chr6 334618 36 + 593897 GGATACTTCTGGCATTCACAGCAGTCAGTTAGGGAA -s simHuman_chr6.simHuman.chr6 356863 36 + 601863 GTACTGTGCTTGCATTCACTGCTGTCAGGTCGGGAA -s simRat_chr6.simRat.chr6 363534 35 + 647215 ATGCTGTGTTGGTGTG-GTTGCGATCAGGAGAGAAG - -a -s simMouse_chr6.simMouse.chr6 371235 5 + 636262 AAGAG -s Anc0.Anc0refChr2 4842 5 + 17989 AAGAG -s Anc1.Anc1refChr6 32876 5 + 197743 AAGAG -s Anc2.Anc2refChr17 26703 5 + 28526 GAGGG -s mr.mrrefChr5 218154 5 + 294540 AAGAG -s simCow_chr6.simCow.chr6 344457 3 + 602619 --GGG -s simDog_chr6.simDog.chr6 334655 5 + 593897 GAGGG -s simHuman_chr6.simHuman.chr6 356900 5 + 601863 AGGAG -s simRat_chr6.simRat.chr6 363570 5 + 647215 AAGAG - -a -s simMouse_chr6.simMouse.chr6 371240 23 + 636262 GCTGCCTGTTGTCAACTTATACT -s Anc0.Anc0refChr2 4847 23 + 17989 TCTGCCCGGTGTCAACTTATATT -s Anc1.Anc1refChr6 32881 23 + 197743 TCTGCCCGGTGTCAACTTATATT -s Anc2.Anc2refChr17 26708 23 + 28526 TCTACCCAGTGTCAACTTATATT -s mr.mrrefChr5 218159 23 + 294540 GCTGCCTGTTGTCAACTTATACT -s simCow_chr6.simCow.chr6 344460 23 + 602619 TCTAAGCAGTGTCAATTTATATT -s simDog_chr6.simDog.chr6 334660 23 + 593897 TCTACCCAGTGTCAACCTATATC -s simDog_chr6.simDog.chr6 157151 2 - 593897 TC--------------------- -s simHuman_chr6.simHuman.chr6 356905 23 + 601863 TCTGCCCGGTGTCAACTTATATT -s simRat_chr6.simRat.chr6 363575 23 + 647215 GCTGCCTGTTGTCAACTTATACT - -a -s simMouse_chr6.simMouse.chr6 371263 3 + 636262 CCA -s Anc0.Anc0refChr2 4870 3 + 17989 CCA -s Anc1.Anc1refChr6 32904 3 + 197743 CCA -s Anc2.Anc2refChr17 26732 3 + 28526 CCA -s mr.mrrefChr5 218182 3 + 294540 CCA -s simCow_chr6.simCow.chr6 344484 3 + 602619 TCA -s simDog_chr6.simDog.chr6 334684 3 + 593897 CCA -s simHuman_chr6.simHuman.chr6 356928 3 + 601863 AAA -s simRat_chr6.simRat.chr6 363598 3 + 647215 TTG - -a -s simMouse_chr6.simMouse.chr6 371266 1 + 636262 C -s Anc0.Anc0refChr2 4873 1 + 17989 C -s Anc1.Anc1refChr6 32907 1 + 197743 C -s Anc2.Anc2refChr17 26735 1 + 28526 C -s mr.mrrefChr5 218185 1 + 294540 C -s simCow_chr6.simCow.chr6 344487 1 + 602619 A -s simDog_chr6.simDog.chr6 334687 1 + 593897 C -s simHuman_chr6.simHuman.chr6 356932 1 + 601863 C -s simRat_chr6.simRat.chr6 363601 1 + 647215 C - -a -s simMouse_chr6.simMouse.chr6 371267 14 + 636262 CATCTAATGGCATT -s Anc0.Anc0refChr2 4874 11 + 17989 CAT---GGGGCATC -s Anc1.Anc1refChr6 32908 11 + 197743 CAT---GGGGCATC -s Anc2.Anc2refChr17 26736 11 + 28526 CTT---GGGGCATC -s mr.mrrefChr5 218186 14 + 294540 CATCTAATGGCATT -s simCow_chr6.simCow.chr6 344488 8 + 602619 ------AGGGCATC -s simDog_chr6.simDog.chr6 334707 11 + 593897 CTT---GGGGTATC -s simHuman_chr6.simHuman.chr6 356933 11 + 601863 CAT---GAGGCATC -s simRat_chr6.simRat.chr6 363602 14 + 647215 CATCTAATGGCATT - -a -s simMouse_chr6.simMouse.chr6 371281 36 + 636262 TATGAGTGCTAGGAAATGAGGGAACTGCTAGAACTG -s Anc0.Anc0refChr2 4888 32 + 17989 TTTGAGCATTAGGGATT---TTATCGCCTTGAA-AG -s Anc1.Anc1refChr6 32922 32 + 197743 TTTGAGCATTAGGGATT---TTATCGCCTTGAA-AG -s Anc2.Anc2refChr17 26750 32 + 28526 TTTGGGCATCAGGGATT---TTATTGCATGGTA-AG -s mr.mrrefChr5 218200 36 + 294540 TATGAGTGCTAGGAAATGAGGGAACTGCTTGAACTG -s simCow_chr6.simCow.chr6 344504 32 + 602619 TTTGGGCATCAGGGATT---TTATTGCATGGTA-AG -s simHuman_chr6.simHuman.chr6 356947 32 + 601863 TGTGAGCATTAGAGACT---TTAGCCCCTTGAA-CA -s simRat_chr6.simRat.chr6 363616 36 + 647215 TGTGAGTGCTGGGAAACAAGGGAACTGCTTGAACTG - -a -s simMouse_chr6.simMouse.chr6 371317 42 + 636262 CCTATGAATGGATCCATCCCTGCAATATGAGACAGGATTGGA -s Anc0.Anc0refChr2 4920 41 + 17989 CCTATGAATGGAT-CACCCATGCAATCTGAGGGATCATTTGA -s Anc1.Anc1refChr6 32954 41 + 197743 CCTATGAATGGAT-CACCCATGCAATCTGAGGGATCATTTGA -s Anc2.Anc2refChr17 26782 41 + 28526 CCCATGAGTGAAT-CACACAGGTAATCAGAGGGGTCATTTGT -s mr.mrrefChr5 218236 42 + 294540 CCTATGAATGGATCCATCCCTGCAATCTGAGACAGGATTTGA -s simCow_chr6.simCow.chr6 344536 41 + 602619 CCCATGAGTGAAT-CACACAGGTAATCAGAGGGGTCATTTGT -s simHuman_chr6.simHuman.chr6 356979 41 + 601863 CCTATGAATGGGT-CACCCATGCAATCTGAGGTAACATTTGA -s simRat_chr6.simRat.chr6 363731 42 + 647215 CCTATGAATGGATCCATCCCTGCAATCTGAGACAGGATTTGA - -a -s simMouse_chr6.simMouse.chr6 371359 5 + 636262 ATTAT -s Anc0.Anc0refChr2 4973 5 + 17989 ATTAT -s Anc1.Anc1refChr6 33007 5 + 197743 ATTAT -s Anc2.Anc2refChr17 26835 5 + 28526 ATTAC -s mr.mrrefChr5 218278 5 + 294540 ATTAT -s simCow_chr6.simCow.chr6 344589 5 + 602619 ATTAC -s simHuman_chr6.simHuman.chr6 357032 5 + 601863 ATTAT -s simRat_chr6.simRat.chr6 363773 5 + 647215 ATTAT - -a -s simMouse_chr6.simMouse.chr6 371364 39 + 636262 TGAACTTATGGTTCTGCATGGTGGATGGAACACATGACT -s Anc0.Anc0refChr2 4981 38 + 17989 AGAACTGATGGTT-TGGATGGTGAATGGAACACATGACT -s Anc1.Anc1refChr6 33015 38 + 197743 AGAACTGATGGTT-TGGATGGTGAATGGAACACATGACT -s Anc2.Anc2refChr17 26843 38 + 28526 AGAACTGATGGCT-TAGATGGTGAATGGAGCGCATGACT -s mr.mrrefChr5 218283 39 + 294540 TGAACTTATGGTTCTGCATGGTGAATGGAACACATGACT -s simCow_chr6.simCow.chr6 344597 38 + 602619 AGAACTGATGGCT-TAGATGGTGAATGGAGCGCATGACT -s simHuman_chr6.simHuman.chr6 357040 38 + 601863 GGAACTGATGGTT-TGAATGGTGAAAGAAACAAATGACT -s simRat_chr6.simRat.chr6 363778 39 + 647215 TGAACTTATGGTTCTGCACAGTGAATGGAACACATGGCT - -a -s simMouse_chr6.simMouse.chr6 371403 21 + 636262 CACTGGGATTCCAGCAATATA -s Anc0.Anc0refChr2 5020 21 + 17989 CACTGGGAATCCAGCAATATA -s Anc1.Anc1refChr6 33054 21 + 197743 CACTGGGAATCCAGCAATATA -s Anc2.Anc2refChr17 26882 21 + 28526 CACTGGCAATCTGGCAATGTT -s mr.mrrefChr5 218323 21 + 294540 CACTGGGATTCCAGCAATATA -s simCow_chr6.simCow.chr6 344636 21 + 602619 CACTGGCAATCTGGCAATGTT -s simHuman_chr6.simHuman.chr6 357079 21 + 601863 CACTGGGAATCCAGCAATATA -s simRat_chr6.simRat.chr6 363818 21 + 647215 CACTGGGATTCCAGCAATATG - -a -s simMouse_chr6.simMouse.chr6 371424 32 + 636262 TGAGTACACTTCTCCCATAAGATATCTAACTA -s Anc0.Anc0refChr2 5042 32 + 17989 TGATCACACTTCTGCCTTTTGATATCTGGCTG -s Anc1.Anc1refChr6 33076 32 + 197743 TGATCACACTTCTGCCTTTTGATATCTGGCTG -s Anc2.Anc2refChr17 26904 32 + 28526 TGATCACACTTCTGTCTTTTGCTAACTGGCTG -s mr.mrrefChr5 218344 32 + 294540 TGAGTACACTTCTCCCATAAGATATCTAACTG -s simCow_chr6.simCow.chr6 344658 32 + 602619 TGATCACACTTCTGTCTTTTGCTAACTGGCTG -s simHuman_chr6.simHuman.chr6 357101 32 + 601863 TGATCACATTTCTTCCTTTGGATGTGTGGCTG -s simRat_chr6.simRat.chr6 363839 32 + 647215 TGAGTACTCTTATGTTATAAGTTATTTAACTG - -a -s simMouse_chr6.simMouse.chr6 371456 24 + 636262 AGACAATCATGTAAATAATGTGGT -s Anc0.Anc0refChr2 5075 24 + 17989 ACACAGGCCTTGCATTAATGGGAT -s Anc1.Anc1refChr6 33109 24 + 197743 ACACAGGCCTTGCATTAATGGGAT -s Anc2.Anc2refChr17 26937 24 + 28526 ACACACGCCATGCATTAATGGGAT -s mr.mrrefChr5 218376 24 + 294540 AGACAGTCATGTAAATAATGTGAT -s simCow_chr6.simCow.chr6 344691 24 + 602619 ACACACTCGGCGCATTAATGAGAT -s simDog_chr6.simDog.chr6 334720 15 + 593897 ------GCCATCTATTA---GCAT -s simHuman_chr6.simHuman.chr6 357134 24 + 601863 AAACAGGCCTTGCATTAATGGGAT -s simRat_chr6.simRat.chr6 363871 24 + 647215 AGACGGTCATGTAAACAATCTGAT - -a -s simMouse_chr6.simMouse.chr6 371480 9 + 636262 AAGTATCAG -s Anc0.Anc0refChr2 5102 9 + 17989 TAGTATTAG -s Anc1.Anc1refChr6 33136 9 + 197743 TAGTATTAG -s Anc2.Anc2refChr17 26964 9 + 28526 TAGTATAAG -s mr.mrrefChr5 218400 9 + 294540 AAGTATTAG -s simCow_chr6.simCow.chr6 344718 9 + 602619 AAGAATCAG -s simDog_chr6.simDog.chr6 334738 9 + 593897 TGTTATAAG -s simHuman_chr6.simHuman.chr6 357161 9 + 601863 GAGTATTAG -s simRat_chr6.simRat.chr6 363895 9 + 647215 AAGTATTGG - -a -s simMouse_chr6.simMouse.chr6 371489 13 + 636262 GATGACTTTTATG -s Anc0.Anc0refChr2 5111 13 + 17989 GATCAATTTTTTG -s Anc1.Anc1refChr6 33145 13 + 197743 GATCAATTTTTTG -s Anc2.Anc2refChr17 26973 13 + 28526 GATCAATTCTTTG -s mr.mrrefChr5 218409 13 + 294540 GATGAATTTTATG -s simCow_chr6.simCow.chr6 344727 13 + 602619 TATCAATTACTTA -s simDog_chr6.simDog.chr6 334750 13 + 593897 GATCAAATCTTTG -s simHuman_chr6.simHuman.chr6 357170 13 + 601863 GATCAATTTTTTG -s simRat_chr6.simRat.chr6 363904 13 + 647215 GATGGATTTTATG - -a -s simMouse_chr6.simMouse.chr6 371502 18 + 636262 TTGGATGCAGTTGTTGAT -s Anc0.Anc0refChr2 5125 18 + 17989 CTGCATACAGTTGTTGGT -s Anc1.Anc1refChr6 33159 18 + 197743 CTGCATACAGTTGTTGGT -s Anc2.Anc2refChr17 26987 18 + 28526 CTGCATACAGTTGTTGGT -s mr.mrrefChr5 218422 18 + 294540 TTGGATACAGTTGTTGGT -s simCow_chr6.simCow.chr6 344741 18 + 602619 CTGCATACCGTTGTCAGT -s simDog_chr6.simDog.chr6 334764 18 + 593897 CTGCACACAGTTGTTGGT -s simHuman_chr6.simHuman.chr6 357184 18 + 601863 CTGTATATGGTTGTTGGT -s simRat_chr6.simRat.chr6 363917 18 + 647215 TTAGATACAGTTGTTGGT - -a -s simMouse_chr6.simMouse.chr6 371520 30 + 636262 GCTCAAACCCATATTACTGACATAACAATT -s Anc0.Anc0refChr2 5150 30 + 17989 GCCCAAACCCACATTACTATCATGACAACT -s Anc1.Anc1refChr6 33184 30 + 197743 GCCCAAACCCACATTACTATCATGACAACT -s Anc2.Anc2refChr17 27012 30 + 28526 GCCCAAACCCACATTACTATCATGGCAACT -s mr.mrrefChr5 218440 30 + 294540 GCTCAAACCCATATTACTGTCATGACAATT -s simCow_chr6.simCow.chr6 344766 30 + 602619 GTCAGAATCCACATTACTTACATGGCAACT -s simDog_chr6.simDog.chr6 334789 24 + 593897 GCCCAAACACAGATTACTATCATG------ -s simHuman_chr6.simHuman.chr6 357209 30 + 601863 GCCCAAACCCACATTACTATCATGACAACT -s simRat_chr6.simRat.chr6 363935 30 + 647215 GGTCAAACCCATACCACTGTCAGGTCGATC - -a -s simMouse_chr6.simMouse.chr6 371550 11 + 636262 CACATCAATCA -s Anc0.Anc0refChr2 5201 11 + 17989 TGAATCAATCA -s Anc1.Anc1refChr6 33235 11 + 197743 TGAATCAATCA -s Anc2.Anc2refChr17 27063 11 + 28526 TGCATCAATCA -s mr.mrrefChr5 218470 11 + 294540 CAAATCAATCA -s simCow_chr6.simCow.chr6 344817 11 + 602619 TGCATCGATCA -s simDog_chr6.simDog.chr6 334829 11 + 593897 TTCGTGAATCA -s simHuman_chr6.simHuman.chr6 357260 11 + 601863 TGAATCAATCA -s simRat_chr6.simRat.chr6 363965 11 + 647215 CAAATCAATCC - -a -s simMouse_chr6.simMouse.chr6 371561 13 + 636262 TAAACACTTACCA -s Anc0.Anc0refChr2 5212 13 + 17989 TTGAGATTTAGAG -s Anc1.Anc1refChr6 33246 13 + 197743 TTGAGATTTAGAG -s Anc2.Anc2refChr17 27074 13 + 28526 TTGAGATTTAGAG -s mr.mrrefChr5 218481 13 + 294540 TAAACACTTACCA -s simCow_chr6.simCow.chr6 344828 13 + 602619 TTTAGATTTTGAG -s simDog_chr6.simDog.chr6 334841 13 + 593897 TTGAAATTTAGAG -s simHuman_chr6.simHuman.chr6 357271 13 + 601863 TTGAGAATTAGAT -s simRat_chr6.simRat.chr6 363976 13 + 647215 TAAATACTTACCA - -a -s simMouse_chr6.simMouse.chr6 371574 10 + 636262 ATCAATTGGG -s Anc0.Anc0refChr2 5231 10 + 17989 ATGAATTGGG -s Anc1.Anc1refChr6 33265 10 + 197743 ATGAATTGGG -s Anc2.Anc2refChr17 27093 10 + 28526 ATGAATCAGG -s mr.mrrefChr5 218500 10 + 294540 ATCAATTGGG -s simCow_chr6.simCow.chr6 344847 10 + 602619 ATGAATCAGG -s simDog_chr6.simDog.chr6 334860 10 + 593897 CTGAATCAGG -s simHuman_chr6.simHuman.chr6 357290 10 + 601863 ATGAATTGGG -s simRat_chr6.simRat.chr6 363995 10 + 647215 ATCAATTGGG - -a -s simMouse_chr6.simMouse.chr6 371584 99 + 636262 CCTAGATATGGAATGGAGACGATATGATTAAGAAAATTACTGCAGTGCAGCGAAGCTATTCACCCCCATGTGAAAGAACCTGGATGCAGCAAACAAAGT -s Anc0.Anc0refChr2 5241 54 + 17989 CCTAGACAAGGAGTGGAGAACATATGATTAAACAGGATACTGTGGGGTA--------------------GCAAG------------------------- -s Anc1.Anc1refChr6 33275 54 + 197743 CCTAGACAAGGAGTGGAGAACATATGATTAAACAGGATACTGTGGGGTA--------------------GCAAG------------------------- -s Anc2.Anc2refChr17 27103 54 + 28526 CCTAGATGAGGAGTGGAGAACATATAATAAAACCAGATGGTGTGGGGTA--------------------GCAAG------------------------- -s mr.mrrefChr5 218510 79 + 294540 CCTAGACATGGAATGGAGACCATATGATTAAAAAGGTTACTGCAGGGTA--------------------GTGAGAGAACCTGGATGCAGCAAACAAAGT -s simCow_chr6.simCow.chr6 344857 26 + 602619 CCCAGATGAGAAGTGGAGC----------------------------TA--------------------GCAAG------------------------- -s simDog_chr6.simDog.chr6 334871 54 + 593897 CCTAGATGAGGATTGGAGAACATATAATAAAACCAGATGGTGTGGGGTA--------------------GCAAG------------------------- -s simHuman_chr6.simHuman.chr6 357300 54 + 601863 CCTAGACAAGGAGAGGAGGACATATGATTAAAGAGGATACTGTGGGGTA--------------------GCTAG------------------------- -s simRat_chr6.simRat.chr6 364005 79 + 647215 TCTAGACATGGAACGGAGACCATATGGTTAAAAAGGTTACTGCAGGGTA--------------------GTAAGAGAACTTGAACGCAGCAAACAGAGT - -a -s simMouse_chr6.simMouse.chr6 371683 101 + 636262 AATGGTGCAGCAATGCTACTCATGCAAATGTGAAAGAAGCTGTGATGCTGAGGACAAAGTGAGTTTGTGGTTGCTGGGTTGACACAACAACCTGGTGGAGG -s Anc0.Anc0refChr2 5295 82 + 17989 --------------GCTACTCCTACCAATGTGAAGGAACCTGAGATGCT---GCCAAAGTTAGTTGTTGATTGCT-GATTGACAC-ACAACCCTGTGGAGG -s Anc1.Anc1refChr6 33329 82 + 197743 --------------GCTACTCCTACCAATGTGAAGGAACCTGAGATGCT---GCCAAAGTTAGTTGTTGATTGCT-GATTGACAC-ACAACCCTGTGGAGG -s Anc2.Anc2refChr17 27160 82 + 28526 --------------GCTACTCCTACCAATGTGAAGGAACCTGAGATGCT---GCCAAAGTTAGTTGTTGATTGCT-GATTGACAC-ACAACCCTGTGGAGG -s mr.mrrefChr5 218589 99 + 294540 AATGGTGCAGCAATGCTACTCATGCCAATGTGAAGGAACCTGTGATGCTGAGGACAAAGTGAGTTTGTGATTGCT-GGTTGACAC-ACAACCTGGTGGAGG -s simCow_chr6.simCow.chr6 344886 82 + 602619 --------------GCTGCTTTTACTGCTGTGAAGGAACCTGAGATCCT---GCCAAATTTCGTTGTTGATTCCT-GATTGACTC-ATAACTTAATGTAGG -s simDog_chr6.simDog.chr6 334928 82 + 593897 --------------GCTACTCCCTCCAAAGTGAGGGAACCTGAAGTGCT---GCCAAAGTTAGTTGTTGATTGCT-GATTGACAC-ACAACCCTGTGGAGG -s simHuman_chr6.simHuman.chr6 357354 66 + 601863 --------------GCTACTCCTACCAATGTGAAGGAACCTAAGATGCT---GCCAAAGTTAGTTGTTGATTGCT-AATTGACA----------------- -s simRat_chr6.simRat.chr6 364086 99 + 647215 AATGGAGCAGCAATGGTACTCATGCCAATGTGAAGGAACCTGGGATGCTGAAAACAAAGTGAATTTGTGATTGCT-GGTTGACAC-ACAACATGGTATAAG - -a -s simMouse_chr6.simMouse.chr6 371784 60 + 636262 TTTTGAAGCTGAGGTTTACGTCCTGGTAGGTGCCTCTAGAGGCCTATTCGAATAATGAAT -s Anc0.Anc0refChr2 5377 57 + 17989 TGTTGGT---GGGGTTTACATCCAGATAAGCACCATTAGAGGGCTGTTCAATTAGTACAT -s Anc1.Anc1refChr6 33411 57 + 197743 TGTTGGT---GGGGTTTACATCCAGATAAGCACCATTAGAGGGCTGTTCAATTAGTACAT -s Anc2.Anc2refChr17 27245 57 + 28526 TGTTGGT---GGGGTTTACATCCAGATAAGCACCATTAGAGGGCTGTTCAATTAGTACAT -s mr.mrrefChr5 218688 57 + 294540 TTTTGAA---GAGGTTTACATCCTGGTAGGTGCCTCTAGAGGCCTATTCGAATAATGAAT -s simCow_chr6.simCow.chr6 344971 54 + 602619 TGTCAGT---GGGGTGTACATCCAGATAGGCACCAT---GGAACTGTTCAATTCATACAG -s simDog_chr6.simDog.chr6 335013 57 + 593897 TGTTGGT---GGGGTTTACATCCAGATAAACAAAGGTAGAGGGTTGTTCAATTAGTACAt -s simHuman_chr6.simHuman.chr6 357420 47 + 601863 -------------GTTTACATCTAGATTAGCACCATTAGAGGGCTGTTCAAGTAGTACAT -s simRat_chr6.simRat.chr6 364185 57 + 647215 CTTTGAA---CAGGTTTATATCCTGGTAGGTGCCCCTAGAGGCCTATTTGATTAATGAAT - -a -s simMouse_chr6.simMouse.chr6 371844 6 + 636262 ACTTTT -s Anc0.Anc0refChr2 5434 6 + 17989 AGTTTT -s Anc1.Anc1refChr6 33468 6 + 197743 AGTTTT -s Anc2.Anc2refChr17 27302 6 + 28526 AGTATT -s mr.mrrefChr5 218745 6 + 294540 ACTTTT -s simCow_chr6.simCow.chr6 345025 6 + 602619 GCTCCT -s simDog_chr6.simDog.chr6 335235 6 + 593897 AGTATT -s simHuman_chr6.simHuman.chr6 357467 6 + 601863 ATTTTT -s simRat_chr6.simRat.chr6 364242 6 + 647215 ACTTGT - -a -s simMouse_chr6.simMouse.chr6 371850 30 + 636262 GGAATGGTAAACCAACTTTACTACATTGCC -s Anc0.Anc0refChr2 5440 30 + 17989 GGAATGGCAACTCAATTTTGCTATATGGCC -s Anc1.Anc1refChr6 33474 30 + 197743 GGAATGGCAACTCAATTTTGCTATATGGCC -s Anc2.Anc2refChr17 27308 30 + 28526 GACATGGCAACTCAATTCTGCTATATGGCC -s mr.mrrefChr5 218751 30 + 294540 GGAATGGCAAACCAACTTTGCTACATTGCC -s simCow_chr6.simCow.chr6 345032 30 + 602619 GACATGGCAAGTCAATTCTGCTATATGGCC -s simDog_chr6.simDog.chr6 335241 30 + 593897 GACATGGCAACTCAATTCTGCTATATGGCC -s simHuman_chr6.simHuman.chr6 357473 24 + 601863 AGAATGGCAA------CTTGCTATATGTCC -s simRat_chr6.simRat.chr6 364248 30 + 647215 GGAATGCCAAACCAGTTTTGCTACATTGCC - -a -s simMouse_chr6.simMouse.chr6 371880 10 + 636262 CTTCACCCAA -s Anc0.Anc0refChr2 5470 10 + 17989 CCTCACCCAA -s Anc1.Anc1refChr6 33504 10 + 197743 CCTCACCCAA -s Anc2.Anc2refChr17 27338 10 + 28526 TCTCACTCAA -s mr.mrrefChr5 218781 10 + 294540 CCTCACCCAA -s simCow_chr6.simCow.chr6 345062 10 + 602619 TCTCATTCAA -s simDog_chr6.simDog.chr6 335271 10 + 593897 TCTCACTGAG -s simHuman_chr6.simHuman.chr6 357502 10 + 601863 CCTCTCCCAA -s simRat_chr6.simRat.chr6 364278 10 + 647215 CCTCACCCAA - -a -s simMouse_chr6.simMouse.chr6 371890 49 + 636262 TATGAAGAAAAGTGCCTGGATCCTGGATGTAAGACAAGAAGGGCCCCAG -s Anc0.Anc0refChr2 5482 38 + 17989 TTTTCACATAAATGCC-----------CATTTGACAACATGGGCCAAAA -s Anc1.Anc1refChr6 33516 38 + 197743 TTTTCACATAAATGCC-----------CATTTGACAACATGGGCCAAAA -s Anc2.Anc2refChr17 27350 38 + 28526 CTTTCACATAAATTCA-----------CATTTAGCAACATGGGCCAACA -s mr.mrrefChr5 218791 49 + 294540 TTTGAAGAAAAGTGCCTGGATCCTGGATGTAAGACAAGAAGGGCCCCAG -s simCow_chr6.simCow.chr6 345074 38 + 602619 CTTTCACATATATTCA-----------TATTTAGCAAAATGGGTGAACA -s simDog_chr6.simDog.chr6 335283 38 + 593897 CTTTCACATAAATTCA-----------CATTTAGCAACATGGGCCACCA -s simHuman_chr6.simHuman.chr6 357514 38 + 601863 TTTTCACAGAGATGCC-----------CATTTGACAACATGGGCAAAAA -s simRat_chr6.simRat.chr6 364288 49 + 647215 TTTGAAGAAAAGTGCCTGGATCCTGGATGTAAGACAGGAAGGGCCCCAG - -a -s simMouse_chr6.simMouse.chr6 371939 6 + 636262 AGGATG -s Anc0.Anc0refChr2 5520 6 + 17989 TAGATG -s Anc1.Anc1refChr6 33554 6 + 197743 TAGATG -s Anc2.Anc2refChr17 27388 6 + 28526 TAGATG -s mr.mrrefChr5 218840 6 + 294540 AGGATG -s simCow_chr6.simCow.chr6 345112 6 + 602619 TAAATC -s simDog_chr6.simDog.chr6 319966 6 + 593897 TGGATG -s simDog_chr6.simDog.chr6 335321 6 + 593897 TAGATG -s simHuman_chr6.simHuman.chr6 357552 6 + 601863 TAAATG -s simRat_chr6.simRat.chr6 364337 6 + 647215 AGGATG - -a -s simMouse_chr6.simMouse.chr6 371945 2 + 636262 GC -s Anc0.Anc0refChr2 5526 2 + 17989 AC -s Anc1.Anc1refChr6 33560 2 + 197743 AC -s Anc2.Anc2refChr17 27441 2 + 28526 AC -s mr.mrrefChr5 218846 2 + 294540 GC -s simDog_chr6.simDog.chr6 320007 2 + 593897 AC -s simDog_chr6.simDog.chr6 335374 2 + 593897 AC -s simHuman_chr6.simHuman.chr6 357558 2 + 601863 TG -s simRat_chr6.simRat.chr6 364343 2 + 647215 AC - -a -s simMouse_chr6.simMouse.chr6 371947 2 + 636262 CT -s Anc0.Anc0refChr2 5528 2 + 17989 AT -s Anc1.Anc1refChr6 33562 2 + 197743 AT -s Anc2.Anc2refChr17 27443 2 + 28526 AT -s mr.mrrefChr5 218848 2 + 294540 AT -s simCow_chr6.simCow.chr6 345158 2 + 602619 CT -s simDog_chr6.simDog.chr6 335381 2 + 593897 AT -s simHuman_chr6.simHuman.chr6 357560 2 + 601863 AT -s simRat_chr6.simRat.chr6 364345 2 + 647215 AT - -a -s simMouse_chr6.simMouse.chr6 371949 161 + 636262 ATATGAGAGAAAGCAGAAACCACTCAATATAATACTATCCCAGTGTATAGGTCAACTAATCTGCCAATGCCTTACTGGATGCTTATAGAGCATTTTTCAGGGGTGGAGTGACTTGGTTAAATAGCATGGGATGTGGGAAGAACCTGATTCAGTGGTATACA -s Anc0.Anc0refChr2 5530 134 + 17989 GTT------GAACTAGGAAGCACT---------------------TATAGACCTACTAATCTACGAATGTCTGACTGGATGCTTATGGAACAATTTTCAGCAGTGTAGTGGCTTAGTCAAATTGCATGGGGTGTGAGAAGACCGTTATTAGATGGCATACT -s Anc1.Anc1refChr6 33564 134 + 197743 GTT------GAACTAGGAAGCACT---------------------TATAGACCTACTAATCTACGAATGTCTGACTGGATGCTTATGGAACAATTTTCAGCAGTGTAGTGGCTTAGTCAAATTGCATGGGGTGTGAGAAGACCGTTATTAGATGGCATACT -s Anc2.Anc2refChr17 27445 134 + 28526 GTT------GACCTAGGAAGTGCT---------------------TATCAACCTACTAATTTACGAATGTCTGAATGGATGATTATTGAACAATTTTCAGCAGTGTAATGGCTTAGTCAAATTGCATGGGGTGTGAGAAAACTGTTATCAGATGGCATATT -s mr.mrrefChr5 218850 161 + 294540 ATATGAGAGGAAGCAGAAACCACTCAATATAATACTATCCCAGTGTATAGATCAACTAATCTGCCAATGCCTTACTGGATGCTTATGGAGCAATTTTCAGGAGTGGAGTGACTTGGTCAAATAGCATGGGGTGTGGGAAGAACCTGATTCAGTGGCATACA -s simCow_chr6.simCow.chr6 345160 108 + 602619 GTT------GA------------------------------------------TATTCACTCAGGCA-----ATCTGGACGATTGTTGAAAAGTTTTCAGCAGTGTAATGGCTTAGCCAGATTGCAAGAGGTGTGAGAAAACTGTTATTAGATGGTATATT -s simDog_chr6.simDog.chr6 320009 134 + 593897 GTT------GACCTAGGAAGTGCA---------------------TATAAAACTACTACTTTACTAACGTCTGAATGGATGATTATTGTACAATTTGCAGCAGTGTAAGGGTTTAGTCAAATTGCTTTGAGTGTAAGTAGACTGTTATCAGATGGCATATT -s simDog_chr6.simDog.chr6 335383 134 + 593897 GTT------GACCTCGGAAGAACT---------------------TATCAACCTACTAATTTACGAATGCGTGAATGAGTGAGTATTGAACAATTTTCAGCAGTGCAATGTCTTAGTCAATTTGCATCGGGTGTGAGAAAACTGTTATCAGACGGCATACT -s simHuman_chr6.simHuman.chr6 357562 130 + 601863 GTC------GAACTAGGAAACACT---------------------TATAGAACCACTAGTCTACACATGTCTGACCGGACACTTATGGAACAATTTTGAACAGTGTAGTACCTTAGTCAAAT----TGGGGTGTAAGAAGGCCATTATTAGATGGCATGCT -s simRat_chr6.simRat.chr6 364347 157 + 647215 ATATTGGAGGAAGCTGAAACCACTCAATATAATACTATCCTAGTCTATAGATCAACTCATCTGCCAATGCCTTACTGGATGCTTATGGAGTGATTTTCAGGAGTGGCGTGACT----CAAATAGCATGGGGTGTGGGAAGAGCCTAATTCAGTGGCATACA - -a -s simMouse_chr6.simMouse.chr6 372110 13 + 636262 GTGGATGCAGATA -s Anc0.Anc0refChr2 5664 13 + 17989 ATTGATGCAACTA -s Anc1.Anc1refChr6 33698 13 + 197743 ATTGATGCAACTA -s Anc2.Anc2refChr17 27579 13 + 28526 AGTGATGCAACTA -s mr.mrrefChr5 219011 13 + 294540 GTGGATGCAGATA -s simCow_chr6.simCow.chr6 345268 13 + 602619 AGTGATGCAACTA -s simDog_chr6.simDog.chr6 335517 13 + 593897 AGTGATGCACCTA -s simHuman_chr6.simHuman.chr6 357692 13 + 601863 ATTGATGCAAGTG -s simRat_chr6.simRat.chr6 364504 13 + 647215 TTGGATGCGGATA - -a -s simMouse_chr6.simMouse.chr6 372123 2 + 636262 AG -s Anc0.Anc0refChr2 5677 2 + 17989 AG -s Anc1.Anc1refChr6 33711 2 + 197743 AG -s Anc2.Anc2refChr17 27592 2 + 28526 AG -s mr.mrrefChr5 219024 2 + 294540 AG -s simCow_chr6.simCow.chr6 345281 2 + 602619 AG -s simDog_chr6.simDog.chr6 320143 2 + 593897 AG -s simDog_chr6.simDog.chr6 335530 2 + 593897 AG -s simHuman_chr6.simHuman.chr6 357705 2 + 601863 AG -s simRat_chr6.simRat.chr6 364517 2 + 647215 GG - -a -s simMouse_chr6.simMouse.chr6 372125 18 + 636262 ATCATAGACTATAAGGAC -s Anc0.Anc0refChr2 5679 17 + 17989 AGT-CAGACTACAAGGAC -s Anc1.Anc1refChr6 33713 17 + 197743 AGT-CAGACTACAAGGAC -s Anc2.Anc2refChr17 27595 17 + 28526 TGT-CAGACTAGAGGGAC -s mr.mrrefChr5 219026 18 + 294540 ATCATAGACTACAAGGAC -s simCow_chr6.simCow.chr6 345284 17 + 602619 TGT-CAGACTGGAAGAAC -s simDog_chr6.simDog.chr6 320146 17 + 593897 TGT-CAGTCTAGAGAGAC -s simDog_chr6.simDog.chr6 335533 17 + 593897 TGT-CATAATAGGGGGCC -s simHuman_chr6.simHuman.chr6 357707 17 + 601863 AGT-CAGACTACAAAGAT -s simRat_chr6.simRat.chr6 364519 18 + 647215 ATCATAGACTTCAAGGAC - -a -s simMouse_chr6.simMouse.chr6 372143 49 + 636262 AAAACTGCAATAAGATTGCTCACTACACAAGGCAAGGGACAGTGTTATC -s Anc0.Anc0refChr2 5697 42 + 17989 AAACCTACGATA--ATTGCCCACTGCACAATTCGAGGAACAGTA----- -s Anc1.Anc1refChr6 33731 45 + 197743 AAACCTACGATAATATTGCCCACTGCACAATTCGAGGAACAGTA----C -s Anc2.Anc2refChr17 27613 42 + 28526 AAACCTACAATA--ATTGCCCACTGCACAAATCGAAGAACAATA----- -s mr.mrrefChr5 219045 49 + 294540 AAAACTGCGATAAGATTGCCCACTACACAATGCAAGGGACAGTGTTATC -s simCow_chr6.simCow.chr6 345302 29 + 602619 AAGTCTCCAAT---------------AGAATTTGAAGTACGGTA----- -s simDog_chr6.simDog.chr6 320164 42 + 593897 TGACCTATGATA--TTTGCCAACTGCATAAATCATAGAACAATA----- -s simDog_chr6.simDog.chr6 335551 42 + 593897 GAACCTACAATA--ATTGCCCATAGCACAAATCGAAGGGCAATA----- -s simHuman_chr6.simHuman.chr6 357725 45 + 601863 AAACCTACGATGATATTGCCCACTGCACAATTTGAGGAACAGTA----C -s simRat_chr6.simRat.chr6 364538 49 + 647215 AAAACTGCGATAAAATTGCCCACTACACAATCCAAGGGACAGTGTTGTC - -a -s simMouse_chr6.simMouse.chr6 372192 5 + 636262 ATCTA -s Anc0.Anc0refChr2 5745 5 + 17989 ATCTA -s Anc1.Anc1refChr6 33782 5 + 197743 ATCTA -s Anc2.Anc2refChr17 27661 5 + 28526 ATCTA -s mr.mrrefChr5 219100 5 + 294540 ATCTA -s simCow_chr6.simCow.chr6 345337 5 + 602619 ATAAA -s simDog_chr6.simDog.chr6 335599 5 + 593897 AGCTC -s simHuman_chr6.simHuman.chr6 357776 5 + 601863 ATCTA -s simRat_chr6.simRat.chr6 364593 5 + 647215 ATCTA - -a -s simMouse_chr6.simMouse.chr6 372197 45 + 636262 ATAAGCCGGTGATGCGCAGATGCTGGGGGACACTGTGGTGGAACT -s Anc0.Anc0refChr2 5757 45 + 17989 ATAGGCCTGTATTGCGTAGGTACTGGAGGACATTGTGATGAAGAC -s Anc1.Anc1refChr6 33794 45 + 197743 ATAGGCCTGTATTGCGTAGGTACTGGAGGACATTGTGATGAAGAC -s Anc2.Anc2refChr17 27673 45 + 28526 ATAGACTTGTATTAGGTAGGTACTGGAGGACATAGCTATGAAGGC -s mr.mrrefChr5 219105 45 + 294540 ATAGGCCGGTGATGCGCAGGTGCTGGGGGACACTGTGATGGAGAT -s simCow_chr6.simCow.chr6 345349 45 + 602619 ATAAACTTGTATTAGGTATGTACTTGAGAACATAGCTATGAAGGC -s simDog_chr6.simDog.chr6 335610 45 + 593897 ATAGACTTGCATTAGGTAGGTACTGGAGGACACAGCTCTGGAGGC -s simHuman_chr6.simHuman.chr6 357788 45 + 601863 ATAGGCCCATATCGCATAGGTACTAGAGGACATTGTGATGAAGAC -s simRat_chr6.simRat.chr6 364598 45 + 647215 ATAGGCCAGTGATGGGCAGGTGCTGGGGGACACTGTGATGGAGAT - -a -s simMouse_chr6.simMouse.chr6 372242 34 + 636262 CCAGGCTAGGAGAGTATTCCCATATGAGACATTC -s Anc0.Anc0refChr2 5802 34 + 17989 CCAGGCTAGAAGAGTGCTCCCACAAGAGATACTT -s Anc1.Anc1refChr6 33839 34 + 197743 CCAGGCTAGAAGAGTGCTCCCACAAGAGATACTT -s Anc2.Anc2refChr17 27718 34 + 28526 CCAGGCCAGAAGAGTGCTCCCACAAGAAATACTT -s mr.mrrefChr5 219150 34 + 294540 CCAGGCTAGGAGAGTATTCCCACAAGAGACATTT -s simCow_chr6.simCow.chr6 345396 34 + 602619 CCAGGCCAGAAAAGTGTTCCCACAAGAATTATTT -s simDog_chr6.simDog.chr6 335655 34 + 593897 CCAGGCCAGAAGAGTGCTCCCACATGAAATACTT -s simHuman_chr6.simHuman.chr6 357833 34 + 601863 CCAGGCTGGAAGAGTGATCCTACAAGAGATAATT -s simRat_chr6.simRat.chr6 364643 34 + 647215 CCAGGCCAGTCAAGTATCCCCACAAGAGACATTT - -a -s simMouse_chr6.simMouse.chr6 372276 18 + 636262 AAACTACAGTTGGTACAT -s Anc0.Anc0refChr2 5836 18 + 17989 AAATGCCAGTAAGTACAT -s Anc1.Anc1refChr6 33873 18 + 197743 AAATGCCAGTAAGTACAT -s Anc2.Anc2refChr17 27752 18 + 28526 AGATGCCAGTAAGTACAT -s mr.mrrefChr5 219184 18 + 294540 AAACTACAGTTAGTACAT -s simCow_chr6.simCow.chr6 345430 18 + 602619 GCATGCCAGTAATTACAT -s simDog_chr6.simDog.chr6 335689 18 + 593897 AGATGCTTATAAGTACAT -s simHuman_chr6.simHuman.chr6 357869 18 + 601863 AAATGCCAGTAAGTACAT -s simRat_chr6.simRat.chr6 364677 13 + 647215 AAACCACAGTTAG----- - -a -s simMouse_chr6.simMouse.chr6 372294 1 + 636262 C -s Anc0.Anc0refChr2 5854 1 + 17989 T -s Anc1.Anc1refChr6 33891 1 + 197743 T -s Anc2.Anc2refChr17 27781 1 + 28526 T -s mr.mrrefChr5 219202 1 + 294540 C -s simCow_chr6.simCow.chr6 345459 1 + 602619 T -s simDog_chr6.simDog.chr6 335718 1 + 593897 T -s simHuman_chr6.simHuman.chr6 357887 1 + 601863 T - -a -s simMouse_chr6.simMouse.chr6 372295 2 + 636262 AA -s Anc0.Anc0refChr2 5858 2 + 17989 TA -s Anc1.Anc1refChr6 33895 2 + 197743 TA -s Anc2.Anc2refChr17 27785 2 + 28526 TA -s mr.mrrefChr5 219203 2 + 294540 AA -s simCow_chr6.simCow.chr6 345462 2 + 602619 AA -s simDog_chr6.simDog.chr6 335722 2 + 593897 TG -s simHuman_chr6.simHuman.chr6 357891 2 + 601863 CA - -a -s simMouse_chr6.simMouse.chr6 372297 5 + 636262 TGTGA -s Anc0.Anc0refChr2 5860 5 + 17989 CGGCA -s Anc1.Anc1refChr6 33897 5 + 197743 CGGCA -s Anc2.Anc2refChr17 27787 5 + 28526 CGGCA -s mr.mrrefChr5 219205 5 + 294540 TGTCA -s simCow_chr6.simCow.chr6 345464 5 + 602619 CAGCA -s simDog_chr6.simDog.chr6 335735 5 + 593897 TGACA -s simHuman_chr6.simHuman.chr6 357893 5 + 601863 CGGCA -s simRat_chr6.simRat.chr6 364690 4 + 647215 -GTCA - -a -s simMouse_chr6.simMouse.chr6 372302 89 + 636262 TGTTAGTGGGCCCCAAGCTTTGTAAGGGGTTCCTAAACCAAATAGCCATGATTACGCAGTAATTATGGTATACCGTAATGGTCCAATGG -s Anc0.Anc0refChr2 5867 86 + 17989 CATTGGTGGACCCTAAGCTTTGTTGGGGGTACCTAAACCCAGTAGCCATGA-TATAGGGCATTTGTGATATACGGCTTTTGTCTAGT-- -s Anc1.Anc1refChr6 33904 86 + 197743 CATTGGTGGACCCTAAGCTTTGTTGGGGGTACCTAAACCCAGTAGCCATGA-TATAGGGCATTTGTGATATACGGCTTTTGTCTAGT-- -s Anc2.Anc2refChr17 27794 86 + 28526 CATTGGTGGACCCTAAGCTTTGTTGGGGGTACCTAAACCCAGTTGCCATAG-TTTAGGGCATTTGTGATATACGGCTTTTGTCTAGT-- -s mr.mrrefChr5 219210 89 + 294540 TGTTAGTGGGCCCCAAGCTTTGTAGGGGGTTCCTAAACCAAGTAGCCATGATTATACAGTATTTATGGTATACAGTAATGGTCCAATGG -s simCow_chr6.simCow.chr6 345471 84 + 602619 CATTGGTGGA--CTGATCTTTGTTGGGGGTACCTAAACCCAGTTGCCATGG-TCCAGGGCATTTGTGATATAGGGCATTTGTGTAGT-- -s simDog_chr6.simDog.chr6 335742 86 + 593897 CACTGGTGGACCCTAAGCTTTGTTGGGGTTACCTACACCCAGATATCACAG-TTTAGGGCATTTGTGGTATACAGCTTTTGTCTAGT-- -s simHuman_chr6.simHuman.chr6 357900 62 + 601863 CATTGGTGGACCCTAAGCTTTATTGGGGGTACCTAAACCTAGTAGCCATGA-TATAAGGCATT-------------------------- -s simRat_chr6.simRat.chr6 364694 89 + 647215 TGTCAGTGGGCCCCAAGCTTTGTCGGGAGTTCCTAAACCAAGTAGCCATGATTATACAGTATTCGTGGTACACAGCAATAGTCCAATGG - -a -s simMouse_chr6.simMouse.chr6 372391 25 + 636262 CATGTTTCTGCAGCTCTTACTACTC -s Anc0.Anc0refChr2 5953 21 + 17989 CAAGCTTGGAATGTTCTCA----TT -s Anc1.Anc1refChr6 33990 21 + 197743 CAAGCTTGGAATGTTCTCA----TT -s Anc2.Anc2refChr17 27880 21 + 28526 CAAGCTTGGAATGTTCTCA----TT -s mr.mrrefChr5 219299 25 + 294540 CATGTTTCTGCAGCTCTTACTACTC -s simCow_chr6.simCow.chr6 345557 21 + 602619 CGTGCTTGGGCAGCGCTCA----CC -s simDog_chr6.simDog.chr6 335828 21 + 593897 CAAGCTTGGAATGTTCTCA----TT -s simRat_chr6.simRat.chr6 364783 25 + 647215 CATGTTTCTGCAGTTCTTACCACTT - -a -s simMouse_chr6.simMouse.chr6 372416 24 + 636262 CTTAGTGGGCCCAGACAGGTTTGC -s Anc0.Anc0refChr2 5974 10 + 17989 CTTGGT--------------ATGC -s Anc1.Anc1refChr6 34011 10 + 197743 CTTGGT--------------ATGC -s Anc2.Anc2refChr17 27901 10 + 28526 CTTGGT--------------ATGC -s mr.mrrefChr5 219324 10 + 294540 CTTAGT--------------TTGC -s simCow_chr6.simCow.chr6 345579 10 + 602619 CTTTGT--------------ACGC -s simDog_chr6.simDog.chr6 335849 10 + 593897 CTTGGT--------------ATGC -s simRat_chr6.simRat.chr6 364808 10 + 647215 TTGAGT--------------TAGC - -a -s simMouse_chr6.simMouse.chr6 372440 5 + 636262 TACTA -s Anc0.Anc0refChr2 5984 5 + 17989 TACCA -s Anc1.Anc1refChr6 34021 5 + 197743 TACCA -s Anc2.Anc2refChr17 27920 5 + 28526 TACCA -s mr.mrrefChr5 219334 5 + 294540 TACTA -s simCow_chr6.simCow.chr6 345598 5 + 602619 TACCA -s simDog_chr6.simDog.chr6 335868 5 + 593897 TACCA -s simRat_chr6.simRat.chr6 364818 5 + 647215 TGCTA - -a -s simMouse_chr6.simMouse.chr6 372445 2 + 636262 CA -s Anc0.Anc0refChr2 5989 2 + 17989 CA -s Anc1.Anc1refChr6 34026 2 + 197743 CA -s Anc2.Anc2refChr17 27929 2 + 28526 CA -s mr.mrrefChr5 219339 2 + 294540 CA -s simCow_chr6.simCow.chr6 345607 2 + 602619 CA -s simDog_chr6.simDog.chr6 335877 2 + 593897 CA -s simRat_chr6.simRat.chr6 364823 2 + 647215 TG - -a -s simMouse_chr6.simMouse.chr6 372447 55 + 636262 ATTGAGCTCAGACTCACAGCTGACTGGCCCCAAATCTAGAGGTATTTGCAAAACT -s Anc0.Anc0refChr2 5991 54 + 17989 ACTGAGGTCAGACTCACAAATGGCTGGCCCCAGATCTA-TGGTTTTTGCCAAACT -s Anc1.Anc1refChr6 34028 54 + 197743 ACTGAGGTCAGACTCACAAATGGCTGGCCCCAGATCTA-TGGTTTTTGCCAAACT -s Anc2.Anc2refChr17 27931 54 + 28526 ACTGAGGTCAGACTCACAAATAGCTGGCCCCAGATCTA-TGGTTTTTGGCAAACC -s mr.mrrefChr5 219341 54 + 294540 ATTGAGCTCAGACTCACAGCTGGCTGGCCCCAGATCTA-AGGTATTTGCAAAACT -s simCow_chr6.simCow.chr6 345610 54 + 602619 ACTGGGGTCAGACTCATTAATAGGTGGCCCCAGATCTA-TGGTTTGTGGCACACA -s simDog_chr6.simDog.chr6 335879 54 + 593897 ACTGAGGTCAGACTCACAAACAGCTGGCCCCAGATCTA-TGGTTTTCGGCAAACC -s simHuman_chr6.simHuman.chr6 357962 51 + 601863 --TTGGGTCGGACTGA-AAATGGCTGGTCCTAGATATA-TGGTTTTTGCGAAACT -s simRat_chr6.simRat.chr6 364825 54 + 647215 ATTGAGCTCACACTCACAGCTGGCTGGCCCCAGATCTA-AGGTATTTGCAAAACT - -a -s simMouse_chr6.simMouse.chr6 372502 12 + 636262 GTTAAGCCCAGT -s Anc0.Anc0refChr2 6045 12 + 17989 GTTAATCCCAGT -s Anc1.Anc1refChr6 34082 12 + 197743 GTTAATCCCAGT -s Anc2.Anc2refChr17 27985 12 + 28526 GTTAATCCCAGT -s mr.mrrefChr5 219395 12 + 294540 GTTAAGCCCAGT -s simCow_chr6.simCow.chr6 345664 12 + 602619 GTTACTCCCAGT -s simDog_chr6.simDog.chr6 335937 12 + 593897 ATTAATCCCAGC -s simHuman_chr6.simHuman.chr6 358013 12 + 601863 GTTAACCCCAGT -s simRat_chr6.simRat.chr6 364879 12 + 647215 GTTCAACCCAGT - -a -s simMouse_chr6.simMouse.chr6 372514 105 + 636262 TTACCAGCATACTACACAATGGTGTGGGTAATTTATGGGACAAAGATGTTGTGTAAGCATATTGTCATGACGACATTGCTCTTTTCTTAGCACTACAGGACCAGG -s Anc0.Anc0refChr2 6057 105 + 17989 TTACCAGTATTCTTCACATCAGATTTGGTAGTTGATGGAATAGAAATATTGTGAAAGCATTTTGTCATGGCTACACTGCCCCTCTCCTAGCATTACAGGACCAGG -s Anc1.Anc1refChr6 34094 105 + 197743 TTACCAGTATTCTTCACATCAGATTTGGTAGTTGATGGAATAGAAATATTGTGAAAGCATTTTGTCATGGCTACACTGCCCCTCTCCTAGCATTACAGGACCAGG -s Anc2.Anc2refChr17 28000 105 + 28526 TTACCAGTATTCTTCACATCAGATTTGGTAGTTGATGGAATAGAAATATTATAAAAACATTTTGTCATGGTTACACTGCCCCTTTTCTAGCATTGCAGGACCAGA -s mr.mrrefChr5 219407 105 + 294540 TTACCAGCATACTACACATTGGTGTGGGTAGTTTATGGGACAAAGATGTTGTGTAAGCATATTGTCATGACGACACTGCTCTTCTCTTAGCATTACAGGACCAGG -s simCow_chr6.simCow.chr6 345679 104 + 602619 TTACCAGTATTCTGC-CATCAGAGTTGGTAGTCAATGCAATAAAAGTATTATATAACCATTTTGTCAATGTTACATTGTCCCTTTACTGCGGTTGCAGGACAAGA -s simDog_chr6.simDog.chr6 335952 104 + 593897 CTACCAGTATTCTTCACATCAGGTTTGGTAG-TGATGGGATAGAAATAGAATAAGTATATTCTGTCCTGTTTACACTGCCCCTTTTCTAGCATCGCAAGACCAGA -s simHuman_chr6.simHuman.chr6 358025 100 + 601863 TTACCAGGATTCTTCACATAAGACTTGGTAGATGATGGAA-AGTAATATTGTGCAAGCATTTTGTCATGGCTACACTGC----CCCCTAGCATTACAGGACCAGG -s simRat_chr6.simRat.chr6 364891 96 + 647215 TTACCAGCATGTTCCACATTGGTGTGGGTAGTTTATGGGACAA---------GTTAGCAAGTTGTCATAACAACACTGTTCCTCTCTTAGCCTTGCCAGTCCAGA - -a -s simMouse_chr6.simMouse.chr6 372619 10 + 636262 TCAGCCACTG -s Anc0.Anc0refChr2 6162 10 + 17989 TCTGGCAGTG -s Anc1.Anc1refChr6 34199 10 + 197743 TCTGGCAGTG -s Anc2.Anc2refChr17 28105 10 + 28526 TCTGGCAGGG -s mr.mrrefChr5 219512 10 + 294540 TCAGGCACTG -s simCow_chr6.simCow.chr6 345783 10 + 602619 TCAGGCAGAG -s simDog_chr6.simDog.chr6 336211 10 + 593897 GCTGGCAGGG -s simHuman_chr6.simHuman.chr6 358125 10 + 601863 TCTGGCAGTG -s simRat_chr6.simRat.chr6 364987 10 + 647215 TCAGGCCCCG - -a -s simMouse_chr6.simMouse.chr6 372629 6 + 636262 TAACCC -s Anc0.Anc0refChr2 6173 6 + 17989 CAGCCC -s Anc1.Anc1refChr6 34210 6 + 197743 CAGCCC -s Anc2.Anc2refChr17 28116 6 + 28526 TGGCCC -s mr.mrrefChr5 219523 6 + 294540 CAACCC -s simCow_chr6.simCow.chr6 345794 6 + 602619 TGGCCC -s simDog_chr6.simDog.chr6 336222 6 + 593897 TGGCCC -s simHuman_chr6.simHuman.chr6 358136 6 + 601863 CAGCCC -s simRat_chr6.simRat.chr6 364998 6 + 647215 CAACCC - -a -s simMouse_chr6.simMouse.chr6 372635 6 + 636262 AGTATT -s Anc0.Anc0refChr2 6182 6 + 17989 GTCATT -s Anc1.Anc1refChr6 34219 6 + 197743 GTCATT -s Anc2.Anc2refChr17 28125 6 + 28526 GTCATT -s mr.mrrefChr5 219532 6 + 294540 AGTATT -s simCow_chr6.simCow.chr6 345803 6 + 602619 GTCATT -s simDog_chr6.simDog.chr6 336231 6 + 593897 GTCATT -s simHuman_chr6.simHuman.chr6 358145 6 + 601863 GCCATT -s simRat_chr6.simRat.chr6 365007 6 + 647215 AGGATT - -a -s simMouse_chr6.simMouse.chr6 372641 1 + 636262 G -s Anc0.Anc0refChr2 6198 1 + 17989 G -s Anc1.Anc1refChr6 34235 1 + 197743 G -s Anc2.Anc2refChr17 28141 1 + 28526 G -s mr.mrrefChr5 219538 1 + 294540 G -s simCow_chr6.simCow.chr6 345819 1 + 602619 T -s simDog_chr6.simDog.chr6 336247 1 + 593897 G -s simHuman_chr6.simHuman.chr6 358161 1 + 601863 G -s simRat_chr6.simRat.chr6 365013 1 + 647215 G - -a -s simMouse_chr6.simMouse.chr6 372642 14 + 636262 CGGTTGCAGAGCAA -s Anc0.Anc0refChr2 6199 14 + 17989 CAGTTGCAGAACTA -s Anc1.Anc1refChr6 34236 14 + 197743 CAGTTGCAGAACTA -s Anc2.Anc2refChr17 28142 14 + 28526 CAGTGGCAGAACTA -s mr.mrrefChr5 219539 14 + 294540 CGGTTGCAGAGCAA -s simCow_chr6.simCow.chr6 345820 12 + 602619 CAATATCAGAGT-- -s simDog_chr6.simDog.chr6 336248 14 + 593897 CAGTGGCAGAACTA -s simHuman_chr6.simHuman.chr6 358162 14 + 601863 TAGTTGCAGAACTA -s simRat_chr6.simRat.chr6 365015 14 + 647215 AGGTTGCAGAGTAA - -a -s simMouse_chr6.simMouse.chr6 372656 12 + 636262 TGTAGACCAGCT -s Anc0.Anc0refChr2 6218 8 + 17989 TGCCTCCT---- -s Anc1.Anc1refChr6 34255 12 + 197743 TGCCTCCTTGCC -s Anc2.Anc2refChr17 28161 8 + 28526 TGCCTCCT---- -s mr.mrrefChr5 219553 12 + 294540 TGCAGACCAGCC -s simDog_chr6.simDog.chr6 336267 8 + 593897 TGCCTCCT---- -s simHuman_chr6.simHuman.chr6 358181 12 + 601863 TGCCTCCATGCC -s simRat_chr6.simRat.chr6 365029 12 + 647215 TGCAGACCAGCC - -a -s simMouse_chr6.simMouse.chr6 372668 34 + 636262 GATAAAAAACCGGGTTTAGCATAATGATGTGCTC -s Anc0.Anc0refChr2 6241 3 + 17989 CAG------------------------------- -s Anc1.Anc1refChr6 34286 3 + 197743 CAG------------------------------- -s Anc2.Anc2refChr17 28184 3 + 28526 CCG------------------------------- -s mr.mrrefChr5 219584 34 + 294540 CATAAAAAACCGGGTTTAGCATAATGATGTGCTC -s simDog_chr6.simDog.chr6 336290 3 + 593897 CCG------------------------------- -s simHuman_chr6.simHuman.chr6 358212 3 + 601863 CAG------------------------------- -s simRat_chr6.simRat.chr6 365060 34 + 647215 CATGAAAAACCAGGTTTGGCATGACCATCTTCTC - -a -s simMouse_chr6.simMouse.chr6 372702 40 + 636262 TAAATGCCAGGCTTGGACCCACCAGATCTAGCCAAGGTGA -s Anc0.Anc0refChr2 6244 10 + 17989 ----------------------------AATCCAAG--AA -s Anc1.Anc1refChr6 34289 10 + 197743 ----------------------------AATCCAAG--AA -s Anc2.Anc2refChr17 28187 10 + 28526 ----------------------------AATCCATA--AA -s mr.mrrefChr5 219618 40 + 294540 TAAATGCCAGGCTTGGACCCACCAGATCTAGCCAAGGTGA -s simDog_chr6.simDog.chr6 336293 10 + 593897 ----------------------------AATCCATA--AA -s simHuman_chr6.simHuman.chr6 358215 10 + 601863 ----------------------------CATCCAAG--AA -s simRat_chr6.simRat.chr6 365095 40 + 647215 GGAATGCCAGGCTTGCGCCCACCAGATCCAGCCAAGGTGA - -a -s simMouse_chr6.simMouse.chr6 372742 31 + 636262 GCAGCATCACACTGAAAGGCATTGCTCGGCT -s Anc0.Anc0refChr2 6254 29 + 17989 ACAGCATCACACTGATAGACATCACTTGA-- -s Anc1.Anc1refChr6 34299 31 + 197743 ACAGCATCACACTGATAGACATCACTTGACC -s Anc2.Anc2refChr17 28197 29 + 28526 ACAGCATCACATTGATAGACATCACTTGA-- -s mr.mrrefChr5 219658 31 + 294540 ACAGCATCACACTGAAAGACATTGCTTGACT -s simDog_chr6.simDog.chr6 336553 29 + 593897 ACAGCATCACATTGATAGACATCACTTGA-- -s simHuman_chr6.simHuman.chr6 358225 31 + 601863 ACTGCATCACACTGATAGACATGATTTGACC -s simRat_chr6.simRat.chr6 365135 31 + 647215 ACAACATCACAGTGAAAGACATTGCTTGACT - -a -s simMouse_chr6.simMouse.chr6 372773 31 + 636262 TGTTTTATCACCTACATTGTTCTAATTAGAT -s Anc0.Anc0refChr2 6284 31 + 17989 TTGTTTTTTGACTGCATAGTTCTAACTAGAT -s Anc1.Anc1refChr6 34331 31 + 197743 TTGTTTTTTGACTGCATAGTTCTAACTAGAT -s Anc2.Anc2refChr17 28227 31 + 28526 TGGCTTTTTCACTGTATAGTTCTAACTGGAT -s mr.mrrefChr5 219689 31 + 294540 TTTTTTTTCGACTGCATTGTTCTAATTAGAT -s simCow_chr6.simCow.chr6 345832 13 + 602619 ------------------GTTCTAACTGGAT -s simDog_chr6.simDog.chr6 336583 31 + 593897 TGGCTTTTTCACTGTATAGTTCTAACCGGGT -s simHuman_chr6.simHuman.chr6 358257 31 + 601863 TTGTTTTTTGACTGCATAGTTCTATCTAGAT -s simRat_chr6.simRat.chr6 365166 31 + 647215 TTTTTTTTCGACTGCATTGTTTTAATTAGAT - -a -s simMouse_chr6.simMouse.chr6 372804 2 + 636262 GG -s Anc0.Anc0refChr2 6316 2 + 17989 GG -s Anc1.Anc1refChr6 34363 2 + 197743 GG -s Anc2.Anc2refChr17 28259 2 + 28526 GG -s mr.mrrefChr5 219720 2 + 294540 GG -s simCow_chr6.simCow.chr6 345846 2 + 602619 GA -s simDog_chr6.simDog.chr6 336615 2 + 593897 GG -s simHuman_chr6.simHuman.chr6 358289 2 + 601863 GG -s simRat_chr6.simRat.chr6 365197 2 + 647215 GG - -a -s simMouse_chr6.simMouse.chr6 372806 26 + 636262 AGTTCTCTGTCAAACAACTCAGCTAG -s Anc0.Anc0refChr2 6318 25 + 17989 AATTCTATGTCAAA-AACTTGTTTGC -s Anc1.Anc1refChr6 34365 25 + 197743 AATTCTATGTCAAA-AACTTGTTTGC -s Anc2.Anc2refChr17 28261 25 + 28526 AATCCTATGTTAAT-AACATGTTTGC -s mr.mrrefChr5 219722 26 + 294540 AGTTCTCTGTCAAACAACTTAGCTAG -s simCow_chr6.simCow.chr6 345848 19 + 602619 AATCCTCTGATAAC-AACAT------ -s simDog_chr6.simDog.chr6 336619 25 + 593897 AATCCTATGTTAAT-AACATGTTTGC -s simHuman_chr6.simHuman.chr6 358291 25 + 601863 AATTCCTTGTCAAA-AACTTTTTTGC -s simRat_chr6.simRat.chr6 365199 26 + 647215 AGTCCTCTGTCAAACAACTTGGCTAG - -a -s simMouse_chr6.simMouse.chr6 372832 16 + 636262 CTTGTGCAAGGAAAAT -s Anc0.Anc0refChr2 6343 4 + 17989 TTTG------------ -s Anc1.Anc1refChr6 34390 4 + 197743 TTTG------------ -s Anc2.Anc2refChr17 28286 4 + 28526 TTTG------------ -s mr.mrrefChr5 219748 16 + 294540 TTTGTGCAAGGAAAAT -s simDog_chr6.simDog.chr6 336647 4 + 593897 TTTG------------ -s simHuman_chr6.simHuman.chr6 358316 4 + 601863 TTTG------------ -s simRat_chr6.simRat.chr6 365225 16 + 647215 TTTGTACAGGGAAAAT - -a -s simMouse_chr6.simMouse.chr6 372848 15 + 636262 TCATACAATCAAACA -s Anc0.Anc0refChr2 6347 15 + 17989 TCACACAATTAGGCA -s Anc1.Anc1refChr6 34394 15 + 197743 TCACACAATTAGGCA -s Anc2.Anc2refChr17 28290 15 + 28526 TTATACAATTAGGCA -s mr.mrrefChr5 219764 15 + 294540 TCACACAATCAAACA -s simDog_chr6.simDog.chr6 336681 15 + 593897 TTATACAATTAGGCA -s simHuman_chr6.simHuman.chr6 358320 15 + 601863 TCACTCAGTTAGGCA -s simRat_chr6.simRat.chr6 365241 15 + 647215 TCACACAATCAACGA - -a -s simMouse_chr6.simMouse.chr6 372863 25 + 636262 ATTGGCTCAAACCTCCTTCTTTAAA -s Anc0.Anc0refChr2 6363 25 + 17989 AATGGTTGACATCTTATTCTTTAAA -s Anc1.Anc1refChr6 34410 25 + 197743 AATGGTTGACATCTTATTCTTTAAA -s Anc2.Anc2refChr17 28306 25 + 28526 AATGGTTAACTTCTTATTCTTTGAA -s mr.mrrefChr5 219779 25 + 294540 ATTGGCTGAAACCTCCTTCTTTAAA -s simCow_chr6.simCow.chr6 345867 1 + 602619 ------------------------A -s simDog_chr6.simDog.chr6 336697 25 + 593897 AATGGTTAACTTCTTATTCTTTGAA -s simHuman_chr6.simHuman.chr6 358336 25 + 601863 AATGGTCGACATCTTAGTCTTTAAA -s simRat_chr6.simRat.chr6 365256 25 + 647215 GTTGGATGAGACATCCTTCGCGAAC - -a -s simMouse_chr6.simMouse.chr6 372888 23 + 636262 AGTTTGGTATGACACTCAGGTAT -s Anc0.Anc0refChr2 6390 18 + 17989 GCTT-----CGACACCCAGGGAT -s Anc1.Anc1refChr6 34437 18 + 197743 GCTT-----CGACACCCAGGGAT -s Anc2.Anc2refChr17 28333 18 + 28526 GGTT-----CAATACCCAGGGAT -s mr.mrrefChr5 219804 18 + 294540 ACTT-----TGACACTCAGGTAT -s simCow_chr6.simCow.chr6 345870 18 + 602619 GATT-----CTAGAGTCAGGGCC -s simDog_chr6.simDog.chr6 336724 18 + 593897 GGTC-----CAATACCTAAGGAT -s simHuman_chr6.simHuman.chr6 358363 18 + 601863 GCTT-----CGACACCCAGGGAT -s simRat_chr6.simRat.chr6 365281 18 + 647215 ACTT-----TGAGACTCAGGAGT - -a -s simMouse_chr6.simMouse.chr6 372911 33 + 636262 TATAGACTCCCTCTATTGAAAATCTCCCTTGGT -s Anc0.Anc0refChr2 6408 33 + 17989 TGGAGACTGGCCCCATTTAACACCTCCCTTGGT -s Anc1.Anc1refChr6 34455 33 + 197743 TGGAGACTGGCCCCATTTAACACCTCCCTTGGT -s Anc2.Anc2refChr17 28351 33 + 28526 TGGAGACTCTCCCCATATAACACCTCCCTTGGT -s mr.mrrefChr5 219822 33 + 294540 TGTAGACTGGCCCTATTGAAAACCTCCCTTGGT -s simCow_chr6.simCow.chr6 345891 27 + 602619 TGGATACACATGACATATA------TGCCTGGT -s simDog_chr6.simDog.chr6 336742 29 + 593897 TGGAGACTCTCCCA----AACACCTCCCTTGAT -s simHuman_chr6.simHuman.chr6 358381 33 + 601863 TGCAGACTGGCCCCATTTAACACCTCACTTGGT -s simRat_chr6.simRat.chr6 365299 33 + 647215 TGGAGACTGGCCCTATCAGATTCCTCCCTTGGT - -a -s simMouse_chr6.simMouse.chr6 372944 149 + 636262 AAAGGTGGATTCCGGGGTTAGGACCATGCTGTCGACAGGTTCCATAGGAAATGTGCTACCTCCCAAGTTCATCATCGCTCTAAACTCAAAAATGCATACGGAGCAACTCAAAAATGCTTACGGAGCGGCCCCGGGGATAGCCCAGCTCT -s Anc0.Anc0refChr2 6442 23 + 17989 AAAG------------------------------------------------------------------------------------------------------------------------------GCAATGCTAGTCCAGCCCT -s Anc1.Anc1refChr6 34489 23 + 197743 AAAG------------------------------------------------------------------------------------------------------------------------------GCAATGCTAGTCCAGCCCT -s Anc2.Anc2refChr17 28385 23 + 28526 AATG------------------------------------------------------------------------------------------------------------------------------GCAAAGCTAGTCTAGCCCT -s mr.mrrefChr5 219855 23 + 294540 AAAG------------------------------------------------------------------------------------------------------------------------------CCAATGATAGCCCAGCTCT -s simCow_chr6.simCow.chr6 345919 15 + 602619 AATG------------------------------------------------------------------------------------------------------------------------------GCTGAGC--------CCCT -s simDog_chr6.simDog.chr6 336772 17 + 593897 AA--------------------------------------------------------------------------------------------------------------------------------GCAAAGCTAGTCTAG---- -s simHuman_chr6.simHuman.chr6 358415 23 + 601863 AAAG------------------------------------------------------------------------------------------------------------------------------GAAATGCCAGTCCAGCCCT -s simRat_chr6.simRat.chr6 365332 23 + 647215 AACG------------------------------------------------------------------------------------------------------------------------------CGAATGGTAGCCCAGCTCT - -a -s simMouse_chr6.simMouse.chr6 373093 39 + 636262 TTCTACTGTCCAGTTCTGTAACGTGGTAAATTCAGCTCT -s Anc0.Anc0refChr2 6465 25 + 17989 ATTAACTG--CAGGTCTGTAA-----------AAT-TCT -s Anc1.Anc1refChr6 34512 38 + 197743 ATTAACTGTCCAGGTCTGTAACTTAGTATATTAAT-TCT -s Anc2.Anc2refChr17 28408 25 + 28526 ATTAATTG--CAGGTTTGTAA-----------AAT-TCT -s mr.mrrefChr5 219878 39 + 294540 TTCTACTGTCCAGTTCTGTAACTTAGTAAATTCATCTCT -s simCow_chr6.simCow.chr6 345934 25 + 602619 CTTAGCTG--CAGGTTTGTGA-----------AAT-TCT -s simDog_chr6.simDog.chr6 336800 25 + 593897 ATTAATTG--CAGGTTTGTAA-----------AAT-TCT -s simHuman_chr6.simHuman.chr6 358438 37 + 601863 GT-GACTGTCCAGCCCTATGACTTAGTATATTAAT-TCT -s simRat_chr6.simRat.chr6 365355 39 + 647215 TTCCACTGTCCAGTTCTGTAACTTAGTAAATTCATCCCT - -a -s simMouse_chr6.simMouse.chr6 373132 19 + 636262 TTCCACGTTCTGTATGCTA -s Anc0.Anc0refChr2 6490 7 + 17989 AGCAAGG------------ -s Anc1.Anc1refChr6 34550 19 + 197743 AGCAAGGTACTGCAGACTA -s Anc2.Anc2refChr17 28434 7 + 28526 AGGAAGG------------ -s mr.mrrefChr5 219917 19 + 294540 TTCCACGTTCTGCATGCTA -s simCow_chr6.simCow.chr6 345960 7 + 602619 ACCCAGT------------ -s simDog_chr6.simDog.chr6 336826 7 + 593897 AGGAAGG------------ -s simHuman_chr6.simHuman.chr6 358475 19 + 601863 AGCAAGGTACTGCAGACTA -s simRat_chr6.simRat.chr6 365394 19 + 647215 TTCCATGTTCCGCGTGCTG - -a -s simMouse_chr6.simMouse.chr6 373151 28 + 636262 TTGAGTCAGCCTTGTGAAAAGGAAGGTG -s Anc0.Anc0refChr2 6497 16 + 17989 ----ATCAGCCTGG--------AAGGCA -s Anc1.Anc1refChr6 34569 28 + 197743 TTCAATCAGCCTGGTGAGAGGAAAGGCA -s Anc2.Anc2refChr17 28441 16 + 28526 ----ATCAGGTTTG--------ATGGCA -s mr.mrrefChr5 219936 28 + 294540 TTGAGTCAGCCTTGTGAAAAGGAAGGTG -s simCow_chr6.simCow.chr6 345967 16 + 602619 ----ATCAGGTTTG--------GTGTCC -s simDog_chr6.simDog.chr6 336833 16 + 593897 ----ATCAGGTTTG--------ATGGCA -s simHuman_chr6.simHuman.chr6 358503 28 + 601863 TTCAATCAGCCTGGTGAGAGGAAAGGCA -s simRat_chr6.simRat.chr6 365413 28 + 647215 TTGACTGGGCCTTGTGAAAAGGAAGGTG - -a -s simMouse_chr6.simMouse.chr6 373179 5 + 636262 TACTG -s Anc0.Anc0refChr2 6513 5 + 17989 GACCC -s Anc1.Anc1refChr6 34597 5 + 197743 GACCC -s Anc2.Anc2refChr17 28467 5 + 28526 TATCC -s mr.mrrefChr5 219964 5 + 294540 TACTG -s simCow_chr6.simCow.chr6 345993 5 + 602619 TGTCC -s simDog_chr6.simDog.chr6 336859 5 + 593897 TATCC -s simHuman_chr6.simHuman.chr6 358531 5 + 601863 GACCC -s simRat_chr6.simRat.chr6 365441 5 + 647215 TACTT - -a -s simMouse_chr6.simMouse.chr6 373184 6 + 636262 ACTGTT -s Anc0.Anc0refChr2 6518 6 + 17989 CCTGTT -s Anc1.Anc1refChr6 34602 6 + 197743 CCTGTT -s Anc2.Anc2refChr17 28472 6 + 28526 CCTGTC -s mr.mrrefChr5 219969 6 + 294540 ACTGTT -s simCow_chr6.simCow.chr6 345998 6 + 602619 CCTGGG -s simDog_chr6.simDog.chr6 336865 6 + 593897 CCTGTC -s simHuman_chr6.simHuman.chr6 358536 6 + 601863 CCTGTT -s simRat_chr6.simRat.chr6 365446 6 + 647215 ACTGTT - -a -s simMouse_chr6.simMouse.chr6 373190 6 + 636262 GGGTCA -s Anc0.Anc0refChr2 6524 2 + 17989 AG---- -s Anc1.Anc1refChr6 34608 2 + 197743 AG---- -s Anc2.Anc2refChr17 28478 2 + 28526 AG---- -s mr.mrrefChr5 219975 6 + 294540 GGATGA -s simCow_chr6.simCow.chr6 346004 2 + 602619 AG---- -s simDog_chr6.simDog.chr6 336871 2 + 593897 AG---- -s simHuman_chr6.simHuman.chr6 358542 2 + 601863 AG---- -s simMouse_chr6.simMouse.chr6 373349 6 + 636262 GTATGA -s simRat_chr6.simRat.chr6 365452 6 + 647215 GGATGA - -a -s simMouse_chr6.simMouse.chr6 373196 77 + 636262 GACAGTAATCAGAGGTGTTGTTTGGGTTAGGAGCATCCTTAGCCTGGCCTTTACGGCTACACTTGACGTCTGGCCTG -s mr.mrrefChr5 219981 7 + 294540 A----------------------------------------------------------------------GGCCTG -s simMouse_chr6.simMouse.chr6 373359 7 + 636262 A----------------------------------------------------------------------GGCCTG -s simRat_chr6.simRat.chr6 365458 7 + 647215 A----------------------------------------------------------------------GGCCTG - -a -s simMouse_chr6.simMouse.chr6 373273 45 + 636262 AACATTCTGTCTCATTATTTGATGTTTGAGTTTGATGTCCACTTA -s mr.mrrefChr5 219989 45 + 294540 AACATTCTGACTCATTATTAGATGTTTGATTTTGATGTCCACTTA -s simMouse_chr6.simMouse.chr6 373367 45 + 636262 AAGATTCTGACTCATTATTAGAGGTTTGATGCTCATTGTTACTTA -s simRat_chr6.simRat.chr6 365466 45 + 647215 AAAATTCTGACTCATTATTAGATGTTTGATTTTTGTGTCCCTTTA - -a -s simMouse_chr6.simMouse.chr6 373318 31 + 636262 CAAATTGTACTCCTGTGGGTCATGTTCTCCA -s mr.mrrefChr5 220035 31 + 294540 CAAATTGTACTCCTGTGGGTCATGTTCTCCA -s simMouse_chr6.simMouse.chr6 373413 31 + 636262 CAAATTGTACCCCGGTGGGTCATGTCCTCCA -s simRat_chr6.simRat.chr6 365512 31 + 647215 AAAATAGTACTCCTGTGGGTCATGTTCCCCA - -a -s simMouse_chr6.simMouse.chr6 373355 4 + 636262 TTGC - -a -s simMouse_chr6.simMouse.chr6 373366 1 + 636262 T -s mr.mrrefChr5 219988 1 + 294540 T -s simRat_chr6.simRat.chr6 365465 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 373412 1 + 636262 C -s mr.mrrefChr5 220034 1 + 294540 C -s simRat_chr6.simRat.chr6 365511 1 + 647215 C - -a -s simMouse_chr6.simMouse.chr6 373444 78 + 636262 GGAAGAGCCAGTACATGATCCAACCCAGTTCTGGAGCAGATCCAATCTACCCTTTCTCAGCTATATGAATCATTCTGC -s mr.mrrefChr5 220066 77 + 294540 G-AAGAGCCAGTACATGATCCAACCCAGTTCTGGAGCAGATCCAATCTACCCTTTCTCAGCTATATGAATCATTCTGC -s simRat_chr6.simRat.chr6 365543 77 + 647215 A-ATTAACCTGTACATGATCCAACCCAGTGCTGGAGCAGATGCAATCTGCCCTTTATCAGGTATATGATTCCTTTTGC - -a -s simMouse_chr6.simMouse.chr6 373522 126 + 636262 TATTAGCAAATTTCCTTTTCTATTAGGCTGTTATTACCCTAATACAACATTCTGAGCTGACAGCCTTAACCACTGGCAAACATGCTGGCATGGATGAAATACAGATCCTTACCTTTGGGCCTGCTA -s mr.mrrefChr5 220143 120 + 294540 TATTAGCAAATTTCCTTTTCTATTAGGCTGTTATTACC-TAATACAACATTCTGAGCTGACAGCCTTAACCACTGGCAAACATGCTGGCATGGATGAAATACAGATCCTTACCTTT-----TGCTA -s simRat_chr6.simRat.chr6 365627 120 + 647215 TATTAGGTAATTTCCTTTTCCATTAGGCTGTTATTAAC-TAATACAACATTCTGAGCTGCCAGCCTTAACCACTGGCAAACATGCTGGCATAGAAAAGATAAAGAATCTCACCTTT-----TGCTA - -a -s simMouse_chr6.simMouse.chr6 373669 6 + 636262 GCCTAT -s mr.mrrefChr5 220284 6 + 294540 GCCTAT -s simRat_chr6.simRat.chr6 365768 6 + 647215 GCCAAT - -a -s simMouse_chr6.simMouse.chr6 373874 2 + 636262 AG - -a -s simMouse_chr6.simMouse.chr6 373887 72 + 636262 CTCTATGAGTTGCAATAAAGCCCGCAGAACTGGTAAGAGCCTGCTAACTGGACTAACCCAGATAATAGCCTG -s Anc1.Anc1refChr6 34855 18 + 197743 CT-TCTGAGCCATGACAAA----------------------------------------------------- -s mr.mrrefChr5 220500 72 + 294540 CTCTATGAGTTGCAATAAAGCCCGCAGAACTGGTAAGAGCCTGCTAACTGGACTAACCCAGATAATAGCCTG -s simHuman_chr6.simHuman.chr6 358544 18 + 601863 CT-TCTGAGCCATGACAAA----------------------------------------------------- -s simRat_chr6.simRat.chr6 365984 72 + 647215 TTCTATGAGCTGCAATAAAGCCCACAGAACTGGTAAAAGCTTGCTAACTGAACCAACCCAGATAATAACCTG - -a -s simMouse_chr6.simMouse.chr6 373959 66 + 636262 TTTTAACCCATTCATCTGCCTAACCCATTGGAAATTCTAGACCAACCTATTCTAGACCCCAAAATA -s Anc1.Anc1refChr6 34873 5 + 197743 ------------------------------------------------------------CAA-TA -s mr.mrrefChr5 220572 41 + 294540 TTTTAACCCATTC------------------------TAGACCAACCTATTCTAGACCCCAAA-TA -s simHuman_chr6.simHuman.chr6 358562 5 + 601863 ------------------------------------------------------------CAA-TA -s simRat_chr6.simRat.chr6 366060 41 + 647215 TTCTAGACCATTC------------------------TAGACCAACCTATTCTAGACCCCAAA-TG - -a -s simMouse_chr6.simMouse.chr6 374025 22 + 636262 TGATGTAGCATGGTCTTGCAAT -s Anc0.Anc0refChr5 0 20 + 87904 CGAACAATCAC--TTTTGCAAT -s Anc1.Anc1refChr6 34878 20 + 197743 CGAACAATCAC--TTTTGCAAT -s Anc2.Anc2refChr14 0 20 + 7748 CAAACAATCAC--TTTTGCAAT -s mr.mrrefChr5 220613 22 + 294540 TGATGTAGCATGGTCTTGCAAT -s simCow_chr6.simCow.chr6 346459 20 + 602619 CAAAAACTTCA--TTCTTCAAT -s simDog_chr6.simDog.chr6 248817 20 - 593897 CAAACAATCAC--TTTTGCAAT -s simHuman_chr6.simHuman.chr6 358567 20 + 601863 CGAACGATCAC--TTATGCATT -s simRat_chr6.simRat.chr6 366101 22 + 647215 TAATGTAGCACGGTCTTGTGAT - -a -s simMouse_chr6.simMouse.chr6 374047 10 + 636262 GAGTGAGTGG -s Anc0.Anc0refChr5 20 8 + 87904 GAGTCA-TG- -s Anc1.Anc1refChr6 34898 9 + 197743 GAGTCA-TGC -s Anc2.Anc2refChr14 20 8 + 7748 GAGTCA-GG- -s mr.mrrefChr5 220635 10 + 294540 GAGTGAGTGG -s simCow_chr6.simCow.chr6 346479 8 + 602619 GTGTCA-GG- -s simDog_chr6.simDog.chr6 248837 2 - 593897 GA-------- -s simHuman_chr6.simHuman.chr6 358587 9 + 601863 GGGTTA-TGC -s simRat_chr6.simRat.chr6 366125 10 + 647215 GAGTCAGTGG - -a -s simMouse_chr6.simMouse.chr6 374057 1 + 636262 A -s Anc0.Anc0refChr5 67 1 + 87904 A -s Anc1.Anc1refChr6 34947 1 + 197743 A -s Anc2.Anc2refChr14 67 1 + 7748 A -s mr.mrrefChr5 220676 1 + 294540 A -s simDog_chr6.simDog.chr6 248878 1 - 593897 A -s simHuman_chr6.simHuman.chr6 358636 1 + 601863 A -s simRat_chr6.simRat.chr6 366166 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 374058 6 + 636262 TAAGAT -s Anc0.Anc0refChr5 73 6 + 87904 TAGGAA -s Anc1.Anc1refChr6 34953 6 + 197743 TAGGAA -s Anc2.Anc2refChr14 73 6 + 7748 TAGGAA -s mr.mrrefChr5 220677 6 + 294540 TAGGAT -s simDog_chr6.simDog.chr6 248884 6 - 593897 TAGGAA -s simHuman_chr6.simHuman.chr6 358642 6 + 601863 TGGGGC -s simRat_chr6.simRat.chr6 366167 6 + 647215 TCGGAT - -a -s simMouse_chr6.simMouse.chr6 374064 5 + 636262 ATTGT -s Anc0.Anc0refChr5 81 5 + 87904 ATTGT -s Anc1.Anc1refChr6 34961 5 + 197743 ATTGT -s Anc2.Anc2refChr14 81 5 + 7748 ATTGT -s mr.mrrefChr5 220683 5 + 294540 ATTGT -s simCow_chr6.simCow.chr6 346487 4 + 602619 -TGGT -s simDog_chr6.simDog.chr6 248892 5 - 593897 ATTGT -s simHuman_chr6.simHuman.chr6 358650 5 + 601863 ACCAT -s simRat_chr6.simRat.chr6 366173 3 + 647215 ATT-- - -a -s simMouse_chr6.simMouse.chr6 374069 6 + 636262 TAGTTC -s Anc0.Anc0refChr5 86 6 + 87904 TAGTTC -s Anc1.Anc1refChr6 34966 6 + 197743 TAGTTC -s Anc2.Anc2refChr14 86 6 + 7748 TAGTTC -s mr.mrrefChr5 220688 6 + 294540 TAGTTC -s simCow_chr6.simCow.chr6 346492 6 + 602619 TAGTTT -s simDog_chr6.simDog.chr6 248897 6 - 593897 TAGTTC -s simHuman_chr6.simHuman.chr6 358655 6 + 601863 TAGTTC -s simRat_chr6.simRat.chr6 366176 6 + 647215 TAGTTC - -a -s simMouse_chr6.simMouse.chr6 374075 12 + 636262 ATGGGGGCAAAC -s Anc0.Anc0refChr5 92 12 + 87904 ATGTAGGCAAAC -s Anc1.Anc1refChr6 34972 12 + 197743 ATGTAGGCAAAC -s Anc2.Anc2refChr14 92 12 + 7748 ATGTAGGCAAAC -s mr.mrrefChr5 220694 12 + 294540 ATGTAGGCAAAC -s simCow_chr6.simCow.chr6 346498 12 + 602619 ATGTAGACAAAC -s simDog_chr6.simDog.chr6 248903 12 - 593897 ATGTAGGCACAC -s simHuman_chr6.simHuman.chr6 358669 12 + 601863 ATGTAGGCTAAC -s simRat_chr6.simRat.chr6 366182 12 + 647215 ATGTAGGCAAAC - -a -s simMouse_chr6.simMouse.chr6 374087 41 + 636262 ATAGGTATCATTCTCAGGGCTCGAGGGTGTGAAAATTTATT -s Anc0.Anc0refChr5 104 41 + 87904 TGAGCCTTCAATCTGTAGGCTAGACAGTGTGAAAACTTATT -s Anc1.Anc1refChr6 34984 41 + 197743 TGAGCCTTCAATCTGTAGGCTAGACAGTGTGAAAACTTATT -s Anc2.Anc2refChr14 104 41 + 7748 TGAGCCTCCAATCTGTAGGCTAGTCAGTGTGGAAACTTCTT -s mr.mrrefChr5 220706 41 + 294540 TTAGGTATCATTCTCAGGGCTCGAGGGTGTGAAAATTTATT -s simCow_chr6.simCow.chr6 346512 41 + 602619 TGGGCCTCCGATCTGTAGGGTAGTCAGTGCGGACACTTCTT -s simDog_chr6.simDog.chr6 248915 41 - 593897 TGAGCCTCCAATTTATAGGCTAGTCAGTGTGGAAATTTCTT -s simHuman_chr6.simHuman.chr6 358681 41 + 601863 TGAGCCTTCAATCTGTTGTCTAGACAGCATGAAACCTTACT -s simRat_chr6.simRat.chr6 366194 41 + 647215 TTAGGTGCCACTCTAAGGGCTGAAGGGTGTGGAAATTTATT - -a -s simMouse_chr6.simMouse.chr6 374128 9 + 636262 TATATGTAG -s Anc0.Anc0refChr5 152 9 + 87904 TGTATGTAT -s Anc1.Anc1refChr6 35032 9 + 197743 TGTATGTAT -s Anc2.Anc2refChr14 152 9 + 7748 TGTATGTAT -s mr.mrrefChr5 220754 9 + 294540 TATATGTAG -s simCow_chr6.simCow.chr6 346560 9 + 602619 TGTATGTAT -s simDog_chr6.simDog.chr6 248959 9 - 593897 TGTATGTAT -s simHuman_chr6.simHuman.chr6 358729 9 + 601863 TGTATGTAT -s simRat_chr6.simRat.chr6 366242 9 + 647215 TAGATGTAG - -a -s simMouse_chr6.simMouse.chr6 374137 14 + 636262 TAAAAAGCAAAACT -s Anc0.Anc0refChr5 168 14 + 87904 TAGAGTGCAAAACA -s Anc1.Anc1refChr6 35048 14 + 197743 TAGAGTGCAAAACA -s Anc2.Anc2refChr14 168 14 + 7748 TAGAGTGCAAAACA -s mr.mrrefChr5 220763 14 + 294540 TAGAAAGCAAAACT -s simCow_chr6.simCow.chr6 346576 14 + 602619 TAGAGTGCAAAACA -s simDog_chr6.simDog.chr6 248975 14 - 593897 TAGAGTGCAGGACA -s simHuman_chr6.simHuman.chr6 358745 14 + 601863 TAGAGTGCAAAGCA -s simRat_chr6.simRat.chr6 366251 14 + 647215 TAGAAAGCAAAACT - -a -s simMouse_chr6.simMouse.chr6 374151 68 + 636262 ACTACGACAGTTGTTGCGTTGCTGTGTAGACAAAAGATATAGGTGTCAGATTGTTAGCATATCATGGC -s Anc0.Anc0refChr5 182 57 + 87904 ACTG-----------GATTTGCTGTGTGGGGAAAAGATATAGGCATCAAATTGTTAGCAAGTCATGTC -s Anc1.Anc1refChr6 35062 57 + 197743 ACTG-----------GATTTGCTGTGTGGGGAAAAGATATAGGCATCAAATTGTTAGCAAGTCATGTC -s Anc2.Anc2refChr14 182 57 + 7748 ACTG-----------GATTTGCTGTGTGGGGAAAAGTTATAGGCATCAAATTGGTAGCAAGTCATGTC -s mr.mrrefChr5 220777 68 + 294540 ACTACGACAGTTGTTGAGTTGCTGTGTAGAGAAAAGATATAGGTGTCAAATTGTTAGCATATCATGGC -s simCow_chr6.simCow.chr6 346591 57 + 602619 CCTT-----------GATTTATTGTGTTGGGAAAAGTTATAGGCATAAAATTGCTAGCAAGTCATATC -s simDog_chr6.simDog.chr6 248989 57 - 593897 ACTG-----------GATTTGCTGTGTGGGGAAAAGTTGTAGACATCAAGTTGGCAGCAAGTCATGTC -s simHuman_chr6.simHuman.chr6 358759 57 + 601863 ACTG-----------GATTTGCTGCATGGGGAAAAGATACAGGCATCAAATTGTTAGCAAGTCATGAG -s simRat_chr6.simRat.chr6 366265 68 + 647215 CCTACGACAGTCGTTGAGTTGCTGTGTAGAGAAAAGATATAGGTGTCAAATTCTTAGCATATCATGGC - -a -s simMouse_chr6.simMouse.chr6 374219 15 + 636262 CCACATGTAATACTA -s Anc0.Anc0refChr5 239 15 + 87904 CCACACATAGTGCTA -s Anc1.Anc1refChr6 35119 15 + 197743 CCACACATAGTGCTA -s Anc2.Anc2refChr14 239 15 + 7748 CCACACATAGTGATA -s mr.mrrefChr5 220845 15 + 294540 CCACATGTAATACTA -s simCow_chr6.simCow.chr6 346724 15 + 602619 CCACACATAATGGTA -s simDog_chr6.simDog.chr6 249046 15 - 593897 CCACACATAGTGATA -s simHuman_chr6.simHuman.chr6 358816 15 + 601863 TCACACATAGTGCTA -s simRat_chr6.simRat.chr6 366333 15 + 647215 CCACATGTTATACTA - -a -s simMouse_chr6.simMouse.chr6 374234 43 + 636262 ATCATGCAATACTAATCATGCTGATTGATGTTGCATACTATCT -s Anc0.Anc0refChr5 254 5 + 87904 ATCTT-------------------------------------- -s Anc1.Anc1refChr6 35134 5 + 197743 ATCTT-------------------------------------- -s Anc2.Anc2refChr14 256 5 + 7748 ATCTT-------------------------------------- -s mr.mrrefChr5 220860 34 + 294540 ATCATGCAATACTAATCATGCTGATTGATGTTGC--------- -s simCow_chr6.simCow.chr6 346741 5 + 602619 GTCAT-------------------------------------- -s simDog_chr6.simDog.chr6 249063 5 - 593897 ATCTT-------------------------------------- -s simHuman_chr6.simHuman.chr6 358831 5 + 601863 ATCCT-------------------------------------- -s simRat_chr6.simRat.chr6 366348 34 + 647215 ATCATGCAATACCAATCATGCTGATTGATGTTGC--------- - -a -s simMouse_chr6.simMouse.chr6 374277 62 + 636262 CTACCCTAAAGGTGTGCAGTCATAGTAGGTCTGCAGACTATAGAGATTAAATACTGTCTCAT -s Anc0.Anc0refChr3 8081 61 + 222631 ATACCTTAATGTGATGCTACTGTAGCAGGTTCCCAGACGAGGGAAACTAAACACGATCTCA- -s Anc1.Anc1refChr6 40873 62 + 197743 ATACCTTAATGTGATGCTACTGTAGCAGGTTCCCAGACGAGGGAAACTAAACACGATCTCAT -s Anc2.Anc2refChr13 10625 61 + 96486 ATACCTTAATGTGATACCACTGTAGCAGGTCACCAGATGAGCAAAACTAAATGCGATCTCA- -s mr.mrrefChr5 227991 62 + 294540 CTACCCTAAAGGTATGCTGTCATAGTAGGTTCCCAGACTATGGAGATTAAACACTGTCTCAT -s simCow_chr6.simCow.chr6 366182 61 + 602619 ATACCTTAATGTGATACCACTGTAGCAGGTCACCAGATGAGCAAAACTAAATGCGATCTCA- -s simHuman_chr6.simHuman.chr6 364699 62 + 601863 ATATCTGAGGATGATGCTCCTGTGGCAGGTTCCCAGACCAGGGGAGCTAAACACCATCTCAT -s simRat_chr6.simRat.chr6 373582 62 + 647215 CTACCCTGAAGGCATACTATCATAGTAAGTTCCCAGAATTTGGAGATTAAACACTGTCTCAT - -a -s simMouse_chr6.simMouse.chr6 374339 90 + 636262 TTTGGGTCACTATTACATTCCCTCCTCCTCAATGCATCTTAACAAGTTGGTTTGATTTAGATGAGGCTCTACAAAGTCTTATGAATATGC -s Anc0.Anc0refChr3 8143 81 + 222631 CATACATCACTA--ACATTACCCCTTCTTCAATGTATCTTGACAAGTTCA-TCATTT--TATGAGCCTCTTTAAAGTCTCAC----ATGC -s Anc1.Anc1refChr6 40936 86 + 197743 CATACATCACTA--ACATTACCCCTTCTTCAATGTATCTTGACAAGTTCA-TCATTTTATATGAGCCTCTTTAAAGTCTCAC-AATATGC -s Anc2.Anc2refChr13 10687 81 + 96486 CATACATTGCTC--ACACTACCCCCTCTTCAATGCATCTTGACAAGTTCA-TCATTT--TATGGGCCACCTTAAAGTCCCAC----ATGC -s mr.mrrefChr5 228053 89 + 294540 TGTATGTCACTATTACATTACCCCTTCCTCAATGTATCTTAACAAGTTGA-TTGATTTATATGAGCCTCTACAAAGTCTTATGAATATGC -s simCow_chr6.simCow.chr6 366244 81 + 602619 CATACATTGCTC--ACACTACCCCCTCTTCAATGCATCTTGACAAGTTCA-TCATTT--TATGGGCCACCTTAAAGTCCCAC----ATGC -s simHuman_chr6.simHuman.chr6 364764 86 + 601863 CATGCACCACTA--ACATTACTCCTTTTCCAATGTGTCTTGACAAGTTCA-TCATTTTATATGAGCCTTTGTAATGTCTCAC-AATATGC -s simRat_chr6.simRat.chr6 373644 89 + 647215 TGTATGTTGCTATTACATTAACCCTCCCTCAATGTATCTCAACAAGTTGA-TTGATTGATATGAGCCTCCACGAAGTTTTATGAGTTTGC - -a -s simMouse_chr6.simMouse.chr6 374429 11 + 636262 AGGTTACAAGA -s Anc0.Anc0refChr3 8224 11 + 222631 AAGCAACAAGA -s Anc1.Anc1refChr6 41022 11 + 197743 AAGCAACAAGA -s Anc2.Anc2refChr13 10768 11 + 96486 AAGCAACAAGA -s mr.mrrefChr5 228142 11 + 294540 AAGCTACAAGA -s simCow_chr6.simCow.chr6 366326 11 + 602619 AAGCAACAAGA -s simHuman_chr6.simHuman.chr6 364850 11 + 601863 AAGCACAATGC -s simRat_chr6.simRat.chr6 373733 11 + 647215 AAGCTACAAGA - -a -s simMouse_chr6.simMouse.chr6 374440 23 + 636262 CACCTTTTTTAGGCTCACAGTGT -s Anc0.Anc0refChr3 8236 23 + 222631 TGCCTTTTTTAGGCTCACAGTGC -s Anc1.Anc1refChr6 41034 23 + 197743 TGCCTTTTTTAGGCTCACAGTGC -s Anc2.Anc2refChr13 10780 23 + 96486 TGCCTCTTTTAGGCTCACATTGC -s mr.mrrefChr5 228153 23 + 294540 TGCCTTTTTTAGGCTCACAGTGT -s simCow_chr6.simCow.chr6 366338 23 + 602619 TGCCTCTTTTAGGCTCACATTGC -s simHuman_chr6.simHuman.chr6 364862 23 + 601863 TGCCTTTTTTAGGCTGACAGTGC -s simRat_chr6.simRat.chr6 373744 23 + 647215 TGCCTTTTTTAGTTTCACAGAGT - -a -s simMouse_chr6.simMouse.chr6 374463 40 + 636262 GAAAAGTGAGGATCTAAGTAGAGGTAAACCATAAGGAACA -s Anc0.Anc0refChr3 8259 34 + 222631 CAAAAGTGAGGACA------AAGAAAAGCAATGGTGGAAG -s Anc1.Anc1refChr6 41057 34 + 197743 CAAAAGTGAGGACA------AAGAAAAGCAATGGTGGAAG -s Anc2.Anc2refChr13 10803 34 + 96486 CACATGTGAGAACA------ATGAAAAGCAATGGTAGAAG -s mr.mrrefChr5 228176 40 + 294540 GAAAAGTGAGGATCTAAGTAAAGGTAAACCGTAAGGAACA -s simCow_chr6.simCow.chr6 366361 34 + 602619 CACATGTGAGAACA------ATGAAAAGCAATGGTAGAAG -s simHuman_chr6.simHuman.chr6 364885 34 + 601863 CGAAAGTGAGGACA------AAAAGAAGCAAAGGTGGCAG -s simRat_chr6.simRat.chr6 373768 40 + 647215 GAAAAGTGAGGATCTAAGTAAAGGGAAACCGTAAAGAACA - -a -s simMouse_chr6.simMouse.chr6 374503 106 + 636262 AAAAGAATAAAATCTAGGATAGAGGACACAAGAGTCAACTTTGTTCTTACCAAGGACAATTTTTAGATACTTTCACTCACTCAAGACGCCCCTAAGAATACTGAGC -s Anc0.Anc0refChr3 8293 100 + 222631 TAAAGAACAAGAACTGAGGTAGCAAACA-AACAGTTAGCTTGCC-CTTACCCAAGACAATTTTTAGATAC----ATTCACTTGAGGCCCCACTAAGTATACTGAGC -s Anc1.Anc1refChr6 41091 100 + 197743 TAAAGAACAAGAACTGAGGTAGCAAACA-AACAGTTAGCTTGCC-CTTACCCAAGACAATTTTTAGATAC----ATTCACTTGAGGCCCCACTAAGTATACTGAGC -s Anc2.Anc2refChr13 10837 100 + 96486 TAAAGAACAAGAACTGAGGCAGCAAACA-AACAGTTTGCTTGCC-CTTACACAAGACAATTTTTAGATAG----ATTTGCTTGAGGCCCCACCAAGTATACTGAGC -s mr.mrrefChr5 228216 106 + 294540 AAAAGAACAAAGTCTAGGATAGAGGACACAAGAGTTAACTTTGCTCTTACCAAAGACAATTTTTAGATACTTTCACTCACTCAAGACGCCACTAAGTATACTGAGC -s simCow_chr6.simCow.chr6 366396 93 + 602619 TAAAGAACAGGAACTAAGGGAGATAACA-GACAGTTTGCTTTTC-CTTAC------CGATTTTTAAATAG----ACTTGCTTAAGGCCTCACCAATTATACTCAG- -s simDog_chr6.simDog.chr6 356971 94 + 593897 ------ACCACAGCTGAGTCAGCAGCCC-AACAGTGTGCTTGCC-CTTACACAAGACAAGTTCTAGATAG----GTTTGCTTGAGGCCCTACCAAGTATACTGAAC -s simHuman_chr6.simHuman.chr6 364919 97 + 601863 CAAAGAAGAAGAACTGAGGTAAGAAACA----AGTTAGCGTGAC-CTTGCCCGAGACAATTTTTATATAC----ATTCACTTGAAGTCCCACTAAGTATACTGAGC -s simRat_chr6.simRat.chr6 373808 106 + 647215 AAAAGAACAACGACTAGGAGAGAGCACACAAGAGTTGACTTTGCACTTACCAAAGACAATTTTTAGAGCCTTTCGCTCGCTCAAGACACCACTAAGTATACTGGGC - -a -s simMouse_chr6.simMouse.chr6 374609 14 + 636262 TTTAAGCTACATAG -s Anc0.Anc0refChr3 8393 14 + 222631 TTTATGTTACTCAG -s Anc1.Anc1refChr6 41191 14 + 197743 TTTATGTTACTCAG -s Anc2.Anc2refChr13 10937 14 + 96486 TTTATGTTACTCAG -s mr.mrrefChr5 228322 14 + 294540 TTTAAGTTACTTAG -s simCow_chr6.simCow.chr6 366489 14 + 602619 TGTATGTTACTCAG -s simDog_chr6.simDog.chr6 357075 14 + 593897 TTTATGTTACCCAG -s simHuman_chr6.simHuman.chr6 365016 14 + 601863 TCTATGTTACTCAG -s simRat_chr6.simRat.chr6 373914 14 + 647215 TTAAAGTTACTTAG - -a -s simMouse_chr6.simMouse.chr6 374623 3 + 636262 AAA -s Anc0.Anc0refChr3 8407 3 + 222631 AAA -s Anc1.Anc1refChr6 41205 3 + 197743 AAA -s Anc2.Anc2refChr13 10951 3 + 96486 AAA -s mr.mrrefChr5 228336 3 + 294540 AAA -s simCow_chr6.simCow.chr6 366503 3 + 602619 AAA -s simDog_chr6.simDog.chr6 357090 3 + 593897 AAA -s simHuman_chr6.simHuman.chr6 365030 3 + 601863 AAT -s simRat_chr6.simRat.chr6 373928 3 + 647215 AAA - -a -s simMouse_chr6.simMouse.chr6 374626 11 + 636262 TGCATGGATCG -s Anc0.Anc0refChr3 8410 11 + 222631 TGCACAGATAA -s Anc1.Anc1refChr6 41208 11 + 197743 TGCACAGATAA -s Anc2.Anc2refChr13 10955 11 + 96486 TGCACAGATAA -s mr.mrrefChr5 228339 11 + 294540 TGCATGGATAG -s simCow_chr6.simCow.chr6 366507 11 + 602619 TGCACAGATAA -s simDog_chr6.simDog.chr6 357094 11 + 593897 TGCACAGATGA -s simHuman_chr6.simHuman.chr6 365033 11 + 601863 TGCAGAGATAA -s simRat_chr6.simRat.chr6 373931 11 + 647215 TGCATGGATAG - -a -s simMouse_chr6.simMouse.chr6 374637 50 + 636262 TCTTGTATTCCCATCAATTCCAGCTCTCTTAGGACCCCACTATGGGCAAA -s Anc0.Anc0refChr3 8424 50 + 222631 TTTCGCCTTCCCCTCAATTGCAGGTATCCCCAAACCCTGTTTTTGGCAAA -s Anc1.Anc1refChr6 41222 50 + 197743 TTTCGCCTTCCCCTCAATTGCAGGTATCCCCAAACCCTGTTTTTGGCAAA -s Anc2.Anc2refChr13 10969 50 + 96486 TTTCACCTTCTCCTCAATTGCAGCTATCCCCAAACTCTGTTTTTGGCAAA -s mr.mrrefChr5 228350 50 + 294540 TTTTGTATTCCCCTCAATTCCAGGTCTCTCAGGACCTCACTTTGGGCAAA -s simCow_chr6.simCow.chr6 366521 50 + 602619 TTAATCCTTCTCCTCAATTGCATATCTCCCCAAACTCTGTTTCCAGGAAA -s simDog_chr6.simDog.chr6 357108 50 + 593897 CTTCACCTTCTCCTCAATTGGAGCTATCCCCAAACTCTGTTTTTGGCAAA -s simHuman_chr6.simHuman.chr6 365047 50 + 601863 TTTCGCCTTCCCCTGACTTGCAGGTTTTCCCCACACCTGTTTTTGGCAAA -s simRat_chr6.simRat.chr6 373942 50 + 647215 CTTTGTATTCCCCTCAATTCCAGGTCTCACATGACCTAACTTTGGGCAAA - -a -s simMouse_chr6.simMouse.chr6 374687 20 + 636262 AGACCAGAATCACACAGGTA -s Anc0.Anc0refChr3 8475 20 + 222631 CTCCCAGAATCACCCAGGCA -s Anc1.Anc1refChr6 41273 20 + 197743 CTCCCAGAATCACCCAGGCA -s Anc2.Anc2refChr13 11020 20 + 96486 CTCCCAGAATCACCCAGGCT -s mr.mrrefChr5 228400 20 + 294540 AGACCAGAATCACACAGGTA -s simCow_chr6.simCow.chr6 366572 20 + 602619 CTCCCAGAATCACCCAGGCA -s simDog_chr6.simDog.chr6 357159 20 + 593897 ATTCCAGAACCGCCCAGGCT -s simHuman_chr6.simHuman.chr6 365098 20 + 601863 CTCCCAGAATCACCCAGGCA -s simRat_chr6.simRat.chr6 373992 20 + 647215 AGACCAGAATCACACAGGTA - -a -s simMouse_chr6.simMouse.chr6 374707 23 + 636262 TAATCAGCTGTGTTATGCATGTC -s Anc0.Anc0refChr3 8495 23 + 222631 TAATCAGCTCTATTGTGTATGTC -s Anc1.Anc1refChr6 41293 23 + 197743 TAATCAGCTCTATTGTGTATGTC -s Anc2.Anc2refChr13 11040 23 + 96486 TAATCAGCTCTATTGTGTATATC -s mr.mrrefChr5 228420 23 + 294540 TAATCAGCTGTGTTGTGCATGTC -s simCow_chr6.simCow.chr6 366592 23 + 602619 TAATAAGGTTTATTGTGTATATC -s simDog_chr6.simDog.chr6 357179 13 + 593897 TAATCAGCTCTA----------A -s simHuman_chr6.simHuman.chr6 365126 23 + 601863 TAACCAGCTCTATTGTATATGTC -s simRat_chr6.simRat.chr6 374012 23 + 647215 TAATCAGCTGTGTTGTGCATGTC - -a -s simMouse_chr6.simMouse.chr6 374730 5 + 636262 AGGGA -s Anc0.Anc0refChr3 8519 5 + 222631 AGCTA -s Anc1.Anc1refChr6 41317 5 + 197743 AGCTA -s Anc2.Anc2refChr13 11064 5 + 96486 AGCTA -s mr.mrrefChr5 228443 5 + 294540 AGCGA -s simCow_chr6.simCow.chr6 366618 5 + 602619 AACTA -s simDog_chr6.simDog.chr6 357193 5 + 593897 AGCTA -s simHuman_chr6.simHuman.chr6 365150 5 + 601863 AGCAA -s simRat_chr6.simRat.chr6 374035 5 + 647215 AGCTA - -a -s simMouse_chr6.simMouse.chr6 374735 130 + 636262 TGGTGCAACTGTTAATATGCAATCCTGAATGGCTATTACATACCATTTAATTTCTTGGCATGCTTATTTTTTGGCATGCTTCATTGTCTTTCAACAGCTGTGGAATTCGTGTCTATAACATCCCCTGGAC -s Anc0.Anc0refChr3 8524 37 + 222631 TTGTGCAACTCTCATTATGCAATTCTGATTG---------------------------------------------------------------------------------------------CTACAC -s Anc1.Anc1refChr6 41322 37 + 197743 TTGTGCAACTCTCATTATGCAATTCTGATTG---------------------------------------------------------------------------------------------CTACAC -s Anc2.Anc2refChr13 11069 37 + 96486 TTGTGCAACTCTCATTATGCAGTTCTAATCG---------------------------------------------------------------------------------------------CCACAC -s mr.mrrefChr5 228448 114 + 294540 TGGTGCAACTCTTATTATGCAATCCTGAATGGCTATTACATACCATTTA----------------ATTTTTTGGCATGCTTCATTGTCTTTCAACAGCTGTGGAATTCGTGTCTATAACATCCCCTGGAC -s simCow_chr6.simCow.chr6 366627 37 + 602619 TTGTGCAACTTTCGTTTTGCAGTCCTCATCA---------------------------------------------------------------------------------------------CAACAC -s simDog_chr6.simDog.chr6 357198 37 + 593897 CTGTGCAATTCTCATTATGCAGTTCCAATCG---------------------------------------------------------------------------------------------TCACAC -s simHuman_chr6.simHuman.chr6 365155 37 + 601863 TTGTGCAACTCTCATTATGCAATTCTGATTG---------------------------------------------------------------------------------------------CTACAC -s simRat_chr6.simRat.chr6 374040 114 + 647215 TGGTGAACCTCTTATTACACAATCCTGTATAACACTCATGTAACAGTTA----------------ATCTTTTGGCATGCTTCAGTGTCTTTCAACAGCTGCAGAATTGGTGTCTATAAAATTCTGTGAAC - -a -s simMouse_chr6.simMouse.chr6 374865 134 + 636262 CCAGTCTTCTTTTACCTTTACTCCTACGTTTGACTGGCATGTTCAAAGGGAGTGAGAAAATTCCCATATCTCTCAAGTGTGGGACCAACCTGTGACATATTCACTGAAAGGGTGTTAAGCAACTATGTCTATTC -s Anc0.Anc0refChr3 8561 94 + 222631 CCAGTCTCCTCTAACCCATACTGCCATG-----------------------------------TTATA--TCTCAGGAGCAGGACCTAACTGCGAAACGTTCACTGATTAG--GCCAAGCAATTAGGTCTAA-C -s Anc1.Anc1refChr6 41359 116 + 197743 CCAGTCTCCTCTAACCCATACTGCCATGTTTGA-----------AAGGGG---GAGCTAATTCTTATA--TCTCAGGAGCAGGACCTAACTGCGAAACGTTCACTGATTAG--GCCAAGCAATTAGGTCTAATC -s Anc2.Anc2refChr13 11107 94 + 96486 TCAGTCGCCTCCAACCCATACTGCCATG-----------------------------------TTACT--TCTCAGGAGCAGGACCTTACTGCAAAACATTCACTGATTAG--GCCAAGCAATTAGGTCTTA-C -s mr.mrrefChr5 228562 130 + 294540 CCAGTCTTCTTTTACCTTTACTCCCATGTTTGACTGGCATGTTCAAAGGGAGTGAGAAAATTCCTATA--TCTCAAGTGTGGGACCAACCTGTGACATGTTCACTGAAAGG--GTTAAGCAACTATGTCTATTC -s simCow_chr6.simCow.chr6 366665 81 + 602619 TCAGTCGTCTCCCACTCATATTGTCACG-----------------------------------TTACC--TTTC-------GGAGCTCAC------ACATTCACAGGTCAG--GCCAAGCAATTAGGTCTTT-C -s simDog_chr6.simDog.chr6 357236 94 + 593897 TCAGTTGCCTCCAATCTGTACTGCCATG-----------------------------------TTACT--TCTCAGGAGCAGGACCTTCCTGCAAAACACTCACTGACTAG--TCCAAGCGATTAGGTTTTA-C -s simHuman_chr6.simHuman.chr6 365192 116 + 601863 CCAGTCTCATCTAACCCATACTGCCATGTTTGA-----------AAGGGG---GAGCTAATTCTTATA--TCTCAGGAGCAGGGCCTAACTGCGATACGTACACTGATTAG--GCCAAGCAAATAGATCTAATC -s simRat_chr6.simRat.chr6 374154 130 + 647215 CCAGTCATCTTCTATCTTTACTCCCATGTTTAAGTGGCATGTTCAAAGCGAGTGAGTCAACTCCTATA--TCTCAAGTATGGGACCAACCTGTGACATGTTCACTGAAAGG--GTTAAGCAAGTATGTCTTTTC - -a -s simMouse_chr6.simMouse.chr6 374999 30 + 636262 TTCCATCTTGAGACATCCAGTTTCTGCTAT -s Anc0.Anc0refChr3 8655 30 + 222631 TTTCATCTTGAACCTTTTAGTTTTTGCTAT -s Anc1.Anc1refChr6 41475 30 + 197743 TTTCATCTTGAACCTTTTAGTTTTTGCTAT -s Anc2.Anc2refChr13 11201 30 + 96486 CTTCATCTTGAACCTTTTTGTTTTTGCTAT -s mr.mrrefChr5 228692 30 + 294540 TTTCATCTTGAGACATCTAGTTTCTGCTAT -s simCow_chr6.simCow.chr6 366746 30 + 602619 CTTCATTTTGACACTTTTTGTTTTTGTTAT -s simDog_chr6.simDog.chr6 357330 30 + 593897 CTGCATCTTGAACCTTATTGTTTTTGCCAT -s simHuman_chr6.simHuman.chr6 365321 30 + 601863 CTTCATCTTGATCCTTTTAGTTTTTGCTAT -s simRat_chr6.simRat.chr6 374284 30 + 647215 TTTCATCTTGAGACATCTAGTTTCTGCTAT - -a -s simMouse_chr6.simMouse.chr6 375029 2 + 636262 GG -s Anc0.Anc0refChr3 8686 2 + 222631 GG -s Anc1.Anc1refChr6 41506 2 + 197743 GG -s Anc2.Anc2refChr13 11232 2 + 96486 GG -s mr.mrrefChr5 228722 2 + 294540 GG -s simCow_chr6.simCow.chr6 366777 2 + 602619 GG -s simDog_chr6.simDog.chr6 357361 2 + 593897 GG -s simHuman_chr6.simHuman.chr6 365352 2 + 601863 GG -s simRat_chr6.simRat.chr6 374314 2 + 647215 GA - -a -s simMouse_chr6.simMouse.chr6 375031 16 + 636262 TGTGAATCAAGTGTTC -s Anc0.Anc0refChr3 8688 16 + 222631 TGTGAGTCAGGTGTTC -s Anc1.Anc1refChr6 41508 16 + 197743 TGTGAGTCAGGTGTTC -s Anc2.Anc2refChr13 11235 16 + 96486 TGTGAGTCAGGTGTGG -s mr.mrrefChr5 228724 16 + 294540 TGTGAATCAAGTGTTC -s simCow_chr6.simCow.chr6 366780 16 + 602619 TGTGAGTCAAGTCTCG -s simDog_chr6.simDog.chr6 357364 16 + 593897 TGTGAGTTAGGTGTGG -s simHuman_chr6.simHuman.chr6 365354 16 + 601863 AGTTAGTCAGATGTTC -s simRat_chr6.simRat.chr6 374316 15 + 647215 TGTGAATCAA-TGTTT - -a -s simMouse_chr6.simMouse.chr6 375047 7 + 636262 ACTGGCT -s Anc0.Anc0refChr3 8713 7 + 222631 ACTGGCT -s Anc1.Anc1refChr6 41533 7 + 197743 ACTGGCT -s Anc2.Anc2refChr13 11260 7 + 96486 ACTGGCT -s mr.mrrefChr5 228748 7 + 294540 ACTGGCT -s simCow_chr6.simCow.chr6 366805 7 + 602619 ACTGGCT -s simDog_chr6.simDog.chr6 357389 7 + 593897 ACTGGCT -s simHuman_chr6.simHuman.chr6 365379 7 + 601863 ACTGGCT -s simRat_chr6.simRat.chr6 374339 7 + 647215 ACTGGCT - -a -s simMouse_chr6.simMouse.chr6 375054 34 + 636262 TTATTAGCTGTCAAGTTTTTATAATTGAATGTGC -s Anc0.Anc0refChr3 8726 26 + 222631 TTCTAACCTGTGTAGTTTATACTAT--------C -s Anc1.Anc1refChr6 41546 26 + 197743 TTCTAACCTGTGTAGTTTATACTAT--------C -s Anc2.Anc2refChr13 11273 26 + 96486 TTCTAACCTGTGTAGTTTATAACAT--------C -s mr.mrrefChr5 228755 34 + 294540 TTATTAGCTGTGAAGTTTATACTATTGAATGTGC -s simCow_chr6.simCow.chr6 366818 26 + 602619 CTCTGACCTGCGTAGTTTATAACAT--------C -s simDog_chr6.simDog.chr6 357402 26 + 593897 TTCTAACCTGTTTAGTTTATAACAC--------C -s simHuman_chr6.simHuman.chr6 365392 19 + 601863 T-------AATGTAGTTTATTCTAT--------C -s simRat_chr6.simRat.chr6 374346 34 + 647215 TTCATAGCTGTGAAGTTTACACTATCAGATGTGC - -a -s simMouse_chr6.simMouse.chr6 375088 96 + 636262 CTTCAGCCCAGCAAACTGGGAACTCCAAGATTTTCAACTGGGTATACCTACTAACATCCTCTACCTGCATAGTTCTCTCAGGATTTAGACAAGAGT -s Anc0.Anc0refChr3 8752 91 + 222631 CTTCACTTCAAAAGTGTAGGAACACCAAGATTTTCAATGGGATATCCCTATCCACATCCTCTATCTG-----TTCTCTCAGGCTTAAGATGAGAGT -s Anc1.Anc1refChr6 41572 91 + 197743 CTTCACTTCAAAAGTGTAGGAACACCAAGATTTTCAATGGGATATCCCTATCCACATCCTCTATCTG-----TTCTCTCAGGCTTAAGATGAGAGT -s Anc2.Anc2refChr13 11306 91 + 96486 CTTCACTTCAAAGGTGTAGGAACACCAAGATTTTCAATGGGATATCCCTATCCACATCCTCCATCTG-----TTTCCTCAGGCTTAACATGCGAGT -s mr.mrrefChr5 228789 96 + 294540 CTTCAGCCCAGCAGTGTGGGAACTCCAAGATTTTCAACTGGATATCCCTACTAACATCCTCTACCTGCATAGTTCTCTCAGGATTTAGACAAGAGT -s simCow_chr6.simCow.chr6 366851 57 + 602619 CTTCACTTCATTGGTGTAGCAACTCCAGAATCTTCGACGGGATATCCCTAACTACAT--------------------------------------- -s simDog_chr6.simDog.chr6 357435 91 + 593897 CTTCACTTCAAAGGTATATGGACACTGAGATTTTCAATGGCAAAGCCCTATCCACATCCTCCATCTG-----TTTCCTCAGGCTTAACATGCGAGT -s simHuman_chr6.simHuman.chr6 365411 91 + 601863 TCTCACTGCAAAAGTGTAGGAACACCAAGACTTTCAATGAGATATCCCTATCCTCATCCTCTATCTG-----TTCTCTCGGGCTTAAGATGAGAGT -s simRat_chr6.simRat.chr6 374380 96 + 647215 CTTCAGCTCAGCAGTGTGGGAACTCCAAGATCTTCAACTGGATGTCCCTACTAACATCCTCTACCTGCACAGTTTTCTCAGGGTTTAGACAATAGT - -a -s simMouse_chr6.simMouse.chr6 375184 44 + 636262 TACATTATTCAAGGGGAGGTATTAGTCAAGCGTATTCAATTGAA -s Anc0.Anc0refChr3 8844 34 + 222631 TACATTTTTCAATTGGGGGTATTGTTTTGCAGTG---------- -s Anc1.Anc1refChr6 41664 34 + 197743 TACATTTTTCAATTGGGGGTATTGTTTTGCAGTG---------- -s Anc2.Anc2refChr13 11398 34 + 96486 TACATTTTTCAATTGGGGGTATTGTTTTGCAGTG---------- -s mr.mrrefChr5 228885 44 + 294540 TACATTATTCAAGTGGAGGTATTGGTCTAGCGTATTCAATTGAA -s simDog_chr6.simDog.chr6 357527 34 + 593897 TACATTTTTCAATTGGGGGTATTGTTTTGCAGTG---------- -s simHuman_chr6.simHuman.chr6 365503 34 + 601863 GACATGTTTCGAATGGGGGTGTTGCTTTGTAGTG---------- -s simRat_chr6.simRat.chr6 374476 43 + 647215 TACATTATTCAAGTGG-GGTATTGTTCTAGTGTATTCAATTGAA - -a -s simMouse_chr6.simMouse.chr6 375228 3 + 636262 GAT -s Anc0.Anc0refChr3 8885 3 + 222631 ATC -s Anc1.Anc1refChr6 41705 3 + 197743 ATC -s Anc2.Anc2refChr13 11439 3 + 96486 GTC -s mr.mrrefChr5 228936 3 + 294540 ATT -s simDog_chr6.simDog.chr6 357568 3 + 593897 GTC -s simHuman_chr6.simHuman.chr6 365544 3 + 601863 ATC -s simRat_chr6.simRat.chr6 374527 3 + 647215 ATT - -a -s simMouse_chr6.simMouse.chr6 375231 5 + 636262 CAATC -s Anc0.Anc0refChr3 8889 5 + 222631 TAATA -s Anc1.Anc1refChr6 41709 5 + 197743 TAATA -s Anc2.Anc2refChr13 11443 5 + 96486 TAATA -s mr.mrrefChr5 228939 5 + 294540 CAATC -s simCow_chr6.simCow.chr6 366908 5 + 602619 TAATA -s simDog_chr6.simDog.chr6 357572 5 + 593897 TAACA -s simHuman_chr6.simHuman.chr6 365548 5 + 601863 TAATA -s simRat_chr6.simRat.chr6 374530 5 + 647215 CAATT - -a -s simMouse_chr6.simMouse.chr6 375236 13 + 636262 AGTGTCTATCAAC -s Anc0.Anc0refChr3 8901 13 + 222631 AGTCCTGATCAAC -s Anc1.Anc1refChr6 41721 13 + 197743 AGTCCTGATCAAC -s Anc2.Anc2refChr13 11455 13 + 96486 AGTCCTGATCAAC -s mr.mrrefChr5 228951 13 + 294540 AGTGTCTATCAAC -s simCow_chr6.simCow.chr6 366920 13 + 602619 CGTCCTGGTCAAC -s simDog_chr6.simDog.chr6 357584 13 + 593897 AGTCGTGATCAAC -s simHuman_chr6.simHuman.chr6 365560 13 + 601863 AGTCCAGATCAAC -s simRat_chr6.simRat.chr6 374542 13 + 647215 AGGGTCTATCAAC - -a -s simMouse_chr6.simMouse.chr6 375249 35 + 636262 ACCATGCTCACTATACATTTCAGTGAACATAAGTA -s Anc0.Anc0refChr3 8914 33 + 222631 ACCATGCTCACTGTGTATTTCAGAAAAC--ATGTA -s Anc1.Anc1refChr6 41734 33 + 197743 ACCATGCTCACTGTGTATTTCAGAAAAC--ATGTA -s Anc2.Anc2refChr13 11468 33 + 96486 ACCATGCTCACTGTGTATTACAGAAACC--ATGAA -s mr.mrrefChr5 228964 33 + 294540 ACCATGCTCACTATACATTTCAGTGAAC--AAGTA -s simCow_chr6.simCow.chr6 366933 32 + 602619 ACTA-GCTCACTGTATATTACAGTAAGT--ATAGA -s simDog_chr6.simDog.chr6 357597 32 + 593897 ACCATG-TCACTGTGTATTACTGAAACC--ATGAG -s simHuman_chr6.simHuman.chr6 365573 33 + 601863 ACCATGCTCACTGTCTATTTCAGAAAAC--ATGTA -s simRat_chr6.simRat.chr6 374556 30 + 647215 ACCATGGTCACAATACATTTTAGTG-----AAGTA - -a -s simMouse_chr6.simMouse.chr6 375284 35 + 636262 ATGTATAATCTAGTTAGGAACAAACCTGTTTATTG -s Anc0.Anc0refChr3 8949 35 + 222631 ATGTGTGATTTAGTTGGGAAGTATCTCTTTCATTG -s Anc1.Anc1refChr6 41769 35 + 197743 ATGTGTGATTTAGTTGGGAAGTATCTCTTTCATTG -s Anc2.Anc2refChr13 11503 35 + 96486 ATTTGTGATTTAGTTGGGAAGTATCTCTTTCATTG -s mr.mrrefChr5 228997 35 + 294540 ATGTATAATCTAGTTGGGAACAAACCCGTTTATTG -s simCow_chr6.simCow.chr6 366967 35 + 602619 ATATGTAATTTGGTCGGGAAGTATCTCTTTCATTA -s simDog_chr6.simDog.chr6 357631 35 + 593897 ATTTGTGATTTAGTTGGGTAGTAGCTGTTTAATTG -s simHuman_chr6.simHuman.chr6 365608 33 + 601863 ATGTGTGG--TAGGTGAGAATTATCTCTTCCATTG -s simRat_chr6.simRat.chr6 374586 35 + 647215 ATGTATAATCTAGTTGGGAAGAAACCCGTTTATTG - -a -s simMouse_chr6.simMouse.chr6 375319 31 + 636262 ATAGTTTGTGACTCATAGACCTCAGTGGCAC -s Anc0.Anc0refChr3 8984 31 + 222631 ATAATTTGTGGTCCCTTGACGTGAGTGGCTC -s Anc1.Anc1refChr6 41804 31 + 197743 ATAATTTGTGGTCCCTTGACGTGAGTGGCTC -s Anc2.Anc2refChr13 11538 31 + 96486 ATAATTTGTGGTCCCTTGATGTGAGTGGCTC -s mr.mrrefChr5 229032 31 + 294540 ATAGTTTGTGATTCCTTGACCTCAGTGGCAC -s simCow_chr6.simCow.chr6 367050 31 + 602619 ATAAATTGTAGTTCCTTCATGTCAGTGGCTC -s simDog_chr6.simDog.chr6 357666 28 + 593897 ATCGT---GGGTCCTTTGATCCGAGTGGCTC -s simHuman_chr6.simHuman.chr6 365641 31 + 601863 ATAATTTGTGGTCCCTTGACGTGAATGGCTC -s simRat_chr6.simRat.chr6 374621 31 + 647215 ATAGTTTGTGTTTCCTTGACCTCAGTGGCAC - -a -s simMouse_chr6.simMouse.chr6 375350 76 + 636262 AAATTAAGAATATGTCTGGCTTCAACGGAGGATGCTGTTACTACTATATATTATTATTGTACATATTACTACTGTA -s Anc0.Anc0refChr3 9017 76 + 222631 AGACTGAGAATGTATCTGTCTTCTTTGATAGATGCTGCTACTTCTATGTATTATTACTACACATACTACAGATGAA -s Anc1.Anc1refChr6 41837 76 + 197743 AGACTGAGAATGTATCTGTCTTCTTTGATAGATGCTGCTACTTCTATGTATTATTACTACACATACTACAGATGAA -s Anc2.Anc2refChr13 11571 76 + 96486 AGACTGAGAATGTATCAATCTTCTTTAATAGACGCTACTACTTCTATGTATTCTTGCTACACATACTACAGATGAA -s mr.mrrefChr5 229065 76 + 294540 AAATTAAGAATATGTCTGGCTTCAACGGAGGATGCTGTTACTACTATATATTATTACTGTACATATTACTAATGTA -s simCow_chr6.simCow.chr6 367083 73 + 602619 AGACTGAGAATGCATCAGTCGTCT---ATAGAAGACACAACTTCTATGTATTCTTGCTGCACATATTACAGATGAA -s simDog_chr6.simDog.chr6 357696 76 + 593897 AGGCCATGCATGTATCAATCTTCTTTAATAGACGCTACTACTTCTATGTATTCTTGCTACACACACTGCAAATGAA -s simHuman_chr6.simHuman.chr6 365674 72 + 601863 AGACTGAGAATGTATCTGCTT----TGTGAGATGTTGCTTCTTCTATGTATTATTACTACACATACTACAGATGAA -s simRat_chr6.simRat.chr6 374654 76 + 647215 AAATTAAGAATATGTCTGTCTTCAATGCAGGATGCTGTCACTGCTATATATTGTTACTCTACATTTTACCAATGTA - -a -s simMouse_chr6.simMouse.chr6 375426 12 + 636262 GTCAAAGGGGTA -s Anc0.Anc0refChr3 9094 10 + 222631 GTCAGAGG--TA -s Anc1.Anc1refChr6 41914 10 + 197743 GTCAGAGG--TA -s Anc2.Anc2refChr13 11648 10 + 96486 ATCAAAGG--CA -s mr.mrrefChr5 229141 12 + 294540 GTCAGAGGGGTA -s simCow_chr6.simCow.chr6 367157 10 + 602619 ATCCCGGG--AA -s simDog_chr6.simDog.chr6 357773 10 + 593897 ATCAAAGG--CA -s simHuman_chr6.simHuman.chr6 365747 10 + 601863 GTCAGAGG--TA -s simRat_chr6.simRat.chr6 374730 12 + 647215 ATCAGAGGGGTG - -a -s simMouse_chr6.simMouse.chr6 375438 10 + 636262 AGCTAACTCC -s Anc0.Anc0refChr3 9104 10 + 222631 AAAGAGCTTA -s Anc1.Anc1refChr6 41924 10 + 197743 AAAGAGCTTA -s Anc2.Anc2refChr13 11658 10 + 96486 AAAGAGCTTA -s mr.mrrefChr5 229153 10 + 294540 AGCTAACTCC -s simCow_chr6.simCow.chr6 367167 10 + 602619 AAAGAGCCTA -s simDog_chr6.simDog.chr6 357784 10 + 593897 ATAGTGCTTA -s simHuman_chr6.simHuman.chr6 365757 10 + 601863 AAACAGCTTA -s simRat_chr6.simRat.chr6 374742 10 + 647215 AGCTAACTCC - -a -s simMouse_chr6.simMouse.chr6 375448 27 + 636262 ATGATCATTTTTTCAAGTGAGAAAAGA -s Anc0.Anc0refChr3 9114 27 + 222631 AGGATCACGTTGTCAACTGTGGATAGA -s Anc1.Anc1refChr6 41934 27 + 197743 AGGATCACGTTGTCAACTGTGGATAGA -s Anc2.Anc2refChr13 11668 27 + 96486 AGGATCACGTTGTCAACTGTGGATAGA -s mr.mrrefChr5 229163 27 + 294540 ATGATCATTTTTTCAAGTGAGAAAAGA -s simCow_chr6.simCow.chr6 367179 27 + 602619 AGAATCACTTTGTCAACTGTGGATAGA -s simDog_chr6.simDog.chr6 357794 27 + 593897 AGGATCATGTTGTCAACTGTGGATAGA -s simHuman_chr6.simHuman.chr6 365767 27 + 601863 AGGATCACGTTATCAACTGTGGATAGA -s simRat_chr6.simRat.chr6 374752 27 + 647215 ATTATCATCTTGTCGAGTGAGCAAAAA - -a -s simMouse_chr6.simMouse.chr6 375475 3 + 636262 CCA -s Anc0.Anc0refChr3 9141 3 + 222631 GCA -s Anc1.Anc1refChr6 41961 3 + 197743 GCA -s Anc2.Anc2refChr13 11695 3 + 96486 GCA -s mr.mrrefChr5 229190 3 + 294540 CCA -s simCow_chr6.simCow.chr6 367206 3 + 602619 GCA -s simDog_chr6.simDog.chr6 357826 3 + 593897 GCA -s simHuman_chr6.simHuman.chr6 365794 3 + 601863 GCA -s simRat_chr6.simRat.chr6 374779 3 + 647215 CCA - -a -s simMouse_chr6.simMouse.chr6 375478 1 + 636262 A -s Anc0.Anc0refChr3 9145 1 + 222631 A -s Anc1.Anc1refChr6 41965 1 + 197743 A -s Anc2.Anc2refChr13 11699 1 + 96486 A -s mr.mrrefChr5 229193 1 + 294540 A -s simCow_chr6.simCow.chr6 367210 1 + 602619 A -s simDog_chr6.simDog.chr6 357830 1 + 593897 A -s simHuman_chr6.simHuman.chr6 365798 1 + 601863 A -s simRat_chr6.simRat.chr6 374782 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 375479 103 + 636262 TCCTGCCATGTCCTATTGTTCGAGGTGTCAACTGGTTTGTTTAATGGTACCAGGGTGTTATGATCTCTCTAAATGCATCTTGGCTTTTCTAGTTTCAGACCTG -s Anc0.Anc0refChr3 9146 6 + 222631 T----CCT---------------------------------------------------------------------------------------------TG -s Anc1.Anc1refChr6 41966 10 + 197743 TCCTGCCT---------------------------------------------------------------------------------------------TG -s Anc2.Anc2refChr13 11700 6 + 96486 T----CCT---------------------------------------------------------------------------------------------TG -s mr.mrrefChr5 229194 10 + 294540 TCCTGCCA---------------------------------------------------------------------------------------------TG -s simCow_chr6.simCow.chr6 367216 6 + 602619 T----GCT---------------------------------------------------------------------------------------------TA -s simDog_chr6.simDog.chr6 357831 6 + 593897 T----CCT---------------------------------------------------------------------------------------------TG -s simHuman_chr6.simHuman.chr6 365799 10 + 601863 TAATGCCT---------------------------------------------------------------------------------------------TG -s simRat_chr6.simRat.chr6 374783 10 + 647215 TCCTGCCA---------------------------------------------------------------------------------------------TG - -a -s simMouse_chr6.simMouse.chr6 375582 14 + 636262 TCCTATTGTTGGAG -s Anc0.Anc0refChr3 9178 8 + 222631 GCTTAT------AG -s Anc1.Anc1refChr6 42002 8 + 197743 GCTTAT------AG -s Anc2.Anc2refChr13 11736 8 + 96486 GTTTAT------AG -s mr.mrrefChr5 229204 14 + 294540 TCCTATTGTTGGAG -s simCow_chr6.simCow.chr6 367252 8 + 602619 GTTTAT------AG -s simDog_chr6.simDog.chr6 357867 8 + 593897 GTTTAT------GG -s simHuman_chr6.simHuman.chr6 365835 8 + 601863 GCTTAT------AG -s simRat_chr6.simRat.chr6 374793 14 + 647215 TCCTATTTTTGGAG - -a -s simMouse_chr6.simMouse.chr6 375596 40 + 636262 GTGTCAATCTGGTTTGTTTAATGGTACAAGGGTGCTATGA -s Anc0.Anc0refChr3 9186 40 + 222631 GTGTTATTCTGCCTTATTTGCTAGTCCCAGTATCTCTTGA -s Anc1.Anc1refChr6 42010 40 + 197743 GTGTTATTCTGCCTTATTTGCTAGTCCCAGTATCTCTTGA -s Anc2.Anc2refChr13 11744 40 + 96486 ATGTTATTCTGCCTTATTCACTAGTCCCAGTAGCTCTTGA -s mr.mrrefChr5 229218 40 + 294540 GTGTCAATCTGGTTTGTTTGATGGTACAAGGGTCCTATGA -s simCow_chr6.simCow.chr6 367260 40 + 602619 ATGCCGTTCTAGCTTATGTATTCGTCCTATGGAGCCTTGA -s simDog_chr6.simDog.chr6 357876 40 + 593897 ATGTTATTCTGCCTTATTCACTAGTCCCAGTAGCTTTTGA -s simHuman_chr6.simHuman.chr6 365843 35 + 601863 GTGTTATTCTGCCTTATTTG---GTTTCAATCTCTCT--A -s simRat_chr6.simRat.chr6 374807 39 + 647215 GTGTCAGTCTGGGTTGTTTGATGGTAC-CGGGTCCTGTGA - -a -s simMouse_chr6.simMouse.chr6 375636 59 + 636262 TCTCTTTAAATGCATCTTGACTTTTCTAGTCTCAGACTTGAGCTTATAGGGGCCATCCA -s Anc0.Anc0refChr3 9226 57 + 222631 TCTCTATAG-CACATCATGA-TCCTCTAATTTCAGACTCCAGCTTGCAGGGGCCATATA -s Anc1.Anc1refChr6 42050 57 + 197743 TCTCTATAG-CACATCATGA-TCCTCTAATTTCAGACTCCAGCTTGCAGGGGCCATATA -s Anc2.Anc2refChr13 11786 57 + 96486 TCTCTATAG-CACACCATAA-TCCTCTAATCTCAGACACCAGCTTGCAGGGGCGATATG -s mr.mrrefChr5 229258 59 + 294540 TCTCTTTAAATGCATCTTGACTTTTCTAGTTTCAGACTTGAGCTTATAGGGGCCATCCA -s simCow_chr6.simCow.chr6 367302 56 + 602619 TCTCTGTAG-CACACTATTA-TCCTCTAATGTCATAC-CTAGCTAGCAGGGACAATGTG -s simDog_chr6.simDog.chr6 357918 57 + 593897 GTTCAATAG-CACACCATAA-GCCTCCAACCTCAGGCACCTGCTTGCAGGGGCGTTATG -s simHuman_chr6.simHuman.chr6 365878 57 + 601863 TCTCTATAG-CACATCATGA-TCCTCTAATTTTAGACTCCAGCTTTCAGCGGCCATATA -s simRat_chr6.simRat.chr6 374846 58 + 647215 TCTCTTTAAATGCATCTTGCCTTTTCTAGTTTCGGACTGGATC-TATAGGGACCATGAA - -a -s simMouse_chr6.simMouse.chr6 375695 17 + 636262 GACTACATAATGGTTGC -s Anc0.Anc0refChr3 9284 17 + 222631 GTTGATGTAATGTCGCC -s Anc1.Anc1refChr6 42108 17 + 197743 GTTGATGTAATGTCGCC -s Anc2.Anc2refChr13 11844 17 + 96486 GCTGATGTAATGTTGCC -s mr.mrrefChr5 229317 17 + 294540 GTCTACATAATGGCTGC -s simCow_chr6.simCow.chr6 367359 17 + 602619 GCTGATAGAATGTTGCC -s simDog_chr6.simDog.chr6 357976 17 + 593897 GCTGATGTAATGTTGCC -s simHuman_chr6.simHuman.chr6 365936 17 + 601863 GTTGATCTAATGTCGCC -s simRat_chr6.simRat.chr6 374904 17 + 647215 GTCTGCATAATGGCTTC - -a -s simMouse_chr6.simMouse.chr6 375712 26 + 636262 CCTATTTCTAAGTTGGCCAAGCAAAG -s Anc0.Anc0refChr3 9311 26 + 222631 CATATTCCTAGCTTAGCCAAGCAAAG -s Anc1.Anc1refChr6 42135 26 + 197743 CATATTCCTAGCTTAGCCAAGCAAAG -s Anc2.Anc2refChr13 11871 26 + 96486 TACATTCCTTGCTTAGCCAAGCAAAA -s mr.mrrefChr5 229334 26 + 294540 CATATTCCTAAGTTGGCCAAGCAAAG -s simCow_chr6.simCow.chr6 367386 22 + 602619 TACACTCCCTGGTTAGGCAAGC---- -s simDog_chr6.simDog.chr6 358003 26 + 593897 TACATTCTTTGCTTAGCCAAGCAAAA -s simHuman_chr6.simHuman.chr6 365963 26 + 601863 CATTTTCCTAGCATAGCCAAGTGAAG -s simRat_chr6.simRat.chr6 374921 26 + 647215 CATATGCCTAAGTTTGCCAAGCAAAG - -a -s simMouse_chr6.simMouse.chr6 375738 14 + 636262 TGAGTAAGAGTAGG -s Anc0.Anc0refChr3 9337 14 + 222631 TGAGTAAGAGGCGC -s Anc1.Anc1refChr6 42161 14 + 197743 TGAGTAAGAGGCGC -s Anc2.Anc2refChr13 11897 14 + 96486 TGAGTAAGAGGCAC -s mr.mrrefChr5 229360 14 + 294540 TGAGTAAGAGTAGG -s simDog_chr6.simDog.chr6 358051 14 + 593897 TGAGTAAGAGGCAC -s simHuman_chr6.simHuman.chr6 365989 14 + 601863 TAAGAAAGAGGTGC -s simRat_chr6.simRat.chr6 374947 14 + 647215 TGAGTAAGAGTAGG - -a -s simMouse_chr6.simMouse.chr6 375752 26 + 636262 TAGTACTAAACTTGTTTAAGACTCCT -s Anc0.Anc0refChr3 9353 26 + 222631 TAGTCCTAAATTGGTATGAGACTCCT -s Anc1.Anc1refChr6 42177 26 + 197743 TAGTCCTAAATTGGTATGAGACTCCT -s Anc2.Anc2refChr13 11913 26 + 96486 TAGTCCTAAACTGGCATGAGACTCCT -s mr.mrrefChr5 229374 26 + 294540 TAGTACTAAATTGGTTTAAGACTCCT -s simCow_chr6.simCow.chr6 367409 26 + 602619 TAGTCCAAGTCTGGCATGAGACTCCT -s simDog_chr6.simDog.chr6 358067 26 + 593897 TATTCCTGAACAGGCACGAGACTCCT -s simHuman_chr6.simHuman.chr6 366005 26 + 601863 TAGCTTTATATTGGTATGAGACTCCT -s simRat_chr6.simRat.chr6 374961 26 + 647215 TAGTCCTAAATTGGCTTAAGACTCCT - -a -s simMouse_chr6.simMouse.chr6 375778 20 + 636262 GCTTATATACTCGTACTTAA -s Anc0.Anc0refChr3 9379 18 + 222631 GCTTGTGTATTTGCATCT-- -s Anc1.Anc1refChr6 42203 18 + 197743 GCTTGTGTATTTGCATCT-- -s Anc2.Anc2refChr13 11939 18 + 96486 GCTTGTGTATTTGCATTG-- -s mr.mrrefChr5 229400 20 + 294540 GCTTGTGTACTCGCACCTAA -s simCow_chr6.simCow.chr6 367436 18 + 602619 GCTTGTGTATTCGCATTA-- -s simDog_chr6.simDog.chr6 358093 18 + 593897 GCTTGTGTACTTGCATTG-- -s simHuman_chr6.simHuman.chr6 366031 18 + 601863 GCTTGTGTATTTGCAGCT-- -s simRat_chr6.simRat.chr6 374987 20 + 647215 ACTTGTGTACTCGCACCTAA - -a -s simMouse_chr6.simMouse.chr6 375798 250 + 636262 TGTTATTTAGATTTCAGAACAGTGCCTGGTGCAAAGCTGTAATAAAGGGCAAACACAGCCATGTAACACAGCCATGTACTTTTGGTTATTGCTTGGCCATGAGCCTGCCCACTTTAGGAGATGTTAAGCGATCACAGAAGGAGTCTGCCCACATCATGCAAGAGGTTAGTCATGCACAGCTCCCTACGTACATTCTATATCCCCTGTCCACCTCATGCTAATGCATCTTCATTGTGGTGGCAGAAGCAGG -s Anc0.Anc0refChr3 9397 29 + 222631 -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GGCATCATGATTATGATGGCAGGAAGAAG -s Anc1.Anc1refChr6 42221 29 + 197743 -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GGCATCATGATTATGATGGCAGGAAGAAG -s Anc2.Anc2refChr13 11957 29 + 96486 -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GGCATCATGATTATCATGACAGGAAGAAG -s mr.mrrefChr5 229420 237 + 294540 TGTTATTTAGATTTCAGAACAGTGCCTGGTGCAAAGCTGTAATAAAGGGCA-------------AACACAGCCATGTACTTTTGGTTATTGCTTGGCCATGAGCCTGCCCACTTTAGGAGATGTTAAGCGATCACAGAAGGAGTCTGCCCACATCATGCAAGAGGTTAGTCATGCACAGCTCCCTACGTACATTCTATATCCCCTGTCCACCTCATGCTAATGCATCTTCATTGTGGTGGCAGAAACAAG -s simCow_chr6.simCow.chr6 367454 29 + 602619 -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TGCATCATGATTATCATGACAGGCAGAAG -s simDog_chr6.simDog.chr6 358111 23 + 593897 -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GGCATCATTATTCT------AGGAAGAGG -s simHuman_chr6.simHuman.chr6 366049 29 + 601863 -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CCCATCCTGATCATGATGGCGGGAAGAAT -s simRat_chr6.simRat.chr6 375008 237 + 647215 TGTTGTTTAGATTTCAGCACAGTGCCTGATGCAATGCTATAATAAAAGGCA-------------AACACAGCCATGTACTCATGGTTATTGCATGGCTATCAGTCTGCCCTCTTGAGAAGATGTTTAGCGATCACAGAAGAAGTCTGCCTGCCTCATGCAAGAGGTTTGTCATGCAGAGCTGCCCACGTACATTTGAGATCCCCTGCCCACCTCATGCTTATGCACCTTTATTGTGGTGGCAGAAACAAG - -a -s simMouse_chr6.simMouse.chr6 376048 16 + 636262 GAGAGAAGGAAAGCCT -s Anc0.Anc0refChr3 9430 13 + 222631 G---GAGGGAAAGCCT -s Anc1.Anc1refChr6 42254 13 + 197743 G---GAGGGAAAGCCT -s Anc2.Anc2refChr13 11990 13 + 96486 G---GAGAGAAAGCCT -s mr.mrrefChr5 229661 16 + 294540 GAGAGAAGGAAAGCCT -s simCow_chr6.simCow.chr6 367487 13 + 602619 G---GAGTGAAAGCCT -s simDog_chr6.simDog.chr6 358138 8 + 593897 T---GCCAAAA----- -s simHuman_chr6.simHuman.chr6 366082 13 + 601863 G---GAGGGAAAGCAT -s simRat_chr6.simRat.chr6 375249 16 + 647215 GAAAGAAGGAAAGCCT - -a -s simMouse_chr6.simMouse.chr6 376064 3 + 636262 TCA -s Anc0.Anc0refChr3 9445 3 + 222631 CCA -s Anc1.Anc1refChr6 42269 3 + 197743 CCA -s Anc2.Anc2refChr13 12005 3 + 96486 CCA -s mr.mrrefChr5 229677 3 + 294540 TCA -s simCow_chr6.simCow.chr6 367508 3 + 602619 CCG -s simDog_chr6.simDog.chr6 358147 3 + 593897 CCA -s simHuman_chr6.simHuman.chr6 366097 3 + 601863 CCA -s simRat_chr6.simRat.chr6 375265 3 + 647215 TCA - -a -s simMouse_chr6.simMouse.chr6 376067 13 + 636262 ATGGTAATTTTAT -s Anc0.Anc0refChr3 9448 13 + 222631 ATGAGGATTCTAT -s Anc1.Anc1refChr6 42272 13 + 197743 ATGAGGATTCTAT -s Anc2.Anc2refChr13 12009 13 + 96486 ATGAGGATTCTTT -s mr.mrrefChr5 229680 13 + 294540 ATGGTAATTTTAT -s simCow_chr6.simCow.chr6 367512 13 + 602619 ATAAGGATTCTTT -s simDog_chr6.simDog.chr6 358151 13 + 593897 ATGAGCTTTCTTT -s simHuman_chr6.simHuman.chr6 366100 13 + 601863 ATGAGGATTCTAT -s simRat_chr6.simRat.chr6 375268 11 + 647215 ATGG--GTTTTAT - -a -s simMouse_chr6.simMouse.chr6 376080 1 + 636262 G -s Anc0.Anc0refChr3 9461 1 + 222631 G -s Anc1.Anc1refChr6 42285 1 + 197743 G -s Anc2.Anc2refChr13 12022 1 + 96486 G -s mr.mrrefChr5 229693 1 + 294540 G -s simCow_chr6.simCow.chr6 367525 1 + 602619 G -s simDog_chr6.simDog.chr6 358164 1 + 593897 G -s simHuman_chr6.simHuman.chr6 366113 1 + 601863 G -s simRat_chr6.simRat.chr6 375336 1 + 647215 G - -a -s simMouse_chr6.simMouse.chr6 376081 9 + 636262 AAACTTTTC -s Anc0.Anc0refChr3 9464 9 + 222631 AAACTCTCA -s Anc1.Anc1refChr6 42288 9 + 197743 AAACTCTCA -s Anc2.Anc2refChr13 12025 9 + 96486 AAACTCTCA -s mr.mrrefChr5 229694 9 + 294540 AAACTCTTC -s simCow_chr6.simCow.chr6 367528 9 + 602619 TATCCCTAA -s simDog_chr6.simDog.chr6 358167 9 + 593897 AAACTCCCA -s simHuman_chr6.simHuman.chr6 366116 9 + 601863 AAGCTCTCA -s simRat_chr6.simRat.chr6 375337 9 + 647215 AAATTCTTC - -a -s simMouse_chr6.simMouse.chr6 376090 9 + 636262 AGTTCCTTC -s Anc0.Anc0refChr3 9473 9 + 222631 AGATCCCTA -s Anc1.Anc1refChr6 42297 9 + 197743 AGATCCCTA -s Anc2.Anc2refChr13 12034 9 + 96486 AGATACCCA -s mr.mrrefChr5 229703 9 + 294540 AGTTCCTTA -s simCow_chr6.simCow.chr6 367542 9 + 602619 AGATACCCA -s simHuman_chr6.simHuman.chr6 366125 9 + 601863 AGATCCCTA -s simRat_chr6.simRat.chr6 375346 9 + 647215 ACTTACTTA - -a -s simMouse_chr6.simMouse.chr6 376099 15 + 636262 AGGAGACTGGAACTA -s Anc0.Anc0refChr3 9483 12 + 222631 ---AGCCTAGAAATA -s Anc1.Anc1refChr6 42307 15 + 197743 AGCAGCCTAGAAATA -s Anc2.Anc2refChr13 12044 12 + 96486 ---AGCCTAGAAATA -s mr.mrrefChr5 229713 15 + 294540 AGGAGACTAGAAATA -s simCow_chr6.simCow.chr6 367552 9 + 602619 ------CTAGAAATA -s simDog_chr6.simDog.chr6 358176 12 + 593897 ---AGCTTAGTAATA -s simHuman_chr6.simHuman.chr6 366135 15 + 601863 AACAGCCCAGAAATA -s simRat_chr6.simRat.chr6 375356 15 + 647215 AGAAAACTATAAATA - -a -s simMouse_chr6.simMouse.chr6 376114 38 + 636262 GTTGCATCCCACAGCATACACAGAAAGGTAACTGGTGT -s Anc0.Anc0refChr3 9495 38 + 222631 GTTCCATCCCATAGCATATCCAGCAAGCTAATTGCTGT -s Anc1.Anc1refChr6 42322 38 + 197743 GTTCCATCCCATAGCATATCCAGCAAGCTAATTGCTGT -s Anc2.Anc2refChr13 12056 38 + 96486 GTTCCATCCCATAGCATATCCATCAATCTAATTGCTGT -s mr.mrrefChr5 229728 38 + 294540 GTTGCATCCCACAGCATACACAGAAAGGTAACTGGTGT -s simCow_chr6.simCow.chr6 367561 38 + 602619 GTTCCACCCCAGAGCATATCCATTTATCTAACTGGCGT -s simDog_chr6.simDog.chr6 358188 38 + 593897 GTTCCATTCCATAGCATATCCATCAATGTAGTTGCTGT -s simHuman_chr6.simHuman.chr6 366151 38 + 601863 GTTTCATCCCATTGCATAGCCAGCAAGCCAAGTAATGT -s simRat_chr6.simRat.chr6 375371 38 + 647215 GTTGCACTGCACAGCATGCACAGTGAGGTGACTGGGGT - -a -s simMouse_chr6.simMouse.chr6 376152 13 + 636262 AGTTTGTACTCAG -s Anc0.Anc0refChr3 9544 13 + 222631 AGTTAATACTCTG -s Anc1.Anc1refChr6 42371 13 + 197743 AGTTAATACTCTG -s Anc2.Anc2refChr13 12105 13 + 96486 AGTTAATGCTCTG -s mr.mrrefChr5 229766 13 + 294540 AGTTTATACTCAG -s simCow_chr6.simCow.chr6 367610 13 + 602619 AGTTGATGCTCTG -s simDog_chr6.simDog.chr6 358233 13 + 593897 AGTCAATGCTGCG -s simHuman_chr6.simHuman.chr6 366200 13 + 601863 AGTTAATACTCTG -s simRat_chr6.simRat.chr6 375409 13 + 647215 AGTTTATGCTCAG - -a -s simMouse_chr6.simMouse.chr6 376165 40 + 636262 CCCTCACTTTGCAGCCCTGACTTACTCTCTCACAAACTGA -s Anc0.Anc0refChr3 9560 40 + 222631 CCCTCACTTTGCAAGGCAGACTGATTCTCCCATAAACTGA -s Anc1.Anc1refChr6 42387 40 + 197743 CCCTCACTTTGCAAGGCAGACTGATTCTCCCATAAACTGA -s Anc2.Anc2refChr13 12121 40 + 96486 CCCTCACTTTACAAGGCAGACTGATTCTCCCATAAACAGT -s mr.mrrefChr5 229779 40 + 294540 CCCTCACTTTGCAGCGCTGACTGATTCTCTCACAAACTGA -s simCow_chr6.simCow.chr6 367626 39 + 602619 CCCCC-CTTTATTATGCAGACCAACTCTCCCAAAAACAGG -s simDog_chr6.simDog.chr6 358249 40 + 593897 CCCTCACTTTACAAGGCAGACTGATTCTCCCATAAACAGT -s simHuman_chr6.simHuman.chr6 366216 40 + 601863 CCCTCACTTTGCAAGGCAGACTGATTCCCCCAGAAACTGA -s simRat_chr6.simRat.chr6 375422 40 + 647215 CCCTCACATTGCAGCGCCAACTGGTTCTCTCACAAACTGA - -a -s simMouse_chr6.simMouse.chr6 376205 37 + 636262 TAAACATTAAACTATATTGTGTCCATCACTAGGACAG -s Anc0.Anc0refChr3 9601 35 + 222631 TAAAGATCAAATTATGTCAAGTCCATCAC--AGAAAG -s Anc1.Anc1refChr6 42428 35 + 197743 TAAAGATCAAATTATGTCAAGTCCATCAC--AGAAAG -s Anc2.Anc2refChr13 12162 35 + 96486 TAAAGATCAAATTATGTCAAGTCCATCAC--AGTAAG -s mr.mrrefChr5 229820 35 + 294540 TAAACATCAAACTATATTGAGTCCATCAC--AGACAG -s simCow_chr6.simCow.chr6 367666 35 + 602619 TAGAAATCAAATTATGTCAAGTTCATCAC--AGGACG -s simDog_chr6.simDog.chr6 358290 34 + 593897 CAAAGATCAAATTAT-TTAAGTCTATCAC--AGTTAG -s simHuman_chr6.simHuman.chr6 366257 35 + 601863 TAATGATCAAATTATGTCAAGCCCATCAC--ATAAAA -s simRat_chr6.simRat.chr6 375463 35 + 647215 TAAATATCAAACTATATTGAGTCCATCAC--AGACGG - -a -s simMouse_chr6.simMouse.chr6 376242 56 + 636262 CAGTAACATAAGAAAAGCTAAAGTTTTCAGTGTAATGTACAAGCAAAAAAAATCAC -s Anc0.Anc0refChr3 9636 51 + 222631 CAATAACATAATAAAAGCTAAAGTTCTCAGTGTAATTCCCATGCAA-----TTTGA -s Anc1.Anc1refChr6 42463 56 + 197743 CAATAACATAATAAAAGCTAAAGTTCTCAGTGTAATTCCCATGCAAGAGTGTTTGA -s Anc2.Anc2refChr13 12198 51 + 96486 CAATAACATAATAAAACCTAAAGTTCTCATTGTAATTCCCATGCAA-----TTGGA -s mr.mrrefChr5 229855 56 + 294540 CAGTAACATAAGAAAAGCTAAAGTTTTCAGTGTAATTTCCATGCAAAAGAATTTGA -s simCow_chr6.simCow.chr6 367702 51 + 602619 CAATAACATAACAAGACCTAAAGTTCTCATTGTAGTTACCATGCAC-----ACAAA -s simDog_chr6.simDog.chr6 358325 51 + 593897 AAATAACATAATGAAACCTAAAGTTCTCATTGTAATTCCTATGAAA-----TTGGA -s simHuman_chr6.simHuman.chr6 366292 56 + 601863 CAATAGCATAATAAAAGCTAAATTCCTCAGTGTAATTCCCATGCAAGAGTGTTTGA -s simRat_chr6.simRat.chr6 375498 56 + 647215 CAGTACCATAAGAAAAGGTAAAGTTTTCAGTGTAATTTCCATGCAAAAGACTTTGA - -a -s simMouse_chr6.simMouse.chr6 376298 11 + 636262 TTGACAAACAT -s Anc0.Anc0refChr3 9687 11 + 222631 TTGACAAACAT -s Anc1.Anc1refChr6 42519 11 + 197743 TTGACAAACAT -s Anc2.Anc2refChr13 12249 11 + 96486 TTGAAAAGAAT -s mr.mrrefChr5 229911 11 + 294540 TTGACAAACAT -s simCow_chr6.simCow.chr6 367753 8 + 602619 C---AAAGAAT -s simDog_chr6.simDog.chr6 358376 11 + 593897 TTGAAAAGAAT -s simHuman_chr6.simHuman.chr6 366375 11 + 601863 TTGACAAACAT -s simRat_chr6.simRat.chr6 375554 11 + 647215 TTGACAAGCAT - -a -s simMouse_chr6.simMouse.chr6 376309 37 + 636262 TCAGTGGTCCCATGCTGACTGAAAGTGTATACAAAGC -s Anc0.Anc0refChr3 9698 1 + 222631 T------------------------------------ -s Anc1.Anc1refChr6 42530 24 + 197743 TCAGCG-TCACATGCTGACCAACAG------------ -s Anc2.Anc2refChr13 12260 1 + 96486 T------------------------------------ -s mr.mrrefChr5 229922 37 + 294540 TCAGTGGTCCCATGCTGACTGAAAGTGTATACAAAGC -s simCow_chr6.simCow.chr6 367763 1 + 602619 T------------------------------------ -s simDog_chr6.simDog.chr6 358387 1 + 593897 T------------------------------------ -s simHuman_chr6.simHuman.chr6 366386 24 + 601863 TCAGCG-TCACATGCTGACCAACAG------------ -s simRat_chr6.simRat.chr6 375565 37 + 647215 TCAGTAGTCCAATGCTGCCTGAAATTGTATACAAAGC - -a -s simMouse_chr6.simMouse.chr6 376346 43 + 636262 TTACATAATAGAAGGAGGCCTTCCCACCCCTTCTGTAGTAGAC -s Anc0.Anc0refChr3 9706 42 + 222631 TCGCACAGTTGGGGGAGGTTTT-CCATCCCTCGTGTAGGTGTC -s Anc1.Anc1refChr6 42561 43 + 197743 TCGCACAGTTGGGGGAGGTTTTCCCATCCCTCGTGTAGGTGTC -s Anc2.Anc2refChr13 12268 42 + 96486 TCGCACAGTTGGGGGAGGTTTT-CCATCTCTCATGTAGGTGTC -s mr.mrrefChr5 229967 43 + 294540 TTGCATAATAGGAGGAGGCCTTCCCACCCCTTGTGTAGTAGAC -s simCow_chr6.simCow.chr6 367771 42 + 602619 TCGCACAGTTGGGGGAGGTTTT-CCATCTCTCCTGCAGGTGAC -s simDog_chr6.simDog.chr6 358395 42 + 593897 TCGTGTAGTTGGAGGAGGTTTT-CCATCTTTCATGTAGGCGTA -s simHuman_chr6.simHuman.chr6 366417 43 + 601863 TCGCACAGTTGGGGAAGGTTCTCCCATCCCTCGTGTGAGTGTC -s simRat_chr6.simRat.chr6 375612 43 + 647215 ATGCATAATAGGACGAGGCCTTCCCACCTCTTGTGTAGTAGAA - -a -s simMouse_chr6.simMouse.chr6 376389 9 + 636262 TTGTTTGAG -s Anc0.Anc0refChr3 9748 8 + 222631 ATATTTGA- -s Anc1.Anc1refChr6 42604 8 + 197743 ATATTTGA- -s Anc2.Anc2refChr13 12310 8 + 96486 ATATTGGA- -s mr.mrrefChr5 230010 8 + 294540 TTGTTTGA- -s simCow_chr6.simCow.chr6 367813 8 + 602619 ATGTTGGA- -s simDog_chr6.simDog.chr6 358443 8 + 593897 ATATTGGA- -s simHuman_chr6.simHuman.chr6 366460 8 + 601863 ACATTTGC- -s simRat_chr6.simRat.chr6 375655 8 + 647215 TTGTTTGA- - -a -s simMouse_chr6.simMouse.chr6 376398 3 + 636262 GAT -s Anc0.Anc0refChr3 9756 3 + 222631 GAT -s Anc1.Anc1refChr6 42612 3 + 197743 GAT -s Anc2.Anc2refChr13 12319 3 + 96486 GAT -s mr.mrrefChr5 230018 3 + 294540 GAT -s simCow_chr6.simCow.chr6 367822 3 + 602619 GAA -s simDog_chr6.simDog.chr6 358452 3 + 593897 GAT -s simHuman_chr6.simHuman.chr6 366468 3 + 601863 AAT -s simRat_chr6.simRat.chr6 375663 3 + 647215 GAT - -a -s simMouse_chr6.simMouse.chr6 376401 53 + 636262 CACATGCACAGGTGACCCATGGGAACTACTGTCTGTGTCCTCTTGATTGTACA -s Anc0.Anc0refChr3 9759 53 + 222631 CACATGCACAGGTGACTGATGGAAGCTACTGCTCATATCCTTTTGATTATGTG -s Anc1.Anc1refChr6 42615 53 + 197743 CACATGCACAGGTGACTGATGGAAGCTACTGCTCATATCCTTTTGATTATGTG -s Anc2.Anc2refChr13 12322 53 + 96486 CAGATCCACAGGTGACTGATAGAAGCTACTGCTCATATCCTTTTGATTATGTG -s mr.mrrefChr5 230021 53 + 294540 CACATGCACAGGTGACTCATGGGAACTACTGTCTGTATCCTTTTGATTGTACA -s simCow_chr6.simCow.chr6 367825 52 + 602619 CAGATCAACAGGTGACTGATAAAAGCAACTGCTCATATCCATTTGA-GAAGAA -s simDog_chr6.simDog.chr6 358455 53 + 593897 CAGATCCACAGGTGACTGATAGGAGTTACTGCTCATACCCTTTTGATTGTATG -s simHuman_chr6.simHuman.chr6 366472 53 + 601863 TACATGCACAGGTGACTGATGGAAGCTACCGCTCATATGCCTTTGATTATGGG -s simRat_chr6.simRat.chr6 375666 52 + 647215 CACATGAGTGGGTGACTCATGAGGACTACTGTCTG-ATCCTTTTGATTGTACA - -a -s simMouse_chr6.simMouse.chr6 376454 23 + 636262 ATCCAAAACATACTGAAAATACA -s Anc0.Anc0refChr3 9812 9 + 222631 TAC--------------AATCAG -s Anc1.Anc1refChr6 42668 9 + 197743 TAC--------------AATCAG -s Anc2.Anc2refChr13 12375 9 + 96486 TAC--------------CAGCAG -s mr.mrrefChr5 230074 23 + 294540 ATCCAAAATATACTGAAAATACA -s simCow_chr6.simCow.chr6 367877 9 + 602619 TAC--------------TAACAG -s simDog_chr6.simDog.chr6 358509 9 + 593897 TAA--------------CAGCAC -s simHuman_chr6.simHuman.chr6 366525 9 + 601863 TAC--------------AATCTG -s simRat_chr6.simRat.chr6 375718 23 + 647215 ATACAAAGTATACTGAAAATACA - -a -s simMouse_chr6.simMouse.chr6 376477 20 + 636262 AACACTATAAAGGTGCCATG -s Anc0.Anc0refChr3 9821 20 + 222631 AATGCTATAAAGGTGTCATC -s Anc1.Anc1refChr6 42677 20 + 197743 AATGCTATAAAGGTGTCATC -s Anc2.Anc2refChr13 12384 20 + 96486 AATGCCATAAAGGTGTCAAC -s mr.mrrefChr5 230097 20 + 294540 AACACTATAAAGGTGCCATG -s simCow_chr6.simCow.chr6 367889 20 + 602619 AATGCCTCAAAGGTGCCAAC -s simDog_chr6.simDog.chr6 358518 20 + 593897 AATGCCATATAGGTGTCTAC -s simHuman_chr6.simHuman.chr6 366534 20 + 601863 AAATATATAAAGGTGTCATA -s simRat_chr6.simRat.chr6 375741 20 + 647215 AATGCCATAAAGCTGCCATG - -a -s simMouse_chr6.simMouse.chr6 376497 21 + 636262 GAGATGGGAAGTCGTAACAAA -s Anc0.Anc0refChr3 9848 21 + 222631 GGGACAGCAAGTCATATCAAC -s Anc1.Anc1refChr6 42704 21 + 197743 GGGACAGCAAGTCATATCAAC -s Anc2.Anc2refChr13 12411 21 + 96486 GGGGCAGCAAGTCATATTAAC -s mr.mrrefChr5 230117 21 + 294540 GAGATGGGAAGTCATAACAAA -s simCow_chr6.simCow.chr6 367916 20 + 602619 GGGGCATCAAGTCAT-CAAAT -s simDog_chr6.simDog.chr6 358545 21 + 593897 GGGGCAGCAAGTCATATTAAC -s simHuman_chr6.simHuman.chr6 366561 21 + 601863 GGGACAGCAAGTCATATCAAC -s simRat_chr6.simRat.chr6 375761 20 + 647215 G-TATGGTCAGTCATAACAAT - -a -s simMouse_chr6.simMouse.chr6 376518 1 + 636262 A -s Anc0.Anc0refChr3 9869 1 + 222631 A -s Anc1.Anc1refChr6 42725 1 + 197743 A -s Anc2.Anc2refChr13 12439 1 + 96486 T -s mr.mrrefChr5 230138 1 + 294540 A -s simCow_chr6.simCow.chr6 367943 1 + 602619 C -s simDog_chr6.simDog.chr6 358573 1 + 593897 T -s simHuman_chr6.simHuman.chr6 366582 1 + 601863 A -s simRat_chr6.simRat.chr6 375781 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 376519 57 + 636262 ATTCTTAACAGTGCCCTACCATTCCTATATTTTGGGTCATAAAAAAACCCATCTTAT -s Anc0.Anc0refChr3 9870 57 + 222631 ACTCTTGGCAACACTCTCTCATTCCTATATCTTGGTTCAGGCTAAAATCCACTTTAT -s Anc1.Anc1refChr6 42726 57 + 197743 ACTCTTGGCAACACTCTCTCATTCCTATATCTTGGTTCAGGCTAAAATCCACTTTAT -s Anc2.Anc2refChr13 12440 57 + 96486 ACTCTTGGCAACACTCTCTCATTCCTAGAGCTTGGTCCAGGCTAAAATCCACTCTAC -s mr.mrrefChr5 230139 57 + 294540 ACTCTTAACAATACCCTACCATTCCTATATTTTGGTTCATAAAAAAATCCATTTTAT -s simCow_chr6.simCow.chr6 367944 57 + 602619 ACTCTTGGCACAACCCTCTCATTCTCGGCGCTTGGTCCAAGCATAAGTCCATTCTGC -s simDog_chr6.simDog.chr6 358574 49 + 593897 TCTCTGGGCAACAATCTCTTATTACTAGA--------CTGGCTAAAATCCACTCCAC -s simHuman_chr6.simHuman.chr6 366613 57 + 601863 ACTCGTGGCAACACTTTTTCATTCCTATATCTCAGTTCAGGCGAAAATCCACTTTAT -s simRat_chr6.simRat.chr6 375782 57 + 647215 ACTCTAAACAATACCCTACCATTCCTATATTTTGGTTCAAAAAACAATCCATTTTAT - -a -s simMouse_chr6.simMouse.chr6 376576 52 + 636262 CCTTTATCCGCACACCTTGCCAGCATAAATATAGAATCTTTCTCTCTAAGTG -s Anc0.Anc0refChr3 9929 52 + 222631 CCCTTCTCCATCGACCTGTCCAGTGTAACTATAGCATCTTGCTCTTTAAGTG -s Anc1.Anc1refChr6 42785 52 + 197743 CCCTTCTCCATCGACCTGTCCAGTGTAACTATAGCATCTTGCTCTTTAAGTG -s Anc2.Anc2refChr13 12499 52 + 96486 CCCTTCTCCATCGACCTGTTAAGTGTGACTATAACACCTTGCTCTTTAAGTG -s mr.mrrefChr5 230198 52 + 294540 CCTTTATCCACACACCTTGCCAGCATAACTATAGAATCTTGCTCTCTAAGTG -s simCow_chr6.simCow.chr6 368003 52 + 602619 CCCTTCTCCATCAACCCACTAATTGTCACTATAACACCTTGCTCTTTAAGTG -s simDog_chr6.simDog.chr6 358625 49 + 593897 CCTGTCATTGTCGACCTGT---GTGTGGCCATAACACCTTGCTTTTTAAGTG -s simHuman_chr6.simHuman.chr6 366672 52 + 601863 CCCTTTTCCATCTCCCTCTCCAGTGTAACTACAGCATCTTGCTCCTTAAGTG -s simRat_chr6.simRat.chr6 375841 52 + 647215 CCTTTATCCACACACCTTGCCAGCATGACTATAGAACCTTGCTCTCTAAGAG - -a -s simMouse_chr6.simMouse.chr6 376628 15 + 636262 AAATGCATGCATTGT -s Anc0.Anc0refChr3 9981 15 + 222631 AAATGCACTCATTGT -s Anc1.Anc1refChr6 42837 15 + 197743 AAATGCACTCATTGT -s Anc2.Anc2refChr13 12551 15 + 96486 AAATGCACTGATTGT -s mr.mrrefChr5 230250 15 + 294540 AAATGCACGCATTGT -s simCow_chr6.simCow.chr6 368055 15 + 602619 GAACGCACTGAGTGT -s simDog_chr6.simDog.chr6 358674 15 + 593897 AAATGTACTGATTGT -s simHuman_chr6.simHuman.chr6 366724 15 + 601863 CAATGCACCCATTGT -s simRat_chr6.simRat.chr6 375894 15 + 647215 AAATGGACGCAATGC - -a -s simMouse_chr6.simMouse.chr6 376643 77 + 636262 ACAACACTGACCCTATGCATGTGAAACTAGCAGCTTATTATCCTTTGTCCAGCAATATTTTTGGTAATTGTGTGTAC -s Anc0.Anc0refChr3 9996 61 + 222631 ATAACTGTGAA---------------CTTGTACCTTACTGACCTGTGAACAGGAGTATTTTTG-CAATTGCATGCAT -s Anc1.Anc1refChr6 42852 71 + 197743 ATAACTGTGAACTAATACCTT-----CTTGTACCTTACTGACCTGTGAACAGGAGTATTTTTG-CAATTGCATGCAT -s Anc2.Anc2refChr13 12566 61 + 96486 ATAACTGTAAA---------------CTTGTACCTTCCTGACCTGTGTACAGGAGTATTTTAG-CAATTGCATGCGT -s mr.mrrefChr5 230265 77 + 294540 ACAACACTGACCCTATGCATGTGAAACTTGCACCTTATTATCCTTTGACCAGCAATATTTTTGGTAATTGTGTGTAC -s simCow_chr6.simCow.chr6 368073 58 + 602619 ATTACTGTAAA---------------CTCGTAC---CCTGACCTCTGTACACAGGTATTTTGG-CATTTACTTGCTT -s simDog_chr6.simDog.chr6 358689 61 + 593897 ATAGCTGTAAA---------------ATTGTACCTTCCTGAAGTGGGTACAGGAATTTTTTAG-CAATGGCAAACGT -s simHuman_chr6.simHuman.chr6 366739 71 + 601863 ATAACTGTGAACTAATACCTT-----CTTGTACCTTACATACCTGTGAACAGGAGCATGTTTG-CCATTGCATGGAT -s simRat_chr6.simRat.chr6 375909 77 + 647215 AAAACGCTGACCCTATGCATGTGAAATGTGCACCTTAGTATTCTTTGACCAGCAATATTTTTAGTAATTGTGTGTAC - -a -s simMouse_chr6.simMouse.chr6 376720 31 + 636262 CTAGCATCAGACAGTGATATCTCCATAGACA -s Anc0.Anc0refChr3 10058 29 + 222631 CT--TGTTTGATACTGATTTCTCCATGCATA -s Anc1.Anc1refChr6 42924 29 + 197743 CT--TGTTTGATACTGATTTCTCCATGCATA -s Anc2.Anc2refChr13 12628 29 + 96486 CC--TGTTTGATTCTGATCTCTCCATGCATA -s mr.mrrefChr5 230342 31 + 294540 CTAGTGTTAGACAGTGATTTCTCCATAGATA -s simCow_chr6.simCow.chr6 368132 29 + 602619 TA--TATTCTATGCTGTTACCTCCATGCATA -s simDog_chr6.simDog.chr6 358751 29 + 593897 CC--TGTTTGATTCTGACCTCTCCATGCATG -s simHuman_chr6.simHuman.chr6 366811 29 + 601863 CT--TGTTTGATACTGATTTCTCCATGCATA -s simRat_chr6.simRat.chr6 375986 31 + 647215 CTAATGCTGAACAGTCATTTCTCCATATGTA - -a -s simMouse_chr6.simMouse.chr6 376751 8 + 636262 CATGGTGA -s Anc0.Anc0refChr3 10087 8 + 222631 AATGTTAA -s Anc1.Anc1refChr6 42953 8 + 197743 AATGTTAA -s Anc2.Anc2refChr13 12657 8 + 96486 AATGTTAA -s mr.mrrefChr5 230373 8 + 294540 CATGGTGA -s simCow_chr6.simCow.chr6 368162 8 + 602619 AACATTAA -s simDog_chr6.simDog.chr6 358780 5 + 593897 CATGT--- -s simHuman_chr6.simHuman.chr6 366840 8 + 601863 AATGTCAA -s simRat_chr6.simRat.chr6 376017 8 + 647215 CATGGTGA - -a -s simMouse_chr6.simMouse.chr6 376759 49 + 636262 CCACCAGGCTTTTGATAATTGGGAGTATGGAACCCTAGTAGCTACGAGC -s Anc0.Anc0refChr3 10095 48 + 222631 ACACCAGGCTTTTCAAAATAGGGTGTATAGG-CTATAGTAGCTATGAAG -s Anc1.Anc1refChr6 42961 48 + 197743 ACACCAGGCTTTTCAAAATAGGGTGTATAGG-CTATAGTAGCTATGAAG -s Anc2.Anc2refChr13 12665 48 + 96486 ACACCAGTCTTTTCCAAATAGGGTGTATAGG-CTACAGGAGCTATGGAG -s mr.mrrefChr5 230381 49 + 294540 CCACCAGGCTTTTCATAATTGGGAGTATGGAACCCTAGTAGCTACGAGC -s simCow_chr6.simCow.chr6 368178 48 + 602619 ACACCAGTCATTCCGAGATAGGGTGTATGTG-CTGCTGCAGCAATGGAA -s simDog_chr6.simDog.chr6 358785 43 + 593897 ----TAG-TTTCTTCAAATAGGAAGTATAGG-CTACAGGAGCTATGGAG -s simHuman_chr6.simHuman.chr6 366848 47 + 601863 AGAGCAGGCTTTTCAAAATAGGGTGCATTGG-CTATAGTAGCTTGGA-T -s simRat_chr6.simRat.chr6 376025 47 + 647215 CCACCAGGCTTCTCATAATTGGGAGTATAAGACCCTAGTAGC--CGAGC - -a -s simMouse_chr6.simMouse.chr6 376808 81 + 636262 AAACCCATCTGTCATTTGCATGGGAGAGTATATTCTTCTCAGCATGATGATACCTTCCTTTTTCCAGAATACACCAGCTGG -s Anc0.Anc0refChr3 10143 73 + 222631 GAGCCAATCAGCCACTTGC------GTGGATTATCTTATCTGCATGGTGAGACCTGGCTTT--CCAGAATAGACCAGACGG -s Anc1.Anc1refChr6 43009 79 + 197743 GAGCCAATCAGCCACTTGCACCCGAGTGGATTATCTTATCTGCATGGTGAGACCTGGCTTT--CCAGAATAGACCAGACGG -s Anc2.Anc2refChr13 12713 73 + 96486 GAGCCAATCAGCCGCTTGT------GTGGATTATCTTATCTGCATGGTGAGCCCTGGGTTT--CCAGAATACACTAGACAG -s mr.mrrefChr5 230430 81 + 294540 AAACCCATCAGTCATTTGCATGGGAGAGTATATTCTTCTCAGCATGATGATACCTTCCTTTTTCCAGAATAGACCAGCTGG -s simCow_chr6.simCow.chr6 368226 73 + 602619 AAACTAATCAGCCGCTTGT------GTGCATTATCTTGTCTGCATGGTGGGCCCTGTGTTT--CCAGAATACGCTAGACAG -s simDog_chr6.simDog.chr6 358830 73 + 593897 GAGCCAATCAGCTGCTTGT------ATCGATTATCTTATCTGCATAGTGAGCCATGGGTTT--CCAGAATACACTAGACAG -s simHuman_chr6.simHuman.chr6 366895 77 + 601863 CAGCCAATCAGCCACC--CACCCGAGTGGATTATCTTATGTGCAGGGTGAGACCTAGCCTT--CCAGAATTGACCAGGGGG -s simRat_chr6.simRat.chr6 376072 81 + 647215 AAACCCTTCAGTCATTTGAGTGGGTGGGTGTATTCTTCTCAGCATGATGATAGCCTTCTTTTTCCAGAATAGACCAGCTGA - -a -s simMouse_chr6.simMouse.chr6 376889 15 + 636262 GCAGACCCACACGAG -s Anc0.Anc0refChr3 10216 11 + 222631 G----CCCACATAAC -s Anc1.Anc1refChr6 43088 11 + 197743 G----CCCACATAAC -s Anc2.Anc2refChr13 12786 11 + 96486 G----CCCACATAAC -s mr.mrrefChr5 230511 15 + 294540 GCAGACCCACACAAG -s simCow_chr6.simCow.chr6 368299 11 + 602619 G----CCCACATAAG -s simDog_chr6.simDog.chr6 358903 11 + 593897 G----CTCACACAAC -s simHuman_chr6.simHuman.chr6 366972 11 + 601863 G----CCCGCATAAA -s simRat_chr6.simRat.chr6 376166 15 + 647215 GCAGACCCACACAAT - -a -s simMouse_chr6.simMouse.chr6 376904 1 + 636262 C -s Anc0.Anc0refChr3 10227 1 + 222631 C -s Anc1.Anc1refChr6 43099 1 + 197743 C -s Anc2.Anc2refChr13 12797 1 + 96486 C -s mr.mrrefChr5 230526 1 + 294540 C -s simCow_chr6.simCow.chr6 368310 1 + 602619 C -s simDog_chr6.simDog.chr6 358914 1 + 593897 C -s simHuman_chr6.simHuman.chr6 366983 1 + 601863 C -s simRat_chr6.simRat.chr6 376182 1 + 647215 C - -a -s simMouse_chr6.simMouse.chr6 376905 3 + 636262 AAT -s Anc0.Anc0refChr3 10228 3 + 222631 AAT -s Anc1.Anc1refChr6 43100 3 + 197743 AAT -s Anc2.Anc2refChr13 12799 3 + 96486 AAT -s mr.mrrefChr5 230527 3 + 294540 AAT -s simCow_chr6.simCow.chr6 368312 3 + 602619 AAT -s simDog_chr6.simDog.chr6 358916 3 + 593897 AAT -s simHuman_chr6.simHuman.chr6 366984 3 + 601863 TAT -s simRat_chr6.simRat.chr6 376183 3 + 647215 AAT - -a -s simMouse_chr6.simMouse.chr6 376908 15 + 636262 GTTTATACCTAGTAC -s Anc0.Anc0refChr3 10231 15 + 222631 GTTTATACCCCGCCC -s Anc1.Anc1refChr6 43103 15 + 197743 GTTTATACCCCGCCC -s Anc2.Anc2refChr13 12802 15 + 96486 GTTTATACCCCAGCC -s mr.mrrefChr5 230530 15 + 294540 GTTTATACCCAGCAC -s simCow_chr6.simCow.chr6 368315 15 + 602619 GTTTGTACCCCAGCC -s simDog_chr6.simDog.chr6 358919 15 + 593897 GTTTATACCCCAGCC -s simHuman_chr6.simHuman.chr6 366989 15 + 601863 GTTCATCCTCTGCCC -s simRat_chr6.simRat.chr6 376186 15 + 647215 GTTGATGCCCAACAC - -a -s simMouse_chr6.simMouse.chr6 376923 50 + 636262 TGGATTTGGTATTTATGGGGGATAGGGGCTCACAGCAACAATAGGAGACT -s Anc0.Anc0refChr3 10247 49 + 222631 AGGATTTGGGATTTATAGGGGATGGGTGGTCAGGGCAAGAAGTAG-GACC -s Anc1.Anc1refChr6 43119 50 + 197743 AGGATTTGGGATTTATAGGGGATGGGTGGTCAGGGCAAGAAGTAGCGACC -s Anc2.Anc2refChr13 12818 49 + 96486 AGGATTTGGGATCTATAGGGGAGGGGTGGTCAGGGCAAGAAGTAG-GACC -s mr.mrrefChr5 230545 50 + 294540 TGGATTTGGTATTTATAGGGGATAGGGGCTCAGGGCAACAATAGGAGACC -s simCow_chr6.simCow.chr6 368331 49 + 602619 AGGATTTGGGATCTACAGGGGAAGAGTGATCAGGGCAAGAGCTGG-GGCC -s simDog_chr6.simDog.chr6 358935 49 + 593897 AGGATTTTGGATCTATAGGGGAGAGGTGGTCACGGCAGGAAGTAG-GACC -s simHuman_chr6.simHuman.chr6 367005 50 + 601863 AAGATTTGGGAGTTATAGGGGATGTGTGGTCAGGGCAAGAAGTCGCATCC -s simRat_chr6.simRat.chr6 376201 50 + 647215 TTCATTTGGTATTTATAGGGGATAGGGGCTCAGGGCAACAACAGGAGACC - -a -s simMouse_chr6.simMouse.chr6 376973 6 + 636262 ATTGAC -s Anc0.Anc0refChr3 10298 6 + 222631 GCCCAC -s Anc1.Anc1refChr6 43171 6 + 197743 GCCCAC -s Anc2.Anc2refChr13 12869 6 + 96486 GCCCAC -s mr.mrrefChr5 230595 6 + 294540 ATTGAC -s simCow_chr6.simCow.chr6 368382 6 + 602619 GTCCAC -s simDog_chr6.simDog.chr6 358986 6 + 593897 CCCCAC -s simHuman_chr6.simHuman.chr6 367057 6 + 601863 GCCCAC -s simRat_chr6.simRat.chr6 376251 6 + 647215 ATTGAC - -a -s simMouse_chr6.simMouse.chr6 376979 18 + 636262 ATAAAAAAATCGTTGTAG -s Anc0.Anc0refChr3 10304 18 + 222631 TTGAAAAAATTGTCATGA -s Anc1.Anc1refChr6 43177 18 + 197743 TTGAAAAAATTGTCATGA -s Anc2.Anc2refChr13 12875 18 + 96486 TTGAAAAAATTGTCATGA -s mr.mrrefChr5 230601 18 + 294540 ATAAAAAAATTGTTGTGG -s simCow_chr6.simCow.chr6 368389 18 + 602619 TTGAAAAAGGTGCTGTGA -s simDog_chr6.simDog.chr6 358992 18 + 593897 TTGAAAAAATTGTCATGA -s simHuman_chr6.simHuman.chr6 367063 18 + 601863 CTGAAGAAATTGTCATGA -s simRat_chr6.simRat.chr6 376257 18 + 647215 ATCGAAAAATTGCGGTGG - -a -s simMouse_chr6.simMouse.chr6 376997 21 + 636262 GGGTATGCACGTGGACAGACT -s Anc0.Anc0refChr3 10322 18 + 222631 GGGTATGCTTCTGGC---ACT -s Anc1.Anc1refChr6 43195 18 + 197743 GGGTATGCTTCTGGC---ACT -s Anc2.Anc2refChr13 12893 18 + 96486 GGTCAGGCTTCTGGC---ACT -s mr.mrrefChr5 230619 21 + 294540 GGGTATGCATGTGGACAGACT -s simCow_chr6.simCow.chr6 368408 18 + 602619 GGTCAGGTTTCTGGC---ACT -s simDog_chr6.simDog.chr6 359010 18 + 593897 GGTCAGACTTCTGGT---ACT -s simHuman_chr6.simHuman.chr6 367081 18 + 601863 GAGTATGCTTTTGTC---ACT -s simRat_chr6.simRat.chr6 376275 21 + 647215 GGGCATGCATGTGGGCAGACT - -a -s simMouse_chr6.simMouse.chr6 377018 36 + 636262 AAAAGAGAGGTGAGTATTTTTGAACATTCCAATTGC -s Anc0.Anc0refChr3 10340 5 + 222631 AAA-------------------------------GC -s Anc1.Anc1refChr6 43213 5 + 197743 AAA-------------------------------GC -s Anc2.Anc2refChr13 12913 5 + 96486 AAA-------------------------------TG -s mr.mrrefChr5 230640 36 + 294540 AAAAGAGAGGTGAGTATTTTTGAACATTCCAATTGC -s simCow_chr6.simCow.chr6 368428 5 + 602619 AAA-------------------------------TG -s simDog_chr6.simDog.chr6 359030 5 + 593897 AAA-------------------------------TG -s simHuman_chr6.simHuman.chr6 367099 5 + 601863 AAA-------------------------------GC -s simRat_chr6.simRat.chr6 376296 36 + 647215 GAAAGAAAGGTGAGTATTTCTGAACACTCCGATTGC - -a -s simMouse_chr6.simMouse.chr6 377054 3 + 636262 AGT -s Anc0.Anc0refChr3 10346 3 + 222631 AGT -s Anc1.Anc1refChr6 43219 3 + 197743 AGT -s Anc2.Anc2refChr13 12919 3 + 96486 AGT -s mr.mrrefChr5 230676 3 + 294540 AGT -s simCow_chr6.simCow.chr6 368434 3 + 602619 AGT -s simDog_chr6.simDog.chr6 359036 3 + 593897 AGT -s simHuman_chr6.simHuman.chr6 367105 3 + 601863 AGT -s simRat_chr6.simRat.chr6 376332 3 + 647215 AGT - -a -s simMouse_chr6.simMouse.chr6 377057 5 + 636262 CTGTT -s Anc0.Anc0refChr3 10349 5 + 222631 TATGT -s Anc1.Anc1refChr6 43222 5 + 197743 TATGT -s Anc2.Anc2refChr13 12922 5 + 96486 TATGT -s mr.mrrefChr5 230679 5 + 294540 CTGTT -s simCow_chr6.simCow.chr6 368437 5 + 602619 CATAT -s simDog_chr6.simDog.chr6 359041 5 + 593897 TGTGT -s simHuman_chr6.simHuman.chr6 367108 5 + 601863 AATGT -s simRat_chr6.simRat.chr6 376335 5 + 647215 CTGTT - -a -s simMouse_chr6.simMouse.chr6 377062 32 + 636262 AGGAAGGTTTGTTTACAGTATCAAGAGATGGA -s Anc0.Anc0refChr3 10354 31 + 222631 AAGAAGGTTTG-TTACAGTATCAAAAGATGAA -s Anc1.Anc1refChr6 43227 31 + 197743 AAGAAGGTTTG-TTACAGTATCAAAAGATGAA -s Anc2.Anc2refChr13 12927 31 + 96486 AAGGAGGTTTG-TTACAGTATCAAAAGATGAA -s mr.mrrefChr5 230684 31 + 294540 AGGAAGGTTTG-TTACAGTATCAAGAGATGAA -s simCow_chr6.simCow.chr6 368442 31 + 602619 AAGGAGATCAG-TTACAATAATAAAAGATGAC -s simDog_chr6.simDog.chr6 359046 31 + 593897 AACGAGGTTTG-TTACAGTATCGAAAGATAAA -s simHuman_chr6.simHuman.chr6 367113 24 + 601863 AAGAGGGTTTG--------ATCAAAAGATGAA -s simRat_chr6.simRat.chr6 376341 31 + 647215 AGGGAGGTTTG-TTACAGTATTAAGAGATGAA - -a -s simMouse_chr6.simMouse.chr6 377094 114 + 636262 ATGAATCAGGTTCCACTATGGATGATATACAGCATTTAATAACAACTATCTGAGCGACATGGTGATCAACTTTTGAAATCAAAAATGACAGTAAGGGAAATCTGGCATGCAGCA -s Anc0.Anc0refChr3 10385 114 + 222631 ATAAAGAAGGATTTGCTATGGATGATATACAACTTTTTATTACAACTACCTGACAGTTAGGGTGATCAACTTTTGGAGTTAAAAATGATAGTAAGGTGAATATGCCATGTGGTG -s Anc1.Anc1refChr6 43258 114 + 197743 ATAAAGAAGGATTTGCTATGGATGATATACAACTTTTTATTACAACTACCTGACAGTTAGGGTGATCAACTTTTGGAGTTAAAAATGATAGTAAGGTGAATATGCCATGTGGTG -s Anc2.Anc2refChr13 12958 114 + 96486 ATAAAGAAGGATTTGCTATTGATGATACACAACTTTTTATTACAACTACCTGACAGTTTGGGAGACCAACTTTTGGAGTTAAAAATGTTAGTAAGGTGAATATGCCATGTGGTG -s mr.mrrefChr5 230715 114 + 294540 ATGAATAAGGTTCCGCTATGGATGATATACAGCATTTAATAACAACTACCTGAGCGTTATGGTGATCAACTTTTGAAATTAAAAATGACAGTAAGGGAAATCTGGCATGCAGCA -s simCow_chr6.simCow.chr6 368473 74 + 602619 ATAAACAAGGATTTACT-----TGATAAACAGCTTTCCATTATAACTAGATGAC-----------------------------------AGGAAGGTGAGTGCGCCATGTTGTG -s simDog_chr6.simDog.chr6 359077 114 + 593897 ATAAAGGAGGATATGCTATTGAACAGACACAACTTTTTGTTACAACTGCCTTATAGTTTGGGAGACCAACTTTTGGAGTTAAAAATGTTAGTCAGGCAAATATGCCATGTGGTG -s simHuman_chr6.simHuman.chr6 367137 107 + 601863 ATAAAGAATGATTTGCTATGGATGATATAAAACTTTTGAATACACCTACCTGACAGTTAAGGTGATTAACTTTTGGAGTTGGAGATGATTATAAGGTGAATATGCCA------- -s simRat_chr6.simRat.chr6 376373 114 + 647215 ATGAGTAAGGTTCCGCTATGGATGATCTACAGTGTTCAATAACGACTACCTGAGGGTTACAGCGAACAACTTTTGAAATTAAAAATGCCAGTATGGCAAATCTGGCATGCAGCA - -a -s simMouse_chr6.simMouse.chr6 377208 1 + 636262 A -s Anc0.Anc0refChr3 10499 1 + 222631 A -s Anc1.Anc1refChr6 43372 1 + 197743 A -s Anc2.Anc2refChr13 13072 1 + 96486 A -s mr.mrrefChr5 230829 1 + 294540 A -s simDog_chr6.simDog.chr6 359204 1 + 593897 A -s simHuman_chr6.simHuman.chr6 367244 1 + 601863 G -s simRat_chr6.simRat.chr6 376487 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 377209 30 + 636262 CATCATAAGCCTTAATTCTATAGTTAATCG -s Anc0.Anc0refChr3 10500 26 + 222631 CATCATAAGCCTTAATTCCATATT----GG -s Anc1.Anc1refChr6 43373 26 + 197743 CATCATAAGCCTTAATTCCATATT----GG -s Anc2.Anc2refChr13 13074 26 + 96486 CATCATAAGCCTTAATTCCATATT----GG -s mr.mrrefChr5 230830 30 + 294540 CATCATAAGCCTTAATTCTATAGTTAATGG -s simCow_chr6.simCow.chr6 368548 26 + 602619 CATCATGAGCCTTAATTCCATATT----GG -s simDog_chr6.simDog.chr6 359206 26 + 593897 CAGCATAAGCCCTAATTCCATATT----GG -s simHuman_chr6.simHuman.chr6 367245 26 + 601863 CATCACAAGCCTTAATTCCATATC----GG -s simRat_chr6.simRat.chr6 376488 30 + 647215 CATCTTAGGCCTTAGATCTATAGTGAATGG - -a -s simMouse_chr6.simMouse.chr6 377239 16 + 636262 GCAGCAAAGTGGGTGT -s Anc0.Anc0refChr3 10526 12 + 222631 GCAG----GTGGGTAT -s Anc1.Anc1refChr6 43399 12 + 197743 GCAG----GTGGGTAT -s Anc2.Anc2refChr13 13112 12 + 96486 GCAG----GTGGGTAT -s mr.mrrefChr5 230860 16 + 294540 GCAGCAAAGTGGGTGT -s simCow_chr6.simCow.chr6 368586 12 + 602619 GCAG----GTGGGTAT -s simDog_chr6.simDog.chr6 359244 12 + 593897 GCAG----GTGGGTAT -s simHuman_chr6.simHuman.chr6 367271 12 + 601863 GCAG----GTGAGTAT -s simRat_chr6.simRat.chr6 376518 16 + 647215 GCAGCAAAGTGGGTGT - -a -s simMouse_chr6.simMouse.chr6 377255 91 + 636262 GGACATCTCAGAAGGAGGGGACTCCAAGAGACTATGCCTGCAGATAGTACTAGCAAGTTAGGAGGATTTAGCCGGTTATGAGGGGGAGAAC -s Anc0.Anc0refChr3 10538 27 + 222631 GGACAGCCCAGAAGGAGGGG----------------------------------------------------------------GAGGACC -s Anc1.Anc1refChr6 43411 27 + 197743 GGACAGCCCAGAAGGAGGGG----------------------------------------------------------------GAGGACC -s Anc2.Anc2refChr13 13124 27 + 96486 GGACAGCCCAGAAGGAGGGG----------------------------------------------------------------GAGGACG -s mr.mrrefChr5 230876 74 + 294540 GGACATCCCAGAAGGAGGGGACTCCAAGAGACTATGCCTGCAGATAGTACTAGCAAGTTAGGAG-----------------GGGGAGGAAC -s simCow_chr6.simCow.chr6 368599 27 + 602619 GAACAGCCCAGAAAGAGGGG----------------------------------------------------------------GAGAACC -s simDog_chr6.simDog.chr6 359256 27 + 593897 GGACAGCCCAGAAGGAGGGG----------------------------------------------------------------GGGGACG -s simHuman_chr6.simHuman.chr6 367283 27 + 601863 GGACAGCCCAGAAGGAGGGG----------------------------------------------------------------GAGGACC -s simRat_chr6.simRat.chr6 376534 74 + 647215 GGACATCCCACAAGGAGGGGTCTGCAAGAGACCATGCCTGCAGATAGAACTAGCAAGTTAGGAG-----------------GGGGAGGATT - -a -s simMouse_chr6.simMouse.chr6 377346 32 + 636262 CCAAGAGGCTATGCCTACAGATTGTTTGAGAG -s Anc0.Anc0refChr3 10565 32 + 222631 CTGAGAGGCTATGGCTGTGGATTGTTTTAGGA -s Anc1.Anc1refChr6 43438 32 + 197743 CTGAGAGGCTATGGCTGTGGATTGTTTTAGGA -s Anc2.Anc2refChr13 13156 32 + 96486 CTGAGAGGCTATGGCTGTGGATTGTATTCAGA -s mr.mrrefChr5 230950 32 + 294540 CCAAGAGGCTATGCCTGCAGATTGTTTGAGGG -s simCow_chr6.simCow.chr6 368652 25 + 602619 CTGAGCAGCTATGGCTGTAGA-------CAGA -s simDog_chr6.simDog.chr6 359288 32 + 593897 CTGAGAGGCAATGGCCATGGATTGTATTCAGA -s simHuman_chr6.simHuman.chr6 367310 32 + 601863 CTGAGAGGCTACGGCTGTGGATATTTTTAGGA -s simRat_chr6.simRat.chr6 376608 32 + 647215 CCAAGGTGTTATGCCTGCAGATTATTTAAGGG - -a -s simMouse_chr6.simMouse.chr6 377378 116 + 636262 TTAAATTCTGAAAAGTGGATTTCCAGATGGTTTGCAGAAGTTAGCATGGATGCCATGATCCTGATGTACCACAAGGGCATACTTAACACCAAGGCAGAGTGCTCCTGAGATACTGT -s Anc0.Anc0refChr3 10599 116 + 222631 TTAATTTCTGAATAATGGATTTCCAAGTGATTTGTGGAAGTCCGCACAGATGCCCTGATTCTGACATACCACAAGGGCATACTTGACACCAAGGCAGATTGATCCCAAGTTACTAT -s Anc1.Anc1refChr6 43472 116 + 197743 TTAATTTCTGAATAATGGATTTCCAAGTGATTTGTGGAAGTCCGCACAGATGCCCTGATTCTGACATACCACAAGGGCATACTTGACACCAAGGCAGATTGATCCCAAGTTACTAT -s Anc2.Anc2refChr13 13190 116 + 96486 TTAATTTCTGAATAATGGATTTCCTAGTAATTTGTGGAAGTCCGCACAGATGCCCTGATCTTGGCATACCACAAGGGCATACTTGACAACAAGGCAGATTGATCCCAAGTTACTAT -s mr.mrrefChr5 230982 116 + 294540 TTAAATTCTGAAAAGTGGATTTCCAGATGGTTTGTAGAAGTCAGCATGGATGCCCTGATTCTGATATACCACAAGGGCATACTTAACACCAAGGCAGAGTGCTCCCAAGATACTAT -s simCow_chr6.simCow.chr6 368679 116 + 602619 TTAATTTCTGAATAATGGATTTCTCAGTTATTTGTTGAAGTCCGCAAAGATTCCCTGGTCTTGGCATACCACAAGGGCATACTTGACAACAAGGCAGTTTGATCCCACGCCACTGT -s simDog_chr6.simDog.chr6 359322 110 + 593897 TCATTTTCTGTGTGATGGATTTCCTAGTAAATTGTGGAAA------CAGATGCCCTGATCTTGGCATGCCACAAGAGCATACTTGACAACAAGGCAGATTAATCCCAAGTTACTAG -s simHuman_chr6.simHuman.chr6 367344 116 + 601863 TTAAGTTCTGAATAACAAATTTCCAAGTGATTTGTGGTAGTCCACTCAGCTGCCCTGATTCCAACATACTACAAGGGAATATTGGACACCAAGGTAGATTGACCCCAAGTTACTAT -s simRat_chr6.simRat.chr6 376640 112 + 647215 TTAAATACTGAAAAGTGGATTTCCAGATTGTTTATAGGAGTCAGCATGGATGCACTGATTTTGATATACC----GGGCATACTTAATGTCAAGGCAGAGTGCTCCCAAGGTATTAT - -a -s simMouse_chr6.simMouse.chr6 377494 13 + 636262 TGGCCCAATCTAA -s Anc0.Anc0refChr3 10723 13 + 222631 CCAACTATTCAAG -s Anc1.Anc1refChr6 43596 13 + 197743 CCAACTATTCAAG -s Anc2.Anc2refChr13 13314 13 + 96486 CCAACTATTCAAG -s mr.mrrefChr5 231098 13 + 294540 CGGACCATTCTAA -s simCow_chr6.simCow.chr6 368803 3 + 602619 TCA---------- -s simDog_chr6.simDog.chr6 359440 13 + 593897 CCAACTATTCAAG -s simHuman_chr6.simHuman.chr6 367468 13 + 601863 TCAACTATCTGAG -s simRat_chr6.simRat.chr6 376752 13 + 647215 CAGACCATTCCAA - -a -s simMouse_chr6.simMouse.chr6 377507 48 + 636262 GGAACTGACCGATAAGCAATGTTGTGACAAAGATAGAAATGTGTGTTA -s Anc0.Anc0refChr3 10747 47 + 222631 GGGAGTGA-GTAATAGTGATGTGGTGACAGATTGAGACTTGTGTGTAA -s Anc1.Anc1refChr6 43620 48 + 197743 GGGAGTGACGTAATAGTGATGTGGTGACAGATTGAGACTTGTGTGTAA -s Anc2.Anc2refChr13 13338 47 + 96486 GGGAGTGA-GTAATAGTGATGTGGTGACAGATTGAGACTTGTGTGTAA -s mr.mrrefChr5 231111 48 + 294540 GGGAGTGACCGATAAGCAATGTTGTGACAAAGATAGAAATGTGTGTTA -s simCow_chr6.simCow.chr6 368806 46 + 602619 -GGATTGA-CTAATAGTGATATGGCAACAGGTTGAGATTTGTGTGTAA -s simDog_chr6.simDog.chr6 359464 47 + 593897 GGGAGTGA-GTAATAGTGATGTGGTGACAGATGGAGACTTGTGTGTAC -s simHuman_chr6.simHuman.chr6 367517 48 + 601863 GAGAGTGACTTAATAATGATGTGCGGACAGATTGAGACTTGTGTATGA -s simRat_chr6.simRat.chr6 376765 48 + 647215 GGGAGTGACCAATAACCAATGTTGTGACGAAGATAGAAACTTGTGTTG - -a -s simMouse_chr6.simMouse.chr6 377555 48 + 636262 CTTGTACAAGAGTCAACATTATAAGAAGTATGTAGGTAGGGTTGAGTT -s Anc0.Anc0refChr3 10795 48 + 222631 CTTGTGCAAGAGTCAACATCATAAGTAGTATAGTGGTAGTATTCAGTT -s Anc1.Anc1refChr6 43669 48 + 197743 CTTGTGCAAGAGTCAACATCATAAGTAGTATAGTGGTAGTATTCAGTT -s Anc2.Anc2refChr13 13386 48 + 96486 CTGGTGCAAGAGTCAACATCATATGTAGTATAGTGGTAGTATTCAGTC -s mr.mrrefChr5 231159 48 + 294540 CTTGTGCAAGAGTCAACATTATAAGAAGTATATAGGTAGGGTTGAGTT -s simCow_chr6.simCow.chr6 368853 48 + 602619 CTAGTGCAAGGGTCAGCATCATATGTAGTACAGTGGTAGTATTCAGCC -s simDog_chr6.simDog.chr6 359512 48 + 593897 CTGGCACAAGAGGCAACTTCATATGTAGTATAGTGGTAGTATTTAGTC -s simHuman_chr6.simHuman.chr6 367566 48 + 601863 CTTGTGCAAAAATCAACATCATAAGTAGTATACTGGTGGTCTTCAGTT -s simRat_chr6.simRat.chr6 376813 48 + 647215 CTTTTGCAAGAGTCAACATTATAAGAAGTATATAGGTAGGGTTGAGTC - -a -s simMouse_chr6.simMouse.chr6 377603 1 + 636262 A -s Anc0.Anc0refChr3 10843 1 + 222631 A -s Anc1.Anc1refChr6 43717 1 + 197743 A -s Anc2.Anc2refChr13 13452 1 + 96486 A -s mr.mrrefChr5 231207 1 + 294540 A -s simCow_chr6.simCow.chr6 368919 1 + 602619 C -s simDog_chr6.simDog.chr6 359578 1 + 593897 A -s simHuman_chr6.simHuman.chr6 367614 1 + 601863 A -s simRat_chr6.simRat.chr6 376861 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 377604 2 + 636262 TT -s Anc0.Anc0refChr3 10851 2 + 222631 TT -s Anc1.Anc1refChr6 43725 2 + 197743 TT -s Anc2.Anc2refChr13 13460 2 + 96486 TT -s mr.mrrefChr5 231208 2 + 294540 TT -s simCow_chr6.simCow.chr6 368927 1 + 602619 -T -s simDog_chr6.simDog.chr6 359586 2 + 593897 TT -s simHuman_chr6.simHuman.chr6 367622 2 + 601863 TT -s simRat_chr6.simRat.chr6 376862 2 + 647215 TT - -a -s simMouse_chr6.simMouse.chr6 377606 33 + 636262 TACTTATAGTGACTGTAAATGATATCAATATTG -s Anc0.Anc0refChr3 10853 29 + 222631 GACTAATA----TTGTAAACCATATGGAAATTG -s Anc1.Anc1refChr6 43727 29 + 197743 GACTAATA----TTGTAAACCATATGGAAATTG -s Anc2.Anc2refChr13 13462 29 + 96486 GACTAGTG----TTGTAAACCATATGGAAATTG -s mr.mrrefChr5 231210 33 + 294540 TACTTATAGTGACTGTAAATGATATCAATATTG -s simCow_chr6.simCow.chr6 368928 29 + 602619 GACTAGTG----TTGTAAATCATATGGAAATTG -s simDog_chr6.simDog.chr6 359588 23 + 593897 GAC----------TGTGAACCATATGGAAACTG -s simHuman_chr6.simHuman.chr6 367624 29 + 601863 GACTAATA----TTGTAAACCATCTGGAAATTG -s simRat_chr6.simRat.chr6 376902 33 + 647215 TACTTATAGTGACTGTAAATGATATCATGATTG - -a -s simMouse_chr6.simMouse.chr6 377639 35 + 636262 AATGCTACTATAACATGACGGGGTTTCTTTTTCCT -s Anc0.Anc0refChr3 10989 33 + 222631 AATGCT-CAATAACATG-GGGGGTTTCTTTTTTCA -s Anc1.Anc1refChr6 43863 34 + 197743 AATGCT-CAATAACATGGGGGGGTTTCTTTTTTCA -s Anc2.Anc2refChr13 13598 33 + 96486 AGTGCG-CAAAGGCATG-GGAAATTTTTTTTTTCA -s mr.mrrefChr5 231243 35 + 294540 AATGCTACTATAACATGAGGGGGTTTCTTTTTCCT -s simCow_chr6.simCow.chr6 369013 33 + 602619 AGTGCG-CAAAGGCATG-GGAAATTTTTTTTTTCA -s simDog_chr6.simDog.chr6 359721 4 + 593897 -------------------------------TTCA -s simHuman_chr6.simHuman.chr6 367816 34 + 601863 AATGCT-CAATAATATTGGGGGGTTTCTTATTTCA -s simRat_chr6.simRat.chr6 376935 35 + 647215 AATGCTACTATAACATGAGGAGGTTTCTTTTTCCC - -a -s simMouse_chr6.simMouse.chr6 377674 37 + 636262 CAGGGCTGTATGGATATATGTATGCCCTTCTTCCATA -s Anc0.Anc0refChr3 11022 37 + 222631 TCAGCCTGCAGGGATATCTCCATGCCATTCTTCTTCT -s Anc1.Anc1refChr6 43897 37 + 197743 TCAGCCTGCAGGGATATCTCCATGCCATTCTTCTTCT -s Anc2.Anc2refChr13 13634 37 + 96486 TCGGCCTGCAGGGATGTCTCCATGCCATTCTTCTTCT -s mr.mrrefChr5 231278 37 + 294540 CAAGGCTGTATGGATATATGTATGCCCTTCTTCCATA -s simCow_chr6.simCow.chr6 369049 36 + 602619 TCGGCCTGTGGAGATGT-TCCGTGCCATTCTTCTTCT -s simDog_chr6.simDog.chr6 359728 28 + 593897 TCGGCCTGCAGGAATGTCCCCA--------TTCT-CA -s simHuman_chr6.simHuman.chr6 367850 37 + 601863 TCAGTCTGCTGGGACATCTCCATGCAATTTTTCTGCT -s simRat_chr6.simRat.chr6 376970 37 + 647215 CAAGCCTATATGGATATATGTATGCCCTTCTTCCATC - -a -s simMouse_chr6.simMouse.chr6 377711 24 + 636262 CTTAACTATTTATTGAGGTTGGCT -s Anc0.Anc0refChr3 11059 24 + 222631 TATTATTAATTAGCAAAGTTGGTT -s Anc1.Anc1refChr6 43934 24 + 197743 TATTATTAATTAGCAAAGTTGGTT -s Anc2.Anc2refChr13 13671 24 + 96486 TAATAATAATTAGCAAAGTTGGTT -s mr.mrrefChr5 231315 24 + 294540 CTTAATTATTTATTGAGGTTGGCT -s simCow_chr6.simCow.chr6 369086 24 + 602619 TTCTAATACTTAGTAAGGTTGGTG -s simDog_chr6.simDog.chr6 359756 24 + 593897 TAATAATTATTAGCAAAGTCAGTT -s simHuman_chr6.simHuman.chr6 367887 24 + 601863 TCTTATTAATTAACAAAGTTGGTT -s simRat_chr6.simRat.chr6 377007 24 + 647215 CTTAATTATTTATTGAGGTTGGCT - -a -s simMouse_chr6.simMouse.chr6 377735 49 + 636262 AAGGTTTTTGTGATCCTGGCTTAACCAGTGGACGATTGTTTGAGGAAAA -s Anc0.Anc0refChr3 11083 49 + 222631 CAGATTTTTGTGATCTCTGCTTAGTCAGTGGACCATTGTTTGAGGAAAG -s Anc1.Anc1refChr6 43958 49 + 197743 CAGATTTTTGTGATCTCTGCTTAGTCAGTGGACCATTGTTTGAGGAAAG -s Anc2.Anc2refChr13 13695 49 + 96486 CAGATTTTTGTGATCTCTGCTTAGTCAGTGGACCATTGTTTGAGGAAAG -s mr.mrrefChr5 231339 49 + 294540 AAGGTTTTTGTGATCCTGGCTTAACCAGTGGACCATTGTTTGAGGAAAG -s simCow_chr6.simCow.chr6 369110 49 + 602619 TGGATTTTTATGATCTCTGCGTAGTCAGCAGAGCATTGTTTGAGGAAAG -s simDog_chr6.simDog.chr6 359780 47 + 593897 CAGATTTTTGAGGCCTCTGCTTAGTCAGTGGGCCTTTGTTTGAG--AAG -s simHuman_chr6.simHuman.chr6 367912 49 + 601863 CAGATTCTTGTAATCTCTGCTTAGTCAGTGGACCATTGTTTGAGCACAG -s simRat_chr6.simRat.chr6 377031 49 + 647215 AAGGTTTCTGTGATCCAGGGTTAACTAGTGGACCATTGTTTAAGGAAAG - -a -s simMouse_chr6.simMouse.chr6 377784 16 + 636262 TCTGTTATGCCTAGAT -s Anc0.Anc0refChr3 11132 16 + 222631 CCTGGTATTCATAGAT -s Anc1.Anc1refChr6 44007 16 + 197743 CCTGGTATTCATAGAT -s Anc2.Anc2refChr13 13744 16 + 96486 CCTGGTATTCATAAAC -s mr.mrrefChr5 231388 16 + 294540 CCTGGTATGCCTAGAT -s simCow_chr6.simCow.chr6 369159 16 + 602619 CCTGGTATTCATAAAC -s simDog_chr6.simDog.chr6 359827 16 + 593897 CCTGGTATTCATGAAC -s simHuman_chr6.simHuman.chr6 367961 16 + 601863 CCTGGTATTTATAGAT -s simRat_chr6.simRat.chr6 377090 16 + 647215 CCTGGTGTGCTTAGAT - -a -s simMouse_chr6.simMouse.chr6 377800 20 + 636262 GTGATTCCATCCAATCCTTT -s Anc0.Anc0refChr3 11148 20 + 222631 CCTATTAGGTCTAACCCTTT -s Anc1.Anc1refChr6 44023 20 + 197743 CCTATTAGGTCTAACCCTTT -s Anc2.Anc2refChr13 13760 20 + 96486 CCTATTAGGTCTAACCCTTT -s mr.mrrefChr5 231404 20 + 294540 GTGATTCCATCCAATCCTTT -s simCow_chr6.simCow.chr6 369176 18 + 602619 CTTATTAGGTCAAACCCT-- -s simDog_chr6.simDog.chr6 359843 20 + 593897 CCTATTAGGTCTAGCCCTTT -s simHuman_chr6.simHuman.chr6 367977 20 + 601863 CCTATTAGTTCTAACCCTTT -s simRat_chr6.simRat.chr6 377106 20 + 647215 GTGATTCCATCCAATCCACT - -a -s simMouse_chr6.simMouse.chr6 377820 12 + 636262 AATGGCATTAGC -s Anc0.Anc0refChr3 11181 12 + 222631 ATTGACCTTGAC -s Anc1.Anc1refChr6 44056 12 + 197743 ATTGACCTTGAC -s Anc2.Anc2refChr13 13793 12 + 96486 TTTGACCCCGAC -s mr.mrrefChr5 231424 12 + 294540 AATGGCATTAGC -s simCow_chr6.simCow.chr6 369201 5 + 602619 TTTGA------- -s simDog_chr6.simDog.chr6 359876 12 + 593897 TTTGACCCCGAC -s simHuman_chr6.simHuman.chr6 368010 12 + 601863 ATTGACCTTGAC -s simRat_chr6.simRat.chr6 377126 12 + 647215 AATGGCACTAGC - -a -s simMouse_chr6.simMouse.chr6 377832 1 + 636262 T -s Anc0.Anc0refChr3 11194 1 + 222631 T -s Anc1.Anc1refChr6 44069 1 + 197743 T -s Anc2.Anc2refChr13 13806 1 + 96486 A -s mr.mrrefChr5 231436 1 + 294540 T -s simDog_chr6.simDog.chr6 359889 1 + 593897 A -s simHuman_chr6.simHuman.chr6 368023 1 + 601863 T -s simRat_chr6.simRat.chr6 377138 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 377833 9 + 636262 TGCCCTCAA -s Anc0.Anc0refChr3 11195 9 + 222631 TGCCCTCAG -s Anc1.Anc1refChr6 44070 9 + 197743 TGCCCTCAG -s Anc2.Anc2refChr13 13807 9 + 96486 TCCTCTCAG -s mr.mrrefChr5 231437 9 + 294540 TGCCCTCAA -s simCow_chr6.simCow.chr6 369784 1 + 602619 --------G -s simDog_chr6.simDog.chr6 359893 9 + 593897 TCCTCTCAG -s simHuman_chr6.simHuman.chr6 368024 9 + 601863 TGCCCTCAG -s simRat_chr6.simRat.chr6 377139 9 + 647215 TGCCCTCAA - -a -s simMouse_chr6.simMouse.chr6 377842 5 + 636262 TTGAG -s Anc0.Anc0refChr3 11204 5 + 222631 TTGGA -s Anc1.Anc1refChr6 44079 5 + 197743 TTGGA -s Anc2.Anc2refChr13 13816 5 + 96486 TTGGA -s mr.mrrefChr5 231446 5 + 294540 TTGAA -s simCow_chr6.simCow.chr6 369206 5 + 602619 TTCAG -s simCow_chr6.simCow.chr6 369785 5 + 602619 TTGGG -s simDog_chr6.simDog.chr6 359902 5 + 593897 TCGGA -s simHuman_chr6.simHuman.chr6 368033 5 + 601863 TTGGA -s simRat_chr6.simRat.chr6 377148 5 + 647215 CTGAA - -a -s simMouse_chr6.simMouse.chr6 377847 10 + 636262 ATGAGCATCG -s Anc0.Anc0refChr3 11214 9 + 222631 ATGAGCAT-G -s Anc1.Anc1refChr6 44089 9 + 197743 ATGAGCAT-G -s Anc2.Anc2refChr13 13826 9 + 96486 ATGAGCTT-G -s mr.mrrefChr5 231451 10 + 294540 ATGAGCATCG -s simCow_chr6.simCow.chr6 369216 9 + 602619 ATGACCTT-G -s simCow_chr6.simCow.chr6 369795 9 + 602619 GTGAATGT-G -s simDog_chr6.simDog.chr6 359912 9 + 593897 ATGAGCTT-G -s simHuman_chr6.simHuman.chr6 368043 9 + 601863 ATGAGCAT-G -s simRat_chr6.simRat.chr6 377153 10 + 647215 AGATGCATAG - -a -s simMouse_chr6.simMouse.chr6 377857 30 + 636262 GAGTTCTACGGTCAACCTTTCCTACCTAAC -s Anc0.Anc0refChr3 11223 18 + 222631 GAGTTTTACAGTCAGCCT------------ -s Anc1.Anc1refChr6 44098 18 + 197743 GAGTTTTACAGTCAGCCT------------ -s Anc2.Anc2refChr13 13835 18 + 96486 GAGTTTTACAGTCAGCCA------------ -s mr.mrrefChr5 231461 30 + 294540 GAGTTCTACAGTCAACCTTTCCTACCTAAC -s simCow_chr6.simCow.chr6 369229 18 + 602619 GACTTTTACAGTCAGCCA------------ -s simCow_chr6.simCow.chr6 369804 18 + 602619 GACTTTTGCAGTCAGCCA------------ -s simDog_chr6.simDog.chr6 359921 18 + 593897 GAGTTTTACAGCCGGCCC------------ -s simHuman_chr6.simHuman.chr6 368052 18 + 601863 GAGTTTTACAATCAGCCT------------ -s simRat_chr6.simRat.chr6 377163 30 + 647215 TAGCTCTACAGTCAACCTCACCTATCTAAC - -a -s simMouse_chr6.simMouse.chr6 377887 49 + 636262 TATTCAGGGAGTATCTTCTGTGTTTTTTTGAAGAGACTATTTTCCGCTG -s Anc0.Anc0refChr3 11241 19 + 222631 ------------------------------GGGGGAATATTTCATGCCT -s Anc1.Anc1refChr6 44116 19 + 197743 ------------------------------GGGGGAATATTTCATGCCT -s Anc2.Anc2refChr13 13853 19 + 96486 ------------------------------GGGGAAATATTTCATACCT -s mr.mrrefChr5 231491 49 + 294540 TATTCAGGGAGTATCTTCTGTGTTTTTTTGAAGAGACTATTTTCCGCTG -s simCow_chr6.simCow.chr6 369247 19 + 602619 ------------------------------AGGGAAACATTTCATGTCT -s simCow_chr6.simCow.chr6 369822 18 + 602619 ------------------------------GGGAG-ATAGTCGGTACCT -s simDog_chr6.simDog.chr6 359939 19 + 593897 ------------------------------TGGGAAATGTTTCACACCT -s simHuman_chr6.simHuman.chr6 368070 19 + 601863 ------------------------------GGGGGTACATTTCATGCCA -s simRat_chr6.simRat.chr6 377199 49 + 647215 TATCTAGAGAGTATCTTCTGTGTTGTTTTGAAGAGACTATCTACCAATG - -a -s simMouse_chr6.simMouse.chr6 377936 15 + 636262 GTAATGGACACTCAA -s Anc0.Anc0refChr3 11272 15 + 222631 GAAATGGACACTCAA -s Anc1.Anc1refChr6 44147 15 + 197743 GAAATGGACACTCAA -s Anc2.Anc2refChr13 13884 15 + 96486 AAACTGGACACTCAA -s mr.mrrefChr5 231552 15 + 294540 GTAATGGACACTCAA -s simCow_chr6.simCow.chr6 369278 15 + 602619 GAACTGGACACACAT -s simCow_chr6.simCow.chr6 369852 15 + 602619 AAGAAGGACACTCAA -s simDog_chr6.simDog.chr6 359970 15 + 593897 AAACTGGACAGTCAA -s simHuman_chr6.simHuman.chr6 368101 15 + 601863 GAAAAGGATACTTGA -s simRat_chr6.simRat.chr6 377260 15 + 647215 GTAATGGACACTCAA - -a -s simMouse_chr6.simMouse.chr6 377951 1 + 636262 G -s Anc0.Anc0refChr3 11287 1 + 222631 G -s Anc1.Anc1refChr6 44162 1 + 197743 G -s Anc2.Anc2refChr13 13899 1 + 96486 G -s mr.mrrefChr5 231567 1 + 294540 G -s simCow_chr6.simCow.chr6 369867 1 + 602619 C -s simDog_chr6.simDog.chr6 359985 1 + 593897 G -s simHuman_chr6.simHuman.chr6 368116 1 + 601863 G -s simRat_chr6.simRat.chr6 377275 1 + 647215 G - -a -s simMouse_chr6.simMouse.chr6 377952 55 + 636262 TAACTGGTGAACCTGAGCAGTAGTCAGGCATGCATGAAACGGTCTTACTAAGTTG -s Anc0.Anc0refChr3 11288 55 + 222631 TTTATGGCAAACCTGGGAGGCAGTCAGGCAAGCATGGAAGCACCTTACTAAGTTG -s Anc1.Anc1refChr6 44163 55 + 197743 TTTATGGCAAACCTGGGAGGCAGTCAGGCAAGCATGGAAGCACCTTACTAAGTTG -s Anc2.Anc2refChr13 13900 55 + 96486 TTTATGGCAAACCTGGGAGGCAGTCAGGCAAGCATGGAAGCACCTCACTAAGTTG -s mr.mrrefChr5 231568 55 + 294540 TAACTGGTAAACCTGAGCAGTAGTCAGGCATGCATGAAACGGTCTTACTAAGTTG -s simCow_chr6.simCow.chr6 369293 51 + 602619 TTTC----AAACCTGAGAGACTGACAGGCAAGCCTGGAATCACCTCAGTCAGTAG -s simCow_chr6.simCow.chr6 369868 51 + 602619 TACA----AAACCCGAGAGGCTGTCAGGCAAACATGGAAGCAGCTCACTAAGATG -s simDog_chr6.simDog.chr6 359986 38 + 593897 TTTATGGCAAATGTGGAAGGCAA-----------------CACCTCACTAAGTTG -s simHuman_chr6.simHuman.chr6 368117 55 + 601863 TTTATGGCAAACCTGGGAGGCAGTCAGGCAAGTATGGAAGCACCTTACTAAGCTG -s simRat_chr6.simRat.chr6 377276 55 + 647215 TCGCTGGTAGACCTGAGCAGTAATCAGGCATGCATGAAACAGGCTTACTAAGTTG - -a -s simMouse_chr6.simMouse.chr6 378007 69 + 636262 TTGCAGGGCATTCTAGCCATGGAAATGCACCAATTAGTGGGGAGACCATTATTTTAGGCAGAAACTTGT -s Anc0.Anc0refChr3 11351 69 + 222631 TTGCAGGTCATTCTCAAAACCAAAACGCACCTGTTGGTGTGGGCACTATTTGTTTAGGAAGATATTGGT -s Anc1.Anc1refChr6 44226 69 + 197743 TTGCAGGTCATTCTCAAAACCAAAACGCACCTGTTGGTGTGGGCACTATTTGTTTAGGAAGATATTGGT -s Anc2.Anc2refChr13 13963 69 + 96486 TTGCTGGTCATTCTCAAAACCAAAACACCCCTGTTGGTGTGTGCATTATTTGTTTGGGAAGATATTGGT -s mr.mrrefChr5 231623 69 + 294540 TTGCAGGGCATTCTAGCCATGAAAATGCACCAATTAGTGGGGAGACCATTTTTTTAGGCAGAAACTTGT -s simCow_chr6.simCow.chr6 369352 69 + 602619 TTGCTAGTTGTTCTTAAAGCCAAAGCACCCCTGTCGGAGTGTGCATTATATGTTTAGGAAGACGTTGTT -s simCow_chr6.simCow.chr6 369927 69 + 602619 TTGTGGGTCATTCTTAAAACCAAAGCGCCCCTGTTGATGGGTGTGCCATCTGTGAGTTAAGGTATGGGT -s simDog_chr6.simDog.chr6 360032 69 + 593897 CTGCTGTTCATTCCCCAAACTAAAACACCACTGTTGGTATGTGCATTATTTGTTTGGGAAGATATTGGC -s simHuman_chr6.simHuman.chr6 368180 69 + 601863 TTGCAGATCAGTCTCATAACCAAAACGCACCTGTTGGAGTGGGCGCTATTTGTTTAGGAAGATATTGGT -s simRat_chr6.simRat.chr6 377331 58 + 647215 ----------TTCTTGCCATGAAAATGTACCAATTAGTGAGAAGACCATTTTTCTAGGCCGAAA-TTGT - -a -s simMouse_chr6.simMouse.chr6 378076 44 + 636262 GTATGGTTTTTTAGGCTGAAACTCATGTTGGTTTGCTGTACAAA -s Anc0.Anc0refChr3 11420 19 + 222631 GACTGGCA-------------------------TGCTCCATAAG -s Anc1.Anc1refChr6 44295 19 + 197743 GACTGGCA-------------------------TGCTCCATAAG -s Anc2.Anc2refChr13 14032 19 + 96486 GATTAGCA-------------------------CGCTCCATATG -s mr.mrrefChr5 231692 44 + 294540 GTCTGGTTTTTTAGGCTGAAACTCATGTTGGTTTGCTGTACAAG -s simCow_chr6.simCow.chr6 369421 19 + 602619 GATTAGCA-------------------------CGTTCCATACG -s simCow_chr6.simCow.chr6 369996 19 + 602619 GCTTAGTG-------------------------TGCTCTCTATG -s simDog_chr6.simDog.chr6 360103 18 + 593897 GATCCTCC-------------------------CGCTCC-CATG -s simHuman_chr6.simHuman.chr6 368249 19 + 601863 GACTGGCA-------------------------TGCTCCGTAAG -s simRat_chr6.simRat.chr6 377389 44 + 647215 GTCTGGTCTTCTAGGTAGAAACTTGTGTTGAGTTGCTGTACAAG - -a -s simMouse_chr6.simMouse.chr6 378120 28 + 636262 AGTAAATATCTAATATCAGCACAGAGTG -s Anc0.Anc0refChr3 11439 28 + 222631 TTTAAATATCTAACATGGGAAAAGAGTC -s Anc1.Anc1refChr6 44314 28 + 197743 TTTAAATATCTAACATGGGAAAAGAGTC -s Anc2.Anc2refChr13 14051 28 + 96486 TTGAAATATCTAACATGGGAAAAGAGTC -s mr.mrrefChr5 231736 28 + 294540 AGTAAATATCTAATATCAGCATAGAGTG -s simCow_chr6.simCow.chr6 369440 28 + 602619 TTGAAATACCTAACGCTCGAAAAGAGTT -s simCow_chr6.simCow.chr6 370015 19 + 602619 ---------CCAACATGGGAAAAGAGTT -s simDog_chr6.simDog.chr6 360123 28 + 593897 TTGAAATATCTAATATGGGAAGAGAGTC -s simHuman_chr6.simHuman.chr6 368268 11 + 601863 TTTAAAGGTCT----------------- -s simRat_chr6.simRat.chr6 377433 28 + 647215 GATAAATATCTAATATCAGAATACAGTG - -a -s simMouse_chr6.simMouse.chr6 378148 6 + 636262 CTATAA -s Anc0.Anc0refChr3 11467 6 + 222631 TTATAA -s Anc1.Anc1refChr6 44342 6 + 197743 TTATAA -s Anc2.Anc2refChr13 14079 6 + 96486 TTATCA -s mr.mrrefChr5 231764 6 + 294540 CTATAA -s simCow_chr6.simCow.chr6 369468 6 + 602619 CCATCA -s simCow_chr6.simCow.chr6 370034 6 + 602619 TTATCA -s simDog_chr6.simDog.chr6 360151 6 + 593897 TTATCA -s simHuman_chr6.simHuman.chr6 368279 5 + 601863 -CATAG -s simRat_chr6.simRat.chr6 377467 6 + 647215 CTATTA - -a -s simMouse_chr6.simMouse.chr6 378154 12 + 636262 TATGAGATTAAA -s Anc0.Anc0refChr3 11473 12 + 222631 AGTGAGAATAAA -s Anc1.Anc1refChr6 44348 12 + 197743 AGTGAGAATAAA -s Anc2.Anc2refChr13 14085 12 + 96486 AGTGGGAATAAA -s mr.mrrefChr5 231770 12 + 294540 TATGAGATTAAA -s simCow_chr6.simCow.chr6 369476 12 + 602619 AGTGGGAATAGA -s simCow_chr6.simCow.chr6 370040 12 + 602619 AGTGGAAATAGA -s simDog_chr6.simDog.chr6 360157 12 + 593897 AATGGGCAAAAA -s simHuman_chr6.simHuman.chr6 368284 12 + 601863 AGTGAGAATAAT -s simRat_chr6.simRat.chr6 377473 12 + 647215 TATGAGACTAAA - -a -s simMouse_chr6.simMouse.chr6 378166 12 + 636262 ACGTCTTTGTAC -s Anc0.Anc0refChr3 11485 11 + 222631 -TGTCTTCCTAC -s Anc1.Anc1refChr6 44360 11 + 197743 -TGTCTTCCTAC -s Anc2.Anc2refChr13 14097 11 + 96486 -TGTCTTCCTAC -s mr.mrrefChr5 231782 12 + 294540 ATGTCTTTGTAC -s simCow_chr6.simCow.chr6 369488 11 + 602619 -TGTCTTCCCAC -s simCow_chr6.simCow.chr6 370052 11 + 602619 -TGTCTTCCCAC -s simDog_chr6.simDog.chr6 360169 11 + 593897 -TGTCTTCCTAT -s simHuman_chr6.simHuman.chr6 368296 11 + 601863 -TGCATTCCTAC -s simRat_chr6.simRat.chr6 377487 12 + 647215 ATGTCTTTGTAC - -a -s simMouse_chr6.simMouse.chr6 378178 12 + 636262 AGGTTGTGTTCT -s Anc0.Anc0refChr3 11496 12 + 222631 AGGCAGTGTCCC -s Anc1.Anc1refChr6 44371 12 + 197743 AGGCAGTGTCCC -s Anc2.Anc2refChr13 14108 12 + 96486 AGGCAGTGTCCC -s mr.mrrefChr5 231794 12 + 294540 AGGCTGTGTTCT -s simCow_chr6.simCow.chr6 369499 12 + 602619 CGGCAGTGTCCC -s simCow_chr6.simCow.chr6 370063 12 + 602619 AGGCAGGGCCCC -s simDog_chr6.simDog.chr6 360185 12 + 593897 ATGCAGTGTCCC -s simHuman_chr6.simHuman.chr6 368307 12 + 601863 AGGCAGCGTCCA -s simRat_chr6.simRat.chr6 377499 12 + 647215 CGGCTGTGTTCT - -a -s simMouse_chr6.simMouse.chr6 378190 153 + 636262 TAATTGATTTATCATAGTGCAGTGTGACTGCACAGAGGAATACCAGGTCGCTCCAAGTCAAGGATTTTCCCCAGTAAGTGTTTAATGTATAAAGGGTACATGCGAAATGTTGATATCATATTAAGTAGTGCAAGCAGTGGGAGTAATACAAGT -s Anc0.Anc0refChr3 11508 153 + 222631 AAACCAATTTATCATAATACATTGTGTCTGCACAGAGAGATACTATGTTACTTCGAATCAAGAATATTCTCCAACAAGTTTTTAGTGCACAAAGGGTACATGCCTAATGTCCTTATTATATTAGGTAGTGCAGACGGTTGGGGTGACACAAGC -s Anc1.Anc1refChr6 44383 153 + 197743 AAACCAATTTATCATAATACATTGTGTCTGCACAGAGAGATACTATGTTACTTCGAATCAAGAATATTCTCCAACAAGTTTTTAGTGCACAAAGGGTACATGCCTAATGTCCTTATTATATTAGGTAGTGCAGACGGTTGGGGTGACACAAGC -s Anc2.Anc2refChr13 14120 153 + 96486 AAACCAATTTCTCATAATATGTTGTGTCTGCACAGAGAGATACTATGTTACTTCGAATCAAGAGTATTCTCCAACAAGTTTTTAATACACAAAGGCTACATGCCTAATGTCCTTACTATATTGGGTAATGCAGATGGTTGGGGTGACACAAGC -s mr.mrrefChr5 231806 153 + 294540 TAATTGATTTATCATAGTGCAGTGTGACTGCACAGAGGAATACCAGGTTACTCCAAGTCAAGGATTTTCCCCAGCAAGTGTTTAGTGTACAAAGGGTACATGCGTAATGTTGTTATCATATTAAGTAGTGCAAGCAGTTGGGGTAATACAAGT -s simCow_chr6.simCow.chr6 369511 153 + 602619 AAACCAATTTCTCATAATATGTTGTGTCTTCACAGAGAGATACTGTGTTGCTCCAACTCAAGAGGATTTTACAACAAGTTTTTAATACACTAAGGCTACTTGCCTAATGTCATTGCTATATTGGGTACTTCAGATGGTTGAGGTAACACGAGT -s simCow_chr6.simCow.chr6 370076 148 + 602619 AAACCAATTTCTGATAATATGGTGTCTCTCCACAGAGAGATACTATGTTACTCCAAATCAATGGTATT----AGCAAGTTTTTAATACACAAAGGCTACATGCCCAATGTCTTTGCTA-GTTAAGAATTGCAGATGGATGGCGAGACACAAGC -s simDog_chr6.simDog.chr6 360197 147 + 593897 AAACCAAATTTTCCTAATGTGTAGTGTCTGAACAGAGAGAGACTACTTTACTT-GAATCA---TTATTCGCCAACATGTTTTT--TACACAAAGGCTACATGGCTAATGTCCTTACCATATTGGGTAATGCAGATGGTTGGGATGACACCACC -s simHuman_chr6.simHuman.chr6 368319 153 + 601863 GAACCAACTCATCATAATACATTGTGTTTGCCCAGAGAGATACTATGTTACTTTGGATTAAGAATATTCTCCAACAAGTCCTTGGTGCACAAATGGTACATGCCTGATGTCCTCATTATATTAGGTAGTGCAGACTGATGGGGTGACACAAAC -s simRat_chr6.simRat.chr6 377511 153 + 647215 AAGTGGATCTATCATAGTGCAGTGTGGCTGCACAGAGGAACACAAAGCTACTCCAAGTCAAGGATCTTCCCCAGCAAGTGTTTAGTGTACAAAGGGTACATGCGTAATGTTGTTATCATATTAAGTGGTGCAAGCAGTTAGGGTAATACAAGT - -a -s simMouse_chr6.simMouse.chr6 378343 8 + 636262 AGTATGTC -s Anc0.Anc0refChr3 11662 8 + 222631 GGTATGAC -s Anc1.Anc1refChr6 44537 8 + 197743 GGTATGAC -s Anc2.Anc2refChr13 14274 8 + 96486 GGTAGGAC -s mr.mrrefChr5 231959 8 + 294540 AGTATGTC -s simCow_chr6.simCow.chr6 369665 8 + 602619 GGTAATAC -s simCow_chr6.simCow.chr6 370225 8 + 602619 GGTAGCAC -s simDog_chr6.simDog.chr6 360345 8 + 593897 GGCAGGAC -s simHuman_chr6.simHuman.chr6 368473 8 + 601863 GGTATGCC -s simRat_chr6.simRat.chr6 377664 8 + 647215 AAGATGTT - -a -s simMouse_chr6.simMouse.chr6 378351 1 + 636262 C -s Anc0.Anc0refChr3 11670 1 + 222631 C -s Anc1.Anc1refChr6 44545 1 + 197743 C -s Anc2.Anc2refChr13 14282 1 + 96486 C -s mr.mrrefChr5 231967 1 + 294540 C -s simCow_chr6.simCow.chr6 370233 1 + 602619 A -s simDog_chr6.simDog.chr6 360353 1 + 593897 C -s simHuman_chr6.simHuman.chr6 368481 1 + 601863 C -s simRat_chr6.simRat.chr6 377672 1 + 647215 C - -a -s simMouse_chr6.simMouse.chr6 378352 4 + 636262 TACA -s Anc0.Anc0refChr3 11671 4 + 222631 TACA -s Anc1.Anc1refChr6 44546 4 + 197743 TACA -s Anc2.Anc2refChr13 14283 4 + 96486 TACA -s mr.mrrefChr5 231968 4 + 294540 TACA -s simCow_chr6.simCow.chr6 369673 4 + 602619 TACC -s simCow_chr6.simCow.chr6 370234 4 + 602619 TACC -s simDog_chr6.simDog.chr6 360354 4 + 593897 TAGA -s simHuman_chr6.simHuman.chr6 368482 4 + 601863 TACA -s simRat_chr6.simRat.chr6 377673 4 + 647215 TACA - -a -s simMouse_chr6.simMouse.chr6 378356 5 + 636262 CACAT -s Anc0.Anc0refChr3 11677 5 + 222631 CATAT -s Anc1.Anc1refChr6 44552 5 + 197743 CATAT -s Anc2.Anc2refChr13 14289 5 + 96486 CCTAT -s mr.mrrefChr5 231972 5 + 294540 CACAT -s simCow_chr6.simCow.chr6 369679 5 + 602619 CAGAT -s simCow_chr6.simCow.chr6 370240 5 + 602619 CCCAT -s simDog_chr6.simDog.chr6 360360 5 + 593897 CCTAT -s simHuman_chr6.simHuman.chr6 368488 5 + 601863 CATAT -s simRat_chr6.simRat.chr6 377677 5 + 647215 CACAT - -a -s simMouse_chr6.simMouse.chr6 378361 58 + 636262 TTAACAGTTGGGCAGGTGAGTATTTAACAGTTGGGCAATCGAGTGAGTGCAACCATTC -s Anc0.Anc0refChr3 11682 46 + 222631 TCAACAGTTGGGCAGGTGAGC------CAG------GACCTACCAGGACCTACCATCC -s Anc1.Anc1refChr6 44557 46 + 197743 TCAACAGTTGGGCAGGTGAGC------CAG------GACCTACCAGGACCTACCATCC -s Anc2.Anc2refChr13 14294 46 + 96486 CCAACAATTGGGCAGCTGAAC------CAG------GACCTACCAGGACCTCCCATCC -s mr.mrrefChr5 231977 58 + 294540 TTAACAGTTGGGCAGGTGAGTATTTAACAGTTGGGCAATCGAGTGGGTGCAACCATTC -s simCow_chr6.simCow.chr6 369684 46 + 602619 CCAATAATTGGGAAGGTAAAC------CAG------GACCTACCCGGACTTACTATCC -s simCow_chr6.simCow.chr6 370246 37 + 602619 CCTAAAATTGGTGAGCTAAAC------CAG------GACCTACC---------CAGCC -s simDog_chr6.simDog.chr6 360365 46 + 593897 GTAACAATTGAGCAGCTGAAC------CAA------GGCCTACCAGGACCTCCCATCC -s simHuman_chr6.simHuman.chr6 368493 36 + 601863 TGAACAGGTGGGCAGGTGAGC------CAG------GACCT----------ACCATCT -s simRat_chr6.simRat.chr6 377682 58 + 647215 TAAACAGTTGGGCACATGAGTATTTAACAGTTGGGCAGGTGGGTGGGGGCAACCATTC - -a -s simMouse_chr6.simMouse.chr6 378419 1 + 636262 A -s Anc0.Anc0refChr3 11728 1 + 222631 A -s Anc1.Anc1refChr6 44603 1 + 197743 A -s Anc2.Anc2refChr13 14340 1 + 96486 A -s mr.mrrefChr5 232035 1 + 294540 A -s simCow_chr6.simCow.chr6 369730 1 + 602619 A -s simCow_chr6.simCow.chr6 370283 1 + 602619 A -s simDog_chr6.simDog.chr6 360411 1 + 593897 A -s simHuman_chr6.simHuman.chr6 368529 1 + 601863 A -s simRat_chr6.simRat.chr6 377746 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 378420 1 + 636262 A -s Anc0.Anc0refChr3 11729 1 + 222631 A -s Anc1.Anc1refChr6 44604 1 + 197743 A -s Anc2.Anc2refChr13 14341 1 + 96486 A -s mr.mrrefChr5 232036 1 + 294540 A -s simCow_chr6.simCow.chr6 370284 1 + 602619 C -s simDog_chr6.simDog.chr6 360412 1 + 593897 A -s simHuman_chr6.simHuman.chr6 368530 1 + 601863 A -s simRat_chr6.simRat.chr6 377747 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 378421 1 + 636262 C -s Anc0.Anc0refChr3 11730 1 + 222631 C -s Anc1.Anc1refChr6 44605 1 + 197743 C -s Anc2.Anc2refChr13 14342 1 + 96486 C -s mr.mrrefChr5 232037 1 + 294540 C -s simCow_chr6.simCow.chr6 369731 1 + 602619 T -s simCow_chr6.simCow.chr6 370285 1 + 602619 C -s simDog_chr6.simDog.chr6 360413 1 + 593897 C -s simHuman_chr6.simHuman.chr6 368531 1 + 601863 C -s simRat_chr6.simRat.chr6 377748 1 + 647215 C - -a -s simMouse_chr6.simMouse.chr6 378422 13 + 636262 GCCTAAATAAAGC -s Anc0.Anc0refChr3 11735 13 + 222631 GCCCAAATTAAAC -s Anc1.Anc1refChr6 44610 13 + 197743 GCCCAAATTAAAC -s Anc2.Anc2refChr13 14347 13 + 96486 GCCCAAATTAAAC -s mr.mrrefChr5 232038 13 + 294540 GCCCAAATAAAGC -s simCow_chr6.simCow.chr6 369736 13 + 602619 TCCTAAATTAAAC -s simCow_chr6.simCow.chr6 370290 13 + 602619 TCCCAAATTGAAC -s simDog_chr6.simDog.chr6 360418 12 + 593897 GCCCAAATT-AAC -s simHuman_chr6.simHuman.chr6 368536 12 + 601863 GCCCAAATTAA-C -s simRat_chr6.simRat.chr6 377749 13 + 647215 ACCCAAATAAGGC - -a -s simMouse_chr6.simMouse.chr6 378435 23 + 636262 AGATAATGTGTTCCAGATTAATG -s Anc0.Anc0refChr3 11748 23 + 222631 AGATAACACATTCCTGAATAATG -s Anc1.Anc1refChr6 44623 23 + 197743 AGATAACACATTCCTGAATAATG -s Anc2.Anc2refChr13 14360 23 + 96486 AGATAACACATTGCTGAATAATG -s mr.mrrefChr5 232051 23 + 294540 AGATAATGTGTTCCAGAATAATG -s simCow_chr6.simCow.chr6 369749 23 + 602619 AGATAATAGATTGCTGAATAATG -s simCow_chr6.simCow.chr6 370303 23 + 602619 AGATAACATATTGCTGAATAACG -s simDog_chr6.simDog.chr6 360430 23 + 593897 AGGTAACACATTGCTGAATAATG -s simHuman_chr6.simHuman.chr6 368548 23 + 601863 AGATAACACCTACTTGTATAATG -s simRat_chr6.simRat.chr6 377764 23 + 647215 AGATAATGTATTCAAGAATAATG - -a -s simMouse_chr6.simMouse.chr6 378458 1 + 636262 G -s Anc0.Anc0refChr3 11771 1 + 222631 A -s Anc1.Anc1refChr6 44646 1 + 197743 A -s Anc2.Anc2refChr13 14383 1 + 96486 A -s mr.mrrefChr5 232074 1 + 294540 G -s simCow_chr6.simCow.chr6 369772 1 + 602619 G -s simCow_chr6.simCow.chr6 370329 1 + 602619 G -s simDog_chr6.simDog.chr6 360453 1 + 593897 A -s simHuman_chr6.simHuman.chr6 368571 1 + 601863 A -s simRat_chr6.simRat.chr6 377787 1 + 647215 G - -a -s simMouse_chr6.simMouse.chr6 378459 8 + 636262 GGTAAAAT -s Anc0.Anc0refChr3 11774 7 + 222631 GTT-AAAC -s Anc1.Anc1refChr6 44649 8 + 197743 GTTAAAAC -s Anc2.Anc2refChr13 14386 7 + 96486 GTT-AAAC -s mr.mrrefChr5 232075 8 + 294540 GTTAAAAT -s simCow_chr6.simCow.chr6 369777 7 + 602619 GCT-CGCA -s simCow_chr6.simCow.chr6 370332 7 + 602619 GTT-AAAC -s simDog_chr6.simDog.chr6 360456 7 + 593897 GTT-AAGC -s simHuman_chr6.simHuman.chr6 368574 8 + 601863 GTTAAAAG -s simRat_chr6.simRat.chr6 377788 8 + 647215 GTTAAAAT - -a -s simMouse_chr6.simMouse.chr6 378467 16 + 636262 CAAGGTATGGGAACAG -s Anc0.Anc0refChr3 11781 16 + 222631 TGAGGGATGAGGACTG -s Anc1.Anc1refChr6 44657 16 + 197743 TGAGGGATGAGGACTG -s Anc2.Anc2refChr13 14393 16 + 96486 TGAGGGATGAGGATTG -s mr.mrrefChr5 232083 16 + 294540 TAAGGGATGAGGACAG -s simCow_chr6.simCow.chr6 370339 10 + 602619 TGAGGGATGC------ -s simDog_chr6.simDog.chr6 360463 16 + 593897 TGGGGGATGAGGATTG -s simHuman_chr6.simHuman.chr6 368582 16 + 601863 TGAGGGATGAGGACGG -s simRat_chr6.simRat.chr6 377796 16 + 647215 TAGGGGATCAGGCTAG - -a -s simMouse_chr6.simMouse.chr6 378483 1 + 636262 T -s Anc0.Anc0refChr3 11802 1 + 222631 T -s Anc1.Anc1refChr6 44678 1 + 197743 T -s Anc2.Anc2refChr13 14414 1 + 96486 T -s mr.mrrefChr5 232099 1 + 294540 T -s simDog_chr6.simDog.chr6 360484 1 + 593897 T -s simHuman_chr6.simHuman.chr6 368603 1 + 601863 T -s simRat_chr6.simRat.chr6 377812 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 378484 8 + 636262 CCCTGAAT -s Anc0.Anc0refChr3 11803 8 + 222631 GCCTTAAT -s Anc1.Anc1refChr6 44679 8 + 197743 GCCTTAAT -s Anc2.Anc2refChr13 14415 8 + 96486 GCCTTATT -s mr.mrrefChr5 232100 8 + 294540 CCCTGAAT -s simCow_chr6.simCow.chr6 370349 8 + 602619 ACCTTATT -s simDog_chr6.simDog.chr6 360486 8 + 593897 GCCTCATT -s simHuman_chr6.simHuman.chr6 368604 6 + 601863 TTCT--AC -s simRat_chr6.simRat.chr6 377813 8 + 647215 CACTGAAT - -a -s simMouse_chr6.simMouse.chr6 378492 28 + 636262 AGGCTGCAAGGATTCCGGGGAAGTAGTA -s Anc0.Anc0refChr3 11811 26 + 222631 GACCC-CAAAGGTTT-AAAGGACCAGTC -s Anc1.Anc1refChr6 44687 26 + 197743 GACCC-CAAAGGTTT-AAAGGACCAGTC -s Anc2.Anc2refChr13 14424 26 + 96486 GACCC-CAAAGGTTT-AAAGGACCAGTC -s mr.mrrefChr5 232108 28 + 294540 AGGCTGCAAGGATTTTGGGGAAGTAGTA -s simCow_chr6.simCow.chr6 370358 26 + 602619 GACCC-CAAAGGCTT-CAAGGATCAGTC -s simDog_chr6.simDog.chr6 360495 26 + 593897 GATTC-TAAAGGTTT-AAAGGACCAGTC -s simHuman_chr6.simHuman.chr6 368610 26 + 601863 GACCC-CTAAGGTTT-AAAGGACCAGTC -s simRat_chr6.simRat.chr6 377821 28 + 647215 AGGCTGCAAGGATTTTGGGGAGGTAGTT - -a -s simMouse_chr6.simMouse.chr6 378520 6 + 636262 CCAAAG -s Anc0.Anc0refChr3 11837 6 + 222631 CAAAAT -s Anc1.Anc1refChr6 44713 6 + 197743 CAAAAT -s Anc2.Anc2refChr13 14450 6 + 96486 CAAAAT -s mr.mrrefChr5 232136 6 + 294540 CCAAAG -s simCow_chr6.simCow.chr6 370384 6 + 602619 CCAAAT -s simDog_chr6.simDog.chr6 360527 6 + 593897 CAAGAT -s simHuman_chr6.simHuman.chr6 368636 6 + 601863 CTAAAT -s simRat_chr6.simRat.chr6 377849 6 + 647215 CCAAAG - -a -s simMouse_chr6.simMouse.chr6 378526 14 + 636262 CGGATGTGTGGTTC -s Anc0.Anc0refChr3 11843 14 + 222631 TTGGTGAGTAGTTC -s Anc1.Anc1refChr6 44719 14 + 197743 TTGGTGAGTAGTTC -s Anc2.Anc2refChr13 14456 14 + 96486 TTGGTGAGTAGTTC -s mr.mrrefChr5 232142 14 + 294540 CTGATGTGTGGTTC -s simCow_chr6.simCow.chr6 370390 14 + 602619 TTGGCATCTTGTTC -s simDog_chr6.simDog.chr6 360536 14 + 593897 TTTGTGAGTAGGTT -s simHuman_chr6.simHuman.chr6 368642 14 + 601863 TTGGTGCGTAGTTC -s simRat_chr6.simRat.chr6 377855 13 + 647215 CTG-TGTGTGGTTC - -a -s simMouse_chr6.simMouse.chr6 378540 5 + 636262 TGAAA -s Anc0.Anc0refChr3 11858 5 + 222631 CATCA -s Anc1.Anc1refChr6 44734 5 + 197743 CATCA -s Anc2.Anc2refChr13 14471 5 + 96486 CATTA -s mr.mrrefChr5 232157 5 + 294540 TAACA -s simCow_chr6.simCow.chr6 370405 5 + 602619 CAATA -s simDog_chr6.simDog.chr6 360551 5 + 593897 TTTTA -s simHuman_chr6.simHuman.chr6 368657 5 + 601863 CAGCA -s simRat_chr6.simRat.chr6 377869 5 + 647215 TAACA - -a -s simMouse_chr6.simMouse.chr6 378545 8 + 636262 TAGAAGCT -s Anc0.Anc0refChr3 11863 8 + 222631 TAGGAATA -s Anc1.Anc1refChr6 44739 8 + 197743 TAGGAATA -s Anc2.Anc2refChr13 14476 8 + 96486 TAGGAATA -s mr.mrrefChr5 232162 8 + 294540 TAGAAGCT -s simCow_chr6.simCow.chr6 370410 8 + 602619 TAGGAATA -s simDog_chr6.simDog.chr6 360594 8 + 593897 TAGCAAtc -s simHuman_chr6.simHuman.chr6 368662 8 + 601863 TAGGAAAA -s simRat_chr6.simRat.chr6 377874 8 + 647215 TAGAAGCT - -a -s simMouse_chr6.simMouse.chr6 378553 26 + 636262 ATGAAACTTGGAATAATGAGCAAGTC -s Anc0.Anc0refChr3 11871 26 + 222631 ATGAACCTGGGAATAATGAGCAAGTG -s Anc1.Anc1refChr6 44747 26 + 197743 ATGAACCTGGGAATAATGAGCAAGTG -s Anc2.Anc2refChr13 14519 26 + 96486 CTGAACATGGGAATAATGAGCAAGTG -s mr.mrrefChr5 232170 26 + 294540 ATGAAACTTGGAATAATGAGCAAGTG -s simCow_chr6.simCow.chr6 370453 26 + 602619 CTGAATATGGGAATAATGAGCAAGTG -s simDog_chr6.simDog.chr6 360646 9 + 593897 CTGAACATG----------------- -s simHuman_chr6.simHuman.chr6 368670 26 + 601863 ATGAACCTCGGAATAATGAGCAAGTG -s simRat_chr6.simRat.chr6 377882 26 + 647215 ACAGAGCTGGGAATAATGAGCAAATG - -a -s simMouse_chr6.simMouse.chr6 378579 10 + 636262 ATTGTTCTTG -s Anc0.Anc0refChr3 11899 10 + 222631 ATTGGTTTTT -s Anc1.Anc1refChr6 44775 10 + 197743 ATTGGTTTTT -s Anc2.Anc2refChr13 14547 10 + 96486 ATCTGTTGTT -s mr.mrrefChr5 232196 10 + 294540 ATTGTTCTTG -s simCow_chr6.simCow.chr6 370481 10 + 602619 ATCTGTTGTT -s simHuman_chr6.simHuman.chr6 368698 10 + 601863 ATTGGTTTTT -s simRat_chr6.simRat.chr6 377908 10 + 647215 ATTGTTCTTG - -a -s simMouse_chr6.simMouse.chr6 378589 52 + 636262 TAAGATCCGAGGGCTGGGGAAGAGGAACATCTGTGAGGGATTGAACATCAGG -s Anc0.Anc0refChr3 11909 21 + 222631 TGA------------------GAGGAACATCTATGAGGG------------- -s Anc1.Anc1refChr6 44785 39 + 197743 TGAGATCTAAAGGCTGGGGAGGAGGAACATCTATGAGGG------------- -s Anc2.Anc2refChr13 14557 21 + 96486 TGA------------------GAGGAACACCTGTAAAGG------------- -s mr.mrrefChr5 232206 52 + 294540 TAAGATCCGAAGGCTGGGGAAGAGGAACATCTATGAGGGATTGAACATCAGG -s simCow_chr6.simCow.chr6 370492 21 + 602619 TGA------------------GAGGAACACCTGTAAAGG------------- -s simHuman_chr6.simHuman.chr6 368708 39 + 601863 TGAGATCTAAAGGCTGGGGAGGAGGAATATTTATGAGGG------------- -s simRat_chr6.simRat.chr6 377918 52 + 647215 TAAGATCCGAAGGCTGGGGAATAGGAACATCTATGAAGGACTGAACATCTGG - -a -s simMouse_chr6.simMouse.chr6 378641 13 + 636262 GGGTTACGATAAG -s Anc0.Anc0refChr3 11930 10 + 222631 ---TACTGAAAAG -s Anc1.Anc1refChr6 44824 10 + 197743 ---TACTGAAAAG -s Anc2.Anc2refChr13 14578 10 + 96486 ---TACTGAAATG -s mr.mrrefChr5 232258 13 + 294540 GGGTAACGAAAAG -s simCow_chr6.simCow.chr6 370513 10 + 602619 ---TACTGAAATG -s simDog_chr6.simDog.chr6 360655 9 + 593897 ----ACCGAAGTG -s simHuman_chr6.simHuman.chr6 368747 10 + 601863 ---TACTGAAAAG -s simRat_chr6.simRat.chr6 377972 13 + 647215 GGGTATCGAAATG - -a -s simMouse_chr6.simMouse.chr6 378654 13 + 636262 CCCCATACTTTGG -s Anc0.Anc0refChr3 11941 11 + 222631 CTTCAGCCT--GA -s Anc1.Anc1refChr6 44835 11 + 197743 CTTCAGCCT--GA -s Anc2.Anc2refChr13 14589 11 + 96486 CTTAAGCCT--AA -s mr.mrrefChr5 232272 13 + 294540 CCTCATACTTTGG -s simCow_chr6.simCow.chr6 370524 11 + 602619 TTTAAACGT--TA -s simDog_chr6.simDog.chr6 360665 11 + 593897 CCTAAGCCT--AA -s simHuman_chr6.simHuman.chr6 368758 11 + 601863 CTTCAGCCT--GA -s simRat_chr6.simRat.chr6 377986 13 + 647215 CCTCATACTTTTG - -a -s simMouse_chr6.simMouse.chr6 378667 37 + 636262 GAGATTGGCCTTTGGGACCACTACAGGACAATACAAC -s Anc0.Anc0refChr3 11953 37 + 222631 GGTCTTAGTGTTTGGTACCACTACATAACAATACAAT -s Anc1.Anc1refChr6 44847 37 + 197743 GGTCTTAGTGTTTGGTACCACTACATAACAATACAAT -s Anc2.Anc2refChr13 14601 37 + 96486 AGTCTTAGTGTTTGGTACCACTGCATAACAAGACAAT -s mr.mrrefChr5 232286 37 + 294540 GAGATTAGTCTTTGGGACCACTACAGGACAATACAAC -s simCow_chr6.simCow.chr6 370536 37 + 602619 AGCCTTAGTGTTTGGTGCCACTGCGTAATGGGACAAT -s simDog_chr6.simDog.chr6 360677 37 + 593897 AGTCTTAGTATTCGGTACCACTGCATAACAAGACAAT -s simHuman_chr6.simHuman.chr6 368770 37 + 601863 GGACTTAGTGTTTGCAACCAATACATAACAATACAAT -s simRat_chr6.simRat.chr6 378000 37 + 647215 GAGATTAGTCTTTGGTACCACTACAGGACAATACAAC - -a -s simMouse_chr6.simMouse.chr6 378704 2 + 636262 AA -s Anc0.Anc0refChr3 11990 2 + 222631 AA -s Anc1.Anc1refChr6 44884 2 + 197743 AA -s Anc2.Anc2refChr13 14638 2 + 96486 AG -s mr.mrrefChr5 232323 2 + 294540 AA -s simCow_chr6.simCow.chr6 370573 2 + 602619 AG -s simDog_chr6.simDog.chr6 360714 2 + 593897 AG -s simHuman_chr6.simHuman.chr6 368818 2 + 601863 AA -s simRat_chr6.simRat.chr6 378037 2 + 647215 AA - -a -s simMouse_chr6.simMouse.chr6 378706 74 + 636262 TGGAAGAGGATCCAGTGATGTTGGGGGGTTGGTACACCACCTGACAGTGTTAGGAGACAAGTATGGTTAGTATA -s Anc0.Anc0refChr3 11993 68 + 222631 TGAAAGTGTGTCCAGTAATGGTGGTGGGTTGGCACACCTCCCAATAGTGTTAG------AGTGTGTTTGGTTTA -s Anc1.Anc1refChr6 44887 74 + 197743 TGAAAGTGTGTCCAGTAATGGTGGTGGGTTGGCACACCTCCCAATAGTGTTAGGATACAAGTGTGTTTGGTTTA -s Anc2.Anc2refChr13 14641 68 + 96486 TGAAAGTGTGTCCAGTAGTGGTGTTGGGTTGTCACACCTCCCAATAGTGTTAG------AGTGTGTTTGGTTTA -s mr.mrrefChr5 232326 74 + 294540 TGGAAGTGTATCCAGTAATGTTGGGGGGTTGGCACACCACCTGACAGTGTTAGGAGACAAGTATGTTTAGTTTA -s simCow_chr6.simCow.chr6 370576 67 + 602619 TGAGTGTGTGTTAAGTAGTGGGGTTGTGGGGT-GCTCCCCTCAATAGTATTAG------GGTGTGTCTAGTTTA -s simDog_chr6.simDog.chr6 360717 68 + 593897 TGAAAGCGTGTCCAGTAGTGGTGTTGGGTTGTCATACCTCCCAATAGTGTTAG------AGTATGTTTGGTTCA -s simHuman_chr6.simHuman.chr6 368821 74 + 601863 TGAAAGTGTGTCCAGTAATGGTGGAGGGTTGGCACAGCTCCAAATAGTGTTAGGATACAAGCGTGTTTGGTTTC -s simRat_chr6.simRat.chr6 378040 74 + 647215 TGGAAGTGTATCCAGTAATGATGGGGGGTTGCCACACCACCTGACAGTGTAAGGAGAGAAATATGTTTAGTTTA - -a -s simMouse_chr6.simMouse.chr6 378780 10 + 636262 CAATGATGTT -s Anc0.Anc0refChr3 12061 9 + 222631 CC-TAATATT -s Anc1.Anc1refChr6 44961 9 + 197743 CC-TAATATT -s Anc2.Anc2refChr13 14709 9 + 96486 CC-TAATATA -s mr.mrrefChr5 232400 10 + 294540 CAATGATATT -s simCow_chr6.simCow.chr6 370643 9 + 602619 CT-TAATATA -s simDog_chr6.simDog.chr6 360785 9 + 593897 CC-TAATATA -s simHuman_chr6.simHuman.chr6 368895 9 + 601863 CC-TAATACT -s simRat_chr6.simRat.chr6 378218 10 + 647215 CAATGATATT - -a -s simMouse_chr6.simMouse.chr6 378790 9 + 636262 GATTAATGA -s Anc0.Anc0refChr3 12070 9 + 222631 GATTATTGC -s Anc1.Anc1refChr6 44970 9 + 197743 GATTATTGC -s Anc2.Anc2refChr13 14718 9 + 96486 GAGTATTGC -s mr.mrrefChr5 232410 9 + 294540 GATTAATGA -s simCow_chr6.simCow.chr6 370658 9 + 602619 GACTACTGC -s simDog_chr6.simDog.chr6 360794 9 + 593897 GAGTATTGC -s simHuman_chr6.simHuman.chr6 368904 8 + 601863 TATTATTG- -s simRat_chr6.simRat.chr6 378228 9 + 647215 GATCACTGA - -a -s simMouse_chr6.simMouse.chr6 378799 5 + 636262 CCCTA -s Anc0.Anc0refChr3 12079 5 + 222631 CCCTA -s Anc1.Anc1refChr6 44979 5 + 197743 CCCTA -s Anc2.Anc2refChr13 14727 5 + 96486 CCCTA -s mr.mrrefChr5 232419 5 + 294540 CCCTA -s simCow_chr6.simCow.chr6 370667 5 + 602619 CCCTA -s simDog_chr6.simDog.chr6 360807 5 + 593897 CCCTA -s simRat_chr6.simRat.chr6 378237 5 + 647215 CCCTA - -a -s simMouse_chr6.simMouse.chr6 378804 28 + 636262 GCTAAAATTCTCAGACGTCTTTATCCAC -s Anc0.Anc0refChr3 12084 28 + 222631 GTTAAAATCATCAAATGTCTTTATTCAG -s Anc1.Anc1refChr6 44984 28 + 197743 GTTAAAATCATCAAATGTCTTTATTCAG -s Anc2.Anc2refChr13 14732 28 + 96486 GTTAAAATCATCCAATGTCTTTATTCAT -s mr.mrrefChr5 232424 28 + 294540 GCTAAAATTCTCAGATGTCTTTATCCAG -s simCow_chr6.simCow.chr6 370672 25 + 602619 GATAAAATC-TACAGTATCTTTATTC-- -s simDog_chr6.simDog.chr6 360815 28 + 593897 GTTGAGATCATCCAATGTCTCTATTCAT -s simHuman_chr6.simHuman.chr6 368912 26 + 601863 --CAAAATCATCACATTTCTTTGTTTAG -s simRat_chr6.simRat.chr6 378242 28 + 647215 GCTAAAGTTCTTATATGTCTTTAACCAG - -a -s simMouse_chr6.simMouse.chr6 378832 33 + 636262 TGTGTAGATAATATTAGGTGGGTCAATTGGTGA -s Anc0.Anc0refChr3 12161 33 + 222631 CAGGTAGGTAATATCAGGTAGGTCAATCAGTGA -s Anc1.Anc1refChr6 45061 33 + 197743 CAGGTAGGTAATATCAGGTAGGTCAATCAGTGA -s Anc2.Anc2refChr13 14809 33 + 96486 CAGGTCAGTAATATCTGGTAGGTCAACCAGTGA -s mr.mrrefChr5 232452 33 + 294540 CAGGTAGATAATATTAGGTGGGTCAATCAGTGA -s simCow_chr6.simCow.chr6 370745 32 + 602619 CAGGTCA-TATAGCCTAGTAAGTCAACCAGCGA -s simDog_chr6.simDog.chr6 360889 33 + 593897 CAGGTCAGTAATATCTGGTAGGACAACCAGTGA -s simHuman_chr6.simHuman.chr6 368987 33 + 601863 CAGGTAGGTAATATCAGGTAGGTTAATCAGTGA -s simRat_chr6.simRat.chr6 378270 29 + 647215 CAGGTAGATAATATTAGGTGGG----TCAATTA - -a -s simMouse_chr6.simMouse.chr6 378865 5 + 636262 GAAAG -s Anc0.Anc0refChr3 12194 5 + 222631 GAGAG -s Anc1.Anc1refChr6 45094 5 + 197743 GAGAG -s Anc2.Anc2refChr13 14842 5 + 96486 GAGAG -s mr.mrrefChr5 232485 5 + 294540 GAAAG -s simCow_chr6.simCow.chr6 370777 4 + 602619 TA-AG -s simDog_chr6.simDog.chr6 360922 5 + 593897 GAGAG -s simHuman_chr6.simHuman.chr6 369020 5 + 601863 GAGAG -s simRat_chr6.simRat.chr6 378303 5 + 647215 GAAGG - -a -s simMouse_chr6.simMouse.chr6 378870 28 + 636262 ACTGGCGTGTTTTCTCAACTACTAGTAT -s Anc0.Anc0refChr3 12199 28 + 222631 AAGGGTGTTTCTACTCATCTACTGAGAT -s Anc1.Anc1refChr6 45099 28 + 197743 AAGGGTGTTTCTACTCATCTACTGAGAT -s Anc2.Anc2refChr13 14848 28 + 96486 AAGGGTGTTTCTACTCATCTACTGAGAT -s mr.mrrefChr5 232490 28 + 294540 AATGGCGTGTTTTCTCAACTACTAATAT -s simCow_chr6.simCow.chr6 370782 28 + 602619 AAGGGTGTTTCTACCCATCTACAGAGAT -s simDog_chr6.simDog.chr6 360928 28 + 593897 AAGGGTGTTTCTACTCATCTACTAAGAT -s simHuman_chr6.simHuman.chr6 369025 28 + 601863 AAGGGTGGTTCCACTTATCGACTGAGAT -s simRat_chr6.simRat.chr6 378308 20 + 647215 AATGG---AGT-----GACTACTAATAT - -a -s simMouse_chr6.simMouse.chr6 378898 36 + 636262 GTCATTTGCTTCCTTGTTGCCTAGCTCGCTATCTTT -s Anc0.Anc0refChr3 12228 35 + 222631 GCAATTTGC-TCCTTATTTCTTAGCTGGTTATCTTT -s Anc1.Anc1refChr6 45128 35 + 197743 GCAATTTGC-TCCTTATTTCTTAGCTGGTTATCTTT -s Anc2.Anc2refChr13 14877 35 + 96486 CCAATCTGC-TCCTTATTTCTTAGCTGGTTGTCTTT -s mr.mrrefChr5 232519 35 + 294540 GCAATTTGC-TCCTTGTTGCCTAGCTCGCTATCTTT -s simCow_chr6.simCow.chr6 370811 35 + 602619 CAAATCTGC-CCCATAATTCTTCGTTGATTTTCTTA -s simDog_chr6.simDog.chr6 360957 35 + 593897 CCCATCTGC-TCCTTATTTCTTAGCCAGTTGTCTTT -s simHuman_chr6.simHuman.chr6 369054 30 + 601863 GCAATTTGC-TCCTT-----TTAGCTGGGTATCTTT -s simRat_chr6.simRat.chr6 378329 35 + 647215 TCAATTTGC-TCCTTGTTTCCTAGCTAGCTACCTTT - -a -s simMouse_chr6.simMouse.chr6 378934 1 + 636262 A -s Anc0.Anc0refChr3 12263 1 + 222631 T -s Anc1.Anc1refChr6 45163 1 + 197743 T -s Anc2.Anc2refChr13 14919 1 + 96486 T -s mr.mrrefChr5 232554 1 + 294540 A -s simCow_chr6.simCow.chr6 370853 1 + 602619 T -s simDog_chr6.simDog.chr6 360999 1 + 593897 T -s simHuman_chr6.simHuman.chr6 369084 1 + 601863 C -s simRat_chr6.simRat.chr6 378364 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 378935 13 + 636262 GCTCTCTTATACT -s Anc0.Anc0refChr3 12265 13 + 222631 GCACGTTATTGCT -s Anc1.Anc1refChr6 45165 13 + 197743 GCACGTTATTGCT -s Anc2.Anc2refChr13 14921 13 + 96486 GGACGTTATCGCT -s mr.mrrefChr5 232555 13 + 294540 GCTCTCTTATACT -s simCow_chr6.simCow.chr6 370855 13 + 602619 GGTCGCGATCGCT -s simDog_chr6.simDog.chr6 361001 13 + 593897 GGACGTTATCACT -s simHuman_chr6.simHuman.chr6 369086 13 + 601863 GCACGTTATTGCT -s simRat_chr6.simRat.chr6 378365 13 + 647215 ACTCTCCCGTACT - -a -s simMouse_chr6.simMouse.chr6 378948 5 + 636262 GTCAT -s Anc0.Anc0refChr3 12278 5 + 222631 ATCAT -s Anc1.Anc1refChr6 45178 5 + 197743 ATCAT -s Anc2.Anc2refChr13 14934 5 + 96486 ATCAT -s mr.mrrefChr5 232568 5 + 294540 GTCAT -s simCow_chr6.simCow.chr6 370868 5 + 602619 ATCAT -s simDog_chr6.simDog.chr6 361014 5 + 593897 CTCAA -s simHuman_chr6.simHuman.chr6 369099 5 + 601863 ATCAT -s simRat_chr6.simRat.chr6 378388 5 + 647215 GTCAT - -a -s simMouse_chr6.simMouse.chr6 378953 22 + 636262 GCGGCCGATCTCAACCACCGCA -s Anc0.Anc0refChr3 12285 17 + 222631 ACGGCCGACG-----CCTTGCG -s Anc1.Anc1refChr6 45185 22 + 197743 ACGGCCGACGCCATACCTTGCG -s Anc2.Anc2refChr13 14941 17 + 96486 CCACCCGACG-----ACTAGCG -s mr.mrrefChr5 232573 22 + 294540 ACGGCCGATCTCATCCACTGCA -s simCow_chr6.simCow.chr6 370875 17 + 602619 CCATTCGACG-----GCCAACG -s simDog_chr6.simDog.chr6 361021 17 + 593897 CCACCCGACG-----ACTAGCG -s simHuman_chr6.simHuman.chr6 369106 22 + 601863 ACGGCCCACACCATACCATCCG -s simRat_chr6.simRat.chr6 378393 22 + 647215 ACGGCCGATGTCATCCACTGCA - -a -s simMouse_chr6.simMouse.chr6 378975 27 + 636262 CGGCTCGTGGCCGGTGCAACGAGCATG -s Anc0.Anc0refChr3 12302 27 + 222631 CGGCTCGTTACTGGTGCACCCAGCGTG -s Anc1.Anc1refChr6 45207 27 + 197743 CGGCTCGTTACTGGTGCACCCAGCGTG -s Anc2.Anc2refChr13 14958 27 + 96486 CGGCTCGTTACTGGTGCACCCAGCGTG -s mr.mrrefChr5 232595 27 + 294540 CGGCTCGTTGCTGGTGCACCGAGCGTG -s simCow_chr6.simCow.chr6 370904 24 + 602619 CGACTCGTTACTGGT-CGTCCAGCG-- -s simDog_chr6.simDog.chr6 361038 27 + 593897 CGGCTCGTTACTGATGCACCCAGCGTG -s simHuman_chr6.simHuman.chr6 369128 27 + 601863 CGGCTCGTTACTGGTGCACCCAGCGTG -s simRat_chr6.simRat.chr6 378415 25 + 647215 CGGCTCGTTGCTAGTGCACC--GCGTG - -a -s simMouse_chr6.simMouse.chr6 379002 125 + 636262 AACCCGACTCAAGAAATTGCACTGAGTAGCACTCGTCCGAAGCCCTGGCGAGCACAAACTCAATCCCAAATTCGCCCCCATTAGCCGCATTGTCCTAGTGGCATAAGATCTCTAGGTCCCCAAAC -s Anc0.Anc0refChr3 12331 120 + 222631 AACGTGACTCAAGAAATTGCAGCAGGCGGCC-TCGTCCGAAGCCTTGGCCTGCAAAA----CGTCCCAGAATAGCCTCCATGAGCTGTACTGCTGTACTGGCGTCGGATCGCTGGGTCCCACAAG -s Anc1.Anc1refChr6 45236 120 + 197743 AACGTGACTCAAGAAATTGCAGCAGGCGGCC-TCGTCCGAAGCCTTGGCCTGCAAAA----CGTCCCAGAATAGCCTCCATGAGCTGTACTGCTGTACTGGCGTCGGATCGCTGGGTCCCACAAG -s Anc2.Anc2refChr13 14987 120 + 96486 AATGTGACTCAAGAAATTGCAGCAGATGGCC-TCGTCCGAAGCCTTGGCCTACAAAA----CGTCCTAGAATAGCCTCCATGAGCTGTACTGCTGTACTGGCGTCGGATCGCTGGCCCCCACAAG -s mr.mrrefChr5 232622 121 + 294540 AACCCGACTCAAGAAATTGCAGCGAGCGGCCCTCGTCCGAAGCCCTGGCGAGCACAA----AATCCCAAATTAGCCCCCATGAGCCGCATTGTCCTAGTGGCATAGGATCTCTAGGTCCCCAAAC -s simCow_chr6.simCow.chr6 370930 120 + 602619 AATGCGAATCAAGAAATTGCAGCATATGTCC-TCGTCTGAAGCCTTGGACTACAAAA----CGTCTTAGATTAGCCTCCATGAGCTGTATTGCTGTACTGACGTCGGATCCCTGGCACCCACAAG -s simDog_chr6.simDog.chr6 361065 114 + 593897 ---ATGACTCAAGAAATTGTAGTAGATGGGC-TCATTCGAAGCCTTGGCCTACTAAA----CGTCCT---ATAACCTCCATAAGCTGTACTGCTGTACTGGCTTCGGACCGCTGGCCCCCACAAG -s simHuman_chr6.simHuman.chr6 369159 119 + 601863 AACGTGACTCAAGAAATT-CAGCAGGCGGCC-TCGTCCGAAGCCTTCGCCTGCAAAA----CGTCCCACAATAGCCGCCATGAAGTGTACTGCTGTACTGGCGTCGGATCGCTGGGTCCCACAAG -s simRat_chr6.simRat.chr6 378440 121 + 647215 AACACGACTCAAGGTATTGCAGCGAGCGGCCCTCGTCCGAAGGCGTGTCGAGCACAA----AATCCCAAATTAGCCTCCATGAGCCGCATTGTCCAATTGGCACAGGATCACTAGGTCTCCAAGT - -a -s simMouse_chr6.simMouse.chr6 379127 37 + 636262 CCCCTCTCGAGCACCAACTGGTGCCTAAGGCTGCAGC -s Anc0.Anc0refChr3 12451 37 + 222631 CCCCTCTCGATCACCAACTGGTGCCGCAGACTGCACC -s Anc1.Anc1refChr6 45356 37 + 197743 CCCCTCTCGATCACCAACTGGTGCCGCAGACTGCACC -s Anc2.Anc2refChr13 15108 37 + 96486 CCCCTCTCGATCACCAACTGGTACCGCAGACTGCACC -s mr.mrrefChr5 232743 37 + 294540 CCCCTCTCGATCACCAACTGGTGCCGAAGACTGCACC -s simCow_chr6.simCow.chr6 371051 37 + 602619 TCCCTCTCGATCATCAACTGGTTCCGCAAACTGCACC -s simDog_chr6.simDog.chr6 361180 37 + 593897 CCCCCTTCGATCACCACCTGGTATCGCAGATTGCACC -s simHuman_chr6.simHuman.chr6 369278 37 + 601863 TCCCTCTAGATCACCAACTGGTGCCGCAGACTTCACC -s simRat_chr6.simRat.chr6 378561 37 + 647215 CCCCTCTTGATCACCAACTGATGCCGAAAACTGGACC - -a -s simMouse_chr6.simMouse.chr6 379164 250 + 636262 CTCGGTACTCTTCACAGGTCCCTCTCAAGCACCAACTGGTGCCTAAGACTGCAGCCTTGGTACTCTTCACAGGTCGCCCTACTCAAGCGCCCAAGGTCAATCCTGGGCCGCACATACTGGGTGCATGGTAGTTCCAGTACGAATACTATGATCCCGTGGATAGGTGGAACAAATCCTGTGCCCGCGGAATCGAAACAAAGTGGTTTGTTGTAAAGCACCCTGTTGGAAATATTATTCCTTTTTGCAGTAA -s Anc0.Anc0refChr3 12489 59 + 222631 CAC-------------------------------------------------------GGTATTCTTGACAGATCCGCCTACTCGAGCACTTAAAGTCACTCGCTAGCCGGACA---------------------------------------------------------------------------------------------------------------------------------------- -s Anc1.Anc1refChr6 45394 59 + 197743 CAC-------------------------------------------------------GGTATTCTTGACAGATCCGCCTACTCGAGCACTTAAAGTCACTCGCTAGCCGGACA---------------------------------------------------------------------------------------------------------------------------------------- -s Anc2.Anc2refChr13 15146 59 + 96486 CAC-------------------------------------------------------GGTATTCTTGACAGAACCGCCCACTCGTGCACTTAAAGTCACTCGCTAGCCGGACA---------------------------------------------------------------------------------------------------------------------------------------- -s mr.mrrefChr5 232780 68 + 294540 CTC-------------------------------------------------------GGTACTCTTCACAGGTCGCCCTACTCAAGCGCCCAAGGTCAATCGTTGGCCGCACATACTGGGTG------------------------------------------------------------------------------------------------------------------------------- -s simCow_chr6.simCow.chr6 371089 59 + 602619 CAT-------------------------------------------------------GGTATTCTTGACAGCACCGCCCACTAGTTCACTTAAAATTACTCGCGAACCGATCA---------------------------------------------------------------------------------------------------------------------------------------- -s simDog_chr6.simDog.chr6 361218 58 + 593897 CAC-------------------------------------------------------GGCATTATTGACACAAGCGCC-ACTCGTGCTCTTACAGGCACTCGCTAGCCAGAGA---------------------------------------------------------------------------------------------------------------------------------------- -s simHuman_chr6.simHuman.chr6 369316 59 + 601863 CAC-------------------------------------------------------GGTATTCTTGACAGATCCGCCTGCTCGAGCACATGAAGTCACTTGCTTGCCGGACA---------------------------------------------------------------------------------------------------------------------------------------- -s simRat_chr6.simRat.chr6 378598 68 + 647215 CTC-------------------------------------------------------GGTACTCTTCACAGGTCGCCCTACTCACGCGCCCAACGGCAATCGTTGGCCGCACAGACTGGGTG------------------------------------------------------------------------------------------------------------------------------- - -a -s simMouse_chr6.simMouse.chr6 379449 36 + 636262 CTTGTACGATTAGTTACTCCAGTAATGTTATTGCGA - -a -s simMouse_chr6.simMouse.chr6 379485 15 + 636262 AAAAAAATAATATTT -s mr.mrrefChr5 232883 15 + 294540 AAAAAAATAATATTT -s simRat_chr6.simRat.chr6 378679 15 + 647215 AAAAGAATAATATTT -s simRat_chr6.simRat.chr6 193946 15 - 647215 ACGATCATAAGATTT - -a -s simMouse_chr6.simMouse.chr6 379500 9 + 636262 CCAAAAGGG -s mr.mrrefChr5 232898 9 + 294540 CCAAAAGGG -s simRat_chr6.simRat.chr6 378694 9 + 647215 CCAACAGGG -s simRat_chr6.simRat.chr6 193964 9 - 647215 CTTAAAGGG - -a -s simMouse_chr6.simMouse.chr6 379509 21 + 636262 TGTTGTACAACATACCATTTT -s Anc0.Anc0refChr3 12680 3 + 222631 ------------------CTG -s Anc1.Anc1refChr6 45585 3 + 197743 ------------------CTG -s Anc2.Anc2refChr13 15343 3 + 96486 ------------------CTG -s mr.mrrefChr5 232907 21 + 294540 TGTTGTACAACATACTGTTTT -s simCow_chr6.simCow.chr6 371291 3 + 602619 ------------------TCC -s simDog_chr6.simDog.chr6 361408 3 + 593897 ------------------CTG -s simRat_chr6.simRat.chr6 378703 21 + 647215 TGCTTTACAACAAACTGCTTT -s simRat_chr6.simRat.chr6 193976 17 - 647215 TGTTGTTGGAGACACTG---- - -a -s simMouse_chr6.simMouse.chr6 379530 6 + 636262 GTTTTG -s Anc0.Anc0refChr3 12683 6 + 222631 ACACTG -s Anc1.Anc1refChr6 45588 6 + 197743 ACACTG -s Anc2.Anc2refChr13 15346 6 + 96486 ACACAG -s mr.mrrefChr5 232928 6 + 294540 GTTTTG -s simCow_chr6.simCow.chr6 371299 6 + 602619 ACGCAA -s simDog_chr6.simDog.chr6 361411 6 + 593897 ACACAG -s simRat_chr6.simRat.chr6 378724 6 + 647215 GTCTCA - -a -s simMouse_chr6.simMouse.chr6 379536 3 + 636262 ATT -s Anc0.Anc0refChr3 12689 2 + 222631 GA- -s Anc1.Anc1refChr6 45594 2 + 197743 GA- -s Anc2.Anc2refChr13 15427 2 + 96486 GC- -s mr.mrrefChr5 232934 3 + 294540 ATC -s simCow_chr6.simCow.chr6 371444 2 + 602619 GC- -s simDog_chr6.simDog.chr6 361493 2 + 593897 GC- -s simRat_chr6.simRat.chr6 378730 3 + 647215 ATC -s simRat_chr6.simRat.chr6 193993 3 - 647215 ATC - -a -s simMouse_chr6.simMouse.chr6 379539 10 + 636262 CCATGGGCAC -s Anc1.Anc1refChr6 31407 10 - 197743 GCACGGGCAC -s mr.mrrefChr3 108419 10 - 181027 GCACATGCAT -s mr.mrrefChr5 232937 10 + 294540 CCACGGGCAC -s simMouse_chr6.simMouse.chr6 116009 10 - 636262 GCACATGCAT -s simRat_chr6.simRat.chr6 115531 10 - 647215 ACACATGCAT -s simRat_chr6.simRat.chr6 378733 10 + 647215 CCACGGACAC -s simRat_chr6.simRat.chr6 193996 10 - 647215 ACACAAGCAT - -a -s simMouse_chr6.simMouse.chr6 379729 4 + 636262 TTAT -s Anc1.Anc1refChr6 31590 4 - 197743 TTTT -s mr.mrrefChr3 108604 4 - 181027 TTTC -s mr.mrrefChr5 233137 4 + 294540 TTTT -s simMouse_chr6.simMouse.chr6 116194 4 - 636262 TTTC -s simRat_chr6.simRat.chr6 115735 4 - 647215 TCTC -s simRat_chr6.simRat.chr6 378925 4 + 647215 TTTT -s simRat_chr6.simRat.chr6 194279 4 - 647215 TTTT - -a -s simMouse_chr6.simMouse.chr6 379733 2 + 636262 GC -s mr.mrrefChr5 233141 2 + 294540 GT -s simRat_chr6.simRat.chr6 378929 2 + 647215 GT -s simRat_chr6.simRat.chr6 194283 2 - 647215 GT - -a -s simMouse_chr6.simMouse.chr6 379797 14 + 636262 ACTGCTGGCCTTTT -s Anc1.Anc1refChr6 31647 14 - 197743 AGTGCTGGCCTTCT -s mr.mrrefChr3 108661 14 - 181027 AGTGCTGGTCCTCT -s mr.mrrefChr5 233215 14 + 294540 ACTGCTGGCCTTTT -s simMouse_chr6.simMouse.chr6 116258 14 - 636262 AGTGCTGGTCCTCT -s simRat_chr6.simRat.chr6 115835 14 - 647215 ACTGCTGGTCCTCT -s simRat_chr6.simRat.chr6 379003 14 + 647215 ACTGCAGGCTTTTT -s simRat_chr6.simRat.chr6 194329 14 - 647215 ACCACTGTTCCTTT - -a -s simMouse_chr6.simMouse.chr6 379829 11 + 636262 AGGTTTTTTAA -s Anc1.Anc1refChr6 31683 11 - 197743 AGGTTTTTTAA -s mr.mrrefChr3 108726 11 - 181027 AGGCTTCTTAA -s mr.mrrefChr5 233251 11 + 294540 AGGTTTTTTAA -s simMouse_chr6.simMouse.chr6 116323 11 - 636262 AGGCTTCTTAA -s simRat_chr6.simRat.chr6 115900 11 - 647215 AGGTTTCTTAA -s simRat_chr6.simRat.chr6 379039 11 + 647215 AAGTTTTTTAA -s simRat_chr6.simRat.chr6 194365 7 - 647215 GGGTCTC---- - -a -s simMouse_chr6.simMouse.chr6 379840 2 + 636262 TC -s mr.mrrefChr5 233262 2 + 294540 TC -s simRat_chr6.simRat.chr6 379050 2 + 647215 TT - -a -s simMouse_chr6.simMouse.chr6 379842 22 + 636262 GTCCTTCTTATGGCTCTTCAGA -s Anc1.Anc1refChr6 31694 22 - 197743 GTCCTTCTAATGGCTCTTCAGA -s mr.mrrefChr3 108737 22 - 181027 GTCCTTCTAATGGCTCTTCAGA -s mr.mrrefChr5 233264 22 + 294540 GTCCTTCTTATGGCTCTTCAGA -s simMouse_chr6.simMouse.chr6 116334 22 - 636262 GTCCTTCTAATGGCTCTTCAGA -s simRat_chr6.simRat.chr6 115911 22 - 647215 GTCCTTTTCATGGGTCTTCAGA -s simRat_chr6.simRat.chr6 379052 22 + 647215 GCTCTTCTTATGGCTCTTCAGA -s simRat_chr6.simRat.chr6 194372 19 - 647215 ---CTTCTTATGGCTCTTCAGA - -a -s simMouse_chr6.simMouse.chr6 379864 13 + 636262 GTATCACCTCTCC -s Anc1.Anc1refChr6 31716 13 - 197743 GTATCACTCCCAC -s mr.mrrefChr3 108759 13 - 181027 GTATCGCTCCCAC -s mr.mrrefChr5 233286 13 + 294540 GTATCACCCCCAC -s simMouse_chr6.simMouse.chr6 116356 13 - 636262 GTATCGCTCCCAC -s simRat_chr6.simRat.chr6 115933 13 - 647215 GTAACACCCCCAC -s simRat_chr6.simRat.chr6 379074 13 + 647215 GTATCACCCCCAC -s simRat_chr6.simRat.chr6 194392 13 - 647215 GTATCGGCCCCAC - -a -s simMouse_chr6.simMouse.chr6 379877 3 + 636262 TCA -s Anc1.Anc1refChr6 31729 3 - 197743 TCA -s mr.mrrefChr3 108773 3 - 181027 TCA -s mr.mrrefChr5 233299 3 + 294540 TCA -s simMouse_chr6.simMouse.chr6 116370 3 - 636262 TCA -s simRat_chr6.simRat.chr6 115948 3 - 647215 TTA -s simRat_chr6.simRat.chr6 379087 3 + 647215 TTT -s simRat_chr6.simRat.chr6 194405 1 - 647215 T-- - -a -s simMouse_chr6.simMouse.chr6 379880 21 + 636262 CAGTTCAGATATCAACCGTTT -s Anc1.Anc1refChr6 31732 21 - 197743 CAGTGCAGATATCAACGGTTT -s mr.mrrefChr3 108811 21 - 181027 TAGTGCAGATATCAGCGGCTT -s mr.mrrefChr5 233302 21 + 294540 CAGTTCAGATATCAACCGTTT -s simMouse_chr6.simMouse.chr6 116408 21 - 636262 TAGTGCAGATATCAGCGGCTT -s simRat_chr6.simRat.chr6 115986 21 - 647215 ATGTGCACATATCGACTGCTT -s simRat_chr6.simRat.chr6 379090 21 + 647215 CAGTCCAGAAATCAACCACTT - -a -s simMouse_chr6.simMouse.chr6 379912 4 + 636262 GCAT -s Anc1.Anc1refChr6 31762 4 - 197743 ACAT -s mr.mrrefChr3 108841 4 - 181027 ACAT -s mr.mrrefChr5 233334 4 + 294540 GCAT -s simMouse_chr6.simMouse.chr6 116460 4 - 636262 ACAT -s simRat_chr6.simRat.chr6 116016 4 - 647215 ACAT -s simRat_chr6.simRat.chr6 379122 4 + 647215 GCAT -s simRat_chr6.simRat.chr6 194417 4 - 647215 GTGT - -a -s simMouse_chr6.simMouse.chr6 379916 1 + 636262 A -s mr.mrrefChr5 233338 1 + 294540 A -s simRat_chr6.simRat.chr6 379126 1 + 647215 A -s simRat_chr6.simRat.chr6 194421 1 - 647215 G - -a -s simMouse_chr6.simMouse.chr6 379955 1 + 636262 t -s Anc1.Anc1refChr6 31795 1 - 197743 t -s mr.mrrefChr3 108878 1 - 181027 t -s mr.mrrefChr5 233377 1 + 294540 t -s simMouse_chr6.simMouse.chr6 116497 1 - 636262 t -s simRat_chr6.simRat.chr6 116053 1 - 647215 t -s simRat_chr6.simRat.chr6 379165 1 + 647215 t -s simRat_chr6.simRat.chr6 194468 1 - 647215 t - -a -s simMouse_chr6.simMouse.chr6 380026 1 + 636262 c -s Anc0.Anc0refChr3 12701 1 + 222631 A -s Anc1.Anc1refChr6 45606 1 + 197743 A -s Anc2.Anc2refChr13 15439 1 + 96486 A -s mr.mrrefChr5 233448 1 + 294540 t -s simCow_chr6.simCow.chr6 371456 1 + 602619 A -s simDog_chr6.simDog.chr6 361505 1 + 593897 A -s simHuman_chr6.simHuman.chr6 369795 1 + 601863 A -s simRat_chr6.simRat.chr6 379235 1 + 647215 t -s simRat_chr6.simRat.chr6 194536 1 - 647215 t - -a -s simMouse_chr6.simMouse.chr6 380027 5 + 636262 agccc -s Anc0.Anc0refChr3 12702 5 + 222631 CCCCC -s Anc1.Anc1refChr6 45607 5 + 197743 CCCCC -s Anc2.Anc2refChr13 15441 5 + 96486 CCCCC -s mr.mrrefChr5 233449 5 + 294540 agccc -s simCow_chr6.simCow.chr6 371458 5 + 602619 TCCTC -s simDog_chr6.simDog.chr6 361507 5 + 593897 CCCCC -s simHuman_chr6.simHuman.chr6 369796 5 + 601863 CCCCT -s simRat_chr6.simRat.chr6 379236 5 + 647215 agccc -s simRat_chr6.simRat.chr6 194537 5 - 647215 agccc - -a -s simMouse_chr6.simMouse.chr6 380062 2 + 636262 tg -s mr.mrrefChr5 233486 2 + 294540 tg -s simRat_chr6.simRat.chr6 379271 2 + 647215 tg -s simRat_chr6.simRat.chr6 194574 2 - 647215 tg - -a -s simMouse_chr6.simMouse.chr6 380064 5 + 636262 atttc -s mr.mrrefChr5 233488 5 + 294540 atctc -s simRat_chr6.simRat.chr6 379273 5 + 647215 atctc -s simRat_chr6.simRat.chr6 194577 5 - 647215 atctc - -a -s simMouse_chr6.simMouse.chr6 380087 122 + 636262 ctgtgcaaccaggccactctcagacgaatatgtggcaaaatgttactcttaattggtatattcacagttggctgtggcaacagtcttttgttcctatgacccacacagcatgttatggacca -s mr.mrrefChr5 233511 94 + 294540 ctgtgca--------------------------ggcaaaatgttactcttaattggtatattcacagttgg--gtggcaacagtcttttgttcctatgacccacacagcatgttatggacca -s simRat_chr6.simRat.chr6 379296 94 + 647215 ccatgaa--------------------------ggcgacattcctgtcttaattggtaggtacacacctgg--gtggtaacgggcttttgatcctttggcccacacaGCAcattatggacct - -a -s simMouse_chr6.simMouse.chr6 380252 6 + 636262 gtccca -s mr.mrrefChr5 233648 6 + 294540 gtccca -s simRat_chr6.simRat.chr6 379433 6 + 647215 gtccca -s simRat_chr6.simRat.chr6 194643 6 - 647215 gtccca - -a -s simMouse_chr6.simMouse.chr6 380258 2 + 636262 ag -s mr.mrrefChr5 233654 2 + 294540 ag -s simRat_chr6.simRat.chr6 194649 2 - 647215 at - -a -s simMouse_chr6.simMouse.chr6 380260 24 + 636262 tggcaggtttgcagttggctgtgg -s mr.mrrefChr5 233656 18 + 294540 tggcaggtttgcag------gtgg -s simRat_chr6.simRat.chr6 379439 18 + 647215 tggtatgtttggtt------gtgg -s simRat_chr6.simRat.chr6 194651 18 - 647215 tggcaggtttgcgg------gtgg - -a -s simMouse_chr6.simMouse.chr6 380284 77 + 636262 taacaatctcttgctcctttgccccacactatgctttttacttaataatatcccactcccctttgttgattcacagc -s mr.mrrefChr5 233674 77 + 294540 taatagtctcttgctcctttgccccacacaatgcctttgacttaataatatcccactcccgtttgttgattcgcagc -s simRat_chr6.simRat.chr6 379457 77 + 647215 taatggtctattgctcctttgccctacacaatgccattgacttaataatatcccactcctgtttgctgattcgcagc -s simRat_chr6.simRat.chr6 194697 76 - 647215 ttat-gtttgttgctgctttgacccacacagtgtctttgacttaatgatatcaaactcacgtttgtcaattcgtggt - -a -s simMouse_chr6.simMouse.chr6 380361 16 + 636262 ttcacatcttttctgg -s mr.mrrefChr5 233757 16 + 294540 ttcgcatctttttttg -s simRat_chr6.simRat.chr6 379540 16 + 647215 ttcgcagctgtttttg -s simRat_chr6.simRat.chr6 194792 16 - 647215 tttgcaactttttttg - -a -s simMouse_chr6.simMouse.chr6 380399 4 + 636262 agta -s mr.mrrefChr5 233798 4 + 294540 agta -s simRat_chr6.simRat.chr6 379581 4 + 647215 agta -s simRat_chr6.simRat.chr6 194833 4 - 647215 agtt - -a -s simMouse_chr6.simMouse.chr6 380413 3 + 636262 gga -s mr.mrrefChr5 233812 3 + 294540 gga -s simRat_chr6.simRat.chr6 194847 3 - 647215 gga - -a -s simMouse_chr6.simMouse.chr6 380417 58 + 636262 tagaaggtcaatttccctagcaccagttattgaagagggactcctgtggccattgatt -s mr.mrrefChr5 233937 58 + 294540 tagaaggccaattcccctagcaccaggtattgaagagggactcctgtggccattgatt -s simRat_chr6.simRat.chr6 379734 58 + 647215 tgaatggccaattcccctggcatcacgtattgaagaggggcttctggggctattgatt -s simRat_chr6.simRat.chr6 194972 58 - 647215 tagaaggccaattcctccagtaccatgtattgaaaaaggaatcctgtgcccattgatt - -a -s simMouse_chr6.simMouse.chr6 380606 22 + 636262 ttggaaccaaaaaagggagccc - -a -s simMouse_chr6.simMouse.chr6 380646 3 + 636262 ggt - -a -s simMouse_chr6.simMouse.chr6 380754 22 + 636262 tcatgctctcagtgccttgttg -s mr.mrrefChr5 234504 22 + 294540 tcatgctctgactgctttgctg -s simRat_chr6.simRat.chr6 380264 22 + 647215 gcatgctctgactgctttgctg -s simRat_chr6.simRat.chr6 195564 22 - 647215 tcatgctctgactggtttgctg - -a -s simMouse_chr6.simMouse.chr6 380776 17 + 636262 attcttctacaagaaag -s mr.mrrefChr5 234526 17 + 294540 attcttctacaagaaag -s simRat_chr6.simRat.chr6 380286 17 + 647215 attctactacaagaaag -s simRat_chr6.simRat.chr6 195589 17 - 647215 atttttatacaaaaaag - -a -s simMouse_chr6.simMouse.chr6 380945 5 + 636262 tatac -s mr.mrrefChr5 234697 5 + 294540 gatac -s simRat_chr6.simRat.chr6 380456 5 + 647215 gatac -s simRat_chr6.simRat.chr6 195786 5 - 647215 gatac - -a -s simMouse_chr6.simMouse.chr6 381154 1 + 636262 a - -a -s simMouse_chr6.simMouse.chr6 381198 15 + 636262 tccaatgttaagaca -s mr.mrrefChr5 234968 15 + 294540 tccaatgttaagatc -s simRat_chr6.simRat.chr6 380707 15 + 647215 tccaacgttaagatc -s simRat_chr6.simRat.chr6 196069 15 - 647215 tccaatgtcagaatc - -a -s simMouse_chr6.simMouse.chr6 381254 20 + 636262 tgggccatgctggcattccc -s mr.mrrefChr5 235044 20 + 294540 tgggccatcctggcattcct -s simRat_chr6.simRat.chr6 380763 20 + 647215 tgtgccatcctggcagtact -s simRat_chr6.simRat.chr6 196145 20 - 647215 tgagccaccctggcattcct - -a -s simMouse_chr6.simMouse.chr6 381274 6 + 636262 agggtg -s mr.mrrefChr5 235064 6 + 294540 agggtg -s simRat_chr6.simRat.chr6 196165 6 - 647215 ggggtg - -a -s simMouse_chr6.simMouse.chr6 381280 28 + 636262 aagtctaagtcatcataatgtattaact -s mr.mrrefChr5 235070 28 + 294540 aattctaagtgatcataatgtattagct -s simRat_chr6.simRat.chr6 380783 28 + 647215 aattctaagtgatcataatgttttggct -s simRat_chr6.simRat.chr6 196171 28 - 647215 aattctaagtgatcataaggtatcagct - -a -s simMouse_chr6.simMouse.chr6 381308 5 + 636262 ttctg -s mr.mrrefChr5 235098 5 + 294540 cactg -s simRat_chr6.simRat.chr6 380811 5 + 647215 cactg -s simRat_chr6.simRat.chr6 196202 5 - 647215 caatg - -a -s simMouse_chr6.simMouse.chr6 381313 21 + 636262 atgatttgttggtacgatttt -s mr.mrrefChr5 235103 19 + 294540 atgatttgttggta--atttc -s simRat_chr6.simRat.chr6 380816 19 + 647215 acaatttgatggtg--gtttc -s simRat_chr6.simRat.chr6 196218 19 - 647215 atgatttgctggta--atttc - -a -s simMouse_chr6.simMouse.chr6 381334 6 + 636262 attgac -s mr.mrrefChr5 235123 6 + 294540 attggc -s simRat_chr6.simRat.chr6 380836 6 + 647215 gctggc -s simRat_chr6.simRat.chr6 196238 6 - 647215 attggc - -a -s simMouse_chr6.simMouse.chr6 381340 4 + 636262 ttta -s mr.mrrefChr5 235134 4 + 294540 tttg -s simRat_chr6.simRat.chr6 380847 4 + 647215 tttg -s simRat_chr6.simRat.chr6 196249 4 - 647215 ttcg - -a -s simMouse_chr6.simMouse.chr6 381344 34 + 636262 tcaaaagacagactttccgactcatagacccagg -s mr.mrrefChr5 235140 34 + 294540 tcaaattaccgtcttggcgaatcaaaagcccagg -s simRat_chr6.simRat.chr6 380853 34 + 647215 tcaaattctcgtcttggcaaattgaaagcccagg -s simRat_chr6.simRat.chr6 196255 34 - 647215 tcaggttgccatcttgggcaatcaaaagcacagg - -a -s simMouse_chr6.simMouse.chr6 381378 56 + 636262 ggagtgttttttgaacctttatacctttaagctcaaattttattttagtaatttgc -s mr.mrrefChr5 235176 54 + 294540 tagctgtctgttgtatcatcatggcttta--ctcgaattggatatcagtactatgc -s simRat_chr6.simRat.chr6 380889 54 + 647215 tagctcgctgtcgtatcatcgtggcttta--cttgacttggatatcagtacgatgc -s simRat_chr6.simRat.chr6 196291 54 - 647215 tagctttctgttgtctcatcatggcctta--ctcgatttggatatcagtacaatgc - -a -s simMouse_chr6.simMouse.chr6 381434 27 + 636262 tgctgccaattcacccttgcatgagta -s mr.mrrefChr5 235230 16 + 294540 agct-----------cttgcagaaatg -s simRat_chr6.simRat.chr6 380993 16 + 647215 agct-----------cttgcagatatg -s simRat_chr6.simRat.chr6 196345 16 - 647215 agct-----------ctagcagaaatg - -a -s simMouse_chr6.simMouse.chr6 381461 203 + 636262 agctcttactcatgtagccctttcatcttgcacaagaatcaccatttgtgctatcccttgctcactttttcttgcattgttcagtgcatagggtgcttcctaaaacagtccaatgaacctcccaagtgttttcgtaagtggggtcctgatccttgttgtcatcaggaaaaatatagtatttgcttcacatattgaatgaattg -s mr.mrrefChr5 235251 30 + 294540 agcttctcttcgtgtagt-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------ttgaataaaatt -s simRat_chr6.simRat.chr6 381014 30 + 647215 aacttctctttgtgtagt-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------ttagagaaaatt -s simRat_chr6.simRat.chr6 196366 30 - 647215 agcatctcttcgtatcgt-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------ttgtaaaatatt - -a -s simMouse_chr6.simMouse.chr6 381664 2 + 636262 aa -s mr.mrrefChr5 235281 2 + 294540 aa -s simRat_chr6.simRat.chr6 196396 2 - 647215 ac - -a -s simMouse_chr6.simMouse.chr6 381666 20 + 636262 tggttaggggccagatgatt -s mr.mrrefChr5 235283 17 + 294540 tggt---aggccaggtagtt -s simRat_chr6.simRat.chr6 381044 17 + 647215 cagt---aggccaggtagtt -s simRat_chr6.simRat.chr6 196398 17 - 647215 tggt---aagctgggtagtt - -a -s simMouse_chr6.simMouse.chr6 381686 45 + 636262 ctgtgtcgcagccatatcatccaggcgtaattttatagagctctg -s mr.mrrefChr5 235726 45 + 294540 ctgtgtcgcagccatatcatccaggcgtaattttatagagctctg -s simRat_chr6.simRat.chr6 381674 45 + 647215 ctgtgtcacagccctggcctccaggctttactttatagagctctg - -a -s simMouse_chr6.simMouse.chr6 381731 21 + 636262 tctgcaaggcaattagagatg -s mr.mrrefChr5 235771 21 + 294540 tctgcaaggcaattagagatg -s simRat_chr6.simRat.chr6 381720 21 + 647215 tctccaaggcaattagtgatg - -a -s simMouse_chr6.simMouse.chr6 381752 183 + 636262 tcagagttcttacgtttgtgcaccagggctttgctccctgcgatgtagccacttcttaaatatgcacgatgtggagcagcaaagaataagtacccagcataaatataaacggggtgaaaagtctcattgatctcaatcaactcagcttggtgaaaacctgtattcagctcagggtatgtagtg -s mr.mrrefChr5 235792 177 + 294540 tcagagttcttacgtttgtgcaccagggctttgctccctgcgatgtagccacttcttaaatatgcacgatgtggagcagcaaagaataagtacccagcataaat------ggggtgaaaagtctcattgatctcaatcaactcagcttggtgaaaacctgtattcagctcagggtatgtagtg -s simRat_chr6.simRat.chr6 381744 177 + 647215 tcagagttcttacattcacgcactagagctttgctcactacgatgtagctaatttttaagtatgcatgatatggagcaccaaagaatgagtacccagattaaat------ggggtgaaaagtctcattgatcgcaatcaagtcagtttggtgtaaaactgcaatcagctcgtggtatgtattg - -a -s simMouse_chr6.simMouse.chr6 381935 75 + 636262 cttcatgttgatctatccacagtcgatagtggcgtgttgacatcacccttgacccactgtatgtgagtgtgggcc -s mr.mrrefChr5 235969 75 + 294540 cttcatgttgatctatccacagtcgatagtggcgtgttgacatcacccttgacccactgtatgtgagtgtgggcc -s simRat_chr6.simRat.chr6 381927 75 + 647215 ctttgtgttgatctattcacagtcgatagtggcgagttgacatcacccttgactcactgtatgtgagtgtgggcc - -a -s simMouse_chr6.simMouse.chr6 382014 143 + 636262 tgaggttacatcccaggcctcaaaagccttcacacacctgtgttgggtttatgcacattcaatacagttgatttttctgattgtatagaaccttctagcgttatggattgcccttcccggtcccttctcacactagcagattt -s mr.mrrefChr5 236049 143 + 294540 tgaggttacatcccaggcctcaaaagccttcacacacctgtgttgggtttatgcacattcaatacagttgatttttctgattgtatagaaccttctagcgttatggattgcccttcccggtcccttctcacactagcagattt -s simRat_chr6.simRat.chr6 263299 143 - 647215 tgaagttagatcccatgcctcaaaagcctttgcacacctgcgttgggtttgtgcatgttcaatacagttgttttttctgattgtgtagaatcttcaaccattattgttcgcccctctcggtcccctctcgcactagcagattt - -a -s simMouse_chr6.simMouse.chr6 382157 21 + 636262 aacctaaagtctgccttgtcg -s mr.mrrefChr5 236192 21 + 294540 aacctaaagtctgccttgtcg -s simRat_chr6.simRat.chr6 263443 21 - 647215 aacccaaagtctaacttgtca - -a -s simMouse_chr6.simMouse.chr6 382178 100 + 636262 tttttcttttctcctttcccaataatctggtgttccttctcctagcccttcacctcgagcttacgagtgtgcctgcatgcaaggtgcatcttatggatgt -s mr.mrrefChr5 236213 100 + 294540 tttttcttttctcctttcccaataatctggtgttccttctcctagcccttcacctcgagcttacgagtgtgcctgcatgcaaggtgcatcttatggatgt -s simRat_chr6.simRat.chr6 263488 100 - 647215 ttcttcttttctccttttccatgaatctggtggttgttctcccaaaccttcaccttgagtttacagatttgccggcatgtaaggtgcatcttttggatgt - -a -s simMouse_chr6.simMouse.chr6 382278 434 + 636262 tgagcaatactgacttctatagctaatctgtgtggctggatcaaagattttattcccatgaccttttgctcaacgaatttactcatatgactggggcgaatatggtgacatatgggtgggattagctcatggcacatgctgcaaccaccccttctctatgaagtgtgggctcatgtctgggttctgttggatcaatgttttgtcttgcaataagtggttacaatctagaaacatagactgaatgtaaaaagcctcatgtaggcataaaaagtccctgcctaatgaacaataccaacccctaattaccatttggcacattgatgcaatagatgatagggactcctttgtgtgttcaaggcctcttttattatttctccaagagtaggcctgcccagaacaaaatcccacaaaccttactcgtcagtgaaatattt -s mr.mrrefChr5 236313 377 + 294540 tgagcaatactgacttctatagctaatctgtgtggct----caaagattttattcccatgaccttttgctcaacgaatttactcatatgactggggcgaatatggtgacatatgggtgggattagctcatggcacatg------------------------------------gtctgggttctgttggatc------ttgtcttgcaataagtggttacaatctagaaacatagactgaatgtaaaaagcctcatgtaggcataaaaagtccctgcctaatgaacaataccaacccctaattac-atttggcacattgatgcaatagatgatagggactcctttgtgtgttcaag----------ttatttctccaagagtaggcctgcccagaacaaaatcccacaaaccttactcgtcagtgaaatattt -s simRat_chr6.simRat.chr6 263617 377 - 647215 tcagcatccctgatttttatagctactctgtgtctct----caaagagttcaatcctatgacctcttgatcaaagaggttaatcctatgaccagggtgaatttggtcacatacacgtggggttcattcatggcacatg------------------------------------gtctgggtttagttgtacc------ttgtcttgccataagtggttacaatccagaaacattgacagaatgtaaagtgccccatgtaggcacagagaatccccgtctaataaatgataccaacccctagttag-atttggcatattgatgcaataaatgatagggattcttatgtatatttaag----------ttatttctccaagagtaggcctgcctggtacaaagtcctacaaggcttgcttatctgtgaaatattt - -a -s simMouse_chr6.simMouse.chr6 382712 373 + 636262 gatattcccttcactaacaaagctgagcttacctggttatggaattttgaaggtctgacatttttttccctcaagatattgaagaagggtccccattttgccttttgatcaatgggatctgttaagtggtctgttactcacagtttccctttccttgtcatctagtcctcttctgttggagcacttagcacaccctgcacctatacctggacattggctcctttgattatcgtacaaaaattctgttgtataatgtcacggagctcttcctccaattttgcaccattccacctttcttgatccggcacccctaagagtgatgatgacacaagttgggcctctggtagtcccaaatctcttggggcccatgctt -s mr.mrrefChr5 236690 362 + 294540 gatattcccttcactaacaaagctgagcttacctggttatggaattttg--ggtctgacatttttttcc-tcaagatattgaagaagggtccccattttgccttttgatcaatgggatctgttaagtggtctgttactcacagtttccctttccttgtcatctagtcctcttctgttggagcacttagcacaccctgcacctatacctggacattggctcctttgattatcgtacaaaaattctgttgtataatgtcacggagctcttcctccaattttgcaccattccacctttcttgatccggcacccctaagagt--------cacaagttgggcctctggtagtcccaaatctcttggggcccatgctt -s simRat_chr6.simRat.chr6 263995 362 - 647215 gatatttccttcactaacaaagctgagccaacctggctgtggaattttg--ggtctgacatttttttcc-taacgatattgaagatgggtccccattttggctttcaattgacggtatctgttaaatagtctgatactcattgtttccctttagtggtcatctagtcctcttccgttggagcgcttaacatagcctgcacttttgcctggttacagggtcctttaattatcgcagaagaattcttttgtataatgtcctggagctcattctccaatttcatgctgttctgcctttctttatccggcacctctgagagt--------cacaagttgggcctttgatagtcccagctctcttgagacccatgctt - -a -s simMouse_chr6.simMouse.chr6 383085 14 + 636262 atcctgtgttaggg -s mr.mrrefChr5 237052 14 + 294540 atcctgtgttaggg -s simRat_chr6.simRat.chr6 264358 14 - 647215 attccgttttaggg - -a -s simMouse_chr6.simMouse.chr6 383099 95 + 636262 ctatttccttagaatctctctctcagttcattttggtttccccgtccctggtaatcagatcctccctctgttcaaaatggtcaaaaaggctactg -s mr.mrrefChr5 237066 93 + 294540 ctatttccttagaatctctctc--agttcattttggtttccccgtccctggtaatcagatcctccctctgttcaaaatggtcaaaaaggctactg -s simRat_chr6.simRat.chr6 264377 93 - 647215 ctttctccttgaaaactctctc--agctcgttttcatctccccatccccagtaaccagatcctccctgctgtcaaaatggtcagaatagctactg - -a -s simMouse_chr6.simMouse.chr6 383194 244 + 636262 aaactcctgcaatcataatgtgtcttaggcaagcttgtcttgggtttagttagctcttgagataatctttagtcttcttaactattataatccatttgtctagtttgttgaagctgtggaggtgcctagcattcgctcatatctcttcccaaagcttgacgtagtatgaatgaatggttagagtctttctccctcaatttgtcagagtcattaccggtcttggtcatgtctactaagggtgcgg -s mr.mrrefChr5 237159 216 + 294540 aaactcctgcaatcataatgtgtcttaggcaagcttgtct---gtttagttagctcttgagataatctttagtcttcttaact--------------------tttgttgaagctgtggaggtgcctagcattcgctcatatctctt--caaagcttgacgtagtatg---gaatggttagagtctttctccctcaatttgtcagagtcattaccggtcttggtcatgtctactaagggtgcgg -s simRat_chr6.simRat.chr6 264639 216 - 647215 AAactcctgcaagcataatgtgtcttaagcagccttgtct---gtatagttatctcttgagaggatctttagtgttcttactt--------------------tttgtcgaagctgtggaggtatctgtcattcgctcgcatctctt--caaagcttggcgtagttca---gagtagctaaagtctttctccctcaatttgtcaaagtcattaccagccttggtcttgtctactaaaggtgggg - -a -s simMouse_chr6.simMouse.chr6 383438 184 + 636262 gcaaaggcacagcgccattgatctatgaattgttacagtagtgtgctcagcccatgtgctcattcttacaagttacagtgatccaatcttagacaggtggcaaattctgacTGTGCATAGTGGACATGATGTGGCCATGCATAGCCAGTCATGGAGGGGGGGTGGAGCAGGTTGGATAAGGCTT -s mr.mrrefChr5 237375 154 + 294540 gcaaaggcacagcgccattgatctatgaattgttacagtagtgtgctcagcccatgtgctcattc--acaagttacagtg---------------------------tgacTGTGCATAGTGGACATGATGTGGCCATGCATAG-CAGTCATGGAGGGGGGGTGGAGCAGGTTGGATAAGGCTT -s simRat_chr6.simRat.chr6 264871 154 - 647215 ccaaaggtgaagcaccattgttgtttgaattgtcacagttgtgtcctcagcccatTTGCCCATCC--ACAAGTTACAGTA---------------------------TGACTGTGCATAGTGGCCATGGTGGGGCCATACATAG-CGGCCGTGGTGGGGGGGTGGAGCAGGTTGGATAAGGCTT - -a -s simMouse_chr6.simMouse.chr6 383622 48 + 636262 CACATTATTAATCCCATCTTAATCCCCATGCATACATATCGTTAGATA -s mr.mrrefChr5 237529 48 + 294540 CACATTATTAATCCCATCTTAATCCCCATGCATACATATCGTTAGATA -s simRat_chr6.simRat.chr6 265027 48 - 647215 CCCACTCTTAATCCCACCTTAATCTCTATGTATACATATCCTTAGATA - -a -s simMouse_chr6.simMouse.chr6 383670 135 + 636262 TGTGGTTCCTGAATTGCGACATGTCACTCTACACTCTCATAGAGAACAACAGTCACGATGTCTGTGATAGTTCCTCGGCCTACGATTGCGGGGCTTACGCGTCAGATTTTTCAGTGGTCAAATACTCTAGCTGAG -s mr.mrrefChr5 237577 132 + 294540 TGTGGTTCCTGAATTGCGACATGTCACTCTACACTCTCATAGAGAACAACAGTCACGATGTCTGTGATAGTTCCTCGGCCTACGATTGCGGGGCTTACGCGT-AGATTTTTCAGTGGTCAAATACTCTAGctg-- -s simRat_chr6.simRat.chr6 265076 132 - 647215 TGTGGTGCCTGCATATTGTCAGGTCGCTCTACACTCTCACAAAAAGCAACTGTTACAGTGTCCACGATCATTTCTCAGCCTACAATTCCGGGGCTCACCCGT-AGATTTTTCAGTGGTCAAATACTCTAGctg-- - -a -s simMouse_chr6.simMouse.chr6 383805 68 + 636262 AACTTGTCGTGGGGCTTCACTATCTCCTCTGAGAGCCGTTGAGGTTGTTGAGAACATCGTCATTTCTT -s Anc0.Anc0refChr3 12713 25 + 222631 -------------------------------------------GTAGGAAGGAATACTTTTATTTTTT -s Anc1.Anc1refChr6 45618 25 + 197743 -------------------------------------------GTAGGAAGGAATACTTTTATTTTTT -s Anc2.Anc2refChr13 15452 25 + 96486 -------------------------------------------GTAGCAAGGAATACTGTTGTTTTTT -s mr.mrrefChr5 237709 68 + 294540 aACTTGTAGTGGGGCTTCACTATCTCCTCTGAGAGCCGTTGAGGTTGGTAAGAACATCTTCATTTCTT -s simCow_chr6.simCow.chr6 371469 25 + 602619 -------------------------------------------GGAGCAAGGATTGCTGTTGCTTTCT -s simDog_chr6.simDog.chr6 361518 20 + 593897 -------------------------------------------GTAGCAAGGAATAC-----TTTTTA -s simHuman_chr6.simHuman.chr6 369807 25 + 601863 -------------------------------------------GTGGGAAGGCAAACTTTTATTTTTT -s simRat_chr6.simRat.chr6 383917 68 + 647215 aACTTGCAGTGGGGCTTCACGCTCTCCTCTGAGAGCCGTTCAGGCTGGCAAGAATATCTTCATTTCTT - -a -s simMouse_chr6.simMouse.chr6 383873 4 + 636262 GAGA -s Anc0.Anc0refChr3 12739 4 + 222631 GATA -s Anc1.Anc1refChr6 45644 4 + 197743 GATA -s Anc2.Anc2refChr13 15478 4 + 96486 GATA -s mr.mrrefChr5 237777 4 + 294540 GATA -s simCow_chr6.simCow.chr6 371495 4 + 602619 GACA -s simDog_chr6.simDog.chr6 361539 4 + 593897 GATA -s simHuman_chr6.simHuman.chr6 369833 4 + 601863 GATA -s simRat_chr6.simRat.chr6 383985 4 + 647215 GATA - -a -s simMouse_chr6.simMouse.chr6 383877 8 + 636262 TTGGGACA -s Anc0.Anc0refChr3 12747 8 + 222631 TTGAAACA -s Anc1.Anc1refChr6 45652 8 + 197743 TTGAAACA -s Anc2.Anc2refChr13 15486 8 + 96486 TTGAACCA -s mr.mrrefChr5 237781 8 + 294540 TTGAGACA -s simCow_chr6.simCow.chr6 371503 8 + 602619 TTGAATCT -s simDog_chr6.simDog.chr6 361547 8 + 593897 TTGAGCCA -s simHuman_chr6.simHuman.chr6 369841 8 + 601863 TTGAAACA -s simRat_chr6.simRat.chr6 383989 8 + 647215 TAGAGACA - -a -s simMouse_chr6.simMouse.chr6 383885 24 + 636262 TAGCATCAAAGAAAGCTATGCTTA -s Anc0.Anc0refChr3 12755 22 + 222631 TAACAGCCAAACAAGCTATGCT-- -s Anc1.Anc1refChr6 45660 24 + 197743 TAACAGCCAAACAAGCTATGCTTA -s Anc2.Anc2refChr13 15494 22 + 96486 TAACAGCCAAACAAGCTATGTT-- -s mr.mrrefChr5 237789 24 + 294540 TAGCAGCAAAAAAAGCTATGCTTA -s simCow_chr6.simCow.chr6 371511 22 + 602619 TAATGGACAAACAAGCTATGTT-- -s simDog_chr6.simDog.chr6 361555 20 + 593897 TAACAGCCAAGCAGGCTATG---- -s simHuman_chr6.simHuman.chr6 369852 24 + 601863 TAACAGCCGAACAAGCTATGCATA -s simRat_chr6.simRat.chr6 383997 24 + 647215 TAGTAGCAAAAAAAACTATGCTTA - -a -s simMouse_chr6.simMouse.chr6 383909 29 + 636262 CTTTTAAGGGCACCAATACGTCCATATCC -s Anc0.Anc0refChr3 12780 29 + 222631 CTTTTAAAGGGACCAGCATATCCCAATCT -s Anc1.Anc1refChr6 45687 29 + 197743 CTTTTAAAGGGACCAGCATATCCCAATCT -s Anc2.Anc2refChr13 15519 29 + 96486 CTTCTAAAAGGACCAACATATCCCAATCT -s mr.mrrefChr5 237813 29 + 294540 CTTTTAAAGGCACCAGTACGTCCATATCC -s simCow_chr6.simCow.chr6 371536 29 + 602619 CTTCTAAAAGGACCAACTTGTCCCAGTCT -s simDog_chr6.simDog.chr6 361575 29 + 593897 TTGCTAAAACAACCGAAATATCCCAATCT -s simHuman_chr6.simHuman.chr6 369879 29 + 601863 CTTTCAAAGGGACCAGCAGCTCCCGATCT -s simRat_chr6.simRat.chr6 384021 29 + 647215 CTTTTAAAGGCACTAGTGTGTCCATATCC - -a -s simMouse_chr6.simMouse.chr6 383938 58 + 636262 AGTAGTCTATTAATGTTAGTCCATGAGAGGTCAGACATGTTAACTTGAGGGATTGGGA -s Anc0.Anc0refChr3 12816 58 + 222631 GGTTGACTATTAGTGTTAAACCATGATGGGTCAGGCATGTTTGTTTGAGTGATTGATA -s Anc1.Anc1refChr6 45723 58 + 197743 GGTTGACTATTAGTGTTAAACCATGATGGGTCAGGCATGTTTGTTTGAGTGATTGATA -s Anc2.Anc2refChr13 15555 58 + 96486 GGTTGACTATTAGTGTTTAACCATGATGGGTCAGGCATGTGAGTTTGAGTGATTGATT -s mr.mrrefChr5 237842 58 + 294540 AGTAGTCTATTAGTGTTAGTCCATGATAGGTCAGACATGTTTACTTGAGGGATTGGGA -s simCow_chr6.simCow.chr6 371572 58 + 602619 GGTTGACTATTAGTGTTGAACCAGGATGAGTTAGGCATGTGAGTTGGAGTGCTTGACT -s simDog_chr6.simDog.chr6 361611 55 + 593897 GGTTGACTATTAGAGTTTGAAC-TGAGGG-TCAAGCATGTGAATGTGAGT-ATTGATT -s simHuman_chr6.simHuman.chr6 369915 58 + 601863 GGTTGGCTATTAGTGTTAAACCATGATGGCTCAGGCATGCTTGTTTGAGTGATTGAAA -s simRat_chr6.simRat.chr6 384050 58 + 647215 AGTAGTCTATTAGCTTTAGTCCATGATAGGTCAGACATGTTTACCTCAGGGATTGGGA - -a -s simMouse_chr6.simMouse.chr6 383996 12 + 636262 TGAGGGGATATT -s Anc0.Anc0refChr3 12875 12 + 222631 TGGGGGGATCTT -s Anc1.Anc1refChr6 45782 12 + 197743 TGGGGGGATCTT -s Anc2.Anc2refChr13 15614 12 + 96486 TGGGGGGATGTT -s mr.mrrefChr5 237900 12 + 294540 TGAGGGGATCTT -s simCow_chr6.simCow.chr6 371631 12 + 602619 TGGGGGGATGTT -s simDog_chr6.simDog.chr6 361667 12 + 593897 CGGGGGGATGTT -s simHuman_chr6.simHuman.chr6 369974 12 + 601863 TGGGGGGACCTT -s simRat_chr6.simRat.chr6 384108 12 + 647215 TGAGGGGATCTT - -a -s simMouse_chr6.simMouse.chr6 384008 6 + 636262 CATTTC -s Anc0.Anc0refChr3 12887 6 + 222631 CATTTC -s Anc1.Anc1refChr6 45794 6 + 197743 CATTTC -s Anc2.Anc2refChr13 15626 6 + 96486 CATTAC -s mr.mrrefChr5 237912 6 + 294540 CATTTC -s simCow_chr6.simCow.chr6 371643 4 + 602619 CACT-- -s simDog_chr6.simDog.chr6 361679 6 + 593897 CATTAC -s simHuman_chr6.simHuman.chr6 370006 6 + 601863 CCTTTC -s simRat_chr6.simRat.chr6 384120 6 + 647215 CGTTTC - -a -s simMouse_chr6.simMouse.chr6 384014 21 + 636262 CATAACTTATAGAAGTGTGAC -s Anc0.Anc0refChr3 12893 21 + 222631 CACAACTTGTAAAAGGGTGAC -s Anc1.Anc1refChr6 45800 21 + 197743 CACAACTTGTAAAAGGGTGAC -s Anc2.Anc2refChr13 15632 21 + 96486 CACAACTTGTAAAAGGGTGGT -s mr.mrrefChr5 237918 21 + 294540 CATAACTTATAGAAGTGTGAC -s simCow_chr6.simCow.chr6 371647 12 + 602619 ---------TAGAAGGGTGGT -s simDog_chr6.simDog.chr6 361685 14 + 593897 CACAACTTGTGAGA------- -s simHuman_chr6.simHuman.chr6 370021 21 + 601863 CACAACTGGTAAAAGGGTGAC -s simRat_chr6.simRat.chr6 384126 21 + 647215 CATAATTTTTAGAACTGTAAC - -a -s simMouse_chr6.simMouse.chr6 384035 8 + 636262 ATATTTAC -s Anc0.Anc0refChr3 12914 8 + 222631 ATTTTTTT -s Anc1.Anc1refChr6 45821 8 + 197743 ATTTTTTT -s Anc2.Anc2refChr13 15653 8 + 96486 ATGTTTTT -s mr.mrrefChr5 237939 8 + 294540 ATTTTTAT -s simCow_chr6.simCow.chr6 371678 8 + 602619 ATGTTTTT -s simHuman_chr6.simHuman.chr6 370042 8 + 601863 ATTTTTCT -s simRat_chr6.simRat.chr6 384147 8 + 647215 ATTTTTAT - -a -s simMouse_chr6.simMouse.chr6 384043 23 + 636262 AAGAGGGGGGTGTAGGGCTGACT -s Anc0.Anc0refChr3 12952 23 + 222631 AAGAGAGGGATGTAGGGCTCACT -s Anc1.Anc1refChr6 45859 23 + 197743 AAGAGAGGGATGTAGGGCTCACT -s Anc2.Anc2refChr13 15691 23 + 96486 AAGAGGTGGATGTAGGGCCCACT -s mr.mrrefChr5 237947 23 + 294540 AAGAGAGGGGTGTAGGGCTCACT -s simCow_chr6.simCow.chr6 371716 23 + 602619 AAGAGGTGGATGTAGGGCCCACT -s simHuman_chr6.simHuman.chr6 370080 23 + 601863 AAGAAAGGGATGTAGGGTTCACT -s simRat_chr6.simRat.chr6 384155 23 + 647215 AAAAGAAGGGTGTAGGGATCACT - -a -s simMouse_chr6.simMouse.chr6 384066 3 + 636262 CAC -s Anc0.Anc0refChr3 12975 3 + 222631 CAC -s Anc1.Anc1refChr6 45882 3 + 197743 CAC -s Anc2.Anc2refChr13 15714 3 + 96486 CAT -s mr.mrrefChr5 237970 3 + 294540 CAC -s simCow_chr6.simCow.chr6 371743 3 + 602619 CAT -s simHuman_chr6.simHuman.chr6 370103 3 + 601863 CAC -s simRat_chr6.simRat.chr6 384178 3 + 647215 CAC - -a -s simMouse_chr6.simMouse.chr6 384069 29 + 636262 ATCCGAGTGAAATCCAAAAAACTGTCACA -s Anc0.Anc0refChr3 12978 29 + 222631 ATTCGTGGGATATCCAAAAAACCGTCACA -s Anc1.Anc1refChr6 45885 29 + 197743 ATTCGTGGGATATCCAAAAAACCGTCACA -s Anc2.Anc2refChr13 15717 29 + 96486 ACTTGTGGGATATCCAAGCAACCATCACA -s mr.mrrefChr5 237973 29 + 294540 ATTCGAGTGAAATCCAAAAAACTGTCACA -s simCow_chr6.simCow.chr6 371747 29 + 602619 ACTTGTGGGATATCCAAGCAACCATCACA -s simDog_chr6.simDog.chr6 243087 4 + 593897 -------------------------CACA -s simHuman_chr6.simHuman.chr6 370106 29 + 601863 ATTCGTTCAAGATCTAAAAGACCGTCACA -s simRat_chr6.simRat.chr6 384181 29 + 647215 ATTCGAGTGAAGTCCAAAAAACTGTCACA - -a -s simMouse_chr6.simMouse.chr6 384098 18 + 636262 CCTCAGCCTCCTTACCTT -s Anc0.Anc0refChr3 13007 18 + 222631 CAGCAGCCTCACAACCTT -s Anc1.Anc1refChr6 45914 18 + 197743 CAGCAGCCTCACAACCTT -s Anc2.Anc2refChr13 15746 18 + 96486 CAGCAGCCACACAACCAT -s mr.mrrefChr5 238002 18 + 294540 CCTCAGCCTCCTAACCTT -s simCow_chr6.simCow.chr6 371776 18 + 602619 CAGCAGCCAATAACCCTT -s simDog_chr6.simDog.chr6 243091 18 + 593897 CAGCAGCCTCATTACCAT -s simDog_chr6.simDog.chr6 361699 15 + 593897 GGGTGGCCACAC---CAT -s simHuman_chr6.simHuman.chr6 370135 18 + 601863 TAGCAGCCTCACAACCTC -s simRat_chr6.simRat.chr6 384210 18 + 647215 CCTCAGCCTGTTATCCTT - -a -s simMouse_chr6.simMouse.chr6 384116 29 + 636262 GTAGGGGCCTTTTTTGCGACTCCCTAACC -s Anc0.Anc0refChr3 13030 29 + 222631 GTAGGAGCCTTTTTTGTAACACCCTATCC -s Anc1.Anc1refChr6 45937 29 + 197743 GTAGGAGCCTTTTTTGTAACACCCTATCC -s Anc2.Anc2refChr13 15769 29 + 96486 GTGGGAGCCTTTTTTGTGACACCCTATCC -s mr.mrrefChr5 238020 29 + 294540 GTAGGGGCCTTTTTTGCAACTCCCTAACC -s simCow_chr6.simCow.chr6 371799 7 + 602619 GTGGGAG---------------------- -s simDog_chr6.simDog.chr6 243114 29 + 593897 ATGGGAGCCTTTTTTGTGACACCCTACCT -s simDog_chr6.simDog.chr6 361719 29 + 593897 GTGAGAGCCTTTTCTGCGACACCCTATCC -s simHuman_chr6.simHuman.chr6 370158 29 + 601863 GTAGGACCCTTTTTTGAAACACTCTAGCC -s simRat_chr6.simRat.chr6 384228 29 + 647215 TTAGGGGCCTTATTTACAACTCCCTAACC - -a -s simMouse_chr6.simMouse.chr6 384145 20 + 636262 AAAACTGCACCCAGTTCTAT -s Anc0.Anc0refChr3 13059 20 + 222631 AAAACTGCCCCTAGTTTTTT -s Anc1.Anc1refChr6 45966 20 + 197743 AAAACTGCCCCTAGTTTTTT -s Anc2.Anc2refChr13 15798 20 + 96486 ATAACTACCCCTGGTTTTTT -s mr.mrrefChr5 238049 20 + 294540 AAAACTGCACCCAGTTCTTT -s simDog_chr6.simDog.chr6 243143 20 + 593897 AGAAGTACCCCTGGTTTTTT -s simDog_chr6.simDog.chr6 361768 20 + 593897 GTAACTACCCCTGGTTTTCT -s simHuman_chr6.simHuman.chr6 370187 20 + 601863 AAAACTGCCCCTAGTTTTTT -s simRat_chr6.simRat.chr6 384257 20 + 647215 AAAACTGCACCCAGTTCTTT - -a -s simMouse_chr6.simMouse.chr6 384165 2 + 636262 AA -s Anc0.Anc0refChr3 13079 1 + 222631 -A -s Anc1.Anc1refChr6 45986 2 + 197743 AA -s Anc2.Anc2refChr13 15818 1 + 96486 -A -s mr.mrrefChr5 238069 2 + 294540 AA -s simDog_chr6.simDog.chr6 243163 1 + 593897 -A -s simDog_chr6.simDog.chr6 361788 1 + 593897 -A -s simHuman_chr6.simHuman.chr6 370209 2 + 601863 AA -s simRat_chr6.simRat.chr6 384277 2 + 647215 AA - -a -s simMouse_chr6.simMouse.chr6 384167 33 + 636262 TCAGCCCCAATTTTTGGTGGATGCAACATTGCC -s Anc0.Anc0refChr3 13080 33 + 222631 CCAGCCTCAAATCTTGGAGGATGTGCTGTAAGT -s Anc1.Anc1refChr6 45988 33 + 197743 CCAGCCTCAAATCTTGGAGGATGTGCTGTAAGT -s Anc2.Anc2refChr13 15819 33 + 96486 CTAACATCAAATCTTGGAGGATGCACTGTAAGG -s mr.mrrefChr5 238071 33 + 294540 TCAGCCCCAATTTTTGGTGGATGTGACATTACT -s simCow_chr6.simCow.chr6 371806 11 + 602619 ----------------------GCACTATAAGT -s simDog_chr6.simDog.chr6 243164 33 + 593897 CTAACATCAAATCTTGGAGGATGCACTGTAAGG -s simDog_chr6.simDog.chr6 361789 33 + 593897 CTAACATCAAATCTTGTAGGTTGCACTGTAGAG -s simHuman_chr6.simHuman.chr6 370211 33 + 601863 CCAGCCTCAAATCCTGGAGGATCTGCTGTCAGT -s simRat_chr6.simRat.chr6 384280 33 + 647215 TCAGCCCCAATTTTTGGTGGACGTGAACTTATT - -a -s simMouse_chr6.simMouse.chr6 384200 2 + 636262 AT -s Anc0.Anc0refChr3 13117 2 + 222631 AT -s Anc1.Anc1refChr6 46025 2 + 197743 AT -s Anc2.Anc2refChr13 15856 2 + 96486 AT -s mr.mrrefChr5 238108 2 + 294540 AT -s simCow_chr6.simCow.chr6 371821 2 + 602619 GT -s simDog_chr6.simDog.chr6 243201 2 + 593897 AT -s simDog_chr6.simDog.chr6 361826 2 + 593897 AT -s simHuman_chr6.simHuman.chr6 370248 2 + 601863 AT -s simRat_chr6.simRat.chr6 384321 2 + 647215 GT - -a -s simMouse_chr6.simMouse.chr6 384202 1 + 636262 G -s Anc0.Anc0refChr3 13119 1 + 222631 G -s Anc1.Anc1refChr6 46027 1 + 197743 G -s Anc2.Anc2refChr13 15858 1 + 96486 G -s mr.mrrefChr5 238110 1 + 294540 G -s simCow_chr6.simCow.chr6 371825 1 + 602619 G -s simDog_chr6.simDog.chr6 361828 1 + 593897 T -s simHuman_chr6.simHuman.chr6 370250 1 + 601863 G -s simRat_chr6.simRat.chr6 384323 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 384203 27 + 636262 AGCCCTTGTTTTGTTCCATTTAGGAGG -s Anc0.Anc0refChr3 13120 27 + 222631 GGACCCTATTCTCTCCTGCTTGGGAAA -s Anc1.Anc1refChr6 46028 27 + 197743 GGACCCTATTCTCTCCTGCTTGGGAAA -s Anc2.Anc2refChr13 15859 27 + 96486 GGACTCTATTCTCTCCTGCTTGGAAAA -s mr.mrrefChr5 238111 27 + 294540 AGCCCTTGTTCTGTTCCACTTAGGAAG -s simCow_chr6.simCow.chr6 371826 27 + 602619 GGACTCCATTTTCCCTTGCTTGGAAAA -s simDog_chr6.simDog.chr6 243203 27 + 593897 TGACTCTATTCTCTCCTGCTTTCAAAG -s simDog_chr6.simDog.chr6 361829 23 + 593897 GGACTCTATTCTCTCCTGCT----AAA -s simHuman_chr6.simHuman.chr6 370251 27 + 601863 TGACCCTAGGCTCTGCTGCTTGGGAAA -s simRat_chr6.simRat.chr6 384324 27 + 647215 CGCCCTTGTTCTTTTCCACCTAGGAAG - -a -s simMouse_chr6.simMouse.chr6 384230 14 + 636262 ATTGCTAAGTTTAT -s Anc0.Anc0refChr3 13147 14 + 222631 ATTCCTGAATATGT -s Anc1.Anc1refChr6 46055 14 + 197743 ATTCCTGAATATGT -s Anc2.Anc2refChr13 15899 14 + 96486 ATTTCTGAATATGT -s mr.mrrefChr5 238138 14 + 294540 ATTCCTGAATATGT -s simCow_chr6.simCow.chr6 371854 13 + 602619 -TTTCTGAGTATTT -s simDog_chr6.simDog.chr6 243243 14 + 593897 GTTTCTGAATATGT -s simDog_chr6.simDog.chr6 361865 14 + 593897 ATTTCTGAATATGT -s simHuman_chr6.simHuman.chr6 370278 14 + 601863 ATTCCTGAATATGT -s simRat_chr6.simRat.chr6 384351 14 + 647215 ATTCCAGAATATGT - -a -s simMouse_chr6.simMouse.chr6 384244 14 + 636262 TACAGACTGTATCC -s Anc0.Anc0refChr3 13167 14 + 222631 TACAGATAACACCT -s Anc1.Anc1refChr6 46075 14 + 197743 TACAGATAACACCT -s Anc2.Anc2refChr13 15919 14 + 96486 TTTAGATAACACCT -s mr.mrrefChr5 238152 14 + 294540 TACAGATTGTATCC -s simCow_chr6.simCow.chr6 371873 14 + 602619 TTTGGAGAACACCT -s simDog_chr6.simDog.chr6 243263 14 + 593897 TTTAGATAACACCT -s simDog_chr6.simDog.chr6 361885 14 + 593897 TTTAGATAACACCT -s simHuman_chr6.simHuman.chr6 370298 14 + 601863 TACCGATATCACCT -s simRat_chr6.simRat.chr6 384365 14 + 647215 TACAGATTGTATCC - -a -s simMouse_chr6.simMouse.chr6 384258 84 + 636262 ATGTTGTAGCACCTACTTACCATCCAGCTACTAGTGAAGCAGATAAGCGAGTGTCATTTTCACAAGCCTGGTGAAATACAGTTC -s Anc0.Anc0refChr3 13181 83 + 222631 ATGTTGTTGCACCTCCTTACCATCCTGCCACTAACAAGGCAGAGAGGGGAGGGTCATTTTCATATGCCAGTTGAAATACAG-TT -s Anc1.Anc1refChr6 46089 84 + 197743 ATGTTGTTGCACCTCCTTACCATCCTGCCACTAACAAGGCAGAGAGGGGAGGGTCATTTTCATATGCCAGTTGAAATACAGTTT -s Anc2.Anc2refChr13 15933 83 + 96486 GTCCTGTTGTGCCTCATTACTGTCCTGACAATAACAAGGCAGAGAGGGGAGGGTCACTTTCCTATGTCAGTTGAAGTACAG-TT -s mr.mrrefChr5 238166 84 + 294540 ATGTTGTAGCACCTACTTACCATCCAGCCACTAGTGAAGCAGATAAGCGAGTGTCATTTTCACAAGCCTGGTGAAATACAGTTT -s simCow_chr6.simCow.chr6 371887 83 + 602619 GTACTGTAATGTCACCTTACCATCGTGCCCATAACAAGGCAGAGCAGGGAGGGTCATATTCCTACGCCCATTGAAGTACAT-TT -s simDog_chr6.simDog.chr6 243277 83 + 593897 GTCCTACTCCACCTCATTACTGTCCTGACAATAACAAGGCAGAGAGGGGAGGGTCACTATTGTATATCAGTTGAAGTACAG-TC -s simDog_chr6.simDog.chr6 361899 83 + 593897 GTCCTGTCGTGCCTAATGACTGTCCTGACAATAACCAAGCAGAGAGTGGAGGGTCACTGTCCTATGTTAGTTGAAGTACAG-TG -s simHuman_chr6.simHuman.chr6 370316 73 + 601863 ATGTT----CACCTTCTTAACATCCTGCCACTATCAAGGCAGAGGGGGGAGGATCATTTTCATGTGCC-------ATGTTGTTT -s simRat_chr6.simRat.chr6 384379 84 + 647215 ATATTGTAGCACCTACTTCCCATCTAGCCCCTAATGCAGCAGATAAGCGAGTTCCATTTTCACAAGCCTGGTGAAATACAGTTT - -a -s simMouse_chr6.simMouse.chr6 384342 10 + 636262 TTGTGGATGC -s Anc0.Anc0refChr3 13266 10 + 222631 TTGTGACTGC -s Anc1.Anc1refChr6 46175 10 + 197743 TTGTGACTGC -s Anc2.Anc2refChr13 16018 10 + 96486 TTGTGACTGC -s mr.mrrefChr5 238250 10 + 294540 TTGTGGATGC -s simCow_chr6.simCow.chr6 371972 10 + 602619 TTCTAACTCC -s simDog_chr6.simDog.chr6 243362 10 + 593897 TTGCGACTGC -s simDog_chr6.simDog.chr6 361984 10 + 593897 TTGTGACTGC -s simHuman_chr6.simHuman.chr6 370391 10 + 601863 TTGTGACTGC -s simRat_chr6.simRat.chr6 384463 9 + 647215 TTGTGG-TGC - -a -s simMouse_chr6.simMouse.chr6 384352 36 + 636262 TACATGCAGACTTTGACTCTTTTGGCTCTTATATAA -s Anc0.Anc0refChr3 13281 27 + 222631 TGTATCCAGAATTTGACTGT---------TATACAA -s Anc1.Anc1refChr6 46190 27 + 197743 TGTATCCAGAATTTGACTGT---------TATACAA -s Anc2.Anc2refChr13 16033 27 + 96486 CACATCTGGAATTTACCTGC---------TATACAA -s mr.mrrefChr5 238260 36 + 294540 TGTATGCAGACTTTGACTCTTTTGGCTCTTATATAA -s simCow_chr6.simCow.chr6 371987 27 + 602619 CGTGTCCAGAAGTTGCCTGC---------TCTACAA -s simDog_chr6.simDog.chr6 243377 27 + 593897 CACATCTGGAATTTACCCGC---------TTTACAA -s simDog_chr6.simDog.chr6 361999 27 + 593897 CACATCTGGAATTTACCTGC---------TATACAA -s simHuman_chr6.simHuman.chr6 370406 27 + 601863 TGTGTCCAGAATTTGACTGT---------TATACAA -s simRat_chr6.simRat.chr6 384472 32 + 647215 TGTATGT----TTTGACTCTTTTGACTCTTGTATAA - -a -s simMouse_chr6.simMouse.chr6 384388 2 + 636262 TC -s Anc0.Anc0refChr3 13308 2 + 222631 CC -s Anc1.Anc1refChr6 46217 2 + 197743 CC -s Anc2.Anc2refChr13 16060 2 + 96486 CC -s mr.mrrefChr5 238296 2 + 294540 TC -s simCow_chr6.simCow.chr6 372014 2 + 602619 CC -s simDog_chr6.simDog.chr6 243404 2 + 593897 CC -s simDog_chr6.simDog.chr6 362032 2 + 593897 CC -s simHuman_chr6.simHuman.chr6 370433 2 + 601863 CC -s simRat_chr6.simRat.chr6 384504 2 + 647215 TC - -a -s simMouse_chr6.simMouse.chr6 384390 9 + 636262 CAGGCCCTA -s Anc0.Anc0refChr3 13317 9 + 222631 TAGGCCCCA -s Anc1.Anc1refChr6 46226 9 + 197743 TAGGCCCCA -s Anc2.Anc2refChr13 16069 9 + 96486 TAGACTCCA -s mr.mrrefChr5 238298 9 + 294540 TAGGCCCTA -s simCow_chr6.simCow.chr6 372023 9 + 602619 TAGACTCCA -s simDog_chr6.simDog.chr6 243409 3 + 593897 ------CCA -s simDog_chr6.simDog.chr6 362037 3 + 593897 ------CCA -s simHuman_chr6.simHuman.chr6 370442 9 + 601863 TAAGCCCCA -s simRat_chr6.simRat.chr6 384506 9 + 647215 TAGGCCCTA - -a -s simMouse_chr6.simMouse.chr6 384399 23 + 636262 TCCTTGTTAGAACCTATCGCAAG -s Anc0.Anc0refChr3 13328 23 + 222631 TCCCTGGTAGAACCTAATGCAAG -s Anc1.Anc1refChr6 46237 23 + 197743 TCCCTGGTAGAACCTAATGCAAG -s Anc2.Anc2refChr13 16080 23 + 96486 TCCCTGGTAGAACCCAATGCAAA -s mr.mrrefChr5 238307 23 + 294540 TCCTTGTTAGAACCTATTGCAAG -s simCow_chr6.simCow.chr6 372034 23 + 602619 TCCCTGTTGGAACCCATTGCAAA -s simDog_chr6.simDog.chr6 243414 23 + 593897 TCCCTGGTAGAACCCAATCTAGG -s simDog_chr6.simDog.chr6 362042 23 + 593897 TCCCCGGTAGGGCCCAATGCTAA -s simHuman_chr6.simHuman.chr6 370453 23 + 601863 TCCCTGGTAGAACATAATGCAAG -s simRat_chr6.simRat.chr6 384515 23 + 647215 TCCTTACTGGAACCTCTTGCAAG - -a -s simMouse_chr6.simMouse.chr6 384422 20 + 636262 TGTTTTTGTGAAAGGGATTC -s Anc0.Anc0refChr3 13351 20 + 222631 CCTTTTTGCAGAAAGGCTTT -s Anc1.Anc1refChr6 46260 20 + 197743 CCTTTTTGCAGAAAGGCTTT -s Anc2.Anc2refChr13 16103 20 + 96486 CCTTTTTGCAGAAAGGCTTT -s mr.mrrefChr5 238330 20 + 294540 TGTTTTTGCGAAAAGGATTC -s simCow_chr6.simCow.chr6 372057 20 + 602619 CCTATTTGCAGAAAGGCATT -s simDog_chr6.simDog.chr6 362065 20 + 593897 CCTTTTTGTAGAACGGCTTT -s simHuman_chr6.simHuman.chr6 370476 20 + 601863 CCTTTTTGCAGAAAGGCTTT -s simRat_chr6.simRat.chr6 384538 20 + 647215 TGTTTCTGCGTAAAAGGTTC - -a -s simMouse_chr6.simMouse.chr6 384442 8 + 636262 CACCATTA -s Anc0.Anc0refChr3 13372 8 + 222631 CACCATTA -s Anc1.Anc1refChr6 46281 8 + 197743 CACCATTA -s Anc2.Anc2refChr13 16124 8 + 96486 CACTATTA -s mr.mrrefChr5 238350 8 + 294540 CACCATTA -s simCow_chr6.simCow.chr6 372078 8 + 602619 CACTATTA -s simDog_chr6.simDog.chr6 362086 8 + 593897 CACTATTA -s simHuman_chr6.simHuman.chr6 370497 8 + 601863 CACCATTA -s simRat_chr6.simRat.chr6 384558 8 + 647215 CACCATTA - -a -s simMouse_chr6.simMouse.chr6 384450 48 + 636262 GTGTTTGGGGCATTGTAGCAATTTTAACCTGATAGAATCAGTTTTGAT -s Anc0.Anc0refChr3 13380 27 + 222631 GTATTTGGGG-ATTGTAGCA--------------------GTTTTGAT -s Anc1.Anc1refChr6 46289 27 + 197743 GTATTTGGGG-ATTGTAGCA--------------------GTTTTGAT -s Anc2.Anc2refChr13 16132 27 + 96486 GTATCTGGGG-ATTGTAGCC--------------------GTTTAAAT -s mr.mrrefChr5 238358 48 + 294540 GTATTTGGGGCATTGTAGCAATTTTAATCTGATAGAATCAGTTTTGAT -s simCow_chr6.simCow.chr6 372086 27 + 602619 GCATCTGGGG-ATTGTTGCG--------------------GTTTTAAT -s simDog_chr6.simDog.chr6 362094 27 + 593897 GTATCTGGGA-ATTGTAGCC--------------------GTTTAAAT -s simDog_chr6.simDog.chr6 362491 18 + 593897 ---------G-ATTGTAGCC--------------------GTTTAAAT -s simHuman_chr6.simHuman.chr6 370508 27 + 601863 CTATTTGAGG-GTTGTACCA--------------------GTTTTGAT -s simRat_chr6.simRat.chr6 384566 48 + 647215 GTATTTGGGGCATTGTAGCAATTTTAATCTGATAGAATCAGTTTTGAT - -a -s simMouse_chr6.simMouse.chr6 384498 82 + 636262 CTGATCATTGCTCGGTTTGTGCCCTGTGATAGCAGGCAGTAGATTGATAACAACTTGCGGACTCTTGCATAGCATTGTAATT -s Anc0.Anc0refChr3 13407 17 + 222631 CTGAT-----------------------------------------------------------------AGCATAGTAATT -s Anc1.Anc1refChr6 46316 17 + 197743 CTGAT-----------------------------------------------------------------AGCATAGTAATT -s Anc2.Anc2refChr13 16160 17 + 96486 CTGAT-----------------------------------------------------------------AGTACAGTAATT -s mr.mrrefChr5 238406 17 + 294540 CTGAT-----------------------------------------------------------------AGCATTGTAATT -s simCow_chr6.simCow.chr6 372114 16 + 602619 -TGAT-----------------------------------------------------------------AGCATAGTAATT -s simDog_chr6.simDog.chr6 362122 17 + 593897 TTGAT-----------------------------------------------------------------AGTACAGTAATT -s simDog_chr6.simDog.chr6 362510 17 + 593897 CTGAT-----------------------------------------------------------------AGTACAGTAATT -s simHuman_chr6.simHuman.chr6 370535 17 + 601863 ATGAT-----------------------------------------------------------------AGCATAGTAATT -s simRat_chr6.simRat.chr6 384614 17 + 647215 GTGAT-----------------------------------------------------------------AGCATTGTAATT - -a -s simMouse_chr6.simMouse.chr6 384580 14 + 636262 TGACAGTTCCTCAT -s Anc0.Anc0refChr3 13425 14 + 222631 TGACAATTCCTCAT -s Anc1.Anc1refChr6 46334 14 + 197743 TGACAATTCCTCAT -s Anc2.Anc2refChr13 16178 14 + 96486 TGACAAGTCCTCAT -s mr.mrrefChr5 238423 14 + 294540 TGACAGTTCCTCAT -s simCow_chr6.simCow.chr6 372131 14 + 602619 CGATAAGTCCTTAT -s simDog_chr6.simDog.chr6 362140 14 + 593897 TGACAAGTCCTCAT -s simDog_chr6.simDog.chr6 362528 14 + 593897 TGACAAGTCCTCAT -s simHuman_chr6.simHuman.chr6 370553 14 + 601863 CGACAATTCCTCGC -s simRat_chr6.simRat.chr6 384631 14 + 647215 TGACAGTTTTTTAT - -a -s simMouse_chr6.simMouse.chr6 384594 22 + 636262 ACACTGAGAAGACTGATGAGTG -s Anc0.Anc0refChr3 13439 22 + 222631 TCACTGAGAGGACTGATGAGTG -s Anc1.Anc1refChr6 46348 22 + 197743 TCACTGAGAGGACTGATGAGTG -s Anc2.Anc2refChr13 16195 22 + 96486 CCACTGAAAGGACTGATGAGTG -s mr.mrrefChr5 238437 22 + 294540 TCACTGAGAGGACTGATGAGTG -s simCow_chr6.simCow.chr6 372148 14 + 602619 CT--------GACCGCTGGATG -s simDog_chr6.simDog.chr6 362157 22 + 593897 CCACTGAAAGGACTGATGAGTG -s simDog_chr6.simDog.chr6 362545 22 + 593897 CCACTGAAAGGACTGATGAGTG -s simHuman_chr6.simHuman.chr6 370567 22 + 601863 TCACTGAGAGCACTGTTCAATG -s simRat_chr6.simRat.chr6 384645 17 + 647215 TCACTGAGAGGACTG-----TG - -a -s simMouse_chr6.simMouse.chr6 384616 57 + 636262 CAAACTATGTATAACCATTACTAAATTATAGCCTGCCTTATTGATGGTATTGTATCT -s Anc0.Anc0refChr3 13468 41 + 222631 CAATGTATGGATAAACTTTACTAAATTATAC----------------TATGGCAACT -s Anc1.Anc1refChr6 46377 41 + 197743 CAATGTATGGATAAACTTTACTAAATTATAC----------------TATGGCAACT -s Anc2.Anc2refChr13 16224 41 + 96486 CAATGTGTAGATAGACTTTAATAAATCCCAC----------------TATGACAACT -s mr.mrrefChr5 238459 56 + 294540 CAAACTATGTATAACCATTACTAAATTATAGCC-GCCTTATTGATGGTATTGTATCT -s simCow_chr6.simCow.chr6 372169 37 + 602619 CAGTGTATCATTCAACTTTACCATATCACAC----------------TATGAC---- -s simDog_chr6.simDog.chr6 362186 41 + 593897 CAATGTGTAGATAGACTTTAATAAATCCCAC----------------TATGACAACT -s simDog_chr6.simDog.chr6 362574 41 + 593897 CAATGTGTAGATAGACCTTAATAAATCCCAC----------------TATGACAACT -s simHuman_chr6.simHuman.chr6 370596 41 + 601863 CAATGTATGAATAAACTTTACTAGATTATAC----------------TGTGGCAACC -s simRat_chr6.simRat.chr6 384662 56 + 647215 CAGACTATGTACAACCACTACTAAACTATAGCC-GTCTTATTGATGATATTGTATCT - -a -s simMouse_chr6.simMouse.chr6 384673 16 + 636262 GGTTCATATCATTTTC -s Anc0.Anc0refChr3 13509 16 + 222631 GGTTCAGATCCTTGTC -s Anc1.Anc1refChr6 46418 16 + 197743 GGTTCAGATCCTTGTC -s Anc2.Anc2refChr13 16305 16 + 96486 GGTGCAGCACCTTGTC -s mr.mrrefChr5 238515 16 + 294540 GGTTCATATCCTTGTC -s simCow_chr6.simCow.chr6 372223 14 + 602619 GGAGCACAACCCTT-- -s simDog_chr6.simDog.chr6 362267 16 + 593897 GGTGCAGCACCTTGTC -s simDog_chr6.simDog.chr6 362655 16 + 593897 GGTGCAGCACCTTGTC -s simHuman_chr6.simHuman.chr6 370637 16 + 601863 TATTCAAATCCTTGTT -s simRat_chr6.simRat.chr6 384718 16 + 647215 AGTGCACATCCTTGTC - -a -s simMouse_chr6.simMouse.chr6 384689 63 + 636262 AGTTAGCTTGGGCACTCAGTAGTGGTGTTGATAGTTCCTACTTCATCAACAGAGGCATTTGTG -s Anc0.Anc0refChr3 13525 60 + 222631 ATTTAGCTTGGGCTCTCAATAG-GGTCT--ATATTTCCCACATCATCAATAGAAGCATTTGTG -s Anc1.Anc1refChr6 46434 60 + 197743 ATTTAGCTTGGGCTCTCAATAG-GGTCT--ATATTTCCCACATCATCAATAGAAGCATTTGTG -s Anc2.Anc2refChr13 16323 60 + 96486 ATTTGGCTTAGGCTCTCAACAG-GCTCT--ATTTTTCACACATCATCAATAGAAGTATTTGTG -s mr.mrrefChr5 238531 61 + 294540 AGTTAGCTTGGGCTCTCAGTAGTGGTGT--ATATTTCCTACATCATCAATAGAGGCATTTGTG -s simCow_chr6.simCow.chr6 372238 60 + 602619 ATTTGGCTTGGGCCCTCAATGG-GGTCT--ATATTACCCATATCACCACTAGAAGCAGTTATG -s simDog_chr6.simDog.chr6 362285 60 + 593897 ATTTGGCTTAGGCTCTCAACAG-GCTCT--ATTTTTCACACATCATCAATAGAAGTATTTGTG -s simDog_chr6.simDog.chr6 362673 60 + 593897 ATTTGGCTTAGGCTCTCAACAG-GCTCT--ATTTTTCACACATCATCAATAGAAGTATTTGTG -s simHuman_chr6.simHuman.chr6 370653 60 + 601863 ATTTAGCCTGGGCTCTCAATGG-GGTCT--ATATTTCCGACATCATCAATAGAAGCATTTGTG -s simRat_chr6.simRat.chr6 384734 61 + 647215 AGTTAGTTTAGGCTCCCAGTAGTGGCGT--TTATTCTCCACATCATCAATAGAGGCATTTCTG - -a -s simMouse_chr6.simMouse.chr6 384752 2 + 636262 TG -s Anc0.Anc0refChr3 13585 2 + 222631 TG -s Anc1.Anc1refChr6 46494 2 + 197743 TG -s Anc2.Anc2refChr13 16383 2 + 96486 AG -s mr.mrrefChr5 238592 2 + 294540 TG -s simCow_chr6.simCow.chr6 372298 2 + 602619 AA -s simDog_chr6.simDog.chr6 362345 2 + 593897 AG -s simDog_chr6.simDog.chr6 362733 2 + 593897 AG -s simHuman_chr6.simHuman.chr6 370714 2 + 601863 TG -s simRat_chr6.simRat.chr6 384795 2 + 647215 TG - -a -s simMouse_chr6.simMouse.chr6 384754 44 + 636262 AAAGTTATTCTGACATGCTCCCCCATGTCTTTTGAGAATTGCCC -s Anc0.Anc0refChr3 13587 44 + 222631 GTACTTACTCTGACAGTTCTCCCCATGCTTTCTGAGAATTGCCC -s Anc1.Anc1refChr6 46496 44 + 197743 GTACTTACTCTGACAGTTCTCCCCATGCTTTCTGAGAATTGCCC -s Anc2.Anc2refChr13 16385 44 + 96486 GTCCCTCCCCTGACAGTTCTTCCCATTCTTTCTGAGTATTGCAC -s mr.mrrefChr5 238594 44 + 294540 ATAGTTATTCTGACAGGCTCCCCCATGTCTTTTGAGAATTGCCC -s simCow_chr6.simCow.chr6 372300 44 + 602619 ATCCTTCTTCTGGCAGTTATCCCCATGCTTTCTGAGAATTTCCC -s simDog_chr6.simDog.chr6 362347 43 + 593897 G-CCCTCCCCTGACAGTTCTTCCCATTCTTTCTGAGTATTGCAC -s simDog_chr6.simDog.chr6 362735 43 + 593897 G-CCCTCCCCTGACAGTTCTTCCCATTCTTTCTGAGTATTGCAC -s simHuman_chr6.simHuman.chr6 370716 44 + 601863 GTACTTAGTCCGAAAGTGCTCTCCATGCTTGCTGAGAATTACCC -s simRat_chr6.simRat.chr6 384801 38 + 647215 ATAGTTATCCTGACAG------CAATGTCTCTTGAGAATTGCCA - -a -s simMouse_chr6.simMouse.chr6 384798 10 + 636262 CAGTAGTTTA -s Anc0.Anc0refChr3 13631 10 + 222631 CAGGTGATTA -s Anc1.Anc1refChr6 46540 10 + 197743 CAGGTGATTA -s Anc2.Anc2refChr13 16429 10 + 96486 AAGGTGATTA -s mr.mrrefChr5 238638 10 + 294540 CAGTAGTTTA -s simCow_chr6.simCow.chr6 372378 10 + 602619 ATGGTGTTTA -s simDog_chr6.simDog.chr6 362390 10 + 593897 AAGGTGATTA -s simDog_chr6.simDog.chr6 362778 10 + 593897 AAGGTGATTA -s simHuman_chr6.simHuman.chr6 370760 10 + 601863 CAGGTGATTA -s simRat_chr6.simRat.chr6 384839 10 + 647215 CAGTGGTTTA - -a -s simMouse_chr6.simMouse.chr6 384808 40 + 636262 AGGATTACATAGTCACAATGAGAAAAAGAAGAAAGGTTGG -s Anc0.Anc0refChr3 13642 40 + 222631 AGGATTCCATAGTCACAGTGAGAAAAAGAAGAAAAGTTGG -s Anc1.Anc1refChr6 46551 40 + 197743 AGGATTCCATAGTCACAGTGAGAAAAAGAAGAAAAGTTGG -s Anc2.Anc2refChr13 16440 40 + 96486 AGGATTCCTTAGTCACAGGGGGTAAAAAAAGAAAAGTCAG -s mr.mrrefChr5 238648 40 + 294540 AGGATTACATAGTCACAATGAGAAAAAGAAGAAAGGTTGG -s simCow_chr6.simCow.chr6 372389 35 + 602619 GGGATCCA-----CACAGTGGATAAAGCAGGGAAAGTTAG -s simDog_chr6.simDog.chr6 362401 39 + 593897 AGGATTCCTTAGTCACAGGGGG-AAAAAAAGAAAAGTCAG -s simDog_chr6.simDog.chr6 362789 39 + 593897 AGGATTCCTTAGTCACAGGGGG-AAAAAAAGAAAAGTCAG -s simHuman_chr6.simHuman.chr6 370771 40 + 601863 AGGATTCCATAATCACAGTGAGAAAAGGAAGGAAAGTTGG -s simRat_chr6.simRat.chr6 384849 39 + 647215 -GGATTACATAGTTACAATGAGAAAAAGAAGAAAGGTTGG - -a -s simMouse_chr6.simMouse.chr6 384848 48 + 636262 TAAGGCCATATTGGGAGGTTCCGCGAAACCAGCTATGAGTATATCTTA -s Anc0.Anc0refChr3 13685 48 + 222631 TAGGGCCATGTTGCTAGGGTCCAGGAAACCAACTATGACATTACCTTA -s Anc1.Anc1refChr6 46594 48 + 197743 TAGGGCCATGTTGCTAGGGTCCAGGAAACCAACTATGACATTACCTTA -s Anc2.Anc2refChr13 16483 48 + 96486 TTGGGCTGGATCGCTAGGGCCCAGGAAGCCAACTGTGGCACTATCTTG -s mr.mrrefChr5 238688 48 + 294540 TAAGGCCATGTTGGGAGGTTCCACGAAACCAGCTATGACATTACCTTA -s simCow_chr6.simCow.chr6 372427 48 + 602619 CAGGGCGAGGTTGCTAAGGTCCAGGAAACCAGCTACAATTCTATCTTG -s simDog_chr6.simDog.chr6 362443 48 + 593897 TTGGGCTGGATCGCTAGGGCCCAGGAAGCCAACTGTGGCACTATCTTG -s simDog_chr6.simDog.chr6 362831 48 + 593897 TTGGGCTGGATCGCTAGGGCCCAGGAAGCCAACTGTGGCACTATCTTG -s simHuman_chr6.simHuman.chr6 370814 47 + 601863 TAGGGCCATGTTCT-AGTGTCCAGGCAACAATCTATGACATTACTTGA -s simRat_chr6.simRat.chr6 384888 48 + 647215 CAAGGCCATGCTGGGAGATTCCACAACAGCAGCTATGACATTACCTTA - -a -s simMouse_chr6.simMouse.chr6 384896 14 + 636262 CCTATATCAACAAA -s Anc0.Anc0refChr3 13733 14 + 222631 GCTGTCTTAAGACA -s Anc1.Anc1refChr6 46642 14 + 197743 GCTGTCTTAAGACA -s Anc2.Anc2refChr13 16531 14 + 96486 GCTGTCTTGAGACG -s mr.mrrefChr5 238736 14 + 294540 CCTATATCAACAAA -s simCow_chr6.simCow.chr6 372475 14 + 602619 GCTATCTTGAGACG -s simDog_chr6.simDog.chr6 362879 7 + 593897 GCTGTCG------- -s simHuman_chr6.simHuman.chr6 370861 14 + 601863 GCTGTTTAAGGACA -s simRat_chr6.simRat.chr6 384936 10 + 647215 CCT----CAACAAA - -a -s simMouse_chr6.simMouse.chr6 384910 16 + 636262 GTGGTGTACCATTGTG -s Anc0.Anc0refChr3 13747 16 + 222631 CTACTTTGGCTGTTTG -s Anc1.Anc1refChr6 46656 16 + 197743 CTACTTTGGCTGTTTG -s Anc2.Anc2refChr13 16545 16 + 96486 TTACATTGGCTGTTTG -s mr.mrrefChr5 238750 16 + 294540 CTGGTGTACCATTGTG -s simCow_chr6.simCow.chr6 372489 16 + 602619 TTACATTGGTTGTTTG -s simDog_chr6.simDog.chr6 362886 10 + 593897 ------TAGCTATCTG -s simHuman_chr6.simHuman.chr6 370875 16 + 601863 CTTTTTTGGCTGTTTG -s simRat_chr6.simRat.chr6 384947 16 + 647215 CTGGTGTACCCTCATG - -a -s simMouse_chr6.simMouse.chr6 384926 12 + 636262 AACCAAACACCC -s Anc0.Anc0refChr3 13781 12 + 222631 AAGAAACCACCC -s Anc1.Anc1refChr6 46690 12 + 197743 AAGAAACCACCC -s Anc2.Anc2refChr13 16579 12 + 96486 AAGAAACTACCC -s mr.mrrefChr5 238766 12 + 294540 AACCAAACACCC -s simCow_chr6.simCow.chr6 372523 12 + 602619 AAGAAACTACCC -s simDog_chr6.simDog.chr6 362912 10 + 593897 AAGAAACTAC-- -s simHuman_chr6.simHuman.chr6 370909 12 + 601863 AAGAAACCACCC -s simRat_chr6.simRat.chr6 384963 12 + 647215 AACCAAACTCCC - -a -s simMouse_chr6.simMouse.chr6 384938 6 + 636262 TCATTA -s Anc0.Anc0refChr3 13795 6 + 222631 TCTTAA -s Anc1.Anc1refChr6 46704 6 + 197743 TCTTAA -s Anc2.Anc2refChr13 16593 6 + 96486 TGTTAA -s mr.mrrefChr5 238778 6 + 294540 TCATTA -s simCow_chr6.simCow.chr6 372537 6 + 602619 TGTTAA -s simDog_chr6.simDog.chr6 362922 1 + 593897 -----A -s simHuman_chr6.simHuman.chr6 370923 6 + 601863 TCTTAA -s simRat_chr6.simRat.chr6 384975 6 + 647215 TCATTA - -a -s simMouse_chr6.simMouse.chr6 384944 23 + 636262 GGAGTGGTCAAGGAATGCATACT -s Anc0.Anc0refChr3 13801 22 + 222631 GGAGTGGATTAGGAATCCATAC- -s Anc1.Anc1refChr6 46710 22 + 197743 GGAGTGGATTAGGAATCCATAC- -s Anc2.Anc2refChr13 16599 22 + 96486 GGAGGGGATTAGGAATCCATCT- -s mr.mrrefChr5 238784 23 + 294540 GGAGTGGTCAAGGAATGCATACT -s simCow_chr6.simCow.chr6 372549 22 + 602619 GAAGGGGATGAGGAATGCATCT- -s simDog_chr6.simDog.chr6 362923 22 + 593897 GGAGGGGATTATGAATCCATCT- -s simHuman_chr6.simHuman.chr6 370929 19 + 601863 GGAGTGG---AGGTGACCATAC- -s simRat_chr6.simRat.chr6 384981 23 + 647215 GGCATGGTCAAGGAATGCATCCA - -a -s simMouse_chr6.simMouse.chr6 384967 30 + 636262 TGCCTAACAAATGCCGGCATCTTTGTCACC -s Anc0.Anc0refChr3 13823 15 + 222631 ---------ATTGA------CCATAGAATG -s Anc1.Anc1refChr6 46732 21 + 197743 ---------ATTGATGGCATCCATAGAATG -s Anc2.Anc2refChr13 16621 15 + 96486 ---------ATTGA------CCATAGAATG -s mr.mrrefChr5 238807 30 + 294540 TGCCTAACAAATGCTGGCATCCTTATCACC -s simCow_chr6.simCow.chr6 372571 15 + 602619 ---------ATTGA------CCATAGAATG -s simDog_chr6.simDog.chr6 362945 14 + 593897 ---------ATTGA------CCATAGA-TA -s simHuman_chr6.simHuman.chr6 370948 21 + 601863 ---------ACTGGTGGCATCCATAGAATG -s simRat_chr6.simRat.chr6 385005 30 + 647215 TGTCTAACAAGTGCTTGCATCCTCATCACC - -a -s simMouse_chr6.simMouse.chr6 384997 6 + 636262 TGGCAT -s Anc0.Anc0refChr3 13839 6 + 222631 TGGCAT -s Anc1.Anc1refChr6 46754 6 + 197743 TGGCAT -s Anc2.Anc2refChr13 16637 6 + 96486 TGGCAT -s mr.mrrefChr5 238837 6 + 294540 TGGCAT -s simCow_chr6.simCow.chr6 372587 6 + 602619 TGGCAT -s simDog_chr6.simDog.chr6 362960 6 + 593897 TGGCAT -s simHuman_chr6.simHuman.chr6 370970 6 + 601863 TGGCAC -s simRat_chr6.simRat.chr6 385035 6 + 647215 TGGCAT - -a -s simMouse_chr6.simMouse.chr6 385003 21 + 636262 TCTTGTCACCACGTGAATCAC -s Anc0.Anc0refChr3 13845 21 + 222631 CCTTGTTATCACTTGAATGAC -s Anc1.Anc1refChr6 46760 21 + 197743 CCTTGTTATCACTTGAATGAC -s Anc2.Anc2refChr13 16644 21 + 96486 CCTTTTTCTCACTTGAATGAC -s mr.mrrefChr5 238843 21 + 294540 TCTTGTCACCACTTGAATCAC -s simCow_chr6.simCow.chr6 372594 4 + 602619 CCTT----------------- -s simDog_chr6.simDog.chr6 362967 21 + 593897 CCTCTTTCTCACTTGAATGAC -s simHuman_chr6.simHuman.chr6 370976 21 + 601863 CATTGTTATTACTTGGATAAC -s simRat_chr6.simRat.chr6 385041 21 + 647215 TCTTTTCACCACTTGAGACGT - -a -s simMouse_chr6.simMouse.chr6 385024 15 + 636262 AGCATTTATTCTAGC -s Anc0.Anc0refChr3 13866 15 + 222631 CTTTTTATTTCACGA -s Anc1.Anc1refChr6 46781 15 + 197743 CTTTTTATTTCACGA -s Anc2.Anc2refChr13 16665 15 + 96486 CTTTTTATTACACAA -s mr.mrrefChr5 238864 15 + 294540 AGCATTTATTCTAGC -s simCow_chr6.simCow.chr6 372598 4 + 602619 -----------ACAA -s simDog_chr6.simDog.chr6 362990 15 + 593897 CTTTTTATTACACAA -s simHuman_chr6.simHuman.chr6 370997 15 + 601863 TTTTTTATTTCACGA -s simRat_chr6.simRat.chr6 385062 5 + 647215 AGCAT---------- - -a -s simMouse_chr6.simMouse.chr6 385039 1 + 636262 C -s Anc0.Anc0refChr3 13891 1 + 222631 C -s Anc1.Anc1refChr6 46806 1 + 197743 C -s Anc2.Anc2refChr13 16690 1 + 96486 C -s mr.mrrefChr5 238879 1 + 294540 C -s simCow_chr6.simCow.chr6 372612 1 + 602619 C -s simDog_chr6.simDog.chr6 363015 1 + 593897 C -s simHuman_chr6.simHuman.chr6 371022 1 + 601863 C - -a -s simMouse_chr6.simMouse.chr6 385040 68 + 636262 TATCAGTATGAGTAGCTGGATGGGAATATAAGTCCCACACAGATTTTGAGTCTTGCTGCTGGCTATAT -s Anc0.Anc0refChr3 13892 50 + 222631 TATCAGTATGAATAGCTAGATGAGAATAT-----CACCGTAG--TTCGCATCCTGCC----------- -s Anc1.Anc1refChr6 46807 68 + 197743 TATCAGTATGAATAGCTAGATGAGAATATAAGCACACCGTAGGCTTCGCATCCTGCCGGCAACTACAC -s Anc2.Anc2refChr13 16692 50 + 96486 TATCAGTATGAATAGCTAAAGGAAAATAT-----CACGGTAG--CTCGCATCCTGCC----------- -s mr.mrrefChr5 238880 68 + 294540 TATCAGTATGAGTAGCTGGATGGGAATATAAGCCCCCCATAGATTTCGCGTCCTGCTGCTGGCTATAT -s simCow_chr6.simCow.chr6 372614 39 + 602619 TATCAGTATGAATAGCTAAAGGAATATA------------------CTCATCTTGCC----------- -s simDog_chr6.simDog.chr6 363017 41 + 593897 TAACAGTATGAATGG---------AATGT-----CACGGTAG--CTAGTCTCCTTCC----------- -s simHuman_chr6.simHuman.chr6 371023 68 + 601863 TATCAGCATGAATAGCTAGATGAGAATATAAGCACACCGTAGGCTTCACATCCTGCCGGCAACTACAC -s simRat_chr6.simRat.chr6 385067 58 + 647215 ---------GAGTAGCTGGATGGGAATATGAGCCCTCCATGGATTTCGCTTCCTGTTATTG-CTATAT - -a -s simMouse_chr6.simMouse.chr6 385108 88 + 636262 CATGAACCAAGTTTTGCCTCCTCAGTCAGATAGCATCTTTGACTGCGCAGTCATTTATCTATTATCTGCTTGGTGCAGAGTGGTGCAA -s Anc0.Anc0refChr3 13942 80 + 222631 --------CGATTTTGCCTCCTCAGTCAGATAGCATCTAAGACTACTCTATCATCTATCCATCATCTTCTTGGTACTGAGTGGCACAG -s Anc1.Anc1refChr6 46878 88 + 197743 GATGGAGTCGATTTTGCCTCCTCAGTCAGATAGCATCTAAGACTACTCTATCATCTATCCATCATCTTCTTGGTACTGAGTGGCACAG -s Anc2.Anc2refChr13 16742 80 + 96486 --------CGATTTTGCCTCCTTCGTTAGATAGCATCTAAGACTACTCTATCATCTATCCATCATCTTCATGGTACTGAGTGGCACAG -s mr.mrrefChr5 238951 88 + 294540 CATGAACCAAGTTTTGCCTCCTCAGTCAGATAGCATCTTTGACTGCGCAGTCATTTATCTATCATCTGCTTGGTGCAGAGTGGCACAA -s simCow_chr6.simCow.chr6 372660 79 + 602619 --------CAATTCTCCCTCCTTGGTTAGATAGCCTCTATGACTTCTCTGTCATCTATTCATCACCACC-TGGTACTGAGTGGCACAG -s simDog_chr6.simDog.chr6 363058 80 + 593897 --------TGATCTTGCCTCCTTCTTTAAATAGCATCTAAGACTACTCTATCATCTATCCATAATCTTCATGGTACTGAGTGGCACAG -s simHuman_chr6.simHuman.chr6 371094 72 + 601863 GATGGAGTCGATTTTGCCTCCTCAGTCAGA--GCATCT--GACT------------ATCCATCATCTTCTTGGTACTGAGTGACACAG -s simRat_chr6.simRat.chr6 385128 88 + 647215 CATGAACCAAGTTTTTCATTCTCAGTCTGATAGCATCTATGGCTTCGCAGTCATTTATCTATCATCTGCTTGGTCCAGAATGGCACAA - -a -s simMouse_chr6.simMouse.chr6 385196 22 + 636262 ACTTAACACACGGCAGAGTCCT -s Anc0.Anc0refChr3 14023 20 + 222631 ATCCAACAGAGGAAAGAGTC-- -s Anc1.Anc1refChr6 46967 22 + 197743 ATCCAACAGAGGAAAGAGTCTT -s Anc2.Anc2refChr13 16823 20 + 96486 ATCCAACAGAGGAGAGCCTC-- -s mr.mrrefChr5 239039 22 + 294540 ACTTAACACACGGCAGAGTCTT -s simCow_chr6.simCow.chr6 372740 20 + 602619 ATCTCGCAGAGGAGAGTCTC-- -s simDog_chr6.simDog.chr6 363139 20 + 593897 ATCCAACAGAGGAGAGCCTC-- -s simHuman_chr6.simHuman.chr6 371167 22 + 601863 ATCCAACAGAAAAAAGAGTCTT -s simRat_chr6.simRat.chr6 385216 20 + 647215 ACTTAACACAG--CAGAGTCTT - -a -s simMouse_chr6.simMouse.chr6 385218 15 + 636262 GTCCTTATAGAGCTG -s Anc0.Anc0refChr3 14043 10 + 222631 -----TATCCAGCTA -s Anc1.Anc1refChr6 46989 15 + 197743 GTCCTTATCCAGCTA -s Anc2.Anc2refChr13 16843 10 + 96486 -----TATCCAACTA -s mr.mrrefChr5 239061 15 + 294540 GTCCTTATAGAGCTG -s simCow_chr6.simCow.chr6 372760 10 + 602619 -----TATTTAACTA -s simDog_chr6.simDog.chr6 363159 10 + 593897 -----TGTCCAACAG -s simHuman_chr6.simHuman.chr6 371191 15 + 601863 GTCCTTATCCAGCTA -s simRat_chr6.simRat.chr6 385236 15 + 647215 GTCCTTATAGAGCTG - -a -s simMouse_chr6.simMouse.chr6 385233 20 + 636262 ATGGAAGGACTAGCTGATAA -s Anc0.Anc0refChr3 14053 18 + 222631 TTGGA-GGCCTACCTCAGT- -s Anc1.Anc1refChr6 47004 19 + 197743 TTGGA-GGCCTACCTCAGTC -s Anc2.Anc2refChr13 16853 18 + 96486 TTTGA-GTCCTTCTCCAGT- -s mr.mrrefChr5 239076 20 + 294540 TTGGAAGGACTAGCTCATAA -s simCow_chr6.simCow.chr6 372770 14 + 602619 T-----GCCCTTCTCCAGT- -s simDog_chr6.simDog.chr6 363176 18 + 593897 TTTGA-GTCCTTCTCCAGA- -s simHuman_chr6.simHuman.chr6 371206 19 + 601863 TTGGA-GGCCTAACTCACTC -s simRat_chr6.simRat.chr6 385251 20 + 647215 TTGGAAGGACTAGCTCATAA - -a -s simMouse_chr6.simMouse.chr6 385253 63 + 636262 AAAATCAAGCTATGTTAGATGTCAAGGCTAGTGCCCCTTTCTACCTAGCAACATGCCTATAAA -s Anc0.Anc0refChr3 14076 58 + 222631 AAAATCAAGCCATGATATACACCCAGGTTAGTGCCCCA----AC-TAACAACATACCTATAAC -s Anc1.Anc1refChr6 47029 59 + 197743 AAAATCAAGCCATGATATACACCCAGGTTAGTGCCCCA----ACTTAACAACATACCTATAAC -s Anc2.Anc2refChr13 16876 58 + 96486 AAAATCAAGCCATGATATACACCCAGGTTAGTGTCCCA----AC-TAACAACATACCTATAAC -s mr.mrrefChr5 239102 63 + 294540 AAAATCAAGCTATGTTATATGTCAAGGTTAGTGCCCCATTCTACCTAGCAACATGCCTATAAA -s simCow_chr6.simCow.chr6 372789 58 + 602619 AAAATCAAGCCATGATATGCATCCAGGTTAGTGTCCGA----AC-TAACAATATTCCAATAAT -s simDog_chr6.simDog.chr6 363199 57 + 593897 AAAATCAAGCCATGATATACACTCAGGTCAT-GTCCCA----AC-TAATAACATACGTATAAC -s simHuman_chr6.simHuman.chr6 371231 59 + 601863 AAAATCAAGCCATGGAATACACCGAGGTTAGAGCTCCA----GCTTAACAACACACCCATAAC -s simRat_chr6.simRat.chr6 385278 63 + 647215 AAAATTGAGCTATGTTATATGTCAATGTTAATGCCCCATTCTACCTAGTATCTTGCCTATAAA - -a -s simMouse_chr6.simMouse.chr6 385316 3 + 636262 CTA -s Anc0.Anc0refChr3 14134 3 + 222631 CTA -s Anc1.Anc1refChr6 47088 3 + 197743 CTA -s Anc2.Anc2refChr13 16934 3 + 96486 ATA -s mr.mrrefChr5 239165 3 + 294540 CTA -s simCow_chr6.simCow.chr6 372847 3 + 602619 GTG -s simDog_chr6.simDog.chr6 363256 3 + 593897 ATA -s simHuman_chr6.simHuman.chr6 371290 3 + 601863 CTA -s simRat_chr6.simRat.chr6 385342 3 + 647215 CTA - -a -s simMouse_chr6.simMouse.chr6 385319 45 + 636262 ATTGCGGTAAGCACAGGGTCAAACATTAACATCATGATATCAGCA -s Anc0.Anc0refChr3 14141 38 + 222631 ACTGTGAAAACCTTAGGGCCACACATCAACATCATAAT------- -s Anc1.Anc1refChr6 47095 45 + 197743 ACTGTGAAAACCTTAGGGCCACACATCAACATCATAATATCAGAA -s Anc2.Anc2refChr13 16941 38 + 96486 ACTGTGAAAACCTTAGGGCCACACATCAACATCATAAT------- -s mr.mrrefChr5 239168 45 + 294540 ACTGTGGTAAGCACAGGGTCACACATTAACATCATGATATCAGCA -s simCow_chr6.simCow.chr6 372854 38 + 602619 ATTATGAAAGACTTAGGGCCACACAGCAACATCATAAA------- -s simDog_chr6.simDog.chr6 363301 36 + 593897 ACTGGGAAAACC--AGGGCCACACGTTAGCATGATAAT------- -s simHuman_chr6.simHuman.chr6 371297 36 + 601863 ACTGTGAAAACCTTAGGGCTACACATCAA---------ATCAGAA -s simRat_chr6.simRat.chr6 385345 45 + 647215 ACTGTGGTAAGCACACGGTCACACATTAACATCATGATATCAGCA - -a -s simMouse_chr6.simMouse.chr6 385364 11 + 636262 ATTGGGCATGA -s Anc0.Anc0refChr3 14361 11 + 222631 ATATGGCATGA -s Anc1.Anc1refChr6 47322 11 + 197743 ATATGGCATGA -s Anc2.Anc2refChr13 17168 11 + 96486 ATATGGTATGT -s mr.mrrefChr5 239213 11 + 294540 ATTGGGCATGA -s simCow_chr6.simCow.chr6 373090 11 + 602619 ATATAGTATTT -s simDog_chr6.simDog.chr6 363530 11 + 593897 TTATGGTATGT -s simHuman_chr6.simHuman.chr6 371527 11 + 601863 ATATGGCATGA -s simRat_chr6.simRat.chr6 385390 11 + 647215 ATTGGGCATGA - -a -s simMouse_chr6.simMouse.chr6 385375 3 + 636262 AAA -s Anc0.Anc0refChr3 14378 3 + 222631 AAA -s Anc1.Anc1refChr6 47339 3 + 197743 AAA -s Anc2.Anc2refChr13 17185 3 + 96486 AAA -s mr.mrrefChr5 239224 3 + 294540 AAA -s simCow_chr6.simCow.chr6 373107 3 + 602619 AAA -s simDog_chr6.simDog.chr6 363547 3 + 593897 AAA -s simHuman_chr6.simHuman.chr6 371544 3 + 601863 AAA -s simRat_chr6.simRat.chr6 385401 3 + 647215 AAA - -a -s simMouse_chr6.simMouse.chr6 385378 10 + 636262 GGATTAAAAA -s Anc0.Anc0refChr3 14382 10 + 222631 GAATGAAGAA -s Anc1.Anc1refChr6 47343 10 + 197743 GAATGAAGAA -s Anc2.Anc2refChr13 17189 10 + 96486 GAATGAAGAA -s mr.mrrefChr5 239228 10 + 294540 GGATGAAAAA -s simCow_chr6.simCow.chr6 373111 10 + 602619 GAACGAAGAA -s simDog_chr6.simDog.chr6 363551 10 + 593897 GAATGCAGAA -s simHuman_chr6.simHuman.chr6 371548 10 + 601863 GAATGAAGAA -s simRat_chr6.simRat.chr6 385405 10 + 647215 GGATGAAAAG - -a -s simMouse_chr6.simMouse.chr6 385388 52 + 636262 GAACCTTACATTTAAACATGGAGTGGAGGGATCTAGTGTATGTGTTAAAATA -s Anc0.Anc0refChr3 14398 48 + 222631 AAACCTCACATTTAAATCTGGAG----TAACACTAGTATATGTGTTAGAATT -s Anc1.Anc1refChr6 47359 48 + 197743 AAACCTCACATTTAAATCTGGAG----TAACACTAGTATATGTGTTAGAATT -s Anc2.Anc2refChr13 17205 48 + 96486 AAACCTCACATTTAAATCTGGAG----TAACACTAGCATATGTGTGAGAATT -s mr.mrrefChr5 239238 52 + 294540 GAACCTTACATTTAAACATGGAGTGGAGGGAACTAGTGTATGTGTTAAAATT -s simCow_chr6.simCow.chr6 373127 48 + 602619 AAACCTCACATTCAAATTGGGAG----GATCACTAGGATATGTGTCAGAATT -s simDog_chr6.simDog.chr6 363567 48 + 593897 AAACCTCAGATTTAAATCTGGAG----TGACCCTAGCATATGTGTGATAATT -s simHuman_chr6.simHuman.chr6 371564 48 + 601863 AAACTTCACACTTAAAACTCAAG----AAACACTAGTATATATGTTAGAATT -s simRat_chr6.simRat.chr6 385415 52 + 647215 GAACCTTACATTTAAACATGGAGTGGAGGGAACTAGTCTGTGTGTTAAAGTT - -a -s simMouse_chr6.simMouse.chr6 385440 33 + 636262 TCAATTTATGTGTTAGTATCGCTTTTATGCATT -s Anc0.Anc0refChr3 14446 20 + 222631 GCTATCTTT-------TATCTC------ACATT -s Anc1.Anc1refChr6 47407 20 + 197743 GCTATCTTT-------TATCTC------ACATT -s Anc2.Anc2refChr13 17253 20 + 96486 GCTACCTTT-------TATCTC------ACATT -s mr.mrrefChr5 239290 33 + 294540 TCAATTTATGTGTTAGTATCGCTTTTATGCATT -s simCow_chr6.simCow.chr6 373180 20 + 602619 GCTACCTTC-------TATCTC------ACATA -s simDog_chr6.simDog.chr6 363615 20 + 593897 GCTACCTTT-------TATCTC------ACATT -s simHuman_chr6.simHuman.chr6 371612 20 + 601863 GCTATCTCT-------TATCTC------ACATT -s simRat_chr6.simRat.chr6 385467 33 + 647215 TCAATCTATGTGTTAGTATGGTTTTTGTGTATT - -a -s simMouse_chr6.simMouse.chr6 385473 36 + 636262 TTAGGACTTGACATAGTTGATTGCTAATGATAACAC -s Anc0.Anc0refChr3 14467 35 + 222631 TTAGGACTCCACATAGTCCAT-CTTAATGATCACAC -s Anc1.Anc1refChr6 47428 36 + 197743 TTAGGACTCCACATAGTCCATGCTTAATGATCACAC -s Anc2.Anc2refChr13 17274 35 + 96486 TTAGAACTCCACATGGTCCAC-CTTAATGACCACAC -s mr.mrrefChr5 239323 36 + 294540 TTAGGACTTGACATAGTTGATTGTTAATGATAACAC -s simCow_chr6.simCow.chr6 373201 35 + 602619 TAAGAACTCCACATGGTCCAC-CTTCACAACCACAC -s simDog_chr6.simDog.chr6 363636 35 + 593897 TTAGAACTCCACATGGTCTAC-CTCAATGACCACAC -s simHuman_chr6.simHuman.chr6 371633 36 + 601863 TTAGGACTCCACATAGTCCATGCTTAATGATCACAC -s simRat_chr6.simRat.chr6 385500 36 + 647215 TTAGGACTTGTCATAGTTGATTGTTCATGATAACAC - -a -s simMouse_chr6.simMouse.chr6 385509 14 + 636262 CTGCGTTATACCTG -s Anc0.Anc0refChr3 14503 14 + 222631 CTGCATTATATCTG -s Anc1.Anc1refChr6 47465 14 + 197743 CTGCATTATATCTG -s Anc2.Anc2refChr13 17310 14 + 96486 CTTCATTATATCTA -s mr.mrrefChr5 239359 14 + 294540 CTGCATTATATCTG -s simCow_chr6.simCow.chr6 373237 14 + 602619 CTACATTATATCTA -s simDog_chr6.simDog.chr6 363672 14 + 593897 TTTCATTATATTTA -s simHuman_chr6.simHuman.chr6 371670 14 + 601863 CTGCATTACATCTG -s simRat_chr6.simRat.chr6 385536 14 + 647215 CAGCATTAAATCTG - -a -s simMouse_chr6.simMouse.chr6 385523 26 + 636262 ATGTCCCAGGTTGCAAAGCCCTTAAG -s Anc0.Anc0refChr3 14521 26 + 222631 GGGTCCCAGGTTCTAAAGTCCTTAAG -s Anc1.Anc1refChr6 47483 26 + 197743 GGGTCCCAGGTTCTAAAGTCCTTAAG -s Anc2.Anc2refChr13 17328 26 + 96486 GGGTTCCAGGTTCTAAGGTCATTAAG -s mr.mrrefChr5 239373 26 + 294540 AGGTCCCAGGTTGCAAAGCCCTTAAG -s simCow_chr6.simCow.chr6 373255 26 + 602619 GGGTTCCAGAGTCTAAGTTCATTGAG -s simDog_chr6.simDog.chr6 363690 26 + 593897 AGGTTTTAGGTTCTAAGGCCATTAAG -s simHuman_chr6.simHuman.chr6 371688 26 + 601863 GGGTCCCAGGTTCTAAAGTCCTTAAG -s simRat_chr6.simRat.chr6 385550 26 + 647215 AGGTCCCAGGTTTCAAGAACCTTAAG - -a -s simMouse_chr6.simMouse.chr6 385549 12 + 636262 TATCTGGCTTTC -s Anc0.Anc0refChr3 14556 12 + 222631 TACCTAACCTCT -s Anc1.Anc1refChr6 47518 12 + 197743 TACCTAACCTCT -s Anc2.Anc2refChr13 17363 12 + 96486 TACCTAACCTCT -s mr.mrrefChr5 239399 12 + 294540 TATCTGGCTTTC -s simCow_chr6.simCow.chr6 373290 12 + 602619 AACCTAACCTCT -s simDog_chr6.simDog.chr6 363723 12 + 593897 TACCTAACCTCT -s simHuman_chr6.simHuman.chr6 371725 12 + 601863 TACGCAACCTCT -s simRat_chr6.simRat.chr6 385576 12 + 647215 TATCTGGCTTTC - -a -s simMouse_chr6.simMouse.chr6 385561 105 + 636262 TACCCAGTACTCCAGTATGTGGTGACTTCAAAGCTGATCACAAGTGTGGGTTCAAGTGACATGGGTGCTAAGCCATGGACACTAGGATAGCACAGGAGGTATCGT -s Anc0.Anc0refChr3 14568 93 + 222631 AATCCAGACCTCCAGTAGGAGGTGTCT-CTAAGCCAATGACAATTGTGCCTCCAAGTTTCAAGGGTGCTAAGCTGTGG------T-----GACAGGAGGTTTCTC -s Anc1.Anc1refChr6 47530 98 + 197743 AATCCAGACCTCCAGTAGGAGGTGTCT-CTAAGCCAATGACAATTGTGCCTCCAAGTTTCAAGGGTGCTAAGCTGTGG------TGATAGGACAGGAGGTTTCTC -s Anc2.Anc2refChr13 17375 93 + 96486 AATCCAGACCTTGAGTAGGAGGTGTCT-GTAAGCCAATGACAATTATGCCTCCAAGTTTCAACGGCATTACGCTGAGC------T-----CACAGGAGGTTATTC -s mr.mrrefChr5 239411 105 + 294540 TACCCAGTACTCCAGTATGTGGTGTCTTCAAAGCTAATCACAAGTGTGGGTTCAAGTGACATGGGTGCTAAGCCATGGACACTAGGATAGCACAGGAGGTATCTC -s simCow_chr6.simCow.chr6 373302 38 + 602619 AA-----------AGCAGGAGGTGTCT-GTAAAGCAATCATAATGATGCT------------------------------------------------------- -s simDog_chr6.simDog.chr6 363737 93 + 593897 AATCCAGACCTTGAGTAGGAGGTGTCT-GTAAGCTGATGACAAATATCCCTCCAAGTTTCAACGGCATTACGCTGAGC------T-----CACAGGAGGTTATTC -s simHuman_chr6.simHuman.chr6 371737 98 + 601863 AATCCAGACATCCAGTAGGAGGTGTAT-CTAAGCCATTGACGATTGTGCCTCCAAGATCCAAGGGTGCTGAGCTGTGG------TGATAGGACAGGCGGTGTCTC -s simRat_chr6.simRat.chr6 385588 104 + 647215 CACCCAGTACTCCAGTATGTGGGGTCTTCAAAGCTACTCACA-GTGTGGGTTCAAGTGACGCGGGCGTAACGCCATGGACACTGGGATAGTACAGGAGGTACCTC - -a -s simMouse_chr6.simMouse.chr6 385666 5 + 636262 CAACA -s Anc1.Anc1refChr6 47635 5 + 197743 CAGCA -s mr.mrrefChr5 239523 5 + 294540 CAACA -s simHuman_chr6.simHuman.chr6 371842 5 + 601863 CAGCA -s simRat_chr6.simRat.chr6 385699 5 + 647215 CAACA - -a -s simMouse_chr6.simMouse.chr6 385671 4 + 636262 GATT -s Anc1.Anc1refChr6 47640 4 + 197743 GCTT -s mr.mrrefChr5 239528 4 + 294540 GATT -s simHuman_chr6.simHuman.chr6 371851 4 + 601863 GCTT -s simRat_chr6.simRat.chr6 385704 4 + 647215 GATT - -a -s simMouse_chr6.simMouse.chr6 385675 30 + 636262 CATGCATCTATGTCACCCCCCAAAAGTTAG -s Anc0.Anc0refChr3 14668 29 + 222631 -ACGCTTCTTTGACAAGTCCCAAAAGTTAG -s Anc1.Anc1refChr6 47644 30 + 197743 CACGCTTCTTTGACAAGTCCCAAAAGTTAG -s Anc2.Anc2refChr13 17475 29 + 96486 -ACATTTCTTCCACAAGTCCCAAAAGTTAG -s mr.mrrefChr5 239532 30 + 294540 CATGCATCTATGTCACCCCCCAAAAGTTAG -s simDog_chr6.simDog.chr6 363837 29 + 593897 -ACATTTCTTCCACAAGTCCCAAAAGTTAG -s simHuman_chr6.simHuman.chr6 371871 30 + 601863 CACGCTTCTTTGACAAGTCGCGCAAATTAG -s simRat_chr6.simRat.chr6 385708 8 + 647215 CATGCATC---------------------- - -a -s simMouse_chr6.simMouse.chr6 385705 9 + 636262 ATAATGGCC -s Anc0.Anc0refChr3 14698 9 + 222631 AAAATTATA -s Anc1.Anc1refChr6 47675 9 + 197743 AAAATTATA -s Anc2.Anc2refChr13 17505 9 + 96486 AAAATTATA -s mr.mrrefChr5 239562 9 + 294540 ATAATGGCC -s simDog_chr6.simDog.chr6 363867 9 + 593897 AAAATTATA -s simHuman_chr6.simHuman.chr6 371902 9 + 601863 AAAATTATA - -a -s simMouse_chr6.simMouse.chr6 385714 5 + 636262 CTGTT -s Anc0.Anc0refChr3 14707 5 + 222631 CAATT -s Anc1.Anc1refChr6 47684 5 + 197743 CAATT -s Anc2.Anc2refChr13 17514 5 + 96486 CAACT -s mr.mrrefChr5 239571 5 + 294540 CTGTT -s simDog_chr6.simDog.chr6 363904 5 + 593897 CAACT -s simHuman_chr6.simHuman.chr6 371911 5 + 601863 CAATT - -a -s simMouse_chr6.simMouse.chr6 385719 3 + 636262 TGG -s Anc0.Anc0refChr3 14724 3 + 222631 TGG -s Anc1.Anc1refChr6 47701 3 + 197743 TGG -s Anc2.Anc2refChr13 17531 3 + 96486 TGG -s mr.mrrefChr5 239576 3 + 294540 TGG -s simDog_chr6.simDog.chr6 363921 3 + 593897 TGG -s simHuman_chr6.simHuman.chr6 371928 3 + 601863 TGG - -a -s simMouse_chr6.simMouse.chr6 385722 98 + 636262 TTGGTGAACCGAGCAAAGATGACGTTACTTACTGTGGAAGTGCACGGAAATACAACAAAGAAATACAAAAACTGTCTCCAGGGGTATCGTTAAAAAAC -s Anc0.Anc0refChr3 14727 86 + 222631 TTGGTGAACCTAGTAAAGATGGAGTT-CTTACACTGGATGGGTGC-----------AAAGACACACAAAAAGAGCCTCCAGGGGTATAGTTGAAAAAT -s Anc1.Anc1refChr6 47704 86 + 197743 TTGGTGAACCTAGTAAAGATGGAGTT-CTTACACTGGATGGGTGC-----------AAAGACACACAAAAAGAGCCTCCAGGGGTATAGTTGAAAAAT -s Anc2.Anc2refChr13 17534 86 + 96486 TTGTTGAACCTAGTTAAGTTGGAGTA-CTTACACTGGATGGGTGC-----------AAAGACACACAAAAAGAGCCTCCAGGGGTATAGTTGAAAAAT -s mr.mrrefChr5 239579 87 + 294540 TTGGTGAACCTAGCAAAGATGAAGTTACTTACTGTGGAAGTGTGC-----------AAAGAAATACAAAAACTGTCTCCAGGGGTATCGTTAAAAAAT -s simCow_chr6.simCow.chr6 373340 69 + 602619 -----------------GTTGGAGTA-CTTACACTGGACAGGTAC-----------AGAGACACACAAAAAGAGTGTATAGGGGTATAGTTGAAAAGC -s simDog_chr6.simDog.chr6 363952 86 + 593897 TTGTTGAACCTAGTTAAGTTAGAGTA-CTTACACTTGATGTGTGT-----------TAAGACACAGATAAAGAGCCTCCAGGGGTATACTTAAAAAAT -s simHuman_chr6.simHuman.chr6 371931 86 + 601863 TTAGTGAACGTAGTAAAAATGGAGTT-CCTACACTGGGGGGGTGC-----------AAATACACACAAAAAGAGCCCCCAGGCCCATAGTTGAAAAAT -s simRat_chr6.simRat.chr6 385716 78 + 647215 ---------CTCACAAAGATGAAGCTACTTATGGGGGAAGAGTGC-----------AAGGAAATACAAAAACTGTCTCTAGGGGTATTGTTAGGAAAT - -a -s simMouse_chr6.simMouse.chr6 385820 23 + 636262 AAAGAGAATGGTCATAAGAGACT -s Anc0.Anc0refChr3 14829 23 + 222631 AAAAAAAATAGTCATAAGAGAGT -s Anc1.Anc1refChr6 47806 23 + 197743 AAAAAAAATAGTCATAAGAGAGT -s Anc2.Anc2refChr13 17636 23 + 96486 AAAAAATAGAGTAATCAGAGAGT -s mr.mrrefChr5 239666 23 + 294540 AAAAAAAATGGTCATAAGAGACT -s simCow_chr6.simCow.chr6 373425 23 + 602619 AAAAAACACAGTAATCAGAGAGT -s simDog_chr6.simDog.chr6 364054 22 + 593897 AAAGAATAGAGTAAT-AGAGAGT -s simHuman_chr6.simHuman.chr6 372033 23 + 601863 AAGAAAAATAGACATAAGAGGGT -s simRat_chr6.simRat.chr6 385794 23 + 647215 AAAAAAAATTGTCATAAGAGACT - -a -s simMouse_chr6.simMouse.chr6 385843 3 + 636262 TAC -s Anc0.Anc0refChr3 14853 3 + 222631 TGC -s Anc1.Anc1refChr6 47830 3 + 197743 TGC -s Anc2.Anc2refChr13 17660 3 + 96486 TGC -s mr.mrrefChr5 239689 3 + 294540 TAC -s simCow_chr6.simCow.chr6 373449 3 + 602619 TGC -s simDog_chr6.simDog.chr6 364077 3 + 593897 TGT -s simHuman_chr6.simHuman.chr6 372057 3 + 601863 TGC -s simRat_chr6.simRat.chr6 385817 3 + 647215 AAC - -a -s simMouse_chr6.simMouse.chr6 385846 13 + 636262 ATCTAAGTATGAT -s Anc0.Anc0refChr3 14856 11 + 222631 ATTT--GTATGTT -s Anc1.Anc1refChr6 47833 13 + 197743 ATTTGAGTATGTT -s Anc2.Anc2refChr13 17663 11 + 96486 GTCT--GCATCTT -s mr.mrrefChr5 239692 13 + 294540 ATTTAAGTATGAT -s simCow_chr6.simCow.chr6 373458 11 + 602619 GTGT--ACTACCG -s simDog_chr6.simDog.chr6 364080 11 + 593897 GTCT--GCATCTT -s simHuman_chr6.simHuman.chr6 372060 13 + 601863 ATTTGAATGTGTT -s simRat_chr6.simRat.chr6 385820 13 + 647215 ATTTAAGTATAGT - -a -s simMouse_chr6.simMouse.chr6 385859 72 + 636262 GCAAATAGTTCACCTCAAGCATGTTAACCCCCCGGATTGGTTTTTAAGATTTAGTTTGAGACTCACAGTGCA -s Anc0.Anc0refChr3 14867 56 + 222631 GCCAA------------GACAGGCTCACCCCCCAG----GTTTTTAAAATTTATCCTTGGACTCTTGGTTAA -s Anc1.Anc1refChr6 47846 56 + 197743 GCCAA------------GACAGGCTCACCCCCCAG----GTTTTTAAAATTTATCCTTGGACTCTTGGTTAA -s Anc2.Anc2refChr13 17674 56 + 96486 GTCAA------------GACAGGCCCACCCCCCAG----GTTTTTTAAATTTATCCATGGACACTTGGTTAA -s mr.mrrefChr5 239705 72 + 294540 GCAAATAGTTCACCTCAGGCATGTTAACCCCCCAGATTGGTTTTTAAGATTTAGTTTGGGACTCTTGGTGAA -s simCow_chr6.simCow.chr6 228249 54 - 602619 AGCCA------------GACAGGCCCACCGCCCAA----ATTTTTTAAATTTATTC-TGGACACTTGG-TGA -s simDog_chr6.simDog.chr6 364091 56 + 593897 GTCAA------------GACAAGCCCACCCTCCAG----GCTATTTAAATTTGTCCAGGGAAACTTGGTTAA -s simHuman_chr6.simHuman.chr6 372073 56 + 601863 GCCAA------------GACAGGCTCACCCCCCAG----GTTTTTAAAATTTATCCTTGGACTTTTGGTTAA -s simRat_chr6.simRat.chr6 385833 72 + 647215 GCAGGTGGATTGCCTGAGGCATGTCTACCCCCGAGATTGATTTTTAGGATTTAGTTTAGGACTCTTGGTGAA - -a -s simMouse_chr6.simMouse.chr6 385931 16 + 636262 TTCCCACAGTAAGTGA -s Anc0.Anc0refChr3 14926 16 + 222631 TCATCACAGTAACTGA -s Anc1.Anc1refChr6 47905 16 + 197743 TCATCACAGTAACTGA -s Anc2.Anc2refChr13 17733 16 + 96486 TCATGACAGTAACTGA -s mr.mrrefChr5 239777 16 + 294540 TTACCACAGTAAGTGA -s simCow_chr6.simCow.chr6 228306 16 - 602619 TCCTTACAGTAACTGA -s simDog_chr6.simDog.chr6 364150 16 + 593897 TTATGACAGTAATCAA -s simHuman_chr6.simHuman.chr6 372132 16 + 601863 TCATCACAGTAACTGA -s simRat_chr6.simRat.chr6 385905 16 + 647215 TTACCACAGCAAGTGA - -a -s simMouse_chr6.simMouse.chr6 385947 11 + 636262 CGCTTGATTAG -s Anc0.Anc0refChr3 14942 11 + 222631 CTGTTGATTAG -s Anc1.Anc1refChr6 47921 11 + 197743 CTGTTGATTAG -s Anc2.Anc2refChr13 17749 11 + 96486 CTGTTGATTAG -s mr.mrrefChr5 239793 11 + 294540 CGGTTGATTAG -s simCow_chr6.simCow.chr6 228322 11 - 602619 CTCTTGACGAA -s simDog_chr6.simDog.chr6 364167 11 + 593897 CTGTTGATTAG -s simHuman_chr6.simHuman.chr6 372148 11 + 601863 CTGTCAATTAG -s simRat_chr6.simRat.chr6 385921 11 + 647215 CGGTTGATTAG - -a -s simMouse_chr6.simMouse.chr6 385958 65 + 636262 ACTAAGTTCCATACCTCTACTATTACAATTTGAGACCCCTAGTGCATGAGGACTTATTATTGACT -s Anc0.Anc0refChr3 14953 47 + 222631 ACTTAACTCACAC-----ACCATCACCCGTTAAGACCCCCAGTGCACTTGGA------------- -s Anc1.Anc1refChr6 47932 65 + 197743 ACTTAACTCACACACTCTACCATCACCCGTTAAGACCCCCAGTGCACTTGGATGTAGTGTTAACC -s Anc2.Anc2refChr13 17765 47 + 96486 AATTGACTCACAC-----AACAACACCCATTAAGACCCCCAGTGCACTTGGA------------- -s mr.mrrefChr5 239804 65 + 294540 ACTAAGTTCCATACCTCTACTATTACAAGTTGAGACCCCTAGTGCATGTGGATGTATTATTGACC -s simCow_chr6.simCow.chr6 228338 46 - 602619 AATTTATGCACTT-----AACA-CACCCATTAAGACCACCAGTGCACTTGGA------------- -s simDog_chr6.simDog.chr6 364183 36 + 593897 AATTGACTCACAC-----AACAA-----------ACCCCCAGTGCACTTGGA------------- -s simHuman_chr6.simHuman.chr6 372159 65 + 601863 ACTCAACTCGTACACTCTACGATCATCCGTTAGGACTCCCAGTGCACTTGGATGTAGTGTTAACC -s simRat_chr6.simRat.chr6 385932 65 + 647215 ACTAAGATCTATACCTCTACTATTACAAGTTGAGACCCCAAGTGCATATGGATGCACTATTGACC - -a -s simMouse_chr6.simMouse.chr6 386023 4 + 636262 CATT -s Anc1.Anc1refChr6 47997 4 + 197743 TCTT -s mr.mrrefChr5 239869 4 + 294540 CATT -s simHuman_chr6.simHuman.chr6 372245 4 + 601863 TCTT -s simRat_chr6.simRat.chr6 385997 4 + 647215 CATT - -a -s simMouse_chr6.simMouse.chr6 386027 62 + 636262 GAAGCCTGTGAAGAACCATTTTGGTGATGGTAGTGTAGTACATGTCCAATTCTCAAGTGGGT -s Anc1.Anc1refChr6 48001 56 + 197743 TAAACC--TGAAGATGCATTCTTGTCATATTTGTGTAATA-ATGT---ATTGTCTAGTGGGT -s mr.mrrefChr5 239873 62 + 294540 GAAACCTGTGAAGATGCATTTTGGTGATGGTAGTGTAGTACATGTCCAATTCTCTAGTGGGT -s simHuman_chr6.simHuman.chr6 372249 56 + 601863 TAAACC--TGAAGATGCATTCTTGTCATATTTGTGTAATA-ATGT---ATTGTCTAGTGGGT -s simRat_chr6.simRat.chr6 386002 58 + 647215 GAAACCTGTGAAGATGCATTTTGGTGGTGGTAGAGTAGTACATGTCCAACTCTCTAGT---- - -a -s simMouse_chr6.simMouse.chr6 386089 31 + 636262 TTGCAAGATAAGGGGATATGTGCTGGTGTGG -s Anc0.Anc0refChr3 15000 3 + 222631 ----------------------------CTG -s Anc1.Anc1refChr6 48057 31 + 197743 GTGTGAGATAAGTGAACACGTGTGTACCCTG -s Anc2.Anc2refChr13 17812 3 + 96486 ----------------------------CTC -s mr.mrrefChr5 239935 31 + 294540 TTGCAAGATAAGGGGATATGTGCTGGTGCTG -s simCow_chr6.simCow.chr6 228384 3 - 602619 ----------------------------CTC -s simDog_chr6.simDog.chr6 364219 3 + 593897 ----------------------------CTC -s simHuman_chr6.simHuman.chr6 372306 31 + 601863 GTGTGAGATAAGTGAACACGTGTGTACCCTG -s simRat_chr6.simRat.chr6 386060 23 + 647215 --------CAAGGGGATATCTGCTGCTGCTG - -a -s simMouse_chr6.simMouse.chr6 386120 1 + 636262 G -s Anc0.Anc0refChr3 15004 1 + 222631 G -s Anc1.Anc1refChr6 48089 1 + 197743 G -s Anc2.Anc2refChr13 17816 1 + 96486 G -s mr.mrrefChr5 239967 1 + 294540 G -s simCow_chr6.simCow.chr6 228388 1 - 602619 G -s simDog_chr6.simDog.chr6 364223 1 + 593897 G -s simHuman_chr6.simHuman.chr6 372338 1 + 601863 G -s simRat_chr6.simRat.chr6 386089 1 + 647215 G - -a -s simMouse_chr6.simMouse.chr6 386121 29 + 636262 ACTTGGCCAACTATGGAATGATGGTACCT -s Anc0.Anc0refChr3 15005 19 + 222631 GCTGATCCACCT----TTGTGT------C -s Anc1.Anc1refChr6 48090 23 + 197743 GCTGATCCACCTGCTGTTGTGT------C -s Anc2.Anc2refChr13 17817 19 + 96486 GCTGATCTACCT----TCGTGT------A -s mr.mrrefChr5 239968 29 + 294540 ACTTGGCCAACTATGGATGGATGGTACCC -s simCow_chr6.simCow.chr6 228390 19 - 602619 GCTGGTCTACAT----TAGTGT------G -s simDog_chr6.simDog.chr6 364224 19 + 593897 GCTGATCTACCT----TCGTGT------A -s simHuman_chr6.simHuman.chr6 372339 17 + 601863 ------CCACCTGCTGTTGTGT------C -s simRat_chr6.simRat.chr6 386090 29 + 647215 ACTTGACCAACTATGGATGGATGCTACCC - -a -s simMouse_chr6.simMouse.chr6 386150 23 + 636262 ATCGATGGAGCAAGAGCTTTCTT -s Anc0.Anc0refChr3 15031 16 + 222631 --C-----AGTAACAGCTTGCTT -s Anc1.Anc1refChr6 48120 18 + 197743 ATC-----AGTAACAGCTTGCTT -s Anc2.Anc2refChr13 17843 16 + 96486 --T-----GGTAACAGGTTGCTT -s mr.mrrefChr5 240004 23 + 294540 ATCGATGGAGTAACAGCTTTCTT -s simCow_chr6.simCow.chr6 228416 16 - 602619 --T-----GGTAATGGGCTGTTT -s simDog_chr6.simDog.chr6 364250 16 + 593897 --T-----GGTAACAGGTTGCTT -s simHuman_chr6.simHuman.chr6 372363 18 + 601863 ATC-----AGTAACAGCTTGCTT -s simRat_chr6.simRat.chr6 386126 23 + 647215 ATCGATGGAGTAACAGATTTCTT - -a -s simMouse_chr6.simMouse.chr6 386173 32 + 636262 TATCGTCAAGCTCAGGTTGGCCCTCGGCCCCT -s Anc0.Anc0refChr3 15053 32 + 222631 TATCATAAAACTCAGATTCCCCCTCAAACTGC -s Anc1.Anc1refChr6 48144 32 + 197743 TATCATAAAACTCAGATTCCCCCTCAAACTGC -s Anc2.Anc2refChr13 17865 32 + 96486 TATCATAAAACTCAGATTCCCCCTTAAACTGC -s mr.mrrefChr5 240027 32 + 294540 TATCATCAAGCTCAGGTTGGCCCTCGGCCCCT -s simCow_chr6.simCow.chr6 228438 32 - 602619 TACTAGAAAACTCAGATTTCCCCTTGAACTGC -s simDog_chr6.simDog.chr6 364272 32 + 593897 TATCATAAAAACCAGATTCCCCCTTAGACTAC -s simHuman_chr6.simHuman.chr6 372387 32 + 601863 TATCATAAACCTAAGAGTCACCCTCAAAATGC -s simRat_chr6.simRat.chr6 386149 31 + 647215 TATCATCAAGCTCAGGTTGGCCCTTG-CCCCT - -a -s simMouse_chr6.simMouse.chr6 386205 20 + 636262 ATCAAAGATATCATGGCAGT -s Anc0.Anc0refChr3 15085 16 + 222631 ATCATTGTTATAGTGG---- -s Anc1.Anc1refChr6 48176 16 + 197743 ATCATTGTTATAGTGG---- -s Anc2.Anc2refChr13 17897 16 + 96486 ATCATTATCATAGCAA---- -s mr.mrrefChr5 240059 20 + 294540 ATCAAAGTTATCATGGCAGT -s simCow_chr6.simCow.chr6 228474 16 - 602619 ATTGTTATCATAGCAA---- -s simDog_chr6.simDog.chr6 364304 16 + 593897 ATCATTATCATAACAA---- -s simHuman_chr6.simHuman.chr6 372419 16 + 601863 ATGATTGTTATAGTGG---- -s simRat_chr6.simRat.chr6 386180 20 + 647215 ATCAAAGTTATCATAGCAGT - -a -s simMouse_chr6.simMouse.chr6 386225 3 + 636262 TTT -s Anc0.Anc0refChr3 15101 3 + 222631 TTT -s Anc1.Anc1refChr6 48192 3 + 197743 TTT -s Anc2.Anc2refChr13 17913 3 + 96486 TTT -s mr.mrrefChr5 240079 3 + 294540 TTT -s simCow_chr6.simCow.chr6 228506 3 - 602619 TTT -s simDog_chr6.simDog.chr6 364320 3 + 593897 TTT -s simHuman_chr6.simHuman.chr6 372435 3 + 601863 TTT -s simRat_chr6.simRat.chr6 386200 3 + 647215 TTT - -a -s simMouse_chr6.simMouse.chr6 386228 11 + 636262 TGTGAAACTGA -s Anc0.Anc0refChr3 15104 11 + 222631 TGTAAATATAA -s Anc1.Anc1refChr6 48195 11 + 197743 TGTAAATATAA -s Anc2.Anc2refChr13 17916 11 + 96486 TGTAAATATAA -s mr.mrrefChr5 240082 11 + 294540 TGTGAATATAA -s simCow_chr6.simCow.chr6 228509 11 - 602619 TGTAAATTGAA -s simDog_chr6.simDog.chr6 364324 11 + 593897 TGTAAATATAA -s simHuman_chr6.simHuman.chr6 372438 11 + 601863 TGTAAATATAA -s simRat_chr6.simRat.chr6 386203 11 + 647215 TGTGAATATAA - -a -s simMouse_chr6.simMouse.chr6 386239 20 + 636262 GGTTATCTTCTTATCGGTGG -s Anc0.Anc0refChr3 15119 20 + 222631 TAGCATTTGCCAACTGGTGC -s Anc1.Anc1refChr6 48210 20 + 197743 TAGCATTTGCCAACTGGTGC -s Anc2.Anc2refChr13 17931 20 + 96486 TAGCATTTGCCAACTGGTGC -s mr.mrrefChr5 240097 20 + 294540 TGTTATCTTCTTATTGGTGG -s simCow_chr6.simCow.chr6 228524 20 - 602619 TGGCATTTGCCATCTAGTGC -s simDog_chr6.simDog.chr6 364339 20 + 593897 TAGCATCTACCAACTGGTGC -s simHuman_chr6.simHuman.chr6 372453 20 + 601863 TAGCATTTGCCAACTGGTAT -s simRat_chr6.simRat.chr6 386218 20 + 647215 TGATGTCTTCTGATTGGTGG - -a -s simMouse_chr6.simMouse.chr6 386259 9 + 636262 TTCCAGGAT -s Anc0.Anc0refChr3 15147 9 + 222631 TGTAATGGT -s Anc1.Anc1refChr6 48238 9 + 197743 TGTAATGGT -s Anc2.Anc2refChr13 17959 9 + 96486 TGTAATGGC -s mr.mrrefChr5 240117 9 + 294540 TTCCATGGT -s simCow_chr6.simCow.chr6 228552 9 - 602619 TGTAATGGC -s simDog_chr6.simDog.chr6 364367 9 + 593897 TGCAATGGC -s simHuman_chr6.simHuman.chr6 372481 9 + 601863 TGTAATGGT -s simRat_chr6.simRat.chr6 386238 9 + 647215 TTCCATGGT - -a -s simMouse_chr6.simMouse.chr6 386268 15 + 636262 GTGGAATGCCTTCCA -s Anc0.Anc0refChr3 15156 15 + 222631 TTGGAATGCCATACA -s Anc1.Anc1refChr6 48247 15 + 197743 TTGGAATGCCATACA -s Anc2.Anc2refChr13 17968 15 + 96486 TCAGAATGCCATACA -s mr.mrrefChr5 240126 15 + 294540 GTGGAATGCCTTACA -s simCow_chr6.simCow.chr6 228577 15 - 602619 TCAGAATGCCATACG -s simDog_chr6.simDog.chr6 364376 15 + 593897 TCAGTTTATCATACA -s simHuman_chr6.simHuman.chr6 372490 15 + 601863 TTGGAATGCCATACA -s simRat_chr6.simRat.chr6 386247 15 + 647215 GTACAATGCCTTACA - -a -s simMouse_chr6.simMouse.chr6 386283 5 + 636262 ACCAG -s Anc0.Anc0refChr3 15174 5 + 222631 ATCAG -s Anc1.Anc1refChr6 48265 5 + 197743 ATCAG -s Anc2.Anc2refChr13 17986 5 + 96486 ATCAA -s mr.mrrefChr5 240141 5 + 294540 ACCAG -s simCow_chr6.simCow.chr6 228595 5 - 602619 ATCAA -s simDog_chr6.simDog.chr6 364394 5 + 593897 ATCAA -s simHuman_chr6.simHuman.chr6 372508 5 + 601863 ATCAG -s simRat_chr6.simRat.chr6 386262 5 + 647215 ACCAG - -a -s simMouse_chr6.simMouse.chr6 386288 23 + 636262 AGATGTCTCTGTCCTGGTTGTTG -s Anc0.Anc0refChr3 15188 23 + 222631 AATTGTCTTTTTCCTAGCTGTTG -s Anc1.Anc1refChr6 48279 23 + 197743 AATTGTCTTTTTCCTAGCTGTTG -s Anc2.Anc2refChr13 18000 23 + 96486 AATTGCCTTTTTCCTAGCTGTTG -s mr.mrrefChr5 240146 23 + 294540 AGTTGTCTTTGTCCTGGTTGTTG -s simCow_chr6.simCow.chr6 228609 23 - 602619 AACTGCGTTTATCCTGGTTGTTG -s simDog_chr6.simDog.chr6 364410 23 + 593897 AGTTGCCTCTTTCCTAGCTGTTG -s simHuman_chr6.simHuman.chr6 372522 23 + 601863 AATCGTTTTTTTCCTAGCTGTTG -s simRat_chr6.simRat.chr6 386267 23 + 647215 AGTTGTCATTGTCCTGGTTGTTG - -a -s simMouse_chr6.simMouse.chr6 386311 4 + 636262 CCTC -s Anc0.Anc0refChr3 15211 4 + 222631 CCCC -s Anc1.Anc1refChr6 48302 4 + 197743 CCCC -s Anc2.Anc2refChr13 18023 4 + 96486 CCCC -s mr.mrrefChr5 240169 4 + 294540 CCTC -s simCow_chr6.simCow.chr6 228633 4 - 602619 CTCC -s simDog_chr6.simDog.chr6 364433 4 + 593897 CCTC -s simHuman_chr6.simHuman.chr6 372545 4 + 601863 CCCC -s simRat_chr6.simRat.chr6 386290 4 + 647215 ATTC - -a -s simMouse_chr6.simMouse.chr6 386315 18 + 636262 AAAATGGCTGCTTCATGG -s Anc0.Anc0refChr3 15215 14 + 222631 AAAATCT-TGCTTTG--- -s Anc1.Anc1refChr6 48306 17 + 197743 AAAATCT-TGCTTTGTGA -s Anc2.Anc2refChr13 18027 14 + 96486 AAAATCT-TTGTCTG--- -s mr.mrrefChr5 240173 18 + 294540 AAAATGGCTGCTTCATGG -s simCow_chr6.simCow.chr6 228637 14 - 602619 AAAATCC-TTATGGT--- -s simDog_chr6.simDog.chr6 364437 14 + 593897 AAAATCT-TTGTCTG--- -s simHuman_chr6.simHuman.chr6 372551 17 + 601863 GAAATTT-TGCTTTGTGA -s simRat_chr6.simRat.chr6 386294 18 + 647215 AAAATGGCTGCATCATGG - -a -s simMouse_chr6.simMouse.chr6 386333 16 + 636262 ACTCACCAATACAGAC -s Anc0.Anc0refChr3 15234 16 + 222631 ACTCACCAATACAGAG -s Anc1.Anc1refChr6 48328 16 + 197743 ACTCACCAATACAGAG -s Anc2.Anc2refChr13 18046 16 + 96486 ACTCACCAATACAGAG -s mr.mrrefChr5 240191 16 + 294540 ACTCACCAATACAGAC -s simCow_chr6.simCow.chr6 228656 16 - 602619 AATCACCAATACAGAG -s simDog_chr6.simDog.chr6 364456 16 + 593897 ACTCACCAACACAGGG -s simHuman_chr6.simHuman.chr6 372576 16 + 601863 ACTCACAAATACAGAG -s simRat_chr6.simRat.chr6 386312 16 + 647215 ACTCACTAATACAAAC - -a -s simMouse_chr6.simMouse.chr6 386349 28 + 636262 AAAGTGTGCAGAACTGTTTGGCGTAAAA -s Anc0.Anc0refChr3 15250 13 + 222631 AAAGTGTG---------------TAAAA -s Anc1.Anc1refChr6 48344 13 + 197743 AAAGTGTG---------------TAAAA -s Anc2.Anc2refChr13 18067 13 + 96486 AAAATGTG---------------CAAAA -s mr.mrrefChr5 240207 28 + 294540 AAAGTGTGCAGAACTGTTTGGCGTAAAA -s simCow_chr6.simCow.chr6 228679 13 - 602619 AAAGTGTT---------------CAAAA -s simDog_chr6.simDog.chr6 364477 13 + 593897 AAAATGTG---------------CAAAA -s simHuman_chr6.simHuman.chr6 372592 13 + 601863 AGAGTATG---------------TAAAA -s simRat_chr6.simRat.chr6 386328 28 + 647215 CAAGGGTGCAGAACTGTTTGGCATAAAA - -a -s simMouse_chr6.simMouse.chr6 386377 22 + 636262 TTGTTCTGGGTTTGGGACCATC -s Anc0.Anc0refChr3 15263 22 + 222631 TTGTCCTGCATTTTTGACCATC -s Anc1.Anc1refChr6 48357 22 + 197743 TTGTCCTGCATTTTTGACCATC -s Anc2.Anc2refChr13 18080 22 + 96486 TTGTCCTACATTTTTGACCATC -s mr.mrrefChr5 240235 22 + 294540 TTGTTCTGGATTTGGGACCATC -s simCow_chr6.simCow.chr6 228692 22 - 602619 TTGCCGTCCATGTTTGACCATG -s simDog_chr6.simDog.chr6 364490 22 + 593897 GTGTTCTACATTTATGACAATC -s simHuman_chr6.simHuman.chr6 372605 22 + 601863 TTGTCCTGCATTTTAGACCATC -s simRat_chr6.simRat.chr6 386357 22 + 647215 TTGTTCTGTACTTGGGACCATC - -a -s simMouse_chr6.simMouse.chr6 386399 14 + 636262 TGTGCCCTGCATAT -s Anc0.Anc0refChr3 15289 14 + 222631 TGTTCCATGCATAT -s Anc1.Anc1refChr6 48383 14 + 197743 TGTTCCATGCATAT -s Anc2.Anc2refChr13 18106 14 + 96486 CGTTCCATGCATAT -s mr.mrrefChr5 240261 14 + 294540 TGTGCCCTGCATAT -s simCow_chr6.simCow.chr6 228718 14 - 602619 CGTTTCATGCATAT -s simDog_chr6.simDog.chr6 364516 14 + 593897 CATTCCATGCATAT -s simHuman_chr6.simHuman.chr6 372631 14 + 601863 TGCTCCATGCATAT -s simRat_chr6.simRat.chr6 386383 14 + 647215 TGTGCCTCGTATAT - -a -s simMouse_chr6.simMouse.chr6 386413 61 + 636262 CAAAGCAATTCAAGTCGGCTACCCAATGCATTGAAAGTTAAACCGGGCCCTTGCCAAATGG -s Anc0.Anc0refChr3 15303 58 + 222631 CACAACAAGTCAAGTC---CACTCCATGCATTGAATGTCAATCTGGGCCATAGCCAAATCA -s Anc1.Anc1refChr6 48397 58 + 197743 CACAACAAGTCAAGTC---CACTCCATGCATTGAATGTCAATCTGGGCCATAGCCAAATCA -s Anc2.Anc2refChr13 18120 58 + 96486 CACAACAAGTCAAGTC---CACTCTATGCATCAAATGTCCATCTAGGCCATAGCCAAATCA -s mr.mrrefChr5 240275 61 + 294540 CAAAACAATTCAAGTCGGCTACCCCATGCATTGAATGTTAAACCGGGCCCTTGCCAAATGA -s simCow_chr6.simCow.chr6 228732 57 - 602619 CAAAACAAGACAAGTC---CCCTCTCTGCATCAAATGTCCATCTAGGCTGTTGCCAAG-CA -s simDog_chr6.simDog.chr6 364541 57 + 593897 CACAACAGGTCAGGTC---CACTCTATG-ATCAAATGTCCATCTAGGCCATAGCCAAATCA -s simHuman_chr6.simHuman.chr6 372645 49 + 601863 CAGAACAAATCAAGTT---CACTCCATGCATTGAGTGTCAATCTGG---------AAATCA -s simRat_chr6.simRat.chr6 386397 61 + 647215 CAAAACAATTCAAGTCACCTACCACACGCATTGAATGGTGAACCGGGCCCTTACCAAATGA - -a -s simMouse_chr6.simMouse.chr6 386474 54 + 636262 GCACTAGATGTATAAGTTCGGGTCACCCATCTCCTCCCGATAGCTAATGCCAAC -s Anc0.Anc0refChr3 15362 54 + 222631 TCACTAGATGGAAAAGTTGGAGCCATCCAACTCATCTTGATCTCTGATACCAAC -s Anc1.Anc1refChr6 48456 54 + 197743 TCACTAGATGGAAAAGTTGGAGCCATCCAACTCATCTTGATCTCTGATACCAAC -s Anc2.Anc2refChr13 18179 54 + 96486 TCACTAGATGGAAAAGTTAGAGCCACCCAACTCATCTTGATCTCTGACACCAAC -s mr.mrrefChr5 240336 54 + 294540 GCACTAGATGTATAAGTTGGGGTCATCCATCTCCTCCCGATAGCTAATGCCAAC -s simCow_chr6.simCow.chr6 228790 54 - 602619 TCACCAGACGGAAAAGTAATAGCCACTCACCCCAACTAGATCTCTTACACGAGT -s simDog_chr6.simDog.chr6 364599 52 + 593897 TCACTAGATG--AAACGTAGAGCCACCCAACTCATCTTAATCTATGACACCAAC -s simHuman_chr6.simHuman.chr6 372695 51 + 601863 TCACTAGATGGAAAAGTTGGAGCTATCCGACTGATCTGGATCACTGATACA--- -s simRat_chr6.simRat.chr6 386458 54 + 647215 ACCCTAGATGTATAAGTTGGGGTCATCCATGTCCTCCAAATAGCTAATGCCAAT - -a -s simMouse_chr6.simMouse.chr6 386528 52 + 636262 GTCCATTCAGCAGTCCCAAACCCTATATGATTCAAAAATTTGCCCTCACCAT -s Anc0.Anc0refChr3 15416 47 + 222631 GCCCATTCAGCAACTCCCTATC--ATATGACTCAAGTGT---CCCTCACCAT -s Anc1.Anc1refChr6 48510 49 + 197743 GCCCATTCAGCAACTCCCTATCATATATGACTCAAGTGT---CCCTCACCAT -s Anc2.Anc2refChr13 18234 47 + 96486 GCACATTTAGCAACTCTCTATC--ATATGACTCAGGTGT---CCGTCACCAT -s mr.mrrefChr5 240390 52 + 294540 GCCCATTCAGCAGTCCCAAACCATATATGATTCAAAAATTTGCCCTCACCAT -s simCow_chr6.simCow.chr6 228845 47 - 602619 GCACATATAGCAACTCACAACC--ATAGGACTTAGATGT---CTGTTGTCAT -s simDog_chr6.simDog.chr6 364652 47 + 593897 GCACATTCAGCAACTCTCTATC--ATATGACTCAGGTGT---CCGTCACCAA -s simHuman_chr6.simHuman.chr6 372746 42 + 601863 GCCCGTTCA-------CCTATCATATATGGCTCAAGTGT---CCCTCACCAT -s simRat_chr6.simRat.chr6 386512 52 + 647215 GCCCATCCTGCAGTTCCAAAACATACATGATTCGAAAATTTGTCCTCACAAT - -a -s simMouse_chr6.simMouse.chr6 386580 24 + 636262 TCATTCAAATAATTGTCAGTCTGG -s Anc0.Anc0refChr3 15463 20 + 222631 TCA----AATAATGGTCATTCTAA -s Anc1.Anc1refChr6 48559 20 + 197743 TCA----AATAATGGTCATTCTAA -s Anc2.Anc2refChr13 18281 20 + 96486 TCA----AATAATGGTCATTCTAA -s mr.mrrefChr5 240442 24 + 294540 TCATTCAAATAATGGTCAGTCTGG -s simCow_chr6.simCow.chr6 228894 20 - 602619 ACA----AATAATGGTCATTCTAA -s simDog_chr6.simDog.chr6 364699 20 + 593897 TGA----AATAATGGTCATTCTTA -s simHuman_chr6.simHuman.chr6 372788 20 + 601863 GCA----AATAGTGGCCATTCTAA -s simRat_chr6.simRat.chr6 386564 24 + 647215 ATCTTCGAATAATGGTCAGTCTGG - -a -s simMouse_chr6.simMouse.chr6 386604 69 + 636262 TGGTTCAATGTCTCCTGATTCACTGTGCAGGATGGTAGTACCATAATAGGTTATAGATGACATGCCCTT -s Anc0.Anc0refChr3 15485 60 + 222631 TGATTCAATGCCTCCTGATTCAGTGTCTAGCATGGTATTAGC-TAATTGATGAAGGGCAAG-------- -s Anc1.Anc1refChr6 48581 68 + 197743 TGATTCAATGCCTCCTGATTCAGTGTCTAGCATGGTATTAGC-TAATTGATGAAGGGCAAGGACCATTT -s Anc2.Anc2refChr13 18303 60 + 96486 TGATATAACACGACCTGATTCAGTGTTTTGCATGGGATCAGT-TAGTTCATGAAGGGCAAG-------- -s mr.mrrefChr5 240466 68 + 294540 TGGTTCAATGTCTCCTGATTCACTGTCCAGGATGGTAGTACC-TAATAGGTTATAGACGACATGCCCTT -s simDog_chr6.simDog.chr6 364721 60 + 593897 TGATATAACACGACCTGATTCAGTGTTTTGCATGGGATCAGT-TAGTTCATGAAGGGCAAG-------- -s simHuman_chr6.simHuman.chr6 372810 68 + 601863 TGATTCAATGCCTCCCTATTCAACACCTAGTATGGTGTTAGC-TAATTGATGAAGGGCAAAGACCATTT -s simRat_chr6.simRat.chr6 386588 60 + 647215 TGGTTCAATGTCTCCTGATTCAGAGTCCAGGATGGTAGTA---------GTAATACACGACATGCCCTT - -a -s simMouse_chr6.simMouse.chr6 386673 68 + 636262 CCACGAACAGATAGTATAGCCCTAAGCCCTAACTACGACCTACTACATTCTTCCTGAGAATGACATGA -s Anc0.Anc0refChr3 15545 66 + 222631 --ATCAACTAATAGAATGGACCTAAACCCTAACTAAGACCTACCACAATCTTCCTGAACAACGTATAT -s Anc1.Anc1refChr6 48649 68 + 197743 CCATCAACTAATAGAATGGACCTAAACCCTAACTAAGACCTACCACAATCTTCCTGAACAACGTATAT -s Anc2.Anc2refChr13 18363 66 + 96486 --ATCAACTAATAGAATGAACCTGAAGTCTAACTAAGACCTACCACAATCTACCTGGACAACGTATAT -s mr.mrrefChr5 240534 68 + 294540 CCACGAACAGATAGTATAGCCCTAAGCCCTAACTAAGACCTACCACATTCTTCCTGAAAATGACATGA -s simCow_chr6.simCow.chr6 228915 11 - 602619 ---------------------------------------------------------CCAATGTACAT -s simDog_chr6.simDog.chr6 364781 66 + 593897 --ATCAACTAATAGAATGAACCTGAAGTCTAACTAAGACCTACCACAATCTACCTGGACAACGTATAT -s simHuman_chr6.simHuman.chr6 372878 68 + 601863 CCATCAACTCTTAGGATGGTTTTAAACCATAACCAAGACCCACCACAATCTTCCTGAACAAAGAATAG -s simRat_chr6.simRat.chr6 386650 68 + 647215 CCACAAACAGATAGTATAGCCCTAAGCCCTAACTAAGATCTACCACATTGTCCCTAAAAAGGACATGT - -a -s simMouse_chr6.simMouse.chr6 386741 4 + 636262 TATG -s Anc0.Anc0refChr3 15611 4 + 222631 TATG -s Anc1.Anc1refChr6 48717 4 + 197743 TATG -s Anc2.Anc2refChr13 18429 4 + 96486 TATG -s mr.mrrefChr5 240602 4 + 294540 TATG -s simCow_chr6.simCow.chr6 228926 4 - 602619 TATG -s simDog_chr6.simDog.chr6 364847 4 + 593897 TATG -s simHuman_chr6.simHuman.chr6 372946 4 + 601863 TTTG -s simRat_chr6.simRat.chr6 386720 4 + 647215 TATG - -a -s simMouse_chr6.simMouse.chr6 386745 46 + 636262 CAGGAGAGAATTTAGCTGAGACAGCTCTCCTTTCAGTCTGAAGTGA -s Anc0.Anc0refChr3 15615 46 + 222631 CAAGTGGGAAATTATCTGTGACAGACCTTCTATCAGATTGAGCTGC -s Anc1.Anc1refChr6 48721 46 + 197743 CAAGTGGGAAATTATCTGTGACAGACCTTCTATCAGATTGAGCTGC -s Anc2.Anc2refChr13 18433 46 + 96486 CAAGTTGGAAATTATCTGTGACAGACCTTCTATCAGATTGAGCTGC -s mr.mrrefChr5 240606 46 + 294540 CAGGTGGGAATTTAGCTGAGACAGACCTCCTATCAGTTTGAAGTGA -s simCow_chr6.simCow.chr6 228932 42 - 602619 CACTGTGGAAATTATCTGTGACAGGCCTTCTATCA----GAACTGC -s simDog_chr6.simDog.chr6 364851 46 + 593897 AAAGTTGGAAATTAGCTTTAACAGATCTGCTATTAGATTGAGTCGT -s simHuman_chr6.simHuman.chr6 372950 46 + 601863 CAAGTGGGAAATTATCTGTGACGGACCTTCTATCTGATTGAGCTCC -s simRat_chr6.simRat.chr6 386724 42 + 647215 CTGGTAGGAA----GCTGAGACAGACCTCCTATCAGTTTGAATTAA - -a -s simMouse_chr6.simMouse.chr6 386791 95 + 636262 TGTCAAGCCTAGTAATGCCTTGCACACCTTTCGATTCTGTACTTTGCTCTTTGTGGAGGTTCTACACTTGAAGAATTCCTCCAACATGCATGGGT -s Anc0.Anc0refChr3 15662 90 + 222631 TATCAAGCTCAGTAATGACT--CACTCCTGTCGATTCTGTACTTTGCTCCTTGAGG---TCCTAGTCCTGAAGAATTCTTTCTACAGGCATGGGT -s Anc1.Anc1refChr6 48768 90 + 197743 TATCAAGCTCAGTAATGACT--CACTCCTGTCGATTCTGTACTTTGCTCCTTGAGG---TCCTAGTCCTGAAGAATTCTTTCTACAGGCATGGGT -s Anc2.Anc2refChr13 18480 90 + 96486 TATGAAGCTCGGTAATGACT--CATTCCTGTAGATTGTGAACTTTGCTCCTTGTGG---TCCTAGTCCTGAAGAATTCTTTCTACAGACAAGGGT -s mr.mrrefChr5 240652 95 + 294540 TGTCAAGCCTAGTAATGCCTTGCACACCTTTCGATTCTGTACTTTGCTCTTTGAGGAGGTTCTACACCTGAAGAATTCCTTCAACATGCATGGGT -s simCow_chr6.simCow.chr6 228975 90 - 602619 TGTGGAGCTTTGTAATGATT--AATGCTTGTGGTTTGTGAACTTTGATCCTTATGA---TCCTAGTTCTGAATAATTCTTTCTACAGATAAGGGT -s simDog_chr6.simDog.chr6 364898 89 + 593897 TATGAGACTCGATAGT-ACT--CGTTCCTCTAGATTGTGAACTTTGCTCCTTGTGG---TACTAGTCCTGAAGGCTTCTTACTACAGACAAAGGT -s simHuman_chr6.simHuman.chr6 372997 90 + 601863 TATCAAGCTGAGCAATGACT--CACTCCTGTCGATTCTGTACTTTGCTCCTTGAAG---TCCTAGTCCTGAACAATTCTTTCTACAGGCATGGGT -s simRat_chr6.simRat.chr6 386766 94 + 647215 TGTCAAGCCTAGTAAGGCCTTACATACATTTAGATTGTATACATTGCTCTTCGAGGAGGCACTACACCTGAAGAATTCCTTCAA-ATGCATGGGT - -a -s simMouse_chr6.simMouse.chr6 386886 4 + 636262 TGGT -s Anc0.Anc0refChr3 15752 4 + 222631 GGAT -s Anc1.Anc1refChr6 48858 4 + 197743 GGAT -s Anc2.Anc2refChr13 18575 4 + 96486 GGAT -s mr.mrrefChr5 240747 4 + 294540 TGGT -s simCow_chr6.simCow.chr6 229070 4 - 602619 GGAC -s simDog_chr6.simDog.chr6 364992 4 + 593897 GGGT -s simHuman_chr6.simHuman.chr6 373087 4 + 601863 GGAT -s simRat_chr6.simRat.chr6 386860 4 + 647215 TGCT - -a -s simMouse_chr6.simMouse.chr6 386890 30 + 636262 TGGTAGCGCAATAGATGCAATTGTTCTCAC -s Anc0.Anc0refChr3 15759 25 + 222631 TGACAGGTTGATAG----GATTGTTGTCA- -s Anc1.Anc1refChr6 48865 25 + 197743 TGACAGGTTGATAG----GATTGTTGTCA- -s Anc2.Anc2refChr13 18582 25 + 96486 TGACAGGTTGATAA----GATTGTTGTCA- -s mr.mrrefChr5 240751 30 + 294540 TGGTAGCGCAATAGAAGCAATTGTTCTCAC -s simCow_chr6.simCow.chr6 229077 22 - 602619 TGATAGGTTGATAA----GATTGTTG---- -s simDog_chr6.simDog.chr6 364999 25 + 593897 TGACAGGCTGATCA----GATGGTTGTCA- -s simHuman_chr6.simHuman.chr6 373094 25 + 601863 TGACAGGTTCATAG----GATTATTGTCA- -s simRat_chr6.simRat.chr6 386864 30 + 647215 GAGTTACACAATAAAAGTAATTGTTCTCAC - -a -s simMouse_chr6.simMouse.chr6 386920 14 + 636262 ATTAATCAAGAATT -s Anc0.Anc0refChr3 15784 14 + 222631 ATTAATCAAGAATT -s Anc1.Anc1refChr6 48890 14 + 197743 ATTAATCAAGAATT -s Anc2.Anc2refChr13 18607 14 + 96486 ATTAATCAAGGATT -s mr.mrrefChr5 240781 14 + 294540 ATTAATCAAGAATT -s simCow_chr6.simCow.chr6 229099 12 - 602619 --TAATCAAGTATT -s simDog_chr6.simDog.chr6 365025 14 + 593897 ATTAATCAAGGGTT -s simHuman_chr6.simHuman.chr6 373119 14 + 601863 ATTGATCAAGAATT -s simRat_chr6.simRat.chr6 386894 14 + 647215 ATTAACCAAGAATT - -a -s simMouse_chr6.simMouse.chr6 386934 15 + 636262 GAGGAGGAAAGAGGG -s Anc0.Anc0refChr3 15798 15 + 222631 GAGCAGGGAAGTGGA -s Anc1.Anc1refChr6 48904 15 + 197743 GAGCAGGGAAGTGGA -s Anc2.Anc2refChr13 18621 15 + 96486 GAGCAGGGAAGTGCA -s mr.mrrefChr5 240795 15 + 294540 GAGGAGGAAAGTGGA -s simCow_chr6.simCow.chr6 229111 15 - 602619 GGGCAGGGAAGTGCA -s simDog_chr6.simDog.chr6 365040 15 + 593897 AAGCAGTGAAGTGCA -s simHuman_chr6.simHuman.chr6 373133 15 + 601863 GTGCAGGGAAGTTGA -s simRat_chr6.simRat.chr6 386908 15 + 647215 GAGTAGGAAAGTGGA - -a -s simMouse_chr6.simMouse.chr6 386949 13 + 636262 ACATCACAGTATC -s Anc0.Anc0refChr3 15818 13 + 222631 ATATTACAACATC -s Anc1.Anc1refChr6 48924 13 + 197743 ATATTACAACATC -s Anc2.Anc2refChr13 18641 13 + 96486 ATATTACAACATC -s mr.mrrefChr5 240810 13 + 294540 ACATCACAATATC -s simCow_chr6.simCow.chr6 229131 12 - 602619 ATATTGCAATAT- -s simDog_chr6.simDog.chr6 365060 13 + 593897 ATATTACAACATC -s simHuman_chr6.simHuman.chr6 373153 13 + 601863 ATTTTACAACATC -s simRat_chr6.simRat.chr6 386923 13 + 647215 GCATCACCATATC - -a -s simMouse_chr6.simMouse.chr6 386962 129 + 636262 ATCTGCTGGCCTATTGTGACTAATGGTTGTATTTCTCCTAGCTTGCCTCACAAACACTTATCAATGGGTAGAGACCAAGAACCCATACATAGAGACCAAGAATCCTTACAAAGGCTTAACAGGACGACA -s Anc0.Anc0refChr3 15832 87 + 222631 GTCTGCTGGCTCATTGTGACTATTGATGATCTTTCTCCTATCCTGCCTGACAA------------------------------------------CCAAGAATCCATACCAAGGCTTAACAGTGTGACA -s Anc1.Anc1refChr6 48938 87 + 197743 GTCTGCTGGCTCATTGTGACTATTGATGATCTTTCTCCTATCCTGCCTGACAA------------------------------------------CCAAGAATCCATACCAAGGCTTAACAGTGTGACA -s Anc2.Anc2refChr13 18655 87 + 96486 GTCTGCTGGCTCATTGTGGCTATTGATGATCTTTCTCCTATCCTGCTTGACAA------------------------------------------CCAAGAATCCATACCAAGGCTTAACAGTGTGACA -s mr.mrrefChr5 240823 129 + 294540 ATCTGCTGGCCTATTGTGACTAATGGTTGTATTTCTCCTAGCCTGCCTCACAAACACTTATCAATGGGTAGAGACCAAGAACCCATACATAGAGACCAAGAATCCATACCAAGGCTTAACAGTACGACA -s simCow_chr6.simCow.chr6 374371 73 + 602619 ------------ATAGTGGCTAT-GATTGTTGTTCTCTTATCCCGCCTAACAA------------------------------------------GCATGAATCCTTATCAAGGCTTAACACC-TGACA -s simDog_chr6.simDog.chr6 365074 87 + 593897 GTCTGCTGGCTCATTATGGCTATTGGCGATCTTTCTTCTATCCTGCTTGATGA------------------------------------------CCAAGAATCCATACCAAGGCTTAACAGTGTAACA -s simHuman_chr6.simHuman.chr6 373167 85 + 601863 GTCTACTGGCACATTGTGACCATCGATCAT-TTGCTCCTAACCT-TCTGACAA------------------------------------------CAAAGAATCCATACCAAGGCTTAACAGTGTGACA -s simRat_chr6.simRat.chr6 386936 129 + 647215 ATCTGCTGGCCTATTGTGACTAATGGTTGTGTTTCTACTATCCTGCCTCACAAACACTTATCCATGGGTAGAGACCAAGAATCAACACATTGGGACTGAGAATCCATACCAGGACTGAACAGTACGACA - -a -s simMouse_chr6.simMouse.chr6 387091 1 + 636262 T -s Anc0.Anc0refChr3 15919 1 + 222631 T -s Anc1.Anc1refChr6 49025 1 + 197743 T -s Anc2.Anc2refChr13 18742 1 + 96486 T -s mr.mrrefChr5 240952 1 + 294540 T -s simCow_chr6.simCow.chr6 374444 1 + 602619 T -s simDog_chr6.simDog.chr6 365166 1 + 593897 T -s simHuman_chr6.simHuman.chr6 373252 1 + 601863 T -s simRat_chr6.simRat.chr6 387065 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 387092 49 + 636262 CTGAAGAGGCATGACTAGTAGGGTGGAATACTTATCTTCCAAAAGGCAC -s Anc0.Anc0refChr3 15935 49 + 222631 CAAAAAGGTCATGGCTAGTAGGGTGGAACATTTATTTTACAAGAGGCAC -s Anc1.Anc1refChr6 49041 49 + 197743 CAAAAAGGTCATGGCTAGTAGGGTGGAACATTTATTTTACAAGAGGCAC -s Anc2.Anc2refChr13 18758 49 + 96486 TAAAAAGGTCATGGCTAATAGGGTGGAACATTTTCTTTACAAGAGGCAC -s mr.mrrefChr5 240953 49 + 294540 CTGAAGAGGCATGACTAGTAGGGTGGAATACTTATCTTCCAAAAGGCAC -s simCow_chr6.simCow.chr6 374460 49 + 602619 AGAAGATGCCATGGCTAATAGGATAGAGTCTCTTCTTTACAAGAGGTAC -s simDog_chr6.simDog.chr6 365182 45 + 593897 TAAAAAGATCATGGC----AGGGTGGAACACTTTCTTTAGAAGAGGCAC -s simHuman_chr6.simHuman.chr6 373268 47 + 601863 CAAGAAGGTCATGGCTAGTAGAGTGGAACATTTAT--TACAACAGGCAC -s simRat_chr6.simRat.chr6 387066 49 + 647215 CTGAAGAGGCGTGACTAGTAGGGTGGAATACTTAGCTTTAAAGAGGCAC - -a -s simMouse_chr6.simMouse.chr6 387141 10 + 636262 AAATTTTTCT -s Anc0.Anc0refChr3 15984 10 + 222631 CAATGTTTCT -s Anc1.Anc1refChr6 49090 10 + 197743 CAATGTTTCT -s Anc2.Anc2refChr13 18807 10 + 96486 CAATGTTTTT -s mr.mrrefChr5 241002 10 + 294540 AAATTTTTCT -s simCow_chr6.simCow.chr6 374509 10 + 602619 TAAAGTTTTT -s simDog_chr6.simDog.chr6 365229 10 + 593897 CTCTATTTTT -s simHuman_chr6.simHuman.chr6 373315 10 + 601863 CAATGTTTCT -s simRat_chr6.simRat.chr6 387115 10 + 647215 TAACATTTCT - -a -s simMouse_chr6.simMouse.chr6 387151 83 + 636262 GTAGAACACAAGATGAATTCAGGTGGTTAAATACCAGGGGCTGCCACTAATACTAATCAGGTGGTAAAACCTGACTGCTGAAC -s Anc0.Anc0refChr3 15994 6 + 222631 AAAGGA----------------------------------------------------------------------------- -s Anc1.Anc1refChr6 49100 6 + 197743 AAAGGA----------------------------------------------------------------------------- -s Anc2.Anc2refChr13 18817 6 + 96486 AAAGGA----------------------------------------------------------------------------- -s mr.mrrefChr5 241012 83 + 294540 GTAGAACACAAGATGAATTCAGGTGGTTAAATACCAGGGGCTGCCACTAATACTAATCAGGTGGTAAAACCTGACTGCTGAAC -s simCow_chr6.simCow.chr6 374520 6 + 602619 AAAGGA----------------------------------------------------------------------------- -s simDog_chr6.simDog.chr6 365239 6 + 593897 AAAGAA----------------------------------------------------------------------------- -s simHuman_chr6.simHuman.chr6 373325 6 + 601863 AAAGGA----------------------------------------------------------------------------- -s simRat_chr6.simRat.chr6 387125 83 + 647215 GGAGAATACAAGGTGGATTCAAATGGTTAAATACCAGGGGCTACCACTAATACCAGTCAGGTGGTTAAACCTGCCTGCTGAGC - -a -s simMouse_chr6.simMouse.chr6 387234 93 + 636262 CATCTCTAACATTCATGCATTATACTATGATTGCGATTAGCAGTTATTACTAGTCCACTCCAAAATGAATTTAGCAATTCCATCTACACTGCC -s Anc0.Anc0refChr3 16000 49 + 222631 --------------------------------------------GGTTACTAATCCATTACAAACTGAATTTGGCAATTTTGTCTGCCCAGCC -s Anc1.Anc1refChr6 49106 49 + 197743 --------------------------------------------GGTTACTAATCCATTACAAACTGAATTTGGCAATTTTGTCTGCCCAGCC -s Anc2.Anc2refChr13 18823 49 + 96486 --------------------------------------------GGTTACTAATCCATTACAAACTGAATTTGGCTATTTTGTCTGCCCAGCC -s mr.mrrefChr5 241095 93 + 294540 CATCTCTAACATTCATGCATTATACTATGATTGCGATTAGCAGTTATTACTAGTCCATTCCAAAATGAATTTGGCAATTCCATCTACACTGCC -s simCow_chr6.simCow.chr6 374526 48 + 602619 --------------------------------------------GGTTACAATTCTATTGCAAACTGAATTTGGCCATTTTGTCTGCC-AACC -s simDog_chr6.simDog.chr6 365245 46 + 593897 --------------------------------------------GGTTACTAATTCAATATGAATT-AATTTGGTTTTCTTGTCTGCGCAG-- -s simHuman_chr6.simHuman.chr6 373331 49 + 601863 --------------------------------------------GGTGATTAATCCATTACAAACTGAATTTGGCAACTAACTCTGCCCAGCC -s simRat_chr6.simRat.chr6 387209 93 + 647215 CGTTCCTTACATTCATGCATTATATTATGATTACAAGAAGGAGGTATTACTAGTCCATTCCAAAATGAATGTGGCTATTCCATCTACACTGCC - -a -s simMouse_chr6.simMouse.chr6 387327 10 + 636262 CCCTTATTGT -s Anc0.Anc0refChr3 16050 10 + 222631 CCCTTATAGT -s Anc1.Anc1refChr6 49156 10 + 197743 CCCTTATAGT -s Anc2.Anc2refChr13 18873 10 + 96486 CCCTTGTAGT -s mr.mrrefChr5 241188 10 + 294540 CCCTTATTGT -s simCow_chr6.simCow.chr6 374575 10 + 602619 CCCTTGTAGT -s simDog_chr6.simDog.chr6 365291 1 + 593897 ---------T -s simHuman_chr6.simHuman.chr6 373381 10 + 601863 CCCATATAGT -s simRat_chr6.simRat.chr6 387302 10 + 647215 CCCTTACTGT - -a -s simMouse_chr6.simMouse.chr6 387337 7 + 636262 CAAGGCA -s Anc0.Anc0refChr3 16064 7 + 222631 CCAAGAT -s Anc1.Anc1refChr6 49170 7 + 197743 CCAAGAT -s Anc2.Anc2refChr13 18887 7 + 96486 CCAAGAT -s mr.mrrefChr5 241201 7 + 294540 CCAGGCT -s simCow_chr6.simCow.chr6 374589 7 + 602619 CTGAGGT -s simDog_chr6.simDog.chr6 365296 7 + 593897 CCAAGAT -s simHuman_chr6.simHuman.chr6 373395 7 + 601863 CCAAGAT -s simRat_chr6.simRat.chr6 387315 7 + 647215 ACAGGCT - -a -s simMouse_chr6.simMouse.chr6 387344 2 + 636262 AG -s Anc0.Anc0refChr3 16071 2 + 222631 AA -s Anc1.Anc1refChr6 49177 2 + 197743 AA -s Anc2.Anc2refChr13 18894 2 + 96486 AA -s mr.mrrefChr5 241208 2 + 294540 AA -s simCow_chr6.simCow.chr6 374596 2 + 602619 AG -s simDog_chr6.simDog.chr6 365304 2 + 593897 AA -s simHuman_chr6.simHuman.chr6 373402 2 + 601863 AA -s simRat_chr6.simRat.chr6 387322 2 + 647215 TA - -a -s simMouse_chr6.simMouse.chr6 387346 16 + 636262 TTGGTCCAATTCTCTG -s Anc0.Anc0refChr3 16073 16 + 222631 TCTGTTCAGTTGTCCA -s Anc1.Anc1refChr6 49179 16 + 197743 TCTGTTCAGTTGTCCA -s Anc2.Anc2refChr13 18896 16 + 96486 TCTGTTCAGTTGTCCA -s mr.mrrefChr5 241210 16 + 294540 TCGGTTCAATTCTCTG -s simCow_chr6.simCow.chr6 374604 16 + 602619 TCTGTTCAATGGTCTG -s simDog_chr6.simDog.chr6 365306 16 + 593897 TCTGCTCAGTTGTCCA -s simHuman_chr6.simHuman.chr6 373404 16 + 601863 TCTGTTCAGTTGTTCA -s simRat_chr6.simRat.chr6 387324 16 + 647215 TCGGTTCAATTCTCTG - -a -s simMouse_chr6.simMouse.chr6 387362 15 + 636262 CAGAAAATTTCTCAA -s Anc0.Anc0refChr3 16091 15 + 222631 CATAAAATTTCTCAC -s Anc1.Anc1refChr6 49197 15 + 197743 CATAAAATTTCTCAC -s Anc2.Anc2refChr13 18914 15 + 96486 CATAAAATTTCTCAC -s mr.mrrefChr5 241226 15 + 294540 CAGAAAATTTCTCAA -s simCow_chr6.simCow.chr6 374622 15 + 602619 TATAAAATTTCTCAC -s simDog_chr6.simDog.chr6 365324 15 + 593897 CCTAAGTTTACCCAC -s simHuman_chr6.simHuman.chr6 373422 15 + 601863 CATAAAACCTCTCAC -s simRat_chr6.simRat.chr6 387340 15 + 647215 CAGAAAATTTCTCAG - -a -s simMouse_chr6.simMouse.chr6 387377 46 + 636262 AAACTTATAAAATTAATCATCCTTACAAAATACAACATTCAAAGCC -s Anc0.Anc0refChr3 16108 46 + 222631 AATTTGACAACATTATCCATCCTTACTGAGAATGAACCTTCAACTT -s Anc1.Anc1refChr6 49214 46 + 197743 AATTTGACAACATTATCCATCCTTACTGAGAATGAACCTTCAACTT -s Anc2.Anc2refChr13 18931 46 + 96486 AATTTGACAACATAATCCATCCTTATTGAGAATGAACCTTCAACTT -s mr.mrrefChr5 241241 46 + 294540 AAACTTATAAAATTAACCATCCTTACAAAGAATGACCTTTAAAGCC -s simCow_chr6.simCow.chr6 374639 46 + 602619 AATTTGAGAACATAATCCATCCTTATTGAGAATGAATCTTCAACTT -s simDog_chr6.simDog.chr6 365341 45 + 593897 AATTTGACCACAC-ATCCGTCCCTATTTAGAATGAACCTTCAACTC -s simHuman_chr6.simHuman.chr6 373439 46 + 601863 AATTTGACAACATTATCCATGCTTACTGAGAATGAACCTTCAAATT -s simRat_chr6.simRat.chr6 387355 46 + 647215 AGACTTATTAAATTACCCACCTTTACAAAGAATGATCTTTAGAGCC - -a -s simMouse_chr6.simMouse.chr6 387423 243 + 636262 TGGCTTAAACTCCCGTTGCCAGAGGCTCAGCTTCAACTATTGGAAGAACATCTAAATAATTGAACAATTGCTATATATACCTATTTGTGCCCACTATGTTTAATCAGCATTGATCAGTTGATTTGCTATAGAAGATGAGAACTGGCCAGAAAGGCCTCAGCAGTCAAAAAGCATAAGGACAACCTGCAGATTTTCAAATACCTGTCAACCCAAAGGCTGCTGCTTTAATATTTTATGTATATA -s Anc0.Anc0refChr3 16154 217 + 222631 TGGCTTAAAACCTTATTTTCAGATGCCAAGCTTCAACCCTTGACAGAACACCCAAATAACCCCACAACTGGTATATCTACCTATTTGAGCCCACTATATTTAAT---GGGTGACCAATTGATTCACTGCAGAAGG-ATGAAC---CCAGAAAGG--TCAACAAT--AGAAGTATAAAGACAACTTGCAGGTCTGCAC-TGTCTAGAAAACATAACTCTGGCACCTTT--------------CA -s Anc1.Anc1refChr6 49260 221 + 197743 TGGCTTAAAACCTTATTTTCAGATGCCAAGCTTCAACCCTTGACAGAACACCCAAATAACCCCACAACTGGTATATCTACCTATTTGAGCCCACTATATTTAATTGGGGGTGACCAATTGATTCACTGCAGAAGG-ATGAACT--CCAGAAAGG--TCAACAAT--AGAAGTATAAAGACAACTTGCAGGTCTGCAC-TGTCTAGAAAACATAACTCTGGCACCTTT--------------CA -s Anc2.Anc2refChr13 18977 217 + 96486 TGGCTTAAAACCTTGTTTTCAGATGCCAAGCTTCAACCCTTGACAAAACACCCAAATAACCCCAAAACTACTTCAACTACCTATTTGAGCCTGCAATATTTAAT---GGGTGACCAATTGAATTGCTGCAGAAGG-ATGAAC---CCAGAAAGG--TCAGCAAT--AGAAGTCACAAGACAGCATGCAGGTCTGCAA-GGTCTAGAATACATAACTCTGGCACCTCT--------------CA -s mr.mrrefChr5 241287 239 + 294540 TGGCTTAAACTCCCATTGCCAGAGGCTCAGCTTCAACTATTGGAAGAACACCTAAATAATTGAACAATTGGTATATATACCTATTTGTGCCCACTATATTTAATCAGCAGTGATCAGTTGATTCACTATAGAAGGTGAGAACT--CCAGAAAGG--TCAACAATCAAAAAGCATAAGGACAACTTGCAGATTTGCACATACCTATCAACCCAAAGGCTGCTGCTTTAATATTTTATGTATATA -s simCow_chr6.simCow.chr6 374686 200 + 602619 TGGCTTAAAACCTTGTTCTCAGATGCCAA--TACAACACTTGACACTACACTCCACTAACCGCAAAACTACTTCAACTACCTATTTGAGCCTGCAATATTTAAT---GGGTGACCAATTGACTTGTTGCAGAAGG-ATGAAC-------------------TAT--AAAAGTC-CAAGAGAGTGCTCAGGTCTGCAA-GGCCTAGAATACATGACTCTGGCACCTCT--------------CA -s simDog_chr6.simDog.chr6 365388 151 + 593897 TGGCCTAAAACCCTGTTTTCAGATGTCAAGCTTCTACCCTCAATAAAACACCCAGATAACTCCAA-----------------------------------------------------TGAATTGCC------------------CCAGAAAGG--TCAGCAAT--AGAGGTCACAGAACAGCATGCAGG-CTGCAA-GGTCTAGAATATATAACTC-AGCACCTCT--------------TA -s simHuman_chr6.simHuman.chr6 373485 220 + 601863 TAGCTTAAAGCCTTATTTTCAGATGCCAAGCTTCAACCCCTGACAGAACACCCAAATAGCCCCACAACTGGTATATCTACCTATCTGGGCTCACTATACTTG-TTGGGGGCAACCAATTGATTCACTGCAGAAGG-ATGAACT--CCAGAAAGG--TCAACAAT--ATGAGTATAGAGACAACTTGCGGGTCTGCAC-TGTTTAGAAAACACAAATCTGGCACCTTT--------------CA -s simRat_chr6.simRat.chr6 387401 239 + 647215 TGGCCTAAACTCCCATTGCCAGAGGCTCAGCTTTAACTATTGGAAGAACACCTAATTAATTGAACAATTGGTATATATACCTATTTGTGCCCACTATATTTCATCAGCAGTGATCAGTTGCTTCACTATAGAATGTGAGAGCC--CCAGAAAGG--TCAACAACCAAAAAGCATAAGTATAACTTGCAGATTTGCACATACCTATCACCTCAAAGGCTGCTGCTACAATACTTTATGTAGATA - -a -s simMouse_chr6.simMouse.chr6 387666 38 + 636262 ATATGACTGTGGCAACTTTTGGCATCTTGTACAGGCTC -s Anc0.Anc0refChr3 16371 8 + 222631 GCATGGG------------------------------C -s Anc1.Anc1refChr6 49481 8 + 197743 GCATGGG------------------------------C -s Anc2.Anc2refChr13 19201 8 + 96486 GCATGGG------------------------------C -s mr.mrrefChr5 241526 8 + 294540 ATATGAC------------------------------C -s simCow_chr6.simCow.chr6 374893 8 + 602619 GAATGGG------------------------------C -s simDog_chr6.simDog.chr6 365546 8 + 593897 GCATGGG------------------------------T -s simHuman_chr6.simHuman.chr6 373705 8 + 601863 GCATGGG------------------------------C -s simRat_chr6.simRat.chr6 387640 8 + 647215 TTATGAC------------------------------C - -a -s simMouse_chr6.simMouse.chr6 387704 26 + 636262 TTCATGACATGTTTCGACATCTCAGG -s Anc0.Anc0refChr3 16379 26 + 222631 TTTGCAACACATGTTGACATCTCAAT -s Anc1.Anc1refChr6 49489 26 + 197743 TTTGCAACACATGTTGACATCTCAAT -s Anc2.Anc2refChr13 19215 26 + 96486 TTTGCAACACATGCTGACAACCCAAT -s mr.mrrefChr5 241534 26 + 294540 TTCATAACATATTTTGACATCTCAGG -s simCow_chr6.simCow.chr6 374907 25 + 602619 TT-GCAACATGCGCTGACAACCCAAT -s simDog_chr6.simDog.chr6 365560 26 + 593897 TTTGTAATGCATGCTGACAACCCAAT -s simHuman_chr6.simHuman.chr6 373713 26 + 601863 TTTGCAACACATGTTGACATCTCAAT -s simRat_chr6.simRat.chr6 387648 26 + 647215 TTCATAACATATTTTGACATCACAGA - -a -s simMouse_chr6.simMouse.chr6 387730 30 + 636262 TGTAAGATGGTACAAAGTGTGACAATGGCA -s Anc0.Anc0refChr3 16410 30 + 222631 TGTAAGACCATAGGAAGTGTGTCAACAGCT -s Anc1.Anc1refChr6 49520 30 + 197743 TGTAAGACCATAGGAAGTGTGTCAACAGCT -s Anc2.Anc2refChr13 19246 30 + 96486 TGTAAGACCATTGGCAGTGTGTCAACAGCT -s mr.mrrefChr5 241560 30 + 294540 TGTAAGATGGTAGAAAGTGTGACAATGGCA -s simCow_chr6.simCow.chr6 374937 30 + 602619 TGTAAGCCCTTTGGCAGTGTATAAACTGAT -s simDog_chr6.simDog.chr6 365591 30 + 593897 TGTAAGACCATTGGCAGCGTGTCAACAACT -s simHuman_chr6.simHuman.chr6 373744 29 + 601863 TGCAAAACCATAGCA-GTGTGTCAACAGCT -s simRat_chr6.simRat.chr6 387674 30 + 647215 TGTAAGATGGTAGAAAGTGTGACAATGGCA - -a -s simMouse_chr6.simMouse.chr6 387760 46 + 636262 CCTATGATATTAATACGATTCATATAAGCCGGCTGAATTGTCCCAT -s Anc0.Anc0refChr3 16440 46 + 222631 CCTATGATATTAATGTAATTCACATAGGTAGGTTGACTAGTTCCAT -s Anc1.Anc1refChr6 49550 46 + 197743 CCTATGATATTAATGTAATTCACATAGGTAGGTTGACTAGTTCCAT -s Anc2.Anc2refChr13 19276 46 + 96486 CCCATGATATTAATGTAATTCACATAGATAGGTTGACTAATTCCAT -s mr.mrrefChr5 241590 46 + 294540 CCTATGATATTAATATGATTCATATAAGCAGGTTGAATTGTCCCAT -s simCow_chr6.simCow.chr6 374967 46 + 602619 CCCATGATATTCATGTAATTTACATAGATAGGCTGACTAATTCTAG -s simDog_chr6.simDog.chr6 365627 46 + 593897 CCCATGATATCAATGTAATTCACATAGATAGGTTGACTAATTCCGT -s simHuman_chr6.simHuman.chr6 373773 46 + 601863 CCTATGATACTAATGTAACTCACACAGGTAGGTTGACTAGTACCAT -s simRat_chr6.simRat.chr6 387704 46 + 647215 CCTATGATATTAATATGATTCATATAAGCAGGTTGAATTGTCTCAT - -a -s simMouse_chr6.simMouse.chr6 387806 25 + 636262 TGTTTGTAGAAGCTTTGTTGTCAAA -s Anc0.Anc0refChr3 16486 25 + 222631 TGGTTATACAGATTCTGCTGTAAAA -s Anc1.Anc1refChr6 49596 25 + 197743 TGGTTATACAGATTCTGCTGTAAAA -s Anc2.Anc2refChr13 19324 25 + 96486 TGTTTATACAGATTCAGCTGTAAAA -s mr.mrrefChr5 241636 25 + 294540 TGGTTGTAGAAGTTTTGCTGTCAAA -s simCow_chr6.simCow.chr6 375015 25 + 602619 TATTTACACACATTCAGCCATAAGA -s simDog_chr6.simDog.chr6 365675 25 + 593897 TGTTTATACAGATTTAGCTGCAAAA -s simHuman_chr6.simHuman.chr6 373819 25 + 601863 TAGTTAGAAAGATTCTACTGTTGAA -s simRat_chr6.simRat.chr6 387750 25 + 647215 GGGTTGTAGAAGTTTTGCTGTCAAT - -a -s simMouse_chr6.simMouse.chr6 387831 5 + 636262 CATTT -s Anc0.Anc0refChr3 16511 5 + 222631 GATCT -s Anc1.Anc1refChr6 49621 5 + 197743 GATCT -s Anc2.Anc2refChr13 19349 5 + 96486 GATCT -s mr.mrrefChr5 241661 5 + 294540 CATTT -s simCow_chr6.simCow.chr6 375040 5 + 602619 GATCT -s simDog_chr6.simDog.chr6 365700 5 + 593897 GATCC -s simHuman_chr6.simHuman.chr6 373844 5 + 601863 GATCT -s simRat_chr6.simRat.chr6 387776 5 + 647215 CGTTT - -a -s simMouse_chr6.simMouse.chr6 387836 16 + 636262 TGTTTGTGCTGCACCA -s Anc0.Anc0refChr3 16518 16 + 222631 TGTTTGTGCTGTGCTA -s Anc1.Anc1refChr6 49628 16 + 197743 TGTTTGTGCTGTGCTA -s Anc2.Anc2refChr13 19356 16 + 96486 TGTTTGTGCTGTGCTA -s mr.mrrefChr5 241666 16 + 294540 TGTTTGTGCTGCACCA -s simCow_chr6.simCow.chr6 375047 16 + 602619 TGGTTATGCTGCACCA -s simDog_chr6.simDog.chr6 365707 16 + 593897 TGTTTGTGCTGTGCTA -s simHuman_chr6.simHuman.chr6 373851 16 + 601863 TGTCTGTTCTGTGTAA -s simRat_chr6.simRat.chr6 387781 16 + 647215 TGATTGTGCTGCACCA - -a -s simMouse_chr6.simMouse.chr6 387852 48 + 636262 ACAGTGCCATTCACCCTAACTAAGTACCCTCCAATAGAACTACACCCA -s Anc0.Anc0refChr3 16548 40 + 222631 TCAATGC---TC-TCTAAGCCA----CCCTCCAATGGAACTAGAAATA -s Anc1.Anc1refChr6 49658 41 + 197743 TCAATGC---TCATCTAAGCCA----CCCTCCAATGGAACTAGAAATA -s Anc2.Anc2refChr13 19386 40 + 96486 TCAATGC---TC-TCTAAGCCA----CCCTCCCATGGAACTAGAAATA -s mr.mrrefChr5 241682 48 + 294540 TCAGTGCCATTCACCTTAACCAAGTACCCTCCAATAGAACTACAACCA -s simCow_chr6.simCow.chr6 375077 39 + 602619 TCAATGC---TC-TCTAAGCCA----CT-GCCCATGGAACTAGAAAGA -s simDog_chr6.simDog.chr6 365737 40 + 593897 TCAATGC---TC-TCTAAGCCA----CCCTCCCATAGAACTCAAAATA -s simHuman_chr6.simHuman.chr6 373881 41 + 601863 TCAATGC---TCATCTACGCCA----CCCTCCAATGGAACTAGAAGAA -s simRat_chr6.simRat.chr6 387797 48 + 647215 TCAGTGCCATTCACCTTAACCAAGTACCTTCCAATAGAATTACAAACA - -a -s simMouse_chr6.simMouse.chr6 387900 13 + 636262 GTAGCCATGATGA -s Anc0.Anc0refChr3 16589 13 + 222631 GTGGCCATAACGA -s Anc1.Anc1refChr6 49700 13 + 197743 GTGGCCATAACGA -s Anc2.Anc2refChr13 19427 13 + 96486 GTGATCATAACGA -s mr.mrrefChr5 241731 13 + 294540 GTAGCCATAATGA -s simCow_chr6.simCow.chr6 375117 13 + 602619 GTGATCACAAGGA -s simDog_chr6.simDog.chr6 365778 9 + 593897 GT----ATAACAA -s simHuman_chr6.simHuman.chr6 373923 13 + 601863 CTGGCCATACGAA -s simRat_chr6.simRat.chr6 387846 13 + 647215 GTATTCATAATGA - -a -s simMouse_chr6.simMouse.chr6 387913 9 + 636262 ACCATGACT -s Anc0.Anc0refChr3 16602 9 + 222631 CACCAGGAT -s Anc1.Anc1refChr6 49713 9 + 197743 CACCAGGAT -s Anc2.Anc2refChr13 19441 9 + 96486 CACCAGGAT -s mr.mrrefChr5 241744 9 + 294540 ACCATGACT -s simCow_chr6.simCow.chr6 375131 3 + 602619 CAC------ -s simDog_chr6.simDog.chr6 365788 9 + 593897 CATCAGGAT -s simHuman_chr6.simHuman.chr6 373936 9 + 601863 CTCCAGGAG -s simRat_chr6.simRat.chr6 387859 9 + 647215 TCCATGACC - -a -s simMouse_chr6.simMouse.chr6 387922 20 + 636262 CTGGCCTAAATTAGCGAGTC -s Anc0.Anc0refChr3 16612 14 + 222631 CTGGCATAAACTA------C -s Anc1.Anc1refChr6 49723 14 + 197743 CTGGCATAAACTA------C -s Anc2.Anc2refChr13 19451 14 + 96486 TGGGCATAAACTA------C -s mr.mrrefChr5 241754 20 + 294540 CTGGCCTAAATTAGCGAGTC -s simCow_chr6.simCow.chr6 375134 11 + 602619 ---ACATAAACTA------C -s simDog_chr6.simDog.chr6 365798 14 + 593897 TGGGCATAAACTA------C -s simHuman_chr6.simHuman.chr6 373946 14 + 601863 CTGGCATAAACTA------C -s simRat_chr6.simRat.chr6 387869 20 + 647215 TGGGCCTAAGTTAGTGAGTC - -a -s simMouse_chr6.simMouse.chr6 387942 3 + 636262 TGA -s Anc0.Anc0refChr3 16626 3 + 222631 TAA -s Anc1.Anc1refChr6 49737 3 + 197743 TAA -s Anc2.Anc2refChr13 19465 3 + 96486 TAA -s mr.mrrefChr5 241774 3 + 294540 TGA -s simCow_chr6.simCow.chr6 375145 3 + 602619 TAA -s simDog_chr6.simDog.chr6 365813 3 + 593897 TAA -s simHuman_chr6.simHuman.chr6 373960 3 + 601863 CAA -s simRat_chr6.simRat.chr6 387889 3 + 647215 TCA - -a -s simMouse_chr6.simMouse.chr6 387945 4 + 636262 TTAT -s Anc0.Anc0refChr3 16629 4 + 222631 ACAG -s Anc1.Anc1refChr6 49740 4 + 197743 ACAG -s Anc2.Anc2refChr13 19478 4 + 96486 ACAG -s mr.mrrefChr5 241777 4 + 294540 TTAT -s simCow_chr6.simCow.chr6 375158 4 + 602619 ACAG -s simDog_chr6.simDog.chr6 365826 4 + 593897 ACAG -s simHuman_chr6.simHuman.chr6 373963 4 + 601863 ACAC -s simRat_chr6.simRat.chr6 387892 4 + 647215 TCAT - -a -s simMouse_chr6.simMouse.chr6 387949 18 + 636262 TATTACAGATTGCAAATT -s Anc0.Anc0refChr3 16719 18 + 222631 TATTTGAGATCACAAATT -s Anc1.Anc1refChr6 49830 18 + 197743 TATTTGAGATCACAAATT -s Anc2.Anc2refChr13 19568 18 + 96486 CATTTGTCATCACAAATT -s mr.mrrefChr5 241814 18 + 294540 TATTACAGATTGCAAATT -s simCow_chr6.simCow.chr6 375242 18 + 602619 CATTTGTCATCACAAATT -s simHuman_chr6.simHuman.chr6 374085 18 + 601863 TATTCAAGACCACAAATT -s simRat_chr6.simRat.chr6 387934 18 + 647215 CATTACAGATTGCAAGTT - -a -s simMouse_chr6.simMouse.chr6 387967 4 + 636262 TGGT -s Anc0.Anc0refChr3 16751 4 + 222631 TGGT -s Anc1.Anc1refChr6 49862 4 + 197743 TGGT -s Anc2.Anc2refChr13 19600 4 + 96486 TGGC -s mr.mrrefChr5 241832 4 + 294540 TGGT -s simCow_chr6.simCow.chr6 375274 4 + 602619 TGGC -s simHuman_chr6.simHuman.chr6 374118 4 + 601863 TGGT -s simRat_chr6.simRat.chr6 387952 4 + 647215 TGGT - -a -s simMouse_chr6.simMouse.chr6 387971 9 + 636262 TCAAATTCT -s Anc0.Anc0refChr3 16755 9 + 222631 TCAAATTGT -s Anc1.Anc1refChr6 49866 9 + 197743 TCAAATTGT -s Anc2.Anc2refChr13 19604 9 + 96486 TAAAATTGT -s mr.mrrefChr5 241836 9 + 294540 TCAAATTCT -s simCow_chr6.simCow.chr6 375280 9 + 602619 TTGAACTAT -s simDog_chr6.simDog.chr6 365896 9 + 593897 TAAGATTGG -s simHuman_chr6.simHuman.chr6 374122 9 + 601863 TCAAATTGT -s simRat_chr6.simRat.chr6 387956 9 + 647215 TCAAATTCT - -a -s simMouse_chr6.simMouse.chr6 387980 42 + 636262 CAATAGTGTAAACATTCTCCTGTGAGATTTAGTAATGCTATG -s Anc0.Anc0refChr3 16764 10 + 222631 CAGTAGTGTA-------------------------------- -s Anc1.Anc1refChr6 49875 42 + 197743 CAGTAGTGTATATGTTTCACTCTAAGATTCAGTAGTAGTATG -s Anc2.Anc2refChr13 19613 10 + 96486 TAGTAGTGTA-------------------------------- -s mr.mrrefChr5 241845 42 + 294540 CAATAGTGTAAACATTTTCCTGTGAGATTTAGTAATGCTATG -s simCow_chr6.simCow.chr6 375289 10 + 602619 GTGTAGTGTA-------------------------------- -s simDog_chr6.simDog.chr6 365906 10 + 593897 TAGTGGTGTA-------------------------------- -s simHuman_chr6.simHuman.chr6 374131 42 + 601863 CAGTAGTGCATATGTTTCACTCTAAGATTCAGTAGTAGTATG -s simRat_chr6.simRat.chr6 387965 42 + 647215 CCATAGTGTAAACATTTTTCTGTGAGATTTGGTAATGCTATG - -a -s simMouse_chr6.simMouse.chr6 388022 12 + 636262 CATGAATTGTTG -s Anc0.Anc0refChr3 16774 12 + 222631 CCTGAATTGTTG -s Anc1.Anc1refChr6 49917 12 + 197743 CCTGAATTGTTG -s Anc2.Anc2refChr13 19623 12 + 96486 CCTGAATAGTAG -s mr.mrrefChr5 241887 12 + 294540 CATGAATTGTTG -s simCow_chr6.simCow.chr6 375331 12 + 602619 GCTGAATAGTAG -s simDog_chr6.simDog.chr6 365916 12 + 593897 CCTGAATAGTAG -s simHuman_chr6.simHuman.chr6 374173 12 + 601863 CCTCAATTGTTG -s simRat_chr6.simRat.chr6 388007 12 + 647215 CATGAATTGTTG - -a -s simMouse_chr6.simMouse.chr6 388034 5 + 636262 CTCAG -s Anc0.Anc0refChr3 16786 5 + 222631 TTCAG -s Anc1.Anc1refChr6 49929 5 + 197743 TTCAG -s Anc2.Anc2refChr13 19635 5 + 96486 TTCAA -s mr.mrrefChr5 241899 5 + 294540 CTCAG -s simCow_chr6.simCow.chr6 375344 5 + 602619 TTCGG -s simDog_chr6.simDog.chr6 365928 5 + 593897 TTCAA -s simHuman_chr6.simHuman.chr6 374185 5 + 601863 TTCAG -s simRat_chr6.simRat.chr6 388019 3 + 647215 C--AT - -a -s simMouse_chr6.simMouse.chr6 388039 48 + 636262 AAGGACCACTTTAACCCTAATTGTGCTTGTTGACAGCTGGTCCATCCT -s Anc0.Anc0refChr3 20511 34 + 222631 GAGGATTGGTTGGAC-------------GATCACA-CTGGTTAATCCT -s Anc1.Anc1refChr6 49934 47 + 197743 GAGGATTGGTTGGACCCTAACGAAGCCTGATCACA-CTGGTTAATCCT -s Anc2.Anc2refChr13 23784 34 + 96486 AAAGATTGATTGGAC-------------GATCACA-CTGGTTAATCCT -s mr.mrrefChr5 241904 48 + 294540 AAGGACCAGTTTAACCCTAACTGTGCTTGTTGACAGCTGGTCCATCCT -s simCow_chr6.simCow.chr6 379678 28 + 602619 ------TGAATGGAC-------------CATCATA-CTGGTGAATCCA -s simDog_chr6.simDog.chr6 370288 34 + 593897 AAAGATTAATTGGAC-------------GATCACA-CTGGTTAATCCT -s simHuman_chr6.simHuman.chr6 374190 47 + 601863 GAGGATTGGTTGGACCCTAACGAAGCCTGATTAGA-CTGGTTGATCCT -s simRat_chr6.simRat.chr6 388022 48 + 647215 CAGGACCAGGTTAACCCTAACTTTGCTTGTTGATAGCTGGTCCATCCT - -a -s simMouse_chr6.simMouse.chr6 388087 16 + 636262 ATTAGCCTCCAATGTA -s Anc0.Anc0refChr3 20545 16 + 222631 ATTAGTCTTCAATGAG -s Anc1.Anc1refChr6 49981 16 + 197743 ATTAGTCTTCAATGAG -s Anc2.Anc2refChr13 23818 16 + 96486 TTTAGTCTTCAATGAG -s mr.mrrefChr5 241952 16 + 294540 ATTAGTCTCCAATGTA -s simCow_chr6.simCow.chr6 379706 16 + 602619 TTTAGTCTTCAATAAG -s simDog_chr6.simDog.chr6 370322 16 + 593897 TTTAAGCTCCAATGGG -s simHuman_chr6.simHuman.chr6 374248 16 + 601863 ATGAGTCTTCAATGAG -s simRat_chr6.simRat.chr6 388070 16 + 647215 ATTAGTCTCCAATGTA - -a -s simMouse_chr6.simMouse.chr6 388103 4 + 636262 TTCC -s Anc0.Anc0refChr3 20561 4 + 222631 TTCC -s Anc1.Anc1refChr6 49997 4 + 197743 TTCC -s Anc2.Anc2refChr13 23834 4 + 96486 TTGC -s mr.mrrefChr5 241968 4 + 294540 TTCC -s simCow_chr6.simCow.chr6 379735 4 + 602619 TTTG -s simDog_chr6.simDog.chr6 370338 4 + 593897 ATGC -s simHuman_chr6.simHuman.chr6 374264 4 + 601863 TTCC -s simRat_chr6.simRat.chr6 388086 4 + 647215 TTCC - -a -s simMouse_chr6.simMouse.chr6 388107 26 + 636262 ACCATACCCTTAAGGCTGTTTCTAAT -s Anc0.Anc0refChr3 20574 26 + 222631 ACCATAGCCTTGGGGCTGCTTCTGAT -s Anc1.Anc1refChr6 50010 26 + 197743 ACCATAGCCTTGGGGCTGCTTCTGAT -s Anc2.Anc2refChr13 23847 26 + 96486 ACCACAGTCTTGGGGCTGCTTCTGAT -s mr.mrrefChr5 241972 26 + 294540 ACCATACCCTTAAGGCTGTTTCTGAT -s simCow_chr6.simCow.chr6 379748 26 + 602619 ATCCCAAGCTTGGGATTGCTTCTGGT -s simDog_chr6.simDog.chr6 370351 26 + 593897 ACCACAGTCTTAGGGCTGCGTCTAAT -s simHuman_chr6.simHuman.chr6 374277 26 + 601863 ACCTTAGCCTTGGGCCCACTTCTGAT -s simRat_chr6.simRat.chr6 388090 24 + 647215 ACCATATCCCT--GGCTGTTTCTGAC - -a -s simMouse_chr6.simMouse.chr6 388133 13 + 636262 GGGGTTGATGACT -s Anc0.Anc0refChr3 20608 13 + 222631 GATATTAACTTCT -s Anc1.Anc1refChr6 50044 13 + 197743 GATATTAACTTCT -s Anc2.Anc2refChr13 23927 13 + 96486 GATATTAACTTCT -s mr.mrrefChr5 241998 13 + 294540 GGTGTTGATGACT -s simCow_chr6.simCow.chr6 379832 13 + 602619 AATATTAACCTTT -s simDog_chr6.simDog.chr6 370431 13 + 593897 GATATTAGTTTCT -s simHuman_chr6.simHuman.chr6 374311 13 + 601863 GATATTAACATCT -s simRat_chr6.simRat.chr6 388114 13 + 647215 GGTGCTGATGACT - -a -s simMouse_chr6.simMouse.chr6 388146 29 + 636262 ATGGATAATTTGATTGTGTATTTAATACA -s Anc0.Anc0refChr3 20643 29 + 222631 ATGCATAATTCAGCTGTATATTTAATACA -s Anc1.Anc1refChr6 50079 29 + 197743 ATGCATAATTCAGCTGTATATTTAATACA -s Anc2.Anc2refChr13 23962 29 + 96486 CTGCATAATTCAGCTGTACATTTAATACA -s mr.mrrefChr5 242011 29 + 294540 ATGGATAATTTGATTGTGTATTTAATACA -s simCow_chr6.simCow.chr6 379867 29 + 602619 CTGGATAATTCAGTTGTAGATTTAATACA -s simDog_chr6.simDog.chr6 370468 29 + 593897 CTGCATAATTTAGCTGTACATATAATGCA -s simHuman_chr6.simHuman.chr6 374346 29 + 601863 ATGCTTAATTCAGCTGTATACTTAATACA -s simRat_chr6.simRat.chr6 388127 29 + 647215 ATTGATAAGCTGAGTGTGAATTGAATACA - -a -s simMouse_chr6.simMouse.chr6 388175 3 + 636262 TAT -s Anc0.Anc0refChr3 20675 3 + 222631 TGG -s Anc1.Anc1refChr6 50111 3 + 197743 TGG -s Anc2.Anc2refChr13 23994 3 + 96486 AGG -s mr.mrrefChr5 242040 3 + 294540 TAT -s simCow_chr6.simCow.chr6 379899 3 + 602619 AGG -s simDog_chr6.simDog.chr6 370500 3 + 593897 AGG -s simHuman_chr6.simHuman.chr6 374378 3 + 601863 TGA -s simRat_chr6.simRat.chr6 388156 3 + 647215 TAT - -a -s simMouse_chr6.simMouse.chr6 388178 60 + 636262 AGAGACTGAAAGCCTTAGGCAAAATTGATTACTTGGTTAGCTCACCATCATAACAGTGGG -s Anc0.Anc0refChr3 20678 59 + 222631 AGAGGCTTTAGGC-ATAGGCAAAATTGATTCTTTGTTTTGGTTACCTTCACAACAGTGGG -s Anc1.Anc1refChr6 50114 59 + 197743 AGAGGCTTTAGGC-ATAGGCAAAATTGATTCTTTGTTTTGGTTACCTTCACAACAGTGGG -s Anc2.Anc2refChr13 23998 59 + 96486 AGGGGCTTTAGGC-ATAGGCAAAATTGAATCTTTGTTTTGGTTACCTTCACAGCAGTGGG -s mr.mrrefChr5 242043 59 + 294540 AGAGGCTTAAAGC-TTAGGCAAAATTGATTACTTGGTTAGCTCACCATCATAACAGTGGG -s simCow_chr6.simCow.chr6 379903 57 + 602619 ATGGGCAGTGCAC-ATAAGCAGAATGGACTCTCAGTTTCGGTTACCTCAAC--CAGTGGG -s simDog_chr6.simDog.chr6 370504 58 + 593897 GGGGTATTTAGGC-TTAGGCAAAATTGAATCTTTGTTTTGGTTACCGTC-CAGCAGTGAC -s simHuman_chr6.simHuman.chr6 374381 57 + 601863 AGAGGCTTTAGGC-ATGGGCAAAAT--ATTCTTTGTTATGGTTACCTTCACAACAGTGGG -s simRat_chr6.simRat.chr6 388159 59 + 647215 AGAGGCTTAAAGC-GTAAGCAAAATTGATTACTTGGCTATCTCAGCATTATAACAGTGGG - -a -s simMouse_chr6.simMouse.chr6 388238 2 + 636262 GA -s Anc0.Anc0refChr3 20737 2 + 222631 CG -s Anc1.Anc1refChr6 50173 2 + 197743 CG -s Anc2.Anc2refChr13 24057 2 + 96486 CA -s mr.mrrefChr5 242102 2 + 294540 GG -s simCow_chr6.simCow.chr6 379961 2 + 602619 CT -s simDog_chr6.simDog.chr6 370562 2 + 593897 CA -s simHuman_chr6.simHuman.chr6 374438 2 + 601863 TG -s simRat_chr6.simRat.chr6 388218 2 + 647215 AG - -a -s simMouse_chr6.simMouse.chr6 388240 78 + 636262 AATCATAGGACCACATTTGTGCCTCGGCACGCTGTAACAGTTTTATGCTGATTTCCATCCTACACAATGACTTATAAA -s Anc0.Anc0refChr3 20739 26 + 222631 G-TAATAGGACCAC--------------------------------------------------TG-TGGCTTGTGAT -s Anc1.Anc1refChr6 50175 26 + 197743 G-TAATAGGACCAC--------------------------------------------------TG-TGGCTTGTGAT -s Anc2.Anc2refChr13 24059 26 + 96486 G-TAATAGGATCAA--------------------------------------------------TG-TGGCTTGTGAT -s mr.mrrefChr5 242104 68 + 294540 AATAATAGGACCACATT---------GCACGCTGTAACAGTTTTATGCTGATTTCCATCCTACACA-TGGCTTATGAT -s simCow_chr6.simCow.chr6 379963 26 + 602619 G-TAATAGACTCAT--------------------------------------------------CG-TGGCTTGTGAC -s simDog_chr6.simDog.chr6 370565 26 + 593897 G-CAATAGGATAAA--------------------------------------------------TG-TAGCTTGTGAT -s simHuman_chr6.simHuman.chr6 374440 26 + 601863 G-TAATAGGACCAC--------------------------------------------------TG-TGGCTTGTGAT -s simRat_chr6.simRat.chr6 388220 68 + 647215 AATAATGTAACCATATT---------GCACACAGTAACAGTTTTAGGCTGATTTCCATCCTACACA-TGGTTTAAGAT - -a -s simMouse_chr6.simMouse.chr6 388318 42 + 636262 GACAGCTCAAGTTATTGGGTGTTCCATAAAATCAAGTTGATG -s Anc0.Anc0refChr3 20765 42 + 222631 GATAGTTCAAGGTAGTGAACGCTTAGTAGAATCAGGTTGAAG -s Anc1.Anc1refChr6 50201 42 + 197743 GATAGTTCAAGGTAGTGAACGCTTAGTAGAATCAGGTTGAAG -s Anc2.Anc2refChr13 24085 42 + 96486 GATGGTTCAAGGTAGTTAACGATTAGTAGAATCAGGTTGAAG -s mr.mrrefChr5 242172 42 + 294540 GATAGCTCAAGTTATTGAGTGCTCCATAAAATCAAGTTGATG -s simCow_chr6.simCow.chr6 379999 41 + 602619 GATGGTTCAAGTTAGCTAACAGTTAG-AGAATCAGGATGAAG -s simDog_chr6.simDog.chr6 370591 42 + 593897 GATGGTTTATGGTAGTTAATGATCAATAGAATGAGGTTGAAG -s simHuman_chr6.simHuman.chr6 374466 42 + 601863 GTTAGTTCAAGCTAATGAACTCTTTGTAGAATCAGGTTGCAG -s simRat_chr6.simRat.chr6 388288 42 + 647215 GGTGGCTCAAGTTATTGAGTGCTCCATAAAATCAAGGTAATG - -a -s simMouse_chr6.simMouse.chr6 388360 5 + 636262 TATTT -s Anc0.Anc0refChr3 20807 5 + 222631 TACCT -s Anc1.Anc1refChr6 50243 5 + 197743 TACCT -s Anc2.Anc2refChr13 24127 5 + 96486 TACCA -s mr.mrrefChr5 242214 5 + 294540 TACTT -s simCow_chr6.simCow.chr6 380040 5 + 602619 TACTA -s simDog_chr6.simDog.chr6 370637 5 + 593897 TCCCA -s simHuman_chr6.simHuman.chr6 374508 5 + 601863 TACCT -s simRat_chr6.simRat.chr6 388330 5 + 647215 CACTT - -a -s simMouse_chr6.simMouse.chr6 388365 33 + 636262 AGGAGGAATAGTTATGGCCCAACTCAGTAATTG -s Anc0.Anc0refChr3 20812 32 + 222631 GT-ATGAATAGTTACGGCCTAACTCAATAATTA -s Anc1.Anc1refChr6 50248 32 + 197743 GT-ATGAATAGTTACGGCCTAACTCAATAATTA -s Anc2.Anc2refChr13 24132 32 + 96486 TT-TTGAATAGTTACAGCTTAATTTAATAATTA -s mr.mrrefChr5 242219 33 + 294540 GGGAGGAATAGTTATGGCCCAACTCAGTAATTG -s simCow_chr6.simCow.chr6 380051 32 + 602619 TT-TTGGATAGTTACAGCTTAGTTTAATAATTA -s simDog_chr6.simDog.chr6 370642 32 + 593897 TT-TTGAATAATTACAGCTTAATTTAATAATTG -s simHuman_chr6.simHuman.chr6 374513 32 + 601863 GC-ATGCATAGGTACGGTCTAACTCAATAATTA -s simRat_chr6.simRat.chr6 388335 33 + 647215 GGGAGGAACATTTGTGGCCCAACTCAGTAATTG - -a -s simMouse_chr6.simMouse.chr6 388398 23 + 636262 TCACCTAATTGGCATGAATTTGT -s Anc0.Anc0refChr3 20845 23 + 222631 TCACCTCAATGGCCTGAGGTTGT -s Anc1.Anc1refChr6 50281 23 + 197743 TCACCTCAATGGCCTGAGGTTGT -s Anc2.Anc2refChr13 24165 23 + 96486 TCACCTCAATGGCCTGGGGTTGG -s mr.mrrefChr5 242252 23 + 294540 TCACCTAATTGGCATGAATTTGT -s simCow_chr6.simCow.chr6 380084 23 + 602619 TCAGTTCAATGGCCTGGGGTGGG -s simDog_chr6.simDog.chr6 370675 22 + 593897 TCACCTCCATG-CCTGGGGTTGG -s simHuman_chr6.simHuman.chr6 374546 23 + 601863 GCACCTTAATGGCCCAAGGTTGT -s simRat_chr6.simRat.chr6 388368 23 + 647215 CCACCTAATTGGCATGAATTCGT - -a -s simMouse_chr6.simMouse.chr6 388421 50 + 636262 TGAATTGGTTTGTTCATGGATTGTGTGTTTATGTGTGTTGGTGCATAATA -s Anc0.Anc0refChr3 20868 50 + 222631 TGAATTGGTTTGTCCATGAATTGTATTTATATGGGTGCTAGCGCATAATG -s Anc1.Anc1refChr6 50304 50 + 197743 TGAATTGGTTTGTCCATGAATTGTATTTATATGGGTGCTAGCGCATAATG -s Anc2.Anc2refChr13 24188 50 + 96486 GGAATTGGTTTGTCCATGAATTATCTTCATATGGGTGCTAGCGCATAATG -s mr.mrrefChr5 242275 50 + 294540 TGAATTGGTTTGTTCATGGATTGTATTTTTATGGGTGCTGGTGCATAATG -s simCow_chr6.simCow.chr6 380107 50 + 602619 GTAATTGGCTTGTCCATGACTTATGCTCATATCGGTGTTCGTGCATAATG -s simDog_chr6.simDog.chr6 370697 50 + 593897 GGACATAGTACGTCCATGAATTATCTTCATATGGGTGCTAGCGCATAATG -s simHuman_chr6.simHuman.chr6 374571 50 + 601863 TGAATTGGGTTGTCCATGAATTGTATTTGTATGGGTGCTAGCGGATAATG -s simRat_chr6.simRat.chr6 388391 50 + 647215 TGAATGGGTTTGTTCATGGATCGTATTTTCATGGATGCTTGTGCATAATG - -a -s simMouse_chr6.simMouse.chr6 388471 16 + 636262 TACAGCAACACTTGCC -s Anc0.Anc0refChr3 20918 16 + 222631 TGCAACAATAATTACT -s Anc1.Anc1refChr6 50354 16 + 197743 TGCAACAATAATTACT -s Anc2.Anc2refChr13 24238 16 + 96486 TGCAACAATAATTATT -s mr.mrrefChr5 242325 16 + 294540 TACAGCAACACTTGCC -s simCow_chr6.simCow.chr6 380157 16 + 602619 TGCAACAATAGCTATT -s simDog_chr6.simDog.chr6 370748 16 + 593897 TGCAGCAATAATTATT -s simHuman_chr6.simHuman.chr6 374621 16 + 601863 TGCAACAAGAATTACT -s simRat_chr6.simRat.chr6 388441 16 + 647215 TACAGCAACATTTTCC - -a -s simMouse_chr6.simMouse.chr6 388487 23 + 636262 TATACATATAAATTGGTCTCATA -s Anc0.Anc0refChr3 20934 21 + 222631 GATTCTTATACATAAGTCT--GG -s Anc1.Anc1refChr6 50370 23 + 197743 GATTCTTATACATAAGTCTAAGG -s Anc2.Anc2refChr13 24254 21 + 96486 GGTTCTTATACATAAGTCT--GG -s mr.mrrefChr5 242341 23 + 294540 TATACATATACATTGGTCTAATA -s simCow_chr6.simCow.chr6 380173 16 + 602619 GGTTGCTATACTTA-------GG -s simDog_chr6.simDog.chr6 370766 19 + 593897 GGTTCTTATACATAAGTCT---- -s simHuman_chr6.simHuman.chr6 374637 23 + 601863 GATTCTTATACATAAGTCTAAGG -s simRat_chr6.simRat.chr6 388457 23 + 647215 TATACATATACATTGGTCTAATA - -a -s simMouse_chr6.simMouse.chr6 388510 27 + 636262 GCACAAAAGTATTGTTACTGATAATAT -s Anc0.Anc0refChr3 20963 27 + 222631 ACACAAAGTTGTTGTTAGTAATAACAT -s Anc1.Anc1refChr6 50401 27 + 197743 ACACAAAGTTGTTGTTAGTAATAACAT -s Anc2.Anc2refChr13 24283 27 + 96486 AAACAAAGTTGTTGTTAGTAATAACAT -s mr.mrrefChr5 242364 27 + 294540 GCACAAAGTTGTTGTTACTAATAACAT -s simCow_chr6.simCow.chr6 380197 27 + 602619 GAACAGAGGTGTTGTTAGTCACAACAT -s simDog_chr6.simDog.chr6 370792 27 + 593897 AAACTAAGTGGTAGTTAGTAATGACAT -s simHuman_chr6.simHuman.chr6 374668 27 + 601863 ACACAAAGTTGTTGTTTGTAATAACAT -s simRat_chr6.simRat.chr6 388480 27 + 647215 GCAAAAGGTTGTTATTACTAATAACAT - -a -s simMouse_chr6.simMouse.chr6 388537 64 + 636262 CCCTGAATAGGCTGTGCTTCCTGCTGTGTATCAATATATCAAGGGAATGATAGTTTTACAATGA -s Anc0.Anc0refChr3 20991 60 + 222631 CATTGAATAAGCTGTGCTCCCTGTTGCACAGCAGTTCAAAAAGTGAA----AGCACAACATTGA -s Anc1.Anc1refChr6 50429 60 + 197743 CATTGAATAAGCTGTGCTCCCTGTTGCACAGCAGTTCAAAAAGTGAA----AGCACAACATTGA -s Anc2.Anc2refChr13 24311 60 + 96486 CATTAAATAAGCTGTGCTCCCTGTTGCACAGCAGTTCAAATGGTGGA----AGCACAACATTGA -s mr.mrrefChr5 242391 64 + 294540 CCCTGAATAAGCTGTGCTTCCTGCTGTGTATCAATTTATCAAGGGAATGATAGTTTAACAATGA -s simCow_chr6.simCow.chr6 380225 60 + 602619 CATTAAATAAGCTGTGCTCCCCACACCACAACAGTTCAAATGGTGGA----AGCACAATGGCAA -s simDog_chr6.simDog.chr6 370820 42 + 593897 CATTAAAAAAGCTGTGTACCCTGTTGCACAGCAGT----------------------ACATTGA -s simHuman_chr6.simHuman.chr6 374696 60 + 601863 CATTGAATAAGCTGTGCTACTTGTTGCACAGTGGTTCAAAAAGCAAA----ACCACAACATTGA -s simRat_chr6.simRat.chr6 388507 64 + 647215 ACCTAAATAAGCTGTGCTTCCTGCTGTGTAACAATTTATTGAGGGAGGAATAGTTTAACAATGA - -a -s simMouse_chr6.simMouse.chr6 388601 4 + 636262 TCCG -s Anc0.Anc0refChr3 21081 4 + 222631 TCCA -s Anc1.Anc1refChr6 50519 4 + 197743 TCCA -s Anc2.Anc2refChr13 24401 4 + 96486 CCCA -s mr.mrrefChr5 242455 4 + 294540 TCCA -s simCow_chr6.simCow.chr6 380315 4 + 602619 CCCA -s simHuman_chr6.simHuman.chr6 374830 4 + 601863 TTGA -s simRat_chr6.simRat.chr6 388571 4 + 647215 TCCA - -a -s simMouse_chr6.simMouse.chr6 388605 13 + 636262 AAGATTCAGATTT -s Anc0.Anc0refChr3 21098 13 + 222631 GAGAGTCAGACTT -s Anc1.Anc1refChr6 50536 13 + 197743 GAGAGTCAGACTT -s Anc2.Anc2refChr13 24418 13 + 96486 GAGAGGCAGCCTT -s mr.mrrefChr5 242461 13 + 294540 GAGATTCAGATTT -s simCow_chr6.simCow.chr6 380348 13 + 602619 GAGAGGCACCCTT -s simDog_chr6.simDog.chr6 370865 7 + 593897 ------CAGCCTT -s simHuman_chr6.simHuman.chr6 374847 13 + 601863 GAGAGTCAGACTT -s simRat_chr6.simRat.chr6 388577 13 + 647215 GAGATTCAGATTT - -a -s simMouse_chr6.simMouse.chr6 388618 8 + 636262 TTTGCAGG -s Anc0.Anc0refChr3 21130 8 + 222631 TTTGTAGG -s Anc1.Anc1refChr6 50568 8 + 197743 TTTGTAGG -s Anc2.Anc2refChr13 24450 8 + 96486 TTTGTCGG -s mr.mrrefChr5 242474 8 + 294540 TTTGCAGG -s simCow_chr6.simCow.chr6 380380 8 + 602619 TTTGTTGC -s simDog_chr6.simDog.chr6 370891 8 + 593897 TTTGTCAG -s simHuman_chr6.simHuman.chr6 374879 8 + 601863 TTTGTAGG -s simRat_chr6.simRat.chr6 388590 7 + 647215 TT-GCAGG - -a -s simMouse_chr6.simMouse.chr6 388626 46 + 636262 TCCCTTGAAAGGAGTCTGACTATTTCTAATGACAATCAGTAATCCC -s Anc0.Anc0refChr3 21156 36 + 222631 TCCCCAAGAAGGTATGTTA----------TGAGAGTCAATAACTCC -s Anc1.Anc1refChr6 50594 46 + 197743 TCCCCAAGAAGGTATGTTACTATTTCTAATGAGAGTCAATAACTCC -s Anc2.Anc2refChr13 24476 36 + 96486 ACCCCAAAAATGTATGTTA----------TGAGTGTCAATAACTCC -s mr.mrrefChr5 242482 46 + 294540 TCCCCTGGAAGGTGTGTTACTATTTCTAATGACAGTCAGTAATCCC -s simCow_chr6.simCow.chr6 380406 36 + 602619 CCCCCAAAAATATTTTTTA----------TGAGTGTCAATAACTCC -s simDog_chr6.simDog.chr6 370917 36 + 593897 ACTCTATAAATGAATGTTC----------AGAGTTGATAAAACTCC -s simHuman_chr6.simHuman.chr6 374905 46 + 601863 TCCCCAAGAAGGTATGTTCCTATTTCTAATGAGAGTCAATAACTCC -s simRat_chr6.simRat.chr6 388597 46 + 647215 TCCCCTGGAGGATGTGTTGCTATTTCTAATGACAGTCAGTAATCCT - -a -s simMouse_chr6.simMouse.chr6 388672 95 + 636262 AGATGTTGATGGAATTGAAACTCGCATGGATAGCACCCTGTACTATAGTCTATGAGCCACCATCCCATTGTATGTCCACCACTTACGTAAAAAGC -s Anc0.Anc0refChr3 21206 95 + 222631 AGTTGCTAATGAAATTGAATTTTGCAGAGATGCAACTCTGCACTATAACTCATGTACAACTGTCCCATTATAGGTCCTTTACCTACATAAAAAAC -s Anc1.Anc1refChr6 50654 95 + 197743 AGTTGCTAATGAAATTGAATTTTGCAGAGATGCAACTCTGCACTATAACTCATGTACAACTGTCCCATTATAGGTCCTTTACCTACATAAAAAAC -s Anc2.Anc2refChr13 24526 95 + 96486 AGTTCCTAATGAAACTGAATTTTGCAGAAATGCAATTCTGCACTATAACTCATGTACAACTGTCCCATTATAGGTCCTTTGCCTACATAAAAAAC -s mr.mrrefChr5 242528 95 + 294540 AGATGTTGATGGAATTGAAACTCGCATGGATGGCACCCTGTACTATAGTTTATGTACCACCATCCCATTGTAGGTCCACCACCTACATAAAAAAC -s simCow_chr6.simCow.chr6 380456 92 + 602619 AGTTACTAATGAGAGTGGATCTTTCAGAAATGCAATTCTGTCCCA---CTCATGTATAACAGTACAATTATAGGTCCTTTGCCTTCATATAAAGC -s simDog_chr6.simDog.chr6 370967 95 + 593897 AGTTCATGATGGAACTGAAATTTGCGGGAATGCAATTCTGCACTTTAACTGATATGCAACTGTCCCATTATCAGTTGTTTGCCCACAGAAAAAAC -s simHuman_chr6.simHuman.chr6 374965 90 + 601863 AGTTGCCAATGAAGTTGAATTTTGCAGAGATGCAACTCTGCACTATAACTCATGTACAACTGTGCC----TAGGTCCTTAATCTACATAAAAAA- -s simRat_chr6.simRat.chr6 388643 95 + 647215 AGATGTTGATGGAATTGAACCTCACATGGATGGCACCCTGTACTATATTTTATGTACCACCATCCCATAATAGGTCGACCACCTACATAAAAAAC - -a -s simMouse_chr6.simMouse.chr6 388767 38 + 636262 TGATACATTCGTTTGTCTGTTTATCACCTTGTTTCAGT -s Anc0.Anc0refChr3 21301 38 + 222631 TTATTCCTTGGTTTGTCAAGTTATCATTACTTTTTATT -s Anc1.Anc1refChr6 50749 38 + 197743 TTATTCCTTGGTTTGTCAAGTTATCATTACTTTTTATT -s Anc2.Anc2refChr13 24622 38 + 96486 TTATTCCTTGGTTTGCCAAGTTATCATTACTTTTTATT -s mr.mrrefChr5 242623 38 + 294540 TGATACATTCGTTTGTCTGTTTATCACCATGTTTCAGT -s simCow_chr6.simCow.chr6 380549 38 + 602619 TTATAGCTTGGTTTGCCAGGTTACAATTACTTTCTTTT -s simDog_chr6.simDog.chr6 371063 38 + 593897 TTATTCCCTGGTACGCCAAATTATCATTACTTTTTATT -s simHuman_chr6.simHuman.chr6 375055 38 + 601863 TAATGCCTTGGTTTGTCAAGTGATCATTACTTTTTATT -s simRat_chr6.simRat.chr6 388738 37 + 647215 TGACACATTCATTTGACTGTTC-TCACCATGTTTCAGT - -a -s simMouse_chr6.simMouse.chr6 388805 16 + 636262 CATTTACTCCACTATG -s Anc0.Anc0refChr3 21357 16 + 222631 CACTCCCTTCATCACA -s Anc1.Anc1refChr6 50805 16 + 197743 CACTCCCTTCATCACA -s Anc2.Anc2refChr13 24678 16 + 96486 CACTCCCTTAGTCACA -s mr.mrrefChr5 242661 16 + 294540 CATTCACTCCACTATG -s simCow_chr6.simCow.chr6 380604 16 + 602619 CACTCTTTTAGTCAGA -s simDog_chr6.simDog.chr6 371119 16 + 593897 CATTTCCCTAGTCACA -s simHuman_chr6.simHuman.chr6 375111 16 + 601863 CACTCCCTTCATCACA -s simRat_chr6.simRat.chr6 388775 16 + 647215 CATTCACTCCACTATG - -a -s simMouse_chr6.simMouse.chr6 388821 8 + 636262 TCCTACAG -s Anc0.Anc0refChr3 21395 8 + 222631 TCTAACAG -s Anc1.Anc1refChr6 50843 8 + 197743 TCTAACAG -s Anc2.Anc2refChr13 24738 8 + 96486 TCTAACAG -s mr.mrrefChr5 242677 8 + 294540 TCCAACAG -s simCow_chr6.simCow.chr6 380667 8 + 602619 TGTAACAG -s simDog_chr6.simDog.chr6 371179 8 + 593897 TCTAACAG -s simHuman_chr6.simHuman.chr6 375149 8 + 601863 TCTAACAG -s simRat_chr6.simRat.chr6 388791 8 + 647215 TTCAACAG - -a -s simMouse_chr6.simMouse.chr6 388829 27 + 636262 AGAATATTCTGTGTAACATGAGTGATA -s Anc0.Anc0refChr3 21404 27 + 222631 AGAATATTCTGCTTAACATGAATGATA -s Anc1.Anc1refChr6 50852 27 + 197743 AGAATATTCTGCTTAACATGAATGATA -s Anc2.Anc2refChr13 24747 27 + 96486 AGGATATTCTGCTTAACATAAATAATA -s mr.mrrefChr5 242686 27 + 294540 AGAATATTCTGTTTAACATGAGTGATA -s simCow_chr6.simCow.chr6 380676 27 + 602619 AGCATATCCTGCTTAACATAATTAATA -s simDog_chr6.simDog.chr6 371188 27 + 593897 AGGATATTCTGCTTAACATAAAAAATA -s simHuman_chr6.simHuman.chr6 375158 27 + 601863 AGAATACTCTGCTTCACATGAATGATA -s simRat_chr6.simRat.chr6 388800 27 + 647215 AGAGTATTCTGTTTAACACGAGTGATA - -a -s simMouse_chr6.simMouse.chr6 388856 1 + 636262 T -s Anc0.Anc0refChr3 21431 1 + 222631 T -s Anc1.Anc1refChr6 50879 1 + 197743 T -s Anc2.Anc2refChr13 24774 1 + 96486 T -s mr.mrrefChr5 242713 1 + 294540 T -s simCow_chr6.simCow.chr6 380703 1 + 602619 T -s simDog_chr6.simDog.chr6 371220 1 + 593897 T -s simHuman_chr6.simHuman.chr6 375185 1 + 601863 T -s simRat_chr6.simRat.chr6 388827 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 388857 38 + 636262 TAAAAAATCCATGCTACTAAAAGGGTGACATTCATGGA -s Anc0.Anc0refChr3 21433 35 + 222631 CGAC---TCCATGCTAGCAAGAGGGTGTCATTCATAGA -s Anc1.Anc1refChr6 50881 35 + 197743 CGAC---TCCATGCTAGCAAGAGGGTGTCATTCATAGA -s Anc2.Anc2refChr13 24776 35 + 96486 CGAC---ACCATGCTAGCAAGATGATGTCATTCATACA -s mr.mrrefChr5 242714 35 + 294540 TAAC---TCCATGCTAGCAAAAGGGTGACATTCATGGA -s simCow_chr6.simCow.chr6 380705 35 + 602619 TGGC---ACCATGCTAGCAAGCTGATGTCATTCATACA -s simDog_chr6.simDog.chr6 371222 35 + 593897 CGAC---ACCATGCTAGTAAGATGATGTCATTCATACA -s simHuman_chr6.simHuman.chr6 375187 35 + 601863 CGAC---TCCATGCTAGCAAGAGGGTGTTGTTCATAGA -s simRat_chr6.simRat.chr6 388828 35 + 647215 TTAC---TCCATGCTAGCAAAATGGTGACATACATGGA - -a -s simMouse_chr6.simMouse.chr6 388895 22 + 636262 GTCAGATCAGGGATTTTGACGC -s Anc0.Anc0refChr3 21468 22 + 222631 CTCAGAACTGAAGTTTTAATTT -s Anc1.Anc1refChr6 50916 22 + 197743 CTCAGAACTGAAGTTTTAATTT -s Anc2.Anc2refChr13 24811 22 + 96486 CTCTGAACTGAAGTATTAATTT -s mr.mrrefChr5 242749 22 + 294540 CTCAGATCAGGGATTTTGATGC -s simCow_chr6.simCow.chr6 380740 22 + 602619 CCCTGATCATGAGGATTACTTT -s simDog_chr6.simDog.chr6 371261 22 + 593897 CTCTGAACTGAAATACTAAGTT -s simHuman_chr6.simHuman.chr6 375222 22 + 601863 CTCAGAACTGAAGTTTTAATTT -s simRat_chr6.simRat.chr6 388863 22 + 647215 CTCAGATCAGGGATTTTGATGC - -a -s simMouse_chr6.simMouse.chr6 388917 12 + 636262 CATATCGCCTGT -s Anc0.Anc0refChr3 21491 12 + 222631 CATAACCTATGT -s Anc1.Anc1refChr6 50939 12 + 197743 CATAACCTATGT -s Anc2.Anc2refChr13 24834 12 + 96486 CATAACCTATAT -s mr.mrrefChr5 242771 12 + 294540 CATATCCCCTGT -s simCow_chr6.simCow.chr6 380763 12 + 602619 CAAAGTCTATAT -s simDog_chr6.simDog.chr6 371284 12 + 593897 TTTAACCTATAT -s simHuman_chr6.simHuman.chr6 375245 12 + 601863 CATACCCTTTGT -s simRat_chr6.simRat.chr6 388885 12 + 647215 CATATCCCATGC - -a -s simMouse_chr6.simMouse.chr6 388929 31 + 636262 TTGTGTCTCTCCCATCTTGGGTCAAGCCCAC -s Anc0.Anc0refChr3 21503 31 + 222631 GATGGTCTCTCCCATCTTAGGTCAAGCTCAC -s Anc1.Anc1refChr6 50951 31 + 197743 GATGGTCTCTCCCATCTTAGGTCAAGCTCAC -s Anc2.Anc2refChr13 24847 31 + 96486 GATGGTCTCTCACATCTTAGGTGAAGCTCAC -s mr.mrrefChr5 242783 31 + 294540 TTGGGTCTCTCCCATCTTGGGTCAAGCCCAC -s simCow_chr6.simCow.chr6 380776 31 + 602619 GGTGGGCTTTCACATCTTAGGTTAAGCTCAG -s simDog_chr6.simDog.chr6 371298 30 + 593897 GACG-TCTCTCACATTGTAGGTGAAGCTGAC -s simHuman_chr6.simHuman.chr6 375257 31 + 601863 GATGGTCTCTACCATCTTAGGTCAAGCTCAC -s simRat_chr6.simRat.chr6 388897 31 + 647215 TTGGGTCTCTCCCATCTTGGGTCGAACCCGC - -a -s simMouse_chr6.simMouse.chr6 388960 15 + 636262 ATCCACTTGGCCCTT -s Anc0.Anc0refChr3 21534 11 + 222631 AT----TTGGACCTT -s Anc1.Anc1refChr6 50982 11 + 197743 AT----TTGGACCTT -s Anc2.Anc2refChr13 24878 11 + 96486 AT----TTGGACCTT -s mr.mrrefChr5 242814 15 + 294540 ATCCACTTGGCCCTT -s simCow_chr6.simCow.chr6 380807 11 + 602619 AC----TTGGACCTT -s simDog_chr6.simDog.chr6 371352 11 + 593897 AT----TTTGACCTT -s simHuman_chr6.simHuman.chr6 375288 11 + 601863 AT----TTGGACCTT -s simRat_chr6.simRat.chr6 388928 15 + 647215 ATCCATTTGGCCCTT - -a -s simMouse_chr6.simMouse.chr6 388975 10 + 636262 TTAGAGCTTA -s Anc0.Anc0refChr3 21545 10 + 222631 TTTGAACTCA -s Anc1.Anc1refChr6 50993 10 + 197743 TTTGAACTCA -s Anc2.Anc2refChr13 24889 10 + 96486 TTTGAACTCA -s mr.mrrefChr5 242829 10 + 294540 TTAGAGCTCA -s simCow_chr6.simCow.chr6 380830 10 + 602619 GGTTTACTCA -s simDog_chr6.simDog.chr6 371363 10 + 593897 TTTGAACTCA -s simHuman_chr6.simHuman.chr6 375299 9 + 601863 TTTGAA-TCA -s simRat_chr6.simRat.chr6 388943 10 + 647215 TTAGAGCTCA - -a -s simMouse_chr6.simMouse.chr6 388985 32 + 636262 GTGTATCTTAGGTTCACCACTCCCACTAAAGA -s Anc0.Anc0refChr3 21555 22 + 222631 GGTTATCT-AGGCTTCCT--T-------AACA -s Anc1.Anc1refChr6 51003 22 + 197743 GGTTATCT-AGGCTTCCT--T-------AACA -s Anc2.Anc2refChr13 24900 22 + 96486 GGTTATCT-AGGCTTCCT--T-------AACA -s mr.mrrefChr5 242839 29 + 294540 GTTTATCT-AGGTTCACC--TCCCACTAAAGA -s simCow_chr6.simCow.chr6 380841 22 + 602619 CATTATGT-AGGCTTCCT--T-------AACA -s simDog_chr6.simDog.chr6 371374 22 + 593897 GGTTACCT-AGGGTTCCT--T-------AACA -s simHuman_chr6.simHuman.chr6 375308 22 + 601863 GGTTATCT-AGGCTTCCT--T-------AACA -s simRat_chr6.simRat.chr6 388953 29 + 647215 GTTTATCA-AAGTTCACC--TCCCACTAAAGA - -a -s simMouse_chr6.simMouse.chr6 389017 7 + 636262 GATTCTA -s Anc0.Anc0refChr3 21577 7 + 222631 AGATCTA -s Anc1.Anc1refChr6 51025 7 + 197743 AGATCTA -s Anc2.Anc2refChr13 24922 7 + 96486 AGAACTA -s mr.mrrefChr5 242868 7 + 294540 AATTCTA -s simCow_chr6.simCow.chr6 380863 7 + 602619 AGGACTA -s simDog_chr6.simDog.chr6 371398 7 + 593897 AGAACCA -s simHuman_chr6.simHuman.chr6 375330 7 + 601863 AGATCTA -s simRat_chr6.simRat.chr6 388982 7 + 647215 AATTCTA - -a -s simMouse_chr6.simMouse.chr6 389024 7 + 636262 CTACCTA -s Anc0.Anc0refChr3 21584 7 + 222631 CTGCGCA -s Anc1.Anc1refChr6 51032 7 + 197743 CTGCGCA -s Anc2.Anc2refChr13 24929 7 + 96486 CTGTGCA -s mr.mrrefChr5 242875 7 + 294540 CTACCTA -s simCow_chr6.simCow.chr6 380871 7 + 602619 CTGTCCA -s simDog_chr6.simDog.chr6 371405 7 + 593897 GTGTGCA -s simHuman_chr6.simHuman.chr6 375337 7 + 601863 CTGCGCA -s simRat_chr6.simRat.chr6 388989 7 + 647215 CTACCAA - -a -s simMouse_chr6.simMouse.chr6 389031 90 + 636262 GAGAACATGTAAAGCAAGGGCCATAGCTAATGTTCTGTTCTGCCTCCCATGCAATGTTTAACTGAATTCACAATTGGGAATGCAACTGAA -s Anc0.Anc0refChr3 21592 85 + 222631 ATTGGTATGTGAGGCCAGGGCTATAGCTGATGTTTTG-----CCTTCCATCCAAGGTTTAACTGAATTCACAGCTAGGAACTCAACTTGA -s Anc1.Anc1refChr6 51040 90 + 197743 ATTGGTATGTGAGGCCAGGGCTATAGCTGATGTTTTGTTTCGCCTTCCATCCAAGGTTTAACTGAATTCACAGCTAGGAACTCAACTTGA -s Anc2.Anc2refChr13 24937 85 + 96486 ATTGGCATGTGAGGCCAGAGCTCTAGCTGATGTTTTG-----CCTTCCATCCAAGGTTTAACTGAGTTCACAGCTACGAAGTGTACTTGC -s mr.mrrefChr5 242882 90 + 294540 GTGAGTATGTAAGGCAAGGGCTATAGCTAATGTTCTGTTCCGCCTTCCATGCAATGTTTAACTGAATTCACAACTGGGAACTCAACTGAA -s simCow_chr6.simCow.chr6 380879 85 + 602619 ATTGGCATATGAGGCTAGAACTGTAGTTGATGTTTTT-----CCTTCCACCTAAGGTTTAGCTAAGTTCACAGTTATGAAGTATACTAGC -s simDog_chr6.simDog.chr6 371413 83 + 593897 ATTGGCAAGTGAGGCCAGAGTTCTAGCTATTGTTTTG-----CCTCACATCCAAGGTTTAACTGAGTTCACAGCTACGGAGTGTACTT-- -s simHuman_chr6.simHuman.chr6 375345 90 + 601863 ATTGGTATGTGAGGCCAGGGCTATAGCTCATGTGATGTTTCACCTTCCATCCAAGGTTTATCTGAACTCACAGCTAGGAACTCAACTTGA -s simRat_chr6.simRat.chr6 388996 85 + 647215 GTGAGTGTGTAAGGCAAGGTCTATAGCTAATATTC-----CGCCTTCCTTGCAATGTTTAACTGACTTCACAACTGGGAACTCAACTGAA - -a -s simMouse_chr6.simMouse.chr6 389121 16 + 636262 CTAATACCTACAACAC -s Anc0.Anc0refChr3 21677 16 + 222631 TTGATACTCTCAATGA -s Anc1.Anc1refChr6 51130 16 + 197743 TTGATACTCTCAATGA -s Anc2.Anc2refChr13 25022 16 + 96486 TTGATACTCTCAATGA -s mr.mrrefChr5 242972 16 + 294540 CTAATACCTACAACGC -s simCow_chr6.simCow.chr6 380964 16 + 602619 TTGATACCCTCAACAA -s simDog_chr6.simDog.chr6 371496 9 + 593897 -------TCTCAATGA -s simHuman_chr6.simHuman.chr6 375435 16 + 601863 TTGATACTCTCAATGA -s simRat_chr6.simRat.chr6 389083 16 + 647215 CTAATACCTCCAACGC - -a -s simMouse_chr6.simMouse.chr6 389137 11 + 636262 CAACATAATCA -s Anc0.Anc0refChr3 21695 11 + 222631 CAACATAATTA -s Anc1.Anc1refChr6 51148 11 + 197743 CAACATAATTA -s Anc2.Anc2refChr13 25040 11 + 96486 CAACATAATTA -s mr.mrrefChr5 242988 11 + 294540 CAACATAATCA -s simCow_chr6.simCow.chr6 380982 11 + 602619 CAGCATGATTT -s simDog_chr6.simDog.chr6 371507 11 + 593897 CAACATAACTA -s simHuman_chr6.simHuman.chr6 375453 11 + 601863 CAACATAATTA -s simRat_chr6.simRat.chr6 389099 11 + 647215 CTACATAGTCA - -a -s simMouse_chr6.simMouse.chr6 389148 7 + 636262 TCAGCTG -s Anc0.Anc0refChr3 21706 7 + 222631 TCAGCTA -s Anc1.Anc1refChr6 51159 7 + 197743 TCAGCTA -s Anc2.Anc2refChr13 25052 7 + 96486 TCTGCTA -s mr.mrrefChr5 242999 7 + 294540 TCAGCTG -s simCow_chr6.simCow.chr6 380994 7 + 602619 CCTGCCA -s simDog_chr6.simDog.chr6 371519 7 + 593897 TCTGCTA -s simHuman_chr6.simHuman.chr6 375464 7 + 601863 TCAGCTA -s simRat_chr6.simRat.chr6 389110 6 + 647215 TCAACT- - -a -s simMouse_chr6.simMouse.chr6 389155 21 + 636262 CTAGGTATGTCTTTGAGTTAT -s Anc0.Anc0refChr3 21713 20 + 222631 T-AGGTATGTCTTTGTGTTAT -s Anc1.Anc1refChr6 51166 21 + 197743 TTAGGTATGTCTTTGTGTTAT -s Anc2.Anc2refChr13 25059 20 + 96486 T-AGGTATATCTTTGTGTTAT -s mr.mrrefChr5 243006 21 + 294540 CTAGGTATGTCTTTGAGTTAT -s simCow_chr6.simCow.chr6 381003 20 + 602619 T-AGGTATATCTTTGTGTTAC -s simDog_chr6.simDog.chr6 371526 20 + 593897 T-AGGTAGATCTTTATGTCGT -s simHuman_chr6.simHuman.chr6 375471 21 + 601863 TTAGATATGGCTTTGTGTTAT -s simRat_chr6.simRat.chr6 389116 19 + 647215 --AGGTATATCTTTGAGTTAT - -a -s simMouse_chr6.simMouse.chr6 389176 20 + 636262 GTCCTTGATCAGCTCCCTGG -s Anc0.Anc0refChr3 21733 20 + 222631 TGCCCTGAACAGTACCCTAG -s Anc1.Anc1refChr6 51187 20 + 197743 TGCCCTGAACAGTACCCTAG -s Anc2.Anc2refChr13 25079 20 + 96486 TGCCCTGAACACTATCCCAA -s mr.mrrefChr5 243027 20 + 294540 GTCCTTGATCAGCTCCCTGG -s simCow_chr6.simCow.chr6 381023 15 + 602619 TTCCTTG-----TATCCCAA -s simDog_chr6.simDog.chr6 371546 20 + 593897 TGCCCTGAACACTATCCCAA -s simHuman_chr6.simHuman.chr6 375492 20 + 601863 TGCCCCGAACAGTACTCTAG -s simRat_chr6.simRat.chr6 389137 20 + 647215 GTCCTTGATCAGCTCCCTGG - -a -s simMouse_chr6.simMouse.chr6 389196 68 + 636262 TGAATGCTCCCTGGTGAATTTAGGAGGGTGAGTATGTCCGGGAGGACTATTTAGCAGTTCAATCATTG -s Anc0.Anc0refChr3 21753 53 + 222631 TGGA-----CTGAGGGGATG--------TGAATATCTTAAG--GGTCTGTTCACTAGTCTAGTCATTG -s Anc1.Anc1refChr6 51207 53 + 197743 TGGA-----CTGAGGGGATG--------TGAATATCTTAAG--GGTCTGTTCACTAGTCTAGTCATTG -s Anc2.Anc2refChr13 25099 53 + 96486 TGGA-----CTGAGGGGATG--------TAAACATCTTAAG--GGTCTGTTCACTAGTCTAGTCATTG -s mr.mrrefChr5 243047 60 + 294540 TGAATGCTCCCTGGTGAATT--------TGAGTATGTCCGGGAGGACTATTCAGCAGTTCAATCATTG -s simCow_chr6.simCow.chr6 381039 53 + 602619 AGGG-----CAGAGGGGCTG--------TAATGATCTTAAG--GGTCTGCTCACCAGTCTAGTCATCG -s simDog_chr6.simDog.chr6 371566 53 + 593897 TGCA-----TTGAGGGGACG--------CAAACATTTTAAG--GGTCTGTTCATTAGTTTTGTCATTG -s simHuman_chr6.simHuman.chr6 375512 53 + 601863 TGGA-----CTGAGAAGATG--------TGAATATCTTAAG--GGTGTGTTCACGAGTCTAGTCATTG -s simRat_chr6.simRat.chr6 389157 60 + 647215 TGAATGCTCCCTGGTGAACT--------TGCGTACGTCCCGGAGGACTATTCAACAGTTCAAACAGTG - -a -s simMouse_chr6.simMouse.chr6 389264 6 + 636262 CTCAGT -s Anc0.Anc0refChr3 21806 6 + 222631 GTCAGT -s Anc1.Anc1refChr6 51260 6 + 197743 GTCAGT -s Anc2.Anc2refChr13 25152 6 + 96486 GTCAGT -s mr.mrrefChr5 243107 6 + 294540 CTCAGT -s simCow_chr6.simCow.chr6 381092 6 + 602619 TTAAGT -s simDog_chr6.simDog.chr6 371619 6 + 593897 GTCAAT -s simHuman_chr6.simHuman.chr6 375565 6 + 601863 GTCAGT -s simRat_chr6.simRat.chr6 389218 6 + 647215 CTTAGT - -a -s simMouse_chr6.simMouse.chr6 389270 17 + 636262 ATTGCACACCTGTAAGT -s Anc0.Anc0refChr3 21812 13 + 222631 ATTTCACACCTGA---- -s Anc1.Anc1refChr6 51266 13 + 197743 ATTTCACACCTGA---- -s Anc2.Anc2refChr13 25158 13 + 96486 ATTTCACACTTGA---- -s mr.mrrefChr5 243113 17 + 294540 ATTGCACACCTGTAAGT -s simCow_chr6.simCow.chr6 381100 13 + 602619 ATTTCACACATGA---- -s simDog_chr6.simDog.chr6 371625 13 + 593897 ATTTCACATTTGA---- -s simHuman_chr6.simHuman.chr6 375571 13 + 601863 ATTTCACACCCGA---- -s simRat_chr6.simRat.chr6 389224 17 + 647215 ATTGCACACCTCTATAT - -a -s simMouse_chr6.simMouse.chr6 389287 6 + 636262 TCAAAA -s Anc0.Anc0refChr3 21825 6 + 222631 TCAAAG -s Anc1.Anc1refChr6 51279 6 + 197743 TCAAAG -s Anc2.Anc2refChr13 25171 6 + 96486 TCAAAG -s mr.mrrefChr5 243130 6 + 294540 TCAAAG -s simCow_chr6.simCow.chr6 381113 6 + 602619 TCAAAG -s simDog_chr6.simDog.chr6 371647 6 + 593897 TCAAAG -s simHuman_chr6.simHuman.chr6 375584 6 + 601863 TCAAGG -s simRat_chr6.simRat.chr6 389241 6 + 647215 TCAAAG - -a -s simMouse_chr6.simMouse.chr6 389293 27 + 636262 ATCCATTTTTTTTCTGCCACTCGGTAT -s Anc0.Anc0refChr3 21831 23 + 222631 TTGCATGGAGT----ACCATTTAATTT -s Anc1.Anc1refChr6 51285 23 + 197743 TTGCATGGAGT----ACCATTTAATTT -s Anc2.Anc2refChr13 25177 23 + 96486 TTGCATGGAGT----ATGATTTCATTT -s mr.mrrefChr5 243136 27 + 294540 ATCCATTTTTTTTCTGCCACTCAGTAT -s simCow_chr6.simCow.chr6 381119 22 + 602619 TCGCATGGAGT----AT-ATTTGCTTT -s simDog_chr6.simDog.chr6 371653 23 + 593897 TTGCATAGAGT----ATGATTTCATTT -s simHuman_chr6.simHuman.chr6 375590 23 + 601863 TTACATGAAGT----ACCATTTATTCT -s simRat_chr6.simRat.chr6 389340 27 + 647215 ATCCATTTTTTTTCTGCCACTCAGTAT - -a -s simMouse_chr6.simMouse.chr6 389320 61 + 636262 TCTTCTGCCATTTAGATAAGACCAACCCAGCATGCAAAGAGTGACTGGTACGTGATTTGAG -s Anc0.Anc0refChr3 21854 60 + 222631 TCTTCTGCCACT-ATGGAGGACCTACCTGGCATGTAAAGAGTGGCTGGCTTGTGATTTGAA -s Anc1.Anc1refChr6 51308 60 + 197743 TCTTCTGCCACT-ATGGAGGACCTACCTGGCATGTAAAGAGTGGCTGGCTTGTGATTTGAA -s Anc2.Anc2refChr13 25200 60 + 96486 CCTTCTGCTACT-TTGGGGGACCTACCTGATATGTGAAGAGTGGCAGCCTTGTGATTTGAA -s mr.mrrefChr5 243163 61 + 294540 TCTTCTGCCATTTAGATAAGACCAACCTGGCATGCAAAGAGTGACTGGTATGTGATTTGAG -s simCow_chr6.simCow.chr6 381141 59 + 602619 CACTCTGCTACT-TTGGGAGACCTACATG-TGTGTGAAGCGTGGTGGCTTTGTGACTTGAA -s simDog_chr6.simDog.chr6 371676 60 + 593897 CCTTCCGCTACT-TTGGGGCACCTACCTGATATGTGAAGAGTTGCAGCCTTGTGATTTGAA -s simHuman_chr6.simHuman.chr6 375613 60 + 601863 TCTTCTGCCACT-ATGGAGGACCTACCTGGCATGTAAAGAATGGATGGATTGTGATTCAAC -s simRat_chr6.simRat.chr6 389381 61 + 647215 TCTTTTGCTGTTTAAATAAGATCAGCCTGGCATGCAAAGAGTCACAGATATGTGAATTGGG - -a -s simMouse_chr6.simMouse.chr6 389381 8 + 636262 ATCAAGGA -s Anc0.Anc0refChr3 21914 8 + 222631 ATGTTGGA -s Anc1.Anc1refChr6 51368 8 + 197743 ATGTTGGA -s Anc2.Anc2refChr13 25261 8 + 96486 ATGTTGGA -s mr.mrrefChr5 243224 8 + 294540 ATCTAGGA -s simCow_chr6.simCow.chr6 381201 8 + 602619 ATGTTGGA -s simDog_chr6.simDog.chr6 371737 8 + 593897 ATGGTGAA -s simHuman_chr6.simHuman.chr6 375673 8 + 601863 ATGTTGGA -s simRat_chr6.simRat.chr6 389442 8 + 647215 ATCTAGGA - -a -s simMouse_chr6.simMouse.chr6 389389 52 + 636262 CTGTGCTACCTTGACTGTCTGCTTCCACCTTGTTTGTAGTTGTCATGACGAC -s Anc0.Anc0refChr3 21922 52 + 222631 GTGTGCTATCTTGTCTGTCTCCTTCCACCTTACTTACAGTTGACTTGGAGAG -s Anc1.Anc1refChr6 51376 52 + 197743 GTGTGCTATCTTGTCTGTCTCCTTCCACCTTACTTACAGTTGACTTGGAGAG -s Anc2.Anc2refChr13 25269 52 + 96486 GTATGCCATCTTGTCTGTCTCCTTCCACCTTACTTACAGTTGACTTGGAGAG -s mr.mrrefChr5 243232 52 + 294540 CTGTGCTACCTTGTCTGTCTGCTTCCACCTTGCTTGTAGTTGTCATGACGAC -s simCow_chr6.simCow.chr6 381210 52 + 602619 GTATGCCAGCTTGTCTGTCTCCTTCCACATTACAGACAATTTACTAGGGGAG -s simDog_chr6.simDog.chr6 371745 52 + 593897 GTATGCCATCTGCTCTGTCTCCTTCCACCTTTATTGCAGTTGACTTGGAGAG -s simHuman_chr6.simHuman.chr6 375681 52 + 601863 TTGTGCTGACCTGTCGGTCTCCTTCCAGGTTACTTACAGTTGATGTGGAGAG -s simRat_chr6.simRat.chr6 389450 52 + 647215 CTGTACCACCTCTTCTGTCTGGTTTCACCTTGCTCGTAGTTGTCATTATGAT - -a -s simMouse_chr6.simMouse.chr6 389441 69 + 636262 GTCACCCCTTGATATACTTCAAGAATAGATTTAATATTCACTTTAGTCTTCCCCTTCAGCCTAAAAGCT -s Anc0.Anc0refChr3 21974 68 + 222631 GTCACCCTGTGATATACTACAATAACAGATCCTCTATTTATGTCAGTCTTTCCTTTCAGCCTAAAAA-C -s Anc1.Anc1refChr6 51428 69 + 197743 GTCACCCTGTGATATACTACAATAACAGATCCTCTATTTATGTCAGTCTTTCCTTTCAGCCTAAAAAAC -s Anc2.Anc2refChr13 25324 68 + 96486 GTCACCCTGTGATATACTATAATAACAGATCCTCTATTTATGTCAGTCTTTCCTTTCAGCCTAAAAA-C -s mr.mrrefChr5 243284 69 + 294540 GTCACCCCTTGATATACTTCAATAATAGATTTAATATTCACTTCAGTCTTTCCCTTCAGCCTAAAAGCT -s simCow_chr6.simCow.chr6 381265 62 + 602619 GTCACACCTCAATATGCT------ACAGGTCCTCTATTCAAGTCAGCCTTTCCTTTCGCCCAAAAAA-C -s simDog_chr6.simDog.chr6 371800 68 + 593897 GTCACCCTGTGAGATATTATAATAATAGATCCTCTCTTTGTGTCAGTCTTTCCTTTTAGCGTGAAAA-C -s simHuman_chr6.simHuman.chr6 375733 61 + 601863 AT--------GATGTACTGCAATAACAGATCGTCTATTTATGTCAGTCTTTCCTTTCAGCCCTAAAAAC -s simRat_chr6.simRat.chr6 389502 69 + 647215 GTCACCCCTTGATATACTTCAATAATAGATTTAATATTGACTTCAGTCTTTCCCTTCTGCCTAAAAGCT - -a -s simMouse_chr6.simMouse.chr6 389510 20 + 636262 TCTTAGAGTTCAACACTGTT -s Anc0.Anc0refChr3 22042 20 + 222631 TCTCAGAGTTCAATCCTGTT -s Anc1.Anc1refChr6 51497 20 + 197743 TCTCAGAGTTCAATCCTGTT -s Anc2.Anc2refChr13 25392 20 + 96486 TCTCAGAGCTCAATCCTGTT -s mr.mrrefChr5 243353 20 + 294540 TCTCAGAGTTCAACACTGTT -s simCow_chr6.simCow.chr6 381327 20 + 602619 TCTCAGAGCTCAATCCTGTT -s simDog_chr6.simDog.chr6 371869 20 + 593897 ACCCAGAGCTCAATCCTGTT -s simHuman_chr6.simHuman.chr6 375794 20 + 601863 TCTCAGAGTTCAATCCCGTT -s simRat_chr6.simRat.chr6 389571 20 + 647215 TCTCAGAGTTCAACTCTGTT - -a -s simMouse_chr6.simMouse.chr6 389530 4 + 636262 TACT -s Anc0.Anc0refChr3 22062 4 + 222631 TTAT -s Anc1.Anc1refChr6 51517 4 + 197743 TTAT -s Anc2.Anc2refChr13 25412 4 + 96486 TTAT -s mr.mrrefChr5 243373 4 + 294540 TTCT -s simCow_chr6.simCow.chr6 381347 4 + 602619 TTAT -s simDog_chr6.simDog.chr6 371903 4 + 593897 TTTT -s simHuman_chr6.simHuman.chr6 375814 4 + 601863 CTAT -s simRat_chr6.simRat.chr6 389591 4 + 647215 TTCT - -a -s simMouse_chr6.simMouse.chr6 389534 51 + 636262 CTACTGTAAATACCCTGCCACCTGTTTGTTTGGCTCTGGCTACCATGTGTT -s Anc0.Anc0refChr3 22068 51 + 222631 CTACAGTAGACACCCTGCCACTTATTTATCTGGCTCTGGCGGTCATATGCA -s Anc1.Anc1refChr6 51523 51 + 197743 CTACAGTAGACACCCTGCCACTTATTTATCTGGCTCTGGCGGTCATATGCA -s Anc2.Anc2refChr13 25418 51 + 96486 CTACAGTAGGCACCTTACCACTTATTTATCTGGCTCTGGCGGTCATAGGCA -s mr.mrrefChr5 243377 51 + 294540 CTACTGTAAATACCCTGCCACCTATTTGTTTGGCTCTGGCTACCATGTGTT -s simCow_chr6.simCow.chr6 381353 51 + 602619 CTACAGTAGCCACATTACCACTTATATATCTGGCTCTGGCAGTCAGACGCA -s simDog_chr6.simDog.chr6 371909 51 + 593897 CTACGGTAGGCACCTTACCACTTACTTATCTGGCTCTGGTGACCATAGGCA -s simHuman_chr6.simHuman.chr6 375820 50 + 601863 CTACAGTATACACCCTGCC-CTTATTTATCTGGCTCTGACCGTCACATTCA -s simRat_chr6.simRat.chr6 389595 36 + 647215 CTACTTTAGATACCCTGCCACCTATTTGTTTAGCTT--------------- - -a -s simMouse_chr6.simMouse.chr6 389585 30 + 636262 CAAACTTCAAGTTGAGTCTGAGAAGTCATT -s Anc0.Anc0refChr3 22119 14 + 222631 CAAATT---A-------------AGTCATT -s Anc1.Anc1refChr6 51574 22 + 197743 CAAATT---AGTT---TTTGG--AGTCATT -s Anc2.Anc2refChr13 25469 14 + 96486 CATATT---A-------------AGTCATT -s mr.mrrefChr5 243428 27 + 294540 CAAACT---AGTTGAGTCTGAGAAGTCATT -s simCow_chr6.simCow.chr6 381421 14 + 602619 TATAGT---A-------------AGTCATT -s simDog_chr6.simDog.chr6 371960 14 + 593897 CATATT---A-------------AGTCATT -s simHuman_chr6.simHuman.chr6 375870 15 + 601863 CAAATT---AGTT---TTTGG--------- -s simRat_chr6.simRat.chr6 389631 21 + 647215 ---------AGTTGAGTCTGAGAAGTCATT - -a -s simMouse_chr6.simMouse.chr6 389615 20 + 636262 CTAAGATACTATTTATACAA -s Anc0.Anc0refChr3 22133 20 + 222631 CTAATTCACTATTTATTGAA -s Anc1.Anc1refChr6 51596 20 + 197743 CTAATTCACTATTTATTGAA -s Anc2.Anc2refChr13 25484 20 + 96486 CTAATTCACTATTTATTGGA -s mr.mrrefChr5 243455 20 + 294540 CTAAGATACTATTTATTGAA -s simCow_chr6.simCow.chr6 381436 14 + 602619 CTCACTCACTATTC------ -s simDog_chr6.simDog.chr6 371975 20 + 593897 CTAATTCTCTATTTATTGGA -s simHuman_chr6.simHuman.chr6 375885 19 + 601863 -TATAGAACACTTTATTGAA -s simRat_chr6.simRat.chr6 389652 20 + 647215 CTAAGATATTATTTATTGGA - -a -s simMouse_chr6.simMouse.chr6 389635 140 + 636262 CATGGGCGAATTCTCCAAAAGTAAGTTTAATTCTCTGTCACTCATGTGCTCCTGCTGTGAAATGATGGTGCTGATGGTGATCCATGCTGTGGAACAATGGGGCTCATGGTGTGCTACATCCAGAACCGCCCAATGCTCTC -s Anc0.Anc0refChr3 22153 93 + 222631 CATGGGTGAATTTCCAAATAGCCAGGTTAATTCTGCGTCACTCATGTGCTCCTGTGGC--------------------------------------ATTGAGATCATGGTGATCTACATCCAGAACTGCCC--------- -s Anc1.Anc1refChr6 51616 93 + 197743 CATGGGTGAATTTCCAAATAGCCAGGTTAATTCTGCGTCACTCATGTGCTCCTGTGGC--------------------------------------ATTGAGATCATGGTGATCTACATCCAGAACTGCCC--------- -s Anc2.Anc2refChr13 25504 93 + 96486 CATGGGTGAATTTCCAAATAGCCATGTTGCTTCTGCGTCACTCATGTGCTCCTGTGGC--------------------------------------ATTGAGATCATGGTGATCTACATCCAGAATTGCCC--------- -s mr.mrrefChr5 243475 140 + 294540 CATGGGTGAATTCTCCAAAAGTCAGTTTAATTCTCTGTCACTCATGTGCTCCTGCTGTGAAATGATGGTGCTGATGGTGATCCATGCTGTGGAACAATGGGGCTCATGGTGTGCTACATCCAGAACTGCCCAATGCTCTC -s simCow_chr6.simCow.chr6 381450 91 + 602619 --TAGATGGATTCACAAATAGCCATGTTGTTTCTCTGTCCCCCATGTGCTCCTGTGAC--------------------------------------AGTGAGATAAAGGTGATCTACATCCAGGAGTGCCC--------- -s simDog_chr6.simDog.chr6 371996 83 + 593897 CATGGGTGAATTTCCA------CATGTTGCTTCTGCGTCACTCATGTGCTCATGCGGC--------------------------------------ATTAGGATCATTGTGACCT----CAACAATTGCTC--------- -s simHuman_chr6.simHuman.chr6 375904 93 + 601863 CATGGGTGAATCTCCAAACAGGCAGGTTAATTCTGCATCACTCACATACTCCTGTGGC--------------------------------------ATAGAGATGATGGTGATCTACATCCAGAACTACCC--------- -s simRat_chr6.simRat.chr6 389672 140 + 647215 TTTGGGTGAATTCTCCAAAGGTCAGTTTAATTCTCTGTCACTCATGTGCTCCTGCTGTGAAATGATGGTGCTGATGGTGATCCACGCTGCAAAACAGTGGTGTTCGTGGTGAACTACATCCAAGACTGCCCAACGCTCTC - -a -s simMouse_chr6.simMouse.chr6 389775 111 + 636262 AGTTCTTGGTCGTAGGTGCACTCAATTCTTGTTTGTGACTTCCCTTTTTTGGTGGAGTTACTGCACTTTGTAATTCTAACATATGGTAAGAGCAGGCAGACTATGACAATA -s Anc0.Anc0refChr3 22246 97 + 222631 --------------GGTGCACTTAGTTTTTGTTCCTAATTTCCCTCTTGTAATGTAGTTACTGCACTTGATACTTCTAACATAGGTTAATACATAGCAGGCTGTGAATATG -s Anc1.Anc1refChr6 51709 97 + 197743 --------------GGTGCACTTAGTTTTTGTTCCTAATTTCCCTCTTGTAATGTAGTTACTGCACTTGATACTTCTAACATAGGTTAATACATAGCAGGCTGTGAATATG -s Anc2.Anc2refChr13 25597 97 + 96486 --------------TGTGCACTTAGATTTTGTTCCTAGTTTCCCTCTTGCAATGTAGTTACTTCACTTGATACTTCCAACACAGGTTAATACATAGCAGGCTGTGAATAAG -s mr.mrrefChr5 243615 111 + 294540 AGTTCTTGGTCGTAGGTGCACTCAATTCTTGTTTGTGACTTCCCTTTTTTGGTGGAGTTACTGCACTTTGTAATTCTAACATATGTTAAGAGCTGGCAGGCTATGACAATA -s simCow_chr6.simCow.chr6 381541 92 + 602619 --------------TGTGCACTTAGGTCTTGATCCTAGTTATCCTCTTTCAATGT-----CTTTTCTTATTACTTCCAACACAGGTGAATACATAGCAGTCAATGAATTGG -s simDog_chr6.simDog.chr6 372079 90 + 593897 --------------TGCACACTTAGACTTTGTTACTGGTTTCCCTGTTGCTATGAAGTTACTTCAATTGATACTTCCAA-------TGATGCATGGCAGGATGCAAAAAAG -s simHuman_chr6.simHuman.chr6 375997 97 + 601863 --------------GGTGCACTTAGTTTTCGTTCATAATTCCCCTCTTCTAATGTAATTACTGCACTTGATACTTCTGACATAGTTTAATACATAACAGGCTGTGAATATG -s simRat_chr6.simRat.chr6 389813 96 + 647215 AGTTCTTGCCCTTAGGTGCAC-AAATTCTTGTTTGTGACTTCCCTTTTTTGGTGG--------------GTAATTCTAATATGTGTTAAGAGCTGTCAGGCTATGAGAATA - -a -s simMouse_chr6.simMouse.chr6 389886 32 + 636262 TGTACTGGCCATTTGGAAAAGGTCTGTGAACG -s Anc0.Anc0refChr3 22344 32 + 222631 TATACTGGCCATTGGCCAAAGGTCTGCCAACA -s Anc1.Anc1refChr6 51807 32 + 197743 TATACTGGCCATTGGCCAAAGGTCTGCCAACA -s Anc2.Anc2refChr13 25695 32 + 96486 TAAACTGCCCATTGCCCAAAGGTCTGCCAAGA -s mr.mrrefChr5 243726 32 + 294540 TGTACTGGCCATTTGGAAAAGGTCTGTCAACG -s simCow_chr6.simCow.chr6 381634 30 + 602619 TAAACTGCCCATTGCCAAAAGGTCTTCAAA-- -s simDog_chr6.simDog.chr6 372170 32 + 593897 TAAACTGCCCATTGCCCAAAGGTCTGCCAAGA -s simHuman_chr6.simHuman.chr6 376095 31 + 601863 TATGCTGGCTATT-GTCAAAGGTCTGCCAACA -s simRat_chr6.simRat.chr6 389909 32 + 647215 TGTACTGGACATTTGCAAAAGGTCTGTCAATG - -a -s simMouse_chr6.simMouse.chr6 389918 13 + 636262 ATCCTCTAGCTAC -s Anc0.Anc0refChr3 22385 12 + 222631 GTCCT-TAGCTAA -s Anc1.Anc1refChr6 51848 12 + 197743 GTCCT-TAGCTAA -s Anc2.Anc2refChr13 25736 12 + 96486 GTCCC-AAGCCAA -s mr.mrrefChr5 243758 13 + 294540 ATCCTCTAGCTAC -s simCow_chr6.simCow.chr6 381667 11 + 602619 ATCTC-AAG-CAA -s simDog_chr6.simDog.chr6 372216 12 + 593897 GTCCC-AAGCCAA -s simHuman_chr6.simHuman.chr6 376135 12 + 601863 GTCCT-TAGGTAA -s simRat_chr6.simRat.chr6 389941 13 + 647215 ATCCTCTAGCCTC - -a -s simMouse_chr6.simMouse.chr6 389931 5 + 636262 AATGA -s Anc0.Anc0refChr3 22398 5 + 222631 AAAAA -s Anc1.Anc1refChr6 51861 5 + 197743 AAAAA -s Anc2.Anc2refChr13 25749 5 + 96486 ACAAA -s mr.mrrefChr5 243771 5 + 294540 AATGA -s simCow_chr6.simCow.chr6 381679 5 + 602619 ACAAA -s simDog_chr6.simDog.chr6 372229 5 + 593897 ACCAA -s simHuman_chr6.simHuman.chr6 376148 5 + 601863 AAAAA -s simRat_chr6.simRat.chr6 389954 5 + 647215 AATGA - -a -s simMouse_chr6.simMouse.chr6 389936 14 + 636262 TTTCTGATCCTAAT -s Anc0.Anc0refChr3 22403 14 + 222631 TTTCTAGTCCTAAT -s Anc1.Anc1refChr6 51866 14 + 197743 TTTCTAGTCCTAAT -s Anc2.Anc2refChr13 25758 14 + 96486 TTTCTAGTCCTAGT -s mr.mrrefChr5 243776 14 + 294540 TTTCTGATCCTAAT -s simCow_chr6.simCow.chr6 381688 14 + 602619 TTTCTAATCCTACT -s simDog_chr6.simDog.chr6 372238 14 + 593897 TTTCTGGTTCTAGT -s simHuman_chr6.simHuman.chr6 376153 14 + 601863 TTTCTACTCGTAAC -s simRat_chr6.simRat.chr6 389959 10 + 647215 TTTC----CCTAAT - -a -s simMouse_chr6.simMouse.chr6 389950 19 + 636262 GAACCCAACAATGACATTA -s Anc0.Anc0refChr3 22418 19 + 222631 TAACCTAACGATGAGATCA -s Anc1.Anc1refChr6 51881 19 + 197743 TAACCTAACGATGAGATCA -s Anc2.Anc2refChr13 25773 19 + 96486 TAACCTAATGATGAGATCA -s mr.mrrefChr5 243790 19 + 294540 TAACCCAACAATGACATTA -s simCow_chr6.simCow.chr6 381703 19 + 602619 TAACTTAATAGTTAGATCA -s simDog_chr6.simDog.chr6 372253 19 + 593897 AAACCTAATGATGAGATCA -s simHuman_chr6.simHuman.chr6 376168 19 + 601863 TAACCTAACGATGATATCA -s simRat_chr6.simRat.chr6 389969 19 + 647215 TAATCCAACAATGACATTA - -a -s simMouse_chr6.simMouse.chr6 389969 6 + 636262 CTTTTA -s Anc0.Anc0refChr3 22444 6 + 222631 CTTTTA -s Anc1.Anc1refChr6 51907 6 + 197743 CTTTTA -s Anc2.Anc2refChr13 25799 6 + 96486 CTTTTA -s mr.mrrefChr5 243809 6 + 294540 CTTTTA -s simCow_chr6.simCow.chr6 381729 6 + 602619 CTTTTA -s simDog_chr6.simDog.chr6 372279 6 + 593897 CTTTTA -s simHuman_chr6.simHuman.chr6 376194 6 + 601863 CTTTTA -s simRat_chr6.simRat.chr6 389988 6 + 647215 CATTTA - -a -s simMouse_chr6.simMouse.chr6 389975 18 + 636262 TTAAGATGACATAACAAG -s Anc0.Anc0refChr3 22459 18 + 222631 TTAAGCTGACATTACAAA -s Anc1.Anc1refChr6 51922 18 + 197743 TTAAGCTGACATTACAAA -s Anc2.Anc2refChr13 25814 18 + 96486 TTTAGCTGACATTACAAA -s mr.mrrefChr5 243815 18 + 294540 TTAAGATGACATAACAAG -s simCow_chr6.simCow.chr6 381744 18 + 602619 TTGAGCTGACATGACAAA -s simDog_chr6.simDog.chr6 372292 18 + 593897 TTTGGCTAACATTACAAT -s simHuman_chr6.simHuman.chr6 376209 18 + 601863 TTAAGCTGCTATTATAAA -s simRat_chr6.simRat.chr6 389994 18 + 647215 TCAAGATGACATAACAAT - -a -s simMouse_chr6.simMouse.chr6 389993 28 + 636262 AGAGGAGACTGCAGTTCCTTGGATGGTT -s Anc0.Anc0refChr3 22502 28 + 222631 AGAAGGAATTGCCATCCCTTGGATGGCT -s Anc1.Anc1refChr6 51965 28 + 197743 AGAAGGAATTGCCATCCCTTGGATGGCT -s Anc2.Anc2refChr13 25857 28 + 96486 AGAAGGACTAACCATCCCTTGGATGGCT -s mr.mrrefChr5 243833 28 + 294540 AGAGGAGACTGCAATTCCTTGGATGGTT -s simCow_chr6.simCow.chr6 381857 28 + 602619 AGAATGACTCACTATCCATTGGATGGCT -s simDog_chr6.simDog.chr6 372335 28 + 593897 AGACGGACTAACCATCCCTCGGATAGCT -s simHuman_chr6.simHuman.chr6 376252 28 + 601863 AGAAGCAATTGCCATCCCTTGGATGGCT -s simRat_chr6.simRat.chr6 390012 23 + 647215 AGA-----CTGCAATTCCTTGGGTGGTT - -a -s simMouse_chr6.simMouse.chr6 390021 13 + 636262 AGATAAGGATCAC -s Anc0.Anc0refChr3 22531 13 + 222631 TGATAGAGATAAC -s Anc1.Anc1refChr6 51994 13 + 197743 TGATAGAGATAAC -s Anc2.Anc2refChr13 25886 13 + 96486 GGGTAAATATAAC -s mr.mrrefChr5 243861 13 + 294540 TGATAGAGATCAC -s simCow_chr6.simCow.chr6 381886 13 + 602619 CGGTAAGTATAGC -s simDog_chr6.simDog.chr6 372364 13 + 593897 GAGTAAATATAAC -s simHuman_chr6.simHuman.chr6 376281 8 + 601863 TGATAGAG----- -s simRat_chr6.simRat.chr6 390035 13 + 647215 TGATTGATGTCAC - -a -s simMouse_chr6.simMouse.chr6 390034 19 + 636262 GAATTGTTCAGCGGTCCAG -s Anc0.Anc0refChr3 22544 19 + 222631 AAACTGTTCAGCTGTCCAC -s Anc1.Anc1refChr6 52007 19 + 197743 AAACTGTTCAGCTGTCCAC -s Anc2.Anc2refChr13 25903 19 + 96486 AAACTGTTCAGCTGTCCAC -s mr.mrrefChr5 243874 19 + 294540 GAATTGTTCAGCGGTCCAG -s simCow_chr6.simCow.chr6 381903 19 + 602619 AAACTGTTCAGCTGCCCAC -s simDog_chr6.simDog.chr6 372381 19 + 593897 AAACTGTTCAGCTGTCCTC -s simHuman_chr6.simHuman.chr6 376289 16 + 601863 ---CTGTTCAGTTGTTTAC -s simRat_chr6.simRat.chr6 390048 19 + 647215 AAACTGATCAGCAGTCCAG - -a -s simMouse_chr6.simMouse.chr6 390053 6 + 636262 CTCACC -s Anc0.Anc0refChr3 22585 6 + 222631 CTTGCT -s Anc1.Anc1refChr6 52048 6 + 197743 CTTGCT -s Anc2.Anc2refChr13 25944 6 + 96486 CTTGCT -s mr.mrrefChr5 243893 6 + 294540 CTCACC -s simCow_chr6.simCow.chr6 381944 6 + 602619 CCTTCT -s simDog_chr6.simDog.chr6 372422 6 + 593897 CTTGCT -s simHuman_chr6.simHuman.chr6 376327 6 + 601863 CTTCCT -s simRat_chr6.simRat.chr6 390067 6 + 647215 CTCACC - -a -s simMouse_chr6.simMouse.chr6 390059 39 + 636262 AGCTTCAACCACCATCTGAGTGATGTACACATGAGAGAT -s Anc0.Anc0refChr3 22591 38 + 222631 AGGTTTAACCACCATCTGGGTGATGT-CACATAGCAGAT -s Anc1.Anc1refChr6 52054 38 + 197743 AGGTTTAACCACCATCTGGGTGATGT-CACATAGCAGAT -s Anc2.Anc2refChr13 25950 38 + 96486 AGGTTTAACCACCATCTGGGTGATGT-CACATAGCAGAT -s mr.mrrefChr5 243899 39 + 294540 AGCTTCAACCACCATCTGAGTGATGTACACATGAGAGAT -s simCow_chr6.simCow.chr6 381985 37 + 602619 AGCTTTTACCACCATCTGAGTGATGT-CACAT-GCAGAT -s simDog_chr6.simDog.chr6 372428 38 + 593897 AGGTCTAACCACCATCCGGATGATGT-CATACAGCAGAT -s simHuman_chr6.simHuman.chr6 376333 38 + 601863 AGTTTTAACCATCATCTGTGTGATGT-TACATAGCAGAT -s simRat_chr6.simRat.chr6 390073 39 + 647215 TGCCTAAACCACCATCTGAGTGATGTACACATGAGGGAC - -a -s simMouse_chr6.simMouse.chr6 390098 2 + 636262 AG -s Anc0.Anc0refChr3 22669 2 + 222631 AG -s Anc1.Anc1refChr6 52132 2 + 197743 AG -s Anc2.Anc2refChr13 26028 2 + 96486 AG -s mr.mrrefChr5 243938 2 + 294540 AG -s simCow_chr6.simCow.chr6 382059 2 + 602619 AG -s simDog_chr6.simDog.chr6 372517 2 + 593897 GC -s simHuman_chr6.simHuman.chr6 376411 2 + 601863 AG -s simRat_chr6.simRat.chr6 390112 2 + 647215 AG - -a -s simMouse_chr6.simMouse.chr6 390100 14 + 636262 AGTAAGTCCTTTGG -s Anc0.Anc0refChr3 22671 14 + 222631 AGTAAGTCCTCCGG -s Anc1.Anc1refChr6 52134 14 + 197743 AGTAAGTCCTCCGG -s Anc2.Anc2refChr13 26030 14 + 96486 AATAAGTCCTCCGG -s mr.mrrefChr5 243940 14 + 294540 AGTAAGTCCTTTGG -s simCow_chr6.simCow.chr6 382061 13 + 602619 AATAAGTCCTCCG- -s simDog_chr6.simDog.chr6 372519 14 + 593897 AATAAGTCCTCCAG -s simHuman_chr6.simHuman.chr6 376413 14 + 601863 AGTTAGTCCTCCGG -s simRat_chr6.simRat.chr6 390118 14 + 647215 AATAAGTCCTTTGG - -a -s simMouse_chr6.simMouse.chr6 390114 136 + 636262 ACTATCACTTCATTCTACATGTATGCTGCAGGTAGCTTATAATCCTTGGTGCTCTGAGGCATTGTATTTCCCGCCTATGGCTAGATTATTGGTACTTCCAGTATATTTCCATTCTATGGCTAGATTCTTGGTACTT -s Anc0.Anc0refChr3 22687 87 + 222631 AGTATAACTTCATTGTACATGTATGCTGT----GGCATATAATCATTAGTGCTCTTAGGCATTGAATTTTCTGCCTATAGCTAGATCATTA--------------------------------------------- -s Anc1.Anc1refChr6 52150 87 + 197743 AGTATAACTTCATTGTACATGTATGCTGT----GGCATATAATCATTAGTGCTCTTAGGCATTGAATTTTCTGCCTATAGCTAGATCATTA--------------------------------------------- -s Anc2.Anc2refChr13 26046 87 + 96486 AGTATAACTTCATTGTACATGTATGCTGT----GGCATATAAACATTAGTGCTGTTGGGCATTGAATTTTCTGCCTATAGCTAGATCATCA--------------------------------------------- -s mr.mrrefChr5 243954 136 + 294540 ACTATAACTTCATTCTACATGTATGCTGTAGGTGGCATATAATCCTTGGTGCTCTGAGGCATTGTATTTCCTGCCTATGGCTAGATTATTGGTACTTCCAGTATATTTCCATTCTATGGCTAGATTCTTGGTACTT -s simCow_chr6.simCow.chr6 382076 87 + 602619 AGTATAAACTCATCATGCATGTACTCAGT----TACATATAAGCATTAGTGCTATCGGGCATTGAATTTTCTGCCTATGGCTAGATCCTCC--------------------------------------------- -s simDog_chr6.simDog.chr6 372535 87 + 593897 AGTATAACTCCCTTGTACATGTATGCTGA----GGCGTAAATACAGTGATGCTGTTGGGCATTACATTTTGCACCTATAGCTACATCATCA--------------------------------------------- -s simHuman_chr6.simHuman.chr6 376429 87 + 601863 CATATAACTTCATTGTAGATGCATGCTGT----GTCATATAATCATTAGTGTTCTTAGTCATTGAATTTTCTGCCTACAGCTAGCTCAGTA--------------------------------------------- -s simRat_chr6.simRat.chr6 390132 133 + 647215 ATTATAACTTCACTCAACACGTAT-CTGTAAGTGGCATATAATTCTTGGCACTCTCAGGCATTGTATTTCCTGC--ATGGCTAGATTCATTGTACTTCCAGTATATTTCCTTCCTATGGTTAGATTATTGGTACTT - -a -s simMouse_chr6.simMouse.chr6 390250 18 + 636262 CCAGTACTAGGAGGCTAA -s Anc0.Anc0refChr3 22774 18 + 222631 CCAGTACTGGTAGGTGAA -s Anc1.Anc1refChr6 52237 18 + 197743 CCAGTACTGGTAGGTGAA -s Anc2.Anc2refChr13 26139 18 + 96486 CCAGTACTGCTAGGTGGA -s mr.mrrefChr5 244090 18 + 294540 CCAGTACTAGGAGGCTAA -s simCow_chr6.simCow.chr6 382169 18 + 602619 CCAGCATTACTAGGTGGA -s simDog_chr6.simDog.chr6 372628 18 + 593897 CGAGTACCGCTAGGTGGA -s simHuman_chr6.simHuman.chr6 376516 18 + 601863 CCAGTACTGGTAGGTGAA -s simRat_chr6.simRat.chr6 390265 18 + 647215 CCAGTACTAGGATACTAA - -a -s simMouse_chr6.simMouse.chr6 390268 11 + 636262 TATTATTGGTC -s Anc0.Anc0refChr3 22802 11 + 222631 TCTTATTGGTC -s Anc1.Anc1refChr6 52265 11 + 197743 TCTTATTGGTC -s Anc2.Anc2refChr13 26167 11 + 96486 TCTTATTGGTC -s mr.mrrefChr5 244108 11 + 294540 TATTATTGGTC -s simCow_chr6.simCow.chr6 382197 11 + 602619 TCTTATTGGCC -s simDog_chr6.simDog.chr6 372656 11 + 593897 TCTTTTTGATT -s simHuman_chr6.simHuman.chr6 376544 11 + 601863 TCTTATTGGTC -s simRat_chr6.simRat.chr6 390283 11 + 647215 TATTATTGGTC - -a -s simMouse_chr6.simMouse.chr6 390279 48 + 636262 CATATGGGTCGCTAGAAGAGGCACAAGTGGGCAGGCTGATGAGCCACA -s Anc0.Anc0refChr3 22814 48 + 222631 CATTTGGGTATATAGATGAGGCACAAATGAGCAGGCTAATGAGCCAAG -s Anc1.Anc1refChr6 52277 48 + 197743 CATTTGGGTATATAGATGAGGCACAAATGAGCAGGCTAATGAGCCAAG -s Anc2.Anc2refChr13 26179 48 + 96486 CACTTGGGGATATAGATGACGCACAAATGAGCAGGCTAATGAGCTGAG -s mr.mrrefChr5 244119 48 + 294540 CATATGGGTAGCTAGATGAGGCACAAGTGGGCAGGCTGATGAGCCACA -s simCow_chr6.simCow.chr6 382209 48 + 602619 CCAATTGCAAAATAGATAATCCACAAATGAGCAGGCTAATGAGCTCAG -s simDog_chr6.simDog.chr6 372668 48 + 593897 CACTTGCGGATATAAATGACGCATGGATGTGCAGGCCAATGAACTGAG -s simHuman_chr6.simHuman.chr6 376556 47 + 601863 CATTGGGGTATTTAGATGAGGTACAAATGAGT-GGCTAATTAGCCAAG -s simRat_chr6.simRat.chr6 390294 48 + 647215 CATATGGGTAGCTAAATGAGGCATAGGTGGGCAGGCTGATGGGCCACA - -a -s simMouse_chr6.simMouse.chr6 390327 16 + 636262 ATGTGTGAAGCTCAAG -s Anc0.Anc0refChr3 22863 16 + 222631 ATCTGAGAAGCTCAAC -s Anc1.Anc1refChr6 52326 16 + 197743 ATCTGAGAAGCTCAAC -s Anc2.Anc2refChr13 26228 16 + 96486 ATCTCAGAAGCTCAAC -s mr.mrrefChr5 244167 16 + 294540 ATGTGTGAAGCTCAAG -s simCow_chr6.simCow.chr6 382258 16 + 602619 ATCCAAGAAGCTCGAC -s simDog_chr6.simDog.chr6 372717 16 + 593897 GTCTCAGAAGCTCAAC -s simHuman_chr6.simHuman.chr6 376604 16 + 601863 ATCTGAGAAGCTCAAC -s simRat_chr6.simRat.chr6 390342 16 + 647215 GTGTGTTGAGCTCAAG - -a -s simMouse_chr6.simMouse.chr6 390343 79 + 636262 ATTATGCACTGATGTCCTCAGTCAGTATTAGGTGTAGAAGTTGAATCACATAGTTCAATTACTATACTGCTAAGGCACT -s Anc0.Anc0refChr3 22879 74 + 222631 AATACTTACTGATACTTTCAGT----ATTAGGTGCAGAAGCTAGATCACT-AAGCAAACTACCATATAGCTAGGGCACT -s Anc1.Anc1refChr6 52342 75 + 197743 AATACTTACTGATACTTTCAGT----ATTAGGTGCAGAAGCTAGATCACTTAAGCAAACTACCATATAGCTAGGGCACT -s Anc2.Anc2refChr13 26245 74 + 96486 AATACTTCCTGATACTTTCAAT----ATTAGGTGCAGAAGCTAGATTGCT-AAGCAAACTATCATATAGCTAGGGTACT -s mr.mrrefChr5 244183 75 + 294540 ATTATGCACTGATGCCCTCAGT----ATTAGGTGTAGAAGTTAAATCACATAATTCAATTACCATACTGCTAGGGCACT -s simCow_chr6.simCow.chr6 382275 74 + 602619 CATACTGCCTGATATTTTCACT----ATTAGGTGCATAGGCTAGGTTGCT-AAGCAGACTATCATATAGCCAGGGTACT -s simDog_chr6.simDog.chr6 372734 74 + 593897 AATACTTCCTGATACTTTAAAA----ATTGAGTGCAGAAGCTAGATTGCT-AAGCAAACTATCATACAGCTAGGGTAAT -s simHuman_chr6.simHuman.chr6 376620 75 + 601863 AATACTAATTAATACTTTCAGT----ATTAGATGAAGGAGCTAGCTCACTTAAGCAAGCCACCATATAACTAGTGCACT -s simRat_chr6.simRat.chr6 390358 75 + 647215 ATTGTACACTGATGCCCTCAGT----GTCAGGCGTAGAAGTTAAGTCACGTAATTCAATTACCATACTGCCAGAGTACT - -a -s simMouse_chr6.simMouse.chr6 390422 27 + 636262 GATGTATGCCCAGAAAACCCAATACAT -s Anc0.Anc0refChr3 22953 27 + 222631 GGAGTATGCCCTAGACTCCCATTACAT -s Anc1.Anc1refChr6 52417 27 + 197743 GGAGTATGCCCTAGACTCCCATTACAT -s Anc2.Anc2refChr13 26319 27 + 96486 GGAGTATTCCCTAGACTCCAAATATGT -s mr.mrrefChr5 244258 27 + 294540 GAAGTATGCCCAGAAAACCCATTACAT -s simCow_chr6.simCow.chr6 382352 27 + 602619 GTAGTATTCCCTAGACACTAAATAAGT -s simDog_chr6.simDog.chr6 372808 26 + 593897 GGAGTT-TCCTTGGACTCCAAATATGT -s simHuman_chr6.simHuman.chr6 376695 27 + 601863 GGAGTAAGCACTAGACGTCCATTTCAT -s simRat_chr6.simRat.chr6 390433 26 + 647215 GAAGCATGCTGGGAAAACCCATT-CAT - -a -s simMouse_chr6.simMouse.chr6 390449 7 + 636262 GTGCTTT -s Anc0.Anc0refChr3 22980 7 + 222631 ATGCCTC -s Anc1.Anc1refChr6 52444 7 + 197743 ATGCCTC -s Anc2.Anc2refChr13 26347 7 + 96486 ATGCCTC -s mr.mrrefChr5 244285 7 + 294540 GTGCTTT -s simCow_chr6.simCow.chr6 382390 7 + 602619 ATGCCTC -s simDog_chr6.simDog.chr6 372835 7 + 593897 GTGCTTA -s simHuman_chr6.simHuman.chr6 376722 7 + 601863 ATGCCTC -s simRat_chr6.simRat.chr6 390459 7 + 647215 GTGATTA - -a -s simMouse_chr6.simMouse.chr6 390456 62 + 636262 CTGGGGCTGGCTCTATATACACAAGAATATGTTTGGCTTGTTTCAACCCTAGAAATGTAACA -s Anc0.Anc0refChr3 22989 58 + 222631 CTATGGAT----ATACTTGCACAAGAGTGTGTTTGGTTGTTTTTAGCCCTAGAGAGGTATTA -s Anc1.Anc1refChr6 52453 58 + 197743 CTATGGAT----ATACTTGCACAAGAGTGTGTTTGGTTGTTTTTAGCCCTAGAGAGGTATTA -s Anc2.Anc2refChr13 26356 58 + 96486 CTATGGCT----ATACTTGCACAAGAGTGAGTTTGGTTGTTTTTAGCCCTAGAGAGGTATTG -s mr.mrrefChr5 244294 62 + 294540 CTAGGGATGGCTCTACATACACAAGAGTATGTTTGGCTTGTTTCAACCCTAGAAATGTAATA -s simCow_chr6.simCow.chr6 382399 58 + 602619 CTTGGGCT----CTGCTTGCGCAAGAGTAAGTTTGGTTCTTCTTAGACCTAGAAAGGTATTG -s simDog_chr6.simDog.chr6 372844 58 + 593897 TTATTGCT----ATACTTGCATAGGAGTGAAACTGGTTGACTTCAGCCCTAGAGAGGCATTG -s simHuman_chr6.simHuman.chr6 376731 58 + 601863 CTATGGAT----ATTCTTGTACAAGAGTGTGTTCGGTTGTTTTTAGCTCTAAAGAGATATTA -s simRat_chr6.simRat.chr6 390468 62 + 647215 CTACGGATGGCTCTACATACACAAGAGTATGTTTGGCTTGTTTCAACCCTTCAAACGTAATA - -a -s simMouse_chr6.simMouse.chr6 390518 42 + 636262 ATTAACGAATGCCCACATGCACCCAAGGCTAAAATCAGTACC -s Anc0.Anc0refChr3 23069 42 + 222631 ACCAGTTATTGCCCACATGTACCAATGACTGACATCAGTACC -s Anc1.Anc1refChr6 52533 42 + 197743 ACCAGTTATTGCCCACATGTACCAATGACTGACATCAGTACC -s Anc2.Anc2refChr13 26441 42 + 96486 ACCAGTTATTGTCCACATGTACCAATGACTGACATCAGTACC -s mr.mrrefChr5 244356 42 + 294540 ATTAATGAATGCCCACATGTACCCAAGACTGAAATCAGTACC -s simCow_chr6.simCow.chr6 382484 42 + 602619 ACCAGCTATTGTCCACATGTACAAATGACAGACATCTCTACC -s simDog_chr6.simDog.chr6 372931 42 + 593897 ACCATTTATCTTCCACCTGTACCAATCACTGACATAAGTACC -s simHuman_chr6.simHuman.chr6 376811 42 + 601863 ACCAGTTGCTGCCCACATGTACCAGTGAATGACATCAGTGCC -s simRat_chr6.simRat.chr6 390530 42 + 647215 ATTCATGAAAGCCCAGATATACCCAAGATGGAAATCAGTATC - -a -s simMouse_chr6.simMouse.chr6 390560 38 + 636262 AATTCTTTCCTGTAAAGCTGTAATAATCTTTTTGGATA -s Anc0.Anc0refChr3 23113 38 + 222631 AATTCTCTCCTATAAAACAGTAATGATCTTTTTGGATG -s Anc1.Anc1refChr6 52577 38 + 197743 AATTCTCTCCTATAAAACAGTAATGATCTTTTTGGATG -s Anc2.Anc2refChr13 26485 38 + 96486 AATTCCCCCCTAAAAAACAGTAATGACCTTTTTGGATG -s mr.mrrefChr5 244398 38 + 294540 AATTCTTTCCTGTAAAGCTGTAATAATCTTTTTGGATA -s simCow_chr6.simCow.chr6 382528 38 + 602619 AATTCATCCCCAAAAAACTGTAATGACCTTTTAGGATA -s simDog_chr6.simDog.chr6 372975 38 + 593897 AATTCCCCTCTAAAATACAGTAATGACCTTCTTGAATG -s simHuman_chr6.simHuman.chr6 376855 38 + 601863 AATTCTCTCCTATAAAACAGTAATGATCTTTTTGGGTG -s simRat_chr6.simRat.chr6 390572 38 + 647215 AATTCTTCCCTGTAAAGCTGAAATAATCATCTTGGATA - -a -s simMouse_chr6.simMouse.chr6 390598 5 + 636262 GGAAG -s Anc0.Anc0refChr3 23162 5 + 222631 GGAAG -s Anc1.Anc1refChr6 52626 5 + 197743 GGAAG -s Anc2.Anc2refChr13 26534 5 + 96486 TGAAG -s mr.mrrefChr5 244436 5 + 294540 GGAAG -s simCow_chr6.simCow.chr6 382577 5 + 602619 TGAAG -s simDog_chr6.simDog.chr6 373024 5 + 593897 TGAAG -s simHuman_chr6.simHuman.chr6 376904 5 + 601863 GGACG -s simRat_chr6.simRat.chr6 390610 5 + 647215 GGAAG - -a -s simMouse_chr6.simMouse.chr6 390603 9 + 636262 GTCTGAAAA -s Anc0.Anc0refChr3 23167 9 + 222631 GTGTGGACA -s Anc1.Anc1refChr6 52631 9 + 197743 GTGTGGACA -s Anc2.Anc2refChr13 26540 9 + 96486 GTGTGGACA -s mr.mrrefChr5 244441 9 + 294540 GTCTGAAAA -s simCow_chr6.simCow.chr6 382583 9 + 602619 GTGTCGAAA -s simDog_chr6.simDog.chr6 373030 9 + 593897 GCCTGAACA -s simHuman_chr6.simHuman.chr6 376909 9 + 601863 GTGTGGATG -s simRat_chr6.simRat.chr6 390615 9 + 647215 GCCTAAAAA - -a -s simMouse_chr6.simMouse.chr6 390612 124 + 636262 GTCTAAGGCCCATATGCACCCAAGGGTAAAATCAGTACCAATACTTCCCTGTAAAGCTGTAATAATCTTTTTGAATAGGAAGGTCTGAAAAGTCAGTGTACCCCAACTCATAAACCTTGCGATG -s Anc0.Anc0refChr3 23182 30 + 222631 GTCG-------------------------------------------------------------------------------------------GTGTGCCTCAACTAATAAACCTAGC---T -s Anc1.Anc1refChr6 52646 30 + 197743 GTCG-------------------------------------------------------------------------------------------GTGTGCCTCAACTAATAAACCTAGC---T -s Anc2.Anc2refChr13 26555 30 + 96486 GTCG-------------------------------------------------------------------------------------------GTGTGGCTCAACAAATAAACTTATC---T -s mr.mrrefChr5 244450 32 + 294540 GTCT-------------------------------------------------------------------------------------------GTGTACCCCAACTCATAAACCTTGC-ATT -s simCow_chr6.simCow.chr6 382598 23 + 602619 TT--------------------------------------------------------------------------------------------------GCTCAGCGAATAAACTTATC---T -s simDog_chr6.simDog.chr6 373045 27 + 593897 GTCG-------------------------------------------------------------------------------------------GTGTGGCTCAACAAAGACTCTTA------ -s simHuman_chr6.simHuman.chr6 376924 29 + 601863 GTTG-------------------------------------------------------------------------------------------GTGTTCCTCA-CTAATAAACCTAGC---T -s simRat_chr6.simRat.chr6 390624 31 + 647215 GTCT-------------------------------------------------------------------------------------------GGGAATGCCAACTGATAAACCTTG--ATT - -a -s simMouse_chr6.simMouse.chr6 390736 16 + 636262 CTGCTGGACTCATAGG -s Anc0.Anc0refChr3 23212 16 + 222631 CCAGTGGACTTATAGG -s Anc1.Anc1refChr6 52676 16 + 197743 CCAGTGGACTTATAGG -s Anc2.Anc2refChr13 26585 16 + 96486 CCAGTGGACTTGTAGG -s mr.mrrefChr5 244482 16 + 294540 CCACTGGACTCATAGG -s simCow_chr6.simCow.chr6 382622 16 + 602619 CCAGTAGACTTGTAAA -s simDog_chr6.simDog.chr6 373072 12 + 593897 ----TGGACTTGTGGG -s simHuman_chr6.simHuman.chr6 376953 16 + 601863 CCAGTGGACTTAGAGG -s simRat_chr6.simRat.chr6 390655 16 + 647215 CCACTGGACTCATAGG - -a -s simMouse_chr6.simMouse.chr6 390752 112 + 636262 AAACATGTAAAATACAGGCAAAATATGGGTAAGTTACATGCTAGGTTTCCAACTACTAGCATCTGTGCGTCAATACTATGTGCTCCTACCATTTCCCCACATATGATGGAAC -s Anc0.Anc0refChr3 23230 108 + 222631 GAATATGTAAAATGCAGCCAAAATATGGGTCAGTTATATTGTAGCTTTTCA-CTGCTAGGATCTGTGCAGCAGAATT---TGTTCTTACTTTCTTCTAGAATATGATGGATA -s Anc1.Anc1refChr6 52694 109 + 197743 GAATATGTAAAATGCAGCCAAAATATGGGTCAGTTATATTGTAGCTTTTCAACTGCTAGGATCTGTGCAGCAGAATT---TGTTCTTACTTTCTTCTAGAATATGATGGATA -s Anc2.Anc2refChr13 26603 108 + 96486 CAATATGTAAAATGCAGCCAAAATATGGGTCAGTTATATTGTAGCTTTTCA-CTGTTAGGATCTGTGCAGCAGAATG---TGTTCTTACTTCCTTCTAGAATATGATGGATA -s mr.mrrefChr5 244498 112 + 294540 GAACATGTAAAATGCAGGCAAAATATGGGTAAGTTACATGCTAGGTTTCCAACTACTAGCATCTGTGCATCAATACTATGTGTTCCTACTATCTCCCCAGATATGATGGAAA -s simCow_chr6.simCow.chr6 382640 108 + 602619 CAATATGTAAAATGCAGCCAGAATATGGGTCAGCCATGTTGTAGCTTTTGA-CCGTTAGGATCTGTGCAGGATGATA---TGTTCTGACATCCTCCTAGTATATGATGGATA -s simDog_chr6.simDog.chr6 373086 105 + 593897 CATTATGTA---TGCAGCCAAAATATGGGTCAGTTATATTACAGTTTTACA-CTGTTAGGATCTGTGCAGCAGAACG---TTTTAGTATTTCCTTCTAGAATATGATTGATA -s simHuman_chr6.simHuman.chr6 376971 107 + 601863 GAATATGTAAAATGTAGACAAATTATGGGTCA-TTATATTGTGGCTTTTCAACTGCTAGGATCTGTGCAGAAGAATT---TGTTCTTACTTTCTACTAG-CTATGATGGATA -s simRat_chr6.simRat.chr6 390671 112 + 647215 GAACATGTAAAATGCAGGCAACATGTGGGTAAGTTACAAGCTAGGCTTCCAATTAGTAGCATCTGTGCATCAATACTATGTGTTCCTACTATCTCTCCAGATATGATGGAAA - -a -s simMouse_chr6.simMouse.chr6 390864 7 + 636262 ACTCTAA -s Anc0.Anc0refChr3 23338 7 + 222631 ACTCCAA -s Anc1.Anc1refChr6 52803 7 + 197743 ACTCCAA -s Anc2.Anc2refChr13 26711 7 + 96486 ATTCCAA -s mr.mrrefChr5 244610 7 + 294540 ACTCTAA -s simCow_chr6.simCow.chr6 382750 7 + 602619 ATTCCAA -s simDog_chr6.simDog.chr6 373191 6 + 593897 ATTCCA- -s simHuman_chr6.simHuman.chr6 377078 7 + 601863 ACTCCAG -s simRat_chr6.simRat.chr6 390783 7 + 647215 AATCTAA - -a -s simMouse_chr6.simMouse.chr6 390871 53 + 636262 AGCAGAAAACTTGCTGGAGACCAAATACCAATACAACCCTTCTGCAGACCATA -s Anc0.Anc0refChr3 23363 53 + 222631 AGCAGGGAACTTGCAGGGGACCAAATATCAATCTAATCTGTCTGCAGGCCATG -s Anc1.Anc1refChr6 52828 53 + 197743 AGCAGGGAACTTGCAGGGGACCAAATATCAATCTAATCTGTCTGCAGGCCATG -s Anc2.Anc2refChr13 26736 53 + 96486 AGCAGGGAACTTGCAGGGGACCAAATTTCAATCTAATCTGTCTGCAGGCCATG -s mr.mrrefChr5 244617 53 + 294540 AGCAGAGAACTTGCTGGAGACCAAATACCAATACAACCCTTCTGCAGACCATA -s simCow_chr6.simCow.chr6 382776 53 + 602619 AGTCAGAAACTTTCAGGGGACCACATTTGCATCTAATCTGTCTGTAGCCCATC -s simDog_chr6.simDog.chr6 373214 53 + 593897 AGCAGGGAACTTGCAGGGGACCAAACTTCAGTCAAATCTGTCTGCAGGCCATG -s simHuman_chr6.simHuman.chr6 377103 52 + 601863 AGCAG-GAACTTGCAACGGACCAAATATCAAATTAATCTGTCTGCAGGCTATG -s simRat_chr6.simRat.chr6 390790 53 + 647215 AGCAGAGAACTTGGTGGAGACCAAACACCAATCCAACTCTTCTGCAGACCATA - -a -s simMouse_chr6.simMouse.chr6 390924 6 + 636262 GGTGTT -s Anc0.Anc0refChr3 23416 6 + 222631 GGTTCT -s Anc1.Anc1refChr6 52881 6 + 197743 GGTTCT -s Anc2.Anc2refChr13 26792 6 + 96486 GGTTCA -s mr.mrrefChr5 244670 6 + 294540 GGTGTT -s simCow_chr6.simCow.chr6 382832 6 + 602619 GATTCA -s simDog_chr6.simDog.chr6 373270 6 + 593897 GGTTCA -s simHuman_chr6.simHuman.chr6 377155 6 + 601863 GGTTCT -s simRat_chr6.simRat.chr6 390843 6 + 647215 GGTGTT - -a -s simMouse_chr6.simMouse.chr6 390930 7 + 636262 CACTCCC -s Anc0.Anc0refChr3 23423 7 + 222631 CACTTCT -s Anc1.Anc1refChr6 52888 7 + 197743 CACTTCT -s Anc2.Anc2refChr13 26799 7 + 96486 CACCTTC -s mr.mrrefChr5 244676 7 + 294540 CACTTCT -s simCow_chr6.simCow.chr6 382839 6 + 602619 CAT-TTC -s simDog_chr6.simDog.chr6 373277 7 + 593897 CACCTTC -s simHuman_chr6.simHuman.chr6 377162 7 + 601863 CACTTCT -s simRat_chr6.simRat.chr6 390849 7 + 647215 CATTTGT - -a -s simMouse_chr6.simMouse.chr6 390937 9 + 636262 ATGCAAGGG -s Anc0.Anc0refChr3 23431 9 + 222631 ACGCAAGCA -s Anc1.Anc1refChr6 52896 9 + 197743 ACGCAAGCA -s Anc2.Anc2refChr13 26807 9 + 96486 ACACAAGCA -s mr.mrrefChr5 244683 9 + 294540 ATGCAAGGG -s simCow_chr6.simCow.chr6 382846 9 + 602619 ACACAAGTA -s simDog_chr6.simDog.chr6 373285 9 + 593897 TCACAAGCA -s simHuman_chr6.simHuman.chr6 377170 9 + 601863 AAGCAAGCA -s simRat_chr6.simRat.chr6 390856 9 + 647215 ATGCAAGGG - -a -s simMouse_chr6.simMouse.chr6 390946 23 + 636262 CAAGCTGGTCCAGAATGATTTTT -s Anc0.Anc0refChr3 23440 23 + 222631 GTGGTTGTGTCAGATTGATTTTT -s Anc1.Anc1refChr6 52905 23 + 197743 GTGGTTGTGTCAGATTGATTTTT -s Anc2.Anc2refChr13 26816 23 + 96486 GTGGTTGTGTCAGATTGATTTTT -s mr.mrrefChr5 244692 23 + 294540 CAAGCTGGTCCAGAATGATTTTT -s simCow_chr6.simCow.chr6 382855 23 + 602619 GAGGTTGTGTCAGATTGATTTTT -s simDog_chr6.simDog.chr6 373298 23 + 593897 CTGGTTGTGTCAGATTGGTTTTT -s simHuman_chr6.simHuman.chr6 377179 23 + 601863 GTGGTTGTCTCAGATTGATTGTT -s simRat_chr6.simRat.chr6 390865 23 + 647215 TGAGGTGGTCCAGAATAATTTTT - -a -s simMouse_chr6.simMouse.chr6 390969 17 + 636262 AGGACTATGGGACATCT -s Anc0.Anc0refChr3 23463 17 + 222631 AAGACTTTGGGGCATCC -s Anc1.Anc1refChr6 52928 17 + 197743 AAGACTTTGGGGCATCC -s Anc2.Anc2refChr13 26839 17 + 96486 GAGACTTTGGGGCAGCC -s mr.mrrefChr5 244715 17 + 294540 AGGACTATGGGACATCT -s simCow_chr6.simCow.chr6 382878 17 + 602619 GATACTTTGGGGTACCC -s simDog_chr6.simDog.chr6 373339 17 + 593897 GAGACTTTGGGGCAGCC -s simHuman_chr6.simHuman.chr6 377202 17 + 601863 AAGACTTTGGGGAATCC -s simRat_chr6.simRat.chr6 390888 17 + 647215 ATGACTATAGGACATCT - -a -s simMouse_chr6.simMouse.chr6 390986 46 + 636262 GTAATATGTTTATGCGTGTGGGGGACTTAGAGTTCTTTGTAGTAGT -s Anc0.Anc0refChr3 23482 45 + 222631 GTAATATGTTCATGTGTTAGGGGGACTTAGGCTTCTGTGT-GTAGC -s Anc1.Anc1refChr6 52947 45 + 197743 GTAATATGTTCATGTGTTAGGGGGACTTAGGCTTCTGTGT-GTAGC -s Anc2.Anc2refChr13 26858 45 + 96486 GTAGTATGTTCAAGTGTTAGGGGGACTTAGGCTTTTGTGC-ATAGC -s mr.mrrefChr5 244732 46 + 294540 GTAATATGTTTATGCGTGAGGGGGACTTAGGCTTCTTTGTAGTAGT -s simCow_chr6.simCow.chr6 382896 33 + 602619 ----------TAAGTGTTAGGAGGACTTAGGCTTTTGT---AGAGC -s simDog_chr6.simDog.chr6 373358 42 + 593897 GTAGTATGTTCAAGTTTTGCGGGGACTTAGGCTT---TGC-ATAGC -s simHuman_chr6.simHuman.chr6 377221 45 + 601863 GTAATATGTTCATGGGACAGGGGGACTTAGGCTTCTGTGT-GTAGC -s simRat_chr6.simRat.chr6 390905 46 + 647215 ATAGTATTTTTATGTATGAGAGGGACTTAGGCTTCTCTGTAGCAGT - -a -s simMouse_chr6.simMouse.chr6 391032 6 + 636262 CATTAG -s Anc0.Anc0refChr3 23527 6 + 222631 TGTTGC -s Anc1.Anc1refChr6 52992 6 + 197743 TGTTGC -s Anc2.Anc2refChr13 26903 6 + 96486 TGTTGC -s mr.mrrefChr5 244778 6 + 294540 CATTAG -s simCow_chr6.simCow.chr6 382929 6 + 602619 TGTTGT -s simDog_chr6.simDog.chr6 373409 6 + 593897 TGTTGC -s simHuman_chr6.simHuman.chr6 377266 6 + 601863 TGTTGC -s simRat_chr6.simRat.chr6 390951 6 + 647215 CATTAG - -a -s simMouse_chr6.simMouse.chr6 391038 5 + 636262 GATGG -s Anc0.Anc0refChr3 23534 5 + 222631 GTTGG -s Anc1.Anc1refChr6 52999 5 + 197743 GTTGG -s Anc2.Anc2refChr13 26910 5 + 96486 GTTGG -s mr.mrrefChr5 244784 5 + 294540 GATGG -s simCow_chr6.simCow.chr6 382936 5 + 602619 TTTGG -s simDog_chr6.simDog.chr6 373416 5 + 593897 GTTGG -s simHuman_chr6.simHuman.chr6 377273 5 + 601863 ATTGG -s simRat_chr6.simRat.chr6 390957 5 + 647215 GATGA - -a -s simMouse_chr6.simMouse.chr6 391043 22 + 636262 AGATGATTCTAATGTACAATGT -s Anc0.Anc0refChr3 23539 22 + 222631 AAAAGATTGCAGTTGATAATGT -s Anc1.Anc1refChr6 53004 22 + 197743 AAAAGATTGCAGTTGATAATGT -s Anc2.Anc2refChr13 26915 22 + 96486 CAGAGATTGCAGTTGATAATGT -s mr.mrrefChr5 244789 22 + 294540 AGATGATTCTAGTGTACAATGT -s simCow_chr6.simCow.chr6 382946 22 + 602619 CAGTGACTGCGGTTGAGAATGT -s simDog_chr6.simDog.chr6 373421 22 + 593897 CAGAGATTGCAGTCAATAATGG -s simHuman_chr6.simHuman.chr6 377283 22 + 601863 ACAAGATTGCAGTTGAAAATGT -s simRat_chr6.simRat.chr6 390962 22 + 647215 AGATGATTCTAGTGTCCAATGT - -a -s simMouse_chr6.simMouse.chr6 391065 8 + 636262 ATATTGCG -s Anc0.Anc0refChr3 23561 7 + 222631 CTATTGT- -s Anc1.Anc1refChr6 53026 8 + 197743 CTATTGTG -s Anc2.Anc2refChr13 26937 7 + 96486 CTATTGT- -s mr.mrrefChr5 244811 8 + 294540 ATATTGCG -s simCow_chr6.simCow.chr6 382968 7 + 602619 ACATTGT- -s simDog_chr6.simDog.chr6 373451 7 + 593897 CTGTTGT- -s simHuman_chr6.simHuman.chr6 377305 8 + 601863 TTATTGTG -s simRat_chr6.simRat.chr6 390984 8 + 647215 ATGTTGCA - -a -s simMouse_chr6.simMouse.chr6 391073 16 + 636262 CCAACACAGGCTCCCC -s Anc0.Anc0refChr3 23572 16 + 222631 CCAACAAGTGCTCCCA -s Anc1.Anc1refChr6 53038 16 + 197743 CCAACAAGTGCTCCCA -s Anc2.Anc2refChr13 26948 16 + 96486 TCAACAAGTGCTCCCA -s mr.mrrefChr5 244819 16 + 294540 CCAACACAGGCTCCCC -s simCow_chr6.simCow.chr6 382979 16 + 602619 TCAATAGGTGATCCCA -s simDog_chr6.simDog.chr6 373462 16 + 593897 TCAACCAGTGCTCCCA -s simHuman_chr6.simHuman.chr6 377317 16 + 601863 CTAACAAGCGCCCCCA -s simRat_chr6.simRat.chr6 390992 14 + 647215 TCAACACAGGC--TCC - -a -s simMouse_chr6.simMouse.chr6 391089 21 + 636262 AACCAGTGCTCTGCAACTTCT -s Anc0.Anc0refChr3 23588 21 + 222631 TTATAGTGCTCTGCAACCTCT -s Anc1.Anc1refChr6 53054 21 + 197743 TTATAGTGCTCTGCAACCTCT -s Anc2.Anc2refChr13 26964 21 + 96486 TTATAGCGCTCTGCAACCTCT -s mr.mrrefChr5 244835 21 + 294540 AACCAGTGCTCTGCAACTTCT -s simCow_chr6.simCow.chr6 382995 21 + 602619 TTGGAGCTTTCTGCAACCTTT -s simDog_chr6.simDog.chr6 373478 21 + 593897 TTATAGCGCTCTGCAACCTCT -s simHuman_chr6.simHuman.chr6 377333 21 + 601863 TCATAGTGCTCTACAACCTCT -s simRat_chr6.simRat.chr6 391007 21 + 647215 AACCAATGCTCTGCAACTTTC - -a -s simMouse_chr6.simMouse.chr6 391110 37 + 636262 GTGCATGACATTGAATAAACTTGAACAGTTCACTTGT -s Anc0.Anc0refChr3 23617 37 + 222631 GTGATTGAAATTGTCTAGACTTGAATCGTTTACTTGT -s Anc1.Anc1refChr6 53083 37 + 197743 GTGATTGAAATTGTCTAGACTTGAATCGTTTACTTGT -s Anc2.Anc2refChr13 26993 37 + 96486 GATATTAAAATTGTATAGACTTGAATCATTTGCTCAC -s mr.mrrefChr5 244856 37 + 294540 GTGCTTGACATTGACTAGACTTGAACAGTTCACTTGT -s simCow_chr6.simCow.chr6 383024 34 + 602619 GATCTTAAAATTGT---GACTGGGATAGTTTACTCAC -s simDog_chr6.simDog.chr6 373504 37 + 593897 GATATTAAGATTGTATAGACTTGAATCATCTGCTCAC -s simHuman_chr6.simHuman.chr6 377362 30 + 601863 GTGGTTGAAATTGTCTAGAT-------GTTTACTTGT -s simRat_chr6.simRat.chr6 391028 37 + 647215 GTGTTTACCATTGACTAGGCTTGAACAGTTCACTTGT - -a -s simMouse_chr6.simMouse.chr6 391147 11 + 636262 TGCTACCCAAG -s Anc0.Anc0refChr3 23654 11 + 222631 TGCAGCCCAAG -s Anc1.Anc1refChr6 53120 11 + 197743 TGCAGCCCAAG -s Anc2.Anc2refChr13 27030 11 + 96486 TACAGCCCAAG -s mr.mrrefChr5 244893 11 + 294540 TGCTGCCCAAG -s simCow_chr6.simCow.chr6 383058 11 + 602619 CACAGCCCAAA -s simDog_chr6.simDog.chr6 373541 11 + 593897 TACTGCCTGAG -s simHuman_chr6.simHuman.chr6 377394 11 + 601863 TGCAGCCCAAG -s simRat_chr6.simRat.chr6 391065 11 + 647215 TACTGCCCAAG - -a -s simMouse_chr6.simMouse.chr6 391158 41 + 636262 AGCAACTTACTACTACACACTACAACTTTTTAATGAGAGCC -s Anc0.Anc0refChr3 23666 34 + 222631 AACAACTTAC-------CACTATAAGTTGTTAAGGAGAGCA -s Anc1.Anc1refChr6 53132 34 + 197743 AACAACTTAC-------CACTATAAGTTGTTAAGGAGAGCA -s Anc2.Anc2refChr13 27042 34 + 96486 AATGAATTAT-------TACTATAAGTTGTTTAGGAGGGCA -s mr.mrrefChr5 244904 41 + 294540 AGCAACTTACTACTACACACTATAACTTGTTAATGAGAGCC -s simCow_chr6.simCow.chr6 383070 29 + 602619 AATGATTT------------TATAAGTTGTTTGGGTGGGCA -s simDog_chr6.simDog.chr6 373553 31 + 593897 AATGAATTAT-------TAC---GTGTTGTTTAGGAGGGCA -s simHuman_chr6.simHuman.chr6 377406 34 + 601863 AACAACTTAC-------CACTATAAGTTGTAAAGGAGAACA -s simRat_chr6.simRat.chr6 391076 41 + 647215 AGCAACTTACAACTACACACTATGACTTGTTAACGAGAGCC - -a -s simMouse_chr6.simMouse.chr6 391199 5 + 636262 AGTCA -s Anc0.Anc0refChr3 23700 5 + 222631 GACCA -s Anc1.Anc1refChr6 53166 5 + 197743 GACCA -s Anc2.Anc2refChr13 27081 5 + 96486 GACTA -s mr.mrrefChr5 244945 5 + 294540 AGTCA -s simCow_chr6.simCow.chr6 383101 5 + 602619 GACTA -s simDog_chr6.simDog.chr6 373598 5 + 593897 GAATA -s simHuman_chr6.simHuman.chr6 377440 5 + 601863 GACCA -s simRat_chr6.simRat.chr6 391117 5 + 647215 AGTCA - -a -s simMouse_chr6.simMouse.chr6 391204 11 + 636262 TCTCTACTTCC -s Anc0.Anc0refChr3 23706 11 + 222631 TCTATAAATTC -s Anc1.Anc1refChr6 53172 11 + 197743 TCTATAAATTC -s Anc2.Anc2refChr13 27087 11 + 96486 TCCATAAATTC -s mr.mrrefChr5 244951 11 + 294540 TCTCTACTTCC -s simCow_chr6.simCow.chr6 383107 11 + 602619 TCCACAAATTC -s simDog_chr6.simDog.chr6 373604 11 + 593897 TCCGTGACTTC -s simHuman_chr6.simHuman.chr6 377446 9 + 601863 TAT--AAATTC -s simRat_chr6.simRat.chr6 391123 11 + 647215 TCTCTCCTACC - -a -s simMouse_chr6.simMouse.chr6 391215 25 + 636262 AAGCTCAGTATATAAATAAATGTTT -s Anc0.Anc0refChr3 23717 21 + 222631 AAGCTCAG-A---AAATAACTGTTT -s Anc1.Anc1refChr6 53183 22 + 197743 AAGCTCAGTA---AAATAACTGTTT -s Anc2.Anc2refChr13 27098 21 + 96486 AAGCTCAG-A---AAATAACTCTTC -s mr.mrrefChr5 244962 25 + 294540 AAGCTCAGTATATAAATAAATGTTT -s simCow_chr6.simCow.chr6 383119 21 + 602619 AAACTCAG-T---AACTAACTCTTC -s simDog_chr6.simDog.chr6 373615 21 + 593897 AAGCTCAG-A---AAATAGCTCTTC -s simHuman_chr6.simHuman.chr6 377455 22 + 601863 AAGTTCATTG---AAATCACTGTTT -s simRat_chr6.simRat.chr6 391134 24 + 647215 AAGCCCAGTATATAAA-AAATGTTT - -a -s simMouse_chr6.simMouse.chr6 391240 1 + 636262 C -s Anc0.Anc0refChr3 23740 1 + 222631 C -s Anc1.Anc1refChr6 53207 1 + 197743 C -s Anc2.Anc2refChr13 27121 1 + 96486 C -s mr.mrrefChr5 244987 1 + 294540 C -s simCow_chr6.simCow.chr6 383142 1 + 602619 C -s simDog_chr6.simDog.chr6 373638 1 + 593897 C -s simHuman_chr6.simHuman.chr6 377479 1 + 601863 T -s simRat_chr6.simRat.chr6 391158 1 + 647215 C - -a -s simMouse_chr6.simMouse.chr6 391241 18 + 636262 CATAGGGCCAGCATGAAA -s Anc0.Anc0refChr3 23742 18 + 222631 CATAGGGCCTGCGTGACA -s Anc1.Anc1refChr6 53209 18 + 197743 CATAGGGCCTGCGTGACA -s Anc2.Anc2refChr13 27123 18 + 96486 CATAGGGCCTGCGTTACG -s mr.mrrefChr5 244989 18 + 294540 CATAGGGCCTGCATGAAA -s simCow_chr6.simCow.chr6 383144 16 + 602619 CAC--GTCATGAGATAGC -s simDog_chr6.simDog.chr6 373640 18 + 593897 CATAGGGTCTGCCTTACG -s simHuman_chr6.simHuman.chr6 377481 18 + 601863 CATTGGGCCTGCGTGACA -s simRat_chr6.simRat.chr6 391160 18 + 647215 CATAAGGCCTGCATGAAA - -a -s simMouse_chr6.simMouse.chr6 391259 7 + 636262 AATCACA -s Anc0.Anc0refChr3 23781 7 + 222631 ATTCACA -s Anc1.Anc1refChr6 53248 7 + 197743 ATTCACA -s Anc2.Anc2refChr13 27162 7 + 96486 ATTCACA -s mr.mrrefChr5 245007 7 + 294540 AATCACA -s simCow_chr6.simCow.chr6 383168 5 + 602619 ATTCA-- -s simDog_chr6.simDog.chr6 373712 7 + 593897 ATCCGCA -s simHuman_chr6.simHuman.chr6 377520 7 + 601863 ATTCACA -s simRat_chr6.simRat.chr6 391178 7 + 647215 CACCACA - -a -s simMouse_chr6.simMouse.chr6 391266 4 + 636262 CGCG -s Anc0.Anc0refChr3 23788 4 + 222631 AGAA -s Anc1.Anc1refChr6 53255 4 + 197743 AGAA -s Anc2.Anc2refChr13 27169 4 + 96486 AGAA -s mr.mrrefChr5 245014 4 + 294540 CGCA -s simCow_chr6.simCow.chr6 383173 4 + 602619 ATAT -s simDog_chr6.simDog.chr6 373719 4 + 593897 AGAA -s simHuman_chr6.simHuman.chr6 377527 4 + 601863 AGAA -s simRat_chr6.simRat.chr6 391186 4 + 647215 TGCA - -a -s simMouse_chr6.simMouse.chr6 391270 69 + 636262 ATGATGCCTTTCCTATGTGTTTCCCCTATTAATCGCCTTTTTCCCTCATGCTTTACTAAATATATGATT -s Anc0.Anc0refChr3 23795 68 + 222631 ATGAACATTTTCCTTTGTGTTTCCC-TATTAATTTCCTCTTTTCCTCATTCATTATTAAATGTATGACT -s Anc1.Anc1refChr6 53262 68 + 197743 ATGAACATTTTCCTTTGTGTTTCCC-TATTAATTTCCTCTTTTCCTCATTCATTATTAAATGTATGACT -s Anc2.Anc2refChr13 27176 68 + 96486 ATGAACATTTTCCTTTGTGTTTCCC-TATTAATTTCCTCTTTTCCTCATTCAATATTAAATGTATGACT -s mr.mrrefChr5 245018 69 + 294540 ATGCCAGCTTTCCTATGTGTTTCCCCTATTAATTGCCTCTTTTCCTCATTCTTTATTAAATGTATGATT -s simCow_chr6.simCow.chr6 383180 56 + 602619 ATGAC------------TGTTTCCC-TATTAATTTCCTCTTTTCCCCATTCAATACGTAATGCATGACT -s simDog_chr6.simDog.chr6 373726 68 + 593897 ATGAACATTTTCCTTTGTGTTTCCC-TACTAATTTTCTCTTTTCTTCATTCAATATTAATTATATGACT -s simHuman_chr6.simHuman.chr6 377534 68 + 601863 AGAGACATTTTACTTTATGTTTCTC-TATTAACTTCCTCTTTTCCTCGTTCATTATTAAATGTATGACT -s simRat_chr6.simRat.chr6 391190 69 + 647215 ATGCCAGCTTTCCTATGTGTTCCCCCTATTAATTGCCTCTTTTGCTCATTCTATATTGAATGTATGATC - -a -s simMouse_chr6.simMouse.chr6 391339 28 + 636262 CAGCAACACATATGCATGAGAGTAAGAT -s Anc0.Anc0refChr3 23866 25 + 222631 AG---ACACATATATGTGAGAAATAGAC -s Anc1.Anc1refChr6 53333 28 + 197743 AGTCAACACATATATGTGAGAAATAGAC -s Anc2.Anc2refChr13 27247 25 + 96486 AG---ACACATATATGTGAGAGATAGAC -s mr.mrrefChr5 245087 28 + 294540 AAGCAACACATATGCATGAGAATAAGAC -s simCow_chr6.simCow.chr6 383239 25 + 602619 CG---AGACATATATGTAGGAGATAGAC -s simDog_chr6.simDog.chr6 373797 25 + 593897 AG---ACACATATATGTGAGAGATGAAC -s simHuman_chr6.simHuman.chr6 377605 26 + 601863 AGTCAACA--TATATGTGAGAAACAGAC -s simRat_chr6.simRat.chr6 391259 28 + 647215 AAACAACGCATATGCATGAGAATAAGAC - -a -s simMouse_chr6.simMouse.chr6 391367 16 + 636262 TTTGTTTCTTAATAGA -s Anc0.Anc0refChr3 23898 16 + 222631 TTTCTTTACTTAAAGC -s Anc1.Anc1refChr6 53368 16 + 197743 TTTCTTTACTTAAAGC -s Anc2.Anc2refChr13 27279 16 + 96486 TTTCTTTACTTAAAGC -s mr.mrrefChr5 245115 16 + 294540 TTTGTTTCCTAATAGC -s simCow_chr6.simCow.chr6 383271 16 + 602619 TTTATTTGTTTAGAGC -s simDog_chr6.simDog.chr6 373829 16 + 593897 TTTCTTTACTTAAAGC -s simHuman_chr6.simHuman.chr6 377638 16 + 601863 TTACTTTACTTACAGC -s simRat_chr6.simRat.chr6 391287 16 + 647215 TTTGTTTCCTAATAGC - -a -s simMouse_chr6.simMouse.chr6 391383 13 + 636262 CTGGGGACTTATA -s Anc1.Anc1refChr6 53434 11 + 197743 CAGGggctt--aa -s mr.mrrefChr5 245183 11 + 294540 CTGGGAACT--AA -s simHuman_chr6.simHuman.chr6 377704 11 + 601863 CAGGggctt--aa -s simRat_chr6.simRat.chr6 391358 11 + 647215 CTGGGAACT--AG - -a -s simMouse_chr6.simMouse.chr6 391396 36 + 636262 GTTGACCCTGGGAATGATCTTGAGCATCATGATCTA -s Anc0.Anc0refChr3 23963 23 + 222631 -------------ACTATTTTAAGCAACCTGAAGTA -s Anc1.Anc1refChr6 53445 36 + 197743 TTCTATTTCGGTTACTATTTTAAGCAACCTGAAGTA -s Anc2.Anc2refChr13 27347 23 + 96486 -------------GCTATTCTAAGCAACCTGAAGTA -s mr.mrrefChr5 245194 36 + 294540 GTTGACCCTGGGAATGATCTTGAGCATCATGATCTA -s simCow_chr6.simCow.chr6 383350 23 + 602619 -------------GCTATTCTAAGCAGCATGAAGTA -s simDog_chr6.simDog.chr6 373897 23 + 593897 -------------GCTATTCTAAACAACCTGAAGTA -s simHuman_chr6.simHuman.chr6 377843 36 + 601863 TTCTATTTCGGTTACTATTTGAAGCAACCTGCAGTA -s simRat_chr6.simRat.chr6 391369 36 + 647215 GTTGACCCTAGGACTGAACTTGAGTATCATGATCTA - -a -s simMouse_chr6.simMouse.chr6 391432 16 + 636262 GTACGTGTGGCCACAC -s Anc0.Anc0refChr3 23986 10 + 222631 TTA------ACCGTAT -s Anc1.Anc1refChr6 53481 10 + 197743 TTA------ACCGTAT -s Anc2.Anc2refChr13 27373 10 + 96486 TTA------ACCGTAT -s mr.mrrefChr5 245230 16 + 294540 GTACGTGTGGCCACAC -s simCow_chr6.simCow.chr6 383376 10 + 602619 TTA------ATTGTAT -s simDog_chr6.simDog.chr6 373923 8 + 593897 TTA------ACC--AT -s simHuman_chr6.simHuman.chr6 377879 10 + 601863 TTA------ACCTTAT -s simRat_chr6.simRat.chr6 391405 16 + 647215 GTACGTGTGACCAGAC - -a -s simMouse_chr6.simMouse.chr6 391448 8 + 636262 TGTAGGTA -s Anc0.Anc0refChr3 24003 8 + 222631 TGGAAATA -s Anc1.Anc1refChr6 53498 8 + 197743 TGGAAATA -s Anc2.Anc2refChr13 27390 8 + 96486 TGGGAATG -s mr.mrrefChr5 245246 8 + 294540 TGTAGGTA -s simCow_chr6.simCow.chr6 383393 8 + 602619 TGTGAATC -s simDog_chr6.simDog.chr6 373938 8 + 593897 TGGGAATG -s simHuman_chr6.simHuman.chr6 377896 8 + 601863 TGGAAATA -s simRat_chr6.simRat.chr6 391421 8 + 647215 TGTAGGTA - -a -s simMouse_chr6.simMouse.chr6 391456 65 + 636262 CTAATTAGCTATTACTGCACTTAATTTATTAAGCCCGGCAAGGCCAGCAAGGCCTTGTCATACAC -s Anc0.Anc0refChr3 24013 55 + 222631 CTGACTGGCTACTACAGCAATTG-TTTAGTAACCCTGGGAAGACCA---------TGTTATACAT -s Anc1.Anc1refChr6 53508 56 + 197743 CTGACTGGCTACTACAGCAATTGGTTTAGTAACCCTGGGAAGACCA---------TGTTATACAT -s Anc2.Anc2refChr13 27400 55 + 96486 CTGACTGGCTGCTACAACAATTG-TTTAGTAACCCTGGGAAGACCA---------TGTTATACAT -s mr.mrrefChr5 245254 56 + 294540 CTAATTAGCTATTACTGCACTTAATTTATTAAGCCTGGCAAGGCCA---------TGTCATACAC -s simCow_chr6.simCow.chr6 383403 54 + 602619 CTGACTGGCTGCTACTACGGTTG-TTTAGTGAATCTGGGATCGCCA---------TGT-ATACAT -s simDog_chr6.simDog.chr6 373948 34 + 593897 C--------------AACAA--------GCAACCCTGGGAAGACCA---------TGTTCTACAT -s simHuman_chr6.simHuman.chr6 377906 56 + 601863 CTGACTGACTACTGTAGTAATTGGTTTAGTAACCCTGGGAAGACCA---------TGTTATATAT -s simRat_chr6.simRat.chr6 391429 56 + 647215 CTAATTAGCTATCACTGCACTTAATTTATTAAGCTTGGCAGGGTCA---------TGTCTTACGC - -a -s simMouse_chr6.simMouse.chr6 391521 2 + 636262 AT -s Anc0.Anc0refChr3 24070 1 + 222631 -T -s Anc1.Anc1refChr6 53568 2 + 197743 AT -s Anc2.Anc2refChr13 27457 1 + 96486 -T -s mr.mrrefChr5 245314 2 + 294540 AT -s simCow_chr6.simCow.chr6 383459 1 + 602619 -T -s simDog_chr6.simDog.chr6 373984 1 + 593897 -T -s simHuman_chr6.simHuman.chr6 377966 2 + 601863 AA -s simRat_chr6.simRat.chr6 391489 2 + 647215 AT - -a -s simMouse_chr6.simMouse.chr6 391523 13 + 636262 GGCATACTGGTTA -s Anc0.Anc0refChr3 24071 13 + 222631 GGCATACTAGTTA -s Anc1.Anc1refChr6 53570 13 + 197743 GGCATACTAGTTA -s Anc2.Anc2refChr13 27458 13 + 96486 GGCATACTAGTTG -s mr.mrrefChr5 245316 13 + 294540 GGCATACTAGTTA -s simCow_chr6.simCow.chr6 383462 13 + 602619 GGCATACTAGTTG -s simDog_chr6.simDog.chr6 373985 13 + 593897 GGCATACTAGGTG -s simHuman_chr6.simHuman.chr6 377968 13 + 601863 GGCATACTAGTTA -s simRat_chr6.simRat.chr6 391491 13 + 647215 GGCTTACTAGTTA - -a -s simMouse_chr6.simMouse.chr6 391536 80 + 636262 CAGACTGGAACCACTCCTCATGGCTTACTTGGGATTAGGTGGGGGTAATTCACTTGACATTACCCTGTACAATATTTGAG -s Anc0.Anc0refChr3 24084 80 + 222631 CGGAACAGTGCAACTTCTTGTGGTTTACTGGGGGTGAGTTGGGGGTGATTAACATGACATTGTCCTGCACAATATTCTAT -s Anc1.Anc1refChr6 53583 80 + 197743 CGGAACAGTGCAACTTCTTGTGGTTTACTGGGGGTGAGTTGGGGGTGATTAACATGACATTGTCCTGCACAATATTCTAT -s Anc2.Anc2refChr13 27471 80 + 96486 CGGAACAGTGCAACTTCTTGTGGTTTACTGGGGGTGAGTTGGGGGTGATTAACATGACATGGTCCTACACAATATTCTAT -s mr.mrrefChr5 245329 80 + 294540 CAGACTAGAACCACTCCTCGTGGCTTACTTGGGGTTAGTTGGGGGTGATTCACTTGACATTATCCTGTACAATATTTGAG -s simCow_chr6.simCow.chr6 383475 79 + 602619 TGGA-CAGTGCAACTTCCTGTGATTTACTGGGGGTGAATTTGGTGTGACTAATGTGACATGGTCCTACACACTATTCTAT -s simDog_chr6.simDog.chr6 373998 80 + 593897 CAGAACAGTGCAGCTTATTGTGGATTGCAGAGGGTGAGTAGAGGGCAGTTAACATGGCATGGTCCTACACAATACTCCAT -s simHuman_chr6.simHuman.chr6 377982 80 + 601863 CGGATCATTGCAAATTCTTGTGGTTAACTGGGGGTGAGTTGGGGGTGATTAACATGACATTGTCCTGCACAACGTTCTAT -s simRat_chr6.simRat.chr6 391504 80 + 647215 CAGACTAGAACCACTCCTGGTGGGATACTAGGGGTTAGTTGGGGGTGACTCACTTGTCATTATCCTGTACAATATTTGAG - -a -s simMouse_chr6.simMouse.chr6 391616 52 + 636262 CCTGAAACGTATTTGCTCCACACACGACTTGCCTGAAAATGTAAGGAATACA -s Anc0.Anc0refChr3 24165 52 + 222631 CCTGAAACATATGTACTTCACACGAGATCTGCCGAAAAGCCCAAGTAATACA -s Anc1.Anc1refChr6 53664 52 + 197743 CCTGAAACATATGTACTTCACACGAGATCTGCCGAAAAGCCCAAGTAATACA -s Anc2.Anc2refChr13 27552 52 + 96486 CCTGAAACATATGTACTTCACACAAGATCTGCCGAAAAGCCCAAGTAATACA -s mr.mrrefChr5 245409 52 + 294540 CCTGAAACATATTTGCTCCACACGCGACTTGCCTGAAAATGTAAGGAATACA -s simCow_chr6.simCow.chr6 383555 51 + 602619 CCTGAAACATATGTACCTCATG-AGGACCTGCGGACAACCACAAGTACTACA -s simDog_chr6.simDog.chr6 374079 52 + 593897 CCTGAAGCTTATGTACTTCACACAAGATCTGCCAAAAAGTCCAAGTAATACA -s simHuman_chr6.simHuman.chr6 378063 52 + 601863 CCTGAAACATATGTACTTCACATGAGATCTGCTGAAAAGCCCAAGTAATAAA -s simRat_chr6.simRat.chr6 391584 52 + 647215 CCTGAAACACACTTGTTCCACACGCTACTTGCCAGAATGTGTAAGGAATACA - -a -s simMouse_chr6.simMouse.chr6 391668 34 + 636262 ATTAAAACGATATGGCTACCAATGGGCACTTTGC -s Anc0.Anc0refChr3 24221 32 + 222631 AT--CAACAATATAGCTACAAGTGGGCACTTTGC -s Anc1.Anc1refChr6 53720 34 + 197743 ATAACAACAATATAGCTACAAGTGGGCACTTTGC -s Anc2.Anc2refChr13 27608 32 + 96486 AT--CAACAATATAGCTACAAGTGGGCACCTTGC -s mr.mrrefChr5 245461 34 + 294540 ATTAAAACAATATAGCTACCAATGGGCACTTTGC -s simCow_chr6.simCow.chr6 383610 32 + 602619 GT--TAACAATATAGCTACAAGTGGGCATCTTGT -s simDog_chr6.simDog.chr6 374135 32 + 593897 AT--CAACACTATAGCTACAAATGAGCACCATGC -s simHuman_chr6.simHuman.chr6 378119 34 + 601863 ACAACAACAATATAACTACAAGTGGGCTCTTTGC -s simRat_chr6.simRat.chr6 391636 34 + 647215 ATTAAAACACTATAGCTACCAATGGGCACCTtgc - -a -s simMouse_chr6.simMouse.chr6 391702 20 + 636262 TGAGGATGTGTAGGCCGTTT -s Anc0.Anc0refChr3 24253 20 + 222631 TGAAGGTGACTAGGTCAGTT -s Anc1.Anc1refChr6 53754 20 + 197743 TGAAGGTGACTAGGTCAGTT -s Anc2.Anc2refChr13 27640 20 + 96486 TGAAGGTGACCAGGTCAGTT -s mr.mrrefChr5 245495 20 + 294540 TGAGGGTGTCTAGGCCATTT -s simCow_chr6.simCow.chr6 383642 19 + 602619 TGAAGGTGACCGAGTCAGT- -s simDog_chr6.simDog.chr6 374167 20 + 593897 TCAAGGTGACCAGGTCAGTT -s simHuman_chr6.simHuman.chr6 378153 20 + 601863 TGAAAGCGACTAGGTCAGTT -s simRat_chr6.simRat.chr6 391875 20 + 647215 TGGGGGTGTCTAGGCCATTT - -a -s simMouse_chr6.simMouse.chr6 391722 34 + 636262 GCATTGGGATCTATGGCTTATATCCTGCTTACAA -s Anc0.Anc0refChr3 24273 33 + 222631 GAATTAAAGTCT-TTGCTTAAATCCTTCTCTAAA -s Anc1.Anc1refChr6 53774 33 + 197743 GAATTAAAGTCT-TTGCTTAAATCCTTCTCTAAA -s Anc2.Anc2refChr13 27661 33 + 96486 GAGTTAAAGTCT-TTGCTTAAATCCTTCTCTAAA -s mr.mrrefChr5 245515 34 + 294540 GCATTGGGATCTATTGCTTATATCCTGCTTAAAA -s simCow_chr6.simCow.chr6 383661 33 + 602619 GATTCAGAACCT-TTGCTTAAATCTGTCTCTAAA -s simDog_chr6.simDog.chr6 374188 33 + 593897 CAGTTGAAGTCT-TTGCTTAAATCCTGCTCTGAA -s simHuman_chr6.simHuman.chr6 378173 33 + 601863 GGATTAAAGTCT-TTGCTTAAATCCTTCTCTAAA -s simRat_chr6.simRat.chr6 391895 34 + 647215 GAGTTGGGATCTATTGCTTATATCATGCTTCAAA - -a -s simMouse_chr6.simMouse.chr6 391756 39 + 636262 TAATAAGAAAGCATCATGCATGCAGTAAGGGATCATACT -s Anc0.Anc0refChr3 24306 35 + 222631 CAATAATAAGAAATCATGCAGTCAGTAT----TAATACT -s Anc1.Anc1refChr6 53807 35 + 197743 CAATAATAAGAAATCATGCAGTCAGTAT----TAATACT -s Anc2.Anc2refChr13 27694 35 + 96486 CAATAATAAGAAACCATACAGTCAATAT----TAATACT -s mr.mrrefChr5 245549 39 + 294540 TAATAAGAAAGCATCATGCATGCAGTAAGGGATCATACT -s simCow_chr6.simCow.chr6 383694 35 + 602619 CAATAATTAGAAGGTATACAGTCAATAA----TAATACT -s simDog_chr6.simDog.chr6 374221 35 + 593897 CAATAATAAGAAACCATACAGTTAATAT----TAATACT -s simHuman_chr6.simHuman.chr6 378206 35 + 601863 CAATGACAAGATATCATGCTGTCAGTAG----TTATACT -s simRat_chr6.simRat.chr6 391931 39 + 647215 TAGTAGGAAATCATCATAAATGCAGTAAGTGATCATACT - -a -s simMouse_chr6.simMouse.chr6 391795 58 + 636262 ACATTACACATAGCAAGATGGAGTATTGACTCCCTTTATTTGATTAGGCCATCTGAAT -s Anc0.Anc0refChr3 24344 58 + 222631 ACATTATTCATAGCAAAATTGAGCATTGACCCCCTTTATTTGACTAGGCCAGCTAAAG -s Anc1.Anc1refChr6 53845 58 + 197743 ACATTATTCATAGCAAAATTGAGCATTGACCCCCTTTATTTGACTAGGCCAGCTAAAG -s Anc2.Anc2refChr13 27732 58 + 96486 CCATTATTCATAGCAAAATTGAGCATTGACCCCCTTTGTTTGACTAGGCCAGCTAGAG -s mr.mrrefChr5 245588 58 + 294540 ACATTACACATAGCAAGATGGAGTATTGACTCCCTTTATTTGATTAGGCCATCTGAAG -s simCow_chr6.simCow.chr6 383732 57 + 602619 CAA-TATTCATAGCAAGATAGAGCATTAACCCCCTTTGTTTGACTAGGGCAACTAGAG -s simDog_chr6.simDog.chr6 374259 44 + 593897 CCATTATTCAGAGCAAAATTTAAGAATG----------TTTGAC----CCAGCTAGAT -s simHuman_chr6.simHuman.chr6 378245 58 + 601863 ATATTATTCATAGCAAAATTGAGCATTGACCCCCTTTATTTGACTAGGCCAGTTCAAG -s simRat_chr6.simRat.chr6 391970 57 + 647215 ACATTGCACATAGCGAGATGGAGTACTGTCTCCCTTTGTTTGATT-GGCCATCTGAAG - -a -s simMouse_chr6.simMouse.chr6 391853 22 + 636262 TCAACACGCCAGACAGGCAGCA -s Anc0.Anc0refChr3 24402 22 + 222631 CCAACACACCAGTCAGGTAGTA -s Anc1.Anc1refChr6 53903 22 + 197743 CCAACACACCAGTCAGGTAGTA -s Anc2.Anc2refChr13 27790 22 + 96486 CCAACACCCCAGTCAGGTAGTA -s mr.mrrefChr5 245646 22 + 294540 TCAACACACCAGACAGGCAGTA -s simCow_chr6.simCow.chr6 383790 20 + 602619 CCACCTCCCCAGTCAGGTTG-- -s simDog_chr6.simDog.chr6 374303 22 + 593897 TTAACACCCCAGTTGGGTAGTA -s simHuman_chr6.simHuman.chr6 378303 22 + 601863 CCAACACACCAGTCAGGTAATA -s simRat_chr6.simRat.chr6 392027 22 + 647215 TCAACACACCAGACGGGCAGTA - -a -s simMouse_chr6.simMouse.chr6 391875 23 + 636262 CTTGAACTAAAAGCTTTACAGAT -s Anc0.Anc0refChr3 24443 23 + 222631 CTTGAAACATAAGCTTTACAAGT -s Anc1.Anc1refChr6 53944 23 + 197743 CTTGAAACATAAGCTTTACAAGT -s Anc2.Anc2refChr13 27831 23 + 96486 CCTGAAACATAACCTTTACAAGT -s mr.mrrefChr5 245668 23 + 294540 CTTGAACTAGAAGCTTTACAAAT -s simCow_chr6.simCow.chr6 383827 23 + 602619 CCTGAAACAGAAACTCTACACCT -s simDog_chr6.simDog.chr6 374343 16 + 593897 G-------ATAACCTTTACAAGC -s simHuman_chr6.simHuman.chr6 378344 23 + 601863 CTAGGAACATAAGTTTTACGAGT -s simRat_chr6.simRat.chr6 392049 23 + 647215 CTTGAACTAGAAGCTTTAAAAAT - -a -s simMouse_chr6.simMouse.chr6 391898 92 + 636262 TCTGCTTTTTAGTGCCCGGTGACGGGTCTGGCAAGCGAGACACTCCTGATCTTGGTTGATACAGGATAGCGCTTACCTACGACTCCGTCTCA -s Anc0.Anc0refChr3 24476 87 + 222631 TCTGCTCCCTAGTGCACAGTGTCGCGTTTGGTAAGCGGGAAATTGTTGAT-T-GGTGGCTACATGATAGC-CTTACCCACGACTCCCCTC-- -s Anc1.Anc1refChr6 53977 90 + 197743 TCTGCTCCCTAGTGCACAGTGTCGCGTTTGGTAAGCGGGAAATTGTTGAT-TTGGTGGCTACATGATAGC-CTTACCCACGACTCCCCTCCG -s Anc2.Anc2refChr13 27864 87 + 96486 TCTGCTCCCTAGTGCACAGTATCGCGTTTGGTAAGCGGGAAATTGTTGAT-T-GGTGGCTACACGACAGG-CTTGCCCCCGACTCCCCTC-- -s mr.mrrefChr5 245691 92 + 294540 TCTGCTTCTTAGTGCACGGTGACGGGTCTGGCAAGCGAGACACTCCTGATCTTGGTTGCTACATGATAGCGCTTACCCACGACTCCGTCTCA -s simCow_chr6.simCow.chr6 383860 82 + 602619 TCTGCTACCTAGTTCACAGTAT-----TTGTAAAGCGAGAATCTGTTGGT-T-GGTTCCTACACGACAGG-CTCGGCTCCGGCTCCCCTC-- -s simDog_chr6.simDog.chr6 374369 86 + 593897 TACGCTCC-TAGTGCACAGTATCGCGTTTGGTAGTCGGGAAATTGTTGAT-T-GGTGGCCGTACGACCCG-CTTGCCCCCAACTCCCCTC-- -s simHuman_chr6.simHuman.chr6 378377 85 + 601863 TCTGCTCCCTAGTGCATAGTGCCGCGTGCGGTAAGCGGGAAATTA------TTGGTGGCTACATGATAGC-CTTACCCACGACTCCCCTCCG -s simRat_chr6.simRat.chr6 392072 91 + 647215 TCTGCTACTTAGTGCACGGTGAGGGGTCTGGCAAG-GAGACACTTCTGATCTTGGTTGCTACATGACAGAACCTATCCACGATTTCGTCTCA - -a -s simMouse_chr6.simMouse.chr6 391990 47 + 636262 TACAACGACGAAAAGTAATGGGCGTTCGGTCTAGGAATTTTTCTAGC -s Anc0.Anc0refChr3 24564 46 + 222631 TACAACAAGGATAAAGGATGCACCTTCGGTCTAGGAATTTTTC-TGG -s Anc1.Anc1refChr6 54068 47 + 197743 TACAACAAGGATAAAGGATGCACCTTCGGTCTAGGAATTTTTCCTGG -s Anc2.Anc2refChr13 27952 46 + 96486 TACAACAAGGTTAAAGGGTCCACCTCCGGATTGGGAGTTTTTC-TGG -s mr.mrrefChr5 245783 47 + 294540 TACAACGACGAAAAGTAATGGGCGTTCGGTCTAGGAATTTTTCCAGG -s simCow_chr6.simCow.chr6 383943 38 + 602619 TACATCAAGCTTAAAGGGTCCTC--------TGGGAGTTTTTT-TGG -s simDog_chr6.simDog.chr6 374456 46 + 593897 CACAACACAGTTCAAGGGTCCACCTCCGGATTGGGAGTTTATC-TCA -s simHuman_chr6.simHuman.chr6 378464 47 + 601863 TAAAACAAGGAGAAAGGATGCACCTTCGGTCCAGGAATTTTTCCTGG -s simRat_chr6.simRat.chr6 392163 47 + 647215 TACAACGACGAAAAGTCATGGGCGTTCGGTCTAGGAGTTTTTCCGGG - -a -s simMouse_chr6.simMouse.chr6 392037 3 + 636262 GGT -s Anc0.Anc0refChr3 24611 3 + 222631 AGC -s Anc1.Anc1refChr6 54116 3 + 197743 AGC -s Anc2.Anc2refChr13 27999 3 + 96486 AGC -s mr.mrrefChr5 245830 3 + 294540 AGC -s simCow_chr6.simCow.chr6 383982 2 + 602619 A-C -s simDog_chr6.simDog.chr6 374503 3 + 593897 AGC -s simHuman_chr6.simHuman.chr6 378512 3 + 601863 AGC -s simRat_chr6.simRat.chr6 392210 3 + 647215 AGC - -a -s simMouse_chr6.simMouse.chr6 392040 66 + 636262 GAATACATCAACCAAAAAGAGCTGATGGCGCGGAGGTTATAGACAACAGAGACACAGACATGACCA -s Anc0.Anc0refChr3 24614 60 + 222631 AAATACTCCAACCCCATAGCTTCGAAGACGCGGAGCGTATAGACAGCCAAG-CACAGTCAT----- -s Anc1.Anc1refChr6 54119 63 + 197743 AAATACTCCAACCCCATAGCTTCGAAGACGCGGAGCGTATAGACAGCCAAG-CACAGTCAT--CCA -s Anc2.Anc2refChr13 28002 60 + 96486 AATTACTCCAACTCCATAGCTTCGAAGACGCGGAGCGTATAGACAGCCAAG-CACAGTCAT----- -s mr.mrrefChr5 245833 65 + 294540 GAATACTTCAACCAAAAAGAGCTGAAGGCGCGGAGGTTATAGACAGCAGAG-CACAGACATGACCA -s simCow_chr6.simCow.chr6 383984 58 + 602619 TATTACTCCAACTCCAAAGCGTCCAAGACGCGGAG--TATAGATAGCCCAG-CACTGTCAT----- -s simDog_chr6.simDog.chr6 374506 56 + 593897 AATTACTCCAACTCCATAGCTTCGAACACGCGGAGCGTATAGACACCCAAG-CACAA--------- -s simHuman_chr6.simHuman.chr6 378515 63 + 601863 CAATTCTCCAACCTCATAGGATCGAAGACTCGGAGCGTATAGGCAGCCTAG-CACAGTTAT--CCA -s simRat_chr6.simRat.chr6 392227 65 + 647215 AGATACTTCAATCAAAAGGAGCTGAAGGCGCGGGGGTCATAGACAGCAGAG-CACGGACATGACTG - -a -s simMouse_chr6.simMouse.chr6 392106 69 + 636262 CTGTGTCACAGTTGCTAGGGTTCAACCATTTCAACACATAGTCCCCGTCACAGATTATCTGCATCTCAA -s Anc0.Anc0refChr3 24674 38 + 222631 -----GCAACCCT-------CTCACACATT-------------------ACAGATTAGCTGTGTACCGA -s Anc1.Anc1refChr6 54182 62 + 197743 CTGGGGCAACCCT-------CTCACACATTTCTTGTCATGGTGTCCAATACAGATTAGCTGTGTACCGA -s Anc2.Anc2refChr13 28062 38 + 96486 -----GCAACCTT-------CTCACACATT-------------------ACAGGTGAGCCGTGTACCGA -s mr.mrrefChr5 245898 69 + 294540 CTGGGTCACAGCTGCTAGGGTTCAACCATTTCAACACATAGTCCCCATCACAGATTATCTGCATCTCAA -s simCow_chr6.simCow.chr6 384042 18 + 602619 -----GCAACCTT-------CTCACACATT--------------------------------------- -s simDog_chr6.simDog.chr6 374562 20 + 593897 -------------------------------------------------ACAGGTGAGCCGTGTACCGA -s simHuman_chr6.simHuman.chr6 378579 62 + 601863 CTGGGGCAATCCT-------CTCACACATTTCTTGTCATGGTGTCCAATACAGATTAGCTGTGTTCCGA -s simRat_chr6.simRat.chr6 392292 69 + 647215 CTGGGTCACAACTGCTTGGGTTCAACCATTTCAACACATAGTCCCCATCACAGATTATTTGCATCTCAA - -a -s simMouse_chr6.simMouse.chr6 392175 31 + 636262 ATTGACGACACCCAATTTCTGGGTGGCACTC -s Anc0.Anc0refChr3 24718 31 + 222631 AACATCGACACCTAACATCCGGGTGGCACTC -s Anc1.Anc1refChr6 54250 31 + 197743 AACATCGACACCTAACATCCGGGTGGCACTC -s Anc2.Anc2refChr13 28106 31 + 96486 AACATCGGCACCTAACATCCGGGTGGCACTC -s mr.mrrefChr5 245967 31 + 294540 ATCGTCGACACCTAATTTCCGGGTGGCACTC -s simCow_chr6.simCow.chr6 384063 27 + 602619 ATCAT----ACCTAATAACCGGGTGGTACTC -s simDog_chr6.simDog.chr6 374588 31 + 593897 AACATCGGCACCTATCGTCCTGGTGGCATTC -s simHuman_chr6.simHuman.chr6 378647 31 + 601863 AACATCGACACCTTACATCCGGGTGGCACTT -s simRat_chr6.simRat.chr6 392361 31 + 647215 ATCGTCGACACCTAATTTCCGGGTGGCACTC - -a -s simMouse_chr6.simMouse.chr6 392206 4 + 636262 CTTC -s Anc0.Anc0refChr3 24761 4 + 222631 TTGC -s Anc1.Anc1refChr6 54293 4 + 197743 TTGC -s Anc2.Anc2refChr13 28149 4 + 96486 TTGC -s mr.mrrefChr5 245998 4 + 294540 CTTC -s simCow_chr6.simCow.chr6 384102 4 + 602619 TTGC -s simDog_chr6.simDog.chr6 374626 4 + 593897 TTGC -s simHuman_chr6.simHuman.chr6 378690 4 + 601863 TTAC -s simRat_chr6.simRat.chr6 392392 4 + 647215 CCTC - -a -s simMouse_chr6.simMouse.chr6 392210 8 + 636262 TTGGAGCA -s Anc0.Anc0refChr3 24765 8 + 222631 TTAGCTCA -s Anc1.Anc1refChr6 54297 8 + 197743 TTAGCTCA -s Anc2.Anc2refChr13 28153 8 + 96486 TTAGCTCA -s mr.mrrefChr5 246002 8 + 294540 TTGGAGCA -s simCow_chr6.simCow.chr6 384106 8 + 602619 GCATCTCA -s simDog_chr6.simDog.chr6 374664 8 + 593897 TTAGTTCA -s simHuman_chr6.simHuman.chr6 378694 8 + 601863 TTCGCTCA -s simRat_chr6.simRat.chr6 392396 8 + 647215 CTGGGGCA - -a -s simMouse_chr6.simMouse.chr6 392218 1 + 636262 C -s Anc0.Anc0refChr3 24773 1 + 222631 T -s Anc1.Anc1refChr6 54305 1 + 197743 T -s Anc2.Anc2refChr13 28161 1 + 96486 T -s mr.mrrefChr5 246010 1 + 294540 C -s simCow_chr6.simCow.chr6 384114 1 + 602619 T -s simDog_chr6.simDog.chr6 374672 1 + 593897 T -s simHuman_chr6.simHuman.chr6 378702 1 + 601863 T -s simRat_chr6.simRat.chr6 392412 1 + 647215 C - -a -s simMouse_chr6.simMouse.chr6 392219 4 + 636262 TCGA -s Anc0.Anc0refChr3 24774 4 + 222631 TACA -s Anc1.Anc1refChr6 54306 4 + 197743 TACA -s Anc2.Anc2refChr13 28162 4 + 96486 TACA -s mr.mrrefChr5 246011 4 + 294540 TCGA -s simCow_chr6.simCow.chr6 384121 4 + 602619 TACG -s simDog_chr6.simDog.chr6 374673 4 + 593897 TACA -s simHuman_chr6.simHuman.chr6 378703 4 + 601863 TACA -s simRat_chr6.simRat.chr6 392413 4 + 647215 TCGC - -a -s simMouse_chr6.simMouse.chr6 392223 10 + 636262 ACCCTCCGAG -s Anc0.Anc0refChr3 24786 10 + 222631 ACCTTCAGAG -s Anc1.Anc1refChr6 54318 10 + 197743 ACCTTCAGAG -s Anc2.Anc2refChr13 28174 10 + 96486 ACCTTCAGAG -s mr.mrrefChr5 246015 10 + 294540 ACCCTCCGAG -s simCow_chr6.simCow.chr6 384133 10 + 602619 ACCTTCAGAG -s simDog_chr6.simDog.chr6 374685 10 + 593897 ATCTTCAGAG -s simHuman_chr6.simHuman.chr6 378715 10 + 601863 TCCTTCAAAG -s simRat_chr6.simRat.chr6 392417 10 + 647215 GCCCTCCAAG - -a -s simMouse_chr6.simMouse.chr6 392233 10 + 636262 TCAGCCATGC -s Anc0.Anc0refChr3 24800 10 + 222631 TCAACGCAGC -s Anc1.Anc1refChr6 54332 10 + 197743 TCAACGCAGC -s Anc2.Anc2refChr13 28188 10 + 96486 TCAACGCAGC -s mr.mrrefChr5 246025 10 + 294540 TCAGCCATGC -s simCow_chr6.simCow.chr6 384147 10 + 602619 TCAACGCAGC -s simDog_chr6.simDog.chr6 374699 10 + 593897 TCAACAGAGC -s simHuman_chr6.simHuman.chr6 378729 10 + 601863 TCAATGCAGC -s simRat_chr6.simRat.chr6 392427 10 + 647215 TCTACCGGGC - -a -s simMouse_chr6.simMouse.chr6 392243 4 + 636262 CGAT -s Anc0.Anc0refChr3 24814 4 + 222631 CCGT -s Anc1.Anc1refChr6 54346 4 + 197743 CCGT -s Anc2.Anc2refChr13 28202 4 + 96486 CCGT -s mr.mrrefChr5 246035 4 + 294540 CGAT -s simCow_chr6.simCow.chr6 384161 4 + 602619 CCGC -s simDog_chr6.simDog.chr6 374713 4 + 593897 CCGT -s simHuman_chr6.simHuman.chr6 378743 4 + 601863 CTGT -s simRat_chr6.simRat.chr6 392437 4 + 647215 CGAT - -a -s simMouse_chr6.simMouse.chr6 392247 43 + 636262 TTTCTGATGACGCAATACACCCGGTGTCCAAGGCTTCGTGTGC -s Anc0.Anc0refChr3 24825 20 + 222631 CGTCTGGCGGCGCTAT-----------------------TTAC -s Anc1.Anc1refChr6 54357 20 + 197743 CGTCTGGCGGCGCTAT-----------------------TTAC -s Anc2.Anc2refChr13 28233 20 + 96486 CGTCTGGCGGCGCTAT-----------------------TTAC -s mr.mrrefChr5 246039 43 + 294540 TTTCTGATGACGCAATACACCCGGTGTCCAAGGCTTCGTGTGC -s simCow_chr6.simCow.chr6 384192 20 + 602619 AGTGTGGCGGCGCAAT-----------------------TTCA -s simDog_chr6.simDog.chr6 374744 20 + 593897 CCTCTAGCGGCGCTAT-----------------------ATAC -s simHuman_chr6.simHuman.chr6 378754 20 + 601863 CGTCTGGCGGCGCGAC-----------------------TCAC -s simRat_chr6.simRat.chr6 392441 43 + 647215 TTTCTGACGACGCGACACATTTGGGGTCCAAGGCTTCGTACGA - -a -s simMouse_chr6.simMouse.chr6 392290 5 + 636262 GTGAA -s Anc0.Anc0refChr3 24854 5 + 222631 GCGCC -s Anc1.Anc1refChr6 54386 5 + 197743 GCGCC -s Anc2.Anc2refChr13 28262 5 + 96486 GCGCC -s mr.mrrefChr5 246082 5 + 294540 GTGAA -s simCow_chr6.simCow.chr6 384221 5 + 602619 GCGCC -s simDog_chr6.simDog.chr6 374773 5 + 593897 GCACC -s simHuman_chr6.simHuman.chr6 378783 5 + 601863 GCGCC -s simRat_chr6.simRat.chr6 392484 5 + 647215 GTGAG - -a -s simMouse_chr6.simMouse.chr6 392295 26 + 636262 TTGGCTCACCGTGGGGATTGCCCCGT -s Anc0.Anc0refChr3 24859 19 + 222631 C-------CCTGCGGGATTGCCTCGT -s Anc1.Anc1refChr6 54391 26 + 197743 CTGCCCCTCCTGCGGGATTGCCTCGT -s Anc2.Anc2refChr13 28267 19 + 96486 C-------CATGCGGGATTGCCTCGT -s mr.mrrefChr5 246087 26 + 294540 TTGGCTCACCGTGGGGATTGCCCCGT -s simCow_chr6.simCow.chr6 384227 19 + 602619 T-------CATGCGGGATTGCCTCTC -s simDog_chr6.simDog.chr6 374778 14 + 593897 C-------CAT-----ATTGCCCCGT -s simHuman_chr6.simHuman.chr6 378788 26 + 601863 CTGCCCCTCCAGCAGGGTTGCTTCGT -s simRat_chr6.simRat.chr6 392489 26 + 647215 TTGGCTCACCGTGGGGCTCGCCCCCC - -a -s simMouse_chr6.simMouse.chr6 392321 66 + 636262 CCCTTAGTCCATGTCGCTCTTAAGGTAAAAAGCAAGCTCTGGTAAGGTCTGTAAATTACCCTTGAG -s Anc0.Anc0refChr3 24878 44 + 222631 CCCT-AGT-------------------AACAGCAATC--CAGTAAAAACTCTTAATTACACTTGAG -s Anc1.Anc1refChr6 54417 46 + 197743 CCCT-AGT-------------------AACAGCAATCTCCAGTAAAAACTCTTAATTACACTTGAG -s Anc2.Anc2refChr13 28286 44 + 96486 CCCT-GAT-------------------AACAGCAATC--CAGCAAAAACTCTTAATTACACTTCAG -s mr.mrrefChr5 246113 47 + 294540 CCCTTAGT-------------------AAAAGCAAGCTCTGGTAAGGTCTGTAAATTACCCTTGAG -s simCow_chr6.simCow.chr6 384246 1 + 602619 C----------------------------------------------------------------- -s simDog_chr6.simDog.chr6 374792 44 + 593897 CCCT-GAT-------------------AACAGCAATC--CAGCAAAAACTCTTAATTACACTTCAG -s simHuman_chr6.simHuman.chr6 378814 44 + 601863 CCCT-AGT-------------------AACAGCAATCTCCAATAGACACTCTCAATT--TCTTGAC -s simRat_chr6.simRat.chr6 392516 47 + 647215 CCCCTAGT-------------------AAAAGGATTCTGTGGTAAACACTGTATATTATCCTTGGG - -a -s simMouse_chr6.simMouse.chr6 392387 141 + 636262 TGAACTAGAACAGGTAGAATGAACAGGTAGTATAGAACTGTGCAATGAAAAAAGAATTTTTGAGTGCCAATTGTTGTCCTTCAGTCTTGAAAGACATGCATTAGTAAGGATACTCCTCTTCCTCTGTGTTCTACATCCAGA -s Anc0.Anc0refChr3 24922 1 + 222631 T-------------------------------------------------------------------------------------------------------------------------------------------- -s Anc1.Anc1refChr6 54463 1 + 197743 T-------------------------------------------------------------------------------------------------------------------------------------------- -s Anc2.Anc2refChr13 28331 1 + 96486 T-------------------------------------------------------------------------------------------------------------------------------------------- -s mr.mrrefChr5 246160 141 + 294540 TGAACTAGAACAGGTAGAATGAACAGGTAGTATAGAACTGTGCAATGAAAAAAGAATTTTTGAGTGCCAATTGTTGTCCTTCAGTCTTGAAAGACATGCATTAGTAAGGATACTCCTCTTCCTCTGTGTTCTACATCCAGA -s simDog_chr6.simDog.chr6 374837 1 + 593897 T-------------------------------------------------------------------------------------------------------------------------------------------- -s simHuman_chr6.simHuman.chr6 378858 1 + 601863 T-------------------------------------------------------------------------------------------------------------------------------------------- -s simRat_chr6.simRat.chr6 392563 141 + 647215 TAGAATAGAACAGGTAGAATGAACAGGTAGTATAGGACTGTACAATGAAAACAGAATTTCTCAGTGCCAAATGTGGTCCATCAATTTAGGAAGACATGCATTAGATAAGATACTATTGCGCCTCTGTGTCCTATATCCAGA - -a -s simMouse_chr6.simMouse.chr6 392528 215 + 636262 GGCGATGAAGTGAGGAGCAAAGCCAAACACATAGTACTTTGATTCTGTGGACCTTGTTGATTCCAAATTAGCATGGCTAATCACATTGTCCCCAATCCCATTGTTCCCATTGAGTGTTTGTATCATACATCCCCACCATAAGCCAGAACTAACCTATGCAGCTCAGTAGGTCTACTATTGCACCATGCGCAGGCGAGGACATTTAGCAGCCTGAT -s Anc0.Anc0refChr3 24923 20 + 222631 ----------------------------------------------------------------------------------------------------------------------------ATAGATT-----------------------------------------------------------------------TTCGCAGCCTGAC -s Anc1.Anc1refChr6 54464 26 + 197743 ----------------------------------------------------------------------------------------------------------------------------ATAGATTGG-----------------------------------------------------------------CCTTTTCGCAGCCTGAC -s Anc2.Anc2refChr13 28332 20 + 96486 ----------------------------------------------------------------------------------------------------------------------------ATAGACT-----------------------------------------------------------------------TTCTCAGCCTGGC -s mr.mrrefChr5 246301 150 + 294540 GGCGATGAAGTGAGGAGCAAAGCCAAACACATAGTACTTTGATTCTGTGGACCTTGTTGATTCCAAATTAGCATGGCTAATCACATTGTCCCCAATCCCATTGTTCCCATTGAGTGTTTGTATCATACATCCC-----------------------------------------------------------------ACATTTAGCAGCCTGAT -s simDog_chr6.simDog.chr6 374838 20 + 593897 ----------------------------------------------------------------------------------------------------------------------------ATAGACT-----------------------------------------------------------------------TTCTCAGCCTGGC -s simHuman_chr6.simHuman.chr6 378859 26 + 601863 ----------------------------------------------------------------------------------------------------------------------------ATAACTTGG-----------------------------------------------------------------CCTTTTCGCAGCCTGAC -s simRat_chr6.simRat.chr6 392705 150 + 647215 GGGTATGAAGCAAGGAGCCGAGGCAAACACATAGTACTGTGATTCTTTGGGCCTTGTTGCTTCCAGACTAGGATGGCTAATCACATTGTCCCCAACCACATTGTTCCCATTGAGTGTTTGTATAATACACCCC-----------------------------------------------------------------ACATTTAGCAGCCTGAT - -a -s simMouse_chr6.simMouse.chr6 392743 26 + 636262 TGAAAAGATGACTAACACAACTCCGA -s Anc0.Anc0refChr3 24943 21 + 222631 GGAGTACA-----AGCACAACTCCAA -s Anc1.Anc1refChr6 54490 21 + 197743 GGAGTACA-----AGCACAACTCCAA -s Anc2.Anc2refChr13 28352 21 + 96486 GGAGTACG-----CGCACAACTCCAA -s mr.mrrefChr5 246451 26 + 294540 TGAAAAGATGACTAACACAACTCCGA -s simCow_chr6.simCow.chr6 384247 14 + 602619 -------G-----GGCGGAATGCCAA -s simDog_chr6.simDog.chr6 374863 21 + 593897 GGAGTACG-----CGCACAACTCCAA -s simHuman_chr6.simHuman.chr6 378885 21 + 601863 GGAGTATA-----AGCACAACTCCAA -s simRat_chr6.simRat.chr6 392855 26 + 647215 TGAAAGGATGACTAACACAACTCTAA - -a -s simMouse_chr6.simMouse.chr6 392769 24 + 636262 GCTTACTAAAACTTAGTAGGAGCT -s Anc0.Anc0refChr3 24964 23 + 222631 GCATACTAGAACC-ACTGGGAACC -s Anc1.Anc1refChr6 54511 23 + 197743 GCATACTAGAACC-ACTGGGAACC -s Anc2.Anc2refChr13 28373 23 + 96486 GCATACCAGAACC-ACTGGGAAGC -s mr.mrrefChr5 246477 24 + 294540 GCTTACTAAAACTTAGTAGGAGCT -s simCow_chr6.simCow.chr6 384272 23 + 602619 GAATCGGTGAATC-TGTGGGAAGC -s simDog_chr6.simDog.chr6 374884 23 + 593897 GCATACCAGAACC-ACTGGGCAGC -s simHuman_chr6.simHuman.chr6 378906 23 + 601863 TCCCACTAGAACC-GCTGGGAACC -s simRat_chr6.simRat.chr6 392881 24 + 647215 GCTTACTAAAACTTAGTAGGAGCT - -a -s simMouse_chr6.simMouse.chr6 392793 30 + 636262 CCAATATTGTTAGTAGACAAGTAGGAGATT -s Anc0.Anc0refChr3 25032 30 + 222631 CTAATGTTGCAAGTGGATTGGTAGGAGATT -s Anc1.Anc1refChr6 54579 30 + 197743 CTAATGTTGCAAGTGGATTGGTAGGAGATT -s Anc2.Anc2refChr13 28441 30 + 96486 CTAATGTTGCAAGTGGATTGGTAGGAGATC -s mr.mrrefChr5 246501 30 + 294540 CCAATATTGTTAGTAGACAAGTAGGAGATT -s simCow_chr6.simCow.chr6 384344 30 + 602619 CTGATATTACATGTGGATTGGTAGCAGATC -s simDog_chr6.simDog.chr6 374951 30 + 593897 CTAATGTTGCAAGTGGATTGGTAGGAGATC -s simHuman_chr6.simHuman.chr6 378975 30 + 601863 CTAATGTTGCAACTGCATTTGTAGGAAATT -s simRat_chr6.simRat.chr6 392905 30 + 647215 CCAATATTGTGAGTAGATATGTAGGAGATT - -a -s simMouse_chr6.simMouse.chr6 392823 47 + 636262 GATGTGATTGAGACTGTCAACTAATAAATAGTCATAAAATTGATGGG -s Anc0.Anc0refChr3 25063 43 + 222631 GAAGTGATAGAGACTGCCAATGAATAAAAACCCATAAA---GATCG- -s Anc1.Anc1refChr6 54610 44 + 197743 GAAGTGATAGAGACTGCCAATGAATAAAAACCCATAAA---GATCGG -s Anc2.Anc2refChr13 28472 43 + 96486 GAAGTGGCAGAGACTGCCAATGAATAAAAACCCATAAA---CATCA- -s mr.mrrefChr5 246531 47 + 294540 GATGTGATTGAGACTGTCAACTAATAAATAGTCATAAAATTGATGGG -s simCow_chr6.simCow.chr6 384375 43 + 602619 GAAGTGCCAGAGACTGTCAATTAATAAGAACCCATAGA---AATCA- -s simDog_chr6.simDog.chr6 374982 41 + 593897 CAAGTGGCAGAAACTGCCAATGAA--AAAACTCATAAG---CATCA- -s simHuman_chr6.simHuman.chr6 379006 42 + 601863 GAAGTGATGGAG--TACCAATAAACAAAAACCTATAAA---GATCGG -s simRat_chr6.simRat.chr6 392935 47 + 647215 GATGTGATTGAGACTGTTACCTAATAAATAGCCATAAAGTTGATGGG - -a -s simMouse_chr6.simMouse.chr6 392870 7 + 636262 ATGACAT -s Anc0.Anc0refChr3 25106 7 + 222631 ATGACAT -s Anc1.Anc1refChr6 54654 7 + 197743 ATGACAT -s Anc2.Anc2refChr13 28515 7 + 96486 ATGGCAC -s mr.mrrefChr5 246578 7 + 294540 ATGACAT -s simCow_chr6.simCow.chr6 384426 7 + 602619 ATGGCAT -s simDog_chr6.simDog.chr6 375023 7 + 593897 ATAGTAC -s simHuman_chr6.simHuman.chr6 379048 7 + 601863 ATGACAT -s simRat_chr6.simRat.chr6 392982 7 + 647215 TTGACAT - -a -s simMouse_chr6.simMouse.chr6 392877 14 + 636262 CCGCAGGGATTCTA -s Anc0.Anc0refChr3 25161 14 + 222631 CCTCAGATGGCACA -s Anc1.Anc1refChr6 54709 14 + 197743 CCTCAGATGGCACA -s Anc2.Anc2refChr13 28572 14 + 96486 CCTTGGATGGCACA -s mr.mrrefChr5 246585 14 + 294540 CCGCAGGGATTCTA -s simCow_chr6.simCow.chr6 384497 14 + 602619 CCTTCCATGGTACA -s simDog_chr6.simDog.chr6 375084 14 + 593897 GCTTGGATGGCACA -s simHuman_chr6.simHuman.chr6 222273 14 - 601863 CCTCAGATGCCACA -s simRat_chr6.simRat.chr6 392989 14 + 647215 CTGCTGGGATTCTA - -a -s simMouse_chr6.simMouse.chr6 392891 8 + 636262 GAAGAAGG -s Anc0.Anc0refChr3 25175 8 + 222631 TAAGAATG -s Anc1.Anc1refChr6 54723 8 + 197743 TAAGAATG -s Anc2.Anc2refChr13 28586 8 + 96486 TAAAAATG -s mr.mrrefChr5 246599 8 + 294540 GAAGAAGG -s simCow_chr6.simCow.chr6 384511 8 + 602619 CTAATATG -s simDog_chr6.simDog.chr6 375100 8 + 593897 TAAAAATC -s simHuman_chr6.simHuman.chr6 222287 8 - 601863 TGAGAATG -s simRat_chr6.simRat.chr6 393003 8 + 647215 GAAATAGC - -a -s simMouse_chr6.simMouse.chr6 392899 7 + 636262 ATTATTG -s Anc0.Anc0refChr3 25183 7 + 222631 ATTATGA -s Anc1.Anc1refChr6 54731 7 + 197743 ATTATGA -s Anc2.Anc2refChr13 28594 7 + 96486 ACCAGGA -s mr.mrrefChr5 246607 7 + 294540 ATTATTG -s simCow_chr6.simCow.chr6 384519 7 + 602619 ACCAGGA -s simDog_chr6.simDog.chr6 375108 7 + 593897 ACCAGGA -s simHuman_chr6.simHuman.chr6 222302 7 - 601863 ATTCTGA -s simRat_chr6.simRat.chr6 393011 7 + 647215 ATGCATG - -a -s simMouse_chr6.simMouse.chr6 392906 45 + 636262 CATTCTCTCCACATTTATTGAAGTGCAAGAGGCACCATCACTAGG -s Anc0.Anc0refChr3 25190 45 + 222631 TTCTGTAGCCACATTTATGAAACAATTCTGGCCATCATGGCTAAT -s Anc1.Anc1refChr6 54738 45 + 197743 TTCTGTAGCCACATTTATGAAACAATTCTGGCCATCATGGCTAAT -s Anc2.Anc2refChr13 28602 45 + 96486 TTCTGTAGCCACATTTCAGAAACAATTCTGGCCATCATGGCTAAT -s mr.mrrefChr5 246614 45 + 294540 CATTCTCTCCACATTTATTGAAGTGCAAGAGGCACCATCACTAGG -s simCow_chr6.simCow.chr6 384527 37 + 602619 TACTGTAGGCACATTACACAAACAATTCTGGCCA--------AAT -s simDog_chr6.simDog.chr6 375116 45 + 593897 TTCTGTAGCCACATTTCAGAAACAATTCCGGCCATCATGGCTAAT -s simHuman_chr6.simHuman.chr6 222309 42 - 601863 TTCTGTAGCCACATTGAT---ACAATTGTGACCATTGTGGCTAAT -s simRat_chr6.simRat.chr6 393018 45 + 647215 CATCCTCTCCACATGTATTCAACTGCAACTGGCACCATCACTAGG - -a -s simMouse_chr6.simMouse.chr6 392951 10 + 636262 TGATACACTC -s Anc0.Anc0refChr3 25237 4 + 222631 TTTT------ -s Anc1.Anc1refChr6 54785 10 + 197743 TTTTCCACTC -s Anc2.Anc2refChr13 28649 4 + 96486 TTTT------ -s mr.mrrefChr5 246659 10 + 294540 TGATACACTC -s simCow_chr6.simCow.chr6 384566 4 + 602619 TTTT------ -s simDog_chr6.simDog.chr6 375163 4 + 593897 TCTT------ -s simHuman_chr6.simHuman.chr6 222353 10 - 601863 TTTTCCACTC -s simRat_chr6.simRat.chr6 393063 10 + 647215 TGGTACACAC - -a -s simMouse_chr6.simMouse.chr6 392961 37 + 636262 TTTATACCCTACAATGGCTTCCTAAAATGGTTGTGGT -s Anc0.Anc0refChr3 25241 26 + 222631 ---------TACACTGACCTC--AACCTGGTTATGGT -s Anc1.Anc1refChr6 54795 35 + 197743 TTGATGGTATACACTGACCTC--AACCTGGTTATGGT -s Anc2.Anc2refChr13 28653 26 + 96486 ---------TATGCTGACCTC--AACCTGGTTATGGT -s mr.mrrefChr5 246669 37 + 294540 TTTATACCCTACAATGGCTTCCTAAAATGGTTGTGGT -s simCow_chr6.simCow.chr6 384570 26 + 602619 ---------TGCTCTGCCCTC--AACCTGGTTATGGT -s simDog_chr6.simDog.chr6 375167 26 + 593897 ---------TATGCTGACCTT--AACCTGTTTGAGAC -s simHuman_chr6.simHuman.chr6 222368 35 - 601863 TTGATGGTATGCACTGACCTC--AACCTGGTCATGGT -s simRat_chr6.simRat.chr6 393073 37 + 647215 TTTATACCCTTCAATGGCTTTCTGAAATGGTTGTGGT - -a -s simMouse_chr6.simMouse.chr6 392998 1 + 636262 G -s Anc0.Anc0refChr3 25268 1 + 222631 G -s Anc1.Anc1refChr6 54831 1 + 197743 G -s Anc2.Anc2refChr13 28682 1 + 96486 G -s mr.mrrefChr5 246706 1 + 294540 G -s simCow_chr6.simCow.chr6 384599 1 + 602619 A -s simDog_chr6.simDog.chr6 375196 1 + 593897 G -s simHuman_chr6.simHuman.chr6 222404 1 - 601863 G -s simRat_chr6.simRat.chr6 393110 1 + 647215 G - -a -s simMouse_chr6.simMouse.chr6 392999 9 + 636262 ATCATAGGT -s Anc0.Anc0refChr3 25269 9 + 222631 GTCATATGA -s Anc1.Anc1refChr6 54832 9 + 197743 GTCATATGA -s Anc2.Anc2refChr13 28683 9 + 96486 GTCATATGA -s mr.mrrefChr5 246707 9 + 294540 ATCATAGGT -s simCow_chr6.simCow.chr6 384600 9 + 602619 GTTGCATGA -s simDog_chr6.simDog.chr6 375197 9 + 593897 GTCATGTGA -s simHuman_chr6.simHuman.chr6 222405 9 - 601863 GTCATATGA -s simRat_chr6.simRat.chr6 393112 9 + 647215 ATCATATGT - -a -s simMouse_chr6.simMouse.chr6 393008 1 + 636262 G -s Anc0.Anc0refChr3 25278 1 + 222631 G -s Anc1.Anc1refChr6 54841 1 + 197743 G -s Anc2.Anc2refChr13 28692 1 + 96486 G -s mr.mrrefChr5 246716 1 + 294540 G -s simCow_chr6.simCow.chr6 384609 1 + 602619 G -s simDog_chr6.simDog.chr6 375206 1 + 593897 T -s simHuman_chr6.simHuman.chr6 222414 1 - 601863 G -s simRat_chr6.simRat.chr6 393122 1 + 647215 G - -a -s simMouse_chr6.simMouse.chr6 393009 32 + 636262 CACTATGTTAACCCTGAGCATAGCAGTAAATC -s Anc0.Anc0refChr3 25280 32 + 222631 CATTGTGTAAACTATGAGCTTAACAATACATT -s Anc1.Anc1refChr6 54843 32 + 197743 CATTGTGTAAACTATGAGCTTAACAATACATT -s Anc2.Anc2refChr13 28694 32 + 96486 CATTGAGTAAACTATGAGCTTAACAATACATT -s mr.mrrefChr5 246717 32 + 294540 CACTATGTTAACCCTGAGCATAGCAGTAAATC -s simCow_chr6.simCow.chr6 384611 32 + 602619 CATTGAGTAAATTTTGAGCTTGATGATATAAT -s simDog_chr6.simDog.chr6 375208 32 + 593897 CCTTGAGTAAACTATGATCTTAACAATACATT -s simHuman_chr6.simHuman.chr6 222416 30 - 601863 CAGTGTGTAAACTATGAGCTTAACAATACA-- -s simRat_chr6.simRat.chr6 393123 32 + 647215 CACTATGTTAACTCTGAGCATAGCAATAAAAC - -a -s simMouse_chr6.simMouse.chr6 393041 14 + 636262 CTGTTTTAGATACT -s Anc0.Anc0refChr3 25312 14 + 222631 GCGTTTTTGATACT -s Anc1.Anc1refChr6 54875 14 + 197743 GCGTTTTTGATACT -s Anc2.Anc2refChr13 28726 14 + 96486 GCACTTTTGATACT -s mr.mrrefChr5 246749 14 + 294540 CTGTTTTAGATACT -s simCow_chr6.simCow.chr6 384713 14 + 602619 GCACTTTTAATAAT -s simDog_chr6.simDog.chr6 375240 14 + 593897 GCACTTTTGATACT -s simHuman_chr6.simHuman.chr6 222446 12 - 601863 --GTCAAGAATATT -s simRat_chr6.simRat.chr6 393155 14 + 647215 CTGTTTTAAGTAAT - -a -s simMouse_chr6.simMouse.chr6 393055 15 + 636262 ATTTCACTAAGGCAA -s Anc0.Anc0refChr3 25326 15 + 222631 GTTGTCTTGAGCCAA -s Anc1.Anc1refChr6 54889 15 + 197743 GTTGTCTTGAGCCAA -s Anc2.Anc2refChr13 28747 15 + 96486 GTTGTCTTGAACCAA -s mr.mrrefChr5 246763 15 + 294540 ATTTCACTAAGGCAA -s simCow_chr6.simCow.chr6 384733 10 + 602619 GTTATCTT-----AC -s simDog_chr6.simDog.chr6 375263 15 + 593897 GTTGTCTTGAACCAA -s simHuman_chr6.simHuman.chr6 222458 15 - 601863 GTTGTCTTGGGTCAA -s simRat_chr6.simRat.chr6 393169 15 + 647215 CTTGCACTGAAGCAA - -a -s simMouse_chr6.simMouse.chr6 393070 39 + 636262 GCTGAAAGACAGACAGAATAGAAAATCATGTGGCGCCAT -s Anc0.Anc0refChr3 25341 36 + 222631 GCTT-AAGACCGAGTGAACATAGAATTATGAGATGC--T -s Anc1.Anc1refChr6 54904 36 + 197743 GCTT-AAGACCGAGTGAACATAGAATTATGAGATGC--T -s Anc2.Anc2refChr13 28762 36 + 96486 GCTT-AAGACCAAGTGGACATAGAATTATGAGATGC--T -s mr.mrrefChr5 246778 38 + 294540 GCTG-AAGACAGACAGAATAGAAAATCATGTGGCGCCAT -s simCow_chr6.simCow.chr6 384743 36 + 602619 GCTT-AAGACCAAGTGGACAAAGAATCATGAGGTGC--T -s simDog_chr6.simDog.chr6 375279 36 + 593897 GCTT-AAGTCCAAGTGGAGATAGAATTATGAGATGC--T -s simHuman_chr6.simHuman.chr6 222473 36 - 601863 GCTC-AAGATTGAGTGACCATAGGGTTATGAGATGC--T -s simRat_chr6.simRat.chr6 393184 38 + 647215 GCTG-GAGACAGACAGGGTGGAAAATCATGAGGTGCCAT - -a -s simMouse_chr6.simMouse.chr6 393109 6 + 636262 TGCATG -s Anc0.Anc0refChr3 25377 6 + 222631 TGCATA -s Anc1.Anc1refChr6 54940 6 + 197743 TGCATA -s Anc2.Anc2refChr13 28798 6 + 96486 TGCATA -s mr.mrrefChr5 246816 6 + 294540 TGCATG -s simCow_chr6.simCow.chr6 384781 6 + 602619 TATAGA -s simDog_chr6.simDog.chr6 375315 6 + 593897 TGCATA -s simHuman_chr6.simHuman.chr6 222509 6 - 601863 TGCATT -s simRat_chr6.simRat.chr6 393222 6 + 647215 TGTATG - -a -s simMouse_chr6.simMouse.chr6 393115 36 + 636262 CAGTCATACAATGTGCGCAACTGAGAGCAACCGAGA -s Anc0.Anc0refChr3 25385 21 + 222631 CACCCACCCAATGTGAGCAAT--------------- -s Anc1.Anc1refChr6 54948 21 + 197743 CACCCACCCAATGTGAGCAAT--------------- -s Anc2.Anc2refChr13 28806 21 + 96486 CACCCACCCAATGTGAGCAAT--------------- -s mr.mrrefChr5 246822 21 + 294540 CAGTCATACAATGTGCGCAAC--------------- -s simCow_chr6.simCow.chr6 384789 21 + 602619 TACCCACCCAATGTGTGCAAT--------------- -s simDog_chr6.simDog.chr6 375323 21 + 593897 CACCCACCCAATGTGAGCATT--------------- -s simHuman_chr6.simHuman.chr6 222517 20 - 601863 AACCCA-CCAATGTGAGCAAT--------------- -s simRat_chr6.simRat.chr6 393228 21 + 647215 CAGTCACACAATATGAGCAAC--------------- - -a -s simMouse_chr6.simMouse.chr6 393151 24 + 636262 CAATGTGATGTTGCCAGTGATAGA -s Anc0.Anc0refChr3 25422 24 + 222631 CAATTCGATGTTGCCAATGATACA -s Anc1.Anc1refChr6 54985 24 + 197743 CAATTCGATGTTGCCAATGATACA -s Anc2.Anc2refChr13 28843 24 + 96486 CAATTCGATATTACAAATGATCCA -s mr.mrrefChr5 246843 24 + 294540 CAATGTGATGTTGCCAGTGATAGA -s simCow_chr6.simCow.chr6 384826 24 + 602619 TAATTCGGTATTACAAATGATCAG -s simDog_chr6.simDog.chr6 375360 24 + 593897 CAAATCGATATTACAAATGATCCA -s simHuman_chr6.simHuman.chr6 222554 24 - 601863 CAATTCAAAGTTGCCAATGATACA -s simRat_chr6.simRat.chr6 393249 24 + 647215 CAATATGGTGTTGCCAGTGATAGG - -a -s simMouse_chr6.simMouse.chr6 393175 70 + 636262 ATCACTCATAATCTCACTCACTAGCTTAGTAGTGCAATGTTTGCCTGCATAATGGGAAAAAATTATTAGA -s Anc0.Anc0refChr3 25452 70 + 222631 ATCACTCATAATATCACTCATTGGCTGGGTGGTGCTATGTTGGCCTGCAAATTGCAAATGGCTTACTAGA -s Anc1.Anc1refChr6 55015 70 + 197743 ATCACTCATAATATCACTCATTGGCTGGGTGGTGCTATGTTGGCCTGCAAATTGCAAATGGCTTACTAGA -s Anc2.Anc2refChr13 28873 70 + 96486 ATCGCTCATGATATCACTCATTGACTGGGTGGTGCTCTGTTGGCCTGCAAATTGCAAATGGCTTACTGGA -s mr.mrrefChr5 246867 70 + 294540 ATCACTCATAATCTCACTCACTAGCTTAGTAGTGCAATGTTTGCCTGCATAATGGGAAAAAATTATTAGA -s simCow_chr6.simCow.chr6 384852 65 + 602619 -----TTCAGATATCTCTCATTAACTGGGTGGTGCTCTGTTATCCTACAAATTGCAGCAGGATTACTGGA -s simDog_chr6.simDog.chr6 375390 70 + 593897 ATCGCTCATGATCTCATTCATTGACTGGGTTGTCCTCCGTTGGCCTGCAAATTGCAAATGGCTTATTGGA -s simHuman_chr6.simHuman.chr6 222584 69 - 601863 AACACTCATAATATCACTCGTT-GCTAGGTGGTGCTATGTTGGCCTGTGCATTAAAAAGGGGTTACTAGA -s simRat_chr6.simRat.chr6 393273 70 + 647215 ATCACTCATTATCTCACTCATTAGCTAAGTAGTGCAATGTTAGCCTGCATAATGGGTGTAAATTAGTAGA - -a -s simMouse_chr6.simMouse.chr6 393245 45 + 636262 AATAGCAAAGTATAAGTTAAGTTTTATGTAGTGAAAAGGCACTGG -s Anc0.Anc0refChr3 25522 45 + 222631 TACAGCAAAGTGTGATTTGAATTCTATGTAGTGAATGAGTGCTGA -s Anc1.Anc1refChr6 55085 45 + 197743 TACAGCAAAGTGTGATTTGAATTCTATGTAGTGAATGAGTGCTGA -s Anc2.Anc2refChr13 28943 45 + 96486 TACAGCAAAGTGTGATTTGAATACTATGTAGTAAATGAGTGATAA -s mr.mrrefChr5 246937 45 + 294540 AATAGCAAAGTATAAGTTAAGTTTTATGTAGTGAAAAGGCACTGG -s simCow_chr6.simCow.chr6 384917 45 + 602619 TGCAGCAAAGTGTGATTTGAGTACTATGCAGTCAATAAGTGTTAG -s simDog_chr6.simDog.chr6 375461 45 + 593897 TACAACAGAGCGTGATTTGAATACTATGTAGTAAATGAGTGATAA -s simHuman_chr6.simHuman.chr6 222653 43 - 601863 CACAGCAAATTGTGATTTGGATTCTATGTAGTGAATTAG--CTGA -s simRat_chr6.simRat.chr6 393343 45 + 647215 CATGGCAAAATATAAGTTAAGTTTTATGTAATGAAAAGGTACTAA - -a -s simMouse_chr6.simMouse.chr6 393290 5 + 636262 AGTGC -s Anc0.Anc0refChr3 25567 5 + 222631 AATTC -s Anc1.Anc1refChr6 55130 5 + 197743 AATTC -s Anc2.Anc2refChr13 28989 5 + 96486 AATTG -s mr.mrrefChr5 246982 5 + 294540 AGTGC -s simCow_chr6.simCow.chr6 384963 5 + 602619 CAATG -s simDog_chr6.simDog.chr6 375507 5 + 593897 AATTG -s simHuman_chr6.simHuman.chr6 222696 5 - 601863 AATTC -s simRat_chr6.simRat.chr6 393388 5 + 647215 AGTCC - -a -s simMouse_chr6.simMouse.chr6 393295 6 + 636262 TACTCT -s Anc0.Anc0refChr3 25577 6 + 222631 TATCCC -s Anc1.Anc1refChr6 55140 6 + 197743 TATCCC -s Anc2.Anc2refChr13 28999 6 + 96486 TATCCC -s mr.mrrefChr5 246987 6 + 294540 TACTCT -s simCow_chr6.simCow.chr6 384973 6 + 602619 CAAACC -s simDog_chr6.simDog.chr6 375517 6 + 593897 TATCCC -s simHuman_chr6.simHuman.chr6 222706 6 - 601863 GATCAA -s simRat_chr6.simRat.chr6 393393 6 + 647215 TACTGG - -a -s simMouse_chr6.simMouse.chr6 393301 3 + 636262 CTC -s Anc0.Anc0refChr3 25583 3 + 222631 GTC -s Anc1.Anc1refChr6 55146 3 + 197743 GTC -s Anc2.Anc2refChr13 29005 3 + 96486 GCC -s mr.mrrefChr5 246993 3 + 294540 CTC -s simCow_chr6.simCow.chr6 384980 3 + 602619 GCC -s simDog_chr6.simDog.chr6 375523 3 + 593897 GCC -s simHuman_chr6.simHuman.chr6 222712 3 - 601863 ATC -s simRat_chr6.simRat.chr6 393399 3 + 647215 CTC - -a -s simMouse_chr6.simMouse.chr6 393304 4 + 636262 TTTT -s Anc0.Anc0refChr3 25586 4 + 222631 TGTG -s Anc1.Anc1refChr6 55149 4 + 197743 TGTG -s Anc2.Anc2refChr13 29011 4 + 96486 TGTG -s mr.mrrefChr5 246996 4 + 294540 TTTT -s simCow_chr6.simCow.chr6 384986 4 + 602619 TGTG -s simDog_chr6.simDog.chr6 375529 4 + 593897 TGTG -s simHuman_chr6.simHuman.chr6 222715 4 - 601863 TGTG -s simRat_chr6.simRat.chr6 393402 4 + 647215 TTTT - -a -s simMouse_chr6.simMouse.chr6 393308 5 + 636262 TGTGG -s Anc0.Anc0refChr3 25590 5 + 222631 TGTGG -s Anc1.Anc1refChr6 55153 5 + 197743 TGTGG -s Anc2.Anc2refChr13 29015 5 + 96486 TGTGA -s mr.mrrefChr5 247000 5 + 294540 TGTGG -s simCow_chr6.simCow.chr6 384991 5 + 602619 GGTGG -s simDog_chr6.simDog.chr6 375533 5 + 593897 TGTGA -s simHuman_chr6.simHuman.chr6 222719 5 - 601863 TGTGG -s simRat_chr6.simRat.chr6 393406 5 + 647215 TGTGG - -a -s simMouse_chr6.simMouse.chr6 393313 12 + 636262 ATTCTCCAGTTT -s Anc0.Anc0refChr3 25595 12 + 222631 ATTCTCCAGTTT -s Anc1.Anc1refChr6 55158 12 + 197743 ATTCTCCAGTTT -s Anc2.Anc2refChr13 29020 12 + 96486 ACTTTCCAGTTT -s mr.mrrefChr5 247005 12 + 294540 ATTCTCCAGTTT -s simCow_chr6.simCow.chr6 384996 12 + 602619 GCTTCCGCATTC -s simDog_chr6.simDog.chr6 375538 12 + 593897 ACTTTTCAGTTT -s simHuman_chr6.simHuman.chr6 222725 12 - 601863 ATCCTCCGGTTT -s simRat_chr6.simRat.chr6 393411 12 + 647215 ACTCTCCTGTTT - -a -s simMouse_chr6.simMouse.chr6 393325 32 + 636262 CTTGGGTTATTTGTTGGTTTTGTCACTGCTGG -s Anc0.Anc0refChr3 25608 32 + 222631 CTTGGGCTCTTACTTGGTGTCCTCACTCTCAA -s Anc1.Anc1refChr6 55171 32 + 197743 CTTGGGCTCTTACTTGGTGTCCTCACTCTCAA -s Anc2.Anc2refChr13 29033 32 + 96486 CTTGCGCTCTTACTTACTGTCCTCACTCTCAA -s mr.mrrefChr5 247017 32 + 294540 TTTGGGTTATTTGTTGGTTTTGTCACTGTTAG -s simCow_chr6.simCow.chr6 385009 32 + 602619 CTTGAGCTCCTACTTAGTGTTCTCACTCCCAA -s simDog_chr6.simDog.chr6 375551 32 + 593897 CTTGCACTCTTACTTACTTTCCTCACTTTCAA -s simHuman_chr6.simHuman.chr6 222738 31 - 601863 CTTGGGCTCTTACTTGGGCCC-TCACTCTCAA -s simRat_chr6.simRat.chr6 393423 32 + 647215 TTTGGGTTATTTATTGGTTTTGTCACTGTCAA - -a -s simMouse_chr6.simMouse.chr6 393357 7 + 636262 GTGGACA -s Anc0.Anc0refChr3 25640 7 + 222631 GTGGACA -s Anc1.Anc1refChr6 55203 7 + 197743 GTGGACA -s Anc2.Anc2refChr13 29100 7 + 96486 GTTGACT -s mr.mrrefChr5 247049 7 + 294540 GTGGGCA -s simCow_chr6.simCow.chr6 385081 7 + 602619 GTTGAAT -s simDog_chr6.simDog.chr6 375618 7 + 593897 GTTGACT -s simHuman_chr6.simHuman.chr6 222769 7 - 601863 GTGGACA -s simRat_chr6.simRat.chr6 393455 7 + 647215 GTGGGCA - -a -s simMouse_chr6.simMouse.chr6 393364 5 + 636262 GAATG -s Anc0.Anc0refChr3 25655 5 + 222631 GGGTG -s Anc1.Anc1refChr6 55218 5 + 197743 GGGTG -s Anc2.Anc2refChr13 29119 5 + 96486 GGGTG -s mr.mrrefChr5 247056 5 + 294540 GAATG -s simCow_chr6.simCow.chr6 385101 5 + 602619 AGGTG -s simDog_chr6.simDog.chr6 375637 5 + 593897 GGGTG -s simHuman_chr6.simHuman.chr6 379668 5 + 601863 GGGTG -s simRat_chr6.simRat.chr6 393462 5 + 647215 GAATG - -a -s simMouse_chr6.simMouse.chr6 393369 19 + 636262 CCCAGTTTACAATGTTGTG -s Anc0.Anc0refChr3 25664 19 + 222631 CCCTGTTTACAATACTGTG -s Anc1.Anc1refChr6 55227 19 + 197743 CCCTGTTTACAATACTGTG -s Anc2.Anc2refChr13 29128 19 + 96486 CCCTGTTTACAATACTGTG -s mr.mrrefChr5 247061 19 + 294540 CCCAGTTTACAATGTTGTG -s simCow_chr6.simCow.chr6 385110 19 + 602619 CCATGTTTTCAATACTGTG -s simDog_chr6.simDog.chr6 375646 19 + 593897 CCCTGTTAAGAATGCGGTG -s simHuman_chr6.simHuman.chr6 379677 19 + 601863 TCTGGTTTACATTACTGTG -s simRat_chr6.simRat.chr6 393467 19 + 647215 CCCAGTTTACAATGTTGTG - -a -s simMouse_chr6.simMouse.chr6 393388 13 + 636262 TGTGTCTTAACCT -s Anc0.Anc0refChr3 25694 13 + 222631 TGTATTTTTAGCT -s Anc1.Anc1refChr6 55257 13 + 197743 TGTATTTTTAGCT -s Anc2.Anc2refChr13 29159 13 + 96486 TGTATTTTTAGCT -s mr.mrrefChr5 247080 13 + 294540 TGTATCTTAACCT -s simCow_chr6.simCow.chr6 385141 13 + 602619 GGCATCTTTGACT -s simDog_chr6.simDog.chr6 375677 13 + 593897 TGTATTTTTAGCT -s simHuman_chr6.simHuman.chr6 379707 13 + 601863 TGTATTTTTAGCT -s simRat_chr6.simRat.chr6 393486 13 + 647215 CATATCTCAAACT - -a -s simMouse_chr6.simMouse.chr6 393407 4 + 636262 GAAG -s Anc0.Anc0refChr3 25713 4 + 222631 TAAG -s Anc1.Anc1refChr6 55276 4 + 197743 TAAG -s Anc2.Anc2refChr13 29178 4 + 96486 TAAG -s mr.mrrefChr5 247099 4 + 294540 TAAG -s simCow_chr6.simCow.chr6 385160 4 + 602619 TAAG -s simDog_chr6.simDog.chr6 375696 4 + 593897 CAGG -s simHuman_chr6.simHuman.chr6 379726 4 + 601863 TAAG -s simHuman_chr6.simHuman.chr6 444638 4 + 601863 CAAG -s simRat_chr6.simRat.chr6 393505 4 + 647215 TAAG - -a -s simMouse_chr6.simMouse.chr6 393423 25 + 636262 CTTATCCATGGACCACATACTGCTA -s Anc1.Anc1refChr6 55312 23 + 197743 C--ATCCACAGACCACATTCTGCTA -s mr.mrrefChr5 247135 25 + 294540 CTTATCCATGGACCACATTCTGCTA -s simHuman_chr6.simHuman.chr6 379762 23 + 601863 C--ATCCACAGACCACATTCTGCTA -s simHuman_chr6.simHuman.chr6 444655 23 + 601863 C--ATCCACAGACCACATTCTATTA -s simRat_chr6.simRat.chr6 393542 25 + 647215 CTTATCCATGGAGCACATTCAACTA - -a -s simMouse_chr6.simMouse.chr6 393456 16 + 636262 TCACCTCGTGTGCATG -s mr.mrrefChr5 247168 16 + 294540 TCACCTCGTGTGCATG -s simRat_chr6.simRat.chr6 393575 16 + 647215 TCAGCTCATGGGCATG - -a -s simMouse_chr6.simMouse.chr6 393480 3 + 636262 TTC -s Anc0.Anc0refChr3 25764 3 + 222631 CCC -s Anc1.Anc1refChr6 55351 3 + 197743 CCC -s Anc2.Anc2refChr13 29230 3 + 96486 CCC -s mr.mrrefChr5 247192 3 + 294540 TTC -s simCow_chr6.simCow.chr6 385255 3 + 602619 CCC -s simDog_chr6.simDog.chr6 375748 3 + 593897 CCC -s simHuman_chr6.simHuman.chr6 379801 3 + 601863 CCC -s simHuman_chr6.simHuman.chr6 444694 3 + 601863 TCC -s simRat_chr6.simRat.chr6 393599 3 + 647215 TTC - -a -s simMouse_chr6.simMouse.chr6 393504 4 + 636262 CCCA -s mr.mrrefChr5 247216 4 + 294540 CCCA -s simRat_chr6.simRat.chr6 393623 4 + 647215 CTCA - -a -s simMouse_chr6.simMouse.chr6 393509 54 + 636262 TCAATTTCTACTTACCCCATTCTGTGGTGAATTTGGTCACATGGGATGGGTACA -s Anc0.Anc0refChr3 25789 39 + 222631 CCAATTCCTACTTGCCCCATTCTATTGTTGATTTG---------------TGCA -s Anc1.Anc1refChr6 55376 39 + 197743 CCAATTCCTACTTGCCCCATTCTATTGTTGATTTG---------------TGCA -s Anc2.Anc2refChr13 29263 39 + 96486 CCAATTCCTACTTGCCCCATTCTATTGTTGATTTG---------------TGCA -s mr.mrrefChr5 247221 54 + 294540 CCAATTTCTACTTACCCCATTCTGTTGTGAATTTGGTCACATGGGATGGGTACA -s simCow_chr6.simCow.chr6 385303 39 + 602619 CCAATTCCTGCGCACTGCATTCTATTGTTGATTTG---------------TGCA -s simDog_chr6.simDog.chr6 375780 38 + 593897 C-AATTCCTACCAGCCCGATGATATTGTTGATTTA---------------TGCA -s simHuman_chr6.simHuman.chr6 379826 39 + 601863 CCATTTTCTACTTGCACCATTCTATTGTTGTTTTG---------------TGTA -s simHuman_chr6.simHuman.chr6 444719 39 + 601863 CCAATTCCTACTTATGACATTCTATTGTTGTTTTG---------------CGTA -s simRat_chr6.simRat.chr6 393628 54 + 647215 CCAATTCCTACTTACCTCATTCTGTTGTGAATTTGTTCACATGGGATGGGTTCA - -a -s simMouse_chr6.simMouse.chr6 393563 3 + 636262 TGT -s Anc0.Anc0refChr3 25828 3 + 222631 TGT -s Anc1.Anc1refChr6 55415 3 + 197743 TGT -s Anc2.Anc2refChr13 29302 3 + 96486 TGT -s mr.mrrefChr5 247275 3 + 294540 TGT -s simCow_chr6.simCow.chr6 385342 3 + 602619 TGT -s simDog_chr6.simDog.chr6 375833 3 + 593897 TGT -s simHuman_chr6.simHuman.chr6 379865 3 + 601863 TGT -s simHuman_chr6.simHuman.chr6 444758 3 + 601863 TCT -s simRat_chr6.simRat.chr6 393682 3 + 647215 TGT - -a -s simMouse_chr6.simMouse.chr6 393580 5 + 636262 TAACA -s Anc0.Anc0refChr3 25865 5 + 222631 CCACA -s Anc1.Anc1refChr6 55452 5 + 197743 CCACA -s Anc2.Anc2refChr13 29339 5 + 96486 CCACA -s mr.mrrefChr5 247312 5 + 294540 TAACA -s simCow_chr6.simCow.chr6 385379 5 + 602619 TCACT -s simDog_chr6.simDog.chr6 375870 5 + 593897 CCACA -s simHuman_chr6.simHuman.chr6 379902 5 + 601863 CCACA -s simHuman_chr6.simHuman.chr6 444824 5 + 601863 CCACA -s simRat_chr6.simRat.chr6 393719 5 + 647215 TGACA - -a -s simMouse_chr6.simMouse.chr6 393606 5 + 636262 ATTTA -s Anc0.Anc0refChr3 25893 5 + 222631 TCTTA -s Anc1.Anc1refChr6 55480 5 + 197743 TCTTA -s Anc2.Anc2refChr13 29367 5 + 96486 TCTTA -s mr.mrrefChr5 247338 5 + 294540 ATTTA -s simCow_chr6.simCow.chr6 385407 5 + 602619 TCTTA -s simRat_chr6.simRat.chr6 393745 5 + 647215 GCTTA - -a -s simMouse_chr6.simMouse.chr6 393618 4 + 636262 GCAC -s Anc0.Anc0refChr3 25905 4 + 222631 GCAC -s Anc1.Anc1refChr6 55492 4 + 197743 GCAC -s Anc2.Anc2refChr13 29379 4 + 96486 GTAC -s mr.mrrefChr5 247350 4 + 294540 GCAC -s simCow_chr6.simCow.chr6 385419 4 + 602619 GTAC -s simDog_chr6.simDog.chr6 375886 4 + 593897 GTAC -s simHuman_chr6.simHuman.chr6 379918 4 + 601863 GCAC -s simHuman_chr6.simHuman.chr6 444837 4 + 601863 GCAC -s simRat_chr6.simRat.chr6 393757 4 + 647215 GCAC - -a -s simMouse_chr6.simMouse.chr6 393622 3 + 636262 AAT -s Anc0.Anc0refChr3 25911 3 + 222631 AAT -s Anc1.Anc1refChr6 55498 3 + 197743 AAT -s Anc2.Anc2refChr13 29385 3 + 96486 AAT -s mr.mrrefChr5 247354 3 + 294540 AAT -s simCow_chr6.simCow.chr6 385425 3 + 602619 TTT -s simDog_chr6.simDog.chr6 375892 3 + 593897 AGT -s simHuman_chr6.simHuman.chr6 379924 3 + 601863 AAT -s simHuman_chr6.simHuman.chr6 444843 3 + 601863 AAT -s simRat_chr6.simRat.chr6 393761 3 + 647215 AAT - -a -s simMouse_chr6.simMouse.chr6 393667 5 + 636262 GGTCT -s Anc0.Anc0refChr3 25958 5 + 222631 GGGCT -s Anc1.Anc1refChr6 55545 5 + 197743 GGGCT -s Anc2.Anc2refChr13 29433 5 + 96486 GGGCT -s mr.mrrefChr5 247399 5 + 294540 GGTCT -s simCow_chr6.simCow.chr6 385471 5 + 602619 GGGCG -s simDog_chr6.simDog.chr6 375940 5 + 593897 GGGCT -s simRat_chr6.simRat.chr6 393803 5 + 647215 GGTCT - -a -s simMouse_chr6.simMouse.chr6 393675 2 + 636262 TT -s Anc0.Anc0refChr3 25966 2 + 222631 TT -s Anc1.Anc1refChr6 55553 2 + 197743 TT -s Anc2.Anc2refChr13 29441 2 + 96486 TT -s mr.mrrefChr5 247407 2 + 294540 TT -s simCow_chr6.simCow.chr6 385479 2 + 602619 TT -s simDog_chr6.simDog.chr6 375948 2 + 593897 TT -s simHuman_chr6.simHuman.chr6 380004 2 + 601863 TT -s simHuman_chr6.simHuman.chr6 444893 2 + 601863 TT -s simRat_chr6.simRat.chr6 393811 2 + 647215 TT - -a -s simMouse_chr6.simMouse.chr6 393694 2 + 636262 AT -s Anc0.Anc0refChr3 25985 2 + 222631 AG -s Anc1.Anc1refChr6 55572 2 + 197743 AG -s Anc2.Anc2refChr13 29460 2 + 96486 AG -s mr.mrrefChr5 247426 2 + 294540 AG -s simCow_chr6.simCow.chr6 385498 2 + 602619 AG -s simDog_chr6.simDog.chr6 375967 2 + 593897 AG -s simHuman_chr6.simHuman.chr6 380023 2 + 601863 AG -s simHuman_chr6.simHuman.chr6 444912 2 + 601863 AG -s simRat_chr6.simRat.chr6 393830 2 + 647215 AG - -a -s simMouse_chr6.simMouse.chr6 393700 36 + 636262 TGGGGTGAGCGCCCTTCCCCAATGATGTTACTCAGT - -a -s simMouse_chr6.simMouse.chr6 393749 5 + 636262 AGTAC -s Anc0.Anc0refChr3 26004 5 + 222631 AATGC -s Anc1.Anc1refChr6 55591 5 + 197743 AATGC -s Anc2.Anc2refChr13 29479 5 + 96486 AATGC -s mr.mrrefChr5 247445 5 + 294540 AATAC -s simCow_chr6.simCow.chr6 385517 5 + 602619 AATGC -s simDog_chr6.simDog.chr6 375984 5 + 593897 ACTGC -s simHuman_chr6.simHuman.chr6 380047 5 + 601863 AACGC -s simRat_chr6.simRat.chr6 393849 5 + 647215 AATGC - -a -s simMouse_chr6.simMouse.chr6 393791 1 + 636262 A -s Anc1.Anc1refChr6 55633 1 + 197743 A -s mr.mrrefChr5 247487 1 + 294540 A -s simHuman_chr6.simHuman.chr6 380086 1 + 601863 A -s simHuman_chr6.simHuman.chr6 444965 1 + 601863 A -s simRat_chr6.simRat.chr6 393891 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 393806 7 + 636262 TATTAGG -s Anc0.Anc0refChr3 26057 7 + 222631 TATCAGG -s Anc1.Anc1refChr6 55648 7 + 197743 TATCAGG -s Anc2.Anc2refChr13 29532 7 + 96486 TATCAGG -s mr.mrrefChr5 247502 7 + 294540 TATCAGG -s simCow_chr6.simCow.chr6 385532 7 + 602619 TATCAAG -s simDog_chr6.simDog.chr6 376040 7 + 593897 TATCAGC -s simHuman_chr6.simHuman.chr6 380101 7 + 601863 TATCAGG -s simHuman_chr6.simHuman.chr6 444980 6 + 601863 TATCAA- -s simRat_chr6.simRat.chr6 393906 7 + 647215 TATCAGG - -a -s simMouse_chr6.simMouse.chr6 393848 2 + 636262 CC -s Anc0.Anc0refChr3 26099 2 + 222631 CC -s Anc1.Anc1refChr6 55690 2 + 197743 CC -s Anc2.Anc2refChr13 29574 2 + 96486 CC -s mr.mrrefChr5 247544 2 + 294540 CC -s simCow_chr6.simCow.chr6 385574 2 + 602619 CC -s simDog_chr6.simDog.chr6 376082 2 + 593897 CC -s simHuman_chr6.simHuman.chr6 380143 2 + 601863 CC -s simHuman_chr6.simHuman.chr6 445019 2 + 601863 CC -s simRat_chr6.simRat.chr6 393948 2 + 647215 CT - -a -s simMouse_chr6.simMouse.chr6 393850 8 + 636262 CAATAGTT -s Anc0.Anc0refChr3 26102 8 + 222631 TAATAATT -s Anc1.Anc1refChr6 55693 8 + 197743 TAATAATT -s Anc2.Anc2refChr13 29577 8 + 96486 TAATAATT -s mr.mrrefChr5 247546 8 + 294540 CAATAATT -s simCow_chr6.simCow.chr6 385577 8 + 602619 TAATAGTT -s simDog_chr6.simDog.chr6 376085 8 + 593897 TAATAATT -s simHuman_chr6.simHuman.chr6 380146 8 + 601863 TAATAATT -s simHuman_chr6.simHuman.chr6 445022 8 + 601863 TAATAATT -s simRat_chr6.simRat.chr6 393950 8 + 647215 GAATAATC - -a -s simMouse_chr6.simMouse.chr6 393858 60 + 636262 GAAGATATTGTGATTAGAGAGTTAAGATTCAGATTAAGCTAGAATCTCGATCACACATAG -s Anc0.Anc0refChr3 26110 58 + 222631 GAAGGCA--GTAGTATGGGATCTAAGATTTGGATTAAGCTAGAATCCCAATCATGCATAA -s Anc1.Anc1refChr6 55701 58 + 197743 GAAGGCA--GTAGTATGGGATCTAAGATTTGGATTAAGCTAGAATCCCAATCATGCATAA -s Anc2.Anc2refChr13 29585 58 + 96486 GAAAGCA--GTAGTATTGGACCTAAGATTTGGATTAAGCTAGGATCCCAATCATGCATAA -s mr.mrrefChr5 247554 60 + 294540 GAAGATATTGTGATTAGAGAGTTAAGATTCAGATTAAGCTAGAATCTCGATCACACATAA -s simCow_chr6.simCow.chr6 385585 52 + 602619 GGAAGCA--GTGGTATTAGACCTAACCTTTGGA------AATGATTGCCATTGTGCATAA -s simDog_chr6.simDog.chr6 376093 58 + 593897 GAAAGCA--GTAGCATTGGACCAAGGATTTGGATTAAGCTAGGATCCCAATAATGCATAA -s simHuman_chr6.simHuman.chr6 380154 58 + 601863 GAAGGCT--ATGGTATGGGATCTAAGATTTGGATTAAGCTAGAATCTCAATCATGCATAA -s simHuman_chr6.simHuman.chr6 445031 58 + 601863 GGAGGCT--ATAGTATGGTATCTAACATTTGGATTAAGCTAGAATCCCAATCATGCATAA -s simRat_chr6.simRat.chr6 393958 60 + 647215 GAAGATATTGTTATTTGTGGGTTAAGATGCAGATTAAGCTAGAATCTTGATCACACATAA - -a -s simMouse_chr6.simMouse.chr6 393918 5 + 636262 AAATT -s Anc0.Anc0refChr3 26170 5 + 222631 TAATT -s Anc1.Anc1refChr6 55761 5 + 197743 TAATT -s Anc2.Anc2refChr13 29645 5 + 96486 TTAAT -s mr.mrrefChr5 247614 5 + 294540 AAATT -s simCow_chr6.simCow.chr6 385639 5 + 602619 TTAAT -s simDog_chr6.simDog.chr6 376153 5 + 593897 TTAAT -s simHuman_chr6.simHuman.chr6 380214 5 + 601863 TAATT -s simHuman_chr6.simHuman.chr6 445091 5 + 601863 AAATT -s simRat_chr6.simRat.chr6 394018 5 + 647215 AACTT - -a -s simMouse_chr6.simMouse.chr6 393923 4 + 636262 AGAG -s Anc0.Anc0refChr3 26176 4 + 222631 TGAG -s Anc1.Anc1refChr6 55767 4 + 197743 TGAG -s Anc2.Anc2refChr13 29651 4 + 96486 TGAG -s mr.mrrefChr5 247619 4 + 294540 AGAG -s simCow_chr6.simCow.chr6 385645 4 + 602619 TCAG -s simDog_chr6.simDog.chr6 376159 4 + 593897 TGAG -s simHuman_chr6.simHuman.chr6 380220 4 + 601863 TGAA -s simHuman_chr6.simHuman.chr6 445096 4 + 601863 TGAA -s simRat_chr6.simRat.chr6 394023 4 + 647215 AGAG - -a -s simMouse_chr6.simMouse.chr6 393927 6 + 636262 TTACAA -s Anc0.Anc0refChr3 26183 6 + 222631 TTATCA -s Anc1.Anc1refChr6 55774 6 + 197743 TTATCA -s Anc2.Anc2refChr13 29658 6 + 96486 TAATCA -s mr.mrrefChr5 247623 6 + 294540 TTACAA -s simCow_chr6.simCow.chr6 385652 6 + 602619 TATCTA -s simDog_chr6.simDog.chr6 376166 5 + 593897 TAATC- -s simHuman_chr6.simHuman.chr6 380227 6 + 601863 TTCTCA -s simHuman_chr6.simHuman.chr6 445103 6 + 601863 TTATAA -s simRat_chr6.simRat.chr6 394027 6 + 647215 TTACTA - -a -s simMouse_chr6.simMouse.chr6 393933 2 + 636262 CA -s Anc0.Anc0refChr3 26214 2 + 222631 CA -s Anc1.Anc1refChr6 55805 2 + 197743 CA -s Anc2.Anc2refChr13 29689 2 + 96486 CA -s mr.mrrefChr5 247629 2 + 294540 CA -s simCow_chr6.simCow.chr6 385683 2 + 602619 TA -s simDog_chr6.simDog.chr6 376171 2 + 593897 CA -s simHuman_chr6.simHuman.chr6 380267 2 + 601863 TA -s simHuman_chr6.simHuman.chr6 445109 2 + 601863 CA -s simRat_chr6.simRat.chr6 394033 2 + 647215 CA - -a -s simMouse_chr6.simMouse.chr6 393935 15 + 636262 TCTGTACACTTTCTG -s Anc0.Anc0refChr3 26233 15 + 222631 TCTGCACACTTCCTG -s Anc1.Anc1refChr6 55824 15 + 197743 TCTGCACACTTCCTG -s Anc2.Anc2refChr13 29708 15 + 96486 TCTGCACACTTCCTC -s mr.mrrefChr5 247631 15 + 294540 TCTGTACACTTCCTG -s simCow_chr6.simCow.chr6 385702 12 + 602619 TC---ACACTTCCTC -s simDog_chr6.simDog.chr6 376177 15 + 593897 TTTGCACACTTCCTC -s simHuman_chr6.simHuman.chr6 380286 15 + 601863 CCTGTACACTTCCTG -s simHuman_chr6.simHuman.chr6 445128 15 + 601863 TCTGCACACTTCCTG -s simRat_chr6.simRat.chr6 394035 15 + 647215 TCTGTACCCTTCCTG - -a -s simMouse_chr6.simMouse.chr6 393950 5 + 636262 CTGTT -s Anc0.Anc0refChr3 26248 5 + 222631 CTGTT -s Anc1.Anc1refChr6 55839 5 + 197743 CTGTT -s Anc2.Anc2refChr13 29723 5 + 96486 CTGTT -s mr.mrrefChr5 247646 5 + 294540 CTGTT -s simCow_chr6.simCow.chr6 385845 5 + 602619 CCTTT -s simDog_chr6.simDog.chr6 376192 5 + 593897 CTGGT -s simHuman_chr6.simHuman.chr6 380301 5 + 601863 ATGTT -s simHuman_chr6.simHuman.chr6 445143 5 + 601863 CTGTT -s simRat_chr6.simRat.chr6 394050 5 + 647215 CTGTT - -a -s simMouse_chr6.simMouse.chr6 393964 4 + 636262 ATTT - -a -s simMouse_chr6.simMouse.chr6 393973 4 + 636262 TCGG -s Anc0.Anc0refChr3 26267 4 + 222631 TTTG -s Anc1.Anc1refChr6 55858 4 + 197743 TTTG -s Anc2.Anc2refChr13 29742 4 + 96486 TTTG -s mr.mrrefChr5 247665 4 + 294540 TCTG -s simCow_chr6.simCow.chr6 385864 4 + 602619 TTTG -s simDog_chr6.simDog.chr6 376211 4 + 593897 TTTG -s simHuman_chr6.simHuman.chr6 380320 4 + 601863 CTTG -s simHuman_chr6.simHuman.chr6 445162 4 + 601863 CTTG -s simRat_chr6.simRat.chr6 394069 4 + 647215 TCTG - -a -s simMouse_chr6.simMouse.chr6 393999 2 + 636262 TG -s Anc0.Anc0refChr3 26293 2 + 222631 TG -s Anc1.Anc1refChr6 55884 2 + 197743 TG -s Anc2.Anc2refChr13 29768 2 + 96486 TG -s mr.mrrefChr5 247691 2 + 294540 TG -s simCow_chr6.simCow.chr6 385890 2 + 602619 TA -s simDog_chr6.simDog.chr6 376236 2 + 593897 TG -s simHuman_chr6.simHuman.chr6 380346 2 + 601863 TG -s simHuman_chr6.simHuman.chr6 445188 2 + 601863 TG -s simRat_chr6.simRat.chr6 394095 2 + 647215 TG - -a -s simMouse_chr6.simMouse.chr6 394011 14 + 636262 TTATTAATCAATTC -s mr.mrrefChr5 247703 11 + 294540 TTATTAAT---TTC -s simRat_chr6.simRat.chr6 394107 9 + 647215 TTATCA-----TTC - -a -s simMouse_chr6.simMouse.chr6 394040 5 + 636262 GATGC -s Anc0.Anc0refChr3 26336 5 + 222631 CATTC -s Anc1.Anc1refChr6 55927 5 + 197743 CATTC -s Anc2.Anc2refChr13 29814 5 + 96486 CATTC -s mr.mrrefChr5 247729 5 + 294540 GATGC -s simCow_chr6.simCow.chr6 385939 5 + 602619 CAGTC -s simDog_chr6.simDog.chr6 376288 5 + 593897 CATTC -s simHuman_chr6.simHuman.chr6 445220 5 + 601863 AATTG -s simRat_chr6.simRat.chr6 394131 5 + 647215 GATAC - -a -s simMouse_chr6.simMouse.chr6 394098 1 + 636262 T -s Anc0.Anc0refChr3 26394 1 + 222631 C -s Anc1.Anc1refChr6 55985 1 + 197743 C -s Anc2.Anc2refChr13 29872 1 + 96486 C -s mr.mrrefChr5 247787 1 + 294540 T -s simDog_chr6.simDog.chr6 376471 1 + 593897 G -s simHuman_chr6.simHuman.chr6 380398 1 + 601863 C -s simHuman_chr6.simHuman.chr6 445250 1 + 601863 C -s simRat_chr6.simRat.chr6 394189 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 394161 7 + 636262 AACTTAA -s Anc0.Anc0refChr3 26487 7 + 222631 AACTTAA -s Anc1.Anc1refChr6 56078 7 + 197743 AACTTAA -s Anc2.Anc2refChr13 29965 7 + 96486 AAGTTAA -s mr.mrrefChr5 247850 7 + 294540 AACTTAA -s mr.mrrefChr5 177161 7 - 294540 AACATGA -s simCow_chr6.simCow.chr6 386097 7 + 602619 AAGTAAA -s simDog_chr6.simDog.chr6 376557 7 + 593897 ATGTTAA -s simHuman_chr6.simHuman.chr6 380483 7 + 601863 AACTCAA -s simHuman_chr6.simHuman.chr6 445337 7 + 601863 AACTTGA -s simRat_chr6.simRat.chr6 392661 7 - 647215 AACATGA -s simRat_chr6.simRat.chr6 394276 7 + 647215 AACTCTA - -a -s simMouse_chr6.simMouse.chr6 394197 10 + 636262 GTCAATTGAG - -a -s simMouse_chr6.simMouse.chr6 394251 1 + 636262 C -s mr.mrrefChr5 247930 1 + 294540 C -s simRat_chr6.simRat.chr6 394356 1 + 647215 C - -a -s simMouse_chr6.simMouse.chr6 394272 5 + 636262 GCTCA -s mr.mrrefChr5 247951 5 + 294540 GCTCA -s simRat_chr6.simRat.chr6 394377 5 + 647215 GTCCA - -a -s simMouse_chr6.simMouse.chr6 394302 3 + 636262 TTG - -a -s simMouse_chr6.simMouse.chr6 394309 1 + 636262 A -s Anc0.Anc0refChr3 26645 1 + 222631 A -s Anc1.Anc1refChr6 56236 1 + 197743 A -s Anc2.Anc2refChr13 30127 1 + 96486 A -s mr.mrrefChr5 248077 1 + 294540 A -s simCow_chr6.simCow.chr6 386261 1 + 602619 A -s simDog_chr6.simDog.chr6 376723 1 + 593897 A -s simHuman_chr6.simHuman.chr6 380633 1 + 601863 A -s simHuman_chr6.simHuman.chr6 445495 1 + 601863 A - -a -s simMouse_chr6.simMouse.chr6 394325 1 + 636262 T -s Anc0.Anc0refChr3 26661 1 + 222631 C -s Anc1.Anc1refChr6 56252 1 + 197743 C -s Anc2.Anc2refChr13 30143 1 + 96486 C -s mr.mrrefChr5 248093 1 + 294540 C -s simCow_chr6.simCow.chr6 386310 1 + 602619 C -s simDog_chr6.simDog.chr6 376739 1 + 593897 C -s simHuman_chr6.simHuman.chr6 380649 1 + 601863 C -s simRat_chr6.simRat.chr6 394579 1 + 647215 C - -a -s simMouse_chr6.simMouse.chr6 394332 13 + 636262 TTTGAACTTCCCA -s Anc0.Anc0refChr3 26668 13 + 222631 TTTCATATTTTCA -s Anc1.Anc1refChr6 56259 13 + 197743 TTTCATATTTTCA -s Anc2.Anc2refChr13 30150 13 + 96486 TTTCATATTTTTG -s mr.mrrefChr5 248100 13 + 294540 TTTCAACTTCCCA -s simCow_chr6.simCow.chr6 386317 13 + 602619 TTTCATACTTTTG -s simDog_chr6.simDog.chr6 376746 13 + 593897 TTTCATATCCTTG -s simHuman_chr6.simHuman.chr6 380656 13 + 601863 ATTCATATTTTCA -s simRat_chr6.simRat.chr6 394586 13 + 647215 TTTCAAGTTCCCA - -a -s simMouse_chr6.simMouse.chr6 394345 6 + 636262 ATCTTG -s Anc0.Anc0refChr3 26681 6 + 222631 ACCTCG -s Anc1.Anc1refChr6 56272 6 + 197743 ACCTCG -s Anc2.Anc2refChr13 30163 6 + 96486 ACCCCG -s mr.mrrefChr5 248113 6 + 294540 ACCTTG -s simCow_chr6.simCow.chr6 386331 6 + 602619 GCAATG -s simDog_chr6.simDog.chr6 376759 6 + 593897 ACCCCC -s simHuman_chr6.simHuman.chr6 380669 6 + 601863 ACCTCG -s simRat_chr6.simRat.chr6 394599 6 + 647215 ACTTTG - -a -s simMouse_chr6.simMouse.chr6 394351 10 + 636262 CAGGGTAGGG -s Anc0.Anc0refChr3 26692 10 + 222631 TAGGGTAGGG -s Anc1.Anc1refChr6 56283 10 + 197743 TAGGGTAGGG -s Anc2.Anc2refChr13 30174 10 + 96486 TATTGTGGGG -s mr.mrrefChr5 248124 10 + 294540 CAGGGTAGGG -s simCow_chr6.simCow.chr6 386342 10 + 602619 AATTGTGGAG -s simDog_chr6.simDog.chr6 376770 4 + 593897 T------GGG -s simHuman_chr6.simHuman.chr6 380680 10 + 601863 TAGGGCAGGG -s simRat_chr6.simRat.chr6 394610 10 + 647215 CAGGGTAGGG - -a -s simMouse_chr6.simMouse.chr6 394361 7 + 636262 CTTAGAA -s Anc0.Anc0refChr3 26710 7 + 222631 TTTGGAA -s Anc1.Anc1refChr6 56301 7 + 197743 TTTGGAA -s Anc2.Anc2refChr13 30192 7 + 96486 TTTGGAG -s mr.mrrefChr5 248134 7 + 294540 CTTAGAA -s simCow_chr6.simCow.chr6 386368 7 + 602619 TGTGGAG -s simDog_chr6.simDog.chr6 376782 7 + 593897 TTCAGAG -s simHuman_chr6.simHuman.chr6 380698 7 + 601863 TTTGGAA -s simRat_chr6.simRat.chr6 394620 7 + 647215 CTTAGAA - -a -s simMouse_chr6.simMouse.chr6 394368 3 + 636262 ATT -s Anc0.Anc0refChr3 26717 3 + 222631 ATT -s Anc1.Anc1refChr6 56308 3 + 197743 ATT -s Anc2.Anc2refChr13 30205 3 + 96486 ATT -s mr.mrrefChr5 248141 3 + 294540 ATT -s simCow_chr6.simCow.chr6 386381 3 + 602619 ATT -s simDog_chr6.simDog.chr6 376795 3 + 593897 ATT -s simHuman_chr6.simHuman.chr6 380705 3 + 601863 ATT -s simRat_chr6.simRat.chr6 394627 3 + 647215 ATT - -a -s simMouse_chr6.simMouse.chr6 394371 23 + 636262 TTATGTCCCAACTGCCCCCAGGT -s Anc0.Anc0refChr3 26721 23 + 222631 TGATGTCTTAGCTACCCCCAGGG -s Anc1.Anc1refChr6 56312 23 + 197743 TGATGTCTTAGCTACCCCCAGGG -s Anc2.Anc2refChr13 30209 23 + 96486 TGATGCCTTGGATACCCCCAGGG -s mr.mrrefChr5 248144 23 + 294540 TTATGTCCCAACTGCCCCCAGGG -s simCow_chr6.simCow.chr6 386385 23 + 602619 TGACACCTTGGATACCTATTGGG -s simDog_chr6.simDog.chr6 376799 23 + 593897 TAATGCCTGGGAGCCCCCCAGGA -s simHuman_chr6.simHuman.chr6 380709 23 + 601863 TGATGTGTTAGCTAGTCCCAGGG -s simRat_chr6.simRat.chr6 394630 8 + 647215 T---------------CCCAGGG - -a -s simMouse_chr6.simMouse.chr6 394394 19 + 636262 AAAGTGTGCCATCACTAGC -s Anc0.Anc0refChr3 26801 19 + 222631 TAAGTGTTATAATGTTGGC -s Anc1.Anc1refChr6 56392 19 + 197743 TAAGTGTTATAATGTTGGC -s Anc2.Anc2refChr13 30289 19 + 96486 TAAGTGTTATAATGTTGGC -s mr.mrrefChr5 248167 19 + 294540 TAAGTGTGCCATCGCTGGC -s simCow_chr6.simCow.chr6 386465 19 + 602619 TAAGTGTTATAATGTTGGC -s simDog_chr6.simDog.chr6 376862 19 + 593897 TAAGTGCTATAATGTTGGC -s simHuman_chr6.simHuman.chr6 380791 19 + 601863 TAAGTGTTATAATGTTGGC -s simRat_chr6.simRat.chr6 394638 19 + 647215 TAAGTGTGCCATCGCTGGC - -a -s simMouse_chr6.simMouse.chr6 394413 14 + 636262 ATATGGTTGTGACT -s Anc0.Anc0refChr3 26820 14 + 222631 ATGCATTTGTTACC -s Anc1.Anc1refChr6 56411 14 + 197743 ATGCATTTGTTACC -s Anc2.Anc2refChr13 30308 14 + 96486 ATGCATTTGCTACC -s mr.mrrefChr5 248186 14 + 294540 ATATGGTTGTGACT -s simCow_chr6.simCow.chr6 386484 14 + 602619 GAACATTTGCAACC -s simDog_chr6.simDog.chr6 376882 14 + 593897 ATGGATTTGCTGCC -s simHuman_chr6.simHuman.chr6 380810 14 + 601863 ATTCATTTGTTACG -s simRat_chr6.simRat.chr6 394657 14 + 647215 ATATGGTTGTGACT - -a -s simMouse_chr6.simMouse.chr6 394427 6 + 636262 ATGTCC -s Anc0.Anc0refChr3 26834 6 + 222631 CTGTCC -s Anc1.Anc1refChr6 56425 6 + 197743 CTGTCC -s Anc2.Anc2refChr13 30322 6 + 96486 ATGTCT -s mr.mrrefChr5 248200 6 + 294540 CTGTCC -s simCow_chr6.simCow.chr6 386498 6 + 602619 ATGGGT -s simDog_chr6.simDog.chr6 376898 6 + 593897 ATGTCT -s simHuman_chr6.simHuman.chr6 380824 6 + 601863 CTGATC -s simRat_chr6.simRat.chr6 394671 6 + 647215 CTGTCC - -a -s simMouse_chr6.simMouse.chr6 394433 9 + 636262 TTTATTTAC -s Anc0.Anc0refChr3 26886 9 + 222631 CCTAACTAC -s Anc1.Anc1refChr6 56477 9 + 197743 CCTAACTAC -s Anc2.Anc2refChr13 30374 9 + 96486 CCTAACTAC -s mr.mrrefChr5 248250 9 + 294540 TTTAATTAC -s simCow_chr6.simCow.chr6 386545 7 + 602619 CCTAAAC-- -s simDog_chr6.simDog.chr6 376950 9 + 593897 CCTAACTAC -s simHuman_chr6.simHuman.chr6 380876 9 + 601863 CCTAACTAC -s simRat_chr6.simRat.chr6 394724 9 + 647215 TTTAATAAC - -a -s simMouse_chr6.simMouse.chr6 394442 120 + 636262 TTGTAAGAGATAGACTTGATACCATGTTCTTGGTTGGCACATAACTGAAACTCTGGCATAATTCAGTGTGATCCAAGGTTCCTTGTTCTCAGGATAAGACACACAACTGCCCTAAGCCAG -s Anc0.Anc0refChr3 26898 69 + 222631 TTGAGCAA--------TCATTA---------------------------------GTATAAGCTA--GTGATTCAAGGAT-CTT-------AGATCAGACTCGCAACTTCCCTTGGCCAG -s Anc1.Anc1refChr6 56489 111 + 197743 TTGAGCAAGGTAAACTTCATTACAAGTGCTTGTTTGCCACACTACCTAAAGTCTAGTATAAGCTA--GTGATTCAAGGATTCTT-------AGATCAGACTCGCAACTTCCCTTGGCCAG -s Anc2.Anc2refChr13 30386 69 + 96486 TTGAGCAA--------TCATAA---------------------------------GTATGAGGTG--GTGCTTCAAGGAG-CTC-------AGATCAGATTCTCAGCTTCCCTTGGCCAG -s mr.mrrefChr5 248259 114 + 294540 TTGTAAGAGATAAACTTGATTACATGTTCTTGGTTGGCACATAACTGAAACTCTGGCATAATCCAGTGTGATCCAAGGTTCCTTG------GGATAAGACACGCAACTGCCCTTAGCCAG -s simCow_chr6.simCow.chr6 386552 10 + 602619 --------------------------------------------------------------------------------------------------------------CCTTGGCCTG -s simDog_chr6.simDog.chr6 376962 69 + 593897 TTGAGCAA--------TCATAA---------------------------------GTATGAGGTG--GTGCTTCAAGGAG-CTC-------AGATCAGATTCTCAGCTTCCGTTGGCTAG -s simHuman_chr6.simHuman.chr6 380889 111 + 601863 TTGCGCAAGGTAAACTTCATTACACATGCTTGTTTGCCACACTACCTAAAGTCTAGTGTAAGCAA--GAGATTCAAGGGTTTTT-------CGATCAAACTCGCAACTCCCCTTGGCCAG -s simRat_chr6.simRat.chr6 394733 100 + 647215 TTGTAAGAGATAAACTTGATTACATGTACTTGGTTGGCATATCACTGAAACTCAGGCATAATCCAGTGTGA--------------------GAATAAGACATGCAACTGCCCTTAGCCAT - -a -s simMouse_chr6.simMouse.chr6 394562 85 + 636262 GTCTCCAGGCAAGTGATCAGGCAGTGGGCCCCAGAAGGGTCAGTTGATCCACATTTCGATTGGAGCATCTCTTGGGTGTCTGGGA -s Anc0.Anc0refChr3 26994 79 + 222631 TTC------CAAGTTATTAGGCACTGGGCCCCACCAGGGTCCATCAATCCACACTTTGATTGGAGCATCTCCTGTGATTTTGAGG -s Anc1.Anc1refChr6 56627 79 + 197743 TTC------CAAGTTATTAGGCACTGGGCCCCACCAGGGTCCATCAATCCACACTTTGATTGGAGCATCTCCTGTGATTTTGAGG -s Anc2.Anc2refChr13 30482 79 + 96486 TTC------CAAGTTATTAGGCACTGGGCCCCATCAGGGTCCATCAATCTACACTTTGATTGGAGCATCTCCTGTAATTTTTAGG -s mr.mrrefChr5 248373 79 + 294540 GTC------CAAGTTATCAGGCAGTGGGCCCCACAAGGGTCCGTTGATCCACATTTCGATTGGAGCATCTCCTGGGTGTCTGGGA -s simCow_chr6.simCow.chr6 386589 67 + 602619 TCC------TAAGCTATTGCTCACT------------TGTCCATTAATCTACACTTTGATTGGAGAATCTCTTGGAAGTTTAGGG -s simDog_chr6.simDog.chr6 377058 77 + 593897 TTC------CAGGTTTTTAGGTA--GGGCCCCATCAGGTTCTATCAATCTGCACTTTGATTGGAGCATCTCCAGTAATTTTTAGG -s simHuman_chr6.simHuman.chr6 381050 79 + 601863 TTC------CAAGATATTAGCCACTGGGCCCCACTAGCGTCCACCAATCCACACTTTGATTGGAGCAACTCCTGTGATTTTGAGG -s simRat_chr6.simRat.chr6 394833 79 + 647215 GTC------CAAGCTATCAGGCAGTGGGCCCCACGAGGGTCCGTTGATCCACATTCCTATTGGAGCATCTCCCGGGTGTCTGGGA - -a -s simMouse_chr6.simMouse.chr6 394647 18 + 636262 GTGGACAGGGAGCAGGCT -s Anc0.Anc0refChr3 27076 18 + 222631 GTGGGTAGGAAACAGGTT -s Anc1.Anc1refChr6 56709 18 + 197743 GTGGGTAGGAAACAGGTT -s Anc2.Anc2refChr13 30564 18 + 96486 GTGGGTAGGAAACAGCTT -s mr.mrrefChr5 248452 18 + 294540 GTGGGCAGGAAGCAGGCT -s simCow_chr6.simCow.chr6 386659 18 + 602619 GAGGGCAGGAGACAGCTT -s simDog_chr6.simDog.chr6 377138 18 + 593897 GTGGGTAGGAAACAGCTG -s simHuman_chr6.simHuman.chr6 381132 18 + 601863 GTGGGTTGGAAACAGGTT -s simRat_chr6.simRat.chr6 394912 18 + 647215 GTGGGCAGGAAGCAGGCT - -a -s simMouse_chr6.simMouse.chr6 394665 40 + 636262 TGAAGGACTCTGTTATACTGGAGGTCTTACCGCTGGGTGT -s Anc0.Anc0refChr3 27094 40 + 222631 TGGAGGACCTTGTTATACTGGCAGTCTTACTTCTGGCTGT -s Anc1.Anc1refChr6 56727 40 + 197743 TGGAGGACCTTGTTATACTGGCAGTCTTACTTCTGGCTGT -s Anc2.Anc2refChr13 30582 40 + 96486 TGGAGGACCTTGCTACACTGGCATTCTTACTTCTGGCTGT -s mr.mrrefChr5 248470 40 + 294540 TGAAGGACCCTGTTATACTGGAGGTCTTACTGCTGGGTGT -s simCow_chr6.simCow.chr6 386854 39 + 602619 TGGAGGACCTTCCTGCACTGGCAA-ATTACTTCTGGCTAT -s simDog_chr6.simDog.chr6 377156 40 + 593897 TGGAGGACTTTGCTACACTGGCATTCTTACTTCTGGCTGA -s simHuman_chr6.simHuman.chr6 381150 38 + 601863 TGGAGGACCTAGTTATATTGAGAGTCT--CTTCTGGCTGT -s simRat_chr6.simRat.chr6 394930 40 + 647215 TGAAGGACCCTGTTATACTGTAGGTCGTACTATTGGGTGT - -a -s simMouse_chr6.simMouse.chr6 394705 4 + 636262 CATT -s Anc0.Anc0refChr3 27153 4 + 222631 CTCT -s Anc1.Anc1refChr6 56786 4 + 197743 CTCT -s Anc2.Anc2refChr13 30641 4 + 96486 CTCT -s mr.mrrefChr5 248510 4 + 294540 CATT -s simCow_chr6.simCow.chr6 386912 4 + 602619 CTCT -s simDog_chr6.simDog.chr6 377215 4 + 593897 CTCT -s simHuman_chr6.simHuman.chr6 381207 4 + 601863 CTCT -s simRat_chr6.simRat.chr6 394970 4 + 647215 AATT - -a -s simMouse_chr6.simMouse.chr6 394709 3 + 636262 ACT -s Anc0.Anc0refChr3 27157 3 + 222631 ACT -s Anc1.Anc1refChr6 56790 3 + 197743 ACT -s Anc2.Anc2refChr13 30645 3 + 96486 ACT -s mr.mrrefChr5 248514 3 + 294540 ACT -s simCow_chr6.simCow.chr6 386916 3 + 602619 GCT -s simDog_chr6.simDog.chr6 377219 3 + 593897 ACT -s simHuman_chr6.simHuman.chr6 381211 3 + 601863 ACT -s simRat_chr6.simRat.chr6 394980 3 + 647215 GCT - -a -s simMouse_chr6.simMouse.chr6 394712 35 + 636262 GGTGTCCTCTAACCACCATGATTTGTACTTTGTTT -s Anc0.Anc0refChr3 27160 33 + 222631 GGTGTCTTCCTATCACCATGATTTGGGCTTT--TT -s Anc1.Anc1refChr6 56793 35 + 197743 GGTGTCTTCCTATCACCATGATTTGGGCTTTCTTT -s Anc2.Anc2refChr13 30648 33 + 96486 GGTGTCTTCCTATCACCATGATTGGGGCGTT--TT -s mr.mrrefChr5 248517 35 + 294540 GGTGTCCTCTAACCACCATGATTTGTACTTTGTTT -s simCow_chr6.simCow.chr6 386919 33 + 602619 TAGGTCTTCCTATCACCATGATTGGGTCGTT--TT -s simDog_chr6.simDog.chr6 377222 33 + 593897 GGTGTCTTCCTATCACTGTGATTGTGGTGTC--TT -s simHuman_chr6.simHuman.chr6 381214 35 + 601863 GGTGTCTTCCTATCACCATGATTTGGCCTTTCTTT -s simRat_chr6.simRat.chr6 394985 35 + 647215 GGTGTCCTTTATACACCATGATTTGAGCTTTTTGG - -a -s simMouse_chr6.simMouse.chr6 394747 19 + 636262 CATGTAAAGAGCGGTTGCT -s Anc0.Anc0refChr3 27195 19 + 222631 TAGTAAAGTACTGGTGGCT -s Anc1.Anc1refChr6 56830 19 + 197743 TAGTAAAGTACTGGTGGCT -s Anc2.Anc2refChr13 30683 19 + 96486 TTGTAAAGTTCTGGTGGCT -s mr.mrrefChr5 248554 19 + 294540 CATGTAAAGACTGGTTGCT -s simCow_chr6.simCow.chr6 386955 19 + 602619 TTGGAAAGCTCTTGTGGCT -s simDog_chr6.simDog.chr6 377257 19 + 593897 CTGTAAAGTTCTGGTGGCT -s simHuman_chr6.simHuman.chr6 381251 19 + 601863 TAGCAAAGTACTGGTGGCT -s simRat_chr6.simRat.chr6 395022 13 + 647215 CATGTAATGACTG------ - -a -s simMouse_chr6.simMouse.chr6 394766 29 + 636262 TAACATATGGATTGGCAATTGAATTGTTT -s Anc0.Anc0refChr3 27225 29 + 222631 TAACATATAGATTGACAATTGAATTGTTT -s Anc1.Anc1refChr6 56860 29 + 197743 TAACATATAGATTGACAATTGAATTGTTT -s Anc2.Anc2refChr13 30713 29 + 96486 TAACATATAGATTGACAATTGAATTATTT -s mr.mrrefChr5 248573 29 + 294540 TAACATATGGATTGGCAATTGAATTGTTT -s simCow_chr6.simCow.chr6 386985 29 + 602619 TAACATATAGATTGACAATTGAATTATTT -s simDog_chr6.simDog.chr6 377287 29 + 593897 AAAAATACAGATTTACAATTGAATTATTT -s simHuman_chr6.simHuman.chr6 381281 26 + 601863 TAACATATAGATTGACTATTGAATTG--- -s simRat_chr6.simRat.chr6 395035 25 + 647215 ----ATATGGATTGGCAATTGAATTGTTT - -a -s simMouse_chr6.simMouse.chr6 394795 35 + 636262 TTACTTTGACCCCTAAAGGATGACTGACTAGAGCC -s Anc0.Anc0refChr3 27254 31 + 222631 TGACTTT----CCTACAGTATAACTCGTTAGACCC -s Anc1.Anc1refChr6 56889 31 + 197743 TGACTTT----CCTACAGTATAACTCGTTAGACCC -s Anc2.Anc2refChr13 30744 31 + 96486 TGTATTT----CCTACAGTATAACTCATTAGGCCC -s mr.mrrefChr5 248602 35 + 294540 TTACTTTGACCCCTAAAGGATGACTGGCTAGAGCC -s simCow_chr6.simCow.chr6 387016 28 + 602619 TG---TT----CTTACAGTAAAACTCATAAGGCTG -s simDog_chr6.simDog.chr6 377318 31 + 593897 TGTATTG----CCAACAGTATGACTCAATAGGCCC -s simHuman_chr6.simHuman.chr6 381307 31 + 601863 TGACTTT----CCTACAATATAACCAGTTGGACCA -s simRat_chr6.simRat.chr6 395060 35 + 647215 TTACTTCCGTTGCTAAAGGATGACATGCTAGAGCC - -a -s simMouse_chr6.simMouse.chr6 394830 24 + 636262 CAATCTGAGATTTTCCTGCGGAAC -s Anc0.Anc0refChr3 27289 24 + 222631 CCACCTGAGCTTTTCCTGTATACT -s Anc1.Anc1refChr6 56924 24 + 197743 CCACCTGAGCTTTTCCTGTATACT -s Anc2.Anc2refChr13 30779 24 + 96486 CCGGCCAAGCTTTTCCTGTATACT -s mr.mrrefChr5 248637 24 + 294540 CAACCTGAGATTTTCCTGCAGAAC -s simCow_chr6.simCow.chr6 387048 18 + 602619 CCGTCCAATCTT------TATACC -s simDog_chr6.simDog.chr6 377353 24 + 593897 CCGGCCAAGCTCTTCCTGGATACT -s simHuman_chr6.simHuman.chr6 381342 24 + 601863 CCACCTGACCTTCTCCCATATACT -s simRat_chr6.simRat.chr6 395095 24 + 647215 CTACCTGAGGTTTTCCTGCAGAAC - -a -s simMouse_chr6.simMouse.chr6 394854 11 + 636262 TCCTTTAATCA -s Anc0.Anc0refChr3 27324 11 + 222631 TGCTCTCATGA -s Anc1.Anc1refChr6 56959 11 + 197743 TGCTCTCATGA -s Anc2.Anc2refChr13 30814 11 + 96486 TGCTCTCTTGA -s mr.mrrefChr5 248661 11 + 294540 TCCTTTAATCA -s simCow_chr6.simCow.chr6 387077 11 + 602619 TGCTATCTTGA -s simDog_chr6.simDog.chr6 377388 11 + 593897 GGCTCTTTTGA -s simHuman_chr6.simHuman.chr6 381377 11 + 601863 TGCTCTCATGA -s simRat_chr6.simRat.chr6 395119 11 + 647215 TCCTTTAATCA - -a -s simMouse_chr6.simMouse.chr6 394865 3 + 636262 ATA -s Anc0.Anc0refChr3 27335 3 + 222631 ATA -s Anc1.Anc1refChr6 56970 3 + 197743 ATA -s Anc2.Anc2refChr13 30825 3 + 96486 ATA -s mr.mrrefChr5 248672 3 + 294540 ATA -s simCow_chr6.simCow.chr6 387088 3 + 602619 GCA -s simDog_chr6.simDog.chr6 377403 3 + 593897 ATA -s simHuman_chr6.simHuman.chr6 381388 3 + 601863 ATA -s simRat_chr6.simRat.chr6 395130 3 + 647215 AGA - -a -s simMouse_chr6.simMouse.chr6 394868 28 + 636262 CCACTCTACACCAGGAGTACTCCCCAGT -s Anc0.Anc0refChr3 27338 28 + 222631 CCATTATCCACCAGGAGGACTGTCCAGT -s Anc1.Anc1refChr6 56973 28 + 197743 CCATTATCCACCAGGAGGACTGTCCAGT -s Anc2.Anc2refChr13 30828 28 + 96486 CCATTATCCACGAGGAGGACTGTCCAGT -s mr.mrrefChr5 248675 28 + 294540 CCACTCTACACCAGGAGGACTCTCCAGT -s simCow_chr6.simCow.chr6 387094 28 + 602619 CCATGCTCCACTAGGAGGACCATCCAGT -s simDog_chr6.simDog.chr6 377406 25 + 593897 CCATTATCCAGGAGGAGGATTGTCT--- -s simHuman_chr6.simHuman.chr6 381391 28 + 601863 CCATTTTCCACCAGGAGGACTGTCCAGT -s simRat_chr6.simRat.chr6 395133 28 + 647215 CCACTCTACACCAGATGGACTCTCCAGT - -a -s simMouse_chr6.simMouse.chr6 394896 37 + 636262 GAAGCTACAGCCTAACATGCAGAGTACTCTCATGATG -s Anc0.Anc0refChr3 27367 32 + 222631 GAAGGTTCAGCCTGACTTGCAAGGTGCTCTCT----- -s Anc1.Anc1refChr6 57002 37 + 197743 GAAGGTTCAGCCTGACTTGCAAGGTGCTCTCTTGATG -s Anc2.Anc2refChr13 30857 32 + 96486 GAAGGTTCAGCCTGACTAGCAAGGTGCTCTAT----- -s mr.mrrefChr5 248703 37 + 294540 GAAGCTACAGCCTAACATGCAGAGTACTCTCATGATG -s simCow_chr6.simCow.chr6 387123 32 + 602619 GAAGGTTTAGCCGGACTAGCAAGGTGCTCTAT----- -s simDog_chr6.simDog.chr6 377431 11 + 593897 GAAGA--CAGCCT------------------------ -s simHuman_chr6.simHuman.chr6 381420 37 + 601863 GAAGGTTCAGCCTGATTTGCAAGGTGGTCTCTTGATG -s simRat_chr6.simRat.chr6 395161 37 + 647215 GAAGCCACAGCCTAAGATGCAGAGTACTTTCATGATG - -a -s simMouse_chr6.simMouse.chr6 394933 29 + 636262 GACTTTCTCCATGAAAGGACCATCCTCCA -s Anc0.Anc0refChr3 27399 27 + 222631 ACCTTTCTCCTCCAGAGGG--GCTGTCCA -s Anc1.Anc1refChr6 57039 27 + 197743 ACCTTTCTCCTCCAGAGGG--GCTGTCCA -s Anc2.Anc2refChr13 30889 27 + 96486 ACTGTTCTACTCCACAGGG--GCTGTTCT -s mr.mrrefChr5 248740 27 + 294540 AACTTTCTCCATGAGAGGG--ACCGTCCA -s simCow_chr6.simCow.chr6 387155 27 + 602619 ACTGTTCTACTCCACAGGG--GCTGTTCT -s simHuman_chr6.simHuman.chr6 381460 27 + 601863 ACCTTACTCCTCTAGCTAG--GCTGTCCA -s simRat_chr6.simRat.chr6 395198 27 + 647215 AACCTTCTCCATGAGAAGG--ACCGTACA - -a -s simMouse_chr6.simMouse.chr6 394962 48 + 636262 GAGGGGTACAGACTCATATTCCCCACCCTCTTTTGAGTCCCTACCCTA -s Anc0.Anc0refChr3 27426 48 + 222631 GGGGGGTACAGGCTCTTAATCCCATCTCTCTTTTAAGTCCTTATTCTA -s Anc1.Anc1refChr6 57066 48 + 197743 GGGGGGTACAGGCTCTTAATCCCATCTCTCTTTTAAGTCCTTATTCTA -s Anc2.Anc2refChr13 30916 48 + 96486 AGGGGGTACAAGCTCTTAATCCCATCTCTCTTTTAACTCCTTAACTTA -s mr.mrrefChr5 248767 48 + 294540 GAGGGGTACAGACTCATATTCCCCACCCTCTTTTGAGTCCCTATTCTA -s simCow_chr6.simCow.chr6 387182 41 + 602619 AGGGGGTACAAACTCCTAATTCCATCACTCTTTCAAATCCT------- -s simDog_chr6.simDog.chr6 377442 32 + 593897 -----------GCTCTTAATCCCATCTC-----TAACTTCTTAACTTA -s simHuman_chr6.simHuman.chr6 381489 48 + 601863 GGGGGGTACAGGCCCTTAATCCCATCTCTCTTTTAAGTCCTTATTCTA -s simRat_chr6.simRat.chr6 395225 46 + 647215 GAGGGGTACAGACTCATA--CCCCGCCCTCTTTTGAATCCCTATTCTA - -a -s simMouse_chr6.simMouse.chr6 395010 10 + 636262 TCTTTCTCCT -s Anc0.Anc0refChr3 27474 10 + 222631 TAATTCTTTG -s Anc1.Anc1refChr6 57114 10 + 197743 TAATTCTTTG -s Anc2.Anc2refChr13 30964 10 + 96486 GAATTCTTTG -s mr.mrrefChr5 248815 10 + 294540 TCTTTCTCTT -s simDog_chr6.simDog.chr6 377478 10 + 593897 GAATTCTTTG -s simHuman_chr6.simHuman.chr6 381537 10 + 601863 TTCTTCTTTG -s simRat_chr6.simRat.chr6 395271 10 + 647215 TCTTTCTCTT - -a -s simMouse_chr6.simMouse.chr6 395020 62 + 636262 TTCGTCTCCCTTGTTTATCTTTTACTCATCTTGGGCCAGAGGTAATTTATAATCTACAACAA -s Anc0.Anc0refChr3 27497 58 + 222631 GT-GTCTTCTTTGTTTATTTT---GTCATCTTGAAATAGAGGTAATTTATCGTCTCCAACAA -s Anc1.Anc1refChr6 57137 58 + 197743 GT-GTCTTCTTTGTTTATTTT---GTCATCTTGAAATAGAGGTAATTTATCGTCTCCAACAA -s Anc2.Anc2refChr13 30987 58 + 96486 GC-ATCTTCTTTGTTTATTCA---GTCATCTTGAAATAGAGGTACTTTATCGTCTCCAACAA -s mr.mrrefChr5 248825 61 + 294540 TT-GTCTCCCTTGTTTATCTTTTAGTCATCTTGGGCCAGAGGTAATTTATCATCTCCAACAA -s simCow_chr6.simCow.chr6 387223 55 + 602619 ----CCTTCTTTCTTTATTCA---GTCGTCTAGGAATGGAGGTACCTTATTGTCTCCGACAA -s simDog_chr6.simDog.chr6 377501 58 + 593897 GC-ATCTTCTTTGTTTATTCA---GTCATCTTGAGATAGAGGTACTTTATCATCTCCAATTA -s simHuman_chr6.simHuman.chr6 381560 58 + 601863 AT-GTTTTCTTTGTTTGTTTT---GTCACCTTGAAATAGAGGTAATCCATCGTCTCTATCAA -s simRat_chr6.simRat.chr6 395281 61 + 647215 TT-GTCTCCCTTGCTTATCTTTTAGTCATCTTGGGCCAGAGGTAATTTATCATCCCCAACCA - -a -s simMouse_chr6.simMouse.chr6 395082 13 + 636262 CATTCAGCAGCCA -s Anc0.Anc0refChr3 27570 13 + 222631 CATTCAGCATTTT -s Anc1.Anc1refChr6 57210 13 + 197743 CATTCAGCATTTT -s Anc2.Anc2refChr13 31060 13 + 96486 CGTTCAGCATTTT -s mr.mrrefChr5 248886 13 + 294540 CATTCAGCATTCA -s simCow_chr6.simCow.chr6 387293 12 + 602619 C-TTCAGCATTTT -s simDog_chr6.simDog.chr6 377573 13 + 593897 AGCTCGGCCTTTT -s simHuman_chr6.simHuman.chr6 381633 13 + 601863 CATTCAGCATTTT -s simRat_chr6.simRat.chr6 395342 13 + 647215 CATTCAGCATTCA - -a -s simMouse_chr6.simMouse.chr6 395095 2 + 636262 CT -s Anc0.Anc0refChr3 27584 2 + 222631 CT -s Anc1.Anc1refChr6 57224 2 + 197743 CT -s Anc2.Anc2refChr13 31074 2 + 96486 TT -s mr.mrrefChr5 248900 2 + 294540 CT -s simCow_chr6.simCow.chr6 387306 2 + 602619 TT -s simDog_chr6.simDog.chr6 377587 2 + 593897 TT -s simHuman_chr6.simHuman.chr6 381647 2 + 601863 CT -s simRat_chr6.simRat.chr6 395356 2 + 647215 CT - -a -s simMouse_chr6.simMouse.chr6 395097 96 + 636262 CTACCTTTTAATAGCACTGATGATTGGCACAGAGCCAATAGAAGGCTCACGCATCATGTAGGCACTTGAGAAATTAAATACAGACATGAAGACTGA -s Anc0.Anc0refChr3 27586 84 + 222631 CCACCTGTTAATAACACTGATAATTGGCATTGAGACCATAAAAGGCTAATGGATCATGTAGTTGCTCT------------TGGACACAAAGACCAA -s Anc1.Anc1refChr6 57226 95 + 197743 CCACCTGTTAATAACACTGATAATTGGCATTGAGACCATAAAAGGCTAATGGATCATGTAGTTGCTCTAGAATATAAA-ATGGACACAAAGACCAA -s Anc2.Anc2refChr13 31076 84 + 96486 CCACCTGTTAATAACACTGATAATTAGCATTGTGAGCATAAAAGGCTAATGGATCATGTAGTTGCTCT------------TGGACACAAGAAGAAT -s mr.mrrefChr5 248902 96 + 294540 CTACCTTTTAATAGCACTGATGATTGGCACAGAGCCAATAAAAGGCTCACGCATCATGTAGGCACTCGAGAAATTAAATACAGACATAAAGACCGA -s simCow_chr6.simCow.chr6 387314 83 + 602619 CCACCTGTGGGTAACACTGATAACTAGC-CTGTGAACACAAAAGGCTGATGGATCATATAGTCGCTCT------------TGGACACATGAAGAAT -s simDog_chr6.simDog.chr6 377589 84 + 593897 CTACCTTTTAATAAGACTGATAGTTAACATTGTGAGCATTAAAGGCTAATGTATCATGGAGTTGCTCG------------TGGACACAAGAAGACT -s simHuman_chr6.simHuman.chr6 381649 95 + 601863 CCACCTGTTAATAACACTGCCAATTGGCATTGAGGCCATAAAAGGCTAATGGATCATGTCATTGCTCTAGAATATAAA-AGGGACACAGAGACCAA -s simRat_chr6.simRat.chr6 395358 96 + 647215 CTACTTCTAAATAGCACTGATGATTGGCACAGAGAAAATAAAAAGCTCACATATCATGCAGGCACTCGAGAAATCAAATACAGCCATAAAGACCGA - -a -s simMouse_chr6.simMouse.chr6 395193 146 + 636262 ATCACCCAATACTAGCTCATAGGCCGCAGCGCAAAGGCATATCACTCATGTTTAGCAAGAGGAAACACAACTCACATTAGCATCCAGGGATGATAAGATTTGGATTGACTCTGCAACACCTTCCTGCATCAGCCATGTCCAAATTT -s Anc0.Anc0refChr3 27670 67 + 222631 GTCAAACAACATTAGCTTATA-------------------------------------------------------------------------------TGGAGCAACTCAGCAACTTCTTCCTGCATTGGACATGTCCAAATGT -s Anc1.Anc1refChr6 57321 67 + 197743 GTCAAACAACATTAGCTTATA-------------------------------------------------------------------------------TGGAGCAACTCAGCAACTTCTTCCTGCATTGGACATGTCCAAATGT -s Anc2.Anc2refChr13 31160 67 + 96486 GTCAAACAACATTAGCTTATA-------------------------------------------------------------------------------TGAAGCAACTTAGCAACTTCTTCCTGCATTTGACATGTCCAAATGT -s mr.mrrefChr5 248998 67 + 294540 ATCACACAATACTAGCTCATA-------------------------------------------------------------------------------TGGAGTGACTCTGCAACATCTTCCTGCATCGGCCATGTCCAAATTT -s simCow_chr6.simCow.chr6 387397 67 + 602619 GTCAAGCAACCTTAGCTTATA-------------------------------------------------------------------------------TGAAGGAACTTAGCCACTTCTTCCTCCAATTACCATGTCCAAATGT -s simDog_chr6.simDog.chr6 377675 67 + 593897 GTCAAATTACATTAGCTTGTA-------------------------------------------------------------------------------TGAGGCTACTTAGCAACTTCCTCTTGCATCTGACATGTCCAAATGT -s simHuman_chr6.simHuman.chr6 381744 65 + 601863 GTCAAACAACATTAGCTTATA-------------------------------------------------------------------------------TGGAGCAACTCAGCAACTTCTACCTGCATTGGACATGTCCTAG--T -s simRat_chr6.simRat.chr6 395454 67 + 647215 ATCACACAATACTAGCTCATA-------------------------------------------------------------------------------TGAAGTGTCTCTGCAATATCTTCCTGCATCGGCCATGTCCAGATTT - -a -s simMouse_chr6.simMouse.chr6 395339 7 + 636262 ACCTACC -s Anc0.Anc0refChr3 27737 7 + 222631 GCCTACC -s Anc1.Anc1refChr6 57388 7 + 197743 GCCTACC -s Anc2.Anc2refChr13 31227 7 + 96486 GCCTACC -s mr.mrrefChr5 249065 7 + 294540 ACCTACC -s simCow_chr6.simCow.chr6 387464 7 + 602619 GCCTACC -s simDog_chr6.simDog.chr6 377742 7 + 593897 ACCTACC -s simHuman_chr6.simHuman.chr6 381809 7 + 601863 GCCTACC -s simRat_chr6.simRat.chr6 395526 7 + 647215 ACTCACT - -a -s simMouse_chr6.simMouse.chr6 395346 20 + 636262 CACAAATATACACATAGTTT -s Anc0.Anc0refChr3 27744 12 + 222631 C--------ACACATAGTTT -s Anc1.Anc1refChr6 57395 12 + 197743 C--------ACACATAGTTT -s Anc2.Anc2refChr13 31234 12 + 96486 A--------ACACCTAGTCT -s mr.mrrefChr5 249072 20 + 294540 CACACATATACACATAGTTT -s simCow_chr6.simCow.chr6 387471 12 + 602619 A--------CCACCTAGTCT -s simDog_chr6.simDog.chr6 377749 12 + 593897 A--------ACACCCAGTCT -s simHuman_chr6.simHuman.chr6 381816 12 + 601863 C--------ACACATGGTTT -s simRat_chr6.simRat.chr6 395534 20 + 647215 CACACATACACACATTGTTT - -a -s simMouse_chr6.simMouse.chr6 395366 45 + 636262 AAACCCAATTACTTGTTGATGGAGAGTAGTCAATGTAGTGCCTTG -s Anc0.Anc0refChr3 27756 45 + 222631 AGACCCAATTACTTGTTGATGATCAGTAGTTACTGTAGTACCTTG -s Anc1.Anc1refChr6 57407 45 + 197743 AGACCCAATTACTTGTTGATGATCAGTAGTTACTGTAGTACCTTG -s Anc2.Anc2refChr13 31246 45 + 96486 AGCCCCAATTAGTTGCTGATGATCAGTAGTTACTGTAGTATCTTG -s mr.mrrefChr5 249092 45 + 294540 AAACCCAATTACTTGTTGATGAACAGTAGTTACTGTAGTACCTTG -s simCow_chr6.simCow.chr6 387483 42 + 602619 CACCCCAA-TATTTGTTGATGATCTGTAG--ACTGTAGTAATTTG -s simDog_chr6.simDog.chr6 377761 45 + 593897 AGCCCCAATTAGTTGCTGATGAACAGTAGTTACTGTAGTATCCTG -s simHuman_chr6.simHuman.chr6 381828 43 + 601863 AGACTGAATTTCT--TTGATGATCAGTAGTTACTGTAGTACCTTA -s simRat_chr6.simRat.chr6 395622 45 + 647215 AAACCCAATTACTTGTTGATGAACAGTAGTTACTGTAGTACCTTG - -a -s simMouse_chr6.simMouse.chr6 395411 9 + 636262 GAAAGGGCC -s Anc0.Anc0refChr3 27801 9 + 222631 AAAAGGGTC -s Anc1.Anc1refChr6 57452 9 + 197743 AAAAGGGTC -s Anc2.Anc2refChr13 31291 9 + 96486 AAAAGGGTC -s mr.mrrefChr5 249137 9 + 294540 GAAAGGGCC -s simCow_chr6.simCow.chr6 387525 9 + 602619 TAAAGGATC -s simDog_chr6.simDog.chr6 377809 9 + 593897 AAAAGGGTC -s simHuman_chr6.simHuman.chr6 381871 9 + 601863 AAAAGGGTC -s simRat_chr6.simRat.chr6 395667 9 + 647215 GAAAGGGCC - -a -s simMouse_chr6.simMouse.chr6 395420 11 + 636262 TACTTTAACTA -s Anc0.Anc0refChr3 27810 11 + 222631 TACATTACTCA -s Anc1.Anc1refChr6 57461 11 + 197743 TACATTACTCA -s Anc2.Anc2refChr13 31300 11 + 96486 TTCATCACCCA -s mr.mrrefChr5 249146 11 + 294540 TACTTTAATTA -s simCow_chr6.simCow.chr6 387534 11 + 602619 TTCTTCAAACA -s simDog_chr6.simDog.chr6 377818 11 + 593897 CTTATCACCCA -s simHuman_chr6.simHuman.chr6 381881 11 + 601863 TATCTTATTCA -s simRat_chr6.simRat.chr6 395676 11 + 647215 TACTTTAATTA - -a -s simMouse_chr6.simMouse.chr6 395431 35 + 636262 TAACTATGAGCTTGGCTGTGAGTCAAGACAAGCTA -s Anc0.Anc0refChr3 27821 31 + 222631 TAAG---GAGCTTATCT-TGATTAAAGACATGCTA -s Anc1.Anc1refChr6 57472 32 + 197743 TAAG---GAGCTTATCTGTGATTAAAGACATGCTA -s Anc2.Anc2refChr13 31311 31 + 96486 TAAG---AAGCTTATCT-TGATTAAAGACATGCTA -s mr.mrrefChr5 249157 35 + 294540 TAACTATGAGCTTGTCTGTGAGTCAAGACAAGCTA -s simCow_chr6.simCow.chr6 387545 31 + 602619 TGAC---AACCTTATCT-TGATTAAAGGCATGTTA -s simDog_chr6.simDog.chr6 377829 22 + 593897 TAAG---AAGCTTAT----------AGATTGGCCA -s simHuman_chr6.simHuman.chr6 381915 32 + 601863 TAAA---GAGCTTATCTGTGATTAGAGACATGCTA -s simRat_chr6.simRat.chr6 395687 35 + 647215 TAACTATGACCTTCTCTGTGAGTCAAGACAAGCTA - -a -s simMouse_chr6.simMouse.chr6 395466 7 + 636262 TTAGTTA -s Anc0.Anc0refChr3 27856 7 + 222631 TTAGTTG -s Anc1.Anc1refChr6 57508 7 + 197743 TTAGTTG -s Anc2.Anc2refChr13 31346 7 + 96486 TTAGTTG -s mr.mrrefChr5 249192 7 + 294540 TTAGTTA -s simCow_chr6.simCow.chr6 387580 6 + 602619 GT-GTTG -s simDog_chr6.simDog.chr6 377855 7 + 593897 TTAATTA -s simHuman_chr6.simHuman.chr6 381951 7 + 601863 TTAGTTG -s simRat_chr6.simRat.chr6 395722 7 + 647215 TTAGTTA - -a -s simMouse_chr6.simMouse.chr6 395473 10 + 636262 ATCCATTTCA -s Anc0.Anc0refChr3 27863 10 + 222631 AGCCAATCCA -s Anc1.Anc1refChr6 57515 10 + 197743 AGCCAATCCA -s Anc2.Anc2refChr13 31353 10 + 96486 AGTGGATTCA -s mr.mrrefChr5 249199 10 + 294540 ATCCATTCCA -s simCow_chr6.simCow.chr6 387592 10 + 602619 AGATGATTCA -s simDog_chr6.simDog.chr6 377862 10 + 593897 AGTGGATTCA -s simHuman_chr6.simHuman.chr6 381958 10 + 601863 AGCCAGTCCA -s simRat_chr6.simRat.chr6 395729 10 + 647215 ATCCACTCCA - -a -s simMouse_chr6.simMouse.chr6 395483 29 + 636262 TGAAAGATGTAGAAGTGAAGAGAAAACAT -s Anc0.Anc0refChr3 27873 25 + 222631 TGAAAGATATAGAGGTG----GAAAACAT -s Anc1.Anc1refChr6 57525 25 + 197743 TGAAAGATATAGAGGTG----GAAAACAT -s Anc2.Anc2refChr13 31363 25 + 96486 TGAAAGAGATAGAGATG----GAAAACAT -s mr.mrrefChr5 249209 29 + 294540 TGAAAGATGTAGAAGTGAAGAGAAAACAT -s simCow_chr6.simCow.chr6 387602 25 + 602619 TTAACGAGATATAGATG----GAAAGAAC -s simDog_chr6.simDog.chr6 377873 25 + 593897 TGGAAGAGAAAGAGATA----GAAGACAT -s simHuman_chr6.simHuman.chr6 381968 25 + 601863 TGAAAGATATAGAGGTG----GAAAACAT -s simRat_chr6.simRat.chr6 395739 25 + 647215 ----AGAGGTAGAAGTGAAGGGAAAACAT - -a -s simMouse_chr6.simMouse.chr6 395512 32 + 636262 CTTTTTCAGACCCACAGATGAGATTATTACTT -s Anc0.Anc0refChr3 27898 32 + 222631 TTTTTTCTGAGTGGCAGATGAGATTATTATTT -s Anc1.Anc1refChr6 57550 32 + 197743 TTTTTTCTGAGTGGCAGATGAGATTATTATTT -s Anc2.Anc2refChr13 31394 32 + 96486 TTCTTTCTGAGTGGCAGGTGAGATTATTATTG -s mr.mrrefChr5 249238 32 + 294540 CTTTTTCAGAGCCGCAGATGAGATTATTATTT -s simCow_chr6.simCow.chr6 387633 32 + 602619 TTCTTTCTGAGTGGCAGGTGAGATTATTATCA -s simDog_chr6.simDog.chr6 377904 27 + 593897 CT-----TGAGAGGCAGGCAAGATTATCATTG -s simHuman_chr6.simHuman.chr6 381993 32 + 601863 TTTTTTCTGAGTGGTAGATGAGATTATTATTT -s simRat_chr6.simRat.chr6 395764 32 + 647215 CCCTTTCAGAGCAGCAGATGAGATTATTTTTC - -a -s simMouse_chr6.simMouse.chr6 395544 16 + 636262 AAAAACAAGTCTACAC -s Anc0.Anc0refChr3 27930 15 + 222631 AAAAGCAGCACT-TGC -s Anc1.Anc1refChr6 57582 16 + 197743 AAAAGCAGCACTCTGC -s Anc2.Anc2refChr13 31426 15 + 96486 AAAAGCAGCATT-TGC -s mr.mrrefChr5 249270 16 + 294540 AAAAGCAAGACTATGC -s simCow_chr6.simCow.chr6 387665 15 + 602619 ACAAGCAGCATT-TGC -s simDog_chr6.simDog.chr6 377931 15 + 593897 GAAAACAGCATT-TGC -s simHuman_chr6.simHuman.chr6 382026 16 + 601863 AAAAGCAGCACCCTGC -s simRat_chr6.simRat.chr6 395796 16 + 647215 AAAGGCAAGACTATGC - -a -s simMouse_chr6.simMouse.chr6 395560 1 + 636262 T -s Anc0.Anc0refChr3 27945 1 + 222631 A -s Anc1.Anc1refChr6 57598 1 + 197743 A -s Anc2.Anc2refChr13 31441 1 + 96486 A -s mr.mrrefChr5 249286 1 + 294540 A -s simCow_chr6.simCow.chr6 387746 1 + 602619 G -s simDog_chr6.simDog.chr6 377946 1 + 593897 A -s simHuman_chr6.simHuman.chr6 382042 1 + 601863 A -s simRat_chr6.simRat.chr6 395812 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 395561 3 + 636262 AGA -s Anc0.Anc0refChr3 27965 3 + 222631 AGA -s Anc1.Anc1refChr6 57618 3 + 197743 AGA -s Anc2.Anc2refChr13 31461 3 + 96486 AGA -s mr.mrrefChr5 249287 3 + 294540 AGA -s simCow_chr6.simCow.chr6 387766 3 + 602619 GGA -s simDog_chr6.simDog.chr6 377966 3 + 593897 AAA -s simHuman_chr6.simHuman.chr6 382062 3 + 601863 AGA -s simRat_chr6.simRat.chr6 395813 3 + 647215 AGA - -a -s simMouse_chr6.simMouse.chr6 395564 7 + 636262 CAGTCAT -s Anc0.Anc0refChr3 27968 7 + 222631 GACTCAT -s Anc1.Anc1refChr6 57621 7 + 197743 GACTCAT -s Anc2.Anc2refChr13 31464 7 + 96486 GACCCAT -s mr.mrrefChr5 249290 7 + 294540 CACTCAT -s simCow_chr6.simCow.chr6 387772 7 + 602619 GAAACAC -s simDog_chr6.simDog.chr6 377969 7 + 593897 AACCCAT -s simHuman_chr6.simHuman.chr6 382065 7 + 601863 GACTCAG -s simRat_chr6.simRat.chr6 395816 7 + 647215 CACTCAT - -a -s simMouse_chr6.simMouse.chr6 395571 5 + 636262 GTGAT -s Anc0.Anc0refChr3 27986 5 + 222631 GTGCT -s Anc1.Anc1refChr6 57639 5 + 197743 GTGCT -s Anc2.Anc2refChr13 31482 5 + 96486 GTGCT -s mr.mrrefChr5 249297 5 + 294540 GTGAT -s simCow_chr6.simCow.chr6 387790 5 + 602619 AATGT -s simDog_chr6.simDog.chr6 377988 5 + 593897 GTGCT -s simHuman_chr6.simHuman.chr6 382083 5 + 601863 GTACT -s simRat_chr6.simRat.chr6 395823 5 + 647215 GTGCT - -a -s simMouse_chr6.simMouse.chr6 395576 43 + 636262 TGACATCGTACTGAATAAGGACAATGCTGTATTTTTGCTCTCT -s Anc0.Anc0refChr3 27997 43 + 222631 TCACAGGATACTAAATAAGGAAGAGGTTGCAAATTTGTTCTGT -s Anc1.Anc1refChr6 57650 43 + 197743 TCACAGGATACTAAATAAGGAAGAGGTTGCAAATTTGTTCTGT -s Anc2.Anc2refChr13 31493 43 + 96486 TCACAGGATAGGAAATAAGGAAGAGGTTGCAAATTTGTTCTGT -s mr.mrrefChr5 249302 43 + 294540 TGACATGGTACTGAATAAGGACAATGCTGTATTTTTGTTCTCT -s simCow_chr6.simCow.chr6 387801 41 + 602619 TTACAGGAT--GGAACAAGGAAAAGGTTGCGCACTTGTTCTGT -s simDog_chr6.simDog.chr6 377999 43 + 593897 CCACAAGATAGGAAATAAGGAAGAGGTTGGAAATTTGCTCTGT -s simHuman_chr6.simHuman.chr6 382094 43 + 601863 TCACAGGATACTAAATGAGGAAGAGGTTGCAGATATGTTCTGT -s simRat_chr6.simRat.chr6 395828 43 + 647215 TAACAAGGTACTGAATAAGTATAACGCTGTATTTTAATTCTCT - -a -s simMouse_chr6.simMouse.chr6 395619 92 + 636262 AGCATGTACAATACAGCCCAAGGTACTCCTTATAAAAAACCCCCATCGGTTGTTGAACCACAATTCTTTGTTCCAGTTCTACTTCCACTACT -s Anc0.Anc0refChr3 28040 43 + 222631 AGGATGTACAATTCAGCCCAGTGTACACTTTATGA-------------------------------------------------CCACACCT -s Anc1.Anc1refChr6 57693 43 + 197743 AGGATGTACAATTCAGCCCAGTGTACACTTTATGA-------------------------------------------------CCACACCT -s Anc2.Anc2refChr13 31538 43 + 96486 AGGATGTACAATTCACCCCAGTGTACACTTTATGA-------------------------------------------------CTATACCT -s mr.mrrefChr5 249345 92 + 294540 AGCATGTACAATACAGCCCAAGGTACTCCTTATAAAAAACCCCCATCGGTTGTTGAACCACAATTCTTTGTTCCAGTTCTACTTCCACTACT -s simCow_chr6.simCow.chr6 387844 43 + 602619 AGGATGTGCAATTCATCCCGATGCACTCCTTCTGG-------------------------------------------------CAATGCCT -s simDog_chr6.simDog.chr6 378044 42 + 593897 AGGATGTAGAATTCACCCCAGTGTACACTCTATGA-------------------------------------------------CTA-AGAG -s simHuman_chr6.simHuman.chr6 382137 43 + 601863 AGGATGTACAATTCAGCCCAGTGTACACTTTATGA-------------------------------------------------CCACACCT -s simRat_chr6.simRat.chr6 395871 92 + 647215 AATGTGTACAATACAGTCCAAGCTACTCCTTATAAAAGGGCCCCATCAGTTCTTCAACCACAATTCTTTACTCGAACTCTAATACAACTACT - -a -s simMouse_chr6.simMouse.chr6 395711 76 + 636262 GAGAGTTAGGTTCACCACAACATAGGAGCATTGCAGAGTTCTCAGTACTTGGCGCAATAGCCAATTTGCAATAGAT -s Anc0.Anc0refChr3 28083 34 + 222631 AAG-----------------------------------------GTTCTGGG-ACAATAGACAACTTGGGGCAGAT -s Anc1.Anc1refChr6 57736 34 + 197743 AAG-----------------------------------------GTTCTGGG-ACAATAGACAACTTGGGGCAGAT -s Anc2.Anc2refChr13 31581 34 + 96486 AAG-----------------------------------------GTTCTGGG-ACAATAGACAACTAGGGGCAAAT -s mr.mrrefChr5 249437 76 + 294540 GAGAGTTAGGTTCACCACAACATAGGAGCATTGCAGAGTTCTCAGTTCTTGGCGCAATAGACAATTTGCAATAGAT -s simCow_chr6.simCow.chr6 387892 34 + 602619 AAG-----------------------------------------GTTCCTGG-ACAGTAATCAACTCAGGGCACAT -s simDog_chr6.simDog.chr6 378086 30 + 593897 AAG-----------------------------------------CCATTGTG----ATAGACC-CCAGGTGCCATT -s simHuman_chr6.simHuman.chr6 382180 34 + 601863 AAG-----------------------------------------GTTCTGGG-ACAATAGACAGCTTGGGGCAGAT -s simRat_chr6.simRat.chr6 395963 76 + 647215 GAGAGTTAGGTTCATCACAAGCGAGGAGAATTGCAGAGTTCTTGGTTCTTGGTGCAATAAATAATTTACAATAGAT - -a -s simMouse_chr6.simMouse.chr6 395787 61 + 636262 TTAGACTCCTGAATAAAAGAATCCATTTTGATAACTGTGAGCACCCCCAACATGTGCCCCC -s Anc0.Anc0refChr3 28117 32 + 222631 CAAGACTCT----------AATCCA-TT--------GTGA---CCCCCAACATG------- -s Anc1.Anc1refChr6 57770 46 + 197743 CAAGACTCTTGAAT-GAAGAATCCA-TT--------GTGATTACCCCCAACATGTG----- -s Anc2.Anc2refChr13 31615 32 + 96486 CAGGAATTT----------AATCAA-CT--------GTGA---CTCCCGACATA------- -s mr.mrrefChr5 249513 53 + 294540 TTAGACTCTTGAATAAAAGAATCCATTT--------GTGATCACCCCCAACATGTGCCCCC -s simCow_chr6.simCow.chr6 387952 32 + 602619 CAGGGATTT----------GATCAA-CT--------GTGA---CCATCCATATA------- -s simDog_chr6.simDog.chr6 378116 32 + 593897 GAGGAATTT----------AATCAA-CC--------GTGA---CTCCTGACATA------- -s simHuman_chr6.simHuman.chr6 382214 46 + 601863 CAAGACTCTTGAAT-GAAGAATCCA-TT--------GTGATTGACCCCAACATGTG----- -s simRat_chr6.simRat.chr6 396039 53 + 647215 TTGGACTCTTGAATAAAAGAATCCTTTT--------GTGATCACCTCCAACATGTGCCCCC - -a -s simMouse_chr6.simMouse.chr6 395848 41 + 636262 GTCTGATATTTCATTAAACATCAGTACTGACCCTATCAACA -s Anc0.Anc0refChr3 28149 21 + 222631 --------------------CCATTAGTGTTTCTATCAACA -s Anc1.Anc1refChr6 57816 23 + 197743 ------------------TGCCATTAGTGTTTCTATCAACA -s Anc2.Anc2refChr13 31647 21 + 96486 --------------------CCATTAGTGTTTCTATCAACA -s mr.mrrefChr5 249566 41 + 294540 GTCTGATAGTTGATCAACTGTCAGTCCTGACTCTATCAGCA -s simCow_chr6.simCow.chr6 387984 21 + 602619 --------------------TCATTAGTGTTTCTATAAATA -s simDog_chr6.simDog.chr6 378148 21 + 593897 --------------------CTAATAGTGTTTCAATCAACA -s simHuman_chr6.simHuman.chr6 382260 23 + 601863 ------------------TGCCATTAGTGGTACTATCAACA -s simRat_chr6.simRat.chr6 396092 41 + 647215 GTCAGAAAGTTGATCAACTGTCAGTCCTGACTCTATCAGCA -s simRat_chr6.simRat.chr6 396374 41 + 647215 ATTTGTTGGTTGATCAACTGTCAGTCCTGACTCTATCAGCA - -a -s simMouse_chr6.simMouse.chr6 395889 6 + 636262 AGGACA -s Anc0.Anc0refChr3 28174 6 + 222631 AGGACA -s Anc1.Anc1refChr6 57843 6 + 197743 AGGACA -s Anc2.Anc2refChr13 31672 6 + 96486 AGGAGA -s mr.mrrefChr5 249607 6 + 294540 GGGACA -s simCow_chr6.simCow.chr6 388009 6 + 602619 AGAATA -s simDog_chr6.simDog.chr6 378173 6 + 593897 GGGAGA -s simHuman_chr6.simHuman.chr6 382287 6 + 601863 AGGACA -s simRat_chr6.simRat.chr6 396133 6 + 647215 GAGACA -s simRat_chr6.simRat.chr6 396415 6 + 647215 GGGACA - -a -s simMouse_chr6.simMouse.chr6 395895 8 + 636262 GTAGTTGT -s Anc0.Anc0refChr3 28180 8 + 222631 GTAGTTAT -s Anc1.Anc1refChr6 57849 8 + 197743 GTAGTTAT -s Anc2.Anc2refChr13 31678 8 + 96486 GTAATTAT -s mr.mrrefChr5 249613 8 + 294540 GTAGTTGT -s simCow_chr6.simCow.chr6 388021 8 + 602619 GTAAGTAG -s simDog_chr6.simDog.chr6 378179 8 + 593897 GGAATTAT -s simHuman_chr6.simHuman.chr6 382293 8 + 601863 GTAGATAA -s simRat_chr6.simRat.chr6 396139 8 + 647215 GTAGTTGT -s simRat_chr6.simRat.chr6 396421 8 + 647215 GTAGTTGT - -a -s simMouse_chr6.simMouse.chr6 395903 22 + 636262 GAGTGGTAGACAATAGATTGGA -s Anc0.Anc0refChr3 28188 22 + 222631 CAGTGGTAGAGGTTAGACTAGA -s Anc1.Anc1refChr6 57857 22 + 197743 CAGTGGTAGAGGTTAGACTAGA -s Anc2.Anc2refChr13 31686 22 + 96486 CAGTAGTAGAGGTTAGACTAGA -s mr.mrrefChr5 249621 22 + 294540 GAGTGGTAGACCACAGATTAGA -s simCow_chr6.simCow.chr6 388042 22 + 602619 CAGTAGTAGACGTTAGATCATA -s simDog_chr6.simDog.chr6 378187 22 + 593897 CAGTAGTAGAGATTGGACTAGA -s simHuman_chr6.simHuman.chr6 382301 22 + 601863 CAGGGGAAGAGGTTAGACTGGA -s simRat_chr6.simRat.chr6 396147 22 + 647215 GAGTGGTAGACCACAGATTAGA -s simRat_chr6.simRat.chr6 396429 22 + 647215 GAGTGGTAGACCACAGATTAGA - -a -s simMouse_chr6.simMouse.chr6 395925 36 + 636262 TGAGGAAAAATGGTTGGAGCTGGTGGTTGCAATTCG -s Anc0.Anc0refChr3 28210 33 + 222631 TGAGG---ATTAGTTTGAGCTGGTGCCTGTGACCCA -s Anc1.Anc1refChr6 57879 33 + 197743 TGAGG---ATTAGTTTGAGCTGGTGCCTGTGACCCA -s Anc2.Anc2refChr13 31710 33 + 96486 TGAGG---ATTAGTGCAAGCTGATGCCTGTGACCCA -s mr.mrrefChr5 249643 36 + 294540 TGAGGAAAAATGGTTTGAGCTGGTGCTTGCAATCCA -s simCow_chr6.simCow.chr6 388066 33 + 602619 TGAGG---CTTAGTGAAAGCTGACACTTATGATCCG -s simDog_chr6.simDog.chr6 378211 33 + 593897 TGAGG---ATTAGTGCAAGCTGATGCCTGTGACCCA -s simHuman_chr6.simHuman.chr6 382323 33 + 601863 CAAGG---ATAAGTTTGAGCTGGTGCCTGTGAAATA -s simRat_chr6.simRat.chr6 396169 36 + 647215 TGAGGAAAAATGGTTTGAGCTGGTGCTTGCAATCCA -s simRat_chr6.simRat.chr6 396451 36 + 647215 TGAGGAAAAATGGTTTGAGCTGGTGCTTGCAATCCA - -a -s simMouse_chr6.simMouse.chr6 395961 26 + 636262 AGAAAAAGGACCTGCTAAATGCGTGC -s Anc0.Anc0refChr3 28243 25 + 222631 AC-AGTAGGATCTGCTAAATGCATTC -s Anc1.Anc1refChr6 57912 25 + 197743 AC-AGTAGGATCTGCTAAATGCATTC -s Anc2.Anc2refChr13 31743 25 + 96486 AC-TGTAGGATCTGTTAAATGCTTTC -s mr.mrrefChr5 249679 26 + 294540 ACAAAAAGGACCTGCTAAATGCATGC -s simCow_chr6.simCow.chr6 388099 25 + 602619 CG-TATGGCACCCATTAAATGCTTTC -s simDog_chr6.simDog.chr6 378255 24 + 593897 AC-TGTAGGATCTG-TATATGCTTTC -s simHuman_chr6.simHuman.chr6 382356 25 + 601863 AC-AGCAGGATCTGCTAAATGTATTC -s simRat_chr6.simRat.chr6 396205 26 + 647215 ACAAAAAGGACCTGCTAAATGCCTGC -s simRat_chr6.simRat.chr6 396487 26 + 647215 ACAAAAAGCACCTGCTAAATGCATGC - -a -s simMouse_chr6.simMouse.chr6 395987 19 + 636262 CTGTTGGGTTTGGCTGGCA -s Anc0.Anc0refChr3 28268 19 + 222631 TTGTTGAGTTTGGGGGCTT -s Anc1.Anc1refChr6 57937 19 + 197743 TTGTTGAGTTTGGGGGCTT -s Anc2.Anc2refChr13 31768 19 + 96486 TCGTTGAATTTGGGGCCTT -s mr.mrrefChr5 249705 19 + 294540 CTGTTGGGTTTGGCTGGCA -s simCow_chr6.simCow.chr6 388124 19 + 602619 TCGTCGGTTATGGTGAAGT -s simDog_chr6.simDog.chr6 378280 19 + 593897 TCACTGAACTTCGGCCCTT -s simHuman_chr6.simHuman.chr6 382381 19 + 601863 TTGTTGAGTTTGAGGGCAT -s simRat_chr6.simRat.chr6 396231 19 + 647215 CTGTTGGGTTTGGCTGGCA -s simRat_chr6.simRat.chr6 396513 19 + 647215 CTGTTGGGTTTGGCTGGCA - -a -s simMouse_chr6.simMouse.chr6 396006 22 + 636262 AAGCATAGACAACCCAATATCT -s Anc0.Anc0refChr3 28287 22 + 222631 AGTCATATATCACCTAGCATCT -s Anc1.Anc1refChr6 57956 22 + 197743 AGTCATATATCACCTAGCATCT -s Anc2.Anc2refChr13 31787 22 + 96486 AGTCATATATCGCCTAGCATCT -s mr.mrrefChr5 249724 22 + 294540 AAACATGGACCAACCAGTATCT -s simCow_chr6.simCow.chr6 388143 21 + 602619 AG-CACATATCTCCTAGCATCT -s simDog_chr6.simDog.chr6 378324 20 + 593897 GGTCATACTTCGTCT--CATTA -s simHuman_chr6.simHuman.chr6 382400 22 + 601863 AGTAATATATCACCTGGCATCT -s simRat_chr6.simRat.chr6 396250 22 + 647215 AAACATGGACCAACCAGTCTCT -s simRat_chr6.simRat.chr6 396532 22 + 647215 AAACATGGACCAACCAGTATCT - -a -s simMouse_chr6.simMouse.chr6 396028 13 + 636262 GATACGAGTGTGG -s Anc0.Anc0refChr3 28313 13 + 222631 GTTATGGGTATGG -s Anc1.Anc1refChr6 57982 13 + 197743 GTTATGGGTATGG -s Anc2.Anc2refChr13 31822 13 + 96486 GTTATGGGTATAG -s mr.mrrefChr5 249746 13 + 294540 GATACAGGTGTGG -s simCow_chr6.simCow.chr6 388177 13 + 602619 GCCATGGGTGTAG -s simDog_chr6.simDog.chr6 378357 13 + 593897 GTTATAGCTATAG -s simHuman_chr6.simHuman.chr6 382426 13 + 601863 GGTATGGGTATGG -s simRat_chr6.simRat.chr6 396272 9 + 647215 ----CAGGTGTGG -s simRat_chr6.simRat.chr6 396554 9 + 647215 ----CAGGTGTGG - -a -s simMouse_chr6.simMouse.chr6 396041 14 + 636262 CAAAATCAGGTTGC -s Anc0.Anc0refChr3 28327 14 + 222631 CAAAAATGAGTTCT -s Anc1.Anc1refChr6 57996 14 + 197743 CAAAAATGAGTTCT -s Anc2.Anc2refChr13 31836 14 + 96486 CAATAATGAGTTAT -s mr.mrrefChr5 249759 14 + 294540 CAGAAGTAGGTCCC -s simCow_chr6.simCow.chr6 388191 14 + 602619 CAAGAATCAGATAT -s simDog_chr6.simDog.chr6 378371 14 + 593897 TGGTGACGGGTTAT -s simHuman_chr6.simHuman.chr6 382440 14 + 601863 CAAAAATGAGGTCT -s simRat_chr6.simRat.chr6 396281 14 + 647215 CCGAAGTAGGTCCC -s simRat_chr6.simRat.chr6 396563 14 + 647215 CAGAAGTAGGTCCC - -a -s simMouse_chr6.simMouse.chr6 396055 28 + 636262 TATATTATGAGCAACTATCAGCAACAGG -s Anc0.Anc0refChr3 28342 28 + 222631 TAACTTAAGAGCATCTATCAGTGGCAGA -s Anc1.Anc1refChr6 58011 28 + 197743 TAACTTAAGAGCATCTATCAGTGGCAGA -s Anc2.Anc2refChr13 31851 28 + 96486 GAACTTAAGAGCATCTATCACTGGCAGA -s mr.mrrefChr5 249773 28 + 294540 TACATTATGAGCAGCTATCAGCAACAGA -s simCow_chr6.simCow.chr6 388206 27 + 602619 -AACTTAAGAGCATCTGTCAAAGGCAGA -s simDog_chr6.simDog.chr6 378386 15 + 593897 G-------------CTATAGCTGGTGAA -s simHuman_chr6.simHuman.chr6 382455 28 + 601863 TAACTCAACAGCACTTATCAGTGGCAGA -s simRat_chr6.simRat.chr6 396295 28 + 647215 TACATTATGAGCAGCTATCAGCAACAGA -s simRat_chr6.simRat.chr6 396577 19 + 647215 TACATTATGAGCAGCTATC--------- - -a -s simMouse_chr6.simMouse.chr6 396083 12 + 636262 TGAAGTCATGTA -s Anc0.Anc0refChr3 28420 12 + 222631 GGAAGTCATGCA -s Anc1.Anc1refChr6 58089 12 + 197743 GGAAGTCATGCA -s Anc2.Anc2refChr13 31935 12 + 96486 GGAAGACATGCA -s mr.mrrefChr5 249801 12 + 294540 GAAAGTCATGCA -s simCow_chr6.simCow.chr6 388297 12 + 602619 GGAAGATATACA -s simDog_chr6.simDog.chr6 378469 12 + 593897 GTGTGACATGAA -s simHuman_chr6.simHuman.chr6 382542 12 + 601863 GGAAGTCATGCA -s simRat_chr6.simRat.chr6 396323 12 + 647215 GAAAGTCATGCA -s simRat_chr6.simRat.chr6 396596 12 + 647215 GAAAGTCATGCA - -a -s simMouse_chr6.simMouse.chr6 396095 4 + 636262 CTGG -s Anc0.Anc0refChr3 28432 4 + 222631 CTGG -s Anc1.Anc1refChr6 58101 4 + 197743 CTGG -s Anc2.Anc2refChr13 31947 4 + 96486 CTGG -s mr.mrrefChr5 249813 4 + 294540 TTGG -s simCow_chr6.simCow.chr6 388309 4 + 602619 GTGG -s simDog_chr6.simDog.chr6 378482 4 + 593897 CTGG -s simHuman_chr6.simHuman.chr6 382554 4 + 601863 CTGA -s simRat_chr6.simRat.chr6 396335 4 + 647215 TTGG -s simRat_chr6.simRat.chr6 396608 4 + 647215 TTGG - -a -s simMouse_chr6.simMouse.chr6 396099 10 + 636262 ATTTCACTAT -s Anc0.Anc0refChr3 28437 10 + 222631 ACTTCAATAT -s Anc1.Anc1refChr6 58106 10 + 197743 ACTTCAATAT -s Anc2.Anc2refChr13 31952 10 + 96486 ACTTCAATAT -s mr.mrrefChr5 249817 10 + 294540 ATTTCACTAT -s simCow_chr6.simCow.chr6 388314 10 + 602619 ACTTCAATAT -s simDog_chr6.simDog.chr6 378487 10 + 593897 ACTTCAATAT -s simHuman_chr6.simHuman.chr6 382559 10 + 601863 ACCTTGATAT -s simRat_chr6.simRat.chr6 396339 10 + 647215 ATTTCACTAT -s simRat_chr6.simRat.chr6 396612 10 + 647215 ATTTCACTAT - -a -s simMouse_chr6.simMouse.chr6 396109 25 + 636262 AGTATCAAGCCTCATATAATCTTCA -s Anc0.Anc0refChr3 28447 17 + 222631 AGTAACTGGTCTC-----CT---GT -s Anc1.Anc1refChr6 58116 20 + 197743 AGTAACTGGTCTC-----CTCCTGT -s Anc2.Anc2refChr13 31962 17 + 96486 AGCAACTGGTCTC-----CT---GT -s mr.mrrefChr5 249827 25 + 294540 AGTATCCGGCCTCAAGTAATCCTCA -s simCow_chr6.simCow.chr6 388324 15 + 602619 AGCAACTG--CCA-----CT---GT -s simDog_chr6.simDog.chr6 378498 17 + 593897 AGCGTCTGGTCTC-----GA---GT -s simHuman_chr6.simHuman.chr6 382569 20 + 601863 AGTAACTGGTCTC-----CTCCTAT -s simRat_chr6.simRat.chr6 396349 25 + 647215 AGTATCCGGCCTCAAGTAATCCTCA -s simRat_chr6.simRat.chr6 396622 25 + 647215 AGTATCCGGCCTCAAGTAATCCTCA - -a -s simMouse_chr6.simMouse.chr6 396134 11 + 636262 AGTTGTTGCTG -s Anc0.Anc0refChr3 28464 1 + 222631 A---------- -s Anc1.Anc1refChr6 58136 1 + 197743 A---------- -s Anc2.Anc2refChr13 31979 1 + 96486 A---------- -s mr.mrrefChr5 249852 11 + 294540 AGTTGTTGCTG -s simCow_chr6.simCow.chr6 388339 1 + 602619 A---------- -s simDog_chr6.simDog.chr6 378515 1 + 593897 A---------- -s simHuman_chr6.simHuman.chr6 382589 1 + 601863 A---------- -s simRat_chr6.simRat.chr6 396647 11 + 647215 ACTTGTTGCTG - -a -s simMouse_chr6.simMouse.chr6 396145 95 + 636262 TCCTACCTTCACATATTGCTGAGTCCTATTAGGTTTTGTTTTAGTGAAAAGGAGTGAGGTGCAGTCATTTAGGTTCACTTCGTGAGCTTAACAGG -s Anc0.Anc0refChr3 28465 84 + 222631 ----ATCTTCAAGTATTGCTTAGTCTTATTA-----TGTTTGAGAGAAAAGAAGTGAGGTATAGTCATTT--TTTCACTTTATTATCTTAATGGG -s Anc1.Anc1refChr6 58137 84 + 197743 ----ATCTTCAAGTATTGCTTAGTCTTATTA-----TGTTTGAGAGAAAAGAAGTGAGGTATAGTCATTT--TTTCACTTTATTATCTTAATGGG -s Anc2.Anc2refChr13 31980 84 + 96486 ----ATCTTCAAGTGTTGGCTTGTCTTATTA-----TGATTGAGAGAAAAGAAGTGAGGTATAGTCATTT--TTTCACTTTATTATCTTAGTGGG -s mr.mrrefChr5 249863 95 + 294540 TCCTACCTTCAAGTATTGCTGAGTCCTATTAGGTTTTGTTTTAGTGAAAAGGAGTGAGGTGTAGTCATTTAGGTTCACTTTATGAGCTTAATGGG -s simCow_chr6.simCow.chr6 388340 83 + 602619 ----ACCTTCGAGTGTTAGCTTGGCTTATTA-----TGCTTGAATGAAAAGGAATGAGGTGTAGTCA-TC--TTTCACTCTATAATCTTAGTGGG -s simDog_chr6.simDog.chr6 378516 84 + 593897 ----ATCTACAAGTGTTGGCTTGTCTTATTA-----CGATTGGGAGAAAAAAAGTGAAGTATAGTCATGT--TTTCACTTTATTATGTTAGTGGG -s simHuman_chr6.simHuman.chr6 382590 84 + 601863 ----ATCTTCAAGAATTGCTCAGTCTTGTTA-----TGTTACAGCAAAAAGTAGTGAGGTATGGTCATTT--TTTCACTTTATTATCTTAATGAG -s simRat_chr6.simRat.chr6 396660 95 + 647215 TCCTATCTTCGAGTATTTCTGAATCCTATTACGTTTTGTCTGAGTGAAAAGGGGTGAGGTGTAGTCATATATCTTAACTTTATGAGCTTAATGGG - -a -s simMouse_chr6.simMouse.chr6 396240 14 + 636262 CTTCAGCCATTTCC -s Anc0.Anc0refChr3 28549 14 + 222631 CTTGGGCCATTCCC -s Anc1.Anc1refChr6 58221 14 + 197743 CTTGGGCCATTCCC -s Anc2.Anc2refChr13 32064 14 + 96486 CTTGGGCCATTCCC -s mr.mrrefChr5 249958 14 + 294540 CTTGGGCCATTTCC -s simCow_chr6.simCow.chr6 388423 14 + 602619 CTCGTGCCGGTCCC -s simDog_chr6.simDog.chr6 378600 14 + 593897 CTTGGGCAATTCCC -s simHuman_chr6.simHuman.chr6 382674 14 + 601863 CCTGGGCCACTCCC -s simRat_chr6.simRat.chr6 396757 14 + 647215 AGTGGGCCGTTTAC - -a -s simMouse_chr6.simMouse.chr6 396254 17 + 636262 TTTATGTTGGTATTGTA -s Anc0.Anc0refChr3 28570 17 + 222631 TTTATATTGGTACTATC -s Anc1.Anc1refChr6 58242 17 + 197743 TTTATATTGGTACTATC -s Anc2.Anc2refChr13 32085 17 + 96486 TTTATATTGGTACTATC -s mr.mrrefChr5 249972 17 + 294540 TTTATGTTGGTACTATA -s simCow_chr6.simCow.chr6 388444 17 + 602619 TTTATGTTGGTACTATC -s simDog_chr6.simDog.chr6 378621 17 + 593897 TTTATATTGGTACTACC -s simHuman_chr6.simHuman.chr6 382695 17 + 601863 TCTTTCTTGGTACTATC -s simRat_chr6.simRat.chr6 396771 17 + 647215 TTTATGTTGGTACTATA - -a -s simMouse_chr6.simMouse.chr6 396271 12 + 636262 GGCAACCATTAG -s Anc0.Anc0refChr3 28587 12 + 222631 AGCAGCCCTTTG -s Anc1.Anc1refChr6 58259 12 + 197743 AGCAGCCCTTTG -s Anc2.Anc2refChr13 32102 12 + 96486 AGCAGCCCTTTG -s mr.mrrefChr5 249989 12 + 294540 GGCAACCATTAG -s simCow_chr6.simCow.chr6 388483 12 + 602619 AGCAGCCCTTTA -s simDog_chr6.simDog.chr6 378638 12 + 593897 AGTAGACCTTTG -s simHuman_chr6.simHuman.chr6 382712 12 + 601863 ATCTGCCCTTTG -s simRat_chr6.simRat.chr6 396788 12 + 647215 GACAACCACTAG - -a -s simMouse_chr6.simMouse.chr6 396283 8 + 636262 TTTGTCAA -s Anc0.Anc0refChr3 28599 8 + 222631 TTTGTAAA -s Anc1.Anc1refChr6 58271 8 + 197743 TTTGTAAA -s Anc2.Anc2refChr13 32121 8 + 96486 TTTGTAAT -s mr.mrrefChr5 250001 8 + 294540 TTTGTCAA -s simCow_chr6.simCow.chr6 388502 8 + 602619 TTTGTGAT -s simDog_chr6.simDog.chr6 378657 8 + 593897 TTTGTAAT -s simHuman_chr6.simHuman.chr6 382724 1 + 601863 -------A -s simRat_chr6.simRat.chr6 396800 8 + 647215 TTTGTTAA - -a -s simMouse_chr6.simMouse.chr6 396291 1 + 636262 T -s Anc0.Anc0refChr3 28607 1 + 222631 T -s Anc1.Anc1refChr6 58279 1 + 197743 T -s Anc2.Anc2refChr13 32129 1 + 96486 T -s mr.mrrefChr5 250009 1 + 294540 T -s simCow_chr6.simCow.chr6 388517 1 + 602619 T -s simDog_chr6.simDog.chr6 378665 1 + 593897 T -s simHuman_chr6.simHuman.chr6 382725 1 + 601863 T -s simRat_chr6.simRat.chr6 396808 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 396292 2 + 636262 GT -s Anc0.Anc0refChr3 28608 2 + 222631 GT -s Anc1.Anc1refChr6 58280 2 + 197743 GT -s Anc2.Anc2refChr13 32131 2 + 96486 AT -s mr.mrrefChr5 250010 2 + 294540 GT -s simCow_chr6.simCow.chr6 388519 2 + 602619 AT -s simDog_chr6.simDog.chr6 378667 2 + 593897 AT -s simHuman_chr6.simHuman.chr6 382726 2 + 601863 GT -s simRat_chr6.simRat.chr6 396809 2 + 647215 GT - -a -s simMouse_chr6.simMouse.chr6 396294 3 + 636262 TTA -s Anc0.Anc0refChr3 28610 3 + 222631 TTA -s Anc1.Anc1refChr6 58282 3 + 197743 TTA -s Anc2.Anc2refChr13 32133 3 + 96486 TTA -s mr.mrrefChr5 250012 3 + 294540 TTA -s simCow_chr6.simCow.chr6 388521 3 + 602619 TTA -s simDog_chr6.simDog.chr6 378669 3 + 593897 TTA -s simRat_chr6.simRat.chr6 396815 3 + 647215 TTA - -a -s simMouse_chr6.simMouse.chr6 396297 9 + 636262 CATCATCTA -s Anc0.Anc0refChr3 28613 9 + 222631 CCCCATCTA -s Anc1.Anc1refChr6 58285 9 + 197743 CCCCATCTA -s Anc2.Anc2refChr13 32136 9 + 96486 CCCCTTCTA -s mr.mrrefChr5 250015 9 + 294540 CATCATCTA -s simCow_chr6.simCow.chr6 388524 9 + 602619 CCCCTTCCA -s simDog_chr6.simDog.chr6 378673 9 + 593897 CCCCTTCTG -s simHuman_chr6.simHuman.chr6 382728 5 + 601863 ----AAAGA -s simRat_chr6.simRat.chr6 396818 9 + 647215 CATCCTCTA - -a -s simMouse_chr6.simMouse.chr6 396306 8 + 636262 CTCCAGTC -s Anc0.Anc0refChr3 28622 8 + 222631 CCCCCATA -s Anc1.Anc1refChr6 58294 8 + 197743 CCCCCATA -s Anc2.Anc2refChr13 32147 8 + 96486 CCCCCATA -s mr.mrrefChr5 250024 8 + 294540 CTCCAGTC -s simCow_chr6.simCow.chr6 388535 8 + 602619 CCCCCATG -s simDog_chr6.simDog.chr6 378684 8 + 593897 ACCTCATA -s simHuman_chr6.simHuman.chr6 382733 8 + 601863 CCCCCATT -s simRat_chr6.simRat.chr6 396827 8 + 647215 CCCCGGTC - -a -s simMouse_chr6.simMouse.chr6 396314 24 + 636262 TGATCCTTAGTAATTATGTAATTC -s Anc0.Anc0refChr3 28630 20 + 222631 GGATTCGT-GTGATT---TAATTC -s Anc1.Anc1refChr6 58302 20 + 197743 GGATTCGT-GTGATT---TAATTC -s Anc2.Anc2refChr13 32155 20 + 96486 GGATTTGT-ATGATG---TAATTC -s mr.mrrefChr5 250032 24 + 294540 TGATCCTTAGTAATTATGTAATTC -s simCow_chr6.simCow.chr6 388552 20 + 602619 GGATATGT-ATGATG---TAATCC -s simDog_chr6.simDog.chr6 378692 20 + 593897 AGATTTGT-ATGATG---TAATTC -s simHuman_chr6.simHuman.chr6 382741 20 + 601863 GGATTCGT-GTGATT---CAATTC -s simRat_chr6.simRat.chr6 396835 24 + 647215 TGATCCTTCATAATAACTTAATTG - -a -s simMouse_chr6.simMouse.chr6 396338 39 + 636262 TTCAACACCTAAGCTTTAGACTCTAGTGCTTTGGGTGAG -s Anc0.Anc0refChr3 28664 28 + 222631 CTCAACTCCTGTTCTTAAGA-----------TTATTGGG -s Anc1.Anc1refChr6 58336 28 + 197743 CTCAACTCCTGTTCTTAAGA-----------TTATTGGG -s Anc2.Anc2refChr13 32190 28 + 96486 CTGGACTCCTGTTGCTAAGA-----------TTATTGGG -s mr.mrrefChr5 250056 28 + 294540 TTCAACACCTAAGCTTTAGA-----------TGGGTGAG -s simCow_chr6.simCow.chr6 388587 28 + 602619 CTTGGCTCCTGTTGCTGAGA-----------TAAATGGG -s simDog_chr6.simDog.chr6 378727 28 + 593897 CTGGATTCCTGTTGCTAAGA-----------TTATTGGG -s simHuman_chr6.simHuman.chr6 382775 28 + 601863 CTCAACTCCTGTCCTCAAGG-----------TCATCGGG -s simRat_chr6.simRat.chr6 396859 28 + 647215 TTTAGCACCTCAGCTTTAGA-----------TGAGTGAG - -a -s simMouse_chr6.simMouse.chr6 396377 32 + 636262 TGAGATAGTATGAGTAATATGAGCATTTATTT -s Anc0.Anc0refChr3 28692 27 + 222631 TGAGTGAGTTTG-----TATGAACATTCATTT -s Anc1.Anc1refChr6 58364 27 + 197743 TGAGTGAGTTTG-----TATGAACATTCATTT -s Anc2.Anc2refChr13 32218 27 + 96486 TAAATGAGTTTG-----TATGAACATTCATTT -s mr.mrrefChr5 250084 32 + 294540 TGAGATAGTATGAGTAATATGAGCATTTATTT -s simCow_chr6.simCow.chr6 388615 27 + 602619 TGAATGAGTTTG-----TATCAGTATTTATTT -s simDog_chr6.simDog.chr6 378755 27 + 593897 TAAATGAGTTTG-----TATGAACATTCATTT -s simHuman_chr6.simHuman.chr6 382804 4 + 601863 TGAG---------------------------- -s simRat_chr6.simRat.chr6 396887 32 + 647215 TGAAATCGTATGAGTAGTATGAACATTTCTTT - -a -s simMouse_chr6.simMouse.chr6 396409 133 + 636262 GTTGCTCCCTGCTTATACTGTATGGTTTACCCTTGGGACAGGATCTATCAAAGAGGCACGTGTCAGGGCGCATATGCTGTTTCACTCAAACTCCACTGTAAGCCAACTGACTATATCTTTTCTATTGAGTCAG -s Anc0.Anc0refChr3 28719 74 + 222631 TGTGCT--GGGCTTAAACTGTCTGGTTCATCCTTAGGACATACCCTA---------------------------------------------CCACTTTAAGCC----------ATCATTTCTAAT-AG-ATG -s Anc1.Anc1refChr6 58391 75 + 197743 TGTGCT--GGGCTTAAACTGTCTGGTTCATCCTTAGGACATACCCTA---------------------------------------------CCACTTTAAGCC----------ATCATTTCTAAT-AGGATG -s Anc2.Anc2refChr13 32245 74 + 96486 TGTGCT--GGGCTTAAACTGTCTGGTTCATCCTTAGGACATACCCTA---------------------------------------------CTACATTTAACT----------CTCATTTCTAAC-AG-ATG -s mr.mrrefChr5 250116 131 + 294540 GTTGCTCCCTGCTTATACTGTATGGTTTACCCTTGGGACAGGATCTATCAAAGAGGCACGTGTCAGGGCGCATATGCTGTTTCACTCAAACTCCACTGTAAGCCAA-TGACTATATCTTTTCTATT-AGTCAG -s simCow_chr6.simCow.chr6 388642 73 + 602619 TGTGCT--GGGC-TAAAATGTCTGTTTCATCATTAGGGTATACCCTA---------------------------------------------CTACATTTAACT----------CTCATTTCTAAC-AG-ATG -s simDog_chr6.simDog.chr6 378784 39 + 593897 TGTGCT--GGACTTAAACTGTGTAGTCCATCCTTAAGACAT-------------------------------------------------------------------------------------------- -s simHuman_chr6.simHuman.chr6 382808 67 + 601863 ----------GCTTAAACTGTCTGGTTCGTCCTTAGGACCTTCATTA---------------------------------------------CCATTATAGGCC----------ACCATCTCTAAT-GGGATG -s simRat_chr6.simRat.chr6 396919 131 + 647215 GTTGCTCCAGGCTTATACTGTATGGGTCACCCTTATGACATGATAAATCAAGGGGGTGCTCATCAGAGCGCATGTGCTCTTTCACTCAAACTTTACTGTAAACCAA-TATCAGTATCTTTTCTGTT-AGTCAG - -a -s simMouse_chr6.simMouse.chr6 396542 16 + 636262 GACCCATTTACCTGCT -s Anc0.Anc0refChr3 28796 16 + 222631 AACTGGCTTGTATAGT -s Anc1.Anc1refChr6 58469 16 + 197743 AACTGGCTTGTATAGT -s Anc2.Anc2refChr13 32322 16 + 96486 AACTGGCTTGTATAGT -s mr.mrrefChr5 250247 16 + 294540 GACCCATTTACCTGCT -s simCow_chr6.simCow.chr6 388718 16 + 602619 AACTGGCTTGTATAGT -s simDog_chr6.simDog.chr6 378823 1 + 593897 ---------------T -s simHuman_chr6.simHuman.chr6 382878 16 + 601863 AAATGGGTTGTGTATA -s simRat_chr6.simRat.chr6 397050 16 + 647215 GACCCATTTACCTGCT - -a -s simMouse_chr6.simMouse.chr6 396558 2 + 636262 CA -s Anc0.Anc0refChr3 28812 2 + 222631 CA -s Anc1.Anc1refChr6 58485 2 + 197743 CA -s Anc2.Anc2refChr13 32338 2 + 96486 AA -s mr.mrrefChr5 250263 2 + 294540 CA -s simCow_chr6.simCow.chr6 388734 2 + 602619 AC -s simDog_chr6.simDog.chr6 378824 2 + 593897 CA -s simHuman_chr6.simHuman.chr6 382894 2 + 601863 CA -s simRat_chr6.simRat.chr6 397072 2 + 647215 TA - -a -s simMouse_chr6.simMouse.chr6 396560 26 + 636262 CTACCCACTGCCAGCAGGACAATGGA -s Anc0.Anc0refChr3 28814 20 + 222631 CTGACAAGTGCCAGCAT------AGC -s Anc1.Anc1refChr6 58487 26 + 197743 CTGACAAGTGCCAGCATGACAAGAGC -s Anc2.Anc2refChr13 32340 20 + 96486 CCGACAAGTGCCAGCCT------ACC -s mr.mrrefChr5 250265 26 + 294540 CTACCCACTGCCAGCAGGACAATGGA -s simCow_chr6.simCow.chr6 388736 20 + 602619 CCGACAAGTGCCAGCCT------ACC -s simDog_chr6.simDog.chr6 378826 15 + 593897 GCAACAAG-----GCCT------TGT -s simHuman_chr6.simHuman.chr6 382955 23 + 601863 CTGACAAGAGC---CATGACAAGAGC -s simRat_chr6.simRat.chr6 397074 26 + 647215 CTACCCACTCCTAGCGGGACAATGGA - -a -s simMouse_chr6.simMouse.chr6 396586 27 + 636262 TAGTAGTCAATTTCCTCCCAGGTTGAG -s Anc0.Anc0refChr3 28834 27 + 222631 TGATTTTCCATTACCTCCCTGGTCGAT -s Anc1.Anc1refChr6 58513 27 + 197743 TGATTTTCCATTACCTCCCTGGTCGAT -s Anc2.Anc2refChr13 32360 27 + 96486 TGATTTTCCATTACCTCCCTGGTCGAT -s mr.mrrefChr5 250291 27 + 294540 TAGTAGTCAATTTCCTTCCAGGTTGAG -s simCow_chr6.simCow.chr6 388756 27 + 602619 TCATTTTCCACTGACCCCCTGGCCAAT -s simDog_chr6.simDog.chr6 378841 27 + 593897 TGATTTTCCATTACCTCCCTGGTTGAG -s simHuman_chr6.simHuman.chr6 382983 21 + 601863 TGATTTAAGATTAC------GATCGAT -s simRat_chr6.simRat.chr6 397100 27 + 647215 TAGTGCTCAATTACCTTCCAGGTTGAG - -a -s simMouse_chr6.simMouse.chr6 396613 27 + 636262 AGTATAAGAGTTGCACCCGAATCTTGT -s Anc0.Anc0refChr3 28861 27 + 222631 AGCTTAAGAATTGCACCTGAACCTTGT -s Anc1.Anc1refChr6 58540 27 + 197743 AGCTTAAGAATTGCACCTGAACCTTGT -s Anc2.Anc2refChr13 32387 27 + 96486 AGCTTAAGGATTGCACCTGAACCTTGT -s mr.mrrefChr5 250318 27 + 294540 AGCATAAGAATTGCACCTGAATCTTGT -s simCow_chr6.simCow.chr6 388785 27 + 602619 AGCTTAAGCATTGTACCTGAAGCTTGT -s simDog_chr6.simDog.chr6 378868 27 + 593897 AGTTTAAGGATGGCACTTGAACCTTGT -s simHuman_chr6.simHuman.chr6 383004 27 + 601863 GGCTTAAGAATTGCTACTGAACCTTGT -s simRat_chr6.simRat.chr6 397127 27 + 647215 AGCCCAAGAAGTGCACCTGAATCATGT - -a -s simMouse_chr6.simMouse.chr6 396640 6 + 636262 CTCAAA -s Anc0.Anc0refChr3 28910 6 + 222631 CGCCAA -s Anc1.Anc1refChr6 58589 6 + 197743 CGCCAA -s Anc2.Anc2refChr13 32436 6 + 96486 TGCCAA -s mr.mrrefChr5 250345 6 + 294540 CTCAAA -s simCow_chr6.simCow.chr6 388828 6 + 602619 GGCCAA -s simDog_chr6.simDog.chr6 378917 6 + 593897 TGTCAA -s simHuman_chr6.simHuman.chr6 383053 6 + 601863 CCCCAA -s simRat_chr6.simRat.chr6 397154 6 + 647215 CTCAAA - -a -s simMouse_chr6.simMouse.chr6 396646 13 + 636262 ATCCATGACATGT -s Anc0.Anc0refChr3 28919 13 + 222631 GTCCATGGCTTGT -s Anc1.Anc1refChr6 58598 13 + 197743 GTCCATGGCTTGT -s Anc2.Anc2refChr13 32445 13 + 96486 GCCCATGGCTTGT -s mr.mrrefChr5 250351 13 + 294540 ATCCATGACATGT -s simCow_chr6.simCow.chr6 388837 13 + 602619 GGCCATCACTTAT -s simDog_chr6.simDog.chr6 378926 13 + 593897 GCCCCTGGCTTGC -s simHuman_chr6.simHuman.chr6 383062 13 + 601863 GTCAATGGCTTCT -s simRat_chr6.simRat.chr6 397160 13 + 647215 ATTCATGACGTGT - -a -s simMouse_chr6.simMouse.chr6 396659 3 + 636262 TAT -s Anc0.Anc0refChr3 28932 3 + 222631 TAA -s Anc1.Anc1refChr6 58611 3 + 197743 TAA -s Anc2.Anc2refChr13 32458 3 + 96486 TAA -s mr.mrrefChr5 250364 3 + 294540 TAA -s simCow_chr6.simCow.chr6 388897 3 + 602619 TAC -s simDog_chr6.simDog.chr6 378939 3 + 593897 TGA -s simHuman_chr6.simHuman.chr6 383075 3 + 601863 CAA -s simRat_chr6.simRat.chr6 397173 3 + 647215 TAA - -a -s simMouse_chr6.simMouse.chr6 396662 153 + 636262 TAATCAGGTAATGCACCCTTCAGGACAATGGATAATAGACAATTTTCTCCCAGGTTGAGAGTCTAAGAGTTACACCTGGTTCTTGTCTCAAGATCCCTGACAGGTTAATTAATTAGGTCATGGACCCATCCACCATCAAGTACTTAACTCAAG -s Anc0.Anc0refChr3 28936 34 + 222631 TAATCAGGTAATGCACCTTTT-------------------------------------------------------------------------------------------------------------CAG----------TTAACGCAGG -s Anc1.Anc1refChr6 58615 34 + 197743 TAATCAGGTAATGCACCTTTT-------------------------------------------------------------------------------------------------------------CAG----------TTAACGCAGG -s Anc2.Anc2refChr13 32462 34 + 96486 TAATCAGGTAATGCACCTTTT-------------------------------------------------------------------------------------------------------------CAG----------TCAATGCAGG -s mr.mrrefChr5 250368 44 + 294540 TAATCAGGTAATGCACCTTTC-------------------------------------------------------------------------------------------------------------CAGCATCAAGTACTTAACTCAAG -s simCow_chr6.simCow.chr6 388901 34 + 602619 CAATGTGGTAATGCACCTTTT-------------------------------------------------------------------------------------------------------------CAC----------TCAATGCAGG -s simDog_chr6.simDog.chr6 378943 34 + 593897 TAATCAGGTAATGTACCTTTT-------------------------------------------------------------------------------------------------------------CAG----------TCAATGGGGG -s simHuman_chr6.simHuman.chr6 383079 34 + 601863 TTATCGAGAAATGCACCTGTT-------------------------------------------------------------------------------------------------------------CAG----------TTAACGCAGG -s simRat_chr6.simRat.chr6 397177 44 + 647215 TAATCAGGTAATGCACCTTTC-------------------------------------------------------------------------------------------------------------CAGCATCAAGCAATTAACTCAAG - -a -s simMouse_chr6.simMouse.chr6 396815 138 + 636262 TAGGCACTAATAGGGACTCTAAGGGTGTCTAACAACTGTTCCCATTCAACCGAGGTTTGTGCCAGTGTCAATGCATTAAGCTGTCTCGTATACTCAGCACGCAGACCAACTCAATGTCATGTTAAGTAGTACAGATGC -s Anc0.Anc0refChr3 28972 123 + 222631 CAGGTGCAAATGAGGA---------TTTCAAACATCCGGTCCTGTTCATTTGAAGCTGGAGCCAGTGTGAATGGGTTAAGCTGTTTCGAAG------CACTTGGACAAAGGCAGTGTCATGCTAATTAGGTCAGGGGC -s Anc1.Anc1refChr6 58651 127 + 197743 CAGGTGCAAATGAGGA---------TTTCAAACATCCGGTCCTGTTCATTTGAAGCTGGAGCCAGTGTGAATGGGTTAAGCTGTTTCGAAGA--CAGCACTTGGACAAAGGCAGTGTCATGCTAATTAGGTCAGGGGC -s Anc2.Anc2refChr13 32498 123 + 96486 CATGTGCAAATGAGGG---------TTTCAAACATCCGGCCCTGATCATTTGGAGTTGGAGGAAGTTTGACTGGGTTAGGCTGTTTTGAAG------CACCTGGACAAAGGCAGTGTCATGCTAATTAGGTCAATGGC -s mr.mrrefChr5 250414 138 + 294540 TAGGCGCTAATAAGGACTCTAAGGGTGTCTAACAACTGTTCCCATTCAATTGAGGCTTGAGCCAGTGTCAATGCATTAAGCTGTTTCGTATACTCAGCACTTGGACCAACTCAATGTCATGTTAAGTAGTACAGGTGC -s simCow_chr6.simCow.chr6 388937 116 + 602619 CATGTGCAAATGAGG-----------TTATAACATATGGCCCTGATCATTTGGAGTTGGAGGAAGTTTGACTGGGTTAGGCTGTTTTGAA-------TATCTGGCC----TTTGTGCCATGCTAATTAGGTCAATATC -s simDog_chr6.simDog.chr6 378978 56 + 593897 ---------------G---------TTTCAAACATCCA----------------------------------------------------G------CACCTCGACAAAGGCAGGGTCATGCTAATTAGGGCAATGGC -s simHuman_chr6.simHuman.chr6 383115 127 + 601863 CAGGTGCAATTGAGGA---------TATCCAACACCCGGTCCTGTTGAGTTGAAGCTGAAGCCACTGTAAATGAGTTAAGCTCTTTCAAAGA--CAGCACTTGGACAAATGCAGTGTCATGCTTATTGAATCAGGGGC -s simRat_chr6.simRat.chr6 397223 133 + 647215 TAGGCGCTAATCAGGGTTCAAAGAGGGTCTAACTACTGTTCCCAATCAATTGAGGCTTGAGCCAGTGTTAATGCATTAAGCTGCTT-----ATCCAGCACTTGGATTAACTCAATGTCATGTTGAGTAGGACAGGTGC - -a -s simMouse_chr6.simMouse.chr6 396953 4 + 636262 TAGG -s Anc0.Anc0refChr3 29104 4 + 222631 AAGG -s Anc1.Anc1refChr6 58787 4 + 197743 AAGG -s Anc2.Anc2refChr13 32630 4 + 96486 AAGG -s mr.mrrefChr5 250561 4 + 294540 TAGG -s simCow_chr6.simCow.chr6 389062 4 + 602619 TGGG -s simDog_chr6.simDog.chr6 379043 4 + 593897 AAGG -s simHuman_chr6.simHuman.chr6 383251 4 + 601863 AAGG -s simRat_chr6.simRat.chr6 397365 4 + 647215 TAGG - -a -s simMouse_chr6.simMouse.chr6 396957 81 + 636262 CATTTATTAATGCTAAAAAGACTCATATGACGCTACTCCATGGAGGCTGACAGATCACAGCATATACCACTAGTTTTGGGG -s Anc0.Anc0refChr3 29108 81 + 222631 CACTTATTAATTTGATAAAGCTCCATTTCACTCTACTCCATGGAGGTTGACAAATAACAGCATGTACCACTAGTTCTTGGG -s Anc1.Anc1refChr6 58791 81 + 197743 CACTTATTAATTTGATAAAGCTCCATTTCACTCTACTCCATGGAGGTTGACAAATAACAGCATGTACCACTAGTTCTTGGG -s Anc2.Anc2refChr13 32655 81 + 96486 CACTTATTAATTTGATAAAGCTCCATTTCACTCTACTCCATGAAGATTGACAAATAACAGCATGTACCACTAGTTCTTGGG -s mr.mrrefChr5 250565 81 + 294540 CATTTATTAATGCTATAAAGACTCATATGACGCTACTCCATGGAGGTTGACAGATCACAGCATATACCACTAGTTCTGGGG -s simCow_chr6.simCow.chr6 389087 81 + 602619 CACTTAATAATTTGATAAAGCTCCATTTCACTCTACTCCATGAAGACTGACAAATGACAGCATATCCTACTAGTCTTTGGG -s simDog_chr6.simDog.chr6 379069 78 + 593897 CACTAATTAATTTGATACAGCTCCATTTCA---TGCTCCATTATGATTGATGAATAACAGCTTGAACCACTAGTTCTTGGG -s simHuman_chr6.simHuman.chr6 383255 81 + 601863 CAGTTATTAATTTGATCAAGCTCCATTTCACTCTACTCCATGGAGGTCAACAAATAACAGCATGTACCCCTAGTTCTAGGG -s simRat_chr6.simRat.chr6 397369 79 + 647215 CATTCAATAAT--TATAAAGACTCATATGATGCTACTCCATAGAGGTTGACGGATCATGGCATATACCATTGGCTCTGGGG - -a -s simMouse_chr6.simMouse.chr6 397038 1 + 636262 G -s Anc0.Anc0refChr3 29191 1 + 222631 G -s Anc1.Anc1refChr6 58874 1 + 197743 G -s Anc2.Anc2refChr13 32738 1 + 96486 G -s mr.mrrefChr5 250646 1 + 294540 G -s simCow_chr6.simCow.chr6 389170 1 + 602619 A -s simDog_chr6.simDog.chr6 379149 1 + 593897 G -s simHuman_chr6.simHuman.chr6 383338 1 + 601863 G -s simRat_chr6.simRat.chr6 397448 1 + 647215 C - -a -s simMouse_chr6.simMouse.chr6 397039 48 + 636262 GATATTAGATGTAAATTCCTGACTCTGATTGATTGGCTCGACAATTGT -s Anc0.Anc0refChr3 29192 48 + 222631 GTATGTTTTTGCAGATTTTTGACTCTGACTGATTGACTATACAATTGG -s Anc1.Anc1refChr6 58875 48 + 197743 GTATGTTTTTGCAGATTTTTGACTCTGACTGATTGACTATACAATTGG -s Anc2.Anc2refChr13 32741 48 + 96486 GTATGTTTTTGCAGATCTTTGACTCGAACTGATTGACTATACAATTGG -s mr.mrrefChr5 250647 48 + 294540 GATAGTAGATGTAAATTCTTGACTCTGACTGATTGACTCGACAATTGT -s simCow_chr6.simCow.chr6 389173 48 + 602619 GCATGTTCTTGTAGCTCTTTGACTCGAATTGATTGACTATACAATTGG -s simDog_chr6.simDog.chr6 379152 43 + 593897 ATAAGTTTTTGCAGATCTCTGAC-----CTGATTGACTATATAATTTG -s simHuman_chr6.simHuman.chr6 383339 48 + 601863 GTATGTTTTTGCAGACTTTTGACTCTGACTGATTGACTATACAGTGGG -s simRat_chr6.simRat.chr6 397449 48 + 647215 GATGGTAGATGTAAATCCTTGACTCTGCCTGATTGACTCAACAATTGA - -a -s simMouse_chr6.simMouse.chr6 397087 27 + 636262 GTCCTGCTTGGATTTCTTGTTATCTAA -s Anc0.Anc0refChr3 29243 26 + 222631 GTCCAGATTGG-TTTCCTGTCAAGTCA -s Anc1.Anc1refChr6 58926 26 + 197743 GTCCAGATTGG-TTTCCTGTCAAGTCA -s Anc2.Anc2refChr13 32792 26 + 96486 GTCCAGATTGA-TTTCCTATCAAGTCA -s mr.mrrefChr5 250695 27 + 294540 GTCCAGCTTGGATTTCTTGTTATGTAA -s simCow_chr6.simCow.chr6 389224 26 + 602619 GTCCAGATTGA-TTTCCTTTCAAGTCA -s simDog_chr6.simDog.chr6 379198 26 + 593897 GTCGAGATTAA-TTCCCTATCAAGTCA -s simHuman_chr6.simHuman.chr6 383390 26 + 601863 GTCCAGACTGG-TTTCCTGTCAAGTGT -s simRat_chr6.simRat.chr6 397497 27 + 647215 CTCCAGCTTGGATTTCTCATTATGTAA - -a -s simMouse_chr6.simMouse.chr6 397114 18 + 636262 ATGTCTGGATGGTGATTA -s Anc0.Anc0refChr3 29269 18 + 222631 ATGATTGGATAGTGATGA -s Anc1.Anc1refChr6 58952 18 + 197743 ATGATTGGATAGTGATGA -s Anc2.Anc2refChr13 32820 18 + 96486 ATGATTGGATAGTGGTGA -s mr.mrrefChr5 250722 18 + 294540 ATGTCTGGATAGTGATTA -s simCow_chr6.simCow.chr6 389252 18 + 602619 ATGATTGGATAGTGGTGA -s simDog_chr6.simDog.chr6 379226 18 + 593897 ATGATTGGATAACAGGGA -s simHuman_chr6.simHuman.chr6 383416 18 + 601863 ATGATAGGATAGTGATCA -s simRat_chr6.simRat.chr6 397524 18 + 647215 ATATCTGGACAGTTATTA - -a -s simMouse_chr6.simMouse.chr6 397132 25 + 636262 AGGCTTTCAATGGGGTAGTAACATC -s Anc0.Anc0refChr3 29305 23 + 222631 AGGCCACCAATGAGGTAGTACCA-- -s Anc1.Anc1refChr6 58988 23 + 197743 AGGCCACCAATGAGGTAGTACCA-- -s Anc2.Anc2refChr13 32856 23 + 96486 AGGCCACCAATGATCTAGTACCA-- -s mr.mrrefChr5 250740 25 + 294540 AGGCCTTCAATGGGGTAGTACCATC -s simCow_chr6.simCow.chr6 389288 23 + 602619 AGGCTGCCAATAGTTTAGTACCA-- -s simDog_chr6.simDog.chr6 379262 23 + 593897 AGACCACCAATGATCTAGTACTG-- -s simHuman_chr6.simHuman.chr6 383452 23 + 601863 AGGCCACCAATCAGGTAGTACCA-- -s simRat_chr6.simRat.chr6 397542 25 + 647215 AGGCCTTCACGGGGGTAGTACCATC - -a -s simMouse_chr6.simMouse.chr6 397157 3 + 636262 CTT -s Anc0.Anc0refChr3 29328 3 + 222631 CCT -s Anc1.Anc1refChr6 59011 3 + 197743 CCT -s Anc2.Anc2refChr13 32879 3 + 96486 CCT -s mr.mrrefChr5 250765 3 + 294540 CTT -s simCow_chr6.simCow.chr6 389311 3 + 602619 TCC -s simDog_chr6.simDog.chr6 379286 3 + 593897 CCT -s simHuman_chr6.simHuman.chr6 383475 3 + 601863 CCT -s simRat_chr6.simRat.chr6 397567 3 + 647215 CTT - -a -s simMouse_chr6.simMouse.chr6 397160 9 + 636262 TTCAGGTAA -s Anc0.Anc0refChr3 29331 9 + 222631 CTCAGGTGA -s Anc1.Anc1refChr6 59014 9 + 197743 CTCAGGTGA -s Anc2.Anc2refChr13 32882 9 + 96486 CTCAGGTGA -s mr.mrrefChr5 250768 9 + 294540 TTCAGGTAA -s simCow_chr6.simCow.chr6 389319 9 + 602619 CTCAGGTAA -s simDog_chr6.simDog.chr6 379289 9 + 593897 CTCAGGTGA -s simHuman_chr6.simHuman.chr6 383478 7 + 601863 GTCAGGT-- -s simRat_chr6.simRat.chr6 397570 9 + 647215 ATCAGGTAA - -a -s simMouse_chr6.simMouse.chr6 397169 90 + 636262 ACAAGGCAGTGGACATGGGGTCCAATGAATATGGTGTGGGTTGATGGACTTACCTCAGGATGTTGCCAAAATATGATTTTTGTTTGCTGA -s Anc0.Anc0refChr3 29340 84 + 222631 ATGAGATGATGAACATCGGCTCCGCTAAATATGGTGTGGGTGAGGGGACTTAGCCAAGGA------CTAGTTATAATTTTTATTTGTTGA -s Anc1.Anc1refChr6 59023 90 + 197743 ATGAGATGATGAACATCGGCTCCGCTAAATATGGTGTGGGTGAGGGGACTTAGCCAAGGATGTAGCCTAGTTATAATTTTTATTTGTTGA -s Anc2.Anc2refChr13 32892 84 + 96486 ATGAGATGATGAACATCGGCTCCGCTAAATATGGTGTGGGTGAGGGGACTTAGCCAAGGA------CTAGTTATAGTTTTTACTTGTTGA -s mr.mrrefChr5 250777 90 + 294540 ACAAGGCAGTGGACATGGGGTCCAATAAATATGGTGTGGGTTGGTGGACTTACCTCAGGATGTTGCCAAAATATAATTTTTGTTTGCTGA -s simCow_chr6.simCow.chr6 389329 84 + 602619 CTGAGATGATGCACATTGGGTCTGTGAAATATGGTGTGGGTGAAGGGACTTAGCCAAGGA------CTAGTTATAGTTTCTAGTTGTTGA -s simDog_chr6.simDog.chr6 379299 84 + 593897 ATGAGATGATGAACATCGGCTCCGCTGAGTATGGTGTGGGTGAGAGGACTTAGCTGAGGA------CTAGTTATAGTTTTTACTTGTTGA -s simHuman_chr6.simHuman.chr6 383485 71 + 601863 ATGGG------------------TCTAGATACGGTGTGGGTAAGGGGACCTAGCCAGGGATGTAGCTGAGTCATAATTTTTATTTGGTG- -s simRat_chr6.simRat.chr6 397579 90 + 647215 ATAAGGCAGAGAAGATGGGGTCTGATAAATATGGTGGGGGTTGGACGAATTACCTCAGGATGCTGACAAAATATAATTTTGGCTTGCTGA - -a -s simMouse_chr6.simMouse.chr6 397259 21 + 636262 TATGTCACAGGTCACCCCACT -s Anc0.Anc0refChr3 29424 19 + 222631 T--GTTACCGAACACTTCCCT -s Anc1.Anc1refChr6 59113 19 + 197743 T--GTTACCGAACACTTCCCT -s Anc2.Anc2refChr13 32978 19 + 96486 T--GTTACCGAACACTTCCCT -s mr.mrrefChr5 250867 19 + 294540 T--GTCACAGGTCACCCCACT -s simCow_chr6.simCow.chr6 389415 19 + 602619 T--TTTATAAAACACTTCAAT -s simDog_chr6.simDog.chr6 379385 19 + 593897 T--GTTACCGAACACTTCCCT -s simRat_chr6.simRat.chr6 397669 19 + 647215 T--GTCACAGGTCACTTCTCT - -a -s simMouse_chr6.simMouse.chr6 397280 25 + 636262 TGTGGTTTTTGTGGCAGCAATTGAC -s Anc0.Anc0refChr3 29443 20 + 222631 GGT----GCAGTGGAGATGATTGA- -s Anc1.Anc1refChr6 59132 20 + 197743 GGT----GCAGTGGAGATGATTGA- -s Anc2.Anc2refChr13 33000 20 + 96486 GGT----GCAGTGGAGATGATTGA- -s mr.mrrefChr5 250886 21 + 294540 GGT----TTTGTGGCAGCAATTGAC -s simCow_chr6.simCow.chr6 389437 20 + 602619 TGT----GCAGGGGAAACAATTGA- -s simDog_chr6.simDog.chr6 379407 20 + 593897 GGT----GCAGTGGAGATGATTGA- -s simRat_chr6.simRat.chr6 397688 21 + 647215 GGT----TTGGTGGCAACAATTGAC - -a -s simMouse_chr6.simMouse.chr6 397305 51 + 636262 TTGGTACAGTGGTGCAATGATGATAGAACCTTTGTTGTGGGCTCAACATCA -s Anc0.Anc0refChr3 29463 45 + 222631 TTGGTTCATTGGTGCAATGATGATAGAACA--TGCTATGAGCTCAAC---- -s Anc1.Anc1refChr6 59152 47 + 197743 TTGGTTCATTGGTGCAATGATGATAGAACAATTGCTATGAGCTCAAC---- -s Anc2.Anc2refChr13 33020 45 + 96486 TTGGTTCATTGGTGCAGTGGTGGTAGATCA--TGCTATGAGATCAAC---- -s mr.mrrefChr5 250907 51 + 294540 TTGGTACAGTGGTGCAATGATGATAGAACCTTTGTTGTGGGCTCAACATCA -s simCow_chr6.simCow.chr6 389458 40 + 602619 TTGGGGCATTGGGGCTGTGGTGGTAGATCA-----TTCGAGACCA------ -s simDog_chr6.simDog.chr6 379427 31 + 593897 TTAGTTCATTAGTGCA----------------TGCTATGAGATCTAC---- -s simHuman_chr6.simHuman.chr6 383556 47 + 601863 TTGGTTCATTGGTGCAATGATGATGGAACAATTGCTATGAGCTCACC---- -s simRat_chr6.simRat.chr6 397709 51 + 647215 TTGATGCAGGTGGGCAATGATGATAGAACCTTTGTTGTGGGCACAACATCA - -a -s simMouse_chr6.simMouse.chr6 397356 30 + 636262 TCCACGCTTACTGTTCGGTTCAACAGGAAA -s Anc0.Anc0refChr3 29508 30 + 222631 CTGCCACCCACTGTTCATTTCAATAGAAAA -s Anc1.Anc1refChr6 59199 30 + 197743 CTGCCACCCACTGTTCATTTCAATAGAAAA -s Anc2.Anc2refChr13 33065 30 + 96486 CTGACACCCACTGTTCATTTCAATAGAAAA -s mr.mrrefChr5 250958 30 + 294540 CCCCCGCTTACTGTTCAGTTCAACAGGAAA -s simCow_chr6.simCow.chr6 389498 22 + 602619 ---ACACCCGC-ATCTATTTCAAT----AA -s simDog_chr6.simDog.chr6 379462 30 + 593897 CTGACACCTATTGTTCATCTCAATAGAAAA -s simHuman_chr6.simHuman.chr6 383603 30 + 601863 CTACCACGCACTGTTCATTTCAATACAAAA -s simRat_chr6.simRat.chr6 397760 30 + 647215 CCGCCGCTTACTGTTCAGTTCAACAGGAAA - -a -s simMouse_chr6.simMouse.chr6 397386 49 + 636262 TGTTTATTGATTCATTTCCTTACAAGGTCATAAGGCCAGTTAAGTCAGG -s Anc0.Anc0refChr3 29538 49 + 222631 TATTTATTAATGCATTTCTGTACAGAGTTATGATGTAAGTTGTGTCAGG -s Anc1.Anc1refChr6 59229 49 + 197743 TATTTATTAATGCATTTCTGTACAGAGTTATGATGTAAGTTGTGTCAGG -s Anc2.Anc2refChr13 33096 49 + 96486 TATTAATTGATGCTTTTCTGTACAGAGTTATGATGTAAATTGTGTCAGG -s mr.mrrefChr5 250988 49 + 294540 TGTTTATTAATTCATTTCCTTACAAAGTCATAATGCCAGTTAAGTCAGG -s simCow_chr6.simCow.chr6 389521 49 + 602619 TGTTGATTGATGCCTTGTTGTATACAGTTGTGCTGTAAATTGTGTCATG -s simDog_chr6.simDog.chr6 379493 49 + 593897 TATCAATTGATGTTTCTCTGCACAGAGTTATGATGTAAATTGTGTCAGG -s simHuman_chr6.simHuman.chr6 383633 47 + 601863 --TTTATCAATGCACTTCACTACAGAGTTATTATGGTAGTTGCGCCAGG -s simRat_chr6.simRat.chr6 397790 49 + 647215 CATTTATTAATTCATTTCTTTACAAAGTCCTAATGCAAGTAAAGTCAGG - -a -s simMouse_chr6.simMouse.chr6 397435 14 + 636262 CTCACAGGGTAGGT -s Anc0.Anc0refChr3 29587 14 + 222631 CTCACAGGGTAGGt -s Anc1.Anc1refChr6 59278 14 + 197743 CTCACAGGGTAGGt -s Anc2.Anc2refChr13 33152 14 + 96486 CTCACAAGGTAGGt -s mr.mrrefChr5 251037 14 + 294540 CTCACAGGGTAGGT -s simCow_chr6.simCow.chr6 389577 14 + 602619 CTCACATGGTAGGA -s simDog_chr6.simDog.chr6 379549 14 + 593897 CTCACAAGATaggt -s simHuman_chr6.simHuman.chr6 383680 14 + 601863 CTCACAGGGTAGGt -s simRat_chr6.simRat.chr6 397839 14 + 647215 CTCACAGAGTAGGT - -a -s simMouse_chr6.simMouse.chr6 397449 19 + 636262 AGGTTGCATTTTGCTGTTC -s Anc0.Anc0refChr3 29601 19 + 222631 ggattccatattgctcttc -s Anc1.Anc1refChr6 59292 19 + 197743 ggattccatattgctcttc -s Anc2.Anc2refChr13 33167 19 + 96486 ggattccatattgctcttc -s mr.mrrefChr5 251051 19 + 294540 AGGTTGCATTTTGCTGTTC -s simCow_chr6.simCow.chr6 389592 19 + 602619 GGACTCCAGACCACTCttc -s simDog_chr6.simDog.chr6 379564 19 + 593897 ggattccatattgctcatc -s simHuman_chr6.simHuman.chr6 383694 19 + 601863 ggattccatattggtattc -s simRat_chr6.simRat.chr6 397853 19 + 647215 AGGTTGCATTTTGCTGTTC - -a -s simMouse_chr6.simMouse.chr6 397468 21 + 636262 GTTCAGCTATTGGGGTGCAAG -s Anc0.Anc0refChr3 29622 21 + 222631 gttcagttattaggatgcagg -s Anc1.Anc1refChr6 59313 21 + 197743 gttcagttattaggatgcagg -s Anc2.Anc2refChr13 33188 21 + 96486 gttcaatcactaggatgtagg -s mr.mrrefChr5 251072 21 + 294540 GTTCAGCTATTAGGGTGCAAG -s simCow_chr6.simCow.chr6 389613 21 + 602619 gttgaatcactaggatgtaac -s simDog_chr6.simDog.chr6 379585 21 + 593897 gttcaatcactgggatgtggg -s simHuman_chr6.simHuman.chr6 383718 19 + 601863 gttcagatattaggataca-- -s simRat_chr6.simRat.chr6 397874 21 + 647215 GTAGAGCTATTAGAGTGCAAG - -a -s simMouse_chr6.simMouse.chr6 397489 13 + 636262 GCAGCTTGAAGGT -s Anc0.Anc0refChr3 29643 13 + 222631 acggcttgggggt -s Anc1.Anc1refChr6 59334 13 + 197743 acggcttgggggt -s Anc2.Anc2refChr13 33209 13 + 96486 acagcttgagggt -s mr.mrrefChr5 251093 13 + 294540 GCGGCTTGGAGGT -s simCow_chr6.simCow.chr6 389634 13 + 602619 agagattgagtga -s simDog_chr6.simDog.chr6 379606 13 + 593897 tcagcttgagggt -s simHuman_chr6.simHuman.chr6 383737 12 + 601863 -cgactgaggggt -s simRat_chr6.simRat.chr6 397907 13 + 647215 GCGGCTTTGAGGT - -a -s simMouse_chr6.simMouse.chr6 397502 60 + 636262 CATAGCTTTCAGACTCTTAGCTCATGAGCTCTGTAGGGTTGGCAGGGATAACGGGGGTAT -s Anc0.Anc0refChr3 29656 60 + 222631 cccagttttaagacttgcagcccgtgagcgctggggggttagcaaataaactgagggtat -s Anc1.Anc1refChr6 59347 60 + 197743 cccagttttaagacttgcagcccgtgagcgctggggggttagcaaataaactgagggtat -s Anc2.Anc2refChr13 33223 60 + 96486 cccagtttcaagacttgcaagccgtgggtgctggggggttagcaaataaactgagggtat -s mr.mrrefChr5 251106 60 + 294540 CATAGCTTTCAGACTTTTAGCTCATGAGCTCTGGAGGGTTGGCAGGGATAATGGGGGTAT -s simCow_chr6.simCow.chr6 389648 60 + 602619 cccattttcaagacttgcaagctgtgcgtgatggggagttagaagataacctgagggtat -s simDog_chr6.simDog.chr6 379620 60 + 593897 accagtttcaagaccttcaagtcgtgggtgctggggggttaacaaataaattgatggtat -s simHuman_chr6.simHuman.chr6 383749 60 + 601863 cccagttttaagacttgcagcccgtgagcactggggggttagcaaatacactgtgggtaa -s simRat_chr6.simRat.chr6 397920 60 + 647215 CATAGCTTTCTGACTTTTACCTTATGAGTTCTGGAGGGTTGGCAGGGATAATGGTGGTAT - -a -s simMouse_chr6.simMouse.chr6 397562 13 + 636262 AAACATGGAGAGC -s Anc0.Anc0refChr3 29716 8 + 222631 aaacatg-----c -s Anc1.Anc1refChr6 59407 13 + 197743 aaacatgaggggc -s Anc2.Anc2refChr13 33283 8 + 96486 agaaatg-----c -s mr.mrrefChr5 251166 13 + 294540 AAACATGGGGAGC -s simCow_chr6.simCow.chr6 389708 8 + 602619 agaatta-----c -s simDog_chr6.simDog.chr6 379680 8 + 593897 AAAAATG-----C -s simHuman_chr6.simHuman.chr6 383838 13 + 601863 aagccttaggggc -s simRat_chr6.simRat.chr6 397980 13 + 647215 TAACATGGGGAGT - -a -s simMouse_chr6.simMouse.chr6 397575 1 + 636262 A -s Anc0.Anc0refChr3 29726 1 + 222631 a -s Anc1.Anc1refChr6 59422 1 + 197743 a -s Anc2.Anc2refChr13 33293 1 + 96486 t -s mr.mrrefChr5 251179 1 + 294540 A -s simCow_chr6.simCow.chr6 389718 1 + 602619 t -s simDog_chr6.simDog.chr6 379690 1 + 593897 T -s simHuman_chr6.simHuman.chr6 383853 1 + 601863 a -s simRat_chr6.simRat.chr6 397993 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 397576 34 + 636262 GAGGAAATGATGTCTGCAACACAACCGAACAACT -s Anc0.Anc0refChr3 29727 34 + 222631 gAGGaAATGATGTGAGCGACACAACCATGGAACG -s Anc1.Anc1refChr6 59423 34 + 197743 gAGGaAATGATGTGAGCGACACAACCATGGAACG -s Anc2.Anc2refChr13 33294 34 + 96486 gAGGgAGTGATGTGAACGACACAACCATGGAACG -s mr.mrrefChr5 251180 34 + 294540 GAGGAAATGATGTCAGCAACACAACCAAACAACT -s simCow_chr6.simCow.chr6 389722 34 + 602619 gAGGGACAGATGTGAATGGCACAACCATGACACT -s simDog_chr6.simDog.chr6 379691 33 + 593897 GAGG-AGTGATTTCAACAACACAAATATGGAATG -s simHuman_chr6.simHuman.chr6 383854 34 + 601863 gaggaaatgatgtgagcgacacaaccatggaacc -s simRat_chr6.simRat.chr6 397994 34 + 647215 GAGGAAATGATGTCAGTAACACAACCAAACAACT - -a -s simMouse_chr6.simMouse.chr6 397610 130 + 636262 GAAGTGTAAGGTCTGATCTTAATGAATTCCCATATTACAGTTGAGCCGAATTCTCATATTACAGTTAAGCCCCAACCAGCATCACCGTGTAAGGTCTGATCTTAATGAATTCCCATATTACAGTTGAGCC -s Anc0.Anc0refChr3 29781 18 + 222631 gaagtagAGACTCCAA----------------------------------------------------------------------------------------------------------------AT -s Anc1.Anc1refChr6 59477 18 + 197743 gaagtagAGACTCCAA----------------------------------------------------------------------------------------------------------------AT -s Anc2.Anc2refChr13 33348 18 + 96486 gaagcagAGACTCCAA----------------------------------------------------------------------------------------------------------------AC -s mr.mrrefChr5 251214 18 + 294540 GAAGTATAAGGTCTAA----------------------------------------------------------------------------------------------------------------AT -s simCow_chr6.simCow.chr6 389768 11 + 602619 -------AGAGTCCAA----------------------------------------------------------------------------------------------------------------GC -s simDog_chr6.simDog.chr6 379744 18 + 593897 GAAGCAGAATCTCTAA----------------------------------------------------------------------------------------------------------------AC -s simHuman_chr6.simHuman.chr6 383908 18 + 601863 gaagtagagaatCCAA----------------------------------------------------------------------------------------------------------------AT -s simRat_chr6.simRat.chr6 398028 18 + 647215 GAAGTATAAGGTCTAA----------------------------------------------------------------------------------------------------------------AT - -a -s simMouse_chr6.simMouse.chr6 397740 32 + 636262 AAATTCTCATATTACAGTTGAGCCCCAACCAG -s Anc0.Anc0refChr3 29799 31 + 222631 G-ATTCTCAGGGTACAGTTGGGTCCTAACCTT -s Anc1.Anc1refChr6 59495 31 + 197743 G-ATTCTCAGGGTACAGTTGGGTCCTAACCTT -s Anc2.Anc2refChr13 33366 31 + 96486 G-AGTCTCAGGGTACAGTTGGGTCCTAACCTT -s mr.mrrefChr5 251232 32 + 294540 GAATTCTCATATTACAGTTGAGCCCCAACCTG -s simCow_chr6.simCow.chr6 389779 31 + 602619 A-AGTCTCAGGGTACGGTTGGGACCTAACCTG -s simDog_chr6.simDog.chr6 379763 31 + 593897 G-GGTTCCAGGGTACAGTTGGATCCTAGCCTT -s simHuman_chr6.simHuman.chr6 383926 31 + 601863 G-ATTCTCAAGATACAGTTGGGTCCTAACTTA -s simRat_chr6.simRat.chr6 398046 32 + 647215 GAATTCTCATCTTACAGTTGAGCCCCAACATG - -a -s simMouse_chr6.simMouse.chr6 397772 9 + 636262 CATCACCGA -s Anc0.Anc0refChr3 29831 9 + 222631 CCCCACTAA -s Anc1.Anc1refChr6 59527 9 + 197743 CCCCACTAA -s Anc2.Anc2refChr13 33398 9 + 96486 CCCCACTAA -s mr.mrrefChr5 251264 9 + 294540 CATCACCGA -s simCow_chr6.simCow.chr6 389811 9 + 602619 TCCCACTAA -s simDog_chr6.simDog.chr6 379795 9 + 593897 CCTCAGTAA -s simHuman_chr6.simHuman.chr6 383958 9 + 601863 CCCCACAAA -s simRat_chr6.simRat.chr6 398078 9 + 647215 CATCATTGA - -a -s simMouse_chr6.simMouse.chr6 397781 5 + 636262 GTATA -s Anc0.Anc0refChr3 29840 5 + 222631 CTACA -s Anc1.Anc1refChr6 59536 5 + 197743 CTACA -s Anc2.Anc2refChr13 33407 5 + 96486 CTACA -s mr.mrrefChr5 251273 5 + 294540 GTATA -s simCow_chr6.simCow.chr6 389820 5 + 602619 GTACA -s simDog_chr6.simDog.chr6 379807 5 + 593897 CTAGG -s simHuman_chr6.simHuman.chr6 383967 5 + 601863 CTACA -s simRat_chr6.simRat.chr6 398087 5 + 647215 GTATA - -a -s simMouse_chr6.simMouse.chr6 397786 7 + 636262 AGAGTTT -s Anc0.Anc0refChr3 29845 4 + 222631 A---TCT -s Anc1.Anc1refChr6 59541 4 + 197743 A---TCT -s Anc2.Anc2refChr13 33412 4 + 96486 A---TCT -s mr.mrrefChr5 251278 7 + 294540 AGAGTTT -s simCow_chr6.simCow.chr6 389830 4 + 602619 A---TTG -s simDog_chr6.simDog.chr6 379812 4 + 593897 A---TCT -s simRat_chr6.simRat.chr6 398092 7 + 647215 AGAGTTT - -a -s simMouse_chr6.simMouse.chr6 397793 76 + 636262 GGTGTCAAATACTATGCAGCTGATCTGCTCCAAACATACTTCCAGTTAGTTCACTATGTTAAGAATAATGGATAAG -s Anc0.Anc0refChr3 29849 73 + 222631 GCGG--AGAAACTGTGCAAGAGATCTGCTG-AAACATACTTTCAACCAGTTCTCCAGGATAAGAAAAATGAATAAG -s Anc1.Anc1refChr6 59545 74 + 197743 GCGG--AGAAACTGTGCAAGAGATCTGCTGCAAACATACTTTCAACCAGTTCTCCAGGATAAGAAAAATGAATAAG -s Anc2.Anc2refChr13 33416 73 + 96486 GCGG--AGAAACTGTGCAAGAGATTTGCTG-AGACATACTTTCAACCAATTCTCCAGGATAAGAAAAATGAACAAA -s mr.mrrefChr5 251285 76 + 294540 GGTGTCAAATACTATGCAGCTGATCTGCTCCAAACATACTTCCAATCAGTTCACTAGGTTAAGAATAATGGATAAG -s simCow_chr6.simCow.chr6 389834 72 + 602619 GCGG--ATAATATAGGGAACAGATCAGTTT-AGACAAACTTTCAACCTA-TCTCCGGGATAAGAGCAATGGAAGAA -s simDog_chr6.simDog.chr6 379817 73 + 593897 GTGT--AGAAACTGTGCAAGAGATTTGCTG-AGACATACTTTCAACCAATCCCCCAGGGTAAGAAAAATGAACAAA -s simHuman_chr6.simHuman.chr6 383972 54 + 601863 ----------------------ATCTGCTGCAAAGATACTTTCAACCAGTTCTCCAGGATAAGAAAAATGAATAAG -s simRat_chr6.simRat.chr6 398099 76 + 647215 GGTGGTAAATACTATGCAGCTGATCTGCTCCAAACACACTTCCAATCAGTTCCCTAGGGTAAGAATGATGGATAAG - -a -s simMouse_chr6.simMouse.chr6 397869 54 + 636262 CTCTACTTAAGTTGTCTGGGAGCTTAAGTTGAACCTGAGCTGACAGTGAACCTG -s Anc0.Anc0refChr3 29922 51 + 222631 CTCTGCTTGAAT---CTGAGAGTTGTAGTTAAACCTGAGCTAACAGTAAACCTG -s Anc1.Anc1refChr6 59619 52 + 197743 CTCTGCTTGAAT--TCTGAGAGTTGTAGTTAAACCTGAGCTAACAGTAAACCTG -s Anc2.Anc2refChr13 33489 51 + 96486 CACTGCTTGAAT---CTGAGAGTTGTAGTTAAACCTGAGCTAACAGTAAACCTG -s mr.mrrefChr5 251361 54 + 294540 CTCTACTTGAGTTGTCTGGGAGCTTAAGTTGAACCTGAGCTAACAGTGAACCTG -s simCow_chr6.simCow.chr6 389906 51 + 602619 CACTGCTTGAAT---CTGGAAGTTGAAGTAAAACCTGAGCTAACAGTAAACCTG -s simDog_chr6.simDog.chr6 379904 51 + 593897 CACTGCTTGGAT---CTGAGAGTTGTAGTTAATCCTGAGCTAACAATAAATCAG -s simHuman_chr6.simHuman.chr6 384026 50 + 601863 CTCTGCTTGAAT----TGATAGTTAGAGATAAACCCGAACTAACAGTTATCCTG -s simRat_chr6.simRat.chr6 398175 54 + 647215 CTCTACTTGAGTTCTCTTGGAGCTCAAGTTGAACCTGAGCTAACTGTGAACCTG - -a -s simMouse_chr6.simMouse.chr6 397923 19 + 636262 CATAAAATTAGGACTAAAG -s Anc0.Anc0refChr3 29973 19 + 222631 AATTAAATTAGTGCTAAAG -s Anc1.Anc1refChr6 59671 19 + 197743 AATTAAATTAGTGCTAAAG -s Anc2.Anc2refChr13 33540 19 + 96486 AATTAAATTAGTGCTAAAG -s mr.mrrefChr5 251415 19 + 294540 CATAAAATTAGGACTAAAG -s simCow_chr6.simCow.chr6 389957 18 + 602619 AATAGCATTAG-GCTAAAA -s simDog_chr6.simDog.chr6 379969 19 + 593897 GAGTAAATTAGTACTACAG -s simHuman_chr6.simHuman.chr6 384076 19 + 601863 AATCAAATTAGAGTTAAAG -s simRat_chr6.simRat.chr6 398229 19 + 647215 CATAAAATTGGGACTAAAG - -a -s simMouse_chr6.simMouse.chr6 397942 14 + 636262 AGCTGTAGAGAAGG -s Anc0.Anc0refChr3 29993 14 + 222631 AACCTCAGAGAAGG -s Anc1.Anc1refChr6 59691 14 + 197743 AACCTCAGAGAAGG -s Anc2.Anc2refChr13 33560 14 + 96486 AACCTCAGAGAAGG -s mr.mrrefChr5 251434 14 + 294540 AGCTGTAGAGAAGG -s simCow_chr6.simCow.chr6 389976 14 + 602619 CACCTCAGAGAAGG -s simDog_chr6.simDog.chr6 379989 14 + 593897 AACCTCAGGGCCTG -s simHuman_chr6.simHuman.chr6 384096 14 + 601863 AACCTGAGAGAAGG -s simRat_chr6.simRat.chr6 398248 14 + 647215 AGCTGTATAGAAAG - -a -s simMouse_chr6.simMouse.chr6 397956 66 + 636262 GATACTCAATCTGCAATTATCTCAGAAATCTTAGAAGGGAGTTACAGCAATACAACGATCTTCAAT -s Anc0.Anc0refChr3 30015 45 + 222631 -----------TGTAACTATCTCAGGA----------GGAAATACAGCAGTGTATTCAACTTCAAT -s Anc1.Anc1refChr6 59716 48 + 197743 G--------TTTGTAACTATCTCAGGA----------GGAAATACAGCAGTGTATTCAACTTCAAT -s Anc2.Anc2refChr13 33582 45 + 96486 -----------TGTAACTATCTCAGGA----------GGAAATACAGCAGTGTATTCAACTCCAAT -s mr.mrrefChr5 251459 66 + 294540 GATACTCAATTTGCAATTATCTCAGAAATCTTAGAAGGGAGTTACAGCAATATATCCATCTTCAAT -s simCow_chr6.simCow.chr6 389998 45 + 602619 -----------CCCAACTAACTCATGT----------GGAAAGTCAATAGTGTACTGAACTCCAAT -s simDog_chr6.simDog.chr6 380011 36 + 593897 -----------TGTAACTATATCAGGA----------GGAAATACAGCAGC-TGTTC--------T -s simHuman_chr6.simHuman.chr6 384121 48 + 601863 G--------TTTGTAACTATCTCAGGA----------GGAAATGCAGCAGTGTATTCAACCTCAAT -s simRat_chr6.simRat.chr6 398281 66 + 647215 GATACTCAATTTGCAATTATCTCAGACATCTCAGACGGGAGTTACAGCACCATATCCATCTTGAAT - -a -s simMouse_chr6.simMouse.chr6 398022 31 + 636262 TCTTGAGACACCAGGGGTTGGGACTAGATAT -s Anc0.Anc0refChr3 30060 28 + 222631 C---GGGACATTAGGGGTTGTGATGATGTAT -s Anc1.Anc1refChr6 59764 28 + 197743 C---GGGACATTAGGGGTTGTGATGATGTAT -s Anc2.Anc2refChr13 33627 28 + 96486 T---GGGACATTAGGGGTTGTAATGATGTAT -s mr.mrrefChr5 251525 31 + 294540 CCTTGAGACACTAGGGGTTGGGACTAGATAT -s simCow_chr6.simCow.chr6 390048 28 + 602619 T---GGGGCATTAGGAGTTGTAATGCTGTAT -s simDog_chr6.simDog.chr6 380047 28 + 593897 T---AGGACACTAGGGGTTGTAATGATGTAT -s simHuman_chr6.simHuman.chr6 384169 28 + 601863 C---GGGACATTAGGGGTTGTGATGATGTAT -s simRat_chr6.simRat.chr6 398347 31 + 647215 CCTTGAGACACTAGGGGTTGGGACTACATAT - -a -s simMouse_chr6.simMouse.chr6 398053 12 + 636262 ACATTGGAGGCT -s Anc0.Anc0refChr3 30088 12 + 222631 ATACCTGCGGTA -s Anc1.Anc1refChr6 59792 12 + 197743 ATACCTGCGGTA -s Anc2.Anc2refChr13 33655 12 + 96486 ACACCTGCGGTA -s mr.mrrefChr5 251556 12 + 294540 ATATTGGAGGCA -s simCow_chr6.simCow.chr6 390076 12 + 602619 ACACCTGCAGTA -s simDog_chr6.simDog.chr6 380075 12 + 593897 ACACCTGCGGGA -s simHuman_chr6.simHuman.chr6 384197 12 + 601863 ATACCTGGGGTA -s simRat_chr6.simRat.chr6 398379 12 + 647215 ATATTGGAAGCA - -a -s simMouse_chr6.simMouse.chr6 398065 98 + 636262 AAAAGGGGTGCATTCAAGAACAGAAAAATTCTTGCACTAAAATATACTGAATTGCACAGTACTTACCTCTTTTGATATCATTGCTATCAGCCGAGATG -s Anc0.Anc0refChr3 30100 57 + 222631 AGCAGTGGCACATTCAAGAACAAAAAGACTCTTGTATTGAAATG-----------------------------------------AACAGCCAATATA -s Anc1.Anc1refChr6 59804 57 + 197743 AGCAGTGGCACATTCAAGAACAAAAAGACTCTTGTATTGAAATG-----------------------------------------AACAGCCAATATA -s Anc2.Anc2refChr13 33668 57 + 96486 AGCACTTGCACATTCAAGAACAGAAAGACTCTTGTATTGAAATG-----------------------------------------AACAGCCAATACA -s mr.mrrefChr5 251568 98 + 294540 AAAAGGGGTGCATTCAAGAACAAAAAAATTCTTGCATTAAAATATACTGAATTGCACAGTACTTACCTCTTTTGATATCATTGCTATCAGCCAATATA -s simCow_chr6.simCow.chr6 390089 54 + 602619 AGCAC---CGCATTCAAGAACAGAAAGACTCTTGTATTGAAATG-----------------------------------------AACAGCCAATACA -s simDog_chr6.simDog.chr6 380090 55 + 593897 AGCACTTGCACG--CAAGAACAGAAAAACTCTTGTATTGAAATG-----------------------------------------AACAGCCAATACA -s simHuman_chr6.simHuman.chr6 384209 56 + 601863 AGCAGTGGCACATTCAAGAATGAAAAGACTCTAGAATTGAAATG-----------------------------------------AACAGCCAATAT- -s simRat_chr6.simRat.chr6 398391 98 + 647215 AAAAGGGATGCCCTCAAGAACAAAAAAATTCTTGCATTAAAATATATTGAATTGCAGAGCACTTACCTATCCTGACATCATTGCTATCAACCAATACA - -a -s simMouse_chr6.simMouse.chr6 398163 45 + 636262 GCAAATGAATGAAGAGCTAAGATAAGGTTGCAAAAGTACCAATAC -s Anc0.Anc0refChr3 30157 37 + 222631 GCAAAAATATCAGGA-TAAAAAAAAGGTTACA-------TTGTAA -s Anc1.Anc1refChr6 59861 44 + 197743 GCAAAAATATCAGGA-TAAAAAAAAGGTTACAAAGGTGCTTGTAA -s Anc2.Anc2refChr13 33730 37 + 96486 GCAAAAATATCAGGA-TAAAAAAAAGGTTACA-------TTGAAA -s mr.mrrefChr5 251666 45 + 294540 GCAAATGAATAAAGAGCTAAGATAAGGTTGCAAAAGTGCCGATAC -s simCow_chr6.simCow.chr6 390148 36 + 602619 GC-AAGATATCATGA-TTAAAGAAAGCTCACA-------TTGGAA -s simDog_chr6.simDog.chr6 380148 35 + 593897 --AAAAATATCAGGA-TAAAAAAAAGGTTACA-------TTGAAA -s simHuman_chr6.simHuman.chr6 384265 14 + 601863 -------------------------------AAAGGTGCTAGTAG -s simRat_chr6.simRat.chr6 398489 45 + 647215 GCAAATAAATAAAGAGCTTAGATAAGGTTGCAAACATGCCGATAC - -a -s simMouse_chr6.simMouse.chr6 398208 10 + 636262 AAGCCCGCCG -s Anc0.Anc0refChr3 30194 4 + 222631 CA------AT -s Anc1.Anc1refChr6 59905 4 + 197743 CA------AT -s Anc2.Anc2refChr13 33767 4 + 96486 CA------AT -s mr.mrrefChr5 251711 10 + 294540 AAGCCCGCAG -s simCow_chr6.simCow.chr6 390184 4 + 602619 GG------AT -s simDog_chr6.simDog.chr6 380183 4 + 593897 CA------AT -s simHuman_chr6.simHuman.chr6 384279 4 + 601863 CA------AT -s simRat_chr6.simRat.chr6 398538 10 + 647215 AAGTCAACAG - -a -s simMouse_chr6.simMouse.chr6 398218 4 + 636262 TGGG -s Anc0.Anc0refChr3 30198 4 + 222631 TTTG -s Anc1.Anc1refChr6 59909 4 + 197743 TTTG -s Anc2.Anc2refChr13 33771 4 + 96486 TTTG -s mr.mrrefChr5 251721 4 + 294540 TGGG -s simCow_chr6.simCow.chr6 390188 4 + 602619 CTTA -s simDog_chr6.simDog.chr6 380193 4 + 593897 TTTG -s simHuman_chr6.simHuman.chr6 384283 4 + 601863 TTTG -s simRat_chr6.simRat.chr6 398548 4 + 647215 TGGG - -a -s simMouse_chr6.simMouse.chr6 398222 9 + 636262 AGGCTGCTG -s Anc0.Anc0refChr3 30202 9 + 222631 ATGCAGCAG -s Anc1.Anc1refChr6 59913 9 + 197743 ATGCAGCAG -s Anc2.Anc2refChr13 33793 9 + 96486 ATGTAGCAG -s mr.mrrefChr5 251725 9 + 294540 AGGCTGCTG -s simCow_chr6.simCow.chr6 390210 9 + 602619 ATGTAGCAT -s simDog_chr6.simDog.chr6 380215 9 + 593897 ATGTAGCAG -s simHuman_chr6.simHuman.chr6 384287 9 + 601863 ATGCGGCAG -s simRat_chr6.simRat.chr6 398552 9 + 647215 AGGCTGCTG - -a -s simMouse_chr6.simMouse.chr6 398231 19 + 636262 CATTTACAACCATTTCAGG -s Anc0.Anc0refChr3 30217 19 + 222631 CCCCTCCAATATTCTTGGG -s Anc1.Anc1refChr6 59928 19 + 197743 CCCCTCCAATATTCTTGGG -s Anc2.Anc2refChr13 33808 19 + 96486 ACCCTCCAATATTCTTGGG -s mr.mrrefChr5 251734 19 + 294540 CATTTACAACCATTTCAGG -s simCow_chr6.simCow.chr6 390225 19 + 602619 ACACTCCAATATTCTTAGG -s simDog_chr6.simDog.chr6 380230 19 + 593897 ACCCACCAATATTCTTGTG -s simHuman_chr6.simHuman.chr6 384302 19 + 601863 CCCCTCCAATAGTCTTGGG -s simRat_chr6.simRat.chr6 398561 19 + 647215 TGTTTACAACCATTTCAGG - -a -s simMouse_chr6.simMouse.chr6 398250 3 + 636262 GCT -s Anc0.Anc0refChr3 30237 3 + 222631 CAC -s Anc1.Anc1refChr6 59948 3 + 197743 CAC -s Anc2.Anc2refChr13 33828 3 + 96486 CAC -s mr.mrrefChr5 251754 3 + 294540 GCT -s simCow_chr6.simCow.chr6 390245 3 + 602619 CAC -s simDog_chr6.simDog.chr6 380250 3 + 593897 CAA -s simHuman_chr6.simHuman.chr6 384322 3 + 601863 TAC -s simRat_chr6.simRat.chr6 398581 3 + 647215 GCT - -a -s simMouse_chr6.simMouse.chr6 398253 4 + 636262 TGGT -s Anc0.Anc0refChr3 30240 1 + 222631 C--- -s Anc1.Anc1refChr6 59951 1 + 197743 C--- -s Anc2.Anc2refChr13 33831 1 + 96486 C--- -s mr.mrrefChr5 251757 4 + 294540 TGGC -s simCow_chr6.simCow.chr6 390248 1 + 602619 T--- -s simDog_chr6.simDog.chr6 380253 1 + 593897 C--- -s simHuman_chr6.simHuman.chr6 384325 1 + 601863 C--- -s simRat_chr6.simRat.chr6 398585 4 + 647215 TGGC - -a -s simMouse_chr6.simMouse.chr6 398257 50 + 636262 TGGTGGCTAGTAGTGATATAGACAATTTTGGTAGGGAGCAGAGTATCCAA -s Anc0.Anc0refChr3 30241 48 + 222631 --ATGGCTAGTACTGATGTATACACTTTCGGTAGGCAGCAGTGCATTCAA -s Anc1.Anc1refChr6 59952 48 + 197743 --ATGGCTAGTACTGATGTATACACTTTCGGTAGGCAGCAGTGCATTCAA -s Anc2.Anc2refChr13 33832 48 + 96486 --AGGGCTAGTACTGATGTAGACACTTTCGGCAGGCAGCAGTGCATTCAA -s mr.mrrefChr5 251761 50 + 294540 TGGTGGCTAGTAGTGATATATACAATTTTGGTAGGCAGCAGAGTATTCAA -s simCow_chr6.simCow.chr6 390249 48 + 602619 --AGGGCTAGCGTTGATGTACACACTTCCAGCTGTCAGTGATGTATCCAA -s simDog_chr6.simDog.chr6 380254 48 + 593897 --AGGGCTAGTACTGATGTAGATATTTTCGACAGGCAGCAGTGCACTCTA -s simHuman_chr6.simHuman.chr6 384326 48 + 601863 --ATGGCCAGGACTGATGATTACACTCTCGGTAGGCAGCAGTGCATTCAA -s simMouse_chr6.simMouse.chr6 398505 50 + 636262 TGGTGGCTAGTAGTGATATATATGATTTTGGTGGGTAGGAGAGTATGCAA -s simRat_chr6.simRat.chr6 398589 50 + 647215 TAATGGCTAGTACTGATCTATACAATTTTGGTAGGCAGCAGAGCATTCAA - -a -s simMouse_chr6.simMouse.chr6 398307 38 + 636262 GACCCTTGGAAGTAGATTACATTGGCAATGACTACCAT -s Anc0.Anc0refChr3 30323 32 + 222631 AACCATTGGAAGGATATTGCATTTGCA------ACCAT -s Anc1.Anc1refChr6 60034 32 + 197743 AACCATTGGAAGGATATTGCATTTGCA------ACCAT -s Anc2.Anc2refChr13 33914 32 + 96486 AGCCATTGGAAGGATATTGCATTTGCA------ACCTT -s mr.mrrefChr5 251811 38 + 294540 GACCCTTGGAAGTAGATTACATTGGCAATGACTACCAT -s simCow_chr6.simCow.chr6 390332 32 + 602619 AGCCATTGGAAAGATGTTGCATTTGCA------AGTTC -s simDog_chr6.simDog.chr6 380329 31 + 593897 AGCCCTT-GAAGGGTATTACATTTGCA------ACCTT -s simHuman_chr6.simHuman.chr6 384408 32 + 601863 AACCATTGGAAGGATATTGCATTTTCA------ACCAT -s simMouse_chr6.simMouse.chr6 398555 37 + 636262 GACCCTTGGAAGTAGATTACATTG-CAATGACTACCAT -s simRat_chr6.simRat.chr6 398639 38 + 647215 GACCCTCGAAAGTAGATTACATTGGCAACCACTACCAT - -a -s simMouse_chr6.simMouse.chr6 398345 23 + 636262 ATGAGAAATGCAGGGAGTGTATT -s Anc0.Anc0refChr3 30355 21 + 222631 GAGAG-AATGCA-GCAGTGTATT -s Anc1.Anc1refChr6 60066 21 + 197743 GAGAG-AATGCA-GCAGTGTATT -s Anc2.Anc2refChr13 33946 21 + 96486 GAGAA-AATGCA-GCAGCGTATT -s mr.mrrefChr5 251849 23 + 294540 ATGAGAAATGCAGGCAGTGTATT -s simCow_chr6.simCow.chr6 390364 21 + 602619 AAGAA-AATGCA-GCAGCATATT -s simDog_chr6.simDog.chr6 380360 19 + 593897 GAGGA-AATGCA-GCA--GTATT -s simHuman_chr6.simHuman.chr6 384445 21 + 601863 GAGAG-AATGGA-GCACTGTATT -s simMouse_chr6.simMouse.chr6 398592 23 + 636262 ATGAGAATTGCAGGCTGTGTATT -s simRat_chr6.simRat.chr6 398677 20 + 647215 --GAGAAACGCAGGCAGTG-ACG - -a -s simMouse_chr6.simMouse.chr6 398368 4 + 636262 TCCC -s Anc0.Anc0refChr3 30376 4 + 222631 CCCA -s Anc1.Anc1refChr6 60087 4 + 197743 CCCA -s Anc2.Anc2refChr13 33967 4 + 96486 CCCA -s mr.mrrefChr5 251872 4 + 294540 TCCC -s simCow_chr6.simCow.chr6 390385 4 + 602619 CCCA -s simDog_chr6.simDog.chr6 380414 4 + 593897 CCCA -s simHuman_chr6.simHuman.chr6 384466 4 + 601863 CCCT -s simMouse_chr6.simMouse.chr6 398615 2 + 636262 TC-- -s simRat_chr6.simRat.chr6 398697 2 + 647215 CA-- - -a -s simMouse_chr6.simMouse.chr6 398372 37 + 636262 TTCAATATTCATGGAACAATAGTGCAAGTAATAATTT -s Anc0.Anc0refChr3 30380 37 + 222631 TTCAATATTCTTGAGACACCAGGGCTAGTACTGATGT -s Anc1.Anc1refChr6 60091 37 + 197743 TTCAATATTCTTGAGACACCAGGGCTAGTACTGATGT -s Anc2.Anc2refChr13 33971 37 + 96486 TCTAAAATTCTTGGGACACCAGGGCTAGTACTGATGT -s mr.mrrefChr5 251876 37 + 294540 TTCAATATTCATGAGACAATAGTGCAAGTAATAATTT -s simCow_chr6.simCow.chr6 390394 37 + 602619 CCAAACATTCTTGGGACACCTGGGCTAGTACTGATAT -s simDog_chr6.simDog.chr6 380418 36 + 593897 TCTAAAATTATTGGGACACCACGATTAGTACT-ATGC -s simHuman_chr6.simHuman.chr6 384470 37 + 601863 TTCAATATTCTTGAGACACCAGGGCTAGTACTGATGT -s simMouse_chr6.simMouse.chr6 398617 34 + 636262 ---AATATTCATGAGACAATAGTGCAAGTCATAATTT -s simRat_chr6.simRat.chr6 398699 34 + 647215 ---AATGTCCATGAGACAATAGTACAAGTAGTAATTC - -a -s simMouse_chr6.simMouse.chr6 398409 37 + 636262 GTAGCCACCAGGGTATTCAAGGAACATAGGAAGTCTT -s Anc0.Anc0refChr3 30428 35 + 222631 GTAGGCAGCAGTGCATTCAA--AACACAGGAAGACTG -s Anc1.Anc1refChr6 60139 35 + 197743 GTAGGCAGCAGTGCATTCAA--AACACAGGAAGACTG -s Anc2.Anc2refChr13 34019 35 + 96486 GTAGGCAGCAGTGCATTCAA--GACACAGAAAGACTG -s mr.mrrefChr5 251913 37 + 294540 GTAGCCAGCAGGGCATTCAAGGAACATAGGAAGCCTT -s simCow_chr6.simCow.chr6 390441 35 + 602619 ACAGGCAGCAGTCCATTCAA--GACACAGAAAGACTG -s simDog_chr6.simDog.chr6 380498 35 + 593897 GTAGTCAGCAGTGCAAACAA--GACACAGAAAGACTA -s simHuman_chr6.simHuman.chr6 384518 35 + 601863 GTAGGCAACAGTACATTCAA--AACACAGGAAGATTG -s simMouse_chr6.simMouse.chr6 398651 37 + 636262 GTAGCCAGCAGGACATTCAGGGAACATAGGAAGCCTT -s simRat_chr6.simRat.chr6 398733 37 + 647215 GTAGCCAGCAGGGCATTCAAGAAACACAGGAAGCCTG - -a -s simMouse_chr6.simMouse.chr6 398446 7 + 636262 CATTTTT -s Anc0.Anc0refChr3 30463 7 + 222631 CATTCTT -s Anc1.Anc1refChr6 60174 7 + 197743 CATTCTT -s Anc2.Anc2refChr13 34054 7 + 96486 CATTCTT -s mr.mrrefChr5 251950 7 + 294540 CATTTTT -s simCow_chr6.simCow.chr6 390476 7 + 602619 CTCCTTT -s simDog_chr6.simDog.chr6 380533 7 + 593897 TATTCTT -s simHuman_chr6.simHuman.chr6 384553 7 + 601863 CATTGTT -s simMouse_chr6.simMouse.chr6 398688 7 + 636262 CATTTTT -s simRat_chr6.simRat.chr6 398771 7 + 647215 CATTTTC - -a -s simMouse_chr6.simMouse.chr6 398453 26 + 636262 GTATATGTAAACAGCTGATTAAAGGT -s Anc0.Anc0refChr3 30470 26 + 222631 GTATAGACGAACGGCTGATTAAAGGG -s Anc1.Anc1refChr6 60181 26 + 197743 GTATAGACGAACGGCTGATTAAAGGG -s Anc2.Anc2refChr13 34061 26 + 96486 GTATAGACGAATGGCTGAATCAATGG -s mr.mrrefChr5 251957 26 + 294540 GTATATGTAAACAGCTGATTAAAGGT -s simCow_chr6.simCow.chr6 390483 26 + 602619 GTATAAATGAATGGCTGAATCAATGG -s simDog_chr6.simDog.chr6 380540 22 + 593897 GCATAGACGA----CTGAATCAATGG -s simHuman_chr6.simHuman.chr6 384560 26 + 601863 GTAAAGAAGAGCTGCTAATTAAAGGG -s simMouse_chr6.simMouse.chr6 398695 26 + 636262 GTATATGTAAACAGCTGATTAAAGAT -s simRat_chr6.simRat.chr6 398779 25 + 647215 GTATAT-TAAACAGCTGATTAAAGGT - -a -s simMouse_chr6.simMouse.chr6 398479 10 + 636262 GGACCACACC -s Anc0.Anc0refChr3 30506 10 + 222631 GGACCTCCCT -s Anc1.Anc1refChr6 60217 10 + 197743 GGACCTCCCT -s Anc2.Anc2refChr13 34097 10 + 96486 GTATCTCCCA -s mr.mrrefChr5 251983 10 + 294540 GGACCACACT -s simCow_chr6.simCow.chr6 390519 7 + 602619 GTATCTT--- -s simDog_chr6.simDog.chr6 380572 10 + 593897 ATATCTCCCA -s simHuman_chr6.simHuman.chr6 384596 10 + 601863 GGACCTCCCT -s simMouse_chr6.simMouse.chr6 398721 10 + 636262 GGACCACACT -s simRat_chr6.simRat.chr6 398804 10 + 647215 GGATCACACT - -a -s simMouse_chr6.simMouse.chr6 398489 7 + 636262 AGACAGG -s Anc0.Anc0refChr3 30517 7 + 222631 AGTTAAG -s Anc1.Anc1refChr6 60228 7 + 197743 AGTTAAG -s Anc2.Anc2refChr13 34108 7 + 96486 GGTTAAG -s mr.mrrefChr5 251993 7 + 294540 AGACAGG -s simCow_chr6.simCow.chr6 390526 4 + 602619 ---TTAG -s simDog_chr6.simDog.chr6 380583 7 + 593897 GGTCAAT -s simHuman_chr6.simHuman.chr6 384607 7 + 601863 AGTTAAG -s simMouse_chr6.simMouse.chr6 398731 7 + 636262 AGACAGA -s simRat_chr6.simRat.chr6 398814 7 + 647215 AAACAGG - -a -s simMouse_chr6.simMouse.chr6 398496 9 + 636262 ATGCCATAA -s Anc0.Anc0refChr3 30527 7 + 222631 ATGTCAT-- -s Anc1.Anc1refChr6 60238 7 + 197743 ATGTCAT-- -s Anc2.Anc2refChr13 34118 7 + 96486 ATATCAT-- -s mr.mrrefChr5 252000 9 + 294540 ATGCCATAA -s simCow_chr6.simCow.chr6 390533 7 + 602619 ATACCAT-- -s simDog_chr6.simDog.chr6 380593 7 + 593897 ATATCAT-- -s simHuman_chr6.simHuman.chr6 384617 7 + 601863 ATGTCAT-- -s simMouse_chr6.simMouse.chr6 398738 9 + 636262 ATGCCATAT -s simRat_chr6.simRat.chr6 398821 9 + 647215 ATGACATAA - -a -s simMouse_chr6.simMouse.chr6 398747 31 + 636262 TGACTTTTCAATATCTTCCAGGGGCATGTTT -s Anc0.Anc0refChr3 30534 5 + 222631 --------------------------TGTTA -s Anc1.Anc1refChr6 60245 5 + 197743 --------------------------TGTTA -s Anc2.Anc2refChr13 34125 5 + 96486 --------------------------CATTA -s mr.mrrefChr5 252009 27 + 294540 TGACTTTTCAATATCT----GGGGCATGTTT -s simCow_chr6.simCow.chr6 390540 5 + 602619 --------------------------CATTC -s simDog_chr6.simDog.chr6 380600 5 + 593897 --------------------------CATTA -s simHuman_chr6.simHuman.chr6 384624 5 + 601863 --------------------------TGTTG -s simRat_chr6.simRat.chr6 398830 16 + 647215 TGAATATGCAGTACCC--------------- - -a -s simMouse_chr6.simMouse.chr6 398778 15 + 636262 ACTCATTGGTATTAG -s Anc0.Anc0refChr3 30539 15 + 222631 CCCCATTGCACTGAG -s Anc1.Anc1refChr6 60250 15 + 197743 CCCCATTGCACTGAG -s Anc2.Anc2refChr13 34130 15 + 96486 CCCCATTGCACTGAG -s mr.mrrefChr5 252036 15 + 294540 ACTCATTGGTATTAG -s simCow_chr6.simCow.chr6 390545 15 + 602619 CTTCATTGCACTGAG -s simDog_chr6.simDog.chr6 380611 15 + 593897 CCCCATTGCCCTGAG -s simHuman_chr6.simHuman.chr6 384629 15 + 601863 CCCCATTGCACTGAG -s simRat_chr6.simRat.chr6 398846 6 + 647215 ---------TATTAG - -a -s simMouse_chr6.simMouse.chr6 398793 100 + 636262 CTGAGTAATCTGAAACGGAGTAATGACATGAATGAGCCACTCACATCGGAGTAATGCATTTGACCACAGCCACTCACATTGGAGTAATGCATTTGACCAC -s Anc0.Anc0refChr3 30560 50 + 222631 CTTGGCAGTTTGGATGAGAGTATTGACATGAA----CCACTCATGT----------------------------------------------TTGATCTA -s Anc1.Anc1refChr6 60271 50 + 197743 CTTGGCAGTTTGGATGAGAGTATTGACATGAA----CCACTCATGT----------------------------------------------TTGATCTA -s Anc2.Anc2refChr13 34151 50 + 96486 CTTGGCAGTTTGAATGGGAGTGTTCACATGAG----CCACTCATGT----------------------------------------------TTGATCTA -s mr.mrrefChr5 252051 54 + 294540 CTTAGTAATCTGGATCAGAGTAATGACATGAATGAGCCACTCACAT----------------------------------------------TTGACCAC -s simCow_chr6.simCow.chr6 390566 50 + 602619 CTTGATGGTTTGAATGGGAGGTTTATCACGTG----TAGCTCATTA----------------------------------------------TTTATCTA -s simDog_chr6.simDog.chr6 380632 48 + 593897 CTTGGCAGTTTGAA--GGAGTGTTCACATGAG----CCACTCATGT----------------------------------------------TCGGGCTA -s simHuman_chr6.simHuman.chr6 384650 50 + 601863 CTTGGCATTTTGGATGAGAGTACTGACATGAA----CCACTCATGT----------------------------------------------TTGATCTA -s simRat_chr6.simRat.chr6 398852 54 + 647215 CTTAGTAATCTGGATCAGAGTAATGACATGAATGAGCTACTCACAT----------------------------------------------TTGAGCAG - -a -s simMouse_chr6.simMouse.chr6 398893 9 + 636262 AGCTACAGG -s Anc0.Anc0refChr3 30610 9 + 222631 AGCTACAGG -s Anc1.Anc1refChr6 60321 9 + 197743 AGCTACAGG -s Anc2.Anc2refChr13 34201 9 + 96486 AGCTACAGC -s mr.mrrefChr5 252105 9 + 294540 AGCTACAGG -s simCow_chr6.simCow.chr6 390617 9 + 602619 AGCTACACC -s simDog_chr6.simDog.chr6 380700 9 + 593897 AGCTAGAGC -s simHuman_chr6.simHuman.chr6 384700 9 + 601863 AGCTACAGG -s simRat_chr6.simRat.chr6 398906 9 + 647215 AGCTACAGG - -a -s simMouse_chr6.simMouse.chr6 398902 20 + 636262 TTAGGCATGTAACTGCTACA -s Anc0.Anc0refChr3 30620 20 + 222631 TTAGGCATATAGCTGCTACT -s Anc1.Anc1refChr6 60331 20 + 197743 TTAGGCATATAGCTGCTACT -s Anc2.Anc2refChr13 34211 20 + 96486 TTATGCATATAGCTGTTACA -s mr.mrrefChr5 252114 20 + 294540 TTAGGCATATAGCTGCTACT -s simCow_chr6.simCow.chr6 390627 18 + 602619 --ATGCATATATTTGATTCA -s simDog_chr6.simDog.chr6 380710 20 + 593897 TTATGCACCTAGCTATTACA -s simHuman_chr6.simHuman.chr6 384710 20 + 601863 TTAGGCGTATAGCTGCTATT -s simRat_chr6.simRat.chr6 398915 20 + 647215 TTGGGCATATAGCCGCTACT - -a -s simMouse_chr6.simMouse.chr6 398922 27 + 636262 GAAGTCATTGACCATTCTGTTTTTACT -s Anc0.Anc0refChr3 30640 27 + 222631 GGAGTGATAGACCATATCTGTTTTACT -s Anc1.Anc1refChr6 60351 27 + 197743 GGAGTGATAGACCATATCTGTTTTACT -s Anc2.Anc2refChr13 34231 27 + 96486 GGAGTCATAGACCATATCTGTTTTACT -s mr.mrrefChr5 252134 27 + 294540 GAAGTGATAGACCATTCTGTTTTTACT -s simCow_chr6.simCow.chr6 390645 27 + 602619 GGAGTCAAATCCCACATCTTCTCTATT -s simDog_chr6.simDog.chr6 380730 27 + 593897 GCAGTCATAGACCGTGTTTGTTTTACT -s simHuman_chr6.simHuman.chr6 384730 27 + 601863 GGAATGATAGACCATATCTGTTTTACT -s simRat_chr6.simRat.chr6 398936 27 + 647215 GAAGTGATAGACCATTCTGTTCTTACT - -a -s simMouse_chr6.simMouse.chr6 398949 80 + 636262 CAGAGCCAAGAATAAAACTGAAGGGAGTAGGGTCTTCTTCAGCGTCAACTGGTAATCAAGAGGGTAAAGTGGTGTAGACT -s Anc0.Anc0refChr3 30668 19 + 222631 CAGA-------------------------------------------------------------AGGCTGGTGCAAAAG -s Anc1.Anc1refChr6 60379 19 + 197743 CAGA-------------------------------------------------------------AGGCTGGTGCAAAAG -s Anc2.Anc2refChr13 34259 19 + 96486 CAGA-------------------------------------------------------------AGGCTGGTGCAAAAG -s mr.mrrefChr5 252162 80 + 294540 CAGAGCCAAGAATAAAACTGAAGGGAGTAGGGTCTTCTTCAGCGTCAACTGGTAATCAAGAGGGCAAAGTGGTGTAGACT -s simCow_chr6.simCow.chr6 390673 19 + 602619 CAGA-------------------------------------------------------------ATGCTGGTACAAAAG -s simDog_chr6.simDog.chr6 380758 19 + 593897 GAGA-------------------------------------------------------------AGGCTGGTGTAAAAG -s simHuman_chr6.simHuman.chr6 384758 19 + 601863 CAGA-------------------------------------------------------------AGGCTGGTGCAAAAG -s simRat_chr6.simRat.chr6 398964 80 + 647215 CAGAGCCAACACAAAAACTGAAGGGAGTAAGGTCTTCTTCAGCATCAACGGGTAATCCAGAGCGCAAAGCGGTGTCGACT - -a -s simMouse_chr6.simMouse.chr6 399029 5 + 636262 GCTCA -s Anc0.Anc0refChr3 30687 3 + 222631 GCT-- -s Anc1.Anc1refChr6 60398 5 + 197743 GCTGG -s Anc2.Anc2refChr13 34278 3 + 96486 GCT-- -s mr.mrrefChr5 252242 5 + 294540 GCTCA -s simCow_chr6.simCow.chr6 390692 3 + 602619 GAT-- -s simDog_chr6.simDog.chr6 380777 3 + 593897 ACT-- -s simHuman_chr6.simHuman.chr6 384777 5 + 601863 GCTGG -s simRat_chr6.simRat.chr6 399045 5 + 647215 GCCTA - -a -s simMouse_chr6.simMouse.chr6 399034 39 + 636262 TTGGAGTGAAGATGTGGTTAATGGGCTACACCACCCTCT -s Anc0.Anc0refChr3 30690 28 + 222631 ------TCAAGATTTGGTAAATGGACT-----GCCCCTC -s Anc1.Anc1refChr6 60403 34 + 197743 CTGGAGTCAAGATTTGGTAAATGGACT-----GCCCCTC -s Anc2.Anc2refChr13 34281 28 + 96486 ------TCATTATTGGACAAAAGAACT-----GCTCCTC -s mr.mrrefChr5 252247 39 + 294540 TTGGAGTGAAGATGTGGTTAATGGACTACACCACCCCCT -s simCow_chr6.simCow.chr6 390695 28 + 602619 ------TGATTATTGAAGTAAAGAACT-----GCTCCTC -s simDog_chr6.simDog.chr6 380780 13 + 593897 ------TCATTATTGGACA-------------------- -s simHuman_chr6.simHuman.chr6 384784 34 + 601863 CTGGAGTCAAGATCTGGTAGATAGACT-----GCCCCTC -s simRat_chr6.simRat.chr6 399050 39 + 647215 TTGGAATAAAGATGTGCTTAATGTACTACACCACCCCCT - -a -s simMouse_chr6.simMouse.chr6 399073 25 + 636262 GACCCACCACTCCCAGATGAGAATT -s Anc0.Anc0refChr3 30718 25 + 222631 CTCCATCCACTCCCAGTTGGGGATT -s Anc1.Anc1refChr6 60437 25 + 197743 CTCCATCCACTCCCAGTTGGGGATT -s Anc2.Anc2refChr13 34309 25 + 96486 CTCCATTCACTCCCAGTTGGGAATT -s mr.mrrefChr5 252286 25 + 294540 GACCCACCACTCCCAGATGAGGATT -s simCow_chr6.simCow.chr6 390727 25 + 602619 CTGAATATACTACCAGTTTTGAATT -s simDog_chr6.simDog.chr6 380793 23 + 593897 --CCATTCACTCCCAGCTGGGAATT -s simHuman_chr6.simHuman.chr6 384818 25 + 601863 CTCCACCCACTGCCAGTAGGGGATT -s simRat_chr6.simRat.chr6 399089 25 + 647215 GACCCACCACTCCCAGATGAGGGTT - -a -s simMouse_chr6.simMouse.chr6 399098 50 + 636262 GCTATAGTCTTGTGTGCTAAGAGAATCCCCAGAATTTTACCCATATTGCA -s Anc0.Anc0refChr3 30752 50 + 222631 GTTATAGTCTTACATGTTAGGAGAAACCAGAGAATTTTACCCATATTGCA -s Anc1.Anc1refChr6 60471 50 + 197743 GTTATAGTCTTACATGTTAGGAGAAACCAGAGAATTTTACCCATATTGCA -s Anc2.Anc2refChr13 34343 50 + 96486 GTTATAGTCTTACATGTTAGAAGAAACCAGAGAATTTTACCCATATTCCA -s mr.mrrefChr5 252311 50 + 294540 GTTATAGTCTTGTGTGCTAAGAGAATCCCCAGAATTTTACCCATATTGCA -s simCow_chr6.simCow.chr6 390761 50 + 602619 GTCATAGGATTATGTGTAAGAACAAACCAGAATATTTTACCCATATTACC -s simDog_chr6.simDog.chr6 380822 50 + 593897 GATATAGTCTTACATGTTAAAAGAAACCAGAGAATTTTACCCATATCCCA -s simHuman_chr6.simHuman.chr6 384852 50 + 601863 GTTGTAGTCCTACCTGTTAGGAGAAGCCAGATAATTTTACCTATATTGCA -s simRat_chr6.simRat.chr6 399114 48 + 647215 GTTAAAGTCATG-GTGCTAAGAGA-TTCCCAGAATTTTACCCATATTGCA - -a -s simMouse_chr6.simMouse.chr6 399148 21 + 636262 TAATTCCCAGGTAAATTCAAC -s Anc0.Anc0refChr3 30802 21 + 222631 TAATCCCCAGGTAAATTGAAT -s Anc1.Anc1refChr6 60521 21 + 197743 TAATCCCCAGGTAAATTGAAT -s Anc2.Anc2refChr13 34393 21 + 96486 TAATCCTGAGGTAAATTGAAT -s mr.mrrefChr5 252361 21 + 294540 TAATCCCCAGGTAAATTCAAC -s simCow_chr6.simCow.chr6 390811 20 + 602619 TAA-CCTGAGGTAACTTGAAT -s simDog_chr6.simDog.chr6 380893 21 + 593897 TAATCCTGAGTTAAACTGAAC -s simHuman_chr6.simHuman.chr6 384902 21 + 601863 TAATCCCCAGGTAAATTGAAT -s simRat_chr6.simRat.chr6 399162 21 + 647215 TAATCTCCAGGTAATTTCAAC - -a -s simMouse_chr6.simMouse.chr6 399169 50 + 636262 ACCCTTCAGGATTTCATCACCAAATTTAGCACTCCTTACTTCTCAATTGT -s Anc0.Anc0refChr3 30823 49 + 222631 ACCCAGCAGAGTTTTACCATTGAAATTAGCAGTCCTTGCTTCACAA-TGG -s Anc1.Anc1refChr6 60542 50 + 197743 ACCCAGCAGAGTTTTACCATTGAAATTAGCAGTCCTTGCTTCACAAATGG -s Anc2.Anc2refChr13 34414 49 + 96486 ACCCAGCAGAGTTTTACCATTGTAATCAACAGTTCTTGCTTCACAA-TGG -s mr.mrrefChr5 252382 50 + 294540 ACCCTTCAGGATTTCATCACCAAAATTAGCACTCCTTACTTCACAATTGT -s simCow_chr6.simCow.chr6 390831 48 + 602619 ACCCAGCAGAGTTTTACCATTGGAATGAACAGTTTT-GCTTCACAA-TGT -s simDog_chr6.simDog.chr6 380914 48 + 593897 ATCCAGCAGAGT-TAAACAGTGTAATCTACAGTTCTTATTTCACAA-TGG -s simHuman_chr6.simHuman.chr6 384923 50 + 601863 ACCCAACAGAGTGTTACCATTGAAATTAGCAGTCCTAGCTTTATAAATGG -s simRat_chr6.simRat.chr6 399184 50 + 647215 ACCCTGCAGGATTTCATCACCAAAATTAGCTCTACTTACTTCACAATTGT - -a -s simMouse_chr6.simMouse.chr6 399219 37 + 636262 ATAGTGTCATAAGGTGAAGTAGAAAAGGAAGTATGCT -s Anc0.Anc0refChr3 30909 33 + 222631 ATAGTTGCACAAGGTGAAGTAGAAAGGGAAGT----G -s Anc1.Anc1refChr6 60629 33 + 197743 ATAGTTGCACAAGGTGAAGTAGAAAGGGAAGT----G -s Anc2.Anc2refChr13 34500 33 + 96486 ATAGTTGCACAAGGTGAAGTAGAAAGGGAAGT----G -s mr.mrrefChr5 252432 33 + 294540 ATAGTGTCATAAGGTGAAGTAGAAAAGGAAGT----T -s simCow_chr6.simCow.chr6 390911 33 + 602619 ATATTTCCACAAGGTGAAGTGGAAAGGGAAGT----G -s simDog_chr6.simDog.chr6 380999 33 + 593897 ATAGTTGGACAAGGTGAAGTAGAAAAGGAAGT----G -s simHuman_chr6.simHuman.chr6 385011 31 + 601863 ATAGTTGCACAATGTGAGGTAGAAAGGGAAG------ -s simRat_chr6.simRat.chr6 399234 33 + 647215 ACAGTGTCATAAGGAGAAGTAGAAAAGTAAGT----T - -a -s simMouse_chr6.simMouse.chr6 399256 35 + 636262 AGACCTTGGTCAGCATTCTTGTCTCATAAATGTTT -s Anc0.Anc0refChr3 30942 33 + 222631 GGACCTTGCTC--CATGCTTGTATCATAGATGTTT -s Anc1.Anc1refChr6 60662 35 + 197743 GGACCTTGCTCGGCATGCTTGTATCATAGATGTTT -s Anc2.Anc2refChr13 34537 33 + 96486 GGACCTTGCTC--CATGCTAGTATCATAGATGTTT -s mr.mrrefChr5 252465 35 + 294540 AGACCTTGGTCAGCATTCTTGTCTCATAAATGTTT -s simCow_chr6.simCow.chr6 390948 33 + 602619 GGACCTTGCTC--CATGTTAGTCTCGTAAATGTTT -s simDog_chr6.simDog.chr6 381036 33 + 593897 GGACCCCTCCC--CATGCTAGTATCATAGATGTTT -s simHuman_chr6.simHuman.chr6 385042 27 + 601863 -----TCGATCGGCAT--TTGCTTCATATATG-TT -s simRat_chr6.simRat.chr6 399267 35 + 647215 AAACCTAGGTCAGCATTCTTCTCTTATAAATGTTT - -a -s simMouse_chr6.simMouse.chr6 399291 69 + 636262 TTGGGACTCCAATAGGGGGGCTGATGACGGGATGCACCAACTTTTTTCATTGAGAAGCAATTTTCCATG -s Anc0.Anc0refChr3 30975 28 + 222631 TT----------------------------------------TTTTTCACTAAGGGGC-ATCTTTCACG -s Anc1.Anc1refChr6 60697 28 + 197743 TT----------------------------------------TTTTTCACTAAGGGGC-ATCTTTCACG -s Anc2.Anc2refChr13 34571 28 + 96486 TT----------------------------------------TTTTTCACTAAGGGGC-ATCTTTGGCG -s mr.mrrefChr5 252500 29 + 294540 TT----------------------------------------TTTTTCACTAAGGGGCAATCTTCCATG -s simCow_chr6.simCow.chr6 390982 28 + 602619 TT----------------------------------------TTCTTCACTGAGGGGC-ATCTACTTCA -s simDog_chr6.simDog.chr6 381070 28 + 593897 TT----------------------------------------TTTTTCCCCAAGGGTC-ACCTTTGGTG -s simHuman_chr6.simHuman.chr6 385069 28 + 601863 TT----------------------------------------TTTCATACTAAGGGGT-ATCATTCACG -s simRat_chr6.simRat.chr6 399302 29 + 647215 TT----------------------------------------TTTTTCACTAAGGGGCAATCTTCCATG - -a -s simMouse_chr6.simMouse.chr6 399360 10 + 636262 GTGCTCTCAG -s Anc0.Anc0refChr3 31014 10 + 222631 GTACTCTTAG -s Anc1.Anc1refChr6 60736 10 + 197743 GTACTCTTAG -s Anc2.Anc2refChr13 34610 10 + 96486 GTACTCTTAG -s mr.mrrefChr5 252529 10 + 294540 GTGCTCTCAG -s simCow_chr6.simCow.chr6 391021 10 + 602619 GTACTCTCAG -s simDog_chr6.simDog.chr6 381109 10 + 593897 GTGCTCTTAG -s simHuman_chr6.simHuman.chr6 385108 10 + 601863 GTACTCTTAG -s simRat_chr6.simRat.chr6 399331 10 + 647215 GTGCCCTCAG - -a -s simMouse_chr6.simMouse.chr6 399370 20 + 636262 GGATTAGTATTTGAGTCACA -s Anc0.Anc0refChr3 31024 20 + 222631 AGATAAGCATGGGAATAACA -s Anc1.Anc1refChr6 60746 20 + 197743 AGATAAGCATGGGAATAACA -s Anc2.Anc2refChr13 34620 20 + 96486 AGATAAGCATGGGAATAACG -s mr.mrrefChr5 252539 20 + 294540 GGATTAGTATGTGAGTCACA -s simCow_chr6.simCow.chr6 391037 20 + 602619 AGATAAGCATGGGAAGACCA -s simDog_chr6.simDog.chr6 381119 20 + 593897 AGACAAGTTTGGGATTAATG -s simHuman_chr6.simHuman.chr6 385118 20 + 601863 AGATAAGCACGGGAATAACA -s simRat_chr6.simRat.chr6 399341 20 + 647215 GGACTAGTATGTTGGTCAAA - -a -s simMouse_chr6.simMouse.chr6 399390 62 + 636262 TTGCCTTCTCATACCTCTTTATACTCTTTGCTAACTTTTCATGCAAAACCCATGTGGTTATC -s Anc0.Anc0refChr3 31044 52 + 222631 TG--TTTCCCATAGCT--TCACTCTC------AACATTTTCGTCAACTGCCATACTAATATC -s Anc1.Anc1refChr6 60766 60 + 197743 TG--TTTCCCATAGCTCTTCACTCTCTTTGCTAACATTTTCGTCAACTGCCATACTAATATC -s Anc2.Anc2refChr13 34641 52 + 96486 TG--TTTCCCATAGCT--TCACTCTC------AACATTTTCGTCAACTGCAGCACTAATGTG -s mr.mrrefChr5 252559 62 + 294540 TTGCCTTCTCATACCTCTTTATACTCTTTGCTAACTTTTCATGCAAAAACCATGTTGATATC -s simCow_chr6.simCow.chr6 391058 50 + 602619 TG--TCTCCCATCTCT--TCACTCTC------AATGTTTCAGT--ACTGCATCACTAATGTG -s simDog_chr6.simDog.chr6 381140 52 + 593897 TG--TTTCCCATAGCT--TCACTCTC------AACATTTTCATCAAGTGCAGCACTAATGTG -s simHuman_chr6.simHuman.chr6 385138 48 + 601863 TG--TTTCGCATAGCTGTTCACTCGCTTTGCT------------AACTTTCATAATAAAATC -s simRat_chr6.simRat.chr6 399361 62 + 647215 TTGCCTTCTCATACCTCTTTATACTCTTTACTAACTTTTTGTGCAAAAACCATGTTGATATT - -a -s simMouse_chr6.simMouse.chr6 399452 13 + 636262 TGGACTCTAATTA -s Anc0.Anc0refChr3 31107 3 + 222631 TGT---------- -s Anc1.Anc1refChr6 60837 13 + 197743 TGTACTTTAGTCA -s Anc2.Anc2refChr13 34704 3 + 96486 TGT---------- -s mr.mrrefChr5 252621 13 + 294540 TGGACTCTAATTA -s simCow_chr6.simCow.chr6 391114 3 + 602619 CAT---------- -s simDog_chr6.simDog.chr6 381203 3 + 593897 TGT---------- -s simHuman_chr6.simHuman.chr6 385197 13 + 601863 TGTACTTTAGTCA -s simRat_chr6.simRat.chr6 399423 11 + 647215 --GTCTCTAATTA - -a -s simMouse_chr6.simMouse.chr6 399465 19 + 636262 TTCACATTGACAGACTAGA -s Anc1.Anc1refChr6 60850 19 + 197743 TTCACGTCCAAAGACTAGG -s mr.mrrefChr5 252634 19 + 294540 TTCACATTCACAGACTAGA -s simHuman_chr6.simHuman.chr6 385212 19 + 601863 TTCACGTCCAAAGACTAGG -s simRat_chr6.simRat.chr6 399434 19 + 647215 TTCACATTCCCAGACTAGA - -a -s simMouse_chr6.simMouse.chr6 399484 3 + 636262 GAT -s Anc0.Anc0refChr3 31110 3 + 222631 GAC -s Anc1.Anc1refChr6 60869 3 + 197743 GAC -s Anc2.Anc2refChr13 34707 3 + 96486 TGC -s mr.mrrefChr5 252653 3 + 294540 GAT -s simCow_chr6.simCow.chr6 391117 3 + 602619 TGC -s simDog_chr6.simDog.chr6 381206 3 + 593897 TGC -s simHuman_chr6.simHuman.chr6 385237 3 + 601863 GAC -s simRat_chr6.simRat.chr6 399453 3 + 647215 GAT - -a -s simMouse_chr6.simMouse.chr6 399487 17 + 636262 CTAATTAGTGAATTCCC -s Anc0.Anc0refChr3 31113 17 + 222631 CTCATTAGTAAATACCC -s Anc1.Anc1refChr6 60872 17 + 197743 CTCATTAGTAAATACCC -s Anc2.Anc2refChr13 34710 17 + 96486 CTCATTAGCAAATACCC -s mr.mrrefChr5 252656 17 + 294540 CTAATTAGTGAATACCC -s simCow_chr6.simCow.chr6 391121 17 + 602619 CCCATAAGGAAATGCCC -s simDog_chr6.simDog.chr6 381209 17 + 593897 ATGATTACCAAATACCC -s simHuman_chr6.simHuman.chr6 385240 14 + 601863 CTCATTAGTAAATA--- -s simRat_chr6.simRat.chr6 399456 17 + 647215 CTAATTAGTGAATACCT - -a -s simMouse_chr6.simMouse.chr6 399504 24 + 636262 ATGGCTCAATGTAATAGAGGAGAA -s Anc0.Anc0refChr3 31130 23 + 222631 ATGGCTCAATGCAATAG-GGAGAA -s Anc1.Anc1refChr6 60889 23 + 197743 ATGGCTCAATGCAATAG-GGAGAA -s Anc2.Anc2refChr13 34728 23 + 96486 ATGGCTCAATGCAATAA-AGAGAA -s mr.mrrefChr5 252673 24 + 294540 ATGGCTCAATGTAATAGAGGAGAA -s simCow_chr6.simCow.chr6 391139 23 + 602619 ATGGATCAATGCAATAA-AGAAAA -s simDog_chr6.simDog.chr6 381227 23 + 593897 ATGGCTCAGTGCAATAA-AGAGAA -s simHuman_chr6.simHuman.chr6 385254 21 + 601863 --GGCTCAATGCAATAG-GGACAA -s simRat_chr6.simRat.chr6 399473 23 + 647215 ATGGCCCA-TGTAATAGAGGAGAA - -a -s simMouse_chr6.simMouse.chr6 399528 16 + 636262 GACAAACTCCATCCAG -s Anc0.Anc0refChr3 31155 16 + 222631 GAAAGACTCCAACCAG -s Anc1.Anc1refChr6 60914 16 + 197743 GAAAGACTCCAACCAG -s Anc2.Anc2refChr13 34753 16 + 96486 GAAAGACTCCAAGCAT -s mr.mrrefChr5 252697 16 + 294540 GACAAACTCCAACCAG -s simCow_chr6.simCow.chr6 391164 14 + 602619 GAAAGACTCCA--CAT -s simDog_chr6.simDog.chr6 381252 16 + 593897 GGAAGACTCGAAGAAT -s simHuman_chr6.simHuman.chr6 385277 16 + 601863 GAAAGACTCCAACCAG -s simRat_chr6.simRat.chr6 399496 16 + 647215 GACAAACTCCAACCGG - -a -s simMouse_chr6.simMouse.chr6 399544 12 + 636262 ACTGTCAAAGAA -s Anc0.Anc0refChr3 31171 12 + 222631 ACTGTCACAGAA -s Anc1.Anc1refChr6 60930 12 + 197743 ACTGTCACAGAA -s Anc2.Anc2refChr13 34769 12 + 96486 ACTGTCACAGAA -s mr.mrrefChr5 252713 12 + 294540 ACTGTCAAAGAA -s simCow_chr6.simCow.chr6 391179 12 + 602619 ACTACCACAGAA -s simDog_chr6.simDog.chr6 381268 12 + 593897 ACTGTCACAGGT -s simHuman_chr6.simHuman.chr6 385293 12 + 601863 ACTGTCACAGAA -s simRat_chr6.simRat.chr6 399512 12 + 647215 ACTGTCAAAGAA - -a -s simMouse_chr6.simMouse.chr6 399556 1 + 636262 A -s Anc0.Anc0refChr3 31183 1 + 222631 T -s Anc1.Anc1refChr6 60942 1 + 197743 T -s Anc2.Anc2refChr13 34781 1 + 96486 T -s mr.mrrefChr5 252725 1 + 294540 T -s simCow_chr6.simCow.chr6 391191 1 + 602619 T -s simDog_chr6.simDog.chr6 381289 1 + 593897 T -s simHuman_chr6.simHuman.chr6 385305 1 + 601863 T -s simRat_chr6.simRat.chr6 399524 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 399557 6 + 636262 ACTGGT -s Anc0.Anc0refChr3 31185 6 + 222631 ACTGGT -s Anc1.Anc1refChr6 60944 6 + 197743 ACTGGT -s Anc2.Anc2refChr13 34783 6 + 96486 ACTGGT -s mr.mrrefChr5 252726 6 + 294540 ACTGGT -s simCow_chr6.simCow.chr6 391193 6 + 602619 ACTGGT -s simDog_chr6.simDog.chr6 381291 6 + 593897 ACTGGT -s simHuman_chr6.simHuman.chr6 385307 6 + 601863 ACTGGT -s simRat_chr6.simRat.chr6 399525 6 + 647215 ACTGGT - -a -s simMouse_chr6.simMouse.chr6 399563 98 + 636262 AGGAAAGACAGCTACACCAATTTGATGGCAGATGTGGCTAACTAAATGAATTCTGCTAGATTATCTGAGAACTTATCAGGTGAGAGTGAGAGATGGCA -s Anc0.Anc0refChr3 31191 77 + 222631 GGGCAAGAAAGCTTCATCATGCATGTGGATGGTGATGCTGT----TGGAAACCTG-----------------TCCCCAGGTTTCAGTGACTGCCAGTA -s Anc1.Anc1refChr6 60950 77 + 197743 GGGCAAGAAAGCTTCATCATGCATGTGGATGGTGATGCTGT----TGGAAACCTG-----------------TCCCCAGGTTTCAGTGACTGCCAGTA -s Anc2.Anc2refChr13 34789 77 + 96486 GCACAAGAAAGTTTCATCATGCATGTGGATAGTGATGCTGT----TGGATACCTG-----------------ACCCCAGGATTCAGTGACTGCCAGTA -s mr.mrrefChr5 252732 94 + 294540 AGGAAAGACAGCTACACCAATTTGATGGCAGGTGTGGCTAA----ATGAATTCTGCTAGATTATCTGAGAACTTATCAGGTGAGAGTGAGAGATGACA -s simCow_chr6.simCow.chr6 391199 77 + 602619 GCACAATAAAGTTTCATCATGCATGTGTGAAATGATACTGT----TGGATACCTG-----------------ACCCCAGGAATAAGTGACTGCCAGTA -s simDog_chr6.simDog.chr6 381297 76 + 593897 GCACAAGAGAG-TTCATCATGCATCTGGATAGCAATGCCAT----TGGATATCTA-----------------ACCCTAGGATTCAGGGACTGCCAGTC -s simHuman_chr6.simHuman.chr6 385318 77 + 601863 GGGCAAGAAAGCCTCATCATGCATGTGGATGGTGATGCTGT----TGGAAACCTG-----------------TCCCCAGGTTCCAGTAACTGCAAGTA -s simRat_chr6.simRat.chr6 399531 94 + 647215 AGGAAAGACAGCTACACCAATTTAATAGCAGGTGTGGCGAA----ATGAATTGTGCTAGATTATCTGAGAACTTATCAGGTGAGAGTGAGAGATGACA - -a -s simMouse_chr6.simMouse.chr6 399661 10 + 636262 GATTGGGTTA -s Anc0.Anc0refChr3 31272 10 + 222631 GATTTAGCCA -s Anc1.Anc1refChr6 61031 10 + 197743 GATTTAGCCA -s Anc2.Anc2refChr13 34870 10 + 96486 GATTTAGCCA -s mr.mrrefChr5 252826 10 + 294540 GATTGGGTTA -s simCow_chr6.simCow.chr6 391280 10 + 602619 GAAGTTGCCA -s simDog_chr6.simDog.chr6 381377 10 + 593897 GATTTAGTCA -s simHuman_chr6.simHuman.chr6 385399 10 + 601863 GAGTTAGCCA -s simRat_chr6.simRat.chr6 399625 10 + 647215 GATTAGGTTA - -a -s simMouse_chr6.simMouse.chr6 399671 104 + 636262 TCTGAGAGGCCCATGTGAGAGACAGCGGCTTGCTAACACATGTTACTGGCAGTTCACAGTCACTGTAGCCTGAGGTTAGAAATCTAATAGGATCGTTCTCTTCA -s Anc0.Anc0refChr3 31282 81 + 222631 TACTTTACA-TAGTGTTCTAATCTGCTGTCTGTTAACTGATGAAACT--------------------TCCT--GGATAGTACACTAACAGAATTAATATCCCCA -s Anc1.Anc1refChr6 61041 81 + 197743 TACTTTACA-TAGTGTTCTAATCTGCTGTCTGTTAACTGATGAAACT--------------------TCCT--GGATAGTACACTAACAGAATTAATATCCCCA -s Anc2.Anc2refChr13 34880 81 + 96486 TACTTTACA-TAGTGTTCTAATCTGCTGTCTGTTAATTGATGAACCT--------------------TCTT--GGATAATACACTAGCAGAATTAATATCCCCA -s mr.mrrefChr5 252836 104 + 294540 TTCGAGAGGCTCATGTGAGAGACAGCTGCTTGCTAACACATGATACTGGCAGTTCACAGTCACTGTAGCCTGAGGTTAGAAATCTAATAGGATCAATCTCCTCA -s simCow_chr6.simCow.chr6 391290 54 + 602619 TG--TTACA-TAGTGTTCTAGTCTGCTGTCTGTTAATTGTTGAACA-----------------------------------------------TAATGTCCCCA -s simDog_chr6.simDog.chr6 381389 75 + 593897 GACTTTACA-TACTGCTCCAATCTGCTGTCT------TGATGAACCT--------------------TCTT--GGATAATACACTAGCAGAATTAATATTCCCA -s simHuman_chr6.simHuman.chr6 385409 81 + 601863 TACTTTATA-TAGTGTTCTAATCTACTGTCTCTTGTCTAATAAAACT--------------------TCCT--GGATAGTACACTAACAGAATTAATTTCCCCA -s simRat_chr6.simRat.chr6 399635 104 + 647215 CTCGAAAGGCTCATGTGAGAGACAGCTGTTTGCTGACACAAGATACTGGCAGGTCACAGTCACTGTAGCCTGGGGTTACAGATCTAATAGGATCAATCTCCTCT - -a -s simMouse_chr6.simMouse.chr6 399775 30 + 636262 TGCAAGTTATTGATACCAACAACAAGAAGG -s Anc0.Anc0refChr3 31387 30 + 222631 TACTAGTTCATGATACAAGGCACCAGAAAG -s Anc1.Anc1refChr6 61146 30 + 197743 TACTAGTTCATGATACAAGGCACCAGAAAG -s Anc2.Anc2refChr13 34985 30 + 96486 TATTAGTTCATGATATAAGGCACCAGAGAG -s mr.mrrefChr5 252940 30 + 294540 TGCAAGTTATTGATACAAACAACAAGAAGG -s simCow_chr6.simCow.chr6 391368 30 + 602619 TATTAGCTCATGATATAAGGCACTGAACAG -s simDog_chr6.simDog.chr6 381488 30 + 593897 TATTAGTCCATGATATAAGAAACCAGAGAG -s simHuman_chr6.simHuman.chr6 385514 30 + 601863 TACCAGATTATGATGCAAGGCTTCAGGAAG -s simRat_chr6.simRat.chr6 399739 30 + 647215 TGCAATTTGTTGATACAACCAACAAGAAGG - -a -s simMouse_chr6.simMouse.chr6 399805 2 + 636262 CC -s Anc0.Anc0refChr3 31419 2 + 222631 CG -s Anc1.Anc1refChr6 61178 2 + 197743 CG -s Anc2.Anc2refChr13 35017 2 + 96486 GG -s mr.mrrefChr5 252970 2 + 294540 CC -s simCow_chr6.simCow.chr6 391400 2 + 602619 GG -s simDog_chr6.simDog.chr6 381520 2 + 593897 GG -s simHuman_chr6.simHuman.chr6 385553 2 + 601863 CA -s simRat_chr6.simRat.chr6 399769 2 + 647215 CC - -a -s simMouse_chr6.simMouse.chr6 399807 29 + 636262 TTCCATTGGATACAAATGATGATGTCAAC -s Anc0.Anc0refChr3 31421 29 + 222631 TTCCATTGGATAGAAATGGTGATGTCAGC -s Anc1.Anc1refChr6 61180 29 + 197743 TTCCATTGGATAGAAATGGTGATGTCAGC -s Anc2.Anc2refChr13 35019 29 + 96486 TTCCATTGGATAAAAATGGTGATGTCAGC -s mr.mrrefChr5 252972 29 + 294540 TTCCATTGGATAGAAATGATGATGTCAAC -s simCow_chr6.simCow.chr6 391403 29 + 602619 CTCCAATGGATAAAAGTGCTGATGTCAGT -s simDog_chr6.simDog.chr6 381522 29 + 593897 TTCCATTGGATAAAAATGGTGAGATCAAC -s simHuman_chr6.simHuman.chr6 385555 29 + 601863 TTCCACTGGATAGAATTGGTGATGTCAGC -s simRat_chr6.simRat.chr6 399771 29 + 647215 TTCCATTAGATAGAAATGATGAGATCAAA - -a -s simMouse_chr6.simMouse.chr6 399836 6 + 636262 ATACAG -s Anc0.Anc0refChr3 31460 6 + 222631 CTACAG -s Anc1.Anc1refChr6 61219 6 + 197743 CTACAG -s Anc2.Anc2refChr13 35058 6 + 96486 CTACAA -s mr.mrrefChr5 253001 6 + 294540 ATACAG -s simCow_chr6.simCow.chr6 391442 6 + 602619 CTACAA -s simDog_chr6.simDog.chr6 381561 6 + 593897 CTAGAA -s simHuman_chr6.simHuman.chr6 385607 6 + 601863 CTACAG -s simRat_chr6.simRat.chr6 399800 6 + 647215 ATACAG - -a -s simMouse_chr6.simMouse.chr6 399842 20 + 636262 ATAAATTTAGACTGGTTCCA -s Anc0.Anc0refChr3 31467 20 + 222631 ATAAATATTGATAGGTCCCA -s Anc1.Anc1refChr6 61226 20 + 197743 ATAAATATTGATAGGTCCCA -s Anc2.Anc2refChr13 35065 20 + 96486 ATAAATATTGATAGGTCCCA -s mr.mrrefChr5 253007 20 + 294540 ATAAATTTAGATTGGTTCCA -s simCow_chr6.simCow.chr6 391449 20 + 602619 ATAAATTTTGATAGGTCCCA -s simDog_chr6.simDog.chr6 381568 20 + 593897 ATAAATATTGATACATCCCA -s simHuman_chr6.simHuman.chr6 385614 20 + 601863 ATAAATCTTGATAGGTCCTA -s simRat_chr6.simRat.chr6 399806 20 + 647215 ATAAATTTAGATTCATTCCA - -a -s simMouse_chr6.simMouse.chr6 399862 18 + 636262 CTTCTAAGCCCAAACAAT -s Anc0.Anc0refChr3 31487 12 + 222631 GTTCTAAGATCA------ -s Anc1.Anc1refChr6 61246 15 + 197743 GTTCTAAGATCAGA---T -s Anc2.Anc2refChr13 35086 12 + 96486 GTTCTAAGATCA------ -s mr.mrrefChr5 253027 15 + 294540 CTTCTAAGCCCAAA---T -s simCow_chr6.simCow.chr6 391470 10 + 602619 --TCTAAGATCA------ -s simDog_chr6.simDog.chr6 381589 12 + 593897 GTTCTAAGATCA------ -s simHuman_chr6.simHuman.chr6 385634 15 + 601863 GCTCTTAGATCAGA---T -s simRat_chr6.simRat.chr6 399826 15 + 647215 CTTCTACGCCCAAA---T - -a -s simMouse_chr6.simMouse.chr6 399880 54 + 636262 CAGTTGCAAGACTTCACCAGTGGCCCTTGCCTATGTCTCACTACCGGGGCCCAC -s Anc0.Anc0refChr3 31507 53 + 222631 C-GGGGCAAGCCTTCACCAATGGCCCCTGTCAAAATCTCAGTACTTGGGTCCAC -s Anc1.Anc1refChr6 61270 54 + 197743 CAGGGGCAAGCCTTCACCAATGGCCCCTGTCAAAATCTCAGTACTTGGGTCCAC -s Anc2.Anc2refChr13 35106 53 + 96486 C-GGGGCAAGCTTACACCAATGACCCCTGACAAAAGCTCAGTACTTGTGCCCAC -s mr.mrrefChr5 253042 54 + 294540 CAGTTGCAAGACTTCACCAGTGGCCCTTGTCTATGTCTCAGTACTGGGGTCCAC -s simCow_chr6.simCow.chr6 391489 52 + 602619 C-TGGGCAATCTTCCAACGA-GACCCCTGAGGAAGGCTCAGGACTTGTGCCTAC -s simDog_chr6.simDog.chr6 381609 53 + 593897 C-GGGGCGAGCTTACACCAATGACCTCTGACAAAAGCTCAATACTTGTGCACAT -s simHuman_chr6.simHuman.chr6 385660 54 + 601863 CAGGGGCAAGCCTTCACCAAGGGCCCCTGTCAAAATTTATGTACTTGGGTCCAC -s simRat_chr6.simRat.chr6 399841 54 + 647215 CAGTTGCAAGACTTGACTGCTAGCACTTGTCTATGTCTCAGTACTGGGGTCCAT - -a -s simMouse_chr6.simMouse.chr6 399934 5 + 636262 GGCTG -s Anc0.Anc0refChr3 31563 5 + 222631 GGCTA -s Anc1.Anc1refChr6 61327 5 + 197743 GGCTA -s Anc2.Anc2refChr13 35162 5 + 96486 GGCTA -s mr.mrrefChr5 253096 5 + 294540 GGCTA -s simCow_chr6.simCow.chr6 391544 5 + 602619 GGCTA -s simDog_chr6.simDog.chr6 381665 5 + 593897 GGCTA -s simHuman_chr6.simHuman.chr6 385717 5 + 601863 GGCTA -s simRat_chr6.simRat.chr6 399895 5 + 647215 GGCCA - -a -s simMouse_chr6.simMouse.chr6 399939 10 + 636262 TCACACTATG -s Anc0.Anc0refChr3 31568 10 + 222631 GCTCACTAGG -s Anc1.Anc1refChr6 61332 10 + 197743 GCTCACTAGG -s Anc2.Anc2refChr13 35167 10 + 96486 GCTCACTAGG -s mr.mrrefChr5 253101 10 + 294540 TCACACTATG -s simCow_chr6.simCow.chr6 391551 10 + 602619 GCTCACTAGA -s simDog_chr6.simDog.chr6 381670 10 + 593897 GCTTACTAGG -s simHuman_chr6.simHuman.chr6 385722 10 + 601863 GCTCACTAGG -s simRat_chr6.simRat.chr6 399900 9 + 647215 TC-CATGACG - -a -s simMouse_chr6.simMouse.chr6 399949 3 + 636262 GAG -s Anc0.Anc0refChr3 31579 3 + 222631 GAG -s Anc1.Anc1refChr6 61343 3 + 197743 GAG -s Anc2.Anc2refChr13 35178 3 + 96486 GGG -s mr.mrrefChr5 253111 3 + 294540 GAG -s simCow_chr6.simCow.chr6 391562 3 + 602619 GGG -s simDog_chr6.simDog.chr6 381681 3 + 593897 AGG -s simHuman_chr6.simHuman.chr6 385733 3 + 601863 GAG -s simRat_chr6.simRat.chr6 399909 3 + 647215 GAG - -a -s simMouse_chr6.simMouse.chr6 399952 14 + 636262 GTTATAGGATCGCG -s Anc0.Anc0refChr3 31582 13 + 222631 GTTATA-GATCTCA -s Anc1.Anc1refChr6 61346 13 + 197743 GTTATA-GATCTCA -s Anc2.Anc2refChr13 35184 13 + 96486 GTCATA-GAACTCA -s mr.mrrefChr5 253114 14 + 294540 GTTATAGGATCTCA -s simCow_chr6.simCow.chr6 391568 13 + 602619 GTGAAA-GGACTCA -s simDog_chr6.simDog.chr6 381687 13 + 593897 GTCATA-GAACTCA -s simHuman_chr6.simHuman.chr6 385736 13 + 601863 GTTAGA-TATCTCA -s simRat_chr6.simRat.chr6 399912 14 + 647215 GTTGTAGGATCTCA - -a -s simMouse_chr6.simMouse.chr6 399966 67 + 636262 ACAAGATAGAGAGCCTTTCTCAATTTAAAGTAGGAGAGCACAAACAACAAACAAAGAGATAACAGTA -s Anc0.Anc0refChr3 31595 67 + 222631 TGGAGACACAGAACCTTTCTCAAATAAATACAGGAGAGCACCGACAACAAATAAAAAAATAACAAGT -s Anc1.Anc1refChr6 61359 67 + 197743 TGGAGACACAGAACCTTTCTCAAATAAATACAGGAGAGCACCGACAACAAATAAAAAAATAACAAGT -s Anc2.Anc2refChr13 35197 67 + 96486 TGGAGACACAGAACCTTTCTCAAATAAATGCCGGAGAGCACCGACAACAAATAAAAGAATGACAAGT -s mr.mrrefChr5 253128 67 + 294540 ACAAGATACAGAACCTTTCTCAATTTAAAATAGGAGAGCACAAACAACAAACAAAGAGATAACAGTA -s simCow_chr6.simCow.chr6 391632 63 + 602619 TGGAGACACAGAACCTTTCTCAAGTA----CTGGAGAGCCCCAACAACAAATAACAGGATGACAAGT -s simDog_chr6.simDog.chr6 381700 65 + 593897 TAAGGGCACAGAACCTTTCTCACATTAATGCCAGAGAGCACTGTCGAC--ATAAAAGAATGACAAGT -s simHuman_chr6.simHuman.chr6 385749 67 + 601863 TGGAGACACAGAACTTTTCCCAAATAAATAAAGGAGAGCACCCACAACAAATTAAAAAATAACAAGT -s simRat_chr6.simRat.chr6 399926 59 + 647215 ACAAGATACGGAACCTTTCTCAATTTAAAATCGGAGAGCGCAAATAATAAACAAAGAG--------A - -a -s simMouse_chr6.simMouse.chr6 400033 19 + 636262 CCTCTCAGATTGGGTGATA -s Anc0.Anc0refChr3 31662 17 + 222631 GCTCTTGGATTGGGTG--A -s Anc1.Anc1refChr6 61426 17 + 197743 GCTCTTGGATTGGGTG--A -s Anc2.Anc2refChr13 35264 17 + 96486 GCTCTTGAATTGAGTG--A -s mr.mrrefChr5 253195 19 + 294540 CCTCTCAGATTGGGTGATA -s simCow_chr6.simCow.chr6 391695 17 + 602619 GCTCTTGAATTACATG--A -s simDog_chr6.simDog.chr6 381765 17 + 593897 GCTCTTGAATTGAGCG--A -s simHuman_chr6.simHuman.chr6 385816 16 + 601863 GCTTTTGGA-TGGATA--A -s simRat_chr6.simRat.chr6 399986 19 + 647215 CCTCTCAGATTGGGTGATG - -a -s simMouse_chr6.simMouse.chr6 400052 36 + 636262 CTGAAGGGTATCAAAACTTTTATCTTGTGAATGCTT -s Anc0.Anc0refChr3 31679 36 + 222631 CCAGAGGGTCTCAAAACCCTTATATTGCGTATGCTG -s Anc1.Anc1refChr6 61443 36 + 197743 CCAGAGGGTCTCAAAACCCTTATATTGCGTATGCTG -s Anc2.Anc2refChr13 35281 36 + 96486 CCAGAGGGTCTCAAGACCCTTATATTGCATATGCTG -s mr.mrrefChr5 253214 36 + 294540 CTGAAGGGTATCAAAACTTTTATCTTGTGAATGCTT -s simCow_chr6.simCow.chr6 391712 32 + 602619 CCCT----CCTCAATACCCTTATGCTGCATATGCTG -s simDog_chr6.simDog.chr6 381782 36 + 593897 CCAGAGGGTCCCAAGACCCTTATATTGCATATGCTG -s simHuman_chr6.simHuman.chr6 385832 36 + 601863 CCACAGGGTTTCAAAACCCATGTTTTGCGTATGGTG -s simRat_chr6.simRat.chr6 400018 36 + 647215 CTGAAGGGTCTCAAGACTTTTATCTTGTGAATGCTT - -a -s simMouse_chr6.simMouse.chr6 400088 7 + 636262 ATAAATT -s Anc0.Anc0refChr3 31715 7 + 222631 ATATATT -s Anc1.Anc1refChr6 61479 7 + 197743 ATATATT -s Anc2.Anc2refChr13 35317 7 + 96486 ATATGTT -s mr.mrrefChr5 253250 7 + 294540 ATAAATT -s simCow_chr6.simCow.chr6 391744 7 + 602619 ATATGTT -s simDog_chr6.simDog.chr6 381819 7 + 593897 ATATGCT -s simHuman_chr6.simHuman.chr6 385868 6 + 601863 ATCTAT- -s simRat_chr6.simRat.chr6 400054 7 + 647215 ATAAATT - -a -s simMouse_chr6.simMouse.chr6 400095 70 + 636262 TGTTTTTATTGTTACACTCTCTTTAGTTTTTTTCACACTAAGTCCAGGAAAACCATAGCTGTGTTTTCTA -s Anc0.Anc0refChr3 31722 10 + 222631 TGTGCTTA------------------------------------------------------------CA -s Anc1.Anc1refChr6 61486 10 + 197743 TGTGCTTA------------------------------------------------------------CA -s Anc2.Anc2refChr13 35395 10 + 96486 TGTGCTTA------------------------------------------------------------CA -s mr.mrrefChr5 253257 10 + 294540 TGTTTTTA------------------------------------------------------------TA -s simCow_chr6.simCow.chr6 391896 10 + 602619 TGTGCGTT------------------------------------------------------------AA -s simDog_chr6.simDog.chr6 381901 10 + 593897 TGTGCTTA------------------------------------------------------------CA -s simRat_chr6.simRat.chr6 400061 10 + 647215 TGTTTTAA------------------------------------------------------------TA - -a -s simMouse_chr6.simMouse.chr6 400165 13 + 636262 AGATAGAACACAA -s Anc0.Anc0refChr3 31732 13 + 222631 AGTGAAAATGAAC -s Anc1.Anc1refChr6 61496 13 + 197743 AGTGAAAATGAAC -s Anc2.Anc2refChr13 35408 13 + 96486 AGTGAAAATGAAC -s mr.mrrefChr5 253267 13 + 294540 AGATAGAACACAA -s simCow_chr6.simCow.chr6 391909 13 + 602619 AATGAAAATAAAC -s simDog_chr6.simDog.chr6 381914 13 + 593897 AGTGAAAATGAAC -s simRat_chr6.simRat.chr6 400071 13 + 647215 AGATAAAAGTGAA - -a -s simMouse_chr6.simMouse.chr6 400178 23 + 636262 ATTCCATTTCCATCTTGAGTCAT -s Anc0.Anc0refChr3 31745 21 + 222631 ATACCATTTCCATGTTGAGTC-- -s Anc1.Anc1refChr6 61509 21 + 197743 ATACCATTTCCATGTTGAGTC-- -s Anc2.Anc2refChr13 35421 21 + 96486 ATACCATTTCCATGTTGAGTC-- -s mr.mrrefChr5 253280 23 + 294540 ATTCCATTTCCATCTTGAGTCAT -s simCow_chr6.simCow.chr6 391922 21 + 602619 ATACCATTTTCATGTGGAGTC-- -s simDog_chr6.simDog.chr6 381927 21 + 593897 ATACCATTTCCATGTTGAGTC-- -s simRat_chr6.simRat.chr6 400085 23 + 647215 ATCCCATTTCCATCTTGAGTCAT - -a -s simMouse_chr6.simMouse.chr6 400201 11 + 636262 AAATCCCAGGT -s Anc0.Anc0refChr3 31766 7 + 222631 CAATCTC---- -s Anc1.Anc1refChr6 61530 7 + 197743 CAATCTC---- -s Anc2.Anc2refChr13 35442 7 + 96486 CAATCTC---- -s mr.mrrefChr5 253303 7 + 294540 AAATCCC---- -s simCow_chr6.simCow.chr6 391945 7 + 602619 AAACCTT---- -s simDog_chr6.simDog.chr6 381948 7 + 593897 CAATCTC---- -s simRat_chr6.simRat.chr6 400108 7 + 647215 AAATATC---- - -a -s simMouse_chr6.simMouse.chr6 400212 29 + 636262 GGGCTCTGTTACCTAGACAGAAACTGGGG -s Anc0.Anc0refChr3 31773 29 + 222631 GGGCTCCAATACATGGCCTGAAACTCAGG -s Anc1.Anc1refChr6 61537 29 + 197743 GGGCTCCAATACATGGCCTGAAACTCAGG -s Anc2.Anc2refChr13 35453 29 + 96486 GGGCTCCAATACATGGCCTGAAACTCAGG -s mr.mrrefChr5 253310 29 + 294540 GGGCTCTGTTACCTAGACAGAAACTGGGG -s simCow_chr6.simCow.chr6 391956 29 + 602619 GGGCACCATTACTGAGCCTGAAAATGGGA -s simDog_chr6.simDog.chr6 381959 29 + 593897 GGGCTCCAATACATGGCCTGAAACTCAGG -s simRat_chr6.simRat.chr6 400115 29 + 647215 GGGCTCCACTACCTTGTCAGAAACTGGGA - -a -s simMouse_chr6.simMouse.chr6 400241 26 + 636262 TCTAGTTCTGGCTTAGGGGGGGTGCA -s Anc0.Anc0refChr3 31802 19 + 222631 TCTAGTACCGACTCAGAGT------- -s Anc1.Anc1refChr6 61566 19 + 197743 TCTAGTACCGACTCAGAGT------- -s Anc2.Anc2refChr13 35482 19 + 96486 TCTAGTACCGACTCAGAGT------- -s mr.mrrefChr5 253339 26 + 294540 TCTAGTTCTGGCTTAGGGGGGGTGCA -s simCow_chr6.simCow.chr6 391986 19 + 602619 TCAACTATTGACTCAAGGT------- -s simDog_chr6.simDog.chr6 381988 19 + 593897 TCTAGTACCGACTCAGAGT------- -s simRat_chr6.simRat.chr6 400144 26 + 647215 TCAAGTTCTGGCTTAGGGTGGATGCA - -a -s simMouse_chr6.simMouse.chr6 400267 45 + 636262 CCCAGGCAAAATCTATAGTGGTGCATTATCAGTCAGCGAGAAAAT -s Anc0.Anc0refChr3 31821 37 + 222631 CCCAGCAAAGATCTAT--------GTTATCAATTGGGGATGAAAT -s Anc1.Anc1refChr6 61585 45 + 197743 CCCAGCAAAGATCTATATTGGTATGTTATCAATTGGGGATGAAAT -s Anc2.Anc2refChr13 35501 37 + 96486 CCCAGCAAAGATCTAT--------GTTATCAATTGTGGATGAAAT -s mr.mrrefChr5 253365 45 + 294540 CCCAGGCAAAATCTATAGTGGTGCATTATCAGTCAGCGAGAAAAT -s simCow_chr6.simCow.chr6 392012 37 + 602619 CCCAGCAGAGATCTAC--------GTTATCAATTGAAGAGAAACT -s simDog_chr6.simDog.chr6 382007 37 + 593897 CCCAGCAAAGATCTAT--------GTTGTCCATTATGCCTGAAAC -s simHuman_chr6.simHuman.chr6 385874 44 + 601863 -ACAGCAAGGATTTATATTGGTATGTTATCAATTGGGGAAGAAAT -s simRat_chr6.simRat.chr6 400170 45 + 647215 CCCAGGCGAAATCTATAGTGGTGCATTACCAGTCAGAGAGAAAAT - -a -s simMouse_chr6.simMouse.chr6 400312 5 + 636262 GAACA -s Anc0.Anc0refChr3 31858 5 + 222631 AAAAA -s Anc1.Anc1refChr6 61630 5 + 197743 AAAAA -s Anc2.Anc2refChr13 35538 5 + 96486 AAAAA -s mr.mrrefChr5 253410 5 + 294540 GAACA -s simCow_chr6.simCow.chr6 392049 5 + 602619 GAAAA -s simDog_chr6.simDog.chr6 382092 5 + 593897 AAATA -s simHuman_chr6.simHuman.chr6 385918 5 + 601863 AAAAA -s simRat_chr6.simRat.chr6 400215 5 + 647215 GAACA - -a -s simMouse_chr6.simMouse.chr6 400317 45 + 636262 CAGATCATGGAGTAATTGTGCTGCATAACAGGGACAGGGGATACA -s Anc0.Anc0refChr3 31866 38 + 222631 CAGGCCGGGGAGAGTTCTTGCTGCATAACAGGGAC-------ATA -s Anc1.Anc1refChr6 61638 38 + 197743 CAGGCCGGGGAGAGTTCTTGCTGCATAACAGGGAC-------ATA -s Anc2.Anc2refChr13 35546 38 + 96486 CAGGCTGAGGAGAGTTCTTGCTGCATAACAGGGAC-------ATA -s mr.mrrefChr5 253415 45 + 294540 CAGACCAGGGAGTAATTGTGCTGCATAACAGGGACAGGGGATACA -s simCow_chr6.simCow.chr6 392056 36 + 602619 --GGCTGAGGACAGTTTTTGATGCATAGCAGGGAC-------CAA -s simDog_chr6.simDog.chr6 382100 36 + 593897 CAGG--GAGGAGAGTTCTTGCTGGATAACAGTCAT-------ATA -s simHuman_chr6.simHuman.chr6 385926 36 + 601863 CAGGCCGGGCAGAGTTCATG--GCATAACAGGGAC-------ATA -s simRat_chr6.simRat.chr6 400220 45 + 647215 CAGACCAGGGAGCAATTGTGCTACATAACAGGGATAGGGGATACA - -a -s simMouse_chr6.simMouse.chr6 400362 25 + 636262 TCTCTGAATGCATACTTCCGACCTA -s Anc0.Anc0refChr3 31904 25 + 222631 TCTCTTACAGCATACTCTCTAGCTG -s Anc1.Anc1refChr6 61676 25 + 197743 TCTCTTACAGCATACTCTCTAGCTG -s Anc2.Anc2refChr13 35584 25 + 96486 TCCCTTACAGCATACCCTCTAGCTG -s mr.mrrefChr5 253460 25 + 294540 TCTCTGAATGCATACTTCCGACCTA -s simCow_chr6.simCow.chr6 392092 25 + 602619 TCACTTACAGCATACCCTCTAATTG -s simDog_chr6.simDog.chr6 382141 24 + 593897 TCCCCTACAGTATGCCCTCTAGCT- -s simHuman_chr6.simHuman.chr6 385962 25 + 601863 TCTCTTGCACCATACTCTCTAGCTT -s simRat_chr6.simRat.chr6 400265 25 + 647215 TCTCAGAATGCATACTTCCAAACTA - -a -s simMouse_chr6.simMouse.chr6 400387 12 + 636262 AAAGAAGGTGGG -s Anc0.Anc0refChr3 31934 12 + 222631 AGGGGAGGTGGA -s Anc1.Anc1refChr6 61706 12 + 197743 AGGGGAGGTGGA -s Anc2.Anc2refChr13 35614 12 + 96486 AGGTGAGGTGGA -s mr.mrrefChr5 253485 12 + 294540 AAAGGAGGTGGG -s simCow_chr6.simCow.chr6 392122 12 + 602619 AGGTGAGATGGA -s simDog_chr6.simDog.chr6 382167 12 + 593897 AAGTGAGGTGGA -s simHuman_chr6.simHuman.chr6 385992 12 + 601863 AGGGGAGGTGGA -s simRat_chr6.simRat.chr6 400290 12 + 647215 AAAGGAGGTGGG - -a -s simMouse_chr6.simMouse.chr6 400399 13 + 636262 GGATGCTAGTTCA -s Anc0.Anc0refChr3 31956 13 + 222631 GAATTCTAGTCCA -s Anc1.Anc1refChr6 61728 13 + 197743 GAATTCTAGTCCA -s Anc2.Anc2refChr13 35636 13 + 96486 GAATTCTCATCCA -s mr.mrrefChr5 253497 13 + 294540 GGATGCTAGTCCA -s simCow_chr6.simCow.chr6 392144 13 + 602619 GAATTCACATCCA -s simDog_chr6.simDog.chr6 382189 10 + 593897 ACATTCTCAT--- -s simHuman_chr6.simHuman.chr6 386014 13 + 601863 GAATTCTAGTCCA -s simRat_chr6.simRat.chr6 400302 13 + 647215 GGATGCTAGTCCA - -a -s simMouse_chr6.simMouse.chr6 400412 60 + 636262 CAGAAGCTGCCAACCCCCAACCCCCTAGGGGAAAAGCCCTGATAATATGATACAGGACAC -s Anc0.Anc0refChr3 31970 52 + 222631 CAAAAACTG-------TCAACCC-CTAGAGGAAAAGCCTTGAACATCTGATGCAGGACAT -s Anc1.Anc1refChr6 61742 53 + 197743 CAAAAACTG-------TCAACCCACTAGAGGAAAAGCCTTGAACATCTGATGCAGGACAT -s Anc2.Anc2refChr13 35650 52 + 96486 CCAAAACTG-------TGAACCC-CTAGAGCAACAGCCTTGAACATCTGATGCAGGACAT -s mr.mrrefChr5 253510 60 + 294540 CAGAAGCTGCCAACCCCCAACCCCCTAGGGGAAAAGCCCTGATAATATGATACAGGACAC -s simCow_chr6.simCow.chr6 392158 31 + 602619 CCAAAACTG-------TGAACCC----------------------CCTGAAGCAAAGCTT -s simDog_chr6.simDog.chr6 382199 36 + 593897 ------------------------CTAGAGCAACAGCCTTGAACATCTGATACAGGACAT -s simHuman_chr6.simHuman.chr6 386028 53 + 601863 CAAAATCTG-------TCAACCCACTAAAGGAAAAGCTGTTAATATCTGGTGCAGGACAT -s simRat_chr6.simRat.chr6 400315 60 + 647215 CTGAAGCTGCCAACCCCCCATCCCTTAGGGTAACAGCCTTGATCATATGATACAGGACAC - -a -s simMouse_chr6.simMouse.chr6 400472 5 + 636262 TATCA -s Anc0.Anc0refChr3 32022 5 + 222631 CAGAA -s Anc1.Anc1refChr6 61795 5 + 197743 CAGAA -s Anc2.Anc2refChr13 35702 5 + 96486 CAGAA -s mr.mrrefChr5 253570 5 + 294540 TAGCA -s simCow_chr6.simCow.chr6 392207 5 + 602619 CAGAA -s simDog_chr6.simDog.chr6 382235 5 + 593897 AAGAC -s simHuman_chr6.simHuman.chr6 386081 5 + 601863 CAGGA -s simRat_chr6.simRat.chr6 400375 5 + 647215 TAGTA - -a -s simMouse_chr6.simMouse.chr6 400477 20 + 636262 GATAGAGAGAGGATTCTTTA -s Anc0.Anc0refChr3 32027 20 + 222631 CTTGAATGTATAATACAGTA -s Anc1.Anc1refChr6 61800 20 + 197743 CTTGAATGTATAATACAGTA -s Anc2.Anc2refChr13 35707 20 + 96486 CTTGAATGTACAATACAGTA -s mr.mrrefChr5 253575 20 + 294540 GATGGAGAGATGATTCTTTA -s simCow_chr6.simCow.chr6 392212 14 + 602619 CTTGAGGGAACAAT------ -s simDog_chr6.simDog.chr6 382240 20 + 593897 CTTGAATGTACCTGACAGTA -s simHuman_chr6.simHuman.chr6 386086 20 + 601863 CTTGAACCTATAATACAGTA -s simRat_chr6.simRat.chr6 400387 20 + 647215 GATGGAGAGATGATTCCTTA - -a -s simMouse_chr6.simMouse.chr6 400497 4 + 636262 AGGC -s Anc0.Anc0refChr3 32048 4 + 222631 ATCA -s Anc1.Anc1refChr6 61821 4 + 197743 ATCA -s Anc2.Anc2refChr13 35728 4 + 96486 ATCA -s mr.mrrefChr5 253596 4 + 294540 AGGC -s simCow_chr6.simCow.chr6 392226 4 + 602619 ATTG -s simDog_chr6.simDog.chr6 382261 4 + 593897 ATCA -s simHuman_chr6.simHuman.chr6 386107 4 + 601863 ATCA -s simRat_chr6.simRat.chr6 400408 4 + 647215 AGGC - -a -s simMouse_chr6.simMouse.chr6 400501 39 + 636262 CCACACAATGTGTCTTTTCTGGGGACAGAAGACAGTTGA -s Anc0.Anc0refChr3 32052 30 + 222631 ATGGAAAGAGATTCTCTTC---------ATCACACTTCA -s Anc1.Anc1refChr6 61825 30 + 197743 ATGGAAAGAGATTCTCTTC---------ATCACACTTCA -s Anc2.Anc2refChr13 35734 30 + 96486 ACGGAAAGAGATCCTCTTC---------AACACACTTCA -s mr.mrrefChr5 253600 39 + 294540 CTACACAAAGTGTCTTTTCTGGGGACAGATCACAGTTCA -s simCow_chr6.simCow.chr6 392232 30 + 602619 ACGGAAAGAGATCCTCCTG---------AACACATTTCA -s simDog_chr6.simDog.chr6 382267 30 + 593897 ACAGGAAGGGGTCCTCTTC---------AACACACTTCA -s simHuman_chr6.simHuman.chr6 386111 30 + 601863 ATGGAGAGAGATTCTCTTC---------ATCACAATTCA -s simRat_chr6.simRat.chr6 400412 39 + 647215 CTACACAAAGTGTCATTTCGGGGAACGCATCACAGTTCA - -a -s simMouse_chr6.simMouse.chr6 400540 68 + 636262 TTCAACAGGCTAAGGATATGTGTATGTTGACAGTGTAATTCAGCTGTACAATGATTGTTATTAGATTA -s Anc0.Anc0refChr3 32082 48 + 222631 T---------TGAGGCCTTACTTGA--GGATTGTG---------TGTATGACTAATGTTATTAGATTA -s Anc1.Anc1refChr6 61855 48 + 197743 T---------TGAGGCCTTACTTGA--GGATTGTG---------TGTATGACTAATGTTATTAGATTA -s Anc2.Anc2refChr13 35769 48 + 96486 T---------GGAGGCCTAACTTGA--GATTTGTG---------TATGTGTCTAAGGTTATTGTATTA -s mr.mrrefChr5 253639 66 + 294540 TTCAACAGCCTAAGGATATGTGTAT--TGACAGTGTATTTCAGCTGTATAATGATTGTTATTAGATTA -s simCow_chr6.simCow.chr6 392267 32 + 602619 T---------AGAGGCCTAATTTGA--GATTAGTG---------GAGGACGC---------------- -s simDog_chr6.simDog.chr6 382302 48 + 593897 T---------GGAGACCTAACTTGA--GATTTATG---------TATGTGTATAAGGTTATTGTATTA -s simHuman_chr6.simHuman.chr6 386141 48 + 601863 T---------TGAGGCCTTACTTCC--AGATTGTG---------TGCATGACTAATGTTATTAGATCA -s simRat_chr6.simRat.chr6 400451 66 + 647215 TTCAACAGCCTAAGGATATGTGGAT--TGACAGTGTATTTCAGCCGTATAATGATTGTCATTAGATTA - -a -s simMouse_chr6.simMouse.chr6 400608 6 + 636262 ATGAGG -s Anc0.Anc0refChr3 32131 6 + 222631 ATGAGA -s Anc1.Anc1refChr6 61904 6 + 197743 ATGAGA -s Anc2.Anc2refChr13 35818 6 + 96486 ACTATT -s mr.mrrefChr5 253705 6 + 294540 ATGAGA -s simDog_chr6.simDog.chr6 382351 6 + 593897 ACTATT -s simHuman_chr6.simHuman.chr6 386190 6 + 601863 ATGAGA -s simRat_chr6.simRat.chr6 400517 6 + 647215 ATGGGA - -a -s simMouse_chr6.simMouse.chr6 400614 25 + 636262 ATCAAGGTATTAAATTTGATGCAAA -s Anc0.Anc0refChr3 32143 25 + 222631 ATCAAGGTCTGAAAATTGATGAAAA -s Anc1.Anc1refChr6 61916 25 + 197743 ATCAAGGTCTGAAAATTGATGAAAA -s Anc2.Anc2refChr13 35830 25 + 96486 ATCTAAGCCTGAAAATTGATGAAAA -s mr.mrrefChr5 253711 25 + 294540 ATCAAGGTATTAAATTTGATGCAAA -s simCow_chr6.simCow.chr6 392299 21 + 602619 --CCTAACCCGGAAATTGATT--CA -s simDog_chr6.simDog.chr6 382363 25 + 593897 ATCTAAGCGTGAAAGTTGGTGAAAA -s simHuman_chr6.simHuman.chr6 386202 25 + 601863 ATTAAGGTCTGAAGATTGAAGAAAA -s simRat_chr6.simRat.chr6 400523 25 + 647215 GTCTAGGTATTGAACTTGATGCAAA - -a -s simMouse_chr6.simMouse.chr6 400639 9 + 636262 GTGAGACAT -s Anc0.Anc0refChr3 32171 8 + 222631 GA-ATGCAT -s Anc1.Anc1refChr6 61944 8 + 197743 GA-ATGCAT -s Anc2.Anc2refChr13 35858 8 + 96486 AA-ATGCAT -s mr.mrrefChr5 253736 8 + 294540 GC-ATACAT -s simCow_chr6.simCow.chr6 392323 6 + 602619 AT-ATGC-- -s simDog_chr6.simDog.chr6 382391 8 + 593897 AA-GTGCAT -s simHuman_chr6.simHuman.chr6 386230 8 + 601863 GA-ATGCAT -s simRat_chr6.simRat.chr6 400548 8 + 647215 GC-ATAGTT - -a -s simMouse_chr6.simMouse.chr6 400648 53 + 636262 TGACTCATGGTAGTCAttgcttggtgtacatattctaaagttaatgactgact -s Anc0.Anc0refChr3 32186 12 + 222631 GGATTCATgatg----------------------------------------- -s Anc1.Anc1refChr6 61959 53 + 197743 GGATTCATgatggcctttggttggtgtatcggtcctaaagttattcgctgacc -s Anc2.Anc2refChr13 35873 12 + 96486 GGATTCATGGTG----------------------------------------- -s mr.mrrefChr5 253744 53 + 294540 TGACTCATGGTAGTCAttgcttggtgtacatatcctaaagttaatgactgact -s simCow_chr6.simCow.chr6 392329 9 + 602619 ---TCCATGGTG----------------------------------------- -s simDog_chr6.simDog.chr6 382406 12 + 593897 GGATTCATGGTA----------------------------------------- -s simHuman_chr6.simHuman.chr6 386245 53 + 601863 GGATTCATgatggcctttggttggtgtatcggtcctaaagttattcgctgacc -s simRat_chr6.simRat.chr6 400556 52 + 647215 TGACTCAGGGTAGTCAttgtttggtgtacatatcctaaagtta-tgactgact - -a -s simMouse_chr6.simMouse.chr6 400701 105 + 636262 gccgtcttgacttgaaggttttcaggatggggcccttcaaaacggggcccttcgaaacttcttcctcatacctatgctcacactttttgttagcccctcaagtgg -s Anc1.Anc1refChr6 62012 90 + 197743 gcactcgcaggctgaatgtcttgaagctgtgacccctt---------------aaggcgtatttcaaatacatatcttaaagttatttgcaaaccccccaggaaa -s mr.mrrefChr5 253797 90 + 294540 gccgtcatgacctgaatgttttgaggatggggcccttc---------------aaagcttctttcacatacatatgctcacattttttgttaacccctcaagtag -s simHuman_chr6.simHuman.chr6 386303 90 + 601863 gcactcgcaggctgaatgtcttgaagctgtgacccctt---------------aaggcgtatttcaaatacatatcttaaagttatttgcaaaccccccaggaaa -s simRat_chr6.simRat.chr6 400608 90 + 647215 gtcatcaagacctgaatgttttgaggatggggcccttc---------------aaagcttctttcatgtacatatgctcacattttttgttaacccctcaagtag - -a -s simMouse_chr6.simMouse.chr6 400806 45 + 636262 ttgaagttgcacctttgtaaccaaactagggtaattatatgcaat -s Anc1.Anc1refChr6 62102 45 + 197743 ctgaagtcgcaccctcataaccgatctggtagagttatacaggat -s mr.mrrefChr5 253887 45 + 294540 ttgaagttgcacctttgtaaccaaactagggtagttatatgcaat -s simHuman_chr6.simHuman.chr6 386394 45 + 601863 ctgaagtcgcaccctcataaccgatctggtagagttatacaggat -s simRat_chr6.simRat.chr6 400698 45 + 647215 ttgaagttgcacctttgtaaccatactagggtagttatatgcagt - -a -s simMouse_chr6.simMouse.chr6 400851 125 + 636262 ccaCTGAAAGAGAACAATGACGTGTGTTTGCCAGCCTGCTAAGTGGAATGGGCCAAGGTTGTGAATAGGATTAAGAGAAATATGTGCAAAGAACACTAAAAAAGGTACAAAGAACAAAGAAACAT -s Anc0.Anc0refChr3 32198 90 + 222631 ----------------------------------CCTGCCTAATGGAATGG-CCGAGGATATGAACAGGATTCAGGGAAATATGTGCAAAGAACATAAAAGACAACACACATTACAAAGAAGCAT -s Anc1.Anc1refChr6 62147 125 + 197743 ccactgaactagaagagtgatatggaattGCCaGCCTGCCTAATGGAATGGACCGAGGATATGAACAGGATTCAGGGAAATATGTGCAAAGAACATAAAAGACAACACACATTACAAAGAAGCAT -s Anc2.Anc2refChr13 35885 90 + 96486 ----------------------------------CCTGCCTAAAGGAATGG-CCGAGGATATAAACAGGATTCAGGGAAATATGTGTACAGAACATAAAAGACAGCACACATTGCAAAGAAGCAT -s mr.mrrefChr5 253932 125 + 294540 ccactgaaagagaacaatgacatggGTTtGCCAGCCTGCTAAGTGGAATGGGCCAAGGTTATGAATAGGATTCAGAGAAATATGTGCAAAGAACACTAAAAAAGATACAAAGAACAAAGAAACAT -s simCow_chr6.simCow.chr6 392338 90 + 602619 ----------------------------------CTTGTGTTAGGGAATAG-CCAAGGATACTAACAGGACTCAGAGACATATGTGAACAGAACACGAAAGAAAGCACACGGAGCAAAGAGATAT -s simDog_chr6.simDog.chr6 382418 87 + 593897 ----------------------------------CCTACCTAAAAGAATGG-CTGAGGATATAAACAGGATTCAGGGCAGTATCTGTACAGAACATAAAAGACAGTACACATTGCAA---AGCCT -s simHuman_chr6.simHuman.chr6 386442 125 + 601863 ccactgaactagaagagtgatatggaatctccagcctGCCTACTGGAATGGACCTAGGATATGAACAGGATTCAGGGAGATATGTTCAAAGGAGATAAATGAGAACACACAACACAAAATAGCAT -s simRat_chr6.simRat.chr6 400743 124 + 647215 ccactgaatgagaacaataacatggGTT-GCCTGCCTCTTAAGTGGAGTGGGCCAATGTTATGAATAGGATTCAAAGAATTATGGGCAAAGAATACTAAAAAAGATACAAAGAACGATGAAACAT - -a -s simMouse_chr6.simMouse.chr6 400976 19 + 636262 ATGCTGTGCTTCCTAATAA -s Anc0.Anc0refChr3 32293 19 + 222631 ATGCAGTGCTGTCTCATGA -s Anc1.Anc1refChr6 62277 19 + 197743 ATGCAGTGCTGTCTCATGA -s Anc2.Anc2refChr13 35980 19 + 96486 GTACAGTGCTGTCACATGA -s mr.mrrefChr5 254057 19 + 294540 ATGCTGTGCTTCCTAATAA -s simCow_chr6.simCow.chr6 392433 19 + 602619 GTACAGTGCTGTCACATGA -s simHuman_chr6.simHuman.chr6 386572 19 + 601863 ATGTGCTGCTCACTCATGA -s simRat_chr6.simRat.chr6 400867 19 + 647215 ATGCTGTGCCTTCTAATAA - -a -s simMouse_chr6.simMouse.chr6 400995 34 + 636262 GCACCTTTGCTCCAGTACAGATGTTTGTGATAGC -s Anc0.Anc0refChr3 32312 33 + 222631 G-ACCTTGTGTCTAGTACCAATATTTGTTCAAGC -s Anc1.Anc1refChr6 62296 33 + 197743 G-ACCTTGTGTCTAGTACCAATATTTGTTCAAGC -s Anc2.Anc2refChr13 35999 33 + 96486 T-ATCTTGTGTCTAGTATCAGTATTTGTTCAGAC -s mr.mrrefChr5 254076 34 + 294540 GCACCTTGGCTCCAGTACAGATATTTGTGATAGC -s simCow_chr6.simCow.chr6 392453 33 + 602619 T-ATCTTGTGTCTAGTATCAGTATTAATTCAGAC -s simDog_chr6.simDog.chr6 382505 29 + 593897 ----CTTGTGTC-GGTATCAGTATCTGTTCAGAC -s simHuman_chr6.simHuman.chr6 386591 33 + 601863 G-ACCTTGTTTCAAGTACCAATATTTGTCTAAGT -s simRat_chr6.simRat.chr6 400886 34 + 647215 GCACTTTGGCTCCAGTACAGGTATTTGTGATAGC - -a -s simMouse_chr6.simMouse.chr6 401029 25 + 636262 TGTGAGGTGGAAATATCATGATATG -s Anc0.Anc0refChr3 32346 25 + 222631 CCTAAGTCGGACATATTATCACATG -s Anc1.Anc1refChr6 62330 25 + 197743 CCTAAGTCGGACATATTATCACATG -s Anc2.Anc2refChr13 36033 25 + 96486 CCTAAGTCAGACATATTATCACATG -s mr.mrrefChr5 254110 25 + 294540 TGTGAGGTGGAAATATCATCATATG -s simCow_chr6.simCow.chr6 392487 25 + 602619 GCTAACTCAGACATATTATCACATG -s simDog_chr6.simDog.chr6 382535 25 + 593897 CTGAAGTCAGACACATTAGCACCTG -s simHuman_chr6.simHuman.chr6 386625 25 + 601863 CCTAAGCCGGAGATATTATCCCATG -s simRat_chr6.simRat.chr6 400920 25 + 647215 TGTGAGGTGGGAATATCATCATATG - -a -s simMouse_chr6.simMouse.chr6 401054 4 + 636262 TCTG -s Anc0.Anc0refChr3 32374 4 + 222631 TCTG -s Anc1.Anc1refChr6 62358 4 + 197743 TCTG -s Anc2.Anc2refChr13 36061 4 + 96486 TCTC -s mr.mrrefChr5 254135 4 + 294540 TCTG -s simCow_chr6.simCow.chr6 392512 4 + 602619 TCTC -s simDog_chr6.simDog.chr6 382566 4 + 593897 GCTC -s simHuman_chr6.simHuman.chr6 386653 4 + 601863 TCTG -s simRat_chr6.simRat.chr6 400945 4 + 647215 TCTG - -a -s simMouse_chr6.simMouse.chr6 401058 1 + 636262 A -s Anc0.Anc0refChr3 32380 1 + 222631 A -s Anc1.Anc1refChr6 62364 1 + 197743 A -s Anc2.Anc2refChr13 36067 1 + 96486 T -s mr.mrrefChr5 254139 1 + 294540 A -s simCow_chr6.simCow.chr6 392518 1 + 602619 T -s simDog_chr6.simDog.chr6 382572 1 + 593897 T -s simHuman_chr6.simHuman.chr6 386659 1 + 601863 A -s simRat_chr6.simRat.chr6 400949 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 401059 22 + 636262 GACTTTAGTAAGTAGTGAGCTC -s Anc0.Anc0refChr3 32381 21 + 222631 GTTTTGAG-AAAGGGTGAACTT -s Anc1.Anc1refChr6 62365 22 + 197743 GTTTTGAGCAAAGGGTGAACTT -s Anc2.Anc2refChr13 36068 21 + 96486 GTTTTGAG-AAAGGGTGAACTT -s mr.mrrefChr5 254140 22 + 294540 GACTTTAGTAAGTGGTGAGCTT -s simCow_chr6.simCow.chr6 392519 21 + 602619 AGTTTGAG-AAAGGGTAAACTT -s simDog_chr6.simDog.chr6 382574 21 + 593897 GTTTTGAG-AAAGCCTGAACTT -s simHuman_chr6.simHuman.chr6 386660 22 + 601863 GTTTTGAGCAAAGGGTGAACTT -s simRat_chr6.simRat.chr6 400950 22 + 647215 GACTTAAGTAAGTGGTGAGCTT - -a -s simMouse_chr6.simMouse.chr6 401081 20 + 636262 GTTCTGGTAAGGGGAAAAAA -s Anc0.Anc0refChr3 32425 20 + 222631 TTTCTGGTAAAGGGAAAAAA -s Anc1.Anc1refChr6 62410 20 + 197743 TTTCTGGTAAAGGGAAAAAA -s Anc2.Anc2refChr13 36112 20 + 96486 TTTCTGGTACAGTGAAAAAA -s mr.mrrefChr5 254162 20 + 294540 GTTCTGGTAAGGGGAAAAAA -s simCow_chr6.simCow.chr6 392563 18 + 602619 TTTCTGGTACAAAGTAAA-- -s simDog_chr6.simDog.chr6 382618 20 + 593897 TTTCTGGTACAGTGACAAAA -s simHuman_chr6.simHuman.chr6 386705 20 + 601863 TTTCTGGTAAAGGGAATGAA -s simRat_chr6.simRat.chr6 400972 20 + 647215 GTTCTGGTAAGGGGAAAAAA - -a -s simMouse_chr6.simMouse.chr6 401101 5 + 636262 GTTGG -s Anc0.Anc0refChr3 32445 5 + 222631 GTTAG -s Anc1.Anc1refChr6 62430 5 + 197743 GTTAG -s Anc2.Anc2refChr13 36132 5 + 96486 GTTAG -s mr.mrrefChr5 254182 5 + 294540 GTTGG -s simCow_chr6.simCow.chr6 392581 3 + 602619 --CAG -s simDog_chr6.simDog.chr6 382638 5 + 593897 GTTAG -s simHuman_chr6.simHuman.chr6 386725 5 + 601863 TTTAA -s simRat_chr6.simRat.chr6 400993 5 + 647215 GTTGG - -a -s simMouse_chr6.simMouse.chr6 401106 57 + 636262 AATAAATTAGCCAACCAAGATAATCAAGAAACACTAAGGGAGTTTGATTACATTATC -s Anc0.Anc0refChr3 32450 47 + 222631 T------TTGCTAACCAATACAATTGGAATGCACTAGAGGTGTCTGAC----CTATT -s Anc1.Anc1refChr6 62435 51 + 197743 T------TTGCTAACCAATACAATTGGAATGCACTAGAGGTGTCTGACTAGACTATT -s Anc2.Anc2refChr13 36147 47 + 96486 T------TTGCTAACCAATACAATTGGAATGCACTAGAGGTGTCTGAC----CTATT -s mr.mrrefChr5 254187 51 + 294540 A------TAGCCAACCAAGATAATCAAGAAACACTAAGGGAGTTTGATTAGATTATT -s simCow_chr6.simCow.chr6 392594 47 + 602619 T------TTGCCAACCACTTGAATTGGAATGCACTAGAGGTGTCTGAA----CTATT -s simDog_chr6.simDog.chr6 382653 47 + 593897 T------TTGTTAACCAATACATTTGGAATGCATTAGAGGTGTCTTAC----CTATT -s simHuman_chr6.simHuman.chr6 386730 51 + 601863 T------GTGCTAACCAATACAATTGGAATGCACTAGAGATGACTGACTAGACTCTT -s simRat_chr6.simRat.chr6 400998 51 + 647215 A------CAACCAACCAAGGTAATCAACAAACACTAAGAGAGTTTGATCAGAACATT - -a -s simMouse_chr6.simMouse.chr6 401163 10 + 636262 AACAGTCAAA -s Anc0.Anc0refChr3 32498 10 + 222631 AATGGTGAAA -s Anc1.Anc1refChr6 62487 10 + 197743 AATGGTGAAA -s Anc2.Anc2refChr13 36195 10 + 96486 AATGGTGAGA -s mr.mrrefChr5 254238 10 + 294540 AACAGTGAAA -s simCow_chr6.simCow.chr6 392642 4 + 602619 AATG------ -s simDog_chr6.simDog.chr6 382701 10 + 593897 AATGGTGAGA -s simHuman_chr6.simHuman.chr6 386782 10 + 601863 GATGGCGAAA -s simRat_chr6.simRat.chr6 401049 10 + 647215 AACAGTGAAA - -a -s simMouse_chr6.simMouse.chr6 401173 2 + 636262 GA -s Anc0.Anc0refChr3 32523 2 + 222631 GA -s Anc1.Anc1refChr6 62514 2 + 197743 GA -s Anc2.Anc2refChr13 36220 2 + 96486 TA -s mr.mrrefChr5 254265 2 + 294540 GA -s simCow_chr6.simCow.chr6 392660 2 + 602619 TG -s simDog_chr6.simDog.chr6 382726 2 + 593897 TA -s simHuman_chr6.simHuman.chr6 386809 2 + 601863 GA -s simRat_chr6.simRat.chr6 401076 2 + 647215 GA - -a -s simMouse_chr6.simMouse.chr6 401175 58 + 636262 TGGAACATGGGTACCCACTGAGGTACCTAGCATGCGTCATACATACTAATAGTATGAT -s Anc0.Anc0refChr3 32531 2 + 222631 TG-------------------------------------------------------- -s Anc1.Anc1refChr6 62522 57 + 197743 TGG-ATATGAACAACCACTATGAGATGTAGCGTGAATCACCCATAATGATGGCCCAAT -s Anc2.Anc2refChr13 36228 2 + 96486 TG-------------------------------------------------------- -s mr.mrrefChr5 254273 58 + 294540 TGGAACATGGATACCCACTGAGGTACCTAGCATGCATCATACATACTAATAGTACGAT -s simCow_chr6.simCow.chr6 392668 2 + 602619 TA-------------------------------------------------------- -s simDog_chr6.simDog.chr6 382734 2 + 593897 TG-------------------------------------------------------- -s simHuman_chr6.simHuman.chr6 386817 57 + 601863 TTG-ATATGAACAACCACTATGAGATGTAGCGTGAATCACCCATAATGATGGCCCAAT -s simRat_chr6.simRat.chr6 401084 58 + 647215 TGGAACATGCATGCCCACTGAGGTACCTAACATGCATTGTACATACTAACAGTACGAT - -a -s simMouse_chr6.simMouse.chr6 401233 12 + 636262 ACTGCACTTAGT -s Anc0.Anc0refChr3 32533 11 + 222631 -TTGCACTAAGT -s Anc1.Anc1refChr6 62579 12 + 197743 GTTGCACTAAGT -s Anc2.Anc2refChr13 36230 11 + 96486 -TTGCACTAAGT -s mr.mrrefChr5 254331 12 + 294540 ATTGCACTTAGT -s simCow_chr6.simCow.chr6 392679 11 + 602619 -TTGCACTAAGT -s simDog_chr6.simDog.chr6 382736 11 + 593897 -TTGCACTAAGT -s simHuman_chr6.simHuman.chr6 386877 12 + 601863 GTCGCACTAAGT -s simRat_chr6.simRat.chr6 401142 12 + 647215 ATTGCGGTTAGC - -a -s simMouse_chr6.simMouse.chr6 401245 108 + 636262 TTAAAAGAGTGACATAGGATCAAATATTTCAAGTGCACTATGATTGCCATTAAGGTTTCTGTGAACCATGATTGCCATTAAGGCTCCTATTGCTCTGTCTTAAATAAT -s Anc0.Anc0refChr3 32544 60 + 222631 ATAAATGGGTAACATAGGATTCAAT--TGCAAGTG----------------------------A------------------GCTCGTATTGCTATGTCTTAAGCAAG -s Anc1.Anc1refChr6 62591 60 + 197743 ATAAATGGGTAACATAGGATTCAAT--TGCAAGTG----------------------------A------------------GCTCGTATTGCTATGTCTTAAGCAAG -s Anc2.Anc2refChr13 36241 60 + 96486 CTAAATGGGGAACATAGGATTCAAT--TGCAAGTA----------------------------A------------------ACTCGTATTGCTATGTCTTAAACAAG -s mr.mrrefChr5 254343 78 + 294540 ATAAAAGGGTGACATAGGATCAAAT--TGCAAGTG----------------------------AACCATGATTGCCATTAAGGCTCCTATTGCTCTGTCTTAAGTAAT -s simCow_chr6.simCow.chr6 392690 60 + 602619 TTAAATGGGAGACATTGAACTCAAT--TGTGAGTC----------------------------A------------------ACTCCTATTGCCATGTGTTAAACAGG -s simDog_chr6.simDog.chr6 382750 60 + 593897 CTAAATGGGGAATAGAGGATTCAAT--TGCAAGAA----------------------------A------------------ACTCGTATTGCTATGTCTTAAACAAG -s simHuman_chr6.simHuman.chr6 386889 60 + 601863 ATAAATGGGTCACATAGGATTCAAT--TGCAAGTG----------------------------A------------------GCTCTTATTGCTGCATCCCAAGCGAA -s simRat_chr6.simRat.chr6 401154 78 + 647215 ATAAAAGGGTGACATAGGATCAAAT--TGCAAGTG----------------------------AACTATGATTGCCATTAAGGCTCCTATTGCGCTGTCTTATGTCAT - -a -s simMouse_chr6.simMouse.chr6 401353 13 + 636262 AAAGGGATACCCC -s Anc0.Anc0refChr3 32604 9 + 222631 AAGGGGT----CC -s Anc1.Anc1refChr6 62651 13 + 197743 AAGGGGTTAACCC -s Anc2.Anc2refChr13 36301 9 + 96486 GAATGGT----CC -s mr.mrrefChr5 254421 13 + 294540 AAGGGGTTAACCC -s simCow_chr6.simCow.chr6 392750 9 + 602619 AATTAAT----CC -s simDog_chr6.simDog.chr6 382810 9 + 593897 GAATGGT----CT -s simHuman_chr6.simHuman.chr6 386950 13 + 601863 AAGGGGTTAACCC -s simRat_chr6.simRat.chr6 401232 13 + 647215 AAGTGGTTAACCC - -a -s simMouse_chr6.simMouse.chr6 401366 66 + 636262 TCCTCACCTGGGGTGTTATGTAATTGCATTTCATCCTTTCTACTGTGCTCTAACATATGTTACACT -s Anc0.Anc0refChr3 32614 61 + 222631 TCTTAAAC-----TGTTGTGTGATTGCTCTTCATCCTTTCCACTGTGCTCTAACATATGTTCCATT -s Anc1.Anc1refChr6 62665 61 + 197743 TCTTAAAC-----TGTTGTGTGATTGCTCTTCATCCTTTCCACTGTGCTCTAACATATGTTCCATT -s Anc2.Anc2refChr13 36311 61 + 96486 TCTTAAAC-----TATTGTGTGACTGCTCTTCATCCTTTCCACTCTGCTCTAACATATGTTCCATT -s mr.mrrefChr5 254434 66 + 294540 TCCTCAACTGGGGTGTTATGTAATTGCACTTCATCCTTTCTACTGTGCTCTAACATATGTTACACT -s simCow_chr6.simCow.chr6 392760 61 + 602619 TCTTAAAC-----TATTGTGTCACTGATCTTCACTCGTTCCACTTCACTCTAACCTATGTTCCACT -s simDog_chr6.simDog.chr6 382820 49 + 593897 CCT-----------------TGACTGCTCTTCATCCTTTCCACTCTGCTTTAACATATGTTCCATT -s simHuman_chr6.simHuman.chr6 386964 61 + 601863 TCTTAAAT-----TGTTTTCTGATTGCTCTTCATCCTTTCCACTGTGCACTAACACATGTTTGATT -s simRat_chr6.simRat.chr6 401245 66 + 647215 ACCTCAACTGGGGTGTTATGTAATTGCACTTCATCCTTTCTACTGTGCTCTAACATATGTTACACT - -a -s simMouse_chr6.simMouse.chr6 401432 11 + 636262 AAAGTGCTATT -s Anc0.Anc0refChr3 32676 11 + 222631 AAAGGGCCATT -s Anc1.Anc1refChr6 62727 11 + 197743 AAAGGGCCATT -s Anc2.Anc2refChr13 36373 11 + 96486 AAAGGGTCATT -s mr.mrrefChr5 254500 11 + 294540 AAAGTGCTATT -s simCow_chr6.simCow.chr6 392822 11 + 602619 AGAGATTCACT -s simDog_chr6.simDog.chr6 382870 11 + 593897 AAAGGGTCATT -s simHuman_chr6.simHuman.chr6 387026 11 + 601863 AAAGGGCCAAT -s simRat_chr6.simRat.chr6 401311 11 + 647215 AAAGTACTATT - -a -s simMouse_chr6.simMouse.chr6 401443 76 + 636262 AGTGACCTGGAGTTACCTTACATTATAATTATAAAAAGTTACCTGGAAGCAGAATGTCCTTAAGGAAACTCTGTGT -s Anc0.Anc0refChr3 32689 75 + 222631 AGTGACCTGGAATCACCTGATATTATAACTATGAAAAATTACCTGGAGGTAAAATG-CCTTGAGGAAACTCTGTGT -s Anc1.Anc1refChr6 62740 75 + 197743 AGTGACCTGGAATCACCTGATATTATAACTATGAAAAATTACCTGGAGGTAAAATG-CCTTGAGGAAACTCTGTGT -s Anc2.Anc2refChr13 36386 75 + 96486 AGTGACCTGGAATCCCCTGATATTATCGCTATGAAAAATTATCTGGAGGCCAAATG-CCCTGAGGAAACTCTGTGT -s mr.mrrefChr5 254513 76 + 294540 AGTGACCTGGAGTCACCTGACATTATAACTATAAAAAATTACCTGGAAGTAGAATGTCCTTAAGGAAACTCTGTGT -s simCow_chr6.simCow.chr6 392835 75 + 602619 AGTGACCTGGAGTCCCCTGATATTATTGCTATGAAAAATTAGCTAGAGGCCACCTG-GCCTGGGGAAACTCTGTAT -s simDog_chr6.simDog.chr6 382883 75 + 593897 AGTGACCTGAAATGCCCTGATGTTATCGCTATGAAAAATTATCTGGAGGCCAAATA-CCCTGAGGGATCTCTGTGT -s simHuman_chr6.simHuman.chr6 387039 68 + 601863 AGTAACCTGGACCCACCTG-----ATAACAATGAAAAATTGCCTGGAGGTACAG---CCTTGAGGAAACTCTGTGG -s simRat_chr6.simRat.chr6 401324 76 + 647215 AGTGACCTGGAGTCACCTGATATTATTACTTTAAGAAATTACCTGGAAGTAAGATGACCTTAGGGAAACGCTGTAT - -a -s simMouse_chr6.simMouse.chr6 401519 4 + 636262 CATG -s Anc0.Anc0refChr3 32764 4 + 222631 CATG -s Anc1.Anc1refChr6 62815 4 + 197743 CATG -s Anc2.Anc2refChr13 36461 4 + 96486 CATG -s mr.mrrefChr5 254589 4 + 294540 CATG -s simCow_chr6.simCow.chr6 392910 4 + 602619 CATG -s simDog_chr6.simDog.chr6 382958 4 + 593897 CATG -s simHuman_chr6.simHuman.chr6 387107 4 + 601863 CATG -s simRat_chr6.simRat.chr6 401401 4 + 647215 CATG - -a -s simMouse_chr6.simMouse.chr6 401523 52 + 636262 ACAGGACAGCTGCAATCTCAAGAAAGGGAGTTATACAATGCTTAAGTATTGA -s Anc0.Anc0refChr3 32770 52 + 222631 ACAGGACAGCTCCAATCTCAACAAAGGGAGTTGTACAATGCTTATGTCTTGA -s Anc1.Anc1refChr6 62821 52 + 197743 ACAGGACAGCTCCAATCTCAACAAAGGGAGTTGTACAATGCTTATGTCTTGA -s Anc2.Anc2refChr13 36467 52 + 96486 ACAGGACAGCTCCAATTTCAATTAACGGAGTTGTACAATGCTTATGTATTCA -s mr.mrrefChr5 254593 52 + 294540 ACAGGACAGCTGCAATCTCAACAAAGGGAGTTGTACAATGCTTAAGTCTTGA -s simCow_chr6.simCow.chr6 392916 51 + 602619 ACAGGACAGCTCAAATTTCAATTAAC-GAGTTGAATAATGCTTAAGTATTTA -s simDog_chr6.simDog.chr6 382964 52 + 593897 CCCAGACAGTTCCAAATTTGATTAACGGACTTGTACAGTGCTGATGTATTCA -s simHuman_chr6.simHuman.chr6 387113 52 + 601863 ACAGGACAGCCTCAATCTCAACAAGGTGAGTTGGACAACGCTTATGTCTTGA -s simRat_chr6.simRat.chr6 401405 52 + 647215 ACAGAACAGCTCCAATCTCAACAAAGGGAGTTGTAAAATGCCTAACCCTTGA - -a -s simMouse_chr6.simMouse.chr6 401575 27 + 636262 ACCTTGGGGAAGAGCTACTTGTGTGTG -s Anc0.Anc0refChr3 32827 27 + 222631 ACCTCAGGGAAAAACTAGTTGTGTGTG -s Anc1.Anc1refChr6 62878 27 + 197743 ACCTCAGGGAAAAACTAGTTGTGTGTG -s Anc2.Anc2refChr13 36524 27 + 96486 ACCTCAGGGAGAAATTAGTTGTGTGTG -s mr.mrrefChr5 254645 27 + 294540 ACCTTGGGGAAGAGCTAGTTGTGTGTG -s simCow_chr6.simCow.chr6 392972 26 + 602619 ACCTTAAGAACAAATCGGTTGTAT-TG -s simDog_chr6.simDog.chr6 383020 27 + 593897 ACCTCAGGGAGAAATTAGCTGGGTGGG -s simHuman_chr6.simHuman.chr6 387170 27 + 601863 ACCACAGGGAAAAACTAGTTGTGTGTG -s simRat_chr6.simRat.chr6 401457 27 + 647215 ACCTTCAGGAAGAGCAAGTTGTGTTTG - -a -s simMouse_chr6.simMouse.chr6 401602 42 + 636262 CACTTCACCAGTAACCAAGCACCTGCTGAGTGGAGTTCTGGA -s Anc0.Anc0refChr3 32855 40 + 222631 CAACTCCAC--TAACAAAGCACCTGCTGAGTGGAGTTTGGGA -s Anc1.Anc1refChr6 62906 42 + 197743 CAACTCCACAGTAACAAAGCACCTGCTGAGTGGAGTTTGGGA -s Anc2.Anc2refChr13 36552 40 + 96486 CAACTCCAC--CAACACAGCGCATGCTGAGTGGTGTTTGGGA -s mr.mrrefChr5 254672 42 + 294540 CACTTCACCAGTAACCAAGCACCTGCTGAGTGGAGTTCTGGA -s simCow_chr6.simCow.chr6 392999 40 + 602619 CAACTCAAC--CAACACAGCGCATGCTGAGTGGTGTTTGGGA -s simDog_chr6.simDog.chr6 383048 8 + 593897 CAATGCCA---------------------------------- -s simHuman_chr6.simHuman.chr6 387198 42 + 601863 CAACTCCACAGTAACAAAGAACCTGCTGAGTGGAGTTTGGGA -s simRat_chr6.simRat.chr6 401484 42 + 647215 CACTTCATCGATAACCAAGCACCTGCTGAGTGGAGTTCTGGG - -a -s simMouse_chr6.simMouse.chr6 401644 69 + 636262 TTTCTGTAAGGCAACTGGAATAAATGTGTGCATATTAGTACAATGATTCGTAATTTAGAAGGCAGTAGA -s Anc0.Anc0refChr3 32895 68 + 222631 TTTCTGTGGGCAAACTGGAATAAAGGCTTGTATGTTAGTACCATGATTTGTAAGTTTGAAGACATT-TC -s Anc1.Anc1refChr6 62948 68 + 197743 TTTCTGTGGGCAAACTGGAATAAAGGCTTGTATGTTAGTACCATGATTTGTAAGTTTGAAGACATT-TC -s Anc2.Anc2refChr13 36592 68 + 96486 TGTCTGCGGGCAAGCTGGAATAGGGGCTTGTATGTCAGTACCATAATTTGTGAGATTGAAAACATC-TC -s mr.mrrefChr5 254714 69 + 294540 TTTCTGTAAGGAAACTGGAATAAATGTGTGCATATTAGTACAATGATTCGTAATTTAGAAGGCATTAGA -s simCow_chr6.simCow.chr6 393039 68 + 602619 TGTCTGCGGGCAAGCTGGAATAGGGGCTTGTATGTCAGTACCATAATTTGTGAGATTGAAAACATC-TC -s simHuman_chr6.simHuman.chr6 387241 68 + 601863 TTTCTGTGTGTAGAGTGGAATAAAGGCCTGTATGTTATTGCCATGATTTGTAAGTTGGAAGACATT-TT -s simRat_chr6.simRat.chr6 401526 69 + 647215 TTTCTGTAGGGAAACTGGAATAAATGTGTACATATTAGTACAATAACTCATAATTTCGAAGGCATTAGA - -a -s simMouse_chr6.simMouse.chr6 401713 31 + 636262 CATAAGAGGATACCCTGCTCCTCAGCGGAAT -s Anc0.Anc0refChr3 32963 15 + 222631 CATGTGAGGATATTT---------------- -s Anc1.Anc1refChr6 63016 15 + 197743 CATGTGAGGATATTT---------------- -s Anc2.Anc2refChr13 36660 15 + 96486 CATGTGAGGGTATTT---------------- -s mr.mrrefChr5 254783 15 + 294540 CATGAGAGGATACCC---------------- -s simCow_chr6.simCow.chr6 393108 15 + 602619 CATGTGAGGGTATTT---------------- -s simHuman_chr6.simHuman.chr6 387309 15 + 601863 CATGTGAGGATGTTT---------------- -s simRat_chr6.simRat.chr6 401595 15 + 647215 CATGAGAGGGTACCC---------------- - -a -s simMouse_chr6.simMouse.chr6 401744 10 + 636262 ATGAATGAGC -s Anc0.Anc0refChr3 32978 9 + 222631 -TGAATAAAC -s Anc1.Anc1refChr6 63031 10 + 197743 GTGAATAAAC -s Anc2.Anc2refChr13 36675 9 + 96486 -TGAATAAAC -s mr.mrrefChr5 254798 10 + 294540 ATGAATAAGC -s simDog_chr6.simDog.chr6 383056 9 + 593897 -TGAATAAAC -s simHuman_chr6.simHuman.chr6 387326 10 + 601863 GTGAATAATC -s simRat_chr6.simRat.chr6 401610 10 + 647215 ATGAATAAGC - -a -s simMouse_chr6.simMouse.chr6 401754 21 + 636262 AAGAGGTGGGAGCCACATGCT -s Anc0.Anc0refChr3 32987 20 + 222631 AG-AAGTGGGAACCTCATACA -s Anc1.Anc1refChr6 63041 20 + 197743 AG-AAGTGGGAACCTCATACA -s Anc2.Anc2refChr13 36684 20 + 96486 AG-AAGTGGGAACCTCATACA -s mr.mrrefChr5 254808 21 + 294540 AAGAGGTGGGAGCTACATACA -s simCow_chr6.simCow.chr6 393123 19 + 602619 -A-AGGTGGGAACCTTTTACA -s simDog_chr6.simDog.chr6 383066 20 + 593897 AG-AAGTACAAACCTCATACA -s simHuman_chr6.simHuman.chr6 387336 20 + 601863 AG-AAGTGGGAAGCTAACACA -s simRat_chr6.simRat.chr6 401620 21 + 647215 TAGAGGTGGGAGCTACATACA - -a -s simMouse_chr6.simMouse.chr6 401775 30 + 636262 TCTTAACCCCCCTCTCTGCCTAAGCATAGT -s Anc0.Anc0refChr3 33018 30 + 222631 TCTTTACCCCCCTCTATGCCTAAGCATAAT -s Anc1.Anc1refChr6 63072 30 + 197743 TCTTTACCCCCCTCTATGCCTAAGCATAAT -s Anc2.Anc2refChr13 36715 30 + 96486 TCTATAACCCCCTCTATGCCTAAGCATACT -s mr.mrrefChr5 254829 30 + 294540 TCTTAACCCCCCTCTCTGCCTAAGCATAAT -s simCow_chr6.simCow.chr6 393153 30 + 602619 TCTATATCCCCCCCTATGCCTAAGCATACT -s simDog_chr6.simDog.chr6 383097 27 + 593897 CCT---ATCAGCTGTATAGCTAAGCATACT -s simHuman_chr6.simHuman.chr6 387367 30 + 601863 TCTTGACCCCCCTCTATGCGTAAGCATAAT -s simRat_chr6.simRat.chr6 401641 30 + 647215 TCTTAACCCCCCTCTTTTCCTAAGCATAAT - -a -s simMouse_chr6.simMouse.chr6 401805 45 + 636262 AGTCCCTGTGGTTGTTACAGGTAATTAGAGGCAGTGGTATAGCTT -s Anc0.Anc0refChr3 33048 36 + 222631 AGTTCCTGCAA----TCCGGG-----AACGGGAGAATTATAGCTT -s Anc1.Anc1refChr6 63102 36 + 197743 AGTTCCTGCAA----TCCGGG-----AACGGGAGAATTATAGCTT -s Anc2.Anc2refChr13 36756 36 + 96486 AGTTCCAACAA----TACTGC-----TACGGGAGAATTATAGCTT -s mr.mrrefChr5 254859 45 + 294540 AGTCCCTGTGGTTGTTCCGGGTAATTAGAGGGAGTAGTATAGCTT -s simCow_chr6.simCow.chr6 393195 35 + 602619 TGTCCCAAAAA----CAATTA-----TA-GGGATGAGTTTAGTTT -s simDog_chr6.simDog.chr6 383135 35 + 593897 AGTTCTAACAA----TACTGC-----TAC-AAAGATTTATAACTG -s simHuman_chr6.simHuman.chr6 387397 36 + 601863 AAGGCCTGCAA----TCCGGG-----AATGGGAGCAATGTAGCTT -s simRat_chr6.simRat.chr6 401671 45 + 647215 ACTTCCTGTGGTAGTTCCGGGTTATTAGAGGGAGAAGTAGAGCTT - -a -s simMouse_chr6.simMouse.chr6 401850 59 + 636262 TGATTGTTTTTGAACTGAAGATTGCCCTTAAACATCTCCTTGCAAAGTTTTTGGCAACC -s Anc0.Anc0refChr3 33084 48 + 222631 -G--TGGTTTTGAAAGGGTTAT-------AACTACCAAC-TACAAATCTTGTAGCAAGC -s Anc1.Anc1refChr6 63138 49 + 197743 TG--TGGTTTTGAAAGGGTTAT-------AACTACCAAC-TACAAATCTTGTAGCAAGC -s Anc2.Anc2refChr13 36792 48 + 96486 -G--TGGTTATGAAAGGGTTAT-------AACTACCAAC-TACAAATCTTGCAGCAAGC -s mr.mrrefChr5 254904 59 + 294540 TGATTGTTTTTGAAATGAGGATTGCCCTTAAACATCTCCTTGCAAAGTTTTTGGCAACC -s simCow_chr6.simCow.chr6 393230 48 + 602619 -G--TGGTTCTGGAAGGGTTTT-------AACTACCAGT-TACAAATCTTGCAGCTAGC -s simDog_chr6.simDog.chr6 383170 48 + 593897 -G--TCATTATGACACCTTCAA-------AACTATGAAC-TAAAGTCCTCCCAATACTT -s simHuman_chr6.simHuman.chr6 387433 49 + 601863 TG--TGGTTTTGAAAGGGTTGT-------AATGACCAAC-CACCAATCTTGTAGCCAGC -s simRat_chr6.simRat.chr6 401717 56 + 647215 TGATTGTTTTTGAAACGAGGATTGCCCACAAACATCTCCTTGCAAAGTTTA---CAACC - -a -s simMouse_chr6.simMouse.chr6 401909 1 + 636262 T -s Anc0.Anc0refChr3 33140 1 + 222631 T -s Anc1.Anc1refChr6 63195 1 + 197743 T -s Anc2.Anc2refChr13 36848 1 + 96486 T -s mr.mrrefChr5 254963 1 + 294540 T -s simCow_chr6.simCow.chr6 393286 1 + 602619 G -s simDog_chr6.simDog.chr6 383231 1 + 593897 T -s simHuman_chr6.simHuman.chr6 387490 1 + 601863 T -s simRat_chr6.simRat.chr6 401773 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 401910 9 + 636262 AAATGCACT -s Anc0.Anc0refChr3 33141 9 + 222631 AAAAGGACT -s Anc1.Anc1refChr6 63196 9 + 197743 AAAAGGACT -s Anc2.Anc2refChr13 36849 9 + 96486 AACAGGAAT -s mr.mrrefChr5 254964 9 + 294540 AAATGCACT -s simCow_chr6.simCow.chr6 393287 2 + 602619 AA------- -s simDog_chr6.simDog.chr6 383232 9 + 593897 CACAGGAAT -s simHuman_chr6.simHuman.chr6 387492 9 + 601863 AAAAGGACT -s simRat_chr6.simRat.chr6 401774 9 + 647215 GAGTGCCCT - -a -s simMouse_chr6.simMouse.chr6 401919 70 + 636262 AACCTAGACTTCTTCACAGACTGAAATTTTTTGGGTCATGGGTCTGGCTTGCTATGCCAAACTACAAATA -s Anc1.Anc1refChr6 63209 41 + 197743 AGACGAGACATTCTATCCCAAT-----------------------------CAATGAGCAACTACAAATC -s mr.mrrefChr5 254977 70 + 294540 AACCTAGACTTCTTCACAGACTGAAAATTTTTGGGTCATGGGTCTGGCTTGCAATGCCCAACTACAAATA -s simHuman_chr6.simHuman.chr6 387506 41 + 601863 AGACGAGACATTCTATCCCAAT-----------------------------CAATGAGCAACTACAAATC -s simRat_chr6.simRat.chr6 401787 70 + 647215 AACCCAGACTTCTTCACAGACTGAAAATTTTTGGGTCATGGGTCTGGGTTGCAATGCCCAACTACAAATA - -a -s simMouse_chr6.simMouse.chr6 401989 17 + 636262 TGCAGCCAGCTGTACTA -s Anc0.Anc0refChr3 33151 13 + 222631 ----GCCAGCAGTATTG -s Anc1.Anc1refChr6 63250 17 + 197743 TGCTGCCAGCAGTATTG -s Anc2.Anc2refChr13 36859 13 + 96486 ----GCTAGCAGTGTTG -s mr.mrrefChr5 255047 17 + 294540 TGCAGCCAGCAGTATTA -s simCow_chr6.simCow.chr6 393289 13 + 602619 ----GCTAGCAGTGTTG -s simHuman_chr6.simHuman.chr6 387548 17 + 601863 TGCTGCCAGCAGTATTG -s simRat_chr6.simRat.chr6 401857 17 + 647215 TGCAGCCAGCAGTATTA - -a -s simMouse_chr6.simMouse.chr6 402006 29 + 636262 AATGCAGACTGAGAAAGATTAGATATTGT -s Anc0.Anc0refChr3 33166 29 + 222631 AAACCAGACTGGGAGAGATGAGGCATTCA -s Anc1.Anc1refChr6 63269 29 + 197743 AAACCAGACTGGGAGAGATGAGGCATTCA -s Anc2.Anc2refChr13 36874 29 + 96486 AAACCAAACTGAGAGAGATGAGGCATTCA -s mr.mrrefChr5 255064 29 + 294540 AATGCAGACTGGGAAAGATTAGATATTGA -s simCow_chr6.simCow.chr6 393304 29 + 602619 AAACCAAACTGAGAGAGATGAAGCCTTCA -s simDog_chr6.simDog.chr6 383242 12 + 593897 -----------------ATGAGGCATACA -s simHuman_chr6.simHuman.chr6 387567 29 + 601863 AAAAAGGAATGGAATAGATAAGGCATTCA -s simRat_chr6.simRat.chr6 401874 29 + 647215 AATGCAGACTGGGCAAGATTAGATATTGA - -a -s simMouse_chr6.simMouse.chr6 402035 46 + 636262 TTTTTAATCATTGTCCTTCATCTTGCTATTACCCAGGATGGAAATA -s Anc0.Anc0refChr3 33195 46 + 222631 ATCCCAATCATTGTCTTTCATCTTGATATTCTACATGATGGAAATG -s Anc1.Anc1refChr6 63298 46 + 197743 ATCCCAATCATTGTCTTTCATCTTGATATTCTACATGATGGAAATG -s Anc2.Anc2refChr13 36903 46 + 96486 AACCCAATCATTGATTTTCATCTTGATATTCTACATGATCGAAATG -s mr.mrrefChr5 255093 46 + 294540 TTCCCAATCATTGTCCTTCATCTTGCTATTACCCAGGATGGAAATA -s simCow_chr6.simCow.chr6 393334 46 + 602619 AACCCTATAATAGACTTTCATCTTGCTATTCTAGATGATTGACTTG -s simDog_chr6.simDog.chr6 383254 46 + 593897 AACCTAATCATTGATTTTCATCTTGATATTCTACATGATCCAAATG -s simHuman_chr6.simHuman.chr6 387596 33 + 601863 GTCCCAATGATTGTC-------------TTCTACATGATGGAAATG -s simRat_chr6.simRat.chr6 401903 46 + 647215 TTCCCAATCATTGTCCTTCATCTTGCTAGTACCCAGGATGGGAATA - -a -s simMouse_chr6.simMouse.chr6 402081 21 + 636262 AACAAATACGACTTATAAATG -s Anc0.Anc0refChr3 33241 21 + 222631 AACAAATACGACGTATAAATG -s Anc1.Anc1refChr6 63344 21 + 197743 AACAAATACGACGTATAAATG -s Anc2.Anc2refChr13 36949 21 + 96486 AATAAATACGATGTATAAATG -s mr.mrrefChr5 255139 21 + 294540 AACAAATACGACTTATAAATG -s simCow_chr6.simCow.chr6 393380 19 + 602619 AAGAA--ATGGTGAATAAATG -s simDog_chr6.simDog.chr6 383301 21 + 593897 AATACATACGATGTACAAATG -s simHuman_chr6.simHuman.chr6 387629 21 + 601863 AACAAGTGCAACATATGAATG -s simRat_chr6.simRat.chr6 401949 21 + 647215 AATAAATACGACTTACAAATG - -a -s simMouse_chr6.simMouse.chr6 402102 75 + 636262 TAGGGGCCTAATGATACTCAAGTTGGGAACCTCAAACTATCCCTGCCAGCATCCCCGTCTGCCAGTACAATAATA -s Anc0.Anc0refChr3 33263 60 + 222631 TAGGGGCTTCATGACACTTAAGTCAGGAACTTCAGGC-ATCCCTGCCAACATC--------------CAATAATA -s Anc1.Anc1refChr6 63366 60 + 197743 TAGGGGCTTCATGACACTTAAGTCAGGAACTTCAGGC-ATCCCTGCCAACATC--------------CAATAATA -s Anc2.Anc2refChr13 36971 60 + 96486 TAGGGGCCTCATGACACTTAAATCAGGAACTTCAGGC-ATTCCTGCCAATGTC--------------CAATAATA -s mr.mrrefChr5 255160 70 + 294540 TAGGGGCTTAATGATACTCAAGTTAGGAACCTCAAAC-ATCCCTGCCAGCATCCC----TGCCAGTACAATAATA -s simCow_chr6.simCow.chr6 393400 58 + 602619 TAGGGGTCTCATGATACTTAAATCAGGAACTTCAGGC-AT--CTTCCAATGTC--------------ATATAATA -s simDog_chr6.simDog.chr6 383323 55 + 593897 ---GGGCCTCATGGCACT--AATAAAGAACTTCAGGC-ATTCCCGCCAGTGTC--------------CAAAAATG -s simHuman_chr6.simHuman.chr6 387651 60 + 601863 TAGGGGCTCCATAACACTTGAGTCAGAAGCTTCAGGC-ACCCCTGCCCACATC--------------CAATAACA -s simRat_chr6.simRat.chr6 401970 68 + 647215 TAGGAGCTTAATGCTACTCAAGTTAGGAACCTAAAAC-ATCCCTGCCAGCATCCC----TGCGAGCACAATAA-- - -a -s simMouse_chr6.simMouse.chr6 402177 6 + 636262 GAGATT -s Anc0.Anc0refChr3 33323 6 + 222631 GAGAGT -s Anc1.Anc1refChr6 63426 6 + 197743 GAGAGT -s Anc2.Anc2refChr13 37031 6 + 96486 GAGAGT -s mr.mrrefChr5 255230 6 + 294540 GAGATT -s simCow_chr6.simCow.chr6 393469 6 + 602619 GAGAGT -s simDog_chr6.simDog.chr6 383378 6 + 593897 GAGATT -s simHuman_chr6.simHuman.chr6 387711 6 + 601863 GAGAGT - -a -s simMouse_chr6.simMouse.chr6 402183 8 + 636262 AACACTTG -s Anc0.Anc0refChr3 33331 8 + 222631 AATAATGG -s Anc1.Anc1refChr6 63434 8 + 197743 AATAATGG -s Anc2.Anc2refChr13 37039 8 + 96486 AATAATGG -s mr.mrrefChr5 255236 8 + 294540 AACACTTG -s simCow_chr6.simCow.chr6 393477 8 + 602619 AATAAGGG -s simDog_chr6.simDog.chr6 383386 7 + 593897 TAT-ATGG -s simHuman_chr6.simHuman.chr6 387719 8 + 601863 AATCACGG -s simRat_chr6.simRat.chr6 402038 7 + 647215 -GCACTTG - -a -s simMouse_chr6.simMouse.chr6 402191 2 + 636262 CG -s Anc0.Anc0refChr3 33340 2 + 222631 GA -s Anc1.Anc1refChr6 63443 2 + 197743 GA -s Anc2.Anc2refChr13 37048 2 + 96486 GA -s mr.mrrefChr5 255244 2 + 294540 GG -s simCow_chr6.simCow.chr6 393486 2 + 602619 GA -s simDog_chr6.simDog.chr6 383394 2 + 593897 GA -s simHuman_chr6.simHuman.chr6 387728 2 + 601863 GA -s simRat_chr6.simRat.chr6 402045 2 + 647215 GG - -a -s simMouse_chr6.simMouse.chr6 402193 83 + 636262 CTTTCCTGAGGAAGTCTCTAATTTGCATCTGACTTTCTGACTTCAAAAGGAGACAGGATTGAAAGGTGTGGGTTGGGGTGGAA -s Anc0.Anc0refChr3 33342 77 + 222631 ATTCACTGAGGAAGTCTCCAGTTCGCA------TGGCTGGGTGCTTAAGGATTCAGAGTTGGGAGGTGAAGGCAGGGACGGAA -s Anc1.Anc1refChr6 63445 77 + 197743 ATTCACTGAGGAAGTCTCCAGTTCGCA------TGGCTGGGTGCTTAAGGATTCAGAGTTGGGAGGTGAAGGCAGGGACGGAA -s Anc2.Anc2refChr13 37050 77 + 96486 CTTCACTGAGGAAGTCTCCAGTTCACA------TGGCTGGGTGCTTAAGGATTCAGAGTTGGGAGGTGAAGGCAGGGACGGCA -s mr.mrrefChr5 255246 83 + 294540 ATTCCCTGAGGAAGTCTCCAATTTGCATCTGACTTTCTGACTTCATAAGGAGACAGAATTGGAAGGTGAGGGTAGGGGTGGAA -s simCow_chr6.simCow.chr6 393488 77 + 602619 CTTCACTGAGGAAGTCTCCAGTTCACA------CGCTTTTGTGCTTAAGGAGTCAAAGTTGTGAGATGAAGGAAGGGATGGGA -s simDog_chr6.simDog.chr6 383396 77 + 593897 CTTCTCTGACGAAGTCTCCAGTGCACA------TTGCTGGGTCCTTAATCATTCAGAGTTGGGAGGTGAAGGCAGGGACGGCA -s simHuman_chr6.simHuman.chr6 387730 77 + 601863 ATTCACTGAGAAAGTCTCCAGTTCGCA------TGGCTGGGTGCTTAAGGACTTAGAGTTGGGAGGTGAAGGCAGGGACAGAA -s simRat_chr6.simRat.chr6 402048 83 + 647215 ATTCCCTGAGGAAGTCTCCAATTTGCATCTGACTTTCTGACTTCGTAAGAAGACAGAATTGGAAGGCGAGGGTAGGTGTGGAA - -a -s simMouse_chr6.simMouse.chr6 402276 38 + 636262 AGTTGCACAACCCGAAAAATTCACAACCCTCATCTTGG -s Anc0.Anc0refChr3 33419 38 + 222631 GGCTGCACATCTTGAGAGAATTGTAGCTCACATCTTGG -s Anc1.Anc1refChr6 63522 38 + 197743 GGCTGCACATCTTGAGAGAATTGTAGCTCACATCTTGG -s Anc2.Anc2refChr13 37127 38 + 96486 GGCTGCACATCTTGAGAGAATTGTAGCTCACATCTTGG -s mr.mrrefChr5 255329 38 + 294540 AGTTGCACAACCTGAAAAAATCATAGCTCTCATCTTGG -s simCow_chr6.simCow.chr6 393565 36 + 602619 CGCTGCACA--GTAATTGAATCAAAGCTCACATCCTAG -s simDog_chr6.simDog.chr6 383473 38 + 593897 GGCTACACATCTTGTGAGAATTGTAGCTTACAACTTGT -s simHuman_chr6.simHuman.chr6 387807 38 + 601863 GGCTGCACATCATGAGAGAATACTAGCTCACATCTTGG -s simRat_chr6.simRat.chr6 402148 38 + 647215 AGTTGCACAACTTGAAAAAATTATAGCTCTCATCTTGG - -a -s simMouse_chr6.simMouse.chr6 402314 26 + 636262 CTCTTGTCTCACTATTGAATATCAAA -s Anc0.Anc0refChr3 33458 24 + 222631 ATCTTGTGT--CTCTTGAATATCTGA -s Anc1.Anc1refChr6 63561 24 + 197743 ATCTTGTGT--CTCTTGAATATCTGA -s Anc2.Anc2refChr13 37166 24 + 96486 ATCTTGTCT--CTCTTGGATAGCTGA -s mr.mrrefChr5 255368 26 + 294540 ATCTTGTGTCACTATTGAATATCAAA -s simCow_chr6.simCow.chr6 393602 24 + 602619 ATCTTGTCC--CATTTGGATGGCTGA -s simDog_chr6.simDog.chr6 383512 24 + 593897 ATCTTGTCT--CTCTTAGGTAGCTCA -s simHuman_chr6.simHuman.chr6 387846 24 + 601863 ATCTTGTGT--CTGTTGAATTTCTGA -s simRat_chr6.simRat.chr6 402187 24 + 647215 ATCTTGTGTCACTATTGACC--CAAA - -a -s simMouse_chr6.simMouse.chr6 402340 5 + 636262 CACTT -s Anc0.Anc0refChr3 33482 5 + 222631 CACTT -s Anc1.Anc1refChr6 63585 5 + 197743 CACTT -s Anc2.Anc2refChr13 37190 5 + 96486 CACTT -s mr.mrrefChr5 255394 5 + 294540 CACTT -s simCow_chr6.simCow.chr6 393706 5 + 602619 TACTT -s simDog_chr6.simDog.chr6 383536 5 + 593897 CACTT -s simHuman_chr6.simHuman.chr6 387870 5 + 601863 CACTT -s simRat_chr6.simRat.chr6 402211 5 + 647215 CACTT - -a -s simMouse_chr6.simMouse.chr6 402345 2 + 636262 TC -s Anc0.Anc0refChr3 33505 2 + 222631 TC -s Anc1.Anc1refChr6 63608 2 + 197743 TC -s Anc2.Anc2refChr13 37213 2 + 96486 TC -s mr.mrrefChr5 255399 2 + 294540 TC -s simCow_chr6.simCow.chr6 393729 2 + 602619 TC -s simHuman_chr6.simHuman.chr6 387893 2 + 601863 TC -s simRat_chr6.simRat.chr6 402216 2 + 647215 TC - -a -s simMouse_chr6.simMouse.chr6 402347 9 + 636262 TTCTGACTA -s Anc0.Anc0refChr3 33507 7 + 222631 TTAT--ATA -s Anc1.Anc1refChr6 63610 7 + 197743 TTAT--ATA -s Anc2.Anc2refChr13 37215 7 + 96486 TTAT--ATG -s mr.mrrefChr5 255401 9 + 294540 TTCTGACTA -s simCow_chr6.simCow.chr6 393733 7 + 602619 TTAT--ATG -s simHuman_chr6.simHuman.chr6 387895 7 + 601863 TGGT--TTA -s simRat_chr6.simRat.chr6 402218 9 + 647215 TATTGACTG - -a -s simMouse_chr6.simMouse.chr6 402356 36 + 636262 GCCTGCTATGGCAAAATTTGAGTGCCACACATGTAG -s Anc0.Anc0refChr3 33534 14 + 222631 TCCTGCTGTGGTGG---------------------- -s Anc1.Anc1refChr6 63637 22 + 197743 TCCTGCTGTGGTGGAA--------------GTGCAG -s Anc2.Anc2refChr13 37242 14 + 96486 TCCTGCTGTGGTGG---------------------- -s mr.mrrefChr5 255410 35 + 294540 TCCTGCTATGGCAAAATTTGAGT-CCACACATGTAG -s simCow_chr6.simCow.chr6 393760 14 + 602619 TCCTGCTGTGGTGG---------------------- -s simHuman_chr6.simHuman.chr6 387922 22 + 601863 TCCTGCTGTGGTGGAA--------------GTGCAG -s simRat_chr6.simRat.chr6 402227 35 + 647215 TCCTGCCATGGCAAAATGTAATT-CCAATGATGTAG - -a -s simMouse_chr6.simMouse.chr6 402392 79 + 636262 CAACCTGGCAATCTTCAAAGGATGCAGTTCTTTGATATGGGGGTTGATAGTTGATGCGAAGCGTCAGGCCTAAACAAAG -s Anc0.Anc0refChr3 33553 73 + 222631 GAACCTTGGGCTTATGAAATGATCCAGTTCTTTGCTACAGTAGTTGATAGTTGATACGG---GTCAGGTG---ATAAAT -s Anc1.Anc1refChr6 63664 76 + 197743 GAACCTTGGGCTTATGAAATGATCCAGTTCTTTGCTACAGTAGTTGATAGTTGATACGG---GTCAGGTGTAAATAAAT -s Anc2.Anc2refChr13 37261 73 + 96486 GAACCTTGGGCTTATGAAATGATCCAGTTTTTTGCTACAGTAGTTGATAGTAGACATGG---GTCAGGTG---ATAAAT -s mr.mrrefChr5 255450 78 + 294540 CAACCTGGCGATCTTCAAAGGATGCAGTTCTTTGATATGGGAGTTGATAGTTGATGCGA-GCGTCAGGCCTAAATAAAG -s simCow_chr6.simCow.chr6 393779 72 + 602619 GAACCTTGGGCTTATGACATGATCCAGTTTGTTGCTAAAGTAGTTGGCAGTAGACATGG---GTCAGGTG----TAAAT -s simDog_chr6.simDog.chr6 383554 49 + 593897 -----TGGGGCTTATGAATTGATCCAGTCTTTTCCTACAGTAGTTGAT-------------------------ATAAAT -s simHuman_chr6.simHuman.chr6 387949 76 + 601863 GGACCCTGGGCTTATGGAACAATCCACTTCTTTGCTACAGTAGTTGATAGTTGATCCGG---GTTAGATGTAAATAAAT -s simRat_chr6.simRat.chr6 402267 66 + 647215 CAACCTGGTGATCTTCAAAGGATTCAGCTCCTTGATATGGAAGTTAA-------------GCATCAGGCCTAACTAAAA - -a -s simMouse_chr6.simMouse.chr6 402471 45 + 636262 AAGCTATGACACTAAGTTGGGAATTGTGTATAACGCCTGGCATTC -s Anc0.Anc0refChr3 33626 30 + 222631 AAACTA---------------AGCTGTGCTCAAGATCTGGTATTC -s Anc1.Anc1refChr6 63740 30 + 197743 AAACTA---------------AGCTGTGCTCAAGATCTGGTATTC -s Anc2.Anc2refChr13 37334 30 + 96486 AGACTA---------------AGCTGTGCTCAAGATCTGGTATTC -s mr.mrrefChr5 255528 45 + 294540 AAGCTATGACACTAAGTTGGGAATTGTGTATAACACCTGGCATTC -s simCow_chr6.simCow.chr6 393851 30 + 602619 AGACTA---------------AACTGTATTCAACATCTGGTATTC -s simDog_chr6.simDog.chr6 383603 29 + 593897 AGACTA---------------GG-TGTGCTCAAGAACTGGTGTTC -s simHuman_chr6.simHuman.chr6 388025 30 + 601863 AAACTA---------------AGCTGTGCTCAGTATCTGGTATTC -s simRat_chr6.simRat.chr6 402334 45 + 647215 AAGCTGTGATGTTAAGTTGAGAATTGTGTATAACACCTGGCCTTC - -a -s simMouse_chr6.simMouse.chr6 402516 13 + 636262 CTCAGTTGATTTG -s Anc0.Anc0refChr3 33656 13 + 222631 TTCAGTTGATTTG -s Anc1.Anc1refChr6 63770 13 + 197743 TTCAGTTGATTTG -s Anc2.Anc2refChr13 37364 13 + 96486 TTCAGTTGATGTG -s mr.mrrefChr5 255573 13 + 294540 CTCAGTTGATTTG -s simCow_chr6.simCow.chr6 393881 13 + 602619 TTCAGTTGATGTA -s simDog_chr6.simDog.chr6 383633 13 + 593897 TTCAATTGATGTG -s simHuman_chr6.simHuman.chr6 388055 13 + 601863 TTCAGTTGATTTG -s simRat_chr6.simRat.chr6 402379 13 + 647215 CTCAGTTGATCTG - -a -s simMouse_chr6.simMouse.chr6 402529 53 + 636262 GGACCAAGTCCGAATGGTGTAAGCTGGCTCTAGTATCGGATCCTCTTAGCCAT -s Anc0.Anc0refChr3 33669 53 + 222631 GGAGCAAATGTGACTGAGTCAAACTGGCTCCAGTATCTGGTGCTCTTACATCT -s Anc1.Anc1refChr6 63783 53 + 197743 GGAGCAAATGTGACTGAGTCAAACTGGCTCCAGTATCTGGTGCTCTTACATCT -s Anc2.Anc2refChr13 37377 53 + 96486 GGAGCAAATGTGACTGAGTCAAACTGGCTCCAATATCTGGTGCTCATATATCT -s mr.mrrefChr5 255586 53 + 294540 GGAGCAAATCTGAATGGTGTAAGCTGGCTCTAGTATCGGATCCTCTTACCTAT -s simCow_chr6.simCow.chr6 393894 27 + 602619 TGAGCAAATATGACTGAATCA--------------------------ATATTT -s simDog_chr6.simDog.chr6 383659 53 + 593897 GGAGCAAATGTAACTGAGTAAAACTGGCTCCAATATCTGGTGCTCATTTGACT -s simHuman_chr6.simHuman.chr6 388068 53 + 601863 GGAGCAAATGTGACAGAGTCAAACTAGCCCCAGTCTCTGGAGCTCTTACATCT -s simRat_chr6.simRat.chr6 402392 53 + 647215 GGAGCAAATCTGATTAGTGAAAGCTGGCTCTAGTATTCAATCCTGGTACCTGT - -a -s simMouse_chr6.simMouse.chr6 402582 67 + 636262 ATCTTTGGAAAATCAGATGACCTTTGAGGTCTGGAATACATAGATCCTGCCAAATGAGGAGCTGCTA -s Anc0.Anc0refChr3 33728 67 + 222631 ATATCTGGGAAAACAGATGAAGTGTGACATCAGTCACACCTAAAACATACTGGGTAGGCAGCTGCTT -s Anc1.Anc1refChr6 63842 67 + 197743 ATATCTGGGAAAACAGATGAAGTGTGACATCAGTCACACCTAAAACATACTGGGTAGGCAGCTGCTT -s Anc2.Anc2refChr13 37436 67 + 96486 ACATCTGGGAAAACAGATGAAGTGTGACAACAGTCACACCTAAAACATACTGGGTAGGCAGCTGCTT -s mr.mrrefChr5 255645 67 + 294540 ATCTTTGGAAAATCAGATGAACTTTGAGATCTGGAATACATAAATCCTGCCAAATAAGCAGCTGCTA -s simCow_chr6.simCow.chr6 393927 67 + 602619 ACATCTGGCAAATCAGAAAAATTGTGACTACAGTTGCGCCTGGAACACACTGAGTAGGCAGCTGTGT -s simDog_chr6.simDog.chr6 383718 66 + 593897 ACATCTG-GCAAACAGATGAAGTGTGACAACAGTCACACCTAAGAACTACTTGGTAGTCAGCTGCTC -s simHuman_chr6.simHuman.chr6 388127 67 + 601863 ATATCTGGGAAAACAGATGAAGTGCAACATCAGTGACACCTAAAACATAATGGGTAGGCAGCTGCTT -s simRat_chr6.simRat.chr6 402451 67 + 647215 ATCTTTGGAAAATCGGATGAAATTTGAGATCCAGAATACATAAATCCTGCCTAATAACCAACTACTA - -a -s simMouse_chr6.simMouse.chr6 402649 96 + 636262 ACATAGCTAGTTATGTTGTTATACACCATAAATTAACCTGGTATGTGAAAGATGAGCCAATGAGGGTGGAATGAGGGTGGAATCAACTAATCAGCA -s Anc0.Anc0refChr3 33795 77 + 222631 ACA-----AGATGTGCCATCAGGCACCGTAATTTATCT---TAGGTGAAGGATAATCCAATGAGGGT-----------GGAATCAGCTAATGAGCA -s Anc1.Anc1refChr6 63909 80 + 197743 ACA-----AGATGTGCCATCAGGCACCGTAATTTATCTCAGTAGGTGAAGGATAATCCAATGAGGGT-----------GGAATCAGCTAATGAGCA -s Anc2.Anc2refChr13 37504 77 + 96486 ACA-----AGATGTACCATCAGGCACCGTAATTTATCT---TAGGTGAAGGATGATCCAATGAGGGT-----------GGCATCAGCTAATGAGTG -s mr.mrrefChr5 255712 96 + 294540 ACATAGCTAGTTATGTTGTTATACACCATAAATTAACCCAGTATGTGAAAGATAAGCCAATGAGGGTGGAATGAGGGTGGAATCAACTAATGAGCA -s simCow_chr6.simCow.chr6 393995 77 + 602619 CTG-----AGATGTTCCATCACACACCATACATTATCT---TGCCTGAAGGATGATTCAATGAGGGT-----------GGCATAAGCTAATGAGTG -s simDog_chr6.simDog.chr6 383785 77 + 593897 ACA-----AGATGTACCATTAGGCGCTGTAATTTATCT---TAGGTGAAGGATGATCCAATGAGGGT-----------GGCATCATCTAAGGAGTG -s simHuman_chr6.simHuman.chr6 388194 80 + 601863 ACA-----GGATGTGCCATCAGTCACCGTAAGTTCTCTCAGTAGGTGAAGGAAAAACTACCGCGGGT-----------GGAATCAGCTAATGAACA -s simRat_chr6.simRat.chr6 402518 95 + 647215 ACAAAGCAAGTTATGTTGTTATACACCATAAATTAAGCCAGTATGTGAAAGATAAGCCAATGAGGGCAGAATGAGGGTGTGATCATC-AATGAGCA - -a -s simMouse_chr6.simMouse.chr6 402745 25 + 636262 GTCACGACTGTCTTGTAAGTAGAGG -s Anc0.Anc0refChr3 33872 18 + 222631 TTTGTGACTGTC-------CAGATG -s Anc1.Anc1refChr6 63989 25 + 197743 TTTGTGACTGTCTTCTAAACAGATG -s Anc2.Anc2refChr13 37581 18 + 96486 TTCGCGACTGTC-------CAGATA -s mr.mrrefChr5 255808 25 + 294540 GTTATGACTGTCTTGTAAGTAGAGG -s simCow_chr6.simCow.chr6 394072 18 + 602619 CTCAGGACTGTC-------CAGATA -s simDog_chr6.simDog.chr6 383862 18 + 593897 TTCGCGACTGTC-------CACAGA -s simHuman_chr6.simHuman.chr6 388275 25 + 601863 TTTGTGACTGTCTTCTAAACAGATG -s simRat_chr6.simRat.chr6 402613 25 + 647215 GTTATGACTGTCTTGCAAGTGGAGG - -a -s simMouse_chr6.simMouse.chr6 402770 40 + 636262 ACATAGAATTTGGCCCAGGGGGTGTGTCCCTAGCTAGCTC -s Anc0.Anc0refChr3 33890 36 + 222631 AAGT----TTGGGCCCAGGTGGTGTGACCCCAGCCATTTC -s Anc1.Anc1refChr6 64014 36 + 197743 AAGT----TTGGGCCCAGGTGGTGTGACCCCAGCCATTTC -s Anc2.Anc2refChr13 37599 36 + 96486 GAGT----TTGGGTCCAGGTGGTGTGACCCCAGCCACTGC -s mr.mrrefChr5 255833 40 + 294540 ACATAGAATTTGGCCCAGGTGGTGTGTCCCTAGCTATCTC -s simCow_chr6.simCow.chr6 394090 36 + 602619 GAGT----TAGTGTCCAGGTGGTCTTACCCCAGCCCCTGC -s simDog_chr6.simDog.chr6 383883 29 + 593897 GAGT----ATGGGTC-------CGTGACCCCAGCCACTGC -s simHuman_chr6.simHuman.chr6 388300 36 + 601863 AAGT----TTGGGCCTGGGTGATGTGACCCCAGTAATTTC -s simRat_chr6.simRat.chr6 402638 40 + 647215 ATATAGAATTTGGCCCAGGTGGTGTGCCCCTAGCTATCTC - -a -s simMouse_chr6.simMouse.chr6 402810 18 + 636262 CCCTGCCAACCATCTCTT -s Anc0.Anc0refChr3 33926 18 + 222631 CCCTACCAACCATCTGTT -s Anc1.Anc1refChr6 64050 18 + 197743 CCCTACCAACCATCTGTT -s Anc2.Anc2refChr13 37635 18 + 96486 CCCTACCAACCATCTGTT -s mr.mrrefChr5 255873 18 + 294540 CCCTGCCAACCATCTCTT -s simCow_chr6.simCow.chr6 394126 18 + 602619 CCCTCCCAACCGTCTGTT -s simDog_chr6.simDog.chr6 383912 18 + 593897 CCCTACCAACCATCTGTT -s simHuman_chr6.simHuman.chr6 388357 18 + 601863 CCCTACCAACCACCTGTC -s simRat_chr6.simRat.chr6 402678 18 + 647215 CCCTGCCAGCCATCTCTT - -a -s simMouse_chr6.simMouse.chr6 402828 32 + 636262 GATTTGTTGACCTACCCCCTAAAGTTACAGAA -s Anc0.Anc0refChr3 33955 23 + 222631 GATTTGTTGACCTA--TCGTAAA-------GA -s Anc1.Anc1refChr6 64079 25 + 197743 GATTTGTTGACCTACCTCGTAAA-------GA -s Anc2.Anc2refChr13 37664 23 + 96486 GATTTGCTGACCTA--GTGTTAA-------GA -s mr.mrrefChr5 255891 32 + 294540 GATTTGTTGACCTACCTCCTAAAGTTACAGAA -s simCow_chr6.simCow.chr6 394155 11 + 602619 GATTTGA--------------AA-------GA -s simDog_chr6.simDog.chr6 383941 23 + 593897 GGTTTGCTGACCTA--GTGTTAA-------AA -s simHuman_chr6.simHuman.chr6 388386 25 + 601863 GATTTATTGACCTACCTCGTAAA-------GA -s simRat_chr6.simRat.chr6 402696 32 + 647215 GATTTGTTGACCTACTTGCTAAAGTTACAGAA - -a -s simMouse_chr6.simMouse.chr6 402860 99 + 636262 CTCTAAGTTATGGCCCTCTCCCATGATATAGTTGCTCAAGACTTAGTACATTTTTCTCAGCAACAAGATAACGTGTAGTTTGTCTATGAGGCCCTGGAC -s Anc0.Anc0refChr3 33978 92 + 222631 C------T-TTGGAACTCTCCCATGATATTGCAGCTCAAGACTTAGTACATCTCTCTCACCAAAAACATAAAGAGTAGTCTGTCTATGAGGTCACTGAC -s Anc1.Anc1refChr6 64104 92 + 197743 C------T-TTGGAACTCTCCCATGATATTGCAGCTCAAGACTTAGTACATCTCTCTCACCAAAAACATAAAGAGTAGTCTGTCTATGAGGTCACTGAC -s Anc2.Anc2refChr13 37687 92 + 96486 C------T-TTGGAACTCTCCCATGCTATTGCAGCTCAAGACTTAGTACATCTCTCTCACCTAAAACATAAAGAGAAGTCTGTCTATGAGGTCACTGGC -s mr.mrrefChr5 255923 98 + 294540 CTCTAAGT-ATGGAACTCTCCCATGATATTGTTGCTCAAGACTTAGTACATCTTTCTCACCAAAAAGATAAAGTGTAGTTTGTCTATGAGGTCCTGGAC -s simCow_chr6.simCow.chr6 394166 92 + 602619 C------C-ATAGAACTCACCAATGGTATTGCAGCTCAGTCCTTAGTACATCTCTTTCACCTATAAGATAAAGAGAAGTCTGTCTTTGAGGTTCCTGTC -s simDog_chr6.simDog.chr6 383970 92 + 593897 T------T-TTGGAGCTCTCCCAGACTATTGCAGCTCAAGACTTAGTCCATGTCTCTCACCTAAACCATGAAGAGAAGTCTGTCTATGAGGTCACTGGC -s simHuman_chr6.simHuman.chr6 388411 92 + 601863 C------T-GTGGAACACTCCCATGATCCTGCCGTTCAAGGTTTAGTAGGTCTCTCTCACCAGAAATATAAAGAGTAGTCTCTCTATGATGTCTGCGAT -s simRat_chr6.simRat.chr6 402728 98 + 647215 CTCTCAGT-ATGGAACTCTTCCATGATATTGTTGCTCAAGACTCAGTATATCTTTCTCACCAAAAAGATAGAGTGTAGTTTGTCTATGAGGTCCTGGAC - -a -s simMouse_chr6.simMouse.chr6 402959 9 + 636262 TTGACAGCC -s Anc0.Anc0refChr3 34070 9 + 222631 TTGATAGCT -s Anc1.Anc1refChr6 64196 9 + 197743 TTGATAGCT -s Anc2.Anc2refChr13 37779 9 + 96486 TTGATAGCT -s mr.mrrefChr5 256021 9 + 294540 TTGATAGCT -s simCow_chr6.simCow.chr6 394270 9 + 602619 TTGATAGCT -s simDog_chr6.simDog.chr6 384062 9 + 593897 TTGATAGCT -s simHuman_chr6.simHuman.chr6 388503 9 + 601863 TTGATAGCT -s simRat_chr6.simRat.chr6 402826 9 + 647215 TTGATAGCT - -a -s simMouse_chr6.simMouse.chr6 402968 29 + 636262 ATTAAATGTGGCTCTGGGGAGTGATCAAG -s Anc0.Anc0refChr3 34079 28 + 222631 GAT-AATGTGTCTCTATGGAGTGATCAAG -s Anc1.Anc1refChr6 64205 28 + 197743 GAT-AATGTGTCTCTATGGAGTGATCAAG -s Anc2.Anc2refChr13 37824 28 + 96486 GAT-AATGTGTCTCTATGAAGTGATCAAG -s mr.mrrefChr5 256030 29 + 294540 ATTAAATGTGGCTCTGGGGAGTGATCAAG -s simCow_chr6.simCow.chr6 394315 24 + 602619 GAT-----TGTCTCTATGAAGTGATCAAA -s simDog_chr6.simDog.chr6 384108 28 + 593897 GAT-AATGTGTCTCTATGAAGTGATCAAG -s simHuman_chr6.simHuman.chr6 388512 28 + 601863 GAT-AATCTGTCTCTATGGAGTGATAAAG -s simRat_chr6.simRat.chr6 402835 29 + 647215 ATCAAATGTAGCTCTGAGGAGCGATCAAG - -a -s simMouse_chr6.simMouse.chr6 402997 1 + 636262 G -s Anc0.Anc0refChr3 34111 1 + 222631 G -s Anc1.Anc1refChr6 64237 1 + 197743 G -s Anc2.Anc2refChr13 37856 1 + 96486 G -s mr.mrrefChr5 256063 1 + 294540 G -s simCow_chr6.simCow.chr6 394343 1 + 602619 G -s simDog_chr6.simDog.chr6 384140 1 + 593897 G -s simHuman_chr6.simHuman.chr6 388544 1 + 601863 G -s simRat_chr6.simRat.chr6 402868 1 + 647215 G - -a -s simMouse_chr6.simMouse.chr6 402998 9 + 636262 AGACATATA -s Anc0.Anc0refChr3 34112 9 + 222631 GGACATATA -s Anc1.Anc1refChr6 64238 9 + 197743 GGACATATA -s Anc2.Anc2refChr13 37858 9 + 96486 GGCCACATG -s mr.mrrefChr5 256064 9 + 294540 GGACATATA -s simCow_chr6.simCow.chr6 394345 9 + 602619 AGCCACATG -s simDog_chr6.simDog.chr6 384142 9 + 593897 GGCCACATG -s simHuman_chr6.simHuman.chr6 388545 9 + 601863 GGACATATA -s simRat_chr6.simRat.chr6 402869 9 + 647215 GGAGATATA - -a -s simMouse_chr6.simMouse.chr6 403007 19 + 636262 TTAGCATTCTAACCACATT -s Anc0.Anc0refChr3 34136 19 + 222631 TTCGCATCTTTATTACTTT -s Anc1.Anc1refChr6 64262 19 + 197743 TTCGCATCTTTATTACTTT -s Anc2.Anc2refChr13 37882 19 + 96486 CTCGCATCCTTATTACTTT -s mr.mrrefChr5 256073 19 + 294540 TTAGCATTTTAACCACATT -s simCow_chr6.simCow.chr6 394427 19 + 602619 CCAGCATCCTTATTGCTGT -s simDog_chr6.simDog.chr6 384166 19 + 593897 CTCTCATCCTTATTATCTT -s simHuman_chr6.simHuman.chr6 388569 19 + 601863 TTGGTGTCTCCATTACTTT -s simRat_chr6.simRat.chr6 402878 15 + 647215 TTAGCATTT----AGCATT - -a -s simMouse_chr6.simMouse.chr6 403026 20 + 636262 GGACACTCCTTCCCCATTTC -s Anc0.Anc0refChr3 34155 20 + 222631 GGACACACTCTTTCTTTGCT -s Anc1.Anc1refChr6 64281 20 + 197743 GGACACACTCTTTCTTTGCT -s Anc2.Anc2refChr13 37901 20 + 96486 GGACACACTCTTTCTTTGCT -s mr.mrrefChr5 256092 20 + 294540 GGACACTCTTTCCCCATTTC -s simCow_chr6.simCow.chr6 394446 20 + 602619 GGACACACTCTTTCTTTGCT -s simDog_chr6.simDog.chr6 384185 15 + 593897 ACACACACTCTTTC-----T -s simHuman_chr6.simHuman.chr6 388588 20 + 601863 GGACACACTCTTTCTCGGAT -s simRat_chr6.simRat.chr6 402894 20 + 647215 TGACACTCTTTCCCCATTAC - -a -s simMouse_chr6.simMouse.chr6 403046 295 + 636262 CAAGATAAGACAATGTACACGGAGGGATGTCATTGTTTGACAGTGCGTAAATCCGGACAGGGTCTACAATATATGCGCTGAGATTGCTCGACAGTTCGTTACGCGGGGCAAACTCACAGCCAAGCCCTGAACATTATGGCCGTGCAGGGCAAGCATAGCCAAGCACTGACTGTCTGTACATGGCCACATGGGGAAGGGGCATAGCCAAGCACGAATCATGTGTACATGGCTGCGTTTGCCTTCTTTTGGAGATTTGCACAAGGCACTGTGCAAAGTCTAAGTAATGTTAAAGTCT -s Anc0.Anc0refChr3 34175 17 + 222631 GACAA-AAAACAAGTTA-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------T -s Anc1.Anc1refChr6 64301 17 + 197743 GACAA-AAAACAAGTTA-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------T -s Anc2.Anc2refChr13 37921 17 + 96486 GACAA-ACAACAAGTTA-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------G -s mr.mrrefChr5 256112 17 + 294540 CAAGA-AAGACAAGGTA-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------T -s simCow_chr6.simCow.chr6 394472 17 + 602619 GTCAA-AGCACAAGTTA-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------G -s simDog_chr6.simDog.chr6 384200 16 + 593897 AACAA-ACAA-AAGTTT-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------G -s simHuman_chr6.simHuman.chr6 388608 17 + 601863 GCCAA-AAAATAAGTTA-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------T -s simRat_chr6.simRat.chr6 402914 13 + 647215 CAAGA-----CAAGGTA-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------T - -a -s simMouse_chr6.simMouse.chr6 403341 24 + 636262 GGGGCTGGTCATGATACATGATAA -s Anc0.Anc0refChr3 34194 24 + 222631 GTGGGTGGTCATGATACATGATAA -s Anc1.Anc1refChr6 64320 24 + 197743 GTGGGTGGTCATGATACATGATAA -s Anc2.Anc2refChr13 37940 24 + 96486 GTGGGTGGCCATGATACATGATAA -s mr.mrrefChr5 256129 24 + 294540 GAGGCTGGTCATGATACATGATAA -s simCow_chr6.simCow.chr6 394491 24 + 602619 CCAGGTGGCCATGATACATGATAA -s simDog_chr6.simDog.chr6 384218 24 + 593897 GTGGGTGGCCATGATACATGTTAA -s simHuman_chr6.simHuman.chr6 388627 24 + 601863 GGTGGTGCTCATGATACATGATAA -s simRat_chr6.simRat.chr6 402927 24 + 647215 GAGGCTGATCATGATACATGTTAA - -a -s simMouse_chr6.simMouse.chr6 403365 11 + 636262 ACGTTTGTGAG -s Anc0.Anc0refChr3 34218 11 + 222631 ATGTGTGTAAG -s Anc1.Anc1refChr6 64344 11 + 197743 ATGTGTGTAAG -s Anc2.Anc2refChr13 37964 11 + 96486 ATCTGTGTAAG -s mr.mrrefChr5 256153 11 + 294540 ACGTTTGTGAG -s simCow_chr6.simCow.chr6 394515 11 + 602619 GTCTGTGCAAG -s simDog_chr6.simDog.chr6 384246 11 + 593897 ATCTGTGTTGG -s simHuman_chr6.simHuman.chr6 388651 11 + 601863 ATGTGTGTAAG -s simRat_chr6.simRat.chr6 402951 11 + 647215 ACATTTGTGAG - -a -s simMouse_chr6.simMouse.chr6 403376 11 + 636262 TGAGTCATTGC -s Anc0.Anc0refChr3 34230 11 + 222631 TCAGACATTGC -s Anc1.Anc1refChr6 64356 11 + 197743 TCAGACATTGC -s Anc2.Anc2refChr13 37976 11 + 96486 TCAGACATTGC -s mr.mrrefChr5 256164 11 + 294540 TGAGTCATTGC -s simCow_chr6.simCow.chr6 394527 10 + 602619 CCAGACA-TGC -s simDog_chr6.simDog.chr6 384258 11 + 593897 TCAGACATTGC -s simHuman_chr6.simHuman.chr6 388663 11 + 601863 TCAGACATTGC -s simRat_chr6.simRat.chr6 402962 11 + 647215 TGAGTCATTAC - -a -s simMouse_chr6.simMouse.chr6 403387 6 + 636262 TAAACA -s Anc0.Anc0refChr3 34241 6 + 222631 TAGACA -s Anc1.Anc1refChr6 64367 6 + 197743 TAGACA -s Anc2.Anc2refChr13 37987 6 + 96486 CAGACA -s mr.mrrefChr5 256175 6 + 294540 TAGACA -s simCow_chr6.simCow.chr6 394537 4 + 602619 CAG--A -s simDog_chr6.simDog.chr6 384269 6 + 593897 GAGACA -s simHuman_chr6.simHuman.chr6 388848 6 + 601863 TGGACA -s simRat_chr6.simRat.chr6 402973 6 + 647215 TAGACA - -a -s simMouse_chr6.simMouse.chr6 403393 126 + 636262 AGGCAGCATTACTTATCCAAGATTCAAGGGTTATAAGAGTTGTCAGTTGTGTGTGTATTTATAGGCCTTTCTAGTAAATTGAAATGCTAACTCCCCTGTACAGGCACATCCAGACTAGCCCTATCG -s Anc0.Anc0refChr3 34247 125 + 222631 AGGCAG-TTTAATTTTCAATGAGCCAAGGGTAACAGGAGAGTTCATTCGAGGGTATATTTATGGTCCTTGCTAGTCACTCAAGATACTAATTGCCCTGTGTGGGCACACACAGACTAGCCCCAATG -s Anc1.Anc1refChr6 64373 126 + 197743 AGGCAGATTTAATTTTCAATGAGCCAAGGGTAACAGGAGAGTTCATTCGAGGGTATATTTATGGTCCTTGCTAGTCACTCAAGATACTAATTGCCCTGTGTGGGCACACACAGACTAGCCCCAATG -s Anc2.Anc2refChr13 37995 125 + 96486 AGGCAG-TTTAATTTTCAATGAGCCAAGGGTAACAGGAGAGTTCATTCGAGGGAATATTTATGGTCCTTGCTAGTCACTCAAGATACTAATTGCCCTGTGTGGGCCTACACAGACTAGCCCCAATG -s mr.mrrefChr5 256181 126 + 294540 AGGCAGCATTAATTATCCATGATTCAAGGGTTATAGGAGTTGTCAGTTGAGTGTGTATTTATAGGCCTTTCTAGTAAATTGAAATACTAACTCCCCTGTACAGGCACACCCAGACTAGCCCTATCG -s simCow_chr6.simCow.chr6 394543 122 + 602619 AGGCAC-AATAATTATCAATGAGCCAAA---AACAGGTGAGTTCAGTCAGGGGCATATCTATGGCCCTGGCTAGAGACTCAAGGTGTTAATTGCCCTGTATAGGCCTACCCAGACTAGTCCCGAAG -s simDog_chr6.simDog.chr6 384277 123 + 593897 AGGCAG-TTTAATTTTCAATGAGCCAGGGGTGACATGAGAATTCATTCGAGGGAATATTTATGTTCCTTGCTAGTCAATCAAGATACCAATTGCCCTGTGTGGG--TATACAAACTAGCCCCAATG -s simHuman_chr6.simHuman.chr6 388854 122 + 601863 ATGCAGATTTAATTCTTGATGAGCCGAGGGCAACAGGAGAGATCAATAGAGGGTATAATTATCGACCTTGCTAGTTACTCAAGA-ACTAATTGCCCTGTGTGAGCACACTCAGTCTCGCCTCA--- -s simRat_chr6.simRat.chr6 402979 125 + 647215 AGGCAGCAT-AATTATCCATGATTTAAGGGTTATAGGAGCTGTCAGTTGAGTGTGTATTTATAGTCTTTTCTAATAATTTGGAACACTAACTCCCCTGTACAGACACACCCAGACTAACGCTATCG - -a -s simMouse_chr6.simMouse.chr6 403519 6 + 636262 AGTGGA -s Anc0.Anc0refChr3 34372 6 + 222631 AATGGG -s Anc1.Anc1refChr6 64499 6 + 197743 AATGGG -s Anc2.Anc2refChr13 38121 6 + 96486 AATGGG -s mr.mrrefChr5 256307 6 + 294540 AGTGGA -s simCow_chr6.simCow.chr6 394666 6 + 602619 GATGGA -s simDog_chr6.simDog.chr6 384403 6 + 593897 AATGGG -s simRat_chr6.simRat.chr6 403104 6 + 647215 AACAGG - -a -s simMouse_chr6.simMouse.chr6 403525 13 + 636262 TGAAATTTAACTG -s Anc0.Anc0refChr3 34378 13 + 222631 GAGACCTTAACTA -s Anc1.Anc1refChr6 64505 13 + 197743 GAGACCTTAACTA -s Anc2.Anc2refChr13 38127 13 + 96486 GAGACCTTAACTA -s mr.mrrefChr5 256313 13 + 294540 TGAAATTTAACTG -s simCow_chr6.simCow.chr6 394680 13 + 602619 GGGTCTTTCACTA -s simDog_chr6.simDog.chr6 384409 13 + 593897 GAGACCTTAACTA -s simRat_chr6.simRat.chr6 403110 13 + 647215 CTAAATTTAACTG - -a -s simMouse_chr6.simMouse.chr6 403538 12 + 636262 CCAAAGATAGCA -s Anc0.Anc0refChr3 34391 11 + 222631 C-AAAAACAGTA -s Anc1.Anc1refChr6 64518 11 + 197743 C-AAAAACAGTA -s Anc2.Anc2refChr13 38157 11 + 96486 C-AAAAACAGTA -s mr.mrrefChr5 256326 11 + 294540 C-AAAGATAGCA -s simCow_chr6.simCow.chr6 394710 11 + 602619 C-AAAAGCAGTA -s simDog_chr6.simDog.chr6 384439 11 + 593897 C-AAAAATAATA -s simHuman_chr6.simHuman.chr6 388976 11 + 601863 A-AAAAACAGTA -s simRat_chr6.simRat.chr6 403123 11 + 647215 C-AGAGATAGCA - -a -s simMouse_chr6.simMouse.chr6 403550 19 + 636262 AATATTCAGGGGATGTGGG -s Anc0.Anc0refChr3 34403 19 + 222631 ATCAATCAGGGAACATGGA -s Anc1.Anc1refChr6 64530 19 + 197743 ATCAATCAGGGAACATGGA -s Anc2.Anc2refChr13 38169 19 + 96486 ATCAATCAGGGAACATGGA -s mr.mrrefChr5 256338 19 + 294540 AATATTCAGGGAATGTGGG -s simCow_chr6.simCow.chr6 394722 19 + 602619 ATCAATCAGGGAGCATGGA -s simDog_chr6.simDog.chr6 384451 19 + 593897 ATCAATCAGGGAACATGGA -s simHuman_chr6.simHuman.chr6 388988 19 + 601863 CTCAATCAGGCAACATGGA -s simRat_chr6.simRat.chr6 403135 19 + 647215 AATACTCGGGGAAAGTGGG - -a -s simMouse_chr6.simMouse.chr6 403569 139 + 636262 CATGGACCATCTATATTCTACCCTACTTTCATCTCGCCGAGCATCAGAGCTGAGCAGAGATAATTATGTATAAACATGGTAAGACTATTGCCCAACTATTGAGCATCACATGTGGTCTCTCAAGGATGCAGGATCCTGG -s Anc0.Anc0refChr3 34423 138 + 222631 CACTGACTAAATAAATTCTATCCTGCCTGCATTTTTCAGAGTGTTAG-TCTGAACAGACAATAACATGTTTAAACATAGTTGGACTACTGCCCAAGTATTGAATCTCACATGTGGTCTTTCCAGAAGGCATCAGCCCAA -s Anc1.Anc1refChr6 64550 138 + 197743 CACTGACTAAATAAATTCTATCCTGCCTGCATTTTTCAGAGTGTTAG-TCTGAACAGACAATAACATGTTTAAACATAGTTGGACTACTGCCCAAGTATTGAATCTCACATGTGGTCTTTCCAGAAGGCATCAGCCCAA -s Anc2.Anc2refChr13 38189 138 + 96486 CACTGACCCAATAAATTCCATCCTGGCTGCACTTTTCAGAGTGTTAG-TCTGAACAGACCATAACATGTTTAAACATAGTTGGACCACTACCCAAGTGTTGAACCTCACATGTGATCTTCCCAGAAGGCATCAGCCCAA -s mr.mrrefChr5 256357 138 + 294540 CATGGACTATATATATTCTACCCTACTTTCATCTCGCCGAGCATCAG-GCTGAGCAGAGATAATTATGTATAAACATAGTAAGACTATTGCCCAACTATTGAGTATCACATGTGGTCTCTCAAGGATGCAGGATCCTGA -s simCow_chr6.simCow.chr6 394742 136 + 602619 CAGTGACCTGATAAACTCAATCCTGGCTGCACTTTTCGGAGTGTTAG-TCTGAACAGGTGATAACATGCTTAAAC--AGTAGGACCACCACACAAATTTCGGACCTCACCTATGACCTTCCCTGAGGGCATGAGCCTGC -s simDog_chr6.simDog.chr6 384471 131 + 593897 CGCTGACCCAATAAGTTCCATCCTGGCTGCACTGTTCAGAGT-TTAG-T------ATACCATAACATGTTTAGGCATAGCTCAATCTCTACCCAAGTGTTGAACATCACATGTGATCTTCCAAGAAGGCACCAGCCCAA -s simHuman_chr6.simHuman.chr6 389008 138 + 601863 CAATGACTACATAAAGTCTATCCTGCCTGCATTTTTCAGAGTGTTAG-TCTGAACAGACAATAACGTGTGTAAACATAGTGGGACTAGTGCCCAAGTACTGAATCTCACATGTGGTCTTTCCAGAAGACATCAGTCCAA -s simRat_chr6.simRat.chr6 403154 122 + 647215 GACGGACTATATATATGCTACCCTACTTTCAGC-------GCA----------GCAGAGATAGTTATGTAGAAACAGAGTAAGGATATTACCCAACTATTAAGTGTCATAGACGGTCTCTCAAGGATGCAGGATCCTGA - -a -s simMouse_chr6.simMouse.chr6 403708 55 + 636262 ACTGAGGGCTGGGAAGAACTTTAGCTTTTATGAGTATGAGAAACTAGTTTGGGTT -s Anc0.Anc0refChr3 34569 47 + 222631 ATTGAGA--------AAACTTTAGCTCTAATGAGTGTGGGCAACTAGTTAGGTTT -s Anc1.Anc1refChr6 64696 54 + 197743 ATTGAGAGCTCTG-GAAACTTTAGCTCTAATGAGTGTGGGCAACTAGTTAGGTTT -s Anc2.Anc2refChr13 38335 47 + 96486 ATTGAGA--------AAACTTTACTTCTAATGAGTGTGGGCAACTAGTTAGGTTT -s mr.mrrefChr5 256503 55 + 294540 ACTGAGAGCTGGGAGGAACTTTAGCTTTTATGAGTATGAGAAACTAGTTAGGGTT -s simCow_chr6.simCow.chr6 394886 47 + 602619 ATCAAGA--------GGACTTTACTTCTAATTAGTGTGGGCAACTAGTTGTGTTT -s simDog_chr6.simDog.chr6 384610 36 + 593897 ATTGAGA--------AAAC---------AATGAGCGTGA--GACTAGTTAGGTTT -s simHuman_chr6.simHuman.chr6 389154 54 + 601863 ATTGAAAGCTCTG-GAAGCTTTAGCTCTGATGAGTGAGGACAACTAGTTAGGTCT -s simRat_chr6.simRat.chr6 403284 55 + 647215 ACTGTGAGTTGGGCGGAACCTTAGCTTTAATGAGTATGAGAAACTACTTAGGCTG - -a -s simMouse_chr6.simMouse.chr6 403763 14 + 636262 TTTGAAAACCAGAC -s Anc0.Anc0refChr3 34628 14 + 222631 GTTGAAAACTAGAC -s Anc1.Anc1refChr6 64762 14 + 197743 GTTGAAAACTAGAC -s Anc2.Anc2refChr13 38394 14 + 96486 GTTGAAAACTAGAC -s mr.mrrefChr5 256568 14 + 294540 TTTGAAAACCAGAC -s simCow_chr6.simCow.chr6 394945 14 + 602619 GTTGAAAACTAGAC -s simDog_chr6.simDog.chr6 384658 14 + 593897 GTTGACAAGCAGAC -s simHuman_chr6.simHuman.chr6 389220 14 + 601863 GCCAAAAACTATAT -s simRat_chr6.simRat.chr6 403349 14 + 647215 TTTGAAAACTAGAC - -a -s simMouse_chr6.simMouse.chr6 403777 51 + 636262 TATTAGTGAGCTTTTTGGTCAGTGGTGACACCTGTAATGCACAGCAGCACA -s Anc0.Anc0refChr3 34652 51 + 222631 TATAAGTGGGACTTAGGGTCAGTGGTGATGCATGTAATGCACTGCAGCAGA -s Anc1.Anc1refChr6 64786 51 + 197743 TATAAGTGGGACTTAGGGTCAGTGGTGATGCATGTAATGCACTGCAGCAGA -s Anc2.Anc2refChr13 38418 51 + 96486 TTTAAGTGGGACTTAGGGTCAGTAGTAATGCATGTAATGCACTGCAACAGC -s mr.mrrefChr5 256582 51 + 294540 TATTAGTGAGGTTTTTGGTCAGTGGTGACACCTGTAATGCACAGCAGCACA -s simCow_chr6.simCow.chr6 394967 45 + 602619 ------TGGGACTGAGGGTGAGTAGTATTGTTTGTAATGCATTGCCACAGC -s simDog_chr6.simDog.chr6 384682 50 + 593897 TTTAAGTGGGACTTGGGGTCACTAGTAATGCATGTAGTGTACAGCAACAG- -s simHuman_chr6.simHuman.chr6 389274 49 + 601863 TATAAGTGGATGTTAGGGTCCGTG--GATGGATGTAATGCACTCCAGCAGA -s simRat_chr6.simRat.chr6 403363 51 + 647215 TATCAGTGGGGTTTATGGTCAGTGGTGACACATGTAATGCACGGCAGCACA - -a -s simMouse_chr6.simMouse.chr6 403828 4 + 636262 GTGG -s Anc0.Anc0refChr3 34707 4 + 222631 GTGG -s Anc1.Anc1refChr6 64841 4 + 197743 GTGG -s Anc2.Anc2refChr13 38473 4 + 96486 GTGA -s mr.mrrefChr5 256633 4 + 294540 GTGG -s simCow_chr6.simCow.chr6 395016 4 + 602619 GTGA -s simDog_chr6.simDog.chr6 384735 4 + 593897 GTGA -s simHuman_chr6.simHuman.chr6 389327 4 + 601863 GTGG -s simRat_chr6.simRat.chr6 403414 4 + 647215 GTGA - -a -s simMouse_chr6.simMouse.chr6 403832 13 + 636262 GATTCAGTTCTGG -s Anc0.Anc0refChr3 34711 13 + 222631 CATTCAATGGTGA -s Anc1.Anc1refChr6 64845 13 + 197743 CATTCAATGGTGA -s Anc2.Anc2refChr13 38477 13 + 96486 CATTCAATGGTGA -s mr.mrrefChr5 256637 13 + 294540 GATTCAGTTGTGG -s simCow_chr6.simCow.chr6 395020 13 + 602619 CATTCAATGGCTA -s simDog_chr6.simDog.chr6 384746 13 + 593897 CATTCAATGGTGg -s simHuman_chr6.simHuman.chr6 389331 13 + 601863 TATTCAATGGTGA -s simRat_chr6.simRat.chr6 403418 13 + 647215 GATTCAATCGTGG - -a -s simMouse_chr6.simMouse.chr6 403845 71 + 636262 CTAATATTCTACCATTGTACAGGTGTAATCTTCTTAAGCAAAGTAGGGTTCTTTCAGTAGCCCCAGTGGTG -s Anc0.Anc0refChr3 34724 12 + 222631 TTa-----cgatcac------------------------------------------------------tc -s Anc1.Anc1refChr6 64858 12 + 197743 TTA-----CGATCAC------------------------------------------------------TC -s Anc2.Anc2refChr13 38490 12 + 96486 TTa-----tgatttc------------------------------------------------------tc -s mr.mrrefChr5 256650 71 + 294540 CTAATATTCTATCATTGTACAGGTGTAATCTTCTTAAGCAAAGTAGGGTTCTTTCAGTAGCCCCAGTGGTG -s simCow_chr6.simCow.chr6 395034 12 + 602619 AAa-----tggttcc------------------------------------------------------ta -s simDog_chr6.simDog.chr6 384759 12 + 593897 tta-----tgatttg------------------------------------------------------tc -s simHuman_chr6.simHuman.chr6 389344 12 + 601863 GTA-----CAATCAC------------------------------------------------------TC -s simRat_chr6.simRat.chr6 403431 30 + 647215 CTAATATTCTATCATTG--CAGGTGTA---------------------------------------TGGTG - -a -s simMouse_chr6.simMouse.chr6 403916 16 + 636262 ACTCCTAACCTTAAAG -s Anc0.Anc0refChr3 34736 15 + 222631 ACTCCT-ACATTAAAG -s Anc1.Anc1refChr6 64870 15 + 197743 ACTCCT-ACATTAAAG -s Anc2.Anc2refChr13 38592 15 + 96486 ACTCCT-ACATTAAGG -s mr.mrrefChr5 256721 16 + 294540 ACTCCTAACCTTAAAG -s simCow_chr6.simCow.chr6 395152 15 + 602619 CCTCCT-ACATTCAGG -s simDog_chr6.simDog.chr6 384868 15 + 593897 ACTCAT-ACATCAAGA -s simHuman_chr6.simHuman.chr6 389356 15 + 601863 GCTCCT-ACATTAAAG -s simRat_chr6.simRat.chr6 403461 16 + 647215 ACTCCTAACCTTAAAG - -a -s simMouse_chr6.simMouse.chr6 403932 33 + 636262 CCAACTTGCAAGCATAATCAGCAGATTAGCTTT -s Anc0.Anc0refChr3 34751 33 + 222631 CAAGCCTATAAGTATAGTTCCCAGCTTGGCTTT -s Anc1.Anc1refChr6 64885 33 + 197743 CAAGCCTATAAGTATAGTTCCCAGCTTGGCTTT -s Anc2.Anc2refChr13 38607 33 + 96486 CAGGCCTTTAAGTATAGTACCCAGCTTGGCTTT -s mr.mrrefChr5 256737 33 + 294540 CCAGCTTACAAGCATAGTTAGCAGATTAGCTTT -s simCow_chr6.simCow.chr6 395168 32 + 602619 CA-GCCTGTAAGTATAGTACCCAGCTTGGCTTT -s simDog_chr6.simDog.chr6 384883 31 + 593897 CAGCCTGTTGAGTATAG--CCCAGCTTGGTTTT -s simHuman_chr6.simHuman.chr6 389371 33 + 601863 CAAGCCTATAAGTTTAGTTCCCAGCTTGGCTTT -s simRat_chr6.simRat.chr6 403477 33 + 647215 CCAGCTTACAAGCATAGTTAGCAGATTAGCTTA - -a -s simMouse_chr6.simMouse.chr6 403965 13 + 636262 GAGCAAGGTAACA -s Anc0.Anc0refChr3 34784 13 + 222631 GAGCAAGGTAACA -s Anc1.Anc1refChr6 64918 13 + 197743 GAGCAAGGTAACA -s Anc2.Anc2refChr13 38640 13 + 96486 GAGTGAGGTAACA -s mr.mrrefChr5 256770 13 + 294540 GAGCAAGGTAACA -s simCow_chr6.simCow.chr6 395200 13 + 602619 GTGTGAGGTAATG -s simDog_chr6.simDog.chr6 384916 13 + 593897 GAGTGGGGTGACA -s simHuman_chr6.simHuman.chr6 389404 13 + 601863 GATCAAGACAGCA -s simRat_chr6.simRat.chr6 403510 13 + 647215 GTGTAAGGTAACA - -a -s simMouse_chr6.simMouse.chr6 403978 11 + 636262 CCGTACATCTT -s Anc0.Anc0refChr3 34797 11 + 222631 CCACACATCCT -s Anc1.Anc1refChr6 64931 11 + 197743 CCACACATCCT -s Anc2.Anc2refChr13 38653 11 + 96486 CCACACATCCT -s mr.mrrefChr5 256783 11 + 294540 CCATACATCTT -s simCow_chr6.simCow.chr6 395214 11 + 602619 CCACACGTCCA -s simDog_chr6.simDog.chr6 384929 11 + 593897 CCACACATCCT -s simHuman_chr6.simHuman.chr6 389417 11 + 601863 TCACACATTCT -s simRat_chr6.simRat.chr6 403523 11 + 647215 CCATATATATT - -a -s simMouse_chr6.simMouse.chr6 403989 18 + 636262 CACCCTCATTCAGGATAC -s Anc0.Anc0refChr3 34812 18 + 222631 TAGCCTCATCCAGGATGT -s Anc1.Anc1refChr6 64946 18 + 197743 TAGCCTCATCCAGGATGT -s Anc2.Anc2refChr13 38668 18 + 96486 TGGCCTCATCCAGGCTAT -s mr.mrrefChr5 256798 18 + 294540 CACCCTCATTCAGGATGC -s simCow_chr6.simCow.chr6 395229 18 + 602619 TTGCCTCGTGCAGGCTAT -s simDog_chr6.simDog.chr6 384944 18 + 593897 AGGCCTCATCGAGGCTAT -s simHuman_chr6.simHuman.chr6 389432 18 + 601863 TATCCTCATCCACGATGT -s simRat_chr6.simRat.chr6 403538 18 + 647215 CTCCCTCATTCATGATGC - -a -s simMouse_chr6.simMouse.chr6 404007 30 + 636262 TTATAGGATGTTGGACTATTTATAGCCATC -s Anc0.Anc0refChr3 34858 29 + 222631 GGAGAAGATGTCA-AGCATCTTTAGGTAGC -s Anc1.Anc1refChr6 64992 29 + 197743 GGAGAAGATGTCA-AGCATCTTTAGGTAGC -s Anc2.Anc2refChr13 38714 29 + 96486 GGAGAAAATGTCT-AGCATCTTTAGGTAGT -s mr.mrrefChr5 256816 29 + 294540 TGATAGGATGTCA-ACTATTTATAGCCATC -s simCow_chr6.simCow.chr6 395275 27 + 602619 GG--AAAAAGTTG-AGCCTCTTTAGGTAGT -s simDog_chr6.simDog.chr6 385056 29 + 593897 AGAGAAAGTGTCT-AGTATCTTTAGGTAGT -s simHuman_chr6.simHuman.chr6 389478 29 + 601863 GGACAAGATGTCA-AGCATCTTTTGGTGGC -s simRat_chr6.simRat.chr6 403556 29 + 647215 TGATAGGATGTCA-ACAATTTATAGCCATC - -a -s simMouse_chr6.simMouse.chr6 404037 33 + 636262 CAGATATTTCTAACAGTTTTTATGTTCATCCTT -s Anc0.Anc0refChr3 34909 30 + 222631 CAGACAGTTC-AACT--TTTTATGTCTGTCCTT -s Anc1.Anc1refChr6 65043 32 + 197743 CAGACAGTTC-AACTGTTTTTATGTCTGTCCTT -s Anc2.Anc2refChr13 38765 30 + 96486 CAGTCAGTCG-AACT--TTTTATGTCTGTCCTT -s mr.mrrefChr5 256845 33 + 294540 CAGATAGTTCTAACAGTTTTTATGTTCGTCCTT -s simCow_chr6.simCow.chr6 395324 30 + 602619 CAGCAGTTCA-ATGT--TTTTGTGTCTGTGCTT -s simDog_chr6.simDog.chr6 385107 30 + 593897 CAGTCAGTCG-AACT--CTTTATGTCTCTCCTT -s simHuman_chr6.simHuman.chr6 389529 32 + 601863 CAGACAGTTC-AACTGTTTTTATGTCAGTCCTT -s simRat_chr6.simRat.chr6 403585 33 + 647215 CAGATAGTTCTAAGAGTTTTTATGTTGGTTCTT - -a -s simMouse_chr6.simMouse.chr6 404070 2 + 636262 TG -s Anc0.Anc0refChr3 34942 2 + 222631 TA -s Anc1.Anc1refChr6 65078 2 + 197743 TA -s Anc2.Anc2refChr13 38798 2 + 96486 TA -s mr.mrrefChr5 256878 2 + 294540 TG -s simCow_chr6.simCow.chr6 395357 2 + 602619 TA -s simDog_chr6.simDog.chr6 385140 2 + 593897 TA -s simHuman_chr6.simHuman.chr6 389564 2 + 601863 TA -s simRat_chr6.simRat.chr6 403618 2 + 647215 TG - -a -s simMouse_chr6.simMouse.chr6 404072 7 + 636262 GCCTGCA -s Anc0.Anc0refChr3 34944 7 + 222631 ACCTCAA -s Anc1.Anc1refChr6 65080 7 + 197743 ACCTCAA -s Anc2.Anc2refChr13 38803 7 + 96486 ACCTCAA -s mr.mrrefChr5 256880 7 + 294540 GCCTCAA -s simCow_chr6.simCow.chr6 395362 7 + 602619 GCCCCAA -s simDog_chr6.simDog.chr6 385145 7 + 593897 ACCTCAA -s simHuman_chr6.simHuman.chr6 389566 7 + 601863 ACCTCAA -s simRat_chr6.simRat.chr6 403620 7 + 647215 GCCTCAA - -a -s simMouse_chr6.simMouse.chr6 404079 29 + 636262 TGGTGATTGCAGAGAAAATGGTGATTCCA -s Anc0.Anc0refChr3 34951 29 + 222631 GGGTGAATGCAAATAAAAGGGCTGTGGTA -s Anc1.Anc1refChr6 65087 29 + 197743 GGGTGAATGCAAATAAAAGGGCTGTGGTA -s Anc2.Anc2refChr13 38810 29 + 96486 GGGTGTATGCAAATAAAAGAGATGTGGTA -s mr.mrrefChr5 256887 29 + 294540 TGGTGAATGCAGAGAAAATGGCGATTCCA -s simCow_chr6.simCow.chr6 395369 28 + 602619 GGGTGGATGC-TATAAAAGACGTGTGGTA -s simDog_chr6.simDog.chr6 385152 29 + 593897 AGGTGTAGGGAAATAAAAGAGATGTGGTA -s simHuman_chr6.simHuman.chr6 389574 29 + 601863 GGGTGAATGCAAATAAAGGGGCTGTGTTA -s simRat_chr6.simRat.chr6 403627 29 + 647215 TAGTGAATGAAGAGAAGATGGCGATTCCA - -a -s simMouse_chr6.simMouse.chr6 404108 2 + 636262 CA -s Anc0.Anc0refChr3 34980 2 + 222631 AA -s Anc1.Anc1refChr6 65116 2 + 197743 AA -s Anc2.Anc2refChr13 38839 2 + 96486 AA -s mr.mrrefChr5 256916 2 + 294540 CA -s simCow_chr6.simCow.chr6 395397 2 + 602619 AG -s simDog_chr6.simDog.chr6 385183 2 + 593897 AA -s simHuman_chr6.simHuman.chr6 389603 2 + 601863 AA -s simRat_chr6.simRat.chr6 403656 2 + 647215 CA - -a -s simMouse_chr6.simMouse.chr6 404110 9 + 636262 GATAAGACG -s Anc0.Anc0refChr3 34982 5 + 222631 G----CCCG -s Anc1.Anc1refChr6 65118 5 + 197743 G----CCCG -s Anc2.Anc2refChr13 38841 5 + 96486 G----CCCG -s mr.mrrefChr5 256918 9 + 294540 GATAACACG -s simCow_chr6.simCow.chr6 395460 5 + 602619 G----CCCA -s simDog_chr6.simDog.chr6 385185 5 + 593897 A----TCAG -s simHuman_chr6.simHuman.chr6 389605 5 + 601863 G----CCCG -s simRat_chr6.simRat.chr6 403658 9 + 647215 CATAACATG - -a -s simMouse_chr6.simMouse.chr6 404119 32 + 636262 GATAAATTTCGTTCCCAGTCAGCGCCCCTGGT -s Anc0.Anc0refChr3 34987 25 + 222631 GGTTAATTTTTTCCTCAATCAACTC------- -s Anc1.Anc1refChr6 65123 25 + 197743 GGTTAATTTTTTCCTCAATCAACTC------- -s Anc2.Anc2refChr13 38846 25 + 96486 GGCTAATTTTTTCCTCAATGAACTC------- -s mr.mrrefChr5 256927 32 + 294540 GATAAATTTCGTCCTCAATCAGCGCCCCTGGT -s simCow_chr6.simCow.chr6 395465 25 + 602619 GGACAATTTTTTCCTCAATGAACTC------- -s simDog_chr6.simDog.chr6 385190 5 + 593897 GACTG--------------------------- -s simHuman_chr6.simHuman.chr6 389610 25 + 601863 GGTTAATTTTTTCCTTAATCATCAC------- -s simRat_chr6.simRat.chr6 403682 32 + 647215 GATAAATTTCCTCCTCAATCAGCTCTCCTTGT - -a -s simMouse_chr6.simMouse.chr6 404151 5 + 636262 ACAAT -s Anc0.Anc0refChr3 35012 5 + 222631 ACAAT -s Anc1.Anc1refChr6 65148 5 + 197743 ACAAT -s Anc2.Anc2refChr13 38871 5 + 96486 ACAAT -s mr.mrrefChr5 256959 5 + 294540 ACAAT -s simCow_chr6.simCow.chr6 395497 5 + 602619 ACAAT -s simHuman_chr6.simHuman.chr6 389635 5 + 601863 ACAAT -s simRat_chr6.simRat.chr6 403714 5 + 647215 AGAAT - -a -s simMouse_chr6.simMouse.chr6 404156 1 + 636262 A -s Anc0.Anc0refChr3 35017 1 + 222631 A -s Anc1.Anc1refChr6 65153 1 + 197743 A -s Anc2.Anc2refChr13 38876 1 + 96486 A -s mr.mrrefChr5 256964 1 + 294540 A -s simCow_chr6.simCow.chr6 395503 1 + 602619 A -s simHuman_chr6.simHuman.chr6 389640 1 + 601863 A -s simRat_chr6.simRat.chr6 403719 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 404157 77 + 636262 TGGTTGTCTGCAGAGTTACCAACAGTGGTTTTGGGAGGGCTGATATGTTGGAACAATCCCTCAACCTATTCTGTAGG -s Anc0.Anc0refChr3 35019 77 + 222631 TAATTGGCTACAGATTGACCAACAACGGTTTTAGGAGAGCAGATTTGTTGTAACAACTGCTTAACCTAATATGTAGG -s Anc1.Anc1refChr6 65155 77 + 197743 TAATTGGCTACAGATTGACCAACAACGGTTTTAGGAGAGCAGATTTGTTGTAACAACTGCTTAACCTAATATGTAGG -s Anc2.Anc2refChr13 38878 77 + 96486 CAAGTGGCTACAGATTGACCAAAAACGGTTGTAGGAGAGCAGATTTGTTGTCAGGACTGCTTAATTTAATATATAAG -s mr.mrrefChr5 256965 77 + 294540 TAGTTGGCTGCAGAGTTACCAACAGTGGTTTTGGGAGAGCTGATATGTTGGAACAATCCCTTAACCTATTCTGTAGG -s simCow_chr6.simCow.chr6 395505 77 + 602619 CAAGTGGCTACAGATTGACCCAAAATGGTTGTAGGAGAGCATATTTGTTGTTATGGCTGCTTAATTTAATATATAAG -s simDog_chr6.simDog.chr6 385195 32 + 593897 --------------------AAACACAGTT------GAGAGGGTCTGAAATCAGGACT------------------- -s simHuman_chr6.simHuman.chr6 389642 77 + 601863 TAATTAGCTACAGGCAGACTAACAACGGTTTTAGGAGAGCAGATTTGTTGTAACAACTGCTTAACCTAGTGTGTAGG -s simRat_chr6.simRat.chr6 403720 77 + 647215 TAGTTGGCTGCAGTGTTAGCAACAGTGTTTCTGGAACAGCCATTGTGTTGGAACAATCTCTTAACCTATTCTGCAGA - -a -s simMouse_chr6.simMouse.chr6 404234 12 + 636262 GGGAGTCAGCAA -s Anc0.Anc0refChr3 35097 12 + 222631 GGAATTCAGGTG -s Anc1.Anc1refChr6 65233 12 + 197743 GGAATTCAGGTG -s Anc2.Anc2refChr13 38956 12 + 96486 GAAATTCAGGTG -s mr.mrrefChr5 257042 12 + 294540 GGAATTCAGCAA -s simCow_chr6.simCow.chr6 395583 12 + 602619 TCAATTCAAGTT -s simDog_chr6.simDog.chr6 385227 12 + 593897 GAAACACAGTTG -s simHuman_chr6.simHuman.chr6 389720 12 + 601863 GGAATTCAGGCG -s simRat_chr6.simRat.chr6 403797 12 + 647215 GGACTTCAGCAA - -a -s simMouse_chr6.simMouse.chr6 404246 5 + 636262 GACCA -s Anc0.Anc0refChr3 35109 5 + 222631 GAGGG -s Anc1.Anc1refChr6 65245 5 + 197743 GAGGG -s Anc2.Anc2refChr13 38968 5 + 96486 GAGGG -s mr.mrrefChr5 257054 5 + 294540 GAGCA -s simCow_chr6.simCow.chr6 395595 5 + 602619 GACAG -s simDog_chr6.simDog.chr6 385240 5 + 593897 GAGGG -s simHuman_chr6.simHuman.chr6 389732 5 + 601863 GAGGG -s simRat_chr6.simRat.chr6 403809 5 + 647215 GAGCA - -a -s simMouse_chr6.simMouse.chr6 404251 16 + 636262 GTACGCAGTATGTGGA -s Anc0.Anc0refChr3 35114 14 + 222631 GCAC-CAGTATCTGT- -s Anc1.Anc1refChr6 65250 15 + 197743 GCAC-CAGTATCTGTA -s Anc2.Anc2refChr13 38973 14 + 96486 GCAC-CAGTAACTGT- -s mr.mrrefChr5 257059 16 + 294540 GTACGCAGTATGTGGA -s simCow_chr6.simCow.chr6 395600 14 + 602619 GCAC-CAGTAGCCAT- -s simDog_chr6.simDog.chr6 385245 14 + 593897 TCAT-CAGTAACTGT- -s simHuman_chr6.simHuman.chr6 389737 15 + 601863 GCAC-CAATATCTGCA -s simRat_chr6.simRat.chr6 403817 16 + 647215 GTACGTACTACGTGAA - -a -s simMouse_chr6.simMouse.chr6 404267 19 + 636262 TATTCAAGTAGTTGGAGTC -s Anc0.Anc0refChr3 35128 13 + 222631 TGTCCAAGT------AGTC -s Anc1.Anc1refChr6 65265 13 + 197743 TGTCCAAGT------AGTC -s Anc2.Anc2refChr13 38987 13 + 96486 TGTCCAAGT------AGTC -s mr.mrrefChr5 257075 19 + 294540 TATTCAAGTAGTTGGAGTC -s simCow_chr6.simCow.chr6 395615 13 + 602619 TGTCCAAGC------AGCC -s simDog_chr6.simDog.chr6 385259 13 + 593897 TGTCCAAGT------AGTC -s simHuman_chr6.simHuman.chr6 389752 2 + 601863 -----------------TC -s simRat_chr6.simRat.chr6 403833 19 + 647215 TATTCAAGAAGTTAGAGTC - -a -s simMouse_chr6.simMouse.chr6 404286 53 + 636262 TGGAAGCAGCATCCTTCACAGTTCTTGGCCTTGGCTGCAATAATGGTCAGTAC -s Anc0.Anc0refChr3 35141 52 + 222631 AAGAATCAGTGTCCCTCTCAGTTATTGGCTTTGGCTG-AGTAACAGTTAGTAC -s Anc1.Anc1refChr6 65278 53 + 197743 AAGAATCAGTGTCCCTCTCAGTTATTGGCTTTGGCTGGAGTAACAGTTAGTAC -s Anc2.Anc2refChr13 39000 52 + 96486 AAGAATCAGTGTTCCTCTCAGTTATAGGCATTGGCTA-AGTAACAATTAGTAC -s mr.mrrefChr5 257094 53 + 294540 TAGAAGCAGCATCCTTCACAGTTCTTGGCTTTGGCTGCAATAACAGTCAGTAC -s simCow_chr6.simCow.chr6 395628 40 + 602619 GAGA-----------TCCTAGTTAT-GGCATTGGCTA-AGACACACCTAGTAC -s simDog_chr6.simDog.chr6 385274 43 + 593897 AAGAATCAGTGTTCCTCTCAGTTATAGGC----------ATACCAATTAGTAC -s simHuman_chr6.simHuman.chr6 389754 53 + 601863 AAGAATCAGTGCCCCTCTCAATTATTGGTTTTGGCTGGAGTAACAGTTAGTAC -s simRat_chr6.simRat.chr6 403852 45 + 647215 TAAAAGAAGCCTCCTTCAC--------GCTTTGGCCGCAATAACAGTCAGTAT - -a -s simMouse_chr6.simMouse.chr6 404339 51 + 636262 GATCAAGAATGTTTGTAAAGCTCTAATTGTGCCTCATGCTGATTTGTCTCC -s Anc0.Anc0refChr3 35194 50 + 222631 GATCAAAAACTTTTGTAT-GCCCTGTTTATAGCTCATGCTGCTTTATCTCT -s Anc1.Anc1refChr6 65332 50 + 197743 GATCAAAAACTTTTGTAT-GCCCTGTTTATAGCTCATGCTGCTTTATCTCT -s Anc2.Anc2refChr13 39053 50 + 96486 GATCAAAAACTTTTGTAT-GCCCTGTTTATAGCTCATGCTGCTTTGTCTCT -s mr.mrrefChr5 257147 50 + 294540 GATCAAGAACGTTTGTAT-GCTCTAATTGTACCTCATGCTGATTTATCTCC -s simCow_chr6.simCow.chr6 395669 50 + 602619 GATAAAGGACTTTTGTAT-GCCCTGTTTGTAGCTTGTGATGCTTTGTTTTT -s simDog_chr6.simDog.chr6 385318 50 + 593897 GAACAAAAACTTTCGTAT-GCCCAGTTTATGGCTCATGCTGCTCTGTCTCT -s simHuman_chr6.simHuman.chr6 389808 50 + 601863 AATCAAATACTTTTGTAT-GCCCTGTTTATAACTCATGCTGCTTTATCTCT -s simRat_chr6.simRat.chr6 403897 50 + 647215 GACCAAGAACATTTGTAT-GCTCTAATTGTACCTCATGCTGATTTATCTCC - -a -s simMouse_chr6.simMouse.chr6 404390 22 + 636262 AGATTACTCACTCTGCCATACC -s Anc0.Anc0refChr3 35244 22 + 222631 GGGCTACTCACTATACCGTAAT -s Anc1.Anc1refChr6 65382 22 + 197743 GGGCTACTCACTATACCGTAAT -s Anc2.Anc2refChr13 39103 22 + 96486 GGGCCACTCATTATACCATAAT -s mr.mrrefChr5 257197 22 + 294540 AGACTACTCACTCTGCCGTACT -s simCow_chr6.simCow.chr6 395719 22 + 602619 GGGCAATTGGTGATACCATAAT -s simDog_chr6.simDog.chr6 385377 21 + 593897 GGGCCACTCATTAT-CCATACT -s simHuman_chr6.simHuman.chr6 389858 22 + 601863 GAGCTACCCACTATACCGTAAT -s simRat_chr6.simRat.chr6 403947 22 + 647215 AGTCTACTCACTCTGCCGTACT - -a -s simMouse_chr6.simMouse.chr6 404412 29 + 636262 CATTTGTAGTTGTGGGGCTGACCACATCC -s Anc0.Anc0refChr3 35267 29 + 222631 GGCATGTAGGTATGGAGCTGAGCATAACC -s Anc1.Anc1refChr6 65405 29 + 197743 GGCATGTAGGTATGGAGCTGAGCATAACC -s Anc2.Anc2refChr13 39126 29 + 96486 GGCATGTTGGTATGGAGCTGAGCATAACC -s mr.mrrefChr5 257219 29 + 294540 CGCTTGTAGTTGTGGAGCTGAGCACATCC -s simCow_chr6.simCow.chr6 395742 29 + 602619 GGTATGTTGGTGTCTAGCTGAGTATAACC -s simDog_chr6.simDog.chr6 385399 29 + 593897 GGCATGTTGGCATGGAGTTGACCAGAACC -s simHuman_chr6.simHuman.chr6 389881 29 + 601863 GGCATGTAGGTATGGAGCTGAGCATAAGC -s simRat_chr6.simRat.chr6 403969 29 + 647215 CGCCTGTAGTTGTGGAGCTGAGTGCACCC - -a -s simMouse_chr6.simMouse.chr6 404441 27 + 636262 ATAGGTACACCCTACAATAATCCGAGG -s Anc0.Anc0refChr3 35296 23 + 222631 A----TATAACTCACAATAATCCAAAG -s Anc1.Anc1refChr6 65434 23 + 197743 A----TATAACTCACAATAATCCAAAG -s Anc2.Anc2refChr13 39155 23 + 96486 A----TACAACTCACAACAACCCAAAG -s mr.mrrefChr5 257248 27 + 294540 ATAGGTATACCCTACAATAATCCGAGG -s simCow_chr6.simCow.chr6 395775 21 + 602619 A----TACAACCCACA--AACCCAAAG -s simDog_chr6.simDog.chr6 385428 17 + 593897 A----------TCGCTACAACCCTCCG -s simHuman_chr6.simHuman.chr6 389910 23 + 601863 A----TATAACTCACAATAATCCAAAG -s simRat_chr6.simRat.chr6 403998 27 + 647215 ATAGGTATAGCCTACAATAGTCCGAGG - -a -s simMouse_chr6.simMouse.chr6 404468 41 + 636262 CTGAAAGTGCCATCACTAGCTCTATGTGTCAGTCATGCTAG -s Anc0.Anc0refChr3 35335 41 + 222631 GCAAAAGCACTAGCCCTAGCCCTATGTATCAGATGTGCTAG -s Anc1.Anc1refChr6 65473 41 + 197743 GCAAAAGCACTAGCCCTAGCCCTATGTATCAGATGTGCTAG -s Anc2.Anc2refChr13 39194 41 + 96486 ACAAAAGCATTAGCCCCAGCCCTATATATCAGATGTGCTAG -s mr.mrrefChr5 257275 41 + 294540 GTGAAAGCACCATCCCTAGCTCTATGTGTCAGTCATGCTAG -s simCow_chr6.simCow.chr6 395812 33 + 602619 ACAAAAGCCGTAGCCCAGGC-------AATAGAT-TGCTAG -s simDog_chr6.simDog.chr6 385461 41 + 593897 ACAAAAGCATTAGCCCCAGCCCTATATATCAGATGTGCTAG -s simHuman_chr6.simHuman.chr6 389953 41 + 601863 GCAAAAGCACTAGCCCTAGACCTATGTATCAGATGCACCAG -s simRat_chr6.simRat.chr6 404025 41 + 647215 GTGAAAGCACCATCCCTGGCTCGATGTGTCAGTCATGCTAG - -a -s simMouse_chr6.simMouse.chr6 404509 68 + 636262 TGCTCACTAAACTAGCACTGGCAAAACTTATGGAAAGATAGCTCGGTGGGGACACCAAAGCATATCAG -s Anc0.Anc0refChr3 35391 67 + 222631 CATTCATTAAAGTCACAGTAGTAAGAGTTAAGCAAAGATACCTTGGTGGCCACAACTGTGC-TAGCCA -s Anc1.Anc1refChr6 65529 67 + 197743 CATTCATTAAAGTCACAGTAGTAAGAGTTAAGCAAAGATACCTTGGTGGCCACAACTGTGC-TAGCCA -s Anc2.Anc2refChr13 39250 67 + 96486 CATTCATAAAAGTCACAGTAGTAAGAGTTAAGCAAAGATACCTTGGTGGCCAAAACTGTGC-TAGCCA -s mr.mrrefChr5 257316 68 + 294540 TGCTCACTAAACTCACACTGGCAAAACTTATGGAAAGATAGCTTGGTGGGGACACCAAAGCATATCAG -s simCow_chr6.simCow.chr6 395860 67 + 602619 AATTCATAAAAGTTACACTAATAAGAGGTAAGCAAAGATACCTTGGTGGCCATAACTGTGT-AAATCA -s simDog_chr6.simDog.chr6 385517 63 + 593897 CATTCA-AAAAGTCACAGTAGTAAAAAT---GCAAAAATACCATGGTGGCCAAAACTGTGC-TAGCCA -s simHuman_chr6.simHuman.chr6 390009 54 + 601863 CATTCATTAAAGTCACGTTAGTTAGAGTTAAGTGAAGATACCTTGGTGGCCACA-------------- -s simRat_chr6.simRat.chr6 404066 68 + 647215 TGCTCGCTTAAATCACACTGGCAAAACATATCCAAAGATAGCTTGGTGGGGACACCTATGCATATCAG - -a -s simMouse_chr6.simMouse.chr6 404577 4 + 636262 TGAC -s Anc0.Anc0refChr3 35458 4 + 222631 TGAT -s Anc1.Anc1refChr6 65596 4 + 197743 TGAT -s Anc2.Anc2refChr13 39317 4 + 96486 TGAT -s mr.mrrefChr5 257384 4 + 294540 TGAC -s simCow_chr6.simCow.chr6 395927 4 + 602619 TGAC -s simDog_chr6.simDog.chr6 385585 4 + 593897 TGAT -s simRat_chr6.simRat.chr6 404134 4 + 647215 TGAC - -a -s simMouse_chr6.simMouse.chr6 404581 111 + 636262 ACAACACCCAGCAAATCAAATAGCCCAGTTTCCAGTTTTAAAAAAAATGGCCACATATGCTGTAACGGTGCTAGTGAGCCGAAGAATAACCTGAGAACTTCACTAAGTGTC -s Anc0.Anc0refChr3 35462 100 + 222631 ACAACAC----CAGATCAAATAACACAGTTT-------TAAGTAAAATGACACTATCTGCTGTAAGCGTGTTAGTGAGCTGAAGAATAACTTGAGGACATCCGTATGTGCC -s Anc1.Anc1refChr6 65600 104 + 197743 ACAACACTTGGCAGATCAAATAACACAGTTT-------TAAGTAAAATGACACTATCTGCTGTAAGCGTGTTAGTGAGCTGAAGAATAACTTGAGGACATCCGTATGTGCC -s Anc2.Anc2refChr13 39323 100 + 96486 ACAACTC----CAGATCAGATAACACAGTTT-------TAAGTGAGATGACACTATCTGCTGTACGCATGTTAGTGGGCTGAAGAATAACTTGAGGACATCCGTATATGCC -s mr.mrrefChr5 257388 104 + 294540 ACAACACCCAGCAGATCAAATAGCCCAGTTT-------TAAAAAAAATGGCAATATATGCTGTAAGGGTGTTAGTGAGCCGAAGAATAACCTGAGAACATCAGTAAGTGTC -s simCow_chr6.simCow.chr6 395933 89 + 602619 ACACCAG----CAGATCAGATAACCCATTTT----------------TGACGCTATCTATTGTATG-ATGTTGGTGTGCTGAAGAATAATTTGAGGACAT-CGTAAATGCC -s simDog_chr6.simDog.chr6 385591 100 + 593897 ACAACTC----CAGGTCTGATAACACAGTTT-------TAAGTGAGATGGCATTATCTGCTGTACACATGACAGTGGGTTGAACAATAACTTGAGAACATCAATATATGCC -s simHuman_chr6.simHuman.chr6 390063 99 + 601863 -----ATTTGGCAGATCAAATAACACAGTTT-------TAATTAAAATGACACTATCTGCTATAAGTGTGTTATTTAGCTGAAGACTAACTTGAGGACATCCGTATGTGCT -s simRat_chr6.simRat.chr6 404138 104 + 647215 ACAACACCCAGCAGATCAAATAGCCCAGTTT-------CAAAAGAAATGGCAGTATATGTTGTAAGGGGGTTAGTGACTCAAAGAATAACCTGAGAACATCAGTAAATGTC - -a -s simMouse_chr6.simMouse.chr6 404692 3 + 636262 ACC -s Anc0.Anc0refChr3 35568 3 + 222631 GAC -s Anc1.Anc1refChr6 65710 3 + 197743 GAC -s Anc2.Anc2refChr13 39429 3 + 96486 GAC -s mr.mrrefChr5 257492 3 + 294540 AAC -s simCow_chr6.simCow.chr6 396028 3 + 602619 GAT -s simDog_chr6.simDog.chr6 385697 3 + 593897 GAC -s simHuman_chr6.simHuman.chr6 390168 3 + 601863 GAC -s simRat_chr6.simRat.chr6 404242 3 + 647215 AAC - -a -s simMouse_chr6.simMouse.chr6 404695 11 + 636262 TAAGTTCACAA -s Anc0.Anc0refChr3 35583 11 + 222631 TAAAACCACAA -s Anc1.Anc1refChr6 65725 11 + 197743 TAAAACCACAA -s Anc2.Anc2refChr13 39444 11 + 96486 TAAAACCACAA -s mr.mrrefChr5 257507 11 + 294540 TAAAATCACAA -s simCow_chr6.simCow.chr6 396043 11 + 602619 TAAAACCAGAA -s simDog_chr6.simDog.chr6 385712 11 + 593897 TAAAACCACAA -s simHuman_chr6.simHuman.chr6 390183 11 + 601863 TAAAACCATGT -s simRat_chr6.simRat.chr6 404257 11 + 647215 TAAAAGTACAA - -a -s simMouse_chr6.simMouse.chr6 404706 12 + 636262 CCCAGCCAGTTC -s Anc0.Anc0refChr3 35594 12 + 222631 CCCAGCCATTTT -s Anc1.Anc1refChr6 65736 12 + 197743 CCCAGCCATTTT -s Anc2.Anc2refChr13 39456 12 + 96486 CCCAGCCATTTT -s mr.mrrefChr5 257518 12 + 294540 CCCAGCCAGTTC -s simCow_chr6.simCow.chr6 396055 12 + 602619 CCTAGCCATTGT -s simDog_chr6.simDog.chr6 385724 12 + 593897 CCCGGCCATTTT -s simHuman_chr6.simHuman.chr6 390194 12 + 601863 CCCAGCCATTTT -s simRat_chr6.simRat.chr6 404268 12 + 647215 CCCAGCCAGTTC - -a -s simMouse_chr6.simMouse.chr6 404718 31 + 636262 AGAAGAACTCCGAACTCCCAACATGCATTGA -s Anc0.Anc0refChr3 35607 21 + 222631 A---GACCA-------CCTAGGATACGATGA -s Anc1.Anc1refChr6 65749 21 + 197743 A---GACCA-------CCTAGGATACGATGA -s Anc2.Anc2refChr13 39469 21 + 96486 A---GACCA-------CCTAGGATGCGATGG -s mr.mrrefChr5 257531 24 + 294540 AGAAGAACT-------CCCAAGATACATTGA -s simCow_chr6.simCow.chr6 396070 21 + 602619 A---GATGA-------CTCAGAATGTATTGT -s simDog_chr6.simDog.chr6 385737 21 + 593897 G---TACCA-------CCTAGGATGCGATGG -s simHuman_chr6.simHuman.chr6 390207 21 + 601863 A---GACTA-------CCAGGGACACGCTGA -s simRat_chr6.simRat.chr6 404281 24 + 647215 AGAAGAACC-------CCTATGATACATTGA - -a -s simMouse_chr6.simMouse.chr6 404749 17 + 636262 TACACTGGAGGGGAGCA -s Anc0.Anc0refChr3 35628 17 + 222631 TGCACTGGAAGGGAGCA -s Anc1.Anc1refChr6 65770 17 + 197743 TGCACTGGAAGGGAGCA -s Anc2.Anc2refChr13 39490 17 + 96486 CGCACTGGAAAGGAGCA -s mr.mrrefChr5 257555 17 + 294540 TACACTGGAAGGGAGCA -s simCow_chr6.simCow.chr6 396091 17 + 602619 CGCACTGAAAAGGAGCA -s simDog_chr6.simDog.chr6 385758 17 + 593897 CACACTGGAAAGAAGCA -s simHuman_chr6.simHuman.chr6 390229 17 + 601863 TGCACTGGAAGGGAGTG -s simRat_chr6.simRat.chr6 404305 17 + 647215 TACCTTCATAGGGAGCA - -a -s simMouse_chr6.simMouse.chr6 404766 1 + 636262 T -s Anc0.Anc0refChr3 35645 1 + 222631 T -s Anc1.Anc1refChr6 65787 1 + 197743 T -s Anc2.Anc2refChr13 39508 1 + 96486 G -s mr.mrrefChr5 257572 1 + 294540 T -s simDog_chr6.simDog.chr6 385776 1 + 593897 G -s simHuman_chr6.simHuman.chr6 390246 1 + 601863 T -s simRat_chr6.simRat.chr6 404322 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 404767 37 + 636262 TGTGTTTGGGACCATGCTGATTTAGTTGAGAGCCAGC -s Anc0.Anc0refChr3 35647 37 + 222631 CTTGTTTGGGACTATGCTGATTTGGTTGAGAGCCAGC -s Anc1.Anc1refChr6 65789 37 + 197743 CTTGTTTGGGACTATGCTGATTTGGTTGAGAGCCAGC -s Anc2.Anc2refChr13 39510 37 + 96486 CTGGTTTGAGACTACTGTGATTTGGTTTAGGACCTGC -s mr.mrrefChr5 257573 37 + 294540 CGTGTTTGGGACTATGCTGATTTAGTTGAGAGCCAGC -s simDog_chr6.simDog.chr6 385778 37 + 593897 CTGGTTTGAGACTACTGTGATTTGGTTTAGGACCTGC -s simHuman_chr6.simHuman.chr6 390248 37 + 601863 CTTGTTTGGGACTATGCTGACTTGGTTGAGAGCCAGC -s simRat_chr6.simRat.chr6 404323 37 + 647215 CATATGTGGGACTATGCTGATTTAGTTGAGAGCCAGC - -a -s simMouse_chr6.simMouse.chr6 404804 12 + 636262 TGTTAAAGTTGG -s Anc0.Anc0refChr3 35719 12 + 222631 CTTTATAAGGGG -s Anc1.Anc1refChr6 65861 12 + 197743 CTTTATAAGGGG -s Anc2.Anc2refChr13 39582 12 + 96486 CTTTATAAGGGG -s mr.mrrefChr5 257610 12 + 294540 TGTTAAAGTTGG -s simCow_chr6.simCow.chr6 396136 12 + 602619 TTTTATGGTGGG -s simDog_chr6.simDog.chr6 385850 12 + 593897 CTTTATAAGGGG -s simHuman_chr6.simHuman.chr6 390320 12 + 601863 CTTTATAAAGGA -s simRat_chr6.simRat.chr6 404360 12 + 647215 TGTTAAAGATAG - -a -s simMouse_chr6.simMouse.chr6 404816 6 + 636262 CAAATG -s Anc0.Anc0refChr3 35731 6 + 222631 TTAATT -s Anc1.Anc1refChr6 65873 6 + 197743 TTAATT -s Anc2.Anc2refChr13 39594 6 + 96486 TTAATT -s mr.mrrefChr5 257622 6 + 294540 CAAATG -s simCow_chr6.simCow.chr6 396148 6 + 602619 TTAATC -s simDog_chr6.simDog.chr6 385862 6 + 593897 TTAATT -s simHuman_chr6.simHuman.chr6 390332 6 + 601863 TTAATT -s simRat_chr6.simRat.chr6 404374 6 + 647215 CAAATA - -a -s simMouse_chr6.simMouse.chr6 404822 5 + 636262 TAGAC -s Anc0.Anc0refChr3 35737 5 + 222631 TTGAC -s Anc1.Anc1refChr6 65879 5 + 197743 TTGAC -s Anc2.Anc2refChr13 39600 5 + 96486 TTGAC -s mr.mrrefChr5 257628 5 + 294540 TAGAC -s simCow_chr6.simCow.chr6 396154 5 + 602619 TTAAC -s simDog_chr6.simDog.chr6 385886 5 + 593897 GTGAC -s simHuman_chr6.simHuman.chr6 390338 5 + 601863 TTGAC -s simRat_chr6.simRat.chr6 404380 5 + 647215 TAGTC - -a -s simMouse_chr6.simMouse.chr6 404827 19 + 636262 GAGTGACCGCCGAATTTGG -s Anc0.Anc0refChr3 35745 17 + 222631 GACTGCCC--TGAATTCAA -s Anc1.Anc1refChr6 65887 17 + 197743 GACTGCCC--TGAATTCAA -s Anc2.Anc2refChr13 39608 17 + 96486 GACTGCCC--TGAATTCAA -s mr.mrrefChr5 257633 17 + 294540 GACTGCCC--TGAATTTGG -s simCow_chr6.simCow.chr6 396162 17 + 602619 GGCTGCCC--TGAATACAA -s simDog_chr6.simDog.chr6 385894 17 + 593897 AACTGCCC--TGAGCTCAA -s simHuman_chr6.simHuman.chr6 390346 17 + 601863 GACTGCCC--TAAATTCAA -s simRat_chr6.simRat.chr6 404385 17 + 647215 AACTGCCC--TGAATTTGG - -a -s simMouse_chr6.simMouse.chr6 404846 31 + 636262 CCTAGACAATTAATACATTGTTTGATTGGCA -s Anc0.Anc0refChr3 35762 31 + 222631 CCCAAATTACTAGTACATGGCTTGAATGGGA -s Anc1.Anc1refChr6 65904 31 + 197743 CCCAAATTACTAGTACATGGCTTGAATGGGA -s Anc2.Anc2refChr13 39625 31 + 96486 CCCAAATTACTAGTACATGGCTTAAATGGGG -s mr.mrrefChr5 257650 31 + 294540 CCTAGACAATTAATACATTGTTTGATTGGCA -s simCow_chr6.simCow.chr6 396188 31 + 602619 CACAGATTAATAGTACATCACTGAAATGTCA -s simDog_chr6.simDog.chr6 385911 31 + 593897 TCGGAATTACTAGTACATGGCTTAAATGGGG -s simHuman_chr6.simHuman.chr6 390363 31 + 601863 CCCAACTTACTAGTACACAGCTTGAGTAGGA -s simRat_chr6.simRat.chr6 404402 25 + 647215 CCTAGACAATTAATACATT------TTGGTA - -a -s simMouse_chr6.simMouse.chr6 404877 12 + 636262 ACTAACCCAGTG -s Anc0.Anc0refChr3 35793 12 + 222631 ATTAACCCAGTG -s Anc1.Anc1refChr6 65935 12 + 197743 ATTAACCCAGTG -s Anc2.Anc2refChr13 39658 12 + 96486 ATTGACCCAGTG -s mr.mrrefChr5 257681 12 + 294540 ATTAACCCAGTG -s simCow_chr6.simCow.chr6 396221 12 + 602619 ATTGACCCAGTG -s simDog_chr6.simDog.chr6 385944 12 + 593897 ATTGACCCGGTG -s simHuman_chr6.simHuman.chr6 390394 12 + 601863 ATTAACTCAGTG -s simRat_chr6.simRat.chr6 404427 12 + 647215 ATTAACCCAGTG - -a -s simMouse_chr6.simMouse.chr6 404889 83 + 636262 AGTATTTGATAACGTTATAATAATCCAGCCCACAGGAGATTACATGCCTTCCCCATGAGAGTGGGTGACTGACAGTCCAGCCT -s Anc0.Anc0refChr3 35805 44 + 222631 GTTGTCTAATAATGTGACTATAAT-CAGTCCACACA--------------------------------ATGACA------CAT -s Anc1.Anc1refChr6 65947 50 + 197743 GTTGTCTAATAATGTGACTATAAT-CAGTCCACACA--------------------------------ATGACAGTCTACCAT -s Anc2.Anc2refChr13 39670 44 + 96486 GTTGGCTAAAAATGTGACTATAAT-CAGTTCATACA--------------------------------AGGACA------CAT -s mr.mrrefChr5 257693 83 + 294540 ATTATTTGATAATGTGACAATAATCCAGCCCACAGGAGATTACATGCCTTCCCCATGAGAGTGGGTGACTGACAGTCCAGCCT -s simCow_chr6.simCow.chr6 396241 43 + 602619 GTTGACTGAAAATGTGGCTATAAT-CAGTACATACA--------------------------------GGGACA------CA- -s simDog_chr6.simDog.chr6 385956 44 + 593897 GTTGGCTAAAAAAGTGACTACAAC-CAGTTCATACA--------------------------------AGGACA------CAT -s simHuman_chr6.simHuman.chr6 390406 50 + 601863 GTTGTCTAATAATGTGTCTATTAT-CAGTCCACACA--------------------------------TTAACAGTCTACCAT -s simRat_chr6.simRat.chr6 404439 83 + 647215 ATTCCGTGATAATGTGACAATAATCCAGCCAACGAGAGACTACATCCCTTCTCCATGGGAGTGTGTGACTGACAATACAGCCT - -a -s simMouse_chr6.simMouse.chr6 404972 17 + 636262 ACTAGTGCACTATTGAT -s Anc0.Anc0refChr3 35852 17 + 222631 ACTAGTGCACTATTAGC -s Anc1.Anc1refChr6 66000 17 + 197743 ACTAGTGCACTATTAGC -s Anc2.Anc2refChr13 39717 17 + 96486 ACTAGTGCACTACTAGC -s mr.mrrefChr5 257776 17 + 294540 ACTAGTGCACTATTGAT -s simCow_chr6.simCow.chr6 396284 4 + 602619 -------------TACC -s simDog_chr6.simDog.chr6 386003 17 + 593897 ACTAGTGCACTACCGGC -s simHuman_chr6.simHuman.chr6 390462 17 + 601863 ATTAGTGCCCTATTAGG -s simRat_chr6.simRat.chr6 404522 17 + 647215 ACTAGTGCACTATTGAT - -a -s simMouse_chr6.simMouse.chr6 404989 15 + 636262 GTGTAGGGTACCCTT -s Anc0.Anc0refChr3 35870 15 + 222631 GTGCAGGGAGCCCTA -s Anc1.Anc1refChr6 66018 15 + 197743 GTGCAGGGAGCCCTA -s Anc2.Anc2refChr13 39735 15 + 96486 TTGCAGGGAGACCTA -s mr.mrrefChr5 257794 15 + 294540 GTGTAGGGTACCCTT -s simCow_chr6.simCow.chr6 396289 15 + 602619 TTGCACGAGCACCCA -s simDog_chr6.simDog.chr6 386021 15 + 593897 TTGGAGGGAGACCTC -s simHuman_chr6.simHuman.chr6 390480 15 + 601863 GGGCAGGGAGCCCTA -s simRat_chr6.simRat.chr6 404540 15 + 647215 GTGTGGGGTACCCAT - -a -s simMouse_chr6.simMouse.chr6 405004 31 + 636262 ACCTGGTTGCTATCTGTTCTAATTAAAACCT -s Anc0.Anc0refChr3 35885 31 + 222631 ACTTGTTTGCTACCTGTTCCAATGCAAACCT -s Anc1.Anc1refChr6 66033 31 + 197743 ACTTGTTTGCTACCTGTTCCAATGCAAACCT -s Anc2.Anc2refChr13 39750 31 + 96486 ACTTCTTTATTACCTGTTCCAATGCAAACGT -s mr.mrrefChr5 257809 31 + 294540 ACCTGGTTGCTATCTGTTCTAATTAAAACCT -s simCow_chr6.simCow.chr6 396304 12 + 602619 ----------CACCTGA---------ATCAA -s simDog_chr6.simDog.chr6 386048 31 + 593897 ACTTCTTTATTATCTGTTCCAATGCAAACGT -s simHuman_chr6.simHuman.chr6 390495 31 + 601863 ACTTGTTTGCTGCCTATTCCAATGCCCACCT -s simRat_chr6.simRat.chr6 404555 31 + 647215 ACCTGGTTGCCCTCTGTTCTAATTAAAACCT - -a -s simMouse_chr6.simMouse.chr6 405035 24 + 636262 TCTAATTAATGCTGAGATGGCATG -s Anc0.Anc0refChr3 35925 24 + 222631 TCTATTTGATGTCAAACTGGCATG -s Anc1.Anc1refChr6 66073 24 + 197743 TCTATTTGATGTCAAACTGGCATG -s Anc2.Anc2refChr13 39790 24 + 96486 ACTATTTGATGTCAAACTAGCATG -s mr.mrrefChr5 257840 24 + 294540 TCTAATTGATGCTAAGATGGCATG -s simCow_chr6.simCow.chr6 396325 24 + 602619 ACTACTTGATGTCACATTAGCATG -s simDog_chr6.simDog.chr6 386088 24 + 593897 ACTATTTGAGGTCAAGCTAACATG -s simHuman_chr6.simHuman.chr6 390535 24 + 601863 TCTGGTTGATGTCAAACTGGCATG -s simRat_chr6.simRat.chr6 404586 24 + 647215 TCTAATTGATGCTAAGATGGCATG - -a -s simMouse_chr6.simMouse.chr6 405059 8 + 636262 AACGCACT -s Anc0.Anc0refChr3 35950 8 + 222631 CACGCAGT -s Anc1.Anc1refChr6 66098 8 + 197743 CACGCAGT -s Anc2.Anc2refChr13 39815 8 + 96486 CATGCAGT -s mr.mrrefChr5 257865 8 + 294540 AACGCAGT -s simCow_chr6.simCow.chr6 396350 8 + 602619 CATGCAGT -s simDog_chr6.simDog.chr6 386113 8 + 593897 CATGTAGT -s simHuman_chr6.simHuman.chr6 390560 8 + 601863 TACGCAGT -s simRat_chr6.simRat.chr6 404611 8 + 647215 AATGCAGT - -a -s simMouse_chr6.simMouse.chr6 405067 28 + 636262 CAAAGAATCTGGTTCAAATATGTGTGAT -s Anc0.Anc0refChr3 35963 25 + 222631 GAAAAAATCTGG---AAATACTAGTGAT -s Anc1.Anc1refChr6 66111 28 + 197743 GAAAAAATCTGGTTCAAATACTAGTGAT -s Anc2.Anc2refChr13 39828 25 + 96486 GAAAAAATCTGG---AAATCCTAGTGAT -s mr.mrrefChr5 257873 28 + 294540 GAAAGAATCTGGTTCAAATATGTGTGAT -s simCow_chr6.simCow.chr6 396363 25 + 602619 GAAAAAATCCAG---AAATGCTGATGAT -s simDog_chr6.simDog.chr6 386126 25 + 593897 AAAAAAATCTGG---ACACCCCAGTGAT -s simHuman_chr6.simHuman.chr6 390573 28 + 601863 GAAAAAATCTGGTTCAAATACTAGTGAT -s simRat_chr6.simRat.chr6 404619 28 + 647215 GAAAGAATCCAGTTCAAACATGTGTGAT - -a -s simMouse_chr6.simMouse.chr6 405095 1 + 636262 A -s Anc0.Anc0refChr3 35989 1 + 222631 A -s Anc1.Anc1refChr6 66140 1 + 197743 A -s Anc2.Anc2refChr13 39854 1 + 96486 C -s mr.mrrefChr5 257901 1 + 294540 A -s simCow_chr6.simCow.chr6 396389 1 + 602619 C -s simDog_chr6.simDog.chr6 386152 1 + 593897 C -s simHuman_chr6.simHuman.chr6 390602 1 + 601863 A -s simRat_chr6.simRat.chr6 404647 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 405096 8 + 636262 ATATTAAG -s Anc0.Anc0refChr3 35990 8 + 222631 CTCAGAAG -s Anc1.Anc1refChr6 66141 8 + 197743 CTCAGAAG -s Anc2.Anc2refChr13 39855 8 + 96486 CTCAGAAG -s mr.mrrefChr5 257902 8 + 294540 CTATTAAG -s simCow_chr6.simCow.chr6 396390 8 + 602619 CTCAGAAG -s simDog_chr6.simDog.chr6 386155 8 + 593897 CTCAGAAG -s simHuman_chr6.simHuman.chr6 390603 8 + 601863 CTCAGAAG -s simRat_chr6.simRat.chr6 404648 8 + 647215 CCATAAAG - -a -s simMouse_chr6.simMouse.chr6 405104 49 + 636262 GGTTGGACTCTCTAGCCAGCCAACCTAGTTTGTACCTTCTGCTTTTTGA -s Anc0.Anc0refChr3 35998 49 + 222631 AGTTGAACTCCCTAGCCAGCCACCCTCATTCATACCCTCTGCTTCTTGC -s Anc1.Anc1refChr6 66149 49 + 197743 AGTTGAACTCCCTAGCCAGCCACCCTCATTCATACCCTCTGCTTCTTGC -s Anc2.Anc2refChr13 39863 49 + 96486 AATTGAACTCCCTAGCCAGCCACCCTCATTCATACCCTCTGCTTCTTGC -s mr.mrrefChr5 257910 49 + 294540 AGTTGAACTCTCTAGCCAGCCACCCTAATTTGTACCTTCTGCTTTTTGA -s simCow_chr6.simCow.chr6 396399 47 + 602619 AATTGAACTCCATAGT-AGCCACTCTAATTCATGCCC-CTGCTTCTTGC -s simDog_chr6.simDog.chr6 386163 36 + 593897 AATTGAACTCCCTAGCCATCGACCCTCAC----ACCTTCT--------- -s simHuman_chr6.simHuman.chr6 390611 49 + 601863 AGTTGAACCCCCTAGCCAGCCACCCTCATTCAGACCCTCTGCTCATTGC -s simRat_chr6.simRat.chr6 404656 49 + 647215 AGTTGAACTCTCTAGCCAAGCACCCTAATTGCTACCTTATACTATCTGA - -a -s simMouse_chr6.simMouse.chr6 405153 13 + 636262 TAGTTTTCCATTT -s Anc0.Anc0refChr3 36052 13 + 222631 TTGTTCTTCTTCT -s Anc1.Anc1refChr6 66203 13 + 197743 TTGTTCTTCTTCT -s Anc2.Anc2refChr13 39917 13 + 96486 TTCTTCTTCTTCT -s mr.mrrefChr5 257959 13 + 294540 TAGTTTTCCATTT -s simCow_chr6.simCow.chr6 396451 13 + 602619 TTCTTCATCTTCC -s simDog_chr6.simDog.chr6 386204 13 + 593897 TTCTTTTTTTTGT -s simHuman_chr6.simHuman.chr6 390670 13 + 601863 TTGTTCTTCTTCT - -a -s simMouse_chr6.simMouse.chr6 405166 43 + 636262 ATATTCCCCTGCTTTTTCTGTTAATACTGCCCTGTTGAGTTGG -s Anc0.Anc0refChr3 36078 37 + 222631 CTATTTCCCTTC-TCTCCTGTTGATATTGCCC-----ACATGG -s Anc1.Anc1refChr6 66229 38 + 197743 CTATTTCCCTTCATCTCCTGTTGATATTGCCC-----ACATGG -s Anc2.Anc2refChr13 39943 37 + 96486 CTATTTCCCTTC-TCTCCTGCTGATATTGCCC-----ACATGG -s mr.mrrefChr5 257972 38 + 294540 ATATTCCCCTGCTTTTTCTGTTAATACTGCCC-----AGTTGG -s simCow_chr6.simCow.chr6 396477 36 + 602619 CTGCTTCCCTT--GCCCCTGCTAATATTGCCC-----ACATGG -s simDog_chr6.simDog.chr6 386230 37 + 593897 TTATTTCTCTTC-TCTGTTGCTGATCTTGTCC-----ACGTGA -s simHuman_chr6.simHuman.chr6 390696 38 + 601863 CTATTTCCCTTCATCTCCTGTTGATATTCCCC-----AAATGG - -a -s simMouse_chr6.simMouse.chr6 405209 1 + 636262 A -s Anc0.Anc0refChr3 36115 1 + 222631 A -s Anc1.Anc1refChr6 66267 1 + 197743 A -s Anc2.Anc2refChr13 39980 1 + 96486 A -s mr.mrrefChr5 258010 1 + 294540 A -s simCow_chr6.simCow.chr6 396515 1 + 602619 A -s simDog_chr6.simDog.chr6 386267 1 + 593897 A -s simHuman_chr6.simHuman.chr6 390734 1 + 601863 A - -a -s simMouse_chr6.simMouse.chr6 405210 3 + 636262 ACT -s Anc0.Anc0refChr3 36116 1 + 222631 A-- -s Anc1.Anc1refChr6 66268 1 + 197743 A-- -s Anc2.Anc2refChr13 39983 1 + 96486 A-- -s mr.mrrefChr5 258011 1 + 294540 A-- -s simCow_chr6.simCow.chr6 396518 1 + 602619 A-- -s simDog_chr6.simDog.chr6 386270 1 + 593897 A-- -s simHuman_chr6.simHuman.chr6 390735 1 + 601863 A-- - -a -s simMouse_chr6.simMouse.chr6 405213 9 + 636262 ACCCATAAA -s Anc0.Anc0refChr3 36117 6 + 222631 CCCCAT--- -s Anc1.Anc1refChr6 66269 6 + 197743 CCCCAT--- -s Anc2.Anc2refChr13 39984 6 + 96486 CCCCAT--- -s mr.mrrefChr5 258012 6 + 294540 ACCCAT--- -s simCow_chr6.simCow.chr6 396520 6 + 602619 CCCCAT--- -s simDog_chr6.simDog.chr6 386271 6 + 593897 CCCCAC--- -s simHuman_chr6.simHuman.chr6 390736 6 + 601863 GCCCAT--- - -a -s simMouse_chr6.simMouse.chr6 405222 31 + 636262 GTAGGGCCTTCAAAGGTCAGGACCACCTATC -s Anc0.Anc0refChr3 36123 31 + 222631 GTACAGTCTTCAAGAATCAGGACAACCTCTC -s Anc1.Anc1refChr6 66275 31 + 197743 GTACAGTCTTCAAGAATCAGGACAACCTCTC -s Anc2.Anc2refChr13 39990 31 + 96486 GTACAGTCTTCAAGAATCAGGACAACCTCTC -s mr.mrrefChr5 258018 31 + 294540 GTAGGGCCTTCAAAGGTCAGGACCACCTATC -s simCow_chr6.simCow.chr6 396526 31 + 602619 GTAAAATCTTCAAGAGTCAAGACTACCTCCC -s simDog_chr6.simDog.chr6 386278 30 + 593897 GTACAGTCTTGAAG-ATCAGGACAACCTCTC -s simHuman_chr6.simHuman.chr6 390742 31 + 601863 GTACAGACTTCAAGAATCAGGACAACCACTC - -a -s simMouse_chr6.simMouse.chr6 405253 9 + 636262 TCTCAGCTA -s Anc0.Anc0refChr3 36154 6 + 222631 TCT--GCT- -s Anc1.Anc1refChr6 66306 6 + 197743 TCT--GCT- -s Anc2.Anc2refChr13 40021 6 + 96486 TCT--GCT- -s mr.mrrefChr5 258049 6 + 294540 TCT--GCT- -s simCow_chr6.simCow.chr6 396606 6 + 602619 TCT--GCT- -s simDog_chr6.simDog.chr6 386308 6 + 593897 TCT--GCT- -s simHuman_chr6.simHuman.chr6 390773 6 + 601863 TCT--GCT- - -a -s simMouse_chr6.simMouse.chr6 405262 81 + 636262 TCTGCTCCTTGTGTCCCTATATGTCACTTCATCATCAACACTTTCATGAGATCATGTAAAACCCCTTAAATTGGTGGGAAT -s Anc0.Anc0refChr3 36160 81 + 222631 TCTGCTTTTTTTGTCTCTATCTGTCTCTTTATTATCATCATCTTCACGAGAGTGTATTAATGGCATCAAATTGGTCTGAAT -s Anc1.Anc1refChr6 66312 81 + 197743 TCTGCTTTTTTTGTCTCTATCTGTCTCTTTATTATCATCATCTTCACGAGAGTGTATTAATGGCATCAAATTGGTCTGAAT -s Anc2.Anc2refChr13 40028 81 + 96486 TCTGCTTTTTTTGTCTCGAGCTGTCTCTTTATTATCATCATCTTCACGAGAGTGTATTAATGGCATCAAATTGGTCTGAAT -s mr.mrrefChr5 258055 81 + 294540 TCTGCTCCTTGTGTCCCTATATGTCACTTCATCATCAACACTTTCATGAGATCATGTAAAACCCCTTAAATTGGTGGGAAT -s simCow_chr6.simCow.chr6 396613 80 + 602619 TCTGCTTTTTTTCTCCCAAGCTGTCTCTTTATTGTCATCATTTTCACGAGAGT-TGTTAATGGCATTACATTGGTCCGAAT -s simDog_chr6.simDog.chr6 386315 79 + 593897 TTTGCTTTTTTTGTCTTGTGCTGTTGCCTTGTTATTATCACCTTCATGAAAGTGTATTAA--GCATCAAAATGGTCTGAAT -s simHuman_chr6.simHuman.chr6 390779 81 + 601863 TCTGCTTTTTTTGTCTCTATCTGTCTTTATATTATCATTGTCTTCACGAGACTGTATTAATGGGATCAAATTGGTCTGAAT - -a -s simMouse_chr6.simMouse.chr6 405343 4 + 636262 AAGG -s Anc0.Anc0refChr3 36246 4 + 222631 AAGG -s Anc1.Anc1refChr6 66398 4 + 197743 AAGG -s Anc2.Anc2refChr13 40114 4 + 96486 AGCG -s mr.mrrefChr5 258136 4 + 294540 AAGG -s simCow_chr6.simCow.chr6 396698 4 + 602619 AGAG -s simDog_chr6.simDog.chr6 386399 4 + 593897 AGCG -s simHuman_chr6.simHuman.chr6 390865 4 + 601863 AAGG - -a -s simMouse_chr6.simMouse.chr6 405347 19 + 636262 GCACAATCCTAAAAGTATC -s Anc0.Anc0refChr3 36272 19 + 222631 GCACATTCTTCAAAATGTT -s Anc1.Anc1refChr6 66424 19 + 197743 GCACATTCTTCAAAATGTT -s Anc2.Anc2refChr13 40140 19 + 96486 GCACATTCTTCAAAATGTT -s mr.mrrefChr5 258140 19 + 294540 GCACAATCCTAAAAGTATC -s simCow_chr6.simCow.chr6 396724 19 + 602619 GCACACTCTTCAGAATGCT -s simDog_chr6.simDog.chr6 386426 19 + 593897 GCACATTAGTTAAAATGTC -s simHuman_chr6.simHuman.chr6 390891 19 + 601863 GCACATTCTTCAAAATGTT - -a -s simMouse_chr6.simMouse.chr6 405366 38 + 636262 AATATTGCCACATTTTTGTCTTTCATATTCAAAGGTCC -s Anc0.Anc0refChr3 36297 38 + 222631 CATGTTGCCGCATGAATGTCTTTACTATCCAAATGTCC -s Anc1.Anc1refChr6 66449 38 + 197743 CATGTTGCCGCATGAATGTCTTTACTATCCAAATGTCC -s Anc2.Anc2refChr13 40165 38 + 96486 CATGTTGCTGCATGAATGTCTTTACTATCCAAATGACC -s mr.mrrefChr5 258159 38 + 294540 AATATTGCCACATTTTTGTCTTTCATATTCAAAGGTCC -s simCow_chr6.simCow.chr6 396749 38 + 602619 CACAGGTTTGCATGAATGTCTTTCCTGCCCAAATGCCC -s simDog_chr6.simDog.chr6 386451 38 + 593897 CATGTTGCTGCATAAATGTCTTTATTATCCAAATGACC -s simHuman_chr6.simHuman.chr6 390916 38 + 601863 CATGTTGCCGCATGAACACTGTTACTATCCAAATGTCT - -a -s simMouse_chr6.simMouse.chr6 405404 2 + 636262 AT -s Anc0.Anc0refChr3 36335 2 + 222631 AT -s Anc1.Anc1refChr6 66487 2 + 197743 AT -s Anc2.Anc2refChr13 40203 2 + 96486 AT -s mr.mrrefChr5 258197 2 + 294540 AT -s simCow_chr6.simCow.chr6 396787 2 + 602619 AT -s simDog_chr6.simDog.chr6 386491 2 + 593897 AT -s simHuman_chr6.simHuman.chr6 390954 2 + 601863 AT - -a -s simMouse_chr6.simMouse.chr6 405406 43 + 636262 TTATCATTTAACATATTGCCACAAGAAAGGCACCCTTCAATGA -s Anc0.Anc0refChr3 36337 25 + 222631 TGATCATT-GACATATTGCC-----------------CTATGA -s Anc1.Anc1refChr6 66489 25 + 197743 TGATCATT-GACATATTGCC-----------------CTATGA -s Anc2.Anc2refChr13 40205 25 + 96486 TGATCGAT-GACATATTGCC-----------------CTATGA -s mr.mrrefChr5 258199 25 + 294540 TTATCATT-AACATATTGCC-----------------CAATGA -s simCow_chr6.simCow.chr6 396790 25 + 602619 TGATCTCT-GACATATTACT-----------------CCATGA -s simDog_chr6.simDog.chr6 386493 25 + 593897 TGATTGAT-GACATATTGAC-----------------GTGTGA -s simHuman_chr6.simHuman.chr6 390956 25 + 601863 TGGTCATT-GACATACTCCC-----------------CGATTA - -a -s simMouse_chr6.simMouse.chr6 405449 1 + 636262 T -s Anc0.Anc0refChr3 36362 1 + 222631 T -s Anc1.Anc1refChr6 66514 1 + 197743 T -s Anc2.Anc2refChr13 40236 1 + 96486 T -s mr.mrrefChr5 258224 1 + 294540 T -s simCow_chr6.simCow.chr6 396821 1 + 602619 T -s simDog_chr6.simDog.chr6 386524 1 + 593897 T -s simHuman_chr6.simHuman.chr6 390981 1 + 601863 T - -a -s simMouse_chr6.simMouse.chr6 405450 4 + 636262 TCAT -s Anc0.Anc0refChr3 36363 4 + 222631 TCAT -s Anc1.Anc1refChr6 66515 4 + 197743 TCAT -s Anc2.Anc2refChr13 40237 4 + 96486 TCAT -s mr.mrrefChr5 258225 4 + 294540 TCAT -s simCow_chr6.simCow.chr6 396822 4 + 602619 GCGT -s simDog_chr6.simDog.chr6 386529 4 + 593897 TCAT -s simHuman_chr6.simHuman.chr6 390982 4 + 601863 AACC - -a -s simMouse_chr6.simMouse.chr6 405454 33 + 636262 TCAATTTAACACCCCTATTAAGTAAGGATGAAT -s Anc0.Anc0refChr3 36367 30 + 222631 TTAATGTAACACCTGGAT---GTAAGTATAATT -s Anc1.Anc1refChr6 66519 33 + 197743 TTAATGTAACACCTGGATCAAGTAAGTATAATT -s Anc2.Anc2refChr13 40244 30 + 96486 CTAATGTGACCACTGGTT---GTGACTATATTT -s mr.mrrefChr5 258229 33 + 294540 TCAATTTAACACCCCTATTAAGTAAGGATGAAT -s simCow_chr6.simCow.chr6 396829 30 + 602619 CTAATGTGACCACTGATC---TTCACAATATTT -s simDog_chr6.simDog.chr6 386536 30 + 593897 CTAATGTGACCACTAGTT---GTGACTATATTT -s simHuman_chr6.simHuman.chr6 390986 33 + 601863 TTAATACAACACTTGGATCAAGTAAGCATTAGT - -a -s simMouse_chr6.simMouse.chr6 405487 8 + 636262 CCCCTTAT -s Anc0.Anc0refChr3 36397 8 + 222631 CTTCTTAT -s Anc1.Anc1refChr6 66552 8 + 197743 CTTCTTAT -s Anc2.Anc2refChr13 40274 8 + 96486 CTTCTTGT -s mr.mrrefChr5 258262 8 + 294540 CCCCTTAT -s simCow_chr6.simCow.chr6 396862 8 + 602619 AGCCTTGA -s simDog_chr6.simDog.chr6 386566 8 + 593897 CTTCTCGT -s simHuman_chr6.simHuman.chr6 391019 8 + 601863 CTTCTTAT - -a -s simMouse_chr6.simMouse.chr6 405495 125 + 636262 TATGGATTAAGATCACCCTAAACATACTGTGTTTATGCCCTGTCTTTCTCATTACCAGGTGCAAACGGGAGTGCTGGGGGTTCTTGATCCCTTTAAGAGACAGCTCCCATACATCTTTTCTTAGT -s Anc0.Anc0refChr3 36405 90 + 222631 TATAGAATATGATCACACCAATAATGTAGAGTTTATGCCCCCGCTTTCTCATTCCTTGG---AGACA--------GGGAG--------------GG----------ATACACATCTCTTGTTGGT -s Anc1.Anc1refChr6 66560 114 + 197743 TATAGAATATGATCACACCAATAATGTAGAGTTTATGCCCCCGCTTTCTCATTCCTTGG---AGACA--------GGGAGTCCCTGATCCCTTTGGTAGACAGGTCATACACATCTCTTGTTGGT -s Anc2.Anc2refChr13 40282 90 + 96486 TATAGAATCTAATCGCACCAATAATGTAGAGAATGTGGCCCCGCTTTCTTGATCTTTTG---AGAAG--------GGAAG--------------GG----------ATACACATCTCTAGTTGGT -s mr.mrrefChr5 258270 125 + 294540 TATGGATTATGATCACCCTAATCATGCTGTGTTTATGCCCTGTCTTTCTCATTACTAGGTGCAAACAGGAGTGCTGGGAGTTCTTGATCCCTTTGATAGACAGGTCCCATACATCTTTTCTTAGT -s simCow_chr6.simCow.chr6 396870 9 + 602619 TATAAGACC-------------------------------------------------------------------------------------------------------------------- -s simDog_chr6.simDog.chr6 386574 90 + 593897 TATAGAATCTAATCGCACCAATAATGTAGAGAATGTGGCCCCGCTTTCTTGATCTTTTG---AGAAG--------GGAAG--------------GG----------ATACACATCTCTAGTTGGT -s simHuman_chr6.simHuman.chr6 391044 114 + 601863 TATAGAATATGATCATACAAATTATGTAGAGTTTATGCCCCCCCTTTCACATTCCTTGG---AGACA--------GGGAGTCCCTGATCCCTTTGGTAGACAGGTCTTGCACATCTCTTATTGGT -s simRat_chr6.simRat.chr6 404705 124 + 647215 -ATGGATTATGATCACTCTAATCAAGCTGTGTTTATGCCCTGTGTTTCTCACTACTAGTGGCAAACAATAGTGCTGGGAGCTCTTGATCTCTTTGATAGACAGGTCCCATACATCATTCCTTAGT - -a -s simMouse_chr6.simMouse.chr6 405620 6 + 636262 GAGATT -s Anc0.Anc0refChr3 36640 6 + 222631 GGGATT -s Anc1.Anc1refChr6 66819 6 + 197743 GGGATT -s Anc2.Anc2refChr13 40517 6 + 96486 AGGATT -s mr.mrrefChr5 258395 6 + 294540 GAGATT -s simDog_chr6.simDog.chr6 386811 6 + 593897 AGGATT -s simHuman_chr6.simHuman.chr6 391319 6 + 601863 GGGATT -s simRat_chr6.simRat.chr6 404829 6 + 647215 GAAATT - -a -s simMouse_chr6.simMouse.chr6 405626 8 + 636262 TACAACAT -s Anc0.Anc0refChr3 36646 8 + 222631 GTATATAC -s Anc1.Anc1refChr6 66825 8 + 197743 GTATATAC -s Anc2.Anc2refChr13 40523 8 + 96486 GTATGTAC -s mr.mrrefChr5 258401 8 + 294540 TACAACAT -s simDog_chr6.simDog.chr6 386855 8 + 593897 GTATGTAC -s simHuman_chr6.simHuman.chr6 391325 8 + 601863 CTTTATAC -s simRat_chr6.simRat.chr6 404835 8 + 647215 TACAACAT - -a -s simMouse_chr6.simMouse.chr6 405634 7 + 636262 CCTGTAT -s Anc0.Anc0refChr3 36654 7 + 222631 CCAGTAT -s Anc1.Anc1refChr6 66833 7 + 197743 CCAGTAT -s Anc2.Anc2refChr13 40531 7 + 96486 CCAGTAT -s mr.mrrefChr5 258409 7 + 294540 CCTGTAT -s simDog_chr6.simDog.chr6 386863 7 + 593897 CCAGTAT -s simHuman_chr6.simHuman.chr6 391333 7 + 601863 CCAATAT -s simRat_chr6.simRat.chr6 404861 7 + 647215 CCTGTAT - -a -s simMouse_chr6.simMouse.chr6 405641 1 + 636262 A -s Anc0.Anc0refChr3 36661 1 + 222631 T -s Anc1.Anc1refChr6 66840 1 + 197743 T -s Anc2.Anc2refChr13 40538 1 + 96486 T -s mr.mrrefChr5 258416 1 + 294540 A -s simDog_chr6.simDog.chr6 386871 1 + 593897 T -s simHuman_chr6.simHuman.chr6 391340 1 + 601863 T -s simRat_chr6.simRat.chr6 404868 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 405642 34 + 636262 ACCCCTTAAGTATTGGTTTGCATACAGCTTAAAT -s Anc0.Anc0refChr3 36662 33 + 222631 -CCCCTTAAGTAAAGATTAGCATACAGCTGAACC -s Anc1.Anc1refChr6 66841 34 + 197743 ACCCCTTAAGTAAAGATTAGCATACAGCTGAACC -s Anc2.Anc2refChr13 40539 33 + 96486 -TCCCTCAAGTCAAAATTAGCATATAGCTGAGCC -s mr.mrrefChr5 258417 34 + 294540 ACCCCTTAAGTATTGGTTTGTATGCAGCTTAAAT -s simDog_chr6.simDog.chr6 386872 33 + 593897 -TCCCTCAAGTCAAAATTAGCATATAGCTGAGCC -s simHuman_chr6.simHuman.chr6 391341 33 + 601863 ACCCTTT-TGTAAAGATTAGCACACAGCTAGACC -s simRat_chr6.simRat.chr6 404871 33 + 647215 ACCCCTTAAGTAT-GGTCTGTATGCAGCTTAAAT - -a -s simMouse_chr6.simMouse.chr6 405676 2 + 636262 GA -s Anc0.Anc0refChr3 36695 2 + 222631 CA -s Anc1.Anc1refChr6 66875 2 + 197743 CA -s Anc2.Anc2refChr13 40572 2 + 96486 CA -s mr.mrrefChr5 258451 2 + 294540 GA -s simDog_chr6.simDog.chr6 386917 2 + 593897 CA -s simHuman_chr6.simHuman.chr6 391374 2 + 601863 AA -s simRat_chr6.simRat.chr6 404904 2 + 647215 GA - -a -s simMouse_chr6.simMouse.chr6 405678 78 + 636262 TGTAGAGTCAGCTTCAATGAAATAGAGGTAATTCCTCGCCTAGTGACTAATACGCTGGGGCTCCATCCATGTAAACCA -s Anc0.Anc0refChr3 36798 74 + 222631 TTTATATGCAGCTTAAATGATATAGAGGTAATTCCCTGCATGATGGCTAATATGGTTAAGAGCCA----CGTGATCCA -s Anc1.Anc1refChr6 66978 74 + 197743 TTTATATGCAGCTTAAATGATATAGAGGTAATTCCCTGCATGATGGCTAATATGGTTAAGAGCCA----CGTGATCCA -s Anc2.Anc2refChr13 40675 74 + 96486 TTTATATGCAGCTTAAATGATGTAGAGGTAATTCCCTGCATGATGGCTAATATGGTTAAGAGCCA----CGTGATCCA -s mr.mrrefChr5 258453 74 + 294540 TGTAGAGTCAGCTTAAATGAAATAGAGGTAATTCCTCGCCTAGTGACTAATACGGTGAGGCTCCA----TGTAATCCA -s simCow_chr6.simCow.chr6 396919 70 + 602619 ATCATGAACAGCTTAAATGGTGTAGA-GTAAGTACCTGTGTGAT--CTAATATGGTGAAGATCCA----CGT-ATCCA -s simDog_chr6.simDog.chr6 387022 68 + 593897 TTTATATGCAGTTTAAATGACGTAGAGGTAATTCTCTGCATAATGGCTACTATGGTTAAAGGTC-------TGAC--- -s simHuman_chr6.simHuman.chr6 391508 74 + 601863 TTTATACGCAGCTTAAATGATATGGAGGTGATCCCCTGCATGATGGCTAATATGGTAAAGAACCA----CATGATCCA -s simRat_chr6.simRat.chr6 404906 50 + 647215 TGTAGAGTCAGCTTAAATA------------------------AGACTAATACGGTCAGGCTCCA----TGTAATCCA - -a -s simMouse_chr6.simMouse.chr6 405756 7 + 636262 TGCCACC -s Anc0.Anc0refChr3 36872 7 + 222631 TGCCAAT -s Anc1.Anc1refChr6 67052 7 + 197743 TGCCAAT -s Anc2.Anc2refChr13 40749 7 + 96486 TGCCTAT -s mr.mrrefChr5 258527 7 + 294540 TGCCACT -s simCow_chr6.simCow.chr6 396994 7 + 602619 TGCCTAG -s simDog_chr6.simDog.chr6 387090 1 + 593897 ------T -s simHuman_chr6.simHuman.chr6 391582 7 + 601863 TGCCAAT -s simRat_chr6.simRat.chr6 404956 7 + 647215 TGCCACT - -a -s simMouse_chr6.simMouse.chr6 405763 6 + 636262 TCTTAG -s Anc0.Anc0refChr3 36882 6 + 222631 TTCTTA -s Anc1.Anc1refChr6 67066 6 + 197743 TTCTTA -s Anc2.Anc2refChr13 40759 6 + 96486 TTCTTA -s mr.mrrefChr5 258541 6 + 294540 TCCTTA -s simCow_chr6.simCow.chr6 397004 6 + 602619 TTGTTA -s simDog_chr6.simDog.chr6 387094 6 + 593897 TCCTTA -s simHuman_chr6.simHuman.chr6 391596 6 + 601863 TTCCTA -s simRat_chr6.simRat.chr6 404970 6 + 647215 TCCTTA - -a -s simMouse_chr6.simMouse.chr6 405769 4 + 636262 GTGA -s Anc0.Anc0refChr3 36888 4 + 222631 GTGA -s Anc1.Anc1refChr6 67072 4 + 197743 GTGA -s Anc2.Anc2refChr13 40765 4 + 96486 CTGA -s mr.mrrefChr5 258547 4 + 294540 GTGA -s simCow_chr6.simCow.chr6 397010 4 + 602619 CTGA -s simHuman_chr6.simHuman.chr6 391604 4 + 601863 GTGT -s simRat_chr6.simRat.chr6 404976 4 + 647215 GTGA - -a -s simMouse_chr6.simMouse.chr6 405773 27 + 636262 TTGTCTCTACAATGTAGATTTCATGTA -s Anc0.Anc0refChr3 36892 27 + 222631 TCATCTCTATGATGTAGATTTCATACA -s Anc1.Anc1refChr6 67076 27 + 197743 TCATCTCTATGATGTAGATTTCATACA -s Anc2.Anc2refChr13 40770 27 + 96486 TCATCCCTATGATGTAGATTTCATACA -s mr.mrrefChr5 258551 27 + 294540 TCATCTCTACAATGTAGATTTCATGTA -s simCow_chr6.simCow.chr6 397015 27 + 602619 TCATCACTATAATGTAGTTTTCATACA -s simDog_chr6.simDog.chr6 387100 22 + 593897 -----CCTATGATGCGGATTTAGTATG -s simHuman_chr6.simHuman.chr6 391608 27 + 601863 TCAATTCTATGATGTAGACCTCATACA -s simRat_chr6.simRat.chr6 404980 27 + 647215 TCATCTCTACAACGGAGATTTCATGTA - -a -s simMouse_chr6.simMouse.chr6 405800 88 + 636262 GTTGCAAAATTCTACCAATTATGTGGTGTATTTATCTTACATTAATTTATTCGAGCAAATATAAACAGCATTTCTCTTGTCTACTAAT -s Anc0.Anc0refChr3 36919 82 + 222631 GTTGCCCGAGTTTAGCAGGTATGTG----CTTTATAATACATTAATTAATTTGAGCAAATATGAATA-C-TATCTCTGGTCTATTAAT -s Anc1.Anc1refChr6 67103 82 + 197743 GTTGCCCGAGTTTAGCAGGTATGTG----CTTTATAATACATTAATTAATTTGAGCAAATATGAATA-C-TATCTCTGGTCTATTAAT -s Anc2.Anc2refChr13 40797 82 + 96486 GTTGCCCGAGTTTAGCAGGTATGTG----TTTTATAATACATTGATTAATTTGAGCAAATCTGAATA-C-TAACTCTGGGCTATTAAT -s mr.mrrefChr5 258578 87 + 294540 GTTGCAAAATTCTACCAATTATGTGGTGTCTTTATCTTACATTAATTAATTCGAGCAAATATAAACA-CATTTCTCTGGTCTACTAAT -s simCow_chr6.simCow.chr6 397044 68 + 602619 GTTGCCTGAAATTAGCAGGTCTGAG----TTTTACATTGCATTGATTAATATGA----------------TTACCTTTGACTATTGAT -s simDog_chr6.simDog.chr6 387122 82 + 593897 GGTGCCCTAGTCTAGTAGGTATGTG----TTTTCTAATACATTGATTAATTTGAGCAAATCTGAATA-C-TAACTCTGGGCTGTTAAT -s simHuman_chr6.simHuman.chr6 391635 82 + 601863 GTTGTTCGAGTTTTGCAGGTGTGTG----CTTTATGCTACATTAACCAGTCTGAGCAAAAATGGAAA-T-TATGTCTGGTCTATTAAT -s simRat_chr6.simRat.chr6 405007 87 + 647215 GTTACAAAATTCTACCAATTATGTGGCGTCCGTATCTTACATTAATTAATTCATGCAAATATAAACA-CATTTCTCTGGTGTGCTAAT - -a -s simMouse_chr6.simMouse.chr6 405888 9 + 636262 TAGTATTCG -s Anc0.Anc0refChr3 37007 9 + 222631 TAGTATATG -s Anc1.Anc1refChr6 67191 9 + 197743 TAGTATATG -s Anc2.Anc2refChr13 40885 9 + 96486 TAGTATATG -s mr.mrrefChr5 258665 9 + 294540 TAGTATTTG -s simCow_chr6.simCow.chr6 397118 9 + 602619 CAGTATATG -s simDog_chr6.simDog.chr6 387210 9 + 593897 TAGTATATG -s simHuman_chr6.simHuman.chr6 391723 9 + 601863 TAGTATATG -s simRat_chr6.simRat.chr6 405094 9 + 647215 TGGTATTTG - -a -s simMouse_chr6.simMouse.chr6 405897 96 + 636262 GTCAGCAATCCTGGCTGGCTGATATCTATGTCTATGCTGGCATAATTATGGTATGCAGCTTCCTCACGTCAGAAAACCAATAACAACTTTATTTAG -s Anc0.Anc0refChr3 37029 90 + 222631 GTCAGCAATTATGGCTAGCTGATA------TCTATCCTGGCATAATTATGGTGCATGGATCCATCATTCCAGCAACTCAACAAAAACTCTATCTAG -s Anc1.Anc1refChr6 67213 90 + 197743 GTCAGCAATTATGGCTAGCTGATA------TCTATCCTGGCATAATTATGGTGCATGGATCCATCATTCCAGCAACTCAACAAAAACTCTATCTAG -s Anc2.Anc2refChr13 40907 90 + 96486 GTCAGCAATTATGGCTAGCTTATA------TCTATCCTGGCATAATTATGGTGCATGGATCCATCATTCCAGCAACTCAACAAATACTCTATCTAG -s mr.mrrefChr5 258687 96 + 294540 GTCAGCAATCCTGGCTGGCTGATATCTATGTCTATGCTGGCATAATTATGGTATACAGCTTCATCACTTCAGCAAACCAATAACAACTTTATTTAG -s simCow_chr6.simCow.chr6 397140 77 + 602619 GTCAGCATTTATGGCCAGCTTATG------TCTATCCTGGT-TAGTTATGGTGTATGGATCCTTCAATGCTGCAACTCAACAAA------------ -s simDog_chr6.simDog.chr6 387232 90 + 593897 TCCACCGATCATGGCTGGCTTCTA------TCTATTCTGGCATAATTATGGTTCATGGATGCATCATTCCAGCAACTCAACAACTACTCTATCTAG -s simHuman_chr6.simHuman.chr6 391745 90 + 601863 GTCAGCAATTACAGCTAGCTGATA------TCTGTCCTGGCATAATCATGATGCATGCATCAATCTTTCTAACAACTCAACAAAAACTCTAAAAAG -s simRat_chr6.simRat.chr6 405116 96 + 647215 GCTAGCAATCCTGGCTGGCTGATATCTATGTCTATGCTGGCATAATTATGGTATACAGCTTTATTACTTCAGCAAACCAAAGACAACTTTATTTAA - -a -s simMouse_chr6.simMouse.chr6 405993 66 + 636262 GTGAGCAGAGAGGTTGAAGTGACAATCTTTTGGTGTGACTCTAACATGACTGACATGATCTACTAG -s Anc0.Anc0refChr3 37120 66 + 222631 ATTCACAAGAAGTTAGGAGTGATAATCTTTTGGTGTGAATCTAACACGACTGACTTTGCCTTTCAG -s Anc1.Anc1refChr6 67304 66 + 197743 ATTCACAAGAAGTTAGGAGTGATAATCTTTTGGTGTGAATCTAACACGACTGACTTTGCCTTTCAG -s Anc2.Anc2refChr13 40998 66 + 96486 ATTCACAAGAAATTAGGAGTGATAATCTTTAGATGTGAATCTAACACGACTGACTTTGCCTTTCAG -s mr.mrrefChr5 258783 66 + 294540 GTGAGCAGGGAGGTAGAAGTGACAATCTTTTGGTGTGACTCTAACACGACTGACATGATCTTTTAG -s simCow_chr6.simCow.chr6 397218 66 + 602619 ACTCACAAGAATTCATGAGTGATAATCTTTAGATGCGAATCTAACATGACTGACTTTGCCTTTCTG -s simDog_chr6.simDog.chr6 387323 66 + 593897 ATTAGCAAGACATTAGGAGTGATAATCTTTAGATGTGAGTCTAACACAAGTGACCTTGCTTTTCAG -s simHuman_chr6.simHuman.chr6 391836 66 + 601863 CTTCACAAGAAGTTAGGAGTGATAATATTTTGGTGTGAATCTAACACGACTGGCTTTGCCTTTCAG -s simRat_chr6.simRat.chr6 405212 66 + 647215 GTCAGCAGGGAGGTAGAAGTGACGATCTTATAGTGTGACTCTAACACGACTGACATAATCTTTTAG - -a -s simMouse_chr6.simMouse.chr6 406059 8 + 636262 AATATGCC -s Anc0.Anc0refChr3 37186 8 + 222631 AATTTGTG -s Anc1.Anc1refChr6 67370 8 + 197743 AATTTGTG -s Anc2.Anc2refChr13 41064 8 + 96486 AATTTGTG -s mr.mrrefChr5 258849 8 + 294540 AATATGCC -s simCow_chr6.simCow.chr6 397285 8 + 602619 AATTTTTC -s simDog_chr6.simDog.chr6 387389 8 + 593897 AATTTGTG -s simHuman_chr6.simHuman.chr6 391902 8 + 601863 AATTTGTG -s simRat_chr6.simRat.chr6 405278 8 + 647215 AATGTCCC - -a -s simMouse_chr6.simMouse.chr6 406067 19 + 636262 CATCAGATTCCATTTCATC -s Anc0.Anc0refChr3 37194 19 + 222631 TATCAGAATCCATTCCACC -s Anc1.Anc1refChr6 67378 19 + 197743 TATCAGAATCCATTCCACC -s Anc2.Anc2refChr13 41072 19 + 96486 TAGCAGAATCCATTCCACC -s mr.mrrefChr5 258857 19 + 294540 CATCAGATTCCATTCCACC -s simCow_chr6.simCow.chr6 397293 19 + 602619 TTCCAGACTCCCTTGCACC -s simDog_chr6.simDog.chr6 387409 17 + 593897 TAGCAGAATCCACTCCA-- -s simHuman_chr6.simHuman.chr6 391910 19 + 601863 TATCAGAATCCATTCCACC -s simRat_chr6.simRat.chr6 405286 19 + 647215 GATCAGATTCCATCCCACC - -a -s simMouse_chr6.simMouse.chr6 406086 5 + 636262 TTGCA -s Anc0.Anc0refChr3 37219 5 + 222631 TTTTG -s Anc1.Anc1refChr6 67403 5 + 197743 TTTTG -s Anc2.Anc2refChr13 41097 5 + 96486 TGTTG -s mr.mrrefChr5 258876 5 + 294540 TTGCA -s simCow_chr6.simCow.chr6 397318 5 + 602619 TGTTG -s simHuman_chr6.simHuman.chr6 391935 5 + 601863 TTATG -s simRat_chr6.simRat.chr6 405305 5 + 647215 TTGCA - -a -s simMouse_chr6.simMouse.chr6 406091 30 + 636262 TATGTACTGATGACCAATGCATTACCTGAG -s Anc0.Anc0refChr3 37224 28 + 222631 TATGTACTAC--ACACATGCATTATCTGGG -s Anc1.Anc1refChr6 67408 30 + 197743 TATGTACTACTGACACATGCATTATCTGGG -s Anc2.Anc2refChr13 41102 28 + 96486 CATGCACTAC--ACACGTGCACTATCTGGG -s mr.mrrefChr5 258881 30 + 294540 TATGTACTGATGACCAATGCATTACCTGAG -s simCow_chr6.simCow.chr6 397326 28 + 602619 CATGCACTAC--ACACGTGCACTATCTGGG -s simHuman_chr6.simHuman.chr6 391940 30 + 601863 TATGTATTTTTGACTCATGCATTATTTAGG -s simRat_chr6.simRat.chr6 405310 30 + 647215 TATGTGCTCATAGCCAATGCATTACCTGTG - -a -s simMouse_chr6.simMouse.chr6 406121 17 + 636262 AAGAGTCAAGCTCTACC -s Anc0.Anc0refChr3 37253 17 + 222631 AGGGGGCAAGATCTTCT -s Anc1.Anc1refChr6 67439 17 + 197743 AGGGGGCAAGATCTTCT -s Anc2.Anc2refChr13 41131 17 + 96486 TGTGAGCATGATCTTCT -s mr.mrrefChr5 258911 17 + 294540 AGGAGTCAAGCTCTACT -s simCow_chr6.simCow.chr6 397355 17 + 602619 TGTGAGCATGATCTTCT -s simHuman_chr6.simHuman.chr6 391971 17 + 601863 AGGGGGCGAGATCTTCT -s simRat_chr6.simRat.chr6 405340 17 + 647215 AGGAGTCAAGTTCTACT - -a -s simMouse_chr6.simMouse.chr6 406138 22 + 636262 ACATTAACTCTTAATAAGGCTC -s Anc0.Anc0refChr3 37270 22 + 222631 ACATTCACTCGTAATAAGGCCC -s Anc1.Anc1refChr6 67456 22 + 197743 ACATTCACTCGTAATAAGGCCC -s Anc2.Anc2refChr13 41148 22 + 96486 ACATCCACTCGTAATAAGGCCC -s mr.mrrefChr5 258928 22 + 294540 ACATTAACTCTTAATAAGGCTC -s simCow_chr6.simCow.chr6 397377 22 + 602619 ACATCCACTCGTAGTAAGGCCC -s simDog_chr6.simDog.chr6 387426 10 + 593897 ------------GATAAGGCCC -s simHuman_chr6.simHuman.chr6 391988 22 + 601863 ACTTTCACCTATAATAAGGTCC -s simRat_chr6.simRat.chr6 405357 22 + 647215 GCATTAGCTCTCAATAAGGCTC - -a -s simMouse_chr6.simMouse.chr6 406160 36 + 636262 AATAGGTCCAGGGACTTGGATCATATATATAACCAC -s Anc0.Anc0refChr3 37293 29 + 222631 AAAAAGTCCAGGGATTTGCACCA-------AACCAC -s Anc1.Anc1refChr6 67479 36 + 197743 AAAAAGTCCAGGGATTTGCACCACGGAGTTAACCAC -s Anc2.Anc2refChr13 41171 29 + 96486 AAAAAGTGCAGGAATTTGCACCA-------AACCAC -s mr.mrrefChr5 258950 36 + 294540 AATAAGTCCAGGGATTTGGACCATATATATAACCAC -s simCow_chr6.simCow.chr6 397400 3 + 602619 AAA--------------------------------- -s simDog_chr6.simDog.chr6 387436 29 + 593897 CAAAAGTGCAGGAATTTGCACCA-------AACCAC -s simHuman_chr6.simHuman.chr6 392011 36 + 601863 AAAAAGCCTAGGGATTTGCACAACGGAGTTAACCAC -s simRat_chr6.simRat.chr6 405379 36 + 647215 TATAAGTCCAGGGATTTGGACTATATATATAATCGC - -a -s simMouse_chr6.simMouse.chr6 406196 24 + 636262 TTCATAGTATCAAGGCTAGTACAT -s Anc0.Anc0refChr3 37325 24 + 222631 TGTATAGTATCGTCGCTAGTACAT -s Anc1.Anc1refChr6 67518 24 + 197743 TGTATAGTATCGTCGCTAGTACAT -s Anc2.Anc2refChr13 41203 24 + 96486 TGTACTAAAGCGTCACTACTACAT -s mr.mrrefChr5 258986 24 + 294540 TTCATAGTATCAAGGCTAGTACAT -s simDog_chr6.simDog.chr6 387468 24 + 593897 TGTACTAAAGCGTCACTACTACAT -s simHuman_chr6.simHuman.chr6 392050 24 + 601863 TGTATAGTATGGTTGCTAGTGCAT -s simRat_chr6.simRat.chr6 405415 16 + 647215 TTCATGATATC--------TATAT - -a -s simMouse_chr6.simMouse.chr6 406220 1 + 636262 C -s Anc0.Anc0refChr3 37354 1 + 222631 C -s Anc1.Anc1refChr6 67547 1 + 197743 C -s Anc2.Anc2refChr13 41232 1 + 96486 C -s mr.mrrefChr5 259010 1 + 294540 C -s simDog_chr6.simDog.chr6 387497 1 + 593897 C -s simHuman_chr6.simHuman.chr6 392079 1 + 601863 C -s simRat_chr6.simRat.chr6 405431 1 + 647215 C - -a -s simMouse_chr6.simMouse.chr6 406221 31 + 636262 TCCATCACCACTAACTATTGGTATAGAAGAA -s Anc0.Anc0refChr3 37355 30 + 222631 TCCATCACCATTAACTACTGGTATAGAAGA- -s Anc1.Anc1refChr6 67548 30 + 197743 TCCATCACCATTAACTACTGGTATAGAAGA- -s Anc2.Anc2refChr13 41233 30 + 96486 TTCATCACCATTAACTACTGGTATAGGAGT- -s mr.mrrefChr5 259011 30 + 294540 TCCATCACCACTAACTACTGGTATAGAAGA- -s simDog_chr6.simDog.chr6 387498 30 + 593897 TTCATCACCATTAACTACTGGTATAGGAGT- -s simHuman_chr6.simHuman.chr6 392081 30 + 601863 TCCATCACTATTCACTACCAGTATAGAAGA- -s simRat_chr6.simRat.chr6 405432 30 + 647215 TCCATCACCACTTATTACAGGTATAGAGGA- - -a -s simMouse_chr6.simMouse.chr6 406252 28 + 636262 TCAGTATGAATCTAAGTACTGACATCGC -s Anc0.Anc0refChr3 37385 28 + 222631 TTAAAATGAAGCTAAGTAATTACACCGC -s Anc1.Anc1refChr6 67578 28 + 197743 TTAAAATGAAGCTAAGTAATTACACCGC -s Anc2.Anc2refChr13 41263 28 + 96486 TTAAAATGAAGCTAAGTAACTACACCAC -s mr.mrrefChr5 259041 28 + 294540 TCAGAATGAATCTAAGTACTGACATCGC -s simCow_chr6.simCow.chr6 397403 27 + 602619 -CTAAATGAAGCTAAGTATCTACACCAC -s simDog_chr6.simDog.chr6 387528 28 + 593897 TTAAAATGAAGCTAAGTAACTACACCAC -s simHuman_chr6.simHuman.chr6 392147 26 + 601863 TTAAAATGAAGCTAAGG--TAACTACGC -s simRat_chr6.simRat.chr6 405462 28 + 647215 TCAGAATGAATCTAAGTGCTGACACCGC - -a -s simMouse_chr6.simMouse.chr6 406280 14 + 636262 TGATAGTCAGACAC -s Anc0.Anc0refChr3 37413 14 + 222631 TGATAACCAGTCAC -s Anc1.Anc1refChr6 67606 14 + 197743 TGATAACCAGTCAC -s Anc2.Anc2refChr13 41291 14 + 96486 TAATAACCAGTAAC -s mr.mrrefChr5 259069 14 + 294540 TGATAGTCAGACAC -s simCow_chr6.simCow.chr6 397430 12 + 602619 CAATAATGAG--AC -s simDog_chr6.simDog.chr6 387556 14 + 593897 TACTGACCAATAAC -s simHuman_chr6.simHuman.chr6 392175 14 + 601863 TGATAACCAGGCAC -s simRat_chr6.simRat.chr6 405490 14 + 647215 TGATAGTCAGACAC - -a -s simMouse_chr6.simMouse.chr6 406294 8 + 636262 TACTCACT -s Anc0.Anc0refChr3 37430 8 + 222631 CACTCACT -s Anc1.Anc1refChr6 67623 8 + 197743 CACTCACT -s Anc2.Anc2refChr13 41308 8 + 96486 CACTCACA -s mr.mrrefChr5 259083 8 + 294540 TACTCACT -s simCow_chr6.simCow.chr6 397445 8 + 602619 CACTCACA -s simDog_chr6.simDog.chr6 387572 8 + 593897 CTCTCATA -s simHuman_chr6.simHuman.chr6 392192 8 + 601863 CACTCACT -s simRat_chr6.simRat.chr6 405504 8 + 647215 TACTCAGT - -a -s simMouse_chr6.simMouse.chr6 406302 7 + 636262 CTTTCAC -s Anc0.Anc0refChr3 37449 7 + 222631 CTTTGAC -s Anc1.Anc1refChr6 67642 7 + 197743 CTTTGAC -s Anc2.Anc2refChr13 41327 7 + 96486 CTTAGAC -s mr.mrrefChr5 259091 7 + 294540 CTTTCAC -s simCow_chr6.simCow.chr6 397464 7 + 602619 CCTAGAC -s simDog_chr6.simDog.chr6 387591 7 + 593897 TTCAGAC -s simHuman_chr6.simHuman.chr6 392211 7 + 601863 CTTTGAC -s simRat_chr6.simRat.chr6 405512 7 + 647215 CTTTCAC - -a -s simMouse_chr6.simMouse.chr6 406309 12 + 636262 TAATTAAGACCG -s Anc0.Anc0refChr3 37456 12 + 222631 TAATTAAAGTCA -s Anc1.Anc1refChr6 67649 12 + 197743 TAATTAAAGTCA -s Anc2.Anc2refChr13 41334 12 + 96486 TAATTAAAGTAA -s mr.mrrefChr5 259098 12 + 294540 TAATTAAGGCCA -s simCow_chr6.simCow.chr6 397471 12 + 602619 TAATTAAAGTTA -s simDog_chr6.simDog.chr6 387598 3 + 593897 ---------TAA -s simHuman_chr6.simHuman.chr6 392219 12 + 601863 TAATTGGAGTCA -s simRat_chr6.simRat.chr6 405519 12 + 647215 TAATTAAGGCCA - -a -s simMouse_chr6.simMouse.chr6 406321 1 + 636262 C -s Anc0.Anc0refChr3 37470 1 + 222631 C -s Anc1.Anc1refChr6 67663 1 + 197743 C -s Anc2.Anc2refChr13 41348 1 + 96486 T -s mr.mrrefChr5 259112 1 + 294540 C -s simCow_chr6.simCow.chr6 397485 1 + 602619 T -s simDog_chr6.simDog.chr6 387603 1 + 593897 T -s simHuman_chr6.simHuman.chr6 392233 1 + 601863 C -s simRat_chr6.simRat.chr6 405533 1 + 647215 C - -a -s simMouse_chr6.simMouse.chr6 406322 11 + 636262 TTCGTAATCAA -s Anc0.Anc0refChr3 37482 11 + 222631 TTTGTATTAAA -s Anc1.Anc1refChr6 67675 11 + 197743 TTTGTATTAAA -s Anc2.Anc2refChr13 41360 11 + 96486 TTTGTATTAAA -s mr.mrrefChr5 259113 11 + 294540 TTTGTAATCAA -s simCow_chr6.simCow.chr6 397497 11 + 602619 TTTCTATTAAA -s simDog_chr6.simDog.chr6 387615 11 + 593897 TTAGCATTAAA -s simHuman_chr6.simHuman.chr6 392245 11 + 601863 TTTGTGTTAAA -s simRat_chr6.simRat.chr6 405534 11 + 647215 TTTGTAATCAA - -a -s simMouse_chr6.simMouse.chr6 406333 17 + 636262 GCATACACCTCATACCA -s Anc0.Anc0refChr3 37493 17 + 222631 GCATAGACCACATATCA -s Anc1.Anc1refChr6 67686 17 + 197743 GCATAGACCACATATCA -s Anc2.Anc2refChr13 41371 17 + 96486 GCATAGACCACATATCA -s mr.mrrefChr5 259124 17 + 294540 GCATAGACCTCATACCA -s simCow_chr6.simCow.chr6 397508 17 + 602619 GCATAGACCACATATCA -s simDog_chr6.simDog.chr6 387626 17 + 593897 GCATAGACCACATGTCA -s simHuman_chr6.simHuman.chr6 392256 17 + 601863 GCATAGACCACATATCA -s simRat_chr6.simRat.chr6 405547 17 + 647215 GCATAGACCTCATACCA - -a -s simMouse_chr6.simMouse.chr6 406350 50 + 636262 GCCATACATGGCTTTAGTGACTATTATCTATACTTCCTAGTGTCAACATC -s Anc0.Anc0refChr3 37511 45 + 222631 ACTGTAA----CTTTTCTGTCTATTGACTATAC-ACCTAGAGTTAAGATC -s Anc1.Anc1refChr6 67704 45 + 197743 ACTGTAA----CTTTTCTGTCTATTGACTATAC-ACCTAGAGTTAAGATC -s Anc2.Anc2refChr13 41389 45 + 96486 ACTGTAA----CTTTTCTGTCTCTTGACTATAC-AGCTAGAGTTAAGATC -s mr.mrrefChr5 259141 46 + 294540 GCCATAC----CTTTAGTGACTATTATCTATACTTCCTAGAGTCAACATC -s simCow_chr6.simCow.chr6 397526 45 + 602619 ACTGTAA----CTTTTCCACCTTTTGACTATAC-AGCAAGAGTGTAGATC -s simDog_chr6.simDog.chr6 387644 45 + 593897 ACTGTAA----CTTTTCTGTCTCTTAATTATAT-CGTTTGAGTTAAGGTC -s simHuman_chr6.simHuman.chr6 392274 45 + 601863 ACTGAAG----CTTTCCTGGCTATTGACTATAC-ACCTAGAGTTCCAATC -s simRat_chr6.simRat.chr6 405564 46 + 647215 ACCATAC----CTTTAGTGAATATTATCTACACTTCTTAGAGTCAAGATC - -a -s simMouse_chr6.simMouse.chr6 406400 19 + 636262 TGTGATGACTAAATCATAC -s Anc0.Anc0refChr3 37556 19 + 222631 TGTGATATCCAAATCATGC -s Anc1.Anc1refChr6 67749 19 + 197743 TGTGATATCCAAATCATGC -s Anc2.Anc2refChr13 41434 19 + 96486 TGTAATATCCAAATTATGC -s mr.mrrefChr5 259187 19 + 294540 TGTGATGTCTAAATCATAC -s simCow_chr6.simCow.chr6 397572 19 + 602619 TGTAATATCTGAATTATGC -s simDog_chr6.simDog.chr6 387689 19 + 593897 TGTAATATCCAAATTATGC -s simHuman_chr6.simHuman.chr6 392319 19 + 601863 CAGGACATCCAAATCATGC -s simRat_chr6.simRat.chr6 405610 19 + 647215 TGTGATCTCTAAATCATAC - -a -s simMouse_chr6.simMouse.chr6 406419 9 + 636262 TGTGTATCC -s Anc0.Anc0refChr3 37582 9 + 222631 TATGCTTGG -s Anc1.Anc1refChr6 67775 9 + 197743 TATGCTTGG -s Anc2.Anc2refChr13 41460 9 + 96486 TATGCTTGG -s mr.mrrefChr5 259206 9 + 294540 TGTGCATGC -s simCow_chr6.simCow.chr6 397598 9 + 602619 TAGGCTAGG -s simDog_chr6.simDog.chr6 387715 9 + 593897 TATGCTTGG -s simHuman_chr6.simHuman.chr6 392346 9 + 601863 TATGCTTGG -s simRat_chr6.simRat.chr6 405629 9 + 647215 TGTGCATGC - -a -s simMouse_chr6.simMouse.chr6 406428 5 + 636262 ACATT -s Anc0.Anc0refChr3 37591 5 + 222631 GCATA -s Anc1.Anc1refChr6 67784 5 + 197743 GCATA -s Anc2.Anc2refChr13 41488 5 + 96486 GTATA -s mr.mrrefChr5 259215 5 + 294540 ACATT -s simCow_chr6.simCow.chr6 397627 5 + 602619 GTATA -s simDog_chr6.simDog.chr6 387743 5 + 593897 GTATA -s simHuman_chr6.simHuman.chr6 392355 5 + 601863 GCATG -s simRat_chr6.simRat.chr6 405638 5 + 647215 ACATT - -a -s simMouse_chr6.simMouse.chr6 406433 1 + 636262 G -s Anc0.Anc0refChr3 37599 1 + 222631 G -s Anc1.Anc1refChr6 67792 1 + 197743 G -s Anc2.Anc2refChr13 41496 1 + 96486 G -s mr.mrrefChr5 259220 1 + 294540 G -s simCow_chr6.simCow.chr6 397649 1 + 602619 T -s simDog_chr6.simDog.chr6 387751 1 + 593897 G -s simHuman_chr6.simHuman.chr6 392363 1 + 601863 G -s simRat_chr6.simRat.chr6 405643 1 + 647215 G - -a -s simMouse_chr6.simMouse.chr6 406434 44 + 636262 ACTTCACCTCAGTATATACAACCCATTGTGCTGGTGTGCACAGT -s Anc0.Anc0refChr3 37600 43 + 222631 ACTTCACCTCGGTATAAATGATCTATTGTGATGGTGTG-AAAGA -s Anc1.Anc1refChr6 67793 43 + 197743 ACTTCACCTCGGTATAAATGATCTATTGTGATGGTGTG-AAAGA -s Anc2.Anc2refChr13 41501 43 + 96486 ACTTTGCCTTGGTATAAATGATCTATTGTGATGGTGTC-AATGA -s mr.mrrefChr5 259221 44 + 294540 ACTTCACCTCAGTATATACAATCCATTGTGCTGGTGTGCACAGT -s simCow_chr6.simCow.chr6 397654 43 + 602619 ACGTTGCCTTTGTATAAACGATCTATTGTGATGGTGTC-AATAA -s simDog_chr6.simDog.chr6 387756 42 + 593897 ACTTTGTCTTGATATAAATGATCTATTGTGATGGTATC-AATG- -s simHuman_chr6.simHuman.chr6 392364 43 + 601863 ACTTCACCTCGGTATGCATGATCTATTGCGATGGTGGG-ATAGG -s simRat_chr6.simRat.chr6 405644 39 + 647215 CCTTCACCTCAGTATAAACAATCCATTGTGCTGGTGTTC----- - -a -s simMouse_chr6.simMouse.chr6 406478 10 + 636262 AGATTAGGTG -s Anc0.Anc0refChr3 37643 10 + 222631 AGGTTTAGTG -s Anc1.Anc1refChr6 67836 10 + 197743 AGGTTTAGTG -s Anc2.Anc2refChr13 41544 10 + 96486 AGGTCTAGTG -s mr.mrrefChr5 259265 10 + 294540 AGATTAAGTG -s simCow_chr6.simCow.chr6 397698 10 + 602619 AGGTCTAGTG -s simDog_chr6.simDog.chr6 387798 9 + 593897 -GGTCTACTG -s simHuman_chr6.simHuman.chr6 392407 10 + 601863 AGGTTTAGTG -s simRat_chr6.simRat.chr6 405683 9 + 647215 -GATTCAGTG - -a -s simMouse_chr6.simMouse.chr6 406488 93 + 636262 TTTGTCTTATTTCAGGTAATTGTTAGCATGTTGTTGGAATATAGCATCCTGAACCTGGATCCCCTTTCTCTATAGCATAAACAGTTGGTTTCC -s Anc0.Anc0refChr3 37653 54 + 222631 CTTCTGCTGTTTTAGGTAATTGTAAACATGTTGTTGACATAGAGCATCCTAAC---------------------------------------T -s Anc1.Anc1refChr6 67846 54 + 197743 CTTCTGCTGTTTTAGGTAATTGTAAACATGTTGTTGACATAGAGCATCCTAAC---------------------------------------T -s Anc2.Anc2refChr13 41554 54 + 96486 CTTCTGCTGTTTTAGGTAGTTGTAAACAAGTTGTTGACATAGAGAATCTTAAC---------------------------------------T -s mr.mrrefChr5 259275 93 + 294540 CTTGTCTTATTTCAGGTAATTGTTAGCATGTTGTTGAAATATAGCATCCTAAACCTGGATCCCCTTTCTCTATAGCATAAACAGTTGGTTTCC -s simCow_chr6.simCow.chr6 397708 53 + 602619 CTTGTTCTGTTGTAGGTACTTGTACACAAGTTGTTGAAA-AGTGAAGCATAAC---------------------------------------T -s simDog_chr6.simDog.chr6 387848 54 + 593897 CTTCTGCTGTTTGGGGTAGTTGTAAACAAGTTATTGACATAGAGAATCTTGAC---------------------------------------T -s simHuman_chr6.simHuman.chr6 392417 54 + 601863 CTTCTACTGTACTAGGTAATTGTAACCATGTTGTTGATATAGAGCATTCTAAC---------------------------------------T -s simRat_chr6.simRat.chr6 405692 91 + 647215 CTAGTCTTATTTCACTTAATTGTTAACACGTCG--GAAATATACCATCCTAAACCTGGATGCGCTTACTCTATAGGATAAACAGTTAGTTTCG - -a -s simMouse_chr6.simMouse.chr6 406581 19 + 636262 ACCAGTTTGCTGCACCTGA -s Anc0.Anc0refChr3 37707 19 + 222631 ACAAATTAGTTGGACCTAA -s Anc1.Anc1refChr6 67900 19 + 197743 ACAAATTAGTTGGACCTAA -s Anc2.Anc2refChr13 41608 19 + 96486 ACAAATTAGTTGGACCTAA -s mr.mrrefChr5 259368 19 + 294540 ACCAGTTTGCTGCACCTGA -s simCow_chr6.simCow.chr6 397761 19 + 602619 ACAAATTAGCTGGAACTAA -s simDog_chr6.simDog.chr6 387902 19 + 593897 ACAAGTTAGTTGATCCCAA -s simHuman_chr6.simHuman.chr6 392471 19 + 601863 ATGAATTAGTCGGACCTAG -s simRat_chr6.simRat.chr6 405785 19 + 647215 GCCGGTCTGCTGCACCTAA - -a -s simMouse_chr6.simMouse.chr6 406600 2 + 636262 TA -s Anc0.Anc0refChr3 37726 2 + 222631 TA -s Anc1.Anc1refChr6 67919 2 + 197743 TA -s Anc2.Anc2refChr13 41636 2 + 96486 CA -s mr.mrrefChr5 259387 2 + 294540 TA -s simDog_chr6.simDog.chr6 387930 2 + 593897 CA -s simHuman_chr6.simHuman.chr6 392490 2 + 601863 TA -s simRat_chr6.simRat.chr6 405804 2 + 647215 TA - -a -s simMouse_chr6.simMouse.chr6 406602 2 + 636262 GC -s Anc0.Anc0refChr3 37728 1 + 222631 C- -s Anc1.Anc1refChr6 67921 1 + 197743 C- -s Anc2.Anc2refChr13 41638 1 + 96486 C- -s mr.mrrefChr5 259389 1 + 294540 G- -s simCow_chr6.simCow.chr6 397781 1 + 602619 C- -s simDog_chr6.simDog.chr6 388039 1 + 593897 C- -s simHuman_chr6.simHuman.chr6 392492 1 + 601863 A- -s simRat_chr6.simRat.chr6 405806 1 + 647215 G- - -a -s simMouse_chr6.simMouse.chr6 406604 2 + 636262 AT -s Anc0.Anc0refChr3 37730 2 + 222631 AG -s Anc1.Anc1refChr6 67923 2 + 197743 AG -s Anc2.Anc2refChr13 41640 2 + 96486 AG -s mr.mrrefChr5 259390 2 + 294540 AT -s simCow_chr6.simCow.chr6 397783 2 + 602619 GG -s simDog_chr6.simDog.chr6 388041 2 + 593897 AG -s simHuman_chr6.simHuman.chr6 392494 2 + 601863 AA -s simRat_chr6.simRat.chr6 405807 2 + 647215 GT - -a -s simMouse_chr6.simMouse.chr6 406606 7 + 636262 ATCCTGA -s Anc0.Anc0refChr3 37732 7 + 222631 GTTCTGA -s Anc1.Anc1refChr6 67925 7 + 197743 GTTCTGA -s Anc2.Anc2refChr13 41642 7 + 96486 GTTCTGG -s mr.mrrefChr5 259392 7 + 294540 ATCCTGA -s simCow_chr6.simCow.chr6 397785 7 + 602619 GTTCTGA -s simDog_chr6.simDog.chr6 388045 7 + 593897 GTTCTGG -s simHuman_chr6.simHuman.chr6 392496 7 + 601863 GTTCTGA -s simRat_chr6.simRat.chr6 405809 7 + 647215 ATCCTGA - -a -s simMouse_chr6.simMouse.chr6 406613 3 + 636262 CTT -s Anc0.Anc0refChr3 37739 3 + 222631 CTG -s Anc1.Anc1refChr6 67932 3 + 197743 CTG -s Anc2.Anc2refChr13 41649 3 + 96486 CTG -s mr.mrrefChr5 259399 3 + 294540 CTT -s simCow_chr6.simCow.chr6 397792 3 + 602619 CTG -s simDog_chr6.simDog.chr6 388052 3 + 593897 CTG -s simHuman_chr6.simHuman.chr6 392508 3 + 601863 CTC -s simRat_chr6.simRat.chr6 405816 3 + 647215 CCT - -a -s simMouse_chr6.simMouse.chr6 406616 14 + 636262 ACTTAAACTTTTAT -s Anc0.Anc0refChr3 37742 12 + 222631 ACTC-AACTTT-AC -s Anc1.Anc1refChr6 67935 12 + 197743 ACTC-AACTTT-AC -s Anc2.Anc2refChr13 41652 12 + 96486 TATC-AACTTT-AC -s mr.mrrefChr5 259402 14 + 294540 ACTTAAACTTTTAT -s simCow_chr6.simCow.chr6 397796 12 + 602619 TCCC-CACCCT-AC -s simDog_chr6.simDog.chr6 388055 12 + 593897 TATC-AACTTT-AC -s simHuman_chr6.simHuman.chr6 392511 4 + 601863 ACTG---------- -s simRat_chr6.simRat.chr6 405819 14 + 647215 ATTTAAACCTTAAC - -a -s simMouse_chr6.simMouse.chr6 406630 51 + 636262 TTTAGGGCTTAGCAGCAGCTCAACCACTATGTGATATAACCTGCTGAGGGC -s Anc0.Anc0refChr3 37754 45 + 222631 TTTAGAAATAGGTAG------AACTACTATGTGATGTGATCAGCTGTGGGC -s Anc1.Anc1refChr6 67947 45 + 197743 TTTAGAAATAGGTAG------AACTACTATGTGATGTGATCAGCTGTGGGC -s Anc2.Anc2refChr13 41664 45 + 96486 TTTAGAAATAGTTAG------AACTACTATGTGGTTTGATCAGCTGTGGGC -s mr.mrrefChr5 259416 51 + 294540 TTTAGGGCTTAGCAGCAGCTCAACCACTATGTGATGTAATCTGCTGAGGGC -s simCow_chr6.simCow.chr6 397808 45 + 602619 TTTAGAAATAGCTAG------AACTATTATGTGGTATGATCAGCTAAAGGT -s simDog_chr6.simDog.chr6 388067 45 + 593897 TTTAGAAATAGTTAA------AACTGCTATCTGGTTTGATAAGCTGTGGAC -s simHuman_chr6.simHuman.chr6 392680 45 + 601863 TCTAGTAATAGGAAG------AACTACTATGTGATGTGATCATCTGTGGGC -s simRat_chr6.simRat.chr6 405833 51 + 647215 TGTAGGGTTTAGCAGCAGCTCAGCTAGTAAGTGATGTAATCTGCTAAGGGC - -a -s simMouse_chr6.simMouse.chr6 406681 12 + 636262 GATGCAAAGAGC -s Anc0.Anc0refChr3 37799 12 + 222631 AATGCAGAGAAC -s Anc1.Anc1refChr6 67992 12 + 197743 AATGCAGAGAAC -s Anc2.Anc2refChr13 41710 12 + 96486 AATGCAGTGAAG -s mr.mrrefChr5 259467 12 + 294540 AATGCAAAGAGC -s simCow_chr6.simCow.chr6 397854 12 + 602619 AATGCAGTGAAG -s simDog_chr6.simDog.chr6 388113 12 + 593897 AATGTAGTGATG -s simHuman_chr6.simHuman.chr6 392725 12 + 601863 ATTGCAGAGAAC -s simRat_chr6.simRat.chr6 405884 12 + 647215 AATGCAATGAGT - -a -s simMouse_chr6.simMouse.chr6 406693 13 + 636262 CTATTAAACTAGA -s Anc0.Anc0refChr3 37811 13 + 222631 CTATTAGACTAGG -s Anc1.Anc1refChr6 68004 13 + 197743 CTATTAGACTAGG -s Anc2.Anc2refChr13 41722 13 + 96486 CTAATAGACTAGG -s mr.mrrefChr5 259479 13 + 294540 CTATTAGACTAGA -s simCow_chr6.simCow.chr6 397866 13 + 602619 CTAATAGTCTAGA -s simDog_chr6.simDog.chr6 388125 13 + 593897 TTAATATACTAGG -s simHuman_chr6.simHuman.chr6 392744 13 + 601863 CTATAAGACTAGG -s simRat_chr6.simRat.chr6 405896 13 + 647215 CTTTTAGACTACA - -a -s simMouse_chr6.simMouse.chr6 406706 16 + 636262 TATGTGTAATGCTGAG -s Anc0.Anc0refChr3 37824 14 + 222631 TA--TGCAATGTTGAG -s Anc1.Anc1refChr6 68017 14 + 197743 TA--TGCAATGTTGAG -s Anc2.Anc2refChr13 41735 14 + 96486 CA--TGCAATGTTGAG -s mr.mrrefChr5 259492 16 + 294540 TATGTGTAATGTTGAG -s simCow_chr6.simCow.chr6 397880 14 + 602619 CA--TGCAATGTCAAG -s simDog_chr6.simDog.chr6 388138 14 + 593897 CA--TGCAATATTGAA -s simHuman_chr6.simHuman.chr6 392757 14 + 601863 TA--TGGAATGTTTTT -s simRat_chr6.simRat.chr6 405909 16 + 647215 TATGTGTGCTGTTGAG - -a -s simMouse_chr6.simMouse.chr6 406722 19 + 636262 GTATACTGGTGGGAAACAC -s Anc0.Anc0refChr3 37838 18 + 222631 GTATAAAGTTTG-AAACCA -s Anc1.Anc1refChr6 68031 18 + 197743 GTATAAAGTTTG-AAACCA -s Anc2.Anc2refChr13 41749 18 + 96486 ATATAAAGTTTG-AAATCA -s mr.mrrefChr5 259508 19 + 294540 GTATACAGGTGGGAAACAC -s simCow_chr6.simCow.chr6 397894 18 + 602619 ATGAATAGTTTG-AGTTTG -s simDog_chr6.simDog.chr6 388152 18 + 593897 ACATAAAGTTTG-AAATCA -s simHuman_chr6.simHuman.chr6 392772 18 + 601863 GTCCAAAGTTTG-AAACCA -s simRat_chr6.simRat.chr6 405925 18 + 647215 GTATGCAGGT-GGAAACAC - -a -s simMouse_chr6.simMouse.chr6 406741 23 + 636262 ATATATGATAGTATACCGATATC -s Anc0.Anc0refChr3 37856 23 + 222631 GTACATGATAGTATACCGATACC -s Anc1.Anc1refChr6 68049 23 + 197743 GTACATGATAGTATACCGATACC -s Anc2.Anc2refChr13 41767 23 + 96486 GTATATGATAGTATACCGATACC -s mr.mrrefChr5 259527 23 + 294540 ATACATGATAGTATACCGATATC -s simCow_chr6.simCow.chr6 397912 22 + 602619 GTATATGCTAATGTACCAATA-T -s simDog_chr6.simDog.chr6 388170 23 + 593897 ATATATGACAGTATACCGATACC -s simHuman_chr6.simHuman.chr6 392790 23 + 601863 GCACATGATAGTATACCGATACC -s simRat_chr6.simRat.chr6 405944 22 + 647215 ATACATGATAG-ATACCGAAATC - -a -s simMouse_chr6.simMouse.chr6 406764 7 + 636262 ATCCTGG -s Anc0.Anc0refChr3 37879 7 + 222631 ATGATAG -s Anc1.Anc1refChr6 68072 7 + 197743 ATGATAG -s Anc2.Anc2refChr13 41796 7 + 96486 ATGACAG -s mr.mrrefChr5 259550 7 + 294540 ATCCTGG -s simCow_chr6.simCow.chr6 397940 7 + 602619 ATGAAAG -s simDog_chr6.simDog.chr6 388199 7 + 593897 ATGACTG -s simHuman_chr6.simHuman.chr6 392813 7 + 601863 ATGATAG - -a -s simMouse_chr6.simMouse.chr6 406771 80 + 636262 TGAAAACTTCCTGGCATAACCCATAGATGTGTTGGTAACTCTTGTTCCTGCAACATAGTTTAGTGGCCAATCACACTTGA -s Anc0.Anc0refChr3 37917 78 + 222631 TGCAAAATTTG--GCCTAATCCTTAAGAGTGTTGGCAACAGTTGTGTCTACGGCATAGTTTGGTGGTCTAACACATTATA -s Anc1.Anc1refChr6 68110 80 + 197743 TGCAAAATTTGTGGCCTAATCCTTAAGAGTGTTGGCAACAGTTGTGTCTACGGCATAGTTTGGTGGTCTAACACATTATA -s Anc2.Anc2refChr13 41834 78 + 96486 TGCAAAATTTG--GCCTAATCCTTAAGAGTGTTGGCAACAGTTGTGTCTACGGCATAGTTTGGTGGTCTAACACATTATG -s mr.mrrefChr5 259557 80 + 294540 TGAAAACTTCCTGGCATAACCCCTAAGAGTGTTGGTAACACTTGTTTCTGCAACATAGTTTGGTGGCCTAACACACTTGA -s simCow_chr6.simCow.chr6 397978 78 + 602619 CGCGAAATTTG--GCTCAATCCTTAAGGGCATTGGCAATAGTTGTGTGTACGGCATAGTTTGGTGGCCTGACATATTATG -s simDog_chr6.simDog.chr6 388292 78 + 593897 TGCAAAATTTG--GCCTAATCCTTAAGAGTGTTGGCAACAGTTGTGTCTACGGCATAGTTTAGTGGTCTAACACATTATG -s simHuman_chr6.simHuman.chr6 392851 71 + 601863 TGCAAAATTTGAGA---------TAAGAGTGTTGGCAACAATTGTGTCTATGGCATATTTTGGGGGTTTAACACATTATA -s simRat_chr6.simRat.chr6 405966 73 + 647215 -------TTCCTGGCATAAAGCCTAAGAATCTTGGTAACACTTGCTTCTGCAACATAGTTTGGTGGCCTAACACACTTGA - -a -s simMouse_chr6.simMouse.chr6 406851 12 + 636262 ATGAGCTACATA -s Anc0.Anc0refChr3 37999 12 + 222631 ATGGTTTACATA -s Anc1.Anc1refChr6 68194 12 + 197743 ATGGTTTACATA -s Anc2.Anc2refChr13 41916 12 + 96486 ATGGTTTACACA -s mr.mrrefChr5 259637 12 + 294540 ATGATCTACATA -s simCow_chr6.simCow.chr6 398060 12 + 602619 ATGGTTTACAGA -s simDog_chr6.simDog.chr6 388374 12 + 593897 ATGGTTTATGCA -s simHuman_chr6.simHuman.chr6 392926 12 + 601863 ATGGTTTACATA -s simRat_chr6.simRat.chr6 406039 12 + 647215 ATGATCTACATA - -a -s simMouse_chr6.simMouse.chr6 406863 46 + 636262 TGTTCAGAAGTTCTAAATTGTTATCTCGAAAATGGAACATGTACAT -s Anc0.Anc0refChr3 38011 43 + 222631 TA---GGAAAGTCTAAATTGTTATGTCAAGATTGGAATATGAATAT -s Anc1.Anc1refChr6 68206 43 + 197743 TA---GGAAAGTCTAAATTGTTATGTCAAGATTGGAATATGAATAT -s Anc2.Anc2refChr13 41928 43 + 96486 TA---GGAAAGTCTACATTGTTATGTCAAGATTGGAATATGAGTAT -s mr.mrrefChr5 259649 46 + 294540 TGTTTAGAAGTTCTAAATTGTTATCTCAAAAATGGAACATGTACAT -s simCow_chr6.simCow.chr6 398073 43 + 602619 TA---GCAAAGTCTGGATTGTTAGGTCCTGATCGGAATGTGAGTAT -s simDog_chr6.simDog.chr6 388386 43 + 593897 CT---GGAAAGTCTACATTGTTATGTCAAGATTCGAATATGAGTAT -s simHuman_chr6.simHuman.chr6 392938 43 + 601863 TA---GGAAAGTCTCAATTGTTATGTCAAGACTGGAATATGCATAT -s simRat_chr6.simRat.chr6 406051 46 + 647215 TGTTTAGATGTTCTAAATTGTTATCTCAAAAATGGAACATGTACAT - -a -s simMouse_chr6.simMouse.chr6 406909 24 + 636262 CTGTGGCTGTGCAGTATGCAAGGC -s Anc0.Anc0refChr3 38055 24 + 222631 CCGTGGTTATGTAGTATGCGAGGC -s Anc1.Anc1refChr6 68250 24 + 197743 CCGTGGTTATGTAGTATGCGAGGC -s Anc2.Anc2refChr13 41972 24 + 96486 CCGGGCTTATGTAGAATGCCAGGC -s mr.mrrefChr5 259696 24 + 294540 CTGTGGCTGTGCAGTATGCGAGGC -s simCow_chr6.simCow.chr6 398117 24 + 602619 TGGGGTTTACTTAGCAGGCCAGGC -s simDog_chr6.simDog.chr6 388430 24 + 593897 CCAGGCTAATGTGGAATGCCACGC -s simHuman_chr6.simHuman.chr6 392982 24 + 601863 CCGTGGTTATGTAGTACACGAGGC -s simRat_chr6.simRat.chr6 406098 20 + 647215 CTGTCACTGTGCAGTATCTG---- - -a -s simMouse_chr6.simMouse.chr6 406933 39 + 636262 ACAGTGATTCAGATTGCCATGTATCTCATGTATGAGTAC -s Anc0.Anc0refChr3 38079 26 + 222631 AAAGTAACTCAGAT-------------ATGTATATGTGA -s Anc1.Anc1refChr6 68274 30 + 197743 AAAGTAACTCAGAT---------TCCCATGTATATGTGA -s Anc2.Anc2refChr13 41996 26 + 96486 AAGGTAACTCAGAT-------------ATGTACATATGA -s mr.mrrefChr5 259720 39 + 294540 ACAGTGATTCAGATTGCCATGTATCTCATGTATGAGTAC -s simCow_chr6.simCow.chr6 398141 26 + 602619 AAGGTGACTCAGAT-------------ATGTACATATGA -s simDog_chr6.simDog.chr6 388454 6 + 593897 AAGGTA--------------------------------- -s simHuman_chr6.simHuman.chr6 393006 30 + 601863 AAAGTAACACAGAT---------TCCCATGGGTATGTGA -s simRat_chr6.simRat.chr6 413216 39 + 647215 ACAGCGATGCCAATTGGCATGTATCCCATGTATGAGTAT - -a -s simMouse_chr6.simMouse.chr6 406972 14 + 636262 CCTACCCACTAAAA -s Anc0.Anc0refChr3 38105 14 + 222631 TCGACTCACTAAAA -s Anc1.Anc1refChr6 68304 14 + 197743 TCGACTCACTAAAA -s Anc2.Anc2refChr13 42022 14 + 96486 TCGACTCACTAAAA -s mr.mrrefChr5 259759 14 + 294540 CCTACCCACTAAAA -s simCow_chr6.simCow.chr6 398171 14 + 602619 TCGATCCACTAAAA -s simDog_chr6.simDog.chr6 388460 11 + 593897 ---ACTCACTAAAG -s simHuman_chr6.simHuman.chr6 393036 14 + 601863 TCAACTCATTCAAA -s simRat_chr6.simRat.chr6 413255 14 + 647215 CCTACCCACTAAAA - -a -s simMouse_chr6.simMouse.chr6 406986 78 + 636262 CATCTAGTGTCTTATCTGGGATATAACTCCAGTTGAGCAGGAACTAGTTGAGTCTGGGCTCCAGATACTGCAGCTGAT -s Anc0.Anc0refChr3 38146 78 + 222631 CATCTTGCATGTTATCTGGAGTGTATCTTTAGTTGGGAGGGAACTAGGTGAATCTGGGCCCCAGATACTGCAACTAAT -s Anc1.Anc1refChr6 68345 78 + 197743 CATCTTGCATGTTATCTGGAGTGTATCTTTAGTTGGGAGGGAACTAGGTGAATCTGGGCCCCAGATACTGCAACTAAT -s Anc2.Anc2refChr13 42063 78 + 96486 CATCTTGCATGTTATATGGAGTGCATTTTTAGTTGGGAGGGAACTAGGTGAATCTGGGCCCCAGATACTGCAACTAAT -s mr.mrrefChr5 259773 78 + 294540 CATCTAGTGTCTTATCTGGAGTATAACTCCAGTTGGGCAGGAACTAGTTGAGTCTGGGCTCCAGATACTGCAGCTGAT -s simCow_chr6.simCow.chr6 398212 78 + 602619 CATCTTGCATCTTATATGGAGTGCATTCTCAGTTGGGAGGGAACTAGGTGTATCTGGGCCCCAGATATTGCAACTAAT -s simDog_chr6.simDog.chr6 388497 78 + 593897 CATCTTGCATGTTATACAGGGTGCATTTTTAGTAGGGAGGGAACTAGGTGAAACTGGGCCTCAAATACTGCAACTAAT -s simHuman_chr6.simHuman.chr6 393077 78 + 601863 CATCTTGGATTTTATCTGGAGTGTATCTTTAGTTGGGAGGGACCTAGGTGAATCTGGGCCCCAGATGCTGCGACTAAT -s simRat_chr6.simRat.chr6 413269 77 + 647215 CATGTAGTGCCTCATCTGGAGTATAACTCCATTTAGGCAGGAACTAGTTGAGTCTGGGCTTCA-CTACTGCAGCTGGT - -a -s simMouse_chr6.simMouse.chr6 407064 2 + 636262 CC -s Anc0.Anc0refChr3 38226 2 + 222631 CC -s Anc1.Anc1refChr6 68425 2 + 197743 CC -s Anc2.Anc2refChr13 42143 2 + 96486 CC -s mr.mrrefChr5 259851 2 + 294540 CC -s simCow_chr6.simCow.chr6 398292 2 + 602619 CC -s simDog_chr6.simDog.chr6 388577 2 + 593897 CC -s simHuman_chr6.simHuman.chr6 393157 2 + 601863 CC -s simRat_chr6.simRat.chr6 413346 2 + 647215 GC - -a -s simMouse_chr6.simMouse.chr6 407066 58 + 636262 ATATTACCATTGCACAATCATCATTGCCAAACATTACCATGAAATGACAAGATGAACA -s Anc0.Anc0refChr3 38228 39 + 222631 TTAAACTCATTGCACAGGCATCATAGAGACAGAT---CATGA---------------- -s Anc1.Anc1refChr6 68427 39 + 197743 TTAAACTCATTGCACAGGCATCATAGAGACAGAT---CATGA---------------- -s Anc2.Anc2refChr13 42145 39 + 96486 TTAAACTCATTGCACAGGCATCATAGAGACAGAT---GGAGA---------------- -s mr.mrrefChr5 259853 58 + 294540 ATATAACCATTGCACAAGCATCATAGCCAAAGATTACCATGAAATGACAAGATGAACA -s simCow_chr6.simCow.chr6 398296 38 + 602619 TTAAACTCATTGCACAGG-ATCATTGAGACAGAT---GGATA---------------- -s simDog_chr6.simDog.chr6 388579 35 + 593897 TTGAGTTTATTACACAGGCACCATAGATACACA-------GA---------------- -s simHuman_chr6.simHuman.chr6 393159 39 + 601863 TTAAACTCATTGCACAGGCATCATAGAGACAGAT---CATGA---------------- -s simRat_chr6.simRat.chr6 413348 58 + 647215 ATGTAACCATTGTACAAGCATCATAGCCAAAGATTGCCATTACATAACAAGATTGACA - -a -s simMouse_chr6.simMouse.chr6 407124 38 + 636262 AGACAAGAACACTGGGGTTGGATGCCATACAGGACAGG -s Anc0.Anc0refChr3 38267 31 + 222631 --ACAGGAACACTGAGGTTGCATGCCATATG-----TT -s Anc1.Anc1refChr6 68466 31 + 197743 --ACAGGAACACTGAGGTTGCATGCCATATG-----TT -s Anc2.Anc2refChr13 42184 31 + 96486 --ACAGGAACACTAAGGTTGCATGCCATACA-----TT -s mr.mrrefChr5 259911 38 + 294540 AGACAAGAACACTGGGGTTGCATGCCATATGGGACAGG -s simCow_chr6.simCow.chr6 398334 30 + 602619 --ACAGG-ACACTAATGTTGCATGCCATACA-----TT -s simDog_chr6.simDog.chr6 388614 31 + 593897 --ACATGAACACTAAGGTTGCATGCCATACA-----TT -s simHuman_chr6.simHuman.chr6 393198 31 + 601863 --ACAGGAACACTGAGGTTGCATGCCATATG-----TT -s simRat_chr6.simRat.chr6 413589 38 + 647215 GGACAAGGACGCTGGGGTTGCATGCCATATGCAACCGG - -a -s simMouse_chr6.simMouse.chr6 407162 58 + 636262 GGAAGAGGCATGTAATTTCTACAAAGTTCAGGTTATACCATGTCTGACAGCATGATCG -s Anc0.Anc0refChr3 38298 58 + 222631 GGGAGAGATACATGATTCCCACAACTTTCAGGTTATAACATGTGTGTCAGCATGATCA -s Anc1.Anc1refChr6 68497 58 + 197743 GGGAGAGATACATGATTCCCACAACTTTCAGGTTATAACATGTGTGTCAGCATGATCA -s Anc2.Anc2refChr13 42215 58 + 96486 GGGAGAGATACAAGGTTCCCACAACTTTCAGGTTATAACATGTGTGTCAGCATGATCA -s mr.mrrefChr5 259949 58 + 294540 GGAAGAGGCATGTAATTTCTACAAATTTCAGGTTATACCATGTCTGATAGTATGATCG -s simCow_chr6.simCow.chr6 398364 57 + 602619 GGGAAAGGTACA-GGTTCCCACAATTCTCAAGTTATAACATGTCTGTCAGCACGAACA -s simDog_chr6.simDog.chr6 388650 58 + 593897 GGGAGAGATACAAGGTTCTTACAACTTTCAGGTTATAACATGTGTGTCAGCATAATCA -s simHuman_chr6.simHuman.chr6 393229 46 + 601863 GGGAGAGATACATGATTCCCACCACTTTCAGGTTAC------------AGCTTGACCA -s simRat_chr6.simRat.chr6 413627 58 + 647215 GGAAGAGGCATGTAATTTCTACAAATTTCAGGTTATACCATGTCTGCTAGTATGATCA - -a -s simMouse_chr6.simMouse.chr6 407220 64 + 636262 GACTAAGGACTAAGATTAGAGATAAAGCCAGAACGGCCATTCAAGGATTCCTGACTATTTGAAG -s Anc0.Anc0refChr3 38383 64 + 222631 GAATAAGGACTGAGACTAGAGATAAAGCCATGATGGCCAGCAGAGGACCCTTGACTATCTAAAA -s Anc1.Anc1refChr6 68582 64 + 197743 GAATAAGGACTGAGACTAGAGATAAAGCCATGATGGCCAGCAGAGGACCCTTGACTATCTAAAA -s Anc2.Anc2refChr13 42300 64 + 96486 GAATAAGGACTGAGACTATACATAAAGGCATGTTGGCCAGCAGAGGACCCTTGACTGTCTAAAG -s mr.mrrefChr5 260007 64 + 294540 GACTAAGGACTAAGATTAGAGATAAAGCCAGAATGGCCATTCAAGGATCCCTGACTATTTGAAA -s simCow_chr6.simCow.chr6 398448 64 + 602619 GTATAAGGAGTGAGATTATATATAAAGGTACCCTAGCCATCCTAGAACCCTTGACTGTCCAAAG -s simDog_chr6.simDog.chr6 388735 64 + 593897 GAATTAGGACTGAGACTATACATAAGGGCATGTGGGCCAGCAGAGGACCCTTGACTGTCTAAAG -s simHuman_chr6.simHuman.chr6 393303 64 + 601863 GAATAAGGACTGAAACTAGAGATAAAGCCATGATGGCCAGCAGAGGTCCCTTGACTATCTAAAA -s simRat_chr6.simRat.chr6 413685 64 + 647215 GAGTAAGTACTAAGATTTGGAGTGAAGACAGCATGGCCATTCAAGGATCCCCAACTATTTGAAA - -a -s simMouse_chr6.simMouse.chr6 407284 1 + 636262 C -s Anc0.Anc0refChr3 38448 1 + 222631 T -s Anc1.Anc1refChr6 68647 1 + 197743 T -s Anc2.Anc2refChr13 42365 1 + 96486 T -s mr.mrrefChr5 260072 1 + 294540 T -s simDog_chr6.simDog.chr6 388800 1 + 593897 T -s simHuman_chr6.simHuman.chr6 393368 1 + 601863 T -s simRat_chr6.simRat.chr6 413750 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 407285 22 + 636262 ACCACATTTTCACCGTCACAAA -s Anc0.Anc0refChr3 38472 22 + 222631 ACTACAGTTACACAGTCACAAT -s Anc1.Anc1refChr6 68671 22 + 197743 ACTACAGTTACACAGTCACAAT -s Anc2.Anc2refChr13 42389 22 + 96486 ACTACAGTTACACAGTCACAAT -s mr.mrrefChr5 260073 22 + 294540 ACCACATTTTCACAGTCACAAA -s simCow_chr6.simCow.chr6 398532 22 + 602619 ACTACAGTTATGCAGGCATAAT -s simDog_chr6.simDog.chr6 388824 22 + 593897 AGTACAGTTGCACTATCACAAC -s simHuman_chr6.simHuman.chr6 393392 22 + 601863 ACTACAGGTACACAGTCACAAT -s simRat_chr6.simRat.chr6 413751 18 + 647215 ACCAC----TCACAGCCACAAA - -a -s simMouse_chr6.simMouse.chr6 407307 41 + 636262 CTATTATGGAGAAAATGAGATGGGTTTGTGTTGTCTTGATG -s Anc0.Anc0refChr3 38495 20 + 222631 CTATTATGGAGAAAATG-GAT-------------------- -s Anc1.Anc1refChr6 68694 20 + 197743 CTATTATGGAGAAAATG-GAT-------------------- -s Anc2.Anc2refChr13 42412 20 + 96486 CTATTATGGAGGACATG-GAT-------------------- -s mr.mrrefChr5 260096 40 + 294540 CTATTATGGAGAAAATG-GATGGGTTTGTGTTGTCTTGATG -s simCow_chr6.simCow.chr6 398555 20 + 602619 CTATTATGGAGGAGATG-GAT-------------------- -s simDog_chr6.simDog.chr6 388847 20 + 593897 TTATTATGGAGGACATG-AAG-------------------- -s simHuman_chr6.simHuman.chr6 393415 20 + 601863 CTATTATGGAGAAAATG-GAT-------------------- -s simRat_chr6.simRat.chr6 413770 38 + 647215 CTATTATGGAGAAAG---AAGGAGATTGTGTTGTCTTGGTG - -a -s simMouse_chr6.simMouse.chr6 407348 26 + 636262 GGATCCTATGGATGATTGATTATCAA -s Anc0.Anc0refChr3 38515 14 + 222631 ------------TGATCGGTTATTGG -s Anc1.Anc1refChr6 68714 14 + 197743 ------------TGATCGGTTATTGG -s Anc2.Anc2refChr13 42432 14 + 96486 ------------TGATCGGTTATTGG -s mr.mrrefChr5 260136 26 + 294540 GGATCCTATGGATGATTGGTTATCAA -s simCow_chr6.simCow.chr6 398575 14 + 602619 ------------CAATTGGTGGTTGG -s simDog_chr6.simDog.chr6 388867 14 + 593897 ------------TGATCCATTATTGG -s simHuman_chr6.simHuman.chr6 393435 14 + 601863 ------------TGATCGGTTATTGG -s simRat_chr6.simRat.chr6 413809 26 + 647215 GGTTCCTATGGATGACTGGTTATCAA - -a -s simMouse_chr6.simMouse.chr6 407374 29 + 636262 ATTTAAGCAGTAATAAAATACTCATTATT -s Anc0.Anc0refChr3 38530 29 + 222631 TCTTAAGCAAAAGCAGAACACTAACTATT -s Anc1.Anc1refChr6 68729 29 + 197743 TCTTAAGCAAAAGCAGAACACTAACTATT -s Anc2.Anc2refChr13 42447 29 + 96486 TCCTAAGCAAGTGCAGAACACCAACTATT -s mr.mrrefChr5 260163 29 + 294540 ATTTAAGCAAAAATAAAATACTAATTATT -s simCow_chr6.simCow.chr6 398590 29 + 602619 TCCTAAGCAAGGGCAAAACACAAACTATA -s simDog_chr6.simDog.chr6 388882 29 + 593897 TCCTAGGTTAGTACAGAACACCAAATATT -s simHuman_chr6.simHuman.chr6 393450 29 + 601863 TATTAAGCAAAAGCAGAACACTAACTAGT -s simRat_chr6.simRat.chr6 413836 29 + 647215 ATTTAACCAAAAATAAACTAGTAATTATT - -a -s simMouse_chr6.simMouse.chr6 407403 4 + 636262 TAAT -s Anc0.Anc0refChr3 38559 4 + 222631 TAAG -s Anc1.Anc1refChr6 68758 4 + 197743 TAAG -s Anc2.Anc2refChr13 42476 4 + 96486 TAAG -s mr.mrrefChr5 260192 4 + 294540 TAAT -s simCow_chr6.simCow.chr6 398619 4 + 602619 TAAG -s simDog_chr6.simDog.chr6 388921 4 + 593897 TAAG -s simHuman_chr6.simHuman.chr6 393479 4 + 601863 TTAG -s simRat_chr6.simRat.chr6 413865 4 + 647215 TAAA - -a -s simMouse_chr6.simMouse.chr6 407407 17 + 636262 GGGGTAATTCACTTTAT -s Anc0.Anc0refChr3 38563 17 + 222631 GGGGGAATTCACTTTAT -s Anc1.Anc1refChr6 68762 17 + 197743 GGGGGAATTCACTTTAT -s Anc2.Anc2refChr13 42480 17 + 96486 GGGGGAATTCACTTTAT -s mr.mrrefChr5 260196 17 + 294540 GGGGTAATTCACTTTAT -s simCow_chr6.simCow.chr6 398623 17 + 602619 GGGGGAATTCACTTTAT -s simDog_chr6.simDog.chr6 388925 17 + 593897 GGGGGGATTCGCTTTAT -s simHuman_chr6.simHuman.chr6 393483 17 + 601863 GGGGGAATTTATTTTAT -s simRat_chr6.simRat.chr6 413870 17 + 647215 GAGGTAATTCACTTTAT - -a -s simMouse_chr6.simMouse.chr6 407424 5 + 636262 GGAAG -s Anc0.Anc0refChr3 38580 5 + 222631 CTAAG -s Anc1.Anc1refChr6 68779 5 + 197743 CTAAG -s Anc2.Anc2refChr13 42497 5 + 96486 CTAAG -s mr.mrrefChr5 260213 5 + 294540 GGAAG -s simCow_chr6.simCow.chr6 398640 5 + 602619 GTAAG -s simDog_chr6.simDog.chr6 388943 5 + 593897 CGAGG -s simHuman_chr6.simHuman.chr6 393500 5 + 601863 TTAAG -s simRat_chr6.simRat.chr6 413887 5 + 647215 GGAAG - -a -s simMouse_chr6.simMouse.chr6 407429 21 + 636262 ATATGGTTACATTACTAGAGT -s Anc0.Anc0refChr3 38586 21 + 222631 ATACAGCTACATTACTAGAGT -s Anc1.Anc1refChr6 68785 21 + 197743 ATACAGCTACATTACTAGAGT -s Anc2.Anc2refChr13 42503 21 + 96486 ATACAGCTACATTACTAGAGT -s mr.mrrefChr5 260219 21 + 294540 ATATAGTTACATTACTAGAGT -s simCow_chr6.simCow.chr6 398646 21 + 602619 ATACAACTACATTACAAGAGT -s simDog_chr6.simDog.chr6 388949 21 + 593897 ATACAGCTACAATACTAGAGT -s simHuman_chr6.simHuman.chr6 393506 21 + 601863 ATACAGCTACATTGATAGGGT -s simRat_chr6.simRat.chr6 413893 20 + 647215 ATATAGTCAC-TTACTAGCGT - -a -s simMouse_chr6.simMouse.chr6 407450 18 + 636262 TCTAGTAGAATAACCAAC -s Anc0.Anc0refChr3 38610 18 + 222631 TCTAGCAGAAAGATCAGC -s Anc1.Anc1refChr6 68809 18 + 197743 TCTAGCAGAAAGATCAGC -s Anc2.Anc2refChr13 42527 18 + 96486 TCTAGCAAAAAGATCAAC -s mr.mrrefChr5 260240 18 + 294540 TCTAGTAGAATAACCAGC -s simCow_chr6.simCow.chr6 398670 10 + 602619 TC--------AGATCAAC -s simDog_chr6.simDog.chr6 388973 18 + 593897 TTTAGCAAAATGATAAAC -s simHuman_chr6.simHuman.chr6 393530 18 + 601863 CCTTACAGAAAGATCAGC -s simRat_chr6.simRat.chr6 413913 18 + 647215 TCTAGTGGAATATCCAGC - -a -s simMouse_chr6.simMouse.chr6 407468 25 + 636262 TCAATTTTATCTCCCAAATGTGACA -s Anc0.Anc0refChr3 38663 25 + 222631 TGAATTTTCTATTTCAAAGAAGGTA -s Anc1.Anc1refChr6 68862 25 + 197743 TGAATTTTCTATTTCAAAGAAGGTA -s Anc2.Anc2refChr13 42580 25 + 96486 TGAATTTTCTAGTTCAAAGAAGGTA -s mr.mrrefChr5 260289 25 + 294540 TCAATTTTATCTCCCAAATATGACA -s simCow_chr6.simCow.chr6 398716 25 + 602619 TAAATTTTCTCGCCAAAAGAAGGTA -s simDog_chr6.simDog.chr6 389027 24 + 593897 TGAATTTTCTA-TTCAAAGAAGGTA -s simHuman_chr6.simHuman.chr6 393581 23 + 601863 --TATTGTCTATTTCAAAGAGGGTA -s simRat_chr6.simRat.chr6 413963 25 + 647215 CAAATTTTAGTTCCCAAATATGACA - -a -s simMouse_chr6.simMouse.chr6 407493 67 + 636262 CGCCTAAATTGTAAACTTCTAAATTATTTCTATTTTTCAAGCAGCCAGCCTGGATAAGAGGATTGCT -s Anc0.Anc0refChr3 38692 63 + 222631 TTTCCAAATGTGAAACTTCTAAATTATCTCTATTTTTCAAG----CAGCCTGGATAAGGGGATTGCA -s Anc1.Anc1refChr6 68891 63 + 197743 TTTCCAAATGTGAAACTTCTAAATTATCTCTATTTTTCAAG----CAGCCTGGATAAGGGGATTGCA -s Anc2.Anc2refChr13 42609 63 + 96486 TTTCCAAATGTGAAACTTCTAAATTGCCTCTATTTTTCAAG----CAGCATGAATAAGGGAATTGCA -s mr.mrrefChr5 260314 67 + 294540 TGTCTAAATTGTAAACTTCTAAATTATTTCTATTTTTCAAGCAGCCAGCCTGGATAAGAGGATTGCA -s simCow_chr6.simCow.chr6 398745 63 + 602619 TTTACAAATGTGAATCCTCTAAATTGCCTTTATTTTTCAAG----AAGCATGAATAAGGGAATTGCA -s simDog_chr6.simDog.chr6 389055 63 + 593897 TTTCCAAATGTGAAACTTTTAAAATGCCTCTATTATTCAAA----CAGCATGAATAAGGGAATCACA -s simHuman_chr6.simHuman.chr6 393608 63 + 601863 TTTCCAAATGTGAGACTTCTAAATTATCTCTATTTTTCAAG----CAGCCCGGATAAGGGGATTGCA -s simRat_chr6.simRat.chr6 413988 67 + 647215 TGTCTAAATAGTAAACATCGAAATTATTTTTATGTTTCAAGCAGCCAGCCTAGATAAAAGGATTGCA - -a -s simMouse_chr6.simMouse.chr6 407560 8 + 636262 GACCTCAA -s Anc0.Anc0refChr3 38767 8 + 222631 AACCTCAA -s Anc1.Anc1refChr6 68970 8 + 197743 AACCTCAA -s Anc2.Anc2refChr13 42684 8 + 96486 CACCTCAG -s mr.mrrefChr5 260381 8 + 294540 AACCTCAA -s simCow_chr6.simCow.chr6 398820 8 + 602619 CATCTCAG -s simDog_chr6.simDog.chr6 389130 8 + 593897 CACCTCAG -s simHuman_chr6.simHuman.chr6 393693 8 + 601863 AACTTCAA -s simRat_chr6.simRat.chr6 414055 8 + 647215 AATCTCAA - -a -s simMouse_chr6.simMouse.chr6 407568 30 + 636262 TTGTTAGTATTCCACAGTCTGTTACCCAAG -s Anc0.Anc0refChr3 38776 30 + 222631 TTGTTAGTACTTGTCAGTCTATTACACTAA -s Anc1.Anc1refChr6 68979 30 + 197743 TTGTTAGTACTTGTCAGTCTATTACACTAA -s Anc2.Anc2refChr13 42693 30 + 96486 TTGTGAGTACTTGTTAGTCTATTACACTAA -s mr.mrrefChr5 260389 30 + 294540 TTGTTAGTATTCCACAGTCTGTTACCCAAG -s simCow_chr6.simCow.chr6 398829 30 + 602619 TTGCAACTACTGGCTAGTCTATTGGACTAA -s simDog_chr6.simDog.chr6 389139 30 + 593897 GTGTGAGTCCTTGTTAGTCTATTACACTAA -s simHuman_chr6.simHuman.chr6 393702 30 + 601863 TTGTTAGTAGCTGTCAGTCTATTACACTAA -s simRat_chr6.simRat.chr6 414063 30 + 647215 TTGTTAGTATTACCCAGTCTGTTACCCAAG - -a -s simMouse_chr6.simMouse.chr6 407598 20 + 636262 ATGATTGTTGTCTCAAGGGC -s Anc0.Anc0refChr3 38806 17 + 222631 ATGAGTGTTA---CAAGGGC -s Anc1.Anc1refChr6 69009 17 + 197743 ATGAGTGTTA---CAAGGGC -s Anc2.Anc2refChr13 42727 17 + 96486 GTGAGTGTTA---CAAGGGC -s mr.mrrefChr5 260419 20 + 294540 ATGATTGTTGCCTCAAGGGC -s simCow_chr6.simCow.chr6 398863 17 + 602619 GTGAGTGTTA---CATGGGC -s simDog_chr6.simDog.chr6 389173 17 + 593897 GTGAGTGTTT---CAAGGGC -s simHuman_chr6.simHuman.chr6 393732 16 + 601863 ATGAGTATTA---CAAGGA- -s simRat_chr6.simRat.chr6 414093 20 + 647215 ATGATTGTTGCCTCATGGGC - -a -s simMouse_chr6.simMouse.chr6 407618 15 + 636262 TGTGAATTAGATCTA -s Anc0.Anc0refChr3 38856 3 + 222631 ------------CTA -s Anc1.Anc1refChr6 69082 15 + 197743 CACCCAATAAATCTA -s Anc2.Anc2refChr13 42778 3 + 96486 ------------CTA -s mr.mrrefChr5 260495 15 + 294540 CATGAATTAGATCTA -s simCow_chr6.simCow.chr6 398912 3 + 602619 ------------CTG -s simDog_chr6.simDog.chr6 389224 3 + 593897 ------------CTA -s simHuman_chr6.simHuman.chr6 393804 15 + 601863 CACCCAATAAATTTG -s simRat_chr6.simRat.chr6 414171 15 + 647215 CATGAATTAGATCTA - -a -s simMouse_chr6.simMouse.chr6 407633 13 + 636262 AATACAGAGATTT -s Anc0.Anc0refChr3 38861 4 + 222631 AATA--------- -s Anc1.Anc1refChr6 69099 13 + 197743 AATACAAAGAATT -s Anc2.Anc2refChr13 42783 4 + 96486 AATA--------- -s mr.mrrefChr5 260512 13 + 294540 AATACAGAGATTT -s simDog_chr6.simDog.chr6 389229 4 + 593897 AATA--------- -s simHuman_chr6.simHuman.chr6 393821 13 + 601863 AAATCAAAGAATT -s simRat_chr6.simRat.chr6 414188 13 + 647215 AATACAGAAATTG - -a -s simMouse_chr6.simMouse.chr6 407646 108 + 636262 CTTGTCTTCATGAGTAGTCATTTCACTTATTTTTCTAAGCACCCCACAGTCGCTGTTTCCATAATAACCATTACCCTAGGTGCCTCCAAAATTTAAAGCGGAATAGAA -s Anc0.Anc0refChr3 38865 80 + 222631 ----TCTGGAT-AGTA----------ATCTTTTTCTTAGCCTGCCACAGTAGCTGCCT-------------CCTATTTGGTGCCTCCAAAAGAAAATATAAACCAGAA -s Anc1.Anc1refChr6 69112 94 + 197743 CTTGTCTGGAT-AGTAGTCTTTTCACATCTTTTTCTTAGCCTGCCACAGTAGCTGCCT-------------CCTATTTGGTGCCTCCAAAAGAAAATATAAACCAGAA -s Anc2.Anc2refChr13 42787 80 + 96486 ----TCTGGTT-AGTG----------ATTTTTTTCTTAGCCTGCCACAGTAGCTGCTC-------------CCTACTTAGTGCCTCCAAAAGAAAATATAAACCATAA -s mr.mrrefChr5 260525 95 + 294540 CTTGTCTTCATGAGTAGTCATTTCACTTCTTTTTCTAAGCCCCCCACAGTCGCTGTCT-------------TATCTTAGGTGCCTCCAAAATATAAAGCAGAACAGAA -s simCow_chr6.simCow.chr6 398917 72 + 602619 ------------ATTG----------CTTTTCTTCTTAGCCTGCCACAGTAGATGCTC-------------TTTACTTAGTGCCTCCAAGAGAAAATATGAACTGT-A -s simDog_chr6.simDog.chr6 389233 77 + 593897 ----TCTGGTT-AGTG----------ATTCTTTTCTTAGCCCACCACAATAGCTGCTC-------------CCTACT---TACCTCCAAAAGAAAATAAAAGCCATAA -s simHuman_chr6.simHuman.chr6 393861 94 + 601863 CTTGGCTGAAT-ACCAGTCTTTTCACATCCTTTTCGTAGCCTGCCACAGTAGCTGCCT-------------CCTATTTGGTGTCTCGATACAAAAATATAAACGAGAA -s simRat_chr6.simRat.chr6 414201 95 + 647215 TTTGTTTTCGTGAGTAGTCATTTCAGTTCTCTTTCTAAGCCATGCACAATCTCTGTCC-------------TGTCTTAGGTGCCGCTGAAATATTAAATAGAACAGAA - -a -s simMouse_chr6.simMouse.chr6 407754 25 + 636262 GCAATAGGTGAGCAGATATGAGGAA -s Anc0.Anc0refChr3 38946 25 + 222631 GTAAACTGTAAGGGAATACAAGGAA -s Anc1.Anc1refChr6 69207 25 + 197743 GTAAACTGTAAGGGAATACAAGGAA -s Anc2.Anc2refChr13 42868 25 + 96486 GTAAACTGTAAGGGAATACAAAGAG -s mr.mrrefChr5 260620 25 + 294540 GCAATAGGTGAGCAGATATGAGGAA -s simCow_chr6.simCow.chr6 398990 25 + 602619 GTAAACTGTAAGGGAATACAGAAAT -s simDog_chr6.simDog.chr6 389311 25 + 593897 GTGAATCATAAGAGAATAGGAAGAG -s simHuman_chr6.simHuman.chr6 393956 25 + 601863 ATAAACTGTAAAGGAACACAAGGAA -s simRat_chr6.simRat.chr6 414296 25 + 647215 GCAATAGGTGAGTGGATATGAAGAA - -a -s simMouse_chr6.simMouse.chr6 407779 69 + 636262 TGGCTCTAGCCTTCTTTTACATCCCCAGGGTTGATAATCCAGGTGGTGGATGCAAGACAAGGGGTTCAG -s Anc0.Anc0refChr3 38971 69 + 222631 TGGTTCCAGCCTTCTCTCACATCCCCAGGAATGACAATCCAGGTGACTGATACGGCAGAAGGGATTTAG -s Anc1.Anc1refChr6 69232 69 + 197743 TGGTTCCAGCCTTCTCTCACATCCCCAGGAATGACAATCCAGGTGACTGATACGGCAGAAGGGATTTAG -s Anc2.Anc2refChr13 42893 69 + 96486 TGGCTCCAGCCTTCTCCCATGTCCCCAGAAATGACAATCCAGGTCACTGTGACGGCAGGAGGGATTTAG -s mr.mrrefChr5 260645 69 + 294540 TGGTTCTAGCCTTCTTTCACATCCCCAGGATTGACAATCCAGGTGGTGGATGCAGGAGAAGGGGTTCAG -s simCow_chr6.simCow.chr6 399019 63 + 602619 TAGCTCTAGCCTTCGCCCATGTCCCCAGAAATGACAATCCAGGTA------ACAGCAGTAGGGGTTTAG -s simDog_chr6.simDog.chr6 389336 66 + 593897 TGGCTCCAGACTTCTCCAATGTCCATAGAGGTGACAATCCAGGCCACTGTGAAG---GGATGGATTTAG -s simHuman_chr6.simHuman.chr6 393981 69 + 601863 TGATTCCAGCCTTCTCTCACACCCCCAGGAATGCCAATCCAGGTGACTGATACGGCAGAAGGGATTTAG -s simRat_chr6.simRat.chr6 414321 69 + 647215 AGGTTCTAGTCTTCTTTCACATCCCCAGGATTGACAATCCAAGTGGTAGATGCAGTAGAAGGGTTTCAG - -a -s simMouse_chr6.simMouse.chr6 407848 15 + 636262 AGGTCTCCCAACCCC -s Anc0.Anc0refChr3 39040 14 + 222631 A-GTTTCACAACCGC -s Anc1.Anc1refChr6 69301 14 + 197743 A-GTTTCACAACCGC -s Anc2.Anc2refChr13 42962 14 + 96486 A-GTTTCAGAACAGC -s mr.mrrefChr5 260714 15 + 294540 AGGTTTCCCAACCCC -s simCow_chr6.simCow.chr6 399083 14 + 602619 G-GTTTCAAAGCAGC -s simDog_chr6.simDog.chr6 389402 14 + 593897 A-AATTCAGAACAGC -s simHuman_chr6.simHuman.chr6 394050 14 + 601863 A-GTTTAGCACCCGC -s simRat_chr6.simRat.chr6 414390 15 + 647215 AGGTTTCCCAACCCC - -a -s simMouse_chr6.simMouse.chr6 407863 14 + 636262 ATAGACACGGTCAA -s Anc0.Anc0refChr3 39054 14 + 222631 ATAGACATAGTCAA -s Anc1.Anc1refChr6 69315 14 + 197743 ATAGACATAGTCAA -s Anc2.Anc2refChr13 42976 14 + 96486 ATAGAAATAGTCAA -s mr.mrrefChr5 260729 14 + 294540 ATAGACATGGTCAA -s simCow_chr6.simCow.chr6 399097 14 + 602619 ATAAAAATAGTCAA -s simDog_chr6.simDog.chr6 389416 14 + 593897 ATAGAAATATCCAG -s simHuman_chr6.simHuman.chr6 394077 14 + 601863 ATAGACATAGTCAA -s simRat_chr6.simRat.chr6 414405 14 + 647215 ATAGACATGGTCAA - -a -s simMouse_chr6.simMouse.chr6 407877 24 + 636262 GACCACCTCATTTACGCAGCAGGG -s Anc0.Anc0refChr3 39068 24 + 222631 GGGCATCCAGGTTAACCGGCCATG -s Anc1.Anc1refChr6 69329 24 + 197743 GGGCATCCAGGTTAACCGGCCATG -s Anc2.Anc2refChr13 42990 24 + 96486 GGGCTTCCAGGTGAACCGACCATG -s mr.mrrefChr5 260743 24 + 294540 GACCACCTCATTTACGCAGCAGGG -s simCow_chr6.simCow.chr6 399111 24 + 602619 GAGCTTACAGATGAACCAACTATG -s simDog_chr6.simDog.chr6 389430 24 + 593897 GGGCTTCCAGGTGAACCGACCAGG -s simHuman_chr6.simHuman.chr6 394091 24 + 601863 GGGCATCCAGGTTAACTGGCCATG -s simRat_chr6.simRat.chr6 414420 24 + 647215 GACACCCTCAATTGCACAGCAGGG - -a -s simMouse_chr6.simMouse.chr6 407901 14 + 636262 GTCAGTTTACGTTT -s Anc0.Anc0refChr3 39095 11 + 222631 GTCAG---ACGGTA -s Anc1.Anc1refChr6 69356 11 + 197743 GTCAG---ACGGTA -s Anc2.Anc2refChr13 43017 11 + 96486 GTCGG---ACAGTA -s mr.mrrefChr5 260767 11 + 294540 GTCAG---ACGTTT -s simCow_chr6.simCow.chr6 399139 11 + 602619 GTTGG---ACAGTA -s simDog_chr6.simDog.chr6 389457 11 + 593897 GTCGG---AAAGCA -s simHuman_chr6.simHuman.chr6 394118 11 + 601863 GTCAG---ACGGTG -s simRat_chr6.simRat.chr6 414444 1 + 647215 A------------- - -a -s simMouse_chr6.simMouse.chr6 407915 3 + 636262 ATG -s Anc0.Anc0refChr3 39106 3 + 222631 ACT -s Anc1.Anc1refChr6 69367 3 + 197743 ACT -s Anc2.Anc2refChr13 43028 3 + 96486 ACT -s mr.mrrefChr5 260778 3 + 294540 ATG -s simCow_chr6.simCow.chr6 399151 3 + 602619 CCT -s simDog_chr6.simDog.chr6 389468 3 + 593897 ATT -s simHuman_chr6.simHuman.chr6 394129 3 + 601863 GCA - -a -s simMouse_chr6.simMouse.chr6 407918 37 + 636262 AGCAAGCAAGTCGAGTTTGCCTAGCTATGCTGTGTCA -s Anc0.Anc0refChr3 39113 37 + 222631 AGGCAACAAGTGGTATTAGCCTAGCTGTGCTGTGTCA -s Anc1.Anc1refChr6 69374 37 + 197743 AGGCAACAAGTGGTATTAGCCTAGCTGTGCTGTGTCA -s Anc2.Anc2refChr13 43035 37 + 96486 AGGCAACAAGTGGTCTTAGCCTAGCTGTGCTGTGTCA -s mr.mrrefChr5 260781 37 + 294540 AGCAAGCAAGTCGAATTTGCCTAGCTATGCTGTGTCA -s simCow_chr6.simCow.chr6 399158 37 + 602619 GGGCAACAAGTGGTGTTACCCTAGCAGGGCTGTGTAA -s simDog_chr6.simDog.chr6 389475 37 + 593897 AGGCAGCAAGTGGGCCTAGTCTAGCTGTGCTGTGTCA -s simHuman_chr6.simHuman.chr6 394136 37 + 601863 AGGCCACATGTAGTATTGGCCTAGCTGTGTTGTGTCA -s simRat_chr6.simRat.chr6 414445 34 + 647215 --CAGGCAAGTGGAATTTGCCTAGCT-TGCTGTGTCA - -a -s simMouse_chr6.simMouse.chr6 407955 13 + 636262 GACATTCTCTGTT -s Anc0.Anc0refChr3 39150 13 + 222631 GATGTGCTATTTT -s Anc1.Anc1refChr6 69411 13 + 197743 GATGTGCTATTTT -s Anc2.Anc2refChr13 43072 13 + 96486 GATGTGCTATTTT -s mr.mrrefChr5 260818 13 + 294540 GACATTCTCTGTT -s simCow_chr6.simCow.chr6 399195 13 + 602619 GATGTGACATTTT -s simDog_chr6.simDog.chr6 389512 13 + 593897 GATGTTCTGTTTT -s simHuman_chr6.simHuman.chr6 394173 13 + 601863 GATGTGTTATCTT -s simRat_chr6.simRat.chr6 414480 6 + 647215 GA-------TGTT - -a -s simMouse_chr6.simMouse.chr6 407968 1 + 636262 T -s Anc0.Anc0refChr3 39163 1 + 222631 T -s Anc1.Anc1refChr6 69424 1 + 197743 T -s Anc2.Anc2refChr13 43085 1 + 96486 T -s mr.mrrefChr5 260831 1 + 294540 T -s simCow_chr6.simCow.chr6 399208 1 + 602619 T -s simDog_chr6.simDog.chr6 389531 1 + 593897 C -s simHuman_chr6.simHuman.chr6 394186 1 + 601863 T -s simRat_chr6.simRat.chr6 414486 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 407969 19 + 636262 TTGTGTCTTTAAGGCTAGA -s Anc0.Anc0refChr3 39164 16 + 222631 TGG---CATTAAGGCAAGA -s Anc1.Anc1refChr6 69425 16 + 197743 TGG---CATTAAGGCAAGA -s Anc2.Anc2refChr13 43086 16 + 96486 TGG---CATTAAGGCAAGA -s mr.mrrefChr5 260832 19 + 294540 TTGTGTCTTTAAGGCTAGA -s simCow_chr6.simCow.chr6 399210 12 + 602619 TGG---CATT----CAAGA -s simDog_chr6.simDog.chr6 389532 16 + 593897 TGG---CGTTAAGGCAAAA -s simHuman_chr6.simHuman.chr6 394187 16 + 601863 TGG---CATTTAGGTAAGA -s simRat_chr6.simRat.chr6 414487 19 + 647215 TTGTGTCTTTAAGGCTAGA - -a -s simMouse_chr6.simMouse.chr6 407988 31 + 636262 TTTCAACTCAAAGTGGAGAAGGTGTATTTGA -s Anc0.Anc0refChr3 39186 24 + 222631 CTTGAG-------TGGAGAGGGTGTATTCTA -s Anc1.Anc1refChr6 69447 24 + 197743 CTTGAG-------TGGAGAGGGTGTATTCTA -s Anc2.Anc2refChr13 43108 24 + 96486 CTTGAG-------TGGAGAGGGTGTATTCTA -s mr.mrrefChr5 260851 24 + 294540 TTTCAA-------TGGAGAAGGTGTATTTGA -s simCow_chr6.simCow.chr6 399228 21 + 602619 CTTGAG-------TGGAGA---TGTATTCTA -s simDog_chr6.simDog.chr6 389554 24 + 593897 CTTGAG-------TGGCGAGGGGGTATTCTA -s simHuman_chr6.simHuman.chr6 394209 24 + 601863 CTTGAG-------AGGAGAGGGTGTATTCTT -s simRat_chr6.simRat.chr6 414506 24 + 647215 CTTCAA-------TGGAGAAGATGTATTTGA - -a -s simMouse_chr6.simMouse.chr6 408019 2 + 636262 TT -s Anc0.Anc0refChr3 39210 2 + 222631 TC -s Anc1.Anc1refChr6 69471 2 + 197743 TC -s Anc2.Anc2refChr13 43132 2 + 96486 TC -s mr.mrrefChr5 260875 2 + 294540 TT -s simCow_chr6.simCow.chr6 399272 2 + 602619 TT -s simDog_chr6.simDog.chr6 389578 2 + 593897 TC -s simHuman_chr6.simHuman.chr6 394233 2 + 601863 TC -s simRat_chr6.simRat.chr6 414530 2 + 647215 TT - -a -s simMouse_chr6.simMouse.chr6 408021 61 + 636262 ACGATCACCTTGCACCCCTGGTGTTTCCTTAAGAGCAGAGTAAGAGTGTTCCTGTACCAAC -s Anc0.Anc0refChr3 39215 61 + 222631 ATGATCACACTGCACCCCTGGCATTTCATCAAGAGCAAAATAAGAGGGTTCCTGTCCCAAC -s Anc1.Anc1refChr6 69476 61 + 197743 ATGATCACACTGCACCCCTGGCATTTCATCAAGAGCAAAATAAGAGGGTTCCTGTCCCAAC -s Anc2.Anc2refChr13 43137 61 + 96486 ATGATCACACTGCACCCCTGGCAGTTCATCAAGAGCAAAATAAGGGGTTCCCTCTCCCAAC -s mr.mrrefChr5 260877 61 + 294540 ATGATCACCCTGCACCCCTGGTGTTTCCTCAAGAGCAAAGTAAGAGTGTTCCTGTACCAAC -s simCow_chr6.simCow.chr6 399277 49 + 602619 ATGATCACACTGCACCCCTGGCCATTCATCAAGAGCAACATA------------TTCCAAC -s simDog_chr6.simDog.chr6 389583 61 + 593897 ATGATCACAATGCACCCCTGACAGTTCATTGAGAGCAAAGAGAGGGGTTCCCTCTCCCAAC -s simHuman_chr6.simHuman.chr6 394238 61 + 601863 ATGATCACACTGCACCCCTGGCATTTAATCAAAAGCAAAATAAGAGGGTTGCTGTCCCAAC -s simRat_chr6.simRat.chr6 414532 61 + 647215 ATGCTCACTCTGCACCCCTCGTGCTTCCTCAAGAGCAAAGTGAGAGTATTCCAGTGCCAAC - -a -s simMouse_chr6.simMouse.chr6 408082 6 + 636262 AGACAG -s Anc0.Anc0refChr3 39279 4 + 222631 A--CAG -s Anc1.Anc1refChr6 69540 6 + 197743 AAACAG -s Anc2.Anc2refChr13 43201 4 + 96486 A--CAG -s mr.mrrefChr5 260938 6 + 294540 AGACAG -s simCow_chr6.simCow.chr6 399328 3 + 602619 ---CAG -s simDog_chr6.simDog.chr6 389647 4 + 593897 A--CTG -s simHuman_chr6.simHuman.chr6 394306 6 + 601863 AAACAG -s simRat_chr6.simRat.chr6 414593 3 + 647215 AGA--- - -a -s simMouse_chr6.simMouse.chr6 408088 10 + 636262 AACCTGTTGC -s Anc0.Anc0refChr3 39286 10 + 222631 AACCTGTGGT -s Anc1.Anc1refChr6 69549 10 + 197743 AACCTGTGGT -s Anc2.Anc2refChr13 43208 10 + 96486 AACATGTGGT -s mr.mrrefChr5 260944 10 + 294540 AACCTGTTGC -s simCow_chr6.simCow.chr6 399334 10 + 602619 AACATGTTGC -s simDog_chr6.simDog.chr6 389654 10 + 593897 AACATATGGT -s simHuman_chr6.simHuman.chr6 394315 10 + 601863 AACCTGTCGG -s simRat_chr6.simRat.chr6 414596 9 + 647215 -ACCTGTTGC - -a -s simMouse_chr6.simMouse.chr6 408098 12 + 636262 ACCAAATAGATC -s Anc0.Anc0refChr3 39296 12 + 222631 AAGAAATGGACC -s Anc1.Anc1refChr6 69559 12 + 197743 AAGAAATGGACC -s Anc2.Anc2refChr13 43218 12 + 96486 AAGAAATGGACC -s mr.mrrefChr5 260954 12 + 294540 AACAAATAGATC -s simCow_chr6.simCow.chr6 399344 12 + 602619 AAGAACTGGACC -s simDog_chr6.simDog.chr6 389664 12 + 593897 AAGGAATAGACC -s simHuman_chr6.simHuman.chr6 394326 12 + 601863 AAAACATGGACC -s simRat_chr6.simRat.chr6 414605 12 + 647215 AACAAATAGAAC - -a -s simMouse_chr6.simMouse.chr6 408110 48 + 636262 ACGGTTCTTGAGAGGTAAGGAAGCCTGTGGAGAGAGCCAATATACATT -s Anc0.Anc0refChr3 39311 45 + 222631 G---TTTATGAGAAGTGAGTAAGCCTGTGGAGAGAGCCATGATACATC -s Anc1.Anc1refChr6 69574 48 + 197743 GCGGTTTATGAGAAGTGAGTAAGCCTGTGGAGAGAGCCATGATACATC -s Anc2.Anc2refChr13 43233 45 + 96486 G---TTTATGAGAAGTGAGTAGGCCTATGGAGAGAGCCATGATACATC -s mr.mrrefChr5 260969 48 + 294540 ACGGTTTTTGAGAGGTAAGGAAGCCTGTGGAGAGAGCCAATATACATT -s simCow_chr6.simCow.chr6 399359 44 + 602619 G---TTTCTAAGAAGTGAATAGGCCTATGGAGTG-GACATGATATATC -s simDog_chr6.simDog.chr6 389679 45 + 593897 A---TTTATGCGAAATGAGTAGGCCTATGAAGAGAGCCGTGATACATC -s simHuman_chr6.simHuman.chr6 394341 45 + 601863 GCCGTTTATGAGGAGTGAGCAAGCTTGTGGAGAGATCCATGGTAC--- -s simRat_chr6.simRat.chr6 414620 48 + 647215 ACTGTTTTTGAGAGGTATGTCAGCCTGTGGAGAGAGCTAATATACATT - -a -s simMouse_chr6.simMouse.chr6 408158 30 + 636262 TAAGGTGAAAGGATGATTGAAGTGATTCTA -s Anc0.Anc0refChr3 39356 30 + 222631 TTAAGTGAAAAGATGGTTGGAGTGATGATA -s Anc1.Anc1refChr6 69622 30 + 197743 TTAAGTGAAAAGATGGTTGGAGTGATGATA -s Anc2.Anc2refChr13 43278 30 + 96486 TTAAGTGAAGAGATGGTTAGAATGATGATA -s mr.mrrefChr5 261017 30 + 294540 TAAGGTGAAAGGATGATTGAAGTGATTCTA -s simCow_chr6.simCow.chr6 399403 30 + 602619 TTAAGTGAAGAGATGGTTAGATTGATGATT -s simDog_chr6.simDog.chr6 389724 25 + 593897 TTAAGTG-----ATGGTTAGAATGATGGAA -s simHuman_chr6.simHuman.chr6 394386 30 + 601863 TTAAGTGAGAAAATGGTTGGAGTGATCATA -s simRat_chr6.simRat.chr6 414673 30 + 647215 TAAGGTAAAAGGATGATTGAGGTGATGCTA - -a -s simMouse_chr6.simMouse.chr6 408188 5 + 636262 TGGCA -s Anc0.Anc0refChr3 39386 5 + 222631 ATGTG -s Anc1.Anc1refChr6 69652 5 + 197743 ATGTG -s Anc2.Anc2refChr13 43308 5 + 96486 ATGTG -s mr.mrrefChr5 261047 5 + 294540 TGGCA -s simCow_chr6.simCow.chr6 399433 4 + 602619 -TGTG -s simDog_chr6.simDog.chr6 389749 5 + 593897 ATGAG -s simHuman_chr6.simHuman.chr6 394427 5 + 601863 ATATG -s simRat_chr6.simRat.chr6 414703 5 + 647215 TGGCA - -a -s simMouse_chr6.simMouse.chr6 408193 34 + 636262 AGTGATACTATAGCCAGGGGGCAGTCTTGTCTTG -s Anc0.Anc0refChr3 39393 34 + 222631 AGAGATGATATGAGCTAGCGACGGTTAAGTCTCC -s Anc1.Anc1refChr6 69659 34 + 197743 AGAGATGATATGAGCTAGCGACGGTTAAGTCTCC -s Anc2.Anc2refChr13 43315 34 + 96486 TGAGATGATATGAGCTAGCAAAGGTTAAGTCTCC -s mr.mrrefChr5 261052 34 + 294540 AGTGATGCTATGGGCAGGGGGCAGTCTTGTCTTG -s simCow_chr6.simCow.chr6 399439 34 + 602619 TAAGACAATATGAGCAAGGAAAGGTGAAATCTCC -s simDog_chr6.simDog.chr6 389756 34 + 593897 TGAGATGATATGAGCTAGCAAAGGTTAAGTCTCC -s simHuman_chr6.simHuman.chr6 394434 34 + 601863 AGAGATGATATGAGCCAGCGACTATTGAGTCTCC -s simRat_chr6.simRat.chr6 414708 34 + 647215 AGTGATGCTATGGGCGGGGGGCAGTCTTGTCTTG - -a -s simMouse_chr6.simMouse.chr6 408227 41 + 636262 TTCTGAGCTTAGTTAGTATTCCCCACACTACTAATGAGTTC -s Anc0.Anc0refChr3 39427 41 + 222631 TTCTGATGTCAGGAGGGATTTCCCCCACTTGTAGGGAATCA -s Anc1.Anc1refChr6 69693 41 + 197743 TTCTGATGTCAGGAGGGATTTCCCCCACTTGTAGGGAATCA -s Anc2.Anc2refChr13 43349 41 + 96486 TTCTGATGACAGGAGGGATTTCCCCCACTTGTAGGGAATTG -s mr.mrrefChr5 261086 41 + 294540 TTCTGAGCTTAGTTAGTATTTCCCACACTACTAATGAATCA -s simCow_chr6.simCow.chr6 399478 32 + 602619 TTCTGATCACAGGAGGGATTTACCCCACTTAT--------- -s simDog_chr6.simDog.chr6 389790 34 + 593897 TTCTGATGACA------ATTCCCCCCAC-TGTAGGGAATTG -s simHuman_chr6.simHuman.chr6 394468 41 + 601863 TGCTTATGTCAGGGGGGGTGTCCTCCACTTGTAGGGAATCA -s simRat_chr6.simRat.chr6 414742 41 + 647215 TTCTGAGCTTAGTTAGTATTTCCCACACCACTAATGGATCA - -a -s simMouse_chr6.simMouse.chr6 408268 1 + 636262 A -s Anc0.Anc0refChr3 39470 1 + 222631 T -s Anc1.Anc1refChr6 69736 1 + 197743 T -s Anc2.Anc2refChr13 43392 1 + 96486 T -s mr.mrrefChr5 261127 1 + 294540 T -s simDog_chr6.simDog.chr6 389826 1 + 593897 T -s simHuman_chr6.simHuman.chr6 394511 1 + 601863 T -s simRat_chr6.simRat.chr6 414783 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 408269 18 + 636262 CGTCAGACATCCAATATA -s Anc0.Anc0refChr3 39471 18 + 222631 TAGGGGACATACAATATA -s Anc1.Anc1refChr6 69737 18 + 197743 TAGGGGACATACAATATA -s Anc2.Anc2refChr13 43393 18 + 96486 TAGGGGCCATACAATATA -s mr.mrrefChr5 261128 18 + 294540 TGTCAGACATCCAATATA -s simCow_chr6.simCow.chr6 399510 15 + 602619 ---GTGCTATACAATACA -s simDog_chr6.simDog.chr6 389828 18 + 593897 TAGGGGCCATAGAACATA -s simHuman_chr6.simHuman.chr6 394512 18 + 601863 TAGAGGACAAACAATATA -s simRat_chr6.simRat.chr6 414784 18 + 647215 TGTCAGACATCCAATATA - -a -s simMouse_chr6.simMouse.chr6 408287 25 + 636262 TAGTTTATGGCATAATAGGTGGTAC -s Anc0.Anc0refChr3 39490 25 + 222631 CAGCTGATGGAATAGTATGTTGTGT -s Anc1.Anc1refChr6 69756 25 + 197743 CAGCTGATGGAATAGTATGTTGTGT -s Anc2.Anc2refChr13 43412 25 + 96486 CAGCTGATGGAATAGTATGTTGTGT -s mr.mrrefChr5 261147 25 + 294540 CAGTTTATGGCATAATAGGTTGTAC -s simCow_chr6.simCow.chr6 399526 25 + 602619 CAGCTGATGGAATAGTTTGTTGTGT -s simDog_chr6.simDog.chr6 389847 23 + 593897 TAGCTGATTGAACA--ATGTTGTGT -s simHuman_chr6.simHuman.chr6 394531 25 + 601863 CAGCTGAAGGGATAGTGTGTTGTGT -s simRat_chr6.simRat.chr6 414803 25 + 647215 CAGTTTATGGCATAATAGGTTGTAC - -a -s simMouse_chr6.simMouse.chr6 408312 26 + 636262 TGTTGAGATCTGCTTGGTAAAGGTGC -s Anc0.Anc0refChr3 39519 26 + 222631 CATTAAGATCTGGTAGCTAAACTGGT -s Anc1.Anc1refChr6 69785 26 + 197743 CATTAAGATCTGGTAGCTAAACTGGT -s Anc2.Anc2refChr13 43441 26 + 96486 CATTAAGATTTGGTAGCTAAACTGGT -s mr.mrrefChr5 261176 26 + 294540 TATTGAGATCTGCTTGGTAAAGGGGC -s simCow_chr6.simCow.chr6 399555 26 + 602619 CATTAAGATTTGGTAGCTAAGCTGAT -s simDog_chr6.simDog.chr6 389874 26 + 593897 CATTAAAATTTGGTAGCTAAACTGGT -s simHuman_chr6.simHuman.chr6 394560 25 + 601863 AATTAAGATCTG-TAGCTAAACTGGT -s simRat_chr6.simRat.chr6 414832 26 + 647215 TACTGAGATCTGCTTGGTGAAGGGGC - -a -s simMouse_chr6.simMouse.chr6 408338 128 + 636262 AATGTGTGGAGTTAGCATAGAACAAGAATTATTATGATGGTATCTGAATTATTAAGCTACTCTTATGGTATTGGGCAATTATTTCACACTACAACTAAGCCTATACAAATATATTTATTATGGGATTA -s Anc0.Anc0refChr3 39546 120 + 222631 GACATGT-AAGTTGGCATAGATAAGGAATATTTATAATGGTATCCGAATTATGAACCTATCTTAGTTGTATTGATCCACTATTTCACATTAGTGCTTAGCCTGTACAAATCTCA-------CCCATTA -s Anc1.Anc1refChr6 69812 127 + 197743 GACATGT-AAGTTGGCATAGATAAGGAATATTTATAATGGTATCCGAATTATGAACCTATCTTAGTTGTATTGATCCACTATTTCACATTAGTGCTTAGCCTGTACAAATCTCATTATAATCCCATTA -s Anc2.Anc2refChr13 43468 120 + 96486 GACATGC-AAGTTGGCATAGATAAGGAATATTTATAATACTATCCGAATTATGAACCTATCTTAGTTGAATTGATCCACTATTTCTCATTAGTGCTTAGCCTGTACACATCTCA-------CCCATTA -s mr.mrrefChr5 261203 128 + 294540 AATGTGTGAAGTTAGCATAGAACAAGAATATTTATGATGGTATCTGAATTATTAACCTACTTTTGTGGTATTGGTCAATTATTTCACACTACAACTAAGCCTATACAAATATATTTATTATCGGATTA -s simCow_chr6.simCow.chr6 399582 115 + 602619 GCCATGC-AAGGTGGCATAG-TAAAGAATATTTTTAATTCTATCCGAATTTTACGCCCATCCCAGCCGAATTGATCAACTATTTGGCATTAGTGCTTAGTGTTGCCATAT-----------CCTATTA -s simDog_chr6.simDog.chr6 389901 120 + 593897 GACATGC-CTGTTGCCATAGATAAGGAAGATTTATAATACTATCTAAATGATGAATCTAGCTTAGTTGAATTGAACCACTACTTCTCACTAGTGCTTAACCTGTACACAACTCA-------CTCATCA -s simHuman_chr6.simHuman.chr6 394586 127 + 601863 GACATGT-AAGAAGGCATAAATAAGGAATATTTATAATGGTATCCGAATTATCAACCTATATGAGTTATATTGATCCACTCTTCCACATTCGTGCTTAGCCTGCACAAATCTCATTATAATCCCATTA -s simRat_chr6.simRat.chr6 414859 127 + 647215 AATGTGTGAAGTTAGCATAGAACAAGAATATTTATGATGCAATCTGAAGTATTAACCTACTTTGGTGGTATTGCTCAAGTATCTCACACCGCAACTAAGCCTATACAA-TATATTTTTTGTCGGATTA - -a -s simMouse_chr6.simMouse.chr6 408466 5 + 636262 CAGGC -s Anc0.Anc0refChr3 39667 5 + 222631 CATGG -s Anc1.Anc1refChr6 69940 5 + 197743 CATGG -s Anc2.Anc2refChr13 43589 5 + 96486 GATGG -s mr.mrrefChr5 261331 5 + 294540 CAGGG -s simCow_chr6.simCow.chr6 399698 5 + 602619 AAAGA -s simDog_chr6.simDog.chr6 390022 5 + 593897 GATGG -s simHuman_chr6.simHuman.chr6 394714 5 + 601863 CATGG -s simRat_chr6.simRat.chr6 414986 5 + 647215 CAGGG - -a -s simMouse_chr6.simMouse.chr6 408471 71 + 636262 CAGGAACATTATCCAGAGAGTGGATTGTAGACTGAATTTCATTATATTAAGTCATAGAATAGTACTGGGCG -s Anc0.Anc0refChr3 39675 71 + 222631 CTAGAACATTACTCAAGGAATGAATCATAGAATGAATTTCATTATTATAAGCCATAGAACATTACTCAGGG -s Anc1.Anc1refChr6 69948 71 + 197743 CTAGAACATTACTCAAGGAATGAATCATAGAATGAATTTCATTATTATAAGCCATAGAACATTACTCAGGG -s Anc2.Anc2refChr13 43597 71 + 96486 GTAGAACATTACTCAAGGAATGAATCATAGAATGGATCTCATTATTATAAGCCATAGAACATTTCGCAGGG -s mr.mrrefChr5 261336 71 + 294540 CAAGAACATTATTCAGAGAGTGGATTGTAGACTGAATTTCATTATAATAAGTCATAGAATAGTACTGGGGG -s simCow_chr6.simCow.chr6 399706 71 + 602619 ATACAACATTACTCCAGTAATGGATTATAGAGTGTATCTCATCATTATAAGCCATAGAACCTTGTCCAGCA -s simDog_chr6.simDog.chr6 390030 71 + 593897 GTAGAACACTACTCAAGGAAGGAATCAGAGAATAGATCTCATTATTATAAGCCATAGAACATTTCGCATGG -s simHuman_chr6.simHuman.chr6 394722 71 + 601863 CTAGGACATGACTCAAGGAATGAACCATAGAATGAATTCCATTTTTATATGCCATAGAACATTAATAAGGG -s simRat_chr6.simRat.chr6 414991 71 + 647215 AAAGAACATTAGTCAGAGACTGGATTGTAAACTGCATTTCATTACAATAAGTCATAGCATAGTACTGGGGG - -a -s simMouse_chr6.simMouse.chr6 408542 39 + 636262 CGAACAGTTACAGCCCAAGATCTGAAATTGGGATCGTAA -s Anc0.Anc0refChr3 39786 39 + 222631 TGAACAATTATAGCCCAAGATCTAAAATTGAATCCTAAA -s Anc1.Anc1refChr6 70059 39 + 197743 TGAACAATTATAGCCCAAGATCTAAAATTGAATCCTAAA -s Anc2.Anc2refChr13 43712 39 + 96486 TGGACAATTATAGCCCAAGATCCAAAGTTGAATCCTAAA -s mr.mrrefChr5 261407 39 + 294540 TGAACAATTACAGCCCAAGATCTGAAATTGAGATCGTAA -s simCow_chr6.simCow.chr6 399821 36 + 602619 ---ACAAGTCTAGCCCAAGATCATAAGTTGAAACCTCAG -s simDog_chr6.simDog.chr6 390145 39 + 593897 TGGACAATTATACCCCGAGATCCAAAGCTGAATTCTAAA -s simHuman_chr6.simHuman.chr6 394837 39 + 601863 TGAACAATTAGGGCCCAAGAACTCAAATTGAATCCTAAG -s simRat_chr6.simRat.chr6 415062 39 + 647215 TGAACAATTACAGCCCAAGATCTAAAATTGAGATCCTAC - -a -s simMouse_chr6.simMouse.chr6 408581 17 + 636262 TTGTGACTAGAGGTTTA -s Anc0.Anc0refChr3 39825 17 + 222631 TAGTGACAAGAGTTTTG -s Anc1.Anc1refChr6 70098 17 + 197743 TAGTGACAAGAGTTTTG -s Anc2.Anc2refChr13 43752 17 + 96486 TAGTGACAAGAGTTTTG -s mr.mrrefChr5 261446 17 + 294540 TTGTGACTAGAGGTTTA -s simCow_chr6.simCow.chr6 399858 17 + 602619 TAGTGACCAGAGCTTTA -s simDog_chr6.simDog.chr6 390185 17 + 593897 TAGTGACAAGAATTTTG -s simHuman_chr6.simHuman.chr6 394876 17 + 601863 TAGTGACGAGAGTTTTG -s simRat_chr6.simRat.chr6 415101 17 + 647215 TGTTGGCTAAAGGTTTA - -a -s simMouse_chr6.simMouse.chr6 408598 17 + 636262 AATTTGCATTTTATTGT -s Anc0.Anc0refChr3 39842 17 + 222631 AATTTACATTTTATTTT -s Anc1.Anc1refChr6 70115 17 + 197743 AATTTACATTTTATTTT -s Anc2.Anc2refChr13 43823 17 + 96486 AATTTGCATTGTGATTG -s mr.mrrefChr5 261463 17 + 294540 AATTTACATTTTATTGT -s simCow_chr6.simCow.chr6 175680 17 - 602619 AATTTACATTTTAATTT -s simDog_chr6.simDog.chr6 390270 17 + 593897 AATTTGCATTGTGATTG -s simHuman_chr6.simHuman.chr6 394893 17 + 601863 ATTTTACATTTAATTTT -s simRat_chr6.simRat.chr6 415118 17 + 647215 AATTTACATTTTATTCT - -a -s simMouse_chr6.simMouse.chr6 408615 51 + 636262 ACATACATCACCTGCCCACCCTCATATCTTGGGCATTTTCAACAGACTATA -s Anc0.Anc0refChr3 39861 51 + 222631 ACACATGTTGCCTGACCAATCTCATACCTTGGATATTTTCAATAGATGACA -s Anc1.Anc1refChr6 70134 51 + 197743 ACACATGTTGCCTGACCAATCTCATACCTTGGATATTTTCAATAGATGACA -s Anc2.Anc2refChr13 43842 51 + 96486 ACATATGTTGCTGGACAAATCTCATACCTTGAATATATTCAATAAATGATA -s mr.mrrefChr5 261480 51 + 294540 ACACACATCACCTGCCCACTCTCATACCTTGGGCATTTTCAATAGACTACA -s simCow_chr6.simCow.chr6 175699 51 - 602619 ACATATGTTACTGGACAACCCTTATACGTTGGAGATGCTCTATGAATGATA -s simDog_chr6.simDog.chr6 390289 51 + 593897 ACATATGTTGCTGGACAGATCTCATATCATGAATACATTCAATAAATGATA -s simHuman_chr6.simHuman.chr6 394912 50 + 601863 ACACATGTTCACTGGCCAATCTCGTACCTT-GATATTTTTGATAGATGACA -s simRat_chr6.simRat.chr6 415135 51 + 647215 AGACACATCACCTGCCCATTCTCATACCTTGGGGATTTACAATAAACTGCA - -a -s simMouse_chr6.simMouse.chr6 408666 69 + 636262 ATAAGTTTGTGAGTGGTTATCAATATGGTAGTCACTGCTAGAACTCGTGTTTCTATCCAAGCAGTTATG -s Anc0.Anc0refChr3 39912 51 + 222631 ACAA-TCTGTAAGTGGTGATTGATGTGGTAGTCACATCTACAATTTGTGTTT----------------- -s Anc1.Anc1refChr6 70185 68 + 197743 ACAA-TCTGTAAGTGGTGATTGATGTGGTAGTCACATCTACAATTTGTGTTTCTACTTGGGCAGTGATG -s Anc2.Anc2refChr13 43895 51 + 96486 ACAA-TCTGTATGTGGTGATTGATGTGGTAGTCACATCTACAATTTATTTTT----------------- -s mr.mrrefChr5 261531 69 + 294540 ATAAGTTTGTAAGTGGTTATTAATATGGTAGTCACTGCTAGAACTTGTGTTTCTATCCAAGCAGTTATG -s simCow_chr6.simCow.chr6 175752 45 - 602619 ACAA-TCTGCATGTGGTGATTGTTGTCATAGTCCCATCTACAATTT----------------------- -s simDog_chr6.simDog.chr6 390342 51 + 593897 ATAA-TTTGTATGTGGTGGTTGATGTGGTCGTCACATCTATAATTTATTTTT----------------- -s simHuman_chr6.simHuman.chr6 394962 68 + 601863 ACAA-TCTGTAAATGATGATTGCTGTGGTAGTCAGATCTCCAATTTGTGTTTCTACTTGGGCAGTGATG -s simRat_chr6.simRat.chr6 415186 69 + 647215 ATAAGGTTGTAAGTGGTTATTAATATGGCAGTCACTGCTAGAACTTGTATTTCTATCCAAGCAATTATG - -a -s simMouse_chr6.simMouse.chr6 408735 23 + 636262 CAACTATGCAACTTTTGGTGGCC -s Anc0.Anc0refChr3 39963 23 + 222631 TGACTGTACAACTCCTGACAGAC -s Anc1.Anc1refChr6 70253 23 + 197743 TGACTGTACAACTCCTGACAGAC -s Anc2.Anc2refChr13 43946 23 + 96486 TGAGAGTAAAACTCCTGACAGAC -s mr.mrrefChr5 261600 23 + 294540 CAACTATGCAACTTCTGGTGGCC -s simCow_chr6.simCow.chr6 399929 23 + 602619 TGAGAGTAGAATTCCTGACAGAC -s simDog_chr6.simDog.chr6 390393 16 + 593897 -------GAGACTCCTGACAGAC -s simHuman_chr6.simHuman.chr6 395030 23 + 601863 TGACTGTACAACTCCTTTCAGAC -s simRat_chr6.simRat.chr6 415255 23 + 647215 CAACTATGCAACCTCTGGTGACC - -a -s simMouse_chr6.simMouse.chr6 408758 11 + 636262 TTAAGGCAATA -s Anc0.Anc0refChr3 39986 11 + 222631 TTATGGCAGCT -s Anc1.Anc1refChr6 70276 11 + 197743 TTATGGCAGCT -s Anc2.Anc2refChr13 43969 11 + 96486 TTATGGCAGCT -s mr.mrrefChr5 261623 11 + 294540 TTAAGGCAACA -s simCow_chr6.simCow.chr6 399952 11 + 602619 TTATGACAGCT -s simDog_chr6.simDog.chr6 390409 11 + 593897 TTTTGGCAGCT -s simHuman_chr6.simHuman.chr6 395053 11 + 601863 TTACGGCTGCT -s simRat_chr6.simRat.chr6 415280 11 + 647215 TTATGGCAACA - -a -s simMouse_chr6.simMouse.chr6 408769 50 + 636262 TAATGCTAGGGTCACATACTTATGACACTAGTCCCAGTATCTGAAAGTCT -s Anc0.Anc0refChr3 39997 50 + 222631 TAGCGCTGGGGTCAGGTACCTGTGACAACAGTCCCAGGATCTGAAAGTCC -s Anc1.Anc1refChr6 70287 50 + 197743 TAGCGCTGGGGTCAGGTACCTGTGACAACAGTCCCAGGATCTGAAAGTCC -s Anc2.Anc2refChr13 43980 50 + 96486 TAGCACTGGGGTCAGGTACCTGTGACAACAGTCCCAGGATCTGAGAGTCC -s mr.mrrefChr5 261634 50 + 294540 TAACGCTGGGGTCACGTACTTATGACACCAGTCCCAGTATCTGAAAGTCT -s simCow_chr6.simCow.chr6 399963 50 + 602619 TAGCACTGGGGCTGGGTACATGTCACAACAGTCCTAGTATCTGACAGTCC -s simDog_chr6.simDog.chr6 390424 50 + 593897 TAGCACTGGGGTCAGGTACCTGTGACAACAGTCCCAGGATCCGAGAGTCT -s simHuman_chr6.simHuman.chr6 395064 50 + 601863 CAGCGCTGGGGTCAGGTACCTGCGATAACAGTCCCAGGATCTGGAAGCCC -s simRat_chr6.simRat.chr6 415291 50 + 647215 TAACACTGGGGTCACGTACTTATGAAACCAGTCCCAGTATCTAAAAGTCT - -a -s simMouse_chr6.simMouse.chr6 408819 14 + 636262 AGAGGCTATATTTT -s Anc0.Anc0refChr3 40047 14 + 222631 ATACGTGGTGTATT -s Anc1.Anc1refChr6 70337 14 + 197743 ATACGTGGTGTATT -s Anc2.Anc2refChr13 44030 14 + 96486 ATACATGGCGCATT -s mr.mrrefChr5 261684 14 + 294540 AGAGGCGATATTTT -s simCow_chr6.simCow.chr6 400013 10 + 602619 ATACATGGAG---- -s simDog_chr6.simDog.chr6 390474 13 + 593897 GT-CATAACACATT -s simHuman_chr6.simHuman.chr6 395114 14 + 601863 ATACGTGGTGTATT -s simRat_chr6.simRat.chr6 415343 14 + 647215 AGAGGCGATATTTT - -a -s simMouse_chr6.simMouse.chr6 408833 93 + 636262 TTGCATTGTTGTCACAATGTCAGCTTCTACATTGATACCAGATCAGCTCTTGAAATGATCCAATTCTTACCACAGTTCTGGCATACTGCACAG -s Anc0.Anc0refChr3 40070 74 + 222631 TCACATGGTTGTCACAATATTAGTTTCTACATCAAGA---GATCAACCCTTTACTTGGT----------------TTCTATCATAATGCATGG -s Anc1.Anc1refChr6 70360 77 + 197743 TCACATGGTTGTCACAATATTAGTTTCTACATCAAGACCAGATCAACCCTTTACTTGGT----------------TTCTATCATAATGCATGG -s Anc2.Anc2refChr13 44053 74 + 96486 CCACATGGTTGTCACAATCTTAGTGTCCGACTCAAGA---GATGAACCCTTTGCTGCGG----------------TTCTATCAGAATGCATGG -s mr.mrrefChr5 261698 93 + 294540 TTGCATGGTTGTCACAATATCAGCTTCTACATTGATACCAGATCAACCCTTGAAATGATCCAATTCTTACCACAGTTCTGGCATACTGCACAG -s simCow_chr6.simCow.chr6 400031 28 + 602619 -------------------------------------------------TTTGCAGTTG----------------TTCTATCTGAAGGCACAG -s simDog_chr6.simDog.chr6 390496 74 + 593897 CCACATGGTTGTCACAATCTTAGTGTCCGACTCAAGA---GATGAACCCTTTGCTGCGG----------------TTATATCAGAATGCATGG -s simHuman_chr6.simHuman.chr6 395137 75 + 601863 TCTCATGGTTGTCACAATACTAGTTTCTACATCAAGACCAGTCCAACC--TCAGGTGGT----------------TTCTAACATAATGCATGG -s simRat_chr6.simRat.chr6 415357 88 + 647215 TTGCGTG-----CACAAAATCAGCTTAGACCTTGGTACCAGATCAACCCATGAAATGCTCCATTTCTTACCACAGTTCTGGCATACTGCACAA - -a -s simMouse_chr6.simMouse.chr6 408926 47 + 636262 AACTTGTGAGCTTAGTGAGTATTCCAACAATGTTGTAGGTCATAATT -s Anc0.Anc0refChr3 40144 47 + 222631 GACTTATGAGCCCATTGAGTTTTCCAATGAAGATGTAGGTCATAACT -s Anc1.Anc1refChr6 70437 47 + 197743 GACTTATGAGCCCATTGAGTTTTCCAATGAAGATGTAGGTCATAACT -s Anc2.Anc2refChr13 44127 47 + 96486 GACTTATGAGCCCATTGAGCTTTCCAATGAAGATGTAGGTCATAACT -s mr.mrrefChr5 261791 47 + 294540 AACTTGTGAGCTTAGTGAGTATTCCAACAATGTTGTAGGTCATAACT -s simCow_chr6.simCow.chr6 400059 47 + 602619 GATATATAAGCCCATTAAGCTTTCCACTGAAGATGTAGGTCATAACT -s simDog_chr6.simDog.chr6 390570 47 + 593897 GACTTGTGCACCCATTGAGCTTTGTAATGGAGATGTGGGTCACAGCT -s simHuman_chr6.simHuman.chr6 395215 47 + 601863 GACTTATGAGCACATTGCATTTTCCAATGAAGATGTATGTCATCACT -s simRat_chr6.simRat.chr6 415445 46 + 647215 AACTTGTGAGGTTAGTGAGTATTCCAA-AATGTTGTAGGTCATAACT - -a -s simMouse_chr6.simMouse.chr6 408973 26 + 636262 AAGAGTAAGCCCATTTTTCTATAATT -s Anc0.Anc0refChr3 40230 26 + 222631 AAGAGTAAGTCCATTATTGCTGAAAT -s Anc1.Anc1refChr6 70523 26 + 197743 AAGAGTAAGTCCATTATTGCTGAAAT -s Anc2.Anc2refChr13 44213 26 + 96486 AAGAGTAAGTCCATTATTGCTGTAAT -s mr.mrrefChr5 261876 26 + 294540 AAGAGTAAGCCCATTTTTCCATAATT -s simCow_chr6.simCow.chr6 400209 26 + 602619 AAGAGTAAGTCGATTATTGCTGTAAT -s simDog_chr6.simDog.chr6 390654 26 + 593897 AAGAATGAGTCCATTATTGCTGTAAT -s simHuman_chr6.simHuman.chr6 395301 20 + 601863 TAGAGGAAGTC------TGCTGAAAT -s simRat_chr6.simRat.chr6 415529 26 + 647215 AAGAGTGAGCCCATTTTACCATAATT - -a -s simMouse_chr6.simMouse.chr6 408999 76 + 636262 TAATCTCCAGTACTGTGTCCCCCATCTATGGATCTGGTGCAGTTCGCCCATTGGAATGAGATTAGTCTCTTAAACT -s Anc0.Anc0refChr3 40256 76 + 222631 CAATCTCCAGTACTGCAGCCCATATCTGTGGGTCTGGGGCAGTTTGGCAGTTGAGATAAGATTAGTCCCTTAAACA -s Anc1.Anc1refChr6 70549 76 + 197743 CAATCTCCAGTACTGCAGCCCATATCTGTGGGTCTGGGGCAGTTTGGCAGTTGAGATAAGATTAGTCCCTTAAACA -s Anc2.Anc2refChr13 44239 76 + 96486 CAATCTCCAGTACTGCAGCCCATAGCTGTGGGTCTGAGGCAGTTTGGCAGCTGAGATAGGGTTAGTCCCATAAACA -s mr.mrrefChr5 261902 76 + 294540 TAATCTCCAGTACTGCGTCCCCTATCTATGGGTCTGGTGCAGTTTGCCCATTGGGATGAGATTAGTCTCTTAAACT -s simCow_chr6.simCow.chr6 400235 58 + 602619 TAACATGCAGTACCACAGTCCATACCTATGGGTCTGAGGCAGTTTGGCAGCTTAGA------------------CA -s simDog_chr6.simDog.chr6 390681 75 + 593897 CGATCCCCAGCACTGCAGCTCATAG-TGTGGCTTCAACATAGTTAGGCAGCTGAGATAGGGTTAGTCCCATAAACA -s simHuman_chr6.simHuman.chr6 395321 76 + 601863 CAATCTCCAGTATTGCAGCCCATATCTGTGGGTCTGGGGCTCTTTGGCAGTGGAGATAAGAGAAGTTCCTTCAACC -s simRat_chr6.simRat.chr6 415555 76 + 647215 TAATCTCCAGTACTGCGTCCCCTATCCTTTGGTCTGGTGCAGTTTGCCCATTGGGATGAGATTAGTCTCATAAGAT - -a -s simMouse_chr6.simMouse.chr6 409075 3 + 636262 GTT -s Anc0.Anc0refChr3 40332 3 + 222631 GTT -s Anc1.Anc1refChr6 70625 3 + 197743 GTT -s Anc2.Anc2refChr13 44321 3 + 96486 GTT -s mr.mrrefChr5 261978 3 + 294540 GTT -s simCow_chr6.simCow.chr6 400299 3 + 602619 GTT -s simDog_chr6.simDog.chr6 390762 3 + 593897 GTT -s simHuman_chr6.simHuman.chr6 395397 1 + 601863 A-- -s simRat_chr6.simRat.chr6 415631 3 + 647215 GTT - -a -s simMouse_chr6.simMouse.chr6 409078 78 + 636262 TAAGGCTTATAATATTGGTCATTGTGAGGACTCCTCAACAAGACTTAGAGGTGCCTATTCACATGGGTAATGTTGATG -s Anc0.Anc0refChr3 40335 76 + 222631 AAAGAACTAGACAGAG-GTTATTGTGAGG-CTACCCAACAAGGCCTAGAGGAGCCTATTCAGGTGTGTGATGTTGGCA -s Anc1.Anc1refChr6 70628 76 + 197743 AAAGAACTAGACAGAG-GTTATTGTGAGG-CTACCCAACAAGGCCTAGAGGAGCCTATTCAGGTGTGTGATGTTGGCA -s Anc2.Anc2refChr13 44324 76 + 96486 AAAGAACTATACAGAG-GTTAATCTGATG-CTACCCTACAAGGCCTAGAGGAGCCTATTCAGGTGTGTGATGTTGGCA -s mr.mrrefChr5 261981 77 + 294540 TAAGGCCTAGAATGAT-GTCATTGTGAGGACTCCTCAACAAGACTTAGAGGTGCCTATTCACATGGGTAATGTTGATG -s simCow_chr6.simCow.chr6 400303 75 + 602619 AAAGAACCATACATAG-AATACT-TGACG-CTAACCCACAAGGCCTAGAGGAGCCTATTCAGGTGTGTGATATTGGCA -s simDog_chr6.simDog.chr6 390765 76 + 593897 AAAGACTTATGCAGAG-GTTAATCTGATG-GTACCCTACAAGGCCTAGAGGAGCCTATTCAAGTGTGTGATGTTGGCA -s simHuman_chr6.simHuman.chr6 395398 70 + 601863 ------CTAGACAGAG-GTTATTGTGAGG-CTACCCAACAAGGCCTAGAGGAGCCTATTCAGGCGTGTGATGTTGGCA -s simRat_chr6.simRat.chr6 415634 73 + 647215 TAAGGCCTAGAAGGAT-GTCGTTGAGAGGACT----ATCTAGACTTAGAGGTGCCTATTCACATGGGTAATATTGATG - -a -s simMouse_chr6.simMouse.chr6 409156 2 + 636262 AG -s Anc0.Anc0refChr3 40411 2 + 222631 AG -s Anc1.Anc1refChr6 70704 2 + 197743 AG -s Anc2.Anc2refChr13 44400 2 + 96486 AG -s mr.mrrefChr5 262058 2 + 294540 AG -s simCow_chr6.simCow.chr6 400400 2 + 602619 AG -s simDog_chr6.simDog.chr6 390841 2 + 593897 AT -s simHuman_chr6.simHuman.chr6 395468 2 + 601863 AG -s simRat_chr6.simRat.chr6 415707 2 + 647215 GG - -a -s simMouse_chr6.simMouse.chr6 409158 74 + 636262 TGGCTATATGTCATGGACTTTCAATTGGTCCCCATTCATCAGATCAAATCTTGATATTTAAAGCTGATCTCAGA -s Anc0.Anc0refChr3 40413 74 + 222631 TGACCAATTCTTATGCGTTTTCCATTGGCTCCTGGTCATTAGACTCAATCTTGACATCTAAGACTGATCTCATG -s Anc1.Anc1refChr6 70706 74 + 197743 TGACCAATTCTTATGCGTTTTCCATTGGCTCCTGGTCATTAGACTCAATCTTGACATCTAAGACTGATCTCATG -s Anc2.Anc2refChr13 44402 74 + 96486 TGACCAATTCTTATGCGTTTTCTGTTGGCTCCTGGTTATTAGACTCAAGCTTGGCATCTAAGACTGATCTCATG -s mr.mrrefChr5 262060 74 + 294540 TGGCTATATGTCATGGGCTTTCCATTGGTCCCCAGTCATCAGATTAAATCTTGATATTTAAAGCTGATCTCAGA -s simCow_chr6.simCow.chr6 400402 74 + 602619 TGACCAGTTCTGATGCATTTTTTGTTGGTTTCAAGTTGTCAGACTCAACCCTGGCAGCTAAGACTGATCTCATG -s simDog_chr6.simDog.chr6 390843 74 + 593897 TGACCAATTCTTATGCGTTTCCTGTTGGCCCCTGATTATTAGACTCAAGCTTGGCATCTACGACTTATGTCATG -s simHuman_chr6.simHuman.chr6 395470 74 + 601863 TGACCAATTTTTATCTGTTTTCCATTAGATCCTGGTCACTAGACTCAATCTTGACTTCTAAGACTGATCTCATG -s simRat_chr6.simRat.chr6 415731 72 + 647215 TATCTGCATCTCATGGGCTTTCCATTGGTCTCCAGTCAT--GGTTGAACCTTGATATTTAAAGCTGATCTCAGA - -a -s simMouse_chr6.simMouse.chr6 409232 3 + 636262 AAT -s Anc0.Anc0refChr3 40487 3 + 222631 GAT -s Anc1.Anc1refChr6 70780 3 + 197743 GAT -s Anc2.Anc2refChr13 44476 3 + 96486 GAT -s mr.mrrefChr5 262134 3 + 294540 AAT -s simCow_chr6.simCow.chr6 400476 3 + 602619 GAT -s simDog_chr6.simDog.chr6 390965 3 + 593897 GAT -s simHuman_chr6.simHuman.chr6 395544 3 + 601863 GAC -s simRat_chr6.simRat.chr6 415803 3 + 647215 AAT - -a -s simMouse_chr6.simMouse.chr6 409235 9 + 636262 CATTACGTC -s Anc0.Anc0refChr3 40490 9 + 222631 CTGTTACCC -s Anc1.Anc1refChr6 70783 9 + 197743 CTGTTACCC -s Anc2.Anc2refChr13 44479 9 + 96486 CTGTTACCC -s mr.mrrefChr5 262137 9 + 294540 CATTACGTC -s simCow_chr6.simCow.chr6 400480 9 + 602619 CATTTAATC -s simDog_chr6.simDog.chr6 390968 9 + 593897 CTGTTACCT -s simHuman_chr6.simHuman.chr6 395547 9 + 601863 CGGTTACAC -s simRat_chr6.simRat.chr6 415806 9 + 647215 CACTATGTC - -a -s simMouse_chr6.simMouse.chr6 409244 31 + 636262 TGGTTATTTCCTGGAATAAAATACTGATTGT -s Anc0.Anc0refChr3 40499 30 + 222631 TGATTATT-CTCTGAATAAAAGGCTGATAGT -s Anc1.Anc1refChr6 70792 31 + 197743 TGATTATTTCTCTGAATAAAAGGCTGATAGT -s Anc2.Anc2refChr13 44488 30 + 96486 TGATTATT-CTCTGAATAGAAGGCTGATAGT -s mr.mrrefChr5 262146 31 + 294540 TGATTATTTCCTTGAATAAAATACTGATTGT -s simCow_chr6.simCow.chr6 400489 30 + 602619 TGATAATT-CTTTGAATACAAGACTGACGGT -s simDog_chr6.simDog.chr6 390978 29 + 593897 TGATTATT--TCTGAATAGAAGGCTGGTAAT -s simHuman_chr6.simHuman.chr6 395556 31 + 601863 TGATTATTACTCTGAATAAAAGGCTGATAGT -s simRat_chr6.simRat.chr6 415815 31 + 647215 TGATTATTTTCTTGAATAAAATACTGATTAT - -a -s simMouse_chr6.simMouse.chr6 409275 43 + 636262 ATATACGATTTGTTTTCAGATCTGCAGTTGAGCTACCTAAAGT -s Anc0.Anc0refChr3 40549 43 + 222631 ATATATGAACTGTGTGCAGATCTGAAGTAGAAATACCTAAATT -s Anc1.Anc1refChr6 70846 43 + 197743 ATATATGAACTGTGTGCAGATCTGAAGTAGAAATACCTAAATT -s Anc2.Anc2refChr13 44539 43 + 96486 ATATATGAACTGTGTGCAGATCTGAAGTATAAATACCTAAATT -s mr.mrrefChr5 262200 43 + 294540 ATATATGATTTGTTTTCAGATCTGCAGTTGAGCTACCTAAAGT -s simCow_chr6.simCow.chr6 400541 43 + 602619 ATAGATAAACTATGTGCAGATCTGCAGAAAAAATGCCTAAATT -s simDog_chr6.simDog.chr6 391028 37 + 593897 ATATATGAACTG------GATCTGAAGTGTAAGCACTTAAGTT -s simHuman_chr6.simHuman.chr6 395610 43 + 601863 ATAAATGAACTGTCTGCAGATCTGTGGTAGAAATACCTATATT -s simRat_chr6.simRat.chr6 415874 35 + 647215 ATATATGATTTGGTTTCAGATCTCCAG--------CCTACAGT - -a -s simMouse_chr6.simMouse.chr6 409318 15 + 636262 CTTCAGGTTACACCA -s Anc0.Anc0refChr3 40592 15 + 222631 CTTCAGGTCATACCC -s Anc1.Anc1refChr6 70889 15 + 197743 CTTCAGGTCATACCC -s Anc2.Anc2refChr13 44582 15 + 96486 CTTTAGGTCATACCC -s mr.mrrefChr5 262243 15 + 294540 CTTCAGGTTACACCA -s simCow_chr6.simCow.chr6 400584 15 + 602619 ATTGAGGTCATACCC -s simDog_chr6.simDog.chr6 391066 15 + 593897 CTTTAGGTCATACCC -s simHuman_chr6.simHuman.chr6 395653 15 + 601863 CTTCAGGTCATACCC -s simRat_chr6.simRat.chr6 415909 15 + 647215 CTTCAGGTTACACCA - -a -s simMouse_chr6.simMouse.chr6 409333 9 + 636262 TATAAAAAC -s Anc0.Anc0refChr3 40607 9 + 222631 TATAAGAAA -s Anc1.Anc1refChr6 70904 9 + 197743 TATAAGAAA -s Anc2.Anc2refChr13 44597 9 + 96486 TATAAGAAA -s mr.mrrefChr5 262258 9 + 294540 TATAAAAAC -s simCow_chr6.simCow.chr6 400600 9 + 602619 TATAAGAAA -s simDog_chr6.simDog.chr6 391081 9 + 593897 TATAAGAAA -s simHuman_chr6.simHuman.chr6 395668 9 + 601863 TATAAGGAA -s simRat_chr6.simRat.chr6 415924 9 + 647215 TATAAAAAC - -a -s simMouse_chr6.simMouse.chr6 409342 18 + 636262 TCAGCTATGTGTCTCTGT -s Anc0.Anc0refChr3 40616 18 + 222631 CCAGCTATGTGGCTTTAA -s Anc1.Anc1refChr6 70913 18 + 197743 CCAGCTATGTGGCTTTAA -s Anc2.Anc2refChr13 44607 18 + 96486 CCAGCTATGTAGCTTTAA -s mr.mrrefChr5 262267 18 + 294540 TCAGCTATGTGTCTCTGT -s simCow_chr6.simCow.chr6 400610 18 + 602619 CCAACTGTGCAACTTTAG -s simDog_chr6.simDog.chr6 391091 18 + 593897 CCAGATACATAGATCTAA -s simHuman_chr6.simHuman.chr6 395677 18 + 601863 CCAGCTATGTGGCTTTAA -s simRat_chr6.simRat.chr6 415933 18 + 647215 TCAGCTATGTGTTTCTGC - -a -s simMouse_chr6.simMouse.chr6 409360 1 + 636262 T -s Anc0.Anc0refChr3 40634 1 + 222631 T -s Anc1.Anc1refChr6 70931 1 + 197743 T -s Anc2.Anc2refChr13 44625 1 + 96486 T -s mr.mrrefChr5 262285 1 + 294540 T -s simCow_chr6.simCow.chr6 400629 1 + 602619 T -s simDog_chr6.simDog.chr6 391109 1 + 593897 T -s simHuman_chr6.simHuman.chr6 395695 1 + 601863 T -s simRat_chr6.simRat.chr6 415951 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 409361 12 + 636262 GCCTGCATAATG -s Anc0.Anc0refChr3 40635 2 + 222631 GA---------- -s Anc1.Anc1refChr6 70932 12 + 197743 GACTGCATCGTG -s Anc2.Anc2refChr13 44626 2 + 96486 GA---------- -s mr.mrrefChr5 262286 12 + 294540 GACTGCATAATG -s simCow_chr6.simCow.chr6 400630 2 + 602619 GA---------- -s simDog_chr6.simDog.chr6 391110 2 + 593897 GA---------- -s simHuman_chr6.simHuman.chr6 395696 12 + 601863 GACTGCATCGTG -s simRat_chr6.simRat.chr6 415954 12 + 647215 GACTGCATAATG - -a -s simMouse_chr6.simMouse.chr6 409373 8 + 636262 TGACACTG -s Anc0.Anc0refChr3 40644 8 + 222631 TGACAATG -s Anc1.Anc1refChr6 70951 8 + 197743 TGACAATG -s Anc2.Anc2refChr13 44635 8 + 96486 TGACAATG -s mr.mrrefChr5 262298 8 + 294540 TGACACTG -s simCow_chr6.simCow.chr6 400640 8 + 602619 TGACAATG -s simDog_chr6.simDog.chr6 391119 8 + 593897 TGACAACG -s simHuman_chr6.simHuman.chr6 395720 8 + 601863 TGACAATG -s simRat_chr6.simRat.chr6 415966 8 + 647215 TGATAGTG - -a -s simMouse_chr6.simMouse.chr6 409381 12 + 636262 GAGTTCAATATC -s Anc0.Anc0refChr3 40658 11 + 222631 GAATTGG-CATC -s Anc1.Anc1refChr6 70965 11 + 197743 GAATTGG-CATC -s Anc2.Anc2refChr13 44649 11 + 96486 GAACTGG-CATC -s mr.mrrefChr5 262306 11 + 294540 GAATTCA-TATC -s simCow_chr6.simCow.chr6 400654 11 + 602619 AAAGTGG-CATT -s simDog_chr6.simDog.chr6 391133 11 + 593897 GGACTTG-CATC -s simHuman_chr6.simHuman.chr6 395734 11 + 601863 GAATTGG-CATC -s simRat_chr6.simRat.chr6 415974 11 + 647215 GAATTCA-TATC - -a -s simMouse_chr6.simMouse.chr6 409393 89 + 636262 CAGTCCTGAGCTCTTGACCAGAAATAACAGTTCTGATATAATGGTTACAAAGATGAGAGTTACCAGGATACACCGTGATATTGTGTGGC -s Anc0.Anc0refChr3 40670 89 + 222631 CAGTCCTAAGCATTAGACAATAAATAACAATTCTCAAATTGTAGTTGTAGAGTTGAGTGTCACAAGGATATGACTTAATTTTGTGTATC -s Anc1.Anc1refChr6 70977 89 + 197743 CAGTCCTAAGCATTAGACAATAAATAACAATTCTCAAATTGTAGTTGTAGAGTTGAGTGTCACAAGGATATGACTTAATTTTGTGTATC -s Anc2.Anc2refChr13 44661 89 + 96486 CAGCTCTAAGCATTAGACAACAAATAACTATTCTAAAATTGCAATTGTGGAATTGAGTGTGGCAAGGATATGACATAATTTTCCGTATC -s mr.mrrefChr5 262317 89 + 294540 CAGTCCTGAGCTCTAGACCATAAATAACAGTTCTCATATAATGGTTACAAAGATGAGAGTCACCAGGATACACCTTGATATTGTGTGTC -s simCow_chr6.simCow.chr6 400666 67 + 602619 TAGCTCTAAGCACTTGGTAAAAAATAACTAT-----AATTGCA-----------------GGCAAGGATATGACATACTATTTCGTAAC -s simDog_chr6.simDog.chr6 391145 89 + 593897 CAGCTCTAAGCATTAGACAACAAATAACTATTCTAAAGTTGCAATTGTGGAATTGAGTGTGGCAAAGATATTACATAATTTTCCGTATC -s simHuman_chr6.simHuman.chr6 395746 85 + 601863 CAGTCCCAGG----AGACAATAAATAACAATTCTCACATTGTAGTAGTATAGTTGAGCATCACAAGGTTATGGCTTAGTGTTGTGCATT -s simRat_chr6.simRat.chr6 415985 89 + 647215 CAGTCCTGAGCTCTAGACCATAAATAACAGTTCCCATATAACGATTACAAAGGTGAGAGTCACCTGGATACACCTTGACATTGTGTGTC - -a -s simMouse_chr6.simMouse.chr6 409482 1 + 636262 A -s Anc0.Anc0refChr3 40759 1 + 222631 A -s Anc1.Anc1refChr6 71066 1 + 197743 A -s Anc2.Anc2refChr13 44750 1 + 96486 A -s mr.mrrefChr5 262406 1 + 294540 A -s simCow_chr6.simCow.chr6 400733 1 + 602619 A -s simDog_chr6.simDog.chr6 391234 1 + 593897 A -s simHuman_chr6.simHuman.chr6 395831 1 + 601863 A -s simRat_chr6.simRat.chr6 416075 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 409483 23 + 636262 GATAGATAGTGTCCCCAGGCTGT -s Anc0.Anc0refChr3 40762 23 + 222631 TATAGATGATGCCCCAAGGATAT -s Anc1.Anc1refChr6 71069 23 + 197743 TATAGATGATGCCCCAAGGATAT -s Anc2.Anc2refChr13 44753 23 + 96486 TGTAGATGATGCCCTAAGGATAT -s mr.mrrefChr5 262407 23 + 294540 GATAGATGGTGTCCCAAGGCTGT -s simCow_chr6.simCow.chr6 400736 23 + 602619 TTTAGATGATGCCGTAAGAATAT -s simDog_chr6.simDog.chr6 391237 23 + 593897 TGCAGATGACGCTCTAAGGATAT -s simHuman_chr6.simHuman.chr6 395834 23 + 601863 TATAGATGATGACCCAAAGATAT -s simRat_chr6.simRat.chr6 416076 23 + 647215 GATAGATGGTGTCCCAAGGCTGT - -a -s simMouse_chr6.simMouse.chr6 409506 16 + 636262 GACTGAGTGTTGTACG -s Anc0.Anc0refChr3 40785 16 + 222631 GACTCAATATTGTGCA -s Anc1.Anc1refChr6 71092 16 + 197743 GACTCAATATTGTGCA -s Anc2.Anc2refChr13 44778 16 + 96486 GACTCAATATTGTGCA -s mr.mrrefChr5 262430 16 + 294540 GACTGAGTGTTGTACG -s simCow_chr6.simCow.chr6 400761 16 + 602619 ACCTCAGTGCTGTGCA -s simDog_chr6.simDog.chr6 391262 16 + 593897 GACTCAATATTGTGCA -s simHuman_chr6.simHuman.chr6 395857 16 + 601863 GCCTCGATATTTTGCT -s simRat_chr6.simRat.chr6 416099 16 + 647215 GACTGAGTGTTGTACA - -a -s simMouse_chr6.simMouse.chr6 409522 24 + 636262 TGACAATCACCTTCTGGTTTTTCC -s Anc0.Anc0refChr3 40801 8 + 222631 TG----------------TTTTCC -s Anc1.Anc1refChr6 71108 8 + 197743 TG----------------TTTTCC -s Anc2.Anc2refChr13 44794 8 + 96486 TG----------------TTTTCC -s mr.mrrefChr5 262446 24 + 294540 TGACAATCACCTTCTGGTTTTTCC -s simDog_chr6.simDog.chr6 391308 8 + 593897 TG----------------TTTTCC -s simHuman_chr6.simHuman.chr6 395873 8 + 601863 TG----------------TTCACC -s simRat_chr6.simRat.chr6 416115 24 + 647215 TGACAGTCACCTTCCATTTTTTCG - -a -s simMouse_chr6.simMouse.chr6 409546 18 + 636262 AGGAGTGTATCCTATTGA -s Anc0.Anc0refChr3 40809 18 + 222631 AGGAGTATATCTTATTAA -s Anc1.Anc1refChr6 71116 18 + 197743 AGGAGTATATCTTATTAA -s Anc2.Anc2refChr13 44803 18 + 96486 AATAGTATATCTTGTTAG -s mr.mrrefChr5 262470 18 + 294540 AGGAGTGTATCCTATTGA -s simDog_chr6.simDog.chr6 391317 18 + 593897 AATAGTATATCTTGTTAG -s simHuman_chr6.simHuman.chr6 395881 18 + 601863 AGGAGTATATCTTATCAA -s simRat_chr6.simRat.chr6 416139 18 + 647215 AGGAGTGTATCCCATTGA - -a -s simMouse_chr6.simMouse.chr6 409564 45 + 636262 TGATTGCTCTATGGGTCAGTCCTTAGTCATTTGTGTCAGTTGCTC -s Anc0.Anc0refChr3 40827 25 + 222631 TGACTGGTCCATGGG--------------------TAAGTTGCTA -s Anc1.Anc1refChr6 71134 25 + 197743 TGACTGGTCCATGGG--------------------TAAGTTGCTA -s Anc2.Anc2refChr13 44821 25 + 96486 TGACTGGTTAATGGC--------------------TAAGTCATTA -s mr.mrrefChr5 262488 45 + 294540 TGATTGGTCCATGGGTCAGTCCTTAGTCATTTGTGTCAGTTGCTA -s simDog_chr6.simDog.chr6 391336 25 + 593897 TGACTGGTTAATGGC--------------------TAAGTCATTA -s simHuman_chr6.simHuman.chr6 395899 25 + 601863 TGACTGGTCCATGGG--------------------TAAACTGCAA -s simRat_chr6.simRat.chr6 416157 45 + 647215 TGATTGGTCCATGAGCCAGTCACGAGTCATCAGTGTCAGTTGCTA - -a -s simMouse_chr6.simMouse.chr6 409609 21 + 636262 CTAGGACGTTTAGTAGATGAT -s Anc0.Anc0refChr3 40856 21 + 222631 TTAGGACTTTTTGGAGATATT -s Anc1.Anc1refChr6 71163 21 + 197743 TTAGGACTTTTTGGAGATATT -s Anc2.Anc2refChr13 44850 21 + 96486 TTAAGGCTATTTGGACTTATC -s mr.mrrefChr5 262537 21 + 294540 TTAGGACGTTTAGTAGATGAT -s simDog_chr6.simDog.chr6 391365 21 + 593897 TTAAGGCTATTTGGACTTATC -s simHuman_chr6.simHuman.chr6 395928 21 + 601863 TTAGAACTTCTGGGAGACATT -s simRat_chr6.simRat.chr6 416206 21 + 647215 TTAGGACGTTTTGTAAATGAT - -a -s simMouse_chr6.simMouse.chr6 409630 84 + 636262 CTAGAGTTTAACTAAGACAAACTAAGACAACCTAAGACCAATTAAATCAAAGGAAGTGTGCATATAACGCTGGGCCAGGCATCC -s Anc0.Anc0refChr3 40877 19 + 222631 CAAGGAT------------------------GTAAA-CCAAGAA---------------------------------------- -s Anc1.Anc1refChr6 71184 23 + 197743 CAAGGATCTAA--------------------GTAAA-CCAAGAA---------------------------------------- -s Anc2.Anc2refChr13 44871 19 + 96486 CAGGGAT------------------------GTACA-CCAAGAA---------------------------------------- -s mr.mrrefChr5 262558 43 + 294540 CAAGGGTTTAACTAAGACAAACTAAGACAACCTAAG-CCAATTA---------------------------------------- -s simDog_chr6.simDog.chr6 391467 19 + 593897 CAGGGAT------------------------GTACA-CCAAGAA---------------------------------------- -s simHuman_chr6.simHuman.chr6 395949 23 + 601863 CAAGGATCTAA--------------------GTAAA-CAAAGGA---------------------------------------- -s simRat_chr6.simRat.chr6 416227 43 + 647215 CAAAGCTTTCACTAAGACAAACTAAGACAACCTAAG-TCAATTT---------------------------------------- - -a -s simMouse_chr6.simMouse.chr6 409714 2 + 636262 TG -s Anc0.Anc0refChr3 40896 2 + 222631 TG -s Anc1.Anc1refChr6 71207 2 + 197743 TG -s Anc2.Anc2refChr13 44890 2 + 96486 TA -s mr.mrrefChr5 262601 2 + 294540 TG -s simDog_chr6.simDog.chr6 391486 2 + 593897 TA -s simHuman_chr6.simHuman.chr6 395972 2 + 601863 TG -s simRat_chr6.simRat.chr6 230251 2 - 647215 TG - -a -s simMouse_chr6.simMouse.chr6 409716 3 + 636262 AAC -s Anc0.Anc0refChr3 40898 3 + 222631 AAT -s Anc1.Anc1refChr6 71209 3 + 197743 AAT -s Anc2.Anc2refChr13 44892 3 + 96486 AAT -s mr.mrrefChr5 262603 3 + 294540 AAC -s simDog_chr6.simDog.chr6 391494 3 + 593897 AAT -s simHuman_chr6.simHuman.chr6 395974 3 + 601863 GTT -s simRat_chr6.simRat.chr6 230253 3 - 647215 AAC - -a -s simMouse_chr6.simMouse.chr6 409719 21 + 636262 CACCTCATTTACCTTTACAAC -s Anc0.Anc0refChr3 40901 21 + 222631 CTACCAATTTACCAGTATAAC -s Anc1.Anc1refChr6 71212 21 + 197743 CTACCAATTTACCAGTATAAC -s Anc2.Anc2refChr13 44895 21 + 96486 CCACCAATTCACCAGCATACC -s mr.mrrefChr5 262606 21 + 294540 CTCCTCATTTACCATTACAAC -s simDog_chr6.simDog.chr6 391497 21 + 593897 CCACCAATTCACCAGCATACC -s simHuman_chr6.simHuman.chr6 395977 21 + 601863 CTGCCAATTTATCACTAATAC -s simRat_chr6.simRat.chr6 230268 21 - 647215 CTATACATTTACCATTACAAC - -a -s simMouse_chr6.simMouse.chr6 409740 6 + 636262 CTGGTA -s Anc0.Anc0refChr3 40922 6 + 222631 CTGGTA -s Anc1.Anc1refChr6 71233 6 + 197743 CTGGTA -s Anc2.Anc2refChr13 44916 6 + 96486 CTGGTA -s mr.mrrefChr5 262627 6 + 294540 CTGGTA -s simDog_chr6.simDog.chr6 391518 6 + 593897 CTGGTA -s simHuman_chr6.simHuman.chr6 395998 6 + 601863 CTGGTA -s simRat_chr6.simRat.chr6 230292 6 - 647215 CTGGTA - -a -s simMouse_chr6.simMouse.chr6 409746 12 + 636262 CAGGAGGTGTTT -s Anc0.Anc0refChr3 40944 12 + 222631 CATGTTATGTTT -s Anc1.Anc1refChr6 71255 12 + 197743 CATGTTATGTTT -s Anc2.Anc2refChr13 44938 12 + 96486 CATGTTATGTTT -s mr.mrrefChr5 262633 12 + 294540 TAGGAGATGTTT -s simCow_chr6.simCow.chr6 400777 7 + 602619 -----TATGTTT -s simDog_chr6.simDog.chr6 391540 12 + 593897 CATGTCATGCTT -s simHuman_chr6.simHuman.chr6 396020 12 + 601863 CATGTTATCTTT -s simRat_chr6.simRat.chr6 230298 12 - 647215 TAGGAGATGTTT - -a -s simMouse_chr6.simMouse.chr6 409758 29 + 636262 CACTTACTCTATTAGGGTGATGTTGTATC -s Anc0.Anc0refChr3 40963 28 + 222631 CAATTAGTTTAATATGGTTGT-ATCAATC -s Anc1.Anc1refChr6 71274 28 + 197743 CAATTAGTTTAATATGGTTGT-ATCAATC -s Anc2.Anc2refChr13 44957 28 + 96486 CAATTAGTTTAATATGATTGT-ATCAATT -s mr.mrrefChr5 262645 29 + 294540 CACTTACTCTATTAGGGTGATGATGAATC -s simCow_chr6.simCow.chr6 400791 25 + 602619 CAGTTAGTTTAATA---TTGT-ATCAATT -s simDog_chr6.simDog.chr6 391559 27 + 593897 CAATTAGCCTAATATGATTGT-ACCATT- -s simHuman_chr6.simHuman.chr6 396039 28 + 601863 CAATTAGTTTAATACAGTTGT-ATCAATC -s simRat_chr6.simRat.chr6 230310 29 - 647215 TGCTTACTCTATTAGGTTCATCATTAACC - -a -s simMouse_chr6.simMouse.chr6 409787 29 + 636262 TGTCAGCCTAAACACATGTAGAATGTTTT -s Anc0.Anc0refChr3 40999 28 + 222631 GATCAACCT-AACACATGCACAATGCTTT -s Anc1.Anc1refChr6 71310 29 + 197743 GATCAACCTGAACACATGCACAATGCTTT -s Anc2.Anc2refChr13 44993 28 + 96486 GATCAACCT-AACCCATCCAAAATGCTTT -s mr.mrrefChr5 262682 29 + 294540 GGTCAGCCTAAACACATGTACAATGTTTT -s simCow_chr6.simCow.chr6 400823 28 + 602619 GATTATCTA-AACAGATCCAGAATGCCTT -s simDog_chr6.simDog.chr6 391592 28 + 593897 GAGCAACCT-AACCCATCCAAAATGCTTT -s simHuman_chr6.simHuman.chr6 396075 18 + 601863 GATCAAACTG---ACATGAAC-------- -s simRat_chr6.simRat.chr6 230347 29 - 647215 GGTGAGCCCTAACACATGCACACTGTTTT - -a -s simMouse_chr6.simMouse.chr6 409816 39 + 636262 TGCTTCTATTTAGTTAGGTCCAGTCATCATGCAAGTGTG -s Anc0.Anc0refChr3 41027 39 + 222631 TGAACATGTCTAAGTCAGTCCAGTCGTTGTACATGAGTG -s Anc1.Anc1refChr6 71339 39 + 197743 TGAACATGTCTAAGTCAGTCCAGTCGTTGTACATGAGTG -s Anc2.Anc2refChr13 45022 39 + 96486 TGAACATGTCTAAGTCAGTCCAGCCATTGTACATGAGTG -s mr.mrrefChr5 262711 39 + 294540 TGCTTCTATTTAGTTCAGTCCAGTCGTTGTGCATGTGTG -s simCow_chr6.simCow.chr6 400852 39 + 602619 TGAACACATCTAAGTCAGTCCAGCCATTGTACATGAGTG -s simDog_chr6.simDog.chr6 391621 39 + 593897 TGAACATGTCTAAGTAAGCCCATCCATTGTACATGAGTG -s simHuman_chr6.simHuman.chr6 396093 34 + 601863 -----ATGTCTAAGCCATTCCGGTCGTTGTACATACGTG -s simRat_chr6.simRat.chr6 230376 39 - 647215 TGCTTCTATTTAGTTCAGTCCATTTGTTGAGCATGTGTG - -a -s simMouse_chr6.simMouse.chr6 409855 26 + 636262 TGTACTGTACAGTTACTCTCCCTTCT -s Anc0.Anc0refChr3 41071 26 + 222631 TGCACTATACAGTCTGCCTTCATGCA -s Anc1.Anc1refChr6 71383 26 + 197743 TGCACTATACAGTCTGCCTTCATGCA -s Anc2.Anc2refChr13 45066 26 + 96486 TGCACTATACAGTCTGCCTTCATGCG -s mr.mrrefChr5 262750 26 + 294540 TGCACTGTACAGTTTCCCTTCCTTCA -s simCow_chr6.simCow.chr6 400900 26 + 602619 TGCACTATACAGTTTGCCTTCATGTG -s simDog_chr6.simDog.chr6 391665 26 + 593897 TGCACTGCACCATCTGCCTTCATGCG -s simHuman_chr6.simHuman.chr6 396132 26 + 601863 TGCACTATACAGTCTGCCTTTATGCA -s simRat_chr6.simRat.chr6 230415 26 - 647215 TGCACTGTACAGTTTTCCATCCTTCA - -a -s simMouse_chr6.simMouse.chr6 409881 4 + 636262 GATT -s Anc0.Anc0refChr3 41098 4 + 222631 AATT -s Anc1.Anc1refChr6 71410 4 + 197743 AATT -s Anc2.Anc2refChr13 45093 4 + 96486 AATT -s mr.mrrefChr5 262776 4 + 294540 AATT -s simCow_chr6.simCow.chr6 400927 4 + 602619 AATT -s simDog_chr6.simDog.chr6 391692 4 + 593897 AATT -s simHuman_chr6.simHuman.chr6 396159 4 + 601863 AATT -s simRat_chr6.simRat.chr6 230441 4 - 647215 AATT - -a -s simMouse_chr6.simMouse.chr6 409885 2 + 636262 CA -s Anc0.Anc0refChr3 41102 2 + 222631 CA -s Anc1.Anc1refChr6 71414 2 + 197743 CA -s Anc2.Anc2refChr13 45105 2 + 96486 CA -s mr.mrrefChr5 262780 2 + 294540 CA -s simCow_chr6.simCow.chr6 400939 2 + 602619 CA -s simDog_chr6.simDog.chr6 391704 2 + 593897 CA -s simHuman_chr6.simHuman.chr6 396163 2 + 601863 CA -s simRat_chr6.simRat.chr6 230445 2 - 647215 CA - -a -s simMouse_chr6.simMouse.chr6 409887 4 + 636262 TATG -s Anc0.Anc0refChr3 41104 4 + 222631 CATG -s Anc1.Anc1refChr6 71416 4 + 197743 CATG -s Anc2.Anc2refChr13 45107 4 + 96486 CATT -s mr.mrrefChr5 262782 4 + 294540 TATG -s simCow_chr6.simCow.chr6 400944 4 + 602619 CATT -s simHuman_chr6.simHuman.chr6 396165 4 + 601863 CACG -s simRat_chr6.simRat.chr6 230447 4 - 647215 TATG - -a -s simMouse_chr6.simMouse.chr6 409891 19 + 636262 ATGACAATGCCACTAACAA -s Anc0.Anc0refChr3 41110 19 + 222631 ACTGCATTGCCACTAACAA -s Anc1.Anc1refChr6 71422 19 + 197743 ACTGCATTGCCACTAACAA -s Anc2.Anc2refChr13 45113 19 + 96486 ACTGCATTGCCACTAACAA -s mr.mrrefChr5 262786 19 + 294540 ATTACAATGCCACTAACAA -s simCow_chr6.simCow.chr6 400958 19 + 602619 ACTACATTGCCCCTTACAA -s simDog_chr6.simDog.chr6 391706 18 + 593897 -CTGCATTGCCACTAGCAA -s simHuman_chr6.simHuman.chr6 396171 19 + 601863 ACTTCATTGCCACTAACAA -s simRat_chr6.simRat.chr6 230451 19 - 647215 AGTACAATGCCACTAACAG - -a -s simMouse_chr6.simMouse.chr6 409910 86 + 636262 TCTTAAATCTTTTCTATTATAACAAACTGAGCATCCCATCTCAGCCTCTCTGTGTTATCTGAATGAGGACACACCACCTCTCTCCA -s Anc0.Anc0refChr3 41132 84 + 222631 T-TT-AGTCATTCCTGTACTAATAAACTCAGCGTCCCACGCCAGCCTCTCTGTGTATTTGGGATGAGGTCTCACCACCTCACCCCA -s Anc1.Anc1refChr6 71444 85 + 197743 TCTT-AGTCATTCCTGTACTAATAAACTCAGCGTCCCACGCCAGCCTCTCTGTGTATTTGGGATGAGGTCTCACCACCTCACCCCA -s Anc2.Anc2refChr13 45135 84 + 96486 T-GT-AGTCATTCCTGTACTAATAAACTCAGCGTCCCACGCCAGCCTCTCTGTGTATTTGGGATGAGATCCCACCACCTCACCCTA -s mr.mrrefChr5 262805 86 + 294540 TCTTAAATCTTTCCTATTATAACAAACTGAGCATCCCATCTCAGCCTCTCTGTGTTATCTGGATGAGGTCTCACCACCTCACTCCA -s simCow_chr6.simCow.chr6 400980 73 + 602619 T-GT-AGTCCTTCTTGCACTATT-------GCATCCCTGGC-AGCCTCTCTGTGTATATGGGATG---CCCTACCACCCCACCCTA -s simDog_chr6.simDog.chr6 391724 79 + 593897 ------GTCATTCCTGTTCCAATAAACTCAGTGTCCTACGCCAGCCTCTCT-TGTATTCAGAATGAGATCCCACAATCTCACCTTA -s simHuman_chr6.simHuman.chr6 396193 85 + 601863 TCTT-AGTCATTCCTGTACTAGTAAACTCAGCTTCCCAAGCCCGCCTCTCTGTATATTTGGGATGAGGTCTCACCACCTCACCCCA -s simRat_chr6.simRat.chr6 230470 86 - 647215 CCTTCAATCTTTCCTATTATAACAAACTAAGCATCCCATCTCAGCCTCTCTGTGTTATCTAGATGAGGTCTCACCACCTCACTCCA - -a -s simMouse_chr6.simMouse.chr6 409996 68 + 636262 TTGTCCATAACAGATTTGTCAGCATTGTCCAAGAAGCTTCAAAGAGATATATCTCATGACAGATGGCT -s Anc0.Anc0refChr3 41216 62 + 222631 CCAGCCATACCAGATTTGTCACCATTGTCCAAAAAGTTCCAAAGAGAAATGCA------CAGATGGCT -s Anc1.Anc1refChr6 71529 68 + 197743 CCAGCCATACCAGATTTGTCACCATTGTCCAAAAAGTTCCAAAGAGAAATGCAACAGGACAGATGGCT -s Anc2.Anc2refChr13 45219 62 + 96486 CCAGCCAGACCAGATTAGTCACCAGTGCCCAAAAAGTTCCAAAGAGAAGTGCA------TAGATGGCT -s mr.mrrefChr5 262891 68 + 294540 TTGTCCATAACAGATTTGTCAGCATTGTCCAAGAAGCTCCAAAGAGAAATACCACATGACAGATGGCT -s simCow_chr6.simCow.chr6 401053 54 + 602619 ACAGCCAAAACGGATTAGTATCCAGTACCCAAAAAGTTCCAAAGGATACTGC--------------CT -s simDog_chr6.simDog.chr6 391803 62 + 593897 CCATCCAGACCACATTAGTCACCAGTGCCCAAAAAGTTGTGAAGAGAAGCACA------TAGATGGCT -s simHuman_chr6.simHuman.chr6 396279 68 + 601863 CCAGCCATACCAGATTTGTCACCATTGTCCAAAGAGTTCCAAAGCGAAATGCAACAGGGCAGATGGCT -s simRat_chr6.simRat.chr6 230556 68 - 647215 ATGCCCATAACAGATTAGTCAGTATTGTCCAGGAAACTCCAAAGAGAAATACTACATGACATATGGCT - -a -s simMouse_chr6.simMouse.chr6 410064 2 + 636262 CC -s Anc0.Anc0refChr3 41286 2 + 222631 CC -s Anc1.Anc1refChr6 71605 2 + 197743 CC -s Anc2.Anc2refChr13 45289 2 + 96486 CC -s mr.mrrefChr5 262967 2 + 294540 CC -s simCow_chr6.simCow.chr6 401115 2 + 602619 CC -s simDog_chr6.simDog.chr6 391873 2 + 593897 GT -s simHuman_chr6.simHuman.chr6 396355 2 + 601863 CC -s simRat_chr6.simRat.chr6 230632 2 - 647215 CC - -a -s simMouse_chr6.simMouse.chr6 410066 37 + 636262 ATGGTATTCCAGAGTAATCATGGCCTTGTTGCACATG -s Anc0.Anc0refChr3 41288 26 + 222631 ATGGTATTTGGGGGG---------CTTA--GCAAATG -s Anc1.Anc1refChr6 71607 26 + 197743 ATGGTATTTGGGGGG---------CTTA--GCAAATG -s Anc2.Anc2refChr13 45291 26 + 96486 ATGGTATTTGGGGGG---------CTTA--GCAAATA -s mr.mrrefChr5 262969 26 + 294540 ATGGTATTCCAGAGG---------CTTG--GCAAATG -s simCow_chr6.simCow.chr6 401129 26 + 602619 ATGGTAGTTGGGGGG---------CTTA--GCAAAGA -s simDog_chr6.simDog.chr6 391875 26 + 593897 ATGGTATTTGGGGTG---------CTTA--GCAAATA -s simHuman_chr6.simHuman.chr6 396357 26 + 601863 AGGGTATTTGGGGGG---------CCTA--GCAAATG -s simRat_chr6.simRat.chr6 230634 26 - 647215 ATGGTATTCAAGAAG---------CTTG--GCAAAAG - -a -s simMouse_chr6.simMouse.chr6 410103 171 + 636262 GTTGGTACTTAGCTAACAAGCTTGCCTCGCACTGTCAAGTGAGCACATACAGCTGTAGAAGGAACCTGCCCACCTCACACACTGTTAAGCGATCACAAACACTTGTAGAAGGGCTCAACACACTTCGCCCCATAAAGTGAATGTTATGCTATCTATCACAAGATATTCATG -s Anc0.Anc0refChr3 41316 21 + 222631 TTTGGAA-----------------------------------------------------------------------------------------------------------------------------------------------------TATAaaa-atgcagt -s Anc1.Anc1refChr6 71635 21 + 197743 TTTGGAA-----------------------------------------------------------------------------------------------------------------------------------------------------TATAaaa-atgcagt -s Anc2.Anc2refChr13 45319 21 + 96486 TTTAGAT-----------------------------------------------------------------------------------------------------------------------------------------------------CATAaaa-atgcagt -s mr.mrrefChr5 262995 21 + 294540 TTTGGTA-----------------------------------------------------------------------------------------------------------------------------------------------------TACAAAA-ATTCAGG -s simCow_chr6.simCow.chr6 401157 21 + 602619 TTGAAGT-----------------------------------------------------------------------------------------------------------------------------------------------------CAGAaaa-gtgcagt -s simDog_chr6.simDog.chr6 391903 21 + 593897 TTTAGAT-----------------------------------------------------------------------------------------------------------------------------------------------------CATAaaa-atgcagt -s simHuman_chr6.simHuman.chr6 396385 21 + 601863 TTTGGAA-----------------------------------------------------------------------------------------------------------------------------------------------------TATAaaa-atgcagt -s simRat_chr6.simRat.chr6 230660 21 - 647215 TTTAGTA-----------------------------------------------------------------------------------------------------------------------------------------------------TACAAAA-ATACAGG - -a -s simMouse_chr6.simMouse.chr6 410274 4 + 636262 AAAG -s Anc0.Anc0refChr3 41337 4 + 222631 gaag -s Anc1.Anc1refChr6 71656 4 + 197743 gaag -s Anc2.Anc2refChr13 45340 4 + 96486 gaaa -s mr.mrrefChr5 263016 4 + 294540 AAAG -s simCow_chr6.simCow.chr6 401178 4 + 602619 gaaa -s simDog_chr6.simDog.chr6 391924 4 + 593897 gaaa -s simHuman_chr6.simHuman.chr6 396406 4 + 601863 gaag -s simRat_chr6.simRat.chr6 230684 4 - 647215 ACAG - -a -s simMouse_chr6.simMouse.chr6 410278 6 + 636262 GCATTT -s Anc0.Anc0refChr3 41346 5 + 222631 gta-at -s Anc1.Anc1refChr6 71665 5 + 197743 gta-at -s Anc2.Anc2refChr13 45349 5 + 96486 gta-at -s mr.mrrefChr5 263020 5 + 294540 GCA-TT -s simCow_chr6.simCow.chr6 401187 5 + 602619 gta-at -s simDog_chr6.simDog.chr6 391933 5 + 593897 gaa-at -s simHuman_chr6.simHuman.chr6 396415 5 + 601863 gta-ct -s simRat_chr6.simRat.chr6 230688 5 - 647215 GCA-TT - -a -s simMouse_chr6.simMouse.chr6 410284 19 + 636262 CTTTTGTGCACCATGATGT -s Anc0.Anc0refChr3 41359 19 + 222631 ctcaagtttatggcagagc -s Anc1.Anc1refChr6 71678 19 + 197743 ctcaagtttatggcagagc -s Anc2.Anc2refChr13 45362 19 + 96486 cacaaccttatggcagaac -s mr.mrrefChr5 263025 19 + 294540 CTCTAGTGCACCATGATGT -s simCow_chr6.simCow.chr6 401200 19 + 602619 cactaccttatggcagaac -s simDog_chr6.simDog.chr6 391946 19 + 593897 cacagccatatggcaaaat -s simHuman_chr6.simHuman.chr6 396428 19 + 601863 ctcaagtttatggctgagc -s simRat_chr6.simRat.chr6 230693 19 - 647215 CTCTAGTGCACCATGATGT - -a -s simMouse_chr6.simMouse.chr6 410303 11 + 636262 TCACAACTCTT -s Anc0.Anc0refChr3 41378 11 + 222631 tgaaatttgtt -s Anc1.Anc1refChr6 71697 11 + 197743 tgaaatttgtt -s Anc2.Anc2refChr13 45381 11 + 96486 ggcaatttgtt -s mr.mrrefChr5 263044 11 + 294540 TCACAACTCTT -s simCow_chr6.simCow.chr6 401221 11 + 602619 gacaaattgtt -s simDog_chr6.simDog.chr6 391965 10 + 593897 ggcaattt-tt -s simHuman_chr6.simHuman.chr6 396447 11 + 601863 tgaaatttgtt -s simRat_chr6.simRat.chr6 230712 11 - 647215 TCACAACTCTT - -a -s simMouse_chr6.simMouse.chr6 410314 8 + 636262 GAGGAATA -s Anc0.Anc0refChr3 41404 8 + 222631 gggaataa -s Anc1.Anc1refChr6 71723 8 + 197743 gggaataa -s Anc2.Anc2refChr13 45407 8 + 96486 gggagtaa -s mr.mrrefChr5 263055 8 + 294540 GAGAAATA -s simCow_chr6.simCow.chr6 401247 8 + 602619 gggagtaa -s simDog_chr6.simDog.chr6 391990 8 + 593897 gggagtaa -s simHuman_chr6.simHuman.chr6 396473 8 + 601863 gggaatag -s simRat_chr6.simRat.chr6 230723 8 - 647215 GAGAAATA - -a -s simMouse_chr6.simMouse.chr6 410322 20 + 636262 TGTTTATGGCATTGCATATT -s Anc0.Anc0refChr3 41412 20 + 222631 tgttagtgacagagtacatt -s Anc1.Anc1refChr6 71731 20 + 197743 tgttagtgacagagtacatt -s Anc2.Anc2refChr13 45415 20 + 96486 tgttagcgacagagcacatt -s mr.mrrefChr5 263063 20 + 294540 TGTTTATGGCATTGTACATT -s simCow_chr6.simCow.chr6 401256 20 + 602619 tgttagcagcagagcagact -s simDog_chr6.simDog.chr6 391998 20 + 593897 tgttatcgacagagcacatt -s simHuman_chr6.simHuman.chr6 396481 20 + 601863 tcttagtgacacagtgcatt -s simRat_chr6.simRat.chr6 230731 20 - 647215 TGTTTATGGTATTGTACATT - -a -s simMouse_chr6.simMouse.chr6 410342 13 + 636262 AAAGTAGGGTGCT -s Anc0.Anc0refChr3 41432 13 + 222631 gaagaggGATGAT -s Anc1.Anc1refChr6 71751 13 + 197743 gaagaggGATGAT -s Anc2.Anc2refChr13 45435 13 + 96486 gaagaggGGTGAT -s mr.mrrefChr5 263083 13 + 294540 GAAGTGGGATGCT -s simCow_chr6.simCow.chr6 401348 13 + 602619 GAAGAGGGGTGAT -s simDog_chr6.simDog.chr6 392018 13 + 593897 gaggagggGTGGT -s simHuman_chr6.simHuman.chr6 396501 13 + 601863 gaagaggTATGAT -s simRat_chr6.simRat.chr6 230751 13 - 647215 GGAGTGGGATGCT - -a -s simMouse_chr6.simMouse.chr6 410355 2 + 636262 AT -s Anc0.Anc0refChr3 41451 2 + 222631 GT -s Anc1.Anc1refChr6 71770 2 + 197743 GT -s Anc2.Anc2refChr13 45454 2 + 96486 GG -s mr.mrrefChr5 263102 2 + 294540 AT -s simCow_chr6.simCow.chr6 401367 2 + 602619 GG -s simDog_chr6.simDog.chr6 392037 2 + 593897 GG -s simHuman_chr6.simHuman.chr6 396520 2 + 601863 GT -s simRat_chr6.simRat.chr6 230770 2 - 647215 AT - -a -s simMouse_chr6.simMouse.chr6 410357 106 + 636262 CCTACTAGACTATTACCACCCCAACTTGCCTGCTCATCGTCATGGTGCTCTTGGTTCTAGTGTTTCTTAGTGTCTGGGATTATGCCTGTCACTTACCTGTCTCTCT -s Anc0.Anc0refChr3 41453 99 + 222631 CTTACTTGTTTCTCACCACCACAATTTTCCTGCTCATTGTCAGA-------TGGCTCTAGTGTCCCGTGGTATTTAGGTTGATATCTGTCACTTACTTGCCTGTCA -s Anc1.Anc1refChr6 71772 99 + 197743 CTTACTTGTTTCTCACCACCACAATTTTCCTGCTCATTGTCAGA-------TGGCTCTAGTGTCCCGTGGTATTTAGGTTGATATCTGTCACTTACTTGCCTGTCA -s Anc2.Anc2refChr13 45456 99 + 96486 CTTACTTGTTTCTCACCACCATAATTTTCCTGCTCATTGACAGA-------TGGCTCTGGATTCCCGTGGTATTTAGGTTGATATTTGTCACTTACTAGCCTGCCA -s mr.mrrefChr5 263104 99 + 294540 CTTACTAGACTCTTACCACCCCAATTTGCCTGCTCATTGTCATG-------TGGTTCTAGTGTTTCTTAGTGTCTAGGATTATGCCTGTCACTTACTTGTCTCTCT -s simCow_chr6.simCow.chr6 401369 47 + 602619 CTTACTTGTTTCTCACCACCGTAATTTTCCTGCTCATTGACGGA-------TGG---------------------------------------------------- -s simDog_chr6.simDog.chr6 392039 98 + 593897 CTTACTTGCTTCTCACCAGCATAATCT-CCTGCTCATTGACAAT-------TGGCTCTGGATTCCCGTGGTATTTAGGTTGATATTTGTCACTTACTAGCCTGCCA -s simHuman_chr6.simHuman.chr6 396523 99 + 601863 TTTACTTGTTTCTCACCACCACAATTTTCCTGCTCATTGTCAGA-------TGGCTCTAGTGTCCTATGGTATTTAGGCTGATATCTATCACTTACTTGCCTATCA -s simRat_chr6.simRat.chr6 230772 80 - 647215 CTCACTAG-CTCCTACCACCCCAATTTGCCTGC-CGTTGCCA------------------------TTAGTGTCAAGGATTATGCCTGTCACCTACTTATCTCTCT - -a -s simMouse_chr6.simMouse.chr6 410463 30 + 636262 TCACAATAAGTTAGTTACTGACAGTGTGGC -s Anc0.Anc0refChr3 41552 25 + 222631 CCACCATAAGTTTTCTACTC-----GTAGT -s Anc1.Anc1refChr6 71871 30 + 197743 CCACCATAAGTTTTCTACTCACTATGTAGT -s Anc2.Anc2refChr13 45555 25 + 96486 CTGCCATGAGTTTTCCACTC-----GTAGT -s mr.mrrefChr5 263203 30 + 294540 TCACAATAAGTTAGTTACTGACTGTGTGGC -s simDog_chr6.simDog.chr6 392153 25 + 593897 CTGCCATGAGTTTTCCACTC-----GTAGT -s simHuman_chr6.simHuman.chr6 396622 30 + 601863 CCACCACAAGTTCTCTACCCACTATTTAGT -s simRat_chr6.simRat.chr6 230852 30 - 647215 TCACAATAAGTCTGTTACTGGCTGTGTGGC - -a -s simMouse_chr6.simMouse.chr6 410493 11 + 636262 TATGTGATCAC -s Anc0.Anc0refChr3 41577 11 + 222631 TATGCTATTAC -s Anc1.Anc1refChr6 71901 11 + 197743 TATGCTATTAC -s Anc2.Anc2refChr13 45580 11 + 96486 CATGCAATTAC -s mr.mrrefChr5 263233 11 + 294540 TATGTTATCAC -s simDog_chr6.simDog.chr6 392179 11 + 593897 CATGCAATTAC -s simHuman_chr6.simHuman.chr6 396652 11 + 601863 TATGCTAATAC -s simRat_chr6.simRat.chr6 230882 11 - 647215 TATGTTATAAC - -a -s simMouse_chr6.simMouse.chr6 410504 11 + 636262 AAATCTACTCA -s Anc0.Anc0refChr3 41588 11 + 222631 AAATACACTCA -s Anc1.Anc1refChr6 71912 11 + 197743 AAATACACTCA -s Anc2.Anc2refChr13 45591 11 + 96486 AAGTACAATCT -s mr.mrrefChr5 263244 11 + 294540 AAATCTACTCA -s simDog_chr6.simDog.chr6 392192 11 + 593897 AAGTACAATCT -s simHuman_chr6.simHuman.chr6 396663 11 + 601863 AAATTCACTCA -s simRat_chr6.simRat.chr6 230893 11 - 647215 AAATCTACTCA - -a -s simMouse_chr6.simMouse.chr6 410515 23 + 636262 TCTAAAAATCTGGGTTTAACACA -s Anc0.Anc0refChr3 41600 23 + 222631 TCTCAAACTCCAGATCTAACACA -s Anc1.Anc1refChr6 71924 23 + 197743 TCTCAAACTCCAGATCTAACACA -s Anc2.Anc2refChr13 45603 23 + 96486 TCTCAAACTCCAGATCTAACACA -s mr.mrrefChr5 263255 23 + 294540 TCTAAAAATCTGGGTTTAACACA -s simCow_chr6.simCow.chr6 401416 10 + 602619 -------------ACATAACATG -s simDog_chr6.simDog.chr6 392205 23 + 593897 TCTCAAACTCCAGATCCAACACA -s simHuman_chr6.simHuman.chr6 396675 23 + 601863 TCTCAAATTACAGATCTAACACA -s simRat_chr6.simRat.chr6 230904 23 - 647215 TCTAAAAATCTGGGTTTCGCACA - -a -s simMouse_chr6.simMouse.chr6 410538 5 + 636262 AAAAC -s Anc0.Anc0refChr3 41632 5 + 222631 AGCCC -s Anc1.Anc1refChr6 71956 5 + 197743 AGCCC -s Anc2.Anc2refChr13 45635 5 + 96486 AGCCC -s mr.mrrefChr5 263278 5 + 294540 AAAAC -s simCow_chr6.simCow.chr6 401435 5 + 602619 GGCCC -s simDog_chr6.simDog.chr6 392237 5 + 593897 AGCCC -s simHuman_chr6.simHuman.chr6 396707 5 + 601863 AGCCC -s simRat_chr6.simRat.chr6 230927 5 - 647215 AAAAT - -a -s simMouse_chr6.simMouse.chr6 410543 21 + 636262 CTTGCAAGTAGTTCATCATGT -s Anc0.Anc0refChr3 41637 18 + 222631 CTAGTGACTGGTT---CATGT -s Anc1.Anc1refChr6 71961 18 + 197743 CTAGTGACTGGTT---CATGT -s Anc2.Anc2refChr13 45640 18 + 96486 CTAGTGACTGGTT---CATAT -s mr.mrrefChr5 263283 20 + 294540 CTTGCAAGTAGTT-ATCATGT -s simCow_chr6.simCow.chr6 401441 18 + 602619 CTAGTGACAGTTT---TATAT -s simDog_chr6.simDog.chr6 392242 18 + 593897 CATGTAATTGGTT---CATAT -s simHuman_chr6.simHuman.chr6 396712 18 + 601863 CTAGTGACCGGCT---CATGT -s simRat_chr6.simRat.chr6 230932 13 - 647215 TTTGTAAGTGATT-------- - -a -s simMouse_chr6.simMouse.chr6 410564 1 + 636262 G -s Anc0.Anc0refChr3 41655 1 + 222631 G -s Anc1.Anc1refChr6 71979 1 + 197743 G -s Anc2.Anc2refChr13 45658 1 + 96486 G -s mr.mrrefChr5 263303 1 + 294540 G -s simCow_chr6.simCow.chr6 401459 1 + 602619 G -s simDog_chr6.simDog.chr6 392265 1 + 593897 G -s simHuman_chr6.simHuman.chr6 396730 1 + 601863 G - -a -s simMouse_chr6.simMouse.chr6 410565 7 + 636262 CTCCTGG -s Anc0.Anc0refChr3 41660 7 + 222631 ATTGTTG -s Anc1.Anc1refChr6 71984 7 + 197743 ATTGTTG -s Anc2.Anc2refChr13 45663 7 + 96486 ATTGTTG -s mr.mrrefChr5 263304 7 + 294540 CTCCTGG -s simCow_chr6.simCow.chr6 401464 7 + 602619 ATTGTTG -s simDog_chr6.simDog.chr6 392270 7 + 593897 GTTGTTG -s simHuman_chr6.simHuman.chr6 396735 7 + 601863 ATTGTTG -s simRat_chr6.simRat.chr6 416976 2 + 647215 -----GG - -a -s simMouse_chr6.simMouse.chr6 410572 11 + 636262 TCACCAGTCAT -s Anc0.Anc0refChr3 41667 11 + 222631 TAACTGTCCAT -s Anc1.Anc1refChr6 71991 11 + 197743 TAACTGTCCAT -s Anc2.Anc2refChr13 45679 11 + 96486 TAACTGTCCAT -s mr.mrrefChr5 263311 11 + 294540 TCACCAGTCAT -s simCow_chr6.simCow.chr6 401480 11 + 602619 TTGCCTTCCAT -s simDog_chr6.simDog.chr6 392286 11 + 593897 TAACTGTCCAT -s simHuman_chr6.simHuman.chr6 396742 11 + 601863 TTACAGCCCAT -s simRat_chr6.simRat.chr6 416978 11 + 647215 TCACCAGTTAT - -a -s simMouse_chr6.simMouse.chr6 410583 6 + 636262 ATTGAT -s Anc0.Anc0refChr3 41683 6 + 222631 ATCGAT -s Anc1.Anc1refChr6 72007 6 + 197743 ATCGAT -s Anc2.Anc2refChr13 45695 6 + 96486 CACAGT -s mr.mrrefChr5 263322 6 + 294540 ATTGAT -s simCow_chr6.simCow.chr6 401496 6 + 602619 CCCAGT -s simDog_chr6.simDog.chr6 392302 6 + 593897 CACAGT -s simHuman_chr6.simHuman.chr6 396758 6 + 601863 ATCGAT -s simRat_chr6.simRat.chr6 416989 6 + 647215 ATTGAT - -a -s simMouse_chr6.simMouse.chr6 410589 39 + 636262 CTAGCTTAGGGGCCCCACACAATTTTATTTAACACTAGT -s Anc0.Anc0refChr3 41689 37 + 222631 CTAGCTTAGAGGTCACCTCCAATCTGATTC-T-ACACAT -s Anc1.Anc1refChr6 72013 37 + 197743 CTAGCTTAGAGGTCACCTCCAATCTGATTC-T-ACACAT -s Anc2.Anc2refChr13 45701 37 + 96486 CTAGCTTAGAGGTCACCTCCAATCTGATGC-T-ACACAT -s mr.mrrefChr5 263328 38 + 294540 CTAGCTTAGGGGCCCCCTACAATTTTATTTAA-ACTAGT -s simCow_chr6.simCow.chr6 401517 37 + 602619 CTAGCTTAGAGGTTACCTCCAATCAGATGC-T-ACACAT -s simDog_chr6.simDog.chr6 392308 37 + 593897 TATGTTTAGAGGTCCCCTCCAATCTGATGC-T-ACACAT -s simHuman_chr6.simHuman.chr6 396764 37 + 601863 CTAGCTTAGAGGTCACCTCCAATCTGATTC-T-ACAGAT -s simRat_chr6.simRat.chr6 416995 38 + 647215 CTAGCTTAGGGGCCCCCTGCAAATTTATTTAA-ACTAGA - -a -s simMouse_chr6.simMouse.chr6 410628 12 + 636262 ATAAAAACAACT -s Anc0.Anc0refChr3 41726 9 + 222631 ATAAAAAC---T -s Anc1.Anc1refChr6 72050 9 + 197743 ATAAAAAC---T -s Anc2.Anc2refChr13 45741 9 + 96486 ATAAAAAC---T -s mr.mrrefChr5 263366 9 + 294540 ATAAAAAC---T -s simCow_chr6.simCow.chr6 401557 9 + 602619 ATAAAAAC---T -s simDog_chr6.simDog.chr6 392348 9 + 593897 CTAAAAAC---T -s simHuman_chr6.simHuman.chr6 396801 9 + 601863 ATATAAAC---T -s simRat_chr6.simRat.chr6 417033 9 + 647215 ATAAAAAC---T - -a -s simMouse_chr6.simMouse.chr6 410640 13 + 636262 CTTCCCTGTTCAC -s Anc0.Anc0refChr3 41736 13 + 222631 CTTCCTTGTTCAC -s Anc1.Anc1refChr6 72060 13 + 197743 CTTCCTTGTTCAC -s Anc2.Anc2refChr13 45751 13 + 96486 CTTCCTTATTCAC -s mr.mrrefChr5 263375 13 + 294540 CTTCCTTGTTCAC -s simCow_chr6.simCow.chr6 401567 12 + 602619 ACTCCAT-TTCAG -s simDog_chr6.simDog.chr6 392358 13 + 593897 CTTCCTTAATGAC -s simHuman_chr6.simHuman.chr6 396811 13 + 601863 CTTCCTTGTTCAC -s simRat_chr6.simRat.chr6 417042 13 + 647215 CTTCATTGTTCAC - -a -s simMouse_chr6.simMouse.chr6 410653 21 + 636262 TATCACCCAAGCATGATATTT -s Anc0.Anc0refChr3 41749 18 + 222631 AATTATC---ATATCATATTC -s Anc1.Anc1refChr6 72073 18 + 197743 AATTATC---ATATCATATTC -s Anc2.Anc2refChr13 45764 18 + 96486 AATTATC---ATACCATATTC -s mr.mrrefChr5 263388 21 + 294540 TATTACCCAAGCATGATATTT -s simCow_chr6.simCow.chr6 401579 13 + 602619 A-----C---ATACCATCTTC -s simDog_chr6.simDog.chr6 392376 16 + 593897 AATTATA---AT--CATATTC -s simHuman_chr6.simHuman.chr6 396824 18 + 601863 AATTATC---ATATCATATTC -s simRat_chr6.simRat.chr6 417055 21 + 647215 TAATACTCAACCATAATATTT - -a -s simMouse_chr6.simMouse.chr6 410674 23 + 636262 TCAAATGTTCTGTCACCATGTGC -s Anc0.Anc0refChr3 41767 23 + 222631 TCAAATGTACAGTCACTACTTAC -s Anc1.Anc1refChr6 72091 23 + 197743 TCAAATGTACAGTCACTACTTAC -s Anc2.Anc2refChr13 45782 23 + 96486 TCAGATGTACAGCCACTACTTAC -s mr.mrrefChr5 263409 23 + 294540 TCAAATGTTCTGTCACCATTTGC -s simCow_chr6.simCow.chr6 401592 23 + 602619 TCAGCAGTACAGCCACCATTCAC -s simDog_chr6.simDog.chr6 392393 23 + 593897 TAAGATGGACAGCCACTACTTAC -s simHuman_chr6.simHuman.chr6 396842 19 + 601863 TCAAATGTACAATCACAAG---- -s simRat_chr6.simRat.chr6 417076 23 + 647215 TCAAATGTTCTGGCACCATTTGC - -a -s simMouse_chr6.simMouse.chr6 410697 16 + 636262 ACCCCAACCTCTCCAG -s Anc0.Anc0refChr3 41790 16 + 222631 AGCCAACCTTCTCTGG -s Anc1.Anc1refChr6 72114 16 + 197743 AGCCAACCTTCTCTGG -s Anc2.Anc2refChr13 45806 16 + 96486 AGCCAACCTTCTCTGG -s mr.mrrefChr5 263432 16 + 294540 ACCCCAACCTCTCCAG -s simCow_chr6.simCow.chr6 401616 16 + 602619 AGCCAACCTTCTCTAT -s simDog_chr6.simDog.chr6 392417 16 + 593897 AGCCAACCTTCTTTGG -s simHuman_chr6.simHuman.chr6 396861 14 + 601863 --CCAGCCTTCTCTGG -s simRat_chr6.simRat.chr6 417099 16 + 647215 ACCCCAACCTCTCCAG - -a -s simMouse_chr6.simMouse.chr6 410713 57 + 636262 GTATTTAAACTTTCTTGAGAATCCTCACCATATCTGAGACACCATATAGACGGGGGG -s Anc0.Anc0refChr3 41806 57 + 222631 ATTGTTAAACTTTTTTGTGAATCTTCCCCATGCCTTAGACACCACATGTGTGGGAGG -s Anc1.Anc1refChr6 72130 57 + 197743 ATTGTTAAACTTTTTTGTGAATCTTCCCCATGCCTTAGACACCACATGTGTGGGAGG -s Anc2.Anc2refChr13 45822 57 + 96486 ATTGTTAAACTTTTTTGTGAATCCTCCCCATGCCTTACACACGACATGTGTGGGAGG -s mr.mrrefChr5 263448 57 + 294540 GTATTTAAACTTTCTTGAGAATCTTCACCATATCTGAGACACCATATGGACGGGGGG -s simCow_chr6.simCow.chr6 401675 56 + 602619 ATTGTTAAACTTTTA-ATGAACTCTCTCCATGTCTTAAACCCTACATGTGTGGGGGG -s simDog_chr6.simDog.chr6 392433 57 + 593897 GTTGCTAAACTATTTTGCGAATCCTCCTCATGCCTTACACATGACATGTGTGGGAGG -s simHuman_chr6.simHuman.chr6 396875 57 + 601863 ACTGTCAAACTTTTCTGTGTAACTTTGCCATGCCTTAGACACCGCATGTGTGGGAGG -s simRat_chr6.simRat.chr6 417115 55 + 647215 GTAT--AGACTTTCTTGAGAATCTTCACTGTATCTGAGCCACCATATGGACGGGGAG - -a -s simMouse_chr6.simMouse.chr6 410770 4 + 636262 AGTG -s Anc0.Anc0refChr3 41864 4 + 222631 GGTG -s Anc1.Anc1refChr6 72188 4 + 197743 GGTG -s Anc2.Anc2refChr13 45880 4 + 96486 GGTG -s mr.mrrefChr5 263506 4 + 294540 GGTG -s mr.mrrefChr5 265778 4 + 294540 GGCA -s simCow_chr6.simCow.chr6 401732 4 + 602619 GGTG -s simDog_chr6.simDog.chr6 392491 4 + 593897 GCTG -s simHuman_chr6.simHuman.chr6 396933 4 + 601863 GGTG -s simMouse_chr6.simMouse.chr6 413084 4 + 636262 GGCA -s simRat_chr6.simRat.chr6 419352 4 + 647215 GATA -s simRat_chr6.simRat.chr6 417171 4 + 647215 GGTG - -a -s simMouse_chr6.simMouse.chr6 410774 1 + 636262 C -s Anc0.Anc0refChr3 41868 1 + 222631 C -s Anc1.Anc1refChr6 72192 1 + 197743 C -s Anc2.Anc2refChr13 45884 1 + 96486 C -s mr.mrrefChr5 263510 1 + 294540 C -s mr.mrrefChr5 265782 1 + 294540 C -s simCow_chr6.simCow.chr6 401736 1 + 602619 C -s simDog_chr6.simDog.chr6 392495 1 + 593897 C -s simHuman_chr6.simHuman.chr6 396937 1 + 601863 C -s simMouse_chr6.simMouse.chr6 413093 1 + 636262 C -s simRat_chr6.simRat.chr6 419356 1 + 647215 C -s simRat_chr6.simRat.chr6 417175 1 + 647215 C - -a -s simMouse_chr6.simMouse.chr6 410775 2 + 636262 AA -s Anc0.Anc0refChr3 41869 1 + 222631 A- -s Anc1.Anc1refChr6 72193 2 + 197743 AA -s Anc2.Anc2refChr13 45885 1 + 96486 A- -s mr.mrrefChr5 263511 2 + 294540 AA -s mr.mrrefChr5 265783 2 + 294540 AA -s simCow_chr6.simCow.chr6 401737 1 + 602619 A- -s simDog_chr6.simDog.chr6 392496 1 + 593897 A- -s simHuman_chr6.simHuman.chr6 396958 2 + 601863 AA -s simMouse_chr6.simMouse.chr6 413094 2 + 636262 AA -s simRat_chr6.simRat.chr6 419357 2 + 647215 AA -s simRat_chr6.simRat.chr6 417176 2 + 647215 AA - -a -s simMouse_chr6.simMouse.chr6 410777 9 + 636262 TATTACCAG -s Anc0.Anc0refChr3 41870 9 + 222631 TACGACCTT -s Anc1.Anc1refChr6 72195 9 + 197743 TACGACCTT -s Anc2.Anc2refChr13 45886 9 + 96486 TGCGACCTT -s mr.mrrefChr5 263513 9 + 294540 TATGACCAG -s mr.mrrefChr5 265785 9 + 294540 TTTAACCCA -s simCow_chr6.simCow.chr6 401739 9 + 602619 TGTGCCGTT -s simDog_chr6.simDog.chr6 392497 9 + 593897 AGCAACCTT -s simHuman_chr6.simHuman.chr6 396960 9 + 601863 TACGACCTT -s simMouse_chr6.simMouse.chr6 413096 9 + 636262 TTTAACCCA -s simRat_chr6.simRat.chr6 419359 9 + 647215 TTTAACCCA -s simRat_chr6.simRat.chr6 417178 9 + 647215 TATGACCAG - -a -s simMouse_chr6.simMouse.chr6 410786 35 + 636262 TACCACATATATGTCTGGTGCTTGGGGGTGAAAAG -s Anc0.Anc0refChr3 41879 35 + 222631 TAGCTAGTATATGTGTGGTGCTTGGGGGTCAAAAA -s Anc1.Anc1refChr6 72204 35 + 197743 TAGCTAGTATATGTGTGGTGCTTGGGGGTCAAAAA -s Anc2.Anc2refChr13 45895 35 + 96486 TAGCTAGTAGATGTGTAGTGCATGGGGGTCAAAAT -s mr.mrrefChr5 263522 35 + 294540 TACCAAATATATGTCTGGTGCTTGGGGGTGAAAAG -s mr.mrrefChr5 265794 34 + 294540 TACCTAATATATGTGTGGTGCTTGGGGCTCATAA- -s simCow_chr6.simCow.chr6 401748 35 + 602619 TAGCCAGTACATGTGTAGTGCATGAGGGTCAACAT -s simDog_chr6.simDog.chr6 392506 35 + 593897 TAGCTGGTAGATGTATAGTGCCTGGGGGTCAAAAA -s simHuman_chr6.simHuman.chr6 396969 35 + 601863 CAGCTAGTATATATTTGGTGTGTGAGGCTCAAAAA -s simMouse_chr6.simMouse.chr6 413105 34 + 636262 TACCTAACATGTGTGTGGTGCTTGGGGCTCATGA- -s simRat_chr6.simRat.chr6 419370 34 + 647215 TACCTAATATATGTGTGGTGCGCGGGGCTCATAA- -s simRat_chr6.simRat.chr6 417187 29 + 647215 TACCAAATATGTGTGTAGTGCTTGGGGGT------ - -a -s simMouse_chr6.simMouse.chr6 410821 13 + 636262 GGTGCTTGGGGGT -s Anc0.Anc0refChr3 41914 1 + 222631 A------------ -s Anc1.Anc1refChr6 72239 13 + 197743 AGTGCTTAGGGGT -s Anc2.Anc2refChr13 45930 1 + 96486 A------------ -s mr.mrrefChr5 263557 13 + 294540 GGTGCTTGGGGGT -s mr.mrrefChr5 265828 2 + 294540 -----TT------ -s simCow_chr6.simCow.chr6 401783 1 + 602619 C------------ -s simDog_chr6.simDog.chr6 392541 1 + 593897 A------------ -s simHuman_chr6.simHuman.chr6 397012 13 + 601863 AGTGCATAGGGGT -s simMouse_chr6.simMouse.chr6 413139 2 + 636262 -----TT------ -s simRat_chr6.simRat.chr6 419404 2 + 647215 -----CT------ - -a -s simMouse_chr6.simMouse.chr6 410834 3 + 636262 CAA -s Anc1.Anc1refChr6 72252 3 + 197743 CAA -s mr.mrrefChr5 263570 3 + 294540 CAA -s simHuman_chr6.simHuman.chr6 397025 3 + 601863 CAA -s simRat_chr6.simRat.chr6 417216 3 + 647215 CAA - -a -s simMouse_chr6.simMouse.chr6 410837 2 + 636262 GA -s Anc0.Anc0refChr3 41915 2 + 222631 AA -s Anc1.Anc1refChr6 72255 2 + 197743 AA -s Anc2.Anc2refChr13 45931 2 + 96486 AA -s mr.mrrefChr5 263573 2 + 294540 AA -s mr.mrrefChr5 265830 2 + 294540 AA -s simCow_chr6.simCow.chr6 401784 2 + 602619 AA -s simDog_chr6.simDog.chr6 392542 2 + 593897 AA -s simHuman_chr6.simHuman.chr6 397028 2 + 601863 AA -s simMouse_chr6.simMouse.chr6 413141 2 + 636262 AA -s simRat_chr6.simRat.chr6 419406 2 + 647215 TA -s simRat_chr6.simRat.chr6 417219 2 + 647215 AA - -a -s simMouse_chr6.simMouse.chr6 410839 13 + 636262 GGACTATGACATA -s Anc0.Anc0refChr3 41917 13 + 222631 GGACTATAACATG -s Anc1.Anc1refChr6 72257 13 + 197743 GGACTATAACATG -s Anc2.Anc2refChr13 45933 13 + 96486 GGACTATAACATG -s mr.mrrefChr5 263575 13 + 294540 GGACTATGACATA -s mr.mrrefChr5 265832 13 + 294540 GGAATGTGACATG -s simCow_chr6.simCow.chr6 401786 13 + 602619 AGACTATAACAAG -s simDog_chr6.simDog.chr6 392544 13 + 593897 GGACTGTAACATG -s simHuman_chr6.simHuman.chr6 397034 13 + 601863 GGACTATACCATG -s simMouse_chr6.simMouse.chr6 413143 13 + 636262 GGAATGTGACATG -s simRat_chr6.simRat.chr6 419408 13 + 647215 GGTATATGACATG -s simRat_chr6.simRat.chr6 417221 13 + 647215 AGACCATGACATA - -a -s simMouse_chr6.simMouse.chr6 410852 34 + 636262 GGACCTTGATAACAATGATTAGTTGACCAATAAT -s Anc0.Anc0refChr3 41931 34 + 222631 GGACCTTGACAACACTGATTAGTTGACCAATAAT -s Anc1.Anc1refChr6 72271 34 + 197743 GGACCTTGACAACACTGATTAGTTGACCAATAAT -s Anc2.Anc2refChr13 45947 34 + 96486 GGACCTTGACACCACTGATTAGTTGACCAATAAT -s mr.mrrefChr5 263588 34 + 294540 GGACCTTGATAACAATGATTAGTTGACCAATAAT -s mr.mrrefChr5 265846 34 + 294540 AGACCCCGACATCACTGATTCATTGACCAATAAT -s simCow_chr6.simCow.chr6 401800 33 + 602619 GGACCTTGACACCTGTGCCT-GTTAACCAATAAT -s simDog_chr6.simDog.chr6 392558 34 + 593897 GAACTTTGACACCACTGATTAGTTGACCAATAAC -s simHuman_chr6.simHuman.chr6 397048 34 + 601863 GGCCCTTGATAACACTGATTAGTTGACCAATAGT -s simMouse_chr6.simMouse.chr6 413157 33 + 636262 AGACCCCGACATCACTGATTCATTGACCAATAA- -s simRat_chr6.simRat.chr6 419422 34 + 647215 AGACCCCAACAGCCCTAATCCATGGACCAATAAT -s simRat_chr6.simRat.chr6 417234 34 + 647215 TGACCTTGATAACAATGGTTAGTTGACCAATAAT - -a -s simMouse_chr6.simMouse.chr6 410886 1 + 636262 T -s Anc0.Anc0refChr3 41965 1 + 222631 T -s Anc1.Anc1refChr6 72305 1 + 197743 T -s Anc2.Anc2refChr13 45981 1 + 96486 T -s mr.mrrefChr5 263622 1 + 294540 T -s mr.mrrefChr5 265880 1 + 294540 T -s simCow_chr6.simCow.chr6 401842 1 + 602619 G -s simDog_chr6.simDog.chr6 392592 1 + 593897 T -s simHuman_chr6.simHuman.chr6 397082 1 + 601863 T -s simRat_chr6.simRat.chr6 419456 1 + 647215 T -s simRat_chr6.simRat.chr6 417268 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 410887 4 + 636262 GAAG -s Anc0.Anc0refChr3 41984 4 + 222631 CAAG -s Anc1.Anc1refChr6 72324 4 + 197743 CAAG -s Anc2.Anc2refChr13 46000 4 + 96486 CAAG -s mr.mrrefChr5 263623 4 + 294540 GAAG -s mr.mrrefChr5 265881 4 + 294540 CAAG -s simCow_chr6.simCow.chr6 401861 4 + 602619 CAAG -s simDog_chr6.simDog.chr6 392610 4 + 593897 CAAG -s simHuman_chr6.simHuman.chr6 397101 4 + 601863 CAAG -s simMouse_chr6.simMouse.chr6 413190 1 + 636262 ---G -s simRat_chr6.simRat.chr6 419457 4 + 647215 CAAG -s simRat_chr6.simRat.chr6 417269 4 + 647215 GAGG - -a -s simMouse_chr6.simMouse.chr6 410891 21 + 636262 AGGTCAAAGTGTGGAGTTGAG -s Anc0.Anc0refChr3 41989 21 + 222631 AAGTGAAAGTGTGGAGTTAAG -s Anc1.Anc1refChr6 72329 21 + 197743 AAGTGAAAGTGTGGAGTTAAG -s Anc2.Anc2refChr13 46005 21 + 96486 AAGTGAAAGTGTGGAGTTAAG -s mr.mrrefChr5 263628 21 + 294540 AGGTCAAAGTGTGGTGTTAAG -s mr.mrrefChr5 265887 21 + 294540 AGGTGAAAGTGTGGAGTTAAG -s simCow_chr6.simCow.chr6 401866 21 + 602619 GAGTGAACGTGCGGAGTCAAA -s simDog_chr6.simDog.chr6 392615 21 + 593897 AAGTGAAAGGGTGGAGTTAAG -s simHuman_chr6.simHuman.chr6 397106 21 + 601863 CAGTAAAAGTATGGTGTTAAG -s simMouse_chr6.simMouse.chr6 413193 20 + 636262 GGGTGGAAATGTGGAGTTAG- -s simRat_chr6.simRat.chr6 419463 21 + 647215 AGGTGAATGTGTGGAGTTAAG -s simRat_chr6.simRat.chr6 417274 21 + 647215 AGGTCAAAGTGTGGTCTTAAG - -a -s simMouse_chr6.simMouse.chr6 410912 1 + 636262 G -s mr.mrrefChr5 263649 1 + 294540 G -s simRat_chr6.simRat.chr6 417295 1 + 647215 G - -a -s simMouse_chr6.simMouse.chr6 410913 55 + 636262 ATTGGCCTTTTGTGCCAAGGACATGGGAAAAAGCAACCTCTTAAGAACAGAAACA -s Anc0.Anc0refChr3 42010 55 + 222631 ATTGGCCACATGTCTTAAGGACCTCAGAAAAAACAACCTCTTGAGAACAGAAACA -s Anc1.Anc1refChr6 72350 55 + 197743 ATTGGCCACATGTCTTAAGGACCTCAGAAAAAACAACCTCTTGAGAACAGAAACA -s Anc2.Anc2refChr13 46026 55 + 96486 ATTGGCCACATGTCTTAAGGACCTCAGAAAAAACAACCTCTTGAGAACAGAAACA -s mr.mrrefChr5 263650 55 + 294540 ATTGGCCTTTTGTCTTAAGGACATGGGAAAAAGCAACCTCTTAAGAACAGAAACA -s mr.mrrefChr5 265908 55 + 294540 ATTGGACACTTGTTTTAAGGACTTGTTACAAAGTAACCTCTTGAAACTAGATAGG -s simCow_chr6.simCow.chr6 401887 55 + 602619 ATTAGCCACATGTCTTCAGGACCTCAAAAGACACAACTCCTTGAGAACAAAAGCA -s simDog_chr6.simDog.chr6 392636 55 + 593897 AGTGGCCACATATCTTAAGGACCTCAGAAAAAACAACCTCTTGACAACAGAAACA -s simHuman_chr6.simHuman.chr6 397127 53 + 601863 ATTGGCCACAGGTCTTAAGGCCCTCAGAAAAAACAACATCCTGCGAACAGATA-- -s simMouse_chr6.simMouse.chr6 413213 53 + 636262 --TGGACACTTGTTTTAAGGACTTGTTACAAAGTAACCTCTTGAAACTAGATAGG -s simRat_chr6.simRat.chr6 419484 55 + 647215 ATTGGACACTTGTTTTAAGGACTTGTTACAAAGTAACGTCTTGAGACTATATAGG -s simRat_chr6.simRat.chr6 417296 55 + 647215 ATTCGCCTTTTGTCTTAAAGACTTGGGAAAAAGCAACCTCTTAAGAACAGAAACA - -a -s simMouse_chr6.simMouse.chr6 410968 6 + 636262 CAAACA -s Anc0.Anc0refChr3 42065 5 + 222631 TGAA-G -s Anc1.Anc1refChr6 72405 5 + 197743 TGAA-G -s Anc2.Anc2refChr13 46081 5 + 96486 TGAA-G -s mr.mrrefChr5 263705 6 + 294540 CAAACA -s simCow_chr6.simCow.chr6 401942 5 + 602619 TTAA-G -s simDog_chr6.simDog.chr6 392691 5 + 593897 TGAA-G -s simRat_chr6.simRat.chr6 417351 6 + 647215 CAAACA - -a -s simMouse_chr6.simMouse.chr6 410974 18 + 636262 GAATAAACTTCTGCATGA -s Anc0.Anc0refChr3 42070 18 + 222631 GAAAAAACTCCCAAGTAA -s Anc1.Anc1refChr6 72410 18 + 197743 GAAAAAACTCCCAAGTAA -s Anc2.Anc2refChr13 46086 18 + 96486 GAAAAAACTCCCTAGTAA -s mr.mrrefChr5 263711 18 + 294540 GAATAAACTTCTGAATAA -s mr.mrrefChr5 265963 18 + 294540 GAATACACTCCCACATAA -s simCow_chr6.simCow.chr6 401948 18 + 602619 GAAAATACTCCCTAGTAA -s simDog_chr6.simDog.chr6 392696 18 + 593897 GAAAAAACTCCTTAGTAA -s simHuman_chr6.simHuman.chr6 397180 16 + 601863 --AAAAACTCCCAAGTAA -s simMouse_chr6.simMouse.chr6 413266 18 + 636262 GAATACACTCCCACATAA -s simRat_chr6.simRat.chr6 419539 18 + 647215 GAACACACTCCCACATAA -s simRat_chr6.simRat.chr6 417357 18 + 647215 GAATAAACTTCTGAATAA - -a -s simMouse_chr6.simMouse.chr6 410992 8 + 636262 AAAGTCAT -s Anc0.Anc0refChr3 42088 8 + 222631 AAAGACAT -s Anc1.Anc1refChr6 72428 8 + 197743 AAAGACAT -s Anc2.Anc2refChr13 46104 8 + 96486 AAAGCCAT -s mr.mrrefChr5 263729 8 + 294540 AAAGTCAT -s mr.mrrefChr5 265981 8 + 294540 AGAGATAC -s simCow_chr6.simCow.chr6 401966 8 + 602619 AAAGCCAT -s simDog_chr6.simDog.chr6 392714 8 + 593897 AGAGCCAT -s simHuman_chr6.simHuman.chr6 397196 8 + 601863 AAAGACAT -s simMouse_chr6.simMouse.chr6 413284 8 + 636262 AGAGATCC -s simRat_chr6.simRat.chr6 419614 8 + 647215 AGACAGAC -s simRat_chr6.simRat.chr6 417375 8 + 647215 AAAGTCAT - -a -s simMouse_chr6.simMouse.chr6 411000 18 + 636262 TTGGTAAGGATACTGGAG -s Anc0.Anc0refChr3 42096 18 + 222631 CTGGTAATGATTCTGGAG -s Anc1.Anc1refChr6 72436 18 + 197743 CTGGTAATGATTCTGGAG -s Anc2.Anc2refChr13 46112 18 + 96486 CTGGTAATGATTCTGGCA -s mr.mrrefChr5 263737 18 + 294540 CTGGTAAGGATACTGGAG -s simCow_chr6.simCow.chr6 401974 18 + 602619 CTGGTAATGATACTGCCC -s simDog_chr6.simDog.chr6 392722 18 + 593897 CTGGTACTAATTTTGGCA -s simHuman_chr6.simHuman.chr6 397204 18 + 601863 CTTGTAATGATTCAGGAG -s simRat_chr6.simRat.chr6 417383 18 + 647215 CTGGTAAGGATACTGGAA - -a -s simMouse_chr6.simMouse.chr6 411018 6 + 636262 TAAGGG -s Anc0.Anc0refChr3 42115 6 + 222631 TTAGGA -s Anc1.Anc1refChr6 72455 6 + 197743 TTAGGA -s Anc2.Anc2refChr13 46131 6 + 96486 TTAGGA -s mr.mrrefChr5 263755 6 + 294540 TAAGGG -s simCow_chr6.simCow.chr6 401993 6 + 602619 TTAGGA -s simDog_chr6.simDog.chr6 392741 6 + 593897 CTAGGA -s simHuman_chr6.simHuman.chr6 397223 6 + 601863 TTATGA -s simRat_chr6.simRat.chr6 417401 6 + 647215 TAAGGG - -a -s simMouse_chr6.simMouse.chr6 411024 3 + 636262 GTC -s Anc0.Anc0refChr3 42121 3 + 222631 GAC -s Anc1.Anc1refChr6 72461 3 + 197743 GAC -s Anc2.Anc2refChr13 46137 3 + 96486 GAC -s mr.mrrefChr5 263761 3 + 294540 GTC -s simCow_chr6.simCow.chr6 402000 3 + 602619 GAC -s simDog_chr6.simDog.chr6 392747 3 + 593897 GAC -s simHuman_chr6.simHuman.chr6 397229 3 + 601863 GAT -s simRat_chr6.simRat.chr6 417407 3 + 647215 GGC - -a -s simMouse_chr6.simMouse.chr6 411027 4 + 636262 ACAG -s Anc0.Anc0refChr3 42124 4 + 222631 AAAA -s Anc1.Anc1refChr6 72464 4 + 197743 AAAA -s Anc2.Anc2refChr13 46140 4 + 96486 AAAA -s mr.mrrefChr5 263764 4 + 294540 AAAA -s simCow_chr6.simCow.chr6 402003 4 + 602619 AAAA -s simDog_chr6.simDog.chr6 392750 4 + 593897 AAAA -s simHuman_chr6.simHuman.chr6 397235 4 + 601863 AAAA -s simRat_chr6.simRat.chr6 417410 4 + 647215 AAAA - -a -s simMouse_chr6.simMouse.chr6 411031 1 + 636262 A -s Anc0.Anc0refChr3 42128 1 + 222631 A -s Anc1.Anc1refChr6 72468 1 + 197743 A -s Anc2.Anc2refChr13 46144 1 + 96486 A -s mr.mrrefChr5 263768 1 + 294540 A -s mr.mrrefChr5 265989 1 + 294540 A -s simCow_chr6.simCow.chr6 402007 1 + 602619 A -s simDog_chr6.simDog.chr6 392754 1 + 593897 A -s simHuman_chr6.simHuman.chr6 397239 1 + 601863 A -s simMouse_chr6.simMouse.chr6 413292 1 + 636262 G -s simRat_chr6.simRat.chr6 419622 1 + 647215 A -s simRat_chr6.simRat.chr6 417414 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 411032 21 + 636262 GGAGTGCTGGGTGCTATCCCG -s Anc0.Anc0refChr3 42129 21 + 222631 GGAGCACTGGATGCTCCTTCC -s Anc1.Anc1refChr6 72469 21 + 197743 GGAGCACTGGATGCTCCTTCC -s Anc2.Anc2refChr13 46145 21 + 96486 GGAGCACTGTATGCCCCTTCC -s mr.mrrefChr5 263769 21 + 294540 GGAGTACTGGATGCTATCCCC -s mr.mrrefChr5 265990 21 + 294540 GGTGCACTTGATGCTACTCCC -s simCow_chr6.simCow.chr6 402009 21 + 602619 GGAGCACTGGATGTCACTTCC -s simDog_chr6.simDog.chr6 392755 21 + 593897 GGAACACTGTGTGCCCCTTCC -s simHuman_chr6.simHuman.chr6 397240 21 + 601863 GGAGCAATTCATGCACATTCC -s simMouse_chr6.simMouse.chr6 413293 21 + 636262 GTTGCACCTGAAACTACTCCC -s simRat_chr6.simRat.chr6 419623 21 + 647215 GGGGAACTCAATGCTACTCCC -s simRat_chr6.simRat.chr6 417415 21 + 647215 GCAGTACTGGATGCTACCCCC - -a -s simMouse_chr6.simMouse.chr6 411053 6 + 636262 CATATG -s Anc0.Anc0refChr3 42150 6 + 222631 CATATG -s Anc1.Anc1refChr6 72490 6 + 197743 CATATG -s Anc2.Anc2refChr13 46166 6 + 96486 CATATG -s mr.mrrefChr5 263790 6 + 294540 CATATG -s mr.mrrefChr5 266011 6 + 294540 CATCTA -s simCow_chr6.simCow.chr6 402030 6 + 602619 CACATA -s simDog_chr6.simDog.chr6 392776 6 + 593897 CATATG -s simHuman_chr6.simHuman.chr6 397261 6 + 601863 CATATG -s simMouse_chr6.simMouse.chr6 413314 6 + 636262 CATCTA -s simRat_chr6.simRat.chr6 417436 6 + 647215 CATATG - -a -s simMouse_chr6.simMouse.chr6 411059 26 + 636262 TAAGCTCCCTCTTATGACTTTGCTGA -s Anc0.Anc0refChr3 42156 26 + 222631 TCAGCTCCCTCTCTAGACTTTGCTGA -s Anc1.Anc1refChr6 72496 26 + 197743 TCAGCTCCCTCTCTAGACTTTGCTGA -s Anc2.Anc2refChr13 46172 26 + 96486 TCAACCACCTCTCTAGACTTTGCTAA -s mr.mrrefChr5 263796 26 + 294540 TAAGCTCCCTCTTAAGACTTTGCTGA -s mr.mrrefChr5 266017 26 + 294540 TCACCTCCCTCTTTTTACTTTGCTCA -s simCow_chr6.simCow.chr6 402036 26 + 602619 TCACCCACCTCTCTAGACTTTGCTAA -s simDog_chr6.simDog.chr6 392782 26 + 593897 TCGACCACCTCTTTAGACTTTGCTAA -s simHuman_chr6.simHuman.chr6 397267 26 + 601863 TCAGTTGCCTCTCTAGACTTGGCTGA -s simMouse_chr6.simMouse.chr6 413320 26 + 636262 TCACCTCCCGATTTTTACTTTGCTCA -s simRat_chr6.simRat.chr6 419644 26 + 647215 TCACCTCTTTCTTTTCATTTTGCTCA -s simRat_chr6.simRat.chr6 417442 23 + 647215 TA---TCCCTCTTAAGACTTAGCTGA - -a -s simMouse_chr6.simMouse.chr6 411085 9 + 636262 GAAAAAAAC -s Anc0.Anc0refChr3 42182 9 + 222631 GTGAAGGAC -s Anc1.Anc1refChr6 72522 9 + 197743 GTGAAGGAC -s Anc2.Anc2refChr13 46199 9 + 96486 GTGCAGGAC -s mr.mrrefChr5 263822 9 + 294540 GTAAAGGAC -s mr.mrrefChr5 266043 9 + 294540 GTGAAGGGC -s simCow_chr6.simCow.chr6 402063 9 + 602619 GTGGAGGAC -s simDog_chr6.simDog.chr6 392809 9 + 593897 GTGCAGGGT -s simHuman_chr6.simHuman.chr6 397293 9 + 601863 GTGAAGGAC -s simMouse_chr6.simMouse.chr6 413346 9 + 636262 GTAAAGGAC -s simRat_chr6.simRat.chr6 419670 9 + 647215 GTGAAGGGC -s simRat_chr6.simRat.chr6 417465 9 + 647215 GTAAAGGAC - -a -s simMouse_chr6.simMouse.chr6 411094 3 + 636262 CAC -s Anc0.Anc0refChr3 42191 3 + 222631 CAC -s Anc1.Anc1refChr6 72531 3 + 197743 CAC -s Anc2.Anc2refChr13 46208 3 + 96486 TAC -s mr.mrrefChr5 263831 3 + 294540 CAC -s mr.mrrefChr5 266052 3 + 294540 CAC -s simCow_chr6.simCow.chr6 402072 3 + 602619 AAC -s simDog_chr6.simDog.chr6 392818 3 + 593897 TAC -s simHuman_chr6.simHuman.chr6 397302 3 + 601863 CAC -s simMouse_chr6.simMouse.chr6 413355 3 + 636262 CAC -s simRat_chr6.simRat.chr6 417474 3 + 647215 CAC - -a -s simMouse_chr6.simMouse.chr6 411097 5 + 636262 ACATT -s Anc0.Anc0refChr3 42197 5 + 222631 ACATT -s Anc1.Anc1refChr6 72539 5 + 197743 ACATT -s Anc2.Anc2refChr13 46214 5 + 96486 ACACT -s mr.mrrefChr5 263835 5 + 294540 ACATT -s mr.mrrefChr5 266060 5 + 294540 ACATT -s simCow_chr6.simCow.chr6 402078 5 + 602619 ACACT -s simDog_chr6.simDog.chr6 392824 5 + 593897 ATGCT -s simHuman_chr6.simHuman.chr6 397310 5 + 601863 ATTTT -s simMouse_chr6.simMouse.chr6 413363 5 + 636262 ACATT -s simRat_chr6.simRat.chr6 419684 5 + 647215 ACATT -s simRat_chr6.simRat.chr6 417478 5 + 647215 ACATT - -a -s simMouse_chr6.simMouse.chr6 411102 48 + 636262 GTTAGCCTCACTCTGCCTTTAGTAAAGACTGTGCCATAATAAGGCCCT -s Anc0.Anc0refChr3 42202 48 + 222631 GTTAGCCTCACTCAACCTTTAGTAAGGTCTGTGCCATACCAAGGTCCT -s Anc1.Anc1refChr6 72544 48 + 197743 GTTAGCCTCACTCAACCTTTAGTAAGGTCTGTGCCATACCAAGGTCCT -s Anc2.Anc2refChr13 46219 48 + 96486 GTTAGCCTCACTCAACCTTTAGTGAGGTCTGTGCCATACCAAGGTCTT -s mr.mrrefChr5 263840 48 + 294540 GTTAGCCTCACTCTGCCTTTAGTAAAGACTGTGCCATAATAAGGCCCT -s mr.mrrefChr5 266065 48 + 294540 GTTAGTCTTACTCAACCTATAGCACAGTCTGTGCTACAATGAGGGCCT -s simCow_chr6.simCow.chr6 402083 48 + 602619 GATAGCCTCACTCAACATTTATTGAGGTCTGTGCCAGAAGTGTGTCTT -s simDog_chr6.simDog.chr6 392829 44 + 593897 GTTAGCCTCGCTCA--CTTTAGTGAGATCTGTGCTGTACCAAGTCC-- -s simHuman_chr6.simHuman.chr6 397316 48 + 601863 GTTAGCCTCACTCAACCTTTAGCAAGGTCTCTACCATACCAAGGTCCT -s simMouse_chr6.simMouse.chr6 413368 48 + 636262 GCTAGTCTTACTCGACCTATAGCACAGCCTATGCCACAATGAGGGCCT -s simRat_chr6.simRat.chr6 419689 48 + 647215 GTTAGGGTTACTCAACCTATAGCACAGTCTGTGCTACAATGAGGACCT -s simRat_chr6.simRat.chr6 417483 48 + 647215 GTTAGCCTCGCTCTGCCTTTAGTAAAGACTGTGCCATAATAAGGCCCT - -a -s simMouse_chr6.simMouse.chr6 411150 2 + 636262 AA -s Anc0.Anc0refChr3 42250 2 + 222631 TA -s Anc1.Anc1refChr6 72592 2 + 197743 TA -s Anc2.Anc2refChr13 46267 2 + 96486 TA -s mr.mrrefChr5 263888 2 + 294540 TA -s mr.mrrefChr5 266113 2 + 294540 GA -s simCow_chr6.simCow.chr6 402131 2 + 602619 TA -s simHuman_chr6.simHuman.chr6 397364 2 + 601863 TA -s simMouse_chr6.simMouse.chr6 413416 2 + 636262 GA -s simRat_chr6.simRat.chr6 419740 2 + 647215 GA -s simRat_chr6.simRat.chr6 417531 2 + 647215 TA - -a -s simMouse_chr6.simMouse.chr6 411152 3 + 636262 CCG -s Anc0.Anc0refChr3 42252 3 + 222631 CCA -s Anc1.Anc1refChr6 72594 3 + 197743 CCA -s Anc2.Anc2refChr13 46269 3 + 96486 CGC -s mr.mrrefChr5 263890 3 + 294540 CCA -s simCow_chr6.simCow.chr6 402133 3 + 602619 CGC -s simHuman_chr6.simHuman.chr6 397366 3 + 601863 CCA -s simRat_chr6.simRat.chr6 417533 3 + 647215 CCA - -a -s simMouse_chr6.simMouse.chr6 411155 14 + 636262 TGGGATGGTTTCTT -s Anc0.Anc0refChr3 42255 14 + 222631 TGGGATGCTTTCTC -s Anc1.Anc1refChr6 72597 14 + 197743 TGGGATGCTTTCTC -s Anc2.Anc2refChr13 46272 14 + 96486 TGACAGCCTCTCTC -s mr.mrrefChr5 263893 14 + 294540 TGGGATGGTTTCTT -s mr.mrrefChr5 266115 14 + 294540 TGGGATGCTTTCTT -s simCow_chr6.simCow.chr6 402136 14 + 602619 TGACAGCCTCACTC -s simDog_chr6.simDog.chr6 392873 4 + 593897 ----------TCCT -s simHuman_chr6.simHuman.chr6 397369 14 + 601863 TGGAATTGTTTCTC -s simMouse_chr6.simMouse.chr6 413418 14 + 636262 TGGGATGCTTTCTT -s simRat_chr6.simRat.chr6 419742 14 + 647215 TGGGATGCTTTCTT -s simRat_chr6.simRat.chr6 417536 14 + 647215 TAGGATGGTTTTTT - -a -s simMouse_chr6.simMouse.chr6 411169 20 + 636262 GAGACCTGAGTGAGGAGTGC -s Anc0.Anc0refChr3 42269 20 + 222631 GAGATCTGAGTAAGAAGTGT -s Anc1.Anc1refChr6 72611 20 + 197743 GAGATCTGAGTAAGAAGTGT -s Anc2.Anc2refChr13 46286 20 + 96486 GAGTTCCCAGTAAGAAGTGT -s mr.mrrefChr5 263907 20 + 294540 GGGACCTGAGTGAGGAGTGC -s mr.mrrefChr5 266129 20 + 294540 GAGACCTGAGTAAGGAGTGC -s simCow_chr6.simCow.chr6 402160 20 + 602619 GAGGTCTGTGCAAGAAGTGT -s simDog_chr6.simDog.chr6 392877 20 + 593897 GAGTACCCAGTAAGAAGTGT -s simHuman_chr6.simHuman.chr6 397383 20 + 601863 GGGCTGAAAGTAAGAAGTGT -s simMouse_chr6.simMouse.chr6 413432 20 + 636262 AAGACCTGGACAAGGAGTAC -s simRat_chr6.simRat.chr6 419756 20 + 647215 GAGACCTGAGTGAGGAGTGC -s simRat_chr6.simRat.chr6 417550 20 + 647215 GGGACCTGAGTGAGGAGTGC - -a -s simMouse_chr6.simMouse.chr6 411189 12 + 636262 AATGATCCATAG -s Anc0.Anc0refChr3 42289 12 + 222631 AAAAATCCATAG -s Anc1.Anc1refChr6 72631 12 + 197743 AAAAATCCATAG -s Anc2.Anc2refChr13 46306 12 + 96486 AAAAATCCATAG -s mr.mrrefChr5 263927 12 + 294540 AATGATCCATAG -s mr.mrrefChr5 266149 12 + 294540 AACAATCTACAG -s simCow_chr6.simCow.chr6 402184 12 + 602619 AAAAATCCATAG -s simDog_chr6.simDog.chr6 392897 12 + 593897 AAAAATCCATAG -s simHuman_chr6.simHuman.chr6 397403 12 + 601863 ACAGATCTACAG -s simMouse_chr6.simMouse.chr6 413452 12 + 636262 AACAATCTACAG -s simRat_chr6.simRat.chr6 419776 12 + 647215 AGCAATCTACAG -s simRat_chr6.simRat.chr6 417570 12 + 647215 AGTGATCCATAG - -a -s simMouse_chr6.simMouse.chr6 411201 5 + 636262 ATGGA -s Anc0.Anc0refChr3 42303 5 + 222631 ATGAA -s Anc1.Anc1refChr6 72645 5 + 197743 ATGAA -s Anc2.Anc2refChr13 46320 5 + 96486 ATGAA -s mr.mrrefChr5 263939 5 + 294540 ATGGA -s mr.mrrefChr5 266161 5 + 294540 ATGAA -s simCow_chr6.simCow.chr6 402198 5 + 602619 AAAGA -s simDog_chr6.simDog.chr6 392911 5 + 593897 ATGAA -s simHuman_chr6.simHuman.chr6 397417 5 + 601863 ATGAA -s simMouse_chr6.simMouse.chr6 413464 5 + 636262 ATGAA -s simRat_chr6.simRat.chr6 419788 5 + 647215 ATGAA -s simRat_chr6.simRat.chr6 417582 5 + 647215 ATGGA - -a -s simMouse_chr6.simMouse.chr6 411206 29 + 636262 ACACAATGATCTAAGGGTAATAGATCCTT -s Anc0.Anc0refChr3 42309 4 + 222631 CCA-------------------------T -s Anc1.Anc1refChr6 72651 29 + 197743 CCACAATGACCTAAGGATAAGTGATCCAT -s Anc2.Anc2refChr13 46326 4 + 96486 CCA-------------------------T -s mr.mrrefChr5 263944 29 + 294540 ACACAATGATCTAAGGGTAAGAGATCCTT -s mr.mrrefChr5 266166 29 + 294540 CCGCAGTGACCTAATGATAAATAATCCAT -s simCow_chr6.simCow.chr6 402204 4 + 602619 CCA-------------------------T -s simDog_chr6.simDog.chr6 392917 4 + 593897 CCA-------------------------T -s simHuman_chr6.simHuman.chr6 397423 11 + 601863 CCATGATGACC------------------ -s simMouse_chr6.simMouse.chr6 413469 29 + 636262 CCGCAGTGACCTAATGATAAATAATCCAT -s simRat_chr6.simRat.chr6 419793 29 + 647215 CCACGATGACCTAATGGCAAATGATCCAT -s simRat_chr6.simRat.chr6 417587 29 + 647215 GCATAAAGATCTAATGGTAAGAGATCCTT - -a -s simMouse_chr6.simMouse.chr6 411235 4 + 636262 GTTG -s Anc0.Anc0refChr3 42313 4 + 222631 GATG -s Anc1.Anc1refChr6 72680 4 + 197743 GATG -s Anc2.Anc2refChr13 46330 4 + 96486 GATG -s mr.mrrefChr5 263973 4 + 294540 GTTG -s mr.mrrefChr5 266209 4 + 294540 GATG -s simCow_chr6.simCow.chr6 402208 4 + 602619 GGCG -s simDog_chr6.simDog.chr6 392921 4 + 593897 GATG -s simMouse_chr6.simMouse.chr6 413512 4 + 636262 GATG -s simRat_chr6.simRat.chr6 419836 4 + 647215 GATG -s simRat_chr6.simRat.chr6 417616 4 + 647215 GATG - -a -s simMouse_chr6.simMouse.chr6 411239 39 + 636262 TAATGGTATCACCTAATAGGCAGTTTTACCTTCTATGAG -s Anc0.Anc0refChr3 42317 39 + 222631 TAATGGTATTAGCTAACAGGTAGGTTCACATTCTATGGG -s Anc1.Anc1refChr6 72684 39 + 197743 TAATGGTATTAGCTAACAGGTAGGTTCACATTCTATGGG -s Anc2.Anc2refChr13 46334 39 + 96486 TCATGGCATTAGCTATCTGGTTGGTTCACAGTCCACACG -s mr.mrrefChr5 263977 39 + 294540 TAATGGTATCACCTAATAGGCAGTTTTACCTTCTATGAG -s mr.mrrefChr5 266213 39 + 294540 TAACAGTATTAGCTAACAGTTAGGTTCACATTCTATGGG -s simCow_chr6.simCow.chr6 402306 39 + 602619 TTATGGTATCACCTAATATGTAGGTTCATACTGTACAGG -s simDog_chr6.simDog.chr6 392925 39 + 593897 TCATGGCATTAGCTATCTGGTTGGTTCACAGTCCACACA -s simHuman_chr6.simHuman.chr6 397434 5 + 601863 ----------------------------------ATGGG -s simMouse_chr6.simMouse.chr6 413516 39 + 636262 TAACAGTATCAGCTAACATTTAGGTTCACATTCTATGGG -s simRat_chr6.simRat.chr6 419840 39 + 647215 TAACAGTATTAGCTAATAGTCAAGTTCACATTCTATGGG -s simRat_chr6.simRat.chr6 417620 39 + 647215 TATTGGTATCAGCTAATAGGCAGTGTCACCTTCTATGGG - -a -s simMouse_chr6.simMouse.chr6 411278 1 + 636262 C -s Anc0.Anc0refChr3 42356 1 + 222631 T -s Anc1.Anc1refChr6 72723 1 + 197743 T -s Anc2.Anc2refChr13 46373 1 + 96486 T -s mr.mrrefChr5 264016 1 + 294540 C -s mr.mrrefChr5 266257 1 + 294540 T -s simCow_chr6.simCow.chr6 402345 1 + 602619 C -s simDog_chr6.simDog.chr6 392964 1 + 593897 T -s simHuman_chr6.simHuman.chr6 397439 1 + 601863 T -s simMouse_chr6.simMouse.chr6 413560 1 + 636262 T -s simRat_chr6.simRat.chr6 419884 1 + 647215 T -s simRat_chr6.simRat.chr6 417659 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 411279 1 + 636262 A -s Anc0.Anc0refChr3 42357 1 + 222631 A -s Anc1.Anc1refChr6 72724 1 + 197743 A -s Anc2.Anc2refChr13 46374 1 + 96486 A -s mr.mrrefChr5 264017 1 + 294540 A -s mr.mrrefChr5 266258 1 + 294540 A -s simCow_chr6.simCow.chr6 402346 1 + 602619 A -s simDog_chr6.simDog.chr6 392965 1 + 593897 A -s simHuman_chr6.simHuman.chr6 397440 1 + 601863 A -s simMouse_chr6.simMouse.chr6 413561 1 + 636262 A -s simRat_chr6.simRat.chr6 417660 1 + 647215 C - -a -s simMouse_chr6.simMouse.chr6 411280 9 + 636262 TATGCCTTA -s Anc0.Anc0refChr3 42358 4 + 222631 TGC-----G -s Anc1.Anc1refChr6 72725 4 + 197743 TGC-----G -s Anc2.Anc2refChr13 46375 4 + 96486 TGC-----G -s mr.mrrefChr5 264018 4 + 294540 TAT-----A -s mr.mrrefChr5 266259 4 + 294540 CAT-----G -s simCow_chr6.simCow.chr6 402347 4 + 602619 TGT-----G -s simDog_chr6.simDog.chr6 392966 4 + 593897 CGC-----G -s simHuman_chr6.simHuman.chr6 397441 4 + 601863 TGC-----G -s simMouse_chr6.simMouse.chr6 413562 4 + 636262 TAT-----G -s simRat_chr6.simRat.chr6 419885 4 + 647215 CAT-----G -s simRat_chr6.simRat.chr6 417661 3 + 647215 TCT------ - -a -s simMouse_chr6.simMouse.chr6 411289 28 + 636262 CCAAAAAAGCATAGAACTGTGTATAAAC -s Anc0.Anc0refChr3 42364 28 + 222631 ACAAAAAGGCACAGAACTGTGTGTTAAC -s Anc1.Anc1refChr6 72731 28 + 197743 ACAAAAAGGCACAGAACTGTGTGTTAAC -s Anc2.Anc2refChr13 46381 28 + 96486 ACATTAAGGCACAGAACTGTGTGTTAAC -s mr.mrrefChr5 264022 28 + 294540 CCAAAAAAGCATAGAACTGTGTATTAAC -s mr.mrrefChr5 266263 28 + 294540 ATAAATTAAGGGGGCATCATGTGTCAAC -s simCow_chr6.simCow.chr6 402353 16 + 602619 AGATTAAGCCAC------------TGAC -s simDog_chr6.simDog.chr6 392972 28 + 593897 ACATTAAGGCACAGAACTGTGTGTTAAC -s simHuman_chr6.simHuman.chr6 397447 28 + 601863 ACACAAAGGCACAGAACTGTGTATTAAC -s simMouse_chr6.simMouse.chr6 413566 28 + 636262 ATAAATTAAGGGGGCATCATGTATCAAC -s simRat_chr6.simRat.chr6 419889 28 + 647215 ACAAACTAAGGAGGCATCATGTGTCAAC -s simRat_chr6.simRat.chr6 417664 24 + 647215 ---AAGAAGCATAGAACTGTGTATTA-C - -a -s simMouse_chr6.simMouse.chr6 411317 75 + 636262 TGTAAGTTGACCGTTCAGAATCTATCGCTCTAAACATATGGCAAATTGCCCCATTGTGGACAAATAAAGGAGGCT -s Anc0.Anc0refChr3 42392 63 + 222631 TGTAAGGTGACCACTCAGAAACTATTGCTCCAAATGTATGGTATATTGCCC-ATCCTGGTCAAA----------- -s Anc1.Anc1refChr6 72759 63 + 197743 TGTAAGGTGACCACTCAGAAACTATTGCTCCAAATGTATGGTATATTGCCC-ATCCTGGTCAAA----------- -s Anc2.Anc2refChr13 46409 63 + 96486 TGTAAGGTGACCACTTGGAAACTATTGCTCCAAATGTATGGTATGTTGCCC-CTCCTGGTCAAA----------- -s mr.mrrefChr5 264050 63 + 294540 TGTAAGTTGACCATTCAGAATCTATTGCTCTAAACATATGGCAAATTGCCC-ATTGTGGACAAA----------- -s mr.mrrefChr5 266291 63 + 294540 TGTAAGGTGAACACTCAGAATCTATTGCTCTACACAAATGGTATAGATCCC-ATCATGGACAAA----------- -s simCow_chr6.simCow.chr6 402369 63 + 602619 TGTAAGGAGACCACATTAAAATGATCGCTCCAACCATATGGTATGTTGCCC-CTCTAGGTCAGA----------- -s simDog_chr6.simDog.chr6 393000 63 + 593897 AATAAGGTGACCACTTGGGAACTATTGCACCAAATGTATGGTATGTATCCC-CTTCTGGTCAAA----------- -s simHuman_chr6.simHuman.chr6 397475 63 + 601863 TGTAGGGTGACCACTCAGAAACTTTTGCTCCAGATGTACGGTATATTGCCC-ATCCTGGTGAAA----------- -s simMouse_chr6.simMouse.chr6 413594 63 + 636262 TGTAAGGTGAATACTCAAAATCTGCTGCTCTACACAAATGGTGGAGACCAT-ATCATTGACAAA----------- -s simRat_chr6.simRat.chr6 419920 63 + 647215 TGTAAGGTGAACACTCAGAATCTATTGCTCTACACAAATGGGATAGATCCC-ATCATGGACAAA----------- -s simRat_chr6.simRat.chr6 417688 40 + 647215 TGTAAGTTTCCCATTCAGAATCTATTGCCCTAAACATATG----------------------------------- - -a -s simMouse_chr6.simMouse.chr6 411392 6 + 636262 GCATGC -s Anc0.Anc0refChr3 42466 6 + 222631 GTATGC -s Anc1.Anc1refChr6 72833 6 + 197743 GTATGC -s Anc2.Anc2refChr13 46483 6 + 96486 GTATTC -s mr.mrrefChr5 264113 6 + 294540 GCATGC -s mr.mrrefChr5 266365 6 + 294540 ATATGC -s simCow_chr6.simCow.chr6 402443 6 + 602619 GTATTC -s simDog_chr6.simDog.chr6 393074 6 + 593897 GTATTC -s simHuman_chr6.simHuman.chr6 397538 6 + 601863 GTATGC -s simMouse_chr6.simMouse.chr6 413668 6 + 636262 AAATGT -s simRat_chr6.simRat.chr6 419994 6 + 647215 ATATGC - -a -s simMouse_chr6.simMouse.chr6 411398 28 + 636262 AAGCTCACTTCTGATACCCACAGAATAT -s Anc0.Anc0refChr3 42472 17 + 222631 AAGCTCACTTCT-----------AATAC -s Anc1.Anc1refChr6 72839 17 + 197743 AAGCTCACTTCT-----------AATAC -s Anc2.Anc2refChr13 46489 17 + 96486 AAGCTCACTCCT-----------AATAC -s mr.mrrefChr5 264119 17 + 294540 AAGCTCACTTCT-----------AATAT -s mr.mrrefChr5 266371 17 + 294540 GAGCTTACTACT-----------AATAC -s simCow_chr6.simCow.chr6 402450 17 + 602619 AAGCGCACTCCC-----------AATAC -s simDog_chr6.simDog.chr6 393080 17 + 593897 AAACTCACTCCT-----------AATAC -s simHuman_chr6.simHuman.chr6 397544 17 + 601863 ATGCTCACCTCT-----------AATAT -s simMouse_chr6.simMouse.chr6 413674 17 + 636262 GAGCTTACTACT-----------GATAC -s simRat_chr6.simRat.chr6 420000 17 + 647215 CAGCTTGCTACC-----------AATAC - -a -s simMouse_chr6.simMouse.chr6 411426 3 + 636262 GAA -s Anc0.Anc0refChr3 42494 3 + 222631 GAA -s Anc1.Anc1refChr6 72861 3 + 197743 GAA -s Anc2.Anc2refChr13 46511 3 + 96486 GAA -s mr.mrrefChr5 264136 3 + 294540 GAA -s mr.mrrefChr5 266393 3 + 294540 TAA -s simCow_chr6.simCow.chr6 402472 3 + 602619 GAA -s simDog_chr6.simDog.chr6 393102 3 + 593897 GAA -s simHuman_chr6.simHuman.chr6 397561 3 + 601863 GAA -s simMouse_chr6.simMouse.chr6 413696 3 + 636262 TAA -s simRat_chr6.simRat.chr6 420022 3 + 647215 CAA -s simRat_chr6.simRat.chr6 417728 1 + 647215 --A - -a -s simMouse_chr6.simMouse.chr6 411429 1 + 636262 C -s Anc0.Anc0refChr3 42497 1 + 222631 C -s Anc1.Anc1refChr6 72864 1 + 197743 C -s Anc2.Anc2refChr13 46514 1 + 96486 A -s mr.mrrefChr5 264139 1 + 294540 C -s simCow_chr6.simCow.chr6 402475 1 + 602619 A -s simDog_chr6.simDog.chr6 393105 1 + 593897 A -s simHuman_chr6.simHuman.chr6 397564 1 + 601863 C -s simRat_chr6.simRat.chr6 417729 1 + 647215 C - -a -s simMouse_chr6.simMouse.chr6 411430 1 + 636262 T -s Anc0.Anc0refChr3 42498 1 + 222631 T -s Anc1.Anc1refChr6 72865 1 + 197743 T -s Anc2.Anc2refChr13 46515 1 + 96486 T -s mr.mrrefChr5 264140 1 + 294540 T -s mr.mrrefChr5 266396 1 + 294540 T -s simCow_chr6.simCow.chr6 402476 1 + 602619 T -s simDog_chr6.simDog.chr6 393106 1 + 593897 T -s simHuman_chr6.simHuman.chr6 397565 1 + 601863 T -s simMouse_chr6.simMouse.chr6 413699 1 + 636262 T -s simRat_chr6.simRat.chr6 420025 1 + 647215 T -s simRat_chr6.simRat.chr6 417730 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 411431 104 + 636262 ACGTCAGATGAGATGCCACCTTAACATGAGTTTTAGGAATGGAACTTGCTAGGGTGTTGCACCACACGGCCAAAGTGTAAGCTCACTTCTGATACCCACAGAAT -s mr.mrrefChr5 264141 96 + 294540 ACGTCAGATGAGATGCCACCTTAACATGAGTTTTAGGAATGGAACTTG--------TTGCACCACACGGCCAAAGTGTAAGCTCACTTCTGATACCCACAGAAT -s simRat_chr6.simRat.chr6 417731 96 + 647215 ACATCAGATGAGATGCTACCCCAACATGAGTTTTAGAAAAGGAACCTG--------TTGCACCACACAGCCATAATGCAAGCTCACTTCTGATTTCCAGAGAAT - -a -s simMouse_chr6.simMouse.chr6 411535 5 + 636262 TCAAA -s Anc0.Anc0refChr3 42499 5 + 222631 TAGAA -s Anc1.Anc1refChr6 72866 5 + 197743 TAGAA -s Anc2.Anc2refChr13 46516 5 + 96486 TAGAA -s mr.mrrefChr5 264237 5 + 294540 TCGAA -s mr.mrrefChr5 266397 5 + 294540 TAGAA -s simCow_chr6.simCow.chr6 402477 5 + 602619 TAGAA -s simDog_chr6.simDog.chr6 393107 5 + 593897 TAGAA -s simHuman_chr6.simHuman.chr6 397566 5 + 601863 TAGGG -s simMouse_chr6.simMouse.chr6 413700 5 + 636262 TAGAA -s simRat_chr6.simRat.chr6 420026 5 + 647215 TAAAA -s simRat_chr6.simRat.chr6 417827 5 + 647215 TTGAA - -a -s simMouse_chr6.simMouse.chr6 411540 4 + 636262 TTAC -s Anc0.Anc0refChr3 42504 4 + 222631 TTAT -s Anc1.Anc1refChr6 72871 4 + 197743 TTAT -s Anc2.Anc2refChr13 46521 4 + 96486 TTAT -s mr.mrrefChr5 264242 4 + 294540 TTAC -s mr.mrrefChr5 266402 4 + 294540 TTAT -s simCow_chr6.simCow.chr6 402483 4 + 602619 TTAT -s simDog_chr6.simDog.chr6 393112 4 + 593897 TTAT -s simHuman_chr6.simHuman.chr6 397571 4 + 601863 TTAT -s simMouse_chr6.simMouse.chr6 413705 4 + 636262 TTAT -s simRat_chr6.simRat.chr6 420031 4 + 647215 TTGT -s simRat_chr6.simRat.chr6 417832 4 + 647215 TTAC - -a -s simMouse_chr6.simMouse.chr6 411544 6 + 636262 AACAAA -s Anc0.Anc0refChr3 42508 6 + 222631 AATAGA -s Anc1.Anc1refChr6 72875 6 + 197743 AATAGA -s Anc2.Anc2refChr13 46526 6 + 96486 AATAGA -s mr.mrrefChr5 264246 6 + 294540 AATAAA -s mr.mrrefChr5 266406 6 + 294540 AACAGA -s simCow_chr6.simCow.chr6 402488 6 + 602619 AATGGA -s simDog_chr6.simDog.chr6 393117 6 + 593897 AATACA -s simHuman_chr6.simHuman.chr6 397575 6 + 601863 AATAGA -s simMouse_chr6.simMouse.chr6 413709 6 + 636262 AACAGA -s simRat_chr6.simRat.chr6 420035 6 + 647215 AACAGA -s simRat_chr6.simRat.chr6 417836 6 + 647215 AATAAA - -a -s simMouse_chr6.simMouse.chr6 411550 13 + 636262 TGAGATGCCACCG -s Anc0.Anc0refChr3 42514 13 + 222631 TGAGATGCCACCT -s Anc1.Anc1refChr6 72881 13 + 197743 TGAGATGCCACCT -s Anc2.Anc2refChr13 46532 13 + 96486 TGAGATGCCAGCT -s mr.mrrefChr5 264252 13 + 294540 TGAGATGCCACCT -s mr.mrrefChr5 266412 13 + 294540 TGAGATCACACCT -s simCow_chr6.simCow.chr6 402494 13 + 602619 AGAGATGCCAGCT -s simDog_chr6.simDog.chr6 393123 6 + 593897 TGAGAT------- -s simHuman_chr6.simHuman.chr6 397581 13 + 601863 TGAGATGCCATCT -s simMouse_chr6.simMouse.chr6 413720 13 + 636262 TGCTATGACACCT -s simRat_chr6.simRat.chr6 420041 13 + 647215 TGAGATCACACCT -s simRat_chr6.simRat.chr6 417842 13 + 647215 CGAGATGCTACCT - -a -s simMouse_chr6.simMouse.chr6 411563 9 + 636262 CAACATGGG -s Anc0.Anc0refChr3 42527 9 + 222631 CACTATGAC -s Anc1.Anc1refChr6 72894 9 + 197743 CACTATGAC -s Anc2.Anc2refChr13 46545 9 + 96486 CACTAAGAC -s mr.mrrefChr5 264265 9 + 294540 CAACATGAG -s simCow_chr6.simCow.chr6 402507 9 + 602619 CACTAAGAC -s simDog_chr6.simDog.chr6 393129 1 + 593897 --------C -s simHuman_chr6.simHuman.chr6 397594 9 + 601863 CACTATGAC -s simRat_chr6.simRat.chr6 417855 9 + 647215 CAGCAAGAG - -a -s simMouse_chr6.simMouse.chr6 411572 5 + 636262 AGGAA -s Anc0.Anc0refChr3 42540 5 + 222631 AGAAA -s Anc1.Anc1refChr6 72907 5 + 197743 AGAAA -s Anc2.Anc2refChr13 46558 5 + 96486 AGAAA -s mr.mrrefChr5 264278 5 + 294540 AGGAA -s mr.mrrefChr5 266428 5 + 294540 ATGAA -s simCow_chr6.simCow.chr6 402520 5 + 602619 AGAAG -s simDog_chr6.simDog.chr6 393134 5 + 593897 AGAAA -s simHuman_chr6.simHuman.chr6 397607 5 + 601863 AGAAA -s simMouse_chr6.simMouse.chr6 413745 5 + 636262 ATGAA -s simRat_chr6.simRat.chr6 420057 5 + 647215 ATGAA -s simRat_chr6.simRat.chr6 417868 5 + 647215 AGGAA - -a -s simMouse_chr6.simMouse.chr6 411577 4 + 636262 TGGA -s Anc0.Anc0refChr3 42545 4 + 222631 AGGA -s Anc1.Anc1refChr6 72912 4 + 197743 AGGA -s Anc2.Anc2refChr13 46563 4 + 96486 AGTA -s mr.mrrefChr5 264283 4 + 294540 TGGA -s mr.mrrefChr5 266433 4 + 294540 AGGA -s simCow_chr6.simCow.chr6 402532 4 + 602619 AGTA -s simHuman_chr6.simHuman.chr6 397612 4 + 601863 AGGA -s simMouse_chr6.simMouse.chr6 413750 4 + 636262 AGGA -s simRat_chr6.simRat.chr6 420062 4 + 647215 AGGG -s simRat_chr6.simRat.chr6 417873 4 + 647215 TTGA - -a -s simMouse_chr6.simMouse.chr6 411581 6 + 636262 ACTTGG -s Anc0.Anc0refChr3 42552 6 + 222631 ACTAAG -s Anc1.Anc1refChr6 72919 6 + 197743 ACTAAG -s Anc2.Anc2refChr13 46570 6 + 96486 ACTAAG -s mr.mrrefChr5 264287 6 + 294540 ACTTGG -s mr.mrrefChr5 266437 6 + 294540 ACTCAG -s simCow_chr6.simCow.chr6 402539 6 + 602619 ACTAAG -s simHuman_chr6.simHuman.chr6 397619 6 + 601863 ACTGGG -s simMouse_chr6.simMouse.chr6 413754 6 + 636262 ACTCAG -s simRat_chr6.simRat.chr6 420066 6 + 647215 TCTAAG -s simRat_chr6.simRat.chr6 417877 6 + 647215 AGTTGG - -a -s simMouse_chr6.simMouse.chr6 411587 2 + 636262 TA -s Anc0.Anc0refChr3 42562 2 + 222631 TA -s Anc1.Anc1refChr6 72929 2 + 197743 TA -s Anc2.Anc2refChr13 46580 2 + 96486 TA -s mr.mrrefChr5 264293 2 + 294540 TA -s mr.mrrefChr5 266443 2 + 294540 TA -s simCow_chr6.simCow.chr6 402562 2 + 602619 TA -s simHuman_chr6.simHuman.chr6 397629 2 + 601863 TC -s simMouse_chr6.simMouse.chr6 413760 2 + 636262 TA -s simRat_chr6.simRat.chr6 420072 2 + 647215 TA -s simRat_chr6.simRat.chr6 417883 2 + 647215 TA - -a -s simMouse_chr6.simMouse.chr6 411589 47 + 636262 TTACGCCACACAGCTAAACAAACTGAAGTCATTCCACACTGGCTATC -s Anc0.Anc0refChr3 42569 45 + 222631 T-GCATCACACAGCTAAATAAAGTGAAGTCATCCTACACTAACTAT- -s Anc1.Anc1refChr6 72936 47 + 197743 TTGCATCACACAGCTAAATAAAGTGAAGTCATCCTACACTAACTATC -s Anc2.Anc2refChr13 46587 45 + 96486 T-GCTTCACACGGCTAAATATAGTGAAGTCATCCTCCACTTACTAT- -s mr.mrrefChr5 264300 47 + 294540 TTGCACCACACAGCTAAACAAAGTGAAGTCATTCCACACTGGCTATC -s mr.mrrefChr5 266450 47 + 294540 CTGAGTGAAACAGCTAAACAGGGTGAACTCATCCTGCACTAGCTATC -s simCow_chr6.simCow.chr6 402569 45 + 602619 T-GCTTCACACGGCTAAATATAGTCAAGTCATCCTCCAGTTACTAT- -s simDog_chr6.simDog.chr6 393139 23 + 593897 -----------------------TGAAGTCATCCTCCACCTACCAT- -s simHuman_chr6.simHuman.chr6 397636 47 + 601863 TTGCACCACACAGCCGATTAAAGTGAAGTCATCCCACACTAACAATC -s simMouse_chr6.simMouse.chr6 413767 45 + 636262 CTGAGTGAAACAGCTAAACAGGGT-AGCTCATCCTGCAC-AGCTGCC -s simRat_chr6.simRat.chr6 420079 47 + 647215 TTGAGTGAAATAGCTAAACAAGTTGAACTCATTCTGCACTAGCTATC -s simRat_chr6.simRat.chr6 417890 46 + 647215 TTGCACCACACAGTGAAACAAAGTGAAGATATTCCAC-CTGGCTATC - -a -s simMouse_chr6.simMouse.chr6 411636 3 + 636262 TGT -s Anc1.Anc1refChr6 72983 3 + 197743 TAT -s mr.mrrefChr5 264347 3 + 294540 TGT -s simHuman_chr6.simHuman.chr6 397683 3 + 601863 TAT -s simRat_chr6.simRat.chr6 417936 3 + 647215 TGT - -a -s simMouse_chr6.simMouse.chr6 411639 13 + 636262 AGATCCTATACTA -s Anc0.Anc0refChr3 42614 13 + 222631 AGATCCCATACCA -s Anc1.Anc1refChr6 72986 13 + 197743 AGATCCCATACCA -s Anc2.Anc2refChr13 46632 13 + 96486 AGATCCCATACCA -s mr.mrrefChr5 264350 13 + 294540 AGATCCTATACTA -s mr.mrrefChr5 266497 13 + 294540 AAATTCCATACTA -s simCow_chr6.simCow.chr6 402614 13 + 602619 ATATCCCATACTA -s simDog_chr6.simDog.chr6 393162 13 + 593897 AGATCCCACACCA -s simHuman_chr6.simHuman.chr6 397686 13 + 601863 AGATCTCATCTCA -s simRat_chr6.simRat.chr6 420129 13 + 647215 AAATTCCATACTA -s simRat_chr6.simRat.chr6 417939 13 + 647215 AGATCCTATACTA - -a -s simMouse_chr6.simMouse.chr6 411652 56 + 636262 AGAAATGCACCCAACTATACAAAGCCTAATTGCTAGGCAAGTTACTATAACACAGG -s Anc0.Anc0refChr3 42627 56 + 222631 ACTTATACACCCAACCATGCAAAGCCTAATTGCTAAGCAAGTTACTATAACTCAAG -s Anc1.Anc1refChr6 72999 56 + 197743 ACTTATACACCCAACCATGCAAAGCCTAATTGCTAAGCAAGTTACTATAACTCAAG -s Anc2.Anc2refChr13 46645 56 + 96486 ACTCATACACCCAAACATGCAAAGCCTAATTGCTAAGCAAGTTATTATAACTCAAG -s mr.mrrefChr5 264363 56 + 294540 AGCAATGCACCCAACTATACAAAGCCTAATTGCTAGGCAAGTTACTATAACACAGG -s mr.mrrefChr5 266510 56 + 294540 AGCTGCACACCCAACCGCACAAAGCCTGATTGCTAAGCAAGTTGCTATAACTCAAG -s simCow_chr6.simCow.chr6 402627 56 + 602619 ACTGATACTCCTGAACATGCAATACCTAACTGCTGAGCAAGTTATTATAACTCATA -s simDog_chr6.simDog.chr6 393175 56 + 593897 ATCCATGTACCCAGACATGCGAAGTCTAATTGCTAAGCATGTTATTATAACCCAAG -s simHuman_chr6.simHuman.chr6 397700 56 + 601863 ACTTCATCACGCTACTTTGAAAAGCCTGATTGCTAAGCAAGTTACCTTCACTCAGG -s simMouse_chr6.simMouse.chr6 413812 18 + 636262 --------------------------------------AAGTTGCTATAACTCAAG -s simRat_chr6.simRat.chr6 420142 56 + 647215 AGCTGCACACCCAACCGCACAAAGCCTGATTGCTAAGCAAGTTGCTATAACTCAGG -s simRat_chr6.simRat.chr6 417952 56 + 647215 AGCAATGCACCCAACTATACAAAGCTTAATGGCTAGGCAAGTTACTACAACCCAGG - -a -s simMouse_chr6.simMouse.chr6 411708 1 + 636262 A -s Anc0.Anc0refChr3 42683 1 + 222631 A -s Anc1.Anc1refChr6 73055 1 + 197743 A -s Anc2.Anc2refChr13 46701 1 + 96486 A -s mr.mrrefChr5 264419 1 + 294540 A -s mr.mrrefChr5 266566 1 + 294540 C -s simCow_chr6.simCow.chr6 402683 1 + 602619 A -s simDog_chr6.simDog.chr6 393231 1 + 593897 A -s simHuman_chr6.simHuman.chr6 397756 1 + 601863 A -s simMouse_chr6.simMouse.chr6 413830 1 + 636262 C -s simRat_chr6.simRat.chr6 418008 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 411709 1 + 636262 T -s Anc0.Anc0refChr3 42684 1 + 222631 T -s Anc1.Anc1refChr6 73056 1 + 197743 T -s Anc2.Anc2refChr13 46702 1 + 96486 T -s mr.mrrefChr5 264420 1 + 294540 T -s mr.mrrefChr5 266567 1 + 294540 A -s simCow_chr6.simCow.chr6 402684 1 + 602619 T -s simDog_chr6.simDog.chr6 393232 1 + 593897 T -s simHuman_chr6.simHuman.chr6 397757 1 + 601863 T -s simMouse_chr6.simMouse.chr6 413831 1 + 636262 A -s simRat_chr6.simRat.chr6 420198 1 + 647215 G -s simRat_chr6.simRat.chr6 418009 1 + 647215 G - -a -s simMouse_chr6.simMouse.chr6 411710 12 + 636262 CATAGTGAGGTT -s Anc0.Anc0refChr3 42687 12 + 222631 CATGATGAGATC -s Anc1.Anc1refChr6 73059 12 + 197743 CATGATGAGATC -s Anc2.Anc2refChr13 46705 12 + 96486 CATGATGAGATC -s mr.mrrefChr5 264421 12 + 294540 CATAGTGAGGTT -s mr.mrrefChr5 266570 12 + 294540 TGTGATGAGGTG -s simCow_chr6.simCow.chr6 402687 12 + 602619 CATGACGAGATC -s simDog_chr6.simDog.chr6 393235 12 + 593897 CATGATGAGATT -s simHuman_chr6.simHuman.chr6 397760 12 + 601863 TCTGGTGAGATC -s simMouse_chr6.simMouse.chr6 413834 12 + 636262 TGTGACGAGGTG -s simRat_chr6.simRat.chr6 420201 12 + 647215 TTTGATGAGGTG -s simRat_chr6.simRat.chr6 418010 12 + 647215 AATAATGGGGTT - -a -s simMouse_chr6.simMouse.chr6 411722 22 + 636262 CTTCTGAAGGCCACAAGACTAG -s Anc0.Anc0refChr3 42700 13 + 222631 CTTTGGAAG---------CGAG -s Anc1.Anc1refChr6 73072 13 + 197743 CTTTGGAAG---------CGAG -s Anc2.Anc2refChr13 46718 13 + 96486 TTTTGGACG---------CGAG -s mr.mrrefChr5 264433 13 + 294540 CTTCGGAAG---------CTAG -s mr.mrrefChr5 266582 13 + 294540 CTTTGGAAG---------CCAG -s simCow_chr6.simCow.chr6 402700 13 + 602619 TCTTGGATG---------CTAG -s simDog_chr6.simDog.chr6 393248 13 + 593897 TTTTGGACG---------TGAA -s simHuman_chr6.simHuman.chr6 397773 13 + 601863 CTTAGGGAG---------CAGG -s simMouse_chr6.simMouse.chr6 413846 13 + 636262 CGTTGGAAG---------CCAG -s simRat_chr6.simRat.chr6 420213 13 + 647215 CTTTGGAAG---------CCAG -s simRat_chr6.simRat.chr6 418022 13 + 647215 CTTTGGAAG---------CTAG - -a -s simMouse_chr6.simMouse.chr6 411744 9 + 636262 CTGGCAAAG -s Anc0.Anc0refChr3 42713 9 + 222631 CTAGTGAAG -s Anc1.Anc1refChr6 73085 9 + 197743 CTAGTGAAG -s Anc2.Anc2refChr13 46731 9 + 96486 CTAGTGAAG -s mr.mrrefChr5 264446 9 + 294540 CTGGCAAAG -s simCow_chr6.simCow.chr6 402713 9 + 602619 CTAGTGCAG -s simDog_chr6.simDog.chr6 393261 9 + 593897 CTAGCAAAA -s simRat_chr6.simRat.chr6 418035 9 + 647215 CTGGCACAG - -a -s simMouse_chr6.simMouse.chr6 411753 28 + 636262 GTAAATACATGACATGGAAGGAATAAGA -s Anc0.Anc0refChr3 42722 28 + 222631 GTAGATACATAACATGAAGGAAATAACA -s Anc1.Anc1refChr6 73094 28 + 197743 GTAGATACATAACATGAAGGAAATAACA -s Anc2.Anc2refChr13 46740 28 + 96486 GAAGGGACAGAACATGAGGAAAATTACA -s mr.mrrefChr5 264455 28 + 294540 GTAAATACATGACATGGAAGAAATAAGA -s mr.mrrefChr5 266595 28 + 294540 GTAGATACATACCATGGAAGAAATGACA -s simCow_chr6.simCow.chr6 402722 28 + 602619 GGAGCTACATGACAGGGAGAAAATTATA -s simDog_chr6.simDog.chr6 393270 28 + 593897 GAAGGGACAGAGCATGAGGAAAATTACA -s simHuman_chr6.simHuman.chr6 397786 18 + 601863 CTAG----------TGAAGGAAATAACA -s simMouse_chr6.simMouse.chr6 413859 28 + 636262 GTAGATACATACCAGGGAAGAAGCGACA -s simRat_chr6.simRat.chr6 420226 28 + 647215 GTAGATACATAACATGGAAGAAATGACA -s simRat_chr6.simRat.chr6 418044 28 + 647215 GTAGATACATGACATGGAAGAAATAAGA - -a -s simMouse_chr6.simMouse.chr6 411781 3 + 636262 CAG -s Anc0.Anc0refChr3 42750 3 + 222631 CAG -s Anc1.Anc1refChr6 73122 3 + 197743 CAG -s Anc2.Anc2refChr13 46768 3 + 96486 CAG -s mr.mrrefChr5 264483 3 + 294540 CAG -s mr.mrrefChr5 266623 3 + 294540 CAT -s simCow_chr6.simCow.chr6 402750 3 + 602619 CAG -s simDog_chr6.simDog.chr6 393298 3 + 593897 CAG -s simHuman_chr6.simHuman.chr6 397848 3 + 601863 CAG -s simMouse_chr6.simMouse.chr6 413887 3 + 636262 CAT -s simRat_chr6.simRat.chr6 420254 3 + 647215 CAT -s simRat_chr6.simRat.chr6 418072 3 + 647215 CAG - -a -s simMouse_chr6.simMouse.chr6 411784 64 + 636262 TACAGCTGAAGTCAGCACTGCCTTTTCACTTCAGGCCCTGTGCCTAAATCATGATTCACACCCG -s Anc0.Anc0refChr3 42753 64 + 222631 TACAGTTCAAGTGAGCACCGCCTCCTCACTTAATTCCCTGCATCTAAATCGTGACTCACACCAG -s Anc1.Anc1refChr6 73125 64 + 197743 TACAGTTCAAGTGAGCACCGCCTCCTCACTTAATTCCCTGCATCTAAATCGTGACTCACACCAG -s Anc2.Anc2refChr13 46771 64 + 96486 TACAGTTCAAATGAGCACCGCTTCCTCACTTAATTCCCTGCATCTTAATCGTGACTCACACCAG -s mr.mrrefChr5 264486 64 + 294540 TACAGTTGAAGTCAGCACTGCCTTTTCACTTCAGTCCCTGTGTCTAAATCATGATTCACACCCG -s mr.mrrefChr5 266637 64 + 294540 TACAGTTCAAGTGAGCAATGCCTCCTCACTTAGGCCCCTGAGTCTAAACTGTGATTCACACCAG -s simCow_chr6.simCow.chr6 402753 64 + 602619 TCCAGCTAAAGTGAGCACCGCTGCCTCATTTAATTCCCTGTATCCGAGTTGTGGCTTACACCAG -s simDog_chr6.simDog.chr6 393301 62 + 593897 AATACTTC-CATGGGTACTGCTTCCTCACTTAATTCCCTGCATCTTAACC-TGACTCACAACAG -s simHuman_chr6.simHuman.chr6 397851 64 + 601863 TACAGTTTGATTGAGCACCACCTCCTCACATAATTCCCTTCATCTAAATGGTGACTCACACTGG -s simMouse_chr6.simMouse.chr6 413901 61 + 636262 TACAGTTCAAGTGAGCAATGCCTCCTCACTTAGGC---TGAGTCAAAGCTGTGATTCACACCAG -s simRat_chr6.simRat.chr6 420268 64 + 647215 TACAGTCAGAGTGAGCAATGCCTCCTCACTTAGGCCCCTGAGTCTAAACTGTGCTTCACACCAG -s simRat_chr6.simRat.chr6 418077 64 + 647215 TACAGTTCAAGTCAGCAATGCCTTTTTACTTTGGTTCCTATGTCTAAATTATGATTCAAATCCC - -a -s simMouse_chr6.simMouse.chr6 411848 1 + 636262 G -s Anc0.Anc0refChr3 42817 1 + 222631 G -s Anc1.Anc1refChr6 73189 1 + 197743 G -s Anc2.Anc2refChr13 46835 1 + 96486 G -s mr.mrrefChr5 264550 1 + 294540 G -s mr.mrrefChr5 266701 1 + 294540 C -s simCow_chr6.simCow.chr6 402817 1 + 602619 G -s simDog_chr6.simDog.chr6 393363 1 + 593897 G -s simHuman_chr6.simHuman.chr6 397915 1 + 601863 G -s simMouse_chr6.simMouse.chr6 413962 1 + 636262 C -s simRat_chr6.simRat.chr6 418141 1 + 647215 G - -a -s simMouse_chr6.simMouse.chr6 411849 13 + 636262 TGTGGAATTTGTG -s Anc0.Anc0refChr3 42818 13 + 222631 TGCGTAATGGGTG -s Anc1.Anc1refChr6 73190 13 + 197743 TGCGTAATGGGTG -s Anc2.Anc2refChr13 46836 13 + 96486 TGCCTAATGGTTG -s mr.mrrefChr5 264551 13 + 294540 TGTGTAATGTGTG -s mr.mrrefChr5 266702 13 + 294540 TGTGTAATTAAAG -s simCow_chr6.simCow.chr6 402818 13 + 602619 TGCATAATGGTTG -s simDog_chr6.simDog.chr6 393364 13 + 593897 TGCCTAATGGTTG -s simHuman_chr6.simHuman.chr6 397916 13 + 601863 TGCTTAATGGGTA -s simMouse_chr6.simMouse.chr6 413963 13 + 636262 TATGTAATACATG -s simRat_chr6.simRat.chr6 420332 13 + 647215 GGTGTAATTAAAG -s simRat_chr6.simRat.chr6 418142 13 + 647215 TATGTAATGTATG - -a -s simMouse_chr6.simMouse.chr6 411862 54 + 636262 GAAAGAGGTAGGACAATGCCTACCATTTTAAGACAACCAACTATGTTGTTTTAC -s Anc0.Anc0refChr3 42831 53 + 222631 CTAAGATGTCAGATGATGACTATAATTATGATAAG-GCAACTATGTCATTTTAC -s Anc1.Anc1refChr6 73203 54 + 197743 CTAAGATGTCAGATGATGACTATAATTATGATAAGCGCAACTATGTCATTTTAC -s Anc2.Anc2refChr13 46849 53 + 96486 CTAAGATGTTAGATGATAACTATAAATATGATAAG-GCAACTATGTCATTTTAC -s mr.mrrefChr5 264564 54 + 294540 GAAAGAGGTCAGACAATGACTACCATTTTAAGACAACCAACTATGTTGTTTTAC -s simCow_chr6.simCow.chr6 402831 53 + 602619 CTAGAATATAAGATGAAAACTGTAGATATGACAAA-GCAACTAGGTCATTTTAT -s simDog_chr6.simDog.chr6 393377 53 + 593897 TTAAGAAGTTAGAGGTTAACTATAAATATTATAAG-GCAACTATACCCTTTTGC -s simHuman_chr6.simHuman.chr6 397929 54 + 601863 CTAAGATGTCATCTGATGACTATAATTATGATAAGCTCCACTATGTCATTTTAG -s simRat_chr6.simRat.chr6 418155 54 + 647215 GAAGGAGGTCAGACAATGACTACCATTTTAAGACAACCAGCTATGTTGTTCTGC - -a -s simMouse_chr6.simMouse.chr6 411916 33 + 636262 ACAGCTGTTGCAAGCGATTAGCTGCACTTTCTA -s Anc0.Anc0refChr3 42884 24 + 222631 ATATTTGTTGCAAACTG---------CTCTGTA -s Anc1.Anc1refChr6 73257 24 + 197743 ATATTTGTTGCAAACTG---------CTCTGTA -s Anc2.Anc2refChr13 46902 24 + 96486 ATATTTATTGCAGACTG---------CTCTGTA -s mr.mrrefChr5 264618 33 + 294540 ATAGCTGTTGCAAGCGGTTAGCTGCACTTTCTA -s simCow_chr6.simCow.chr6 402885 24 + 602619 ATATCTAATGCAGACTG---------CTCTGTA -s simDog_chr6.simDog.chr6 393430 24 + 593897 ATATTCATTGTAGATTG---------CTCTGTA -s simHuman_chr6.simHuman.chr6 397983 24 + 601863 GTATTTGGTGCAAACTG---------CTCTATA -s simRat_chr6.simRat.chr6 418209 33 + 647215 ATAGCTGTTGCAAGCAGTTAGCTGCACTTTCTA - -a -s simMouse_chr6.simMouse.chr6 411949 5 + 636262 GGCTC -s Anc0.Anc0refChr3 42908 5 + 222631 GGCTT -s Anc1.Anc1refChr6 73281 5 + 197743 GGCTT -s Anc2.Anc2refChr13 46929 5 + 96486 GGCCT -s mr.mrrefChr5 264651 5 + 294540 GGCTT -s simCow_chr6.simCow.chr6 402912 5 + 602619 GGCCT -s simDog_chr6.simDog.chr6 393457 5 + 593897 GCCCT -s simHuman_chr6.simHuman.chr6 398007 5 + 601863 GGCTT -s simRat_chr6.simRat.chr6 418242 5 + 647215 GGCTT - -a -s simMouse_chr6.simMouse.chr6 411954 3 + 636262 CAG -s Anc0.Anc0refChr3 42913 3 + 222631 CAG -s Anc1.Anc1refChr6 73286 3 + 197743 CAG -s Anc2.Anc2refChr13 46934 3 + 96486 CAG -s mr.mrrefChr5 264656 3 + 294540 CAG -s simCow_chr6.simCow.chr6 402918 3 + 602619 CGG -s simDog_chr6.simDog.chr6 393462 3 + 593897 CAG -s simHuman_chr6.simHuman.chr6 398012 3 + 601863 CAG -s simRat_chr6.simRat.chr6 418247 3 + 647215 CAG - -a -s simMouse_chr6.simMouse.chr6 411957 18 + 636262 GGTCATAGAAAAGAAACA -s Anc0.Anc0refChr3 42916 17 + 222631 GGTCAAGAAAAA-AGACA -s Anc1.Anc1refChr6 73289 17 + 197743 GGTCAAGAAAAA-AGACA -s Anc2.Anc2refChr13 46937 17 + 96486 GGTTAAGAAAAA-AGATT -s mr.mrrefChr5 264659 18 + 294540 GGTCATAGAAAAGAAACA -s simCow_chr6.simCow.chr6 402921 17 + 602619 TGTTAAGAAAAA-AGATT -s simDog_chr6.simDog.chr6 393681 2 + 593897 GG---------------- -s simHuman_chr6.simHuman.chr6 398015 17 + 601863 GGTCAAGAAAAA-AGACA -s simRat_chr6.simRat.chr6 418250 18 + 647215 GGTCATAGAAATGAAATA - -a -s simMouse_chr6.simMouse.chr6 411975 13 + 636262 GTGGACCTACTTA -s Anc0.Anc0refChr3 42940 13 + 222631 GCTGGCCACCCTA -s Anc1.Anc1refChr6 73314 13 + 197743 GCTGGCCACCCTA -s Anc2.Anc2refChr13 46961 13 + 96486 GCTGGCCACACTT -s mr.mrrefChr5 264685 13 + 294540 GTGGGCCACCTTA -s simCow_chr6.simCow.chr6 402945 13 + 602619 GCTGGCCACACTT -s simHuman_chr6.simHuman.chr6 398040 13 + 601863 GCTGGCCACCCTA -s simRat_chr6.simRat.chr6 418276 13 + 647215 GTGGGCCACCTTA - -a -s simMouse_chr6.simMouse.chr6 411988 28 + 636262 CACTTACATTAATACATGCAACAATAGT -s Anc0.Anc0refChr3 42954 27 + 222631 CACCTACATACATACACGCAATA-TAAT -s Anc1.Anc1refChr6 73328 27 + 197743 CACCTACATACATACACGCAATA-TAAT -s Anc2.Anc2refChr13 46975 27 + 96486 CACCTGCATACATATACGCACTA-TAAT -s mr.mrrefChr5 264698 28 + 294540 CACTTACATTAATACATGCAATAATAGT -s simCow_chr6.simCow.chr6 402959 27 + 602619 CACCTGCATACATATACGCACTA-TAAT -s simHuman_chr6.simHuman.chr6 398054 27 + 601863 CACACACATGCATACACATAATG-TAAT -s simRat_chr6.simRat.chr6 418289 26 + 647215 TACTTACATTAA--CATGCAATAATAGT - -a -s simMouse_chr6.simMouse.chr6 412016 47 + 636262 GAGAGTTGAATACATTGCTGGACAACTGATGGGTGGGGAAAGCGCCA -s Anc0.Anc0refChr3 42981 47 + 222631 GAGATTTGAATACATAGTCTGCCAACTGATGTGAGGAGAAAACCCCA -s Anc1.Anc1refChr6 73355 47 + 197743 GAGATTTGAATACATAGTCTGCCAACTGATGTGAGGAGAAAACCCCA -s Anc2.Anc2refChr13 47002 47 + 96486 TAAATTTGAATACATAGTCTACCAACTAATGTAAGGAGAAAACCCTG -s mr.mrrefChr5 264726 47 + 294540 GAGAGTTGAATACATTGCTGGCCAACTGATGGGTGGGGAAAACGCCA -s simCow_chr6.simCow.chr6 402986 47 + 602619 TAAATTTGAATACATAGTCTACCAACTAATGTAAGGAGAAAACCCTG -s simHuman_chr6.simHuman.chr6 398111 47 + 601863 GAGACTTGAATACATCAACTGCTGACTGAAGTGGGGCCAAAACCCCA -s simRat_chr6.simRat.chr6 418315 47 + 647215 GAGAGTAGAATACATTGTTGGCCACCTCACGGGTGGGGAAAACACCA - -a -s simMouse_chr6.simMouse.chr6 412063 10 + 636262 GGGGAACAGA -s Anc0.Anc0refChr3 43028 3 + 222631 TA-------A -s Anc1.Anc1refChr6 73402 3 + 197743 TA-------A -s Anc2.Anc2refChr13 47049 3 + 96486 TA-------A -s mr.mrrefChr5 264773 10 + 294540 GGGGAACAGA -s simCow_chr6.simCow.chr6 403033 3 + 602619 TA-------A -s simHuman_chr6.simHuman.chr6 398158 3 + 601863 TA-------A -s simRat_chr6.simRat.chr6 418367 10 + 647215 GGGGAATAGA - -a -s simMouse_chr6.simMouse.chr6 412073 10 + 636262 TTAATAGTCT -s Anc0.Anc0refChr3 43031 10 + 222631 ATAATGACCT -s Anc1.Anc1refChr6 73405 10 + 197743 ATAATGACCT -s Anc2.Anc2refChr13 47052 10 + 96486 ATAATGACCT -s mr.mrrefChr5 264783 10 + 294540 ATAATAGTCT -s simCow_chr6.simCow.chr6 403047 10 + 602619 ATAATGACCT -s simHuman_chr6.simHuman.chr6 398161 10 + 601863 ATAATCACCT -s simRat_chr6.simRat.chr6 418377 10 + 647215 ATAACGGTCT - -a -s simMouse_chr6.simMouse.chr6 412083 14 + 636262 TGGTTGTTAGCGCT -s Anc0.Anc0refChr3 43041 14 + 222631 TGGTTATAAGAATT -s Anc1.Anc1refChr6 73415 14 + 197743 TGGTTATAAGAATT -s Anc2.Anc2refChr13 47062 14 + 96486 TAGTTATAAGAATT -s mr.mrrefChr5 264793 14 + 294540 TGGTTATAAGCACT -s simCow_chr6.simCow.chr6 403061 14 + 602619 TAGTTATAAGAATT -s simHuman_chr6.simHuman.chr6 398171 14 + 601863 TGATTATAAAAATT -s simRat_chr6.simRat.chr6 418387 14 + 647215 TAGTTATAAGCACT - -a -s simMouse_chr6.simMouse.chr6 412097 27 + 636262 TATAGATCTGTGTACAGCCTGAGGGTC -s Anc0.Anc0refChr3 43055 25 + 222631 TATAC-TCTGTGCATAGCCTGAGG-TC -s Anc1.Anc1refChr6 73429 26 + 197743 TATACATCTGTGCATAGCCTGAGG-TC -s Anc2.Anc2refChr13 47076 25 + 96486 TATAC-TGTATACATAGCCTGACG-TC -s mr.mrrefChr5 264807 26 + 294540 TATAGATCTGTGCACAGCCTGAGG-TC -s simCow_chr6.simCow.chr6 403078 25 + 602619 TATAC-TGTATACATAGCCTGACG-TC -s simHuman_chr6.simHuman.chr6 398185 26 + 601863 TATACATCTGTGCATAGCCTGAGG-TC -s simRat_chr6.simRat.chr6 418401 26 + 647215 TATAGGTCTGTGCACAGCCTGAGG-TC - -a -s simMouse_chr6.simMouse.chr6 412124 45 + 636262 AAAAAGCAGAACTGCAAACCTGTCAATAAATAATCATATAAATCT -s Anc0.Anc0refChr3 43084 44 + 222631 AAAA-GCATAGTTGGAAACCTAAAGATACATAATCATATAAATCT -s Anc1.Anc1refChr6 73459 45 + 197743 AAAAAGCATAGTTGGAAACCTAAAGATACATAATCATATAAATCT -s Anc2.Anc2refChr13 47105 44 + 96486 AAAG-GCATCGTCGGAAAGTTAAAGGTACATAGTCATATAAATCT -s mr.mrrefChr5 264833 45 + 294540 AAAAAGCATAACTGGAAACCTGTCAATAAATAATCATATAAATCT -s simCow_chr6.simCow.chr6 403107 44 + 602619 AAAG-GCATCGTCGGAAAGTTAAAAGTACATATTGTTATAAATCT -s simDog_chr6.simDog.chr6 393683 24 + 593897 ---------------------AAAGGTACATAGACACATAAATCT -s simHuman_chr6.simHuman.chr6 398216 45 + 601863 AGAAAGCATAGTTGGAAACCTAAAGATACAAAATCATATAAATTT -s simRat_chr6.simRat.chr6 418427 45 + 647215 AAAAAACATAACTGGAAACCTGTCAGTAAATAATCATATAAATCT - -a -s simMouse_chr6.simMouse.chr6 412169 1 + 636262 G -s Anc0.Anc0refChr3 43128 1 + 222631 T -s Anc1.Anc1refChr6 73504 1 + 197743 T -s Anc2.Anc2refChr13 47153 1 + 96486 T -s mr.mrrefChr5 264878 1 + 294540 G -s simCow_chr6.simCow.chr6 403155 1 + 602619 G -s simDog_chr6.simDog.chr6 393711 1 + 593897 T -s simHuman_chr6.simHuman.chr6 398261 1 + 601863 T -s simRat_chr6.simRat.chr6 418472 1 + 647215 G - -a -s simMouse_chr6.simMouse.chr6 412170 7 + 636262 CTGCAAT -s Anc0.Anc0refChr3 43134 7 + 222631 TCGCAAT -s Anc1.Anc1refChr6 73510 7 + 197743 TCGCAAT -s Anc2.Anc2refChr13 47159 7 + 96486 TCACAAT -s mr.mrrefChr5 264884 7 + 294540 TTGCAAT -s simCow_chr6.simCow.chr6 403161 7 + 602619 TTCCTCT -s simDog_chr6.simDog.chr6 393717 7 + 593897 TCACAAC -s simHuman_chr6.simHuman.chr6 398267 7 + 601863 TGGCAGT -s simRat_chr6.simRat.chr6 418479 7 + 647215 TTGCAAG - -a -s simMouse_chr6.simMouse.chr6 412177 22 + 636262 AAACTTACATGGAAGAATCACC -s Anc0.Anc0refChr3 43141 22 + 222631 AAACTTATCTGGAATGATCACC -s Anc1.Anc1refChr6 73517 22 + 197743 AAACTTATCTGGAATGATCACC -s Anc2.Anc2refChr13 47166 22 + 96486 AAACTTATCTGAAATGATCACT -s mr.mrrefChr5 264891 22 + 294540 AAACTTACATGGAAGAATCACC -s simCow_chr6.simCow.chr6 403168 22 + 602619 AATCTTAGCTGAAATGATCACC -s simDog_chr6.simDog.chr6 393725 22 + 593897 AAACTTATCTGAAATGATCACT -s simHuman_chr6.simHuman.chr6 398274 22 + 601863 AAACTTATCTGGAATGATTATC -s simRat_chr6.simRat.chr6 418486 7 + 647215 ATACTTA--------------- - -a -s simMouse_chr6.simMouse.chr6 412199 17 + 636262 ACATATGGGGTCTTATT -s Anc0.Anc0refChr3 43163 16 + 222631 A-GTTTGGGGTCTCATT -s Anc1.Anc1refChr6 73539 16 + 197743 A-GTTTGGGGTCTCATT -s Anc2.Anc2refChr13 47189 16 + 96486 A-GTTTGGGGTCTCATT -s mr.mrrefChr5 264913 16 + 294540 A-ATATGGGGTCTTATT -s simCow_chr6.simCow.chr6 403191 16 + 602619 A-GGAAAGGGTGTCATC -s simDog_chr6.simDog.chr6 393748 16 + 593897 A-GTTTGGGGTCTCATT -s simHuman_chr6.simHuman.chr6 398296 16 + 601863 A-GTGTGTGTTCTCAGT - -a -s simMouse_chr6.simMouse.chr6 412216 10 + 636262 ATATTTTATT -s Anc0.Anc0refChr3 43191 10 + 222631 ACACACTACT -s Anc1.Anc1refChr6 73567 10 + 197743 ACACACTACT -s Anc2.Anc2refChr13 47217 10 + 96486 ACACACTACT -s mr.mrrefChr5 264929 10 + 294540 ATATTTTATT -s simCow_chr6.simCow.chr6 403219 10 + 602619 GCACGCTACT -s simDog_chr6.simDog.chr6 393776 10 + 593897 ATACACCACT -s simHuman_chr6.simHuman.chr6 398324 10 + 601863 ACACCCTACT - -a -s simMouse_chr6.simMouse.chr6 412226 2 + 636262 TT -s Anc0.Anc0refChr3 43205 2 + 222631 TT -s Anc1.Anc1refChr6 73581 2 + 197743 TT -s Anc2.Anc2refChr13 47231 2 + 96486 TT -s mr.mrrefChr5 264939 2 + 294540 TT -s simCow_chr6.simCow.chr6 403233 2 + 602619 TT -s simDog_chr6.simDog.chr6 393790 2 + 593897 TT -s simHuman_chr6.simHuman.chr6 398339 2 + 601863 TT - -a -s simMouse_chr6.simMouse.chr6 412228 11 + 636262 TTTCAGAGTTT -s Anc0.Anc0refChr3 43207 11 + 222631 CCTCATACTTT -s Anc1.Anc1refChr6 73583 11 + 197743 CCTCATACTTT -s Anc2.Anc2refChr13 47233 11 + 96486 CCTCATACTTT -s mr.mrrefChr5 264941 11 + 294540 TTTCAGAGTTT -s simCow_chr6.simCow.chr6 403268 11 + 602619 CCTCAGACTTT -s simDog_chr6.simDog.chr6 393792 11 + 593897 TCCCATGCTTT -s simHuman_chr6.simHuman.chr6 398341 11 + 601863 CCTCACACCTT - -a -s simMouse_chr6.simMouse.chr6 412239 14 + 636262 ATCTATAAAGTTGT -s Anc0.Anc0refChr3 43218 14 + 222631 ATTCATCAAATTGT -s Anc1.Anc1refChr6 73594 14 + 197743 ATTCATCAAATTGT -s Anc2.Anc2refChr13 47244 14 + 96486 ATTTATCAAATTGT -s mr.mrrefChr5 264952 14 + 294540 ATCCATAAAGTTGT -s simCow_chr6.simCow.chr6 403279 14 + 602619 ATTTATTGAATTGT -s simDog_chr6.simDog.chr6 393804 14 + 593897 ATTTATCAGTTAGT -s simHuman_chr6.simHuman.chr6 398352 14 + 601863 ATTCACCAAACTGT -s simRat_chr6.simRat.chr6 418493 13 + 647215 -TCCATAAAGTCAT - -a -s simMouse_chr6.simMouse.chr6 412253 32 + 636262 ATCATTTGATAATGCCTAGAAAAAAGCACTAA -s Anc0.Anc0refChr3 43240 29 + 222631 ATTACTTTATAATGCCCAGACAA---CACTAA -s Anc1.Anc1refChr6 73616 29 + 197743 ATTACTTTATAATGCCCAGACAA---CACTAA -s Anc2.Anc2refChr13 47266 29 + 96486 ATTACTTTATAATGCCCAGACAA---CACCAA -s mr.mrrefChr5 264966 32 + 294540 ATCATTTGATAATGCCTAGAAAAAAGCACTAA -s simCow_chr6.simCow.chr6 403301 29 + 602619 ATTATTTTATCATGCTCACACAA---CACGAA -s simDog_chr6.simDog.chr6 393823 29 + 593897 ATTACCTTATAATGCCCAGACAA---CACCAA -s simHuman_chr6.simHuman.chr6 398374 29 + 601863 ATTAGTTTATAATTTGCAGACAA---CACTAA -s simRat_chr6.simRat.chr6 418506 32 + 647215 ATCATTGGATAATGCCTAGGACAAAGCACTAA - -a -s simMouse_chr6.simMouse.chr6 412285 1 + 636262 A -s Anc0.Anc0refChr3 43269 1 + 222631 A -s Anc1.Anc1refChr6 73645 1 + 197743 A -s Anc2.Anc2refChr13 47295 1 + 96486 A -s mr.mrrefChr5 264998 1 + 294540 A -s simCow_chr6.simCow.chr6 403330 1 + 602619 A -s simDog_chr6.simDog.chr6 393852 1 + 593897 A -s simHuman_chr6.simHuman.chr6 398420 1 + 601863 A -s simRat_chr6.simRat.chr6 418538 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 412286 14 + 636262 CCACAAAATATAGG -s Anc0.Anc0refChr3 43270 14 + 222631 CCACAAAATATATG -s Anc1.Anc1refChr6 73646 14 + 197743 CCACAAAATATATG -s Anc2.Anc2refChr13 47296 14 + 96486 CCACAAAATATATG -s mr.mrrefChr5 264999 14 + 294540 CCACAAAATATAGG -s simCow_chr6.simCow.chr6 403333 14 + 602619 CAACAATATACATG -s simDog_chr6.simDog.chr6 393853 14 + 593897 CCATAAAATATATC -s simHuman_chr6.simHuman.chr6 398421 14 + 601863 CTGCAACAAAAATG -s simRat_chr6.simRat.chr6 418539 14 + 647215 CCACAAAATATAGG - -a -s simMouse_chr6.simMouse.chr6 412300 23 + 636262 AAAGAAACCTGATTTGCCTCAAC -s Anc0.Anc0refChr3 43289 22 + 222631 AGC-AAATTGGATGAGCTTCAAC -s Anc1.Anc1refChr6 73665 23 + 197743 AGCGAAATTGGATGAGCTTCAAC -s Anc2.Anc2refChr13 47315 22 + 96486 TGC-AAGTTGGATGAGCTCCAAC -s mr.mrrefChr5 265013 23 + 294540 AAAGAAACCTGATTTGCCTCAAC -s simCow_chr6.simCow.chr6 403352 22 + 602619 TGT-GAGTTGGATCAGGTCCAAT -s simDog_chr6.simDog.chr6 393872 22 + 593897 TGC-AGGTTGGATGAGCTCTGAC -s simHuman_chr6.simHuman.chr6 398440 23 + 601863 AGTGCAATTGGATGAGCTTCAAC -s simRat_chr6.simRat.chr6 418553 23 + 647215 AAAGAAACCTGACTTACCTGAAC - -a -s simMouse_chr6.simMouse.chr6 412323 6 + 636262 AACAGA -s Anc0.Anc0refChr3 43315 6 + 222631 GACAGA -s Anc1.Anc1refChr6 73692 6 + 197743 GACAGA -s Anc2.Anc2refChr13 47341 6 + 96486 GGCAGT -s mr.mrrefChr5 265036 6 + 294540 AACAGA -s simCow_chr6.simCow.chr6 403378 6 + 602619 AGCAGC -s simDog_chr6.simDog.chr6 393898 6 + 593897 GGCAGT -s simHuman_chr6.simHuman.chr6 398467 6 + 601863 GACAGA -s simRat_chr6.simRat.chr6 418576 6 + 647215 AACAGA - -a -s simMouse_chr6.simMouse.chr6 412329 17 + 636262 GCTAGCCAAGAAGAAAA -s Anc0.Anc0refChr3 43329 17 + 222631 GCTAGTCAAGAAGAAGA -s Anc1.Anc1refChr6 73706 17 + 197743 GCTAGTCAAGAAGAAGA -s Anc2.Anc2refChr13 47357 17 + 96486 ACTCATCAAGAAGAAGG -s mr.mrrefChr5 265042 17 + 294540 GCTAGCCAAGAAGAAGA -s simCow_chr6.simCow.chr6 403393 13 + 602619 AC----TAAGGAGAAGG -s simDog_chr6.simDog.chr6 393917 17 + 593897 ACTCATCAAGAAGCAGG -s simHuman_chr6.simHuman.chr6 398481 17 + 601863 GCTAGTCAAGATGAAGA -s simRat_chr6.simRat.chr6 418582 16 + 647215 GCTAACCAAGTAGATG- - -a -s simMouse_chr6.simMouse.chr6 412346 18 + 636262 AGAAATGGGTGCACTGAG -s Anc0.Anc0refChr3 43346 14 + 222631 TG----GGGTGTAAAGGC -s Anc1.Anc1refChr6 73723 14 + 197743 TG----GGGTGTAAAGGC -s Anc2.Anc2refChr13 47374 14 + 96486 TG----GGGTGTCAAGGC -s mr.mrrefChr5 265059 15 + 294540 AG---TGGGTGCACTGAG -s simCow_chr6.simCow.chr6 403406 14 + 602619 AG----GGGCGCCAAGAC -s simDog_chr6.simDog.chr6 393936 14 + 593897 TG----AGGTGTCAAAGC -s simHuman_chr6.simHuman.chr6 398498 14 + 601863 TG----GGGTATAAAGGC -s simRat_chr6.simRat.chr6 418598 13 + 647215 -----TGGGTGCACTGAG - -a -s simMouse_chr6.simMouse.chr6 412364 42 + 636262 ATGCCATGTAAATCTTGCTATGGCACAATAACTCAACTATTA -s Anc0.Anc0refChr3 43362 41 + 222631 AGG-CATGCACATATCGCCATGGCACATTAACCCAACCATTA -s Anc1.Anc1refChr6 73739 41 + 197743 AGG-CATGCACATATCGCCATGGCACATTAACCCAACCATTA -s Anc2.Anc2refChr13 47390 41 + 96486 AGA-CATGCACATCTCTCCATGGAACATTATCCCAACCATTA -s mr.mrrefChr5 265076 41 + 294540 ATG-CATGTAAATATTGCTATGGCACAATAACTCAACTATTA -s simCow_chr6.simCow.chr6 403422 41 + 602619 AGA-CATGCACATCTCACCATAGAACATTTCCCTAGCTTTTA -s simDog_chr6.simDog.chr6 393952 40 + 593897 GAA-CATGCAAATCCCTCTATGGAACATTATC-CGACCATTA -s simHuman_chr6.simHuman.chr6 398514 41 + 601863 AGG-CATGCACATATCGCCATGGCACATTGACGCAACCATTA -s simRat_chr6.simRat.chr6 418613 41 + 647215 ATG-CCAGTAAGTATTGCTATGGCACAATACTTTAACTATTA - -a -s simMouse_chr6.simMouse.chr6 412406 26 + 636262 GGCCTTAAAGTCTAATAACTCCAATC -s Anc0.Anc0refChr3 43409 26 + 222631 GGCCTGAAACTCCCCTAAATCTGATC -s Anc1.Anc1refChr6 73786 26 + 197743 GGCCTGAAACTCCCCTAAATCTGATC -s Anc2.Anc2refChr13 47437 26 + 96486 GGCATGAAACCCCCCTAAATCTGATT -s mr.mrrefChr5 265117 26 + 294540 GGCCTTAAAGTCTAATAACTCTAATC -s simCow_chr6.simCow.chr6 403469 26 + 602619 GGAACGACACCCCCCTAAATCTGATT -s simDog_chr6.simDog.chr6 393998 26 + 593897 GGCATGAAACCCCCCTAAATCTGAAT -s simHuman_chr6.simHuman.chr6 398561 26 + 601863 GGCCTGAAAATCCCCTAAATCTGATC -s simRat_chr6.simRat.chr6 418654 26 + 647215 GGCCTTAAAGTCTAATAACTCTAATG - -a -s simMouse_chr6.simMouse.chr6 412432 55 + 636262 TTTGTGAGTATAAAATCATGGGGCTGGGGCTCTGAAAGTGCTGAGCAATGTCCTC -s Anc0.Anc0refChr3 43435 46 + 222631 TTTGTAAGCAGAAAATC------CTGATGCTCTGAGATTGTCTATCA---CCCTC -s Anc1.Anc1refChr6 73812 49 + 197743 TTTGTAAGCAGAAAATC------CTGATGCTCTGAGATTGTCTATCAATCCCCTC -s Anc2.Anc2refChr13 47463 46 + 96486 TTTGTAAGCAGAAACTC------CTGGTGCTCTGAGATTGTCTATCA---CCCTG -s mr.mrrefChr5 265143 55 + 294540 TTTGTGAGTATAAAATCATGGGGCTGAGGCTCTGAAAGTGCTGAGCAATGTCCTC -s simCow_chr6.simCow.chr6 403499 46 + 602619 TTTGTTAGCGGAAAGTC------CTGGGGTTATGACATTGTTTAACA---CCCTG -s simDog_chr6.simDog.chr6 394024 46 + 593897 TTTGTAAGCAAATACTC------CTGGTGCTCTGAGATTGTCTATCA---GCCTG -s simHuman_chr6.simHuman.chr6 398587 49 + 601863 TTTGTAAGCAGAAAATC------CCGATCCTCTGATATTGTCCATTGATCCCCTC -s simRat_chr6.simRat.chr6 418680 55 + 647215 TTTGTGAGTCTAAAATCATGGGGCTAAGGCTCTGAAAGTGCTGAGCAATGTCCTC - -a -s simMouse_chr6.simMouse.chr6 412487 16 + 636262 CAATAAATGTAAGATT -s Anc0.Anc0refChr3 43481 16 + 222631 CAATAGATGTAAGATC -s Anc1.Anc1refChr6 73861 16 + 197743 CAATAGATGTAAGATC -s Anc2.Anc2refChr13 47509 16 + 96486 TAATAGATGTAAGATC -s mr.mrrefChr5 265198 16 + 294540 CAATAGATGTAAGATT -s simCow_chr6.simCow.chr6 403545 16 + 602619 TAATAAAAGTAAGATC -s simDog_chr6.simDog.chr6 394070 15 + 593897 TAAT-GATGTAAAATC -s simHuman_chr6.simHuman.chr6 398636 16 + 601863 CAATAGATGTAAGATC -s simRat_chr6.simRat.chr6 418739 16 + 647215 CACTAGACGTAAGATT - -a -s simMouse_chr6.simMouse.chr6 412503 1 + 636262 T -s Anc0.Anc0refChr3 43497 1 + 222631 T -s Anc1.Anc1refChr6 73877 1 + 197743 T -s Anc2.Anc2refChr13 47525 1 + 96486 T -s mr.mrrefChr5 265214 1 + 294540 T -s simCow_chr6.simCow.chr6 403576 1 + 602619 T -s simDog_chr6.simDog.chr6 394085 1 + 593897 T -s simHuman_chr6.simHuman.chr6 398652 1 + 601863 C -s simRat_chr6.simRat.chr6 418755 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 412504 21 + 636262 TATCACTCTCATTGGAAGGTT -s Anc0.Anc0refChr3 43499 21 + 222631 TATCATTTTTATTGGTAGGTT -s Anc1.Anc1refChr6 73879 21 + 197743 TATCATTTTTATTGGTAGGTT -s Anc2.Anc2refChr13 47527 21 + 96486 CATCATCTTTATTGGTAGGTT -s mr.mrrefChr5 265216 21 + 294540 TATCATTCTTATTGGAAGGTT -s simCow_chr6.simCow.chr6 403578 21 + 602619 CACTATCTTTATTGGTAGGTT -s simDog_chr6.simDog.chr6 394087 21 + 593897 CATCATCTTTATTGGTAGGTT -s simHuman_chr6.simHuman.chr6 398654 21 + 601863 TATCATTTTTATTGGTAGGTT -s simRat_chr6.simRat.chr6 418757 21 + 647215 TATCATTCTTATTGGAAGGTT - -a -s simMouse_chr6.simMouse.chr6 412525 55 + 636262 ATATGTAATCCAAGGAGACCCACGCACAGGCCTATAGTTTTTGTGACTACTGCAA -s Anc0.Anc0refChr3 43521 46 + 222631 ATCATTAATC---------CCACACCCAGTCATAAAATTTTTGTGACTTTTGCAA -s Anc1.Anc1refChr6 73901 46 + 197743 ATCATTAATC---------CCACACCCAGTCATAAAATTTTTGTGACTTTTGCAA -s Anc2.Anc2refChr13 47549 46 + 96486 ATCATTGATC---------CCACACCCAGTCATAAAGTTTTTGTGACTCTTGCAA -s mr.mrrefChr5 265238 46 + 294540 ATATGTAATC---------CCACGCACAGGCCTAAAATTTTTGTGACTTCTGCAA -s simCow_chr6.simCow.chr6 403599 35 + 602619 --------------------CACACCCGCTCAGAAGGTATTCAGGACTCTTACAT -s simDog_chr6.simDog.chr6 394109 46 + 593897 ATCATTGATC---------CCACACCCAGCCATAAAGTTTTTGTGAGTCTTGCAA -s simHuman_chr6.simHuman.chr6 398676 46 + 601863 ACCATTAATC---------TGACCCCTAGTCACAAAATTTTTGTGACTTTTGCAA -s simRat_chr6.simRat.chr6 418779 46 + 647215 ATATGTAATC---------ATATGCACAGGCCTAAGATTTTTGTAACTTCTGCAA - -a -s simMouse_chr6.simMouse.chr6 412580 4 + 636262 CAAT -s Anc0.Anc0refChr3 43569 4 + 222631 CCCT -s Anc1.Anc1refChr6 73949 4 + 197743 CCCT -s Anc2.Anc2refChr13 47597 4 + 96486 TCCT -s mr.mrrefChr5 265284 4 + 294540 CAAT -s simCow_chr6.simCow.chr6 403636 4 + 602619 TCCT -s simDog_chr6.simDog.chr6 394157 4 + 593897 TCCT -s simHuman_chr6.simHuman.chr6 398724 4 + 601863 CCCT -s simRat_chr6.simRat.chr6 418825 4 + 647215 CACT - -a -s simMouse_chr6.simMouse.chr6 412584 1 + 636262 T -s Anc0.Anc0refChr3 43573 1 + 222631 T -s Anc1.Anc1refChr6 73953 1 + 197743 T -s Anc2.Anc2refChr13 47608 1 + 96486 T -s mr.mrrefChr5 265288 1 + 294540 T -s simCow_chr6.simCow.chr6 403647 1 + 602619 T -s simDog_chr6.simDog.chr6 394168 1 + 593897 T -s simHuman_chr6.simHuman.chr6 398728 1 + 601863 T -s simRat_chr6.simRat.chr6 418829 1 + 647215 G - -a -s simMouse_chr6.simMouse.chr6 412585 1 + 636262 A -s Anc0.Anc0refChr3 43574 1 + 222631 G -s Anc1.Anc1refChr6 73954 1 + 197743 G -s Anc2.Anc2refChr13 47609 1 + 96486 G -s mr.mrrefChr5 265289 1 + 294540 A -s simCow_chr6.simCow.chr6 403648 1 + 602619 G -s simDog_chr6.simDog.chr6 394169 1 + 593897 G -s simHuman_chr6.simHuman.chr6 398729 1 + 601863 G -s simRat_chr6.simRat.chr6 418832 1 + 647215 G - -a -s simMouse_chr6.simMouse.chr6 412586 13 + 636262 GTCTCTTTTCACG -s Anc0.Anc0refChr3 43579 13 + 222631 GTCTTTTTTCACG -s Anc1.Anc1refChr6 73959 13 + 197743 GTCTTTTTTCACG -s Anc2.Anc2refChr13 47614 13 + 96486 GTCTTTCATCACG -s mr.mrrefChr5 265290 13 + 294540 GTCTCTTTTCACG -s simCow_chr6.simCow.chr6 403653 13 + 602619 CTCTTTACTCCCA -s simDog_chr6.simDog.chr6 394174 13 + 593897 GTCTTACACCATG -s simHuman_chr6.simHuman.chr6 398734 10 + 601863 GTA---TTTCTGG -s simRat_chr6.simRat.chr6 418833 13 + 647215 GTCTCTTTCCACA - -a -s simMouse_chr6.simMouse.chr6 412599 2 + 636262 TG -s Anc0.Anc0refChr3 43592 2 + 222631 TT -s Anc1.Anc1refChr6 73972 2 + 197743 TT -s Anc2.Anc2refChr13 47632 2 + 96486 TT -s mr.mrrefChr5 265303 2 + 294540 TG -s simCow_chr6.simCow.chr6 403671 2 + 602619 TT -s simDog_chr6.simDog.chr6 394192 2 + 593897 TT -s simHuman_chr6.simHuman.chr6 398744 2 + 601863 TC -s simRat_chr6.simRat.chr6 418846 2 + 647215 TG - -a -s simMouse_chr6.simMouse.chr6 412601 7 + 636262 ACACTCT -s Anc0.Anc0refChr3 43594 6 + 222631 GCAC-CC -s Anc1.Anc1refChr6 73974 7 + 197743 GCACTCC -s Anc2.Anc2refChr13 47634 6 + 96486 GCAC-CC -s mr.mrrefChr5 265305 7 + 294540 ACACTCT -s simCow_chr6.simCow.chr6 403674 6 + 602619 GCAC-CC -s simDog_chr6.simDog.chr6 394194 6 + 593897 GCAC-CC -s simHuman_chr6.simHuman.chr6 398746 7 + 601863 GCCCTCA -s simRat_chr6.simRat.chr6 418848 7 + 647215 ACACTCT - -a -s simMouse_chr6.simMouse.chr6 412608 9 + 636262 ACTCTGTTT -s Anc0.Anc0refChr3 43600 8 + 222631 ACTCTGTT- -s Anc1.Anc1refChr6 73981 9 + 197743 ACTCTGTTT -s Anc2.Anc2refChr13 47640 8 + 96486 ACTCTGTT- -s mr.mrrefChr5 265312 9 + 294540 ACTCTGTTT -s simCow_chr6.simCow.chr6 403681 8 + 602619 ACTCAATT- -s simDog_chr6.simDog.chr6 394200 8 + 593897 ACTCTGTT- -s simHuman_chr6.simHuman.chr6 398753 9 + 601863 AATGTATTT -s simRat_chr6.simRat.chr6 418855 9 + 647215 ACTTTGTTT - -a -s simMouse_chr6.simMouse.chr6 412617 5 + 636262 TTGAT -s Anc1.Anc1refChr6 74060 5 + 197743 GTGAC -s mr.mrrefChr5 265321 5 + 294540 TTGAT -s simHuman_chr6.simHuman.chr6 398866 5 + 601863 GTGAC -s simRat_chr6.simRat.chr6 418864 5 + 647215 TTAGG - -a -s simMouse_chr6.simMouse.chr6 412622 12 + 636262 TTATAGTGAGAT -s Anc1.Anc1refChr6 74065 11 + 197743 TTATA-TGGAAT -s mr.mrrefChr5 265326 12 + 294540 TTATAGTGAGAT -s simHuman_chr6.simHuman.chr6 398871 11 + 601863 TTATA-TGGAAT -s simRat_chr6.simRat.chr6 418896 12 + 647215 TTATAGTGAGAT - -a -s simMouse_chr6.simMouse.chr6 412634 8 + 636262 GCTGGGCC -s Anc1.Anc1refChr6 74076 8 + 197743 ACTGGCCC -s mr.mrrefChr5 265338 8 + 294540 GCTGGGCC -s simHuman_chr6.simHuman.chr6 398884 8 + 601863 ACTGGCCC -s simRat_chr6.simRat.chr6 418908 8 + 647215 GCTGGGCT - -a -s simMouse_chr6.simMouse.chr6 412642 10 + 636262 CTTTATTAGC -s Anc0.Anc0refChr3 43678 1 + 222631 ---------T -s Anc1.Anc1refChr6 74084 10 + 197743 CTCTCTCAGT -s Anc2.Anc2refChr13 47720 1 + 96486 ---------T -s mr.mrrefChr5 265346 10 + 294540 CTTTATTAGC -s simCow_chr6.simCow.chr6 403710 1 + 602619 ---------T -s simHuman_chr6.simHuman.chr6 398899 10 + 601863 CTCTCTCAGT -s simRat_chr6.simRat.chr6 418916 10 + 647215 GTTTATAAGC - -a -s simMouse_chr6.simMouse.chr6 412652 12 + 636262 ACCCCTAGAGAG -s Anc0.Anc0refChr3 43688 11 + 222631 ACCCTTAGAGA- -s Anc1.Anc1refChr6 74103 11 + 197743 ACCCTTAGAGA- -s Anc2.Anc2refChr13 47730 11 + 96486 ACCCTTAGAGA- -s mr.mrrefChr5 265356 12 + 294540 ACCCCTAGAGAG -s simCow_chr6.simCow.chr6 403720 11 + 602619 ACCCTTAGAGA- -s simHuman_chr6.simHuman.chr6 398918 11 + 601863 ACCCTTAGTGA- -s simRat_chr6.simRat.chr6 418926 12 + 647215 ACCCTTAGAGAG - -a -s simMouse_chr6.simMouse.chr6 412664 136 + 636262 CCCGGCAGTAGCTATCAATGAGGCAGTAGCTATTCAAGGCCACCCCCATAATGTATCTCCTTGCTCTTTTTTGTTTACATTAAGTATAGCTGGTGCCCTTTGAGTTGACCATTAGTGTGGAGGATGACCATTGGTG -s Anc0.Anc0refChr3 43699 27 + 222631 ------------TATCA------CAGTAGCTAT-CAAAGCTACCTC------------------------------------------------------------------------------------------ -s Anc1.Anc1refChr6 74114 27 + 197743 ------------TATCA------CAGTAGCTAT-CAAAGCTACCTC------------------------------------------------------------------------------------------ -s Anc2.Anc2refChr13 47741 27 + 96486 ------------CATCA------CAGTAGCTGT-GCCAACTACCTC------------------------------------------------------------------------------------------ -s mr.mrrefChr5 265368 135 + 294540 CCCGGCAGTAGCTATCAATGAGGCAGTAGCTAT-CAAGGCCACCCCCATAATGTATCTCCTTGCTCTTTTTTGTTTACATTAAGTATAGCTGGTGCCCTTTGAGTTGACCATTAGTGTGGAGGATGACCATTGGTG -s simCow_chr6.simCow.chr6 403731 27 + 602619 ------------CATCA------CAGTAGCTGT-GCCTACTACCGC------------------------------------------------------------------------------------------ -s simDog_chr6.simDog.chr6 394310 21 + 593897 --------------TAA------CAGTGGCTG-----AACTACCTC------------------------------------------------------------------------------------------ -s simHuman_chr6.simHuman.chr6 398929 27 + 601863 ------------TATCA------CAGTAGCTAT-CAACGCTACCTC------------------------------------------------------------------------------------------ -s simRat_chr6.simRat.chr6 418939 135 + 647215 TTTGGCAGCAGCTGCTAATGGGGCAGCAGCTAT-CAACACACCCCCAATAATGCGTCTCTTCGAGCTTCTTTGTCTACATTAAGCATAGCTGGCGCCCTTTGAGTCAACCATTGGTGTGGGGGATGACTATAGGTG - -a -s simMouse_chr6.simMouse.chr6 412800 205 + 636262 AGGGGATATGTACATGAAGTATTGCAGCTAGTGACAGTGGGGACTGAGTTCTGACAATATTTAGCGGTGTCTCACGCCAAGTGATTAGATATTCAATTAATTTGGATTGACTATCAGTTTACTAGGCCACACCCTAGTTTGTTGAACCGCCCTGTTAATTTAACTGGGGGATGAGGTTTATGGAACTATGGGCCTAATTCCCCGA -s mr.mrrefChr5 265503 196 + 294540 AGGGGATATGTACATGAAGTATTGCAGCTAGTGACAGTGGGGACTGAGTTCTGACAATATTTAGCGGTGTCTCACGCCAAGTGATTAGATATTC--------TGGATTGACTATCAGTTT-CTAGGCCACACCCTAGTTTGTTGAACCGCCCTGTTAATTTAACTGGGGGATGAGGTTTATGGAACTATGGGCCTAATTCCCCGA -s simRat_chr6.simRat.chr6 419075 196 + 647215 GGGGGACGTGTACATGAAGTATTGCAACTGGCACCAGTGGGCACTGGGTCCTGAAAATATTTAGCGGTGCCGCACACCAAATGATTAGATGTTC--------TAGATTGACTATGCGTTT-CTAGACCACACCCTAGCTTGTTGAACCCCCCTGTTAATTAAACTGGGGGATAAAGTTTATGGAACTATGGGTCTAATTCCTCAA - -a -s simMouse_chr6.simMouse.chr6 413005 22 + 636262 GTTGCTGACACTCATTTGAGGC -s mr.mrrefChr5 265699 22 + 294540 GTTGCTGACACTCATTTGAGGC -s simRat_chr6.simRat.chr6 419272 22 + 647215 GTTGTTGACATTCTTTTGAGGG - -a -s simMouse_chr6.simMouse.chr6 413027 57 + 636262 CCATGATTGGTTGATCTGCCATAAGCATAGGCTAAGATGAATTCCACTGACTGCAGA -s mr.mrrefChr5 265721 57 + 294540 CCATGATTGGTTGATCTGCCATAAGCATAGGCTAAGATGAATTCCACTGACTGCAGA -s simRat_chr6.simRat.chr6 419295 57 + 647215 CCGTGATTGACTGATCTGCCATGAGCACAGGCCAAGATGAATTCCACTCAATGAAGA - -a -s simMouse_chr6.simMouse.chr6 413088 5 + 636262 TGCCA - -a -s simMouse_chr6.simMouse.chr6 413156 1 + 636262 C -s Anc0.Anc0refChr3 41930 1 + 222631 A -s Anc1.Anc1refChr6 72270 1 + 197743 A -s Anc2.Anc2refChr13 45946 1 + 96486 A -s mr.mrrefChr5 265845 1 + 294540 C -s simCow_chr6.simCow.chr6 401799 1 + 602619 A -s simDog_chr6.simDog.chr6 392557 1 + 593897 A -s simHuman_chr6.simHuman.chr6 397047 1 + 601863 A -s simRat_chr6.simRat.chr6 419421 1 + 647215 C - -a -s simMouse_chr6.simMouse.chr6 413191 1 + 636262 G -s mr.mrrefChr5 265885 1 + 294540 T -s simRat_chr6.simRat.chr6 419461 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 413192 1 + 636262 A -s Anc0.Anc0refChr3 41988 1 + 222631 G -s Anc1.Anc1refChr6 72328 1 + 197743 G -s Anc2.Anc2refChr13 46004 1 + 96486 G -s mr.mrrefChr5 265886 1 + 294540 A -s mr.mrrefChr5 263627 1 + 294540 G -s simCow_chr6.simCow.chr6 401865 1 + 602619 G -s simDog_chr6.simDog.chr6 392614 1 + 593897 T -s simHuman_chr6.simHuman.chr6 397105 1 + 601863 G -s simRat_chr6.simRat.chr6 417273 1 + 647215 G -s simRat_chr6.simRat.chr6 419462 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 413358 4 + 636262 ATCA -s Anc0.Anc0refChr3 42194 2 + 222631 --CA -s Anc1.Anc1refChr6 72534 4 + 197743 AACA -s Anc2.Anc2refChr13 46211 2 + 96486 --CA -s mr.mrrefChr5 266055 4 + 294540 ATCA -s simCow_chr6.simCow.chr6 402075 2 + 602619 --CT -s simDog_chr6.simDog.chr6 392821 2 + 593897 --CA -s simHuman_chr6.simHuman.chr6 397305 4 + 601863 AACA -s simRat_chr6.simRat.chr6 419679 4 + 647215 ATCA - -a -s simMouse_chr6.simMouse.chr6 413362 1 + 636262 C -s Anc0.Anc0refChr3 42196 1 + 222631 C -s Anc1.Anc1refChr6 72538 1 + 197743 C -s Anc2.Anc2refChr13 46213 1 + 96486 C -s mr.mrrefChr5 266059 1 + 294540 C -s mr.mrrefChr5 263834 1 + 294540 C -s simCow_chr6.simCow.chr6 402077 1 + 602619 C -s simDog_chr6.simDog.chr6 392823 1 + 593897 C -s simHuman_chr6.simHuman.chr6 397309 1 + 601863 C -s simRat_chr6.simRat.chr6 417477 1 + 647215 C -s simRat_chr6.simRat.chr6 419683 1 + 647215 C - -a -s simMouse_chr6.simMouse.chr6 413498 14 + 636262 AGACAGAACACCAG -s mr.mrrefChr5 266195 14 + 294540 AGACAGAACACCAG -s simRat_chr6.simRat.chr6 419822 14 + 647215 AGACAGAGCACCAG - -a -s simMouse_chr6.simMouse.chr6 413555 5 + 636262 ATGGG -s mr.mrrefChr5 266252 5 + 294540 ACGGG -s simRat_chr6.simRat.chr6 419879 5 + 647215 ACGGG - -a -s simMouse_chr6.simMouse.chr6 413657 11 + 636262 CTTAAGAGGCC -s Anc0.Anc0refChr3 42455 11 + 222631 TCAAGAAGACT -s Anc1.Anc1refChr6 72822 11 + 197743 TCAAGAAGACT -s Anc2.Anc2refChr13 46472 11 + 96486 TCAAGAAGACT -s mr.mrrefChr5 266354 11 + 294540 TTTAGGAGGCC -s simCow_chr6.simCow.chr6 402432 11 + 602619 TCAAGAAGGCT -s simDog_chr6.simDog.chr6 393063 11 + 593897 TCAAGAAGACT -s simRat_chr6.simRat.chr6 419983 11 + 647215 TTTAGGAGGCC - -a -s simMouse_chr6.simMouse.chr6 413691 5 + 636262 CCTTA -s Anc0.Anc0refChr3 42489 5 + 222631 CCACA -s Anc1.Anc1refChr6 72856 5 + 197743 CCACA -s Anc2.Anc2refChr13 46506 5 + 96486 CCACA -s mr.mrrefChr5 266388 5 + 294540 CCTTA -s simCow_chr6.simCow.chr6 402467 5 + 602619 CCACA -s simDog_chr6.simDog.chr6 393097 5 + 593897 CCACA -s simRat_chr6.simRat.chr6 420017 5 + 647215 CCTTA - -a -s simMouse_chr6.simMouse.chr6 413715 5 + 636262 ACAGG - -a -s simMouse_chr6.simMouse.chr6 413733 12 + 636262 TAAAATGAGCTT -s Anc0.Anc0refChr3 42537 3 + 222631 T---------TA -s Anc1.Anc1refChr6 72904 3 + 197743 T---------TA -s Anc2.Anc2refChr13 46555 3 + 96486 T---------TA -s mr.mrrefChr5 266425 3 + 294540 T---------TT -s mr.mrrefChr5 264275 3 + 294540 T---------TT -s simCow_chr6.simCow.chr6 402517 3 + 602619 T---------TA -s simDog_chr6.simDog.chr6 393131 3 + 593897 T---------TA -s simHuman_chr6.simHuman.chr6 397604 3 + 601863 T---------TA -s simRat_chr6.simRat.chr6 417865 3 + 647215 T---------TT -s simRat_chr6.simRat.chr6 420054 3 + 647215 T---------TT - -a -s simMouse_chr6.simMouse.chr6 413762 5 + 636262 GTCTA -s Anc0.Anc0refChr3 42564 5 + 222631 GTCTA -s Anc1.Anc1refChr6 72931 5 + 197743 GTCTA -s Anc2.Anc2refChr13 46582 5 + 96486 GTAGA -s mr.mrrefChr5 266445 5 + 294540 GTCTA -s mr.mrrefChr5 264295 5 + 294540 GTCTG -s simCow_chr6.simCow.chr6 402564 5 + 602619 GTAGA -s simHuman_chr6.simHuman.chr6 397631 5 + 601863 GTGCC -s simRat_chr6.simRat.chr6 417885 5 + 647215 GTCTG -s simRat_chr6.simRat.chr6 420074 5 + 647215 GTCTA - -a -s simMouse_chr6.simMouse.chr6 413832 2 + 636262 CA -s Anc0.Anc0refChr3 42685 2 + 222631 CG -s Anc1.Anc1refChr6 73057 2 + 197743 CG -s Anc2.Anc2refChr13 46703 2 + 96486 CG -s mr.mrrefChr5 266568 2 + 294540 CG -s simCow_chr6.simCow.chr6 402685 2 + 602619 CA -s simDog_chr6.simDog.chr6 393233 2 + 593897 CG -s simHuman_chr6.simHuman.chr6 397758 2 + 601863 TG -s simRat_chr6.simRat.chr6 420199 2 + 647215 TG - -a -s simMouse_chr6.simMouse.chr6 413890 11 + 636262 CACATAATCGC -s mr.mrrefChr5 266626 11 + 294540 CACATAATCGT -s simRat_chr6.simRat.chr6 420257 11 + 647215 CACATAAGCAT - -a -s simMouse_chr6.simMouse.chr6 413976 210 + 636262 CAACAAGAGTGAGAGTTGAATGTTGGTCTGGGGGATGCATACATAGAATATATCAGCTGGTGACATTTGAATTGGCTCTCAGTCTGAGAGTTATCACACTCTTATTTGCGACCTTTCCCATTAGCTGATCCATAAGACTAACATGAAATTCTGCTAAATGATATGGTGTGCCACATGAGATCCCCCTCTGATCCCCCTCTACCCTTGTAA -s Anc0.Anc0refChr3 43727 10 + 222631 --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AATATTATAA -s Anc1.Anc1refChr6 74142 10 + 197743 --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AATATTATAA -s Anc2.Anc2refChr13 47769 10 + 96486 --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AATATTATAA -s mr.mrrefChr5 266715 169 + 294540 CAACAAGAGTGAGAGTTGAATGTTGGTCTGGGGGATG-----------------AGCTGG-------------GGCTCTCAGTCTGAGAGTTATCACACTCTTATTTGCGACCTTTCCCATTAGCTGATCCATAAGACTAACATGAAATTCTGCTAAATGATATGGTGTGCCACATGAGATCCCCCTCT-----------ACCCTTGTAA -s simCow_chr6.simCow.chr6 403759 10 + 602619 --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AAGATTTTAG -s simDog_chr6.simDog.chr6 394332 7 + 593897 ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TAT-ATAA -s simHuman_chr6.simHuman.chr6 398957 10 + 601863 --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ATTATTATGA -s simRat_chr6.simRat.chr6 420345 169 + 647215 CAACAAGAGTGAGAGTTGAGTTCTTGGATGGCTATTG-----------------GGCCGG-------------GGGGCTCAGTCTGAGGGTCATCACACTCTCATTTGTAAACTCTCCCATTAGCTAATCTGTAAGACTGAGATGGAATTCTTCTTAACAATAAGGTGCACAACGTGAGGTCCCTCTCC-----------ACCCTTGTAA - -a -s simMouse_chr6.simMouse.chr6 414186 96 + 636262 TCACCAGGTTCTGTGTACTTGTCAGGTAATCACGTATGTATCATAAATTGCTAGGGAAGTTGGACCAGCTGGTAAGAAATATGGTGGTAATCCGGT -s Anc0.Anc0refChr3 43738 95 + 222631 TCACTGGGTTTTATGTATTAAACAGGTACCTATGTACAGCTCATAAATTGATAGGGAAGTTGGACCAGCTGGTGGTAAATAAAGTGGTAGCTGG-T -s Anc1.Anc1refChr6 74153 95 + 197743 TCACTGGGTTTTATGTATTAAACAGGTACCTATGTACAGCTCATAAATTGATAGGGAAGTTGGACCAGCTGGTGGTAAATAAAGTGGTAGCTGG-T -s Anc2.Anc2refChr13 47780 95 + 96486 TCACTGGGTTTTACATATTAAACAGGTACCTATGTACAGCTCATAAATCGATAGGGAAGTTGGACCAGCTGGTGGTAAATAAAGTGGTAGCTGG-T -s mr.mrrefChr5 266884 95 + 294540 TCACCAGGTTCTGTGTACTTGTCAGGTAATCATGTATGGCTCATAAATTGCTAGGGAAGTTGGACCAGCTGGTAGGAAATATGGTGGTAGCTCG-T -s simCow_chr6.simCow.chr6 403770 93 + 602619 TCACTTGGTTTTACACATCAAACAGGTACCTTTGCAAAGCTCATAAATCAATGGGGATGTCG--CCAGATAGCGGTAAATAAAGCAATAGCAGG-A -s simDog_chr6.simDog.chr6 394340 94 + 593897 TCACTGGGTTTTACATACTAAACAGGTACCTATGTACAGCTCACACATCG-TAGGGAAGTTGGACCAGCTGGTAGTTAATAAAGTGGTAGCTGG-T -s simHuman_chr6.simHuman.chr6 398968 95 + 601863 TCACTGGGTTTTATGTATTGCAAAGGGACCTATGTACAGCCCATAAATTGGTAGGGAAGTAGGTCCAGGTGGTGGTAAATAAAATGGTAGCTAG-T -s simRat_chr6.simRat.chr6 420514 92 + 647215 TCACCAGGTTCTGTGTACTTGTCAGGTAATCATGTATGGCTTGTAAATTGCT---GAAGCTGTACCAGATGGTAGGAAATATGGTGGTAGCTCG-T - -a -s simMouse_chr6.simMouse.chr6 414282 60 + 636262 TAGGGAGGTCACAATCATGAGGATGCTGGCCCCCTAAATACTTTTTGATTTGGGCTAGAA -s Anc0.Anc0refChr3 43833 60 + 222631 GAAGAAGGCCACAATCATTAGGATGATTGACCCCTAGACACTTTGTGACTTGAGCTTGAA -s Anc1.Anc1refChr6 74248 60 + 197743 GAAGAAGGCCACAATCATTAGGATGATTGACCCCTAGACACTTTGTGACTTGAGCTTGAA -s Anc2.Anc2refChr13 47875 60 + 96486 GAAGAAGGCCACAATCATTGTAATGACTGACCCCTAGACACTTTGTGACTTGAGTTTGAA -s mr.mrrefChr5 266979 60 + 294540 TAGGAAGGCCACAATCATGAGGATGCTTGCCCCCTAGATACTTTTTGACTTGAGCTTGAA -s simCow_chr6.simCow.chr6 403867 60 + 602619 AAGGAAGACCACAATCACTACGATCACTGACCTCCAGATACTTTGTGACTTGGGTTTGAA -s simDog_chr6.simDog.chr6 394434 60 + 593897 GAAGAAGGCCACAATCATTGTAATGACTGCCCCCTAGACACTTCGCGACTTGAGTGTGAA -s simHuman_chr6.simHuman.chr6 399063 57 + 601863 GAAGAAGGCTGCAACC---AGGATGATTGACCCCTAGAAACTATGTGACTTGAGCTTGAA -s simRat_chr6.simRat.chr6 420606 60 + 647215 TAGGAAGACCATAATCATGTGGATGCTTGCCCCCTGGGTATTTTTTGACTTAAGCTTGGA - -a -s simMouse_chr6.simMouse.chr6 414342 9 + 636262 CAAAAACAC -s Anc0.Anc0refChr3 43896 9 + 222631 TAGAAATGG -s Anc1.Anc1refChr6 74311 9 + 197743 TAGAAATGG -s Anc2.Anc2refChr13 47938 9 + 96486 TAGAAATGG -s mr.mrrefChr5 267042 9 + 294540 CAAAAACAG -s simCow_chr6.simCow.chr6 403930 9 + 602619 TGGAAATGG -s simDog_chr6.simDog.chr6 394497 9 + 593897 TAGAAATGG -s simHuman_chr6.simHuman.chr6 399123 9 + 601863 TAGGAATGG -s simRat_chr6.simRat.chr6 420669 9 + 647215 CAAATTCAG - -a -s simMouse_chr6.simMouse.chr6 414351 16 + 636262 CATGACATGTGGTGAG -s Anc0.Anc0refChr3 43907 16 + 222631 AATGACTCCTGGTGGG -s Anc1.Anc1refChr6 74322 16 + 197743 AATGACTCCTGGTGGG -s Anc2.Anc2refChr13 47949 16 + 96486 AATGACTCCTGGTGGG -s mr.mrrefChr5 267051 16 + 294540 CATGACATGTGGTGAG -s simCow_chr6.simCow.chr6 403941 16 + 602619 AATGACTTCTGGTGGG -s simDog_chr6.simDog.chr6 394508 16 + 593897 AACGACTCCTCGTGGG -s simHuman_chr6.simHuman.chr6 399134 16 + 601863 GATGACTCTTGTTGGG -s simRat_chr6.simRat.chr6 420678 16 + 647215 CATGACATGTTGTGAG - -a -s simMouse_chr6.simMouse.chr6 414367 22 + 636262 GTCTAAGCTAGTCACGTGTGCA -s Anc0.Anc0refChr3 43927 22 + 222631 ACCTAGGCTAGTGACCTGTGGA -s Anc1.Anc1refChr6 74344 22 + 197743 ACCTAGGCTAGTGACCTGTGGA -s Anc2.Anc2refChr13 47969 22 + 96486 ACCTAGGCCAGTGACCTGTGGA -s mr.mrrefChr5 267073 22 + 294540 ATCTAAGCTAGTCACCTGTGCA -s simCow_chr6.simCow.chr6 403961 20 + 602619 ACCTAGACCAGTGATCAGTG-- -s simDog_chr6.simDog.chr6 394528 22 + 593897 ACCTGGGCCAGTGACCTGTGGA -s simHuman_chr6.simHuman.chr6 399156 22 + 601863 ACCTATGCTAGTGACCTGTGGA -s simRat_chr6.simRat.chr6 420700 22 + 647215 ATCTAAGCTAGTCACCTGTGCA - -a -s simMouse_chr6.simMouse.chr6 414389 74 + 636262 AAAACTGCTGAATTTCAGTCTATGATTTTGTTATCCCTAATATTGATTAAACATATACACTATATAACCCCATA -s Anc0.Anc0refChr3 43952 69 + 222631 CAAAGTTGTG-----CAGCCCATAATTTTGTTAGCCCTGATAATTATTAAAAATATACATTATACCACCCCAAA -s Anc1.Anc1refChr6 74369 69 + 197743 CAAAGTTGTG-----CAGCCCATAATTTTGTTAGCCCTGATAATTATTAAAAATATACATTATACCACCCCAAA -s Anc2.Anc2refChr13 47994 69 + 96486 GTAAGTTGGG-----CAGCCCATAATTTTGTTAGCCCCGATAATTATTAAAAATGTGCATCATACCACCCCAAA -s mr.mrrefChr5 267095 74 + 294540 CAAACTGGTGAATTTCAGCCCATGATTTTGTTATCCCTAATATTGATTAAACATATACATTATATAACCCCATA -s simCow_chr6.simCow.chr6 403981 54 + 602619 ---------------CAGGCAATAATTCTTTTAGCTCCGGTAGTTATTAGAAATGTG-----TACCACCCTAAA -s simDog_chr6.simDog.chr6 394553 66 + 593897 GTAAGTTGGG-----CAGCCCATAATTTTGTTAGCCCCAATAATGATTAATGATGTGCATCATACC---CCCCA -s simHuman_chr6.simHuman.chr6 399181 69 + 601863 CAAAGTTGTG-----CAGCCCATAATTTTGTTGACGCTGATAACTGTTAAAAATAAACATTATACCACCCCAAA -s simRat_chr6.simRat.chr6 420722 62 + 647215 CAAACTGGTGAAGTTCAGCCCATGATTAT------------ATTGATTAAATATACACATTATATAACCCCATA - -a -s simMouse_chr6.simMouse.chr6 414463 83 + 636262 CTGGCCAACTGCTAGGAGTGTTTGTTGCGATTTCCATCACTGTCCAATTGATTAAGGGAATACAAAGAGCTTATGAGCTTCTC -s Anc0.Anc0refChr3 44028 83 + 222631 CTGCTCAAATTCATTGAGTGTCAGTGGTAATTCTTATCACCATCTGATTGATTCAGGGAATTCAAACCGCTTATAAACTTCTC -s Anc1.Anc1refChr6 74445 83 + 197743 CTGCTCAAATTCATTGAGTGTCAGTGGTAATTCTTATCACCATCTGATTGATTCAGGGAATTCAAACCGCTTATAAACTTCTC -s Anc2.Anc2refChr13 48070 83 + 96486 CTACTAAAATTCATTAAGTGTCAGTGATAATTCTTATTGCCATCTGATTGATTCAGGGAATTCAAACCACTTACAAACTACTC -s mr.mrrefChr5 267176 83 + 294540 CTGGCCAACTGCTAGGAGTGTTTGTGGTGATTTCTATCACTGTCCAATTGATTAAGGGAATACAAAGAGCTTATGAGCTTCTC -s simCow_chr6.simCow.chr6 404042 73 + 602619 CTACTAAAATTCATT----------GATAATTCTCATTGTCACCTGATTGAGTCAGGGAATTCAAACCACTTACAAACTACTC -s simDog_chr6.simDog.chr6 394620 55 + 593897 --------ATTCATTAAGTGTCAGTGACTGTTCTTATTGCCATCTGATTGATTCAGGGTATTC-------------------- -s simHuman_chr6.simHuman.chr6 399257 83 + 601863 CCGCTCAAATTTATTGTGTGTCAGTGGTAATTCTTAGCACCATCTGATTGATTCAGGGAATTCAAATGGCTAATAAACTTCCA -s simRat_chr6.simRat.chr6 420791 83 + 647215 CTGACCAACTCCTAAGAGTGTTCATGGTGTTTTCTATAACTGTCCAATCGATTGAGAGAATGCAAAAAGCTTATGAGCTTCTC - -a -s simMouse_chr6.simMouse.chr6 414546 57 + 636262 CCTTTAAATCACAATTATGTCACAATTGCTCAACTCCTACTCTGAAACTGTAGGAAT -s Anc0.Anc0refChr3 44111 57 + 222631 CCTTTAAATCACTCTTATGTCACAATGTATCACCTCCTTATGTGAGACACAAGGGAT -s Anc1.Anc1refChr6 74528 57 + 197743 CCTTTAAATCACTCTTATGTCACAATGTATCACCTCCTTATGTGAGACACAAGGGAT -s Anc2.Anc2refChr13 48153 57 + 96486 CCTTTAAATCACTCTTATAGCACAATGTATCACCTCCTTATGTGAGACACAAGGGAT -s mr.mrrefChr5 267259 57 + 294540 CCTTTAAATCACTATTATGTCACAATGGCTCAACTCCTAATGTGAAACTGTAGGAAT -s simCow_chr6.simCow.chr6 404121 50 + 602619 CCTTTAAATCCCTTCTATAACACAATGTATC-------TATGTGAGACACAGGGGAT -s simDog_chr6.simDog.chr6 394675 53 + 593897 ----TAAGTAACTCTTGTAGGATAATGTATCACCTCCTTATGTGAGACACAAGGGCT -s simHuman_chr6.simHuman.chr6 399340 57 + 601863 CCCTTAAATCAGTCTTACGTCACAATGTACCACCTCCTCATGTGAGACACAAGGGAT -s simRat_chr6.simRat.chr6 420874 56 + 647215 CATTATATTCACTATTATGACAGAATGGCTCAACTCCTAATGTAAAACC-CAGGATT - -a -s simMouse_chr6.simMouse.chr6 414603 15 + 636262 ATCTTACTAAACAAA -s Anc0.Anc0refChr3 44170 15 + 222631 ATCTTGTGAGACACA -s Anc1.Anc1refChr6 74587 15 + 197743 ATCTTGTGAGACACA -s Anc2.Anc2refChr13 48212 15 + 96486 ATCTTGTGAGACACT -s mr.mrrefChr5 267316 15 + 294540 ATCTTGTTAAACAAA -s simCow_chr6.simCow.chr6 404173 15 + 602619 ATCTTGTGAGTCATG -s simDog_chr6.simDog.chr6 394728 11 + 593897 ----TGTGAGACACT -s simHuman_chr6.simHuman.chr6 399399 15 + 601863 ATCATGTGAGACACA -s simRat_chr6.simRat.chr6 420930 14 + 647215 ATCTTGTCACATAA- - -a -s simMouse_chr6.simMouse.chr6 414618 29 + 636262 ACTTTTCAAAATCCAGACCCATGAGGGCA -s Anc0.Anc0refChr3 44190 27 + 222631 ACGTCTCAAAATCCAGATTCAT-AC-ATA -s Anc1.Anc1refChr6 74607 27 + 197743 ACGTCTCAAAATCCAGATTCAT-AC-ATA -s Anc2.Anc2refChr13 48232 27 + 96486 ATGTCTCAAAATCCAGATTCAC-AC-ATG -s mr.mrrefChr5 267331 28 + 294540 ACTTTTCAAAATCCAGACCCATGAG-GCA -s simCow_chr6.simCow.chr6 404193 27 + 602619 GTCTCCGAAAATCCAGATTCAG-GC-ATG -s simDog_chr6.simDog.chr6 394744 27 + 593897 ATGTCTCAAGATCCACATTCAC-AC-ATG -s simHuman_chr6.simHuman.chr6 399420 27 + 601863 ACACCTCAAAATCCAGATTCAT-AC-ATA -s simRat_chr6.simRat.chr6 420944 3 + 647215 --------------------------GCA - -a -s simMouse_chr6.simMouse.chr6 414647 15 + 636262 GCACAGTTTTTGGTG -s Anc0.Anc0refChr3 44217 13 + 222631 GCACAGTTTT--GTG -s Anc1.Anc1refChr6 74634 13 + 197743 GCACAGTTTT--GTG -s Anc2.Anc2refChr13 48261 13 + 96486 GCATAGTTTT--GTG -s mr.mrrefChr5 267359 15 + 294540 GCACAGTTTTAGGTG -s simCow_chr6.simCow.chr6 404222 13 + 602619 GCATGGTTTT--GTG -s simDog_chr6.simDog.chr6 394773 13 + 593897 GCATAGTCTT--GTG -s simHuman_chr6.simHuman.chr6 399447 13 + 601863 GCACAATTTT--ATG -s simRat_chr6.simRat.chr6 420947 15 + 647215 GCACAGTTTTAGGTG - -a -s simMouse_chr6.simMouse.chr6 414662 26 + 636262 GTCTGCCACTGCTTAAGGGCAATGCA -s Anc0.Anc0refChr3 44230 25 + 222631 ATCTCCCAATTCTT-AGGGCAATACA -s Anc1.Anc1refChr6 74647 25 + 197743 ATCTCCCAATTCTT-AGGGCAATACA -s Anc2.Anc2refChr13 48310 25 + 96486 ATCTCCCCATTCTT-CTGGAAATACA -s mr.mrrefChr5 267374 26 + 294540 GTCTCCCAATGCTTAAGGGCAATGCA -s simCow_chr6.simCow.chr6 404272 24 + 602619 GTC-CCCCATTCTT-CTGGGAATACA -s simDog_chr6.simDog.chr6 394833 25 + 593897 ATCTCCCCATTCTT-CTGCAAAGATA -s simHuman_chr6.simHuman.chr6 399460 25 + 601863 ACCTCCCAATTCTT-AGGGCAATACA -s simRat_chr6.simRat.chr6 420962 26 + 647215 GTCCCCAAATGCTTAAGGGCAATGCA - -a -s simMouse_chr6.simMouse.chr6 414688 7 + 636262 ACCATGG -s Anc0.Anc0refChr3 44277 7 + 222631 TCCATCA -s Anc1.Anc1refChr6 74694 7 + 197743 TCCATCA -s Anc2.Anc2refChr13 48357 7 + 96486 TCCATCA -s mr.mrrefChr5 267400 7 + 294540 TCCATGG -s simCow_chr6.simCow.chr6 404321 5 + 602619 TC--TCA -s simDog_chr6.simDog.chr6 394880 7 + 593897 TCCATCA -s simHuman_chr6.simHuman.chr6 399587 7 + 601863 TCCATCA -s simRat_chr6.simRat.chr6 420988 7 + 647215 TCCATGG - -a -s simMouse_chr6.simMouse.chr6 414695 7 + 636262 CAATGTG -s Anc0.Anc0refChr3 44306 7 + 222631 GAATGTG -s Anc1.Anc1refChr6 74723 7 + 197743 GAATGTG -s Anc2.Anc2refChr13 48386 7 + 96486 GAATGTG -s mr.mrrefChr5 267428 7 + 294540 CAATGTG -s simCow_chr6.simCow.chr6 404349 7 + 602619 AAGTGTG -s simDog_chr6.simDog.chr6 394904 7 + 593897 GAATGTA -s simHuman_chr6.simHuman.chr6 399616 7 + 601863 GGATGCG -s simRat_chr6.simRat.chr6 421016 7 + 647215 CAATGTG - -a -s simMouse_chr6.simMouse.chr6 414702 17 + 636262 TCGAGTGCATTTTGTGA -s Anc0.Anc0refChr3 44319 14 + 222631 T---GTACAATATGCGA -s Anc1.Anc1refChr6 74736 14 + 197743 T---GTACAATATGCGA -s Anc2.Anc2refChr13 48399 14 + 96486 T---GTATAACATGCCA -s mr.mrrefChr5 267441 17 + 294540 TCCAGTGCATTTTGTGA -s simCow_chr6.simCow.chr6 404362 12 + 602619 T---GTAATACAT--TG -s simDog_chr6.simDog.chr6 394917 14 + 593897 G---GTATAGCATGCCA -s simHuman_chr6.simHuman.chr6 399629 14 + 601863 T---ACACAATCCAAGA -s simRat_chr6.simRat.chr6 421029 17 + 647215 TCCAGTGCATTTTGTGA - -a -s simMouse_chr6.simMouse.chr6 414719 18 + 636262 TTTGAATCCATATCCTGG -s Anc0.Anc0refChr3 44335 18 + 222631 TCTGTAGCCATATTGTCA -s Anc1.Anc1refChr6 74752 18 + 197743 TCTGTAGCCATATTGTCA -s Anc2.Anc2refChr13 48415 18 + 96486 TCTGTAGCCATATTATCA -s mr.mrrefChr5 267458 18 + 294540 TTTGAATCCATATCGTCA -s simCow_chr6.simCow.chr6 404376 18 + 602619 GTCATAGCCATATTATCA -s simDog_chr6.simDog.chr6 394933 18 + 593897 TCTGTAGCCATATTATCA -s simHuman_chr6.simHuman.chr6 399645 18 + 601863 TCTGTAGCCATTCTGTCA -s simRat_chr6.simRat.chr6 421046 18 + 647215 TTTGAATCCATATCGTCA - -a -s simMouse_chr6.simMouse.chr6 414737 15 + 636262 ACTTGCGGGACATAG -s Anc0.Anc0refChr3 44353 15 + 222631 ACTTTCAGGAGCTAG -s Anc1.Anc1refChr6 74770 15 + 197743 ACTTTCAGGAGCTAG -s Anc2.Anc2refChr13 48433 15 + 96486 ACTTTCAGGAGCTAG -s mr.mrrefChr5 267476 15 + 294540 ACTTGCAGGACATAG -s simCow_chr6.simCow.chr6 404397 15 + 602619 ACACTCATGAGCTAG -s simDog_chr6.simDog.chr6 394951 15 + 593897 ACTTTCAGGAGCTAG -s simHuman_chr6.simHuman.chr6 399663 15 + 601863 CTGTTCAGGAGCTAT -s simRat_chr6.simRat.chr6 421064 15 + 647215 ACTTGTAGGACATAG - -a -s simMouse_chr6.simMouse.chr6 414752 3 + 636262 AAT -s Anc0.Anc0refChr3 44372 3 + 222631 AAT -s Anc1.Anc1refChr6 74789 3 + 197743 AAT -s Anc2.Anc2refChr13 48452 3 + 96486 AAT -s mr.mrrefChr5 267495 3 + 294540 AAT -s simCow_chr6.simCow.chr6 404416 3 + 602619 AAT -s simDog_chr6.simDog.chr6 394970 3 + 593897 AAT -s simHuman_chr6.simHuman.chr6 399682 3 + 601863 AAT -s simRat_chr6.simRat.chr6 421083 3 + 647215 AAT - -a -s simMouse_chr6.simMouse.chr6 414755 1 + 636262 G -s Anc0.Anc0refChr3 44375 1 + 222631 G -s Anc1.Anc1refChr6 74792 1 + 197743 G -s Anc2.Anc2refChr13 48456 1 + 96486 G -s mr.mrrefChr5 267498 1 + 294540 G -s simCow_chr6.simCow.chr6 404420 1 + 602619 G -s simDog_chr6.simDog.chr6 394974 1 + 593897 G -s simHuman_chr6.simHuman.chr6 399685 1 + 601863 G -s simRat_chr6.simRat.chr6 421086 1 + 647215 G - -a -s simMouse_chr6.simMouse.chr6 414756 16 + 636262 TCCAACCTGCAGTCAA -s Anc0.Anc0refChr3 44376 16 + 222631 CTCAATCTGCATCTAA -s Anc1.Anc1refChr6 74793 16 + 197743 CTCAATCTGCATCTAA -s Anc2.Anc2refChr13 48457 16 + 96486 CTCATTCTGCATCTAA -s mr.mrrefChr5 267499 16 + 294540 TCCAACCTGCAGTCAA -s simCow_chr6.simCow.chr6 404421 16 + 602619 CTCAGTCTGCAGCTAA -s simDog_chr6.simDog.chr6 394975 16 + 593897 CTCATTGTGCATGTAT -s simHuman_chr6.simHuman.chr6 399698 16 + 601863 CTCAATCTGCAACTAA -s simRat_chr6.simRat.chr6 421087 16 + 647215 TCCAACCTGCAGTCAA - -a -s simMouse_chr6.simMouse.chr6 414772 49 + 636262 TTTTGTTATTCTCTCCTCTCTAATAGTGGAGTGATAAAGAGCAGCGTAG -s Anc0.Anc0refChr3 44398 49 + 222631 ATTTATAATTCTATTCTCTCCAATAGTAGAATGATAGGAATCAGGGAAG -s Anc1.Anc1refChr6 74815 49 + 197743 ATTTATAATTCTATTCTCTCCAATAGTAGAATGATAGGAATCAGGGAAG -s Anc2.Anc2refChr13 48479 49 + 96486 ATTTATAATTCTATTCTCTCCAATAGTAAAGTGATAGGAATCAGGGATG -s mr.mrrefChr5 267521 49 + 294540 TTTTGTTATTCTCTTCTCTCTAATAGTGGAATGATAAAGAGCAGCGTAG -s simCow_chr6.simCow.chr6 404448 48 + 602619 ATGAATAATTCTATTCTCTCTAATAGTGAAGCGAT-GGAATTGGGGATG -s simDog_chr6.simDog.chr6 395029 44 + 593897 ATTTATAATTCTGTTCTCTCCGATAGCAAGGTGCTAGGAATCAT----- -s simHuman_chr6.simHuman.chr6 399720 49 + 601863 ATTTATAATTCTACTCCCTGCAATAGTAGAATGATAGGAATCAGGGAAG -s simRat_chr6.simRat.chr6 421111 49 + 647215 TTGTGTTATCTTCTTCTCTCTAATAGTTGAATGATAAAGAGCAGAGTAG - -a -s simMouse_chr6.simMouse.chr6 414821 9 + 636262 GATTGCAAA -s Anc0.Anc0refChr3 44448 9 + 222631 AAATGAAAA -s Anc1.Anc1refChr6 74865 9 + 197743 AAATGAAAA -s Anc2.Anc2refChr13 48529 9 + 96486 AAATGAAAA -s mr.mrrefChr5 267570 9 + 294540 GATTGCAAA -s simCow_chr6.simCow.chr6 404497 9 + 602619 AAATGAAAA -s simHuman_chr6.simHuman.chr6 399770 9 + 601863 AACTGGGAA -s simRat_chr6.simRat.chr6 421160 9 + 647215 GATTGCAAG - -a -s simMouse_chr6.simMouse.chr6 414830 70 + 636262 AATTAGGATGGAAAAAATGTACTAATGTAGGAAATTGAAATTAACCCTGGTGTCCGTAATATTCCACATG -s Anc0.Anc0refChr3 44457 61 + 222631 ACCTAAGGTGGAGAAAAC---CTAAGGTGGAAAATT------GATCCTGGTGTGGGTATTATTCCACAGG -s Anc1.Anc1refChr6 74874 61 + 197743 ACCTAAGGTGGAGAAAAC---CTAAGGTGGAAAATT------GATCCTGGTGTGGGTATTATTCCACAGG -s Anc2.Anc2refChr13 48538 61 + 96486 ACTTAAAGTTGAGAAAAC---CTAAGATGGAAAATT------GATTCTGGTGTGGGTATTATTCCACAGG -s mr.mrrefChr5 267579 64 + 294540 AACTAGGATGGAAAAAATGTACTAATGTAGGAAATT------AATCCTGGTGTCCGTATTATTCCACATG -s simCow_chr6.simCow.chr6 404507 61 + 602619 ACTTAAAGTTGAGAAAGC---CTGAGATGCAAAATT------GATTCCAGTGTTGGTTTTATTGCACAGG -s simDog_chr6.simDog.chr6 395073 46 + 593897 ---------------AAC---ATAAGACAGAAAATC------GATTCTGGTGTGGGTACTATTCCACAGG -s simHuman_chr6.simHuman.chr6 399779 61 + 601863 ACCTAAGGTGGAGAAAAC---CTAAAGTGGAAAATT------GATCCTGGTGTGGGTATTATTCTGTGGG -s simRat_chr6.simRat.chr6 421169 64 + 647215 GTCTAGGATTCAAAAAATGTACTAATGTAGGAAACT------AATCCTGGTGTCCGTATTATTCCACATG - -a -s simMouse_chr6.simMouse.chr6 414900 1 + 636262 T -s Anc0.Anc0refChr3 44518 1 + 222631 C -s Anc1.Anc1refChr6 74935 1 + 197743 C -s Anc2.Anc2refChr13 48600 1 + 96486 C -s mr.mrrefChr5 267643 1 + 294540 T -s simCow_chr6.simCow.chr6 404568 1 + 602619 T -s simDog_chr6.simDog.chr6 395120 1 + 593897 C -s simHuman_chr6.simHuman.chr6 399840 1 + 601863 C -s simRat_chr6.simRat.chr6 421233 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 414901 5 + 636262 CCTCC -s Anc0.Anc0refChr3 44521 5 + 222631 CCACT -s Anc1.Anc1refChr6 74938 5 + 197743 CCACT -s Anc2.Anc2refChr13 48603 5 + 96486 CCACT -s mr.mrrefChr5 267644 5 + 294540 CCTCT -s simCow_chr6.simCow.chr6 404571 5 + 602619 CCACT -s simDog_chr6.simDog.chr6 395123 5 + 593897 CCTCC -s simHuman_chr6.simHuman.chr6 399843 5 + 601863 CCACT -s simRat_chr6.simRat.chr6 421234 5 + 647215 CCTCT - -a -s simMouse_chr6.simMouse.chr6 414906 1 + 636262 T -s Anc0.Anc0refChr3 44529 1 + 222631 T -s Anc1.Anc1refChr6 74946 1 + 197743 T -s Anc2.Anc2refChr13 48611 1 + 96486 T -s mr.mrrefChr5 267652 1 + 294540 T -s simCow_chr6.simCow.chr6 404579 1 + 602619 T -s simDog_chr6.simDog.chr6 395131 1 + 593897 T -s simHuman_chr6.simHuman.chr6 399851 1 + 601863 T -s simRat_chr6.simRat.chr6 421242 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 414907 116 + 636262 GCAGTTGGGTGGCTACATATTGAGCTTTGAGTTGAATACATTTGCTAGAGAGTAGTTATGAATTATCATGGGGCAATTGAATGCAATTGCATGCTGAGTTTTGTGTTGAATATGTT -s Anc0.Anc0refChr3 44530 59 + 222631 GCAA-TGGAAAACTGCATATTGAGC-------TGGACATGTTTGCAAGAGGGTAGCTATAAACTACC------------------------------------------------- -s Anc1.Anc1refChr6 74947 59 + 197743 GCAA-TGGAAAACTGCATATTGAGC-------TGGACATGTTTGCAAGAGGGTAGCTATAAACTACC------------------------------------------------- -s Anc2.Anc2refChr13 48612 59 + 96486 GCAA-CAGAAAACTGCATATTGACC-------TGGACATGTTTGCGTGGGGGTAGCTATAAACTACC------------------------------------------------- -s mr.mrrefChr5 267653 105 + 294540 GCAGTTGGGTGGCTACATATTGAGCTTTGAGTTGAATACATTTGCAAGAGAGTAGCTATGAATTATCATGGGGCAATTG----------CATGCTGAGTTTTG-ATTGAATATGTT -s simCow_chr6.simCow.chr6 404582 59 + 602619 GCAA-CAGAAAACTGCCCATTGAGC-------TGAATCTGTTTGCGGGTGGGTAGTCATGAACTACA------------------------------------------------- -s simDog_chr6.simDog.chr6 395132 58 + 593897 -TAA-CAGAAAACTGCATTTTGACC-------TGGACATGTTCGCGTGGGACTAGCTATAAATCAAC------------------------------------------------- -s simHuman_chr6.simHuman.chr6 399852 49 + 601863 GCAA-TGGACTACTGCAAATTGAG-----------------TTGCAAGAGGGTAGCTATTAACTACC------------------------------------------------- -s simRat_chr6.simRat.chr6 421243 105 + 647215 GCAGTTGGGTGGCTACATATTGAGCTTTGAGTTGAAAATGTTTGCAAGAGAGTGGCTATGACTTATCACAGGGCAATTG----------CATGCTGAGTTTTG-ATTGAATATGTT - -a -s simMouse_chr6.simMouse.chr6 415023 50 + 636262 GAGGGTAGCTATGCATTCTCTCACACAGCCAGGGCATTGAGTCAGTACCA -s Anc0.Anc0refChr3 44589 30 + 222631 --TGGTATATATG-ATTCTCTTA-----------------GTCAGTGCCA -s Anc1.Anc1refChr6 75006 31 + 197743 --TGGTATATATGGATTCTCTTA-----------------GTCAGTGCCA -s Anc2.Anc2refChr13 48671 30 + 96486 --TGGTGTATATG-AGTCTCTGA-----------------GTCAGTGCCA -s mr.mrrefChr5 267758 50 + 294540 GAGGGTAGCTATGCATTCTCTTACACATCCAGGGCATTGGGTCAGTATCA -s simCow_chr6.simCow.chr6 404641 29 + 602619 --AGGTGTATGTG-AGACTCTGA-----------------GTCAGTGC-A -s simDog_chr6.simDog.chr6 395190 30 + 593897 --TGGTGTATATG-AGTCCCTGA-----------------GTCAGTGCCA -s simHuman_chr6.simHuman.chr6 399901 31 + 601863 --TGGTATATTTTGATTCTCTTA-----------------GACAATTCCA -s simRat_chr6.simRat.chr6 421353 50 + 647215 GAGGGTAGCTATAAATTCTCTTACACATCCAAGTCATTGGGTCAATATCC - -a -s simMouse_chr6.simMouse.chr6 415073 2 + 636262 CA -s Anc0.Anc0refChr3 44619 2 + 222631 TA -s Anc1.Anc1refChr6 75037 2 + 197743 TA -s Anc2.Anc2refChr13 48701 2 + 96486 TA -s mr.mrrefChr5 267808 2 + 294540 CA -s simCow_chr6.simCow.chr6 404670 2 + 602619 TA -s simDog_chr6.simDog.chr6 395233 2 + 593897 TA -s simHuman_chr6.simHuman.chr6 399932 2 + 601863 TA -s simRat_chr6.simRat.chr6 421403 2 + 647215 GA - -a -s simMouse_chr6.simMouse.chr6 415075 10 + 636262 AAGTGGTTGT -s Anc0.Anc0refChr3 44633 10 + 222631 TAATGGTTGT -s Anc1.Anc1refChr6 75051 10 + 197743 TAATGGTTGT -s Anc2.Anc2refChr13 48715 10 + 96486 TAATGGTTGT -s mr.mrrefChr5 267810 10 + 294540 AAATGGTTGT -s simCow_chr6.simCow.chr6 404684 10 + 602619 TAATGGTTGG -s simDog_chr6.simDog.chr6 395247 10 + 593897 TAAGGGTTGT -s simHuman_chr6.simHuman.chr6 399946 10 + 601863 TAATGATTGT -s simRat_chr6.simRat.chr6 421405 10 + 647215 AAATGGTTGT - -a -s simMouse_chr6.simMouse.chr6 415085 16 + 636262 TACTATGGCAGAGGAA -s Anc0.Anc0refChr3 44646 16 + 222631 CACTGTGGAAAAGGGA -s Anc1.Anc1refChr6 75064 16 + 197743 CACTGTGGAAAAGGGA -s Anc2.Anc2refChr13 48728 16 + 96486 CACTGTGGAAAATGGA -s mr.mrrefChr5 267820 16 + 294540 TACTATGGCAGAGGAA -s simCow_chr6.simCow.chr6 404697 16 + 602619 CGCTGTGGAAAATGGA -s simDog_chr6.simDog.chr6 395260 16 + 593897 CACTGTGGAATCTGGA -s simHuman_chr6.simHuman.chr6 399959 16 + 601863 CACAGTGGAGAAGGGA -s simRat_chr6.simRat.chr6 421415 16 + 647215 TATTATAGCATAGGAA - -a -s simMouse_chr6.simMouse.chr6 415101 10 + 636262 GGAAAGAATC -s Anc0.Anc0refChr3 44662 5 + 222631 AGG-----GG -s Anc1.Anc1refChr6 75080 5 + 197743 AGG-----GG -s Anc2.Anc2refChr13 48745 5 + 96486 AGG-----GG -s mr.mrrefChr5 267836 5 + 294540 GGG-----TG -s simCow_chr6.simCow.chr6 404714 5 + 602619 AGG-----GG -s simDog_chr6.simDog.chr6 395277 5 + 593897 AGG-----GG -s simHuman_chr6.simHuman.chr6 399975 5 + 601863 AGG-----GG -s simRat_chr6.simRat.chr6 421431 5 + 647215 GGG-----TG - -a -s simMouse_chr6.simMouse.chr6 415111 2 + 636262 GA -s Anc0.Anc0refChr3 44667 2 + 222631 AA -s Anc1.Anc1refChr6 75085 2 + 197743 AA -s Anc2.Anc2refChr13 48750 2 + 96486 AA -s mr.mrrefChr5 267841 2 + 294540 GA -s simCow_chr6.simCow.chr6 404720 2 + 602619 AA -s simDog_chr6.simDog.chr6 395282 2 + 593897 GA -s simHuman_chr6.simHuman.chr6 399980 2 + 601863 AA -s simRat_chr6.simRat.chr6 421436 2 + 647215 GA - -a -s simMouse_chr6.simMouse.chr6 415113 10 + 636262 ATCCACAGGA -s Anc0.Anc0refChr3 44669 10 + 222631 ATCAACAAGA -s Anc1.Anc1refChr6 75087 10 + 197743 ATCAACAAGA -s Anc2.Anc2refChr13 48752 10 + 96486 CTCAACAAGA -s mr.mrrefChr5 267843 10 + 294540 ATCCACAAGA -s simCow_chr6.simCow.chr6 404735 10 + 602619 CTCATCAAGC -s simDog_chr6.simDog.chr6 395284 10 + 593897 CTCAACAAGA -s simHuman_chr6.simHuman.chr6 399982 10 + 601863 ATAAACAAGA -s simRat_chr6.simRat.chr6 421438 10 + 647215 ATCCACAAGA - -a -s simMouse_chr6.simMouse.chr6 415123 27 + 636262 GTAGTTGTTTAAATGAGAGATGCACAG -s Anc0.Anc0refChr3 44683 21 + 222631 CTAGCTGTATA------AGATGCACAG -s Anc1.Anc1refChr6 75101 21 + 197743 CTAGCTGTATA------AGATGCACAG -s Anc2.Anc2refChr13 48766 21 + 96486 CTAGCTGTATA------AAAAGCACAA -s mr.mrrefChr5 267853 27 + 294540 GTAGTTGTATAAATGAGAGATGCACAG -s simCow_chr6.simCow.chr6 404749 20 + 602619 CT-GCTGTATA------AAAAGCACAA -s simDog_chr6.simDog.chr6 395298 4 + 593897 CTAG----------------------- -s simHuman_chr6.simHuman.chr6 399996 21 + 601863 ATAGGTGAATA------AGATGCAGAG -s simRat_chr6.simRat.chr6 421448 27 + 647215 GTAGTTGTATAAAAGAGGGATGCACAG - -a -s simMouse_chr6.simMouse.chr6 415150 2 + 636262 AA -s Anc0.Anc0refChr3 44704 2 + 222631 AA -s Anc1.Anc1refChr6 75122 2 + 197743 AA -s Anc2.Anc2refChr13 48787 2 + 96486 CA -s mr.mrrefChr5 267880 2 + 294540 AA -s simCow_chr6.simCow.chr6 404769 2 + 602619 CA -s simHuman_chr6.simHuman.chr6 400023 2 + 601863 AA -s simRat_chr6.simRat.chr6 421475 2 + 647215 AA - -a -s simMouse_chr6.simMouse.chr6 415152 7 + 636262 TCATTTA -s Anc0.Anc0refChr3 44706 7 + 222631 GTTTTTA -s Anc1.Anc1refChr6 75124 7 + 197743 GTTTTTA -s Anc2.Anc2refChr13 48789 7 + 96486 GTTTTTG -s mr.mrrefChr5 267882 7 + 294540 TCATTTA -s simCow_chr6.simCow.chr6 404771 7 + 602619 GTTTTTG -s simHuman_chr6.simHuman.chr6 400027 7 + 601863 ATTATTA -s simRat_chr6.simRat.chr6 421477 7 + 647215 TCATTTA - -a -s simMouse_chr6.simMouse.chr6 415159 21 + 636262 TCATTTATGTTCAATGTGGTG -s Anc0.Anc0refChr3 44738 21 + 222631 TCATTTATGCTCAACTAGGTG -s Anc1.Anc1refChr6 75156 21 + 197743 TCATTTATGCTCAACTAGGTG -s Anc2.Anc2refChr13 48821 21 + 96486 TCACTTACGCTGAGCTAGATG -s mr.mrrefChr5 267889 21 + 294540 TCATTTATGTTCAACGTGGTG -s simCow_chr6.simCow.chr6 404803 21 + 602619 TCACTTACGCTGAGCTAGATG -s simHuman_chr6.simHuman.chr6 400059 21 + 601863 TCATTTATACTCTACCCAGTG -s simRat_chr6.simRat.chr6 421484 21 + 647215 TCATTTATGTTCAACATGGTG - -a -s simMouse_chr6.simMouse.chr6 415180 19 + 636262 CCTGGAAAAGCTATATGCA -s Anc0.Anc0refChr3 44759 19 + 222631 CCTGTAAAAGCTACTAGGA -s Anc1.Anc1refChr6 75177 19 + 197743 CCTGTAAAAGCTACTAGGA -s Anc2.Anc2refChr13 48842 19 + 96486 CCTGTAATAGCTACTAGGA -s mr.mrrefChr5 267910 19 + 294540 CCTGTAAAAGCTATATGCA -s simCow_chr6.simCow.chr6 404824 19 + 602619 CCTGTAATAGCTACTAGGA -s simHuman_chr6.simHuman.chr6 400080 19 + 601863 CCTGTACAACCTACTATGA -s simRat_chr6.simRat.chr6 421507 19 + 647215 CCTGTAAAAGCTATGCGCA - -a -s simMouse_chr6.simMouse.chr6 415199 48 + 636262 GATTGAGAAGACCAAGTGTGTACTATCTGGGAGATTAATGTTACCATT -s Anc0.Anc0refChr3 44778 48 + 222631 GCATGAAAAAACCAGGTGAATCCTATCAAGGACATTGATATTACCATG -s Anc1.Anc1refChr6 75196 48 + 197743 GCATGAAAAAACCAGGTGAATCCTATCAAGGACATTGATATTACCATG -s Anc2.Anc2refChr13 48861 48 + 96486 GCATGAAAAAGCCGGGTAAATCCTGTCAAGGACATTGACATTGCTATG -s mr.mrrefChr5 267929 48 + 294540 GATTGAGAAGACCAAGTGTGTACTATCTAGGAGATTGATGTTACCATT -s simCow_chr6.simCow.chr6 404843 47 + 602619 GCATGAAAAAGCCGGGTAAATCCTGTCAAGGACATTGACATTGCTGT- -s simDog_chr6.simDog.chr6 395302 5 + 593897 -------------------------------------------CTATG -s simHuman_chr6.simHuman.chr6 400099 48 + 601863 GCATGAAAAAACCAGGTGGCTCCTATGAAATACATTGATATCACCATG -s simRat_chr6.simRat.chr6 421527 48 + 647215 GACTGAGAAGACCAAGTGTGTACTGTCTAGGAAATTGATGTTACCATT - -a -s simMouse_chr6.simMouse.chr6 415247 16 + 636262 ATGGTAGTAGCCTAGG -s Anc0.Anc0refChr3 177476 15 - 222631 ACAGTA-TAGTCTAGA -s Anc1.Anc1refChr6 122169 16 - 197743 ACAGTAGTAGTCTAGA -s Anc2.Anc2refChr13 47239 15 - 96486 ACAGCA-TAGTCTAGA -s mr.mrrefChr5 267977 16 + 294540 ATGGTAGTAGCCTAGG -s simCow_chr6.simCow.chr6 197406 15 - 602619 ACAGCA-TAACCTAGA -s simDog_chr6.simDog.chr6 198272 8 - 593897 --------AGTCTAGA -s simHuman_chr6.simHuman.chr6 201382 16 - 601863 ACAGTGGTGGTCTAGA -s simRat_chr6.simRat.chr6 421575 16 + 647215 ATGATAGTAGCCTAGG - -a -s simMouse_chr6.simMouse.chr6 415263 35 + 636262 GCCACCGAAAGGGAACTTAACTTGGTAACTTTAAG -s Anc0.Anc0refChr3 177498 35 - 222631 GCCACTGAAGGGGGAATGAACTTGGCAACTTAAAA -s Anc1.Anc1refChr6 122192 35 - 197743 GCCACTGAAGGGGGAATGAACTTGGCAACTTAAAA -s Anc2.Anc2refChr13 47261 35 - 96486 GCCACTGAAGGGGGGATGTACTTGGCAACTTAAAA -s mr.mrrefChr5 267993 35 + 294540 GCCACTGAAAGGGGACTTAACTTGGTAACTTTAAG -s simCow_chr6.simCow.chr6 197428 35 - 602619 GACACTGAAGGGGGGATGGATTTGGCATCTTAAAA -s simDog_chr6.simDog.chr6 198287 34 - 593897 GCCACTTAAGTGGGGATGTGCAG-GCAACTTAAAA -s simHuman_chr6.simHuman.chr6 201405 35 - 601863 GCCACTGGAGGAGGAATGAACTTCGCGACTTAAAA -s simRat_chr6.simRat.chr6 421591 35 + 647215 GCCACTGAAAGGGGATTTAACTTGGTAACTTTAAG - -a -s simMouse_chr6.simMouse.chr6 415298 66 + 636262 TGATAAATTGTGCAGCTAGTTCTTTGTACTTCTTTGCAGTGGTACAGAATTATTATGTCAGCAGGG -s Anc0.Anc0refChr3 177533 66 - 222631 TGATAAATTAAGCAACTAGTTATGTGTACCTCTTTGTAGTGGTACAGTACCACAATGTCAGAGGGG -s Anc1.Anc1refChr6 122227 66 - 197743 TGATAAATTAAGCAACTAGTTATGTGTACCTCTTTGTAGTGGTACAGTACCACAATGTCAGAGGGG -s Anc2.Anc2refChr13 47296 66 - 96486 TGATACATTAAGCAACTAGTTTTGTGCACCTCTTTGTAGTGGTACTGTACCACAATGTCAGAGGGG -s mr.mrrefChr5 268028 66 + 294540 TGATAAATTGAGCAGCTAGTTATTTGTACTTCTTTGTAGTGGTACAGAACTATTATGTCAGCAGGG -s simCow_chr6.simCow.chr6 197463 66 - 602619 TGATACATTAATCAACTAATTTTGTGCACCTCTTCGTTGTGGGACTGTAACGCTATGTCAGAGAGA -s simDog_chr6.simDog.chr6 198321 66 - 593897 TGCTACATTTAGCAACCAGTTTTGTGCACCTCTTTGTAGTGGTCCTGCACCACAATGTCAGAGGGG -s simHuman_chr6.simHuman.chr6 201441 66 - 601863 TGATAAATTAAGCACCTAGTTATGTGTATCTCCTTGTGATGGTACAGTACCACCATGTCAAAGGGG -s simRat_chr6.simRat.chr6 421626 65 + 647215 TGATAAATAGAGCAGCTAGTTATTTG-ACTTCTTTGTAGTGGTACAGAACTATTATGTCAGCAGGG - -a -s simMouse_chr6.simMouse.chr6 415364 9 + 636262 TGTGATCAT -s Anc0.Anc0refChr3 177599 9 - 222631 CATGATCCT -s Anc1.Anc1refChr6 122293 9 - 197743 CATGATCCT -s Anc2.Anc2refChr13 47368 9 - 96486 CATGATCCC -s mr.mrrefChr5 268094 9 + 294540 CATGATCAT -s simCow_chr6.simCow.chr6 197535 9 - 602619 CATGATCCC -s simDog_chr6.simDog.chr6 198393 8 - 593897 CCT-ATCCC -s simHuman_chr6.simHuman.chr6 201507 9 - 601863 CATGATCCT -s simRat_chr6.simRat.chr6 421691 9 + 647215 CATGATCAT - -a -s simMouse_chr6.simMouse.chr6 415373 50 + 636262 GCCAAAGCGGAAATATGCCTTGAACTGGTTTCATGTAGGAGTTCTGTGCA -s Anc0.Anc0refChr3 177613 50 - 222631 GTCAAAGGGGAAATATGCCTTGAATTTATGTTAATCTGCAGTTCTGTGCA -s Anc1.Anc1refChr6 122307 50 - 197743 GTCAAAGGGGAAATATGCCTTGAATTTATGTTAATCTGCAGTTCTGTGCA -s Anc2.Anc2refChr13 47382 50 - 96486 GTCAAAGGGGAAATTTGCCTTGAATTTATGCTAACTTGCAGTTCTGTGCA -s mr.mrrefChr5 268103 50 + 294540 GCCAAAGCGGAAATATGCCTTGAACTGGTGTCATTCAGGAGTTCTGTGCA -s simCow_chr6.simCow.chr6 197549 48 - 602619 GTCAAGGGGGAAATTTACCCTGAATTTATACTA--TTGCAGTTCTGTGCA -s simDog_chr6.simDog.chr6 198406 50 - 593897 GCCAAAAAGGAAATTTGCCTCAATTTTAGGCTAACTTGCAGTTCTGTGCA -s simHuman_chr6.simHuman.chr6 201524 50 - 601863 GTTAGAGGGGAAATATGTCTTGAATTTATGTTACTCCGCAGTTCTGTGCA -s simRat_chr6.simRat.chr6 421700 50 + 647215 GCCAAAGCGGAAATATGCCACAAACTGGGGTCATTCAGGAGTTCAGTGCA - -a -s simMouse_chr6.simMouse.chr6 415423 12 + 636262 GCAGACTCATGA -s Anc0.Anc0refChr3 177663 12 - 222631 GCAGATCTGTAA -s Anc1.Anc1refChr6 122357 12 - 197743 GCAGATCTGTAA -s Anc2.Anc2refChr13 47435 12 - 96486 GCAGATCTGCAA -s mr.mrrefChr5 268153 12 + 294540 GCAGATCCATGA -s simCow_chr6.simCow.chr6 197600 12 - 602619 GCAGATCTGCAA -s simDog_chr6.simDog.chr6 198459 12 - 593897 GCAGATCTGCAA -s simHuman_chr6.simHuman.chr6 201574 12 - 601863 GCATATCTGTAA -s simRat_chr6.simRat.chr6 421750 12 + 647215 GTAGATCCATGA - -a -s simMouse_chr6.simMouse.chr6 415435 23 + 636262 GACTGTTATTGTTATCTATATTT -s Anc0.Anc0refChr3 177679 23 - 222631 TAATGTTATGGTTGCCTATATTC -s Anc1.Anc1refChr6 122373 23 - 197743 TAATGTTATGGTTGCCTATATTC -s Anc2.Anc2refChr13 47451 23 - 96486 TTATGTCATGGTTGCCTATATTC -s mr.mrrefChr5 268165 23 + 294540 GACTGTTATTGTTATCTATATTT -s simCow_chr6.simCow.chr6 197616 23 - 602619 TCATCTAATGGTTACCTATTTTC -s simDog_chr6.simDog.chr6 198475 23 - 593897 TTATGTCTTGGCTGCCTAGATTC -s simHuman_chr6.simHuman.chr6 201590 23 - 601863 AAATGTTACAGTTGCCTATATTC -s simRat_chr6.simRat.chr6 421762 23 + 647215 GACTGTTATTGTTATCTATATTT - -a -s simMouse_chr6.simMouse.chr6 415458 9 + 636262 GGCCAATTG -s Anc0.Anc0refChr3 177703 9 - 222631 GGCCAACTG -s Anc1.Anc1refChr6 122397 9 - 197743 GGCCAACTG -s Anc2.Anc2refChr13 47475 9 - 96486 AGCCAGCTG -s mr.mrrefChr5 268188 9 + 294540 GGCCAATTG -s simCow_chr6.simCow.chr6 197640 5 - 602619 AGGCA---- -s simDog_chr6.simDog.chr6 198499 9 - 593897 AGCCAGCTG -s simHuman_chr6.simHuman.chr6 201614 9 - 601863 GACTAACTG -s simRat_chr6.simRat.chr6 421785 9 + 647215 GGCCAATTG - -a -s simMouse_chr6.simMouse.chr6 415467 23 + 636262 AATGAAGTCTTCTGCGGCTAGGA -s Anc0.Anc0refChr3 177728 23 - 222631 AATGTAGTCTTCTACTGCTGAGA -s Anc1.Anc1refChr6 122422 23 - 197743 AATGTAGTCTTCTACTGCTGAGA -s Anc2.Anc2refChr13 47500 23 - 96486 CATGTAGTCTTCTACTGCTGACA -s mr.mrrefChr5 268197 23 + 294540 AATGAAGTCTTCTGCGGCTGGGA -s simCow_chr6.simCow.chr6 197652 23 - 602619 CATGTAGTCTTCTACAGCTGACA -s simDog_chr6.simDog.chr6 198525 23 - 593897 CATGTAGTTTTCTAGTGCTGTCA -s simHuman_chr6.simHuman.chr6 201639 23 - 601863 AATCCAGTCTTCCACTGTTGAGA -s simRat_chr6.simRat.chr6 421794 23 + 647215 AAGGAAGTCTTCTGCGGCTGGGA - -a -s simMouse_chr6.simMouse.chr6 415490 48 + 636262 CCTATGCATGGGCATTGGCCAAAGAGCGTTGAAACTTTTACATGGAGC -s Anc0.Anc0refChr3 177757 48 - 222631 CCTACACTTGGGCACTGATCAAAGAGCATTAAAACTATTGCACTGAGT -s Anc1.Anc1refChr6 122451 48 - 197743 CCTACACTTGGGCACTGATCAAAGAGCATTAAAACTATTGCACTGAGT -s Anc2.Anc2refChr13 47529 48 - 96486 CTTACACTTAGGCATTGATCAAAGAGCATGAAAATTATTGCACTGAGT -s mr.mrrefChr5 268220 48 + 294540 CCTACGCATGGGCACTGGCCAAAGAGCATTGAAACTTTTACATGGAGT -s simCow_chr6.simCow.chr6 197681 48 - 602619 CTCACACTAAGGCATTGGTAGAACGGCATGAAAATTATTCCACCGAGT -s simDog_chr6.simDog.chr6 198554 36 - 593897 ATTACACATAGGCATGAATCAAAGAGC------------GCACTGAGT -s simHuman_chr6.simHuman.chr6 201668 48 - 601863 CCTACACTTGGGCACTGATCAAAAAGCATTAAACCTATTGCACTGAGT -s simRat_chr6.simRat.chr6 421817 48 + 647215 CCTGCGCATGGGCACTGGCCAGAGATCACTGAAACTTTTACATGGAGT - -a -s simMouse_chr6.simMouse.chr6 415538 25 + 636262 GTTAGATGCTTTATCAGGCACATTG -s Anc0.Anc0refChr3 45155 25 + 222631 CCTTGATACTTTATCAGGCACCTTA -s Anc1.Anc1refChr6 75574 25 + 197743 CCTTGATACTTTATCAGGCACCTTA -s Anc2.Anc2refChr13 49247 25 + 96486 CCTTGAAACTTTATCATGCATCTTA -s mr.mrrefChr5 268268 25 + 294540 GTTAGATGCTTTATCAGGCACATTA -s simCow_chr6.simCow.chr6 405213 25 + 602619 CCTAGAAGTTTTATCAAGCATCTTG -s simDog_chr6.simDog.chr6 395625 23 + 593897 --TTGAAACTTTATCATGCATATGA -s simHuman_chr6.simHuman.chr6 400481 25 + 601863 ACTCGATCCTTTAGCAGGTGCCTTA -s simRat_chr6.simRat.chr6 421865 25 + 647215 GTTAGATGTGTTATCAGGCATATTA - -a -s simMouse_chr6.simMouse.chr6 415563 91 + 636262 CTTGTGTGATGTCTGGCCAATCAAGAGTGGGCAGATTCCTGCTCAAACACAGTTTATCATCATGCACTGGGCAGGGTATAAGCCAATTATC -s Anc0.Anc0refChr3 45183 85 + 222631 TTTGT--GATGTGTGTGTAATTAAAA----GCAGAATCCTGCTCAAATGCAGTCCATTCCTACCTACTGGACAGGGTATAAGGCAGATATT -s Anc1.Anc1refChr6 75602 85 + 197743 TTTGT--GATGTGTGTGTAATTAAAA----GCAGAATCCTGCTCAAATGCAGTCCATTCCTACCTACTGGACAGGGTATAAGGCAGATATT -s Anc2.Anc2refChr13 49275 85 + 96486 CTTGT--GATGTGTCTGTAATTAAGA----GCAGAATCCTGCTCAAATGCAGTCCATTCCTACCTACTGGACAGGGTACAAGGCAGAGATT -s mr.mrrefChr5 268293 89 + 294540 TTTGT--GATGTCTGGGCAATCAAAAGTGGGCAGATTCCTGCTCAAATACAGTTTATCATCACGCACTGGGCAGGGTATAAGCCAGTTATT -s simCow_chr6.simCow.chr6 405241 85 + 602619 CTTGT--GATGTGCATGTAATAAAGA----GCAGAATCATGCTCAAATGCAGTCCATACCTGCCTACAGGACAGGTTACTAGGCAGTGATT -s simDog_chr6.simDog.chr6 395651 85 + 593897 CTTGT--GATGTCTCTGTAGTTAAGA----GCAGAACCCTGCTCAAAATCAATCTATTCCTACATAATGCACAGTGTACAGGGCAGAGATT -s simHuman_chr6.simHuman.chr6 400509 84 + 601863 TTTGT--GATGGGTGTGTGATGAAAA----GCAGAATCC-GCTCAAATGCAGTCCATTTCTACCTACTGGACAAGGTATAAGGGAGCTACT -s simRat_chr6.simRat.chr6 421890 89 + 647215 TTTGT--GATGTCTGGGCAATCAAAAGTGGGTGGATTCCTGCTCAACTACAGTTTTTCATCACGCACTGGGCAGGGTATAAACCAGTTATT - -a -s simMouse_chr6.simMouse.chr6 415654 66 + 636262 CGATTGCTCGTAGGGAACCCAGAGCACAACTTCTGCTTAAACAAGATCCATACTTCCACTTAAGAA -s Anc0.Anc0refChr3 45268 45 + 222631 TGATTGCTAATAGGGGACCCAGAGATGAACTTCCACTTA---------------------CAAGAA -s Anc1.Anc1refChr6 75687 45 + 197743 TGATTGCTAATAGGGGACCCAGAGATGAACTTCCACTTA---------------------CAAGAA -s Anc2.Anc2refChr13 49360 45 + 96486 TGGTTGCTAATAGGGGACCCAGAGATGAACTTCCACTTA---------------------CAACAG -s mr.mrrefChr5 268382 66 + 294540 TGATTGCTCGTAGGGGACCCAGAGCACAACTTCTGCTTAAACAAGATCCATACTTCCACTTAAGAA -s simCow_chr6.simCow.chr6 405326 44 + 602619 TGGTCACTACTAGGGGACCCAGAGGTGAACTCCCAATCA---------------------CAAC-T -s simDog_chr6.simDog.chr6 395737 45 + 593897 TGGTTGCTAATAGGGGACCCAGAGATGAGCTTCCACTTA---------------------CAACAG -s simHuman_chr6.simHuman.chr6 400593 40 + 601863 TGATTG-----AGGGGACCCAGAGATGAATTTCCACTTA---------------------CAAGAA -s simRat_chr6.simRat.chr6 421979 66 + 647215 TGGGTGCTTGTAGGAGACCCAGAACACAACTTCTGCTTAAAAAAGATCCATACTCCCACCTAAAAA - -a -s simMouse_chr6.simMouse.chr6 415720 42 + 636262 AGCCCAATTTGATTTTCCCCTGGAGTTTGGCAGATCTTTTGA -s Anc0.Anc0refChr3 45313 33 + 222631 CATCCAATCTGA----CCCTCCAATTTTGG-----CTTTTGA -s Anc1.Anc1refChr6 75732 37 + 197743 CATCCAATCTGATGGTCCCTCCAATTTTGG-----CTTTTGA -s Anc2.Anc2refChr13 49409 33 + 96486 CATCCAATCACA----CCCTCCCATTTTGG-----CTTTTGA -s mr.mrrefChr5 268448 42 + 294540 AGCCCAATTTGATTTTCCCTTGAATTTTGGCAGATCTTTTGA -s simCow_chr6.simCow.chr6 405374 33 + 602619 CATCTGATTGCT----GCCTCCTATTTTAG-----TTTTTGA -s simDog_chr6.simDog.chr6 395786 33 + 593897 TATCCAATCACA----CCCTCTCATTTTGG-----CTTTTTG -s simHuman_chr6.simHuman.chr6 400633 37 + 601863 CATCCAATCTGATGGTCCCTCCAATTTTGG-----CTTTTGA -s simRat_chr6.simRat.chr6 422045 42 + 647215 ACCTCCATTTGATTTTACCTTGAATTTTGGCAGAGCTTTTGA - -a -s simMouse_chr6.simMouse.chr6 415762 56 + 636262 TAGACAACCACATTCGTACATCATGACCAGTTTGTCTAATCACTGTGACTTAACCA -s Anc0.Anc0refChr3 45347 55 + 222631 TAGACCCCAACATTCAGAAGGCATGACAGGTTGATCTAGTCATTGTGAAGT-ACCA -s Anc1.Anc1refChr6 75770 55 + 197743 TAGACCCCAACATTCAGAAGGCATGACAGGTTGATCTAGTCATTGTGAAGT-ACCA -s Anc2.Anc2refChr13 49443 55 + 96486 TAGACCACAACATTCAGAAGGCATGACAGGTTGATCTAGTCATTGTGAAGT-AACC -s mr.mrrefChr5 268490 56 + 294540 TAGACACCCACATTCGTACGTCATGACAAGTTTGTCTAATCACTGTGACTTAACCA -s simCow_chr6.simCow.chr6 405408 55 + 602619 TAGGCCACAACATTTATAAGTCATGACAGGCTGATATAATCATTGTGAAGC-AACC -s simDog_chr6.simDog.chr6 395820 55 + 593897 CAGACCACAATGTTCAGAAGGCATGACAGGTTGATCCAGCCATTGTGAAGT-AACC -s simHuman_chr6.simHuman.chr6 400671 55 + 601863 TAGACCCTAACATTCAGGAGCCATGACATGTTGATCTAGTCGTTGTGAAGT-ACCA -s simRat_chr6.simRat.chr6 422087 56 + 647215 TAGCCACCCGCACTTGTCTGTCATGGCAAATTTTTCTAATCACTGTGACTTAACCA - -a -s simMouse_chr6.simMouse.chr6 415818 15 + 636262 TCATGAATGAAAGGC -s Anc0.Anc0refChr3 45402 15 + 222631 CCATGAATAAAGGGT -s Anc1.Anc1refChr6 75825 15 + 197743 CCATGAATAAAGGGT -s Anc2.Anc2refChr13 49498 15 + 96486 CCATGAATAAAGAGT -s mr.mrrefChr5 268546 15 + 294540 TCATGAATGAAAGGC -s simCow_chr6.simCow.chr6 405464 15 + 602619 CCATGAAAAAGGAGT -s simDog_chr6.simDog.chr6 395875 15 + 593897 CCATGAGTAAAGAGC -s simHuman_chr6.simHuman.chr6 400726 15 + 601863 CCATGAACAAAGGGT -s simRat_chr6.simRat.chr6 422143 15 + 647215 TCATGAAAGAAAGGC - -a -s simMouse_chr6.simMouse.chr6 415833 10 + 636262 TTGCTGATCA -s Anc0.Anc0refChr3 45417 10 + 222631 TAGCCGGTCA -s Anc1.Anc1refChr6 75840 10 + 197743 TAGCCGGTCA -s Anc2.Anc2refChr13 49513 10 + 96486 TAGCCGGTCA -s mr.mrrefChr5 268561 10 + 294540 TTGCTGGTCA -s simCow_chr6.simCow.chr6 405480 10 + 602619 TAGCCGGTGG -s simDog_chr6.simDog.chr6 395890 9 + 593897 -AGTTGGTCA -s simHuman_chr6.simHuman.chr6 400741 10 + 601863 TAGCCAGTAA -s simRat_chr6.simRat.chr6 422158 10 + 647215 TTGCTGGTCA - -a -s simMouse_chr6.simMouse.chr6 415843 9 + 636262 CCAACCCAA -s Anc0.Anc0refChr3 45427 9 + 222631 CCTGCCCAA -s Anc1.Anc1refChr6 75850 9 + 197743 CCTGCCCAA -s Anc2.Anc2refChr13 49523 9 + 96486 CCTGCCCAA -s mr.mrrefChr5 268571 9 + 294540 CCAACCCAA -s simCow_chr6.simCow.chr6 405497 9 + 602619 CCTGCCCCA -s simDog_chr6.simDog.chr6 395899 9 + 593897 CCCGCCCAA -s simHuman_chr6.simHuman.chr6 400751 9 + 601863 ACTGCTGAA -s simRat_chr6.simRat.chr6 422168 9 + 647215 CCGACCCAA - -a -s simMouse_chr6.simMouse.chr6 415852 10 + 636262 GACAGATGTT -s Anc0.Anc0refChr3 45436 9 + 222631 GACAGA-GCA -s Anc1.Anc1refChr6 75859 9 + 197743 GACAGA-GCA -s Anc2.Anc2refChr13 49534 9 + 96486 GACAAA-GCA -s mr.mrrefChr5 268580 10 + 294540 GACAGATGTT -s simCow_chr6.simCow.chr6 405508 9 + 602619 GACAAA-GCT -s simDog_chr6.simDog.chr6 395910 9 + 593897 GAAAAA-GCA -s simHuman_chr6.simHuman.chr6 400760 5 + 601863 GACAG----- -s simRat_chr6.simRat.chr6 422177 10 + 647215 GACAGATGTT - -a -s simMouse_chr6.simMouse.chr6 415862 24 + 636262 CAAAGCTGTCATTACACAGTGTGC -s Anc0.Anc0refChr3 45445 20 + 222631 CAAAACTATCATCACACACT---- -s Anc1.Anc1refChr6 75868 20 + 197743 CAAAACTATCATCACACACT---- -s Anc2.Anc2refChr13 49543 20 + 96486 CAAAACTATCATCACACACT---- -s mr.mrrefChr5 268590 24 + 294540 CAAAGCTGTCATTACACAGTGTGC -s simCow_chr6.simCow.chr6 405517 20 + 602619 CAAAAATATCAGAAACATCT---- -s simDog_chr6.simDog.chr6 395920 20 + 593897 CAAAACTATCATCACACATT---- -s simHuman_chr6.simHuman.chr6 400765 10 + 601863 ----------ATCACACACT---- -s simRat_chr6.simRat.chr6 422187 24 + 647215 CAAGGCTGTCATTACACAGTGTAC - -a -s simMouse_chr6.simMouse.chr6 415886 22 + 636262 TTTGGCCAGTGTGCACTATGGA -s Anc0.Anc0refChr3 45465 22 + 222631 TTTGGCTGCTGTACAGCCTGTA -s Anc1.Anc1refChr6 75888 22 + 197743 TTTGGCTGCTGTACAGCCTGTA -s Anc2.Anc2refChr13 49563 22 + 96486 TTTGGCTGCTGTACAGCCTGTG -s mr.mrrefChr5 268614 22 + 294540 TTTGGCCACTGTACACTATGGA -s simCow_chr6.simCow.chr6 405537 22 + 602619 ATTGACTGCTGTACACCCTGTG -s simDog_chr6.simDog.chr6 395944 22 + 593897 TTTGGCTACTGTACAGCCGGTG -s simHuman_chr6.simHuman.chr6 400775 22 + 601863 TATGGCTGCTCTACATCCTGTA -s simRat_chr6.simRat.chr6 422211 22 + 647215 TTTGACCACTGTACACTACAGA - -a -s simMouse_chr6.simMouse.chr6 415908 20 + 636262 CAAATATGCAAACCAGAGAA -s Anc0.Anc0refChr3 45487 20 + 222631 CAAATAAATCGACCAGAGGA -s Anc1.Anc1refChr6 75910 20 + 197743 CAAATAAATCGACCAGAGGA -s Anc2.Anc2refChr13 49645 20 + 96486 CAAAAAAATCGACCAGAGGT -s mr.mrrefChr5 268636 20 + 294540 CAAATATGCAAACCAGAGAA -s simCow_chr6.simCow.chr6 405621 19 + 602619 CAAAAAAAT-GACCAGAGGT -s simDog_chr6.simDog.chr6 396042 20 + 593897 TAAAAAAGCCAACCAGAGGT -s simHuman_chr6.simHuman.chr6 400797 20 + 601863 CAAATAAATTGACCAGAGGA -s simRat_chr6.simRat.chr6 422233 20 + 647215 CAGAAATGCAAACCAGAGAA - -a -s simMouse_chr6.simMouse.chr6 415928 20 + 636262 CACCTCATTAATGGTATGAC -s Anc0.Anc0refChr3 45524 20 + 222631 CACTTCACTAATGGTACAGC -s Anc1.Anc1refChr6 75947 20 + 197743 CACTTCACTAATGGTACAGC -s Anc2.Anc2refChr13 49682 20 + 96486 CACTTCACTAATGGTGCAGC -s mr.mrrefChr5 268656 20 + 294540 CACCTCATTAATGGTATGAC -s simCow_chr6.simCow.chr6 405657 20 + 602619 CTCTTCACTAATAGTGCAGC -s simDog_chr6.simDog.chr6 396077 20 + 593897 CACTTCACTACTGGTGTGGC -s simHuman_chr6.simHuman.chr6 400834 20 + 601863 CACTTCACTAATGGTACAGC -s simRat_chr6.simRat.chr6 422253 20 + 647215 TACCTAATTAATGATGTGAC - -a -s simMouse_chr6.simMouse.chr6 415948 4 + 636262 TTAT -s Anc0.Anc0refChr3 45544 4 + 222631 TGAT -s Anc1.Anc1refChr6 75967 4 + 197743 TGAT -s Anc2.Anc2refChr13 49702 4 + 96486 TGAT -s mr.mrrefChr5 268676 4 + 294540 TTAT -s simCow_chr6.simCow.chr6 405678 4 + 602619 GGAT -s simDog_chr6.simDog.chr6 396097 4 + 593897 TGAC -s simHuman_chr6.simHuman.chr6 400854 4 + 601863 TGAT -s simRat_chr6.simRat.chr6 422273 4 + 647215 TTAT - -a -s simMouse_chr6.simMouse.chr6 415952 99 + 636262 ATCTGGCTGGAGCACGTCTATTCTCCAGTAGCAATGAAGGGCCCTGCTTAAGGCCGCAAGCTTAATCAGCCCCCAAACAAGGGGTTAATTGTAGCCTAA -s Anc0.Anc0refChr3 45548 94 + 222631 ATCTGGTTGGC--ATCTCTATCCCCCAGTAGGAAAACAGAGCACAGTTTAAGGCTGC---CTTTCTCAGCCTCCACACAGGGGGTTAGTTTTAGGCTAA -s Anc1.Anc1refChr6 75971 99 + 197743 ATCTGGTTGGCGCATCTCTATCCCCCAGTAGGAAAACAGAGCACAGTTTAAGGCTGCTAGCTTTCTCAGCCTCCACACAGGGGGTTAGTTTTAGGCTAA -s Anc2.Anc2refChr13 49706 94 + 96486 ATCTGGTTGGC--ATCTCTATCGCCCAGTAGGAAAACAAAGCACAATTCAAGGTCAC---CTTTCTCAGTGCCCACATAGGGGGTTAGTATTAGGCTAA -s mr.mrrefChr5 268680 99 + 294540 ATCTGGCTGGAGCATGTCTATTCCCCAGTAGCAATAAAGGGCCCTGCTTAAGGCTGCAAGCTTAATCAGCCTCCAAACAAGGGGTTAATTTTAGCCTAA -s simCow_chr6.simCow.chr6 405682 94 + 602619 GTCTGGTTGGC--ATCCCTATCTCCCAGTTGGAAAACAATGCACCAGTCAAGGTCAC---CTTTCTCTGTGCCTACATAGGGGCTTAGTGTTAGGCTGC -s simDog_chr6.simDog.chr6 396101 81 + 593897 ATCTGGTTGGC--ATCTCTTTCGTCCAGTAGGAAAACAAAGCACAATTCA----------------CAGTGCCCACATAAGGGGTTAGTATTAGACTAA -s simHuman_chr6.simHuman.chr6 400858 98 + 601863 -TCTGGTTGGCACATTTCTATCCCCCAGTAGGAAAACAGAGCAAAGATTAAGGCTGCTAGCTGCCTTAGCCTCCAGACAGGGGGTCAGTTTTAGGCCAA -s simRat_chr6.simRat.chr6 422278 99 + 647215 ATCTGGCTAGAGCATGTCTATTTCCCAGTAGCAATAAATGGCCCTTTTTGAGGCTGCAAGCTTGATCAGACTCCACACATGGGGTTAATTTTAGCCTAA - -a -s simMouse_chr6.simMouse.chr6 416051 21 + 636262 ATGACAAGCAGTATTAGGACC -s Anc0.Anc0refChr3 45648 20 + 222631 AGGACAAACAGTGTTAC-ACT -s Anc1.Anc1refChr6 76076 21 + 197743 AGGACAAACAGTGTTACTACT -s Anc2.Anc2refChr13 49806 20 + 96486 AGGACTAACAGTGCTAC-ATT -s mr.mrrefChr5 268779 21 + 294540 ATGACAAGCAGTATTAGGACC -s simCow_chr6.simCow.chr6 405782 19 + 602619 AG-ACTAACAGTGCTAC-ATT -s simDog_chr6.simDog.chr6 396188 18 + 593897 AGGA--ACCAGTGCTAC-ATT -s simHuman_chr6.simHuman.chr6 400962 21 + 601863 AGGACAAACAGTGTTACTACT -s simRat_chr6.simRat.chr6 422377 21 + 647215 ATGACAAGCAGTATTATAGCC - -a -s simMouse_chr6.simMouse.chr6 416072 23 + 636262 TGTGGTCTCCCTGGCCTTTAATG -s Anc0.Anc0refChr3 45668 23 + 222631 TGTGGTCTCTCTCACCTTTAATG -s Anc1.Anc1refChr6 76097 23 + 197743 TGTGGTCTCTCTCACCTTTAATG -s Anc2.Anc2refChr13 49826 23 + 96486 CGTGGTCCCTTTCACCTTTAATG -s mr.mrrefChr5 268800 23 + 294540 TGTGGTCTCCCTGGCCTTTAATG -s simCow_chr6.simCow.chr6 405824 23 + 602619 CATGGTCCCTTTCACCTTTAGTG -s simDog_chr6.simDog.chr6 396206 23 + 593897 CGTGGTCCCTTTTGCCTTTAATG -s simHuman_chr6.simHuman.chr6 400983 22 + 601863 TGCGGTTTCGCTCACT-TTAAAG -s simRat_chr6.simRat.chr6 422398 23 + 647215 TGTAGTCTCCTTGGCCTTTAAAG - -a -s simMouse_chr6.simMouse.chr6 416095 12 + 636262 AATTGCAAAGAG -s Anc0.Anc0refChr3 45693 12 + 222631 AATCACAAAGGG -s Anc1.Anc1refChr6 76122 12 + 197743 AATCACAAAGGG -s Anc2.Anc2refChr13 49851 12 + 96486 AATCACAAAGGA -s mr.mrrefChr5 268823 12 + 294540 AATCACAAAGAG -s simCow_chr6.simCow.chr6 405849 12 + 602619 AATCACAAAGGA -s simDog_chr6.simDog.chr6 396231 12 + 593897 AATTATAAAGGA -s simHuman_chr6.simHuman.chr6 401007 12 + 601863 AATCACAAAGGG -s simRat_chr6.simRat.chr6 422421 12 + 647215 ATGCACAAAGAG - -a -s simMouse_chr6.simMouse.chr6 416107 13 + 636262 CTTCCAACCCTCG -s Anc0.Anc0refChr3 45705 13 + 222631 TCTTTAACTCCTG -s Anc1.Anc1refChr6 76134 13 + 197743 TCTTTAACTCCTG -s Anc2.Anc2refChr13 49863 13 + 96486 TCATTAACTCCTG -s mr.mrrefChr5 268835 13 + 294540 CTTCCAACTCCTG -s simCow_chr6.simCow.chr6 405892 13 + 602619 TCATTAGCTCCTG -s simDog_chr6.simDog.chr6 396243 13 + 593897 CCATCAACTCATG -s simHuman_chr6.simHuman.chr6 401019 13 + 601863 TCTTTGACTCCTG -s simRat_chr6.simRat.chr6 422433 13 + 647215 CTGCCAACTCCTG - -a -s simMouse_chr6.simMouse.chr6 416120 7 + 636262 GATTCAT -s Anc0.Anc0refChr3 45718 3 + 222631 C----AT -s Anc1.Anc1refChr6 76147 3 + 197743 C----AT -s Anc2.Anc2refChr13 49876 3 + 96486 C----AT -s mr.mrrefChr5 268848 7 + 294540 GATTCAT -s simCow_chr6.simCow.chr6 405909 3 + 602619 C----AT -s simDog_chr6.simDog.chr6 396256 3 + 593897 C----AT -s simHuman_chr6.simHuman.chr6 401032 3 + 601863 A----CT -s simRat_chr6.simRat.chr6 422446 7 + 647215 GATTCAT - -a -s simMouse_chr6.simMouse.chr6 416127 44 + 636262 AGGTAGTTTCATTTACACAACATCAGTAAACAGACTGTTATGCA -s Anc0.Anc0refChr3 45721 43 + 222631 AGGTGGTTGCATTTACACAACATAACTAAACAGACTG-TGTGTG -s Anc1.Anc1refChr6 76150 43 + 197743 AGGTGGTTGCATTTACACAACATAACTAAACAGACTG-TGTGTG -s Anc2.Anc2refChr13 49879 43 + 96486 AGGTGGTTGCATTTACACTACATAACTAAACAGACTG-TGTGTG -s mr.mrrefChr5 268855 44 + 294540 AGGTAGTTTCATTTACACAACATCAGTAAACAGACTGTTATGCA -s simCow_chr6.simCow.chr6 405912 43 + 602619 GGGTGCTTGCATTTACACTACATCATTAGACAGACTG-TGTGTG -s simDog_chr6.simDog.chr6 396263 43 + 593897 AGGTGGTTGCATTTAGACTGGATAACTAAATGGACTC-CATGTG -s simHuman_chr6.simHuman.chr6 401035 43 + 601863 AGGTGATTGGATCTACACAACTGAACTAAACAGACTG-TGTGTG -s simRat_chr6.simRat.chr6 422453 42 + 647215 AGGTAGTTTCATTTACACAACACCAG--TACAGACTATTATGCT - -a -s simMouse_chr6.simMouse.chr6 416171 39 + 636262 GAGTTTCCTTTCCCCAAGTTCATCCCCACTGTTAGGCTT -s Anc0.Anc0refChr3 45764 39 + 222631 AAGGTTCCCTCTCTCAGGTACATTCTCACCATTTGGGTT -s Anc1.Anc1refChr6 76193 39 + 197743 AAGGTTCCCTCTCTCAGGTACATTCTCACCATTTGGGTT -s Anc2.Anc2refChr13 49922 39 + 96486 AGGGTTCCCTCTCTCAGGTACATTATCACCATTTGGGTT -s mr.mrrefChr5 268899 39 + 294540 GAGTTTCCCTTCCCCAAGTTCATCCCCACCATTAGGCTT -s simCow_chr6.simCow.chr6 405957 39 + 602619 GGGGCTCCATCTCTCAGGTAGAATTTCACCAATTGGGTT -s simDog_chr6.simDog.chr6 396306 39 + 593897 AGGGTCCACTGTTCCAGGTCCATTATCATCGTTTGGGTT -s simHuman_chr6.simHuman.chr6 401078 39 + 601863 AATCTTCCCCCTCTCAGGTACATTCTCACCATTCGGGTT -s simRat_chr6.simRat.chr6 422495 39 + 647215 GAGTTTCCCTACTCCAAGTTCATCCCCACCACTAGGCGT - -a -s simMouse_chr6.simMouse.chr6 416210 336 + 636262 ACAACTGAACCTTGACAGTGCGTGAACCCGGACAGGGGATCTTCTACAATGTATGCGTGGAGATCGCTCGACATTTTCTCATGCGGGGCACACTCATAGCTGAGCCCTGACCATGTGTACATGGCCGCATGGGGCAGGCATAGCCAAGCACTGGCTGTTTGTACAAAGAGGTGTGGGGAAGGGACATAGCCAAGCACTAACTATGTGTACATGGCTGTGTTTGCCTTTTTTTGGAGATTTGCATGAGGTGCCGTGCAAAGTCCAACTAGTGTTGAACACGAGGTTCTATTTCTCGACAAGACCTAGCGTCCCAAGAACACAGAGTGTTTTTAGTCT -s Anc0.Anc0refChr3 45805 37 + 222631 ACAGTCCAGC----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TACCAAT-CTACAGAGTGAGCTTAGACT -s Anc1.Anc1refChr6 76234 37 + 197743 ACAGTCCAGC----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TACCAAT-CTACAGAGTGAGCTTAGACT -s Anc2.Anc2refChr13 49963 37 + 96486 ACAGTCCAGT----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TACCAAT-CTATGAAGTGAGCTAAGACT -s mr.mrrefChr5 268938 38 + 294540 ACAACTGAGC----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TCCCAAGAATACAGAGTGTTTTTAGTCT -s simCow_chr6.simCow.chr6 405998 37 + 602619 ACAGTACATT----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TAGCAAT-CTATGAAGTGAGCTAAGACT -s simDog_chr6.simDog.chr6 396347 17 + 593897 ATGGTCCAGT----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TACTCAA--------------------- -s simHuman_chr6.simHuman.chr6 401119 37 + 601863 ACAGTCAAGC----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TGCCAAT-CTACAGAGCAAGCTTAGCAG -s simRat_chr6.simRat.chr6 422534 38 + 647215 GCGACTGAGT----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TCCCAAGAGTATAGAGTGTCTTTAGTCT - -a -s simMouse_chr6.simMouse.chr6 416546 4 + 636262 CTTA -s Anc0.Anc0refChr3 45842 4 + 222631 CTCC -s Anc1.Anc1refChr6 76271 4 + 197743 CTCC -s Anc2.Anc2refChr13 50000 4 + 96486 CTCC -s mr.mrrefChr5 268976 4 + 294540 CTTA -s simCow_chr6.simCow.chr6 406035 4 + 602619 CCCC -s simHuman_chr6.simHuman.chr6 88489 4 + 601863 CTGC -s simHuman_chr6.simHuman.chr6 401156 4 + 601863 CTCA -s simRat_chr6.simRat.chr6 422572 4 + 647215 CTTA - -a -s simMouse_chr6.simMouse.chr6 416550 73 + 636262 TTCCCAGTACCATCGTTTGCTGAGGGCCTGTGAACATAGTTAGACAAAATAACACCCAAAGCAGTAGTTTTTT -s Anc0.Anc0refChr3 45850 73 + 222631 TCTCATGTATTGTAATCTTCAGTGGGCCAACACACCTCGCTAGACAAAATTACAGCCAATACAGTATCCTGTT -s Anc1.Anc1refChr6 76279 73 + 197743 TCTCATGTATTGTAATCTTCAGTGGGCCAACACACCTCGCTAGACAAAATTACAGCCAATACAGTATCCTGTT -s Anc2.Anc2refChr13 50008 73 + 96486 TCTCATGTATTGTAATCTTCAGTGGGGCAACACACTTCGCTAGACAAAATTACAGCCAATACAGTATCCTGTT -s mr.mrrefChr5 268980 73 + 294540 TTCCAAGTACCATAATTTGCTGAGGGCCTGTACACCTAGTTAGACAAAATTACAGCCAAAACAGTAGTTTTTT -s simCow_chr6.simCow.chr6 406043 72 + 602619 TCTCCCTGACTGCAATTGACAGTGTGGCACCACATTTTAGTAGACAAACTGACAGCCAATAC-GTATCCTGTT -s simDog_chr6.simDog.chr6 396364 54 + 593897 -------------------CAGTGGTGCAGCATACTTCGTTAGAAAAAATTCCAGTGATTACAGTATCCTGTT -s simHuman_chr6.simHuman.chr6 88493 73 + 601863 TATCATGTCTTGTAATCTTCAGTGGGCCAACACACCTCGCTAGACAACACTACAGCCAATACAGTATCCTGTT -s simHuman_chr6.simHuman.chr6 401164 73 + 601863 TCTCATGTATTGTAATCTTCAGTGGGCCAACACACCTTGCTAGACAACATTACAGCCAATACAGTATCCTGCT -s simRat_chr6.simRat.chr6 422576 72 + 647215 TTGCAAGTACCATAATTAGCTGAGGGC-TGTACACCTAGTTAGACAAAACTACAGCAAACACTTTAGTTTTTT - -a -s simMouse_chr6.simMouse.chr6 416623 28 + 636262 TAATCCATTCCCACCCTCCATAGCACCA -s Anc0.Anc0refChr3 45923 18 + 222631 CAACCTGT----------CATAAAATAG -s Anc1.Anc1refChr6 76352 18 + 197743 CAACCTGT----------CATAAAATAG -s Anc2.Anc2refChr13 50081 18 + 96486 CAACCTGT----------CATAAAATGG -s mr.mrrefChr5 269053 28 + 294540 TAATCCATTCCCACCCTCCATAGCACAA -s simCow_chr6.simCow.chr6 406145 18 + 602619 CAACTTGT----------CATAGATTGG -s simDog_chr6.simDog.chr6 396418 18 + 593897 CAACCCGA----------CATAAAATGG -s simHuman_chr6.simHuman.chr6 88566 18 + 601863 CAACCTGT----------CATAAAATAG -s simHuman_chr6.simHuman.chr6 401237 18 + 601863 CAACCTGT----------CATAAAATAG -s simRat_chr6.simRat.chr6 422648 28 + 647215 TAATGCATACCCACCCTCCATAGCACAA - -a -s simMouse_chr6.simMouse.chr6 416651 2 + 636262 TC -s Anc0.Anc0refChr3 45947 2 + 222631 TC -s Anc1.Anc1refChr6 76376 2 + 197743 TC -s Anc2.Anc2refChr13 50105 2 + 96486 TC -s mr.mrrefChr5 269081 2 + 294540 TC -s simCow_chr6.simCow.chr6 406169 2 + 602619 TC -s simDog_chr6.simDog.chr6 396442 2 + 593897 TA -s simHuman_chr6.simHuman.chr6 88590 2 + 601863 CC -s simHuman_chr6.simHuman.chr6 401261 2 + 601863 CC -s simRat_chr6.simRat.chr6 422676 2 + 647215 CC - -a -s simMouse_chr6.simMouse.chr6 416653 2 + 636262 AA -s Anc0.Anc0refChr3 45949 2 + 222631 AA -s Anc1.Anc1refChr6 76378 2 + 197743 AA -s Anc2.Anc2refChr13 50107 2 + 96486 AA -s mr.mrrefChr5 269083 2 + 294540 AA -s simCow_chr6.simCow.chr6 406201 2 + 602619 AA -s simDog_chr6.simDog.chr6 396444 2 + 593897 AA -s simHuman_chr6.simHuman.chr6 88592 2 + 601863 AA -s simHuman_chr6.simHuman.chr6 401263 2 + 601863 AA -s simRat_chr6.simRat.chr6 422678 2 + 647215 AA - -a -s simMouse_chr6.simMouse.chr6 416655 5 + 636262 TGTTG -s Anc0.Anc0refChr3 45951 5 + 222631 ACATA -s Anc1.Anc1refChr6 76380 5 + 197743 ACATA -s Anc2.Anc2refChr13 50109 5 + 96486 ACATA -s mr.mrrefChr5 269085 5 + 294540 TGTTG -s simCow_chr6.simCow.chr6 406203 5 + 602619 ACATA -s simDog_chr6.simDog.chr6 396446 5 + 593897 ACATA -s simHuman_chr6.simHuman.chr6 88594 5 + 601863 ACATA -s simHuman_chr6.simHuman.chr6 401265 5 + 601863 ATATA -s simRat_chr6.simRat.chr6 422683 5 + 647215 TGTTG - -a -s simMouse_chr6.simMouse.chr6 416660 45 + 636262 TTGAACTTTCTCATTTAATGAACCATAGGTAACTTATTCCTGTTT -s Anc0.Anc0refChr3 45958 37 + 222631 TT--ATTTTACCAATTAATGAGTCATCTTTT------TTCTATTT -s Anc1.Anc1refChr6 76387 39 + 197743 TT--ATTTTACCAATTAATGAGTCATCTTTTA----TTTCTATTT -s Anc2.Anc2refChr13 50116 37 + 96486 TT--ATTTCTACTATTAATGAGTCACCTTTT------TTCTATTT -s mr.mrrefChr5 269092 45 + 294540 TTGAACTTTCCCATTTAATGAGTCATAGGTAACTTATTCCTGTTT -s simCow_chr6.simCow.chr6 406210 37 + 602619 TT--ATTCCTACTATTAATGTGGCACCGTTT------CATTATTT -s simDog_chr6.simDog.chr6 396453 37 + 593897 TT--ATTTCTATTATTAATGAGTCACCTTAT------TTCTATTT -s simHuman_chr6.simHuman.chr6 88601 28 + 601863 TT--ATTTTACTA--TAATAAGTCATCTTTTA------------- -s simHuman_chr6.simHuman.chr6 401272 28 + 601863 TT--ATTTTACTA--TAATAAGTCATCTTTTA------------- -s simRat_chr6.simRat.chr6 422690 45 + 647215 TTGAACTTTCCCATAAAATGAGTCATTGCTAACTCATTCCCGTTT - -a -s simMouse_chr6.simMouse.chr6 416705 8 + 636262 TCCTCTTA -s Anc0.Anc0refChr3 45995 8 + 222631 CCCGTCAA -s Anc1.Anc1refChr6 76426 8 + 197743 CCCGTCAA -s Anc2.Anc2refChr13 50153 8 + 96486 CCCGTCAA -s mr.mrrefChr5 269137 8 + 294540 TCCTCTTA -s simCow_chr6.simCow.chr6 406255 8 + 602619 CCCGTTAA -s simDog_chr6.simDog.chr6 396490 8 + 593897 CCCGTCAA -s simRat_chr6.simRat.chr6 422735 8 + 647215 TCCCCTCA - -a -s simMouse_chr6.simMouse.chr6 416713 20 + 636262 CTTATAAACAAACCCTGCCA -s Anc0.Anc0refChr3 46003 20 + 222631 CCTATAAACAAACCCAGCTA -s Anc1.Anc1refChr6 76434 20 + 197743 CCTATAAACAAACCCAGCTA -s Anc2.Anc2refChr13 50163 20 + 96486 CCTATAAACAAACCCAGCTA -s mr.mrrefChr5 269145 20 + 294540 CTTATAAACAAACCCTGCCA -s simCow_chr6.simCow.chr6 406279 20 + 602619 CCTATTAACCAACCCAGCTA -s simDog_chr6.simDog.chr6 396500 20 + 593897 CCTATAAACAAACCCAGCTA -s simRat_chr6.simRat.chr6 422743 20 + 647215 CTTATAAACAAACCCTGCCA - -a -s simMouse_chr6.simMouse.chr6 416733 21 + 636262 CCACATATTGACAACTTGACA -s Anc0.Anc0refChr3 46023 21 + 222631 ACACTTACTGAGAATTGGACA -s Anc1.Anc1refChr6 76454 21 + 197743 ACACTTACTGAGAATTGGACA -s Anc2.Anc2refChr13 50183 21 + 96486 ACACTTACTTAGAATTGGACA -s mr.mrrefChr5 269165 21 + 294540 CCACATATTGACAACTTGACA -s simCow_chr6.simCow.chr6 406299 7 + 602619 ----TTACTTA---------- -s simDog_chr6.simDog.chr6 396521 21 + 593897 ACACTTACTTAGAACTGGACA -s simHuman_chr6.simHuman.chr6 88629 20 + 601863 -CACTTACTGAGAATTGGACA -s simHuman_chr6.simHuman.chr6 401300 20 + 601863 -CACTTAGTGAGAATTGGACA -s simRat_chr6.simRat.chr6 422763 21 + 647215 CTATGTATTGACAACTTGACA - -a -s simMouse_chr6.simMouse.chr6 416754 35 + 636262 TGCATTCAGGATGTGCATTATGATTTGTCATTTTT -s Anc0.Anc0refChr3 46045 30 + 222631 CACATTCAGGATATACATTATGATTTGTT-----T -s Anc1.Anc1refChr6 76476 30 + 197743 CACATTCAGGATATACATTATGATTTGTT-----T -s Anc2.Anc2refChr13 50205 30 + 96486 CACATTCAGGTTATACATTATGATTTGTT-----T -s mr.mrrefChr5 269186 35 + 294540 TGCATTCAGGATATGCATTATGATTTGTCATTTTT -s simCow_chr6.simCow.chr6 406306 23 + 602619 ------CTAG-TATATATAATGATTTGTT-----T -s simDog_chr6.simDog.chr6 396543 30 + 593897 CACATCCACGTTATTCATTATGATTTGTT-----T -s simHuman_chr6.simHuman.chr6 88650 30 + 601863 CACATTCAGGATATACACTATGATTTGCC-----T -s simHuman_chr6.simHuman.chr6 401321 29 + 601863 CACATTCAGG-TATACATTATGATTTGTT-----T -s simRat_chr6.simRat.chr6 422784 35 + 647215 TGCATTCAGGATATGCATTACGATTTGTTCTTTTT - -a -s simMouse_chr6.simMouse.chr6 416789 33 + 636262 GGCATGTACTAGATGCTAGGGGGGCTGATGGCG -s Anc0.Anc0refChr3 46075 33 + 222631 GACATGTGTTAGTGGCTCATGGGGTTGATGGTG -s Anc1.Anc1refChr6 76506 33 + 197743 GACATGTGTTAGTGGCTCATGGGGTTGATGGTG -s Anc2.Anc2refChr13 50237 33 + 96486 GACATGTGTTATTAGCTCATGGGGTTGATGGTG -s mr.mrrefChr5 269221 33 + 294540 GGCATGTACTAGTTGCTAGGGGGGCTGATGGCG -s simCow_chr6.simCow.chr6 406331 26 + 602619 -TCAT------TTAGCTTGTGGGGTTGATGGTT -s simDog_chr6.simDog.chr6 396578 33 + 593897 GCCATGTGTTATTAGCTCATGGGGTTGGTGGTG -s simHuman_chr6.simHuman.chr6 88680 33 + 601863 GACATGTGTTAGTGGCCCATGGGGTTGATGGTG -s simHuman_chr6.simHuman.chr6 401350 33 + 601863 GAAATATGTTAGTGGCCCATGGGGTTGATGGTG -s simRat_chr6.simRat.chr6 422819 33 + 647215 GGCATGCACTAGTTGCTAGGGGGGCTGTTGGCG - -a -s simMouse_chr6.simMouse.chr6 416822 33 + 636262 GGAACCTTTTTTGCCACAGCTTGATAGTCAGTG -s Anc0.Anc0refChr3 46108 33 + 222631 GAAACCTTTTATGTCATACATTGATAGTCAGTG -s Anc1.Anc1refChr6 76539 33 + 197743 GAAACCTTTTATGTCATACATTGATAGTCAGTG -s Anc2.Anc2refChr13 50270 33 + 96486 GGAACCTTTTATGTCATACATTGATAGTCAGTG -s mr.mrrefChr5 269254 33 + 294540 GAAACCTTTTTTGTCACAGCTTGATAGTCAGTG -s simCow_chr6.simCow.chr6 406357 33 + 602619 GTAACCCTGTATATAATACATTGATGGTCATTG -s simDog_chr6.simDog.chr6 396611 33 + 593897 GGAGCCTTTTATGTCATACATTGATAAACAGAG -s simHuman_chr6.simHuman.chr6 401383 33 + 601863 GAAACCTTTTATGTCAGGTATTGATAGTCTGTG -s simRat_chr6.simRat.chr6 422852 33 + 647215 GAAACCCTTTTTGTCATAGCTTCATAGTCAGTA - -a -s simMouse_chr6.simMouse.chr6 416855 51 + 636262 GTTCATTAGAGTATGTATTTAGATGCACTCACGTCTATTCCCGATGCAAGT -s Anc0.Anc0refChr3 46142 51 + 222631 GACCCTTAAAGTATATATTGGTGTGCCCTCAAGCCTATCCCAGAGGCAAGT -s Anc1.Anc1refChr6 76573 51 + 197743 GACCCTTAAAGTATATATTGGTGTGCCCTCAAGCCTATCCCAGAGGCAAGT -s Anc2.Anc2refChr13 50322 51 + 96486 GACCCTTAAAGTATATGTTGGTGTGCCCTCAAGCCTATCTCAGAGGCAAGT -s mr.mrrefChr5 269287 51 + 294540 GTTCACTAAAGTATGTATTTAGATGCCCTCACGTCTATTCCAGATGCAAGT -s simCow_chr6.simCow.chr6 406409 51 + 602619 GACCCTTAAAGTATATGCTGGTGTGCCCTCAAGCTTATCTCAGAGGCAAGT -s simDog_chr6.simDog.chr6 396673 50 + 593897 GACCCCTAAAGTATATGTTGGTGTGTCCTTA-GCCTATCTCAGAGGCAAGT -s simHuman_chr6.simHuman.chr6 401417 51 + 601863 AACCCTAAAAGCATATATTGGTGTGCCCTCAAGCCTATCCTAGAGTCAAGT -s simRat_chr6.simRat.chr6 422885 51 + 647215 GTTCACCCAAGTATGTATCTAGATGCCCTCATGTCTATTCCAGATGCAAGT - -a -s simMouse_chr6.simMouse.chr6 416906 9 + 636262 ACCAATCCC -s Anc0.Anc0refChr3 46193 9 + 222631 ATCAATCGC -s Anc1.Anc1refChr6 76624 9 + 197743 ATCAATCGC -s Anc2.Anc2refChr13 50373 9 + 96486 ATCAATCGC -s mr.mrrefChr5 269338 9 + 294540 ATCAATCCC -s simCow_chr6.simCow.chr6 406460 9 + 602619 ATCGATCTC -s simDog_chr6.simDog.chr6 396734 9 + 593897 ATCAATCGC -s simHuman_chr6.simHuman.chr6 401468 9 + 601863 ATCAATTGT -s simRat_chr6.simRat.chr6 422936 9 + 647215 ATCAATCTG - -a -s simMouse_chr6.simMouse.chr6 416915 9 + 636262 AGCTGCCAG -s Anc0.Anc0refChr3 46202 9 + 222631 GACTAACAG -s Anc1.Anc1refChr6 76633 9 + 197743 GACTAACAG -s Anc2.Anc2refChr13 50382 9 + 96486 GACTAAAGG -s mr.mrrefChr5 269347 9 + 294540 AGCTACCAG -s simCow_chr6.simCow.chr6 406469 9 + 602619 AATGAAAGG -s simDog_chr6.simDog.chr6 396748 9 + 593897 GACTAAAGG -s simHuman_chr6.simHuman.chr6 401477 9 + 601863 GACTAACAG -s simRat_chr6.simRat.chr6 422945 9 + 647215 AGCTACTGG - -a -s simMouse_chr6.simMouse.chr6 416924 47 + 636262 CTCACCACCAAACAAAAGAGCATATTTGCAATCATGCTGAGGCATTG -s Anc0.Anc0refChr3 46211 47 + 222631 CTCTCTTGGAGTGCAGAAGGCATATTTACCATTATGCTGACGCATTG -s Anc1.Anc1refChr6 76642 47 + 197743 CTCTCTTGGAGTGCAGAAGGCATATTTACCATTATGCTGACGCATTG -s Anc2.Anc2refChr13 50391 47 + 96486 TTCTCTTGGAGTGCAGAAGGCCTATTTACCAATGTGCTGACGCATTG -s mr.mrrefChr5 269356 47 + 294540 CTCACTTCCAAACAAAAGAGCATATTTGCAATCATGCTGAGGCATTG -s simCow_chr6.simCow.chr6 406482 47 + 602619 TTCTCTTGTAGTGCAGAAGGCGTATTTACCGATGTGCTGATGCATTG -s simDog_chr6.simDog.chr6 396757 47 + 593897 TTCTCTTGGAGTGCAGAAAGCCTATTTACCAAGGTGCTGACGCATTG -s simHuman_chr6.simHuman.chr6 401486 47 + 601863 CTCTCTTGGAGTTTAGCAGGCATAACTACCATTATGCTGAAGCATTG -s simRat_chr6.simRat.chr6 422954 47 + 647215 CTCCCTTCCAAACCAAACAGGATATTTGCAATCATGCTGAGGCGTTA - -a -s simMouse_chr6.simMouse.chr6 416971 15 + 636262 GACTACGAAAGTCAA -s Anc0.Anc0refChr3 46261 15 + 222631 AATTACAAAAGTCAC -s Anc1.Anc1refChr6 76692 15 + 197743 AATTACAAAAGTCAC -s Anc2.Anc2refChr13 50441 15 + 96486 AATTACAAAAGTCAC -s mr.mrrefChr5 269403 15 + 294540 GACTACAAAAGTCAA -s simCow_chr6.simCow.chr6 406532 15 + 602619 AACTGCAAATGTGAC -s simDog_chr6.simDog.chr6 396807 15 + 593897 AATTACAACAGTCAC -s simHuman_chr6.simHuman.chr6 401536 15 + 601863 AATTACAAAAGTCAC -s simRat_chr6.simRat.chr6 423001 15 + 647215 GACTACAAAAGTAAA - -a -s simMouse_chr6.simMouse.chr6 416986 50 + 636262 GTCACAGATAAACTCTGCGCATTCTTAAGGTATTCAATAAGGAGAGTTGA -s Anc0.Anc0refChr3 46281 50 + 222631 ATTACTGATAAATTCTGTGAAATCCTAAGGTATTTGATAGAGAGAATTGG -s Anc1.Anc1refChr6 76712 50 + 197743 ATTACTGATAAATTCTGTGAAATCCTAAGGTATTTGATAGAGAGAATTGG -s Anc2.Anc2refChr13 50461 50 + 96486 ATTACTGATAAATTCTGTGAAATCCTAAGGTATTTGATAGAGTGGACTGA -s mr.mrrefChr5 269418 50 + 294540 GTCACTGATAAACTCTGCGCAATCTTAAGGTATTTAATAAAGAGAGTTGG -s simCow_chr6.simCow.chr6 406552 39 + 602619 ATCGCTGATAAACTCCGT-AAATCCTAAGGTATTTTATAA---------- -s simDog_chr6.simDog.chr6 396827 50 + 593897 ATTACCGATAAGTTCTGTGAATTCCTAAGGTATTTGATAGAGTGGACTGA -s simHuman_chr6.simHuman.chr6 401556 50 + 601863 ATTACTGATAAATGCTGTGAAATCGTAAGGTATTTGGTAGAGAGAATTGG -s simRat_chr6.simRat.chr6 423016 50 + 647215 GTCACTGATAACCTCTACATAATCTTAAGGTACTTAACAAAGAGAGTTGG - -a -s simMouse_chr6.simMouse.chr6 417036 3 + 636262 TCT -s Anc0.Anc0refChr3 46331 3 + 222631 TAT -s Anc1.Anc1refChr6 76762 3 + 197743 TAT -s Anc2.Anc2refChr13 50511 3 + 96486 TAT -s mr.mrrefChr5 269468 3 + 294540 TCT -s simDog_chr6.simDog.chr6 396879 3 + 593897 TAT -s simHuman_chr6.simHuman.chr6 401606 3 + 601863 TAT -s simRat_chr6.simRat.chr6 423066 3 + 647215 CCT - -a -s simMouse_chr6.simMouse.chr6 417039 29 + 636262 TAAGGTATCACTAGTCTGAATGCTATCAT -s Anc0.Anc0refChr3 46336 29 + 222631 TAAGGTATTACTTTTTTGATTCCTGTTGG -s Anc1.Anc1refChr6 76767 29 + 197743 TAAGGTATTACTTTTTTGATTCCTGTTGG -s Anc2.Anc2refChr13 50516 29 + 96486 TAAGGTATTACTTTTTTGATTCCTGTTGG -s mr.mrrefChr5 269473 29 + 294540 TAAGGTATCACTAGTCTGAATGCTATCAT -s simCow_chr6.simCow.chr6 406591 26 + 602619 ---GGTATTACTTTTTTGAATGCTGTTGG -s simDog_chr6.simDog.chr6 396884 29 + 593897 TAATGTATTACTTTTTTGATTCCTGTTGG -s simHuman_chr6.simHuman.chr6 401611 29 + 601863 TATGGTATTACTTTTTTGATTTCTGTTGG -s simRat_chr6.simRat.chr6 423071 19 + 647215 TAAGGTATCACTAATCTGG---------- - -a -s simMouse_chr6.simMouse.chr6 417068 1 + 636262 G -s Anc0.Anc0refChr3 46365 1 + 222631 A -s Anc1.Anc1refChr6 76796 1 + 197743 A -s Anc2.Anc2refChr13 50545 1 + 96486 A -s mr.mrrefChr5 269502 1 + 294540 G -s simCow_chr6.simCow.chr6 406617 1 + 602619 A -s simDog_chr6.simDog.chr6 396914 1 + 593897 A -s simHuman_chr6.simHuman.chr6 401640 1 + 601863 A - -a -s simMouse_chr6.simMouse.chr6 417069 26 + 636262 TTGCTATTGGATTTCTCATAAGCAGG -s Anc0.Anc0refChr3 46367 26 + 222631 TTGCTGTTGGATTTCTCTGCAGCAGG -s Anc1.Anc1refChr6 76798 26 + 197743 TTGCTGTTGGATTTCTCTGCAGCAGG -s Anc2.Anc2refChr13 50547 26 + 96486 TTGCTGTTGCATTTCTTTGAAGCCAG -s mr.mrrefChr5 269503 26 + 294540 TTGCTATTGGATTTCTCATCAGCAGG -s simCow_chr6.simCow.chr6 406619 23 + 602619 TTGCTACTGTATTTC---AGAGTTAG -s simDog_chr6.simDog.chr6 396916 26 + 593897 TTGTTGTCGCATCTCTTTGAGGCCAA -s simHuman_chr6.simHuman.chr6 401642 26 + 601863 TCGCTGTTTGATTTCTCTGCAGCAGG -s simRat_chr6.simRat.chr6 423090 25 + 647215 -TGCTATTGGATTTCTCCTCAGCGGG - -a -s simMouse_chr6.simMouse.chr6 417095 6 + 636262 ATTGCT -s Anc0.Anc0refChr3 46394 6 + 222631 ACTGCT -s Anc1.Anc1refChr6 76825 6 + 197743 ACTGCT -s Anc2.Anc2refChr13 50574 6 + 96486 TCTGCT -s mr.mrrefChr5 269529 6 + 294540 ATTGCT -s simCow_chr6.simCow.chr6 406643 6 + 602619 TTTGCT -s simDog_chr6.simDog.chr6 396943 6 + 593897 TCAGCT -s simHuman_chr6.simHuman.chr6 401669 6 + 601863 ACTGCT -s simRat_chr6.simRat.chr6 423115 6 + 647215 ATTGCT - -a -s simMouse_chr6.simMouse.chr6 417101 78 + 636262 CCAGTTGAGCTGGACTGGGGTATCACAAAGTCATTATTTCTCTGTTACCTCCCTATATGTCCAAAGTCACCATCTTGA -s Anc0.Anc0refChr3 46400 67 + 222631 CCAGTTGGGCTAGATAGGGTTATCACGCAGTCATTGTTTCCC--T-------GTATA--TCCACATTGACTAGCATGA -s Anc1.Anc1refChr6 76831 74 + 197743 CCAGTTGGGCTAGATAGGGTTATCACGCAGTCATTGTTTCCC--TTAGATGGGTATA--TCCACATTGACTAGCATGA -s Anc2.Anc2refChr13 50580 67 + 96486 CAAGGTGGGCTAGATAGGGTTATCACGCAGTTATTGTTCCCT--T-------GTAGT--TCCACATTCACTAGCATGA -s mr.mrrefChr5 269535 78 + 294540 CCAGTTGAGCTGGACTGGGGTATCACAAAGTCATTATTTCTCTGTTACCTCCGTATATGTCCAAAGTGACTATCTTGA -s simCow_chr6.simCow.chr6 406649 63 + 602619 CATAGTGGGCCGGATGGGGTTATCACACGGT----GTGGCTC--T-------GTAGG--TCCACATTTACTAGCATGA -s simDog_chr6.simDog.chr6 396949 67 + 593897 CAAGGTGGGCTAGACAAAGTTATCATGCAGTTATTGTTCCCT--T-------GTAGT--TCCACATTCACTATCATGA -s simHuman_chr6.simHuman.chr6 401675 74 + 601863 CCAGTTGGGCAAGATAGGGATATCACTCAATCATTGCTTCCC--TTAGATGGGTATA--TTCACATTGACTAGGATGA -s simRat_chr6.simRat.chr6 423136 78 + 647215 CCGGTTGAGCTGGACCAGGTTATCACAAAGTCTTTATTTATCTCTTACCTCCGTATATGTCCAAGGTGACTATCCTGA - -a -s simMouse_chr6.simMouse.chr6 417179 14 + 636262 CTGCTTTCCAGATG -s Anc0.Anc0refChr3 46467 14 + 222631 CCCTTTTCCAGATG -s Anc1.Anc1refChr6 76905 14 + 197743 CCCTTTTCCAGATG -s Anc2.Anc2refChr13 50647 14 + 96486 CCCTTTTCCAGATG -s mr.mrrefChr5 269613 14 + 294540 CTGCTTTCCAGATG -s simCow_chr6.simCow.chr6 406718 14 + 602619 CCCTTTTCCAGCTC -s simDog_chr6.simDog.chr6 397016 14 + 593897 CTCTCTTCCACATG -s simHuman_chr6.simHuman.chr6 401749 14 + 601863 CCCTTTTCCAGATT -s simRat_chr6.simRat.chr6 423214 14 + 647215 CTGCTTTCCAGATG - -a -s simMouse_chr6.simMouse.chr6 417193 2 + 636262 CA -s Anc0.Anc0refChr3 46481 2 + 222631 CA -s Anc1.Anc1refChr6 76919 2 + 197743 CA -s Anc2.Anc2refChr13 50661 2 + 96486 CA -s mr.mrrefChr5 269627 2 + 294540 CA -s simCow_chr6.simCow.chr6 406734 2 + 602619 CA -s simDog_chr6.simDog.chr6 397030 2 + 593897 CA -s simHuman_chr6.simHuman.chr6 401763 2 + 601863 CA -s simRat_chr6.simRat.chr6 423228 2 + 647215 CA - -a -s simMouse_chr6.simMouse.chr6 417195 33 + 636262 ACATACACACTTTGACCATACCCAGCATATAGA -s Anc0.Anc0refChr3 46487 32 + 222631 ACATGCACACTTTGACTATACTAGCCCTATAG- -s Anc1.Anc1refChr6 76925 32 + 197743 ACATGCACACTTTGACTATACTAGCCCTATAG- -s Anc2.Anc2refChr13 50667 32 + 96486 ACATGCACAGTCTGACTATACTAGCCCTAAAG- -s mr.mrrefChr5 269629 32 + 294540 ACATACACACTTTGACCATACTCACCATATAG- -s simCow_chr6.simCow.chr6 406740 32 + 602619 ACATACACCATATGACTATGCCAGCCCCAGAG- -s simDog_chr6.simDog.chr6 397036 28 + 593897 ACATGCACAGTCTGACTACACT----CTAAAG- -s simHuman_chr6.simHuman.chr6 401769 32 + 601863 ACAGGCCCACTTTGACTATTCTTGCCCTATAG- -s simRat_chr6.simRat.chr6 423230 32 + 647215 ACATACACACTTTGACCATACTCACCATATTG- - -a -s simMouse_chr6.simMouse.chr6 417228 4 + 636262 TCAA -s Anc0.Anc0refChr3 46521 4 + 222631 CCTA -s Anc1.Anc1refChr6 76959 4 + 197743 CCTA -s Anc2.Anc2refChr13 50701 4 + 96486 CCTG -s mr.mrrefChr5 269661 4 + 294540 CCTA -s simCow_chr6.simCow.chr6 406774 2 + 602619 TC-- -s simDog_chr6.simDog.chr6 397066 4 + 593897 CCTG -s simHuman_chr6.simHuman.chr6 401803 4 + 601863 CCTA -s simRat_chr6.simRat.chr6 423262 4 + 647215 CCTG - -a -s simMouse_chr6.simMouse.chr6 417232 1 + 636262 C -s Anc0.Anc0refChr3 46525 1 + 222631 C -s Anc1.Anc1refChr6 76963 1 + 197743 C -s Anc2.Anc2refChr13 50705 1 + 96486 C -s mr.mrrefChr5 269665 1 + 294540 C -s simCow_chr6.simCow.chr6 406776 1 + 602619 C -s simDog_chr6.simDog.chr6 397071 1 + 593897 C -s simHuman_chr6.simHuman.chr6 401807 1 + 601863 C -s simRat_chr6.simRat.chr6 423266 1 + 647215 C - -a -s simMouse_chr6.simMouse.chr6 417233 118 + 636262 TCCATAATTGTCTAGTCATTGGTCAGGTTGCTATTTTGAATCTCACACCCAGTAATGGGCCCTCTAATCATGGAAGCAAGGCAGGGCAACTATTCAAAAGAGCGATCCATGTCAACTA -s Anc0.Anc0refChr3 46526 31 + 222631 TAAAAGATTGTCT----------------------------------------------------------------------------TTACTAAACAGAGGGAAC----------- -s Anc1.Anc1refChr6 76964 31 + 197743 TAAAAGATTGTCT----------------------------------------------------------------------------TTACTAAACAGAGGGAAC----------- -s Anc2.Anc2refChr13 50707 31 + 96486 TAAAAGATTGTGT----------------------------------------------------------------------------TTCCTAAACAGAGGAAAC----------- -s mr.mrrefChr5 269666 116 + 294540 TCAATAATTGTCTAGTCATTGGTCAGGTTGCTATTTTGAATC--ACACCCAGTAATGGGCCCTCTAATCATGGAAGCAAGGCAGGGCAACTACTAAAAAGAGCGATCCATGTCAACTA -s simCow_chr6.simCow.chr6 406778 31 + 602619 TAAAAAATTGTTT----------------------------------------------------------------------------TCTCCAGTAAGATCAAAC----------- -s simDog_chr6.simDog.chr6 397073 31 + 593897 TAAAAGATTGTGT----------------------------------------------------------------------------TTCCTAAACAGAGGAGAC----------- -s simHuman_chr6.simHuman.chr6 401808 31 + 601863 TGAGAGATTTTCT----------------------------------------------------------------------------TTACTAAAGAGAGGGAAC----------- -s simRat_chr6.simRat.chr6 423267 116 + 647215 TCAATAATTGTCTAGTCATTGGTCATGTTGCTATATAGAAAC--ACACGCAATAATGGGCCATCCAATCATGGAAGCAAGGTAGGGCAATTACTAAAAATAGTGTCCCATGTTAACCA - -a -s simMouse_chr6.simMouse.chr6 417351 9 + 636262 TGTAAGGGG -s Anc0.Anc0refChr3 46557 9 + 222631 TGTTGGGGT -s Anc1.Anc1refChr6 76995 9 + 197743 TGTTGGGGT -s Anc2.Anc2refChr13 50740 9 + 96486 TGTTGGGGT -s mr.mrrefChr5 269782 9 + 294540 TGTTGGGGT -s simCow_chr6.simCow.chr6 406811 9 + 602619 TGTTGGAGT -s simDog_chr6.simDog.chr6 397106 9 + 593897 TGTTGGGGT -s simHuman_chr6.simHuman.chr6 401839 9 + 601863 TGTTGGGGT -s simRat_chr6.simRat.chr6 423383 9 + 647215 TGTTGGGGT - -a -s simMouse_chr6.simMouse.chr6 417360 26 + 636262 GCCTGATATACTAAAGTTAGTATGGG -s Anc0.Anc0refChr3 46567 25 + 222631 CCTTC-CTTACTAAAGTTAATATGGA -s Anc1.Anc1refChr6 77005 25 + 197743 CCTTC-CTTACTAAAGTTAATATGGA -s Anc2.Anc2refChr13 50750 25 + 96486 CCTTC-CTTACTAAAGTTACTGTAGA -s mr.mrrefChr5 269791 25 + 294540 GCCTG-CATACTAAAGTTAATATGGG -s simCow_chr6.simCow.chr6 406821 25 + 602619 CCTTC-CTTACTAAAGTTAGTGTAGA -s simDog_chr6.simDog.chr6 397116 25 + 593897 CCTTC-CTTACAATAGTTACTGTAGA -s simHuman_chr6.simHuman.chr6 401851 25 + 601863 CCTTC-CTTACTAAAGCTAATAAGGA -s simRat_chr6.simRat.chr6 423392 25 + 647215 GCCAG-CATACTAAAGTTAATATGGG - -a -s simMouse_chr6.simMouse.chr6 417386 18 + 636262 TTCCATTAATATGGGCCC -s Anc0.Anc0refChr3 46592 5 + 222631 TCCCA------------- -s Anc1.Anc1refChr6 77030 5 + 197743 TCCCA------------- -s Anc2.Anc2refChr13 50775 5 + 96486 TCCCA------------- -s mr.mrrefChr5 269816 18 + 294540 TTCCATTAATATGGGCCC -s simCow_chr6.simCow.chr6 406847 5 + 602619 TCCCA------------- -s simDog_chr6.simDog.chr6 397141 5 + 593897 CCCCA------------- -s simHuman_chr6.simHuman.chr6 401876 5 + 601863 TCCCA------------- -s simRat_chr6.simRat.chr6 423417 18 + 647215 TTCCATTAATATGGGCCC - -a -s simMouse_chr6.simMouse.chr6 417404 63 + 636262 AAGGATCTGGTGATGATTGGGATAAAACGACCCATGCGCTACTCTGCCTGTGGTTGACCAAGG -s Anc0.Anc0refChr3 46598 62 + 222631 AAGCATCTAGTGATGGTTCAAATAAAAGGTGC-ATGTGCTACTCTGGAGGTGGCCAACCAAGG -s Anc1.Anc1refChr6 77036 62 + 197743 AAGCATCTAGTGATGGTTCAAATAAAAGGTGC-ATGTGCTACTCTGGAGGTGGCCAACCAAGG -s Anc2.Anc2refChr13 50781 62 + 96486 AAGCATCTAGTGGTGGTTCAAATAGAAGGTGC-ATGTGCTACTCTGGAGGTGGCCAACCCAGG -s mr.mrrefChr5 269835 62 + 294540 AAGCATCTGGTGATGGTTGGGATAAAACGACC-ATGTGCTACTCTGCCTGTGGTCAACCAAGG -s simCow_chr6.simCow.chr6 406853 56 + 602619 AAGTACCTAGGAGTAG-----AACCAAGGTGC-ATGTGCTACTCTGGAAATG-CCAACTGAGG -s simDog_chr6.simDog.chr6 397147 61 + 593897 AGGCATCCAGTGGTGGTTCAAATAGAAGGTGC-ATGCACCATTTTTGAGGTGGTCAA-CCAAG -s simHuman_chr6.simHuman.chr6 401882 62 + 601863 AAACCTCTTCTGACGGTCCACCTTAAAGGTAC-ATGTGCTACTCTGGAGGTGGCCAACCAAGG -s simRat_chr6.simRat.chr6 423437 62 + 647215 AAGCATCTGGTGATGGTTGGAATAAAACAACC-ATGTGCTACTCTGCCTGTGGTCAACCAAGG - -a -s simMouse_chr6.simMouse.chr6 417467 35 + 636262 GGAATCCAGTATCAAGGCTTCACATTCTCTCCTGC -s Anc0.Anc0refChr3 46661 35 + 222631 GGGAGGCACTACCTAGGCTTTGCATTCTTTCCTGC -s Anc1.Anc1refChr6 77099 35 + 197743 GGGAGGCACTACCTAGGCTTTGCATTCTTTCCTGC -s Anc2.Anc2refChr13 50844 35 + 96486 GGGAGGCACTACTTAGGCTTTGCATTCCTTCCTGC -s mr.mrrefChr5 269897 35 + 294540 GGGAGCCAGTATCAAGGCTTCGCATTCTCTCCTGC -s simCow_chr6.simCow.chr6 406910 35 + 602619 GGAAGGCACTACTTAGGCTTTGCATTCCCTACTGC -s simDog_chr6.simDog.chr6 397209 33 + 593897 GGGAAGCACTA--TAGGCTTTGCATTCCTTCCAGC -s simHuman_chr6.simHuman.chr6 401945 35 + 601863 GGGAGGCACCACCTAGGGTTTGCATTCTTTCCTGC -s simRat_chr6.simRat.chr6 423499 35 + 647215 GGGAGCCAGTATCAAGGCTTCGCATTCTCTCCTGG - -a -s simMouse_chr6.simMouse.chr6 417502 24 + 636262 AACCCTCATCACTTTCACAGTATG -s Anc0.Anc0refChr3 46696 24 + 222631 AACCCTTATCACATTCACAGTATT -s Anc1.Anc1refChr6 77134 24 + 197743 AACCCTTATCACATTCACAGTATT -s Anc2.Anc2refChr13 50879 24 + 96486 AACCCTTATCACAACTACAGTGTT -s mr.mrrefChr5 269932 24 + 294540 AACCCTCATCACTTTCACAGTATG -s simCow_chr6.simCow.chr6 406946 12 + 602619 AACCATTATCAC------------ -s simDog_chr6.simDog.chr6 397242 24 + 593897 CTCCCTTATCACAACTACAGTGTT -s simHuman_chr6.simHuman.chr6 401980 24 + 601863 AACCCTTATCACGTTCACAGTATT -s simRat_chr6.simRat.chr6 423534 24 + 647215 AACCCTCATCACTTTCACAGTATG - -a -s simMouse_chr6.simMouse.chr6 417526 31 + 636262 TACTGCCCACTCTCGTGTCTATCAAACCTTC -s Anc0.Anc0refChr3 46720 29 + 222631 G-CT-CTCACACTCCCGTCCAATGGTCCTTC -s Anc1.Anc1refChr6 77158 29 + 197743 G-CT-CTCACACTCCCGTCCAATGGTCCTTC -s Anc2.Anc2refChr13 50903 29 + 96486 G-CT-CTTACACTCCCGTCCAATGGTCCTTC -s mr.mrrefChr5 269956 30 + 294540 T-CTGCCCACTCTCGTGTCTAATGGACCTTC -s simCow_chr6.simCow.chr6 406958 18 + 602619 -------------CCTGTCTAATGGTCCTTC -s simDog_chr6.simDog.chr6 397267 29 + 593897 G-CT-CTTACACTCCCATCCAATGGTCCTTC -s simHuman_chr6.simHuman.chr6 402004 29 + 601863 G-CT-CTCACACTCCCGCCCAATGGTCCTTC -s simRat_chr6.simRat.chr6 423558 30 + 647215 T-CTGTCCACCCTCTTATCTAATGGACCTTC - -a -s simMouse_chr6.simMouse.chr6 417557 6 + 636262 CCATGA -s Anc0.Anc0refChr3 46753 6 + 222631 CCATGA -s Anc1.Anc1refChr6 77191 6 + 197743 CCATGA -s Anc2.Anc2refChr13 50936 6 + 96486 CCATGA -s mr.mrrefChr5 269986 6 + 294540 CCATGA -s simCow_chr6.simCow.chr6 406981 6 + 602619 CCAAGT -s simDog_chr6.simDog.chr6 397300 6 + 593897 CCATGA -s simHuman_chr6.simHuman.chr6 402037 6 + 601863 CCACAA -s simRat_chr6.simRat.chr6 423588 6 + 647215 CCATGG - -a -s simMouse_chr6.simMouse.chr6 417563 45 + 636262 ATGTTTGCATCACTTCTTGGCCAACAGATATGACCAGTTCTGGTG -s Anc0.Anc0refChr3 46759 45 + 222631 ATGTTATCATTGATCCTTCACCAATGGATATGACCAGTTGTGGTG -s Anc1.Anc1refChr6 77197 45 + 197743 ATGTTATCATTGATCCTTCACCAATGGATATGACCAGTTGTGGTG -s Anc2.Anc2refChr13 50942 45 + 96486 ATGTTATCATTGATCCTTCACCAATGGATATGACCAGTTGTGGTG -s mr.mrrefChr5 269992 45 + 294540 ATGTTTGCATCAATCCTTGGCCAACAGATATGACCAGTTCTGGTG -s simCow_chr6.simCow.chr6 406987 44 + 602619 ATGTTATTGTTGAGACTTCA-CAACAGATATGACCCACTGAGGTG -s simDog_chr6.simDog.chr6 397326 45 + 593897 ATGTTACCACTGATCCTTTGCCAATGGATTTGACCAGTTGTGGTG -s simHuman_chr6.simHuman.chr6 402043 45 + 601863 ATGTTATCATTGATCCTTCATCAATGGATATGACCAGTTGTGGTG -s simRat_chr6.simRat.chr6 423594 45 + 647215 ATGTTTGGATCAATCTTTTGCCAACAGATATGACCAGTTCTGGTG - -a -s simMouse_chr6.simMouse.chr6 417608 6 + 636262 GGGCAT -s Anc0.Anc0refChr3 46804 1 + 222631 G----- -s Anc1.Anc1refChr6 77242 2 + 197743 GG---- -s Anc2.Anc2refChr13 50987 1 + 96486 G----- -s mr.mrrefChr5 270037 6 + 294540 GGGCAT -s simCow_chr6.simCow.chr6 407031 1 + 602619 G----- -s simDog_chr6.simDog.chr6 397371 1 + 593897 G----- -s simHuman_chr6.simHuman.chr6 402090 2 + 601863 GG---- -s simRat_chr6.simRat.chr6 423639 6 + 647215 TCTCAT - -a -s simMouse_chr6.simMouse.chr6 417614 70 + 636262 ACATGAAAGGGATGGAACTGAAACATGGTGCATGTTCCCGAAAGGATGGGAATGTCTCAATAACCATCAT -s Anc0.Anc0refChr3 46805 42 + 222631 ----------------------------TACATATTCTCAAAAGGATGGACATGACTGGAAAAGCATCAA -s Anc1.Anc1refChr6 77244 67 + 197743 ACACGAATGCGTTGGG--TGAG-GATGGTACATATTCTCAAAAGGATGGACATGACTGGAAAAGCATCAA -s Anc2.Anc2refChr13 50988 42 + 96486 ----------------------------TACATATTCTCAAAAGGATGTACATGAAAGGAAAAGAATCAA -s mr.mrrefChr5 270043 69 + 294540 ACACGAAAGGGATGGAACTGAA-CATGGTGCATATTCCCAAAAGGATGGGAATGTCTCAAAAACCATCAT -s simCow_chr6.simCow.chr6 407032 39 + 602619 ----------------------------TGCATAATTGCAACAGGATAAGCAGGAAAATAAAAG---TAA -s simDog_chr6.simDog.chr6 397372 42 + 593897 ----------------------------TACATATTCTCAAAATTATGTACATGGAAGGAAAAAAATCAA -s simHuman_chr6.simHuman.chr6 402371 67 + 601863 ACACGAATGCGTTGGG--TGAG-GATGGTACATATTCTCAAAAGGATGGATGTGACTGGAAAAGCTTCAA -s simRat_chr6.simRat.chr6 423645 69 + 647215 ACACGAAACGGATGGAACTGAA-CATGGTGTATATTCCCATAAGGTTGGGAATGTCTCAAAAACCATCAT - -a -s simMouse_chr6.simMouse.chr6 417684 21 + 636262 CCAGGTGAATGGAGGGGGGTT -s Anc0.Anc0refChr3 46850 21 + 222631 CCAGGTGCACAGAGTATGGTT -s Anc1.Anc1refChr6 77314 21 + 197743 CCAGGTGCACAGAGTATGGTT -s Anc2.Anc2refChr13 51033 21 + 96486 CCTGGTGCACAGGCTATGGTT -s mr.mrrefChr5 270112 21 + 294540 CCAGGTGAATGGAGGGGGGTT -s simCow_chr6.simCow.chr6 407074 10 + 602619 AGTGGTGAGC----------- -s simDog_chr6.simDog.chr6 397417 21 + 593897 CCTGGTTCACAGGCTATGGTT -s simHuman_chr6.simHuman.chr6 402441 21 + 601863 CCAGGTGGACAGAGACAGACT -s simRat_chr6.simRat.chr6 423714 21 + 647215 CCAGGTGTATGGATGGGGGGT - -a -s simMouse_chr6.simMouse.chr6 417705 22 + 636262 GACAGGGTGTCTGTTGCATTGC -s Anc0.Anc0refChr3 46871 15 + 222631 G-------GTTCATTGACCTGC -s Anc1.Anc1refChr6 77335 22 + 197743 GACAGGGTGTTCATTGACCTGC -s Anc2.Anc2refChr13 51054 15 + 96486 G-------GGTCAATGACCTGA -s mr.mrrefChr5 270133 22 + 294540 GACAGGGTGTCTGTTGCATTGC -s simCow_chr6.simCow.chr6 407084 11 + 602619 -----------CAATGACCTGA -s simDog_chr6.simDog.chr6 397438 4 + 593897 G-------GGT----------- -s simHuman_chr6.simHuman.chr6 402466 22 + 601863 GACAGGGTATACATTGACCTCC -s simRat_chr6.simRat.chr6 423735 22 + 647215 AACAGGGTGCCTGTTGTGTTGT - -a -s simMouse_chr6.simMouse.chr6 417727 5 + 636262 ATGTA -s Anc0.Anc0refChr3 46886 5 + 222631 ATGTT -s Anc1.Anc1refChr6 77357 5 + 197743 ATGTT -s Anc2.Anc2refChr13 51069 5 + 96486 ATGTT -s mr.mrrefChr5 270155 5 + 294540 ATGTA -s simCow_chr6.simCow.chr6 407095 5 + 602619 ATATA -s simDog_chr6.simDog.chr6 397442 4 + 593897 -TGTT -s simHuman_chr6.simHuman.chr6 402488 5 + 601863 ATGTT -s simRat_chr6.simRat.chr6 423759 5 + 647215 ATTTA - -a -s simMouse_chr6.simMouse.chr6 417732 57 + 636262 GATCCTGTTGTGACACTACTAATAATAGCTGACATAATTTTAAGTGGAAACGTGAAG -s Anc0.Anc0refChr3 46891 43 + 222631 GATGCTACTACGATATTATTAAT-----------T---CTTAAGGGGAAGTTTTAAG -s Anc1.Anc1refChr6 77362 54 + 197743 GATGCTACTACGATATTATTAATGATAGTTGACAT---CTTAAGGGGAAGTTTTAAG -s Anc2.Anc2refChr13 51074 43 + 96486 GATGCTACTACGATATTATTTAT-----------T---CTTAAGGGGAAGTTTTAAC -s mr.mrrefChr5 270160 57 + 294540 GATCCTGCTGTGACACTACTAATGATAGCTGACATGATTTTAAGTGGAAACGTGAAG -s simCow_chr6.simCow.chr6 407100 43 + 602619 GATTCTACTATGATATTATCTAG-----------T---TTTAAGGGGAGGTTTTGAC -s simDog_chr6.simDog.chr6 397453 43 + 593897 GACGCTACTACGATGTTATTTGT-----------T---CTTAAGGGGAAATCTCAAC -s simHuman_chr6.simHuman.chr6 402493 43 + 601863 GATGCGACTACAATAGTATTAATGATAGTTGACAT--------------GTTTTAAG -s simRat_chr6.simRat.chr6 423764 54 + 647215 GGTCCTGCTGGGACCCT---AATGATAGCTGACATGATTTTAAGTGGAAATATGATG - -a -s simMouse_chr6.simMouse.chr6 417789 82 + 636262 TGTCTCTAGGAATGTAAACCAAACATTCCTCATGGGTGATCAAGGTCAGCAAACCATTATGAGTGGTTGGATCACCAGAAGT -s Anc0.Anc0refChr3 46934 82 + 222631 TGCTTCTAGACATGTTAACCAAAAAATCCTCATGGGTCCTCAAGGTCAACAAAGCATCATGAGTGGTTGGATGACTGGAAGG -s Anc1.Anc1refChr6 77416 82 + 197743 TGCTTCTAGACATGTTAACCAAAAAATCCTCATGGGTCCTCAAGGTCAACAAAGCATCATGAGTGGTTGGATGACTGGAAGG -s Anc2.Anc2refChr13 51117 82 + 96486 TGCTTCTGGACATGTTAACCAAGAAATCCTCATGGGTCCTCAAGGTCAACAAAGCATCATGAGTAGTTAAGAGACTGGAAGG -s mr.mrrefChr5 270217 82 + 294540 TGTCTCTAGGAATGTAAACCAAAAAATCCTCATGGGTGATCAAGGTCAGCAAACCATCATGAGTGGTTGGATGACTGGAAGG -s simCow_chr6.simCow.chr6 407143 82 + 602619 TGCTTCTGGACATGTTAACCAAGAAATCCTCATGGGGCCACAAGGTCAACAAAGTGTGAAGAGTAGTCAAGAGGCTGGAAGT -s simDog_chr6.simDog.chr6 397496 82 + 593897 TGCTTCTGGACATGTTAACCAAGAAATCCTCATGGGTCTTTGAGGTCAACACAGCATCATGGGCAGTTAAGAAAGTGGAAGG -s simHuman_chr6.simHuman.chr6 402538 82 + 601863 TGCTTCTAGTCATGTTAGCCAAAAAATCCTCACGGGACCTCAAGGTCAACAAAGCATCATGAGTGGTTGGATGACTGGGAGG -s simRat_chr6.simRat.chr6 423818 82 + 647215 TGTCTCTAGGAATGTAAACCAAGAAATCCTCATGGGTTATCAAGGTAAGCAAACCATCATGACAGGTTGAATGACTGGAAGG - -a -s simMouse_chr6.simMouse.chr6 417871 49 + 636262 CATAAATGTATCATGTTGATTTCTTATCCCACTGATTTCACATCATTAG -s Anc0.Anc0refChr3 47018 49 + 222631 CATATATGAACCATGTAAATCTCTTACTGCACTGATTTCTTGTCTTTAG -s Anc1.Anc1refChr6 77500 49 + 197743 CATATATGAACCATGTAAATCTCTTACTGCACTGATTTCTTGTCTTTAG -s Anc2.Anc2refChr13 51201 49 + 96486 CATATACGAACCATGTAAGTCTCTTATTGTACTGATTTCTTGTCTTCAG -s mr.mrrefChr5 270299 49 + 294540 CATAAATGTATCATGTTAATTTCTTACCCCACTGATTTCATGTCTTTAG -s simCow_chr6.simCow.chr6 407227 49 + 602619 TATATTCATACCAAGTAAGACTCTTGTTGTCCTGATTTCTTGCCTTGAA -s simDog_chr6.simDog.chr6 397580 49 + 593897 CATATACGAACCATGGAAGTCTCTTATCGTACTGATTTCTTCTCTTCAG -s simHuman_chr6.simHuman.chr6 402622 49 + 601863 CATATGTGGGCCATGTAAATCACTTACTGCACTGATTTCTTGTCTTTAG -s simRat_chr6.simRat.chr6 423900 49 + 647215 CCTAACTGTCTCATGCCAATTTCTTACCTAACTGATTTCATGTCTTTAG - -a -s simMouse_chr6.simMouse.chr6 417920 31 + 636262 CTGAAGTTCGTCTCCATGCAGTTGCCAGAAA -s Anc0.Anc0refChr3 47067 31 + 222631 ATGAATTTCGTCTCTGTGTGATTGCTAGAAA -s Anc1.Anc1refChr6 77549 31 + 197743 ATGAATTTCGTCTCTGTGTGATTGCTAGAAA -s Anc2.Anc2refChr13 51250 31 + 96486 ATGAATTTTGTTTCTGTGTGATTGCTAGAAA -s mr.mrrefChr5 270348 31 + 294540 CTGAAGTTCGTCTCCATGTGGTTGCCAGAAA -s simCow_chr6.simCow.chr6 407276 30 + 602619 ATAAATCTTGT-TCTGCATGATCGCTAAAAA -s simDog_chr6.simDog.chr6 397629 31 + 593897 AGGAATTTTGTTCCTGTGTAACTGCTAGAGA -s simHuman_chr6.simHuman.chr6 402671 31 + 601863 ATGAAATTCGTCTCTTTGTGATTGCTAGAAA -s simRat_chr6.simRat.chr6 423966 31 + 647215 CTGAAGTTCATCTCCATGTGGTTGCAAGAAA - -a -s simMouse_chr6.simMouse.chr6 417951 47 + 636262 TACGAGAAATCTGATGTACACTGATAGGGCTACTAGGCTCCACTGCC -s Anc0.Anc0refChr3 47098 36 + 222631 TACCA---------TGTACAATCATGGCC--ATTAAGTTCTGCTGCC -s Anc1.Anc1refChr6 77580 36 + 197743 TACCA---------TGTACAATCATGGCC--ATTAAGTTCTGCTGCC -s Anc2.Anc2refChr13 51281 36 + 96486 TACCA---------TGTACAATCATGGCC--ATTAAGTTCTGCTGCC -s mr.mrrefChr5 270379 47 + 294540 TACCAGAAATCTGATGTACACTGATAGGCCTACTAAGCTCCACTGCC -s simCow_chr6.simCow.chr6 407306 36 + 602619 TACTA---------TGTACAATCATGGCC--ATTAAATTTTGTTGCC -s simDog_chr6.simDog.chr6 397660 36 + 593897 TGCCA---------TGTTCAATCATGGCC--ATTAAGCTCTGCTGCC -s simHuman_chr6.simHuman.chr6 402702 36 + 601863 CACCA---------TGTACAACCATGAAC--ATTAAGTTCTGCCACC -s simRat_chr6.simRat.chr6 423999 47 + 647215 TACCAGAAATCCAATGTACACTGGTAGGCCTACTGAGCTCCACTGCC - -a -s simMouse_chr6.simMouse.chr6 417998 4 + 636262 TCGC -s Anc0.Anc0refChr3 47135 4 + 222631 TGGT -s Anc1.Anc1refChr6 77617 4 + 197743 TGGT -s Anc2.Anc2refChr13 51318 4 + 96486 TGGT -s mr.mrrefChr5 270426 4 + 294540 TCGT -s simCow_chr6.simCow.chr6 407343 4 + 602619 TGGA -s simDog_chr6.simDog.chr6 397697 4 + 593897 TGGT -s simHuman_chr6.simHuman.chr6 402739 4 + 601863 TGGT -s simRat_chr6.simRat.chr6 424046 4 + 647215 TTGT - -a -s simMouse_chr6.simMouse.chr6 418002 10 + 636262 CTTAGTAGGC -s Anc0.Anc0refChr3 47139 9 + 222631 GCTAGTA-AT -s Anc1.Anc1refChr6 77621 9 + 197743 GCTAGTA-AT -s Anc2.Anc2refChr13 51323 9 + 96486 GCTAGTA-AT -s mr.mrrefChr5 270430 10 + 294540 CTTAGTAGAC -s simCow_chr6.simCow.chr6 407348 9 + 602619 GCTAGTA-TT -s simDog_chr6.simDog.chr6 397702 9 + 593897 GGCAGTA-AC -s simHuman_chr6.simHuman.chr6 402743 9 + 601863 GCTAGTA-AT -s simRat_chr6.simRat.chr6 424050 10 + 647215 CTTGGTTGAC - -a -s simMouse_chr6.simMouse.chr6 418012 2 + 636262 AC -s Anc0.Anc0refChr3 47148 2 + 222631 AC -s Anc1.Anc1refChr6 77630 2 + 197743 AC -s Anc2.Anc2refChr13 51332 2 + 96486 AC -s mr.mrrefChr5 270440 2 + 294540 AC -s simCow_chr6.simCow.chr6 407357 2 + 602619 TC -s simDog_chr6.simDog.chr6 397711 2 + 593897 AC -s simHuman_chr6.simHuman.chr6 402752 2 + 601863 AC -s simRat_chr6.simRat.chr6 424061 2 + 647215 AC - -a -s simMouse_chr6.simMouse.chr6 418014 25 + 636262 CACACTTTGTAAACTATGTTGTGGT -s Anc0.Anc0refChr3 47150 25 + 222631 AACACTTTTTAAGTTGAGTTGTGGA -s Anc1.Anc1refChr6 77632 25 + 197743 AACACTTTTTAAGTTGAGTTGTGGA -s Anc2.Anc2refChr13 51334 25 + 96486 AACCCTTTTTAAGTTGAGTTGTGGA -s mr.mrrefChr5 270442 25 + 294540 CACACTTTGTAAGTTAAGTTGTGGT -s simCow_chr6.simCow.chr6 407359 25 + 602619 AACCCTCTTTAATCTGAGCTGAGGA -s simDog_chr6.simDog.chr6 397714 25 + 593897 AACCCTTTCTAGGTTGGATTGTGGA -s simHuman_chr6.simHuman.chr6 402754 25 + 601863 AACACTTTTTAAGTTGAGTTGTGGA -s simRat_chr6.simRat.chr6 424063 25 + 647215 CACACTCTGTAAGTTAAGATGTGGT - -a -s simMouse_chr6.simMouse.chr6 418039 16 + 636262 GAACCCTACTAACATG -s Anc0.Anc0refChr3 47183 15 + 222631 TAACCTTA-TGACATG -s Anc1.Anc1refChr6 77665 15 + 197743 TAACCTTA-TGACATG -s Anc2.Anc2refChr13 51367 15 + 96486 TAACCTTA-TGGCATA -s mr.mrrefChr5 270475 16 + 294540 GAACCCTACTAACATG -s simCow_chr6.simCow.chr6 407391 15 + 602619 TAACCTTA-CAGCCCA -s simDog_chr6.simDog.chr6 397747 15 + 593897 TAATCTTA-TGGCATA -s simHuman_chr6.simHuman.chr6 402787 15 + 601863 TAGCCTTA-TGACATG -s simRat_chr6.simRat.chr6 424096 16 + 647215 GAACCCTACTAACATG - -a -s simMouse_chr6.simMouse.chr6 418055 1 + 636262 G -s Anc0.Anc0refChr3 47198 1 + 222631 G -s Anc1.Anc1refChr6 77680 1 + 197743 G -s Anc2.Anc2refChr13 51382 1 + 96486 A -s mr.mrrefChr5 270491 1 + 294540 G -s simCow_chr6.simCow.chr6 407406 1 + 602619 A -s simDog_chr6.simDog.chr6 397769 1 + 593897 A -s simHuman_chr6.simHuman.chr6 402802 1 + 601863 G -s simRat_chr6.simRat.chr6 424112 1 + 647215 G - -a -s simMouse_chr6.simMouse.chr6 418056 42 + 636262 CTAATGTCACTACTTTAAATAGCTCATCTTGAATATATGGCC -s Anc0.Anc0refChr3 47204 42 + 222631 TCTTTGTTACTATCCTAGATAGATCATTTTGAACATGTAATC -s Anc1.Anc1refChr6 77686 42 + 197743 TCTTTGTTACTATCCTAGATAGATCATTTTGAACATGTAATC -s Anc2.Anc2refChr13 51395 42 + 96486 TCTTTGTTACTATCCTAGGTGGAATATTTTGAACATGTAATC -s mr.mrrefChr5 270497 42 + 294540 TCAATGTCACTACCTTAAATAGCTCATCTTGAATATATGGCC -s simCow_chr6.simCow.chr6 407419 36 + 602619 CCTCCATTACTATCCTAG------TATTTTGAATGTCTAGTC -s simDog_chr6.simDog.chr6 397782 41 + 593897 TCTTTG-TCCTACCCTAGGTGGAATATCTTGAGCATGTAATC -s simHuman_chr6.simHuman.chr6 402808 42 + 601863 TCTTTGGTACTGTCCTAGACAGATCATTTTGAACATGTAATC -s simRat_chr6.simRat.chr6 424119 42 + 647215 TCAACGCCACTACCTTAAATAGCTCATCTTGAATATATGGCC - -a -s simMouse_chr6.simMouse.chr6 418098 26 + 636262 CCTGGGTATGAGATCTTTGTTTCACG -s Anc0.Anc0refChr3 47246 26 + 222631 CCTAGATACAAGGTCTTCTCCTTATA -s Anc1.Anc1refChr6 77728 26 + 197743 CCTAGATACAAGGTCTTCTCCTTATA -s Anc2.Anc2refChr13 51437 26 + 96486 ACTAAATACAAGGTCTTCTCCTTATA -s mr.mrrefChr5 270539 26 + 294540 CCTGGATATGAGATCTTCGTTTCATA -s simCow_chr6.simCow.chr6 407455 26 + 602619 ACTAAACACAATGTCTCCTCCCCATA -s simDog_chr6.simDog.chr6 397823 26 + 593897 ACTAAATAAAAGACCTTCTCTTTATA -s simHuman_chr6.simHuman.chr6 402870 26 + 601863 CCCAGATACTAGGTCTTCTCCTTATA -s simRat_chr6.simRat.chr6 424161 26 + 647215 TCTGGATATGAGATCTTCGTTTCATA - -a -s simMouse_chr6.simMouse.chr6 418124 75 + 636262 TAAAATAGTCAGAGCTCCCTAATTTGGTTCCAGAAACAGGCATCCCTATTAACCTAGTAGTTCCTGCTCTGCCAC -s Anc0.Anc0refChr3 47273 71 + 222631 TGAAATAGTCAAAACTTCTCAGCCTGATTACAAGCACAGGCTTCCATA----CCCATTAGTTTCTGATCTGCAAC -s Anc1.Anc1refChr6 77755 71 + 197743 TGAAATAGTCAAAACTTCTCAGCCTGATTACAAGCACAGGCTTCCATA----CCCATTAGTTTCTGATCTGCAAC -s Anc2.Anc2refChr13 51464 71 + 96486 TGAAATAGCCAAGACTTCTCATCCTGATTATAAGCACAGGCTTCCATA----CCCATTAGTTTCTGATCTGCAAC -s mr.mrrefChr5 270565 75 + 294540 TAAAATAGTCAGAACTTCCTAGTTTGGTTACAGACACAGGCATCCCTATTAACCTAGTAGTTCCTGCTCTGCCAC -s simCow_chr6.simCow.chr6 407482 71 + 602619 TGAAATAGCCAGGACCCTTCATCCTGATTATTTGCACAGGCTCCCATG----TTTATTAGTTACTGATCTGAAAC -s simDog_chr6.simDog.chr6 397850 71 + 593897 TGAAATAGCCAAGATTTCTCGTCCTGATTATAAGCACAGGCATCCACA----CCCATTAGTTTCTGATTTGCAAC -s simHuman_chr6.simHuman.chr6 402897 71 + 601863 TGATATAGTTAAAACTTCACAGCCTGATTACAACCATAGGCTTCCATA----CCAATTAGTTTCTGACCTGCTAC -s simRat_chr6.simRat.chr6 424187 75 + 647215 TAAAATAGTCAGAACTTCCTAGTTTGGTCACAGACACAGGCATCCCTATGAGCCTAGTAGTGCCTGCTTTTACAC - -a -s simMouse_chr6.simMouse.chr6 418199 17 + 636262 CAGCAGTTTGAGGACCC -s Anc0.Anc0refChr3 47402 17 + 222631 CGGGAGTGTTAGGAACC -s Anc1.Anc1refChr6 77884 17 + 197743 CGGGAGTGTTAGGAACC -s Anc2.Anc2refChr13 51593 17 + 96486 CAGGGGTGTTAGGAACC -s mr.mrrefChr5 270640 17 + 294540 CGGCAGTTTGAGGACCC -s simCow_chr6.simCow.chr6 407612 17 + 602619 CAGGGGTGTTGAGAACC -s simDog_chr6.simDog.chr6 397978 17 + 593897 TAGGGGTGTAAGGACCC -s simHuman_chr6.simHuman.chr6 403026 17 + 601863 CGGGAGTGTTAGGAAGC -s simRat_chr6.simRat.chr6 424262 11 + 647215 CGG------GAGGACCC - -a -s simMouse_chr6.simMouse.chr6 418216 58 + 636262 TCGACTGTTCGTTCTTTTTACACTTGGTGCCATCATTCCCCAGTGTGGTGTGGCAGAT -s Anc0.Anc0refChr3 47419 54 + 222631 TTGACTGTGC----TTTCTGCACTTGACACAATCTTTCCACAATGTGGTGTGACAGAT -s Anc1.Anc1refChr6 77901 54 + 197743 TTGACTGTGC----TTTCTGCACTTGACACAATCTTTCCACAATGTGGTGTGACAGAT -s Anc2.Anc2refChr13 51610 54 + 96486 ATAATTCTGC----CTTCTGCACTTGACACAATTTTTCCACAATGTGGTGTGACAGAC -s mr.mrrefChr5 270657 58 + 294540 TTGACTGTTCGTTCTTTCTACACTTGGTGCCATCTTTCCCCAGTGTGGTGTGGCAGAT -s simCow_chr6.simCow.chr6 407629 54 + 602619 ATAATTCTGC----CTTCTGCACTTCACACAATTTTTCCACGGCATGGTGTGACAGAC -s simDog_chr6.simDog.chr6 195329 34 - 593897 ------------------------TGACACAATTTTTCCACAATGTGGTGTTGCAGAC -s simHuman_chr6.simHuman.chr6 403074 54 + 601863 TTGACTGTCC----TTTCTGCACATGACACTATCTTTCCGCTATGTGGTGTGACAAAT -s simRat_chr6.simRat.chr6 424273 58 + 647215 TTGACTGTTCGTGTTTTCTACAATTGGTGCCATCTTTCCCCAGTGTGGTGTGGCAGAT - -a -s simMouse_chr6.simMouse.chr6 418274 22 + 636262 CAAGTCTACCTATGCTATTCAT -s Anc0.Anc0refChr3 47484 22 + 222631 CAAATGTTCCTATGTAATTCAA -s Anc1.Anc1refChr6 77966 22 + 197743 CAAATGTTCCTATGTAATTCAA -s Anc2.Anc2refChr13 51675 22 + 96486 CAAATGTTCCTATGTAACTAGA -s mr.mrrefChr5 270715 22 + 294540 CAAGTCTACCTATGCTATTCAT -s simCow_chr6.simCow.chr6 407692 22 + 602619 CAAATGTTGCTATGTATCTAGA -s simDog_chr6.simDog.chr6 195374 17 - 593897 CAAATGTTCTTGTGTAA----- -s simHuman_chr6.simHuman.chr6 403139 22 + 601863 CAAATGTTCCCATCTAATTCAA -s simRat_chr6.simRat.chr6 424331 22 + 647215 CAAGTCTACCTATGCTATACAT - -a -s simMouse_chr6.simMouse.chr6 418296 22 + 636262 CTTTTTCTCTATCAGTTGCACT -s Anc0.Anc0refChr3 47515 22 + 222631 CTTCTTCTCTTTCAATTGCACT -s Anc1.Anc1refChr6 77997 22 + 197743 CTTCTTCTCTTTCAATTGCACT -s Anc2.Anc2refChr13 51706 22 + 96486 CTTCTTCTCTTTCAATTGCACT -s mr.mrrefChr5 270737 22 + 294540 CTTTTTCTCTATCAATTGCACT -s simCow_chr6.simCow.chr6 407723 22 + 602619 CCTCTTCTCTTTCGAATGCACT -s simDog_chr6.simDog.chr6 195400 22 - 593897 CTTTTCCTTTTTAAATTGCATT -s simHuman_chr6.simHuman.chr6 403170 22 + 601863 CTTCTTTTCTTTCAATTACACT -s simRat_chr6.simRat.chr6 424353 22 + 647215 CTTTATCTCTATCAATTGCACT - -a -s simMouse_chr6.simMouse.chr6 418318 1 + 636262 C -s Anc0.Anc0refChr3 47537 1 + 222631 T -s Anc1.Anc1refChr6 78019 1 + 197743 T -s Anc2.Anc2refChr13 51728 1 + 96486 T -s mr.mrrefChr5 270759 1 + 294540 C -s simCow_chr6.simCow.chr6 407745 1 + 602619 C -s simDog_chr6.simDog.chr6 195422 1 - 593897 T -s simHuman_chr6.simHuman.chr6 403192 1 + 601863 T -s simRat_chr6.simRat.chr6 424382 1 + 647215 C - -a -s simMouse_chr6.simMouse.chr6 418319 3 + 636262 AAA -s Anc0.Anc0refChr3 47585 3 + 222631 CAA -s Anc1.Anc1refChr6 78067 3 + 197743 CAA -s Anc2.Anc2refChr13 51776 3 + 96486 CAA -s mr.mrrefChr5 270760 3 + 294540 CAA -s simCow_chr6.simCow.chr6 407785 3 + 602619 TAA -s simDog_chr6.simDog.chr6 195471 3 - 593897 CAA -s simHuman_chr6.simHuman.chr6 403240 3 + 601863 CAA -s simRat_chr6.simRat.chr6 424383 3 + 647215 CAA - -a -s simMouse_chr6.simMouse.chr6 418322 4 + 636262 TACT -s Anc0.Anc0refChr3 47588 4 + 222631 TACA -s Anc1.Anc1refChr6 78070 4 + 197743 TACA -s Anc2.Anc2refChr13 51780 4 + 96486 TACA -s mr.mrrefChr5 270763 4 + 294540 TACT -s simCow_chr6.simCow.chr6 407789 4 + 602619 TACA -s simDog_chr6.simDog.chr6 195475 4 - 593897 CACA -s simHuman_chr6.simHuman.chr6 403243 4 + 601863 TACA -s simRat_chr6.simRat.chr6 424386 4 + 647215 TACC - -a -s simMouse_chr6.simMouse.chr6 418326 5 + 636262 CTCTA -s Anc0.Anc0refChr3 47601 5 + 222631 CTCTA -s Anc1.Anc1refChr6 78083 5 + 197743 CTCTA -s Anc2.Anc2refChr13 51793 5 + 96486 CCCTA -s mr.mrrefChr5 270776 5 + 294540 CTCTA -s simCow_chr6.simCow.chr6 407802 5 + 602619 CCCCA -s simDog_chr6.simDog.chr6 195488 5 - 593897 CCCTA -s simHuman_chr6.simHuman.chr6 403256 5 + 601863 CTCTA -s simRat_chr6.simRat.chr6 424399 5 + 647215 CTCTA - -a -s simMouse_chr6.simMouse.chr6 418331 10 + 636262 CAGCATTGAG -s Anc0.Anc0refChr3 47606 10 + 222631 CAGCACTGAT -s Anc1.Anc1refChr6 78088 10 + 197743 CAGCACTGAT -s Anc2.Anc2refChr13 51798 10 + 96486 CAGGACTGAT -s mr.mrrefChr5 270781 10 + 294540 CAGCATTGAG -s simCow_chr6.simCow.chr6 407810 10 + 602619 TAGTACTGAC -s simDog_chr6.simDog.chr6 195493 10 - 593897 CAGGACTGAT -s simHuman_chr6.simHuman.chr6 403261 10 + 601863 CAGCACTGAA -s simRat_chr6.simRat.chr6 424404 10 + 647215 CAGCATTGAG - -a -s simMouse_chr6.simMouse.chr6 418341 18 + 636262 ATAATGAGCAGACCATGT -s Anc0.Anc0refChr3 47616 10 + 222631 ATAAT--------TATGC -s Anc1.Anc1refChr6 78098 10 + 197743 ATAAT--------TATGC -s Anc2.Anc2refChr13 51808 10 + 96486 ATAAT--------TATGC -s mr.mrrefChr5 270791 18 + 294540 ATAATGAGCAGACCATGT -s simCow_chr6.simCow.chr6 407820 10 + 602619 ATAAT--------TATGT -s simDog_chr6.simDog.chr6 195504 10 - 593897 ATAGT--------GATGC -s simHuman_chr6.simHuman.chr6 403271 10 + 601863 ATCAT--------TATGC -s simRat_chr6.simRat.chr6 424414 18 + 647215 ATAATGAGCAGACCATGT - -a -s simMouse_chr6.simMouse.chr6 418359 4 + 636262 ATCC -s Anc0.Anc0refChr3 47627 4 + 222631 ATCA -s Anc1.Anc1refChr6 78109 4 + 197743 ATCA -s Anc2.Anc2refChr13 51819 4 + 96486 CTTA -s mr.mrrefChr5 270809 4 + 294540 ATCC -s simCow_chr6.simCow.chr6 407831 4 + 602619 CATG -s simDog_chr6.simDog.chr6 195515 4 - 593897 CTTA -s simHuman_chr6.simHuman.chr6 403282 4 + 601863 ATCA -s simRat_chr6.simRat.chr6 424432 4 + 647215 ATCC - -a -s simMouse_chr6.simMouse.chr6 418363 3 + 636262 TTT -s Anc0.Anc0refChr3 47631 3 + 222631 TTT -s Anc1.Anc1refChr6 78113 3 + 197743 TTT -s Anc2.Anc2refChr13 51845 3 + 96486 TTT -s mr.mrrefChr5 270813 3 + 294540 TTT -s simCow_chr6.simCow.chr6 407857 3 + 602619 TTT -s simDog_chr6.simDog.chr6 195547 3 - 593897 TTT -s simHuman_chr6.simHuman.chr6 403286 3 + 601863 TCA -s simRat_chr6.simRat.chr6 424436 3 + 647215 TTT - -a -s simMouse_chr6.simMouse.chr6 418366 15 + 636262 CTTGATGACCATGCT -s Anc0.Anc0refChr3 47634 15 + 222631 CTTGATGCCCATGCT -s Anc1.Anc1refChr6 78116 15 + 197743 CTTGATGCCCATGCT -s Anc2.Anc2refChr13 51848 15 + 96486 CTTGATGCCCATGCT -s mr.mrrefChr5 270816 15 + 294540 CTTGATGCCCATGCT -s simCow_chr6.simCow.chr6 407860 14 + 602619 -TTGATACCCATGCT -s simDog_chr6.simDog.chr6 195554 15 - 593897 CCTGATGCCCATGTT -s simHuman_chr6.simHuman.chr6 403289 15 + 601863 TTTGATGCACATGCT -s simRat_chr6.simRat.chr6 424439 15 + 647215 CCTGATGCTCATGCT - -a -s simMouse_chr6.simMouse.chr6 418381 11 + 636262 ATTGTAGTATT -s Anc0.Anc0refChr3 47650 11 + 222631 ATTGCTGTGTC -s Anc1.Anc1refChr6 78132 11 + 197743 ATTGCTGTGTC -s Anc2.Anc2refChr13 51864 11 + 96486 ATTGGTGTGCC -s mr.mrrefChr5 270831 11 + 294540 ATTGCAGTATT -s simCow_chr6.simCow.chr6 407875 11 + 602619 GTTGAAGTGCC -s simDog_chr6.simDog.chr6 195570 11 - 593897 ATTGGTGTGCC -s simHuman_chr6.simHuman.chr6 403305 11 + 601863 ATTCCTGCTTC -s simRat_chr6.simRat.chr6 424454 11 + 647215 ATTGCAGTATG - -a -s simMouse_chr6.simMouse.chr6 418392 12 + 636262 TGCTGGGAAGTT -s Anc0.Anc0refChr3 47661 12 + 222631 TGCTTGGTACTG -s Anc1.Anc1refChr6 78143 12 + 197743 TGCTTGGTACTG -s Anc2.Anc2refChr13 51875 12 + 96486 TGCTTGGTAGTG -s mr.mrrefChr5 270842 12 + 294540 TGCTTGGAACTT -s simCow_chr6.simCow.chr6 407886 12 + 602619 TGCTTGGTAGTT -s simDog_chr6.simDog.chr6 195581 12 - 593897 TGCTTGGTAGTG -s simHuman_chr6.simHuman.chr6 403317 12 + 601863 TGCTTGGGACTA -s simRat_chr6.simRat.chr6 424465 12 + 647215 TGTTTGGAACTT - -a -s simMouse_chr6.simMouse.chr6 418404 29 + 636262 TTACAGGGCTAGAATGCACAAAGGTGCCC -s Anc0.Anc0refChr3 47677 24 + 222631 CTAGG-AGCTAGAATGCACAAAAGT---- -s Anc1.Anc1refChr6 78159 25 + 197743 CTAGGGAGCTAGAATGCACAAAAGT---- -s Anc2.Anc2refChr13 51891 24 + 96486 CTAGG-AGTTAGAATGCACAAAAGT---- -s mr.mrrefChr5 270854 29 + 294540 TTACAGGGCTAGAATGCACAAAAGTGCCC -s simCow_chr6.simCow.chr6 407902 24 + 602619 CTAAG-AGTTAGAATGCACAAAAGT---- -s simDog_chr6.simDog.chr6 195597 24 - 593897 CTAGG-AGTTAGGATGCATAAAAGT---- -s simHuman_chr6.simHuman.chr6 403333 23 + 601863 CTAGGGAGCTAGAATGCACAACA------ -s simRat_chr6.simRat.chr6 424477 29 + 647215 TCACTAGGCTAGGATGCACAAAAGTGCCC - -a -s simMouse_chr6.simMouse.chr6 418433 35 + 636262 AAACAATTTATTTATATCCTGAGCCATAAATTAGT -s Anc0.Anc0refChr3 47701 35 + 222631 CAACTATCTATGTATATCCTGAGCCTTAACTCAGC -s Anc1.Anc1refChr6 78184 35 + 197743 CAACTATCTATGTATATCCTGAGCCTTAACTCAGC -s Anc2.Anc2refChr13 51915 35 + 96486 CAACTATCAGGGAATATCCTGAGTCTTAACTCAGC -s mr.mrrefChr5 270883 35 + 294540 AAACAATTTATTTATATCCTGAGCCATAACTTAGT -s simCow_chr6.simCow.chr6 407926 24 + 602619 -----------GCATATCCTGAGTCTTAAGTCAGC -s simDog_chr6.simDog.chr6 195625 35 - 593897 CAACTATCAGGGAATATCCTGAGTCTTAACTCAGC -s simHuman_chr6.simHuman.chr6 403356 33 + 601863 --ACTATCTATGTATATCCCGAGCTTTAACTCAGC -s simRat_chr6.simRat.chr6 424506 35 + 647215 AAACAATTTATTTATATCCTGAATCATAACTTAAT - -a -s simMouse_chr6.simMouse.chr6 418468 22 + 636262 TTAGTGAGATCTACAGGATTTC -s Anc0.Anc0refChr3 47736 22 + 222631 CAAGGGAAACCTACAGGCTTGC -s Anc1.Anc1refChr6 78219 22 + 197743 CAAGGGAAACCTACAGGCTTGC -s Anc2.Anc2refChr13 51950 22 + 96486 CAAGGGAAACCTACAGGCTTGC -s mr.mrrefChr5 270918 22 + 294540 TTAGGGAGATCTACAGGATTTC -s simCow_chr6.simCow.chr6 407950 22 + 602619 CAGGGGAAACCTACAGGCTTGC -s simDog_chr6.simDog.chr6 195665 22 - 593897 CAAAGGAAACCTACAGGGTTGC -s simHuman_chr6.simHuman.chr6 403389 22 + 601863 AGAGGGGAACCCACAGGCTTGC -s simRat_chr6.simRat.chr6 424541 22 + 647215 TAAGGGAGATCTACAGGGTTTC - -a -s simMouse_chr6.simMouse.chr6 418490 27 + 636262 ATGTTCACATGTTTCACTAGAGTTCTC -s Anc0.Anc0refChr3 47758 27 + 222631 ATGTCCGCATGTTCCACTAAAGTCCTT -s Anc1.Anc1refChr6 78241 27 + 197743 ATGTCCGCATGTTCCACTAAAGTCCTT -s Anc2.Anc2refChr13 51972 27 + 96486 ATGTCCGCACGTTCCACTAAAGTCCTT -s mr.mrrefChr5 270940 27 + 294540 ATGTTCACATGTTTCACTAGAGTTCTC -s simCow_chr6.simCow.chr6 407972 27 + 602619 TTGTTCACACGTTCCACTAAAGTCTTT -s simDog_chr6.simDog.chr6 195689 27 - 593897 ATTTCCGCACGGCTCACTAAAGTCCTT -s simHuman_chr6.simHuman.chr6 403411 19 + 601863 ATGTCTGAATGTTCCACCA-------- -s simRat_chr6.simRat.chr6 424563 27 + 647215 ATGTTCACATGTCCCACTAGAGTTCCC - -a -s simMouse_chr6.simMouse.chr6 418517 38 + 636262 ATGTTGTGCCCTAACCATTCCTCCCAACTGCATGGATA -s Anc0.Anc0refChr3 47785 38 + 222631 GTGTTGTGGCTTAAGCGCCCCCCTCAACTGCAAGGGTG -s Anc1.Anc1refChr6 78268 38 + 197743 GTGTTGTGGCTTAAGCGCCCCCCTCAACTGCAAGGGTG -s Anc2.Anc2refChr13 52000 38 + 96486 GTGTTGTGGCTTAAGCGCCCCCCTCAACTGCAAGGGTG -s mr.mrrefChr5 270967 38 + 294540 ATGTTGTGCCCTAACCATTCCTCCCAACTGCATGGATA -s simCow_chr6.simCow.chr6 408000 38 + 602619 GACAGGTTGCTCAAGGATCACCTTCAACAGCAAGGGTG -s simDog_chr6.simDog.chr6 195717 38 - 593897 GTGTTGTGGCTTAAGCGCCCCCCTCAACTGCAAGGGTG -s simRat_chr6.simRat.chr6 424590 38 + 647215 ATCTTTTGCTATAATCATTCCTCCCAAATGCATTGATG - -a -s simMouse_chr6.simMouse.chr6 418555 6 + 636262 ACTCTA -s Anc0.Anc0refChr3 47823 6 + 222631 ATTGTA -s Anc1.Anc1refChr6 78306 6 + 197743 ATTGTA -s Anc2.Anc2refChr13 52042 6 + 96486 ATTGTA -s mr.mrrefChr5 271005 6 + 294540 ACTCTA -s simCow_chr6.simCow.chr6 408042 6 + 602619 ATTCTA -s simDog_chr6.simDog.chr6 195766 6 - 593897 ATTGTA -s simRat_chr6.simRat.chr6 424628 6 + 647215 ACTCAA - -a -s simMouse_chr6.simMouse.chr6 418561 30 + 636262 CGTTTTAGAAATATCTGGTGTAGGATGGTG -s Anc0.Anc0refChr3 47829 27 + 222631 TGT---AGAATCATCTGGAGCATGTTTGTG -s Anc1.Anc1refChr6 78312 27 + 197743 TGT---AGAATCATCTGGAGCATGTTTGTG -s Anc2.Anc2refChr13 52048 27 + 96486 TGT---AGAATCATCTGGAGCATGTTTGTG -s mr.mrrefChr5 271011 30 + 294540 CGTTTTAGAAATATCTGGTGTAGGATGGTG -s simCow_chr6.simCow.chr6 408054 27 + 602619 TGG---ACCAACATCTGGTGCATGTTTGTG -s simDog_chr6.simDog.chr6 195772 27 - 593897 TGT---AGAATCATCTGGAGCATGTTTGTG -s simRat_chr6.simRat.chr6 424634 30 + 647215 CATTGTAGAAATATCTGGTGTATGTTGGTG - -a -s simMouse_chr6.simMouse.chr6 418591 5 + 636262 GTGTG -s Anc0.Anc0refChr3 47856 5 + 222631 GTATG -s Anc1.Anc1refChr6 78339 5 + 197743 GTATG -s Anc2.Anc2refChr13 52075 5 + 96486 GTATG -s mr.mrrefChr5 271041 5 + 294540 GTGTG -s simCow_chr6.simCow.chr6 408081 5 + 602619 GCATG -s simDog_chr6.simDog.chr6 195799 5 - 593897 GTATG -s simRat_chr6.simRat.chr6 424666 5 + 647215 GTGTG - -a -s simMouse_chr6.simMouse.chr6 418596 11 + 636262 GTACTTTCCCT -s Anc0.Anc0refChr3 47861 11 + 222631 ACACTTTCCCT -s Anc1.Anc1refChr6 78344 11 + 197743 ACACTTTCCCT -s Anc2.Anc2refChr13 52081 11 + 96486 ACACTTTCCCT -s mr.mrrefChr5 271046 11 + 294540 GTACTTTCCCT -s simCow_chr6.simCow.chr6 408087 11 + 602619 GTACTTTCACT -s simDog_chr6.simDog.chr6 195805 11 - 593897 ACACTTTCCCT -s simHuman_chr6.simHuman.chr6 403430 8 + 601863 ---CTTTCCCT -s simRat_chr6.simRat.chr6 424671 11 + 647215 GTCCTTTCCCT - -a -s simMouse_chr6.simMouse.chr6 418607 3 + 636262 TTC -s Anc0.Anc0refChr3 47872 3 + 222631 TTC -s Anc1.Anc1refChr6 78355 3 + 197743 TTC -s Anc2.Anc2refChr13 52096 3 + 96486 TTC -s mr.mrrefChr5 271057 3 + 294540 TTC -s simCow_chr6.simCow.chr6 408099 2 + 602619 -TC -s simDog_chr6.simDog.chr6 195820 3 - 593897 TTT -s simHuman_chr6.simHuman.chr6 403438 3 + 601863 TTC -s simRat_chr6.simRat.chr6 424682 3 + 647215 TTC - -a -s simMouse_chr6.simMouse.chr6 418610 4 + 636262 TCTT -s Anc0.Anc0refChr3 47879 4 + 222631 CCTT -s Anc1.Anc1refChr6 78362 4 + 197743 CCTT -s Anc2.Anc2refChr13 52103 4 + 96486 CCTT -s mr.mrrefChr5 271060 4 + 294540 TCTT -s simCow_chr6.simCow.chr6 408105 4 + 602619 CCTC -s simDog_chr6.simDog.chr6 195827 4 - 593897 CCTT -s simHuman_chr6.simHuman.chr6 403445 4 + 601863 CCTT -s simRat_chr6.simRat.chr6 424685 4 + 647215 TCTC - -a -s simMouse_chr6.simMouse.chr6 418614 5 + 636262 GGCAC -s Anc0.Anc0refChr3 47884 5 + 222631 GGCAC -s Anc1.Anc1refChr6 78367 5 + 197743 GGCAC -s Anc2.Anc2refChr13 52108 5 + 96486 AGCCC -s mr.mrrefChr5 271064 5 + 294540 GGCAC -s simCow_chr6.simCow.chr6 408110 5 + 602619 TGCCC -s simDog_chr6.simDog.chr6 195832 5 - 593897 AGCCC -s simHuman_chr6.simHuman.chr6 403450 5 + 601863 GGCAT -s simRat_chr6.simRat.chr6 424689 4 + 647215 GGCA- - -a -s simMouse_chr6.simMouse.chr6 418619 50 + 636262 TATGAAGGCTTTTCTAATCTGGTGAGAACATCTGAAGGTTAACTGACTAT -s Anc0.Anc0refChr3 47891 50 + 222631 TATGAAGTCTTTTCCAATCTTTGGAGAAGATATGGAGGTTGACTGACTGT -s Anc1.Anc1refChr6 78374 50 + 197743 TATGAAGTCTTTTCCAATCTTTGGAGAAGATATGGAGGTTGACTGACTGT -s Anc2.Anc2refChr13 52115 50 + 96486 TATGATGTCTTTCCCAATCTTTGGAGAAGATATAGAGGTTGACTGACTGT -s mr.mrrefChr5 271069 50 + 294540 TATGAAGGCTTTTCTAATCTGTTGAGAACATCTGAAGGTTAACTGACTAT -s simCow_chr6.simCow.chr6 408117 28 + 602619 TACGATGCCTTTCCCAATCTT----------------------TAAGTGT -s simDog_chr6.simDog.chr6 195839 50 - 593897 TGTGATGTCTTTCTCCATCTTTGGAGAAGATATAGAGGTTGACTGACTGT -s simHuman_chr6.simHuman.chr6 403457 50 + 601863 TATGAAGTCTTTTCCAATCTTTGGAGAATATATGGGGTTTCGCAGACTGT -s simRat_chr6.simRat.chr6 424693 49 + 647215 -ACTAGGGCTTTCCTGGTCGGTTGAGAACATCTGAAGGTTAACTGACTAT - -a -s simMouse_chr6.simMouse.chr6 418669 8 + 636262 TGGCATGA -s Anc0.Anc0refChr3 47949 8 + 222631 TGGCATGG -s Anc1.Anc1refChr6 78432 8 + 197743 TGGCATGG -s Anc2.Anc2refChr13 52173 8 + 96486 TGGCATGG -s mr.mrrefChr5 271119 8 + 294540 TGGCATGA -s simCow_chr6.simCow.chr6 408153 8 + 602619 TTGCATGG -s simDog_chr6.simDog.chr6 195896 6 - 593897 TGTTAT-- -s simHuman_chr6.simHuman.chr6 403515 8 + 601863 TGGCATGG -s simRat_chr6.simRat.chr6 424742 8 + 647215 TGGCAGGT - -a -s simMouse_chr6.simMouse.chr6 418677 40 + 636262 CTGGATCCTCTGAGGTGACAGCAAAACATAAACACTTAAA -s Anc0.Anc0refChr3 47957 39 + 222631 CTG-ATTCTCTGAGGTCACAATGAAACATCAACACTTACA -s Anc1.Anc1refChr6 78440 39 + 197743 CTG-ATTCTCTGAGGTCACAATGAAACATCAACACTTACA -s Anc2.Anc2refChr13 52181 39 + 96486 CTG-ATTCTCTGAGGTCACAATGAAACATCAACACTTACC -s mr.mrrefChr5 271127 40 + 294540 CTGGATCCTCTGAGGTGACAGCAAAACATAAACACTTAAA -s simCow_chr6.simCow.chr6 408161 39 + 602619 CTG-TTTCTCTGAGGTCACAATCAAACATCAAAACTTACC -s simDog_chr6.simDog.chr6 398587 39 + 593897 CTG-ATCCTCTGAGGTCTCAACGAGACATAAACTCTTACC -s simHuman_chr6.simHuman.chr6 403523 39 + 601863 CTG-ATTCTGTGAGGTCACAATGAAACATCAACACTTACA -s simRat_chr6.simRat.chr6 424750 40 + 647215 TTGGATCCCTTGAGGTGACAGCAAAACATTCACACTTAAA - -a -s simMouse_chr6.simMouse.chr6 418717 1 + 636262 C -s Anc0.Anc0refChr3 48001 1 + 222631 T -s Anc1.Anc1refChr6 78484 1 + 197743 T -s Anc2.Anc2refChr13 52225 1 + 96486 T -s mr.mrrefChr5 271167 1 + 294540 T -s simCow_chr6.simCow.chr6 408205 1 + 602619 T -s simDog_chr6.simDog.chr6 398631 1 + 593897 C -s simHuman_chr6.simHuman.chr6 403567 1 + 601863 T -s simRat_chr6.simRat.chr6 424790 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 418718 48 + 636262 CACCTCAGGCTGTTCCTTGGAGGTGAAAGAAGTTATTGCTGTGAGCAA -s Anc0.Anc0refChr3 48002 48 + 222631 CACTTCTGGTTGTTCAAGGGTTACATAGGAAATGAATGCCGAGTGCTA -s Anc1.Anc1refChr6 78485 48 + 197743 CACTTCTGGTTGTTCAAGGGTTACATAGGAAATGAATGCCGAGTGCTA -s Anc2.Anc2refChr13 52226 48 + 96486 CACTTCAGGTTGTTCAAGGGTTACATGGGAAATGAATGCCGACTGCTA -s mr.mrrefChr5 271168 48 + 294540 CACCTCTGGCTGTTCCTTGGATGTGAAAGAAATGATTGCTGAGAGCAA -s simCow_chr6.simCow.chr6 408206 38 + 602619 C----CAGGTTGTGCAAAAATTGCAGTGGAAGTGAGCGTC------CA -s simDog_chr6.simDog.chr6 398634 48 + 593897 CACTTCAGGTTGTTCAAGGGTCACATGGGAAACCAATGCCGACTGCTA -s simHuman_chr6.simHuman.chr6 403568 48 + 601863 CTCTTCTGGTTGTTCAGGGGGTACACAGAAAATGGATGCCGAGTACTA -s simRat_chr6.simRat.chr6 424791 48 + 647215 CACCTCTGGCTGTTCCTTGGATGTGAGAGAAATGATTGCAGAGAGCAA - -a -s simMouse_chr6.simMouse.chr6 418766 14 + 636262 CATTGGCAGCTATG -s Anc0.Anc0refChr3 48063 14 + 222631 TGCTGGCTGCTATG -s Anc1.Anc1refChr6 78567 14 + 197743 TGCTGGCTGCTATG -s Anc2.Anc2refChr13 52287 14 + 96486 TGCTGGCTGCTATG -s mr.mrrefChr5 271250 14 + 294540 CATTGGCAGCTATG -s simCow_chr6.simCow.chr6 408265 14 + 602619 TGCTAGCTGCTGTG -s simDog_chr6.simDog.chr6 398695 14 + 593897 TGCTGGCTGCTATG -s simHuman_chr6.simHuman.chr6 403659 14 + 601863 TGCTGGCTGCCATG -s simRat_chr6.simRat.chr6 424881 14 + 647215 CATTGGCGGCTATA - -a -s simMouse_chr6.simMouse.chr6 418780 21 + 636262 ATGTGGAAGAATCTCCAATTC -s Anc0.Anc0refChr3 48077 21 + 222631 ATCTGGAAAAGGGCCCAGCTA -s Anc1.Anc1refChr6 78581 21 + 197743 ATCTGGAAAAGGGCCCAGCTA -s Anc2.Anc2refChr13 52301 21 + 96486 ATCTGGAAAAGGGCCCAGCTA -s mr.mrrefChr5 271264 21 + 294540 ATGTGGAAGAGTCTCCAGTTA -s simCow_chr6.simCow.chr6 408281 21 + 602619 ATCTGGAAAAGGGTCCAGCTA -s simDog_chr6.simDog.chr6 398709 21 + 593897 ATCTGGCAAAGGGCCCAACTA -s simHuman_chr6.simHuman.chr6 403673 21 + 601863 ATCTGGAAAAGGGCCCAGGTA -s simRat_chr6.simRat.chr6 424895 21 + 647215 ATGTGGAAGAGTCTCCAGTTA - -a -s simMouse_chr6.simMouse.chr6 418801 35 + 636262 CAAAGGAGGATCCCATCCAGGACATCAGGACCCAT -s Anc0.Anc0refChr3 48098 35 + 222631 TAATGGAGGGTCACAACCAGGATGGACCAGCTCAT -s Anc1.Anc1refChr6 78602 35 + 197743 TAATGGAGGGTCACAACCAGGATGGACCAGCTCAT -s Anc2.Anc2refChr13 52322 35 + 96486 TAATGCAGGGTCACAACCGGGATGGACCAGCTCAT -s mr.mrrefChr5 271285 35 + 294540 CAAAGGAGGATCCCATCCAGGACATCAGGACCCAT -s simCow_chr6.simCow.chr6 408302 35 + 602619 TAATGCCGAGTCACAGCCGGGATGGACCAGCTCAT -s simDog_chr6.simDog.chr6 398730 32 + 593897 TAATGCAGGGATGTAACAGGGAAGGACCAGCT--- -s simHuman_chr6.simHuman.chr6 403695 35 + 601863 TAATGGAGGGTCACAACCAGGATGGATCAGCTCAT -s simRat_chr6.simRat.chr6 424916 35 + 647215 CAAAGCAAGATACCATCCAGCACATCAGGACCCAT - -a -s simMouse_chr6.simMouse.chr6 418836 17 + 636262 AAAGGAGAGACAACTGA -s Anc0.Anc0refChr3 48141 17 + 222631 AAGGGAAAGATAAATAA -s Anc1.Anc1refChr6 78645 17 + 197743 AAGGGAAAGATAAATAA -s Anc2.Anc2refChr13 52365 17 + 96486 CAGGGAAAGATAAATAA -s mr.mrrefChr5 271320 17 + 294540 AAAGGAGAGACAACTGA -s simCow_chr6.simCow.chr6 408345 17 + 602619 CAGGGAAAGATAAATAA -s simHuman_chr6.simHuman.chr6 403738 17 + 601863 AAGGGAAAGATAAGTAG -s simRat_chr6.simRat.chr6 424951 17 + 647215 AAAGGAGAGACAACTGA - -a -s simMouse_chr6.simMouse.chr6 418853 20 + 636262 CCAAGCAATTCTATACTTAA -s Anc0.Anc0refChr3 48158 20 + 222631 CAAGGCAATTCTATACTCAA -s Anc1.Anc1refChr6 78662 20 + 197743 CAAGGCAATTCTATACTCAA -s Anc2.Anc2refChr13 52382 20 + 96486 TAAGGCAATTCTATACTCAA -s mr.mrrefChr5 271337 20 + 294540 CAAAGCAATTCTATACTCAA -s simCow_chr6.simCow.chr6 408365 20 + 602619 TGAAGTAATTCTATACTCAA -s simDog_chr6.simDog.chr6 398762 19 + 593897 -AAGGCAATTCTATACTCAA -s simHuman_chr6.simHuman.chr6 403755 20 + 601863 CAAGGCAATTCTATAGTCAA -s simRat_chr6.simRat.chr6 424968 20 + 647215 CAAAGTGATTCTATACTCAA - -a -s simMouse_chr6.simMouse.chr6 418873 15 + 636262 CCAGAGGGCAAGATA -s Anc0.Anc0refChr3 48178 15 + 222631 CCTGAGAGCAAAGTA -s Anc1.Anc1refChr6 78682 15 + 197743 CCTGAGAGCAAAGTA -s Anc2.Anc2refChr13 52419 15 + 96486 CCTGAGAGCAAAGTA -s mr.mrrefChr5 271357 15 + 294540 CCAGAGGGCAAGATA -s simCow_chr6.simCow.chr6 408402 15 + 602619 TCTGAGAGTAAAGTT -s simDog_chr6.simDog.chr6 398798 15 + 593897 CCTGAGAGCAAAATA -s simHuman_chr6.simHuman.chr6 403775 15 + 601863 CCTGAGAGCAAAGTA -s simRat_chr6.simRat.chr6 424988 15 + 647215 CCAGAGGGCAAGATA - -a -s simMouse_chr6.simMouse.chr6 418888 41 + 636262 CAGTGCAACATGCATCACAGGAAGCATATTCAGAGTCATGA -s Anc0.Anc0refChr3 48193 41 + 222631 CAGTGAGGCATGTGGTACAGGAAGCATAATCAAAATCACAA -s Anc1.Anc1refChr6 78697 41 + 197743 CAGTGAGGCATGTGGTACAGGAAGCATAATCAAAATCACAA -s Anc2.Anc2refChr13 52475 41 + 96486 CAGTGAGGCATGTGGTGCAGGAAGTGTGATTAACATCACAA -s mr.mrrefChr5 271372 41 + 294540 CAGTGCAACATGCATCACAGGAAGCATAATCAGAGTCATGA -s simCow_chr6.simCow.chr6 408458 34 + 602619 -----CGGCATGTGGTGCAGGAAG--TGATTAATGATACAA -s simDog_chr6.simDog.chr6 398914 40 + 593897 CAGTGAGGCA-GTGGTGCAGGAGGTGTGATTCACATCACGA -s simHuman_chr6.simHuman.chr6 403790 41 + 601863 CAGTGAGGCATGTGGTATAGGTAGCATAATCACAATCACAA -s simRat_chr6.simRat.chr6 425003 41 + 647215 TAGTGCACTATACATCACAGACAACGAGATCAGAGTCATGA - -a -s simMouse_chr6.simMouse.chr6 418929 6 + 636262 TGGTGC -s Anc0.Anc0refChr3 48245 6 + 222631 TGGTAA -s Anc1.Anc1refChr6 78749 6 + 197743 TGGTAA -s Anc2.Anc2refChr13 52527 6 + 96486 GGGCAA -s mr.mrrefChr5 271413 6 + 294540 TGGTAC -s simDog_chr6.simDog.chr6 398965 6 + 593897 GGGCAA -s simHuman_chr6.simHuman.chr6 403842 6 + 601863 TGGTAA -s simRat_chr6.simRat.chr6 425044 6 + 647215 GGGTAT - -a -s simMouse_chr6.simMouse.chr6 418935 3 + 636262 GCA -s Anc0.Anc0refChr3 48251 3 + 222631 ACA -s Anc1.Anc1refChr6 78755 3 + 197743 ACA -s Anc2.Anc2refChr13 52533 3 + 96486 ACA -s mr.mrrefChr5 271419 3 + 294540 GCA -s simDog_chr6.simDog.chr6 398972 3 + 593897 ACA -s simHuman_chr6.simHuman.chr6 403848 3 + 601863 ACA -s simRat_chr6.simRat.chr6 425050 3 + 647215 CCA - -a -s simMouse_chr6.simMouse.chr6 418938 51 + 636262 CATCACAGGACCACATGCTCTAGTTTAGAGAGAGATTTGCCCTGCTGCGTG -s Anc0.Anc0refChr3 48268 27 + 222631 CATCAC-GTACCACATGCTTTAGTTTAG----------------------- -s Anc1.Anc1refChr6 78772 49 + 197743 CATCACAGTACCACATGCTTTAGTTTAGGGAGA--ATTGTCTCATTGTGTA -s Anc2.Anc2refChr13 52550 27 + 96486 CATCAT-GTATCACATGATTTAGTTTAT----------------------- -s mr.mrrefChr5 271436 49 + 294540 CATCACAGGACCACATGCTCTAGTTTAGAGAGA--TTTGCCCTGCTGTGTG -s simCow_chr6.simCow.chr6 408499 20 + 602619 --------TATCACATCATTTAGTTTAT----------------------- -s simDog_chr6.simDog.chr6 398989 20 + 593897 CATCAT-G-------TGATTTAATTTAT----------------------- -s simHuman_chr6.simHuman.chr6 403865 49 + 601863 CATCACAACACCACATGCTTTAGTTTAGGGAGA--ATTGTCTCATTGTGTA -s simRat_chr6.simRat.chr6 425067 49 + 647215 CATCACAGGGCCACGGGCTCTAGTTTAGAGAGA--TTTGCCCTGCTGTGTG - -a -s simMouse_chr6.simMouse.chr6 418989 12 + 636262 AGACAATCACCA -s Anc1.Anc1refChr6 78821 12 + 197743 AGGGAAGCAAAA -s mr.mrrefChr5 271485 12 + 294540 AGAGAATCACCA -s simHuman_chr6.simHuman.chr6 403920 12 + 601863 AGGGAAGCAAAA -s simRat_chr6.simRat.chr6 425116 12 + 647215 AGAGAATCACCA - -a -s simMouse_chr6.simMouse.chr6 419001 49 + 636262 TAAGTGTCGTCCGCCCTAATCGACAACGTGTTTGGCCACGTGGTACAGA -s Anc1.Anc1refChr6 78833 44 + 197743 TAAGTGTGCAAAGCACATGCCAGTGACG-----GGCTATGTATTGAAGA -s mr.mrrefChr5 271497 44 + 294540 TAAGTGTCGTCCGCCCTAATCGACAACG-----GGCCACGTGGTACAGA -s simHuman_chr6.simHuman.chr6 403934 44 + 601863 TAAGTGTGCAAAGCACATGCCAGTGACG-----GGCTATGTATTGAAGA -s simRat_chr6.simRat.chr6 425128 6 + 647215 TAAGC-------------------------------------------A - -a -s simMouse_chr6.simMouse.chr6 419050 5 + 636262 CAGAG -s Anc0.Anc0refChr3 48295 2 + 222631 ---TG -s Anc1.Anc1refChr6 78877 5 + 197743 CAGTG -s Anc2.Anc2refChr13 52577 2 + 96486 ---TG -s mr.mrrefChr5 271541 5 + 294540 CAGTG -s simCow_chr6.simCow.chr6 408519 2 + 602619 ---CG -s simDog_chr6.simDog.chr6 399009 2 + 593897 ---TG -s simHuman_chr6.simHuman.chr6 403979 5 + 601863 CAGTG -s simRat_chr6.simRat.chr6 425134 5 + 647215 CAGTG - -a -s simMouse_chr6.simMouse.chr6 419055 9 + 636262 TGTAAGTAA -s Anc0.Anc0refChr3 48297 9 + 222631 TGTAATTAA -s Anc1.Anc1refChr6 78882 9 + 197743 TGTAATTAA -s Anc2.Anc2refChr13 52579 9 + 96486 TATTATTTA -s mr.mrrefChr5 271546 9 + 294540 TGTAAGTAA -s simCow_chr6.simCow.chr6 408521 7 + 602619 GGTGTTT-- -s simDog_chr6.simDog.chr6 399011 9 + 593897 TATTATTTA -s simHuman_chr6.simHuman.chr6 403985 9 + 601863 CGCAATTAA -s simRat_chr6.simRat.chr6 425139 9 + 647215 TGTAAGTAA - -a -s simMouse_chr6.simMouse.chr6 419064 30 + 636262 GAATGATATCGATTCTGCATTAAGTCACTA -s Anc0.Anc0refChr3 48311 30 + 222631 GAATGATATCCATTTTGCATTAAGGCACTA -s Anc1.Anc1refChr6 78896 30 + 197743 GAATGATATCCATTTTGCATTAAGGCACTA -s Anc2.Anc2refChr13 52593 30 + 96486 GAATGTTATCCATTTTGCATTAAGGCACTA -s mr.mrrefChr5 271555 30 + 294540 GAATGATATCGATTTTGCATTAAGTCACTA -s simCow_chr6.simCow.chr6 408531 29 + 602619 GAATGGTATTGAGTTTGCATTAATGCAT-A -s simDog_chr6.simDog.chr6 399025 30 + 593897 GAATGTCATCCATTTTGCATTAAGGCCCTA -s simHuman_chr6.simHuman.chr6 403999 30 + 601863 AAATGATATCCATTTTGCATTAAGGAACTA -s simRat_chr6.simRat.chr6 425148 30 + 647215 GAATGATATCAATTTTGCATTAAGTCACTA - -a -s simMouse_chr6.simMouse.chr6 419094 51 + 636262 TACATACACCAGCCTAGATAGGAGGAGAAAAATCAAATGAAAATTGACGGT -s Anc0.Anc0refChr3 48354 48 + 222631 TAGATATACCAGCCTAGA---AAGAAGAAAAACTAAATGGAAATTACTGAT -s Anc1.Anc1refChr6 78939 48 + 197743 TAGATATACCAGCCTAGA---AAGAAGAAAAACTAAATGGAAATTACTGAT -s Anc2.Anc2refChr13 52637 48 + 96486 TAGATGTGCGAGCTTAGA---AAGAAGAAAGACTAGATGGAGATTACTGAT -s mr.mrrefChr5 271585 51 + 294540 TACATACACCAGCCTAGATAGGAGGAGAAAAATTAAATGAAAATTGACGGT -s simCow_chr6.simCow.chr6 408574 48 + 602619 TAGATGTGGTTGCTTAGA---AAGAATAACGACTAGATCAAGACTACCGAT -s simDog_chr6.simDog.chr6 399066 48 + 593897 TAGATGTGCGAGCTTAGA---AAGAAGAAAGACTAGATGGAGTTTACTGAT -s simHuman_chr6.simHuman.chr6 404042 41 + 601863 TAGACATACCAGCCTATA----------ATAACTAAATGGAAATTACTGAT -s simRat_chr6.simRat.chr6 425178 50 + 647215 TACATGCACCAGC-TAGATAGGAGGACAAAAATTGAATGAAAATTGACAGT - -a -s simMouse_chr6.simMouse.chr6 419145 3 + 636262 GTT -s Anc0.Anc0refChr3 48403 3 + 222631 GTT -s Anc1.Anc1refChr6 78988 3 + 197743 GTT -s Anc2.Anc2refChr13 52686 3 + 96486 CCT -s mr.mrrefChr5 271636 3 + 294540 GTT -s simCow_chr6.simCow.chr6 408623 3 + 602619 TGT -s simDog_chr6.simDog.chr6 399115 3 + 593897 CCT -s simHuman_chr6.simHuman.chr6 404084 3 + 601863 GTT -s simRat_chr6.simRat.chr6 425228 3 + 647215 GCT - -a -s simMouse_chr6.simMouse.chr6 419148 5 + 636262 CGTAC -s Anc0.Anc0refChr3 48406 5 + 222631 TGCCT -s Anc1.Anc1refChr6 78991 5 + 197743 TGCCT -s Anc2.Anc2refChr13 52689 5 + 96486 TGCCT -s mr.mrrefChr5 271639 5 + 294540 CGTAC -s simCow_chr6.simCow.chr6 408626 4 + 602619 CACC- -s simDog_chr6.simDog.chr6 399118 5 + 593897 TGTCT -s simHuman_chr6.simHuman.chr6 404087 5 + 601863 TGCCT -s simRat_chr6.simRat.chr6 425250 5 + 647215 CGTGC - -a -s simMouse_chr6.simMouse.chr6 419153 131 + 636262 AAGGCTCCAATAAAAGGCAAATCTGGTCATATAGACATGGTTAGTACCTAGCTATGATCTTGCCCAGCTTGTCACACTTCAGCTGTGAATGTTGTGATGGAATGAATGGCCATAACCAGAGGAGATTATCT -s Anc0.Anc0refChr3 48411 11 + 222631 AGGACT------------------------------------------------------------------------------------------------------------------------ATTTT -s Anc1.Anc1refChr6 78996 11 + 197743 AGGACT------------------------------------------------------------------------------------------------------------------------ATTTT -s Anc2.Anc2refChr13 52694 11 + 96486 AGGATA------------------------------------------------------------------------------------------------------------------------ATTTA -s mr.mrrefChr5 271644 11 + 294540 AAGGCT------------------------------------------------------------------------------------------------------------------------TTTTT -s simCow_chr6.simCow.chr6 408630 11 + 602619 AGGATC------------------------------------------------------------------------------------------------------------------------ATTTA -s simDog_chr6.simDog.chr6 399124 11 + 593897 GGGATA------------------------------------------------------------------------------------------------------------------------ATTTA -s simHuman_chr6.simHuman.chr6 404092 11 + 601863 AGGACT------------------------------------------------------------------------------------------------------------------------ATTTT -s simRat_chr6.simRat.chr6 425255 11 + 647215 AAGGCT------------------------------------------------------------------------------------------------------------------------TTTTT - -a -s simMouse_chr6.simMouse.chr6 419284 9 + 636262 CTACTTGAT -s Anc0.Anc0refChr3 48423 9 + 222631 CTTCTTGAG -s Anc1.Anc1refChr6 79008 9 + 197743 CTTCTTGAG -s Anc2.Anc2refChr13 52706 9 + 96486 CTTCTTGGG -s mr.mrrefChr5 271655 9 + 294540 CTACTTGAT -s simCow_chr6.simCow.chr6 408642 9 + 602619 TTTCCTGGG -s simDog_chr6.simDog.chr6 399136 9 + 593897 CTCTTTAGG -s simHuman_chr6.simHuman.chr6 404104 9 + 601863 CTTCTTGAG -s simRat_chr6.simRat.chr6 425266 9 + 647215 CTACTTGAT - -a -s simMouse_chr6.simMouse.chr6 419293 7 + 636262 AGAAAAG -s Anc0.Anc0refChr3 48510 7 + 222631 AGAAAAG -s Anc1.Anc1refChr6 79095 7 + 197743 AGAAAAG -s Anc2.Anc2refChr13 52793 7 + 96486 AGAAAAG -s mr.mrrefChr5 271664 7 + 294540 AGAAAAG -s simCow_chr6.simCow.chr6 408729 7 + 602619 GGAAAAG -s simDog_chr6.simDog.chr6 399223 7 + 593897 AAAAAAG -s simHuman_chr6.simHuman.chr6 404191 7 + 601863 AGAAAAG -s simRat_chr6.simRat.chr6 425275 7 + 647215 AGAAAAG - -a -s simMouse_chr6.simMouse.chr6 419300 8 + 636262 TTGGAAAG -s Anc0.Anc0refChr3 48525 8 + 222631 TTGAAAAG -s Anc1.Anc1refChr6 79110 8 + 197743 TTGAAAAG -s Anc2.Anc2refChr13 52808 8 + 96486 TTGAAAAG -s mr.mrrefChr5 271671 8 + 294540 TTGAAAAG -s simCow_chr6.simCow.chr6 408744 8 + 602619 TTGAAAAG -s simDog_chr6.simDog.chr6 399238 8 + 593897 TCGAAAAC -s simHuman_chr6.simHuman.chr6 404206 8 + 601863 TTGAAAAG -s simRat_chr6.simRat.chr6 425282 8 + 647215 TTTAAAAG - -a -s simMouse_chr6.simMouse.chr6 419308 11 + 636262 TTCTAATTGAC -s Anc0.Anc0refChr3 48540 4 + 222631 TTCA------- -s Anc1.Anc1refChr6 79125 7 + 197743 TTCAACT---- -s Anc2.Anc2refChr13 52823 4 + 96486 TTAA------- -s mr.mrrefChr5 271679 11 + 294540 TTCTAATTGAC -s simCow_chr6.simCow.chr6 408770 4 + 602619 CTAA------- -s simDog_chr6.simDog.chr6 399253 4 + 593897 TTAA------- -s simHuman_chr6.simHuman.chr6 404221 7 + 601863 TTCAACT---- -s simRat_chr6.simRat.chr6 425290 11 + 647215 TTCTAATTGTC - -a -s simMouse_chr6.simMouse.chr6 419319 8 + 636262 CAGTGCAC -s Anc0.Anc0refChr3 48647 8 + 222631 TAGCACAC -s Anc1.Anc1refChr6 79236 8 + 197743 TAGCACAC -s Anc2.Anc2refChr13 52930 8 + 96486 TATCACAC -s mr.mrrefChr5 271690 8 + 294540 TAGTGCAC -s simCow_chr6.simCow.chr6 408874 8 + 602619 TATCACAC -s simDog_chr6.simDog.chr6 399360 8 + 593897 TATCACAC -s simHuman_chr6.simHuman.chr6 404443 8 + 601863 TAGCACAC -s simRat_chr6.simRat.chr6 425301 8 + 647215 TAGTGCAC - -a -s simMouse_chr6.simMouse.chr6 419327 6 + 636262 TATAAG -s Anc0.Anc0refChr3 48655 6 + 222631 TATAAG -s Anc1.Anc1refChr6 79244 6 + 197743 TATAAG -s Anc2.Anc2refChr13 52938 6 + 96486 TATAAG -s mr.mrrefChr5 271698 6 + 294540 TATAAG -s simCow_chr6.simCow.chr6 408882 6 + 602619 TATAAA -s simDog_chr6.simDog.chr6 399368 6 + 593897 TATTAG -s simHuman_chr6.simHuman.chr6 404451 6 + 601863 TATAAG -s simRat_chr6.simRat.chr6 425378 6 + 647215 TATAAG - -a -s simMouse_chr6.simMouse.chr6 419333 46 + 636262 TATCCAAACTCAGGTGGCTGCTGAGGCCAAGAATGTGATCATTATA -s Anc0.Anc0refChr3 48662 41 + 222631 TATCCACACTAAGGTGGCTAC--AG---TAAAATGTGTTCAATGTA -s Anc1.Anc1refChr6 79251 44 + 197743 TATCCACACTAAGGTGGCTAC--AGGTGTAAAATGTGTTCAATGTA -s Anc2.Anc2refChr13 52945 41 + 96486 TAGCCACACTAAGGTGGCTAC--AA---TAAAACGTGTTCAATGTG -s mr.mrrefChr5 271704 46 + 294540 TATCCAAACTCAGGTGGCTGCTGAGGCCAAAAATGTGTTCATTATA -s simCow_chr6.simCow.chr6 408889 29 + 602619 TAACCATGCTAAGTTGA-----------------ATGTTCAATATG -s simDog_chr6.simDog.chr6 399375 40 + 593897 TAGCGACACTAAGGTGGCTAC--AA---TAAAACGTGGTGA-TGTG -s simHuman_chr6.simHuman.chr6 404458 44 + 601863 TATGCACACTAAGGTGGCAAC--AGGTGTAAACTGTGTTCAGTGTA -s simRat_chr6.simRat.chr6 425384 46 + 647215 TATCAAAACTCAGGTGGCTTTTGAGGCAAAAAATGTATTCATTATA - -a -s simMouse_chr6.simMouse.chr6 419379 21 + 636262 TACGTGTAACTTCTATGCAAA -s Anc0.Anc0refChr3 48704 21 + 222631 TAAGTGTAACTGCTATGCAGA -s Anc1.Anc1refChr6 79296 21 + 197743 TAAGTGTAACTGCTATGCAGA -s Anc2.Anc2refChr13 52987 21 + 96486 TAAGTGAAACTGCCATGCAGA -s mr.mrrefChr5 271750 21 + 294540 TACGTGTAACTTCTATGCAAA -s simCow_chr6.simCow.chr6 408919 21 + 602619 CAAGTGAGGCTTCCATTTAAC -s simDog_chr6.simDog.chr6 399416 21 + 593897 TAAGTGAAACTGCCATGCAGA -s simHuman_chr6.simHuman.chr6 404503 21 + 601863 TAAGTGTAATTCCTGTGCAGA -s simRat_chr6.simRat.chr6 425430 21 + 647215 TACGTGTAACTTCTATGCAAA - -a -s simMouse_chr6.simMouse.chr6 419400 9 + 636262 ACTACATTT -s Anc0.Anc0refChr3 48725 8 + 222631 AT-AAATTT -s Anc1.Anc1refChr6 79317 8 + 197743 AT-AAATTT -s Anc2.Anc2refChr13 53110 8 + 96486 AC-AAATTT -s mr.mrrefChr5 271771 9 + 294540 ATTACATTT -s simCow_chr6.simCow.chr6 409047 8 + 602619 AC-AAATTC -s simDog_chr6.simDog.chr6 399558 8 + 593897 AC-AGATTT -s simHuman_chr6.simHuman.chr6 404524 8 + 601863 GT-AAATTT -s simRat_chr6.simRat.chr6 425451 9 + 647215 ATTACATTT - -a -s simMouse_chr6.simMouse.chr6 419409 16 + 636262 AATATTCCTGATGACA -s Anc0.Anc0refChr3 48733 16 + 222631 AATGTTCCTGATGGCC -s Anc1.Anc1refChr6 79325 16 + 197743 AATGTTCCTGATGGCC -s Anc2.Anc2refChr13 53118 16 + 96486 AAAGGTACAGATTGTC -s mr.mrrefChr5 271780 16 + 294540 AATATTCCTGATGACA -s simCow_chr6.simCow.chr6 409055 4 + 602619 TAAG------------ -s simDog_chr6.simDog.chr6 399570 16 + 593897 AGAGGTACAGATTGTC -s simHuman_chr6.simHuman.chr6 404532 16 + 601863 AATCTTCCTGATGGCC -s simRat_chr6.simRat.chr6 425460 16 + 647215 AATATTCCTTATGACA - -a -s simMouse_chr6.simMouse.chr6 419425 1 + 636262 G -s Anc0.Anc0refChr3 48749 1 + 222631 T -s Anc1.Anc1refChr6 79341 1 + 197743 T -s Anc2.Anc2refChr13 53134 1 + 96486 T -s mr.mrrefChr5 271796 1 + 294540 G -s simCow_chr6.simCow.chr6 409059 1 + 602619 T -s simDog_chr6.simDog.chr6 399588 1 + 593897 T -s simHuman_chr6.simHuman.chr6 404548 1 + 601863 T -s simRat_chr6.simRat.chr6 425476 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 419426 48 + 636262 GTTGTCTGTCCAGATTGTGTTTCCAGACACTGTACACAGGGATATAGA -s Anc0.Anc0refChr3 48750 40 + 222631 GATG--------GGTCATGTTTCTAGCTGCTATACACAGTGATCTATA -s Anc1.Anc1refChr6 79342 40 + 197743 GATG--------GGTCATGTTTCTAGCTGCTATACACAGTGATCTATA -s Anc2.Anc2refChr13 53136 40 + 96486 GATG--------GGTCATGTTTCTAGCTGTTATACACAGTGATCTATG -s mr.mrrefChr5 271797 48 + 294540 GTTGTCTGTCCAGATTGTGTTTCCAGATGCTGTACACAGGGATATAGA -s simCow_chr6.simCow.chr6 409061 38 + 602619 GATG--------GGTCATGTTTCTAGCTA-TATACACAGTGATCT-TG -s simDog_chr6.simDog.chr6 399590 40 + 593897 GATG--------GGTCATGTTTCTAGCTGTTATACACAGTGATCTATG -s simHuman_chr6.simHuman.chr6 404549 35 + 601863 GATG--------GGTCATGTTTCTAGCTGCTATACACAG-----TGCA -s simRat_chr6.simRat.chr6 425477 48 + 647215 GTTGTCTTTCCAGATTGTGTCTCCAGATGCTGTATACAGGGACTTAAA - -a -s simMouse_chr6.simMouse.chr6 419474 7 + 636262 CTTTAAT -s Anc0.Anc0refChr3 48790 7 + 222631 ATGTAAT -s Anc1.Anc1refChr6 79382 7 + 197743 ATGTAAT -s Anc2.Anc2refChr13 53176 7 + 96486 ATGAAAT -s mr.mrrefChr5 271845 7 + 294540 CTTTAAT -s simCow_chr6.simCow.chr6 409106 7 + 602619 ATTATAT -s simDog_chr6.simDog.chr6 399630 7 + 593897 ATGAAAT -s simHuman_chr6.simHuman.chr6 404584 7 + 601863 ATCTATT -s simRat_chr6.simRat.chr6 425525 7 + 647215 CTTTAAT - -a -s simMouse_chr6.simMouse.chr6 419481 62 + 636262 TAATGAAAGCTCGTGCCTACATCTGACACTGAGCTGATATAACTTAAATCAATCGAGCAAGA -s Anc0.Anc0refChr3 48797 50 + 222631 TATCCACGG------------TCTGGTGCTGAGCTAATGCGACCTAAATCGATCAACCAAAA -s Anc1.Anc1refChr6 79389 50 + 197743 TATCCACGG------------TCTGGTGCTGAGCTAATGCGACCTAAATCGATCAACCAAAA -s Anc2.Anc2refChr13 53192 50 + 96486 TATCCACGA------------TCTAGTGCTGAGCCAGTGCGACCTAAATCGATCAACAAAAA -s mr.mrrefChr5 271852 62 + 294540 TAATGAAGGCTCGTGCCTACATCTGACACTGAGCTGATGCAACTTAAATCAATCGAGCAAGA -s simCow_chr6.simCow.chr6 409122 50 + 602619 TATCCATGA------------TCTAGTGCCGAGCCAGTACAACTGAAATCAATAAACAAAAA -s simDog_chr6.simDog.chr6 399646 47 + 593897 TACTCACAA------------CCCAGTACTGAGTCGGCGCGTCCTAAGTTGATCA---AAAA -s simHuman_chr6.simHuman.chr6 404591 50 + 601863 TATCCACGG------------TCTGGTGCTGAGCTAATGCTACCTAAATCGATCAACCAAAA -s simRat_chr6.simRat.chr6 425532 62 + 647215 TAATGAAGGCTTGTGCTTACATCTAACACTGAGCTGATGCAACTTAAATCAATTGAGCAAGA - -a -s simMouse_chr6.simMouse.chr6 419543 22 + 636262 CTAACCTGCTAGTAGTGAACGG -s Anc0.Anc0refChr3 48847 20 + 222631 CTCATTTGGC--TGGGCAACTG -s Anc1.Anc1refChr6 79439 20 + 197743 CTCATTTGGC--TGGGCAACTG -s Anc2.Anc2refChr13 53242 20 + 96486 TTCATCTGGC--TGGGCAATTG -s mr.mrrefChr5 271914 22 + 294540 CTAACTTGCTAGTAGTGAACTG -s simCow_chr6.simCow.chr6 409172 20 + 602619 ATCACCTGGC--TGGGCAATTG -s simDog_chr6.simDog.chr6 399693 20 + 593897 TTCGTCTGGC--CGGACAATTT -s simHuman_chr6.simHuman.chr6 404641 20 + 601863 CTGATTCGGC--TGGGAAACTG -s simRat_chr6.simRat.chr6 425598 22 + 647215 TTAGCTTGCTAGTAGTGAACTG - -a -s simMouse_chr6.simMouse.chr6 419565 4 + 636262 TAGA -s Anc0.Anc0refChr3 48867 4 + 222631 TAGA -s Anc1.Anc1refChr6 79459 4 + 197743 TAGA -s Anc2.Anc2refChr13 53268 4 + 96486 TAGA -s mr.mrrefChr5 271936 4 + 294540 TAGA -s simCow_chr6.simCow.chr6 409198 4 + 602619 TAGA -s simDog_chr6.simDog.chr6 399719 4 + 593897 TAAA -s simHuman_chr6.simHuman.chr6 404661 4 + 601863 TGAA -s simRat_chr6.simRat.chr6 425620 4 + 647215 TAGA - -a -s simMouse_chr6.simMouse.chr6 419569 4 + 636262 GATA -s Anc0.Anc0refChr3 48871 4 + 222631 GATA -s Anc1.Anc1refChr6 79463 4 + 197743 GATA -s Anc2.Anc2refChr13 53275 4 + 96486 GGTA -s mr.mrrefChr5 271940 4 + 294540 GATA -s simCow_chr6.simCow.chr6 409205 4 + 602619 GGAA -s simDog_chr6.simDog.chr6 399726 4 + 593897 GGTA -s simHuman_chr6.simHuman.chr6 404665 4 + 601863 GACA -s simRat_chr6.simRat.chr6 425624 4 + 647215 TATA - -a -s simMouse_chr6.simMouse.chr6 419573 2 + 636262 GA -s Anc0.Anc0refChr3 48875 2 + 222631 GA -s Anc1.Anc1refChr6 79467 2 + 197743 GA -s Anc2.Anc2refChr13 53279 2 + 96486 GA -s mr.mrrefChr5 271944 2 + 294540 GA -s simCow_chr6.simCow.chr6 409209 2 + 602619 GA -s simDog_chr6.simDog.chr6 399730 2 + 593897 GA -s simHuman_chr6.simHuman.chr6 404670 2 + 601863 GG -s simRat_chr6.simRat.chr6 425628 2 + 647215 GA - -a -s simMouse_chr6.simMouse.chr6 419575 39 + 636262 AAATTTATGTCTCCAAGTCAGTACACTTGATACAGTATC -s Anc0.Anc0refChr3 48877 38 + 222631 AAACTTATGTCTTCAGATCAGAA-AATTGGTACAGTGTG -s Anc1.Anc1refChr6 79469 38 + 197743 AAACTTATGTCTTCAGATCAGAA-AATTGGTACAGTGTG -s Anc2.Anc2refChr13 53281 38 + 96486 AAACTTATGTCTTCAGATAGGAA-AACTGGTACAGTGTG -s mr.mrrefChr5 271946 39 + 294540 AAATTTATGTCTCCAAGTCAGTACACTTGATACAGTATG -s simCow_chr6.simCow.chr6 409213 38 + 602619 AGACTTATGACTTCAGGTAGGAA-ATCTGGTACAGTATG -s simDog_chr6.simDog.chr6 399732 37 + 593897 AAACTTTTGTCTCCAGAGA-GAA-AACTTATGCAGAGAG -s simHuman_chr6.simHuman.chr6 404672 38 + 601863 AAGCTTATGCCTTCAGATCAGAA-AGTTGGTACAGTGTG -s simRat_chr6.simRat.chr6 425630 39 + 647215 AAATTTATGTCTCCAAGTCAGTACACGTGATACAGCATG - -a -s simMouse_chr6.simMouse.chr6 419614 47 + 636262 TGGAAGAGGCACAACCAGGCACTAGGCATATGGATTGTGGGTCACAT -s Anc0.Anc0refChr3 48915 47 + 222631 TGGGAGAGGCCCAACTAGCCACTAGGCATATGGCTAATGGGTCACAT -s Anc1.Anc1refChr6 79507 47 + 197743 TGGGAGAGGCCCAACTAGCCACTAGGCATATGGCTAATGGGTCACAT -s Anc2.Anc2refChr13 53319 47 + 96486 TAGGAGAGACCCAAATAGCCACTAGGCATATGGCTAATGGGTCACAT -s mr.mrrefChr5 271985 47 + 294540 TGGAAGAGGCACAACTAGGCACTAGGCATATGGATTGTGGGTCACAT -s simCow_chr6.simCow.chr6 409251 47 + 602619 AAGGAGAGATCCAGAAGGCCACTAGGCATATGGCTAATGGGTCACAT -s simDog_chr6.simDog.chr6 399776 47 + 593897 TAAGAGAGACCCAAATAGCCACTAGGCAGATGGATAGTGGGTCACAT -s simHuman_chr6.simHuman.chr6 404710 47 + 601863 TGGGGGAGGCTCAACTAGCGACTAGGCATACGGCTAATGGGTCATAT -s simRat_chr6.simRat.chr6 425669 47 + 647215 TGGAAGCGACACAACTAGGCACTAGGCACATGGATTGTTGTTCACAT - -a -s simMouse_chr6.simMouse.chr6 419661 7 + 636262 ACCTTTT -s Anc0.Anc0refChr3 48962 7 + 222631 ACCTCTT -s Anc1.Anc1refChr6 79554 7 + 197743 ACCTCTT -s Anc2.Anc2refChr13 53366 7 + 96486 ACCTCTT -s mr.mrrefChr5 272032 7 + 294540 ACCTTTT -s simCow_chr6.simCow.chr6 409298 7 + 602619 ACCTCTT -s simDog_chr6.simDog.chr6 399823 7 + 593897 ACCTGCT -s simHuman_chr6.simHuman.chr6 404757 7 + 601863 ACCTCTT -s simRat_chr6.simRat.chr6 425732 7 + 647215 ACCTATA - -a -s simMouse_chr6.simMouse.chr6 419668 80 + 636262 GATGCTCTTAGGCAGGGGTGCTTAGTGGCTACCTCGAATTCTCGAATCAACCAGGATGTCTTAACCTATCTGGTAAGTTA -s Anc0.Anc0refChr3 49144 72 + 222631 GATG--------CAAGGGGGTTTAACAGCTACCTTAAATTTTCAAGCCAATCTTGTCATCTTAACCTATCTAGTAGGTTG -s Anc1.Anc1refChr6 79736 72 + 197743 GATG--------CAAGGGGGTTTAACAGCTACCTTAAATTTTCAAGCCAATCTTGTCATCTTAACCTATCTAGTAGGTTG -s Anc2.Anc2refChr13 53548 72 + 96486 GATG--------CAAGGAGGTTTAACAGCTACCTTAAATTTTCAAGCCAATCTTGTCATCTTAACCTATCTAGTAGGTTG -s mr.mrrefChr5 272039 80 + 294540 GATGCTCTTAGACAGGGGTGCTTAGTGGCTACCTCAAATTTTCAAACCAACCAGGATGTCTTAACCTATCTAGTAAGTTA -s simCow_chr6.simCow.chr6 409480 71 + 602619 GATG--------CAAGGCAGTTTAACATTTGCCTTAAA-TTTCAGAACAGCTTGGTCACATTGACCTGTCTAGAAGCGTG -s simDog_chr6.simDog.chr6 400005 72 + 593897 GATT--------TAGGGAGATTCAACAGCTACCTTAAATTTTCAAGCCAATCTTGTCATCTTAACCTATCTAGTAGGTTA -s simHuman_chr6.simHuman.chr6 404950 50 + 601863 GGTG--------CAAGGGGGTTTAACAGCAACCTTAAATTT----------------------ACCTATTTAGCAGGTCG -s simRat_chr6.simRat.chr6 425739 80 + 647215 GAAGCTCTTAGACAGGGGTGCTTAGTGGGTACCTCATATCTTCAAACCAACCAGGATGTCTTGACCTATATAGTGAGTTA - -a -s simMouse_chr6.simMouse.chr6 419748 34 + 636262 CAGTAGCCTGAACACCAGGCTGACCATCTCTCTG -s Anc0.Anc0refChr3 49216 34 + 222631 TAAAATCTTGAGCATCAGGCAAGTCAACTTTCTG -s Anc1.Anc1refChr6 79808 34 + 197743 TAAAATCTTGAGCATCAGGCAAGTCAACTTTCTG -s Anc2.Anc2refChr13 53620 34 + 96486 TAAAATCTTGAGCATCAGGCAAGTCAACTTTCTG -s mr.mrrefChr5 272119 34 + 294540 CAGTAGCCTGAACACCAGGCTAACCATCTCTCTG -s simCow_chr6.simCow.chr6 409556 34 + 602619 CAAAATCGTGAGCATCAGGCAAGTCAACTTTCTG -s simDog_chr6.simDog.chr6 400077 34 + 593897 TAAAATCTTGAGCATCAGGCAAGTCAACTTTCTG -s simHuman_chr6.simHuman.chr6 405000 34 + 601863 TAAGGACATGAGCATCTGCCGAGTCAACTTCCTG -s simRat_chr6.simRat.chr6 425819 34 + 647215 CAGTACCCTGAACACTAACCCAAACAGCTCTCTG - -a -s simMouse_chr6.simMouse.chr6 419782 3 + 636262 ATT -s Anc0.Anc0refChr3 49251 3 + 222631 ATT -s Anc1.Anc1refChr6 79843 3 + 197743 ATT -s Anc2.Anc2refChr13 53655 3 + 96486 ATT -s mr.mrrefChr5 272153 3 + 294540 ATT -s simCow_chr6.simCow.chr6 409591 3 + 602619 ATT -s simDog_chr6.simDog.chr6 400112 3 + 593897 ATT -s simHuman_chr6.simHuman.chr6 405035 3 + 601863 AAC -s simRat_chr6.simRat.chr6 425853 3 + 647215 ATT - -a -s simMouse_chr6.simMouse.chr6 419785 2 + 636262 GA -s Anc0.Anc0refChr3 49257 2 + 222631 GA -s Anc1.Anc1refChr6 79849 2 + 197743 GA -s Anc2.Anc2refChr13 53661 2 + 96486 GA -s mr.mrrefChr5 272159 2 + 294540 GA -s simCow_chr6.simCow.chr6 409597 2 + 602619 AG -s simDog_chr6.simDog.chr6 400118 2 + 593897 GA -s simHuman_chr6.simHuman.chr6 405041 2 + 601863 GA -s simRat_chr6.simRat.chr6 425859 2 + 647215 GA - -a -s simMouse_chr6.simMouse.chr6 419787 19 + 636262 CTAGCAACCCAGATTCCAG -s Anc0.Anc0refChr3 49259 19 + 222631 CCATTCGTCTCGATTCCAG -s Anc1.Anc1refChr6 79851 19 + 197743 CCATTCGTCTCGATTCCAG -s Anc2.Anc2refChr13 53664 19 + 96486 CCATTCGTCTCGATTCCAG -s mr.mrrefChr5 272161 19 + 294540 CTAGCCACCTAGATTCCAG -s simCow_chr6.simCow.chr6 409600 19 + 602619 CCATTCGTCTCGATTCCAG -s simDog_chr6.simDog.chr6 400121 3 + 593897 CCA---------------- -s simHuman_chr6.simHuman.chr6 405043 19 + 601863 CCATTTGACTGCATTTCAG -s simRat_chr6.simRat.chr6 425861 19 + 647215 CTAGCCACATAGATTCAAG - -a -s simMouse_chr6.simMouse.chr6 419806 28 + 636262 CTCATTCACAACTGGAAGAATTGTGATC -s Anc0.Anc0refChr3 49278 28 + 222631 CTTATACACACCTAGAAGAATTGTCAGC -s Anc1.Anc1refChr6 79870 28 + 197743 CTTATACACACCTAGAAGAATTGTCAGC -s Anc2.Anc2refChr13 53683 28 + 96486 CTGATACACACCTAGAAGAATTGTCAGC -s mr.mrrefChr5 272180 28 + 294540 CTCATTCACAACTGGAAGAATTGTGATC -s mr.mrrefChr5 272324 28 + 294540 CTTAGACACATCCAGCAGCACAGCCCCC -s simCow_chr6.simCow.chr6 409619 28 + 602619 CTGATACACACCTAGAAGAATGGCCGGC -s simDog_chr6.simDog.chr6 400124 7 + 593897 ---------------------TGTCAGC -s simHuman_chr6.simHuman.chr6 405062 28 + 601863 CTTATATGCACCTGGAGGAATTGTTAGC -s simMouse_chr6.simMouse.chr6 419954 28 + 636262 CTTAGACACATCCAGCAGCACAGCCCCC -s simRat_chr6.simRat.chr6 426174 28 + 647215 CTTAGATGCGTCCAGCCGCCCAGCCCAC -s simRat_chr6.simRat.chr6 425880 28 + 647215 CTTACACACATCTGGAAGAATTGTGAGT - -a -s simMouse_chr6.simMouse.chr6 419834 6 + 636262 CATACT -s Anc0.Anc0refChr3 49315 6 + 222631 CATCCT -s Anc1.Anc1refChr6 79907 6 + 197743 CATCCT -s Anc2.Anc2refChr13 53720 6 + 96486 CATCCT -s mr.mrrefChr5 272208 6 + 294540 CATACT -s mr.mrrefChr5 272352 6 + 294540 CAGTCT -s simCow_chr6.simCow.chr6 409654 4 + 602619 --TCTC -s simDog_chr6.simDog.chr6 400140 6 + 593897 CATCCT -s simHuman_chr6.simHuman.chr6 405099 6 + 601863 CATCCT -s simMouse_chr6.simMouse.chr6 419982 6 + 636262 CAGTCT -s simRat_chr6.simRat.chr6 426202 6 + 647215 CAGCCT -s simRat_chr6.simRat.chr6 425908 6 + 647215 GATACA - -a -s simMouse_chr6.simMouse.chr6 419840 15 + 636262 TGTAGAGGATTAAGA -s Anc0.Anc0refChr3 49321 11 + 222631 A---AAGGATT-AGA -s Anc1.Anc1refChr6 79913 11 + 197743 A---AAGGATT-AGA -s Anc2.Anc2refChr13 53726 11 + 96486 A---AAGGATT-AGA -s mr.mrrefChr5 272214 11 + 294540 T---AAGGATT-AGA -s mr.mrrefChr5 272363 11 + 294540 A---AAGGAGC-AAA -s simCow_chr6.simCow.chr6 409658 11 + 602619 A---AAAGATT-AGA -s simDog_chr6.simDog.chr6 400146 11 + 593897 G---AAGGATT-AGA -s simHuman_chr6.simHuman.chr6 405105 11 + 601863 A---AAGGATT-AGA -s simMouse_chr6.simMouse.chr6 419993 11 + 636262 A---AAGGAGC-AAA -s simRat_chr6.simRat.chr6 426213 11 + 647215 A---AAGGAGC-AAA -s simRat_chr6.simRat.chr6 425914 11 + 647215 T---AAGGATT-AGA - -a -s simMouse_chr6.simMouse.chr6 419855 20 + 636262 AGACCAAAGTTATACTCTGT -s Anc0.Anc0refChr3 49332 20 + 222631 AAACCAAAGCCATATTTTAC -s Anc1.Anc1refChr6 79924 20 + 197743 AAACCAAAGCCATATTTTAC -s Anc2.Anc2refChr13 53737 20 + 96486 AAACCAAAGCCATATTTTAC -s mr.mrrefChr5 272225 20 + 294540 AGACCAAAGCTATATTTTGT -s mr.mrrefChr5 272374 20 + 294540 GGAGCTAAGAAATATATTAT -s simCow_chr6.simCow.chr6 409669 20 + 602619 GAACCTAAACCATATTTTAC -s simDog_chr6.simDog.chr6 400157 20 + 593897 AAACCAAAGCCAAATCTTAG -s simHuman_chr6.simHuman.chr6 405116 20 + 601863 AAACCAAGGCCATATTTTGC -s simMouse_chr6.simMouse.chr6 420007 20 + 636262 GGAGCTAAGAAATATATTAT -s simRat_chr6.simRat.chr6 426224 20 + 647215 GGAGCTCATAAATGTAATAT -s simRat_chr6.simRat.chr6 425925 20 + 647215 AGACCAAAGCTCTATTTGGC - -a -s simMouse_chr6.simMouse.chr6 419875 15 + 636262 TTCAGAATAGCACCT -s Anc0.Anc0refChr3 49352 15 + 222631 TTCACAATTGGGCCT -s Anc1.Anc1refChr6 79944 15 + 197743 TTCACAATTGGGCCT -s Anc2.Anc2refChr13 53757 15 + 96486 TTCACAATTGGGCCT -s mr.mrrefChr5 272245 15 + 294540 TTCAGAGTAGCACCT -s mr.mrrefChr5 272396 15 + 294540 TTTACTCTTGTAATC -s simCow_chr6.simCow.chr6 409689 14 + 602619 TACACAATTCGGC-T -s simDog_chr6.simDog.chr6 400177 15 + 593897 TTCACAGGTGGGCCT -s simHuman_chr6.simHuman.chr6 405136 15 + 601863 TTCACAATTGGGCTT -s simMouse_chr6.simMouse.chr6 420029 15 + 636262 TTTACTCTTGTAATC -s simRat_chr6.simRat.chr6 426246 15 + 647215 TTTACTCTTTTAACC -s simRat_chr6.simRat.chr6 425945 15 + 647215 TTTAGAGTAGCACCC - -a -s simMouse_chr6.simMouse.chr6 419890 26 + 636262 TAGTTGCAAACTCAGTACACTAGATT -s Anc0.Anc0refChr3 49367 26 + 222631 CAGTCAGGTACTCAGTATAATAGGGT -s Anc1.Anc1refChr6 79959 26 + 197743 CAGTCAGGTACTCAGTATAATAGGGT -s Anc2.Anc2refChr13 53772 26 + 96486 CAGTCAAGTACTCAGTATAATAGGGT -s mr.mrrefChr5 272260 26 + 294540 TAGTCGCAAACTCAGTACACTAGATT -s mr.mrrefChr5 272417 26 + 294540 TTCTTAGGGACCTCTCAGAATGGGGT -s simCow_chr6.simCow.chr6 409703 26 + 602619 CAGTCATGTACTCAGTATAATAATGT -s simDog_chr6.simDog.chr6 400192 26 + 593897 CAGTCGAGTACTCAGTATAATAGGGA -s simHuman_chr6.simHuman.chr6 405151 26 + 601863 CACTAAGGTACTCAGTATACTGGGCT -s simMouse_chr6.simMouse.chr6 420050 26 + 636262 TTCTTAGGGACCTCTCAGAATGGGGT -s simRat_chr6.simRat.chr6 426267 26 + 647215 TTCTTGGGGATCTCTCTAAATGAGGT -s simRat_chr6.simRat.chr6 425960 26 + 647215 TAGTCACAAACTCAGTACGCTAGATT - -a -s simMouse_chr6.simMouse.chr6 419916 4 + 636262 AGTG -s Anc0.Anc0refChr3 49393 4 + 222631 AGTT -s Anc1.Anc1refChr6 79985 4 + 197743 AGTT -s Anc2.Anc2refChr13 53798 4 + 96486 AGTT -s mr.mrrefChr5 272286 4 + 294540 AGTG -s mr.mrrefChr5 272443 4 + 294540 ATAT -s simCow_chr6.simCow.chr6 409729 4 + 602619 AGTT -s simDog_chr6.simDog.chr6 400218 4 + 593897 AATT -s simHuman_chr6.simHuman.chr6 405177 4 + 601863 AGTC -s simMouse_chr6.simMouse.chr6 420076 4 + 636262 ATAT -s simRat_chr6.simRat.chr6 426294 4 + 647215 ATGT -s simRat_chr6.simRat.chr6 425986 4 + 647215 AGTA - -a -s simMouse_chr6.simMouse.chr6 419920 1 + 636262 A -s Anc0.Anc0refChr3 49397 1 + 222631 A -s Anc1.Anc1refChr6 79989 1 + 197743 A -s Anc2.Anc2refChr13 53802 1 + 96486 A -s mr.mrrefChr5 272290 1 + 294540 A -s simCow_chr6.simCow.chr6 409733 1 + 602619 A -s simDog_chr6.simDog.chr6 400222 1 + 593897 A -s simHuman_chr6.simHuman.chr6 405181 1 + 601863 A -s simRat_chr6.simRat.chr6 425990 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 419921 3 + 636262 TCT -s Anc0.Anc0refChr3 49398 3 + 222631 TGT -s Anc1.Anc1refChr6 79990 3 + 197743 TGT -s Anc2.Anc2refChr13 53803 3 + 96486 TGT -s mr.mrrefChr5 272291 3 + 294540 TCT -s mr.mrrefChr5 272447 3 + 294540 TGT -s simCow_chr6.simCow.chr6 409734 3 + 602619 TGT -s simDog_chr6.simDog.chr6 400223 3 + 593897 TGA -s simHuman_chr6.simHuman.chr6 405182 3 + 601863 TGT -s simMouse_chr6.simMouse.chr6 420080 3 + 636262 TGT -s simRat_chr6.simRat.chr6 426298 3 + 647215 TGG -s simRat_chr6.simRat.chr6 425991 3 + 647215 TAT - -a -s simMouse_chr6.simMouse.chr6 419924 9 + 636262 GTTCCTAAC -s Anc0.Anc0refChr3 49401 9 + 222631 GCTCCCAAC -s Anc1.Anc1refChr6 79993 9 + 197743 GCTCCCAAC -s Anc2.Anc2refChr13 53806 9 + 96486 GCTCCCAAC -s mr.mrrefChr5 272294 9 + 294540 GTTCCCAAC -s simCow_chr6.simCow.chr6 409737 6 + 602619 GATCCC--- -s simDog_chr6.simDog.chr6 400226 9 + 593897 GCTCCCAAC -s simHuman_chr6.simHuman.chr6 405185 8 + 601863 A-TCCCAAC -s simRat_chr6.simRat.chr6 425994 9 + 647215 GTTCCCAAC - -a -s simMouse_chr6.simMouse.chr6 419933 7 + 636262 TAAGGTA -s Anc0.Anc0refChr3 49410 3 + 222631 TAA---- -s Anc1.Anc1refChr6 80002 7 + 197743 TAACGTA -s Anc2.Anc2refChr13 53815 3 + 96486 TAA---- -s mr.mrrefChr5 272303 7 + 294540 TAAGGTA -s mr.mrrefChr5 272450 7 + 294540 CAGTATA -s simCow_chr6.simCow.chr6 409743 2 + 602619 -AA---- -s simDog_chr6.simDog.chr6 400235 3 + 593897 TAA---- -s simHuman_chr6.simHuman.chr6 405193 7 + 601863 TAACGTA -s simMouse_chr6.simMouse.chr6 420083 7 + 636262 CAGTATA -s simRat_chr6.simRat.chr6 426301 7 + 647215 CATTATA -s simRat_chr6.simRat.chr6 426003 7 + 647215 TAAAGTA - -a -s simMouse_chr6.simMouse.chr6 419940 3 + 636262 CTT -s mr.mrrefChr5 272310 3 + 294540 CTT -s simRat_chr6.simRat.chr6 426010 3 + 647215 CAT - -a -s simMouse_chr6.simMouse.chr6 419943 3 + 636262 TAC -s Anc1.Anc1refChr6 80009 3 + 197743 TAC -s mr.mrrefChr5 272313 3 + 294540 TAC -s mr.mrrefChr5 272457 3 + 294540 GAC -s simHuman_chr6.simHuman.chr6 405200 3 + 601863 TAC -s simMouse_chr6.simMouse.chr6 420090 3 + 636262 GAC -s simRat_chr6.simRat.chr6 426308 3 + 647215 GGC -s simRat_chr6.simRat.chr6 426013 3 + 647215 TAT - -a -s simMouse_chr6.simMouse.chr6 419946 1 + 636262 T -s Anc0.Anc0refChr3 49413 1 + 222631 T -s Anc1.Anc1refChr6 80013 1 + 197743 T -s Anc2.Anc2refChr13 53818 1 + 96486 T -s mr.mrrefChr5 272316 1 + 294540 T -s mr.mrrefChr5 272461 1 + 294540 T -s simCow_chr6.simCow.chr6 409745 1 + 602619 T -s simDog_chr6.simDog.chr6 400238 1 + 593897 G -s simHuman_chr6.simHuman.chr6 405204 1 + 601863 T -s simMouse_chr6.simMouse.chr6 420094 1 + 636262 T -s simRat_chr6.simRat.chr6 426312 1 + 647215 T -s simRat_chr6.simRat.chr6 426016 1 + 647215 G - -a -s simMouse_chr6.simMouse.chr6 419947 3 + 636262 CTG -s Anc0.Anc0refChr3 49414 3 + 222631 CTG -s Anc1.Anc1refChr6 80014 3 + 197743 CTG -s Anc2.Anc2refChr13 53819 3 + 96486 CTG -s mr.mrrefChr5 272317 3 + 294540 CTG -s mr.mrrefChr5 272462 3 + 294540 CTG -s simCow_chr6.simCow.chr6 409746 3 + 602619 TTG -s simDog_chr6.simDog.chr6 400239 3 + 593897 CTG -s simHuman_chr6.simHuman.chr6 405205 3 + 601863 CAG -s simMouse_chr6.simMouse.chr6 420095 3 + 636262 CTG -s simRat_chr6.simRat.chr6 426313 3 + 647215 CTA -s simRat_chr6.simRat.chr6 426167 3 + 647215 CTG - -a -s simMouse_chr6.simMouse.chr6 419950 4 + 636262 GAAA -s mr.mrrefChr5 272320 4 + 294540 AGAA -s simRat_chr6.simRat.chr6 426170 4 + 647215 AGAA - -a -s simMouse_chr6.simMouse.chr6 419988 5 + 636262 CTGTC -s mr.mrrefChr5 272358 5 + 294540 CTGTC -s simRat_chr6.simRat.chr6 426208 5 + 647215 CTGGC - -a -s simMouse_chr6.simMouse.chr6 420004 3 + 636262 CAT - -a -s simMouse_chr6.simMouse.chr6 420027 2 + 636262 AG -s mr.mrrefChr5 272394 2 + 294540 AG -s simRat_chr6.simRat.chr6 426244 2 + 647215 AG - -a -s simMouse_chr6.simMouse.chr6 420044 6 + 636262 ACCAGA -s mr.mrrefChr5 272411 6 + 294540 ACCAGA -s simRat_chr6.simRat.chr6 426261 6 + 647215 ACCAGA - -a -s simMouse_chr6.simMouse.chr6 420093 1 + 636262 A -s Anc1.Anc1refChr6 80012 1 + 197743 A -s mr.mrrefChr5 272460 1 + 294540 A -s simHuman_chr6.simHuman.chr6 405203 1 + 601863 A -s simRat_chr6.simRat.chr6 426311 1 + 647215 G - -a -s simMouse_chr6.simMouse.chr6 420098 7 + 636262 CTCTCAG -s Anc0.Anc0refChr3 49417 7 + 222631 CTCCCAG -s Anc1.Anc1refChr6 80017 7 + 197743 CTCCCAG -s Anc2.Anc2refChr13 53822 7 + 96486 CTCCCAG -s mr.mrrefChr5 272465 7 + 294540 CTCTCAG -s simCow_chr6.simCow.chr6 409749 7 + 602619 CTCCCAG -s simDog_chr6.simDog.chr6 400242 7 + 593897 CCTCCAG -s simHuman_chr6.simHuman.chr6 405208 7 + 601863 CTCCCAG -s simRat_chr6.simRat.chr6 426316 7 + 647215 CTCTCAG - -a -s simMouse_chr6.simMouse.chr6 420105 27 + 636262 TACTCTGCTTAAGTTATCTTATCACTT -s Anc0.Anc0refChr3 49424 22 + 222631 TTCCCTACTTGAATTCTCA-----GTT -s Anc1.Anc1refChr6 80024 27 + 197743 TTCCCTACTTGAATTCTCAAATCAGTT -s Anc2.Anc2refChr13 53829 22 + 96486 TTCCCTACTTAAATTCTCA-----GTT -s mr.mrrefChr5 272472 27 + 294540 TACTCTGCTTGAGTTATCTTATCACTT -s simCow_chr6.simCow.chr6 409756 22 + 602619 AGTCCTACTTAAAGCCTCA-----GTT -s simDog_chr6.simDog.chr6 400250 17 + 593897 TTCCCTGCTTAAATTC----------T -s simHuman_chr6.simHuman.chr6 405215 27 + 601863 TTCCCTACTTGAATTCTCAAATCAGTT -s simRat_chr6.simRat.chr6 426323 27 + 647215 TACTCTGCTGGAGTTATGTCATCACTT - -a -s simMouse_chr6.simMouse.chr6 420132 16 + 636262 AGCATGAAGAGATATG -s Anc0.Anc0refChr3 49447 16 + 222631 AGTCTGGAGACATATG -s Anc1.Anc1refChr6 80052 16 + 197743 AGTCTGGAGACATATG -s Anc2.Anc2refChr13 53852 16 + 96486 AGTCTGGAGTCATATG -s mr.mrrefChr5 272500 16 + 294540 AGCATGAAGACATATG -s simCow_chr6.simCow.chr6 409779 16 + 602619 AGTCTGAAATCATATG -s simDog_chr6.simDog.chr6 400268 16 + 593897 AGTCCAGAGTCATATG -s simHuman_chr6.simHuman.chr6 405243 16 + 601863 AGACTGGAGACATATG -s simRat_chr6.simRat.chr6 426351 16 + 647215 AGCATGAAGACATATG - -a -s simMouse_chr6.simMouse.chr6 420148 14 + 636262 GCTTCTTGAGCGAT -s Anc0.Anc0refChr3 49469 14 + 222631 GCTCCTTAAGGATT -s Anc1.Anc1refChr6 80074 14 + 197743 GCTCCTTAAGGATT -s Anc2.Anc2refChr13 53874 14 + 96486 GCTCCTTAAGGATT -s mr.mrrefChr5 272522 14 + 294540 GCTTCTTGAGCGAT -s simCow_chr6.simCow.chr6 409815 14 + 602619 GCTCCTTAGGGATT -s simDog_chr6.simDog.chr6 400290 14 + 593897 GCTGCTTAAGGATT -s simHuman_chr6.simHuman.chr6 405265 12 + 601863 GC--CTTAAGGATT -s simRat_chr6.simRat.chr6 426373 14 + 647215 GCATCTTTAGCAAT - -a -s simMouse_chr6.simMouse.chr6 420162 4 + 636262 AATG -s Anc0.Anc0refChr3 49491 4 + 222631 AGTG -s Anc1.Anc1refChr6 80096 4 + 197743 AGTG -s Anc2.Anc2refChr13 53896 4 + 96486 GGTG -s mr.mrrefChr5 272536 4 + 294540 AATG -s simCow_chr6.simCow.chr6 409837 4 + 602619 GGTG -s simDog_chr6.simDog.chr6 400312 3 + 593897 -GTG -s simHuman_chr6.simHuman.chr6 405285 4 + 601863 AGTG -s simRat_chr6.simRat.chr6 426387 4 + 647215 AATG - -a -s simMouse_chr6.simMouse.chr6 420166 41 + 636262 TAAGGTTAGGAGGTGCCCATTCTATATGCATGCATGGGCTA -s Anc0.Anc0refChr3 49497 41 + 222631 CAAGGTTAGGTGACACCCATTCTACATGCTCATCTGGGCTT -s Anc1.Anc1refChr6 80102 41 + 197743 CAAGGTTAGGTGACACCCATTCTACATGCTCATCTGGGCTT -s Anc2.Anc2refChr13 53902 41 + 96486 CAAGGTTAGGTGGCACCCATTCTACATGCTCATCTGGGCTT -s mr.mrrefChr5 272540 41 + 294540 TAAGGTTAGGAGATGCCCATTCTATATGCATGCATGGGCTA -s simCow_chr6.simCow.chr6 409843 41 + 602619 CAAGGCTAGGTGGTAACCATTCTACATGCTCATCTAGGCTT -s simDog_chr6.simDog.chr6 400317 41 + 593897 CAAGGTTAGGAGGCCCCCATTCTACATGCTAATCTGGACTT -s simHuman_chr6.simHuman.chr6 405291 41 + 601863 CAAGGTTAGGTCACACCCATTGTGCATGCTCATCTGGGCTT -s simRat_chr6.simRat.chr6 426391 41 + 647215 TAAGGTTAGGAGATGCCCATTCTATATGTATGCATGGGCTA - -a -s simMouse_chr6.simMouse.chr6 420207 132 + 636262 TACACCTTTATCCCCTGGTATGCTAAGGTCCCCGTGACAAACTGCGCTTGACCAACCTAGCTCAATGTGGAACAGAGGCAGCAATCAGAGTAAAATGTCATATCAGTAAGATACATATAAATTTTCTACACT -s Anc0.Anc0refChr3 49538 121 + 222631 TACACCTTTATCCC-TGGTATGCCAAGGTTCCTGTGATGAACTGTATTGGATTGAACTGCTCATTT-TGTGAAATGAGCAACCATCAGGGTGAATT-----ATCAGTAAGATACA----AAACTTCTAGACC -s Anc1.Anc1refChr6 80143 121 + 197743 TACACCTTTATCCC-TGGTATGCCAAGGTTCCTGTGATGAACTGTATTGGATTGAACTGCTCATTT-TGTGAAATGAGCAACCATCAGGGTGAATT-----ATCAGTAAGATACA----AAACTTCTAGACC -s Anc2.Anc2refChr13 53953 121 + 96486 TACACATTTATCCC-TGGTATGCCAAGGTTCCTGTGATGAAATGTATTGGATTGAACTGCTCATTT-TGTGAAATGAGCAACCATCAGGGTGAATT-----ATCAGTAAGATACA----AGACTTCTAGACC -s mr.mrrefChr5 272581 122 + 294540 TACACCTTTATCCCCTGGTATGCCAAGGTCCCTGTGATAAACTGCGCTTGACCAAACTGGCTCTAT-TGGAACAGAGGCAACAATCAGAGTAAAAT-----ATCAGTAAGATACA----AATTTTCTACACT -s simCow_chr6.simCow.chr6 409894 117 + 602619 TACACATTTATCCC-TAGTATGTCAAGGTCCCTGTGATGAAGTGGATTAGATTAAACTGCTCGTCT-TGTGACACACACAACCATCAGGGTGAATT-----ATCCGTA----ACA----AACTGTCTGGACC -s simDog_chr6.simDog.chr6 400368 121 + 593897 CACACATTTATCTC-TGGTATACCAAGGTTCCTGTGGTGAAATGTATTGGATTGAACTGTTCATTT-TGTGAAATGAGCAACCATCAGGCTGAATT-----ATCAGTAAGATACA----AGACTTCTAGACC -s simHuman_chr6.simHuman.chr6 405332 120 + 601863 TACACCTTTATCCC-TGGTATGCCAAGGCTCCTGTGATGAACCGAATTGTATTGAACTGCTCTTTT-TGTGATATGAGTAACCATCAGGGTGAATG-----ATTAGTGAGATAGA----GAA-TTTCATACC -s simRat_chr6.simRat.chr6 426432 122 + 647215 TACACCTTAATCCCCTGGTATGCCAAGGTCCCTGTGATAAACTGGGCCTGACCAAACTGACTCTCT-TGGAACACAGGCAATTATTAGAGTAAAAT-----ATCCATAAAATACA----AATTTTCTACACT - -a -s simMouse_chr6.simMouse.chr6 420339 40 + 636262 GAGTTTTGTCATATGAGGAACCAGGCATGCCGGGTGAATA -s Anc0.Anc0refChr3 49665 31 + 222631 AACTGTTGTCATGTGGGGGATCAGG---------TGTATG -s Anc1.Anc1refChr6 80270 31 + 197743 AACTGTTGTCATGTGGGGGATCAGG---------TGTATG -s Anc2.Anc2refChr13 54080 31 + 96486 AACTGTTGTCATGTGGGGGATCAGG---------TGTATG -s mr.mrrefChr5 272709 40 + 294540 GAGTTTTGTCATATGAGGAATCAGGCATGCCGGGTGTATA -s simCow_chr6.simCow.chr6 410017 21 + 602619 AACTGTTGTCATGTGGTGGAT------------------- -s simDog_chr6.simDog.chr6 400493 29 + 593897 --CTGGTGTCATGTGGGGGATCAGG---------TGTATG -s simHuman_chr6.simHuman.chr6 405458 31 + 601863 ACCTGTAGTCTTGTGGGGGATCAGG---------TGTATG -s simRat_chr6.simRat.chr6 426560 40 + 647215 GAGTTTTGTCATACGAGAAATCAGGCAAGCCAGGTGTATA - -a -s simMouse_chr6.simMouse.chr6 420379 49 + 636262 ATCACCAATAATCATAAAAGGTTCACCAGCCTTAGGTTGATAAGTATCT -s Anc0.Anc0refChr3 49701 42 + 222631 TCCACCACTAATTGTATA-GGTCCACTATCCTTAGGTAC------AGCA -s Anc1.Anc1refChr6 80306 48 + 197743 TCCACCACTAATTGTATA-GGTCCACTATCCTTAGGTACGTGTGTAGCA -s Anc2.Anc2refChr13 54116 42 + 96486 TCCACCACTAATTGTATA-GGTCCACTATCCTTAGGTAC------AGTA -s mr.mrrefChr5 272754 49 + 294540 ATCACCAATAATCATAAAAGGTTCACCAGCCTTAGGTAGGTAAGTATCA -s simCow_chr6.simCow.chr6 410040 42 + 602619 TCCACCACTAATTGCATA-GGTCCAATATCCTTGGGTAC------AGTA -s simDog_chr6.simDog.chr6 400527 42 + 593897 TCCAGCACTAATTGTGTA-GGTCCACTATCCTTAGGTAC------AGTA -s simHuman_chr6.simHuman.chr6 405494 48 + 601863 TCTGCCACTAACTGTATA-GATCCACTACCCTTAGGTAAGTGTGTACCA -s simRat_chr6.simRat.chr6 426605 49 + 647215 ATCACCAGTAATCATAAAAGGGTCACCAGCCTTAGGTAGGTAAGTATCA - -a -s simMouse_chr6.simMouse.chr6 420428 19 + 636262 GGTCAATTGTTCAGCCATT -s Anc0.Anc0refChr3 49743 15 + 222631 GTT----TGTCCTGACATT -s Anc1.Anc1refChr6 80354 15 + 197743 GTT----TGTCCTGACATT -s Anc2.Anc2refChr13 54158 15 + 96486 GTT----TTTCCTGACATC -s mr.mrrefChr5 272803 19 + 294540 GGTCAATTGTTCTGCCATT -s simCow_chr6.simCow.chr6 410085 15 + 602619 ATT----TTTCCTAACCTC -s simDog_chr6.simDog.chr6 400569 15 + 593897 GCG----CTTGCTGACATC -s simHuman_chr6.simHuman.chr6 405542 15 + 601863 GTT----TGTCCTGACATT -s simRat_chr6.simRat.chr6 426654 19 + 647215 GGTCAACTCTTCTGCCATT - -a -s simMouse_chr6.simMouse.chr6 420447 12 + 636262 CTAATGTCAAAG -s Anc0.Anc0refChr3 49759 12 + 222631 CAAGTGCCAGAG -s Anc1.Anc1refChr6 80370 12 + 197743 CAAGTGCCAGAG -s Anc2.Anc2refChr13 54174 12 + 96486 CAAGTACCAGAG -s mr.mrrefChr5 272822 12 + 294540 CTAATGTCAAAG -s simCow_chr6.simCow.chr6 410101 12 + 602619 CAACTACCAGAG -s simDog_chr6.simDog.chr6 400585 12 + 593897 CAAGTACCAGAG -s simHuman_chr6.simHuman.chr6 405558 12 + 601863 CAAGTGCCAGAG -s simRat_chr6.simRat.chr6 426673 9 + 647215 CT---GTTAAAG - -a -s simMouse_chr6.simMouse.chr6 420459 62 + 636262 TTGGCAGCATACACACTTGCCATGTGCCTTGAGGGTCATTGTGTAGCGACCCTGGACAAAGT -s Anc0.Anc0refChr3 49771 54 + 222631 TAGGCAACATTAACA-------TGTGCCTCCAGGGACACTATCTACCGACCCTGGACAA-GG -s Anc1.Anc1refChr6 80382 54 + 197743 TAGGCAACATTAACA-------TGTGCCTCCAGGGACACTATCTACCGACCCTGGACAA-GG -s Anc2.Anc2refChr13 54186 54 + 96486 TAGGCAACGTTAACA-------TGTGCCTCCAGGGAAGCTATCTACCCATCCTGTACAA-GG -s mr.mrrefChr5 272834 61 + 294540 TTGGCAGCATAAACACTTGCCATGTGCCTTGAGGGACATTGTGTAGCGACCCTGGACAA-GG -s simCow_chr6.simCow.chr6 410115 22 + 602619 TAGGCAATTTTAACA-------TGTGGCT--------------------------------- -s simDog_chr6.simDog.chr6 400597 54 + 593897 CAGGCAACGTAGACA-------CATGCCTCCAGGGAAGCTATCTACCCATCCTGTACAA-GG -s simHuman_chr6.simHuman.chr6 405570 54 + 601863 TAGGCATCATTAACA-------TGTGCCTCCAGGTACACCATCTAATGACCCTGGATAA-GG -s simRat_chr6.simRat.chr6 426682 58 + 647215 TGTGCAGCATAAACACTTGCCATGTGCCTTG--GGACATTGTGAGGAGATCCTGGACG--GG - -a -s simMouse_chr6.simMouse.chr6 420521 4 + 636262 ACAA -s Anc0.Anc0refChr3 49825 4 + 222631 ATAA -s Anc1.Anc1refChr6 80436 4 + 197743 ATAA -s Anc2.Anc2refChr13 54241 4 + 96486 ACCA -s mr.mrrefChr5 272895 4 + 294540 ATAA -s simDog_chr6.simDog.chr6 400652 4 + 593897 ACCA -s simHuman_chr6.simHuman.chr6 405624 4 + 601863 ATAA -s simRat_chr6.simRat.chr6 426740 4 + 647215 ATAA - -a -s simMouse_chr6.simMouse.chr6 420525 14 + 636262 CACAGAGAATTCCT -s Anc0.Anc0refChr3 49829 14 + 222631 CACACTGAATTCGT -s Anc1.Anc1refChr6 80440 14 + 197743 CACACTGAATTCGT -s Anc2.Anc2refChr13 54245 14 + 96486 CCAACTGAATTTGT -s mr.mrrefChr5 272899 14 + 294540 CACAGAGAATTCCT -s simDog_chr6.simDog.chr6 400656 14 + 593897 CCAACTGAATTTGT -s simHuman_chr6.simHuman.chr6 405635 14 + 601863 CACTCTGAGTTCAT -s simRat_chr6.simRat.chr6 426744 14 + 647215 CACAGAGAATTCCT - -a -s simMouse_chr6.simMouse.chr6 420539 21 + 636262 TGGAAACAATACACTTTCCTT -s Anc0.Anc0refChr3 49843 21 + 222631 GTGAAACAATACAATATCATT -s Anc1.Anc1refChr6 80454 21 + 197743 GTGAAACAATACAATATCATT -s Anc2.Anc2refChr13 54259 21 + 96486 GTGAAACAATACAATATCATT -s mr.mrrefChr5 272913 21 + 294540 TGGAAACAATACACTTTCATT -s simCow_chr6.simCow.chr6 410137 12 + 602619 ---------TACAATATTTTT -s simDog_chr6.simDog.chr6 400675 21 + 593897 GTGAAACAACACAATATCATT -s simHuman_chr6.simHuman.chr6 405649 21 + 601863 ATGAAACAGTACAATATCATT -s simRat_chr6.simRat.chr6 426758 21 + 647215 TGAAAACTATACATTTTCATC - -a -s simMouse_chr6.simMouse.chr6 420560 9 + 636262 TGTGTCCCT -s Anc0.Anc0refChr3 49864 5 + 222631 G----TACT -s Anc1.Anc1refChr6 80475 5 + 197743 G----TACT -s Anc2.Anc2refChr13 54280 5 + 96486 G----TACT -s mr.mrrefChr5 272934 9 + 294540 TGTGTTCCT -s simCow_chr6.simCow.chr6 410149 5 + 602619 G----TACT -s simDog_chr6.simDog.chr6 400696 5 + 593897 A----TACT -s simHuman_chr6.simHuman.chr6 405670 5 + 601863 G----TACT -s simRat_chr6.simRat.chr6 426783 9 + 647215 TGTGTTCCC - -a -s simMouse_chr6.simMouse.chr6 420569 5 + 636262 TGCAA -s Anc0.Anc0refChr3 49869 5 + 222631 TGCAC -s Anc1.Anc1refChr6 80480 5 + 197743 TGCAC -s Anc2.Anc2refChr13 54285 5 + 96486 TGCAC -s mr.mrrefChr5 272943 5 + 294540 TGCAA -s simCow_chr6.simCow.chr6 410157 5 + 602619 TACAC -s simDog_chr6.simDog.chr6 400734 5 + 593897 TGCAC -s simHuman_chr6.simHuman.chr6 405675 5 + 601863 TGCAT -s simRat_chr6.simRat.chr6 426792 5 + 647215 TTCAA - -a -s simMouse_chr6.simMouse.chr6 420574 23 + 636262 GTTACATGTTACAAGAACTTAGG -s Anc0.Anc0refChr3 49874 23 + 222631 GGAACACGTCAGAAGGCCTTTGG -s Anc1.Anc1refChr6 80485 23 + 197743 GGAACACGTCAGAAGGCCTTTGG -s Anc2.Anc2refChr13 54290 23 + 96486 AGAACACTTCAGAAGGCCTTTGG -s mr.mrrefChr5 272948 23 + 294540 GTAACATGTTACAAGAACTTAGG -s simCow_chr6.simCow.chr6 410163 23 + 602619 AGCACACTTCACTAGGACTTTGG -s simDog_chr6.simDog.chr6 400739 23 + 593897 AGAACAATTCAGAGTGCTTTTGG -s simHuman_chr6.simHuman.chr6 405680 23 + 601863 GGAACACGTCAAAAGTCCTTTGA -s simRat_chr6.simRat.chr6 426797 23 + 647215 GCAGCATTTTGCAAGAACTTAGG - -a -s simMouse_chr6.simMouse.chr6 420597 9 + 636262 TCTTGATAA -s Anc0.Anc0refChr3 49897 9 + 222631 CCTTCATGA -s Anc1.Anc1refChr6 80508 9 + 197743 CCTTCATGA -s Anc2.Anc2refChr13 54313 9 + 96486 CCTTCATGA -s mr.mrrefChr5 272971 9 + 294540 TCTTGATAA -s simCow_chr6.simCow.chr6 410186 9 + 602619 CCTTCTTGA -s simDog_chr6.simDog.chr6 400762 9 + 593897 CCCTCATGA -s simHuman_chr6.simHuman.chr6 405714 9 + 601863 CCTTCATGA -s simRat_chr6.simRat.chr6 426820 9 + 647215 TCTTGGTAA - -a -s simMouse_chr6.simMouse.chr6 420606 15 + 636262 TGTACATTTAATTTT -s Anc0.Anc0refChr3 49906 15 + 222631 TGTACATTTAATTAT -s Anc1.Anc1refChr6 80517 15 + 197743 TGTACATTTAATTAT -s Anc2.Anc2refChr13 54322 15 + 96486 TGTATGTTAAATTAT -s mr.mrrefChr5 272980 15 + 294540 TGTACATTTAATTTT -s simCow_chr6.simCow.chr6 410195 14 + 602619 TGTATGTACAACTA- -s simDog_chr6.simDog.chr6 400868 15 + 593897 TGTATGTTAAATTAT -s simHuman_chr6.simHuman.chr6 405723 15 + 601863 TGTACATTTAATTAT -s simRat_chr6.simRat.chr6 426829 15 + 647215 TGTACATTTAATTTT - -a -s simMouse_chr6.simMouse.chr6 420621 16 + 636262 AGATGTCAACTTGACC -s Anc0.Anc0refChr3 49923 16 + 222631 AGATGTCATCTGGATC -s Anc1.Anc1refChr6 80534 16 + 197743 AGATGTCATCTGGATC -s Anc2.Anc2refChr13 54339 16 + 96486 AGATGTCATATGGATC -s mr.mrrefChr5 272995 16 + 294540 AGATGTCAACTTGACC -s simCow_chr6.simCow.chr6 410209 15 + 602619 -GATGTCATGTGGGTC -s simDog_chr6.simDog.chr6 400885 14 + 593897 AG--GTAATATGGATC -s simHuman_chr6.simHuman.chr6 405740 16 + 601863 GGATGTCCTCTGGATC -s simRat_chr6.simRat.chr6 426844 16 + 647215 AGTTGTCAGCTAGACC - -a -s simMouse_chr6.simMouse.chr6 420637 24 + 636262 ACACTTAAGAAAGTCCCGATGATC -s Anc0.Anc0refChr3 49946 22 + 222631 ACTCTTAAGAGA--TTTGACTATC -s Anc1.Anc1refChr6 80557 24 + 197743 ACTCTTAAGAGAGATTTGACTATC -s Anc2.Anc2refChr13 54362 22 + 96486 ACTTTTAAGAGA--TTTGACTATC -s mr.mrrefChr5 273011 24 + 294540 ACACTTAAGAAAGTCCTGATGATC -s simCow_chr6.simCow.chr6 410231 22 + 602619 ACTTTTAATAGA--AATGACTATC -s simDog_chr6.simDog.chr6 400907 22 + 593897 ACTTAAAAGAGA--TTTGACTATC -s simHuman_chr6.simHuman.chr6 405763 22 + 601863 ACTCTTAAGACAGGATTG--TATC -s simRat_chr6.simRat.chr6 426860 24 + 647215 ACACTTAAGAGAGTCCTGATGATC - -a -s simMouse_chr6.simMouse.chr6 420661 5 + 636262 ATCTG -s Anc0.Anc0refChr3 49968 5 + 222631 ATCTG -s Anc1.Anc1refChr6 80581 5 + 197743 ATCTG -s Anc2.Anc2refChr13 54384 5 + 96486 ATCTG -s mr.mrrefChr5 273035 5 + 294540 ATCTG -s simCow_chr6.simCow.chr6 410253 5 + 602619 ATCCA -s simDog_chr6.simDog.chr6 400940 5 + 593897 ATTTG -s simHuman_chr6.simHuman.chr6 405785 5 + 601863 ATCTG -s simRat_chr6.simRat.chr6 426884 5 + 647215 ATCTG - -a -s simMouse_chr6.simMouse.chr6 420666 12 + 636262 TTATTTTCAATT -s Anc0.Anc0refChr3 49973 12 + 222631 TTATTTTCAATG -s Anc1.Anc1refChr6 80586 12 + 197743 TTATTTTCAATG -s Anc2.Anc2refChr13 54389 12 + 96486 TTATTTTCAGTG -s mr.mrrefChr5 273040 12 + 294540 TTATTTTCAATT -s simCow_chr6.simCow.chr6 410258 12 + 602619 TTATTTTCAGTG -s simDog_chr6.simDog.chr6 400951 12 + 593897 CTCTTTTCAGTG -s simHuman_chr6.simHuman.chr6 405790 12 + 601863 TTATTTTTAACG -s simRat_chr6.simRat.chr6 426889 12 + 647215 TTATCTTCAATT - -a -s simMouse_chr6.simMouse.chr6 420678 7 + 636262 TTTCCTC -s Anc0.Anc0refChr3 49985 7 + 222631 TCTCCTC -s Anc1.Anc1refChr6 80598 7 + 197743 TCTCCTC -s Anc2.Anc2refChr13 54401 7 + 96486 TCTTCCC -s mr.mrrefChr5 273052 7 + 294540 TTTCCTC -s simCow_chr6.simCow.chr6 410270 7 + 602619 TCTTCCC -s simDog_chr6.simDog.chr6 400963 7 + 593897 TCTTTCC -s simHuman_chr6.simHuman.chr6 405802 5 + 601863 T--CCTC -s simRat_chr6.simRat.chr6 426908 7 + 647215 TTTCCTC - -a -s simMouse_chr6.simMouse.chr6 420685 18 + 636262 TCATATATCCACATTGTA -s Anc0.Anc0refChr3 49992 18 + 222631 TCAGTTATACACATTGTC -s Anc1.Anc1refChr6 80605 18 + 197743 TCAGTTATACACATTGTC -s Anc2.Anc2refChr13 54408 18 + 96486 TTAGTTATACACATTGTC -s mr.mrrefChr5 273059 18 + 294540 TCATATATCCACATTGTA -s simCow_chr6.simCow.chr6 410277 17 + 602619 TTCGTTATA-ACGTTGTC -s simDog_chr6.simDog.chr6 400970 18 + 593897 CTAGTTATACACATTGTC -s simHuman_chr6.simHuman.chr6 405897 18 + 601863 TCAGTTATATACATTGTC -s simRat_chr6.simRat.chr6 426915 18 + 647215 TCATATACACACATTGTA - -a -s simMouse_chr6.simMouse.chr6 420703 1 + 636262 T -s Anc0.Anc0refChr3 50010 1 + 222631 C -s Anc1.Anc1refChr6 80623 1 + 197743 C -s Anc2.Anc2refChr13 54426 1 + 96486 C -s mr.mrrefChr5 273077 1 + 294540 T -s simCow_chr6.simCow.chr6 410295 1 + 602619 C -s simDog_chr6.simDog.chr6 400988 1 + 593897 C -s simHuman_chr6.simHuman.chr6 405915 1 + 601863 C -s simRat_chr6.simRat.chr6 426933 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 420704 20 + 636262 GATTCTGCTTAAACAAGGTC -s Anc0.Anc0refChr3 50011 19 + 222631 -ATTCTGCACTTATAAGATC -s Anc1.Anc1refChr6 80624 20 + 197743 TATTCTGCACTTATAAGATC -s Anc2.Anc2refChr13 54427 19 + 96486 -ATTCTGCACTTATAAGATC -s mr.mrrefChr5 273078 20 + 294540 GATTCTGCTTAAACAAGGTC -s simCow_chr6.simCow.chr6 410296 19 + 602619 -ATCCTGCGCTTATAAGAAC -s simDog_chr6.simDog.chr6 400989 19 + 593897 -ATTCTGCACTTATATGATA -s simHuman_chr6.simHuman.chr6 405917 20 + 601863 TATTGTACACTTAAAAGATC -s simRat_chr6.simRat.chr6 426934 20 + 647215 GATTCTGCTCAAACAAGATC - -a -s simMouse_chr6.simMouse.chr6 420724 15 + 636262 TCCTTGACCCATAAT -s Anc0.Anc0refChr3 50033 12 + 222631 TCC---ATGCATAAT -s Anc1.Anc1refChr6 80647 12 + 197743 TCC---ATGCATAAT -s Anc2.Anc2refChr13 54449 12 + 96486 TCC---ATGCATAAT -s mr.mrrefChr5 273098 14 + 294540 TCC-TGACCCATAAT -s simCow_chr6.simCow.chr6 410318 12 + 602619 TCA---ATGCATAAT -s simDog_chr6.simDog.chr6 401011 12 + 593897 TCC---ACACATAAA -s simHuman_chr6.simHuman.chr6 405940 12 + 601863 TCC---ATGTGTAAT -s simRat_chr6.simRat.chr6 426954 14 + 647215 TCC-TAACTAGTAAC - -a -s simMouse_chr6.simMouse.chr6 420739 5 + 636262 TGTCT -s Anc0.Anc0refChr3 50050 5 + 222631 TATAT -s Anc1.Anc1refChr6 80664 5 + 197743 TATAT -s Anc2.Anc2refChr13 54466 5 + 96486 TATAT -s mr.mrrefChr5 273112 5 + 294540 TGTCT -s simCow_chr6.simCow.chr6 410335 5 + 602619 CATGT -s simDog_chr6.simDog.chr6 401028 5 + 593897 TATAT -s simHuman_chr6.simHuman.chr6 405957 5 + 601863 TATAT -s simRat_chr6.simRat.chr6 426968 5 + 647215 TGTTG - -a -s simMouse_chr6.simMouse.chr6 420744 15 + 636262 AAGTGCAGCCTTAAT -s Anc0.Anc0refChr3 50055 11 + 222631 ----GCTGCCTTAAT -s Anc1.Anc1refChr6 80669 15 + 197743 ATATGCTGCCTTAAT -s Anc2.Anc2refChr13 54471 11 + 96486 ----GCTGCCTTAAT -s mr.mrrefChr5 273117 15 + 294540 AAGTGCAGCCTTAAT -s simCow_chr6.simCow.chr6 410340 11 + 602619 ----GCTGCTTTGAT -s simDog_chr6.simDog.chr6 401033 11 + 593897 ----GGTGCCTTAAT -s simHuman_chr6.simHuman.chr6 405962 15 + 601863 ATATGCTGCCTTAAT -s simRat_chr6.simRat.chr6 426974 15 + 647215 AAATGCAGCCTTAAT - -a -s simMouse_chr6.simMouse.chr6 420759 7 + 636262 TGAGTCC -s Anc0.Anc0refChr3 50082 4 + 222631 TGAG--- -s Anc1.Anc1refChr6 80700 4 + 197743 TGAG--- -s Anc2.Anc2refChr13 54498 4 + 96486 TGAG--- -s mr.mrrefChr5 273132 4 + 294540 TGAG--- -s simCow_chr6.simCow.chr6 410364 4 + 602619 TGAA--- -s simDog_chr6.simDog.chr6 401060 4 + 593897 TGAG--- -s simHuman_chr6.simHuman.chr6 405993 4 + 601863 TGAG--- -s simRat_chr6.simRat.chr6 426989 4 + 647215 TGAG--- - -a -s simMouse_chr6.simMouse.chr6 420766 22 + 636262 CTAGCATTGGCAACTTGAGCTA -s Anc0.Anc0refChr3 50089 22 + 222631 CTAGGACTGGCAACTTGTTCTA -s Anc1.Anc1refChr6 80707 22 + 197743 CTAGGACTGGCAACTTGTTCTA -s Anc2.Anc2refChr13 54505 22 + 96486 GTAGGACTGGCAACTTGTTCAA -s mr.mrrefChr5 273136 22 + 294540 CTAGCATTGGCAACTTGAGCTA -s simCow_chr6.simCow.chr6 410371 22 + 602619 TTAGTACTCGCAACCTGTTCTG -s simDog_chr6.simDog.chr6 401067 22 + 593897 GCAGGACTGCCAACTTGTTCAA -s simHuman_chr6.simHuman.chr6 406000 22 + 601863 CTAGGACTGGCAACTTGGTCTA -s simRat_chr6.simRat.chr6 426993 22 + 647215 CTAGCATTGGCAACTTGAGCTA - -a -s simMouse_chr6.simMouse.chr6 420788 15 + 636262 TTTGGTCTGTAGTAC -s Anc0.Anc0refChr3 50111 15 + 222631 TTATACTTGTAGTAC -s Anc1.Anc1refChr6 80729 15 + 197743 TTATACTTGTAGTAC -s Anc2.Anc2refChr13 54527 15 + 96486 TTATACTTATGGTAC -s mr.mrrefChr5 273158 15 + 294540 TTTGGTCTGTAGTAC -s simCow_chr6.simCow.chr6 410393 15 + 602619 ATATGCTTATGGTGC -s simDog_chr6.simDog.chr6 401089 15 + 593897 TTAGACTTATGGTAC -s simHuman_chr6.simHuman.chr6 406032 15 + 601863 TGATCCTTGAAGAAG -s simRat_chr6.simRat.chr6 427015 15 + 647215 TTAGGCGTGTGGTAC - -a -s simMouse_chr6.simMouse.chr6 420803 1 + 636262 G -s Anc0.Anc0refChr3 50126 1 + 222631 G -s Anc1.Anc1refChr6 80744 1 + 197743 G -s Anc2.Anc2refChr13 54542 1 + 96486 A -s mr.mrrefChr5 273173 1 + 294540 G -s simDog_chr6.simDog.chr6 401104 1 + 593897 A -s simHuman_chr6.simHuman.chr6 406047 1 + 601863 G -s simRat_chr6.simRat.chr6 427031 1 + 647215 G - -a -s simMouse_chr6.simMouse.chr6 420804 17 + 636262 TTCAGAACTAAGACATA -s Anc0.Anc0refChr3 50132 15 + 222631 TCCT-AA-TAAGACACA -s Anc1.Anc1refChr6 80750 16 + 197743 TCCTGAA-TAAGACACA -s Anc2.Anc2refChr13 54548 15 + 96486 TCTT-AA-TAAGACACA -s mr.mrrefChr5 273174 17 + 294540 TTCAGAACTAAGACATA -s simCow_chr6.simCow.chr6 410413 15 + 602619 TCTT-AA-TAAGACACA -s simDog_chr6.simDog.chr6 401108 15 + 593897 TATT-AA-TAAGACACA -s simHuman_chr6.simHuman.chr6 406053 13 + 601863 TCCTGGA----GACAGA -s simRat_chr6.simRat.chr6 427032 17 + 647215 TCCCATACTAAGACAGA - -a -s simMouse_chr6.simMouse.chr6 420821 18 + 636262 TGAGACACTTCACACAAT -s Anc0.Anc0refChr3 50149 18 + 222631 TGCGACACATTGCACAAC -s Anc1.Anc1refChr6 80768 18 + 197743 TGCGACACATTGCACAAC -s Anc2.Anc2refChr13 54565 18 + 96486 CACAACACATTGCACAAC -s mr.mrrefChr5 273191 18 + 294540 TGAGACACTTCACACAAT -s simCow_chr6.simCow.chr6 410430 8 + 602619 ----------TGTCTAAC -s simDog_chr6.simDog.chr6 401125 18 + 593897 CACAACACATTGCACAAT -s simHuman_chr6.simHuman.chr6 406068 18 + 601863 TGGGACACATTGAACAAC -s simRat_chr6.simRat.chr6 427049 18 + 647215 TGAGGCACTTCGTGCAAT - -a -s simMouse_chr6.simMouse.chr6 420839 16 + 636262 CTGAATAACTAGTATG -s Anc0.Anc0refChr3 50167 16 + 222631 GTGAATTACCTGCATG -s Anc1.Anc1refChr6 80786 16 + 197743 GTGAATTACCTGCATG -s Anc2.Anc2refChr13 54586 16 + 96486 GTGAATTACCTGCATG -s mr.mrrefChr5 273209 16 + 294540 CTGAATAACTAGTATG -s simCow_chr6.simCow.chr6 410441 16 + 602619 GTGAATCACTTTCACA -s simDog_chr6.simDog.chr6 401146 16 + 593897 TTGAATTACCTGCATG -s simHuman_chr6.simHuman.chr6 406086 16 + 601863 GTGAAATACCTACATG -s simRat_chr6.simRat.chr6 427067 16 + 647215 TTGAATAACTAGTCTG - -a -s simMouse_chr6.simMouse.chr6 420855 23 + 636262 TCTAATAGACAACTGGGATGCAG -s Anc0.Anc0refChr3 50207 23 + 222631 TATAATTGACAACTGGGATATAT -s Anc1.Anc1refChr6 80826 23 + 197743 TATAATTGACAACTGGGATATAT -s Anc2.Anc2refChr13 54626 23 + 96486 TATAATTGACAACTGGGATATAT -s mr.mrrefChr5 273225 23 + 294540 TCTAATAGACAACTGGGATGTAG -s simCow_chr6.simCow.chr6 410480 23 + 602619 ATTAAGTAACAACTGGGATATGC -s simDog_chr6.simDog.chr6 401186 23 + 593897 TATAGTTGACAACTGGGATTTAT -s simHuman_chr6.simHuman.chr6 406126 23 + 601863 TATAATTGACAACTGGGATATAT -s simRat_chr6.simRat.chr6 427083 23 + 647215 TATAATAGACAACTGGGATGTAG - -a -s simMouse_chr6.simMouse.chr6 420878 3 + 636262 GGA -s Anc0.Anc0refChr3 50241 3 + 222631 GGA -s Anc1.Anc1refChr6 80864 3 + 197743 GGA -s Anc2.Anc2refChr13 54660 3 + 96486 GGA -s mr.mrrefChr5 273248 3 + 294540 GGA -s simCow_chr6.simCow.chr6 410514 3 + 602619 GGA -s simDog_chr6.simDog.chr6 401220 3 + 593897 GAA -s simHuman_chr6.simHuman.chr6 406190 3 + 601863 GGA -s simRat_chr6.simRat.chr6 427106 3 + 647215 GGA - -a -s simMouse_chr6.simMouse.chr6 420881 2 + 636262 AT -s Anc0.Anc0refChr3 50244 2 + 222631 AT -s Anc1.Anc1refChr6 80867 2 + 197743 AT -s Anc2.Anc2refChr13 54663 2 + 96486 AT -s mr.mrrefChr5 273251 2 + 294540 AT -s simCow_chr6.simCow.chr6 410522 2 + 602619 AT -s simDog_chr6.simDog.chr6 401223 2 + 593897 AA -s simHuman_chr6.simHuman.chr6 406193 2 + 601863 AT -s simRat_chr6.simRat.chr6 427109 2 + 647215 AT - -a -s simMouse_chr6.simMouse.chr6 420883 93 + 636262 CATCTAACATAATAAGTATATATTATTGGTTATGTGAGCTATATAGTTTATATCTGTAAGTATATGTATTTGGGCTAGAGCCCTTGTCATGAC -s Anc0.Anc0refChr3 50268 91 + 222631 AACCTGATA--ATAAGTATATAATAATGACTATGTGTGCCATTTAGTTTATAACTGTAAGGATCTGCACTGAAGCTAGAGGCCTTACCATGGC -s Anc1.Anc1refChr6 80891 93 + 197743 AACCTGATATAATAAGTATATAATAATGACTATGTGTGCCATTTAGTTTATAACTGTAAGGATCTGCACTGAAGCTAGAGGCCTTACCATGGC -s Anc2.Anc2refChr13 54687 91 + 96486 AACCTGATA--ATAAGTATATAATAATGACTATGTGTACCATTAAGCTTTTAACTATAAGGACCTGCACTGAAGATAGAGGCCTTACCATGGC -s mr.mrrefChr5 273275 93 + 294540 CACCTAATATAATAAGTATATATTATTGGTTATGTGAGCTATATAGTTTATATCTGTAAGTATATGTATTTAGGCTAGAGCCCTTGTCATGAC -s simCow_chr6.simCow.chr6 410546 82 + 602619 GACCCAATA--ATGAGGATATGGTAATGACTATGTGTCCCATCAGGCTTGT--------GGACCTGCACTGAAG-TACAGGCCTCACCATCGC -s simDog_chr6.simDog.chr6 401247 80 + 593897 ACCCTGGTG--ATAATTATATAATAATGATTATGCATATAATTAAGCTTTTAACTATAAG-----------AACATAGAGGCCTTACCATGGC -s simHuman_chr6.simHuman.chr6 406217 93 + 601863 AACCTCCTATAATAAGTATATAATGATGACTATGTGTGCCATTTAGTTTATGACTGTAAGGATGTACACTCAAGCTAGAGGCATTACCATGGC -s simRat_chr6.simRat.chr6 427133 93 + 647215 CACTTAATATATTAAGTAAATATTATCGGTTATGTGAGCTACCTAATTAATACCTGTAAGCATATGTTTTTAGGCTACAGTCCCTGTCATAAC - -a -s simMouse_chr6.simMouse.chr6 420976 74 + 636262 CATACATAGGATCCAGAACAATCACAGCTTTTCAAACCGGTATTATCTGTATATGCCTATAGTATGTAGCTTGA -s Anc0.Anc0refChr3 50359 71 + 222631 CATCCATAGATTC-AGAACCATTGCAGCCT--CATACTAGTGTTAAGTGTATATGCCCATAATATGTAAGTCAA -s Anc1.Anc1refChr6 80984 74 + 197743 CATCCATAGATTCCAGAACCATTGCAGCCTTACATACTAGTGTTAAGTGTATATGCCCATAATATGTAAGTCAA -s Anc2.Anc2refChr13 54778 71 + 96486 CACCCATAGATTC-AGAACCATTGCAGCCT--CATACCAGTGTTAAGTGTATATGCCCATAATATGTAAGTCAA -s mr.mrrefChr5 273368 74 + 294540 CATACATAGAATCCAGAACAATTGCAGCTTTACAAACTGGTATTATCTGTATATGCCTATAGTATGTAGCTTGA -s simCow_chr6.simCow.chr6 410628 71 + 602619 CACCTATAGATTT-AGAACCATTGTAGCCT--CACACCAGTGTTAAGTGTATATGCTCATAATATGTATGTCAA -s simDog_chr6.simDog.chr6 401327 71 + 593897 CACCCATAGATTC-AGAACCATTGCAGGCT--CATACCAGTATTAAGCGTATATGCCCAAAATAGGTAAGTCAA -s simHuman_chr6.simHuman.chr6 406315 71 + 601863 GATCCATAGATTCCAGAACCATTGCAGCCTTA---AGTAGTGATAAGTATATTTGCCCATAATGTGTAAGTCAA -s simRat_chr6.simRat.chr6 427226 74 + 647215 CATAGATAGAATCCAGAACAATTGCAGCTTTACAAACTGGTATTACCTGAATATGCCTATAGTATGTAGCTTGA - -a -s simMouse_chr6.simMouse.chr6 421050 55 + 636262 CCCTAGCCCTACGATTCCTCCACACATATCTGTCTGACCTTTTCCTGGCCTCATG -s Anc0.Anc0refChr3 50430 47 + 222631 CCCTAAA------ATTCGTCCAGA--TATCTGTCTGAACTTTTCCTTGCCTCATG -s Anc1.Anc1refChr6 81058 49 + 197743 CCCTAAA------ATTCGTCCAGAAATATCTGTCTGAACTTTTCCTTGCCTCATG -s Anc2.Anc2refChr13 54849 47 + 96486 CCCTAAA------ATTTGCCTGGA--TATCTGTCTGAACTTTTCCTTGCCTTATG -s mr.mrrefChr5 273442 49 + 294540 CCCTAGC------ATTCCTCCACACATATCTGTCTGACCTTTTCCTGGCCTCATG -s simCow_chr6.simCow.chr6 410700 47 + 602619 CCCTAAA------ATTTGACTGGA--TATCTGTCTGAACTTCTCCTTGCCTTAAA -s simDog_chr6.simDog.chr6 401398 47 + 593897 CCCTAAA------ATGTGCCTGGA--TGTCTGTCTGATCTTTTCCTTGGCTTATG -s simHuman_chr6.simHuman.chr6 406386 49 + 601863 CCCTAAA------ATTCTTCCAGAAATATCTGTCTGAACTTTTCCTTACCTCATG -s simRat_chr6.simRat.chr6 427300 49 + 647215 CCCTAGT------ATTCCTTTACACATGACTGTCTGACCTTCTCCTAGACTCATG - -a -s simMouse_chr6.simMouse.chr6 421105 20 + 636262 ATGCTTTGTTGTTATGATTG -s Anc0.Anc0refChr3 50478 20 + 222631 GTGCTTTGAGGTTCTGAGTG -s Anc1.Anc1refChr6 81108 20 + 197743 GTGCTTTGAGGTTCTGAGTG -s Anc2.Anc2refChr13 54897 20 + 96486 GTGCTTTGAGGTTCTGAGTG -s mr.mrrefChr5 273491 20 + 294540 ATGCTTTGTTGTTCTGATTG -s simCow_chr6.simCow.chr6 410748 20 + 602619 ATGCTTTGAGGTTCTGTGTG -s simDog_chr6.simDog.chr6 401446 20 + 593897 GTACTTTGAGGTTCTCAGTG -s simHuman_chr6.simHuman.chr6 406436 20 + 601863 GTGCTTTTGGGTTCTGAGTG -s simRat_chr6.simRat.chr6 427349 20 + 647215 ATGCTTTGTTGTTCTGATTG - -a -s simMouse_chr6.simMouse.chr6 421125 18 + 636262 TGTGTGCTACCCTTTGAA -s Anc0.Anc0refChr3 50503 17 + 222631 TATA-GCTACCTTTCAAT -s Anc1.Anc1refChr6 81133 17 + 197743 TATA-GCTACCTTTCAAT -s Anc2.Anc2refChr13 54922 17 + 96486 GATA-GCCACCTTTCAAG -s mr.mrrefChr5 273511 17 + 294540 TGTG-GCTACCCTTTGAT -s simCow_chr6.simCow.chr6 410771 11 + 602619 -------CACCTATCTAA -s simDog_chr6.simDog.chr6 401471 17 + 593897 GATA-GCCACCTTTCAAG -s simHuman_chr6.simHuman.chr6 406461 17 + 601863 TATT-TCTACCTTTCAGT -s simRat_chr6.simRat.chr6 427369 17 + 647215 TGTG-ACCACCCTTTGAT - -a -s simMouse_chr6.simMouse.chr6 421143 37 + 636262 CTGAAGTAGAACTTCAGTGTGTGAGGTGTGGCCAAGC -s Anc0.Anc0refChr3 50520 37 + 222631 GTGAAGTTTAACTCCAATATGTGTGATGTGGACAAGC -s Anc1.Anc1refChr6 81150 37 + 197743 GTGAAGTTTAACTCCAATATGTGTGATGTGGACAAGC -s Anc2.Anc2refChr13 54939 37 + 96486 GTGAAGTTTAACTCCAATATGTGTGATTTGGACAAGC -s mr.mrrefChr5 273528 37 + 294540 CTGAAGTAGAACTTCAGTGTGTGAGGTGTGGCCAAGC -s simCow_chr6.simCow.chr6 410785 37 + 602619 GTGAAGTCTAACTCCAATATATGATATTCAAATGACC -s simDog_chr6.simDog.chr6 401488 37 + 593897 GTGAAGTTTAGCCTCAATATGAGTGATTTGGGCAAGC -s simHuman_chr6.simHuman.chr6 406478 37 + 601863 GTGAAGCTAAACTCCAATATGTGGGATGTGGACAGCT -s simRat_chr6.simRat.chr6 427386 37 + 647215 CTGAAGTGGAACTTCAGTGTGTAAAGTGTGGCCAAGC - -a -s simMouse_chr6.simMouse.chr6 421180 26 + 636262 CAATCACAAGATATGACAGGCTCATG -s Anc0.Anc0refChr3 50557 26 + 222631 CAGTCACAAGAGATCATGCTTTCATG -s Anc1.Anc1refChr6 81187 26 + 197743 CAGTCACAAGAGATCATGCTTTCATG -s Anc2.Anc2refChr13 54977 26 + 96486 CGGTCATAAGAGATCATGCTTTCATG -s mr.mrrefChr5 273565 26 + 294540 CAATCACAAGATATGACAGGCTCATG -s simCow_chr6.simCow.chr6 410823 26 + 602619 CTGTCAAAAGAGATCATGCTATCATG -s simDog_chr6.simDog.chr6 401526 25 + 593897 CGG-CATAAGAGATAATGCTTTCATG -s simHuman_chr6.simHuman.chr6 406518 26 + 601863 TAGTCACAAGAGATCATGCTTTCATG -s simRat_chr6.simRat.chr6 427423 26 + 647215 CAATCACAAGATATGACAGCCTCATG - -a -s simMouse_chr6.simMouse.chr6 421206 30 + 636262 GGCATTTCCTAAGCACCACTGGGTTTTGGT -s Anc0.Anc0refChr3 50583 30 + 222631 AGCATGTGCTAAAGACAGTTGGGTTTTGGG -s Anc1.Anc1refChr6 81213 30 + 197743 AGCATGTGCTAAAGACAGTTGGGTTTTGGG -s Anc2.Anc2refChr13 55003 30 + 96486 AGCATGTGCTAAAGAAAGTTGGGTTTTGGG -s mr.mrrefChr5 273591 30 + 294540 GGCATTTCCTAAGCACCACTGGGTTTTGGT -s simCow_chr6.simCow.chr6 410849 30 + 602619 AGCAGGTGCACAAGAAAGTCGAGTTTTGGG -s simDog_chr6.simDog.chr6 401552 30 + 593897 GGCATGTGCTAAAGCAAGTTTGGTTGTGGG -s simHuman_chr6.simHuman.chr6 406544 30 + 601863 AGCATGTGCTAAAGACAGTTGGGTTTTAGG -s simRat_chr6.simRat.chr6 427449 30 + 647215 GGCATTTCCCAAGAACCACTGGGTTTTGGT - -a -s simMouse_chr6.simMouse.chr6 421236 3 + 636262 GCT -s Anc0.Anc0refChr3 50613 3 + 222631 GCT -s Anc1.Anc1refChr6 81243 3 + 197743 GCT -s Anc2.Anc2refChr13 55033 3 + 96486 GCT -s mr.mrrefChr5 273621 3 + 294540 GCT -s simCow_chr6.simCow.chr6 410879 2 + 602619 G-T -s simDog_chr6.simDog.chr6 401589 3 + 593897 GCT -s simHuman_chr6.simHuman.chr6 406574 3 + 601863 GCT -s simRat_chr6.simRat.chr6 427479 3 + 647215 GCT - -a -s simMouse_chr6.simMouse.chr6 421239 22 + 636262 AAGATTACCATATCATGTTTGA -s Anc0.Anc0refChr3 50616 22 + 222631 AAGACTACCATCTCATGATGGA -s Anc1.Anc1refChr6 81246 22 + 197743 AAGACTACCATCTCATGATGGA -s Anc2.Anc2refChr13 55036 22 + 96486 AAGACTGCCATCTCATGATGGA -s mr.mrrefChr5 273624 22 + 294540 AAGATTACCATATCATGTTGGA -s simCow_chr6.simCow.chr6 410881 22 + 602619 AAGACTGCCGTCTCATGATGGC -s simDog_chr6.simDog.chr6 401608 16 + 593897 AAGACTGACA------GCTGGA -s simHuman_chr6.simHuman.chr6 406577 22 + 601863 AAGACTACCATCTCAGGATGGA -s simRat_chr6.simRat.chr6 427482 22 + 647215 AAGATTGCCATATCATGGAGGA - -a -s simMouse_chr6.simMouse.chr6 421261 15 + 636262 ATAATTTATGTGATA -s Anc0.Anc0refChr3 50641 15 + 222631 AAGGTTTATGTCATA -s Anc1.Anc1refChr6 81271 15 + 197743 AAGGTTTATGTCATA -s Anc2.Anc2refChr13 55061 15 + 96486 GAGGCTTATGTCATA -s mr.mrrefChr5 273646 15 + 294540 ATAGTTTATGTGATA -s simCow_chr6.simCow.chr6 410906 15 + 602619 GAGGCTTATGTCATA -s simDog_chr6.simDog.chr6 401627 15 + 593897 GAGGCTTATGTCATA -s simHuman_chr6.simHuman.chr6 406602 15 + 601863 AAGGTTTATGTCATA -s simRat_chr6.simRat.chr6 427504 14 + 647215 ATAGTTTATG-GCTA - -a -s simMouse_chr6.simMouse.chr6 421276 56 + 636262 CTAGTAAGGACTGAAATTGATACAGTTATGGAGGCTGACTGTTCCCCCCAGCTAGG -s Anc0.Anc0refChr3 50656 56 + 222631 CTAGTAAGAATTAAAATGGATACATTTATTAGAACTAACTGATCTCCCTGGCTAGG -s Anc1.Anc1refChr6 81286 56 + 197743 CTAGTAAGAATTAAAATGGATACATTTATTAGAACTAACTGATCTCCCTGGCTAGG -s Anc2.Anc2refChr13 55076 56 + 96486 CTAGTAAGAATTAAAATGGATACATTTATTAGAAGTAACTGATCTCCCTGGCTAGG -s mr.mrrefChr5 273661 56 + 294540 CTAGTAAGGACTGAAATTGATACAGTTATGGAGGCTGACTGTTCCCCCTGGCTAGG -s simCow_chr6.simCow.chr6 410926 56 + 602619 CTAGTAAGGATCAAAATGGATACGGTCATTGAAAGTGACTGATCTCCCTGGCTAGG -s simDog_chr6.simDog.chr6 401642 56 + 593897 CTAGTAAGAATTTAAATGGATAGATTTATCAGAAGTAACTGATCTCCCTGGCTAGG -s simHuman_chr6.simHuman.chr6 406617 56 + 601863 CTAGTGAGAATAAATGTGGATTCATTTACTATAACTAACTGATCTCTATGGCTGGG -s simRat_chr6.simRat.chr6 427518 56 + 647215 TTAGTAGGGACTGAAATTGATACACTTATGGAGGCTGACTGTTCCCCCTGGCTAGG - -a -s simMouse_chr6.simMouse.chr6 421332 28 + 636262 ACCTCTGAGACATACCCCAGAAGGCTTT -s Anc0.Anc0refChr3 50719 27 + 222631 ACCA-TTAGGCCTGCCTCAGAAGGCTTT -s Anc1.Anc1refChr6 81349 28 + 197743 ACCAATTAGGCCTGCCTCAGAAGGCTTT -s Anc2.Anc2refChr13 55139 27 + 96486 ACCA-TTAGGCCTGCCTTGGAAGGCTTT -s mr.mrrefChr5 273717 28 + 294540 ACCTATGAGACATGCCCCAGAAGGCTTT -s simCow_chr6.simCow.chr6 410989 27 + 602619 GCCA-TCAGGCCTGCTGTGGAAGGCTTT -s simDog_chr6.simDog.chr6 401705 27 + 593897 ATCA-TTGGGCCTATCTTGGAAGGCTTT -s simHuman_chr6.simHuman.chr6 406680 28 + 601863 ACCAATTAGGCCTGCCTCAGGAGGCTTT -s simRat_chr6.simRat.chr6 427574 28 + 647215 ACCTATGAGATATGACCCAGAAGGCTTT - -a -s simMouse_chr6.simMouse.chr6 421360 26 + 636262 TAGAGAGCACTGCTTTAGCATGGATA -s Anc0.Anc0refChr3 50746 25 + 222631 TACAGAGCACTGCATCAGCCTGGG-A -s Anc1.Anc1refChr6 81377 25 + 197743 TACAGAGCACTGCATCAGCCTGGG-A -s Anc2.Anc2refChr13 55166 25 + 96486 TACAGAGCACTGCATCAGCCTGGG-A -s mr.mrrefChr5 273745 26 + 294540 TAGAGAGCACTGCTTTAGCCTGGATA -s simCow_chr6.simCow.chr6 411016 24 + 602619 TACAGAGCATTGT-TCTGACTGGG-A -s simDog_chr6.simDog.chr6 401747 25 + 593897 TACAGAGCACTACAGCAGCCCGGG-A -s simHuman_chr6.simHuman.chr6 406708 25 + 601863 TACAGAGCACTGCATCAGCCTGGG-A -s simRat_chr6.simRat.chr6 427602 26 + 647215 TAGAGAGCACTGGTTTAGCCTGGATA - -a -s simMouse_chr6.simMouse.chr6 421386 21 + 636262 ATCATAACTATTGCCCTATCG -s Anc0.Anc0refChr3 50771 21 + 222631 ATCATAACTATCGCTGTGTCT -s Anc1.Anc1refChr6 81402 21 + 197743 ATCATAACTATCGCTGTGTCT -s Anc2.Anc2refChr13 55193 21 + 96486 ATCATAACTATCACTGTGTCT -s mr.mrrefChr5 273771 21 + 294540 ATCATAACTATTGCCCTGTCT -s simCow_chr6.simCow.chr6 411042 21 + 602619 ATCACAACTAGCACTGTGTCC -s simDog_chr6.simDog.chr6 401774 21 + 593897 ACCATAACTATTATTGTGTCT -s simHuman_chr6.simHuman.chr6 406733 21 + 601863 ATCATAACTACCGCTGTGTCT -s simRat_chr6.simRat.chr6 427628 21 + 647215 ATCATAACTATTGCAATGTAT - -a -s simMouse_chr6.simMouse.chr6 421407 9 + 636262 TTTTCCAAA -s Anc0.Anc0refChr3 50792 9 + 222631 TTTTCCAAC -s Anc1.Anc1refChr6 81423 9 + 197743 TTTTCCAAC -s Anc2.Anc2refChr13 55214 9 + 96486 TTATCCAAC -s mr.mrrefChr5 273792 9 + 294540 TTTTCCAAA -s simCow_chr6.simCow.chr6 411063 9 + 602619 TTCTTCAAA -s simDog_chr6.simDog.chr6 401834 9 + 593897 TTAGCCAAC -s simHuman_chr6.simHuman.chr6 406754 9 + 601863 TTTTCCAAC -s simRat_chr6.simRat.chr6 427649 9 + 647215 TTTTCCAAA - -a -s simMouse_chr6.simMouse.chr6 421416 48 + 636262 GTTAGCATCATGTTTGCCAGGCAGCCCATGGGACAAACAGAATGTCTA -s Anc0.Anc0refChr3 50810 45 + 222631 ATTAGCATCACAGTTGCCAGGCAGTGCAGTG---CAACATAATGTTCA -s Anc1.Anc1refChr6 81441 45 + 197743 ATTAGCATCACAGTTGCCAGGCAGTGCAGTG---CAACATAATGTTCA -s Anc2.Anc2refChr13 55232 45 + 96486 ACTAGCATCACAGTTGCCAGGCAGTGCAGTG---CAATGTAATGTTCT -s mr.mrrefChr5 273801 48 + 294540 GTTAGCATCATGTTTGCCAGGCAGTCCATTGGACAAACAGAATGTTTA -s simCow_chr6.simCow.chr6 411081 45 + 602619 TGTAGCACTGGGGTTGCCAGGCAGTGCCGTG---CAGTGTATTATTCT -s simDog_chr6.simDog.chr6 401852 45 + 593897 ACTAAAATCACAGTGGCCACGCTGCACAGTA---CAATGTAATGTTCT -s simHuman_chr6.simHuman.chr6 406772 45 + 601863 ATTCGCATCACAGTTGCCAGGCAGTGTAGTG---CAACATAGTGTTCA -s simRat_chr6.simRat.chr6 427658 48 + 647215 GTTAACATCAGGTTTGTCGGGCAGTCCATTGGACAAACAGAATGTTAA - -a -s simMouse_chr6.simMouse.chr6 421464 9 + 636262 CCTCCTCCC -s Anc0.Anc0refChr3 50855 9 + 222631 CCTTCTCCC -s Anc1.Anc1refChr6 81486 9 + 197743 CCTTCTCCC -s Anc2.Anc2refChr13 55277 9 + 96486 CCTTCTCCC -s mr.mrrefChr5 273849 9 + 294540 CCTCCTCCC -s simCow_chr6.simCow.chr6 411140 9 + 602619 CCTTCTCTC -s simDog_chr6.simDog.chr6 401897 9 + 593897 CCTTCTCCC -s simHuman_chr6.simHuman.chr6 406817 9 + 601863 CCTTCTTCC -s simRat_chr6.simRat.chr6 427706 9 + 647215 CCTCTTCGC - -a -s simMouse_chr6.simMouse.chr6 421473 6 + 636262 CAACCA -s Anc0.Anc0refChr3 50864 6 + 222631 CAACGA -s Anc1.Anc1refChr6 81495 6 + 197743 CAACGA -s Anc2.Anc2refChr13 55286 6 + 96486 CAACGA -s mr.mrrefChr5 273858 6 + 294540 CAACCA -s simCow_chr6.simCow.chr6 411149 6 + 602619 CAACGA -s simDog_chr6.simDog.chr6 401906 3 + 593897 TCA--- -s simHuman_chr6.simHuman.chr6 406826 6 + 601863 CAACTA -s simRat_chr6.simRat.chr6 427718 6 + 647215 CAACCA - -a -s simMouse_chr6.simMouse.chr6 421479 64 + 636262 TCTGCATGATAATAGATGAGCCATATGAGTCAGTCCTATCTTCAGTTTTTGAGTACCAGAATGC -s Anc0.Anc0refChr3 50871 64 + 222631 TTTGCATGCTGCAATATAAGATGTTTGATTCAATCCTATCCCCAGTCTTTGAGCCCCAGAAAAC -s Anc1.Anc1refChr6 81502 64 + 197743 TTTGCATGCTGCAATATAAGATGTTTGATTCAATCCTATCCCCAGTCTTTGAGCCCCAGAAAAC -s Anc2.Anc2refChr13 55293 64 + 96486 TTTGTGTGTTACAATATAAGATGCTTGATTCAATCCTATCCCCAGTCTTTTGGCCCCAGAAAAC -s mr.mrrefChr5 273864 64 + 294540 TCTGCATGCTGATAGATAAGCTGTATGAGTCAATCCTATCTTCAGTTTTTGAGCACCAGAAAAC -s simCow_chr6.simCow.chr6 411156 64 + 602619 TTTGTGTGTTACAATATATGATGCTTGATTCAATCCTATCCCCAGTTTTGCGGCCCCAGGAAAC -s simDog_chr6.simDog.chr6 401909 61 + 593897 ---GTGTGTTACAATATAAGATGCTTGAGTCTATCCTCTCCCCAGGCTTTTGGCTCCAGAAAAC -s simHuman_chr6.simHuman.chr6 406833 64 + 601863 TTTGCATCCTGCAATATAAGATGTTTGATTCAATTGTATGCCCAGTCTTTGAGCCCCAGAAAAC -s simRat_chr6.simRat.chr6 427724 64 + 647215 TCTGTATGCTGATACATAAGCTGCATGAGTCAATCCTATCGTCAGTGTTTGAGCACCAGAAAAC - -a -s simMouse_chr6.simMouse.chr6 421543 3 + 636262 TAG -s Anc0.Anc0refChr3 50935 3 + 222631 TAG -s Anc1.Anc1refChr6 81566 3 + 197743 TAG -s Anc2.Anc2refChr13 55357 3 + 96486 CAG -s mr.mrrefChr5 273928 3 + 294540 TAG -s simCow_chr6.simCow.chr6 411220 3 + 602619 AAG -s simDog_chr6.simDog.chr6 401970 3 + 593897 CAG -s simHuman_chr6.simHuman.chr6 406900 3 + 601863 TAG -s simRat_chr6.simRat.chr6 427788 3 + 647215 TAG - -a -s simMouse_chr6.simMouse.chr6 421546 181 + 636262 GAGGAGTACCAGGCCATTCACATCTACATGCTCGTTACCTAGTGTTGTTTAGATTTTGCATAGCAAATCGTGCAAGCAAATCGTGCAAAGCACACATATCGGGGGATTTCATGCCTCAAGAGGTATACTAATTAACTTCCTAATTATCCAAGCACCGAGACCTGGAAATGAGGTTCCTCAA -s Anc0.Anc0refChr3 50938 91 + 222631 GGTGTATACCAGGCTATTTGCATC-----------TACCT--------------------------------------------------------TAAC---------------TCAATATGCTTGTT----AACTTCCCAGTTATTGGACCACTGAAACCCAGACAGG----TTCACAT -s Anc1.Anc1refChr6 81569 117 + 197743 GGTGTATACCAGGCTATTTGCATCAACATACTTGTTACCT--------------------------------------------------------TAACAGAGG-CTATTTGCATCAATATGCTTGTT---TAACTTCCCAGTTATTGGACCACTGAAACCCAGACAGG----TTCACAT -s Anc2.Anc2refChr13 55360 91 + 96486 GGTTTACACCAGGCTACTTGCATC-----------TGCCT--------------------------------------------------------CAAT---------------TCAATGTGCTTGTT----AACTTCCCAGTTATTGGACCACTGAAACCCAGGCAGG----TTCACAT -s mr.mrrefChr5 273931 168 + 294540 GAGGAGTACCAGGCCATTCACATCAACATGCTTGTTACCTAGTGTTGTTTAGATTTTGCATAGCAAATCGTGCAA-------------AGCACACATATCAGGGGATTTTTTGCATCAAGAGGTATACTAATTAACTTCCTAGTTATCCGAGCACCGAAACCTGGAAATGAGGTTCCTCAA -s simCow_chr6.simCow.chr6 411225 75 + 602619 GGTTTACACCAGGGTACTTGTAT--------------------------------------------------------------------------------------------------TACTTGTT----AACTTGCCAATTATTGGACCACTGAAACCCAGGAGAG----TTCAGAT -s simDog_chr6.simDog.chr6 401973 75 + 593897 GCT------CAGGCTACTTGCCTC-----------TGCCT--------------------------------------------------------CAAT---------------TCAATGTGCTTATT----AACTTCACAGTT----------TGAAACCCAGGCAGG----ATCACAT -s simHuman_chr6.simHuman.chr6 406903 117 + 601863 GGTGTATACCAGGCTATTTGCATCAACATACTTGTTAACT--------------------------------------------------------TCCCAGAGG-CTATTTGCATCAACATGCTTGTT---TAACTTCCCAGTTATTGGACCACTGAAACCCTTAGAGG----TTCACAT -s simRat_chr6.simRat.chr6 427791 168 + 647215 CAGGAGTACCAGACCATTCACATCAACATGCTTGTTACCTAATGTTGTTTAGATTTTGCATAGCAAATCGTGCAA-------------AGCACACATATCAGGGAATTTTTTGCATTGAGAAGTGTACTAATTAAATTCCTAGTTATCAGAGTACCGAAACCTGGAAATGAAGTTCCTCAA - -a -s simMouse_chr6.simMouse.chr6 421727 19 + 636262 TAAATGCCTGTTAATGTCA -s Anc0.Anc0refChr3 51029 16 + 222631 TA--TGCTTGCAA-CGTTG -s Anc1.Anc1refChr6 81686 17 + 197743 TA--TGCTTGCAAACGTTG -s Anc2.Anc2refChr13 55451 16 + 96486 CC--TGCTTGCAA-CATTG -s mr.mrrefChr5 274099 17 + 294540 TA--TGCCTGTTAACGTCA -s simCow_chr6.simCow.chr6 411300 7 + 602619 -----------AA-CCTCA -s simDog_chr6.simDog.chr6 402048 16 + 593897 CC--TGCTTGCAA-CATTG -s simHuman_chr6.simHuman.chr6 407037 17 + 601863 TA--TGCTGGGAAACGTTG -s simRat_chr6.simRat.chr6 427959 12 + 647215 TA-------TTGAGCTTCA - -a -s simMouse_chr6.simMouse.chr6 421746 9 + 636262 AATGGATGA -s Anc0.Anc0refChr3 51045 9 + 222631 AGTGGTTGA -s Anc1.Anc1refChr6 81703 9 + 197743 AGTGGTTGA -s Anc2.Anc2refChr13 55467 9 + 96486 AGTGGTTGA -s mr.mrrefChr5 274116 9 + 294540 AATGGATGA -s simCow_chr6.simCow.chr6 411307 9 + 602619 AGTGGCTGA -s simDog_chr6.simDog.chr6 402064 9 + 593897 AGTGGTTGA -s simHuman_chr6.simHuman.chr6 407056 9 + 601863 AGTGGGTGA -s simRat_chr6.simRat.chr6 427971 2 + 647215 CA------- - -a -s simMouse_chr6.simMouse.chr6 421755 5 + 636262 ATACT -s Anc0.Anc0refChr3 51055 5 + 222631 ATACT -s Anc1.Anc1refChr6 81713 5 + 197743 ATACT -s Anc2.Anc2refChr13 55477 5 + 96486 ATACT -s mr.mrrefChr5 274125 5 + 294540 ATACT -s simCow_chr6.simCow.chr6 411332 5 + 602619 ATACT -s simDog_chr6.simDog.chr6 402074 5 + 593897 ATACT -s simHuman_chr6.simHuman.chr6 407066 5 + 601863 ATACT -s simRat_chr6.simRat.chr6 427973 4 + 647215 ATAC- - -a -s simMouse_chr6.simMouse.chr6 421760 52 + 636262 TCCATTTGTAATTTCCACAGGTAAGTCGCTAACTTCCAGAATACCAATTAAG -s Anc0.Anc0refChr3 51067 52 + 222631 TCCATTTGTGATTTCCACAAGCAATTACCAAACTTCCAAAATACCAATTATG -s Anc1.Anc1refChr6 81725 52 + 197743 TCCATTTGTGATTTCCACAAGCAATTACCAAACTTCCAAAATACCAATTATG -s Anc2.Anc2refChr13 55489 52 + 96486 TCCATTCCTGATTTCCACAAGCAATTACCAAACTCCCAAAATACCAATTATG -s mr.mrrefChr5 274130 52 + 294540 TCCATTTGTGATTTCCACAGGCAAGTCGCTAACTTCCAAAATACCAATTATG -s simCow_chr6.simCow.chr6 411344 48 + 602619 TCTATTCATAATTCCCACAAGTAAGTTCAGA----CCAAAGTACCAATTACG -s simDog_chr6.simDog.chr6 402086 52 + 593897 TCCAATCCTGATTTCCATGAGCTATTAACAAACTCCCAGAATACCAATTATG -s simHuman_chr6.simHuman.chr6 407078 52 + 601863 TCCATTTGTGGTTTCCACAAGCAATTACTAAACTTCCGAAATACCAATTGTG -s simRat_chr6.simRat.chr6 427977 49 + 647215 ---ATTTGTGATTTCTGCAGGCAAGTCGCTAACTTCCAAAATACCAATTATG - -a -s simMouse_chr6.simMouse.chr6 421812 20 + 636262 TTTCGCCCTCATGATCTTCT -s Anc0.Anc0refChr3 51119 20 + 222631 TTCTGCCTCCATGATCCTAT -s Anc1.Anc1refChr6 81777 20 + 197743 TTCTGCCTCCATGATCCTAT -s Anc2.Anc2refChr13 55541 20 + 96486 TTCTGCCTCCATCATCCTAT -s mr.mrrefChr5 274182 20 + 294540 TTTTGCCTTCATGATCCTCT -s simCow_chr6.simCow.chr6 411392 20 + 602619 TTCAGCCTTCGTCATCCCAT -s simDog_chr6.simDog.chr6 402138 20 + 593897 TTTTGCCTCCATCATCTTAA -s simHuman_chr6.simHuman.chr6 407133 20 + 601863 TTCTGCCTCCATGATCCTAT -s simRat_chr6.simRat.chr6 428026 20 + 647215 TTTTGCCTTCATGATCCTCT - -a -s simMouse_chr6.simMouse.chr6 421832 42 + 636262 AAATTGGTTGGATCATCGCTTAAACTGGTTGGGCTGTTGAAG -s Anc0.Anc0refChr3 51139 20 + 222631 AAACGG----------------------TTAGTCTGTTAAAG -s Anc1.Anc1refChr6 81797 20 + 197743 AAACGG----------------------TTAGTCTGTTAAAG -s Anc2.Anc2refChr13 55561 20 + 96486 ACTTGG----------------------TTAGTCTGTTAACA -s mr.mrrefChr5 274202 42 + 294540 AAACTGGTTGGATCATCGCTTAAACTGGTTGGGCTGTTAAAG -s simCow_chr6.simCow.chr6 411413 20 + 602619 ACCGGG----------------------TTGGTCTGTCAACT -s simDog_chr6.simDog.chr6 402158 20 + 593897 ACTTGG----------------------TCAGTTTGCTAGCA -s simHuman_chr6.simHuman.chr6 407153 20 + 601863 AAACCG----------------------TTAGTCTGTTAAAG -s simRat_chr6.simRat.chr6 428046 42 + 647215 AAACTGGTTAGATCATCCTCTAAACTGGTTGGGCTGTTAAAG - -a -s simMouse_chr6.simMouse.chr6 421874 16 + 636262 ATAGCTCAGTGTGCTG -s Anc0.Anc0refChr3 51159 16 + 222631 GTAGCCCAGTGTAACA -s Anc1.Anc1refChr6 81817 16 + 197743 GTAGCCCAGTGTAACA -s Anc2.Anc2refChr13 55581 16 + 96486 GTAGCCAAGTGTAACA -s mr.mrrefChr5 274244 16 + 294540 ATAGCCCAGTGTACTG -s simCow_chr6.simCow.chr6 411433 16 + 602619 GTGGTTAAGCGCAACA -s simDog_chr6.simDog.chr6 402178 16 + 593897 GTAACCAAGTGTAGCA -s simHuman_chr6.simHuman.chr6 407173 16 + 601863 GGAGCCCCGTGTAACA -s simRat_chr6.simRat.chr6 428089 16 + 647215 ATAGCCCAGTGTATTG - -a -s simMouse_chr6.simMouse.chr6 421890 4 + 636262 TGTG -s Anc0.Anc0refChr3 51189 4 + 222631 TGCA -s Anc1.Anc1refChr6 81847 4 + 197743 TGCA -s Anc2.Anc2refChr13 55611 4 + 96486 TGCA -s mr.mrrefChr5 274274 4 + 294540 TGTG -s simCow_chr6.simCow.chr6 411481 4 + 602619 TGTA -s simDog_chr6.simDog.chr6 402208 4 + 593897 TGCA -s simHuman_chr6.simHuman.chr6 407203 4 + 601863 TGCA -s simRat_chr6.simRat.chr6 428119 4 + 647215 TGTG - -a -s simMouse_chr6.simMouse.chr6 421894 50 + 636262 GGGCCTTCAGACTTGATATAAGGGTCCTAACCTTGGCAATATCATGGAGT -s Anc0.Anc0refChr3 51193 49 + 222631 GGACTCTCTGACTTGAGATA-TGGTCCTAATATCTGCTGCATCATAAGCT -s Anc1.Anc1refChr6 81851 49 + 197743 GGACTCTCTGACTTGAGATA-TGGTCCTAATATCTGCTGCATCATAAGCT -s Anc2.Anc2refChr13 55615 49 + 96486 GGACTCTCTGACTTGAGATA-TGGTCCTAATATCTGCTGCACCATAAGCT -s mr.mrrefChr5 274278 49 + 294540 GGGCTTTCAGACTTGATATA-TGGTCCTAACCTCGGCAACATCATAAAGT -s simCow_chr6.simCow.chr6 411485 49 + 602619 GGACTCCTGGACTTGAGATA-GGGTCCTAATATCTGCTGCACTATATGCT -s simDog_chr6.simDog.chr6 402223 49 + 593897 GGACCCTCTAACTTGAGATA-TGGTCCTAATATCTGCTGCACCATGAACA -s simHuman_chr6.simHuman.chr6 407207 49 + 601863 GGATTCTCTGACTTGGGATA-TTACCCTAAGATCAGCTGCATCATAAGCT -s simRat_chr6.simRat.chr6 428123 49 + 647215 GGGCTTTTAGACTTGATGTA-TGGTCCTATCCTCGGCAACATCATAAAGT - -a -s simMouse_chr6.simMouse.chr6 421944 49 + 636262 ATATAATCTAACAACTCAATATGAAAGCTACACACCATTGAGTGACCAT -s Anc0.Anc0refChr3 51242 48 + 222631 A-ATACTCTAATAACACAAGGTTAACTCCACACAGTATTGAGTGACCAC -s Anc1.Anc1refChr6 81900 48 + 197743 A-ATACTCTAATAACACAAGGTTAACTCCACACAGTATTGAGTGACCAC -s Anc2.Anc2refChr13 55667 48 + 96486 A-ATACTCTAATGACACAAGGTTAACTCCACACAGTATTAAGTGTCCAC -s mr.mrrefChr5 274327 49 + 294540 ATATAATCTAACAACTCAATATTAACTCTACACACTATTGAGTGACCAT -s simCow_chr6.simCow.chr6 411537 45 + 602619 A-ATACTCTAT---CAAAATGTTAACTCCACACAGTATTAAGTGCTCAC -s simDog_chr6.simDog.chr6 402275 48 + 593897 A-ATACTCTAATGACGCAAGGTTAACTCTATGCAGTATCAAGTGTCCGC -s simHuman_chr6.simHuman.chr6 407256 48 + 601863 A-ATACCGTAGTAACACAAGGTTAACTCCACACAGTATTGAGTGAACAC -s simRat_chr6.simRat.chr6 428172 49 + 647215 ACATAATCTAACAACTCATTATTAACTCTGCACACTATTGAGTGACCAT - -a -s simMouse_chr6.simMouse.chr6 421993 77 + 636262 GCCTGCAGCATTGGTAACCAGCTGAGGTCTGTGATCAAACTGCTTGAACTTAGTGCCTTGTGGTTTCTAAGAGTAGC -s Anc0.Anc0refChr3 51290 77 + 222631 TCCTGCAGCATTGGTAACCAGCCAAGGAAGGTAATCAAAATGCTTGAACTTAGTGCCTTGTGGTTTCTAGGAGAAGC -s Anc1.Anc1refChr6 81948 77 + 197743 TCCTGCAGCATTGGTAACCAGCCAAGGAAGGTAATCAAAATGCTTGAACTTAGTGCCTTGTGGTTTCTAGGAGAAGC -s Anc2.Anc2refChr13 55715 77 + 96486 TCCCACAGCATTGGTAACCAGCCAAGGAGGGTAATCAAAATACTTAAACTTAGTGCCTTGTGGTTTCTAGGAGAAGC -s mr.mrrefChr5 274376 77 + 294540 GCCTGCAGCATTGGTAACCAGCTGAGGTATGTGATCAAAATGCTTGAACTTAGTGCCTTGTGGTTTCTAAGAGTAGC -s simCow_chr6.simCow.chr6 411582 77 + 602619 TTCCACAGCATTGGTAACCAGCCAAAGATGGTCAGCAAAATACTTAAACTTAGTGTTTTGTGGTTTCTAGGAAAAGC -s simDog_chr6.simDog.chr6 402323 77 + 593897 TCCCACATTTTTGGTTACCAGTCAAGAAGGGGAATCAAAATACTTAAACTTAGTGCCTTGTGGTTTCTAAGAGAAGC -s simHuman_chr6.simHuman.chr6 407304 76 + 601863 TCCTGCAGCATCAGTAGCCAGCCAGGGCAAGTACTCAAAATGCTTGAACTTAGTACCTTGTAGTTT-TAGCAGAAGG -s simRat_chr6.simRat.chr6 428224 77 + 647215 GCCTGCAGCATTGGTAACCACCTGAGTTACATGATCAAAATGCTTGAAGTTAGTGCCTTGTGGTTTCTAAGAGCAGC - -a -s simMouse_chr6.simMouse.chr6 422070 35 + 636262 ATATGAAATAGACATTTATCAATCAGTTAAAGGCC -s Anc0.Anc0refChr3 51367 35 + 222631 ATATGACATGGTCATTCATCAATATGTTAATGGAC -s Anc1.Anc1refChr6 82025 35 + 197743 ATATGACATGGTCATTCATCAATATGTTAATGGAC -s Anc2.Anc2refChr13 55792 35 + 96486 ATATGACATGGTCATTCACCAATATTTTAATGGAT -s mr.mrrefChr5 274453 35 + 294540 ATATGAAATAGTCATTTATCAATCAGTTAAAGGCC -s simCow_chr6.simCow.chr6 411659 35 + 602619 ATATGGCATGGTCATTCACCAATATTTTAATGGAT -s simDog_chr6.simDog.chr6 402400 30 + 593897 ATATGACATGGGCATTCACTA-----TTTCTGGAT -s simHuman_chr6.simHuman.chr6 407380 35 + 601863 ATATGACATGGTCATTCATCAATAGGTTAATGGAC -s simRat_chr6.simRat.chr6 428314 35 + 647215 ATATGAAATAGTCATTTATCAATGAGTTAAAGGCT - -a -s simMouse_chr6.simMouse.chr6 422105 83 + 636262 ATTGTGGCCATAATTGAGGTGGCCATGCAGATGAGCTAAGGGGAATGCTTTTACTCCTAAATAATAATGAATGTCTGCCTGCT -s Anc0.Anc0refChr3 51403 78 + 222631 ATCATGGCCACCATTGAGGTGGCTATGGAGATGATCTCAGTGGTGTACTTTTACCCCCAAATAATATTGACTATCGGC----- -s Anc1.Anc1refChr6 82061 83 + 197743 ATCATGGCCACCATTGAGGTGGCTATGGAGATGATCTCAGTGGTGTACTTTTACCCCCAAATAATATTGACTATCGGCCTGCT -s Anc2.Anc2refChr13 55828 78 + 96486 ATCATGGCCACCATTGAGGTGGCTATGGAGATGATCTCAGTGGTGTACTTTTACCCCCAAATAATATTGACTATTGGT----- -s mr.mrrefChr5 274488 83 + 294540 ATTGTGGCCACAATTGAGGTGGCCATGCAGATGAGCTAAGGGGTATACTTTTACTCCTAAATAATATTGAATGTCTGCCTGCT -s simCow_chr6.simCow.chr6 411695 78 + 602619 ACCATGGCCATCATTGAGTTAACTATGGAGAAGATCTCAGTGGTGTACTTTTACCCCCAAATAATATTGACTATTGGT----- -s simDog_chr6.simDog.chr6 402431 78 + 593897 ATCATGGCCACCATTGAGGTGGCTATGGAGATGATCCGAGCTGTGTACTTTTACCCCCAAGTAATATTGACTATTGGT----- -s simHuman_chr6.simHuman.chr6 407416 83 + 601863 ATCATGGCCACCATCCAGGAGGCTATGGGGATGATCTCATTGGTGTACTTTTACCCCCAAATAATGTTGACTATCGGCCTGCT -s simRat_chr6.simRat.chr6 428349 83 + 647215 ATTGTGGCCACAATTGAGGTGGCCATGCAGATGAGCCGAGGGGTACACTTGTACTCTGGAATAACATAGAATGTCTGCCTGCT - -a -s simMouse_chr6.simMouse.chr6 422188 31 + 636262 AGGTCTGTCAATTAGATGTCTATGTTACACA -s Anc0.Anc0refChr3 51481 21 + 222631 -A---------TTGGATGTGGATATTTGACC -s Anc1.Anc1refChr6 82144 22 + 197743 AA---------TTGGATGTGGATATTTGACC -s Anc2.Anc2refChr13 55906 21 + 96486 -A---------CTGGATGTGGATATTTGTCC -s mr.mrrefChr5 274571 31 + 294540 AAGTCTGTCAATTAGATGTCGATGTTACACA -s simCow_chr6.simCow.chr6 411773 21 + 602619 -A---------CTGGTTGTGGATATTTGTCT -s simDog_chr6.simDog.chr6 402509 21 + 593897 -A---------CTGAATGTGGATATTTGTCC -s simHuman_chr6.simHuman.chr6 407499 22 + 601863 AA---------TTGGCCCCAGATATTTGACT -s simRat_chr6.simRat.chr6 428433 31 + 647215 AAGTCTACCAATAAGATGTCGATGTCACACA - -a -s simMouse_chr6.simMouse.chr6 422219 6 + 636262 AACACA -s Anc0.Anc0refChr3 51502 6 + 222631 AACTCA -s Anc1.Anc1refChr6 82166 6 + 197743 AACTCA -s Anc2.Anc2refChr13 55927 6 + 96486 CACTCC -s mr.mrrefChr5 274602 6 + 294540 AACACA -s simCow_chr6.simCow.chr6 411795 6 + 602619 CACTCC -s simDog_chr6.simDog.chr6 402530 6 + 593897 CATTCC -s simHuman_chr6.simHuman.chr6 407521 6 + 601863 ACAGGA -s simRat_chr6.simRat.chr6 428464 6 + 647215 AACACA - -a -s simMouse_chr6.simMouse.chr6 422225 54 + 636262 CGCATACCTACCCTAATCTACATCATACCTACCCTAATCTGCATAGGGACATGA -s Anc0.Anc0refChr3 51508 37 + 222631 TGCACACCCAC-----------------CTACCCTATTCTGCATAGGGACATTG -s Anc1.Anc1refChr6 82172 37 + 197743 TGCACACCCAC-----------------CTACCCTATTCTGCATAGGGACATTG -s Anc2.Anc2refChr13 55938 37 + 96486 TGCACACACAC-----------------CTACCCTATTCTGCATAGGGACATTG -s mr.mrrefChr5 274608 50 + 294540 CGCATACCTACCC----CTACATCATACCTACCCTAATCTGCATAGGGACATGA -s simCow_chr6.simCow.chr6 411806 32 + 602619 TGCACACACAC-----------------CTATCATAGTCT-----GGGGCATTG -s simDog_chr6.simDog.chr6 402541 37 + 593897 TGCACACACAC-----------------CTACCCCATTCTGCATAGGGACATTG -s simHuman_chr6.simHuman.chr6 407527 32 + 601863 TGCACACCCAC-----------------CTACCCTATTCTGCATAGGTT----- -s simRat_chr6.simRat.chr6 428470 50 + 647215 CACATACCTACCC----CCGAATCATACCTACCTTAATCTGCATAGGGACATGA - -a -s simMouse_chr6.simMouse.chr6 422279 9 + 636262 GAAATAGTA -s Anc0.Anc0refChr3 51545 9 + 222631 GATATAGTA -s Anc1.Anc1refChr6 82209 9 + 197743 GATATAGTA -s Anc2.Anc2refChr13 55978 9 + 96486 GATATAGTA -s mr.mrrefChr5 274658 9 + 294540 GAAATAGTA -s simCow_chr6.simCow.chr6 411839 9 + 602619 GATAAAGCA -s simDog_chr6.simDog.chr6 402587 9 + 593897 GAAATAGTA -s simHuman_chr6.simHuman.chr6 407559 9 + 601863 GATATAGTA -s simRat_chr6.simRat.chr6 428520 9 + 647215 GAAATAGTA - -a -s simMouse_chr6.simMouse.chr6 422288 12 + 636262 TGCAATATATGT -s Anc0.Anc0refChr3 51554 12 + 222631 TGCAGTATGGGT -s Anc1.Anc1refChr6 82218 12 + 197743 TGCAGTATGGGT -s Anc2.Anc2refChr13 55987 12 + 96486 TGCAGTATGGGT -s mr.mrrefChr5 274667 12 + 294540 TGCAATATATGT -s simCow_chr6.simCow.chr6 411848 12 + 602619 TGCAGTATGGGT -s simDog_chr6.simDog.chr6 402603 12 + 593897 TGCAGTATAAGT -s simHuman_chr6.simHuman.chr6 407568 12 + 601863 TGCAGTATGGGT -s simRat_chr6.simRat.chr6 428529 12 + 647215 TGCAATATATGT - -a -s simMouse_chr6.simMouse.chr6 422300 54 + 636262 CCTGTAGCATGCTTATGACCACGCTGTCAAACTTTAATTACACTGCAGAGTAAA -s Anc0.Anc0refChr3 51566 54 + 222631 ATAGTAGGAGGCTTATGAGCATGCTATCAATTTTGAATTATGCTGAGGAATAAG -s Anc1.Anc1refChr6 82230 54 + 197743 ATAGTAGGAGGCTTATGAGCATGCTATCAATTTTGAATTATGCTGAGGAATAAG -s Anc2.Anc2refChr13 56000 54 + 96486 ATAGTAGGAGGCTTATGAGCATGCTATCACTTTTGAATTATGCTGAGGAATGGG -s mr.mrrefChr5 274679 54 + 294540 CCTGTAGCATGCTTATGACCATGCTGTCAATCTTTAATTACACTGCAGAGTAAA -s simCow_chr6.simCow.chr6 411861 40 + 602619 ATGGTAGAGGGGTTATGTGC--------------GGATTATGCTGATGAATGTG -s simDog_chr6.simDog.chr6 402616 54 + 593897 ATAGTAGGAGGCTAATGAGCATGCTATCACTTTTGAATTATGCTGAGAAATGGG -s simHuman_chr6.simHuman.chr6 407580 54 + 601863 ATCGTAGGAGGCTTATGAGCATGTCACCAATTTTAAATTATGCTAAGGAATAAG -s simRat_chr6.simRat.chr6 428541 54 + 647215 CCTGTAGTATGCTTATGATCATGCTGTCAATCTTTAATTACACTGCAAAGTAAA - -a -s simMouse_chr6.simMouse.chr6 422354 13 + 636262 CCTGCCCCTGCAT -s Anc0.Anc0refChr3 51620 8 + 222631 CCTCCCC-----T -s Anc1.Anc1refChr6 82284 13 + 197743 CCTCCCCCCACGT -s Anc2.Anc2refChr13 56054 8 + 96486 CCTCCCC-----T -s mr.mrrefChr5 274733 13 + 294540 CCTGCCCCCGCAT -s simCow_chr6.simCow.chr6 411918 8 + 602619 CCTCCCA-----T -s simDog_chr6.simDog.chr6 402670 8 + 593897 CCTCCCC-----T -s simHuman_chr6.simHuman.chr6 407634 13 + 601863 CCTCCCTCCACGT -s simRat_chr6.simRat.chr6 428595 13 + 647215 CCTGCCCCCCCCC - -a -s simMouse_chr6.simMouse.chr6 422367 3 + 636262 AGA -s Anc0.Anc0refChr3 51628 3 + 222631 AGA -s Anc1.Anc1refChr6 82297 3 + 197743 AGA -s Anc2.Anc2refChr13 56062 3 + 96486 AGA -s mr.mrrefChr5 274746 3 + 294540 AGA -s simCow_chr6.simCow.chr6 411926 3 + 602619 AGA -s simDog_chr6.simDog.chr6 402678 3 + 593897 AGA -s simHuman_chr6.simHuman.chr6 407647 3 + 601863 AGC -s simRat_chr6.simRat.chr6 428613 3 + 647215 AGA - -a -s simMouse_chr6.simMouse.chr6 422370 16 + 636262 ATTAATATCATACTGG -s Anc0.Anc0refChr3 51632 14 + 222631 ATTAATGTCAGACC-- -s Anc1.Anc1refChr6 82301 14 + 197743 ATTAATGTCAGACC-- -s Anc2.Anc2refChr13 56066 14 + 96486 ATTATTGTCAGACC-- -s mr.mrrefChr5 274749 16 + 294540 ATTAATATCATACTGG -s simCow_chr6.simCow.chr6 411930 14 + 602619 ATTAGTGTCAGACT-- -s simDog_chr6.simDog.chr6 402682 14 + 593897 ATTATTGTTAGGTC-- -s simHuman_chr6.simHuman.chr6 407651 14 + 601863 AACAATGTCAGACC-- -s simRat_chr6.simRat.chr6 428616 16 + 647215 GCTAATATCATACTGG - -a -s simMouse_chr6.simMouse.chr6 422386 82 + 636262 TTACAAGTGGGGTGAGAGGTAGGCACCCTTCTTTGCAGGATGCACACACCCAGCCAACAAAATGTGCGATTTTTTCATTTTG -s Anc0.Anc0refChr3 51646 82 + 222631 CCATAAGTGGGATGAGAGGTACGCTCCCCTCATTGCATGATGCACATACCCATCCAACAAAATGTATGTTTTTCCAATTTTG -s Anc1.Anc1refChr6 82315 82 + 197743 CCATAAGTGGGATGAGAGGTACGCTCCCCTCATTGCATGATGCACATACCCATCCAACAAAATGTATGTTTTTCCAATTTTG -s Anc2.Anc2refChr13 56080 82 + 96486 CCATAAGTGGGATGAGAGGTACGCTCGCCTTGATGCATGATGCACATGCCCATCTAACAAAATGTATGTTTTTCCAATTTCG -s mr.mrrefChr5 274765 82 + 294540 TTACAAGTGGGATGAGAGGTAGGCACCCTTCATTGCAGGATGCACACACCCAGCCAACAAAATGTGCGATTTTTTCATTTTG -s simCow_chr6.simCow.chr6 411944 72 + 602619 ----------GATGAGGGGTATGGTCTCCTTGATGCATGATGCACATGCTCAGTTAACAAAATATTTGATGTATCAGGTTCG -s simDog_chr6.simDog.chr6 402698 82 + 593897 CCATAAGTGGGTTGAGAAATACGCTCGCTTTGATGCATGATGCACCTGCCCATCTAAGAAAATGCATGTTTTTCCAATTTCA -s simHuman_chr6.simHuman.chr6 407665 82 + 601863 CCATAAGTGGGATGAGAGGTAAACTCCCCTCATTGCATGATGCACATATCTATCCACCAAAATGTATGGTTCTCCAATCTTG -s simRat_chr6.simRat.chr6 428632 67 + 647215 TTACAAGTGGGATCAGAGATAGGCACCCTTCATTACAGGATGCACACACCCAGCCAGCAAAATGTGC--------------- - -a -s simMouse_chr6.simMouse.chr6 422468 2 + 636262 CC -s Anc0.Anc0refChr3 51728 2 + 222631 CA -s Anc1.Anc1refChr6 82397 2 + 197743 CA -s Anc2.Anc2refChr13 56162 2 + 96486 CA -s mr.mrrefChr5 274847 2 + 294540 CC -s simCow_chr6.simCow.chr6 412046 2 + 602619 CA -s simDog_chr6.simDog.chr6 402780 2 + 593897 CA -s simHuman_chr6.simHuman.chr6 407747 2 + 601863 CA - -a -s simMouse_chr6.simMouse.chr6 422470 44 + 636262 TATCTTGGCTGTGCATCATCGTGAAAGGTGATCTTTCAATCGGG -s Anc0.Anc0refChr3 51731 44 + 222631 TGTATAGGCAGTGTGTCAGTGTGTAAGATGGTCTTCCAACAGGG -s Anc1.Anc1refChr6 82400 44 + 197743 TGTATAGGCAGTGTGTCAGTGTGTAAGATGGTCTTCCAACAGGG -s Anc2.Anc2refChr13 56165 44 + 96486 TGTATAGGCAATGTGCCAGTATGTGAGATGGTCTTCCAACAGGG -s mr.mrrefChr5 274849 44 + 294540 TATCTTGGCTGTGCATCATTGTGAAAGGTGATCTTTCAATCGGG -s simCow_chr6.simCow.chr6 412049 39 + 602619 CATGTAGGCTATGT-----TATGTGAGATGGCCTTCCCATGGAG -s simDog_chr6.simDog.chr6 402783 40 + 593897 TGTATAGGCAATGTGCCAGTATGTGAGATGGT----CACCAGGA -s simHuman_chr6.simHuman.chr6 407750 44 + 601863 TGTATAGGCCGTCTGTTAGTGTGCAAGCTAGTCTTCCAACAGGG -s simRat_chr6.simRat.chr6 428699 27 + 647215 ----------------CATTGTGAAAGATGATCTTT-AATTGAC - -a -s simMouse_chr6.simMouse.chr6 422514 17 + 636262 TTGTGGATTTAGGCATG -s Anc0.Anc0refChr3 51775 17 + 222631 TTGTTAGTTTGGGCATA -s Anc1.Anc1refChr6 82444 17 + 197743 TTGTTAGTTTGGGCATA -s Anc2.Anc2refChr13 56209 17 + 96486 TTGTTAGTTTGGGCATA -s mr.mrrefChr5 274893 17 + 294540 TTGTGGATTTAGGCATG -s simCow_chr6.simCow.chr6 412088 12 + 602619 TTGTTAGCTCGG----- -s simDog_chr6.simDog.chr6 402825 17 + 593897 TAGTTAGTTTGAGCATA -s simHuman_chr6.simHuman.chr6 407794 17 + 601863 TTGTTAGAGTGGGCATA -s simRat_chr6.simRat.chr6 428726 17 + 647215 TTGTGCATTTAGGCATG - -a -s simMouse_chr6.simMouse.chr6 422531 2 + 636262 TG -s Anc0.Anc0refChr3 51792 2 + 222631 TA -s Anc1.Anc1refChr6 82461 2 + 197743 TA -s Anc2.Anc2refChr13 56226 2 + 96486 TA -s mr.mrrefChr5 274910 2 + 294540 TG -s simCow_chr6.simCow.chr6 412100 2 + 602619 TA -s simDog_chr6.simDog.chr6 402843 2 + 593897 TA -s simHuman_chr6.simHuman.chr6 407811 2 + 601863 TA -s simRat_chr6.simRat.chr6 428743 2 + 647215 TG - -a -s simMouse_chr6.simMouse.chr6 422533 9 + 636262 CTAGGTGTC -s Anc0.Anc0refChr3 51797 9 + 222631 CCATTTATT -s Anc1.Anc1refChr6 82466 9 + 197743 CCATTTATT -s Anc2.Anc2refChr13 56231 9 + 96486 CCATTTATT -s mr.mrrefChr5 274912 9 + 294540 CCATGTGTC -s simCow_chr6.simCow.chr6 412105 9 + 602619 CCATCTCTT -s simDog_chr6.simDog.chr6 402848 9 + 593897 CTCTTTATT -s simHuman_chr6.simHuman.chr6 407816 9 + 601863 CCATTTTTT -s simRat_chr6.simRat.chr6 428745 9 + 647215 CCATGTGTC - -a -s simMouse_chr6.simMouse.chr6 422542 12 + 636262 TTAGATTAGAGG -s Anc0.Anc0refChr3 51806 12 + 222631 TGACTAAAGGGG -s Anc1.Anc1refChr6 82475 12 + 197743 TGACTAAAGGGG -s Anc2.Anc2refChr13 56240 12 + 96486 GGACTAAAGGGG -s mr.mrrefChr5 274921 12 + 294540 TTAGATTAGAGG -s simCow_chr6.simCow.chr6 412114 12 + 602619 TCATGAATTGGG -s simDog_chr6.simDog.chr6 402857 12 + 593897 GGACTAAAGGGG -s simHuman_chr6.simHuman.chr6 407825 3 + 601863 TGA--------- -s simRat_chr6.simRat.chr6 428782 12 + 647215 TTAGATTAAAGG - -a -s simMouse_chr6.simMouse.chr6 422554 11 + 636262 GAGATGTGACT -s Anc0.Anc0refChr3 51818 11 + 222631 AGGAGGCAAAA -s Anc1.Anc1refChr6 82487 11 + 197743 AGGAGGCAAAA -s Anc2.Anc2refChr13 56252 11 + 96486 AGGAGGCAAAA -s mr.mrrefChr5 274933 11 + 294540 GAGATGTGACT -s simCow_chr6.simCow.chr6 412126 11 + 602619 AGGGCGCAAGA -s simDog_chr6.simDog.chr6 402869 11 + 593897 AGGAGGCAAAA -s simRat_chr6.simRat.chr6 428798 11 + 647215 GAGATAGGACT - -a -s simMouse_chr6.simMouse.chr6 422565 98 + 636262 AACACACAAGTCAAATCAGGCTTAAGATTCCAATGAGAGTGGCTTGTATGTAAACACAAAGGCAAAACAGAGCACACCTGTCAGTGGAGTACATGTAT -s Anc0.Anc0refChr3 51829 98 + 222631 TGCATACCAATCAAGTGAGGCTCAAGATTTCAATAAAAGTAGTATGTATAGACAGACAAAGACAAATCAAAGGACATCTGTCTATGGGGTATATGTAT -s Anc1.Anc1refChr6 82498 98 + 197743 TGCATACCAATCAAGTGAGGCTCAAGATTTCAATAAAAGTAGTATGTATAGACAGACAAAGACAAATCAAAGGACATCTGTCTATGGGGTATATGTAT -s Anc2.Anc2refChr13 56263 98 + 96486 TGCATACCAATCAAGTGAGGCCCAAGATTTCAATAGAAGTAGTATATATAGACAGAAAAAGACAAATCAAAGGACATCTGTCTATGGGGTATATGTAA -s mr.mrrefChr5 274944 98 + 294540 AACACACAAGTCAAATCAGGCTCAAGATTCCAATGAGAGTGGCTTGTATATAAACACAAAGGCAAAACAGAGCACACCTGTCAGTGGGGTACATGTAT -s simCow_chr6.simCow.chr6 412139 98 + 602619 TGCATACCAATCAAGTGAGGCCCAAGATCTCAATACAGGTAGCATACATCAACAGAAAAAGACAGATTAAAGTACGTCTGTCTATGGGGTACATGAAA -s simDog_chr6.simDog.chr6 402880 98 + 593897 TGCATACCAATCAAATGAGGCCCAAGATTTCAATGGAAGTAGTATATATAGGCAGAAAAAAACAAATCAAAGGACATCTGACTATGGGGTATATGTAA -s simHuman_chr6.simHuman.chr6 407828 79 + 601863 ---ATATCAATCAAGTAAGGCTCAAGATTTCAATAAAAGCAGAATGTGTAGACAGACGCAG----------------TGATCTATGGGGTATACGTAT -s simRat_chr6.simRat.chr6 428809 98 + 647215 AACACACAAGTCAAATCAAGATCAAGCTGCTAATGAGATTGGCCTGTATATAAACACAAAAGCAAAACAGAGCACACCTGTTAGCAGGGTACATGTAT - -a -s simMouse_chr6.simMouse.chr6 422663 118 + 636262 CAAGCGCAAGCTTAGCTCGGCTACTTGGTACTTGGGCCCATAAGATGTCTCTACAACTGTTCCACCTAGCAAATTTTTAGGAAACAACTTGTGGCCATAAAACCATTGTAACAGAGTA -s Anc0.Anc0refChr3 51927 85 + 222631 ACAGA------TCAGCTCAGTTACTTG-------GGCCCATTAGATGTTTTTACAATTGTCTCA------------------AATGATTTGTAGCCATAA--TTAGTGTACCAGAGAA -s Anc1.Anc1refChr6 82596 85 + 197743 ACAGA------TCAGCTCAGTTACTTG-------GGCCCATTAGATGTTTTTACAATTGTCTCA------------------AATGATTTGTAGCCATAA--TTAGTGTACCAGAGAA -s Anc2.Anc2refChr13 56361 85 + 96486 ACAGA------TCAGCTCAGTTACTTG-------GGCCCAATAGATGTTTTTACAATTGTCTCA------------------AATGATTTGTAGCTGTAA--TCAGTGTACCAGAGAA -s mr.mrrefChr5 275042 110 + 294540 CAAGC------TTAGCTCGGCTACTTGGTACTTGGGCCCATAAGATGTCTTTACAATTGTCCCACCTAGCAAATTTTTAGGAAACAACTTGTGGCCATAA--TTATTGTAACAGAGTA -s simCow_chr6.simCow.chr6 412239 74 + 602619 ACAGA------TGAACTCAGTTACTTA-------G--------GATGATTTTACAATTGTCTCA------------------GATGATTTATATCT---A--TCAGTTTAACAGAGAA -s simDog_chr6.simDog.chr6 402978 85 + 593897 ATGGA------TCAGCTCAGTTACTTG-------GGCCCAATAAATGTTTTTACAACTATCTTA------------------AATGATTTGTAGCTGTAA--TCAGAGTACCAGGGAA -s simHuman_chr6.simHuman.chr6 407907 85 + 601863 ACAGA------TCACGTCAGTTACTTG-------GGTCCATTAGATGTTTTTACAATTGTCTCA------------------AATGATTTGCTGCCATAG--TTAGTGTAGCAGAGCA -s simRat_chr6.simRat.chr6 428907 107 + 647215 CAAGC------TTAGCCTCGCTACTTGGTACTTGGGCCCATAAGATCTCTTTACAATTGTCCCACCTATCAAATTTTTAGAAAACAA--TATGCCCATAA--TTGTTGTAACAGAG-A - -a -s simMouse_chr6.simMouse.chr6 422781 6 + 636262 CCGCTT -s Anc0.Anc0refChr3 52018 6 + 222631 CCACTT -s Anc1.Anc1refChr6 82687 6 + 197743 CCACTT -s Anc2.Anc2refChr13 56452 6 + 96486 CCACTT -s mr.mrrefChr5 275152 6 + 294540 CCGCTT -s simCow_chr6.simCow.chr6 412319 3 + 602619 CCA--- -s simDog_chr6.simDog.chr6 403069 6 + 593897 CCACTT -s simHuman_chr6.simHuman.chr6 407998 6 + 601863 CCACTT -s simRat_chr6.simRat.chr6 429014 6 + 647215 CTGCTT - -a -s simMouse_chr6.simMouse.chr6 422787 20 + 636262 ATAACTAGGAGCTAGCTAGT -s Anc0.Anc0refChr3 52024 18 + 222631 GTAGGTGGGGGCGAGCTA-- -s Anc1.Anc1refChr6 82693 18 + 197743 GTAGGTGGGGGCGAGCTA-- -s Anc2.Anc2refChr13 56458 18 + 96486 GTAGGTGGGGGTGGGCTA-- -s mr.mrrefChr5 275158 20 + 294540 ATAGCTAGGAGCTAGCTAGT -s simDog_chr6.simDog.chr6 403075 18 + 593897 GTAGGTGGGGGTGGGCTA-- -s simHuman_chr6.simHuman.chr6 408004 18 + 601863 GCAGGTGGGGACAAGCTA-- -s simRat_chr6.simRat.chr6 429024 20 + 647215 ATAGCTTGGAGCCAGCTCGT - -a -s simMouse_chr6.simMouse.chr6 422807 43 + 636262 ATTGGGACACTGGGCCATTTATTATTTAATAGGAACAGTTGAG -s Anc0.Anc0refChr3 52042 43 + 222631 ACTAGGATATTAGACTAGTTACTATTTACTAGAACCAGGTGAA -s Anc1.Anc1refChr6 82711 43 + 197743 ACTAGGATATTAGACTAGTTACTATTTACTAGAACCAGGTGAA -s Anc2.Anc2refChr13 56476 43 + 96486 ACTATGATGTTAAACTAGTTACTATTTATTAAATCCAGGTGAA -s mr.mrrefChr5 275178 43 + 294540 ATTGGGACACTGGGCCATTTATTATTTACTAGGAACAGGTGAG -s simDog_chr6.simDog.chr6 403095 43 + 593897 ACTATGATGTTAAACTAGTTACTATTTATTAAATCCAGGTGAA -s simHuman_chr6.simHuman.chr6 408022 43 + 601863 ACTAGGGTATAAGACTAGATACTATTTACTAGAACCAGGTGAA -s simRat_chr6.simRat.chr6 429044 42 + 647215 ATTGGGACAC-GGGCCATTTATTTTTTACTTGGAATAGGTGAG - -a -s simMouse_chr6.simMouse.chr6 422850 24 + 636262 TAGCTGAGCTTTTCTATATTTGTT -s Anc0.Anc0refChr3 52086 21 + 222631 TAAGTTTGCA---CTAAATTTAAT -s Anc1.Anc1refChr6 82755 21 + 197743 TAAGTTTGCA---CTAAATTTAAT -s Anc2.Anc2refChr13 56520 21 + 96486 TGAGTTTACA---CGAAATTTAAT -s mr.mrrefChr5 275221 24 + 294540 TAGCTGAGCTTTTCTATATTTGTT -s simDog_chr6.simDog.chr6 403139 21 + 593897 TGAGTTTACA---CGAAATTTAAT -s simHuman_chr6.simHuman.chr6 408066 21 + 601863 TACGTTTGCC---CTAAATTTAAT -s simRat_chr6.simRat.chr6 429086 24 + 647215 TAGCTGAGTTTTACTATATTTGTT - -a -s simMouse_chr6.simMouse.chr6 422874 32 + 636262 TGCATTTAGTATCATAACCTCTGGTTTGATCT -s Anc0.Anc0refChr3 52107 22 + 222631 GGAT----GAA------CAAAGGGATAGATCC -s Anc1.Anc1refChr6 82776 28 + 197743 GGAT----GAATTGCAACAAAGGGATAGATCC -s Anc2.Anc2refChr13 56541 22 + 96486 GAAT----GAA------CCAAGCGATAGATCC -s mr.mrrefChr5 275245 32 + 294540 TGCATTTAGTATTACAACATCTGGTTTGATCT -s simDog_chr6.simDog.chr6 403160 22 + 593897 GAAT----GAA------CCAAGCGATAGATCC -s simHuman_chr6.simHuman.chr6 408087 28 + 601863 GGAC----GAATTGCACCAAAAGGATGGATCC -s simRat_chr6.simRat.chr6 429114 32 + 647215 TGCAATTAGTATTACAACATCTAGTTTGATCT - -a -s simMouse_chr6.simMouse.chr6 422906 14 + 636262 CTCCCACAGTTCAC -s Anc0.Anc0refChr3 52138 14 + 222631 TTACGGCACTAAAT -s Anc1.Anc1refChr6 82813 14 + 197743 TTACGGCACTAAAT -s Anc2.Anc2refChr13 56572 14 + 96486 TTATGGTACTAAAT -s mr.mrrefChr5 275277 14 + 294540 CTACCACAGTTCAC -s simDog_chr6.simDog.chr6 403191 14 + 593897 TTATGGTACTAAAT -s simHuman_chr6.simHuman.chr6 408124 14 + 601863 TTACAGCCCTAAAT -s simRat_chr6.simRat.chr6 429146 14 + 647215 CTACCACAGTTTAC - -a -s simMouse_chr6.simMouse.chr6 422920 16 + 636262 CCGGGAAAATTGCAGT -s Anc0.Anc0refChr3 52155 11 + 222631 CCA-----AATGCAGG -s Anc1.Anc1refChr6 82830 16 + 197743 CCATAACAAATGCAGG -s Anc2.Anc2refChr13 56589 11 + 96486 CCA-----AATGCGGG -s mr.mrrefChr5 275291 16 + 294540 CCGGTAAATTTGCAGT -s simCow_chr6.simCow.chr6 412324 11 + 602619 CCA-----AATGTAGG -s simDog_chr6.simDog.chr6 403208 11 + 593897 CCA-----AATGCGGG -s simHuman_chr6.simHuman.chr6 408141 16 + 601863 CCATAACAAATATAGG -s simRat_chr6.simRat.chr6 429160 16 + 647215 CCAGTAAGTTTGCAGT - -a -s simMouse_chr6.simMouse.chr6 422936 12 + 636262 GCTGCATAAAAC -s Anc0.Anc0refChr3 52166 12 + 222631 ACCACATTGACT -s Anc1.Anc1refChr6 82846 12 + 197743 ACCACATTGACT -s Anc2.Anc2refChr13 56601 12 + 96486 ACCACATTGGCT -s mr.mrrefChr5 275307 12 + 294540 GCTGCATAAAAT -s simCow_chr6.simCow.chr6 412336 12 + 602619 ACCATATTGTTT -s simDog_chr6.simDog.chr6 403220 12 + 593897 ACCACATTGGCA -s simHuman_chr6.simHuman.chr6 408157 12 + 601863 ATCACATTGAGT -s simRat_chr6.simRat.chr6 429176 12 + 647215 GCTGCATAAAAT - -a -s simMouse_chr6.simMouse.chr6 422948 28 + 636262 ACTAAAGTCTGCAACATCAGCCTGCCAA -s Anc0.Anc0refChr3 52184 28 + 222631 AGTCAAGACTTCAACATTATCCTGCTCA -s Anc1.Anc1refChr6 82864 28 + 197743 AGTCAAGACTTCAACATTATCCTGCTCA -s Anc2.Anc2refChr13 56619 28 + 96486 AGTCAAGACTTCAACATTATCCTGCTCA -s mr.mrrefChr5 275319 28 + 294540 ACTAAAGTCTTCAACATTAGCCTGCCAA -s simCow_chr6.simCow.chr6 412354 26 + 602619 AGTCAAGACTTCAACATTAT--TGTTCA -s simDog_chr6.simDog.chr6 403238 28 + 593897 CGTCATGATTCCAACATTATCCTGCTCA -s simHuman_chr6.simHuman.chr6 408175 28 + 601863 AGTCAAGACTTCAACGTTATCCCTCTCA -s simRat_chr6.simRat.chr6 429188 21 + 647215 ACTAAAGTCTTCGACATTAGC------- - -a -s simMouse_chr6.simMouse.chr6 422976 32 + 636262 ACTTATTATCCCACACAGTCTCCAGTGTGATC -s Anc0.Anc0refChr3 52212 32 + 222631 ACAAAATATCCCACACAGTTTCCAGTGGGAAC -s Anc1.Anc1refChr6 82892 32 + 197743 ACAAAATATCCCACACAGTTTCCAGTGGGAAC -s Anc2.Anc2refChr13 56647 32 + 96486 ACAAAATATCCCACACAGTTTCCAATGGGAAC -s mr.mrrefChr5 275347 32 + 294540 ACTTAATATCCCACACAGTCTCCAGTGGGATC -s simCow_chr6.simCow.chr6 412380 32 + 602619 ACAAAATATACCACACTGCTTCCTATAAGAAA -s simDog_chr6.simDog.chr6 403280 32 + 593897 AAAAAATATCCCACACATTTTGCAATGGGAAC -s simHuman_chr6.simHuman.chr6 408203 32 + 601863 GCAAAATATCCCACACAGTTTCCAGTGGGAAC -s simRat_chr6.simRat.chr6 429209 30 + 647215 --TTAATATCCCATACAGTCTCTAGTGGGATC - -a -s simMouse_chr6.simMouse.chr6 423008 63 + 636262 TAGAGACACTGTTGGCTCCATCTTGTGGCTCATCAGTACAGATAAACAATAAAATGCTACACT -s Anc0.Anc0refChr3 52249 50 + 222631 CAGGAACCTTGTTG------CCTCCT----CATCGATAAGGATATGAAATAAGATGCTG---T -s Anc1.Anc1refChr6 82929 50 + 197743 CAGGAACCTTGTTG------CCTCCT----CATCGATAAGGATATGAAATAAGATGCTG---T -s Anc2.Anc2refChr13 56684 50 + 96486 CAGGAACCCTGTTG------CCTCCT----CATTGATAAGAATATGAAATATGATCCTA---T -s mr.mrrefChr5 275379 51 + 294540 TAGAGACATTGTTG------TCTTGT----CATCAGTACAGATAAACAATAAAATGCTGC--T -s simCow_chr6.simCow.chr6 412417 50 + 602619 CAGGAACCCTGTTG------ACTCAT----CCTTGATAGGACTATACAATATGATACTA---T -s simDog_chr6.simDog.chr6 403317 50 + 593897 CAGTAACTCTGTTG------CCTCCT----CATTGATAAGAACATGAAGTATGATCCTA---T -s simHuman_chr6.simHuman.chr6 408240 50 + 601863 CAGGAACCTTGTTG------CCTCTT----CATCGATAAGGATAGGTGATAAGATGCTG---T -s simRat_chr6.simRat.chr6 429239 51 + 647215 TAGAGACATTGTTG------TCTTGT----CATCAGTACAGATGAACAATAAAATTCTGC--T - -a -s simMouse_chr6.simMouse.chr6 423071 21 + 636262 TAAGCAAGTCCTCTGTGACTG -s Anc0.Anc0refChr3 52299 20 + 222631 TGACCAATCT-TAGTTGATTG -s Anc1.Anc1refChr6 82979 20 + 197743 TGACCAATCT-TAGTTGATTG -s Anc2.Anc2refChr13 56734 20 + 96486 TGACCAATCT-TAGTTGATTG -s mr.mrrefChr5 275430 20 + 294540 TAAGCAAGTC-TCTGTGACTG -s simCow_chr6.simCow.chr6 412469 20 + 602619 TGACAAATCT-TAGTTGGTTA -s simDog_chr6.simDog.chr6 403367 20 + 593897 TGACCAATCT-TGATTGATTG -s simHuman_chr6.simHuman.chr6 408290 10 + 601863 -----AACCA-TAGTT----- -s simRat_chr6.simRat.chr6 429290 20 + 647215 TAAGCAAGTC-TCTGTGACTG - -a -s simMouse_chr6.simMouse.chr6 423092 5 + 636262 GTGGA -s Anc0.Anc0refChr3 52319 2 + 222631 AC--- -s Anc1.Anc1refChr6 82999 2 + 197743 AC--- -s Anc2.Anc2refChr13 56754 2 + 96486 AC--- -s mr.mrrefChr5 275450 5 + 294540 GTGGA -s simCow_chr6.simCow.chr6 412489 2 + 602619 AC--- -s simDog_chr6.simDog.chr6 403389 2 + 593897 AC--- -s simRat_chr6.simRat.chr6 429310 5 + 647215 GTGGA - -a -s simMouse_chr6.simMouse.chr6 423097 64 + 636262 CCATTAATCTATTGACTCATCCCAGTGCAACACACATAGTCCCTGTAATTTGCACTAAGTGAGT -s Anc0.Anc0refChr3 52324 50 + 222631 TCATCC-TCTAATGTCTCATGT-------------ATTGTGCCCATGATATGCACCTAGTGAGC -s Anc1.Anc1refChr6 83004 50 + 197743 TCATCC-TCTAATGTCTCATGT-------------ATTGTGCCCATGATATGCACCTAGTGAGC -s Anc2.Anc2refChr13 56759 50 + 96486 TCATCC-TTTAATGTCTCATGT-------------ATTGTGCCCATAATATGCATCTAGTGAGT -s mr.mrrefChr5 275458 63 + 294540 CCATTA-TCTATTGACTCATGCCAGTGCAACACACATAGTCCCTGTGATTTGCACTAAGTGAGC -s simCow_chr6.simCow.chr6 412494 46 + 602619 TC-TTT-TTAATTGTCTCATGT-------------ATTGTGCCCACATTAAGCA---AGTGGGC -s simDog_chr6.simDog.chr6 403394 50 + 593897 TCATCC-TTTAATATCTTATGT-------------ATTGTGCCCATAATATGTATCTACTGAGT -s simHuman_chr6.simHuman.chr6 408300 48 + 601863 --ATCC-TCTAATGTCTCATGT-------------ATTGTGCCCATGATATGCACCCAGAGCGC -s simRat_chr6.simRat.chr6 429319 63 + 647215 CCGTTA-TTTATTGACTCATGCCAGTGAAGCACATTTAGTCTCTGTGATTTGCACTAGGTGAGC - -a -s simMouse_chr6.simMouse.chr6 423161 38 + 636262 TGATTGTACATGAAACCTCTCATAATCTCTCTGGTAAC -s Anc0.Anc0refChr3 52374 38 + 222631 TGATTGTACATGACCTCTCTCATAATGCCTCTGGCACA -s Anc1.Anc1refChr6 83054 38 + 197743 TGATTGTACATGACCTCTCTCATAATGCCTCTGGCACA -s Anc2.Anc2refChr13 56809 38 + 96486 TGATTGTACATCACCTCTCCCATAATGCCTCTGGCACA -s mr.mrrefChr5 275521 38 + 294540 TGATTGTACATGAAATCTCTCATAATCTCTCTGGTACC -s simCow_chr6.simCow.chr6 412540 38 + 602619 TGATTGTACACAACCCCTTCCACAATCCCTCTGCGTCA -s simDog_chr6.simDog.chr6 403444 36 + 593897 TGATTATACATCA--TCTCCCATAATGCCCCTGGCACA -s simHuman_chr6.simHuman.chr6 408352 38 + 601863 TGATTGTACATGACTTCTCTCATAATTCCTCTGGCACA -s simRat_chr6.simRat.chr6 429382 38 + 647215 TAATTGTGCATGAACTCTCTTATAATCACTCTGGTACC - -a -s simMouse_chr6.simMouse.chr6 423199 15 + 636262 AAAATAATTCCTACT -s Anc0.Anc0refChr3 52412 15 + 222631 CAAGCAACCCCTCCT -s Anc1.Anc1refChr6 83092 15 + 197743 CAAGCAACCCCTCCT -s Anc2.Anc2refChr13 56847 15 + 96486 CAAGCAACCCCCCCT -s mr.mrrefChr5 275559 15 + 294540 AAAATAACTCCTACT -s simCow_chr6.simCow.chr6 412579 15 + 602619 TAAGCAACCCCCTCT -s simDog_chr6.simDog.chr6 403480 15 + 593897 CAAGCCACCGCCCCT -s simHuman_chr6.simHuman.chr6 408390 15 + 601863 CAAGCAACCCCTCAT -s simRat_chr6.simRat.chr6 429420 15 + 647215 AAAATAACTCACACT - -a -s simMouse_chr6.simMouse.chr6 423214 24 + 636262 ACTAAGTGTGATCTGTGCATACAC -s Anc0.Anc0refChr3 52429 24 + 222631 ATCAAGTGGGGTTTTTGCATGCAC -s Anc1.Anc1refChr6 83109 24 + 197743 ATCAAGTGGGGTTTTTGCATGCAC -s Anc2.Anc2refChr13 56864 24 + 96486 ATCAAGTTGGGTTTTTGCATGAAC -s mr.mrrefChr5 275574 24 + 294540 ACCAAGTGTGATCTGTGCATACAC -s simCow_chr6.simCow.chr6 412596 22 + 602619 ATCAA--TGTGTTCTTGCATGAAC -s simDog_chr6.simDog.chr6 403497 24 + 593897 ATCAAGTTGGGTTTTTACATGAAC -s simHuman_chr6.simHuman.chr6 408407 24 + 601863 ATCAAGTGGGGTTATTGCATGCAC -s simRat_chr6.simRat.chr6 429435 24 + 647215 ACCAAGTGTGATCTGTGCATACAC - -a -s simMouse_chr6.simMouse.chr6 423238 4 + 636262 TAGT -s Anc0.Anc0refChr3 52453 3 + 222631 CAG- -s Anc1.Anc1refChr6 83133 4 + 197743 CAGT -s Anc2.Anc2refChr13 56888 3 + 96486 AAG- -s mr.mrrefChr5 275598 4 + 294540 CAGT -s simCow_chr6.simCow.chr6 412618 3 + 602619 AGG- -s simDog_chr6.simDog.chr6 403521 3 + 593897 AAG- -s simHuman_chr6.simHuman.chr6 408437 4 + 601863 CCAT -s simRat_chr6.simRat.chr6 429459 4 + 647215 CAGT - -a -s simMouse_chr6.simMouse.chr6 423242 52 + 636262 ACCTTATAGATGCCAACAATTGTGATCACCCATAGAAAGACAAAAGACTTAC -s Anc0.Anc0refChr3 52456 51 + 222631 ACCATACAGAT-CCAACAATTGGAATTACCTACAGAGCCCAAAGAAAAGACC -s Anc1.Anc1refChr6 83137 52 + 197743 ACCATACAGATTCCAACAATTGGAATTACCTACAGAGCCCAAAGAAAAGACC -s Anc2.Anc2refChr13 56891 51 + 96486 ACCATACAGAT-CTGGCCACTGGAATTCTGTATAGAGCCCAAGGAAAAGACT -s mr.mrrefChr5 275602 52 + 294540 ACCTTATAGATTCCAACAATTGGGATCACCTACAGAGAGACAAAAAACGTAC -s simCow_chr6.simCow.chr6 412622 13 + 602619 ATCATATAGAT-CT-------------------------------------- -s simDog_chr6.simDog.chr6 403524 51 + 593897 ACCAAACAGAT-CTGGCCACTGGAATTCTGTATAGAGCCCAAGGAAAAGACT -s simHuman_chr6.simHuman.chr6 408441 52 + 601863 ACCATACAGATTCCAACAATTGGAATTACCTACAGAGCCCAAAGAATTGACC -s simRat_chr6.simRat.chr6 429463 52 + 647215 ACCTTATAGATTCCAACAATCGGGATCACCTACAGAGAGACAAAAAACGTAC - -a -s simMouse_chr6.simMouse.chr6 423294 9 + 636262 CTGTTATGT -s Anc0.Anc0refChr3 52511 9 + 222631 CTGTTTAGT -s Anc1.Anc1refChr6 83193 9 + 197743 CTGTTTAGT -s Anc2.Anc2refChr13 56946 9 + 96486 CTGTTTAGT -s mr.mrrefChr5 275658 9 + 294540 CTGTTTTGT -s simCow_chr6.simCow.chr6 412636 9 + 602619 CTGTGGAGT -s simDog_chr6.simDog.chr6 403579 9 + 593897 CTATTTAGT -s simHuman_chr6.simHuman.chr6 408497 9 + 601863 CTGTTTAGT -s simRat_chr6.simRat.chr6 429519 9 + 647215 CTGTTTTGT - -a -s simMouse_chr6.simMouse.chr6 423303 25 + 636262 CCCCTCTTCTATATCGTGGGTTCAT -s Anc0.Anc0refChr3 52522 25 + 222631 CCCCTATTGTGTGTCGTAGGTCCAT -s Anc1.Anc1refChr6 83204 25 + 197743 CCCCTATTGTGTGTCGTAGGTCCAT -s Anc2.Anc2refChr13 56957 25 + 96486 CCCCTATTGTGTGTCATAGGTCCAT -s mr.mrrefChr5 275667 25 + 294540 CCCCTCTTCTATGTCGTAGGTTCAT -s simCow_chr6.simCow.chr6 412647 25 + 602619 CCCCTACTCTGTGTCATAGGTCCAT -s simDog_chr6.simDog.chr6 403590 25 + 593897 CCCCTATTGTATTTCATAGGTCTAT -s simHuman_chr6.simHuman.chr6 408508 25 + 601863 CCCCTGTTGTGTGCCGTAGATCCAT -s simRat_chr6.simRat.chr6 429528 20 + 647215 CCACTCTTCTAGGTCATAGG----- - -a -s simMouse_chr6.simMouse.chr6 423328 9 + 636262 AAAGACTAG -s Anc0.Anc0refChr3 52547 9 + 222631 AAATACTAG -s Anc1.Anc1refChr6 83229 9 + 197743 AAATACTAG -s Anc2.Anc2refChr13 56982 9 + 96486 AAATACTAG -s mr.mrrefChr5 275692 9 + 294540 AAAGACTAG -s simCow_chr6.simCow.chr6 412676 9 + 602619 AAATACTAG -s simDog_chr6.simDog.chr6 403615 9 + 593897 AAATACTGG -s simHuman_chr6.simHuman.chr6 408533 9 + 601863 AAATACTAG -s simRat_chr6.simRat.chr6 429548 7 + 647215 --GGACTAG - -a -s simMouse_chr6.simMouse.chr6 423337 16 + 636262 CACATGAGGACATAGA -s Anc0.Anc0refChr3 52557 16 + 222631 CACTTAATGACATAGG -s Anc1.Anc1refChr6 83239 16 + 197743 CACTTAATGACATAGG -s Anc2.Anc2refChr13 56992 16 + 96486 CACTTAATGACATAGG -s mr.mrrefChr5 275702 16 + 294540 CACATGAGGACATAGA -s simCow_chr6.simCow.chr6 412686 16 + 602619 GGCTTAAAGACATGGG -s simDog_chr6.simDog.chr6 403625 16 + 593897 CAATTCATGACATAAG -s simHuman_chr6.simHuman.chr6 408543 16 + 601863 CACTCAATGACATAGG -s simRat_chr6.simRat.chr6 429556 16 + 647215 CGGGTGAAGACATAGA - -a -s simMouse_chr6.simMouse.chr6 423353 19 + 636262 AGATGAGTACTGTACATTT -s Anc0.Anc0refChr3 52573 19 + 222631 AGATGGGTACCATAAATTT -s Anc1.Anc1refChr6 83255 19 + 197743 AGATGGGTACCATAAATTT -s Anc2.Anc2refChr13 57008 19 + 96486 AGATGGGTACCATAAATTT -s mr.mrrefChr5 275718 19 + 294540 AGATGAGTACTGTACATTT -s simCow_chr6.simCow.chr6 412703 19 + 602619 AGAGGGGTACCATAAATCT -s simDog_chr6.simDog.chr6 403641 19 + 593897 AGATGGATACCATCAATTG -s simHuman_chr6.simHuman.chr6 408559 19 + 601863 CAATGGGTAACAGAAATTT -s simRat_chr6.simRat.chr6 429572 19 + 647215 AGATGAGTATTGTACATTT - -a -s simMouse_chr6.simMouse.chr6 423372 1 + 636262 C -s Anc0.Anc0refChr3 52592 1 + 222631 C -s Anc1.Anc1refChr6 83274 1 + 197743 C -s Anc2.Anc2refChr13 57027 1 + 96486 C -s mr.mrrefChr5 275737 1 + 294540 C -s simCow_chr6.simCow.chr6 412722 1 + 602619 C -s simDog_chr6.simDog.chr6 403661 1 + 593897 A -s simHuman_chr6.simHuman.chr6 408578 1 + 601863 C -s simRat_chr6.simRat.chr6 429591 1 + 647215 C - -a -s simMouse_chr6.simMouse.chr6 423373 1 + 636262 C -s Anc0.Anc0refChr3 52593 1 + 222631 C -s Anc1.Anc1refChr6 83275 1 + 197743 C -s Anc2.Anc2refChr13 57028 1 + 96486 C -s mr.mrrefChr5 275738 1 + 294540 C -s simCow_chr6.simCow.chr6 412733 1 + 602619 C -s simDog_chr6.simDog.chr6 403662 1 + 593897 C -s simHuman_chr6.simHuman.chr6 408579 1 + 601863 C -s simRat_chr6.simRat.chr6 429592 1 + 647215 C - -a -s simMouse_chr6.simMouse.chr6 423374 33 + 636262 CATGTAATACATACCCAGCGAAGGAAGTCTGGT -s Anc0.Anc0refChr3 52598 28 + 222631 CAT-----ACATATCCAGCTAATGAAGTCTGAC -s Anc1.Anc1refChr6 83280 28 + 197743 CAT-----ACATATCCAGCTAATGAAGTCTGAC -s Anc2.Anc2refChr13 57033 28 + 96486 CAT-----CCATATCCAGGTAATGAAGTCTGAC -s mr.mrrefChr5 275739 28 + 294540 CAT-----ACATACCCAGCGAAGGAAGTCTGGT -s simCow_chr6.simCow.chr6 412738 28 + 602619 TCT-----TCCTATGCAGGGAATGAGGCCTCAC -s simDog_chr6.simDog.chr6 403667 28 + 593897 CAT-----CCAGATCCAGGTAATGAAGTCTGAC -s simHuman_chr6.simHuman.chr6 408584 28 + 601863 CAC-----ACATATCCAGCAGATGAAGTCCGAC -s simRat_chr6.simRat.chr6 429593 28 + 647215 CAT-----ACAAACTCAGTGAAGGAAGTTTGGT - -a -s simMouse_chr6.simMouse.chr6 423407 71 + 636262 ATAGGATTACAATCCCATTCATCCACCATGGGCCATCAGTCAACTCAACTGATCTGGTCTCAAATTAAACA -s Anc0.Anc0refChr3 52629 71 + 222631 ATAGAATTAAAATTTTATTTACCCACTACAGGCCATCAATCAAATCTTCACCACTGGTCATGAGGTAAAAA -s Anc1.Anc1refChr6 83311 71 + 197743 ATAGAATTAAAATTTTATTTACCCACTACAGGCCATCAATCAAATCTTCACCACTGGTCATGAGGTAAAAA -s Anc2.Anc2refChr13 57064 71 + 96486 ATAGAATTAATATTTTATTTACTCACTACAGACCATCAATCAAATCTTCAGCACTGGTCATGAGGTAAAAG -s mr.mrrefChr5 275767 71 + 294540 ATAGGATTACAATTCCATTCATCCACCACGGGCCATCAGTCAACTCAACTCATCTGGTCTCAAATTAAACA -s simCow_chr6.simCow.chr6 412769 67 + 602619 ATGGAATTA----TTTATTTATTTACTACACAGCATCAATCAAATCCTCAGGTCTGTTCAGGAATTAAGAT -s simDog_chr6.simDog.chr6 403698 70 + 593897 ATAGAATTAATATTTTG-TAACTCACTACAGACCATCATTCAAATTTCCAGCACCGGACATAAGGTAAAAG -s simHuman_chr6.simHuman.chr6 408615 71 + 601863 ATAGAACTAAAATTTTATTTACCCATTGCTGGCCATTAATCAAATCTTCACCCCTGGTCATGAGCTAAAAA -s simRat_chr6.simRat.chr6 429621 64 + 647215 ATAGGATTACAAGTCCGTTCATCCACCACAGGCCA-------ACTCAAATCAACTGATCTCAAATTAAATA - -a -s simMouse_chr6.simMouse.chr6 423478 11 + 636262 TAACTTGGCAG -s Anc0.Anc0refChr3 52700 11 + 222631 TAATTTCCCGC -s Anc1.Anc1refChr6 83382 11 + 197743 TAATTTCCCGC -s Anc2.Anc2refChr13 57135 11 + 96486 TAATTGGCCGC -s mr.mrrefChr5 275838 11 + 294540 TAACTTCGCAC -s simCow_chr6.simCow.chr6 412837 11 + 602619 TAATTGAGCAC -s simDog_chr6.simDog.chr6 403768 11 + 593897 TAATTGGCTGC -s simHuman_chr6.simHuman.chr6 408686 11 + 601863 TAATTTCCCGC -s simRat_chr6.simRat.chr6 429685 11 + 647215 TATCTTCGCAC - -a -s simMouse_chr6.simMouse.chr6 423489 11 + 636262 CCTCTAAGTAT -s Anc0.Anc0refChr3 52711 11 + 222631 CCTCTAAGTCC -s Anc1.Anc1refChr6 83393 11 + 197743 CCTCTAAGTCC -s Anc2.Anc2refChr13 57146 11 + 96486 CCTCCAAGCCC -s mr.mrrefChr5 275849 11 + 294540 CCTCTAAGTAT -s simCow_chr6.simCow.chr6 412848 11 + 602619 TCTCCAAGAGC -s simDog_chr6.simDog.chr6 403779 11 + 593897 CCTCCAAGCCC -s simHuman_chr6.simHuman.chr6 408710 11 + 601863 CCTCTAAGTGC -s simRat_chr6.simRat.chr6 429696 11 + 647215 CCTCTAAGTAT - -a -s simMouse_chr6.simMouse.chr6 423500 1 + 636262 C -s Anc0.Anc0refChr3 52722 1 + 222631 C -s Anc1.Anc1refChr6 83404 1 + 197743 C -s Anc2.Anc2refChr13 57157 1 + 96486 A -s mr.mrrefChr5 275860 1 + 294540 C -s simCow_chr6.simCow.chr6 412859 1 + 602619 C -s simDog_chr6.simDog.chr6 403790 1 + 593897 A -s simHuman_chr6.simHuman.chr6 408721 1 + 601863 C -s simRat_chr6.simRat.chr6 429762 1 + 647215 C - -a -s simMouse_chr6.simMouse.chr6 423501 8 + 636262 CTTTGTAC -s Anc0.Anc0refChr3 52723 8 + 222631 CGATGTAC -s Anc1.Anc1refChr6 83405 8 + 197743 CGATGTAC -s Anc2.Anc2refChr13 57158 8 + 96486 AGATGTAC -s mr.mrrefChr5 275861 8 + 294540 CTTTGTAC -s simCow_chr6.simCow.chr6 412860 8 + 602619 ACATGCAC -s simDog_chr6.simDog.chr6 403791 8 + 593897 AGATGTAC -s simHuman_chr6.simHuman.chr6 408730 8 + 601863 CAATGTAC -s simRat_chr6.simRat.chr6 429763 8 + 647215 CTTCTTAC - -a -s simMouse_chr6.simMouse.chr6 423509 55 + 636262 CAACCATTTGAAAGCTATAAAGCATGAACATTGCCAAAACTTTAAGAGAGACCTT -s Anc0.Anc0refChr3 52731 54 + 222631 AAACTATTTGAAAGATTCAGGGCATGAACATTGCCAGAA-TCTAAGGGAGACCTT -s Anc1.Anc1refChr6 83413 55 + 197743 AAACTATTTGAAAGATTCAGGGCATGAACATTGCCAGAAATCTAAGGGAGACCTT -s Anc2.Anc2refChr13 57166 54 + 96486 AAACTATTTAAAAGATTCAGGCTATGAACATTGCCAGTA-TCTGAGGGAGACCCT -s mr.mrrefChr5 275869 55 + 294540 CAACCATTTGAAAGCTATAAAGCATGAACATTGCCAAAACTTTAAGAGAGACCTT -s simCow_chr6.simCow.chr6 412868 33 + 602619 AAACCATTTAAAAGCTTTAGA----------------------GGGAGAGACCCT -s simDog_chr6.simDog.chr6 403799 54 + 593897 AAATTACTTAAAAGATTCAGGCTATGAACATTGCCAGTA-TCTGAGGGAGACCCT -s simHuman_chr6.simHuman.chr6 408738 55 + 601863 AAACTATTTGAAAGGTTCGGGGCACGAACATTGCCTGAAATCTAAGGGGGACCTT -s simRat_chr6.simRat.chr6 429779 12 + 647215 CTACCATCTGAG------------------------------------------- - -a -s simMouse_chr6.simMouse.chr6 423564 5 + 636262 AGACT -s Anc0.Anc0refChr3 52785 5 + 222631 GAACT -s Anc1.Anc1refChr6 83468 5 + 197743 GAACT -s Anc2.Anc2refChr13 57220 5 + 96486 GAACT -s mr.mrrefChr5 275924 5 + 294540 AGACT -s simCow_chr6.simCow.chr6 412901 5 + 602619 GAACT -s simDog_chr6.simDog.chr6 403875 5 + 593897 GAACT -s simHuman_chr6.simHuman.chr6 408793 5 + 601863 GAAAT - -a -s simMouse_chr6.simMouse.chr6 423569 39 + 636262 TAGGATGAGAGGCATCTGAACTGTGCTGTGACTCCACTT -s Anc0.Anc0refChr3 52790 39 + 222631 TAGGATGAGGGGCACCTGGACTGTGCTGAGACTCCACTT -s Anc1.Anc1refChr6 83473 39 + 197743 TAGGATGAGGGGCACCTGGACTGTGCTGAGACTCCACTT -s Anc2.Anc2refChr13 57225 39 + 96486 TGGCATGAGGGGCACCTGGACTTGGCTGAGACTCCACTT -s mr.mrrefChr5 275929 39 + 294540 TAGGATGAGAGGCATCTGAACTGTGCTGTGACTCCACTT -s simCow_chr6.simCow.chr6 412913 39 + 602619 GGGCACCTGGGGCACCTGGACTTAGCTGAGACTCTACTT -s simDog_chr6.simDog.chr6 403880 39 + 593897 TGGCATGAGGGGCCCCTGAACTTGGCTGAGACTCCACTT -s simHuman_chr6.simHuman.chr6 408798 39 + 601863 TAAGATGGGGGGCAACTGGACTGTGCTGAGACTCCAATT - -a -s simMouse_chr6.simMouse.chr6 423608 41 + 636262 GGGGCTGTTTAAGCATTACAATCAAGGATGGTAGATGGTGA -s Anc0.Anc0refChr3 52829 41 + 222631 GAGGCTGTTTAAGGATGACAATCAAGAATGGTAAAAGGTGA -s Anc1.Anc1refChr6 83512 41 + 197743 GAGGCTGTTTAAGGATGACAATCAAGAATGGTAAAAGGTGA -s Anc2.Anc2refChr13 57264 41 + 96486 GAGGCTGTTTAAAGATGATAATCAAGAATGGTAAAAGGTGA -s mr.mrrefChr5 275968 41 + 294540 GGGGCTGTTTAAGCATTACAATCAAGGATGGTAGATGGTGA -s simCow_chr6.simCow.chr6 412952 27 + 602619 GAGGCTGTT--------------AAGTATGGTAAAAGGTGA -s simDog_chr6.simDog.chr6 403920 41 + 593897 GGGGCTGTTTAAAGATGATAATCAAGAATGGTAAAAGGTGA -s simHuman_chr6.simHuman.chr6 408837 41 + 601863 GAGGCTCTTTAAGGATAACAATCAAGACTGGTAAAAGATCA - -a -s simMouse_chr6.simMouse.chr6 423649 20 + 636262 AGTAAGGAGCCTTTAAAATG -s Anc0.Anc0refChr3 52870 10 + 222631 AATGAGAAG----------G -s Anc1.Anc1refChr6 83553 10 + 197743 AATGAGAAG----------G -s Anc2.Anc2refChr13 57305 10 + 96486 AATGAGAAG----------G -s mr.mrrefChr5 276009 10 + 294540 AGTAAGGAG----------G -s simCow_chr6.simCow.chr6 412982 10 + 602619 GATGAGAAG----------A -s simDog_chr6.simDog.chr6 403961 10 + 593897 AGTGAGAAG----------G -s simHuman_chr6.simHuman.chr6 408878 10 + 601863 AATGAGAAG----------G - -a -s simMouse_chr6.simMouse.chr6 423669 1 + 636262 A -s Anc0.Anc0refChr3 52880 1 + 222631 A -s Anc1.Anc1refChr6 83563 1 + 197743 A -s Anc2.Anc2refChr13 57323 1 + 96486 G -s mr.mrrefChr5 276019 1 + 294540 A -s simCow_chr6.simCow.chr6 412999 1 + 602619 G -s simDog_chr6.simDog.chr6 403981 1 + 593897 G -s simHuman_chr6.simHuman.chr6 408888 1 + 601863 A - -a -s simMouse_chr6.simMouse.chr6 423670 48 + 636262 TGTTATTAATCTAAGTGGGGCAATGGTTGTGTAGATATAGGATGAACA -s Anc0.Anc0refChr3 52881 47 + 222631 TGGTATTAATCTATG-GGAGAGAGGGGGGTGTAGATATAGGAGGAGCA -s Anc1.Anc1refChr6 83564 47 + 197743 TGGTATTAATCTATG-GGAGAGAGGGGGGTGTAGATATAGGAGGAGCA -s Anc2.Anc2refChr13 57324 47 + 96486 TGGTATTAATCTATG-GGAGAGAGGGGGGTGTGGATAAAGGAGGAGCA -s mr.mrrefChr5 276020 47 + 294540 TGTTATTAATCTAAG-GGGGCAATGGTTGTGTAGATATAGGATGAACA -s simCow_chr6.simCow.chr6 413000 44 + 602619 TGGTATTAATCTGTG-GGAGAGAGGGGGATATGGATA---GAGGAGCA -s simDog_chr6.simDog.chr6 403982 47 + 593897 TGCTATCAATCTATG-TGAGAGAGGGGGGTGTGGATAAAGGAGGAGAA -s simHuman_chr6.simHuman.chr6 408890 47 + 601863 TGGTATTAATCTACG-GGAGAGAGGGGGGTGTAGATATGCAAGGAGCA -s simRat_chr6.simRat.chr6 429791 5 + 647215 -------------------------------------------GAACA - -a -s simMouse_chr6.simMouse.chr6 423718 8 + 636262 TCCTCTAC -s Anc0.Anc0refChr3 52968 8 + 222631 TCATCCAC -s Anc1.Anc1refChr6 83651 8 + 197743 TCATCCAC -s Anc2.Anc2refChr13 57411 8 + 96486 TGATCCAC -s mr.mrrefChr5 276067 8 + 294540 TCCTCTAC -s simCow_chr6.simCow.chr6 413084 8 + 602619 TTGTCTGC -s simDog_chr6.simDog.chr6 404069 8 + 593897 TGATCCAC -s simHuman_chr6.simHuman.chr6 408977 8 + 601863 TCATCAGA -s simRat_chr6.simRat.chr6 429796 8 + 647215 TCCTCTAC - -a -s simMouse_chr6.simMouse.chr6 423726 24 + 636262 CCAGTATTGTGTCGTGGTCATCAT -s Anc0.Anc0refChr3 52976 24 + 222631 CAAAAATTGTATTGTGGTTATCAG -s Anc1.Anc1refChr6 83659 24 + 197743 CAAAAATTGTATTGTGGTTATCAG -s Anc2.Anc2refChr13 57420 24 + 96486 CAAAAATTGTATTATGGTTATCAG -s mr.mrrefChr5 276075 24 + 294540 CCAGTATTGTATTGTGGTTATCAT -s simCow_chr6.simCow.chr6 413093 23 + 602619 CAAAAATTGTATT-TGATTATCAG -s simDog_chr6.simDog.chr6 404078 24 + 593897 CAAAAATCATACTATGGTCATAAG -s simHuman_chr6.simHuman.chr6 408985 24 + 601863 CACCAACTGTATTGTGGTTATCAG -s simRat_chr6.simRat.chr6 429804 24 + 647215 ACAGTATTGTATTATGGTTATCAT - -a -s simMouse_chr6.simMouse.chr6 423750 4 + 636262 GTGG -s Anc0.Anc0refChr3 53000 4 + 222631 GGGG -s Anc1.Anc1refChr6 83683 4 + 197743 GGGG -s Anc2.Anc2refChr13 57444 4 + 96486 GGGG -s mr.mrrefChr5 276099 4 + 294540 GTGG -s simCow_chr6.simCow.chr6 413116 4 + 602619 GTGG -s simDog_chr6.simDog.chr6 404103 4 + 593897 AGGG -s simHuman_chr6.simHuman.chr6 409009 4 + 601863 GGGG -s simRat_chr6.simRat.chr6 429828 4 + 647215 GTGG - -a -s simMouse_chr6.simMouse.chr6 423754 18 + 636262 ACTCACCATGATGCATAG -s Anc0.Anc0refChr3 53004 18 + 222631 ACTCACTGTGACATAAAA -s Anc1.Anc1refChr6 83687 18 + 197743 ACTCACTGTGACATAAAA -s Anc2.Anc2refChr13 57448 18 + 96486 ACTCACTGTGACATAAAA -s mr.mrrefChr5 276103 18 + 294540 ACTCACCATGATGCACAG -s simCow_chr6.simCow.chr6 413133 18 + 602619 ACTGACTGTGACGGAATG -s simDog_chr6.simDog.chr6 404107 18 + 593897 ACTCACTGTGACATAAAA -s simHuman_chr6.simHuman.chr6 409013 13 + 601863 ACTCATACCAACA----- -s simRat_chr6.simRat.chr6 429832 18 + 647215 ACTCACTATGATGCACAG - -a -s simMouse_chr6.simMouse.chr6 423772 1 + 636262 T -s Anc0.Anc0refChr3 53022 1 + 222631 T -s Anc1.Anc1refChr6 83705 1 + 197743 T -s Anc2.Anc2refChr13 57479 1 + 96486 T -s mr.mrrefChr5 276121 1 + 294540 T -s simCow_chr6.simCow.chr6 413164 1 + 602619 T -s simDog_chr6.simDog.chr6 404142 1 + 593897 T -s simRat_chr6.simRat.chr6 429850 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 423773 1 + 636262 A -s Anc0.Anc0refChr3 53023 1 + 222631 A -s Anc1.Anc1refChr6 83706 1 + 197743 A -s Anc2.Anc2refChr13 57480 1 + 96486 A -s mr.mrrefChr5 276122 1 + 294540 A -s simCow_chr6.simCow.chr6 413165 1 + 602619 A -s simDog_chr6.simDog.chr6 404143 1 + 593897 A -s simRat_chr6.simRat.chr6 429861 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 423774 41 + 636262 CATCAAAGCCAGTCATCTCCAACAGTCAAATTGCCTAATCT -s Anc0.Anc0refChr3 53024 41 + 222631 CATAAGGGCCAGTCATGTGTAACAGTAAAATTGTGTACACT -s Anc1.Anc1refChr6 83707 41 + 197743 CATAAGGGCCAGTCATGTGTAACAGTAAAATTGTGTACACT -s Anc2.Anc2refChr13 57481 41 + 96486 CATAAGGGCCTATCATGTGTAACAGTAATATTGTGTACAAT -s mr.mrrefChr5 276123 41 + 294540 CATCAAAGCCAGTCATGTGCAACAGTAAAATTGTCTAATCT -s simCow_chr6.simCow.chr6 413166 31 + 602619 CATAAAGGCCCCTCATGTGTTACA----------GTACAAT -s simDog_chr6.simDog.chr6 404152 41 + 593897 CATAAGTGCCTAACATGTGTAACAGTAATATTGTGTATAAT -s simHuman_chr6.simHuman.chr6 409026 36 + 601863 -----TGGCCAGTCGTGTGTAACAGTAAAACTGTGTACACT -s simRat_chr6.simRat.chr6 429862 41 + 647215 AATCAAAGCCAGTCATGTGCTACAGTAATATTGTCTAATCT - -a -s simMouse_chr6.simMouse.chr6 423815 24 + 636262 TACTCCTTGTCTGCAAGAACATTC -s Anc0.Anc0refChr3 53068 24 + 222631 TACCGCTCATCTCCTGGAGTGCTC -s Anc1.Anc1refChr6 83751 24 + 197743 TACCGCTCATCTCCTGGAGTGCTC -s Anc2.Anc2refChr13 57525 24 + 96486 TACCGTTCATCTCCTGGAGTGCTC -s mr.mrrefChr5 276164 24 + 294540 TACTCCTTGTCTGCAAGAACACTC -s simCow_chr6.simCow.chr6 413200 23 + 602619 TGCTG-TCATCTCCTGGAGTGCTC -s simDog_chr6.simDog.chr6 404196 24 + 593897 TATCGTTCCTCTCCTAGAGTGTTC -s simHuman_chr6.simHuman.chr6 409065 24 + 601863 TACAGCTCATCTTCTGGTGTGCTT -s simRat_chr6.simRat.chr6 429903 24 + 647215 TACTCCTTGTCTGCCAGACCACTC - -a -s simMouse_chr6.simMouse.chr6 423839 55 + 636262 CTCTAACATCCTGATAGATTTAAATTCCTTACGAGACATCACGTTGTGTTGTATT -s Anc0.Anc0refChr3 53096 55 + 222631 CTCTAACATCCTGACACATGTATATTTCTTACTAGAGATCATGTTGTCTTGTATT -s Anc1.Anc1refChr6 83779 55 + 197743 CTCTAACATCCTGACACATGTATATTTCTTACTAGAGATCATGTTGTCTTGTATT -s Anc2.Anc2refChr13 57553 55 + 96486 CTCTAACATCATGACACATGTATATTTCTTACTAGAGGTCATGTTGTCTTGTACC -s mr.mrrefChr5 276188 55 + 294540 CTCTAACATCCTGATAGATTTAAATTCCTTACGAGACATCATGTTGTGTTGTATT -s simCow_chr6.simCow.chr6 413227 55 + 602619 CTCTGACATCTTGACACATTGATATTTCTTACTAGAGGGCATGTTATCTTGTACC -s simDog_chr6.simDog.chr6 404224 55 + 593897 CTCTAATATCATGACACATGTTTATTTCTTACTATAAGTCATATTGTCTTGTACC -s simHuman_chr6.simHuman.chr6 409093 55 + 601863 CTCTAACATCCTGACACATCTATATTTCTTACAAGAGAACTTGTTGCCTCGTATT -s simRat_chr6.simRat.chr6 429927 55 + 647215 CTCTAACATCCTGATAGGTTTAACTTCCTTCCGAGACAGCATATTGTGGTGTATT - -a -s simMouse_chr6.simMouse.chr6 423894 13 + 636262 CTCCTTTTGGAAC -s Anc0.Anc0refChr3 53152 13 + 222631 CTTCTTTAAGAAC -s Anc1.Anc1refChr6 83835 13 + 197743 CTTCTTTAAGAAC -s Anc2.Anc2refChr13 57609 13 + 96486 CATCTTTAAGAAC -s mr.mrrefChr5 276243 13 + 294540 CTCCTTTAGGAAC -s simCow_chr6.simCow.chr6 413283 13 + 602619 CATCTTTAAGAAT -s simDog_chr6.simDog.chr6 404280 13 + 593897 CACCTATACGAAC -s simHuman_chr6.simHuman.chr6 409149 13 + 601863 CTTCTTTAAGAAT -s simRat_chr6.simRat.chr6 429982 13 + 647215 CCCCTTTAGGAAC - -a -s simMouse_chr6.simMouse.chr6 423907 9 + 636262 AATGTATGA -s Anc0.Anc0refChr3 53165 6 + 222631 ---CAATGA -s Anc1.Anc1refChr6 83848 9 + 197743 AACCAATGA -s Anc2.Anc2refChr13 57622 6 + 96486 ---CAGTGC -s mr.mrrefChr5 276256 9 + 294540 AATGTATGA -s simCow_chr6.simCow.chr6 413296 6 + 602619 ---GACTGT -s simDog_chr6.simDog.chr6 404293 6 + 593897 ---CAGAGC -s simHuman_chr6.simHuman.chr6 409170 9 + 601863 AACTAATGA -s simRat_chr6.simRat.chr6 429995 9 + 647215 AATGTATGG - -a -s simMouse_chr6.simMouse.chr6 423916 27 + 636262 CTGAACCTGCACACCCTGCATGTGGCA -s Anc0.Anc0refChr3 53176 27 + 222631 CCAGATCCACAAACTATGCTGGATGCA -s Anc1.Anc1refChr6 83862 27 + 197743 CCAGATCCACAAACTATGCTGGATGCA -s Anc2.Anc2refChr13 57633 27 + 96486 CCAGATCCACAAACTATGCTGGATGCA -s mr.mrrefChr5 276265 27 + 294540 CTGAACCTGCACACCCTGCAAGTGGCA -s simCow_chr6.simCow.chr6 413307 27 + 602619 CCAGATGCACAAACTAAGCTGTATGCA -s simDog_chr6.simDog.chr6 404304 27 + 593897 CCAGGCCCACAAACTATGCTGGATGCA -s simHuman_chr6.simHuman.chr6 409184 27 + 601863 CCAGATCCACAAATTATGCTGCCTGCA -s simRat_chr6.simRat.chr6 430004 27 + 647215 CTGAACCTACAAGCTCTGCAAGTGTTA - -a -s simMouse_chr6.simMouse.chr6 423943 27 + 636262 ATGCTACAAGCTGATTGAGTACCTTAC -s Anc0.Anc0refChr3 53203 13 + 222631 ATA--------------GTCACCTTAT -s Anc1.Anc1refChr6 83889 13 + 197743 ATA--------------GTCACCTTAT -s Anc2.Anc2refChr13 57677 13 + 96486 ATA--------------GTCACCTTAT -s mr.mrrefChr5 276292 27 + 294540 ATGCTACAAGTTGATTGATCACCTTAC -s simCow_chr6.simCow.chr6 413351 13 + 602619 AGA--------------GTCACCTCAT -s simDog_chr6.simDog.chr6 404348 13 + 593897 ATA--------------GTTACCTTAT -s simHuman_chr6.simHuman.chr6 409211 13 + 601863 ATA--------------GTCACTTTAT -s simRat_chr6.simRat.chr6 430031 27 + 647215 ATGCTGCAAGTTGATTGATCATCTTAC - -a -s simMouse_chr6.simMouse.chr6 423970 37 + 636262 ATCTTTAGTGAAGTGCAGACTTTTTTTAGTCTTCATG -s Anc0.Anc0refChr3 53217 32 + 222631 ACCA--GGTGAGATGCTG-CTTTTCT-AGTCT-CATG -s Anc1.Anc1refChr6 83903 32 + 197743 ACCA--GGTGAGATGCTG-CTTTTCT-AGTCT-CATG -s Anc2.Anc2refChr13 57691 32 + 96486 ACCA--GGTGAGATGCTG-CTTTTCT-AGTTT-CCTG -s mr.mrrefChr5 276319 35 + 294540 ACCATTAGTGAAATGCAG-CTTTTTTTAGTCT-CATG -s simCow_chr6.simCow.chr6 413365 32 + 602619 ACCA--GGGGAGATCCTG-CTTTTCC-AGTGT-CCTG -s simDog_chr6.simDog.chr6 404362 32 + 593897 ACCA--GGTGAAGTGCTG-CTTTTCT-AGTTT-CCTG -s simHuman_chr6.simHuman.chr6 409225 25 + 601863 ACCA--GGTAAGATGGTG-GTTT-------CT-CA-G -s simRat_chr6.simRat.chr6 430058 35 + 647215 ACCATGAGTGAAATGTGG-CTTTTTTTAGTCC-CATA - -a -s simMouse_chr6.simMouse.chr6 424007 21 + 636262 CTGAAAACCATCACTATAAAG -s Anc0.Anc0refChr3 53249 21 + 222631 CAGAAAACCCTCCCTATAGAG -s Anc1.Anc1refChr6 83935 21 + 197743 CAGAAAACCCTCCCTATAGAG -s Anc2.Anc2refChr13 57724 21 + 96486 CAGAAACCCCTCCCTATAGAG -s mr.mrrefChr5 276354 21 + 294540 CTGAAAACCCTCACTATAAAG -s simCow_chr6.simCow.chr6 413398 21 + 602619 CAGATAGCCCTCCCTACACAG -s simDog_chr6.simDog.chr6 404395 21 + 593897 CAGAAACCCCTCCCTATAGAG -s simHuman_chr6.simHuman.chr6 409250 21 + 601863 CAAAAAACCCTCCATCTAGAG -s simRat_chr6.simRat.chr6 430093 21 + 647215 CTGACAACCCTCACTATAAAG - -a -s simMouse_chr6.simMouse.chr6 424028 6 + 636262 TTTTTA -s Anc0.Anc0refChr3 53272 6 + 222631 TCTTTG -s Anc1.Anc1refChr6 83958 6 + 197743 TCTTTG -s Anc2.Anc2refChr13 57747 6 + 96486 TCCTTG -s mr.mrrefChr5 276375 6 + 294540 TCTTTA -s simCow_chr6.simCow.chr6 413421 6 + 602619 TCCTTG -s simDog_chr6.simDog.chr6 404434 6 + 593897 TCCTTG -s simHuman_chr6.simHuman.chr6 409273 6 + 601863 TCTTTG -s simRat_chr6.simRat.chr6 430114 6 + 647215 TCTTTA - -a -s simMouse_chr6.simMouse.chr6 424034 10 + 636262 CTAGACACAG -s Anc0.Anc0refChr3 53278 10 + 222631 AAAGACACTG -s Anc1.Anc1refChr6 83964 10 + 197743 AAAGACACTG -s Anc2.Anc2refChr13 57753 10 + 96486 AAAGACACTG -s mr.mrrefChr5 276381 10 + 294540 CTAGACACAG -s simCow_chr6.simCow.chr6 413470 10 + 602619 AAATACATTG -s simDog_chr6.simDog.chr6 404440 10 + 593897 AAAGATACTG -s simHuman_chr6.simHuman.chr6 409279 10 + 601863 TGAGACACTG -s simRat_chr6.simRat.chr6 430120 10 + 647215 ATAGACACAG - -a -s simMouse_chr6.simMouse.chr6 424044 12 + 636262 TACATATATAAG -s Anc0.Anc0refChr3 53293 12 + 222631 TATAGATATAAG -s Anc1.Anc1refChr6 83979 12 + 197743 TATAGATATAAG -s Anc2.Anc2refChr13 57768 12 + 96486 TATAGATATAAG -s mr.mrrefChr5 276391 12 + 294540 TACATATATAAG -s simCow_chr6.simCow.chr6 413485 12 + 602619 TATAGATATAAC -s simDog_chr6.simDog.chr6 404455 12 + 593897 TATACATATAAG -s simHuman_chr6.simHuman.chr6 409294 12 + 601863 TATAGACATAAG -s simRat_chr6.simRat.chr6 430130 12 + 647215 TAAATATACAAG - -a -s simMouse_chr6.simMouse.chr6 424056 21 + 636262 ATGAACAACATAAACAAAGCA -s Anc0.Anc0refChr3 53305 21 + 222631 ATGAACCACAAAAACAAAGCA -s Anc1.Anc1refChr6 83991 21 + 197743 ATGAACCACAAAAACAAAGCA -s Anc2.Anc2refChr13 57780 21 + 96486 ATGAACCACAAAAACAAAGCA -s mr.mrrefChr5 276403 21 + 294540 ATGAACCACATAAACAAAGCA -s simCow_chr6.simCow.chr6 413497 14 + 602619 ATTAACCAC-------AATTG -s simDog_chr6.simDog.chr6 404467 21 + 593897 ATGAACCAGAAAAACAAAGCA -s simHuman_chr6.simHuman.chr6 409308 21 + 601863 ATGAGCCACGAAAAGAAGGCA -s simRat_chr6.simRat.chr6 430142 21 + 647215 CTGGACCACATAAACAAAGGA - -a -s simMouse_chr6.simMouse.chr6 424077 8 + 636262 CCAACTAA -s Anc0.Anc0refChr3 53326 8 + 222631 CCAAATGT -s Anc1.Anc1refChr6 84012 8 + 197743 CCAAATGT -s Anc2.Anc2refChr13 57806 8 + 96486 CCAAATGT -s mr.mrrefChr5 276424 8 + 294540 CCAACTAA -s simCow_chr6.simCow.chr6 413516 8 + 602619 CCTGACGT -s simDog_chr6.simDog.chr6 404493 8 + 593897 TCAAATGT -s simHuman_chr6.simHuman.chr6 409329 8 + 601863 CCAAATGT -s simRat_chr6.simRat.chr6 430163 8 + 647215 CCGAGTAC - -a -s simMouse_chr6.simMouse.chr6 424085 19 + 636262 GGTCTCGCATCATGACCTG -s Anc0.Anc0refChr3 53340 19 + 222631 GTTCCAGTATCATGGCCTG -s Anc1.Anc1refChr6 84026 19 + 197743 GTTCCAGTATCATGGCCTG -s Anc2.Anc2refChr13 57820 19 + 96486 ATTCCAGTATCATGGGCCA -s mr.mrrefChr5 276437 19 + 294540 GGTCTCGTATCATGGCCTG -s simCow_chr6.simCow.chr6 413530 19 + 602619 ATTCCCGTACCATGGGACA -s simDog_chr6.simDog.chr6 404507 19 + 593897 AGTCCAGTATAATGGGCCA -s simHuman_chr6.simHuman.chr6 409343 19 + 601863 GTTCCAGTATCATGGCCTG -s simRat_chr6.simRat.chr6 430176 19 + 647215 GGTCTGGTGTCATGGCCTG - -a -s simMouse_chr6.simMouse.chr6 424104 4 + 636262 CATA -s Anc0.Anc0refChr3 53367 4 + 222631 CAGG -s Anc1.Anc1refChr6 84053 4 + 197743 CAGG -s Anc2.Anc2refChr13 57847 4 + 96486 CAGG -s mr.mrrefChr5 276456 4 + 294540 CATG -s simCow_chr6.simCow.chr6 413557 4 + 602619 CATG -s simDog_chr6.simDog.chr6 404534 4 + 593897 CAGG -s simHuman_chr6.simHuman.chr6 409370 4 + 601863 CAGG -s simRat_chr6.simRat.chr6 430195 4 + 647215 CATG - -a -s simMouse_chr6.simMouse.chr6 424108 1 + 636262 C -s Anc0.Anc0refChr3 53375 1 + 222631 C -s Anc1.Anc1refChr6 84061 1 + 197743 C -s Anc2.Anc2refChr13 57855 1 + 96486 C -s mr.mrrefChr5 276460 1 + 294540 C -s simCow_chr6.simCow.chr6 413565 1 + 602619 C -s simDog_chr6.simDog.chr6 404542 1 + 593897 C -s simHuman_chr6.simHuman.chr6 409378 1 + 601863 C -s simRat_chr6.simRat.chr6 430199 1 + 647215 C - -a -s simMouse_chr6.simMouse.chr6 424109 24 + 636262 ATTCCCAAAAATAGGTGATGTTGG -s Anc0.Anc0refChr3 53377 23 + 222631 ATCCCCAAAGGCAG-TGATGTCAG -s Anc1.Anc1refChr6 84063 23 + 197743 ATCCCCAAAGGCAG-TGATGTCAG -s Anc2.Anc2refChr13 57857 23 + 96486 ATCCCCAAAGGCAG-TGATGTCAA -s mr.mrrefChr5 276462 23 + 294540 ATCCCCAAAAATAG-TGATGTTGG -s simCow_chr6.simCow.chr6 413567 23 + 602619 CTCCCCCAAGGCAG-TAATGCCAA -s simDog_chr6.simDog.chr6 404544 20 + 593897 ATCCCCAAAGGCAG-TGATGT--- -s simHuman_chr6.simHuman.chr6 409380 23 + 601863 ATCCCCAAAGGCAG-TGAAATCAG -s simRat_chr6.simRat.chr6 430201 23 + 647215 ATCCCCACAAATAG-TGATGTTGG - -a -s simMouse_chr6.simMouse.chr6 424133 35 + 636262 CTATTGCCTTCTTGTGTCTATTCTGCCCTCATCTT -s Anc0.Anc0refChr3 53404 35 + 222631 CTATTGCTATTCTGTGTCATCTCTACTTTCTTCTT -s Anc1.Anc1refChr6 84090 35 + 197743 CTATTGCTATTCTGTGTCATCTCTACTTTCTTCTT -s Anc2.Anc2refChr13 57884 35 + 96486 CCATTGCTATTCTGTGTGATTTCTACTTTCTTCTT -s mr.mrrefChr5 276485 35 + 294540 CTATTGCTTTTTTGTGTCTTCTCTGCCCTCTTCTT -s simCow_chr6.simCow.chr6 413594 34 + 602619 CCATTGCTAATC-GTGTGATTCCTTCTTACTTCTT -s simDog_chr6.simDog.chr6 404568 35 + 593897 CCATCACTATTGTATGTGGTTTCTACCTTCTTCTT -s simHuman_chr6.simHuman.chr6 409407 35 + 601863 CTATTGCTATTCTGTATCATCTCTACTTTCTTCTT -s simRat_chr6.simRat.chr6 430224 35 + 647215 CTATTGCTTTTTGGCGTCTTCTCTGCCCTCTTCTT - -a -s simMouse_chr6.simMouse.chr6 424168 19 + 636262 ATTCTTGGTCCACACTCAA -s Anc0.Anc0refChr3 53439 13 + 222631 TATCATGT------CTTAA -s Anc1.Anc1refChr6 84125 13 + 197743 TATCATGT------CTTAA -s Anc2.Anc2refChr13 57919 13 + 96486 TATCATCT------CTTAA -s mr.mrrefChr5 276520 19 + 294540 ATTCTTGTTCCACACTCAA -s simCow_chr6.simCow.chr6 413628 13 + 602619 TATCCTCT------CTTAC -s simDog_chr6.simDog.chr6 404609 13 + 593897 TATCATCT------CTTAA -s simHuman_chr6.simHuman.chr6 409442 13 + 601863 CGACAAGT------CTTAT -s simRat_chr6.simRat.chr6 430259 19 + 647215 ATTCTTGTTCCACACTCAA - -a -s simMouse_chr6.simMouse.chr6 424187 93 + 636262 TAGCTTGCCAACCAATTCTTTCACAGGTATTGTCAACTTCCAACGGTTAGTCAATGGAACACTGGTCAAAATAGCACTTTAATAGCAGTTCAA -s Anc0.Anc0refChr3 53464 91 + 222631 TAGCTTGTCAACTGGTTCTTTCACAGGTTCTGTCAGCGTACAAAAGCGATTCAAGGTGACA-GGGTTTCATCAGAGC-CCAATAGCTGTTCAA -s Anc1.Anc1refChr6 84150 91 + 197743 TAGCTTGTCAACTGGTTCTTTCACAGGTTCTGTCAGCGTACAAAAGCGATTCAAGGTGACA-GGGTTTCATCAGAGC-CCAATAGCTGTTCAA -s Anc2.Anc2refChr13 57944 91 + 96486 TAGTTTGTCAACTGGCTCTTTCACAGGTTCTCTCAGTGTACAAAAGCGATGCAAGGTGACA-GGGTTTCATCAGAGC-CCTATAGCTGTTCAA -s mr.mrrefChr5 276551 93 + 294540 TAGCTTGTCAACCAATTCTTTCACAGGTATTGTCAACTTCCAACGGTTAGTCAATGGAACACTGGTCAAAATAGCACTCTAATAGCAGTTCAA -s simCow_chr6.simCow.chr6 413653 91 + 602619 TAGTTTGTCAATTGACTCTTTCACAGGTTCTCTCAGCATCCAAACGCAATACAAGTATACA-GTGTATAATTGGAGC-CCCATAGATGCGCAA -s simDog_chr6.simDog.chr6 404634 87 + 593897 TGGTTTGCCAACTGG----TTCACAGGTTCTCTCAGTGTACAAAAGTGATGCAAGGTGACA-GGGTTTCTTCAGAGA-CCTGCCACTGTTTGA -s simHuman_chr6.simHuman.chr6 409467 81 + 601863 CAACTTGTCAACTGGTTCCTTCACTGGTTCTGTCAGCG----------ATTTGAGGTGAGA-GAGTTTCATCAGAGC-CAAATAGCTATTCAA -s simRat_chr6.simRat.chr6 430290 85 + 647215 TAGTGTGTCAACCAATTCTTTCACAGGTGTTGTCAACATCCAACAGTAAGTCCATGGAACACTGAGCAAAAAAGCAGTCCAACAG-------- - -a -s simMouse_chr6.simMouse.chr6 424280 12 + 636262 AGCACAATACTA -s Anc0.Anc0refChr3 53556 12 + 222631 AGAATAGTACTA -s Anc1.Anc1refChr6 84242 12 + 197743 AGAATAGTACTA -s Anc2.Anc2refChr13 58036 12 + 96486 GGAACAGTAATA -s mr.mrrefChr5 276644 12 + 294540 AGCATAATACTA -s simCow_chr6.simCow.chr6 413745 12 + 602619 GTGACAGTAACA -s simDog_chr6.simDog.chr6 404722 12 + 593897 GGAACAGTAATA -s simHuman_chr6.simHuman.chr6 409549 12 + 601863 AGAATAGTACTG -s simRat_chr6.simRat.chr6 430375 9 + 647215 ---ATAATACTA - -a -s simMouse_chr6.simMouse.chr6 424292 12 + 636262 TATTTTTTAACA -s Anc0.Anc0refChr3 53570 12 + 222631 CATTCTATAGCT -s Anc1.Anc1refChr6 84256 12 + 197743 CATTCTATAGCT -s Anc2.Anc2refChr13 58050 12 + 96486 AATTCTATAGCT -s mr.mrrefChr5 276656 12 + 294540 CATTTTTTAACA -s simCow_chr6.simCow.chr6 413759 12 + 602619 ACTTCTATAACA -s simDog_chr6.simDog.chr6 404736 12 + 593897 AATCCTGTAGCT -s simHuman_chr6.simHuman.chr6 409563 12 + 601863 CATTCTATGGCG -s simRat_chr6.simRat.chr6 430384 12 + 647215 CATTTTTTAACA - -a -s simMouse_chr6.simMouse.chr6 424304 41 + 636262 AAGTCAAATACTATGTCTTTGAACATCTAGGGCTTTGAACA -s Anc0.Anc0refChr3 53582 20 + 222631 GAGTCAAGTACTATG---------------------GAAGA -s Anc1.Anc1refChr6 84268 20 + 197743 GAGTCAAGTACTATG---------------------GAAGA -s Anc2.Anc2refChr13 58062 20 + 96486 GAATCAAGTACTATG---------------------CCAGA -s mr.mrrefChr5 276668 41 + 294540 AAGTCAAGTACTATGTCTTTGAACATCTAGGGCTTTGAACA -s simCow_chr6.simCow.chr6 413771 19 + 602619 TATTCAAGTACTAT----------------------TCACA -s simDog_chr6.simDog.chr6 404748 20 + 593897 GAATCAAGTACTATG---------------------CCAGA -s simHuman_chr6.simHuman.chr6 409589 20 + 601863 CAGTCAAGTACTATG---------------------GACGA -s simRat_chr6.simRat.chr6 430396 41 + 647215 AAGTCGGGTCCTATGCCTTTGAACATCTATGGCTTTGAACA - -a -s simMouse_chr6.simMouse.chr6 424345 11 + 636262 TTGAACTGGCC -s Anc0.Anc0refChr3 53602 11 + 222631 TTGAACCAGCC -s Anc1.Anc1refChr6 84288 11 + 197743 TTGAACCAGCC -s Anc2.Anc2refChr13 58082 11 + 96486 TTGTACCAGCC -s mr.mrrefChr5 276709 11 + 294540 TTGAACTGGCC -s simCow_chr6.simCow.chr6 413790 11 + 602619 CAGTACCAGCC -s simDog_chr6.simDog.chr6 404773 11 + 593897 TTGTACTAACC -s simHuman_chr6.simHuman.chr6 409609 11 + 601863 TTGAACCAGCC -s simRat_chr6.simRat.chr6 430437 11 + 647215 TTGAACTGGCC - -a -s simMouse_chr6.simMouse.chr6 424356 58 + 636262 TAAGCCCTGACATCTGTGATAGCCCTAGCCATGCAAAATAATCCAAGCTTGTGGTGCA -s Anc0.Anc0refChr3 53613 54 + 222631 TAGCACC----AACTGGGCTAGCCCTAACCAGGCAGAATAACCAAAGCTCTTGATACA -s Anc1.Anc1refChr6 84299 54 + 197743 TAGCACC----AACTGGGCTAGCCCTAACCAGGCAGAATAACCAAAGCTCTTGATACA -s Anc2.Anc2refChr13 58094 54 + 96486 TAGCACC----AACTGGGCTAGCCCTAACCAGGCAGAATAACCAAAGTTCTTGATACA -s mr.mrrefChr5 276720 58 + 294540 TAAGCCCTGACATCTGTGATAGCCCTAGCCATGCAAAATAATCCAAGCTTGTGGTACA -s simCow_chr6.simCow.chr6 413802 52 + 602619 TAGCACC----AACTGGG--AGCCCTAACCAAGCAGAATAACCCAAGATCCCGATACA -s simDog_chr6.simDog.chr6 404785 54 + 593897 TAACATC----AACTGGGCTAGGACTAGCCAGGCAGAATACCCAAAGTTCTTGATACA -s simHuman_chr6.simHuman.chr6 409620 53 + 601863 TAGCACC----AACTGGGCTAGCCCTAACTAGGTGGTATGACCAAAACTCTTG-TACA -s simRat_chr6.simRat.chr6 430448 58 + 647215 AGAGCCCTGGCATCTGTGATAGCCTTTGCCACACAAAATAATCCAAGTTTGGGGTACA - -a -s simMouse_chr6.simMouse.chr6 424414 20 + 636262 TGGCAATAGGATCCTCATCT -s Anc0.Anc0refChr3 53667 20 + 222631 TGGCAGTGGCATCCTAATCT -s Anc1.Anc1refChr6 84353 20 + 197743 TGGCAGTGGCATCCTAATCT -s Anc2.Anc2refChr13 58148 20 + 96486 TGGCAGTGGCATTTTAATCT -s mr.mrrefChr5 276778 20 + 294540 TGGCAGTGGGATCCTCATCT -s simCow_chr6.simCow.chr6 413856 20 + 602619 GGGCAGTGGCATTTTAATCT -s simDog_chr6.simDog.chr6 404839 19 + 593897 TGGCAGTGACATTTT-ATCC -s simHuman_chr6.simHuman.chr6 409673 20 + 601863 TGACAGTGGCATCCTAATCT -s simRat_chr6.simRat.chr6 430506 20 + 647215 TGGCAGTGGGATCCTTATCT - -a -s simMouse_chr6.simMouse.chr6 424434 10 + 636262 GTGATACTCT -s Anc0.Anc0refChr3 53691 10 + 222631 GAGACACTTT -s Anc1.Anc1refChr6 84377 10 + 197743 GAGACACTTT -s Anc2.Anc2refChr13 58172 10 + 96486 GAGACACCTT -s mr.mrrefChr5 276798 10 + 294540 GTGACACTCT -s simCow_chr6.simCow.chr6 413880 10 + 602619 GAGACGCTTC -s simDog_chr6.simDog.chr6 404862 10 + 593897 GAGACACCTT -s simHuman_chr6.simHuman.chr6 409697 10 + 601863 GAGACCCTTT -s simRat_chr6.simRat.chr6 430526 10 + 647215 GTGACACTCT - -a -s simMouse_chr6.simMouse.chr6 424444 4 + 636262 GATC -s Anc0.Anc0refChr3 53701 4 + 222631 GATT -s Anc1.Anc1refChr6 84387 4 + 197743 GATT -s Anc2.Anc2refChr13 58183 4 + 96486 GATT -s mr.mrrefChr5 276808 4 + 294540 GATC -s simCow_chr6.simCow.chr6 413891 4 + 602619 GATT -s simDog_chr6.simDog.chr6 404873 4 + 593897 GACT -s simHuman_chr6.simHuman.chr6 409707 4 + 601863 GATT -s simRat_chr6.simRat.chr6 430536 4 + 647215 AATC - -a -s simMouse_chr6.simMouse.chr6 424448 189 + 636262 AGTGACCCCTTTGGACCTGGGATGAAGGGTGTCGTGTCCTTCTAAAGGTGCTTGCAATCAGATGACAGCATGTGAAGTGGGCACATGAGCCAGGCAGGGTCCTCCTACAGGTGCCTGTAATCACTTGAGAGCGCATAAGTGGGGCCGGCTCAGAGCCACGCACTAACCATGTGCACATGGCCACATTTG -s Anc0.Anc0refChr3 53705 1 + 222631 A-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- -s Anc1.Anc1refChr6 84391 1 + 197743 A-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- -s Anc2.Anc2refChr13 58187 1 + 96486 A-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- -s mr.mrrefChr5 276812 189 + 294540 AGTGACCCCTTTGGACCTGGGATGAAGGGTGTCGTGTCCTTCTAAAGGTGCTTGCAATCAGATGACAGCATGTGAAGTGGGCACATGAGCCAGGCAGGGTCCTCCTACAGGTGCCTGTAATCACTTGAGAGCGCATAAGTGGGGCCGGCTCAGAGCCACGCACTAACCATGTGCACATGGCCACATTTG -s simCow_chr6.simCow.chr6 413895 1 + 602619 A-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- -s simDog_chr6.simDog.chr6 404877 1 + 593897 A-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- -s simHuman_chr6.simHuman.chr6 409711 1 + 601863 A-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- -s simRat_chr6.simRat.chr6 430542 189 + 647215 AGTGAACCCTTTCGACTTGGGATGAATGACGTTGTGTCCCTCTAAAGGTGCTTGCAATCACTTGACAGCATGTGACATGGGCACGTGAGGCAGGCAGGGTCCTCCTACAAGAGCTTGTAATCATTCGAGAGTGCATAAGTGGGGCAGGCTCAGAGCTACATGCTAACCACGTGTATGTGGCCACATTTG - -a -s simMouse_chr6.simMouse.chr6 424637 16 + 636262 CCTTTCATTGGAGCTT -s mr.mrrefChr5 277001 16 + 294540 CCTTTCATTGGAGCTT -s simRat_chr6.simRat.chr6 430740 16 + 647215 TCATACAGTTCAACTA - -a -s simMouse_chr6.simMouse.chr6 424653 50 + 636262 TACATGAGGTGCTGTGCAAAATCTCAACAATGTTAAGATTGTTTCTTCTA -s Anc0.Anc0refChr3 53706 1 + 222631 -------------------------------------------------A -s Anc1.Anc1refChr6 84392 1 + 197743 -------------------------------------------------A -s Anc2.Anc2refChr13 58188 1 + 96486 -------------------------------------------------T -s mr.mrrefChr5 277017 36 + 294540 TACATGAGG-GCTGTGCAA-------------TTAAGATTGTTTCTTCTA -s simCow_chr6.simCow.chr6 413896 1 + 602619 -------------------------------------------------T -s simDog_chr6.simDog.chr6 404878 1 + 593897 -------------------------------------------------T -s simHuman_chr6.simHuman.chr6 409712 1 + 601863 -------------------------------------------------A -s simRat_chr6.simRat.chr6 430759 36 + 647215 CACTTGTAG-GCGGTGTAA-------------TTGAGTCTTTCACTGCAA - -a -s simMouse_chr6.simMouse.chr6 424703 4 + 636262 TAGG -s Anc0.Anc0refChr3 53707 4 + 222631 TAGG -s Anc1.Anc1refChr6 84393 4 + 197743 TAGG -s Anc2.Anc2refChr13 58189 4 + 96486 TAGA -s mr.mrrefChr5 277053 4 + 294540 TAGG -s simCow_chr6.simCow.chr6 413902 4 + 602619 TAGA -s simDog_chr6.simDog.chr6 404879 4 + 593897 TACA -s simHuman_chr6.simHuman.chr6 409713 4 + 601863 TAGG -s simRat_chr6.simRat.chr6 430795 4 + 647215 CAGG - -a -s simMouse_chr6.simMouse.chr6 424707 24 + 636262 CTTCTAAGGTGCCTGTTGGAATGA -s Anc0.Anc0refChr3 53711 24 + 222631 CTTATAAGGTGCCCTTTGTAATGA -s Anc1.Anc1refChr6 84397 24 + 197743 CTTATAAGGTGCCCTTTGTAATGA -s Anc2.Anc2refChr13 58193 24 + 96486 CTTATAAGGTGCCCTTTGTAATGA -s mr.mrrefChr5 277057 24 + 294540 CTTCTAAGGTGCCTGTTGGAATGA -s simCow_chr6.simCow.chr6 413906 24 + 602619 CTTATCAGGTGCCCTTCATAATGA -s simDog_chr6.simDog.chr6 404886 24 + 593897 CTTATAGGGCACCCTTTGTAATGA -s simHuman_chr6.simHuman.chr6 409717 24 + 601863 CTTATTAGGTGCCCTTTGTAATGA -s simRat_chr6.simRat.chr6 430799 24 + 647215 CACCTAAGAAGCCTATAGGAAACA - -a -s simMouse_chr6.simMouse.chr6 424731 3 + 636262 AGA -s Anc0.Anc0refChr3 53736 2 + 222631 TG- -s Anc1.Anc1refChr6 84422 3 + 197743 TGA -s Anc2.Anc2refChr13 58218 2 + 96486 TG- -s mr.mrrefChr5 277081 3 + 294540 TGA -s simCow_chr6.simCow.chr6 413931 2 + 602619 TG- -s simDog_chr6.simDog.chr6 404911 2 + 593897 TG- -s simHuman_chr6.simHuman.chr6 409742 3 + 601863 TGA -s simRat_chr6.simRat.chr6 430823 3 + 647215 TGA - -a -s simMouse_chr6.simMouse.chr6 424734 25 + 636262 CTCGACAACACCTCCTAAAAGTTTA -s Anc0.Anc0refChr3 53738 25 + 222631 CTCAGTTACACCTCCTATAGGTTTA -s Anc1.Anc1refChr6 84425 25 + 197743 CTCAGTTACACCTCCTATAGGTTTA -s Anc2.Anc2refChr13 58220 25 + 96486 CTCAGTTACACCTCCTATAGGGTTA -s mr.mrrefChr5 277084 25 + 294540 CTCAACAACACCTCCTAAAAGTTTA -s simCow_chr6.simCow.chr6 413933 25 + 602619 CTCAATTACACCTCCTATAAGCATA -s simDog_chr6.simDog.chr6 404913 25 + 593897 CTCAGTCACACCTCCTATAGGGTTA -s simHuman_chr6.simHuman.chr6 409751 25 + 601863 CTCAGTTACACCTCCTATAGGTGTA -s simRat_chr6.simRat.chr6 430826 21 + 647215 TTTAACA----TTGTTGAGAATTTG - -a -s simMouse_chr6.simMouse.chr6 424759 14 + 636262 GTTGACCTGTATGA -s Anc0.Anc0refChr3 53766 13 + 222631 GGTGCCCT-TTGTG -s Anc1.Anc1refChr6 84453 13 + 197743 GGTGCCCT-TTGTG -s Anc2.Anc2refChr13 58248 13 + 96486 GGTTCCCT-ATGTG -s mr.mrrefChr5 277109 14 + 294540 GTTGACCTGTAGGG -s simCow_chr6.simCow.chr6 413961 4 + 602619 GGTT---------- -s simDog_chr6.simDog.chr6 404941 13 + 593897 GGTTCCCT-ATGTG -s simHuman_chr6.simHuman.chr6 409779 13 + 601863 GGTGCCCT-TGGCG -s simRat_chr6.simRat.chr6 430847 14 + 647215 CACAGCACCTTGTG - -a -s simMouse_chr6.simMouse.chr6 424773 9 + 636262 TAAATGTTC -s Anc0.Anc0refChr3 53779 9 + 222631 TGAATGCTC -s Anc1.Anc1refChr6 84466 9 + 197743 TGAATGCTC -s Anc2.Anc2refChr13 58261 9 + 96486 AGAGTGCTC -s mr.mrrefChr5 277123 9 + 294540 TAAATGTTC -s simDog_chr6.simDog.chr6 404955 9 + 593897 AGAGTGCTC -s simHuman_chr6.simHuman.chr6 409792 9 + 601863 TGAATGCTC -s simRat_chr6.simRat.chr6 430861 9 + 647215 TAAAGCTCC - -a -s simMouse_chr6.simMouse.chr6 424782 14 + 636262 CTGGGCCACACAAT -s Anc0.Anc0refChr3 53788 14 + 222631 CAGAACCACACAGT -s Anc1.Anc1refChr6 84475 14 + 197743 CAGAACCACACAGT -s Anc2.Anc2refChr13 58270 14 + 96486 CAGAACCACACAGT -s mr.mrrefChr5 277132 14 + 294540 CTGGGCCACACAGT -s simCow_chr6.simCow.chr6 413965 13 + 602619 -AGTATCACTCAGG -s simDog_chr6.simDog.chr6 404964 14 + 593897 CAGAACCACACGGT -s simHuman_chr6.simHuman.chr6 409801 14 + 601863 CAGAACCACATAGT -s simRat_chr6.simRat.chr6 430879 14 + 647215 CTGGTCCACAAAGT - -a -s simMouse_chr6.simMouse.chr6 424796 27 + 636262 ATGTAGTCTGAAGTATCAGTTAGAGTA -s Anc0.Anc0refChr3 53802 24 + 222631 AGGTATTTTTATGTATCAGTTAGG--- -s Anc1.Anc1refChr6 84489 24 + 197743 AGGTATTTTTATGTATCAGTTAGG--- -s Anc2.Anc2refChr13 58284 24 + 96486 GGGAATTTTTATGTATCAATCAGG--- -s mr.mrrefChr5 277146 27 + 294540 ATGTAGTCTGAAGTATCAGTTAGAGTA -s simCow_chr6.simCow.chr6 413978 8 + 602619 CGGGGTCT------------------- -s simDog_chr6.simDog.chr6 404978 24 + 593897 GGGAATTTTTATGTATCAATCAGG--- -s simHuman_chr6.simHuman.chr6 409815 24 + 601863 AGGTATTTTTGGGTATCAGTTAGG--- -s simRat_chr6.simRat.chr6 430894 27 + 647215 ACATAGTCTGAAGTATTGGTTAGAGTC - -a -s simMouse_chr6.simMouse.chr6 424823 30 + 636262 CAGTTACCTAGGGATGAGTGGCTGTGGGGT -s Anc0.Anc0refChr3 53826 8 + 222631 ----------------------TGTGGGGC -s Anc1.Anc1refChr6 84513 8 + 197743 ----------------------TGTGGGGC -s Anc2.Anc2refChr13 58308 8 + 96486 ----------------------TAGGGGCC -s mr.mrrefChr5 277173 30 + 294540 CAGTTACCTAGGGATGAGTGGCTGTGGGGT -s simDog_chr6.simDog.chr6 405002 8 + 593897 ----------------------TAGGGGCC -s simHuman_chr6.simHuman.chr6 409839 8 + 601863 ----------------------TGTGGAGG -s simRat_chr6.simRat.chr6 430922 30 + 647215 CAGTTACCTGGGGATGAGTGGCTATTGGGT - -a -s simMouse_chr6.simMouse.chr6 424853 32 + 636262 ATATCCCTGTCTAAATGCAGTGGATCAGTGGT -s Anc0.Anc0refChr3 53834 22 + 222631 AGGGATC-GTCTAAACT---------AGTTGC -s Anc1.Anc1refChr6 84521 22 + 197743 AGGGATC-GTCTAAACT---------AGTTGC -s Anc2.Anc2refChr13 58316 22 + 96486 AGGGATT-GTATAAACC---------AGTTAC -s mr.mrrefChr5 277203 32 + 294540 AGGTCCCTGTCTAAACTCAGTGGATCAGTGGT -s simCow_chr6.simCow.chr6 413986 22 + 602619 AGGGATT-GTATAACCC---------AGTTAC -s simDog_chr6.simDog.chr6 405010 22 + 593897 AGGGAAT-GTATGAACC---------AATTAC -s simHuman_chr6.simHuman.chr6 409847 22 + 601863 AGGATTC-GTCTAAACT---------AGTTGG -s simRat_chr6.simRat.chr6 430989 32 + 647215 AGGTCCCTGTCGAAACTCAGTGTCTCAGTGGC - -a -s simMouse_chr6.simMouse.chr6 424885 4 + 636262 CTGA -s Anc0.Anc0refChr3 53856 4 + 222631 TTGG -s Anc1.Anc1refChr6 84543 4 + 197743 TTGG -s Anc2.Anc2refChr13 58340 4 + 96486 TTAG -s mr.mrrefChr5 277235 4 + 294540 TTGA -s simCow_chr6.simCow.chr6 414010 4 + 602619 GTAG -s simDog_chr6.simDog.chr6 405034 4 + 593897 TTAG -s simHuman_chr6.simHuman.chr6 409869 4 + 601863 TTGG -s simRat_chr6.simRat.chr6 431021 4 + 647215 TTGA - -a -s simMouse_chr6.simMouse.chr6 424889 4 + 636262 GCGC -s Anc0.Anc0refChr3 53860 4 + 222631 GTGC -s Anc1.Anc1refChr6 84547 4 + 197743 GTGC -s Anc2.Anc2refChr13 58344 4 + 96486 ATGT -s mr.mrrefChr5 277239 4 + 294540 GCGC -s simCow_chr6.simCow.chr6 414037 4 + 602619 ATGT -s simDog_chr6.simDog.chr6 405038 4 + 593897 ATGT -s simHuman_chr6.simHuman.chr6 409873 4 + 601863 GAGC -s simRat_chr6.simRat.chr6 431025 3 + 647215 -GGC - -a -s simMouse_chr6.simMouse.chr6 424893 48 + 636262 TGATGAATGGGCACAGATAAACCTGATGCATAAAAGGTGCAGCCTTAT -s Anc0.Anc0refChr3 53864 48 + 222631 GGATGAATGGGTGCAGATGAAACCAATGTGGGAGGGGTGCAGTTCTAT -s Anc1.Anc1refChr6 84551 48 + 197743 GGATGAATGGGTGCAGATGAAACCAATGTGGGAGGGGTGCAGTTCTAT -s Anc2.Anc2refChr13 58348 48 + 96486 GGCAGCTTTGGTGCAGATGAAACCAGTGTGGGAGGGGTGAAGTTCTAT -s mr.mrrefChr5 277243 48 + 294540 TGATGAATGGGTGCAGATAAACCTGATGCATGAAGGGTGCAGCCCTAT -s simCow_chr6.simCow.chr6 414043 48 + 602619 GGTGGCCTCGGTGCAGATGAAACAAGTGTGTAGAGGGTGAAGTTCTGT -s simDog_chr6.simDog.chr6 405042 47 + 593897 GACAGCTTTGGTGCC-ATGAAACCAGTGTGGGAGGGGTGAAGTTCTAC -s simHuman_chr6.simHuman.chr6 409877 48 + 601863 AGATGAATGGGTGCAGATGAAACCAATGTGGGAGGGGTGCAGTTCTAT -s simRat_chr6.simRat.chr6 431028 48 + 647215 TGATGAATAGGTGCAGATAAATCAGATGCATGGAGAGTGGAGCCCTAT - -a -s simMouse_chr6.simMouse.chr6 424941 22 + 636262 AATCCAGCCCTCCATTATGTCT -s Anc0.Anc0refChr3 53917 20 + 222631 AATCCTGGCC--CATTGTGTCT -s Anc1.Anc1refChr6 84604 20 + 197743 AATCCTGGCC--CATTGTGTCT -s Anc2.Anc2refChr13 58401 20 + 96486 AATCGTGGCT--CACTGTGTCT -s mr.mrrefChr5 277296 22 + 294540 AATCCAGCCCTCCATTATGTCT -s simCow_chr6.simCow.chr6 414096 20 + 602619 AATCGTGGCG--CAGTATGCCT -s simDog_chr6.simDog.chr6 405094 20 + 593897 AATTGTGGCT--CACTGTGTCT -s simHuman_chr6.simHuman.chr6 409930 20 + 601863 AATCCTGGCC--CATTGTCTCT -s simRat_chr6.simRat.chr6 431085 22 + 647215 AACCCAGCCCTCCATTATTTCT - -a -s simMouse_chr6.simMouse.chr6 424963 17 + 636262 CTTGCGAGCTATATAAG -s Anc0.Anc0refChr3 53937 17 + 222631 ATTGCCAGTTATCAAAG -s Anc1.Anc1refChr6 84624 17 + 197743 ATTGCCAGTTATCAAAG -s Anc2.Anc2refChr13 58421 17 + 96486 ATTGCCAGCTATCAAAG -s mr.mrrefChr5 277318 17 + 294540 CTTGCCAGTTATATAAG -s simCow_chr6.simCow.chr6 414116 17 + 602619 ATTACCAGCTATCAAAG -s simDog_chr6.simDog.chr6 405114 17 + 593897 AATGCCAGCTATCAAAA -s simHuman_chr6.simHuman.chr6 409950 17 + 601863 GTTGCCTGTTATCAAGG -s simRat_chr6.simRat.chr6 431108 17 + 647215 CTTGGCAGTTATTTGAG - -a -s simMouse_chr6.simMouse.chr6 424980 81 + 636262 TCGTCTTTGTTACTGCTTCTGGGTGCCTTCTGTCTTTTGGGCTGACAGTCAAAGCAACAACAAGGCTAAGTAGTAGGCAGA -s Anc0.Anc0refChr3 53974 81 + 222631 TTATCCTTGTTAGTACTTATGGCTGTCTTCTCTGTTTTTGGCTAACAGCAAAATTAAGAGTCAGGTTAAGTGTTAGGTGAG -s Anc1.Anc1refChr6 84661 81 + 197743 TTATCCTTGTTAGTACTTATGGCTGTCTTCTCTGTTTTTGGCTAACAGCAAAATTAAGAGTCAGGTTAAGTGTTAGGTGAG -s Anc2.Anc2refChr13 58459 81 + 96486 TTATCCTTGTTAGTACTTATGGCTGTCTTCTCTGTTTTTGCCCAACAGCAAAATTAAGAGTCAGGTAAAGTGTTAAGTGAA -s mr.mrrefChr5 277335 81 + 294540 TCATCTTTGTTAGTGCTTATGGGTGCCTTCTGTCTTTTGGGCTGACAGTCAAAGCAAGAACCAGGCTAAGTAGTAGGCAGG -s simCow_chr6.simCow.chr6 414155 72 + 602619 ATATCCTTGTTAGTACTTATGGTTGTCTTTTCTGA--TAGCCCAACAGCAAAATT-----TCAGGTAGAATTTTA--TGGT -s simDog_chr6.simDog.chr6 405154 81 + 593897 TTATGTTTGTTAGTATCTATGGCTGCCTTCTCTGTTTTTGCCCAATAGCAAAATTAAGAGTTAGGTAAAGTGCTAAGTGAA -s simHuman_chr6.simHuman.chr6 409987 81 + 601863 TTATCCTTGTTAGTCCTTATGGATGTCTTCTCTGTTTTTAGGTAACAACAAAATTTGGAGTCAGGTTTATTCTTAGGTGTG -s simRat_chr6.simRat.chr6 431125 67 + 647215 TCATCTTTGTTAGTGCCTA-------CCTCTGTCTTTTG-A------GTCAAAGCAAGAACCAGGCTAAGTTGTAAGCAGG - -a -s simMouse_chr6.simMouse.chr6 425061 6 + 636262 AGTAGG -s Anc0.Anc0refChr3 54058 6 + 222631 AGTAAG -s Anc1.Anc1refChr6 84745 6 + 197743 AGTAAG -s Anc2.Anc2refChr13 58543 6 + 96486 AGTAAG -s mr.mrrefChr5 277419 6 + 294540 AGTAGG -s simCow_chr6.simCow.chr6 414230 6 + 602619 AGTAAG -s simDog_chr6.simDog.chr6 405238 6 + 593897 GGTAAG -s simHuman_chr6.simHuman.chr6 410071 6 + 601863 AGTAAG -s simRat_chr6.simRat.chr6 431195 6 + 647215 AGTAGG - -a -s simMouse_chr6.simMouse.chr6 425067 7 + 636262 TGAGTGG -s Anc0.Anc0refChr3 54065 7 + 222631 TGATTAG -s Anc1.Anc1refChr6 84752 7 + 197743 TGATTAG -s Anc2.Anc2refChr13 58550 7 + 96486 GGATTAG -s mr.mrrefChr5 277425 7 + 294540 TGAGTGG -s simCow_chr6.simCow.chr6 414237 7 + 602619 GGATTAG -s simDog_chr6.simDog.chr6 405245 7 + 593897 GGATTAG -s simHuman_chr6.simHuman.chr6 410078 7 + 601863 TGATTAG -s simRat_chr6.simRat.chr6 431201 7 + 647215 TTAGTGG - -a -s simMouse_chr6.simMouse.chr6 425074 58 + 636262 AATCTTAACTATGTCTAACCCCTGATAGCCAACAACAGGTTAGTTTAATCAGCAACAT -s Anc0.Anc0refChr3 54116 57 + 222631 AATCTTTACTATGCCTACTCCATGATAGTCA-CAATAGGCTAATTAAATCAGAAATAT -s Anc1.Anc1refChr6 84803 57 + 197743 AATCTTTACTATGCCTACTCCATGATAGTCA-CAATAGGCTAATTAAATCAGAAATAT -s Anc2.Anc2refChr13 58601 57 + 96486 AATCTTTACTGTGCCTACCCTACAATAGTCA-CAATGGGCTAATTAAATCAGAAATAT -s mr.mrrefChr5 277432 58 + 294540 AATCTTAACTATGTCTAATCCCTGATAGCCAACAACAGGCTAGTTTAATCAGCAACAT -s simCow_chr6.simCow.chr6 414286 57 + 602619 AATTGTTACTGTGACTGTGCTACAATAGTCA-CAATTGGCTATCTAAATCACAAATAT -s simDog_chr6.simDog.chr6 405297 57 + 593897 AATCTCCATTGTGCTTACCTTACAATAGTCA-CAATGGGCTAATTAAATCAGAGAATT -s simHuman_chr6.simHuman.chr6 410130 56 + 601863 AATCTTTGCTATGCCTACTCCATGATGATT--TCATAGGCTACTTAAATTGGAAATAT -s simRat_chr6.simRat.chr6 431208 58 + 647215 AATTTTAACTATGTCTAATCTCTGATAGCCAACAACAGGCCAGTTTAATCAGCAACCT - -a -s simMouse_chr6.simMouse.chr6 425132 3 + 636262 ATT -s Anc0.Anc0refChr3 54173 3 + 222631 ATT -s Anc1.Anc1refChr6 84860 3 + 197743 ATT -s Anc2.Anc2refChr13 58658 3 + 96486 ATC -s mr.mrrefChr5 277490 3 + 294540 ATT -s simCow_chr6.simCow.chr6 414416 3 + 602619 ATC -s simDog_chr6.simDog.chr6 405354 3 + 593897 ATC -s simHuman_chr6.simHuman.chr6 410186 3 + 601863 ACT -s simRat_chr6.simRat.chr6 431266 3 + 647215 ATT - -a -s simMouse_chr6.simMouse.chr6 425135 45 + 636262 TTTATTGCTGGGTCCCCTTGGATCTACTATTTAGAGTGGCTCTTG -s Anc0.Anc0refChr3 54176 32 + 222631 T-------------CCCTTGGATCTACTTCTTGAGTAAGCTCTTG -s Anc1.Anc1refChr6 84863 32 + 197743 T-------------CCCTTGGATCTACTTCTTGAGTAAGCTCTTG -s Anc2.Anc2refChr13 58665 32 + 96486 T-------------CCCTTGGATCTACTTCTTGAGTAAGCTCTTG -s mr.mrrefChr5 277493 45 + 294540 TTTATTGCTGGGTCCCCTTGGATCTACTACTTAGAGTGGCTCTTG -s simCow_chr6.simCow.chr6 414423 32 + 602619 C-------------CCCTTGGACCGATTTCTTGAGTAAGTCTTTG -s simDog_chr6.simDog.chr6 405361 32 + 593897 T-------------GCACTAGATCTACTTCTTAAGTAAGCTCTTG -s simHuman_chr6.simHuman.chr6 410189 32 + 601863 T-------------CCCTTGGATCTGCTTCTTGAGTGAGCTCTTG -s simRat_chr6.simRat.chr6 431269 45 + 647215 TTTATTGCTATGCCCCCTTGGGTCTACTGCCTAGACCGGCTCTTG - -a -s simMouse_chr6.simMouse.chr6 425180 4 + 636262 TATC -s Anc0.Anc0refChr3 54210 4 + 222631 TCTC -s Anc1.Anc1refChr6 84897 4 + 197743 TCTC -s Anc2.Anc2refChr13 58699 4 + 96486 TCCC -s mr.mrrefChr5 277538 4 + 294540 TATC -s simCow_chr6.simCow.chr6 414457 4 + 602619 TCCT -s simDog_chr6.simDog.chr6 405395 4 + 593897 TCCC -s simHuman_chr6.simHuman.chr6 410223 4 + 601863 TCTC -s simRat_chr6.simRat.chr6 431314 4 + 647215 TATC - -a -s simMouse_chr6.simMouse.chr6 425184 11 + 636262 TTAATCTGTAG -s Anc0.Anc0refChr3 54214 11 + 222631 TCAATCTGTAA -s Anc1.Anc1refChr6 84901 11 + 197743 TCAATCTGTAA -s Anc2.Anc2refChr13 58703 11 + 96486 TCAATCTGTAA -s mr.mrrefChr5 277542 11 + 294540 TTAATCTGTAA -s simCow_chr6.simCow.chr6 414461 11 + 602619 TCAATCTGTAG -s simDog_chr6.simDog.chr6 405400 11 + 593897 TCAATTGGTAA -s simHuman_chr6.simHuman.chr6 410227 11 + 601863 TGAATCTGTAA -s simRat_chr6.simRat.chr6 431318 11 + 647215 TTACTCTGTAA - -a -s simMouse_chr6.simMouse.chr6 425195 35 + 636262 GTAAACATCTGGCTGCAGACATTCAAGGCGTGTTA -s Anc0.Anc0refChr3 54225 28 + 222631 ATAAGAAATTGGCTGCAGTCATACA-------CTC -s Anc1.Anc1refChr6 84912 35 + 197743 ATAAGAAATTGGCTGCAGTCATACATAACATACTC -s Anc2.Anc2refChr13 58714 28 + 96486 ACTAGAAATTGGCTGCAGTCATACC-------CTC -s mr.mrrefChr5 277553 35 + 294540 GTAAACATCTGGCTGCAGACATTCAAGGCATGTTA -s simCow_chr6.simCow.chr6 414567 28 + 602619 CCTAGCAATTGGCTGCAGACATACC-------CTC -s simDog_chr6.simDog.chr6 405411 21 + 593897 ACTAGA-------CGCAGTCATACC-------CTC -s simHuman_chr6.simHuman.chr6 410238 35 + 601863 ATAAGAACTTGACTGCACTAATGCATAACATACTC -s simRat_chr6.simRat.chr6 431329 26 + 647215 GTC---------CTGCATACATTCAAGGCACGTTA - -a -s simMouse_chr6.simMouse.chr6 425230 2 + 636262 CT -s Anc0.Anc0refChr3 54288 2 + 222631 AT -s Anc1.Anc1refChr6 84982 2 + 197743 AT -s Anc2.Anc2refChr13 58777 2 + 96486 AT -s mr.mrrefChr5 277623 2 + 294540 CT -s simCow_chr6.simCow.chr6 414630 2 + 602619 AT -s simDog_chr6.simDog.chr6 405462 2 + 593897 AT -s simHuman_chr6.simHuman.chr6 410308 2 + 601863 AT -s simRat_chr6.simRat.chr6 431390 2 + 647215 CT - -a -s simMouse_chr6.simMouse.chr6 425232 145 + 636262 CATGGCCATGTGACGGGTACAGTGTACGACACAGCATTCCCCATGAGGCAAATTCCCCTCAGTGGTCTTATTAATTCCAGCTATGCATACCCTTTACTGTGACCTTATGCCCCTACTTAACAGCAGTATTGTCAATCCTAGAACT -s Anc0.Anc0refChr3 54291 144 + 222631 CATGACCATGTGAAAGATATAGGGTACCACCCAGCAATCCCC-TGAAACAAGCTCCCTTCTGTTGTCATACTAACCTCAGCTGTACATGCCCTCTACTGTGACCTTATGTGACTACTTACCTGAGGTATCATCAATCCTAGAACT -s Anc1.Anc1refChr6 84985 144 + 197743 CATGACCATGTGAAAGATATAGGGTACCACCCAGCAATCCCC-TGAAACAAGCTCCCTTCTGTTGTCATACTAACCTCAGCTGTACATGCCCTCTACTGTGACCTTATGTGACTACTTACCTGAGGTATCATCAATCCTAGAACT -s Anc2.Anc2refChr13 58780 144 + 96486 TCTGACTCTGTGAAAGATATAGGGAACCACCTAGCAATCCCC-TGAAACAAGCTCTCTTCTGTTGACATACTAACCTCAGCTGTACATGCCCTCTGCTGTGACCTTATGTGACTACTTACCTGAGGCATCATCAATCCTAGAACT -s mr.mrrefChr5 277625 145 + 294540 CATGGCCATGTGACAGGTACAGTGTACGACACAGCATTCCCCATGAGGCAAGTTCCCTTCAGTGGTCTTACTAATTCCAGCTATACATGCCCTTTACTGTGACCTTATGCCCCTACTTACCAGCAGTATTGTCAATCCTAGAACT -s simCow_chr6.simCow.chr6 414633 143 + 602619 TGTGACTGTATGAAACATATGGGGAACCACCTAGCAATCCAC-TGCAACAAGGTCTCTTGTGTTGACATACTTACCTCAGCTGTATCTGCCGTCTGTTGTGACCTTATGTGACCACTTACCTGAGGCA-AATTAATCCTGGAACT -s simDog_chr6.simDog.chr6 405465 133 + 593897 TCTGACTCTGTGAAGGATATAAG-----------CAATCTCC-TGAATCAAGCTCTCTCCGGTTAACATACTAACTTCAGTTGTACATGCTCTCTGCAGTGACTTTATGTAACTACTTTCCTGGGGCATCAACAGTCCCAGAACT -s simHuman_chr6.simHuman.chr6 410311 144 + 601863 CATACCCAAGTGAAAGATATAGGGTACCGCCCAAGGATCCCC-TGGAACAAGCCCCCTTCTGTTGTCAGACTAACCTTGGCTGTACATGCCCTATAATGTGACCAAACTTGACTACTTACCTGAGGTATCATCAATCCTAGAACT -s simRat_chr6.simRat.chr6 431392 145 + 647215 CACGGCCATGTGACAGGTACAGTGTACGACACTGCATTCCCCATGAGGTAAGTTCCCTTCAGTGGTCTTACTGATTCCAGCTATACATGCCCTTTACTGTAACCTTATGCACCTACTTACCAGCAGTATTGGCAATCATAGAACT - -a -s simMouse_chr6.simMouse.chr6 425377 11 + 636262 CTATTAACGCT -s Anc0.Anc0refChr3 54435 1 + 222631 C---------- -s Anc1.Anc1refChr6 85129 1 + 197743 C---------- -s Anc2.Anc2refChr13 58924 1 + 96486 T---------- -s mr.mrrefChr5 277770 11 + 294540 CTATTAACGCT -s simCow_chr6.simCow.chr6 414776 1 + 602619 T---------- -s simDog_chr6.simDog.chr6 405598 1 + 593897 T---------- -s simHuman_chr6.simHuman.chr6 410455 1 + 601863 C---------- -s simRat_chr6.simRat.chr6 431541 11 + 647215 CTATTAACGCT - -a -s simMouse_chr6.simMouse.chr6 425388 3 + 636262 GGT -s Anc0.Anc0refChr3 54436 2 + 222631 -CT -s Anc1.Anc1refChr6 85130 2 + 197743 -CT -s Anc2.Anc2refChr13 58925 2 + 96486 -CT -s mr.mrrefChr5 277781 3 + 294540 GGT -s simCow_chr6.simCow.chr6 414777 2 + 602619 -CT -s simDog_chr6.simDog.chr6 405599 2 + 593897 -CT -s simHuman_chr6.simHuman.chr6 410456 2 + 601863 -AT -s simRat_chr6.simRat.chr6 431554 3 + 647215 GGT - -a -s simMouse_chr6.simMouse.chr6 425391 30 + 636262 GTGCTTGAAATTGTTCCTTATCATAATCTT -s Anc0.Anc0refChr3 54441 30 + 222631 GTGCTTGGAATCCCACCTTGTTATAAAATT -s Anc1.Anc1refChr6 85135 30 + 197743 GTGCTTGGAATCCCACCTTGTTATAAAATT -s Anc2.Anc2refChr13 58930 30 + 96486 GTACTTGGAATCCCACCTTGTTATGAAATT -s mr.mrrefChr5 277787 30 + 294540 GTGCTTGAAATTGTACCTTATTATAATCTT -s simCow_chr6.simCow.chr6 414782 26 + 602619 GTCCTTGGGATTTCGCTTTGTT----AGTT -s simDog_chr6.simDog.chr6 405604 30 + 593897 GTACTTGAAATCCCAACTTGCTATGAAATT -s simHuman_chr6.simHuman.chr6 410461 30 + 601863 GTGTTCGGAATCACACCTTCTTACAAAATT -s simRat_chr6.simRat.chr6 431560 30 + 647215 GTGCTTAAAATTGTACCTTATTATAATCTT - -a -s simMouse_chr6.simMouse.chr6 425421 16 + 636262 ATCTTCCTAGTCTAAA -s Anc0.Anc0refChr3 54471 16 + 222631 TTCAGCCCAGTCTAAA -s Anc1.Anc1refChr6 85165 16 + 197743 TTCAGCCCAGTCTAAA -s Anc2.Anc2refChr13 58960 16 + 96486 TTCAGCCCAGCCTAAA -s mr.mrrefChr5 277817 16 + 294540 ATCTGCCTAGTCTAAA -s simCow_chr6.simCow.chr6 414808 16 + 602619 GTCAGTCCAGCCTAAA -s simDog_chr6.simDog.chr6 405634 16 + 593897 TTCAGCCGAGCCTAAA -s simHuman_chr6.simHuman.chr6 410491 16 + 601863 TTTGGCCCAGTCTAAA -s simRat_chr6.simRat.chr6 431591 16 + 647215 CTCTGCCTAGTCAAGG - -a -s simMouse_chr6.simMouse.chr6 425437 111 + 636262 GGGTTGTCAGATAAATGAGCCTAGTTCCTGTCTTGTAAGAAAAATAGCGTAGTTCTTCGAGTTTTGCCTGTACTACCGCGCATTAAACAGTGTCTGTGGTAACTATTGCAT -s Anc0.Anc0refChr3 54488 50 + 222631 GACTTGTTAGATAAATTAGTTTTGTTCCTCT------------------------------------------------------------GTTTGTG-TAACCATGATGT -s Anc1.Anc1refChr6 85182 50 + 197743 GACTTGTTAGATAAATTAGTTTTGTTCCTCT------------------------------------------------------------GTTTGTG-TAACCATGATGT -s Anc2.Anc2refChr13 58977 50 + 96486 GACTTGTTAGATAAATTAGTTTTGTTCCTCT------------------------------------------------------------ATTTGTG-TAACCATGATGT -s mr.mrrefChr5 277833 50 + 294540 GGCTTGTCAGATAAATTAGCTTAGTTCCTGT------------------------------------------------------------GTCTGTG-TAACTATTGCAT -s simCow_chr6.simCow.chr6 414825 50 + 602619 GACTTGTTACATAAATTAGCTTAGCTTCTCT------------------------------------------------------------ATTTATG-TAACCATGTTGT -s simDog_chr6.simDog.chr6 405651 46 + 593897 ----TGTTAGATAAGTTAGTTTTGTCCCTCT------------------------------------------------------------ATTTGTG-CAACCATGATGT -s simHuman_chr6.simHuman.chr6 410508 50 + 601863 GACCCATTGGGTAAATTGGTTTGGTTCCTCT------------------------------------------------------------GTTTGTG-TAACCATGATGT -s simRat_chr6.simRat.chr6 431607 24 + 647215 GGCTTGTCAGTTAAATTAGCTTAG--------------------------------------------------------------------------------------- - -a -s simMouse_chr6.simMouse.chr6 425548 115 + 636262 CCCCCTTCAGTTTAACATGGATACCCTGATCACCCAAGTCTCACTCTTATAGTACTGACTTCTATATTATCCAGTGGACATGCATGTCAGGAGACATGACATACTCAAAATGGAG -s Anc0.Anc0refChr3 54538 73 + 222631 CCCCCTG-AGTTTAAGATGGACAA--TACTTGCTCAAGAGTCACTCTGATAGTTTTTAAT---------------------------------------CATGCTCAACATCCAG -s Anc1.Anc1refChr6 85232 112 + 197743 CCCCCTG-AGTTTAAGATGGACAA--TACTTGCTCAAGAGTCACTCTGATAGTTTTTAATTTAATATTCTGCAGAGGGCATGCACGGCAGTAGGGATGACATGCTCAACATCCAG -s Anc2.Anc2refChr13 59027 73 + 96486 CCCCTTG-AGTTTAAGATGGACCA--TACTTGCTTGTGAGTCACTCTGATAGTTTTTAAT---------------------------------------CATGCTCAACATCCGG -s mr.mrrefChr5 277883 112 + 294540 CCCCCTT-AGTTTAACATGGATAC--TGATTGCCCAAGTGTCACTCTTATAGTTCTGACTTTTATATTATCCAGAGGACATGCATGTCAGGAGACATGACATACTCAAAATGGAG -s simCow_chr6.simCow.chr6 414875 73 + 602619 CCCCTTG-GATATAGGAGGGACCC--TACCTGCTTGTGAGACACTCTGATAGTTTTTAAC---------------------------------------CATGCTCTACATCCGG -s simDog_chr6.simDog.chr6 405698 69 + 593897 CCCTTTG-AGTTTAAGATGTACCA--TACTTGCTT----GTCCTTCTGATGTATCTTAAT---------------------------------------CATGCTCAACATCTGG -s simHuman_chr6.simHuman.chr6 410558 111 + 601863 CCTCCTG-AGTCTAAGATGGACAT--TACTTGGTCAAGAGTCACTTTGATAGTTTTTAATTTAATATTCTGCAGAGGGCATGCACGGCAGTAGGGATGACAT-CTCATCATTCAG -s simRat_chr6.simRat.chr6 431631 87 + 647215 ----------------------------ATTGCCCAAGTGTCACGCCTATAGTTCTGTCTTTTATATTATCCAGAGAACATGCATTTCAGGAGACATGACATGCCCAAAATGGAG - -a -s simMouse_chr6.simMouse.chr6 425663 5 + 636262 TGACA -s Anc0.Anc0refChr3 54611 5 + 222631 ATGCA -s Anc1.Anc1refChr6 85344 5 + 197743 ATGCA -s Anc2.Anc2refChr13 59100 5 + 96486 ATGTG -s mr.mrrefChr5 277995 5 + 294540 TGGCA -s simCow_chr6.simCow.chr6 414951 5 + 602619 ATGTG -s simDog_chr6.simDog.chr6 405767 5 + 593897 ACGTG -s simHuman_chr6.simHuman.chr6 410669 5 + 601863 ATGCA -s simRat_chr6.simRat.chr6 431718 5 + 647215 TGGCA - -a -s simMouse_chr6.simMouse.chr6 425668 9 + 636262 TCTGCTGTT -s Anc0.Anc0refChr3 54616 9 + 222631 TGTTTTGTT -s Anc1.Anc1refChr6 85349 9 + 197743 TGTTTTGTT -s Anc2.Anc2refChr13 59105 9 + 96486 TGTTTTGTT -s mr.mrrefChr5 278000 9 + 294540 TGTGCTGTT -s simCow_chr6.simCow.chr6 414970 9 + 602619 TGATTCGTT -s simDog_chr6.simDog.chr6 405772 9 + 593897 TGTTTTGTC -s simHuman_chr6.simHuman.chr6 410674 9 + 601863 TGCTTTGTT -s simRat_chr6.simRat.chr6 431723 8 + 647215 TGT-CTATT - -a -s simMouse_chr6.simMouse.chr6 425677 9 + 636262 GTCTGTCTT -s Anc0.Anc0refChr3 54631 9 + 222631 GCTTGTCTT -s Anc1.Anc1refChr6 85364 9 + 197743 GCTTGTCTT -s Anc2.Anc2refChr13 59120 9 + 96486 GCTCATCTT -s mr.mrrefChr5 278015 9 + 294540 GTCTGTCTT -s simCow_chr6.simCow.chr6 414985 9 + 602619 GCCCATCTA -s simDog_chr6.simDog.chr6 405787 9 + 593897 GCTCATCTT -s simHuman_chr6.simHuman.chr6 410689 9 + 601863 ACTTGTCTT -s simRat_chr6.simRat.chr6 431737 8 + 647215 GTCTGTCT- - -a -s simMouse_chr6.simMouse.chr6 425686 61 + 636262 TCCTGGCCCATGTAGATTATGGGAGGGAGCATCTAGCAGAAAGGTTTTCAGTCACAAATTA -s Anc0.Anc0refChr3 54642 61 + 222631 ACCTATACCATGCAGTGTCTGGCAGGGAGTCTCTATAGGGAGGGTTTTCTACCACAAATTA -s Anc1.Anc1refChr6 85375 61 + 197743 ACCTATACCATGCAGTGTCTGGCAGGGAGTCTCTATAGGGAGGGTTTTCTACCACAAATTA -s Anc2.Anc2refChr13 59131 61 + 96486 ACCTATACTATGCAGTGTCTGGCAAGGAGTCTCTATAGGGAGGGTTTTCTACCATAAACTA -s mr.mrrefChr5 278024 61 + 294540 TCCTGGCCCATGTAGATTATGGGAGGGAGCATCTAGCAGAAGGGTTTTCAGCCACAAATTA -s simCow_chr6.simCow.chr6 414996 45 + 602619 ACCAATGCTATGCAGTGTTTGGCAAGGGGTTTCTATAGGGAGGTT---------------- -s simDog_chr6.simDog.chr6 405798 61 + 593897 ACCTATACTGTACATTGTCTAGCAAGGAGGCTCTATAGGGAGGGTTTTCTACCATAAACTA -s simHuman_chr6.simHuman.chr6 410700 61 + 601863 GCCTATACCACGCAGTGTCTGGCTGGGAGTCTCCATGGGGAGGGTTTTCTTCCACAAATTA -s simRat_chr6.simRat.chr6 431745 56 + 647215 -----ACCCATGTAGATTATGGAAGGGAGCATCTAGAAGAAGGGTTTTTGGCCACAAATTA - -a -s simMouse_chr6.simMouse.chr6 425747 1 + 636262 G -s Anc0.Anc0refChr3 54703 1 + 222631 G -s Anc1.Anc1refChr6 85436 1 + 197743 G -s Anc2.Anc2refChr13 59192 1 + 96486 G -s mr.mrrefChr5 278085 1 + 294540 G -s simDog_chr6.simDog.chr6 405859 1 + 593897 G -s simHuman_chr6.simHuman.chr6 410764 1 + 601863 G -s simRat_chr6.simRat.chr6 431801 1 + 647215 G - -a -s simMouse_chr6.simMouse.chr6 425748 29 + 636262 TTGCTTACCAGAAACTTGTAGCAGGTGCA -s Anc0.Anc0refChr3 54704 29 + 222631 TTGTTTGCCAGCAACTCGCTGCATCTGTG -s Anc1.Anc1refChr6 85437 29 + 197743 TTGTTTGCCAGCAACTCGCTGCATCTGTG -s Anc2.Anc2refChr13 59195 29 + 96486 TTGTATACCAGCAACCCGCTGCATCTGTG -s mr.mrrefChr5 278086 29 + 294540 TTGCTTGCCAGAAACTTGTAGCAGGTGTA -s simCow_chr6.simCow.chr6 415041 22 + 602619 -------CAAGGAACCCGCTGCATCTGAG -s simDog_chr6.simDog.chr6 405862 29 + 593897 TTGTATAGCAGCAACCTTCTGCATTTGTG -s simHuman_chr6.simHuman.chr6 410765 29 + 601863 TTGTTCGCGATTCACTCGATCCATCTGTG -s simRat_chr6.simRat.chr6 431802 29 + 647215 TTGCTTGTCAAAAACTTGTAAAAGGTGTA - -a -s simMouse_chr6.simMouse.chr6 425777 24 + 636262 GGGAGCGTCCCTGTAATTGATCCA -s Anc0.Anc0refChr3 54736 24 + 222631 GGGAAATTCCCTCTAATAGATGAG -s Anc1.Anc1refChr6 85469 24 + 197743 GGGAAATTCCCTCTAATAGATGAG -s Anc2.Anc2refChr13 59227 24 + 96486 AGAAAATTCCCTCTAACAGATGAG -s mr.mrrefChr5 278115 24 + 294540 GGGAGCGTCCCTGTAATTGATCCA -s simCow_chr6.simCow.chr6 415066 24 + 602619 AGAAAGTTCCCTCTAACAGGACAG -s simDog_chr6.simDog.chr6 405894 24 + 593897 AGAAAATTCCCTCGAACAGATGAG -s simHuman_chr6.simHuman.chr6 410797 24 + 601863 GGGAAATTCCTTCTCCTGGATGAG -s simRat_chr6.simRat.chr6 431831 24 + 647215 GAGAGCATCCCTGTAACTGATCCA - -a -s simMouse_chr6.simMouse.chr6 425801 1 + 636262 G -s Anc0.Anc0refChr3 54760 1 + 222631 G -s Anc1.Anc1refChr6 85493 1 + 197743 G -s Anc2.Anc2refChr13 59251 1 + 96486 G -s mr.mrrefChr5 278139 1 + 294540 G -s simCow_chr6.simCow.chr6 415092 1 + 602619 G -s simDog_chr6.simDog.chr6 405918 1 + 593897 G -s simHuman_chr6.simHuman.chr6 410821 1 + 601863 G -s simRat_chr6.simRat.chr6 431855 1 + 647215 G - -a -s simMouse_chr6.simMouse.chr6 425802 40 + 636262 GTATTATTCTCAGGTGTCACCATCTCAGATGTAGGGCTGG -s Anc0.Anc0refChr3 54761 33 + 222631 ATGCTATGCTCAGGGACCTCAATTTAAAA-------CTTC -s Anc1.Anc1refChr6 85494 33 + 197743 ATGCTATGCTCAGGGACCTCAATTTAAAA-------CTTC -s Anc2.Anc2refChr13 59252 33 + 96486 ATGCTATGCTCAGGGACCTCAATTTACAA-------CTTC -s mr.mrrefChr5 278140 40 + 294540 GTATTATTCTCAGGTGTCACCATCTCAAATGTAGGGCTGG -s simCow_chr6.simCow.chr6 415093 33 + 602619 CTGTTATTCTCTGGGACCAAAATGTTGAA-------CTTT -s simDog_chr6.simDog.chr6 405924 33 + 593897 ATGCTATGCTCAGGGACCTCAATTTACAA-------CTTC -s simHuman_chr6.simHuman.chr6 410822 27 + 601863 ATGCTATCCTCAGGGACCCCAATATAA------------- -s simRat_chr6.simRat.chr6 431856 40 + 647215 GTATTATTCTCAGGTGTTACCATCTCAAATGTAGGGCTGA - -a -s simMouse_chr6.simMouse.chr6 425842 19 + 636262 TGATGTATTCCAGGATTCT -s Anc0.Anc0refChr3 54794 17 + 222631 AGATACATTTCGGGAT--G -s Anc1.Anc1refChr6 85527 19 + 197743 AGATACATTTCGGGATTTG -s Anc2.Anc2refChr13 59285 17 + 96486 AGATACATTTGGGGAT--G -s mr.mrrefChr5 278180 19 + 294540 TGATGTATTCCAGGATTCT -s simCow_chr6.simCow.chr6 415138 17 + 602619 AGACGCAATTGGGGAT--G -s simDog_chr6.simDog.chr6 405957 17 + 593897 AGATACATTTAGGGAC--A -s simHuman_chr6.simHuman.chr6 410849 10 + 601863 ---------TCGGGATTTG -s simRat_chr6.simRat.chr6 431896 19 + 647215 TGGTGTATTCTAGGATTCT - -a -s simMouse_chr6.simMouse.chr6 425861 11 + 636262 GCAAGATAAGA -s Anc0.Anc0refChr3 54811 11 + 222631 CCCAGCTATGA -s Anc1.Anc1refChr6 85546 11 + 197743 CCCAGCTATGA -s Anc2.Anc2refChr13 59302 11 + 96486 CCCATCTATTA -s mr.mrrefChr5 278199 11 + 294540 GCAAGATAAGA -s simCow_chr6.simCow.chr6 415164 11 + 602619 ACCATCTCTTA -s simDog_chr6.simDog.chr6 405974 10 + 593897 CTCATC-ATTA -s simHuman_chr6.simHuman.chr6 410859 11 + 601863 CCCAGCTTTGA -s simRat_chr6.simRat.chr6 431915 11 + 647215 GCAAGATGAGA - -a -s simMouse_chr6.simMouse.chr6 425872 17 + 636262 TTGAAAGTGGCTAGTCA -s Anc0.Anc0refChr3 54822 16 + 222631 CTGATA-TAGCTACTAA -s Anc1.Anc1refChr6 85557 16 + 197743 CTGATA-TAGCTACTAA -s Anc2.Anc2refChr13 59313 16 + 96486 CTGATA-TAGCTACTAC -s mr.mrrefChr5 278210 17 + 294540 TTGAAAGTGGCTAGTCA -s simCow_chr6.simCow.chr6 415177 16 + 602619 CTGATA-TAACTATTAC -s simDog_chr6.simDog.chr6 405984 16 + 593897 CTGATA-GAGGTACTAC -s simHuman_chr6.simHuman.chr6 410870 16 + 601863 CTGATA-TAGCCACTTA -s simRat_chr6.simRat.chr6 431926 17 + 647215 TTGAAAGTGGCTAGCCA - -a -s simMouse_chr6.simMouse.chr6 425889 44 + 636262 TACCTGTTGAGTGGAGAGATGCTGAACTTTTCCTATTGTTTCTA -s Anc0.Anc0refChr3 54843 36 + 222631 TCGCATTGCAAT----AGCC----TGCCTCCATCATCAGTTCTG -s Anc1.Anc1refChr6 85578 36 + 197743 TCGCATTGCAAT----AGCC----TGCCTCCATCATCAGTTCTG -s Anc2.Anc2refChr13 59334 36 + 96486 TCACATTGCAAT----AGCC----TGCCTCTATCATCAGCTCTG -s mr.mrrefChr5 278227 40 + 294540 TAGCTGTTGAGT----AGCCGCTGTACTTTCCCTATTGTTTCTA -s simCow_chr6.simCow.chr6 415198 36 + 602619 TCACATTGCAAT----TGCC----TACCTTTATCATCAGCTGTG -s simDog_chr6.simDog.chr6 406005 35 + 593897 TCACATTGCAAT----AGCC----TGCCTCTAG-ATCAGCTCTA -s simHuman_chr6.simHuman.chr6 410891 36 + 601863 TCGCCTTGTAAT----AGCC----TGCCTACATCATCAGTTCTG -s simRat_chr6.simRat.chr6 431943 40 + 647215 GAGCTGTTGAGC----AGCCGCTGTTCTTTCCCTATTGTTTCTA - -a -s simMouse_chr6.simMouse.chr6 425933 6 + 636262 CCCTTA -s Anc0.Anc0refChr3 54880 6 + 222631 CCCTTA -s Anc1.Anc1refChr6 85615 6 + 197743 CCCTTA -s Anc2.Anc2refChr13 59371 6 + 96486 CCCTTA -s mr.mrrefChr5 278267 6 + 294540 CCCTTA -s simCow_chr6.simCow.chr6 415235 6 + 602619 CCCTTA -s simDog_chr6.simDog.chr6 406041 6 + 593897 TCCTTA -s simHuman_chr6.simHuman.chr6 410928 6 + 601863 CCCTTA -s simRat_chr6.simRat.chr6 431983 6 + 647215 CCCTTA - -a -s simMouse_chr6.simMouse.chr6 425939 75 + 636262 TGCCCCTATTTTACTATATATGTGTAGTAGTTGATTTACTATATATGTGTAGTAGTTGATCCTGTTAGCCAGCCG -s Anc0.Anc0refChr3 54886 50 + 222631 TTCCCCTAATTCACTTTATCTTTATCCTAGGTGAT-------------------------GCCATTAGCCACCCA -s Anc1.Anc1refChr6 85621 50 + 197743 TTCCCCTAATTCACTTTATCTTTATCCTAGGTGAT-------------------------GCCATTAGCCACCCA -s Anc2.Anc2refChr13 59377 50 + 96486 TTCCTCTAATTCACTTTATCTTTATCCTAGGTGAT-------------------------GCCATTTGCCACCCA -s mr.mrrefChr5 278273 50 + 294540 TGCCCCTATTTTACTATATCTGTGTAGTAGTTGAT-------------------------CCTGTTAGCCAGCCA -s simCow_chr6.simCow.chr6 415241 50 + 602619 TTCCTCTAATTCATTTTATCCTTATCCTAGTTGAT-------------------------GCTGTTTGGGACCCA -s simDog_chr6.simDog.chr6 406047 50 + 593897 TTCCTCTGAGTCACTTTATCTTTATGCTAGGTGAT-------------------------GCCACTTGCCACCCA -s simHuman_chr6.simHuman.chr6 410935 50 + 601863 TCCCCCTAATTCACTTTCTCTTCACCTTAACCGAT-------------------------GCCATTAGCCACCCA -s simRat_chr6.simRat.chr6 431989 50 + 647215 TGCCGCTATTTTACTGTATCTGTGTAGTAGTTGAT-------------------------TCTGTTAGCCAGCCA - -a -s simMouse_chr6.simMouse.chr6 426014 28 + 636262 TGCTGCTATGCAGGACAGAAGACCTAGC -s Anc0.Anc0refChr3 54936 23 + 222631 GGCTGCTATATGGGACATCAGAC----- -s Anc1.Anc1refChr6 85671 28 + 197743 GGCTGCTATATGGGACATCAGACCAAGC -s Anc2.Anc2refChr13 59427 23 + 96486 GGCTGCTACATGGGACATCAGAC----- -s mr.mrrefChr5 278323 28 + 294540 TGCTGCTATGCGGGACAGAAGACCAAGC -s simCow_chr6.simCow.chr6 415291 23 + 602619 GGCTGCTACATAGGAAATCAGGC----- -s simDog_chr6.simDog.chr6 406097 23 + 593897 GGCTGCTACATGGGACATCACAC----- -s simHuman_chr6.simHuman.chr6 410985 28 + 601863 GGCTGCTATATGGGACATCAGATCAAGC -s simRat_chr6.simRat.chr6 432040 26 + 647215 TACTGCTATGCGGGACAG--GACCAAGT - -a -s simMouse_chr6.simMouse.chr6 426042 14 + 636262 CAAACAAGGAAAAG -s Anc1.Anc1refChr6 85699 14 + 197743 CAAACAAGAAAGAG -s mr.mrrefChr5 278351 14 + 294540 CAAACAAGGAAAAG -s simHuman_chr6.simHuman.chr6 411017 14 + 601863 CAAACAAGAAAGAG -s simRat_chr6.simRat.chr6 432066 14 + 647215 CGAACAAGGAAAAG - -a -s simMouse_chr6.simMouse.chr6 426056 78 + 636262 AACTTATGGAGATTTGGGTATACCATAAGAGCAGTGGTCTGGGTTTGCTGTGCACCAGTGACTGGACTGAGGGTCTTC -s Anc0.Anc0refChr3 54959 40 + 222631 --------------------------------------TTTGGGTACTTGTCCAGCTGGGACTGGATTGAGGGTCTTT -s Anc1.Anc1refChr6 85713 77 + 197743 AAGTT-TGGGCATTTGTGTCTATTGTAAGAGCAATGATTTTGGGTACTTGTCCAGCTGGGACTGGATTGAGGGTCTTT -s Anc2.Anc2refChr13 59450 40 + 96486 --------------------------------------TGTGTGTACTTGTCAAGCAAGAACTGGATTGAGGGTCTTT -s mr.mrrefChr5 278365 78 + 294540 AACTTATGGAGATTTGGGTATACCATAAGAGCAGTGGTCTGGGTTTGCTGTGCACCTGTGACTGGACTGAGGGTCTTC -s simCow_chr6.simCow.chr6 415314 36 + 602619 ------------------------------------------TGAACATATCAAGCAAGAACTGAATGAAGAGTCCTT -s simDog_chr6.simDog.chr6 406120 38 + 593897 --------------------------------------TGTGTGTGCTTGCCAAGCAAGAACTAGATTGAGGGTCT-- -s simHuman_chr6.simHuman.chr6 411034 77 + 601863 AAGTT-TGGGCATTTGTGTCTATTGTAAGAGCAATGATTTTGGATACTTGTACAGCTGGGACTGGATTGAGGGTCTTT -s simRat_chr6.simRat.chr6 432080 78 + 647215 AACTTATGGAGATTTGCATATACCATAAGAGCAGTGGTCTGGTTTTGCTGTGCACCTGTGACTGGACTGAGGGTCTTC - -a -s simMouse_chr6.simMouse.chr6 426134 5 + 636262 ACCAC -s Anc0.Anc0refChr3 54999 5 + 222631 ACCAC -s Anc1.Anc1refChr6 85790 5 + 197743 ACCAC -s Anc2.Anc2refChr13 59490 5 + 96486 ACCAG -s mr.mrrefChr5 278443 5 + 294540 ACCAC -s simCow_chr6.simCow.chr6 415350 5 + 602619 ACCAG -s simHuman_chr6.simHuman.chr6 411111 5 + 601863 ACCAC -s simRat_chr6.simRat.chr6 432161 5 + 647215 GCCAC - -a -s simMouse_chr6.simMouse.chr6 426139 8 + 636262 TGGCTCCT -s Anc0.Anc0refChr3 55006 8 + 222631 TGGCTTCT -s Anc1.Anc1refChr6 85797 8 + 197743 TGGCTTCT -s Anc2.Anc2refChr13 59497 8 + 96486 TTGTTTCT -s mr.mrrefChr5 278448 8 + 294540 TGGCTCCT -s simCow_chr6.simCow.chr6 415357 8 + 602619 TTGTTTCT -s simHuman_chr6.simHuman.chr6 411118 8 + 601863 TGGCTTAT -s simRat_chr6.simRat.chr6 432166 8 + 647215 TGGCTCCT - -a -s simMouse_chr6.simMouse.chr6 426147 9 + 636262 TATAATGAC -s Anc0.Anc0refChr3 55050 9 + 222631 CCTAATGAC -s Anc1.Anc1refChr6 85841 9 + 197743 CCTAATGAC -s Anc2.Anc2refChr13 59541 9 + 96486 CCTAATGAC -s mr.mrrefChr5 278456 9 + 294540 TATAATGAC -s simDog_chr6.simDog.chr6 406175 9 + 593897 CCTAATGAC -s simHuman_chr6.simHuman.chr6 411185 9 + 601863 CCTAATGAC -s simRat_chr6.simRat.chr6 432174 9 + 647215 TATGATGAC - -a -s simMouse_chr6.simMouse.chr6 426156 6 + 636262 CAGGAA -s Anc0.Anc0refChr3 55066 6 + 222631 CAGAAA -s Anc1.Anc1refChr6 85857 6 + 197743 CAGAAA -s Anc2.Anc2refChr13 59557 6 + 96486 CAGAAA -s mr.mrrefChr5 278472 6 + 294540 CAGAAA -s simDog_chr6.simDog.chr6 406191 6 + 593897 CAGAAA -s simHuman_chr6.simHuman.chr6 411201 6 + 601863 TAGAAA -s simRat_chr6.simRat.chr6 432190 6 + 647215 CAGACA - -a -s simMouse_chr6.simMouse.chr6 426162 14 + 636262 GCAGAGAAGGGAGG -s Anc0.Anc0refChr3 55073 14 + 222631 GCAGAGAAAGGAAG -s Anc1.Anc1refChr6 85864 14 + 197743 GCAGAGAAAGGAAG -s Anc2.Anc2refChr13 59564 14 + 96486 GCAGAGAAAAGAAG -s mr.mrrefChr5 278478 14 + 294540 GCAGAGAAGGGAGG -s simCow_chr6.simCow.chr6 415384 14 + 602619 GCAGAGAAAAGAAG -s simDog_chr6.simDog.chr6 406198 14 + 593897 GCAGACAAAACAGG -s simHuman_chr6.simHuman.chr6 411208 14 + 601863 GCAGAGAAAGGAAG -s simRat_chr6.simRat.chr6 432196 14 + 647215 GCAGAAAAGAGAGG - -a -s simMouse_chr6.simMouse.chr6 426176 8 + 636262 AGTTTCTG -s Anc0.Anc0refChr3 55088 8 + 222631 AATTGCTG -s Anc1.Anc1refChr6 85879 8 + 197743 AATTGCTG -s Anc2.Anc2refChr13 59579 8 + 96486 TATTGCTG -s mr.mrrefChr5 278492 8 + 294540 AGTTGCTG -s simCow_chr6.simCow.chr6 415399 8 + 602619 TATTGTTG -s simDog_chr6.simDog.chr6 406213 8 + 593897 TGTTGCTG -s simHuman_chr6.simHuman.chr6 411223 8 + 601863 AATTGCTG -s simRat_chr6.simRat.chr6 432210 8 + 647215 ACTTGCTT - -a -s simMouse_chr6.simMouse.chr6 426184 39 + 636262 GAGTACCTGGAAATTGCTGACACATGCTTTGCATATGAA -s Anc0.Anc0refChr3 55096 39 + 222631 AAGTACCTTGAAATTGCTGATAAAAATGTTACAAATGAA -s Anc1.Anc1refChr6 85887 39 + 197743 AAGTACCTTGAAATTGCTGATAAAAATGTTACAAATGAA -s Anc2.Anc2refChr13 59594 39 + 96486 AAGTACCCTGAAATTGCTGATAAAAATGTTACAAATGAA -s mr.mrrefChr5 278500 39 + 294540 GAGTACCTGGAAATTGCTGATACATATTTTGCATATGAA -s simCow_chr6.simCow.chr6 415414 39 + 602619 AAGTACCCTGAAATTGCTGATAAAAATGTTACGAATGAA -s simDog_chr6.simDog.chr6 406228 39 + 593897 AAGTACCCTAAAATTGCTGATAAAAATGTTACAAGTGGA -s simHuman_chr6.simHuman.chr6 411231 39 + 601863 AAGTACCTTGAAACTGCTGATAAAAATACTACCAATGAA -s simRat_chr6.simRat.chr6 432218 39 + 647215 GAGTACCTGGAAATTGCCAATATACATTTTGCATATGAA - -a -s simMouse_chr6.simMouse.chr6 426223 72 + 636262 CAAAAGATTCATTCTTCAGCTTCATAGGTGCTAGATCAGCTTTTAACATTGAACTTAATTAAGGAGGATTCC -s Anc0.Anc0refChr3 55136 72 + 222631 TAGTAGAATCATTCTCCAGTAGTATAGGTGCTAGATAGTCTTGTAACATTGGGTTTGCTTGGGAGTAATTCC -s Anc1.Anc1refChr6 85927 72 + 197743 TAGTAGAATCATTCTCCAGTAGTATAGGTGCTAGATAGTCTTGTAACATTGGGTTTGCTTGGGAGTAATTCC -s Anc2.Anc2refChr13 59634 72 + 96486 TTAAGCAACCATTCTCCAGTAGTATAGGTGCTAGATAGTCTTGTAAGATTGGGTATGCTTGGGAGTAATTCC -s mr.mrrefChr5 278540 72 + 294540 CAGTAGAATCATTCTTCAGTTGCATAGGTGCTAGATCAGCTTTTAACATTGAGCTTACTTAGGGATGATTCC -s simCow_chr6.simCow.chr6 415454 67 + 602619 TTAAGCAACCATTCTACAGTAGTGTAGGTGCTAGAG-GTTTTGTAAGACTGGGTATTC----GGGTTAATTC -s simDog_chr6.simDog.chr6 406268 65 + 593897 TTAAGCAACCATTCTCCAGTAGTATAGAGGCTAGATAGTCT-------TTGGGTATGCTTGGTAGTAATTCC -s simHuman_chr6.simHuman.chr6 411271 72 + 601863 TAGTAGAATCATTTTCCAGTAGTATACGTGCTAGATGGCCTTGTAACATTGTGTTTGCTTGGGAGTCATTCC -s simRat_chr6.simRat.chr6 432258 72 + 647215 CAGTAGAATCATCCTTCAGTTGCATAGGCGCTAGATCATCTTTTAACATTGAGCTTACTTAGGGATAATTCC - -a -s simMouse_chr6.simMouse.chr6 426295 19 + 636262 TCAAGATGGTGTGAACAGA -s Anc0.Anc0refChr3 55211 19 + 222631 TCAATCCAGTGTGAACAGA -s Anc1.Anc1refChr6 86002 19 + 197743 TCAATCCAGTGTGAACAGA -s Anc2.Anc2refChr13 59709 19 + 96486 TCAATCCAGTGTGAACAGA -s mr.mrrefChr5 278612 19 + 294540 TCAAGATGGTGTGAACAGA -s simCow_chr6.simCow.chr6 415524 19 + 602619 ACATTCCAGTTTTAACGGA -s simDog_chr6.simDog.chr6 406336 19 + 593897 TCAATCCTGAGTGTACAGA -s simHuman_chr6.simHuman.chr6 411346 19 + 601863 TCAATCCAATGTGAACAGA -s simRat_chr6.simRat.chr6 432330 19 + 647215 TCAAGATGGTGTGAACAGA - -a -s simMouse_chr6.simMouse.chr6 426314 23 + 636262 TGTGTGTTATACTTGGGGCCCCC -s Anc0.Anc0refChr3 55230 23 + 222631 TGTTCTTTATACTTGGGATAAAA -s Anc1.Anc1refChr6 86021 23 + 197743 TGTTCTTTATACTTGGGATAAAA -s Anc2.Anc2refChr13 59728 23 + 96486 TGTTCTTTATACTTGGGATAAAA -s mr.mrrefChr5 278631 23 + 294540 TGTGTGTTATACTTGGGGTCCAC -s simCow_chr6.simCow.chr6 415543 18 + 602619 TGTTC-----ACGCGGGTTCAAA -s simDog_chr6.simDog.chr6 406363 23 + 593897 TGTTCTTTATACTTGGGACAAAA -s simHuman_chr6.simHuman.chr6 411365 23 + 601863 TGCTCTTTATACTTGGGATAAAA -s simRat_chr6.simRat.chr6 432349 23 + 647215 TGTGTGTTATACTTGGGGTCCAC - -a -s simMouse_chr6.simMouse.chr6 426337 4 + 636262 TGCT -s Anc0.Anc0refChr3 55268 4 + 222631 TGCT -s Anc1.Anc1refChr6 86060 4 + 197743 TGCT -s Anc2.Anc2refChr13 59766 4 + 96486 TGCT -s mr.mrrefChr5 278669 4 + 294540 TGCT -s simCow_chr6.simCow.chr6 415576 4 + 602619 TGCT -s simDog_chr6.simDog.chr6 406401 4 + 593897 TGCT -s simHuman_chr6.simHuman.chr6 411404 4 + 601863 CACT -s simRat_chr6.simRat.chr6 432387 4 + 647215 TGCT - -a -s simMouse_chr6.simMouse.chr6 426341 19 + 636262 TGAGGGTACAGTGATTATA -s Anc0.Anc0refChr3 55275 19 + 222631 TGATAGTACAGTGGCTTTA -s Anc1.Anc1refChr6 86067 19 + 197743 TGATAGTACAGTGGCTTTA -s Anc2.Anc2refChr13 59773 19 + 96486 TGATAGTACAGTGGCTTTA -s mr.mrrefChr5 278676 19 + 294540 TGAGGGTACAGTGATTATA -s simCow_chr6.simCow.chr6 415583 19 + 602619 TGATAATACAATGGCTTTA -s simDog_chr6.simDog.chr6 406408 19 + 593897 CTATAGTACAGTAGCTTTA -s simHuman_chr6.simHuman.chr6 411411 19 + 601863 TGATAGTACATTGGCTTTA -s simRat_chr6.simRat.chr6 432394 19 + 647215 TTAGTGTACAGTGATTATA - -a -s simMouse_chr6.simMouse.chr6 426360 19 + 636262 ACTTCTCAAGAGAAATTCT -s Anc0.Anc0refChr3 55294 19 + 222631 ATTTGCTCTCAGAAATCCT -s Anc1.Anc1refChr6 86086 19 + 197743 ATTTGCTCTCAGAAATCCT -s Anc2.Anc2refChr13 59823 19 + 96486 GTTTGCTCTCTATGATCGT -s mr.mrrefChr5 278695 19 + 294540 ACTTCTCAAGAGAAATTCT -s simCow_chr6.simCow.chr6 415651 19 + 602619 GTTCCCATTCCGTGATCAT -s simDog_chr6.simDog.chr6 406458 19 + 593897 GTTTGCTCTCTATGATCGT -s simHuman_chr6.simHuman.chr6 411430 19 + 601863 ATGTGGTGTTAGAAATCCT -s simRat_chr6.simRat.chr6 432413 19 + 647215 ACTTCTCAAGAGTAATTCT - -a -s simMouse_chr6.simMouse.chr6 426379 8 + 636262 GATTAAGC -s Anc0.Anc0refChr3 55313 8 + 222631 GACCAAGT -s Anc1.Anc1refChr6 86105 8 + 197743 GACCAAGT -s Anc2.Anc2refChr13 59848 8 + 96486 GACCAAGT -s mr.mrrefChr5 278714 8 + 294540 GATTAAGC -s simCow_chr6.simCow.chr6 415676 8 + 602619 GACCAAGT -s simDog_chr6.simDog.chr6 406483 8 + 593897 GACCAAGT -s simHuman_chr6.simHuman.chr6 411449 6 + 601863 GA--AAGT -s simRat_chr6.simRat.chr6 432432 8 + 647215 GACTAAGC - -a -s simMouse_chr6.simMouse.chr6 426387 14 + 636262 CATGATATGGTATA -s Anc0.Anc0refChr3 55322 14 + 222631 TATGATCTGGCATA -s Anc1.Anc1refChr6 86114 14 + 197743 TATGATCTGGCATA -s Anc2.Anc2refChr13 59857 14 + 96486 TGTGATCTGGCATA -s mr.mrrefChr5 278722 14 + 294540 CATGATATGGTATA -s simCow_chr6.simCow.chr6 415685 14 + 602619 GGTGATTTGGCCTG -s simDog_chr6.simDog.chr6 406492 14 + 593897 TGCGATCTAGCATA -s simHuman_chr6.simHuman.chr6 411456 14 + 601863 TATGATCTGGCATA -s simRat_chr6.simRat.chr6 432440 14 + 647215 CATGATATGGTATA - -a -s simMouse_chr6.simMouse.chr6 426401 74 + 636262 GCAATCATACCTGTCCCTTGGTATCTTGGGTGAAAGGGAATCAAACACAGTTTCAATACTAGTACCACCTGATA -s Anc0.Anc0refChr3 55336 74 + 222631 GCGATCTTACCTGCTTCTTGGTATCATGGGTGGAGGGGAAGCTAATACAGGCTCAATAGTATTACCTGGTAATC -s Anc1.Anc1refChr6 86128 74 + 197743 GCGATCTTACCTGCTTCTTGGTATCATGGGTGGAGGGGAAGCTAATACAGGCTCAATAGTATTACCTGGTAATC -s Anc2.Anc2refChr13 59871 74 + 96486 GCGATCTTACCTGCTTCTAGGTATCATGGGTGGAGGAGAAGCTAATACAGGCTCAATAGTATCACCTGGTAATC -s mr.mrrefChr5 278736 74 + 294540 GCAATCATACCTGTTCCTTGGTATCTTGGGTGGAAGGGAATCAAACACAGTTTCAATACTAGTACCTGCTGATC -s simCow_chr6.simCow.chr6 415699 72 + 602619 GCGATCTTACCTACTT-TGGGTATCATGGGTGGG-ATGAAGCTAATGCAGGCTCAATAGTACCACCTGGTAATC -s simDog_chr6.simDog.chr6 406506 73 + 593897 GCAATCTCACCTGCTTCTAGGTATCATGGGTGGAGGACAGCTAAATACAGGCTCAATCGTATCACCCGG-AATC -s simHuman_chr6.simHuman.chr6 411471 74 + 601863 GCGACCTTACCTGCTTCTTGTGATTGTGGGTGGAGGGGAAGCTATTACAAGGTCATTAGTATTATCTGGTCATC -s simRat_chr6.simRat.chr6 432454 73 + 647215 GCAATCATACCAATTCCTTGGTATCTTGGGTGGA-TGGAATCAAACACAGTTTCAATACTAGTACCTGAAGTTC - -a -s simMouse_chr6.simMouse.chr6 426475 22 + 636262 AACATCTCCTGTTGTGATAATA -s Anc0.Anc0refChr3 55411 22 + 222631 GACATCTCCTTTTGTCATCACA -s Anc1.Anc1refChr6 86203 22 + 197743 GACATCTCCTTTTGTCATCACA -s Anc2.Anc2refChr13 59946 22 + 96486 GACATCTCCTTTTGTCATCACA -s mr.mrrefChr5 278810 22 + 294540 GACATCTCCTGTTGTGATAATA -s simCow_chr6.simCow.chr6 415772 22 + 602619 GACATCTCCTTTTGTCACCGCA -s simDog_chr6.simDog.chr6 406580 22 + 593897 GACATCTACTTTTGTCATCACG -s simHuman_chr6.simHuman.chr6 411546 22 + 601863 GATATCTCCTTTCATCATCACA -s simRat_chr6.simRat.chr6 432527 22 + 647215 GGCATCTCATGTTGTGATGATC - -a -s simMouse_chr6.simMouse.chr6 426497 32 + 636262 AGCAAGCTCGGGAAATGGCATAATCAGCTGGT -s Anc0.Anc0refChr3 55434 32 + 222631 AGTAAACTCAGGAAATGGCCTAAAAAGTTGTT -s Anc1.Anc1refChr6 86226 32 + 197743 AGTAAACTCAGGAAATGGCCTAAAAAGTTGTT -s Anc2.Anc2refChr13 59969 32 + 96486 AGTACACTCATGAAATGGCCTAAAAAGTTATT -s mr.mrrefChr5 278832 32 + 294540 AGCAAGCTCAGGAAATGGCCTAAAAAGTTGGT -s simCow_chr6.simCow.chr6 415795 22 + 602619 A-------CTTCAAATGGCTT---CTGTTTTG -s simDog_chr6.simDog.chr6 406603 32 + 593897 AGTACACTCATGAAATGGCCTAAAAAGTCATT -s simHuman_chr6.simHuman.chr6 411569 32 + 601863 AGTAAATTCAGGAAATGGTCTAAAAAGTTGTT -s simRat_chr6.simRat.chr6 432549 27 + 647215 AGC----TCAGGAAATAGCCTAGAAAGTTG-T - -a -s simMouse_chr6.simMouse.chr6 426529 16 + 636262 TTTCAATTGGATACTG -s Anc0.Anc0refChr3 55466 16 + 222631 TTACAATCAGATACTG -s Anc1.Anc1refChr6 86258 16 + 197743 TTACAATCAGATACTG -s Anc2.Anc2refChr13 60001 16 + 96486 TTATAATCAGATACAG -s mr.mrrefChr5 278864 16 + 294540 TTTCAATTGGATACTG -s simCow_chr6.simCow.chr6 230324 16 + 602619 TTATATTTGCATACAG -s simCow_chr6.simCow.chr6 415817 16 + 602619 TCCCGACATGATGCTA -s simDog_chr6.simDog.chr6 406635 16 + 593897 TTATAGTCAAACACAG -s simHuman_chr6.simHuman.chr6 411601 16 + 601863 TTCCGATCAGAAACTG -s simRat_chr6.simRat.chr6 432576 16 + 647215 TTTTAATTGAATACTG - -a -s simMouse_chr6.simMouse.chr6 426545 3 + 636262 TTA -s Anc0.Anc0refChr3 55482 3 + 222631 CTA -s Anc1.Anc1refChr6 86274 3 + 197743 CTA -s Anc2.Anc2refChr13 60017 3 + 96486 CTA -s mr.mrrefChr5 278880 3 + 294540 TTA -s simCow_chr6.simCow.chr6 415833 3 + 602619 CTA -s simDog_chr6.simDog.chr6 406651 3 + 593897 TTA -s simHuman_chr6.simHuman.chr6 411617 3 + 601863 CTA -s simRat_chr6.simRat.chr6 432592 3 + 647215 TTA - -a -s simMouse_chr6.simMouse.chr6 426548 1 + 636262 T -s Anc0.Anc0refChr3 55485 1 + 222631 C -s Anc1.Anc1refChr6 86277 1 + 197743 C -s Anc2.Anc2refChr13 60020 1 + 96486 C -s mr.mrrefChr5 278883 1 + 294540 T -s simCow_chr6.simCow.chr6 230340 1 + 602619 C -s simCow_chr6.simCow.chr6 415836 1 + 602619 C -s simDog_chr6.simDog.chr6 406654 1 + 593897 C -s simHuman_chr6.simHuman.chr6 411620 1 + 601863 C -s simRat_chr6.simRat.chr6 432595 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 426549 2 + 636262 GT -s Anc0.Anc0refChr3 55486 2 + 222631 GT -s Anc1.Anc1refChr6 86278 2 + 197743 GT -s Anc2.Anc2refChr13 60021 2 + 96486 GT -s mr.mrrefChr5 278884 2 + 294540 GT -s simCow_chr6.simCow.chr6 415841 2 + 602619 GT -s simHuman_chr6.simHuman.chr6 411621 2 + 601863 AT -s simRat_chr6.simRat.chr6 432596 2 + 647215 GT - -a -s simMouse_chr6.simMouse.chr6 426551 7 + 636262 GCAGATA -s Anc0.Anc0refChr3 55488 7 + 222631 ACAAATA -s Anc1.Anc1refChr6 86280 7 + 197743 ACAAATA -s Anc2.Anc2refChr13 60023 7 + 96486 ACAAATA -s mr.mrrefChr5 278886 7 + 294540 GCAAATA -s simCow_chr6.simCow.chr6 230341 7 + 602619 ACAGGCA -s simCow_chr6.simCow.chr6 415843 4 + 602619 ACAA--- -s simDog_chr6.simDog.chr6 406655 7 + 593897 ACAAATA -s simHuman_chr6.simHuman.chr6 411623 7 + 601863 ACAAATG -s simRat_chr6.simRat.chr6 432598 7 + 647215 GCAAATA - -a -s simMouse_chr6.simMouse.chr6 426558 5 + 636262 CAAGA -s Anc0.Anc0refChr3 55515 5 + 222631 CAAAA -s Anc1.Anc1refChr6 86307 5 + 197743 CAAAA -s Anc2.Anc2refChr13 60050 5 + 96486 CAAAA -s mr.mrrefChr5 278913 5 + 294540 CAAGA -s simCow_chr6.simCow.chr6 230357 5 + 602619 CCAGG -s simCow_chr6.simCow.chr6 415862 5 + 602619 CAGAA -s simDog_chr6.simDog.chr6 406682 5 + 593897 CAAAA -s simHuman_chr6.simHuman.chr6 411650 5 + 601863 CAATA -s simRat_chr6.simRat.chr6 432625 5 + 647215 CAAAA - -a -s simMouse_chr6.simMouse.chr6 426563 2 + 636262 AG -s Anc0.Anc0refChr3 55521 2 + 222631 AG -s Anc1.Anc1refChr6 86313 2 + 197743 AG -s Anc2.Anc2refChr13 60056 2 + 96486 AG -s mr.mrrefChr5 278918 2 + 294540 AG -s simCow_chr6.simCow.chr6 230363 2 + 602619 GG -s simCow_chr6.simCow.chr6 415868 2 + 602619 AG -s simDog_chr6.simDog.chr6 406688 2 + 593897 AA -s simHuman_chr6.simHuman.chr6 411656 2 + 601863 AG -s simRat_chr6.simRat.chr6 432630 2 + 647215 AG - -a -s simMouse_chr6.simMouse.chr6 426565 9 + 636262 AAGCTATCC -s Anc0.Anc0refChr3 55523 9 + 222631 AAGCTATTC -s Anc1.Anc1refChr6 86315 9 + 197743 AAGCTATTC -s Anc2.Anc2refChr13 60058 9 + 96486 ATGCCATTC -s mr.mrrefChr5 278920 9 + 294540 AAGCTATTC -s simCow_chr6.simCow.chr6 230365 9 + 602619 ACTCTGTTA -s simCow_chr6.simCow.chr6 415876 9 + 602619 AGGCCATTC -s simDog_chr6.simDog.chr6 406690 9 + 593897 CTGCCATTC -s simHuman_chr6.simHuman.chr6 411658 9 + 601863 AAGCTATTC -s simRat_chr6.simRat.chr6 432632 9 + 647215 AAGCTATTC - -a -s simMouse_chr6.simMouse.chr6 426574 4 + 636262 AAAG -s Anc0.Anc0refChr3 55532 4 + 222631 AAAG -s Anc1.Anc1refChr6 86324 4 + 197743 AAAG -s Anc2.Anc2refChr13 60067 4 + 96486 AAAG -s mr.mrrefChr5 278929 4 + 294540 AAAG -s simCow_chr6.simCow.chr6 230374 4 + 602619 AAAG -s simCow_chr6.simCow.chr6 415889 4 + 602619 AATG -s simDog_chr6.simDog.chr6 406699 4 + 593897 AAAC -s simHuman_chr6.simHuman.chr6 411667 4 + 601863 AAAG -s simRat_chr6.simRat.chr6 432641 4 + 647215 AAAG - -a -s simMouse_chr6.simMouse.chr6 426578 2 + 636262 CA -s Anc0.Anc0refChr3 55536 2 + 222631 TA -s Anc1.Anc1refChr6 86328 2 + 197743 TA -s Anc2.Anc2refChr13 60071 2 + 96486 TA -s mr.mrrefChr5 278933 2 + 294540 CA -s simCow_chr6.simCow.chr6 415893 2 + 602619 TC -s simDog_chr6.simDog.chr6 406703 2 + 593897 AA -s simHuman_chr6.simHuman.chr6 411671 2 + 601863 TT -s simRat_chr6.simRat.chr6 432645 1 + 647215 C- - -a -s simMouse_chr6.simMouse.chr6 426580 15 + 636262 GCTTAATTGATGATT -s Anc0.Anc0refChr3 55538 15 + 222631 GCTTAATGGATGGTT -s Anc1.Anc1refChr6 86330 15 + 197743 GCTTAATGGATGGTT -s Anc2.Anc2refChr13 60073 15 + 96486 GATTAGTGGATAGTT -s mr.mrrefChr5 278935 15 + 294540 GCTTAATGGATGATT -s simCow_chr6.simCow.chr6 230378 15 + 602619 GATTATTGTAAAGGC -s simCow_chr6.simCow.chr6 415898 15 + 602619 GATTAGTGGATGGTT -s simDog_chr6.simDog.chr6 406705 15 + 593897 AATTAGTAAACAGTT -s simHuman_chr6.simHuman.chr6 411673 15 + 601863 GCTTAATGGATGGTT -s simRat_chr6.simRat.chr6 432646 12 + 647215 ---TTGTGCAAATTT - -a -s simMouse_chr6.simMouse.chr6 426595 16 + 636262 TGTGCAAATAGTTTGT -s Anc0.Anc0refChr3 55553 4 + 222631 A------------TGT -s Anc1.Anc1refChr6 86345 4 + 197743 A------------TGT -s Anc2.Anc2refChr13 60088 4 + 96486 A------------TGT -s mr.mrrefChr5 278950 16 + 294540 TGTGCAAATAGTTTGT -s simCow_chr6.simCow.chr6 230393 4 + 602619 C------------TGC -s simCow_chr6.simCow.chr6 415914 4 + 602619 A------------TCT -s simDog_chr6.simDog.chr6 406720 4 + 593897 A------------TGT -s simHuman_chr6.simHuman.chr6 411688 4 + 601863 A------------TGT -s simRat_chr6.simRat.chr6 432658 16 + 647215 TGTGCAACTAGTTTGT - -a -s simMouse_chr6.simMouse.chr6 426611 9 + 636262 GTCTTAATC -s Anc0.Anc0refChr3 55557 9 + 222631 GTATTATTC -s Anc1.Anc1refChr6 86349 9 + 197743 GTATTATTC -s Anc2.Anc2refChr13 60092 9 + 96486 TTATTATTC -s mr.mrrefChr5 278966 9 + 294540 GTCTTAATC -s simCow_chr6.simCow.chr6 230401 9 + 602619 TTGTTGTTC -s simCow_chr6.simCow.chr6 415918 9 + 602619 TTGTTGCTC -s simDog_chr6.simDog.chr6 406724 9 + 593897 ACATTATTC -s simHuman_chr6.simHuman.chr6 411692 9 + 601863 GTATTATGC -s simRat_chr6.simRat.chr6 432674 9 + 647215 GTCTTAATC - -a -s simMouse_chr6.simMouse.chr6 426620 15 + 636262 TCGTGCCACCAACAG -s Anc0.Anc0refChr3 55566 15 + 222631 TCATGTCACAAACAG -s Anc1.Anc1refChr6 86358 15 + 197743 TCATGTCACAAACAG -s Anc2.Anc2refChr13 60101 15 + 96486 TCATGTCACAAGCAG -s mr.mrrefChr5 278975 15 + 294540 TCATGTCACCAACAG -s simCow_chr6.simCow.chr6 230410 15 + 602619 TCATGCCACATGCAC -s simCow_chr6.simCow.chr6 415927 2 + 602619 TC------------- -s simDog_chr6.simDog.chr6 406733 15 + 593897 CCATGTCACAAGTGG -s simHuman_chr6.simHuman.chr6 411701 15 + 601863 TCATGTCACACACAG -s simRat_chr6.simRat.chr6 432684 15 + 647215 TCATGTCATCAGCAG - -a -s simMouse_chr6.simMouse.chr6 426635 6 + 636262 TTAGAG -s Anc0.Anc0refChr3 55586 6 + 222631 TTAGAA -s Anc1.Anc1refChr6 86378 6 + 197743 TTAGAA -s Anc2.Anc2refChr13 60121 6 + 96486 TTACAA -s mr.mrrefChr5 278990 6 + 294540 TTAGAG -s simCow_chr6.simCow.chr6 230430 6 + 602619 TTATGA -s simDog_chr6.simDog.chr6 406753 6 + 593897 TTACAA -s simHuman_chr6.simHuman.chr6 411721 6 + 601863 TTAGAA -s simRat_chr6.simRat.chr6 432699 6 + 647215 TTAGAG - -a -s simMouse_chr6.simMouse.chr6 426641 1 + 636262 C -s Anc0.Anc0refChr3 55592 1 + 222631 C -s Anc1.Anc1refChr6 86384 1 + 197743 C -s Anc2.Anc2refChr13 60127 1 + 96486 C -s mr.mrrefChr5 278996 1 + 294540 C -s simCow_chr6.simCow.chr6 230436 1 + 602619 C -s simDog_chr6.simDog.chr6 406759 1 + 593897 C -s simHuman_chr6.simHuman.chr6 411727 1 + 601863 C -s simRat_chr6.simRat.chr6 432711 1 + 647215 C - -a -s simMouse_chr6.simMouse.chr6 426642 10 + 636262 CCCAGGATTC -s Anc0.Anc0refChr3 55593 10 + 222631 CCTAGGATTC -s Anc1.Anc1refChr6 86385 10 + 197743 CCTAGGATTC -s Anc2.Anc2refChr13 60128 10 + 96486 CCTAGGATTC -s mr.mrrefChr5 278997 10 + 294540 CCCAGGATTC -s simCow_chr6.simCow.chr6 230442 10 + 602619 CCAAGGATTC -s simCow_chr6.simCow.chr6 415929 9 + 602619 -CAAGGATTC -s simDog_chr6.simDog.chr6 406760 10 + 593897 CCTAGGATTC -s simHuman_chr6.simHuman.chr6 411728 10 + 601863 TCTAGTATTC -s simRat_chr6.simRat.chr6 432712 10 + 647215 CCCAGAATTC - -a -s simMouse_chr6.simMouse.chr6 426652 20 + 636262 AACTATTCAGCCTTTTTCTG -s Anc0.Anc0refChr3 55607 20 + 222631 GACTACTCAGCCTCTTTCCA -s Anc1.Anc1refChr6 86399 20 + 197743 GACTACTCAGCCTCTTTCCA -s Anc2.Anc2refChr13 60142 20 + 96486 GACTACTCAGCCTCCCTCGA -s mr.mrrefChr5 279007 20 + 294540 AACTATTCAGCCTTTTTCCG -s simCow_chr6.simCow.chr6 230456 20 + 602619 AACTACCCAGCCTCTCTCAA -s simCow_chr6.simCow.chr6 415942 20 + 602619 AACTACCCAGCCTCCTCCGA -s simDog_chr6.simDog.chr6 406774 20 + 593897 GAATATTGAGCCTCCCTCGA -s simHuman_chr6.simHuman.chr6 411742 20 + 601863 GACTAATTAGGCACTTTCCT -s simRat_chr6.simRat.chr6 432722 20 + 647215 AACTATTCAGCCTATTTCCG - -a -s simMouse_chr6.simMouse.chr6 426672 27 + 636262 AAAAACCACAAAATAGAACCAACAGCT -s Anc0.Anc0refChr3 55631 22 + 222631 AAAAACCA-----TAGAAACATCATCT -s Anc1.Anc1refChr6 86423 22 + 197743 AAAAACCA-----TAGAAACATCATCT -s Anc2.Anc2refChr13 60166 22 + 96486 AAACACCA-----TAGAAACATCATGT -s mr.mrrefChr5 279027 27 + 294540 AAAAACCACAAAATAGAACCAACAGCT -s simCow_chr6.simCow.chr6 230480 22 + 602619 AAACGTCA-----TGAACACATCATGT -s simCow_chr6.simCow.chr6 415966 22 + 602619 AAATACCA-----TGGAAACATCATGT -s simDog_chr6.simDog.chr6 406798 22 + 593897 GAACACCA-----TAGAAACATCATGT -s simHuman_chr6.simHuman.chr6 411766 22 + 601863 AAAAACCA-----TAGAAACATCATCT -s simRat_chr6.simRat.chr6 432742 27 + 647215 AAAAACCACCAAATAGAACCAACAGCT - -a -s simMouse_chr6.simMouse.chr6 426699 49 + 636262 TATATTAATAAGCAAATAAACTGACTCAGGGACTCAGGTCCTGCAACTC -s Anc0.Anc0refChr3 55653 33 + 222631 TGTAATCATAAACAGATAAAGTGATTCAGC----------------CTA -s Anc1.Anc1refChr6 86445 33 + 197743 TGTAATCATAAACAGATAAAGTGATTCAGC----------------CTA -s Anc2.Anc2refChr13 60190 33 + 96486 TGTAATCATAAACAGATGAAGTGCTACATC----------------CTA -s mr.mrrefChr5 279054 41 + 294540 TGTATTAATAAGCAAATAAACTGACTCAGG--------TCCTGCAACTC -s simCow_chr6.simCow.chr6 230504 10 + 602619 TGTGACATTG--------------------------------------- -s simCow_chr6.simCow.chr6 415990 10 + 602619 TGTAATCATG--------------------------------------- -s simDog_chr6.simDog.chr6 406820 33 + 593897 TGGAATCATAAACAGATGAAGTGCTACATC----------------CTA -s simHuman_chr6.simHuman.chr6 411788 33 + 601863 TGTAATCACAAAAAGATACAGTGAGTGAGT----------------CTG -s simRat_chr6.simRat.chr6 432769 41 + 647215 TGTATTAATAAGCCAATAAACTGACTCAGG--------TCCTGCAACTC - -a -s simMouse_chr6.simMouse.chr6 426748 9 + 636262 TTCATGGTA -s Anc0.Anc0refChr3 55686 9 + 222631 ATTATGGTA -s Anc1.Anc1refChr6 86478 9 + 197743 ATTATGGTA -s Anc2.Anc2refChr13 60223 9 + 96486 ATTATGGTA -s mr.mrrefChr5 279095 9 + 294540 TTCATGGTA -s simDog_chr6.simDog.chr6 406859 9 + 593897 ATTATGGTA -s simHuman_chr6.simHuman.chr6 411821 9 + 601863 ATTATGGTA -s simRat_chr6.simRat.chr6 432810 4 + 647215 T-----GTA - -a -s simMouse_chr6.simMouse.chr6 426757 65 + 636262 CTCAAAAATAGCTGTCCATATGCAAGCTTGGATTAACTGACTTGTCTCAGCTTAAATTGCTAAGA -s Anc0.Anc0refChr3 55695 65 + 222631 CTAGAAAATAGGTGCTTATTGGCAGGCTTGTATGACCTGATTTGTCTCTGCCCAAATCGCAAAGA -s Anc1.Anc1refChr6 86487 65 + 197743 CTAGAAAATAGGTGCTTATTGGCAGGCTTGTATGACCTGATTTGTCTCTGCCCAAATCGCAAAGA -s Anc2.Anc2refChr13 60232 65 + 96486 CTAGAGAATGGGTGTTTTATGTCAGGCATGTATGACCTGATTTGTCTTTGCCCAAATCTCAAAGA -s mr.mrrefChr5 279104 65 + 294540 CTCAAAAATAGCTGCCCATTTGCAAGCTTGGATTACCTGACTTGTCTCAGCTTAAATTGCAAAGA -s simCow_chr6.simCow.chr6 230514 28 + 602619 -------------------------------------TGATTTGTCTTTGCTCAAGTCTAAAAGA -s simCow_chr6.simCow.chr6 416000 27 + 602619 -------------------------------------TGGGTCGTCTTTGCTCAAGTC-CAAAGG -s simDog_chr6.simDog.chr6 406872 65 + 593897 CTAGAGAATGGGTGTTTTATGTCAGGCATGTATGACCTGAATTGTTTTTGCCTAAATCTTAAAGA -s simHuman_chr6.simHuman.chr6 411830 65 + 601863 CTTCAAAATAAGTGCTTATTGGCAGGCTTTCGTGACCTGATTTGTCTCCACCCAAATCGCACAGG -s simRat_chr6.simRat.chr6 432814 65 + 647215 CTCAAAAATAGCTGCCCATTTGCAAGCTTGGATAACCTGACTTATCTGAGCTTGAATTGCAAAGA - -a -s simMouse_chr6.simMouse.chr6 426822 30 + 636262 AGATTTTGTACATAGGGTAGATGCTTTCCA -s Anc0.Anc0refChr3 55762 30 + 222631 AGATTTTGCATGTAGGGTAGATGTTCTTAA -s Anc1.Anc1refChr6 86554 30 + 197743 AGATTTTGCATGTAGGGTAGATGTTCTTAA -s Anc2.Anc2refChr13 60299 30 + 96486 AGACATTGCATTTAGGGTAGATGTTCTTAA -s mr.mrrefChr5 279169 30 + 294540 AGATTTTGTATGTAGGGTAGATGCTTTCCA -s simCow_chr6.simCow.chr6 230544 30 + 602619 AGACATGGCATTTAAGGCAAATGTTCTTCA -s simCow_chr6.simCow.chr6 416029 16 + 602619 AGACATGGCATTTAGG-------------- -s simDog_chr6.simDog.chr6 406939 30 + 593897 AGACATTGTGTTTAGGGTAGATGCTCTCAA -s simHuman_chr6.simHuman.chr6 411897 29 + 601863 AGATTTTGCATGTAGGGTA-ATGTTCTTAA -s simRat_chr6.simRat.chr6 432879 30 + 647215 AGATCTTGTATGCAGGGTACATGCTTTCCA - -a -s simMouse_chr6.simMouse.chr6 426852 32 + 636262 AAAGATGGTTTAAGTCGACTTTTTTGACATGG -s Anc0.Anc0refChr3 55794 32 + 222631 GAAGATGGTTTAAGTCGATTTTACTGAGATGG -s Anc1.Anc1refChr6 86586 32 + 197743 GAAGATGGTTTAAGTCGATTTTACTGAGATGG -s Anc2.Anc2refChr13 60331 32 + 96486 GAAGATGGTTTAAATTGATATTACTGAGATGG -s mr.mrrefChr5 279199 32 + 294540 AAAGATGGTTTAAGTCGACTTTTTTGACATGG -s simCow_chr6.simCow.chr6 230576 31 + 602619 GAAGATGGTTTAA-TTGATGTTTTTGAGATGG -s simDog_chr6.simDog.chr6 406971 32 + 593897 GAAGTTGGTTTAAATTAACATTACTGAGATGG -s simHuman_chr6.simHuman.chr6 411928 21 + 601863 GAAGATAGTTTAAGTCGATT-----------A -s simRat_chr6.simRat.chr6 432909 32 + 647215 ATCGATGGTTTAAATTGACTTTTTTGACATGG - -a -s simMouse_chr6.simMouse.chr6 426884 4 + 636262 GTTA -s Anc0.Anc0refChr3 55826 4 + 222631 GTAG -s Anc1.Anc1refChr6 86618 4 + 197743 GTAG -s Anc2.Anc2refChr13 60365 4 + 96486 GTAG -s mr.mrrefChr5 279231 4 + 294540 GTTA -s simCow_chr6.simCow.chr6 230607 1 + 602619 ---G -s simDog_chr6.simDog.chr6 407006 4 + 593897 GTAG -s simHuman_chr6.simHuman.chr6 411949 4 + 601863 GCAG -s simRat_chr6.simRat.chr6 432941 4 + 647215 GTTA - -a -s simMouse_chr6.simMouse.chr6 426888 5 + 636262 TTCTT -s Anc0.Anc0refChr3 55830 5 + 222631 TTCTT -s Anc1.Anc1refChr6 86622 5 + 197743 TTCTT -s Anc2.Anc2refChr13 60369 5 + 96486 TTCTT -s mr.mrrefChr5 279235 5 + 294540 TTCTT -s simCow_chr6.simCow.chr6 230608 5 + 602619 TTCTT -s simDog_chr6.simDog.chr6 407021 5 + 593897 TTCTT -s simHuman_chr6.simHuman.chr6 411953 5 + 601863 TTCTT -s simRat_chr6.simRat.chr6 432945 5 + 647215 TTCTT - -a -s simMouse_chr6.simMouse.chr6 426893 3 + 636262 CTG -s Anc0.Anc0refChr3 55835 3 + 222631 TTA -s Anc1.Anc1refChr6 86627 3 + 197743 TTA -s Anc2.Anc2refChr13 60374 3 + 96486 TTA -s mr.mrrefChr5 279240 3 + 294540 CTG -s simCow_chr6.simCow.chr6 230615 3 + 602619 TTA -s simDog_chr6.simDog.chr6 407026 3 + 593897 TTA -s simHuman_chr6.simHuman.chr6 411958 3 + 601863 TTA -s simRat_chr6.simRat.chr6 432950 3 + 647215 CTG - -a -s simMouse_chr6.simMouse.chr6 426896 2 + 636262 AC -s Anc0.Anc0refChr3 55838 2 + 222631 TC -s Anc1.Anc1refChr6 86630 2 + 197743 TC -s Anc2.Anc2refChr13 60377 2 + 96486 TC -s mr.mrrefChr5 279243 2 + 294540 AC -s simCow_chr6.simCow.chr6 230618 2 + 602619 TC -s simDog_chr6.simDog.chr6 407030 2 + 593897 TT -s simHuman_chr6.simHuman.chr6 411961 2 + 601863 TC -s simRat_chr6.simRat.chr6 432953 2 + 647215 AA - -a -s simMouse_chr6.simMouse.chr6 426898 8 + 636262 AACACTCA -s Anc0.Anc0refChr3 55840 8 + 222631 ATCCTTCA -s Anc1.Anc1refChr6 86632 8 + 197743 ATCCTTCA -s Anc2.Anc2refChr13 60379 8 + 96486 ATCCTTCA -s mr.mrrefChr5 279245 8 + 294540 AACACTCA -s simCow_chr6.simCow.chr6 230643 8 + 602619 ATTCTTCA -s simDog_chr6.simDog.chr6 407032 8 + 593897 GTCCTTCA -s simHuman_chr6.simHuman.chr6 411963 8 + 601863 ATCCTTCA -s simRat_chr6.simRat.chr6 432955 8 + 647215 AACACTCA - -a -s simMouse_chr6.simMouse.chr6 426906 63 + 636262 TAAGATTCACATCCGCCAATGTTTTATATGGTTTTAGTAGCCTGCTTGCCTTTATTCATGCTT -s Anc0.Anc0refChr3 55848 2 + 222631 CC------------------------------------------------------------- -s Anc1.Anc1refChr6 86640 2 + 197743 CC------------------------------------------------------------- -s Anc2.Anc2refChr13 60388 2 + 96486 CC------------------------------------------------------------- -s mr.mrrefChr5 279253 62 + 294540 TAAGATTCACATCCGCCAATGTTTTATAAGGTTC-AGTAGCCTGGTTGCCTTTTTTCATGCTT -s simCow_chr6.simCow.chr6 230652 2 + 602619 TG------------------------------------------------------------- -s simDog_chr6.simDog.chr6 407041 2 + 593897 CC------------------------------------------------------------- -s simHuman_chr6.simHuman.chr6 411971 2 + 601863 CC------------------------------------------------------------- -s simRat_chr6.simRat.chr6 432963 62 + 647215 TGGGATTCATATCCGCCAATGATTTATAAGGTTC-AGTAGCCTGGTTGCCTTTTTTCATGCTT - -a -s simMouse_chr6.simMouse.chr6 426969 6 + 636262 CAATGT -s Anc0.Anc0refChr3 55850 1 + 222631 -----T -s Anc1.Anc1refChr6 86642 1 + 197743 -----T -s Anc2.Anc2refChr13 60390 1 + 96486 -----T -s mr.mrrefChr5 279315 6 + 294540 CAGTGT -s simCow_chr6.simCow.chr6 230654 1 + 602619 -----T -s simDog_chr6.simDog.chr6 407043 1 + 593897 -----T -s simHuman_chr6.simHuman.chr6 411973 1 + 601863 -----T -s simRat_chr6.simRat.chr6 433026 6 + 647215 CAGTGT - -a -s simMouse_chr6.simMouse.chr6 426975 4 + 636262 TCGT -s Anc0.Anc0refChr3 55852 4 + 222631 TTGT -s Anc1.Anc1refChr6 86644 4 + 197743 TTGT -s Anc2.Anc2refChr13 60392 4 + 96486 TTAT -s mr.mrrefChr5 279322 4 + 294540 TCGT -s simCow_chr6.simCow.chr6 230656 4 + 602619 TTAT -s simDog_chr6.simDog.chr6 407045 4 + 593897 TCAT -s simHuman_chr6.simHuman.chr6 411975 4 + 601863 TTGT -s simRat_chr6.simRat.chr6 433033 4 + 647215 TTGG - -a -s simMouse_chr6.simMouse.chr6 426979 13 + 636262 CACACTCCAGACT -s Anc0.Anc0refChr3 55856 13 + 222631 CACACTCCAGAGG -s Anc1.Anc1refChr6 86648 13 + 197743 CACACTCCAGAGG -s Anc2.Anc2refChr13 60396 13 + 96486 CACACTACAGAGG -s mr.mrrefChr5 279326 13 + 294540 CACACTCCAGACT -s simCow_chr6.simCow.chr6 230661 13 + 602619 CTTGTTTCTCAAG -s simDog_chr6.simDog.chr6 407049 12 + 593897 CACAC-ACAGAGG -s simHuman_chr6.simHuman.chr6 411979 13 + 601863 TGCACTCCAAAGG -s simRat_chr6.simRat.chr6 433037 13 + 647215 CACACTCCAGACT - -a -s simMouse_chr6.simMouse.chr6 426992 4 + 636262 CAGG -s Anc0.Anc0refChr3 55870 4 + 222631 CAGG -s Anc1.Anc1refChr6 86662 4 + 197743 CAGG -s Anc2.Anc2refChr13 60410 4 + 96486 CAGG -s mr.mrrefChr5 279339 4 + 294540 CAGG -s simCow_chr6.simCow.chr6 230675 3 + 602619 CAG- -s simDog_chr6.simDog.chr6 407062 4 + 593897 CAGG -s simHuman_chr6.simHuman.chr6 411993 4 + 601863 CAGG -s simRat_chr6.simRat.chr6 433050 4 + 647215 CAGG - -a -s simMouse_chr6.simMouse.chr6 426996 56 + 636262 TGTGATATTGCTGCTACAAGAAACTCACTCATGTAGGATTTAGACTTTCATGACCC -s Anc0.Anc0refChr3 55905 52 + 222631 TAT----TGGCTGTAATAAAAAACTTAGTGATATAAGATTTAACCTTTTATTACCT -s Anc1.Anc1refChr6 86697 56 + 197743 TATAATATGGCTGTAATAAAAAACTTAGTGATATAAGATTTAACCTTTTATTACCT -s Anc2.Anc2refChr13 60449 52 + 96486 TAT----TGCATGTAATAAAATACTTAGTGTTATAAGCTTTAACTTTTTATTACTT -s mr.mrrefChr5 279343 56 + 294540 TGTAATATTGCTGCAACAAGAAACTCACTCATGTAGGATTTAGACTTTCATTACCC -s simCow_chr6.simCow.chr6 230709 52 + 602619 TCA----TGCTTGTAACAAAAGACTTAATGGTATGTGCTTTGTCTTTTTCTCTCTT -s simDog_chr6.simDog.chr6 407101 52 + 593897 TAT----TGCATGTTCTTAAGTACTTAGTCTTACAACCTTTAACTTTTTATTACTT -s simHuman_chr6.simHuman.chr6 412028 56 + 601863 TATAATCGGGCTGTAATAAAAAACTTAGTGATATAAGACTTAACCTTTTATTGCCT -s simRat_chr6.simRat.chr6 433054 56 + 647215 TGCAATGTTGTTGCAACAAGAAACCCACTCATGTAGGATTTAGACTATCATTACTC - -a -s simMouse_chr6.simMouse.chr6 427052 20 + 636262 ATAAAGCTGGAGCAAGCAGC -s Anc0.Anc0refChr3 55957 20 + 222631 GCAAAGCCGCAGCAAGCAGC -s Anc1.Anc1refChr6 86753 20 + 197743 GCAAAGCCGCAGCAAGCAGC -s Anc2.Anc2refChr13 60501 20 + 96486 GCAAAGTCGCAGCTAACAAC -s mr.mrrefChr5 279399 20 + 294540 ATAAAGCTGGAGCAAGCAGC -s simCow_chr6.simCow.chr6 230762 17 + 602619 GCTAAGTCTCAGCTATT--- -s simDog_chr6.simDog.chr6 407153 20 + 593897 GCAAAGTGGCCGCTAACAAC -s simHuman_chr6.simHuman.chr6 412084 17 + 601863 G---AGCCACAGCAAGCGGC -s simRat_chr6.simRat.chr6 433110 20 + 647215 TCAAAGTTGGAGCAGGCTGC - -a -s simMouse_chr6.simMouse.chr6 427072 38 + 636262 AAGTCAATGTAGTAGGCTATGAGCCACAAATGAGTCTT -s Anc0.Anc0refChr3 55978 38 + 222631 ATGTGATTGTATTAGGCTATGAGCTGCAAGTAAGTCTT -s Anc1.Anc1refChr6 86774 38 + 197743 ATGTGATTGTATTAGGCTATGAGCTGCAAGTAAGTCTT -s Anc2.Anc2refChr13 60522 38 + 96486 GTGTGATTGTATTAGGCTATGAGCTGCAAGTAAGTCTT -s mr.mrrefChr5 279420 38 + 294540 AAGTGAATGTAGTAGGCTATGAGCCACAAATGAGTCTT -s simCow_chr6.simCow.chr6 416045 34 + 602619 ----GATTGTATTAGGCTATGTGCTGCAAGTAAGTCTT -s simDog_chr6.simDog.chr6 407174 38 + 593897 GTGTCATTGTATTACGCTATGAGCTGAAAGTAAGTCAT -s simHuman_chr6.simHuman.chr6 412102 36 + 601863 ATGTGATTGT--CAGGCTACAAGCTGCAAGTAAGTCTT -s simRat_chr6.simRat.chr6 433131 38 + 647215 AAGTGAATGTATAAGGCCATGAGCCACAAATGAGTCTT - -a -s simMouse_chr6.simMouse.chr6 427110 12 + 636262 CGTCAATAGCCT -s Anc0.Anc0refChr3 56016 12 + 222631 CATCACTAGCCC -s Anc1.Anc1refChr6 86812 12 + 197743 CATCACTAGCCC -s Anc2.Anc2refChr13 60560 12 + 96486 CACCACTAGCCC -s mr.mrrefChr5 279458 12 + 294540 CATCAATAGCCC -s simCow_chr6.simCow.chr6 416090 12 + 602619 CACCACCAGCAC -s simDog_chr6.simDog.chr6 407212 12 + 593897 CACAACTAGCCC -s simHuman_chr6.simHuman.chr6 412138 12 + 601863 CATCACTCACCC -s simRat_chr6.simRat.chr6 433169 12 + 647215 CATCAATAGCCC - -a -s simMouse_chr6.simMouse.chr6 427122 38 + 636262 AGAAATTCATAGCTCTCAGTTATCCTGAAGCATGATTC -s Anc0.Anc0refChr3 56034 37 + 222631 AGAAATTAGTATCCCTCAGTTGCCCTGAGC-ATTTATC -s Anc1.Anc1refChr6 86830 37 + 197743 AGAAATTAGTATCCCTCAGTTGCCCTGAGC-ATTTATC -s Anc2.Anc2refChr13 60578 37 + 96486 AGAAGTTAGTATCCCTCTGTTGCCCTAAGA-ATTTATC -s mr.mrrefChr5 279470 38 + 294540 AGAAATTCATAGCCCTCAGTTATCCTGAACCATGATTC -s simCow_chr6.simCow.chr6 416108 36 + 602619 AGAAGTC-GTTTCCCTCTGTCGTCTTAAGT-GTGTATC -s simDog_chr6.simDog.chr6 407230 34 + 593897 GGAAGTTAGTATC---CTGTTGCCCTAAGA-ACTTATC -s simHuman_chr6.simHuman.chr6 412156 37 + 601863 AGAAATTAGTATCCCTTAGTTGCCGTGAGC-ATTTATC -s simRat_chr6.simRat.chr6 433181 38 + 647215 AGACATTCATAGCCCTCAGTTAGCCTGAACCATGATCC - -a -s simMouse_chr6.simMouse.chr6 427160 10 + 636262 CATTGGGGAA -s Anc0.Anc0refChr3 56071 10 + 222631 CATTAGGGAA -s Anc1.Anc1refChr6 86867 10 + 197743 CATTAGGGAA -s Anc2.Anc2refChr13 60615 10 + 96486 CATTAGGGAA -s mr.mrrefChr5 279508 10 + 294540 CATTGGGGAA -s simCow_chr6.simCow.chr6 416327 10 + 602619 AATTAAGGAA -s simDog_chr6.simDog.chr6 407264 10 + 593897 CATTAGGGAA -s simHuman_chr6.simHuman.chr6 412193 10 + 601863 CATTAGGGAA -s simRat_chr6.simRat.chr6 433219 10 + 647215 CATTGGGGAA - -a -s simMouse_chr6.simMouse.chr6 427170 1 + 636262 G -s Anc0.Anc0refChr3 56081 1 + 222631 G -s Anc1.Anc1refChr6 86877 1 + 197743 G -s Anc2.Anc2refChr13 60625 1 + 96486 G -s mr.mrrefChr5 279518 1 + 294540 G -s simCow_chr6.simCow.chr6 230779 1 + 602619 C -s simCow_chr6.simCow.chr6 416337 1 + 602619 C -s simDog_chr6.simDog.chr6 407274 1 + 593897 G -s simHuman_chr6.simHuman.chr6 412203 1 + 601863 G -s simRat_chr6.simRat.chr6 433229 1 + 647215 C - -a -s simMouse_chr6.simMouse.chr6 427171 62 + 636262 GCGTTTATAGTAATCAAAGTGGGTACACTCCTGGCCCCCATCCTTGTCCCCTGTGATGTCAC -s Anc0.Anc0refChr3 56082 47 + 222631 GAGTTAATAGTCATCA--GTAAGTAGACTACTG-------------TCCCCAGTGATGTCAC -s Anc1.Anc1refChr6 86878 47 + 197743 GAGTTAATAGTCATCA--GTAAGTAGACTACTG-------------TCCCCAGTGATGTCAC -s Anc2.Anc2refChr13 60626 47 + 96486 GAGTTAATAGTCATCA--TTAAGTAGACTACTG-------------TCCCCAGTGAGGTCAC -s mr.mrrefChr5 279519 49 + 294540 GAGTTTATAGTCATCAAAGTGGGTACACTCCTG-------------TCCCCTGTGATGTCAC -s simCow_chr6.simCow.chr6 416338 47 + 602619 AAGTTAACAGTCAGCA--ATGAGTAAACTACTG-------------TCCTCAGTCAGGTCAC -s simDog_chr6.simDog.chr6 407275 44 + 593897 GAATCAATAGTCATCA--TTAAGTAGACTACTG-------------TCCCCAGTG---CCAC -s simHuman_chr6.simHuman.chr6 412204 47 + 601863 TAGTTATTAGACATCA--GTAAGTAGACTGCTG-------------TCCCCAGTGATGTCAC -s simRat_chr6.simRat.chr6 433230 49 + 647215 GAGTTTATAGCCATCAAAGTGGGTGCATTACTG-------------TCCCCTGTGGTGTCAC - -a -s simMouse_chr6.simMouse.chr6 427233 12 + 636262 ATGGCCCAAACA -s Anc0.Anc0refChr3 56129 12 + 222631 ATGGCCTTAACA -s Anc1.Anc1refChr6 86925 12 + 197743 ATGGCCTTAACA -s Anc2.Anc2refChr13 60673 12 + 96486 ATGGCTTTAACC -s mr.mrrefChr5 279568 12 + 294540 ATGGCCCAAACA -s simCow_chr6.simCow.chr6 416387 12 + 602619 ATTGCTCTACTC -s simDog_chr6.simDog.chr6 407319 12 + 593897 ATGGCTTTAACC -s simHuman_chr6.simHuman.chr6 412251 10 + 601863 GTGGAC--AATA -s simRat_chr6.simRat.chr6 433279 12 + 647215 ATGGCACAAACT - -a -s simMouse_chr6.simMouse.chr6 427245 5 + 636262 AGTGA -s Anc0.Anc0refChr3 56141 5 + 222631 AGTGC -s Anc1.Anc1refChr6 86937 5 + 197743 AGTGC -s Anc2.Anc2refChr13 60685 5 + 96486 ACTGC -s mr.mrrefChr5 279580 5 + 294540 AGTGA -s simCow_chr6.simCow.chr6 416404 5 + 602619 ACTGT -s simDog_chr6.simDog.chr6 407331 5 + 593897 ACTGC -s simHuman_chr6.simHuman.chr6 412261 2 + 601863 AG--- -s simRat_chr6.simRat.chr6 433291 5 + 647215 AGTGA - -a -s simMouse_chr6.simMouse.chr6 427250 2 + 636262 TT -s Anc0.Anc0refChr3 56146 2 + 222631 AC -s Anc1.Anc1refChr6 86942 2 + 197743 AC -s Anc2.Anc2refChr13 60690 2 + 96486 AC -s mr.mrrefChr5 279585 2 + 294540 TT -s simCow_chr6.simCow.chr6 416409 2 + 602619 AC -s simDog_chr6.simDog.chr6 407337 2 + 593897 AC -s simRat_chr6.simRat.chr6 433296 2 + 647215 TT - -a -s simMouse_chr6.simMouse.chr6 427252 20 + 636262 AAGATGTCTATGCGAATCGT -s Anc0.Anc0refChr3 56148 20 + 222631 AATAGGTCTATGCAAACTTT -s Anc1.Anc1refChr6 86944 20 + 197743 AATAGGTCTATGCAAACTTT -s Anc2.Anc2refChr13 60692 20 + 96486 AATAGGTGTATGCAAACTTT -s mr.mrrefChr5 279587 20 + 294540 AAGATGTCTATGCAAACTGT -s simCow_chr6.simCow.chr6 416411 20 + 602619 AATTGGTGTATGCAAACTTT -s simDog_chr6.simDog.chr6 407339 20 + 593897 AATAGGTGTATACAACTTTT -s simHuman_chr6.simHuman.chr6 412263 15 + 601863 -----GTCTAGGCAAACTTT -s simRat_chr6.simRat.chr6 433299 20 + 647215 AAAACGTCCTTGCAAACTGT - -a -s simMouse_chr6.simMouse.chr6 427272 30 + 636262 GTCTATTTTGATCCAATACCTTAGCCCTAA -s Anc0.Anc0refChr3 56168 30 + 222631 GCTTATTTTGATCAAATAGCTTGGCCCTGG -s Anc1.Anc1refChr6 86964 30 + 197743 GCTTATTTTGATCAAATAGCTTGGCCCTGG -s Anc2.Anc2refChr13 60712 30 + 96486 GCTTGTTTTCATCAAATAGCTTGGCCCTGG -s mr.mrrefChr5 279607 30 + 294540 GTCTATTTTGATCCAATACCTTAGCCCTGA -s simCow_chr6.simCow.chr6 416432 24 + 602619 GCTTGTTTTTATCAGGTAGCTTGG------ -s simDog_chr6.simDog.chr6 407359 30 + 593897 GCTTGATTTCATGAAATAGTTTGGCCCTGG -s simHuman_chr6.simHuman.chr6 412278 30 + 601863 GCTTATTTTGATCAAATAGCTTGGCCCTGG -s simRat_chr6.simRat.chr6 433319 30 + 647215 GGCTATTCTTATTGCATATCTTAGCCCTGA - -a -s simMouse_chr6.simMouse.chr6 427302 2 + 636262 GC -s Anc0.Anc0refChr3 56200 2 + 222631 CA -s Anc1.Anc1refChr6 86996 2 + 197743 CA -s Anc2.Anc2refChr13 60744 2 + 96486 CT -s mr.mrrefChr5 279639 2 + 294540 GA -s simDog_chr6.simDog.chr6 407391 2 + 593897 CT -s simHuman_chr6.simHuman.chr6 412310 2 + 601863 CA -s simRat_chr6.simRat.chr6 433351 2 + 647215 GA - -a -s simMouse_chr6.simMouse.chr6 427304 5 + 636262 ACCCT -s Anc0.Anc0refChr3 56202 5 + 222631 ACCCT -s Anc1.Anc1refChr6 86998 5 + 197743 ACCCT -s Anc2.Anc2refChr13 60761 5 + 96486 ACCCT -s mr.mrrefChr5 279641 5 + 294540 ACCCT -s simCow_chr6.simCow.chr6 416471 5 + 602619 ATCCT -s simDog_chr6.simDog.chr6 407411 5 + 593897 GCCTT -s simHuman_chr6.simHuman.chr6 412312 5 + 601863 ACCCT -s simRat_chr6.simRat.chr6 433353 5 + 647215 GCCCT - -a -s simMouse_chr6.simMouse.chr6 427309 17 + 636262 AAACAGGACACATAGTA -s Anc0.Anc0refChr3 56211 17 + 222631 AAACAACACACAATGTA -s Anc1.Anc1refChr6 87007 17 + 197743 AAACAACACACAATGTA -s Anc2.Anc2refChr13 60770 17 + 96486 AGGCAACACAAAATGTA -s mr.mrrefChr5 279646 17 + 294540 AAACAAGACACATAGTA -s simCow_chr6.simCow.chr6 416480 17 + 602619 AGGCAAGATGGAATGTC -s simDog_chr6.simDog.chr6 407420 12 + 593897 G-----CGCAAAATGTA -s simHuman_chr6.simHuman.chr6 412321 17 + 601863 AAAAAACACACAATGTA -s simRat_chr6.simRat.chr6 433358 17 + 647215 GAACAAGAGACATAGTA - -a -s simMouse_chr6.simMouse.chr6 427326 16 + 636262 GTAGGGTGATTTCTGC -s Anc0.Anc0refChr3 56228 16 + 222631 GTAGGATGTTTTCTGC -s Anc1.Anc1refChr6 87024 16 + 197743 GTAGGATGTTTTCTGC -s Anc2.Anc2refChr13 60787 16 + 96486 GTAGGATGTTTTCTGC -s mr.mrrefChr5 279663 16 + 294540 GTAGGATGATTTCTGC -s simCow_chr6.simCow.chr6 416497 16 + 602619 GTAGGACATCATCTGC -s simDog_chr6.simDog.chr6 407439 16 + 593897 GTAGGTTGTTTCATGC -s simHuman_chr6.simHuman.chr6 412338 16 + 601863 GTAGGATGCTTTCTGT -s simRat_chr6.simRat.chr6 433375 16 + 647215 GTAGGATGTTTTCTGC - -a -s simMouse_chr6.simMouse.chr6 427342 25 + 636262 AGGTGCACAATCCATCCCCATAGGG -s Anc0.Anc0refChr3 56244 25 + 222631 AGGTGCTCAATCCATCCTCATAGAG -s Anc1.Anc1refChr6 87040 25 + 197743 AGGTGCTCAATCCATCCTCATAGAG -s Anc2.Anc2refChr13 60804 25 + 96486 AGGTGTTCAATCCATTCTTATAGAG -s mr.mrrefChr5 279679 25 + 294540 AGGTGCACAATCCATCCTCATAGGG -s simCow_chr6.simCow.chr6 416514 25 + 602619 GGGTGTTCAATCCATTATGATAGAG -s simDog_chr6.simDog.chr6 407456 25 + 593897 AGGTGTTCAATCCATTCTTATAGAG -s simHuman_chr6.simHuman.chr6 412354 25 + 601863 TGGTGCGCTATCCGTCCTCATAGCT -s simRat_chr6.simRat.chr6 433391 25 + 647215 GGGTGCACAATCCATCCTCATAAGA - -a -s simMouse_chr6.simMouse.chr6 427367 29 + 636262 ATAATCTCAGGAATGCTTACTCCATATCA -s Anc0.Anc0refChr3 56269 29 + 222631 GTAATCTTAAGAAGGCTTACTCCTTATGA -s Anc1.Anc1refChr6 87065 29 + 197743 GTAATCTTAAGAAGGCTTACTCCTTATGA -s Anc2.Anc2refChr13 60830 29 + 96486 GTAATTTTAAGAAGGCTTAGTCCTTATGA -s mr.mrrefChr5 279704 29 + 294540 GTAATCTCAGGAATGCTTACTCCATATCA -s simCow_chr6.simCow.chr6 416540 29 + 602619 GTAATTTTAAGTAGGCTGAGTCCATATAA -s simDog_chr6.simDog.chr6 407482 29 + 593897 GTAATTTTAAGAAGGCTTAGACCTTATGA -s simHuman_chr6.simHuman.chr6 412379 29 + 601863 GTGATCTTAAGAAGGCCTACTCTCAGTGA -s simRat_chr6.simRat.chr6 433416 29 + 647215 GTAATCTCAGGAATACTCACTCCATATCA - -a -s simMouse_chr6.simMouse.chr6 427396 44 + 636262 ACCTTTTTGCTGCCTTTCTGTGCATTCGCTGTTGGTATTAATAC -s Anc0.Anc0refChr3 56298 41 + 222631 GCCCCTTTAATTTCCTACTTT---TTGGCTGCTGGTAGTACTAT -s Anc1.Anc1refChr6 87094 41 + 197743 GCCCCTTTAATTTCCTACTTT---TTGGCTGCTGGTAGTACTAT -s Anc2.Anc2refChr13 60866 41 + 96486 GCCCCTTTAATTTTCCACTTT---TTGGCTGCTGGTAGCACTAT -s mr.mrrefChr5 279733 44 + 294540 ACCTCTTTGCTGCCCTTCTGTGCATTCGCTGTTGGTATTAATAT -s simCow_chr6.simCow.chr6 416576 34 + 602619 GCCCCTTTAATTT-------T---TTGGCTGCTGGTGGCAAGCT -s simDog_chr6.simDog.chr6 407518 41 + 593897 GCCCTTTTGACTTTCCACTTG---TTGGCTGGTGGTAACACTAT -s simHuman_chr6.simHuman.chr6 412408 41 + 601863 GTCCCTCTAATTTCCTGCCTT---TTGGGTCCTGGTAGTAGTAT -s simRat_chr6.simRat.chr6 433445 44 + 647215 ACCTCTTTGCTGCCCCTCTATGCATTCACTGTTGGTAATAATAT - -a -s simMouse_chr6.simMouse.chr6 427440 1 + 636262 A -s Anc0.Anc0refChr3 56344 1 + 222631 A -s Anc1.Anc1refChr6 87140 1 + 197743 A -s Anc2.Anc2refChr13 60912 1 + 96486 G -s mr.mrrefChr5 279784 1 + 294540 A -s simCow_chr6.simCow.chr6 416615 1 + 602619 T -s simDog_chr6.simDog.chr6 407564 1 + 593897 G -s simHuman_chr6.simHuman.chr6 412454 1 + 601863 A -s simRat_chr6.simRat.chr6 433502 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 427441 19 + 636262 GGTGTTTCATAAATTGATG -s Anc0.Anc0refChr3 56345 17 + 222631 GGTGTAACA--AATTGAGG -s Anc1.Anc1refChr6 87141 17 + 197743 GGTGTAACA--AATTGAGG -s Anc2.Anc2refChr13 60933 17 + 96486 AGTGTAACA--AAGTGAGG -s mr.mrrefChr5 279785 19 + 294540 GGTGTAGCATAAATTGATG -s simCow_chr6.simCow.chr6 416636 17 + 602619 AGTACTACA--CAGTGAGA -s simDog_chr6.simDog.chr6 407585 17 + 593897 AGTGTAACA--AAGTGAGG -s simHuman_chr6.simHuman.chr6 412455 7 + 601863 GG----------GTTGA-- -s simRat_chr6.simRat.chr6 433503 19 + 647215 GGTGTAGCATAAATTGATG - -a -s simMouse_chr6.simMouse.chr6 427460 1 + 636262 C -s Anc0.Anc0refChr3 56362 1 + 222631 C -s Anc1.Anc1refChr6 87158 1 + 197743 C -s Anc2.Anc2refChr13 60950 1 + 96486 C -s mr.mrrefChr5 279804 1 + 294540 C -s simCow_chr6.simCow.chr6 416653 1 + 602619 C -s simDog_chr6.simDog.chr6 407602 1 + 593897 C -s simRat_chr6.simRat.chr6 433523 1 + 647215 C - -a -s simMouse_chr6.simMouse.chr6 427461 28 + 636262 AGTAGACTATGGGATTAGTTTGCTGTCT -s Anc0.Anc0refChr3 56363 28 + 222631 AGCAGACTATGGGTTCAGTATGCTATCT -s Anc1.Anc1refChr6 87159 28 + 197743 AGCAGACTATGGGTTCAGTATGCTATCT -s Anc2.Anc2refChr13 60952 28 + 96486 AGCATACTATGGGTTCAATATGCTATCT -s mr.mrrefChr5 279805 28 + 294540 AGTAGACTATGGGATTAGTATGCTATCT -s simCow_chr6.simCow.chr6 416655 28 + 602619 AGCATAATATGGAGTCAATGTGCTTCCT -s simDog_chr6.simDog.chr6 407604 28 + 593897 AGCATACTATGGGTTCAATATGCTATCT -s simHuman_chr6.simHuman.chr6 412462 25 + 601863 ---GGGCTGGAGGTTCAGTATGCTATCT -s simRat_chr6.simRat.chr6 433524 27 + 647215 AGTAGATCATGG-ATTAGTATGCCATCT - -a -s simMouse_chr6.simMouse.chr6 427489 136 + 636262 TCTAAACCTAAAGCATTCCATTCACATCATCCTGAGGTATGAACACGACCGGAGCGTATTGCAATTTTCACTGGCCATACTAAGTCTATTAGAGTTGTCTAAGTAGTCATGTTTGCTACCATTTGGATAACCTATT -s Anc0.Anc0refChr3 56391 67 + 222631 TCTGCACCTATAGCAGTTTACTCACCTCATCCCTAAATGAGAATACTATTTGAGC--------------------------------------------------------------------TAT-TGCCTTATT -s Anc1.Anc1refChr6 87187 68 + 197743 TCTGCACCTATAGCAGTTTACTCACCTCATCCCTAAATGAGAATACTATTTGAGC--------------------------------------------------------------------TATATGCCTTATT -s Anc2.Anc2refChr13 60980 67 + 96486 TCTGCACTTATACCAGTTTACTTACCTCATCACTAAATGAAAGTACTATTTGAAC--------------------------------------------------------------------TAT-TGCCTTATT -s mr.mrrefChr5 279833 136 + 294540 TCTACACCTATAGCAGTCCATTCACATCATCCTGAGGTAAGAATACGACTGGAGCGTATTGCAATTTTCACTGGCCATACTAAGTCTATTAGAGTTGTTTAAGTAGTCATGTTTGCTACCATTTGGATAACTTATT -s simCow_chr6.simCow.chr6 416684 66 + 602619 TCTGCACTTA-ACCAGTTTACTTATCTTGTCATTAAGTGAAAGTACTATTTGAAA--------------------------------------------------------------------GGC-TACCTTGTT -s simDog_chr6.simDog.chr6 407632 67 + 593897 TCTACACTTATACCAGTTTCCTTACCTCATCACTAAATGAAAGTATTATCTGAAC--------------------------------------------------------------------TAT-TGCCTTATT -s simHuman_chr6.simHuman.chr6 412487 68 + 601863 TCTGCCCCTATAGTGGTTTACTCCCCGCAGCCCAAATTGAGCATACTATTTGAGC--------------------------------------------------------------------TATATGGCTTATT -s simRat_chr6.simRat.chr6 433551 136 + 647215 TCTACACCTATAGCAGTCCATTCACATCATCCTGATGCTAGACTACAACTGGAGCCTGTTTCAGTATTCACTGGCCGTACTAAGTCTATTAGAGTTGTTTATGTAGTGATGTTTGCTACCATTTAGATAACTTATT - -a -s simMouse_chr6.simMouse.chr6 427625 7 + 636262 ATTAATG -s Anc0.Anc0refChr3 56477 7 + 222631 ATTACTG -s Anc1.Anc1refChr6 87274 7 + 197743 ATTACTG -s Anc2.Anc2refChr13 61125 7 + 96486 ATTACTG -s mr.mrrefChr5 279969 7 + 294540 ATTAATG -s simCow_chr6.simCow.chr6 416829 7 + 602619 ATCGCTG -s simDog_chr6.simDog.chr6 407785 7 + 593897 ATTACTG -s simHuman_chr6.simHuman.chr6 412574 7 + 601863 ATTATTA -s simRat_chr6.simRat.chr6 433687 7 + 647215 GTTAAAG - -a -s simMouse_chr6.simMouse.chr6 427632 65 + 636262 TTGTTTGACAGGACTTGGACGCATCCTCTCAATGAGAGAGGTACCCTGTTCCCAATCTGAATGAG -s Anc0.Anc0refChr3 56484 64 + 222631 TTGTTAAACTGGACTTTGAAGTATCCTGGAAAAGGGAGAGGGACCCTGCTTCCATTT-GTGTGTA -s Anc1.Anc1refChr6 87281 65 + 197743 TTGTTAAACTGGACTTTGAAGTATCCTGGAAAAGGGAGAGGGACCCTGCTTCCATTTTGTGTGTA -s Anc2.Anc2refChr13 61133 64 + 96486 TTGTTAAATTGGACTTTGAAGTGTCGTGGAAAAGGGAGAGGGACCCTGCTTCCATTT-ATGCATA -s mr.mrrefChr5 279976 65 + 294540 TTGTTTAACTGGACTTGGACGCATCCTCTCAATGAGAGAGGTACCCTGTTCCCAATTTGAATGAG -s simCow_chr6.simCow.chr6 416837 56 + 602619 TCATTAAATTGGACTTTGAAGTG--------AAGAGAGAGCGACCCTGCTTCCACCT-ATGCATA -s simDog_chr6.simDog.chr6 407793 63 + 593897 TTGTTAAATCGGACTTC-AACCGTCGTGGAAAAGGGAGAGGGAACCTGCTTCCATTT-ATGCATA -s simHuman_chr6.simHuman.chr6 412581 65 + 601863 TTGATAACCTGGACTTTGAAGTACTCTGGTAGAGTGCCAGGACCCCTGCTGCCATCTTGGGTGTA -s simRat_chr6.simRat.chr6 433694 65 + 647215 TTATCTAATTAGACTTAGACGCATCCTCTCAATGAGAGAGGTACCCTATTTCCAATTTGAATGAG - -a -s simMouse_chr6.simMouse.chr6 427697 14 + 636262 CACTACTATATAGT -s Anc0.Anc0refChr3 56556 14 + 222631 CGCACACATGTAGT -s Anc1.Anc1refChr6 87354 14 + 197743 CGCACACATGTAGT -s Anc2.Anc2refChr13 61205 14 + 96486 CGCACACATGTAGT -s mr.mrrefChr5 280049 14 + 294540 CACTCACATATAGT -s simCow_chr6.simCow.chr6 416901 14 + 602619 CGTGCATATGTAGT -s simDog_chr6.simDog.chr6 407864 14 + 593897 CACATACACATAGT -s simHuman_chr6.simHuman.chr6 412658 14 + 601863 TGCACACATGTAGT -s simRat_chr6.simRat.chr6 433767 14 + 647215 CACTCACATATAGT - -a -s simMouse_chr6.simMouse.chr6 427711 72 + 636262 CTTGGCAAGATCTGTAAAAGAATGATTCTTCTGATGGAAAATATAGGTTGGGCTAACTGCTAATGATAAATT -s Anc0.Anc0refChr3 56608 71 + 222631 TAGAGGGGGATCTGTCAGAGAATAATGTTTCTAACGGAAAATGCAGGTTGAGCTTGCTGGGAGT-ATAAGTC -s Anc1.Anc1refChr6 87406 71 + 197743 TAGAGGGGGATCTGTCAGAGAATAATGTTTCTAACGGAAAATGCAGGTTGAGCTTGCTGGGAGT-ATAAGTC -s Anc2.Anc2refChr13 61257 71 + 96486 TAGAGGGGGATCTGCCAGAGAATAATGTTTCGAATGGAGGATGCAGGTTGAGCTTGCCGGGGGT-ATGAGTC -s mr.mrrefChr5 280101 72 + 294540 CAGGGCAAGATCTGTAAAAGAATGATTCTTCTGACGGAAAATATAGGTTGGGCTAGCTGGTAATGAAAAATC -s simCow_chr6.simCow.chr6 416953 57 + 602619 TGGAGGTCAGTCTTCCAGGGAAAAATATTTCCACTGAAGGATGCAGGTTGATCT---------------GTT -s simDog_chr6.simDog.chr6 407917 70 + 593897 TATAGGGGGATCAGCCAGAGCATAA-GTTTCGGATGGAGGATGCATGTTGAGCTTGCCGGGGGT-ATGAATC -s simHuman_chr6.simHuman.chr6 412714 71 + 601863 TAGAGGGGGATCTGTCAGACAATAATGTTTCTAACGGAAAAGGCAGGATGAGCTTGCTGGGAGT-AGAAGTC -s simRat_chr6.simRat.chr6 433819 71 + 647215 CAGGGCAAGATCTGTAAAAGAAC-ATTCTTTTGACGGAGGATATAGGTTTGGCTGGCTGGTAATGAAAAATC - -a -s simMouse_chr6.simMouse.chr6 427783 46 + 636262 TCATGTCAGTGGATGTGAAGATATAATAGACTTCATTGTATTATCA -s Anc0.Anc0refChr3 56960 46 + 222631 TCATAACAGTATAAATGTAGGTACCATAGACTTTACTGTATTATAA -s Anc1.Anc1refChr6 87758 46 + 197743 TCATAACAGTATAAATGTAGGTACCATAGACTTTACTGTATTATAA -s Anc2.Anc2refChr13 61618 46 + 96486 TTATAACAGTATAAATGTAGGTACCATAGACTTTACTGTATTCTAA -s mr.mrrefChr5 280173 46 + 294540 TCATGTCAGTGGATGTGAAGGTATAATAGACTTCATTGTATTATCA -s simCow_chr6.simCow.chr6 417194 43 + 602619 TTATAACAGTATAAATGCAGGCACCATCGAC---ACTGTATCCTCC -s simDog_chr6.simDog.chr6 408276 45 + 593897 TTATAACAGAATAAAAGTGGGTACCTTAGA-TTTACCTTATTCCAA -s simHuman_chr6.simHuman.chr6 413092 46 + 601863 TCATAACAGTATAAATGGAGGTACCATAGACTTTACTGTATAATAA -s simRat_chr6.simRat.chr6 433890 46 + 647215 TCATGTCAGTGGAGGTGAGGGTATAACAGACTACATTGTATCATCA - -a -s simMouse_chr6.simMouse.chr6 427829 7 + 636262 ACTTTGT -s Anc0.Anc0refChr3 57006 7 + 222631 ACTTTAT -s Anc1.Anc1refChr6 87804 7 + 197743 ACTTTAT -s Anc2.Anc2refChr13 61664 7 + 96486 GCTTTAT -s mr.mrrefChr5 280219 7 + 294540 ACTTTGT -s simCow_chr6.simCow.chr6 417237 7 + 602619 CCTTTAT -s simDog_chr6.simDog.chr6 408321 7 + 593897 GCTTTAC -s simHuman_chr6.simHuman.chr6 413153 7 + 601863 ACTTTAT -s simRat_chr6.simRat.chr6 433936 7 + 647215 GCTTTGT - -a -s simMouse_chr6.simMouse.chr6 427836 8 + 636262 TTAGGCTT -s Anc0.Anc0refChr3 57016 8 + 222631 TTAGGCTT -s Anc1.Anc1refChr6 87814 8 + 197743 TTAGGCTT -s Anc2.Anc2refChr13 61674 8 + 96486 TTAGGCTT -s mr.mrrefChr5 280226 8 + 294540 TTAGGCTT -s simCow_chr6.simCow.chr6 417247 8 + 602619 TTAGACTT -s simDog_chr6.simDog.chr6 408331 8 + 593897 TTAGGATC -s simHuman_chr6.simHuman.chr6 413163 8 + 601863 TTAGGCTT -s simRat_chr6.simRat.chr6 433943 7 + 647215 ACAGG-TT - -a -s simMouse_chr6.simMouse.chr6 427844 23 + 636262 GGAACTTGGGCAACATACTATAC -s Anc0.Anc0refChr3 57026 23 + 222631 GTATCTGGGTAAACATTTTATAT -s Anc1.Anc1refChr6 87824 23 + 197743 GTATCTGGGTAAACATTTTATAT -s Anc2.Anc2refChr13 61684 23 + 96486 GTATTTGGGTAAGCATTTTATAT -s mr.mrrefChr5 280234 23 + 294540 GGAACTTGGGCAACATACTATAC -s simCow_chr6.simCow.chr6 417257 23 + 602619 GTATTTGAGGAGTCACTTTATAT -s simDog_chr6.simDog.chr6 408341 23 + 593897 GGATTTGGGTAAGCATTTTATAT -s simHuman_chr6.simHuman.chr6 413173 23 + 601863 GTATCTAGATAAAGATCTTATAA -s simRat_chr6.simRat.chr6 433950 23 + 647215 GGACCTTGGGCAGCACTATATCC - -a -s simMouse_chr6.simMouse.chr6 427867 26 + 636262 TGTATCTGCTTGCATAAGATTGTTGG -s Anc0.Anc0refChr3 57049 22 + 222631 CATATTTATCTGTATAATAT----GG -s Anc1.Anc1refChr6 87847 22 + 197743 CATATTTATCTGTATAATAT----GG -s Anc2.Anc2refChr13 61707 22 + 96486 CATATTTATCTGTAGAGTAT----GG -s mr.mrrefChr5 280257 26 + 294540 TGTATTTGCTTGCATAAGATTGTTGG -s simCow_chr6.simCow.chr6 417285 22 + 602619 CATATGCACCTGTAGAGTTT----GG -s simDog_chr6.simDog.chr6 408364 21 + 593897 CATATTTATCTGTAGAGTAT----G- -s simHuman_chr6.simHuman.chr6 413196 22 + 601863 CATATTTATCTGTATAATAT----GG -s simRat_chr6.simRat.chr6 433973 26 + 647215 TCCATTTGCTTGCATAAGGTTGTTGG - -a -s simMouse_chr6.simMouse.chr6 427893 18 + 636262 TTAATGTGGCATTAGTAT -s Anc0.Anc0refChr3 57071 18 + 222631 CTAACATGGCATAAGTGT -s Anc1.Anc1refChr6 87869 18 + 197743 CTAACATGGCATAAGTGT -s Anc2.Anc2refChr13 61729 18 + 96486 CTGACATGGCATAGGTGC -s mr.mrrefChr5 280283 18 + 294540 TTAACATGGCATTAGTAT -s simCow_chr6.simCow.chr6 417311 18 + 602619 CTGATATGGCATAGGTGC -s simDog_chr6.simDog.chr6 408385 4 + 593897 ----CTTG---------- -s simHuman_chr6.simHuman.chr6 413218 18 + 601863 CAAACATGGCATAAATGT -s simRat_chr6.simRat.chr6 433999 18 + 647215 TTAACATGGCATGAGTAT - -a -s simMouse_chr6.simMouse.chr6 427911 38 + 636262 GACCTTGCTGGCCATGTTTCCAGATATGTATCCTGTTT -s Anc0.Anc0refChr3 57117 38 + 222631 GGTCTCTTTGGCTATGTTTCCAGATATGTATCCTCTTT -s Anc1.Anc1refChr6 87915 38 + 197743 GGTCTCTTTGGCTATGTTTCCAGATATGTATCCTCTTT -s Anc2.Anc2refChr13 61775 38 + 96486 GGTCTCTTTGGCTATGTTTCCAGATATGTGTCCTCTTT -s mr.mrrefChr5 280301 38 + 294540 GACCTTGCTGGCCATGTTTCCAGATATGTATCCTGTTT -s simCow_chr6.simCow.chr6 417360 36 + 602619 AGTCTCT--GGCTACGTTGCCAGATATGTGTCCTTTTT -s simDog_chr6.simDog.chr6 408415 38 + 593897 GATCTCTTTGGCCATGTTTCCAAATGTGTGTCCTCTTT -s simHuman_chr6.simHuman.chr6 413266 38 + 601863 GGTCTCTTTGGCTATGTTTCCAGGAATCTATTCTCTCT -s simRat_chr6.simRat.chr6 434017 32 + 647215 GACCT------CAATGTTTCGAAATATGTATCCTGTTT - -a -s simMouse_chr6.simMouse.chr6 427949 15 + 636262 TCTATTAAGTCTGAT -s Anc0.Anc0refChr3 57155 15 + 222631 TCTACTAAGTTTGAT -s Anc1.Anc1refChr6 87953 15 + 197743 TCTACTAAGTTTGAT -s Anc2.Anc2refChr13 61813 15 + 96486 TCTACTAAGTTTGAT -s mr.mrrefChr5 280339 15 + 294540 TCTATTAAGTCTGAT -s simCow_chr6.simCow.chr6 417396 15 + 602619 TCTACTGAGTTTGAT -s simDog_chr6.simDog.chr6 408455 15 + 593897 TCTACTAAGTTTGAT -s simHuman_chr6.simHuman.chr6 413304 15 + 601863 TCTACTAAGTTTGAT -s simRat_chr6.simRat.chr6 434049 10 + 647215 TCGATTAAGT----- - -a -s simMouse_chr6.simMouse.chr6 427964 8 + 636262 CTTATAAT -s Anc0.Anc0refChr3 57177 8 + 222631 TTTCCAAT -s Anc1.Anc1refChr6 87975 8 + 197743 TTTCCAAT -s Anc2.Anc2refChr13 61835 8 + 96486 TTTCCAAT -s mr.mrrefChr5 280354 8 + 294540 CTTCCAAT -s simCow_chr6.simCow.chr6 417419 8 + 602619 TTTCCAAT -s simDog_chr6.simDog.chr6 408477 8 + 593897 TTTCCAAT -s simHuman_chr6.simHuman.chr6 413326 8 + 601863 TTTCCACT -s simRat_chr6.simRat.chr6 434059 7 + 647215 -TTCCAAC - -a -s simMouse_chr6.simMouse.chr6 427972 3 + 636262 AAT -s Anc0.Anc0refChr3 57185 3 + 222631 AAT -s Anc1.Anc1refChr6 87983 3 + 197743 AAT -s Anc2.Anc2refChr13 61858 3 + 96486 ACT -s mr.mrrefChr5 280362 3 + 294540 AAT -s simCow_chr6.simCow.chr6 417442 3 + 602619 AGT -s simDog_chr6.simDog.chr6 408505 3 + 593897 ACT -s simHuman_chr6.simHuman.chr6 413334 3 + 601863 AAT -s simRat_chr6.simRat.chr6 434066 3 + 647215 AAT - -a -s simMouse_chr6.simMouse.chr6 427975 9 + 636262 AGTGAACCT -s Anc0.Anc0refChr3 57188 9 + 222631 TATGAACCT -s Anc1.Anc1refChr6 87986 9 + 197743 TATGAACCT -s Anc2.Anc2refChr13 61861 9 + 96486 TATGAACCT -s mr.mrrefChr5 280365 9 + 294540 AGTGAACCT -s simCow_chr6.simCow.chr6 417448 9 + 602619 TATGAAACT -s simDog_chr6.simDog.chr6 408508 9 + 593897 TATGAACCT -s simHuman_chr6.simHuman.chr6 413337 9 + 601863 TATGAATCT -s simRat_chr6.simRat.chr6 434069 9 + 647215 AGTGGACCT - -a -s simMouse_chr6.simMouse.chr6 427984 18 + 636262 CTACATACTTGGCTGGCC -s Anc0.Anc0refChr3 57252 15 + 222631 CCATTAACTTGGTTG--- -s Anc1.Anc1refChr6 88050 15 + 197743 CCATTAACTTGGTTG--- -s Anc2.Anc2refChr13 61969 15 + 96486 CCATTAACCTGGTAT--- -s mr.mrrefChr5 280429 18 + 294540 CTACATACTTGGCTGGCC -s simCow_chr6.simCow.chr6 417543 15 + 602619 CCATTAACCTGGCGC--- -s simDog_chr6.simDog.chr6 408607 15 + 593897 CCATGAATCTGGTAT--- -s simHuman_chr6.simHuman.chr6 413401 15 + 601863 TCAGTAACTTGGTTG--- -s simRat_chr6.simRat.chr6 434166 18 + 647215 CTATATACCTGGCTGTAC - -a -s simMouse_chr6.simMouse.chr6 428002 33 + 636262 TCCAGGAGTATTCCACTCCTGAGACGACTGACG -s Anc0.Anc0refChr3 57267 32 + 222631 -TTGTAACTACTCCACTCCTGAGCCAACTGACC -s Anc1.Anc1refChr6 88065 32 + 197743 -TTGTAACTACTCCACTCCTGAGCCAACTGACC -s Anc2.Anc2refChr13 61984 32 + 96486 -TTGTTACTACTCCACTCCTGAGCAAAATGACC -s mr.mrrefChr5 280447 33 + 294540 TCTAGAAGTATTCCACTCCTGAGACGACTGACC -s simCow_chr6.simCow.chr6 417558 32 + 602619 -TTGTTACTACCCCACTCCAGAATTGAAGAATC -s simDog_chr6.simDog.chr6 408622 30 + 593897 -TTGTTAGTACTCCACTCCTCAGCAA--TGTCC -s simHuman_chr6.simHuman.chr6 413416 32 + 601863 -GTGTAACTACTCCACTCTTGAGCCAACTGACC -s simRat_chr6.simRat.chr6 434192 33 + 647215 TCTACAAGTATTCCACTCCTGAGATGATTAACC - -a -s simMouse_chr6.simMouse.chr6 428035 20 + 636262 TTGGCTCATCTTCAAGTACA -s Anc0.Anc0refChr3 57299 17 + 222631 AGCACCCATAGTCAAGT--- -s Anc1.Anc1refChr6 88097 20 + 197743 AGCACCCATAGTCAAGTACA -s Anc2.Anc2refChr13 62016 17 + 96486 AGCACCCATAGTTGAGT--- -s mr.mrrefChr5 280480 20 + 294540 TTGGCCCATCTTCAAGTACA -s simCow_chr6.simCow.chr6 417592 17 + 602619 GGCACCCTGAATTGGGA--- -s simDog_chr6.simDog.chr6 408652 17 + 593897 AGCACCCATGGTTGAGT--- -s simHuman_chr6.simHuman.chr6 413448 20 + 601863 CACACCCATAGTCAAGTACA -s simRat_chr6.simRat.chr6 434225 20 + 647215 TTGGCCCAACTTCAAGTACA - -a -s simMouse_chr6.simMouse.chr6 428055 15 + 636262 CACCAAGGGGCAGTC -s Anc0.Anc0refChr3 57316 2 + 222631 -------------GC -s Anc1.Anc1refChr6 88117 15 + 197743 CCCCATGTGGCTGGC -s Anc2.Anc2refChr13 62033 2 + 96486 -------------GC -s mr.mrrefChr5 280500 15 + 294540 CACCAAGGGGCAGTC -s simCow_chr6.simCow.chr6 417609 2 + 602619 -------------GC -s simDog_chr6.simDog.chr6 408669 2 + 593897 -------------GC -s simHuman_chr6.simHuman.chr6 413472 15 + 601863 CCCCATGTGGCTGGC -s simRat_chr6.simRat.chr6 434245 15 + 647215 CACCAAGGGGCAGTC - -a -s simMouse_chr6.simMouse.chr6 428070 4 + 636262 CAGG -s Anc0.Anc0refChr3 57318 4 + 222631 CAGG -s Anc1.Anc1refChr6 88132 4 + 197743 CAGG -s Anc2.Anc2refChr13 62035 4 + 96486 CAGG -s mr.mrrefChr5 280515 4 + 294540 CAGG -s simCow_chr6.simCow.chr6 417616 4 + 602619 CAGG -s simDog_chr6.simDog.chr6 408671 4 + 593897 TAGC -s simHuman_chr6.simHuman.chr6 413487 4 + 601863 CAGG -s simRat_chr6.simRat.chr6 434260 4 + 647215 GAGG - -a -s simMouse_chr6.simMouse.chr6 428074 5 + 636262 CAGGT -s Anc0.Anc0refChr3 57329 5 + 222631 CAATT -s Anc1.Anc1refChr6 88143 5 + 197743 CAATT -s Anc2.Anc2refChr13 62046 5 + 96486 CAATT -s mr.mrrefChr5 280519 5 + 294540 CAGGT -s simCow_chr6.simCow.chr6 417626 5 + 602619 CAATT -s simDog_chr6.simDog.chr6 408682 5 + 593897 CGATT -s simHuman_chr6.simHuman.chr6 413498 5 + 601863 CAATT -s simRat_chr6.simRat.chr6 434264 5 + 647215 CAGGT - -a -s simMouse_chr6.simMouse.chr6 428079 7 + 636262 ACCCTGG -s Anc0.Anc0refChr3 57338 7 + 222631 ACCCTAG -s Anc1.Anc1refChr6 88152 7 + 197743 ACCCTAG -s Anc2.Anc2refChr13 62055 7 + 96486 ACCCTAG -s mr.mrrefChr5 280524 7 + 294540 ACCCTGG -s simCow_chr6.simCow.chr6 417635 7 + 602619 ACCCCAG -s simDog_chr6.simDog.chr6 408691 7 + 593897 ACTCTGA -s simHuman_chr6.simHuman.chr6 413507 7 + 601863 ACCCTAG -s simRat_chr6.simRat.chr6 434269 7 + 647215 ACCCCGG - -a -s simMouse_chr6.simMouse.chr6 428086 16 + 636262 GAAGCTGACCAGGATT -s Anc1.Anc1refChr6 88169 16 + 197743 GAGGCTAGCCAGGACT -s mr.mrrefChr5 280531 16 + 294540 GAAGCTGACCAGGATT -s simHuman_chr6.simHuman.chr6 413526 16 + 601863 GAGGCTAGCCAGGACT -s simRat_chr6.simRat.chr6 434276 16 + 647215 GAAGCTGACCAGGATT - -a -s simMouse_chr6.simMouse.chr6 428102 61 + 636262 CTCCAATTTTTCATCTTAATGCCAAGGACATTGCATATGAGCTTTGCAGGCTTACTATGTG -s Anc0.Anc0refChr3 57355 30 + 222631 -------------------TGCCAAGTACAATT-----GCACATC-------CACTATGTG -s Anc1.Anc1refChr6 88185 61 + 197743 CTCCAATTTTTCACCCTAGTGCCAAGTACAATTTTTATGCACATCGTATAGTCACTATGTG -s Anc2.Anc2refChr13 62072 30 + 96486 -------------------TGCCAAGTACAATT-----GCACATC-------CACTATGTG -s mr.mrrefChr5 280547 61 + 294540 CTCCAATTTTTCATCCTAATGCCAAGGACATTGCATATGAGCTTTGTAGGCTCACTATGTG -s simCow_chr6.simCow.chr6 417652 19 + 602619 ------------------------------ATC-----AAACATT-------CACTGTGTT -s simDog_chr6.simDog.chr6 408708 30 + 593897 -------------------TGCCAAGTACATTT-----GCACATC-------CACTATGTG -s simHuman_chr6.simHuman.chr6 413544 56 + 601863 CTCCAATTTTTCACCCTAGTGCCAAGTACAATTTTTATGGACATCGTATAGTCACC----- -s simRat_chr6.simRat.chr6 434292 61 + 647215 CTCCAATTTGTCATCCTAATGCCAAGGACATTGCATATGAGCTTTGTAGGCTCACTATGTG - -a -s simMouse_chr6.simMouse.chr6 428163 69 + 636262 CAGTGTCCAGAGGTTAACTTGTTATACAATGTCCTATCTTTGACAATGGCTAATCTAGTCTATGGTTCT -s Anc0.Anc0refChr3 57385 61 + 222631 CA-------AATATCAACTCATTATACAG-GTTCTATTTTCCACAATGGTTAATCTGGTCCATTGCTCT -s Anc1.Anc1refChr6 88246 66 + 197743 CA--GTCCAAATATCAACTCATTATACAG-GTTCTATTTTCCACAATGGTTAATCTGGTCCATTGCTCT -s Anc2.Anc2refChr13 62102 61 + 96486 CA-------AATATCAACTCATTATACAG-ATTCTATTTTCCACAATGGTAAATCTGGTCTATTTCACT -s mr.mrrefChr5 280608 68 + 294540 CAGTGTCCAGAGGTTAACTTGTTATACAA-GTCCTATCTTTGACAATGGCTAATCTAGTCCATTGTTCT -s simCow_chr6.simCow.chr6 417671 50 + 602619 CA-------AATGTCAACTTATTATACAG-ATTCTATTTTCCATAATGGTAAAGCTGG----------- -s simDog_chr6.simDog.chr6 408738 61 + 593897 CA-------AATATCAACTCATTATACAT-ATTCTATTTTCCACGATGGTAGATTTAGTCTATTTCACT -s simHuman_chr6.simHuman.chr6 413600 64 + 601863 ----GTCCAAATAACAACTCATTATACAG-GTTCTCTTTCCCACAATGTTTAATCTGGCCCATTGCTCT -s simRat_chr6.simRat.chr6 434358 33 + 647215 CCATGTGCAGAGGTTGACTT------------------------------------AGTCCTATGTTCT - -a -s simMouse_chr6.simMouse.chr6 428232 6 + 636262 ATTTCT -s Anc0.Anc0refChr3 57446 6 + 222631 ATTACT -s Anc1.Anc1refChr6 88312 6 + 197743 ATTACT -s Anc2.Anc2refChr13 62163 6 + 96486 ATTACC -s mr.mrrefChr5 280676 6 + 294540 ATTTCT -s simCow_chr6.simCow.chr6 418381 6 + 602619 AATGCC -s simDog_chr6.simDog.chr6 408799 6 + 593897 ATTATC -s simHuman_chr6.simHuman.chr6 413664 6 + 601863 ATTACT -s simRat_chr6.simRat.chr6 434391 6 + 647215 ATTTCT - -a -s simMouse_chr6.simMouse.chr6 428238 20 + 636262 GAACAGAAGAAAGCAGATCC -s Anc0.Anc0refChr3 57452 20 + 222631 GGACAGAAGAAATTAGATTC -s Anc1.Anc1refChr6 88318 20 + 197743 GGACAGAAGAAATTAGATTC -s Anc2.Anc2refChr13 62169 20 + 96486 GGACAGAAGAAATTAGATTC -s mr.mrrefChr5 280682 20 + 294540 GAACAGAAGAAAGCAGATTC -s simCow_chr6.simCow.chr6 418460 20 + 602619 GGATAGAAGAAATTAGACTC -s simDog_chr6.simDog.chr6 408805 20 + 593897 TGACAGAAGAAATTAGATTT -s simHuman_chr6.simHuman.chr6 413670 20 + 601863 GGACAGAAAAAATTACATTC -s simRat_chr6.simRat.chr6 434397 20 + 647215 GCATAGAAGAAAACAAATTC - -a -s simMouse_chr6.simMouse.chr6 428258 26 + 636262 TATTTTACATTGATTAAAACATTAAG -s Anc0.Anc0refChr3 57472 26 + 222631 TAGTTCATATTTGCAAAAACACTAAG -s Anc1.Anc1refChr6 88338 26 + 197743 TAGTTCATATTTGCAAAAACACTAAG -s Anc2.Anc2refChr13 62189 26 + 96486 TAGTGCATATTTACAAAAACACAAAG -s mr.mrrefChr5 280702 26 + 294540 TAGTTTACATTGGTTAAAACATTAAG -s simCow_chr6.simCow.chr6 418480 26 + 602619 TAGTACCTAATGACAAAAACACAAAG -s simDog_chr6.simDog.chr6 408825 26 + 593897 TAGTGCATATTTACAAGAACACAAAG -s simHuman_chr6.simHuman.chr6 413690 26 + 601863 TAGATCATATTTGCAAAAACACTAAG -s simRat_chr6.simRat.chr6 434421 26 + 647215 TAGTTTACATTGGTTTAAACATTAAG - -a -s simMouse_chr6.simMouse.chr6 428284 5 + 636262 TACTA -s Anc0.Anc0refChr3 57499 5 + 222631 TGCTC -s Anc1.Anc1refChr6 88365 5 + 197743 TGCTC -s Anc2.Anc2refChr13 62216 5 + 96486 TGCTC -s mr.mrrefChr5 280728 5 + 294540 TGCTC -s simCow_chr6.simCow.chr6 418507 5 + 602619 TGTTC -s simDog_chr6.simDog.chr6 408852 5 + 593897 TACTC -s simHuman_chr6.simHuman.chr6 413717 5 + 601863 TGCCC -s simRat_chr6.simRat.chr6 434447 5 + 647215 TGCTC - -a -s simMouse_chr6.simMouse.chr6 428289 71 + 636262 TAAGATGACATGTTTTTCATCCATGGAGTAATTCCAGAGTGACAAAGACCTGGGTATTGTACCATTTGTAG -s Anc0.Anc0refChr3 57505 70 + 222631 TGAGATAATATGGTGT-CCCACATGAACAAATTCCAGAGTGACATAGGCCTTGGGATTGCATTATTTGTAG -s Anc1.Anc1refChr6 88371 70 + 197743 TGAGATAATATGGTGT-CCCACATGAACAAATTCCAGAGTGACATAGGCCTTGGGATTGCATTATTTGTAG -s Anc2.Anc2refChr13 62222 70 + 96486 TGAGATAATATGGTGC-CCCACATGAACAAAGTCTGGAGTGACATCAGCCTTGGGATAGCATTATCTGTGG -s mr.mrrefChr5 280733 70 + 294540 TAAGATGACATGTTTT-CACCCATGGAGTAATTCCAGAGTGACAAAGACCTGGGTATTGTATTATTTGTAG -s simCow_chr6.simCow.chr6 418513 70 + 602619 TGAGATAATATGGTGC-CCCATATGAATAAAGTCTGGAGTGACATCAGCCTTTGGACATCATTATCTATGG -s simDog_chr6.simDog.chr6 408858 64 + 593897 TGAGATTATATGGTAC-TCCACCTGAACAAAGTCTGGAGTGA------CCTTGGGGTAGCATTATCTGTGG -s simHuman_chr6.simHuman.chr6 413723 70 + 601863 TTAGGTAATATGGTGT-CTCACATAAACAAATTCCAGACTGATACAGGCCTTGGGATTGCATTACTTGTAG -s simRat_chr6.simRat.chr6 434452 70 + 647215 TAATATGACACGTTTT-CACCCATGGAGTAATTCCAGGGTGACAGAGAGCTGGGTATTGTATTATTTGTAG - -a -s simMouse_chr6.simMouse.chr6 428360 23 + 636262 TCTTTCATGCTATCTGAAGGCTT -s Anc0.Anc0refChr3 57575 23 + 222631 TCTTTTATGCTATGAGGAAGCAT -s Anc1.Anc1refChr6 88441 23 + 197743 TCTTTTATGCTATGAGGAAGCAT -s Anc2.Anc2refChr13 62292 23 + 96486 TCTTTTATGCTATGAGGAAGCAT -s mr.mrrefChr5 280803 23 + 294540 TCTTTCATGCTATCTGGAGGCTT -s simCow_chr6.simCow.chr6 418649 23 + 602619 TTTTCTAAGTTATGAGGAAGCAT -s simDog_chr6.simDog.chr6 408922 23 + 593897 TCTGTTATACTATGAGGAAACAC -s simHuman_chr6.simHuman.chr6 413793 23 + 601863 TCTTTTATGCTATGAGGCAGCAT -s simRat_chr6.simRat.chr6 434522 23 + 647215 TCTTTCATGCTACATGGTGACTT - -a -s simMouse_chr6.simMouse.chr6 428383 10 + 636262 TTGGTGTAGC -s Anc0.Anc0refChr3 57598 10 + 222631 GGGGTTTAGC -s Anc1.Anc1refChr6 88464 10 + 197743 GGGGTTTAGC -s Anc2.Anc2refChr13 62315 10 + 96486 GGGGTTTAGC -s mr.mrrefChr5 280826 10 + 294540 TTGGTGTAGC -s simCow_chr6.simCow.chr6 418673 10 + 602619 GGGGCTTAAC -s simDog_chr6.simDog.chr6 408945 10 + 593897 GGGGTTCAGC -s simHuman_chr6.simHuman.chr6 413816 10 + 601863 AGGGTTTAGC -s simRat_chr6.simRat.chr6 434545 10 + 647215 GTGGTGTAGC - -a -s simMouse_chr6.simMouse.chr6 428393 11 + 636262 CTCAAATTGCA -s Anc0.Anc0refChr3 57608 11 + 222631 CTTAAATTCCA -s Anc1.Anc1refChr6 88474 11 + 197743 CTTAAATTCCA -s Anc2.Anc2refChr13 62325 11 + 96486 CTTAAATTCCG -s mr.mrrefChr5 280836 11 + 294540 CTCAAATTGCA -s simCow_chr6.simCow.chr6 418683 11 + 602619 CTTAAATTCCG -s simDog_chr6.simDog.chr6 408979 11 + 593897 CTTAAATCCCG -s simHuman_chr6.simHuman.chr6 413826 11 + 601863 CTTAAATTCCA -s simRat_chr6.simRat.chr6 434555 11 + 647215 CTCACATTGCA - -a -s simMouse_chr6.simMouse.chr6 428404 11 + 636262 TCTTGGCTGGT -s Anc0.Anc0refChr3 57623 11 + 222631 TCTTGGCTGGT -s Anc1.Anc1refChr6 88489 11 + 197743 TCTTGGCTGGT -s Anc2.Anc2refChr13 62340 11 + 96486 TTTTGGCTGAT -s mr.mrrefChr5 280847 11 + 294540 TCTTGGCTGGT -s simCow_chr6.simCow.chr6 418698 11 + 602619 TTTTATCTGAT -s simDog_chr6.simDog.chr6 408994 11 + 593897 TTTTGGATTAT -s simHuman_chr6.simHuman.chr6 413841 11 + 601863 TCTTGGCTGGT -s simRat_chr6.simRat.chr6 434566 11 + 647215 TCTTAGCTCAT - -a -s simMouse_chr6.simMouse.chr6 428415 94 + 636262 GATTTTCAATACCTCACATGTATGGCAAGCTAAGGAATCCACTAAAAGAGGAGAGTAACATTGAATCTCTAGTCTGGTGGATGTACATATGTGC -s Anc0.Anc0refChr3 57639 51 + 222631 GATATGTAATATGCCA--TGTATGGCAAACTGAAG-----------------------------------------GTGTGTGTATGTATGCAC -s Anc1.Anc1refChr6 88505 51 + 197743 GATATGTAATATGCCA--TGTATGGCAAACTGAAG-----------------------------------------GTGTGTGTATGTATGCAC -s Anc2.Anc2refChr13 62356 51 + 96486 GATATGTAATATGCCA--TGTGTGGCAAACTGAAA-----------------------------------------TTGTGTGGATGTATGCAC -s mr.mrrefChr5 280858 91 + 294540 GATTTTCAATACCTCACATGTATGGCAAACTAAAGAATCCACTAAAAGAGGAGAGTAGCAT---ATCTCTAGCCTGGTGGATGTACATATGTGC -s simCow_chr6.simCow.chr6 418714 44 + 602619 GGTATTTAATATGC---------AGCAAACTGAAA-----------------------------------------TTGAGTGCAGGTATGAGC -s simDog_chr6.simDog.chr6 409010 51 + 593897 GATATGTAAGATGCCA--TGTGTGGCAAGCTGAAA-----------------------------------------TCGTTTGGATGCATGCAC -s simHuman_chr6.simHuman.chr6 413857 51 + 601863 GATATATAATATGCTA--CGTATGGCAAACCGAAG-----------------------------------------GTGTGTGTGTGTGTGCAT -s simRat_chr6.simRat.chr6 434577 91 + 647215 GATTTTCAATACCTCACATGTATGGCAAACTTAAGAATCCACTAAAAGAGGAGAGTAGTAT---ATCTCTAGCCTGATGTGTGTACCTATGGAC - -a -s simMouse_chr6.simMouse.chr6 428509 2 + 636262 AG -s Anc0.Anc0refChr3 57690 2 + 222631 AT -s Anc1.Anc1refChr6 88556 2 + 197743 AT -s Anc2.Anc2refChr13 62407 2 + 96486 AT -s mr.mrrefChr5 280949 2 + 294540 AG -s simCow_chr6.simCow.chr6 418758 2 + 602619 AT -s simDog_chr6.simDog.chr6 409061 2 + 593897 AT -s simHuman_chr6.simHuman.chr6 414000 2 + 601863 AT -s simRat_chr6.simRat.chr6 434668 2 + 647215 AG - -a -s simMouse_chr6.simMouse.chr6 428511 33 + 636262 TCCACCCACCTTTTGAAACACAGAGCTGTAGGT -s Anc0.Anc0refChr3 57695 33 + 222631 TCTACCCACTTTCAGAAAGACAGTGATTTGAGT -s Anc1.Anc1refChr6 88561 33 + 197743 TCTACCCACTTTCAGAAAGACAGTGATTTGAGT -s Anc2.Anc2refChr13 62412 33 + 96486 TCTACCCACTTTCAGAAAGACAGTCATTTGAGT -s mr.mrrefChr5 280951 33 + 294540 TCCACCCACTTTCTGAAACACAGAGCTTTAGGT -s simCow_chr6.simCow.chr6 418763 33 + 602619 TCTACCCACTTACAGAAGAACAGTCATTTGAGT -s simDog_chr6.simDog.chr6 409066 31 + 593897 TCCACCCACTTT--GAAAGACAGTCAGTAGAGT -s simHuman_chr6.simHuman.chr6 414005 32 + 601863 TGTACCCACTTTCAGAAAGA-AGTGTTTTGAGT -s simRat_chr6.simRat.chr6 434670 33 + 647215 TCCACCGACTTTCTGAAACACAGAGCTTTAGGT - -a -s simMouse_chr6.simMouse.chr6 428544 48 + 636262 TGGGTCTTGAAATGTGGCTCTTGTCACAAGCAGGCTGTATACTCTAAC -s Anc0.Anc0refChr3 57742 48 + 222631 TGGGTCTGATAATGTGTTTCTTGTCAAAAACAGGTAGTAGACTTTGAT -s Anc1.Anc1refChr6 88608 48 + 197743 TGGGTCTGATAATGTGTTTCTTGTCAAAAACAGGTAGTAGACTTTGAT -s Anc2.Anc2refChr13 62459 48 + 96486 TGGGTCTGATAATGTGTTTCTTGTCATAAACAGGTAGTAGACTTTGAT -s mr.mrrefChr5 280998 48 + 294540 TGGGTCTTGAAATGTGGTTCTTGTCAAAAACAGGCAGTAGACTCTAAC -s simCow_chr6.simCow.chr6 418810 48 + 602619 TGGGTCTGTAAATGTGGTTTTTGTCATATACAGGTAGTAGACTTTGAT -s simDog_chr6.simDog.chr6 409111 48 + 593897 TGAGTCTGATGATGTATTTCCTGCCATAAACAGGTAGTAGACTTTGAT -s simHuman_chr6.simHuman.chr6 414051 48 + 601863 TGGGTCTAATAATGCGTTTCTCATCAAAAACAGTTAGTAGACTTGGAT -s simRat_chr6.simRat.chr6 434717 48 + 647215 TGGGTCTGGAAATGTGGTTCTTGTCAAAAACAGACAGTAGACACTAAC - -a -s simMouse_chr6.simMouse.chr6 428592 3 + 636262 GAA -s Anc0.Anc0refChr3 57791 3 + 222631 AAA -s Anc1.Anc1refChr6 88657 3 + 197743 AAA -s Anc2.Anc2refChr13 62508 3 + 96486 AAG -s mr.mrrefChr5 281046 3 + 294540 AAA -s simCow_chr6.simCow.chr6 418859 3 + 602619 AAG -s simDog_chr6.simDog.chr6 409160 3 + 593897 GAG -s simHuman_chr6.simHuman.chr6 414100 3 + 601863 AGA -s simRat_chr6.simRat.chr6 434765 2 + 647215 AA- - -a -s simMouse_chr6.simMouse.chr6 428595 62 + 636262 GTCCGAGTTAGCTGAAGGTTCAAACCGTAAGTGACTAAGCTTGCAATGCTTTTAGCCTTTAC -s Anc0.Anc0refChr3 57794 8 + 222631 ATTCAAGT------------------------------------------------------ -s Anc1.Anc1refChr6 88660 19 + 197743 ATTCAAGTTAGGTAGAGGC------------------------------------------- -s Anc2.Anc2refChr13 62511 8 + 96486 ATTCAAGT------------------------------------------------------ -s mr.mrrefChr5 281049 62 + 294540 GTCCGAGTTAGCTGAAGGTTCAAACCGTAAGTGACTAAGCTTGCAATGCTTTTAGCCTTTAC -s simCow_chr6.simCow.chr6 418863 8 + 602619 ATTGAAGT------------------------------------------------------ -s simDog_chr6.simDog.chr6 409163 8 + 593897 ATCCAAGT------------------------------------------------------ -s simHuman_chr6.simHuman.chr6 414103 19 + 601863 ATTCAAGTTAGGTAGAGGC------------------------------------------- -s simRat_chr6.simRat.chr6 434767 56 + 647215 ------GTTATCTGAAGGCTCAAACCCTAAGTGACTGAGCTTGCAATGATTTTAGCCCTTAC - -a -s simMouse_chr6.simMouse.chr6 428657 64 + 636262 AAGAACGCTCTATGTCAAGGCTGAAAATCTCCAGCTGTTAGCTTTTAGTGCTTACAAGGACACT -s Anc1.Anc1refChr6 88679 7 + 197743 ---------------------------------------------------------GGAAATT -s mr.mrrefChr5 281111 64 + 294540 AAGAACGCTCTATGTCAAGGCTGAAAATCTCCAGGTGTTAGCTTTTAGTGCTTACAAGGACACT -s simHuman_chr6.simHuman.chr6 414122 7 + 601863 ---------------------------------------------------------GGAAATT -s simRat_chr6.simRat.chr6 434829 64 + 647215 AAGGACACTCCATGTCAAGGCTGAAAATCTCCAGGTGTTATCCTTTAGTGCTGACAAGGACACT - -a -s simMouse_chr6.simMouse.chr6 428721 45 + 636262 TCCATGTCATGGCTGAAAATCTCCAGGTATCCGCCTTATCAAAAG -s Anc0.Anc0refChr3 57802 43 + 222631 --CAGGTAAAGGCTGAAATTCTCCAGGGGCTAGCCATGCCAAAAG -s Anc1.Anc1refChr6 88686 45 + 197743 TCCAGGTAAAGGCTGAAATTCTCCAGGGGCTAGCCATGCCAAAAG -s Anc2.Anc2refChr13 62519 43 + 96486 --CAGGTAAAGGCTGAAATTCTCCAGGGGCTAGCCATGCCAAAAG -s mr.mrrefChr5 281175 45 + 294540 TCCATGTCAAGGCTGAAAATCTCCAGGTGTTAGCCATATCAAAAG -s simCow_chr6.simCow.chr6 418871 43 + 602619 --TGGGTAAAAGTTGACATTTTCCAGGGGTTAGCCATGCCAAAAG -s simDog_chr6.simDog.chr6 409171 43 + 593897 --CAGGAAAAGGCTAAAATTCTCTGAGGGCTGGCCATGTCGAAAG -s simHuman_chr6.simHuman.chr6 414130 45 + 601863 TCCAGGTAAATGCTGAAATTCTCCAGGAGCTAGCCATGCCAAAAG -s simRat_chr6.simRat.chr6 434893 45 + 647215 TCCATGTCAAGACTGAAAATCTCCAGGTGTTAGCCATATCAAAAG - -a -s simMouse_chr6.simMouse.chr6 428766 58 + 636262 TAAATGCAAAGGGTTAGGTATACCTTGACTGGAGATCTTGCCAATTGCCAAGTTGGCA -s Anc0.Anc0refChr3 57850 58 + 222631 TAAATATGAAGGGTTAGGTATGCCTTCTCACGAGCTCTGGTCAATTGCCGCATTGGCA -s Anc1.Anc1refChr6 88736 58 + 197743 TAAATATGAAGGGTTAGGTATGCCTTCTCACGAGCTCTGGTCAATTGCCGCATTGGCA -s Anc2.Anc2refChr13 62567 58 + 96486 TAAATATGAAGGGCTAGGTATGCCTTCTCACAAGCCCTGGTCAATTGCTACATTGGCA -s mr.mrrefChr5 281220 58 + 294540 TAAATATGAAGGGTTAGGTATACCTTGACTGGAGATCTTGTCAATTGCCGAATTGGCA -s simCow_chr6.simCow.chr6 418919 58 + 602619 AAAATGTGAAGGGTTAGATATACCTTCACAGTAGTCCTGGCCAATTGGTACAGTGGCA -s simDog_chr6.simDog.chr6 409219 58 + 593897 TAAATATGAAGGGCTAGGTATGCCTTCTCACAAGCCCTGGTCAATTGCTACATTGGGA -s simHuman_chr6.simHuman.chr6 414180 45 + 601863 TAAATATGAGGGGTT-------------CAAGAGCTTTGATCAATTGACGTACTGGCA -s simRat_chr6.simRat.chr6 434938 58 + 647215 TGAATATGAAGGGATAGGTATACCTTGAGGGGAGATCTAGTCAATCACTGAATTCGCA - -a -s simMouse_chr6.simMouse.chr6 428824 18 + 636262 GCATTCCAATCGGCACTG -s Anc0.Anc0refChr3 57908 18 + 222631 ACATTTTCATTTGCACTG -s Anc1.Anc1refChr6 88794 18 + 197743 ACATTTTCATTTGCACTG -s Anc2.Anc2refChr13 62625 18 + 96486 ACATTTTCATTTCTACTG -s mr.mrrefChr5 281278 18 + 294540 ACATTCCCATCGGCACCG -s simCow_chr6.simCow.chr6 418977 18 + 602619 ACATTCACATTTCTACCA -s simDog_chr6.simDog.chr6 409277 13 + 593897 ACATTTTC-----TATTG -s simHuman_chr6.simHuman.chr6 414225 18 + 601863 ACATTTGCATTTGCACTG -s simRat_chr6.simRat.chr6 435001 18 + 647215 ACACTCCCATCGGCACCC - -a -s simMouse_chr6.simMouse.chr6 428842 5 + 636262 CCCAG -s Anc0.Anc0refChr3 57929 5 + 222631 CCCAG -s Anc1.Anc1refChr6 88815 5 + 197743 CCCAG -s Anc2.Anc2refChr13 62646 5 + 96486 CCCTC -s mr.mrrefChr5 281296 5 + 294540 CCCAG -s simCow_chr6.simCow.chr6 418998 5 + 602619 CCCTC -s simDog_chr6.simDog.chr6 409293 5 + 593897 CCTTC -s simHuman_chr6.simHuman.chr6 414246 5 + 601863 CCCAG -s simRat_chr6.simRat.chr6 435019 5 + 647215 TCCAG - -a -s simMouse_chr6.simMouse.chr6 428847 6 + 636262 GATGAA -s Anc0.Anc0refChr3 57938 6 + 222631 GAGGAA -s Anc1.Anc1refChr6 88824 6 + 197743 GAGGAA -s Anc2.Anc2refChr13 62655 6 + 96486 GAGGAA -s mr.mrrefChr5 281301 6 + 294540 GAGGAA -s simCow_chr6.simCow.chr6 419007 6 + 602619 GAATAT -s simDog_chr6.simDog.chr6 409302 6 + 593897 GAGGAA -s simHuman_chr6.simHuman.chr6 414255 6 + 601863 AAGGAA -s simRat_chr6.simRat.chr6 435024 6 + 647215 GAGGAA - -a -s simMouse_chr6.simMouse.chr6 428853 5 + 636262 CGATG -s Anc0.Anc0refChr3 57944 5 + 222631 GAATG -s Anc1.Anc1refChr6 88830 5 + 197743 GAATG -s Anc2.Anc2refChr13 62661 5 + 96486 GAATA -s mr.mrrefChr5 281307 5 + 294540 CAATG -s simCow_chr6.simCow.chr6 419013 5 + 602619 AATAT -s simDog_chr6.simDog.chr6 409317 5 + 593897 GAATA -s simHuman_chr6.simHuman.chr6 414261 5 + 601863 GAATG -s simRat_chr6.simRat.chr6 435030 5 + 647215 CAATG - -a -s simMouse_chr6.simMouse.chr6 428858 23 + 636262 GCTGGCATTAGGGAATAGTCATA -s Anc0.Anc0refChr3 57964 23 + 222631 GCCAGTATTAGGGAAAAGTCTTA -s Anc1.Anc1refChr6 88850 23 + 197743 GCCAGTATTAGGGAAAAGTCTTA -s Anc2.Anc2refChr13 62681 23 + 96486 GCCAGTATTAGGGAAAAGTCTTT -s mr.mrrefChr5 281312 23 + 294540 GCCAGCATTAGGGAATAGTCATA -s simCow_chr6.simCow.chr6 419033 23 + 602619 CCCAGTATTAGAGAAAAGGCTTC -s simDog_chr6.simDog.chr6 409337 23 + 593897 GCCAGTATTAGGGAAAAGTCTTT -s simHuman_chr6.simHuman.chr6 414281 23 + 601863 GTCAGTATTAGTGAAAAGTCTTA -s simRat_chr6.simRat.chr6 435035 23 + 647215 GCCAGCATTAGGGAATAGTCATA - -a -s simMouse_chr6.simMouse.chr6 428881 32 + 636262 ATTCCATGGTTATGGTATCTCGGGAGTACTGC -s Anc0.Anc0refChr3 57987 25 + 222631 ATT------T-ATAGTAGGCAGGGGATACTGC -s Anc1.Anc1refChr6 88873 26 + 197743 ATT------TTATAGTAGGCAGGGGATACTGC -s Anc2.Anc2refChr13 62704 25 + 96486 ATT------T-ATAGTGGGCAGGGGATGCTGC -s mr.mrrefChr5 281335 32 + 294540 ATTCCATGGTTATGGTATGTAGGGAGTACTGC -s simCow_chr6.simCow.chr6 419056 25 + 602619 ATT------T-ATAATGTGCAGGGGGTGCTGC -s simDog_chr6.simDog.chr6 409360 25 + 593897 ATT------T-ATAGTGGGCAGGGGATGATGC -s simHuman_chr6.simHuman.chr6 414305 26 + 601863 ATT------TTATAGTAGGCAGGGGATACTGC -s simRat_chr6.simRat.chr6 435058 32 + 647215 ATTCCATGGTAGTGGTTCGTAGGGAGTGCTGC - -a -s simMouse_chr6.simMouse.chr6 428913 44 + 636262 ATGGACACACCACTCAAAAACACAATAGTGGATAGACTAGAACT -s Anc0.Anc0refChr3 58012 44 + 222631 ATAATCACACAGACCAAAAACACAAGAATGAATAAGTTAAAATT -s Anc1.Anc1refChr6 88899 44 + 197743 ATAATCACACAGACCAAAAACACAAGAATGAATAAGTTAAAATT -s Anc2.Anc2refChr13 62735 44 + 96486 ATAATCACACAGACCAAAAACACAAGAATGAATAAGTTTAAATT -s mr.mrrefChr5 281367 44 + 294540 ATGAACACACCACTCAAAAACACAATAGTGGATAGACTAAAACT -s simCow_chr6.simCow.chr6 419087 21 + 602619 ATAATCACACAGACCAACAAC----------------------- -s simDog_chr6.simDog.chr6 409391 44 + 593897 ATAATCACACAGACCAAAAACACAAGAATGAATAAGTTTAAATT -s simHuman_chr6.simHuman.chr6 414331 44 + 601863 ATAATCACAATGACCAAGAATGCAAGAATGCATAAGTTAAAATT -s simRat_chr6.simRat.chr6 435090 44 + 647215 ATGAACACACCACTCACAAACACAACAGTGGATAGACTAAAACT - -a -s simMouse_chr6.simMouse.chr6 428957 2 + 636262 AG -s Anc0.Anc0refChr3 58058 2 + 222631 AA -s Anc1.Anc1refChr6 88945 2 + 197743 AA -s Anc2.Anc2refChr13 62781 2 + 96486 AA -s mr.mrrefChr5 281411 2 + 294540 AG -s simDog_chr6.simDog.chr6 409437 2 + 593897 AA -s simHuman_chr6.simHuman.chr6 414377 2 + 601863 AA -s simRat_chr6.simRat.chr6 435134 2 + 647215 AG - -a -s simMouse_chr6.simMouse.chr6 428959 21 + 636262 ATGCAACAACATACAACACTG -s Anc0.Anc0refChr3 58068 21 + 222631 GAACAACGCTGTACAAAATTG -s Anc1.Anc1refChr6 88955 21 + 197743 GAACAACGCTGTACAAAATTG -s Anc2.Anc2refChr13 62791 21 + 96486 GAACATGGCTGCAAAAAATGG -s mr.mrrefChr5 281420 21 + 294540 GTGCAACAATGTACAACACTG -s simDog_chr6.simDog.chr6 409449 21 + 593897 GAACATGGCTGCAAAAAATGG -s simHuman_chr6.simHuman.chr6 414387 21 + 601863 GAACAACGTTGTACAAAATTG -s simRat_chr6.simRat.chr6 435143 21 + 647215 GTGCAACAATGTACCGTGCTG - -a -s simMouse_chr6.simMouse.chr6 428980 5 + 636262 ATATT -s Anc0.Anc0refChr3 58160 5 + 222631 TTACT -s Anc1.Anc1refChr6 89047 5 + 197743 TTACT -s Anc2.Anc2refChr13 62883 5 + 96486 TTACT -s mr.mrrefChr5 281441 5 + 294540 TTATT -s simCow_chr6.simCow.chr6 419124 5 + 602619 TTACT -s simDog_chr6.simDog.chr6 409541 5 + 593897 TTACT -s simHuman_chr6.simHuman.chr6 414479 5 + 601863 TTACT -s simRat_chr6.simRat.chr6 435164 5 + 647215 TTATT - -a -s simMouse_chr6.simMouse.chr6 428985 69 + 636262 TCACTATGTGCACTATGTGTGATACAGAGGATCACTGGAACTCAATATGCCACATGTTTGACAATCTTT -s Anc0.Anc0refChr3 58165 58 + 222631 ACATTCTATA-----------ATAGAAAGGACCACTGGAACTCCCCCAGTCACATGTTTAACAATCTTT -s Anc1.Anc1refChr6 89052 58 + 197743 ACATTCTATA-----------ATAGAAAGGACCACTGGAACTCCCCCAGTCACATGTTTAACAATCTTT -s Anc2.Anc2refChr13 62888 58 + 96486 ACATTCTATA-----------ATAGGTAGGACCACTGGAACTCCCCCAGTCACATGCTTAACAACCTTT -s mr.mrrefChr5 281446 60 + 294540 TCATTATGTG---------TGATACAAAGGATCACTGGAACTCACTAAGCCACATGTTTGACAATCTTT -s simCow_chr6.simCow.chr6 419129 58 + 602619 AGATTCCATA-----------ATAGGGAGGATCACTGGAACTCCCCAAGTCACATGCTTGACAACCTTT -s simDog_chr6.simDog.chr6 409548 58 + 593897 ACATTCTGTA-----------ACAGGTAGGACCACTGGGACTACCCCAGACACATGCTTAACAACCTTT -s simHuman_chr6.simHuman.chr6 414484 58 + 601863 GCATTCTATA-----------ATAGAAAAGACCACTGGAACTCCCCCAGTCAGATGTTTCACAATCTTT -s simRat_chr6.simRat.chr6 435169 60 + 647215 TGATTATGTG---------TGATACAAAGCATCACTGGAACTAACTAAGCCACATGTTTAACAATCTTT - -a -s simMouse_chr6.simMouse.chr6 429054 67 + 636262 CCAAAGAGGTAGGTCACCCAATATGGCACTGGCAGGCAAAGACTTGCCTTTACAGTGAGGTCAAAAT -s Anc0.Anc0refChr3 58223 67 + 222631 AAAAAGAGATAGATCACCTAACAATGGACCTGCAGACCAAAACTTGCCCTTACAATGAAGTCAAAAT -s Anc1.Anc1refChr6 89110 67 + 197743 AAAAAGAGATAGATCACCTAACAATGGACCTGCAGACCAAAACTTGCCCTTACAATGAAGTCAAAAT -s Anc2.Anc2refChr13 62946 67 + 96486 AAAGAGAGATAGATCACCTAGCAATGGACCTGCAGACCAAACCTTGCACTTACAATGAAATCAAAAT -s mr.mrrefChr5 281506 67 + 294540 CCAAAGAGGTAGGTCACCTAATATGGCACTGGCAGGCAAAGACTTGCCTTTACAGTGAAGTCAAAAT -s simCow_chr6.simCow.chr6 419189 66 + 602619 AAAGAGAGATAGATCACCTAGCAATGGATCTGCAG-CCAACTCTGGCACTCACAATGAAATCAAAAT -s simDog_chr6.simDog.chr6 409606 67 + 593897 AAAGAGAGATAGATCACCTAGCAATGGACGTGCAGACCTAACCTTGCACTTACAAAGAAATCAAAGT -s simHuman_chr6.simHuman.chr6 414542 67 + 601863 AAAAAGAGTTAAATCACCTGACAACTGACCTGCAGACCAAAACTTGCCCTTAGAATGAAGTCAAAAT -s simRat_chr6.simRat.chr6 435229 46 + 647215 CTAAAGAGGTAGGTCACCTAATATGCCACTGGCA---------------------GGAAGTCAAAAT - -a -s simMouse_chr6.simMouse.chr6 429121 29 + 636262 ATTTGTTGTACACTTCTTGGTCACCCAAG -s Anc0.Anc0refChr3 58290 29 + 222631 ATTTGGTGTACACTTGATGGTCACTCAAG -s Anc1.Anc1refChr6 89177 29 + 197743 ATTTGGTGTACACTTGATGGTCACTCAAG -s Anc2.Anc2refChr13 63013 29 + 96486 ATTTGGTGTACACTTGATGGTCACTCAAG -s mr.mrrefChr5 281573 29 + 294540 ATTTGTTGTACACTTGATGGTCACTCAAG -s simCow_chr6.simCow.chr6 419259 29 + 602619 ATATGTGACACCACTTATGGTCACTCAAG -s simDog_chr6.simDog.chr6 409673 29 + 593897 ATTTTGTGTACACTTGATGGCCACTCAAG -s simHuman_chr6.simHuman.chr6 414609 29 + 601863 ATTTGGTGTACACTTGATGATCACTCAAG -s simRat_chr6.simRat.chr6 435275 29 + 647215 ATCTGTTGCACACTTGATGGTCACTCAAG - -a -s simMouse_chr6.simMouse.chr6 429150 2 + 636262 GA -s Anc0.Anc0refChr3 58322 2 + 222631 GA -s Anc1.Anc1refChr6 89209 2 + 197743 GA -s Anc2.Anc2refChr13 63045 2 + 96486 GA -s mr.mrrefChr5 281602 2 + 294540 GA -s simCow_chr6.simCow.chr6 419291 2 + 602619 GA -s simDog_chr6.simDog.chr6 409705 2 + 593897 GA -s simHuman_chr6.simHuman.chr6 414641 2 + 601863 GA -s simRat_chr6.simRat.chr6 435304 1 + 647215 T- - -a -s simMouse_chr6.simMouse.chr6 429152 33 + 636262 AATTTGTTGGTTGTTCTAACTCTTTTATCTGAA -s Anc0.Anc0refChr3 58324 32 + 222631 AATTCTTTGGTT-CCTTAACTCTATTATTTGAA -s Anc1.Anc1refChr6 89211 33 + 197743 AATTCTTTGGTTTCCTTAACTCTATTATTTGAA -s Anc2.Anc2refChr13 63047 32 + 96486 GATTCTTTGGTT-CCTTGACTCTATGATTTGAA -s mr.mrrefChr5 281604 33 + 294540 AATTTGTTGGTTGTTTTAACTCTTTTATCTGAA -s simCow_chr6.simCow.chr6 419293 32 + 602619 CATTCTTTGTTA-TTTTGACTCTATGATTTGAA -s simDog_chr6.simDog.chr6 409708 29 + 593897 GAGACTTTAGGT-CCTTG--TCTA-GATTTAAA -s simHuman_chr6.simHuman.chr6 414643 33 + 601863 AATTCTTTGGTTTCCTAAACTCTGTTATTTGAA -s simRat_chr6.simRat.chr6 435305 27 + 647215 ------TCAGCTGTTTTGACTCTTTTATCTGAA - -a -s simMouse_chr6.simMouse.chr6 429185 36 + 636262 ATTTGCATGAAGAATGAAATTTGAAAGAGAAAAGAC -s Anc0.Anc0refChr3 58356 36 + 222631 ATCTGCATGAGGTGTGAAATTTGAATAAGATTAGAA -s Anc1.Anc1refChr6 89244 36 + 197743 ATCTGCATGAGGTGTGAAATTTGAATAAGATTAGAA -s Anc2.Anc2refChr13 63079 36 + 96486 ATCTACATGAGGGCTGAAATTTGAATAAGATTTGAA -s mr.mrrefChr5 281637 36 + 294540 ATCTGCATGAAGTGTGAAATTTGAAAGAGAAAAGAC -s simCow_chr6.simCow.chr6 419325 36 + 602619 ATCTACATGAGGCATGAAATTTGAACAAGAATTGAA -s simDog_chr6.simDog.chr6 409750 36 + 593897 ATATACACCCAGGCTGAAAGTTATATGCAATATGCA -s simHuman_chr6.simHuman.chr6 414676 36 + 601863 ATCTGCATGAGTTGTGAAATTTGAAGAAGAGTAGAA -s simRat_chr6.simRat.chr6 435332 36 + 647215 ATCTGCATGAAGTGTGAAATTTGAAAGAGAAAATAC - -a -s simMouse_chr6.simMouse.chr6 429221 1 + 636262 A -s Anc0.Anc0refChr3 58395 1 + 222631 A -s Anc1.Anc1refChr6 89283 1 + 197743 A -s Anc2.Anc2refChr13 63118 1 + 96486 C -s mr.mrrefChr5 281676 1 + 294540 A -s simCow_chr6.simCow.chr6 419364 1 + 602619 T -s simDog_chr6.simDog.chr6 409788 1 + 593897 C -s simHuman_chr6.simHuman.chr6 414715 1 + 601863 A -s simRat_chr6.simRat.chr6 435371 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 429222 68 + 636262 TTATAGTCTTCAACCAAAGAGGCCTGACCCACTGGATATGTGTATGTGTCTACCCATGACATTATATT -s Anc0.Anc0refChr3 58411 64 + 222631 TGTCGGTCTTCAACTAAAGAGGTCCAGGTCACTGGACAC----ATGAGTCGACACATAACGTTATATT -s Anc1.Anc1refChr6 89299 64 + 197743 TGTCGGTCTTCAACTAAAGAGGTCCAGGTCACTGGACAC----ATGAGTCGACACATAACGTTATATT -s Anc2.Anc2refChr13 63134 64 + 96486 TGTCGGTCCTCATCTAAAGAGGTCCAGGTAACTGGACAC----ATGAGTCGACATAAAACAGTATATT -s mr.mrrefChr5 281691 68 + 294540 TTATGGTCTTCAACCAAAGAGGCCTGACTCACTGGATATGTGTATGTGTCTACCCATAACGTTATATT -s simCow_chr6.simCow.chr6 419380 62 + 602619 TGTTGTTCCTCATCCAAAGAGGTCCAGGTAAGTGG--AC----ATGAGTCCGCATGAAACAGTAGACT -s simDog_chr6.simDog.chr6 409804 64 + 593897 TGTCGGTCCTCATCTAAAGAGGTCCAGGCAACTGGACAC----ATGAGTCGACATAAAACAATATATT -s simHuman_chr6.simHuman.chr6 414731 59 + 601863 TGTCGGTCTTTAACTAAAGAGGTCCAGGTCACTGGACAC----ATCATT----TCATAAAGT-ATATT -s simRat_chr6.simRat.chr6 435386 63 + 647215 TTATGGGCTTCAACCAAAGAG-CCTGACTCACTG----TGGATATGTGTCTACCTATAACGTTATATT - -a -s simMouse_chr6.simMouse.chr6 429290 13 + 636262 GTGTAAGCCTTCA -s Anc0.Anc0refChr3 58475 13 + 222631 GTATAACTCTTCA -s Anc1.Anc1refChr6 89363 13 + 197743 GTATAACTCTTCA -s Anc2.Anc2refChr13 63198 13 + 96486 GTATAACTCTTGG -s mr.mrrefChr5 281759 13 + 294540 GTGTAACCCTTCA -s simCow_chr6.simCow.chr6 419442 13 + 602619 GTACAACTCTTGG -s simDog_chr6.simDog.chr6 409868 13 + 593897 GTATAATGCCTGG -s simHuman_chr6.simHuman.chr6 414790 13 + 601863 GTATAACTCTTCA -s simRat_chr6.simRat.chr6 435450 13 + 647215 GTGTAGCCCTTCA - -a -s simMouse_chr6.simMouse.chr6 429303 20 + 636262 TTCAATCTAAATTTGGCATG -s Anc0.Anc0refChr3 58506 20 + 222631 TTATGTCTATAGCTGGCACT -s Anc1.Anc1refChr6 89394 20 + 197743 TTATGTCTATAGCTGGCACT -s Anc2.Anc2refChr13 63229 20 + 96486 CCATGTCTATAGCTGGCACT -s mr.mrrefChr5 281790 20 + 294540 TTCTATCTAAATTTGGCATG -s simCow_chr6.simCow.chr6 419462 17 + 602619 ---TGTCTATAGCTGGCACT -s simDog_chr6.simDog.chr6 409899 20 + 593897 CCATCTCTAAATCTGGCACT -s simHuman_chr6.simHuman.chr6 414826 20 + 601863 TTGTGTCTATAGCTGGCACT -s simRat_chr6.simRat.chr6 435481 20 + 647215 TTCTATCTAAATTTGGCGTG - -a -s simMouse_chr6.simMouse.chr6 429323 7 + 636262 TACACAA -s Anc0.Anc0refChr3 58530 7 + 222631 TACACAA -s Anc1.Anc1refChr6 89418 7 + 197743 TACACAA -s Anc2.Anc2refChr13 63253 7 + 96486 TACACAA -s mr.mrrefChr5 281810 7 + 294540 TACACAA -s simCow_chr6.simCow.chr6 419483 7 + 602619 AACATAA -s simDog_chr6.simDog.chr6 409923 7 + 593897 TAGACAA -s simHuman_chr6.simHuman.chr6 414850 7 + 601863 TACACAA -s simRat_chr6.simRat.chr6 435501 7 + 647215 TACACAA - -a -s simMouse_chr6.simMouse.chr6 429330 9 + 636262 ATACGCAGT -s Anc0.Anc0refChr3 58537 9 + 222631 CTACCTAGA -s Anc1.Anc1refChr6 89425 9 + 197743 CTACCTAGA -s Anc2.Anc2refChr13 63260 9 + 96486 CTACCTAGA -s mr.mrrefChr5 281817 9 + 294540 ATACGCAGT -s simCow_chr6.simCow.chr6 419494 9 + 602619 TTCCCTGGA -s simDog_chr6.simDog.chr6 409930 9 + 593897 CTACCTAGT -s simHuman_chr6.simHuman.chr6 414857 9 + 601863 CTACCTAGA -s simRat_chr6.simRat.chr6 435508 9 + 647215 ATACACAGT - -a -s simMouse_chr6.simMouse.chr6 429339 10 + 636262 ACCAGGCAAT -s Anc0.Anc0refChr3 58547 10 + 222631 ACCAGACAAT -s Anc1.Anc1refChr6 89435 10 + 197743 ACCAGACAAT -s Anc2.Anc2refChr13 63270 10 + 96486 ACCAGAAAAT -s mr.mrrefChr5 281827 10 + 294540 ACCAGGCAAT -s simCow_chr6.simCow.chr6 419504 10 + 602619 ACCAGGGAAT -s simDog_chr6.simDog.chr6 409940 10 + 593897 ATCAAAAAAT -s simHuman_chr6.simHuman.chr6 414867 10 + 601863 ACCAGACAAT -s simRat_chr6.simRat.chr6 435518 10 + 647215 ACCAGGCAAT - -a -s simMouse_chr6.simMouse.chr6 429349 85 + 636262 GCAGAATCAATACAGAGAAATTGTTTCAGTATGTTGCCAGGGTCATTATCTGGTGTCTGGTGGACTGGTTAAGAAGCCTTGCAGG -s Anc0.Anc0refChr3 58557 74 + 222631 ACAGA--------AGAATTATTGGTAAGATATGAAGCTGGTATCCTTATCTG---TCTGGCAGACAGCCTAAAAGGCCTTGTGGG -s Anc1.Anc1refChr6 89445 76 + 197743 ACAGA------GCAGAATTATTGGTAAGATATGAAGCTGGTATCCTTATCTG---TCTGGCAGACAGCCTAAAAGGCCTTGTGGG -s Anc2.Anc2refChr13 63280 74 + 96486 ACAGG--------AGAATTATTGGTAAGATACGAAGTTAGTATCCTTATCTG---TCTGGCAGACAGCCTAAAAGGCCTTGTGGG -s mr.mrrefChr5 281837 85 + 294540 GCAGAATCAATGCAGAAAAATTGTTTCAGTATGTTGCCGGGGTCATTATCTGGTGTCTGGTGGACTGGTTAAGAAGCCTTGCAGG -s simCow_chr6.simCow.chr6 419515 74 + 602619 ACAGG--------AGGATCATTGATAAGAGACGAAGTCAGTATACTCATGTG---TTTGGCAGACAGCCTACAAGACCTTGTGGG -s simDog_chr6.simDog.chr6 409950 73 + 593897 ACAGG--------AGACTTATCGGTAAGGTACAAAGTTAGTATCCTTATCTG---TCTGGCAGACAGCCCAAAAGGCCCTGTGG- -s simHuman_chr6.simHuman.chr6 414877 75 + 601863 ATAGA------GCAGAACTATTAGTAAGATATGAAGCTGGTATC-TTATTTG---TCTTGCAGACGGCCTAGAAGCTCTTGTGGG -s simRat_chr6.simRat.chr6 435528 83 + 647215 GCAGGAGCAATGCAGAATAATTGTTTCAGTATGTTACCGGGGTCATTATGTGGTGCCTGGTCGACTGGTTAAG--GCCTTACAGG - -a -s simMouse_chr6.simMouse.chr6 429434 14 + 636262 GGCCCATGTATATA -s Anc0.Anc0refChr3 58632 14 + 222631 GGTCCATGTCTTGG -s Anc1.Anc1refChr6 89522 14 + 197743 GGTCCATGTCTTGG -s Anc2.Anc2refChr13 63355 14 + 96486 GATCCTTGTCTTGG -s mr.mrrefChr5 281922 14 + 294540 GGCCCATGTATATA -s simCow_chr6.simCow.chr6 419590 14 + 602619 GATCCTTGTCTTGG -s simHuman_chr6.simHuman.chr6 414953 14 + 601863 GGGCTATGTGTGAG -s simRat_chr6.simRat.chr6 435611 14 + 647215 GGCCCATGTATATA - -a -s simMouse_chr6.simMouse.chr6 429448 44 + 636262 CACTGAGAATGCACATGGTGTAAGTTATTAAGTTCCTATTTCCC -s Anc0.Anc0refChr3 58792 40 + 222631 CACTGATGATGTAAATGGTCTAAGTTATCAAGT----GTTTGCC -s Anc1.Anc1refChr6 89682 40 + 197743 CACTGATGATGTAAATGGTCTAAGTTATCAAGT----GTTTGCC -s Anc2.Anc2refChr13 63564 40 + 96486 CACTGATGATTTAAATGGTCTAAGTTATCAAGT----GTCTGCC -s mr.mrrefChr5 281936 40 + 294540 CACTGAGGATGCACATGGTGTAAGTTATTAAGT----ATTTCCC -s simCow_chr6.simCow.chr6 419823 40 + 602619 CATAGGTGATTTAAATGGTCTAGGTTAGCAAGT----GCCTGCC -s simDog_chr6.simDog.chr6 410206 40 + 593897 CACTCATGACTGAAATTGTCTAAGTTATCAAGT----GTCCACT -s simHuman_chr6.simHuman.chr6 415116 40 + 601863 CACTGATGATGTAAATGGTCTAAGTTATCACAT----GTTTGCC -s simRat_chr6.simRat.chr6 435625 40 + 647215 CACTGAGGATGCACATGGTGTAAGTTATTAAGC----AGTTTCC - -a -s simMouse_chr6.simMouse.chr6 429492 37 + 636262 CAGAATCAGACAAATAAACTGCATCCCGCAACACTGT -s Anc0.Anc0refChr3 58832 37 + 222631 CACAATCAGGCTAACACACCTCATCTAACAACACTTT -s Anc1.Anc1refChr6 89722 37 + 197743 CACAATCAGGCTAACACACCTCATCTAACAACACTTT -s Anc2.Anc2refChr13 63604 37 + 96486 CACAATTAGGATAACACACCTCATCCAACAACACTTT -s mr.mrrefChr5 281976 37 + 294540 CAGAATCAGACAAACAAACTGCATCTCACAACACTGT -s simCow_chr6.simCow.chr6 419865 36 + 602619 CACAATTCGGATAACATA-CTCATCCAACAACACTTT -s simDog_chr6.simDog.chr6 410246 37 + 593897 GACAATTATGATAACACACCTCAATCAACAACATTTT -s simHuman_chr6.simHuman.chr6 415156 37 + 601863 CCCCATCAGGCTAACACATCCCATCTGATGACACTTT -s simRat_chr6.simRat.chr6 435665 37 + 647215 CAGTATCAGACAAACAAACTGCATCTAACAACACTCT - -a -s simMouse_chr6.simMouse.chr6 429529 65 + 636262 AGGAACTTCAAAGAATGACTTGGACTGTGCGACACCTTGTGAACTTTTTGATGATACTTGAGACC -s Anc0.Anc0refChr3 58869 65 + 222631 AGGTGCTTCAAGGGATGACTTGGATTGTGTGACACCTTGGGAACCTTTTGATGGCACTTGAGCCT -s Anc1.Anc1refChr6 89759 65 + 197743 AGGTGCTTCAAGGGATGACTTGGATTGTGTGACACCTTGGGAACCTTTTGATGGCACTTGAGCCT -s Anc2.Anc2refChr13 63641 65 + 96486 AGGTGCTTCAAGGGATGACTTGGATTGTGTGACACCTTGGGAACCTTTTGATGGCACTTGAGCCT -s mr.mrrefChr5 282013 65 + 294540 AGGAACTTCAAAGAATGACTTGGACTGTGCGACACCTTGTGAACTTTTTGATGGCACTTGAGACT -s simCow_chr6.simCow.chr6 419901 65 + 602619 AGGTGCTTTGAGGGATGACTTGAATTGTTTGACACCTTGTGAACTTTCTGATGGCACTTGAGCGT -s simDog_chr6.simDog.chr6 410283 64 + 593897 AGGTGCTTCAAGGGG-GACTTGGATTGTGTGGCACCTTGGGAACCTTTTGATGGCACTTGAGCCT -s simHuman_chr6.simHuman.chr6 415253 65 + 601863 AGGTGCGTCAGGGGATGACTTGGATTGCATGAGACCTGGCGAACCTTTTGATGGCACTTGATCCT -s simRat_chr6.simRat.chr6 435702 54 + 647215 AG-AACTTCAAAGAATGACTCAGACTGTG----------TGAACTTTTCGACGGCCCTTGAGACT - -a -s simMouse_chr6.simMouse.chr6 429594 19 + 636262 TCTCCACCAGAGCCAAGTT -s Anc0.Anc0refChr3 58934 19 + 222631 TCCCCATCAGAACCAAGTA -s Anc1.Anc1refChr6 89824 19 + 197743 TCCCCATCAGAACCAAGTA -s Anc2.Anc2refChr13 63706 19 + 96486 ACCCCATCAAAACCAAGTA -s mr.mrrefChr5 282078 19 + 294540 TCCCCACCAGAGCCAAGTA -s simCow_chr6.simCow.chr6 419966 19 + 602619 ACCCCATCAAAGCCAAGTA -s simDog_chr6.simDog.chr6 410347 19 + 593897 ACCCCATCAAAAGCAAGTA -s simHuman_chr6.simHuman.chr6 415340 19 + 601863 TCCCCATCAGAACCAAGTA -s simRat_chr6.simRat.chr6 435756 19 + 647215 TCCCCAACAGAGCCAAGTA - -a -s simMouse_chr6.simMouse.chr6 429613 12 + 636262 TCAGACTGTTTG -s Anc0.Anc0refChr3 58953 12 + 222631 TCAAATTGATTC -s Anc1.Anc1refChr6 89843 12 + 197743 TCAAATTGATTC -s Anc2.Anc2refChr13 63725 12 + 96486 TCAAATTGATTT -s mr.mrrefChr5 282097 12 + 294540 TCAAACTGTTTC -s simCow_chr6.simCow.chr6 419986 12 + 602619 TCAAATTGGTTT -s simDog_chr6.simDog.chr6 410366 12 + 593897 TCAAAGTGATTT -s simHuman_chr6.simHuman.chr6 415359 12 + 601863 TCAAATGGATTC -s simRat_chr6.simRat.chr6 435775 12 + 647215 TCAAACTGTTTC - -a -s simMouse_chr6.simMouse.chr6 429625 33 + 636262 CACCAGTACCCAGTACCAAACTTATTTTTGATA -s Anc0.Anc0refChr3 58965 4 + 222631 CACA----------------------------- -s Anc1.Anc1refChr6 89855 26 + 197743 CACAAG-AACCAGTATCAAATTAATTT------ -s Anc2.Anc2refChr13 63737 4 + 96486 CACA----------------------------- -s mr.mrrefChr5 282109 33 + 294540 CACCAGTACCCAGTACCAAACTTATTTTTGATA -s simCow_chr6.simCow.chr6 419999 4 + 602619 CATA----------------------------- -s simDog_chr6.simDog.chr6 410378 4 + 593897 CTCA----------------------------- -s simHuman_chr6.simHuman.chr6 415371 26 + 601863 CACAAG-AACCAGTATCAAATTAATTT------ -s simRat_chr6.simRat.chr6 435787 33 + 647215 CACCAGTACCCAGTACCAAACTTATTTTTGACC - -a -s simMouse_chr6.simMouse.chr6 429658 34 + 636262 AAGAAACGACATACAGCAGCAAACAATGTACAGC -s Anc0.Anc0refChr3 58969 25 + 222631 ---------CTTTGATGAGGAAACAATGGACAGT -s Anc1.Anc1refChr6 89881 30 + 197743 ----ACTGACTTTGATGAGGAAACAATGGACAGT -s Anc2.Anc2refChr13 63741 25 + 96486 ---------CTTTGATGAAGAAACAACAGACAGT -s mr.mrrefChr5 282142 34 + 294540 AAGAAACGACATACAGCAGCAAACAATGTACAGC -s simCow_chr6.simCow.chr6 420003 25 + 602619 ---------CTTTCATAGAGAAACAACAGATAGT -s simDog_chr6.simDog.chr6 410382 25 + 593897 ---------CTTTGATGAAGAAGCAACAGACAGT -s simHuman_chr6.simHuman.chr6 415397 30 + 601863 ----ACTGACTTTGGTGAGAAAACAATGGACAGT -s simRat_chr6.simRat.chr6 435822 34 + 647215 AAAAGACAACATATAGCAGCAAACAACATACAGC - -a -s simMouse_chr6.simMouse.chr6 429692 68 + 636262 AGCCAGAAGAAGACATACAAGAAGCAAGGGCCAAGGTATGAAGAGTTCAGATTCACCTACAGCAAAAT -s Anc0.Anc0refChr3 58994 65 + 222631 GGCCAAAACAGTACATAAAGGA--TCATG-CTTAGGTATAAAAAGTTAAGCTTCAGGTACAGCAAAAT -s Anc1.Anc1refChr6 89911 65 + 197743 GGCCAAAACAGTACATAAAGGA--TCATG-CTTAGGTATAAAAAGTTAAGCTTCAGGTACAGCAAAAT -s Anc2.Anc2refChr13 63766 65 + 96486 GGCCAAAACAGTACATAAAGAA--TTGTG-CTTAGGTATAAAGAGTTAAGCTTCAGGTACAGCAAAAA -s mr.mrrefChr5 282176 66 + 294540 AGCCAAAAGAAGACATACAAGA--CCATGGCCAAGGTATAAAAAGTTCAGATTCACCTACAGCAAAAT -s simCow_chr6.simCow.chr6 420050 65 + 602619 GTCTAGAACAGTACATCCAGTA--TTGTG-CTTTAGTATAAAGGGTTTGGCTTCAGATACAGCAAAAA -s simDog_chr6.simDog.chr6 410407 61 + 593897 GGACAAA----TACATAAAGAA--TTGTG-CATAGGTATAAGGAGTTAAGTGCCAGGTACAGCAAAAA -s simHuman_chr6.simHuman.chr6 415427 64 + 601863 GGCCAAAACATTACATATAGGA--TCATG-CTGAGGTAAAAAAAGTT-AGCTTCAGGTACAGGAAACT -s simRat_chr6.simRat.chr6 435856 66 + 647215 AGCCAAAAGAAGACATACAAGA--CCATGGCCAAGGTATAACAAGTTCAAATTCACATACAGCAAAAT - -a -s simMouse_chr6.simMouse.chr6 429760 47 + 636262 TTGCTCTCGGCAATTACTATATCTTCCTTACCTACATATGGTCAAAC -s Anc0.Anc0refChr3 59059 45 + 222631 TTTGCTTCAGGAACAACTGTTTGGTTTTTA--GAGAGGGAGACAACC -s Anc1.Anc1refChr6 89976 45 + 197743 TTTGCTTCAGGAACAACTGTTTGGTTTTTA--GAGAGGGAGACAACC -s Anc2.Anc2refChr13 63836 45 + 96486 TTTGCTTCAGGTACAGCTGTTTGGTATTTA--GAGAGGGAGGCAACC -s mr.mrrefChr5 282242 45 + 294540 TTGGTTTCGGCAATTACTATATGTTTCTTA--TACAGATGGACAACC -s simCow_chr6.simCow.chr6 420121 45 + 602619 TTTGCTTAACATACAGCTATTTGGTGTCTA--GAGAGGGAGGTGACC -s simDog_chr6.simDog.chr6 410473 45 + 593897 TTAGTTTCAGGTACAGCTGTTTATCACTTA--GAGAGGGATGCAACC -s simHuman_chr6.simHuman.chr6 415491 45 + 601863 TTTGCTTCAGGAGCAACCGTTTGGTTTTTA--GAGAGGCTGACACCC -s simRat_chr6.simRat.chr6 435922 45 + 647215 TTAGTTTCCGCAATTAATAAATGTTTGTTA--TATAGATGAACAACC - -a -s simMouse_chr6.simMouse.chr6 429807 16 + 636262 TTGATGCTCAGACAAT -s Anc0.Anc0refChr3 59105 15 + 222631 ATGTTGTGTTCA-AAT -s Anc1.Anc1refChr6 90022 15 + 197743 ATGTTGTGTTCA-AAT -s Anc2.Anc2refChr13 63882 15 + 96486 ATATTATGTTCA-AAG -s mr.mrrefChr5 282288 15 + 294540 TTGTTGTTTTGA-AAT -s simCow_chr6.simCow.chr6 420167 15 + 602619 ACATTATGATCA-CAG -s simDog_chr6.simDog.chr6 410519 15 + 593897 ATATTATGTTCA-AAG -s simHuman_chr6.simHuman.chr6 415537 15 + 601863 ATGTTGTGTTCA-TCT -s simRat_chr6.simRat.chr6 435968 15 + 647215 TTGTTGTTTTGA-AAT - -a -s simMouse_chr6.simMouse.chr6 429823 9 + 636262 TAGCATTGC -s Anc0.Anc0refChr3 59123 9 + 222631 TAGTACTGT -s Anc1.Anc1refChr6 90040 9 + 197743 TAGTACTGT -s Anc2.Anc2refChr13 63900 9 + 96486 TAGTACTGT -s mr.mrrefChr5 282306 9 + 294540 TAGCATTGC -s simCow_chr6.simCow.chr6 420185 9 + 602619 TATGACTGC -s simDog_chr6.simDog.chr6 410537 9 + 593897 TAGTATCGT -s simHuman_chr6.simHuman.chr6 415555 9 + 601863 CAGTACTGT -s simRat_chr6.simRat.chr6 435986 9 + 647215 TAGAAATGC - -a -s simMouse_chr6.simMouse.chr6 429832 9 + 636262 CTCACAATA -s Anc0.Anc0refChr3 59133 9 + 222631 GAGGCAAGG -s Anc1.Anc1refChr6 90050 9 + 197743 GAGGCAAGG -s Anc2.Anc2refChr13 63910 9 + 96486 AAGGCAAGG -s mr.mrrefChr5 282315 9 + 294540 GAGGCAATG -s simCow_chr6.simCow.chr6 420195 9 + 602619 AAGGCAAGG -s simDog_chr6.simDog.chr6 410547 9 + 593897 AAGGTAAGG -s simHuman_chr6.simHuman.chr6 415565 9 + 601863 GAGGCAAGG -s simRat_chr6.simRat.chr6 435995 9 + 647215 GAGGCAATG - -a -s simMouse_chr6.simMouse.chr6 429841 9 + 636262 CTAAAAATT -s Anc0.Anc0refChr3 59147 9 + 222631 CCACCCACA -s Anc1.Anc1refChr6 90064 9 + 197743 CCACCCACA -s Anc2.Anc2refChr13 63924 9 + 96486 CCACCCACA -s mr.mrrefChr5 282324 9 + 294540 CCAAAAATT -s simCow_chr6.simCow.chr6 420209 9 + 602619 CCAGCCACA -s simDog_chr6.simDog.chr6 410561 9 + 593897 TCACTCACA -s simHuman_chr6.simHuman.chr6 415579 7 + 601863 CCACCCA-- -s simRat_chr6.simRat.chr6 436004 9 + 647215 TCAATTGTA - -a -s simMouse_chr6.simMouse.chr6 429850 4 + 636262 TGAA -s Anc0.Anc0refChr3 59156 4 + 222631 TGAC -s Anc1.Anc1refChr6 90073 4 + 197743 TGAC -s Anc2.Anc2refChr13 63933 4 + 96486 TGAC -s mr.mrrefChr5 282333 4 + 294540 TGAA -s simCow_chr6.simCow.chr6 420227 4 + 602619 TGAT -s simDog_chr6.simDog.chr6 410570 4 + 593897 TGAC -s simRat_chr6.simRat.chr6 436013 4 + 647215 TGAG - -a -s simMouse_chr6.simMouse.chr6 429854 18 + 636262 ACCAATGATGGTTGTCTA -s Anc0.Anc0refChr3 59161 18 + 222631 ATCAAAGCTGATAATGTA -s Anc1.Anc1refChr6 90078 18 + 197743 ATCAAAGCTGATAATGTA -s Anc2.Anc2refChr13 63938 18 + 96486 ATCAAAGCTGATAATGTA -s mr.mrrefChr5 282338 18 + 294540 ACCAATGATGATAATCTA -s simCow_chr6.simCow.chr6 420232 18 + 602619 TTAAAAGCTGATAATGTA -s simDog_chr6.simDog.chr6 410575 18 + 593897 ATCAAAGTTGATAATGTA -s simHuman_chr6.simHuman.chr6 415586 17 + 601863 -GGAAAGCTAATAATGTA -s simRat_chr6.simRat.chr6 436018 18 + 647215 ATCAAGGTTGATAATTTG - -a -s simMouse_chr6.simMouse.chr6 429872 10 + 636262 AAACATATGC -s Anc0.Anc0refChr3 59187 10 + 222631 CAGCACATGC -s Anc1.Anc1refChr6 90104 10 + 197743 CAGCACATGC -s Anc2.Anc2refChr13 63964 10 + 96486 CAGCACATGC -s mr.mrrefChr5 282364 10 + 294540 AAACATATGC -s simCow_chr6.simCow.chr6 420258 10 + 602619 CAGCATCTGC -s simDog_chr6.simDog.chr6 410601 10 + 593897 AAGCACATGC -s simHuman_chr6.simHuman.chr6 415611 10 + 601863 CAGCACATGC -s simRat_chr6.simRat.chr6 436044 10 + 647215 GAAGATATGC - -a -s simMouse_chr6.simMouse.chr6 429882 68 + 636262 ATACATGGAATAAGAGAAGTATATATAATGTTTGGTTTTAAGCAGACACATGAGCCTAAGCGCATGTG -s Anc0.Anc0refChr3 59197 68 + 222631 TTACATGGAATAAAAAAAGCACATATACTGTTTGGATTTAAGCAGACACTTGAGCCTAAGCACACATG -s Anc1.Anc1refChr6 90114 68 + 197743 TTACATGGAATAAAAAAAGCACATATACTGTTTGGATTTAAGCAGACACTTGAGCCTAAGCACACATG -s Anc2.Anc2refChr13 63974 68 + 96486 TTACATGGAATAAAAAAAGCACATATACTGTTTGAATTTAAGCAGACACTTGGGCTTAAGCACACATG -s mr.mrrefChr5 282374 68 + 294540 ATACATGGAATAAGAAAAGTATATATAATGTTTGGATTTAAGCAGACACATGAGCCTAAGCACATGTG -s simCow_chr6.simCow.chr6 420268 67 + 602619 TTACATGGAATAAAAAAGGAACACACACTGTTTGAATTCAAGCA-ACACTTGCACTTAAGCATACATG -s simDog_chr6.simDog.chr6 410624 66 + 593897 TTACATGGAATAACAAAAGCACATATACCGTTTGAATTTAA--AGACACTTTGGCTTAGGCACACATG -s simHuman_chr6.simHuman.chr6 415621 68 + 601863 TTACATGTAAGAAAAAAAGCTCATGTACTGTTTGGATTTAAACAGACACTTGAGCCTAAGCACACATG -s simRat_chr6.simRat.chr6 436054 68 + 647215 AGACATGGAATAAGAAAAGTGTATATAATGTTTGGATTTAACCAGACACACGAGCCTAAGGACATGTG - -a -s simMouse_chr6.simMouse.chr6 429950 39 + 636262 GCTGCTATTCATTAGTTTAAATACTGATAGGCCACAGGA -s Anc0.Anc0refChr3 59295 39 + 222631 GCTGCTGGTCATCAGTCTAGGTGCTGATGGGCCATTGGA -s Anc1.Anc1refChr6 90212 39 + 197743 GCTGCTGGTCATCAGTCTAGGTGCTGATGGGCCATTGGA -s Anc2.Anc2refChr13 64072 39 + 96486 GCTGCTGGTCACAAGTCTTGGTGCTGATGGGCCATTGGA -s mr.mrrefChr5 282442 39 + 294540 GCTGCTATTCATCAGTTTAAATACTGATAGGCCACAGGA -s simCow_chr6.simCow.chr6 420352 37 + 602619 GCTG-TAGTCACAAGT-TTGGTGCTGATGGGCCATTGAA -s simDog_chr6.simDog.chr6 410711 35 + 593897 ----CTGGTCTCAAGTCTTGGTGTTGATAGGCCATTGGA -s simHuman_chr6.simHuman.chr6 415728 39 + 601863 GCTGCTGGTTATCAGTCTAGGTGCTGATGGGCCATTGGA -s simRat_chr6.simRat.chr6 436122 35 + 647215 GCTGCTATTCATCAGTTTAAATAC----AGGCCTCAAGA - -a -s simMouse_chr6.simMouse.chr6 429989 45 + 636262 AGTACTAACTAAAGAGCAAAAAATTGCTGTCTGAATGTCTTATCA -s Anc0.Anc0refChr3 59335 41 + 222631 AGT-CTAACTAAATAGCAAAA---TACTATCTCAATTTCTGCTCA -s Anc1.Anc1refChr6 90252 42 + 197743 AGTGCTAACTAAATAGCAAAA---TACTATCTCAATTTCTGCTCA -s Anc2.Anc2refChr13 64112 41 + 96486 ACT-CTAACTAAATAGCAAAA---TACTATCTCAATTTCTGCTCA -s mr.mrrefChr5 282481 45 + 294540 AGTACTAACTAAATAGCAAAAAATTGCTGTCTAAATGTCTTATCA -s simCow_chr6.simCow.chr6 420390 41 + 602619 TTT-CTAACTAAATAGCAAAA---TACTATTTCAATATCTCCTCA -s simDog_chr6.simDog.chr6 410747 41 + 593897 ACT-CTAACTAAATAGCAAAA---TACTATCTTACTTTCTGCTTA -s simHuman_chr6.simHuman.chr6 415768 42 + 601863 AGGGCTTACCAAGTAGCAAAA---TACAATCTCAATTCCTGTTCA -s simRat_chr6.simRat.chr6 436157 41 + 647215 A----TCACTAAATAGCAAAAATTTGCTGTCTAAATATCTCATCG - -a -s simMouse_chr6.simMouse.chr6 430034 30 + 636262 TATTTACTTTACAGAGTACCAATTACTAGC -s Anc0.Anc0refChr3 59389 30 + 222631 TGTTTACAGTTTCTACTACTAATAACTAAC -s Anc1.Anc1refChr6 90307 30 + 197743 TGTTTACAGTTTCTACTACTAATAACTAAC -s Anc2.Anc2refChr13 64166 30 + 96486 TGTATACAGTTTCTACTACTAATAACTGAC -s mr.mrrefChr5 282526 30 + 294540 TATTTACTTTACAGACTACCAATTACTAGC -s simCow_chr6.simCow.chr6 420444 29 + 602619 TGTG-ACAGTTTTTACTACCAATTACTGAC -s simDog_chr6.simDog.chr6 410801 29 + 593897 AGTATACAGTTTCTACTACT-ATACCTGAC -s simHuman_chr6.simHuman.chr6 415823 30 + 601863 TGTTTACAGTTTCCACTACTAATGACTAAC -s simRat_chr6.simRat.chr6 436198 30 + 647215 TATTTACTTTAGAGACTACCAATTAATAGC - -a -s simMouse_chr6.simMouse.chr6 430064 20 + 636262 ATAATTTTCTGCTGGAGCAG -s Anc0.Anc0refChr3 59419 20 + 222631 ATGATTTTATACCAGGGCAG -s Anc1.Anc1refChr6 90337 20 + 197743 ATGATTTTATACCAGGGCAG -s Anc2.Anc2refChr13 64196 20 + 96486 ATGATATTATACCAGGGCAG -s mr.mrrefChr5 282556 20 + 294540 ATAATTTTCTGCTGGAGCAG -s simCow_chr6.simCow.chr6 420473 20 + 602619 ATGATATTATACCAGGGCAG -s simDog_chr6.simDog.chr6 410844 20 + 593897 ACGATATTCTACCAGGGCAG -s simHuman_chr6.simHuman.chr6 415853 20 + 601863 ATGATTCTATACCAGGGCAA -s simRat_chr6.simRat.chr6 436228 20 + 647215 GTAATTTTCTGCTGGAGCAG - -a -s simMouse_chr6.simMouse.chr6 430084 8 + 636262 TTATTATA -s Anc0.Anc0refChr3 59440 8 + 222631 TCATTATT -s Anc1.Anc1refChr6 90358 8 + 197743 TCATTATT -s Anc2.Anc2refChr13 64217 8 + 96486 TCATTATT -s mr.mrrefChr5 282577 8 + 294540 TTATTATA -s simCow_chr6.simCow.chr6 420494 8 + 602619 ACGTGATT -s simDog_chr6.simDog.chr6 410865 8 + 593897 TCATTATT -s simHuman_chr6.simHuman.chr6 415874 8 + 601863 TCATTTTT -s simRat_chr6.simRat.chr6 436249 8 + 647215 TTATTATA - -a -s simMouse_chr6.simMouse.chr6 430092 23 + 636262 ATTTTGTGGGTAATAGGAATTTA -s Anc0.Anc0refChr3 59448 20 + 222631 ATTTTGTGGGT---GGGAAAATA -s Anc1.Anc1refChr6 90366 23 + 197743 ATTTTGTGGGTAATGGGAAAATA -s Anc2.Anc2refChr13 64225 20 + 96486 ATTTTGTGGGT---GTGTAAACA -s mr.mrrefChr5 282585 23 + 294540 ATTTTGTGGGTAATAGGAATTTA -s simCow_chr6.simCow.chr6 420502 20 + 602619 ATTTTGGGGTC---ATACAAACA -s simDog_chr6.simDog.chr6 410873 20 + 593897 ATTTTGTGGGT---GTGTAAACA -s simHuman_chr6.simHuman.chr6 415885 23 + 601863 ATTTTGTCGATAATGGGAACATA -s simRat_chr6.simRat.chr6 436257 23 + 647215 ATTTTGTGGGTAATAGGAATTTA - -a -s simMouse_chr6.simMouse.chr6 430115 23 + 636262 GGATACACGCAACTTATCTTCAC -s Anc0.Anc0refChr3 59468 23 + 222631 GTATACATACAACATATCTCCAG -s Anc1.Anc1refChr6 90389 23 + 197743 GTATACATACAACATATCTCCAG -s Anc2.Anc2refChr13 64245 23 + 96486 GTATCCATACAACATATCTCGAG -s mr.mrrefChr5 282608 23 + 294540 GGATACATGCAACTTATCTTCAC -s simCow_chr6.simCow.chr6 420524 23 + 602619 GTATGGATACAACTTATCTCAAA -s simDog_chr6.simDog.chr6 410893 23 + 593897 GGGTCCATACAGCATATCCTGAG -s simHuman_chr6.simHuman.chr6 415908 23 + 601863 GTATACATAAAACATACCTCCAG -s simRat_chr6.simRat.chr6 436280 23 + 647215 GGATACATGCAACTTATCTTCAC - -a -s simMouse_chr6.simMouse.chr6 430138 16 + 636262 CACGAGCAAGTTAAAG -s Anc0.Anc0refChr3 59492 16 + 222631 CATAAGTAATTTAAAA -s Anc1.Anc1refChr6 90413 16 + 197743 CATAAGTAATTTAAAA -s Anc2.Anc2refChr13 64269 16 + 96486 CATAAATAATTTGAAA -s mr.mrrefChr5 282631 16 + 294540 CACGAGCAATTTAAAG -s simCow_chr6.simCow.chr6 420548 16 + 602619 CATAATTAATCTGAAG -s simDog_chr6.simDog.chr6 410917 16 + 593897 CGTAAATAATTTGAAA -s simHuman_chr6.simHuman.chr6 415932 16 + 601863 CATAAGTAATTTAAAA -s simRat_chr6.simRat.chr6 436303 16 + 647215 CAGGAGCAATTTAAAG - -a -s simMouse_chr6.simMouse.chr6 430154 14 + 636262 AAGCTTACTGTAAT -s Anc0.Anc0refChr3 59510 14 + 222631 AAGTTAACTGAAAT -s Anc1.Anc1refChr6 90431 14 + 197743 AAGTTAACTGAAAT -s Anc2.Anc2refChr13 64287 14 + 96486 AAGTTAACTGAAAT -s mr.mrrefChr5 282647 14 + 294540 AAGCTTACTGTAAT -s simCow_chr6.simCow.chr6 420566 14 + 602619 AACTCAGCTGTAAT -s simDog_chr6.simDog.chr6 410935 14 + 593897 AAGGTAACTCATGC -s simHuman_chr6.simHuman.chr6 415950 14 + 601863 CAATTAATTGGAAT -s simRat_chr6.simRat.chr6 436319 14 + 647215 AAGCTTACTGTAAT - -a -s simMouse_chr6.simMouse.chr6 430168 1 + 636262 A -s Anc0.Anc0refChr3 59524 1 + 222631 T -s Anc1.Anc1refChr6 90445 1 + 197743 T -s Anc2.Anc2refChr13 64301 1 + 96486 T -s mr.mrrefChr5 282661 1 + 294540 A -s simCow_chr6.simCow.chr6 420581 1 + 602619 T -s simDog_chr6.simDog.chr6 410949 1 + 593897 T -s simHuman_chr6.simHuman.chr6 415964 1 + 601863 T -s simRat_chr6.simRat.chr6 436333 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 430169 8 + 636262 GAAGTGTA -s Anc0.Anc0refChr3 59525 8 + 222631 AGTGCATA -s Anc1.Anc1refChr6 90446 8 + 197743 AGTGCATA -s Anc2.Anc2refChr13 64302 8 + 96486 AGTGCAAA -s mr.mrrefChr5 282662 8 + 294540 GAAGTGTA -s simCow_chr6.simCow.chr6 420582 8 + 602619 AATGTACA -s simDog_chr6.simDog.chr6 410952 8 + 593897 AGTGCAAA -s simHuman_chr6.simHuman.chr6 415965 8 + 601863 AGGGCATA -s simRat_chr6.simRat.chr6 436334 8 + 647215 GAAGTGTA - -a -s simMouse_chr6.simMouse.chr6 430177 7 + 636262 ATTAAAC -s Anc0.Anc0refChr3 59533 7 + 222631 ATTAACC -s Anc1.Anc1refChr6 90454 7 + 197743 ATTAACC -s Anc2.Anc2refChr13 64310 7 + 96486 AGTAACC -s mr.mrrefChr5 282670 7 + 294540 ATTAAAC -s simCow_chr6.simCow.chr6 420590 7 + 602619 GGTAGTC -s simDog_chr6.simDog.chr6 410981 7 + 593897 AGTAACT -s simHuman_chr6.simHuman.chr6 415973 7 + 601863 ATTAACC -s simRat_chr6.simRat.chr6 436342 7 + 647215 TTTAAAC - -a -s simMouse_chr6.simMouse.chr6 430184 4 + 636262 ACTG -s Anc0.Anc0refChr3 59541 4 + 222631 ACTG -s Anc1.Anc1refChr6 90462 4 + 197743 ACTG -s Anc2.Anc2refChr13 64318 4 + 96486 AGTG -s mr.mrrefChr5 282677 4 + 294540 ACTG -s simCow_chr6.simCow.chr6 420598 4 + 602619 ATGG -s simDog_chr6.simDog.chr6 410989 4 + 593897 AGTG -s simHuman_chr6.simHuman.chr6 415981 4 + 601863 ACTG -s simRat_chr6.simRat.chr6 436349 4 + 647215 GCTG - -a -s simMouse_chr6.simMouse.chr6 430188 2 + 636262 AA -s Anc0.Anc0refChr3 59545 2 + 222631 CA -s Anc1.Anc1refChr6 90466 2 + 197743 CA -s Anc2.Anc2refChr13 64322 2 + 96486 CA -s mr.mrrefChr5 282681 2 + 294540 AA -s simCow_chr6.simCow.chr6 420724 2 + 602619 CA -s simDog_chr6.simDog.chr6 410993 2 + 593897 CA -s simHuman_chr6.simHuman.chr6 415985 2 + 601863 CA -s simRat_chr6.simRat.chr6 436353 2 + 647215 AA - -a -s simMouse_chr6.simMouse.chr6 430190 3 + 636262 GTG -s Anc0.Anc0refChr3 59547 3 + 222631 GTG -s Anc1.Anc1refChr6 90468 3 + 197743 GTG -s Anc2.Anc2refChr13 64335 3 + 96486 GTG -s mr.mrrefChr5 282683 3 + 294540 GTG -s simCow_chr6.simCow.chr6 420737 3 + 602619 AAG -s simDog_chr6.simDog.chr6 411006 3 + 593897 GTG -s simHuman_chr6.simHuman.chr6 415987 3 + 601863 TTG -s simRat_chr6.simRat.chr6 436355 3 + 647215 GTG - -a -s simMouse_chr6.simMouse.chr6 430193 3 + 636262 AAT -s Anc0.Anc0refChr3 59550 3 + 222631 AAT -s Anc1.Anc1refChr6 90471 3 + 197743 AAT -s Anc2.Anc2refChr13 64338 3 + 96486 AAT -s mr.mrrefChr5 282686 3 + 294540 AAT -s simCow_chr6.simCow.chr6 420750 3 + 602619 AAT -s simDog_chr6.simDog.chr6 411009 3 + 593897 AAT -s simHuman_chr6.simHuman.chr6 415990 3 + 601863 CCT -s simRat_chr6.simRat.chr6 436358 3 + 647215 AAT - -a -s simMouse_chr6.simMouse.chr6 430196 21 + 636262 GGAAACACATTTAATTTGAAT -s Anc0.Anc0refChr3 59553 2 + 222631 AG------------------- -s Anc1.Anc1refChr6 90474 2 + 197743 AG------------------- -s Anc2.Anc2refChr13 64350 2 + 96486 AC------------------- -s mr.mrrefChr5 282689 21 + 294540 GGAAACACATTTAATTTGAAT -s simCow_chr6.simCow.chr6 420762 2 + 602619 AT------------------- -s simDog_chr6.simDog.chr6 411021 2 + 593897 AC------------------- -s simHuman_chr6.simHuman.chr6 415993 2 + 601863 AG------------------- -s simRat_chr6.simRat.chr6 436361 21 + 647215 TGAAATGCATTTGACTTGACT - -a -s simMouse_chr6.simMouse.chr6 430217 21 + 636262 ATTAGTTTTGTAGCATGCCAT -s mr.mrrefChr5 282715 21 + 294540 ATTAGTTTTGTAGCATGCCAT -s simRat_chr6.simRat.chr6 436387 21 + 647215 AGTAGTTTTATAGTGTGCCAT - -a -s simMouse_chr6.simMouse.chr6 430238 104 + 636262 ATTATTCACATACACTAATCATTGTTTTAGAGTGCACTTCTGTTGTTAATGAACAAATATCCGTGCAATCCTGGCTCACACTCCTATTTGTGTGAGCTTAGTTG -s Anc0.Anc0refChr3 59555 33 + 222631 ---------------------------------------------------------------------CCTGTCTCACACTGTTATT-GTGTGAGCTA-TCTT -s Anc1.Anc1refChr6 90476 34 + 197743 ---------------------------------------------------------------------CCTGTCTCACACTGTTATT-GTGTGAGCTAATCTT -s Anc2.Anc2refChr13 64352 33 + 96486 ---------------------------------------------------------------------CCTGTCTCACACTGTTATT-GTGTGAGCTA-TCTT -s mr.mrrefChr5 282736 101 + 294540 ATTATTCACATACAGTAATCATTGTTTTAGAGTGCACTTTTGTTATTAATGAACAAA---CTGTGGAATCCTGTCTCACACTCTTATTTGTGTGAGCTAAGCTT -s simCow_chr6.simCow.chr6 420764 33 + 602619 ---------------------------------------------------------------------TTTGTCTCACACTGATGTT-GTGTGAGTGA-TCTT -s simDog_chr6.simDog.chr6 411023 33 + 593897 ---------------------------------------------------------------------CCTGTTTCACCCTGTCATT-GCGTGAGCTA-TCTT -s simHuman_chr6.simHuman.chr6 415995 34 + 601863 ---------------------------------------------------------------------CCGGCCTCAGACTGTTATT-GTGTGAGCTAATCCT -s simRat_chr6.simRat.chr6 436415 101 + 647215 ATTATTCACATACAGTAATCATTGTTTTAGAGTGCACTTTTTCCATTAATGAGCAGA---TTGTGGAATCCTGTCTCACACTCTTATTTGTGTGGGCTAGGCTT - -a -s simMouse_chr6.simMouse.chr6 430342 49 + 636262 GCAGAGGACTTGATCCAAGGCAGGATGTGCTGCACATATCTTAGACTTC -s Anc0.Anc0refChr3 59589 49 + 222631 ATAGAGTATTTGATCCAAGGCAGGATGTGCTCCACAGATCTGAAGCTTT -s Anc1.Anc1refChr6 90511 49 + 197743 ATAGAGTATTTGATCCAAGGCAGGATGTGCTCCACAGATCTGAAGCTTT -s Anc2.Anc2refChr13 64386 49 + 96486 ATAGAGTATTTGATCCAAGGCAGGATGTGCTCCACAGATCTGAAGCCTT -s mr.mrrefChr5 282837 49 + 294540 GCAAAGGACTTGATCCAAGGCAGGATGTGCTGCACAGATCTTAGACTTT -s simCow_chr6.simCow.chr6 420798 49 + 602619 TTAGGATATTGGATCCAAGGCAAGGTGTTCTCCACAGATCCGAAGCCTT -s simDog_chr6.simDog.chr6 411057 49 + 593897 ATAGAGTATTTGATCCAAGGCAGGACGTGCTGCACAGATTTGAAGCCTT -s simHuman_chr6.simHuman.chr6 416030 49 + 601863 ATACAGCATTTGATCCACGGCAGAATGTGCTCTATGGATCTGAAGCTCT -s simRat_chr6.simRat.chr6 436516 49 + 647215 GGCATGGACTTGATCCAGGGCAGGATGTGCTGCACAGATCTTAGACTTT - -a -s simMouse_chr6.simMouse.chr6 430391 32 + 636262 ATCTAATGTGGCTCTAAAGACAGGAACAGATC -s Anc0.Anc0refChr3 59638 32 + 222631 GTCTAGTCTGGCTCTAAAAATAGGAATAGATT -s Anc1.Anc1refChr6 90560 32 + 197743 GTCTAGTCTGGCTCTAAAAATAGGAATAGATT -s Anc2.Anc2refChr13 64436 32 + 96486 GTCTAGTCTGGCTCTAAAATTAGGAAGAGATT -s mr.mrrefChr5 282886 32 + 294540 GTCTAATCTGGCTCTAAAGACAGGAATAGATT -s simCow_chr6.simCow.chr6 420848 32 + 602619 GTCTGGTCCAGCTCCAGAATTAGGAAGTGATT -s simDog_chr6.simDog.chr6 411107 32 + 593897 GTCTAGTCTGGCTTTCAAATTAGGAAGAGATT -s simHuman_chr6.simHuman.chr6 416079 32 + 601863 GTCTAGTCTGGCTCTAAGAATAAGTATACATT -s simRat_chr6.simRat.chr6 436565 32 + 647215 GTCTAATCTGGCTAAAAAGACAGGAATAGATT - -a -s simMouse_chr6.simMouse.chr6 430423 9 + 636262 AGATGGGAT -s Anc0.Anc0refChr3 59671 9 + 222631 AGGTGGGTT -s Anc1.Anc1refChr6 90593 9 + 197743 AGGTGGGTT -s Anc2.Anc2refChr13 64469 9 + 96486 AGGTGGGTT -s mr.mrrefChr5 282918 9 + 294540 AGATGGGAT -s simCow_chr6.simCow.chr6 420881 9 + 602619 AGATGGGTT -s simDog_chr6.simDog.chr6 411140 9 + 593897 AGGTGGGTT -s simHuman_chr6.simHuman.chr6 416112 9 + 601863 AGGTGGGTT -s simRat_chr6.simRat.chr6 436597 9 + 647215 AGATGGGAT - -a -s simMouse_chr6.simMouse.chr6 430432 3 + 636262 TGC -s Anc0.Anc0refChr3 59680 3 + 222631 TTC -s Anc1.Anc1refChr6 90602 3 + 197743 TTC -s Anc2.Anc2refChr13 64486 3 + 96486 TTT -s mr.mrrefChr5 282927 3 + 294540 TGC -s simCow_chr6.simCow.chr6 420898 3 + 602619 TTT -s simDog_chr6.simDog.chr6 411158 3 + 593897 TTT -s simHuman_chr6.simHuman.chr6 416121 3 + 601863 TAC -s simRat_chr6.simRat.chr6 436606 3 + 647215 TGC - -a -s simMouse_chr6.simMouse.chr6 430435 85 + 636262 TTAAATATCTGTACAAACGAAATAATCTATTACAGACAGTTACCACAACCTAGGGTTTTGGATACAACTGTGGCTTTACAAATAG -s Anc0.Anc0refChr3 59683 53 + 222631 TTAAATATTTGCATCAAAGACACAATCCACTACA-----------CAC---------------------GTGGCTTCAAAAATAG -s Anc1.Anc1refChr6 90605 74 + 197743 TTAAATATTTGCATCAAAGACACAATCCACTACA-----------CACCCCATGGTTTTGCATACAAATGTGGCTTCAAAAATAG -s Anc2.Anc2refChr13 64489 53 + 96486 CTAAATATTTGCATCAAAGACACAATCCACTACA-----------TAC---------------------GCGTCTTCCAAAATAG -s mr.mrrefChr5 282930 74 + 294540 TTAAATATCTGTACAAAAGAAATAATCTACTACA-----------CAACCCAGGGTTTTGGATACAACTGTGGCTTTACAAATAG -s simCow_chr6.simCow.chr6 420901 34 + 602619 CCAAATATTTGCATCAAAGACACAATTCACTACA--------------------------------------------------- -s simDog_chr6.simDog.chr6 411162 53 + 593897 CTGAATATTTGCATCAAAGGTGTGATCCACTACA-----------TAC---------------------GCGTCTTCCAAAATAG -s simHuman_chr6.simHuman.chr6 416124 68 + 601863 TTAAATATTTGCATCAAAGACACA------CATA-----------CACCCCATGGTTTTGCATACAAATTTGGCTTCAAAAATAG -s simRat_chr6.simRat.chr6 436609 74 + 647215 TTAAATATCTGTACAAAAGAGATAATCTACTACA-----------CAACTCAGGGTTTTGGCTACAACTGTGGCTTTACATATAG - -a -s simMouse_chr6.simMouse.chr6 430520 60 + 636262 TTTGAAGCCCTTCTCTTCCTATTTTGCCTCTGGACTCCTAATGCAGCATGCTATGATAGT -s Anc0.Anc0refChr3 59736 57 + 222631 GTTGAAGCATTTCCTTTCCTATTTTGCCACTGGACTGCCAAGACAGTGTACCATGAC--- -s Anc1.Anc1refChr6 90679 60 + 197743 GTTGAAGCATTTCCTTTCCTATTTTGCCACTGGACTGCCAAGACAGTGTACCATGACAGT -s Anc2.Anc2refChr13 64542 57 + 96486 GTTGAAGCATTTCCTTTCCCATTCTGCCACTGGATTGCCAAGACAGTGTACCATGAC--- -s mr.mrrefChr5 283004 60 + 294540 GTTGAAGCCCTTCTCTTCCTATTTTGCCACTGGACTCCCAAGGCAGCATGCCATGATAGT -s simCow_chr6.simCow.chr6 420935 46 + 602619 -----------TCCTTTCCCATTCTGCCAATGGATTGCCAAGGCAGCGTATGATGAC--- -s simDog_chr6.simDog.chr6 411215 46 + 593897 GTTGAAGCATTTCCCT-----------TACTGGATTGCCAAGACAGTGTACCATGGC--- -s simHuman_chr6.simHuman.chr6 416193 60 + 601863 GATAAAGTGTTTCATTTCCTATGTTGCCACTGGACTGTCAAGACAGTCCACCATGACAGT -s simRat_chr6.simRat.chr6 436683 60 + 647215 GTTGGAGCCCTTCTCTTCCTACTTTGCCATTGGACTCCCAAGGCAGCATGCCATGATAGT - -a -s simMouse_chr6.simMouse.chr6 430580 14 + 636262 CACCCTAAATGACC -s Anc0.Anc0refChr3 59793 2 + 222631 ------------CA -s Anc1.Anc1refChr6 90739 14 + 197743 CACAATGCTTGACA -s Anc2.Anc2refChr13 64599 2 + 96486 ------------CA -s mr.mrrefChr5 283064 14 + 294540 CACCCTAAATGACC -s simCow_chr6.simCow.chr6 420981 2 + 602619 ------------AA -s simDog_chr6.simDog.chr6 411261 2 + 593897 ------------CA -s simHuman_chr6.simHuman.chr6 416254 14 + 601863 CACAATGCTTGACA -s simRat_chr6.simRat.chr6 436743 14 + 647215 CACCGTAAATGATC - -a -s simMouse_chr6.simMouse.chr6 430594 54 + 636262 TGAGAGTTGTAAATCCTTTCTTTACTCTATTTGCTATATATAATAGATGCCTAT -s Anc0.Anc0refChr3 59803 54 + 222631 TGATAGTTGAAAATCCTGCTTTTATTCTATTTGCTATATATAATATATGTCTAG -s Anc1.Anc1refChr6 90761 54 + 197743 TGATAGTTGAAAATCCTGCTTTTATTCTATTTGCTATATATAATATATGTCTAG -s Anc2.Anc2refChr13 64609 54 + 96486 TGATAGTTAAAAATCCTGCTTTTATTATCTTTGCTATATATAACATATGTCTAG -s mr.mrrefChr5 283086 54 + 294540 TGAGAGTTGTAAATCCTTTCTTTACTCTATTTGCTATATATAATATATGCCTAT -s simCow_chr6.simCow.chr6 420986 54 + 602619 TAACCGTCAAAAGTCCTGCTTATGTTCTGTATGCTAGATGTAACATACCTCTAG -s simDog_chr6.simDog.chr6 411271 54 + 593897 TGGTAGTTAAAAACCTCCCTTTGATCATCTTTGCTATATATAACATTTGTCTAG -s simHuman_chr6.simHuman.chr6 416276 53 + 601863 TGATAGTTGAAAATACTGCTTTTATTCCATT-CATATATACACTATAGGTCTAG -s simRat_chr6.simRat.chr6 436765 54 + 647215 TGAGAGTTGTAAATCCTTTCTTTACTCTATTTGCTATATATAATATGTGCCTAA - -a -s simMouse_chr6.simMouse.chr6 430648 53 + 636262 CATGACAGCACCTCACAGCTATAATAAGGGGTAGAGACAATGGATAACCTGGT -s Anc0.Anc0refChr3 59857 53 + 222631 TCTGACAGCAACTGACAGCAATAATAGGAGGTAGAAATGATGGGTAACCTGTG -s Anc1.Anc1refChr6 90815 53 + 197743 TCTGACAGCAACTGACAGCAATAATAGGAGGTAGAAATGATGGGTAACCTGTG -s Anc2.Anc2refChr13 64663 53 + 96486 TCTGACAGCAACTGACAGCAATAATAGGGGGTAGAAATGATGGGTAACCTGTG -s mr.mrrefChr5 283140 53 + 294540 CATGACAGCACCTGACAGCAATAATAAGAGGTAGAGACAATGGATAACCTGTG -s simCow_chr6.simCow.chr6 421042 53 + 602619 TCTAACAGCAATTGACAGCAATAATTGGGGGTAGTGATGATGGGTAACAGGTG -s simDog_chr6.simDog.chr6 411325 53 + 593897 TCTGACAGCAACTGACAGCAATAATAGGGGGTAGAAATGGCAGGTAACCTGTT -s simHuman_chr6.simHuman.chr6 416329 52 + 601863 TCTGACAGC-TCTGACAGCAATAGTAGTAGATCAAACTGATGGGTAACCTGTG -s simRat_chr6.simRat.chr6 436819 52 + 647215 CATGCCAGC-CCTGACAGCAATAATAAGAAGTAGAGACAATAGATAACCTGTG - -a -s simMouse_chr6.simMouse.chr6 430701 5 + 636262 GGCTA -s Anc0.Anc0refChr3 59917 5 + 222631 GACTA -s Anc1.Anc1refChr6 90875 5 + 197743 GACTA -s Anc2.Anc2refChr13 64723 5 + 96486 GACTA -s mr.mrrefChr5 283193 5 + 294540 GGCTA -s simCow_chr6.simCow.chr6 421102 5 + 602619 GACTA -s simDog_chr6.simDog.chr6 411385 5 + 593897 GACCA -s simHuman_chr6.simHuman.chr6 416388 5 + 601863 GACTA -s simRat_chr6.simRat.chr6 436871 5 + 647215 GGCTA - -a -s simMouse_chr6.simMouse.chr6 430706 43 + 636262 AAGCAGGATCCCAAGCACATTCTTAAGTGCCTATACTTTGCCC -s Anc0.Anc0refChr3 59951 43 + 222631 AAGCAGGCTGCCAAGCATATTCTTATGTGCCCATGATTTGCCC -s Anc1.Anc1refChr6 90909 43 + 197743 AAGCAGGCTGCCAAGCATATTCTTATGTGCCCATGATTTGCCC -s Anc2.Anc2refChr13 64757 43 + 96486 AAGCAGACTGCCAAGCATATTCTTATGTGCCCATGATTGGCCA -s mr.mrrefChr5 283228 43 + 294540 AAGCAGGATCCCAAGCACATTCTTAAGTGCCCATAATTTGCCC -s simCow_chr6.simCow.chr6 421137 43 + 602619 AAGCAGACTGCCATGCACACTCTTATGTGCCCATGATTGGCCA -s simDog_chr6.simDog.chr6 411420 43 + 593897 AAGCAGACTGCCAAGCCTTTTCTTATGTGTCCATGACTGTCCA -s simHuman_chr6.simHuman.chr6 416422 43 + 601863 AAGTAGGCTGCCAAGCATATTTTTATCTGCCCATGATTTGCCC -s simRat_chr6.simRat.chr6 436906 43 + 647215 AACCAGGATCCGAAGCACATTGTTAAGTGCCCATAATTTGCCC - -a -s simMouse_chr6.simMouse.chr6 430749 16 + 636262 CTTTTGGAGCCAACTA -s Anc0.Anc0refChr3 59995 16 + 222631 TTTTTGTAACCAACTA -s Anc1.Anc1refChr6 90953 16 + 197743 TTTTTGTAACCAACTA -s Anc2.Anc2refChr13 64801 16 + 96486 TGTCTGTAACCAATTA -s mr.mrrefChr5 283271 16 + 294540 CTTTTGGAGCCAACTA -s simCow_chr6.simCow.chr6 421181 16 + 602619 TGTCTGGAGCCAATTG -s simDog_chr6.simDog.chr6 411464 16 + 593897 TGTCTGTAACCAGTTA -s simHuman_chr6.simHuman.chr6 416466 16 + 601863 TTTTTGTGACCAACAA -s simRat_chr6.simRat.chr6 436949 16 + 647215 CATTTGGAGCCAACTA - -a -s simMouse_chr6.simMouse.chr6 430765 11 + 636262 TACTACAATGA -s Anc0.Anc0refChr3 60014 11 + 222631 CATCAATGTGC -s Anc1.Anc1refChr6 90972 11 + 197743 CATCAATGTGC -s Anc2.Anc2refChr13 64820 11 + 96486 CATCGATGTAC -s mr.mrrefChr5 283287 11 + 294540 TACTAAAGTGA -s simCow_chr6.simCow.chr6 421200 11 + 602619 CATCGATGTAC -s simDog_chr6.simDog.chr6 411483 7 + 593897 C----ATGTAC -s simHuman_chr6.simHuman.chr6 416485 11 + 601863 CATCAATGTGC -s simRat_chr6.simRat.chr6 436965 11 + 647215 TACTAAAGTGA - -a -s simMouse_chr6.simMouse.chr6 430776 15 + 636262 AAACAGCTTGTGAAA -s Anc0.Anc0refChr3 60033 15 + 222631 ACATAACTTGAGATA -s Anc1.Anc1refChr6 90991 15 + 197743 ACATAACTTGAGATA -s Anc2.Anc2refChr13 64839 15 + 96486 TCATAACTTGTGATA -s mr.mrrefChr5 283298 15 + 294540 AAACAGCTTGAGAAA -s simCow_chr6.simCow.chr6 421219 15 + 602619 TCAAAATTGGTGATA -s simDog_chr6.simDog.chr6 411498 15 + 593897 TCCTAACTTGCAATA -s simHuman_chr6.simHuman.chr6 416504 9 + 601863 ACA----TTGATA-- -s simRat_chr6.simRat.chr6 436976 15 + 647215 AAAGAGCTTGAGAAA - -a -s simMouse_chr6.simMouse.chr6 430791 2 + 636262 AA -s Anc0.Anc0refChr3 60048 2 + 222631 TA -s Anc1.Anc1refChr6 91006 2 + 197743 TA -s Anc2.Anc2refChr13 64854 2 + 96486 TA -s mr.mrrefChr5 283313 2 + 294540 AA -s simCow_chr6.simCow.chr6 421235 2 + 602619 TA -s simDog_chr6.simDog.chr6 411513 2 + 593897 TA -s simHuman_chr6.simHuman.chr6 416513 2 + 601863 TA -s simRat_chr6.simRat.chr6 436991 2 + 647215 AA - -a -s simMouse_chr6.simMouse.chr6 430793 5 + 636262 CCATA -s Anc0.Anc0refChr3 60052 5 + 222631 CTAAA -s Anc1.Anc1refChr6 91010 5 + 197743 CTAAA -s Anc2.Anc2refChr13 64858 5 + 96486 CTAAA -s mr.mrrefChr5 283315 5 + 294540 CCATA -s simCow_chr6.simCow.chr6 421239 5 + 602619 CTGAC -s simDog_chr6.simDog.chr6 411517 5 + 593897 CCAAA -s simHuman_chr6.simHuman.chr6 416517 5 + 601863 CTAAA -s simRat_chr6.simRat.chr6 436993 5 + 647215 TCATA - -a -s simMouse_chr6.simMouse.chr6 430798 7 + 636262 GAATGGA -s Anc0.Anc0refChr3 60057 7 + 222631 GGAGGGA -s Anc1.Anc1refChr6 91015 7 + 197743 GGAGGGA -s Anc2.Anc2refChr13 64870 7 + 96486 GGAGAGA -s mr.mrrefChr5 283320 7 + 294540 GGATGGA -s simCow_chr6.simCow.chr6 421251 7 + 602619 GAAAAAA -s simDog_chr6.simDog.chr6 411529 7 + 593897 GGAGAGA -s simHuman_chr6.simHuman.chr6 416522 7 + 601863 GGAGGCA -s simRat_chr6.simRat.chr6 436998 7 + 647215 GGATGGA - -a -s simMouse_chr6.simMouse.chr6 430805 2 + 636262 GG -s Anc0.Anc0refChr3 60064 2 + 222631 GG -s Anc1.Anc1refChr6 91022 2 + 197743 GG -s Anc2.Anc2refChr13 64885 2 + 96486 GG -s mr.mrrefChr5 283327 2 + 294540 GG -s simCow_chr6.simCow.chr6 421266 2 + 602619 GG -s simDog_chr6.simDog.chr6 411544 2 + 593897 GG -s simHuman_chr6.simHuman.chr6 416529 2 + 601863 GT -s simRat_chr6.simRat.chr6 437005 2 + 647215 AG - -a -s simMouse_chr6.simMouse.chr6 430807 1 + 636262 A -s Anc0.Anc0refChr3 60066 1 + 222631 A -s Anc1.Anc1refChr6 91024 1 + 197743 A -s Anc2.Anc2refChr13 64887 1 + 96486 A -s mr.mrrefChr5 283329 1 + 294540 A -s simCow_chr6.simCow.chr6 421274 1 + 602619 A -s simDog_chr6.simDog.chr6 411546 1 + 593897 A -s simHuman_chr6.simHuman.chr6 416531 1 + 601863 A -s simRat_chr6.simRat.chr6 437007 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 430808 183 + 636262 GCATAATGGCAGTGTTGCAGGGAAAGAACAAATGCAGGATCCATGGGTGAGTGGCAAGGTATCCTGGTTCGAACTCTCATCGCGAGACTATATAGTAGTGCTGACGGGTCGAGACGTGGATTCCGGGGTTAGGACCATGCTGTTGACGGGTTCCATAGGAATTGTGCTCCCTCCCAAATTGTA -s Anc0.Anc0refChr3 60069 51 + 222631 GTGTAATGACAGTGCCACAGGGAGA----AAA--AAAGTTGAATAAGAGAGTGGAAA------------------------------------------------------------------------------------------------------------------------------ -s Anc1.Anc1refChr6 91027 53 + 197743 GTGTAATGACAGTGCCACAGGGAGAG--CAAA--AAAGTTGAATAAGAGAGTGGAAA------------------------------------------------------------------------------------------------------------------------------ -s Anc2.Anc2refChr13 64890 51 + 96486 GTGTAATGACAGTGCCACAGGGGGA----AAA--AGAGTGGAATAAGAGAGTGGGAG------------------------------------------------------------------------------------------------------------------------------ -s mr.mrrefChr5 283330 55 + 294540 GCGTAATGACAGTGTTGCAGGGAAAG--CAAATGCAGGATGCATAGGTGAGTGGAAA------------------------------------------------------------------------------------------------------------------------------ -s simCow_chr6.simCow.chr6 421277 51 + 602619 GTGTAATGACAGTGCCACAGGGGGA----GAA--AGAGTAGAATGAGGTAGAGAGAG------------------------------------------------------------------------------------------------------------------------------ -s simDog_chr6.simDog.chr6 411549 51 + 593897 GTGTAAAGACAGTGCCACAGGGGGA----AGA--AGAGTGGAATAACAGCATGGGAG------------------------------------------------------------------------------------------------------------------------------ -s simHuman_chr6.simHuman.chr6 416534 53 + 601863 GTGTAATGATAGTGCCACAGGGAGAG--CAAA--AAAGCTGAATAAGAGAGTGGAAA------------------------------------------------------------------------------------------------------------------------------ -s simRat_chr6.simRat.chr6 437008 55 + 647215 GCGTAATGACAGTGTTGCAGGGCAGG--CAAATGCAGAATGCATAGGTGAGTGGAAA------------------------------------------------------------------------------------------------------------------------------ - -a -s simMouse_chr6.simMouse.chr6 430991 25 + 636262 TCAAAGTTGATAGGTTAGGTATAGC -s Anc0.Anc0refChr3 62245 25 + 222631 ACGTGGTCTATAGCTTAGGTATAGC -s Anc1.Anc1refChr6 93262 25 + 197743 ACGTGGTCTATAGCTTAGGTATAGC -s Anc2.Anc2refChr13 67113 25 + 96486 ACATGGTCTATAGCTCAGATATAGC -s mr.mrrefChr5 285623 25 + 294540 TCGAAGTTGATAGCTTAGGTATAGC -s simCow_chr6.simCow.chr6 424481 25 + 602619 ACATGGTCTATAACTCAAACATTGC -s simDog_chr6.simDog.chr6 414308 25 + 593897 GCATGGTCTACAGCTCAGATATAGC -s simHuman_chr6.simHuman.chr6 418742 25 + 601863 ATGTGGTACATGTCTTAGGTATAAA -s simRat_chr6.simRat.chr6 439531 25 + 647215 TCGCAGTTGATAGCTAAGGTATAGC - -a -s simMouse_chr6.simMouse.chr6 431016 28 + 636262 ATCCATGATGTTAGCACAGACAGGCATA -s Anc0.Anc0refChr3 62270 21 + 222631 ACCC-------TAGTCCAAACACGCTCA -s Anc1.Anc1refChr6 93287 21 + 197743 ACCC-------TAGTCCAAACACGCTCA -s Anc2.Anc2refChr13 67146 21 + 96486 ACCC-------TAGTCCAAACACGCTCA -s mr.mrrefChr5 285648 28 + 294540 ATCCATGATATTAGCACAGACGAGCATG -s simCow_chr6.simCow.chr6 424513 21 + 602619 CCCT-------TAGTACAAATGCGCTCA -s simDog_chr6.simDog.chr6 414341 21 + 593897 ACCC-------TAGTCAAAACATGCCCA -s simHuman_chr6.simHuman.chr6 418767 21 + 601863 CCCC-------TATACCGAACACGCTCA -s simRat_chr6.simRat.chr6 439556 28 + 647215 AGCCATGATATTAGCACAGACGAGCATG - -a -s simMouse_chr6.simMouse.chr6 431044 42 + 636262 CTCGCTATATATGGTAAATATGGGGATAGCAATATTGCTGCT -s Anc0.Anc0refChr3 62292 31 + 222631 CCCTCAATACATGGTCAATACTGGGGTAACA----------- -s Anc1.Anc1refChr6 93309 31 + 197743 CCCTCAATACATGGTCAATACTGGGGTAACA----------- -s Anc2.Anc2refChr13 67168 31 + 96486 TCCACCATACATAGTCAATACTGGGGTAACA----------- -s mr.mrrefChr5 285677 42 + 294540 CCCTCAATATATGGTCAATATGGGGATAGCAATATTGCTGCT -s simCow_chr6.simCow.chr6 424535 31 + 602619 TCCGCCATACATAGTTAATACTGGGCCAACA----------- -s simDog_chr6.simDog.chr6 414363 31 + 593897 TCCACCATACATAGCCGATACTGGGGTAACA----------- -s simHuman_chr6.simHuman.chr6 418789 26 + 601863 C--TCAATACATGGTCAATACTGCAGTC-------------- -s simRat_chr6.simRat.chr6 439585 42 + 647215 CCCTCAATATATGGGCGATATGGGCATAGCAATCTTGTTGTT - -a -s simMouse_chr6.simMouse.chr6 431086 44 + 636262 GTAATACTGAAATGATGAAGCATATTGTTGTTTCAGGACAGCAC -s Anc0.Anc0refChr3 62323 43 + 222631 TTAATATTGGGATAAC-AATATTATTGTTGTTTCAAGTTAGTGC -s Anc1.Anc1refChr6 93340 43 + 197743 TTAATATTGGGATAAC-AATATTATTGTTGTTTCAAGTTAGTGC -s Anc2.Anc2refChr13 67199 43 + 96486 TTGATATTGGGATAAC-AATATTATTGTTGTTTCGAGTTAATGC -s mr.mrrefChr5 285719 44 + 294540 GTAATACTGAAATGATGAATCATATTGTTGTTTCAAGATAGCAC -s simDog_chr6.simDog.chr6 414397 43 + 593897 TTGATATTGGGATAAC-AATATTATTGTTGTTTCGAGTTAATGC -s simHuman_chr6.simHuman.chr6 418815 42 + 601863 -CATTCTGGGGATAAC-AATATTATTGTCATTTGAAGGTAGTGC -s simRat_chr6.simRat.chr6 439627 44 + 647215 GTAATACTGAAATAATGAATCATATTGTAGTTTCGAGATAACAC - -a -s simMouse_chr6.simMouse.chr6 431130 53 + 636262 TGTTTTAAAAGATTCAATGGGCTAGAACTGTGTTTGCATTGGTGTTCACATCT -s Anc0.Anc0refChr3 62372 41 + 222631 -GTTTTCTAAGATTTAGTGGGGTGGATTTG-----------ATTTTTCCAGCG -s Anc1.Anc1refChr6 93390 42 + 197743 TGTTTTCTAAGATTTAGTGGGGTGGATTTG-----------ATTTTTCCAGCG -s Anc2.Anc2refChr13 67248 41 + 96486 -GTTTTCTAAGATTTAGTGTGGTGGATTTG-----------AATCTCCTGGCG -s mr.mrrefChr5 285770 53 + 294540 TGTTTTAAAAGATTCAATGGGCTAGAACTGTGTTTGCATTGGTGTTTACATCT -s simDog_chr6.simDog.chr6 414447 41 + 593897 -GTTTTCTAAGATTTAGTGTGGTGGATTTG-----------AATCTCCTGGCG -s simHuman_chr6.simHuman.chr6 418864 42 + 601863 TGTTTTGTAAGGTTTAGTAGGGTGGATTTG-----------ATTTCTCCAGTG -s simRat_chr6.simRat.chr6 439678 53 + 647215 TGTTTTAAAAGATTCAATGGGCTACGTGGGTGTTTGGATTTTCGTTTACATGT - -a -s simMouse_chr6.simMouse.chr6 431183 14 + 636262 AATGATGCCAATTG -s Anc0.Anc0refChr3 62413 14 + 222631 AGTAATGGCAGTTG -s Anc1.Anc1refChr6 93432 14 + 197743 AGTAATGGCAGTTG -s Anc2.Anc2refChr13 67289 14 + 96486 AGTCATGGCAGTTG -s mr.mrrefChr5 285823 14 + 294540 AATAATGCCAGTTG -s simDog_chr6.simDog.chr6 414489 14 + 593897 AGTCATGGCAGTTG -s simHuman_chr6.simHuman.chr6 418906 14 + 601863 AGTAATGGCAGTTG -s simRat_chr6.simRat.chr6 439731 14 + 647215 AATACTGCCAGTTG - -a -s simMouse_chr6.simMouse.chr6 431197 15 + 636262 TTGCGTTGTTGTTGG -s Anc0.Anc0refChr3 62427 11 + 222631 TG----TATTGCTAA -s Anc1.Anc1refChr6 93446 11 + 197743 TG----TATTGCTAA -s Anc2.Anc2refChr13 67303 11 + 96486 TG----TATTGCTAA -s mr.mrrefChr5 285837 15 + 294540 TTGCGTTGTTGCTGG -s simDog_chr6.simDog.chr6 414505 11 + 593897 TG----TATTGCTAA -s simHuman_chr6.simHuman.chr6 418920 11 + 601863 TG----TATTGCTAA -s simRat_chr6.simRat.chr6 439745 15 + 647215 TTGTGTTGTTGCTGG - -a -s simMouse_chr6.simMouse.chr6 431212 3 + 636262 GCT -s Anc0.Anc0refChr3 62441 3 + 222631 GCT -s Anc1.Anc1refChr6 93460 3 + 197743 GCT -s Anc2.Anc2refChr13 67317 3 + 96486 GCT -s mr.mrrefChr5 285855 3 + 294540 GCT -s simDog_chr6.simDog.chr6 414524 3 + 593897 GCT -s simHuman_chr6.simHuman.chr6 418934 3 + 601863 GCT -s simRat_chr6.simRat.chr6 439763 3 + 647215 GCT - -a -s simMouse_chr6.simMouse.chr6 431215 45 + 636262 TTATGATGTAGATTTTTCAACGGTGGCGGTGGTTTGAATAGTTCA -s Anc0.Anc0refChr3 62447 45 + 222631 TTATGATGTAGAACTTTCAAGGGTGTCACTGGTTTGGATGATTAA -s Anc1.Anc1refChr6 93466 45 + 197743 TTATGATGTAGAACTTTCAAGGGTGTCACTGGTTTGGATGATTAA -s Anc2.Anc2refChr13 67323 45 + 96486 TTATAATGTAGAACTTTCAAGTGTGTCACTGTTTTCGGTGATTAA -s mr.mrrefChr5 285858 45 + 294540 TTATGATGTAGATTTTTCAACGGTGGCAGTGGTTTGAATAGTTCA -s simDog_chr6.simDog.chr6 414530 45 + 593897 TTATAATGTAGAACTTTCAAGTGTGTCACTGTTTTCGGTGATTAA -s simHuman_chr6.simHuman.chr6 418940 45 + 601863 TTATGATGTGGAAATTTAAAAGGTGTTACTGGTTTGGATGTTTAA -s simRat_chr6.simRat.chr6 439766 45 + 647215 TTATGATGTAGATGTCTCAAGGGTGGCAGTGGTTTGAAAAATTCA - -a -s simMouse_chr6.simMouse.chr6 431260 54 + 636262 GTCAAATAGATTGGCCCAAGATTAGTAAGATAATCTAGCATGAAAGCTTCATTT -s Anc0.Anc0refChr3 62499 47 + 222631 GCAGACTAAGATGGCCCAGGCTTA-------AGTCCAGGCTTTGAGGTTAATTT -s Anc1.Anc1refChr6 93518 54 + 197743 GCAGACTAAGATGGCCCAGGCTTAGTAAGATAGTCCAGGCTTTGAGGTTAATTT -s Anc2.Anc2refChr13 67375 47 + 96486 GTAGACTAAGACGGGCCAGCCTTA-------AGTCCAGGCTTTGAGGTTAATTT -s mr.mrrefChr5 285903 54 + 294540 GCCAAATAGGTTGGCCCAAGATTAGTAAGATAGTCTAGCATGTGAGCTTCATTT -s simCow_chr6.simCow.chr6 424566 12 + 602619 ------------------------------------------TGTGGTTATTTT -s simDog_chr6.simDog.chr6 414582 47 + 593897 GTAGACTAAGACGGGCCAGCCTTA-------AGTCCAGGCTTAGATGTTAATTT -s simHuman_chr6.simHuman.chr6 418992 54 + 601863 GCAGATTAAGATGGCCCGGGCTTAGTAAGATAGTCCAGGCTTTGAGGTTAATTT -s simRat_chr6.simRat.chr6 439811 54 + 647215 GCTAAATGGGTGGGCCCAAGGTTAGTAAGGTAGTCTAGCATGTGAGATTTGTTT - -a -s simMouse_chr6.simMouse.chr6 431314 28 + 636262 AGGTCTCATAACACATATAGGAGGGATA -s Anc0.Anc0refChr3 62546 28 + 222631 ATACTTCAGAATGCATATACGAGGGACA -s Anc1.Anc1refChr6 93572 28 + 197743 ATACTTCAGAATGCATATACGAGGGACA -s Anc2.Anc2refChr13 67423 28 + 96486 ATACTTCAGAATGCATATTCCTGGGAAA -s mr.mrrefChr5 285957 28 + 294540 AGGTCTCATAACACATATAGGAGGGACA -s simCow_chr6.simCow.chr6 424579 28 + 602619 CGACATGCTAATGTGTATTCATGAGAAA -s simDog_chr6.simDog.chr6 414630 28 + 593897 ATACTTCAGAATACATATTCCTGGGAAA -s simHuman_chr6.simHuman.chr6 419046 28 + 601863 ATACTTTACAATGCATGCACGAGGGGCT -s simRat_chr6.simRat.chr6 439865 28 + 647215 AACTCTCATAACACACATTGGAGGGACC - -a -s simMouse_chr6.simMouse.chr6 431342 3 + 636262 GGT -s Anc0.Anc0refChr3 62574 3 + 222631 GGT -s Anc1.Anc1refChr6 93600 3 + 197743 GGT -s Anc2.Anc2refChr13 67461 3 + 96486 GGT -s mr.mrrefChr5 285985 3 + 294540 GGT -s simCow_chr6.simCow.chr6 424617 3 + 602619 GGT -s simDog_chr6.simDog.chr6 414668 3 + 593897 AAT -s simHuman_chr6.simHuman.chr6 419074 3 + 601863 GGT -s simRat_chr6.simRat.chr6 439893 3 + 647215 GGT - -a -s simMouse_chr6.simMouse.chr6 431345 33 + 636262 GGTAGCTGTAGAGAATGTAGGAAACCACATTAA -s Anc0.Anc0refChr3 62580 33 + 222631 GGTAGCTGTAGAGATTGTAGGAAATCTCATTGA -s Anc1.Anc1refChr6 93606 33 + 197743 GGTAGCTGTAGAGATTGTAGGAAATCTCATTGA -s Anc2.Anc2refChr13 67467 33 + 96486 GGTAGCTGTAAAGATTGTCGGAAATCTCATTGA -s mr.mrrefChr5 285988 33 + 294540 GGTAGCTGTAGAGAATGTAGGAAACCACATTAA -s simCow_chr6.simCow.chr6 424623 33 + 602619 GGTAGCAGTAAAGATTTCTGGAAATCTCATTGA -s simDog_chr6.simDog.chr6 414674 33 + 593897 TATAGCTGTAAAGATTGTCGGAAATATCATTGA -s simHuman_chr6.simHuman.chr6 419080 33 + 601863 GGTAGCTGTAGAGATCATAGGAAATCTTATTGA -s simRat_chr6.simRat.chr6 439896 33 + 647215 GGTAGCTGTAGAGAGTGTAGGAAACCACATTAA - -a -s simMouse_chr6.simMouse.chr6 431378 52 + 636262 GGTTATTGGTAGTCTGTTAGCAGGATGACCCATTTTGTTTCGTTTTAAAGCC -s Anc0.Anc0refChr3 62613 52 + 222631 GGTAACTGTTAGTTTGTTAGCAGGATGCCCCATTTTATTTTTTCATAAAGCT -s Anc1.Anc1refChr6 93639 52 + 197743 GGTAACTGTTAGTTTGTTAGCAGGATGCCCCATTTTATTTTTTCATAAAGCT -s Anc2.Anc2refChr13 67500 52 + 96486 GGTAACAGTTAGTTTGTTAGCAGGATGCCCTATTTTACTTTTTCATAAATCT -s mr.mrrefChr5 286021 52 + 294540 GGTTATTGGTAGTTTGTTAGCAGGATGACCCATTTTGTTTCGTCTTAAAGCC -s simCow_chr6.simCow.chr6 424656 52 + 602619 GGTAACAGCCAGTTTGTTAGCAGAGTGCCCTATTTTACTTTTTCATAAATCT -s simDog_chr6.simDog.chr6 414707 49 + 593897 GGTAACAGTTTGTTTCTCAGAAGGATGC---ATTTTACTTTTTCATAGGTCT -s simHuman_chr6.simHuman.chr6 419113 52 + 601863 GGTAACTGTTAATTTGTTAGCAGGATGCCCCATTGTATTTTTTCATAAAGCT -s simRat_chr6.simRat.chr6 439931 52 + 647215 GGTTATTGGTAGTTTGTTAGCAGGATGACCCATCTTGTGTCATCTAAAAGCC - -a -s simMouse_chr6.simMouse.chr6 431430 86 + 636262 TTACCTCAAAGTCACAGTTCATTATAGTTTTCAAAAATCTGCTTTGCCACACCTGTGACCGCCCTTTGAGCTAGGCCAAACACTGT -s Anc0.Anc0refChr3 62674 85 + 222631 TTACTTCAGAGTTGCAGTTCATTATAGTCTC-AAAAATCTGCATTGCAACACCTGTGACTGCCCTTTGAACTAGGTCAAGCATTGT -s Anc1.Anc1refChr6 93700 86 + 197743 TTACTTCAGAGTTGCAGTTCATTATAGTCTCCAAAAATCTGCATTGCAACACCTGTGACTGCCCTTTGAACTAGGTCAAGCATTGT -s Anc2.Anc2refChr13 67561 85 + 96486 TTACTTCAGAGTTGCAGTTCATAATAGTCTC-AAAAATCTGCATTGCAACACCTGTGAGTGCCCTTTGAACTAGGTCAAGCAGTTG -s mr.mrrefChr5 286073 86 + 294540 TTACCTCAAAGTCACAGTTCATTATAGTTTTCAAAAATCTGCTTTGCAACACCTGTGACTGCCCTTTGAGCTAGGCCAAACATTGT -s simCow_chr6.simCow.chr6 424717 85 + 602619 CTACTTCAGAGTATCAATTCACAACTTTCTG-GAAAATTTACTTTGAAACACCAGTGAGTGCCCATTGAACAAAGTCAAGCAATTG -s simDog_chr6.simDog.chr6 414765 82 + 593897 TTCCTTAGGAGTTGCAGTTCATAATAGTCTC-AAAAATCTGGATTGCAAC---TGTGAGTGCCCTTGGAACTAGGTCAAGAAGTTG -s simHuman_chr6.simHuman.chr6 419190 86 + 601863 TTACTCCAGAGTTGCAGTTCATTATAATCTCCAAGGACCTGCATTGCAACACCTATGACTGCCCTTTGAAATAGGTCCAGCATTGT -s simRat_chr6.simRat.chr6 439983 86 + 647215 TTACCTCAAAGTCACAGTTCATTATAGTGTTCAGAAATCTGGTTTGCAACACCTGTGACTGCCTGTTGAGCTGGGCCAAACATTGT - -a -s simMouse_chr6.simMouse.chr6 431516 55 + 636262 CTTCTGAGGTAAAAAGATTCGAGCTAGGCCAAACATTGTCATCTGGAGTAAAAAG -s Anc0.Anc0refChr3 62759 16 + 222631 ATTC------------------------------------ATTTGTAGT---AAG -s Anc1.Anc1refChr6 93786 16 + 197743 ATTC------------------------------------ATTTGTAGT---AAG -s Anc2.Anc2refChr13 67646 16 + 96486 ATTC------------------------------------TTTTGTAGT---AAG -s mr.mrrefChr5 286159 54 + 294540 CTTCTG-GGTAAAAAGATTCGAGCTAGGCCAAACATTGTCATCTGGAGTAAAAAG -s simCow_chr6.simCow.chr6 424803 16 + 602619 CTTC------------------------------------CTTTGTAGT---ATG -s simDog_chr6.simDog.chr6 414847 16 + 593897 ATTT------------------------------------TTTTGTAGT---AAG -s simHuman_chr6.simHuman.chr6 419276 16 + 601863 TTAC------------------------------------ATTTGTAGC---ACG -s simRat_chr6.simRat.chr6 440069 54 + 647215 CTTCTT-GGTAAATAGATTTGAGCTAGGCCAAACATTGTCTTCTGCAGTAAAAAG - -a -s simMouse_chr6.simMouse.chr6 431571 10 + 636262 GTTTCCCTCA -s Anc0.Anc0refChr3 62776 10 + 222631 GTTTCACTTA -s Anc1.Anc1refChr6 93803 10 + 197743 GTTTCACTTA -s Anc2.Anc2refChr13 67663 10 + 96486 GTTTCACTTA -s mr.mrrefChr5 286214 10 + 294540 GTTTCCCTCA -s simCow_chr6.simCow.chr6 424820 10 + 602619 GTTTCACTCA -s simDog_chr6.simDog.chr6 414864 10 + 593897 GTTTCACTTA -s simHuman_chr6.simHuman.chr6 419293 10 + 601863 GTTTCACTTA -s simRat_chr6.simRat.chr6 440124 10 + 647215 GTTTCCCTCA - -a -s simMouse_chr6.simMouse.chr6 431581 24 + 636262 CCACCATCTGAGCTATAAGACTAT -s Anc0.Anc0refChr3 62787 24 + 222631 CAAACATCTGAGATATAAGACTAT -s Anc1.Anc1refChr6 93814 24 + 197743 CAAACATCTGAGATATAAGACTAT -s Anc2.Anc2refChr13 67674 24 + 96486 CAAACATCTGAGATATAAGACTGT -s mr.mrrefChr5 286224 24 + 294540 CCACCATCTGAGCTATAAGACTAT -s simCow_chr6.simCow.chr6 424831 24 + 602619 CAAACATCTGAGATATAAGACTGT -s simDog_chr6.simDog.chr6 414875 15 + 593897 TAAACATCTATGAAA--------- -s simHuman_chr6.simHuman.chr6 419304 24 + 601863 CTAACACCTGAGATATAAGACTAT -s simRat_chr6.simRat.chr6 440134 24 + 647215 CAACCATCTGGGCCATAAGACAGT - -a -s simMouse_chr6.simMouse.chr6 431605 38 + 636262 TGCTGGGGATCTCTAATGGGCTCACATAAGGTCATCTG -s Anc0.Anc0refChr3 62811 28 + 222631 TGCAAAAAAGC---------CTTACA-ACACTTAACCT -s Anc1.Anc1refChr6 93838 28 + 197743 TGCAAAAAAGC---------CTTACA-ACACTTAACCT -s Anc2.Anc2refChr13 67698 28 + 96486 TGGAAAACTGC---------CTTACA-GCACTTAACCT -s mr.mrrefChr5 286248 38 + 294540 TGCTGGGAAGCTCTACTGGGCTCACATAAGCTTATCCG -s simCow_chr6.simCow.chr6 424858 28 + 602619 TGGAAGGCTAC---------CTCACA-GCACTTAACCT -s simDog_chr6.simDog.chr6 414890 24 + 593897 ----AAACTGC---------CTTACA-GGACTTAACCT -s simHuman_chr6.simHuman.chr6 419328 28 + 601863 TGCCAAAAAGC---------CTTCCA-ACACTTAACCT -s simRat_chr6.simRat.chr6 440158 38 + 647215 ATTTGGGAAGCTCTACTGGGCTCACATAAGCCTATCCG - -a -s simMouse_chr6.simMouse.chr6 431643 75 + 636262 TCAATGGAATGCCAAGGTCTTTTGTAGTAACCCTTGTATATGGACCTGTCAGGCCGCCTTACAATACTTAGCCCA -s Anc0.Anc0refChr3 62840 37 + 222631 CAAATGCA-------------------TAACCTTTA--CA---------CAGGCTGCATACAAA--------TCA -s Anc1.Anc1refChr6 93867 37 + 197743 CAAATGCA-------------------TAACCTTTA--CA---------CAGGCTGCATACAAA--------TCA -s Anc2.Anc2refChr13 67727 37 + 96486 CAAATTCA-------------------GAACCTTTA--CA---------CAGGCTGCAAACAAA--------TCA -s mr.mrrefChr5 286287 73 + 294540 TCAATGGAATGCCAGGGTATTTTGTAGTAACCCTTG--TATGGACCTGTCAGGCCGCCTTACAATACTTAGCCCA -s simCow_chr6.simCow.chr6 424887 36 + 602619 CAAATACA-------------------GA-CCTTTA--CA---------CAGGCTGCACACAAA--------TCA -s simDog_chr6.simDog.chr6 414915 37 + 593897 CAAACTCA-------------------GAACCTTTA--CA---------CAGGCTGCAAACAAA--------TCA -s simHuman_chr6.simHuman.chr6 419357 37 + 601863 CAAATGCA-------------------TAACCTATA--CA---------CAAGCTGCATGCAAA--------TCA -s simRat_chr6.simRat.chr6 440197 73 + 647215 TCAATGGAATGCCCGGGTATTTTGTAGTAACCCTTG--TATGGACCTATCAGGCCGCCTTACAGTACTTAGCTCA - -a -s simMouse_chr6.simMouse.chr6 431718 36 + 636262 TTTACAGAAGCCTCATAGTCACTTCAAAGAGCATCC -s Anc0.Anc0refChr3 62877 25 + 222631 TGTACAA-----------TGACTTAAGATATCATCC -s Anc1.Anc1refChr6 93904 25 + 197743 TGTACAA-----------TGACTTAAGATATCATCC -s Anc2.Anc2refChr13 67764 25 + 96486 TGTATAA-----------TGGCTGAAGATATCACCC -s mr.mrrefChr5 286360 36 + 294540 TTTACAGAAGCCTCATAGTCACTTCAAAGAGCATCC -s simCow_chr6.simCow.chr6 424923 25 + 602619 TGTATAA-----------TAGCTCAAGATAGCACCC -s simDog_chr6.simDog.chr6 414952 21 + 593897 TGTATAG-----------TGGATGAAGG-ATCA--- -s simHuman_chr6.simHuman.chr6 419394 25 + 601863 TGTTCAA-----------TGACTTAATATATCATCC -s simRat_chr6.simRat.chr6 440282 36 + 647215 CTTACTGAAGCCTGATAGTTACGTCAAGGAGCATCC - -a -s simMouse_chr6.simMouse.chr6 431754 15 + 636262 TTACATAAAAGATAT -s Anc0.Anc0refChr3 62902 13 + 222631 CCAAC--AAGGATCT -s Anc1.Anc1refChr6 93929 13 + 197743 CCAAC--AAGGATCT -s Anc2.Anc2refChr13 67789 13 + 96486 CCAAC--AAGGATCT -s mr.mrrefChr5 286396 15 + 294540 TTAAATAAAAGATAT -s simCow_chr6.simCow.chr6 424989 13 + 602619 CCCAC--AAGGATCC -s simDog_chr6.simDog.chr6 414973 12 + 593897 -CAAC--AAGGATCT -s simHuman_chr6.simHuman.chr6 419419 13 + 601863 CCGAC--AAGGATCT -s simRat_chr6.simRat.chr6 440318 15 + 647215 TTAAATAAAAGATAT - -a -s simMouse_chr6.simMouse.chr6 431769 47 + 636262 TGGTTGTCCCACAGGAAATCTACTCAGTGCCTCTTTTTCGATGGACA -s Anc0.Anc0refChr3 62915 47 + 222631 TGGTTGTCACATAGGAAATCCACTCAGTGACTCGTTTTCGTTGGAAA -s Anc1.Anc1refChr6 93942 47 + 197743 TGGTTGTCACATAGGAAATCCACTCAGTGACTCGTTTTCGTTGGAAA -s Anc2.Anc2refChr13 67802 47 + 96486 TCGTTGTCACATAGGAAATCCACTCAGTGACTCTTTTTCGTTGGGAA -s mr.mrrefChr5 286411 47 + 294540 TGGTTGTCCCACAGGAAATCTACTCAGTGCCTCGTTTTCGATGGAAA -s simCow_chr6.simCow.chr6 425002 40 + 602619 TTGTT-------AAAAAATTCACTCAGTGACTCTGTTTAATTGGGAA -s simDog_chr6.simDog.chr6 414985 47 + 593897 TCGTTGTCACATAGGAAAACCACTCAGTGACCTTTTTTCGTTGGGGA -s simHuman_chr6.simHuman.chr6 419432 43 + 601863 TGGTTGTCACGTAGGAAATCCACTCAGTGACTCGTGTT----GGAAA -s simRat_chr6.simRat.chr6 440343 47 + 647215 TGGTTGTCCCACAGGAAGTTTACTCAGTGCCTCGTTTTCGATGGGAA - -a -s simMouse_chr6.simMouse.chr6 431816 35 + 636262 TAACTAAGATAAGAGTTACATGAAAGGTTGCTGCA -s Anc0.Anc0refChr3 62962 31 + 222631 TAG----GATGGGAGTAATATGAAAGGTTGTTACA -s Anc1.Anc1refChr6 93989 31 + 197743 TAG----GATGGGAGTAATATGAAAGGTTGTTACA -s Anc2.Anc2refChr13 67850 31 + 96486 TAG----GATGGGAGTAATATGAAAGGCTGTTACA -s mr.mrrefChr5 286458 35 + 294540 TAACTAAGATAAGAGTTACATGAAAGGTTGCTACA -s simCow_chr6.simCow.chr6 425042 31 + 602619 TAG----GATGGGAGTAACATGAAAGGCTGTTACA -s simDog_chr6.simDog.chr6 415033 27 + 593897 TAG----GATGGGAGTAATATGA----CTGCTGCA -s simHuman_chr6.simHuman.chr6 419475 31 + 601863 TAG----GATGGGAGTACTATGAAAGGTTGTTACA -s simRat_chr6.simRat.chr6 440390 35 + 647215 TAGCTAAGATAAGAGTGACATGAAAGGTTGCTACA - -a -s simMouse_chr6.simMouse.chr6 431851 30 + 636262 TTTGAAATAGTCCATCCAAGTAGTTGTGTG -s Anc0.Anc0refChr3 62993 30 + 222631 CTTGAAATAGTCCATCCTGGTGGCTGATTG -s Anc1.Anc1refChr6 94020 30 + 197743 CTTGAAATAGTCCATCCTGGTGGCTGATTG -s Anc2.Anc2refChr13 67881 30 + 96486 CTTGAAATAGTCCACCCTGGTGGCTGATTG -s mr.mrrefChr5 286493 30 + 294540 TTTGAAATAGTCCATCCAAGTAGTTGTGTG -s simCow_chr6.simCow.chr6 425073 28 + 602619 CT--ACATAGTCCAACCTAGTGGCTGAGTG -s simDog_chr6.simDog.chr6 415060 30 + 593897 CTTGAACTAGTTCACCCTGGTGGCTGATTG -s simHuman_chr6.simHuman.chr6 419506 18 + 601863 CTTGGAATCGTCCATC------------TG -s simRat_chr6.simRat.chr6 440426 30 + 647215 TTTGAAAAAGTCCACCTGATTAGTTGTGTG - -a -s simMouse_chr6.simMouse.chr6 431881 4 + 636262 TCCC -s Anc0.Anc0refChr3 63023 4 + 222631 TCCC -s Anc1.Anc1refChr6 94050 4 + 197743 TCCC -s Anc2.Anc2refChr13 67911 4 + 96486 CGAG -s mr.mrrefChr5 286523 4 + 294540 TCCC -s simCow_chr6.simCow.chr6 425115 4 + 602619 CGAG -s simDog_chr6.simDog.chr6 415090 4 + 593897 CGAG -s simHuman_chr6.simHuman.chr6 419524 4 + 601863 TCCC -s simRat_chr6.simRat.chr6 440456 4 + 647215 TCCC - -a -s simMouse_chr6.simMouse.chr6 431885 5 + 636262 TTATG -s Anc0.Anc0refChr3 63027 4 + 222631 TCAT- -s Anc1.Anc1refChr6 94054 5 + 197743 TCATT -s Anc2.Anc2refChr13 67915 4 + 96486 TCAT- -s mr.mrrefChr5 286527 5 + 294540 TTATG -s simCow_chr6.simCow.chr6 425119 3 + 602619 -CAT- -s simDog_chr6.simDog.chr6 415098 4 + 593897 TCAT- -s simHuman_chr6.simHuman.chr6 419528 5 + 601863 TCATT -s simRat_chr6.simRat.chr6 440460 5 + 647215 CTATG - -a -s simMouse_chr6.simMouse.chr6 431890 11 + 636262 ACCACGTGGTG -s Anc0.Anc0refChr3 63046 11 + 222631 ACCCCATGGTT -s Anc1.Anc1refChr6 94074 11 + 197743 ACCCCATGGTT -s Anc2.Anc2refChr13 67934 11 + 96486 ACCCCATGGTT -s mr.mrrefChr5 286532 11 + 294540 ACCACATGGTG -s simCow_chr6.simCow.chr6 425137 11 + 602619 AACACATGGTT -s simDog_chr6.simDog.chr6 415117 9 + 593897 ACACCATGG-- -s simHuman_chr6.simHuman.chr6 419553 11 + 601863 ACCGCATGGTC -s simRat_chr6.simRat.chr6 440465 11 + 647215 ACCACATGTTG - -a -s simMouse_chr6.simMouse.chr6 431901 48 + 636262 AATAATAGCTCTATCTCTCCTCATCATTATGGCACACATTCTTGATAG -s Anc0.Anc0refChr3 63057 48 + 222631 AATAGTATCTCTATTTCTCCACACTAACATAGTACACACCCTTGATAG -s Anc1.Anc1refChr6 94085 48 + 197743 AATAGTATCTCTATTTCTCCACACTAACATAGTACACACCCTTGATAG -s Anc2.Anc2refChr13 67945 48 + 96486 AATAGTATCTCTATTTCTCCACACTAACGTACTACACACCCTTGATAG -s mr.mrrefChr5 286543 48 + 294540 AATAATATCTCTATCTCTCCTCACTATCATGGCACACATTCTTGATAG -s simCow_chr6.simCow.chr6 425148 48 + 602619 AATCTTATCTCTTATTCTCCACACTAACGAATTACACACCTTTGATGG -s simDog_chr6.simDog.chr6 415126 46 + 593897 -ATAG-ATCTCTATTCCTCCACACTAATGTACTACACACCCTTGACAG -s simHuman_chr6.simHuman.chr6 419564 41 + 601863 AATAGTATCTATATTTCTCCACACTAACATAGTACA-------GATAG -s simRat_chr6.simRat.chr6 440477 47 + 647215 AATAATATCTCTATCTCTCCTCACTATCATGACACACACTCTT-ATAG - -a -s simMouse_chr6.simMouse.chr6 431949 21 + 636262 GAACCTCTTCCTAGGATTTCA -s Anc0.Anc0refChr3 63105 21 + 222631 GCACCTCTACATAAGATCTGA -s Anc1.Anc1refChr6 94133 21 + 197743 GCACCTCTACATAAGATCTGA -s Anc2.Anc2refChr13 67993 21 + 96486 GCACCTCTACATAAGAACAGA -s mr.mrrefChr5 286591 21 + 294540 GAACCTCTTCATAAGATTTCA -s simCow_chr6.simCow.chr6 425196 21 + 602619 GCACCTCTACATGAGAACAGA -s simDog_chr6.simDog.chr6 415173 21 + 593897 GCCCCTATACATAAAAACAGA -s simHuman_chr6.simHuman.chr6 419605 21 + 601863 GCACCCCAACATAAGATCTGA -s simRat_chr6.simRat.chr6 440524 21 + 647215 GAACCTCTTCATAAGATTGCA - -a -s simMouse_chr6.simMouse.chr6 431970 4 + 636262 GTTC -s Anc0.Anc0refChr3 63136 4 + 222631 GTGC -s Anc1.Anc1refChr6 94164 4 + 197743 GTGC -s Anc2.Anc2refChr13 68032 4 + 96486 GTAC -s mr.mrrefChr5 286613 4 + 294540 GTGC -s simCow_chr6.simCow.chr6 425263 4 + 602619 GTAC -s simDog_chr6.simDog.chr6 415212 4 + 593897 ATAC -s simHuman_chr6.simHuman.chr6 419636 4 + 601863 GTGC -s simRat_chr6.simRat.chr6 440546 4 + 647215 GTGC - -a -s simMouse_chr6.simMouse.chr6 431974 80 + 636262 AATCTAAAGCACCTGTAGCGTGGGAAATGTACATTATTATCGTGAATCAGGAATAGGGCACTGATAACCAGTCCCTGGTA -s Anc0.Anc0refChr3 63291 78 + 222631 AATCTAG--CACCCATATTATTGCAGTTATACATTATTTTCAGGATTAGGGAATATGGCACCAATATCCAGTCCCCTGAA -s Anc1.Anc1refChr6 94319 80 + 197743 AATCTAGAGCACCCATATTATTGCAGTTATACATTATTTTCAGGATTAGGGAATATGGCACCAATATCCAGTCCCCTGAA -s Anc2.Anc2refChr13 68193 78 + 96486 AAACTAG--CACCCATATTATTGCAGTCATACATTATTCTCAAGGATCAGGAATGTTCCACCAATATCCAATCCCCTGAA -s mr.mrrefChr5 286617 80 + 294540 AATCTAAAGCACCTGTAGCATGGGAAATGTACATTATTTTCATGAATCGGGAATAGGGCACTAATAACCAGTCCCTGGTA -s simCow_chr6.simCow.chr6 425451 77 + 602619 AACCTA---CACCTGTATTATCGCAGACATACATTATTCTCAACGGTCAGGAATGTTAGACCAAAGTCCAAACCCCTGAA -s simDog_chr6.simDog.chr6 415392 74 + 593897 AAAC--G--CACCCATATTATTGGAGTCATACATCATCCTCAAGGATCAGGACTGTTCCACTATTAACAGATACA--GCA -s simHuman_chr6.simHuman.chr6 419794 80 + 601863 GATCTAGAGCACCCATATTATTGCAGGTATACATTATTTTAAGGATTAGGAAACACGGCACCAACATCCAGTCCCATGAA -s simRat_chr6.simRat.chr6 440550 80 + 647215 AATCTAAAGCACCTGTAGCATGGGAAATGTACATTATTTTCAAGAATCGGGAATAGGGCACTAATAACCAGTCCCTGGTA - -a -s simMouse_chr6.simMouse.chr6 432054 6 + 636262 TTTTCA -s Anc0.Anc0refChr3 63381 6 + 222631 CTTTTA -s Anc1.Anc1refChr6 94411 6 + 197743 CTTTTA -s Anc2.Anc2refChr13 68283 6 + 96486 CCATTG -s mr.mrrefChr5 286697 6 + 294540 CTTTCA -s simCow_chr6.simCow.chr6 425541 6 + 602619 CCATCG -s simDog_chr6.simDog.chr6 415478 6 + 593897 CCACTG -s simHuman_chr6.simHuman.chr6 419886 6 + 601863 CTTTTA -s simRat_chr6.simRat.chr6 440630 6 + 647215 CTCTCA - -a -s simMouse_chr6.simMouse.chr6 432060 6 + 636262 TCTCAT -s Anc0.Anc0refChr3 63401 6 + 222631 TGGCAT -s Anc1.Anc1refChr6 94431 6 + 197743 TGGCAT -s Anc2.Anc2refChr13 68303 6 + 96486 TGGCAT -s mr.mrrefChr5 286703 6 + 294540 TGTCAT -s simCow_chr6.simCow.chr6 425561 6 + 602619 TGGCAT -s simDog_chr6.simDog.chr6 415498 6 + 593897 TGGCAT -s simHuman_chr6.simHuman.chr6 419906 6 + 601863 TGGTAT -s simRat_chr6.simRat.chr6 440636 6 + 647215 AGTCAT - -a -s simMouse_chr6.simMouse.chr6 432066 4 + 636262 CTCA -s Anc0.Anc0refChr3 63408 4 + 222631 CTCA -s Anc1.Anc1refChr6 94438 4 + 197743 CTCA -s Anc2.Anc2refChr13 68310 4 + 96486 CTTA -s mr.mrrefChr5 286709 4 + 294540 CTCA -s simCow_chr6.simCow.chr6 425568 4 + 602619 CTTT -s simDog_chr6.simDog.chr6 415505 4 + 593897 CTTA -s simHuman_chr6.simHuman.chr6 419913 4 + 601863 CTCA -s simRat_chr6.simRat.chr6 440642 4 + 647215 CCCG - -a -s simMouse_chr6.simMouse.chr6 432070 1 + 636262 T -s Anc0.Anc0refChr3 63412 1 + 222631 T -s Anc1.Anc1refChr6 94442 1 + 197743 T -s Anc2.Anc2refChr13 68314 1 + 96486 T -s mr.mrrefChr5 286713 1 + 294540 T -s simCow_chr6.simCow.chr6 425804 1 + 602619 T -s simDog_chr6.simDog.chr6 415509 1 + 593897 T -s simHuman_chr6.simHuman.chr6 419917 1 + 601863 C -s simRat_chr6.simRat.chr6 440646 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 432071 19 + 636262 CTCATTGCACGATGAAGTT -s Anc0.Anc0refChr3 63413 19 + 222631 CTCAGTGTACAATGAAGTT -s Anc1.Anc1refChr6 94443 19 + 197743 CTCAGTGTACAATGAAGTT -s Anc2.Anc2refChr13 68316 19 + 96486 CTCAGTGTAGAATGAAGTT -s mr.mrrefChr5 286714 19 + 294540 CTCAGTGTACAATGAAGTT -s simCow_chr6.simCow.chr6 425806 19 + 602619 ATCGGTATAGAATGGAGTT -s simDog_chr6.simDog.chr6 415511 19 + 593897 CTCAGTGTAGAATGAAGTT -s simHuman_chr6.simHuman.chr6 419918 19 + 601863 CTCAGTGTACAACAAAGTT -s simRat_chr6.simRat.chr6 440647 19 + 647215 CTCGGTGTGCAATGAAGTT - -a -s simMouse_chr6.simMouse.chr6 432090 17 + 636262 AGACGCAAATAAATGTT -s Anc0.Anc0refChr3 63432 17 + 222631 AGATGCAAATATATGTT -s Anc1.Anc1refChr6 94462 17 + 197743 AGATGCAAATATATGTT -s Anc2.Anc2refChr13 68335 17 + 96486 AGATGCAAATATATGTT -s mr.mrrefChr5 286733 17 + 294540 AGATGCAAATAAATGTT -s simCow_chr6.simCow.chr6 425826 17 + 602619 AGATGCAAATACAAGTT -s simDog_chr6.simDog.chr6 415530 17 + 593897 AGATGCAAATATATGTT -s simHuman_chr6.simHuman.chr6 419937 17 + 601863 AGATGCAAAGATATACC -s simRat_chr6.simRat.chr6 440666 17 + 647215 AGATGCAAATAAATTTT - -a -s simMouse_chr6.simMouse.chr6 432107 3 + 636262 CCA -s Anc0.Anc0refChr3 63449 3 + 222631 CCA -s Anc1.Anc1refChr6 94479 3 + 197743 CCA -s Anc2.Anc2refChr13 68352 3 + 96486 ACC -s mr.mrrefChr5 286750 3 + 294540 CCA -s simCow_chr6.simCow.chr6 425843 3 + 602619 ACC -s simDog_chr6.simDog.chr6 415547 3 + 593897 ACC -s simHuman_chr6.simHuman.chr6 419961 3 + 601863 CCA -s simRat_chr6.simRat.chr6 440683 3 + 647215 CCA - -a -s simMouse_chr6.simMouse.chr6 432110 18 + 636262 GGCAATATTAGATTTGAT -s Anc0.Anc0refChr3 63452 18 + 222631 GGCAATACTTTATCTGAC -s Anc1.Anc1refChr6 94482 18 + 197743 GGCAATACTTTATCTGAC -s Anc2.Anc2refChr13 68355 18 + 96486 GGCAATACTTTAGCTGAC -s mr.mrrefChr5 286753 18 + 294540 GGCAATATTAGATTTGAT -s simCow_chr6.simCow.chr6 425847 18 + 602619 GGCAACATTTTAGCTGAC -s simDog_chr6.simDog.chr6 415550 18 + 593897 GGCAATACTTTAGCTATG -s simHuman_chr6.simHuman.chr6 419964 18 + 601863 GGCAAGACTTTGTCTGAC -s simRat_chr6.simRat.chr6 440686 18 + 647215 GGCAGTTTTAGATTTGAT - -a -s simMouse_chr6.simMouse.chr6 432128 1 + 636262 A -s Anc0.Anc0refChr3 63471 1 + 222631 A -s Anc1.Anc1refChr6 94501 1 + 197743 A -s Anc2.Anc2refChr13 68374 1 + 96486 A -s mr.mrrefChr5 286772 1 + 294540 A -s simCow_chr6.simCow.chr6 425866 1 + 602619 A -s simDog_chr6.simDog.chr6 415569 1 + 593897 A -s simHuman_chr6.simHuman.chr6 419983 1 + 601863 A -s simRat_chr6.simRat.chr6 440705 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 432129 1 + 636262 C -s Anc0.Anc0refChr3 63473 1 + 222631 C -s Anc1.Anc1refChr6 94503 1 + 197743 C -s Anc2.Anc2refChr13 68376 1 + 96486 C -s mr.mrrefChr5 286773 1 + 294540 C -s simCow_chr6.simCow.chr6 425868 1 + 602619 C -s simDog_chr6.simDog.chr6 415571 1 + 593897 C -s simHuman_chr6.simHuman.chr6 419985 1 + 601863 C -s simRat_chr6.simRat.chr6 440706 1 + 647215 C - -a -s simMouse_chr6.simMouse.chr6 432130 17 + 636262 GGACGCATTCAGGACGC -s Anc0.Anc0refChr3 63474 17 + 222631 AAACCCACTTAGCACAC -s Anc1.Anc1refChr6 94504 17 + 197743 AAACCCACTTAGCACAC -s Anc2.Anc2refChr13 68377 17 + 96486 AAATCCACTTAGCATAC -s mr.mrrefChr5 286774 17 + 294540 AAACGCATTCAGGACAC -s simCow_chr6.simCow.chr6 425876 17 + 602619 ACATCCACTTAGTATGC -s simDog_chr6.simDog.chr6 415572 17 + 593897 AAATACATTTAGCATAC -s simHuman_chr6.simHuman.chr6 419986 17 + 601863 AAACCCACATAGCACAT -s simRat_chr6.simRat.chr6 440707 17 + 647215 AAACGCATCCAGGACAC - -a -s simMouse_chr6.simMouse.chr6 432147 27 + 636262 ATTACACTTGTTGCTGCTGGTACAGGT -s Anc0.Anc0refChr3 63492 21 + 222631 ATTACCCTT-C-----CTGCCACAGGT -s Anc1.Anc1refChr6 94522 21 + 197743 ATTACCCTT-C-----CTGCCACAGGT -s Anc2.Anc2refChr13 68395 21 + 96486 ATTACCCTT-C-----CTCCCACAGGT -s mr.mrrefChr5 286792 26 + 294540 ATTACACTT-CTGCTGCTGCTACAGGT -s simCow_chr6.simCow.chr6 425894 21 + 602619 ATCACCCTC-C-----CTCCCACAGGC -s simDog_chr6.simDog.chr6 415590 21 + 593897 ATTACCCTT-A-----CTCCCACGGGT -s simHuman_chr6.simHuman.chr6 420004 21 + 601863 ATTACCCTT-C-----CTGCCACAGGT -s simRat_chr6.simRat.chr6 440725 26 + 647215 ATTACATTT-CTGCTGCTGCTACAGGT - -a -s simMouse_chr6.simMouse.chr6 432174 108 + 636262 TTTCTCTACTAAGTCTCAAGCTCTCACTGACATAAAAGACTTTGGGGTTGGGTACTATAGACATAGGTCATCTAGGCACATAGCACTAAGAGATTTTGGGTGTTCATT -s Anc0.Anc0refChr3 63513 22 + 222631 TTT-TCTCCCA-------------------------------------------------------------------------------------GCAAAGTTTAGC -s Anc1.Anc1refChr6 94543 22 + 197743 TTT-TCTCCCA-------------------------------------------------------------------------------------GCAAAGTTTAGC -s Anc2.Anc2refChr13 68416 22 + 96486 TCT-TCTCCCA-------------------------------------------------------------------------------------TCAAAGCTTAGC -s mr.mrrefChr5 286818 25 + 294540 TTTCTCTACTA-----------------------------------------------------------------------------------TTGGGGTGTTCATT -s simCow_chr6.simCow.chr6 425915 22 + 602619 TCT-GCTCCCA-------------------------------------------------------------------------------------TCAAAGCTTAAC -s simDog_chr6.simDog.chr6 415614 22 + 593897 TCC-TCTCTCA-------------------------------------------------------------------------------------TCAAAGCTTAGC -s simHuman_chr6.simHuman.chr6 420025 22 + 601863 TTT-TCTCCCA-------------------------------------------------------------------------------------GCAAAGTTTAGC -s simRat_chr6.simRat.chr6 440751 25 + 647215 GTTCTCTACTA-----------------------------------------------------------------------------------CTGTGGTGGTCATT - -a -s simMouse_chr6.simMouse.chr6 432282 17 + 636262 CCCGTGGTGGCAGAGTG -s Anc0.Anc0refChr3 63535 9 + 222631 CTCTC--------AGCA -s Anc1.Anc1refChr6 94565 9 + 197743 CTCTC--------AGCA -s Anc2.Anc2refChr13 68524 9 + 96486 CTCTC--------AGCA -s mr.mrrefChr5 286843 9 + 294540 CCCGT--------AGCG -s simCow_chr6.simCow.chr6 426033 9 + 602619 CTCTC--------AGCA -s simDog_chr6.simDog.chr6 415723 9 + 593897 CTTTC--------AGTA -s simHuman_chr6.simHuman.chr6 420047 9 + 601863 CTCTC--------AGCA -s simRat_chr6.simRat.chr6 440776 9 + 647215 CCCAT--------AGCG - -a -s simMouse_chr6.simMouse.chr6 432299 3 + 636262 GCA -s Anc0.Anc0refChr3 63544 3 + 222631 CAA -s Anc1.Anc1refChr6 94574 3 + 197743 CAA -s Anc2.Anc2refChr13 68539 3 + 96486 CAA -s mr.mrrefChr5 286852 3 + 294540 GCA -s simCow_chr6.simCow.chr6 426048 3 + 602619 CAA -s simDog_chr6.simDog.chr6 415738 3 + 593897 CAA -s simHuman_chr6.simHuman.chr6 420056 3 + 601863 CAA -s simRat_chr6.simRat.chr6 440785 3 + 647215 GCA - -a -s simMouse_chr6.simMouse.chr6 432302 13 + 636262 GGACCAGCCAACA -s Anc0.Anc0refChr3 63548 13 + 222631 GAAAAAAATAATT -s Anc1.Anc1refChr6 94578 13 + 197743 GAAAAAAATAATT -s Anc2.Anc2refChr13 68543 13 + 96486 GAAAAAAATAATT -s mr.mrrefChr5 286855 13 + 294540 GAACCAGCTAATA -s simCow_chr6.simCow.chr6 426052 13 + 602619 GGAAGAAATGATT -s simDog_chr6.simDog.chr6 415742 13 + 593897 GAATAAAATAATT -s simHuman_chr6.simHuman.chr6 420060 13 + 601863 GAAAAAATTAATT -s simRat_chr6.simRat.chr6 440788 13 + 647215 GAACTAGCTAATG - -a -s simMouse_chr6.simMouse.chr6 432315 10 + 636262 TGTACTCAGA -s Anc0.Anc0refChr3 63574 10 + 222631 TGCACTCAGG -s Anc1.Anc1refChr6 94604 10 + 197743 TGCACTCAGG -s Anc2.Anc2refChr13 68569 10 + 96486 TGCTCTCATG -s mr.mrrefChr5 286868 10 + 294540 TGCACTCAGA -s simDog_chr6.simDog.chr6 415768 10 + 593897 TGCTCTCATG -s simHuman_chr6.simHuman.chr6 420086 10 + 601863 TGCACTCAGT -s simRat_chr6.simRat.chr6 440801 10 + 647215 TGCACTCAGA - -a -s simMouse_chr6.simMouse.chr6 432325 14 + 636262 ACTAGTGTCCTTAT -s Anc0.Anc0refChr3 63618 14 + 222631 ATTAGTGGAGATGT -s Anc1.Anc1refChr6 94648 14 + 197743 ATTAGTGGAGATGT -s Anc2.Anc2refChr13 68613 14 + 96486 ATTAGTGGAGATCT -s mr.mrrefChr5 286885 14 + 294540 ATTAGTGTTCATGT -s simDog_chr6.simDog.chr6 415812 14 + 593897 ATTAGTGGAGATCT -s simHuman_chr6.simHuman.chr6 420130 14 + 601863 ATTAGTAAAGATGT -s simRat_chr6.simRat.chr6 440818 14 + 647215 ATTAGTGTTCATGA - -a -s simMouse_chr6.simMouse.chr6 432339 57 + 636262 TGAACCTTCCAATTATTGTGTGAGCTGGGTTATGAGTTGCATTAAAACTAAGTCCTA -s Anc0.Anc0refChr3 63636 57 + 222631 TGAACTTTTCACTTACAGTCTAAGGTGAGTGACTTGTTGCATTAAAACCAAGTCCTA -s Anc1.Anc1refChr6 94666 57 + 197743 TGAACTTTTCACTTACAGTCTAAGGTGAGTGACTTGTTGCATTAAAACCAAGTCCTA -s Anc2.Anc2refChr13 68631 57 + 96486 TGAACTTTTCACTTACAGTATGAGGTGAGGGACTTGTTGCATCAAAGACAAGTCCTA -s mr.mrrefChr5 286899 57 + 294540 TGAACCTTCCAATTATTGTCTAAGGTGAGTTATGAGTTGCATTAAAACTAAGTCCTA -s simDog_chr6.simDog.chr6 415830 57 + 593897 TGAACTTTTCACTTACAGTATGAGGTGAGGGACTTGTTGCATCAAAGACAAGTCCTA -s simHuman_chr6.simHuman.chr6 420148 57 + 601863 TGAACATTTCACTTACAGTCTAAGGTGAGTGACTCATAATATTAAAACCAAGTTCTA -s simRat_chr6.simRat.chr6 440832 57 + 647215 TGAACCTTCCGACTATTGTCCAAGGTGAGGTATGAGTTGCATTAAAACTAAGTCCTA - -a -s simMouse_chr6.simMouse.chr6 432396 30 + 636262 ACACTGCAAGGAATAGATCTCTCAGGAGTA -s Anc0.Anc0refChr3 63693 7 + 222631 ACATTGA----------------------- -s Anc1.Anc1refChr6 94723 7 + 197743 ACATTGA----------------------- -s Anc2.Anc2refChr13 68688 7 + 96486 ACATTGA----------------------- -s mr.mrrefChr5 286956 30 + 294540 ACACTGCAAGGAATAGATCTCTCAGGAGTA -s simCow_chr6.simCow.chr6 426078 7 + 602619 ATGGTGA----------------------- -s simDog_chr6.simDog.chr6 415955 7 + 593897 ACATTGA----------------------- -s simRat_chr6.simRat.chr6 440889 30 + 647215 ACACTACGACGAATAGATGTCTCAAGAGGA - -a -s simMouse_chr6.simMouse.chr6 432426 59 + 636262 ATAGTGGCTGCAAATTTTGAGACTATGCTCTGCCACTCAACAGCAACAATACTCATCCA -s Anc0.Anc0refChr3 63700 32 + 222631 --------------------------GCTCTTACAATC-ACACCAATAAAAGTGATTCA -s Anc1.Anc1refChr6 94730 32 + 197743 --------------------------GCTCTTACAATC-ACACCAATAAAAGTGATTCA -s Anc2.Anc2refChr13 68695 32 + 96486 --------------------------GCTCTTACAATC-ACACCAATAAAAGTGATTCA -s mr.mrrefChr5 286986 53 + 294540 ATAGTGGCTGC-----TTGAGACTATGCTCTGCCACTC-ACAGCAACAATACTCATCCA -s simCow_chr6.simCow.chr6 426085 32 + 602619 --------------------------CCTCTTACAATC-ACACCAATAATGATGATTCA -s simDog_chr6.simDog.chr6 415962 32 + 593897 --------------------------GCTCTTACAATC-ACACCAATAAAAGTGATTCA -s simRat_chr6.simRat.chr6 440920 53 + 647215 ATAGGAGCTGC-----TTGAGACTGTGCTCTGCCACTC-ACATCAACAATACTTAACCC - -a -s simMouse_chr6.simMouse.chr6 432485 10 + 636262 TCAGTTAGAC -s Anc0.Anc0refChr3 63732 8 + 222631 TCAGAT--AC -s Anc1.Anc1refChr6 94762 8 + 197743 TCAGAT--AC -s Anc2.Anc2refChr13 68731 8 + 96486 TCAGAT--AC -s mr.mrrefChr5 287039 9 + 294540 TCAGTT-GAC -s simCow_chr6.simCow.chr6 426121 8 + 602619 TCAGAT--AT -s simDog_chr6.simDog.chr6 415998 8 + 593897 TCAGAT--AC -s simRat_chr6.simRat.chr6 440973 9 + 647215 TTGATT-GAC - -a -s simMouse_chr6.simMouse.chr6 432495 27 + 636262 ATAGGGCTCATATCTCATGATATAGAC -s Anc0.Anc0refChr3 63740 16 + 222631 GTAG---TCATATGCCAAG-------- -s Anc1.Anc1refChr6 94770 16 + 197743 GTAG---TCATATGCCAAG-------- -s Anc2.Anc2refChr13 68739 16 + 96486 GTAG---TCATATGCCAAG-------- -s mr.mrrefChr5 287048 27 + 294540 ATAGGGCTCATATCTCATGATATAGAC -s simCow_chr6.simCow.chr6 426130 16 + 602619 GGAC---ACATGTACCAAG-------- -s simDog_chr6.simDog.chr6 416006 16 + 593897 GTAG---TCATATGCCAAG-------- -s simRat_chr6.simRat.chr6 440982 27 + 647215 ATAGGGCTCATATCCCAGGAAATAGAC - -a -s simMouse_chr6.simMouse.chr6 432522 46 + 636262 TGTTTAGTCTCCACAAGGCTTAGAGCTACAAACCTGCTGATGTAAA -s Anc0.Anc0refChr3 63756 46 + 222631 TGACTAGTCCACACACGGCCTAAAGGTGCAAATCTGCAGCTATAAA -s Anc1.Anc1refChr6 94786 46 + 197743 TGACTAGTCCACACACGGCCTAAAGGTGCAAATCTGCAGCTATAAA -s Anc2.Anc2refChr13 68755 46 + 96486 TGACTAGTCCACACACGTCCTTACAGTGCAAATCTGCAGCTATAAA -s mr.mrrefChr5 287075 46 + 294540 TGTTTAGTCTCCACAAGGCTTAGAGCTACAAACCTGCTGATGTAAA -s simCow_chr6.simCow.chr6 426151 29 + 602619 TGACTAGTCCAC--------------TGCAGATCTCAA---ATGAA -s simDog_chr6.simDog.chr6 416022 46 + 593897 TGACTAGTCCACACACGTCCTTACAGTACCAATCTGCAGCTTTAAA -s simHuman_chr6.simHuman.chr6 420205 46 + 601863 TGACTAGTTCACAAATGGCCTAAAGACGCAAATCTGCAGGCATAAA -s simRat_chr6.simRat.chr6 441009 46 + 647215 TGTCTAGTCTGCACAAGGCTTGGAGCTGCAAACCTATGGATGTAAA - -a -s simMouse_chr6.simMouse.chr6 432568 19 + 636262 TTCTGTCGCTAGTACATAC -s Anc0.Anc0refChr3 63816 19 + 222631 TTCTGTCGTCATCACATAC -s Anc1.Anc1refChr6 94846 19 + 197743 TTCTGTCGTCATCACATAC -s Anc2.Anc2refChr13 68815 19 + 96486 TTGTGTCCTCATCACATAA -s mr.mrrefChr5 287121 19 + 294540 TTCTGTCGCTAGTACATAC -s simCow_chr6.simCow.chr6 426194 19 + 602619 TTGTGACCTCATCACAGAA -s simDog_chr6.simDog.chr6 416080 19 + 593897 TTGTGTCCTCATCACATAA -s simHuman_chr6.simHuman.chr6 420265 19 + 601863 TTCTGTCGTCACCACATAC -s simRat_chr6.simRat.chr6 441055 19 + 647215 TTCTGTAGCCAACACATAC - -a -s simMouse_chr6.simMouse.chr6 432587 32 + 636262 ATTTAGCCTAGTCACAACCCACAGGGGCATGT -s Anc0.Anc0refChr3 63836 32 + 222631 GTTCAACCCAGTCTCAACCCACAGCTGCGTAT -s Anc1.Anc1refChr6 94866 32 + 197743 GTTCAACCCAGTCTCAACCCACAGCTGCGTAT -s Anc2.Anc2refChr13 68835 32 + 96486 GTTCAACCCAGTCTTAACCCACAGCTGTGTAT -s mr.mrrefChr5 287140 32 + 294540 ATTTAGCCTAGTCACAACCCACAGGGGCATGT -s simCow_chr6.simCow.chr6 426214 7 + 602619 GTTC-------------------------TAT -s simDog_chr6.simDog.chr6 416100 32 + 593897 GTCCAACCCAGTCTTAACCCACAGCTGTGTGT -s simHuman_chr6.simHuman.chr6 420285 32 + 601863 GTTCACCCCATCCTCCACCAACACCTGCGTAT -s simRat_chr6.simRat.chr6 441074 32 + 647215 ATCTAGCCTAGTAGCAAACCAGAGGGGTGTGT - -a -s simMouse_chr6.simMouse.chr6 432619 29 + 636262 AAGAATCAAGAGTGTTTTTTATAAGAGGT -s Anc0.Anc0refChr3 63868 29 + 222631 AAAAAATAAAAGTTTTTTATATAATGCGT -s Anc1.Anc1refChr6 94898 29 + 197743 AAAAAATAAAAGTTTTTTATATAATGCGT -s Anc2.Anc2refChr13 68867 29 + 96486 GAAAAATAAAAGTTTTTTATATAATGCGT -s mr.mrrefChr5 287172 29 + 294540 AAGAATCAAGAGTGTTTTTTATAAGAGGT -s simCow_chr6.simCow.chr6 426221 29 + 602619 GACAATCCATAGCTTTTTAAACAATGGGT -s simDog_chr6.simDog.chr6 416186 29 + 593897 GaaaaataaaaattttttatataatGCGT -s simHuman_chr6.simHuman.chr6 420317 29 + 601863 AAAAAATAAAGGTTCTCTATATAATGCGT -s simRat_chr6.simRat.chr6 441106 29 + 647215 AAGAATCAAGAGTGTTTTTTATAAGAGGC - -a -s simMouse_chr6.simMouse.chr6 432648 125 + 636262 TGATAATGAGTTTATCAATACACTGTGATAGATAAACAACCCCCATAACTAGAGCAATGAAACACTTTTATAAGAGATTGACAATGGGTTAGTCAATATGCTATGATTGACATGCCAACGATATG -s Anc0.Anc0refChr3 63898 15 + 222631 TGATTAAGAGCTTAT-------------------------------------------------------------------------------------------------------------- -s Anc1.Anc1refChr6 94928 15 + 197743 TGATTAAGAGCTTAT-------------------------------------------------------------------------------------------------------------- -s Anc2.Anc2refChr13 68897 15 + 96486 TGATTAAGAACCTAT-------------------------------------------------------------------------------------------------------------- -s mr.mrrefChr5 287201 124 + 294540 TGATAATGAGTTTATCAAT-CACTGTGATAGATAAACAACCCCCATAACTAGAGCAATGAAACACTTTTATAAGAGATTGACAATGGGTTAGTCAATATGCTATGATTGACATGCCAACGATATG -s simCow_chr6.simCow.chr6 426251 15 + 602619 CAATTAAGAACCGTT-------------------------------------------------------------------------------------------------------------- -s simDog_chr6.simDog.chr6 416216 9 + 593897 TGATTA------TAT-------------------------------------------------------------------------------------------------------------- -s simHuman_chr6.simHuman.chr6 420347 15 + 601863 TGATTCAGAGCTCAT-------------------------------------------------------------------------------------------------------------- -s simRat_chr6.simRat.chr6 441135 124 + 647215 TGATAATGAGTTGATCAAC-CACTGTGATAGATAAGCAACCCCCATAACTAGAGCAAGGAAGTGCCTTTATAAGACCTGGACAATGGATTAGTCAGTACGCTATGATTGATATGCCAGTGATATG - -a -s simMouse_chr6.simMouse.chr6 432773 114 + 636262 AGGGGCCTCATAACTAGAGTAAGGACACGCCTTAATAAAAGTCTTATAATGGATTGATCCAAATGCTAAGGTAGACTTGCAGGCCCACCTACTAGAGTAATGACACACTGGTTT -s Anc0.Anc0refChr3 63913 69 + 222631 ---------------------------------------------GCAACGGATTGATCAACACCTTATGATAGATATTCAGGCCCAATTAATATAGTAATTACACACTGGTTT -s Anc1.Anc1refChr6 94943 69 + 197743 ---------------------------------------------GCAACGGATTGATCAACACCTTATGATAGATATTCAGGCCCAATTAATATAGTAATTACACACTGGTTT -s Anc2.Anc2refChr13 68912 69 + 96486 ---------------------------------------------GCAACAGTTTGATCAGCACCTTATGATAGATATTCGGGCCCGATTAATATAGTAATTACACACTCGTTT -s mr.mrrefChr5 287325 114 + 294540 AGGGGCCTCATAACTAGAGTAAGGACACGCCTTAATAAAAGTCTTATAATGGATTGATCAAAATGCTATGGTAGACTTGCAGGCCCACCTACTAGAGTAATGACACACTGGTTT -s simCow_chr6.simCow.chr6 426266 69 + 602619 ---------------------------------------------GCAATCGTTTGATCAGAACCTTATGATAGATACTCGGGCACCATAAATATAGTAGTAGCACACTTGTTT -s simDog_chr6.simDog.chr6 416225 68 + 593897 ---------------------------------------------GCAACAGTTTGATTGGCACCTTATT-TAGATATGCGGGCCTGATTAATATAATAATTACACAGCCGTTT -s simHuman_chr6.simHuman.chr6 420362 64 + 601863 ---------------------------------------------GCAACGGATTGATCAACACCTTATGACAGATATTCAGGCCCA-----TATAGCAATTATACACTGATTT -s simRat_chr6.simRat.chr6 441260 97 + 647215 CAGGGCCCCATAGGTAGAGTAATGATACACCTTAATAAAA-----------------TCAAAATGCTGTGGTAGTCTTATAGGCTCACTTACTAGAGTAACGAAACACTGGTTT - -a -s simMouse_chr6.simMouse.chr6 432887 68 + 636262 GACTAGTTGATACCAGACTGTTAGACAACATCAATGAATAGTTTCTAGGCCATGAGTATTCATAATAT -s Anc0.Anc0refChr3 63983 58 + 222631 AACAAAATGATACCAGATTTTTAGACAACATCAATAAA-AGTCTCTAGGCCATGAG---------TAT -s Anc1.Anc1refChr6 95013 58 + 197743 AACAAAATGATACCAGATTTTTAGACAACATCAATAAA-AGTCTCTAGGCCATGAG---------TAT -s Anc2.Anc2refChr13 68982 58 + 96486 AACAAAATGATACCAGATTTCTAGACAACATCAATAAA-AGTCTCTAGGCCATGAG---------TAA -s mr.mrrefChr5 287439 59 + 294540 GACTAGTTGATACCAGACTGTTAGACAACATCAATGAATAGTTTCTAGGCCATGAG---------TAT -s simCow_chr6.simCow.chr6 426336 50 + 602619 --------GATACCATATTTCTACACAACATCAATAAA-AGTCTCTAGCCCATGAC---------TAC -s simDog_chr6.simDog.chr6 416294 58 + 593897 AACAAAATGATACCAGTTTTCTAGACCACATCACTAAA-ATTCTCTAGGCCATGAG---------TAA -s simHuman_chr6.simHuman.chr6 420428 58 + 601863 AGCAATATGATACCAGATTTTCAAACAAGATCTATATA-AGTCTCTAGGCAATGAG---------CAT -s simRat_chr6.simRat.chr6 441357 59 + 647215 GACTAGTTGATACCAGACTGTTAGACAACAGCAATGAACAGTTTCTAGGCCATGAG---------TAT - -a -s simMouse_chr6.simMouse.chr6 432955 53 + 636262 TCATAATTATTGTGAACTACAGCAAAGAAAAATGCAATGGGGACATCTGAGAA -s Anc0.Anc0refChr3 64043 53 + 222631 TGGAAATTATAGTCAATCACAGGCAAGTTAAATGCAATGGGAATGTCTGGGCA -s Anc1.Anc1refChr6 95073 53 + 197743 TGGAAATTATAGTCAATCACAGGCAAGTTAAATGCAATGGGAATGTCTGGGCA -s Anc2.Anc2refChr13 69042 53 + 96486 TGGAAATTATAGTCAATCACAGGCAAGTTAATTGCAAGGGGAATGACTGGGCA -s mr.mrrefChr5 287498 53 + 294540 TCATAATTATTGTGAACTACAGCAAAGAAAAATGCAATGGGGACGTCTGAGAA -s simCow_chr6.simCow.chr6 426388 53 + 602619 TGGAAATTTTAGTCAGTCCCAGGCACGTTAGCTGCAAAGGGCACAACTGGGAA -s simDog_chr6.simDog.chr6 416354 49 + 593897 CAGAGATTATACTGAATCAC----AAGCTAATTGCAAGGGGAATGACTGGGCG -s simHuman_chr6.simHuman.chr6 420488 53 + 601863 TGGAAATTATAGTCAATCACTGACAAGTTATATGCAATGGGTGTGTTTGGGGA -s simRat_chr6.simRat.chr6 441416 53 + 647215 TCATAATTAGTTTGAACTACAGTAAAGAAAAATGCAATGGGGACGTCTGAGAA - -a -s simMouse_chr6.simMouse.chr6 433008 102 + 636262 GAATCGATGCCAAAGACAGAAAACAACTCCAACCTGGCATAAATGAAATAAATATTAGCTAGAATCTTTCTCTTGGTAGAAAGGGAGCAAGATGCTCCACAC -s Anc0.Anc0refChr3 64096 5 + 222631 GAATC------------------------------------------------------------------------------------------------- -s Anc1.Anc1refChr6 95126 5 + 197743 GAATC------------------------------------------------------------------------------------------------- -s Anc2.Anc2refChr13 69101 5 + 96486 AAATC------------------------------------------------------------------------------------------------- -s mr.mrrefChr5 287551 101 + 294540 GAATCGATGCCAAAGACAG-AAACAACTCCAACCTGGCATAAATGAAATAAATATTAGCTAGAATCTTTCTCTTGGTAGAAAGGGAGCAAGATGCTCCACAC -s simCow_chr6.simCow.chr6 426447 5 + 602619 AAATC------------------------------------------------------------------------------------------------- -s simDog_chr6.simDog.chr6 416410 5 + 593897 AAATC------------------------------------------------------------------------------------------------- -s simHuman_chr6.simHuman.chr6 420541 5 + 601863 GAACC------------------------------------------------------------------------------------------------- -s simRat_chr6.simRat.chr6 441469 101 + 647215 GAATCAATGCCAAAGACAG-CAACAAATCAAACCTGGCGTAAATGAAATAAATAGTACCTAGAATCTTTTTCTGGGTACAGAGGAAGCAAGATGCTCCACAT - -a -s simMouse_chr6.simMouse.chr6 433110 9 + 636262 ATTCCTGGA -s Anc0.Anc0refChr3 64196 9 + 222631 GTTTATAGC -s Anc1.Anc1refChr6 95226 9 + 197743 GTTTATAGC -s Anc2.Anc2refChr13 69215 9 + 96486 GTTTATAGC -s mr.mrrefChr5 287734 9 + 294540 GTTTATGGA -s simCow_chr6.simCow.chr6 426554 9 + 602619 GTTTATAGC -s simDog_chr6.simDog.chr6 416654 9 + 593897 ATTTATAGG -s simHuman_chr6.simHuman.chr6 420641 9 + 601863 GTCTATAGC -s simRat_chr6.simRat.chr6 441745 9 + 647215 GTTTATGGA - -a -s simMouse_chr6.simMouse.chr6 433119 43 + 636262 TATATTCTTGTGCCTTATACAAACAGATTAATTCCAAGAGTGA -s Anc0.Anc0refChr3 64207 43 + 222631 TAGAGTCTTGTGCTATAGGCAAATCGATAAAATCCAAGAGTGG -s Anc1.Anc1refChr6 95237 43 + 197743 TAGAGTCTTGTGCTATAGGCAAATCGATAAAATCCAAGAGTGG -s Anc2.Anc2refChr13 69226 43 + 96486 TAGAGTCTAGTGCTATAGGCAAATAGAAAAAATCCAAGAGTGG -s mr.mrrefChr5 287745 43 + 294540 TATATTCTTGTGCCTTAGACAAACCGATAAATTCCAAGAGTGA -s simCow_chr6.simCow.chr6 426565 42 + 602619 TATAGTC-ATTCCTTCAGGGAAACTCAGGAAATCCTGGAGTGG -s simDog_chr6.simDog.chr6 416665 43 + 593897 TAGAGTCTAGTGCTATAGGCAAATAGAAAAAGTCAAAGAGTGG -s simHuman_chr6.simHuman.chr6 420652 43 + 601863 TAGAGTCCTGTGCTATAGGTGAATCAATAAGATCCAAGAGTGG -s simRat_chr6.simRat.chr6 441756 43 + 647215 TATAATCTTGTGCCTTAGACAAACCGATAAACTCCAAGAGTGA - -a -s simMouse_chr6.simMouse.chr6 433162 131 + 636262 CCAGCACACGGGAGCAGCCACCTTTCACATTTTTCCATATGGTGTTGTGCCCCAGATATTCAGTTACTGTATAGTTGCTGTAAGAAATTAAAAAGTTAGGTATTAAAAATGGGCATAGGTCCAAACAGGAA -s Anc0.Anc0refChr3 64252 129 + 222631 CCAGGACTCATGAATAGCCACCTTGCGCATTTTTTCCTAGAGCATAGTGTCACTGATATTTGGTTACTGTA--GTTGCTGTAATAACTCAAAAAGTCAAGTATCAAAAATTGGCATGCATTAAAAAGGGAA -s Anc1.Anc1refChr6 95282 129 + 197743 CCAGGACTCATGAATAGCCACCTTGCGCATTTTTTCCTAGAGCATAGTGTCACTGATATTTGGTTACTGTA--GTTGCTGTAATAACTCAAAAAGTCAAGTATCAAAAATTGGCATGCATTAAAAAGGGAA -s Anc2.Anc2refChr13 69271 129 + 96486 CTTGGACTCATGAACAGCCACCTTACGCATTTCTTCCTAGAGCATAGTGTCACTGATATTTGAGTACTGTA--GTTGCTGTAATAACTCAAAAAGTCAAGTATCAAAATTTGGCATGCATTAAAAAGGGAA -s mr.mrrefChr5 287788 131 + 294540 CCAGCACACAGGAGTAGCCACCTTGCACATTTTTCCATATAGTGTTGTGTCACAGATATTCAGTTACTGTATAGTTGCTGTAAGAAATCAAAAAGTTAGGTATCAAAAATTGGCATAGGTCCAAACAGGAA -s simCow_chr6.simCow.chr6 426609 128 + 602619 CTGGAACTCATGAGCAGCCAGCTCACACAGTTCTCTCTAAGGCATAGTGTCACTCATATTTGAGTACTGTA--GTTGCTGTAATAATTCAAAGAGCAAAGTATCAAAATTTGGAATGCATTAAAAATGGA- -s simDog_chr6.simDog.chr6 416710 129 + 593897 GTTGGACTTATGAACAGCCACCTTATGCATTTCTTCCTAGAACATGGTGTCACTGATATTTGAGAACTGTA--GTTGCTATAATCACTCAAAAAGTCAAGTGTGAAAATTTGGCATGCAACAAAAAGGGAA -s simHuman_chr6.simHuman.chr6 420697 122 + 601863 CCAGGACTCATGACTAGCCACATTGCTCATTTTG------AGCATATTGTCACTGATATTTGGTTACTGTA--GTTGCTGTAACAACTCATAAAGC-AAGTATCAAAAATTGGCATGCATTAAAAAGGGGC -s simRat_chr6.simRat.chr6 441799 131 + 647215 CCAGCACACAGGAGTGGCCACCTTGTACATTCTTCCATACAGTGTTGTGTTACAGATATTCAGTTACTGTGTAGTTGCTGTAATAAATCAAAAAGTTGGGTAACAAAAATTGGCACAGGTCTAAACAGAAA - -a -s simMouse_chr6.simMouse.chr6 433293 5 + 636262 TAACT -s Anc0.Anc0refChr3 64381 4 + 222631 TAA-T -s Anc1.Anc1refChr6 95411 4 + 197743 TAA-T -s Anc2.Anc2refChr13 69400 4 + 96486 AAA-T -s mr.mrrefChr5 287919 5 + 294540 TAACT -s simCow_chr6.simCow.chr6 426956 4 + 602619 AAG-T -s simDog_chr6.simDog.chr6 416839 4 + 593897 AAA-T -s simHuman_chr6.simHuman.chr6 420819 4 + 601863 TGA-T -s simRat_chr6.simRat.chr6 441930 5 + 647215 TAACA - -a -s simMouse_chr6.simMouse.chr6 433298 3 + 636262 GCC -s Anc0.Anc0refChr3 64385 3 + 222631 CCC -s Anc1.Anc1refChr6 95415 3 + 197743 CCC -s Anc2.Anc2refChr13 69404 3 + 96486 CCC -s mr.mrrefChr5 287924 3 + 294540 GCC -s simCow_chr6.simCow.chr6 426960 3 + 602619 CAC -s simDog_chr6.simDog.chr6 416852 3 + 593897 CCC -s simHuman_chr6.simHuman.chr6 420823 3 + 601863 CCC -s simRat_chr6.simRat.chr6 441935 3 + 647215 TAC - -a -s simMouse_chr6.simMouse.chr6 433301 4 + 636262 AGGG -s Anc0.Anc0refChr3 64388 4 + 222631 AGGG -s Anc1.Anc1refChr6 95418 4 + 197743 AGGG -s Anc2.Anc2refChr13 69407 4 + 96486 AGGG -s mr.mrrefChr5 287927 4 + 294540 AGGG -s simCow_chr6.simCow.chr6 426965 4 + 602619 AGGG -s simDog_chr6.simDog.chr6 416855 4 + 593897 AGGG -s simHuman_chr6.simHuman.chr6 420826 4 + 601863 AGGG -s simRat_chr6.simRat.chr6 441938 4 + 647215 AAGG - -a -s simMouse_chr6.simMouse.chr6 433305 11 + 636262 AGATAGATACA -s Anc0.Anc0refChr3 64398 11 + 222631 ACATAGGTACA -s Anc1.Anc1refChr6 95428 11 + 197743 ACATAGGTACA -s Anc2.Anc2refChr13 69417 11 + 96486 ACATAGGTACA -s mr.mrrefChr5 287931 11 + 294540 AGATAGATACA -s simCow_chr6.simCow.chr6 426975 11 + 602619 ACATAAGTTTA -s simDog_chr6.simDog.chr6 416865 11 + 593897 ACATAGGTACT -s simHuman_chr6.simHuman.chr6 420836 11 + 601863 ACATAGGTACA -s simRat_chr6.simRat.chr6 441942 11 + 647215 AGATAGAGACA - -a -s simMouse_chr6.simMouse.chr6 433316 71 + 636262 AATTCTCAGTATTATGTCTTGGTCTCTAGAGTTATCCAGCAGTGGTACATAACCCATGACTTGTACTGGCT -s Anc0.Anc0refChr3 64428 55 + 222631 AATTCT--GTATTATG--------------GTGACCCAACAGCCATATGTGACCACTAACTCCTATTATCT -s Anc1.Anc1refChr6 95458 65 + 197743 AATTCTCAGTATTATG-CTTGATC-----AGTGACCCAACAGCCATATGTGACCACTAACTCCTATTATCT -s Anc2.Anc2refChr13 69447 55 + 96486 AATTTT--GCACTGTG--------------GTGACCCAACAACCATATGTGGCCACTAACTCCTATTATGT -s mr.mrrefChr5 287961 71 + 294540 AATTCTCAGTATTATGTCTTGATCTCTAGAGTTATCCAGCAGCGGTACATAACCCATGACTTCTACTATCT -s simCow_chr6.simCow.chr6 427007 55 + 602619 CATTCT--GCACTGCG--------------GTGACCCAACGACCATATGTGGCCACTAACTCCTATTATGT -s simDog_chr6.simDog.chr6 416895 25 + 593897 AATTTT--GCACTGTG--------------GCGACCCAACA------------------------------ -s simHuman_chr6.simHuman.chr6 420867 64 + 601863 AATTCCCAGTATCAT--CTTGATC-----AGTGACCCAAAAGCTATATGTGAGCACTAACTCCTATTATCT -s simRat_chr6.simRat.chr6 441972 71 + 647215 AAATCTGAGTATTATGACTAGATCTTGAAGCTTATCCAGTGGCAGCACATAACCCATGACTACTACCATCT - -a -s simMouse_chr6.simMouse.chr6 433387 56 + 636262 AAGACATCTTTTATTAGCTGACATGCTGAAGGTTGTCTTGTCCAATGCTCTTCATA -s Anc0.Anc0refChr3 64483 55 + 222631 TAGGTCT-TTTTATGAGATAACATGCTGAAGGTTGTATTGTCCTATGCTCTTCTTC -s Anc1.Anc1refChr6 95523 55 + 197743 TAGGTCT-TTTTATGAGATAACATGCTGAAGGTTGTATTGTCCTATGCTCTTCTTC -s Anc2.Anc2refChr13 69502 55 + 96486 TCGGTCT-TTTTATGAGATAACATGCTGAAAGTTGTATTGTCCTATGCTCTTCTTC -s mr.mrrefChr5 288032 55 + 294540 TAGACAT-TTTTATTAGCTGACATGCTGAAGGTTGTCTTGTCCAATGCTCTTCATA -s simCow_chr6.simCow.chr6 427062 55 + 602619 TCGGTCT-TCTTACGAGATTCCAGGCTTAAAGTTGTATTGTCCTATGCTCTTCTTC -s simDog_chr6.simDog.chr6 416920 51 + 593897 ----TCT-TTCTATGAGGTAAGATGCAGAAAGTTGTATTGACCTATGCTCTTCTGC -s simHuman_chr6.simHuman.chr6 420938 55 + 601863 TAGGTCT-TTTTATCGGATCACATGCTGTAGGTTGTATTGTTCTTTGCGCTTCTTG -s simRat_chr6.simRat.chr6 442043 51 + 647215 TAGACAT-TTCTATTAGCCGACATGCTGAAGGTTGTCTTGTCCAATGCTCTT---- - -a -s simMouse_chr6.simMouse.chr6 433443 21 + 636262 ACAATTTAAGCTCCGTATCCA -s Anc0.Anc0refChr3 64541 21 + 222631 ACCACTTCAGGCAAGTATTCA -s Anc1.Anc1refChr6 95581 21 + 197743 ACCACTTCAGGCAAGTATTCA -s Anc2.Anc2refChr13 69560 21 + 96486 GCCACTTCGGGCAAGTATTCA -s mr.mrrefChr5 288087 21 + 294540 ACAATTTCAGCTCCGTATTCA -s simCow_chr6.simCow.chr6 427120 19 + 602619 GCCATT--GGGTAAATATTCA -s simDog_chr6.simDog.chr6 416974 21 + 593897 GCAACTTCGGCCAAGTACTCA -s simHuman_chr6.simHuman.chr6 420996 21 + 601863 ACCAATTCAGGCATGTATTCA -s simRat_chr6.simRat.chr6 442094 19 + 647215 --GTTTTCAGCTCCGTAGTCA - -a -s simMouse_chr6.simMouse.chr6 433464 25 + 636262 ACCAATAGCAACCTAAACCTAGTGC -s Anc0.Anc0refChr3 64562 19 + 222631 ACCGATAAC------AACCTGGTGC -s Anc1.Anc1refChr6 95602 19 + 197743 ACCGATAAC------AACCTGGTGC -s Anc2.Anc2refChr13 69581 19 + 96486 GTCGATAAC------AACCTGGTGC -s mr.mrrefChr5 288108 19 + 294540 ACCAATAGC------AACCTAGTGC -s simCow_chr6.simCow.chr6 427140 19 + 602619 ACCAACAGC------AACCTACTGG -s simDog_chr6.simDog.chr6 416995 19 + 593897 GTCGATAAC------CACCTGGCGC -s simHuman_chr6.simHuman.chr6 421017 12 + 601863 AC-------------AACCTGGTGC -s simRat_chr6.simRat.chr6 442113 19 + 647215 ACTTACAGC------AACCTAGTGC - -a -s simMouse_chr6.simMouse.chr6 433489 42 + 636262 AAATGATTATGTTGTTCATTTAAATTATGTGACTTTGGTGAC -s Anc0.Anc0refChr3 64585 42 + 222631 GAATGACTGTGTTGTTAAGGGAAGGTGTGTGACCATGTTGCC -s Anc1.Anc1refChr6 95625 42 + 197743 GAATGACTGTGTTGTTAAGGGAAGGTGTGTGACCATGTTGCC -s Anc2.Anc2refChr13 69604 42 + 96486 GATTGACTGTGTTGTTAAGGGGAGGTGTGTGACCATGTTGCC -s mr.mrrefChr5 288127 42 + 294540 AAATGACTGTGTTGTTCATTGAAAGTGTGTGACTTTGTTGAC -s simCow_chr6.simCow.chr6 427163 39 + 602619 GATTGACTGTGTTGTTA---GGAGGTGTGTGAACATTTTACC -s simDog_chr6.simDog.chr6 417018 41 + 593897 GATTGATTGTATTGTTAAGGGGAGGTATGTGGCCATGT-GCC -s simHuman_chr6.simHuman.chr6 421034 42 + 601863 GAATGGCTGTGATGGCAAGGGAAGGTGTGTGACCATATTGCC -s simRat_chr6.simRat.chr6 442132 42 + 647215 AACTGACTGTGTTGTTCATTGAAAGTGTGTGACTTTGTTGAC - -a -s simMouse_chr6.simMouse.chr6 433531 8 + 636262 TCAAGGTA -s Anc0.Anc0refChr3 64628 8 + 222631 TCTTGGTA -s Anc1.Anc1refChr6 95668 8 + 197743 TCTTGGTA -s Anc2.Anc2refChr13 69647 8 + 96486 TCTTGGTA -s mr.mrrefChr5 288169 8 + 294540 TCAAGGTA -s simCow_chr6.simCow.chr6 427203 8 + 602619 TCTTGGTA -s simDog_chr6.simDog.chr6 417060 8 + 593897 TCTTGATA -s simHuman_chr6.simHuman.chr6 421077 8 + 601863 TCTTGGTA -s simRat_chr6.simRat.chr6 442174 6 + 647215 TCA--GTA - -a -s simMouse_chr6.simMouse.chr6 433539 8 + 636262 CAGCCACC -s Anc0.Anc0refChr3 64650 8 + 222631 TATCCACA -s Anc1.Anc1refChr6 95690 8 + 197743 TATCCACA -s Anc2.Anc2refChr13 69669 8 + 96486 CATCCACA -s mr.mrrefChr5 288177 8 + 294540 TATCCACA -s simCow_chr6.simCow.chr6 427225 8 + 602619 AATCCATA -s simDog_chr6.simDog.chr6 417082 8 + 593897 CATCCACA -s simHuman_chr6.simHuman.chr6 421099 8 + 601863 TATTCACA -s simRat_chr6.simRat.chr6 442180 8 + 647215 TGTCTCCA - -a -s simMouse_chr6.simMouse.chr6 433547 26 + 636262 GGAAAGGAAGTTAAGGGCTTGAGATA -s Anc0.Anc0refChr3 64668 26 + 222631 GGGGAGGAAGTTAAGGGCCTTAAATA -s Anc1.Anc1refChr6 95708 26 + 197743 GGGGAGGAAGTTAAGGGCCTTAAATA -s Anc2.Anc2refChr13 69687 26 + 96486 GGGGAGGAAGTTAAGGGCCTTAAATA -s mr.mrrefChr5 288185 26 + 294540 GGAGAGGAAGTTAAGGGCTTTAGATA -s simCow_chr6.simCow.chr6 427235 26 + 602619 GGGGAGGAAATCAAGGGTTTGAAATA -s simDog_chr6.simDog.chr6 417100 26 + 593897 GGGGAGGAAGTTAAGGGCCTTAAATA -s simHuman_chr6.simHuman.chr6 421117 26 + 601863 GGGGAGGAAGTTAACAGCCTTAAACA -s simRat_chr6.simRat.chr6 442188 26 + 647215 GGAGAGGAAGTTAAGGGTTTTAGATA - -a -s simMouse_chr6.simMouse.chr6 433573 6 + 636262 ACAGAC -s Anc0.Anc0refChr3 64694 6 + 222631 ATAAGG -s Anc1.Anc1refChr6 95734 6 + 197743 ATAAGG -s Anc2.Anc2refChr13 69713 6 + 96486 ATAAGG -s mr.mrrefChr5 288211 6 + 294540 ATAGAG -s simCow_chr6.simCow.chr6 427261 6 + 602619 GTAAGA -s simDog_chr6.simDog.chr6 417129 6 + 593897 AGAAGG -s simHuman_chr6.simHuman.chr6 421143 6 + 601863 ATAAGG -s simRat_chr6.simRat.chr6 442214 6 + 647215 ATAGAG - -a -s simMouse_chr6.simMouse.chr6 433579 7 + 636262 AATTGCA -s Anc0.Anc0refChr3 64700 7 + 222631 GGTTTCA -s Anc1.Anc1refChr6 95740 7 + 197743 GGTTTCA -s Anc2.Anc2refChr13 69719 7 + 96486 GGCTTCA -s mr.mrrefChr5 288217 7 + 294540 AATTGCA -s simCow_chr6.simCow.chr6 427267 7 + 602619 GGATTCA -s simDog_chr6.simDog.chr6 417136 7 + 593897 GGCTTCA -s simHuman_chr6.simHuman.chr6 421149 7 + 601863 GGTTTTA -s simRat_chr6.simRat.chr6 442220 7 + 647215 AACCGCA - -a -s simMouse_chr6.simMouse.chr6 433586 408 + 636262 TCAGCAAATTTTATTTCATATCAGGACAATGAGAAAACAACACAGTTGTGGGTGAGCAGCCTTATGATCCTATGTCTGGCTATTGATCTTCGGGTGATAGACCTTCTTGTTCAGCGTACTTAGTCTGCAAGTTCAGTTGATGTATGGGTTCAATACCGAATCGCTCAAAAACGTCGCCGGGTCACTGGTACCTCATGAATCCCCTGTATAATTACACGTCTATAACGTGGGTGCAAGATAATGTCCCCTAGTCCAACAGAAAACTCTAATGGTCCCAGTTGTATTACTTTATGTATATGTCCCCCAGGCCAATAACCAGCTCAGTGCCAGTTCAACTTTATGTCTTGAAAAAAGATTGAAGAGGCATGCCCACGGTTCTTTAAGGCTGTTGGTAGTATTAGTTACTAC -s Anc0.Anc0refChr3 64712 106 + 222631 GAGGCAAATTTTATTTCATATCTGGACAATGAGATAATAACAAAGCTGTGGGTGTGCAACCCTGTGATCCTAG--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CCACTGCTCTCTTAGGTACTTGGTAGTATCAGT------ -s Anc1.Anc1refChr6 95752 106 + 197743 GAGGCAAATTTTATTTCATATCTGGACAATGAGATAATAACAAAGCTGTGGGTGTGCAACCCTGTGATCCTAG--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CCACTGCTCTCTTAGGTACTTGGTAGTATCAGT------ -s Anc2.Anc2refChr13 69731 106 + 96486 TAGGCAAGTTTTATTTCACATCTGGGCAATGAGATAATAACAAAGCTGTCGGTGTGCAACCCTGTGGTCCTAG--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CCACTGCTCTCTTAGGTACTTGGTAGTATCAGT------ -s mr.mrrefChr5 288224 325 + 294540 GCGGCAAATTTTATTTCATATCAGGACAATGAGAAAACAACACAGTTGTGGGTGTGCAGCCTTATGATCCTATGTCTGGCTATTGATCTTCGGGTGATAGACCTTCTTGTTCAGCGTACTTAGTCTGCAAGTTCAGTTGATGTATGGGTTCAATA--------------------------------------------------------------------AACGTGGGTGCAAG---------CCTAGTCCAACAGAAAACTCTAATGGTCCCAGTTGTATTACTTTATGTATATGTCCCCCAGGCCAATAACCAGCTCAGTGCCAGTTCAACTTTATGTCT-----AAAGATTGAAGAGGCATGCCCACGGTTCTTTAAGGCTGTTGGTAGTATTAGT-ACTAC -s simCow_chr6.simCow.chr6 427279 101 + 602619 CAGGCTATTTTTATTTCACATTGGGGCAATGAGATATCA-----GTTGTAGGTGTGCTGCCCCATGGTCCTAT--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CCACAGCTCCTTAAGGTACTTGGTAGCATCAGG------ -s simDog_chr6.simDog.chr6 417148 106 + 593897 TAGGCAGGTTTCATATTACATCTGGGCAATGGAAAAATAACAAAGCTGTCAGTGTGCAATGTTGTGGTCCTAG--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CCACTGCTCTCTTAGGTGCTTGGTAGTATCAGT------ -s simHuman_chr6.simHuman.chr6 421161 67 + 601863 GAGCCAAATCTTATTTCATATCTGGACAATGAGATAAGAACAGAGCTGTGGGCATGCAACCCTGTGA----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- -s simRat_chr6.simRat.chr6 442227 325 + 647215 GTGGCAAGTTTTGTTTCATATCAGGACAGTGAGAAAACGACACAGTTGTGGGTGTGCAGCCTTATGGTCCTAGGTCTAACTATTAATCTTCAGGTAACAGACCTTCTTGTTCAGCAGACTTAGACTGCAAGTTTTGTTGAGGTAGGGGTTCAATA--------------------------------------------------------------------AACATGGGCACAAG---------CCTAGTCCAACAACCAACTCTAATGGATCCAGTTGTATTACTTCATATATATGTCCCCCAGGCCAATAGGCAACTTAGTGCCAGTTCTACTTTATGTCT-----AAAGATTGAAGAGGCATGCTCACAGTTCTTTTAGGTTGTTGGTAGTATTAGT-ACTGT - -a -s simMouse_chr6.simMouse.chr6 433994 37 + 636262 CAGAGGGTAAAGTGGTTCTACCTAATATCTTCCTCTA -s Anc0.Anc0refChr3 64818 21 + 222631 ----------------TCTACCTAGTATTCTCCTATA -s Anc1.Anc1refChr6 95858 21 + 197743 ----------------TCTACCTAGTATTCTCCTATA -s Anc2.Anc2refChr13 69837 21 + 96486 ----------------TTTATTTAGTATTCCACTATA -s mr.mrrefChr5 288549 37 + 294540 CAGAGGGTAAAGTGGTTCTACCTAATATCTTCCTCTA -s simCow_chr6.simCow.chr6 427380 21 + 602619 ----------------CTCACCTAATATTCCTTTATA -s simDog_chr6.simDog.chr6 417278 21 + 593897 ----------------TTTATTTAGTATTCCACTATA -s simHuman_chr6.simHuman.chr6 421228 20 + 601863 -----------------CTACCCATGAGTGTCAGGTA -s simRat_chr6.simRat.chr6 442554 37 + 647215 TAGAGGGTAGAGTGGCTCTACCTAATATTTTCTTCTC - -a -s simMouse_chr6.simMouse.chr6 434031 2 + 636262 GG -s Anc0.Anc0refChr3 64839 2 + 222631 AG -s Anc1.Anc1refChr6 95879 2 + 197743 AG -s Anc2.Anc2refChr13 69858 2 + 96486 AG -s mr.mrrefChr5 288586 2 + 294540 GG -s simCow_chr6.simCow.chr6 427401 2 + 602619 AT -s simDog_chr6.simDog.chr6 417301 2 + 593897 AG -s simHuman_chr6.simHuman.chr6 421248 2 + 601863 TG -s simRat_chr6.simRat.chr6 442591 2 + 647215 GA - -a -s simMouse_chr6.simMouse.chr6 434033 7 + 636262 ACAGGAT -s Anc0.Anc0refChr3 64841 7 + 222631 AGAGGGT -s Anc1.Anc1refChr6 95881 7 + 197743 AGAGGGT -s Anc2.Anc2refChr13 69860 7 + 96486 AGGGGGT -s mr.mrrefChr5 288588 7 + 294540 ACAGGAT -s simCow_chr6.simCow.chr6 427403 7 + 602619 AGGGTGG -s simDog_chr6.simDog.chr6 417303 7 + 593897 AGGGGGT -s simHuman_chr6.simHuman.chr6 421252 7 + 601863 ATAGGGT -s simRat_chr6.simRat.chr6 442593 7 + 647215 AAAGGAT - -a -s simMouse_chr6.simMouse.chr6 434040 23 + 636262 TATTTAGCTCAGTACTCTGatat -s Anc0.Anc0refChr3 64848 23 + 222631 TACTTTGTTCAATACTTTGACAT -s Anc1.Anc1refChr6 95888 23 + 197743 TACTTTGTTCAATACTTTGACAT -s Anc2.Anc2refChr13 69870 23 + 96486 TACTTTGTTGAATAGTTTGACAT -s mr.mrrefChr5 288595 23 + 294540 TACTTTGCTCAGTACTCTGACAT -s simCow_chr6.simCow.chr6 427413 22 + 602619 TACTTAGTTGATTCGTT-GACAT -s simDog_chr6.simDog.chr6 417313 23 + 593897 TACTTTATTGAATAGTTTGACAT -s simHuman_chr6.simHuman.chr6 421259 23 + 601863 TACTTTGTTCACTACTTTGACAT -s simRat_chr6.simRat.chr6 442600 23 + 647215 TACATTGCTCAGTGGTCTGACAT - -a -s simMouse_chr6.simMouse.chr6 434063 44 + 636262 tatactatcaattcggttaaaacctgagtagggtgtgccacagc -s Anc0.Anc0refChr3 64871 44 + 222631 CATACTGTTAATTAGTTTAAACCCttattagggtgtgacacagc -s Anc1.Anc1refChr6 95911 44 + 197743 CATACTGTTAATTAGTTTAAACCCttattagggtgtgacacagc -s Anc2.Anc2refChr13 69893 44 + 96486 CATACTGTTGAGTAGTTTAAACCCttattaaggtgtgacacagc -s mr.mrrefChr5 288618 44 + 294540 TATACTATTAATTCGGTTAAAACCtgattagggtgtgccacagc -s simCow_chr6.simCow.chr6 427436 44 + 602619 CATTCTGTTGACTAGTTTAAACCCttaccaaggtgatgcaccgc -s simDog_chr6.simDog.chr6 417336 44 + 593897 CATACTGTTGAGTAGTTTACACTCttattaaggtatgacacagc -s simHuman_chr6.simHuman.chr6 421282 44 + 601863 CATACTCCTAATTAGCTTAAACCCttatgagagagccacacagc -s simRat_chr6.simRat.chr6 442623 44 + 647215 TATATTATTAGTTCAGTTAGAACCTGATTAGTGTTTGCCACAGC - -a -s simMouse_chr6.simMouse.chr6 434107 7 + 636262 ctaagat -s Anc0.Anc0refChr3 64915 7 + 222631 ttgaggg -s Anc1.Anc1refChr6 95955 7 + 197743 ttgaggg -s Anc2.Anc2refChr13 69937 7 + 96486 ttgaggg -s mr.mrrefChr5 288662 7 + 294540 ctaagag -s simCow_chr6.simCow.chr6 427480 7 + 602619 tgaaggg -s simDog_chr6.simDog.chr6 417380 7 + 593897 ttgaggg -s simHuman_chr6.simHuman.chr6 421326 7 + 601863 tcgaggg -s simRat_chr6.simRat.chr6 442669 7 + 647215 CTAACAG - -a -s simMouse_chr6.simMouse.chr6 434114 27 + 636262 ttcaagtcttttaggacatagttatag -s Anc0.Anc0refChr3 64930 27 + 222631 tttaagactttcaggatatacttagga -s Anc1.Anc1refChr6 95970 27 + 197743 tttaagactttcaggatatacttagga -s Anc2.Anc2refChr13 69952 27 + 96486 tttaagactttcaggatgtacttcgga -s mr.mrrefChr5 288669 27 + 294540 tttaagtctttcaggacatagttatga -s simCow_chr6.simCow.chr6 427495 27 + 602619 tttaagaatttcaggccgtactttgga -s simDog_chr6.simDog.chr6 417395 26 + 593897 tctacgactttcaggatgca-ttcaga -s simHuman_chr6.simHuman.chr6 421341 27 + 601863 tttaagactttcaggatataattagga -s simRat_chr6.simRat.chr6 442676 27 + 647215 TTTCAGCCTATCAGGACACAGTTAAGA - -a -s simMouse_chr6.simMouse.chr6 434141 112 + 636262 tattagatacagcttgaagggtcccagtttaaagactttggacacacaactgctgtgggtttagtaaatgagttcaggattgtaaggtaggcatacggcagtgatgagggct -s Anc0.Anc0refChr3 64960 92 + 222631 aatatagaacaag-----gggtcccagttttaagactttcaggtcacaagtgctggggaattagcaaataaattcaggat----atgtacaca---------aat--taact -s Anc1.Anc1refChr6 96000 92 + 197743 aatatagaacaag-----gggtcccagttttaagactttcaggtcacaagtgctggggaattagcaaataaattcaggat----atgtacaca---------aat--taaCT -s Anc2.Anc2refChr13 69982 92 + 96486 gatatagattaag-----aggttccagttttaagactttcaggtcgccagttctggggaattagcaaataaatttaggat----atgtacaca---------aat--caagt -s mr.mrrefChr5 288696 105 + 294540 aattagatacagc-----gggtcccagtttaaagactttgggcacacaactgctgtgggtttagtaaatgagttcaggattgtaaggtagacatacggcagtgat--tggCT -s simCow_chr6.simCow.chr6 427525 92 + 602619 gatatagtttgaa-----aggttccagttctaagaccttcatgttgtgagtaccaggggattagcagataaatttagaat----atgctcaca---------aat--caagt -s simDog_chr6.simDog.chr6 417424 92 + 593897 gatatagattaag-----aggctcgggttttaagactttcaggccgccagttctggggaatcatccaacaaaattaagat----atgtacaca---------aat--caggt -s simHuman_chr6.simHuman.chr6 421371 92 + 601863 aatacagcacaag-----gggtcccagttttaaaactatcagatcacaagcgctgaggcactagcaaataaattcaggat----aagtacaca---------aat--taaCT -s simRat_chr6.simRat.chr6 442703 104 + 647215 AATTAGATACAGC-----GGGTCTCAG-TTAAAGACTTCAGGCACACGACTGCTGGGGGTTTAGTAAATGGCTTCAGGATTTTAAGGTAGACACACTGCAGTGGT--TGGCT - -a -s simMouse_chr6.simMouse.chr6 434253 57 + 636262 cagcttggcatcacatcattatggcggaaatgtaatttTGTCTGAAGATGGCATGGT -s Anc0.Anc0refChr3 65052 37 + 222631 cg--ttagtgtcacaaccttatggcggaaatgaaatttt------------------ -s Anc1.Anc1refChr6 96092 37 + 197743 Cg--TTAGTGTCacaaccttatggcggaaatgaaatttt------------------ -s Anc2.Anc2refChr13 70116 37 + 96486 cg--tcagtgacacaaccttatgatggaaatgaaatttc------------------ -s mr.mrrefChr5 288801 55 + 294540 Ca--TTGGCATCacatcattatggcggaaatgtaatttTGTCTGAAGATGGCATGGT -s simCow_chr6.simCow.chr6 427661 29 + 602619 cc--tcagtaacaagaccgtatgatggaaat-------------------------- -s simDog_chr6.simDog.chr6 417560 36 + 593897 cg--tcagtgacacacccttatg-tgctaatgaaatttc------------------ -s simHuman_chr6.simHuman.chr6 421463 36 + 601863 C---TTAAAGTAacaacctcatggcggaaatgaaatttt------------------ -s simRat_chr6.simRat.chr6 442807 51 + 647215 CA--TTGGCAACACATCACTATGGTGGAAATG----TTTGTCTGAGGCTGACAAGGT - -a -s simMouse_chr6.simMouse.chr6 434310 43 + 636262 TGGCTCGGCCTCTGGACAGGAGCTGTTTGCAGGCCCCTGAATG -s Anc0.Anc0refChr3 65089 37 + 222631 ------tGCCTCCAGGCAGGAGCCGTTTGCAGGCCCCTCAATG -s Anc1.Anc1refChr6 96129 37 + 197743 ------tGCCTCCAGGCAGGAGCCGTTTGCAGGCCCCTCAATG -s Anc2.Anc2refChr13 70153 37 + 96486 ------tGCCTCCAGGCAGGAGCCCTGTGCAGGCCCCTCAATG -s mr.mrrefChr5 288856 43 + 294540 TGGCTCTGCCTCTGGACAGGAGCTGTTTGCAGGCCCCTCAATG -s simCow_chr6.simCow.chr6 427690 34 + 602619 ---------CTCCAGGTAGGAGTTCTGTGCAGGCCTCTAAATG -s simDog_chr6.simDog.chr6 417708 37 + 593897 ------TGCCTCCAGGCAGGGGCCCTGTGCATGCCCCTCAATC -s simHuman_chr6.simHuman.chr6 421499 37 + 601863 ------tATCTCCAGGCAGGAGCAGTTTGCAGGCGCCTCAATG -s simRat_chr6.simRat.chr6 442860 43 + 647215 TGGCTCTGCCTCAGGATAGGAACTGTTTGCAGGCCCCTCAATG - -a -s simMouse_chr6.simMouse.chr6 434353 6 + 636262 AGATGT -s Anc0.Anc0refChr3 65128 6 + 222631 AGATGT -s Anc1.Anc1refChr6 96168 6 + 197743 AGATGT -s Anc2.Anc2refChr13 70192 6 + 96486 AGATGT -s mr.mrrefChr5 288899 6 + 294540 AGATGT -s simCow_chr6.simCow.chr6 427726 6 + 602619 AGATGT -s simDog_chr6.simDog.chr6 417747 6 + 593897 AGATGT -s simHuman_chr6.simHuman.chr6 421538 6 + 601863 AGATGT -s simRat_chr6.simRat.chr6 442903 6 + 647215 AGATGT - -a -s simMouse_chr6.simMouse.chr6 434359 44 + 636262 CAAAAGAGTGGAATGTAAGACAAGGTAGCTTGCAATCAGGATCT -s Anc0.Anc0refChr3 65134 44 + 222631 CAAAAATAGGAAACAGAGGGCAAGGTAGCATCCAATCAGGACCT -s Anc1.Anc1refChr6 96174 44 + 197743 CAAAAATAGGAAACAGAGGGCAAGGTAGCATCCAATCAGGACCT -s Anc2.Anc2refChr13 70199 44 + 96486 CAAAAATAGCAAGCAGATGGCAGGGCAGCATCCAATCAGGACCT -s mr.mrrefChr5 288905 44 + 294540 CAAAAATATGGAACATAGGACAAGGTAGCTTCCAATCAGGATCT -s simCow_chr6.simCow.chr6 427733 44 + 602619 CAAAAATATAAACCAGATGGTGGGCCAGCATCCAATCAGGAGCT -s simDog_chr6.simDog.chr6 417754 44 + 593897 CAGAAATGGCATGCAGGTGACAGGGCAGCATTCAATCAGGACCA -s simHuman_chr6.simHuman.chr6 421544 44 + 601863 CAAAAATAGGAAACACAGTGCAAGGTAGCGTCCAGTCAGGACCT -s simRat_chr6.simRat.chr6 442909 44 + 647215 CAAAAATATGGGACATAGAACAAGGTAGCCTCCAATCAGGATCT - -a -s simMouse_chr6.simMouse.chr6 434403 13 + 636262 CAAACAACAAGAG -s Anc0.Anc0refChr3 65181 11 + 222631 CAAGCAAC--TAG -s Anc1.Anc1refChr6 96221 11 + 197743 CAAGCAAC--TAG -s Anc2.Anc2refChr13 70246 11 + 96486 GAAGTAAC--TAG -s mr.mrrefChr5 288952 13 + 294540 CAAACAACAAGAG -s simCow_chr6.simCow.chr6 427780 10 + 602619 -AAGTAAC--TAG -s simDog_chr6.simDog.chr6 417801 11 + 593897 GAAGTAAC--CAA -s simHuman_chr6.simHuman.chr6 421591 11 + 601863 CAAGCAAC--TAG -s simRat_chr6.simRat.chr6 442956 13 + 647215 CAAACAACAAGAG - -a -s simMouse_chr6.simMouse.chr6 434416 25 + 636262 TCACCTAAAAGAAACCCGTGGTCTC -s Anc0.Anc0refChr3 65192 25 + 222631 CCACATACTAGAAACCTGTGGTCCT -s Anc1.Anc1refChr6 96232 25 + 197743 CCACATACTAGAAACCTGTGGTCCT -s Anc2.Anc2refChr13 70257 25 + 96486 CCACATACTTGAAACCTGTGGTCCT -s mr.mrrefChr5 288965 25 + 294540 CCACATAAAAGAAACCCGTGGTCCC -s simCow_chr6.simCow.chr6 427792 25 + 602619 CCAAAGACTTGAAACCTGTGGTCCC -s simDog_chr6.simDog.chr6 417812 25 + 593897 AGCCATACTTGAAACCTGTGGTCCT -s simHuman_chr6.simHuman.chr6 421602 25 + 601863 CCATATATTAGAAACCTGTGATCCT -s simRat_chr6.simRat.chr6 442969 25 + 647215 CCACATAACGCGAGCCAGTGGTCCC - -a -s simMouse_chr6.simMouse.chr6 434441 14 + 636262 TGGGGTTGTGGTGA -s Anc0.Anc0refChr3 65220 14 + 222631 TAAGAGCGTGCTGA -s Anc1.Anc1refChr6 96260 14 + 197743 TAAGAGCGTGCTGA -s Anc2.Anc2refChr13 70294 14 + 96486 TAACAGCCTGCTAG -s mr.mrrefChr5 288990 14 + 294540 TGGGGGTGTGCTGA -s simCow_chr6.simCow.chr6 427829 14 + 602619 TAACATCCTGCTCG -s simDog_chr6.simDog.chr6 417849 14 + 593897 TATCAGCCTGCTAG -s simHuman_chr6.simHuman.chr6 421630 14 + 601863 TAAGTGCGTACTGA -s simRat_chr6.simRat.chr6 442994 14 + 647215 TGGGGGTGTGCTGT - -a -s simMouse_chr6.simMouse.chr6 434455 182 + 636262 TTGTGAGTCCGTGCCCCTCCTTCGCTGAGCTGCACCGGAGGTACCAACCCTAACTTTGTGCTTATCATTAATCCCTGCCCCTCCTACACTGGGCTGTGCCAGGGGTACCAACGTGTCACCAGAGGCACTGTCGGAATGCACCAGGGATACCAACATGTCCCAGAATTTAGAGGTCCGGGAAT -s Anc0.Anc0refChr3 65547 13 + 222631 TGGTCTGTCCATG------------------------------------------------------------------------------------------------------------------------------------------------------------------------- -s Anc1.Anc1refChr6 96587 13 + 197743 TGGTCTGTCCATG------------------------------------------------------------------------------------------------------------------------------------------------------------------------- -s Anc2.Anc2refChr13 71223 13 + 96486 TGGTCCATCCATG------------------------------------------------------------------------------------------------------------------------------------------------------------------------- -s mr.mrrefChr5 289004 178 + 294540 TTGTGAGTCCGTGCCCCTCCTTCGCTGAGCTGCACCGGAGGTACCAACCCTAACTTTGTGCTTATCATTAATCCCTGCCCCTCCTACACTGGGCTGTGCCAGGGGTACCAACGTGTC-CCAGAGGCACTGTCGGAATGCACCAGGGATACCAACATGTCCCAGAATTTAGAGGTCCGGG--- -s simCow_chr6.simCow.chr6 428686 13 + 602619 TGTTCCATCCCTG------------------------------------------------------------------------------------------------------------------------------------------------------------------------- -s simDog_chr6.simDog.chr6 419415 13 + 593897 GGGTCCATGCATG------------------------------------------------------------------------------------------------------------------------------------------------------------------------- -s simHuman_chr6.simHuman.chr6 422656 13 + 601863 TGGTCTGTCCATG------------------------------------------------------------------------------------------------------------------------------------------------------------------------- -s simRat_chr6.simRat.chr6 443008 178 + 647215 CCGTGAGTCCGTGCCCCTCCTATACTGGGCCAGGCCAGGGGTCCCCACCCTAACTTTGTGTTGATCGTTAATCTGTGCCCCTCCTATGCCGGGCTGTGCCAGAGGAATCAACGTGTC-CCAGAAGCACCATTGGGCTGCGCCAGGGGTACCAACATGGCCCAGAATTTAGTGGTGCAGG--- - -a -s simMouse_chr6.simMouse.chr6 434637 27 + 636262 CGACACATGGTACCCAAATGCCAAAGT -s mr.mrrefChr5 289182 27 + 294540 CGACACATGGTACCCAAATGCCAAAGT -s simRat_chr6.simRat.chr6 202249 27 - 647215 CTACACATGGTACCCAAAAGCCGAAGT - -a -s simMouse_chr6.simMouse.chr6 434664 80 + 636262 GGGATGTCCACGCATGGTTCATCATGAGGAGGGTGCAATACACTGCAGAAAACACACCAGTGTCGGTGCCACCACCAGGG -s mr.mrrefChr5 289209 62 + 294540 GGGATGTCCACGCAT------------------TGCAATACACTGCAGAAAACACACCAGTGTCGGTGCCACCACCAGGG -s simRat_chr6.simRat.chr6 202278 62 - 647215 GGGATATCTACGCGT------------------TGCAATACAACGCAGAAAACACACCAGCGTCGGTGCCACTACCTGGG - -a -s simMouse_chr6.simMouse.chr6 434744 219 + 636262 TGCCACCACCAGGCACTTTGTGTGgtcgaaaagagggtggtgtaaaatttgtcattgtttactagatgaaacgagacgctcaatgcacagttatcatagttgacctcatcattcgttgaagcattatcagaagactatatattaagagcagtgttaacaagacttcatcccatctcctaagcgttaaggatgccactggaatagacgtagagggaggtg -s mr.mrrefChr5 289271 201 + 294540 TGCCACCACCAGGCACTTTGTGTGgtcgaaaagagggtggtgtaaaatt-gtcattgtttactagatgaaa-----------atgcacagttatcatagttgacctcatc------tgaagcattatcagaagactatatattaagagcagtgttaacaagacttcatcccatctcctaagcgttaaggatgccactggaatagacgtagagggaggtg -s simRat_chr6.simRat.chr6 202351 201 - 647215 TGCCACTACCTGGGACATGGAGTGCtcaaaaagagggtgaggtacaatt-gtcactgtttactagatgcaa-----------atgtatggtcgtcatagctaaccccatc------cgaagcattatccaaagagtatatagcaggagcagtgtcaacatgacttcatcccatcacctaggtgttaaagatgccactggaatagatgtagaggcgggtg - -a -s simMouse_chr6.simMouse.chr6 434963 454 + 636262 tccgggtgccagctgacgaggctggggagataaacggagttgccacagaggcggtcgagttgggctcctgatgacagtacgttatgctccttcttgtttcctgtttctccttctctctaatattgcagtacggcacctcatctattgattatgataatcgaagcaaactaatcatggtttgctcaatctcgcaaaaagctgttatgattttaaatgattggaaggtatttatatcgtctagcatcataagtcctcaacaaatgtccaaataaagcttatttccctgcactgaggccagattatcaggtggcaaacattctagtggtaaatgtttgcttggcactgaggcttctccctcatcctaaccgtcatctgggtgcagatgatcacatcccctgatcccaatgctcatcagtacctcttgcaccaagcgttttaaggttgtatcaattag -s mr.mrrefChr5 289472 450 + 294540 tccgggtgccagctgacga--ctggggagataaacggagttgccacagaggcggtcgagttgggctcctgatgacagtacgttatgctccttcttgtttcctgtttctccttctctctaatattgcagtacggcacctcatctattgattatgataatcgaagcaaactaatcatggtttgctcaatctcgcaaaaagctgttatgattttaaatgattggaaggtatttatatcgtctagcatcataagtcctcaacaaatgtccaaataaagcttatttccctgcactgaggccagattatcaggtggcaaac-ttctagtggtaaatgtttgcttggcactgaggcttctccctcatcctaaccgtcatctgggtgcagatgatcacatcccctgatcccaatgctcatc-gtacctcttgcaccaagcgttttaaggttgtatcaattag -s simRat_chr6.simRat.chr6 202553 450 - 647215 tccaggcactggctgatga--ctggggagataaacggagtcaccgtagaagcagtcaggctggggtcgtaatgacagtacgttgtattacctcctgtttcctgtttttccacctctctaatattgcagtattgcccctcatctattgattgttttaattgaagcaaacaaatcatggtttgctctttattgccaaaagatgttatgattttaaataaccagaaggtaattatattatctagcatcataagtcctcagcaaatgtctgaagaagggttatttcctcacactaatgtcagattgttgggtgggaaat-ttctagtggtaaatgtttgcttggcactgaggcttcaccctcctcctaattgtcatcggggggtagatgatcgcatgccctgaccccaatgctcatc-gtacctcttgtgccgaccgttttaacgtcatatcaattag - -a -s simMouse_chr6.simMouse.chr6 435417 213 + 636262 gtatgtattatgcgcttcattatgtccttaataggggggatcatgtatgctgacgtctcaggacacagtcttctccaacatcagttcatggcacctggttcattttgtttggcaggctgatcagtgatgttgattgcatcgctgattgaatccttccaaaggctgataatgttacccttaatggatgggattctcttcagtcatgttcacacc -s mr.mrrefChr5 289922 205 + 294540 gtatgtattatgcgcttcattatgtccttaataggggggatcat-tatgc---cgtctcaggacacagtcttctccaacatcagttcatggcacctggttcattttgtttggcaggctgatcagtgatgttgattgcatcgctgattgaatccttccaaaggctgataatgttacccttaatgg----gattctcttcagtcatgttcacacc -s simRat_chr6.simRat.chr6 203017 205 - 647215 gtatctactatgcacttcattatgaccttaaagggtgggatcat-tatcc---catcccaggacgcagtcttttccaacaccaactcatggtacctggttcattttgcctggtgggctgatcagtgacttggatggggttgtcgatcgaatccttccaaagcctgataatgttaccctaaatga----gatgcacttcagtcatgttcacacc - -a -s simMouse_chr6.simMouse.chr6 435630 214 + 636262 atagcgtgtcaaatatagagaacatcattaaatgttcttgtgactcttgtctaatcaaggggtctgatgtattgggagatacatagaccacctctacacctacaaatgtaaatccatgagaatctgcatagcttggagcattgtccaggacctgaagtaccagtaggggcctacaattgttcctccctgagaatatgcaaacgtgaaggtagcc -s mr.mrrefChr5 290127 202 + 294540 atagcgtgtcaaatatagagaacatcattaaatgttct-gtgactcttgt--aatcaaggggtctgatgtattgggagatacatag------tctacacctacaaatgtaaatccatgagaatctgcatagct---agcattgtccaggacctgaagtaccagtaggggcctacaattgttcctccctgagaatatgcaaacgtgaaggtagcc -s simRat_chr6.simRat.chr6 203229 202 - 647215 atggcgtgtcaaacatagagaacatcattaaatgtcct-gtgactcttgg--aggcctgagcgctaatgtattagtcgatatgtag------tctacacctacaaacgtaaatccatgagaatctgcatagct---gacattgtccaggacctgaagtacctgtaggggcctatagtagttcccccccgagaatatgtgaatgtcaaggaaacc - -a -s simMouse_chr6.simMouse.chr6 435844 46 + 636262 ttgaaaccagtcccaggaaaaagtattagctgtcaaccaagcagtt -s mr.mrrefChr5 290329 25 + 294540 ttgaaaccag---------------------gtcaaccaagcagtt -s simRat_chr6.simRat.chr6 203432 25 - 647215 ttgaaaccag---------------------gacgactaagtggtt - -a -s simMouse_chr6.simMouse.chr6 435890 97 + 636262 tttttgtacgtgtaaatccgaagtactggagtgatttcatgcctatatttagactttagcctttaaatgtcaagggttggtagtctggcatactaaa -s mr.mrrefChr5 290354 90 + 294540 tttttgtacgtgtaaatccgaagtactggagtgatttcatgcctatatttag-------cctttaaatgtcaagggttggtagtctggcatactaaa -s simRat_chr6.simRat.chr6 203460 90 - 647215 ttattgtacatgtaaatccagagaattgtagcaatttcatgcctatatttag-------cctttaggtgttgagtgttggtagtatggcatactaaa - -a -s simMouse_chr6.simMouse.chr6 435987 44 + 636262 tattttttagcatcagatgaaccgaatgcttgcaatatagcgac -s mr.mrrefChr5 290444 43 + 294540 tattttttag-atcagatgaaccgaatgcttgcaatatagcgac -s simRat_chr6.simRat.chr6 203551 43 - 647215 tgttttttag-atcagttgagctgaattcttgcaatatagtgac - -a -s simMouse_chr6.simMouse.chr6 436031 7 + 636262 ataagct -s mr.mrrefChr5 290487 7 + 294540 ataagct -s simRat_chr6.simRat.chr6 203599 7 - 647215 gtaagct - -a -s simMouse_chr6.simMouse.chr6 436038 21 + 636262 gtagcttgccccacggtaaat -s mr.mrrefChr5 290494 21 + 294540 gtagcttgccccacggtaaat -s simRat_chr6.simRat.chr6 203608 21 - 647215 gtagttctccccccagtaact - -a -s simMouse_chr6.simMouse.chr6 436059 791 + 636262 ccagggtcttgcatttcctctttgctagttgaagttctcaagggggtcttctgcctccagaataatgagactcttccattgtcaaacacctgtatagggaagtaccctttttcctcaacaatgtcctctatggggttgctgaattcattgggggatcctagcccagaggacactcctccaccagtgactttggcatgtgcccgactccgtatattgggtgcaaggcacctcaatcctgaggattggtgtccatatgtcagctggtttttcaaagtagcttgcttccgataaatttccagacagtccttatttccattgcactcacaagactctgggccctctcctttttccctctatgagttgtcctccaagcccttgccctctcttggtttgtgtttgtgtgaactgcaaaacctttgtcgtaagtgctagatcgcaacagattcctgcctgggattctctattcctagaacttacatatttctgagaaaatgagaacttttaacaccggcagtccatttccctgacactgcaaactcacaaatgcctctcttgatcgtaacatttgacgtcagtccaccagttacagtgctcgaatcattaattagtgcgcaggccagggctgatgctgctctcagttgtgtgtgtgtttcgtcaggaaactccaccttcatttctagcaatgtcaacaccccgtgttgcttctgatatgccttgcatgtgttgatcgtgatgcttcttatggagcctatgtggtgtcactgacagagcGTCACTTTAATGACTGAGTG -s mr.mrrefChr5 290515 100 + 294540 ccagggtcttgcatttcctctttgctagttgaagttctcaagggggtcttctgcctccagaataatgagactcttccattgtc---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------cGTCACTTTAATGACTG---- -s simRat_chr6.simRat.chr6 203630 100 - 647215 ccaggggcttgcatttcttctttgctagttggagttctcaagggggtcttctgcctccaggacaatgagattcttccggtAGC---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CTTGGATCTAATGACAG---- - -a -s simMouse_chr6.simMouse.chr6 436850 23 + 636262 AGCTCTACACATATACTGGTGTA -s mr.mrrefChr5 290615 23 + 294540 AGCTCTACACATATACTGGTGTA -s simRat_chr6.simRat.chr6 443196 23 + 647215 AGCTCTACACAAATACTGGTGTC - -a -s simMouse_chr6.simMouse.chr6 436873 54 + 636262 GGCAGAGCATCACCTTAATGACTGACTTAGCTCTACACAAGTATGTTATGTAGT -s mr.mrrefChr5 290638 52 + 294540 GGCAGAGCATCACCTTAATGACTGACTTAGCTCTACACAAGTATGTTATG--GT -s simRat_chr6.simRat.chr6 443222 52 + 647215 GACATAGTGTCACTTTAATAACTTCCTGAGCTCCATGCAAATATGTTATG--GT - -a -s simMouse_chr6.simMouse.chr6 436927 30 + 636262 GTGAGAAGCATACCACATACTGTGGGCATC -s mr.mrrefChr5 290690 30 + 294540 GTGAGAAGCATACCACATACTGTGGGCATC -s simRat_chr6.simRat.chr6 443275 30 + 647215 ATGACAAATATACCACATACCGTGAACATA - -a -s simMouse_chr6.simMouse.chr6 436957 8 + 636262 CATGATAA -s mr.mrrefChr5 290720 8 + 294540 CATGATAA -s simRat_chr6.simRat.chr6 443307 8 + 647215 AACAATAA - -a -s simMouse_chr6.simMouse.chr6 436965 23 + 636262 GTTAAGGGTATGGCGGCAACTTG -s mr.mrrefChr5 290728 20 + 294540 GTTAAGGGTAT---GGCAACTTG -s simRat_chr6.simRat.chr6 443316 20 + 647215 GTTAAGGGTAT---GGCAACTTG - -a -s simMouse_chr6.simMouse.chr6 436988 181 + 636262 GGGCAGATAGCAACACCACCGTTCCATTTCATACTATATAAATGAGGGAAACAGGGGGTAACATGACGTCAAAATCTAGAAGTAGTTCTTTGTCTCTTCATCCCTATATTGGTAAGAGGTGCCTTCCATTGGGTTTTAAGCTGAATCTCTGTTATTCTTAGGATAACCTAAGGCTGGAGTA -s mr.mrrefChr5 290748 148 + 294540 GGGCAGATAGCAACACCACCGTTCCATTTCATACTATATAAATGAGGGAAACAGGGGGTAACATGACGTCAAAATCTAGAAGTAGTTCTTTGTCTCTTCATCCCTATATTGGTAAGAGGTGCCTTCCATTGGGTTTTAAGCTGAATCT--------------------------------- -s simRat_chr6.simRat.chr6 443337 148 + 647215 GGGCATATAGCAACACCACTGTTCCATTGCTCACTATGTGAATGAACACAACAGGGGGTAACACAACATCAAAATTTAGAAGTAGCTCTTTGTCACTTCATCCCTATAATGGTCAGAGGTGCCTTCTGTTGGGTTTTAAGCTGAATGT--------------------------------- - -a -s simMouse_chr6.simMouse.chr6 437169 60 + 636262 GACCCAGTTATATGGTATTTAGACGCTGGTAGTGCATTGCAGGGGATGAGTTCCTCATCC -s mr.mrrefChr5 290896 60 + 294540 GACCCAGTTATATGGTATTTAGACGCTGGTAGTGCATTGCAGGGGATGAGTTCCTCATCC -s simRat_chr6.simRat.chr6 445709 60 + 647215 GACTCAGTTATAAGGTTTTTGGATGCTGGTAGTGCATTGCAAGGGATGGATTCCTCACCC - -a -s simMouse_chr6.simMouse.chr6 437229 232 + 636262 CACACATATGTCCTGAGGGCCTGGTAGCTTGAGAGGTCAGTTTATTCAGGTGTCAGGTGAGGCTGCTATAATATGGCTCACGCTCTCAGAATCCAGGCGTTTAGTACTAGTAATGCACAAGAAACCATTAGTTCAACTTTCTTCAGTGTTCTTCTACACGAACTGTTTTCAGCAAGTGCTGCATCCATGGTTGGGTATTGGTTTTGAACTACATTTTGCCTTCCCCCAGTTC -s mr.mrrefChr5 290956 213 + 294540 CACACATATGTCCTGAGGGCCTGGTAGC---AGAGGT-AGTTTATTCAGG--------GAGGCTGCTATAATATGGCTCACGCTCTCAGAATCCAGGCGTTTAGTACTAGTAATGCACAAGAAACCATTAGTTCAACTTTCTTCAGTGTTCTTCTACACGAACTGTTTTCAGCAAGTGCTGCATCCATGGTTGGGTATTGGTTT-------CATTTTGCCTTCCCCCAGTTC -s simRat_chr6.simRat.chr6 445773 213 + 647215 CCCACATATGTCCTGGGGGCCTGATAGT---AGAGGT-AATTTATTCAGG--------GAGGCTGCCATAATATGACTCAAGCTCTCAGAAACCAGGAGTTTAGTACTAGTGATGCGCAAGAAACTGTTAGTTCAACTTTCTTCAGTGTTCTTCAACACGAATTGTTTTCAGCAACTGCTGCATCCATGGTTAGGTATTGAATT-------CATTTTGCCTTCCTCCTGATC - -a -s simMouse_chr6.simMouse.chr6 437461 42 + 636262 GGGGTTCGATTTTAGAGTATTGTCTATGAGAAATTCAGAACC -s mr.mrrefChr5 291169 42 + 294540 GGGGTTCGATTTTAGAGTATTGTCTATGAGAAATTCAGAACC -s simRat_chr6.simRat.chr6 446000 42 + 647215 AGCGTTTGATTCTTAAGAATTGTCTATGGGAAATTCAGGGCC - -a -s simMouse_chr6.simMouse.chr6 437503 234 + 636262 TCTAAGTAAAGTCCAGTGATGGCCACCATGCCACCTATAGTGTTTTGATCAGCCAACATGGGCAACAGGCATTTACTCACAGCCAGTCAATATGGAGAACTTGAGTGTGATCTCAGGAAGGTCTCGAACATCGAGGGATGACCAGTCCATGCCCTACCTTAGATCCTGTGTATACACAAGCTACCCTTCTTGCTAACAACACATTTCTTTGCTCGAAGAGTAGAAAGAAGTCCA -s mr.mrrefChr5 291211 234 + 294540 TCTAAGTAAAGTCCAGTGATGGCCACCATGCCACCTATAGTGTTTTGATCAGCCAACATGGGCAACAGGCATTTACTCACAGCCAGTCAATATGGAGAACTTGAGTGTGATCTCAGGAAGGTCTCGAACATCGAGGGATGACCAGTCCATGCCCTACCTTAGATCCTGTGTATACACAAGCTACCCTTCTTGCTAACAACACATTTCTTTGCTCGAAGAGTAGAAAGAAGTCCA -s simRat_chr6.simRat.chr6 446044 234 + 647215 TCTCAGTAAAGTCCAGTGACAGCCACCACAGCACCTCTAGTGTTTTGACCAGCCCGCATAGGCAATAGGCGTTTGTCCACAGACAGTTAATATGGGGAACTTGAGCATGATCTCAGCAAGGCCTAGGACATTGAGGGATGAACAGTCCATGCCCTGCCTTAGATCCCATGTATAAGCAAGCTACCCTTCTTGCTAACAACACATTTCTTTACTTGAAGAGTAGAAAGAAGTCCA - -a -s simMouse_chr6.simMouse.chr6 437737 17 + 636262 TAGATGTCTCTAAGCCT -s mr.mrrefChr5 291445 17 + 294540 TAGATGTCTCTAAGCCT -s simRat_chr6.simRat.chr6 446292 17 + 647215 TAGATGTCTCTAAGCCT - -a -s simMouse_chr6.simMouse.chr6 437754 29 + 636262 GCTACTGCATATAATAGGGTAACTATCTG -s mr.mrrefChr5 291462 28 + 294540 GCTACTGCATATAATAGGGTAA-TATCTG -s simRat_chr6.simRat.chr6 446311 28 + 647215 GATACTGCTTATACTAGAGTAA-TATCTG - -a -s simMouse_chr6.simMouse.chr6 437783 17 + 636262 TCTTTTGTACTATGGAG -s mr.mrrefChr5 291490 17 + 294540 TCTTTTGTACTATGGAG -s simRat_chr6.simRat.chr6 446340 17 + 647215 TCTTTTGTGCTATGGAG - -a -s simMouse_chr6.simMouse.chr6 437800 213 + 636262 TGCCCTCCTGCCATCAAGCAATGTATGGAAAGTCTGTGGTCTAAGTAGTCACTTGATAATTGGTTCTGTCAAAGTGATCATGCCATGGTTATATGAATCCCCATGGATATCCCTACAATTCACTCTGTTAGGAACCCTGATAACAATCCCTAGAATTCAGCTTCTATCCACAGACTGGTGACTATTCCCAGAGCTCATCTTTTATCCAGGCAC -s mr.mrrefChr5 291507 205 + 294540 TGCCCTCCTGCCATCAAGCAATGTATGG--------TGGTCTAAGTAGTCACTTGATAATTGGTTCTGTCAAAGTGATCATGCCATGGTTATATGAATCCCCATGGATATCCCTACAATTCACTCTGTTAGGAACCCTGATAACAATCCCTAGAATTCAGCTTCTATCCACAGACTGGTGACTATTCCCAGAGCTCATCTTTTATCCAGGCAC -s simRat_chr6.simRat.chr6 446358 205 + 647215 TGTCATTTTTCCTTCAAGCTATATGTAG--------CGGTCTAAGCATTCACTTGATAATGGGTTATGTCAGAGAGATTATGCCATGGTTATATGAATCCCCATGGATATCCCTACAATTCACTCTGTGAGGAACCCTGATAGTTGCCCCTAGATTTCATTTTCTATCCACAGACTGGTGACTATCTCCAGAGCTCATCTTTTATCCAGGCAC - -a -s simMouse_chr6.simMouse.chr6 438013 31 + 636262 ACCCTTGCTATGGTGAGTGAGAACTTTTTAC -s Anc0.Anc0refChr3 65560 13 + 222631 ------------------AAGAGCTTTCCCC -s Anc1.Anc1refChr6 96600 13 + 197743 ------------------AAGAGCTTTCCCC -s Anc2.Anc2refChr13 71236 13 + 96486 ------------------AAGAGCTTTCCCC -s mr.mrrefChr5 291712 31 + 294540 ACCCTTGCTATGGTGAGTGAGAACTTTTTAC -s simCow_chr6.simCow.chr6 428699 13 + 602619 ------------------AAGAGCTTTTCCC -s simDog_chr6.simDog.chr6 419428 13 + 593897 ------------------AAGAGCTCTCCCC -s simHuman_chr6.simHuman.chr6 422669 13 + 601863 ------------------AAGAGTTTTCCTC -s simRat_chr6.simRat.chr6 446570 31 + 647215 GCCGTTGCTGTTGTGGGTGAGAACTTTTTAC - -a -s simMouse_chr6.simMouse.chr6 438044 65 + 636262 CATGCCCATGGAGTCAAATTCTGAGGTGGAGCCTCTAACAGATCATGTGCCTATTGCCTCAAACA -s Anc0.Anc0refChr3 65573 27 + 222631 TGTTCCTATGGAATCAAATTTTGAGGT-------------------------------------- -s Anc1.Anc1refChr6 96613 27 + 197743 TGTTCCTATGGAATCAAATTTTGAGGT-------------------------------------- -s Anc2.Anc2refChr13 71250 27 + 96486 TGTTCCTATAGAATCAAACTTTGAGGT-------------------------------------- -s mr.mrrefChr5 291743 65 + 294540 CATGCCCATGGAGTCAAATTCTGAGGTGGAGCCTCTAACAGATCATGTGCCTATTGCCTCAAACA -s simCow_chr6.simCow.chr6 428713 27 + 602619 TATTCTCATTGAATCAAACTTTGAGGT-------------------------------------- -s simDog_chr6.simDog.chr6 419442 27 + 593897 TGTTCCTCTAAAATCAAACTTTGAGGT-------------------------------------- -s simHuman_chr6.simHuman.chr6 422682 27 + 601863 TGTTCCTATGGACTCAAATTGTGAGGT-------------------------------------- -s simRat_chr6.simRat.chr6 446601 65 + 647215 CATGCCTATGGAGTCGAATTCTGAGGTAGAGCCACTAATAGATTATGTGGCTATTGTCTCAAACA - -a -s simMouse_chr6.simMouse.chr6 438109 48 + 636262 CTAAATTTTGGGGTCGAGCAGAGAGGCTTTTTTCAGGAAGTAAAGAAG -s Anc0.Anc0refChr3 65600 7 + 222631 -----------------------------------------AGAGAGG -s Anc1.Anc1refChr6 96640 7 + 197743 -----------------------------------------AGAGAGG -s Anc2.Anc2refChr13 71277 7 + 96486 -----------------------------------------AGAGAGG -s mr.mrrefChr5 291808 48 + 294540 CTAAATTTTGGGGTCGAGCAGAGAGGCTTTTTTCAGGAAGTAGAGAAG -s simCow_chr6.simCow.chr6 428740 7 + 602619 -----------------------------------------AGAGAGG -s simDog_chr6.simDog.chr6 419469 7 + 593897 -----------------------------------------GGAGAAG -s simHuman_chr6.simHuman.chr6 422709 7 + 601863 -----------------------------------------AGAGGGG -s simRat_chr6.simRat.chr6 446667 48 + 647215 CTAAATCTTGTGGTAGTGAAGTGAGGCTCCTTTCAGGATGTAGAGAAA - -a -s simMouse_chr6.simMouse.chr6 438157 47 + 636262 CAGTTATGCTGTTGATTGTTCCAATCACTGACTTACCTCTTGTAATA -s Anc0.Anc0refChr3 65619 47 + 222631 CAGTTATGCTGTTTATTGTCCCAATCACTGCCCTACCTTCAGTCATG -s Anc1.Anc1refChr6 96659 47 + 197743 CAGTTATGCTGTTTATTGTCCCAATCACTGCCCTACCTTCAGTCATG -s Anc2.Anc2refChr13 71296 47 + 96486 CATTTATGCTGTTTATTGACCCAATCACTGCCATACTTTCAGTCATA -s mr.mrrefChr5 291868 47 + 294540 CAGTTATGCTGTTGATTGTTCCAATCACTGACCTACCTCTTGTTATG -s simCow_chr6.simCow.chr6 428758 43 + 602619 ----TATGCTGTTCATTGACCCAATCCCTACCGTACTTCCAGTAATA -s simDog_chr6.simDog.chr6 419488 47 + 593897 CATTTATGCTGTTTATTGACCCAATCACTGCCATACTTTTTGTCATA -s simHuman_chr6.simHuman.chr6 422728 47 + 601863 CAGTTATGGTGTTTATTGTCCCAATCACTGCCCTACCTTCAGTCAGG -s simRat_chr6.simRat.chr6 446727 47 + 647215 CAGTTATGCCATGGATTGTTCCAATCAATGACCTACCCCTTGTTATG - -a -s simMouse_chr6.simMouse.chr6 438204 56 + 636262 CCTCTTCTGAGATATTTTTATTCATTTTTCTTTTTCTGAGATGCTGAAAAATCCCC -s Anc0.Anc0refChr3 65670 46 + 222631 CTACTTCTGAGA---T-------ATTGTTCTTCTCCTGAGATACTGGGGAATCCCC -s Anc1.Anc1refChr6 96710 46 + 197743 CTACTTCTGAGA---T-------ATTGTTCTTCTCCTGAGATACTGGGGAATCCCC -s Anc2.Anc2refChr13 71347 46 + 96486 CTACTTCTAAGA---T-------ATTGTTCTTCTCCTGAGATACCAGGGAATCCCC -s mr.mrrefChr5 291915 52 + 294540 CTTCTTCTGAGA---TTTTATT-ATTTTTCTTCTCCTGAGATACTGGAAAATCCCC -s simCow_chr6.simCow.chr6 428805 45 + 602619 CTACTTCTCAG----T-------ATTGTCCTTCTCCTGAGGTATCAGGAAGTCCCC -s simDog_chr6.simDog.chr6 419539 46 + 593897 CTACTTCTAAAA---T-------AATATTCTTCTCCTGAGATACCAGGGAATCCCT -s simHuman_chr6.simHuman.chr6 422779 46 + 601863 CTAGTTCTGGGA---T-------ATTGTTCTTCTCCTGAGATACTGGGGAATCCCC -s simRat_chr6.simRat.chr6 446774 49 + 647215 CTCCTTCTGAGA---TTCCATT--TTTTTTTTCTCCTGAGATAACGGAAAATCC-- - -a -s simMouse_chr6.simMouse.chr6 438260 16 + 636262 TCCTCAACCCTCCAAT -s Anc0.Anc0refChr3 65718 14 + 222631 TCCTCCATCTTCC--T -s Anc1.Anc1refChr6 96758 14 + 197743 TCCTCCATCTTCC--T -s Anc2.Anc2refChr13 71395 14 + 96486 TCTTCCATCTTCC--T -s mr.mrrefChr5 291967 16 + 294540 TCCTCAACCCTCCAAT -s simCow_chr6.simCow.chr6 428852 14 + 602619 TGTTCTATATTCC--T -s simDog_chr6.simDog.chr6 419587 14 + 593897 TCTTCCATCCTCG--T -s simHuman_chr6.simHuman.chr6 422827 14 + 601863 TCCTCCATCTTCC--T -s simRat_chr6.simRat.chr6 446823 12 + 647215 ----CAACTCTCCAAT - -a -s simMouse_chr6.simMouse.chr6 438276 3 + 636262 GGC -s Anc0.Anc0refChr3 65732 1 + 222631 G-- -s Anc1.Anc1refChr6 96772 3 + 197743 GGC -s Anc2.Anc2refChr13 71409 1 + 96486 A-- -s mr.mrrefChr5 291983 3 + 294540 GGC -s simCow_chr6.simCow.chr6 428873 1 + 602619 A-- -s simDog_chr6.simDog.chr6 419601 1 + 593897 A-- -s simHuman_chr6.simHuman.chr6 422841 3 + 601863 GGC -s simRat_chr6.simRat.chr6 446835 3 + 647215 GGC - -a -s simMouse_chr6.simMouse.chr6 438279 5 + 636262 ATCTC -s Anc0.Anc0refChr3 65733 2 + 222631 ---TA -s Anc1.Anc1refChr6 96775 5 + 197743 ATCTA -s Anc2.Anc2refChr13 71410 2 + 96486 ---CA -s mr.mrrefChr5 291986 5 + 294540 ATCTC -s simCow_chr6.simCow.chr6 428874 2 + 602619 ---CA -s simDog_chr6.simDog.chr6 419602 2 + 593897 ---CA -s simHuman_chr6.simHuman.chr6 422845 5 + 601863 ATCTT -s simRat_chr6.simRat.chr6 446838 5 + 647215 ATCTG - -a -s simMouse_chr6.simMouse.chr6 438284 37 + 636262 TATGCTAACTGTTTGTCTTGAACATTCCTTCATACCT -s Anc0.Anc0refChr3 65735 37 + 222631 TGTTGTGTCCACTTGCCTTCAATGTTCTTTTATAACT -s Anc1.Anc1refChr6 96780 37 + 197743 TGTTGTGTCCACTTGCCTTCAATGTTCTTTTATAACT -s Anc2.Anc2refChr13 71412 37 + 96486 TATTGTGTCCACTTGCCTTCAATGTTCTTTTATAACT -s mr.mrrefChr5 291991 37 + 294540 TGTGGTAACTGTTTGTCTTGAACATTCTTTCATACCT -s simCow_chr6.simCow.chr6 428876 32 + 602619 TACAATGTCCGCTT-----CAATATTCTTTCATAACT -s simDog_chr6.simDog.chr6 419604 37 + 593897 TATTGTGTCCACTTGCCTTCAATGTCCTTTTGTAACT -s simHuman_chr6.simHuman.chr6 422863 37 + 601863 TGTTGTGCCCACTTGCCTTCAATGTTCTTTTATAACT -s simRat_chr6.simRat.chr6 446843 37 + 647215 TGTGGTAAGTGTTTGTCTTGAACATTCTTTCATACCT - -a -s simMouse_chr6.simMouse.chr6 438321 25 + 636262 CTGTTATAAGGAGTATGTTGACTGC -s Anc0.Anc0refChr3 65772 25 + 222631 CTGCAAGAACAAGCACTTGGTATGT -s Anc1.Anc1refChr6 96817 25 + 197743 CTGCAAGAACAAGCACTTGGTATGT -s Anc2.Anc2refChr13 71450 25 + 96486 CTGCAAGAACAAGCACTTGGTATGT -s mr.mrrefChr5 292028 25 + 294540 CTGTTATAAGAAGCATGTTGATTGC -s simCow_chr6.simCow.chr6 428909 25 + 602619 TTGCAGGAGAAAGCACTTGATATGT -s simDog_chr6.simDog.chr6 419642 20 + 593897 CTGCAACAACAAGCACTTTG----- -s simHuman_chr6.simHuman.chr6 422900 25 + 601863 GTGCAAGAATAAGCACTTGGGATAT -s simRat_chr6.simRat.chr6 446880 25 + 647215 CTGTGATAAGAAGCAGATTGATTGC - -a -s simMouse_chr6.simMouse.chr6 438346 49 + 636262 AGATATCGGTATTTGAAGGTAAATAGGCACCCACATTGTAGTCTGCAGG -s Anc0.Anc0refChr3 65800 49 + 222631 AGATTTTGGTATTTGAGGGAGAATATGCAGTCAGAATGCATTGAGCAGA -s Anc1.Anc1refChr6 96845 49 + 197743 AGATTTTGGTATTTGAGGGAGAATATGCAGTCAGAATGCATTGAGCAGA -s Anc2.Anc2refChr13 71478 49 + 96486 AGACTTTGGTATTTCAGGGAGAAAATGCAGTCAGAATGCATTGAGCAGA -s mr.mrrefChr5 292053 49 + 294540 AGATATCGGTATTTGAAGGTAAATAGGCACTCACAATGCAGTCTGCAGG -s simCow_chr6.simCow.chr6 428937 49 + 602619 TGACATTGATATATCAGAGAGGACATGCAGTCAGAATGCATCCTCCAGT -s simDog_chr6.simDog.chr6 419664 49 + 593897 AGACTTTGGTATTTCAGGAAAAGAATGCAGTCAGAATGCATTGAGCATA -s simHuman_chr6.simHuman.chr6 422928 49 + 601863 AGATTTTGGTATTTGGGGGAGAATAAGCAGTTGGGATGCATTTAGCAGA -s simRat_chr6.simRat.chr6 446905 48 + 647215 AGATCTCAGTATTTGAAGGC-AATAGGCACTCACAATGCAAACTGCAGG - -a -s simMouse_chr6.simMouse.chr6 438395 17 + 636262 GCCTTTTGGTCAGCTCC -s Anc0.Anc0refChr3 65859 16 + 222631 GACCTTGGGTCTGCCC- -s Anc1.Anc1refChr6 96904 17 + 197743 GACCTTGGGTCTGCCCC -s Anc2.Anc2refChr13 71538 16 + 96486 GACCTTGGGTCTGCCC- -s mr.mrrefChr5 292102 17 + 294540 GCCTTTGGGTCAGCCCC -s simCow_chr6.simCow.chr6 428997 3 + 602619 GAG-------------- -s simDog_chr6.simDog.chr6 419724 16 + 593897 GACCTTGGGTCTGCCC- -s simHuman_chr6.simHuman.chr6 422987 17 + 601863 GGCCTTGGGTATGCCCC -s simRat_chr6.simRat.chr6 446953 17 + 647215 GCTTTTGGGTTAGTCCC - -a -s simMouse_chr6.simMouse.chr6 438412 3 + 636262 TAT -s Anc0.Anc0refChr3 65875 3 + 222631 TAT -s Anc1.Anc1refChr6 96921 3 + 197743 TAT -s Anc2.Anc2refChr13 71554 3 + 96486 TAT -s mr.mrrefChr5 292119 3 + 294540 TAT -s simCow_chr6.simCow.chr6 417723 3 + 602619 TAT -s simDog_chr6.simDog.chr6 419740 3 + 593897 TAT -s simHuman_chr6.simHuman.chr6 423004 3 + 601863 TAT -s simRat_chr6.simRat.chr6 446970 3 + 647215 TAT - -a -s simMouse_chr6.simMouse.chr6 438415 11 + 636262 GTAAGTTGGTT -s Anc0.Anc0refChr3 65878 11 + 222631 GTTAGTTGATA -s Anc1.Anc1refChr6 96924 11 + 197743 GTTAGTTGATA -s Anc2.Anc2refChr13 71557 11 + 96486 GTTAATTGATA -s mr.mrrefChr5 292122 11 + 294540 GTAAGTTGGTA -s simCow_chr6.simCow.chr6 417730 11 + 602619 GTTTATCTATA -s simDog_chr6.simDog.chr6 419743 11 + 593897 ATTAATTGATA -s simHuman_chr6.simHuman.chr6 423007 11 + 601863 GTTGGTTGATA -s simRat_chr6.simRat.chr6 446973 10 + 647215 TTAAG-TGGTA - -a -s simMouse_chr6.simMouse.chr6 438426 54 + 636262 TGTAGGATTTATTTCTCTTGGCCAGACTACCCAGACTACCCTATACTGATATTT -s Anc0.Anc0refChr3 65890 44 + 222631 TGTAG-ATTTATATCTCTTGGGATG---------ACTACCCTACACCAATATTT -s Anc1.Anc1refChr6 96936 44 + 197743 TGTAG-ATTTATATCTCTTGGGATG---------ACTACCCTACACCAATATTT -s Anc2.Anc2refChr13 71569 44 + 96486 TGTAG-ATTTATAGCTCTTGGGATG---------ACTACCCTACACCAATATTT -s mr.mrrefChr5 292133 45 + 294540 TGTAGGATTTATTTCTCTTGGGCTG---------ACTACCCTATACTAATATTT -s simCow_chr6.simCow.chr6 417742 44 + 602619 TGTGG-GTTCATAGCTCTTGAGATG---------ACCACCCTATGCCAATATTT -s simDog_chr6.simDog.chr6 419755 44 + 593897 TGTAG-ATTTCTAGCTCTTGGGATG---------ACTACTCTACACCAATCTTT -s simHuman_chr6.simHuman.chr6 423019 44 + 601863 TGTAG-ATTTATATCTCTTGGGATG---------ACTACCCTACACAAATATCT -s simRat_chr6.simRat.chr6 446983 45 + 647215 TGTACAATTTATTTCTCTTGGGCTG---------ACTACCCTATACTAATATTG - -a -s simMouse_chr6.simMouse.chr6 438480 36 + 636262 TCCATAATACTTCTAAAATCATACTCCATCAATTTC -s Anc0.Anc0refChr3 65939 33 + 222631 CCC---ACACTTCCAAAATCATACTCCCTCAATTTG -s Anc1.Anc1refChr6 96985 33 + 197743 CCC---ACACTTCCAAAATCATACTCCCTCAATTTG -s Anc2.Anc2refChr13 71618 33 + 96486 CAC---ACACTTCCAAAATCATAATCCCTTAATTTG -s mr.mrrefChr5 292178 33 + 294540 TCC---ATACTTCTAAAATCATACTCCATCAATTTC -s simCow_chr6.simCow.chr6 417791 33 + 602619 CAC---ACACTTCCAAAATCATAATCCCTTAATTTG -s simDog_chr6.simDog.chr6 419804 24 + 593897 CAC---ACACTTCTAAAATCATA---------TTTG -s simHuman_chr6.simHuman.chr6 423068 33 + 601863 CCC---AGACTTCCAAAAGCATACTCCCTCAATTTA -s simRat_chr6.simRat.chr6 447028 26 + 647215 TCC---GTACTTGTAAAA-------CCATCAATTTG - -a -s simMouse_chr6.simMouse.chr6 438516 44 + 636262 AGTGGTTCTGTTGCCTATGTGTACTCAGGTTTGTAACCAGGTGT -s Anc0.Anc0refChr3 65972 31 + 222631 AATGGTTCTGTTGCCTATGTGTACACAGGTG------------- -s Anc1.Anc1refChr6 97018 31 + 197743 AATGGTTCTGTTGCCTATGTGTACACAGGTG------------- -s Anc2.Anc2refChr13 71651 31 + 96486 AATGGTTCTGTTGCCCATGTGTACACAGGTG------------- -s mr.mrrefChr5 292211 44 + 294540 AGTGGTTCTGTTGCCTATGTGTACTCAGGTACATAACTGGGTGT -s simCow_chr6.simCow.chr6 417828 31 + 602619 AGTGGTTCTGTTGCCCATATGTATACAAGTG------------- -s simDog_chr6.simDog.chr6 419828 31 + 593897 GATGGTTTCATTGCCCATGTGTACGCAGGTG------------- -s simHuman_chr6.simHuman.chr6 423101 31 + 601863 AATGATTCTGTTGCTTATGGGTACACAGGTG------------- -s simRat_chr6.simRat.chr6 447054 41 + 647215 AGTGGTTCTGTTGCCC---TACACCTGGATACAAACCTGAGTAT - -a -s simMouse_chr6.simMouse.chr6 438560 1 + 636262 G -s Anc0.Anc0refChr3 66003 1 + 222631 G -s Anc1.Anc1refChr6 97049 1 + 197743 G -s Anc2.Anc2refChr13 71683 1 + 96486 A -s mr.mrrefChr5 292255 1 + 294540 G -s simCow_chr6.simCow.chr6 417860 1 + 602619 A -s simDog_chr6.simDog.chr6 419860 1 + 593897 A -s simHuman_chr6.simHuman.chr6 423132 1 + 601863 G -s simRat_chr6.simRat.chr6 447095 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 438561 81 + 636262 GGTTGTTTAGCAGTATCCATTATGATAGGGGAGGGGCAAATTATGTATTTTGCGGTTTCGCAATTGTTACTACAGGCCTTT -s Anc0.Anc0refChr3 66004 81 + 222631 GGAGGTCTAGCAATTTGCTTTATGGTGGGAGGAGATAATATTCTTTTGCTGTTTCTTGCAGGAATGTTACTACGGGCCTAT -s Anc1.Anc1refChr6 97050 81 + 197743 GGAGGTCTAGCAATTTGCTTTATGGTGGGAGGAGATAATATTCTTTTGCTGTTTCTTGCAGGAATGTTACTACGGGCCTAT -s Anc2.Anc2refChr13 71684 81 + 96486 GGAGGTCTAGCAATTTGCTTTATGGTGAGAGGGGATCATGTTCTTTTGCTGTTTCTTGCAGGAATGCTAGTACGGGCCTAT -s mr.mrrefChr5 292256 81 + 294540 GGTTGTCTAGCAGTATCCTTTATGATAGGGGAAGGGAAAATTATGTATTTTGCGGTTTCAGAAATGTTACTACAGGCCTTT -s simCow_chr6.simCow.chr6 417861 81 + 602619 GGAGGTTTTCCAATTTGCTTTATGGTAAGAGATCATCATGCTCTTTTGCTGTTTTTAGCAGGAGTACTAATACAGGTCTAT -s simDog_chr6.simDog.chr6 419861 81 + 593897 GGAGGCCTAGCAATTGGCTTTATGGTGAGAGGGGATCACGTTCTTTTGCTGTTTCTTACAGGAATGCTAGTACGGGCTTAG -s simHuman_chr6.simHuman.chr6 423133 81 + 601863 GGAGGTCTAGCAATTTTCTATATGGTGGGAGCAGATAATATTCCATCGCTGCTCCCTGCAGGGATGTTACTATGGGCCTCT -s simRat_chr6.simRat.chr6 447099 81 + 647215 AGTTGTCTAGCAGTATCCTTCATGATACAGGAAGGGAAAATTATGTATTTTGCTGTTTTAGAAATGTTACTACAGGCCCTT - -a -s simMouse_chr6.simMouse.chr6 438642 157 + 636262 GCAGTGAATGAAGCCAGCCCAAAGATTGAAATGGGGTTACAACATTAAAGCAGTCATTATAGCAGTTGAATTAGAGGACAGGATTATTACAGTTGAGTTACAGGACAGGAGACATCAACAAACATTAATATCCAAAAAGTAGGCTGATTGATATTCT -s Anc0.Anc0refChr3 66085 82 + 222631 GCAGTTAATGGAGCCAGTCAAGGGATTCACATGAGATTATGATATTAAAGCAG------------TTGAA---------------------------TTATA----AGAAGACATCAACAAA--------------------------------GGT -s Anc1.Anc1refChr6 97131 85 + 197743 GCAGTTAATGGAGCCAGTCAAGGGATTCACATGAGATTATGATATTAAAGCAG------------TTGAA---------------------------TTATAG-ACAGAAGACATCAACAAA--------------------------------GGT -s Anc2.Anc2refChr13 71765 82 + 96486 GCAGTTAATGGAGCCAGTCAAGGGATTCACATGAGATCATGATATTAAAGCAG------------TTGAA---------------------------TTATA----AGAAGACATCAACAAA--------------------------------GGT -s mr.mrrefChr5 292337 126 + 294540 GCAGTGAATGAAGCCAGCCCAAAGATTGAAATGAGGTTACAACATTAAAGCAGTCATTATAGCAGTTGAA---------------------------TTACAGGACAGGAGACATCAACAAACATTAATATCCAAAAAGTAGG----TTGATATTGT -s simCow_chr6.simCow.chr6 417942 82 + 602619 ACAGTTAACAGAGCCAGTCAAGGAATTCACATGAGATCATGACATTAAAGCAG------------TTGAA---------------------------TTATA----AGACAATATCAACAAA--------------------------------AGT -s simDog_chr6.simDog.chr6 419942 79 + 593897 GCAGTTACTGGTGCCAGTCAAGGGATTCACATGTGATC-TTATATTAAAGCAG------------TTGAA---------------------------TCATA----GGCAGACAACTACCAA--------------------------------G-- -s simHuman_chr6.simHuman.chr6 423216 85 + 601863 GCACTTAATGGAGCCAATCAAGGCATCCACATGAGATTATGATATTAAAGCAG------------TTGAA---------------------------TTATAG-ACAGAAGACATCAACAAA--------------------------------GGT -s simRat_chr6.simRat.chr6 447180 126 + 647215 GCAGTGAATGAAACCATCCCAAAGAGTGAAATGAGGTTACAACATCAAAGCAGTCATTATTGCAGTTAAA---------------------------TTACAGGATGGGAGACATAAACAAACATTTCTATCCTAACAGTAGG----TTGTGATTGT - -a -s simMouse_chr6.simMouse.chr6 438799 48 + 636262 TTGTTTAAGCTAGCAACTTACTAAACTCACTAAATTGGATTGCATAAA -s Anc0.Anc0refChr3 66167 38 + 222631 CTGTTTGAGGTT----------CAACTTACCAAATTGGATTTCATAAA -s Anc1.Anc1refChr6 97216 38 + 197743 CTGTTTGAGGTT----------CAACTTACCAAATTGGATTTCATAAA -s Anc2.Anc2refChr13 71847 38 + 96486 CTGTTTGAGGTT----------CAACCTACCAAATTGGATTTCATAAA -s mr.mrrefChr5 292463 48 + 294540 TTGTTTAAGCTAGCAACTTACTAAACTTACTAAATTGGATTGCATAAA -s simCow_chr6.simCow.chr6 418033 38 + 602619 CTGTTTAAGGTT----------CAACCTACCAAATTGGATTTCATAAA -s simDog_chr6.simDog.chr6 420021 15 + 593897 -----TGGG----------------------------GGTTTCATAAA -s simHuman_chr6.simHuman.chr6 423301 38 + 601863 CTGTTTGAGATG----------CAATTTACCGAATTTGATTTCATAAA -s simRat_chr6.simRat.chr6 447306 48 + 647215 GTGTTTAAGCTAGCAACTTGCTAAACTTACTAAATTGGATTGCATAAA - -a -s simMouse_chr6.simMouse.chr6 438847 45 + 636262 ATAGGGACACCAGTCAGGTTTTTGGTGTGTTTCTCTCTACAACCA -s Anc0.Anc0refChr3 66221 29 + 222631 AGAGGGACACCAGTCAGGCTGTTGGTGCA---------------- -s Anc1.Anc1refChr6 97270 42 + 197743 AGAGGGACACCAGTCAGGCTGTTGGTGCA---CTCATAACAACTG -s Anc2.Anc2refChr13 71901 29 + 96486 AGAAGGACACCAGGCAGGCTGTTGGTGCA---------------- -s mr.mrrefChr5 292511 45 + 294540 ATAGGGACACCAGTCAGGTTTTTGGTGTGTTTCTCTCTACAACCA -s simCow_chr6.simCow.chr6 418088 29 + 602619 AGAAGGACACTAGGCAGGCTGTTGGTCCA---------------- -s simDog_chr6.simDog.chr6 420046 27 + 593897 AGAAGGATACCA--CAGGCTGTTGGTGCA---------------- -s simHuman_chr6.simHuman.chr6 423355 42 + 601863 ACAGGGGCAACAGTCAGGCAGTTGGTGCA---CTCATAACAACTG -s simRat_chr6.simRat.chr6 447354 44 + 647215 ATAAGGACACCAGTTAGGTTTTTAGTGTGTTTCTCCCC-CAACCA - -a -s simMouse_chr6.simMouse.chr6 438892 29 + 636262 TTTTGGGAGATTTTAACTCCAAGGAATCT -s Anc0.Anc0refChr3 66250 20 + 222631 ---------ACTTTAAGTCTTAATAATCT -s Anc1.Anc1refChr6 97312 29 + 197743 TTCTGGACAACTTTAAGTCTTAATAATCT -s Anc2.Anc2refChr13 71930 20 + 96486 ---------ACTTTAAGTTTTAATAATCT -s mr.mrrefChr5 292556 29 + 294540 TTCTGGGAGATTTTAACTCCAAGGAATCT -s simCow_chr6.simCow.chr6 418117 20 + 602619 ---------AGTTTAAATTTTAATAATCT -s simDog_chr6.simDog.chr6 420073 20 + 593897 ---------ACCTTAAGTTTGATTGATCT -s simHuman_chr6.simHuman.chr6 423398 29 + 601863 TTCTGGACAACTTTAAGTCTTAATAATCT -s simRat_chr6.simRat.chr6 447398 29 + 647215 TTCTGGGAGATTTTAACTCCAAGGGGTCT - -a -s simMouse_chr6.simMouse.chr6 438921 25 + 636262 GGGGGTGGAAAGCAGTCCACACCTG -s Anc0.Anc0refChr3 66270 25 + 222631 GGAGGTGGAAAGCAGGCCACACACG -s Anc1.Anc1refChr6 97341 25 + 197743 GGAGGTGGAAAGCAGGCCACACACG -s Anc2.Anc2refChr13 71950 25 + 96486 GGAGGTGGAAAGCAGGCCATAGACG -s mr.mrrefChr5 292585 25 + 294540 GGAGGTGGAAAGCAGTCCACACATG -s simCow_chr6.simCow.chr6 418142 25 + 602619 GGAGGTGCAGAGCAGGTAATAGACG -s simDog_chr6.simDog.chr6 420093 25 + 593897 GGAGATGGAAAGCAGGCCATAGGTG -s simHuman_chr6.simHuman.chr6 423427 25 + 601863 GGAGGTGGAAAGCAGGCCACACACG -s simRat_chr6.simRat.chr6 447427 25 + 647215 GGAGGTGGAAAGCAGTCCACACATA - -a -s simMouse_chr6.simMouse.chr6 438946 31 + 636262 TCTGGAAAAGCAAATCTATAAATATTGTGAG -s Anc0.Anc0refChr3 66296 31 + 222631 TCTAGAAATGAGAATGTGTAAATATTCTAAA -s Anc1.Anc1refChr6 97367 31 + 197743 TCTAGAAATGAGAATGTGTAAATATTCTAAA -s Anc2.Anc2refChr13 71976 31 + 96486 TCTAGAAATGAGAATGTGCAAATATTCTAAA -s mr.mrrefChr5 292610 31 + 294540 TCTGGAAAAGCAAATCTATAAATATTGTGAG -s simCow_chr6.simCow.chr6 418168 31 + 602619 TTTAGCAATGAAAATATGCGAATATTCTAAA -s simDog_chr6.simDog.chr6 420119 31 + 593897 CCTAGAATTGAGAAGGCGCAAATGTTCTACA -s simHuman_chr6.simHuman.chr6 423453 31 + 601863 TCTAGAAAGGAGAATGTGTAGATATTCTAAA -s simRat_chr6.simRat.chr6 447452 31 + 647215 CCTGGAAAAGCAAAGCTATACATGTTGTGAG - -a -s simMouse_chr6.simMouse.chr6 438977 25 + 636262 GTACGGGCATATCTCGCAACTTTTA -s Anc0.Anc0refChr3 66327 24 + 222631 CAATATCCATATCT-GCTACTTTCT -s Anc1.Anc1refChr6 97398 24 + 197743 CAATATCCATATCT-GCTACTTTCT -s Anc2.Anc2refChr13 72007 24 + 96486 CAATATCCATATCT-GGTACTTTCT -s mr.mrrefChr5 292641 25 + 294540 GTATGGGCATATCTCGCAACTTTCT -s simCow_chr6.simCow.chr6 418204 24 + 602619 CTATATCCATATCT-GGTACTTTCT -s simDog_chr6.simDog.chr6 420150 24 + 593897 TAATATCCACATCT-GGTACTTTCT -s simHuman_chr6.simHuman.chr6 423484 24 + 601863 CCATATCCATATCT-GCTACTTTCT -s simRat_chr6.simRat.chr6 447483 25 + 647215 GTATGGGCATATCTGGCAACTTTCT - -a -s simMouse_chr6.simMouse.chr6 439002 15 + 636262 AGTTGATGCCTAAAC -s Anc0.Anc0refChr3 66351 15 + 222631 AGTTGTTCCCAAAAC -s Anc1.Anc1refChr6 97422 15 + 197743 AGTTGTTCCCAAAAC -s Anc2.Anc2refChr13 72031 15 + 96486 AGTTGTTCCCAAAAC -s mr.mrrefChr5 292666 15 + 294540 AGTTGATGCCAAAAC -s simCow_chr6.simCow.chr6 418256 15 + 602619 AGTTGATGCCAACAA -s simDog_chr6.simDog.chr6 420174 15 + 593897 AATCGTTCCTAAAGC -s simHuman_chr6.simHuman.chr6 423508 15 + 601863 AGTTGCTACCAAAAC -s simRat_chr6.simRat.chr6 447508 15 + 647215 AGTTGACGCTAAAAG - -a -s simMouse_chr6.simMouse.chr6 439017 19 + 636262 GCTTAAACACACAGGCTAT -s Anc0.Anc0refChr3 66368 19 + 222631 GTGTAAACAGGCAAGCCAT -s Anc1.Anc1refChr6 97439 19 + 197743 GTGTAAACAGGCAAGCCAT -s Anc2.Anc2refChr13 72048 19 + 96486 GTGTAAACAGGTAAGCCAT -s mr.mrrefChr5 292681 19 + 294540 GCTTAAACACACAGGCTAT -s simCow_chr6.simCow.chr6 418273 19 + 602619 GTGTTACCAGGTCAGCCAT -s simDog_chr6.simDog.chr6 420191 19 + 593897 GTGTAAACAGGTAGGGCTT -s simHuman_chr6.simHuman.chr6 423525 19 + 601863 GGGCAAACAGGCAAGCCAT -s simRat_chr6.simRat.chr6 447523 19 + 647215 GCATAGACATACAGGCTAT - -a -s simMouse_chr6.simMouse.chr6 439036 15 + 636262 CAGCAGTCTATGGCG -s Anc0.Anc0refChr3 66387 15 + 222631 ATGCAGCCTATGGTA -s Anc1.Anc1refChr6 97458 15 + 197743 ATGCAGCCTATGGTA -s Anc2.Anc2refChr13 72067 15 + 96486 ATGCAGCCTATGGTA -s mr.mrrefChr5 292700 15 + 294540 CAGCAGTCTATGGCA -s simCow_chr6.simCow.chr6 418293 15 + 602619 ATCCAGCCTATGGTA -s simDog_chr6.simDog.chr6 420210 15 + 593897 AAGCAGCCAATGGTG -s simHuman_chr6.simHuman.chr6 423544 15 + 601863 GTACAACCTAGGGTA -s simRat_chr6.simRat.chr6 447542 15 + 647215 CCGCTGTCTATGGCA - -a -s simMouse_chr6.simMouse.chr6 439051 4 + 636262 TCTT -s Anc0.Anc0refChr3 66403 4 + 222631 TCTT -s Anc1.Anc1refChr6 97474 4 + 197743 TCTT -s Anc2.Anc2refChr13 72083 4 + 96486 TCTT -s mr.mrrefChr5 292715 4 + 294540 TCTT -s simCow_chr6.simCow.chr6 418309 4 + 602619 TCTT -s simDog_chr6.simDog.chr6 420226 4 + 593897 TCTT -s simHuman_chr6.simHuman.chr6 423560 4 + 601863 TGGT -s simRat_chr6.simRat.chr6 447557 4 + 647215 TCTT - -a -s simMouse_chr6.simMouse.chr6 439055 8 + 636262 GGCTCTAA -s Anc0.Anc0refChr3 66407 8 + 222631 GCATCTAA -s Anc1.Anc1refChr6 97478 8 + 197743 GCATCTAA -s Anc2.Anc2refChr13 72106 8 + 96486 GCATCTAA -s mr.mrrefChr5 292719 8 + 294540 GGCTCTAA -s simCow_chr6.simCow.chr6 418332 8 + 602619 GCATCTAA -s simDog_chr6.simDog.chr6 420249 8 + 593897 GCATCTAA -s simHuman_chr6.simHuman.chr6 423564 8 + 601863 GCATCTAA -s simRat_chr6.simRat.chr6 447561 8 + 647215 GGCTCTAA - -a -s simMouse_chr6.simMouse.chr6 439063 31 + 636262 TAAATCAGTTGAGCTATGATGGCCGTTACAT -s Anc0.Anc0refChr3 66415 31 + 222631 GAAACCAGATGAAGTACAATGGCCCTTGCAT -s Anc1.Anc1refChr6 97486 31 + 197743 GAAACCAGATGAAGTACAATGGCCCTTGCAT -s Anc2.Anc2refChr13 72114 31 + 96486 GAAACCAGATGAAGTACAACAGCCCTTGCAT -s mr.mrrefChr5 292727 31 + 294540 TAAATCAGTTGAAGTACAATGGCCGTTACAT -s simCow_chr6.simCow.chr6 418340 31 + 602619 GAAATCTGATGAATTACAACAGCCCCAGCAT -s simDog_chr6.simDog.chr6 420257 31 + 593897 GAATCTAGATGAAGTACAACAGCCCTTACAC -s simHuman_chr6.simHuman.chr6 423572 31 + 601863 GAAAACAGATGAAGTACAATGGCCCTTGCAT -s simRat_chr6.simRat.chr6 447577 31 + 647215 TAAATCAGTTGAAGTACAATGGCCATCACAT - -a -s simMouse_chr6.simMouse.chr6 439094 21 + 636262 AATGGCAATTACATAGACAGA -s Anc0.Anc0refChr3 66446 1 + 222631 T-------------------- -s Anc1.Anc1refChr6 97517 1 + 197743 T-------------------- -s Anc2.Anc2refChr13 72150 1 + 96486 T-------------------- -s mr.mrrefChr5 292758 21 + 294540 AATGGCAATTACATAGACAGA -s simCow_chr6.simCow.chr6 418376 1 + 602619 C-------------------- -s simDog_chr6.simDog.chr6 420293 1 + 593897 T-------------------- -s simHuman_chr6.simHuman.chr6 423603 1 + 601863 T-------------------- -s simRat_chr6.simRat.chr6 447608 21 + 647215 AATGGCAATTACATAGACACA - -a -s simMouse_chr6.simMouse.chr6 439115 167 + 636262 TCCCATGACACATAATGACTGGAGACTAAGTCTGCATAGAATAACTAGTGCATATAGCCATTTGATGAAATGATCCACTTGTGGCTAGCCTAGATAACTTTACTACTCTTTCAGTGCCATGCCAATATTGACCAGTTGGAAGGGTACCATTCAGTCCAGATTACCAT -s Anc0.Anc0refChr3 66447 108 + 222631 TTTTATGAGT-----------------------GTATAGACTAACTACTGCACATAGCCCTTTAAGGGAACGTGCCACTTGTGGTTAGCCCAAATAAGTTGACCTGTCTTTCCATTCTA---------------------AGGGAAC---------------ACCAC -s Anc1.Anc1refChr6 97518 108 + 197743 TTTTATGAGT-----------------------GTATAGACTAACTACTGCACATAGCCCTTTAAGGGAACGTGCCACTTGTGGTTAGCCCAAATAAGTTGACCTGTCTTTCCATTCTA---------------------AGGGAAC---------------ACCAC -s Anc2.Anc2refChr13 72151 108 + 96486 TTTCTTGTTT-----------------------TTATACACTAACTACTGCGCATAGCCCTTTAAGGGAACGTGCAACTTGTGGTTAGCCCAAATAAGTTTACTTGTCTTTCCATTCTA---------------------AGGAAAC---------------ACCAC -s mr.mrrefChr5 292779 167 + 294540 TTCTATGAGACATAATGACTGGAGACTAAGTCTGCATAGAATAACTAGTGCATATAGCCCTTTAATGAAATGATCCACTTGTGGCTAGCCTAGATAACTTGACCACTCTTTCAGTGCCATGCCAATATTGACCAGTTGGAAGGGTACCATTCAGTCCGGATTACCAT -s simCow_chr6.simCow.chr6 429000 108 + 602619 TTTCTAGTTT-----------------------TTATACACTAACTACTGCGCATAGACCTTCAAGGTCATGATCAACCTGGGATTAGCCTAAATAAGTTTACTTCTCTTTCGATTCTA---------------------AGGAAAC---------------ACCAC -s simDog_chr6.simDog.chr6 420294 82 + 593897 TGTCTTGT-------------------------------------------------CCCCTTAAGGGAACGTGCAACTTGTAGTCAGCCCAGAGAGGGCTACTTGTCTTTCCATTCTA---------------------AAGAAAC---------------ACCAC -s simHuman_chr6.simHuman.chr6 423604 94 + 601863 TTTTATGAGG-----------------------GTATAGACTACCTACCACACATAGCCCTTTA----------TCCCTTGTGGTTAGCCCAAATAAGTTGACC----TCTTTATTCTA---------------------AGGGAAC---------------ACCAC -s simRat_chr6.simRat.chr6 447629 167 + 647215 ATCTATGAGACATAATGACTGGAGACTAAGTTTGAATATAATAACTAGTGCATACAGTCCTTTAATGAGATGATCCACTTGTGGCTAGCCTGCATAACTTGACCACTCTTTTGGTGCCATGCCAATATTGACCAGTTGGAAGTGTACCATTCAGCCTGGATTACCAT - -a -s simMouse_chr6.simMouse.chr6 439282 44 + 636262 TCAGTTCAGACGAGTAGCTTACCATCACAACATAGATCATCTTT -s Anc0.Anc0refChr3 66556 42 + 222631 TCA--TCAGTTGAGTAGCTTACCATTATAACACATAACATCTTT -s Anc1.Anc1refChr6 97627 42 + 197743 TCA--TCAGTTGAGTAGCTTACCATTATAACACATAACATCTTT -s Anc2.Anc2refChr13 72260 42 + 96486 TCA--TCAGTTGAGTAGCTTACCATTATAACACATAACATCTTT -s mr.mrrefChr5 292946 44 + 294540 TCAGTTCAGACGAGTAGCTTACCATCACAACATAGATCATCTTT -s simCow_chr6.simCow.chr6 429109 42 + 602619 TCA--ATGGCTGACCAGCTTACCATTACAACATATAACATCTTT -s simDog_chr6.simDog.chr6 420377 42 + 593897 TCA--TCAGTCATGTAGCTTACCATTATTTCACATAACATCTTT -s simHuman_chr6.simHuman.chr6 423699 42 + 601863 TCA--TCAGGTGAGAAACTTACTTTTATAAGAGATAACATCTTT -s simRat_chr6.simRat.chr6 447796 44 + 647215 TCAGTTCAAAAGAGTAGCTTACCATCACAACATAGATCATCTTT - -a -s simMouse_chr6.simMouse.chr6 439326 73 + 636262 CTATTAACCCCACTAGTGCAATGGAGAGACACATATTCGCCTTAAGATCCTACGTTGTAGTACTTACTAAGAA -s Anc0.Anc0refChr3 66598 24 + 222631 CTATTAGTCCA-TTAGTCCAA------------------------------------------------AAAA -s Anc1.Anc1refChr6 97669 32 + 197743 CTATTAGTCCAGTTAGTCCAA-----------------------------------------CCTGCACAAAA -s Anc2.Anc2refChr13 72302 24 + 96486 CTATTGGTCTA-TTGGTCCAA------------------------------------------------AAAA -s mr.mrrefChr5 292990 73 + 294540 CTATTAACCCCACTAGTGCAATGGAGAGACACATATTCGCCTTAAGATCCTACGTTGTAGTACTTACTCAGAA -s simCow_chr6.simCow.chr6 429151 24 + 602619 CTATTGATCTA-TTGGTCCAT------------------------------------------------ATAA -s simDog_chr6.simDog.chr6 420419 24 + 593897 CTATTGGTCTA-TTGGTCCAA------------------------------------------------GAAA -s simHuman_chr6.simHuman.chr6 423742 32 + 601863 CTATTAGTCCAGTTAGTACAA-----------------------------------------CCTGCACAAAA -s simRat_chr6.simRat.chr6 447840 66 + 647215 CTATTAA-------AGTGCAGTGGAGGGACGTGTATTCGTCTTAAGATCCTATGTTGTACTACTTACTCAGAA - -a -s simMouse_chr6.simMouse.chr6 439399 24 + 636262 ACAAACTGAGACAGTGTAGTCTCT -s Anc0.Anc0refChr3 66622 23 + 222631 CCACACTGAAACTGTATGGTCTC- -s Anc1.Anc1refChr6 97701 23 + 197743 CCACACTGAAACTGTATGGTCTC- -s Anc2.Anc2refChr13 72326 23 + 96486 CTGCACTGAAACTGTATGGTCTC- -s mr.mrrefChr5 293063 23 + 294540 ACAAACTGAGACAGTATAGTCTC- -s simCow_chr6.simCow.chr6 429181 22 + 602619 CTCCACT-ACACTGTATAGTCTT- -s simDog_chr6.simDog.chr6 420443 23 + 593897 CTGCACTGAAACAGTATGGTCTC- -s simHuman_chr6.simHuman.chr6 423774 23 + 601863 CCATGCCGAAACTGTATGGTCTC- -s simRat_chr6.simRat.chr6 447906 23 + 647215 ACAATCTGAGACAGTATAGTCTC- - -a -s simMouse_chr6.simMouse.chr6 439423 5 + 636262 AGCGT -s mr.mrrefChr3 108058 5 + 181027 AGTGA -s simMouse_chr6.simMouse.chr6 558136 5 + 636262 AATGA -s simRat_chr6.simRat.chr6 33294 5 - 647215 AGTGG - -a -s simMouse_chr6.simMouse.chr6 439428 73 + 636262 GTAACACATGAGGTGGATAGGTTCCTTCTTGAGATGCCTGTGATTACTTGACAGCACATGAAGCGGGCAGGCT -s mr.mrrefChr3 108070 73 + 181027 ATAACACATGAGGTGGATAGGCTCCTTCTAGAGATGCCTGTGATTACTTGACAGCACATGAAGCGGGCAGGCT -s simMouse_chr6.simMouse.chr6 558148 73 + 636262 ATAACACATGAGGTGGATAGGCTCCTTCTAGAGATGCCTGTGATTACTTGACAGCACATGAAGCGGGCAGGCT -s simRat_chr6.simRat.chr6 33306 73 - 647215 ACAACACATGAGGTGGATAGGCTCCTTCTACAGATGCTGGTGATTATTTGGCAGCACATGAGGCAGGTGGGCT - -a -s simMouse_chr6.simMouse.chr6 439501 58 + 636262 CAGCAGCCAAGTAATGACCGCATGCACATGGCCGTGTTTGCCTTTGATGGGAGCTTGG -s mr.mrrefChr3 108143 58 + 181027 CAGCAGCCAAGTAATGACTGCATGCACATGGCCGTGTTTGCCTTTAATGGGAGCTTTG -s simMouse_chr6.simMouse.chr6 558222 58 + 636262 CAGCAGCCAAGTAATGACTACATGCACATGGCCGTGTTTGCCCTTAATGGGAGCTTTG -s simRat_chr6.simRat.chr6 33379 58 - 647215 CACCAGCCAAGTAATGACAGCACGCACATGGCCATGTTTTCCTTTAATGGGAGCTTTG - -a -s simMouse_chr6.simMouse.chr6 439559 67 + 636262 CACAAGGGGCACTTGAAATTTCGACAACATTAAGGAGGTCCGAAAAGAGTTTAAGAATGTAGGATAT -s mr.mrrefChr3 108201 67 + 181027 CACAAGGGGCACTTGAAATTTCGACAACATTAAGGAGGTCCGAAAAGAGTTTAAGAATGTAGGAAAC -s simMouse_chr6.simMouse.chr6 558280 67 + 636262 CACATGGGGCACTTGAAATTTCGACAACATTAAGGAGGTCCGAAAAGAGTTTAAGAATGTAGGAAAC -s simRat_chr6.simRat.chr6 33438 67 - 647215 CACAAGGAGCACTTGAAATCTTGACAACATTAAGGAGGTCCAAAAAGAGTTTAAGAATGTAGGAAAC - -a -s simMouse_chr6.simMouse.chr6 439626 45 + 636262 ACAGATCAGCCCATAAGAACCAACATGAATATACAGACTACACAT -s Anc0.Anc0refChr3 66653 31 + 222631 ACCCAGCAGCCCATAATAGCCAATATGGATG-------------- -s Anc1.Anc1refChr6 97732 45 + 197743 ACCCAGCAGCCCATAATAGCCAATATGGATGTACAATCTGAACCA -s Anc2.Anc2refChr13 72357 31 + 96486 ACCCAGCAGCCCATGATAGCCAATATGGATT-------------- -s mr.mrrefChr5 293094 45 + 294540 ACCGAGCAGCCCATAAGAACCAACATGAATGTACAAACTACACAA -s simCow_chr6.simCow.chr6 429211 31 + 602619 ACCTAGCAGTCCAGGATAGCCAATATTGCCT-------------- -s simDog_chr6.simDog.chr6 420474 31 + 593897 TCCCAGGACCCCATGATAGCCAATAGGGATT-------------- -s simHuman_chr6.simHuman.chr6 423805 45 + 601863 ACCAAGCAGCCCACAATAGCCGATATGGATGTACAATCTGAACCA -s simRat_chr6.simRat.chr6 447937 45 + 647215 ATCCAGCAGCCCATAACAACCAAAATGAATGTACAAAGTACACAA - -a -s simMouse_chr6.simMouse.chr6 439671 7 + 636262 GATTCCC -s Anc1.Anc1refChr6 97777 7 + 197743 GATGGCC -s mr.mrrefChr5 293139 7 + 294540 GATTCCC -s simHuman_chr6.simHuman.chr6 423866 7 + 601863 GATGGCC -s simRat_chr6.simRat.chr6 447982 7 + 647215 GATTCCT - -a -s simMouse_chr6.simMouse.chr6 439678 24 + 636262 ACATGACCAGCGGCATAGACAACA -s Anc0.Anc0refChr3 66684 3 + 222631 ---------------------ATA -s Anc1.Anc1refChr6 97784 24 + 197743 ACAGACCCAGCAGCCCAGCCAATA -s Anc2.Anc2refChr13 72388 3 + 96486 ---------------------GTA -s mr.mrrefChr5 293146 24 + 294540 ACATAACCAGCAGCACAGACAATA -s simCow_chr6.simCow.chr6 429242 3 + 602619 ---------------------GTA -s simDog_chr6.simDog.chr6 420505 3 + 593897 ---------------------GTG -s simHuman_chr6.simHuman.chr6 423879 24 + 601863 ACAGACCCAGCAGCCCAGCCAATA -s simRat_chr6.simRat.chr6 447989 23 + 647215 -TAAAACCAGCAGCACAGACAGTA - -a -s simMouse_chr6.simMouse.chr6 439702 37 + 636262 CAGGTTCCACCTGTTATAGTATCCTGGATATTAGGAA -s Anc0.Anc0refChr3 66687 24 + 222631 CAGGTTC-ACATGT---AGTATCCTGG---------A -s Anc1.Anc1refChr6 97808 28 + 197743 CAGGTTC-ACATGTTGTAGTATCCTGGT--------A -s Anc2.Anc2refChr13 72391 24 + 96486 CGGGTTA-ACATGT---GGTATCCTGG---------A -s mr.mrrefChr5 293170 37 + 294540 CAGGTTCCACCTGTTATAGTATCCTGGTTATTAGGAA -s simCow_chr6.simCow.chr6 429245 22 + 602619 AGG--TC-ATATTT---GGGGTCCTGG---------A -s simDog_chr6.simDog.chr6 420508 22 + 593897 CGGGTTA-ACATGT---GGTATCATG----------- -s simHuman_chr6.simHuman.chr6 423910 21 + 601863 CAGGTTC-ACATGTTGTA------CGGT--------- -s simRat_chr6.simRat.chr6 448012 37 + 647215 CAGGTTCCACCTGCTGCAGTGTGCTGGTTATTTGGAA - -a -s simMouse_chr6.simMouse.chr6 439739 29 + 636262 CTAGATGAAATGCCCAGGGGATATATGGT -s Anc0.Anc0refChr3 66711 29 + 222631 CTGAATCAAATGCCCTGGGTATGTAAGGC -s Anc1.Anc1refChr6 97836 29 + 197743 CTGAATCAAATGCCCTGGGTATGTAAGGC -s Anc2.Anc2refChr13 72415 29 + 96486 CTGAATCAAATGCCCTGGGTATGTAAGGC -s mr.mrrefChr5 293207 29 + 294540 CTAGATGAAATGCCCAGGGGATATATGGT -s simCow_chr6.simCow.chr6 429274 29 + 602619 CTGAATCAAATGCCCTGGTTGTATATGCC -s simDog_chr6.simDog.chr6 420530 29 + 593897 CTGAATCAAATGCCCTGGGTATGTAAGGC -s simHuman_chr6.simHuman.chr6 423931 13 + 601863 ------------CCCTGGATATTGA---- -s simRat_chr6.simRat.chr6 448049 29 + 647215 CTAGATGAAATGCCCAGGGGATGAATGGT - -a -s simMouse_chr6.simMouse.chr6 439768 7 + 636262 ATCTTAG -s Anc0.Anc0refChr3 66740 7 + 222631 TTCTTAG -s Anc1.Anc1refChr6 97865 7 + 197743 TTCTTAG -s Anc2.Anc2refChr13 72444 7 + 96486 TTCTTAA -s mr.mrrefChr5 293236 7 + 294540 ATCTTAG -s simCow_chr6.simCow.chr6 429319 7 + 602619 TTCTTAA -s simDog_chr6.simDog.chr6 420559 7 + 593897 TTCTTAA -s simHuman_chr6.simHuman.chr6 423944 2 + 601863 -----AG -s simRat_chr6.simRat.chr6 448078 7 + 647215 TTCTTAG - -a -s simMouse_chr6.simMouse.chr6 439775 13 + 636262 CAAACAACAATAC -s Anc0.Anc0refChr3 66747 13 + 222631 CTAACAACAATAC -s Anc1.Anc1refChr6 97872 13 + 197743 CTAACAACAATAC -s Anc2.Anc2refChr13 72451 13 + 96486 CTAACAACAAAAC -s mr.mrrefChr5 293243 13 + 294540 CAAACAACAATAC -s simCow_chr6.simCow.chr6 429326 13 + 602619 CTAACAACAACAC -s simDog_chr6.simDog.chr6 420567 13 + 593897 CTAACAACAAAAA -s simHuman_chr6.simHuman.chr6 423946 13 + 601863 TCCACAACAATAC -s simRat_chr6.simRat.chr6 448085 13 + 647215 CGAACAACAATAC - -a -s simMouse_chr6.simMouse.chr6 439788 53 + 636262 TACAAAGGCTACAAGAAGTGGGTTGCCCAATACTAAAATATCCAGATTTGTTT -s Anc0.Anc0refChr3 66761 53 + 222631 TGCACAGGCTACAAGAAATGGATTGTCCAATGTTAAAACAGCTAGGGTTGTTT -s Anc1.Anc1refChr6 97886 53 + 197743 TGCACAGGCTACAAGAAATGGATTGTCCAATGTTAAAACAGCTAGGGTTGTTT -s Anc2.Anc2refChr13 72465 53 + 96486 TGCACAGACTACAGGAAAAGGCTTGTCCAATGTTAAAACAGGTAGGGTTGTTT -s mr.mrrefChr5 293256 53 + 294540 TACAAAGGCTACAAGAAGTGGATTGCCCAATGCTAAAACATCCAGGTTTGTTT -s simCow_chr6.simCow.chr6 429340 52 + 602619 TACACACACTACGGGAAACGGCTTATCCTAAGTTAGAACAGTTA-GGTTGTTT -s simDog_chr6.simDog.chr6 420581 53 + 593897 TGCACAGACTACAGGGAAAGACTTGTCCAATCTTAAAACAGGTAGATTTGTTT -s simHuman_chr6.simHuman.chr6 423960 53 + 601863 TTCGCAGGCTCCAAGAGATGGATTGTCCAGTGTTATAGCAGCTAGGGTTGTTT -s simRat_chr6.simRat.chr6 448098 53 + 647215 TACAAAGGTTACCAGAAGTGGATTGCCTAATGCTAAAACATTCATGTTTGTTT - -a -s simMouse_chr6.simMouse.chr6 439841 13 + 636262 TATCTGTTCTCCC -s Anc0.Anc0refChr3 66814 13 + 222631 CATTTTTTCCCCC -s Anc1.Anc1refChr6 97939 13 + 197743 CATTTTTTCCCCC -s Anc2.Anc2refChr13 72518 13 + 96486 CATTTTTTCCCCC -s mr.mrrefChr5 293309 13 + 294540 CATCTGTTCTCCC -s simCow_chr6.simCow.chr6 429392 12 + 602619 CATTGTTTCCCC- -s simDog_chr6.simDog.chr6 420634 13 + 593897 CATTTTTGCCCCC -s simHuman_chr6.simHuman.chr6 424016 13 + 601863 CATTACTTCCCCC -s simRat_chr6.simRat.chr6 448151 13 + 647215 CATCTGTTCTCTC - -a -s simMouse_chr6.simMouse.chr6 439854 1 + 636262 T -s Anc0.Anc0refChr3 66827 1 + 222631 A -s Anc1.Anc1refChr6 97952 1 + 197743 A -s Anc2.Anc2refChr13 72531 1 + 96486 A -s mr.mrrefChr5 293322 1 + 294540 T -s simCow_chr6.simCow.chr6 562900 1 - 602619 A -s simCow_chr6.simCow.chr6 429405 1 + 602619 A -s simHuman_chr6.simHuman.chr6 424029 1 + 601863 A -s simRat_chr6.simRat.chr6 448164 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 439855 20 + 636262 ATTTGAGTCAAGTCCATGAA -s Anc0.Anc0refChr3 66828 20 + 222631 ATTTGTATCAAGTTCACACC -s Anc1.Anc1refChr6 97953 20 + 197743 ATTTGTATCAAGTTCACACC -s Anc2.Anc2refChr13 72613 20 + 96486 ATTTGTATCAATTTCACACC -s mr.mrrefChr5 293323 20 + 294540 ATTTGAATCAAGTCCACAAA -s simCow_chr6.simCow.chr6 429487 20 + 602619 GTTTGTATCAGATTCACACC -s simDog_chr6.simDog.chr6 420648 19 + 593897 ATTGGTATCAATTTCCCAT- -s simHuman_chr6.simHuman.chr6 424030 20 + 601863 ATTTGTATCAAGTTCACACC -s simRat_chr6.simRat.chr6 448165 20 + 647215 ATTTGAATCAAGCCCACAAA - -a -s simMouse_chr6.simMouse.chr6 439875 51 + 636262 AGGAAAAATGGAAAGGGGAGACACTAACTTTAACATAGAGACTATTACACT -s Anc0.Anc0refChr3 66848 49 + 222631 T--AAATAGCAAAAGAGGAGAAACTAACTCTACTGAAAAGACTATTATCCT -s Anc1.Anc1refChr6 97973 49 + 197743 T--AAATAGCAAAAGAGGAGAAACTAACTCTACTGAAAAGACTATTATCCT -s Anc2.Anc2refChr13 72633 49 + 96486 T--AAATAGCAAAAGAGGAGAAACTAGCTCTACTGGAAAGACAATTGTCTT -s mr.mrrefChr5 293343 51 + 294540 AGGAAAAATGGAAAGAGAAGACACTAACTTTAACGAAAAGACTATTACACT -s simCow_chr6.simCow.chr6 429514 49 + 602619 T--AAGTAGCAACAGAGGGGAAATTATCACTACTAGATAGACAATTGTCTC -s simDog_chr6.simDog.chr6 420667 47 + 593897 ----GAAGGAAAAAATGGAGAAACTAGCTCTGCTGGAAAGACAATTGTTTT -s simHuman_chr6.simHuman.chr6 424050 49 + 601863 C--AAATAGCAATAGAAGAGTGACTAATTCTACTGAAAAGACTAATATCCT -s simRat_chr6.simRat.chr6 448185 51 + 647215 AGGAAAAATGGAAAGAGAAGACACTAACTTTAAGGAAAGGACTATTGCACT - -a -s simMouse_chr6.simMouse.chr6 439926 21 + 636262 GTGCTAGTTTATGTGAAGGAC -s Anc0.Anc0refChr3 66904 21 + 222631 TTGCCAGTTTATGTGAAGCAC -s Anc1.Anc1refChr6 98029 21 + 197743 TTGCCAGTTTATGTGAAGCAC -s Anc2.Anc2refChr13 72689 21 + 96486 TTGCCAGTTGATGTGAAGCAC -s mr.mrrefChr5 293397 21 + 294540 GTGCCAGTTTATGTGAAGGAC -s simCow_chr6.simCow.chr6 429570 21 + 602619 TTGCCAGTTGATGTGAAACAC -s simDog_chr6.simDog.chr6 420720 9 + 593897 ------------GTGAAGCAC -s simHuman_chr6.simHuman.chr6 424106 21 + 601863 TTGCCAGTTTACATGAGGTAC -s simRat_chr6.simRat.chr6 448239 21 + 647215 GTGCCAGTTTATGTGAAGGAC - -a -s simMouse_chr6.simMouse.chr6 439947 36 + 636262 GCTTTGTATAAGCTATTGGAGATACTACTCTGTTCC -s Anc0.Anc0refChr3 66925 36 + 222631 AGTTTGTATTGGCTATTGGACATGTTACTCCGTTTT -s Anc1.Anc1refChr6 98050 36 + 197743 AGTTTGTATTGGCTATTGGACATGTTACTCCGTTTT -s Anc2.Anc2refChr13 72710 36 + 96486 AGTTCGTATTGGCTATTGGACATGTTACTCCGTTTT -s mr.mrrefChr5 293418 36 + 294540 ACTTTGTATAAGCTATTGGAGATACTACTCTGTTCC -s simCow_chr6.simCow.chr6 429593 36 + 602619 AGTTCATATAGGCTTTTGGGCACGTTACTCCCTTTT -s simDog_chr6.simDog.chr6 420729 36 + 593897 AGTTCGTATTGGCTATTGGAGTTGTTATTCTGTTTT -s simHuman_chr6.simHuman.chr6 424127 36 + 601863 AGTTTGCATTGACTATTGGACATGTTACTCCATTTT -s simRat_chr6.simRat.chr6 448260 36 + 647215 ACTTTGTATCAGTTATTGGAGATACTATTCTGTTCC - -a -s simMouse_chr6.simMouse.chr6 439983 6 + 636262 ACATTT -s Anc0.Anc0refChr3 66963 6 + 222631 ACATTT -s Anc1.Anc1refChr6 98088 6 + 197743 ACATTT -s Anc2.Anc2refChr13 72748 6 + 96486 ATATTG -s mr.mrrefChr5 293454 6 + 294540 ACATTT -s simCow_chr6.simCow.chr6 429631 6 + 602619 ATATTG -s simDog_chr6.simDog.chr6 420767 6 + 593897 ATGGTG -s simHuman_chr6.simHuman.chr6 424165 6 + 601863 ACATTT -s simRat_chr6.simRat.chr6 448296 6 + 647215 TCATTG - -a -s simMouse_chr6.simMouse.chr6 439989 21 + 636262 TCATGACAGCACAGGGTCCCA -s Anc0.Anc0refChr3 66969 21 + 222631 TCATTACAGCACAGCATCCCA -s Anc1.Anc1refChr6 98094 21 + 197743 TCATTACAGCACAGCATCCCA -s Anc2.Anc2refChr13 72754 21 + 96486 TGATTACAGCACCGCATCCCA -s mr.mrrefChr5 293460 21 + 294540 TCATGACAGCACAGGGTCCCA -s simCow_chr6.simCow.chr6 429637 21 + 602619 TGATTGCAACACTGCATCCCA -s simDog_chr6.simDog.chr6 420773 21 + 593897 TGATTACAGCACCACATCCTA -s simHuman_chr6.simHuman.chr6 424178 21 + 601863 TCATTACAGCACAGCATCCCA -s simRat_chr6.simRat.chr6 448302 21 + 647215 TCATGACACCAAAGGCCCCCA - -a -s simMouse_chr6.simMouse.chr6 440010 105 + 636262 ACTCACCTCTTCATTCTCCTCTTTATTTACTAGCGCATATACATGTTTCGCGAAGCTGTTAATTTGTTGTACTTGTAGTACTCATATTGTTACTTTGCCTCATGT -s Anc0.Anc0refChr3 66990 100 + 222631 ACCCC-A---TCAATCTGTTCTTTATTCATGAATGCACATATGT-TTTGGGGAAGAGACTGATATTTTATATCTGCAGTACTGAAGTTGTTTCTTTGTTTCACAT -s Anc1.Anc1refChr6 98115 101 + 197743 ACCCCCA---TCAATCTGTTCTTTATTCATGAATGCACATATGT-TTTGGGGAAGAGACTGATATTTTATATCTGCAGTACTGAAGTTGTTTCTTTGTTTCACAT -s Anc2.Anc2refChr13 72775 100 + 96486 ACCCC-A---TCAATCTGTTCTTTATTCATGAATGCACATATGT-TTTGGGAAAAAGACTAATATTTTATATCTGTAGCACTGAAGTTGTTTCTTTGTTTCACAT -s mr.mrrefChr5 293481 105 + 294540 ACTCACCTCTTCATTCTCCTCTTTATTTATGAATGCATATATGTGTTTCGCGAAGCTGTTGATTTGTTGTACTTGCAGTACTCATATTGTTACTTTGCCTCATGT -s simCow_chr6.simCow.chr6 429671 100 + 602619 ACCTT-G---TCAATCTGCTCTTTATTTATGAATGCAAATACGT-TTTGGGAAAAAGACTAATTTTTTATATTTGTGGCACTGAAGTTGTTTCTTTGTTTCACCT -s simDog_chr6.simDog.chr6 420794 88 + 593897 ACCCC-A---TCAATCTGTCCTTTATTCATGAATGCACATATC------------AGACCAATATTTTATATCTGTAGCACTGAAG-TAATTCTTCATTTTACAT -s simHuman_chr6.simHuman.chr6 424199 99 + 601863 ACCCCCA-----GATCTGTTCTTTATTCATGAATGCACATATGT-CTTGGGGAAGAGACTGATCTTTTATATCTTCACTACTGACGCTGTTTCTTTGTTTCACAT -s simRat_chr6.simRat.chr6 448323 104 + 647215 ACTCACTTCTTCATTCTCCTCTTCATTTGTGAATGCATATATGTGTTTCAAGAAGCTGTTGCTTTGCTGTACTTGCAGCACTCATATTGTTA-TTTGCCACATGA - -a -s simMouse_chr6.simMouse.chr6 440115 40 + 636262 TTTAATTGTATGTGTTAGTTTGATATTTAAACTGTTGAAT -s Anc0.Anc0refChr3 67091 40 + 222631 TTTAGTGGTCTGGGTTAGTCTGATACTCAAACTCTTAAAT -s Anc1.Anc1refChr6 98217 40 + 197743 TTTAGTGGTCTGGGTTAGTCTGATACTCAAACTCTTAAAT -s Anc2.Anc2refChr13 72876 40 + 96486 TTTAGTGGTCTGGGTCAGTCTGATATTCAAACTCTTAAGT -s mr.mrrefChr5 293586 40 + 294540 TTTAATTGTATGTGTTAGTTTGATACTTAAACTGTTGAAT -s simCow_chr6.simCow.chr6 429772 40 + 602619 TTTAGTGGTCTGGGTCAGTCTGATATTCAAACTCTTAAGT -s simDog_chr6.simDog.chr6 420883 31 + 593897 TTTAGTGGTCTGGGACAGTCTAATATTTAAA--------- -s simHuman_chr6.simHuman.chr6 424299 40 + 601863 TTTAGTGGTCTGGGTTAGTCTGAAACTCAAACTCTTAAAT -s simRat_chr6.simRat.chr6 448427 40 + 647215 ATTAATTGTATGTTTAAGTTTAATACTTAACCTGTTGAAG - -a -s simMouse_chr6.simMouse.chr6 440155 18 + 636262 GTTATGATCATAAACTTA -s Anc0.Anc0refChr3 67131 5 + 222631 T-------------CTTA -s Anc1.Anc1refChr6 98257 5 + 197743 T-------------CTTA -s Anc2.Anc2refChr13 72916 5 + 96486 T-------------CTTA -s mr.mrrefChr5 293626 18 + 294540 GTTATGATCATAAACTTA -s simCow_chr6.simCow.chr6 429825 5 + 602619 T-------------CTTA -s simDog_chr6.simDog.chr6 420914 5 + 593897 T-------------CGTA -s simHuman_chr6.simHuman.chr6 424339 5 + 601863 T-------------CTTA -s simRat_chr6.simRat.chr6 448467 18 + 647215 GTTCTGATGCTTAACTGA - -a -s simMouse_chr6.simMouse.chr6 440173 36 + 636262 ACTGTTACCTCTCACTAGATGGGATCATATGGTCTA -s Anc0.Anc0refChr3 67136 36 + 222631 AATGTTACCTTTCTTAAGAAGGGATCTTGTGGTGAT -s Anc1.Anc1refChr6 98262 36 + 197743 AATGTTACCTTTCTTAAGAAGGGATCTTGTGGTGAT -s Anc2.Anc2refChr13 73007 36 + 96486 AGGAGTACCTTTCTTAAGAAGGGATCTCGTGATCAT -s mr.mrrefChr5 293644 36 + 294540 ACTGTTACCTCTCTCAAGAAGGGATCATATGGTGAA -s simCow_chr6.simCow.chr6 429974 36 + 602619 GGTAGTACCTTTCTCAAGAGGGGATCTGGTGATCAT -s simDog_chr6.simDog.chr6 421130 28 + 593897 AGGAGTACCTGTTTTAAGAAGGGATCTC-------- -s simHuman_chr6.simHuman.chr6 424344 36 + 601863 AATGTTACTTTTCTGAAGAAGGGATCTTGTGGTGAT -s simRat_chr6.simRat.chr6 448485 36 + 647215 TCTGTTACCTCTCTCAAGAAGGGATCATATGGTGAC - -a -s simMouse_chr6.simMouse.chr6 440209 65 + 636262 GTTTTCAATTTCAGGCTACATTTAGGTTGGTTCAGCAGCTCCAATTGAGGTGTTTCCCGAGTGTC -s Anc0.Anc0refChr3 67174 65 + 222631 GTTTTCAATTTCAGTCTACTTCTAAGTTGAGTCTGCAGCTCCAATTTAGATGTCTGCCAAGCATC -s Anc1.Anc1refChr6 98300 65 + 197743 GTTTTCAATTTCAGTCTACTTCTAAGTTGAGTCTGCAGCTCCAATTTAGATGTCTGCCAAGCATC -s Anc2.Anc2refChr13 73045 65 + 96486 GATTTCAACTTCAGTCTACTTCTAAGTGGAGTCTGCTGCACCAATTTAAATGTCTGCCAAGCATC -s mr.mrrefChr5 293680 65 + 294540 GTTTTCAATTTCAGGCTACATCTAGGTTGGTTCAGCAGCTCCAATTGAGGTGTTTCCCAAGTATC -s simCow_chr6.simCow.chr6 430012 62 + 602619 GATTTCAACCTCAATCTACT---AAGTGGAGTCTGTCGTGCCAATTTAAATGTTTGCCAAGAGTC -s simDog_chr6.simDog.chr6 421158 58 + 593897 ------AACTTCAGTCTACCTCTAACTGGAGTCTGCTCCACAAATTTA-ATGTCTGCCAGGCATC -s simHuman_chr6.simHuman.chr6 424382 65 + 601863 ATTTTAAATTTCAGCCTACTTCGAAGTTGTGTTTGCAGCTCCAATTCAGATGTCGGTCAAGCATC -s simRat_chr6.simRat.chr6 448521 61 + 647215 GTCTTCAATTTCAGGCTCCATCTAGGT-GGTTCCGCAGCTCCAATTGAG---TTTCCCAAGTATC - -a -s simMouse_chr6.simMouse.chr6 440274 20 + 636262 AGGTGGTGCTTTTGACAAAG -s Anc0.Anc0refChr3 67242 20 + 222631 GGTTAGTGTTTTTGACTAGG -s Anc1.Anc1refChr6 98368 20 + 197743 GGTTAGTGTTTTTGACTAGG -s Anc2.Anc2refChr13 73113 20 + 96486 GGTTAGTGTTATTGACTAGG -s mr.mrrefChr5 293745 20 + 294540 AGGTGGTGCTTTTGACAAAG -s simCow_chr6.simCow.chr6 430077 20 + 602619 GATTAGTGTCATTAACTAGG -s simDog_chr6.simDog.chr6 421219 20 + 593897 GGTTAGTGTTATTGGCTAGG -s simHuman_chr6.simHuman.chr6 424450 20 + 601863 GGTTAGTGTTTATGACTAGG -s simRat_chr6.simRat.chr6 448582 20 + 647215 TGGCGGTGCTTTTGACACAG - -a -s simMouse_chr6.simMouse.chr6 440294 25 + 636262 GATATGATACAGATGTCCTGCCAGT -s Anc0.Anc0refChr3 67273 25 + 222631 GATAAGGTGCTAATATGCTGCCAGT -s Anc1.Anc1refChr6 98399 25 + 197743 GATAAGGTGCTAATATGCTGCCAGT -s Anc2.Anc2refChr13 73144 25 + 96486 GATAAGGTGCTAACATGCCTCCTGG -s mr.mrrefChr5 293776 25 + 294540 GATATGATACAGATGTCCTGCCAGT -s simCow_chr6.simCow.chr6 430108 25 + 602619 GAAAAGATGCTAACATACTTTCTGA -s simDog_chr6.simDog.chr6 421250 25 + 593897 GGTAAGGTGCAAACATGCCTCCAGG -s simHuman_chr6.simHuman.chr6 424481 22 + 601863 GACAAGGTGCTAAT---CTGCCAAT -s simRat_chr6.simRat.chr6 448613 25 + 647215 GGTAGGATAGAGTTGTCCTGCCAGT - -a -s simMouse_chr6.simMouse.chr6 440319 12 + 636262 GGGCTAAGCACA -s Anc0.Anc0refChr3 67298 12 + 222631 GGACTGAGTACA -s Anc1.Anc1refChr6 98424 12 + 197743 GGACTGAGTACA -s Anc2.Anc2refChr13 73169 12 + 96486 GGACTGAGTACA -s mr.mrrefChr5 293801 12 + 294540 GGACTAAGCACA -s simCow_chr6.simCow.chr6 430133 12 + 602619 GGACTGAGTACA -s simDog_chr6.simDog.chr6 421275 12 + 593897 GGACTGAGTACA -s simHuman_chr6.simHuman.chr6 424510 12 + 601863 AGACTGAGTATA -s simRat_chr6.simRat.chr6 448638 12 + 647215 GAACTAACCACA - -a -s simMouse_chr6.simMouse.chr6 440331 14 + 636262 ATTTAAGTGTAAAC -s Anc0.Anc0refChr3 67312 14 + 222631 ATTTAAGTCCAAGT -s Anc1.Anc1refChr6 98438 14 + 197743 ATTTAAGTCCAAGT -s Anc2.Anc2refChr13 73183 14 + 96486 ATTTAAGTCCAAGT -s mr.mrrefChr5 293813 14 + 294540 ATTTAAGTGTAAAC -s simCow_chr6.simCow.chr6 430147 14 + 602619 ATTTAAGCCCAAGT -s simDog_chr6.simDog.chr6 421289 14 + 593897 ATTTGAGTCCAAGC -s simHuman_chr6.simHuman.chr6 424524 14 + 601863 ATTTAAGTCCAAGT -s simRat_chr6.simRat.chr6 448650 14 + 647215 TTTTAAGTATCAAC - -a -s simMouse_chr6.simMouse.chr6 440345 6 + 636262 CAGTCA -s Anc0.Anc0refChr3 67330 6 + 222631 CAGAGG -s Anc1.Anc1refChr6 98456 6 + 197743 CAGAGG -s Anc2.Anc2refChr13 73201 6 + 96486 CAGAGG -s mr.mrrefChr5 293831 6 + 294540 CAGTCA -s simCow_chr6.simCow.chr6 430165 6 + 602619 CAGAGA -s simDog_chr6.simDog.chr6 421307 6 + 593897 CAGAGG -s simHuman_chr6.simHuman.chr6 424542 6 + 601863 CAGAGG -s simRat_chr6.simRat.chr6 448668 6 + 647215 CAGTCA - -a -s simMouse_chr6.simMouse.chr6 440351 3 + 636262 TAA -s Anc0.Anc0refChr3 67336 3 + 222631 CAC -s Anc1.Anc1refChr6 98462 3 + 197743 CAC -s Anc2.Anc2refChr13 73207 3 + 96486 CAC -s mr.mrrefChr5 293837 3 + 294540 TAA -s simCow_chr6.simCow.chr6 430173 3 + 602619 CAC -s simDog_chr6.simDog.chr6 421313 3 + 593897 CAC -s simHuman_chr6.simHuman.chr6 424548 3 + 601863 CAC -s simRat_chr6.simRat.chr6 448674 3 + 647215 TAG - -a -s simMouse_chr6.simMouse.chr6 440354 10 + 636262 TATTTTAGAC -s Anc0.Anc0refChr3 67340 10 + 222631 TAATTTGGAT -s Anc1.Anc1refChr6 98466 10 + 197743 TAATTTGGAT -s Anc2.Anc2refChr13 73211 10 + 96486 TAATTTGGAT -s mr.mrrefChr5 293841 10 + 294540 TAATTTAGAC -s simCow_chr6.simCow.chr6 430177 10 + 602619 TAAATTGGAT -s simDog_chr6.simDog.chr6 421317 10 + 593897 TAATTCGGAT -s simHuman_chr6.simHuman.chr6 424552 10 + 601863 TAATTTGGAT -s simRat_chr6.simRat.chr6 448678 10 + 647215 TAATTTAGAC - -a -s simMouse_chr6.simMouse.chr6 440364 7 + 636262 CAGTACA -s Anc0.Anc0refChr3 67350 7 + 222631 CAGTACA -s Anc1.Anc1refChr6 98476 7 + 197743 CAGTACA -s Anc2.Anc2refChr13 73225 7 + 96486 CAGTACT -s mr.mrrefChr5 293851 7 + 294540 CAGTACA -s simCow_chr6.simCow.chr6 430187 7 + 602619 CAGTGCT -s simDog_chr6.simDog.chr6 421331 7 + 593897 CAATACT -s simHuman_chr6.simHuman.chr6 424562 7 + 601863 CAGCACA -s simRat_chr6.simRat.chr6 448688 7 + 647215 CAGTGTA - -a -s simMouse_chr6.simMouse.chr6 440371 64 + 636262 AAAATAAGTCATGTAAGCCATTTTTAATATTCCAACACACACAAACTTTACAACTGTAATGTCT -s Anc0.Anc0refChr3 67357 64 + 222631 AGAACCAGTCACGTAGGCTACTTTTAATAATCCAATGCATTCAAAGTTTATGATAGTAACCTCT -s Anc1.Anc1refChr6 98483 64 + 197743 AGAACCAGTCACGTAGGCTACTTTTAATAATCCAATGCATTCAAAGTTTATGATAGTAACCTCT -s Anc2.Anc2refChr13 73232 64 + 96486 AGATCCAGTCACTTAGGCTACTTTTAATAATCCAATGCATTCAAAGTTTTTGACAGTAGCCTCT -s mr.mrrefChr5 293858 64 + 294540 AAAATAAGTCATGTAAGCCATTTTTAATATTCCAACGCACACAAACTTTACAATTGTAATGTCT -s simCow_chr6.simCow.chr6 430194 64 + 602619 AGGTCCAGTCACTTAGGCTAATTCTAATAATTCAATACATTCAAAGCTTTTGTCATTAGCCTCT -s simDog_chr6.simDog.chr6 421338 64 + 593897 AGATCCAGCCACTTAGTCTACTTTTAATAATCCAATGCATTCAACGTTTTTGACAGTGGCCTGT -s simHuman_chr6.simHuman.chr6 424675 64 + 601863 AGAACTCGTCACGTGGGCTACTCATAATAATCCAATGCATTCAAAATTTATGATAGTAACCTCT -s simRat_chr6.simRat.chr6 448695 64 + 647215 AAAATGAGTCATGTAAGCCGTTTTTAATATTCCAACGCACACAGACTATACAATTGTAATATCT - -a -s simMouse_chr6.simMouse.chr6 440435 6 + 636262 CTCAAA -s Anc0.Anc0refChr3 67421 6 + 222631 CTCAAC -s Anc1.Anc1refChr6 98547 6 + 197743 CTCAAC -s Anc2.Anc2refChr13 73296 6 + 96486 CTCTAC -s mr.mrrefChr5 293922 6 + 294540 CTCAAA -s simCow_chr6.simCow.chr6 430259 6 + 602619 CTCTAT -s simDog_chr6.simDog.chr6 421402 6 + 593897 CTCTAC -s simHuman_chr6.simHuman.chr6 424739 6 + 601863 CTCAAC -s simRat_chr6.simRat.chr6 448759 6 + 647215 CTCAAA - -a -s simMouse_chr6.simMouse.chr6 440441 267 + 636262 AAACCAAGTTTTAAGGTTTCGTCAAGTTAACAGGGACACTTATCATACATGCAATCAGATTGTCTGTATTTTAAGAATACCAGTGTTTTTGGTGGATTCATCCAAACCTCAGGTTGACTAGGTATTTGCTGTGGAGTAAGTACATGCATATGACATTAATATCATATTAAGGACTTCTGTAGTATAATGTGTAACCATTGACTTGACTAATATGTAGTGCAAGCTTGTTTACTATCCACATTACCTTCCATCAACTGGGAATTCATT -s Anc0.Anc0refChr3 67427 41 + 222631 AAAGCAGGTTTTAAGGTTTAGTCATGTGAACAGGGA----TATCA------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ -s Anc1.Anc1refChr6 98553 41 + 197743 AAAGCAGGTTTTAAGGTTTAGTCATGTGAACAGGGA----TATCA------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ -s Anc2.Anc2refChr13 73302 41 + 96486 AGAGCAGGTTTTAAGGCTTAGTCATGTGAACAGGGA----TATCA------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ -s mr.mrrefChr5 293928 267 + 294540 AAACCAAGTTTTAAGGTTTCGTCAAGTGAACAGGGACACTTATCATACATGCAATCAGATTGTCTGTATTTTAAGAATACCAGTGTTTTTGGTGGATTCATCCAAACCTCAGGTTGACTAGGTATTTGCTGTGGAGTAAGTACATGCATATGACATTAATATCATATTAAGGACTTCTGTAGTATAATGTGTAACCATTGACTTGACTAATATGTAGTGCAAGCTTGTTTACTATCCACATTACCTTCCATCAACTGGGAATTCATT -s simCow_chr6.simCow.chr6 430265 37 + 602619 AGACTGGGTTTTAA----TAGTCCTGTGCACATAGG----TATCT------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ -s simDog_chr6.simDog.chr6 421408 41 + 593897 AGAGCAGGTTGTAAGGCTTAGTCATGTGAACAGGGA----TATCA------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ -s simHuman_chr6.simHuman.chr6 424745 41 + 601863 AAATCAGGTTTTAAGGTTTAGTCATGTGAACAGGGA----TATAA------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ -s simRat_chr6.simRat.chr6 448783 267 + 647215 AAACTAAGTTTTACGGTTTCGTCAGGTGAACAGGGAGACTTATCAGACATGCAGTCAGATTCACTGTATTTTGAAAGTATCAGTGCTTTTGCTGGATTCATCCAATTCTCAGGTTGACAAGGAATTTGCAGTGAAGTCAGTACAGGCACATAACACTAATGTCATATTAGGGACTTCTGTAATAAAATGTGTAACCATTCACTTGACTGACATGTAGTGCAAGCTTGTTTACTATCTACACTACCTTCCATCAACTAGGAATGCGTT - -a -s simMouse_chr6.simMouse.chr6 440708 5 + 636262 ATGCT -s mr.mrrefChr5 294195 5 + 294540 ATGCT -s simRat_chr6.simRat.chr6 449051 5 + 647215 ATGCT - -a -s simMouse_chr6.simMouse.chr6 440713 7 + 636262 ATGAGGT -s mr.mrrefChr5 294200 7 + 294540 ATGAGGT -s simRat_chr6.simRat.chr6 449058 7 + 647215 ATGACGT - -a -s simMouse_chr6.simMouse.chr6 440720 57 + 636262 GCTGTTCAAGGTGCTGATGATTTTAGGGAGTGCCTTAACCCTGAAAGTTCCCAATAG -s mr.mrrefChr5 294207 57 + 294540 GCTGTTCAAGGTGCTGATGATTTTAGGGAGTGCCTTAACCCTGAAAGTTCCCAATAG -s simRat_chr6.simRat.chr6 449137 57 + 647215 GCTGTTCGAAGTGCTGCTGACTTTAAGAAGTGCCTTAACCCCCAGAGCTCCCAATAG - -a -s simMouse_chr6.simMouse.chr6 440777 21 + 636262 GTTGGAGGGAATCAGCATTGT -s mr.mrrefChr5 294264 21 + 294540 GTTGGAGGGAATCAGCATTGT -s simRat_chr6.simRat.chr6 449197 21 + 647215 GGAGGGGGGAATCAGCATTGT - -a -s simMouse_chr6.simMouse.chr6 440798 8 + 636262 CTTCTTGC -s Anc1.Anc1refChr6 146750 8 + 197743 CTTCTTGC -s mr.mrrefChr3 50704 8 + 181027 CTCCTTGC -s mr.mrrefChr5 294285 8 + 294540 CTTCTTGC -s simMouse_chr6.simMouse.chr6 496692 8 + 636262 CTCCTTGC -s simRat_chr6.simRat.chr6 509340 8 + 647215 CTCCTTAC -s simRat_chr6.simRat.chr6 449218 8 + 647215 CTTCTTAT - -a -s simMouse_chr6.simMouse.chr6 440806 3 + 636262 CTT -s Anc0.Anc0refChr3 112937 3 + 222631 TTC -s Anc1.Anc1refChr6 146758 3 + 197743 TTC -s Anc2.Anc2refChr1 25045 3 + 142988 TTC -s mr.mrrefChr3 50712 3 + 181027 TTC -s mr.mrrefChr5 294293 3 + 294540 CTT -s simCow_chr6.simCow.chr6 481464 3 + 602619 TTC -s simDog_chr6.simDog.chr6 471408 3 + 593897 TCC -s simMouse_chr6.simMouse.chr6 496700 3 + 636262 TTC -s simRat_chr6.simRat.chr6 509348 3 + 647215 TTC -s simRat_chr6.simRat.chr6 449226 3 + 647215 CTT - -a -s simMouse_chr6.simMouse.chr6 440809 1 + 636262 A -s Anc0.Anc0refChr3 112940 1 + 222631 A -s Anc1.Anc1refChr6 146761 1 + 197743 A -s Anc2.Anc2refChr1 25048 1 + 142988 A -s mr.mrrefChr3 50715 1 + 181027 A -s mr.mrrefChr5 294296 1 + 294540 A -s simCow_chr6.simCow.chr6 481467 1 + 602619 A -s simDog_chr6.simDog.chr6 471411 1 + 593897 A -s simMouse_chr6.simMouse.chr6 496703 1 + 636262 A -s simRat_chr6.simRat.chr6 197396 1 - 647215 A -s simRat_chr6.simRat.chr6 509351 1 + 647215 A -s simRat_chr6.simRat.chr6 449229 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 440810 6 + 636262 ACAGAC -s Anc0.Anc0refChr3 112941 6 + 222631 GGAGGT -s Anc1.Anc1refChr6 146762 6 + 197743 GGAGGT -s Anc2.Anc2refChr1 25049 6 + 142988 GGGGGT -s mr.mrrefChr3 50716 6 + 181027 GAAGGT -s mr.mrrefChr5 294297 6 + 294540 ACAGAC -s simCow_chr6.simCow.chr6 481468 6 + 602619 AGGGGT -s simDog_chr6.simDog.chr6 471412 6 + 593897 GAGGGC -s simMouse_chr6.simMouse.chr6 496714 6 + 636262 GAAGGT -s simRat_chr6.simRat.chr6 197397 6 - 647215 GGAAGC -s simRat_chr6.simRat.chr6 509352 6 + 647215 GAAGAT -s simRat_chr6.simRat.chr6 449230 6 + 647215 ACAGAC - -a -s simMouse_chr6.simMouse.chr6 440816 10 + 636262 TATCAAACAA -s Anc0.Anc0refChr3 112950 10 + 222631 TAGTAGCCAT -s Anc1.Anc1refChr6 146771 10 + 197743 TAGTAGCCAT -s Anc2.Anc2refChr1 25058 10 + 142988 TAGTAGCAAT -s mr.mrrefChr3 50725 10 + 181027 TAGTAGTCAT -s mr.mrrefChr5 294303 10 + 294540 TATCAAACAA -s simCow_chr6.simCow.chr6 481477 10 + 602619 TAATAGGAAT -s simDog_chr6.simDog.chr6 471421 10 + 593897 TAGTTGCAAT -s simMouse_chr6.simMouse.chr6 496723 10 + 636262 TAGTAGTCAT -s simRat_chr6.simRat.chr6 509361 10 + 647215 TAGTAGGCTT -s simRat_chr6.simRat.chr6 449236 10 + 647215 TATCAAACAA - -a -s simMouse_chr6.simMouse.chr6 440826 10 + 636262 ACTTAACCTG -s Anc0.Anc0refChr3 112960 10 + 222631 ACTTGTCTTG -s Anc1.Anc1refChr6 146781 10 + 197743 ACTTGTCTTG -s Anc2.Anc2refChr1 25068 10 + 142988 CCATTTCTTG -s mr.mrrefChr3 50735 10 + 181027 AGTTGTCTTG -s mr.mrrefChr5 294313 10 + 294540 ACTTAACCTG -s simCow_chr6.simCow.chr6 481487 10 + 602619 CTGTTTCATG -s simDog_chr6.simDog.chr6 471431 10 + 593897 CCATTTCTTG -s simHuman_chr6.simHuman.chr6 478633 9 + 601863 -GGTGTCTTT -s simMouse_chr6.simMouse.chr6 496733 10 + 636262 AGTTGTCTTG -s simRat_chr6.simRat.chr6 509371 10 + 647215 AGTTGTCTTT -s simRat_chr6.simRat.chr6 449310 10 + 647215 GCTTAACCTG - -a -s simMouse_chr6.simMouse.chr6 440836 2 + 636262 TG -s mr.mrrefChr5 294323 2 + 294540 TG -s simRat_chr6.simRat.chr6 449320 2 + 647215 TG - -a -s simMouse_chr6.simMouse.chr6 440838 10 + 636262 GGCATCCAAA -s Anc0.Anc0refChr3 112970 6 + 222631 GG----CAGC -s Anc1.Anc1refChr6 146791 10 + 197743 GGCATCCAGC -s Anc2.Anc2refChr1 25078 6 + 142988 GG----CAGC -s mr.mrrefChr3 50745 10 + 181027 GCTATCCAGT -s mr.mrrefChr5 294325 10 + 294540 GGCATCCAAA -s simCow_chr6.simCow.chr6 481497 6 + 602619 GG----CATC -s simDog_chr6.simDog.chr6 471441 6 + 593897 GG----CAGC -s simHuman_chr6.simHuman.chr6 478642 10 + 601863 AGCAGCCGGC -s simMouse_chr6.simMouse.chr6 496743 10 + 636262 GCTATCCAGT -s simRat_chr6.simRat.chr6 509381 10 + 647215 GCCATGCAAT -s simRat_chr6.simRat.chr6 449322 10 + 647215 GGCATGCAAC - -a -s simMouse_chr6.simMouse.chr6 440848 14 + 636262 TCTTTAAATCTGGG -s Anc0.Anc0refChr3 112978 13 + 222631 TCTGCACCTA-GGG -s Anc1.Anc1refChr6 146803 14 + 197743 TCTGCACCTATGGG -s Anc2.Anc2refChr1 25086 13 + 142988 TCTGCACCTA-GGG -s mr.mrrefChr3 50755 14 + 181027 TTGGTACCTCTGGG -s mr.mrrefChr5 294335 14 + 294540 TCTTTAAATCTGGG -s simCow_chr6.simCow.chr6 481508 13 + 602619 TCCACACCTG-GGG -s simDog_chr6.simDog.chr6 471449 13 + 593897 GCTGGACCTA-GGG -s simHuman_chr6.simHuman.chr6 478654 14 + 601863 TCTGCACCTAGGGG -s simMouse_chr6.simMouse.chr6 496753 14 + 636262 TTGGTACCTCTGGG -s simRat_chr6.simRat.chr6 509391 14 + 647215 TTGTTACCTCTGGG -s simRat_chr6.simRat.chr6 449332 14 + 647215 TCTTTAAATCTGGG - -a -s simMouse_chr6.simMouse.chr6 440862 9 + 636262 ATTGAATGA -s Anc0.Anc0refChr3 112991 9 + 222631 ACTGAGTGA -s Anc1.Anc1refChr6 146817 9 + 197743 ACTGAGTGA -s Anc2.Anc2refChr1 25099 9 + 142988 ACTAAGTGT -s mr.mrrefChr3 50769 9 + 181027 GCCGAGTGA -s mr.mrrefChr5 294349 9 + 294540 ATTGAATGA -s simCow_chr6.simCow.chr6 481521 8 + 602619 -CCAGGTGG -s simDog_chr6.simDog.chr6 471462 9 + 593897 AATAAGAAT -s simHuman_chr6.simHuman.chr6 478669 9 + 601863 GCTGAGTGA -s simMouse_chr6.simMouse.chr6 496767 9 + 636262 GCCGAGTGG -s simRat_chr6.simRat.chr6 509405 9 + 647215 GCCAAGTGA -s simRat_chr6.simRat.chr6 449346 9 + 647215 GCTGAGTGG - -a -s simMouse_chr6.simMouse.chr6 440871 1 + 636262 T -s Anc0.Anc0refChr3 113000 1 + 222631 T -s Anc1.Anc1refChr6 146826 1 + 197743 T -s Anc2.Anc2refChr1 25108 1 + 142988 T -s mr.mrrefChr3 50778 1 + 181027 T -s mr.mrrefChr5 294358 1 + 294540 T -s simCow_chr6.simCow.chr6 481529 1 + 602619 C -s simDog_chr6.simDog.chr6 471471 1 + 593897 T -s simHuman_chr6.simHuman.chr6 478678 1 + 601863 T -s simMouse_chr6.simMouse.chr6 496776 1 + 636262 T -s simRat_chr6.simRat.chr6 449355 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 440872 12 + 636262 ATTCATTGAAAC -s Anc0.Anc0refChr3 113001 12 + 222631 ATTCACCAAAAC -s Anc1.Anc1refChr6 146827 12 + 197743 ATTCACCAAAAC -s Anc2.Anc2refChr1 25109 12 + 142988 ATTCACCAAAAC -s mr.mrrefChr3 50779 12 + 181027 ATTCACCAAATC -s mr.mrrefChr5 294359 12 + 294540 ATTCATTGAAAC -s simCow_chr6.simCow.chr6 481530 12 + 602619 ATTCACCAAAAC -s simDog_chr6.simDog.chr6 471472 12 + 593897 ATTCACCAAGAC -s simHuman_chr6.simHuman.chr6 478679 12 + 601863 ATCCGCCAAAAC -s simMouse_chr6.simMouse.chr6 496777 12 + 636262 ATTCACCAAATC -s simRat_chr6.simRat.chr6 509414 12 + 647215 ATTCACCAAATC -s simRat_chr6.simRat.chr6 449356 12 + 647215 TTTCATCAAAAC - -a -s simMouse_chr6.simMouse.chr6 440884 10 + 636262 TTGTCCTTCA -s Anc0.Anc0refChr3 113013 10 + 222631 TTATCCTTCA -s Anc1.Anc1refChr6 146839 10 + 197743 TTATCCTTCA -s Anc2.Anc2refChr1 25121 10 + 142988 TTATCCTTCA -s mr.mrrefChr3 50791 10 + 181027 TCATTTTTCA -s mr.mrrefChr5 294371 10 + 294540 TTGTCCTTCA -s simCow_chr6.simCow.chr6 481542 10 + 602619 TAATCCTTCA -s simDog_chr6.simDog.chr6 471484 10 + 593897 TTATCCTGCC -s simHuman_chr6.simHuman.chr6 478693 10 + 601863 TTATCTTTCA -s simMouse_chr6.simMouse.chr6 496789 10 + 636262 TCATTTTTCA -s simRat_chr6.simRat.chr6 509426 10 + 647215 TCATTTTTCA -s simRat_chr6.simRat.chr6 449368 10 + 647215 TTGTCTTGCA - -a -s simMouse_chr6.simMouse.chr6 440894 52 + 636262 AGAGCCCTCATCTCACTCCAACACCGCTAGTGTCGTTTGGGTCAACTCTCAC -s Anc0.Anc0refChr3 113024 52 + 222631 GGAGTTGTTATCTGACACCAAGAATGCTTGAACGGTTTAGGTGGACTCTCAC -s Anc1.Anc1refChr6 146850 52 + 197743 GGAGTTGTTATCTGACACCAAGAATGCTTGAACGGTTTAGGTGGACTCTCAC -s Anc2.Anc2refChr1 25132 52 + 142988 GGAGTTGTTGTCTGACACAAAGAATGCTTGAAAGGTTTAAGCAGACTCACAC -s mr.mrrefChr3 50802 52 + 181027 GGAGTTGTTATCTCACTCCTACAACGCTAGTCCGTTTCAGGTGGACTCTCAC -s mr.mrrefChr5 294381 52 + 294540 AGAGCCCTCATCTCACTCCAACACCGCTAGTGTCGTTTGGGTCAACTCTCAC -s simCow_chr6.simCow.chr6 481553 51 + 602619 GGAGTTGTTCTCTGACACTGAGAATGCCTGAAAGGTGTAAGCAGACTC-CAT -s simDog_chr6.simDog.chr6 471495 51 + 593897 AGAGTTGTTGTCTGGCACAAGCAATGCTCCAGAGGTT-AAGCAGACTGACAC -s simHuman_chr6.simHuman.chr6 478704 51 + 601863 GGAG-TGTTATCTGACACCAAGATTGTTTGAACGGTTTGGGTGGATTCGCAC -s simMouse_chr6.simMouse.chr6 496800 52 + 636262 GGAGTTGTTGGCTCCTTCCTGCAACACTAGTCCATTTCAGGTGGGCTCTCAC -s simRat_chr6.simRat.chr6 509437 52 + 647215 GGAATTGCTATCTCACTCCTACAACGCTAGTCAGTTTCAGGTGGACTCTCAC -s simRat_chr6.simRat.chr6 449378 52 + 647215 AGAGCCAGTATCTGACTCCAACAGTGCTAGTATCATTTGGGTGGACTCTCAC - -a -s simMouse_chr6.simMouse.chr6 440946 3 + 636262 ATG -s Anc0.Anc0refChr3 113076 3 + 222631 ATT -s Anc1.Anc1refChr6 146902 3 + 197743 ATT -s Anc2.Anc2refChr1 25184 3 + 142988 ATT -s mr.mrrefChr3 50854 3 + 181027 ATA -s mr.mrrefChr5 294433 3 + 294540 ATG -s simCow_chr6.simCow.chr6 481608 3 + 602619 ATT -s simDog_chr6.simDog.chr6 471546 3 + 593897 GTT -s simHuman_chr6.simHuman.chr6 478755 3 + 601863 ATT -s simMouse_chr6.simMouse.chr6 496852 3 + 636262 AAA -s simRat_chr6.simRat.chr6 509489 3 + 647215 ATA -s simRat_chr6.simRat.chr6 449430 3 + 647215 ATG - -a -s simMouse_chr6.simMouse.chr6 440949 16 + 636262 TTGAGGATCCAGAGCC -s Anc0.Anc0refChr3 113119 16 + 222631 TTGGTATTCAAGCTCC -s Anc1.Anc1refChr6 146945 16 + 197743 TTGGTATTCAAGCTCC -s Anc2.Anc2refChr1 25239 16 + 142988 TTAGTATTGAAGCTCC -s mr.mrrefChr3 50857 16 + 181027 TTGAGGATCCAAAGCC -s mr.mrrefChr5 294436 16 + 294540 TTGAGGATCCAGAGCC -s simCow_chr6.simCow.chr6 481673 16 + 602619 TTAGTATTGAAGCTCC -s simDog_chr6.simDog.chr6 471635 16 + 593897 TCAGTGTTGAAGTTCC -s simHuman_chr6.simHuman.chr6 478798 16 + 601863 TTGGTATTCAAGCTCC -s simMouse_chr6.simMouse.chr6 496855 16 + 636262 TTGAAGATCCAAAGCC -s simRat_chr6.simRat.chr6 509492 16 + 647215 TTGAGGATCCAAAGCC -s simRat_chr6.simRat.chr6 449433 16 + 647215 TTGAAAATCCGAAGCC - -a -s simMouse_chr6.simMouse.chr6 440965 1 + 636262 A -s Anc0.Anc0refChr3 113135 1 + 222631 G -s Anc1.Anc1refChr6 146961 1 + 197743 G -s Anc2.Anc2refChr1 25255 1 + 142988 G -s mr.mrrefChr3 50873 1 + 181027 A -s mr.mrrefChr5 294452 1 + 294540 A -s simCow_chr6.simCow.chr6 481689 1 + 602619 G -s simDog_chr6.simDog.chr6 471661 1 + 593897 G -s simHuman_chr6.simHuman.chr6 478814 1 + 601863 G -s simMouse_chr6.simMouse.chr6 496871 1 + 636262 A -s simRat_chr6.simRat.chr6 509508 1 + 647215 A -s simRat_chr6.simRat.chr6 449449 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 440966 12 + 636262 CCTGCTCAGAGC -s Anc0.Anc0refChr3 113136 12 + 222631 CCTGCTTTGGAC -s Anc1.Anc1refChr6 146962 12 + 197743 CCTGCTTTGGAC -s Anc2.Anc2refChr1 25256 12 + 142988 CCTGCTTTGGAC -s mr.mrrefChr3 50874 12 + 181027 CCTGCTATGGAC -s mr.mrrefChr5 294453 12 + 294540 CCTGCTCAGAGC -s simCow_chr6.simCow.chr6 481696 12 + 602619 CTTGCTTTGGAC -s simDog_chr6.simDog.chr6 471662 12 + 593897 CCTGCTTTGGAC -s simHuman_chr6.simHuman.chr6 478815 12 + 601863 CCTGCTTTGGAC -s simMouse_chr6.simMouse.chr6 496872 12 + 636262 CCTGCTATGGAC -s simRat_chr6.simRat.chr6 509509 12 + 647215 CCTGCTGTGGAC -s simRat_chr6.simRat.chr6 449450 12 + 647215 TCCGCTCTGGGC - -a -s simMouse_chr6.simMouse.chr6 440978 1 + 636262 G -s mr.mrrefChr5 294465 1 + 294540 G -s simRat_chr6.simRat.chr6 449462 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 440979 2 + 636262 TT -s Anc0.Anc0refChr3 113148 2 + 222631 AT -s Anc1.Anc1refChr6 146974 2 + 197743 AT -s Anc2.Anc2refChr1 25268 2 + 142988 AT -s mr.mrrefChr3 50886 2 + 181027 TT -s mr.mrrefChr5 294466 2 + 294540 TT -s simCow_chr6.simCow.chr6 481708 2 + 602619 AT -s simDog_chr6.simDog.chr6 471674 1 + 593897 -T -s simHuman_chr6.simHuman.chr6 478827 2 + 601863 AT -s simMouse_chr6.simMouse.chr6 496884 2 + 636262 TT -s simRat_chr6.simRat.chr6 509521 2 + 647215 TT -s simRat_chr6.simRat.chr6 449463 2 + 647215 TT - -a -s simMouse_chr6.simMouse.chr6 440981 5 + 636262 TCTGT -s Anc0.Anc0refChr3 113150 5 + 222631 TATGT -s Anc1.Anc1refChr6 146976 5 + 197743 TATGT -s Anc2.Anc2refChr1 25270 5 + 142988 TATGT -s mr.mrrefChr3 50888 5 + 181027 TCTGT -s mr.mrrefChr5 294468 5 + 294540 TCTGT -s simCow_chr6.simCow.chr6 481710 5 + 602619 TATGT -s simDog_chr6.simDog.chr6 471675 5 + 593897 AATAT -s simHuman_chr6.simHuman.chr6 478829 5 + 601863 TATGT -s simMouse_chr6.simMouse.chr6 496886 5 + 636262 TCTGT -s simRat_chr6.simRat.chr6 509523 5 + 647215 TCTGT -s simRat_chr6.simRat.chr6 449484 5 + 647215 TCTAT - -a -s simMouse_chr6.simMouse.chr6 440986 66 + 636262 CAGTGCATTTGCATGTATGATGGTGACAGTAACAAAGAAAATCTGATACATGTGCTGAAGAATGGT -s Anc0.Anc0refChr3 113175 66 + 222631 TAGAGCATTTGTATATATTGTGGTGATAGTAATAAAGATGATCAGATACAAGACCTCAAGAATGGA -s Anc1.Anc1refChr6 147001 66 + 197743 TAGAGCATTTGTATATATTGTGGTGATAGTAATAAAGATGATCAGATACAAGACCTCAAGAATGGA -s Anc2.Anc2refChr1 25295 66 + 142988 TAGAGCATTTGTATATATTGTGGTGATAGTAATAAAGATGATCAGATACAAGACCTCAAGAATGGA -s mr.mrrefChr3 50913 66 + 181027 TAGAGCATTTGTATATATTGTGGTGATAGTAACAAAGATGATCAGATACAAGATCTGAAGAATGGT -s mr.mrrefChr5 294473 66 + 294540 CAGTGCATTTGCATGTATGATGGTGACAGTAACAAAGAAAATCTGATACATGTGCTGAAGAATGGT -s simCow_chr6.simCow.chr6 481735 66 + 602619 CAGAGCATTCGTATCTATTGTGGTGATAGTAATAAAGAAGATCAGATACAAGACCTCAAGAATGAA -s simDog_chr6.simDog.chr6 471700 66 + 593897 TAGAGCATTTGTATATATTGTGGTGATAGTAATAAAGATGATCAGATACAAGACCTCAGGAATGGA -s simHuman_chr6.simHuman.chr6 478854 66 + 601863 TAGAGCATTTGTATATATTGTGGCGATATTAATAAAGATGATCAGTTACAAGACCTCAAGAATGGA -s simMouse_chr6.simMouse.chr6 496911 66 + 636262 TAGAGCATCTGTATACATTGTGGTGATAGTAACAAAGATGATCAGATACAAGATCTGAAGAATGGT -s simRat_chr6.simRat.chr6 509548 66 + 647215 TAAAGCATTTGTATATATTGTGGTGATAGTAACAAAGATGATCAGATACAAGATCTGAAGAATGGT -s simRat_chr6.simRat.chr6 449489 66 + 647215 CAGTGCATTTGCATATATTGTCCTAACAGAAACAAAGAGGATCAGATACAATTGCTGAAGAGTGGT - -a -s simMouse_chr6.simMouse.chr6 441052 1 + 636262 G -s Anc0.Anc0refChr3 113244 1 + 222631 G -s Anc1.Anc1refChr6 147070 1 + 197743 G -s Anc2.Anc2refChr1 25364 1 + 142988 G -s mr.mrrefChr3 50982 1 + 181027 G -s mr.mrrefChr5 294539 1 + 294540 G -s simCow_chr6.simCow.chr6 481804 1 + 602619 G -s simDog_chr6.simDog.chr6 471769 1 + 593897 G -s simHuman_chr6.simHuman.chr6 478923 1 + 601863 G -s simMouse_chr6.simMouse.chr6 496980 1 + 636262 G -s simRat_chr6.simRat.chr6 449558 1 + 647215 G -s simRat_chr6.simRat.chr6 509617 1 + 647215 G -s simRat_chr6.simRat.chr6 449555 1 + 647215 G - -a -s simMouse_chr6.simMouse.chr6 441053 6 + 636262 TAGATA -s Anc0.Anc0refChr3 109925 6 - 222631 ATAAAG -s Anc1.Anc1refChr6 51229 6 - 197743 ATAAAG -s Anc2.Anc2refChr1 118198 6 - 142988 ATAACG -s mr.mrrefChr3 130564 6 - 181027 ATAAAA -s simCow_chr6.simCow.chr6 121402 6 - 602619 ATAACG -s simDog_chr6.simDog.chr6 122746 1 - 593897 A----- -s simHuman_chr6.simHuman.chr6 123462 6 - 601863 ATAAAG -s simMouse_chr6.simMouse.chr6 139810 6 - 636262 ACAGAG -s simRat_chr6.simRat.chr6 450077 6 + 647215 ATAGAA -s simRat_chr6.simRat.chr6 138334 6 - 647215 ATGACA - -a -s simMouse_chr6.simMouse.chr6 441059 53 + 636262 CAAATCTCCCATGTGTTTCTGTTCACTTCCACAGATTGGGGCCATGGCTGTGT -s Anc0.Anc0refChr3 109944 28 - 222631 CAAA-CTGCTGTGTGTTTCTGTTG-CTTCC----------------------- -s Anc1.Anc1refChr6 51248 30 - 197743 CAAAGCTGCTGTGTGTTTCTGTTGGCTTCC----------------------- -s Anc2.Anc2refChr1 118217 28 - 142988 GAAA-CTGCTGAGTGTTTCTGTTG-CTTCC----------------------- -s mr.mrrefChr3 130583 53 - 181027 CAAAGCTCCCATGTGTTTCTGTTGGCTTCCATGGCTTGGGGTCATGACTTGTG -s simCow_chr6.simCow.chr6 121421 25 - 602619 GAAA-CTGCTGAGTGTTCCT---G-CTTCC----------------------- -s simDog_chr6.simDog.chr6 122747 9 - 593897 --------------GTTTCTGTT------------------------------ -s simHuman_chr6.simHuman.chr6 123482 30 - 601863 CAAAGCTGTTGTGTGATTCTGTTGGCTGCT----------------------- -s simMouse_chr6.simMouse.chr6 139829 53 - 636262 CCAAGTTTCCGTGTGTCTCTGTTGGCTTCAATGACTTGGGGTCACGACTTGTG -s simRat_chr6.simRat.chr6 450096 53 + 647215 TAAATCTCCCATGTGTTTCTGTTCACTTCCATGGCTTGGGGCCATGACTTGTG -s simRat_chr6.simRat.chr6 138353 53 - 647215 CCAAGTTTCCATGCGTTTCTGTTGGCTTCAATGACTTGGGGTCATGACTTGTA - -a -s simMouse_chr6.simMouse.chr6 441112 7 + 636262 TTCTATT -s mr.mrrefChr3 130643 7 - 181027 TTCTATT -s simMouse_chr6.simMouse.chr6 139889 7 - 636262 TTCAATT -s simRat_chr6.simRat.chr6 450149 7 + 647215 TTCTATT -s simRat_chr6.simRat.chr6 138413 7 - 647215 TGCTATT - -a -s simMouse_chr6.simMouse.chr6 441119 12 + 636262 GCTTCCATGATA -s Anc0.Anc0refChr3 109972 6 - 222631 ------ATGACT -s Anc1.Anc1refChr6 51278 6 - 197743 ------ATGACT -s Anc2.Anc2refChr1 118245 6 - 142988 ------ATGACT -s mr.mrrefChr3 130651 12 - 181027 GCTTCCATGACT -s simCow_chr6.simCow.chr6 121446 6 - 602619 ------ATGACT -s simDog_chr6.simDog.chr6 122756 5 - 593897 -------TGACT -s simHuman_chr6.simHuman.chr6 123512 6 - 601863 ------ATGACT -s simMouse_chr6.simMouse.chr6 139897 12 - 636262 GCTTCCAGGTCT -s simRat_chr6.simRat.chr6 450156 12 + 647215 ACTTCCATGACA -s simRat_chr6.simRat.chr6 138421 12 - 647215 GCTTCTATCACT - -a -s simMouse_chr6.simMouse.chr6 441131 11 + 636262 GGAGTAATGAA -s Anc0.Anc0refChr3 109978 11 - 222631 GGAGTAATGAA -s Anc1.Anc1refChr6 51284 11 - 197743 GGAGTAATGAA -s Anc2.Anc2refChr1 118251 11 - 142988 GGAGTAATGAA -s mr.mrrefChr3 130663 11 - 181027 GGAGTAATGAA -s simCow_chr6.simCow.chr6 121452 11 - 602619 CGAGTAATGAA -s simDog_chr6.simDog.chr6 122761 11 - 593897 GGAGCAACGAG -s simHuman_chr6.simHuman.chr6 123518 11 - 601863 GCAGTAATGAA -s simMouse_chr6.simMouse.chr6 139913 11 - 636262 GGGGTAATGAA -s simRat_chr6.simRat.chr6 450168 11 + 647215 GGAGTGATGAA -s simRat_chr6.simRat.chr6 138433 11 - 647215 GGGGTAATGAA - -a -s simMouse_chr6.simMouse.chr6 441142 44 + 636262 CCTGGAAGTTGATATGGTAAAATGTTCAATCTATGATGGAGCTA -s Anc0.Anc0refChr3 109989 43 - 222631 TGTGTAAATTTAAGGTGTAAGGTGGGCAAAATGTG-TTAGGGCA -s Anc1.Anc1refChr6 51295 43 - 197743 TGTGTAAATTTAAGGTGTAAGGTGGGCAAAATGTG-TTAGGGCA -s Anc2.Anc2refChr1 118262 43 - 142988 TGTGTAAGTTTAAGGTGTAAGGTGGGCAAAATGTG-TTAGGGCA -s mr.mrrefChr3 130674 44 - 181027 CCTGTAAATTGAAGTTGTAAAATGTGCAAACTATGATTAAGGTA -s simCow_chr6.simCow.chr6 121463 41 - 602619 CTTGTAAGATTAAGGTGTAAGGTGGGCAAAATCTG-TTAGTG-- -s simDog_chr6.simDog.chr6 122781 43 - 593897 TGTGTGAGTTTAAGGTGTAAGGTGTGCAAAATGTG-TTAGGGCA -s simHuman_chr6.simHuman.chr6 123529 43 - 601863 TATGTAAATTTGAGGTGCAAGGTGGGCAAAATGTG-CAAGGGCA -s simMouse_chr6.simMouse.chr6 139924 40 - 636262 CTTTTGAATTGAAGTTGTCAAAAGTGCCAAGTGTG-TTATG--- -s simRat_chr6.simRat.chr6 450179 44 + 647215 CCTGTAAGTTGATATAGTAAAATGTTCAATCTATGATTGAGGTA -s simRat_chr6.simRat.chr6 138444 40 - 647215 CCTGTGAATTGAAGTTGTCAGATGTGCAAAGTCTA-CCAGG--- - -a -s simMouse_chr6.simMouse.chr6 441186 52 + 636262 GGCCTTATCCTTGGGAATGAACTAGTGGGACATGGGACAACACACCAGAGTT -s Anc0.Anc0refChr3 110033 35 - 222631 GGCCTTAT-ATTGGGAACA-------------TGCCTCCAATTA---AGGGA -s Anc1.Anc1refChr6 51339 35 - 197743 GGCCTTAT-ATTGGGAACA-------------TGCCTCCAATTA---AGGGA -s Anc2.Anc2refChr1 118306 35 - 142988 GGCCTTAT-ATTGGGAACA-------------TGCCTCTAATTA---GGGGG -s mr.mrrefChr3 130719 44 - 181027 GGCCTTAT-CTTGGGAATAAACTAG-------TGCCTCCACTTACTAAGGTA -s simCow_chr6.simCow.chr6 121504 31 - 602619 ----TGGT-ACTGGGAACA-------------TGCCTCGAATTA---GGGAG -s simDog_chr6.simDog.chr6 122825 35 - 593897 GGCCTTAT-ATTGGGAACA-------------TGCCTCTGATTA---GGGGG -s simHuman_chr6.simHuman.chr6 123573 35 - 601863 GGCCTTAT-ATTAGGAACA-------------TGCCTCCAACTA---AGGGA -s simMouse_chr6.simMouse.chr6 139965 38 - 636262 GGGCTTAT-ATTGGGAATA-------------TGCCTTCACTTACTGAGATA -s simRat_chr6.simRat.chr6 450224 44 + 647215 GGCCTTAT-CTTGGGAATAAATTAG-------TGACCCAACATACCATAGTT -s simRat_chr6.simRat.chr6 138485 38 - 647215 GGGCTTAT-GTTGGGAATA-------------TGTCTTCGATTACTGAGATA - -a -s simMouse_chr6.simMouse.chr6 441238 11 + 636262 AGTTCTAGAAG -s Anc0.Anc0refChr3 110081 11 - 222631 AGTTCTAGATG -s Anc1.Anc1refChr6 51387 11 - 197743 AGTTCTAGATG -s Anc2.Anc2refChr1 118359 11 - 142988 AGTTCTAGATG -s mr.mrrefChr3 130776 11 - 181027 AGTTCTAGAAG -s simCow_chr6.simCow.chr6 121553 11 - 602619 AGTTCAAGATG -s simDog_chr6.simDog.chr6 122878 11 - 593897 AGATCTAGATG -s simHuman_chr6.simHuman.chr6 123608 11 - 601863 AGTTCCAGATG -s simMouse_chr6.simMouse.chr6 140016 11 - 636262 AGTTCTACAAG -s simRat_chr6.simRat.chr6 450268 11 + 647215 AGTCCTAGAAG -s simRat_chr6.simRat.chr6 138536 11 - 647215 AGTTCTACAAG - -a -s simMouse_chr6.simMouse.chr6 441249 34 + 636262 CTAAGTGTAAAGGCAATTGGGAATACAAGGATGA -s Anc0.Anc0refChr3 110092 34 - 222631 CTGAATGTAAAGAAAACCAGGTATTCAGAGATAA -s Anc1.Anc1refChr6 51398 34 - 197743 CTGAATGTAAAGAAAACCAGGTATTCAGAGATAA -s Anc2.Anc2refChr1 118370 34 - 142988 TGGAATGTAAGGAAAACTGGGTACTCAGAGTTAA -s mr.mrrefChr3 130787 34 - 181027 CTGAATGTAAAGGAAATCAGGAATTCAAAGATGA -s simCow_chr6.simCow.chr6 121565 34 - 602619 TGGAATGTAAGGAAAACTGGGTACTCAGAGTTAA -s simDog_chr6.simDog.chr6 122889 4 - 593897 TGGA------------------------------ -s simHuman_chr6.simHuman.chr6 123619 34 - 601863 CTGAATGTAAAGTAAACCAGGTGTTCAGAGATAC -s simMouse_chr6.simMouse.chr6 140027 34 - 636262 CTGAATGTAAAGGAAATCAGGAATTTAAAAATGA -s simRat_chr6.simRat.chr6 450279 34 + 647215 CTGAGTGTAAAGGCAATTGGGAATTCAAAGATGA -s simRat_chr6.simRat.chr6 138547 34 - 647215 CTGAATGCAAAGGAACTCAGGAATTCAGAAACGA - -a -s simMouse_chr6.simMouse.chr6 441283 40 + 636262 AAGTCCCATGCTCTTTTTCCCTGGGAACAAGAATCAGGAG -s Anc0.Anc0refChr3 110127 40 - 222631 AAACCCCATGCTTTTCAACGCTGAGAACGGGAATCAGGAA -s Anc1.Anc1refChr6 51433 40 - 197743 AAACCCCATGCTTTTCAACGCTGAGAACGGGAATCAGGAA -s Anc2.Anc2refChr1 118405 40 - 142988 TAACTCCATACTTTTCAATGCTGTGGATGGGAATTAGTAA -s mr.mrrefChr3 130822 40 - 181027 AACCCCCGTGCTCTTCAACCCTGAGAACAAGAATCAGGAA -s simCow_chr6.simCow.chr6 121600 40 - 602619 TAACTCCATACTTTTCAATGCTGTGGATGGGAATTAGTAA -s simHuman_chr6.simHuman.chr6 123654 40 - 601863 AAACCCTATGTTGTCCAACACTCAGAACGGGAATCAGGAA -s simMouse_chr6.simMouse.chr6 140062 10 - 636262 TACCC------------AC------------------GAA -s simRat_chr6.simRat.chr6 450313 40 + 647215 AAGTCTCGTGCTCTACGACCATGAGAACAAGAATTAGGAG -s simRat_chr6.simRat.chr6 138582 22 - 647215 TACCCCGGCTCTCTGCAAT------------------GAA - -a -s simMouse_chr6.simMouse.chr6 441323 16 + 636262 AATAGGTGTTGCAAAT -s Anc0.Anc0refChr3 110167 16 - 222631 GGTAAGTGTGGCAAGC -s Anc1.Anc1refChr6 51473 16 - 197743 GGTAAGTGTGGCAAGC -s Anc2.Anc2refChr1 118445 16 - 142988 GATAAGTGTGGCAAGC -s mr.mrrefChr3 130862 16 - 181027 AGTATGTGTTGCAAGT -s simCow_chr6.simCow.chr6 121640 16 - 602619 GATAAGTGTGGCAAGC -s simHuman_chr6.simHuman.chr6 123694 16 - 601863 GGTAGGTGTGGCAAGG -s simMouse_chr6.simMouse.chr6 140072 16 - 636262 AGTATGCATAGCAAGT -s simRat_chr6.simRat.chr6 450356 16 + 647215 AATATGTGTTGCAAGT -s simRat_chr6.simRat.chr6 138604 13 - 647215 AGTA-GCATAGCA--T - -a -s simMouse_chr6.simMouse.chr6 441339 9 + 636262 TATGATTGT -s Anc0.Anc0refChr3 110183 9 - 222631 CATGATCAT -s Anc1.Anc1refChr6 51489 9 - 197743 CATGATCAT -s Anc2.Anc2refChr1 118461 9 - 142988 CATGATCAT -s mr.mrrefChr3 130878 9 - 181027 CATGATCAT -s simCow_chr6.simCow.chr6 121656 9 - 602619 CATGATCAT -s simHuman_chr6.simHuman.chr6 123710 9 - 601863 CACAATCAC -s simMouse_chr6.simMouse.chr6 140088 9 - 636262 CATAATCAT -s simRat_chr6.simRat.chr6 138617 9 - 647215 CATGATGAT - -a -s simMouse_chr6.simMouse.chr6 441348 26 + 636262 GCCACTAGTGTTAATACCTAGGCAAG -s Anc0.Anc0refChr3 110192 26 - 222631 GCCACTAGTGTTAAGGTCTAGGCAAG -s Anc1.Anc1refChr6 51498 26 - 197743 GCCACTAGTGTTAAGGTCTAGGCAAG -s Anc2.Anc2refChr1 118470 26 - 142988 GCCACCAGTGTTAAGGTCTACGCAAG -s mr.mrrefChr3 130887 26 - 181027 GCCACTAGTGTTAATATCTAGGCAAG -s simCow_chr6.simCow.chr6 121665 26 - 602619 GCCACCAGTGTTAAGGTCTACGCAAG -s simHuman_chr6.simHuman.chr6 123719 26 - 601863 GTCATTGGTGTTAAGGTCTAGGCAAT -s simMouse_chr6.simMouse.chr6 140097 26 - 636262 GCCACTAGTGCTAATCTCTAGGCAAG -s simRat_chr6.simRat.chr6 453269 26 + 647215 GCCACTAGTGTTAATATCTGGGCAAG -s simRat_chr6.simRat.chr6 138626 26 - 647215 GCCACTGGCGCTAATGTCTAGGCAAA - -a -s simMouse_chr6.simMouse.chr6 441374 30 + 636262 GAGAGGATACCCTTTGATAGACAAGCTGCC -s Anc0.Anc0refChr3 110218 25 - 222631 GA-----TGCCCTTTGATAGGTATGTTACC -s Anc1.Anc1refChr6 51524 25 - 197743 GA-----TGCCCTTTGATAGGTATGTTACC -s Anc2.Anc2refChr1 118496 25 - 142988 GA-----TGATCTTTGGTAGGTATGTAAAC -s mr.mrrefChr3 130913 30 - 181027 GAGAGGATACCCTTTGATAGATAAGCTACC -s simCow_chr6.simCow.chr6 121693 25 - 602619 GA-----TGATCTTTGGTAGGTATGTAAAC -s simHuman_chr6.simHuman.chr6 123745 25 - 601863 TA-----TGCCCTTTGATAGGTAGGTTACC -s simMouse_chr6.simMouse.chr6 140123 22 - 636262 AAGAGGATACCCTTTGATAGAT-------- -s simRat_chr6.simRat.chr6 453295 30 + 647215 GAGAGGATACCCTTTGATAGATGAGCCACC -s simRat_chr6.simRat.chr6 138652 29 - 647215 AAGAGGATACCCTTTGATACA-AGATTACC - -a -s simMouse_chr6.simMouse.chr6 441404 4 + 636262 AGTT -s Anc0.Anc0refChr3 110256 4 - 222631 AGAG -s Anc1.Anc1refChr6 51562 4 - 197743 AGAG -s Anc2.Anc2refChr1 118534 4 - 142988 AGGG -s mr.mrrefChr3 130943 4 - 181027 AGAT -s simCow_chr6.simCow.chr6 121732 4 - 602619 AGGG -s simHuman_chr6.simHuman.chr6 123783 4 - 601863 GGAG -s simRat_chr6.simRat.chr6 453325 4 + 647215 AGAT -s simRat_chr6.simRat.chr6 138681 4 - 647215 AGAT - -a -s simMouse_chr6.simMouse.chr6 441408 2 + 636262 AC -s Anc0.Anc0refChr3 110260 2 - 222631 GC -s Anc1.Anc1refChr6 51566 2 - 197743 GC -s Anc2.Anc2refChr1 118538 2 - 142988 GC -s mr.mrrefChr3 130947 2 - 181027 AC -s simCow_chr6.simCow.chr6 121744 2 - 602619 GC -s simHuman_chr6.simHuman.chr6 123787 2 - 601863 GC -s simRat_chr6.simRat.chr6 453329 2 + 647215 AT -s simRat_chr6.simRat.chr6 138685 2 - 647215 AC - -a -s simMouse_chr6.simMouse.chr6 441410 26 + 636262 AACCTTAGAGACCATTTGTGATGTGA -s Anc0.Anc0refChr3 110265 26 - 222631 CACCTACAAGTCTTTTTGTGATATAA -s Anc1.Anc1refChr6 51571 26 - 197743 CACCTACAAGTCTTTTTGTGATATAA -s Anc2.Anc2refChr1 118543 26 - 142988 CACCAACAAATCTTTTGGTGCTATAA -s mr.mrrefChr3 130952 26 - 181027 TACCTCAGAGACCATTTGTGATGTGA -s simCow_chr6.simCow.chr6 121749 26 - 602619 CACCAACAAATCTTTTGGTGCTATAA -s simHuman_chr6.simHuman.chr6 123792 26 - 601863 AACCTAGAAGTCTTTTTGCAATAAAA -s simRat_chr6.simRat.chr6 453334 26 + 647215 TACCTCAGGGACCAATTGTGATGTGA -s simRat_chr6.simRat.chr6 138690 26 - 647215 TACCTCAGAGACCATTTATGATGTAA - -a -s simMouse_chr6.simMouse.chr6 441436 5 + 636262 CATCA -s Anc0.Anc0refChr3 110292 2 - 222631 T-T-- -s Anc1.Anc1refChr6 51598 4 - 197743 T-TCA -s Anc2.Anc2refChr1 118570 2 - 142988 T-T-- -s mr.mrrefChr3 130979 5 - 181027 CATCT -s simCow_chr6.simCow.chr6 121776 2 - 602619 T-T-- -s simHuman_chr6.simHuman.chr6 123819 4 - 601863 T-TCA -s simRat_chr6.simRat.chr6 453360 5 + 647215 CATCT -s simRat_chr6.simRat.chr6 138717 5 - 647215 CATCT - -a -s simMouse_chr6.simMouse.chr6 441441 38 + 636262 TATGTTGCAAAAAAATTGCTGATGGCCCACCTCTCTTC -s Anc0.Anc0refChr3 110297 38 - 222631 TGAGATGCAATAAAATTGCTGATGATCCACCTCTCTTG -s Anc1.Anc1refChr6 51606 38 - 197743 TGAGATGCAATAAAATTGCTGATGATCCACCTCTCTTG -s Anc2.Anc2refChr1 118575 38 - 142988 TGAGATGTAATAAAATTACTGATAATCCCCCTGTTTTG -s mr.mrrefChr3 130988 38 - 181027 TATGCTGCAAAAAAACTGCTGATGATCCACCTCTCTTC -s simCow_chr6.simCow.chr6 121781 38 - 602619 TGAGATGTAATAAAATTACTGATAATCCCCCTGTTTTG -s simHuman_chr6.simHuman.chr6 123827 38 - 601863 TGAGATGCAATAAAATTGCTGATGATCCACCTCGCTGG -s simMouse_chr6.simMouse.chr6 140149 38 - 636262 TGTGCTGCAATAAAACTGCTGATGATTGAGCTATCTAC -s simRat_chr6.simRat.chr6 453369 38 + 647215 CATGTTGCAAAAAAACTGCTGATGGCCTACCTCTCTTC -s simRat_chr6.simRat.chr6 138726 38 - 647215 TATACTGCAACAAAACTGCCAATGATCAAGCTATCTAC - -a -s simMouse_chr6.simMouse.chr6 441479 14 + 636262 TGCCTAATTAGTAG -s Anc0.Anc0refChr3 110335 14 - 222631 TGCTTATTAGATAG -s Anc1.Anc1refChr6 51644 14 - 197743 TGCTTATTAGATAG -s Anc2.Anc2refChr1 118613 14 - 142988 GGCTTATTAGATAG -s mr.mrrefChr3 131026 14 - 181027 TGCATAACTAAGAG -s simCow_chr6.simCow.chr6 121819 14 - 602619 GGCTTATTAGATAG -s simHuman_chr6.simHuman.chr6 123865 14 - 601863 TGCTTATTGGATAG -s simMouse_chr6.simMouse.chr6 140187 14 - 636262 TGCATAACTAAGAA -s simRat_chr6.simRat.chr6 453407 14 + 647215 TGCTTAACTAACAG -s simRat_chr6.simRat.chr6 138770 14 - 647215 TGCATAACTAAGAG - -a -s simMouse_chr6.simMouse.chr6 441493 2 + 636262 AT -s Anc0.Anc0refChr3 110349 2 - 222631 AT -s Anc1.Anc1refChr6 51658 2 - 197743 AT -s Anc2.Anc2refChr1 118627 2 - 142988 AC -s mr.mrrefChr3 131040 2 - 181027 AT -s simCow_chr6.simCow.chr6 121833 2 - 602619 AC -s simHuman_chr6.simHuman.chr6 123879 2 - 601863 CT -s simMouse_chr6.simMouse.chr6 140201 2 - 636262 AC -s simRat_chr6.simRat.chr6 138784 2 - 647215 AT - -a -s simMouse_chr6.simMouse.chr6 441495 7 + 636262 TTTGATT -s Anc0.Anc0refChr3 110351 7 - 222631 TATGATT -s Anc1.Anc1refChr6 51660 7 - 197743 TATGATT -s Anc2.Anc2refChr1 118629 7 - 142988 TATGAAT -s mr.mrrefChr3 131042 7 - 181027 TCTGATT -s simCow_chr6.simCow.chr6 121835 7 - 602619 TATGAAT -s simHuman_chr6.simHuman.chr6 123881 7 - 601863 CTTGATT -s simMouse_chr6.simMouse.chr6 140203 7 - 636262 TCTCTTC -s simRat_chr6.simRat.chr6 453421 7 + 647215 TTTGATT -s simRat_chr6.simRat.chr6 138786 7 - 647215 TCTGATA - -a -s simMouse_chr6.simMouse.chr6 441502 2 + 636262 AT -s Anc0.Anc0refChr3 110359 2 - 222631 AT -s Anc1.Anc1refChr6 51668 2 - 197743 AT -s Anc2.Anc2refChr1 118637 2 - 142988 GT -s mr.mrrefChr3 131049 2 - 181027 AT -s simCow_chr6.simCow.chr6 121843 2 - 602619 GT -s simHuman_chr6.simHuman.chr6 123889 2 - 601863 AT -s simMouse_chr6.simMouse.chr6 140210 2 - 636262 AT -s simRat_chr6.simRat.chr6 453428 2 + 647215 AT -s simRat_chr6.simRat.chr6 138793 2 - 647215 AT - -a -s simMouse_chr6.simMouse.chr6 441504 6 + 636262 ACATGG -s Anc0.Anc0refChr3 110361 6 - 222631 CCATGA -s Anc1.Anc1refChr6 51670 6 - 197743 CCATGA -s Anc2.Anc2refChr1 118639 6 - 142988 CTATGA -s mr.mrrefChr3 131051 6 - 181027 ACATGG -s simCow_chr6.simCow.chr6 121860 6 - 602619 CTATGA -s simHuman_chr6.simHuman.chr6 123891 6 - 601863 CCATGT -s simMouse_chr6.simMouse.chr6 140212 6 - 636262 ACATGG -s simRat_chr6.simRat.chr6 453430 6 + 647215 ACATGG -s simRat_chr6.simRat.chr6 138795 6 - 647215 ACATGG - -a -s simMouse_chr6.simMouse.chr6 441510 4 + 636262 CAAC -s Anc0.Anc0refChr3 110368 4 - 222631 TAGC -s Anc1.Anc1refChr6 51677 4 - 197743 TAGC -s Anc2.Anc2refChr1 118646 4 - 142988 TTGT -s mr.mrrefChr3 131058 4 - 181027 CAAC -s simCow_chr6.simCow.chr6 121867 4 - 602619 TTGT -s simHuman_chr6.simHuman.chr6 123898 4 - 601863 GAGC -s simMouse_chr6.simMouse.chr6 140219 4 - 636262 CGGC -s simRat_chr6.simRat.chr6 453436 4 + 647215 CAAC -s simRat_chr6.simRat.chr6 138802 4 - 647215 CAAA - -a -s simMouse_chr6.simMouse.chr6 441514 44 + 636262 CGGATTTATAATTTATATATGATTACAGATGCAGAACCTGGTAG -s Anc0.Anc0refChr3 110375 34 - 222631 TG-------TA---ATATATCATGACAAATGTAGAACATGGCAG -s Anc1.Anc1refChr6 51684 37 - 197743 TG-------TATTTATATATCATGACAAATGTAGAACATGGCAG -s Anc2.Anc2refChr1 118653 34 - 142988 TG-------TA---ACATATCATGACAAATGTAGAACATAGCAC -s mr.mrrefChr3 131062 37 - 181027 TG-------AATTTATATAGGATGACAGATGTAGAACCTGGCAG -s simCow_chr6.simCow.chr6 121874 34 - 602619 TG-------TA---ACATATCATGACAAATGTAGAACATAGAAC -s simDog_chr6.simDog.chr6 122893 10 - 593897 ----------------------------------AACGTAGCAC -s simHuman_chr6.simHuman.chr6 123905 37 - 601863 TG-------TATTTATATAACATGACAAATCTGGAACATGGCAG -s simMouse_chr6.simMouse.chr6 140223 29 - 636262 TG-------AATTTGTATAG--------CCATAGAACCTGGCAG -s simRat_chr6.simRat.chr6 453440 37 + 647215 TA-------AATTCATATAGGATCACAGATGCATAACCTGGCAG -s simRat_chr6.simRat.chr6 138806 37 - 647215 TG-------ATTTTGTATAACATGACTAATATAGAACCTGGCAG - -a -s simMouse_chr6.simMouse.chr6 441558 15 + 636262 AGAATTAACTATTGA -s Anc0.Anc0refChr3 110409 15 - 222631 AGCCTTAACAGTTGG -s Anc1.Anc1refChr6 51721 15 - 197743 AGCCTTAACAGTTGG -s Anc2.Anc2refChr1 118687 15 - 142988 AGCCTTAACAGTTGG -s mr.mrrefChr3 131099 15 - 181027 AGCCTTAACAATTGG -s simCow_chr6.simCow.chr6 121911 15 - 602619 CGCCTTGATGGCTGG -s simDog_chr6.simDog.chr6 122903 15 - 593897 AACCTTATCAATTCG -s simHuman_chr6.simHuman.chr6 123942 15 - 601863 AGCCTTAACAGTTGG -s simMouse_chr6.simMouse.chr6 140252 15 - 636262 AGCCTCAAGAATTGG -s simRat_chr6.simRat.chr6 453477 15 + 647215 AGCATTCACTGTAGG -s simRat_chr6.simRat.chr6 138843 15 - 647215 TACCTCAAGAATTGG - -a -s simMouse_chr6.simMouse.chr6 441573 20 + 636262 AATATCCTCATTGATATAAC -s Anc0.Anc0refChr3 110424 11 - 222631 AATATCCTAA---------C -s Anc1.Anc1refChr6 51736 11 - 197743 AATATCCTAA---------C -s Anc2.Anc2refChr1 118702 11 - 142988 AATATCATAA---------C -s mr.mrrefChr3 131114 11 - 181027 AATATCCTCA---------C -s simCow_chr6.simCow.chr6 121927 10 - 602619 AATATCGTAA---------- -s simDog_chr6.simDog.chr6 122918 11 - 593897 AATATCACAA---------C -s simHuman_chr6.simHuman.chr6 123957 11 - 601863 ATTATCCTAA---------C -s simMouse_chr6.simMouse.chr6 140267 11 - 636262 AATTTCCTCA---------C -s simRat_chr6.simRat.chr6 453492 11 + 647215 AATGTCCTCA---------C -s simRat_chr6.simRat.chr6 138858 11 - 647215 AATATCCTCA---------C - -a -s simMouse_chr6.simMouse.chr6 441593 18 + 636262 TGATATAACTTACTATAC -s Anc0.Anc0refChr3 110435 18 - 222631 TGATTTGACTTATTATAT -s Anc1.Anc1refChr6 51747 18 - 197743 TGATTTGACTTATTATAT -s Anc2.Anc2refChr1 118713 18 - 142988 TGATTTGACTTATTATAT -s mr.mrrefChr3 131125 18 - 181027 TGATTTCACTTACTGTAT -s simCow_chr6.simCow.chr6 121937 14 - 602619 ----TTGGCTCAAAGTAT -s simDog_chr6.simDog.chr6 122932 18 - 593897 TGATTTGACTTATTATAT -s simHuman_chr6.simHuman.chr6 123968 18 - 601863 AGATTTGACTTATGATTT -s simMouse_chr6.simMouse.chr6 140278 18 - 636262 TGTTTCCACTTATTGTAT -s simRat_chr6.simRat.chr6 453503 18 + 647215 TGATATGACTTACTTTAC -s simRat_chr6.simRat.chr6 138869 18 - 647215 TGTTTTCACTTGCTGTAT - -a -s simMouse_chr6.simMouse.chr6 441611 23 + 636262 AACTTGTCCTTTTCTAAATACAG -s Anc0.Anc0refChr3 110453 23 - 222631 GGCTTTTCCTTTTTCAAAACCAG -s Anc1.Anc1refChr6 51765 23 - 197743 GGCTTTTCCTTTTTCAAAACCAG -s Anc2.Anc2refChr1 118731 23 - 142988 GGCTTTTCCTTTTTCAAAACCAG -s mr.mrrefChr3 131143 23 - 181027 AGCTTTTCCTTTTTTAAATACAG -s simCow_chr6.simCow.chr6 121951 23 - 602619 GGCTTATCTTTTTTTAGAATCAG -s simDog_chr6.simDog.chr6 122950 23 - 593897 GGCTTTTCCTTTTTCAAAACCAG -s simHuman_chr6.simHuman.chr6 123987 23 - 601863 GGCTTTTCCTTTCTCAAAACCAG -s simMouse_chr6.simMouse.chr6 140296 20 - 636262 CGCTTTTCTTCTTTTAA---CAA -s simRat_chr6.simRat.chr6 453521 23 + 647215 AACTTTTCTTTGTCTAAATACCG -s simRat_chr6.simRat.chr6 138887 23 - 647215 GGCTTTTCCTCATTTCAATCCAA - -a -s simMouse_chr6.simMouse.chr6 441634 5 + 636262 TTATA -s Anc0.Anc0refChr3 110476 5 - 222631 TTATA -s Anc1.Anc1refChr6 51788 5 - 197743 TTATA -s Anc2.Anc2refChr1 118754 5 - 142988 TTATA -s mr.mrrefChr3 131166 5 - 181027 TTATA -s simCow_chr6.simCow.chr6 121974 5 - 602619 TTATA -s simDog_chr6.simDog.chr6 122973 5 - 593897 TCCTA -s simHuman_chr6.simHuman.chr6 124010 5 - 601863 CTATA -s simMouse_chr6.simMouse.chr6 140316 5 - 636262 TTATA -s simRat_chr6.simRat.chr6 453544 5 + 647215 TTTTG -s simRat_chr6.simRat.chr6 138960 5 - 647215 CTAAT - -a -s simMouse_chr6.simMouse.chr6 441639 6 + 636262 ATGTTT -s Anc0.Anc0refChr3 110481 5 - 222631 ATACC- -s Anc1.Anc1refChr6 51793 6 - 197743 ATACCT -s Anc2.Anc2refChr1 118759 5 - 142988 ATACC- -s mr.mrrefChr3 131171 6 - 181027 ACGTCT -s simCow_chr6.simCow.chr6 121979 5 - 602619 ATACC- -s simDog_chr6.simDog.chr6 122978 5 - 593897 ATACA- -s simHuman_chr6.simHuman.chr6 124015 6 - 601863 ATCCCT -s simMouse_chr6.simMouse.chr6 140322 6 - 636262 ACTTCT -s simRat_chr6.simRat.chr6 453549 6 + 647215 ACGTTT -s simRat_chr6.simRat.chr6 138965 6 - 647215 ACCACT - -a -s simMouse_chr6.simMouse.chr6 441645 28 + 636262 GAGTCATGAACAGTTCACACTAGCCATT -s Anc0.Anc0refChr3 110487 28 - 222631 AAGATGTGGAAAGTTTACTCTAGCCAAC -s Anc1.Anc1refChr6 51800 28 - 197743 AAGATGTGGAAAGTTTACTCTAGCCAAC -s Anc2.Anc2refChr1 118765 28 - 142988 AAGATAAGGAAAGTTTACTCTAGCTAAC -s mr.mrrefChr3 131178 28 - 181027 GAGATGTGGACAGTTCACTCTAGCCAAT -s simCow_chr6.simCow.chr6 121985 28 - 602619 AGGACCATGAAAGTTTACTCTAGCAAAC -s simDog_chr6.simDog.chr6 122984 28 - 593897 AAGATAAGGAAAGTTTACCCTAGCTAGC -s simHuman_chr6.simHuman.chr6 124022 28 - 601863 AAGATGTGGAAAGTTTACTCTAGCCAAC -s simMouse_chr6.simMouse.chr6 140329 28 - 636262 AAAATGTAGATAGTCCACTCTACCAAAT -s simRat_chr6.simRat.chr6 453555 28 + 647215 GAGATGTGGACAGTTCACACTAGCCATT -s simRat_chr6.simRat.chr6 138972 28 - 647215 TAAATGTGGACAGCTCACTCTACCACAT - -a -s simMouse_chr6.simMouse.chr6 441673 1 + 636262 C -s Anc0.Anc0refChr3 110515 1 - 222631 C -s Anc1.Anc1refChr6 51828 1 - 197743 C -s Anc2.Anc2refChr1 118793 1 - 142988 C -s mr.mrrefChr3 131206 1 - 181027 C -s simCow_chr6.simCow.chr6 122013 1 - 602619 C -s simDog_chr6.simDog.chr6 123018 1 - 593897 C -s simHuman_chr6.simHuman.chr6 124050 1 - 601863 C -s simMouse_chr6.simMouse.chr6 140357 1 - 636262 C -s simRat_chr6.simRat.chr6 453583 1 + 647215 C -s simRat_chr6.simRat.chr6 139000 1 - 647215 C - -a -s simMouse_chr6.simMouse.chr6 441674 5 + 636262 CACCA -s Anc0.Anc0refChr3 110696 5 - 222631 CACCA -s Anc1.Anc1refChr6 52009 5 - 197743 CACCA -s Anc2.Anc2refChr1 118974 5 - 142988 TGCCA -s mr.mrrefChr3 131378 5 - 181027 CACCA -s simCow_chr6.simCow.chr6 122171 5 - 602619 TGCCA -s simDog_chr6.simDog.chr6 123217 5 - 593897 TGCCA -s simHuman_chr6.simHuman.chr6 124231 5 - 601863 CACCA -s simMouse_chr6.simMouse.chr6 140526 4 - 636262 T-TCA -s simRat_chr6.simRat.chr6 453757 5 + 647215 CATTG -s simRat_chr6.simRat.chr6 139161 5 - 647215 CACCA - -a -s simMouse_chr6.simMouse.chr6 441679 1 + 636262 A -s mr.mrrefChr3 0 1 + 181027 A -s simRat_chr6.simRat.chr6 453762 1 + 647215 G - -a -s simMouse_chr6.simMouse.chr6 441680 14 + 636262 CTGTCCTTATACAG -s Anc0.Anc0refChr3 110702 14 - 222631 TTGTCTCTATACAG -s Anc1.Anc1refChr6 52015 14 - 197743 TTGTCTCTATACAG -s Anc2.Anc2refChr1 118980 14 - 142988 TTTTTTCTATACAG -s mr.mrrefChr3 1 14 + 181027 CTGTCCTTATACAG -s mr.mrrefChr3 131384 14 - 181027 CTGCCCTTATAAAG -s simCow_chr6.simCow.chr6 122180 14 - 602619 TTTTTTCTATGCAG -s simDog_chr6.simDog.chr6 123223 14 - 593897 CTTTTTCCTTACAG -s simHuman_chr6.simHuman.chr6 124237 14 - 601863 TTATCTCTATACAG -s simMouse_chr6.simMouse.chr6 140531 14 - 636262 CTGCCCTTACAAAG -s simRat_chr6.simRat.chr6 139167 14 - 647215 Ccgcccttataagg -s simRat_chr6.simRat.chr6 453763 14 + 647215 CTGTCCCTATACAG - -a -s simMouse_chr6.simMouse.chr6 441694 1 + 636262 C -s Anc0.Anc0refChr3 110716 1 - 222631 C -s Anc1.Anc1refChr6 52029 1 - 197743 C -s Anc2.Anc2refChr1 118994 1 - 142988 C -s mr.mrrefChr3 15 1 + 181027 C -s simCow_chr6.simCow.chr6 122194 1 - 602619 C -s simDog_chr6.simDog.chr6 123237 1 - 593897 C -s simHuman_chr6.simHuman.chr6 124251 1 - 601863 C -s simRat_chr6.simRat.chr6 453777 1 + 647215 C - -a -s simMouse_chr6.simMouse.chr6 441695 28 + 636262 TTTTTGTGTCTATCCTGGTGAAAAAATT -s Anc0.Anc0refChr3 110717 28 - 222631 TTTTTTTGTTTATCCTGTTGACAAAAGT -s Anc1.Anc1refChr6 52030 28 - 197743 TTTTTTTGTTTATCCTGTTGACAAAAGT -s Anc2.Anc2refChr1 118995 28 - 142988 TTATTTTGTTTATCATGTTGACAAAAGT -s mr.mrrefChr3 16 28 + 181027 TTTTTGTGTCTATCCTGGTGAAAAAATT -s mr.mrrefChr3 131398 28 - 181027 TTTTTTTGTTGATCCTGTTGAAGAAGGT -s simCow_chr6.simCow.chr6 122195 28 - 602619 ATGTTTTGTGTATCCTGTTGACCAAAGA -s simDog_chr6.simDog.chr6 123238 28 - 593897 TAATTTTGTTTATCATGGTGGCAAAAGT -s simHuman_chr6.simHuman.chr6 124252 28 - 601863 TTCTTTTGTTTATCTTGTTGACAAACGT -s simMouse_chr6.simMouse.chr6 140545 28 - 636262 TTTTTTTATTGATACTGTTGAAGTAGGT -s simRat_chr6.simRat.chr6 139181 28 - 647215 tttttttgttaatcctgttgaagaaggg -s simRat_chr6.simRat.chr6 453778 28 + 647215 TTTTTTTGTTTATCCTGTTTAAAAAATT - -a -s simMouse_chr6.simMouse.chr6 441723 3 + 636262 AAG -s Anc0.Anc0refChr3 110745 3 - 222631 AAA -s Anc1.Anc1refChr6 52058 3 - 197743 AAA -s Anc2.Anc2refChr1 119023 3 - 142988 AGA -s mr.mrrefChr3 44 3 + 181027 AAG -s mr.mrrefChr3 131426 3 - 181027 aAA -s simCow_chr6.simCow.chr6 122223 3 - 602619 AGA -s simDog_chr6.simDog.chr6 123268 3 - 593897 AGA -s simHuman_chr6.simHuman.chr6 124280 3 - 601863 CAA -s simMouse_chr6.simMouse.chr6 140573 3 - 636262 AAA -s simRat_chr6.simRat.chr6 139209 3 - 647215 aaa -s simRat_chr6.simRat.chr6 453806 3 + 647215 AAA - -a -s simMouse_chr6.simMouse.chr6 441726 35 + 636262 CTGATTGGAGCTCTAGTGGCGTAAAAGAAATCAGA -s Anc0.Anc0refChr3 110748 35 - 222631 CTGGTTGGAGCTTTAAGAGCATCCAAGAAATCAGA -s Anc1.Anc1refChr6 52061 35 - 197743 CTGGTTGGAGCTTTAAGAGCATCCAAGAAATCAGA -s Anc2.Anc2refChr1 119026 35 - 142988 CTGGTTGGAGCTTTAAGAGTTGCCAAGAAATCAGA -s mr.mrrefChr3 47 35 + 181027 CTGATTGGAGCTCTAGTGGCGTAAAAGAAATCAGA -s mr.mrrefChr3 131430 35 - 181027 CTCATTCGAGCTTCAGCGGCATCCAGGAGATCAGA -s simCow_chr6.simCow.chr6 122226 35 - 602619 CTGGTTGAATCTTTAAGAGTGATCAAGAAATCAGA -s simDog_chr6.simDog.chr6 123271 35 - 593897 CTGGTTGGAGCTTTGAGGTTTGCCAAGAAGTCAGA -s simHuman_chr6.simHuman.chr6 124283 35 - 601863 CTGGTTAGAGCTCCAAGAGCATCCAAGAAATTGGA -s simMouse_chr6.simMouse.chr6 140577 35 - 636262 CTCATTCGAGCTTCAGCGGCATCCAGGAGATCAGA -s simRat_chr6.simRat.chr6 139213 35 - 647215 ctcaatggagcttcagcggcacccaggatacccga -s simRat_chr6.simRat.chr6 453809 35 + 647215 CTGGTTGGAGCTTTAGTGGCATCCAGGAAACCAGA - -a -s simMouse_chr6.simMouse.chr6 441761 14 + 636262 ATGGGAATCATACA -s Anc0.Anc0refChr3 110783 14 - 222631 AAAGGAATAACAAA -s Anc1.Anc1refChr6 52096 14 - 197743 AAAGGAATAACAAA -s Anc2.Anc2refChr1 119061 14 - 142988 AAAGGACGAACAAA -s mr.mrrefChr3 82 14 + 181027 ATGGGAATCATACA -s mr.mrrefChr3 131465 14 - 181027 ACAGGAATAATACA -s simCow_chr6.simCow.chr6 122261 14 - 602619 AATGGACCAATACA -s simDog_chr6.simDog.chr6 123306 14 - 593897 AAATAACGAACAAA -s simHuman_chr6.simHuman.chr6 124318 14 - 601863 AAAGGAATTACAAA -s simMouse_chr6.simMouse.chr6 140612 14 - 636262 ACAGGAATAATACA -s simRat_chr6.simRat.chr6 143731 14 - 647215 ACAGTAATCGTACA -s simRat_chr6.simRat.chr6 453844 14 + 647215 ATGGGAGTCATACA - -a -s simMouse_chr6.simMouse.chr6 441775 1 + 636262 T -s Anc0.Anc0refChr3 110797 1 - 222631 T -s Anc1.Anc1refChr6 52110 1 - 197743 T -s Anc2.Anc2refChr1 119075 1 - 142988 T -s mr.mrrefChr3 96 1 + 181027 T -s mr.mrrefChr3 131479 1 - 181027 T -s simCow_chr6.simCow.chr6 122379 1 - 602619 T -s simDog_chr6.simDog.chr6 123320 1 - 593897 T -s simHuman_chr6.simHuman.chr6 124332 1 - 601863 T -s simMouse_chr6.simMouse.chr6 140626 1 - 636262 T -s simRat_chr6.simRat.chr6 143745 1 - 647215 T -s simRat_chr6.simRat.chr6 453858 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 441776 4 + 636262 ACAG -s Anc0.Anc0refChr3 110800 4 - 222631 AAGA -s Anc1.Anc1refChr6 52113 4 - 197743 AAGA -s Anc2.Anc2refChr1 119080 4 - 142988 AAGC -s mr.mrrefChr3 97 4 + 181027 ACAA -s mr.mrrefChr3 131480 4 - 181027 AAGG -s simCow_chr6.simCow.chr6 122384 4 - 602619 GAGG -s simDog_chr6.simDog.chr6 123325 4 - 593897 AAGC -s simHuman_chr6.simHuman.chr6 124335 4 - 601863 AAGA -s simMouse_chr6.simMouse.chr6 140627 4 - 636262 AAGG -s simRat_chr6.simRat.chr6 143746 4 - 647215 AAGG -s simRat_chr6.simRat.chr6 453859 4 + 647215 ACAA - -a -s simMouse_chr6.simMouse.chr6 441780 16 + 636262 GGGGGCTTGGTTGCAC -s Anc0.Anc0refChr3 67468 16 + 222631 GTGGATCTTATCACAC -s Anc1.Anc1refChr6 98594 16 + 197743 GTGGATCTTATCACAC -s Anc2.Anc2refChr13 73343 16 + 96486 GTGGATCCTATCACAC -s mr.mrrefChr3 101 16 + 181027 GGGGGCTTGGTCGCAC -s simCow_chr6.simCow.chr6 430302 16 + 602619 GCAGATCCTATTGCAC -s simDog_chr6.simDog.chr6 421449 16 + 593897 GTGGATCCTATCACGT -s simHuman_chr6.simHuman.chr6 424786 16 + 601863 GTGGATCTTATCATAC -s simRat_chr6.simRat.chr6 453863 16 + 647215 GGGGGCTTGGGCTCAC - -a -s simMouse_chr6.simMouse.chr6 441796 19 + 636262 TCCCCGCAACTACTTTAGA -s Anc0.Anc0refChr3 67485 19 + 222631 TGCCTGCAACTTCCTCAAA -s Anc1.Anc1refChr6 98611 19 + 197743 TGCCTGCAACTTCCTCAAA -s Anc2.Anc2refChr13 73360 19 + 96486 TGCCTGCAACTTCCTCAAA -s mr.mrrefChr3 117 19 + 181027 TCCCTGCAACTACTTTAGA -s simCow_chr6.simCow.chr6 430319 19 + 602619 TGACCACAACTTCCTCAAA -s simDog_chr6.simDog.chr6 421466 19 + 593897 TGCCTGCTACTTCCCAAGA -s simHuman_chr6.simHuman.chr6 424803 19 + 601863 TTTCTGCAACTTCCTCAAA -s simRat_chr6.simRat.chr6 453879 19 + 647215 TGCCTGCAACTACTTTAGA - -a -s simMouse_chr6.simMouse.chr6 441815 40 + 636262 AAATTTAAGAAGGAAAGATAGGACTTGAGGGCTAGGATGC -s Anc0.Anc0refChr3 67505 40 + 222631 GCTGCTAAGAAGGAAGGATAGGACTAGAGCACTAGGATAT -s Anc1.Anc1refChr6 98631 40 + 197743 GCTGCTAAGAAGGAAGGATAGGACTAGAGCACTAGGATAT -s Anc2.Anc2refChr13 73380 40 + 96486 GCTGCTAAGAAGGAAGAATAGGACTAGAGCACCAGGATAT -s mr.mrrefChr3 137 40 + 181027 ACAGCTAAGAAGGAAAGATAGGACTTGAGGGCTAGGATGC -s simCow_chr6.simCow.chr6 430339 38 + 602619 GGTG-TAAGAAGGAAGACTAGG-CTAGAGCACCAGGATGG -s simDog_chr6.simDog.chr6 421486 40 + 593897 ACCACTAAGAAGGAAGAATAGGACTAGAGCGCCGGGATAT -s simHuman_chr6.simHuman.chr6 424823 40 + 601863 GCTGCTAAGAAGGAAGGATAAGACTATAACATTAGGATAT -s simRat_chr6.simRat.chr6 453899 40 + 647215 ACAGCTAAGAAGGAAAGATAGGACTGGAGGGCTAGCATGC - -a -s simMouse_chr6.simMouse.chr6 441855 14 + 636262 TCCACACTGTTGTG -s Anc0.Anc0refChr3 67547 14 + 222631 CCCATGCTTTTGTG -s Anc1.Anc1refChr6 98673 14 + 197743 CCCATGCTTTTGTG -s Anc2.Anc2refChr13 73422 14 + 96486 CCCATGCTTTTGCA -s mr.mrrefChr3 177 14 + 181027 TCCACACTGTTGTG -s simCow_chr6.simCow.chr6 430379 13 + 602619 CCCGTGATTTT-CA -s simDog_chr6.simDog.chr6 421528 14 + 593897 CCCACGCTTTTGCA -s simHuman_chr6.simHuman.chr6 424869 14 + 601863 CCCATGCTCTTGTG -s simRat_chr6.simRat.chr6 453939 14 + 647215 TCAACACTTTTGTG - -a -s simMouse_chr6.simMouse.chr6 441869 13 + 636262 TTTTAACCTGCAA -s Anc0.Anc0refChr3 67573 13 + 222631 TTCAAACATTCAA -s Anc1.Anc1refChr6 98699 13 + 197743 TTCAAACATTCAA -s Anc2.Anc2refChr13 73448 13 + 96486 TTCAAACATTCAA -s mr.mrrefChr3 191 13 + 181027 TTTTAACCTGCAA -s simCow_chr6.simCow.chr6 430404 13 + 602619 TGCAAACAGGCAA -s simDog_chr6.simDog.chr6 421553 13 + 593897 TTCAAACATTCGG -s simHuman_chr6.simHuman.chr6 424895 13 + 601863 TTCAAATATTCAA -s simRat_chr6.simRat.chr6 453953 13 + 647215 TTTTAACCTGCAA - -a -s simMouse_chr6.simMouse.chr6 441882 105 + 636262 CACCCAATCCATCACCTACCTCACCTTATCAATACGTTTTACTGTGCCCGGTAGGAGTGCACACTTTTTGCCGCATTTGACAGGACACTGACTTTTTCTCTTTGT -s Anc0.Anc0refChr3 67586 91 + 222631 TGGCATATCCATCATTTACCTT----------TTCCTCTGTCA----CTGCTAAGAGCACACACCTTATGGCTTATTTTACTGGAGGCTGCAATCTTCTTTGCAT -s Anc1.Anc1refChr6 98712 93 + 197743 TGGCATATCCATCATTTACCTT----------TTCCTCTGTCACT--CTGCTAAGAGCACACACCTTATGGCTTATTTTACTGGAGGCTGCAATCTTCTTTGCAT -s Anc2.Anc2refChr13 73461 91 + 96486 TGGCATATCCATCATTTACCCT----------TTACTCTGTCA----CTGCTAAGAGCACACATCTAATGGCTCATTTTACTGGAGGCTGCAATCTTCTTTGCAT -s mr.mrrefChr3 204 103 + 181027 CACCCAATCCATCACCTACCTCACCTTATCAATTCGTTTTACTGT--CTGGTAGGAGTGCACACTTTTTGCCTTATTTGACAGGACACTGACTTTTTCTCTTTGT -s simCow_chr6.simCow.chr6 430417 60 + 602619 TGGCCCATCTATCATTT------------------CCATGTCA----CTGCTAAGATCAC-------------------ACTGGAGGCTTCA----TCTTAGCAT -s simDog_chr6.simDog.chr6 421566 91 + 593897 TGGCATATTCATCATTGACCCT----------TTACTCTGTAA----CAGCTAAGTGCCCACATCTAATGGCTCATTTTACTGGGGGCTGCCATCTTCTCTGCAT -s simHuman_chr6.simHuman.chr6 424908 93 + 601863 TGGCATATCCATCATTTACCTT----------TTCAACTGTCACT--CTGATAAGAACACACACCTTCTGGCTTACTTTACTGGAGGCTGCACCCCTCTTCGCAT -s simRat_chr6.simRat.chr6 453967 103 + 647215 CACCCAATCCATCACCTCCCTCACCTTGTCGATTTGTTTTACTGT--CTGGTAGGAGAGCACACTCTTTCCCTTATTTAACAGGACACTGACTTTTTCTATATGT - -a -s simMouse_chr6.simMouse.chr6 441987 13 + 636262 TGTCAGTAATGTT -s Anc0.Anc0refChr3 67677 13 + 222631 TGTCACTAGCATT -s Anc1.Anc1refChr6 98805 13 + 197743 TGTCACTAGCATT -s Anc2.Anc2refChr13 73554 13 + 96486 TGTCACTAGCATT -s mr.mrrefChr3 307 13 + 181027 TGTCAGTAATGTT -s simCow_chr6.simCow.chr6 430479 13 + 602619 TGTCTCTAACATT -s simDog_chr6.simDog.chr6 421659 13 + 593897 TGTCACTAGCATT -s simHuman_chr6.simHuman.chr6 425001 3 + 601863 TGT---------- -s simRat_chr6.simRat.chr6 454070 13 + 647215 TGTCAGTAATATT - -a -s simMouse_chr6.simMouse.chr6 442000 4 + 636262 TTGC -s Anc0.Anc0refChr3 67690 4 + 222631 TCCC -s Anc1.Anc1refChr6 98818 4 + 197743 TCCC -s Anc2.Anc2refChr13 73569 4 + 96486 TCCC -s mr.mrrefChr3 320 4 + 181027 TTGC -s simCow_chr6.simCow.chr6 430494 4 + 602619 TCCC -s simDog_chr6.simDog.chr6 421674 4 + 593897 TCCC -s simRat_chr6.simRat.chr6 454083 4 + 647215 GCGT - -a -s simMouse_chr6.simMouse.chr6 442004 10 + 636262 CTCTCTGTTA -s Anc0.Anc0refChr3 67694 9 + 222631 CTCTCT-TTG -s Anc1.Anc1refChr6 98822 9 + 197743 CTCTCT-TTG -s Anc2.Anc2refChr13 73573 9 + 96486 CTCTCT-TTG -s mr.mrrefChr3 324 10 + 181027 CTCTCTGTTA -s simCow_chr6.simCow.chr6 430498 9 + 602619 CTCTTG-TTG -s simDog_chr6.simDog.chr6 421678 9 + 593897 CTCTCT-TTG -s simRat_chr6.simRat.chr6 454088 10 + 647215 CTCTCTGTTA - -a -s simMouse_chr6.simMouse.chr6 442014 77 + 636262 CTTCTCATCGAGTTTTGTTTGAAGCTACTCCTTTCGAACAGTCTTTAATTGTCCAAACTGAATGAAACAAAGCATAA -s Anc0.Anc0refChr3 67703 25 + 222631 CTGCTAAACAAATTATGTTTGA----------------------------------------------------TAT -s Anc1.Anc1refChr6 98831 25 + 197743 CTGCTAAACAAATTATGTTTGA----------------------------------------------------TAT -s Anc2.Anc2refChr13 73582 25 + 96486 CTGCTAAACAAATTACGTTTGA----------------------------------------------------CAT -s mr.mrrefChr3 334 77 + 181027 CTTCTCATCGAGTTTTGTTTGAAGCTACTCCTTTCGAACAGTCTTTAATTGTCCAAACTGAATGAAACAAAGCATAA -s simCow_chr6.simCow.chr6 430507 25 + 602619 CTGCTTAATGAGTTTCAATTGA----------------------------------------------------TAA -s simDog_chr6.simDog.chr6 421692 25 + 593897 CTGCTAAACAAATTACGTTTGA----------------------------------------------------CAT -s simHuman_chr6.simHuman.chr6 425004 13 + 601863 ------------GTATGCCTCA----------------------------------------------------TAT -s simRat_chr6.simRat.chr6 454098 77 + 647215 CTGCTCATTGAGTTTTGGTTGAAACTACTCTTTGTGAACAGTCTTTAATTATCCAAACGAAATGAGACAAAACATAC - -a -s simMouse_chr6.simMouse.chr6 442091 8 + 636262 ACATACGT -s Anc0.Anc0refChr3 67728 8 + 222631 TCATCACT -s Anc1.Anc1refChr6 98856 8 + 197743 TCATCACT -s Anc2.Anc2refChr13 73614 8 + 96486 TCTTCACT -s mr.mrrefChr3 411 8 + 181027 ACATACCT -s simCow_chr6.simCow.chr6 430539 8 + 602619 TCTGCCCT -s simDog_chr6.simDog.chr6 421724 8 + 593897 TCTTCACT -s simHuman_chr6.simHuman.chr6 425017 8 + 601863 TCATGACT -s simRat_chr6.simRat.chr6 454175 8 + 647215 ACATACCT - -a -s simMouse_chr6.simMouse.chr6 442099 9 + 636262 TATGTTCAT -s Anc0.Anc0refChr3 67737 9 + 222631 CATATTCAT -s Anc1.Anc1refChr6 98865 9 + 197743 CATATTCAT -s Anc2.Anc2refChr13 73623 9 + 96486 CATATTAAT -s mr.mrrefChr3 419 9 + 181027 TATATTCAT -s simDog_chr6.simDog.chr6 421733 9 + 593897 CATATTAAT -s simHuman_chr6.simHuman.chr6 425026 9 + 601863 CATATGCAT -s simRat_chr6.simRat.chr6 454183 9 + 647215 TATATTCAT - -a -s simMouse_chr6.simMouse.chr6 442108 2 + 636262 GG -s Anc0.Anc0refChr3 67746 2 + 222631 GA -s Anc1.Anc1refChr6 98874 2 + 197743 GA -s Anc2.Anc2refChr13 73645 2 + 96486 GA -s mr.mrrefChr3 428 2 + 181027 GG -s simDog_chr6.simDog.chr6 421755 2 + 593897 GA -s simHuman_chr6.simHuman.chr6 425035 2 + 601863 GA - -a -s simMouse_chr6.simMouse.chr6 442110 83 + 636262 CTGCTGGTCATCTAATTACAGAGAGTGATAAGCGAGATAACTCACTGAAAACTCCCTTCCCTATATTTCCATCCTAGTGGCAC -s Anc0.Anc0refChr3 67748 67 + 222631 CTGCTAGTCATGTAGTGACAGAGAGCCATGAGGTAGATAACTC----------------CCTATTGTTTCATCCTATTGGTGT -s Anc1.Anc1refChr6 98876 67 + 197743 CTGCTAGTCATGTAGTGACAGAGAGCCATGAGGTAGATAACTC----------------CCTATTGTTTCATCCTATTGGTGT -s Anc2.Anc2refChr13 73647 67 + 96486 CTGCTAGTCATGTAGTGACAGAGAGCCATGACTTAGATAACTC----------------CATATTGTTTCATGATATTGGTGT -s mr.mrrefChr3 430 73 + 181027 CTGCTGGTCATCTAATTACAGAGAGTGATAAGGTAGATAACTCAC----------CTTCCCTATATTTCCATCCTAGTGGCAT -s simDog_chr6.simDog.chr6 421758 67 + 593897 CTGCTAGTCATGTAGTGACAGAGAGCCATGACTTAGATAACTC----------------CATATTGTTTCATGATATTGGTGT -s simHuman_chr6.simHuman.chr6 425037 67 + 601863 CTGCTAGCCATGTAGTGACAGAGAGCCATGAGGTATTTAACTC----------------CCTATTGTTTTATCCTATTGGTGT -s simRat_chr6.simRat.chr6 454192 70 + 647215 ---CTGGTCATCTAATTACCAAAAGAGATAAGGTAGATAACTCAC----------CTTCCCTATATTTCCATCCTAATGGCAT - -a -s simMouse_chr6.simMouse.chr6 442193 4 + 636262 AGTA -s Anc0.Anc0refChr3 67816 4 + 222631 AGTG -s Anc1.Anc1refChr6 98944 4 + 197743 AGTG -s Anc2.Anc2refChr13 73715 4 + 96486 ATGG -s mr.mrrefChr3 503 4 + 181027 AGTA -s simCow_chr6.simCow.chr6 430547 3 + 602619 -TGG -s simDog_chr6.simDog.chr6 421826 4 + 593897 ATGG -s simHuman_chr6.simHuman.chr6 425105 4 + 601863 AGTG -s simRat_chr6.simRat.chr6 454262 4 + 647215 AGTA - -a -s simMouse_chr6.simMouse.chr6 442197 2 + 636262 GC -s Anc0.Anc0refChr3 67820 2 + 222631 GA -s Anc1.Anc1refChr6 98948 2 + 197743 GA -s Anc2.Anc2refChr13 73719 2 + 96486 GA -s mr.mrrefChr3 507 2 + 181027 GC -s simCow_chr6.simCow.chr6 430550 2 + 602619 GA -s simDog_chr6.simDog.chr6 421837 2 + 593897 GA -s simHuman_chr6.simHuman.chr6 425109 2 + 601863 GG -s simRat_chr6.simRat.chr6 454266 2 + 647215 GC - -a -s simMouse_chr6.simMouse.chr6 442199 13 + 636262 TTTTGTGGAGCCA -s Anc0.Anc0refChr3 67822 13 + 222631 TTTCTTGAATGCA -s Anc1.Anc1refChr6 98950 13 + 197743 TTTCTTGAATGCA -s Anc2.Anc2refChr13 73721 13 + 96486 TTTCTTGAGTGCA -s mr.mrrefChr3 509 13 + 181027 TTTCGTGGAGCCA -s simCow_chr6.simCow.chr6 430554 13 + 602619 TTTCTTGAGTGTG -s simDog_chr6.simDog.chr6 421839 13 + 593897 TTAATTTGGGGCA -s simHuman_chr6.simHuman.chr6 425111 13 + 601863 TTTCTTGAATGCA -s simRat_chr6.simRat.chr6 454268 13 + 647215 CTTCATAGAGCCA - -a -s simMouse_chr6.simMouse.chr6 442212 25 + 636262 TCTGCTGGGGGCCCAGGACTCAGTT -s Anc0.Anc0refChr3 67835 25 + 222631 CTTGTCGGGGGCCCAGGACTCAATT -s Anc1.Anc1refChr6 98963 25 + 197743 CTTGTCGGGGGCCCAGGACTCAATT -s Anc2.Anc2refChr13 73734 25 + 96486 CTTGTCGGGGACCCAGGACTCAAAT -s mr.mrrefChr3 522 25 + 181027 TCTGCTGGGGGCCCAGGACTCAGTT -s simCow_chr6.simCow.chr6 430567 25 + 602619 CTTCTTGGGGACCCAGGACTCAAAT -s simDog_chr6.simDog.chr6 421960 6 + 593897 TTTGTC------------------- -s simHuman_chr6.simHuman.chr6 425124 25 + 601863 CTTGTCGGGTGGCCAGGAGTCAATT -s simRat_chr6.simRat.chr6 454281 25 + 647215 TCTGCTGGGGGCCAAGGACTCAGTT - -a -s simMouse_chr6.simMouse.chr6 442237 5 + 636262 GCAGC -s Anc0.Anc0refChr3 67906 5 + 222631 GCAAT -s Anc1.Anc1refChr6 99034 5 + 197743 GCAAT -s Anc2.Anc2refChr13 73805 5 + 96486 CCAAT -s mr.mrrefChr3 547 5 + 181027 GCAGC -s simDog_chr6.simDog.chr6 421993 5 + 593897 CCAAT -s simHuman_chr6.simHuman.chr6 425220 5 + 601863 GCAAT -s simRat_chr6.simRat.chr6 454306 5 + 647215 GCAGC - -a -s simMouse_chr6.simMouse.chr6 442242 4 + 636262 AGCT -s Anc0.Anc0refChr3 67911 4 + 222631 AGAT -s Anc1.Anc1refChr6 99039 4 + 197743 AGAT -s Anc2.Anc2refChr13 73810 4 + 96486 AGAT -s mr.mrrefChr3 552 4 + 181027 AGCT -s simCow_chr6.simCow.chr6 430627 3 + 602619 -GAT -s simDog_chr6.simDog.chr6 422003 4 + 593897 AGGT -s simHuman_chr6.simHuman.chr6 425225 4 + 601863 GGAT -s simRat_chr6.simRat.chr6 454311 4 + 647215 AGCT - -a -s simMouse_chr6.simMouse.chr6 442246 15 + 636262 AAATCTCAACAACCT -s Anc0.Anc0refChr3 67921 15 + 222631 AAATCTAAACAGCTT -s Anc1.Anc1refChr6 99049 15 + 197743 AAATCTAAACAGCTT -s Anc2.Anc2refChr13 73820 15 + 96486 AAATCTAAACAGCTT -s mr.mrrefChr3 560 15 + 181027 AAATCTCAACAACCT -s simCow_chr6.simCow.chr6 430636 15 + 602619 AAATCCATTCAGCTT -s simDog_chr6.simDog.chr6 422013 15 + 593897 AAATCTTAAAAACCC -s simHuman_chr6.simHuman.chr6 425235 15 + 601863 AGATCTAAACAGCTT -s simRat_chr6.simRat.chr6 454319 15 + 647215 AAATCTCCACAACCT - -a -s simMouse_chr6.simMouse.chr6 442261 42 + 636262 AGACCCCCTAGCCTTAGATAGTGTATAAAGTGATGCTTGTTT -s Anc0.Anc0refChr3 67937 42 + 222631 AGAACCTCTAGCCTTGAATAGTGTGCAAAGTAGAACTCATCT -s Anc1.Anc1refChr6 99065 42 + 197743 AGAACCTCTAGCCTTGAATAGTGTGCAAAGTAGAACTCATCT -s Anc2.Anc2refChr13 73836 42 + 96486 ATAAGCTCTAGCCTTGAATAGTGTGCAAAGTAGAACTCATCT -s mr.mrrefChr3 576 42 + 181027 AGACCCCCTAGCCTTAAATAGTGTATAAAGTGATGCTTGTTT -s simCow_chr6.simCow.chr6 430655 42 + 602619 AATAACTCTAATCTTGAATAGTTTGCAAAGCAGAACTCATCT -s simDog_chr6.simDog.chr6 422029 42 + 593897 ATAAGTCCTAGCCTTGGATAGTGTGCAAAGTAGAATGCATCT -s simHuman_chr6.simHuman.chr6 425251 42 + 601863 AGGACCTCTAGCCTTGAATAGTGTGCAAAGTAGAACTCATCT -s simRat_chr6.simRat.chr6 454335 42 + 647215 AGACTCCCAAGCCTTAAATAGTGTATCAAGTGATGTATGCAT - -a -s simMouse_chr6.simMouse.chr6 442303 57 + 636262 CCAAAAATAACTTAGAACAACAAGGGTGATTAACATTACTCATGTTAGGTTCTGTTG -s Anc0.Anc0refChr3 67979 32 + 222631 CTAGAAATAAGTTAGGACAACAAG-------AATATT------------------TG -s Anc1.Anc1refChr6 99107 32 + 197743 CTAGAAATAAGTTAGGACAACAAG-------AATATT------------------TG -s Anc2.Anc2refChr13 73878 32 + 96486 CTAGGTATAAGTTTGGACAACAAG-------AATATT------------------TG -s mr.mrrefChr3 618 57 + 181027 CCAGAAATAACTTAGAACAACAAGGGTGATTAACATTACTCATGTTAGGTTCTGTTG -s simCow_chr6.simCow.chr6 430697 32 + 602619 CCAATGGTAAGCTCATATACCAAA-------AATATT------------------TG -s simDog_chr6.simDog.chr6 422101 32 + 593897 CTTGGTATCAATATGGGCAAGAAG-------ACCACA------------------TG -s simHuman_chr6.simHuman.chr6 425293 32 + 601863 CTAGAAATAAGTTAGCACAACAAG-------AATATT------------------TG -s simRat_chr6.simRat.chr6 454377 57 + 647215 CCAGAAATAACTTAGAACAATAAGGGTGATTAACATTACTCATGGAAGGTACTGTTG - -a -s simMouse_chr6.simMouse.chr6 442360 1 + 636262 G -s Anc0.Anc0refChr3 68011 1 + 222631 G -s Anc1.Anc1refChr6 99139 1 + 197743 G -s Anc2.Anc2refChr13 73910 1 + 96486 G -s mr.mrrefChr3 675 1 + 181027 G -s simCow_chr6.simCow.chr6 430753 1 + 602619 G -s simDog_chr6.simDog.chr6 422133 1 + 593897 G -s simHuman_chr6.simHuman.chr6 425325 1 + 601863 G -s simRat_chr6.simRat.chr6 454434 1 + 647215 G - -a -s simMouse_chr6.simMouse.chr6 442361 3 + 636262 GTA -s Anc0.Anc0refChr3 68012 3 + 222631 GTA -s Anc1.Anc1refChr6 99140 3 + 197743 GTA -s Anc2.Anc2refChr13 73911 3 + 96486 GTA -s mr.mrrefChr3 676 3 + 181027 GTA -s simCow_chr6.simCow.chr6 430754 3 + 602619 GTA -s simDog_chr6.simDog.chr6 422141 3 + 593897 ATA -s simHuman_chr6.simHuman.chr6 425326 3 + 601863 GTA -s simRat_chr6.simRat.chr6 454435 3 + 647215 GTA - -a -s simMouse_chr6.simMouse.chr6 442364 10 + 636262 CTATACTGGG -s Anc0.Anc0refChr3 68016 10 + 222631 CTGTATTGGG -s Anc1.Anc1refChr6 99144 10 + 197743 CTGTATTGGG -s Anc2.Anc2refChr13 73915 10 + 96486 CTGTATTGGG -s mr.mrrefChr3 679 10 + 181027 CTATACTGGG -s simCow_chr6.simCow.chr6 430758 10 + 602619 CCTCATTGGG -s simDog_chr6.simDog.chr6 422145 10 + 593897 GTGTAATGGA -s simHuman_chr6.simHuman.chr6 425330 10 + 601863 CTCTATTGGG -s simRat_chr6.simRat.chr6 454438 10 + 647215 CTATACTGGG - -a -s simMouse_chr6.simMouse.chr6 442374 52 + 636262 TAGAGTGCATATAGTCAGTACATTCATACGCTGAAAACCTGGGCAGGAAAGG -s Anc0.Anc0refChr3 68026 52 + 222631 AAGAAGGCACATGGTCAGTAAATACCTACCCTGAATACCTGGGCAGGGCAAG -s Anc1.Anc1refChr6 99154 52 + 197743 AAGAAGGCACATGGTCAGTAAATACCTACCCTGAATACCTGGGCAGGGCAAG -s Anc2.Anc2refChr13 73925 52 + 96486 AAGAAGACACATGGTGAGTAAATACCTACCATGAATACCTAGGAAGGGCAAG -s mr.mrrefChr3 689 52 + 181027 AAGAATGCATATAGTCAGTACATTCATACGCTGAATACCTGGGCAGGAAAGG -s simCow_chr6.simCow.chr6 430768 52 + 602619 AAGAAGACACATAATAAATACATACCTATCACGAATATCTAGGAAAGGTGAG -s simDog_chr6.simDog.chr6 422156 52 + 593897 AAGAAGACACATGGTGAGAAAATACCCACCATGAATACCTAGGAAGGTCAAG -s simHuman_chr6.simHuman.chr6 425340 52 + 601863 AAGAAAGCACATCGTCACTATATACCTACACTGAATACCTGGGCAGGGCAAG -s simRat_chr6.simRat.chr6 454448 52 + 647215 AAGAATGCATATAGTCAGTACATTGATGTCATGAATACCTGGACAGGATGGG - -a -s simMouse_chr6.simMouse.chr6 442426 12 + 636262 ATCCATCTTGAA -s Anc0.Anc0refChr3 68078 12 + 222631 AACTATCTTAGG -s Anc1.Anc1refChr6 99206 12 + 197743 AACTATCTTAGG -s Anc2.Anc2refChr13 73977 12 + 96486 AACTAGCTTAGG -s mr.mrrefChr3 741 12 + 181027 ATCCATCTTGGA -s simCow_chr6.simCow.chr6 430820 12 + 602619 AACTACCTTAGA -s simDog_chr6.simDog.chr6 422209 12 + 593897 AACTAGCTTAGG -s simHuman_chr6.simHuman.chr6 425392 12 + 601863 AACTATCTTAGG -s simRat_chr6.simRat.chr6 454500 12 + 647215 ATCCATCTTTGA - -a -s simMouse_chr6.simMouse.chr6 442438 6 + 636262 TTGATA -s Anc0.Anc0refChr3 68118 6 + 222631 TTGATC -s Anc1.Anc1refChr6 99246 6 + 197743 TTGATC -s Anc2.Anc2refChr13 74017 6 + 96486 TTGACC -s mr.mrrefChr3 781 6 + 181027 TTGATA -s simCow_chr6.simCow.chr6 430860 6 + 602619 TTGACC -s simDog_chr6.simDog.chr6 422249 6 + 593897 TTGACC -s simHuman_chr6.simHuman.chr6 425432 6 + 601863 TTGatc -s simRat_chr6.simRat.chr6 454541 6 + 647215 TTGTGA - -a -s simMouse_chr6.simMouse.chr6 442444 20 + 636262 TAGGGACATGTAGTGCACCC -s Anc0.Anc0refChr3 68124 7 + 222631 T-------------GTACCC -s Anc1.Anc1refChr6 99252 7 + 197743 T-------------GTACCC -s Anc2.Anc2refChr13 74023 7 + 96486 T-------------GTACCC -s mr.mrrefChr3 787 20 + 181027 TAGGGACATGTAGTGCACCC -s simCow_chr6.simCow.chr6 430866 7 + 602619 T-------------GTACCC -s simDog_chr6.simDog.chr6 422256 7 + 593897 T-------------ATCCCC -s simHuman_chr6.simHuman.chr6 425438 7 + 601863 t-------------gtaccc -s simRat_chr6.simRat.chr6 454547 20 + 647215 TAAGGACCTGTAGTGTACCC - -a -s simMouse_chr6.simMouse.chr6 442464 8 + 636262 TCAGTCCA -s Anc0.Anc0refChr3 68131 3 + 222631 TCA----- -s Anc1.Anc1refChr6 99259 8 + 197743 TCAgttca -s Anc2.Anc2refChr13 74030 3 + 96486 TCA----- -s mr.mrrefChr3 807 8 + 181027 TCAGTCCA -s simCow_chr6.simCow.chr6 430881 3 + 602619 TCA----- -s simDog_chr6.simDog.chr6 422263 3 + 593897 TCA----- -s simHuman_chr6.simHuman.chr6 425445 8 + 601863 tcagttca -s simRat_chr6.simRat.chr6 454567 8 + 647215 ACAGCACA - -a -s simMouse_chr6.simMouse.chr6 442472 35 + 636262 GTATCAAAAGACAGATGTTAAAGGGGTTGATAGTT -s Anc0.Anc0refChr3 68134 31 + 222631 -TA-C-AAAGGCAGAGATTAATAGAGTGGAAC-TT -s Anc1.Anc1refChr6 99267 34 + 197743 gTA-CAAAAGGCAGAGATTAATAGAGTGGAACATT -s Anc2.Anc2refChr13 74033 31 + 96486 -TA-C-AAAGGCAGAGATTTATAGAGTGTAAC-TT -s mr.mrrefChr3 815 35 + 181027 GTATCAAAAGACAGATGTTAAAGGGGTTGATAGTT -s simCow_chr6.simCow.chr6 430884 31 + 602619 -TA-G-AAAGAAAGAGTTTAATGGTGTAGAGC-AT -s simDog_chr6.simDog.chr6 422266 31 + 593897 -TA-C-AAAGGCAGAGATTTATAGAGTGTAAC-TT -s simHuman_chr6.simHuman.chr6 430359 34 + 601863 gta-cagaaaGCACAGATTAACAGTGTAGAGCATC -s simRat_chr6.simRat.chr6 454575 35 + 647215 GCATTAAAAGTCAGAGGTTAATGGGGTTGATAATT - -a -s simMouse_chr6.simMouse.chr6 442507 27 + 636262 TTTTCTGTGGTGTGAGGCAGTTTTGTA -s Anc0.Anc0refChr3 68165 26 + 222631 TTTTCAGTGACATGAGGCGGTTTTGT- -s Anc1.Anc1refChr6 99301 27 + 197743 TTTTCAGTGACATGAGGCGGTTTTGTA -s Anc2.Anc2refChr13 74064 26 + 96486 TATTCAGTGACATGAAGTGGTCTTGT- -s mr.mrrefChr3 850 27 + 181027 TTTTCTGTGGTGTGAGGCAGTTTTGTA -s simCow_chr6.simCow.chr6 430922 26 + 602619 TTTTCAGTAACATGAGGGTGTTTTGC- -s simDog_chr6.simDog.chr6 422297 26 + 593897 TATTCAGTGACATGAAGTGGTCTTGT- -s simHuman_chr6.simHuman.chr6 430393 27 + 601863 TTAGCAGTGACATGAGGCTGTTTTGTA -s simRat_chr6.simRat.chr6 454610 27 + 647215 TTTTCTGTGGTGTGGGGCAGTTTTATA - -a -s simMouse_chr6.simMouse.chr6 442534 1 + 636262 A -s Anc0.Anc0refChr3 68191 1 + 222631 A -s Anc1.Anc1refChr6 99328 1 + 197743 A -s Anc2.Anc2refChr13 74090 1 + 96486 A -s mr.mrrefChr3 877 1 + 181027 A -s simCow_chr6.simCow.chr6 430948 1 + 602619 A -s simDog_chr6.simDog.chr6 422323 1 + 593897 A -s simHuman_chr6.simHuman.chr6 430480 1 + 601863 A -s simRat_chr6.simRat.chr6 454637 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 442535 5 + 636262 AACAT -s Anc0.Anc0refChr3 68192 5 + 222631 AACAC -s Anc1.Anc1refChr6 99329 5 + 197743 AACAC -s Anc2.Anc2refChr13 74091 5 + 96486 GACAC -s mr.mrrefChr3 878 5 + 181027 AACAT -s simCow_chr6.simCow.chr6 430950 5 + 602619 GGCAC -s simDog_chr6.simDog.chr6 422324 5 + 593897 GACAC -s simHuman_chr6.simHuman.chr6 430481 5 + 601863 TATGC -s simRat_chr6.simRat.chr6 454638 5 + 647215 TACAG - -a -s simMouse_chr6.simMouse.chr6 442540 9 + 636262 CTAGCGAAC -s Anc0.Anc0refChr3 68197 9 + 222631 TTAGGGAAA -s Anc1.Anc1refChr6 99334 9 + 197743 TTAGGGAAA -s Anc2.Anc2refChr13 74096 9 + 96486 TTGGGGAAA -s mr.mrrefChr3 883 9 + 181027 CTAGCGAAC -s simCow_chr6.simCow.chr6 430994 9 + 602619 TTAGGGCAA -s simDog_chr6.simDog.chr6 422329 9 + 593897 TTGGGGAAA -s simHuman_chr6.simHuman.chr6 430486 9 + 601863 TTAGGGAAG -s simRat_chr6.simRat.chr6 454643 9 + 647215 TTAGTGAGC - -a -s simMouse_chr6.simMouse.chr6 442549 63 + 636262 CTCAGCTTCCAATAAAAGGATCACACATTAATGTTGCACCAATGGCACCAACCAGTGATACAG -s Anc0.Anc0refChr3 68371 57 + 222631 CGC--CTT--ATCAAAAAGACCACATGTTAATGTTACACCAAAGGCCCCAGCCAGTGATGC-- -s Anc1.Anc1refChr6 99508 61 + 197743 CGCAGCTT--ATCAAAAAGACCACATGTTAATGTTACACCAAAGGCCCCAGCCAGTGATGCAG -s Anc2.Anc2refChr13 74308 57 + 96486 CGC--CTT--ATCAAGAAGACTACATGATAATGGAACACCGAAGGCCCCAGCCAGTGATGC-- -s mr.mrrefChr3 892 61 + 181027 CTCAGCTT--AATAAAAGGATCACACATTAATGTTGCACCAATGGCACCAACCAGTGATACAG -s simDog_chr6.simDog.chr6 422526 57 + 593897 CGC--CTT--ATCAAGAAGACTACATGATAATGGAACACCGAAGGCCCCAGCCAGTGATGC-- -s simHuman_chr6.simHuman.chr6 430665 61 + 601863 CACAGCTC--ATCAAAAAGACCCCATGTAAATGTTATGCCAAAGGCCCTCGTTAGTGATCCAG -s simRat_chr6.simRat.chr6 454652 61 + 647215 CGCAGGTT--AATAAAAAGATTGCACATTAATGTTGCACCAACGGCACCGGCCAGGGATACAG - -a -s simMouse_chr6.simMouse.chr6 442612 37 + 636262 ATCCAGCATGTCAGTTCAACTCTCTATTACACATCAA -s Anc0.Anc0refChr3 68428 22 + 222631 ---------------TCAATTCTCTATTACCATTCAA -s Anc1.Anc1refChr6 99569 28 + 197743 ATCTAG---------TCAATTCTCTATTACCATTCAA -s Anc2.Anc2refChr13 74365 22 + 96486 ---------------TCAGTTCTCTATTATCATTCAA -s mr.mrrefChr3 953 34 + 181027 ATCCAGCATG---GTTCAACTCTCTATTACACATCAA -s simDog_chr6.simDog.chr6 422583 22 + 593897 ---------------TCAGTTCTCTATTATCATTCAA -s simHuman_chr6.simHuman.chr6 430729 28 + 601863 ATCTAG---------TCAATACGCTAGTACCATTCAA -s simRat_chr6.simRat.chr6 454713 34 + 647215 ATCCAGCATG---GTTCATCTCTCTATTACACATCAA - -a -s simMouse_chr6.simMouse.chr6 442649 3 + 636262 ACC -s Anc0.Anc0refChr3 68450 3 + 222631 TCC -s Anc1.Anc1refChr6 99597 3 + 197743 TCC -s Anc2.Anc2refChr13 74387 3 + 96486 TCA -s mr.mrrefChr3 987 3 + 181027 ACC -s simDog_chr6.simDog.chr6 422606 3 + 593897 TCA -s simHuman_chr6.simHuman.chr6 430757 3 + 601863 TCC -s simRat_chr6.simRat.chr6 454747 3 + 647215 ACC - -a -s simMouse_chr6.simMouse.chr6 442652 26 + 636262 CTCAGTAATGAAAGAGTCTCATTTTA -s Anc0.Anc0refChr3 68455 23 + 222631 C--CTTTACAAAAGAGTCTCAACT-A -s Anc1.Anc1refChr6 99602 23 + 197743 C--CTTTACAAAAGAGTCTCAACT-A -s Anc2.Anc2refChr13 74392 23 + 96486 C--CTATACAAGAAAGTCTTAACT-A -s mr.mrrefChr3 990 23 + 181027 C--AGTAATGAAAGAGTCTCATTT-A -s simDog_chr6.simDog.chr6 422611 23 + 593897 C--CTATACAAGAAAGTCTTAACT-A -s simHuman_chr6.simHuman.chr6 430762 23 + 601863 C--GTTTGCAAAAGAGTCTCAACT-A -s simRat_chr6.simRat.chr6 454750 23 + 647215 C--ATTAATAAAAGAGGCTCATTT-A - -a -s simMouse_chr6.simMouse.chr6 442678 11 + 636262 CAGTGTGAGAG -s Anc0.Anc0refChr3 68487 11 + 222631 CATTGTTCTGG -s Anc1.Anc1refChr6 99634 11 + 197743 CATTGTTCTGG -s Anc2.Anc2refChr13 74424 11 + 96486 CATTGTTCTGG -s mr.mrrefChr3 1013 11 + 181027 CAGTGTGAGAG -s simDog_chr6.simDog.chr6 422643 11 + 593897 CATTGTTCTGG -s simHuman_chr6.simHuman.chr6 430794 11 + 601863 TATTGTTCTGG -s simRat_chr6.simRat.chr6 454773 11 + 647215 TGGTGTGAGAG - -a -s simMouse_chr6.simMouse.chr6 442689 2 + 636262 AT -s Anc0.Anc0refChr3 68498 2 + 222631 TT -s Anc1.Anc1refChr6 99645 2 + 197743 TT -s Anc2.Anc2refChr13 74435 2 + 96486 TT -s mr.mrrefChr3 1024 2 + 181027 AT -s simDog_chr6.simDog.chr6 422655 2 + 593897 TT -s simHuman_chr6.simHuman.chr6 430805 2 + 601863 TT -s simRat_chr6.simRat.chr6 454784 2 + 647215 AT - -a -s simMouse_chr6.simMouse.chr6 442691 17 + 636262 GCATTTGCATAGCATAA -s Anc0.Anc0refChr3 68579 17 + 222631 GCATTAGCATAGTAGAA -s Anc1.Anc1refChr6 99726 17 + 197743 GCATTAGCATAGTAGAA -s Anc2.Anc2refChr13 74516 17 + 96486 TAATTAGAATAGTAGAA -s mr.mrrefChr3 1026 17 + 181027 GCATTAGCATAGCATAA -s simDog_chr6.simDog.chr6 422736 17 + 593897 TAATTAGAATAGTAGAA -s simHuman_chr6.simHuman.chr6 430904 17 + 601863 GCATTAGCGTGGTACAA -s simRat_chr6.simRat.chr6 454786 17 + 647215 GTATTAGCATAGCATAA - -a -s simMouse_chr6.simMouse.chr6 442708 122 + 636262 CTCATAAGGATGGATCGTCTTTTCTGTCCAATATGGGCTTGTAACATCCTACTATATAGGGCTAGCTAAAGTCAATATTATAATGTGTAGGTAGTACAAAGACTGATTCTCAATTACTTCCT -s Anc0.Anc0refChr3 68606 56 + 222631 CTTATAAGGATGGATGTTCATTTCTGACTGATA-------------------------------------------------------AGGTGGTACAGGAACTGGTTCT-----------T -s Anc1.Anc1refChr6 99753 85 + 197743 CTTATAAGGATGGATGTTCATTTCTGACTGATATG---------------------TAAGAGTGACTTAAA-----AGTACAGTTGGTAGGTGGTACAGGAACTGGTTCT-----------T -s Anc2.Anc2refChr13 74543 56 + 96486 CTTATAAAGATGGATGTTCATCTGTGACTGACA-------------------------------------------------------GGGTGATACAGGGACTGGTTCC-----------C -s mr.mrrefChr3 1043 122 + 181027 CTCATAAGGATGGATGGTCATTTCTGTCTGATATGGGCTTGTAACATCCTACTATATAGGGCTGACTAAAGTCAATATTACAATGTGTAGGTAGTACAAAAACTGATTCTCAATTACTTTCT -s simDog_chr6.simDog.chr6 422763 56 + 593897 CTTATAAAGATGGATGTTCATCTGTGACTGACA-------------------------------------------------------GGGTGATACAGGGACTGGTTCC-----------C -s simHuman_chr6.simHuman.chr6 430931 85 + 601863 CTTATAAGAATGGATGTGCATTTCCAACTGATATG---------------------TAAGAGTGACTTAAA-----AGTACAGTTGGTAGGTGGTACAGGAACTGTTCTT-----------T -s simRat_chr6.simRat.chr6 454803 121 + 647215 CACATAGGGATGG-TGGTCATTTTTGTCTGATATGGCCGTGTACCATCCTACTATATAGGGCTGATTACAGTCAACATTACAATGTGCAGGTAGTACAAAAACTGATTCTCAATTACTTTCT - -a -s simMouse_chr6.simMouse.chr6 442830 13 + 636262 GCTTCTTACAAGG -s Anc0.Anc0refChr3 68662 13 + 222631 GTTTCTTACAGGG -s Anc1.Anc1refChr6 99838 13 + 197743 GTTTCTTACAGGG -s Anc2.Anc2refChr13 74599 13 + 96486 ATTTCTTATAGGG -s mr.mrrefChr3 1165 13 + 181027 GCTTCTTACAAGG -s simDog_chr6.simDog.chr6 422819 13 + 593897 ATTTCTTATAGGG -s simHuman_chr6.simHuman.chr6 431016 13 + 601863 GTTTCTTACAGGG -s simRat_chr6.simRat.chr6 454925 13 + 647215 AATTTTTAGAAGG - -a -s simMouse_chr6.simMouse.chr6 442843 10 + 636262 GGTGCCTTGC -s Anc0.Anc0refChr3 68684 10 + 222631 GGGGCCTTGC -s Anc1.Anc1refChr6 99860 10 + 197743 GGGGCCTTGC -s Anc2.Anc2refChr13 74621 10 + 96486 GGGGGCTTGC -s mr.mrrefChr3 1178 10 + 181027 GGTGCCTTGC -s simDog_chr6.simDog.chr6 422846 10 + 593897 GGGGGCTTGC -s simHuman_chr6.simHuman.chr6 431038 10 + 601863 GGGGCCTTGC -s simRat_chr6.simRat.chr6 454938 10 + 647215 GGTCCCTTGC - -a -s simMouse_chr6.simMouse.chr6 442853 30 + 636262 TGGGTAGAGGCCCACACACATATACCCCAC -s Anc0.Anc0refChr3 68702 28 + 222631 GGGGCAAAGACG--TACACATATACACCAC -s Anc1.Anc1refChr6 99878 28 + 197743 GGGGCAAAGACG--TACACATATACACCAC -s Anc2.Anc2refChr13 74639 28 + 96486 GGATCAAAGATG--CACAGTCATACTCCAC -s mr.mrrefChr3 1196 30 + 181027 GGGGTAGAGACCCATACACATATACACCAC -s simDog_chr6.simDog.chr6 422864 28 + 593897 GGATCAAAGATG--CACAGTCATACTCCAC -s simHuman_chr6.simHuman.chr6 431056 28 + 601863 GGGGCAAAGACA--TACACATATACACCAT -s simRat_chr6.simRat.chr6 454956 29 + 647215 GGTA-AGAGACCCATATATATATACACCAC - -a -s simMouse_chr6.simMouse.chr6 442883 22 + 636262 GGAAACCATGACCGTCCAAATG -s Anc0.Anc0refChr3 68730 5 + 222631 GGAAA----------------- -s Anc1.Anc1refChr6 99906 22 + 197743 GGAAACCATGGTAAACCAAATG -s Anc2.Anc2refChr13 74667 5 + 96486 AGACA----------------- -s mr.mrrefChr3 1226 22 + 181027 GGAAACCATGGTCGACCAAATG -s simDog_chr6.simDog.chr6 422892 5 + 593897 AGACA----------------- -s simHuman_chr6.simHuman.chr6 431087 22 + 601863 GGAAACCATGGTAAACCAAATG -s simRat_chr6.simRat.chr6 454985 22 + 647215 GGATAGCAAGGTGGACCAAATG - -a -s simMouse_chr6.simMouse.chr6 442905 61 + 636262 ACCTTAATAAGACTGGCAAATGTTTCTTCAAAGGGCAAAATAGGCAGCCTACTATAACAGC -s Anc0.Anc0refChr3 68735 57 + 222631 ---TGTATAAGGCTATCGAGTGTTTCTACAAAATACTAAAGAGGCAGACTACTATA-CAGC -s Anc1.Anc1refChr6 99928 60 + 197743 ATCTGTATAAGGCTATCGAGTGTTTCTACAAAATACTAAAGAGGCAGACTACTATA-CAGC -s Anc2.Anc2refChr13 74672 57 + 96486 ---TGTGTGGGGCTATCGAGTGTACCTACAATATACTAAAGAGCCAGACTACTATA-CAGC -s mr.mrrefChr3 1248 61 + 181027 ATCTTAATAAGACTGGCAAATGTTTCTTCAAAGGGCTAAATAGGCAGCCTACTATAACAGC -s simDog_chr6.simDog.chr6 422897 57 + 593897 ---TGTGTGGGGCTATCGAGTGTACCTACAATATACTAAAGAGCCAGACTACTATA-CAGC -s simHuman_chr6.simHuman.chr6 431114 60 + 601863 ATCTGCATAAGGCTCTTGAGTGTTTCTACAAAATTCTATAGAGGCAGACTTCTATA-CAGC -s simRat_chr6.simRat.chr6 455007 50 + 647215 ATCTTAATAATACTAGCAAATGT-----------GCTAAATGGGCAGCCTACTATAACAGC - -a -s simMouse_chr6.simMouse.chr6 442966 7 + 636262 AAGGGGC -s Anc0.Anc0refChr3 68793 7 + 222631 AAGGCTT -s Anc1.Anc1refChr6 99989 7 + 197743 AAGGCTT -s Anc2.Anc2refChr13 74730 7 + 96486 AAGGCTT -s mr.mrrefChr3 1310 7 + 181027 AAGGGGC -s simDog_chr6.simDog.chr6 422956 7 + 593897 AAGGCTT -s simHuman_chr6.simHuman.chr6 431175 7 + 601863 AAGGCTT -s simRat_chr6.simRat.chr6 455058 7 + 647215 AAGGGGC - -a -s simMouse_chr6.simMouse.chr6 442973 24 + 636262 TCACGCATTAATCAGTATCCATGT -s Anc0.Anc0refChr3 68800 24 + 222631 TCCCAGGTTGATTGGTATCCAGGT -s Anc1.Anc1refChr6 99996 24 + 197743 TCCCAGGTTGATTGGTATCCAGGT -s Anc2.Anc2refChr13 74737 24 + 96486 TCCCAGGTAGATTGGTATCCGGAT -s mr.mrrefChr3 1317 24 + 181027 TCACGCATTAATCAGTATCCATGT -s simDog_chr6.simDog.chr6 422964 24 + 593897 TCCCAGGTAGATTGGTATCCGGAT -s simHuman_chr6.simHuman.chr6 431182 24 + 601863 TCCCAAGTTGAGTGGTATCCAGGT -s simRat_chr6.simRat.chr6 455065 24 + 647215 TCATCCTTCAATCAGTATCCAAGT - -a -s simMouse_chr6.simMouse.chr6 442997 30 + 636262 GCTGTATGCACATAGAATTCTTACTTAAGG -s Anc0.Anc0refChr3 68824 22 + 222631 GTGGGATGCAC-------TCTTAAGTA-GG -s Anc1.Anc1refChr6 100020 30 + 197743 GTGGGATGCACAGAGGCTTCTTAAGTAGGG -s Anc2.Anc2refChr13 74761 22 + 96486 GTGGGATGCAC-------TCTCAAGTA-GG -s mr.mrrefChr3 1341 30 + 181027 GCTGTATGCACATAGAATTCTTACTTAAGG -s simCow_chr6.simCow.chr6 298484 11 + 602619 ------------------TCTCAAATA-GG -s simDog_chr6.simDog.chr6 422989 20 + 593897 GTGGGATGCAC---------TCAAGTA-GG -s simHuman_chr6.simHuman.chr6 431206 30 + 601863 GTGGGATGCACAGAGGCTTCTTAAGAAGGG -s simRat_chr6.simRat.chr6 455089 30 + 647215 GCTGTATGCACATAGAACTCTTACTTAAGG - -a -s simMouse_chr6.simMouse.chr6 443027 10 + 636262 AAGGATATGA -s Anc0.Anc0refChr3 68894 10 + 222631 AAGGCAATAA -s Anc1.Anc1refChr6 100098 10 + 197743 AAGGCAATAA -s Anc2.Anc2refChr13 74831 10 + 96486 AATACAACAA -s mr.mrrefChr3 1371 10 + 181027 AAGGATATGA -s simCow_chr6.simCow.chr6 298543 10 + 602619 AATACAACAA -s simDog_chr6.simDog.chr6 423057 10 + 593897 GGTACAACAA -s simHuman_chr6.simHuman.chr6 431287 10 + 601863 AAGGCAATAA -s simRat_chr6.simRat.chr6 455119 10 + 647215 AAAGATATGC - -a -s simMouse_chr6.simMouse.chr6 443037 4 + 636262 TAGC -s Anc0.Anc0refChr3 68906 2 + 222631 TT-- -s Anc1.Anc1refChr6 100110 4 + 197743 TTGC -s Anc2.Anc2refChr13 74843 2 + 96486 CT-- -s mr.mrrefChr3 1381 4 + 181027 TAGC -s simCow_chr6.simCow.chr6 298555 2 + 602619 CT-- -s simDog_chr6.simDog.chr6 423069 2 + 593897 CT-- -s simHuman_chr6.simHuman.chr6 431299 4 + 601863 TTGC -s simRat_chr6.simRat.chr6 455129 4 + 647215 TAGC - -a -s simMouse_chr6.simMouse.chr6 443041 15 + 636262 TTAGTTTGGATGCAA -s Anc0.Anc0refChr3 68908 15 + 222631 TTAGTGTAAATGCTA -s Anc1.Anc1refChr6 100114 15 + 197743 TTAGTGTAAATGCTA -s Anc2.Anc2refChr13 74845 15 + 96486 TTAGTGTAAATACTA -s mr.mrrefChr3 1385 15 + 181027 TTAGTTTGAATGCAA -s simDog_chr6.simDog.chr6 423083 15 + 593897 TTAGTGTAAATACTA -s simHuman_chr6.simHuman.chr6 431303 13 + 601863 ATGGTC--AAGGCTA -s simRat_chr6.simRat.chr6 455133 15 + 647215 TTAGTGTGAATGCAA - -a -s simMouse_chr6.simMouse.chr6 443056 91 + 636262 TAGCCTCACATGATCAAATCGTACTTTCAGGTGAGGTTCCACAGCAATAAAATGGAGTAGACTGACCTTTGGAAAGTCACTTTACACTCTG -s Anc0.Anc0refChr3 68923 83 + 222631 TAACCTCACATGCTCAAATTGTACTTTACAGT----TTCCAAAGTAATAAAATGGAGCAGACTGACCCTT----AGACTCATTACACTCCA -s Anc1.Anc1refChr6 100129 83 + 197743 TAACCTCACATGCTCAAATTGTACTTTACAGT----TTCCAAAGTAATAAAATGGAGCAGACTGACCCTT----AGACTCATTACACTCCA -s Anc2.Anc2refChr13 74860 83 + 96486 TGACCTCACATGCTCAAATTGTACTTTACAAA----TTCCAAAGTAATAAAATGGAGCAGACTGACCCTT----GGACTCATAACACCCCA -s mr.mrrefChr3 1400 91 + 181027 TAGCCTCACATGATCAAATTGTACTTTCAAGTGAGGTTCCACAGCAATAAAATGGAGTAGACTGACCTTTGGAAAGACACTTTACACTCCG -s simCow_chr6.simCow.chr6 298557 76 + 602619 -------ATAAGCAAAAATTGTCCTTTACACA----TTCCAAAGGAGTAAAATGGAGCAGAATGACCCTT----GGGCCCATCACACCCTG -s simDog_chr6.simDog.chr6 423099 76 + 593897 TGACCTCACATGCTCAA----TACTTTACAAA----TTCC---GTAATAAAATGGAGCAGACTGATCCTT----GGACTCATAACACCCCA -s simHuman_chr6.simHuman.chr6 431316 83 + 601863 TAACCTTACATGGTCAATTTGTACTTTACAGT----TTCCAAAATCATAAAATGGAGCAGAGTGACCCTT----AGATTCATTACACTCCA -s simRat_chr6.simRat.chr6 455148 91 + 647215 TAGCCTCACATGAACAAATTGTACTTTCAAGTGAGGTTCCACGGCTATAAAATGGAGTAGACTGACCTCTGGAAAGAAACTCTACACTCCG - -a -s simMouse_chr6.simMouse.chr6 443147 32 + 636262 TCAGGTCAATACTGTCTTAAGTAACATCTCAG -s Anc0.Anc0refChr3 69006 32 + 222631 CCAGGTGAATGTTAGCTTAAGTTACAACCCAG -s Anc1.Anc1refChr6 100212 32 + 197743 CCAGGTGAATGTTAGCTTAAGTTACAACCCAG -s Anc2.Anc2refChr13 74943 32 + 96486 CCAGGTGAATGTTAGCTTAAGTTACAACCCAG -s mr.mrrefChr3 1491 32 + 181027 TCAGGTCAATATTGTCTTAAGTTACATCTCAG -s simCow_chr6.simCow.chr6 298652 21 + 602619 CCAGGTGA----------AAGTTACAG-ACAA -s simDog_chr6.simDog.chr6 423175 32 + 593897 TAAGGCGAATGTTAGCTTAAGTTACAACCCAG -s simHuman_chr6.simHuman.chr6 431399 32 + 601863 CCAGGTGAATGTCAGTTTAAGGTACTCACCAG -s simRat_chr6.simRat.chr6 455239 32 + 647215 GCAGGTCAATATTGTCTTAAGCTACATCTCAG - -a -s simMouse_chr6.simMouse.chr6 443179 42 + 636262 CAGCCCTTTTCCCACTCAAGCCAGAGTTATAACCACACTTGG -s Anc0.Anc0refChr3 69040 39 + 222631 CGGCCCTAATTCC---CAAGCCGGAGTTATACCTATGCTTTG -s Anc1.Anc1refChr6 100246 41 + 197743 CGGCCCTAATTCC-CACAAGCCGGAGTTATACCTATGCTTTG -s Anc2.Anc2refChr13 74977 39 + 96486 CGGCCCTAATTCC---CAAGTCGGAGTTACACCTATGCTTTG -s mr.mrrefChr3 1525 42 + 181027 CAGCCCTTTTCCCACTCAAGCCGGAGTTATAACTACACTTGG -s simCow_chr6.simCow.chr6 298675 39 + 602619 CGGTCATAACTCC---CTAGTTGGAGTTACATGGATGCTTTG -s simDog_chr6.simDog.chr6 423209 39 + 593897 CGGCACTAATTCC---CAAGTCGAAGTTACTCCTATGCTCTG -s simHuman_chr6.simHuman.chr6 431433 34 + 601863 TGGCCC--------CACAAGCCGGAGTTATACCTATGATTTG -s simRat_chr6.simRat.chr6 455273 42 + 647215 CAGCCCCATTCCCACTCAAGCCGGAGTTATAACTACACTCAG - -a -s simMouse_chr6.simMouse.chr6 443221 3 + 636262 ACC -s Anc0.Anc0refChr3 69082 3 + 222631 ACG -s Anc1.Anc1refChr6 100290 3 + 197743 ACG -s Anc2.Anc2refChr13 75019 3 + 96486 ACG -s mr.mrrefChr3 1570 3 + 181027 ACC -s simCow_chr6.simCow.chr6 298717 3 + 602619 ACG -s simDog_chr6.simDog.chr6 423251 3 + 593897 TCG -s simHuman_chr6.simHuman.chr6 431470 3 + 601863 ACA -s simRat_chr6.simRat.chr6 455318 3 + 647215 GCC - -a -s simMouse_chr6.simMouse.chr6 443224 10 + 636262 ATGAAAACCA -s Anc0.Anc0refChr3 69090 10 + 222631 GGCAAAACCA -s Anc1.Anc1refChr6 100298 10 + 197743 GGCAAAACCA -s Anc2.Anc2refChr13 75027 10 + 96486 GGCAAAACAA -s mr.mrrefChr3 1573 10 + 181027 AGCAAAACCA -s simCow_chr6.simCow.chr6 298725 10 + 602619 TGCAAAACAA -s simDog_chr6.simDog.chr6 423259 10 + 593897 GGCTAAACAA -s simHuman_chr6.simHuman.chr6 431478 10 + 601863 GGCAAAACCA -s simRat_chr6.simRat.chr6 455321 10 + 647215 AGCAAAACCA - -a -s simMouse_chr6.simMouse.chr6 443234 37 + 636262 TTAGTATCAACACACCAACGCGGCGGTAAAGTGCATG -s Anc0.Anc0refChr3 69108 37 + 222631 TTAGCATCGATGCACCATTGGGGCTGGAAGCAACAGG -s Anc1.Anc1refChr6 100316 37 + 197743 TTAGCATCGATGCACCATTGGGGCTGGAAGCAACAGG -s Anc2.Anc2refChr13 75045 37 + 96486 TTAGCATCGATGCATCATTGGGGCTGGAAGCAACAGG -s mr.mrrefChr3 1590 37 + 181027 TTAGTATCAATACACCAACGCGGCGGGAAAGTACATG -s simCow_chr6.simCow.chr6 298743 34 + 602619 TTTGCATGGATGCAATACCAGAGCC---AACAACAGT -s simDog_chr6.simDog.chr6 423277 37 + 593897 TTAGCATCGATGTATCATTGTGGCTGGAGGCAACAGG -s simHuman_chr6.simHuman.chr6 431496 37 + 601863 TTAGCATCGGTGCACCATAGGGGCTGGAACCAACAGG -s simRat_chr6.simRat.chr6 455338 37 + 647215 TGAGTATCAATCCACCAACGCGGCGGGAAAGTACATG - -a -s simMouse_chr6.simMouse.chr6 443271 2 + 636262 TT -s Anc0.Anc0refChr3 69148 2 + 222631 TC -s Anc1.Anc1refChr6 100356 2 + 197743 TC -s Anc2.Anc2refChr13 75085 2 + 96486 TC -s mr.mrrefChr3 1630 2 + 181027 TT -s simCow_chr6.simCow.chr6 298780 2 + 602619 TC -s simDog_chr6.simDog.chr6 423317 2 + 593897 TC -s simHuman_chr6.simHuman.chr6 431536 2 + 601863 TC -s simRat_chr6.simRat.chr6 455378 2 + 647215 TT - -a -s simMouse_chr6.simMouse.chr6 443273 5 + 636262 GCGGG -s Anc0.Anc0refChr3 69152 5 + 222631 GCGGG -s Anc1.Anc1refChr6 100360 5 + 197743 GCGGG -s Anc2.Anc2refChr13 75089 5 + 96486 GCGGG -s mr.mrrefChr3 1632 5 + 181027 GCGGG -s simCow_chr6.simCow.chr6 298784 5 + 602619 GGGGG -s simDog_chr6.simDog.chr6 423321 5 + 593897 GCGCG -s simHuman_chr6.simHuman.chr6 431540 5 + 601863 GCGGG -s simRat_chr6.simRat.chr6 455380 5 + 647215 GTGGG - -a -s simMouse_chr6.simMouse.chr6 443278 20 + 636262 TGCTCCGCCTCCACGTTTTC -s Anc0.Anc0refChr3 69163 4 + 222631 C----------------TTC -s Anc1.Anc1refChr6 100371 20 + 197743 CGCTTCACTGCCACTCTTTC -s Anc2.Anc2refChr13 75100 4 + 96486 C----------------TTC -s mr.mrrefChr3 1637 20 + 181027 TGCTCCGCCGCCACGTTTTC -s simDog_chr6.simDog.chr6 423332 4 + 593897 C----------------TTC -s simHuman_chr6.simHuman.chr6 431551 20 + 601863 CGCTTCACTGCCACTCTTTC -s simRat_chr6.simRat.chr6 455385 20 + 647215 TGCTCCGCCGCCACGTTTTC - -a -s simMouse_chr6.simMouse.chr6 443298 49 + 636262 GCCTGTCGTGATGCTCGCGTTCATGTCCGCAGGACCCGCCCGGGGCTCT -s Anc0.Anc0refChr3 69167 41 + 222631 GCCGGGCGTGGCGCAGGCGTTCATATCCTC------CACCCGGG--CCT -s Anc1.Anc1refChr6 100391 41 + 197743 GCCGGGCGTGGCGCAGGCGTTCATATCCTC------CACCCGGG--CCT -s Anc2.Anc2refChr13 75104 41 + 96486 GCCGGGCGTTGCGCAGGCATTCGTATCCTC------AACGCCGG--CCT -s mr.mrrefChr3 1657 49 + 181027 GCCGGTCGTGATGCTCGCGTTCATGTCCGCAGGACCCGCCCGGGGCCCT -s simCow_chr6.simCow.chr6 431779 28 + 602619 -------------CAGGCATTCGAATCCTC------AACGCCGG--CTT -s simDog_chr6.simDog.chr6 423336 40 + 593897 GCCGGGCGTTGCGCAAGCATT-GTATCCCC------AATGTCGG--CCT -s simHuman_chr6.simHuman.chr6 431571 41 + 601863 GCCGGCCCTGGCGCAGACGCTAATATCCTC------CACCCGGA--CCT -s simRat_chr6.simRat.chr6 455475 49 + 647215 GCCGGTCGTGATGGTCGTGTTCATGTCCGCGAAACCCGCCCGAGGCCCC - -a -s simMouse_chr6.simMouse.chr6 443347 10 + 636262 ACTCCCTTGA -s Anc0.Anc0refChr3 69208 10 + 222631 GCGCCCTTTA -s Anc1.Anc1refChr6 100432 10 + 197743 GCGCCCTTTA -s Anc2.Anc2refChr13 75145 10 + 96486 GAGTGCTTTG -s mr.mrrefChr3 1706 10 + 181027 ACTCCCTTGA -s simCow_chr6.simCow.chr6 431814 10 + 602619 AAGTATTTTT -s simDog_chr6.simDog.chr6 423376 10 + 593897 GAATGCTTTG -s simHuman_chr6.simHuman.chr6 431612 10 + 601863 GCGCCCTTCA -s simRat_chr6.simRat.chr6 455524 10 + 647215 ACTCCCTTGA - -a -s simMouse_chr6.simMouse.chr6 443357 23 + 636262 CCAACGATATCTCGTCGCACTGG -s Anc0.Anc0refChr3 69218 22 + 222631 CACACGAAGTATCCTCGCAC-GG -s Anc1.Anc1refChr6 100442 22 + 197743 CACACGAAGTATCCTCGCAC-GG -s Anc2.Anc2refChr13 75155 22 + 96486 TACACGAAGTATCCTCGCAC-GG -s mr.mrrefChr3 1716 22 + 181027 CCAACGATATCTCGTCGCAC-GG -s simCow_chr6.simCow.chr6 431828 22 + 602619 TACACGATATCTCCTCGTGC-CC -s simDog_chr6.simDog.chr6 423386 17 + 593897 -----GAAGTAAAGTCGCAC-GG -s simHuman_chr6.simHuman.chr6 431622 22 + 601863 CACACGAGTTTTCCTCCCAC-AT -s simRat_chr6.simRat.chr6 455534 14 + 647215 CCAACGTTATCACG--------- - -a -s simMouse_chr6.simMouse.chr6 443380 39 + 636262 ACGGGCGGAAACTGAACGTTGCATTTTCCGCGCAATGGA -s Anc0.Anc0refChr3 69240 39 + 222631 ATGGGCAGATACTGAATGTTGCACTTTTACAGCATCGGG -s Anc1.Anc1refChr6 100464 39 + 197743 ATGGGCAGATACTGAATGTTGCACTTTTACAGCATCGGG -s Anc2.Anc2refChr13 75178 39 + 96486 ATGGGCAGATACTGAATGTTGCACTTTTACAGCATCGGG -s mr.mrrefChr3 1738 39 + 181027 ACGGGCGGAAACTGAATGTTGCATTTTCCGCGCAATGGA -s simCow_chr6.simCow.chr6 431851 39 + 602619 AGGGGCAGAAACTGAATGTTGCACTTTTACAGCATCGGG -s simDog_chr6.simDog.chr6 423404 39 + 593897 ATGGGCAGGTACTGAATGCTTCACCTTTACTGCATCGGT -s simHuman_chr6.simHuman.chr6 431644 39 + 601863 ATGGGCAGAGACTGGATGTTGCGATTTTACAGCATCGGG -s simRat_chr6.simRat.chr6 455548 37 + 647215 --GGGTCGAAACTGAATGTTGCACTTTCCGCGCAATGGA - -a -s simMouse_chr6.simMouse.chr6 443419 17 + 636262 CACGTGTTATATCAGAT -s Anc0.Anc0refChr3 69280 17 + 222631 GACCTGCCATACCAGAT -s Anc1.Anc1refChr6 100504 17 + 197743 GACCTGCCATACCAGAT -s Anc2.Anc2refChr13 75218 17 + 96486 GGCCTACCATACAAGAT -s mr.mrrefChr3 1777 17 + 181027 GACGTGCTATATCAGAT -s simCow_chr6.simCow.chr6 431891 17 + 602619 GGTCTACTATATATGAT -s simDog_chr6.simDog.chr6 423444 17 + 593897 GGCATACCATACAAGAT -s simHuman_chr6.simHuman.chr6 431684 17 + 601863 GACCCGCCATGCCAGAT -s simRat_chr6.simRat.chr6 455585 17 + 647215 GATTTGCTACATCAGAT - -a -s simMouse_chr6.simMouse.chr6 443436 23 + 636262 GACATAGGTCAAAATATTCCGGC -s Anc0.Anc0refChr3 69297 23 + 222631 GTCACAAGTCACAATGTTGCGGT -s Anc1.Anc1refChr6 100521 23 + 197743 GTCACAAGTCACAATGTTGCGGT -s Anc2.Anc2refChr13 75235 23 + 96486 GCCACAAGTCACAATGTTGCGGT -s mr.mrrefChr3 1794 23 + 181027 GTCATAGGTCAAAATATTCCGGT -s simCow_chr6.simCow.chr6 431908 23 + 602619 GCCGCAAGTCACAACGTTGCGGC -s simDog_chr6.simDog.chr6 423461 23 + 593897 GCCACAAGTCACGATTTCGCGGT -s simHuman_chr6.simHuman.chr6 431701 23 + 601863 GTCACAAGGCACAATGTTGCGCT -s simRat_chr6.simRat.chr6 455603 23 + 647215 GTCAAAGGTCGAAATACTCCGGT - -a -s simMouse_chr6.simMouse.chr6 443459 7 + 636262 CGCTGGG -s Anc0.Anc0refChr3 69320 4 + 222631 CGA---G -s Anc1.Anc1refChr6 100544 4 + 197743 CGA---G -s Anc2.Anc2refChr13 75258 4 + 96486 CGA---G -s mr.mrrefChr3 1817 7 + 181027 CGATGGG -s simCow_chr6.simCow.chr6 431931 4 + 602619 CCA---G -s simDog_chr6.simDog.chr6 423486 4 + 593897 TGG---G -s simHuman_chr6.simHuman.chr6 431724 4 + 601863 CGA---G -s simRat_chr6.simRat.chr6 455626 7 + 647215 CGATGGG - -a -s simMouse_chr6.simMouse.chr6 443466 10 + 636262 GCGGCTAAAG -s Anc0.Anc0refChr3 69324 10 + 222631 GCGGCTAATG -s Anc1.Anc1refChr6 100548 10 + 197743 GCGGCTAATG -s Anc2.Anc2refChr13 75262 10 + 96486 GCGGCTAATA -s mr.mrrefChr3 1824 10 + 181027 GCGGCTAAAG -s simCow_chr6.simCow.chr6 431944 10 + 602619 GCAGTCGAGC -s simDog_chr6.simDog.chr6 423490 10 + 593897 GTGGCTAATA -s simHuman_chr6.simHuman.chr6 431728 10 + 601863 GCGGCTAATG -s simRat_chr6.simRat.chr6 455633 10 + 647215 GCGGCTAAAA - -a -s simMouse_chr6.simMouse.chr6 443476 10 + 636262 CAATTCATGC -s Anc0.Anc0refChr3 69334 10 + 222631 CAATAAGTGT -s Anc1.Anc1refChr6 100558 10 + 197743 CAATAAGTGT -s Anc2.Anc2refChr13 75273 10 + 96486 CATCAAGTGT -s mr.mrrefChr3 1834 10 + 181027 CAATTCATGC -s simCow_chr6.simCow.chr6 431955 10 + 602619 CATCAAAAAT -s simDog_chr6.simDog.chr6 423501 10 + 593897 CATCAAGTGT -s simHuman_chr6.simHuman.chr6 431738 10 + 601863 CAATGAGTGT -s simRat_chr6.simRat.chr6 455643 10 + 647215 CAATTCATGC - -a -s simMouse_chr6.simMouse.chr6 443486 8 + 636262 GTTAGCCT -s Anc0.Anc0refChr3 69348 8 + 222631 GCTGGCCT -s Anc1.Anc1refChr6 100572 8 + 197743 GCTGGCCT -s Anc2.Anc2refChr13 75287 8 + 96486 GCTGGCCT -s mr.mrrefChr3 1844 8 + 181027 GTTGGCCT -s simCow_chr6.simCow.chr6 431969 8 + 602619 GCTGTCGT -s simDog_chr6.simDog.chr6 423515 8 + 593897 GCTGGCCT -s simHuman_chr6.simHuman.chr6 431752 8 + 601863 GGTGGCTT -s simRat_chr6.simRat.chr6 455653 8 + 647215 GTTGACCT - -a -s simMouse_chr6.simMouse.chr6 443494 8 + 636262 TTTAAATA -s Anc0.Anc0refChr3 69356 8 + 222631 CTCATATA -s Anc1.Anc1refChr6 100580 8 + 197743 CTCATATA -s Anc2.Anc2refChr13 75295 8 + 96486 CTCATAGA -s mr.mrrefChr3 1852 8 + 181027 TTTAAATA -s simCow_chr6.simCow.chr6 431994 8 + 602619 CTCATAAA -s simDog_chr6.simDog.chr6 423523 8 + 593897 TTCAAGGA -s simHuman_chr6.simHuman.chr6 431760 8 + 601863 CTCATATA -s simRat_chr6.simRat.chr6 455661 8 + 647215 TTTGAATA - -a -s simMouse_chr6.simMouse.chr6 443502 1 + 636262 G -s Anc0.Anc0refChr3 69364 1 + 222631 A -s Anc1.Anc1refChr6 100588 1 + 197743 A -s Anc2.Anc2refChr13 75303 1 + 96486 A -s mr.mrrefChr3 1860 1 + 181027 A -s simCow_chr6.simCow.chr6 432003 1 + 602619 A -s simDog_chr6.simDog.chr6 423531 1 + 593897 A -s simHuman_chr6.simHuman.chr6 431768 1 + 601863 A -s simRat_chr6.simRat.chr6 455669 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 443503 20 + 636262 CCTTCTAAAATCAATACTTG -s Anc0.Anc0refChr3 69365 19 + 222631 T-TTCTAAAATGAATACTTG -s Anc1.Anc1refChr6 100589 19 + 197743 T-TTCTAAAATGAATACTTG -s Anc2.Anc2refChr13 75306 19 + 96486 T-TTCTAAAATGAATACTTG -s mr.mrrefChr3 1861 20 + 181027 CCTTCTAAAATCAATACTTG -s simCow_chr6.simCow.chr6 432006 19 + 602619 T-TTCTAAAATGAATACTTG -s simDog_chr6.simDog.chr6 423534 17 + 593897 T-TGTTGAAATGAATA--TA -s simHuman_chr6.simHuman.chr6 431769 19 + 601863 T-TTCTAGAATGAATATTTG -s simRat_chr6.simRat.chr6 455670 20 + 647215 CCTTCTAAAATCAATACTTG - -a -s simMouse_chr6.simMouse.chr6 443523 29 + 636262 TTACTCATTTTTTTGATGTACTGACTGGT -s Anc0.Anc0refChr3 69384 27 + 222631 GTACTCATTTTTA--ATCCACTGATTGGT -s Anc1.Anc1refChr6 100608 27 + 197743 GTACTCATTTTTA--ATCCACTGATTGGT -s Anc2.Anc2refChr13 75325 27 + 96486 GTACTCATTTTTA--ATCCACAGATTGGT -s mr.mrrefChr3 1881 29 + 181027 TTACTCATTTTTTTGATCTACTGATTGGT -s simCow_chr6.simCow.chr6 432027 27 + 602619 GTACTCCTTTTTG--TTCCACAGATTGGT -s simDog_chr6.simDog.chr6 423551 27 + 593897 GCGCACACTTTTA--AACCACAGATGGGC -s simHuman_chr6.simHuman.chr6 431788 27 + 601863 GTACTCATTTCTC--ATCCACTCATTGGT -s simRat_chr6.simRat.chr6 455690 29 + 647215 TTACTCATTTTTTTGATCTACAGATTGGT - -a -s simMouse_chr6.simMouse.chr6 443552 54 + 636262 TGACTTGCAACAGTCCCATAGTGATTTGAGAAGCAGCAACAAGCATCAGTCCCA -s Anc0.Anc0refChr3 69412 29 + 222631 TGACTTACAACAGCATCTT------------------------CCATACTTAC- -s Anc1.Anc1refChr6 100636 29 + 197743 TGACTTACAACAGCATCTT------------------------CCATACTTAC- -s Anc2.Anc2refChr13 75353 29 + 96486 TGACTTACAACAGCATGTC------------------------CCATACTTAC- -s mr.mrrefChr3 1910 46 + 181027 TGACTTGCAACAGTCCCATAGTGATTTGA--------AACAAGCCACAGTTCCA -s simCow_chr6.simCow.chr6 432055 29 + 602619 GAACTTACAATGGCGTGTC------------------------CCATACTTAC- -s simDog_chr6.simDog.chr6 423579 29 + 593897 TGGCTTACAACAGCATGTC------------------------TCATACTTAC- -s simHuman_chr6.simHuman.chr6 431816 29 + 601863 TGACTTATAACAGCTTCTT------------------------CCATACCTAC- -s simRat_chr6.simRat.chr6 455719 46 + 647215 CAACTTGCAACAGTCCCATAGTGGTTTGA--------AACAAGCCACAGTTCCA - -a -s simMouse_chr6.simMouse.chr6 443606 60 + 636262 TAGTGGTTTAACATTTAAACCACGTTGAACAAAAATGTCCTGTCATATCTGGTCCGTATC -s Anc0.Anc0refChr3 69441 46 + 222631 TAGAAATTCTGTA--------------AGCAAGAATGTACTGGCCTACCTGGTCAGTATC -s Anc1.Anc1refChr6 100665 46 + 197743 TAGAAATTCTGTA--------------AGCAAGAATGTACTGGCCTACCTGGTCAGTATC -s Anc2.Anc2refChr13 75382 46 + 96486 TGGAAATTCTGTA--------------AGTAAGAATGCACTGGCCTACCTGGTAAGTATC -s mr.mrrefChr3 1956 46 + 181027 TAGTGGTTTAACA--------------AGCAAGAATGTCCTGTCCTATCTGGTCCGTATC -s simCow_chr6.simCow.chr6 432084 46 + 602619 TTGAAATTCTGTA--------------AGTAAGAATGCAATGGCTTACCTGATAAGTATC -s simDog_chr6.simDog.chr6 423609 46 + 593897 TGGAAATCCCATA--------------AGTCAGAATGCACTGGCCTACCTGGTAAGTATC -s simHuman_chr6.simHuman.chr6 431845 46 + 601863 TAGATATTGTGTA--------------TGCAAGAATGTACTGGCCTACCTGGTCAGTATC -s simRat_chr6.simRat.chr6 455765 46 + 647215 TAGTGGTTTGACA--------------AGAAAGAATGTGCTGACCTATCTGGTCTGTACC - -a -s simMouse_chr6.simMouse.chr6 443666 53 + 636262 ACCCCTGTGATCTATAGACATCTCAGATTCTATACATTAATAGACTTAAATTG -s Anc0.Anc0refChr3 69488 53 + 222631 ACCTCAGTGATCAATAGACATCTCAGATTCAATACATCAATAGGCTGGAATTG -s Anc1.Anc1refChr6 100712 53 + 197743 ACCTCAGTGATCAATAGACATCTCAGATTCAATACATCAATAGGCTGGAATTG -s Anc2.Anc2refChr13 75429 53 + 96486 ACCTCAGTGATTAATAGATATTTCAGATTCAGTACATCAATAGGCTGGAATTG -s mr.mrrefChr3 2002 53 + 181027 ACCTCTGTGATCTATAGACATCTCAGATTCAATACATTAATAGACTTAAATTG -s simCow_chr6.simCow.chr6 432131 53 + 602619 ACCTCAGTTATTAGTAGATATTTCAGATTCAGTACATCAATAGGCTGGAATTG -s simDog_chr6.simDog.chr6 423656 16 + 593897 ACATCAG-GGTTAATAG------------------------------------ -s simHuman_chr6.simHuman.chr6 431892 53 + 601863 ACCTCAGTGATCAATAAACATCTCAGATTCAACACGTCAAGAGGCTGGGATTA -s simRat_chr6.simRat.chr6 455811 51 + 647215 AACTCTGTGATCTACGGACAACTAAGAG-CAATACATTAATGGACT-AAATTG - -a -s simMouse_chr6.simMouse.chr6 443719 14 + 636262 GGTCATGCAGCTCA -s Anc0.Anc0refChr3 69554 14 + 222631 GATCATAGTTATAA -s Anc1.Anc1refChr6 100778 14 + 197743 GATCATAGTTATAA -s Anc2.Anc2refChr13 75495 14 + 96486 GATCACAGTTATAG -s mr.mrrefChr3 2055 14 + 181027 GGTCATGCAGCTCA -s simCow_chr6.simCow.chr6 432200 14 + 602619 GATCACCGCTATAG -s simDog_chr6.simDog.chr6 423684 14 + 593897 GATCACAGTTATAG -s simHuman_chr6.simHuman.chr6 431958 14 + 601863 GATTATAGTTATAA -s simRat_chr6.simRat.chr6 455862 14 + 647215 AGTCATGCAGCTCA - -a -s simMouse_chr6.simMouse.chr6 443733 12 + 636262 AATTTTGAGGCA -s Anc0.Anc0refChr3 69568 12 + 222631 AATTTTGGAACA -s Anc1.Anc1refChr6 100792 12 + 197743 AATTTTGGAACA -s Anc2.Anc2refChr13 75631 12 + 96486 AATTTTGGAGGT -s mr.mrrefChr3 2069 12 + 181027 AATTTTGAGACA -s simCow_chr6.simCow.chr6 432343 12 + 602619 AATTATGGAGGT -s simDog_chr6.simDog.chr6 423822 12 + 593897 AATTTTGGAGGT -s simHuman_chr6.simHuman.chr6 431972 12 + 601863 TGTTTTTGTACA -s simRat_chr6.simRat.chr6 455876 12 + 647215 AATTTTGAGACA - -a -s simMouse_chr6.simMouse.chr6 443745 15 + 636262 GCCCAGCACTGCAGT -s Anc0.Anc0refChr3 69580 15 + 222631 GCCTAGCACTGCAGC -s Anc1.Anc1refChr6 100804 15 + 197743 GCCTAGCACTGCAGC -s Anc2.Anc2refChr13 75643 15 + 96486 GCCTAGCACTGTAGC -s mr.mrrefChr3 2081 15 + 181027 GCCTAGCACTGCAGT -s simCow_chr6.simCow.chr6 432355 15 + 602619 GCCTAGCACCATAGC -s simDog_chr6.simDog.chr6 423834 15 + 593897 GCCTAGCACTGTCCC -s simHuman_chr6.simHuman.chr6 431991 15 + 601863 GCCTAGCACTGCAGC -s simRat_chr6.simRat.chr6 455888 15 + 647215 GCCTAGCACTGCAGT - -a -s simMouse_chr6.simMouse.chr6 443760 14 + 636262 GAGGAACATGGGTC -s Anc0.Anc0refChr3 69597 14 + 222631 GAGCACCACAAGCC -s Anc1.Anc1refChr6 100821 14 + 197743 GAGCACCACAAGCC -s Anc2.Anc2refChr13 75660 14 + 96486 GAGCACCACAAGCA -s mr.mrrefChr3 2096 14 + 181027 GAGGAACATGGGCC -s simCow_chr6.simCow.chr6 432372 14 + 602619 GAGCACCACAAGTA -s simDog_chr6.simDog.chr6 423851 14 + 593897 GAGCACTACAAGCA -s simHuman_chr6.simHuman.chr6 432008 14 + 601863 GAATACCACAAACC -s simRat_chr6.simRat.chr6 455903 14 + 647215 GAGGAACATGTGCC - -a -s simMouse_chr6.simMouse.chr6 443774 8 + 636262 TAATGCTT -s Anc0.Anc0refChr3 69614 8 + 222631 TGATGGCC -s Anc1.Anc1refChr6 100838 8 + 197743 TGATGGCC -s Anc2.Anc2refChr13 75677 8 + 96486 TGATGGCC -s mr.mrrefChr3 2110 8 + 181027 TAATGCTT -s simCow_chr6.simCow.chr6 432388 4 + 602619 ----GGCA -s simDog_chr6.simDog.chr6 423868 8 + 593897 TGATGGCC -s simHuman_chr6.simHuman.chr6 432025 8 + 601863 TGATGACC -s simRat_chr6.simRat.chr6 455917 8 + 647215 TAATGTTT - -a -s simMouse_chr6.simMouse.chr6 443782 8 + 636262 CATACCAT -s Anc0.Anc0refChr3 69623 8 + 222631 TGCACTGT -s Anc1.Anc1refChr6 100847 8 + 197743 TGCACTGT -s Anc2.Anc2refChr13 75686 8 + 96486 TGCACTGT -s mr.mrrefChr3 2119 8 + 181027 CATACCAT -s simCow_chr6.simCow.chr6 432393 8 + 602619 CGCACTGT -s simDog_chr6.simDog.chr6 423877 8 + 593897 TGCACTGT -s simHuman_chr6.simHuman.chr6 432034 8 + 601863 GTCACTGT -s simRat_chr6.simRat.chr6 455926 8 + 647215 CATACCAT - -a -s simMouse_chr6.simMouse.chr6 443790 194 + 636262 AGCATAACCATTTCGTATATAACTTGGCTATGAAGTTATGGTTTTAATGTGACCCAGTTAAAGAATTGGAAGTCAAATTACTGGGCTCACCAGTGATCGGTGTTACACGATCGGTTTGTATAGTTGCATGCCTCAGCACTAGGCATGTTTGCAAGCCTGACAACGGCTACAAGAAAAAAGGCAAAACAGGAGGA -s Anc0.Anc0refChr3 69631 135 + 222631 CCCACAACCAACTTATATATAGTTTGGCAATGAAAAGATAATATCAAAGTTGCCCAGCAAAGG---------------------------------------------------------TAGTTGCATGTGTCAGTACTAGGCATATTTGCAAGCATAAGCAAGGTTACAAGA--GGAGGATGAACTGGAAGG -s Anc1.Anc1refChr6 100855 135 + 197743 CCCACAACCAACTTATATATAGTTTGGCAATGAAAAGATAATATCAAAGTTGCCCAGCAAAGG---------------------------------------------------------TAGTTGCATGTGTCAGTACTAGGCATATTTGCAAGCATAAGCAAGGTTACAAGA--GGAGGATGAACTGGAAGG -s Anc2.Anc2refChr13 75694 135 + 96486 CCCACAACCAACTTACATATAGTTTGGCAATGAAATGATAATATCAAAATTGCTTAGAAAAGG---------------------------------------------------------TAGTTGCATGTGTCAGTACTAAGCCTATTTGCAAGCAGAAGCAAGGTTACAAGA--GGAGGATGAAATGGGAGG -s mr.mrrefChr3 2127 194 + 181027 AGCATAACCATTTCGTATATAATTTGGCTATGAAGATATAGTTTTAATGTGACCCAGCTAAAGAATTGGAAGTCAAATTACTGGGCTCACCAGTGATCGGTGTTACACGATCGGTTTGTATAGTTGCATGCCTCAGCACTAGGCATGTTTGCAAGCCTAACCAAGGCTACAAGAAAGAAGGCAAAACAGGAGGA -s simCow_chr6.simCow.chr6 432405 124 + 602619 CCCACAATCAACTTACATAAAATTTGGTGATGGAATGATAATATCGAA----------AATGG---------------------------------------------------------TAGTTGCATATGCCAGTACTATGTGTAT-TGCAAGCAGACACAAGGTTACAAGA--GGAGGGTGAAATGGGAAG -s simDog_chr6.simDog.chr6 423885 129 + 593897 CCCACAACCATC------ATAGTTTGGCAATAAATTGATCATTTCAAAATTGCTTAGAGAAGG---------------------------------------------------------TAGTGGTATGTGTCAGTGCTTAACCCATTTGCAGGCAGAAGGAAGGTTATAAGG--GGACGATGAAATGGGAGG -s simHuman_chr6.simHuman.chr6 432042 135 + 601863 CCCACAACCAACTTATGTATAGTTCAGCAATGAAAAAACAATATCAAAGTAGCCCAGCAAAGG---------------------------------------------------------TAGTTGCATGTGTCAGTACTAGGCATATATGCAAGCATAAGCAAAGGTACAAGA--GGAGGTTGAACTGGAAGG -s simRat_chr6.simRat.chr6 455934 194 + 647215 GTCTTTATCACTTCGTATCTAATCTGGCTATGAAGATATAGTGTTAATATGACCCAGCGAAAGAATTGGAAGTCTGATTACTAGGCTCACCAGTGGACGGTGTTGCATGTTCCGTCCATATAGCTGCATGCCTCAGAACTAGGCATGTCTGCAAGCCCAACCAAGGCTACAAGAAAGAAGGCAATGCAGGAGGA - -a -s simMouse_chr6.simMouse.chr6 443984 59 + 636262 TTACTGGGCTATAGCAACATAGTACTACATGACCGGTGGGAGCAATACAAAGTTTCTGC -s Anc0.Anc0refChr3 69772 59 + 222631 TTACTAGGCTATATCAACATAGCAATTCATGTCCATGTGTAGCAATGTGGAATTCCTAT -s Anc1.Anc1refChr6 100996 59 + 197743 TTACTAGGCTATATCAACATAGCAATTCATGTCCATGTGTAGCAATGTGGAATTCCTAT -s Anc2.Anc2refChr13 75835 59 + 96486 TTACCAGGCTACATCAACCTAACAATTCATGTCCATGTGTAGCGATATGGAATTCCTAT -s mr.mrrefChr3 2321 59 + 181027 TTACTGGGCTATAGCAACATAGTACTACATGACCAGGTGGAGCAATGCAAAATTTCTGC -s simCow_chr6.simCow.chr6 432535 59 + 602619 TTACCAGGCTACATCAACCTGATAATTTGTGTCCATGTGTAGAGATATGGTATCCCGCC -s simDog_chr6.simDog.chr6 424020 59 + 593897 TTACCAGGTTACATCAACCTAACCATTCACACCCATGTGTAGCGGTAGGGAATTCCTAT -s simHuman_chr6.simHuman.chr6 432183 59 + 601863 TTACTAGGCTATACCAACATAGCAATTCATGTCCATGTGTAGCAACGTGGAATTCATTT -s simRat_chr6.simRat.chr6 456128 59 + 647215 TTACTGGGCTATATTAACATAGTACTACATGACCAGGTGAAGTATTGCAAAATTTTTGC - -a -s simMouse_chr6.simMouse.chr6 444043 54 + 636262 ACGCTTGGTGTTAGCTGGTCAAGACAAGCCTTAAGTTTAGATTGTGAATACTGG -s Anc0.Anc0refChr3 69831 52 + 222631 A-GCTTG-TGTTAGGTAGATCAAGCAAGCCTTAACTTTGGTTTATAGATGCTGC -s Anc1.Anc1refChr6 101055 53 + 197743 ATGCTTG-TGTTAGGTAGATCAAGCAAGCCTTAACTTTGGTTTATAGATGCTGC -s Anc2.Anc2refChr13 75894 52 + 96486 A-GCCTG-TGTTGGGCAGATCAAGCAAGCCTTAACTTTGGTTTACAGATGCTGC -s mr.mrrefChr3 2380 53 + 181027 ATGCTTG-TGTTAGCTGGTCCAGACAAGCCTTAAGTTTAGATTATGAATACTGG -s simCow_chr6.simCow.chr6 432594 47 + 602619 A-ATCTG-TGTTGGGCAAACCAAGCATGCCTTGACTTTGGTTTACAG-----GC -s simDog_chr6.simDog.chr6 424080 52 + 593897 G-GCCTG-AGTTGAGCAGATCAAGCAACCCTTAACTTGGGATTGCAGATGCTGC -s simHuman_chr6.simHuman.chr6 432242 51 + 601863 ATGCTTG-T--TAGGTAGGTCAAGCGAGCTTTAAATTTGGTTTATAGATCCTGC -s simRat_chr6.simRat.chr6 456187 53 + 647215 ATGCCTG-TGTTGGCTGGTCCAGACAAGCCTTAACTTTAGATCATGAATACTGG - -a -s simMouse_chr6.simMouse.chr6 444097 47 + 636262 ATCTAGTCCAACTGAGATACCTGGAGACAGTAGTAGGGTCCGTAATT -s Anc0.Anc0refChr3 69913 47 + 222631 ACTCAACCTGACAAAGATCCCTAAATGTAGTACACCAGTCCACAATT -s Anc1.Anc1refChr6 101138 47 + 197743 ACTCAACCTGACAAAGATCCCTAAATGTAGTACACCAGTCCACAATT -s Anc2.Anc2refChr13 75990 47 + 96486 ACTCATTCTGACAAAGATCCCCAAATGTAGTACACCAGTCCACAATT -s mr.mrrefChr3 2433 47 + 181027 ATCTAACCTAACAGAGATACCTGGAGATAGTACTAGGGTCCGTAATT -s simCow_chr6.simCow.chr6 432685 47 + 602619 ACTCAGTGTGATAAAGGTCCCCAAATGTAATATACCAGTCCACAATT -s simDog_chr6.simDog.chr6 424176 47 + 593897 ACTCATTCTGACAAAGATCCTCAAATGTAGTGCACCAGTCCCAAATT -s simHuman_chr6.simHuman.chr6 432323 47 + 601863 ACACAACCTGACAAAGATCCCTAAGTGTAGTACACCAGTCCACAATT -s simRat_chr6.simRat.chr6 456240 47 + 647215 ATTTAACCTTACAGAGATACCTTGAGATAGTACTTGTGTCTGTAATT - -a -s simMouse_chr6.simMouse.chr6 444144 21 + 636262 CAAGTTCATTTCAGTAGCCAA -s Anc0.Anc0refChr3 69964 21 + 222631 GATGTAAATTTTACTTGCTAA -s Anc1.Anc1refChr6 101189 21 + 197743 GATGTAAATTTTACTTGCTAA -s Anc2.Anc2refChr13 76041 21 + 96486 GATGTAAATTTTACTTGCTAA -s mr.mrrefChr3 2480 21 + 181027 GAAGTTAATTTCAGTAGCTAA -s simCow_chr6.simCow.chr6 432736 21 + 602619 GAAGTAAATTTTGATTGCTAA -s simDog_chr6.simDog.chr6 424227 21 + 593897 GATGTAAATTTTACTTGCTAA -s simHuman_chr6.simHuman.chr6 432374 21 + 601863 GAGGTCAATTTTACTTGCTAA -s simRat_chr6.simRat.chr6 456287 21 + 647215 GAAGTTAACTTCAGTAGTTAA - -a -s simMouse_chr6.simMouse.chr6 444165 38 + 636262 TAGTAATGCCTGCATGATGGCATGGAAGCATTGTTGGC -s Anc0.Anc0refChr3 69986 38 + 222631 CAATTTTGCTTGCCCACTGGCATGATAACACTGTTGGC -s Anc1.Anc1refChr6 101211 38 + 197743 CAATTTTGCTTGCCCACTGGCATGATAACACTGTTGGC -s Anc2.Anc2refChr13 76063 38 + 96486 CAATTTTGCTTGCCCACTAACATGATAGCACTGTTGGC -s mr.mrrefChr3 2501 38 + 181027 CAATAATGCCTGCATGATGGCATGAAAACATTGTTGGC -s simCow_chr6.simCow.chr6 432758 24 + 602619 CAATTTT--------------ATGATATCACTGTTGGC -s simDog_chr6.simDog.chr6 424249 38 + 593897 CATTTTTGCTTGCCCACTAACATGATGGCACTGATGGT -s simHuman_chr6.simHuman.chr6 432396 38 + 601863 CAATTGTGCTTGCTCACTGGCACGATAACACTATTGGC -s simRat_chr6.simRat.chr6 456308 38 + 647215 CAATAATGCCTGCATGATGGCATGAAAACATTCTTGGC - -a -s simMouse_chr6.simMouse.chr6 444203 4 + 636262 TTTA -s Anc0.Anc0refChr3 70030 4 + 222631 TTTA -s Anc1.Anc1refChr6 101255 4 + 197743 TTTA -s Anc2.Anc2refChr13 76107 4 + 96486 TTTG -s mr.mrrefChr3 2539 4 + 181027 TTTA -s simCow_chr6.simCow.chr6 432788 4 + 602619 TTTC -s simDog_chr6.simDog.chr6 424293 4 + 593897 TTTG -s simHuman_chr6.simHuman.chr6 432440 4 + 601863 TTTA -s simRat_chr6.simRat.chr6 456346 4 + 647215 TTTA - -a -s simMouse_chr6.simMouse.chr6 444207 24 + 636262 CACTCACATTTTCCAGTTATAGGG -s Anc0.Anc0refChr3 70034 24 + 222631 TGTTCATTTCTTCCAGTTATGGGG -s Anc1.Anc1refChr6 101259 24 + 197743 TGTTCATTTCTTCCAGTTATGGGG -s Anc2.Anc2refChr13 76111 24 + 96486 TGTTCATTTCTTCCAGTTATGGGG -s mr.mrrefChr3 2543 24 + 181027 TGTTCACATTTTCCAGTTATAGGG -s simCow_chr6.simCow.chr6 432792 24 + 602619 AGTGCAATTTTTCCAGTTATAGGG -s simDog_chr6.simDog.chr6 424299 24 + 593897 TATTCATTTCTTCCAGTTCTGGGA -s simHuman_chr6.simHuman.chr6 432444 24 + 601863 TGTTCATTTCTTCCAATTATGGGG -s simRat_chr6.simRat.chr6 456350 24 + 647215 TGTTTACACTTTCCAGTTATAGGG - -a -s simMouse_chr6.simMouse.chr6 444231 50 + 636262 GAACTTGTAGTGCACAGCTTGCATTACCTCCTTTATATTGGCTGGAGTCT -s Anc0.Anc0refChr3 70058 50 + 222631 GAGCTTGTAACACACAGCTTGCATTATTTCTCCTGTATTTGCTGGTACCT -s Anc1.Anc1refChr6 101283 50 + 197743 GAGCTTGTAACACACAGCTTGCATTATTTCTCCTGTATTTGCTGGTACCT -s Anc2.Anc2refChr13 76135 50 + 96486 GAGCTTGTAACACAAAGCTTGCACTATTTCTCCTGTATTTGCTGGTACTT -s mr.mrrefChr3 2567 50 + 181027 GAACTTGTAGTGCACAGCTTGCATTACCTCCTTTATATTGGCTGGAATCT -s simCow_chr6.simCow.chr6 432816 49 + 602619 GAGCTTGTAGCACAAAGCTCA-ACTATTTCTCCGGTATGTGCTGGTACTT -s simDog_chr6.simDog.chr6 424328 50 + 593897 GAGCTTGTAACACAAAGCGTGCACTATCTCTCCTGTATTTGCTGATACTT -s simHuman_chr6.simHuman.chr6 432468 50 + 601863 GAGCTTGTAACACACAGCTTGCATTATTTCTCCTGTATTTGCTGGTACCT -s simRat_chr6.simRat.chr6 456374 50 + 647215 GAACTTGTAGTGCCCAGCTTGCATAACCTCCTTTATATCGGCTGGAATCT - -a -s simMouse_chr6.simMouse.chr6 444281 32 + 636262 TACAACAAACAATATGCGAACCTCCTTACCAT -s Anc0.Anc0refChr3 70109 14 + 222631 TACAACAA----TAAG--------------AT -s Anc1.Anc1refChr6 101334 28 + 197743 TACAACAA----TAAGCAGTTCTCATTGCAAT -s Anc2.Anc2refChr13 76186 14 + 96486 TACAACAA----AAAG--------------AT -s mr.mrrefChr3 2617 32 + 181027 TACAACAAACAATATGCGGACCTCATTACCAT -s simCow_chr6.simCow.chr6 432866 14 + 602619 TACAACAA----AAAG--------------AT -s simDog_chr6.simDog.chr6 424379 14 + 593897 TGCAACAA----AAAG--------------AT -s simHuman_chr6.simHuman.chr6 432519 28 + 601863 TACAACAA----TAGGCAGTTCTCATTGCAAT -s simRat_chr6.simRat.chr6 456424 32 + 647215 TACAACAAACAACATGTGGACCTCATTACCAT - -a -s simMouse_chr6.simMouse.chr6 444313 29 + 636262 CTAAGATTTGTAGTGTGACACTGACACTC -s Anc0.Anc0refChr3 70124 29 + 222631 CTAAGATTTGTAATGTGACACTTAATCTC -s Anc1.Anc1refChr6 101363 29 + 197743 CTAAGATTTGTAATGTGACACTTAATCTC -s Anc2.Anc2refChr13 76201 29 + 96486 CTAAGATTTGTAATGTGACACTTTATCTC -s mr.mrrefChr3 2649 29 + 181027 CTAAGATTTGTAGTGTGACACTGACACTC -s simCow_chr6.simCow.chr6 432881 29 + 602619 CTAAGGTTTGTAATGTTACACTTTATCTT -s simDog_chr6.simDog.chr6 424394 29 + 593897 CTTAGATTTATAATGTGACACTTTATCCC -s simHuman_chr6.simHuman.chr6 432548 29 + 601863 CTAAGATTTGTGATGTAACATTTAATCTC -s simRat_chr6.simRat.chr6 456456 29 + 647215 CTAAGATTTGTAGTGTGCCACTAATACTT - -a -s simMouse_chr6.simMouse.chr6 444342 42 + 636262 GGCATCAAGCATAGGCCTCAGGGAATGCTGTTTCCCAGTGTG -s Anc0.Anc0refChr3 70155 42 + 222631 TATACCCAGCACAGACCTCAGGGAGTGTTGTTTCCCAGGGTG -s Anc1.Anc1refChr6 101394 42 + 197743 TATACCCAGCACAGACCTCAGGGAGTGTTGTTTCCCAGGGTG -s Anc2.Anc2refChr13 76232 42 + 96486 TATACCCAGCACAGACCTCAGGGAGTGTTGTTTCCCTGGGTG -s mr.mrrefChr3 2678 42 + 181027 GACATCAAGCATAGGCCTCAGGGAATGCTGTTTCCCAGTGTG -s simCow_chr6.simCow.chr6 432912 42 + 602619 GATACCCAGCATAGACTTCACGGAGTGTAGCTTCCCTGGGTG -s simDog_chr6.simDog.chr6 424425 37 + 593897 TACA-----CACAGATCTCAGGGGTCGTTGTTTCCCTGAGTC -s simHuman_chr6.simHuman.chr6 432579 42 + 601863 TATACCCAGCAAAGCCCCCAGGCAGTGTCATTTCCTAGGGTG -s simRat_chr6.simRat.chr6 456486 42 + 647215 GACATCAAGCATAAGCCTCAGGGAATGCTGTTTACCTGTGTG - -a -s simMouse_chr6.simMouse.chr6 444384 25 + 636262 CACAAAAAAATCCTTAACACTCCTT -s Anc0.Anc0refChr3 70197 25 + 222631 CAAAAACAAGTTCGTAACACCCCTT -s Anc1.Anc1refChr6 101436 25 + 197743 CAAAAACAAGTTCGTAACACCCCTT -s Anc2.Anc2refChr13 76274 25 + 96486 CAAAAACAAGTTCGTAACACCCCCT -s mr.mrrefChr3 2720 25 + 181027 CACAAAAAAATTCTTAACACTCCTT -s simCow_chr6.simCow.chr6 432954 25 + 602619 CACAGACAAGTCCTTAACGCCCCCT -s simDog_chr6.simDog.chr6 424462 25 + 593897 CAAAAACAAGTTTGTGCCACCCCCT -s simHuman_chr6.simHuman.chr6 432622 25 + 601863 CATAAACAGGTTCCTAACACCCCTT -s simRat_chr6.simRat.chr6 456528 25 + 647215 CACAAAAAAATTGTTAAGACTCCTT - -a -s simMouse_chr6.simMouse.chr6 444409 1 + 636262 T -s Anc0.Anc0refChr3 70222 1 + 222631 C -s Anc1.Anc1refChr6 101461 1 + 197743 C -s Anc2.Anc2refChr13 76304 1 + 96486 C -s mr.mrrefChr3 2745 1 + 181027 T -s simCow_chr6.simCow.chr6 432984 1 + 602619 C -s simDog_chr6.simDog.chr6 424492 1 + 593897 C -s simHuman_chr6.simHuman.chr6 432647 1 + 601863 C -s simRat_chr6.simRat.chr6 456553 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 444410 10 + 636262 AATCATGGGT -s Anc0.Anc0refChr3 70223 10 + 222631 ATTCATGGTA -s Anc1.Anc1refChr6 101462 10 + 197743 ATTCATGGTA -s Anc2.Anc2refChr13 76305 10 + 96486 ATGCATTGTA -s mr.mrrefChr3 2746 10 + 181027 AATCATGGGT -s simCow_chr6.simCow.chr6 432985 5 + 602619 -----TTGAT -s simDog_chr6.simDog.chr6 424497 10 + 593897 ATGCATTGTA -s simHuman_chr6.simHuman.chr6 432648 10 + 601863 GTTTATGGTA -s simRat_chr6.simRat.chr6 456554 10 + 647215 AATCATGGCT - -a -s simMouse_chr6.simMouse.chr6 444420 28 + 636262 GCATGGTAGACGAATTTCTTAAATAAAC -s Anc0.Anc0refChr3 70233 28 + 222631 GCATAGTAGACGAATTTCTTAACTAAAC -s Anc1.Anc1refChr6 101472 28 + 197743 GCATAGTAGACGAATTTCTTAACTAAAC -s Anc2.Anc2refChr13 76315 28 + 96486 GCATAGTAGATCAATTTCTTAACTAAAC -s mr.mrrefChr3 2756 28 + 181027 GCATGGTAGACGAATTTCTTAAATAAAC -s simCow_chr6.simCow.chr6 432990 28 + 602619 GCATAGTGGATAAATTTGTTCACTGAAT -s simDog_chr6.simDog.chr6 424515 28 + 593897 GCATTGTAGATCAACTTCTTAACTAAAC -s simHuman_chr6.simHuman.chr6 432658 28 + 601863 GCATAGTAGACGAATTTCTTAAGGAAAC -s simRat_chr6.simRat.chr6 456564 28 + 647215 TCATGGTAGACAAATTTCTTGAATAAAC - -a -s simMouse_chr6.simMouse.chr6 444448 1 + 636262 C -s Anc0.Anc0refChr3 70261 1 + 222631 T -s Anc1.Anc1refChr6 101500 1 + 197743 T -s Anc2.Anc2refChr13 76348 1 + 96486 T -s mr.mrrefChr3 2784 1 + 181027 T -s simCow_chr6.simCow.chr6 433023 1 + 602619 A -s simDog_chr6.simDog.chr6 424548 1 + 593897 T -s simHuman_chr6.simHuman.chr6 432686 1 + 601863 T -s simRat_chr6.simRat.chr6 456592 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 444449 48 + 636262 GTTGTGTTATCTCAGTATCTGATGTTGGGTGTGGGAATGGTAAGTTTA -s Anc0.Anc0refChr3 70262 48 + 222631 GTTTTGTTGTGCCAGTATTAGATGCTGGGTGTGCAAATGATGGGTTTA -s Anc1.Anc1refChr6 101501 48 + 197743 GTTTTGTTGTGCCAGTATTAGATGCTGGGTGTGCAAATGATGGGTTTA -s Anc2.Anc2refChr13 76349 48 + 96486 GTTTTGTTGTGCCAGTATTAGATCCTGGGTGTGCAAATGATGGGTTTA -s mr.mrrefChr3 2785 48 + 181027 GTTGTGTTGTCTCAGTATCTGATGTTGGGTGTGGGAATGATAAGTTTA -s simCow_chr6.simCow.chr6 433024 48 + 602619 GTTTTGTTGTGCCAGTATTAGATAGTGGGTGTGTAAATAATGGGTGTA -s simDog_chr6.simDog.chr6 424549 48 + 593897 GTTTCATTGTATCTTTATTAAGTCCTGGGTGTGCAAATGATGGGTTCA -s simHuman_chr6.simHuman.chr6 432689 48 + 601863 GTTTTGTGGTGCCAGTCTTAGATGCTGGGTGTGCAAGTGATGGGTTTA -s simRat_chr6.simRat.chr6 456593 48 + 647215 GTTGTGTTGTCTCAGCATCTGATGTTGGGTGTGGGTATGATAAGTTTA - -a -s simMouse_chr6.simMouse.chr6 444497 4 + 636262 CCTG -s Anc0.Anc0refChr3 70399 4 + 222631 TCTT -s Anc1.Anc1refChr6 101656 4 + 197743 TCTT -s Anc2.Anc2refChr13 76486 4 + 96486 ACTT -s mr.mrrefChr3 2918 4 + 181027 TCTG -s simCow_chr6.simCow.chr6 433138 2 + 602619 --TT -s simDog_chr6.simDog.chr6 424686 4 + 593897 ACTT -s simHuman_chr6.simHuman.chr6 432866 4 + 601863 TCTT -s simRat_chr6.simRat.chr6 456732 4 + 647215 TCTG - -a -s simMouse_chr6.simMouse.chr6 444501 8 + 636262 GTGGATTG -s Anc0.Anc0refChr3 70403 8 + 222631 GTGGATTC -s Anc1.Anc1refChr6 101660 8 + 197743 GTGGATTC -s Anc2.Anc2refChr13 76490 8 + 96486 GTGGTTTC -s mr.mrrefChr3 2922 8 + 181027 GTGGATTG -s simCow_chr6.simCow.chr6 433140 8 + 602619 GTGGTTTC -s simDog_chr6.simDog.chr6 424690 8 + 593897 GTGGTCCC -s simHuman_chr6.simHuman.chr6 432871 8 + 601863 GTGGATTC -s simRat_chr6.simRat.chr6 456736 8 + 647215 TTGGATTG - -a -s simMouse_chr6.simMouse.chr6 444509 12 + 636262 GTAAATGTGCAT -s Anc0.Anc0refChr3 70418 12 + 222631 GCAACAGTATAT -s Anc1.Anc1refChr6 101675 12 + 197743 GCAACAGTATAT -s Anc2.Anc2refChr13 76505 12 + 96486 GCAACAGTATAT -s mr.mrrefChr3 2930 12 + 181027 GTAAATGTGTAT -s simCow_chr6.simCow.chr6 433155 12 + 602619 GCAATAGTATAT -s simDog_chr6.simDog.chr6 424705 12 + 593897 GCAACAGTATAT -s simHuman_chr6.simHuman.chr6 432886 12 + 601863 GCAGCGGTATAT -s simRat_chr6.simRat.chr6 456744 12 + 647215 GTAAATGTGTAT - -a -s simMouse_chr6.simMouse.chr6 444521 7 + 636262 ATCAACT -s Anc0.Anc0refChr3 70431 4 + 222631 ATC---T -s Anc1.Anc1refChr6 101688 7 + 197743 ATCCCAT -s Anc2.Anc2refChr13 76518 4 + 96486 ATC---T -s mr.mrrefChr3 2942 7 + 181027 ATCATAT -s simCow_chr6.simCow.chr6 433168 4 + 602619 ATC---T -s simDog_chr6.simDog.chr6 424718 4 + 593897 ATC---T -s simHuman_chr6.simHuman.chr6 432899 7 + 601863 ATCCCAT -s simRat_chr6.simRat.chr6 456756 7 + 647215 ATCATAT - -a -s simMouse_chr6.simMouse.chr6 444528 15 + 636262 ACTGGGAGATGGTTG -s Anc0.Anc0refChr3 70435 15 + 222631 CTTGGGAGAGGCTGG -s Anc1.Anc1refChr6 101695 15 + 197743 CTTGGGAGAGGCTGG -s Anc2.Anc2refChr13 76522 15 + 96486 CTTGGGAGAGCCTGG -s mr.mrrefChr3 2949 15 + 181027 CCTGGGAGAGGGTTG -s simCow_chr6.simCow.chr6 433172 15 + 602619 CTTCAGGGAGACTGG -s simDog_chr6.simDog.chr6 424722 15 + 593897 CTTGGGAGAGCCTGT -s simHuman_chr6.simHuman.chr6 432911 15 + 601863 CATGGGAGAGGCTGG -s simRat_chr6.simRat.chr6 456763 15 + 647215 CCTTGGAGAGGGTTG - -a -s simMouse_chr6.simMouse.chr6 444543 1 + 636262 G -s Anc0.Anc0refChr3 70450 1 + 222631 A -s Anc1.Anc1refChr6 101710 1 + 197743 A -s Anc2.Anc2refChr13 76537 1 + 96486 A -s mr.mrrefChr3 2964 1 + 181027 G -s simCow_chr6.simCow.chr6 433187 1 + 602619 A -s simDog_chr6.simDog.chr6 424751 1 + 593897 A -s simHuman_chr6.simHuman.chr6 432926 1 + 601863 A - -a -s simMouse_chr6.simMouse.chr6 444544 103 + 636262 TTGCAGGCTTTTCTTCAGTGCTAGGGCAATAGAAATTTTAGCAGCTTAGTATCTACGATAAGTTATCTTTAACATCACAAATTATAACAGTCAGGTGTACTGT -s Anc0.Anc0refChr3 70452 99 + 222631 TTACA----TCTCTTCAGTGCCAGGACAACAGGAAATATCACAGTTTGGCACCGATATTAAATTATCTGTAGCATCACGAAATACAACAGTGGTGTGTACTGT -s Anc1.Anc1refChr6 101712 99 + 197743 TTACA----TCTCTTCAGTGCCAGGACAACAGGAAATATCACAGTTTGGCACCGATATTAAATTATCTGTAGCATCACGAAATACAACAGTGGTGTGTACTGT -s Anc2.Anc2refChr13 76539 99 + 96486 TTACA----TCTATTTAGTTCCAGGACTACAGGAAATATCACAGTTTGGCACCGATATTAAATTATCTGTAGCACCATGAAATTCAACAGTTGTGTGTACTGT -s mr.mrrefChr3 2965 103 + 181027 TTGCAGGCTTTTCTTCAGTGCCAGGGCAATAGAAATTTTAGCAGTTTAGTATCTACGATAAATTATCTTTAACATCACAAATTATAACAGTGAGGTGTACTGT -s simCow_chr6.simCow.chr6 433189 99 + 602619 TTATA----CCTGTTTGGTTGCAGGACAACAAGCAATATTACAGTTAAGCACCAATAAAAAATTGCATGCAACACCATAAAATCTAACAGTTGCATGTACCGT -s simDog_chr6.simDog.chr6 424753 99 + 593897 TTCCG----TTTATCTAGTTCCAGAACTACAGGAAATATCACAGTTTGGCACCGATATTAAATCATCTGTAGTGCCATGAAATTCAACAGTTGTGTGCACTGT -s simHuman_chr6.simHuman.chr6 432928 67 + 601863 TTACA----TCTCTTCAGTGCAAGGACAA--------------------------------ATTATCTGTATCATCCCGGCATACAACAGTGGTGTGTATTTT -s simRat_chr6.simRat.chr6 456778 93 + 647215 ---CAGGCTTTTCTTCAGGGCCAGGGCGAGCAAAATTTTGGTGGTTTAGTTT-------AGATTATCTTTAACATCACAAATTCTGACCGTGAGGTGTACTGT - -a -s simMouse_chr6.simMouse.chr6 444647 3 + 636262 CAT -s Anc0.Anc0refChr3 70552 3 + 222631 CAT -s Anc1.Anc1refChr6 101812 3 + 197743 CAT -s Anc2.Anc2refChr13 76639 3 + 96486 CAT -s mr.mrrefChr3 3069 3 + 181027 CAT -s simCow_chr6.simCow.chr6 433289 3 + 602619 TGT -s simDog_chr6.simDog.chr6 424853 3 + 593897 CAT -s simHuman_chr6.simHuman.chr6 432996 3 + 601863 CAT -s simRat_chr6.simRat.chr6 456872 3 + 647215 CAT - -a -s simMouse_chr6.simMouse.chr6 444650 8 + 636262 GGTACTCT -s Anc0.Anc0refChr3 70568 8 + 222631 GTTGCTCT -s Anc1.Anc1refChr6 101828 8 + 197743 GTTGCTCT -s Anc2.Anc2refChr13 76655 8 + 96486 ATAGCTCT -s mr.mrrefChr3 3072 8 + 181027 GGTACTCT -s simCow_chr6.simCow.chr6 433306 8 + 602619 ATAGCTCT -s simDog_chr6.simDog.chr6 424869 8 + 593897 ACAGCTCG -s simHuman_chr6.simHuman.chr6 433012 8 + 601863 GTTGCTCT -s simRat_chr6.simRat.chr6 456875 8 + 647215 GGTACTTT - -a -s simMouse_chr6.simMouse.chr6 444658 30 + 636262 ATCACAGCAGTAATAAGAAGTCTAGGAACA -s Anc0.Anc0refChr3 70577 27 + 222631 ATCACAGTAGTAA---GAAATTGTGGGACA -s Anc1.Anc1refChr6 101837 27 + 197743 ATCACAGTAGTAA---GAAATTGTGGGACA -s Anc2.Anc2refChr13 76664 27 + 96486 ATCACAGTAGTAA---GTAGTTGTGGGACA -s mr.mrrefChr3 3081 30 + 181027 ATCACAGCAGTAATAAGAAATCTAGGGACA -s simCow_chr6.simCow.chr6 433315 23 + 602619 ATCACAGTAGTAA---GGAGCTGCGG---- -s simDog_chr6.simDog.chr6 424878 27 + 593897 ATCACAGTAGTAA---TTAGTTGTGGGACA -s simHuman_chr6.simHuman.chr6 433021 27 + 601863 ATCAAAGTAGTAT---GAAATTCTGGGACA -s simRat_chr6.simRat.chr6 456884 27 + 647215 ATCACAG---TAATAAGAAATCTAGAGACA - -a -s simMouse_chr6.simMouse.chr6 444688 49 + 636262 GTGTATGAGAATTCTCAGTACTGTAAGCTTGTGGTGAACATATGCTACT -s Anc0.Anc0refChr3 70611 49 + 222631 GCATATGGTAATGCTGAATACTGTATGCTGGGGGTTAACATGTCCTACT -s Anc1.Anc1refChr6 101871 49 + 197743 GCATATGGTAATGCTGAATACTGTATGCTGGGGGTTAACATGTCCTACT -s Anc2.Anc2refChr13 76698 49 + 96486 GCATATGGTAATGCTGAATACAGTATGCTGGGGGTTAGCATGTCCTACT -s mr.mrrefChr3 3111 49 + 181027 GTGTATGGTAATTCTCAGTACTGTATGCTTGTGGTGAACATGTGCTACT -s simCow_chr6.simCow.chr6 433344 43 + 602619 GCATATAGTAATGTTGAATCCAGTATGCCAGGGGTTA------CCTACT -s simDog_chr6.simDog.chr6 424912 49 + 593897 GCGTAAGGTAACTCCGGATACAGTATGCTGGGGGTTGGCATGTCCCACT -s simHuman_chr6.simHuman.chr6 433055 49 + 601863 GCATATGGTAGTGCTAAATACTGTATGCTGGGGGGTAACATGTCCTACT -s simRat_chr6.simRat.chr6 456911 49 + 647215 GTGTATGGTAATTCTCAGTACTGTATGCTAGTGGTGAACATGTGCTACT - -a -s simMouse_chr6.simMouse.chr6 444737 52 + 636262 CCTGTCTACCCCTTTTCCAAGTGCTGAATCAAGTTAGCCAAGATCCTATATG -s Anc0.Anc0refChr3 70660 48 + 222631 CCTT----CCTCTTTTCTAGGTGCTGAATTGAGTTAACCAAGATTTCATACA -s Anc1.Anc1refChr6 101920 48 + 197743 CCTT----CCTCTTTTCTAGGTGCTGAATTGAGTTAACCAAGATTTCATACA -s Anc2.Anc2refChr13 76747 48 + 96486 CCTT----CCTCTTTTCTAGGTGCTGAATTGAGTCAACCAATATTTCATACA -s mr.mrrefChr3 3160 52 + 181027 CCTGTCTACCCCTTTTCCAAGTGCTGAATCGAGTTAACCAAGATTCTATATA -s simCow_chr6.simCow.chr6 433387 46 + 602619 --TA----CCTCTTTCCTAAGTGATGAATTGACTCAACTAATATTTTGTACA -s simDog_chr6.simDog.chr6 424965 48 + 593897 CCTT----CCTCTTTTCTAGATGCTGAATTGAGTCAACCAATATTTCATACA -s simHuman_chr6.simHuman.chr6 433104 24 + 601863 CCTT----CCTCTTTTC-----------------TCCCTAAGGTT------- -s simRat_chr6.simRat.chr6 456960 43 + 647215 CCTGT--------TATCCAA-TGCTGAATGGAGTTAACTGAGATTCTATATA - -a -s simMouse_chr6.simMouse.chr6 444789 43 + 636262 TAGTCCCTATTTTTGCCATCCTATGTACAGGATGTAGCATGCA -s Anc0.Anc0refChr3 70708 38 + 222631 T-----CTAAATTTGGAACTCTATATACACAATATAGCATGCT -s Anc1.Anc1refChr6 101968 38 + 197743 T-----CTAAATTTGGAACTCTATATACACAATATAGCATGCT -s Anc2.Anc2refChr13 76795 38 + 96486 T-----CTAAATTTGGAACTCTATATACACAATATAGCTTGCT -s mr.mrrefChr3 3212 43 + 181027 TAGTCCTTATTTTTGCCATCCTATGTACAGGATGTAGCATGCA -s simCow_chr6.simCow.chr6 433433 35 + 602619 T-----TTAGATTTGGCTTTCTATCAACACAATAT---CTGCT -s simDog_chr6.simDog.chr6 425018 38 + 593897 T-----CTAAATTTGGAACTCTATATACACAATATAGCTTGTT -s simHuman_chr6.simHuman.chr6 433128 10 + 601863 ---------------------------------TTACCATGCT -s simRat_chr6.simRat.chr6 457003 43 + 647215 TAGTCCTTATCGTTGACATCCTATGTACAAGGTGTAGCATGCA - -a -s simMouse_chr6.simMouse.chr6 444832 30 + 636262 ATTCCTGGGATGTGTTTCAATCTTGATCCA -s Anc0.Anc0refChr3 70764 30 + 222631 ATTTCTGGAATTTCTTTGAATTTTGATTCA -s Anc1.Anc1refChr6 102024 30 + 197743 ATTTCTGGAATTTCTTTGAATTTTGATTCA -s Anc2.Anc2refChr13 76851 30 + 96486 ATTTCTGTAATTTCTTTGGTTTCTGATTCA -s mr.mrrefChr3 3273 30 + 181027 ATTCCTGGAATGTGTTTCAATCTTGATCCA -s simCow_chr6.simCow.chr6 433486 14 + 602619 GTATCTGTAATTTC---------------- -s simDog_chr6.simDog.chr6 425074 24 + 593897 ATT------ATTTCTTTGGTTTCTGATTCA -s simHuman_chr6.simHuman.chr6 433156 30 + 601863 ATTTCTGGAATTTCTTTTAATTTTGATTCA -s simRat_chr6.simRat.chr6 457065 30 + 647215 ATTCCTGGAATGTGTTTCATTCTTGATCTA - -a -s simMouse_chr6.simMouse.chr6 444862 6 + 636262 CTCAAT -s Anc0.Anc0refChr3 70802 6 + 222631 TTTAAC -s Anc1.Anc1refChr6 102062 6 + 197743 TTTAAC -s Anc2.Anc2refChr13 76889 6 + 96486 TTTAAC -s mr.mrrefChr3 3303 6 + 181027 CTTAAC -s simCow_chr6.simCow.chr6 433508 6 + 602619 GTTAAC -s simDog_chr6.simDog.chr6 425106 6 + 593897 TTTACC -s simHuman_chr6.simHuman.chr6 433195 6 + 601863 TTTAAC -s simRat_chr6.simRat.chr6 457095 6 + 647215 CTTAAC - -a -s simMouse_chr6.simMouse.chr6 444868 20 + 636262 ATGAATGGGACTTTGCTGAG -s Anc0.Anc0refChr3 70812 17 + 222631 CT---GTACTTTTTAGTGAG -s Anc1.Anc1refChr6 102072 20 + 197743 CTGTAGTACTTTTTAGTGAG -s Anc2.Anc2refChr13 76899 17 + 96486 CT---GTACTTTTTAGTGAG -s mr.mrrefChr3 3309 20 + 181027 CTGTATGACATTTTGCTGAG -s simCow_chr6.simCow.chr6 433515 14 + 602619 ------TACTTTTTAGTGAG -s simDog_chr6.simDog.chr6 425116 17 + 593897 CT---GTACTTGTTAGTGGG -s simHuman_chr6.simHuman.chr6 433205 20 + 601863 CTGTAGTACTTTTTAGTGAG -s simRat_chr6.simRat.chr6 457101 20 + 647215 CTGTACGACATTTTGCTGAG - -a -s simMouse_chr6.simMouse.chr6 444888 30 + 636262 TACATCTTGGGGTATATTCACAGACTGAAG -s Anc0.Anc0refChr3 70829 30 + 222631 TTCATCTCGGGATATATTGACAGGCAGAAG -s Anc1.Anc1refChr6 102092 30 + 197743 TTCATCTCGGGATATATTGACAGGCAGAAG -s Anc2.Anc2refChr13 76916 30 + 96486 TTCATCTTGGGATATATTGACAGGCAGAAG -s mr.mrrefChr3 3329 30 + 181027 TACATCTCGGGATATATTCACAGACTGAAG -s simCow_chr6.simCow.chr6 433541 30 + 602619 TTCACCTTAGGATATATCAACAGACAGGAG -s simDog_chr6.simDog.chr6 425133 30 + 593897 TTCATCTTGGAATATGTTGACAGGCTGAAG -s simHuman_chr6.simHuman.chr6 433225 27 + 601863 TTCATCTCGGGATATATTGCCAGG---AAG -s simRat_chr6.simRat.chr6 457121 30 + 647215 TACGTCTCGGGATATATTCATAGACTGAAG - -a -s simMouse_chr6.simMouse.chr6 444918 27 + 636262 TTGGCAATTCACAGACTGAAGTCCACA -s Anc0.Anc0refChr3 70859 5 + 222631 CCG--------------------CA-- -s Anc1.Anc1refChr6 102122 5 + 197743 CCG--------------------CA-- -s Anc2.Anc2refChr13 76947 5 + 96486 CCA--------------------CA-- -s mr.mrrefChr3 3359 24 + 181027 CTGGCAATTCACA-ACTGAAGTCCA-- -s simCow_chr6.simCow.chr6 433572 5 + 602619 CAA--------------------CA-- -s simDog_chr6.simDog.chr6 425164 5 + 593897 CCA--------------------CA-- -s simHuman_chr6.simHuman.chr6 433252 5 + 601863 CAG--------------------CA-- -s simRat_chr6.simRat.chr6 457151 23 + 647215 C-GGTAATCCACA-ACTGAAGTCCA-- - -a -s simMouse_chr6.simMouse.chr6 444945 34 + 636262 TTGTGCAGCTATCATTGTCAGGTAATTCTGAACA -s Anc0.Anc0refChr3 70864 34 + 222631 TTGATAGGCTAAGATTATCAATTAATTCAGCGCA -s Anc1.Anc1refChr6 102127 34 + 197743 TTGATAGGCTAAGATTATCAATTAATTCAGCGCA -s Anc2.Anc2refChr13 76952 34 + 96486 TTGATAGGCTAAGATTAGGAATTAATTCAGCACA -s mr.mrrefChr3 3383 34 + 181027 TTGTGCAGCTATCATTGTCAGGTAATTCTGAGCA -s simCow_chr6.simCow.chr6 433578 34 + 602619 TTGATAGGCCAAGATGAGGAATTGATTGAGCAGG -s simDog_chr6.simDog.chr6 425169 34 + 593897 TTGATAGGCTAAGACTAGGTATTAATTCAGCACA -s simHuman_chr6.simHuman.chr6 433257 34 + 601863 CTGAAAGGCTAAGATTCTCAATTAATTCAGGGCA -s simRat_chr6.simRat.chr6 457174 34 + 647215 TTGTGCAGCTAGTACTGTCAGGTAAATCTGAGCA - -a -s simMouse_chr6.simMouse.chr6 444979 8 + 636262 GGCCCGAA -s Anc0.Anc0refChr3 70898 5 + 222631 AGC---AG -s Anc1.Anc1refChr6 102161 8 + 197743 AGCATAAG -s Anc2.Anc2refChr13 76986 5 + 96486 AGC---AA -s mr.mrrefChr3 3417 8 + 181027 GGCCTAAG -s simCow_chr6.simCow.chr6 433613 5 + 602619 AGC---GA -s simDog_chr6.simDog.chr6 425203 5 + 593897 AGC---AA -s simHuman_chr6.simHuman.chr6 433291 8 + 601863 AGCATAAG -s simRat_chr6.simRat.chr6 457208 8 + 647215 GGCCTAAG - -a -s simMouse_chr6.simMouse.chr6 444987 46 + 636262 TTCCCATTTCAAGGCAATTGAAAGATTTGAGTGGAAGGTGTCACCT -s Anc0.Anc0refChr3 70903 46 + 222631 TACCTATTTCAGGGCAGTCAAAGGACTTAAGTGGGTGGTGTGACCT -s Anc1.Anc1refChr6 102169 46 + 197743 TACCTATTTCAGGGCAGTCAAAGGACTTAAGTGGGTGGTGTGACCT -s Anc2.Anc2refChr13 76991 46 + 96486 TACCTATTTCAGGGCAGTCAGCGGACTTATGTGGGTGGTGTGACCT -s mr.mrrefChr3 3425 46 + 181027 TACCCATTTCAAGGCAGTTGAAAGATTTGAGTGGAAGGTGTCACCT -s simCow_chr6.simCow.chr6 433618 46 + 602619 TTCCCATTTCAGGGCGGCAACCAGGATTAAACGGCAGGCGTTACTT -s simDog_chr6.simDog.chr6 425208 46 + 593897 TAATTTTTTCAGGGCAGTCAGCGGACTTATGTGGGTGGTGTGACCT -s simHuman_chr6.simHuman.chr6 433299 42 + 601863 TACCAACTGCAGGGCAGTGAAAGGACTTAAGTAG----TGTGACCT -s simRat_chr6.simRat.chr6 457226 39 + 647215 TACCCATTTCAAGGCGGTTTGAAGATTTGAGT-------GTCACCT - -a -s simMouse_chr6.simMouse.chr6 445033 14 + 636262 CCATGTAACACTTC -s Anc0.Anc0refChr3 70949 14 + 222631 CCATGTAGCAATCC -s Anc1.Anc1refChr6 102215 14 + 197743 CCATGTAGCAATCC -s Anc2.Anc2refChr13 77050 14 + 96486 CAAGATAGCAATCC -s mr.mrrefChr3 3471 14 + 181027 CCATGTAACACTTC -s simCow_chr6.simCow.chr6 433678 14 + 602619 CAAAATTGAGGTCC -s simDog_chr6.simDog.chr6 425267 14 + 593897 CAAGATAGCAATCC -s simHuman_chr6.simHuman.chr6 433341 14 + 601863 CCATGTCGCAATCC -s simRat_chr6.simRat.chr6 457265 14 + 647215 CCATGTAACACCTC - -a -s simMouse_chr6.simMouse.chr6 445047 16 + 636262 TTAAGAATCCAAGTCC -s Anc0.Anc0refChr3 70963 16 + 222631 TAGAAGGTATAAGTCC -s Anc1.Anc1refChr6 102229 16 + 197743 TAGAAGGTATAAGTCC -s Anc2.Anc2refChr13 77064 16 + 96486 TAGAAGGTATTTGTCC -s mr.mrrefChr3 3488 16 + 181027 TTGAGAATCCAAGTCC -s simCow_chr6.simCow.chr6 433692 16 + 602619 TAGAAGGTATTGGTCC -s simDog_chr6.simDog.chr6 425281 16 + 593897 CAGAAAGTATTTGTCC -s simHuman_chr6.simHuman.chr6 433355 16 + 601863 TAGAAGGTATAAGTCC -s simRat_chr6.simRat.chr6 457282 16 + 647215 TTGAGAATCCAGGTCC - -a -s simMouse_chr6.simMouse.chr6 445063 23 + 636262 TAATTACTGCCCTATATGTGTGG -s Anc0.Anc0refChr3 70980 23 + 222631 TAATTAATGCCCTATACGTCTAA -s Anc1.Anc1refChr6 102246 23 + 197743 TAATTAATGCCCTATACGTCTAA -s Anc2.Anc2refChr13 77081 23 + 96486 TAATTAATGCCCTATACGTCTAA -s mr.mrrefChr3 3504 23 + 181027 TAATTACTGCCCTATATGTGTGG -s simCow_chr6.simCow.chr6 433709 23 + 602619 TAATTAACGCCCTATACGTCTAA -s simDog_chr6.simDog.chr6 425298 22 + 593897 TAATTAATG-ACTATACATCTAA -s simHuman_chr6.simHuman.chr6 433372 23 + 601863 TAATTAATGTCCTACACGTCTAA -s simRat_chr6.simRat.chr6 457298 23 + 647215 TAATTACTACCCTATATGTGTGG - -a -s simMouse_chr6.simMouse.chr6 445086 13 + 636262 CTTTAATGTGTCA -s Anc0.Anc0refChr3 71003 13 + 222631 ACTTAATATGTCA -s Anc1.Anc1refChr6 102269 13 + 197743 ACTTAATATGTCA -s Anc2.Anc2refChr13 77104 13 + 96486 ACCTAATATGTCA -s mr.mrrefChr3 3527 13 + 181027 ATTTAATGTGTCA -s simCow_chr6.simCow.chr6 433732 13 + 602619 ATCTAATATGTCA -s simDog_chr6.simDog.chr6 425321 13 + 593897 CCCCAATATGTCA -s simHuman_chr6.simHuman.chr6 433395 13 + 601863 ACTTAATATGTCA -s simRat_chr6.simRat.chr6 457321 13 + 647215 ATCTAATGTGTCA - -a -s simMouse_chr6.simMouse.chr6 445099 2 + 636262 AG -s Anc0.Anc0refChr3 71016 2 + 222631 GG -s Anc1.Anc1refChr6 102282 2 + 197743 GG -s Anc2.Anc2refChr13 77120 2 + 96486 GG -s mr.mrrefChr3 3540 2 + 181027 GG -s simCow_chr6.simCow.chr6 433748 2 + 602619 GC -s simDog_chr6.simDog.chr6 425337 2 + 593897 GG -s simHuman_chr6.simHuman.chr6 433408 2 + 601863 GA -s simRat_chr6.simRat.chr6 457334 2 + 647215 GG - -a -s simMouse_chr6.simMouse.chr6 445101 33 + 636262 TAGGTCACAAGTATAAGGACCTAACAAAGCCAA -s Anc0.Anc0refChr3 71020 32 + 222631 TAGGTCAGAAGTG-CCAGGCCTGAGAAAGCTAA -s Anc1.Anc1refChr6 102286 32 + 197743 TAGGTCAGAAGTG-CCAGGCCTGAGAAAGCTAA -s Anc2.Anc2refChr13 77124 32 + 96486 TAGGTCAGAAGTG-CCAGGCCTGAGAAAGCTAA -s mr.mrrefChr3 3544 32 + 181027 TAGGTCACAAGTA-AAGGACCTAACAAAGCCAA -s simCow_chr6.simCow.chr6 433752 32 + 602619 TAGGTCTGTAGTA-CAAGGCCTGACAAAGATAG -s simDog_chr6.simDog.chr6 425341 32 + 593897 TAGGTCAGAAGTG-CCAGGCCTGAGAAAACTGA -s simHuman_chr6.simHuman.chr6 433412 32 + 601863 TAGATCAAGAGTG-TCAGGCATGAAAAAGCTAA -s simRat_chr6.simRat.chr6 457338 32 + 647215 TAGGTGACAAGTA-AAGGACCTAACAAAGCCAA - -a -s simMouse_chr6.simMouse.chr6 445134 15 + 636262 CTTACTTCACTAAAT -s Anc0.Anc0refChr3 71052 15 + 222631 CTATGCTAGCAGGAT -s Anc1.Anc1refChr6 102318 15 + 197743 CTATGCTAGCAGGAT -s Anc2.Anc2refChr13 77159 15 + 96486 CTATGCTAGCAGGAT -s mr.mrrefChr3 3576 15 + 181027 CTTACTTCGCTAAAT -s simCow_chr6.simCow.chr6 433787 15 + 602619 CCTTGCTAGCAGAAT -s simDog_chr6.simDog.chr6 425376 15 + 593897 CTATGCTAGCAGGAT -s simHuman_chr6.simHuman.chr6 433444 1 + 601863 C-------------- -s simRat_chr6.simRat.chr6 457370 15 + 647215 CATACTTTGCTAAAT - -a -s simMouse_chr6.simMouse.chr6 445149 30 + 636262 AGATCCTGTCTTACCCAAAGCAATATATTC -s Anc0.Anc0refChr3 71067 30 + 222631 TGCTCCTGCCTTACCCGTAGCAAAATATTT -s Anc1.Anc1refChr6 102333 30 + 197743 TGCTCCTGCCTTACCCGTAGCAAAATATTT -s Anc2.Anc2refChr13 77174 30 + 96486 TGCTCCTGCCTTACCCGTAGCAAAATATTT -s mr.mrrefChr3 3591 30 + 181027 AGATCCTGTCTTACCCAAAGCAATATATTC -s simCow_chr6.simCow.chr6 433803 30 + 602619 TCCTCCTGTCTTACCCACAGCAATATATTT -s simDog_chr6.simDog.chr6 425391 30 + 593897 TGCTCCTGCCTTACCTGTAGCAAAATATTT -s simHuman_chr6.simHuman.chr6 433445 14 + 601863 ---------------CCTAGCATAATATT- -s simRat_chr6.simRat.chr6 457385 30 + 647215 GGATCCTGTCTTATCCACAGCAATATATTC - -a -s simMouse_chr6.simMouse.chr6 445179 11 + 636262 TTGTTCATAAT -s Anc0.Anc0refChr3 71097 11 + 222631 TTGTTGATGAT -s Anc1.Anc1refChr6 102363 11 + 197743 TTGTTGATGAT -s Anc2.Anc2refChr13 77216 11 + 96486 TTGTTGATGAT -s mr.mrrefChr3 3621 11 + 181027 TTGTTCATAAT -s simDog_chr6.simDog.chr6 425437 11 + 593897 TTGTTGATGAT -s simHuman_chr6.simHuman.chr6 433459 10 + 601863 -GGTTTATGGT -s simRat_chr6.simRat.chr6 457415 11 + 647215 TTGTCTATAAT - -a -s simMouse_chr6.simMouse.chr6 445190 10 + 636262 AAATAATTAT -s Anc0.Anc0refChr3 71108 5 + 222631 AGATT----- -s Anc1.Anc1refChr6 102374 5 + 197743 AGATT----- -s Anc2.Anc2refChr13 77227 5 + 96486 AGACT----- -s mr.mrrefChr3 3632 10 + 181027 AAGTAATTAT -s simDog_chr6.simDog.chr6 425449 5 + 593897 AGACT----- -s simHuman_chr6.simHuman.chr6 433469 5 + 601863 AGTTT----- -s simRat_chr6.simRat.chr6 457426 10 + 647215 AAGTAATCAT - -a -s simMouse_chr6.simMouse.chr6 445200 5 + 636262 AGAAG -s Anc0.Anc0refChr3 71113 1 + 222631 ----G -s Anc1.Anc1refChr6 102379 1 + 197743 ----G -s Anc2.Anc2refChr13 77232 1 + 96486 ----G -s mr.mrrefChr3 3642 5 + 181027 AGAAG -s simDog_chr6.simDog.chr6 425454 1 + 593897 ----G -s simHuman_chr6.simHuman.chr6 433474 1 + 601863 ----G -s simRat_chr6.simRat.chr6 457527 5 + 647215 AGAAG - -a -s simMouse_chr6.simMouse.chr6 445205 10 + 636262 TTCCAGACAT -s Anc0.Anc0refChr3 71114 10 + 222631 TTCCAGACAT -s Anc1.Anc1refChr6 102380 10 + 197743 TTCCAGACAT -s Anc2.Anc2refChr13 77233 10 + 96486 TTGCAGATGT -s mr.mrrefChr3 3647 10 + 181027 TTCCAGACAT -s simDog_chr6.simDog.chr6 425461 10 + 593897 TTGCAGATGT -s simHuman_chr6.simHuman.chr6 433475 10 + 601863 TTCCAGACAT -s simRat_chr6.simRat.chr6 457532 10 + 647215 TACCAGACAT - -a -s simMouse_chr6.simMouse.chr6 445215 61 + 636262 AGTTGACATGTTTCCAATGTCTTACTTGTGATTCACAGGTGAAAGGGTCACCAGCATTTCT -s Anc0.Anc0refChr3 71136 52 + 222631 CATGAACATGTTTCCAATGTCTTCCC--TGATGGACAGGTTAAA-------CATCACTTCT -s Anc1.Anc1refChr6 102402 58 + 197743 CATGAACATGTTTCCAATGTCTTCCC--TGATGGACAGGTTAAAGG-TCATCATCACTTCT -s Anc2.Anc2refChr13 77255 52 + 96486 CATGAGCATGTTTTCAATGTCCTCCC--TGATGGACAGGCTGAA-------CATCACTTCC -s mr.mrrefChr3 3657 59 + 181027 AATTGACATGTTTCCAATGTCTTACT--TGATGCACAGGTTAAAGGGTCACCAGCATTTCT -s simCow_chr6.simCow.chr6 433846 18 + 602619 ---------------AATGTCCTCCC--TAATTG--------------------------G -s simDog_chr6.simDog.chr6 425483 52 + 593897 CATGAGCATGTTTTCAATGTCCACCC--CGATGGACAGGCTGAA-------CATCACTTCC -s simHuman_chr6.simHuman.chr6 433497 56 + 601863 GACAAACATGTCTCTAATGCCTTCCC--TGACAGATAGATTAAAGG-TCATC--CACTTCT -s simRat_chr6.simRat.chr6 457542 59 + 647215 AATTGACATGTTTCCAATGGCTTACT--GGATGCACAGGTTAAAAGGTCACCAGCATTTCT - -a -s simMouse_chr6.simMouse.chr6 445276 11 + 636262 GAGAGTGGGTT -s Anc0.Anc0refChr3 71199 10 + 222631 GAGTATG-ATT -s Anc1.Anc1refChr6 102471 11 + 197743 GAGTATGAATT -s Anc2.Anc2refChr13 77318 10 + 96486 CACTATG-ATT -s mr.mrrefChr3 3716 11 + 181027 GAGAGTGGGTT -s simCow_chr6.simCow.chr6 433864 3 + 602619 --------ATT -s simDog_chr6.simDog.chr6 425546 10 + 593897 CACTATG-AAT -s simHuman_chr6.simHuman.chr6 433564 11 + 601863 GAGTATGAATT -s simRat_chr6.simRat.chr6 457601 11 + 647215 ATGGGTGGATT - -a -s simMouse_chr6.simMouse.chr6 445287 6 + 636262 CATAAT -s Anc0.Anc0refChr3 71214 6 + 222631 CATGAT -s Anc1.Anc1refChr6 102487 6 + 197743 CATGAT -s Anc2.Anc2refChr13 77333 6 + 96486 CATGAT -s mr.mrrefChr3 3727 6 + 181027 CATAAT -s simCow_chr6.simCow.chr6 433872 6 + 602619 CATGGT -s simDog_chr6.simDog.chr6 425561 6 + 593897 TATAAT -s simHuman_chr6.simHuman.chr6 433580 6 + 601863 CGTGAT -s simRat_chr6.simRat.chr6 457612 6 + 647215 CACAAG - -a -s simMouse_chr6.simMouse.chr6 445293 17 + 636262 CAATCGGCTGCTGGCGG -s Anc0.Anc0refChr3 71231 16 + 222631 C-ATAAGCTGCTGGTGA -s Anc1.Anc1refChr6 102504 16 + 197743 C-ATAAGCTGCTGGTGA -s Anc2.Anc2refChr13 77353 16 + 96486 T-ATAAGCTGCTAGTAA -s mr.mrrefChr3 3733 16 + 181027 C-ATCAGCTGCTGGCGA -s simCow_chr6.simCow.chr6 433890 13 + 602619 ----ACACTGTTAGGAG -s simDog_chr6.simDog.chr6 425581 16 + 593897 T-ATAAGCTGCTAGTAA -s simHuman_chr6.simHuman.chr6 433597 16 + 601863 C-TTAAGCTGCTGGAGA -s simRat_chr6.simRat.chr6 457618 16 + 647215 C-ATCAGCGGCTGGCGA - -a -s simMouse_chr6.simMouse.chr6 445310 16 + 636262 AAGTCTACCCTCTATC -s Anc0.Anc0refChr3 71247 10 + 222631 AAGTCGACCC------ -s Anc1.Anc1refChr6 102520 16 + 197743 AAGTCGACCCTCTATT -s Anc2.Anc2refChr13 77369 10 + 96486 AAGTCGCCCC------ -s mr.mrrefChr3 3749 16 + 181027 AAGTTTACCCTCTATC -s simCow_chr6.simCow.chr6 433903 10 + 602619 GAATCAGCTT------ -s simDog_chr6.simDog.chr6 425598 10 + 593897 AAGTTGCCCC------ -s simHuman_chr6.simHuman.chr6 433613 16 + 601863 AAGTCGACCCTCTATT -s simRat_chr6.simRat.chr6 457634 16 + 647215 AAGTTTACCCTCTATC - -a -s simMouse_chr6.simMouse.chr6 445326 4 + 636262 TCAC -s Anc0.Anc0refChr3 71260 4 + 222631 TCAC -s Anc1.Anc1refChr6 102539 4 + 197743 TCAC -s Anc2.Anc2refChr13 77382 4 + 96486 TCAT -s mr.mrrefChr3 3765 4 + 181027 TCAC -s simCow_chr6.simCow.chr6 433916 4 + 602619 TCAT -s simDog_chr6.simDog.chr6 425611 4 + 593897 TCAT -s simHuman_chr6.simHuman.chr6 433632 4 + 601863 TCCC -s simRat_chr6.simRat.chr6 457650 4 + 647215 TCAT - -a -s simMouse_chr6.simMouse.chr6 445330 30 + 636262 TCAACTGCTAGGCCTAGCAAGAGAATTGGC -s Anc0.Anc0refChr3 71264 20 + 222631 CCAACTGCTAGGCCCAGC---C-------C -s Anc1.Anc1refChr6 102543 20 + 197743 CCAACTGCTAGGCCCAGC---C-------C -s Anc2.Anc2refChr13 77386 20 + 96486 CCAACTGCTTGGCCCAGC---C-------C -s mr.mrrefChr3 3769 27 + 181027 TCAACTGCTAGGCCTAGC---AGAATTGGC -s simCow_chr6.simCow.chr6 433920 20 + 602619 CCCACTGCTCAGCCCTGA---C-------C -s simDog_chr6.simDog.chr6 425617 20 + 593897 CCAACTGCTTGACCCAGC---C-------C -s simHuman_chr6.simHuman.chr6 433636 20 + 601863 CTAACTGCTAGGCCCAGC---C-------C -s simRat_chr6.simRat.chr6 457654 22 + 647215 TCAACTGC-ATGCT-------GGAATTGTC - -a -s simMouse_chr6.simMouse.chr6 445360 32 + 636262 CCTAGTATTGGCTAGTCCCCTTGGCTTATATC -s Anc0.Anc0refChr3 71284 32 + 222631 ACTGGAATTGGCTAGTCATCTGGGCTGATATC -s Anc1.Anc1refChr6 102563 32 + 197743 ACTGGAATTGGCTAGTCATCTGGGCTGATATC -s Anc2.Anc2refChr13 77406 32 + 96486 ACTGGAATTGGCTAGTCATCTGTGCTGATATC -s mr.mrrefChr3 3796 32 + 181027 CCTAGTATTGGCTAGTCCCCTTGGTTTATATC -s simCow_chr6.simCow.chr6 433940 32 + 602619 ACTGAAATTGGCTAGTCATCTGTGCTGCTATC -s simDog_chr6.simDog.chr6 425642 32 + 593897 ACTTGAATTGGCTAGTCATCTGTGTTGATATC -s simHuman_chr6.simHuman.chr6 433656 32 + 601863 ACTGGAATTGGCTAATCATCCAGGCTGATATC -s simRat_chr6.simRat.chr6 457676 32 + 647215 CCTAGTATTATCTAGTCCCCTTGGTTTATATC - -a -s simMouse_chr6.simMouse.chr6 445392 17 + 636262 CTTTAGATCCCACTTCA -s Anc0.Anc0refChr3 71317 11 + 222631 CTGTAGATTCC------ -s Anc1.Anc1refChr6 102596 17 + 197743 CTGTAGATTCCAGTACA -s Anc2.Anc2refChr13 77439 11 + 96486 CTGTAGATTCC------ -s mr.mrrefChr3 3829 17 + 181027 CTTTAGATCCCACTTCA -s simCow_chr6.simCow.chr6 433973 11 + 602619 CTGTAGATTCC------ -s simHuman_chr6.simHuman.chr6 433689 8 + 601863 A---------CAGTACA -s simRat_chr6.simRat.chr6 457709 17 + 647215 CTTTAGATCCCACTTCA - -a -s simMouse_chr6.simMouse.chr6 445409 24 + 636262 GTCCCACTTCAAGCAACATGTAAG -s Anc0.Anc0refChr3 71328 2 + 222631 ----------------------AG -s Anc1.Anc1refChr6 102613 6 + 197743 GTCT------------------AG -s Anc2.Anc2refChr13 77450 2 + 96486 ----------------------AG -s mr.mrrefChr3 3846 24 + 181027 GTCCCACTTCAAGCAACATGTAAG -s simCow_chr6.simCow.chr6 433984 2 + 602619 ----------------------AG -s simHuman_chr6.simHuman.chr6 433697 6 + 601863 GTCT------------------AG -s simRat_chr6.simRat.chr6 457727 24 + 647215 GTCCCACTTCATGCAACATGTAAG - -a -s simMouse_chr6.simMouse.chr6 445433 31 + 636262 TTCCATAGAAGTGCTTATCACATCTAGTTTC -s Anc0.Anc0refChr3 71330 31 + 222631 TTCCATAAAAGTACTGATAAAGTCCAGTTCC -s Anc1.Anc1refChr6 102619 31 + 197743 TTCCATAAAAGTACTGATAAAGTCCAGTTCC -s Anc2.Anc2refChr13 77452 31 + 96486 TTCCATGAAAGTACTGGTAAAGTCCAGTACC -s mr.mrrefChr3 3870 31 + 181027 TTCCATAGAAGTGCTTATCACATCTAGTTTC -s simCow_chr6.simCow.chr6 434002 31 + 602619 TTCCATGAAAGTAGTGGTCAAGGCTAGTCCC -s simDog_chr6.simDog.chr6 425674 18 + 593897 ------------ACTG-TAGATTCCAGTATC -s simHuman_chr6.simHuman.chr6 433703 31 + 601863 TTCCATAAAAGTACTGATAAAGTCCAGTTCC -s simRat_chr6.simRat.chr6 457751 31 + 647215 TTCCATACGAGAGCTTATCACATATAGTTTC - -a -s simMouse_chr6.simMouse.chr6 445464 35 + 636262 AAAATTCTCTAAACCTATAAGTATAGAAGCATACA -s Anc0.Anc0refChr3 71361 35 + 222631 AAAACTCTCAAATCCTGTGACTACATGGACATGCC -s Anc1.Anc1refChr6 102650 35 + 197743 AAAACTCTCAAATCCTGTGACTACATGGACATGCC -s Anc2.Anc2refChr13 77483 35 + 96486 AAAACTCTCAAATCCTGTGACTACATGGACAAGCC -s mr.mrrefChr3 3901 35 + 181027 AAAATTCTCTAAACCTATAACTACAGAGGCATACA -s simCow_chr6.simCow.chr6 434036 33 + 602619 AAAACTCTGTAACTCTGTGACTACATGGACA--CC -s simDog_chr6.simDog.chr6 425692 35 + 593897 AAAATTCTCAAATCCTGTGACCACAAAGACAAGCA -s simHuman_chr6.simHuman.chr6 433734 29 + 601863 AAAGCTCTCCA------TTACTATATGGATATGCC -s simRat_chr6.simRat.chr6 457782 35 + 647215 AGAATTCCCTAGGCCTATAACTACACAGGCATACA - -a -s simMouse_chr6.simMouse.chr6 445499 56 + 636262 CTCTTCTGCAGGCTTCCAAACATAGGAAGAGACCTGCTGTGGTGGGCTCATCGGTC -s Anc0.Anc0refChr3 71399 56 + 222631 TTACACTGGAGGCTTCCAAATAAAGGGGGGGACCTGCCATGGTAAGCTAATCATTC -s Anc1.Anc1refChr6 102688 56 + 197743 TTACACTGGAGGCTTCCAAATAAAGGGGGGGACCTGCCATGGTAAGCTAATCATTC -s Anc2.Anc2refChr13 77521 56 + 96486 TTACACTGGAGGCTTCCAAGTAAAGGGGGGGAACTGCCATGGTAAACAAATCATTC -s mr.mrrefChr3 3939 56 + 181027 CTCTTCTGCAGGCTTCCAAACAAAGGAAGAGACCTGCTGTGGTGGGCTCATCAGTC -s simCow_chr6.simCow.chr6 434072 54 + 602619 TTGCACTGAATGCTTCCA--TAAATGAAGGGATCTGCCATGCCAAACCCCTCTTCC -s simDog_chr6.simDog.chr6 425730 56 + 593897 CTACATTGGAGGTTTCCAAGCAAAGGGGGGGAACTGCAATGGTGAACAAATCATTC -s simHuman_chr6.simHuman.chr6 433766 48 + 601863 TTACACTGGGGGCTTCCAAATG--------GACCTGCCATGGTAAGCTGATCATTT -s simRat_chr6.simRat.chr6 457820 56 + 647215 CTTTTCTACAGGCTTCCAAACAAAGGAACAGACCTGCTTTGGTGTGTTCATCAGAC - -a -s simMouse_chr6.simMouse.chr6 445555 69 + 636262 ACTCTCTATATCCTGGATTGTGTTCAGAGGCATTACAATAATTGCCCCAATGATTCCCATGGGGGTTTA -s Anc0.Anc0refChr3 71455 59 + 222631 A----------CCTGAATTGTGTTTAGTGGCATTGGAACAGTTGCCCCAGCAGCTTCTATGGAAGTAAT -s Anc1.Anc1refChr6 102744 65 + 197743 ACCATC--T--CCTGAATTGTGTTTAGTGGCATTGGAACAGTTGCCCCAGCAGCTTCTATGGAAGTAAT -s Anc2.Anc2refChr13 77577 59 + 96486 A----------ACTGACATGTGTTTAGTGGCATTGGAACAGTTCCCCCAGCAGCTTCTATGGAAGTAAT -s mr.mrrefChr3 3995 67 + 181027 ACTCTC--TATCCTGGATTGTGTTTAGTGGCATTACAATAATTGCCCCAATGATTCCCATGGGGGTTTC -s simCow_chr6.simCow.chr6 434126 59 + 602619 A----------ACTGGCATGTTTGTGGCAGCATTGGAACAGTTCGCCCATCAGCTTCTGTGGAAGTAAT -s simDog_chr6.simDog.chr6 425786 57 + 593897 A----------ACTGACAT--GTTTAGTGGCATTGGCACAGTTCCACCCGCAGCTTCTAGGGAAGTAGT -s simHuman_chr6.simHuman.chr6 433815 65 + 601863 ACCATC--T--CCTGAATTGGGTTTTGTGAGATCGGAACAGTTGCCACAGAAGCATCTATGCAAGTAAG -s simRat_chr6.simRat.chr6 457876 67 + 647215 ATGCCC--TAGTGTGGATTGTGCTTGGTGGCATTACAATAATTGCTCCAATGATTCCCATGGGGGTTTC - -a -s simMouse_chr6.simMouse.chr6 445624 13 + 636262 AAGTCATACTTCG -s Anc0.Anc0refChr3 71514 12 + 222631 AAGTCATACTTT- -s Anc1.Anc1refChr6 102809 12 + 197743 AAGTCATACTTT- -s Anc2.Anc2refChr13 77639 12 + 96486 AAGTTATACTTT- -s mr.mrrefChr3 4062 12 + 181027 AAGTCATACTTC- -s simCow_chr6.simCow.chr6 434213 12 + 602619 CGGTTACATTTT- -s simDog_chr6.simDog.chr6 425846 12 + 593897 AAGTTATACTTT- -s simHuman_chr6.simHuman.chr6 433880 12 + 601863 CACTCATACTTT- -s simRat_chr6.simRat.chr6 457943 12 + 647215 AAGTCAAACTTC- - -a -s simMouse_chr6.simMouse.chr6 445637 2 + 636262 TT -s Anc0.Anc0refChr3 71526 2 + 222631 TT -s Anc1.Anc1refChr6 102821 2 + 197743 TT -s Anc2.Anc2refChr13 77651 2 + 96486 TG -s mr.mrrefChr3 4074 2 + 181027 TT -s simCow_chr6.simCow.chr6 434225 2 + 602619 TG -s simDog_chr6.simDog.chr6 425858 2 + 593897 TG -s simHuman_chr6.simHuman.chr6 433893 2 + 601863 TT - -a -s simMouse_chr6.simMouse.chr6 445639 10 + 636262 CTCAATTTCT -s Anc0.Anc0refChr3 71528 10 + 222631 CTTGATTTTT -s Anc1.Anc1refChr6 102823 10 + 197743 CTTGATTTTT -s Anc2.Anc2refChr13 77653 10 + 96486 CTTGATTTTT -s mr.mrrefChr3 4076 10 + 181027 CTCAATTTCT -s simCow_chr6.simCow.chr6 434231 10 + 602619 CTTAATTTTA -s simDog_chr6.simDog.chr6 425860 10 + 593897 CTTGATTTTT -s simHuman_chr6.simHuman.chr6 433895 10 + 601863 CTTGATCTTT -s simRat_chr6.simRat.chr6 457955 4 + 647215 ------TTCT - -a -s simMouse_chr6.simMouse.chr6 445649 23 + 636262 AAGTGAAAATTTTTCTATGCCAC -s Anc0.Anc0refChr3 71538 21 + 222631 AAG--AAAGGGCCCTGATGCCAG -s Anc1.Anc1refChr6 102833 21 + 197743 AAG--AAAGGGCCCTGATGCCAG -s Anc2.Anc2refChr13 77689 21 + 96486 AAG--AAAGGGCCCTGATGCCTG -s mr.mrrefChr3 4086 23 + 181027 AAGTGAAAGGTTTTCTATGCCAC -s simCow_chr6.simCow.chr6 434267 21 + 602619 AAG--AAAGGACCCTGATGCCTG -s simDog_chr6.simDog.chr6 425896 21 + 593897 AAT--AAAGGGTTCTGATGCCTG -s simHuman_chr6.simHuman.chr6 433905 21 + 601863 GAG--AATGGGCCCTAATGCCAA -s simRat_chr6.simRat.chr6 457959 23 + 647215 AAGTGAAAGGCTTTCTATGCCAC - -a -s simMouse_chr6.simMouse.chr6 445672 8 + 636262 CTACCATG -s Anc0.Anc0refChr3 71559 8 + 222631 CTGTGCTG -s Anc1.Anc1refChr6 102854 8 + 197743 CTGTGCTG -s Anc2.Anc2refChr13 77710 8 + 96486 CTGTGCTG -s mr.mrrefChr3 4109 8 + 181027 CTACCCTG -s simCow_chr6.simCow.chr6 434288 8 + 602619 ATGCCCTG -s simDog_chr6.simDog.chr6 425924 8 + 593897 CTGTGCTG -s simHuman_chr6.simHuman.chr6 433926 8 + 601863 CTGTGCTG -s simRat_chr6.simRat.chr6 457982 8 + 647215 CTACCCTG - -a -s simMouse_chr6.simMouse.chr6 445680 1 + 636262 G -s Anc0.Anc0refChr3 71568 1 + 222631 G -s Anc1.Anc1refChr6 102863 1 + 197743 G -s Anc2.Anc2refChr13 77719 1 + 96486 G -s mr.mrrefChr3 4117 1 + 181027 G -s simCow_chr6.simCow.chr6 434297 1 + 602619 G -s simDog_chr6.simDog.chr6 425932 1 + 593897 G -s simHuman_chr6.simHuman.chr6 433935 1 + 601863 G -s simRat_chr6.simRat.chr6 457990 1 + 647215 G - -a -s simMouse_chr6.simMouse.chr6 445681 16 + 636262 TCCAGAACATCTCAGT -s Anc0.Anc0refChr3 71569 16 + 222631 TCCAGACAGTCTCAGT -s Anc1.Anc1refChr6 102864 16 + 197743 TCCAGACAGTCTCAGT -s Anc2.Anc2refChr13 77720 16 + 96486 TCCAGACAGTCTCAGT -s mr.mrrefChr3 4118 16 + 181027 TCCAGAACATCTCAGT -s simCow_chr6.simCow.chr6 434301 16 + 602619 TCAGGACAGTATCATT -s simDog_chr6.simDog.chr6 425933 16 + 593897 TCCAGGCAGTCTCAGT -s simHuman_chr6.simHuman.chr6 433936 16 + 601863 TCCAGAGAGTCTCTGC -s simRat_chr6.simRat.chr6 457991 16 + 647215 TCCAGATCATTTCAGT - -a -s simMouse_chr6.simMouse.chr6 445697 29 + 636262 AGCGGTCAGTGCTGTAGAAAAATGAATCA -s Anc0.Anc0refChr3 71585 28 + 222631 AGCAATCAGTGATCTATGTGAAT-AGTCA -s Anc1.Anc1refChr6 102880 29 + 197743 AGCAATCAGTGATCTATGTGAATGAGTCA -s Anc2.Anc2refChr13 77738 28 + 96486 GGCAATCAATGATCTGTGTGAAC-AGTCA -s mr.mrrefChr3 4134 29 + 181027 AGCGATCAGTGATGTAGAAAAATGAATCA -s simCow_chr6.simCow.chr6 434319 28 + 602619 GGGATTCACTGATCTGTGTAACA-AGTCA -s simDog_chr6.simDog.chr6 425951 26 + 593897 -GCGATTAATGATCTGTGTGAAC-AGTC- -s simHuman_chr6.simHuman.chr6 433952 29 + 601863 AGTAATCAGTGATCTATGTGAATGAGTCA -s simRat_chr6.simRat.chr6 458007 29 + 647215 AGCGATCGGTGATGTAGAAAAATGAATCA - -a -s simMouse_chr6.simMouse.chr6 445726 22 + 636262 TCATCAATCAACTGTGGGAGTT -s Anc0.Anc0refChr3 71627 22 + 222631 TTATAAATCACCTATGAGAATT -s Anc1.Anc1refChr6 102923 22 + 197743 TTATAAATCACCTATGAGAATT -s Anc2.Anc2refChr13 77780 22 + 96486 TTATAAATTACCTATGAGAATT -s mr.mrrefChr3 4163 22 + 181027 TTATCAATCAACTGTGGGAGTT -s simCow_chr6.simCow.chr6 434361 22 + 602619 TCATAAATTACCTTTGAGAATT -s simDog_chr6.simDog.chr6 425986 22 + 593897 TTGTAACTTACCTATGAGAACT -s simHuman_chr6.simHuman.chr6 433995 22 + 601863 TTATAAATCACCCATGAAAATT -s simRat_chr6.simRat.chr6 458036 14 + 647215 TTAT--------TGTGGGAGTT - -a -s simMouse_chr6.simMouse.chr6 445748 158 + 636262 GATTGGTGGAGGTTCCTATGCAGGTAACATGTTACGCTTTGTCTTCACTTTTTACGAAAAAGGGCTTCAATGCCTCATATGCTGTGTGCAGGTGATCTAAGTAGTCATCAGTGGTGTGGAAAAATGGATCATTTTAACTCATCCTGTGAGAGTTTAGT -s Anc0.Anc0refChr3 71650 6 + 222631 GATTGT-------------------------------------------------------------------------------------------------------------------------------------------------------- -s Anc1.Anc1refChr6 102946 6 + 197743 GATTGT-------------------------------------------------------------------------------------------------------------------------------------------------------- -s Anc2.Anc2refChr13 77803 6 + 96486 GATTGT-------------------------------------------------------------------------------------------------------------------------------------------------------- -s mr.mrrefChr3 4185 34 + 181027 GATTGGTGGAGATTCCTATG----------------------------------------------------------------------------------------------------------------------------TGTGAGAGTTTAGT -s simCow_chr6.simCow.chr6 434384 6 + 602619 GATTGT-------------------------------------------------------------------------------------------------------------------------------------------------------- -s simDog_chr6.simDog.chr6 426009 5 + 593897 G-TTGT-------------------------------------------------------------------------------------------------------------------------------------------------------- -s simHuman_chr6.simHuman.chr6 434018 6 + 601863 GATTGT-------------------------------------------------------------------------------------------------------------------------------------------------------- -s simRat_chr6.simRat.chr6 458050 34 + 647215 GATTGGTGGAGATTCCTATG----------------------------------------------------------------------------------------------------------------------------GGTGAGAGTTTAGT - -a -s simMouse_chr6.simMouse.chr6 445906 4 + 636262 CATG -s mr.mrrefChr3 4219 4 + 181027 CATG -s simRat_chr6.simRat.chr6 458094 4 + 647215 CATG - -a -s simMouse_chr6.simMouse.chr6 445910 5 + 636262 GAGAC -s Anc0.Anc0refChr3 71656 5 + 222631 GAGAC -s Anc1.Anc1refChr6 102952 5 + 197743 GAGAC -s Anc2.Anc2refChr13 77810 5 + 96486 GAGAT -s mr.mrrefChr3 4223 5 + 181027 GAGAC -s simCow_chr6.simCow.chr6 434391 5 + 602619 GAGCT -s simDog_chr6.simDog.chr6 426015 5 + 593897 GAGAT -s simHuman_chr6.simHuman.chr6 434024 5 + 601863 GAGAC -s simRat_chr6.simRat.chr6 458106 5 + 647215 GAAAC - -a -s simMouse_chr6.simMouse.chr6 445915 21 + 636262 ATCAAACTTTGAGTTGGAGAT -s Anc0.Anc0refChr3 71661 21 + 222631 ATCAAAATGTGAGTTAGAGAT -s Anc1.Anc1refChr6 102957 21 + 197743 ATCAAAATGTGAGTTAGAGAT -s Anc2.Anc2refChr13 77815 21 + 96486 GGCAAAATGTGAGTTAGAGAT -s mr.mrrefChr3 4228 21 + 181027 ATCAAACTTTGAGTTGGAGAT -s simCow_chr6.simCow.chr6 434396 21 + 602619 GGCAAAATGTGAGTTAGAGAT -s simDog_chr6.simDog.chr6 426020 21 + 593897 GGCAAAATGTGAGTTGGACAT -s simHuman_chr6.simHuman.chr6 434029 21 + 601863 ATCAAAATATGAGTTAGAGAC -s simRat_chr6.simRat.chr6 458118 21 + 647215 ATCAAACTGTGAGTTGGAGAT - -a -s simMouse_chr6.simMouse.chr6 445936 23 + 636262 TACTAAACTAATTTTCACAGCTA -s Anc0.Anc0refChr3 71682 21 + 222631 GT--AATCTAACTTTCACAATTT -s Anc1.Anc1refChr6 102978 21 + 197743 GT--AATCTAACTTTCACAATTT -s Anc2.Anc2refChr13 77836 21 + 96486 GT--ACTCTAACTTTCACAATTT -s mr.mrrefChr3 4249 23 + 181027 TACTAAACTAATTTTCACAGCTA -s simCow_chr6.simCow.chr6 434417 17 + 602619 GT--TTTCTAACTTTC----TTT -s simDog_chr6.simDog.chr6 426041 21 + 593897 GT--ACCCTGACTTTCACAAACT -s simHuman_chr6.simHuman.chr6 434050 21 + 601863 GG--AATCTAACTTTCACAATTC -s simRat_chr6.simRat.chr6 458142 23 + 647215 TACTAAACTAATTTTCATGACTC - -a -s simMouse_chr6.simMouse.chr6 445959 24 + 636262 AGAGGTTCAGTCACAAGGTGCAAT -s Anc0.Anc0refChr3 71704 24 + 222631 AGGGATCCAGTCACAAGCCACAAC -s Anc1.Anc1refChr6 103000 24 + 197743 AGGGATCCAGTCACAAGCCACAAC -s Anc2.Anc2refChr13 77858 24 + 96486 AGGGATCCAGTCACAAGCCACAAC -s mr.mrrefChr3 4272 24 + 181027 AGAGGTTCAGTCACAAGGTGCAAT -s simCow_chr6.simCow.chr6 434435 21 + 602619 AGAGATCCAGTGACA---CACAAC -s simDog_chr6.simDog.chr6 426063 24 + 593897 AAGGGTCCAGTCACAAGCCACAAC -s simHuman_chr6.simHuman.chr6 434072 24 + 601863 AGGGATCGGGTCACAAGCCAAAAC -s simRat_chr6.simRat.chr6 458165 24 + 647215 AGAGATCCAGTCACAAGCTGGAAT - -a -s simMouse_chr6.simMouse.chr6 445983 16 + 636262 AGTGATTTTAATGATA -s Anc0.Anc0refChr3 71729 16 + 222631 ACTGATATTAATGATA -s Anc1.Anc1refChr6 103025 16 + 197743 ACTGATATTAATGATA -s Anc2.Anc2refChr13 77883 16 + 96486 ACTGATATTGATGATC -s mr.mrrefChr3 4296 16 + 181027 AGTGATTTTAATGATA -s simCow_chr6.simCow.chr6 434457 16 + 602619 ACTGATATTGATGATT -s simDog_chr6.simDog.chr6 426088 16 + 593897 ATTGATATTGATGATC -s simHuman_chr6.simHuman.chr6 434097 16 + 601863 ACTGAGATAAATGAGA -s simRat_chr6.simRat.chr6 458189 16 + 647215 AGTGATTTTAATGATA - -a -s simMouse_chr6.simMouse.chr6 445999 28 + 636262 TTATCTATTGTTTAATTATTCCATGATC -s Anc0.Anc0refChr3 71745 22 + 222631 CTATAT------TAATTAGTCAATGTTC -s Anc1.Anc1refChr6 103041 22 + 197743 CTATAT------TAATTAGTCAATGTTC -s Anc2.Anc2refChr13 77906 22 + 96486 CTGTAT------CAATTAGTCAATGTTC -s mr.mrrefChr3 4312 28 + 181027 TTATCTATTGTTTAATTATTCCATGATC -s simCow_chr6.simCow.chr6 434480 21 + 602619 CT-TAT------CATTAAGACAATGTTC -s simDog_chr6.simDog.chr6 426111 22 + 593897 CTGCGT------CAATTGGTTATTGGTC -s simHuman_chr6.simHuman.chr6 434113 22 + 601863 CTATAT------TAAATAGTCAATGTTC -s simRat_chr6.simRat.chr6 458205 28 + 647215 TTATCTATTGTTCAATTATTCTATGACC - -a -s simMouse_chr6.simMouse.chr6 446027 47 + 636262 AGATACAATGAAGATGTCTGAGACAATCTATCCAACCTGCAAACAAT -s Anc0.Anc0refChr3 71767 47 + 222631 AGTGCAAATGTAGATGTCTGAGGAAATCTATTCAACCTGCAAGCAAT -s Anc1.Anc1refChr6 103063 47 + 197743 AGTGCAAATGTAGATGTCTGAGGAAATCTATTCAACCTGCAAGCAAT -s Anc2.Anc2refChr13 77928 47 + 96486 AGTGCAGATGTAGATTTCTAAGGAAATCCATTCAACCTGCAAGCAAT -s mr.mrrefChr3 4340 47 + 181027 AGATACAATGAAGATGTCTGAGACAATCTATCCAACCTGCAAACAAT -s simCow_chr6.simCow.chr6 434509 47 + 602619 AGTGCAGATGTAGATTTCTAAAGAAATCCATTCAACCTGCAAGCAAT -s simDog_chr6.simDog.chr6 426133 32 + 593897 AGTGT---------------AGGACATCCATTCAGCCTGCAAGCAAT -s simHuman_chr6.simHuman.chr6 434135 47 + 601863 TGTGCAAATGCAGATGTCTGAGGAAATCTATTAAACCTGCAAGCAAG -s simRat_chr6.simRat.chr6 458233 47 + 647215 AGATCAAATGCAAATGTTTGAGACAATCTAGTCAACCTGTAACTAAT - -a -s simMouse_chr6.simMouse.chr6 446074 20 + 636262 GCAAATTACTTCTAACATGT -s Anc0.Anc0refChr3 71814 19 + 222631 GCAAATTGCTT-TAACATGT -s Anc1.Anc1refChr6 103110 20 + 197743 GCAAATTGCTTCTAACATGT -s Anc2.Anc2refChr13 77976 19 + 96486 GTAAATTGCTG-TAACTTGT -s mr.mrrefChr3 4387 20 + 181027 GCAAATTACTTCTAACATGT -s simCow_chr6.simCow.chr6 434557 19 + 602619 GTAAATTGTTG-TGGCTTGT -s simDog_chr6.simDog.chr6 426166 19 + 593897 GTAAATTGCTG-TAACTTGT -s simHuman_chr6.simHuman.chr6 434182 12 + 601863 AC--------TCTAACATCT -s simRat_chr6.simRat.chr6 458281 20 + 647215 GTAAATTATCTCTAACATGT - -a -s simMouse_chr6.simMouse.chr6 446094 231 + 636262 AGTGTAAGGAGGCAGTGAAGGGCTCCATGATGTTTTATATTATTGGTACAAAGAGAGGGGGGTCCCAGTTTCAAGGATTTCGGTTGATGAGTTCCTTAATGTTATTTAGATCACATTGTATAGATTTCGAACAAGGTCTCATGCAAAGCTCCAAAAAAAGGCAAATGTGGCTATGTACACATGGTTAGTGCTTGGCTATGAGCCTGCCCCACGTGGCCATGTACACTCAGT -s Anc0.Anc0refChr3 71835 89 + 222631 ATTGACAGGAGGAAGTGAAGTACTCAATGATGTAT-AT-TTATTAGTACAATATGAgagtggtcccagttttaaggctttcgggttgcaag-------------------------------------------------------------------------------------------------------------------------------------------- -s Anc1.Anc1refChr6 103132 89 + 197743 ATTGACAGGAGGAAGTGAAGTACTCAATGATGTAT-AT-TTATTAGTACAATATGAgagtggtcccagttttaaggctttcgggttgcaag-------------------------------------------------------------------------------------------------------------------------------------------- -s Anc2.Anc2refChr13 77997 89 + 96486 CTTGACAGGAGAAAGTGTAGTACACAATGATGTAT-AT-TTATTAGTACAATATGAgagtggtcccagttttaagactttcaggttgcaag-------------------------------------------------------------------------------------------------------------------------------------------- -s mr.mrrefChr3 4407 215 + 181027 AGTGTAAGGAGGCAGTGAAGGGCTCCATGATGTTT-ATATTATTGGTACAAAGAGAGGGGGGTCCCAGTTTTAAGGATTTCGGGTGATGAGTTCCTTAATGTTATTTAGAT--------------TTCGAACAAGGTCTCATGCAAAGCTCCAAAAAAAGGCAAATGTGGCTATGTACACATGGTTAGTGCTTGGCTATGAGCCTGCCCCACGTGGCC-TGTACACTCAGT -s simCow_chr6.simCow.chr6 434582 87 + 602619 CTTGACTGGAGCAAGT--TGAAGCCAACAATGTAC-AT-TTATGAGAACAATAGGAgagtggtcccagttttaagattttcaggttgcaag-------------------------------------------------------------------------------------------------------------------------------------------- -s simDog_chr6.simDog.chr6 426187 89 + 593897 CTTGACAGGAGAAAGTGTAGTGCACAATGATGAAT-AT-CTGCTGATACAATATGAgaggggtcccagttttacgactttcaggtcataag-------------------------------------------------------------------------------------------------------------------------------------------- -s simHuman_chr6.simHuman.chr6 434196 89 + 601863 ATTCACAGGGGGAAATGAGGTACTCAATGATGTCT-AT-TTATTAGTACAATTTGAgagtggtcccagtcttaaggcttttgggttgcaag-------------------------------------------------------------------------------------------------------------------------------------------- -s simRat_chr6.simRat.chr6 458301 215 + 647215 AGTTAAAGGAGCCAGTCAAGGGCTCAGTGATGTTT-ATATTTTTGGTACAAGAAGAGGGGGGTCCCAGTTTTAAGGATTTCAGGTCATGAGTTCCCTAATGTTGTTTAGAT--------------TTCGCACAGGGCCTCATGCAAAGCTCCAAAAAAAGGCAAATGTGGCAATGTACACATGGTTAGTGCTTGGCCATGGGCCTGCCCCGTACGGCC-TGTGCACACAGT - -a -s simMouse_chr6.simMouse.chr6 446325 33 + 636262 TAGTACTTGGCTATGAGCCCACCCCGCTTGACT -s Anc0.Anc0refChr3 71924 4 + 222631 -----------------------c------act -s Anc1.Anc1refChr6 103221 4 + 197743 -----------------------c------act -s Anc2.Anc2refChr13 78086 4 + 96486 -----------------------t------acc -s mr.mrrefChr3 4622 27 + 181027 TAGTACTTGGCTATGAGCCCACCC------act -s simCow_chr6.simCow.chr6 434669 4 + 602619 -----------------------t------gtg -s simDog_chr6.simDog.chr6 426276 4 + 593897 -----------------------t------acc -s simHuman_chr6.simHuman.chr6 434285 4 + 601863 -----------------------c------act -s simRat_chr6.simRat.chr6 458525 24 + 647215 TAGTGTTTGACTATGAGCCTGCCC--------- - -a -s simMouse_chr6.simMouse.chr6 446358 12 + 636262 AGGGGATTAGCA -s Anc0.Anc0refChr3 71928 12 + 222631 aggggcttagca -s Anc1.Anc1refChr6 103225 12 + 197743 aggggcttagca -s Anc2.Anc2refChr13 78090 12 + 96486 aggggcttagca -s mr.mrrefChr3 4649 12 + 181027 aGGGGATTAGCA -s simCow_chr6.simCow.chr6 434673 7 + 602619 agg-----agcc -s simDog_chr6.simDog.chr6 426280 12 + 593897 aggggcttagca -s simHuman_chr6.simHuman.chr6 434290 12 + 601863 agggggttagca -s simRat_chr6.simRat.chr6 458549 11 + 647215 -GGGGATTAGCA - -a -s simMouse_chr6.simMouse.chr6 446370 14 + 636262 AATACCAGCTGCTT -s Anc0.Anc0refChr3 71945 14 + 222631 aATGTGAGATATCA -s Anc1.Anc1refChr6 103242 14 + 197743 AATGTGAGATATCA -s Anc2.Anc2refChr13 78107 14 + 96486 aATGTGAGATATCA -s mr.mrrefChr3 4661 14 + 181027 AATATCAGCTGCTT -s simCow_chr6.simCow.chr6 434685 14 + 602619 aATGTGAGATATCA -s simDog_chr6.simDog.chr6 426297 14 + 593897 aattcaggatatCA -s simHuman_chr6.simHuman.chr6 434307 14 + 601863 AATGTGAGATATCA -s simRat_chr6.simRat.chr6 458560 14 + 647215 AATATCAGCTGCTT - -a -s simMouse_chr6.simMouse.chr6 446384 6 + 636262 TGATAA -s Anc0.Anc0refChr3 71959 6 + 222631 TGATAA -s Anc1.Anc1refChr6 103256 6 + 197743 TGATAA -s Anc2.Anc2refChr13 78128 6 + 96486 TGATAA -s mr.mrrefChr3 4675 6 + 181027 TGATAA -s simCow_chr6.simCow.chr6 434706 6 + 602619 TGATAC -s simDog_chr6.simDog.chr6 426318 6 + 593897 TGATAA -s simHuman_chr6.simHuman.chr6 434321 6 + 601863 TAATTA -s simRat_chr6.simRat.chr6 458574 6 + 647215 TGATGA - -a -s simMouse_chr6.simMouse.chr6 446390 9 + 636262 TAGGGAGTG -s Anc0.Anc0refChr3 71965 9 + 222631 TAGGGAGTG -s Anc1.Anc1refChr6 103262 9 + 197743 TAGGGAGTG -s Anc2.Anc2refChr13 78134 9 + 96486 TAGGGAGCG -s mr.mrrefChr3 4681 9 + 181027 TAGGGAGTG -s simCow_chr6.simCow.chr6 434712 9 + 602619 TAGGGCAGG -s simDog_chr6.simDog.chr6 426324 9 + 593897 TAGGGAGCA -s simHuman_chr6.simHuman.chr6 434331 9 + 601863 TACAGCATG -s simRat_chr6.simRat.chr6 458580 9 + 647215 TAAGGAGTG - -a -s simMouse_chr6.simMouse.chr6 446399 7 + 636262 TATTCAT -s Anc0.Anc0refChr3 71975 7 + 222631 TATCCTT -s Anc1.Anc1refChr6 103272 7 + 197743 TATCCTT -s Anc2.Anc2refChr13 78144 7 + 96486 TATCCTT -s mr.mrrefChr3 4691 7 + 181027 TATTCTT -s simCow_chr6.simCow.chr6 434722 7 + 602619 TGTCCTT -s simDog_chr6.simDog.chr6 426334 7 + 593897 TATCCCT -s simHuman_chr6.simHuman.chr6 434341 7 + 601863 TATCCTT -s simRat_chr6.simRat.chr6 458590 7 + 647215 TTTTCTT - -a -s simMouse_chr6.simMouse.chr6 446406 23 + 636262 CAAAAAAGACTTTTGGGTAGATT -s Anc0.Anc0refChr3 72021 23 + 222631 CTAAAAAGACTTGTGTGTTGATT -s Anc1.Anc1refChr6 103318 23 + 197743 CTAAAAAGACTTGTGTGTTGATT -s Anc2.Anc2refChr13 78190 23 + 96486 CTAAAAAGACTTGTGTGTTGATC -s mr.mrrefChr3 4698 23 + 181027 CAAAAAAGACTTTTGGGTAGATT -s simCow_chr6.simCow.chr6 434766 23 + 602619 ACTAAAGGACTTGTGTGTTGATC -s simDog_chr6.simDog.chr6 426373 22 + 593897 CTAAAAATACTTGTGTGCTGTT- -s simHuman_chr6.simHuman.chr6 434393 23 + 601863 CTGAAAAGATTTATGTGTTGACT -s simRat_chr6.simRat.chr6 458597 23 + 647215 CAAATAAGACTTGTGGGTGACTT - -a -s simMouse_chr6.simMouse.chr6 446429 36 + 636262 AAACTTCTGGCATGGATCTCGGCTGCAGCATCAGGT -s Anc0.Anc0refChr3 72044 36 + 222631 AACCCTCTAGCTTCTATCTTGGGTGCTGAATTATGT -s Anc1.Anc1refChr6 103341 36 + 197743 AACCCTCTAGCTTCTATCTTGGGTGCTGAATTATGT -s Anc2.Anc2refChr13 78213 36 + 96486 AACTCTTTAGCTTCTATCTTGGGTGCTGAATTATGT -s mr.mrrefChr3 4721 36 + 181027 AAACTTCTGGCATGGATCTCGGCTGCTGCATCAGGT -s simCow_chr6.simCow.chr6 434789 36 + 602619 AACTCCTTAGCTTCTGTCTTGACTGCTCGATTTTCT -s simDog_chr6.simDog.chr6 426395 34 + 593897 AACTCTTTAGTTTCTATCTTGGG--ATGAATTATGG -s simHuman_chr6.simHuman.chr6 434416 36 + 601863 ATTCATCTAGCTTCTACCTTGGTTCCTATATTATGT -s simRat_chr6.simRat.chr6 458632 36 + 647215 AAATTTCTGGCATGGATCTCGGCTGCTGCATGAGGT - -a -s simMouse_chr6.simMouse.chr6 446465 5 + 636262 GTCAA -s Anc0.Anc0refChr3 72081 5 + 222631 GTCAA -s Anc1.Anc1refChr6 103378 5 + 197743 GTCAA -s Anc2.Anc2refChr13 78250 5 + 96486 GTCAA -s mr.mrrefChr3 4757 5 + 181027 GTCAA -s simCow_chr6.simCow.chr6 434826 5 + 602619 ATCAA -s simDog_chr6.simDog.chr6 426430 5 + 593897 GTCAA -s simHuman_chr6.simHuman.chr6 434453 5 + 601863 GTCAT -s simRat_chr6.simRat.chr6 458668 5 + 647215 GTCAG - -a -s simMouse_chr6.simMouse.chr6 446470 40 + 636262 CCCTGCAGTCTTGACAGTATGCAGAGAGACCAGGGCGTTA -s Anc0.Anc0refChr3 72086 36 + 222631 CCCATCAGCCTTGGAAGCACACAGAAAGACCA----GTTT -s Anc1.Anc1refChr6 103383 36 + 197743 CCCATCAGCCTTGGAAGCACACAGAAAGACCA----GTTT -s Anc2.Anc2refChr13 78256 36 + 96486 CCCATCAGTCCTTGAAGCACACAGAAAGACCA----GATT -s mr.mrrefChr3 4762 36 + 181027 CCCTGCAGCCTTGACAGCATACAGAGAGACCA----GTTA -s simCow_chr6.simCow.chr6 434832 26 + 602619 CCAATCAGTCGTTGAAGCACACAGAA-------------- -s simDog_chr6.simDog.chr6 426436 35 + 593897 CCCATCAGTCCT-GAAGCACACAGAAAGACCA----GATT -s simHuman_chr6.simHuman.chr6 434458 36 + 601863 CCTGTCAGCCTTGGAAGCACACAGAAAGACCA----GTTT -s simRat_chr6.simRat.chr6 458673 33 + 647215 CC---CAGCCTTGACAGCCTACAGAGAGATCA----GTTA - -a -s simMouse_chr6.simMouse.chr6 446510 49 + 636262 CCTTTTAAGAGGCTAGAACCTACACAGGGAGGTAATAGCAGCAAGAAGT -s Anc0.Anc0refChr3 72126 40 + 222631 T-TTTTCCTTGGCGAGAAT-------TGGAGGTAGTA-TAGTATGAAAT -s Anc1.Anc1refChr6 103423 41 + 197743 TCTTTTCCTTGGCGAGAAT-------TGGAGGTAGTA-TAGTATGAAAT -s Anc2.Anc2refChr13 78296 40 + 96486 T-TTCTCCTTGGTGAGAAT-------TGGAGCTAGTA-TAGTATGAAAT -s mr.mrrefChr3 4798 49 + 181027 CCTTTTAAGAGGCTAGAACCTACACAGGGAGGTAATAGTAGCAAGAAGT -s simCow_chr6.simCow.chr6 434858 8 + 602619 -----------------------------------------TCTGAAGT -s simDog_chr6.simDog.chr6 426475 40 + 593897 T-TTCTCCTTGGTGAGAAT-------TGGAGCTAGTA-TAGTAGGAAAT -s simHuman_chr6.simHuman.chr6 434498 41 + 601863 TCTTTTTCTTTGCCAGAGT-------AGGTGGTAGTA-TAGTATGGGAT -s simRat_chr6.simRat.chr6 458706 47 + 647215 --TTTTAAAAGGGTACAACCTCCACAGGGAGGTAATAGTAGCAAGAATT - -a -s simMouse_chr6.simMouse.chr6 446559 7 + 636262 TCTATAA -s Anc0.Anc0refChr3 72166 7 + 222631 TCCAAAA -s Anc1.Anc1refChr6 103464 7 + 197743 TCCAAAA -s Anc2.Anc2refChr13 78336 7 + 96486 TTCCAAA -s mr.mrrefChr3 4847 7 + 181027 TCTATAA -s simCow_chr6.simCow.chr6 434866 5 + 602619 AT--AAG -s simDog_chr6.simDog.chr6 426523 7 + 593897 TTCCTAA -s simHuman_chr6.simHuman.chr6 434539 7 + 601863 TCCAAAA -s simRat_chr6.simRat.chr6 458753 7 + 647215 TCTATAA - -a -s simMouse_chr6.simMouse.chr6 446566 81 + 636262 CTGCCCAAAGGGAGCCCAAAGGGAAAGCACATGGAGGGGCTTGACTTTAAGATTTTAAAAATGGGGTGAACACATGCAACT -s Anc0.Anc0refChr3 72174 69 + 222631 CTGTCCAAAGGGAGGCCA-----------CATATGAGTGCTTGGATGTAAGATCTTAAGATTGTGGTGA-CAGATGCAACA -s Anc1.Anc1refChr6 103472 69 + 197743 CTGTCCAAAGGGAGGCCA-----------CATATGAGTGCTTGGATGTAAGATCTTAAGATTGTGGTGA-CAGATGCAACA -s Anc2.Anc2refChr13 78344 69 + 96486 CTGTCCAAACAGAGGCCA-----------CACATGAGTGCTTGGAAGTTAAATCTTAAGATCTTGGTGG-CAGATGCGATG -s mr.mrrefChr3 4854 81 + 181027 CTGCCCAAAGGGAGCCCAAAGGGAAAGCACATGGAGGTGCTTGACTTTAAGATTTTAAAAATGGGGTGAACACATGCAACA -s simCow_chr6.simCow.chr6 434872 38 + 602619 CTGTCCAGAC----------------------ATGATTGCTTGGAACTTAAATGTCTGGA--------------------- -s simDog_chr6.simDog.chr6 426531 69 + 593897 CTATCCAAACAGAGGCCA-----------CACATCAGTGCTTGGAAGTTAAGTCCTAAGATCTTGGTGG-CAGATGCGATG -s simHuman_chr6.simHuman.chr6 434547 69 + 601863 CTGTCCAAAGGGAGGCCA-----------CATACGAGTGCTTAGATGTAAGATCTTAAGATTGTGGTGA-CAGATGCAACA -s simRat_chr6.simRat.chr6 458760 81 + 647215 CTGCCCAAAAGGAGCCAAAAGGGAGAGCACATGTAGGTGCTTGACTTTAAGATTTTAAAAATGGGGTGAACACATGCAACA - -a -s simMouse_chr6.simMouse.chr6 446647 187 + 636262 TCATGTGCAATTAGCAGCTGGGATCTAGCACCCCTAGGATTTATCCAAGGTATGCATCAATCAATCATAGACAGTCACACCGGCTGGGATTGTGTTGAGTTGAGGGATCCTAGCCTAGTTAGGTCGAACCCAAATAACTAGTATCACTGGATTGATCTACTGTAACAGAACTGTTATTAGTCCCAGC -s Anc0.Anc0refChr3 72246 5 + 222631 CCATG-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- -s Anc1.Anc1refChr6 103544 133 + 197743 CCATGTGTAATTACCAGATGGGATCTAACATCCACAGCACTTATCAAACGCATGTGCT----GAGCACAGACAGTTGTA--------------------------------------------------TCAAACTATTTGTGTTGCAACATTAATTTACTGTTACAGAACCTTTTGCAGTCCCAAC -s Anc2.Anc2refChr13 78416 5 + 96486 CCATG-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- -s mr.mrrefChr3 4935 137 + 181027 TCATGTGCAATTAGCAGCTGGGATCTAGCATCCCTAGCACTTATCCAAGGTATGCATCAATCAATCATAGACAGTTATA--------------------------------------------------CCAAATAACTAGTATCACTGGATTGATCTACTGTAACAGAACTGTTATCAGTCCCAGC -s simDog_chr6.simDog.chr6 426603 5 + 593897 CCATG-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- -s simHuman_chr6.simHuman.chr6 434619 133 + 601863 CCATATGTGATTACCAGATGGGATCTAACATCCACAGCACTTATCAAACGCATGTGCT----GAGCACAGACAGTTGTA--------------------------------------------------TCAAACTATTTGTGTTGCAACATTAATTTACTGTTACAGAACCTTTTGCAGTCCCAAC -s simRat_chr6.simRat.chr6 458841 137 + 647215 TGATGGGCAATTGGCACCTGGGATCTAGCATCCCTAGCACTTACCTAAGGTATGCATGAATTCATCATACACAGTTATA--------------------------------------------------CTAAATAACTAGTATCACTGGATTGATCTACTGTCATAGGAATGTTATCAGTCCCAGC - -a -s simMouse_chr6.simMouse.chr6 446834 14 + 636262 TATAATAAACCTAA -s Anc1.Anc1refChr6 103677 14 + 197743 GACAGCAATTGCAA -s mr.mrrefChr3 5072 14 + 181027 TATAACAAACGTAA -s simHuman_chr6.simHuman.chr6 434756 14 + 601863 GACAGCAATTGCAA -s simRat_chr6.simRat.chr6 458978 14 + 647215 TATAACAAAAGTAA - -a -s simMouse_chr6.simMouse.chr6 446848 34 + 636262 TGAATACTTGATACACAGTGTTAATAGAATTGCA -s Anc1.Anc1refChr6 103691 34 + 197743 TGAACGCCTCATACACAATCCAAAGAGAACTACA -s mr.mrrefChr3 5086 34 + 181027 TGAATACCTCATACACAGTCCTAATAGAATTGCA -s simHuman_chr6.simHuman.chr6 434771 34 + 601863 TGAACGCCTCATACACAATCCAAAGAGAACTACA -s simRat_chr6.simRat.chr6 458992 30 + 647215 TG----CCTCATGCACAGCCCTAATAGAATTGCA - -a -s simMouse_chr6.simMouse.chr6 446882 19 + 636262 ATCATCTGGAAAGTAAGCT -s Anc1.Anc1refChr6 103726 19 + 197743 GCCGCCTGGAAACTAAGTT -s mr.mrrefChr3 5121 19 + 181027 GTCATCTGGAAAGTAAGCT -s simHuman_chr6.simHuman.chr6 434806 19 + 601863 GCCGCCTGGAAACTAAGTT -s simRat_chr6.simRat.chr6 459023 19 + 647215 GTCATCTGGAAAGTAAGCT - -a -s simMouse_chr6.simMouse.chr6 446901 13 + 636262 TCACAACATTACC -s Anc1.Anc1refChr6 103745 13 + 197743 TTGTAACATTATT -s mr.mrrefChr3 5140 13 + 181027 TCACAACATTACT -s simHuman_chr6.simHuman.chr6 434826 13 + 601863 TTGTAACATTATT -s simRat_chr6.simRat.chr6 459042 13 + 647215 TCACAACATTACT - -a -s simMouse_chr6.simMouse.chr6 446914 4 + 636262 TGTT -s Anc1.Anc1refChr6 103758 4 + 197743 TTGT -s mr.mrrefChr3 5153 4 + 181027 TGTT -s simHuman_chr6.simHuman.chr6 434848 4 + 601863 TTGT -s simRat_chr6.simRat.chr6 459055 4 + 647215 TGTT - -a -s simMouse_chr6.simMouse.chr6 446918 22 + 636262 GTCTTATGGAATGGTATCCTCC -s Anc1.Anc1refChr6 103762 22 + 197743 GTGTTACCAAGTCTCACCCTCC -s mr.mrrefChr3 5157 22 + 181027 GTCTTATGGAGTGGTATCCTCC -s simHuman_chr6.simHuman.chr6 434852 22 + 601863 GTGTTACCAAGTCTCACCCTCC -s simRat_chr6.simRat.chr6 459091 22 + 647215 CTCTCATAGGGTGGTATCCTCC - -a -s simMouse_chr6.simMouse.chr6 446940 85 + 636262 CATAGGATGGTATAGTTAAAATTTCTTCCTCTTCACTCCATTCCCTATCCACTATCATTGCTCACTTCATGTTATAGTGGTTTGC -s Anc0.Anc0refChr3 72251 16 + 222631 ---------------------------------------------------------------------CGTGAGCTGGTGTTGC -s Anc1.Anc1refChr6 103784 83 + 197743 CATATGATTGGGTCATTAACATAACTCCCTCTCCATTCCA--CCTCAACATGTACCACCCCCCACCACACGTGAGCTGGTGTTGC -s Anc2.Anc2refChr13 78421 16 + 96486 ---------------------------------------------------------------------CGTAAGCTGGTGTTGC -s mr.mrrefChr3 5179 85 + 181027 CATAGGATGGTATAATTAAAATTTCTTCCTCTTCACTCCATTCCCTATCCAGTACCATTGCTCACTTCACGTTATAGTGGTTTGC -s simCow_chr6.simCow.chr6 434910 15 + 602619 ----------------------------------------------------------------------GTAAGTTTGAGTTGC -s simDog_chr6.simDog.chr6 426608 16 + 593897 ---------------------------------------------------------------------CATAAGCTGGTGTTGC -s simHuman_chr6.simHuman.chr6 434894 83 + 601863 CATATGATTGGGTCATTAACATAACTCCCTCTCCATTCCA--CCTCAACATGTACCACCCCCCACCACACGTGAGCTCGTGCTGC -s simRat_chr6.simRat.chr6 459113 85 + 647215 CATAGAATGGCATAATAAATATTTCTTCCTCTTCACTTCATCTTCTATTCAGTACCATTGCTCAATCTACGTTATAGTGGTTTGC - -a -s simMouse_chr6.simMouse.chr6 447025 40 + 636262 TAGGATGACTCCATCTCCACTCAGCAGGGTATCCAGCATG -s Anc0.Anc0refChr3 72271 36 + 222631 ----ATTACTCCCCCTTCACTGTTGATAATATCCAGCCTG -s Anc1.Anc1refChr6 103871 36 + 197743 ----ATTACTCCCCCTTCACTGTTGATAATATCCAGCCTG -s Anc2.Anc2refChr13 78441 36 + 96486 ----ATTACTTCCCTTTCACTGGTGATAATATCCACCCTG -s mr.mrrefChr3 5268 40 + 181027 TAGGATGACTCCCTCTCCACTCTGCAGAGTATCCAGCATG -s simCow_chr6.simCow.chr6 434929 33 + 602619 ----ATCACTTCC---TGACTGGTGATAAAATCCACCCTG -s simDog_chr6.simDog.chr6 426628 28 + 593897 ----ATTACGTCCCTTGCACTGGTCATAATAT-------- -s simHuman_chr6.simHuman.chr6 434981 36 + 601863 ----ATTATTCCCCCATCACTGTCGTCAATATCCAGCCTG -s simRat_chr6.simRat.chr6 459203 35 + 647215 TAAAGTAACATGCTGGATACTCTGCAGAGT-----GGAGA - -a -s simMouse_chr6.simMouse.chr6 447065 27 + 636262 TTACTTCCTTAGCCATGTTGCATCCCA -s Anc0.Anc0refChr3 72322 27 + 222631 TGACTCCCTGAGCCATATTGCATCCTA -s Anc1.Anc1refChr6 103922 27 + 197743 TGACTCCCTGAGCCATATTGCATCCTA -s Anc2.Anc2refChr13 78492 27 + 96486 GGACTCTCTGAGCTATATTGCATCCTA -s mr.mrrefChr3 5308 27 + 181027 TGACTTCCTGAGCCATGTTGCATCCCA -s simCow_chr6.simCow.chr6 434977 27 + 602619 GGGCTCTCTGAGCTATATTGCATCCTA -s simDog_chr6.simDog.chr6 426671 26 + 593897 GGACGCTCT-AGCTATATTGCATCCTA -s simHuman_chr6.simHuman.chr6 435032 27 + 601863 TGACTCCCTGAGCCATATCGCATCTTA -s simRat_chr6.simRat.chr6 459238 27 + 647215 TGGAGTCCTGAGTCATGTTGCATCCCA - -a -s simMouse_chr6.simMouse.chr6 447092 35 + 636262 AGCCTGCACTAGAAGGTTCAGAAGGCAATGTATTA -s Anc0.Anc0refChr3 72350 26 + 222631 AAACTGCACTAAAAGG---------CAATGTATTA -s Anc1.Anc1refChr6 103950 26 + 197743 AAACTGCACTAAAAGG---------CAATGTATTA -s Anc2.Anc2refChr13 78520 26 + 96486 AAACTGAACTAAGAGG---------CAATGTATTT -s mr.mrrefChr3 5335 35 + 181027 AGCCTGCACTAGAAGGTTCAGAAGGCAATGTATTA -s simCow_chr6.simCow.chr6 435005 26 + 602619 AAACTGGACCTATAGT---------CAAGGCATTG -s simDog_chr6.simDog.chr6 426698 26 + 593897 TAATTAAACTAAGAGG---------CAATTTATTT -s simHuman_chr6.simHuman.chr6 435060 26 + 601863 AAACTGCACTAAAAGG---------CAATGTATTA -s simRat_chr6.simRat.chr6 459265 29 + 647215 A------ACTAGAAGGTTCAGAACACAATGTATTC - -a -s simMouse_chr6.simMouse.chr6 447127 3 + 636262 GTA -s Anc0.Anc0refChr3 72376 3 + 222631 GGA -s Anc1.Anc1refChr6 103976 3 + 197743 GGA -s Anc2.Anc2refChr13 78546 3 + 96486 GGA -s mr.mrrefChr3 5370 3 + 181027 GTA -s simCow_chr6.simCow.chr6 435031 3 + 602619 GGA -s simDog_chr6.simDog.chr6 426725 3 + 593897 GGA -s simHuman_chr6.simHuman.chr6 435086 3 + 601863 AGG -s simRat_chr6.simRat.chr6 459294 3 + 647215 GTA - -a -s simMouse_chr6.simMouse.chr6 447130 23 + 636262 GTGAGTTATATGGAACTATAACA -s Anc0.Anc0refChr3 72383 23 + 222631 TTGAGTTATATGGAATCAAAACC -s Anc1.Anc1refChr6 103983 23 + 197743 TTGAGTTATATGGAATCAAAACC -s Anc2.Anc2refChr13 78553 23 + 96486 TCAAGTTATATGGAATCAAAACC -s mr.mrrefChr3 5377 23 + 181027 GTGAGTTATATGGAACTATAACC -s simCow_chr6.simCow.chr6 435038 22 + 602619 TCAAATTATATGGAATC-AACCC -s simDog_chr6.simDog.chr6 426732 23 + 593897 TCAAGTTATAGGGGATCAAAACC -s simHuman_chr6.simHuman.chr6 435093 18 + 601863 TTGAGTTATATGGAATCA----- -s simRat_chr6.simRat.chr6 459301 14 + 647215 GTGAGTGATAT---------ATC - -a -s simMouse_chr6.simMouse.chr6 447153 6 + 636262 GACAAG -s Anc0.Anc0refChr3 72407 5 + 222631 -ACTAA -s Anc1.Anc1refChr6 104007 5 + 197743 -ACTAA -s Anc2.Anc2refChr13 78577 5 + 96486 -ACTAA -s mr.mrrefChr3 5401 6 + 181027 GACAAG -s simCow_chr6.simCow.chr6 435061 5 + 602619 -ATTCA -s simDog_chr6.simDog.chr6 426756 5 + 593897 -ACTAA -s simRat_chr6.simRat.chr6 459316 6 + 647215 GTCAAG - -a -s simMouse_chr6.simMouse.chr6 447159 15 + 636262 CATGGCAGCCTAGTT -s Anc0.Anc0refChr3 72412 15 + 222631 CATTTTGGCCTAATT -s Anc1.Anc1refChr6 104012 15 + 197743 CATTTTGGCCTAATT -s Anc2.Anc2refChr13 78582 15 + 96486 CATTTTGGCCTAATT -s mr.mrrefChr3 5407 15 + 181027 CATTGCAGCCTAGTT -s simCow_chr6.simCow.chr6 435066 15 + 602619 CCTTGTGGTGTAATT -s simDog_chr6.simDog.chr6 426762 15 + 593897 CATTTTGGCCTAATT -s simHuman_chr6.simHuman.chr6 435111 14 + 601863 -ATTATGGCCTAATT -s simRat_chr6.simRat.chr6 459322 15 + 647215 CATTGCAGCCTAGTT - -a -s simMouse_chr6.simMouse.chr6 447174 30 + 636262 TTAGGTTTAGAACTGAGCCTGTGTTAACTG -s Anc0.Anc0refChr3 72427 22 + 222631 G-AGGTTTGGAACTGATTCTG-------TG -s Anc1.Anc1refChr6 104027 27 + 197743 G-AGGTTTGGAACTGATTCTGTGTC--CTG -s Anc2.Anc2refChr13 78597 22 + 96486 G-AGGTTTGGAACTGATTCTG-------TG -s mr.mrrefChr3 5422 29 + 181027 T-AGGTTTAGAACTGAGTCTGTGTTAACTG -s simCow_chr6.simCow.chr6 435081 20 + 602619 G-AGGTTTGGATCTGATTCTG--------- -s simDog_chr6.simDog.chr6 426777 22 + 593897 G-AGGTTTGGAACTTATTCTG-------TG -s simHuman_chr6.simHuman.chr6 435128 27 + 601863 G-AGATTTGGAACTGATTCCATGTC--CTG -s simRat_chr6.simRat.chr6 459337 28 + 647215 T-AGGTTTAGAACTGAGTCTGTGTAAT-TT - -a -s simMouse_chr6.simMouse.chr6 447204 4 + 636262 GTGG -s Anc0.Anc0refChr3 72449 4 + 222631 GTGG -s Anc1.Anc1refChr6 104054 4 + 197743 GTGG -s Anc2.Anc2refChr13 78619 4 + 96486 GTAG -s mr.mrrefChr3 5451 4 + 181027 GTGG -s simCow_chr6.simCow.chr6 435101 4 + 602619 GTGG -s simDog_chr6.simDog.chr6 426806 4 + 593897 GTAG -s simHuman_chr6.simHuman.chr6 435155 3 + 601863 GTG- -s simRat_chr6.simRat.chr6 459365 4 + 647215 GTAG - -a -s simMouse_chr6.simMouse.chr6 447208 20 + 636262 GGGCAAAGACACAGAATCTG -s Anc0.Anc0refChr3 72453 20 + 222631 TGATAGATATATGGACTCTG -s Anc1.Anc1refChr6 104058 20 + 197743 TGATAGATATATGGACTCTG -s Anc2.Anc2refChr13 78623 20 + 96486 TGATAGATATATGGACTCTG -s mr.mrrefChr3 5455 20 + 181027 TGACAGAGATATAGAATCTG -s simCow_chr6.simCow.chr6 435105 20 + 602619 TGTAAAATATACAGAATCTA -s simDog_chr6.simDog.chr6 426810 20 + 593897 TGATAGATATATGGACTCTG -s simRat_chr6.simRat.chr6 459370 12 + 647215 TAAGAGAAGTAT-------- - -a -s simMouse_chr6.simMouse.chr6 447228 31 + 636262 TAGATAAGAGAAGGACTCATTTGATGACAAT -s Anc0.Anc0refChr3 72473 29 + 222631 TAGATAAGGAAGGAAATTACTTGACAAC--C -s Anc1.Anc1refChr6 104078 29 + 197743 TAGATAAGGAAGGAAATTACTTGACAAC--C -s Anc2.Anc2refChr13 78644 29 + 96486 TAGATAAGGAAGGAAATTACTTGACAAC--C -s mr.mrrefChr3 5475 29 + 181027 TAGATAAGAGAAGGACTCATTTGATGAC--T -s simCow_chr6.simCow.chr6 435126 29 + 602619 TGGATAAGAAGGGAAATTGCTTCAAGAC--C -s simDog_chr6.simDog.chr6 426831 29 + 593897 TAGATAAGGAAGGAAATTACTTGACAAC--C - -a -s simMouse_chr6.simMouse.chr6 447259 84 + 636262 ATTGACTATGAGCTAAATCAGAAATCAGGAAATCATCTTAAATAATTCAAGTGTGATTACAAGTTACCTGTGGGTGCTGGGAGT -s Anc0.Anc0refChr3 72502 76 + 222631 ATCAATGAGGAGTAGCATTGGAC--------TTCATCTGAAATAATTCAAGTTTAACTACAAATTACTGCCGGGTGCTGGGAAA -s Anc1.Anc1refChr6 104107 81 + 197743 ATCAATGAGGAGTAGCATTGGACGTCA---ATTCATCTGAAATAATTCAAGTTTAACTACAAATTACTGCCGGGTGCTGGGAAA -s Anc2.Anc2refChr13 78673 76 + 96486 ATCAATGAGGAGTAGCAGTGGAC--------TTCATCTGAAATAGTTCGCGTTTAGCTATAGATTATGGCCGGGTGCTGGGAAA -s mr.mrrefChr3 5504 84 + 181027 ATTAACTACAAGCTGAATTGGAAATCAGGAAATCATCTTAAATAATTCAAGTGTGATTACAAGTTACTTGTGGGTGCTGGGAGT -s simCow_chr6.simCow.chr6 435157 52 + 602619 ATCAAATATGAGTATCAGTGGGA--------TTCATCTGAAATA------------------------GCCGGGTGCTGGGAAA -s simDog_chr6.simDog.chr6 426860 74 + 593897 ATCAATGAGGAGTAGCAGTGGAC--------TTCATCTGAA--AGTTCGCGTTTAGCTATAGATTATGTCCAGGTGCTGGGAAA -s simHuman_chr6.simHuman.chr6 435158 65 + 601863 ----------------ATTCCATGTCA---ATTCACCTGAAATAATGTAAATTCAACTACAAATTACTGCAGGGTGCTGGGAAA -s simRat_chr6.simRat.chr6 459382 81 + 647215 ---AACTACAAGCTGTATTGGAAATCAGGCAATCATCTTAAATAATTCAGGTGTGATTACAACTTACTTGTAGGTGCTGGAAGT - -a -s simMouse_chr6.simMouse.chr6 447343 3 + 636262 CTC -s Anc0.Anc0refChr3 72581 3 + 222631 TTC -s Anc1.Anc1refChr6 104191 3 + 197743 TTC -s Anc2.Anc2refChr13 78752 3 + 96486 TTC -s mr.mrrefChr3 5591 3 + 181027 TTC -s simCow_chr6.simCow.chr6 435212 3 + 602619 TTG -s simDog_chr6.simDog.chr6 426937 3 + 593897 TTC -s simHuman_chr6.simHuman.chr6 435226 3 + 601863 TTC -s simRat_chr6.simRat.chr6 459466 3 + 647215 TTC - -a -s simMouse_chr6.simMouse.chr6 447346 98 + 636262 CCTTGCAAAGAGAACAGAGGGGGAATAACAAGAGCAACTTTCCTTGAGCATAAAGGCTATCTTGCAAAGGACTAAACTTCATAACACAAGTCTATTCC -s Anc0.Anc0refChr3 72584 55 + 222631 TCTTACAAAGAGAGTATAAGAGGAATAACAAAAGCAATTTTCCTAGAGCTTCAAG------------------------------------------- -s Anc1.Anc1refChr6 104194 55 + 197743 TCTTACAAAGAGAGTATAAGAGGAATAACAAAAGCAATTTTCCTAGAGCTTCAAG------------------------------------------- -s Anc2.Anc2refChr13 78755 55 + 96486 TCATACAAAGAGAGTATAAGAGGAATAACAAAAGCAATTTTCCTAGAGCTTCAAG------------------------------------------- -s mr.mrrefChr3 5594 74 + 181027 CCTTGCAAAGAGAACAGAGGAGGAATAACAAGAGCAACTTTCCTTGAGCATAAAG------------------------CATAACACAAGTCTATTCC -s simCow_chr6.simCow.chr6 435215 55 + 602619 TCATATAAAGAGAGAAGGAGAGGAATAATAAAAGTAAATTTCCTATATCTTCAAG------------------------------------------- -s simDog_chr6.simDog.chr6 426940 55 + 593897 TCATGCAGAGAGAGTATAAGAGGAATAACAAAAGCAATTTTCCTAGAGCTCCAGG------------------------------------------- -s simHuman_chr6.simHuman.chr6 435229 55 + 601863 TCTTACAAGGAGAGTAAAAGAGGAATAACAGAAGCAATTTTCCTAGAGCCTCAAG------------------------------------------- -s simRat_chr6.simRat.chr6 459506 74 + 647215 CCATGCAAAGAGAACAGAGGAGGAATAACAAGAGCAACTTTCCTCGAGCATAAAG------------------------CATAATAGAACTCTATTTC - -a -s simMouse_chr6.simMouse.chr6 447444 150 + 636262 ATCAATTTTTACGATGTACCTATAGAATCTTTTTTAGCTAATTCAAACAATGTCATCACCAATCTATTCAACTGAGGTGACCACAATGGATTGGTTTATAATAATACATAATTGTGAAAGAAAAACACTAGGCCAGCAGACTACAATTAA -s Anc0.Anc0refChr3 72639 55 + 222631 -----------------------------------------------------------------------------------------------GTACAGTAATAGGTAATTCAGACAGGGAGGAACCAGGCCAGCATACCACAACCAA -s Anc1.Anc1refChr6 104249 55 + 197743 -----------------------------------------------------------------------------------------------GTACAGTAATAGGTAATTCAGACAGGGAGGAACCAGGCCAGCATACCACAACCAA -s Anc2.Anc2refChr13 78810 55 + 96486 -----------------------------------------------------------------------------------------------GTACAGTAACAGGTACTTCAGACAGGGAGGAACCAGGCCAACATAACCCCACCAA -s mr.mrrefChr3 5668 150 + 181027 ATCAATTTTTACGATGTACCTATAGAATCTTTTTTAGCTAATTCAAACAATGTCATCACCAATCTATTCAACTGAGGTGACCACAATGGATTGCTTTATAATAATACATAATTGTGAAAGAAAAGAACCAGGCCAGCAGACCACAATTAA -s simCow_chr6.simCow.chr6 435270 55 + 602619 -----------------------------------------------------------------------------------------------ATACAATAAGAGGTATTTCAAAAAAGGAGGAAGCAAGCCAACACAACCCCAACAA -s simDog_chr6.simDog.chr6 426995 55 + 593897 -----------------------------------------------------------------------------------------------GTACAGTAACAGGTACTTCAGACAGGAAGTAACCAGGCCAACATAACCCCACCAC -s simHuman_chr6.simHuman.chr6 435284 55 + 601863 -----------------------------------------------------------------------------------------------GTACAGTAATAGGTAATCCAGAGAGGGAGGAACCAGGCCAGCATACCACAACCAA -s simRat_chr6.simRat.chr6 459581 150 + 647215 ACCACTTTTTACAGTGTACCTAAAGGATTTCTCTTAGCTAGTTTAGACAATGTCATCCCAAACCTATTCATCTGAGGTGGCCACAATGGATCGCTTTATAATAGTACATAACTATGAAAGAAATGAACCAGGCCGGCAGACCACAATTAA - -a -s simMouse_chr6.simMouse.chr6 447594 31 + 636262 GGTAACTTATGGGGTACGTGGCTCTGAGGAT -s Anc0.Anc0refChr3 72700 31 + 222631 GGTGACTCATAGGGTGAGTGGCTCAGAGGAT -s Anc1.Anc1refChr6 104310 31 + 197743 GGTGACTCATAGGGTGAGTGGCTCAGAGGAT -s Anc2.Anc2refChr13 78871 31 + 96486 GGTGACACAAAGGGTGAGAGGATCAGAGGAT -s mr.mrrefChr3 5818 31 + 181027 GGTAACTCATGGGGTGCGTGGCTCTGAGGAT -s simCow_chr6.simCow.chr6 435331 31 + 602619 GGTGACACAAGTGGTGAGGGGGTCACAGGAT -s simDog_chr6.simDog.chr6 427056 31 + 593897 CGTGACACGAAGGATGAAAGGATCAGAGGAT -s simHuman_chr6.simHuman.chr6 435345 31 + 601863 GGTGACTCATAGGGTGAGTGGCTCAAAGGGT -s simRat_chr6.simRat.chr6 459731 31 + 647215 GGTAACTCACGGGGTGTGTGGCTCTGAGGAT - -a -s simMouse_chr6.simMouse.chr6 447625 21 + 636262 ATAAACACAACAGTAGTATGA -s Anc0.Anc0refChr3 72731 18 + 222631 ATAAGCGCA---GTAGTATGA -s Anc1.Anc1refChr6 104341 18 + 197743 ATAAGCGCA---GTAGTATGA -s Anc2.Anc2refChr13 78902 18 + 96486 CCAAGCACA---GTAATATGA -s mr.mrrefChr3 5849 21 + 181027 ATAAGCGCAACAGTAGTATGA -s simCow_chr6.simCow.chr6 435362 18 + 602619 CAATGCACA---GTAACATGA -s simDog_chr6.simDog.chr6 427087 18 + 593897 CCAAGCACA---GTCATATGA -s simHuman_chr6.simHuman.chr6 435377 18 + 601863 ATAAGCGCA---GTAGTGTAA -s simRat_chr6.simRat.chr6 459762 21 + 647215 ATAAGTGCAACAGCAGTATGA - -a -s simMouse_chr6.simMouse.chr6 447646 6 + 636262 CCACCA -s Anc0.Anc0refChr3 72749 6 + 222631 CAATCA -s Anc1.Anc1refChr6 104359 6 + 197743 CAATCA -s Anc2.Anc2refChr13 78920 6 + 96486 CAGTCA -s mr.mrrefChr3 5870 6 + 181027 CCACCA -s simCow_chr6.simCow.chr6 435380 6 + 602619 CAGTCA -s simDog_chr6.simDog.chr6 427114 6 + 593897 CAGTCA -s simHuman_chr6.simHuman.chr6 435395 6 + 601863 CAATCA -s simRat_chr6.simRat.chr6 459783 6 + 647215 GCACCA - -a -s simMouse_chr6.simMouse.chr6 447652 5 + 636262 GAATA -s Anc0.Anc0refChr3 72756 5 + 222631 GGATG -s Anc1.Anc1refChr6 104366 5 + 197743 GGATG -s Anc2.Anc2refChr13 78927 5 + 96486 GGATG -s mr.mrrefChr3 5876 5 + 181027 GAATA -s simCow_chr6.simCow.chr6 435387 5 + 602619 GGGTG -s simDog_chr6.simDog.chr6 427121 5 + 593897 GGATA -s simHuman_chr6.simHuman.chr6 435402 5 + 601863 GGATG -s simRat_chr6.simRat.chr6 459789 5 + 647215 AAATA - -a -s simMouse_chr6.simMouse.chr6 447657 5 + 636262 TACAT -s Anc0.Anc0refChr3 72768 5 + 222631 TACAT -s Anc1.Anc1refChr6 104378 5 + 197743 TACAT -s Anc2.Anc2refChr13 78939 5 + 96486 TACAT -s mr.mrrefChr3 5881 5 + 181027 TACAT -s simCow_chr6.simCow.chr6 435399 5 + 602619 TACAT -s simDog_chr6.simDog.chr6 427133 5 + 593897 TACAT -s simHuman_chr6.simHuman.chr6 435414 5 + 601863 TACAT -s simRat_chr6.simRat.chr6 459794 5 + 647215 TACAG - -a -s simMouse_chr6.simMouse.chr6 447662 63 + 636262 GATTCTGATAGGGAGGGGAACGGATACCACAGAGATCTTAGACACACCTGAGTTTGGGAAGAC -s Anc0.Anc0refChr3 72774 60 + 222631 GGTGAAGCCTGAGAGGGGAACTGATAACACACAG--TTTAGACAGGCATGAGTTTGGGAAGG- -s Anc1.Anc1refChr6 104384 60 + 197743 GGTGAAGCCTGAGAGGGGAACTGATAACACACAG--TTTAGACAGGCATGAGTTTGGGAAGG- -s Anc2.Anc2refChr13 78945 60 + 96486 GGTGAAGCCTGAGAGGGGGACTGATAACACACAG--TTTAGACAGGCATGAGTTTGGGAAAG- -s mr.mrrefChr3 5886 60 + 181027 GATTCTGATAGGGAGGGGAACGGATACCACAGAG--TTTAGACACGCCTGAGTTTGGGAAGG- -s simCow_chr6.simCow.chr6 435405 60 + 602619 GGTGAAGCCTGAGAGGGGGACTCCATACGCAAAG--TTTCAATGGGCATGAGTTTGCGGAAG- -s simDog_chr6.simDog.chr6 427139 60 + 593897 AAGGAAGCTTCAGATGGCGACTGATAACACACAG--TCTAGACAGGCAGGAGTTTGGGAAAG- -s simHuman_chr6.simHuman.chr6 435420 60 + 601863 GGTCAAGCCTGAGAGGGGAACTGATAACACATAG--TTAAGACAGGGATGAGTTTGAGAAGG- -s simRat_chr6.simRat.chr6 459799 56 + 647215 GATGTTGAGAGGGA----GACAGACACCACAGAG--TTTAGACATGCTTAAGTCTGGGAAGG- - -a -s simMouse_chr6.simMouse.chr6 447725 69 + 636262 CCAACTCTATACTAAGTAATGGTACATAAGTGCTATCACCTTGCTGGCAGAACAGAATGATAAGCAGAA -s Anc0.Anc0refChr3 72836 68 + 222631 CTGACTCTATACTAAGTTATTGTATATCACTGCTGTTGCCTTGCTGGTACAATAGAATGAG-ACATGAG -s Anc1.Anc1refChr6 104446 69 + 197743 CTGACTCTATACTAAGTTATTGTATATCACTGCTGTTGCCTTGCTGGTACAATAGAATGAGAACATGAG -s Anc2.Anc2refChr13 79007 68 + 96486 CTGACACTATACTAAGTTGTTGTATATCACTGCTGGTGCCTTGTTGGTACAATAGAATGAG-ACCTGAG -s mr.mrrefChr3 5946 69 + 181027 CCAACTCTATACTAAGTAATGGTACATAAGTGCTGTCGCCTTGCTGGCACAACAGAATGATAAGCAGAA -s simCow_chr6.simCow.chr6 435467 66 + 602619 CCGGCCCTATGCTAAGTTGTCGTATATCACTCCTGGTGCCTT--TGGTACAAGAGAATAAG-AACTGAG -s simDog_chr6.simDog.chr6 427201 68 + 593897 CTAACACTACACTAAGTTGTTATATATCACTGCTAGTGCCGTGTTGGTATAATAGAATGAG-ACCTGGA -s simHuman_chr6.simHuman.chr6 435482 69 + 601863 CTGACTATATCCTAAGTGATTGTATATCACTGCTGTTGCCTTGCTGGTACAATAAAATGAGAACATGAG -s simRat_chr6.simRat.chr6 459855 69 + 647215 CCAACTCTATACTAAGTAATCGTACATTATTGCTGTCGCCACACTGGGACAGCAGAATGGTAAGGAGAA - -a -s simMouse_chr6.simMouse.chr6 447794 19 + 636262 CATGTTGTTAAGGAATAAT -s Anc0.Anc0refChr3 72905 13 + 222631 CATGTTGT------GTAAT -s Anc1.Anc1refChr6 104516 13 + 197743 CATGTTGT------GTAAT -s Anc2.Anc2refChr13 79076 13 + 96486 CATGTTGT------GTAAA -s mr.mrrefChr3 6015 13 + 181027 CATGTTGT------ATAAT -s simCow_chr6.simCow.chr6 435533 13 + 602619 AATGTTGT------GTAAG -s simDog_chr6.simDog.chr6 427270 13 + 593897 CATGCAGT------GTAGA -s simHuman_chr6.simHuman.chr6 435552 13 + 601863 CATGTTGT------GTAAT -s simRat_chr6.simRat.chr6 459924 7 + 647215 CATGTCT------------ - -a -s simMouse_chr6.simMouse.chr6 447813 5 + 636262 AAGTA -s Anc0.Anc0refChr3 72918 5 + 222631 GAGAA -s Anc1.Anc1refChr6 104529 5 + 197743 GAGAA -s Anc2.Anc2refChr13 79089 5 + 96486 GAGAA -s mr.mrrefChr3 6028 5 + 181027 AAGTA -s simCow_chr6.simCow.chr6 435546 5 + 602619 GAGAA -s simDog_chr6.simDog.chr6 427312 5 + 593897 GAGAA -s simHuman_chr6.simHuman.chr6 435565 5 + 601863 GAGAA - -a -s simMouse_chr6.simMouse.chr6 447818 27 + 636262 TCTAATCAATCTATCTGTTAAAGGCCA -s Anc0.Anc0refChr3 72927 27 + 222631 TCCAATCAACCTGTCTGCTGAAGGCCA -s Anc1.Anc1refChr6 104538 27 + 197743 TCCAATCAACCTGTCTGCTGAAGGCCA -s Anc2.Anc2refChr13 79098 27 + 96486 TCCATTCTGCCTGTCTGCTGAAGGCCA -s mr.mrrefChr3 6033 27 + 181027 TCCAATCAATCTATCTGTTAAAGGCCA -s simCow_chr6.simCow.chr6 435555 27 + 602619 TCTGTTCTGCCTGTCTACTGAAGGCCA -s simDog_chr6.simDog.chr6 427321 27 + 593897 TCCATTCTGCCTGTCTGCTCAAGGCCA -s simHuman_chr6.simHuman.chr6 435574 27 + 601863 TCCAATCAACCTGTCTGCTGGAGGCTA -s simRat_chr6.simRat.chr6 459931 27 + 647215 CCCAATCCTTTTCTTGGTTAATGTAGA - -a -s simMouse_chr6.simMouse.chr6 447845 2 + 636262 CA -s Anc0.Anc0refChr3 72987 2 + 222631 AT -s Anc1.Anc1refChr6 104598 2 + 197743 AT -s Anc2.Anc2refChr13 79158 2 + 96486 AT -s mr.mrrefChr3 6060 2 + 181027 AT -s simCow_chr6.simCow.chr6 435623 2 + 602619 GT -s simDog_chr6.simDog.chr6 427381 2 + 593897 AT -s simHuman_chr6.simHuman.chr6 435634 2 + 601863 AT -s simRat_chr6.simRat.chr6 459958 2 + 647215 AT - -a -s simMouse_chr6.simMouse.chr6 447847 34 + 636262 CCCTCATGTCAAGCTATAGCTCCCCCAGTCCTTT -s Anc0.Anc0refChr3 72989 25 + 222631 TCCTTG-GTTATTGTGCATT--------ATATTT -s Anc1.Anc1refChr6 104600 25 + 197743 TCCTTG-GTTATTGTGCATT--------ATATTT -s Anc2.Anc2refChr13 79160 25 + 96486 TCCTTG-GTTATTGTGCATT--------ATATTT -s mr.mrrefChr3 6062 25 + 181027 TCCTTA-GTTAATGTACATT--------TTCTTT -s simCow_chr6.simCow.chr6 435626 23 + 602619 TCCTTG-GTGATTATGC--T--------ATATCT -s simDog_chr6.simDog.chr6 427383 24 + 593897 TCCTTG-GTT-TTGTACATT--------ATATTT -s simHuman_chr6.simHuman.chr6 435636 25 + 601863 TCCCTG-GTTACTGTGCATT--------ATATTT -s simRat_chr6.simRat.chr6 459960 25 + 647215 TCCTTA-GTTAGTGTACATT--------GTCTTT - -a -s simMouse_chr6.simMouse.chr6 447881 57 + 636262 CAAAACCAGCAAGCCTAAAATATCACTTCAAGAAACCCTTACTAGATGACCATAAAT -s Anc0.Anc0refChr3 73014 56 + 222631 TAAAACCAGCAAGCTTGAAATATCACTTTAA-AAATCCTTAATAGACGATCATAAAC -s Anc1.Anc1refChr6 104625 56 + 197743 TAAAACCAGCAAGCTTGAAATATCACTTTAA-AAATCCTTAATAGACGATCATAAAC -s Anc2.Anc2refChr13 79192 56 + 96486 TAAAACCAGCAAGCTTGAAGTATCACTTTAA-GAATCCTTAATAAACGATCATAAAC -s mr.mrrefChr3 6087 57 + 181027 TAAAACCAGCAAGCCTAAAATATCACTTCAAGAAACCCTTACTAGATGATCATAAAT -s simCow_chr6.simCow.chr6 435656 56 + 602619 TAAAATCAGCAAGCTTAAAGTATAACTTCAA-GAGTCTTTAATAAACGCTCACAAAT -s simDog_chr6.simDog.chr6 427414 56 + 593897 TAAAACCAGCAAGCTTGAGGTATCACTCTAA-GAATCCTCAATGAATGATCATAAAC -s simHuman_chr6.simHuman.chr6 435661 56 + 601863 TTTAATCTACAAGCATGAAATATCACTTTAA-AGAGCCTTAGTAGACGATCATAAAC -s simRat_chr6.simRat.chr6 459985 57 + 647215 TAAAACCAGCAAGCCTAAAATATCACTTCAAGAAATCCTTATTAGATGATCATAAAT - -a -s simMouse_chr6.simMouse.chr6 447938 2 + 636262 CT -s Anc0.Anc0refChr3 73070 2 + 222631 AT -s Anc1.Anc1refChr6 104681 2 + 197743 AT -s Anc2.Anc2refChr13 79248 2 + 96486 AT -s mr.mrrefChr3 6144 2 + 181027 CT -s simCow_chr6.simCow.chr6 435730 2 + 602619 AT -s simDog_chr6.simDog.chr6 427470 2 + 593897 AT -s simHuman_chr6.simHuman.chr6 435717 2 + 601863 AT -s simRat_chr6.simRat.chr6 460042 2 + 647215 CT - -a -s simMouse_chr6.simMouse.chr6 447940 49 + 636262 ACGTCTTGCACCCAGGGACAGCATCATAGTATCCTTCCTGCTGTATGTT -s Anc0.Anc0refChr3 73072 45 + 222631 TG-CATTGCATACAAAGT---CAGCATAGTATCCTTGTGGTTATATTTT -s Anc1.Anc1refChr6 104683 45 + 197743 TG-CATTGCATACAAAGT---CAGCATAGTATCCTTGTGGTTATATTTT -s Anc2.Anc2refChr13 79251 45 + 96486 TG-CAATGCATACTAAGT---TAGCATAGGATCCTTGTGGTTATATTTT -s mr.mrrefChr3 6146 45 + 181027 AC-TCTTGCACCCAGAGA---CATCATAGTATCCTTCCTGCTGTATGTT -s simCow_chr6.simCow.chr6 435733 45 + 602619 TG-CAATGCATACTGAGT---TAGTACAGGATCCTTGTTGCTATATTTT -s simDog_chr6.simDog.chr6 427473 44 + 593897 TA-CAATACATACTAAGT---TAGCATTAGA-CCTTGTGGTTTCCTTTT -s simHuman_chr6.simHuman.chr6 435719 44 + 601863 TG-CATTGCATTCA-AGT---CAGCAGAGTACCCTTATAGTTATATTTT -s simRat_chr6.simRat.chr6 460044 45 + 647215 AC-TCTTGGGACCAGAGA---CACCATAGTATTCTTGCCGCTGTATGTT - -a -s simMouse_chr6.simMouse.chr6 447989 10 + 636262 TAAGATCCCA -s Anc0.Anc0refChr3 73119 10 + 222631 TTAGAACCCA -s Anc1.Anc1refChr6 104730 10 + 197743 TTAGAACCCA -s Anc2.Anc2refChr13 79298 10 + 96486 TTAAAACCCA -s mr.mrrefChr3 6191 10 + 181027 TAAGATCCCA -s simCow_chr6.simCow.chr6 435780 10 + 602619 TTAAAACCCA -s simDog_chr6.simDog.chr6 427519 10 + 593897 TTAAGACCCA -s simHuman_chr6.simHuman.chr6 435765 10 + 601863 TCAGAACCCA -s simRat_chr6.simRat.chr6 460089 10 + 647215 TAAATCCCCA - -a -s simMouse_chr6.simMouse.chr6 447999 2 + 636262 AA -s Anc0.Anc0refChr3 73134 2 + 222631 AG -s Anc1.Anc1refChr6 104745 2 + 197743 AG -s Anc2.Anc2refChr13 79313 2 + 96486 AG -s mr.mrrefChr3 6201 2 + 181027 AA -s simCow_chr6.simCow.chr6 435795 2 + 602619 AG -s simDog_chr6.simDog.chr6 427547 2 + 593897 TG -s simHuman_chr6.simHuman.chr6 435780 2 + 601863 AG -s simRat_chr6.simRat.chr6 460099 2 + 647215 AA - -a -s simMouse_chr6.simMouse.chr6 448001 15 + 636262 ATTGATATTCACTGT -s Anc0.Anc0refChr3 73136 15 + 222631 ACTGAGCTTCAAGGA -s Anc1.Anc1refChr6 104747 15 + 197743 ACTGAGCTTCAAGGA -s Anc2.Anc2refChr13 79315 15 + 96486 ACTGAGCTTCAAGGA -s mr.mrrefChr3 6203 15 + 181027 ATTGATATTCAAGGT -s simCow_chr6.simCow.chr6 435797 15 + 602619 CTTGAGCTACAAGGT -s simDog_chr6.simDog.chr6 427561 15 + 593897 ACTGAGCTTCAAGGA -s simHuman_chr6.simHuman.chr6 435782 15 + 601863 ACTGCGCTTCAAGGA -s simRat_chr6.simRat.chr6 460101 15 + 647215 ATTAATATTCGAGGT - -a -s simMouse_chr6.simMouse.chr6 448016 53 + 636262 TTTGTATCCCTTGTTGTTGGTTCGACTATTATGGGTGGCACAGCGGGGGTTCC -s Anc0.Anc0refChr3 73151 49 + 222631 TTTGTGTAATTCATTGTTGCTTTGGCTA-TACAGGTAGCACAG---TGTTTCT -s Anc1.Anc1refChr6 104762 50 + 197743 TTTGTGTAATTCATTGTTGCTTTGGCTATTACAGGTAGCACAG---TGTTTCT -s Anc2.Anc2refChr13 79331 49 + 96486 TTTATGTAATACATTGTTGCTTTGGCTA-TACAGGTAGCATAG---AGTTTCT -s mr.mrrefChr3 6218 53 + 181027 TTTGTATCCTTTGTTGTTGGTTTGACTATTATGGGTGGCACAGCAGTGTTTCC -s simCow_chr6.simCow.chr6 435813 49 + 602619 CCTCTGTAATACGTTGTCGCTTTGACTA-TACAGGTAGCATGG---CACTTCT -s simDog_chr6.simDog.chr6 427577 49 + 593897 TTCATGTAATATATTGTTGTTTTGGCTA-CACAGGTAGCATAG---AGTTTCT -s simHuman_chr6.simHuman.chr6 435797 50 + 601863 TTTGTGTAATTCATTGTTGCTTTGGCTATTACAGGTAGGACAG---TGTTTCT -s simRat_chr6.simRat.chr6 460116 53 + 647215 TTTGTATTCTTTGTCATTCGTTTGACTATTATGGGTGTTACAGCAGTGTTTCC - -a -s simMouse_chr6.simMouse.chr6 448069 35 + 636262 TCATCACACGATATTTCGGAGGGTCAACCATGGAG -s Anc0.Anc0refChr3 73201 35 + 222631 TGATCACACCAAATTTTGGATGGCCAATCATGGAG -s Anc1.Anc1refChr6 104813 35 + 197743 TGATCACACCAAATTTTGGATGGCCAATCATGGAG -s Anc2.Anc2refChr13 79381 35 + 96486 GGATCATACCAAATTTTGGATGGCCAATCATGGAG -s mr.mrrefChr3 6272 35 + 181027 TCATCACACGATATTTTGGAGGGCCAACCATGGAG -s simCow_chr6.simCow.chr6 435863 35 + 602619 GGATTATACCTGATTTTCAATGGCCCATCATGGGG -s simDog_chr6.simDog.chr6 427627 35 + 593897 GGATCATACCAAATTTTGGAGAGCCAATCATGGAG -s simHuman_chr6.simHuman.chr6 435848 34 + 601863 TGATCACACAA-ATTCTGGATGGCGAATCATGGAG -s simRat_chr6.simRat.chr6 460170 35 + 647215 GCATCACATGAGATTTTGGAGTGCCAAACATGGAG - -a -s simMouse_chr6.simMouse.chr6 448104 7 + 636262 GTTTGCA -s Anc0.Anc0refChr3 73236 7 + 222631 GTTTGCA -s Anc1.Anc1refChr6 104848 7 + 197743 GTTTGCA -s Anc2.Anc2refChr13 79418 7 + 96486 GTTTGCA -s mr.mrrefChr3 6307 7 + 181027 GTTTGCA -s simCow_chr6.simCow.chr6 435900 7 + 602619 GTTTGCA -s simDog_chr6.simDog.chr6 427664 7 + 593897 GTTTGCA -s simHuman_chr6.simHuman.chr6 435882 7 + 601863 GTTTGCa -s simRat_chr6.simRat.chr6 460205 6 + 647215 GTTT-CA - -a -s simMouse_chr6.simMouse.chr6 448111 81 + 636262 ACTTTGCATCGCACGACAATTATCTAGTATCCAACAATTCTCTAGTATCAGGGTGTATGCATTCCAATAAGATCCTTAGTT -s Anc0.Anc0refChr3 73243 63 + 222631 ATTTTGCACTGCA-----------------C-AACAGTTATTCCATGTCAGTGAGTATACATTCCGCTTCAATACTCAACA -s Anc1.Anc1refChr6 104855 63 + 197743 ATTTTGCACTGCA-----------------C-AACAGTTATTCCATGTCAGTGAGTATACATTCCGCTTCAATACTCAACA -s Anc2.Anc2refChr13 79425 63 + 96486 ATTTTGCACTACA-----------------C-AACAGTTATTCCATGTCAGTCAGTATCTATTATGCTTCAACACTTAACA -s mr.mrrefChr3 6314 64 + 181027 ACTTTGCATCGCA-----------------CCAACAATTATCTAGTATCAGGGTGTATACATTCCAATAAGATACTCAATT -s simCow_chr6.simCow.chr6 435907 33 + 602619 ATTTTGCTCCACA-----------------C-AACAGTGATTCCGTGTCAT------------------------------ -s simDog_chr6.simDog.chr6 427671 63 + 593897 ATTTTGCACTATA-----------------C-AACACTTATTTGATGTCAGTCAGTATCTATTATGCTTCAACACTTAACA -s simHuman_chr6.simHuman.chr6 435929 63 + 601863 gTTTTGCACTGCA-----------------C-AACAGTTATTCCATGTCAGAGATTGCACATTCCGCTCCAATACTCAACA -s simRat_chr6.simRat.chr6 460211 64 + 647215 ACTTTGCATCACA-----------------CCAACAATTAGCTAGTATCAGGGTGAATATATTCCAATAAGATACTCAATT - -a -s simMouse_chr6.simMouse.chr6 448192 17 + 636262 GGAATAGGGGACTAAGA -s Anc0.Anc0refChr3 73306 17 + 222631 GGAATAGGAGACGAATA -s Anc1.Anc1refChr6 104918 17 + 197743 GGAATAGGAGACGAATA -s Anc2.Anc2refChr13 79488 17 + 96486 GGAGTGTGAGATGAATA -s mr.mrrefChr3 6378 17 + 181027 GGAATAGGGGACTAATA -s simCow_chr6.simCow.chr6 435940 3 + 602619 --------------AGA -s simDog_chr6.simDog.chr6 427734 17 + 593897 GGAGTGTGAGATGAATA -s simHuman_chr6.simHuman.chr6 435993 17 + 601863 GGAATAGGAGACAAATA -s simRat_chr6.simRat.chr6 460275 17 + 647215 GGAATAGGGGACTAGTA - -a -s simMouse_chr6.simMouse.chr6 448209 5 + 636262 ACACA -s Anc0.Anc0refChr3 73325 5 + 222631 ACACA -s Anc1.Anc1refChr6 104937 5 + 197743 ACACA -s Anc2.Anc2refChr13 79507 5 + 96486 ACACA -s mr.mrrefChr3 6395 5 + 181027 ACACA -s simCow_chr6.simCow.chr6 435945 5 + 602619 TCATA -s simDog_chr6.simDog.chr6 427753 5 + 593897 ACACA -s simHuman_chr6.simHuman.chr6 436012 5 + 601863 ACACA -s simRat_chr6.simRat.chr6 460292 5 + 647215 ACACA - -a -s simMouse_chr6.simMouse.chr6 448214 150 + 636262 TGAGCTACATGAAAGACCTGAGCTAGGCCCCATGAGAAAGAAGCAAACAAGGTACGTTCTTTACTGGAAGGAAATAGAAGATGAAATATCTTTCATGGCTGATAGTGAAAGATCACCTGAATAACATCAATAACAGCATTCATTGTCTTA -s Anc0.Anc0refChr3 73330 139 + 222631 TGGGTT-GATAAAATACCTGGGCTTGGCCCTGGAAGAAAGAAGGGAGCAAGGCA-TTCCTTC---------AAATGGAAGTTGAAGTCTTCTTTATGGTTTATAATGAAAGATCAATGGTTTGAAAACAAGAACAACATTTATTGTCTTA -s Anc1.Anc1refChr6 104942 150 + 197743 TGGGTTAGATAAAATACCTGGGCTTGGCCCTGGAAGAAAGAAGGGAGCAAGGCACTTCCTTCTCTTGAAGGAAATGGAAGTTGAAGTCTTCTTTATGGTTTATAATGAAAGATCAATGGTTTGAAAACAAGAACAACATTTATTGTCTTA -s Anc2.Anc2refChr13 79512 139 + 96486 TGGTTT-GATAGAATACCTGGGCTTGGCCTTGGAAGAAAGAAGAGAGCAAGACA-TTCCTTC---------ATATGGAAGTTGAAGTCTTCTTTACGGTTTATAATGAAAGATCAATAGTTTGAAAACAAGAGTAACATTTATTGTCTTA -s mr.mrrefChr3 6400 150 + 181027 TGAGTTACATGAAAGACCTGAGCTAGGCCCCATGAGAAAGAAGGAAACAAGGTACGTTCTTTACTGGAAGGAAATAGAAGATGAAATCTCTTTTATGGCTGATAGTGAAAGATCACCGGAATAACAACAAGAACAGCATTTATTGTCTTA -s simCow_chr6.simCow.chr6 435952 112 + 602619 TGCTTT-CATAGGATAT---------GCCTTGGAAAAAAGAGGAGAGCAAGACG-TTCCTTC---------ATATGCAAGTTGAAGTCTT--------TTTACAACGAAAG----------TGAAAACGAGAGTAACATTTACTGTCTTA -s simDog_chr6.simDog.chr6 427758 135 + 593897 TGGTCT-GATAGAATACCTGGGCTTGGCCTTGGGAGAAATAAGAAAACAAGACA-TTCCTTC---------ATATTGAAGTGGAAGTCTCCTTTACGGTTCTTAATGGAAGATCAATAGTTTGAAAACAAG----ACATGTTTTGTCTTA -s simHuman_chr6.simHuman.chr6 436017 148 + 601863 TAGGTTATGTAAAACACCTGGGCTGGGCCCTGGAAGAAAGAAGGGGGCA--GATCTTCCTTCTCTTGAAGGAAATGGAAGTTGAAGTCTTCTTTTTGGTTTATAATGAATGATCAATGATCTTAAGACAAGAACAACATTTATTGTCATA -s simRat_chr6.simRat.chr6 460297 127 + 647215 TGAGTTACATGAAAGAC--------------------AAGACGGAAACAACGTACGTTCTTTA---TAAGGAAATAGAAGATGAAATCTCTTTTGTGGCTGATAGTTAAAGATTACCGTAATAACAACAAGAACAGCATTTGTTGTCTTA - -a -s simMouse_chr6.simMouse.chr6 448364 7 + 636262 CTTCTAT -s Anc0.Anc0refChr3 73469 3 + 222631 CTG---- -s Anc1.Anc1refChr6 105092 3 + 197743 CTG---- -s Anc2.Anc2refChr13 79651 3 + 96486 CTG---- -s mr.mrrefChr3 6550 7 + 181027 CTTCTAT -s simCow_chr6.simCow.chr6 436064 3 + 602619 CTG---- -s simDog_chr6.simDog.chr6 427902 3 + 593897 CTA---- -s simHuman_chr6.simHuman.chr6 436165 3 + 601863 CTG---- -s simRat_chr6.simRat.chr6 460424 7 + 647215 CTTGTAT - -a -s simMouse_chr6.simMouse.chr6 448371 18 + 636262 TCTTGTACCAATCTGACT -s Anc0.Anc0refChr3 73472 15 + 222631 TCTTGGATCA---TAACT -s Anc1.Anc1refChr6 105095 15 + 197743 TCTTGGATCA---TAACT -s Anc2.Anc2refChr13 79654 15 + 96486 TCTTGGATCA---TAGCT -s mr.mrrefChr3 6557 18 + 181027 TCTTGTACCAATCTGACT -s simCow_chr6.simCow.chr6 436071 15 + 602619 TCCTGCATCA---CAGTT -s simDog_chr6.simDog.chr6 427905 15 + 593897 GATTGGACCC---TAGCT -s simHuman_chr6.simHuman.chr6 436168 15 + 601863 TCTTGAATCA---TCACT -s simRat_chr6.simRat.chr6 460431 18 + 647215 TCTTGTACTAAACTGAAT - -a -s simMouse_chr6.simMouse.chr6 448389 16 + 636262 GAATCTCACATAGATA -s Anc0.Anc0refChr3 73487 16 + 222631 GAATCTCACACAGGAC -s Anc1.Anc1refChr6 105110 16 + 197743 GAATCTCACACAGGAC -s Anc2.Anc2refChr13 79669 16 + 96486 GAATCTGACACAGGAC -s mr.mrrefChr3 6575 16 + 181027 GAATCTCACATAGATA -s simCow_chr6.simCow.chr6 436086 16 + 602619 CAATCTGACACAGGAC -s simDog_chr6.simDog.chr6 427921 16 + 593897 GTACCTGAGACAGGAT -s simHuman_chr6.simHuman.chr6 436183 16 + 601863 GAGTCTCACACAGGCC -s simRat_chr6.simRat.chr6 460449 16 + 647215 GAATCTCACATAGATA - -a -s simMouse_chr6.simMouse.chr6 448405 49 + 636262 ATTATCAATACCCTGACAAATGTATGTGGAACAATGTCAAAAAAGGGAG -s Anc0.Anc0refChr3 73503 34 + 222631 ATTGCCAGC---CTTGCT--------AGGAAC----CCCAAAAAGGGAG -s Anc1.Anc1refChr6 105126 34 + 197743 ATTGCCAGC---CTTGCT--------AGGAAC----CCCAAAAAGGGAG -s Anc2.Anc2refChr13 79685 34 + 96486 ATTGCCAGT---TTTGCC--------AGGAAC----CCCAGAAAGGGAG -s mr.mrrefChr3 6591 49 + 181027 ATTATCAACACCCTGACTAATGTATGTGGAACAATGTCCAAAAAGGGAG -s simCow_chr6.simCow.chr6 436105 33 + 602619 ATTGTCA-T---TCTGCC--------AGGAAC----CCCAGGGATGGCT -s simDog_chr6.simDog.chr6 427937 34 + 593897 ATTGCCAGT---TTTGTC--------AGCAAC----CCCAGAAAGGAAG -s simHuman_chr6.simHuman.chr6 436199 34 + 601863 ATTGCCAGC---CTTGCT--------AGGAAC----CCCAATAAGGGAG -s simRat_chr6.simRat.chr6 460465 49 + 647215 ATTATGAACACCCTGACTAATGTATGTGGAACGAGGTCCAAAGAGAGAG - -a -s simMouse_chr6.simMouse.chr6 448454 4 + 636262 ACCT -s Anc0.Anc0refChr3 73665 4 + 222631 ACCT -s Anc1.Anc1refChr6 105288 4 + 197743 ACCT -s Anc2.Anc2refChr13 79847 4 + 96486 AACT -s mr.mrrefChr3 6640 4 + 181027 ACCT -s simCow_chr6.simCow.chr6 436437 3 + 602619 A-TT -s simDog_chr6.simDog.chr6 428078 4 + 593897 AACT -s simHuman_chr6.simHuman.chr6 436372 4 + 601863 ACCT -s simRat_chr6.simRat.chr6 460514 4 + 647215 ACCT - -a -s simMouse_chr6.simMouse.chr6 448458 13 + 636262 TGGGGGTTTGAAA -s Anc0.Anc0refChr3 73669 13 + 222631 TGGGAGTACCAAT -s Anc1.Anc1refChr6 105292 13 + 197743 TGGGAGTACCAAT -s Anc2.Anc2refChr13 79852 13 + 96486 TGGGAGTACCAAT -s mr.mrrefChr3 6644 13 + 181027 TGGGGGTTTGAAA -s simCow_chr6.simCow.chr6 436441 13 + 602619 TGGGAGTACCATT -s simDog_chr6.simDog.chr6 428083 13 + 593897 TGGGAGTATAAAT -s simHuman_chr6.simHuman.chr6 436376 13 + 601863 ATGGAGTACCAAT -s simRat_chr6.simRat.chr6 460518 13 + 647215 TGGGGGTTTGAAA - -a -s simMouse_chr6.simMouse.chr6 448471 12 + 636262 CAGAATAATGGA -s Anc0.Anc0refChr3 73682 12 + 222631 CAGAACAATGGA -s Anc1.Anc1refChr6 105305 12 + 197743 CAGAACAATGGA -s Anc2.Anc2refChr13 79865 12 + 96486 CAGAACAATGGA -s mr.mrrefChr3 6657 12 + 181027 CAGAATAATGGA -s simCow_chr6.simCow.chr6 436454 12 + 602619 TAGAGTGATAGG -s simDog_chr6.simDog.chr6 428096 12 + 593897 CAGAACAATGGA -s simHuman_chr6.simHuman.chr6 436389 12 + 601863 CAGAACAATGAA -s simRat_chr6.simRat.chr6 460545 12 + 647215 CAGAATAATGGA - -a -s simMouse_chr6.simMouse.chr6 448483 130 + 636262 ATGTCAGTTTAGTATTGATATAGGGAACTTTGCTCTTGGAGGCAAAGTCTCTACAATCTGACCAATCAGATAACTGTGGTGGAAACTCAGCCCTCTGCCACGTCCACAATGTGGATGTATAGATATTAAG -s Anc0.Anc0refChr3 73697 28 + 222631 ATTGCATTTTAT----------------------------------------------------------------------------------------------CAATGTA--------GAGATCATG -s Anc1.Anc1refChr6 105320 28 + 197743 ATTGCATTTTAT----------------------------------------------------------------------------------------------CAATGTA--------GAGATCATG -s Anc2.Anc2refChr13 79880 28 + 96486 TTTGCATTGTAT----------------------------------------------------------------------------------------------CAATGTA--------GAGAACATG -s mr.mrrefChr3 6669 122 + 181027 ATGTCAGTTTAGTATTGATATAGCGAACTTTGCTCTTGAAGGCAAAGTCTCTACAATCTGACCAATCAGATAACTGTGGTGGAAACTCAGCCCTCTGCCACGTCCACAATGTG--------GATATCAAG -s simCow_chr6.simCow.chr6 436469 28 + 602619 TTTGTATTGTAT----------------------------------------------------------------------------------------------CAATGAA--------AAGAACATG -s simDog_chr6.simDog.chr6 428110 27 + 593897 TCTTCATTGTGT-----------------------------------------------------------------------------------------------ACTGTA--------GCAAACATG -s simHuman_chr6.simHuman.chr6 436404 28 + 601863 ATTGCATTTTAT----------------------------------------------------------------------------------------------CAATGTA--------GAGATCATG -s simRat_chr6.simRat.chr6 460557 122 + 647215 ATTTCAGTTTAGTATTGATGTAGCGAACTTTGCTCGTGAAGGCAAAGTCTCAACAATTCTACCAATCAGATAACAGTTGTGGAAACTCAGCCCTCCGCCACATCCACAATGTG--------GATATCAAT - -a -s simMouse_chr6.simMouse.chr6 448613 6 + 636262 TGAAGA -s Anc0.Anc0refChr3 73725 6 + 222631 TGAAGA -s Anc1.Anc1refChr6 105348 6 + 197743 TGAAGA -s Anc2.Anc2refChr13 79968 6 + 96486 TGAAGA -s mr.mrrefChr3 6791 6 + 181027 TGAAGA -s simCow_chr6.simCow.chr6 436559 6 + 602619 TAAAGG -s simDog_chr6.simDog.chr6 428259 6 + 593897 TGAAGA -s simHuman_chr6.simHuman.chr6 436432 6 + 601863 TGTAAA -s simRat_chr6.simRat.chr6 460679 6 + 647215 TGAAGA - -a -s simMouse_chr6.simMouse.chr6 448619 7 + 636262 AAAAGCC -s Anc0.Anc0refChr3 73731 7 + 222631 AAAATCC -s Anc1.Anc1refChr6 105354 7 + 197743 AAAATCC -s Anc2.Anc2refChr13 79974 7 + 96486 ATAATTC -s mr.mrrefChr3 6797 7 + 181027 AAAAGCC -s simCow_chr6.simCow.chr6 436565 7 + 602619 ACAAATC -s simDog_chr6.simDog.chr6 428266 7 + 593897 ATAATTC -s simHuman_chr6.simHuman.chr6 436438 7 + 601863 AATATCC -s simRat_chr6.simRat.chr6 460685 7 + 647215 AAAAGCC - -a -s simMouse_chr6.simMouse.chr6 448626 41 + 636262 ACAGCCACTCCCTTAAGCTGGGATGGTATGGAACTTTGCCA -s Anc0.Anc0refChr3 73755 39 + 222631 ACAGACATTTGGTTACGCTGGTGTGGTGTGT--CTTTGCCA -s Anc1.Anc1refChr6 105378 39 + 197743 ACAGACATTTGGTTACGCTGGTGTGGTGTGT--CTTTGCCA -s Anc2.Anc2refChr13 80006 39 + 96486 ACAGACATTTGGCTACGCCAGTGTTGTGTGT--ACTTGCCA -s mr.mrrefChr3 6804 41 + 181027 ACAGCCATTCCCTTAAGCTGGGATGGTATGGAACTTTGCCA -s simCow_chr6.simCow.chr6 436597 27 + 602619 ACAGACATTTGGCTACGCCAGTGTTGT-------------- -s simDog_chr6.simDog.chr6 428298 16 + 593897 ACA-----------------------TGTGT--ACTTGCCA -s simHuman_chr6.simHuman.chr6 436462 39 + 601863 AGAGACATTTGGTTCGGCTGGTGTGGTGTGT--CTTTGTCA -s simRat_chr6.simRat.chr6 460692 41 + 647215 ACAGCCATTCCCTTAAGCTGGGATGGCATGGACGTATGCCA - -a -s simMouse_chr6.simMouse.chr6 448667 30 + 636262 TAAACATAACAACATGTGTTGTTACTGATC -s Anc0.Anc0refChr3 73796 30 + 222631 TAAACACAACAAAATTTGCTGTTATCTATA -s Anc1.Anc1refChr6 105419 30 + 197743 TAAACACAACAAAATTTGCTGTTATCTATA -s Anc2.Anc2refChr13 80047 30 + 96486 TAAGCACAACAAAACATACTGTTATCTATA -s mr.mrrefChr3 6845 30 + 181027 TAAACATAACAACATTTGTTGTTACTGATC -s simDog_chr6.simDog.chr6 428316 30 + 593897 TAAGCACAACAAAACATACTGTTATCTATA -s simHuman_chr6.simHuman.chr6 436503 30 + 601863 TATACACAACAAAATTTGCTGTTATATATA -s simRat_chr6.simRat.chr6 460733 30 + 647215 TAAACATAACAACATTTGTTGTTACTGATC - -a -s simMouse_chr6.simMouse.chr6 448697 44 + 636262 TTATATTCTGAAGTGGGACCGTATTAATTTCTAAAATGTACTCT -s Anc0.Anc0refChr3 73826 30 + 222631 C-ATATTCTGTAGCCAGAG------------TAACATGTGTTC- -s Anc1.Anc1refChr6 105449 42 + 197743 C-ATATTCTGTAGCCAGAGTGTGAAACTTTCTAACATGTGTTC- -s Anc2.Anc2refChr13 80077 30 + 96486 C-TTATTGTGTAGCCAGAG------------TAACATGTGTTC- -s mr.mrrefChr3 6875 44 + 181027 TTATATTCTGAAGTGGGACTGTATAAATTTCTAAAATGTACTCT -s simDog_chr6.simDog.chr6 428347 30 + 593897 C-TTATTGTGTAGCCAGAG------------TAACATGTGTTC- -s simHuman_chr6.simHuman.chr6 436533 42 + 601863 C-ATATTCCATAGCCAGAGTGTGAAACTTTCTAAGATGTGTTC- -s simRat_chr6.simRat.chr6 460763 44 + 647215 TTATATTCTGGAGTGGGACTGTATAAATTTCTAAAATGTACTCT - -a -s simMouse_chr6.simMouse.chr6 448741 43 + 636262 AAAATGTACTCAATTGAAGGATCTAGTAGTTGTTGAGCCTAAT -s Anc0.Anc0refChr3 73856 30 + 222631 -----------AATCAATGAATTTAATAGTTGTGGAACCTA-- -s Anc1.Anc1refChr6 105491 30 + 197743 -----------AATCAATGAATTTAATAGTTGTGGAACCTA-- -s Anc2.Anc2refChr13 80107 30 + 96486 -----------AATCAATAAACTTAATAGTTGTGGAACCTA-- -s mr.mrrefChr3 6920 41 + 181027 AAAATGTACTCAATTGAAGGATCTAGTAGTTGTTGAGCCTA-- -s simDog_chr6.simDog.chr6 428377 30 + 593897 -----------AATCAATAAACTTAATAGTTGTGGAACCTA-- -s simHuman_chr6.simHuman.chr6 436575 30 + 601863 -----------AACCAATGAATTTAACAGTTATGGAATCCA-- -s simRat_chr6.simRat.chr6 460808 41 + 647215 AAAGTGTATTCAATTGAAGAATCTAGGAGTTTATAAGCCTA-- - -a -s simMouse_chr6.simMouse.chr6 448784 7 + 636262 TAGAGCT -s Anc0.Anc0refChr3 73886 7 + 222631 CACAGCT -s Anc1.Anc1refChr6 105521 7 + 197743 CACAGCT -s Anc2.Anc2refChr13 80139 7 + 96486 TACAGCT -s mr.mrrefChr3 6961 7 + 181027 CAGAGCT -s simDog_chr6.simDog.chr6 428409 7 + 593897 TACAGCT -s simHuman_chr6.simHuman.chr6 436605 7 + 601863 CCAAACT -s simRat_chr6.simRat.chr6 460849 7 + 647215 CGGAACT - -a -s simMouse_chr6.simMouse.chr6 448791 34 + 636262 TCATAATGGTTAGGAAAGGTAGTTTCCCCCATGA -s Anc0.Anc0refChr3 73893 22 + 222631 TTATAATGATTAGG-TAG-----------TGTGG -s Anc1.Anc1refChr6 105528 33 + 197743 TTATAATGATTAGG-TAGGTAGTTTCTCCTGTGG -s Anc2.Anc2refChr13 80146 22 + 96486 CTATAATGATTAAG-TAG-----------TGCGG -s mr.mrrefChr3 6968 33 + 181027 TCATAATGGTTAGG-AAGGTAGTTTCTCCCATGG -s simCow_chr6.simCow.chr6 436624 16 + 602619 ------TGGATAAG-TGA-----------TACAG -s simDog_chr6.simDog.chr6 428416 22 + 593897 CTATAATGATTAAA-TAG-----------TGCGG -s simHuman_chr6.simHuman.chr6 436692 33 + 601863 TTATAATGATTAGG-TAGGTAGTTTCTCCTGTGG -s simRat_chr6.simRat.chr6 460856 33 + 647215 TCATAGTGGTTAGG-CAGGTAGTTCCTCCCATGG - -a -s simMouse_chr6.simMouse.chr6 448825 19 + 636262 CTTATTGATAATCTAGGCC -s Anc0.Anc0refChr3 73915 19 + 222631 CTTGTTGATACTGCAGACC -s Anc1.Anc1refChr6 105561 19 + 197743 CTTGTTGATACTGCAGACC -s Anc2.Anc2refChr13 80168 19 + 96486 CTTGTTAACACTGCAGACC -s mr.mrrefChr3 7001 19 + 181027 CTTATTGATAATCTAGGCC -s simCow_chr6.simCow.chr6 436641 15 + 602619 CTTGTT----CTGCACACT -s simDog_chr6.simDog.chr6 428438 19 + 593897 CTTATTAACACTGCAGCCC -s simHuman_chr6.simHuman.chr6 436725 19 + 601863 CTTGTTGATACTGCAGACC -s simRat_chr6.simRat.chr6 460889 19 + 647215 CTTATTGATAATATAGGCC - -a -s simMouse_chr6.simMouse.chr6 448844 9 + 636262 TAAAGCTAG -s Anc0.Anc0refChr3 73938 9 + 222631 TGAAGCTTG -s Anc1.Anc1refChr6 105584 9 + 197743 TGAAGCTTG -s Anc2.Anc2refChr13 80191 9 + 96486 TGAAGCTTG -s mr.mrrefChr3 7024 9 + 181027 TAAAGCTAG -s simCow_chr6.simCow.chr6 436660 8 + 602619 T-AAGTTTT -s simDog_chr6.simDog.chr6 428461 9 + 593897 TGAAGCATG -s simHuman_chr6.simHuman.chr6 436748 9 + 601863 TGAAGCTTG -s simRat_chr6.simRat.chr6 460912 9 + 647215 TAATGCTAG - -a -s simMouse_chr6.simMouse.chr6 448853 7 + 636262 ACCATAC -s Anc0.Anc0refChr3 73947 7 + 222631 CTCATAC -s Anc1.Anc1refChr6 105593 7 + 197743 CTCATAC -s Anc2.Anc2refChr13 80200 7 + 96486 CTCATAC -s mr.mrrefChr3 7033 7 + 181027 ACCATAC -s simCow_chr6.simCow.chr6 436668 7 + 602619 CTCATAA -s simDog_chr6.simDog.chr6 428472 7 + 593897 CACATAC -s simHuman_chr6.simHuman.chr6 436757 7 + 601863 CTGATAC -s simRat_chr6.simRat.chr6 460921 5 + 647215 ACCAT-- - -a -s simMouse_chr6.simMouse.chr6 448860 136 + 636262 ACCATACTGATGAATCTGTGTAAAGGACTAATGCAGTTATCGCTCTTAGCTGTCCCACTTCCATATGTTCTAGTCTTCTATCCCGCAGTCAGTCTGACGTTCCATGGTAGTTCTCCCATGCAATCTGCCATGGTCC -s Anc0.Anc0refChr3 73954 87 + 222631 TCCATGCTGATAAATTTGTGAAAAAAATCAATGCAGCTATCACTTTTAGCTATTCCACATCCATGTGATCTAGTTTTCTATCCCCTA------------------------------------------------- -s Anc1.Anc1refChr6 105600 119 + 197743 TCCATGCTGATAAATTTGTGAAAAAAATCAATGCAGCTATCACTTTTAGCTATTCCACATCCATGTGATCTAGTTTTCTATCCCCTAATTGG----GCACTCCATG-------------ACAGGCTGCCAACAGCC -s Anc2.Anc2refChr13 80207 87 + 96486 TCCGTGCTGATAAATTTGCAAAAAAAATCCATGCAGCTATCACTTTTAGCTATTCCACAACCATGTGATCTAGTTTTCTAACCCCTA------------------------------------------------- -s mr.mrrefChr3 7040 136 + 181027 ACCATACTGATGAATTTGTGTAAAGGACTAATGCAGCTATCACTCTTAGCTGTCCCACTTCCATGTGTTCTAGTCTTCTATCCCCCAGTCAGTCTGACGTTCCATGGTAGTTCTCCCACACAATCTGCCATGGTCC -s simCow_chr6.simCow.chr6 436675 83 + 602619 TCCGTGCTGACGAACTTGCAATCAAAATC--TGCAGCTATCACTATGATCTATTCCACAG--ATGTGACCTAGTTGTCTATGCATTG------------------------------------------------- -s simDog_chr6.simDog.chr6 428509 86 + 593897 TCCGTGCTGATAAATATGCAAAAAGAATCCATGCGGCTATCACCT-TAGCTATTTCACAACCAAGTGATCTAGTTTTCTAACCCCTA------------------------------------------------- -s simHuman_chr6.simHuman.chr6 436764 118 + 601863 TCCATGCTGATAA-TTTGTGAAAAAAATCAATGCAGCTTTCACTTATAGCTATTCCATATACATGTGGTCTAGTTTACTATCCCCTAATTGG----GCACTCCATG-------------ACAGGCTGCCAACAGCC -s simRat_chr6.simRat.chr6 460926 126 + 647215 ---GTACTTATGAATTCGTGTAAAGGACTTATGCTGCTATCACTCTTAGCCG-------TCAATGTGCTCTAGTCTTCTATCCCCCAGTTGTGCTGAAGTTCGATGGTAGTTCTCCCACACAATCTGCCATGGCCG - -a -s simMouse_chr6.simMouse.chr6 448996 31 + 636262 AAGCATGCTGGCTGATAAACCCTGACAAAGA -s Anc1.Anc1refChr6 105719 28 + 197743 AAGCAAGCTTACTGATAAGTC---ACAAAGA -s mr.mrrefChr3 7176 31 + 181027 AAGCATGCTGGCTGATAAACCCTGACAAAGA -s simHuman_chr6.simHuman.chr6 436887 28 + 601863 AAGCAAGCTTACTGATAAGTC---ACAAAGA -s simRat_chr6.simRat.chr6 461052 31 + 647215 AAGCATGCTGGCTGATTAACCTTGACAAAGA - -a -s simMouse_chr6.simMouse.chr6 449027 61 + 636262 ATCCACTATCATTCTTAGCTATTAGTTTTAATCATGAGATTTAGTTTTTCATTTCCACATT -s Anc0.Anc0refChr3 74041 3 + 222631 ----------------------------------------------------------ATT -s Anc1.Anc1refChr6 105747 57 + 197743 ACTCCCTATCACTCTTAGCTACTATTCTACATCC----ATTTGATCTATCTACTCCCTATT -s Anc2.Anc2refChr13 80294 3 + 96486 ----------------------------------------------------------ATT -s mr.mrrefChr3 7207 61 + 181027 ATCCACTATCACTCTTAGCTATTAGTTTTAATCATGAGATTTAGTTTTTCATTTCCACATT -s simCow_chr6.simCow.chr6 436758 3 + 602619 ----------------------------------------------------------ATT -s simDog_chr6.simDog.chr6 428595 3 + 593897 ----------------------------------------------------------ATT -s simHuman_chr6.simHuman.chr6 436965 57 + 601863 ACTCCCTATCACTCTTAGCTACTATTCTACATCC----ATTTGATCTATCTACTCCCTATT -s simRat_chr6.simRat.chr6 461083 59 + 647215 ATCCACTAT-GCTCTTAG-TATTAATTTTAGTCATGTGAATTAGTTTTTTATTTCCACATT - -a -s simMouse_chr6.simMouse.chr6 449088 35 + 636262 GGGCTTGCAATCCATCACAGTTCTCTCATACAGGT -s Anc0.Anc0refChr3 74044 35 + 222631 GGGCTCAAGATCCTTAACAGGTCTTTCACACAAGC -s Anc1.Anc1refChr6 105804 35 + 197743 GGGCTCAAGATCCTTAACAGGTCTTTCACACAAGC -s Anc2.Anc2refChr13 80297 35 + 96486 GGGCTCAAGATCCTCAACAGGTCTTTCACACAAGC -s mr.mrrefChr3 7268 35 + 181027 GGGCTTGCAATCCATCACAGTTCTTTCACACAAGC -s simCow_chr6.simCow.chr6 436761 35 + 602619 GGGGTTAAGACCCTCCACAGGTCTTTTGGAGGAGC -s simDog_chr6.simDog.chr6 428598 35 + 593897 GGGCTCAAGATCCACAACAGGTCTTTCACACAAGC -s simHuman_chr6.simHuman.chr6 437023 35 + 601863 GGGTGCAACATCCTTGACAGGTCTTTCACACAAGC -s simRat_chr6.simRat.chr6 461142 35 + 647215 GGCCCTGCAATCCGTCACAGTTCTTTCACACAAGC - -a -s simMouse_chr6.simMouse.chr6 449123 18 + 636262 TACCAACTTCATGAACTG -s Anc0.Anc0refChr3 74100 18 + 222631 CACTCACTGAATGAAATG -s Anc1.Anc1refChr6 105860 18 + 197743 CACTCACTGAATGAAATG -s Anc2.Anc2refChr13 80353 18 + 96486 CACTCACTGAATGAAATG -s mr.mrrefChr3 7303 18 + 181027 CACCAACTTCATGAACTG -s simDog_chr6.simDog.chr6 428654 18 + 593897 CACTCACTGAATGAAATG -s simHuman_chr6.simHuman.chr6 437079 18 + 601863 AGCATACAAAATGGGATT -s simRat_chr6.simRat.chr6 461177 18 + 647215 CACCAACTTCATGAACTG - -a -s simMouse_chr6.simMouse.chr6 449141 6 + 636262 TCAAAT -s Anc0.Anc0refChr3 74125 6 + 222631 TCAAAC -s Anc1.Anc1refChr6 105885 6 + 197743 TCAAAC -s Anc2.Anc2refChr13 80378 6 + 96486 TCAAAC -s mr.mrrefChr3 7321 6 + 181027 TCAAAT -s simDog_chr6.simDog.chr6 428679 6 + 593897 TCAAAC -s simHuman_chr6.simHuman.chr6 437104 6 + 601863 TTGAAA -s simRat_chr6.simRat.chr6 461195 6 + 647215 TCAAAC - -a -s simMouse_chr6.simMouse.chr6 449147 9 + 636262 TTGAACTTG -s Anc0.Anc0refChr3 74133 9 + 222631 TTGAACATG -s Anc1.Anc1refChr6 105893 9 + 197743 TTGAACATG -s Anc2.Anc2refChr13 80386 9 + 96486 CTGGACATG -s mr.mrrefChr3 7327 9 + 181027 TTGAACTTG -s simCow_chr6.simCow.chr6 436796 8 + 602619 -TGTACATG -s simDog_chr6.simDog.chr6 428687 9 + 593897 CTGGACATG -s simHuman_chr6.simHuman.chr6 437112 9 + 601863 TTGAACATG -s simRat_chr6.simRat.chr6 461201 9 + 647215 TTGAAGTTG - -a -s simMouse_chr6.simMouse.chr6 449156 35 + 636262 GACCTGAATGGTTAACCCCAAGTACTACCTGTGGT -s Anc0.Anc0refChr3 74148 33 + 222631 GACTAGAATGCCTAAACTCAT--ATTTCATGGGGG -s Anc1.Anc1refChr6 105908 35 + 197743 GACTAGAATGCCTAAACTCATTGATTTCATGGGGG -s Anc2.Anc2refChr13 80401 33 + 96486 GACTAGAATGCCTAAATTCAT--GTTTCATGGAGG -s mr.mrrefChr3 7336 35 + 181027 GACCTGAATGGTTAACCCCAAGTACTACCTGTGGT -s simCow_chr6.simCow.chr6 436810 33 + 602619 ACCTAGAATGCCCAAGTTCAT--GTTTCATGGAGG -s simDog_chr6.simDog.chr6 428703 21 + 593897 GATAAGAA---CTAAA-----------CATTGAGG -s simHuman_chr6.simHuman.chr6 437127 35 + 601863 GACTAGAAGGCCTAAACTCATTGATTTCATGGGGG -s simRat_chr6.simRat.chr6 461210 35 + 647215 ACCTTGAATGGTTATTGCCAAGTACTACCTGTACT - -a -s simMouse_chr6.simMouse.chr6 449191 31 + 636262 CCTCATTCGGAACTTAGAAAATGTGCTGCAT -s Anc0.Anc0refChr3 74212 29 + 222631 --TCATTCTCAGGTTGGAAAATGTGATGCAT -s Anc1.Anc1refChr6 105975 31 + 197743 CTTCATTCTCAGGTTGGAAAATGTGATGCAT -s Anc2.Anc2refChr13 80475 29 + 96486 --TTACCTCCGGGTTGCAAAATGTGATGCAT -s mr.mrrefChr3 7371 31 + 181027 CCTCATTCTGAGCTTAGAAAATGTGCTGCAT -s simCow_chr6.simCow.chr6 436884 28 + 602619 --TTA-GTCCAGGTTGCAGAATGTGATGCAT -s simDog_chr6.simDog.chr6 428765 29 + 593897 --TTACCACCGGGTTGCAAGATATGATGTAT -s simHuman_chr6.simHuman.chr6 437218 30 + 601863 CTTCTTTCTCAGATT-GAAAATGTGATGCCT -s simRat_chr6.simRat.chr6 461245 24 + 647215 CCTCATTCTGAGGTTGG-------GCTGCAT - -a -s simMouse_chr6.simMouse.chr6 449222 16 + 636262 CAACAAATGCAGAAAT -s Anc0.Anc0refChr3 74247 9 + 222631 T-------GGGGACAA -s Anc1.Anc1refChr6 106012 9 + 197743 T-------GGGGACAA -s Anc2.Anc2refChr13 80510 9 + 96486 T-------AGGAACAA -s mr.mrrefChr3 7408 16 + 181027 CAACAAATGCAGAAAT -s simCow_chr6.simCow.chr6 436918 9 + 602619 T-------AGGAATAA -s simDog_chr6.simDog.chr6 428800 9 + 593897 G-------AGGAACAA -s simHuman_chr6.simHuman.chr6 437254 9 + 601863 T-------GGGGACAA -s simRat_chr6.simRat.chr6 461282 16 + 647215 CAAGAACTGCAGAAAT - -a -s simMouse_chr6.simMouse.chr6 449238 13 + 636262 TCTACCAAAGTAC -s Anc0.Anc0refChr3 74256 13 + 222631 ACTACCAGAGAAG -s Anc1.Anc1refChr6 106021 13 + 197743 ACTACCAGAGAAG -s Anc2.Anc2refChr13 80524 13 + 96486 ACTACCAGAGAGG -s mr.mrrefChr3 7424 13 + 181027 TCTACCAAAGTAC -s simCow_chr6.simCow.chr6 436932 13 + 602619 ACTACCAAAGAGG -s simDog_chr6.simDog.chr6 428814 13 + 593897 ACTACCAGAGAGG -s simHuman_chr6.simHuman.chr6 437263 13 + 601863 ACTACCAGAGAAG -s simRat_chr6.simRat.chr6 461298 13 + 647215 TCTACCAAAGTAC - -a -s simMouse_chr6.simMouse.chr6 449251 52 + 636262 TCCAAAGACGCCTGTCTTGCTATCAAATGGGAAGCTATTACAAGAAAGGAGT -s Anc0.Anc0refChr3 74269 52 + 222631 TTCAAGGTTGCCTATCTTGTGATTGAATGGGCATTTGTTGCATGAAAGGAAT -s Anc1.Anc1refChr6 106034 52 + 197743 TTCAAGGTTGCCTATCTTGTGATTGAATGGGCATTTGTTGCATGAAAGGAAT -s Anc2.Anc2refChr13 80537 52 + 96486 CTCAAGGTTGCCTATCTTCTGCTTGACTGGGCATCTGTTGCATGAAAGGGAT -s mr.mrrefChr3 7437 52 + 181027 TCCAAAGATGCCTATCTTGCTATCAAATGGGAAGTTGTTGCAAGAAAGGAGT -s simCow_chr6.simCow.chr6 436955 49 + 602619 CTCAAGGTTGCCTATCATTTA---GTCTAGGCATCCATCCCATGAAAGGGAT -s simDog_chr6.simDog.chr6 428827 52 + 593897 CTCAAGGTTACCTACGTTCTGCTTGACTGGGCATCTGTTGCATGACAGGGAG -s simHuman_chr6.simHuman.chr6 437276 52 + 601863 TTCAAGGTTGCCCATCTTGTGATTGGATGGGCACTTGCTGTATGAAAGGAAT -s simRat_chr6.simRat.chr6 461311 50 + 647215 TCCAAAGATCCCTATCTTGCTA--AAATGGGGATTTGTTGCAAGGAAGGGGT - -a -s simMouse_chr6.simMouse.chr6 449303 54 + 636262 AGACAAATACTGAAAGGCTGATTGACTGATAGAGGCATTAATCCAGGATATGCA -s Anc0.Anc0refChr3 74321 54 + 222631 AGACTAATACTGGAAGGCTGGTTGGTTGATTGAGGAATTAATCCAGGATAGGCA -s Anc1.Anc1refChr6 106086 54 + 197743 AGACTAATACTGGAAGGCTGGTTGGTTGATTGAGGAATTAATCCAGGATAGGCA -s Anc2.Anc2refChr13 80589 54 + 96486 AGACTAATACTGGAAGGCTGGTTGGTTGATTGAGGAATTAATCCAGGATAGGCA -s mr.mrrefChr3 7489 54 + 181027 AGACAAATACTGAAAGGCTGATTGACTGATAGAGGCATTAATCCAGGATATGCA -s simCow_chr6.simCow.chr6 437006 54 + 602619 GGACTAGTGCTGGATGGCCAGTTGATAGATTGAAGAATTGCTCCACAATAGGCA -s simDog_chr6.simDog.chr6 428879 54 + 593897 AGGCTAATACTGGAAGGCTGGTTGGTTGATTGAGGAATTAAGCCAGGATAGGCA -s simHuman_chr6.simHuman.chr6 437328 39 + 601863 TGACTAATACT---------------TGATTGGGTAATTAATCCATGATACACA -s simRat_chr6.simRat.chr6 461361 54 + 647215 AGACAAATACTGAAAGACTGACTAACTGATAGAGGCATTAAATCAGGAAATGCA - -a -s simMouse_chr6.simMouse.chr6 449357 8 + 636262 CCTTCAGA -s Anc0.Anc0refChr3 74375 8 + 222631 CTTTCAGA -s Anc1.Anc1refChr6 106140 8 + 197743 CTTTCAGA -s Anc2.Anc2refChr13 80643 8 + 96486 CTTTCAGA -s mr.mrrefChr3 7543 8 + 181027 CCTTCAGA -s simCow_chr6.simCow.chr6 437060 6 + 602619 CTCT--GA -s simDog_chr6.simDog.chr6 429035 8 + 593897 CTTTCAGA -s simHuman_chr6.simHuman.chr6 437367 8 + 601863 CTTTCAGA -s simRat_chr6.simRat.chr6 461415 8 + 647215 CCTTCAGA - -a -s simMouse_chr6.simMouse.chr6 449365 20 + 636262 CTCGAGTTCATGGCTAATTT -s Anc0.Anc0refChr3 74383 20 + 222631 CTCCAGATCATGGCCAACTT -s Anc1.Anc1refChr6 106148 20 + 197743 CTCCAGATCATGGCCAACTT -s Anc2.Anc2refChr13 80655 20 + 96486 CTCCAGATTATGGCCAACTT -s mr.mrrefChr3 7551 20 + 181027 CTCCAGTTCATGGCTAATTT -s simCow_chr6.simCow.chr6 437070 20 + 602619 CTCAAAATTATGACCAACTT -s simDog_chr6.simDog.chr6 429047 20 + 593897 CTCCAGCTTATGGCCAACTT -s simHuman_chr6.simHuman.chr6 437375 20 + 601863 CTCCAGATCATGGACAACTT -s simRat_chr6.simRat.chr6 461423 20 + 647215 CTCCAGTACATGGCTAATTT - -a -s simMouse_chr6.simMouse.chr6 449385 9 + 636262 CATACCTGC -s Anc0.Anc0refChr3 74410 9 + 222631 CACACATGC -s Anc1.Anc1refChr6 106175 9 + 197743 CACACATGC -s Anc2.Anc2refChr13 80682 9 + 96486 CACAAATGC -s mr.mrrefChr3 7578 9 + 181027 CACACCTGC -s simCow_chr6.simCow.chr6 437097 9 + 602619 CACAAATGC -s simDog_chr6.simDog.chr6 429074 5 + 593897 CACAA---- -s simHuman_chr6.simHuman.chr6 437402 9 + 601863 CACACATGC -s simRat_chr6.simRat.chr6 461450 9 + 647215 TACAGCTGC - -a -s simMouse_chr6.simMouse.chr6 449394 29 + 636262 AACTTACTAAAAATGTGGAGATTATTCAC -s Anc0.Anc0refChr3 74419 29 + 222631 AAGTTACTAAGAATGCGGAGATTATTCAG -s Anc1.Anc1refChr6 106184 29 + 197743 AAGTTACTAAGAATGCGGAGATTATTCAG -s Anc2.Anc2refChr13 80691 29 + 96486 AAACTACTAAGAATGCGGAGATTATTCAG -s mr.mrrefChr3 7587 29 + 181027 AAGTTACTAAAAATGTGGAGATTATTCAC -s simCow_chr6.simCow.chr6 437181 29 + 602619 AAACTACTAAGAATGCAGAGACTATTCAG -s simDog_chr6.simDog.chr6 429079 18 + 593897 -----------AATGTGGTGATTATTCAG -s simHuman_chr6.simHuman.chr6 437411 29 + 601863 AAGTTATTAATAATGCGGAGATTATTCAA -s simRat_chr6.simRat.chr6 461459 29 + 647215 AAGTTACTAAAAATGTGGAAACTATTCAC - -a -s simMouse_chr6.simMouse.chr6 449423 122 + 636262 ACATCTATGTTTAGATTCCACTGCCAGACTGAAAAGGAGTAGGTAACCAGACATGCACTGATTGTTATGGATATGTTGCATTAAGTTGACACAAGGGGGGGTATGATGATTTACAGATCTTA -s Anc0.Anc0refChr3 74449 122 + 222631 ACACCTATGCTTTGATTTTACTGCCAGACTAAAAAGGTGTAGAGAACTTGACTTGTGCTGATTGTTATGGCTATGTTGTAATAAGTCAACATGAGGGGTGGGCTGGTGAGTTACAGGGCTAA -s Anc1.Anc1refChr6 106214 122 + 197743 ACACCTATGCTTTGATTTTACTGCCAGACTAAAAAGGTGTAGAGAACTTGACTTGTGCTGATTGTTATGGCTATGTTGTAATAAGTCAACATGAGGGGTGGGCTGGTGAGTTACAGGGCTAA -s Anc2.Anc2refChr13 80721 122 + 96486 ACACCTCTGCTTTGATTTTACTGCCAGACTAAAAAGGTGTAGAGAACTTGGCTTGTGCTGATTGTTATGGCTATGTTGTAATAAGACAACATGAGGGGTGGGCTGGTGAGTTACAGGGCTAA -s mr.mrrefChr3 7616 122 + 181027 ACATCTATGTTTAGATTTCACTGCCAGACTAAAAAGGAGTAGGTAACTAGACATGCACTGATTGTTATGGATATGTTGCATTAAGTTGACACAAGGGGGGGGATGATGATTTACAGATCTTA -s simCow_chr6.simCow.chr6 437211 122 + 602619 TGATGTCAGTTTTGATTTTACTACCAGACTAAAAAGGTGTAGGGAACTTGGCTTGTGCTAATGGTTATGGTTATGTTGCAATAAGACAACACAAGGGGTGTGCTGGTGATTTACTGGCCTAA -s simDog_chr6.simDog.chr6 429098 119 + 593897 ACACCTCTACTTTGATTATACTGCCAGACTAAAAAGGTGTAGAGAGCTTGGCT--TGCTGATTGTTATGGCTGAGTTGTATTAG-ACAACATGGGGGGTGGGCTGGTGAGTTACAGGGCTAA -s simHuman_chr6.simHuman.chr6 437441 105 + 601863 ACACCTATGCTTGGATTTTACTGCCAGACTAAAAAGGTGTTGAGAACTTAACTTGTGCTGCTTGTTATTGCTATGTTGTAATAATTCAACATGAGGGGTGGGCTG----------------- -s simRat_chr6.simRat.chr6 461488 120 + 647215 ACATCCATGTTTAGATTTCACTGCCAGACTAAAAAGGAGTAGCTAACTAGACATGCACTGATTATTATGGATATGTTGCA--AAGTTGATAAAAAGGGAGGGATGATGATTTATAGATCTTA - -a -s simMouse_chr6.simMouse.chr6 449545 26 + 636262 TTAAGGCATTACAGGTTTAGTTGAAA -s Anc0.Anc0refChr3 74571 25 + 222631 T-AAGGTATTAAAGTTTTAGTTGGAA -s Anc1.Anc1refChr6 106336 25 + 197743 T-AAGGTATTAAAGTTTTAGTTGGAA -s Anc2.Anc2refChr13 80843 25 + 96486 T-AAGGCATTAAAGTGTTAGATGGAA -s mr.mrrefChr3 7738 26 + 181027 TTAAGGTATTACAGTTTTAGTTGAAA -s simCow_chr6.simCow.chr6 437333 25 + 602619 T-AAGGCATCAAAGTGTTAGATTGAC -s simDog_chr6.simDog.chr6 429218 25 + 593897 T-AAGGCATTAAACTGGTAGATGGAA -s simHuman_chr6.simHuman.chr6 437546 22 + 601863 ----GGTATTGATGTTTTAGTTGGAA -s simRat_chr6.simRat.chr6 461608 26 + 647215 TTAAGGTATTACAGTGTTAGTTGAAA - -a -s simMouse_chr6.simMouse.chr6 449571 42 + 636262 GTGCAGCATGACAGCCACAGATACCTTCTAATAAACATTGTC -s Anc0.Anc0refChr3 74613 40 + 222631 GTACAATATGATGGTGA--GTTACATTCAAGTAATCACTACC -s Anc1.Anc1refChr6 106378 40 + 197743 GTACAATATGATGGTGA--GTTACATTCAAGTAATCACTACC -s Anc2.Anc2refChr13 80885 40 + 96486 GTGCAATATGATGGTGA--GTTACATTCAAGTAATCACTACC -s mr.mrrefChr3 7764 42 + 181027 GTACAGCATGACAGCCACAGATACCTTCTAATAAACATTGTC -s simCow_chr6.simCow.chr6 437375 40 + 602619 GTGTAATATGATGATGG--GTTACGTTCAATTAAGCACTGTA -s simDog_chr6.simDog.chr6 429260 40 + 593897 GTGCACTATGATGGCCA--GCAACATTCAAGTAATCACTACC -s simHuman_chr6.simHuman.chr6 437585 40 + 601863 GTACAATATGGAGGTGA--ATTACATTCCACTGACGACCACC -s simRat_chr6.simRat.chr6 461634 40 + 647215 GTACAGCATGACAACCACAGATTCCTTCTAATAAACATTG-- - -a -s simMouse_chr6.simMouse.chr6 449613 3 + 636262 TTG -s Anc0.Anc0refChr3 74653 3 + 222631 CTG -s Anc1.Anc1refChr6 106418 3 + 197743 CTG -s Anc2.Anc2refChr13 80925 3 + 96486 CTG -s mr.mrrefChr3 7806 3 + 181027 TTG -s simCow_chr6.simCow.chr6 437416 3 + 602619 CTG -s simDog_chr6.simDog.chr6 429300 3 + 593897 CTG -s simHuman_chr6.simHuman.chr6 437625 3 + 601863 CTG - -a -s simMouse_chr6.simMouse.chr6 449616 13 + 636262 TTTCTCCACCTTG -s Anc0.Anc0refChr3 74656 13 + 222631 TTCCTCCATCTAG -s Anc1.Anc1refChr6 106421 13 + 197743 TTCCTCCATCTAG -s Anc2.Anc2refChr13 80928 13 + 96486 TTCCTCCATCTAG -s mr.mrrefChr3 7809 13 + 181027 TTTCTCCACCTTG -s simCow_chr6.simCow.chr6 437419 13 + 602619 TTACTGCATCTAG -s simDog_chr6.simDog.chr6 429304 13 + 593897 TCCCTCTATCTAG -s simHuman_chr6.simHuman.chr6 437628 13 + 601863 TTCCTCCATTTAG - -a -s simMouse_chr6.simMouse.chr6 449629 42 + 636262 TAATATCAATAGCCATATAGTACATGTCCTGCCCAAATTGTA -s Anc0.Anc0refChr3 74671 42 + 222631 GAATATACATAGGCTCATAGTACATGTCTTGCTCACATTTTA -s Anc1.Anc1refChr6 106436 42 + 197743 GAATATACATAGGCTCATAGTACATGTCTTGCTCACATTTTA -s Anc2.Anc2refChr13 80943 42 + 96486 GTATATACATAGGCTCATAGTACATGTCTTGCTCACATTTTA -s mr.mrrefChr3 7822 42 + 181027 TAATATCAATAGCCATATAGTACATGTCCTGCCCAAATTGTA -s simCow_chr6.simCow.chr6 437434 39 + 602619 GT--ATGCATAGGC-CAAAGTACATAGCTTGCTCACACTTTA -s simDog_chr6.simDog.chr6 429319 35 + 593897 GTATATA-------TTATAATACATGTCTTGCTCCCTTTGCA -s simHuman_chr6.simHuman.chr6 437643 42 + 601863 GAGTATACATAGGCTCACAGTACATGTCTTGCTCACATTTTA -s simRat_chr6.simRat.chr6 461674 15 + 647215 -----------------------ATGTCCCACCC----TATA - -a -s simMouse_chr6.simMouse.chr6 449671 333 + 636262 GCTGTGAGGAGTCCCTATGATCTAGTGACTGGGTCCCATGCATCTTCACGGAACCATTGGGATACTGCTTTACTGGCTGCCTCAGGTGATCGTTGAATACCTGACTTGTTAGTAGCCTGAAGAGTTTGCTGGGTCCCAGCATCCTGCACCTTGACAGGAGAACCTTGAGTTCCAACCTCCTGTACTTTAACAGAGCGTTGTGTCCCAGTGTCTCGAGGCTCCACTGGTCGTTGTGTGCCAGCTTCCCTCACAGCTATTGAGGAGCGCTTAGTCCTGGATTTCTGTGTGGCTACATCTTTAGCAAGGGCTTTCCCTGAACCTTGCAATGTTATG -s Anc0.Anc0refChr3 74713 333 + 222631 GCGCTAAAGAGTCGCTATGATCTAGTGACTGGGTCCCATGCATCTTCACAGAACCATTGGGACACTGCTTTACTGGCTGCTTCAGGTGATCGTTGGATCCCTGACTTATTAGCAGCCTGAAGAGATTGCTGAGTCCCAGCATCCTGCACCTTAACAGGAGAACCTTGAGTTCCAACCTCCTGTACTTTAACAGAGCGTTGTGTCCCAGTGTCTCGAGGCTCCACTGGTCGTTGTGTGCCAGCTTCCCTCACAGCTATTGAGGAGCGCTGAGTCTTGGATTTCTGAGTGGCTACATCTTGGGCAAGGGCTTTCCCCGAACCTTGAGACTTTATG -s Anc1.Anc1refChr6 106478 333 + 197743 GCGCTAAAGAGTCGCTATGATCTAGTGACTGGGTCCCATGCATCTTCACAGAACCATTGGGACACTGCTTTACTGGCTGCTTCAGGTGATCGTTGGATCCCTGACTTATTAGCAGCCTGAAGAGATTGCTGAGTCCCAGCATCCTGCACCTTAACAGGAGAACCTTGAGTTCCAACCTCCTGTACTTTAACAGAGCGTTGTGTCCCAGTGTCTCGAGGCTCCACTGGTCGTTGTGTGCCAGCTTCCCTCACAGCTATTGAGGAGCGCTGAGTCTTGGATTTCTGAGTGGCTACATCTTGGGCAAGGGCTTTCCCCGAACCTTGAGACTTTATG -s Anc2.Anc2refChr13 80985 333 + 96486 GCGCTAAAGAGTCGCTATGATCTAGTGACTGGGTCCCATGCATCTTCACAGAACCATTGGGACACTGCTTTACTGGCTGCTTCAGGTGATCGTTGGATCCCTGACTTATTTGCAGCCTGAAGAGATTGCTGAGTCCCAGCATCCTGCACCTCAACAGGAGAACCTTGAGTTCCAACCTCCTGTACTTTAACAGAGCGTTGTGTCCCAGTGTCTCGAGGCTCCACTGGTCGTTGTGTGCCAGCTTCCCTCACAGCTATGGAGGAGCGCTGAGTCTTGGATTTCTGAGTGGCTACATCTTGGGCAAGGGCTTTCCCAGAACCTTGAGACTTTATG -s mr.mrrefChr3 7864 333 + 181027 GCTGTGAAGAGTCCCTATGATCTAGTGACTGGGTCCCATGCATCTTCACAGAACCATTGGGATACTGCTTTACTGGCTGCTTCAGGTGATCGTTGAATACCTGACTTGTTAGTAGCCTGAAGAGTTTGCTGGGTCCCAGCATCCTGCACCTTGACAGGAGAACCTTGAGTTCCAACCTCCTGTACTTTAACAGAGCGTTGTGTCCCAGTGTCTCGAGGCTCCACTGGTCGTTGTGTGCCAGCTTCCCTCACAGCTATTGAGGAGCGCTTAGTCTTGGATTTCTGTGTGGCTACATCTTTAGCAAGGGCTTTCCCCGAACCTTGCAATGTTATG -s simCow_chr6.simCow.chr6 437475 329 + 602619 GCGCTAAAGAGTCCCTATGATCTAGTGACTGGGTCCCATGCATCTTCACAGAACCACTGGGAGACTGCTTTACTGGCTGCTTCAGGCGATCGTTGAATACCTGACTTATTTGCAGCCTGAAGAGATTGCTGAGTCCCAGCATCCTGCACCTCCACCGGAGATCCTTGAGTTCCGACCTCCTGCACTTTAACAGAGCGTTGTGTCCCAGTGTCACGAGGCTCCACTGGTCGTTGTGTACCAGCTTCCCTCACAGCTATAGAGGAGCACTGCGTCTTGGATTTCTGATTGGCTACATCTTGAGCAAGAGCCTTCCCTGAACCTCGAGACTT---- -s simDog_chr6.simDog.chr6 429354 323 + 593897 GC-------AATTGCTATGATCTAGTAACTGGGTCCCATGCATCTTCACAGAACCATTGGGACACTGCTTTACTGGCTGCTTCAGGTGATCTTTGGATCCCTGACTTATTTGCAGCCTGAAGGGATTGCTGAGTCCCAGCATCATGTACCTCAACAGGAGAACCTTGAGTGCCAACCTCCTGTACTTTAACAGAGCGTTGTGTCCCAGTGTCTCGAGGCTCCACTGGTCGTTGTGTGCCAGCTTC---CACAGCTATGGAGGAGCGCTGAGTCTTGGATTTCTGAGTGGCTACATCTTGGGCAAGGGCTTTTCCAGAACCTTGAGACTTTATG -s simHuman_chr6.simHuman.chr6 437685 333 + 601863 GCACCAAAGAGTCTTTAGGATCTAGTGACTGGATCCCATGCATCTTCACAGAACCATTGTGACACTGCTTTACTGGCTGCTTCAGGTGATCGTTGGATCCCAGACTTATTAGCAGCCTGAAGAGATTGCTGAGTCTCAGCATCCTGCACCTTTACAGGAGAACCTTGAGTTCCAACCTCCTGTACTTTAACAGAGCGTTGCGTCCCTGTGTCTCGAGGCTCCACTGGTCGTTGTGTCCCAGCTTCCCTCACAGCTATTGAAGAATGCTGAGTCTTGGATTTCTGAGTGGCTACATCTTGGGCAAGGACTTTCCCCGAACCTTGAGACTTTATG -s simRat_chr6.simRat.chr6 461689 333 + 647215 GTTGTGAAGAGTCCCTATGATCTAGTGACTGGGTCCCAAGCATCTTCACAGAACCATTGGGATACTGCTTTACTGGCTGCTTCTGGTGAGCGTTGAATACCTGACTTGTTAGTGGCCTGAAGAGTTTGCTGGGTCCCAGCATCCTGCACCTTGACAGGAGAACCTTGAGTTCCAACCTCCTGTACTTTAACAGAGCGTTGTGTCCCAGTGTCTCGAGGCTCCACTGGACGTTGTGTACCAGCTTCCCTCACAGCTATTGAGGAGCGCTTAGTCTTGGATTTTTGTGTGGCTACATCTTTAGCAAGGGCTTTCCCCGAACCTTGCAATGTTATG - -a -s simMouse_chr6.simMouse.chr6 450004 5 + 636262 AAACA -s Anc0.Anc0refChr3 75049 5 + 222631 AAACA -s Anc1.Anc1refChr6 106814 5 + 197743 AAACA -s Anc2.Anc2refChr13 81321 5 + 96486 AAATG -s mr.mrrefChr3 8197 5 + 181027 AAACA -s simDog_chr6.simDog.chr6 429680 5 + 593897 AAATG -s simHuman_chr6.simHuman.chr6 438021 5 + 601863 AAACA -s simRat_chr6.simRat.chr6 462022 5 + 647215 AAATA - -a -s simMouse_chr6.simMouse.chr6 450009 45 + 636262 TACCATGTCTATTTGTTTCCTCATGAGCTGTAGTGGAAACATGCC -s Anc0.Anc0refChr3 75055 45 + 222631 TATCATGTCTATATGCCCACAAATGAGCTGTAGTAGAAACATCAC -s Anc1.Anc1refChr6 106820 45 + 197743 TATCATGTCTATATGCCCACAAATGAGCTGTAGTAGAAACATCAC -s Anc2.Anc2refChr13 81327 45 + 96486 TATCATGTCTATACCCCCACTAATGAGCTGCAGTAAAAACATCCC -s mr.mrrefChr3 8202 45 + 181027 TACCATGTCTATTTGTCTCCACATGAGCTGTAGTGGAAACATGAC -s simCow_chr6.simCow.chr6 437805 43 + 602619 TACCACATCTACAC--CCACTAATAAGCTAGTATAAAACCATCCC -s simDog_chr6.simDog.chr6 429686 45 + 593897 CATTATGTCTATGCCCACTCTGACGAACCGCAGTAAAAACATCCC -s simHuman_chr6.simHuman.chr6 438027 45 + 601863 TGACATGTCTATATGCCCACAAATGAGCTGTGGTAGAAACCACAC -s simRat_chr6.simRat.chr6 462027 45 + 647215 TACCGTGTCTAATTGTCACCACGTGAGCTGTAGTGGAAACATGAC - -a -s simMouse_chr6.simMouse.chr6 450054 19 + 636262 CATTCAATACTTCTTAGAC -s Anc0.Anc0refChr3 75107 16 + 222631 CACCTAA---TTCTTGGAC -s Anc1.Anc1refChr6 106872 16 + 197743 CACCTAA---TTCTTGGAC -s Anc2.Anc2refChr13 81379 16 + 96486 CACCTAA---CTTTTGGGC -s mr.mrrefChr3 8254 16 + 181027 CATTCAA---TTCTTAGAC -s simCow_chr6.simCow.chr6 437855 16 + 602619 CACCCAA---ATGTTGGTT -s simDog_chr6.simDog.chr6 429738 16 + 593897 TGCCTAA---CTTTTGGGC -s simHuman_chr6.simHuman.chr6 438079 16 + 601863 CACCTAA---TTCATGAAC -s simRat_chr6.simRat.chr6 462079 16 + 647215 CAGTCAG---TTCTTAGAC - -a -s simMouse_chr6.simMouse.chr6 450073 32 + 636262 AGGTCATGTATTCCAACAGGTTGATAAGTGTT -s Anc0.Anc0refChr3 75123 32 + 222631 AGGTCAGGTATTTTGACAGGTCAAGATGAGTT -s Anc1.Anc1refChr6 106888 32 + 197743 AGGTCAGGTATTTTGACAGGTCAAGATGAGTT -s Anc2.Anc2refChr13 81395 32 + 96486 AGGTCAGGTATTTTGACTGGTCAAGATGAATT -s mr.mrrefChr3 8270 32 + 181027 AGGTCATGTATTCCAACAGGTCAATAAGTGTT -s simCow_chr6.simCow.chr6 437871 32 + 602619 AGGTCAGGTATTGTGACTGGTCAAGATGAATT -s simDog_chr6.simDog.chr6 429763 32 + 593897 AGGTCTGGTATTTTGCCTGGTCAAGATGAACT -s simHuman_chr6.simHuman.chr6 438095 32 + 601863 AGGTCAGGTATTTTGACAGGACAAGATGAGTC -s simRat_chr6.simRat.chr6 462095 32 + 647215 AGGTCATGTATTCCTACAGATCAACAAGTGTT - -a -s simMouse_chr6.simMouse.chr6 450105 2 + 636262 TA -s Anc0.Anc0refChr3 75155 2 + 222631 TA -s Anc1.Anc1refChr6 106920 2 + 197743 TA -s Anc2.Anc2refChr13 81429 2 + 96486 TA -s mr.mrrefChr3 8302 2 + 181027 TA -s simCow_chr6.simCow.chr6 437905 2 + 602619 CA -s simDog_chr6.simDog.chr6 429797 2 + 593897 TA -s simHuman_chr6.simHuman.chr6 438127 2 + 601863 TA -s simRat_chr6.simRat.chr6 462127 2 + 647215 TA - -a -s simMouse_chr6.simMouse.chr6 450107 83 + 636262 GTGCCCTACCATGATTGGTAATGAAGACTTGCCTAGCAGTTGAAATTAAAACATAAACCATTTCTTAGTTTCCACAGCCTTTG -s Anc0.Anc0refChr3 75157 82 + 222631 GTACCCAACCATGATTAT-AAAGCAGTCCTGCCCACCAAACGGAGCTAAGACATAAATGGTATCATAGTTTCTACAGCTTTTG -s Anc1.Anc1refChr6 106922 82 + 197743 GTACCCAACCATGATTAT-AAAGCAGTCCTGCCCACCAAACGGAGCTAAGACATAAATGGTATCATAGTTTCTACAGCTTTTG -s Anc2.Anc2refChr13 81431 82 + 96486 GTACCCAGCCATGATTAT-GAAGCAGTCCTGCCCCCCAAACGAAGCTGAGACATAAATGGCACTATAGCTTCTACAGTTTTTG -s mr.mrrefChr3 8304 83 + 181027 GTGCCCTACCATGATTGGTAAAGAAGACCTGCCTAGCAGATGGAATTAAGACATAAACCATTTCATAGTTTCCACAGCCTTTG -s simCow_chr6.simCow.chr6 437907 78 + 602619 GTACTCAGCCATAATT-----AGCAGCCATGCCTGCCAAACTCAGCTAAAGCATAAATGGCAGTATATCTTCCACAGTTAATG -s simDog_chr6.simDog.chr6 429799 82 + 593897 GTGCCCAGCCATGTTTAT-GAAGCGGTCCTGCCCCCCAAACGAAGCTGAGAGATAAATGGCACTACAGCTTCTACAGTTTTTG -s simHuman_chr6.simHuman.chr6 438132 81 + 601863 AAACCCAACCATGATCAA-AAAACAGTCCTGCCCACGATAAGGATCTA-GACATAAATGGTCTCATAGTGCTTACAGCTTTTG -s simRat_chr6.simRat.chr6 462129 82 + 647215 GTGCCCTACCATAATTGGTAAAGAGGACCTGACTAGCAGATGGAATTAAGACATAAACCATTTCAAAGTTT-CACATCCTTTG - -a -s simMouse_chr6.simMouse.chr6 450190 28 + 636262 AACAACATCACCAGCTCAAACTGACTAG -s Anc0.Anc0refChr3 75239 15 + 222631 CATAACATTACCAGC------------- -s Anc1.Anc1refChr6 107004 15 + 197743 CATAACATTACCAGC------------- -s Anc2.Anc2refChr13 81513 15 + 96486 CATAACATTACCAGC------------- -s mr.mrrefChr3 8387 28 + 181027 AACAACATTACCAGCTCAAACTGACTAG -s simCow_chr6.simCow.chr6 437985 15 + 602619 CACTACAGGATCTGC------------- -s simDog_chr6.simDog.chr6 429881 15 + 593897 TATAACATTACCAGC------------- -s simHuman_chr6.simHuman.chr6 438213 15 + 601863 CATAACATTAGCCAC------------- -s simRat_chr6.simRat.chr6 462215 28 + 647215 AACAACATTACCAGCTCAAACTGTCTAG - -a -s simMouse_chr6.simMouse.chr6 450218 8 + 636262 CCACACAG -s Anc0.Anc0refChr3 75254 8 + 222631 CCAACCAG -s Anc1.Anc1refChr6 107019 8 + 197743 CCAACCAG -s Anc2.Anc2refChr13 81528 8 + 96486 CCAACCAG -s mr.mrrefChr3 8415 8 + 181027 CCACACAG -s simCow_chr6.simCow.chr6 438000 8 + 602619 CCAACCAG -s simDog_chr6.simDog.chr6 429896 8 + 593897 CTAACCTG -s simHuman_chr6.simHuman.chr6 438228 8 + 601863 CCAACCAG -s simRat_chr6.simRat.chr6 462244 8 + 647215 CCACACGG - -a -s simMouse_chr6.simMouse.chr6 450226 74 + 636262 AAAACCTCCTGCCCAATTTAACACTACTTAGACTTCGCACAGTGCCACGTGCAAATCTCCAAAAGCAAGTGATG -s Anc0.Anc0refChr3 75262 27 + 222631 AAAACCCTTTGCCT-----------------------------------------------GTAGCAAGTGATG -s Anc1.Anc1refChr6 107027 27 + 197743 AAAACCCTTTGCCT-----------------------------------------------GTAGCAAGTGATG -s Anc2.Anc2refChr13 81539 27 + 96486 AAAACCCTTTGCCT-----------------------------------------------GTAGCAAGTGATG -s mr.mrrefChr3 8423 27 + 181027 AAAACCTTTTGCCC-----------------------------------------------AAAGCAAGTGATG -s simCow_chr6.simCow.chr6 438011 27 + 602619 AAAACCCTTCGCCT-----------------------------------------------GTAGCAAGTGGTG -s simDog_chr6.simDog.chr6 429907 27 + 593897 AAAACCCTTTGCCT-----------------------------------------------GTAGCAAATGATG -s simHuman_chr6.simHuman.chr6 438236 27 + 601863 AGAACCCTTTGCCT-----------------------------------------------GGAGCAAGTGATG -s simRat_chr6.simRat.chr6 462252 27 + 647215 AAAACCTTTTGCCC-----------------------------------------------AAAGCAAGTGATG - -a -s simMouse_chr6.simMouse.chr6 450300 162 + 636262 CAGGTTCATAATCATTTTTATGTCTTCCTGGAAGGAAGATCTTACAAATATCAGGATTTCTGCTTCACCATTAGGATCTAGGCGATTGACATGAACTAAGATTTGAGACATACCCTGGACATGTGGAATACGTTCCCCACCCCGGCCTGTGTGGGATGGACT -s Anc0.Anc0refChr3 75298 162 + 222631 CAGGTTCATGATCATTTTTACATCTTCCTGGTAGGAAGGTCTTCCAAATACCAGGATTTCTGCTTCACCATTAGGATCTAAGCGATTCACATGAATCAAGATTTGAGACATACCCTGGACATGTGGAATGCGCTCCCCGCCCCGGCCTGTGTGGGTTGCAGT -s Anc1.Anc1refChr6 107063 162 + 197743 CAGGTTCATGATCATTTTTACATCTTCCTGGTAGGAAGGTCTTCCAAATACCAGGATTTCTGCTTCACCATTAGGATCTAAGCGATTCACATGAATCAAGATTTGAGACATACCCTGGACATGTGGAATGCGCTCCCCGCCCCGGCCTGTGTGGGTTGCAGT -s Anc2.Anc2refChr13 81575 162 + 96486 TAGGTTCATGATCATTTTTACATCTTCCTGGTAGGAAGGTCTTCCAAATACCAGGATTTCTGCTTCACCATTAGGATCTAAGCGATTCACATGAATCAAGATTTGAGACATACCCTGGACATGTGGAATGCGCTCCCCGCCCCGGCCTGTGGGGGTTGCAGT -s mr.mrrefChr3 8459 162 + 181027 CAGGTTCATAATCATTTTTATGTCTTCCTGGAAGGAAGATCTTCCAAATACCAGGATTTCTGCTTCACCATTAGGATCTAGGCGATTGACATGAACTAAGATTTGAGACATACCCTGGACATGTGGAATACGTTCCCCACCCCGGCCTGTGTGGGATGGACT -s simCow_chr6.simCow.chr6 438047 162 + 602619 TAGGTTCATGATCATTTTTACATCTTCCTGGTAAGATGGTCTTCCAAATACTAGTATTTCTGCTTCACCATTCGGATCTAAGTGATTCACATGAATTAAGATTTGAGACATACCCTTGACATGTGGAATGCGTTCCCCACCCTGGCCTGTGGGGGTCGCAGT -s simDog_chr6.simDog.chr6 429943 162 + 593897 TAGGTTCATAATCATCTTTACATCCTCCTGGTAGGCAGGTCTTCCAAATACCAGGATCTCTGCATCACCATTAGGATCTAAACGATTCACATGAATCAAGATTTGTGACATACCCTGAACATGTGGAATGCGCTCCCCGCCCCGGCCTGTCGTGTTTGCAGT -s simHuman_chr6.simHuman.chr6 438272 159 + 601863 CAGATTCATGATCATTTTTACATCTTCCTGATATGAAGGTCTTCCAAATACCAGGATTTCTGCTTCACCATTAGGATCTAAGCGATTCACGTGAA---AGATTTGAGACATACCTTGGACATGTGGAATTCGCTCTCCGCCCCGGCCTGTGTGGGTTGCAGT -s simRat_chr6.simRat.chr6 462288 162 + 647215 CAGGTTCATAATCATTGTTATGTCTTCCCAGAAGGAAGATCTTCCAATTACCAGGAATACTGCTTCACCATTAGGATCTAGGCAATTGACATGAACTAGGATTTGAGACATACCCTGGACATGTGGAATACGTTCCCCACCCCGGCCTGTGTGGGATGTATT - -a -s simMouse_chr6.simMouse.chr6 450462 208 + 636262 ATGACCTCTTACCAAAGATCTTGTCCACCAACCAGACCTCCAGGCGTACTACTTTTGGATTCTTGAGGAACTCTGAGTGAAACCAAGAAAATTGCTGAGGGAGGTGACTGAGCACCTCTACTGGCATTGCCCTAAGCTGCATCAAATGTACAAGCGATGGGCTGGGAGCATCCATAGCAGACAGGCAATCATAAGGTACTTACTTGAA -s Anc0.Anc0refChr3 75564 204 + 222631 ATCACCTTTTACCAAAGATCTTGTCCACCAACCAAACCTCCAGCCGTACTACTTTTGGATTCTTGAGGAACTCTGAGTGAAACCAAGAAAATTGCTGAGGGAGGTGACTGAGCACCTCTACTGGCATTGCCCTAGGCTGCATCAAGTGTACAAGAGATGGGCTGGGAGCATCCATAGCAGACAGGCAATCATAAGATACTT----GAA -s Anc1.Anc1refChr6 107332 204 + 197743 ATCACCTTTTACCAAAGATCTTGTCCACCAACCAAACCTCCAGCCGTACTACTTTTGGATTCTTGAGGAACTCTGAGTGAAACCAAGAAAATTGCTGAGGGAGGTGACTGAGCACCTCTACTGGCATTGCCCTAGGCTGCATCAAGTGTACAAGAGATGGGCTGGGAGCATCCATAGCAGACAGGCAATCATAAGATACTT----GAA -s Anc2.Anc2refChr13 81841 204 + 96486 ATCACCTTTTACCAAAGATCTTGTCCACCAACCAAACCTCAAGCCGTACTACTTTTGGATTCTTGAGGAACTCTGAGTGAAACCAAGAAAATTGCTGAGGGAGGTGACTGAGAACCTCAACTGGCATTGCCCTAGGCTGCATCAAGTGTACAAGAGATGGGCTGGGTGCATCCATAGCAGACAGGCAATCATAAGATACCT----GAA -s mr.mrrefChr3 8725 208 + 181027 ATCACCTCTTACCAAAGATCTTGTCCACCAACCAGACCTCCAGCCGTACTACTTTTGGATTCTTGAGGAACTCTGAGTGAAACCAAGAAAATTGCTGAGGGAGGTGACTGAGCACCTCTACTGGCATTGCCCTAAGCTGCATCAAATGTACAAGCGATGGGCTGGGAGCATCCATAGCAGACAGGCAATCATAAGGTACTTACTTGAA -s simCow_chr6.simCow.chr6 438305 204 + 602619 ATCATCTATTACCAAAAATCTTGTGCACCAACCAAACCTCAAGCCGTACCACTTTTGGATTCTTGAGGAACTCTGAGTGAAACCAAGAAAATTGCTGAGGGAGGTGACTGAGAACTTCCACTGGCATTGCCCTAGGCTGCATCAAGTGTACAAGAGATGGGCTAGGTGCATCCATAGCAGACAGGTAATCGTAAGATACCT----GAA -s simDog_chr6.simDog.chr6 430194 204 + 593897 GTCACCTTTTACCGAAGACCTTGTCCACCAACCAAACCTCAAGCCGTACTACTTTTGGATTCTTGAGGAACTCCAAGTGGAACCAAGAAAATTGCTGAGGGAGGTGACTGAGAACCTCAACTGGCATTGCCCTAGGCTGCATCGAATGTACGAGAGATGGACTGGGTGCATCCATAGCAGACAGGCAATCATAGGATACCT----AAA -s simHuman_chr6.simHuman.chr6 438538 204 + 601863 ATCACCTTTTACCAAAGATCTTGCCCACCAACCAAACCTTCAACCGTACTACTTTTGGATTCTTGAGGAACTCTGAGTGAAACCAAGAAAATTGCTGGGGGAGGTGACTGAGCACCTCTACTGGCATTGCCCTAGGCTGTGTCAAGTGTACAAGAGATGGGCTGGGAGCATCCATAGCAGACAGGCAATCATAAGAGACTT----GAA -s simRat_chr6.simRat.chr6 462554 202 + 647215 ATCACCTCTCACC------CTTGTCCACCAACCAGACCTCCAGCTGTACTACTTTTGGATTCTTGAGGAACTCTAAGTGAAACCAAGAAAACTGCTGAGGGAGGTGACTGAGCACCTCTACTGGCATTGCCCTAAGCTGCATCAAATGTACAAGTGGTGGGCCGGGAGCATCCATGGCAGACAGGCAGACATAAGGTACCTGCTTGAA - -a -s simMouse_chr6.simMouse.chr6 450670 4 + 636262 ACTT -s Anc0.Anc0refChr3 75768 3 + 222631 AC-T -s Anc1.Anc1refChr6 107536 4 + 197743 ACTT -s Anc2.Anc2refChr13 82045 3 + 96486 AC-T -s mr.mrrefChr3 8933 4 + 181027 ACTT -s simCow_chr6.simCow.chr6 438509 3 + 602619 AC-T -s simDog_chr6.simDog.chr6 430398 3 + 593897 AC-T -s simHuman_chr6.simHuman.chr6 438742 4 + 601863 AATT -s simRat_chr6.simRat.chr6 462759 4 + 647215 ACTT - -a -s simMouse_chr6.simMouse.chr6 450674 7 + 636262 CTCCTGG -s Anc0.Anc0refChr3 75771 6 + 222631 TGC-TGG -s Anc1.Anc1refChr6 107540 6 + 197743 TGC-TGG -s Anc2.Anc2refChr13 82048 6 + 96486 TGC-TGG -s mr.mrrefChr3 8937 7 + 181027 CGCCTGG -s simCow_chr6.simCow.chr6 438514 6 + 602619 TCC-TGG -s simDog_chr6.simDog.chr6 430401 3 + 593897 TGC---- -s simHuman_chr6.simHuman.chr6 438746 6 + 601863 TGC-TAG -s simRat_chr6.simRat.chr6 462763 7 + 647215 CGCCTGG - -a -s simMouse_chr6.simMouse.chr6 450681 18 + 636262 CCTGCAAGATTCAACTAC -s Anc0.Anc0refChr3 75784 18 + 222631 ACTTCAAAATCCAAGCAC -s Anc1.Anc1refChr6 107553 18 + 197743 ACTTCAAAATCCAAGCAC -s Anc2.Anc2refChr13 82061 18 + 96486 ACTTCAAAATCCAAGCAC -s mr.mrrefChr3 8951 18 + 181027 CCTGCAAGATTCAACTAC -s simCow_chr6.simCow.chr6 438527 18 + 602619 CCATCAAAACTGAAGCAG -s simDog_chr6.simDog.chr6 430411 18 + 593897 AGTTCAAAATCCAATCAC -s simHuman_chr6.simHuman.chr6 438759 18 + 601863 ACTTCAAAATCCAAGCAC -s simRat_chr6.simRat.chr6 462777 18 + 647215 CCTGTAATATTCGACTAC - -a -s simMouse_chr6.simMouse.chr6 450699 8 + 636262 TTCCCTAG -s Anc0.Anc0refChr3 75802 8 + 222631 GTCCCTAG -s Anc1.Anc1refChr6 107571 8 + 197743 GTCCCTAG -s Anc2.Anc2refChr13 82093 8 + 96486 GTCCCTAG -s mr.mrrefChr3 8969 8 + 181027 TTCCCTAG -s simCow_chr6.simCow.chr6 438559 8 + 602619 TGCCCTAA -s simDog_chr6.simDog.chr6 430443 8 + 593897 GTCCCTAG -s simHuman_chr6.simHuman.chr6 438777 5 + 601863 ACTGC--- -s simRat_chr6.simRat.chr6 462795 8 + 647215 TGCTCTAG - -a -s simMouse_chr6.simMouse.chr6 450707 25 + 636262 AAGTCCATCACAGTAGAACTGAGGA -s Anc0.Anc0refChr3 75810 25 + 222631 AAGTGCATGAAAGCTGGGCTGGGTG -s Anc1.Anc1refChr6 107579 25 + 197743 AAGTGCATGAAAGCTGGGCTGGGTG -s Anc2.Anc2refChr13 82109 25 + 96486 AAGTGCATGAAAGCTGGGCTGGGTG -s mr.mrrefChr3 8977 25 + 181027 AAGTGCATCACAGTAGAACTGAGGG -s simCow_chr6.simCow.chr6 438575 25 + 602619 AATTGACTGAGAGCTGGGCTGTGTG -s simDog_chr6.simDog.chr6 430459 25 + 593897 AAGTGCATGAAAGCTGGGCTGGGTG -s simRat_chr6.simRat.chr6 462803 25 + 647215 AAATGCATCATAGTACAACTTAGGG - -a -s simMouse_chr6.simMouse.chr6 450732 91 + 636262 ACATAAGCAGGCAGGGCCACTATAATATTATTGAGACTCCTGCTGCAATAGAAACTTTGCAATTAAGCAGTCTTGATGTGAGTGAAGTGTT -s Anc0.Anc0refChr3 75835 86 + 222631 ATCAAAGCAAGCAGGGCAATCATAAGATCCTTGAAAATTCTGCTGGAATAAGGAGTTTAAAATTGATTAATATTGGTGC-----TTGTATC -s Anc1.Anc1refChr6 107604 86 + 197743 ATCAAAGCAAGCAGGGCAATCATAAGATCCTTGAAAATTCTGCTGGAATAAGGAGTTTAAAATTGATTAATATTGGTGC-----TTGTATC -s Anc2.Anc2refChr13 82135 86 + 96486 ATCAAAGCAAGCAGGGCAATCATAAGATCCTTGAAAATTCTGCTGGAATAAGGAGTTTAAAATTGATTAATATTGGTGC-----TTGTATC -s mr.mrrefChr3 9002 86 + 181027 ATATAAGCAGGCAGGGCCACTATAAGATTATTGAGACTTCTGCTGCAATAGAGACTTTGCAATTAAGCAGTCTTGGTGT-----AAGTGTT -s simCow_chr6.simCow.chr6 438601 86 + 602619 ATCAAAGCAGGTAGGACAATCACAAGACTCTTGAAAATTAAGCTGGAGTAGAAACTTCAAAATTGGGGAGTCTTGGTGT-----TTGTATT -s simDog_chr6.simDog.chr6 430485 86 + 593897 ATCAAAGCAAGCAGGGCAATCATAAGATCCTTGAAAATTCTGCTGGAATAAGGAGTTTAAAATTGATTAATATTGGTGC-----TTGTATC -s simRat_chr6.simRat.chr6 462828 86 + 647215 ATATAAGCAGGCAGAACCACTAAAAGATTATCAAGACTTCTATTGCAATAGAGACGTCGCAATTAAGCAGAGTTGGTGT-----AAGTGTT - -a -s simMouse_chr6.simMouse.chr6 450823 84 + 636262 AGGTCTTTTGCTTAGTTGCTTTTAGCGTTGTGTCTTGGCCCTTATTCGCTTCATACAACCACAGAAACACAGTTTCAGCTATAC -s Anc0.Anc0refChr3 75921 55 + 222631 TGGGCTGT-GAATAGTTG---------TAGTGGCTAAGT--------------TACATCCATTGAGATACATTTTAGGC----- -s Anc1.Anc1refChr6 107690 55 + 197743 TGGGCTGT-GAATAGTTG---------TAGTGGCTAAGT--------------TACATCCATTGAGATACATTTTAGGC----- -s Anc2.Anc2refChr13 82221 55 + 96486 TGGGCTGT-GAATAGTTG---------TAGTGGCTAAGT--------------TACATCCATTGAGATACATTTTAGGC----- -s mr.mrrefChr3 9088 84 + 181027 AGGTCTTTTGCTTAGTTGCTTTTAGCGTTGTGTCTTGGCCCTTATTCGCTTCATACAACCACACAGACACATTTTCAGCTATAC -s simCow_chr6.simCow.chr6 438688 55 + 602619 TGAACCAG-GATAATCTG---------CAGTAACTAAGC--------------CACATCCATGGGGATTCATTTGGGGC----- -s simDog_chr6.simDog.chr6 430571 55 + 593897 TGGGCTGT-GAATAGTTG---------TAGTGGCTAAGT--------------TACATCCATTCAGATACTTTTTAGGC----- -s simRat_chr6.simRat.chr6 462914 83 + 647215 ATGTCTTGTGCACAGTCACTGTTAGTGTTATGTCTTG-CCCTTAGTTGCTTAGCACAACTACACAGACAGATTAACAGCTATAA - -a -s simMouse_chr6.simMouse.chr6 450907 53 + 636262 TAACACCATGTTTGTATGAGAATCCATTGTCTTCCAAGGGGAAGGACGTGTAT -s Anc0.Anc0refChr3 75976 51 + 222631 --ACACCATGCCTCTATGGGAGTCCATTATCTTCCAGAGTGAAACACTTATAT -s Anc1.Anc1refChr6 107745 51 + 197743 --ACACCATGCCTCTATGGGAGTCCATTATCTTCCAGAGTGAAACACTTATAT -s Anc2.Anc2refChr13 82276 51 + 96486 --ACACCATGCCTCTATGGGAGTCCATTATCTTCCAGAGTGAAACACTTATAT -s mr.mrrefChr3 9172 53 + 181027 TAACACCATGTCTGTATGAGAATCCATTGTCTTCCAAGGGGAAGCACTTGTAT -s simCow_chr6.simCow.chr6 438744 50 + 602619 --ACACCATACCTCAATGGGAGTCC-TTTTCTTCCAGAGTGAAACACTTACAT -s simDog_chr6.simDog.chr6 430626 51 + 593897 --AGACCATGCCTCTGTGGAAGTCCATTATCTCCCAGAGTGCAACACTTATGT -s simRat_chr6.simRat.chr6 462998 53 + 647215 TAACACCATGACTATATGACAATCCATTGTCTTCCAAGGGGAAGCACTTGTAA - -a -s simMouse_chr6.simMouse.chr6 450960 16 + 636262 TGAGTCTACTATTCAC -s Anc0.Anc0refChr3 76027 16 + 222631 GGAGTTTACTATTCAT -s Anc1.Anc1refChr6 107796 16 + 197743 GGAGTTTACTATTCAT -s Anc2.Anc2refChr13 82327 16 + 96486 GGAGTTTACTATTCAT -s mr.mrrefChr3 9225 16 + 181027 TGAGTCTACTATTCAT -s simCow_chr6.simCow.chr6 438794 16 + 602619 GGTGTTTCCTATTCAT -s simDog_chr6.simDog.chr6 430677 16 + 593897 GGAGTTTACTATTCAT -s simRat_chr6.simRat.chr6 463052 16 + 647215 TGAGTCTACTATTCAT - -a -s simMouse_chr6.simMouse.chr6 450976 8 + 636262 TGGGCTAG -s Anc0.Anc0refChr3 76043 8 + 222631 TGGGTTAG -s Anc1.Anc1refChr6 107812 8 + 197743 TGGGTTAG -s Anc2.Anc2refChr13 82343 8 + 96486 TGGGTTAG -s mr.mrrefChr3 9241 8 + 181027 TGGGCTAG -s simCow_chr6.simCow.chr6 438831 8 + 602619 TGGGTTAG -s simDog_chr6.simDog.chr6 430693 8 + 593897 TGGGTTAG -s simRat_chr6.simRat.chr6 463068 8 + 647215 TGGGCTAG - -a -s simMouse_chr6.simMouse.chr6 450984 4 + 636262 TGCC -s Anc0.Anc0refChr3 76052 4 + 222631 TTAC -s Anc1.Anc1refChr6 107821 4 + 197743 TTAC -s Anc2.Anc2refChr13 82352 4 + 96486 TTAC -s mr.mrrefChr3 9250 4 + 181027 TGCC -s simCow_chr6.simCow.chr6 438840 4 + 602619 CTCC -s simDog_chr6.simDog.chr6 430702 4 + 593897 TTAC -s simRat_chr6.simRat.chr6 463077 4 + 647215 TGCC - -a -s simMouse_chr6.simMouse.chr6 450988 4 + 636262 TGTG -s Anc0.Anc0refChr3 76056 4 + 222631 TATG -s Anc1.Anc1refChr6 107825 4 + 197743 TATG -s Anc2.Anc2refChr13 82356 4 + 96486 TGTG -s mr.mrrefChr3 9254 4 + 181027 TATG -s simCow_chr6.simCow.chr6 438848 4 + 602619 TGTG -s simDog_chr6.simDog.chr6 430706 4 + 593897 TATG -s simHuman_chr6.simHuman.chr6 438782 3 + 601863 -ATT -s simRat_chr6.simRat.chr6 463081 4 + 647215 TATA - -a -s simMouse_chr6.simMouse.chr6 450992 19 + 636262 TATGCATGTTTCAAACTTT -s Anc0.Anc0refChr3 76060 19 + 222631 TTTACATGTTGTAAATCAT -s Anc1.Anc1refChr6 107829 19 + 197743 TTTACATGTTGTAAATCAT -s Anc2.Anc2refChr13 82362 19 + 96486 TTTACATGTTGTAAATCAT -s mr.mrrefChr3 9258 19 + 181027 TTTACATGTTTCAAACTAT -s simCow_chr6.simCow.chr6 438854 19 + 602619 TTTACATGTTGTAAATCAT -s simDog_chr6.simDog.chr6 430712 19 + 593897 TTTACATGTTGTAAATCAT -s simHuman_chr6.simHuman.chr6 438785 19 + 601863 TTTATGCAATGTAAATCTT -s simRat_chr6.simRat.chr6 463085 19 + 647215 TTTACACATTTCAAACTAT - -a -s simMouse_chr6.simMouse.chr6 451011 6 + 636262 AATGCA -s Anc0.Anc0refChr3 76096 6 + 222631 AATGCA -s Anc1.Anc1refChr6 107865 6 + 197743 AATGCA -s Anc2.Anc2refChr13 82398 6 + 96486 AATGCA -s mr.mrrefChr3 9277 6 + 181027 AATGCA -s simCow_chr6.simCow.chr6 438895 6 + 602619 ATTGCA -s simDog_chr6.simDog.chr6 430754 6 + 593897 AATACA -s simHuman_chr6.simHuman.chr6 438821 6 + 601863 AATGCA -s simRat_chr6.simRat.chr6 463104 6 + 647215 AATGCA - -a -s simMouse_chr6.simMouse.chr6 451017 67 + 636262 TGTTCTAGTCTAACGTGCTACCCCTTTCTACAGGTCATCCCCTCGAGCAGATGAATACTATCTCTAT -s Anc0.Anc0refChr3 76110 65 + 222631 TGTTTCAGTTTGAAATGTTACGTTTCTCTGCAGGTCATCTACTCGAGAGAATAAATACCACCTCT-- -s Anc1.Anc1refChr6 107879 65 + 197743 TGTTTCAGTTTGAAATGTTACGTTTCTCTGCAGGTCATCTACTCGAGAGAATAAATACCACCTCT-- -s Anc2.Anc2refChr13 82412 65 + 96486 TGTTTCAGTTTGAAATGTTACGTTTCTCTGGAGGTGATCTACCTGAGAGAATAAACATCACCTCC-- -s mr.mrrefChr3 9283 67 + 181027 TGTTCTAGTTTAACTTGCTTTGCTTTTCTGCAGGTCATCCCCTCGAGCAGATGAATACTATCTCTAT -s simCow_chr6.simCow.chr6 438909 65 + 602619 TGTTTCAAGTCAAAATTTTACGCTTCTCTGTCAGCAACTTCCTTGAGAGAATAAACATCACCTCC-- -s simDog_chr6.simDog.chr6 430768 59 + 593897 TGTTT-AGTTTGAAGTG-----TTTCTCTGGAGGTGATCTACCTGAGAGGATAGGCATTACCTCC-- -s simHuman_chr6.simHuman.chr6 438835 63 + 601863 TGTTTCAGTATGCAATGTTGCCTTGCTCTGCTGGTCATCT--TCAAGAGAACAAATACCACCTCT-- -s simRat_chr6.simRat.chr6 463110 67 + 647215 TCTTCTAGTTTAGGTTGCTTTGCTTTTCTGCAGGTCAGCCCCTCGAGCAGATGAATACTATCTCTAT - -a -s simMouse_chr6.simMouse.chr6 451084 11 + 636262 TAATGGCTACA -s Anc0.Anc0refChr3 76175 6 + 222631 -----GCTACA -s Anc1.Anc1refChr6 107944 6 + 197743 -----GCTACA -s Anc2.Anc2refChr13 82477 6 + 96486 -----ACTACA -s mr.mrrefChr3 9350 11 + 181027 TAATGGCTACA -s simCow_chr6.simCow.chr6 438974 6 + 602619 -----ACTACA -s simDog_chr6.simDog.chr6 430827 6 + 593897 -----ACTACA -s simHuman_chr6.simHuman.chr6 438898 6 + 601863 -----GCTACA -s simRat_chr6.simRat.chr6 463192 11 + 647215 TAATGGCTACA - -a -s simMouse_chr6.simMouse.chr6 451095 64 + 636262 GGCAAGAACAGAAATTTATTAGGTGTAAGATCCGAGAGACATCTCTATGACTAGAGATCTCCAA -s Anc0.Anc0refChr3 76182 61 + 222631 GGGAACAA---AAGCTTATTAAATGGAAGATCCTATAGATAGCTGTTTGGCTATTAATCCCCAA -s Anc1.Anc1refChr6 107951 61 + 197743 GGGAACAA---AAGCTTATTAAATGGAAGATCCTATAGATAGCTGTTTGGCTATTAATCCCCAA -s Anc2.Anc2refChr13 82484 61 + 96486 GGGAACAA---CAACTTATTGAATGGAAAATCCTATAGATAGCTGTTTGGCTATTAATCCCCAA -s mr.mrrefChr3 9362 64 + 181027 GGCAACAACAGAAGCTTATTAGGTGTAAGATCCGAGAGACATCTCTATGACTACTAATCTACAA -s simCow_chr6.simCow.chr6 438981 61 + 602619 GAGAATGA---TGACTTATTGATAGCAAAATCCTATAGATATCTATTTGGTTTCTAATCCATAG -s simDog_chr6.simDog.chr6 430834 61 + 593897 GGGGGCAA---CAACTTATTGGATGGGAAATCCTATGGATAGCTGTTTGGCTATTAATCCCCAA -s simHuman_chr6.simHuman.chr6 438905 36 + 601863 GGGAACAA---AAGCTTATTAAATGGAAGCTCATATAGC------------------------- -s simRat_chr6.simRat.chr6 463204 47 + 647215 GGCAACAACAGAAGCTTACAA-----------------ACATTTCTATGACTACTAATCCACAA - -a -s simMouse_chr6.simMouse.chr6 451159 36 + 636262 GAACTATAATCTGCAGCTCTCAGCCAGCTCATACCT -s Anc0.Anc0refChr3 76243 31 + 222631 CGACTATAATCTGGAGCTCTCAGG----TCAAAC-C -s Anc1.Anc1refChr6 108012 31 + 197743 CGACTATAATCTGGAGCTCTCAGG----TCAAAC-C -s Anc2.Anc2refChr13 82545 31 + 96486 CGACTATAATCTGGAGCTCTCAGG----TCAAAC-C -s mr.mrrefChr3 9426 31 + 181027 GAACTATAATCTGCAGCTCTCAGC----TCATAC-T -s simCow_chr6.simCow.chr6 439043 31 + 602619 CAACTATAAGCTGGTGCTCTCAGG----TCAAAC-C -s simDog_chr6.simDog.chr6 430895 31 + 593897 CGACTATAATCCGGAGCTCTCAGG----TCAAAC-A -s simHuman_chr6.simHuman.chr6 438941 29 + 601863 --ACTATTACCTGAGGCTCTTCAG----TCAAAC-C -s simRat_chr6.simRat.chr6 463251 31 + 647215 GAACTATAATCTGCAGCTCTCAGC----TCATAC-T - -a -s simMouse_chr6.simMouse.chr6 451195 150 + 636262 CGGAGTCTGTACTATGCAATTACAGAACCCTGGTATAGGGCTGTGAAGATACTGTCATGTTAATTTCATTATTGTCATATCATGATGAACTAATCCCTGTGCTATCCATAGAAGTTAATAGGCTAGGCATAAATAAACAGATCTTGTTTT -s Anc0.Anc0refChr3 76288 146 + 222631 CAGATT---TACTATGAATCTGGAGAACCTTGGTATAGGTCAGATAAAATGTTGTCATGTTGTCCTCATTACTTTCATTTTA-TGTTAATTGATCCCTATTTTGTTCATAGTAGTTAATAGGCCACGAATAGATGCTCATAGCTTGTTTT -s Anc1.Anc1refChr6 108057 146 + 197743 CAGATT---TACTATGAATCTGGAGAACCTTGGTATAGGTCAGATAAAATGTTGTCATGTTGTCCTCATTACTTTCATTTTA-TGTTAATTGATCCCTATTTTGTTCATAGTAGTTAATAGGCCACGAATAGATGCTCATAGCTTGTTTT -s Anc2.Anc2refChr13 82590 146 + 96486 CAGCTA---TGCTATGAATCTGGAGAACCTTGGCATGGATCAGATAAAATGTTGTCATGTTGTCCTCATTATTTTTATTTTA-TGTTAATTGATCCCCAGTTTATTCATAGTAGTTAATAGGCCACGAATAGATGATCATAGTTTGTTTT -s mr.mrrefChr3 9457 150 + 181027 CGGATTCTGTACTATGAATTTACAGAACCCTGGTATAGGTCTGTGAAAATGTTGTCATGTTAATTTCATTACTGTCATATCATGATGAATTAATCCCTGTGCTGTCCATAGAAGTTAATAGGCTAGGCATAAATACACAGATCTTGTTTT -s simCow_chr6.simCow.chr6 439088 125 + 602619 CAGC-------------------AGAACCTTGGCATTGATCTAAGAAAATGTTGTCATGTTGTACTCACTATTTTTATTTTA-TGTGAAATGATCCACAGCTTATTCATAGCAGGTAATAGGCCAGGAATAGATGAT-----TTTGTTTA -s simDog_chr6.simDog.chr6 430940 143 + 593897 CAGCTA---TGCTATGAATCTGGAGAACCTTGGCCTG---CAGATAAAATGTTGTCATGTTATCCTCATTATTATTACTTTA-TGTTACTCGATCCCCGGTTTATTCATAGTAGTTAATGGGCCACGAATTGATGATCATAGTTTGTTTT -s simHuman_chr6.simHuman.chr6 438984 146 + 601863 CAGATT---TACAATGAATCTGGAGAACCTTGGTATAGGTCCGAAGAAATGTTGTCATGTTGTCCTCATTACTTTCATTTTA-ATTAAATTGATCCCTATAATGTTCATAGGAATTAATAGCCCAAGAATAGATGCTCATACCTTGTTTT -s simRat_chr6.simRat.chr6 463282 147 + 647215 CGGATTCTGTACTATGAATTTAAAGAACCCTGGTATAGGTCTGTGAAAATGTTGTCATGTTAAGTTTATTACTGTTGTATCATGATGAATCAATTCCTGTGCTGTCCATCGAAGTTAATAG---GGGCATAAATACACAGATCTTGTTCT - -a -s simMouse_chr6.simMouse.chr6 451345 3 + 636262 GGG -s Anc0.Anc0refChr3 76434 2 + 222631 -GG -s Anc1.Anc1refChr6 108203 3 + 197743 GGG -s Anc2.Anc2refChr13 82736 2 + 96486 -GG -s mr.mrrefChr3 9607 3 + 181027 GGG -s simCow_chr6.simCow.chr6 439213 2 + 602619 -GG -s simDog_chr6.simDog.chr6 431083 2 + 593897 -GA -s simHuman_chr6.simHuman.chr6 439131 3 + 601863 AGG -s simRat_chr6.simRat.chr6 463429 3 + 647215 GGG - -a -s simMouse_chr6.simMouse.chr6 451348 9 + 636262 TCTTAAGGT -s Anc0.Anc0refChr3 76436 9 + 222631 TCTTAAGAT -s Anc1.Anc1refChr6 108206 9 + 197743 TCTTAAGAT -s Anc2.Anc2refChr13 82738 9 + 96486 TCTTAAGAT -s mr.mrrefChr3 9610 9 + 181027 TCTTAAGAT -s simCow_chr6.simCow.chr6 439216 9 + 602619 TCTTGAGAC -s simDog_chr6.simDog.chr6 431085 9 + 593897 TCTTAAGAT -s simHuman_chr6.simHuman.chr6 439134 9 + 601863 TCTTAAAAT -s simRat_chr6.simRat.chr6 463432 9 + 647215 TCTTAGGAT - -a -s simMouse_chr6.simMouse.chr6 451357 31 + 636262 GTCAGATGGAGAAAACACTCTAAATCATTGC -s Anc0.Anc0refChr3 76449 24 + 222631 GTCCAATGCAGAAAAC-----CAATCATT-- -s Anc1.Anc1refChr6 108219 29 + 197743 GTCCAATGCAGAAAACACCATCAATCATT-- -s Anc2.Anc2refChr13 82753 24 + 96486 GTCCAATGCAGAAGAC-----CATTCATT-- -s mr.mrrefChr3 9619 29 + 181027 GTCAGATGGAGAAAACACTCTAAATCATT-- -s simCow_chr6.simCow.chr6 439231 23 + 602619 GTCCAAAGCA-AGGAA-----CATTCATT-- -s simDog_chr6.simDog.chr6 431100 24 + 593897 GTCCAATGTGGAAAAC-----CATTTATT-- -s simHuman_chr6.simHuman.chr6 439147 29 + 601863 GTCCAATGCAGATAAGACCATCAATCATT-- -s simRat_chr6.simRat.chr6 463441 29 + 647215 GTCAGATGGAGAAAACACTCTAAATCATT-- - -a -s simMouse_chr6.simMouse.chr6 451388 10 + 636262 CTACTTACCA -s Anc0.Anc0refChr3 76473 10 + 222631 CCCCTTAAAT -s Anc1.Anc1refChr6 108248 10 + 197743 CCCCTTAAAT -s Anc2.Anc2refChr13 82777 10 + 96486 CCCCTTAAAT -s mr.mrrefChr3 9648 10 + 181027 CTACTTACCT -s simCow_chr6.simCow.chr6 439254 10 + 602619 CCCCTCTAAG -s simDog_chr6.simDog.chr6 431124 10 + 593897 CCCCTTAAGT -s simHuman_chr6.simHuman.chr6 439177 10 + 601863 CCTCTTAAAT -s simRat_chr6.simRat.chr6 463470 10 + 647215 CTACTTACCT - -a -s simMouse_chr6.simMouse.chr6 451398 4 + 636262 TGGT -s Anc0.Anc0refChr3 76483 4 + 222631 TGGT -s Anc1.Anc1refChr6 108258 4 + 197743 TGGT -s Anc2.Anc2refChr13 82799 4 + 96486 TGGT -s mr.mrrefChr3 9658 4 + 181027 TGGT -s simCow_chr6.simCow.chr6 439276 4 + 602619 TTTT -s simDog_chr6.simDog.chr6 431146 4 + 593897 TGGT -s simHuman_chr6.simHuman.chr6 439187 4 + 601863 TAGG -s simRat_chr6.simRat.chr6 463480 4 + 647215 CGGT - -a -s simMouse_chr6.simMouse.chr6 451402 50 + 636262 GTTTTCCCTCAAGACAAGCGCAGTCAAGCGCAGTGGTATGCAAATAAATA -s Anc0.Anc0refChr3 76487 40 + 222631 GTTTTCCTTCAGAAGAAGCAC----------AGTTGAGTGCAAATAATTA -s Anc1.Anc1refChr6 108262 41 + 197743 GTTTTCCTTCAGAAGAAGCACA---------AGTTGAGTGCAAATAATTA -s Anc2.Anc2refChr13 82803 40 + 96486 GTTTGCCTTCAGAAGAAGCAC----------AGTTGAGTGCAAATAATTA -s mr.mrrefChr3 9662 41 + 181027 GTTTTCCCTCAAGACAAGCGCA---------AGTGGTATGCAAATAATTA -s simCow_chr6.simCow.chr6 439305 40 + 602619 GTTTCCTTTCAGAAGATGCAG----------AGTTGAGTGCAAATAATTA -s simDog_chr6.simDog.chr6 431150 40 + 593897 ATTTGCCTTCAGAAGAAAGAC----------AGTTGCATGCAAATAGTTA -s simHuman_chr6.simHuman.chr6 439191 41 + 601863 TGTTTCCTTCAGAAGAAGCACA---------AGTCCAGTATAAATAATTA -s simRat_chr6.simRat.chr6 463484 39 + 647215 GTTTTCCCTCAAGATAAGTGCA----------GTGGTATGCAAATAGT-A - -a -s simMouse_chr6.simMouse.chr6 451452 12 + 636262 CTGATAGGTTGA -s Anc0.Anc0refChr3 76527 12 + 222631 CTGATAGATTCA -s Anc1.Anc1refChr6 108303 12 + 197743 CTGATAGATTCA -s Anc2.Anc2refChr13 82843 12 + 96486 CTGATAGGTTCA -s mr.mrrefChr3 9703 12 + 181027 CTGATAGATTGA -s simCow_chr6.simCow.chr6 439373 12 + 602619 CTGACAGGTTCA -s simDog_chr6.simDog.chr6 431190 12 + 593897 CTGATAGGTCCA -s simHuman_chr6.simHuman.chr6 439232 12 + 601863 CTAATAGATTCA -s simRat_chr6.simRat.chr6 463523 12 + 647215 CTGATAGATTGA - -a -s simMouse_chr6.simMouse.chr6 451464 12 + 636262 TGGGAAGTGATG -s Anc0.Anc0refChr3 76564 12 + 222631 TGGGAAGTGTCC -s Anc1.Anc1refChr6 108340 12 + 197743 TGGGAAGTGTCC -s Anc2.Anc2refChr13 82880 12 + 96486 TGGGAAGTGTCC -s mr.mrrefChr3 9736 12 + 181027 TGGGAAGTGACG -s simCow_chr6.simCow.chr6 439414 12 + 602619 TGGGAAGTGTTC -s simDog_chr6.simDog.chr6 431227 12 + 593897 TGGGAAGTGTCC -s simHuman_chr6.simHuman.chr6 439269 12 + 601863 TGGGAAGTGTCC -s simRat_chr6.simRat.chr6 463556 12 + 647215 TGGGAAGTGACG - -a -s simMouse_chr6.simMouse.chr6 451476 22 + 636262 ACTAACTTGAGTCCAGGTAATG -s Anc0.Anc0refChr3 76576 1 + 222631 G--------------------- -s Anc1.Anc1refChr6 108352 1 + 197743 G--------------------- -s Anc2.Anc2refChr13 82892 1 + 96486 G--------------------- -s mr.mrrefChr3 9748 19 + 181027 ACTATCTTGA---CAGGTAATG -s simCow_chr6.simCow.chr6 439454 1 + 602619 G--------------------- -s simDog_chr6.simDog.chr6 431239 1 + 593897 A--------------------- -s simHuman_chr6.simHuman.chr6 439281 1 + 601863 G--------------------- -s simRat_chr6.simRat.chr6 463568 19 + 647215 ACTATCTTGA---CAGGGAATG - -a -s simMouse_chr6.simMouse.chr6 451498 126 + 636262 TCTTACTAGCCACAGTGAAGATTATCTTGAACCCAGCTAATTATTATATGTCTTACTAGTCACTGTACTAGTGGAAACCGGACCAGTTGGGATTCCTAGATATGGGTCAGGTGGTCCCTGTATGCA -s Anc0.Anc0refChr3 76577 96 + 222631 ---------------------TTTTCTTGTACCCACGTAATTGTGAAATGTCCTATTAGTCACTGTACTAGGGGAAGCAAGGCCAGT-GT--------GATATAGGTTGGGTGGGCCCTGTGTGCA -s Anc1.Anc1refChr6 108353 104 + 197743 ---------------------TTTTCTTGTACCCACGTAATTGTGAAATGTCCTATTAGTCACTGTACTAGGGGAAGCAAGGCCAGT-GTCATTCCTAGATATAGGTTGGGTGGGCCCTGTGTGCA -s Anc2.Anc2refChr13 82893 96 + 96486 ---------------------TTTTCTCATACCCACGTAATTGTGGAATGTCCTATCAGTCACTGTACTAGTGGAAGCAAGGCCAGT-AT--------GGTATAGGTTGGGTGGGCGCTGTGTGCA -s mr.mrrefChr3 9767 126 + 181027 TCTTACTAGCCACAGTGAAGATTATCTTGAACCCAGGTAATTATTAAATGTCTTACTAGTCACTGTACTAGGGGAAGCCGGACCAGTTGGGATTCCTAGATATGGGTCAGGTGGTCCCTGTATGCA -s simCow_chr6.simCow.chr6 439455 96 + 602619 ---------------------TTTTCTCATACCCACGTAATTGTGGAATGTCCTATCAGCCACTATACTAGTGGAAGCAGGGCCAGT-AT--------GGTATAGGTTGCATAGGTACTGTGAGCA -s simDog_chr6.simDog.chr6 431240 65 + 593897 ---------------------GTTCCTC-------------------------------TTACTGAACTAGTGGCAGCAAGGCCAGT-AT--------GGTATAGGTTGGGTGGGCGTAGTGTGCA -s simHuman_chr6.simHuman.chr6 439282 104 + 601863 ---------------------TTTTTTTGTACACATGTAATGGTGAAACGTCCTATTAGTCACTGTAGTAGGGGAAGTTAGGCCAAT-GTCATTCCTAGATATATGTTGGGTGGGGCCTGTGTGCA -s simRat_chr6.simRat.chr6 463595 100 + 647215 CCACACTAGCCACAGTGATGACTATCCTGAACCCAGGCAATTATTAAATGTCTTACTAGTCACTGTACTAGGGGAAGCCTAACCAGTTGGGATTCCTAGA-------------------------- - -a -s simMouse_chr6.simMouse.chr6 451624 20 + 636262 TTTTCATATTCAATAGTTCA -s Anc0.Anc0refChr3 76673 20 + 222631 TTTCCATACTCAATAATTCA -s Anc1.Anc1refChr6 108457 20 + 197743 TTTCCATACTCAATAATTCA -s Anc2.Anc2refChr13 82989 20 + 96486 TTTCCATGCTCAATAACTCA -s mr.mrrefChr3 9893 20 + 181027 TTTTCATATTCAATAGTTCA -s simCow_chr6.simCow.chr6 439551 20 + 602619 TTTCCATGCCCAATAAATCA -s simDog_chr6.simDog.chr6 431306 20 + 593897 TTTCCATGCTTAATAACTCA -s simHuman_chr6.simHuman.chr6 439386 20 + 601863 TATCAATACTCAATAATTCA - -a -s simMouse_chr6.simMouse.chr6 451644 20 + 636262 CATGCGAATGCTCTGTGGAA -s Anc0.Anc0refChr3 76693 20 + 222631 TGTGAGAATGCTCTTTGGAA -s Anc1.Anc1refChr6 108477 20 + 197743 TGTGAGAATGCTCTTTGGAA -s Anc2.Anc2refChr13 83009 20 + 96486 TGTCAGGATGCTTTTTGGGA -s mr.mrrefChr3 9913 20 + 181027 CATGCGAATGCTCTGTGGAA -s simCow_chr6.simCow.chr6 439571 20 + 602619 TGTCAGGATGCTTTTTGGGA -s simDog_chr6.simDog.chr6 431326 18 + 593897 TGCCAGGATGCTTT--GGGA -s simHuman_chr6.simHuman.chr6 439407 20 + 601863 TGTGAGAATGCTCTCGGGAA - -a -s simMouse_chr6.simMouse.chr6 451664 27 + 636262 GCTAATGAGCGATACTGTCTTCTGGTA -s Anc0.Anc0refChr3 76718 27 + 222631 ACTAACAAACAGTACTGTCTTCTGGTA -s Anc1.Anc1refChr6 108502 27 + 197743 ACTAACAAACAGTACTGTCTTCTGGTA -s Anc2.Anc2refChr13 83034 27 + 96486 ACAAACAAACAGTATTGTGTTCTGGCA -s mr.mrrefChr3 9933 27 + 181027 GCTAATGAGCGATACTGTCTTCTGGTA -s simCow_chr6.simCow.chr6 439596 27 + 602619 GCAAACAAACAGTTTCACATTCTGGCA -s simDog_chr6.simDog.chr6 431349 17 + 593897 AC----------TATTGTGTTCTGGCA -s simHuman_chr6.simHuman.chr6 439432 27 + 601863 ACTAACAAACAGTACTGTCTTCTGGTA - -a -s simMouse_chr6.simMouse.chr6 451691 2 + 636262 CT -s Anc0.Anc0refChr3 76746 2 + 222631 CT -s Anc1.Anc1refChr6 108530 2 + 197743 CT -s Anc2.Anc2refChr13 83062 2 + 96486 CT -s mr.mrrefChr3 9960 2 + 181027 CT -s simCow_chr6.simCow.chr6 439624 2 + 602619 CT -s simDog_chr6.simDog.chr6 431367 2 + 593897 CT -s simHuman_chr6.simHuman.chr6 439460 2 + 601863 CT - -a -s simMouse_chr6.simMouse.chr6 451693 49 + 636262 GGTCGGCCTTTGGTTGGGACAACCATTAATCATCAACACAAGCTTTTGA -s Anc0.Anc0refChr3 76748 45 + 222631 TATC----TTTGGTTGGGACAACCACTAATTAACAGTACAGCCTTCTGG -s Anc1.Anc1refChr6 108532 45 + 197743 TATC----TTTGGTTGGGACAACCACTAATTAACAGTACAGCCTTCTGG -s Anc2.Anc2refChr13 83064 45 + 96486 TATC----TTTGGTTGGGACAACCGCTAATTAACAGTACAGCCTTCTGG -s mr.mrrefChr3 9962 45 + 181027 GGTC----TTTGGTTGGGACAACCATTAATCATCAACACAAGCTTTTGA -s simCow_chr6.simCow.chr6 439653 45 + 602619 TATC----TTTGGTTAGGACAACTGCTAATAAACATCACAGGATTCTGG -s simDog_chr6.simDog.chr6 431369 45 + 593897 TATC----TTTGGTTGGGACAACCGCTAAGTAACAGTACAACCTTCTGG -s simHuman_chr6.simHuman.chr6 439462 43 + 601863 TATC----TCTGGTTGGGACAACCAATAGTA--CAGTATAGACTTCTGG - -a -s simMouse_chr6.simMouse.chr6 451742 9 + 636262 GTACATTCT -s Anc0.Anc0refChr3 76804 9 + 222631 ATACATTCC -s Anc1.Anc1refChr6 108588 9 + 197743 ATACATTCC -s Anc2.Anc2refChr13 83120 9 + 96486 ATACATTCC -s mr.mrrefChr3 10007 9 + 181027 GTACATTCT -s simCow_chr6.simCow.chr6 439710 9 + 602619 ATACAGTCC -s simDog_chr6.simDog.chr6 431425 9 + 593897 ACACATGCC -s simHuman_chr6.simHuman.chr6 439516 9 + 601863 ATACATTCC - -a -s simMouse_chr6.simMouse.chr6 451751 50 + 636262 AAAAACTCAACTTTCCTATCTAGTGTGAATGTTGTTGAACTCCTGTTTTG -s Anc0.Anc0refChr3 76822 45 + 222631 CAGAACTCAACTTAC-----TAGTTTTAAGGTCATAGCACTCCCCTATTG -s Anc1.Anc1refChr6 108606 45 + 197743 CAGAACTCAACTTAC-----TAGTTTTAAGGTCATAGCACTCCCCTATTG -s Anc2.Anc2refChr13 83138 45 + 96486 CAGAACTCAACTTAT-----TAGTTTTGAGGCCATAGCACTCCCCAATTG -s mr.mrrefChr3 10016 45 + 181027 AAAAACTCAACTTTC-----TAGTGTGAATGTTGTTGAACTCCTGTTTTG -s simCow_chr6.simCow.chr6 439728 45 + 602619 CAGAACACAACTGCT-----AAGTTTTGAGGCCATAGCACTCCCAAATCG -s simDog_chr6.simDog.chr6 431438 42 + 593897 --GAACTCCACTTA------TAAAGCTGAGGCCATAGCACTCACCAATTG -s simHuman_chr6.simHuman.chr6 439534 45 + 601863 CAGAACTCAACTTAC-----TAGTTTCAAGATCATAGCACTCCCCTATTG - -a -s simMouse_chr6.simMouse.chr6 451801 9 + 636262 TTAATGGTT -s Anc0.Anc0refChr3 76881 9 + 222631 CTAATGATT -s Anc1.Anc1refChr6 108665 9 + 197743 CTAATGATT -s Anc2.Anc2refChr13 83197 9 + 96486 CTAATGAAT -s mr.mrrefChr3 10061 9 + 181027 TTAATGGTT -s simCow_chr6.simCow.chr6 439787 9 + 602619 CTAATAAGT -s simDog_chr6.simDog.chr6 431494 9 + 593897 TTAGTGAAC -s simHuman_chr6.simHuman.chr6 439593 9 + 601863 CTAATGATT - -a -s simMouse_chr6.simMouse.chr6 451810 16 + 636262 CAAAAACAGCCTTCCC -s Anc0.Anc0refChr3 76891 16 + 222631 CAAACATTGCCTACTA -s Anc1.Anc1refChr6 108675 16 + 197743 CAAACATTGCCTACTA -s Anc2.Anc2refChr13 83207 16 + 96486 CAAACATTGCCTACTA -s mr.mrrefChr3 10070 16 + 181027 CAAAAACAGCCTTCCC -s simCow_chr6.simCow.chr6 439797 16 + 602619 CAAACTTTGCCTACCA -s simDog_chr6.simDog.chr6 431504 16 + 593897 CAAACATTGCCTACTA -s simHuman_chr6.simHuman.chr6 439603 16 + 601863 CAAACATTGCCTGCGG - -a -s simMouse_chr6.simMouse.chr6 451826 12 + 636262 TTGGTTTAAATA -s Anc0.Anc0refChr3 76907 12 + 222631 TTTTTTTAATAG -s Anc1.Anc1refChr6 108691 12 + 197743 TTTTTTTAATAG -s Anc2.Anc2refChr13 83223 12 + 96486 TTTTTTTGATAG -s mr.mrrefChr3 10086 12 + 181027 TTGGTTTAAATA -s simCow_chr6.simCow.chr6 439813 12 + 602619 TTTTGGTGAAAC -s simDog_chr6.simDog.chr6 431520 12 + 593897 TTTTTTTGATAG -s simHuman_chr6.simHuman.chr6 439620 12 + 601863 TTTTGTTAATGG - -a -s simMouse_chr6.simMouse.chr6 451838 18 + 636262 AATCATTATGAGGTATTG -s Anc0.Anc0refChr3 76924 10 + 222631 GATTATT-------CTT- -s Anc1.Anc1refChr6 108708 10 + 197743 GATTATT-------CTT- -s Anc2.Anc2refChr13 83240 10 + 96486 GATTACT-------CTT- -s mr.mrrefChr3 10103 18 + 181027 AATCATTATGAGGTATTG -s simCow_chr6.simCow.chr6 439830 10 + 602619 TATTAGT-------CTT- -s simDog_chr6.simDog.chr6 431537 10 + 593897 GATTGCT-------CTT- -s simHuman_chr6.simHuman.chr6 439637 10 + 601863 GAGAATC-------CTT- -s simRat_chr6.simRat.chr6 463724 18 + 647215 AATCATGATGAGGTTTTG - -a -s simMouse_chr6.simMouse.chr6 451856 7 + 636262 CCCACAA -s Anc0.Anc0refChr3 76934 7 + 222631 CCCTTAA -s Anc1.Anc1refChr6 108718 7 + 197743 CCCTTAA -s Anc2.Anc2refChr13 83250 7 + 96486 CCCTTAA -s mr.mrrefChr3 10121 7 + 181027 CCCACAA -s simCow_chr6.simCow.chr6 439840 7 + 602619 CCATTCA -s simDog_chr6.simDog.chr6 431549 7 + 593897 TCCTCAA -s simHuman_chr6.simHuman.chr6 439647 7 + 601863 CCCTTTA -s simRat_chr6.simRat.chr6 463742 7 + 647215 CCCACAA - -a -s simMouse_chr6.simMouse.chr6 451863 10 + 636262 ATCAAATGCT -s Anc0.Anc0refChr3 76942 5 + 222631 AT-----GTT -s Anc1.Anc1refChr6 108726 5 + 197743 AT-----GTT -s Anc2.Anc2refChr13 83258 5 + 96486 AG-----GTT -s mr.mrrefChr3 10128 5 + 181027 AT-----GCT -s simCow_chr6.simCow.chr6 439848 5 + 602619 AG-----GTT -s simDog_chr6.simDog.chr6 431557 5 + 593897 GG-----TTT -s simHuman_chr6.simHuman.chr6 439655 5 + 601863 AT-----GTT -s simRat_chr6.simRat.chr6 463749 5 + 647215 AT-----ACT - -a -s simMouse_chr6.simMouse.chr6 451873 26 + 636262 AATGGGTTGACTTAGGGGGGCTACTG -s Anc0.Anc0refChr3 76949 26 + 222631 AATATATCATTACCGAGCAGCTAGAG -s Anc1.Anc1refChr6 108733 26 + 197743 AATATATCATTACCGAGCAGCTAGAG -s Anc2.Anc2refChr13 83265 26 + 96486 AATATATCATTACCAAGCAGCTAGAA -s mr.mrrefChr3 10133 26 + 181027 AATGGGTTGACTTAGGGGGGCTACTG -s simCow_chr6.simCow.chr6 439855 26 + 602619 CATATGTCAATACCAAGCTGCTAGAA -s simDog_chr6.simDog.chr6 431564 26 + 593897 AACATATCATTACCAAGTAGCTAGAA -s simHuman_chr6.simHuman.chr6 439662 26 + 601863 GATATACCATTGCTGAGCAGCTAGAG -s simRat_chr6.simRat.chr6 463754 26 + 647215 AATGGGTTGACTTAGGGGGCCTACTG - -a -s simMouse_chr6.simMouse.chr6 451899 58 + 636262 CCACAAATATCAGTGGGGTGACATACGGGGACTGGTGTAAGCCCCCTCGTAGACCAAG -s Anc0.Anc0refChr3 76979 58 + 222631 CCACAAATATTAGTAGGTTGACATAGGGGGTCTAGTGTGAGCCCCCCTGTGGACCAAG -s Anc1.Anc1refChr6 108763 58 + 197743 CCACAAATATTAGTAGGTTGACATAGGGGGTCTAGTGTGAGCCCCCCTGTGGACCAAG -s Anc2.Anc2refChr13 83295 58 + 96486 CCACAAATACTAGTGGGTTGACATAGAGGGTCTTGTGTGAGCCCCCCTGTGAACCAAG -s mr.mrrefChr3 10159 58 + 181027 CCACAAATATCAGTAGGGTGACATACGGGGACTAGTGTAAGCCCCCTTGTAGACCAAG -s simCow_chr6.simCow.chr6 439885 58 + 602619 CTACAGACTCCAATGGGTTGACATAGAGGGACTTGTGTGAGCCCCCCTTTGAACCAAG -s simDog_chr6.simDog.chr6 431594 58 + 593897 CCAAAAATACTAGTGGGTTAACAAAGAGGGTTTTGTGTGAGCCCCTGTGTGAACCAAG -s simHuman_chr6.simHuman.chr6 439692 58 + 601863 CCACAAATATTGGTAGACTGACGTTGGGGGGCTAGTGTGGGCCTTCCTGTGGACCAGG -s simRat_chr6.simRat.chr6 463780 58 + 647215 TCGCAAATATCAGTAGGGTGACATATAGGCACTACTGTTAGCCCCCTTGTAGACCAAG - -a -s simMouse_chr6.simMouse.chr6 451957 4 + 636262 ATAA -s Anc0.Anc0refChr3 77037 4 + 222631 AAAA -s Anc1.Anc1refChr6 108821 4 + 197743 AAAA -s Anc2.Anc2refChr13 83353 4 + 96486 AAAA -s mr.mrrefChr3 10217 4 + 181027 ATAA -s simCow_chr6.simCow.chr6 439943 4 + 602619 AACA -s simDog_chr6.simDog.chr6 431652 4 + 593897 AAAA -s simHuman_chr6.simHuman.chr6 439751 4 + 601863 AAAA -s simRat_chr6.simRat.chr6 463838 4 + 647215 ATAA - -a -s simMouse_chr6.simMouse.chr6 451961 17 + 636262 CAGATTGCTATAAAATG -s Anc0.Anc0refChr3 77044 17 + 222631 CACATCGGTACATAATG -s Anc1.Anc1refChr6 108828 17 + 197743 CACATCGGTACATAATG -s Anc2.Anc2refChr13 83360 17 + 96486 CACCTCTGTACATAATG -s mr.mrrefChr3 10224 17 + 181027 CAGATTGCTATAAAATG -s simCow_chr6.simCow.chr6 439950 17 + 602619 TACCTCTGTACATAATG -s simDog_chr6.simDog.chr6 431659 17 + 593897 CACCTCTTTACATAATG -s simHuman_chr6.simHuman.chr6 439758 16 + 601863 CACATCG-TACATAATG -s simRat_chr6.simRat.chr6 463845 17 + 647215 CAGATTGCTATAAAATG - -a -s simMouse_chr6.simMouse.chr6 451978 3 + 636262 CAT -s Anc0.Anc0refChr3 77061 2 + 222631 TA- -s Anc1.Anc1refChr6 108845 2 + 197743 TA- -s Anc2.Anc2refChr13 83377 2 + 96486 TA- -s mr.mrrefChr3 10241 3 + 181027 CAT -s simCow_chr6.simCow.chr6 439967 2 + 602619 TA- -s simDog_chr6.simDog.chr6 431683 2 + 593897 CA- -s simHuman_chr6.simHuman.chr6 439774 2 + 601863 TG- -s simRat_chr6.simRat.chr6 463862 3 + 647215 CAT - -a -s simMouse_chr6.simMouse.chr6 451981 7 + 636262 GTGATAT -s Anc0.Anc0refChr3 77063 7 + 222631 GTGATGC -s Anc1.Anc1refChr6 108847 7 + 197743 GTGATGC -s Anc2.Anc2refChr13 83379 7 + 96486 GTGATAC -s mr.mrrefChr3 10244 7 + 181027 GTGATGT -s simCow_chr6.simCow.chr6 439970 7 + 602619 GTGATAC -s simDog_chr6.simDog.chr6 431685 7 + 593897 GGGTCAC -s simHuman_chr6.simHuman.chr6 439776 7 + 601863 GTGATGC -s simRat_chr6.simRat.chr6 463865 7 + 647215 GTGATGT - -a -s simMouse_chr6.simMouse.chr6 451988 69 + 636262 TCATACTATACCAGTATTCGAGGTGTCTCCCAAATCCTATGTTCCCTTTTTGATCTAAGCTCCTGTCTC -s Anc0.Anc0refChr3 77071 69 + 222631 TTATAATGCACCAGTATACAACATTTCTTCCTAACTCCCTGTTCTCTATCTGTTGTAATTTCCTGTCCA -s Anc1.Anc1refChr6 108855 69 + 197743 TTATAATGCACCAGTATACAACATTTCTTCCTAACTCCCTGTTCTCTATCTGTTGTAATTTCCTGTCCA -s Anc2.Anc2refChr13 83387 69 + 96486 TTATAATGCACTTGTATACAACATTTCATCCTCACTCCCTGTTCTCTATCTGTTGTAATTTCCTGTCCA -s mr.mrrefChr3 10251 69 + 181027 TCATACTATACCAGTATTCAAGGTGTCTCCCTAACTCTATGTTCCCTTTTTGATCTAAGCTCCTGTCTC -s simCow_chr6.simCow.chr6 439978 69 + 602619 TTATAATGCATTTGTATTTAACATTACAGCCTCACTCTCTGTTCTCTATCTGTTGTGATTCCCTGGCCA -s simDog_chr6.simDog.chr6 431693 69 + 593897 TTGTAATGCACTTGTATACAATGTTTCATCCCCACTCCCTGTTCTATATTTGCTGTAATTTCCTGTTCA -s simHuman_chr6.simHuman.chr6 439784 62 + 601863 TTATAATGCACCAACA-------TCGCTTGCTAACTCCCTGTTTTCTATCTGTTGTAATTTCCTGTCCA -s simRat_chr6.simRat.chr6 463872 69 + 647215 TCATACTATACCAGTACTCAAGGTGTCTCCCTAACTCTATGTTCCCATTTTGATCTAAGCTTCTGTCTC - -a -s simMouse_chr6.simMouse.chr6 452057 11 + 636262 CCTGTAATCAG -s Anc0.Anc0refChr3 77140 11 + 222631 CCTGTAGTCCT -s Anc1.Anc1refChr6 108924 11 + 197743 CCTGTAGTCCT -s Anc2.Anc2refChr13 83465 11 + 96486 CCTGTGGTGCT -s mr.mrrefChr3 10320 11 + 181027 CCTGTAATCCT -s simCow_chr6.simCow.chr6 440069 11 + 602619 CCTGTGGTGCT -s simDog_chr6.simDog.chr6 431771 11 + 593897 TCTGTGGTGTT -s simHuman_chr6.simHuman.chr6 439846 11 + 601863 CCTATAGTCCC -s simRat_chr6.simRat.chr6 463941 11 + 647215 CCTGTACTCCT - -a -s simMouse_chr6.simMouse.chr6 452068 27 + 636262 CCTGCCCCAGTTTCCCTAGTGTATCAC -s Anc0.Anc0refChr3 77154 21 + 222631 ------GCGCCTCCCCTAGTGCGCCAA -s Anc1.Anc1refChr6 108938 21 + 197743 ------GCGCCTCCCCTAGTGCGCCAA -s Anc2.Anc2refChr13 83479 21 + 96486 ------GCGCCTCCCCTGGTGCGCCAA -s mr.mrrefChr3 10334 27 + 181027 CCTGCCCCAGCTTCCCCAGTGTATCAA -s simCow_chr6.simCow.chr6 440083 21 + 602619 ------GGGCCCTCCTTGGCGTGCCGA -s simDog_chr6.simDog.chr6 431785 21 + 593897 ------GCGCCTCCCCTGGTGCGCCAA -s simHuman_chr6.simHuman.chr6 439860 21 + 601863 ------GAGCCTCCCCTAGTGCGCCAA -s simRat_chr6.simRat.chr6 463955 27 + 647215 CCTTCCCCAGCTTCCCCAGTGTATCAA - -a -s simMouse_chr6.simMouse.chr6 452095 26 + 636262 CCAAGAATTGGATAACCTGGATAAAT -s Anc0.Anc0refChr3 77176 10 + 222631 C----------------TGAACAAAT -s Anc1.Anc1refChr6 108960 26 + 197743 CTGAGAATTGAAAAGGTTGAACAAAT -s Anc2.Anc2refChr13 83501 10 + 96486 C----------------TAAACAAAT -s mr.mrrefChr3 10361 26 + 181027 CCAAGAATTGAATAACCTGAATAAAT -s simCow_chr6.simCow.chr6 440105 10 + 602619 C----------------TAAACAAAG -s simDog_chr6.simDog.chr6 431807 10 + 593897 C----------------TAAACAAAT -s simHuman_chr6.simHuman.chr6 439882 26 + 601863 CTGAGAATTGAAAAGGTTGAGCAAAT -s simRat_chr6.simRat.chr6 463982 26 + 647215 CCAAGAATTGAATCACCTAAATAAAT - -a -s simMouse_chr6.simMouse.chr6 452121 7 + 636262 TGCACGA -s Anc0.Anc0refChr3 77188 6 + 222631 TGCA-GA -s Anc1.Anc1refChr6 108988 6 + 197743 TGCA-GA -s Anc2.Anc2refChr13 83513 6 + 96486 TGCA-AA -s mr.mrrefChr3 10387 7 + 181027 TGCACGA -s simCow_chr6.simCow.chr6 440117 6 + 602619 TGCA-AA -s simDog_chr6.simDog.chr6 431819 6 + 593897 TGCA-AA -s simHuman_chr6.simHuman.chr6 439910 6 + 601863 TGCA-GA -s simRat_chr6.simRat.chr6 464008 7 + 647215 TGCACGA - -a -s simMouse_chr6.simMouse.chr6 452128 64 + 636262 TTTCTGTGTATAGCTGGAAACCAGTATATTCATGGTTCACCTGCACTGGTGAGGCATTTTCCAT -s Anc0.Anc0refChr3 77194 35 + 222631 TTTTTGGATATTGCTG-----------------------------CTCTTGAACCTTTTTCTAT -s Anc1.Anc1refChr6 108994 35 + 197743 TTTTTGGATATTGCTG-----------------------------CTCTTGAACCTTTTTCTAT -s Anc2.Anc2refChr13 83519 35 + 96486 TTTTTGGATATTGCTG-----------------------------CACTTGAACCTTGTTCTAT -s mr.mrrefChr3 10394 64 + 181027 TTTCTGTGTATAGCTGGAAACCAGTATATTTATGGTTCACCTGCATTGGTGAACCATTTTCCAT -s simCow_chr6.simCow.chr6 440124 34 + 602619 TTTTTGGATATTGCTG-----------------------------TGCTTG-ACCTTGTTCCAT -s simDog_chr6.simDog.chr6 431825 35 + 593897 GTTTTGGATATTGCTG-----------------------------CACTGGAGCCTTGTTTTGC -s simHuman_chr6.simHuman.chr6 439916 35 + 601863 TTTTTGGATATTGCTG-----------------------------CTCTTGAACCTTTTTCTAT -s simRat_chr6.simRat.chr6 464015 64 + 647215 TTTCTGTGTGTAGCTGGAAACCAATATATTTATGGTTCACCTGCATTGGTGAACCATTCTCAAT - -a -s simMouse_chr6.simMouse.chr6 452192 5 + 636262 AAGTA -s Anc0.Anc0refChr3 77235 2 + 222631 AA--- -s Anc1.Anc1refChr6 109035 5 + 197743 AAGTA -s Anc2.Anc2refChr13 83560 2 + 96486 AA--- -s mr.mrrefChr3 10458 5 + 181027 AAGTA -s simCow_chr6.simCow.chr6 440164 2 + 602619 TA--- -s simDog_chr6.simDog.chr6 431866 2 + 593897 AA--- -s simHuman_chr6.simHuman.chr6 439957 5 + 601863 AAGTA -s simRat_chr6.simRat.chr6 464079 5 + 647215 AAGTA - -a -s simMouse_chr6.simMouse.chr6 452197 9 + 636262 TGTACACCG -s Anc0.Anc0refChr3 77237 6 + 222631 ---GCAATG -s Anc1.Anc1refChr6 109040 9 + 197743 CATGCAATG -s Anc2.Anc2refChr13 83562 6 + 96486 ---GCAATG -s mr.mrrefChr3 10463 9 + 181027 TGTACACCA -s simCow_chr6.simCow.chr6 440166 5 + 602619 ----CAGTA -s simDog_chr6.simDog.chr6 431868 6 + 593897 ---GCAATG -s simHuman_chr6.simHuman.chr6 439963 9 + 601863 CATGCAATG -s simRat_chr6.simRat.chr6 464084 9 + 647215 TGTACACCA - -a -s simMouse_chr6.simMouse.chr6 452206 41 + 636262 GGAAACTAATGGAATTCCGGGAAACTGATGGAATTTCTTTT -s Anc0.Anc0refChr3 77243 23 + 222631 GCATACTAATGGAA------------------TTACATAGT -s Anc1.Anc1refChr6 109049 23 + 197743 GCATACTAATGGAA------------------TTACATAGT -s Anc2.Anc2refChr13 83568 23 + 96486 GCATACTAATGGAA------------------TTACATAGT -s mr.mrrefChr3 10472 23 + 181027 GCAAAGTAATGGAA------------------ATTTCTTTT -s simCow_chr6.simCow.chr6 440171 23 + 602619 GCATACAAGTGGAA------------------GTACATACT -s simDog_chr6.simDog.chr6 431875 23 + 593897 GCATACTAATGGAA------------------TTACATAGT -s simHuman_chr6.simHuman.chr6 439972 23 + 601863 GCGTACTAAGGGAA------------------TTACATCAT -s simRat_chr6.simRat.chr6 464093 23 + 647215 GCAAAGTAATGGAA------------------ATTTCTCAT - -a -s simMouse_chr6.simMouse.chr6 452247 7 + 636262 TGTGTGA -s Anc0.Anc0refChr3 77302 7 + 222631 TGTGAGA -s Anc1.Anc1refChr6 109108 7 + 197743 TGTGAGA -s Anc2.Anc2refChr13 83627 7 + 96486 TGTGAGA -s mr.mrrefChr3 10495 7 + 181027 TGTGTGA -s simCow_chr6.simCow.chr6 440230 4 + 602619 TT---GA -s simDog_chr6.simDog.chr6 431934 7 + 593897 AGTGAGA -s simHuman_chr6.simHuman.chr6 440031 7 + 601863 TGTGAGA -s simRat_chr6.simRat.chr6 464116 7 + 647215 TGTGTGT - -a -s simMouse_chr6.simMouse.chr6 452254 18 + 636262 TATGAACTGTAGACCCCC -s Anc0.Anc0refChr3 77309 18 + 222631 TGTGAAGTGTAGACCCCC -s Anc1.Anc1refChr6 109115 18 + 197743 TGTGAAGTGTAGACCCCC -s Anc2.Anc2refChr13 83634 18 + 96486 TGTCAAATGCAGACCCCC -s mr.mrrefChr3 10502 18 + 181027 TGTGAAGTGTAGACCCCC -s simCow_chr6.simCow.chr6 440234 18 + 602619 TGTAGAATGTCGATCCCC -s simDog_chr6.simDog.chr6 431941 18 + 593897 TGTCAAATGCAGACCCCC -s simHuman_chr6.simHuman.chr6 440039 13 + 601863 TGTGAGGTGTGAA----- -s simRat_chr6.simRat.chr6 464123 18 + 647215 TGTGAAGTGTAGACCCCA - -a -s simMouse_chr6.simMouse.chr6 452272 92 + 636262 GTAGCAAGTACAGAGAGTAGAAGGTATTACTGCGCTTGGGTTTGTGGACTAGAAATGACAATCAGGGATGATCATTGTCCCTTGAAGAGTTG -s Anc0.Anc0refChr3 77327 91 + 222631 GTGAAAAGCACAGGGTGTAGAAG-TATTACAATATTTGGGTGTGTGGACTTGCAATGACAGTCAGTGCTCATCATTGCCATTTGCAAAATTG -s Anc1.Anc1refChr6 109133 91 + 197743 GTGAAAAGCACAGGGTGTAGAAG-TATTACAATATTTGGGTGTGTGGACTTGCAATGACAGTCAGTGCTCATCATTGCCATTTGCAAAATTG -s Anc2.Anc2refChr13 83660 91 + 96486 GTGAAGAACACAGGGTGTAGAAG-TATTGCAATAATTGGATGTGAGTACTTGCAATGACAGACAGTGCTCATCATTGCCATTTGCAAAATTG -s mr.mrrefChr3 10520 92 + 181027 GTGGCAAGTACAGAGAGTAGAAGGTATTACTGTGTTTGGGTTTGTGGACTTGAAATGACAATCAGGGATGATCATTGTCCCTTGAAGAGTTG -s simCow_chr6.simCow.chr6 440260 83 + 602619 GTGAAGAATGCAATGTGTAGAAG-TACTGCAATAATTGGATGTAC-------CACTGACAGACAGTGCTCATTTATGAT-TTTGTGAAATTT -s simDog_chr6.simDog.chr6 431967 91 + 593897 GTGAAGAACACAGGGTGTAGAAG-TATTGTGATAACTGGATGTGAGTACTTGCAAGGATAGACAATGCTCATCATTGCCATTTGCAAAATTG -s simHuman_chr6.simHuman.chr6 440052 83 + 601863 -----AAGCACTGGGTGTAGAAG-TATTACAATATTTAGGTGCGTGGTTTTGCA-TGACAGTCAGA-CTTATCGTTACCATTTGGAAAAT-G -s simRat_chr6.simRat.chr6 464141 90 + 647215 GAGGTAAGTACAGAAAGTAGATGGTATCAGTGTGTTTGGGTTTGTGGACTTGAAATGACAATCACGAA-GATCATTGTCTCCAGA-GAGTTG - -a -s simMouse_chr6.simMouse.chr6 452364 24 + 636262 ACCAGTATTTCCACAACTCTTGCC -s Anc0.Anc0refChr3 77418 24 + 222631 AGTAGTATTACCACTACTATAGCC -s Anc1.Anc1refChr6 109224 24 + 197743 AGTAGTATTACCACTACTATAGCC -s Anc2.Anc2refChr13 83754 24 + 96486 AGTACTATTACCACTACTATAGCC -s mr.mrrefChr3 10612 24 + 181027 AGCAGTATTTCCACAACTCTTGCC -s simCow_chr6.simCow.chr6 440346 20 + 602619 ----ATATTTCCACTATTATAGCC -s simDog_chr6.simDog.chr6 432061 24 + 593897 AGTACTATCACCACTGCTATAGCC -s simHuman_chr6.simHuman.chr6 440135 24 + 601863 AGTAGTATTCCCACTACTATAGCC -s simRat_chr6.simRat.chr6 464231 24 + 647215 AGCAGTATTTTAACAAGTCTTGCC - -a -s simMouse_chr6.simMouse.chr6 452388 16 + 636262 ACAGTGATAATTGGCT -s Anc0.Anc0refChr3 77443 16 + 222631 GCATCAACTGTTAGCT -s Anc1.Anc1refChr6 109249 16 + 197743 GCATCAACTGTTAGCT -s Anc2.Anc2refChr13 83779 16 + 96486 GCATCAACTGTTAGCA -s mr.mrrefChr3 10636 16 + 181027 ATAGTGATAATTGGCT -s simCow_chr6.simCow.chr6 440367 16 + 602619 GCATCAACTAGTAGCA -s simDog_chr6.simDog.chr6 432086 16 + 593897 GCCTGAGCTGTTAGCA -s simHuman_chr6.simHuman.chr6 440160 16 + 601863 GCATCAACTGTTCCCT -s simRat_chr6.simRat.chr6 464255 16 + 647215 ATAGTGGCAATTGGCT - -a -s simMouse_chr6.simMouse.chr6 452404 96 + 636262 GTGCTTAGAACTACTACTCTTTGTCAAGAGTACAACACCATTAAACTTATGCATGTCTTAACATTGATCCTTACTAGGACATGTTATTTAATTTGT -s Anc0.Anc0refChr3 77459 84 + 222631 GTG-ATGGTAGTGCTACTCTATGACAAGAGTACAACTCTGTTAGGAATATGCACTTCTTAACATTGATTATTACTAAAATGAGTT----------- -s Anc1.Anc1refChr6 109265 96 + 197743 GTGCATGGTAGTGCTACTCTATGACAAGAGTACAACTCTGTTAGGAATATGCACTTCTTAACATTGATTATTACTAAAATGAGTTATGGTATGTCC -s Anc2.Anc2refChr13 83795 84 + 96486 GTG-ATGGTAGTGCCACTCTATTATAAAGGTACAACTTTGTTAGGAATATGCACTTCTTAACATTGATTATTACTAAAATGAGGT----------- -s mr.mrrefChr3 10652 96 + 181027 GTGCTCAGCAGTGCTACTCTATGTCAAGAGTACAACTCCATTAAAAATATGCATGTCTTAACATTGATCATTACTAGGACATGTTATTGAATTTGC -s simCow_chr6.simCow.chr6 440384 84 + 602619 GTA-ATGCTAGTGCCATCCTATCGTATCGGTACAACTTTGTTAAGAATATACACCTCTTAACATTGATAATTGCTAAAATGAGAG----------- -s simDog_chr6.simDog.chr6 432102 83 + 593897 ATG-ATGGTAGTGCCACTCTATTATAAAGGTACAACTTTGTTAGGAAGATGCGCTTCTAAACATTGA-TATGACTAAAATGAGGT----------- -s simHuman_chr6.simHuman.chr6 440176 94 + 601863 G--CATGGTAGCGCTACTCTATGCCAAGAGTACACCTCTGTTATGAATATGCAATTCTTAATGTTGAGTATTACTCAAATGAATTATGGTATGTCC -s simRat_chr6.simRat.chr6 464271 96 + 647215 GCCCTCAACAGTGCTACTCCATGTCAAGAGTGCAACTCCATTAAAAATATGCATGTCTTAACAATCATAATTACCAGGACTCGTTATTGAATTTGC - -a -s simMouse_chr6.simMouse.chr6 452500 22 + 636262 CATTTTGCAGGTGGAGTAATGA -s Anc1.Anc1refChr6 109362 22 + 197743 AACTTTGTAGATATAGAATTGA -s mr.mrrefChr3 10749 22 + 181027 AATTTTGCAGGTGTAGTAATGA -s simHuman_chr6.simHuman.chr6 440271 22 + 601863 AACTTTGTAGATATAGAATTGA -s simRat_chr6.simRat.chr6 464368 22 + 647215 AATTTTGCAGGTGTAGTAATGA - -a -s simMouse_chr6.simMouse.chr6 452522 108 + 636262 AACTAGCTTGCATACGAAGGGACTTGTTTCCTTGTTAAAACAGGAGCAAAGCTGTGGACTTCATTGATCAAATCAGTATAACAACAGGAACAGGGATGTGAATTCTAC -s Anc1.Anc1refChr6 109384 65 + 197743 GATTAGCATGTGTGTGGGGGAATTGATATCTTTGTTAAAACAGGA-CAGAGATGCAAAT------------------------------------------ATTGTAC -s mr.mrrefChr3 10771 108 + 181027 AACTAGCTTGCATATGAAGGGACTTGTTTCCTTGTTAAAACAGGAGCAGAGCTGTGAATTTCATTGATCAAATCAGTATAACAACAGGAACAGGGATGTGAATTCTAC -s simHuman_chr6.simHuman.chr6 440298 65 + 601863 GATTAGCATGTGTGTGGGGGAATTGATATCTTTGTTAAAACAGGA-CAGAGATGCAAAT------------------------------------------ATTGTAC -s simRat_chr6.simRat.chr6 464390 108 + 647215 AACTAGCTTGCTTATGAAGGGACCTGTTTCCTTGTTAAAACAGGAGCAGAGCTGTGAATTTTATTGATTAAATCAGTATAGCAACAGGAACAGGGATGTGAATTCTAC - -a -s simMouse_chr6.simMouse.chr6 452630 102 + 636262 ATACATGGGTTCAATCAAAGTAAGAGCCTACATTTTATACACATGAGCACAATTTTCACTCAATACCAATGTCAATGGTCATGTCAAGATGCCTGGTCTTGC -s Anc1.Anc1refChr6 109449 85 + 197743 ATACATAAGCTCAATCAGAAACACAGCATAAATTCTATATACATGAGCTCAA-T----------------GTCAATGTTCATGATTTGCTGTCTTGTCTTGC -s mr.mrrefChr3 10879 101 + 181027 ATACATGGGTTCAATCAAAGTAAGAGCCTACATTTTATACACATGAGCTCAA-TTTCACTCAATACCAATGTCAATGGTCATGTCAAGATGCCTGGTCTTGC -s simHuman_chr6.simHuman.chr6 440363 85 + 601863 ATACATAAGCTCAATCAGAAACACAGCATAAATTCTATATACATGAGCTCAA-T----------------GTCAATGTTCATGATTTGCTGTCTTGTCTTGC -s simRat_chr6.simRat.chr6 464511 101 + 647215 ATACATGGGTCCAATCAAAGGAAGAGCCTACATTTTATAGACATGAGCTCAA-TAACGCTCAATACAAACATTAATGCTCATGTCAAGATGCCTGGACTTGC - -a -s simMouse_chr6.simMouse.chr6 452732 9 + 636262 TGATTGGTT -s Anc1.Anc1refChr6 109534 9 + 197743 AGACTGATT -s mr.mrrefChr3 10980 9 + 181027 TGATTGGTT -s simHuman_chr6.simHuman.chr6 440448 9 + 601863 AGACTGATT -s simRat_chr6.simRat.chr6 464613 9 + 647215 TGATTGATT - -a -s simMouse_chr6.simMouse.chr6 452741 3 + 636262 CAG -s Anc1.Anc1refChr6 109543 3 + 197743 CAG -s mr.mrrefChr3 10989 3 + 181027 CAG -s simHuman_chr6.simHuman.chr6 440461 3 + 601863 CAG -s simRat_chr6.simRat.chr6 464622 3 + 647215 CAG - -a -s simMouse_chr6.simMouse.chr6 452744 4 + 636262 CTGA -s Anc1.Anc1refChr6 109546 4 + 197743 CTGA -s mr.mrrefChr3 10992 4 + 181027 CTGA -s simHuman_chr6.simHuman.chr6 440466 4 + 601863 CTGA -s simRat_chr6.simRat.chr6 464625 4 + 647215 CTAA - -a -s simMouse_chr6.simMouse.chr6 452748 62 + 636262 AAGAGGTGTAGTGTTTAGAAAATCCTCTTAACAGAAGGCACCATATCCATAATAAATCAATA -s Anc1.Anc1refChr6 109550 62 + 197743 ATGAGGAGTACCAGGTAGAAGATCCCCTTAATGGATGATATGTTATCCTTAATCAATCAACA -s mr.mrrefChr3 10996 62 + 181027 AAGAGGTGTAGTGTTTAGAAAATCCTCTTAATGGATGGCATGTTATCCTTAATAAATCAATA -s simHuman_chr6.simHuman.chr6 440472 62 + 601863 ATGAGGAGTACCAGGTAGAAGATCCCCTTAATGGATGATATGTTATCCTTAATCAATCAACA -s simRat_chr6.simRat.chr6 464629 62 + 647215 AAGAGGTGTAATGTTTAGAAAAACCTCTTAATGGATGGAATGTTATCCTTAAAAAATTAATA - -a -s simMouse_chr6.simMouse.chr6 452810 4 + 636262 AAGT -s Anc1.Anc1refChr6 109612 4 + 197743 AACT -s mr.mrrefChr3 11058 4 + 181027 AAGT -s simHuman_chr6.simHuman.chr6 440534 4 + 601863 AACT -s simRat_chr6.simRat.chr6 464692 4 + 647215 AAGT - -a -s simMouse_chr6.simMouse.chr6 452814 46 + 636262 GGCACATCAAACAAGAACCATATAATTCCAAAGAGTGGCAATCCTG -s Anc1.Anc1refChr6 109618 46 + 197743 GGCACATAATATGAGCACCACACAAATATAGAGGGTGGTACTCAGG -s mr.mrrefChr3 11064 46 + 181027 GGCACATCAAACAAGAACCATATAATTCCAAAGAGTGGCAATCCTG -s simHuman_chr6.simHuman.chr6 440540 46 + 601863 GGCACATAATATGAGCACCACACAAATATAGAGGGTGGTACTCAGG -s simRat_chr6.simRat.chr6 464698 46 + 647215 GGCACATCAAACTAGAGCCATATAAGTGCAACGAGTGGCAATCCTG - -a -s simMouse_chr6.simMouse.chr6 452860 34 + 636262 TGATAACCAGAGACAATGGGGGTGTCTATAGCCT -s Anc0.Anc0refChr3 77543 27 + 222631 ----AGAGGGCGCAGATGGGCCTG---TCACCCC -s Anc1.Anc1refChr6 109664 34 + 197743 TGCAAGAGGGCGCAGATGGGCCTGTCATCACCCC -s Anc2.Anc2refChr13 83879 27 + 96486 ----AGTGGGCGCAGATGAGCCTG---TAACCCC -s mr.mrrefChr3 11110 34 + 181027 TGATAGCCAGAGACAATGGGGCTGTCTACAGCCT -s simCow_chr6.simCow.chr6 440468 27 + 602619 ----AGTGGGCGCAGATGAGCTTG---TAACCCC -s simDog_chr6.simDog.chr6 432185 22 + 593897 ----AGTGGGCACAGATGAGACTG--------CC -s simHuman_chr6.simHuman.chr6 440619 34 + 601863 TGCAAGAGGGTGTAGATGGGCCTGTCATCACCCC -s simRat_chr6.simRat.chr6 464744 34 + 647215 TGATAGCCTGCGACAATAGGGCTGTCTACAGCTT - -a -s simMouse_chr6.simMouse.chr6 452894 10 + 636262 GGCAGTGTAT -s Anc0.Anc0refChr3 77571 4 + 222631 GGCA------ -s Anc1.Anc1refChr6 109699 10 + 197743 GGCACCTTAC -s Anc2.Anc2refChr13 83907 4 + 96486 GTCA------ -s mr.mrrefChr3 11144 10 + 181027 GGCAGTGTAT -s simCow_chr6.simCow.chr6 440496 4 + 602619 GACA------ -s simDog_chr6.simDog.chr6 432208 4 + 593897 GTCA------ -s simHuman_chr6.simHuman.chr6 440654 10 + 601863 GGCACCTTAC -s simRat_chr6.simRat.chr6 464778 9 + 647215 -GCAGTGTAT - -a -s simMouse_chr6.simMouse.chr6 452904 38 + 636262 TCCCAGGTGCAGCATCAAGGTTTCTATAATCTCAGTAA -s Anc0.Anc0refChr3 77575 32 + 222631 TGTCAAAAAC-----CAGGTTAAGTGTGTCCT-AGTAG -s Anc1.Anc1refChr6 109709 34 + 197743 TGTCAAAAAC---ATCAGGTTAAGTGTGTCCT-AGTAG -s Anc2.Anc2refChr13 83911 32 + 96486 TGTCAAAAAC-----CAGGTTAAGTGTGTCCC-AGTAG -s mr.mrrefChr3 11154 38 + 181027 TCCCAGATACAGCATCAAGGTTTCTATAATCTCAGTAG -s simCow_chr6.simCow.chr6 440508 32 + 602619 TGTCAAAAAC-----TAGGTTAAGAGTGTCCC-AGTAT -s simDog_chr6.simDog.chr6 432212 32 + 593897 TGTCAAAAGC-----CAGGTTGGGTGTCTCCC-AGTAG -s simHuman_chr6.simHuman.chr6 440664 33 + 601863 TGTCAAAAA----ATAAGGTTAAATGTGGCCT-AGTAG -s simRat_chr6.simRat.chr6 464787 38 + 647215 TCCCAGATACAGCACCAAGGTTTCTATAATCGCAGTAG - -a -s simMouse_chr6.simMouse.chr6 452942 2 + 636262 TT -s Anc0.Anc0refChr3 77616 2 + 222631 TA -s Anc1.Anc1refChr6 109752 2 + 197743 TA -s Anc2.Anc2refChr13 83953 2 + 96486 AA -s mr.mrrefChr3 11194 2 + 181027 TT -s simCow_chr6.simCow.chr6 440550 2 + 602619 AA -s simDog_chr6.simDog.chr6 432254 2 + 593897 AA -s simHuman_chr6.simHuman.chr6 440706 2 + 601863 TA -s simRat_chr6.simRat.chr6 464827 2 + 647215 TT - -a -s simMouse_chr6.simMouse.chr6 452944 4 + 636262 ATTT -s Anc0.Anc0refChr3 77618 4 + 222631 ATTT -s Anc1.Anc1refChr6 109754 4 + 197743 ATTT -s Anc2.Anc2refChr13 83955 4 + 96486 GGTT -s mr.mrrefChr3 11196 4 + 181027 ATTT -s simCow_chr6.simCow.chr6 440552 4 + 602619 GGTT -s simDog_chr6.simDog.chr6 432257 4 + 593897 GGTT -s simHuman_chr6.simHuman.chr6 440708 4 + 601863 ATTT -s simRat_chr6.simRat.chr6 464829 4 + 647215 ATTT - -a -s simMouse_chr6.simMouse.chr6 452948 4 + 636262 TAAA -s Anc0.Anc0refChr3 77622 4 + 222631 TGAA -s Anc1.Anc1refChr6 109758 4 + 197743 TGAA -s Anc2.Anc2refChr13 83977 4 + 96486 TGAA -s mr.mrrefChr3 11200 4 + 181027 TAAA -s simCow_chr6.simCow.chr6 440579 4 + 602619 TAAA -s simDog_chr6.simDog.chr6 432279 4 + 593897 TGAA -s simHuman_chr6.simHuman.chr6 440712 4 + 601863 TGGA -s simRat_chr6.simRat.chr6 464833 4 + 647215 TAAA - -a -s simMouse_chr6.simMouse.chr6 452952 30 + 636262 TTGGAACACATGTGGTGGAGTAAAATGTAA -s Anc0.Anc0refChr3 77626 29 + 222631 CAG-AACAAATGTAGTAAAGTATAATGTAA -s Anc1.Anc1refChr6 109762 29 + 197743 CAG-AACAAATGTAGTAAAGTATAATGTAA -s Anc2.Anc2refChr13 83981 29 + 96486 CAG-AGCAAATGTAGTAAAGTATAGTGTAA -s mr.mrrefChr3 11204 30 + 181027 TTGGAAAACATGTGGTGAAGTAAAATGTAA -s simCow_chr6.simCow.chr6 440583 29 + 602619 TAG-AGCAAATGGAGTAAAGTATAGTATAA -s simDog_chr6.simDog.chr6 432286 29 + 593897 CAG-AGCAAGTTTTCAAAAGTATAGTGTAG -s simHuman_chr6.simHuman.chr6 440716 29 + 601863 CAG-CACAAATGTAGTAAAGTACAATGTAA -s simRat_chr6.simRat.chr6 464837 30 + 647215 TTGGAAAACATGTGGTGAAGTAAAGTGTAA - -a -s simMouse_chr6.simMouse.chr6 452982 30 + 636262 ACATGTCCTCCTGATCCCTGGCCTTTGCAG -s Anc0.Anc0refChr3 77658 30 + 222631 ATATGCCCTCCTATTCCCTGGATTTTGCAG -s Anc1.Anc1refChr6 109794 30 + 197743 ATATGCCCTCCTATTCCCTGGATTTTGCAG -s Anc2.Anc2refChr13 84013 30 + 96486 GTATGCTCTCCTGTTCCCTGGATTTTTTAG -s mr.mrrefChr3 11234 30 + 181027 ACATGTCCTCCTAATCCCTGGCCTTTGCAG -s simCow_chr6.simCow.chr6 440615 20 + 602619 GTATGCTCTCCTGTTCCCTG---------- -s simDog_chr6.simDog.chr6 432318 30 + 593897 GTATGCTATCCTGTTCCATGGATTTTTTAG -s simHuman_chr6.simHuman.chr6 440748 30 + 601863 ATGTGCCCTCCCACTCCCTGGAATTCGCAG -s simRat_chr6.simRat.chr6 464867 30 + 647215 ACCTGATCTCCTAATTCTTGGCCTTTGCAG - -a -s simMouse_chr6.simMouse.chr6 453012 23 + 636262 AAAATGTTGTCATGATGATATCC -s Anc0.Anc0refChr3 77688 21 + 222631 AT--TTTTGTTGAGATGATATGA -s Anc1.Anc1refChr6 109824 21 + 197743 AT--TTTTGTTGAGATGATATGA -s Anc2.Anc2refChr13 84043 21 + 96486 AT--CTCTGTTGACAGAATATGA -s mr.mrrefChr3 11264 23 + 181027 AAAATGTTGTCATGATGATATCC -s simCow_chr6.simCow.chr6 440635 14 + 602619 ---------TTGACACAATCAGA -s simDog_chr6.simDog.chr6 432350 21 + 593897 AT--CTCTGCTGACAGAATATGA -s simHuman_chr6.simHuman.chr6 440778 21 + 601863 AT--TTTTATTGAGATGATAAAA -s simRat_chr6.simRat.chr6 464897 23 + 647215 AAAATCTTGTCATGATGGTACCC - -a -s simMouse_chr6.simMouse.chr6 453035 16 + 636262 TTGACACCTATATCAG -s Anc0.Anc0refChr3 77709 14 + 222631 GACACACTTCTG--TG -s Anc1.Anc1refChr6 109845 14 + 197743 GACACACTTCTG--TG -s Anc2.Anc2refChr13 84065 14 + 96486 GACACTCATCTG--TG -s mr.mrrefChr3 11287 16 + 181027 TTGACACTTATATCAG -s simCow_chr6.simCow.chr6 440650 14 + 602619 GGCACCCATCTG--TG -s simDog_chr6.simDog.chr6 432372 14 + 593897 GACACTTATCTG--TG -s simHuman_chr6.simHuman.chr6 440799 14 + 601863 GACACACTTCAG--TG -s simRat_chr6.simRat.chr6 464920 16 + 647215 TTGACACTTATATCAG - -a -s simMouse_chr6.simMouse.chr6 453051 8 + 636262 TATCAGTT -s Anc0.Anc0refChr3 77724 8 + 222631 TATCTGGT -s Anc1.Anc1refChr6 109860 8 + 197743 TATCTGGT -s Anc2.Anc2refChr13 84080 8 + 96486 CATCTGGT -s mr.mrrefChr3 11304 8 + 181027 TATCAGGT -s simCow_chr6.simCow.chr6 440665 8 + 602619 GATCTGGT -s simDog_chr6.simDog.chr6 432387 8 + 593897 CATCCAGT -s simHuman_chr6.simHuman.chr6 440814 8 + 601863 TACCTGGT -s simRat_chr6.simRat.chr6 464937 8 + 647215 TATCAGGT - -a -s simMouse_chr6.simMouse.chr6 453059 58 + 636262 TTTGGAGGTTTCACTCCAATGAGAACCTATAATAGTTCCTTTCTTCCAAATACACTGA -s Anc0.Anc0refChr3 77732 58 + 222631 TTTGGAGGTCACACTCCAATAAGAAGATATGCTAGTTTCTTACACCCAAATGCACTGA -s Anc1.Anc1refChr6 109868 58 + 197743 TTTGGAGGTCACACTCCAATAAGAAGATATGCTAGTTTCTTACACCCAAATGCACTGA -s Anc2.Anc2refChr13 84088 58 + 96486 CGTGGAGGTCACACTCTATTAAGAAGATATACTAGTTTCTTACACCCAAATGCACTGA -s mr.mrrefChr3 11312 58 + 181027 TTTGGAGGTTTCACTCCAATGAGAACCTATGCTAGTTCCTTTCTTCCAAATACACTGA -s simCow_chr6.simCow.chr6 440673 58 + 602619 CGTGGAGGTCTCACCCAAATAAGAAGATATATTAAATTCTTACACCCAAACGGACTGA -s simDog_chr6.simDog.chr6 432395 58 + 593897 CGTGGAGGTCACACTCTATTAAGAAGATATACTAGTTTCTTACACCCAGATGCACTGA -s simHuman_chr6.simHuman.chr6 440822 51 + 601863 TTTGGAGGT-------CAATAAGAAGAGATGCTAGTTTCTTACACCCAAATGTACTGA -s simRat_chr6.simRat.chr6 464947 58 + 647215 TTTGGAAATTTTACTCCAATGAGAACCTATGCTAGTTCCTTTCTTCCAAATACACTGA - -a -s simMouse_chr6.simMouse.chr6 453117 2 + 636262 AG -s Anc0.Anc0refChr3 77818 2 + 222631 AA -s Anc1.Anc1refChr6 109955 2 + 197743 AA -s Anc2.Anc2refChr13 84174 2 + 96486 AA -s mr.mrrefChr3 11397 2 + 181027 AG -s simCow_chr6.simCow.chr6 440759 2 + 602619 AA -s simHuman_chr6.simHuman.chr6 440905 2 + 601863 AA -s simRat_chr6.simRat.chr6 465032 2 + 647215 AG - -a -s simMouse_chr6.simMouse.chr6 453119 29 + 636262 TAACCGTGAGTATAACTAATCGGGGTGAG -s Anc0.Anc0refChr3 77820 27 + 222631 AAAATCTGAGGGTAACTGATGGGGGAG-- -s Anc1.Anc1refChr6 109957 29 + 197743 AAAATCTGAGGGTAACTGATGGGGGAGAA -s Anc2.Anc2refChr13 84177 27 + 96486 AAAATCTGAGGGTAGCTGATGGGACAG-- -s mr.mrrefChr3 11399 29 + 181027 AAATCGTGAGTGTAACTGATCGGGGTGAG -s simCow_chr6.simCow.chr6 440771 27 + 602619 AGAATCTAAGGGTGGCTGATGGGACAG-- -s simDog_chr6.simDog.chr6 432478 25 + 593897 AAAATCCGAGGGCAGTTGATGGT--AG-- -s simHuman_chr6.simHuman.chr6 440907 29 + 601863 AAAGGTTGAGGGTAACTGATGGGGGAGAA -s simRat_chr6.simRat.chr6 465034 29 + 647215 AAATCCTGAGTGTAACTGATCAGGGTGCG - -a -s simMouse_chr6.simMouse.chr6 453148 85 + 636262 TGAATTAGACATTACATCCATACACATTTACCCAGCCTATACAATAAACTCCCCGTAAAAACTGCAACAAAAATGAAGCCTTTGA -s Anc0.Anc0refChr3 77847 42 + 222631 -------AACCTGATA---GTACATGTTTACCTGGCCTATACGACAGAGT---------------------------------GC -s Anc1.Anc1refChr6 109986 49 + 197743 TGATTTAAACCTGATA---GTACATGTTTACCTGGCCTATACGACAGAGT---------------------------------GC -s Anc2.Anc2refChr13 84204 42 + 96486 -------AAACTGATA---GTACATGTTTACCCAGTCTATATGACAGAGT---------------------------------GC -s mr.mrrefChr3 11428 85 + 181027 TGGATTAGACATTACATCCATACATATTTACCTGGCCTATACAATAAACTCCCCCTAAAAACTGCAACAAAAATGAAGCCTTTGA -s simCow_chr6.simCow.chr6 440798 42 + 602619 -------AAACTGACA---GTGAATGTTTACCCAGTCTATATGAGAGAGT---------------------------------GC -s simDog_chr6.simDog.chr6 432503 42 + 593897 -------AAACTGATA---GTACAAGTCCACCCAGTCTATATGACAGGGC---------------------------------GC -s simHuman_chr6.simHuman.chr6 440985 49 + 601863 TGATTTAAACCGGATA---GTACTTGTTTACCTGGCCTATGCCACAGAAT---------------------------------GC -s simRat_chr6.simRat.chr6 465063 83 + 647215 TGGACTAGACATTACATCCATGCATATTTA--TGGCCTATACAATAACCTCCCCCTAAAAACTGCAACAAAAATGAAGCCTTTGA - -a -s simMouse_chr6.simMouse.chr6 453233 1 + 636262 A -s Anc0.Anc0refChr3 77889 1 + 222631 A -s Anc1.Anc1refChr6 110035 1 + 197743 A -s Anc2.Anc2refChr13 84252 1 + 96486 A -s mr.mrrefChr3 11513 1 + 181027 A -s simCow_chr6.simCow.chr6 440846 1 + 602619 A -s simDog_chr6.simDog.chr6 432551 1 + 593897 A -s simHuman_chr6.simHuman.chr6 441034 1 + 601863 A -s simRat_chr6.simRat.chr6 465147 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 453234 35 + 636262 AACTGTCAGACAAATGAAATTGCTTATCAGTAGTC -s Anc0.Anc0refChr3 77890 33 + 222631 AACTTTAACACAAATGAA--GGCTTGTTAGTAGTT -s Anc1.Anc1refChr6 110036 33 + 197743 AACTTTAACACAAATGAA--GGCTTGTTAGTAGTT -s Anc2.Anc2refChr13 84253 33 + 96486 AACTTTAACACAAATGAA--GGCTTGTTACTAGTT -s mr.mrrefChr3 11514 35 + 181027 AACTGTAAGACAAATGAAATGGCTTGTCAGTAGTC -s simCow_chr6.simCow.chr6 440849 33 + 602619 AACTTTCATACAAATGAA--GTCTTGTTACTAGTT -s simDog_chr6.simDog.chr6 432552 33 + 593897 TCCTTTAACTCAAATGAA--GGCTTGTTACTAGTT -s simHuman_chr6.simHuman.chr6 441035 33 + 601863 AACTTTAACACGAATGAA--GGTCTGTTGGTAGTG -s simRat_chr6.simRat.chr6 465148 35 + 647215 AACCATAATACAAATGAACTGGCTTGTCATTAGTT - -a -s simMouse_chr6.simMouse.chr6 453269 5 + 636262 AAATA -s Anc0.Anc0refChr3 77923 5 + 222631 GTACA -s Anc1.Anc1refChr6 110069 5 + 197743 GTACA -s Anc2.Anc2refChr13 84286 5 + 96486 GTACA -s mr.mrrefChr3 11549 5 + 181027 GAATA -s simCow_chr6.simCow.chr6 440915 5 + 602619 GAACA -s simDog_chr6.simDog.chr6 432585 5 + 593897 GTATA -s simHuman_chr6.simHuman.chr6 441068 5 + 601863 GTACA -s simRat_chr6.simRat.chr6 465183 5 + 647215 GAATA - -a -s simMouse_chr6.simMouse.chr6 453274 42 + 636262 AGCCTAACCAATGCAAAAAATATCCACAGGTCACTTGAAGCG -s Anc0.Anc0refChr3 77931 42 + 222631 AGCCTCACCAATGCAGAAAATATTTACAGGTCACTTGAAGCT -s Anc1.Anc1refChr6 110077 42 + 197743 AGCCTCACCAATGCAGAAAATATTTACAGGTCACTTGAAGCT -s Anc2.Anc2refChr13 84294 42 + 96486 AGCCTCACCAATGCAGAAAGTATTTACAGGTCACTTGAAGCT -s mr.mrrefChr3 11554 42 + 181027 AGCCTAACCAATGCAAAAAATATCCACAGGTCACTTGAAGCT -s simCow_chr6.simCow.chr6 440923 42 + 602619 AGCCTTACCAATGCAGAAAGTATTTACAGGTCTCATGAAGTT -s simDog_chr6.simDog.chr6 432592 42 + 593897 AGCCTCGCCAATGCTAAAAGTATTCACATGTCACTCAAAGCT -s simHuman_chr6.simHuman.chr6 441076 42 + 601863 AGTATCACTAATGTAGAAAATATTTACAGGTCACTTGAAGCT -s simRat_chr6.simRat.chr6 465188 42 + 647215 AGCCTAACCAATGCAAAAAATATCCACAGGTCACTTGAGGCT - -a -s simMouse_chr6.simMouse.chr6 453316 53 + 636262 GTGTACCAGGCCTAGCTTGAATTTCCTATCTCTGGCTGATGCTGGTGAGAAGC -s Anc0.Anc0refChr3 77973 53 + 222631 GTATAGCAGGCCCAGTTTGGACATCCCATCCCTTACTGCTGCAGGTGAGAAAC -s Anc1.Anc1refChr6 110119 53 + 197743 GTATAGCAGGCCCAGTTTGGACATCCCATCCCTTACTGCTGCAGGTGAGAAAC -s Anc2.Anc2refChr13 84336 53 + 96486 GTATAGCATGCCCAGTTTGGACATCCCATCCCTTACCGCTGCAGGTGGGAAAA -s mr.mrrefChr3 11596 53 + 181027 GTGTACCAGGCCTAGCTTGGATTTCCTATCTCTGGCTGATGCTGGTGAGAAGC -s simCow_chr6.simCow.chr6 440966 53 + 602619 GTATAGCAGGCCCAGTTTGGATGTCCCATCCCTTACCGCTGCAGGTGTTAAAA -s simDog_chr6.simDog.chr6 432634 45 + 593897 GTATAGCATGCCC-------ACATCCCATCCTTTGCCGCTGCAGGTGGGAAA- -s simHuman_chr6.simHuman.chr6 441118 52 + 601863 GCATATCAG-CCCAGTTAGGACATCCCATCCCTCACTGCTGCAGGTGAGAAAC -s simRat_chr6.simRat.chr6 465230 51 + 647215 GTGTACCAGGCCTAACTTGGATTTTCTATCTCTGGCT--TGCTGGTGGGAAGC - -a -s simMouse_chr6.simMouse.chr6 453369 42 + 636262 TCTGCACAGGTACCAATACCAATAGAACACTTGATCCCTCAG -s Anc0.Anc0refChr3 78028 31 + 222631 ACCTCACAGGCTCCAA-----------CACTGGCCCCCACAG -s Anc1.Anc1refChr6 110174 33 + 197743 ACCTCACAGGCTCCAA---------ATCACTGGCCCCCACAG -s Anc2.Anc2refChr13 84391 31 + 96486 ACCTCATAGGCTCCAA-----------CACTGGCCTCTATAG -s mr.mrrefChr3 11649 42 + 181027 TCTGCACAGGCACCAATACCAATAGAACACTTGCCCCCTCAG -s simCow_chr6.simCow.chr6 441021 31 + 602619 ACCTCATAGGCTCCAA-----------CACTGGCCTCTATAG -s simDog_chr6.simDog.chr6 432679 14 + 593897 --------------AA-----------CCCTGGTTTATA--- -s simHuman_chr6.simHuman.chr6 441172 33 + 601863 CCCCCACAGACCCCAA---------ATCACTAGCCCCCACAG -s simRat_chr6.simRat.chr6 465281 42 + 647215 TCAGCACAGGCACCAATACTAATAGAACACTTGCCCCCTCAG - -a -s simMouse_chr6.simMouse.chr6 453411 12 + 636262 GCAATGGTTACA -s Anc0.Anc0refChr3 78059 9 + 222631 ---TTGGTTACA -s Anc1.Anc1refChr6 110207 12 + 197743 GGATTGGTTACA -s Anc2.Anc2refChr13 84422 9 + 96486 ---TTGGTGACC -s mr.mrrefChr3 11691 12 + 181027 GCAATGGTTACA -s simCow_chr6.simCow.chr6 441052 9 + 602619 ---TTGGTGACC -s simHuman_chr6.simHuman.chr6 441206 12 + 601863 GGATTGGTTACA -s simRat_chr6.simRat.chr6 465323 12 + 647215 GCTACGGTTACC - -a -s simMouse_chr6.simMouse.chr6 453423 24 + 636262 ACCACGTGGAAAATTCATCTGGAT -s Anc0.Anc0refChr3 78068 9 + 222631 ACCACATGG--------------- -s Anc1.Anc1refChr6 110219 9 + 197743 ACCACATGG--------------- -s Anc2.Anc2refChr13 84432 9 + 96486 ACCACATGG--------------- -s mr.mrrefChr3 11703 24 + 181027 ACCACATGGAAAATTCATCTGGAT -s simCow_chr6.simCow.chr6 441062 9 + 602619 ACAATACAG--------------- -s simDog_chr6.simDog.chr6 432693 9 + 593897 ACCACATGA--------------- -s simHuman_chr6.simHuman.chr6 441218 9 + 601863 TCCACATGG--------------- -s simRat_chr6.simRat.chr6 465335 24 + 647215 ACCACATGGGAAAGTCATCTGGAT - -a -s simMouse_chr6.simMouse.chr6 453447 71 + 636262 CCATCTTGATTATAATTGAAGGACATGTGGTTATACAATGGGCAGCATGCTACAAAAAGTTGTGGAAACAC -s Anc0.Anc0refChr3 78083 15 + 222631 CCATCTTGATCAGAA-------------------------------------------------------- -s Anc1.Anc1refChr6 110234 35 + 197743 CCATCTTGATCAGAAT------------------------------------CAGAGGGTCGTCTCAACAT -s Anc2.Anc2refChr13 84447 15 + 96486 CCATCTTGATCAGAA-------------------------------------------------------- -s mr.mrrefChr3 11733 71 + 181027 CCATCTTGATTATAATTGAGGGACATGTGATTATACAATGGGCATCATGCTACAAAAAGTTGTGGAAACAC -s simCow_chr6.simCow.chr6 441077 15 + 602619 CCATCTTGATCAGAA-------------------------------------------------------- -s simDog_chr6.simDog.chr6 432708 15 + 593897 CCATCTCACTCAAAG-------------------------------------------------------- -s simHuman_chr6.simHuman.chr6 441233 35 + 601863 CCATCTTGATCAGAAT------------------------------------CAGAGGGTCGTCTCAACAT -s simRat_chr6.simRat.chr6 465371 71 + 647215 CCATCTTGATTATGATTGAGGGACATGTGATTATACAATGGGCATCATGTGACAAAAAGGTGTAGAAATAG - -a -s simMouse_chr6.simMouse.chr6 453518 39 + 636262 TCAGTAAGCAGAAAGTTTATTGGACAGGTGAATGTATCA -s Anc0.Anc0refChr3 78098 32 + 222631 -------TCAGAAAGTTGTTTGGACAGGTGACTGTATCA -s Anc1.Anc1refChr6 110269 38 + 197743 TCAG-AATCAGAAAGTTGTTTGGACAGGTGACTGTATCA -s Anc2.Anc2refChr13 84462 32 + 96486 -------TCAGAAAGTTGTGTGGACAGGTGACTGTATCA -s mr.mrrefChr3 11804 39 + 181027 TCAGTAAGCAGAAAGTTTTTTGGACAGGTGAATGTATCA -s simCow_chr6.simCow.chr6 441092 31 + 602619 -------TCAGAAAGTTGTGTGGACACGTG-CCGTATCA -s simDog_chr6.simDog.chr6 432723 32 + 593897 -------TCAGAAAGTTGTGTGGACAGCCGACTGTATCA -s simHuman_chr6.simHuman.chr6 441273 38 + 601863 TCAG-AATCAGAAGGTTGTTTGGACAGGTGATTTTATCA -s simRat_chr6.simRat.chr6 465442 39 + 647215 TCAGTAAGCAGAAAGTTTTTTGGATGGGTGTATGTATCA - -a -s simMouse_chr6.simMouse.chr6 453557 1 + 636262 A -s Anc0.Anc0refChr3 78130 1 + 222631 A -s Anc1.Anc1refChr6 110307 1 + 197743 A -s Anc2.Anc2refChr13 84495 1 + 96486 A -s mr.mrrefChr3 11843 1 + 181027 A -s simCow_chr6.simCow.chr6 441124 1 + 602619 A -s simDog_chr6.simDog.chr6 432756 1 + 593897 A -s simHuman_chr6.simHuman.chr6 441311 1 + 601863 A -s simRat_chr6.simRat.chr6 465481 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 453558 2 + 636262 AA -s Anc0.Anc0refChr3 78134 2 + 222631 GA -s Anc1.Anc1refChr6 110311 2 + 197743 GA -s Anc2.Anc2refChr13 84499 2 + 96486 GA -s mr.mrrefChr3 11844 2 + 181027 AA -s simCow_chr6.simCow.chr6 441128 2 + 602619 GA -s simDog_chr6.simDog.chr6 432760 2 + 593897 GA -s simHuman_chr6.simHuman.chr6 441315 2 + 601863 GA -s simRat_chr6.simRat.chr6 465482 2 + 647215 AA - -a -s simMouse_chr6.simMouse.chr6 453560 12 + 636262 AATGTACTGCAT -s Anc0.Anc0refChr3 78136 12 + 222631 CCTCTCCTGCAG -s Anc1.Anc1refChr6 110313 12 + 197743 CCTCTCCTGCAG -s Anc2.Anc2refChr13 84508 12 + 96486 CCCCTCCTGCAG -s mr.mrrefChr3 11846 12 + 181027 AATCTACTGCAT -s simCow_chr6.simCow.chr6 441136 12 + 602619 CCCCCCATGCCG -s simDog_chr6.simDog.chr6 432769 12 + 593897 CCCATCCTGCAA -s simHuman_chr6.simHuman.chr6 441317 12 + 601863 CCTCTGCTACAG -s simRat_chr6.simRat.chr6 465484 12 + 647215 AATCTACTGCAT - -a -s simMouse_chr6.simMouse.chr6 453572 13 + 636262 GACCACATGATGA -s Anc0.Anc0refChr3 78148 11 + 222631 CACCATGTGA--A -s Anc1.Anc1refChr6 110325 11 + 197743 CACCATGTGA--A -s Anc2.Anc2refChr13 84520 11 + 96486 CACCATCTTA--C -s mr.mrrefChr3 11858 13 + 181027 GACCATGTGATGA -s simCow_chr6.simCow.chr6 441149 11 + 602619 GACCATTTAA--G -s simDog_chr6.simDog.chr6 432781 11 + 593897 CCCCATCCTA--C -s simHuman_chr6.simHuman.chr6 441329 11 + 601863 TACCATGTGA--A -s simRat_chr6.simRat.chr6 465496 13 + 647215 GACCATGTGATGA - -a -s simMouse_chr6.simMouse.chr6 453585 19 + 636262 AAATATGCTGGTTAAGGGC -s Anc0.Anc0refChr3 78159 19 + 222631 GAATATGCAGGTTATGGGC -s Anc1.Anc1refChr6 110336 19 + 197743 GAATATGCAGGTTATGGGC -s Anc2.Anc2refChr13 84531 19 + 96486 AAATATGCAGGTAATGGGC -s mr.mrrefChr3 11871 19 + 181027 GAATATGCAGGTTAAGGGC -s simCow_chr6.simCow.chr6 441160 19 + 602619 CAATATGCACGTAATGGGC -s simDog_chr6.simDog.chr6 432797 19 + 593897 AAAGATGCAGGTAATGGGC -s simHuman_chr6.simHuman.chr6 441340 19 + 601863 GAATATGCAGGTTATGGGC -s simRat_chr6.simRat.chr6 465509 19 + 647215 GGATAAACAGGTTAAGGGC - -a -s simMouse_chr6.simMouse.chr6 453604 4 + 636262 CAGA -s Anc0.Anc0refChr3 78178 4 + 222631 CATA -s Anc1.Anc1refChr6 110355 4 + 197743 CATA -s Anc2.Anc2refChr13 84552 4 + 96486 CATA -s mr.mrrefChr3 11890 4 + 181027 CAGA -s simCow_chr6.simCow.chr6 441181 4 + 602619 CATA -s simDog_chr6.simDog.chr6 432818 4 + 593897 CATA -s simHuman_chr6.simHuman.chr6 441364 4 + 601863 CATT -s simRat_chr6.simRat.chr6 465528 4 + 647215 CTGA - -a -s simMouse_chr6.simMouse.chr6 453608 14 + 636262 CTCTAAGATGTTCA -s Anc0.Anc0refChr3 78185 14 + 222631 ATCTAATAGGTTTG -s Anc1.Anc1refChr6 110362 14 + 197743 ATCTAATAGGTTTG -s Anc2.Anc2refChr13 84559 14 + 96486 ATCTAATAGATTTG -s mr.mrrefChr3 11897 14 + 181027 ATCTAATAGGTTTA -s simCow_chr6.simCow.chr6 441188 14 + 602619 ATCTAATAGATTTG -s simDog_chr6.simDog.chr6 432825 14 + 593897 CTCTGATAGATTTG -s simHuman_chr6.simHuman.chr6 441371 14 + 601863 ATCTAATAGGTTTG -s simRat_chr6.simRat.chr6 465535 14 + 647215 AACTAATAGAAGTT - -a -s simMouse_chr6.simMouse.chr6 453622 42 + 636262 ACAGGTATGAACACTCTTTGATAATTTACAACAAAGAAACAA -s Anc0.Anc0refChr3 78226 1 + 222631 -----------------------------------------A -s Anc1.Anc1refChr6 110403 1 + 197743 -----------------------------------------A -s Anc2.Anc2refChr13 84600 1 + 96486 -----------------------------------------A -s mr.mrrefChr3 11972 42 + 181027 ACAGGTGTGAACACTCTTTAATAATTTACAACAAAGAAACAA -s simCow_chr6.simCow.chr6 441229 1 + 602619 -----------------------------------------C -s simDog_chr6.simDog.chr6 432868 1 + 593897 -----------------------------------------A -s simRat_chr6.simRat.chr6 465610 42 + 647215 ACAGGTGTGAACACTCTTTAATAATTTACAACAAAGAAACAA - -a -s simMouse_chr6.simMouse.chr6 453664 21 + 636262 GTGGTAAACTATAGGGAATGC -s Anc0.Anc0refChr3 78235 20 + 222631 GTGGGAAATTATAAGGAA-CC -s Anc1.Anc1refChr6 110412 20 + 197743 GTGGGAAATTATAAGGAA-CC -s Anc2.Anc2refChr13 84609 20 + 96486 GTGGGAAATTATAAGGAA-CC -s mr.mrrefChr3 12022 20 + 181027 GTGGTAAACTATAGGGAA-GC -s simCow_chr6.simCow.chr6 441238 18 + 602619 GTAGAAAATTAGAAGGAA--- -s simDog_chr6.simDog.chr6 432881 20 + 593897 GTGGGAAATTATGAGGAA-CC -s simRat_chr6.simRat.chr6 465660 20 + 647215 GTGGGAAACTATAGGGAA-AC - -a -s simMouse_chr6.simMouse.chr6 453685 23 + 636262 AGTCAGCTAGGCTTATTAAAAAC -s Anc0.Anc0refChr3 78255 22 + 222631 AGT-AGCTTGGCTTATTTAAAAC -s Anc1.Anc1refChr6 110432 22 + 197743 AGT-AGCTTGGCTTATTTAAAAC -s Anc2.Anc2refChr13 84635 22 + 96486 AGT-AGCTTGGCTTATTTAAAAC -s mr.mrrefChr3 12042 23 + 181027 AGTCAGCTAGGCTTATTAAAAAC -s simCow_chr6.simCow.chr6 441256 22 + 602619 ATT-AGATTGGCTTTTTTAAAAC -s simDog_chr6.simDog.chr6 432907 22 + 593897 AGT-AGCTTGGCTTATTTAAAGC -s simHuman_chr6.simHuman.chr6 441400 22 + 601863 AGT-AGCTTGGCTTATTTAAAAC -s simRat_chr6.simRat.chr6 465680 23 + 647215 AGTCAGCTAGGCTTATTAAAGAC - -a -s simMouse_chr6.simMouse.chr6 453708 67 + 636262 CTGGCAGTTTTGAAGGTCAGAATATGGGGGGTGCGACTACAAGCAACTATGGGGAACCTGGACACCC -s Anc0.Anc0refChr3 78277 51 + 222631 CTGGCAGTTT----------------GAGGGTTCGACTACAAGCAACCATGGGGAACCTTCGCAGTT -s Anc1.Anc1refChr6 110454 51 + 197743 CTGGCAGTTT----------------GAGGGTTCGACTACAAGCAACCATGGGGAACCTTCGCAGTT -s Anc2.Anc2refChr13 84657 51 + 96486 CTGGCAGTTT----------------GAGGGTTTGACTACAATTATCCATGGGGAACCTTCGCAGTT -s mr.mrrefChr3 12065 67 + 181027 CTGGCAGTTTTGAAGGTCAGAATATGGGGGGTGCGACTACAAGCAACTATGGGGAAGCTGGACACTT -s simCow_chr6.simCow.chr6 441287 51 + 602619 TGGGCAGTTT----------------GAGGGTTTGACTACAATTATCCATGGTGGACCTTCGCAGTT -s simDog_chr6.simDog.chr6 432929 24 + 593897 CTG-------------------------------------------CCATGGGGAACCTTCAGAGTT -s simHuman_chr6.simHuman.chr6 441422 51 + 601863 CTGGCAGTTT----------------GAGGGTACTGTTACAAGCAACCACAGGGACCCTATGCAGTT -s simRat_chr6.simRat.chr6 465703 67 + 647215 CTGGCAGTTTTGAAAGTCAGAATATGGGGGGTGCAACTACAAGCAACTATGGGGAAGCTAGACACTT - -a -s simMouse_chr6.simMouse.chr6 453775 19 + 636262 GGCAGTCAGGACTAGACAA -s Anc0.Anc0refChr3 78328 8 + 222631 GGCAATCA----------- -s Anc1.Anc1refChr6 110505 19 + 197743 GGCAATCAGACCTTAACAG -s Anc2.Anc2refChr13 84708 8 + 96486 GGCAATCA----------- -s mr.mrrefChr3 12132 19 + 181027 GGCAGTCAGGACTGGACAA -s simCow_chr6.simCow.chr6 441343 8 + 602619 GGGTCTGA----------- -s simDog_chr6.simDog.chr6 432953 8 + 593897 GGCAATCA----------- -s simHuman_chr6.simHuman.chr6 441473 19 + 601863 GGCAACAAGACCTTAACAG -s simRat_chr6.simRat.chr6 465770 15 + 647215 GGCAGTCAGGTCTGG---- - -a -s simMouse_chr6.simMouse.chr6 453794 53 + 636262 GAGAGACATGGATGATATGTGTCTAAGCCTGACTTAGCCGGCAAGTGATTGTT -s Anc0.Anc0refChr3 78350 33 + 222631 GATGG----------TATGTGTATAAGCCTGACTTGGCCGGCA---------- -s Anc1.Anc1refChr6 110538 33 + 197743 GATGG----------TATGTGTATAAGCCTGACTTGGCCGGCA---------- -s Anc2.Anc2refChr13 84730 33 + 96486 GATGG----------TATGGGCATAAGCCTGATTTGGCCAGCA---------- -s mr.mrrefChr3 12151 33 + 181027 GAGAG----------TATGTGTCTAAGCCTGACTTAGCCGGCA---------- -s simCow_chr6.simCow.chr6 441365 33 + 602619 GATGG----------TATGTGTAGAAGCCTTATTTGGCCAACA---------- -s simDog_chr6.simDog.chr6 432971 28 + 593897 ---------------TATGGGCATAAGCCTGATTAGGTCAGCA---------- -s simHuman_chr6.simHuman.chr6 441517 27 + 601863 GATGG----------TATGTGTAT------GACTTGGCTGGCA---------- - -a -s simMouse_chr6.simMouse.chr6 453847 22 + 636262 CTATCAGACAATCACAGGAGAG -s Anc0.Anc0refChr3 78393 16 + 222631 CTATCAAGCAATGGCA------ -s Anc1.Anc1refChr6 110581 16 + 197743 CTATCAAGCAATGGCA------ -s Anc2.Anc2refChr13 84773 16 + 96486 TTATCAAGCAATGGCA------ -s mr.mrrefChr3 12184 16 + 181027 CTATCAGACAATCACA------ -s simCow_chr6.simCow.chr6 441408 15 + 602619 TTATCAAGCAAGCG-A------ -s simDog_chr6.simDog.chr6 433000 14 + 593897 -TATCAAGCAATGGC------- -s simHuman_chr6.simHuman.chr6 441554 16 + 601863 CTATCAAGTGCTAGCA------ - -a -s simMouse_chr6.simMouse.chr6 453869 19 + 636262 GCTGACAGGCTGCAATGAA -s Anc0.Anc0refChr3 78415 19 + 222631 GGTGACAGGCTGTAATGAT -s Anc1.Anc1refChr6 110603 19 + 197743 GGTGACAGGCTGTAATGAT -s Anc2.Anc2refChr13 84795 19 + 96486 GGTAACAGGCTATAATAAT -s mr.mrrefChr3 12200 19 + 181027 GCTGACAGGCTGCAATGAA -s simCow_chr6.simCow.chr6 441429 14 + 602619 GGTAACAGGCTATA----- -s simDog_chr6.simDog.chr6 433014 5 + 593897 --------------ATAAT -s simHuman_chr6.simHuman.chr6 441576 19 + 601863 GGTGACAGGCTGTGATGTG -s simRat_chr6.simRat.chr6 465785 19 + 647215 GCTGACAGGCTGCAATGAA - -a -s simMouse_chr6.simMouse.chr6 453888 1 + 636262 T -s Anc0.Anc0refChr3 78434 1 + 222631 C -s Anc1.Anc1refChr6 110622 1 + 197743 C -s Anc2.Anc2refChr13 84814 1 + 96486 C -s mr.mrrefChr3 12219 1 + 181027 T -s simDog_chr6.simDog.chr6 433019 1 + 593897 C -s simHuman_chr6.simHuman.chr6 441655 1 + 601863 C -s simRat_chr6.simRat.chr6 465804 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 453889 54 + 636262 ATTCATTCAGTAAAATTTACTCCATGGAAGAATGGAAGATATGATTTTGATTGC -s Anc0.Anc0refChr3 78435 41 + 222631 A--------GTAGATTTTACTCGATGGA-----GGGAGATATGATATGGATTCT -s Anc1.Anc1refChr6 110623 43 + 197743 A--------GTAGATTTTACTCGATGGAAT---GGGAGATATGATATGGATTCT -s Anc2.Anc2refChr13 84819 41 + 96486 A--------GTAGATTTTACTTGAAGGA-----GGGGAATATGATATAGATTAC -s mr.mrrefChr3 12220 46 + 181027 A--------GTAAAATTTACTCCATGGAATAATGGAAGATATGATTTGGATTCT -s simCow_chr6.simCow.chr6 441443 9 + 602619 ---------------------------------------------GTAGATAAC -s simDog_chr6.simDog.chr6 433024 41 + 593897 A--------GTAGATTTTACTTGAAGGA-----GGGGAATATGATATAGATTAC -s simHuman_chr6.simHuman.chr6 441656 43 + 601863 A--------GGAGGTTTTGCCCAATGGTAT---GGGAGACTTGATATGGATTCT -s simRat_chr6.simRat.chr6 465805 46 + 647215 A--------GTAAAATCTACTCCACAGAATAATGGCAGATGTGATTTGGATTCT - -a -s simMouse_chr6.simMouse.chr6 453943 44 + 636262 CCTGGCTTGGCCTATTTTGTTGTTCTTGCTATGTGGTTTGTGAG -s Anc0.Anc0refChr3 78476 44 + 222631 CCTGGCCCGCCCTATTTTCTTTTTCTTGATATTTCATTGGTGAG -s Anc1.Anc1refChr6 110666 44 + 197743 CCTGGCCCGCCCTATTTTCTTTTTCTTGATATTTCATTGGTGAG -s Anc2.Anc2refChr13 84860 44 + 96486 TCTGGCCCACCTTATTTTTCTTTTCTGGATATTTCATCGGTGAG -s mr.mrrefChr3 12266 44 + 181027 CCTGGCTTGGCCTATTTTCTTGTTCTTGCTATGTGGTTTGTGAG -s simCow_chr6.simCow.chr6 441453 30 + 602619 TCTGGTCCACCTTAT--------------TATTTCATAGGTGAA -s simDog_chr6.simDog.chr6 433065 37 + 593897 TCTGGCCC-------TTTTCTTTTCTGGATATGGCATCGGTGAG -s simHuman_chr6.simHuman.chr6 441699 44 + 601863 CCCGCCCCGCCCTATTTTCTTTTTCTTGATATTTCATTGGTGAG -s simRat_chr6.simRat.chr6 465851 44 + 647215 CCTGGCTTGGCCTATTCTCTTGTTCTTGCTATGTTGTTCGTGAG - -a -s simMouse_chr6.simMouse.chr6 453987 21 + 636262 ATATATGGTGTCCATCAGAAA -s Anc0.Anc0refChr3 78520 21 + 222631 AGATGTGGTTTTCCCCAGAAA -s Anc1.Anc1refChr6 110710 21 + 197743 AGATGTGGTTTTCCCCAGAAA -s Anc2.Anc2refChr13 84905 21 + 96486 AGATGTGGTTTTCCCCAGAAA -s mr.mrrefChr3 12310 21 + 181027 ATATATGGTGTCCATCAGAAA -s simCow_chr6.simCow.chr6 441484 21 + 602619 AGATATGATTTTCCCCAGAAA -s simDog_chr6.simDog.chr6 433103 21 + 593897 AGATGTGGTTCTCATCGGAGA -s simHuman_chr6.simHuman.chr6 441743 21 + 601863 AAAAGCGGTTTTCCCCAAAAA -s simRat_chr6.simRat.chr6 465895 20 + 647215 A-ATATGGTGCCCATGAGAAA - -a -s simMouse_chr6.simMouse.chr6 454008 19 + 636262 TTATACTAGTCATCTGATT -s Anc0.Anc0refChr3 78542 19 + 222631 TGATTGCAGCAACCTGATT -s Anc1.Anc1refChr6 110732 19 + 197743 TGATTGCAGCAACCTGATT -s Anc2.Anc2refChr13 84927 19 + 96486 TGGTTGCAACAACCTGATC -s mr.mrrefChr3 12331 19 + 181027 TTATTCTAGTAATCTGATT -s simCow_chr6.simCow.chr6 441506 19 + 602619 TGCTTGCAACAACCTGATC -s simDog_chr6.simDog.chr6 433125 18 + 593897 TGGTTG-AACAACCTGATC -s simHuman_chr6.simHuman.chr6 441765 19 + 601863 TGACTGCAGCAAGCTGATT -s simRat_chr6.simRat.chr6 465915 19 + 647215 TTATTCTAGTAATCTGATC - -a -s simMouse_chr6.simMouse.chr6 454027 162 + 636262 AGTAGAAAGGGATAAGAAGGGTAAGGTTCAACAGTGTGACAAGTTAGGTCCACTAACTAGTTGTTAAGATCACATCCCATGGTTGGAACTCTCTTTCATCTGCCTCTGGGGTCTTTTATTAATAGTTCGATGCTCAGTCAGAGTTGTTTTGGCCTGGTGTCT -s Anc0.Anc0refChr3 78564 68 + 222631 AGTAGAAAGAAATAAGAGAAAGGAAGTGGAACAGTGAGACA--------------------------GATCACATCCTTAAGTTGTA--------------------------------------------------------------------GGAGTCT -s Anc1.Anc1refChr6 110754 68 + 197743 AGTAGAAAGAAATAAGAGAAAGGAAGTGGAACAGTGAGACA--------------------------GATCACATCCTTAAGTTGTA--------------------------------------------------------------------GGAGTCT -s Anc2.Anc2refChr13 84949 68 + 96486 AGGAGAAAGAAATAAGAGAAAGGAAGTGGGACAGTGACACA--------------------------GTTCACACCCTTAAGTTGTA--------------------------------------------------------------------GGAGTCT -s mr.mrrefChr3 12350 162 + 181027 AGTAGAAAGGGATAAGAAGAATAAGGTTCAACAGTGAGACAAGTTAGGTCCACTAACTAGTTGTTCAGATCACATCCCATGGTTGGAACTCTCTTTCATCTGCCTCTGGGGTCTCTTATTAATAGTTCGATGCTCAGTCAGAGTTGTTTTGGCCTGGTGTCT -s simCow_chr6.simCow.chr6 441528 67 + 602619 AGAAGAAAGAA-TAAGAGAAAGGAATGATGATACAGGTTAG--------------------------GTCCAGAAACTAGAGGTGTA--------------------------------------------------------------------GGAGTAC -s simDog_chr6.simDog.chr6 433146 68 + 593897 AGGAGAAAGAAATAATAGAAAGAAAGTGGGACAGTGACACA--------------------------GTTCACACCCTTAAGTTGTA--------------------------------------------------------------------GGAGTCT -s simHuman_chr6.simHuman.chr6 441787 53 + 601863 AGTATAAAGAAGTAAGATAAAGGTACTCGAACAGTGAGACA--------------------------GATTGAGTCCAC----------------------------------------------------------------------------------- -s simRat_chr6.simRat.chr6 465934 162 + 647215 AGCACAAAGGGATCTGACTAATAAGGCTCAACAGTGATACAAGTTAGGTCCACTAACTAGTTGTTCAGATCACATCCCATGGTTGGAACTCTTATTCGTCTGCCTGTGGGGTCTCTTATCAATTGTTCAATCTTCAGTCAGAACTGTGTTGGCCTGGTTTCT - -a -s simMouse_chr6.simMouse.chr6 454189 20 + 636262 TTAACGTTTCAATGCATTAA -s Anc0.Anc0refChr3 78632 15 + 222631 TTAGTGTTCAAATGC----- -s Anc1.Anc1refChr6 110822 18 + 197743 TTAGTGTTCAAATGCA--AA -s Anc2.Anc2refChr13 85018 15 + 96486 TTAGTGTTCAAATGC----- -s mr.mrrefChr3 12512 20 + 181027 TTAATGTTTCAATGCATTAA -s simCow_chr6.simCow.chr6 441596 15 + 602619 CTGATGTTCTAATGC----- -s simDog_chr6.simDog.chr6 433215 15 + 593897 TTAGTGTTCAAATGC----- -s simHuman_chr6.simHuman.chr6 441840 2 + 601863 ------------------AA -s simRat_chr6.simRat.chr6 466096 20 + 647215 TTAATGTTTTAATCCATTAG - -a -s simMouse_chr6.simMouse.chr6 454209 2 + 636262 AC -s Anc0.Anc0refChr3 78647 2 + 222631 AC -s Anc1.Anc1refChr6 110840 2 + 197743 AC -s Anc2.Anc2refChr13 85033 2 + 96486 AC -s mr.mrrefChr3 12532 2 + 181027 AC -s simCow_chr6.simCow.chr6 441616 2 + 602619 AC -s simDog_chr6.simDog.chr6 433230 2 + 593897 AC -s simHuman_chr6.simHuman.chr6 441842 2 + 601863 AC -s simRat_chr6.simRat.chr6 466116 2 + 647215 AC - -a -s simMouse_chr6.simMouse.chr6 454211 30 + 636262 CCTTAATGCCCCCATCATTGGTATACCCAT -s Anc0.Anc0refChr3 78649 27 + 222631 CCCTAATGCATCCAACACTGATACACT--- -s Anc1.Anc1refChr6 110842 27 + 197743 CCCTAATGCATCCAACACTGATACACT--- -s Anc2.Anc2refChr13 85035 27 + 96486 CCCTAGTGCATCCAACACTGATACACT--- -s mr.mrrefChr3 12534 30 + 181027 CCTTAATGCCCCCATCATTGGTACACTCAT -s simCow_chr6.simCow.chr6 441618 27 + 602619 CCCCCGTGCATCCAACACTGGTACACC--- -s simDog_chr6.simDog.chr6 433232 27 + 593897 CCCTAGTGCATCCAAGATTGATACACT--- -s simHuman_chr6.simHuman.chr6 441850 27 + 601863 CTCTAATGCATCCAACGCTCATACACA--- -s simRat_chr6.simRat.chr6 466118 30 + 647215 CCTAAATGCCCCTGGCATTGGTACACTCAT - -a -s simMouse_chr6.simMouse.chr6 454241 74 + 636262 TAATGACAAATACAGTGACTTTCTATAAAAGTGATAAAAAGTAATCATCATAGAAGTCTCAATCATTCTGTGGA -s Anc0.Anc0refChr3 78676 59 + 222631 ----GACAAA-AGGGTGACTTCCAACAAAAGTGAT----------CATTATAGCAATTCTGGCTATTCAATGGA -s Anc1.Anc1refChr6 110869 60 + 197743 ----GACAAATAGGGTGACTTCCAACAAAAGTGAT----------CATTATAGCAATTCTGGCTATTCAATGGA -s Anc2.Anc2refChr13 85062 59 + 96486 ----GACAAA-AGGGTGACTTCCAACAAAAGTTAT----------TATTATAGCAATTCTGGCTGTTCAATGGA -s mr.mrrefChr3 12564 74 + 181027 TAATGACAAATACAGTGACTTTCCACAAAAGTGATAAAAAGTAATCATCATAGAAGTTTCAATCATTCTATGGA -s simCow_chr6.simCow.chr6 441645 58 + 602619 ----AACAAA-AGGTTCACTTCCAAC-AAAGTTAT----------TATTATAGTACTTCTGACTGTTCACTGAA -s simDog_chr6.simDog.chr6 433259 59 + 593897 ----GACAAA-AGGGTGACTTCTCACAAAAGCTAT----------TATTATAGCAATTGTGGATGTGCAATAGA -s simHuman_chr6.simHuman.chr6 441877 60 + 601863 ----GACAAATAGGGTAACTTCCATCAAAAGTGAT----------CATTATAGCAACCCTGGCTATTCGATGGA -s simRat_chr6.simRat.chr6 466153 74 + 647215 CACTTACAAATACAGTAACTTTCCACGAAAGTGATAAAAAGTAATCATCTTAGGATTTCCAATCATTCCATGAA - -a -s simMouse_chr6.simMouse.chr6 454315 10 + 636262 GGGTTCTTTG -s Anc0.Anc0refChr3 78735 10 + 222631 GGGATCTTTG -s Anc1.Anc1refChr6 110929 10 + 197743 GGGATCTTTG -s Anc2.Anc2refChr13 85121 10 + 96486 GGGATCTTTG -s mr.mrrefChr3 12638 10 + 181027 GGGTTCTTTG -s simCow_chr6.simCow.chr6 441704 10 + 602619 GGGATCTTTG -s simDog_chr6.simDog.chr6 433318 10 + 593897 GGGATCTTTG -s simHuman_chr6.simHuman.chr6 441937 10 + 601863 GGGATCTTTG -s simRat_chr6.simRat.chr6 466227 10 + 647215 GGGTTCTTTG - -a -s simMouse_chr6.simMouse.chr6 454325 4 + 636262 ATGT -s Anc0.Anc0refChr3 78745 4 + 222631 GTGT -s Anc1.Anc1refChr6 110939 4 + 197743 GTGT -s Anc2.Anc2refChr13 85131 4 + 96486 GTGT -s mr.mrrefChr3 12648 4 + 181027 ATGT -s simCow_chr6.simCow.chr6 441714 4 + 602619 GTGT -s simDog_chr6.simDog.chr6 433328 4 + 593897 GTGT -s simHuman_chr6.simHuman.chr6 441947 4 + 601863 GTGT -s simRat_chr6.simRat.chr6 466243 4 + 647215 AAAT - -a -s simMouse_chr6.simMouse.chr6 454329 13 + 636262 TAAGATTTATGAC -s Anc0.Anc0refChr3 78753 12 + 222631 TATATGTAATG-T -s Anc1.Anc1refChr6 110947 13 + 197743 TATATGTAATGAT -s Anc2.Anc2refChr13 85139 12 + 96486 CATATGTACTG-T -s mr.mrrefChr3 12652 13 + 181027 TATGAGTCATGAC -s simCow_chr6.simCow.chr6 441722 12 + 602619 CATGGGTAGTC-T -s simDog_chr6.simDog.chr6 433336 12 + 593897 CATATATACTG-T -s simHuman_chr6.simHuman.chr6 441955 13 + 601863 TATATGTAATCAT -s simRat_chr6.simRat.chr6 466247 13 + 647215 TATGAGTCATTGC - -a -s simMouse_chr6.simMouse.chr6 454342 16 + 636262 CGAGCACCCCTAATAA -s Anc0.Anc0refChr3 78765 14 + 222631 CC--CCTCCCCAAAGA -s Anc1.Anc1refChr6 110960 14 + 197743 CC--CCTCCCCAAAGA -s Anc2.Anc2refChr13 85151 14 + 96486 TC--CCTCCCCAAAGA -s mr.mrrefChr3 12665 16 + 181027 CGAGCACCCCTAATAA -s simCow_chr6.simCow.chr6 441734 14 + 602619 TC--ACACCTCAAAGA -s simDog_chr6.simDog.chr6 433348 14 + 593897 TC--CCTCCCCAAAGA -s simHuman_chr6.simHuman.chr6 441968 2 + 601863 CC-------------- -s simRat_chr6.simRat.chr6 466276 15 + 647215 CACGCACCC-TAATAG - -a -s simMouse_chr6.simMouse.chr6 454358 11 + 636262 ACCAATGTTAA -s Anc0.Anc0refChr3 78779 11 + 222631 ATCAGGGTGGA -s Anc1.Anc1refChr6 110974 11 + 197743 ATCAGGGTGGA -s Anc2.Anc2refChr13 85193 11 + 96486 ATCAGGGTGGA -s mr.mrrefChr3 12681 11 + 181027 ACCAATGTGGA -s simCow_chr6.simCow.chr6 441778 11 + 602619 TTCAGCGTGTA -s simDog_chr6.simDog.chr6 433395 11 + 593897 ATCAGGGTGGA -s simRat_chr6.simRat.chr6 466291 11 + 647215 GCCAATGTGGA - -a -s simMouse_chr6.simMouse.chr6 454369 26 + 636262 ACCCTACTCAACCAGAGAGTGCCAAA -s Anc0.Anc0refChr3 78790 23 + 222631 CGCTTATTCAACCAAGGAG---CCCT -s Anc1.Anc1refChr6 110985 23 + 197743 CGCTTATTCAACCAAGGAG---CCCT -s Anc2.Anc2refChr13 85204 23 + 96486 CGCTTATTCAACCAAGGAG---CCCT -s mr.mrrefChr3 12692 26 + 181027 ACCCTACTCAACCAGAGAGTGCCCAA -s simCow_chr6.simCow.chr6 441789 23 + 602619 CTTATACTCAACCAAGGAG---CCCT -s simDog_chr6.simDog.chr6 433421 23 + 593897 CGCTTATTCAACCAAGGAG---CCCT -s simRat_chr6.simRat.chr6 466302 26 + 647215 ACTGCACTTAACTAGAGAGAGCCCAT - -a -s simMouse_chr6.simMouse.chr6 454395 13 + 636262 CTGTGTTATATCC -s Anc0.Anc0refChr3 78813 13 + 222631 CTAAGGTAAGACC -s Anc1.Anc1refChr6 111008 13 + 197743 CTAAGGTAAGACC -s Anc2.Anc2refChr13 85227 13 + 96486 CTAAGGTAAGACC -s mr.mrrefChr3 12718 13 + 181027 CTGTGTTATGTCC -s simCow_chr6.simCow.chr6 441812 13 + 602619 TTGAGTTAAGACC -s simDog_chr6.simDog.chr6 433445 13 + 593897 CTAAGGTAAGACC -s simRat_chr6.simRat.chr6 466328 13 + 647215 CTGTGTTATGTCC - -a -s simMouse_chr6.simMouse.chr6 454408 34 + 636262 TTTATTCTTAGAATCTAGATCAGAGATATGTTTG -s Anc0.Anc0refChr3 78826 26 + 222631 TCTGCTCTCAGAACCCAGATCAGA--------TG -s Anc1.Anc1refChr6 111021 26 + 197743 TCTGCTCTCAGAACCCAGATCAGA--------TG -s Anc2.Anc2refChr13 85240 26 + 96486 TCTGCTCTCAGAACCCAGATCAGA--------TG -s mr.mrrefChr3 12731 26 + 181027 TTTATTCTTAGAATCTAGATCAGA--------TG -s simCow_chr6.simCow.chr6 441825 26 + 602619 TTTGCTCACAGAATGGAGAATAGA--------TG -s simDog_chr6.simDog.chr6 433458 26 + 593897 TCTGCTCTCAGAACCCAGATCAGA--------TG -s simRat_chr6.simRat.chr6 466342 9 + 647215 TTTATTGTT------------------------- - -a -s simMouse_chr6.simMouse.chr6 454442 6 + 636262 GTGTTT -s Anc0.Anc0refChr3 78852 6 + 222631 GTGTTT -s Anc1.Anc1refChr6 111047 6 + 197743 GTGTTT -s Anc2.Anc2refChr13 85266 6 + 96486 GTGTTT -s mr.mrrefChr3 12757 6 + 181027 GTGTTT -s simCow_chr6.simCow.chr6 441853 6 + 602619 GTGTTT -s simDog_chr6.simDog.chr6 433484 6 + 593897 GTGTTT - -a -s simMouse_chr6.simMouse.chr6 454448 20 + 636262 AGATACCAACTCAAGGTGAT -s Anc0.Anc0refChr3 78858 20 + 222631 AGACTCCAATCTGAGAAGAT -s Anc1.Anc1refChr6 111053 20 + 197743 AGACTCCAATCTGAGAAGAT -s Anc2.Anc2refChr13 85279 20 + 96486 AGACTCCAATCTGAGAAGAT -s mr.mrrefChr3 12763 20 + 181027 AGATACCAACCTAAGGTGAT -s simCow_chr6.simCow.chr6 441866 20 + 602619 AAGCTCCAATCTGAGATGAC -s simDog_chr6.simDog.chr6 433497 20 + 593897 AGACTCCAATCTGAGAAGAT -s simRat_chr6.simRat.chr6 466351 15 + 647215 -----CCCACCTAAGGTCAT - -a -s simMouse_chr6.simMouse.chr6 454468 26 + 636262 GTGCTCTCTCCTAGCTTGGTCAGAAA -s Anc0.Anc0refChr3 78878 18 + 222631 ATCCTCTGTTTTAGC--------AGG -s Anc1.Anc1refChr6 111073 26 + 197743 ATCCTCTGTTTTAGCTTCTCCAGAGG -s Anc2.Anc2refChr13 85304 18 + 96486 ATCCTCTGTTTTAGC--------AGG -s mr.mrrefChr3 12783 26 + 181027 GTGCTCTCTCCTAGCTTGGTCAGAAA -s simCow_chr6.simCow.chr6 441894 18 + 602619 ATCCCCTGTTTTGGT--------AGG -s simDog_chr6.simDog.chr6 433524 18 + 593897 ATCCTCTGTTTTAGC--------AGG -s simHuman_chr6.simHuman.chr6 441970 12 + 601863 --------------CTTCTCCAGAGG -s simRat_chr6.simRat.chr6 466366 26 + 647215 GTGTTTTCCCCTAGCTTGGTTAGACG - -a -s simMouse_chr6.simMouse.chr6 454494 10 + 636262 AACTTTTGTG -s Anc0.Anc0refChr3 78900 10 + 222631 AACTTTTATG -s Anc1.Anc1refChr6 111103 10 + 197743 AACTTTTATG -s Anc2.Anc2refChr13 85326 10 + 96486 AACTTTTATA -s mr.mrrefChr3 12809 10 + 181027 AACTTTTATG -s simCow_chr6.simCow.chr6 441916 10 + 602619 AACTTTTATA -s simDog_chr6.simDog.chr6 433546 8 + 593897 AACT--TATA -s simHuman_chr6.simHuman.chr6 441986 10 + 601863 AACTTTTATG -s simRat_chr6.simRat.chr6 466393 10 + 647215 AACTTTCATG - -a -s simMouse_chr6.simMouse.chr6 454504 37 + 636262 GGCAAACACAGATACTAATTCCAATGAATATGAGTGT -s Anc0.Anc0refChr3 78912 33 + 222631 GGCAAACGCTGAT----ATTCCACTGAGTCTGGGTCT -s Anc1.Anc1refChr6 111115 37 + 197743 GGCAAACGCTGATATTCATTCCACTGAGTCTGGGTCT -s Anc2.Anc2refChr13 85338 33 + 96486 GGCAAATGCTGAT----ATTCCACTAAGTCTGGGTCT -s mr.mrrefChr3 12819 37 + 181027 GGCAAACACAGATAGCAATTCCAATGAATATGAGTGT -s simCow_chr6.simCow.chr6 441928 26 + 602619 CACAAATACTGAT----ATT------AGT-TGCATCA -s simDog_chr6.simDog.chr6 433556 33 + 593897 GGCAAATGTTGCT----ATTCCACTAAGTCCAGGTCT -s simHuman_chr6.simHuman.chr6 441998 37 + 601863 GGCAAACGCTGATATTCATCCCCTTGAGTCTGGGTCT -s simRat_chr6.simRat.chr6 466403 35 + 647215 GGCA--CACAGATAGCAATTCCAATGAATTTGAGTGT - -a -s simMouse_chr6.simMouse.chr6 454541 61 + 636262 TAACCTGACATGTGAACTTAAGTAGTAAGCAGTTAGTAGCACACTGGGGGACATCCGGGTC -s Anc0.Anc0refChr3 78945 50 + 222631 GATCCTAGTAAGTACACTTAAGTAGC-----------AGCATAATAGGGGAAATTCATGTA -s Anc1.Anc1refChr6 111152 50 + 197743 GATCCTAGTAAGTACACTTAAGTAGC-----------AGCATAATAGGGGAAATTCATGTA -s Anc2.Anc2refChr13 85371 50 + 96486 GATCCTAGTAAGTACACTTAAGTGGC-----------AGTATAATAGGGGAAATTCATGTA -s mr.mrrefChr3 12856 54 + 181027 TAACCTGATAAGTAAACTTAAGTAGT-------TAGTAGCACACTGGGGGACATTCGGGTC -s simCow_chr6.simCow.chr6 441954 50 + 602619 AATGTTAGTAGGCATACTTAAGCTGT-----------AGTATAACAGGGGACAGTCAGGTA -s simDog_chr6.simDog.chr6 433590 50 + 593897 GATCCTAGTAATTACACTTAAGTGGC-----------AGTTTAATGGGGCAAATTCATGTA -s simHuman_chr6.simHuman.chr6 442035 50 + 601863 CACACTTGTGAGTACACTTATGTATC-----------AGCATAATAGGGGAGATTCATGTA -s simRat_chr6.simRat.chr6 466438 54 + 647215 TAACCTGATAAGTAAACTTAAGTCAT-------TAGTAGCACATTGGGGGACATTTTGGTC - -a -s simMouse_chr6.simMouse.chr6 454602 54 + 636262 TAACCAAGTATGAAAAAGGGAGGATCCCTCGTGTTTACAAGCCAACCTCCTACC -s Anc0.Anc0refChr3 79001 52 + 222631 TGTCAAAGTATGAAAAAGGAAGGTTCCTTCATATCCCCAATCCAACCTCC--AT -s Anc1.Anc1refChr6 111208 54 + 197743 TGTCAAAGTATGAAAAAGGAAGGTTCCTTCATATCCCCAATCCAACCTCCTAAT -s Anc2.Anc2refChr13 85427 52 + 96486 TGTCAAAGTATGAAAAAGGAAGGTTCCTTCATATCCCCAATCCAACTTCC--AT -s mr.mrrefChr3 12910 54 + 181027 TAACCAAGTATGAAAAAGGGAGGTTCCCTCGTGTTTACAAGCCAACCTCCTACC -s simCow_chr6.simCow.chr6 442010 34 + 602619 TATCAAAGTAAGAAAAAGTAAGGTTCCTTCATAT-------------------- -s simDog_chr6.simDog.chr6 433646 52 + 593897 TGTCATAGTATGAAAAAGGAAGGTCCCTTCATATCCCCAATCCAACTTCC--AT -s simHuman_chr6.simHuman.chr6 442091 54 + 601863 TGTCTAAGTATGAAAAGGAAAGGTTCCATCATACCCCCGATCCAACCTCCTAAT -s simRat_chr6.simRat.chr6 466492 54 + 647215 CAACCAAATATGACAAAGGGAGGTTCTCTTGTGTTTACAAGCCAACCTCCTAAC - -a -s simMouse_chr6.simMouse.chr6 454656 46 + 636262 CTGTAGCCTGTTTTGCATCCATGAGGAATTAATAAATTACTGAATT -s Anc0.Anc0refChr3 79053 41 + 222631 ---TAGCCTGCCTTGCATCTATTAGTAATTAA--AATTACTGCTGT -s Anc1.Anc1refChr6 111262 44 + 197743 TTGTAGCCTGCCTTGCATCTATTAGTAATTAA--AATTACTGCTGT -s Anc2.Anc2refChr13 85479 41 + 96486 ---TAGCCTGCCTTGCATCTATTAGTAATTAA--AATTACTGCTGT -s mr.mrrefChr3 12964 46 + 181027 CTGTAGCCTGTTTTGCATCCATGAGTAATTAATAAATTACTGAAGT -s simCow_chr6.simCow.chr6 442044 38 + 602619 ------CTTGCCCTGCATCCATTAGTAATTCA--AATTACTGCTGT -s simDog_chr6.simDog.chr6 433698 41 + 593897 ---TAGCCTGCCTTGCAACTATTAGTAATTAA--AGTTACTGCTGT -s simHuman_chr6.simHuman.chr6 442146 41 + 601863 TTGTAGCCAGCATCACATCTATTAGGAATTAA--AATTATTGC--- -s simRat_chr6.simRat.chr6 466546 46 + 647215 CTGTAGCCTGTTTTGCATCCATGGGTAATTAGAAAATCAGTGAAGT - -a -s simMouse_chr6.simMouse.chr6 454702 3 + 636262 GGC -s Anc0.Anc0refChr3 79094 3 + 222631 AAC -s Anc1.Anc1refChr6 111306 3 + 197743 AAC -s Anc2.Anc2refChr13 85527 3 + 96486 AAC -s mr.mrrefChr3 13010 3 + 181027 GGC -s simCow_chr6.simCow.chr6 442082 3 + 602619 AAC -s simDog_chr6.simDog.chr6 433751 3 + 593897 AAC -s simRat_chr6.simRat.chr6 466592 3 + 647215 GGC - -a -s simMouse_chr6.simMouse.chr6 454705 9 + 636262 CTTTTTACA -s Anc0.Anc0refChr3 79103 9 + 222631 TTTATAACA -s Anc1.Anc1refChr6 111315 9 + 197743 TTTATAACA -s Anc2.Anc2refChr13 85536 9 + 96486 TTTATAACA -s mr.mrrefChr3 13019 9 + 181027 CTTTTTACA -s simCow_chr6.simCow.chr6 442091 9 + 602619 GTTATAATA -s simDog_chr6.simDog.chr6 433763 9 + 593897 TTTATAACA -s simHuman_chr6.simHuman.chr6 442192 5 + 601863 AG----ATA -s simRat_chr6.simRat.chr6 466601 9 + 647215 CCTTTTACA - -a -s simMouse_chr6.simMouse.chr6 454714 27 + 636262 ATGCTGCAGAGATCCTTTAGGTTCTTC -s Anc0.Anc0refChr3 79112 16 + 222631 ATGCCA-----------TAAATTCTTC -s Anc1.Anc1refChr6 111324 16 + 197743 ATGCCA-----------TAAATTCTTC -s Anc2.Anc2refChr13 85550 16 + 96486 ATTCCA-----------TAAATTTTTC -s mr.mrrefChr3 13028 27 + 181027 ATGCCACAGAGATCCTTTAAGTTCTTC -s simCow_chr6.simCow.chr6 442106 16 + 602619 ATTCCA-----------TAAGTTCTTC -s simDog_chr6.simDog.chr6 433777 16 + 593897 ATTCCT-----------TAAATTTTTC -s simHuman_chr6.simHuman.chr6 442197 16 + 601863 ATGCCA-----------TCCATGCCTT -s simRat_chr6.simRat.chr6 466610 27 + 647215 ATGCCACAGAGATCCTTTAAGCTCTTC - -a -s simMouse_chr6.simMouse.chr6 454741 19 + 636262 CCCTCGACACTATAGATAT -s Anc0.Anc0refChr3 79128 18 + 222631 T-CTAAACTGTTGAGATAT -s Anc1.Anc1refChr6 111340 19 + 197743 TCCTAAACTGTTGAGATAT -s Anc2.Anc2refChr13 85566 18 + 96486 T-CTAAACTGTTGAGATAT -s mr.mrrefChr3 13055 19 + 181027 TTCTCAACTGTATAGATAT -s simCow_chr6.simCow.chr6 442122 18 + 602619 T-CTAAACTGTTGACATAT -s simDog_chr6.simDog.chr6 433794 18 + 593897 T-CTAAACTGTTGAGATAT -s simHuman_chr6.simHuman.chr6 442213 2 + 601863 TC----------------- -s simRat_chr6.simRat.chr6 466637 19 + 647215 TTCTCAACTGTATAGATAT - -a -s simMouse_chr6.simMouse.chr6 454760 11 + 636262 TGCGTGCTGTA -s Anc0.Anc0refChr3 79146 11 + 222631 TGCCTGCTTTT -s Anc1.Anc1refChr6 111359 11 + 197743 TGCCTGCTTTT -s Anc2.Anc2refChr13 85584 11 + 96486 TGCCTGCTTTT -s mr.mrrefChr3 13074 11 + 181027 TGCGTGCTGTA -s simCow_chr6.simCow.chr6 442142 11 + 602619 TACCTGCTTTT -s simDog_chr6.simDog.chr6 433812 11 + 593897 TGCCTGCTTTT -s simRat_chr6.simRat.chr6 466656 11 + 647215 TGCGTCCTGTC - -a -s simMouse_chr6.simMouse.chr6 454771 24 + 636262 AATATTCTATTGTTTATGCGGGGC -s Anc0.Anc0refChr3 79157 22 + 222631 ATT--TCCATTGTCCATGAGGGAA -s Anc1.Anc1refChr6 111370 22 + 197743 ATT--TCCATTGTCCATGAGGGAA -s Anc2.Anc2refChr13 85595 22 + 96486 ATT--TCCATTGCCCCTGAGGGAA -s mr.mrrefChr3 13085 24 + 181027 AATATTCCATTGTTTATGCGGGGC -s simCow_chr6.simCow.chr6 442154 22 + 602619 ATT--TGAATAACCACTGAGTGAA -s simDog_chr6.simDog.chr6 433823 22 + 593897 ATT--TCCATTGCCCCTGAGGCCA -s simHuman_chr6.simHuman.chr6 442215 19 + 601863 -----TCCATTGTCCATTATGGAA -s simRat_chr6.simRat.chr6 466667 24 + 647215 ACTATTCCATTGTTTGTGCTGAGC - -a -s simMouse_chr6.simMouse.chr6 454795 5 + 636262 TTGTT -s Anc0.Anc0refChr3 79181 5 + 222631 ATGTT -s Anc1.Anc1refChr6 111394 5 + 197743 ATGTT -s Anc2.Anc2refChr13 85620 5 + 96486 ATGTT -s mr.mrrefChr3 13109 5 + 181027 ATGTT -s simCow_chr6.simCow.chr6 442179 5 + 602619 ATGTC -s simDog_chr6.simDog.chr6 433850 5 + 593897 ATGTT -s simHuman_chr6.simHuman.chr6 442236 5 + 601863 ATGTA -s simRat_chr6.simRat.chr6 466691 5 + 647215 ATGTT - -a -s simMouse_chr6.simMouse.chr6 454800 69 + 636262 CATAAACCTCTCAGTCTCAGTCATATATGACAACTTACTATTCAAGCACCCTAATCTGCTGCCCTGATT -s Anc0.Anc0refChr3 79187 59 + 222631 AATCAATTTCTCAGTCGTA----TATAAGAGGCCCTGCAATTTG------CTACTTGGGCACCCTGATT -s Anc1.Anc1refChr6 111400 59 + 197743 AATCAATTTCTCAGTCGTA----TATAAGAGGCCCTGCAATTTG------CTACTTGGGCACCCTGATT -s Anc2.Anc2refChr13 85626 59 + 96486 AATCAATTTCTCAGTTGTA----TATAAGAGGCCCTGCAATTTG------CTACTTGGGCACCCTCATT -s mr.mrrefChr3 13115 69 + 181027 CATAAACTTCTCAGTCTCAGTCATATATGACAACTTACTATTTAAGCACCCTAATTTGCTGCCCTGATT -s simCow_chr6.simCow.chr6 442185 43 + 602619 AACCAATTTC-----TGTA----TATAAGAGGCCCTACA--TTA------CTACTTG--------CAT- -s simDog_chr6.simDog.chr6 433856 59 + 593897 AATCAATTTCTCAGTTGTA----TATAAGAGGTCCTGCAATTTG------ATACTTGGGCACCCTCATT -s simHuman_chr6.simHuman.chr6 442242 59 + 601863 AATTAATTTCTCAGGCATA----TAGAGGAGGCCCTGCAACTTG------CTACTGGGGCACTCTGATT -s simRat_chr6.simRat.chr6 466697 69 + 647215 TGTAATCTCCTCAGTGTCAGTCATATATGACAACTTACTACTTAGGCACCCTAATTTGCTGCCCTGACT - -a -s simMouse_chr6.simMouse.chr6 454869 13 + 636262 CCAGCTGCCCTAG -s Anc0.Anc0refChr3 79246 13 + 222631 TCAGCTGTCCCAG -s Anc1.Anc1refChr6 111459 13 + 197743 TCAGCTGTCCCAG -s Anc2.Anc2refChr13 85685 13 + 96486 TCAGCTGTCCCAG -s mr.mrrefChr3 13184 13 + 181027 TCAGCTGCCCTAG -s simCow_chr6.simCow.chr6 442228 10 + 602619 ---GATGTCCCAG -s simDog_chr6.simDog.chr6 433915 13 + 593897 TCAGCTGCCCCAG -s simHuman_chr6.simHuman.chr6 442315 13 + 601863 TCAGCTGTCCCAG -s simRat_chr6.simRat.chr6 466766 13 + 647215 TCGGCTGCCCTAG - -a -s simMouse_chr6.simMouse.chr6 454882 64 + 636262 CTCCACTCTAGGAGGTCAATGACTGGTATTGACCATGTTTGAACTGGCATTAACCATGTATGAG -s Anc0.Anc0refChr3 79262 43 + 222631 CTCCACTCTAAGGGGTTAATGACTGC---------------------CATTACCCATCCAGGAG -s Anc1.Anc1refChr6 111475 43 + 197743 CTCCACTCTAAGGGGTTAATGACTGC---------------------CATTACCCATCCAGGAG -s Anc2.Anc2refChr13 85701 43 + 96486 CTTCACTCTAAGGGGTTAATGACTGC---------------------CATTACCCATCCAGGAG -s mr.mrrefChr3 13197 64 + 181027 CTCCACTCTAGGAGGTCAATGACTGGCATTGACCATGTTTGAACTGGCATTAACCATGTATGAG -s simCow_chr6.simCow.chr6 442241 42 + 602619 CTTCACTCTAAGAGGTTAATAACAG----------------------CACTACCCATCTTGGAC -s simDog_chr6.simDog.chr6 433928 43 + 593897 CTTCATTCTAAGGGGTTAATGACTGC---------------------CATTTCCCATCCAGGAG -s simHuman_chr6.simHuman.chr6 442331 43 + 601863 CTCCACTCTAAGGGATTAATGACTGC---------------------CATTACACATTGAGGAG -s simRat_chr6.simRat.chr6 466779 64 + 647215 CTCCACTGTAGGAGATCAATGACTGGCATTAACCATGTTTGAACTGGCATTAACCATGTATGAG - -a -s simMouse_chr6.simMouse.chr6 454946 67 + 636262 CCTCAGGTACGTCTTTCTTAATTTTATACTACTATGTATATCAAATAGATGAATAATGCTTGCTTGT -s Anc0.Anc0refChr3 79305 65 + 222631 CATTAGACATGTCTTTGTGAGATTTGTACAATTATTTATAGCA--TATATGAAGGGTGCTTGCAACT -s Anc1.Anc1refChr6 111518 65 + 197743 CATTAGACATGTCTTTGTGAGATTTGTACAATTATTTATAGCA--TATATGAAGGGTGCTTGCAACT -s Anc2.Anc2refChr13 85744 65 + 96486 TATTAGACATGTCTTTGTGAGATTTGCACAGTTGTTTATAGCA--TATATGGAGGGTACATACAACT -s mr.mrrefChr3 13261 67 + 181027 CCTCAGGTACGTCTTTCTTAATTTTATACTACTATGTATATCAAATAGATGAATAATGCTTGCTTGT -s simCow_chr6.simCow.chr6 442283 65 + 602619 TGTTAGACATGTATTTGTGTGATATGCACAGTTGTTTATAGCA--TATATGGAGGGTACATATACCT -s simDog_chr6.simDog.chr6 433972 63 + 593897 TATTATACAGGTCTT--TGACATTTGCACAGTTGTTTTTAACA--CATATGGCGGGTACACACAACT -s simHuman_chr6.simHuman.chr6 442374 65 + 601863 CATTGGACATGTCTCTGTGGGATTTGTAACATTAGTTATCGCA--TATATGAAGGGTGCTTGCAACT -s simRat_chr6.simRat.chr6 466843 67 + 647215 CCTCAGGTACATCTTTGTTAGCTTTATACTACTATGTATGTCAAATTGATGAATCATTCTTGCTTGT - -a -s simMouse_chr6.simMouse.chr6 455013 27 + 636262 AGTGAGAATAAGAAATACCTATATAGC -s Anc0.Anc0refChr3 79588 26 + 222631 GGTGAGAATAA-GCATACATATCTAGC -s Anc1.Anc1refChr6 111801 27 + 197743 GGTGAGAATAAGGCATACATATCTAGC -s Anc2.Anc2refChr13 86027 26 + 96486 GGTTAGAATAA-GCATACATTTCTAGC -s mr.mrrefChr3 13328 27 + 181027 AGTGAGAATAAGAAATACCTATATAGC -s simDog_chr6.simDog.chr6 434256 26 + 593897 GGTTAGAATAA-GCATACATTTCTAGC -s simHuman_chr6.simHuman.chr6 442699 27 + 601863 GGTGAGAATTAGGCATACTTATCTAGC -s simRat_chr6.simRat.chr6 466910 27 + 647215 GGTGAGAATAAGAAATACCTATATAGC - -a -s simMouse_chr6.simMouse.chr6 455040 73 + 636262 CCCTTACAAATTTTGTCAATACGATTAAGAGTTAGTCCTCTCCAGGGCAATAGATTAGCAGAAGTAAAATTGT -s Anc0.Anc0refChr3 79614 30 + 222631 CCCTCTAAAGTCC----------------------------------CAACAGGCT----AAAGTA-----TT -s Anc1.Anc1refChr6 111828 34 + 197743 CCCTCTAAAGTCC----------------------------------CAACAGGCTAGCAAAAGTA-----TT -s Anc2.Anc2refChr13 86053 30 + 96486 CCCCCTAAAGTCC----------------------------------CAACAGGCC----AAAGTA-----TT -s mr.mrrefChr3 13355 73 + 181027 CCCTTACAAATTTTGTCAATACGATTAAGAGTTAGTCCTCTCTAGGGCAATAGGTTAGCAGAAGTAAAATTGT -s simCow_chr6.simCow.chr6 442395 10 + 602619 ------------------------------------------------------CC----AAATTA-----CA -s simDog_chr6.simDog.chr6 434331 25 + 593897 CCCCCTAAAGTCC----------------------------------CAACAGG---------GCA-----TT -s simHuman_chr6.simHuman.chr6 442726 34 + 601863 CCCTCTATAGACC----------------------------------CAGCAGGCTAGCAAAAGTA-----TC -s simRat_chr6.simRat.chr6 466937 73 + 647215 CCCTTACAAATTTTGTCAAAACATGTAAAAGTCAGCCCCCTTTAGGGCAATAGGTTAACATAAGAAAAAATGG - -a -s simMouse_chr6.simMouse.chr6 455113 19 + 636262 GCTGAAGATGTAAATTGTG -s Anc0.Anc0refChr3 79644 19 + 222631 GCTGTGGATGTAAATTGTG -s Anc1.Anc1refChr6 111862 19 + 197743 GCTGTGGATGTAAATTGTG -s Anc2.Anc2refChr13 86083 19 + 96486 GCTGTGAATGTAAAGTGTG -s mr.mrrefChr3 13428 19 + 181027 GCTGAAGATGTAAATTGTG -s simCow_chr6.simCow.chr6 442405 19 + 602619 GCTGAGTATGCAACATGTG -s simDog_chr6.simDog.chr6 434356 19 + 593897 GCTGTGAATGTAAAGTGTG -s simHuman_chr6.simHuman.chr6 442766 19 + 601863 GCTGTGGATGTAGGTTGTG -s simRat_chr6.simRat.chr6 467010 19 + 647215 GCTGAAAATGTAAATTGTG - -a -s simMouse_chr6.simMouse.chr6 455132 11 + 636262 TGCTACATCCC -s Anc0.Anc0refChr3 79663 11 + 222631 TGCTACAACCT -s Anc1.Anc1refChr6 111881 11 + 197743 TGCTACAACCT -s Anc2.Anc2refChr13 86102 11 + 96486 TGCTAGAACTT -s mr.mrrefChr3 13447 11 + 181027 TGCTACATCCC -s simCow_chr6.simCow.chr6 442424 11 + 602619 TGCTAGTACTT -s simDog_chr6.simDog.chr6 434375 11 + 593897 TGCAAGAACTT -s simHuman_chr6.simHuman.chr6 442785 11 + 601863 TGCTACAACCT -s simRat_chr6.simRat.chr6 467030 11 + 647215 TGCTACATCCC - -a -s simMouse_chr6.simMouse.chr6 455143 40 + 636262 CAGTATAAGGTTAGGAAGTAACAAAAGTAAAATTCTCTCT -s Anc0.Anc0refChr3 79704 38 + 222631 CAATATAAGGTGAGGAA-CAACAAAAATGAA-TCCTCCCT -s Anc1.Anc1refChr6 111922 38 + 197743 CAATATAAGGTGAGGAA-CAACAAAAATGAA-TCCTCCCT -s Anc2.Anc2refChr13 86143 38 + 96486 CAATATAAGGTGAGGAA-CAACAAAAATGAA-TCCTCCCT -s mr.mrrefChr3 13458 40 + 181027 CAGTATAAGGTTAGGAAGCAACAAAAGTAAAATTCTCTCT -s simCow_chr6.simCow.chr6 442465 38 + 602619 CAGTGTAAGGTGAGGAA-CAATAAAAATGCA-TCCTCCGT -s simDog_chr6.simDog.chr6 434414 37 + 593897 -AATATATGGTGAGGAA-CAACATAAGTGAA-TCCTCCCT -s simHuman_chr6.simHuman.chr6 442826 38 + 601863 CAATATAAGGTGAGGAA-CAGCAAAAATGAA-TCCTCCCT -s simRat_chr6.simRat.chr6 467041 40 + 647215 CAGTAAAAGGTTAGGAAACAAGAAAAGTAAAATTCCCTCT - -a -s simMouse_chr6.simMouse.chr6 455183 6 + 636262 TGGGGT -s Anc0.Anc0refChr3 79742 6 + 222631 TAAGGT -s Anc1.Anc1refChr6 111960 6 + 197743 TAAGGT -s Anc2.Anc2refChr13 86181 6 + 96486 AAAGGT -s mr.mrrefChr3 13498 6 + 181027 TAGGGT -s simCow_chr6.simCow.chr6 442504 6 + 602619 AAAGGT -s simDog_chr6.simDog.chr6 434451 6 + 593897 AAAGGC -s simHuman_chr6.simHuman.chr6 442864 6 + 601863 TAAGGT -s simRat_chr6.simRat.chr6 467081 6 + 647215 CAGGGT - -a -s simMouse_chr6.simMouse.chr6 455189 1 + 636262 T -s Anc0.Anc0refChr3 79749 1 + 222631 T -s Anc1.Anc1refChr6 111967 1 + 197743 T -s Anc2.Anc2refChr13 86188 1 + 96486 T -s mr.mrrefChr3 13504 1 + 181027 T -s simCow_chr6.simCow.chr6 442511 1 + 602619 C -s simDog_chr6.simDog.chr6 434458 1 + 593897 T -s simHuman_chr6.simHuman.chr6 442871 1 + 601863 T -s simRat_chr6.simRat.chr6 467087 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 455190 5 + 636262 AGTTG -s Anc0.Anc0refChr3 79751 5 + 222631 AGTTG -s Anc1.Anc1refChr6 111969 5 + 197743 AGTTG -s Anc2.Anc2refChr13 86190 5 + 96486 AGTGG -s mr.mrrefChr3 13506 5 + 181027 AGTTG -s simCow_chr6.simCow.chr6 442513 5 + 602619 ATCGG -s simDog_chr6.simDog.chr6 434460 5 + 593897 AGTGG -s simHuman_chr6.simHuman.chr6 442873 5 + 601863 AGTTG -s simRat_chr6.simRat.chr6 467089 5 + 647215 AGTGG - -a -s simMouse_chr6.simMouse.chr6 455195 15 + 636262 ACAAGCCAACATTGA -s Anc0.Anc0refChr3 79757 14 + 222631 GCAAG-TAATACAGA -s Anc1.Anc1refChr6 111975 15 + 197743 GCAAGTTAATACAGA -s Anc2.Anc2refChr13 86196 14 + 96486 GCAAG-TAATACAGA -s mr.mrrefChr3 13511 15 + 181027 GCAAGTCAACATTGA -s simCow_chr6.simCow.chr6 442519 11 + 602619 GAAAG-TGATAC--- -s simDog_chr6.simDog.chr6 434466 14 + 593897 GCGAG-CACTACAGA -s simHuman_chr6.simHuman.chr6 442879 15 + 601863 GCAAGTTAATACAGA -s simRat_chr6.simRat.chr6 467094 15 + 647215 GCAAGTCAACATTGA - -a -s simMouse_chr6.simMouse.chr6 455210 82 + 636262 GAAATCTACATTGACAATAATTTCTTGCATGCACATTCTGTTATGTCACTCAGAGCAGAAAAACATCAAATCATACCAGTAA -s Anc0.Anc0refChr3 79774 66 + 222631 GAAATCTTCATTGCCAATAATTTGTTGCAGGAACCTTCTGTTTTGTAGCTCAGAACAGAG-----------TAAGCT----- -s Anc1.Anc1refChr6 111993 66 + 197743 GAAATCTTCATTGCCAATAATTTGTTGCAGGAACCTTCTGTTTTGTAGCTCAGAACAGAG-----------TAAGCT----- -s Anc2.Anc2refChr13 86213 66 + 96486 GAAATCTTCATTGCCAATAATTTGTTGCAGGAACCTTCTGTTTTGTAGCTCAGAACAGAG-----------TCAGCT----- -s mr.mrrefChr3 13526 71 + 181027 GAAATCTTCATTGACAATAATTTCTTGCATGAACATTCTGTTATGTCACTCAGAGCAGAA-----------CATACCAGTAA -s simCow_chr6.simCow.chr6 442531 58 + 602619 GAATTTTTCATTGCCAATAATTTGTTGCA-----CTTGTGTTCTGTAG--CAGAACAGAG-----------C-AGCT----- -s simDog_chr6.simDog.chr6 434483 66 + 593897 GAAATCTTCATTGCTAATCATTTATTGCAGGAACCTTCTGTTTTGTAGCTTGGAACAGAG-----------TCAGCT----- -s simHuman_chr6.simHuman.chr6 442897 66 + 601863 GAACTCTTCATTGCCAATAATTTGTTGCAGGAACCTTCTGTTGTGTAGCTCAGAACAAAG-----------TAGGCT----- -s simRat_chr6.simRat.chr6 467109 71 + 647215 GAAATCTTCATTGACAATAATTTTTTGGGTGAACATTCTGTTATGTCCTTAGGATTTGAA-----------CATACAAGCAA - -a -s simMouse_chr6.simMouse.chr6 455292 6 + 636262 TAAGAG -s Anc0.Anc0refChr3 79840 1 + 222631 -----T -s Anc1.Anc1refChr6 112059 1 + 197743 -----T -s Anc2.Anc2refChr13 86279 1 + 96486 -----T -s mr.mrrefChr3 13597 6 + 181027 TAGGAT -s simCow_chr6.simCow.chr6 442589 1 + 602619 -----T -s simDog_chr6.simDog.chr6 434549 1 + 593897 -----T -s simHuman_chr6.simHuman.chr6 442963 1 + 601863 -----T -s simRat_chr6.simRat.chr6 467240 6 + 647215 TAGGAT - -a -s simMouse_chr6.simMouse.chr6 455298 38 + 636262 TTGAAAATACAAGAATTTCATAAGTAGCCTGTGATCTT -s Anc0.Anc0refChr3 79841 19 + 222631 CTGAACCTACAAGA----CATAA--------------- -s Anc1.Anc1refChr6 112060 19 + 197743 CTGAACCTACAAGA----CATAA--------------- -s Anc2.Anc2refChr13 86291 19 + 96486 CTGAACCTACAAGA----CATAA--------------- -s mr.mrrefChr3 13603 38 + 181027 TTGAACATACAAGAATTTCATAAGTAGCCTGTGATCTT -s simCow_chr6.simCow.chr6 442601 19 + 602619 ATCGACCTAGAAGA----CAAAA--------------- -s simDog_chr6.simDog.chr6 434561 19 + 593897 CTGAACTGACCAGA----GATAA--------------- -s simHuman_chr6.simHuman.chr6 442964 19 + 601863 CTGTACCTACAAGA----CATGA--------------- -s simRat_chr6.simRat.chr6 467246 38 + 647215 TTGAACATACAAGAATTTTATAGGTGGCCTGTGGCCTT - -a -s simMouse_chr6.simMouse.chr6 455336 44 + 636262 TCACCATTAGTCCTAGGCTTAGGACCTAAGATAGACCTACAAGG -s Anc0.Anc0refChr3 79860 7 + 222631 -------------------------------------TACATGA -s Anc1.Anc1refChr6 112079 7 + 197743 -------------------------------------TACATGA -s Anc2.Anc2refChr13 86310 7 + 96486 -------------------------------------AACATGA -s mr.mrrefChr3 13641 44 + 181027 TCACCATTAGTCCTAGGCTTAGGACCTAAGATAGACCTACAAGG -s simCow_chr6.simCow.chr6 442620 7 + 602619 -------------------------------------AACATGG -s simDog_chr6.simDog.chr6 434580 7 + 593897 -------------------------------------AACATTA -s simHuman_chr6.simHuman.chr6 442983 7 + 601863 -------------------------------------TACATGA -s simRat_chr6.simRat.chr6 467286 44 + 647215 TTACCATGAGTTCTAGGCTTAAGACCTAGGCTAGACCTACAAGG - -a -s simMouse_chr6.simMouse.chr6 455380 66 + 636262 GCCTACCAGTATCACACAAAATAACCAAGAAACAAATATGACCAATCTTCTGTCAGTTGAGAAAAA -s Anc0.Anc0refChr3 79875 62 + 222631 GTCTACCCATATTGCACAAAA----CAAGAATTGAATGATACCAATCCTCTATCAGTTGAAAAAAG -s Anc1.Anc1refChr6 112094 66 + 197743 GTCTACCCATATTGCACAAAACAACCAAGAATTGAATGATACCAATCCTCTATCAGTTGAAAAAAG -s Anc2.Anc2refChr13 86325 62 + 96486 GTCCACCCATATTGCACACAG----CAAGAATTGAATGATACCAATCCTCTATCAGTTGAAAAAAG -s mr.mrrefChr3 13685 66 + 181027 GCCTACCAGTATCACACAAAATAACCAAGAAACAAATATGACCAATCTTCTGTCAGTTGAGAAAAA -s simCow_chr6.simCow.chr6 442635 62 + 602619 GACAACCCATATTGCACACAG----CAAGTATTGAATAATACCACTTTTGTATCAGTTGAAAAAAG -s simDog_chr6.simDog.chr6 434595 62 + 593897 GTCCACCCATATTGCACACAG----CAAGAATTGAATGATACCAATCCTCTATCAGTTGAAAAAAG -s simHuman_chr6.simHuman.chr6 442998 31 + 601863 GTCTATCCATATTGCACAAAACAACCATATA----------------------------------- -s simRat_chr6.simRat.chr6 467330 66 + 647215 GTCTACCAGTATCACACGAAACAATCAAGAAACAGATATGATCAATCTTCTGTCAGTTAAGAAAAT - -a -s simMouse_chr6.simMouse.chr6 455446 63 + 636262 GCATGTGTTGCTATACGATTTCTCAAACACCTGCCATCTGTGCATGTGTGTGTAAAAATACAG -s Anc0.Anc0refChr3 79937 24 + 222631 GCATATGTGTGTGTGC---------------------------------------AATTACAG -s Anc1.Anc1refChr6 112160 24 + 197743 GCATATGTGTGTGTGC---------------------------------------AATTACAG -s Anc2.Anc2refChr13 86388 24 + 96486 GCATATGTGTGTGTGT---------------------------------------GATTACAG -s mr.mrrefChr3 13751 63 + 181027 GCATGTGTTGCTATACGATTTCTCAAACACCTGCCATCTGTGCATGTGTGTGTAAAAATACAG -s simCow_chr6.simCow.chr6 442735 24 + 602619 GCATATTTTTGTGTGT---------------------------------------GATTACAG -s simDog_chr6.simDog.chr6 434658 24 + 593897 GTGTGTGTGTGTGTGT---------------------------------------GATTACAG -s simHuman_chr6.simHuman.chr6 443029 23 + 601863 -CATATGTGCGGGTGC---------------------------------------AAGTACAG -s simRat_chr6.simRat.chr6 467396 63 + 647215 CCACTTGTTGCTATCTGATTTCTTAACCGCCTGCCACATGTGCATGTATTTGTGAAAATACAG - -a -s simMouse_chr6.simMouse.chr6 455509 15 + 636262 AATCACGGAAAATAA -s Anc0.Anc0refChr3 79961 10 + 222631 AATTCC-----ATAA -s Anc1.Anc1refChr6 112184 10 + 197743 AATTCC-----ATAA -s Anc2.Anc2refChr13 86423 10 + 96486 AATTCC-----ATAA -s mr.mrrefChr3 13814 10 + 181027 AATCAC-----ATAA -s simCow_chr6.simCow.chr6 442770 10 + 602619 GATTCC-----ATAG -s simDog_chr6.simDog.chr6 434694 10 + 593897 AATTCC-----ATAA -s simHuman_chr6.simHuman.chr6 443052 3 + 601863 AGC------------ -s simRat_chr6.simRat.chr6 467459 10 + 647215 AATTAC-----ATTA - -a -s simMouse_chr6.simMouse.chr6 455524 53 + 636262 TGCATGTTCTACACCTGGAGCCACCCTCATGATTTTAGTGCGTCCTAGTCCTG -s Anc0.Anc0refChr3 79971 53 + 222631 TGTATGTTCTACACTCAGAGCCACCCTCATGCCTTTAATGCAACCTTGTATTT -s Anc1.Anc1refChr6 112194 53 + 197743 TGTATGTTCTACACTCAGAGCCACCCTCATGCCTTTAATGCAACCTTGTATTT -s Anc2.Anc2refChr13 86443 53 + 96486 TGTATGTTATAAGCTCAAAGTCACCCTCATGCCTTTAATGCAACCTTTTATTT -s mr.mrrefChr3 13824 53 + 181027 TGCATGTTCTACACCTGGAGCCACCCTCATGATTTTAGTGCGTCCTAGTCCTG -s simCow_chr6.simCow.chr6 442790 53 + 602619 CGTATGTTATAAGCCCAAAACCACCCTCATGCCTTTAATCTGACCTAATATTT -s simDog_chr6.simDog.chr6 434714 52 + 593897 TGTATGTTATAAGCTCAAAGTGACCCTCCTGACATCAATGCATCTTTTTAT-T -s simHuman_chr6.simHuman.chr6 443055 47 + 601863 ------TGCTCCAGAAAGGACCACCCTCATGCCTTTAATGCAACCTGGTATTT -s simRat_chr6.simRat.chr6 467469 53 + 647215 TGTATGTTCTACACCTAAAGCCACCCTCATGATTTTAGTGTATCCTAGTCTTG - -a -s simMouse_chr6.simMouse.chr6 455577 47 + 636262 TTGCCGTAATACACATTAGAATGTGCTCCACCAAATGTGATAATGAT -s Anc0.Anc0refChr3 80024 47 + 222631 TTGTAGTAGTGCACATTTGAATGTGCTAAGCAAAATGTGATAATGAT -s Anc1.Anc1refChr6 112247 47 + 197743 TTGTAGTAGTGCACATTTGAATGTGCTAAGCAAAATGTGATAATGAT -s Anc2.Anc2refChr13 86496 47 + 96486 TTGTAGTGGTGCACATTTAAATGTGCTAAGCAGAATGTGATAATGAT -s mr.mrrefChr3 13877 47 + 181027 TTGCCGTAATACACATTAGAATGTGCTCCACCAAATGTGATAATGAT -s simCow_chr6.simCow.chr6 442849 45 + 602619 TTCTAGTGGTGTACGTTT--GTGTGGTAAGCAGAATGTGATAATGAT -s simDog_chr6.simDog.chr6 434766 47 + 593897 TTGCAGTGGTGCACACTTAAATGTGCCAAACAGGATGTGATAATGAT -s simHuman_chr6.simHuman.chr6 443102 45 + 601863 TTGTAGTAGTGCA--TTGGAATGGACTAAGTAAAATGTGATAATGAT -s simRat_chr6.simRat.chr6 467522 47 + 647215 TTGCAGTAATGCACATTATAATGGGCTCCACCAATTGTAATAATGAG - -a -s simMouse_chr6.simMouse.chr6 455624 3 + 636262 ACT -s Anc0.Anc0refChr3 80071 3 + 222631 ACT -s Anc1.Anc1refChr6 112294 3 + 197743 ACT -s Anc2.Anc2refChr13 86548 3 + 96486 ACT -s mr.mrrefChr3 13924 3 + 181027 ACT -s simCow_chr6.simCow.chr6 442899 3 + 602619 GCT -s simDog_chr6.simDog.chr6 434818 3 + 593897 ACT -s simHuman_chr6.simHuman.chr6 443147 3 + 601863 GTT -s simRat_chr6.simRat.chr6 467569 3 + 647215 ACT - -a -s simMouse_chr6.simMouse.chr6 455627 22 + 636262 GATGGATGTTTATGCTACTACT -s Anc0.Anc0refChr3 80075 22 + 222631 GACAATTGTTTATCATATTACT -s Anc1.Anc1refChr6 112298 22 + 197743 GACAATTGTTTATCATATTACT -s Anc2.Anc2refChr13 86552 22 + 96486 GACAATTGTTTATCATGTTACT -s mr.mrrefChr3 13927 22 + 181027 GATGGATGTTTATGCTACTACT -s simCow_chr6.simCow.chr6 442903 13 + 602619 GACA---------CATGTTACT -s simDog_chr6.simDog.chr6 434822 22 + 593897 GACAATTGTTTATTATGCTACT -s simHuman_chr6.simHuman.chr6 443151 22 + 601863 GACAACTGTTTACCACATTTCT -s simRat_chr6.simRat.chr6 467573 22 + 647215 GATGGATGTTTATCCTACTACT - -a -s simMouse_chr6.simMouse.chr6 455649 19 + 636262 TAAGGAACATGAAATCATA -s Anc0.Anc0refChr3 80097 10 + 222631 TAAGGTATA---------A -s Anc1.Anc1refChr6 112320 10 + 197743 TAAGGTATA---------A -s Anc2.Anc2refChr13 86574 10 + 96486 TAAGGTATA---------T -s mr.mrrefChr3 13949 10 + 181027 TAAGGAACA---------A -s simCow_chr6.simCow.chr6 442918 10 + 602619 TAAAGTATA---------T -s simDog_chr6.simDog.chr6 434844 10 + 593897 TAAGGTATA---------T -s simHuman_chr6.simHuman.chr6 443173 10 + 601863 TAAGGCATA---------A -s simRat_chr6.simRat.chr6 467595 10 + 647215 TAAGCAATA---------A - -a -s simMouse_chr6.simMouse.chr6 455668 51 + 636262 AGTAAATTGAGTGAGGGTGTATAGAGCTGAAGATCTTAGGCTACAGGCAAT -s Anc0.Anc0refChr3 80116 48 + 222631 ATCAAGTTGGGGGAAGCTGCACAGAGAC--AGAGCTCAGGATACAG-CAAC -s Anc1.Anc1refChr6 112339 48 + 197743 ATCAAGTTGGGGGAAGCTGCACAGAGAC--AGAGCTCAGGATACAG-CAAC -s Anc2.Anc2refChr13 86593 48 + 96486 ATCAAGTTGGGGGAAGCTGCACAGAGAC--AGAGCTCAGGATACAG-CCAC -s mr.mrrefChr3 13959 51 + 181027 AGTAAATTGAGTGAGGGTGTATAGAGCTGAAGATCTTAGGCTACAGGCAAT -s simCow_chr6.simCow.chr6 442937 48 + 602619 ATCAAGTTGGGTGAAGCTGCACAGAGAC--AGAGCTCAGGATACAG-CCAA -s simDog_chr6.simDog.chr6 434863 48 + 593897 TTCAAGTTGGCGGAAGCTGTGCAGAGAT--AGTGCTCAGGATACAG-CCAC -s simHuman_chr6.simHuman.chr6 443192 47 + 601863 ATCAATTTGGGGGAAG-TGCACAGAGAC--AGAGCTCAGGACACAG-CAAC -s simRat_chr6.simRat.chr6 467605 51 + 647215 ACTAAGTTGATGGAGGGTGCATAGAGACAGAGCTCCTAGGATACAGGCAAT - -a -s simMouse_chr6.simMouse.chr6 455719 38 + 636262 GGGTGCCAAAAGTGTTCATTACCTAAACTAAATCATTA -s Anc0.Anc0refChr3 80195 38 + 222631 GAGTGCTAAAAGTGTTTATGCCGTTAACCAAATCATTA -s Anc1.Anc1refChr6 112418 38 + 197743 GAGTGCTAAAAGTGTTTATGCCGTTAACCAAATCATTA -s Anc2.Anc2refChr13 86672 38 + 96486 GAGAGCTAAAAGTGCCTATGCCGTTACCCAAATTATTA -s mr.mrrefChr3 14010 38 + 181027 GGGTGCCAAAAGTGTTCATTACCTAAACTAAATCATTA -s simCow_chr6.simCow.chr6 443004 21 + 602619 -----------------ATGCCGTTACCCAAATTATTA -s simDog_chr6.simDog.chr6 434942 29 + 593897 GAGAGCTAAAAGTGCCTATGCT---------GTTATTA -s simHuman_chr6.simHuman.chr6 443303 38 + 601863 GAGTGCTAAAAATGTTTATGCCTTGAACCAGATCATTA -s simRat_chr6.simRat.chr6 467656 38 + 647215 GAGTGTCAAAAGTGTCCCTGACTTAAAATAAATTGTTA - -a -s simMouse_chr6.simMouse.chr6 455757 22 + 636262 AGCACCTGGGACTGTTATTTTT -s Anc0.Anc0refChr3 80233 22 + 222631 ATAGCCTGGGACTGTCATTTTT -s Anc1.Anc1refChr6 112456 22 + 197743 ATAGCCTGGGACTGTCATTTTT -s Anc2.Anc2refChr13 86710 22 + 96486 ATAGCCTGGGACTGTCATTTTT -s mr.mrrefChr3 14048 22 + 181027 AGCACCTGGGACTGTTATTTTT -s simCow_chr6.simCow.chr6 443027 22 + 602619 AGAGCCTGGGACTGTCATTTTT -s simDog_chr6.simDog.chr6 434971 22 + 593897 ATGGCTCAGGACTGTCATTTTT -s simHuman_chr6.simHuman.chr6 443341 22 + 601863 ATAGCCTGAGACTGTCATTTTT -s simRat_chr6.simRat.chr6 467694 22 + 647215 AGCACCTGGGACTGTTATTTTT - -a -s simMouse_chr6.simMouse.chr6 455779 68 + 636262 TTTGGATGTGTGTAGGTGTTGGCAACTTAGGGTTTGATCCACATTGAGATCACAGGATATATATTATA -s Anc0.Anc0refChr3 80257 67 + 222631 TTTGGCTGGGAGTAGGCTTTGGAAACCTAGGGTTT-ACCCGCCTTGAGATAGCAGGGTGTTTATTTAA -s Anc1.Anc1refChr6 112480 68 + 197743 TTTGGCTGGGAGTAGGCTTTGGAAACCTAGGGTTTGACCCGCCTTGAGATAGCAGGGTGTTTATTTAA -s Anc2.Anc2refChr13 86734 67 + 96486 TTTGGCTGGGAGTAGGCTTTGGAAACCAAGGGTGT-ACCTGCCTTGAGAGAGCAGGGTGTTTATCTAA -s mr.mrrefChr3 14070 68 + 181027 TTTGGATGTGTGTAGGTGTTGGCAACTTAGGGTTTGATCCACATTGAGATCACAGGATATATATTATA -s simCow_chr6.simCow.chr6 443051 67 + 602619 TTTGGCTAGGAGCAGACTTTGTAAACCAAGGGTGT-ACCTGTCTTGAGAGAGCAGGTTGTTTATCTAT -s simDog_chr6.simDog.chr6 434995 67 + 593897 TTTAGCTGGGAGTAGGCTTTTGAAACCTAGGGTGT-ATCTGCCTTGAGAGAGCTGGGGCTCTATCTAA -s simHuman_chr6.simHuman.chr6 443365 65 + 601863 TTTGGCTGGGACTGGGCTTTGGAA---TAGGGTTAGACCCGCCTTGAGATAGCAGGGTGTTTATTTAA -s simRat_chr6.simRat.chr6 467716 68 + 647215 TTTGGATGGGTGTAGGTGTTGGCAACTTAGGGTTTGATCCAGATTGAGAGCACAGGATATATACCATA - -a -s simMouse_chr6.simMouse.chr6 455847 31 + 636262 CTAGTTCAGTCATGGGACACTGCCTTGTTGG -s Anc0.Anc0refChr3 80331 31 + 222631 CTGGTCCAGTAATGGGACTCTATCATGATAG -s Anc1.Anc1refChr6 112555 31 + 197743 CTGGTCCAGTAATGGGACTCTATCATGATAG -s Anc2.Anc2refChr13 86808 31 + 96486 CTGGTCCAGTAATGGGACTCTATCATGATAG -s mr.mrrefChr3 14138 31 + 181027 CTAGTTCAGTCATGGGACACTGCCTTGTTGG -s simCow_chr6.simCow.chr6 443125 31 + 602619 TTGGTCCATTATTGGGACACTGTCATGATAG -s simDog_chr6.simDog.chr6 435069 31 + 593897 CTGGTCCAGAAATGGCACTCTATCATGATAG -s simHuman_chr6.simHuman.chr6 443437 31 + 601863 CTGGTACAGTTATGGGGGGCTTTCATGATAG -s simRat_chr6.simRat.chr6 467784 31 + 647215 CTGGTTCAATCATGGGACACCATTTTGGTGG - -a -s simMouse_chr6.simMouse.chr6 455878 67 + 636262 GATTGTAAAAGTCATGTCCCAATGGGATAATTCTAGGACAGTGATCTAGGACGGTGCAGATGAACTT -s Anc0.Anc0refChr3 80375 67 + 222631 GACTGTAAAGATTATATTCCGCTGGATTAACTCTAGCCCAGTGATCTTGGAAAGGGCAGGTTAAGTT -s Anc1.Anc1refChr6 112599 67 + 197743 GACTGTAAAGATTATATTCCGCTGGATTAACTCTAGCCCAGTGATCTTGGAAAGGGCAGGTTAAGTT -s Anc2.Anc2refChr13 86852 67 + 96486 GACTGTAAAGATTATATTTTGCTGGATTCACTCTAGCCCAGTGATCTTTGAAAGGACAGGCTAAGTT -s mr.mrrefChr3 14169 67 + 181027 GATTGTAAAAGTCATGTCCCAATGGGATAATTCTAGGACAGTGATCTAGGACGGTGCAGATGAACTT -s simCow_chr6.simCow.chr6 443169 67 + 602619 GACAGTAAAGATTTTATTTTGATGGATTCACTTTATCCCAGTGATCTTCGAGAGGACAGGCTAAGCT -s simDog_chr6.simDog.chr6 435113 66 + 593897 GACTGTAAAGCTTACATTTTGCTGGATGCACTCTAGCCCTGTGATCTTTGAAAGCAC-GGCTAAGTT -s simHuman_chr6.simHuman.chr6 443481 67 + 601863 GACTGTAAAGATTATACTCCGCTGGATTAACTCTAGCCCAGTGATCTTGGAAAGGGCAGGTTAAGTT -s simRat_chr6.simRat.chr6 467815 67 + 647215 GATTGTAAAAGTTATGTCTCGATGGAACAATTCAAGAATAGTAATCTTGGAAAGCATAGACAAACTT - -a -s simMouse_chr6.simMouse.chr6 455945 20 + 636262 CAAGTACATGGAGTCCAAAG -s Anc0.Anc0refChr3 80453 20 + 222631 CAAGTACATGGAATCCAAAG -s Anc1.Anc1refChr6 112677 20 + 197743 CAAGTACATGGAATCCAAAG -s Anc2.Anc2refChr13 86930 20 + 96486 CAAGTACATGGAATCCAATG -s mr.mrrefChr3 14236 20 + 181027 CAAGTACATGGAGTCCAAAG -s simCow_chr6.simCow.chr6 443247 20 + 602619 CAAGTACAGGGAATCCAATG -s simDog_chr6.simDog.chr6 435190 20 + 593897 GAATTAGATGGACTGAAATG -s simHuman_chr6.simHuman.chr6 443559 20 + 601863 CAAGTACATGGAATCCAAAG -s simRat_chr6.simRat.chr6 467882 20 + 647215 CAAGTACATCGAGTCCAAAG - -a -s simMouse_chr6.simMouse.chr6 455965 2 + 636262 TA -s Anc0.Anc0refChr3 80535 1 + 222631 G- -s Anc1.Anc1refChr6 112759 1 + 197743 G- -s Anc2.Anc2refChr13 87012 1 + 96486 G- -s mr.mrrefChr3 14256 1 + 181027 T- -s simCow_chr6.simCow.chr6 443328 1 + 602619 G- -s simDog_chr6.simDog.chr6 435272 1 + 593897 G- -s simHuman_chr6.simHuman.chr6 443651 1 + 601863 G- -s simRat_chr6.simRat.chr6 467902 1 + 647215 T- - -a -s simMouse_chr6.simMouse.chr6 455967 26 + 636262 TAAATTTAATGATATACCAGCTGAAA -s Anc0.Anc0refChr3 160386 25 - 222631 TATAATTA-TGATATCTCAGGTGGAA -s Anc1.Anc1refChr6 104481 25 - 197743 TATAATTA-TGATATCTCAGGTGGAA -s Anc2.Anc2refChr13 29373 25 - 96486 TATGATTA-TGATATCTCAAGTGGAA -s mr.mrrefChr5 8917 25 - 294540 TAAAATTA-TGATATACCAGCTGAAA -s simCow_chr6.simCow.chr6 178138 25 - 602619 TATGAATA-TGATATCTCAAGTGGAA -s simDog_chr6.simDog.chr6 179589 25 - 593897 TGTGATTG-TGATATCCCAAGTGGGA -s simHuman_chr6.simHuman.chr6 183121 25 - 601863 TATAATTA-TGATATCTCAGGTGGAA -s simRat_chr6.simRat.chr6 207684 25 - 647215 TACAATCA-TGATATACTAACTGAAA - -a -s simMouse_chr6.simMouse.chr6 455993 18 + 636262 TAGTACCAGATAGATCTC -s Anc0.Anc0refChr3 160413 12 - 222631 TAGTGCAAGATT------ -s Anc1.Anc1refChr6 104508 12 - 197743 TAGTGCAAGATT------ -s Anc2.Anc2refChr13 29400 12 - 96486 TAGTGCAAGATT------ -s mr.mrrefChr5 8942 12 - 294540 TAGTGCAAGATA------ -s simCow_chr6.simCow.chr6 178165 12 - 602619 TAGTGCAAGACT------ -s simDog_chr6.simDog.chr6 179616 12 - 593897 TAGCGCAAGATT------ -s simHuman_chr6.simHuman.chr6 183148 12 - 601863 TGGTGCAAGATC------ -s simRat_chr6.simRat.chr6 207709 12 - 647215 TCGTGCAAGATA------ - -a -s simMouse_chr6.simMouse.chr6 456011 2 + 636262 AA -s Anc0.Anc0refChr3 160434 2 - 222631 AC -s Anc1.Anc1refChr6 104529 2 - 197743 AC -s Anc2.Anc2refChr13 29421 2 - 96486 AC -s mr.mrrefChr5 8954 2 - 294540 AA -s simCow_chr6.simCow.chr6 178186 2 - 602619 AC -s simDog_chr6.simDog.chr6 179637 2 - 593897 AT -s simHuman_chr6.simHuman.chr6 183169 2 - 601863 AC -s simRat_chr6.simRat.chr6 207721 2 - 647215 AA - -a -s simMouse_chr6.simMouse.chr6 456013 13 + 636262 CCATTACTCATAA -s Anc0.Anc0refChr3 160436 13 - 222631 TAAGCACTAATAA -s Anc1.Anc1refChr6 104531 13 - 197743 TAAGCACTAATAA -s Anc2.Anc2refChr13 29423 13 - 96486 TAAGCATTAATAA -s mr.mrrefChr5 8956 13 - 294540 CCATTACTCATAA -s simCow_chr6.simCow.chr6 178193 13 - 602619 TAAGCATTAATAC -s simDog_chr6.simDog.chr6 179639 13 - 593897 CAAGCATTAATAA -s simHuman_chr6.simHuman.chr6 183171 13 - 601863 TAAGCACTAATAA -s simRat_chr6.simRat.chr6 207723 13 - 647215 CCATTACTCATAA - -a -s simMouse_chr6.simMouse.chr6 456026 54 + 636262 AAGAAGCCCAGAAAAAAACCTAAGTTTGCCTCATCCACCAGAGAAAGCAAGGAT -s Anc0.Anc0refChr3 160450 20 - 222631 AGGGAGATCAGGAG--------------CT--------------------GGAT -s Anc1.Anc1refChr6 104545 20 - 197743 AGGGAGATCAGGAG--------------CT--------------------GGAT -s Anc2.Anc2refChr13 29437 20 - 96486 AGGGAGATCAGGAG--------------CT--------------------GGAT -s mr.mrrefChr5 8970 40 - 294540 AAGAAGCCCAGAAA--------------CCTCATCCACCAGAGAAAGTAAGGAT -s simCow_chr6.simCow.chr6 178207 20 - 602619 AGGGAGATGAGGAG--------------CT--------------------GGAT -s simDog_chr6.simDog.chr6 179653 15 - 593897 A-----ACCAGAAG--------------CA--------------------CGAT -s simHuman_chr6.simHuman.chr6 183185 20 - 601863 AGGGAGATCAGGAG--------------CT--------------------GGAT -s simRat_chr6.simRat.chr6 207737 40 - 647215 AAGAAGCCCAGAAA--------------CGTTAACCTCCAAAGAAAGTAAGGAT - -a -s simMouse_chr6.simMouse.chr6 456080 21 + 636262 TGTATTGTGTCATATACCACA -s Anc0.Anc0refChr3 160471 21 - 222631 GGTGTGGAAATTTGAAGTTCA -s Anc1.Anc1refChr6 104566 21 - 197743 GGTGTGGAAATTTGAAGTTCA -s Anc2.Anc2refChr13 29458 21 - 96486 GGTGTGGAAATTTGAAGTTCA -s mr.mrrefChr5 9010 21 - 294540 TGTATTGAGTCATATACCACA -s simCow_chr6.simCow.chr6 178227 21 - 602619 GGTGTGGAAGTTTGAAGTTCA -s simDog_chr6.simDog.chr6 179669 13 - 593897 --------AACTCAGCATCAA -s simHuman_chr6.simHuman.chr6 183206 21 - 601863 GGTGTGGAAATTTGAAGTTCA -s simRat_chr6.simRat.chr6 207777 21 - 647215 TGTGTTGAGTCCTATGCCACA - -a -s simMouse_chr6.simMouse.chr6 456101 23 + 636262 CTTGGTGACTGTTTGGGGTCAGC -s Anc0.Anc0refChr3 160493 6 - 222631 CTTAAT----------------- -s Anc1.Anc1refChr6 104588 13 - 197743 CTTAATT----------GCCAAA -s Anc2.Anc2refChr13 29480 6 - 96486 CTTAAT----------------- -s mr.mrrefChr5 9031 23 - 294540 CTTAGTTACTGTTTGGGGTCAGC -s simCow_chr6.simCow.chr6 178249 6 - 602619 CTTAAT----------------- -s simDog_chr6.simDog.chr6 179683 6 - 593897 AGTAGT----------------- -s simHuman_chr6.simHuman.chr6 183228 13 - 601863 CTTAATT----------GCCAAA -s simRat_chr6.simRat.chr6 207798 23 - 647215 CTTAGTTACTGTTTGGGGTGAGC - -a -s simMouse_chr6.simMouse.chr6 456124 18 + 636262 TGAATACATTATGTTTTT -s Anc0.Anc0refChr3 160499 18 - 222631 TGAATAAATTATGTTCTG -s Anc1.Anc1refChr6 104601 18 - 197743 TGAATAAATTATGTTCTG -s Anc2.Anc2refChr13 29486 18 - 96486 TGAATAAACTATATTCTG -s mr.mrrefChr5 9054 18 - 294540 TGAATACATTATGTTTTT -s simCow_chr6.simCow.chr6 178336 18 - 602619 TGAATACACTATGTTCTG -s simDog_chr6.simDog.chr6 179689 18 - 593897 TGAATAAACAATATTCTG -s simHuman_chr6.simHuman.chr6 183241 16 - 601863 GAAATATATTGGG--CTG -s simRat_chr6.simRat.chr6 207821 17 - 647215 TGAAT-CATAATGTTTCT - -a -s simMouse_chr6.simMouse.chr6 456142 18 + 636262 GTATTCCTATACCGTCTT -s Anc0.Anc0refChr3 160517 18 - 222631 GCATGCAAAAAGCCTTTT -s Anc1.Anc1refChr6 104619 18 - 197743 GCATGCAAAAAGCCTTTT -s Anc2.Anc2refChr13 29504 18 - 96486 GCATGCAAAAAGCCTTCT -s mr.mrrefChr5 9072 18 - 294540 GTATTCATATAGCGTCTT -s simCow_chr6.simCow.chr6 178354 18 - 602619 GCATTCAAAAAACCTTCG -s simDog_chr6.simDog.chr6 179707 18 - 593897 GCATGCAAAGAGCCTCCT -s simHuman_chr6.simHuman.chr6 183257 18 - 601863 GCATGCAGAAAGCCTTTT -s simRat_chr6.simRat.chr6 207849 18 - 647215 GGATTCACATAGTGACTT - -a -s simMouse_chr6.simMouse.chr6 456160 27 + 636262 TTCTCAATCTAATAAAAAGACACAACA -s Anc0.Anc0refChr3 160535 27 - 222631 TTCTCAACCTATTCAGGAAACAAAATA -s Anc1.Anc1refChr6 104637 27 - 197743 TTCTCAACCTATTCAGGAAACAAAATA -s Anc2.Anc2refChr13 29523 27 - 96486 TTCTCAACCTATTCAGGAAACAAAATA -s mr.mrrefChr5 9090 27 - 294540 TTCTCAACCTAATAAAAAGACACAATA -s simCow_chr6.simCow.chr6 178373 27 - 602619 CTCTCAATCTATTCAGGTAACACCACA -s simDog_chr6.simDog.chr6 179726 27 - 593897 TGCTCAACATATTCTGGAAACAAAATA -s simHuman_chr6.simHuman.chr6 183275 27 - 601863 ATTCCAACCTATTCAGGAAACATAATA -s simRat_chr6.simRat.chr6 207867 27 - 647215 TTCTGAACCTAATAAAAAGACACAATA - -a -s simMouse_chr6.simMouse.chr6 456187 32 + 636262 TGGTGGAATATTTGTGAGATGGCCAGCAAACA -s Anc0.Anc0refChr3 160562 30 - 222631 AGGTGCAGTATTGGTGAAAAGTCTAAC--ACA -s Anc1.Anc1refChr6 104664 30 - 197743 AGGTGCAGTATTGGTGAAAAGTCTAAC--ACA -s Anc2.Anc2refChr13 29550 30 - 96486 AGGTGCAGTATTGGTGAAAAGTCTGAA--ACA -s mr.mrrefChr5 9117 32 - 294540 TGGTGGAGTATTTGTGAAATGGCCAGCAAACA -s simCow_chr6.simCow.chr6 178400 28 - 602619 GGGTGCAGTATTGGTGAAGAGAC--AA--ACA -s simDog_chr6.simDog.chr6 179755 30 - 593897 AGGTGCAGTATTGGTGACAAGTCTGAA--AAA -s simHuman_chr6.simHuman.chr6 183302 30 - 601863 ATGTGCAGTATTGGTGAATAGTCTAAC--ACA -s simRat_chr6.simRat.chr6 207894 32 - 647215 CGGTGGAGTATTCGTGAAATGGCCAGCAAACA - -a -s simMouse_chr6.simMouse.chr6 456219 31 + 636262 AGAGCATAGTACCTAACATGGGTTTAGTTTC -s Anc0.Anc0refChr3 160592 31 - 222631 AGAACTTAGTATCTAACATTGGTTTAGCCTC -s Anc1.Anc1refChr6 104694 31 - 197743 AGAACTTAGTATCTAACATTGGTTTAGCCTC -s Anc2.Anc2refChr13 29580 31 - 96486 AGAACTTAGTATTGAACATTGGTTTAGCCAC -s mr.mrrefChr5 9149 31 - 294540 AGAGCATAGTACCTAACATGGGTTTAGTTTC -s simCow_chr6.simCow.chr6 178428 31 - 602619 AGAACTCAGCATTGAACATGAGTTTAGCCAC -s simDog_chr6.simDog.chr6 179788 28 - 593897 AGAACTTAGTA---TACATTGGTTTAGCCAC -s simHuman_chr6.simHuman.chr6 183332 31 - 601863 AGAACCTAGTAACTAACATAGGTTTAGCCTC -s simRat_chr6.simRat.chr6 207926 31 - 647215 AGAGCATAGAACCTAACATGGGTCTAATTTC - -a -s simMouse_chr6.simMouse.chr6 456250 20 + 636262 TCCGGCCGCCTAATGTGTCA -s Anc0.Anc0refChr3 160623 19 - 222631 TTT-GCCATCTAATTTGTCA -s Anc1.Anc1refChr6 104725 19 - 197743 TTT-GCCATCTAATTTGTCA -s Anc2.Anc2refChr13 29612 19 - 96486 TTT-GCCATCTGACTTGTCA -s mr.mrrefChr5 9180 19 - 294540 TCC-GCCACCTAATGTGTCA -s simCow_chr6.simCow.chr6 178460 19 - 602619 TTT-GCCATCTGCCTTGACA -s simDog_chr6.simDog.chr6 179817 19 - 593897 TTT-GCCGTCTGACTTGTCA -s simHuman_chr6.simHuman.chr6 183363 19 - 601863 TTT-GCCATCTAATTTATCA -s simRat_chr6.simRat.chr6 207957 17 - 647215 TC---CCACCTAATGTGTCA - -a -s simMouse_chr6.simMouse.chr6 456270 33 + 636262 TTCCAGAATGCCTATCATCCCAGGATGACAGAA -s Anc0.Anc0refChr3 160642 14 - 222631 TCC-------------------GAATGACAGAA -s Anc1.Anc1refChr6 104744 14 - 197743 TCC-------------------GAATGACAGAA -s Anc2.Anc2refChr13 29633 14 - 96486 TCC-------------------GAATGACATGA -s mr.mrrefChr5 9199 33 - 294540 TCCCAGAATGCCTATCATCCCAGGATGACAGAA -s simCow_chr6.simCow.chr6 178481 14 - 602619 CCC-------------------AAATAACCTGA -s simDog_chr6.simDog.chr6 179838 14 - 593897 TCT-------------------GAATGACATGA -s simHuman_chr6.simHuman.chr6 183382 14 - 601863 TCC-------------------GAATGACAGAA -s simRat_chr6.simRat.chr6 207974 33 - 647215 TCCCAGACTGCATATGATTGCAGGATGACAGAA - -a -s simMouse_chr6.simMouse.chr6 456303 1 + 636262 G -s Anc0.Anc0refChr3 160656 1 - 222631 G -s Anc1.Anc1refChr6 104758 1 - 197743 G -s Anc2.Anc2refChr13 29650 1 - 96486 G -s mr.mrrefChr5 9232 1 - 294540 G -s simCow_chr6.simCow.chr6 178498 1 - 602619 A -s simDog_chr6.simDog.chr6 179855 1 - 593897 G -s simHuman_chr6.simHuman.chr6 183396 1 - 601863 G -s simRat_chr6.simRat.chr6 208007 1 - 647215 G - -a -s simMouse_chr6.simMouse.chr6 456304 18 + 636262 TTTTCAAACAGCTGTACC -s Anc0.Anc0refChr3 160658 18 - 222631 ATTTTAAACAACATTACC -s Anc1.Anc1refChr6 104760 18 - 197743 ATTTTAAACAACATTACC -s Anc2.Anc2refChr13 29652 18 - 96486 ATTTTACACAAGATTACC -s mr.mrrefChr5 9233 18 - 294540 ATTTCAAACAGCTGTACC -s simCow_chr6.simCow.chr6 178500 18 - 602619 ATTTTATTCAAACTTACC -s simDog_chr6.simDog.chr6 179857 15 - 593897 GATATACACTAGAAT--- -s simHuman_chr6.simHuman.chr6 183398 18 - 601863 ATTTTAAACAACATTTTC -s simRat_chr6.simRat.chr6 208008 18 - 647215 ATTTCAAGCAGCTGTACC - -a -s simMouse_chr6.simMouse.chr6 456322 7 + 636262 TTGTCCC -s Anc0.Anc0refChr3 160676 7 - 222631 TTGTCTC -s Anc1.Anc1refChr6 104778 7 - 197743 TTGTCTC -s Anc2.Anc2refChr13 29670 7 - 96486 TTGTCCC -s mr.mrrefChr5 9251 7 - 294540 TTGTCTC -s simCow_chr6.simCow.chr6 178518 7 - 602619 TTGTCCC -s simDog_chr6.simDog.chr6 180023 7 - 593897 TTGTCCC -s simHuman_chr6.simHuman.chr6 183416 7 - 601863 TTGTCTC -s simRat_chr6.simRat.chr6 208026 7 - 647215 TTGTCTC - -a -s simMouse_chr6.simMouse.chr6 456329 24 + 636262 AAAAATCTCTGTAAAAACTTTGCT -s Anc0.Anc0refChr3 160683 16 - 222631 A--------TGTAAAATCCTTCCT -s Anc1.Anc1refChr6 104785 16 - 197743 A--------TGTAAAATCCTTCCT -s Anc2.Anc2refChr13 29678 16 - 96486 A--------TGTAAAATCCTTCCA -s mr.mrrefChr5 9258 24 - 294540 AAAAATCTCTGTAAAAACTTTGCT -s simCow_chr6.simCow.chr6 178526 16 - 602619 A--------TCTAAAATCCCTCCA -s simDog_chr6.simDog.chr6 180031 16 - 593897 A--------TGCAAAAACTTTCCA -s simHuman_chr6.simHuman.chr6 183423 16 - 601863 A--------TGTAAAATCCTTCAT -s simRat_chr6.simRat.chr6 208033 24 - 647215 AAAAATCTCTGTAAAAACTTTGCC - -a -s simMouse_chr6.simMouse.chr6 456353 20 + 636262 CACCCTAGGGCCCACAAAGA -s Anc0.Anc0refChr3 160699 20 - 222631 CACCTAATGCTCACCAGAGA -s Anc1.Anc1refChr6 104801 20 - 197743 CACCTAATGCTCACCAGAGA -s Anc2.Anc2refChr13 29694 20 - 96486 CACTTAATGCTCACCAGAGA -s mr.mrrefChr5 9282 20 - 294540 CACCCTAGGGCCCACAAAGA -s simCow_chr6.simCow.chr6 178542 20 - 602619 CAATTAACGCTTACCACAGG -s simDog_chr6.simDog.chr6 180047 20 - 593897 CACTTAATGCACACCAGGGA -s simHuman_chr6.simHuman.chr6 183444 20 - 601863 CACCTCATGCTCACCAGAGT -s simRat_chr6.simRat.chr6 208057 20 - 647215 AACCCTAGGGCTCGTGTAAA - -a -s simMouse_chr6.simMouse.chr6 456373 2 + 636262 TT -s Anc0.Anc0refChr3 160719 2 - 222631 TT -s Anc1.Anc1refChr6 104821 2 - 197743 TT -s Anc2.Anc2refChr13 29716 2 - 96486 TT -s mr.mrrefChr5 9302 2 - 294540 TT -s simCow_chr6.simCow.chr6 178564 2 - 602619 TT -s simDog_chr6.simDog.chr6 180069 2 - 593897 TC -s simHuman_chr6.simHuman.chr6 183464 2 - 601863 GT -s simRat_chr6.simRat.chr6 208077 2 - 647215 CT - -a -s simMouse_chr6.simMouse.chr6 456375 7 + 636262 TAACTTG -s Anc0.Anc0refChr3 160723 7 - 222631 AAACATG -s Anc1.Anc1refChr6 104825 7 - 197743 AAACATG -s Anc2.Anc2refChr13 29720 7 - 96486 AAACATG -s mr.mrrefChr5 9304 7 - 294540 TAACTTG -s simCow_chr6.simCow.chr6 178568 7 - 602619 TAATGTG -s simDog_chr6.simDog.chr6 180073 7 - 593897 AAACATG -s simHuman_chr6.simHuman.chr6 183468 7 - 601863 AAACATG -s simRat_chr6.simRat.chr6 208079 7 - 647215 TAACTTT - -a -s simMouse_chr6.simMouse.chr6 456382 2 + 636262 TG -s Anc0.Anc0refChr3 160730 1 - 222631 T- -s Anc1.Anc1refChr6 104832 1 - 197743 T- -s Anc2.Anc2refChr13 29729 1 - 96486 T- -s mr.mrrefChr5 9311 2 - 294540 TG -s simCow_chr6.simCow.chr6 178577 1 - 602619 T- -s simDog_chr6.simDog.chr6 180082 1 - 593897 T- -s simHuman_chr6.simHuman.chr6 183475 1 - 601863 T- -s simRat_chr6.simRat.chr6 208086 2 - 647215 TG - -a -s simMouse_chr6.simMouse.chr6 456384 25 + 636262 AACAGTGCTCCATAACCTGGGTAAC -s Anc0.Anc0refChr3 160731 20 - 222631 -----TACACCATAGCTTGCATTCG -s Anc1.Anc1refChr6 104833 20 - 197743 -----TACACCATAGCTTGCATTCG -s Anc2.Anc2refChr13 29730 20 - 96486 -----TAAATCATAGCATGCATTCG -s mr.mrrefChr5 9313 25 - 294540 AACAGTGCTCCATAACTTGGGTAAC -s simCow_chr6.simCow.chr6 178578 20 - 602619 -----CATATCGTAGCATGCATGCG -s simDog_chr6.simDog.chr6 180083 20 - 593897 -----TAAATCATAGAATGCATTCA -s simHuman_chr6.simHuman.chr6 183476 20 - 601863 -----TACACCATAGCTTGCATTGG -s simRat_chr6.simRat.chr6 208089 25 - 647215 GACAGTGTTCCATAACTTGTGTAAC - -a -s simMouse_chr6.simMouse.chr6 456409 70 + 636262 GACAACTTGTACAACAGTGTTAATAGTGCATCATTTATTATAAATCGAATTCATGCTGCTATGCCATTTG -s Anc0.Anc0refChr3 160751 52 - 222631 GTTGATTTGT------------------AATCATTCATTCTTGATTAAATATATGTTGCCACACCATTTG -s Anc1.Anc1refChr6 104853 52 - 197743 GTTGATTTGT------------------AATCATTCATTCTTGATTAAATATATGTTGCCACACCATTTG -s Anc2.Anc2refChr13 29755 52 - 96486 GTTGATTTTT------------------AATCATTCATTCTTGATTAATTATATGTTGCCACACCATTTG -s mr.mrrefChr5 9338 70 - 294540 GATAATTTGTACAACAGTGTTAATAGTGCATCATTTATTATTAATCAAATTCATGCTGCTATGCCATTTG -s simCow_chr6.simCow.chr6 178603 52 - 602619 GTTGATTTTT------------------AATCCTTCATTCTTGATTAATAATAATCTGACACACCATCTG -s simDog_chr6.simDog.chr6 180108 52 - 593897 GTTGATTTTT------------------AATCATTCATTCTTGATTAATTATATGTTGCCATGCCATTTG -s simHuman_chr6.simHuman.chr6 183496 51 - 601863 GTTGATATGT------------------ACTCATTCATT-CTGATTAAATATATGTTGCCTCACCATTTG -s simRat_chr6.simRat.chr6 208114 69 - 647215 AATAATTTGTGTCACAGTGTTAATAGTGCATCATATAATATTAATCAAGTCCATGCTGCTATGCCACTT- - -a -s simMouse_chr6.simMouse.chr6 456479 38 + 636262 TATATCTCATTTAAAGGTGAGTATTTGTCTTGAGTTTA -s Anc0.Anc0refChr3 160803 24 - 222631 TATGTCTTCTCCTAGGTTGAATAT-------------- -s Anc1.Anc1refChr6 104905 24 - 197743 TATGTCTTCTCCTAGGTTGAATAT-------------- -s Anc2.Anc2refChr13 29807 24 - 96486 CATGTCTTCTCCTAAGTTAAATAT-------------- -s mr.mrrefChr5 9408 38 - 294540 TATATCTTATCTAAGGGTGAGTATTTGTCTTGAGTTTA -s simCow_chr6.simCow.chr6 178655 16 - 602619 CATTGCTC-TCATAAGT--------------------- -s simDog_chr6.simDog.chr6 180160 24 - 593897 CATGTCTTCTCCTAAGTTAAATAT-------------- -s simHuman_chr6.simHuman.chr6 183547 24 - 601863 TATGTCTTGTCCTAGGTTGTATAT-------------- -s simRat_chr6.simRat.chr6 208394 38 - 647215 AGTATTCTACCAAAGACTCAGTATTTGTCTTGTGGCCC - -a -s simMouse_chr6.simMouse.chr6 456517 50 + 636262 TCTTCTGATGGCTACTTTATGCCTGTTCTTGTTCACCCTTTGCCTACGCC -s Anc0.Anc0refChr3 160827 30 - 222631 TCTTCCAAGGGTTACTTTTTGCTTGTTGTT-------------------- -s Anc1.Anc1refChr6 104929 30 - 197743 TCTTCCAAGGGTTACTTTTTGCTTGTTGTT-------------------- -s Anc2.Anc2refChr13 29831 30 - 96486 CCTGCCAAGAGTTACTTTTGGCTTGTTGTC-------------------- -s mr.mrrefChr5 9446 50 - 294540 TCTTCTGATGGCTACTTTATGCCTGTTCTTGTTCACCCTTTGCCTACGCC -s simCow_chr6.simCow.chr6 178671 21 - 602619 ---------AATTACTTGAGGCTTGTTATC-------------------- -s simDog_chr6.simDog.chr6 180197 30 - 593897 CCTGCCAAGAGTTACTCTTGGCTTGTTGTC-------------------- -s simHuman_chr6.simHuman.chr6 183571 30 - 601863 TCTTCCACGGGTTAATTTGTGCTTGCTTTT-------------------- -s simRat_chr6.simRat.chr6 208432 50 - 647215 TCTTCTGATGGCTACTTTATGCCTGTTCTTGCTCACCCTTTGACTGTTCC - -a -s simMouse_chr6.simMouse.chr6 456567 39 + 636262 TGTTCTCTATTCACTGCCCTATCATATGAAATGCTCCTT -s Anc0.Anc0refChr3 160857 25 - 222631 --------------TACTCTATCTTATGGATTGTTCATA -s Anc1.Anc1refChr6 104959 25 - 197743 --------------TACTCTATCTTATGGATTGTTCATA -s Anc2.Anc2refChr13 29861 25 - 96486 --------------TACTTTATCTTCTGGATTGTCCATA -s mr.mrrefChr5 9496 39 - 294540 TGTTCTCTATTCACTGCCCTATCATATGAAATGCTCCTT -s simCow_chr6.simCow.chr6 178692 21 - 602619 --------------TACTTTATCTTCTGGATTGTC---- -s simDog_chr6.simDog.chr6 180227 25 - 593897 --------------TTCTTTATCTTCCAGTATGTCCATA -s simHuman_chr6.simHuman.chr6 183601 25 - 601863 --------------TACTCTATCTTATGGATTGTTAATC -s simRat_chr6.simRat.chr6 208483 39 - 647215 TGTTTTCCATTCTCTGTCCTATCATACGAAATGCTCCTT - -a -s simMouse_chr6.simMouse.chr6 456606 24 + 636262 ATCAAGGACCTTATCCACATTTGG -s Anc0.Anc0refChr3 160883 18 - 222631 AACAAGGACCTTACCCAT------ -s Anc1.Anc1refChr6 104985 24 - 197743 AACAAGGACCTTACCCATTTCTGG -s Anc2.Anc2refChr13 29887 18 - 96486 AACAACGACCTTACCTAT------ -s mr.mrrefChr5 9535 24 - 294540 ATCAAGGACCTTATCCATATTTGG -s simDog_chr6.simDog.chr6 180253 18 - 593897 AACAACGACCTTACCTAT------ -s simHuman_chr6.simHuman.chr6 183627 24 - 601863 ACCAAGGACCCTGCCCATTTCTGG -s simRat_chr6.simRat.chr6 208522 24 - 647215 ATCAAGGGCCTTAGCCATATTTGG - -a -s simMouse_chr6.simMouse.chr6 456630 49 + 636262 CAATATGTTAGTACACATTGATAAAACAGCTGGTGCCCTGTTCTAAGGT -s Anc0.Anc0refChr3 160901 14 - 222631 ---------------------------------TGCCT--TTCAAAGAC -s Anc1.Anc1refChr6 105009 49 - 197743 TAACATGCTAGCACACGTTAATGAATCAGTTAATGCCTTGTTCAAAGAC -s Anc2.Anc2refChr13 29905 14 - 96486 ---------------------------------TGCCT--ATCAAAGAC -s mr.mrrefChr5 9559 49 - 294540 CAATATGTTAGTACACATTGATGAATCAGCTGGTGCCCTGTTCAAAGAT -s simCow_chr6.simCow.chr6 178713 7 - 602619 ------------------------------------------CAAAGAC -s simDog_chr6.simDog.chr6 180271 14 - 593897 ---------------------------------TGCCT--ATCAAAGAC -s simHuman_chr6.simHuman.chr6 183655 49 - 601863 TAACATGCTAGCACACGTTAATGAATCAGTTAATTCCTTGTTCAAAGAC -s simRat_chr6.simRat.chr6 208546 49 - 647215 CAATATGTTAGTACACATTGATGAGTCAGCTGGTAACCTGTTCAAAGAT - -a -s simMouse_chr6.simMouse.chr6 456679 27 + 636262 TCAAATCCTCTTGGAATCTTGGTCAAA -s Anc0.Anc0refChr3 160917 24 - 222631 TCTAATCCCC---ACATCATTGTCAGA -s Anc1.Anc1refChr6 105060 24 - 197743 TCTAATCCCC---ACATCATTGTCAGA -s Anc2.Anc2refChr13 29921 24 - 96486 TCTAACCCCC---ACGTCATTGTCAGA -s mr.mrrefChr5 9608 27 - 294540 TCAAATCCTCTTGGAATCTTGGTCAAA -s simCow_chr6.simCow.chr6 178724 24 - 602619 TCTATCTCCC---ATGTCATTGTCAGA -s simDog_chr6.simDog.chr6 180287 22 - 593897 T--AACCCCC---GCGTGATCTTCATA -s simHuman_chr6.simHuman.chr6 183706 24 - 601863 TCTAATCTCC---ACATCATTGGCAGA -s simRat_chr6.simRat.chr6 208595 27 - 647215 TTGAATCCTCTTGTAATCTTGTTCTAG - -a -s simMouse_chr6.simMouse.chr6 456706 91 + 636262 GTCTGCTCAAAACTCAGTCAACAATAAAGCCACTCACTAAAGCTACTCAGTCAAAACTGGACACATGCTAGACATCTAGCAAGGATAGTGA -s Anc0.Anc0refChr3 160943 78 - 222631 GGCTATGGGAATCTCAGTCAACAATAGGACCACGCAACAAAGCCACCTGATT--AACTGGACA-ATACAAGGCGC----------CAGTCA -s Anc1.Anc1refChr6 105086 79 - 197743 GGCTATGGGAATCTCAGTCAACAATAGGACCACGCAACAAAGCCACCTGATT--AACTGGACAGATACAAGGCGC----------CAGTCA -s Anc2.Anc2refChr13 29947 78 - 96486 AGCTATGGGAATCTCGGGCAACAATAGGACCAAGCAACAAAGCCACCTGATT--AACTAGACA-ATACAAGGTGC----------CAGTAA -s mr.mrrefChr5 9635 81 - 294540 GTCTATTCGAATCTCAGTCAACAATAAAACCACTCACTAAAGCCACTCAATCAAAACTGGACACATGCAAGACAT----------TAGTCA -s simCow_chr6.simCow.chr6 178750 76 - 602619 TGCCTTGGGAA-CTCGGCCAACAATATGACCAAGCAATAAAGCCGTCTAATT--AAATAGACA--TACAAGGTAC----------CAGCAA -s simDog_chr6.simDog.chr6 180311 77 - 593897 AGCTATGGGAATATTGGGCAACAATAGGACCAAGCAACAAAGCCACCTG-CT--AACTAGACA-ACACAAGGTGC----------CAGTAG -s simHuman_chr6.simHuman.chr6 183734 79 - 601863 GGCTATCGGAGTCTCAGTCAACAGTAGTACCACACAGCCAAGCCACCTGATT--AACTGGACAGATACAAGGCGC----------CAGTCA -s simRat_chr6.simRat.chr6 208622 81 - 647215 GTCTATTCGAATCTCAATCAACAATAAGACTACTCACGAAAGCCACTCAACCAAAAATGGACACATGCAAGACAT----------TAGTCA - -a -s simMouse_chr6.simMouse.chr6 456797 21 + 636262 AGACCCCAGATCATTTCCAAA -s Anc0.Anc0refChr3 161021 19 - 222631 AGTCCTAAA--CAATACAACA -s Anc1.Anc1refChr6 105165 21 - 197743 AGTCCTAAAATCAATACAACA -s Anc2.Anc2refChr13 30030 19 - 96486 AGTTCTAAA--CCATACAACA -s mr.mrrefChr5 9716 21 - 294540 AGACCCCAGATCATTTCCAAA -s simCow_chr6.simCow.chr6 178838 19 - 602619 AGTTCTAAA--CCATGCACCA -s simDog_chr6.simDog.chr6 180393 19 - 593897 AGTTCTAAA--CCATACAACA -s simHuman_chr6.simHuman.chr6 183813 21 - 601863 AGGCCTAAAATCAATCCAACA -s simRat_chr6.simRat.chr6 208703 21 - 647215 AGACCCCAGGTCATTTCTAAA - -a -s simMouse_chr6.simMouse.chr6 456818 11 + 636262 CCAGACACAAC -s Anc0.Anc0refChr3 161054 11 - 222631 CCAAGAACATT -s Anc1.Anc1refChr6 105200 11 - 197743 CCAAGAACATT -s Anc2.Anc2refChr13 30063 11 - 96486 CAAAGAACATT -s mr.mrrefChr5 9737 11 - 294540 CCAGAAACAAT -s simCow_chr6.simCow.chr6 178871 11 - 602619 CTAAGAACATC -s simDog_chr6.simDog.chr6 180426 11 - 593897 CAGTGAACATT -s simHuman_chr6.simHuman.chr6 183848 11 - 601863 CCAAGCCCATT -s simRat_chr6.simRat.chr6 208724 11 - 647215 CCAGAAACAAT - -a -s simMouse_chr6.simMouse.chr6 456829 72 + 636262 GAACTAGTGCATTCATGACCTCTACTGAGTGTGGTAGGAACCTAATGATCAGGAACTTTGCCTGCTTGGCCT -s Anc0.Anc0refChr3 161074 46 - 222631 AAGTACGGGCACTGACAAA--------------------------AGTTCAGGAAACCTGCCCACTACTACT -s Anc1.Anc1refChr6 105220 46 - 197743 AAGTACGGGCACTGACAAA--------------------------AGTTCAGGAAACCTGCCCACTACTACT -s Anc2.Anc2refChr13 30083 46 - 96486 AAGTACAGGCACTGACAAA--------------------------AGTTCAGTAAACCTGCCCACTACTACT -s mr.mrrefChr5 9748 46 - 294540 GAATTAGTGCATTGACAAC--------------------------TGATCAGGAACTTTGCCTGCTTGGCCT -s simCow_chr6.simCow.chr6 178891 46 - 602619 AAGTACTGGTGGCGACAAA--------------------------AGTTCAGTCTCCCTGCCTGTTACTGCT -s simDog_chr6.simDog.chr6 180450 46 - 593897 AAGTACAGGCACTGACAAA--------------------------AGATCAGTAAACCTGCCCACTACTACT -s simHuman_chr6.simHuman.chr6 183868 37 - 601863 AAGTACGGGCAATGACAAA--------------------------AGTTCAGG---------CACTGCTACT -s simRat_chr6.simRat.chr6 208735 35 - 647215 GAATTAGTATGTTGACAAC--------------------------CT-----------TGCCAGCTTGTCCT - -a -s simMouse_chr6.simMouse.chr6 456901 24 + 636262 TTTGAAGCTATCACAACTGGTGAA -s Anc0.Anc0refChr3 161120 24 - 222631 TTTGATGCCATTAGGTCAGGTGAG -s Anc1.Anc1refChr6 105266 24 - 197743 TTTGATGCCATTAGGTCAGGTGAG -s Anc2.Anc2refChr13 30129 24 - 96486 TTTGATGCCATTAGGTCAGGTGAA -s mr.mrrefChr5 9794 24 - 294540 TTTGAAGCTATTACGACTGGTGAG -s simCow_chr6.simCow.chr6 178937 24 - 602619 TTTGATGCCATTGGGTCAGGTGAA -s simDog_chr6.simDog.chr6 180496 24 - 593897 TTTGATGCCATTAGGGCACAAGAA -s simHuman_chr6.simHuman.chr6 183907 24 - 601863 TTTGAGGCCATTAGGTCAGGTGAG -s simRat_chr6.simRat.chr6 208770 24 - 647215 TTTGAAGCTATTGTGACTGGTGAG - -a -s simMouse_chr6.simMouse.chr6 456925 22 + 636262 AACACAACCCCTCCAAAGAATC -s Anc0.Anc0refChr3 161145 22 - 222631 TACACAACCCCTCCTCAGAATC -s Anc1.Anc1refChr6 105291 22 - 197743 TACACAACCCCTCCTCAGAATC -s Anc2.Anc2refChr13 30154 22 - 96486 CAGACAACCCTTACTCAGACTT -s mr.mrrefChr5 9818 22 - 294540 TACACAACCCCTCCTAAGAATC -s simCow_chr6.simCow.chr6 178962 20 - 602619 CAGACAACCCT--CTCAGAGGA -s simDog_chr6.simDog.chr6 180521 22 - 593897 CAGACAACCCTTACCAAGACTT -s simHuman_chr6.simHuman.chr6 183932 22 - 601863 TACACAACCCCTCCTCAGAATC -s simRat_chr6.simRat.chr6 208794 22 - 647215 TACACAACCCCTCCTGAGAATC - -a -s simMouse_chr6.simMouse.chr6 456947 19 + 636262 TTGTCAGAGAGGTTCAACA -s Anc0.Anc0refChr3 161167 19 - 222631 TGGCGCGAGGTGTGAAATG -s Anc1.Anc1refChr6 105313 19 - 197743 TGGCGCGAGGTGTGAAATG -s Anc2.Anc2refChr13 30176 19 - 96486 TGGCGCGAAGTATGAAATG -s mr.mrrefChr5 9840 19 - 294540 TTGTCAGAGAGGTTAAACA -s simCow_chr6.simCow.chr6 178982 19 - 602619 TGGTGAGAAAGATGAAACG -s simDog_chr6.simDog.chr6 180545 19 - 593897 TGACACGAAGTATGAACTG -s simHuman_chr6.simHuman.chr6 183954 19 - 601863 TGGGGGGAGGTGTGAAATG -s simRat_chr6.simRat.chr6 208816 19 - 647215 ATGTCAGAGAGGTTAGACA - -a -s simMouse_chr6.simMouse.chr6 456966 10 + 636262 AGCAGTCTAC -s Anc0.Anc0refChr3 161186 10 - 222631 AGACATCTAC -s Anc1.Anc1refChr6 105332 10 - 197743 AGACATCTAC -s Anc2.Anc2refChr13 30195 10 - 96486 AGACATCTAC -s mr.mrrefChr5 9859 10 - 294540 AGAAGTCTAC -s simCow_chr6.simCow.chr6 179001 10 - 602619 AGACATCTAC -s simDog_chr6.simDog.chr6 180849 10 - 593897 AGATATTTAC -s simHuman_chr6.simHuman.chr6 183973 10 - 601863 GGACATCCAC -s simRat_chr6.simRat.chr6 208835 10 - 647215 AGAAGTCTAC - -a -s simMouse_chr6.simMouse.chr6 456976 19 + 636262 AGAAGTTGTAGACACTAAT -s Anc0.Anc0refChr3 161196 19 - 222631 AGAACTCTTAAACACTAAT -s Anc1.Anc1refChr6 105342 19 - 197743 AGAACTCTTAAACACTAAT -s Anc2.Anc2refChr13 30207 19 - 96486 AGAACTCTTCAGTACTAAT -s mr.mrrefChr5 9869 19 - 294540 AGAAGTTTTAAACACTAAT -s simCow_chr6.simCow.chr6 179013 11 - 602619 AGGACTCTTCA-------- -s simDog_chr6.simDog.chr6 180861 19 - 593897 AGAACTCCTCAGTACTAAT -s simHuman_chr6.simHuman.chr6 183983 19 - 601863 AGAACTCTTAAACACTTAT -s simRat_chr6.simRat.chr6 208845 19 - 647215 AGAAATTTTCAGCAATAGT - -a -s simMouse_chr6.simMouse.chr6 456995 11 + 636262 TTGCCTCCTTG -s Anc0.Anc0refChr3 161216 11 - 222631 TTGTCCAGTCG -s Anc1.Anc1refChr6 105362 11 - 197743 TTGTCCAGTCG -s Anc2.Anc2refChr13 30227 11 - 96486 TTGTCCAGGAG -s mr.mrrefChr5 9888 11 - 294540 TTGCCTCCTCG -s simCow_chr6.simCow.chr6 179024 8 - 602619 ---TCCAAGTG -s simDog_chr6.simDog.chr6 180881 11 - 593897 TTGTCCAGGAG -s simHuman_chr6.simHuman.chr6 184003 11 - 601863 TTGTCCAGTCG -s simRat_chr6.simRat.chr6 208864 11 - 647215 TTGCCTCCTCG - -a -s simMouse_chr6.simMouse.chr6 457006 14 + 636262 GTGCACATGGTGAA -s Anc0.Anc0refChr3 161231 14 - 222631 GCACACACAGAGAA -s Anc1.Anc1refChr6 105377 14 - 197743 GCACACACAGAGAA -s Anc2.Anc2refChr13 30242 14 - 96486 GCACACACAGAGAA -s mr.mrrefChr5 9899 14 - 294540 GTGCACACGGTGAA -s simCow_chr6.simCow.chr6 179036 1 - 602619 A------------- -s simDog_chr6.simDog.chr6 180896 14 - 593897 GCACACACAGAGAA -s simHuman_chr6.simHuman.chr6 184018 14 - 601863 GCACACTAAGAGAC -s simRat_chr6.simRat.chr6 208875 14 - 647215 GTGCATGCAGTGAA - -a -s simMouse_chr6.simMouse.chr6 457020 3 + 636262 GTT -s Anc0.Anc0refChr3 161246 3 - 222631 TTT -s Anc1.Anc1refChr6 105392 3 - 197743 TTT -s Anc2.Anc2refChr13 30257 3 - 96486 TTC -s mr.mrrefChr5 9913 3 - 294540 TTT -s simDog_chr6.simDog.chr6 180911 3 - 593897 TTC -s simHuman_chr6.simHuman.chr6 184033 3 - 601863 TCT -s simRat_chr6.simRat.chr6 208889 3 - 647215 TTT - -a -s simMouse_chr6.simMouse.chr6 457023 25 + 636262 CAGCTGCTGCATGCGTGACAGGGGC -s Anc0.Anc0refChr3 161249 22 - 222631 CTGCTTCTGCA---ATGTAAGGTGC -s Anc1.Anc1refChr6 105395 22 - 197743 CTGCTTCTGCA---ATGTAAGGTGC -s Anc2.Anc2refChr13 30260 22 - 96486 CTGCTTCTGCA---ATGTAAGGTGC -s mr.mrrefChr5 9916 25 - 294540 CAGCTGCTGCATGCGTGACAGGGGC -s simCow_chr6.simCow.chr6 179037 21 - 602619 -TGCTTCTATA---ATGTAAGGTGC -s simDog_chr6.simDog.chr6 180916 22 - 593897 CTGCTTCTGCA---ATGTAAGGCGC -s simHuman_chr6.simHuman.chr6 184036 22 - 601863 CTGCGTCTGCA---ATGTAAGGTGC -s simRat_chr6.simRat.chr6 208892 25 - 647215 CGGCTGCTGCATTTGTCACAGAGGC - -a -s simMouse_chr6.simMouse.chr6 457048 18 + 636262 CAGATGTTCCATTGTGCA -s Anc0.Anc0refChr3 161271 18 - 222631 CAAATGTCCCATTGCTCA -s Anc1.Anc1refChr6 105417 18 - 197743 CAAATGTCCCATTGCTCA -s Anc2.Anc2refChr13 30282 18 - 96486 CTAATGACCCATTGCTCA -s mr.mrrefChr5 9941 18 - 294540 CAGATGTTCCATTGTGCA -s simCow_chr6.simCow.chr6 179058 9 - 602619 C---------ATTGCTCA -s simDog_chr6.simDog.chr6 181081 18 - 593897 CTAATGACCCATTGCTAA -s simHuman_chr6.simHuman.chr6 184058 18 - 601863 CACATGTCCCATTGCCCA -s simRat_chr6.simRat.chr6 208917 18 - 647215 CAGATGTTCCATTATTCA - -a -s simMouse_chr6.simMouse.chr6 457066 23 + 636262 TTGGTATTTAATTGAACAGCATT -s Anc0.Anc0refChr3 161289 23 - 222631 GTGGTGTCTAATTGAATAGCATT -s Anc1.Anc1refChr6 105435 23 - 197743 GTGGTGTCTAATTGAATAGCATT -s Anc2.Anc2refChr13 30300 23 - 96486 GTGGTGTCTAATTGAGTAGCATC -s mr.mrrefChr5 9959 23 - 294540 TTGGTATTTAATTGAACAGCATT -s simCow_chr6.simCow.chr6 179067 23 - 602619 ATGGTGTCTACTTGAGTGACAAG -s simDog_chr6.simDog.chr6 181099 23 - 593897 GTGGTGCCGAATCTAGCAGCATC -s simHuman_chr6.simHuman.chr6 184076 23 - 601863 GTGGTGTCTAATTGAATAGCATT -s simRat_chr6.simRat.chr6 208946 23 - 647215 TGGTTACTTAATGGAACAACATT - -a -s simMouse_chr6.simMouse.chr6 457089 18 + 636262 GTAGTCATTGCTCACTTG -s Anc0.Anc0refChr3 161328 18 - 222631 GAAGGCATTGCTCAGCTG -s Anc1.Anc1refChr6 105474 18 - 197743 GAAGGCATTGCTCAGCTG -s Anc2.Anc2refChr13 30339 18 - 96486 GAAGGCATTGCTCAGCTG -s mr.mrrefChr5 9982 18 - 294540 GTAGTCATTGCTCACCTG -s simCow_chr6.simCow.chr6 179126 18 - 602619 GAAGGCATTGCTCAGCTG -s simDog_chr6.simDog.chr6 181123 17 - 593897 -AAGGCATTATTCAGCTC -s simHuman_chr6.simHuman.chr6 184115 18 - 601863 GAAGGCATTGCTCAGCTG -s simRat_chr6.simRat.chr6 208969 18 - 647215 TTAGTCATTGCTCAACTG - -a -s simMouse_chr6.simMouse.chr6 457107 4 + 636262 GTGA -s Anc1.Anc1refChr0 11631 4 + 16026 gtga -s mr.mrrefChr0 82737 4 - 130230 GTGA -s simHuman_chr6.simHuman.chr6 13326 4 + 601863 gtga -s simRat_chr6.simRat.chr6 604719 4 - 647215 GTGC - -a -s simMouse_chr6.simMouse.chr6 457111 1 + 636262 T -s Anc0.Anc0refChr9 11167 1 - 35212 c -s Anc1.Anc1refChr0 11635 1 + 16026 c -s Anc2.Anc2refChr0 11893 1 + 56053 t -s mr.mrrefChr0 82741 1 - 130230 C -s simCow_chr6.simCow.chr6 15715 1 + 602619 t -s simHuman_chr6.simHuman.chr6 13330 1 + 601863 c -s simRat_chr6.simRat.chr6 604723 1 - 647215 C - -a -s simMouse_chr6.simMouse.chr6 457112 63 + 636262 TAGTGCAGTGAAAAGGGAAGTAGAGTGGGAGTATCATAGAATAATGAGTTGCAAAGTGCAATT -s Anc0.Anc0refChr9 11169 51 - 35212 cagtgcagtgaagaggg------------agtaatatACAATGAAAAGTCAAGAAGTGCAAAT -s Anc1.Anc1refChr0 11637 51 + 16026 cagtgcagtgaagaggg------------agtaatatACAATGAAAAGTCAAGAAGTGCAAAT -s Anc2.Anc2refChr0 11895 51 + 56053 cggcacagtgaaggtgg------------agtaatatACAGTGAAAAGTCAAGAGGTGCAGAT -s mr.mrrefChr0 82742 63 - 130230 TAGTGCAGTGAAAAGGGAAGTGAAGTGGGAGTATCATAGAATAATGAGTTGCAAAGTGCAATT -s simCow_chr6.simCow.chr6 15717 51 + 602619 cggcACAGTGAAGGTGG------------AGTAATATACAGTGAAAAGTCAAGAGGTGCAGAT -s simHuman_chr6.simHuman.chr6 13332 51 + 601863 cagtgcagtgaacaggg------------agtgatgtGCAATGGAATATCATGAATTGCAAAT -s simRat_chr6.simRat.chr6 604724 63 - 647215 TAGTGCAGTGAAAAGGGAAGTGAAGTTGGAGCATCATACAATAATGAGTTGCAAGGTGCAATT - -a -s simMouse_chr6.simMouse.chr6 457175 9 + 636262 CACAATACT -s Anc0.Anc0refChr9 11221 9 - 35212 CACAAAACC -s Anc1.Anc1refChr0 11689 9 + 16026 CACAAAACC -s Anc2.Anc2refChr0 11947 9 + 56053 CACCAAGCC -s mr.mrrefChr0 82805 9 - 130230 CACAAAACT -s simCow_chr6.simCow.chr6 15769 9 + 602619 CACCAAGCC -s simHuman_chr6.simHuman.chr6 13384 9 + 601863 CACAAAACC -s simRat_chr6.simRat.chr6 604787 9 - 647215 CACAAAACT - -a -s simMouse_chr6.simMouse.chr6 457184 68 + 636262 AATAGAACTATGTGTGTAAGATACCTACAAACCAAAGGCCTACCTCTTCTTGAAATGATCTGTATGAT -s Anc0.Anc0refChr9 11230 66 - 35212 AATAGAATCATGGGTGTAAAATACCTATAAACGATAGGCCCA--TCTTCTTAGAATTATGCCTATAAT -s Anc1.Anc1refChr0 11698 66 + 16026 AATAGAATCATGGGTGTAAAATACCTATAAACGATAGGCCCA--TCTTCTTAGAATTATGCCTATAAT -s Anc2.Anc2refChr0 11956 66 + 56053 TATAGAGTCATGGGGGTAAAAGACCTATAAGCGATAGGCCCA--TCTTCTTAGTATTATGCCTATAAA -s mr.mrrefChr0 82814 66 - 130230 AATAGAACCATGTGTGTAAGATACCTACAAACCATAGGCCTA--TCTTCTTGAAATGATCTGTATAAT -s simCow_chr6.simCow.chr6 15779 66 + 602619 TATAGAGTCATGGGGGTAAAAGACCTATAAGCAATCTGCGCA--TCTTCTTGGGAATACGCATATAAA -s simDog_chr6.simDog.chr6 12052 40 + 593897 --------------------------ATAAGCGGTAGGCCCA--TCTTCTTAGTATTATGCCCATAAA -s simHuman_chr6.simHuman.chr6 13393 66 + 601863 AATAGAATCATGGGTGTAAAATATCTATAGAGGATAGGCTAA--TCTTCTTAGAATTATTCCTATAGT -s simRat_chr6.simRat.chr6 604796 66 - 647215 GATAGAACCATGTGTGTAAGATACCTACAAACACTAGGCCTA--TCCTCTTGAAATGATCTGTATAAT - -a -s simMouse_chr6.simMouse.chr6 457252 31 + 636262 TGAGAAAAAGAATACCCACTACGTAAGTGAC -s Anc0.Anc0refChr9 11296 30 - 35212 GAAGAAGAAGCATACCCACTA-TTCAGTGAC -s Anc1.Anc1refChr0 11764 31 + 16026 GAAGAAGAAGCATACCCACTAATTCAGTGAC -s Anc2.Anc2refChr0 12022 30 + 56053 GAAGAAGAAGCATACCCACTA-TTCAGTGAC -s mr.mrrefChr0 82880 31 - 130230 TGAGAAAAAGCATACCCACTACGTAAGTGAC -s simCow_chr6.simCow.chr6 15857 19 + 602619 GAAGAAAAGGGATAGCCTC------------ -s simDog_chr6.simDog.chr6 12092 30 + 593897 GAAGAAGAAGCATACCCACTA-TTCAGTGAC -s simHuman_chr6.simHuman.chr6 13459 31 + 601863 AAAGAAGAAGCTTACCTACTAATTCAAAGAC -s simRat_chr6.simRat.chr6 604862 31 - 647215 TGAGAGAAAGCGTACCCACTATGTAAGTGAC - -a -s simMouse_chr6.simMouse.chr6 457283 50 + 636262 AATATACATTCTCCAATATAAGTAATCAGCAACCTCGGCTTAAAAAACTG -s Anc0.Anc0refChr9 11327 38 - 35212 TATATAAATTCTCCAAGAACAGGAATTAGCAACTTCTG------------ -s Anc1.Anc1refChr0 11796 38 + 16026 TATATAAATTCTCCAAGAACAGGAATTAGCAACTTCTG------------ -s Anc2.Anc2refChr0 12053 38 + 56053 TACATAAATTCTCCAAGAACAGGAATTTGCAACTTCTG------------ -s mr.mrrefChr0 82912 38 - 130230 AATATAAATTCTCCAATATAAGTAATTAGCAACCTCTG------------ -s simCow_chr6.simCow.chr6 15876 29 + 602619 --------TTCTCCAAGTGCAGG-ATCGACAACTTATG------------ -s simDog_chr6.simDog.chr6 12123 38 + 593897 TACATAAATTCTCCAAGAACAGGAAATTGCAATTGCAG------------ -s simHuman_chr6.simHuman.chr6 13491 38 + 601863 TATATAAATTCTCCAAGACCAGGTATTAGCAGCATCTG------------ -s simRat_chr6.simRat.chr6 604894 38 - 647215 GATATAAATTCTCCAACATAAGTAATTAGCAACCTTTG------------ - -a -s simMouse_chr6.simMouse.chr6 457333 3 + 636262 AGA -s Anc0.Anc0refChr3 161346 3 - 222631 ACA -s Anc1.Anc1refChr6 105492 3 - 197743 ACA -s Anc2.Anc2refChr13 30357 3 - 96486 ACA -s mr.mrrefChr5 10000 3 - 294540 ACA -s simCow_chr6.simCow.chr6 179144 3 - 602619 ACA -s simDog_chr6.simDog.chr6 181140 3 - 593897 ACA -s simHuman_chr6.simHuman.chr6 184133 3 - 601863 ACA -s simRat_chr6.simRat.chr6 208987 3 - 647215 ACA - -a -s simMouse_chr6.simMouse.chr6 457336 11 + 636262 CCCATATTACG -s Anc0.Anc0refChr3 161350 11 - 222631 CCCATACTGGG -s Anc1.Anc1refChr6 105496 11 - 197743 CCCATACTGGG -s Anc2.Anc2refChr13 30361 11 - 96486 CCCATACTGGG -s mr.mrrefChr5 10003 11 - 294540 CCCATACTACG -s simCow_chr6.simCow.chr6 179148 11 - 602619 CCCATACCAGG -s simDog_chr6.simDog.chr6 181144 11 - 593897 CCCATATTGGG -s simHuman_chr6.simHuman.chr6 184137 11 - 601863 CCCATACTGGG -s simRat_chr6.simRat.chr6 208990 11 - 647215 CCCATACTAAG - -a -s simMouse_chr6.simMouse.chr6 457347 112 + 636262 CTCTTCTTACAATCCACTCAACATGTAGCTACTTCAACTGGGGACTACCCATGATCTAACACCACAGCATAATTATTTCTAACTCTTATATAAGTGTAAGAACTTTATAGTC -s Anc0.Anc0refChr3 161361 54 - 222631 C----CTTACGA----------------------------------------GCTGTAAGATCACAATAT-------------CCTCATAATAGTGT-CATACATGGTTGCC -s Anc1.Anc1refChr6 105507 54 - 197743 C----CTTACGA----------------------------------------GCTGTAAGATCACAATAT-------------CCTCATAATAGTGT-CATACATGGTTGCC -s Anc2.Anc2refChr13 30375 54 - 96486 C----CTTACGA----------------------------------------GCTGTAAGATCACAATAT-------------CCTCATAATAGTGT-GATACATGGTTGCA -s mr.mrrefChr5 10014 112 - 294540 CTCTTCTTACAATCCACTCAACATGTAGCTACTTCAACTGGGGACTACCCATGATCTAACACCACAGCATAATTATTTCTAACCCTTATATAAGTGTACGAACTTTATAGTC -s simCow_chr6.simCow.chr6 179167 54 - 602619 C----CCTACAG----------------------------------------GCTGTAAGATCACAAGAT-------------CCCCATGATGGGGT-GATACATGGTTGCA -s simDog_chr6.simDog.chr6 181158 54 - 593897 C----CTAACGA----------------------------------------GCTGTAGGATCCCAATTT-------------CCTTATAAGAGTGT-GATCAATGGTTGCA -s simHuman_chr6.simHuman.chr6 184148 54 - 601863 C----CTTACGA----------------------------------------GCTTTAAGATCACAATAT-------------CCACATACTAGTGT-CATACATGGTTGCC -s simRat_chr6.simRat.chr6 209001 112 - 647215 CTCTTCTTACAATCCAATCAACACGTGACTACTCCAATTGGGGCCTACCCATGATCTAACACCAGGGCATAGTTATTTCTAACCCTTGTATAAGTGTACCATCCTTATAGTC - -a -s simMouse_chr6.simMouse.chr6 457459 55 + 636262 TTTACAGGATGACACAGATAGGTCATGGACCAGATGGCTGTCTGCAAACTTTATA -s Anc0.Anc0refChr3 161415 45 - 222631 CTTTGGGCTTCATA-----AGATCATGGGCCATACAGCGGTCTGTG-----CAAA -s Anc1.Anc1refChr6 105561 45 - 197743 CTTTGGGCTTCATA-----AGATCATGGGCCATACAGCGGTCTGTG-----CAAA -s Anc2.Anc2refChr13 30429 45 - 96486 CTTTGGGCTTCATA-----AGCTCATGGGCCATACAGCGGTTCATG-----CAAA -s mr.mrrefChr5 10126 55 - 294540 TTTACGGGATGACACAGATAGATCATGGACCATATGGCTGTCTGCAAACTTTAAA -s simCow_chr6.simCow.chr6 179221 45 - 602619 CTACTGGGTTCATA-----AGGTCATGGACCATAAAGTGGTACAGC-----CAAA -s simDog_chr6.simDog.chr6 181212 45 - 593897 CATTGGGCTTCATA-----AGCTCATGGGCCATACAGCATTTCATG-----TAAA -s simHuman_chr6.simHuman.chr6 184202 45 - 601863 GTTTGGGATTTATA-----AGAGCATGTGCCATACAGCGGTCTGAG-----CAAA -s simRat_chr6.simRat.chr6 209115 55 - 647215 ATTATGGGGTGACACAGATAGATCATGGACCATATGGCTGCCTGCAAACTTTAAA - -a -s simMouse_chr6.simMouse.chr6 457514 17 + 636262 CTTTGTTAATTCTTCTT -s Anc0.Anc0refChr3 161460 17 - 222631 CTTTGTTAATTCATCAT -s Anc1.Anc1refChr6 105606 17 - 197743 CTTTGTTAATTCATCAT -s Anc2.Anc2refChr13 30474 17 - 96486 CTTTGTTAGTTTATCAT -s mr.mrrefChr5 10181 17 - 294540 CTTTGTTAATTCTTCTT -s simCow_chr6.simCow.chr6 179266 13 - 602619 CTTTGCTA----ATCAT -s simDog_chr6.simDog.chr6 181258 17 - 593897 TTATGTTAGTTTATAAT -s simHuman_chr6.simHuman.chr6 184247 17 - 601863 CTTCGTTAATTCATCAT -s simRat_chr6.simRat.chr6 209170 17 - 647215 CTTTGTTAATTCTTCTT - -a -s simMouse_chr6.simMouse.chr6 457531 6 + 636262 GCCTAT -s Anc0.Anc0refChr3 161477 6 - 222631 ACCTAT -s Anc1.Anc1refChr6 105623 6 - 197743 ACCTAT -s Anc2.Anc2refChr13 30491 6 - 96486 ACCTAT -s mr.mrrefChr5 10198 6 - 294540 GCCTAT -s simCow_chr6.simCow.chr6 179279 6 - 602619 ACCTTT -s simDog_chr6.simDog.chr6 181275 6 - 593897 ACCTAT -s simHuman_chr6.simHuman.chr6 184269 6 - 601863 ACCTAT -s simRat_chr6.simRat.chr6 209187 6 - 647215 GCCTAT - -a -s simMouse_chr6.simMouse.chr6 457537 54 + 636262 GAACTATTGAAACTGTGCTGTAATTACATGGAAAGCTTACTGACAACATACCAA -s Anc0.Anc0refChr3 161483 51 - 222631 GAACTATTTAGACTGTGCAGCAATTACATGCAAAACT---TTACATAACCACAA -s Anc1.Anc1refChr6 105629 51 - 197743 GAACTATTTAGACTGTGCAGCAATTACATGCAAAACT---TTACATAACCACAA -s Anc2.Anc2refChr13 30497 51 - 96486 GAACTATTTGGACTATGCAGCAATTACATGCAAAACT---TTCCATAACCACAA -s mr.mrrefChr5 10204 54 - 294540 GAACTATTTAAACTGTGCTGTAATTACATGGAAAGCTTACTGACAACATAACAA -s simCow_chr6.simCow.chr6 179285 50 - 602619 GAACCATTTGGACTATGCAGCAATTGCATGCAAAACT---ATGAA-GACAACAA -s simDog_chr6.simDog.chr6 181282 51 - 593897 GACCTATTTGGACCATGCAGCCATTACATGGAAAACT---TACCATAACCACAA -s simHuman_chr6.simHuman.chr6 184275 51 - 601863 GAACTATTTAGACTGTGCAGCAATTACACACATAACT---CTACACAAATACAA -s simRat_chr6.simRat.chr6 209193 54 - 647215 GAACTATTTAAACTGTACTATAATTACATGGAAAGCCTACTGGCATCATAACAA - -a -s simMouse_chr6.simMouse.chr6 457591 51 + 636262 AGAACAAGACAGTCCTGACAATAGAGAAATGTAAAATATAAATCACCATCT -s Anc0.Anc0refChr3 161534 51 - 222631 AAAACAAGGCATCCTGCTCAATGAACAAATGTAAGATGTAAACCATCACCT -s Anc1.Anc1refChr6 105680 51 - 197743 AAAACAAGGCATCCTGCTCAATGAACAAATGTAAGATGTAAACCATCACCT -s Anc2.Anc2refChr13 30548 51 - 96486 AAAACAAGGCATCCTGCTCAGTGAACAAATGTAAGATGTAGACCATCAGCT -s mr.mrrefChr5 10258 51 - 294540 AGAACAAGGCAGTCCTGTCAATAGAGAAATGTAAAATATAAATCACCACCT -s simCow_chr6.simCow.chr6 179335 51 - 602619 AATACAAGGGGTCCTGCTCAGTGAACAAATGTAAAACATACACCCTCAACT -s simDog_chr6.simDog.chr6 181336 51 - 593897 AAAACGAGGCATCCTGCTCAGTGGACAAACGTATGATGTAGACTATCAGGT -s simHuman_chr6.simHuman.chr6 184326 51 - 601863 ATGACAAGGCATCCTGCTCCATGAACAAATGTAAGATGTAAGCCATCACCT -s simRat_chr6.simRat.chr6 209247 51 - 647215 AGAACAAGGCAGTCCTGTCATTTGAGGAATGTAAAATATAAATCACCACCT - -a -s simMouse_chr6.simMouse.chr6 457642 46 + 636262 AAGTAAACAAACCTCATCGGTTTTAATACCACAAAGCATGAACTAG -s Anc0.Anc0refChr3 161585 44 - 222631 ATGTAGACGAACCTGAT-AGCTTTACTTCAAAAGAGC-TGGACTAG -s Anc1.Anc1refChr6 105731 44 - 197743 ATGTAGACGAACCTGAT-AGCTTTACTTCAAAAGAGC-TGGACTAG -s Anc2.Anc2refChr13 30599 44 - 96486 ATGTAGACGAACCTGAT-AGCTTTACTTCAAAAGAGC-CTGACTAG -s mr.mrrefChr5 10309 45 - 294540 AAGTAAACAAACCTCAT-GGTTTTAATACAACAGAGCATGAACTAG -s simCow_chr6.simCow.chr6 179386 44 - 602619 ATGTAGAGGAACCAAGT-AGCTTTACTACAATAGAGC-CTGACTAG -s simDog_chr6.simDog.chr6 181387 44 - 593897 ATGTAGACGAACCTGAT-GGCTTTACTTCAAAAGAAC-CTGACTGG -s simHuman_chr6.simHuman.chr6 184377 44 - 601863 ATGTAGACGAACCTTAT-AGCTTTACTCCAAAAGAGC-TGGACTAG -s simRat_chr6.simRat.chr6 209299 36 - 647215 AAGGAAACAAACTTCA---GTTTTAATACAACAGAGCAT------- - -a -s simMouse_chr6.simMouse.chr6 457688 77 + 636262 TTCCATTTTCAACAGAATCTCTGTGAATGGGCCAGATTCCAGATTTAGAGAATGGTTCAAACCCTGAGTCTACCATG -s Anc0.Anc0refChr3 161698 53 - 222631 TTCCATTTTCAACAGAATCTTGGTGAG------------------------GAGGTTCAGACCCCTGGTCTATTATG -s Anc1.Anc1refChr6 105844 58 - 197743 TTCCATTTTCAACAGAATCTTGGTGAGGGG-------------T------AGAGGTTCAGACCCCTGGTCTATTATG -s Anc2.Anc2refChr13 30712 53 - 96486 TTCTATTTTCAACAGAATCTTGGTGAG------------------------GAGGTCAAGACCCCTGGGCTATTATG -s mr.mrrefChr5 10354 64 - 294540 TTCCATTTTCAACAGAATCTCTGTGAATGG-------------TTTAGAGAATGGTTCAAACCCTGAGTCTACCATG -s simCow_chr6.simCow.chr6 179490 53 - 602619 TTCTATTCTTAACAGAACCTTGGTGAG------------------------GAGGTCAAGACCCCTGGGCTACTAAG -s simDog_chr6.simDog.chr6 181500 33 - 593897 TTCTATATTCAACAGAATCTTAGTG--------------------------------------------CTATTATG -s simHuman_chr6.simHuman.chr6 184490 58 - 601863 TTCCATTTACAAAAGAATCTTGGTGAGGGG-------------T------AGAGGGTCATACCCCTGGTCTATTATG -s simRat_chr6.simRat.chr6 209335 34 - 647215 -------------------------------------------TTCTGAGAATGGTTCACACCCTGAGTTTACCATG - -a -s simMouse_chr6.simMouse.chr6 457765 26 + 636262 TTTCTCACACAAATTCTCACATAAAT -s Anc0.Anc0refChr3 161751 15 - 222631 TT-----------TTCTCATACACCA -s Anc1.Anc1refChr6 105902 15 - 197743 TT-----------TTCTCATACACCA -s Anc2.Anc2refChr13 30765 15 - 96486 TC-----------TTCTCATAGACCA -s mr.mrrefChr5 10418 26 - 294540 TTTCTCACACAAATTCTCACACAAAT -s simCow_chr6.simCow.chr6 179543 15 - 602619 TC-----------TTCTCATAACCCA -s simDog_chr6.simDog.chr6 181533 15 - 593897 TC-----------TTCTCATAGACCA -s simHuman_chr6.simHuman.chr6 184548 15 - 601863 TT-----------TTCTCATACACCG -s simRat_chr6.simRat.chr6 209431 26 - 647215 TTTCTCACACAAATTCTCACACAAAT - -a -s simMouse_chr6.simMouse.chr6 457791 3 + 636262 GGG -s Anc0.Anc0refChr3 161766 3 - 222631 GGG -s Anc1.Anc1refChr6 105917 3 - 197743 GGG -s Anc2.Anc2refChr13 30781 3 - 96486 GGG -s mr.mrrefChr5 10444 3 - 294540 GGG -s simCow_chr6.simCow.chr6 179559 3 - 602619 GGG -s simDog_chr6.simDog.chr6 181549 3 - 593897 GGA -s simHuman_chr6.simHuman.chr6 184563 3 - 601863 GAG -s simRat_chr6.simRat.chr6 209457 3 - 647215 GGG - -a -s simMouse_chr6.simMouse.chr6 457794 4 + 636262 ACTT -s Anc0.Anc0refChr3 161770 4 - 222631 GCTT -s Anc1.Anc1refChr6 105921 4 - 197743 GCTT -s Anc2.Anc2refChr13 30785 4 - 96486 GCTT -s mr.mrrefChr5 10447 4 - 294540 GCTT -s simCow_chr6.simCow.chr6 179563 4 - 602619 GCTT -s simDog_chr6.simDog.chr6 181553 4 - 593897 GCTT -s simHuman_chr6.simHuman.chr6 184567 4 - 601863 GCTT -s simRat_chr6.simRat.chr6 209460 4 - 647215 GCTT - -a -s simMouse_chr6.simMouse.chr6 457798 40 + 636262 CCCTTGTGTACTGAATAAAATTCAATAGCCTATCAAAAAG -s Anc0.Anc0refChr3 161777 40 - 222631 CCCTGGTGTACTCAATGAAACCTAAAGGCCTACCAATAAA -s Anc1.Anc1refChr6 105928 40 - 197743 CCCTGGTGTACTCAATGAAACCTAAAGGCCTACCAATAAA -s Anc2.Anc2refChr13 30792 40 - 96486 CCCTGGTGTACTCAGTGAAACCTAAAGGCCTACCAATCAG -s mr.mrrefChr5 10453 40 - 294540 CCCTGGTGTACTCAATAAAATTCAATAGCCTATCAATAAA -s simCow_chr6.simCow.chr6 179570 28 - 602619 CATTGGTATACTCAGTGAAACCTGAAGG------------ -s simDog_chr6.simDog.chr6 181560 40 - 593897 CCCTGGTGTACTCAGTGAAACCTAAAGACCTACCAATCAG -s simHuman_chr6.simHuman.chr6 184574 40 - 601863 CCCTGGTGTACTCAATGAAACCTAAAGGCCTACCAATACA -s simRat_chr6.simRat.chr6 209466 40 - 647215 CCCTGTTGTACTCAATAAAATTCAAGAGCCTATCAATAGA - -a -s simMouse_chr6.simMouse.chr6 457838 48 + 636262 TAAGATCCGTTAGTCATTACATTACCTAAAGTATCAGGAACTGACACA -s Anc0.Anc0refChr3 161817 48 - 222631 TAGCATTTGTTGGTCACACCCCTAGCCAGAGTATCAGGTACTGACATA -s Anc1.Anc1refChr6 105968 48 - 197743 TAGCATTTGTTGGTCACACCCCTAGCCAGAGTATCAGGTACTGACATA -s Anc2.Anc2refChr13 30832 48 - 96486 GAGCATTTGCTGGTCACACCCCTAGCCAGAGTGTGAGGTACTGACATA -s mr.mrrefChr5 10493 48 - 294540 TAAGATCTGTTAGTCATTCCACTACCTAAAGTATCAGGAACTGACACA -s simCow_chr6.simCow.chr6 180570 48 - 602619 CAGCATTTGCTGGTCACGCTCCTAGCTAGAGTCATAGGTACTGACATA -s simDog_chr6.simDog.chr6 181600 48 - 593897 GAGCATTTGCTGCTCACACCCCTAGACAGAGGGTGAAGGACTGACACA -s simHuman_chr6.simHuman.chr6 184614 48 - 601863 TAGCATTTGTAGGCTGCACCCCTAGCCAGAGTATCAGGTACTGACATA -s simRat_chr6.simRat.chr6 209506 39 - 647215 TGAGATCTGTTAGTCATTCCGC---------CAGCAGGAACTGATACA - -a -s simMouse_chr6.simMouse.chr6 457886 42 + 636262 TCCTTATACACTTATTAGGGAAAAGATGACTGTTGATACCTA -s Anc0.Anc0refChr3 161869 41 - 222631 T-CTTATGCACTCATTAAGACAAAGAGTACCACTAAGGACTA -s Anc1.Anc1refChr6 106020 41 - 197743 T-CTTATGCACTCATTAAGACAAAGAGTACCACTAAGGACTA -s Anc2.Anc2refChr13 30890 41 - 96486 T-CTTATGCACTCATTAAGACAAAGAGGACCACTAAGGACTA -s mr.mrrefChr5 10541 41 - 294540 T-CTTATACACTTATTAGGAAAAAGATTACTATTAATACCTA -s simCow_chr6.simCow.chr6 180628 41 - 602619 T-CTTACTCACTCATCAATTCAAAGAGGACTAGTAAGGACTA -s simDog_chr6.simDog.chr6 181658 41 - 593897 T-CTTATGTACTCATTGAGAGAAAGAGGACCACCAATAAATG -s simHuman_chr6.simHuman.chr6 184666 41 - 601863 T-CTTATGCACTCATTAAGACAAAGACTATCACTAAGGACTA -s simRat_chr6.simRat.chr6 209545 41 - 647215 T-CGTATACACTTATTAGGAAAAAGATTGCTATTAATACCTA - -a -s simMouse_chr6.simMouse.chr6 457928 8 + 636262 CTAATTCA -s Anc0.Anc0refChr3 161910 8 - 222631 CTAATTCT -s Anc1.Anc1refChr6 106061 8 - 197743 CTAATTCT -s Anc2.Anc2refChr13 30931 8 - 96486 CTAATTCT -s mr.mrrefChr5 10582 8 - 294540 CTAATTCA -s simCow_chr6.simCow.chr6 180670 8 - 602619 CAAATCCT -s simDog_chr6.simDog.chr6 181699 8 - 593897 CTCCTTTT -s simHuman_chr6.simHuman.chr6 184707 8 - 601863 CTAATTCT -s simRat_chr6.simRat.chr6 209586 8 - 647215 CTAATTCA - -a -s simMouse_chr6.simMouse.chr6 457936 28 + 636262 TATCTAGTTACCTCTGTCACTAGCTGTC -s Anc0.Anc0refChr3 161918 28 - 222631 CTCTTAGTTACATCTGTTCTTAGCTGTT -s Anc1.Anc1refChr6 106069 28 - 197743 CTCTTAGTTACATCTGTTCTTAGCTGTT -s Anc2.Anc2refChr13 30939 28 - 96486 CTCTTAGTCACATCTGTTCTTAGTTGTT -s mr.mrrefChr5 10590 28 - 294540 TATTTAGTTACATCTGTCACTAGCTGTC -s simCow_chr6.simCow.chr6 180678 28 - 602619 CTCTTAGCCACATCCTTCCTTAGGTGTT -s simDog_chr6.simDog.chr6 181711 28 - 593897 CTTTTATTCACATCTGTTCTTAGTTGCT -s simHuman_chr6.simHuman.chr6 184715 28 - 601863 CTCTTAGTTACATCTGTTGTTAGCTGTT -s simRat_chr6.simRat.chr6 209594 28 - 647215 TGTTTGGTTACATCTATCACTAGCTGTC - -a -s simMouse_chr6.simMouse.chr6 457964 25 + 636262 TGTCAATCTATGTATACCATACATC -s Anc0.Anc0refChr3 161946 25 - 222631 TGTCTATCCATGTTTAACATTTATC -s Anc1.Anc1refChr6 106097 25 - 197743 TGTCTATCCATGTTTAACATTTATC -s Anc2.Anc2refChr13 30967 25 - 96486 TTTCTATTCATGTTCAACATTTATC -s mr.mrrefChr5 10618 25 - 294540 TGTCAATCTATGTATACCATACATC -s simCow_chr6.simCow.chr6 180706 24 - 602619 TTCTTATTCATGTT-AGCATTTATC -s simDog_chr6.simDog.chr6 181739 25 - 593897 TTTCTATTCATGTTCAACAATCACT -s simHuman_chr6.simHuman.chr6 184763 25 - 601863 TGTTTAGCCATGTTTATAATTTATC -s simRat_chr6.simRat.chr6 209622 24 - 647215 TGTCAATCTATGTA-ACCATACCTC - -a -s simMouse_chr6.simMouse.chr6 457989 49 + 636262 AATGAACGAAGAATATCCTTTAGTAAGGGTCTGAATTTTGTGTGCCACC -s Anc0.Anc0refChr3 161976 49 - 222631 TATAAACAAAGAACATCCATAATTATCGATCTAAACTTTGTGTGTCACC -s Anc1.Anc1refChr6 106127 49 - 197743 TATAAACAAAGAACATCCATAATTATCGATCTAAACTTTGTGTGTCACC -s Anc2.Anc2refChr13 30997 49 - 96486 TATAAACAAAGAACATCCATAATCATCGATCTAAACTTTGTGTGTCACT -s mr.mrrefChr5 10643 49 - 294540 TATGAACAAAGAATATCCATTAGTAAGGATCTGAACTTTGTGTGCCACC -s simCow_chr6.simCow.chr6 180735 49 - 602619 TATAAACAAAGAACATCCATAGTCATGGGCCTAAAGTTTGTGTGTCACT -s simDog_chr6.simDog.chr6 181769 49 - 593897 CATAACCATAGAATATCCATAATCATCGATCTAAACTTTGTGTGTCACT -s simHuman_chr6.simHuman.chr6 184793 49 - 601863 TATAAACAAAGAACATCCATACTTACAGATCTACCCTTTGTGTGTCACC -s simRat_chr6.simRat.chr6 209646 49 - 647215 TATGAGCAAAGAATTTCCATTAGTATGAATCTGAACTTTGTGTGCCACC - -a -s simMouse_chr6.simMouse.chr6 458038 42 + 636262 CTCTCCAACTAGCTCAACTTAAAACAAGAGACCACCTTGGGG -s Anc0.Anc0refChr3 162025 42 - 222631 TTCTGTTTTTTGCCCATCCTGATACAAGAAACCACCTTTGGA -s Anc1.Anc1refChr6 106176 42 - 197743 TTCTGTTTTTTGCCCATCCTGATACAAGAAACCACCTTTGGA -s Anc2.Anc2refChr13 31046 42 - 96486 TGCTATTTTCTGCCCATCCTGATACAAGAAACCAGCTTTGGA -s mr.mrrefChr5 10692 42 - 294540 TTCTGCAACTAGCTCAACTTAAAACAAGAGACCACCTTGGGG -s simCow_chr6.simCow.chr6 180784 42 - 602619 TGCTTTTTTCTGCCGATCTTAATACAAGGAACTAGCTTCAGG -s simDog_chr6.simDog.chr6 181818 42 - 593897 TGCTATTTTCTGACCATCCAGATACAAGAAACCAGCTGTGGA -s simHuman_chr6.simHuman.chr6 184843 42 - 601863 TTCTGTTTGTTGCCCATCCTGCGACAAGAAACCACCTTTGGA -s simRat_chr6.simRat.chr6 209695 42 - 647215 TTCTGCAACTAGCTCAACTTAAAACTAGAGACCACCCTGGGT - -a -s simMouse_chr6.simMouse.chr6 458080 42 + 636262 CAGGCGTTCTGGAGAACTTCACCTAGTGGAAGAGCATAGATG -s Anc0.Anc0refChr3 162068 42 - 222631 CAGATGTTGTAGAGAACTTCTTCCAGTAATAGAATATCAATG -s Anc1.Anc1refChr6 106219 42 - 197743 CAGATGTTGTAGAGAACTTCTTCCAGTAATAGAATATCAATG -s Anc2.Anc2refChr13 31089 42 - 96486 TGGATGTTGTAGAGAACTTCTTGCAGGAATAGGATATCAATG -s mr.mrrefChr5 10734 42 - 294540 CAGGTGTTCTGGAGAACTTCACCTAGTGAAAGAGCATAAATG -s simCow_chr6.simCow.chr6 180827 42 - 602619 TGGATGTTCTAGAGAATTTCTTGCAGGAATAGGACATCAATG -s simDog_chr6.simDog.chr6 181861 42 - 593897 TGGATCTTGTAGAGAACTTCTTGGAGGGATAGGATATCAATG -s simHuman_chr6.simHuman.chr6 184886 42 - 601863 CAGATGTTTTAGACGACACCTTCCAGTAATAGAATATCAATG -s simRat_chr6.simRat.chr6 209737 42 - 647215 CAAGTGTTCTGGAAAACTTCACCTAGTGAGAGGGCATAAGTG - -a -s simMouse_chr6.simMouse.chr6 458122 13 + 636262 TGCACACTGAGAC -s Anc0.Anc0refChr3 162114 13 - 222631 TGCTCACTGAGGC -s Anc1.Anc1refChr6 106265 13 - 197743 TGCTCACTGAGGC -s Anc2.Anc2refChr13 31135 13 - 96486 TGCTCACTGAGGC -s mr.mrrefChr5 10776 13 - 294540 TGCACACTGAGAC -s simCow_chr6.simCow.chr6 180873 11 - 602619 TGCTCAC--AGGC -s simDog_chr6.simDog.chr6 181907 13 - 593897 TGCTCACTGACAC -s simHuman_chr6.simHuman.chr6 184932 13 - 601863 TGCTCACTTAGGC -s simRat_chr6.simRat.chr6 209779 8 - 647215 TGCA-----AGAC - -a -s simMouse_chr6.simMouse.chr6 458135 20 + 636262 ATTCAGGGGCCACACACACT -s Anc0.Anc0refChr3 162128 20 - 222631 ACTCTTTCGCCACAAGCAAT -s Anc1.Anc1refChr6 106279 20 - 197743 ACTCTTTCGCCACAAGCAAT -s Anc2.Anc2refChr13 31149 20 - 96486 ACTCTTTCGCCACAAGCAAC -s mr.mrrefChr5 10789 20 - 294540 ATTCAGGGGCCACACACAAT -s simCow_chr6.simCow.chr6 180885 8 - 602619 ATTCTTTC------------ -s simDog_chr6.simDog.chr6 181921 20 - 593897 ACCCTGTAGCCACAAGCAAC -s simHuman_chr6.simHuman.chr6 184946 20 - 601863 ACTCTTTCGCCACATGCAAT -s simRat_chr6.simRat.chr6 209787 20 - 647215 CTTCAGGGGGCACACAAAAT - -a -s simMouse_chr6.simMouse.chr6 458155 12 + 636262 TCACTTCTTTCA -s Anc0.Anc0refChr3 162148 12 - 222631 TCATTTCCCTCA -s Anc1.Anc1refChr6 106299 12 - 197743 TCATTTCCCTCA -s Anc2.Anc2refChr13 31169 12 - 96486 TCTTTTCCCTCA -s mr.mrrefChr5 10809 12 - 294540 TCACTTCTTTCA -s simCow_chr6.simCow.chr6 180893 5 - 602619 -------CCTCA -s simDog_chr6.simDog.chr6 181941 12 - 593897 TCTTTTCCCTCA -s simHuman_chr6.simHuman.chr6 184975 12 - 601863 TCATTTCCCTCA -s simRat_chr6.simRat.chr6 209807 12 - 647215 TCATTTCTTTCA - -a -s simMouse_chr6.simMouse.chr6 458167 93 + 636262 GACTCTAAGTGCACTAGTCTTGTCCTGTTACTGTGCCCATTGACATTTAACTCATGTTAGACAATCTTTTATAGTGATGTCTATGCCCATAGA -s Anc0.Anc0refChr3 162160 84 - 222631 TGCTTA----CCACTAATGTTGTTTTCTCAGCAGTCCCTTTGGCATTTTTTGGATATTAGGCAGTTCTATATATTGAGGTCCAGGCAT----- -s Anc1.Anc1refChr6 106311 84 - 197743 TGCTTA----CCACTAATGTTGTTTTCTCAGCAGTCCCTTTGGCATTTTTTGGATATTAGGCAGTTCTATATATTGAGGTCCAGGCAT----- -s Anc2.Anc2refChr13 31194 84 - 96486 TGCATA----CCACTAATGTTGTTTTCTCGGTAATCCCTTTGGCATTTTTTGGATATTAGGCAGTTCTATATATTGAGGTCCAGGCAT----- -s mr.mrrefChr5 10821 93 - 294540 TACTCAGAGTGCACTAGTCTTGTTCTCTTACCAGGCCCATTGGCATTTTACTCATGTTAGGCAATCTTTTATAGTGATGTCTATGCCCATAGA -s simCow_chr6.simCow.chr6 180911 83 - 602619 TGCGT-----CCACTAACATTGTTTTCCCGGTAATCCCTTTGGCATTTTTCGGACATTAGGCATTCTTAGATATTGAGGTCCAGGCAC----- -s simDog_chr6.simDog.chr6 181966 72 - 593897 TACATA----TCACTTATGTTGTTTTTT------------TGGCATTTTTTGGATATTAGGCAGTTCTATATATTGAGGTCCAGGCAT----- -s simHuman_chr6.simHuman.chr6 184987 44 - 601863 GGCTTA----CCACTAATGTTGCTTGCTCAGCAGCCCCTCTGGCATTT--------------------------------------------- -s simRat_chr6.simRat.chr6 209819 93 - 647215 TACTCAGAGTGCACTAGTCTTATTCTCCTACCAGGCCCGTTAGCATTTTACTCATGCTAAGCAATCTTTTACAGTGACGTCTATGACCATAGA - -a -s simMouse_chr6.simMouse.chr6 458260 65 + 636262 TAGAAGCAAACCCGATCCTGGTATGGCTACATATAGGATGTGCCAACAGGCTCCGGGCATTGAGG -s Anc0.Anc0refChr3 162244 65 - 222631 CAGAGACAAACTTGATCCCATTAGGGCGTCACATAGGATGTGCCAGTAGGATCCAAGCATTGGGG -s Anc1.Anc1refChr6 106395 65 - 197743 CAGAGACAAACTTGATCCCATTAGGGCGTCACATAGGATGTGCCAGTAGGATCCAAGCATTGGGG -s Anc2.Anc2refChr13 31278 65 - 96486 CAGAGACAAACTTGATCCCATTAGGGCGTCACATTACATGTGCTAGTAAAATTCAAGCATTGGGG -s mr.mrrefChr5 10914 65 - 294540 TAGAAACAAACCCGATCCTGGTATGGCTACATATAGGATGTGCCAACAGGCTCCGGGCATTGGGG -s simCow_chr6.simCow.chr6 180999 65 - 602619 CAGGGACAAACTTTGTCCTGTTATGGCACCACATAGGATGTGCTAGCAAAAGCAAAGCATTGGGG -s simDog_chr6.simDog.chr6 182038 65 - 593897 CAGAGACAAACTTGATCCCATTAGGGCGTCACATTACATGTGCTAGTAAAATTCAAGCATTGGGG -s simHuman_chr6.simHuman.chr6 185031 31 - 601863 ---------------------------------TAGGATGTACCAGT-GGAACCAAGCATCAGGG -s simRat_chr6.simRat.chr6 209912 65 - 647215 TAGAAACAAACCCAATCCTGGTAGGGCTACATATGGGATGTGCTAACAGGCTCCTGGCATTGGGG - -a -s simMouse_chr6.simMouse.chr6 458325 31 + 636262 CAAGTAAGGAGATGGTTTGAATTAACCTATG -s Anc0.Anc0refChr3 162311 30 - 222631 AAATTAATGAGGTGA-TTGTCTGAACCTGTT -s Anc1.Anc1refChr6 106462 30 - 197743 AAATTAATGAGGTGA-TTGTCTGAACCTGTT -s Anc2.Anc2refChr13 31345 30 - 96486 AGATTAATGAGGTGA-TTGTCTGAACCTGTT -s mr.mrrefChr5 10979 31 - 294540 CAAGTAAGGAGGTGGTTTGAATTAACCTGTG -s simCow_chr6.simCow.chr6 181094 30 - 602619 AGATTAATGAGGCGA-TTGTCTGAACCAGTA -s simDog_chr6.simDog.chr6 182105 30 - 593897 AGATTAATGGGGTGA-TTGTCTGAATGTGCT -s simHuman_chr6.simHuman.chr6 185064 30 - 601863 AAATTAATGAGGTGA-TTGTCTGAACCTGTT -s simRat_chr6.simRat.chr6 209977 31 - 647215 CATGTAAGGAGGTGGTTTGAATTAACCTGTG - -a -s simMouse_chr6.simMouse.chr6 458356 45 + 636262 CTAAAAATGCCAGAATCCTTCCAATGAAACTCAACTCTATCACAA -s Anc0.Anc0refChr3 162341 44 - 222631 CT-AAAATGCTGGTGGACTTCCAGTGAAATACAAATCTGCCACAA -s Anc1.Anc1refChr6 106492 44 - 197743 CT-AAAATGCTGGTGGACTTCCAGTGAAATACAAATCTGCCACAA -s Anc2.Anc2refChr13 31375 44 - 96486 CT-AAAATGCTGGTGGACTTCCAGTGAAATACAAATCTACCATAG -s mr.mrrefChr5 11010 45 - 294540 CTAAAAATGCCAGAATCCTTCCAATGAAACTCAACTCTGTCACAA -s simCow_chr6.simCow.chr6 181124 44 - 602619 CT-AAAATGCTGGTGGACTTCCGCAGCAACATAAATCTACCATAG -s simDog_chr6.simDog.chr6 182146 39 - 593897 CT-AAGATGCAGGCGGACTTCAAGTGAAATACCAATCTAC----- -s simHuman_chr6.simHuman.chr6 185094 44 - 601863 CT-TAAATACTGGTGGATTTCCATTGAAATACAAATCTGCCACAA -s simRat_chr6.simRat.chr6 210008 45 - 647215 CTAAAAATGCCAGCATCCCTCCTGTTAAACTCAATTCTGTCGCGA - -a -s simMouse_chr6.simMouse.chr6 458401 8 + 636262 TTATTGCT -s Anc0.Anc0refChr3 162392 7 - 222631 -GTTTGCT -s Anc1.Anc1refChr6 106543 8 - 197743 TGTTTGCT -s Anc2.Anc2refChr13 31426 7 - 96486 -GTTTGCC -s mr.mrrefChr5 11055 8 - 294540 TTATTGCT -s simCow_chr6.simCow.chr6 181175 7 - 602619 -GTTTGCC -s simHuman_chr6.simHuman.chr6 185156 8 - 601863 TGCTTGCT -s simRat_chr6.simRat.chr6 210053 8 - 647215 TTATTGCT - -a -s simMouse_chr6.simMouse.chr6 458409 53 + 636262 TCTCTCCTATGCGGTCGCTGAACTAACACCATAGAGGTATACACCTGTACATT -s Anc0.Anc0refChr3 162412 53 - 222631 GCTCTCACATTCGGTGGCTGAGCTAATACCATAGAGGTATACAACTGTAAATT -s Anc1.Anc1refChr6 106564 53 - 197743 GCTCTCACATTCGGTGGCTGAGCTAATACCATAGAGGTATACAACTGTAAATT -s Anc2.Anc2refChr13 31446 53 - 96486 GATCCCACATTTGGTGGCTGAGCTAATACCATAGAGGTATACAAGTGGAAATT -s mr.mrrefChr5 11076 53 - 294540 GCTCTCCCATGCGGTGGCTGAGCTAACACCATAGAGGTATACACCTGTACATT -s simCow_chr6.simCow.chr6 181195 50 - 602619 GATCCCAGATTTTGTGGCTGAGCTGATACCATAAAGG---ACAAGTGGAATTT -s simDog_chr6.simDog.chr6 182198 53 - 593897 TATCCCACATTTGGTGGCTAAGCCAATACCATGGAGGTATACAAGTGGACATT -s simHuman_chr6.simHuman.chr6 185177 53 - 601863 GCTCTCACATTCAATGAATGAGCTAATGCCATAGAGGTATACAACTGTAAATC -s simRat_chr6.simRat.chr6 210074 53 - 647215 GATCTCCCATGCGGTGGCTGAGCTAAGACCATAGAAGTATACACCTGTACACT - -a -s simMouse_chr6.simMouse.chr6 458462 17 + 636262 AACATGGCCGTTTGGCA -s Anc0.Anc0refChr3 162465 17 - 222631 ACCATGGTTGTACAGCA -s Anc1.Anc1refChr6 106617 17 - 197743 ACCATGGTTGTACAGCA -s Anc2.Anc2refChr13 31499 17 - 96486 ACCATGATTATACAGCA -s mr.mrrefChr5 11129 17 - 294540 AACATGGCCGTTTGGCA -s simCow_chr6.simCow.chr6 181245 17 - 602619 ACCATGATGATACAGCT -s simDog_chr6.simDog.chr6 182251 17 - 593897 ACCATGATTATACAGCA -s simHuman_chr6.simHuman.chr6 185230 17 - 601863 ACCAAGGTTGAACAGCA -s simRat_chr6.simRat.chr6 210128 17 - 647215 AACATGAACTTTTGGCA - -a -s simMouse_chr6.simMouse.chr6 458479 5 + 636262 GATGG -s Anc0.Anc0refChr3 162500 5 - 222631 GCTGG -s Anc1.Anc1refChr6 106652 5 - 197743 GCTGG -s Anc2.Anc2refChr13 31534 5 - 96486 GCTAG -s mr.mrrefChr5 11146 5 - 294540 GATGG -s simCow_chr6.simCow.chr6 181280 5 - 602619 GCTAG -s simDog_chr6.simDog.chr6 182286 5 - 593897 ACTAG -s simHuman_chr6.simHuman.chr6 185265 5 - 601863 GCTGG -s simRat_chr6.simRat.chr6 210145 3 - 647215 G--GA - -a -s simMouse_chr6.simMouse.chr6 458484 43 + 636262 GACCGCTCCATGAGCATTTTTGAGTTTAGAGCAATAGTGAAAT -s Anc0.Anc0refChr3 162507 4 - 222631 GAAC--------------------------------------- -s Anc1.Anc1refChr6 106659 4 - 197743 GAAC--------------------------------------- -s Anc2.Anc2refChr13 31541 4 - 96486 GAAC--------------------------------------- -s mr.mrrefChr5 11151 4 - 294540 GACC--------------------------------------- -s simCow_chr6.simCow.chr6 181287 4 - 602619 GAGC--------------------------------------- -s simDog_chr6.simDog.chr6 182293 4 - 593897 AAAC--------------------------------------- -s simHuman_chr6.simHuman.chr6 185272 4 - 601863 GAAG--------------------------------------- -s simRat_chr6.simRat.chr6 210148 4 - 647215 TACC--------------------------------------- - -a -s simMouse_chr6.simMouse.chr6 458527 42 + 636262 AGGACCCTTATCTCAGATTATAAGTAAACCCCAACAGACTGG -s Anc0.Anc0refChr3 80536 41 + 222631 AAGACTCTTGTCTCAGATTATAAGTTAACCCCCACACACTA- -s Anc1.Anc1refChr6 112760 41 + 197743 AAGACTCTTGTCTCAGATTATAAGTTAACCCCCACACACTA- -s Anc2.Anc2refChr13 87013 41 + 96486 AACACTCTTGTCTCAGATTATAAGTTAGCAGCCACGCACTA- -s mr.mrrefChr3 14257 41 + 181027 AGGACCCTTATCTCAGATTATAAGTAAACCCCAACAGACTG- -s simCow_chr6.simCow.chr6 443329 36 + 602619 AACACTCTTGTCTCAGATT-----TTAGTTTCCACGCACTA- -s simDog_chr6.simDog.chr6 435273 41 + 593897 AACACTTTAGTTTCAGACTATAAGCTAGCAGCCACGCACTT- -s simHuman_chr6.simHuman.chr6 443652 41 + 601863 AAGACTCTTGTCTCAGATTATAAATTAACCCCCGCACACTA- -s simRat_chr6.simRat.chr6 467927 41 + 647215 AGGACTCTTATCTCAGGTTTTAAGCGAGCCCCAACAGACTG- - -a -s simMouse_chr6.simMouse.chr6 458569 31 + 636262 TTTATGATTGTTGGAAAGGGCTAACTGGGAT -s Anc0.Anc0refChr3 80580 28 + 222631 TTTGTGATTGATAGAA-TGGCAAACTGGA-- -s Anc1.Anc1refChr6 112804 29 + 197743 TTTGTGATTGATAGAATTGGCAAACTGGA-- -s Anc2.Anc2refChr13 87057 28 + 96486 TTTGTGATTGATAGAA-TGGCAAACTGGA-- -s mr.mrrefChr3 14298 31 + 181027 TTTATGATTGTTGGAAAGGGCTAACTGGGAT -s simCow_chr6.simCow.chr6 443368 24 + 602619 TTTGTG-TTGATAA----GGCAAACTGGA-- -s simDog_chr6.simDog.chr6 435317 28 + 593897 TTTTTGATTGATGGAA-TGGCAGACTGGA-- -s simHuman_chr6.simHuman.chr6 443696 29 + 601863 TTTGTTATTGATAGACTTTGCAAACTGGA-- -s simRat_chr6.simRat.chr6 467968 31 + 647215 TTTGTGATTGTTGGAAAGGGCTAACTACAAT - -a -s simMouse_chr6.simMouse.chr6 458600 20 + 636262 TCGTCATCCAAAGATTTGCC -s Anc0.Anc0refChr3 80608 20 + 222631 TCCTCATCCAAAGATCTGCT -s Anc1.Anc1refChr6 112833 20 + 197743 TCCTCATCCAAAGATCTGCT -s Anc2.Anc2refChr13 87086 20 + 96486 TCCTCATCCAAAGATCTGCT -s mr.mrrefChr3 14329 20 + 181027 TCGTCATCCAAAGATTTGCC -s simCow_chr6.simCow.chr6 443393 20 + 602619 TCCTAGTCAACAGATCTGCT -s simDog_chr6.simDog.chr6 435346 20 + 593897 TCCCCATCCAAAGTTTTACT -s simHuman_chr6.simHuman.chr6 443725 20 + 601863 TCCTCATCCAAAGACCTGCT -s simRat_chr6.simRat.chr6 467999 20 + 647215 TCGTCATCCAAAGATCTGCC - -a -s simMouse_chr6.simMouse.chr6 458620 31 + 636262 TTTGAGCGTTCTAGACCACGGTTTGATACTG -s Anc0.Anc0refChr3 80631 31 + 222631 TTTGAATAGTCTAGGCCAGACTTTGACATTG -s Anc1.Anc1refChr6 112856 31 + 197743 TTTGAATAGTCTAGGCCAGACTTTGACATTG -s Anc2.Anc2refChr13 87109 31 + 96486 TTCAAATAGTCTGAGCCAGACTTTGACGTTG -s mr.mrrefChr3 14349 31 + 181027 TTTGAGCGTTCTAGACCACGGTTTGATACTG -s simCow_chr6.simCow.chr6 443416 31 + 602619 TTCAAGAAGTCTGTGCCAGACTTTGACTTTG -s simDog_chr6.simDog.chr6 435369 31 + 593897 TTCAAATAGCCAGAGCCAGATTTTGACGTTG -s simHuman_chr6.simHuman.chr6 443748 31 + 601863 TTTGAATCATCTAGCTCAGACTTTGACATTT -s simRat_chr6.simRat.chr6 468019 31 + 647215 TTTGAACAGTCTAGACCATTGTTTGACACTG - -a -s simMouse_chr6.simMouse.chr6 458713 1 + 636262 T -s Anc0.Anc0refChr4 19534 1 + 45765 t -s Anc1.Anc1refChr2 86622 1 - 144309 t -s Anc2.Anc2refChr7 5832 1 - 32194 t -s mr.mrrefChr0 51958 1 - 130230 t -s mr.mrrefChr3 14442 1 + 181027 T -s simCow_chr6.simCow.chr6 518059 1 - 602619 t -s simDog_chr6.simDog.chr6 408104 1 - 593897 t -s simHuman_chr6.simHuman.chr6 523499 1 - 601863 t -s simRat_chr6.simRat.chr6 572275 1 - 647215 T -s simRat_chr6.simRat.chr6 468112 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 458850 1 + 636262 C - -a -s simMouse_chr6.simMouse.chr6 458860 1 + 636262 T - -a -s simMouse_chr6.simMouse.chr6 458869 1 + 636262 T -s Anc0.Anc0refChr4 19692 1 + 45765 T -s Anc1.Anc1refChr2 86785 1 - 144309 T -s Anc2.Anc2refChr7 5991 1 - 32194 T -s mr.mrrefChr0 52118 1 - 130230 T -s mr.mrrefChr3 14596 1 + 181027 T -s simCow_chr6.simCow.chr6 518200 1 - 602619 T -s simDog_chr6.simDog.chr6 408263 1 - 593897 T -s simHuman_chr6.simHuman.chr6 523855 1 - 601863 T -s simRat_chr6.simRat.chr6 572450 1 - 647215 T -s simRat_chr6.simRat.chr6 468271 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 458899 11 + 636262 CTATCTGATCA - -a -s simMouse_chr6.simMouse.chr6 458939 2 + 636262 AA -s Anc0.Anc0refChr4 19763 2 + 45765 AA -s Anc1.Anc1refChr2 86857 2 - 144309 AA -s Anc2.Anc2refChr7 6064 2 - 32194 AA -s mr.mrrefChr0 52180 2 - 130230 AA -s mr.mrrefChr3 14655 2 + 181027 AA -s simCow_chr6.simCow.chr6 518272 2 - 602619 AA -s simDog_chr6.simDog.chr6 408336 2 - 593897 AG -s simHuman_chr6.simHuman.chr6 523922 2 - 601863 AA -s simRat_chr6.simRat.chr6 572496 2 - 647215 AA -s simRat_chr6.simRat.chr6 468330 2 + 647215 AA - -a -s simMouse_chr6.simMouse.chr6 458958 3 + 636262 TGA -s Anc0.Anc0refChr4 19782 3 + 45765 GGA -s Anc1.Anc1refChr2 86876 3 - 144309 GGA -s Anc2.Anc2refChr7 6083 3 - 32194 GGA -s mr.mrrefChr3 14674 3 + 181027 TGA -s simCow_chr6.simCow.chr6 518291 3 - 602619 AGA -s simDog_chr6.simDog.chr6 408355 3 - 593897 GGA -s simHuman_chr6.simHuman.chr6 523942 3 - 601863 GGA -s simRat_chr6.simRat.chr6 468349 3 + 647215 TCA - -a -s simMouse_chr6.simMouse.chr6 458966 1 + 636262 T -s Anc0.Anc0refChr4 19790 1 + 45765 T -s Anc1.Anc1refChr2 86884 1 - 144309 T -s Anc2.Anc2refChr7 6091 1 - 32194 T -s mr.mrrefChr3 14682 1 + 181027 T -s simCow_chr6.simCow.chr6 518298 1 - 602619 T -s simDog_chr6.simDog.chr6 408363 1 - 593897 T -s simHuman_chr6.simHuman.chr6 523950 1 - 601863 T -s simRat_chr6.simRat.chr6 468357 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 459063 47 + 636262 ATATAGGGTCACTTTAAGGTTGTGTTTTATCTAGGAGTCAAATTTGT -s Anc0.Anc0refChr3 80664 44 + 222631 -TT--AGGCCACTTTGATGATGGCTTCTATCTAGAGATCAAGTTTGT -s Anc1.Anc1refChr6 112889 44 + 197743 -TT--AGGCCACTTTGATGATGGCTTCTATCTAGAGATCAAGTTTGT -s Anc2.Anc2refChr13 87142 44 + 96486 -TT--AGGCCACTTTGATGATGGCTTCTATCTAGAGATCAAGTTTGT -s mr.mrrefChr3 14779 47 + 181027 ATATAGGGTCACTTTAAGGTTGTGTCTTATCTAGGAGTCAAATTTGT -s simCow_chr6.simCow.chr6 443449 44 + 602619 -GT--AGGCCACTTTGAGGGTGGGTTCTATTTAGGGATCAAGTCTGT -s simDog_chr6.simDog.chr6 435402 44 + 593897 -TT--AGGTCACTTTGATGATGGCTTCTATCTAGAGATCAAGTTTGT -s simHuman_chr6.simHuman.chr6 443781 12 + 601863 -TT--AGGCCACTTT-------------------------------- -s simMouse_chr6.simMouse.chr6 459191 47 + 636262 ATATGCGTCCACTTTAAGGTTGTGTCTTATCTAGGAGTCAAATTTGT -s simRat_chr6.simRat.chr6 468454 45 + 647215 GTATAGGGTCACTTTAAGGTTGT--CTAATCTAGGAGTCAAATTTGT - -a -s simMouse_chr6.simMouse.chr6 459110 12 + 636262 CGACTTGTAAGT -s Anc0.Anc0refChr3 80708 12 + 222631 GGATTTACAAAT -s Anc1.Anc1refChr6 112933 12 + 197743 GGATTTACAAAT -s Anc2.Anc2refChr13 87186 12 + 96486 GGATTTACAAAT -s mr.mrrefChr3 14826 12 + 181027 CGACTTGTAAGT -s simCow_chr6.simCow.chr6 443502 12 + 602619 GGATTTAAAAAT -s simDog_chr6.simDog.chr6 435446 12 + 593897 GGATTTACAAAT -s simMouse_chr6.simMouse.chr6 459238 12 + 636262 CGACTTGTAAGT -s simRat_chr6.simRat.chr6 468499 12 + 647215 CGATTTGTAAGT - -a -s simMouse_chr6.simMouse.chr6 459122 1 + 636262 T -s Anc0.Anc0refChr3 80720 1 + 222631 T -s Anc1.Anc1refChr6 112945 1 + 197743 T -s Anc2.Anc2refChr13 87202 1 + 96486 T -s mr.mrrefChr3 14838 1 + 181027 T -s simCow_chr6.simCow.chr6 443518 1 + 602619 T -s simDog_chr6.simDog.chr6 435462 1 + 593897 T -s simMouse_chr6.simMouse.chr6 459250 1 + 636262 T -s simRat_chr6.simRat.chr6 468511 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 459123 9 + 636262 GTACAGATG -s Anc0.Anc0refChr3 80721 9 + 222631 GAAAGGATG -s Anc1.Anc1refChr6 112946 9 + 197743 GAAAGGATG -s Anc2.Anc2refChr13 87203 9 + 96486 GAAAGGATG -s mr.mrrefChr3 14839 9 + 181027 GTACAGATG -s simCow_chr6.simCow.chr6 443519 9 + 602619 GAAAGGATG -s simDog_chr6.simDog.chr6 435463 9 + 593897 GAAAGGATG -s simMouse_chr6.simMouse.chr6 459251 9 + 636262 GTACAGATG -s simRat_chr6.simRat.chr6 468536 9 + 647215 GTATAAATG - -a -s simMouse_chr6.simMouse.chr6 459132 1 + 636262 C -s Anc0.Anc0refChr3 80730 1 + 222631 T -s Anc1.Anc1refChr6 112955 1 + 197743 T -s Anc2.Anc2refChr13 87212 1 + 96486 T -s mr.mrrefChr3 14848 1 + 181027 C -s simCow_chr6.simCow.chr6 443528 1 + 602619 T -s simDog_chr6.simDog.chr6 435485 1 + 593897 T -s simMouse_chr6.simMouse.chr6 459260 1 + 636262 C -s simRat_chr6.simRat.chr6 468545 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 459133 51 + 636262 TATTGGTGCTGTCCCAACACACACACAAGCCTGAGATCACATTTTGCAAGC -s Anc0.Anc0refChr3 80731 35 + 222631 TGTTGGTCTTGT----------------GCATGGAATCATATATCTCAAGC -s Anc1.Anc1refChr6 112956 35 + 197743 TGTTGGTCTTGT----------------GCATGGAATCATATATCTCAAGC -s Anc2.Anc2refChr13 87225 35 + 96486 TGTTGGTCTTGT----------------GCATGGAATCATATATCTCAAGC -s mr.mrrefChr3 14849 46 + 181027 TATTGGTGCTGCCCAA-----CGCACAAGCCTGAGATCACATTTTACAAGC -s simCow_chr6.simCow.chr6 443541 35 + 602619 TGTTTGTCTTGT----------------GCATGAGCTCGTACATCTCAATC -s simDog_chr6.simDog.chr6 435498 35 + 593897 TGTTGGTCTTGT----------------GCATGGAATCATATATCTCAAGC -s simMouse_chr6.simMouse.chr6 459261 46 + 636262 TATTGGCGCTGCCCAA-----CGCACAAGCTTGAGATCTCATTTTACAAGC -s simRat_chr6.simRat.chr6 468546 44 + 647215 TATTGGTG-GACTCAA-----TGC-CAAGCCTGAGTGCACATGTCTCAAGC - -a -s simMouse_chr6.simMouse.chr6 459184 4 + 636262 ATGT -s Anc0.Anc0refChr3 80766 4 + 222631 CTTA -s Anc1.Anc1refChr6 112991 4 + 197743 CTTA -s Anc2.Anc2refChr13 87260 4 + 96486 CTTA -s mr.mrrefChr3 14895 4 + 181027 ATTA -s simCow_chr6.simCow.chr6 443581 4 + 602619 TTTA -s simDog_chr6.simDog.chr6 435533 4 + 593897 CTTA -s simMouse_chr6.simMouse.chr6 459307 4 + 636262 ATTA -s simRat_chr6.simRat.chr6 468590 4 + 647215 ATTA - -a -s simMouse_chr6.simMouse.chr6 459311 57 + 636262 CTCAGTACACCTTGATTTCTAAACTATGCAGCATCCAGACCATATCACCCAGCATGA -s Anc0.Anc0refChr3 80770 46 + 222631 CTTGGTATGCCTTAATGGCTAAACTAT----A--CCATACCT-----CCCACCATGA -s Anc1.Anc1refChr6 112995 50 + 197743 CTTGGTATGCCTTAATGGCTAAACTATCTAGA--CCATACCT-----CCCACCATGA -s Anc2.Anc2refChr13 87264 46 + 96486 CTTGGTATGCCTTAATGGCTAAACTAT----A--CCATATCT-----CTCACCATGA -s mr.mrrefChr3 14899 52 + 181027 CTCAGTACACCTTGATTTCTAAACTATGCAGCATCCAGACCA-----CCCAGCATGA -s simCow_chr6.simCow.chr6 443585 46 + 602619 TTCGATATGCCTTGATAACTGAACTTG----A--CCGTGCCT-----CTCACTATGA -s simDog_chr6.simDog.chr6 435537 46 + 593897 CTTGGTATGCCTTAATGGCTAAACTAT----A--CCATATCT-----CTCACCATGA -s simHuman_chr6.simHuman.chr6 443793 32 + 601863 ------------------TGAAAATAACTAGA--CCATACCT-----CCCACCATGA -s simRat_chr6.simRat.chr6 468594 52 + 647215 CCCAATATATCTAGATATCTAAACTATGCAACATCCAGACTG-----CCCAGCATGA - -a -s simMouse_chr6.simMouse.chr6 459368 16 + 636262 GATATAACATTTAGAG -s Anc0.Anc0refChr3 80816 16 + 222631 GAAGTAACAATCAGAG -s Anc1.Anc1refChr6 113045 16 + 197743 GAAGTAACAATCAGAG -s Anc2.Anc2refChr13 87310 16 + 96486 AGAGTAACAATCAGAG -s mr.mrrefChr3 14951 16 + 181027 GATATAACATTTAGAG -s simCow_chr6.simCow.chr6 443631 16 + 602619 ACAATAACAATCTGAG -s simDog_chr6.simDog.chr6 435583 16 + 593897 AGAGTAACAATCAGAG -s simHuman_chr6.simHuman.chr6 443928 16 + 601863 GAGTTGACAATCAGAG -s simRat_chr6.simRat.chr6 468646 16 + 647215 GATATAACATTTAGAG - -a -s simMouse_chr6.simMouse.chr6 459384 6 + 636262 CTCGAT -s Anc0.Anc0refChr3 80832 5 + 222631 CTCTA- -s Anc1.Anc1refChr6 113061 5 + 197743 CTCTA- -s Anc2.Anc2refChr13 87326 5 + 96486 CTATA- -s mr.mrrefChr3 14967 5 + 181027 CTCGA- -s simCow_chr6.simCow.chr6 443664 5 + 602619 TTATA- -s simDog_chr6.simDog.chr6 435599 5 + 593897 CTATA- -s simHuman_chr6.simHuman.chr6 443944 5 + 601863 GTCAA- -s simRat_chr6.simRat.chr6 468662 5 + 647215 CTCGA- - -a -s simMouse_chr6.simMouse.chr6 459390 4 + 636262 GTTG -s Anc0.Anc0refChr3 80839 4 + 222631 GTAG -s Anc1.Anc1refChr6 113068 4 + 197743 GTAG -s Anc2.Anc2refChr13 87333 4 + 96486 ACAG -s mr.mrrefChr3 14972 4 + 181027 GTTG -s simCow_chr6.simCow.chr6 443671 4 + 602619 ATAG -s simDog_chr6.simDog.chr6 435606 4 + 593897 ACAG -s simHuman_chr6.simHuman.chr6 443951 4 + 601863 GTAG -s simRat_chr6.simRat.chr6 468667 4 + 647215 GTTG - -a -s simMouse_chr6.simMouse.chr6 459394 3 + 636262 TAT -s Anc0.Anc0refChr3 80843 3 + 222631 TAT -s Anc1.Anc1refChr6 113072 3 + 197743 TAT -s Anc2.Anc2refChr13 87337 3 + 96486 CAT -s mr.mrrefChr3 14976 3 + 181027 TAT -s simCow_chr6.simCow.chr6 443675 3 + 602619 CAT -s simDog_chr6.simDog.chr6 435610 3 + 593897 CAT -s simHuman_chr6.simHuman.chr6 443956 3 + 601863 TAT -s simRat_chr6.simRat.chr6 468671 3 + 647215 TAT - -a -s simMouse_chr6.simMouse.chr6 459397 16 + 636262 GAGCTTTTATAACATA -s Anc0.Anc0refChr3 80846 16 + 222631 GAACCTTTATAACATA -s Anc1.Anc1refChr6 113075 16 + 197743 GAACCTTTATAACATA -s Anc2.Anc2refChr13 87399 16 + 96486 GAACCTTGATATCATC -s mr.mrrefChr3 14979 16 + 181027 GAGCTTTTATAACATA -s simCow_chr6.simCow.chr6 443800 16 + 602619 GATCCATGTTCTCACC -s simDog_chr6.simDog.chr6 435672 16 + 593897 GAACCTTGATATCATC -s simHuman_chr6.simHuman.chr6 443959 13 + 601863 G---CTTTATAACATA -s simRat_chr6.simRat.chr6 468674 16 + 647215 ATGCTCTTATAACATA - -a -s simMouse_chr6.simMouse.chr6 459413 4 + 636262 CCAT -s Anc0.Anc0refChr3 80862 4 + 222631 CCAT -s Anc1.Anc1refChr6 113091 4 + 197743 CCAT -s Anc2.Anc2refChr13 87418 4 + 96486 CCAT -s mr.mrrefChr3 14995 4 + 181027 CCAT -s simCow_chr6.simCow.chr6 443819 4 + 602619 CTAT -s simDog_chr6.simDog.chr6 435691 4 + 593897 CCTT -s simHuman_chr6.simHuman.chr6 443972 4 + 601863 CCAT -s simRat_chr6.simRat.chr6 468690 4 + 647215 CCAT - -a -s simMouse_chr6.simMouse.chr6 459417 18 + 636262 ATGAGTATGTAAACTCAT -s Anc0.Anc0refChr3 80867 18 + 222631 ATAAGAATCTAAACTCAT -s Anc1.Anc1refChr6 113096 18 + 197743 ATAAGAATCTAAACTCAT -s Anc2.Anc2refChr13 87423 18 + 96486 AGAAGAATCTAAACTCAT -s mr.mrrefChr3 14999 18 + 181027 ATGAGTATGTAAACTCAT -s simCow_chr6.simCow.chr6 443824 17 + 602619 AGAAGCATTCAAACTCA- -s simDog_chr6.simDog.chr6 435696 18 + 593897 AGAGGAAGCTAAACTCAT -s simHuman_chr6.simHuman.chr6 443977 18 + 601863 ATTAGGATCTAAACTCAT -s simRat_chr6.simRat.chr6 468694 18 + 647215 ATGAGGGTGTAAACTCAT - -a -s simMouse_chr6.simMouse.chr6 459435 45 + 636262 CAAGTTTTAGTACGTACAGACAATCTCCCATAAGTTTCAAGGATG -s Anc0.Anc0refChr3 80886 44 + 222631 CAAGATCTAGTTTATACAGTTAATCTCCCA-AAGTGTCAGAGTTA -s Anc1.Anc1refChr6 113115 44 + 197743 CAAGATCTAGTTTATACAGTTAATCTCCCA-AAGTGTCAGAGTTA -s Anc2.Anc2refChr13 87442 44 + 96486 CAAGATCTAGTTTATCCAGTTAATCTCCAT-AAGTGTCAGAGTTA -s mr.mrrefChr3 15017 45 + 181027 CAAGTTTTAGTACGTACAGACAATCTCCCATAAGTTTCAAGGATG -s simCow_chr6.simCow.chr6 443842 44 + 602619 CAAGATCTAGCTTGTCTAGTCAATCTCCAT-AAGCGTCAGAATTG -s simDog_chr6.simDog.chr6 435715 41 + 593897 T---ATCTAGTTCATCCAGTTAATATCCAT-ACGTGTCAAAGTCA -s simHuman_chr6.simHuman.chr6 443996 44 + 601863 CAAGATCTAATTTTTACAGTTGACCTCCCA-AAGTGTGAGAGTTA -s simRat_chr6.simRat.chr6 468712 45 + 647215 CAAGGTTTAGTATGTACAAATAACCCCCCATAAGTTTCAAAGATG - -a -s simMouse_chr6.simMouse.chr6 459480 72 + 636262 CCCTTCAAGCACTGTCATTTAAACTGCCATTAAAGCTGATGCCATATATAATAACTAGTGGCTATCAAGATT -s Anc0.Anc0refChr3 80931 20 + 222631 CCCTTTG----------------------------------------------------GGTTAACAGCATT -s Anc1.Anc1refChr6 113160 20 + 197743 CCCTTTG----------------------------------------------------GGTTAACAGCATT -s Anc2.Anc2refChr13 87487 20 + 96486 CCTTTTG----------------------------------------------------GTTTAACAGCATT -s mr.mrrefChr3 15062 72 + 181027 CCCTTCAAGCACTGTCATTTAAACTGCCATTAAAGCTGATGCCATATATAATAACTAGTGGCTATCAAGATT -s simCow_chr6.simCow.chr6 443887 20 + 602619 CCTTTTA----------------------------------------------------GTTTAACAGCATT -s simDog_chr6.simDog.chr6 435757 20 + 593897 CCTTTTG----------------------------------------------------GTTTAACAGCATT -s simHuman_chr6.simHuman.chr6 444041 20 + 601863 CCCTTTG----------------------------------------------------GGTTAACAGAATT -s simRat_chr6.simRat.chr6 468757 72 + 647215 ACCTTTCAGCTCTGTCATTTAAACTGCTATTAAGACTGAGGCCATCTATGATAATTGGTGGCTATCAAGTTT - -a -s simMouse_chr6.simMouse.chr6 459552 27 + 636262 TTTGGTTCTACAAACACTCATGCATTC -s Anc0.Anc0refChr3 80954 15 + 222631 TCTGGTTCC------------GCCTTC -s Anc1.Anc1refChr6 113183 15 + 197743 TCTGGTTCC------------GCCTTC -s Anc2.Anc2refChr13 87575 15 + 96486 TCTGGATCC------------GCCTTC -s mr.mrrefChr3 15134 27 + 181027 TTTGGTTCTACAAACACTCATGCATTC -s simCow_chr6.simCow.chr6 443975 15 + 602619 CCTGTATCT------------GCCTGC -s simDog_chr6.simDog.chr6 435868 15 + 593897 TCTGGATCC------------CACTTC -s simHuman_chr6.simHuman.chr6 444064 15 + 601863 TCTGGTTCC------------GCCTTC -s simRat_chr6.simRat.chr6 468829 27 + 647215 TTTGGTTCTACAAATACTCATGCATTC - -a -s simMouse_chr6.simMouse.chr6 459579 6 + 636262 TGTTGT -s Anc0.Anc0refChr3 80969 6 + 222631 TGGTAT -s Anc1.Anc1refChr6 113198 6 + 197743 TGGTAT -s Anc2.Anc2refChr13 87590 6 + 96486 TGGTAT -s mr.mrrefChr3 15161 6 + 181027 TGTTGT -s simCow_chr6.simCow.chr6 444001 6 + 602619 TGGTTT -s simDog_chr6.simDog.chr6 435883 6 + 593897 TGGTAT -s simHuman_chr6.simHuman.chr6 444079 6 + 601863 TGGTAT -s simRat_chr6.simRat.chr6 468856 6 + 647215 TGTTGT - -a -s simMouse_chr6.simMouse.chr6 459585 1 + 636262 A -s Anc0.Anc0refChr3 80975 1 + 222631 A -s Anc1.Anc1refChr6 113204 1 + 197743 A -s Anc2.Anc2refChr13 87596 1 + 96486 A -s mr.mrrefChr3 15167 1 + 181027 A -s simCow_chr6.simCow.chr6 444009 1 + 602619 A -s simDog_chr6.simDog.chr6 435889 1 + 593897 A -s simHuman_chr6.simHuman.chr6 444085 1 + 601863 A -s simRat_chr6.simRat.chr6 468862 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 459586 50 + 636262 CATTTTTGTTGGGAAATCCCTCCCTTAGCATCTGAATTGTCTTAGCAACA -s Anc0.Anc0refChr3 80979 44 + 222631 CATTATTG--GG-AAAT---GCCATCACCATCTTAATTCCCATTGTAACA -s Anc1.Anc1refChr6 113208 44 + 197743 CATTATTG--GG-AAAT---GCCATCACCATCTTAATTCCCATTGTAACA -s Anc2.Anc2refChr13 87600 44 + 96486 CATTATTG--GG-AAAT---GCCATCACCAGCTTACTTCCCATTGTAACA -s mr.mrrefChr3 15168 49 + 181027 CATTTTTGTTGG-AAATCCCTCCCTTAGCATCTGAATTGTCTTAGCAACA -s simCow_chr6.simCow.chr6 444013 44 + 602619 TGTTATCA--GG-AAAT---ACCATCACCAGCTTACTTCCCATTGTAACA -s simDog_chr6.simDog.chr6 435893 32 + 593897 CATTATTG--GG-AAAT---GCCATCACCAGC------------ATAACA -s simHuman_chr6.simHuman.chr6 444089 44 + 601863 CATGATTG--GG-AAAT---GCCATCACCGTCTAAATTCCCATGGTAACA -s simRat_chr6.simRat.chr6 468863 49 + 647215 CATTTTCGTTGG-AAATCCCCCCCTTAGCGTCTGAATTGTCTTGGTAAAA - -a -s simMouse_chr6.simMouse.chr6 459636 12 + 636262 TCATTCCTTAAT -s Anc0.Anc0refChr3 81023 12 + 222631 tCATTCACTAAT -s Anc1.Anc1refChr6 113252 12 + 197743 TCATTCACTAAT -s Anc2.Anc2refChr13 87864 12 + 96486 gCATTCACTAAT -s mr.mrrefChr3 15217 12 + 181027 TCATTCCTTAAT -s simCow_chr6.simCow.chr6 444280 12 + 602619 TCATTCACTAAT -s simDog_chr6.simDog.chr6 436210 12 + 593897 gcagtcaCTAAT -s simHuman_chr6.simHuman.chr6 444133 12 + 601863 TCATTAACTAAT -s simRat_chr6.simRat.chr6 468912 12 + 647215 TCATTCCTTAAT - -a -s simMouse_chr6.simMouse.chr6 459648 28 + 636262 TGGAGGATGCCCACAACAAGATGCACAC -s Anc0.Anc0refChr3 81036 28 + 222631 TAAAGGATGCCCAGAACTAATGAAATTT -s Anc1.Anc1refChr6 113265 28 + 197743 TAAAGGATGCCCAGAACTAATGAAATTT -s Anc2.Anc2refChr13 87877 28 + 96486 GAAAGGATGCCCAGAACTAATGAAATTT -s mr.mrrefChr3 15229 28 + 181027 TGGAGGATGCCCACAACAAGATGCACAC -s simCow_chr6.simCow.chr6 444293 28 + 602619 GAAAGGATGCACAGAGCTAATGGAATTT -s simDog_chr6.simDog.chr6 436223 28 + 593897 GAAAGGATGCCCACGACTGACGAAATTT -s simHuman_chr6.simHuman.chr6 444146 28 + 601863 TAAAGGATGCCCAGAACTAATGAAATTT -s simRat_chr6.simRat.chr6 468924 28 + 647215 GGAAAGATGCCCTCACCAAGAGGCACAC - -a -s simMouse_chr6.simMouse.chr6 459676 11 + 636262 CTTATCCTCCC -s Anc0.Anc0refChr3 81069 9 + 222631 CTTAC--TTAA -s Anc1.Anc1refChr6 113298 9 + 197743 CTTAC--TTAA -s Anc2.Anc2refChr13 87910 9 + 96486 CTTAC--TTAA -s mr.mrrefChr3 15257 9 + 181027 CTTAT--TCCC -s simCow_chr6.simCow.chr6 444326 9 + 602619 CTTGT--TTAA -s simDog_chr6.simDog.chr6 436256 9 + 593897 ATTAC--CTAA -s simHuman_chr6.simHuman.chr6 444179 9 + 601863 CTTAC--TTAG -s simRat_chr6.simRat.chr6 468952 9 + 647215 CTTAT--TCCC - -a -s simMouse_chr6.simMouse.chr6 459687 15 + 636262 TGTCTCAGCCTGATC -s Anc0.Anc0refChr3 81081 15 + 222631 TGGCTGAGCCTGATG -s Anc1.Anc1refChr6 113310 15 + 197743 TGGCTGAGCCTGATG -s Anc2.Anc2refChr13 87922 15 + 96486 GGGCCGAGCCTAAAG -s mr.mrrefChr3 15266 15 + 181027 TGTCTCAGCCTGATC -s simCow_chr6.simCow.chr6 444338 15 + 602619 GGGCAGAGCCTAAAG -s simDog_chr6.simDog.chr6 436268 14 + 593897 GGGCC-AGCCTAAAG -s simHuman_chr6.simHuman.chr6 444191 15 + 601863 TGGCTAAGCCTGATG -s simRat_chr6.simRat.chr6 468961 15 + 647215 TGTCTCAGCCTGATC - -a -s simMouse_chr6.simMouse.chr6 459702 32 + 636262 AGTTCATTGAACTTGACATGGAAGAAAATTTT -s Anc0.Anc0refChr3 81097 32 + 222631 AGTTCATTGAACTTCACATGGAAGCAAACTTT -s Anc1.Anc1refChr6 113326 32 + 197743 AGTTCATTGAACTTCACATGGAAGCAAACTTT -s Anc2.Anc2refChr13 87938 32 + 96486 AGTCAGTTGAATTTCACATGGAGACAAACTTT -s mr.mrrefChr3 15281 32 + 181027 AGTTCATTGAACTTGACATGGAAGAAAATTTT -s simCow_chr6.simCow.chr6 444354 31 + 602619 AGTG-GTTGAAATTCCCATGGATACAAAGTTA -s simDog_chr6.simDog.chr6 436283 32 + 593897 GTTCAGTTGAATTTCACACAGAGACCAACTTT -s simHuman_chr6.simHuman.chr6 444207 32 + 601863 AGTTCACGGAACCCCACATGGAAGCAAACTTT -s simRat_chr6.simRat.chr6 468976 32 + 647215 GGTTAATTGAACTTGACATGGGAGAAAATTTT - -a -s simMouse_chr6.simMouse.chr6 459734 1 + 636262 T -s Anc0.Anc0refChr3 81130 1 + 222631 T -s Anc1.Anc1refChr6 113359 1 + 197743 T -s Anc2.Anc2refChr13 87971 1 + 96486 T -s mr.mrrefChr3 15313 1 + 181027 T -s simCow_chr6.simCow.chr6 444386 1 + 602619 T -s simDog_chr6.simDog.chr6 436316 1 + 593897 C -s simHuman_chr6.simHuman.chr6 444240 1 + 601863 T -s simRat_chr6.simRat.chr6 469008 1 + 647215 G - -a -s simMouse_chr6.simMouse.chr6 459735 22 + 636262 GCAAGGCTGCCCTTCAATTGCA -s Anc0.Anc0refChr3 81131 22 + 222631 GCAAGGTTACCCTTCAGTTATG -s Anc1.Anc1refChr6 113360 22 + 197743 GCAAGGTTACCCTTCAGTTATG -s Anc2.Anc2refChr13 87972 22 + 96486 TCAAGGTTACCCTCCAGTTATG -s mr.mrrefChr3 15314 22 + 181027 GCAAGGCTGCCCTTCAATTGCA -s simCow_chr6.simCow.chr6 444387 18 + 602619 TCAAGATTACCCTCCAGT---- -s simDog_chr6.simDog.chr6 436317 22 + 593897 TCAAGGTCACCCTCTGATTATG -s simHuman_chr6.simHuman.chr6 444241 20 + 601863 GCA--GTTACTGTTCAGTTATG -s simRat_chr6.simRat.chr6 469049 22 + 647215 GCAAGGCTGCCCCTCAATTGCA - -a -s simMouse_chr6.simMouse.chr6 459757 85 + 636262 TGGCAACCTTCTGATCAAACCAGTGAACAATCTGATACATACTTCCCCATAGGGCCAAAAATCGAGTTGGTTGAAATTGACAGCC -s Anc0.Anc0refChr3 81154 41 + 222631 TGGCAGCCTACAGATCAAACCAATGAATAATCTGATG--------------------------------------------AACC -s Anc1.Anc1refChr6 113383 41 + 197743 TGGCAGCCTACAGATCAAACCAATGAATAATCTGATG--------------------------------------------AACC -s Anc2.Anc2refChr13 87995 41 + 96486 TGGCAGCCTACAGACCAAATCAATGAATAATCCAATG--------------------------------------------CACC -s mr.mrrefChr3 15336 74 + 181027 TGGCAACCTTCTGATCAAACCAGTGAACAATCTGATAC-----------TAGGGCCAAAAATCGAGTTGGTTGAAATTGACAGCC -s simCow_chr6.simCow.chr6 444405 40 + 602619 TGGGAG-CTACAGACTAAATCACCGAATAAGCCAATG--------------------------------------------TCCC -s simDog_chr6.simDog.chr6 436364 41 + 593897 TGGCAGCCTACAGACCAAATCAATGAATAGTCCAAGG--------------------------------------------CACC -s simHuman_chr6.simHuman.chr6 444262 41 + 601863 TGGCAGTCTACAGATCAAGCCAATGAATAATCTGATG--------------------------------------------AACC -s simRat_chr6.simRat.chr6 469071 74 + 647215 TGGCAACCTTCTGATCGAACCAGTGAACAATCCCATAC-----------TAGGGCGAAAGATCGGGTTAGTTGAAATTGACAGCC - -a -s simMouse_chr6.simMouse.chr6 459842 19 + 636262 ACTTCCCCACAGAGTAAAA -s Anc0.Anc0refChr3 81195 19 + 222631 ACTTTCCCACAGAGCAAAA -s Anc1.Anc1refChr6 113424 19 + 197743 ACTTTCCCACAGAGCAAAA -s Anc2.Anc2refChr13 88036 19 + 96486 ACTTTCCCACAGAGCAAAA -s mr.mrrefChr3 15410 19 + 181027 ACTTCCCCACAGAGTAAAA -s simCow_chr6.simCow.chr6 444445 19 + 602619 ATTTTCTGATGGGGCAAAA -s simDog_chr6.simDog.chr6 436406 19 + 593897 ACCTTCCCACAGAGCAAAA -s simHuman_chr6.simHuman.chr6 444303 19 + 601863 ACTTTCCCACAGAGCAAAA -s simRat_chr6.simRat.chr6 469145 19 + 647215 ACTCCCCCATAGAGCAAAA - -a -s simMouse_chr6.simMouse.chr6 459861 36 + 636262 CAGTTTCATGCCCTGCATGCCACTCCTCAAGTTTGG -s Anc0.Anc0refChr3 81217 36 + 222631 CGGTTTCAGGCCCTGCATATCACTCCTCTAGTTTGG -s Anc1.Anc1refChr6 113446 36 + 197743 CGGTTTCAGGCCCTGCATATCACTCCTCTAGTTTGG -s Anc2.Anc2refChr13 88058 36 + 96486 CGGTTTCGGGCTCTGCATATCACTCCTCTAATTTGG -s mr.mrrefChr3 15429 36 + 181027 CAGTTTCATGCCCTGCATGCCACTCCTCAAGTTTGG -s simCow_chr6.simCow.chr6 444467 35 + 602619 CGGGTTC-GGCTCTGTATATAACTCTTCTAATTTGA -s simDog_chr6.simDog.chr6 436428 36 + 593897 CGGTTTCGCGCTCTGCATATCACTCCTCTAATTTGG -s simHuman_chr6.simHuman.chr6 444325 36 + 601863 CGGTTTCAGGGCCTGCACCTCATTCCTCTAGTTTGG -s simRat_chr6.simRat.chr6 469164 36 + 647215 CAGTTTCATGGCCTGCATATCACTCTTCTAGTGTGG - -a -s simMouse_chr6.simMouse.chr6 459897 112 + 636262 TGATTCAGAACACTTGCCTATCGTGTCCACATCATCGCTAGGCCAACCAAAAACCTTGATGAGTCTGAGTTTTACAATTTTCAAATCACTACTGCTGGAAGGGCTGCAAGCA -s Anc0.Anc0refChr3 81254 76 + 222631 TAAtagaatgcagt------------------------------------aaaccttgttgagtcccagttttacgactttgaggttgtgaccactgggggggttgcaagta -s Anc1.Anc1refChr6 113483 76 + 197743 TAATAGAATGCAGT------------------------------------AAaccttgttgagtcccagttttacgactttgaggttgtgaccactgggggggttgcaagta -s Anc2.Anc2refChr13 88095 76 + 96486 TAGtagaatgcggt------------------------------------atacctaatggagtcccagttttatgaccttgaggttgtgaccactggggggttagcaagta -s mr.mrrefChr3 15465 112 + 181027 TGATTCAGAACACTTGCCTATCGTGTCCACATCATCGCTAGGCCAACCAAAAaccttgatgagtctgagttttacaattttcaaatcactactgctggaagggctgcaagca -s simCow_chr6.simCow.chr6 444503 76 + 602619 Tactaaaatgcgat------------------------------------atacctcaaggagtcccagttctatgacctttaggtcaggacccatgggaggttagcaagta -s simDog_chr6.simDog.chr6 436465 76 + 593897 TAGtagaatatggt------------------------------------atacctaatggagtcccagttttatgaccttgaggttgtgaccactggggggttagcaagta -s simHuman_chr6.simHuman.chr6 444362 57 + 601863 TAATAGAATGCAGT------------------------------------AAACCTTGGTGAGTCCATGTCACACGACTTCAA-------------------GTTGCAAGTA -s simRat_chr6.simRat.chr6 469200 112 + 647215 TGATTCAGAACACTTGCCTATCATGTCCACATCATCACTAGGCCAACCAAAAaccttgatgagtctgaactttgcgactttcaaatcactagtgctggaagggctgcaaaca - -a -s simMouse_chr6.simMouse.chr6 460009 4 + 636262 AGTT -s Anc0.Anc0refChr3 81330 4 + 222631 atat -s Anc1.Anc1refChr6 113559 4 + 197743 atat -s Anc2.Anc2refChr13 88171 4 + 96486 atat -s mr.mrrefChr3 15577 4 + 181027 agtt -s simCow_chr6.simCow.chr6 444579 4 + 602619 aaat -s simDog_chr6.simDog.chr6 436546 4 + 593897 atat -s simHuman_chr6.simHuman.chr6 444419 4 + 601863 ACAT -s simRat_chr6.simRat.chr6 469312 4 + 647215 agtt - -a -s simMouse_chr6.simMouse.chr6 460013 18 + 636262 GATTGTCTAAAATGTTGT -s Anc0.Anc0refChr3 81337 17 + 222631 ggatatTT-AAATGTAGT -s Anc1.Anc1refChr6 113566 18 + 197743 GGATATTTAAAATGTAGT -s Anc2.Anc2refChr13 88178 17 + 96486 ggatatTC-AAATGTAGT -s mr.mrrefChr3 15581 18 + 181027 GATTGTCTAAAATGTTGT -s simCow_chr6.simCow.chr6 444586 17 + 602619 gggtatTA-TAATGTGCT -s simDog_chr6.simDog.chr6 436553 17 + 593897 ggatattc-aagtgcagt -s simHuman_chr6.simHuman.chr6 444426 18 + 601863 GGCTATTTAAAATGTAGT -s simRat_chr6.simRat.chr6 469316 18 + 647215 GATTTTGTAAAATGATGT - -a -s simMouse_chr6.simMouse.chr6 460031 13 + 636262 AAAGAGGGAGTAA -s Anc0.Anc0refChr3 81355 12 + 222631 AA-GAGGGTATAA -s Anc1.Anc1refChr6 113585 12 + 197743 AA-GAGGGTATAA -s Anc2.Anc2refChr13 88196 12 + 96486 AA-GTGGATATAA -s mr.mrrefChr3 15599 12 + 181027 AA-GAGGGAGTAA -s simCow_chr6.simCow.chr6 444604 12 + 602619 AA-AGGGATATAA -s simDog_chr6.simDog.chr6 436571 12 + 593897 aa-gtgcaattaa -s simHuman_chr6.simHuman.chr6 444445 12 + 601863 AA-GAGGGTATAA -s simRat_chr6.simRat.chr6 469334 12 + 647215 AA-GAGGGAGTAA - -a -s simMouse_chr6.simMouse.chr6 460044 4 + 636262 GTCA -s Anc0.Anc0refChr3 81367 4 + 222631 GtCA -s Anc1.Anc1refChr6 113597 4 + 197743 GTCA -s Anc2.Anc2refChr13 88209 4 + 96486 GtCA -s mr.mrrefChr3 15611 4 + 181027 GTCA -s simCow_chr6.simCow.chr6 444617 4 + 602619 GTAA -s simDog_chr6.simDog.chr6 436584 4 + 593897 gtcA -s simHuman_chr6.simHuman.chr6 444457 4 + 601863 TGCA -s simRat_chr6.simRat.chr6 469346 4 + 647215 GTCA - -a -s simMouse_chr6.simMouse.chr6 460048 32 + 636262 GTGACACAACCTTATTGTAAGTTAGACAGTGA -s Anc0.Anc0refChr3 81371 32 + 222631 GTGACACAACCTTACTCTAAGAGAGACATTTA -s Anc1.Anc1refChr6 113601 32 + 197743 GTGACACAACCTTACTCTAAGAGAGACATTTA -s Anc2.Anc2refChr13 88213 32 + 96486 GTGACACAACCTTGCTCTAAGAGAGACATTTA -s mr.mrrefChr3 15615 32 + 181027 GTGACACAACCTTATTGTAAGTTAGACAGTGA -s simCow_chr6.simCow.chr6 444623 32 + 602619 TTGATACAGCATTTGTCTAAGAAAGACATTTA -s simDog_chr6.simDog.chr6 436588 32 + 593897 GTGACACAACCTTGCTCCGTGAGAGACATTTA -s simHuman_chr6.simHuman.chr6 444461 32 + 601863 GTGACACAACCTTACTCTAAGACAGAAATTTA -s simRat_chr6.simRat.chr6 469350 32 + 647215 GTGACACAACCTTATTGTAAGACAGACATTGA - -a -s simMouse_chr6.simMouse.chr6 460080 2 + 636262 AA -s Anc0.Anc0refChr3 81403 2 + 222631 AG -s Anc1.Anc1refChr6 113633 2 + 197743 AG -s Anc2.Anc2refChr13 88245 2 + 96486 GG -s mr.mrrefChr3 15647 2 + 181027 AA -s simCow_chr6.simCow.chr6 444656 2 + 602619 GG -s simDog_chr6.simDog.chr6 436620 2 + 593897 GG -s simHuman_chr6.simHuman.chr6 444493 2 + 601863 AG -s simRat_chr6.simRat.chr6 469382 2 + 647215 AA - -a -s simMouse_chr6.simMouse.chr6 460082 3 + 636262 AGG -s Anc0.Anc0refChr3 81417 3 + 222631 AGT -s Anc1.Anc1refChr6 113647 3 + 197743 AGT -s Anc2.Anc2refChr13 88259 3 + 96486 AGT -s mr.mrrefChr3 15649 3 + 181027 AGG -s simCow_chr6.simCow.chr6 444670 3 + 602619 AGT -s simDog_chr6.simDog.chr6 436634 3 + 593897 GGT -s simHuman_chr6.simHuman.chr6 444507 3 + 601863 AGT -s simRat_chr6.simRat.chr6 469384 3 + 647215 AGG - -a -s simMouse_chr6.simMouse.chr6 460085 7 + 636262 AGATTCT -s Anc0.Anc0refChr3 81420 7 + 222631 GGGTTTC -s Anc1.Anc1refChr6 113650 7 + 197743 GGGTTTC -s Anc2.Anc2refChr13 88262 7 + 96486 GGGTTTC -s mr.mrrefChr3 15652 7 + 181027 AGATTCT -s simCow_chr6.simCow.chr6 444673 7 + 602619 CGGTTTC -s simDog_chr6.simDog.chr6 436733 7 + 593897 GGGTTTT -s simHuman_chr6.simHuman.chr6 444510 7 + 601863 GGGCTTC -s simRat_chr6.simRat.chr6 469387 7 + 647215 AGATTTT - -a -s simMouse_chr6.simMouse.chr6 460092 6 + 636262 AACAGC -s Anc0.Anc0refChr3 81427 6 + 222631 AGGAGC -s Anc1.Anc1refChr6 113657 6 + 197743 AGGAGC -s Anc2.Anc2refChr13 88269 6 + 96486 AGGAGC -s mr.mrrefChr3 15659 6 + 181027 AACAGC -s simCow_chr6.simCow.chr6 444680 6 + 602619 AGGAGC -s simDog_chr6.simDog.chr6 436742 2 + 593897 AG---- -s simHuman_chr6.simHuman.chr6 444517 6 + 601863 AGGAGC -s simRat_chr6.simRat.chr6 469394 6 + 647215 AATAGC - -a -s simMouse_chr6.simMouse.chr6 460098 4 + 636262 TCCA -s Anc0.Anc0refChr3 81433 4 + 222631 TTAA -s Anc1.Anc1refChr6 113663 4 + 197743 TTAA -s Anc2.Anc2refChr13 88275 4 + 96486 TTAA -s mr.mrrefChr3 15665 4 + 181027 TCCA -s simCow_chr6.simCow.chr6 444686 4 + 602619 TTAA -s simDog_chr6.simDog.chr6 123548 4 + 593897 TTAA -s simDog_chr6.simDog.chr6 436858 4 + 593897 TTAA -s simHuman_chr6.simHuman.chr6 444523 4 + 601863 TTAA -s simRat_chr6.simRat.chr6 469400 4 + 647215 TCCA - -a -s simMouse_chr6.simMouse.chr6 460102 28 + 636262 TAGCTTTATGTCAAGATACTTACCTTAC -s Anc0.Anc0refChr3 81498 28 + 222631 TAGCTCTACGTCAAGATACTTACCTTAC -s Anc1.Anc1refChr6 113728 28 + 197743 TAGCTCTACGTCAAGATACTTACCTTAC -s Anc2.Anc2refChr13 88341 28 + 96486 TAGCTCTACGACAAGATGCTTACCTTAC -s mr.mrrefChr3 15669 28 + 181027 TAGCTTTATGTCAAGATACTTACCTTAC -s simCow_chr6.simCow.chr6 444764 28 + 602619 TAGCTCTACGTCAATAAACTTACGTTAC -s simDog_chr6.simDog.chr6 123614 28 + 593897 TAGCTCCACGACAAGATGCTTACCTTGG -s simDog_chr6.simDog.chr6 436924 28 + 593897 TAGCTCTATGACAAGATGCTTACCTTAC -s simHuman_chr6.simHuman.chr6 444588 28 + 601863 TGGCTGTACGTCAAGATACTTACCTTAC -s simRat_chr6.simRat.chr6 469404 28 + 647215 TAGCTTTATGTCAAGATACTTACCTTAC - -a -s simMouse_chr6.simMouse.chr6 460130 2 + 636262 AG -s Anc0.Anc0refChr3 81526 2 + 222631 AA -s Anc1.Anc1refChr6 113756 2 + 197743 AA -s Anc2.Anc2refChr13 88369 2 + 96486 GA -s mr.mrrefChr3 15697 2 + 181027 AG -s simCow_chr6.simCow.chr6 444792 2 + 602619 AA -s simDog_chr6.simDog.chr6 123642 2 + 593897 CT -s simDog_chr6.simDog.chr6 436952 2 + 593897 GA -s simHuman_chr6.simHuman.chr6 444616 2 + 601863 AA -s simRat_chr6.simRat.chr6 469433 2 + 647215 AG - -a -s simMouse_chr6.simMouse.chr6 460132 9 + 636262 TTACACCAA -s Anc0.Anc0refChr3 81531 9 + 222631 TTACATCAA -s Anc1.Anc1refChr6 113761 9 + 197743 TTACATCAA -s Anc2.Anc2refChr13 88374 9 + 96486 CTACGTCGA -s mr.mrrefChr3 15699 9 + 181027 TTACACCAA -s simCow_chr6.simCow.chr6 444797 9 + 602619 CTACGTCGA -s simDog_chr6.simDog.chr6 436957 9 + 593897 CTACGTCGA -s simHuman_chr6.simHuman.chr6 444621 9 + 601863 TTAGATAAA -s simRat_chr6.simRat.chr6 469435 9 + 647215 TTATACTAA - -a -s simMouse_chr6.simMouse.chr6 460141 1 + 636262 G -s Anc0.Anc0refChr3 81540 1 + 222631 G -s Anc1.Anc1refChr6 113770 1 + 197743 G -s Anc2.Anc2refChr13 88383 1 + 96486 G -s mr.mrrefChr3 15708 1 + 181027 G -s simCow_chr6.simCow.chr6 444806 1 + 602619 G -s simDog_chr6.simDog.chr6 436966 1 + 593897 G -s simHuman_chr6.simHuman.chr6 444630 1 + 601863 G -s simRat_chr6.simRat.chr6 469445 1 + 647215 G - -a -s simMouse_chr6.simMouse.chr6 460142 16 + 636262 CATATAGGAGCCAGTA -s Anc0.Anc0refChr3 81542 16 + 222631 AAGTTAAAAGCCAGAA -s Anc1.Anc1refChr6 113772 16 + 197743 AAGTTAAAAGCCAGAA -s Anc2.Anc2refChr13 88385 16 + 96486 AAGTTAAAAGCCAGAA -s mr.mrrefChr3 15709 16 + 181027 CATATAGGAGCCAGTA -s simCow_chr6.simCow.chr6 444808 16 + 602619 CAGTGAAAAGCCAGAA -s simDog_chr6.simDog.chr6 436968 16 + 593897 AAGTTAAAAGCCAGAA -s simRat_chr6.simRat.chr6 469446 16 + 647215 CATATACAAGCCAGTA - -a -s simMouse_chr6.simMouse.chr6 460158 18 + 636262 GGTGGGTCGGGCCATTCA -s Anc0.Anc0refChr3 81560 18 + 222631 GGCAACACATGCCAGTCA -s Anc1.Anc1refChr6 113790 18 + 197743 GGCAACACATGCCAGTCA -s Anc2.Anc2refChr13 88403 18 + 96486 GGCAACACATGCCAGTCA -s mr.mrrefChr3 15725 18 + 181027 GGTGGGTCGGGCCATTCA -s simCow_chr6.simCow.chr6 444826 18 + 602619 GGCAACTCAGGCCAGTCA -s simDog_chr6.simDog.chr6 436986 18 + 593897 GGCAACACATGTCAGTCA -s simHuman_chr6.simHuman.chr6 445525 18 + 601863 ACAAACCCAAGCCACTCA -s simRat_chr6.simRat.chr6 469462 18 + 647215 GGTGGGTCGAGCCATCTA - -a -s simMouse_chr6.simMouse.chr6 460176 15 + 636262 TAGCTAAGATTACAC -s Anc0.Anc0refChr3 81613 15 + 222631 TGGTTAAGTGCACAC -s Anc1.Anc1refChr6 113843 15 + 197743 TGGTTAAGTGCACAC -s Anc2.Anc2refChr13 88456 15 + 96486 TGGTTAAGTGCACAC -s mr.mrrefChr3 15743 15 + 181027 TAGTTAAGAGCACAC -s simCow_chr6.simCow.chr6 444879 15 + 602619 TGGCTAAGTGCACAC -s simDog_chr6.simDog.chr6 437039 15 + 593897 TGGTTGAGTGGACAC -s simHuman_chr6.simHuman.chr6 445578 15 + 601863 TGGTTAAGTGCACAC -s simRat_chr6.simRat.chr6 469480 15 + 647215 TAGTTAAGAGCACAC - -a -s simMouse_chr6.simMouse.chr6 460191 8 + 636262 GTGGGGCA -s Anc0.Anc0refChr3 81628 8 + 222631 TTTGGTGG -s Anc1.Anc1refChr6 113858 8 + 197743 TTTGGTGG -s Anc2.Anc2refChr13 88471 8 + 96486 TTTGGTGG -s mr.mrrefChr3 15758 8 + 181027 GTGGGGCA -s simCow_chr6.simCow.chr6 444894 8 + 602619 TCTGGTGA -s simDog_chr6.simDog.chr6 437054 8 + 593897 TTTAGTGG -s simHuman_chr6.simHuman.chr6 445594 8 + 601863 TTTGGTGG -s simRat_chr6.simRat.chr6 469495 8 + 647215 ATGGGGCA - -a -s simMouse_chr6.simMouse.chr6 460199 7 + 636262 AGGAATG -s Anc0.Anc0refChr3 81637 7 + 222631 AGGACTA -s Anc1.Anc1refChr6 113867 7 + 197743 AGGACTA -s Anc2.Anc2refChr13 88480 7 + 96486 GGGACTA -s mr.mrrefChr3 15766 7 + 181027 AGGAATG -s simCow_chr6.simCow.chr6 444903 7 + 602619 GGGATCA -s simDog_chr6.simDog.chr6 437063 7 + 593897 GTAACTA -s simHuman_chr6.simHuman.chr6 445603 7 + 601863 AGGACTA -s simRat_chr6.simRat.chr6 469503 7 + 647215 AGGAATG - -a -s simMouse_chr6.simMouse.chr6 460206 9 + 636262 TCTTAAGCT -s Anc0.Anc0refChr3 81647 9 + 222631 CCTTCAGCA -s Anc1.Anc1refChr6 113877 9 + 197743 CCTTCAGCA -s Anc2.Anc2refChr13 88490 9 + 96486 CTTTCACCA -s mr.mrrefChr3 15773 9 + 181027 TCTTAAGCT -s simCow_chr6.simCow.chr6 444913 8 + 602619 CTTTC-CCA -s simDog_chr6.simDog.chr6 437073 9 + 593897 CTTCCACCA -s simHuman_chr6.simHuman.chr6 445613 9 + 601863 CCTTCAGCA -s simRat_chr6.simRat.chr6 469510 9 + 647215 TCTTAAGCT - -a -s simMouse_chr6.simMouse.chr6 460215 53 + 636262 GTTGAGAAGCATAAATGAAAACCTCAGATGACGCAGATGAGACACGGATGGCT -s Anc0.Anc0refChr3 81660 31 + 222631 GTTG---------------------AGA-AACGCAGATGAGCCACCGATGGCT -s Anc1.Anc1refChr6 113890 46 + 197743 GTTGAGAAGCTA------AAAGTTTAGA-AACGCAGATGAGCCACCGATGGCT -s Anc2.Anc2refChr13 88503 31 + 96486 GTTG---------------------AGA-ACCGCAGATGAGCCACCGATGGCT -s mr.mrrefChr3 15782 47 + 181027 GTTGAGAAGCAT------AAAGTTCAGATGACGCAGATGAGACACCGATGGCT -s simCow_chr6.simCow.chr6 444925 31 + 602619 GTGA---------------------AGA-ACCGCAGATGACCCATCGATGGCT -s simDog_chr6.simDog.chr6 437086 31 + 593897 CTTG---------------------AGC-ACCGCAGATGAGCCACCAATGGCT -s simHuman_chr6.simHuman.chr6 445626 46 + 601863 GTTGAGGAGCTA------AAAGTTTAGA-AACGTAGATGGGCCACCGATGGCT -s simRat_chr6.simRat.chr6 469519 42 + 647215 GTTGAGAAGCAT------AAAGT-----TGAAAAAGATAAAACAGCGTTGGCT - -a -s simMouse_chr6.simMouse.chr6 460268 18 + 636262 GGTAGCGTGAGGCGCCAT -s Anc0.Anc0refChr3 81691 17 + 222631 GGTGGGATGGGGCGCCG- -s Anc1.Anc1refChr6 113936 17 + 197743 GGTGGGATGGGGCGCCG- -s Anc2.Anc2refChr13 88534 17 + 96486 GGTGGGATGGGGCGCCG- -s mr.mrrefChr3 15829 18 + 181027 GGTAGCGTGAGGCGCCAT -s simCow_chr6.simCow.chr6 444957 17 + 602619 GGTAGGGTGGGGCGGCG- -s simDog_chr6.simDog.chr6 437117 15 + 593897 GGTGGGATGAGGCGC--- -s simHuman_chr6.simHuman.chr6 445672 17 + 601863 GGTGAGTTGGGGTGCCG- -s simRat_chr6.simRat.chr6 469561 18 + 647215 GGTAGCGTGAGGCGTCAT - -a -s simMouse_chr6.simMouse.chr6 460286 36 + 636262 GTAACCCCAGGCGACTAGGTAAGTTGCAGGTATCTC -s Anc0.Anc0refChr3 81708 35 + 222631 GTGAGCC-AAGCGACGGGGTAAGATGCAGGTATCTC -s Anc1.Anc1refChr6 113953 35 + 197743 GTGAGCC-AAGCGACGGGGTAAGATGCAGGTATCTC -s Anc2.Anc2refChr13 88551 35 + 96486 GTGAGTT-GAAAAACGGGGTAAAATGCAGGTATTTC -s mr.mrrefChr3 15847 36 + 181027 GTAACCCCAAGCGACTAGGTAAGTTGCAGGTATCTC -s simCow_chr6.simCow.chr6 445004 35 + 602619 GTGAGTT-GAAAAACGGGGTAAAATGCAGGTATTTC -s simDog_chr6.simDog.chr6 437132 1 + 593897 -----------------------------------T -s simHuman_chr6.simHuman.chr6 445689 35 + 601863 GTGAGCC-AAGCGACGGGGTCAGATGCAGGTTTCTC -s simRat_chr6.simRat.chr6 469579 36 + 647215 GTAACCCCAAGCGATTAAGTAAGGTGCAAGTATTTC - -a -s simMouse_chr6.simMouse.chr6 460322 4 + 636262 TCCG -s Anc0.Anc0refChr3 81743 4 + 222631 TTCG -s Anc1.Anc1refChr6 113988 4 + 197743 TTCG -s Anc2.Anc2refChr13 88586 4 + 96486 TTCA -s mr.mrrefChr3 15883 4 + 181027 TTCG -s simCow_chr6.simCow.chr6 445044 4 + 602619 TTCA -s simDog_chr6.simDog.chr6 437133 4 + 593897 CTCA -s simHuman_chr6.simHuman.chr6 445724 4 + 601863 TTCG -s simRat_chr6.simRat.chr6 469615 4 + 647215 TTCG - -a -s simMouse_chr6.simMouse.chr6 460326 60 + 636262 GACCAGTCAGAATAGCAACGAAGCTGGATGCTCAATCTAACGTTCAGGCCAGCGGGCCCG -s Anc0.Anc0refChr3 81747 60 + 222631 CACCAGCCAGAATAGCAAGGGAACTGGGGGTTCAATCTATCGTTCAGGGCAGGTGTCTGG -s Anc1.Anc1refChr6 113992 60 + 197743 CACCAGCCAGAATAGCAAGGGAACTGGGGGTTCAATCTATCGTTCAGGGCAGGTGTCTGG -s Anc2.Anc2refChr13 88590 60 + 96486 CACCAGCCAGAATAGCAAGGGAGTAGGGGGTTCAATCTATCGTTCAGGGCAGGTGTTTGG -s mr.mrrefChr3 15887 60 + 181027 GACCAGTCAGAATAGCAACGAAACTGGATGCTCAATCTAACGTTCAGGCCAGCGGGCCCG -s simCow_chr6.simCow.chr6 445055 60 + 602619 CACCAGCAAGAATAGCACGGGAGTAGGGACTTCAATCTATCGTTTAGGGCAGGTGGTTCA -s simDog_chr6.simDog.chr6 437137 60 + 593897 CACCAGCCAGAATAGCAAGGGAGTAGGGGGTTTAATGTATCGTTCAGGGCCGAGGTTTGG -s simHuman_chr6.simHuman.chr6 445728 60 + 601863 CACAAGCCAGAGTAGCAAGGGAACTGGGGGTTCTAGCTATGGTTCAGGGCAGGTGCCTGG -s simRat_chr6.simRat.chr6 469619 60 + 647215 GACCAGTCAGAATAGCAAAGAAATTGGCTGCTCAATCTAACGTTCGAGCTACAGGTCCCG - -a -s simMouse_chr6.simMouse.chr6 460386 1 + 636262 C -s Anc0.Anc0refChr3 81807 1 + 222631 T -s Anc1.Anc1refChr6 114052 1 + 197743 T -s Anc2.Anc2refChr13 88650 1 + 96486 T -s mr.mrrefChr3 15947 1 + 181027 T -s simCow_chr6.simCow.chr6 445115 1 + 602619 T -s simDog_chr6.simDog.chr6 437197 1 + 593897 T -s simHuman_chr6.simHuman.chr6 445793 1 + 601863 T -s simRat_chr6.simRat.chr6 469679 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 460387 27 + 636262 TGGAGATCAATAATAAGTCATAGCTAA -s Anc0.Anc0refChr3 81808 23 + 222631 CGGAGATGA----TGAGTTGGAGCCAA -s Anc1.Anc1refChr6 114053 27 + 197743 CGGAGATGAGGAGTGAGTTGGAGCCAA -s Anc2.Anc2refChr13 88651 23 + 96486 CGGATCTGA----CGAGTTGGAGCCAA -s mr.mrrefChr3 15948 27 + 181027 TGGAGATCAGGAGTGAGTCATAGCCAA -s simCow_chr6.simCow.chr6 445116 16 + 602619 CGGA---GA----C----TGGGGCCAA -s simDog_chr6.simDog.chr6 437198 23 + 593897 CGGATCTGA----CGAGTTGGAGCCAA -s simHuman_chr6.simHuman.chr6 445794 27 + 601863 CGGAGATGGGGAGCGAGTTGGAGACAA -s simRat_chr6.simRat.chr6 469682 27 + 647215 GAGAGATCAGGAGTGAGTCATAGCCGA - -a -s simMouse_chr6.simMouse.chr6 460414 28 + 636262 ACTCTGGAGGTGGATTACATAGCACTCT -s Anc0.Anc0refChr3 81840 28 + 222631 GGTATGaggttggattccatatcactct -s Anc1.Anc1refChr6 114089 28 + 197743 GGTATGaggttggattccatatcactct -s Anc2.Anc2refChr13 88683 28 + 96486 GGTATGaggttggattccatatcactct -s mr.mrrefChr3 15984 28 + 181027 AGTCTGGAGGTGGATTACATAGCACTCT -s simCow_chr6.simCow.chr6 445141 28 + 602619 GGTATGaggtcagattccatatcactct -s simDog_chr6.simDog.chr6 437230 28 + 593897 GGTGTGaggttggattccatataactct -s simHuman_chr6.simHuman.chr6 445830 28 + 601863 GGTATGaggctgtattccatatcactgt -s simRat_chr6.simRat.chr6 469718 28 + 647215 AGTCTGGAGATGGATTACATTGCACTTT - -a -s simMouse_chr6.simMouse.chr6 460442 91 + 636262 TCTAGCACAGTTACCTTGGACACACTAGAGCTCAACAGGCTCCAATTGTGTAACCTCTAAGCTGCAAGTGACAGAGGGTTAGCTAGCAATA -s Anc0.Anc0refChr3 81868 89 + 222631 tctagctcagttat-ttggatgcaacgtagctcaaagggttccaggtttatgactttcaggttgtaagtgctggggggttagctagtaat- -s Anc1.Anc1refChr6 114117 89 + 197743 tctagctcagttat-ttggatgcaacgtagctcaaagggTtccaggtttatgactttcaggttgtaagtgctggggggttagctagtaat- -s Anc2.Anc2refChr13 88711 89 + 96486 tctagctcagttat-ttggatgcaacgtagcttgaagagttccaggtttatgactttcaggttgcaagtgctggggggtttgctagtaat- -s mr.mrrefChr3 16012 91 + 181027 TCTAGCACAGTTACCTTGGACACACTATAGCTCAACAGGCTCCAATTGTGTAACCTCTAAGCTGTAAGTGACAGAGGGTTAGCTAGTAATA -s simCow_chr6.simCow.chr6 445169 80 + 602619 tctagctcagctat-tttgatgcaaagtagattgaggagctccaggtttatgacttttaggttgcaagtgcTGGGG---------TCAAT- -s simDog_chr6.simDog.chr6 437258 89 + 593897 tctagcttggttat-tcggatgtaccgtagcttgaagagttccaggtttataactttcagaccgcaagtgctgatgggtttgctagtaat- -s simHuman_chr6.simHuman.chr6 445858 80 + 601863 tctagctcagttat-ttggatccaacgtggctcaa--ggAtc-------atgactctgaggttgttagtgctggggggttagctagtaat- -s simRat_chr6.simRat.chr6 469775 91 + 647215 CCTAGCACAGTTACCTTGGACACACTATAGCTCAACATGCTCCAATTGCTTAACCTCTAAGCTGTAAGTGACAGAGTGTTAGCTAGTAATA - -a -s simMouse_chr6.simMouse.chr6 460533 14 + 636262 TTGATGATGTTAAA -s Anc0.Anc0refChr3 81957 14 + 222631 ttgaggatatTAAA -s Anc1.Anc1refChr6 114206 14 + 197743 ttgaggatatTAAA -s Anc2.Anc2refChr13 88800 14 + 96486 ttgaggatatTAAA -s mr.mrrefChr3 16103 14 + 181027 TTGAGGATGTTAAA -s simCow_chr6.simCow.chr6 445249 9 + 602619 CT-----TATGAAA -s simDog_chr6.simDog.chr6 437348 14 + 593897 ttgaggatatTaga -s simHuman_chr6.simHuman.chr6 445938 14 + 601863 ttgaggatatTAAA -s simRat_chr6.simRat.chr6 469866 14 + 647215 TTGAGGATGTTAAA - -a -s simMouse_chr6.simMouse.chr6 460547 5 + 636262 AGATA -s Anc0.Anc0refChr3 81971 5 + 222631 ATGCa -s Anc1.Anc1refChr6 114220 5 + 197743 ATGCa -s Anc2.Anc2refChr13 88814 5 + 96486 ATGCa -s mr.mrrefChr3 16117 5 + 181027 AGACA -s simCow_chr6.simCow.chr6 445258 5 + 602619 ATGCA -s simDog_chr6.simDog.chr6 437362 5 + 593897 atgct -s simHuman_chr6.simHuman.chr6 445960 5 + 601863 aagca -s simRat_chr6.simRat.chr6 469880 5 + 647215 AGACA - -a -s simMouse_chr6.simMouse.chr6 460552 10 + 636262 GGGGGGGATG -s Anc0.Anc0refChr3 81976 10 + 222631 gggagtaatg -s Anc1.Anc1refChr6 114225 10 + 197743 gggagtaatg -s Anc2.Anc2refChr13 88826 10 + 96486 gggagtaatg -s mr.mrrefChr3 16122 10 + 181027 GGGGGGGAtg -s simCow_chr6.simCow.chr6 445270 10 + 602619 GGGAGTAATG -s simDog_chr6.simDog.chr6 437374 10 + 593897 gggagtaaca -s simHuman_chr6.simHuman.chr6 445965 10 + 601863 ggaagcaatg -s simRat_chr6.simRat.chr6 469885 8 + 647215 GGGGGGGG-- - -a -s simMouse_chr6.simMouse.chr6 460562 36 + 636262 GCTGTGGCAATACAAATATATGTGGAGTGGAGTATG -s Anc0.Anc0refChr3 81986 33 + 222631 tcagtgaca---caatcatatgtggaatgaaacatg -s Anc1.Anc1refChr6 114235 33 + 197743 tcagtgaca---caatcatatgtggaatgaaacatg -s Anc2.Anc2refChr13 88836 33 + 96486 tcagtgaca---cagtcatatgtggaatgaaacatg -s mr.mrrefChr3 16132 36 + 181027 gctGTGACAATACAAATATATGTGGAATGGAGTATG -s simCow_chr6.simCow.chr6 445281 27 + 602619 TCAGTCAC---------ATATATGGAAGGAGATATG -s simDog_chr6.simDog.chr6 437384 33 + 593897 tcagagaca---cagtcataagtggaatgaaacatg -s simHuman_chr6.simHuman.chr6 445975 33 + 601863 tcagtgaca---caacaatatgtggaataaaacacg -s simRat_chr6.simRat.chr6 469893 33 + 647215 ---GGGACAATACAAGCATATGCGGAATGGAGTATG - -a -s simMouse_chr6.simMouse.chr6 460598 22 + 636262 AGAGACAAAACGGAGTGGGAAT -s Anc0.Anc0refChr3 82020 22 + 222631 aaaggcacaacaaggagggaat -s Anc1.Anc1refChr6 114269 22 + 197743 aaaggcacaacaaggagggaat -s Anc2.Anc2refChr13 88870 22 + 96486 aagggcacaacaaggagggaat -s mr.mrrefChr3 16168 22 + 181027 AGAGgcaaaacggagtgggaat -s simCow_chr6.simCow.chr6 445309 17 + 602619 AAGGGCACGACAAGGAG----- -s simDog_chr6.simDog.chr6 437418 22 + 593897 gagagcacaactaggagggaat -s simHuman_chr6.simHuman.chr6 446009 22 + 601863 aaaggcacaacaaggagggaat -s simRat_chr6.simRat.chr6 469956 22 + 647215 AGAGgcaaaatggagggggaat - -a -s simMouse_chr6.simMouse.chr6 460620 14 + 636262 GTTTGCAACACAAC -s Anc0.Anc0refChr3 82045 7 + 222631 gttagca------- -s Anc1.Anc1refChr6 114294 14 + 197743 gttagcaacacaat -s Anc2.Anc2refChr13 88895 7 + 96486 gttagca------- -s mr.mrrefChr3 16190 14 + 181027 gttagcaacacaac -s simDog_chr6.simDog.chr6 437443 7 + 593897 gttagcA------- -s simHuman_chr6.simHuman.chr6 446034 14 + 601863 gttagcgacacaat -s simRat_chr6.simRat.chr6 469978 14 + 647215 gttagcaacacaac - -a -s simMouse_chr6.simMouse.chr6 460634 79 + 636262 CATTCATCAGGGAGTAATGTACTGACCCTCTACGGTACACGATCAGGACGTCCTACCCTTCGAGAATTAATTAATATGA -s Anc1.Anc1refChr6 114309 31 + 197743 cattgaagagtaagtaatgtCCTGAAATTAT------------------------------------------------ -s mr.mrrefChr3 16205 79 + 181027 cattcatgagggagtaatgtACTGACCCTATACGGTACACGATCAGGACGTCCTACCCTTCGAGAATAAATTAATATGA -s simHuman_chr6.simHuman.chr6 446049 31 + 601863 cattgaagagtaagtaatgtCCTGAAATTAT------------------------------------------------ -s simRat_chr6.simRat.chr6 469993 79 + 647215 cactcatgagggagtaacatACTGACCCTATACGGTACACGATCAGGACGTCCTACCCTTCGAGAATATATTAATATGA - -a -s simMouse_chr6.simMouse.chr6 460713 1 + 636262 A -s Anc0.Anc0refChr8 6195 1 + 17196 A -s Anc1.Anc1refChr8 2854 1 + 57822 A -s Anc2.Anc2refChr8 6419 1 + 12804 A -s mr.mrrefChr3 16532 1 + 181027 A -s simCow_chr6.simCow.chr6 285734 1 + 602619 G -s simDog_chr6.simDog.chr6 267155 1 + 593897 A -s simHuman_chr6.simHuman.chr6 232748 1 + 601863 A - -a -s simMouse_chr6.simMouse.chr6 460714 4 + 636262 GAGA -s Anc0.Anc0refChr8 6200 4 + 17196 GAGG -s Anc1.Anc1refChr8 2859 4 + 57822 GAGG -s Anc2.Anc2refChr8 6424 4 + 12804 GAGG -s mr.mrrefChr3 16533 4 + 181027 GAGA -s simCow_chr6.simCow.chr6 285739 4 + 602619 GAGG -s simDog_chr6.simDog.chr6 267160 4 + 593897 GAGG -s simHuman_chr6.simHuman.chr6 232753 4 + 601863 AAGG - -a -s simMouse_chr6.simMouse.chr6 460718 16 + 636262 TTCTGGTCTTTGAATG -s Anc0.Anc0refChr8 6204 13 + 17196 TTTCACTCTTT---TT -s Anc1.Anc1refChr8 2863 13 + 57822 TTTCACTCTTT---TT -s Anc2.Anc2refChr8 6430 13 + 12804 TTTCACTCTCT---TT -s mr.mrrefChr3 16537 13 + 181027 TTCTGGTCTTT---TG -s simCow_chr6.simCow.chr6 285745 13 + 602619 CTTCCATCTCT---TT -s simDog_chr6.simDog.chr6 267166 13 + 593897 TTTCACTCTCT---TT -s simHuman_chr6.simHuman.chr6 232757 13 + 601863 TGTCAACATTT---AC - -a -s simMouse_chr6.simMouse.chr6 460734 7 + 636262 ATTGACC -s Anc0.Anc0refChr8 6217 7 + 17196 CTACAGC -s Anc1.Anc1refChr8 2876 7 + 57822 CTACAGC -s Anc2.Anc2refChr8 6443 7 + 12804 CTACAGC -s mr.mrrefChr3 16550 7 + 181027 ATTGACC -s simCow_chr6.simCow.chr6 285758 7 + 602619 CTACAAC -s simDog_chr6.simDog.chr6 267180 7 + 593897 CTACAGC -s simHuman_chr6.simHuman.chr6 232770 7 + 601863 CTATAGT - -a -s simMouse_chr6.simMouse.chr6 460741 58 + 636262 CACACTTCTGTTCATCAGAGTTTTTACCGAGTATGGATGATGGTCCCGGGAACAACAC -s Anc0.Anc0refChr3 82052 46 + 222631 ---------gtccgtcagggtTTATTCCG--TATAT-TCATGGCCCCCGCAACGACAT -s Anc1.Anc1refChr6 114340 55 + 197743 CAAAACTCCGTCCGTCAGGGTTTATTCCG--TATAT-TCATGGCCCCCGCAACGACAT -s Anc2.Anc2refChr13 88902 46 + 96486 ---------gcccgtcagtgtTTATTCCG--TATAT-TCATGGCCCCCACAACAACAT -s mr.mrrefChr3 16557 56 + 181027 CACACTTCTGTTCATCAGGGTTTTTACCG--TATGGATGATGGTCCCGGCAACGACAC -s simCow_chr6.simCow.chr6 445326 29 + 602619 ---------------------TTTTCCCA--CGTAT-TCAAAACCCTCACAAC----- -s simDog_chr6.simDog.chr6 437450 46 + 593897 ---------GCCCGTCAGTGTTTATTCCG--TATAT-TCATGGCCCCCACGACAACAT -s simHuman_chr6.simHuman.chr6 446317 47 + 601863 CAAAACTCCGTCCGCCAAGGTTTCTTCCG-----------GGGCCACCGCAACGACAT -s simRat_chr6.simRat.chr6 470337 48 + 647215 --------TGTTCATTAGGGTTTTTACCG--TATGGATGATGGTCCCGACAACGACAC - -a -s simMouse_chr6.simMouse.chr6 460799 32 + 636262 GTCACACACGGATAGACGGATAGGTCAAAAAG -s Anc0.Anc0refChr3 82105 24 + 222631 GAAGCTCACGGATAA--------GTAAAATAG -s Anc1.Anc1refChr6 114402 24 + 197743 GAAGCTCACGGATAA--------GTAAAATAG -s Anc2.Anc2refChr13 88955 24 + 96486 CAAGCTCACGGATAA--------GTAAAATAG -s mr.mrrefChr3 16613 24 + 181027 GTCACACACGGATAG--------GTCAAAAAG -s simCow_chr6.simCow.chr6 445359 24 + 602619 TAAACTCACGGATAA--------CTAACATGG -s simDog_chr6.simDog.chr6 437504 24 + 593897 CAAGCACACGGATAA--------GTAAAAAAG -s simHuman_chr6.simHuman.chr6 446371 24 + 601863 GAAGCTCACGAACAA--------GGAAAATAG -s simRat_chr6.simRat.chr6 470385 24 + 647215 GTCACACACGGATTG--------GTCAAGAAG - -a -s simMouse_chr6.simMouse.chr6 460831 31 + 636262 GGGTCAGTCATTTGTACTGGTAGAATCTATT -s Anc0.Anc0refChr3 82143 31 + 222631 AGGTCTTTTATAGCTGCTGCTAGAATCTATT -s Anc1.Anc1refChr6 114440 31 + 197743 AGGTCTTTTATAGCTGCTGCTAGAATCTATT -s Anc2.Anc2refChr13 88993 31 + 96486 AGGTCTTTTGTAGCTGCTGCTAGAATCTTTT -s mr.mrrefChr3 16637 31 + 181027 GGGTCAGTCATTTCTACTGGTAGAATCTATT -s simCow_chr6.simCow.chr6 445397 31 + 602619 AGGTCTATCGCAGCTACTGCCAGAGTCTTCC -s simDog_chr6.simDog.chr6 437542 31 + 593897 AGGTCTTTTGTAGCTGCTGCTAGAATCTTTT -s simHuman_chr6.simHuman.chr6 446409 31 + 601863 AGGTCTTTTATAGCTGCTGCTAGAATCTATT -s simRat_chr6.simRat.chr6 470409 30 + 647215 GGGTCAGTCATTTCTACTGGTAGAATCCAG- - -a -s simMouse_chr6.simMouse.chr6 460862 5 + 636262 GACAT -s Anc0.Anc0refChr3 82175 5 + 222631 GACCT -s Anc1.Anc1refChr6 114472 5 + 197743 GACCT -s Anc2.Anc2refChr13 89025 5 + 96486 GACTT -s mr.mrrefChr3 16668 5 + 181027 GACCT -s simCow_chr6.simCow.chr6 445429 5 + 602619 GACTT -s simDog_chr6.simDog.chr6 437574 5 + 593897 GACTT -s simHuman_chr6.simHuman.chr6 446441 5 + 601863 GACCT -s simRat_chr6.simRat.chr6 470439 5 + 647215 GACCT - -a -s simMouse_chr6.simMouse.chr6 460867 50 + 636262 ATTGTCAGCGTGCATACGAATGCAAAGTCATTCCCTCCATGTTATATGCC -s Anc0.Anc0refChr3 82180 49 + 222631 ATCGTAAGCGTGCAAGCGCATGCAGCCGC-TTCCATCCACGTCATATGCC -s Anc1.Anc1refChr6 114477 49 + 197743 ATCGTAAGCGTGCAAGCGCATGCAGCCGC-TTCCATCCACGTCATATGCC -s Anc2.Anc2refChr13 89036 49 + 96486 ATCGTAAGCGTGCAAGCGCATGCAGCCGC-TTCTATCCACGTCATATGCC -s mr.mrrefChr3 16673 50 + 181027 ATTGTCAGCGTGCATACGAATGCAAACTCATTCCCTCCATGTTATATGCC -s simCow_chr6.simCow.chr6 445440 49 + 602619 ATCAGAACCGAGCAAGCGCATGCAGCCGC-TTATATCCACGTCATACGCC -s simDog_chr6.simDog.chr6 437585 48 + 593897 ATCGTAAGCGTGCAAGCGCATGCAGTC-C-TTCTATCCACGTCACATGGC -s simHuman_chr6.simHuman.chr6 446446 49 + 601863 ATCGTAAGCGCGCAAGCGCATACAGCCGC-TTCCATCCACGTCATATGCC -s simRat_chr6.simRat.chr6 470444 50 + 647215 ATAGTGAGCGTGCCTACGAATGCAAACTTACTCCCTCCATGTTATATGCT - -a -s simMouse_chr6.simMouse.chr6 460917 35 + 636262 TTTTAACCCACCCGAAACGAAGAGTAGCCGGATCA -s Anc0.Anc0refChr3 82231 35 + 222631 CTTGAACCCCCTTGAAGCGGAGAAGATTTGGATCA -s Anc1.Anc1refChr6 114528 35 + 197743 CTTGAACCCCCTTGAAGCGGAGAAGATTTGGATCA -s Anc2.Anc2refChr13 89087 35 + 96486 CTTGAGCCCCCTTGAAGCGGCGAAGATTTGGATCA -s mr.mrrefChr3 16723 35 + 181027 CTTTAACCCACCCGAAACGAAGAGTAGCCGGATCA -s simCow_chr6.simCow.chr6 445491 35 + 602619 CTTTAGCTTCCTTGAAGCGCGGAAGATTTGCATCA -s simDog_chr6.simDog.chr6 437634 35 + 593897 CTCGAGTCCCCTTGTAGCGGCGAAGGTTTGGATCA -s simHuman_chr6.simHuman.chr6 446497 35 + 601863 CCTGAACCCTCTTGAAGCGGAGAAGACAGGGATCA -s simRat_chr6.simRat.chr6 470494 35 + 647215 CTATAACCCACCCGAAAGGAAGAGTATCCGGATCA - -a -s simMouse_chr6.simMouse.chr6 460952 59 + 636262 GAAGAACTTGATGGCAGCAGGCCCAATAGATTGCTGTCTAGCCGGGCTAGACTTAGAGG -s Anc0.Anc0refChr3 82266 55 + 222631 GAAGACCGTGATGGCTGCAGACCCGATAAATTACTA--TGG-CGGGCC-GACTTAGAGG -s Anc1.Anc1refChr6 114563 57 + 197743 GAAGACCGTGATGGCTGCAGACCCGATAAATTACTATCTGG-CGGGCC-GACTTAGAGG -s Anc2.Anc2refChr13 89122 55 + 96486 GAAGACCGTGATCGCTGTAGATCCGATAAATTACTA--TGG-CGGGAC-GACTTAGAGG -s mr.mrrefChr3 16758 59 + 181027 GAAGAACTTGATGGCAGCAGGCCCAATAGATTGCTGTCTAGCCGGGCCAGACTTAGAGG -s simCow_chr6.simCow.chr6 445526 55 + 602619 GAAGACCGTGTTCGCTGTAGATCCGATAGATTACTA--TGG-CGAGGC-GACTTAGAGG -s simDog_chr6.simDog.chr6 437670 46 + 593897 AAAGACCGTGATCGA---------GATAAACCACTA--TAG-CGGGAC-GACTTAGAGG -s simHuman_chr6.simHuman.chr6 446532 57 + 601863 GAAGACCGTGATGGCTGCATACCCGATAATTTACTATCTGG-CGGGCC-GTCTTTGAGG -s simRat_chr6.simRat.chr6 470529 59 + 647215 GAAGAATTAGATGGCAGCAGGCCCAATACATTGCAGTCTAGCCGGGCCAGACTTAGAGG - -a -s simMouse_chr6.simMouse.chr6 461011 4 + 636262 TGTG -s Anc0.Anc0refChr3 82321 4 + 222631 TGTT -s Anc1.Anc1refChr6 114620 4 + 197743 TGTT -s Anc2.Anc2refChr13 89177 4 + 96486 TGTT -s mr.mrrefChr3 16817 4 + 181027 TGTG -s simCow_chr6.simCow.chr6 445581 4 + 602619 TAGT -s simDog_chr6.simDog.chr6 437719 4 + 593897 CGTT -s simHuman_chr6.simHuman.chr6 446589 4 + 601863 TGTT -s simRat_chr6.simRat.chr6 470588 4 + 647215 TGTG - -a -s simMouse_chr6.simMouse.chr6 461015 39 + 636262 GACACTGAATAGAGAATTGTAGGTGTTTTGGTAAATCGT -s Anc0.Anc0refChr3 82326 39 + 222631 GACGCTAAATAGAGAATTATAGGTATATTGGTAAATCGT -s Anc1.Anc1refChr6 114625 39 + 197743 GACGCTAAATAGAGAATTATAGGTATATTGGTAAATCGT -s Anc2.Anc2refChr13 89182 39 + 96486 GACGCTAAATAGAGAATTGTAGGTATATTGTTAAATTGT -s mr.mrrefChr3 16821 39 + 181027 GACACTGAATAGAGAATTATAGGTATTTTGGTAAATCGT -s simCow_chr6.simCow.chr6 445586 33 + 602619 GACACT-----GAGAATTGTAGGTAT-TTTTTTAATGGT -s simDog_chr6.simDog.chr6 437724 37 + 593897 GACGCTAAATAGAGAATTGT--TTGTATTGTCAGGTTCT -s simHuman_chr6.simHuman.chr6 446594 39 + 601863 GACGATAAATTGAGAATTATAGGTATATTGGTAAATCGT -s simRat_chr6.simRat.chr6 470592 39 + 647215 GACATTGAATAGCAATTTATATGTATTTTGGTAAATCGT - -a -s simMouse_chr6.simMouse.chr6 461054 75 + 636262 CGACCAGGCACAGGAAGTCGTAGAACCGCGCCACGGGAGGGGCGGCGGCCAGGGACATTCCGTGACAAGTGGGAT -s Anc0.Anc0refChr3 82371 69 + 222631 CGACCATGCTCAGTATGTCGCAGAATCGCGCCGCGAGCGCGGAGGGAAACAAAACGGTTCCGGGACA------AT -s Anc1.Anc1refChr6 114670 69 + 197743 CGACCATGCTCAGTATGTCGCAGAATCGCGCCGCGAGCGCGGAGGGAAACAAAACGGTTCCGGGACA------AT -s Anc2.Anc2refChr13 89227 69 + 96486 CGACCATGCTCTGTATGTCGCAGAATCGCGCCGCGAGCGCGGAGGGAAACAAAACGGTTCCGGGACA------AC -s mr.mrrefChr3 16860 75 + 181027 CGACCATGCACAGGAAGTCGTAGAACCGCGCCGCGGGAGCGGCGGCGGCCAGAACCATTCCGTGACAAGTGGGAT -s simCow_chr6.simCow.chr6 445625 52 + 602619 CTACC-----------------GAATCACGCCGTGAGCGCGGAGGGAAACAAGACGGTTTCGGGACA------AC -s simDog_chr6.simDog.chr6 437767 69 + 593897 CGACCATGCTCTGTATGTCGCAGAATCGAGCAGCGAACACGGAGGGAAGCAAAACGGTTCCGGGGCA------AC -s simHuman_chr6.simHuman.chr6 446639 69 + 601863 CAACCATACTCAGTATGTCGCAGAATCGCCCCGCGAGCGCGGAGGGAAACAAAACGGTTCCGGGACA------AT -s simRat_chr6.simRat.chr6 470631 75 + 647215 CGACCATGCACAGGAAGTCGTAGAACCACGCCGCGGGAGCGGCGGCGGCCAGAACCATTCCGTGACAAGTGGGAT - -a -s simMouse_chr6.simMouse.chr6 461129 21 + 636262 TTCAGCTACCTAGTAACTCGT -s Anc0.Anc0refChr3 82441 21 + 222631 TTCAGCAGGCCTGTTTCTCGT -s Anc1.Anc1refChr6 114740 21 + 197743 TTCAGCAGGCCTGTTTCTCGT -s Anc2.Anc2refChr13 89297 21 + 96486 TTCAGCAGGCCTGTTTCTCGT -s mr.mrrefChr3 16936 21 + 181027 TTCAGCAACCTAGTATCTCGT -s simCow_chr6.simCow.chr6 445678 21 + 602619 TTCAGCAGGCCTGTCTCTCGT -s simDog_chr6.simDog.chr6 437837 21 + 593897 TTCAGCAGGCCTGATTCTCGT -s simHuman_chr6.simHuman.chr6 446709 21 + 601863 TTCAGCAGGCCTGTTTCTCGT -s simRat_chr6.simRat.chr6 470707 21 + 647215 TTCAACAACCTCGTATCTCGT - -a -s simMouse_chr6.simMouse.chr6 461150 25 + 636262 TTCCACTAGCATACACACCTGACAG -s Anc0.Anc0refChr3 82462 25 + 222631 TGCAACTTGCACACACTCCTGACAA -s Anc1.Anc1refChr6 114761 25 + 197743 TGCAACTTGCACACACTCCTGACAA -s Anc2.Anc2refChr13 89318 25 + 96486 TGCAGCTTGCACACACTCCTGACAA -s mr.mrrefChr3 16957 25 + 181027 TGCCACTAGCACACACACCTGACAG -s simCow_chr6.simCow.chr6 445699 25 + 602619 TGCTGCTTGCACACACTCCTGACAA -s simDog_chr6.simDog.chr6 437858 25 + 593897 TGCAGCTTGCACATACTCCTGACAC -s simHuman_chr6.simHuman.chr6 446736 25 + 601863 TGCAACTTGCACACACTCCTGATAA -s simRat_chr6.simRat.chr6 470728 25 + 647215 TGCCACTAGCACACAGACCTGTCGG - -a -s simMouse_chr6.simMouse.chr6 461175 1 + 636262 T -s Anc0.Anc0refChr3 82491 1 + 222631 T -s Anc1.Anc1refChr6 114790 1 + 197743 T -s Anc2.Anc2refChr13 89347 1 + 96486 C -s mr.mrrefChr3 16986 1 + 181027 T -s simCow_chr6.simCow.chr6 445728 1 + 602619 T -s simDog_chr6.simDog.chr6 437887 1 + 593897 C -s simHuman_chr6.simHuman.chr6 446765 1 + 601863 T -s simRat_chr6.simRat.chr6 470757 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 461176 7 + 636262 TACTCGC -s Anc0.Anc0refChr3 82492 6 + 222631 TAC-CGC -s Anc1.Anc1refChr6 114791 6 + 197743 TAC-CGC -s Anc2.Anc2refChr13 89348 6 + 96486 TAC-TTT -s mr.mrrefChr3 16987 7 + 181027 TACTCGC -s simCow_chr6.simCow.chr6 445729 6 + 602619 GAC-TTT -s simDog_chr6.simDog.chr6 437888 3 + 593897 TAC---- -s simHuman_chr6.simHuman.chr6 446767 6 + 601863 TAC-CGC -s simRat_chr6.simRat.chr6 470758 7 + 647215 TACTTGC - -a -s simMouse_chr6.simMouse.chr6 461183 50 + 636262 AGCCCTTTAAGATTAAATGAAGTTGTTGAACTTTCAACAACAGCCATGCA -s Anc0.Anc0refChr3 82499 50 + 222631 ATCTCCTTGAGATAACCTGAAGTTGTTGAACTTTTAGTAACAACCATTCA -s Anc1.Anc1refChr6 114798 50 + 197743 ATCTCCTTGAGATAACCTGAAGTTGTTGAACTTTTAGTAACAACCATTCA -s Anc2.Anc2refChr13 89355 50 + 96486 ATCTCCTTGAAATAACCTGGAGTTGTTGGACTTTTAGTGACAATCCTTCA -s mr.mrrefChr3 16994 50 + 181027 AGCCCTTTAAGATTAAATGAAGTTGTTGAACTTTTAACAACAACCATGCA -s simCow_chr6.simCow.chr6 445736 50 + 602619 AGCTCCTTGAAATAACCTGGTGCTGTTAGACTTTTAGTGACAATACTCCA -s simDog_chr6.simDog.chr6 437891 48 + 593897 ATCTCCTTGAAATAAACCGGAGTTGTTGGACTTTTAG--GCACTCCTTTG -s simHuman_chr6.simHuman.chr6 446774 49 + 601863 ACCTCCTTGAGATAACCTGACGTTGTTCAA-TTGTAGTAACAACCATTCA -s simRat_chr6.simRat.chr6 470765 50 + 647215 AGCCCTTTAAGACTAAATGAAGTTGTTAGACTTTTAACAACAACCATCTA - -a -s simMouse_chr6.simMouse.chr6 461233 17 + 636262 GGTATGCTGCAAGCAGG -s Anc0.Anc0refChr3 82564 14 + 222631 GG---GGTGCGAGTAGG -s Anc1.Anc1refChr6 114863 17 + 197743 GGCCCGGTGCGAGTAGG -s Anc2.Anc2refChr13 89420 14 + 96486 GA---GGTGTGTGTAGT -s mr.mrrefChr3 17044 17 + 181027 GGTATGCTGCAAGCAGG -s simCow_chr6.simCow.chr6 445800 3 + 602619 GA--------------T -s simDog_chr6.simDog.chr6 155131 12 - 593897 -----GGTGTGTGTAGT -s simHuman_chr6.simHuman.chr6 446845 17 + 601863 GGCCCGGTGCGAGTAGG -s simRat_chr6.simRat.chr6 470815 17 + 647215 GGTATATTATAGGCAGG - -a -s simMouse_chr6.simMouse.chr6 461250 4 + 636262 CACA -s Anc0.Anc0refChr3 82578 1 + 222631 C--- -s Anc1.Anc1refChr6 114880 4 + 197743 CTCA -s Anc2.Anc2refChr13 89434 1 + 96486 T--- -s mr.mrrefChr3 17061 4 + 181027 CACA -s simCow_chr6.simCow.chr6 445803 1 + 602619 G--- -s simDog_chr6.simDog.chr6 155143 1 - 593897 T--- -s simHuman_chr6.simHuman.chr6 446868 4 + 601863 CTCA -s simRat_chr6.simRat.chr6 470832 4 + 647215 CACA - -a -s simMouse_chr6.simMouse.chr6 461254 46 + 636262 GGAAGGGTTTACAGTGAGTTGGACAGTGGAGGCAGTGAACTAGGAG -s Anc0.Anc0refChr3 82579 45 + 222631 -GAAGGGTTTACAGTGAGTTTTACAATGGGGGCTGTTAACTTGAAG -s Anc1.Anc1refChr6 114884 46 + 197743 GGAAGGGTTTACAGTGAGTTTTACAATGGGGGCTGTTAACTTGAAG -s Anc2.Anc2refChr13 89435 45 + 96486 -GAAGGGTTTATAGTGAGTTTTACAATGGGGCCTGTTAACTTGAAG -s mr.mrrefChr3 17065 46 + 181027 GGAAGGGTTTACAGTGAGTTGTACAATGGAGGCAGTGAACTAGGAG -s simCow_chr6.simCow.chr6 445804 45 + 602619 -GAAGGGTTTGTTGTGAGTCTTACAATGGAGCCTGCTAAGTTGAGG -s simDog_chr6.simDog.chr6 155144 45 - 593897 -GAAGGGTTTATAGAGAGTTTTACGATGGGGCCTGTTAGCTTGAAA -s simHuman_chr6.simHuman.chr6 446872 46 + 601863 GCAAGGGTTTACAGTGAGTTTTACAATGGGGGTGGTTAACTTGAAG -s simRat_chr6.simRat.chr6 470847 46 + 647215 GGACGAGTTTAGAGTGAGTTGTACAACGGAGGCAGTGAACTAGGAG - -a -s simMouse_chr6.simMouse.chr6 461300 2 + 636262 GC -s Anc0.Anc0refChr3 82624 2 + 222631 GG -s Anc1.Anc1refChr6 114930 2 + 197743 GG -s Anc2.Anc2refChr13 89480 2 + 96486 GG -s mr.mrrefChr3 17111 2 + 181027 GC -s simCow_chr6.simCow.chr6 445890 2 + 602619 AG -s simDog_chr6.simDog.chr6 155189 2 - 593897 GG -s simHuman_chr6.simHuman.chr6 446918 2 + 601863 GT -s simRat_chr6.simRat.chr6 470893 2 + 647215 GC - -a -s simMouse_chr6.simMouse.chr6 461302 4 + 636262 TCAT -s Anc0.Anc0refChr3 82627 4 + 222631 ACAA -s Anc1.Anc1refChr6 114933 4 + 197743 ACAA -s Anc2.Anc2refChr13 89483 4 + 96486 ACTA -s mr.mrrefChr3 17114 4 + 181027 TCAA -s simCow_chr6.simCow.chr6 445893 4 + 602619 ACCA -s simDog_chr6.simDog.chr6 155192 4 - 593897 ACTA -s simHuman_chr6.simHuman.chr6 446921 4 + 601863 CCAA -s simRat_chr6.simRat.chr6 470896 4 + 647215 TTAA - -a -s simMouse_chr6.simMouse.chr6 461306 12 + 636262 GGTTTTGACACA -s Anc0.Anc0refChr3 82679 12 + 222631 GTGAATGTCAAT -s Anc1.Anc1refChr6 114985 12 + 197743 GTGAATGTCAAT -s Anc2.Anc2refChr13 89568 12 + 96486 CTGAATTTCAAT -s mr.mrrefChr3 17118 12 + 181027 GGTTTTGACACA -s simCow_chr6.simCow.chr6 445976 12 + 602619 CTGAATTTCCAC -s simDog_chr6.simDog.chr6 155277 12 - 593897 CTGGATTTCAAT -s simHuman_chr6.simHuman.chr6 446973 12 + 601863 GTGAATGTCAAT -s simRat_chr6.simRat.chr6 470900 12 + 647215 GGTTTTGCCAGG - -a -s simMouse_chr6.simMouse.chr6 461318 11 + 636262 ACCTTTGATTA -s Anc0.Anc0refChr3 82691 7 + 222631 GGTATTG---- -s Anc1.Anc1refChr6 114997 7 + 197743 AGCATTG---- -s Anc2.Anc2refChr13 89580 7 + 96486 GGTTTTG---- -s Anc2.Anc2refChr13 89775 7 + 96486 GGTCTTG---- -s mr.mrrefChr3 17130 11 + 181027 ACCATTGATTA -s simCow_chr6.simCow.chr6 446198 7 + 602619 GTCCTTG---- -s simCow_chr6.simCow.chr6 445988 7 + 602619 GGTTTTG---- -s simDog_chr6.simDog.chr6 155492 7 - 593897 GGTCTTG---- -s simDog_chr6.simDog.chr6 155289 7 - 593897 GGTTTTG---- -s simHuman_chr6.simHuman.chr6 446985 7 + 601863 AGCATTG---- -s simRat_chr6.simRat.chr6 470912 11 + 647215 AACAATGATTG - -a -s simMouse_chr6.simMouse.chr6 461329 1 + 636262 T -s Anc0.Anc0refChr3 82704 1 + 222631 T -s Anc1.Anc1refChr6 115004 1 + 197743 T -s Anc2.Anc2refChr13 89593 1 + 96486 T -s Anc2.Anc2refChr13 89788 1 + 96486 T -s mr.mrrefChr3 17141 1 + 181027 T -s simCow_chr6.simCow.chr6 446211 1 + 602619 T -s simCow_chr6.simCow.chr6 446001 1 + 602619 T -s simDog_chr6.simDog.chr6 155505 1 - 593897 T -s simDog_chr6.simDog.chr6 155302 1 - 593897 T -s simRat_chr6.simRat.chr6 470923 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 461330 14 + 636262 AATGCAACCCTAAT -s Anc0.Anc0refChr3 82715 14 + 222631 AATGCCTCCCTAAT -s Anc1.Anc1refChr6 115015 14 + 197743 AATGCCTCCCTAAT -s Anc2.Anc2refChr13 89604 14 + 96486 AATGCCTCCCTAAT -s Anc2.Anc2refChr13 89799 14 + 96486 AATGCCTCCCTAAC -s mr.mrrefChr3 17142 14 + 181027 AATGCAACCCTAAT -s simCow_chr6.simCow.chr6 446222 14 + 602619 AATGCCTGTTTAAT -s simCow_chr6.simCow.chr6 446012 14 + 602619 AATGCCTCCCTAAT -s simDog_chr6.simDog.chr6 155516 14 - 593897 AATGCCTCCCTAAC -s simDog_chr6.simDog.chr6 155313 14 - 593897 ATTGTCTGCATAAT -s simHuman_chr6.simHuman.chr6 447002 14 + 601863 AATGCCTCTCTAAT -s simRat_chr6.simRat.chr6 470924 14 + 647215 AATGCTACCCTAAT - -a -s simMouse_chr6.simMouse.chr6 461344 27 + 636262 ATGGTAATCTCAGCGCCAATTGTTTGG -s Anc0.Anc0refChr3 82731 27 + 222631 ATGGTAATCTCAGCTCTCATTGTTTGG -s Anc1.Anc1refChr6 115031 27 + 197743 ATGGTAATCTCAGCTCTCATTGTTTGG -s Anc2.Anc2refChr13 89620 27 + 96486 ATGGTAATCTCAGCCCTCATTGTTTGG -s Anc2.Anc2refChr13 89815 27 + 96486 ATAGCCATTGCAGATCTCATTGTTTGG -s mr.mrrefChr3 17156 27 + 181027 ATGGTAATCTCAGCGCCAATTGTTTGG -s simCow_chr6.simCow.chr6 446238 27 + 602619 GTAGTAGCCTCAGATCTTATTGTTCAG -s simCow_chr6.simCow.chr6 446028 27 + 602619 ATGGTAATCTCAGCCCTCCAAGTTTGG -s simDog_chr6.simDog.chr6 155532 27 - 593897 ATAGCCATTGCAGATCTCATTGTTTGG -s simDog_chr6.simDog.chr6 155329 27 - 593897 ATAGTACTCTCAGCCCTAATTGTATGG -s simHuman_chr6.simHuman.chr6 447018 27 + 601863 ATGGTAATGTCAGCTCTCATTGTTTGG -s simRat_chr6.simRat.chr6 470938 27 + 647215 ATGGTAGATTCAGCACGAATTGTTTGG - -a -s simMouse_chr6.simMouse.chr6 461371 1 + 636262 A -s Anc0.Anc0refChr3 82758 1 + 222631 T -s Anc1.Anc1refChr6 115058 1 + 197743 T -s Anc2.Anc2refChr13 89647 1 + 96486 A -s mr.mrrefChr3 17183 1 + 181027 T -s simCow_chr6.simCow.chr6 446055 1 + 602619 G -s simDog_chr6.simDog.chr6 155356 1 - 593897 A -s simHuman_chr6.simHuman.chr6 447045 1 + 601863 T -s simRat_chr6.simRat.chr6 470965 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 461372 1 + 636262 A -s Anc0.Anc0refChr3 82759 1 + 222631 A -s Anc1.Anc1refChr6 115059 1 + 197743 A -s Anc2.Anc2refChr13 89648 1 + 96486 A -s Anc2.Anc2refChr13 89842 1 + 96486 A -s mr.mrrefChr3 17184 1 + 181027 A -s simCow_chr6.simCow.chr6 446265 1 + 602619 A -s simCow_chr6.simCow.chr6 446056 1 + 602619 A -s simDog_chr6.simDog.chr6 155559 1 - 593897 A -s simDog_chr6.simDog.chr6 155357 1 - 593897 A -s simHuman_chr6.simHuman.chr6 447046 1 + 601863 A -s simRat_chr6.simRat.chr6 470966 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 461373 12 + 636262 CCATCAAGCCCA -s Anc0.Anc0refChr3 82760 12 + 222631 CCTTCAGACCCA -s Anc1.Anc1refChr6 115060 12 + 197743 CCTTCAGACCCA -s Anc2.Anc2refChr13 89649 12 + 96486 CCTTCAGACCCA -s Anc2.Anc2refChr13 89843 12 + 96486 CCTTCAGAACCA -s mr.mrrefChr3 17185 12 + 181027 CCATCAGACCCA -s simCow_chr6.simCow.chr6 446266 12 + 602619 CCCTCACATCCA -s simCow_chr6.simCow.chr6 446057 12 + 602619 CCTTCAGACCCA -s simDog_chr6.simDog.chr6 155564 12 - 593897 CCTTCAGAACCA -s simDog_chr6.simDog.chr6 155358 12 - 593897 CTTTCAGAGCCA -s simHuman_chr6.simHuman.chr6 447047 12 + 601863 CCTTCAGACCCA -s simRat_chr6.simRat.chr6 470967 12 + 647215 CCATCAGACTCA - -a -s simMouse_chr6.simMouse.chr6 461385 1 + 636262 G -s Anc0.Anc0refChr3 82772 1 + 222631 G -s Anc1.Anc1refChr6 115072 1 + 197743 G -s Anc2.Anc2refChr13 89661 1 + 96486 G -s mr.mrrefChr3 17197 1 + 181027 G -s simCow_chr6.simCow.chr6 446069 1 + 602619 A -s simDog_chr6.simDog.chr6 155370 1 - 593897 G -s simHuman_chr6.simHuman.chr6 447059 1 + 601863 G -s simRat_chr6.simRat.chr6 470979 1 + 647215 G - -a -s simMouse_chr6.simMouse.chr6 461386 10 + 636262 AACATCCAGA -s Anc0.Anc0refChr3 82773 10 + 222631 AGCATTCAGA -s Anc1.Anc1refChr6 115073 10 + 197743 AACATTCAGA -s Anc2.Anc2refChr13 89662 10 + 96486 AGCATTCAGA -s Anc2.Anc2refChr13 89855 10 + 96486 AGCACTCAGA -s mr.mrrefChr3 17198 10 + 181027 AACATTCAGA -s simCow_chr6.simCow.chr6 446278 10 + 602619 AGGATTCAGA -s simCow_chr6.simCow.chr6 446070 10 + 602619 AGCATTTACA -s simDog_chr6.simDog.chr6 155577 10 - 593897 AGCACTCAGA -s simDog_chr6.simDog.chr6 155371 10 - 593897 AGCTTTCAGA -s simHuman_chr6.simHuman.chr6 447060 10 + 601863 AACATTCAGA -s simRat_chr6.simRat.chr6 470980 10 + 647215 AACATTCAGC - -a -s simMouse_chr6.simMouse.chr6 461396 13 + 636262 CCAAGGGAATGCT -s Anc0.Anc0refChr3 82783 9 + 222631 CCAAGGGA----A -s Anc1.Anc1refChr6 115083 13 + 197743 CCAAGGGAACATA -s Anc2.Anc2refChr13 89672 9 + 96486 CCAAGGGA----A -s Anc2.Anc2refChr13 89865 9 + 96486 CCAAAGAA----C -s mr.mrrefChr3 17208 13 + 181027 CCAAGGGAATGCA -s simCow_chr6.simCow.chr6 446290 9 + 602619 CCAAAGAT----C -s simCow_chr6.simCow.chr6 446080 9 + 602619 CCAAGTGA----T -s simDog_chr6.simDog.chr6 155587 9 - 593897 CCAAAGAA----G -s simDog_chr6.simDog.chr6 155381 9 - 593897 CCAAGGGA----A -s simHuman_chr6.simHuman.chr6 447070 13 + 601863 CCACAGGAACATA -s simRat_chr6.simRat.chr6 470990 13 + 647215 CCAAGGAAATGCA - -a -s simMouse_chr6.simMouse.chr6 461409 20 + 636262 GGAGTAGCTCCAAAACAACT -s Anc0.Anc0refChr3 82792 20 + 222631 GGAACTACTTCTCCACAACT -s Anc1.Anc1refChr6 115096 20 + 197743 GGAACTACTTCTCCACAACT -s Anc2.Anc2refChr13 89681 20 + 96486 GAAACTACTTCTCCACAACC -s Anc2.Anc2refChr13 89874 20 + 96486 ATATTAACTACTCCACAACT -s mr.mrrefChr3 17221 20 + 181027 GGAGCAGCTCCAAAACAACT -s simCow_chr6.simCow.chr6 446299 20 + 602619 ATAATAACTACTCCATAATT -s simCow_chr6.simCow.chr6 446089 20 + 602619 GAGACCACTCTGCAACTAAC -s simDog_chr6.simDog.chr6 155596 20 - 593897 ATATTAACTACTCCCCAACT -s simDog_chr6.simDog.chr6 155394 20 - 593897 GAAACTACTTCTCCACAACC -s simHuman_chr6.simHuman.chr6 447083 17 + 601863 GGAACTA---CTCCACAACT -s simRat_chr6.simRat.chr6 471003 20 + 647215 GGAGCAGCTCCAAAAAAGCT - -a -s simMouse_chr6.simMouse.chr6 461429 13 + 636262 AACACAAGGGGAG -s Anc0.Anc0refChr3 82812 13 + 222631 AACACAAAGGGAG -s Anc1.Anc1refChr6 115116 13 + 197743 AACACAAAGGGAG -s Anc2.Anc2refChr13 89894 13 + 96486 AACACAAAGGGAG -s mr.mrrefChr3 17241 13 + 181027 AACACAAAGGGAG -s simCow_chr6.simCow.chr6 446319 13 + 602619 AATACAAACGGAG -s simDog_chr6.simDog.chr6 155616 13 - 593897 AACACATAGAGAG -s simHuman_chr6.simHuman.chr6 447100 13 + 601863 TACACAAAAGGAG -s simRat_chr6.simRat.chr6 471023 13 + 647215 AACACAAAGGGAG - -a -s simMouse_chr6.simMouse.chr6 461442 5 + 636262 CCTTA -s Anc0.Anc0refChr3 82825 5 + 222631 CTTTA -s Anc1.Anc1refChr6 115129 5 + 197743 CTTTA -s Anc2.Anc2refChr13 89907 5 + 96486 CTTTA -s mr.mrrefChr3 17254 5 + 181027 CCTTA -s simCow_chr6.simCow.chr6 446332 5 + 602619 CCTAA -s simDog_chr6.simDog.chr6 155629 5 - 593897 CTTTA -s simHuman_chr6.simHuman.chr6 447123 5 + 601863 CATTT -s simRat_chr6.simRat.chr6 471036 5 + 647215 CCTTA - -a -s simMouse_chr6.simMouse.chr6 461447 1 + 636262 A -s Anc0.Anc0refChr3 82830 1 + 222631 A -s Anc1.Anc1refChr6 115134 1 + 197743 A -s Anc2.Anc2refChr13 89701 1 + 96486 G -s Anc2.Anc2refChr13 89912 1 + 96486 A -s mr.mrrefChr3 17259 1 + 181027 A -s simCow_chr6.simCow.chr6 446337 1 + 602619 C -s simCow_chr6.simCow.chr6 446109 1 + 602619 A -s simDog_chr6.simDog.chr6 155634 1 - 593897 A -s simDog_chr6.simDog.chr6 155414 1 - 593897 G -s simHuman_chr6.simHuman.chr6 447128 1 + 601863 G -s simRat_chr6.simRat.chr6 471041 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 461448 12 + 636262 AGATTGTGTCAG -s Anc0.Anc0refChr3 82835 12 + 222631 AGACTGCATAGG -s Anc1.Anc1refChr6 115139 12 + 197743 AGACTGCATAGG -s Anc2.Anc2refChr13 89706 12 + 96486 AGGGTGCATAGG -s Anc2.Anc2refChr13 89917 12 + 96486 AGACTGCACAGG -s mr.mrrefChr3 17260 12 + 181027 AGATTGTGTAGG -s simCow_chr6.simCow.chr6 446342 12 + 602619 AGAATGCACAGG -s simCow_chr6.simCow.chr6 446129 12 + 602619 AGAGTCCATAAG -s simDog_chr6.simDog.chr6 155639 12 - 593897 AGGCTGCACAGG -s simDog_chr6.simDog.chr6 155419 12 - 593897 AGGGTGCATAGG -s simHuman_chr6.simHuman.chr6 447133 12 + 601863 GGAGGTCATAGG -s simRat_chr6.simRat.chr6 471042 12 + 647215 AGATTACATAGG - -a -s simMouse_chr6.simMouse.chr6 461460 2 + 636262 AC -s Anc0.Anc0refChr3 82867 2 + 222631 CC -s Anc1.Anc1refChr6 115171 2 + 197743 CC -s Anc2.Anc2refChr13 89949 2 + 96486 CC -s mr.mrrefChr3 17292 2 + 181027 AC -s simCow_chr6.simCow.chr6 446374 2 + 602619 CC -s simDog_chr6.simDog.chr6 155671 2 - 593897 CT -s simHuman_chr6.simHuman.chr6 447165 2 + 601863 CC -s simRat_chr6.simRat.chr6 471074 2 + 647215 AC - -a -s simMouse_chr6.simMouse.chr6 461462 41 + 636262 CAAGCTAAAGTTGGCTCAGATCTTTTGCATAGCCATTTGCT -s Anc0.Anc0refChr3 82869 39 + 222631 CTAGCTTAGGTTGGGTGAGATCTTTAGCACTGCC--TTGCT -s Anc1.Anc1refChr6 115173 41 + 197743 CTAGCTTAGGTTGGTTGAGATCTTTAGCACTGCCATTTGCT -s Anc2.Anc2refChr13 89736 39 + 96486 CTAGGTTTGGTTGGGTGAGATCTTTAACATTGCA--TTAAT -s Anc2.Anc2refChr13 89951 39 + 96486 CTAGCTTAGGTTGGGTGAGATCTTTAGCACTGCC--TTGCT -s mr.mrrefChr3 17294 41 + 181027 CAAGCTAAAGTTGGTTCAGATCTTTTGCATAGCCATTTGCT -s simCow_chr6.simCow.chr6 446376 39 + 602619 CTAACTTAGGTTGGATGAGATCTATGGCACTGCC--TTGCT -s simCow_chr6.simCow.chr6 446159 39 + 602619 CTAGCCTAGGTTGAGTGAAATCTTTAGCACAGCC--TTAAT -s simDog_chr6.simDog.chr6 155673 39 - 593897 CTAGCTTAGATTGGGTGAGACCTTTAGCACTGCC--TTGTT -s simDog_chr6.simDog.chr6 155453 39 - 593897 CTAGGTTTGGTTGGGTGAGATCTTTAACATTGCA--TTAAT -s simHuman_chr6.simHuman.chr6 447167 41 + 601863 CTGGCTTAGGTTGGTTGAGATATTTAGTACTGCCATTTGCT -s simRat_chr6.simRat.chr6 471076 41 + 647215 CAAGCTAAAGTTGGTTCGGATCTTTTGCATAGCCATTTACT - -a -s simMouse_chr6.simMouse.chr6 461503 22 + 636262 ACAAAAGACCAAACCACAGAGT -s Anc0.Anc0refChr3 82908 22 + 222631 ACAAAAAACCAATCCCCAGAGG -s Anc1.Anc1refChr6 115214 22 + 197743 ACAAAAAACCAATCCCCAGAGG -s Anc2.Anc2refChr13 89990 22 + 96486 ACAAAAAACCAGTCCCCATAGG -s mr.mrrefChr3 17335 22 + 181027 ACAAAAGACCAAACCACAGAGT -s simCow_chr6.simCow.chr6 446415 22 + 602619 ACAAAAAACCAGTCCCCATAGG -s simDog_chr6.simDog.chr6 155712 22 - 593897 ACAAAAAACTGGTCCCCATAGG -s simHuman_chr6.simHuman.chr6 447208 22 + 601863 GCAAAAAACCAATCGCCAGAGC -s simRat_chr6.simRat.chr6 471117 22 + 647215 ACAAAAGACCAAATCACAGAGT - -a -s simMouse_chr6.simMouse.chr6 461525 21 + 636262 TCTTAGACCTTTCCATATTCT -s Anc0.Anc0refChr3 82949 21 + 222631 TCTCATACCATTTCATGATTT -s Anc1.Anc1refChr6 115255 21 + 197743 TCTCATACCATTTCATGATTT -s Anc2.Anc2refChr13 90032 21 + 96486 TCTCCTACCACTTTATGATTT -s mr.mrrefChr3 17357 21 + 181027 TCTCAGACCTTTTCATAATTT -s simCow_chr6.simCow.chr6 446453 21 + 602619 TCTTGTACCACCTTATGATTC -s simDog_chr6.simDog.chr6 155754 17 - 593897 TCCCCTACCACT----AACTT -s simHuman_chr6.simHuman.chr6 447249 21 + 601863 TCTCATAGCATTTCATGATTT -s simRat_chr6.simRat.chr6 471139 21 + 647215 GCTCAGAACTTTTCAAAATTT - -a -s simMouse_chr6.simMouse.chr6 461546 128 + 636262 CAGTATGGTTTGAGGGCAGCACCTACTTATGAGAGAATGAATGTCGTGTTAGTGATCTCTAAGCTTCACATTTGTGGCCCTGGCCCTGTTTTCTTCATCCGTCTGCCATGCAAAACTCCCAATGACTA -s Anc0.Anc0refChr3 82970 125 + 222631 CAGTATGGGTTGAGGGTAAAGCCTTATGATGAGAGTTTGAATGTCATTTTAGCAATCTCTATGCTTCCCATGTGTGGCTCTGGCTGTTTT---CTCCTCCATCTACCATGAAAGACCCCCCATGACTA -s Anc1.Anc1refChr6 115276 125 + 197743 CAGTATGGGTTGAGGGTAAAGCCTTATGATGAGAGTTTGAATGTCATTTTAGCAATCTCTATGCTTCCCATGTGTGGCTCTGGCTGTTTT---CTCCTCCATCTACCATGAAAGACCCCCCATGACTA -s Anc2.Anc2refChr13 90053 125 + 96486 CAATATGGGTTGAGGTTAAAGCCTTATGATGAGAGTTTTAATGGTATTTTAGCAATCTCTATGCTTCCCATGTGTGGCTCTGGCTGTTGT---TTCCTCCATCTACCATGAAAGACCCTCCATGACCC -s mr.mrrefChr3 17378 128 + 181027 CAGTATGGTTTGAGGGCAGCACCTACTTATGAGAGTTTGAATGTCATGTTAGCAATCTCTAAGCTTCACATGTGTGGCTCTGGCCCTTTTTTCCTCATCCATCTACCATGCAAAACTCCCAATGACTA -s simCow_chr6.simCow.chr6 446496 124 + 602619 CAATATGGGTTGAGGTCAGGGCATTATGATGAGCGCTTTAAGGCTATTTTATTAATTTCTATGTTCCACATGTGAAGCTCTTACTGTTGC---TCCCTGCATCTACCATGAGACACCCTCCATGACC- -s simDog_chr6.simDog.chr6 155771 124 - 593897 CAATATTAGTTGAGGTTGAAGCCTTATGATGAGAGTTTTAATGGTATTTTAGCAATCTCTATGCTTCCCATATGTGGCCCAGGCTGTTGT---TTCCTCCACCTACCA-GAAAGACCCTCCATGACCC -s simHuman_chr6.simHuman.chr6 447270 125 + 601863 CGGTATGGGTTGAGGGAAAAGCCTTGTGATGAGAGTTTGAATATCATTTTAGCAATCTCTGTGCATTGCATGTGTGGCTGTGGCTGTTTT---CTTGTACATCTACCATGAAAGACCCCGTATGACTA -s simRat_chr6.simRat.chr6 471160 128 + 647215 CAGGATGGTTTGTGGGCAGCACCTAATTATGGGAGTTTGAATGTCATGTTAGCAATCTCTAGGCTTCACATGTGTGGCTCTGGCCATTTTTTCCTCATCCATCTACCACGCAAAACTCCCCATGACTA - -a -s simMouse_chr6.simMouse.chr6 461674 48 + 636262 AGGTCAGAAGATCTATGTGGACTTGTTAGATTGGCACAGTTTGTATAA -s Anc0.Anc0refChr3 83102 42 + 222631 AGGTTAGAAGATCTATGTAGGGACATTAGACTGGCAAGG------CAA -s Anc1.Anc1refChr6 115408 42 + 197743 AGGTTAGAAGATCTATGTAGGGACATTAGACTGGCAAGG------CAA -s Anc2.Anc2refChr13 90185 42 + 96486 AAGTTAGAAGATCTATGTAGGGACATTAGCCTGGTAAGG------CAA -s mr.mrrefChr3 17506 48 + 181027 AGGTCAGAAGATCTATGTGGACTCGTTAGATTGGCACGGTTTGTATAA -s simCow_chr6.simCow.chr6 446620 42 + 602619 AAGTTAGAAGACATATGCAGGGACATTGGTCTGCTAGGG------CAA -s simDog_chr6.simDog.chr6 155905 41 - 593897 AAGTTAAAAGATCTA-GTAGCGACATTAACCTGGTAAGG------TGA -s simHuman_chr6.simHuman.chr6 447402 42 + 601863 AGGTTAGAAGGTCTACGTTGGGACATTAGACTGGCAAGG------CAA -s simRat_chr6.simRat.chr6 471288 45 + 647215 AGGTGAGAAGATCTATTAGG---CTTTAGATTGGCACGGTTTGTATAT - -a -s simMouse_chr6.simMouse.chr6 461722 1 + 636262 A -s Anc0.Anc0refChr3 83144 1 + 222631 A -s Anc1.Anc1refChr6 115450 1 + 197743 A -s Anc2.Anc2refChr13 90229 1 + 96486 A -s mr.mrrefChr3 17554 1 + 181027 A -s simCow_chr6.simCow.chr6 446664 1 + 602619 A -s simDog_chr6.simDog.chr6 155948 1 - 593897 A -s simHuman_chr6.simHuman.chr6 447444 1 + 601863 A -s simRat_chr6.simRat.chr6 471333 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 461723 5 + 636262 TCCAT -s Anc0.Anc0refChr3 83145 5 + 222631 CCCAT -s Anc1.Anc1refChr6 115451 5 + 197743 CCCAT -s Anc2.Anc2refChr13 90230 5 + 96486 CCCAT -s mr.mrrefChr3 17555 5 + 181027 TCCAT -s simCow_chr6.simCow.chr6 446669 5 + 602619 CCCAT -s simDog_chr6.simDog.chr6 155949 5 - 593897 CTCGT -s simHuman_chr6.simHuman.chr6 447445 5 + 601863 CCCAT -s simRat_chr6.simRat.chr6 471334 5 + 647215 TCCAT - -a -s simMouse_chr6.simMouse.chr6 461728 34 + 636262 GTTTGATGTCGTGATCAGTATATCGTTGGCCTGA -s Anc0.Anc0refChr3 83150 25 + 222631 GTTTGATG---------ATAGAACATTCACCTAA -s Anc1.Anc1refChr6 115456 25 + 197743 GTTTGATG---------ATAGAACATTCACCTAA -s Anc2.Anc2refChr13 90235 25 + 96486 GTTTGAGT---------ATAGAATGTTCACCTAA -s mr.mrrefChr3 17560 34 + 181027 GTTTGATGTCGTGATCAGTATATCATTGGCCTGA -s simCow_chr6.simCow.chr6 446674 24 + 602619 GTTTGAGT---------ATAGAATGCTCAT-TAA -s simDog_chr6.simDog.chr6 438767 25 + 593897 GTTTGAGT---------ACAGAATGTTCACCTAA -s simHuman_chr6.simHuman.chr6 447450 25 + 601863 GTTTGATG---------ATAAAACATTCACCTAA -s simRat_chr6.simRat.chr6 471339 34 + 647215 CTTTGATGTTGTTATCAGTATATCATTGGCCTGG - -a -s simMouse_chr6.simMouse.chr6 461762 108 + 636262 CGATTAGTTGTGGGACATTCTCTTCTCGCAGAAGAAGTAACTCTTCCAGACAGCACTGCTATACAGCACACCCTACACTATCCTCAGGTTAGGTGACTATTCTAGAAT -s Anc0.Anc0refChr3 83248 35 + 222631 CAACCAGTTG-------------------------------------------------------------------------TCAGGCCTAATGATAGACTGATAAC -s Anc1.Anc1refChr6 115554 35 + 197743 CAACCAGTTG-------------------------------------------------------------------------TCAGGCCTAATGATAGACTGATAAC -s Anc2.Anc2refChr13 90339 35 + 96486 CAACCAGTTG-------------------------------------------------------------------------TTAGGCCTAATGATAGACTGATAGC -s mr.mrrefChr3 17594 105 + 181027 CAACTAGTTGTGAGGTATTCTCTTATCGCAGAAG---TAACTCTTCCAGACAGCATTGCTATACAGCACACCCTACACTATCCTCAGGTTAGGTGACTATTTTATAAT -s simCow_chr6.simCow.chr6 446776 34 + 602619 TGACCAGTTG-------------------------------------------------------------------------T-GGGCCTTGTGATATACTGATAGC -s simDog_chr6.simDog.chr6 438869 35 + 593897 CAACCAGTTG-------------------------------------------------------------------------GTAATCATAATGGTAGACTGATAGC -s simHuman_chr6.simHuman.chr6 447553 35 + 601863 CAACCAGTTG-------------------------------------------------------------------------TCAGGCCCAATGATACACTGATAAC -s simRat_chr6.simRat.chr6 471373 105 + 647215 CAACTCGTTGTGAGGTATTCTCTTATCGCAGAAG---TAACTCTTCCAGACAGCATTGCAATACAGCACACTCTACGCTATCCTCAGGTTAGGTGACTATTTTATAAT - -a -s simMouse_chr6.simMouse.chr6 461870 6 + 636262 CATGTT -s Anc0.Anc0refChr3 83296 6 + 222631 CATGTT -s Anc1.Anc1refChr6 115602 6 + 197743 CATGTT -s Anc2.Anc2refChr13 90387 6 + 96486 CACATT -s mr.mrrefChr3 17699 6 + 181027 CATGTT -s simCow_chr6.simCow.chr6 446822 6 + 602619 AACATT -s simDog_chr6.simDog.chr6 438923 6 + 593897 CACATT -s simHuman_chr6.simHuman.chr6 447601 6 + 601863 CATGTT -s simRat_chr6.simRat.chr6 471478 6 + 647215 CATGTT - -a -s simMouse_chr6.simMouse.chr6 461876 4 + 636262 TTGT -s Anc0.Anc0refChr3 83302 4 + 222631 ATGT -s Anc1.Anc1refChr6 115608 4 + 197743 ATGT -s Anc2.Anc2refChr13 90393 4 + 96486 ATGT -s mr.mrrefChr3 17705 4 + 181027 TTGT -s simCow_chr6.simCow.chr6 446830 4 + 602619 ATGT -s simDog_chr6.simDog.chr6 438929 4 + 593897 ATGT -s simHuman_chr6.simHuman.chr6 447607 4 + 601863 CTAT -s simRat_chr6.simRat.chr6 471484 4 + 647215 TTGT - -a -s simMouse_chr6.simMouse.chr6 461880 52 + 636262 CTTTTTGTTTTGACTGGTACACTCTTGACTCGTTTGGAATTGGTTCAGTTGC -s Anc0.Anc0refChr3 83307 51 + 222631 TTTTTTG-TGGGATTGTTTAACTCTTGACTATTTTTGAATTGGGTCAattcc -s Anc1.Anc1refChr6 115613 51 + 197743 TTTTTTG-TGGGATTGTTTAACTCTTGACTATTTTTGAATTGGGTCAATTCC -s Anc2.Anc2refChr13 90398 51 + 96486 TTTCGTT-TGGGATTGTTTAACTCTTAACTATTTTTGAATTGGGTAAaaccg -s mr.mrrefChr3 17710 52 + 181027 CTTTTTGTTTTGATTGTTAAACTCTTGACTCGTTTGGAATTGGTTCAGTTGC -s simCow_chr6.simCow.chr6 446835 51 + 602619 TTTCATT-TGGGATTGTTCAACACTTAACTGTTTTCGAATTGGGTaaaattt -s simDog_chr6.simDog.chr6 438934 51 + 593897 TTTCGTT-TGGGATTGTTTAACTCTCAACTATTTTTGGACTGGGCAAAACCG -s simHuman_chr6.simHuman.chr6 447612 49 + 601863 TTTTTTG-TGAGATTGTTTAACTCTTGGATA--TTTGAATTGGGTCAATTCC -s simRat_chr6.simRat.chr6 471489 52 + 647215 CTTTTTGTTTCAATTGTTAAACTCTTGACTGGTTTGGGATTGGTTCAGTTGC - -a -s simMouse_chr6.simMouse.chr6 461932 4 + 636262 ACTT -s Anc0.Anc0refChr3 83360 4 + 222631 gcct -s Anc1.Anc1refChr6 115666 4 + 197743 GCCT -s Anc2.Anc2refChr13 90459 4 + 96486 gcct -s mr.mrrefChr3 17762 4 + 181027 ACTT -s simCow_chr6.simCow.chr6 446896 4 + 602619 tcct -s simDog_chr6.simDog.chr6 438995 4 + 593897 GCCT -s simHuman_chr6.simHuman.chr6 447663 4 + 601863 GCCT -s simRat_chr6.simRat.chr6 471541 4 + 647215 ACTC - -a -s simMouse_chr6.simMouse.chr6 461936 82 + 636262 TTGACCTGTACCAATATCATACATTGCAAAGCACTAATCATCTTCTAAGTTTATGTTATTGAGATTGAAGATCATCTTCCTG -s Anc0.Anc0refChr3 83364 2 + 222631 tt-------------------------------------------------------------------------------- -s Anc1.Anc1refChr6 115670 2 + 197743 TT-------------------------------------------------------------------------------- -s Anc2.Anc2refChr13 90640 2 + 96486 ct-------------------------------------------------------------------------------- -s mr.mrrefChr3 17766 52 + 181027 TTGACCTGTACCAATATCATACATTGCAAAGCACTAATCAT------------------------------TCATCTTCCTG -s simCow_chr6.simCow.chr6 447091 2 + 602619 CA-------------------------------------------------------------------------------- -s simDog_chr6.simDog.chr6 439236 2 + 593897 ct-------------------------------------------------------------------------------- -s simHuman_chr6.simHuman.chr6 447667 2 + 601863 TT-------------------------------------------------------------------------------- -s simRat_chr6.simRat.chr6 471545 52 + 647215 TTGACCTGTACTGACTGCATATATTGCAAAGTGCTAATCAT------------------------------TCATCTTCCTG - -a -s simMouse_chr6.simMouse.chr6 462018 27 + 636262 CCAGCCTTGGATAGATTAGTTCTCCCC -s mr.mrrefChr3 17818 25 + 181027 CCAGCCTTGGA--GATTAGTTCTCCCC -s simRat_chr6.simRat.chr6 471598 25 + 647215 CCAGCCTGGAA--GTTTAGTTCTCCCC - -a -s simMouse_chr6.simMouse.chr6 462045 101 + 636262 TTAATAACTTGAATGGTCCTCACCAGAGGAAGAACTTAAGCTTTTGGCTGCATAATGTTTGAATACTGGTGTTTAGATTTAACTGGTTGCCCGTACACTAG -s mr.mrrefChr3 17843 101 + 181027 TTAATAACTTGAATGGTCCTCACCAGAGGAAGAACTTAAGCTTTTGGCTGCATAATGTTTGAATACTGGTGTTTAGATTTAAGTGGTTGCCTGTACACTAG -s simRat_chr6.simRat.chr6 471643 101 + 647215 TTCATGACTTGAATGATCCTCACCAGAGGAAGAACCTCATCTTCTGGGCCAATATTGTTTGAATACTTGTGTTCAGATTTAAGTGGTTGCCTGGTCACTAG - -a -s simMouse_chr6.simMouse.chr6 462146 57 + 636262 CCAGTACTTGAGGAAAATTATAGAATTGCCTGTAAATAAATGTCAAATCTGTGAAGT -s mr.mrrefChr3 17951 57 + 181027 CCAGCACTTGAGGAAAATTATTGAATTGCCTGTAAATAAATGTCAAATCTGTGAAGT -s simRat_chr6.simRat.chr6 471751 57 + 647215 CTGGCACTTGAGGCAACTTATTGAATTGCCTGTAAATAAATGTCAAATCTGTGAAGT - -a -s simMouse_chr6.simMouse.chr6 462203 231 + 636262 CATCCCAGTAAATGTTCTCAGAACCTGTGCATTACATAGACCTGCATCAACCTGTAAGATGCAGAACATCCTATGTCAAATGTAATTAGTATAATAGGGTGCAATAAGTAGCTTTTCTGGTTATCACTATGAATGTGTAGGCAAGTGTGTAGACCTAACAACCTAACAATTGTACTCGTTGCACATTTCCATACCCTTCAATATCCTTCTGCATGAGTGGAGCTAGCCCCT -s mr.mrrefChr3 18008 231 + 181027 CATTTTAGTAAATATTCTCAGAAGCTGTGCATTACATAGATCAGCATCAACCTGTAAGATGCAGAACATCCTATGTCAAATTTAATTAGTATAATAGGGTGCAATAAGTAGCTTTTCTGGTCATCACTATGAATGTGTAGGCAAGTGTGTAGACCTAAAAACCTAACAATTGTACTCGTTGCACATTTCTATATCCTTCAATATCCTTCTGCATGAGTGGAGCTAGCCCCT -s simRat_chr6.simRat.chr6 471819 231 + 647215 TATTTTAGTAAACAGTCTTAGAAGCTATGCATTACATAGATCAGAATTAACCTGTAAGATACAGAACATTCTATGTTAAACTTAATTAGTATGATAGCGTGCAATAAGTAGGTTTTCGGGCCATCACGATTAGTGTGTAGGCCAGTGCGAAAACCTAAAAACCTGACAATTGTACTCATTGCACATTTCTATATCCCTCAATACCTGGATTCATGAGTTGAGCTAGTCCCT - -a -s simMouse_chr6.simMouse.chr6 462434 70 + 636262 CATTGTCCACCTTCATTAACTTCAGATATGGTTGGTCGTAATAGTGCTTACTCTCTTATCCATTAAAACA -s mr.mrrefChr3 18239 70 + 181027 CATTGTCCACCTTCATTAACTTCAGATATGGTTGGTCGTAATAGTGCTTACTCTCTTATCCATTAAAACA -s simRat_chr6.simRat.chr6 472131 70 + 647215 CCTTAGCCATCTTTATTAACTTCAGATATGGTTAGTTGTAATAGTGCTTACTCTCTTATCTGTTAAAACA - -a -s simMouse_chr6.simMouse.chr6 462504 41 + 636262 ATTTTAGCTAAATTGGTCAAAACATGGCATACACTGCAAGC -s mr.mrrefChr3 18309 41 + 181027 ATTTTAGCTAAATTGGTCAAAACATGGCATACACTGCAAGC -s simRat_chr6.simRat.chr6 472203 41 + 647215 ATTTTAGCTAGATTGGTCAAAACATGGCACACACTGCAAGT - -a -s simMouse_chr6.simMouse.chr6 462545 11 + 636262 AGTGACGCCAC -s Anc0.Anc0refChr3 83366 1 + 222631 ----------c -s Anc1.Anc1refChr6 115672 1 + 197743 ----------C -s Anc2.Anc2refChr13 90642 1 + 96486 ----------c -s mr.mrrefChr3 18350 11 + 181027 AGTGACGCCAC -s simCow_chr6.simCow.chr6 447093 1 + 602619 ----------A -s simDog_chr6.simDog.chr6 439238 1 + 593897 ----------c -s simHuman_chr6.simHuman.chr6 447669 1 + 601863 ----------C -s simRat_chr6.simRat.chr6 472246 11 + 647215 AGTGACACCAC - -a -s simMouse_chr6.simMouse.chr6 462556 3 + 636262 AGA -s Anc0.Anc0refChr3 83367 3 + 222631 AAA -s Anc1.Anc1refChr6 115673 3 + 197743 AAA -s Anc2.Anc2refChr13 4989 3 - 96486 AGA -s mr.mrrefChr3 18361 3 + 181027 AGA -s simCow_chr6.simCow.chr6 154734 3 - 602619 AGG -s simDog_chr6.simDog.chr6 153645 3 - 593897 AGA -s simHuman_chr6.simHuman.chr6 447670 3 + 601863 AAA -s simRat_chr6.simRat.chr6 472257 3 + 647215 AGA - -a -s simMouse_chr6.simMouse.chr6 462559 29 + 636262 TTTTACTACAGTGTAAAACTTGAACTGCA -s Anc0.Anc0refChr3 83370 19 + 222631 TTTTACACTAGAGTAAAAT---------- -s Anc1.Anc1refChr6 115676 19 + 197743 TTTTACACTAGAGTAAAAT---------- -s Anc2.Anc2refChr13 4992 19 - 96486 TTCCACAGTATAGTAAAAT---------- -s mr.mrrefChr3 18364 29 + 181027 TTTTACTACAGTGTAAAACTTGAACTGCA -s simCow_chr6.simCow.chr6 154847 19 - 602619 TTCCACAGTATAGAAGAGT---------- -s simCow_chr6.simCow.chr6 154737 19 - 602619 TTCCACAGTGTTGCAGAAT---------- -s simDog_chr6.simDog.chr6 153648 19 - 593897 TTCCACAGTCTAGTAAAAC---------- -s simHuman_chr6.simHuman.chr6 447673 19 + 601863 TTCTACACTATAGTAAAAT---------- -s simRat_chr6.simRat.chr6 472260 29 + 647215 TTTTACTACAGTGTAGAACTTGAACTGCA - -a -s simMouse_chr6.simMouse.chr6 462588 4 + 636262 GACC -s Anc0.Anc0refChr3 84092 1 + 222631 G--- -s Anc1.Anc1refChr6 116406 4 + 197743 GATC -s Anc2.Anc2refChr13 5838 1 - 96486 A--- -s mr.mrrefChr3 18393 4 + 181027 GACC -s simCow_chr6.simCow.chr6 155520 1 - 602619 A--- -s simDog_chr6.simDog.chr6 154653 1 - 593897 g--- -s simHuman_chr6.simHuman.chr6 448541 4 + 601863 GATC -s simRat_chr6.simRat.chr6 472289 4 + 647215 GAGC - -a -s simMouse_chr6.simMouse.chr6 462592 34 + 636262 CCCAGGGCATCTGAATCATCAGTTAAACTGCTCA -s Anc0.Anc0refChr3 84093 34 + 222631 CACAGGGAAACTGAATAATGTCTGAAACTATTTG -s Anc1.Anc1refChr6 116410 34 + 197743 CACAGGGAAACTGAATAATGTCTGAAACTATTTG -s Anc2.Anc2refChr13 91509 34 + 96486 CAAAGGGAAACTGAATAATGTCTGAAACTATTTG -s mr.mrrefChr3 18397 34 + 181027 CCCAGGGCATCTGAATCATCAGTTAAACTACTCA -s simCow_chr6.simCow.chr6 447897 34 + 602619 CAGAGGGAAACTGAATAATGTCTGGAACTCTCTG -s simDog_chr6.simDog.chr6 440264 28 + 593897 CAAAGGGAAATTGA------TTTGAAACTATTTG -s simHuman_chr6.simHuman.chr6 448545 34 + 601863 CGCTGGGAAACTGAACAGTTCCTGAAATTATTAG -s simRat_chr6.simRat.chr6 472293 34 + 647215 CCCAGGGTATCTGAATTATCAGTAAAACTACTCA - -a -s simMouse_chr6.simMouse.chr6 462626 15 + 636262 CGGATACAACGTACA -s Anc0.Anc0refChr3 84127 15 + 222631 AGCATACAATGCACA -s Anc1.Anc1refChr6 116444 15 + 197743 AGCATACAATGCACA -s Anc2.Anc2refChr13 91543 15 + 96486 AGCAGACAATGTACA -s mr.mrrefChr3 18431 15 + 181027 AGGATACAATGCACA -s simCow_chr6.simCow.chr6 447931 14 + 602619 AGCAAACAA-GTATA -s simDog_chr6.simDog.chr6 440661 15 + 593897 AGTGGACAATGTACA -s simHuman_chr6.simHuman.chr6 448579 15 + 601863 AGCATACAATGCACA -s simRat_chr6.simRat.chr6 472327 15 + 647215 AGGATACAATGCACA - -a -s simMouse_chr6.simMouse.chr6 462641 29 + 636262 CTAATGTGCCCCTTATATGTTATTGACTT -s Anc0.Anc0refChr3 84143 27 + 222631 TTAAAGCATTTTTTATATGTTATTGA--T -s Anc1.Anc1refChr6 116460 29 + 197743 TTAAAGCATTTTTTATATGTTATTGACTT -s Anc2.Anc2refChr13 91559 27 + 96486 TTAAAGCATTTTTTATATGTTATTGA--T -s mr.mrrefChr3 18447 29 + 181027 TTAATGTGCCCCTTATATGTTATTGACTT -s simCow_chr6.simCow.chr6 447946 27 + 602619 TAAAAGCATCCTGTATCTGTTATTGA--C -s simDog_chr6.simDog.chr6 440677 27 + 593897 TTAAAGCATTTTTTATATGTTATTGA--T -s simHuman_chr6.simHuman.chr6 448595 5 + 601863 TT------------------------CTT -s simRat_chr6.simRat.chr6 472343 29 + 647215 TTAATGTGCCCCTAATATGTCATTGACTT - -a -s simMouse_chr6.simMouse.chr6 462670 11 + 636262 CTTTTCATGAG -s Anc0.Anc0refChr3 84170 11 + 222631 TTTCTTACAAG -s Anc1.Anc1refChr6 116489 11 + 197743 TTTCTTACAAG -s Anc2.Anc2refChr13 91586 11 + 96486 TTTCTTACAAG -s mr.mrrefChr3 18476 11 + 181027 CTTTTCATGAG -s simCow_chr6.simCow.chr6 447973 10 + 602619 TTTCTTCCAA- -s simDog_chr6.simDog.chr6 440706 11 + 593897 TTTCTCAAGAG -s simHuman_chr6.simHuman.chr6 448600 11 + 601863 TTTATTACAAG -s simRat_chr6.simRat.chr6 472372 11 + 647215 ATTTTCATGAG - -a -s simMouse_chr6.simMouse.chr6 462681 33 + 636262 TCTGACATGTTATATTTCTACCGTATGTTAAAC -s Anc0.Anc0refChr3 84192 33 + 222631 CCATTCATCTCAGATGTCTCTCCTTTGTACATC -s Anc1.Anc1refChr6 116511 33 + 197743 CCATTCATCTCAGATGTCTCTCCTTTGTACATC -s Anc2.Anc2refChr13 91608 33 + 96486 CCATTCATCTCAGATGTCACTCTGTTGTACATC -s mr.mrrefChr3 18487 33 + 181027 TCTGACATCTTATATGTCTATCCTATGTTAAAC -s simCow_chr6.simCow.chr6 447994 33 + 602619 CCATCCATCGCAGATGTCACTCTGTTATACACC -s simDog_chr6.simDog.chr6 440728 33 + 593897 CCATTCATCTCAAATTGCACTCTGTTGTACATC -s simHuman_chr6.simHuman.chr6 448622 33 + 601863 CCACTCATCTCAGATGTCTCTCCTTTGTACATC -s simRat_chr6.simRat.chr6 472383 33 + 647215 TCAGACATCTTATGTGTCAATCCTATGTTACAC - -a -s simMouse_chr6.simMouse.chr6 462714 13 + 636262 ACAATGTCTAGCA -s Anc0.Anc0refChr3 84230 13 + 222631 ACAATGTCTAGCA -s Anc1.Anc1refChr6 116549 13 + 197743 ACAATGTCTAGCA -s Anc2.Anc2refChr13 91646 13 + 96486 ATAATGTCCAGAA -s mr.mrrefChr3 18520 13 + 181027 ACAATGTCTAGCA -s simCow_chr6.simCow.chr6 448032 13 + 602619 AAAATGTTCAGAA -s simDog_chr6.simDog.chr6 440766 13 + 593897 ATAATGCCCAGAA -s simHuman_chr6.simHuman.chr6 448660 13 + 601863 ACAATGTCTAGCG -s simRat_chr6.simRat.chr6 472416 2 + 647215 TA----------- - -a -s simMouse_chr6.simMouse.chr6 462727 33 + 636262 AGTATGGACCTTCCAGGTTGATTCCTCCTCAGT -s Anc0.Anc0refChr3 84243 33 + 222631 AGTCAGGATCATCCAGGTTGTTTCATCCTTGGT -s Anc1.Anc1refChr6 116562 33 + 197743 AGTCAGGATCATCCAGGTTGTTTCATCCTTGGT -s Anc2.Anc2refChr13 91659 33 + 96486 AGTCAGGATCATCTAGCTTGTTTCATCCTTGGT -s mr.mrrefChr3 18533 33 + 181027 AGTATGGACCTTCCAGGTTGATTCCTCCTCAGT -s simCow_chr6.simCow.chr6 448046 33 + 602619 AGTCAGGATTGTCTAGCTTATTTTATCCTTAGT -s simDog_chr6.simDog.chr6 440779 32 + 593897 AGTCAGGACCATCT-GCTTGCTTCATCCTTGGT -s simHuman_chr6.simHuman.chr6 448673 33 + 601863 AGTCAGGATCATCCAGGTTGTTGCATCCTTGGT - -a -s simMouse_chr6.simMouse.chr6 462760 21 + 636262 CCTTATCAGAAAGACTGGTGA -s Anc0.Anc0refChr3 84277 21 + 222631 CCTCATAAAAAAGACAGGTGA -s Anc1.Anc1refChr6 116596 21 + 197743 CCTCATAAAAAAGACAGGTGA -s Anc2.Anc2refChr13 91693 21 + 96486 CCTCATAAAAAAGACAGGTGA -s mr.mrrefChr3 18566 21 + 181027 CCTCATCAGAAAGACTGGTGA -s simCow_chr6.simCow.chr6 448080 21 + 602619 CCCCATAAAAAAGACGCATGA -s simDog_chr6.simDog.chr6 440812 20 + 593897 CCTTGTAGAAAAGA-AGGTGA -s simHuman_chr6.simHuman.chr6 448707 21 + 601863 CCTCATAAAAAAGACAGGTGA -s simRat_chr6.simRat.chr6 472418 21 + 647215 CCTCATCAGAACGACTGATGA - -a -s simMouse_chr6.simMouse.chr6 462781 28 + 636262 AAAACCCACTTTTAACATCACTGTGCTC -s Anc0.Anc0refChr3 84298 20 + 222631 GAATTCTGTTTTTA--------GTGTTC -s Anc1.Anc1refChr6 116617 20 + 197743 GAATTCTGTTTTTA--------GTGTTC -s Anc2.Anc2refChr13 91715 20 + 96486 GAATTCTGTTTTTA--------CTGTTC -s mr.mrrefChr3 18587 28 + 181027 AAAATCCACTTTTAACATCACTGTGCTC -s simCow_chr6.simCow.chr6 448102 20 + 602619 AGATTTTGTTTTTA--------CCAGTC -s simDog_chr6.simDog.chr6 440833 20 + 593897 GAATTCTGCTTTTA--------CTGTCC -s simHuman_chr6.simHuman.chr6 448728 20 + 601863 GAATTCTGTTTTTA--------GTGTTC -s simRat_chr6.simRat.chr6 472439 28 + 647215 AAAATCCACTTTTAACATCATTGTGCTT - -a -s simMouse_chr6.simMouse.chr6 462809 35 + 636262 AAGGGCGGGCTGTGGATATACCCTTAGGGCCTGGG -s Anc0.Anc0refChr3 84318 16 + 222631 AA-------------------CCCTCAGGCCTGTG -s Anc1.Anc1refChr6 116637 16 + 197743 AA-------------------CCCTCAGGCCTGTG -s Anc2.Anc2refChr13 91735 16 + 96486 CA-------------------CCCTCAGACCTGTG -s mr.mrrefChr3 18615 35 + 181027 AAGGGCGGGCTGTGGATATACCCTTAGGGCCTGGG -s simCow_chr6.simCow.chr6 448122 16 + 602619 CA-------------------CCCTCAGACCTGTG -s simDog_chr6.simDog.chr6 440853 16 + 593897 CA-------------------CCTCCAGACCTGTG -s simHuman_chr6.simHuman.chr6 448748 16 + 601863 AA-------------------TCCTCAGGCCTGTG -s simRat_chr6.simRat.chr6 472484 35 + 647215 AAGTGTGGGCTACCAATCTACCTTTAGGGCCAGGG - -a -s simMouse_chr6.simMouse.chr6 462844 20 + 636262 AGACCATGGTCACTGTACGT -s Anc0.Anc0refChr3 84334 20 + 222631 AGACCATGGTTACTGTATGT -s Anc1.Anc1refChr6 116653 20 + 197743 AGACCATGGTTACTGTATGT -s Anc2.Anc2refChr13 91751 20 + 96486 AGACCATGCTTGTTGTATAT -s mr.mrrefChr3 18650 20 + 181027 AGACCATGGTCACTGTATGT -s simCow_chr6.simCow.chr6 448138 20 + 602619 AGACAATGCTTGTTGTATAT -s simDog_chr6.simDog.chr6 440871 5 + 593897 GGACC--------------- -s simHuman_chr6.simHuman.chr6 448764 20 + 601863 AGACCCTGGTTACTGTATGT -s simRat_chr6.simRat.chr6 472519 20 + 647215 AGACCATGGTCACTGTATAT - -a -s simMouse_chr6.simMouse.chr6 462864 14 + 636262 TGAAACTGCTGAAT -s Anc0.Anc0refChr3 84354 11 + 222631 T--AACTGT-GAAT -s Anc1.Anc1refChr6 116673 14 + 197743 TGGAACTGTGGAAT -s Anc2.Anc2refChr13 91771 11 + 96486 T--AATTGT-GAGT -s mr.mrrefChr3 18670 14 + 181027 TGAAACTGTTGAAT -s mr.mrrefChr3 18882 14 + 181027 AGCAACTGGGGAAT -s simCow_chr6.simCow.chr6 448158 11 + 602619 T--AATTGT-GAGT -s simHuman_chr6.simHuman.chr6 448784 13 + 601863 TAGGAGTGT-GAAT -s simMouse_chr6.simMouse.chr6 463095 14 + 636262 AGCAACTGGGGAAT -s simRat_chr6.simRat.chr6 472790 14 + 647215 AGCAGTTGAGGTAT -s simRat_chr6.simRat.chr6 472539 14 + 647215 TGAAACTGTTGAAT - -a -s simMouse_chr6.simMouse.chr6 462878 5 + 636262 AAAGA -s Anc0.Anc0refChr3 84365 5 + 222631 CTAGA -s Anc1.Anc1refChr6 116687 5 + 197743 CTAGA -s Anc2.Anc2refChr13 91782 5 + 96486 CTAGA -s mr.mrrefChr3 18684 5 + 181027 AAAGA -s mr.mrrefChr3 18905 5 + 181027 AAAGA -s simCow_chr6.simCow.chr6 448169 5 + 602619 CTAGA -s simHuman_chr6.simHuman.chr6 448797 5 + 601863 CTAGA -s simMouse_chr6.simMouse.chr6 463118 5 + 636262 AAAGA -s simRat_chr6.simRat.chr6 472813 5 + 647215 TAAGA -s simRat_chr6.simRat.chr6 472553 5 + 647215 AAAGA - -a -s simMouse_chr6.simMouse.chr6 462883 52 + 636262 AACAATGGTCCCTGAATGCCACCCAGGTAGTGGAACACTAAATGCGATAGGT -s mr.mrrefChr3 18689 52 + 181027 AACAATGGTCCCTGAATGCCACCCAGGTAGTGGAACACTAAATGCGATAGGT -s simRat_chr6.simRat.chr6 472558 52 + 647215 AACAATGGTCCCTAAATGCCACCCAGCTAGTGGGACACTAAATGTGCTAGGT - -a -s simMouse_chr6.simMouse.chr6 462935 17 + 636262 ACTTTATTGAGCTTGAG -s mr.mrrefChr3 18741 17 + 181027 ACTTTATTGAGTCTGAA -s simRat_chr6.simRat.chr6 472650 17 + 647215 ACTGTATTGAGTCTGAA - -a -s simMouse_chr6.simMouse.chr6 462952 12 + 636262 TTGTAGATAGGG -s Anc0.Anc0refChr3 84370 12 + 222631 TTGTAGATACTG -s Anc1.Anc1refChr6 116692 12 + 197743 TTGTAGATACTG -s Anc2.Anc2refChr13 91787 12 + 96486 TTATAGATACTG -s mr.mrrefChr3 18758 12 + 181027 TTGTAGATAGGG -s mr.mrrefChr3 18910 12 + 181027 CTCTAGATTGTG -s simCow_chr6.simCow.chr6 448174 12 + 602619 TTTTAGATACTG -s simDog_chr6.simDog.chr6 440876 11 + 593897 -TATAGATACTG -s simHuman_chr6.simHuman.chr6 448802 12 + 601863 TTGTAGATACTG -s simMouse_chr6.simMouse.chr6 463123 12 + 636262 CTCTAGATTGTG -s simRat_chr6.simRat.chr6 472818 12 + 647215 CTCTAGCTTATG -s simRat_chr6.simRat.chr6 472667 12 + 647215 TTGTAGGTAGGG - -a -s simMouse_chr6.simMouse.chr6 462964 1 + 636262 A -s Anc0.Anc0refChr3 84382 1 + 222631 T -s Anc1.Anc1refChr6 116704 1 + 197743 T -s Anc2.Anc2refChr13 91799 1 + 96486 T -s mr.mrrefChr3 18770 1 + 181027 A -s simCow_chr6.simCow.chr6 448186 1 + 602619 T -s simDog_chr6.simDog.chr6 440887 1 + 593897 T -s simHuman_chr6.simHuman.chr6 448814 1 + 601863 T -s simRat_chr6.simRat.chr6 472679 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 462965 11 + 636262 TGTGTAAACCA -s Anc0.Anc0refChr3 84383 11 + 222631 TCTGTAAAGCA -s Anc1.Anc1refChr6 116705 11 + 197743 TCTGTAAAGCA -s Anc2.Anc2refChr13 91800 11 + 96486 TCTGTAAAGCA -s mr.mrrefChr3 18771 11 + 181027 TGTGTAAACCA -s mr.mrrefChr3 18922 11 + 181027 TCCAGAAAGCA -s simCow_chr6.simCow.chr6 448187 11 + 602619 GCTGTAAAGCA -s simDog_chr6.simDog.chr6 440888 11 + 593897 TTTGTAAAGCA -s simHuman_chr6.simHuman.chr6 448815 11 + 601863 ACTGTGAAGCA -s simMouse_chr6.simMouse.chr6 463135 11 + 636262 TCCAGAAAGCA -s simRat_chr6.simRat.chr6 472830 11 + 647215 TCCAGAAAGCA -s simRat_chr6.simRat.chr6 472680 11 + 647215 TTTGTCATCCA - -a -s simMouse_chr6.simMouse.chr6 462976 10 + 636262 TCATAGAATT -s Anc0.Anc0refChr3 84394 10 + 222631 TCACATAATT -s Anc1.Anc1refChr6 116716 10 + 197743 TCACATAATT -s Anc2.Anc2refChr13 91811 10 + 96486 CCACATAATT -s mr.mrrefChr3 18782 10 + 181027 TCATAGAATT -s mr.mrrefChr3 18933 10 + 181027 TTACAAAATC -s simCow_chr6.simCow.chr6 448199 10 + 602619 CCATTTAATT -s simDog_chr6.simDog.chr6 440899 10 + 593897 CCACATAATT -s simHuman_chr6.simHuman.chr6 448826 10 + 601863 TCACATAACT -s simMouse_chr6.simMouse.chr6 463146 10 + 636262 TTACAAAATC -s simRat_chr6.simRat.chr6 472841 10 + 647215 TTACAAAAAG -s simRat_chr6.simRat.chr6 472691 6 + 647215 ----AGGATT - -a -s simMouse_chr6.simMouse.chr6 462986 1 + 636262 T -s Anc0.Anc0refChr3 84404 1 + 222631 T -s Anc1.Anc1refChr6 116726 1 + 197743 T -s Anc2.Anc2refChr13 91821 1 + 96486 T -s mr.mrrefChr3 18792 1 + 181027 T -s simCow_chr6.simCow.chr6 448209 1 + 602619 T -s simDog_chr6.simDog.chr6 440909 1 + 593897 T -s simHuman_chr6.simHuman.chr6 448836 1 + 601863 T -s simRat_chr6.simRat.chr6 472697 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 462987 7 + 636262 AATAGTA -s Anc0.Anc0refChr3 84405 5 + 222631 AATAG-- -s Anc1.Anc1refChr6 116727 5 + 197743 AATAG-- -s Anc2.Anc2refChr13 91822 5 + 96486 AATAG-- -s mr.mrrefChr3 18793 7 + 181027 AATAGTA -s simCow_chr6.simCow.chr6 448211 5 + 602619 AATAG-- -s simDog_chr6.simDog.chr6 440910 5 + 593897 AATAG-- -s simHuman_chr6.simHuman.chr6 448837 5 + 601863 AATAG-- -s simRat_chr6.simRat.chr6 472698 7 + 647215 AGTGGTA - -a -s simMouse_chr6.simMouse.chr6 462994 2 + 636262 CA -s Anc0.Anc0refChr3 84410 1 + 222631 -A -s Anc1.Anc1refChr6 116732 2 + 197743 CA -s Anc2.Anc2refChr13 91827 1 + 96486 -A -s mr.mrrefChr3 18800 2 + 181027 CA -s mr.mrrefChr3 18943 2 + 181027 AA -s simCow_chr6.simCow.chr6 448220 1 + 602619 -A -s simDog_chr6.simDog.chr6 440982 1 + 593897 -A -s simHuman_chr6.simHuman.chr6 448842 1 + 601863 -A -s simMouse_chr6.simMouse.chr6 463156 2 + 636262 AA -s simRat_chr6.simRat.chr6 472851 2 + 647215 AG -s simRat_chr6.simRat.chr6 472705 2 + 647215 CA - -a -s simMouse_chr6.simMouse.chr6 462996 12 + 636262 TGTGGTGAATCC -s Anc0.Anc0refChr3 84411 12 + 222631 TGTGATGATTCC -s Anc1.Anc1refChr6 116734 12 + 197743 TGTGATGATTCC -s Anc2.Anc2refChr13 91828 12 + 96486 TGTGATGATTCC -s mr.mrrefChr3 18802 12 + 181027 TGTGGTGAATCC -s mr.mrrefChr3 18945 12 + 181027 TGTGATGACCCC -s simCow_chr6.simCow.chr6 448221 12 + 602619 GGTGCTGACTCA -s simDog_chr6.simDog.chr6 440983 12 + 593897 TGTCATGATTCC -s simHuman_chr6.simHuman.chr6 448843 12 + 601863 TGTGATGATCCC -s simMouse_chr6.simMouse.chr6 463158 12 + 636262 TGTGATGACACC -s simRat_chr6.simRat.chr6 472853 12 + 647215 TGCGATGACCCC -s simRat_chr6.simRat.chr6 472708 12 + 647215 TATGGTGAATCC - -a -s simMouse_chr6.simMouse.chr6 463008 30 + 636262 TGAAATAGGATGTTTGTTTCTTTTGGGGTC -s Anc0.Anc0refChr3 84429 16 + 222631 AAAAAAAG------TGTTTCTG-------- -s Anc1.Anc1refChr6 116752 16 + 197743 AAAAAAAG------TGTTTCTG-------- -s Anc2.Anc2refChr13 91846 16 + 96486 AAAAAAAG------TGTTTCTG-------- -s mr.mrrefChr3 18814 16 + 181027 TGAAATAG------TGTTTCTT-------- -s mr.mrrefChr3 18963 16 + 181027 AAAAGGTG------CAGCTCTG-------- -s simCow_chr6.simCow.chr6 448239 16 + 602619 AAAAAGAG------TGTTTATT-------- -s simDog_chr6.simDog.chr6 441001 16 + 593897 AATAGATG------TGTTTCTG-------- -s simHuman_chr6.simHuman.chr6 448861 16 + 601863 ATAGAAAG------TATTTCTG-------- -s simMouse_chr6.simMouse.chr6 463176 13 + 636262 AAAAGGTC------C---TCTG-------- -s simRat_chr6.simRat.chr6 472871 16 + 647215 AAAAGGTG------CAGCTCTG-------- -s simRat_chr6.simRat.chr6 472720 16 + 647215 TAAAATAG------TGAATCCT-------- - -a -s simMouse_chr6.simMouse.chr6 463038 1 + 636262 A -s Anc0.Anc0refChr3 84462 1 + 222631 G -s Anc1.Anc1refChr6 116785 1 + 197743 G -s Anc2.Anc2refChr13 91879 1 + 96486 G -s mr.mrrefChr3 18830 1 + 181027 A -s mr.mrrefChr3 18990 1 + 181027 G -s simCow_chr6.simCow.chr6 448268 1 + 602619 G -s simDog_chr6.simDog.chr6 441034 1 + 593897 G -s simHuman_chr6.simHuman.chr6 448894 1 + 601863 G -s simMouse_chr6.simMouse.chr6 463200 1 + 636262 G -s simRat_chr6.simRat.chr6 472898 1 + 647215 G -s simRat_chr6.simRat.chr6 472736 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 463039 8 + 636262 CTAGACTG -s Anc0.Anc0refChr3 84464 8 + 222631 CTAGGCAG -s Anc1.Anc1refChr6 116787 8 + 197743 CTAGGCAG -s Anc2.Anc2refChr13 91881 8 + 96486 CTTGGTAG -s mr.mrrefChr3 18831 8 + 181027 CTAGACTG -s mr.mrrefChr3 18991 8 + 181027 CTAGGCGG -s simCow_chr6.simCow.chr6 448270 8 + 602619 CTGGGGAG -s simDog_chr6.simDog.chr6 441036 8 + 593897 CCTGGTGG -s simHuman_chr6.simHuman.chr6 448896 8 + 601863 CTAGACAG -s simMouse_chr6.simMouse.chr6 463201 8 + 636262 CTAGGCGG -s simRat_chr6.simRat.chr6 472899 8 + 647215 CTAGGCGG -s simRat_chr6.simRat.chr6 472737 8 + 647215 AAAGACTA - -a -s simMouse_chr6.simMouse.chr6 463047 2 + 636262 CC -s mr.mrrefChr3 18839 2 + 181027 CC -s simRat_chr6.simRat.chr6 472745 2 + 647215 CC - -a -s simMouse_chr6.simMouse.chr6 463049 10 + 636262 CAGGCAACAT -s Anc0.Anc0refChr3 84472 5 + 222631 CAT-----AT -s Anc1.Anc1refChr6 116795 5 + 197743 CAT-----AT -s Anc2.Anc2refChr13 91889 5 + 96486 CAT-----AT -s mr.mrrefChr3 18841 5 + 181027 CAG-----AT -s mr.mrrefChr3 18999 5 + 181027 CAG-----GT -s simCow_chr6.simCow.chr6 448278 5 + 602619 CAT-----AT -s simDog_chr6.simDog.chr6 441044 5 + 593897 CCT-----GT -s simHuman_chr6.simHuman.chr6 448904 5 + 601863 CAT-----AT -s simMouse_chr6.simMouse.chr6 463209 1 + 636262 C--------- -s simRat_chr6.simRat.chr6 472907 5 + 647215 CAG-----GT -s simRat_chr6.simRat.chr6 472747 5 + 647215 CAA-----AT - -a -s simMouse_chr6.simMouse.chr6 463059 2 + 636262 AG -s mr.mrrefChr3 18846 2 + 181027 AG -s simRat_chr6.simRat.chr6 472752 2 + 647215 AG - -a -s simMouse_chr6.simMouse.chr6 463061 34 + 636262 GAACTCAACAATAACTGGAGTACCTTAGGTAATG -s Anc0.Anc0refChr3 84477 34 + 222631 GAATTCAACAATGACCTGAGTAACTTATACAATG -s Anc1.Anc1refChr6 116800 34 + 197743 GAATTCAACAATGACCTGAGTAACTTATACAATG -s Anc2.Anc2refChr13 91894 34 + 96486 GAATTCAACAATGACCTGAGTAACTTATACAATG -s mr.mrrefChr3 18848 34 + 181027 GAACTCAACAATAACTGGAGTACCTTAGGTAATG -s mr.mrrefChr3 19004 34 + 181027 GAGTCCAGCAATGACCTGAGTAACTTACACGATG -s simCow_chr6.simCow.chr6 448283 34 + 602619 TGATTCAACTCTGGCCTGAGTAACTTATATAATG -s simDog_chr6.simDog.chr6 441049 34 + 593897 GAACCCAACAATGACCTGAGTAACTTTTACAATG -s simHuman_chr6.simHuman.chr6 448909 34 + 601863 GAATTCAGCAATAACTGGAGTAACTTATACAATG -s simMouse_chr6.simMouse.chr6 463210 34 + 636262 GAGTCCAGCAATGACCTGAGTAACTTACACGATG -s simRat_chr6.simRat.chr6 472912 34 + 647215 GGGTCCAGAAATGGCCTGAGCAACTTACATGATG -s simRat_chr6.simRat.chr6 472754 34 + 647215 GAATTCAAGAATAACTGGAGTAGCCTGCAATATG - -a -s simMouse_chr6.simMouse.chr6 463109 9 + 636262 TTTACTGTA -s mr.mrrefChr3 18896 9 + 181027 TTTACTGTA -s simRat_chr6.simRat.chr6 472804 9 + 647215 TTTACTTCG - -a -s simMouse_chr6.simMouse.chr6 463170 6 + 636262 ATAAGG -s Anc0.Anc0refChr3 84423 6 + 222631 ATAAAG -s Anc1.Anc1refChr6 116746 6 + 197743 ATAAAG -s Anc2.Anc2refChr13 91840 6 + 96486 ATAAAG -s mr.mrrefChr3 18957 6 + 181027 ATAAGG -s simCow_chr6.simCow.chr6 448233 6 + 602619 GAGAGG -s simDog_chr6.simDog.chr6 440995 6 + 593897 ATAAAT -s simHuman_chr6.simHuman.chr6 448855 6 + 601863 ATAAAG -s simRat_chr6.simRat.chr6 472865 6 + 647215 ATAAGC - -a -s simMouse_chr6.simMouse.chr6 463189 3 + 636262 TTA -s Anc0.Anc0refChr3 84445 3 + 222631 TTA -s Anc1.Anc1refChr6 116768 3 + 197743 TTA -s Anc2.Anc2refChr13 91862 3 + 96486 TTA -s mr.mrrefChr3 18979 3 + 181027 TTA -s simCow_chr6.simCow.chr6 448255 3 + 602619 TTA -s simDog_chr6.simDog.chr6 441017 3 + 593897 CTA -s simHuman_chr6.simHuman.chr6 448877 3 + 601863 TCG -s simRat_chr6.simRat.chr6 472887 3 + 647215 TTA - -a -s simMouse_chr6.simMouse.chr6 463192 8 + 636262 GAACAGCT -s Anc0.Anc0refChr3 84454 8 + 222631 GAACTACT -s Anc1.Anc1refChr6 116777 8 + 197743 GAACTACT -s Anc2.Anc2refChr13 91871 8 + 96486 GAAGTACT -s mr.mrrefChr3 18982 8 + 181027 GAACAGCT -s simCow_chr6.simCow.chr6 448264 4 + 602619 GA----CT -s simDog_chr6.simDog.chr6 441026 8 + 593897 GAAGTATT -s simHuman_chr6.simHuman.chr6 448886 8 + 601863 AAACTACT -s simRat_chr6.simRat.chr6 472890 8 + 647215 GAACAGCT - -a -s simMouse_chr6.simMouse.chr6 463244 8 + 636262 ATTTGAGT -s Anc0.Anc0refChr3 84511 8 + 222631 ACCTGAGT -s Anc1.Anc1refChr6 116834 8 + 197743 ACCTGAGT -s Anc2.Anc2refChr13 91928 8 + 96486 ACCTGAGT -s mr.mrrefChr3 19038 8 + 181027 ATCTGAGT -s simCow_chr6.simCow.chr6 448317 8 + 602619 ACCTGAGT -s simDog_chr6.simDog.chr6 441083 8 + 593897 CCCTGAGC -s simHuman_chr6.simHuman.chr6 448943 8 + 601863 ACCTTAGT -s simRat_chr6.simRat.chr6 472946 8 + 647215 AACTGAGT - -a -s simMouse_chr6.simMouse.chr6 463252 30 + 636262 ACCATATGTATATATAGATGTCAGCATCCA -s Anc0.Anc0refChr3 84519 25 + 222631 ACTCTACATG-----AAATGTCAGCAGCCA -s Anc1.Anc1refChr6 116842 26 + 197743 ACTCTACATGT----AAATGTCAGCAGCCA -s Anc2.Anc2refChr13 91936 25 + 96486 ACCCTACATG-----AAATGTCAGCAGCCA -s mr.mrrefChr3 19046 30 + 181027 ACTATATATATATATAGATGTCAGCATCCA -s simCow_chr6.simCow.chr6 448326 25 + 602619 ATACTACATG-----GCATGCCAACAGCCA -s simDog_chr6.simDog.chr6 441091 25 + 593897 ACCCTACATG-----AAATGTTAGCAGCAA -s simHuman_chr6.simHuman.chr6 448951 24 + 601863 ACTGTACATGT------ATGTCAGCAGCCA -s simRat_chr6.simRat.chr6 472954 30 + 647215 ACTATATATATATATAAATGTCAGCATCCA - -a -s simMouse_chr6.simMouse.chr6 463282 8 + 636262 TAGAATTT -s Anc0.Anc0refChr3 84547 8 + 222631 TTGAGTTT -s Anc1.Anc1refChr6 116871 8 + 197743 TTGAGTTT -s Anc2.Anc2refChr13 91966 8 + 96486 TTGAGTTT -s mr.mrrefChr3 19076 8 + 181027 TAGAATTT -s simCow_chr6.simCow.chr6 448356 8 + 602619 ATGAGTTT -s simDog_chr6.simDog.chr6 441121 8 + 593897 TTGAGCTT -s simHuman_chr6.simHuman.chr6 448978 8 + 601863 TTGAGTTT -s simRat_chr6.simRat.chr6 472984 8 + 647215 CAGATTTT - -a -s simMouse_chr6.simMouse.chr6 463290 8 + 636262 TTCCATTC -s Anc0.Anc0refChr3 84557 8 + 222631 TTTCATCT -s Anc1.Anc1refChr6 116881 8 + 197743 TTTCATCT -s Anc2.Anc2refChr13 91976 8 + 96486 TTCCATCT -s mr.mrrefChr3 19084 8 + 181027 TTTCATTC -s simCow_chr6.simCow.chr6 448366 8 + 602619 TTCCATTT -s simDog_chr6.simDog.chr6 441131 8 + 593897 TTCCATCC -s simHuman_chr6.simHuman.chr6 448988 8 + 601863 TGTCACCT -s simRat_chr6.simRat.chr6 472992 8 + 647215 CTTCATTC - -a -s simMouse_chr6.simMouse.chr6 463298 6 + 636262 TAGTCT -s Anc0.Anc0refChr3 84565 6 + 222631 TATTTT -s Anc1.Anc1refChr6 116889 6 + 197743 TATTTT -s Anc2.Anc2refChr13 91984 6 + 96486 TGTTTT -s mr.mrrefChr3 19092 6 + 181027 TAGTCT -s simCow_chr6.simCow.chr6 448374 1 + 602619 T----- -s simDog_chr6.simDog.chr6 441147 6 + 593897 TGTTTT -s simHuman_chr6.simHuman.chr6 448996 6 + 601863 TATTTT -s simRat_chr6.simRat.chr6 473000 6 + 647215 TAGTCT - -a -s simMouse_chr6.simMouse.chr6 463304 25 + 636262 CTGGAGTCTCCTTGAGACTTTATGA -s Anc0.Anc0refChr3 84571 25 + 222631 TGGGCACCCCCTTGAGACATCATTA -s Anc1.Anc1refChr6 116895 25 + 197743 TGGGCACCCCCTTGAGACATCATTA -s Anc2.Anc2refChr13 91993 25 + 96486 TGGGCACCCCCTTGAGACATCCTTA -s mr.mrrefChr3 19098 25 + 181027 CTGGAGTCTCCTTGAGACTTTATGA -s simCow_chr6.simCow.chr6 448375 25 + 602619 TGGGCCCCCCCTTGAAACATCCTTA -s simDog_chr6.simDog.chr6 441159 20 + 593897 TGGGTAACCCCTTGAGACAT----- -s simHuman_chr6.simHuman.chr6 449002 25 + 601863 GCAGCTCTGCCTTGACACCTGATTA -s simRat_chr6.simRat.chr6 473006 25 + 647215 ATGGAATCTCCTTGAGACTTTATGA - -a -s simMouse_chr6.simMouse.chr6 463329 10 + 636262 ACATAAATGG -s Anc0.Anc0refChr3 84603 7 + 222631 AAATAAA--- -s Anc1.Anc1refChr6 116927 7 + 197743 AAATAAA--- -s Anc2.Anc2refChr13 92025 7 + 96486 AAATAAA--- -s mr.mrrefChr3 19123 10 + 181027 ACATAAATGG -s simCow_chr6.simCow.chr6 448407 7 + 602619 AAATAAA--- -s simDog_chr6.simDog.chr6 441185 7 + 593897 AAATAAA--- -s simHuman_chr6.simHuman.chr6 449034 7 + 601863 GAATAAA--- -s simRat_chr6.simRat.chr6 473031 10 + 647215 ACATAAATGG - -a -s simMouse_chr6.simMouse.chr6 463339 88 + 636262 CAGCATTAAAAGTTTTGTAACTTTACCTATGTACTGCCATAGATGTGTTATTTCACTAAGTTGACTCTTGTGTCATGTGGTAATACTT -s Anc0.Anc0refChr3 84610 88 + 222631 CAGCATTAGATGTTTTGTAGGTTCATCTATGTGCTGTTAGAGGTGTATTACCTCAATAAGCCTACTCTTGTGTCATCAGGTATTACTT -s Anc1.Anc1refChr6 116934 88 + 197743 CAGCATTAGATGTTTTGTAGGTTCATCTATGTGCTGTTAGAGGTGTATTACCTCAATAAGCCTACTCTTGTGTCATCAGGTATTACTT -s Anc2.Anc2refChr13 92032 88 + 96486 CAGCATTAGATGTTTTGTAGGTTCATCTATGTGCTGTTAGAGGTGCATTACCTCAATGAGCCTACTCTTGTATTATCAGGTATTACTT -s mr.mrrefChr3 19133 88 + 181027 CAGCATTAGAAGTTTTGTAGCTTTACCTATGTACTGCCATAGGTGTATTATCTCACTAAGTCGACTCTTGTGTCATGTGGTAATACTT -s simCow_chr6.simCow.chr6 448414 80 + 602619 CAACATTAGATATCCTGCAGGTTCATCTATGTGCTGTTAAAGCTGCATTGCCTCAATGAGCCTACTCTTG--------GGTATTACTT -s simDog_chr6.simDog.chr6 441195 88 + 593897 CAGCATTGGATGTTTTGTAGGTTAATCTATGTGTTATTAGAGGTGCATTACCTCAATGAGCCTACTCTTGTATTATCAGGTATTACTT -s simHuman_chr6.simHuman.chr6 449041 88 + 601863 CAGCATTAGATGTTTTATAGGTTCATCTATGTGCTGTTAGAGGTGTATAACCTCAATAAGCCTACTCTTGTGTCAGTCGGTACCACTT -s simRat_chr6.simRat.chr6 473041 80 + 647215 CAGCATTAGAAGTTTTGCAGTTTTACCTA--------CATAGGTGTATTATCTCACTTAGTCAACTCTTGTGTCATGGGGTATTACTT - -a -s simMouse_chr6.simMouse.chr6 463427 32 + 636262 TATAGGCTTCACCTCAGCACCCGCATTGCTCA -s Anc0.Anc0refChr3 84698 32 + 222631 TATAGTATTTACCTCAGCAACTGAACTGCTCA -s Anc1.Anc1refChr6 117022 32 + 197743 TATAGTATTTACCTCAGCAACTGAACTGCTCA -s Anc2.Anc2refChr13 92120 32 + 96486 TTTAGTATTTCCCTCAGCAACTGAACTGCTCA -s mr.mrrefChr3 19221 32 + 181027 TATAGGATTCACCTCAGCACCTGCATTGCTCA -s simCow_chr6.simCow.chr6 448494 32 + 602619 TTTAGTATTTGCCTTAGCAACTGAACTACTCA -s simDog_chr6.simDog.chr6 441283 32 + 593897 TTTAGTATTTCCCCCGGCAACTGAACAGTTCT -s simHuman_chr6.simHuman.chr6 449130 32 + 601863 TATAGTATATACCTCAGCAACTGTACTGCTCA -s simRat_chr6.simRat.chr6 473121 32 + 647215 GATAGGATTCACCTCAGTACCTGCATTACTCA - -a -s simMouse_chr6.simMouse.chr6 463459 21 + 636262 CCATTGAACTGATAGAGGCAA -s Anc0.Anc0refChr3 84734 21 + 222631 TTATTGGGCTGATGGAGGTAA -s Anc1.Anc1refChr6 117058 21 + 197743 TTATTGGGCTGATGGAGGTAA -s Anc2.Anc2refChr13 92156 21 + 96486 TTATTGGGCTGATGGAGGTAA -s mr.mrrefChr3 19253 21 + 181027 CCATTGAACTGATGGAGGTAA -s simCow_chr6.simCow.chr6 448530 21 + 602619 TTTTTGGGCTGATGGAGGTAG -s simDog_chr6.simDog.chr6 441319 21 + 593897 TTATTGGACTGATGGAGGTAA -s simHuman_chr6.simHuman.chr6 449166 20 + 601863 TTATTGGG-TGATGGAGGTAA -s simRat_chr6.simRat.chr6 473153 21 + 647215 CAGTTGAACTGATGGAGCTGA - -a -s simMouse_chr6.simMouse.chr6 463480 1 + 636262 C -s Anc0.Anc0refChr3 84755 1 + 222631 C -s Anc1.Anc1refChr6 117079 1 + 197743 C -s Anc2.Anc2refChr13 92177 1 + 96486 C -s mr.mrrefChr3 19274 1 + 181027 C -s simCow_chr6.simCow.chr6 448551 1 + 602619 C -s simDog_chr6.simDog.chr6 441340 1 + 593897 C -s simHuman_chr6.simHuman.chr6 449186 1 + 601863 C -s simRat_chr6.simRat.chr6 473178 1 + 647215 C - -a -s simMouse_chr6.simMouse.chr6 463481 13 + 636262 AAGTCAACCTGCT -s Anc0.Anc0refChr3 84764 13 + 222631 AAGTTTACCAGTT -s Anc1.Anc1refChr6 117088 13 + 197743 AAGTTTACCAGTT -s Anc2.Anc2refChr13 92186 13 + 96486 AAGTTTACCAGAT -s mr.mrrefChr3 19275 13 + 181027 AAGTCAACCTGTT -s simCow_chr6.simCow.chr6 448560 13 + 602619 AAGTTTACCAGCT -s simDog_chr6.simDog.chr6 441349 13 + 593897 AAGTCTATCAGAT -s simHuman_chr6.simHuman.chr6 449195 13 + 601863 AAGTTGACCAGTT -s simRat_chr6.simRat.chr6 473179 13 + 647215 AAGTCAACCTGTT - -a -s simMouse_chr6.simMouse.chr6 463494 1 + 636262 C -s Anc0.Anc0refChr3 84870 1 + 222631 C -s Anc1.Anc1refChr6 117198 1 + 197743 C -s Anc2.Anc2refChr13 92293 1 + 96486 C -s mr.mrrefChr3 19338 1 + 181027 C -s simCow_chr6.simCow.chr6 448659 1 + 602619 C -s simDog_chr6.simDog.chr6 441557 1 + 593897 C -s simHuman_chr6.simHuman.chr6 449305 1 + 601863 C -s simRat_chr6.simRat.chr6 473245 1 + 647215 C - -a -s simMouse_chr6.simMouse.chr6 463495 43 + 636262 ACAATGATATGCTAGTACTCAGAGATGAAAACAGCATTTACAT -s Anc0.Anc0refChr3 84872 40 + 222631 ACAATGGTCTGGTAC---TCAGAGAAGAAAAGAGCATTAACAT -s Anc1.Anc1refChr6 117200 40 + 197743 ACAATGGTCTGGTAC---TCAGAGAAGAAAAGAGCATTAACAT -s Anc2.Anc2refChr13 92295 40 + 96486 ATAATAGTCTGGTAC---TCAGAGAAGAAAGGAGTGTTAACAT -s mr.mrrefChr3 19339 40 + 181027 ACAATGATATGCTAG---TCAGAGATGAAAACAGCATTTACAT -s simCow_chr6.simCow.chr6 448661 32 + 602619 ATAATAGTCTGATAC---TCAGAGAAGGAGGGAGA-------- -s simDog_chr6.simDog.chr6 441559 40 + 593897 ATTATAGTCTGGTAC---CCAGAGAAGAAAGGGGTGTTAACAT -s simHuman_chr6.simHuman.chr6 449307 40 + 601863 GCAATGGTGTAGTAC---TCAGAAAAAAAAAGAGCATTAACAT -s simRat_chr6.simRat.chr6 473246 38 + 647215 ACAATGATACGCTTG---TGAGA--CGAAACCAGAATTCACGT - -a -s simMouse_chr6.simMouse.chr6 463538 16 + 636262 TTTGTCTCACAAAACT -s Anc0.Anc0refChr3 84933 16 + 222631 TTTGACTCACAACACT -s Anc1.Anc1refChr6 117261 16 + 197743 TTTGACTCACAACACT -s Anc2.Anc2refChr13 92356 16 + 96486 CTTGACTCACAGCGCC -s mr.mrrefChr3 19400 16 + 181027 TTTGTCTCACAAAACT -s simCow_chr6.simCow.chr6 448693 16 + 602619 CTTGGCTCACAGCCCT -s simDog_chr6.simDog.chr6 441620 16 + 593897 CTTGACTCACAGCGCC -s simHuman_chr6.simHuman.chr6 449368 13 + 601863 TTTG---CTCAAGACT -s simRat_chr6.simRat.chr6 473305 16 + 647215 TTTGTCTCACACAATT - -a -s simMouse_chr6.simMouse.chr6 463554 4 + 636262 GGAC -s Anc0.Anc0refChr3 84949 4 + 222631 GGAC -s Anc1.Anc1refChr6 117277 4 + 197743 GGAC -s Anc2.Anc2refChr13 92372 4 + 96486 GCAA -s mr.mrrefChr3 19416 4 + 181027 GGAC -s simCow_chr6.simCow.chr6 448709 4 + 602619 GCAA -s simDog_chr6.simDog.chr6 441636 4 + 593897 GCAC -s simHuman_chr6.simHuman.chr6 449381 4 + 601863 TGAC -s simRat_chr6.simRat.chr6 473331 4 + 647215 AAAC - -a -s simMouse_chr6.simMouse.chr6 463558 9 + 636262 TTCCTAAGT -s Anc0.Anc0refChr3 84953 9 + 222631 TACCTAATT -s Anc1.Anc1refChr6 117281 9 + 197743 TACCTAATT -s Anc2.Anc2refChr13 92376 9 + 96486 TACCCAATT -s mr.mrrefChr3 19420 9 + 181027 TTCTTAAGT -s simCow_chr6.simCow.chr6 448713 9 + 602619 TACCCAATT -s simDog_chr6.simDog.chr6 441640 9 + 593897 TACCCAGTT -s simHuman_chr6.simHuman.chr6 449390 9 + 601863 TCCCTGCAC -s simRat_chr6.simRat.chr6 473335 9 + 647215 TTCTTAAGT - -a -s simMouse_chr6.simMouse.chr6 463567 3 + 636262 TTG -s Anc0.Anc0refChr3 84962 3 + 222631 TTG -s Anc1.Anc1refChr6 117290 3 + 197743 TTG -s Anc2.Anc2refChr13 92451 3 + 96486 CTG -s mr.mrrefChr3 19429 3 + 181027 TTG -s simCow_chr6.simCow.chr6 448791 3 + 602619 AAA -s simDog_chr6.simDog.chr6 441715 3 + 593897 CTG -s simHuman_chr6.simHuman.chr6 449399 3 + 601863 TTG -s simRat_chr6.simRat.chr6 473344 3 + 647215 TTG - -a -s simMouse_chr6.simMouse.chr6 463570 2 + 636262 AG -s Anc0.Anc0refChr3 84968 2 + 222631 AC -s Anc1.Anc1refChr6 117296 2 + 197743 AC -s Anc2.Anc2refChr13 92457 2 + 96486 AC -s mr.mrrefChr3 19432 2 + 181027 AG -s simCow_chr6.simCow.chr6 448797 2 + 602619 AC -s simDog_chr6.simDog.chr6 441721 2 + 593897 AC -s simHuman_chr6.simHuman.chr6 449405 2 + 601863 AT -s simRat_chr6.simRat.chr6 473347 2 + 647215 AG - -a -s simMouse_chr6.simMouse.chr6 463572 74 + 636262 TTTGCAGAAATAAACGGCAATTGCTGTGATCCCGTAGAGGTAAATGTGAAAGGTAACATTATCAACTGCTAATA -s Anc0.Anc0refChr3 84970 74 + 222631 TTTGTAGAAACTAAAGGAAAGTGAAGTGATCCCTTACAAATAGATTTGATACGTCACATTATCAACTGATGACA -s Anc1.Anc1refChr6 117298 74 + 197743 TTTGTAGAAACTAAAGGAAAGTGAAGTGATCCCTTACAAATAGATTTGATACGTCACATTATCAACTGATGACA -s Anc2.Anc2refChr13 92459 74 + 96486 TTTGTAGAAACTAAAGGAAGGTGAAATGATCCATTACAAATAGATTCAATGCTTCACATTATCAACTGATGACC -s mr.mrrefChr3 19434 74 + 181027 TTTGTAGAAATAAAAGGCAATTGCTGTGATCCCGTAGAGATAAATGTGAAAGGTAACATTATCAACTGCTAATA -s simCow_chr6.simCow.chr6 448812 73 + 602619 TTTGTAGAAACCAAAGGAAGGTGAAATGATGTGTTACAAGTAAATTCAATCCCTCGT-TTATCAACTGATGACC -s simDog_chr6.simDog.chr6 441723 73 + 593897 TTTGTAGAAACTAAAGGAA-GTAAAATGATCCATTAAAAATAGATTCAATGATTCACATTATCAACTGATGACC -s simHuman_chr6.simHuman.chr6 449407 74 + 601863 TTTGTAGGAACTAAAGGAAAGTGAAGTAATCCCTTACATATAGATTTGATACGTGACATTACCAACTGATGACA -s simRat_chr6.simRat.chr6 473349 74 + 647215 TTTGTAGAAATAAAAGGCAATTGCTATGGTCCTGTAGAGATAAATGTGAAAGGTAACATTATCAACTGCTAATA - -a -s simMouse_chr6.simMouse.chr6 463646 26 + 636262 GTAAATGCTACCAAGGTTGGAGATGG -s Anc0.Anc0refChr3 85045 25 + 222631 GTAAATG-TATCAAAGTTAGTGATCA -s Anc1.Anc1refChr6 117373 26 + 197743 GTAAATGTTATCAAAGTTAGTGATCA -s Anc2.Anc2refChr13 92534 25 + 96486 GTAAGTG-TATCAAACTTAGTGATCA -s mr.mrrefChr3 19508 26 + 181027 GTAAATGTTATCAAGGTTAGAGATGG -s simCow_chr6.simCow.chr6 448886 23 + 602619 GTAAGTG-TATCA--CCTAGAGGTTA -s simDog_chr6.simDog.chr6 441797 25 + 593897 GTGAGTG-TATTGAACTTAATGATCA -s simHuman_chr6.simHuman.chr6 449482 26 + 601863 GTAAAAGTTATCAAAGTTAGTGATCA -s simRat_chr6.simRat.chr6 473423 26 + 647215 GTAAATGTTGTCGAGGTTAGAGATGG - -a -s simMouse_chr6.simMouse.chr6 463672 5 + 636262 AGTTA -s Anc0.Anc0refChr3 85070 5 + 222631 AGAAA -s Anc1.Anc1refChr6 117399 5 + 197743 AGAAA -s Anc2.Anc2refChr13 92559 5 + 96486 AGAAA -s mr.mrrefChr3 19534 5 + 181027 AGTTA -s simCow_chr6.simCow.chr6 448911 5 + 602619 AGCCA -s simDog_chr6.simDog.chr6 441822 5 + 593897 AGAAG -s simHuman_chr6.simHuman.chr6 449508 5 + 601863 AGAAA -s simRat_chr6.simRat.chr6 473449 5 + 647215 AGCTA - -a -s simMouse_chr6.simMouse.chr6 463677 6 + 636262 CATACC -s Anc0.Anc0refChr3 85082 6 + 222631 CATACC -s Anc1.Anc1refChr6 117411 6 + 197743 CATACC -s Anc2.Anc2refChr13 92571 6 + 96486 GACACC -s mr.mrrefChr3 19539 6 + 181027 CATACC -s simCow_chr6.simCow.chr6 448923 6 + 602619 AACACC -s simDog_chr6.simDog.chr6 441834 6 + 593897 GACACC -s simHuman_chr6.simHuman.chr6 449520 6 + 601863 CATGCT -s simRat_chr6.simRat.chr6 473454 6 + 647215 CACACC - -a -s simMouse_chr6.simMouse.chr6 463683 34 + 636262 GATTACATATCAGACATATAAATGACACCAAAAT -s Anc0.Anc0refChr3 85088 34 + 222631 TAGTAGGCATCAGCCATACAAGTAACACCAAAAT -s Anc1.Anc1refChr6 117417 34 + 197743 TAGTAGGCATCAGCCATACAAGTAACACCAAAAT -s Anc2.Anc2refChr13 92577 34 + 96486 TAGTAGGAATTAGCCATACAAGTAACACCAAAGC -s mr.mrrefChr3 19545 34 + 181027 TATTAGACATCAGACATATAAGTGACACCAAAAT -s simCow_chr6.simCow.chr6 448938 32 + 602619 TAATCGAAATTTG--ACACATGGAACCTTCAAGC -s simDog_chr6.simDog.chr6 441840 34 + 593897 TAGTAGGAATTAGCCATACAAATAACACCAAAGC -s simHuman_chr6.simHuman.chr6 449526 34 + 601863 TAGTAGGCATCAGCTATCCAAGTAACACCATTAT -s simRat_chr6.simRat.chr6 473460 34 + 647215 TATTAGACATCAGGCATATAAGTGACCCCAAAAT - -a -s simMouse_chr6.simMouse.chr6 463717 2 + 636262 TT -s Anc0.Anc0refChr3 85122 2 + 222631 TT -s Anc1.Anc1refChr6 117451 2 + 197743 TT -s Anc2.Anc2refChr13 92612 2 + 96486 TT -s mr.mrrefChr3 19579 2 + 181027 TT -s simCow_chr6.simCow.chr6 448971 2 + 602619 CT -s simDog_chr6.simDog.chr6 441875 2 + 593897 TT -s simHuman_chr6.simHuman.chr6 449560 2 + 601863 TT -s simRat_chr6.simRat.chr6 473494 2 + 647215 TT - -a -s simMouse_chr6.simMouse.chr6 463719 7 + 636262 GATATTG -s Anc0.Anc0refChr3 85124 7 + 222631 CATGTTG -s Anc1.Anc1refChr6 117453 7 + 197743 CATGTTG -s Anc2.Anc2refChr13 92614 7 + 96486 CATGTTG -s mr.mrrefChr3 19581 7 + 181027 GATGTTG -s simCow_chr6.simCow.chr6 448998 7 + 602619 CATCTTG -s simDog_chr6.simDog.chr6 441877 7 + 593897 CATGTTA -s simHuman_chr6.simHuman.chr6 449562 7 + 601863 CATGCTG -s simRat_chr6.simRat.chr6 473496 7 + 647215 GGTGTTG - -a -s simMouse_chr6.simMouse.chr6 463726 10 + 636262 CCTAAGGGAA -s Anc0.Anc0refChr3 85136 10 + 222631 GGTAAAGAAA -s Anc1.Anc1refChr6 117465 10 + 197743 GGTAAAGAAA -s Anc2.Anc2refChr13 92626 10 + 96486 GGAAAAGAAG -s mr.mrrefChr3 19593 10 + 181027 CGTAAGGAAA -s simCow_chr6.simCow.chr6 449010 10 + 602619 GGAAAAGAAG -s simDog_chr6.simDog.chr6 441889 10 + 593897 AGAAACGAAG -s simHuman_chr6.simHuman.chr6 449574 10 + 601863 GGTAAAGAGA -s simRat_chr6.simRat.chr6 473510 10 + 647215 AGTAAGGAAA - -a -s simMouse_chr6.simMouse.chr6 463736 98 + 636262 CATATGGAGTTCGAGCCCCCAACACAGATCAGCATCAAACATCTCTGTGCGAAATTATGCTAGACACAGCTGGATACTGAGACTGGCCTGGTTTAAAC -s Anc0.Anc0refChr3 85146 96 + 222631 CATACA--GTTTGAGCCTTTGACACAGGTCAGCATCAAATATCACTATGGCAAATTATACTTGGCACACCTGGATTCTAAGACCAGCCTGGTTGAGAT -s Anc1.Anc1refChr6 117475 96 + 197743 CATACA--GTTTGAGCCTTTGACACAGGTCAGCATCAAATATCACTATGGCAAATTATACTTGGCACACCTGGATTCTAAGACCAGCCTGGTTGAGAT -s Anc2.Anc2refChr13 92636 96 + 96486 TATACA--GTTTGAGCCTTTGTCACAGGGCAGCATCAAATATCACTATGGCAAATTGCCCTTGGCATATCCAAATTTTGAGACCAGCCTGGTTGACAT -s mr.mrrefChr3 19603 98 + 181027 CATATGGAGTTTGAGCCCCTGACACAGATCAGCATCAAATATCTCTGTGCCAAATTATACTAGGCACACCTGGATACTAAGACTGGCCTGGTTTAGAT -s simCow_chr6.simCow.chr6 449020 95 + 602619 TCTACA--GTTAGAGCCTTTGGGACAGGCCAGCATCAAATACTACTGTGGCAAATTGCC-TTGGCATATCCAAATTTTGAGACCAGCCTGGCCAATAT -s simDog_chr6.simDog.chr6 441899 71 + 593897 TATACA--GTTT--------GTCACAGGGCGGCATCAAATATCGTTATGGCTAATAGCCCT-----------------GAGACCAGCCTGGTTGACAT -s simHuman_chr6.simHuman.chr6 449584 96 + 601863 CAAACT--GTTTCAGCCTTTGATGTAGGTCAGCATCAAATATCACTATGGCAAATTATACTTGGCACACCTGGATTCCAAGACCAGCCTGGTTGAGAT -s simRat_chr6.simRat.chr6 473523 96 + 647215 CGTATGGAGTTTGAGCACCTGACACAGATCAGCATCAAATGCCTCTGTGTCAAATTACACTAGGCACACCTGGACACTAAGACAGGC--GGTGTAGAT - -a -s simMouse_chr6.simMouse.chr6 463834 23 + 636262 AGCTTGTCCCAATATTTATGCAC -s Anc0.Anc0refChr3 85253 21 + 222631 AGCTTGTCC--ACATTTGTGAAC -s Anc1.Anc1refChr6 117582 23 + 197743 AGCTTGTCCCAACATTTGTGAAC -s Anc2.Anc2refChr13 92744 21 + 96486 AGTCTGTCC--AAATTTGTGAAC -s mr.mrrefChr3 19701 23 + 181027 AGCTTGTCCCAATATTTATGCAC -s simCow_chr6.simCow.chr6 449127 21 + 602619 AGTCTGTCC--ACATTTGTGAAC -s simDog_chr6.simDog.chr6 441982 21 + 593897 AGTCTGTCC--AAATCTGTGAAC -s simHuman_chr6.simHuman.chr6 449691 23 + 601863 AGCTTGTGCCAACATTTGTGAAC -s simRat_chr6.simRat.chr6 473619 23 + 647215 AGCTCGTCCCAATATTTATGCAC - -a -s simMouse_chr6.simMouse.chr6 463857 5 + 636262 ACATT -s Anc0.Anc0refChr3 85274 5 + 222631 CTATC -s Anc1.Anc1refChr6 117605 5 + 197743 CTATC -s Anc2.Anc2refChr13 92765 5 + 96486 CTATC -s mr.mrrefChr3 19724 5 + 181027 ACATT -s simCow_chr6.simCow.chr6 449148 5 + 602619 CTATG -s simDog_chr6.simDog.chr6 442010 5 + 593897 CTATC -s simRat_chr6.simRat.chr6 473642 5 + 647215 ACATT - -a -s simMouse_chr6.simMouse.chr6 463862 65 + 636262 TATGAAGGGTGGAAAAGATGAGACAAGGGATCTAATAATATCAGTAGAGAGGTCTGCAAAAGTCC -s Anc0.Anc0refChr3 85279 54 + 222631 TCTGGTGGGAGGGACAGATAAGACAAGGTATCTAAAAACACCTGTAGAGAGG-----------CC -s Anc1.Anc1refChr6 117610 54 + 197743 TCTGGTGGGAGGGACAGATAAGACAAGGTATCTAAAAACACCTGTAGAGAGG-----------CC -s Anc2.Anc2refChr13 92776 54 + 96486 TCTGGTGAGAGGGACAGATAAGACAAGGTATCTAAAAACACCTATAGAGAGG-----------CC -s mr.mrrefChr3 19729 65 + 181027 TATGAAGGGTGGGAAAGATGAGACAAGGGATCTAATAATATCAGTAGAGAGGTCTGCAAAAGTCC -s simCow_chr6.simCow.chr6 449159 46 + 602619 CCTGGGTGGAGGGACAGATGACACAA--------AAAAGTCCCATAGAAAAG-----------CC -s simDog_chr6.simDog.chr6 442022 54 + 593897 TCTGGTGAGAGGGACAGATAAGACGAGGTATCTAAAATCACCTATGGGGAGA-----------CC -s simHuman_chr6.simHuman.chr6 449714 49 + 601863 -----GAGGAGGGACAGATAAGACAAGGAATCTAAAAACACTTGTAGAGAGG-----------CC -s simRat_chr6.simRat.chr6 473647 65 + 647215 TATGAAGAGTGGGAAAGATGAGATGAGGGATCTGAGACTGTCCGTGGAGGGGTCTGCAAGAGGCC - -a -s simMouse_chr6.simMouse.chr6 463927 21 + 636262 TAGTGGTTTTGGGTGTGTTGG -s Anc0.Anc0refChr3 85333 10 + 222631 TAGCAGCTTT----------- -s Anc1.Anc1refChr6 117664 10 + 197743 TAGCAGCTTT----------- -s Anc2.Anc2refChr13 92830 10 + 96486 TAGCAGCTTC----------- -s mr.mrrefChr3 19794 21 + 181027 TAGTAGTTTTGGGTGTGTTGG -s simCow_chr6.simCow.chr6 449205 10 + 602619 TGGCAGGCTC----------- -s simDog_chr6.simDog.chr6 442114 10 + 593897 TAGTGGCTTC----------- -s simHuman_chr6.simHuman.chr6 449763 10 + 601863 TAGCAGCTTT----------- -s simRat_chr6.simRat.chr6 473712 21 + 647215 TAGTAGTTTCAGGTGTGTTGG - -a -s simMouse_chr6.simMouse.chr6 463948 5 + 636262 GTGTG -s Anc0.Anc0refChr3 85343 5 + 222631 GTGGG -s Anc1.Anc1refChr6 117674 5 + 197743 GTGGG -s Anc2.Anc2refChr13 92842 5 + 96486 GTGGG -s mr.mrrefChr3 19815 5 + 181027 GTGTG -s simCow_chr6.simCow.chr6 449217 5 + 602619 CCAGA -s simDog_chr6.simDog.chr6 442126 5 + 593897 GTGGG -s simHuman_chr6.simHuman.chr6 449773 5 + 601863 GTGGG -s simRat_chr6.simRat.chr6 473733 5 + 647215 GTATG - -a -s simMouse_chr6.simMouse.chr6 463953 18 + 636262 GTGGAATATCTCTCCTGA -s Anc0.Anc0refChr3 85348 18 + 222631 GTAGAATATTTCTTCTGT -s Anc1.Anc1refChr6 117679 18 + 197743 GTAGAATATTTCTTCTGT -s Anc2.Anc2refChr13 92847 18 + 96486 GTAAAATATTTCTTCTGT -s mr.mrrefChr3 19820 18 + 181027 GTGGAATATCTCTCCTGA -s simCow_chr6.simCow.chr6 449222 18 + 602619 GGAAAATATTTCTTGTGT -s simDog_chr6.simDog.chr6 442131 18 + 593897 GTAAAGTCTTCCTCCTGT -s simHuman_chr6.simHuman.chr6 449778 18 + 601863 GTAGAATATTTCTTCTGG -s simRat_chr6.simRat.chr6 473740 18 + 647215 GTGGAATATCTCTCCTGA - -a -s simMouse_chr6.simMouse.chr6 463971 114 + 636262 ACATGTCAGTTCATATAGGCTCCATATACTTCCCACGATTGGATACACACACACATCGTGTGAGTGTAGATGATGAGAGGTTGTTAGGTTGGCAAAACTGCCATATGGAGTTTT -s Anc0.Anc0refChr3 85366 49 + 222631 ACATGTCAGTTCATACAGGTTTCATACCATTCCCAAGACTGCA--------------------------------------------------------GCCAC---------C -s Anc1.Anc1refChr6 117697 49 + 197743 ACATGTCAGTTCATACAGGTTTCATACCATTCCCAAGACTGCA--------------------------------------------------------GCCAC---------C -s Anc2.Anc2refChr13 92865 49 + 96486 ACAAGTCAGTTCATACAGGTTTCATACCATTCCTGCGACTGCA--------------------------------------------------------GCCAC---------C -s mr.mrrefChr3 19838 114 + 181027 ACATGTCAGTTCATACAGGCTCCATATAATTCCCAAGATTGGATACACACACACATCGTGTGAGTGTAGATGATGAGAGGTTGTTAGGTTGGCAAAACTGCCATATGGAGTTTT -s simCow_chr6.simCow.chr6 449240 49 + 602619 ACAAGTCAGTTTGTGCAGGCTTCATAACATTCCTGTGACTGTA--------------------------------------------------------TGCAC---------C -s simDog_chr6.simDog.chr6 442149 49 + 593897 ATAAGTTAGTTCATACAGCTTTCATACTATTCCTGCAGCTACA--------------------------------------------------------GCCGC---------C -s simHuman_chr6.simHuman.chr6 449797 49 + 601863 ACATGTCAGTTCATACAGGTTTCATACCATTCCCAAGACTGCA--------------------------------------------------------GACAC---------C -s simRat_chr6.simRat.chr6 473758 114 + 647215 ACATGTCAGTTCATACCGGCTCCATATAATTCCCAAGATTGTATACACACACACATTGTGTGAGTGTGGACCCTGAGAGGTTGTGAGCTTGGCGAAGCTGGCATATGGGATGTT - -a -s simMouse_chr6.simMouse.chr6 464085 42 + 636262 AACCACAGCTACCTAACAGTATTATTAATACCAGAGTGGAGC -s Anc0.Anc0refChr3 85415 42 + 222631 AACCAAAGCAAGAGAAAAAGATTATTAATACCACAGTAGAGC -s Anc1.Anc1refChr6 117746 42 + 197743 AACCAAAGCAAGAGAAAAAGATTATTAATACCACAGTAGAGC -s Anc2.Anc2refChr13 92914 42 + 96486 TAGAAAAGCAAGAGAAAAAGATTATTAATACCACAGTAGAGC -s mr.mrrefChr3 19952 42 + 181027 AACCACAGCTACCTAACAGTATTATTAATACCAGAGTGGAGC -s simCow_chr6.simCow.chr6 449289 42 + 602619 TATAAAAGCAAGAGAAAAATACTATTAATACCATAGTAGGGC -s simDog_chr6.simDog.chr6 442198 42 + 593897 TAGAAAAGCAAGAGAAAAAGATTATTAATACCACAGTAGAGC -s simHuman_chr6.simHuman.chr6 449846 30 + 601863 AACCAGAGCAAGAGAAAAA------------CACAGTAGACC -s simRat_chr6.simRat.chr6 473882 42 + 647215 AGCCACAGCTACCCAACAATGTTATTCGTACCAGAGTGGAGT - -a -s simMouse_chr6.simMouse.chr6 464127 21 + 636262 TGGAAAAATGCTAGACCATCT -s Anc0.Anc0refChr3 85457 21 + 222631 TGGAAATTTGCCAGACCATCT -s Anc1.Anc1refChr6 117788 21 + 197743 TGGAAATTTGCCAGACCATCT -s Anc2.Anc2refChr13 92956 21 + 96486 TGGAAATTTACCAGACCATCT -s mr.mrrefChr3 19994 21 + 181027 TGGAAAAATGCTAGACCATCT -s simCow_chr6.simCow.chr6 449331 21 + 602619 AGGAAATGTACTAAACCATCT -s simDog_chr6.simDog.chr6 442245 21 + 593897 TGGAAATTCAACAGACCATCT -s simHuman_chr6.simHuman.chr6 449876 21 + 601863 TAAAAATTTGCGAGATCATCC -s simRat_chr6.simRat.chr6 473924 21 + 647215 TGGAAAAATGCTAGACCATCG - -a -s simMouse_chr6.simMouse.chr6 464148 13 + 636262 TGTTACACTTAGA -s Anc0.Anc0refChr3 85482 13 + 222631 CATTACACTTAGG -s Anc1.Anc1refChr6 117813 13 + 197743 CATTACACTTAGG -s Anc2.Anc2refChr13 92981 13 + 96486 CATTATACTTAGG -s mr.mrrefChr3 20019 13 + 181027 TGTTACACTTAGA -s simCow_chr6.simCow.chr6 449356 13 + 602619 CATTATGCTTAAA -s simDog_chr6.simDog.chr6 442270 13 + 593897 CATTATACTTAGG -s simHuman_chr6.simHuman.chr6 449901 13 + 601863 CATTACACTTAGG -s simRat_chr6.simRat.chr6 473949 13 + 647215 TGTAACACTTGGA - -a -s simMouse_chr6.simMouse.chr6 464161 6 + 636262 CCTGGT -s Anc0.Anc0refChr3 85495 6 + 222631 TTTAGT -s Anc1.Anc1refChr6 117826 6 + 197743 TTTAGT -s Anc2.Anc2refChr13 92994 6 + 96486 TTTAGT -s mr.mrrefChr3 20032 6 + 181027 CCTGGT -s simCow_chr6.simCow.chr6 449369 6 + 602619 TCTAGC -s simDog_chr6.simDog.chr6 442287 6 + 593897 CTTGGT -s simHuman_chr6.simHuman.chr6 449914 6 + 601863 TTTAGT -s simRat_chr6.simRat.chr6 473962 6 + 647215 CCTGGT - -a -s simMouse_chr6.simMouse.chr6 464167 58 + 636262 AAGGGGATGATGTTTAGTTGAGGAAGTTTAATGCTAAGACCTTAGTCAATCTATAACA -s Anc0.Anc0refChr3 85501 44 + 222631 AAGGTGGAGAGGT-------------TATGATGCTATGACCTGTGTTGATCAGAAGC- -s Anc1.Anc1refChr6 117832 45 + 197743 AAGGTGGAGAGGT-------------TATGATGCTATGACCTGTGTTGATCAGAAGCA -s Anc2.Anc2refChr13 93000 44 + 96486 AAGGTGGAGAGGT-------------TATGATGCTATGACATGTGTTGATCAGAAGC- -s mr.mrrefChr3 20038 57 + 181027 AAGGGGAAGATGTTTA-TTGAGGAAGTTTAATGCTAAGACCTGAGTCAATCTATAGCA -s simCow_chr6.simCow.chr6 449375 40 + 602619 ATGGTGAGGAAGT-------------TATGACGCTGTGAATTGTGTTGATCAG----- -s simDog_chr6.simDog.chr6 442294 44 + 593897 AAGAATGAGAGGT-------------TATGATGCTATGACAGGTGTTGGTTAAAAGC- -s simHuman_chr6.simHuman.chr6 449920 45 + 601863 AAGGTGGAGAGGT-------------TATGATGCTATGACCTGTGTTGATCAGAAGCA -s simRat_chr6.simRat.chr6 473968 56 + 647215 AAGGGGAAGATGTTTA-TTGAGGAAGTTTAAAGTGAAGAC-TGAGTCAATCCAAAGCA - -a -s simMouse_chr6.simMouse.chr6 464225 39 + 636262 CTCCAAGAATGAGTTGTCTGTCCATTGTTTTTATAGTGA -s Anc0.Anc0refChr3 85552 39 + 222631 CTCCAAAAGTGGGCTGATTGTCCATTGTTTTCTTAGTGA -s Anc1.Anc1refChr6 117884 39 + 197743 CTCCAAAAGTGGGCTGATTGTCCATTGTTTTCTTAGTGA -s Anc2.Anc2refChr13 93051 39 + 96486 CTCCTAAAGTGGGCTGATTGTCCATTGTTTTTTTGGTGA -s mr.mrrefChr3 20095 39 + 181027 CTCCAAAAATGAGTTGTCTGTCCATTGTTTTCATAGTGA -s simCow_chr6.simCow.chr6 449421 39 + 602619 CTCCTAAAGTGGCCTGATTGTCCACTGTTTTTTTTGTGA -s simDog_chr6.simDog.chr6 442339 28 + 593897 -----------GGATGCTTGTCCATTGTTCCTTTGGTGA -s simHuman_chr6.simHuman.chr6 450021 39 + 601863 CTCCAAAAGTTGGCTGATTGTCCATTGTTTTCTTAGGGA -s simRat_chr6.simRat.chr6 474024 39 + 647215 CTCTAAAACTGAGTTGTCTGTCCATTGTTTTCATAGTGA - -a -s simMouse_chr6.simMouse.chr6 464264 4 + 636262 GCCC -s Anc0.Anc0refChr3 85600 4 + 222631 GCCC -s Anc1.Anc1refChr6 117932 4 + 197743 GCCC -s Anc2.Anc2refChr13 93099 4 + 96486 CCCC -s mr.mrrefChr3 20134 4 + 181027 GCCC -s simCow_chr6.simCow.chr6 449469 4 + 602619 TCCC -s simDog_chr6.simDog.chr6 442376 4 + 593897 CCCC -s simHuman_chr6.simHuman.chr6 450069 4 + 601863 GCCC -s simRat_chr6.simRat.chr6 474063 4 + 647215 GCCC - -a -s simMouse_chr6.simMouse.chr6 464268 15 + 636262 TAGTGCGTGAAAGTT -s Anc0.Anc0refChr3 85615 15 + 222631 TAGTGTGTGAAATTT -s Anc1.Anc1refChr6 117947 15 + 197743 TAGTGTGTGAAATTT -s Anc2.Anc2refChr13 93116 15 + 96486 TAGTGTGTGTAATTT -s mr.mrrefChr3 20138 15 + 181027 TAGTGCGTGAAAGTT -s simCow_chr6.simCow.chr6 449486 15 + 602619 TGGGGTGTGTAATAT -s simDog_chr6.simDog.chr6 442393 15 + 593897 TAGTGTGTGTAATTT -s simHuman_chr6.simHuman.chr6 450084 13 + 601863 TAGT--GTGAAATTT -s simRat_chr6.simRat.chr6 474067 15 + 647215 TAGTGCATGAAAATT - -a -s simMouse_chr6.simMouse.chr6 464283 27 + 636262 TAGAATAGTAAAACTAGATGGGGGAGG -s Anc0.Anc0refChr3 85684 27 + 222631 TAAAAGAGTAAAGCCAACTTGGGGAGA -s Anc1.Anc1refChr6 118016 27 + 197743 TAAAAGAGTAAAGCCAACTTGGGGAGA -s Anc2.Anc2refChr13 93185 27 + 96486 TAAGAGAGTAAAGCCATCTTGGGGAGA -s mr.mrrefChr3 20153 27 + 181027 TAGAATAGTAAAACCAAATTGGGGAGG -s simCow_chr6.simCow.chr6 449550 27 + 602619 TAAGATAGTAAAGCCAGCCTGGGGGGA -s simDog_chr6.simDog.chr6 442462 23 + 593897 TAGG-GAGTGAAGCAATCTTG---AGA -s simHuman_chr6.simHuman.chr6 450151 27 + 601863 TAAAAGAATAAAGCCAACTTGGGGAGA -s simRat_chr6.simRat.chr6 474082 27 + 647215 TAGGATAGTAAAATCAAATTGAGGAGG - -a -s simMouse_chr6.simMouse.chr6 464310 32 + 636262 GGGAGGGTCAAATCACTTCTGACGAAATAGTA -s Anc0.Anc0refChr3 85711 32 + 222631 GGGAGGATCAAATCACTTGTTATAATATAGTT -s Anc1.Anc1refChr6 118043 32 + 197743 GGGAGGATCAAATCACTTGTTATAATATAGTT -s Anc2.Anc2refChr13 93212 32 + 96486 TCGAGGATCAAATCACTTGTTAGAATATAGTT -s mr.mrrefChr3 20180 32 + 181027 GGGAGGGTCAAATCACTTCTGATGATATAGTA -s simCow_chr6.simCow.chr6 449577 24 + 602619 T-GAGGATCAAAT-------TAAAATATAGTT -s simDog_chr6.simDog.chr6 442485 32 + 593897 TCGAGGATCAAATCACTTGTTAGGATATAGTT -s simHuman_chr6.simHuman.chr6 450180 32 + 601863 GGGGGAATCAAATCACTTTTTATAATGTAGTC -s simRat_chr6.simRat.chr6 474109 32 + 647215 GGGAGGGTCAAGTCACTTCTGATGATACAGTT - -a -s simMouse_chr6.simMouse.chr6 464342 56 + 636262 TTTTTATCATTCACCTGAGTAGGGTACATATGTGAAGGTGTAAGAGCATACATGGG -s Anc0.Anc0refChr3 85744 56 + 222631 TTATAGTCATTCTGCATAGTAATGTGCATATATACAGGTGTAGGAACATTTATGTG -s Anc1.Anc1refChr6 118076 56 + 197743 TTATAGTCATTCTGCATAGTAATGTGCATATATACAGGTGTAGGAACATTTATGTG -s Anc2.Anc2refChr13 93245 56 + 96486 TTATAGTCATTCTGCATAGTAATGCGCATATATACAGGTGTAGGAACATTTATGTG -s mr.mrrefChr3 20212 56 + 181027 TTTTTATCATTCACCTTAGTAGTGTACATATGTGCAGGTGTAAGAACATACATGGG -s simCow_chr6.simCow.chr6 449602 56 + 602619 TGATTGTCATTCTGCATAGTGATGCGCATGTAAAAAGATGTGGGAACTTTTATGTG -s simDog_chr6.simDog.chr6 442518 55 + 593897 TTTTAGTAATTCTGCATAGTA-TGCACTAATATACAGGTGTAGGAACATTCGTGAG -s simHuman_chr6.simHuman.chr6 450213 56 + 601863 TTACAGTCATTCTGCATAGTAATGTGCATATATACAGGTGTTGGAACATTTATGTG -s simRat_chr6.simRat.chr6 474141 56 + 647215 TTTTTATAATTCACCTTAGTGGTGTACATATGTGCAGGTGTGAGGACATACATGGA - -a -s simMouse_chr6.simMouse.chr6 464398 18 + 636262 GCTACATAAATATCTGTA -s Anc0.Anc0refChr3 85800 18 + 222631 ACTAAATATGTATCTGCA -s Anc1.Anc1refChr6 118132 18 + 197743 ACTAAATATGTATCTGCA -s Anc2.Anc2refChr13 93301 18 + 96486 ACTAAATATGTATCTGCA -s mr.mrrefChr3 20268 18 + 181027 GCTACATAAATATCTGTA -s simCow_chr6.simCow.chr6 449658 18 + 602619 ATTAAATAATTATCTGCA -s simDog_chr6.simDog.chr6 442573 18 + 593897 ACTAAATATGTATCAGCT -s simHuman_chr6.simHuman.chr6 450269 18 + 601863 ACTAAATAGGTATCTGCA -s simRat_chr6.simRat.chr6 474198 18 + 647215 GCTAGATAAATATCTGTA - -a -s simMouse_chr6.simMouse.chr6 464416 3 + 636262 CAT -s Anc0.Anc0refChr3 85821 3 + 222631 CAT -s Anc1.Anc1refChr6 118153 3 + 197743 CAT -s Anc2.Anc2refChr13 93322 3 + 96486 CAT -s mr.mrrefChr3 20289 3 + 181027 CAT -s simCow_chr6.simCow.chr6 449679 3 + 602619 CAT -s simDog_chr6.simDog.chr6 442594 3 + 593897 CAT -s simHuman_chr6.simHuman.chr6 450290 3 + 601863 CAT -s simRat_chr6.simRat.chr6 474219 3 + 647215 CAT - -a -s simMouse_chr6.simMouse.chr6 464419 11 + 636262 TGTTGACAGAT -s Anc0.Anc0refChr3 85831 11 + 222631 TACTGACAGAT -s Anc1.Anc1refChr6 118163 11 + 197743 TACTGACAGAT -s Anc2.Anc2refChr13 93332 11 + 96486 TACTGACAGAT -s mr.mrrefChr3 20292 11 + 181027 TGTTGACAGAT -s simCow_chr6.simCow.chr6 449689 11 + 602619 TACTGACAGAT -s simDog_chr6.simDog.chr6 442604 11 + 593897 TACTGACAGAT -s simHuman_chr6.simHuman.chr6 450300 11 + 601863 TACTGACAGAT -s simRat_chr6.simRat.chr6 474222 11 + 647215 CGTTGACAGAT - -a -s simMouse_chr6.simMouse.chr6 464430 22 + 636262 AGGAGCTATAATATCTTGTTAA -s Anc0.Anc0refChr3 85842 19 + 222631 A---GCTAGAATATGTTTTTGT -s Anc1.Anc1refChr6 118174 19 + 197743 A---GCTAGAATATGTTTTTGT -s Anc2.Anc2refChr13 93343 19 + 96486 A---GCTAGAATAAGTTTTTGT -s mr.mrrefChr3 20303 22 + 181027 AGGAGCTATAATATCTTGTTAA -s simCow_chr6.simCow.chr6 449720 19 + 602619 A---GCTAGAATGACTTTTTGT -s simDog_chr6.simDog.chr6 442615 19 + 593897 T---GCTAAAACAAGTTCTTGT -s simHuman_chr6.simHuman.chr6 450311 19 + 601863 A---GCTAGAATATTTTTTTTT -s simRat_chr6.simRat.chr6 474233 22 + 647215 AGAAGCTACAAGATCTTGCTGA - -a -s simMouse_chr6.simMouse.chr6 464452 12 + 636262 GAAAACTTCTAT -s Anc0.Anc0refChr3 85861 12 + 222631 TGAGCTAAATAT -s Anc1.Anc1refChr6 118193 12 + 197743 TGAGCTAAATAT -s Anc2.Anc2refChr13 93362 12 + 96486 TGAGCTAAACAT -s mr.mrrefChr3 20325 12 + 181027 GAAAACTTCTAT -s simCow_chr6.simCow.chr6 449739 12 + 602619 AGAGCTAAACAT -s simDog_chr6.simDog.chr6 442634 12 + 593897 TGAGGTAAACAT -s simHuman_chr6.simHuman.chr6 450330 12 + 601863 TGGGCTCATTAT -s simRat_chr6.simRat.chr6 474261 12 + 647215 GAAAATGTCTAC - -a -s simMouse_chr6.simMouse.chr6 464464 17 + 636262 TCACAAGCTCCTTAGAT -s Anc0.Anc0refChr3 85873 17 + 222631 GGGCCAGCTTGCCAACT -s Anc1.Anc1refChr6 118205 17 + 197743 GGGCCAGCTTGCCAACT -s Anc2.Anc2refChr13 93400 17 + 96486 GGGCCAGCTTGCCAACT -s mr.mrrefChr3 20337 17 + 181027 TCACAAGCTCCTTAGAT -s simCow_chr6.simCow.chr6 449777 17 + 602619 GAGCCAATTTACCAACT -s simDog_chr6.simDog.chr6 442672 17 + 593897 GGGCCAGCTTGCCAACT -s simHuman_chr6.simHuman.chr6 450342 17 + 601863 GGGCCACCATGCCAACT -s simRat_chr6.simRat.chr6 474273 17 + 647215 TCTCAAGCTCATTAGTT - -a -s simMouse_chr6.simMouse.chr6 464481 7 + 636262 CTACTTA -s Anc0.Anc0refChr3 85893 3 + 222631 ---C-TA -s Anc1.Anc1refChr6 118225 6 + 197743 CTAC-TA -s Anc2.Anc2refChr13 93420 3 + 96486 ---C-TA -s mr.mrrefChr3 20354 7 + 181027 CTACTTA -s simCow_chr6.simCow.chr6 449797 3 + 602619 ---C-TA -s simDog_chr6.simDog.chr6 442692 3 + 593897 ---T-TA -s simHuman_chr6.simHuman.chr6 450362 6 + 601863 CTAC-TA -s simRat_chr6.simRat.chr6 474290 7 + 647215 CTACTTA - -a -s simMouse_chr6.simMouse.chr6 464488 20 + 636262 GTCTTTATGACTTTCCAGCC -s Anc0.Anc0refChr3 85896 20 + 222631 GTCTTTATTTCTTTCTGGCC -s Anc1.Anc1refChr6 118231 20 + 197743 GTCTTTATTTCTTTCTGGCC -s Anc2.Anc2refChr13 93423 20 + 96486 GTCTTTATTTCTTCCTGGTC -s mr.mrrefChr3 20361 20 + 181027 GTCTTTATGACTTTCCAGCC -s simCow_chr6.simCow.chr6 449800 18 + 602619 GTCTTT--TTTTTCCTGGTT -s simDog_chr6.simDog.chr6 442695 20 + 593897 GTCTTTATTTCTTCCTGTTC -s simHuman_chr6.simHuman.chr6 450368 20 + 601863 GTCCTTATTTCTTTCTGGCC -s simRat_chr6.simRat.chr6 474298 20 + 647215 GCCTTTATGTCTTCCTGGCC - -a -s simMouse_chr6.simMouse.chr6 464508 2 + 636262 TT -s Anc0.Anc0refChr3 85923 2 + 222631 TA -s Anc1.Anc1refChr6 118258 2 + 197743 TA -s Anc2.Anc2refChr13 93450 2 + 96486 TA -s mr.mrrefChr3 20381 2 + 181027 TT -s simCow_chr6.simCow.chr6 449825 2 + 602619 TA -s simDog_chr6.simDog.chr6 442722 2 + 593897 TG -s simHuman_chr6.simHuman.chr6 450395 2 + 601863 TA -s simRat_chr6.simRat.chr6 474318 2 + 647215 TT - -a -s simMouse_chr6.simMouse.chr6 464510 37 + 636262 CCTATTCCAAATGTAAATTGATTTGAACTAGGCAACA -s Anc0.Anc0refChr3 85925 23 + 222631 TTTTTTATAAATGTATA--------------GCAACA -s Anc1.Anc1refChr6 118260 23 + 197743 TTTTTTATAAATGTATA--------------GCAACA -s Anc2.Anc2refChr13 93452 23 + 96486 TTTTTTATTAATGTATA--------------GCAACA -s mr.mrrefChr3 20383 37 + 181027 CCTATTCCAAATGTAAATTGATTTGAACTAGGCAACA -s simCow_chr6.simCow.chr6 449827 23 + 602619 TTTTTTACTAATGTATA--------------GTAATA -s simDog_chr6.simDog.chr6 442724 23 + 593897 TTTTTCGTTAATGTATA--------------GCAACA -s simHuman_chr6.simHuman.chr6 450397 23 + 601863 TTTTTTATAAATGTATA--------------GCAACA -s simRat_chr6.simRat.chr6 474334 37 + 647215 CCTTTTCCAAATGTATATTGACTTGAACTAGATGATG - -a -s simMouse_chr6.simMouse.chr6 464547 3 + 636262 GGG -s Anc0.Anc0refChr3 85948 3 + 222631 GTA -s Anc1.Anc1refChr6 118283 3 + 197743 GTA -s Anc2.Anc2refChr13 93475 3 + 96486 GTA -s mr.mrrefChr3 20420 3 + 181027 GGG -s simCow_chr6.simCow.chr6 449850 3 + 602619 GTA -s simDog_chr6.simDog.chr6 442749 3 + 593897 GGA -s simHuman_chr6.simHuman.chr6 450420 3 + 601863 GTA -s simRat_chr6.simRat.chr6 474371 3 + 647215 GGG - -a -s simMouse_chr6.simMouse.chr6 464550 11 + 636262 TCACCTAAAAT -s Anc0.Anc0refChr3 85955 11 + 222631 TCTCTTGAACT -s Anc1.Anc1refChr6 118290 11 + 197743 TCTCTTGAACT -s Anc2.Anc2refChr13 93482 11 + 96486 TCTATTGAACT -s mr.mrrefChr3 20423 11 + 181027 TCACCTAAAAT -s simCow_chr6.simCow.chr6 449857 11 + 602619 TCTAATAAACT -s simDog_chr6.simDog.chr6 442756 11 + 593897 TCTATTGAACT -s simHuman_chr6.simHuman.chr6 450427 11 + 601863 TCTCTTGAACC -s simRat_chr6.simRat.chr6 474374 11 + 647215 TCAACTAAAAT - -a -s simMouse_chr6.simMouse.chr6 464561 141 + 636262 ATAACCTGGACACTATATTATGTCACCCAACTAAACAGAAGGCAGACTTCCTATTTCACCCAGATGTGCACTATGAGTACTATCAATGGTACAAATACAGTCAGCATGACACTGAATTACCACAATGGTAGTGAGGGAGAA -s Anc0.Anc0refChr3 85966 23 + 222631 AGAAGTTGTGTCA----------------------------------------------------------------------------------------------------------------------CAAGGGCAAA -s Anc1.Anc1refChr6 118301 23 + 197743 AGAAGTTGTGTCA----------------------------------------------------------------------------------------------------------------------CAAGGGCAAA -s Anc2.Anc2refChr13 93493 23 + 96486 AGAGGTTTTGTCA----------------------------------------------------------------------------------------------------------------------CAAGGGCAAA -s mr.mrrefChr3 20434 23 + 181027 ATAACCTGGACAC----------------------------------------------------------------------------------------------------------------------TGAGGGAGAA -s simCow_chr6.simCow.chr6 449868 23 + 602619 AAAGGTTTTGTCA----------------------------------------------------------------------------------------------------------------------CAAGGGCAAA -s simDog_chr6.simDog.chr6 442767 23 + 593897 AGAGGCTTTGTCA----------------------------------------------------------------------------------------------------------------------CAAGGGCAAA -s simHuman_chr6.simHuman.chr6 450438 23 + 601863 AGAAGTTGTGTCA----------------------------------------------------------------------------------------------------------------------CAAGAGCAAA -s simRat_chr6.simRat.chr6 474391 23 + 647215 AAAACCTGGACAC----------------------------------------------------------------------------------------------------------------------TGAGGGAGAA - -a -s simMouse_chr6.simMouse.chr6 464702 4 + 636262 CCAC -s Anc0.Anc0refChr3 85993 4 + 222631 CCAT -s Anc1.Anc1refChr6 118328 4 + 197743 CCAT -s Anc2.Anc2refChr13 93520 4 + 96486 CCAT -s mr.mrrefChr3 20457 4 + 181027 CCAC -s simCow_chr6.simCow.chr6 449895 4 + 602619 CAAT -s simDog_chr6.simDog.chr6 442794 4 + 593897 CCAT -s simHuman_chr6.simHuman.chr6 450465 4 + 601863 CCAT -s simRat_chr6.simRat.chr6 474414 4 + 647215 CCTC - -a -s simMouse_chr6.simMouse.chr6 464706 14 + 636262 ATGGTCTTTCCCGT -s Anc0.Anc0refChr3 85997 14 + 222631 GTTGTCTCTCTCGT -s Anc1.Anc1refChr6 118332 14 + 197743 GTTGTCTCTCTCGT -s Anc2.Anc2refChr13 93524 14 + 96486 GTTGCCCCTCTCTT -s mr.mrrefChr3 20461 14 + 181027 ATGGTCTTTCCCGT -s simCow_chr6.simCow.chr6 449899 4 + 602619 TATG---------- -s simDog_chr6.simDog.chr6 442798 14 + 593897 GTTGCCCCTCTCTT -s simHuman_chr6.simHuman.chr6 450469 14 + 601863 GTTGTCTCCCTCGT -s simRat_chr6.simRat.chr6 474420 14 + 647215 ATGACATTTCCTGT - -a -s simMouse_chr6.simMouse.chr6 464720 41 + 636262 GTTAATTGTCTTGGATGGAAAGCACGGGATTCCTGAATTAT -s Anc0.Anc0refChr3 86180 26 + 222631 GTTGATGGTCTTGGATGCCACTCAC-----T---------- -s Anc1.Anc1refChr6 118515 26 + 197743 GTTGATGGTCTTGGATGCCACTCAC-----T---------- -s Anc2.Anc2refChr13 93707 26 + 96486 GTTGATGGTCTTGGATGCCACTGGC-----T---------- -s mr.mrrefChr3 20475 31 + 181027 GTTAATTGTCTTGGATGGAAAGCACTGGATT---------- -s simDog_chr6.simDog.chr6 443014 26 + 593897 GTTGATGGTCTTGGATGCCACTGGC-----T---------- -s simHuman_chr6.simHuman.chr6 450710 26 + 601863 GTTCATAGTCCTGGACACCACTCAC-----T---------- -s simRat_chr6.simRat.chr6 474434 31 + 647215 GTTAATTGTCTTGGATGGAAAGCACTGGATC---------- - -a -s simMouse_chr6.simMouse.chr6 464761 68 + 636262 AGTTCATTAGCACTCCAAACCCAATGTTGTTCAGGCAGCATATCAAGACTCTTGCTGAACAACTTTCA -s Anc0.Anc0refChr3 86206 55 + 222631 AGTTCATTA-AGCTCCAGACTCAGCATTGTTCA--TAGTATTTCAA-ATTC---------AATTTTTG -s Anc1.Anc1refChr6 118541 58 + 197743 AGTTCATTAGAGCTCCAGACTCAGCATTGTTCAGGTAGTATTTCAA-ATTC---------AATTTTTG -s Anc2.Anc2refChr13 93733 55 + 96486 AGTTTGTTA-AGCTCCACATTCAGCATTGATCA--TGGTATGTCAA-ATGC---------ACTCTTTG -s mr.mrrefChr3 20506 59 + 181027 AGTTCATTAGAACTCCAGACTCAATGTTGTTCAGGCAGCATTTCAAGACTC---------AACTTTCA -s simDog_chr6.simDog.chr6 443051 55 + 593897 AGTTTGTTA-AGCTCCACATTCAGCATTGATCA--TGGTATGTCAA-ATGC---------ACTCTTTG -s simHuman_chr6.simHuman.chr6 450736 58 + 601863 AGTCCATTAGAGTTCCAGACTCAGCACTATTCAGGTAATATTTCAA-ATTC---------AATTTTTG -s simRat_chr6.simRat.chr6 474465 50 + 647215 ---------GAACTCCAGGCTCAATGTTGTCGAGTCAGCATTTTAAGACTC---------AACTTTCA - -a -s simMouse_chr6.simMouse.chr6 464829 52 + 636262 ATATATTACAATGTTTAACAGACAGTTGGTATTAGAGGATGTGACTGCTAAG -s Anc0.Anc0refChr3 86275 52 + 222631 ATATGTTATGATACTTCACATACAGTTGGTACTGGAGGTAGTGACTACTAGG -s Anc1.Anc1refChr6 118613 52 + 197743 ATATGTTATGATACTTCACATACAGTTGGTACTGGAGGTAGTGACTACTAGG -s Anc2.Anc2refChr13 93802 52 + 96486 ATATGTTCTGACAATCCACATACAGTTGGTACTATAGGTAGTGACTATTAGG -s mr.mrrefChr3 20565 52 + 181027 ATATATTACGATACTTAACAGACAGTTGGTATTGGAGGATGTGACTGCTAGG -s simDog_chr6.simDog.chr6 443120 52 + 593897 ATATGTTCTGACAATCCACATACAGTTGGTACTATAGGTAGTGACTATTAGG -s simHuman_chr6.simHuman.chr6 450808 52 + 601863 ATATGTTAAGATACTTCACATACAGTTAGTACTGGAGGTGATGACTACTAGG -s simRat_chr6.simRat.chr6 474515 52 + 647215 ATATATTAGGATACTTAACAGACAGTTGGTATTGGAGGCTGTGACTGTCAGG - -a -s simMouse_chr6.simMouse.chr6 464881 45 + 636262 GTTTACCACATAGATCAACACCAGCCAGTGGATGCCTTAACTTAT -s Anc0.Anc0refChr3 86328 35 + 222631 CTTGACCACATAGATCAATACCA-----TGGATACTTAC-----T -s Anc1.Anc1refChr6 118666 45 + 197743 CTTGACCACATAGATCAATACCAACCAGTGGATACTTACGCTTGT -s Anc2.Anc2refChr13 93855 35 + 96486 CTTGACCACATAGATCAATACCA-----TTGATACTTAC-----T -s mr.mrrefChr3 20617 45 + 181027 GTTTACCACATAGATCAATACCAACCAGTGGATACCTTAGCTTGT -s simDog_chr6.simDog.chr6 443173 35 + 593897 CTTGACCACATAGATCAATACCA-----TTGATACTTAC-----T -s simHuman_chr6.simHuman.chr6 450861 45 + 601863 ATTCACCACATAGATCAATACCAACCAGTGGCTACTTACGCTTGT -s simRat_chr6.simRat.chr6 474567 45 + 647215 GTTTAGCACATAGATCAATACCAACCAGTGGGTACCTTAGCTTGT - -a -s simMouse_chr6.simMouse.chr6 464926 13 + 636262 GGCATCATCCAGC -s Anc0.Anc0refChr3 86364 13 + 222631 AGAATCATCTAGT -s Anc1.Anc1refChr6 118712 13 + 197743 AGAATCATCTAGT -s Anc2.Anc2refChr13 93891 13 + 96486 AGAGTCATCCAAT -s mr.mrrefChr3 20662 13 + 181027 AGCATCATCTAGT -s simDog_chr6.simDog.chr6 443209 13 + 593897 AGAGTCATCCAAT -s simHuman_chr6.simHuman.chr6 450907 13 + 601863 AGAATCATCTAGT -s simRat_chr6.simRat.chr6 474612 13 + 647215 AGCATCGTCTAGT - -a -s simMouse_chr6.simMouse.chr6 464939 95 + 636262 CCAAATTGTATGTTAGTCAGTTCAAGAACCTCCAAGCACTAATGTAGCCACTTACTCGAACACTAGATAATAGCCATTATCTTTAGAGTACCACT -s Anc0.Anc0refChr3 86384 95 + 222631 ACAAATTGTGCTTTAGTAAGTTCAAGAACCTTCAATTATTAACATAGCAGATTACTCAATCACCACACAATAGACCTTATTTATAGAGTTCTATT -s Anc1.Anc1refChr6 118732 95 + 197743 ACAAATTGTGCTTTAGTAAGTTCAAGAACCTTCAATTATTAACATAGCAGATTACTCAATCACCACACAATAGACCTTATTTATAGAGTTCTATT -s Anc2.Anc2refChr13 93911 95 + 96486 ACAAATTGCGCTTTAGCAAGTTCAAGAACTTTCAATTATTAATATAGCAGATTACTCAATCACCACACAATAGACCTTATTCATAAAGTTCTATT -s mr.mrrefChr3 20675 95 + 181027 ACAAATTGTATGTTAGTCAGTTCAAGAACCTCCAAGCACTAACATAGCCACTTACTCAAACACTAGATAATAGCCATTATCTTTAGAGTACTACT -s simCow_chr6.simCow.chr6 449910 92 + 602619 GCAAATT---CATTAGCAAGTTCAAGAACGTTCAGTTATTAGGATAGCAAATTTCCCAATCACTCCACAATAGACCTTATCAATGAAGTATTTTT -s simDog_chr6.simDog.chr6 443222 92 + 593897 ACAAATTGCGCTTAGGCAAGCTCAAGAGCTCTTAATTATTAATATAGCAGATTACTCAATCACCACATAAT---CCTTAATCATAAAGTTCTATT -s simHuman_chr6.simHuman.chr6 450935 95 + 601863 ACAAATTGTGCTTTAATAAGTTCAAGAACCTTCAATGATTAACATAGCAGATTACTCAATCACCACACAATAGTCCTTATTTATAGAGTGCTAAT -s simRat_chr6.simRat.chr6 474625 95 + 647215 ACAAATTGTATGATAGTCAGTTCAAGAATTTCCATGTACTAACATAGCCACTTACTCAAACACTAGATAATAGCCATTATCTTTAGAGTACTACT - -a -s simMouse_chr6.simMouse.chr6 465034 76 + 636262 CCCTTGCTCACACCTGAATGGTAAGAGATCACTGAAAAGCACTGAAAAGTTATTATAATCACAGATGAGCTATCTT -s Anc0.Anc0refChr3 86483 63 + 222631 CCC---CTCACACCAGTTGGATTAGAGATTGCTG----------AAAAGTTGTTATAATATCAGTTGAGTTATCTT -s Anc1.Anc1refChr6 118831 66 + 197743 CCCTTGCTCACACCAGTTGGATTAGAGATTGCTG----------AAAAGTTGTTATAATATCAGTTGAGTTATCTT -s Anc2.Anc2refChr13 94010 63 + 96486 CCC---CTTGCACCAGTTGGATTAGAGATTGCAG----------AAAAGTTGTTATTATATCAGTTGAGTTATCTT -s mr.mrrefChr3 20770 66 + 181027 CCCTTGCTCACACCTGAATGGTAAGAGATCACTG----------AAAAGTTATTATAATAACAGATGAGTTATCTT -s simCow_chr6.simCow.chr6 450006 48 + 602619 ATT---CA----------GGATTAGAGATTCCAG----------ATAAGTTGTCATCAT-----TTGAGTTATCTT -s simDog_chr6.simDog.chr6 443318 63 + 593897 CCC---CTTGCACCAGTTGGATTAGAGATTGCAG----------AAAAGTTGTTATTATATCAGTTGAGTTGTCTT -s simHuman_chr6.simHuman.chr6 451034 66 + 601863 CCATTGCTCACTCCAGTTGGATCAGAAATTGCTG----------AAAAGTTGTTATAATATCAGTTCAGTCATCTT -s simRat_chr6.simRat.chr6 474720 66 + 647215 CCCTTGATCACACCTTAATGGTTAGAGATCACCG----------AGTAGTTATTATATTAACAGGTGAGTTATCTT - -a -s simMouse_chr6.simMouse.chr6 465110 15 + 636262 CCCCAATAATTGGTT -s Anc0.Anc0refChr3 86546 10 + 222631 CCCAAGTTA-----T -s Anc1.Anc1refChr6 118897 10 + 197743 CCCAAGTTA-----T -s Anc2.Anc2refChr13 94073 10 + 96486 CCCAAGTTA-----T -s mr.mrrefChr3 20836 15 + 181027 CCCAAGTAATTGGTT -s simCow_chr6.simCow.chr6 450054 4 + 602619 ACCG----------- -s simDog_chr6.simDog.chr6 443408 10 + 593897 CTCAAGTTA-----T -s simHuman_chr6.simHuman.chr6 451100 10 + 601863 CCCAAGTTA-----C -s simRat_chr6.simRat.chr6 474786 15 + 647215 CCCAAGTAGTTGGTT - -a -s simMouse_chr6.simMouse.chr6 465125 20 + 636262 TCTCTTGGTGACTGTGTTGT -s Anc0.Anc0refChr3 86556 19 + 222631 TCCCTA-GTAAATGTGTTCT -s Anc1.Anc1refChr6 118907 20 + 197743 TCCCTAGGTAAATGTGTTCT -s Anc2.Anc2refChr13 94083 19 + 96486 TCCCTA-GTAAATGTGTTCT -s mr.mrrefChr3 20851 20 + 181027 TCTCTTGGTAACTGTGTTGT -s simCow_chr6.simCow.chr6 450058 18 + 602619 -CCCTA-GGAAATGTGTTCT -s simDog_chr6.simDog.chr6 443420 19 + 593897 TCCCTA-GTAAATGTGTTCT -s simHuman_chr6.simHuman.chr6 451110 20 + 601863 TCCCTAGTAAAATGTGTTCT -s simRat_chr6.simRat.chr6 474801 20 + 647215 CCTCTTAGTAACTGTGTTGT - -a -s simMouse_chr6.simMouse.chr6 465145 90 + 636262 GAACAGTCATTTTCTTCCAGTCAGTGGGATGAGTATTTTGGTTGTAACAGTACAACTGATATGAGTTCTTGTGCCATTAACAATGCATTC -s Anc0.Anc0refChr3 86575 45 + 222631 --------------------------------------------TGAAAGTACAACTACTGTAAGTACTTGTGCAATATCC-TTGCATTC -s Anc1.Anc1refChr6 118927 89 + 197743 GGGCACTTGTCTTCTCCCAGTTAATAGGGCGAGCATTTGGGATATGAAAGTACAACTACTGTAAGTACTTGTGCAATATCC-TTGCATTC -s Anc2.Anc2refChr13 94102 45 + 96486 --------------------------------------------TGAAAGTACAGCTACTGTAAGTACTTGTGCAATATCC-TTTCATTC -s mr.mrrefChr3 20871 90 + 181027 GAACAGTTATTTTCTTCCAGTCAGTGGGATGAGCATTTTGGTTGTGACAGTACAACTGATATGAGTTCTTGTGCCATTAACAATGCATTC -s simCow_chr6.simCow.chr6 450127 40 + 602619 --------------------------------------------TGAAAGGATAGGCAC---AAGTACTTG--CAATAGCT-GTACTGTC -s simDog_chr6.simDog.chr6 443439 45 + 593897 --------------------------------------------TTACAGTACAGCTTCTGTGAGTACTTGTGCAATATCC-TTTCATTC -s simHuman_chr6.simHuman.chr6 451131 89 + 601863 GGGCACTTGTCTTCTCCCAGTTAATAGGGCGAGCATTTGGGATATGAAAGTACAACTACTGAAAAGACCTGTGCTATGTTC-TTGCATTC -s simRat_chr6.simRat.chr6 474821 90 + 647215 GAACAGTTATTTACTTCCAGTCAGTGGGATGAGCGTTTTGGTAGTGACAGTACAACTGATATGAGTTCTTGTGCCATTAACAATACATTC - -a -s simMouse_chr6.simMouse.chr6 465235 4 + 636262 ACTT -s Anc0.Anc0refChr3 86620 4 + 222631 ACTT -s Anc1.Anc1refChr6 119016 4 + 197743 ACTT -s Anc2.Anc2refChr13 94147 4 + 96486 ACTT -s mr.mrrefChr3 20961 4 + 181027 ACTT -s simCow_chr6.simCow.chr6 450167 4 + 602619 ACAT -s simDog_chr6.simDog.chr6 443484 4 + 593897 ACTT -s simHuman_chr6.simHuman.chr6 451220 4 + 601863 ACTT -s simRat_chr6.simRat.chr6 474913 4 + 647215 ACTT - -a -s simMouse_chr6.simMouse.chr6 465239 85 + 636262 GAGGTTGTGCAGCACTGCTGAATCTAATAGTGTCGTGTTGAAGTCAGTAGCATGCATTGGGCTAATGACATGTGATATTGCTGCT -s Anc0.Anc0refChr3 86624 83 + 222631 GAGGTCGTGCAGCATTTTTTAATTTGAAGATGTTATTTTGAAGTCA--AGCAGGCAATGTGCTAATGTTGTGTCACATTATTACT -s Anc1.Anc1refChr6 119020 83 + 197743 GAGGTCGTGCAGCATTTTTTAATTTGAAGATGTTATTTTGAAGTCA--AGCAGGCAATGTGCTAATGTTGTGTCACATTATTACT -s Anc2.Anc2refChr13 94151 83 + 96486 GGGCTCGTGCAGCATTTTTTAATTTGAAGATGTTATTTTGAAGTCA--AGCAGGCAATGTGCTAATGTTGTGTCACATTATTACT -s mr.mrrefChr3 20965 85 + 181027 GAGGTTGTGCAGCACTGTTTAATCTAATAGTGTTGTGTTGAAGTCAGTAGCATGCATTGGGCTAATGACATGTGATATTGCTACT -s simCow_chr6.simCow.chr6 450176 72 + 602619 GTGCTCGT-----CTTACTGACTGGGAAAAAACAACT-----GTCA--AGCACATATCGTGCTGATGTT-TGTCACATCATTCCT -s simDog_chr6.simDog.chr6 443488 83 + 593897 GGGCTCATGCAGCAATTTTTTATTTGAGGATGTTATTTTGAAGTCA--AGCAGGCAATGTGCTATCAATGTGTCACATTATTACT -s simHuman_chr6.simHuman.chr6 451224 82 + 601863 GAGGTCGTGTAGGATTCTTTAATTCGAACATGTTATTTTGAAGTCA--AGCAGGCAATATGTTAATGTTGTG-ACCATTAGTACT -s simRat_chr6.simRat.chr6 474917 85 + 647215 GAGTTTGAGCAGCACTGTTTAATCAAATAGTGTTGTGTTGAAGTCAGTAGCATGCGTTGGGCTAATGAGGTGTGATGTTGCTACT - -a -s simMouse_chr6.simMouse.chr6 465324 53 + 636262 TGCTTAAGGATGGCAGTTACAGGTTGCTACTTGTTAAGGACCACATAATAGAA -s Anc0.Anc0refChr3 86708 53 + 222631 TGCTTAAGAATGTGAGTAACCAGGTATTACTTTTCCAGGGCCACATCATAACA -s Anc1.Anc1refChr6 119104 53 + 197743 TGCTTAAGAATGTGAGTAACCAGGTATTACTTTTCCAGGGCCACATCATAACA -s Anc2.Anc2refChr13 94235 53 + 96486 TGCTTAAAAATGTGAGTAACCAGGTATTACTTTTCCATGGCCACATCATAACA -s mr.mrrefChr3 21050 53 + 181027 TGCTTAAGGATGTCAGTAACAAGTTGCTACTTGTTAAGGACCACATAATAAAA -s simCow_chr6.simCow.chr6 450249 53 + 602619 TGCTTAAAAAAGTGAGTAACCAGGTACTATTTTTCCCTGGTCACATCATACCA -s simDog_chr6.simDog.chr6 443572 52 + 593897 TGATTAAAAATGTGTGCAAC-AGTTATTACCTGCCCATATCCACATTATAATA -s simHuman_chr6.simHuman.chr6 451307 53 + 601863 TGCTTAAGAATGTGAGTAACCAGGTAATACTTTTCCAGGGCCACATCATAACA -s simRat_chr6.simRat.chr6 475002 53 + 647215 TGCTTAGGGACATCAGTAATGAGTTGGTACTTGTTAAGGACCTCATGACAAAT - -a -s simMouse_chr6.simMouse.chr6 465377 7 + 636262 CAGCCCA -s Anc0.Anc0refChr3 86761 7 + 222631 CAGCCTA -s Anc1.Anc1refChr6 119157 7 + 197743 CAGCCTA -s Anc2.Anc2refChr13 94288 7 + 96486 CAGCCTA -s mr.mrrefChr3 21103 7 + 181027 CAGCCTA -s simCow_chr6.simCow.chr6 450581 7 + 602619 CAGCCTA -s simDog_chr6.simDog.chr6 443624 7 + 593897 CAGCATA -s simHuman_chr6.simHuman.chr6 451360 7 + 601863 CAGCCTA -s simRat_chr6.simRat.chr6 475055 7 + 647215 CAGCCTA - -a -s simMouse_chr6.simMouse.chr6 465384 40 + 636262 CTGGCATCAAACTTTTTAACACCATGATTCTTGGAGAGCC -s Anc0.Anc0refChr3 86776 40 + 222631 CTACAATCAAAGACTTTCACACCATGAGTCTTGCTAATCT -s Anc1.Anc1refChr6 119172 40 + 197743 CTACAATCAAAGACTTTCACACCATGAGTCTTGCTAATCT -s Anc2.Anc2refChr13 94303 40 + 96486 CTGCAGTCAAAGACTTTCACGTCATGGGTCTTGCTAATCT -s mr.mrrefChr3 21118 40 + 181027 CTAGCATCAAACTTTTTAACACCATGATTCTTGGAGAGCC -s simCow_chr6.simCow.chr6 450596 39 + 602619 CTCCAGTTAAACTCTTTCATGACATGGGTCTTGCTAATC- -s simDog_chr6.simDog.chr6 443639 40 + 593897 CTGTGGTCAAAGACATTCACGTGATGGGTAGTGCTAATCT -s simHuman_chr6.simHuman.chr6 451375 40 + 601863 CCACAATCAAATGCTTTCACACCCTGAGCCTTGCTAATCT -s simRat_chr6.simRat.chr6 475070 40 + 647215 CTAGTATCAAACTTTTTAACACCATGAATCTTGGAGAGCC - -a -s simMouse_chr6.simMouse.chr6 465424 28 + 636262 CAAATTAATACTAATGCAAGGGATCCGT -s Anc0.Anc0refChr3 86817 28 + 222631 CATTATAATCCTAATGTGAGGGAACCAA -s Anc1.Anc1refChr6 119213 28 + 197743 CATTATAATCCTAATGTGAGGGAACCAA -s Anc2.Anc2refChr13 94344 28 + 96486 CATTATAATCCTAATGTGACGGAACCCA -s mr.mrrefChr3 21158 28 + 181027 CAAATTAATACTAATGTGAGGGATCCAA -s simCow_chr6.simCow.chr6 450636 27 + 602619 CATAATA-TCCTTTTACTGCAGTAACCA -s simDog_chr6.simDog.chr6 443680 28 + 593897 CATTTTTAACCTAATGTGACGGAACCCA -s simHuman_chr6.simHuman.chr6 451416 28 + 601863 CATGATAATCATAATGTGAGGGACCCAA -s simRat_chr6.simRat.chr6 475110 28 + 647215 CAAATTAACACTAATGTGAGAGATCCAA - -a -s simMouse_chr6.simMouse.chr6 465452 102 + 636262 TTGAAGATCCAACAGTCAATGGGACCTGAGGTGGCTCAGGTCCATACGGGAGAAATACATGTCAATTAGAGCCACATGCTCTTGGCATTTAATTTAACTATG -s Anc0.Anc0refChr3 86845 83 + 222631 C---AGATTCA----------------GGGGTAGCCCAGGTCCATGGGGGAGAAACTCATATGGATTTGGGCAACATGCTATTGGCTATTAATTTATCTATG -s Anc1.Anc1refChr6 119241 83 + 197743 C---AGATTCA----------------GGGGTAGCCCAGGTCCATGGGGGAGAAACTCATATGGATTTGGGCAACATGCTATTGGCTATTAATTTATCTATG -s Anc2.Anc2refChr13 94372 83 + 96486 C---ACATTTG----------------GGGGTAGCCCAGGTCTATGGGGGAAGAACTCATATGGCTTTGGGCAACATGATATTGGCTAGTAATTTGTCTATG -s mr.mrrefChr3 21186 102 + 181027 TTGAAGATCCAACAGTCAATGGGACCTGAGGTGGCTCAGGTCCATACGGGAGAAATACATGTGGATTAGAGCCACATGCTCTTGGCATTTAATTTAACTATG -s simCow_chr6.simCow.chr6 450664 81 + 602619 C---CAATGTG----------------GGGGTAACCCAGGCCTATGGGAG--GAACTCACATGGCTTTGGGCAACACAATATTGGCTAGTCATTTGACTATG -s simDog_chr6.simDog.chr6 443708 83 + 593897 C---ACAATTG----------------GGAGTAGCCCAGGTCTATGGGGGAAGAACTCGTGTGGCTTTGGTCAAGATGATATTGGCTAGTAATTTGTGTATG -s simHuman_chr6.simHuman.chr6 451444 80 + 601863 C---AGATTCA----------------GGGGTAGGCGAGGTCCATGAGGGAGAAACTAATATGGATTTGGGTAACATGCTGTTGG---TTAATTTAGCTATG -s simRat_chr6.simRat.chr6 475138 102 + 647215 TGTAAGCTCCAACAGCAAATGGGACGTGAGGTGGCTCAGGTCTATAGGAGAGAAATACATGTGGATTAGAGCCACATGCTCTTGGCTTTTAATTTAACTATG - -a -s simMouse_chr6.simMouse.chr6 465554 28 + 636262 CACAATCCCTTATTGTGAAAGTGTTAGA -s Anc0.Anc0refChr3 86948 28 + 222631 CACAATTCCTAATTGTTAAAGCCTTAGG -s Anc1.Anc1refChr6 119344 28 + 197743 CACAATTCCTAATTGTTAAAGCCTTAGG -s Anc2.Anc2refChr13 94475 28 + 96486 CACCATTCCTAACTATTAGAGCCTTAAG -s mr.mrrefChr3 21308 28 + 181027 CACAATCCCTAATTGTGAAAGCGTTAGA -s simCow_chr6.simCow.chr6 450765 28 + 602619 CACCATTCCTAAATCATTGAGCCTTAAG -s simDog_chr6.simDog.chr6 443811 28 + 593897 CACCATTCCAAACTATTAGAGCCTCAAG -s simHuman_chr6.simHuman.chr6 451544 28 + 601863 CACAAGGCTTAATTGCAAAAGCCCTAGG -s simRat_chr6.simRat.chr6 475260 28 + 647215 CGCTATCCCTAATTTTGAAAACTTTTGA - -a -s simMouse_chr6.simMouse.chr6 465582 93 + 636262 ACATTAGGTCCTATAAGGTTATACATGAGTTTTCTGTCATTATCATCAGGAGCTAGGAACCAGTCAGGGACCATAACCAGCTTTACCTCAATA -s Anc0.Anc0refChr3 86978 81 + 222631 ACAATTGGTCCTAAAAGGCCAGACATGAGCTTTCTGTCA-TATCATTAGTAGTTAGGAACTA-----------TACCCATTTTTAGATAAACA -s Anc1.Anc1refChr6 119374 81 + 197743 ACAATTGGTCCTAAAAGGCCAGACATGAGCTTTCTGTCA-TATCATTAGTAGTTAGGAACTA-----------TACCCATTTTTAGATAAACA -s Anc2.Anc2refChr13 94505 81 + 96486 ACAATTAGTCCTGAAAGACCAGACATGAGCTTTCTGTCA-TATCATTAGTAGTTAGCAACTG-----------TACCCATTTTTAGATAAACA -s mr.mrrefChr3 21336 85 + 181027 ACATTTGGTCCTATAAGGCCATACATGAGTTTTCTGTCATTATCATTAGGAGCTAGGAACCAGTC--------TAACCAGCTTTAGCTAAATA -s simCow_chr6.simCow.chr6 450795 73 + 602619 ACAATTTATCCTGCATGACTAGACATGAGCT--CTGTCA-TACCATTAGTAGTTA------C-----------TAGCCATTTTTCGATACACA -s simDog_chr6.simDog.chr6 443841 81 + 593897 ACAATTAGTCATGAAAGACCCAACATGGGCTTTCTGTCA-AATCATTAGTTGTTAGCAACTG-----------TGCCCATTGCTAGATAAACA -s simHuman_chr6.simHuman.chr6 451574 81 + 601863 GCAATTGGTACTAAAAGGCCAGACATGAGCTTTCTGTCA-TATCATTAGTAGTTAGGAACTA-----------TACCCATTTTTGGGTATACA -s simRat_chr6.simRat.chr6 475288 77 + 647215 ACATTTGGGCCTATAAGGCCATATGCGAGTTTTCCGTCATTGTCAATAGGAGCTAGGGACCAGTC----------------TTTAGCTAAATA - -a -s simMouse_chr6.simMouse.chr6 465675 83 + 636262 AAATGATGATGTGATTTGTCATGGTTTGCACCTTGAAGCAGGATCTGCCCCATGTTGTCCGACTGGGGATAAAGGATGGAGTG -s Anc0.Anc0refChr3 87060 30 + 222631 AAGTGC-----TCATTTGTCATGAGTTG------------------------------------------------TTGAGTG -s Anc1.Anc1refChr6 119456 30 + 197743 AAGTGC-----TCATTTGTCATGAGTTG------------------------------------------------TTGAGTG -s Anc2.Anc2refChr13 94587 30 + 96486 AAGTGC-----TCATTTGTAATGAGTTG------------------------------------------------TTGAGTG -s mr.mrrefChr3 21422 74 + 181027 AAGTGCTGATGTGATTTGTCATGATTTG---------GCAGGATCTGCCCCATGTTGTCCGACTGGGGATAAAGGATGGAGTG -s simCow_chr6.simCow.chr6 450869 30 + 602619 TGGTGC-----TCATCTGTAATGTGTTG------------------------------------------------TTGAGTG -s simDog_chr6.simDog.chr6 443923 30 + 593897 AAGGGT-----TCATTTGTAACAAGTTG------------------------------------------------TGGAGAG -s simHuman_chr6.simHuman.chr6 451656 30 + 601863 AAGTGC-----TAACTTGTCATGAGTTG------------------------------------------------TTGAGTG -s simRat_chr6.simRat.chr6 475366 74 + 647215 AAGTGCTGATGTGATTTGTCATGATTTG---------GCAAGATCTGCCCCATATTGTCAGACTGGGGACAAAGGATGTAGTG - -a -s simMouse_chr6.simMouse.chr6 465758 3 + 636262 CAT -s Anc0.Anc0refChr3 87090 3 + 222631 CAC -s Anc1.Anc1refChr6 119486 3 + 197743 CAC -s Anc2.Anc2refChr13 94617 3 + 96486 CAC -s mr.mrrefChr3 21496 3 + 181027 CAT -s simCow_chr6.simCow.chr6 450899 3 + 602619 CAC -s simDog_chr6.simDog.chr6 443953 3 + 593897 CAC -s simRat_chr6.simRat.chr6 475512 3 + 647215 CGT - -a -s simMouse_chr6.simMouse.chr6 465761 28 + 636262 TGAATGGTACCAGTGACATTGGAATTAC -s Anc0.Anc0refChr3 87093 28 + 222631 TGAATGCTACCACTTGTACCAAAATCAC -s Anc1.Anc1refChr6 119489 28 + 197743 TGAATGCTACCACTTGTACCAAAATCAC -s Anc2.Anc2refChr13 94621 28 + 96486 AGGGTGCTACCACTTGTACCAAAACCAC -s mr.mrrefChr3 21499 28 + 181027 TGAATGGTACCAGTGACATTGGAATTAC -s simCow_chr6.simCow.chr6 450903 28 + 602619 GAGGTTCTACCAGTACCACCAAGAACAC -s simDog_chr6.simDog.chr6 443957 28 + 593897 AGGGTGCTACCACTTGTACCAAAACCAC -s simHuman_chr6.simHuman.chr6 451686 19 + 601863 TAAACAA---------TACCAAAATCGC -s simRat_chr6.simRat.chr6 475515 28 + 647215 TGAAAGGTACCCGTGTCATTGGAATTAC - -a -s simMouse_chr6.simMouse.chr6 465789 62 + 636262 CAGGGATCCTCATAGCCAATAGACAAAGTACTACACTGTCAAAGCTATTTCTAGTTCGTCAG -s Anc0.Anc0refChr3 87121 61 + 222631 CAGGGAGACTCATAGC-AAGAGACAAAGCAATACATTGGAAAAGCCAGTTGCAGTTGGTCAG -s Anc1.Anc1refChr6 119517 61 + 197743 CAGGGAGACTCATAGC-AAGAGACAAAGCAATACATTGGAAAAGCCAGTTGCAGTTGGTCAG -s Anc2.Anc2refChr13 94649 61 + 96486 CAGGGAGACTCATAGC-AAGGGACAAAGCAATACATTGGAAAAGCCAGTTGCAGTTGGTCAG -s mr.mrrefChr3 21527 61 + 181027 CAGGGATACTCATAGC-AATAGACAAAGCACTACACTGTCAAAGCCATTTGCAGTTCGTCAG -s simCow_chr6.simCow.chr6 450938 59 + 602619 CAGGGAGACTCATACC-TTAGGACAAAGCAATACATTGGAAAGGCTTGTT--AGCTGATCAG -s simDog_chr6.simDog.chr6 443985 61 + 593897 CAGGGAAACTCATAGC-AAGGCACATAGCAAGGCATTGAAAAAGCCAGTTGCAGTTGGTTAG -s simHuman_chr6.simHuman.chr6 451705 61 + 601863 CAGGGAGACTCATAGC-CAGAGACAAAGCAGTATGTTGGAAAAGCCAGTTGCAGTTGGTCAG -s simRat_chr6.simRat.chr6 475543 55 + 647215 CAGGGATACTCATAGC-ATTGGACAAAGCAATACACTTTCAAAGCCATTTGCAGTT------ - -a -s simMouse_chr6.simMouse.chr6 465851 8 + 636262 GAACTTGA -s Anc0.Anc0refChr3 87182 8 + 222631 GAACTTGA -s Anc1.Anc1refChr6 119578 8 + 197743 GAACTTGA -s Anc2.Anc2refChr13 94710 8 + 96486 GAACTTGC -s mr.mrrefChr3 21588 8 + 181027 GAACTTGA -s simCow_chr6.simCow.chr6 450997 8 + 602619 GTACATGC -s simDog_chr6.simDog.chr6 444046 8 + 593897 GAACTTGC -s simHuman_chr6.simHuman.chr6 451769 8 + 601863 TACCCTTA -s simRat_chr6.simRat.chr6 475598 6 + 647215 --GCTTGA - -a -s simMouse_chr6.simMouse.chr6 465859 52 + 636262 CTTAATAAGTTCATCCAGTTGTACTTGCAGCACCAAGCAGTACAACCTGACT -s Anc0.Anc0refChr3 87190 51 + 222631 CTTTATGAGTTTATTCAGTTGAGGGCTCAGCACCAGCCAGTATAATCTGAC- -s Anc1.Anc1refChr6 119586 52 + 197743 CTTTATGAGTTTATTCAGTTGAGGGCTCAGCACCAGCCAGTATAATCTGACT -s Anc2.Anc2refChr13 94718 51 + 96486 TCTTATGAGTTCATTCAGTTGAGGGCTCAGCACCAGCCAGTATAATCTGAC- -s mr.mrrefChr3 21596 52 + 181027 CTTAATAAGTTTATCCAGTTGTACTTGCAGCACCAAGCAGTACAACCTGACT -s simCow_chr6.simCow.chr6 451005 44 + 602619 TTTTA-------ATTCAGTTGTGAACTCAGCACCAGCCTGTATAATGTGAA- -s simDog_chr6.simDog.chr6 444054 51 + 593897 TCTCATGAGTTCATACAGTTGAGGGCTCAGCACCAGCCAGTATAATCCGAC- -s simHuman_chr6.simHuman.chr6 451783 41 + 601863 CTTTATGAGTTTATTCAGTTGGGGGCTCAGCACTAGCCC-----------CT -s simRat_chr6.simRat.chr6 475604 52 + 647215 CTTAATAAGTTTATCCAGCTGTACTTGCAGTACCAAGCTGTACAATCTGACT - -a -s simMouse_chr6.simMouse.chr6 465911 40 + 636262 GGACTTTGCCTCTCTCCTAGATAAGACTTTTAAGGTAATA -s Anc0.Anc0refChr3 87241 39 + 222631 GGACTTTGGCTTCCTCTTAGATAACAC-TTTAAGATAATA -s Anc1.Anc1refChr6 119638 39 + 197743 GGACTTTGGCTTCCTCTTAGATAACAC-TTTAAGATAATA -s Anc2.Anc2refChr13 94769 39 + 96486 GAACTTCAGCTTCCTCTTCGATAACCC-ACTAAAATAATA -s mr.mrrefChr3 21648 40 + 181027 GGACTTTGCCTCTCTCCTAGATAAGACTTTTAAGGTAATA -s simCow_chr6.simCow.chr6 451049 39 + 602619 GATCTTTAGCTCTCTCTTAGATAACCC-CGCAGAATAATA -s simDog_chr6.simDog.chr6 444106 39 + 593897 GAACTTCAGCTTCCTCTTCACTAACCC-ACTAAAATGGTA -s simHuman_chr6.simHuman.chr6 451824 29 + 601863 GGAATTTG----------AGATAACAC-TTTAAGATAATA -s simRat_chr6.simRat.chr6 475656 40 + 647215 GGACTCTGCCTCTGCCCTAGATAAAACTTTTAAGGTAATA - -a -s simMouse_chr6.simMouse.chr6 465951 7 + 636262 GCAAAAT -s Anc0.Anc0refChr3 87280 7 + 222631 GCAGAAT -s Anc1.Anc1refChr6 119677 7 + 197743 GCAGAAT -s Anc2.Anc2refChr13 94808 7 + 96486 GCAGAGT -s mr.mrrefChr3 21688 7 + 181027 GCAAAAT -s simCow_chr6.simCow.chr6 451088 7 + 602619 GCAGCGT -s simDog_chr6.simDog.chr6 444145 7 + 593897 ATAGAGT -s simHuman_chr6.simHuman.chr6 451853 7 + 601863 GCGGAAT -s simRat_chr6.simRat.chr6 475699 7 + 647215 GCAAGAT - -a -s simMouse_chr6.simMouse.chr6 465958 6 + 636262 TTGGGT -s Anc0.Anc0refChr3 87290 6 + 222631 GTGGGT -s Anc1.Anc1refChr6 119687 6 + 197743 GTGGGT -s Anc2.Anc2refChr13 94818 6 + 96486 GTGGGC -s mr.mrrefChr3 21695 6 + 181027 TTGGGT -s simDog_chr6.simDog.chr6 444156 6 + 593897 GTGGGC -s simHuman_chr6.simHuman.chr6 451863 6 + 601863 GTAGGT -s simRat_chr6.simRat.chr6 475706 6 + 647215 TTGGGT - -a -s simMouse_chr6.simMouse.chr6 465964 37 + 636262 TTGCCTCTGTGATCACCTGGAGTACAACGTTCTGCAT -s Anc0.Anc0refChr3 87305 37 + 222631 TTCCCTCTGTGATCACTGGTAGTATGATGCTCTGCAC -s Anc1.Anc1refChr6 119702 37 + 197743 TTCCCTCTGTGATCACTGGTAGTATGATGCTCTGCAC -s Anc2.Anc2refChr13 94833 37 + 96486 TTCCCTCTTTGATCACTGGTGGTTTGATGCTCTGCAC -s mr.mrrefChr3 21701 37 + 181027 TTCCCTCTGTGATCACCTGGAGTACAACGCTCTGCAC -s simCow_chr6.simCow.chr6 451102 16 + 602619 TTTCCTCTATGATCAC--------------------- -s simDog_chr6.simDog.chr6 444171 37 + 593897 TTCCCTCTTTGATTACTGGTGGTTTGATGCTCTGCAC -s simHuman_chr6.simHuman.chr6 451878 37 + 601863 TCCCCTCTGTGATCACTGACAGCATCATGCTTTGCAC -s simRat_chr6.simRat.chr6 475712 37 + 647215 TTCCCTCTGTGACCACCTGAAGTACAACGCTCTGCAC - -a -s simMouse_chr6.simMouse.chr6 466001 32 + 636262 CTGCGGCCCTGATTAACATCATAGTGGAAACA -s Anc0.Anc0refChr3 87343 28 + 222631 CTG----CCCAATTGTCACCATAGAGGAAATA -s Anc1.Anc1refChr6 119740 32 + 197743 CTGTGATCCCAATTGTCACCATAGAGGAAATA -s Anc2.Anc2refChr13 94871 28 + 96486 CTG----CACAATTGTCACCATAGAGGAAATA -s mr.mrrefChr3 21738 32 + 181027 CTGTGGTCCTGATTATCATCATAGTGGAAACA -s simCow_chr6.simCow.chr6 451118 3 + 602619 -----------------------------ATA -s simDog_chr6.simDog.chr6 444209 28 + 593897 CTG----CACAATTGTCACCATAGAGGAAATA -s simHuman_chr6.simHuman.chr6 451916 32 + 601863 CTGTGATCCCCATTGTGACCATTAGGGGAATA -s simRat_chr6.simRat.chr6 475749 32 + 647215 CCGTGGTCCTGAGTATCATCATAGTGGCAACA - -a -s simMouse_chr6.simMouse.chr6 466033 2 + 636262 TA -s Anc0.Anc0refChr3 87371 2 + 222631 TG -s Anc1.Anc1refChr6 119772 2 + 197743 TG -s Anc2.Anc2refChr13 94899 2 + 96486 TG -s mr.mrrefChr3 21770 2 + 181027 TA -s simCow_chr6.simCow.chr6 451121 2 + 602619 TG -s simDog_chr6.simDog.chr6 444237 2 + 593897 TG -s simHuman_chr6.simHuman.chr6 451948 2 + 601863 TG -s simRat_chr6.simRat.chr6 475969 2 + 647215 TT - -a -s simMouse_chr6.simMouse.chr6 466035 10 + 636262 GCTGACATAC -s Anc0.Anc0refChr3 87373 10 + 222631 GTTAATATAC -s Anc1.Anc1refChr6 119774 10 + 197743 GTTAATATAC -s Anc2.Anc2refChr13 94901 10 + 96486 GTTAATACAC -s mr.mrrefChr3 21772 10 + 181027 GCTGACATAC -s simCow_chr6.simCow.chr6 451123 10 + 602619 GTTAATACAC -s simDog_chr6.simDog.chr6 444241 10 + 593897 GTTAATACAT -s simHuman_chr6.simHuman.chr6 451950 10 + 601863 GTTAATATAC -s simRat_chr6.simRat.chr6 475971 10 + 647215 GGTGACTTGC - -a -s simMouse_chr6.simMouse.chr6 466045 3 + 636262 TAG -s Anc0.Anc0refChr3 87383 3 + 222631 TAG -s Anc1.Anc1refChr6 119784 3 + 197743 TAG -s Anc2.Anc2refChr13 94911 3 + 96486 CAG -s mr.mrrefChr3 21782 3 + 181027 TAG -s simCow_chr6.simCow.chr6 451133 2 + 602619 CA- -s simDog_chr6.simDog.chr6 444251 3 + 593897 CAG -s simHuman_chr6.simHuman.chr6 451960 3 + 601863 TAG -s simRat_chr6.simRat.chr6 475994 3 + 647215 TGA - -a -s simMouse_chr6.simMouse.chr6 466048 27 + 636262 GGCCTCAATGGATGTGATTGTATAATT -s Anc0.Anc0refChr3 87386 18 + 222631 GAC--------A-GTGATTGCACACTT -s Anc1.Anc1refChr6 119787 18 + 197743 GAC--------A-GTGATTGCACACTT -s Anc2.Anc2refChr13 94914 18 + 96486 GAC--------C-ATGATTGCACACCT -s mr.mrrefChr3 21785 26 + 181027 GGCCTCAATGGA-GTGATTGTATAATT -s simCow_chr6.simCow.chr6 451135 17 + 602619 -AC--------C-ACGATTGCATAACA -s simDog_chr6.simDog.chr6 444255 18 + 593897 GAC--------C-ATGATTGCACACCT -s simHuman_chr6.simHuman.chr6 451963 18 + 601863 GAC--------A-GTGTTTGCACAGTT -s simRat_chr6.simRat.chr6 475997 23 + 647215 AGTCTAAATAGC----GTTAAATAATT - -a -s simMouse_chr6.simMouse.chr6 466075 84 + 636262 ATGCGATCTGGCCTACAAACAGTCCTATCTGACTACAATGACGTGTAGCGGAACAGGGATCCCTTATGGTGTAATATGCGTTGA -s Anc0.Anc0refChr3 87404 29 + 222631 ACA---------------------------------AGTGATGTCTGGGGGAACTgggagcc---------------------- -s Anc1.Anc1refChr6 119805 51 + 197743 ACA---------------------------------AGTGATGTCTGGGGGAACTgggagcccttgtggcgttttttgtgcaca -s Anc2.Anc2refChr13 94932 29 + 96486 ACA---------------------------------TGTGATGTCTGGGGGGACTGACAGCC---------------------- -s mr.mrrefChr3 21811 84 + 181027 ATGCGATCTGGCCTACAAACAGTCCTATCTGACTACAATGATGTGTAGGGGAACAgggatcccttatggtgtaatatgtgttga -s simCow_chr6.simCow.chr6 451165 29 + 602619 AAC---------------------------------TGTGATGCCTTGGCCTATAAACAGTC---------------------- -s simDog_chr6.simDog.chr6 444273 25 + 593897 ACA---------------------------------TGC----TCTGGTGGGCCTGACAGCC---------------------- -s simHuman_chr6.simHuman.chr6 451981 51 + 601863 ACA---------------------------------AGTAATGTTTGGGggaactgggaccccttgtggcgttttttgtgcaca -s simRat_chr6.simRat.chr6 476020 84 + 647215 ATGTGCCCTGGCCTACAAACCGTCCTATCTGACTATATTGATGTGTAGGGGAACAgggatccctccttgtgtaatatgtgttga - -a -s simMouse_chr6.simMouse.chr6 466159 55 + 636262 TACTTTAAAATTGTATGCTGATCCTACTGTATGGCCTGGAGTCTTAAACTCATAA -s Anc1.Anc1refChr6 119856 53 + 197743 tatctcaaaattgttcgctaaccccccagggcaacctgaagtc--acacccataa -s mr.mrrefChr3 21895 55 + 181027 tattttaaaattgtatgctgatcctcctgtatggcctgaagtcTTAAACTCATAA -s simHuman_chr6.simHuman.chr6 452043 53 + 601863 tatctcaaaattgttcgctaaccccccagggcaacctgaagtc--acacccataa -s simRat_chr6.simRat.chr6 476104 55 + 647215 ttttgtaaagttatatgctgatcctcctgtatggcctgaagtcTTAAACTAATAA - -a -s simMouse_chr6.simMouse.chr6 466214 18 + 636262 GGAATCCTAATCTTGTCT -s Anc0.Anc0refChr3 87433 3 + 222631 ---------------ctt -s Anc1.Anc1refChr6 119909 12 + 197743 ggaatcc------agctt -s Anc2.Anc2refChr13 94961 3 + 96486 ---------------CTA -s mr.mrrefChr3 21950 18 + 181027 GGAATCCTAATCTTGTCT -s simCow_chr6.simCow.chr6 451194 3 + 602619 ---------------CTG -s simDog_chr6.simDog.chr6 444298 3 + 593897 ---------------CTA -s simHuman_chr6.simHuman.chr6 452143 12 + 601863 ggaatcc------agctt -s simRat_chr6.simRat.chr6 476159 18 + 647215 GGAACCCTAATCTTGTCT - -a -s simMouse_chr6.simMouse.chr6 466232 4 + 636262 CATC -s Anc0.Anc0refChr3 87436 4 + 222631 CATA -s Anc1.Anc1refChr6 119921 4 + 197743 CATA -s Anc2.Anc2refChr13 94964 4 + 96486 CCTA -s mr.mrrefChr3 21968 4 + 181027 CATC -s simCow_chr6.simCow.chr6 451222 4 + 602619 CCTA -s simHuman_chr6.simHuman.chr6 452155 4 + 601863 CATG -s simRat_chr6.simRat.chr6 476177 4 + 647215 CATC - -a -s simMouse_chr6.simMouse.chr6 466236 20 + 636262 TACATGCACAGTAACTAAGC -s Anc0.Anc0refChr3 87446 20 + 222631 TGCATGGACATAAACGAAGC -s Anc1.Anc1refChr6 119931 20 + 197743 TGCATGGACATAAACGAAGC -s Anc2.Anc2refChr13 94974 20 + 96486 TGCATGGACATAAATGAAGC -s mr.mrrefChr3 21972 20 + 181027 TACATGCACATTAACTAAGC -s simCow_chr6.simCow.chr6 451232 18 + 602619 TGCATGG--ATAAATGAAGC -s simDog_chr6.simDog.chr6 444678 20 + 593897 TGCATGGACATAAATGAAGC -s simHuman_chr6.simHuman.chr6 452165 20 + 601863 TGCATGGGCATCAACAAAGC -s simRat_chr6.simRat.chr6 476181 20 + 647215 TACATGAACATTAGCTAAGC - -a -s simMouse_chr6.simMouse.chr6 466256 5 + 636262 AAATC -s Anc0.Anc0refChr3 87467 5 + 222631 ATTTT -s Anc1.Anc1refChr6 119952 5 + 197743 ATTTT -s Anc2.Anc2refChr13 94995 5 + 96486 ATTTT -s mr.mrrefChr3 21992 5 + 181027 AAATC -s simCow_chr6.simCow.chr6 451251 5 + 602619 ATTTT -s simDog_chr6.simDog.chr6 444699 5 + 593897 ATTTT -s simHuman_chr6.simHuman.chr6 452186 5 + 601863 ACTTT -s simRat_chr6.simRat.chr6 476201 5 + 647215 AAATC - -a -s simMouse_chr6.simMouse.chr6 466261 113 + 636262 CTATTTCGGCAAAAAGGTTAAGCAGAGCGCAAAAAAATCTAGAAGAATGGGAAGCACAAACTAATAGTTAAGAAAGCAGAAAGAGCAGTGGTGGAGTAGGGAAAAGAAAGCAT -s Anc0.Anc0refChr3 87472 103 + 222631 CTATTTCATTGGAAAGGTCAAGCAAAACACAAAACACTCC--AAGTATGGGCAGCACAAATTAG-------AATAGCAGCAAAGGCAGCAGTGGAGTAGATGAAACAA-ACAC -s Anc1.Anc1refChr6 119957 103 + 197743 CTATTTCATTGGAAAGGTCAAGCAAAACACAAAACACTCC--AAGTATGGGCAGCACAAATTAG-------AATAGCAGCAAAGGCAGCAGTGGAGTAGATGAAACAA-ACAC -s Anc2.Anc2refChr13 95000 103 + 96486 CTATTTCATTGGAAAGGTCAAGAAAAACACAAAACTCTTG--AAGTATGGGCAGCAAAAATTAG-------AATAGGAGCAGAGGCTGCAATGGAGAAGATGAAACAA-ACAC -s mr.mrrefChr3 21997 112 + 181027 CTATTTCATTAAAAAGGTTAAGCAAAGCACAAAAAAATCCAGAAGAATGGGAAGCACAAACTAGTAGTTAAGAAAGCAGAAAGAGCAGTGGTGGAGTAGGGAAAAGAA-GCAT -s simCow_chr6.simCow.chr6 451256 96 + 602619 ATATTTCATGAGAAAGGTAAAGT-------AAGGCCCTTA--AAGTATGGGCAGCATGAATAAG-------AATAGGAGCAGAGGCTGCAAGGGAGAATATGAAAAAA-ACAC -s simDog_chr6.simDog.chr6 444705 88 + 593897 CTATCTCATTGGAAAGGTCAGGAAAAACACAAAACTCCTG--AAATTTGGGTATTAAAAATTGG-------AAC---------------AATATAGAAGATGAAACAA-ACAC -s simHuman_chr6.simHuman.chr6 452191 103 + 601863 CTATTTCATTGGAATGGTCAAGCAAAACACAGAACATTCC--AAGTATGGGCAGCACAAATTAG-------AATAACAAGAAAGACAAAAGAGGAGTAGCTGAGATAA-ATGC -s simRat_chr6.simRat.chr6 476206 112 + 647215 CCATTTCATTATAAAGGTTAAGCAAAGCACAAAAAACTTCTGATGAATGGGAAGCACAAACAAGTACTTAAGAAAGCAGGAAGACCAGTGATGGAGTAGGGAAAAGAA-GCAT - -a -s simMouse_chr6.simMouse.chr6 466374 13 + 636262 GTCAGATTATAAT -s Anc0.Anc0refChr3 87578 13 + 222631 GTCAGACAATTGG -s Anc1.Anc1refChr6 120063 13 + 197743 GTCAGACAATTGG -s Anc2.Anc2refChr13 95106 13 + 96486 GTCAGACAATTAG -s mr.mrrefChr3 22112 13 + 181027 GTCAGATTATAGT -s simCow_chr6.simCow.chr6 451355 13 + 602619 GTCAGACAATTAG -s simDog_chr6.simDog.chr6 444796 13 + 593897 GTCAGATGATTAG -s simHuman_chr6.simHuman.chr6 452297 13 + 601863 GTCAGACAATTGG -s simRat_chr6.simRat.chr6 476321 13 + 647215 GTCAGATTATAGC - -a -s simMouse_chr6.simMouse.chr6 466387 17 + 636262 TAAGTCTGGATTTCCAA -s Anc0.Anc0refChr3 87591 17 + 222631 TGATTTTGGAGTACAAC -s Anc1.Anc1refChr6 120076 17 + 197743 TGATTTTGGAGTACAAC -s Anc2.Anc2refChr13 95127 17 + 96486 TGATTTTGGAGTACAAC -s mr.mrrefChr3 22125 17 + 181027 TAATTCTGGATTACCAA -s simCow_chr6.simCow.chr6 451376 17 + 602619 TGATTTTGGAGTACAAC -s simDog_chr6.simDog.chr6 444817 17 + 593897 TGATTTTGCAGTACAAC -s simHuman_chr6.simHuman.chr6 452310 17 + 601863 TGCTTTTCGAGTATAAC -s simRat_chr6.simRat.chr6 476334 17 + 647215 TAATTCTGGACTAGCAA - -a -s simMouse_chr6.simMouse.chr6 466404 12 + 636262 TCTTCGATAGCT -s Anc0.Anc0refChr3 87608 9 + 222631 TCTAGGAT---A -s Anc1.Anc1refChr6 120093 9 + 197743 TCTAGGAT---A -s Anc2.Anc2refChr13 95144 9 + 96486 TTTAGGGT---A -s mr.mrrefChr3 22142 12 + 181027 TCTTCGATAGCA -s simCow_chr6.simCow.chr6 451394 9 + 602619 TTTAGGGT---A -s simDog_chr6.simDog.chr6 444834 5 + 593897 TTCAG------- -s simHuman_chr6.simHuman.chr6 452327 9 + 601863 CCTGGGAT---A -s simRat_chr6.simRat.chr6 476351 12 + 647215 TCATAGATTGTA - -a -s simMouse_chr6.simMouse.chr6 466416 40 + 636262 CTATATCCAACAAGTAGTCGGCATTTTACACCTGACAGCC -s Anc0.Anc0refChr3 87617 40 + 222631 CTGCATCCTATTAATAGTTGGCCCTTTGCACCTGATCTCT -s Anc1.Anc1refChr6 120102 40 + 197743 CTGCATCCTATTAATAGTTGGCCCTTTGCACCTGATCTCT -s Anc2.Anc2refChr13 95153 40 + 96486 TTGCATCTTATTGATAGTTAGCCCTTTGCACCTAATCTCT -s mr.mrrefChr3 22154 40 + 181027 CTATATCCTACAAGTAGTCGGCATTTTACACCTGACAGCC -s simCow_chr6.simCow.chr6 451406 34 + 602619 TTGCACCTTATA------TAGCCTTTTACACCTAATCTCT -s simDog_chr6.simDog.chr6 444839 39 + 593897 -TGTATCTTACTGATAGTTAGTCCTTTGCACCTAATCTCT -s simHuman_chr6.simHuman.chr6 452336 40 + 601863 CTGCATCCTATGAATAATTGGCCATTTGCACCTGATTTCT -s simRat_chr6.simRat.chr6 476363 37 + 647215 CTATATTTTACTAGTAGTCAGCATTTTACACC---CAGCC - -a -s simMouse_chr6.simMouse.chr6 466456 14 + 636262 ATCAAATATAAAGT -s Anc0.Anc0refChr3 87660 14 + 222631 GGAAACTGTGCACT -s Anc1.Anc1refChr6 120145 14 + 197743 GGAAACTGTGCACT -s Anc2.Anc2refChr13 95196 14 + 96486 GGAAGCTGTGCACT -s mr.mrrefChr3 22194 14 + 181027 ATCAAATATAAAGT -s simCow_chr6.simCow.chr6 451443 14 + 602619 CGGAGCTGTGCACT -s simDog_chr6.simDog.chr6 444881 14 + 593897 GGAAGCTGCACATT -s simHuman_chr6.simHuman.chr6 452379 14 + 601863 GGTAACTGTGTACT -s simRat_chr6.simRat.chr6 476400 14 + 647215 ATCAAATGAAAAGT - -a -s simMouse_chr6.simMouse.chr6 466470 18 + 636262 GCCACAAGGGTGACAGCA -s Anc0.Anc0refChr3 87682 15 + 222631 GCCACAA--GTAGC-GGG -s Anc1.Anc1refChr6 120167 18 + 197743 GCCACAAGGGTAGCAGGG -s Anc2.Anc2refChr13 95313 15 + 96486 ACCACAA--GTAGT-GAG -s mr.mrrefChr3 22208 18 + 181027 GCCACAAGGGTAACAGGG -s simCow_chr6.simCow.chr6 451574 15 + 602619 CTTATAA--GTTGT-GTG -s simDog_chr6.simDog.chr6 148480 15 - 593897 ACCACAA--GTAGT-GAG -s simHuman_chr6.simHuman.chr6 452401 18 + 601863 GGCCGAGGGGTAGCAAGG -s simRat_chr6.simRat.chr6 476414 18 + 647215 GCCACAAGGGTAACAGGG - -a -s simMouse_chr6.simMouse.chr6 466488 11 + 636262 CAGGCTCAGAA -s Anc0.Anc0refChr3 87697 11 + 222631 CAGTCTCTGAA -s Anc1.Anc1refChr6 120185 11 + 197743 CAGTCTCTGAA -s Anc2.Anc2refChr13 95328 11 + 96486 CATTCTCTGAA -s mr.mrrefChr3 22226 11 + 181027 CAGGCTCAGAA -s simCow_chr6.simCow.chr6 451590 11 + 602619 CATTCTCTGAA -s simDog_chr6.simDog.chr6 148495 1 - 593897 ----------A -s simHuman_chr6.simHuman.chr6 452419 11 + 601863 CAGTCTCTCAA -s simRat_chr6.simRat.chr6 476432 11 + 647215 CACGCTCAGAA - -a -s simMouse_chr6.simMouse.chr6 466499 43 + 636262 AGCTTAAATGGCGGTGACTGTTCGTTAAACAAATTGCAGATAC -s Anc0.Anc0refChr3 87709 43 + 222631 AGCTTAAATGGCTGAGATTGTTGGTTAAAACAAATGTGGACAC -s Anc1.Anc1refChr6 120197 43 + 197743 AGCTTAAATGGCTGAGATTGTTGGTTAAAACAAATGTGGACAC -s Anc2.Anc2refChr13 95340 43 + 96486 AGCTTAAATGGCTGAGATTGTTGGTTAAAACAAATGTGGACAC -s mr.mrrefChr3 22237 43 + 181027 AGCTTAAATGGCTGTGACTGTTGGTTAAACAAAATGCAGATAC -s simCow_chr6.simCow.chr6 451602 43 + 602619 AGCTTACATGGCTTAAATTGCGGGTTACAACAAATGTGGACTC -s simDog_chr6.simDog.chr6 148497 43 - 593897 AGACTCAATGGCTGGGATCGTTGGTTAAAATAAATGGGGACAC -s simHuman_chr6.simHuman.chr6 452431 43 + 601863 AGCTTAAATGGCTGAGATTGTTGGTTAAAACACATGTGGACAC -s simRat_chr6.simRat.chr6 476443 43 + 647215 GGCTTAAATGGCTGTGACCGTTGGTTACACAAAATGCAGATAC - -a -s simMouse_chr6.simMouse.chr6 466542 52 + 636262 TGCACCCTATCAGACAGTGCTTTACCTCGGTAATAACATATGTATATATTAC -s Anc0.Anc0refChr3 87754 50 + 222631 TGGACTCCACCA--CATGGGTTGCTTCTGGAAGTGACATAACCATATATCAC -s Anc1.Anc1refChr6 120242 50 + 197743 TGGACTCCACCA--CATGGGTTGCTTCTGGAAGTGACATAACCATATATCAC -s Anc2.Anc2refChr13 95385 50 + 96486 TGGGCTCCACCA--CATGGATTGCTTCTGGGAGTGGCATAACCATATATTAC -s mr.mrrefChr3 22282 52 + 181027 TGCACCCCATCACTCAGTGGTTGCTCTTGGAAATGACATATGCATATATCAC -s simCow_chr6.simCow.chr6 451647 50 + 602619 TGGGCTCCAGCA--GATGGATGGCTTGTGGGAGTGGCATAATCCTATGTTAC -s simDog_chr6.simDog.chr6 148542 45 - 593897 TGGGCTCCTCAA--C--GGATTG---CTGGGAGTGGCATGACCATATATTAC -s simHuman_chr6.simHuman.chr6 452476 50 + 601863 TGGACGCCACCA--CAAGAGTTGCTTCTGGAAGTGAGATAACCATATATCGC -s simRat_chr6.simRat.chr6 476489 52 + 647215 TGTGCCCCATCACTCAGTGGTTGCTCTTGCAAATGACATATGCATATATCAT - -a -s simMouse_chr6.simMouse.chr6 466594 71 + 636262 TGTCTACATGGTGGCTACCTAAGTGCCTAGGGCTTGTGCTCCGTCATAAAGACTGCTTCAAGGAGTGCGAA -s Anc0.Anc0refChr3 87816 68 + 222631 TG--TATAT-GCTCCTACCTCAGTGCCTAGGGCTTGCTTTCCATCGCAAGGACTGCTTCAAGGAGTGGCAT -s Anc1.Anc1refChr6 120304 70 + 197743 TGTCTATAT-GCTCCTACCTCAGTGCCTAGGGCTTGCTTTCCATCGCAAGGACTGCTTCAAGGAGTGGCAT -s Anc2.Anc2refChr13 95447 68 + 96486 TG--TATAT-GCTCCTACCCCAGTGCTGAGGGCTTGCTTTCCATCGCAAGGACTGCTTCGAGGAGCGGCAT -s mr.mrrefChr3 22334 71 + 181027 TGTCTACATGGCTGCTACCTAAGTGCCTAGGGCTTGTGCTCCGTCATAAAGACTGCTTCAAGGAGTGCAAT -s simCow_chr6.simCow.chr6 451709 67 + 602619 TG--TGCAT-GCCCCTACGCCAGTGCT-AGGGCTTGCTTTGCATCATAAGAACTGCCTCCAGGAGGAACAC -s simDog_chr6.simDog.chr6 148594 65 - 593897 -----ATAT-ACTTGCCCCCCAGTGCTGAGGGCTTGCTTTCCATCGCAGGGACTGCTTCGAGGAGCGGCAT -s simHuman_chr6.simHuman.chr6 452538 60 + 601863 TGTCAATGT-GCTCCTACCTCAGTGCCTAGGGCTTG----------CAAGGACTGCTTCAAGCAATGGCAT -s simRat_chr6.simRat.chr6 476541 69 + 647215 TGTCTATATTGCTGC--GCCAAGTGTCTTAGGCTTGTGCTCCGTCATAAAGACTGCTTCAAGGAGTGCAAT - -a -s simMouse_chr6.simMouse.chr6 466665 6 + 636262 AAACAG -s Anc0.Anc0refChr3 87884 5 + 222631 AACC-A -s Anc1.Anc1refChr6 120374 5 + 197743 AACC-A -s Anc2.Anc2refChr13 95515 5 + 96486 AACC-A -s mr.mrrefChr3 22405 5 + 181027 AAAC-G -s simCow_chr6.simCow.chr6 451785 5 + 602619 AACC-A -s simDog_chr6.simDog.chr6 148659 5 - 593897 AACA-A -s simHuman_chr6.simHuman.chr6 452598 5 + 601863 AACC-A -s simRat_chr6.simRat.chr6 476610 5 + 647215 AATC-G - -a -s simMouse_chr6.simMouse.chr6 466671 4 + 636262 ATAC -s Anc0.Anc0refChr3 87890 4 + 222631 ATAC -s Anc1.Anc1refChr6 120380 4 + 197743 ATAC -s Anc2.Anc2refChr13 95521 4 + 96486 ATAC -s mr.mrrefChr3 22410 4 + 181027 ATAC -s simCow_chr6.simCow.chr6 451791 4 + 602619 ATAC -s simDog_chr6.simDog.chr6 148665 4 - 593897 ATAC -s simHuman_chr6.simHuman.chr6 452604 4 + 601863 ATAC -s simRat_chr6.simRat.chr6 476615 4 + 647215 ATAC - -a -s simMouse_chr6.simMouse.chr6 466675 2 + 636262 TT -s Anc0.Anc0refChr3 87894 2 + 222631 CT -s Anc1.Anc1refChr6 120384 2 + 197743 CT -s Anc2.Anc2refChr13 95530 2 + 96486 CT -s mr.mrrefChr3 22414 2 + 181027 TT -s simCow_chr6.simCow.chr6 451800 2 + 602619 TT -s simDog_chr6.simDog.chr6 148674 2 - 593897 CT -s simHuman_chr6.simHuman.chr6 452608 2 + 601863 CT -s simRat_chr6.simRat.chr6 476619 2 + 647215 TT - -a -s simMouse_chr6.simMouse.chr6 466677 50 + 636262 CATATTTTATGTAAATACTCCAAGCCTACATTTTAGGCCAGGGTTTCCCA -s Anc0.Anc0refChr3 87896 50 + 222631 CATGTCTTATGAACATACTCCAATCCCAGGTCTTAGGGCAGGGTTTTCCA -s Anc1.Anc1refChr6 120386 50 + 197743 CATGTCTTATGAACATACTCCAATCCCAGGTCTTAGGGCAGGGTTTTCCA -s Anc2.Anc2refChr13 95532 50 + 96486 AATTTCTTATGAACATACTCCAATCCCAGGTCTTAAGGCAGGGTTCTCCA -s mr.mrrefChr3 22416 50 + 181027 CATGTTTTATGTAAATACTCCAAGCCAACATTTTAGGGCAGGGTTTCCCA -s simCow_chr6.simCow.chr6 451803 46 + 602619 CATCTCCCATAAACATACTCCAATCTCA----CTAAGGCAGGGTTATCCA -s simDog_chr6.simDog.chr6 148676 50 - 593897 AATTTCTTATGAACATACTATAACCCAAGGTCTTAAGGCAGGGTTCTCCA -s simHuman_chr6.simHuman.chr6 452610 46 + 601863 CATG----GTGAACATACTCCAATCCCAGCTCTTAGGGCAGGGTTTTCCA -s simRat_chr6.simRat.chr6 476621 49 + 647215 TATGTTTTATACAAATACTTCAAGCCAACATTATA-GGCCGGGTTTCCCA - -a -s simMouse_chr6.simMouse.chr6 466727 4 + 636262 TTAT -s Anc0.Anc0refChr3 87946 4 + 222631 CTAT -s Anc1.Anc1refChr6 120436 4 + 197743 CTAT -s Anc2.Anc2refChr13 95582 4 + 96486 CTAT -s mr.mrrefChr3 22466 4 + 181027 TTAT -s simCow_chr6.simCow.chr6 451851 4 + 602619 ATAT -s simDog_chr6.simDog.chr6 148726 4 - 593897 CTAT -s simHuman_chr6.simHuman.chr6 452656 4 + 601863 CTAT -s simRat_chr6.simRat.chr6 476670 4 + 647215 TTAT - -a -s simMouse_chr6.simMouse.chr6 466731 3 + 636262 GAG -s Anc0.Anc0refChr3 87950 3 + 222631 GAG -s Anc1.Anc1refChr6 120440 3 + 197743 GAG -s Anc2.Anc2refChr13 95587 3 + 96486 AAG -s mr.mrrefChr3 22470 3 + 181027 GAG -s simCow_chr6.simCow.chr6 451856 3 + 602619 AAG -s simDog_chr6.simDog.chr6 148731 3 - 593897 AAG -s simHuman_chr6.simHuman.chr6 452660 3 + 601863 GAA -s simRat_chr6.simRat.chr6 476674 3 + 647215 AAG - -a -s simMouse_chr6.simMouse.chr6 466734 57 + 636262 AGTAGTGATCATTGTCCCAATTACTGCCAATTCTATAGTCCTTACATGCCACCTTGA -s Anc0.Anc0refChr3 87953 57 + 222631 AGAAGTGATCATTGAACAAATTACAGCCAGTTCTCTAGTCTTTACACTAGACCTTAG -s Anc1.Anc1refChr6 120443 57 + 197743 AGAAGTGATCATTGAACAAATTACAGCCAGTTCTCTAGTCTTTACACTAGACCTTAG -s Anc2.Anc2refChr13 95590 57 + 96486 AGAAGTGATCATTGAAGAAATTACGGCCAGGTGTCTAGTCTTTACACTAGGCCTTAG -s mr.mrrefChr3 22473 57 + 181027 AGTAGTGATCATTGTCCAAATTACAGCCAGTTCTATAGTCCTTACACTCCACCTTGA -s simCow_chr6.simCow.chr6 451859 44 + 602619 AGAAGTGATCA-------------GGCTAAGTGTCAAGTCCTTACACTGGGCCTTAG -s simDog_chr6.simDog.chr6 148734 57 - 593897 AGAAGTGATCTTTGAAGAAATTACGGCCAGGGGTCTAGTTTTTACACTAAGCCTTAG -s simHuman_chr6.simHuman.chr6 452683 57 + 601863 AGAAGTGATCATTGAGCAAATAAGACTCAGTTCTGTAGTCTTTACACTAGACCTTAG -s simRat_chr6.simRat.chr6 476677 57 + 647215 AGTAATGATCATGGTCCAAATTACAGCCAGTTTTATAGTCCTTATACTTCACCTTCA - -a -s simMouse_chr6.simMouse.chr6 466791 4 + 636262 ACAG -s Anc0.Anc0refChr3 88013 4 + 222631 AAGG -s Anc1.Anc1refChr6 120503 4 + 197743 AAGG -s Anc2.Anc2refChr13 95650 4 + 96486 AAGG -s mr.mrrefChr3 22530 4 + 181027 ACAG -s simCow_chr6.simCow.chr6 451906 4 + 602619 GGGG -s simDog_chr6.simDog.chr6 148794 4 - 593897 AAGA -s simHuman_chr6.simHuman.chr6 452743 4 + 601863 AAGG -s simRat_chr6.simRat.chr6 476734 4 + 647215 ACAG - -a -s simMouse_chr6.simMouse.chr6 466795 13 + 636262 GCCATATCAGCCA -s Anc0.Anc0refChr3 88017 13 + 222631 GCCACATTTAGCA -s Anc1.Anc1refChr6 120507 13 + 197743 GCCACATTTAGCA -s Anc2.Anc2refChr13 95654 13 + 96486 GCCACATTTAGTA -s mr.mrrefChr3 22534 13 + 181027 GCCACATTAACCA -s simCow_chr6.simCow.chr6 451910 13 + 602619 GCCACATTTAGTA -s simDog_chr6.simDog.chr6 148801 13 - 593897 GCCACATTTAGTA -s simHuman_chr6.simHuman.chr6 452747 13 + 601863 GCCAGATTTAGCA -s simRat_chr6.simRat.chr6 476738 13 + 647215 GCCACATTGACCA - -a -s simMouse_chr6.simMouse.chr6 466808 5 + 636262 ACAGT -s Anc0.Anc0refChr3 88030 5 + 222631 ACAGT -s Anc1.Anc1refChr6 120520 5 + 197743 ACAGT -s Anc2.Anc2refChr13 95667 5 + 96486 ACAGT -s mr.mrrefChr3 22549 5 + 181027 ACAGT -s simCow_chr6.simCow.chr6 451923 5 + 602619 ATAGT -s simDog_chr6.simDog.chr6 148816 5 - 593897 ACAGT -s simHuman_chr6.simHuman.chr6 452760 5 + 601863 ACAGT -s simRat_chr6.simRat.chr6 476753 5 + 647215 ACTGT - -a -s simMouse_chr6.simMouse.chr6 466813 5 + 636262 CGGGC -s Anc0.Anc0refChr3 88035 5 + 222631 AATCT -s Anc1.Anc1refChr6 120525 5 + 197743 AATCT -s Anc2.Anc2refChr13 95672 5 + 96486 AATCT -s mr.mrrefChr3 22554 5 + 181027 CGGGC -s simCow_chr6.simCow.chr6 451930 5 + 602619 AACCT -s simDog_chr6.simDog.chr6 148821 5 - 593897 AATCT -s simHuman_chr6.simHuman.chr6 452765 1 + 601863 T---- -s simRat_chr6.simRat.chr6 476758 5 + 647215 CGGGC - -a -s simMouse_chr6.simMouse.chr6 466818 10 + 636262 ATGTCAGTTA -s Anc0.Anc0refChr3 88040 8 + 222631 ACGGGAGT-- -s Anc1.Anc1refChr6 120530 8 + 197743 ACGGGAGT-- -s Anc2.Anc2refChr13 95677 8 + 96486 ACGGGAGT-- -s mr.mrrefChr3 22559 10 + 181027 ATGTCAGTTA -s simCow_chr6.simCow.chr6 451941 8 + 602619 GCAGCAGT-- -s simDog_chr6.simDog.chr6 148826 8 - 593897 ACGGGAGT-- -s simRat_chr6.simRat.chr6 476763 10 + 647215 ATGTCAGTTA - -a -s simMouse_chr6.simMouse.chr6 466828 7 + 636262 TCCTAAA -s Anc0.Anc0refChr3 88048 7 + 222631 CCCTAAA -s Anc1.Anc1refChr6 120538 7 + 197743 CCCTAAA -s Anc2.Anc2refChr13 95685 7 + 96486 CCCTAAA -s mr.mrrefChr3 22569 7 + 181027 TCCTAAA -s simCow_chr6.simCow.chr6 451950 7 + 602619 CCCCCAA -s simDog_chr6.simDog.chr6 148834 7 - 593897 CCCTAAA -s simRat_chr6.simRat.chr6 476773 7 + 647215 TCCTAAA - -a -s simMouse_chr6.simMouse.chr6 466835 5 + 636262 AGCAG -s Anc0.Anc0refChr3 88055 5 + 222631 AGACA -s Anc1.Anc1refChr6 120545 5 + 197743 AGACA -s Anc2.Anc2refChr13 95696 5 + 96486 AGACA -s mr.mrrefChr3 22576 5 + 181027 AGCAG -s simCow_chr6.simCow.chr6 451961 5 + 602619 AGAGA -s simDog_chr6.simDog.chr6 148845 5 - 593897 AGACA -s simRat_chr6.simRat.chr6 476780 5 + 647215 AGCAG - -a -s simMouse_chr6.simMouse.chr6 466840 7 + 636262 AATCAGA -s Anc0.Anc0refChr3 88060 7 + 222631 AATCAGA -s Anc1.Anc1refChr6 120550 7 + 197743 AATCAGA -s Anc2.Anc2refChr13 95701 7 + 96486 AATCAGA -s mr.mrrefChr3 22581 7 + 181027 AATCAGA -s simCow_chr6.simCow.chr6 451967 7 + 602619 AGTTAGA -s simDog_chr6.simDog.chr6 148850 7 - 593897 AATCAGA -s simRat_chr6.simRat.chr6 476785 7 + 647215 AATCTGA - -a -s simMouse_chr6.simMouse.chr6 466847 21 + 636262 TTAACTCCCTACTTGTCACAC -s Anc0.Anc0refChr3 88067 13 + 222631 GCTATTTACT--------CCC -s Anc1.Anc1refChr6 120557 13 + 197743 GCTATTTACT--------CCC -s Anc2.Anc2refChr13 95708 13 + 96486 GCTATTTACT--------CCC -s mr.mrrefChr3 22588 21 + 181027 TTAACTTACTACTTGTCACAC -s simCow_chr6.simCow.chr6 451982 13 + 602619 ACTATTTGCT--------ACA -s simDog_chr6.simDog.chr6 148857 13 - 593897 GCTATTTACT--------CCC -s simRat_chr6.simRat.chr6 476792 17 + 647215 ----CTTACTACATGTCATGC - -a -s simMouse_chr6.simMouse.chr6 466868 36 + 636262 CAAAATTAACTTGACGAAAAGATGGTGTCGAACCAG -s Anc0.Anc0refChr3 88080 35 + 222631 TGGAATCAAATCTAGGTAAAGATAGTGACTAGCCA- -s Anc1.Anc1refChr6 120570 35 + 197743 TGGAATCAAATCTAGGTAAAGATAGTGACTAGCCA- -s Anc2.Anc2refChr13 95721 35 + 96486 TGGAATCAAATCTAGGTAAAGATAGTGACTAGCCA- -s mr.mrrefChr3 22609 36 + 181027 TAAAATTAACTTTAGGTAAAGATAGTGTCTAACCAG -s simCow_chr6.simCow.chr6 451996 33 + 602619 TGCAATTAATTTTAACCAATGATCGTGATTAGC--- -s simDog_chr6.simDog.chr6 148870 35 - 593897 TGGAATCAAATCTAGGTGAAAACAGTGGCTGGCCA- -s simHuman_chr6.simHuman.chr6 452766 22 + 601863 -------------GGAGATAGATAGTGACTAGCCA- -s simRat_chr6.simRat.chr6 476809 35 + 647215 TAAAATTTATTTTAGGTAAAGATAGTG-TTAACCAG - -a -s simMouse_chr6.simMouse.chr6 466904 45 + 636262 TGACTATTCAGTGTACTAACCAGTGACCAGCCAGCCAACGTGCAC -s Anc0.Anc0refChr3 88115 41 + 222631 TGACTATCCGATATACTAGCCAGTGAC----TAGCCAACATGCAC -s Anc1.Anc1refChr6 120605 41 + 197743 TGACTATCCGATATACTAGCCAGTGAC----TAGCCAACATGCAC -s Anc2.Anc2refChr13 95756 41 + 96486 TGACTATCCGATATACTAGCCAGTGAC----TAGCCAACATGCAC -s mr.mrrefChr3 22645 41 + 181027 TGACTATTCAATATACTAACCAGTGAC----CAGCCAACGTGCAC -s simCow_chr6.simCow.chr6 452029 41 + 602619 TGAATATTTGATATACTAGCCAGTGAC----TAGTGAACTTGTGC -s simDog_chr6.simDog.chr6 148906 41 - 593897 TGACTGTCCGACATATTAGCCAGTGAC----TAGCCAACATGCAC -s simHuman_chr6.simHuman.chr6 452788 36 + 601863 CCACTATCCGATAAGCCAGCCAGTGAG----TAGCC-----GCAC -s simRat_chr6.simRat.chr6 476844 41 + 647215 TGACTATTCAATATACTAACGAGTGAC----CAACCAACGTGCAC - -a -s simMouse_chr6.simMouse.chr6 466949 5 + 636262 CATGC -s Anc0.Anc0refChr3 88156 5 + 222631 CATGC -s Anc1.Anc1refChr6 120646 5 + 197743 CATGC -s Anc2.Anc2refChr13 95797 5 + 96486 CATGC -s mr.mrrefChr3 22686 5 + 181027 CATGC -s simCow_chr6.simCow.chr6 452072 5 + 602619 TCTGC -s simDog_chr6.simDog.chr6 148947 5 - 593897 CATGC -s simHuman_chr6.simHuman.chr6 452824 5 + 601863 CATGC -s simRat_chr6.simRat.chr6 476885 5 + 647215 CATAC - -a -s simMouse_chr6.simMouse.chr6 466954 1 + 636262 T -s Anc0.Anc0refChr3 88163 1 + 222631 T -s Anc1.Anc1refChr6 120653 1 + 197743 T -s Anc2.Anc2refChr13 95804 1 + 96486 T -s mr.mrrefChr3 22691 1 + 181027 T -s simCow_chr6.simCow.chr6 452079 1 + 602619 C -s simDog_chr6.simDog.chr6 148954 1 - 593897 T -s simHuman_chr6.simHuman.chr6 452831 1 + 601863 T -s simRat_chr6.simRat.chr6 476890 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 466955 24 + 636262 GCTTCTGGTAGAACATGCTGTAAT -s Anc0.Anc0refChr3 88164 23 + 222631 GCTTCACCTA-CACAACCTTTCAT -s Anc1.Anc1refChr6 120654 23 + 197743 GCTTCACCTA-CACAACCTTTCAT -s Anc2.Anc2refChr13 95805 23 + 96486 GCTTCACCTA-CGGAACCTTTCAT -s mr.mrrefChr3 22692 24 + 181027 GCTTCTGGTAGAACATGCTGTCAT -s simCow_chr6.simCow.chr6 452080 23 + 602619 GCCTTAGTTG-CCAATGCTATCAT -s simDog_chr6.simDog.chr6 148962 23 - 593897 GCTGCCCCTA-TGGCACCTTTTAT -s simHuman_chr6.simHuman.chr6 452832 23 + 601863 GCTTCACATA-CACACACTCTCAT -s simRat_chr6.simRat.chr6 476891 24 + 647215 GCTTCTGGTAGAAAAGGCCGTCAT - -a -s simMouse_chr6.simMouse.chr6 466979 2 + 636262 AC -s Anc0.Anc0refChr3 88187 2 + 222631 TC -s Anc1.Anc1refChr6 120677 2 + 197743 TC -s Anc2.Anc2refChr13 95828 2 + 96486 TC -s mr.mrrefChr3 22716 2 + 181027 AC -s simCow_chr6.simCow.chr6 452104 2 + 602619 GC -s simDog_chr6.simDog.chr6 148985 2 - 593897 TC -s simHuman_chr6.simHuman.chr6 452855 2 + 601863 TC -s simRat_chr6.simRat.chr6 476915 2 + 647215 AC - -a -s simMouse_chr6.simMouse.chr6 466981 6 + 636262 TTAACT -s Anc0.Anc0refChr3 88189 4 + 222631 GTA--T -s Anc1.Anc1refChr6 120679 4 + 197743 GTA--T -s Anc2.Anc2refChr13 95830 4 + 96486 GTA--T -s mr.mrrefChr3 22718 6 + 181027 TTAACT -s simCow_chr6.simCow.chr6 452106 4 + 602619 TTA--T -s simDog_chr6.simDog.chr6 148991 4 - 593897 GCT--G -s simHuman_chr6.simHuman.chr6 452857 4 + 601863 ATA--T -s simRat_chr6.simRat.chr6 476917 6 + 647215 TTAACT - -a -s simMouse_chr6.simMouse.chr6 466987 5 + 636262 CAACT -s Anc0.Anc0refChr3 88193 5 + 222631 TGACT -s Anc1.Anc1refChr6 120683 5 + 197743 TGACT -s Anc2.Anc2refChr13 95834 5 + 96486 TGACT -s mr.mrrefChr3 22724 5 + 181027 CAACT -s simCow_chr6.simCow.chr6 452111 5 + 602619 TGACC -s simDog_chr6.simDog.chr6 148995 5 - 593897 TAACT -s simHuman_chr6.simHuman.chr6 452861 5 + 601863 TGACT -s simRat_chr6.simRat.chr6 476923 5 + 647215 CATCT - -a -s simMouse_chr6.simMouse.chr6 466992 14 + 636262 GATTACGAGGCAAG -s Anc0.Anc0refChr3 88198 13 + 222631 TCTTA-GATGCAAG -s Anc1.Anc1refChr6 120688 13 + 197743 TCTTA-GATGCAAG -s Anc2.Anc2refChr13 95839 13 + 96486 TCTTG-GATGCAAG -s mr.mrrefChr3 22729 14 + 181027 GATTAGGAGGCAAG -s simCow_chr6.simCow.chr6 452116 13 + 602619 TCTTG-CATGCAAG -s simDog_chr6.simDog.chr6 445589 13 + 593897 TTTTG-GATGCAAT -s simHuman_chr6.simHuman.chr6 452866 13 + 601863 TCTTA-GACGCAAG -s simRat_chr6.simRat.chr6 476928 14 + 647215 GATTAGGAGGCAAG - -a -s simMouse_chr6.simMouse.chr6 467006 7 + 636262 AGATCTT -s Anc0.Anc0refChr3 88217 7 + 222631 AGATATT -s Anc1.Anc1refChr6 120707 7 + 197743 AGATATT -s Anc2.Anc2refChr13 95858 7 + 96486 AGATATT -s mr.mrrefChr3 22749 7 + 181027 AGATCTT -s simCow_chr6.simCow.chr6 452135 7 + 602619 AGACATT -s simDog_chr6.simDog.chr6 445608 7 + 593897 AGATACT -s simHuman_chr6.simHuman.chr6 452885 7 + 601863 AGATGTT -s simRat_chr6.simRat.chr6 476948 7 + 647215 AAATCAT - -a -s simMouse_chr6.simMouse.chr6 467013 15 + 636262 TCCAAGTTATGTATA -s Anc0.Anc0refChr3 88232 15 + 222631 CTCAACTTATGTATA -s Anc1.Anc1refChr6 120722 15 + 197743 CTCAACTTATGTATA -s Anc2.Anc2refChr13 95873 15 + 96486 CTCAACTTATGTATA -s mr.mrrefChr3 22756 15 + 181027 TTCAAGTTATGTATA -s simCow_chr6.simCow.chr6 452150 15 + 602619 CTCAACTTATGTATA -s simDog_chr6.simDog.chr6 445616 15 + 593897 CTCAACTTATCTATA -s simHuman_chr6.simHuman.chr6 452900 15 + 601863 CTCAATTTATGTATA -s simRat_chr6.simRat.chr6 476955 15 + 647215 TTCAAGTTATGTATA - -a -s simMouse_chr6.simMouse.chr6 467028 3 + 636262 TCT -s Anc0.Anc0refChr3 88247 3 + 222631 TCT -s Anc1.Anc1refChr6 120737 3 + 197743 TCT -s Anc2.Anc2refChr13 95888 3 + 96486 TCT -s mr.mrrefChr3 22771 3 + 181027 TCT -s simCow_chr6.simCow.chr6 452165 3 + 602619 TCT -s simDog_chr6.simDog.chr6 445638 3 + 593897 TCT -s simHuman_chr6.simHuman.chr6 452915 3 + 601863 TCT -s simRat_chr6.simRat.chr6 476970 3 + 647215 TCT - -a -s simMouse_chr6.simMouse.chr6 467031 24 + 636262 CTAAGTTTAACTAGGAGCCAGATG -s Anc0.Anc0refChr3 88259 18 + 222631 CTGGGCTTAGC------CCAGATT -s Anc1.Anc1refChr6 120749 24 + 197743 CTGGGCTTAGCCAGGCACCAGATT -s Anc2.Anc2refChr13 95900 18 + 96486 TTGGGCTTAGC------CCACATT -s mr.mrrefChr3 22774 24 + 181027 CTGAGTTTAGCTAGGAGCCAGATG -s simCow_chr6.simCow.chr6 452177 17 + 602619 TTGATCTTAG-------ACGCTTT -s simDog_chr6.simDog.chr6 445650 18 + 593897 TTGGGCTTAGC------CCACATT -s simHuman_chr6.simHuman.chr6 452927 24 + 601863 CTGGGCTTAGCCAGGCAGCAGATT -s simRat_chr6.simRat.chr6 476973 23 + 647215 CTGAGTTTAGCTAGGAGCCAGGC- - -a -s simMouse_chr6.simMouse.chr6 467055 60 + 636262 AAGTGACTATGCACTAGATGGGGTGTGGTATGGGCTGCTATATCTCTTTCACTAGGTAGC -s Anc0.Anc0refChr3 88278 45 + 222631 AAAAGACTATGTTCTAAATTGGGTGTGGTATAGGCAGTTATACCT--------------- -s Anc1.Anc1refChr6 120774 45 + 197743 AAAAGACTATGTTCTAAATTGGGTGTGGTATAGGCAGTTATACCT--------------- -s Anc2.Anc2refChr13 95919 45 + 96486 AAAAGACCAAGTTCCAAATTGGGTGTGGTAGAGGCAGTTGGACCT--------------- -s mr.mrrefChr3 22798 53 + 181027 AAGTGACTATGCACTAGATGGGGTGTGGTATGGGCTGCTATATCT-------TAGGTAGC -s simCow_chr6.simCow.chr6 452195 34 + 602619 ATATGACCAAGTAGCTAAAGGAATGCGAAAAAGG-------------------------- -s simDog_chr6.simDog.chr6 445669 45 + 593897 AAAAAACCAAGGTCCAAATTGGGCATGGTAGAGGCAGTTGGACCT--------------- -s simHuman_chr6.simHuman.chr6 452952 45 + 601863 AAAAGACTATGTTATAAACTTGGTGTGGTATAAACAGTTATGCTT--------------- -s simRat_chr6.simRat.chr6 476996 19 + 647215 AACTGACTATG-----------------------------------------TGGGTAGC - -a -s simMouse_chr6.simMouse.chr6 467115 14 + 636262 TAGAGTAAGGGTAC -s Anc0.Anc0refChr3 88323 14 + 222631 TACAATAAGGGGCC -s Anc1.Anc1refChr6 120819 14 + 197743 TACAATAAGGGGCC -s Anc2.Anc2refChr13 95964 14 + 96486 TACAAAAAGGGGCC -s mr.mrrefChr3 22851 14 + 181027 TAGAGTAAGGGTAC -s simCow_chr6.simCow.chr6 452229 10 + 602619 ----ACAGCGGGCC -s simDog_chr6.simDog.chr6 445729 14 + 593897 TACAGAAAGGGTCC -s simHuman_chr6.simHuman.chr6 452997 14 + 601863 TACAATGAGGGGCC -s simRat_chr6.simRat.chr6 477015 14 + 647215 TAGAGTAAGAGTAC - -a -s simMouse_chr6.simMouse.chr6 467129 3 + 636262 AAA -s Anc0.Anc0refChr3 88337 3 + 222631 AAG -s Anc1.Anc1refChr6 120833 3 + 197743 AAG -s Anc2.Anc2refChr13 95978 3 + 96486 AAG -s mr.mrrefChr3 22865 3 + 181027 AAA -s simCow_chr6.simCow.chr6 452239 3 + 602619 AGG -s simDog_chr6.simDog.chr6 445746 3 + 593897 AAA -s simHuman_chr6.simHuman.chr6 453011 3 + 601863 AAG -s simRat_chr6.simRat.chr6 477029 3 + 647215 AAA - -a -s simMouse_chr6.simMouse.chr6 467132 17 + 636262 GAGGTCCATGTTACCCA -s Anc0.Anc0refChr3 88340 4 + 222631 TTGG------------- -s Anc1.Anc1refChr6 120836 4 + 197743 TTGG------------- -s Anc2.Anc2refChr13 95984 4 + 96486 TGGG------------- -s mr.mrrefChr3 22868 17 + 181027 GTGGTCCATGTTACCCA -s simCow_chr6.simCow.chr6 452245 4 + 602619 TGGG------------- -s simDog_chr6.simDog.chr6 445752 4 + 593897 TGGG------------- -s simHuman_chr6.simHuman.chr6 453014 4 + 601863 TTGG------------- -s simRat_chr6.simRat.chr6 477032 17 + 647215 GTGGCCCATGTTCTCCA - -a -s simMouse_chr6.simMouse.chr6 467149 43 + 636262 AGGACTGCTCAAAGTGAAAGCATTGAAGAGTATTAGACAGGAA -s Anc0.Anc0refChr3 88344 39 + 222631 AAGACTG----GGAGGGAAGCACCGGAGAGTATCATAAATGAA -s Anc1.Anc1refChr6 120840 39 + 197743 AAGACTG----GGAGGGAAGCACCGGAGAGTATCATAAATGAA -s Anc2.Anc2refChr13 95988 39 + 96486 AAGACTG----GGAGAGAAGCACAGGAGAGTATCATAAATGAA -s mr.mrrefChr3 22885 43 + 181027 AGGACTGCTCAAAGTGAAAGCATCGAAGAGTATTAGACAGGAA -s simCow_chr6.simCow.chr6 452249 38 + 602619 TAGACTG----GGGGAGGATCATT-GAGAGTATCATAAAAGAA -s simDog_chr6.simDog.chr6 445763 31 + 593897 AAGACTG----GGAGAAAAGCACAGGAGAG--------ATGAT -s simHuman_chr6.simHuman.chr6 453018 39 + 601863 AAGACTG----GGAGGGAAGTACCGGGGAATATCATAAATGAA -s simRat_chr6.simRat.chr6 477049 31 + 647215 AGGACTGCTCAAAGTGAAAGCAGCGAAGATT------------ - -a -s simMouse_chr6.simMouse.chr6 467192 17 + 636262 AACAGGTGTGAGTGAAT -s Anc0.Anc0refChr3 88383 16 + 222631 A-CAGGTAGGAGTTAAT -s Anc1.Anc1refChr6 120879 16 + 197743 A-CAGGTAGGAGTTAAT -s Anc2.Anc2refChr13 96027 16 + 96486 A-CAGGTAGGAGTTAAT -s mr.mrrefChr3 22928 16 + 181027 A-CAGGTGTGAGTTAAT -s simCow_chr6.simCow.chr6 452292 16 + 602619 A-CAGGTAGGAGTTAAT -s simDog_chr6.simDog.chr6 445794 16 + 593897 A-CAGGTAGGAGGTAAT -s simHuman_chr6.simHuman.chr6 453057 16 + 601863 A-CAGGTAGGATTTAGT -s simRat_chr6.simRat.chr6 477080 15 + 647215 --CAGGTGTGAGTTAAT - -a -s simMouse_chr6.simMouse.chr6 467209 19 + 636262 ATCACCTATATTGAAAATT -s Anc0.Anc0refChr3 88399 19 + 222631 ATAGCCTATATCAAAAGTT -s Anc1.Anc1refChr6 120895 19 + 197743 ATAGCCTATATCAAAAGTT -s Anc2.Anc2refChr13 96043 19 + 96486 ATAGTCTATATCAGAAGTT -s mr.mrrefChr3 22944 19 + 181027 ATCACCTATATTGAAAGTT -s simCow_chr6.simCow.chr6 452309 19 + 602619 ATAGTCTTTAACACAAGTT -s simDog_chr6.simDog.chr6 445810 19 + 593897 GTAGTCTATATCAGATATA -s simHuman_chr6.simHuman.chr6 453073 19 + 601863 ATAGCGTATATCAAAAGTT -s simRat_chr6.simRat.chr6 477095 19 + 647215 ATCACTTATATTGAAGGTT - -a -s simMouse_chr6.simMouse.chr6 467228 5 + 636262 ACTAT -s Anc0.Anc0refChr3 88429 5 + 222631 ACTAT -s Anc1.Anc1refChr6 120925 5 + 197743 ACTAT -s Anc2.Anc2refChr13 96073 5 + 96486 ACTAT -s mr.mrrefChr3 22963 5 + 181027 ACTAT -s simCow_chr6.simCow.chr6 452340 5 + 602619 ACTAT -s simDog_chr6.simDog.chr6 445840 5 + 593897 ACTAC -s simHuman_chr6.simHuman.chr6 453103 5 + 601863 ACTAT -s simRat_chr6.simRat.chr6 477114 5 + 647215 ACTAT - -a -s simMouse_chr6.simMouse.chr6 467233 34 + 636262 CAGAAATACTACCACCAAAAACATAAAAACATAC -s Anc0.Anc0refChr3 88454 23 + 222631 CAGAAATGCTACTTGC-----TGTAAA------C -s Anc1.Anc1refChr6 120950 23 + 197743 CAGAAATGCTACTTGC-----TGTAAA------C -s Anc2.Anc2refChr13 96098 23 + 96486 CAGAAATGCTACTTGC-----TGTAAA------C -s mr.mrrefChr3 22968 23 + 181027 CAGAAATACTACTACC-----CATAAA------C -s simCow_chr6.simCow.chr6 452365 22 + 602619 CAAACATGCT-TTTGC-----TGTAAA------C -s simDog_chr6.simDog.chr6 445865 23 + 593897 CAGAAATACTACTTGT-----TGTGAA------C -s simHuman_chr6.simHuman.chr6 453128 23 + 601863 CAGAGATGCTACTTGC-----TGTAAA------C -s simRat_chr6.simRat.chr6 477119 23 + 647215 CAGAAATACTACTGCC-----CATAAA------C - -a -s simMouse_chr6.simMouse.chr6 467267 15 + 636262 CTAATAAAACATAGC -s Anc0.Anc0refChr3 88479 15 + 222631 TGAGTTCCAGGGTGA -s Anc1.Anc1refChr6 120975 15 + 197743 TGAGTTCCAGGGTGA -s Anc2.Anc2refChr13 96123 15 + 96486 TGAGTTCCAGGGTGA -s mr.mrrefChr3 22991 15 + 181027 TTAATAAAACATAGC -s simCow_chr6.simCow.chr6 452389 15 + 602619 TGAGCTCCAGGGAGA -s simDog_chr6.simDog.chr6 445890 15 + 593897 TGAATTCCAGGGTGA -s simHuman_chr6.simHuman.chr6 453153 15 + 601863 TGAGTTCCAGGGGGA -s simRat_chr6.simRat.chr6 477142 13 + 647215 TTAA--AAACATAGC - -a -s simMouse_chr6.simMouse.chr6 467282 23 + 636262 TAATAATCTCAACTTTCTATCCA -s Anc0.Anc0refChr3 88494 23 + 222631 TAAAAATGCCAACTAACTATCTG -s Anc1.Anc1refChr6 120990 23 + 197743 TAAAAATGCCAACTAACTATCTG -s Anc2.Anc2refChr13 96138 23 + 96486 TAAAAATGCTAACTAACTATCTG -s mr.mrrefChr3 23006 23 + 181027 TAATAATCCCAACTTTCTATCCA -s simCow_chr6.simCow.chr6 452409 23 + 602619 TAAAAATGCTAACTGGCTATCTG -s simDog_chr6.simDog.chr6 445905 23 + 593897 TAAAAACACTAATCAAGTATCCA -s simHuman_chr6.simHuman.chr6 453168 23 + 601863 TAAAAATGCCAACTAACTATCTG -s simRat_chr6.simRat.chr6 477155 23 + 647215 TAATAATCCCAACTGTCTATCCA - -a -s simMouse_chr6.simMouse.chr6 467305 35 + 636262 GAGGGAGTTCATTCATGCCGCAAAGATGCTGTTGA -s Anc0.Anc0refChr3 88517 35 + 222631 CAGAGGGATCAACCATGCTACAAAGATGCTATCAA -s Anc1.Anc1refChr6 121013 35 + 197743 CAGAGGGATCAACCATGCTACAAAGATGCTATCAA -s Anc2.Anc2refChr13 96161 35 + 96486 CAGAGGGATCAACCATGCTACAAATATGCTATCAA -s mr.mrrefChr3 23029 35 + 181027 GAGGGGGTTCATTCATGCCACAAAGATGCTGTCAA -s simCow_chr6.simCow.chr6 452432 35 + 602619 CAGAGCATCCAACCTTGCTACAAACACACTATCAT -s simDog_chr6.simDog.chr6 445928 35 + 593897 CAGAGGGATCAACCATGCTACACATATGATATCAA -s simHuman_chr6.simHuman.chr6 453191 34 + 601863 CAGAGGGCTCAACCATGCTA-AAAGATGCTATCAA -s simRat_chr6.simRat.chr6 477180 35 + 647215 GAGGGGGTTCATTCAGGCCACAACAATGCTGTCAA - -a -s simMouse_chr6.simMouse.chr6 467340 12 + 636262 TAAGCCAGTTGA -s Anc0.Anc0refChr3 88555 11 + 222631 TATGTGAGCTG- -s Anc1.Anc1refChr6 121051 11 + 197743 TATGTGAGCTG- -s Anc2.Anc2refChr13 96199 11 + 96486 TATGTGAGCTG- -s mr.mrrefChr3 23064 12 + 181027 TAAGCCAGTTGA -s simCow_chr6.simCow.chr6 452470 11 + 602619 TGTTCAAGCTG- -s simDog_chr6.simDog.chr6 445966 11 + 593897 TATGTGAGCTG- -s simHuman_chr6.simHuman.chr6 453228 11 + 601863 TATGAGAGCTG- -s simRat_chr6.simRat.chr6 477215 12 + 647215 TAGGCCAGTTGA - -a -s simMouse_chr6.simMouse.chr6 467352 4 + 636262 GCCC -s Anc0.Anc0refChr3 88566 4 + 222631 GCAC -s Anc1.Anc1refChr6 121062 4 + 197743 GCAC -s Anc2.Anc2refChr13 96210 4 + 96486 GCAC -s mr.mrrefChr3 23076 4 + 181027 GCCC -s simCow_chr6.simCow.chr6 452481 4 + 602619 GCTT -s simDog_chr6.simDog.chr6 445989 4 + 593897 GCAC -s simHuman_chr6.simHuman.chr6 453239 4 + 601863 GCGC -s simRat_chr6.simRat.chr6 477227 4 + 647215 GTCC - -a -s simMouse_chr6.simMouse.chr6 467356 25 + 636262 AGTGAAGGGCACAATAGCCATGGAG -s Anc0.Anc0refChr3 88570 18 + 222631 A-------GAACAGCAGTCAAGGAG -s Anc1.Anc1refChr6 121066 18 + 197743 A-------GAACAGCAGTCAAGGAG -s Anc2.Anc2refChr13 96214 18 + 96486 A-------GATCAGCAGTCAAGGAC -s mr.mrrefChr3 23080 25 + 181027 AGTGAAGGGCACAATAGCCATGGAG -s simCow_chr6.simCow.chr6 452485 18 + 602619 A-------GATCATCAGCCACAGCC -s simDog_chr6.simDog.chr6 446012 18 + 593897 A-------AATCAGATGTCAAGGAC -s simHuman_chr6.simHuman.chr6 453243 18 + 601863 A-------GAACACCAGTCAGAATG -s simRat_chr6.simRat.chr6 477231 25 + 647215 ACTGGAGGTCTCAATGGCCACGGAG - -a -s simMouse_chr6.simMouse.chr6 467381 8 + 636262 GGTCCCTA -s Anc0.Anc0refChr3 88588 8 + 222631 GGTGCCAC -s Anc1.Anc1refChr6 121084 8 + 197743 GGTGCCAC -s Anc2.Anc2refChr13 96232 8 + 96486 CGTGCCAC -s mr.mrrefChr3 23105 8 + 181027 GGTCCCTA -s simCow_chr6.simCow.chr6 452507 8 + 602619 TGTACCAC -s simDog_chr6.simDog.chr6 446030 8 + 593897 CGTGCCAC -s simHuman_chr6.simHuman.chr6 453261 8 + 601863 GGGGCCGC -s simRat_chr6.simRat.chr6 477256 8 + 647215 GGTCCCTC - -a -s simMouse_chr6.simMouse.chr6 467389 38 + 636262 AAGAAATTGACACTACGAAGTGGGACATGTTCAGGTAG -s Anc0.Anc0refChr3 88596 3 + 222631 AAC----------------------------------- -s Anc1.Anc1refChr6 121092 11 + 197743 AACGAGTGGAT--------------------------- -s Anc2.Anc2refChr13 96240 3 + 96486 AAC----------------------------------- -s mr.mrrefChr3 23113 11 + 181027 AAGAAATTGAC--------------------------- -s simCow_chr6.simCow.chr6 452517 3 + 602619 AAT----------------------------------- -s simDog_chr6.simDog.chr6 446038 3 + 593897 AAC----------------------------------- -s simHuman_chr6.simHuman.chr6 453269 11 + 601863 AATGAGAGGAT--------------------------- -s simRat_chr6.simRat.chr6 477264 11 + 647215 AGGAAACCATC--------------------------- - -a -s simMouse_chr6.simMouse.chr6 467427 1 + 636262 A -s Anc0.Anc0refChr3 39377 1 - 222631 G -s Anc1.Anc1refChr1 47154 1 - 69767 G -s Anc2.Anc2refChr1 44215 1 - 142988 G -s mr.mrrefChr3 23124 1 + 181027 A -s mr.mrrefChr3 49362 1 - 181027 G -s simCow_chr6.simCow.chr6 45911 1 - 602619 G -s simHuman_chr6.simHuman.chr6 48057 1 - 601863 G -s simMouse_chr6.simMouse.chr6 54411 1 - 636262 G -s simRat_chr6.simRat.chr6 589827 1 + 647215 G -s simRat_chr6.simRat.chr6 477275 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 467428 5 + 636262 TGCCG -s Anc0.Anc0refChr3 39378 5 - 222631 TGGGG -s Anc1.Anc1refChr1 47155 5 - 69767 TGGGG -s Anc2.Anc2refChr1 44216 5 - 142988 TGGGG -s mr.mrrefChr3 23125 5 + 181027 TGCCG -s mr.mrrefChr3 49363 5 - 181027 ATAAT -s simCow_chr6.simCow.chr6 45924 5 - 602619 TGGGG -s simDog_chr6.simDog.chr6 48634 5 - 593897 TGGGG -s simHuman_chr6.simHuman.chr6 48058 5 - 601863 TAGGT -s simMouse_chr6.simMouse.chr6 54412 5 - 636262 ATAAT -s simRat_chr6.simRat.chr6 589828 5 + 647215 AAGCC -s simRat_chr6.simRat.chr6 477276 5 + 647215 TGCAG - -a -s simMouse_chr6.simMouse.chr6 467433 47 + 636262 CTTGTATTTTAAAAGTGGGCAAACAAATTCTCTGCTGTTATCACTGG -s Anc0.Anc0refChr3 39383 27 - 222631 CTTCTACTTTAAAATTTACCAAATAA--------------------G -s Anc1.Anc1refChr1 47160 47 - 69767 CTTCTACTTTAAAATTTACCAAATAAATACTGTGCTGTCAGAACTGG -s Anc2.Anc2refChr1 44221 27 - 142988 CTTCTACTTTAAAAGTTACCAAAACA--------------------G -s mr.mrrefChr3 23130 47 + 181027 CTTGTATTTTAAAAGTGGGCAAACAAATTCTCTGCTGTTATCACTGG -s mr.mrrefChr3 49368 47 - 181027 CTTCCACTTTAAAATTTACCCAATAAATAGAGTGCTGTTAGAATTGG -s simCow_chr6.simCow.chr6 45929 27 - 602619 CTTCTATTGTAAAAGTTACCAAAACC--------------------A -s simDog_chr6.simDog.chr6 48639 27 - 593897 CTTCTACTTTAAAAGTTACCGAGACA--------------------G -s simHuman_chr6.simHuman.chr6 48063 28 - 601863 CCAATCCATTACA-------------------TGCTGTCAGAACTGG -s simMouse_chr6.simMouse.chr6 54417 47 - 636262 CTTCCACTTTAAAATTTACCCAACAAATAGAGTGCTGTTAGAATTGG -s simRat_chr6.simRat.chr6 589834 47 + 647215 CTTCCCCATTAAAACTTACCCAATTAATCCAGTGGTGTTAGAATTGG -s simRat_chr6.simRat.chr6 477281 47 + 647215 CTTCTATTTTAATAGTTAGCGAGCAAATTCTATGCTGTTATCACTGG - -a -s simMouse_chr6.simMouse.chr6 467480 4 + 636262 GGCT -s Anc0.Anc0refChr3 39410 4 - 222631 GGCT -s Anc1.Anc1refChr1 47207 4 - 69767 GGCT -s Anc2.Anc2refChr1 44248 4 - 142988 GCCT -s mr.mrrefChr3 23177 4 + 181027 GGCT -s mr.mrrefChr3 49415 4 - 181027 GACT -s simCow_chr6.simCow.chr6 45985 4 - 602619 GCCT -s simHuman_chr6.simHuman.chr6 48091 3 - 601863 -GCT -s simMouse_chr6.simMouse.chr6 54464 4 - 636262 GACT -s simRat_chr6.simRat.chr6 589881 4 + 647215 GATT -s simRat_chr6.simRat.chr6 477328 4 + 647215 CACT - -a -s simMouse_chr6.simMouse.chr6 467484 1 + 636262 T -s Anc0.Anc0refChr3 39414 1 - 222631 T -s Anc1.Anc1refChr1 47211 1 - 69767 T -s Anc2.Anc2refChr1 44252 1 - 142988 T -s mr.mrrefChr3 23181 1 + 181027 T -s mr.mrrefChr3 49419 1 - 181027 T -s simCow_chr6.simCow.chr6 45989 1 - 602619 T -s simHuman_chr6.simHuman.chr6 48094 1 - 601863 T -s simMouse_chr6.simMouse.chr6 54468 1 - 636262 T -s simRat_chr6.simRat.chr6 589886 1 + 647215 C -s simRat_chr6.simRat.chr6 477332 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 467485 6 + 636262 TGAACT -s Anc0.Anc0refChr3 39438 6 - 222631 TGAGAC -s Anc1.Anc1refChr1 47235 6 - 69767 TGAGAC -s Anc2.Anc2refChr1 44276 6 - 142988 TAAGAC -s mr.mrrefChr3 23182 6 + 181027 TGAACT -s mr.mrrefChr3 49448 6 - 181027 AGAGAC -s simCow_chr6.simCow.chr6 46013 6 - 602619 TAAAGC -s simDog_chr6.simDog.chr6 48744 6 - 593897 TAAGAC -s simHuman_chr6.simHuman.chr6 48118 6 - 601863 TGAGTG -s simMouse_chr6.simMouse.chr6 54497 6 - 636262 AGATAC -s simRat_chr6.simRat.chr6 589915 6 + 647215 AGAGAC -s simRat_chr6.simRat.chr6 477355 6 + 647215 TGAGCT - -a -s simMouse_chr6.simMouse.chr6 467491 14 + 636262 GCTCTCAATGGTAC -s Anc0.Anc0refChr3 39444 13 - 222631 ACTCTCAACGGC-C -s Anc1.Anc1refChr1 47241 13 - 69767 ACTCTCAACGGC-C -s Anc2.Anc2refChr1 44282 13 - 142988 ACTCTCAACTGC-C -s mr.mrrefChr3 23188 13 + 181027 GCTCTCAATGGT-C -s mr.mrrefChr3 49454 13 - 181027 CCTCTCAGTGGC-A -s simCow_chr6.simCow.chr6 46020 13 - 602619 ACTCTCATTAGC-A -s simDog_chr6.simDog.chr6 48750 13 - 593897 ACTCTCAACTGC-C -s simHuman_chr6.simHuman.chr6 48124 13 - 601863 ACTCTCAACGGC-C -s simMouse_chr6.simMouse.chr6 54503 13 - 636262 CCCCTCAGTGGC-A -s simRat_chr6.simRat.chr6 589921 13 + 647215 CCTCTCAGTGAC-A -s simRat_chr6.simRat.chr6 477361 13 + 647215 GCTCTCAGTGGT-C - -a -s simMouse_chr6.simMouse.chr6 467505 1 + 636262 A -s Anc0.Anc0refChr3 39459 1 - 222631 A -s Anc1.Anc1refChr1 47256 1 - 69767 A -s Anc2.Anc2refChr1 44297 1 - 142988 A -s mr.mrrefChr3 23201 1 + 181027 A -s mr.mrrefChr3 49469 1 - 181027 A -s simCow_chr6.simCow.chr6 46035 1 - 602619 A -s simDog_chr6.simDog.chr6 48765 1 - 593897 A -s simHuman_chr6.simHuman.chr6 48137 1 - 601863 A -s simMouse_chr6.simMouse.chr6 54518 1 - 636262 G -s simRat_chr6.simRat.chr6 589936 1 + 647215 A -s simRat_chr6.simRat.chr6 477374 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 467506 1 + 636262 A -s mr.mrrefChr3 23202 1 + 181027 A -s simRat_chr6.simRat.chr6 477375 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 467507 22 + 636262 GGAACCTATGCATTCCTTCCCC -s Anc0.Anc0refChr3 39460 22 - 222631 GGGTCCTATGCATTTCTTCCCC -s Anc1.Anc1refChr1 47257 22 - 69767 GGGTCCTATGCATTTCTTCCCC -s Anc2.Anc2refChr1 44298 22 - 142988 GAGTCCTATGCATTTCTTTCCC -s mr.mrrefChr3 23203 22 + 181027 GGAACCTATGCATTCCTTCCCC -s mr.mrrefChr3 49470 22 - 181027 GGTACCTATGCATTCCTTCCCC -s simCow_chr6.simCow.chr6 46036 22 - 602619 GAACCCTATGCATTCCTTTCCC -s simDog_chr6.simDog.chr6 48766 22 - 593897 TAGTCTTGTGCATTTCTTTGCC -s simHuman_chr6.simHuman.chr6 48138 22 - 601863 GGGTCCTATGCATTTTTTCCCC -s simMouse_chr6.simMouse.chr6 54519 22 - 636262 GGTACCTATGCATTCCTTCCCC -s simRat_chr6.simRat.chr6 589937 22 + 647215 GGTACCTGTGCATTCATTCCCC -s simRat_chr6.simRat.chr6 477376 22 + 647215 GGTACCTATGTATTCCTTCCCC - -a -s simMouse_chr6.simMouse.chr6 467529 10 + 636262 CCCTTGTTCA -s Anc0.Anc0refChr3 39482 5 - 222631 C-----TGCA -s Anc1.Anc1refChr1 47279 5 - 69767 C-----TGCA -s Anc2.Anc2refChr1 44320 5 - 142988 C-----TGCA -s mr.mrrefChr3 23225 10 + 181027 CCCTTGTTCA -s simCow_chr6.simCow.chr6 46058 5 - 602619 C-----TGCA -s simHuman_chr6.simHuman.chr6 48160 5 - 601863 T-----TGCA -s simRat_chr6.simRat.chr6 477398 10 + 647215 CCCTTGCACA - -a -s simMouse_chr6.simMouse.chr6 467539 13 + 636262 CTCACTGTTACCA -s Anc0.Anc0refChr3 39487 13 - 222631 CTTACTATTAGCA -s Anc1.Anc1refChr1 47284 13 - 69767 CTTACTATTAGCA -s Anc2.Anc2refChr1 44325 13 - 142988 CTTATTATTAGCA -s mr.mrrefChr3 23235 13 + 181027 CTCACTGTTACCA -s mr.mrrefChr3 49492 13 - 181027 CCTACTGTTAGCA -s simCow_chr6.simCow.chr6 46063 13 - 602619 CTTATTATTAGCA -s simHuman_chr6.simHuman.chr6 48165 13 - 601863 CTTACTATTAGCA -s simMouse_chr6.simMouse.chr6 54541 13 - 636262 CCTACTGTTAGCA -s simRat_chr6.simRat.chr6 589959 13 + 647215 CCTACCGTTAGCA -s simRat_chr6.simRat.chr6 477408 13 + 647215 CTCACTGTTAGCA - -a -s simMouse_chr6.simMouse.chr6 467552 1 + 636262 G -s Anc0.Anc0refChr3 39500 1 - 222631 G -s Anc1.Anc1refChr1 47297 1 - 69767 G -s Anc2.Anc2refChr1 44338 1 - 142988 G -s mr.mrrefChr3 23248 1 + 181027 G -s mr.mrrefChr3 49505 1 - 181027 G -s simCow_chr6.simCow.chr6 46076 1 - 602619 G -s simHuman_chr6.simHuman.chr6 48178 1 - 601863 G -s simMouse_chr6.simMouse.chr6 54554 1 - 636262 G -s simRat_chr6.simRat.chr6 477421 1 + 647215 G - -a -s simMouse_chr6.simMouse.chr6 467553 8 + 636262 GGGGCTGG -s Anc0.Anc0refChr3 39501 6 - 222631 GGTGCT-- -s Anc1.Anc1refChr1 47298 8 - 69767 GGTGCTGC -s Anc2.Anc2refChr1 44339 6 - 142988 GGTGCT-- -s mr.mrrefChr3 23249 8 + 181027 GGGGCTGG -s mr.mrrefChr3 49506 8 - 181027 GGGGCTGC -s simCow_chr6.simCow.chr6 46077 6 - 602619 GGTGCT-- -s simHuman_chr6.simHuman.chr6 48179 6 - 601863 GGTGC--C -s simMouse_chr6.simMouse.chr6 54555 8 - 636262 GGGGCTGG -s simRat_chr6.simRat.chr6 589972 8 + 647215 GGGGCTGC -s simRat_chr6.simRat.chr6 477422 8 + 647215 GGGGCTGG - -a -s simMouse_chr6.simMouse.chr6 467561 7 + 636262 AATGTAT -s Anc0.Anc0refChr3 39507 7 - 222631 CATGTCT -s Anc1.Anc1refChr1 47306 7 - 69767 CATGTCT -s Anc2.Anc2refChr1 44345 7 - 142988 CGTGTCT -s mr.mrrefChr3 23257 7 + 181027 AATGTAT -s mr.mrrefChr3 49514 7 - 181027 CATGTAT -s simCow_chr6.simCow.chr6 46085 7 - 602619 CGTGTCT -s simHuman_chr6.simHuman.chr6 48185 7 - 601863 CATGGCT -s simMouse_chr6.simMouse.chr6 54563 7 - 636262 CATGTAT -s simRat_chr6.simRat.chr6 589980 7 + 647215 CATGCAT -s simRat_chr6.simRat.chr6 477430 7 + 647215 CATATAT - -a -s simMouse_chr6.simMouse.chr6 467568 40 + 636262 TGGTTATTAAGCATGCTACTGGTATCAAATTCCAGGGTGC -s Anc0.Anc0refChr3 39517 40 - 222631 TGGCTGTTAAGCATAACTATAGTATCAAATTCTAAGGTGC -s Anc1.Anc1refChr1 47316 40 - 69767 TGGCTGTTAAGCATAACTATAGTATCAAATTCTAAGGTGC -s Anc2.Anc2refChr1 44355 40 - 142988 TGACGGTTAAGCATAACTATAGTCTCAAGTTCTAAGGTGC -s mr.mrrefChr3 23264 40 + 181027 TGGTTATTAAGCATGCTACTGGTATCAAATTCCAGGGTGC -s mr.mrrefChr3 49521 40 - 181027 TGGCTGTTAAGCATACCTCTGATATGAAATTCTAAGGTGC -s simCow_chr6.simCow.chr6 46095 40 - 602619 TGACGGTCAAGCATGACTATAGTCTCAAGTCCCAAAGTGC -s simDog_chr6.simDog.chr6 48788 34 - 593897 ------TTAAGCATAACTATGGTCTCAAGTTCTAAGGTGC -s simHuman_chr6.simHuman.chr6 48195 40 - 601863 TGGCTGTTAATCATAATCATAGTATCAAATTCTGAGGCTC -s simMouse_chr6.simMouse.chr6 54570 40 - 636262 TGGCTGTTAAGCATACCTCTGATATGAAATTCTAAGGTGC -s simRat_chr6.simRat.chr6 589987 40 + 647215 TGGCAATTAAGCATACCTCTGATATGAAATTCTAAGGTGT -s simRat_chr6.simRat.chr6 477437 40 + 647215 TCATTATTAAGCATGCTACTGATATCAAATCCTAGGGCGC - -a -s simMouse_chr6.simMouse.chr6 467608 6 + 636262 TGTGGT -s Anc0.Anc0refChr3 39557 6 - 222631 TGTGCT -s Anc1.Anc1refChr1 47356 6 - 69767 TGTGCT -s Anc2.Anc2refChr1 44395 6 - 142988 TATGCT -s mr.mrrefChr3 23304 6 + 181027 TGTGGT -s mr.mrrefChr3 49561 6 - 181027 TGTGGT -s simCow_chr6.simCow.chr6 46135 6 - 602619 TAAAGT -s simDog_chr6.simDog.chr6 48822 6 - 593897 TATGCT -s simHuman_chr6.simHuman.chr6 48245 6 - 601863 TGTGCT -s simMouse_chr6.simMouse.chr6 54610 6 - 636262 TGTGGT -s simRat_chr6.simRat.chr6 590027 6 + 647215 TGTGGT -s simRat_chr6.simRat.chr6 477477 6 + 647215 TGTGGT - -a -s simMouse_chr6.simMouse.chr6 467614 1 + 636262 G -s Anc0.Anc0refChr3 39563 1 - 222631 G -s Anc1.Anc1refChr1 47362 1 - 69767 G -s Anc2.Anc2refChr1 44401 1 - 142988 G -s mr.mrrefChr3 23310 1 + 181027 G -s mr.mrrefChr3 49567 1 - 181027 G -s simCow_chr6.simCow.chr6 46141 1 - 602619 G -s simDog_chr6.simDog.chr6 48828 1 - 593897 A -s simHuman_chr6.simHuman.chr6 48251 1 - 601863 G -s simMouse_chr6.simMouse.chr6 54616 1 - 636262 G -s simRat_chr6.simRat.chr6 477483 1 + 647215 G - -a -s simMouse_chr6.simMouse.chr6 467615 6 + 636262 ACACCC -s Anc0.Anc0refChr3 39564 6 - 222631 ACATTC -s Anc1.Anc1refChr1 47363 6 - 69767 ACATTC -s Anc2.Anc2refChr1 44402 6 - 142988 ACATTC -s mr.mrrefChr3 23311 6 + 181027 ACACCC -s mr.mrrefChr3 49568 6 - 181027 AAATTC -s simCow_chr6.simCow.chr6 46142 6 - 602619 ACATTC -s simDog_chr6.simDog.chr6 48829 6 - 593897 ACATTC -s simHuman_chr6.simHuman.chr6 48252 6 - 601863 ACATTC -s simMouse_chr6.simMouse.chr6 54617 6 - 636262 AAATTC -s simRat_chr6.simRat.chr6 590033 6 + 647215 AAATTC -s simRat_chr6.simRat.chr6 477484 6 + 647215 ACATTC - -a -s simMouse_chr6.simMouse.chr6 467621 2 + 636262 AG -s Anc0.Anc0refChr3 39570 2 - 222631 AG -s Anc1.Anc1refChr1 47369 2 - 69767 AG -s Anc2.Anc2refChr1 44408 2 - 142988 AG -s mr.mrrefChr3 23317 2 + 181027 AG -s mr.mrrefChr3 49574 2 - 181027 AG -s simCow_chr6.simCow.chr6 46148 2 - 602619 AG -s simDog_chr6.simDog.chr6 48838 2 - 593897 AG -s simHuman_chr6.simHuman.chr6 48258 2 - 601863 AG -s simMouse_chr6.simMouse.chr6 54623 2 - 636262 GG -s simRat_chr6.simRat.chr6 590039 2 + 647215 AG -s simRat_chr6.simRat.chr6 477490 2 + 647215 AG - -a -s simMouse_chr6.simMouse.chr6 467623 2 + 636262 GG -s Anc0.Anc0refChr3 39572 2 - 222631 GC -s Anc1.Anc1refChr1 47371 2 - 69767 GC -s Anc2.Anc2refChr1 44410 2 - 142988 GC -s mr.mrrefChr3 23319 2 + 181027 GG -s mr.mrrefChr3 49576 2 - 181027 CT -s simCow_chr6.simCow.chr6 46150 2 - 602619 GC -s simDog_chr6.simDog.chr6 48840 2 - 593897 GC -s simHuman_chr6.simHuman.chr6 48260 2 - 601863 GC -s simMouse_chr6.simMouse.chr6 54671 2 - 636262 CT -s simRat_chr6.simRat.chr6 590041 2 + 647215 CT -s simRat_chr6.simRat.chr6 477492 2 + 647215 GG - -a -s simMouse_chr6.simMouse.chr6 467625 6 + 636262 GAAACA -s Anc0.Anc0refChr3 39577 6 - 222631 CAGATA -s Anc1.Anc1refChr1 47376 6 - 69767 CAGATA -s Anc2.Anc2refChr1 44415 6 - 142988 CAGATA -s mr.mrrefChr3 23321 6 + 181027 GAAACA -s mr.mrrefChr3 49578 6 - 181027 CAAACA -s simCow_chr6.simCow.chr6 46155 6 - 602619 CAGATA -s simDog_chr6.simDog.chr6 48845 6 - 593897 CAGAAA -s simHuman_chr6.simHuman.chr6 48265 6 - 601863 CAGATA -s simMouse_chr6.simMouse.chr6 54673 6 - 636262 CAAACA -s simRat_chr6.simRat.chr6 590043 6 + 647215 CAAACA -s simRat_chr6.simRat.chr6 477494 6 + 647215 CAAACA - -a -s simMouse_chr6.simMouse.chr6 467631 206 + 636262 AAAGTATAACCTGGCATAACTCATTTGCTTAAAAAGCACCAAAAGATGTGTCCTTAACTAATTATAATAACTTACTATGCAGGTTCTATGTATCAAGGAATTACCTCTGCCTAACTTATTAACCGTTATCAGTTTCTCTTTTCAGTCTGGGAGATCTACCCTGCCTGATGGCTAAGGGTCTTTAAGACTGGGCAACTACCCTTCAC -s Anc1.Anc1refChr6 121103 37 + 197743 CCAGCAAAAGATGCTAGAACAAATCCCTTCAAGATGC------------------------------------------------------------------------------------------------------------------------------------------------------------------------- -s mr.mrrefChr3 23327 206 + 181027 AAAGTATAACCTGGCATAACTCATTTGCTTAAAAAGCACCAAAAGATGTGTCCTTAACTAATTATAATAACTTACTATGCAGGTTCTATGTATCAAGGAATTACCTCTGCCTAACTTATTAACCGTTATCAGTTTCTCTTTTCAGTCTGGGAGATCTACCCTGCCTGATGGCTAAGGGTCTTTAAGACTGGGCAACTACCCTTCAC -s simHuman_chr6.simHuman.chr6 453283 37 + 601863 CCAGCAAAAGATGCTAGAACAAATCCCTTCAAGATGC------------------------------------------------------------------------------------------------------------------------------------------------------------------------- -s simRat_chr6.simRat.chr6 477500 206 + 647215 AAAGTACAACCTGGCATAATTCATTTGCTTAAAAAGCACTAGAAGGTGTGTTCCTCACTAATTACAATAACTTACTATGAGGGTTTTATGTGTCAAGGATTAACTTCTGCCTAACTTATGAAGTGTTATCAGTTTCTCTTTTCAGTCTGGGAGATCTATACTGCCTGATGGCTGAGGGTCTTTGAGACTGGGCAACTACATTTCAC - -a -s simMouse_chr6.simMouse.chr6 467837 27 + 636262 AATTGGCTAATCATGTTTCCATGTGGC -s mr.mrrefChr3 23533 27 + 181027 AATTGGCTAATCATGTTTCCATGTGGC -s simRat_chr6.simRat.chr6 477707 27 + 647215 TTTTGGCTAATCAGGGTTCCAAATTGT - -a -s simMouse_chr6.simMouse.chr6 467864 58 + 636262 AATCAGGAATATTGGCTATGATCCTTTTTACTTCCACTCACCATAACTGCACCCCAAG -s mr.mrrefChr3 23560 51 + 181027 AATCAGGAATATTGGCTATGATCCTTTTTAC-------CACCATAACTGCACCCCAAG -s simRat_chr6.simRat.chr6 477786 51 + 647215 AATCAGCAGTATTGGCTATGATCCTCTTTAC-------AGCCATAACTACACCCCAAG - -a -s simMouse_chr6.simMouse.chr6 467922 186 + 636262 AGTTAGCTAAGTGATGTGTAAAGAAACCAACTGCCAAAGTGTCTCAACAATACAATCATGACATTTTGTTCCCAAGATTGTCTTAGTATAGAGGTGAGTTCCCAATTTCCCTATGCTTACCTGGGATCTTATCAGCACCCTTTTAAGAGAATACCTTCCTTTGCAAGGTCTTGTTTTAAGGCACTT -s Anc1.Anc1refChr6 121140 49 + 197743 -----------------------------------------------------------------------------------------------------------------------------------------TCCTTTCGACAGGAGAGCTTCCCCCACAAGGACTTGTATTAAAAGACTT -s mr.mrrefChr3 23611 180 + 181027 AGTTAGCTAAG---TGTGTAAAGAAACCAACTGCCAAAGTGTCTCAACAATACAATCATGACATTTTGTTCCCAAGATTGTCTTAGTATAGAGGTGAGTTCCCAATTTCCCTATGCTTAC---GGATCTTATCAGCACCCTTTTAAGAGGATACCTTCCCTTGCAAGGACTTGTTTTAAAGCACTT -s simHuman_chr6.simHuman.chr6 453320 49 + 601863 -----------------------------------------------------------------------------------------------------------------------------------------TCCTTTCGACAGGAGAGCTTCCCCCACAAGGACTTGTATTAAAAGACTT -s simRat_chr6.simRat.chr6 477840 180 + 647215 AGTTAGCTAAG---CGCGGCAAGATACCAACTGCCAAAGTGTCTCAACAATACAATCATGACATTTTGTTCCCAAGCTTGTCTTATTATAGAGGTGAGTTCCCAATTTTCCTATGCTTAT---GGATTGTATTAGCACTGTCTTAAGAGGATACCTTCCCTTGCAAGGACATGTTTAAAAGCACTT - -a -s simMouse_chr6.simMouse.chr6 468108 89 + 636262 CACTGGCTGGGCTGCCCCAGGGATGTGTATTATCATATTAGACATATCAATGCGCGTAAAACACAAGCCTCAGACAGCTTAATGCTCCA -s Anc0.Anc0refChr3 88599 36 + 222631 ----------------------------ATCATCA-------------------------ACACAAACCTCAAGAAGTTTGACTTCCCA -s Anc1.Anc1refChr6 121189 64 + 197743 TACCGTCTGGGCTGGCTGAGGACTGTGTATCATCA-------------------------ACACAAACCTCAAGAAGTTTGACTTCCCA -s Anc2.Anc2refChr13 4757 36 + 96486 ----------------------------ATCATGA-------------------------ACACAAACCTCAAGAACTTTGACTTCCCA -s mr.mrrefChr3 23791 64 + 181027 CACTGTCTGGGCTGCCCCAGGGATGTGTATTATCA-------------------------ACACAAACCTCAGACAGTTTAACTCTCCA -s simCow_chr6.simCow.chr6 360175 36 + 602619 ----------------------------TTCACAA-------------------------ACACCAGTCTCAAGAAATTCAACTACTCA -s simDog_chr6.simDog.chr6 144649 36 - 593897 ----------------------------ATTATGA-------------------------ACACAAACCTCAAGAACTCTGACTTACTG -s simHuman_chr6.simHuman.chr6 453373 64 + 601863 TACCGTCTGGGCTGGCTGAGGACTGTGTATCATCA-------------------------TCACAAACCTCAACAAGTTTGACTTCCCA -s simRat_chr6.simRat.chr6 478020 64 + 647215 CACTCTCTGGGCTACTCAAGGGACATGTATTATCA-------------------------ACACAAACCTCAGACAGTTTAACTCTCCA - -a -s simMouse_chr6.simMouse.chr6 468197 3 + 636262 GGC -s Anc0.Anc0refChr3 88635 3 + 222631 GGT -s Anc1.Anc1refChr6 121253 3 + 197743 GGT -s Anc2.Anc2refChr13 4793 3 + 96486 GGT -s mr.mrrefChr3 23855 3 + 181027 GGC -s simCow_chr6.simCow.chr6 360224 3 + 602619 GGT -s simDog_chr6.simDog.chr6 144685 3 - 593897 GGG -s simHuman_chr6.simHuman.chr6 453437 3 + 601863 GGT -s simRat_chr6.simRat.chr6 478084 3 + 647215 GGC - -a -s simMouse_chr6.simMouse.chr6 468200 65 + 636262 ACAGTTCCATTCAGATGGGCAGGGGCTATGGACCTGCCGCTTCCACAGTTGCATCTGCCGCTTCC -s Anc0.Anc0refChr3 88676 38 + 222631 ------CAGTTCAG---G-------------CCCAGCTCAGTCC-----TACATTTGCCGCTTAA -s Anc1.Anc1refChr6 121298 47 + 197743 ACAGCCCAGTTCAGTCCG-------------CCCAGCTCAGTCC-----TACATTTGCCGCTTAA -s Anc2.Anc2refChr13 4834 38 + 96486 ------CAGTTTAG---G-------------CCCAGCTCAGACC-----TACATTTGCCGCTCAA -s mr.mrrefChr3 23884 65 + 181027 ACAGCTCCATTCAGATGGGCAGGGGCTATGGACCTGCTGCTTCCACAGTTGCATCTGCCGCTTCC -s simCow_chr6.simCow.chr6 360279 38 + 602619 ------CAGCGTAG---G-------------CCCAGCTCAGACC-----TCCATTTGCTGCTCAA -s simDog_chr6.simDog.chr6 144725 37 - 593897 ------CAGTTTAG---G-------------CCCAGAACAG-AC-----TACACTTGCCACTCAA -s simHuman_chr6.simHuman.chr6 453482 47 + 601863 ACAGCCCAGCTCAGTCCG-------------CCCAGCTCAGTCC-----TACTTTTGCCGCTTAT -s simRat_chr6.simRat.chr6 478117 65 + 647215 ACAGCTCCATTCAGATGTGCATTGGCTATGGACCTGCTGCTTCGACAGTTGCATCTGCTGCTTCC - -a -s simMouse_chr6.simMouse.chr6 468265 27 + 636262 CACAGTTGCCATAAGCTGTATATCGAA -s Anc0.Anc0refChr3 88721 27 + 222631 CACAAGTGACATAAGCTGTATATAGAT -s Anc1.Anc1refChr6 121352 27 + 197743 CACAAGTGACATAAGCTGTATATAGAT -s Anc2.Anc2refChr13 4879 27 + 96486 CACAAGTGACATAAGCTGTATATAGGT -s mr.mrrefChr3 23949 27 + 181027 CACAGTTGCCATAAGCTGTATATCGAA -s simCow_chr6.simCow.chr6 360324 27 + 602619 CACGAGGGGAATACGCTGTATATAGGT -s simDog_chr6.simDog.chr6 144769 27 - 593897 CACAAGTGACATAAGCTGCACACGGGA -s simHuman_chr6.simHuman.chr6 453536 27 + 601863 TGCAAGTGATGTAAGCTGTATCTACAT -s simRat_chr6.simRat.chr6 478182 27 + 647215 CACAGTTGCCATAGGTTGTATATCAAC - -a -s simMouse_chr6.simMouse.chr6 468292 10 + 636262 CCCACCATGA -s Anc0.Anc0refChr3 88767 1 + 222631 ---------G -s Anc1.Anc1refChr6 121398 1 + 197743 ---------G -s Anc2.Anc2refChr13 4925 1 + 96486 ---------G -s mr.mrrefChr3 23995 10 + 181027 CCCACCATGA -s simCow_chr6.simCow.chr6 360376 1 + 602619 ---------C -s simDog_chr6.simDog.chr6 144816 1 - 593897 ---------G -s simHuman_chr6.simHuman.chr6 453582 1 + 601863 ---------G -s simRat_chr6.simRat.chr6 478228 10 + 647215 CCCACCCTGA - -a -s simMouse_chr6.simMouse.chr6 468302 6 + 636262 CAGAAT -s Anc0.Anc0refChr3 88768 6 + 222631 CATGAT -s Anc1.Anc1refChr6 121399 6 + 197743 CATGAT -s Anc2.Anc2refChr13 4927 6 + 96486 CATGAC -s mr.mrrefChr3 24005 6 + 181027 CAGGAT -s simCow_chr6.simCow.chr6 360378 6 + 602619 CATGGC -s simDog_chr6.simDog.chr6 144818 6 - 593897 CATGAC -s simHuman_chr6.simHuman.chr6 453583 6 + 601863 CATGAT -s simRat_chr6.simRat.chr6 478238 6 + 647215 CAGGAT - -a -s simMouse_chr6.simMouse.chr6 468308 14 + 636262 GAGAACCACAAGTA -s Anc0.Anc0refChr3 88774 14 + 222631 GAGAGCCACTAGTA -s Anc1.Anc1refChr6 121405 14 + 197743 GAGAGCCACTAGTA -s Anc2.Anc2refChr13 4933 14 + 96486 GAGAGCCACTAGTC -s mr.mrrefChr3 24011 14 + 181027 GAGAACCACAAGTA -s simCow_chr6.simCow.chr6 360388 14 + 602619 GAGAGCCATTAGTC -s simDog_chr6.simDog.chr6 144824 14 - 593897 TAGAGCAACTAGTC -s simHuman_chr6.simHuman.chr6 453589 14 + 601863 GAAAGCCACTGATA -s simRat_chr6.simRat.chr6 478244 14 + 647215 GAGAACCACAAGTA - -a -s simMouse_chr6.simMouse.chr6 468322 45 + 636262 TTCCCAGGATTTGCAGCTGTTTGCCATGCACAACCTTAGGGGCAA -s Anc0.Anc0refChr3 88792 45 + 222631 TGTCCAGGATGTGCAAATATTTACTCTAAGTAATTTTGGAGCCAA -s Anc1.Anc1refChr6 121423 45 + 197743 TGTCCAGGATGTGCAAATATTTACTCTAAGTAATTTTGGAGCCAA -s Anc2.Anc2refChr1 0 14 + 142988 -------------------------------AATTTTGGAGCCAA -s Anc2.Anc2refChr13 4951 31 + 96486 TGTTCAGGATGTGCACATATTTACCCTAAGT-------------- -s mr.mrrefChr3 24025 45 + 181027 TTCCCAGGATGTGCAACTGTTTACCATGCACAACCTTAGGGGCAA -s simCow_chr6.simCow.chr6 360406 31 + 602619 CACTCAGGATGCGCACATATTTACGCTAAGT-------------- -s simDog_chr6.simDog.chr6 144842 45 - 593897 TGTTCGGGATGTGCACATATTTACCCAAAATAATTTTGGAGCCAA -s simHuman_chr6.simHuman.chr6 453607 45 + 601863 TGTCCAGGATGTGCAAATATTTACTCTAAGTAATTTTGGAGAAAA -s simRat_chr6.simRat.chr6 478258 45 + 647215 TTCCCAGGATGCATGACTGTTCACCATGCACAACCTTAAGGGCAA - -a -s simMouse_chr6.simMouse.chr6 468367 67 + 636262 GTAAAAACTTATGTATCTGCTTCTTGTATAGTTTGACAATTCAGCAGGGCTCTGATGTGGGGTCAAG -s Anc0.Anc0refChr3 88837 64 + 222631 GTCCAAACTTATATATTTGGTTCTT---TAGTTATATAATTCTTCAGGTCTCCGATATGAGATCAAC -s Anc1.Anc1refChr6 121468 64 + 197743 GTCCAAACTTATATATTTGGTTCTT---TAGTTATATAATTCTTCAGGTCTCCGATATGAGATCAAC -s Anc2.Anc2refChr1 14 64 + 142988 GTCCAAACTTATATATTTGGTTCTA---TAGTTATATAGTTCTTCAGGTCTCCGATATGAGATCAAC -s mr.mrrefChr3 24070 67 + 181027 GTAAAAACTTATGTATCTGCTTCTTGTATAGTTTGACAATTCATCAGGGCTCCGATGTGGGGTCAAC -s simCow_chr6.simCow.chr6 453396 64 + 602619 GTCCAAGTTGATATATTTGGTTCCA---TGGTTACATAGTACTTCAGGTCTCTGATGTGAGATCAAC -s simDog_chr6.simDog.chr6 144887 64 - 593897 GTCCCAACTTATATATTAGGTTCTA---TAGTTATATAGTTCTTCAGGTCCCCAATATGAGATCAAC -s simHuman_chr6.simHuman.chr6 453652 58 + 601863 GTCCAAACTTATATAGTTGGTTCTT---TAGTTATATAATTCTTCAGGTCTCCGA------ATCAGC -s simRat_chr6.simRat.chr6 478303 67 + 647215 GTAAAAACTAATCTGTCTGCTTCCAGTATAATTTGACAATTCATCAGGGCTCCGATGTGGGGTCAAC - -a -s simMouse_chr6.simMouse.chr6 468434 35 + 636262 CATCACTACCAAGGATCAACCATCATTCCAGGCTG -s Anc0.Anc0refChr3 88901 15 + 222631 CATCACT--------------------CTAAGCTG -s Anc1.Anc1refChr6 121532 15 + 197743 CATCACT--------------------CTAAGCTG -s Anc2.Anc2refChr1 78 15 + 142988 CATTGCT--------------------CTAAGCAA -s mr.mrrefChr3 24137 35 + 181027 CATCACTATCAAGGATCAACCAAAATTCCAGGCTG -s simCow_chr6.simCow.chr6 453460 15 + 602619 CAGTGCT--------------------CCAAGCAA -s simDog_chr6.simDog.chr6 144952 15 - 593897 CATTGCT--------------------CTAGGCAA -s simHuman_chr6.simHuman.chr6 453710 15 + 601863 CATCACT--------------------CTAAGCTG -s simRat_chr6.simRat.chr6 478370 35 + 647215 CATCACTATGACAGATCACCCAAAATTCCATGCCA - -a -s simMouse_chr6.simMouse.chr6 468469 6 + 636262 GGTGTT -s Anc0.Anc0refChr3 88919 6 + 222631 GTTGTC -s Anc1.Anc1refChr6 121550 6 + 197743 GTTGTC -s Anc2.Anc2refChr1 96 6 + 142988 GTTGTC -s mr.mrrefChr3 24172 6 + 181027 GGTGTC -s simCow_chr6.simCow.chr6 453478 6 + 602619 TTTGTC -s simDog_chr6.simDog.chr6 144970 6 - 593897 GTTGTT -s simHuman_chr6.simHuman.chr6 453728 6 + 601863 GTTGTC -s simRat_chr6.simRat.chr6 478405 6 + 647215 GGTGTC - -a -s simMouse_chr6.simMouse.chr6 468475 24 + 636262 GCATTGTCTTTCTTCACACTCCAA -s Anc0.Anc0refChr3 88935 24 + 222631 ACTTTTACATTTTGCACACTTCAA -s Anc1.Anc1refChr6 121566 24 + 197743 ACTTTTACATTTTGCACACTTCAA -s Anc2.Anc2refChr1 112 24 + 142988 TCTTTTATACTTGGCACACTTCAA -s mr.mrrefChr3 24178 24 + 181027 ACATTGTCTTTCTTCACACTTCAA -s simCow_chr6.simCow.chr6 453494 24 + 602619 TCTTTTATACTTGGCAAACTCCTC -s simDog_chr6.simDog.chr6 144986 24 - 593897 TCTTTTATACTTGGCACATATGAA -s simHuman_chr6.simHuman.chr6 453744 24 + 601863 ACTTTTACATTTTGCACACTTCAA -s simRat_chr6.simRat.chr6 478411 24 + 647215 ACCTTGTCTCTCTTCACACTTCAA - -a -s simMouse_chr6.simMouse.chr6 468499 30 + 636262 GCTGTGGTACATGCAGGTATAATTTAGGCA -s Anc0.Anc0refChr3 88967 30 + 222631 GCTATGGTTCAATCAGGTACAATTTGAACA -s Anc1.Anc1refChr6 121598 30 + 197743 GCTATGGTTCAATCAGGTACAATTTGAACA -s Anc2.Anc2refChr1 144 30 + 142988 GCTATGGTTCAATCAGGTACAATTTGAACA -s mr.mrrefChr3 24202 30 + 181027 GCTGTGGTACATGCAGGTATAATTTAGACA -s simCow_chr6.simCow.chr6 453526 30 + 602619 GTTATGGTTCAACCAGGTACAAGTCAGACA -s simDog_chr6.simDog.chr6 145018 30 - 593897 GCTATACCTCAATTGGGTACAATGTGAACA -s simHuman_chr6.simHuman.chr6 453776 30 + 601863 GCTTTGGTCCGATCAGGTACAATTTGAACA -s simRat_chr6.simRat.chr6 478435 27 + 647215 GCTGTG---CACCCAGGTATAATTTAGACA - -a -s simMouse_chr6.simMouse.chr6 468529 8 + 636262 TTCATATT -s Anc0.Anc0refChr3 88999 8 + 222631 TCCATATT -s Anc1.Anc1refChr6 121630 8 + 197743 TCCATATT -s Anc2.Anc2refChr1 176 8 + 142988 TCCATATT -s mr.mrrefChr3 24232 8 + 181027 TTCATATT -s simCow_chr6.simCow.chr6 453558 8 + 602619 TCCACACT -s simDog_chr6.simDog.chr6 145050 8 - 593897 TCCCTATT -s simHuman_chr6.simHuman.chr6 453808 8 + 601863 TCCATAAT -s simRat_chr6.simRat.chr6 478462 8 + 647215 TTCAAATT - -a -s simMouse_chr6.simMouse.chr6 468537 1 + 636262 T -s Anc0.Anc0refChr3 89007 1 + 222631 A -s Anc1.Anc1refChr6 121638 1 + 197743 A -s Anc2.Anc2refChr1 184 1 + 142988 A -s mr.mrrefChr3 24240 1 + 181027 T -s simCow_chr6.simCow.chr6 453566 1 + 602619 A -s simDog_chr6.simDog.chr6 145058 1 - 593897 A -s simHuman_chr6.simHuman.chr6 453816 1 + 601863 A -s simRat_chr6.simRat.chr6 478472 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 468538 6 + 636262 GGTGGT -s Anc0.Anc0refChr3 89008 6 + 222631 GTTTGT -s Anc1.Anc1refChr6 121639 6 + 197743 GTTTGT -s Anc2.Anc2refChr1 185 6 + 142988 GTCTTG -s mr.mrrefChr3 24241 6 + 181027 GGTGGT -s simCow_chr6.simCow.chr6 453568 6 + 602619 GTCTTG -s simDog_chr6.simDog.chr6 145059 6 - 593897 GTCTTG -s simHuman_chr6.simHuman.chr6 453817 6 + 601863 ATTTGT -s simRat_chr6.simRat.chr6 478473 6 + 647215 GGTGGT - -a -s simMouse_chr6.simMouse.chr6 468544 27 + 636262 CCATAATCTAAAGTTACTACAACACAG -s Anc0.Anc0refChr3 89014 24 + 222631 TC---ATCTAAAGTTACCACACCACAG -s Anc1.Anc1refChr6 121645 24 + 197743 TC---ATCTAAAGTTACCACACCACAG -s Anc2.Anc2refChr1 191 24 + 142988 TA---ATCTAAAGTTACCACACCACAG -s mr.mrrefChr3 24247 27 + 181027 CCATAATCTAAAGTTACCACACCACAG -s simCow_chr6.simCow.chr6 453578 24 + 602619 TA---ATCTAAAGTTAGCTCACCACAG -s simDog_chr6.simDog.chr6 145065 24 - 593897 TA---ATCTAGTGTTACCATACCACAG -s simHuman_chr6.simHuman.chr6 453823 24 + 601863 AC---ATCTAAAGTTACCACACCACAG -s simRat_chr6.simRat.chr6 478479 27 + 647215 CCATAATCTAAAGTTACCACACCACAG - -a -s simMouse_chr6.simMouse.chr6 468571 6 + 636262 CTGTTC -s Anc0.Anc0refChr3 89039 6 + 222631 CCCTTC -s Anc1.Anc1refChr6 121670 6 + 197743 CCCTTC -s Anc2.Anc2refChr1 216 6 + 142988 CTCTTC -s mr.mrrefChr3 24274 6 + 181027 CCGTTC -s simCow_chr6.simCow.chr6 453603 6 + 602619 ATCCTC -s simDog_chr6.simDog.chr6 145090 6 - 593897 CTCTCC -s simHuman_chr6.simHuman.chr6 453848 6 + 601863 CCCTTC -s simRat_chr6.simRat.chr6 478506 6 + 647215 CCTTTC - -a -s simMouse_chr6.simMouse.chr6 468577 17 + 636262 CCACCTTTGGGGTAAAA -s Anc0.Anc0refChr3 89045 17 + 222631 GCACCTTTGAGGTAAAA -s Anc1.Anc1refChr6 121676 17 + 197743 GCACCTTTGAGGTAAAA -s Anc2.Anc2refChr1 222 17 + 142988 GCACCTTTGAGGTATAA -s mr.mrrefChr3 24280 17 + 181027 CCACCTTTGGGGTAAAA -s simCow_chr6.simCow.chr6 453609 17 + 602619 CCACCTTTGAGGCATAA -s simDog_chr6.simDog.chr6 145100 17 - 593897 GCATTTTTGAGATGTAA -s simHuman_chr6.simHuman.chr6 453854 17 + 601863 TCACCTTTGAGGTAATA -s simRat_chr6.simRat.chr6 478512 17 + 647215 CCACCTTTGGGGTAAAA - -a -s simMouse_chr6.simMouse.chr6 468594 17 + 636262 ATGTGTCAAGAGTGGGC -s Anc0.Anc0refChr3 89062 17 + 222631 ATCCACCAAGAGGGGGC -s Anc1.Anc1refChr6 121693 17 + 197743 ATCCACCAAGAGGGGGC -s Anc2.Anc2refChr1 239 17 + 142988 ATCCACCAAGAGGGGGC -s mr.mrrefChr3 24297 17 + 181027 ATGTGTCAAGAGTGGGC -s simCow_chr6.simCow.chr6 453629 17 + 602619 ACCTAGCAAGAGGGGGC -s simDog_chr6.simDog.chr6 145117 17 - 593897 ATCCACCAAGAGGAGGG -s simHuman_chr6.simHuman.chr6 453871 17 + 601863 ATCCACCAAGGGGGGGC -s simRat_chr6.simRat.chr6 478529 17 + 647215 ATGTGTCAAGAGTGGGC - -a -s simMouse_chr6.simMouse.chr6 468611 12 + 636262 AAGTGGAACTCC -s Anc0.Anc0refChr3 89088 12 + 222631 AAACGGCACTCT -s Anc1.Anc1refChr6 121719 12 + 197743 AAACGGCACTCT -s Anc2.Anc2refChr1 265 12 + 142988 AAACGGCACCCT -s mr.mrrefChr3 24314 12 + 181027 AAATGGAACTCC -s simCow_chr6.simCow.chr6 453655 10 + 602619 AAATG--ACTTT -s simDog_chr6.simDog.chr6 145143 12 - 593897 AAACGGCACCCT -s simHuman_chr6.simHuman.chr6 453897 12 + 601863 AAAAGGCACTCT -s simRat_chr6.simRat.chr6 478546 12 + 647215 AAATTGGACTCC - -a -s simMouse_chr6.simMouse.chr6 468623 46 + 636262 TCTGCAGTGTGCTTTCCCGTGCTCTGTAATGACTTGTGGGATGATC -s Anc0.Anc0refChr3 89100 46 + 222631 GCATCATTGTGCTTTCCTGTGCTCTATATTGATTCAAGAGATGATC -s Anc1.Anc1refChr6 121731 46 + 197743 GCATCATTGTGCTTTCCTGTGCTCTATATTGATTCAAGAGATGATC -s Anc2.Anc2refChr1 277 46 + 142988 GCATCACTGTGCCTTCCTGTGCTCTATATTGATTCAAGAGATGCTC -s mr.mrrefChr3 24326 46 + 181027 TCTGCATTGTGCTTTCCTGTGCTCTGTAATGACTTGTGGGATGATC -s simCow_chr6.simCow.chr6 453665 46 + 602619 GCATCACTGTGCATTCCTGTGCCCTATAGTGATCCAAGAGATGCTC -s simDog_chr6.simDog.chr6 145155 46 - 593897 GCACTACTGTGCCTTCCTATGTTCTATATTGATTCAAGAGATACTC -s simHuman_chr6.simHuman.chr6 453914 46 + 601863 ACATCATTGTGCTTTCCTGTGCTCTATCCAAATTCAAGCGATGACC -s simRat_chr6.simRat.chr6 478558 46 + 647215 TCTACATTGTACTTTGCTGTGCTCTGTAAGGGCTTGGGGGATAATC - -a -s simMouse_chr6.simMouse.chr6 468669 18 + 636262 CCATTGTATGAACTCAAG -s Anc0.Anc0refChr3 89146 18 + 222631 CCCTTGAATCAGCTAAAG -s Anc1.Anc1refChr6 121777 18 + 197743 CCCTTGAATCAGCTAAAG -s Anc2.Anc2refChr1 323 18 + 142988 CTCTTGAGTCAGCTAAAG -s mr.mrrefChr3 24372 18 + 181027 CCATTGTATGAACTAAAG -s simCow_chr6.simCow.chr6 453711 18 + 602619 CTCTTGAGTCAGCTAAAG -s simDog_chr6.simDog.chr6 145201 18 - 593897 CTCTTGAGTCAGCTAAAG -s simHuman_chr6.simHuman.chr6 453977 18 + 601863 CCCTTGAATCTGCTAAGA -s simRat_chr6.simRat.chr6 478604 18 + 647215 CCATTGTGTGAACTAAAG - -a -s simMouse_chr6.simMouse.chr6 468687 12 + 636262 TACCGATGCCAC -s Anc0.Anc0refChr3 89164 12 + 222631 TACTTATGCCAT -s Anc1.Anc1refChr6 121795 12 + 197743 TACTTATGCCAT -s Anc2.Anc2refChr1 343 12 + 142988 TACTTGTGTGAT -s mr.mrrefChr3 24390 12 + 181027 TACTGATGCCAT -s simCow_chr6.simCow.chr6 453731 10 + 602619 T--TTGTGTGAT -s simDog_chr6.simDog.chr6 145221 12 - 593897 GACTTGTGTGAT -s simHuman_chr6.simHuman.chr6 453995 11 + 601863 TACT-ATGCCAT -s simRat_chr6.simRat.chr6 478622 12 + 647215 TACTTTTGCCAT - -a -s simMouse_chr6.simMouse.chr6 468699 6 + 636262 TGACCA -s Anc0.Anc0refChr3 89176 6 + 222631 TGTACA -s Anc1.Anc1refChr6 121807 6 + 197743 TGTACA -s Anc2.Anc2refChr1 355 6 + 142988 TGTACC -s mr.mrrefChr3 24402 6 + 181027 TGAACA -s simCow_chr6.simCow.chr6 453746 6 + 602619 TATAAC -s simDog_chr6.simDog.chr6 145233 6 - 593897 TGTACC -s simHuman_chr6.simHuman.chr6 454006 6 + 601863 TGTACA -s simRat_chr6.simRat.chr6 478634 6 + 647215 TGAACC - -a -s simMouse_chr6.simMouse.chr6 468705 1 + 636262 C -s Anc0.Anc0refChr3 89182 1 + 222631 C -s Anc1.Anc1refChr6 121813 1 + 197743 C -s Anc2.Anc2refChr1 361 1 + 142988 C -s mr.mrrefChr3 24408 1 + 181027 C -s simCow_chr6.simCow.chr6 453752 1 + 602619 G -s simDog_chr6.simDog.chr6 145239 1 - 593897 C -s simHuman_chr6.simHuman.chr6 454013 1 + 601863 C -s simRat_chr6.simRat.chr6 478640 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 468706 6 + 636262 AACGGG -s Anc0.Anc0refChr3 89183 6 + 222631 AAGAGG -s Anc1.Anc1refChr6 121814 6 + 197743 AAGAGG -s Anc2.Anc2refChr1 364 6 + 142988 GAGAGG -s mr.mrrefChr3 24409 6 + 181027 AAGGGG -s simCow_chr6.simCow.chr6 453755 6 + 602619 GAGCGG -s simDog_chr6.simDog.chr6 145242 6 - 593897 GTGAGG -s simHuman_chr6.simHuman.chr6 454014 6 + 601863 AAGAGG -s simRat_chr6.simRat.chr6 478641 6 + 647215 AAGGCA - -a -s simMouse_chr6.simMouse.chr6 468712 4 + 636262 TTAC -s Anc0.Anc0refChr3 89189 4 + 222631 TTAC -s Anc1.Anc1refChr6 121820 4 + 197743 TTAC -s Anc2.Anc2refChr1 370 4 + 142988 TTAC -s mr.mrrefChr3 24415 4 + 181027 TTAC -s simCow_chr6.simCow.chr6 453765 4 + 602619 TTAC -s simDog_chr6.simDog.chr6 145248 4 - 593897 TTAC -s simHuman_chr6.simHuman.chr6 454020 4 + 601863 CTAC -s simRat_chr6.simRat.chr6 478647 4 + 647215 TTAC - -a -s simMouse_chr6.simMouse.chr6 468716 30 + 636262 GAGTGGACATAAGACTCTCTCCTGCAACTT -s Anc0.Anc0refChr3 89194 30 + 222631 GTGTGAACATAAGAGTGAGCCCTTGGATTT -s Anc1.Anc1refChr6 121825 30 + 197743 GTGTGAACATAAGAGTGAGCCCTTGGATTT -s Anc2.Anc2refChr1 375 30 + 142988 GTGTGAACATAAGAGTGAGCCCTTGGATTT -s mr.mrrefChr3 24420 30 + 181027 GAGTGGACATAAGACTGTGTCCTGCAACTT -s simCow_chr6.simCow.chr6 453770 30 + 602619 ATGTAAACCTAAGAGTGTGTCCTTTGAACT -s simDog_chr6.simDog.chr6 145253 30 - 593897 GTGCGAATATAAGAGTGAGCCCTCGCATTT -s simHuman_chr6.simHuman.chr6 454025 30 + 601863 GTGTGAACATAAGAGTGAGCCCTTGGATTT -s simRat_chr6.simRat.chr6 478652 30 + 647215 GAATGGACATAAGACTGTGTCCTGCAACTT - -a -s simMouse_chr6.simMouse.chr6 468746 11 + 636262 GGACAACATCT -s Anc0.Anc0refChr3 89225 11 + 222631 GAACAACATCT -s Anc1.Anc1refChr6 121856 11 + 197743 GAACAACATCT -s Anc2.Anc2refChr1 406 11 + 142988 GAACAACATCT -s mr.mrrefChr3 24450 11 + 181027 GGACAACATCT -s simCow_chr6.simCow.chr6 453801 11 + 602619 AAACAACATCT -s simDog_chr6.simDog.chr6 145284 11 - 593897 GAACAACATCT -s simHuman_chr6.simHuman.chr6 454056 11 + 601863 GAACAACATCT -s simRat_chr6.simRat.chr6 478682 11 + 647215 CAACCACGTCT - -a -s simMouse_chr6.simMouse.chr6 468757 9 + 636262 TTAAGGATT -s Anc0.Anc0refChr3 89240 9 + 222631 TCAAGAAGT -s Anc1.Anc1refChr6 121871 9 + 197743 TCAAGAAGT -s Anc2.Anc2refChr1 421 9 + 142988 TCTAAAAGT -s mr.mrrefChr3 24465 9 + 181027 TTAAGGATT -s simCow_chr6.simCow.chr6 453816 9 + 602619 ACCGTAAGT -s simDog_chr6.simDog.chr6 145299 9 - 593897 TCTAAAAGT -s simHuman_chr6.simHuman.chr6 454071 9 + 601863 TCAAGAAGT -s simRat_chr6.simRat.chr6 478697 9 + 647215 TAAAGGACA - -a -s simMouse_chr6.simMouse.chr6 468766 19 + 636262 GTTATTAATGCTCCAATCC -s Anc0.Anc0refChr3 89249 18 + 222631 TTTATGGA-AAGGCAAATT -s Anc1.Anc1refChr6 121880 19 + 197743 TTTATGGATAAGGCAAATT -s Anc2.Anc2refChr1 430 18 + 142988 TTTATGGA-AAGGCAAATT -s mr.mrrefChr3 24474 19 + 181027 GTTATTAATACTGCAATCC -s simCow_chr6.simCow.chr6 453832 18 + 602619 TTTATCTA-CAAGGACATT -s simDog_chr6.simDog.chr6 145308 18 - 593897 GTTATGGA-AAGGCAAATT -s simHuman_chr6.simHuman.chr6 454080 19 + 601863 TTTATGTGTAAGGCAAGTT -s simRat_chr6.simRat.chr6 478706 19 + 647215 GTTATTAACAGTGCAATCC - -a -s simMouse_chr6.simMouse.chr6 468785 4 + 636262 ATTT -s Anc0.Anc0refChr3 89267 4 + 222631 ATCT -s Anc1.Anc1refChr6 121899 4 + 197743 ATCT -s Anc2.Anc2refChr1 449 4 + 142988 ATCT -s mr.mrrefChr3 24493 4 + 181027 ATTT -s simCow_chr6.simCow.chr6 453851 4 + 602619 ATCT -s simDog_chr6.simDog.chr6 145327 4 - 593897 ATCT -s simHuman_chr6.simHuman.chr6 454099 4 + 601863 ATCT -s simRat_chr6.simRat.chr6 478725 4 + 647215 ATTT - -a -s simMouse_chr6.simMouse.chr6 468789 52 + 636262 GCAATTTGGCTCTTTAATTGGATGCTTGATAACTAACATTGTCACCCTCCAA -s Anc0.Anc0refChr3 89272 32 + 222631 GCACTTTAGTTCATTAATTATGTACACGTTAG-------------------- -s Anc1.Anc1refChr6 121904 32 + 197743 GCACTTTAGTTCATTAATTATGTACACGTTAG-------------------- -s Anc2.Anc2refChr1 454 32 + 142988 GCACTTTAATTCATTAATTATGTACACGTAGG-------------------- -s mr.mrrefChr3 24497 52 + 181027 GCACTTTGGCTCTTTAATTAGATACTTGATAACTAACATTGTCACCCTCCAA -s simCow_chr6.simCow.chr6 453856 32 + 602619 GCACTTTAACTCATCTATTATGTACATGTAGG-------------------- -s simDog_chr6.simDog.chr6 145332 29 - 593897 TC---TTAATTGACTAATTACATACACGTAGG-------------------- -s simHuman_chr6.simHuman.chr6 454104 32 + 601863 GCACTTTAGTTCATTCATTATGTACAAGTTAG-------------------- -s simRat_chr6.simRat.chr6 478729 52 + 647215 GCACTTTGGCCCTTTAACTAGATAATTCGTGACTAACATTGTCCCTCTCCAA - -a -s simMouse_chr6.simMouse.chr6 468841 1 + 636262 G -s Anc0.Anc0refChr3 89304 1 + 222631 G -s Anc1.Anc1refChr6 121936 1 + 197743 G -s Anc2.Anc2refChr1 486 1 + 142988 G -s mr.mrrefChr3 24549 1 + 181027 G -s mr.mrrefChr5 95811 1 + 294540 G -s simCow_chr6.simCow.chr6 453888 1 + 602619 G -s simDog_chr6.simDog.chr6 145361 1 - 593897 G -s simMouse_chr6.simMouse.chr6 695 1 - 636262 G -s simRat_chr6.simRat.chr6 352583 1 + 647215 G -s simRat_chr6.simRat.chr6 478781 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 468842 1 + 636262 G -s Anc1.Anc1refChr6 121937 1 + 197743 G -s mr.mrrefChr3 24550 1 + 181027 G -s mr.mrrefChr5 95812 1 + 294540 A -s simMouse_chr6.simMouse.chr6 696 1 - 636262 A -s simRat_chr6.simRat.chr6 352584 1 + 647215 T -s simRat_chr6.simRat.chr6 66882 1 - 647215 A -s simRat_chr6.simRat.chr6 478782 1 + 647215 G - -a -s simMouse_chr6.simMouse.chr6 468845 1 + 636262 G - -a -s simMouse_chr6.simMouse.chr6 468976 20 + 636262 GAGTACCCAGACCTGACTTA -s mr.mrrefChr3 24683 12 + 181027 G--------GACCTGACTTA -s simRat_chr6.simRat.chr6 478915 12 + 647215 G--------GACCTGGCTTA - -a -s simMouse_chr6.simMouse.chr6 469005 1 + 636262 A - -a -s simMouse_chr6.simMouse.chr6 469034 1 + 636262 T -s mr.mrrefChr3 24733 1 + 181027 T - -a -s simMouse_chr6.simMouse.chr6 469050 2 + 636262 AT -s Anc1.Anc1refChr6 122123 2 + 197743 AT -s mr.mrrefChr3 24749 2 + 181027 AT -s mr.mrrefChr3 157339 2 + 181027 AT -s simMouse_chr6.simMouse.chr6 609417 2 + 636262 AT -s simRat_chr6.simRat.chr6 83974 2 - 647215 AT -s simRat_chr6.simRat.chr6 478965 2 + 647215 AC - -a -s simMouse_chr6.simMouse.chr6 469054 1 + 636262 C -s mr.mrrefChr3 24753 1 + 181027 C -s simRat_chr6.simRat.chr6 478969 1 + 647215 G - -a -s simMouse_chr6.simMouse.chr6 469055 2 + 636262 CC -s Anc1.Anc1refChr6 122127 2 + 197743 CT -s mr.mrrefChr3 24754 2 + 181027 CT -s mr.mrrefChr3 157343 2 + 181027 CT -s mr.mrrefChr5 96000 2 + 294540 CT -s simMouse_chr6.simMouse.chr6 609422 2 + 636262 CT -s simMouse_chr6.simMouse.chr6 994 2 - 636262 CT -s simRat_chr6.simRat.chr6 83978 2 - 647215 TT -s simRat_chr6.simRat.chr6 352673 2 + 647215 CT -s simRat_chr6.simRat.chr6 67048 2 - 647215 CT -s simRat_chr6.simRat.chr6 478970 2 + 647215 CT - -a -s simMouse_chr6.simMouse.chr6 469067 4 + 636262 GGCC -s Anc0.Anc0refChr3 89351 4 + 222631 AATA -s Anc1.Anc1refChr6 122206 4 + 197743 AATA -s Anc2.Anc2refChr1 533 4 + 142988 AATA -s mr.mrrefChr3 24766 4 + 181027 AGCC -s simCow_chr6.simCow.chr6 453935 4 + 602619 AATG -s simDog_chr6.simDog.chr6 145407 4 - 593897 AATA -s simHuman_chr6.simHuman.chr6 454184 4 + 601863 AAAA -s simRat_chr6.simRat.chr6 478982 4 + 647215 AGCC - -a -s simMouse_chr6.simMouse.chr6 469071 14 + 636262 AAAGCAGTAAGAAT -s Anc0.Anc0refChr3 89355 13 + 222631 AAAGCAAT-AGAAC -s Anc1.Anc1refChr6 122210 13 + 197743 AAAGCAAT-AGAAC -s Anc2.Anc2refChr1 537 13 + 142988 AAAGCAAT-AAAAC -s mr.mrrefChr3 24770 14 + 181027 AAAGCAGTAAGAAT -s simCow_chr6.simCow.chr6 453939 13 + 602619 GAAGAGAT-AAAAA -s simDog_chr6.simDog.chr6 145419 13 - 593897 AAAGCAGT-AAAAC -s simHuman_chr6.simHuman.chr6 454188 13 + 601863 AAAGCAAA-AGAAC -s simRat_chr6.simRat.chr6 478986 14 + 647215 AAAGCAGCAAGGAT - -a -s simMouse_chr6.simMouse.chr6 469085 37 + 636262 CTTTAACAGCGCTGTCTGCAAGGTAGGCCGAATACAA -s Anc0.Anc0refChr3 89368 36 + 222631 TATTAATAGCACTGCCTGCAAGGTAAGCCTAA-TAGA -s Anc1.Anc1refChr6 122223 37 + 197743 TATTAATAGCACTGCCTGCAAGGTAAGCCTAACTAGA -s Anc2.Anc2refChr1 552 36 + 142988 TATTAGTGACACTGCCTGCAAGGTAAGGCTAG-TAGA -s mr.mrrefChr3 24784 37 + 181027 CTTTAACAGCGCTGTCTGCAAGGTAGGCCGAATACAA -s simCow_chr6.simCow.chr6 453954 36 + 602619 TATTACTGACAGAGCCCGCAAGGTAAGTCTAG-TAGA -s simDog_chr6.simDog.chr6 145434 36 - 593897 TGTTAGTGACACTGCCTGCAAGGTAGGGCTAG-TAGA -s simHuman_chr6.simHuman.chr6 454201 37 + 601863 TAATAATAGCACTGCCTGCAAGGTCAGCCAAACTAGA -s simRat_chr6.simRat.chr6 479000 37 + 647215 CTTTAGCAGCTCTGTCTGCAAGGGAGGTTGAGTACAA - -a -s simMouse_chr6.simMouse.chr6 469122 82 + 636262 TGAAGGCTTTGGTTTCATCACAGGATAGTCACATGCTAATGAATAGTGTTAGTGGCAGCTCTACAATAAATAAGTTATTTTG -s Anc0.Anc0refChr3 89405 81 + 222631 TGAAGGCTTCAACTTCATCACAGGATTGTGACATGCTAACGAATAGTGTT-GTACCAGCTCCATGATAAATACGTTCTTTAG -s Anc1.Anc1refChr6 122261 82 + 197743 TGAAGGCTTCAACTTCATCACAGGATTGTGACATGCTAACGAATAGTGTTTGTACCAGCTCCATGATAAATACGTTCTTTAG -s Anc2.Anc2refChr1 589 81 + 142988 TAATTGCCTCAACTTCATCACAGGATTGTGACATGCTGACAAATAGTGTT-GTACCAGCTCCATGATAAATACGTTCTTTAG -s mr.mrrefChr3 24822 82 + 181027 TGAAGGCTTTGATTTCATCACAGGATAGTCACATGCTAATGAATAGTGTTAGTGGCAGCTCTACAATAAATAAGTTATTTTG -s simCow_chr6.simCow.chr6 453991 76 + 602619 TCAGAGCATCAACTTTATCACAGGATTGTGACATGCTGCCAAATAGTGTT--CACCAGCTCCA----AGATTTATTCTTTAC -s simDog_chr6.simDog.chr6 145471 81 - 593897 CACTTGCCTCAATGTCATCACAGAATTATGACATGTTGACAAATAGTGTG-GTATCAGCTCCATGATAAATACGTTTTTGAG -s simHuman_chr6.simHuman.chr6 454239 82 + 601863 TGAAGGCTTCAACTTCATCACAAGATTGTGACATGCCAACGAAGAGTGTTTGTACCAGATCAATGTTAAATACGTTCTTTAA -s simRat_chr6.simRat.chr6 479038 81 + 647215 TGAAGGTTTTGATTTCATCACAGG-TGGGTACATGCTAATGAATAGTGTTGGTTACAGCTCTACAATAAATAAGTTATTTTG - -a -s simMouse_chr6.simMouse.chr6 469204 74 + 636262 GGCTTGTTTTAGCAATGTAAGTCTCCACAAGATATTGAGGTAATGGAAAATAAACAGTGTCAACGCGAGGTGAT -s Anc0.Anc0refChr3 89488 74 + 222631 GGTATGATCCAGTGGGCTGAATCTCCACAAGATACTGAGGTGCTGGAAAACAAGGAGTACCAATGAGAAATGAT -s Anc1.Anc1refChr6 122345 74 + 197743 GGTATGATCCAGTGGGCTGAATCTCCACAAGATACTGAGGTGCTGGAAAACAAGGAGTACCAATGAGAAATGAT -s Anc2.Anc2refChr1 672 74 + 142988 GGTATGATCCAGTGGGCTGAACCTCCACAAGATACTGAGGTGCTGGAAAGCAAGGAGCACCAATGAGAAAAGAT -s mr.mrrefChr3 24906 74 + 181027 GGTTTGTTCTAGTAGTGTAAATCTCCACAAGATATTGAGGTAATGGAAAATAAACAGTGTCAACGCGAGGTGAT -s simCow_chr6.simCow.chr6 454069 72 + 602619 GGTATGATCCAATGGGCAGGGCCTCC--AAGATACTGAGGGGCTGGAAATGAAGTAGCACCAATGAGACACAAT -s simDog_chr6.simDog.chr6 145554 74 - 593897 GGTATGATCTAGTGGGTTGAACATCCACAAGATACTGAGGTTCTGGAAAGCAAGGAGCACCAATGAGAAAAGAT -s simHuman_chr6.simHuman.chr6 454323 74 + 601863 GGTATGATCCAGTGGGCTGAATCTCCAGAAGATACTGAGGTGCTGGAAGACAAGGAGTACCAATAAGAAATGAT -s simRat_chr6.simRat.chr6 479121 52 + 647215 AGTTTGTTCTGGTAGTTTAGATCTCCACAAGATATTGCAGTAATGGAAAATA---------------------- - -a -s simMouse_chr6.simMouse.chr6 469278 4 + 636262 TGCT -s Anc0.Anc0refChr3 89567 4 + 222631 TACT -s Anc1.Anc1refChr6 122424 4 + 197743 TACT -s Anc2.Anc2refChr1 751 4 + 142988 TACT -s mr.mrrefChr3 24980 4 + 181027 TGCT -s simCow_chr6.simCow.chr6 454146 4 + 602619 TACT -s simDog_chr6.simDog.chr6 145633 4 - 593897 TACT -s simHuman_chr6.simHuman.chr6 454402 4 + 601863 TACT -s simRat_chr6.simRat.chr6 479173 3 + 647215 -GCT - -a -s simMouse_chr6.simMouse.chr6 469282 5 + 636262 CAGCT -s Anc0.Anc0refChr3 89571 5 + 222631 CTTTA -s Anc1.Anc1refChr6 122428 5 + 197743 CTTTA -s Anc2.Anc2refChr1 755 5 + 142988 CTTTG -s mr.mrrefChr3 24984 5 + 181027 CTTTA -s simCow_chr6.simCow.chr6 454150 5 + 602619 CTTTG -s simDog_chr6.simDog.chr6 145638 5 - 593897 CTTTG -s simHuman_chr6.simHuman.chr6 454406 5 + 601863 CTTTA -s simRat_chr6.simRat.chr6 479176 5 + 647215 TTTTA - -a -s simMouse_chr6.simMouse.chr6 469287 6 + 636262 TATAAT -s Anc0.Anc0refChr3 89589 6 + 222631 TATAAT -s Anc1.Anc1refChr6 122446 6 + 197743 TATAAT -s Anc2.Anc2refChr1 773 6 + 142988 AGTGAT -s mr.mrrefChr3 24989 6 + 181027 TATAAT -s simCow_chr6.simCow.chr6 454168 6 + 602619 AGTGAT -s simDog_chr6.simDog.chr6 145656 6 - 593897 AGTGAT -s simHuman_chr6.simHuman.chr6 454424 6 + 601863 TATAAT -s simRat_chr6.simRat.chr6 479181 6 + 647215 TATAAT - -a -s simMouse_chr6.simMouse.chr6 469293 28 + 636262 GGAATGTATATATAAGCTCTAATATGCT -s Anc0.Anc0refChr3 89599 28 + 222631 GGTAAGTAAGCATAATATATAATAGGAT -s Anc1.Anc1refChr6 122456 28 + 197743 GGTAAGTAAGCATAATATATAATAGGAT -s Anc2.Anc2refChr1 783 28 + 142988 GGTAAGTCAGCATAATATATAATGGGAT -s mr.mrrefChr3 24995 28 + 181027 GGAATGTATATATAAGCTCTAATATGCT -s simCow_chr6.simCow.chr6 454178 28 + 602619 AGTAAGTCGGCATAATATATAATGAGAT -s simDog_chr6.simDog.chr6 145666 28 - 593897 GGTAGAACACCATAATATGTAATGGGAT -s simHuman_chr6.simHuman.chr6 454434 28 + 601863 GGTAAGTAAGCATAATATATAATAGAAT -s simRat_chr6.simRat.chr6 479187 28 + 647215 GGAATGCATATATAAGCCCTAAAATGCT - -a -s simMouse_chr6.simMouse.chr6 469321 45 + 636262 TGACACACATTTGAGACATTTGATACCAAACTACAAGAAATGCTC -s Anc0.Anc0refChr3 89633 45 + 222631 TCAGACACATTTGAGACTTGACATATTGAACTATGTGGAAAGCTT -s Anc1.Anc1refChr6 122490 45 + 197743 TCAGACACATTTGAGACTTGACATATTGAACTATGTGGAAAGCTT -s Anc2.Anc2refChr1 823 45 + 142988 TCTGACACATTTGAGACTCAACATATTGGACTATGTGGAGAGCTT -s mr.mrrefChr3 25023 45 + 181027 TGACACACATTTGAGACATGTGATACTGAACTACAAGAAATGCTC -s simCow_chr6.simCow.chr6 454218 43 + 602619 TCTG--ACTTTTGAGACTCAGCATGTTGGACTATTTGGACACCTC -s simDog_chr6.simDog.chr6 145706 45 - 593897 TCTGACACATCTGAGATGCAATATATTGGACTATGTGGGGAGCTT -s simHuman_chr6.simHuman.chr6 454468 45 + 601863 TCAGACACATTTGAGACTTGACATATTGAACTATGTGGAAAGCTT -s simRat_chr6.simRat.chr6 479215 45 + 647215 TGACACACATTTTAGACATGTGATACTGTACTACAAGAGATGCTC - -a -s simMouse_chr6.simMouse.chr6 469366 26 + 636262 ACAATTGCTAGACTTTGTATTATTTT -s Anc0.Anc0refChr3 89679 26 + 222631 ATAATTGCTGGGCAGAGCATTATTTT -s Anc1.Anc1refChr6 122536 26 + 197743 ATAATTGCTGGGCAGAGCATTATTTT -s Anc2.Anc2refChr1 869 26 + 142988 ATAATTGCTGGGTAGAGCATTATTTT -s mr.mrrefChr3 25068 26 + 181027 ACAATTGCTAGGCTTTGTATTATTTT -s simCow_chr6.simCow.chr6 454262 26 + 602619 ATAATTGCTGGGTAGAGCAGTTTCTT -s simDog_chr6.simDog.chr6 145752 26 - 593897 ATAATTGCTGGGTAGGGCATTATTTT -s simHuman_chr6.simHuman.chr6 454515 26 + 601863 AGATTTGCTGGGCAAAGCATTATTTT -s simRat_chr6.simRat.chr6 479260 26 + 647215 ACAACTGCTAGGTTTTGTATTATTTT - -a -s simMouse_chr6.simMouse.chr6 469392 13 + 636262 GGATGATGATTAA -s Anc0.Anc0refChr3 89706 13 + 222631 GGATAGTGATTAA -s Anc1.Anc1refChr6 122563 13 + 197743 GGATAGTGATTAA -s Anc2.Anc2refChr1 896 13 + 142988 AGATAGTGATTAA -s mr.mrrefChr3 25094 13 + 181027 GGATGATGATTAA -s simCow_chr6.simCow.chr6 454289 13 + 602619 AGATAGTGATTAA -s simDog_chr6.simDog.chr6 145779 13 - 593897 AGATTGAGAATAA -s simHuman_chr6.simHuman.chr6 454542 13 + 601863 GGATAGTGATTGA -s simRat_chr6.simRat.chr6 479286 13 + 647215 GGATGATGATTAA - -a -s simMouse_chr6.simMouse.chr6 469405 42 + 636262 TTATCCTGTGGTACGACTCATGTTGATTCTCAGTATATACTA -s Anc0.Anc0refChr3 89723 36 + 222631 CTATCCTG------GTCTCATGTCAATTCTCACTATATACTA -s Anc1.Anc1refChr6 122580 36 + 197743 CTATCCTG------GTCTCATGTCAATTCTCACTATATACTA -s Anc2.Anc2refChr1 913 36 + 142988 CTATCCTG------GTCCCATGTCAATTCTCACTATCTACTC -s mr.mrrefChr3 25107 42 + 181027 TTATCCTGTGGTACGACTCATGTTGATTCTCAGTATATACTA -s simCow_chr6.simCow.chr6 454306 30 + 602619 CTATCCTG------GTCCCATTTCAATTCTCTCTAT------ -s simDog_chr6.simDog.chr6 145796 36 - 593897 TTATCCTG------GTCCCATGCCAATTCTCACCATCTACTC -s simHuman_chr6.simHuman.chr6 454559 36 + 601863 CTATCCTA------GTCTCATGTCCATTCTTACTATATACCA -s simRat_chr6.simRat.chr6 479299 42 + 647215 TTATCCTGTGGTATCATTCATATTGACTCTCAGTACATACTA - -a -s simMouse_chr6.simMouse.chr6 469447 5 + 636262 GAACC -s Anc1.Anc1refChr6 122636 5 + 197743 GATCT -s mr.mrrefChr3 25149 5 + 181027 GAACT -s simHuman_chr6.simHuman.chr6 454615 5 + 601863 GATCT -s simRat_chr6.simRat.chr6 479341 5 + 647215 GAGCT - -a -s simMouse_chr6.simMouse.chr6 469452 4 + 636262 ACCT -s Anc0.Anc0refChr3 89779 2 + 222631 --CA -s Anc1.Anc1refChr6 122643 4 + 197743 ACCA -s Anc2.Anc2refChr1 969 2 + 142988 --CA -s mr.mrrefChr3 25156 4 + 181027 ACCA -s simCow_chr6.simCow.chr6 454356 2 + 602619 --CA -s simDog_chr6.simDog.chr6 145851 2 - 593897 --CA -s simHuman_chr6.simHuman.chr6 454622 4 + 601863 ACCA -s simRat_chr6.simRat.chr6 479348 4 + 647215 ACCA - -a -s simMouse_chr6.simMouse.chr6 469456 63 + 636262 ATAGTGGTCCATGAATACCTCCCTGTGCCTATCTTCTCGTATTTCAAGCATGTGTTACCTGGA -s Anc0.Anc0refChr3 89781 60 + 222631 ATAGTGGTGCAGGAAAACCTCCCTGTGCCTACCTTCTGGTCTTTAAGGCATATATT---GAGA -s Anc1.Anc1refChr6 122647 60 + 197743 ATAGTGGTGCAGGAAAACCTCCCTGTGCCTACCTTCTGGTCTTTAAGGCATATATT---GAGA -s Anc2.Anc2refChr1 971 60 + 142988 GAATGGGTGCAGGAAAACCTCCGTGTGCCTACCTTCTGGTCTTTAAGGCACATATT---GAAA -s mr.mrrefChr3 25160 60 + 181027 ATAGTGGTCCATGAATACCTCCCTGTGCCTATCTTCTCGTCTTTCAAGCATATGTT---TGGA -s simCow_chr6.simCow.chr6 454359 51 + 602619 GAAAAGGTGCAGGAAAATCTCCTTGTGACTACCTTCTGGTATTTAAGGCA------------A -s simDog_chr6.simDog.chr6 145853 60 - 593897 GAATGTGTCCAGAAAAACTTCCGTTTTCCCACCTTCTGCTCTCTGGGGCACATATT---GAAA -s simHuman_chr6.simHuman.chr6 454626 60 + 601863 ATAGTGGTGCAGGAAAACCTCCCTGAGCCTACTTTTTGGTCTTCAAGGCATATCGT---GAGA -s simRat_chr6.simRat.chr6 479352 60 + 647215 ATAGTGGTCCATGAATGCCTTGCTGTGCCTATCTTCTTGTCTTTGAACCATATGTT---TGAA - -a -s simMouse_chr6.simMouse.chr6 469519 5 + 636262 ATGGA -s Anc0.Anc0refChr3 89846 5 + 222631 CTGGA -s Anc1.Anc1refChr6 122716 5 + 197743 CTGGA -s Anc2.Anc2refChr1 1036 5 + 142988 CTCGA -s mr.mrrefChr3 25229 5 + 181027 CTGGA -s simCow_chr6.simCow.chr6 454415 5 + 602619 CTGGA -s simDog_chr6.simDog.chr6 145921 5 - 593897 CTCAA -s simHuman_chr6.simHuman.chr6 454695 5 + 601863 CTGGA -s simRat_chr6.simRat.chr6 479421 5 + 647215 CTGGA - -a -s simMouse_chr6.simMouse.chr6 469524 28 + 636262 GATGTTACTATGACTGTGCCTGATTTGC -s Anc0.Anc0refChr3 89855 28 + 222631 AATGTTGCTATGACTGTACCTAATTTGA -s Anc1.Anc1refChr6 122725 28 + 197743 AATGTTGCTATGACTGTACCTAATTTGA -s Anc2.Anc2refChr1 1045 28 + 142988 AATGTTGCTATGACTGTACCTAATTTGA -s mr.mrrefChr3 25238 28 + 181027 GATGTTACTATGACTGTGCCTGATTTGC -s simCow_chr6.simCow.chr6 454424 28 + 602619 AATATAGCCATGACTGTACCTGATTTGA -s simDog_chr6.simDog.chr6 145930 27 - 593897 AATGTTGCTATAACTGTACCTAATTC-A -s simHuman_chr6.simHuman.chr6 454704 28 + 601863 AATGTTGCTATGACAGTACCTAATTTGG -s simRat_chr6.simRat.chr6 479430 26 + 647215 GATCTTACTATG--TGTGCCTGATTTGC - -a -s simMouse_chr6.simMouse.chr6 469552 8 + 636262 TGGAGGAG -s Anc0.Anc0refChr3 89883 8 + 222631 ATGGGGTG -s Anc1.Anc1refChr6 122753 8 + 197743 ATGGGGTG -s Anc2.Anc2refChr1 1073 8 + 142988 ATGGGGTG -s mr.mrrefChr3 25266 8 + 181027 TGGAGGAG -s simCow_chr6.simCow.chr6 454453 8 + 602619 AGAGGGTG -s simDog_chr6.simDog.chr6 145957 8 - 593897 ATGGGGTG -s simHuman_chr6.simHuman.chr6 454732 8 + 601863 ACGGGGGG -s simRat_chr6.simRat.chr6 479456 8 + 647215 TGGAGGAG - -a -s simMouse_chr6.simMouse.chr6 469560 5 + 636262 TGTAG -s Anc0.Anc0refChr3 89896 5 + 222631 TGTAG -s Anc1.Anc1refChr6 122766 5 + 197743 TGTAG -s Anc2.Anc2refChr1 1086 5 + 142988 TGTAG -s mr.mrrefChr3 25274 5 + 181027 TGTAG -s simCow_chr6.simCow.chr6 454466 5 + 602619 AGTAA -s simDog_chr6.simDog.chr6 145970 5 - 593897 TTTAG -s simHuman_chr6.simHuman.chr6 454745 5 + 601863 TGTAC -s simRat_chr6.simRat.chr6 479464 5 + 647215 TGTAG - -a -s simMouse_chr6.simMouse.chr6 469565 38 + 636262 TGGCACCATATAAGGTAGGGAGACCCTTTATTTATAAT -s Anc0.Anc0refChr3 89902 36 + 222631 TAATACCACA--AGGTAGGGGGTCTCCTTGTTTTCAAT -s Anc1.Anc1refChr6 122772 38 + 197743 TAATACCACATAAGGTAGGGGGTCTCCTTGTTTTCAAT -s Anc2.Anc2refChr1 1092 36 + 142988 TAATACCACA--AGGTAGGGTGTCTCCTTGTTTTCAAT -s mr.mrrefChr3 25280 38 + 181027 TGGCACCATATAAGGTAGGGGGTCCCTTTGTTTATAAT -s simCow_chr6.simCow.chr6 454472 36 + 602619 TAATACCACA--AAGTAGTGCATCTCCTTCTTTACACT -s simDog_chr6.simDog.chr6 145976 36 - 593897 TAATACCACA--AGGTATGGTGTCTCCTTGTTTTTAAT -s simHuman_chr6.simHuman.chr6 454751 38 + 601863 TAATACCACATGAGGTAGGGGGTCTCCTTGCTTTCAAT -s simRat_chr6.simRat.chr6 479470 38 + 647215 TGGCACCATATAAGGTAGGGGGTCCCTTTGTTTATAAT - -a -s simMouse_chr6.simMouse.chr6 469603 12 + 636262 CACAAATACGCA -s Anc0.Anc0refChr3 89939 9 + 222631 CAGAAATAT--- -s Anc1.Anc1refChr6 122811 9 + 197743 CAGAAATAT--- -s Anc2.Anc2refChr1 1129 9 + 142988 AAGAAATAT--- -s mr.mrrefChr3 25319 12 + 181027 CACAAATACGCA -s simCow_chr6.simCow.chr6 454509 4 + 602619 ACGA-------- -s simDog_chr6.simDog.chr6 146013 9 - 593897 AAGAAATAT--- -s simHuman_chr6.simHuman.chr6 454790 9 + 601863 CAGAGATAT--- -s simRat_chr6.simRat.chr6 479509 12 + 647215 CACAAATACACA - -a -s simMouse_chr6.simMouse.chr6 469615 42 + 636262 TGTACCATTGAAACACACCAAAGCCCTGCGTACACAAGCTTG -s Anc0.Anc0refChr3 89948 42 + 222631 TACATCATGGGAACACACCAAAACCCTGTATATACAAGCCTG -s Anc1.Anc1refChr6 122820 42 + 197743 TACATCATGGGAACACACCAAAACCCTGTATATACAAGCCTG -s Anc2.Anc2refChr1 1138 42 + 142988 TGCATGATGGGAACACACCAAAACCGTGTATATACAAGCCTG -s mr.mrrefChr3 25331 42 + 181027 TATACCATTGAAACACACCAAAACCCTGCGTACACAAGCCTG -s simCow_chr6.simCow.chr6 454513 31 + 602619 -----------ACCACACCAAAGCCTTGTATATACAACCATG -s simDog_chr6.simDog.chr6 146025 42 - 593897 TGCATGATGGGAAAACACCAAAACCGTGTATATACAAGCCTC -s simHuman_chr6.simHuman.chr6 454799 42 + 601863 TACATCCAAGGAACACACCAAAACCCAGTACATACAAGCCTG -s simRat_chr6.simRat.chr6 479521 38 + 647215 CATACCATTGAAACACACCAAAACTCTGCGTACAC----CTG - -a -s simMouse_chr6.simMouse.chr6 469657 10 + 636262 GTGATAGCTA -s Anc0.Anc0refChr3 90015 10 + 222631 GTAATAGCTA -s Anc1.Anc1refChr6 122887 10 + 197743 GTAATAGCTA -s Anc2.Anc2refChr1 1205 10 + 142988 GTAAGAGCTA -s mr.mrrefChr3 25373 10 + 181027 GTAATAGCTA -s simCow_chr6.simCow.chr6 454569 10 + 602619 GCAAAAGCTT -s simDog_chr6.simDog.chr6 146092 10 - 593897 GTAAGAACTA -s simHuman_chr6.simHuman.chr6 454866 10 + 601863 GTAATAGCTA -s simRat_chr6.simRat.chr6 479559 10 + 647215 ATAATAGCTA - -a -s simMouse_chr6.simMouse.chr6 469667 74 + 636262 ATATTAACTTGCAAGATTGGAACACAGGATTGGCCAGGTTACCTGGCTGGCAGGAGAGACCCTTTAGCACTGGC -s Anc0.Anc0refChr3 90025 68 + 222631 ACTTAAACTTACAATATTGGAATACAAAACTGG---GGTT---CAGCGGCCAGGAGAGATCATTTAGTGTTGGC -s Anc1.Anc1refChr6 122897 68 + 197743 ACTTAAACTTACAATATTGGAATACAAAACTGG---GGTT---CAGCGGCCAGGAGAGATCATTTAGTGTTGGC -s Anc2.Anc2refChr1 1215 68 + 142988 ACTTAAACTTACAATATTGGAATATAAAACTGG---GGTT---CATCGGCCAGGAGAGATCATCTAGTGGTGGC -s mr.mrrefChr3 25383 74 + 181027 ATATTAACTTGCAAGATTGGAACACAGGATTGGCCAGGTTACCTGGCTGGCAGGAGAGACCCTTTAGCATTGGC -s simCow_chr6.simCow.chr6 454579 67 + 602619 ACTT-AATTTAGAATATTGGGATATAAAACTGG---GGTT---CACCTGCCCCGAGAGTTCGTCTAGTGGTGGC -s simDog_chr6.simDog.chr6 146102 68 - 593897 ACTTAAACTTACAATATTGGAATATAAAACGGG---GGTC---CATCGGTCAGGGAAGATCATCTAGGGGGGGC -s simHuman_chr6.simHuman.chr6 454884 68 + 601863 GCCTAAACTTACAATATTGGAATACAAAACTGG---GGTT---CAGTCACCAGGAGAGATCATTTAGTGTTGGC -s simRat_chr6.simRat.chr6 479569 74 + 647215 ATATTAACTTGAAAGATTGGAACACAGGATTGGCAAGGTCACCTGGCTGACAGTAGAGACCCTTTAGCATTGGC - -a -s simMouse_chr6.simMouse.chr6 469741 43 + 636262 ATCCCTTGATAGCCTGAGTTGATGATGTAGGATTAATCTACAA -s Anc0.Anc0refChr3 90093 43 + 222631 ATCCCTTGACAACCTAAGTCTATGAGTTAGAGTTCGTTTACAA -s Anc1.Anc1refChr6 122965 43 + 197743 ATCCCTTGACAACCTAAGTCTATGAGTTAGAGTTCGTTTACAA -s Anc2.Anc2refChr1 1283 43 + 142988 ATCCCTTGGCAACCTAAGTCTATGAGTTAGAGTTCATTTACGA -s mr.mrrefChr3 25457 43 + 181027 ATCCCTTGACAGCCTGAGTTGATGATTTAGGGTTAGTCTACAA -s simCow_chr6.simCow.chr6 454646 43 + 602619 ATGCTTTGGTCACATCAGTCTATGAGTTAGAGGTCATTTACGA -s simDog_chr6.simDog.chr6 146183 43 - 593897 ATCCCTTGGCAACCTAAGTCTATGATTTAGAGTTCATCTACGA -s simHuman_chr6.simHuman.chr6 454952 43 + 601863 ATTCCTTCACAACCTAAGTCTATGAGTTAGAGTTTGTTTACAT -s simRat_chr6.simRat.chr6 479643 41 + 647215 ATCC--TGGCAGCCTGAATTGATGATTTACGGTCAGTCTATGA - -a -s simMouse_chr6.simMouse.chr6 469784 59 + 636262 AAAACAATAAATGTAAGAACCATCATTTTTCTCATACAGTTAATTGTCTCATACAGTTG -s Anc0.Anc0refChr3 90136 52 + 222631 GGATCAATGAATGTAAGAACCAACAC------CATTGTGAAAATTG-GACTTACAGGGG -s Anc1.Anc1refChr6 123008 58 + 197743 GGATCAATGAATGTAAGAACCAACACTCACCTCATTGTGAAAATTG-GACTTACAGGGG -s Anc2.Anc2refChr1 1338 52 + 142988 GGATGAATGAATGTGGGAACCAATAC------CATTGTGAAAATGG-GACTTACAGTGG -s mr.mrrefChr3 25500 59 + 181027 AAAACAATAAATGTAAGAACCATCATTTTTCTCATACAGTTAATTGTCTCATACAGGTG -s simCow_chr6.simCow.chr6 454701 45 + 602619 AGATGCAT---TGTTCAAAATTA----------ATTGTGAAAATAG-AACTTACCGAGG -s simDog_chr6.simDog.chr6 146238 52 - 593897 GAATGAATGAATGTGGGAACCAATAC------CATCAGGAAAATGG-GACTTACAATGG -s simHuman_chr6.simHuman.chr6 454995 58 + 601863 GGAGCAATGGATGTAAGGACCAACACTCACCTCATTGTGAATATTG-TATTTACTGGAG -s simRat_chr6.simRat.chr6 479684 42 + 647215 AAACCAATAAATGTAAGAACCACCATTT-----------------GCCTCATTCAGGTA - -a -s simMouse_chr6.simMouse.chr6 469843 25 + 636262 AAGGTAGTGTAGAGGCTGCAGTTTC -s Anc0.Anc0refChr3 90188 25 + 222631 AAGGCAGTCTAAAGACCACATTTTC -s Anc1.Anc1refChr6 123066 25 + 197743 AAGGCAGTCTAAAGACCACATTTTC -s Anc2.Anc2refChr1 1391 25 + 142988 AAGGCAGTCTAAAGACCACATTTTC -s mr.mrrefChr3 25559 25 + 181027 AAGGTAGTCTAAAGGCTGCAGTTTC -s simCow_chr6.simCow.chr6 454747 25 + 602619 CAGGCAGTCTAGAGACTGCATTTTC -s simDog_chr6.simDog.chr6 146291 25 - 593897 ACAGCAGTCTAAAGACCACATTGTC -s simHuman_chr6.simHuman.chr6 455053 25 + 601863 AAGGCAGTCTAAAGACCACATGTTC -s simRat_chr6.simRat.chr6 479726 25 + 647215 AAGGTAGTCCAATGGCTCCAGTTTC - -a -s simMouse_chr6.simMouse.chr6 469868 14 + 636262 TTTAACTAAACTCA -s Anc0.Anc0refChr3 90216 14 + 222631 TTTAATAAAACTCA -s Anc1.Anc1refChr6 123094 14 + 197743 TTTAATAAAACTCA -s Anc2.Anc2refChr1 1419 14 + 142988 TGTAATAAAGCTCA -s mr.mrrefChr3 25584 14 + 181027 TTTAACTAAACTCA -s simCow_chr6.simCow.chr6 454774 10 + 602619 ----ATAAAGCTCA -s simDog_chr6.simDog.chr6 146331 14 - 593897 TGTATTAAAGCTCA -s simHuman_chr6.simHuman.chr6 455081 14 + 601863 TTTAATGGAACTCA -s simRat_chr6.simRat.chr6 479751 14 + 647215 TTTAACTAAACTCA - -a -s simMouse_chr6.simMouse.chr6 469882 13 + 636262 AAGCTGACCTTGT -s Anc0.Anc0refChr3 90235 13 + 222631 AAGTTTACCTTGA -s Anc1.Anc1refChr6 123113 13 + 197743 AAGTTTACCTTGA -s Anc2.Anc2refChr1 1438 13 + 142988 AGGTTTACCTTGA -s mr.mrrefChr3 25598 13 + 181027 AAGCTGACCTTGT -s simCow_chr6.simCow.chr6 454789 13 + 602619 AGGTTTAACCTGG -s simDog_chr6.simDog.chr6 146350 13 - 593897 AGGGGCACCTTGA -s simHuman_chr6.simHuman.chr6 455100 13 + 601863 AAGTTTACCTTGA -s simRat_chr6.simRat.chr6 479765 13 + 647215 AAGCTCATCTTGT - -a -s simMouse_chr6.simMouse.chr6 469895 4 + 636262 TTTA -s Anc0.Anc0refChr3 90248 4 + 222631 TTTA -s Anc1.Anc1refChr6 123126 4 + 197743 TTTA -s Anc2.Anc2refChr1 1451 4 + 142988 TCTA -s mr.mrrefChr3 25611 4 + 181027 TTTA -s simCow_chr6.simCow.chr6 454804 4 + 602619 TCTG -s simDog_chr6.simDog.chr6 146363 4 - 593897 TCTA -s simHuman_chr6.simHuman.chr6 455113 4 + 601863 TTTA -s simRat_chr6.simRat.chr6 479778 4 + 647215 TTTA - -a -s simMouse_chr6.simMouse.chr6 469899 29 + 636262 CAAAGCTGGTGTGTTTGGGCTTTATGAGT -s Anc0.Anc0refChr3 90253 29 + 222631 CAAGGATGGTTTGTTTGGACTTTACCATT -s Anc1.Anc1refChr6 123131 29 + 197743 CAAGGATGGTTTGTTTGGACTTTACCATT -s Anc2.Anc2refChr1 1456 29 + 142988 CAAGGATGGTTTGTTTGGACTTTACCATT -s mr.mrrefChr3 25615 29 + 181027 CAAGGCTGGTGTGTTTGGGCTTTATGAGT -s simCow_chr6.simCow.chr6 454809 29 + 602619 CAAGGATGGTTAATTTGGACTGTACCATT -s simDog_chr6.simDog.chr6 146368 29 - 593897 CATGGATGGTTTGTTTGGACTTTACTATT -s simHuman_chr6.simHuman.chr6 455118 29 + 601863 CGAGGATGGTTTGTTTGGACTTTACCATT -s simRat_chr6.simRat.chr6 479782 29 + 647215 CAAGGCTGGTGTGTTTGGGCTTTATGAGT - -a -s simMouse_chr6.simMouse.chr6 469928 22 + 636262 ACCAGTCTTTAGGTAGAATAAT -s Anc0.Anc0refChr3 90283 5 + 222631 AATAG----------------- -s Anc1.Anc1refChr6 123161 22 + 197743 AATAGTCTTCATATTGATTTAT -s Anc2.Anc2refChr1 1486 5 + 142988 AATAG----------------- -s mr.mrrefChr3 25645 22 + 181027 ACCAGTCTTTAGGTAGAATAAT -s simCow_chr6.simCow.chr6 454839 5 + 602619 ACTAG----------------- -s simDog_chr6.simDog.chr6 146398 5 - 593897 AATAG----------------- -s simHuman_chr6.simHuman.chr6 455148 22 + 601863 AATAGTCTTCATATTGATTTAT -s simRat_chr6.simRat.chr6 479812 22 + 647215 ACCAGTCTTTAGGTAGAATACT - -a -s simMouse_chr6.simMouse.chr6 469950 7 + 636262 TAAAATT -s Anc1.Anc1refChr6 123183 7 + 197743 CAAGGAT -s mr.mrrefChr3 25667 7 + 181027 TAAAATT -s simHuman_chr6.simHuman.chr6 455170 7 + 601863 CAAGGAT -s simRat_chr6.simRat.chr6 438821 7 + 647215 TAAAATT -s simRat_chr6.simRat.chr6 479834 7 + 647215 TAAAATT - -a -s simMouse_chr6.simMouse.chr6 469957 4 + 636262 AATT -s Anc0.Anc0refChr3 90305 4 + 222631 AATT -s Anc1.Anc1refChr6 123238 4 + 197743 AATT -s Anc2.Anc2refChr1 1508 4 + 142988 AACT -s mr.mrrefChr3 25725 4 + 181027 AATT -s simCow_chr6.simCow.chr6 454862 4 + 602619 AACT -s simDog_chr6.simDog.chr6 146420 4 - 593897 AACT -s simHuman_chr6.simHuman.chr6 455228 3 + 601863 AAT- -s simRat_chr6.simRat.chr6 438878 4 + 647215 TGTC -s simRat_chr6.simRat.chr6 479892 4 + 647215 AATT - -a -s simMouse_chr6.simMouse.chr6 469961 5 + 636262 CGTAC -s Anc0.Anc0refChr3 90309 5 + 222631 CATGC -s Anc1.Anc1refChr6 123242 5 + 197743 CATGC -s Anc2.Anc2refChr1 1512 5 + 142988 CATGT -s mr.mrrefChr3 25729 5 + 181027 CATAC -s simCow_chr6.simCow.chr6 454866 5 + 602619 CATTT -s simDog_chr6.simDog.chr6 146424 5 - 593897 CATGC -s simHuman_chr6.simHuman.chr6 455231 4 + 601863 -ATGC -s simRat_chr6.simRat.chr6 438886 5 + 647215 CACAC -s simRat_chr6.simRat.chr6 479896 5 + 647215 CATAC - -a -s simMouse_chr6.simMouse.chr6 469966 57 + 636262 ATCTTTGTCATAGACATGGCCCAGTGTAAACCTAGCATTGTAAAAACTTTGATTTCC -s Anc0.Anc0refChr3 90314 57 + 222631 ATTTATGTCAGAGAGATGGCCCAGTGTACACTTAGGGTTGTATAAACTTTTGTTTCA -s Anc1.Anc1refChr6 123247 57 + 197743 ATTTATGTCAGAGAGATGGCCCAGTGTACACTTAGGGTTGTATAAACTTTTGTTTCA -s Anc2.Anc2refChr1 1519 57 + 142988 ATTTATGTCAGAGAGATGGCCCAGTGTACACTTAGGGTTGTATAAACTTGTGCTTCA -s mr.mrrefChr3 25734 57 + 181027 ATTTTTGTCAGAGACATGGCCCAGTGTAAACTTAGCATCATAAAAACTTTTATTTCT -s simCow_chr6.simCow.chr6 454871 53 + 602619 ATTTAGGTCAGAGAGATGGCCCAGTTTACACTCAGGGATGTAAAAACT----CTTCA -s simDog_chr6.simDog.chr6 146431 57 - 593897 TTTTATGTCAGAGAGCTGGCCCAGTGTACACTTAGGCTTGTATAAACTTGTGCATCA -s simHuman_chr6.simHuman.chr6 455235 57 + 601863 ATTGATGACAGAGAAAAGGCTCTGTGTACGCCTAGGGTTGTCTAAACTTTTGTTTCA -s simRat_chr6.simRat.chr6 438891 57 + 647215 ATTTTTGTCAGAGACATGGCCCAGTATGAACTTAGCATCATATAAATTTTTATTTCT -s simRat_chr6.simRat.chr6 479901 54 + 647215 ATTTTTGTCAGAGGTATGACCAAGTGTAAACTTAGCATCATAAAAACTTTTA---CT - -a -s simMouse_chr6.simMouse.chr6 470023 20 + 636262 TGTACATTTATACTATGCCA -s Anc0.Anc0refChr3 90371 20 + 222631 CATGCATTTATACTGTGTCA -s Anc1.Anc1refChr6 123304 20 + 197743 CATGCATTTATACTGTGTCA -s Anc2.Anc2refChr1 1578 20 + 142988 CATGCATTTATACTGTGTCA -s mr.mrrefChr3 25791 20 + 181027 GGTACATTTATACTATGTCA -s simCow_chr6.simCow.chr6 454926 20 + 602619 CATGCATTTACACTGTGTCA -s simDog_chr6.simDog.chr6 146490 20 - 593897 CACACATGTATACAGTGTCA -s simHuman_chr6.simHuman.chr6 455292 20 + 601863 CATGAATTTATACTGTGTCA -s simRat_chr6.simRat.chr6 438948 20 + 647215 GGTACATTTATACTATGTAA -s simRat_chr6.simRat.chr6 479955 20 + 647215 GGTACATTTATACTACATCA - -a -s simMouse_chr6.simMouse.chr6 470043 34 + 636262 CTAAAGTAAGAATTTTACTACTTGAGTAGGTTCT -s Anc0.Anc0refChr3 90392 34 + 222631 TTACAGTAAAATCTTTACTTTTTGAATAGGTTGT -s Anc1.Anc1refChr6 123325 34 + 197743 TTACAGTAAAATCTTTACTTTTTGAATAGGTTGT -s Anc2.Anc2refChr1 1599 34 + 142988 TGACAGTAAAATCTTTACTTTTTGAATAGGTTGT -s mr.mrrefChr3 25812 34 + 181027 CTAAAGTAAGAATTTTACTACTTGAGTAGGTTGT -s simCow_chr6.simCow.chr6 454947 34 + 602619 GGATGGTAACAACTTTACTCTTTGAATAGGTTGC -s simDog_chr6.simDog.chr6 146511 34 - 593897 TGGCAATAAAATCTTAACTTTTTGAATAGGTTGT -s simHuman_chr6.simHuman.chr6 455313 34 + 601863 TTACAGTAAAATCTATACTTTTTGAATAGGTTGT -s simRat_chr6.simRat.chr6 438969 34 + 647215 CTAAAGTAAGAATTTTGCTACTGGAGGAGTTTGT -s simRat_chr6.simRat.chr6 479976 34 + 647215 CTAAAGTAAGAATTTTACTACTTGAGTAGGTTGT - -a -s simMouse_chr6.simMouse.chr6 470077 6 + 636262 GAATTT -s Anc0.Anc0refChr3 90429 6 + 222631 GAATTT -s Anc1.Anc1refChr6 123362 6 + 197743 GAATTT -s Anc2.Anc2refChr1 1636 6 + 142988 GAATTT -s mr.mrrefChr3 25846 6 + 181027 GAATTT -s simCow_chr6.simCow.chr6 454984 6 + 602619 GAATTT -s simDog_chr6.simDog.chr6 146548 6 - 593897 AAATTT -s simHuman_chr6.simHuman.chr6 455350 6 + 601863 GGATTT -s simRat_chr6.simRat.chr6 439003 6 + 647215 GAATTT -s simRat_chr6.simRat.chr6 480010 6 + 647215 GAATTC - -a -s simMouse_chr6.simMouse.chr6 470083 11 + 636262 CTACCAAAGCA -s Anc0.Anc0refChr3 90437 11 + 222631 CTACTAAAGAA -s Anc1.Anc1refChr6 123370 11 + 197743 CTACTAAAGAA -s Anc2.Anc2refChr1 1644 11 + 142988 CCACTTAAGAA -s mr.mrrefChr3 25852 11 + 181027 CTACCAAAGCA -s simCow_chr6.simCow.chr6 454992 11 + 602619 CCACAGACAAA -s simDog_chr6.simDog.chr6 146556 11 - 593897 CCACTTAAGAA -s simHuman_chr6.simHuman.chr6 455358 11 + 601863 CTACTAAAGAA -s simRat_chr6.simRat.chr6 439009 10 + 647215 CTATCCAAG-C -s simRat_chr6.simRat.chr6 480016 10 + 647215 CTACCAAAG-A - -a -s simMouse_chr6.simMouse.chr6 470094 10 + 636262 ATCTCCCAAA -s Anc0.Anc0refChr3 90448 10 + 222631 GTCTCCCAAA -s Anc1.Anc1refChr6 123381 10 + 197743 GTCTCCCAAA -s Anc2.Anc2refChr1 1655 10 + 142988 GTCACCCAAA -s mr.mrrefChr3 25863 10 + 181027 ATCTCCCAAA -s simCow_chr6.simCow.chr6 455003 10 + 602619 GTTGCCCAAA -s simDog_chr6.simDog.chr6 146567 10 - 593897 CTCAGCCAAA -s simHuman_chr6.simHuman.chr6 455369 10 + 601863 GTCTCCCAAA -s simRat_chr6.simRat.chr6 439022 10 + 647215 ATCTCCCGAA -s simRat_chr6.simRat.chr6 480026 10 + 647215 ATCTCACAAA - -a -s simMouse_chr6.simMouse.chr6 470104 116 + 636262 AATGAGTTTGTAAAATCAATGGATTGATGGTGGTGGGGTTGTATGTAGGACTCCTTTCACTCTGCATGCTAACATTGTTCAGAATTTATTTTTGTAGATGACTTTTCATGTTATGG -s Anc0.Anc0refChr3 90458 95 + 222631 AATGAGTTAGTAAAATGAGTA----GATAGTCAT-----TGTATATATGATT-------TTCTG-TTATTA-CTTAGATTAGTAT---TTTTAGTGGTCAACTTTTCATATTACAG -s Anc1.Anc1refChr6 123391 104 + 197743 AATGAGTTAGTAAAATGAGTA----GATAGTCATGGGGTTGTATATATGATT-------TTCTG-TTATTAACTTAGATTAGTATGTTTTTTAGTGGTCAACTTTTCATATTACAG -s Anc2.Anc2refChr1 1665 95 + 142988 AATGAGTTAGTAAGATGAGTA----GACCATCAC-----TGTATATATGATT-------TTATA-TTATTA-CTTAGATTAGTAT---TTATAGTGGTCAACTTTTCATATTACAA -s mr.mrrefChr3 25873 116 + 181027 AATGAGTTTGTAAAATCAATGGATTGATAGTGATGGGGTTGTATATATGACTCCTTTCACTCTGCATGCTAACATTGTTCAGAATTTATTTTTGTAGATGACTTTTCATGTTATGG -s simCow_chr6.simCow.chr6 455013 37 + 602619 AATGAGGTAGTA-------------------------------------------------------------------------------TAGTGGCAAACTTTTCATATATTGA -s simDog_chr6.simDog.chr6 146577 92 - 593897 G---AGTTAGTAAGATGAGTA----GACCATCAC-----TGTATATATGATT-------TTATA-TTATTA-CTTAGATTAGTAT---TTATAGTGGTCTACATTTCATATTACAA -s simHuman_chr6.simHuman.chr6 455379 104 + 601863 ATTAAGTTAGTAAAATGATTA----GGTAGTTATGGGGTGATATATATGATT-------TTCTG-GTATTAACTTCGATTACTATGTTTTTTAGTGGTCAACTTCTACTATTACAG -s simRat_chr6.simRat.chr6 480036 116 + 647215 AATGAGTTTGTAAAATCGATGGATTAATAGTGATTGGGTTGTATATGTGACTCCCGTCACTTTGCATGCTAATCTTGTTCAGAATCTATTTTTGTAGGTGACTATTCTTGTTATGA - -a -s simMouse_chr6.simMouse.chr6 470220 16 + 636262 CAAGAGTATTAATTGG -s Anc0.Anc0refChr3 90556 16 + 222631 CAGGAGTACCAATTGG -s Anc1.Anc1refChr6 123498 16 + 197743 CAGGAGTACCAATTGG -s Anc2.Anc2refChr1 1763 16 + 142988 CAGGAGTACCAATTGG -s mr.mrrefChr3 25989 16 + 181027 CAGGAGTATCAATTGG -s simCow_chr6.simCow.chr6 455053 16 + 602619 CAGGAGTACCAATTGG -s simDog_chr6.simDog.chr6 146672 16 - 593897 TAGGAGTACCAATCAG -s simHuman_chr6.simHuman.chr6 455486 16 + 601863 CAGGAGCACCAATTGG -s simRat_chr6.simRat.chr6 480152 16 + 647215 CTGGAGTATCAATTGG - -a -s simMouse_chr6.simMouse.chr6 470236 35 + 636262 CTTGAGCCATCAGAAAATTGTTGATCCTTGAATAG -s Anc0.Anc0refChr3 90573 33 + 222631 CATGAGCTGCCAGAAAATTGCCCATCCCTGACT-- -s Anc1.Anc1refChr6 123515 33 + 197743 CATGAGCTGCCAGAAAATTGCCCATCCCTGACT-- -s Anc2.Anc2refChr1 1780 33 + 142988 CATGAGCTGCCAGAAAATTGCCCTTCCCTAACT-- -s mr.mrrefChr3 26005 35 + 181027 CTTGAGCCATCAGAAAATTGTTCATCCCTGAATAG -s simCow_chr6.simCow.chr6 455070 29 + 602619 CATGAACTGCCAGAAAACTGCCCTTCCCT------ -s simDog_chr6.simDog.chr6 146689 33 - 593897 CATGAGTTGCCAGAAAATTGCCCTTCCCTAACT-- -s simHuman_chr6.simHuman.chr6 455503 33 + 601863 CATAAGCTGCAAGAAAGTTGCCCATGCCTGACT-- -s simRat_chr6.simRat.chr6 480168 35 + 647215 CTTGGGCCATCAGAAAAATGTTCATCCCTGAATAG - -a -s simMouse_chr6.simMouse.chr6 470271 16 + 636262 CTTGTACACTTGGAAA -s Anc0.Anc0refChr3 90606 15 + 222631 CTTGTGCACCTGGC-A -s Anc1.Anc1refChr6 123548 16 + 197743 CTTGTGCACCTGGCGA -s Anc2.Anc2refChr1 1813 15 + 142988 CTTCCCTAACTGGC-C -s mr.mrrefChr3 26040 16 + 181027 CTTGTGCACTTGGAGA -s simCow_chr6.simCow.chr6 455399 15 + 602619 TGTTACTTAGTAAC-C -s simDog_chr6.simDog.chr6 146724 15 - 593897 CTTCCCTAACTGGC-C -s simHuman_chr6.simHuman.chr6 455536 16 + 601863 CTAGTGCACCTGGCGA -s simRat_chr6.simRat.chr6 480203 16 + 647215 CTTGTGCACTTGGAGA - -a -s simMouse_chr6.simMouse.chr6 470287 14 + 636262 CAGCTGTGATCTCT -s Anc0.Anc0refChr3 90621 8 + 222631 CAGCGG------CA -s Anc1.Anc1refChr6 123564 11 + 197743 CAGCGGTTA---CA -s Anc2.Anc2refChr1 1828 8 + 142988 CAGGGG------CA -s mr.mrrefChr3 26056 14 + 181027 CAGCTGTGATCTCT -s simCow_chr6.simCow.chr6 455414 8 + 602619 TAGAGA------CA -s simDog_chr6.simDog.chr6 146743 8 - 593897 CAGGGG------CA -s simHuman_chr6.simHuman.chr6 455552 9 + 601863 CATCACTTA----- -s simRat_chr6.simRat.chr6 480219 14 + 647215 CAGCTATGACCTCT - -a -s simMouse_chr6.simMouse.chr6 470301 38 + 636262 GAGTGAACCTCTTAGACAAGATAGCTACATAAACCTAT -s Anc0.Anc0refChr3 90629 38 + 222631 GAGAGAACCTTTTAGAGCACATTGGTACATGAGGCTTG -s Anc1.Anc1refChr6 123575 38 + 197743 GAGAGAACCTTTTAGAGCACATTGGTACATGAGGCTTG -s Anc2.Anc2refChr1 1836 38 + 142988 GAGAGAACCTTTTAGAGCACATTGGTACATGAGGCTTG -s mr.mrrefChr3 26070 38 + 181027 GAGTGAACCTCTTAGACAAGATAGCTACATAAACCTAT -s simCow_chr6.simCow.chr6 455422 38 + 602619 GAGAGAAGCTTTTAGGTAAGATAGTTACATGAGGCTTG -s simDog_chr6.simDog.chr6 146756 38 - 593897 GAGAGAACCTTTTAGAGCACATTGGTACATGAGGCTTA -s simHuman_chr6.simHuman.chr6 455561 2 + 601863 ------------------------------------TG -s simRat_chr6.simRat.chr6 480233 38 + 647215 GAGTGAGCTTTATAGACAAGATTGCTACATAAACCTTG - -a -s simMouse_chr6.simMouse.chr6 470339 62 + 636262 AGAGTATACCTAAGTTCTCTTTGTGCTACCCCTCAGATCTATTGTAAACTCAGAGCTGTCCA -s Anc0.Anc0refChr3 90669 60 + 222631 GAA--ACACCAAAGTACTCTTCTCACTACCACCCAGATCTATTCTTTGCTGATAGCTGCCTC -s Anc1.Anc1refChr6 123615 62 + 197743 GAACCACACCAAAGTACTCTTCTCACTACCACCCAGATCTATTCTTTGCTGATAGCTGCCTC -s Anc2.Anc2refChr1 1876 60 + 142988 GAA--ACCCCAAAGTACTCTTCTCACTACTACCCAGATCTATTCTTTGCTGATAGCTGCCTC -s mr.mrrefChr3 26108 62 + 181027 AGAGTACACCTAAGTTCTCTTTGCACTACCCCTCAGATCTATTGTAAACTCAGAGCTGTCCA -s simCow_chr6.simCow.chr6 455462 60 + 602619 GGA--ACTCCAAAGTATTCTCCTCACTACTCCCCAGATCTATTCTTCACTGATAGCTGCCTC -s simDog_chr6.simDog.chr6 146796 60 - 593897 AAA--ATCCCAAAGTACTCTTCTCACTACTACCCAGATCTATTCTTTGCTGATAGCTGGCTT -s simHuman_chr6.simHuman.chr6 455565 62 + 601863 GAACCACACCAAAATACTGTTCTCACTACCGCCCAGATCTATTCTTTTCTGATAGTTGCCTC -s simRat_chr6.simRat.chr6 480271 62 + 647215 ATAGTACACCCAAGTTCTTTTTGCACCACCCCTCGGATCTATTGTAAACTCAGAGCTGTCCA - -a -s simMouse_chr6.simMouse.chr6 470401 20 + 636262 ACGTCCTAAATCACTTACAG -s Anc0.Anc0refChr3 90730 20 + 222631 AAGTCCTAAATTACTTACAC -s Anc1.Anc1refChr6 123678 20 + 197743 AAGTCCTAAATTACTTACAC -s Anc2.Anc2refChr1 1937 20 + 142988 AAGTCCTGAATTACTTCCAC -s mr.mrrefChr3 26171 20 + 181027 ACGTCCTAAATTACTTACAC -s simCow_chr6.simCow.chr6 455523 20 + 602619 AAGTCCTGAAATACTTTCGC -s simDog_chr6.simDog.chr6 146857 20 - 593897 AAGCCCTGAATCACTTCCAC -s simHuman_chr6.simHuman.chr6 455628 20 + 601863 GAGTCCTAAACTACATACAC -s simRat_chr6.simRat.chr6 480334 20 + 647215 AGATCCTAAATTACTTAAAC - -a -s simMouse_chr6.simMouse.chr6 470421 125 + 636262 TGCAAAAAGCCACTGATGTTGCTAAGTCTTATGTACATTCAAATCCACCCCACACTCTGGATCACTATGTTATCAAAACCACTACAAATCTCCACATGTTTCACATAAGGCCGCTTGTGGGCGCT -s Anc0.Anc0refChr3 90752 122 + 222631 TGCATAAAGCCACTGTTTCTGTCAAGTCTTATATGTGTTCCTGTTCACCCAGCACTGTGGATTGCAATGTTATCAAAACCTCGAAAGATCACCATTTGTTTTGTACTGGGCA---TATGGGAACT -s Anc1.Anc1refChr6 123700 122 + 197743 TGCATAAAGCCACTGTTTCTGTCAAGTCTTATATGTGTTCCTGTTCACCCAGCACTGTGGATTGCAATGTTATCAAAACCTCGAAAGATCACCATTTGTTTTGTACTGGGCA---TATGGGAACT -s Anc2.Anc2refChr1 1959 122 + 142988 TGCATAAAGCCATTGTTTCTATCAAGTCTTATATGTATTGCTGTTCACCCAGCATTGTGGATTGCAGTGTTATCAAAACCTCGAAAGATCACCATTTGCTTTGTACTGGGCA---TCTGGCAACT -s mr.mrrefChr3 26191 122 + 181027 TGCAAAAAGCCACTGATGTTGCTAAGTCTTATGTGTGTTCAAGTCCACCCAACACTCTGGATCACTATGTTATCAAAACCACTACAAATCTCCACATGTTTCGCATTAGGCA---TATGGGCACT -s simCow_chr6.simCow.chr6 455545 116 + 602619 TGCATAAAGCCATTGTTTGTCTCAAATCTTATGTGTATTGCTGTTTACCCAGCAGTGTGGATTGCAGTGTTATCAGTACCACTAAAGATCACAAGC------GCATTCAGCA---CCTGGCGACT -s simDog_chr6.simDog.chr6 146879 118 - 593897 TGCATCAAGCC--TGTTTCTATCAAGTCTTATATGTATTGCTGTTCACCCA--GTTGCGGACTGCAGTGTTATCAAAACCTCGAAAGATCATCATTTGCTTTATACTGGGTA---TCTGCCAACT -s simHuman_chr6.simHuman.chr6 455650 122 + 601863 CACATAAAGCCACTGTTTCTGTCAAGTCTTATATGTGTCCCTGTTCACCCATCACCGTGCATTGCAATGTTATCAAAACCCCCAAAGATCACTAATTGTTTTGTGGTGGGCA---TATGGGTACT -s simRat_chr6.simRat.chr6 480354 122 + 647215 TGCAAAAAGCCACTGATGTTGCTAAGTCTTATGTGTGTTCAAGTCCACCCAGTACTCTGAATCATTATTTTATCAAAACCACTACACACCTCCAGGTGTTTCGCATTAGGCA---TATGGGCACT - -a -s simMouse_chr6.simMouse.chr6 470546 11 + 636262 TGCTATGACCA -s Anc0.Anc0refChr3 90874 11 + 222631 AACTATGACCA -s Anc1.Anc1refChr6 123822 11 + 197743 AACTATGACCA -s Anc2.Anc2refChr1 2081 11 + 142988 AACTATGACCC -s mr.mrrefChr3 26313 11 + 181027 TGCTATGACCA -s simCow_chr6.simCow.chr6 455661 11 + 602619 TACTGTGACCC -s simDog_chr6.simDog.chr6 146998 11 - 593897 AACTATGACCC -s simHuman_chr6.simHuman.chr6 455772 11 + 601863 AACTATGACCA -s simRat_chr6.simRat.chr6 480476 11 + 647215 TGCTATGACTA - -a -s simMouse_chr6.simMouse.chr6 470557 34 + 636262 CTACTTGAGGAATGGTAGGTAGAGCGAGGAGTGG -s Anc0.Anc0refChr3 90885 24 + 222631 CTGCCTGAGAAGGAGTAGGTAAAA---------- -s Anc1.Anc1refChr6 123833 24 + 197743 CTGCCTGAGAAGGAGTAGGTAAAA---------- -s Anc2.Anc2refChr1 2092 24 + 142988 CTGCCTGAGAATGAGTAGGTAAAA---------- -s mr.mrrefChr3 26324 34 + 181027 CTACCTGAGGAGTGGTAGGTAGAGCGAGGAGTGG -s simCow_chr6.simCow.chr6 455673 23 + 602619 CTGCCTGAGTA-GGGTAGGTAAAA---------- -s simDog_chr6.simDog.chr6 147009 24 - 593897 CTGCTTGCGAATGAGTAGGTAAAA---------- -s simHuman_chr6.simHuman.chr6 455783 24 + 601863 CTGCCTGAGAAGCAGTACATGAAA---------- -s simRat_chr6.simRat.chr6 480487 34 + 647215 CTACCTGAGGAGTGGTAGGTAGATTGAGGAGTAG - -a -s simMouse_chr6.simMouse.chr6 470591 10 + 636262 AGGTAGAATA -s Anc0.Anc0refChr3 90909 6 + 222631 ----TGACTA -s Anc1.Anc1refChr6 123857 6 + 197743 ----TGACTA -s Anc2.Anc2refChr1 2116 6 + 142988 ----TGGCTA -s mr.mrrefChr3 26358 10 + 181027 AGGTAGAATA -s simCow_chr6.simCow.chr6 455696 6 + 602619 ----TGGCTA -s simDog_chr6.simDog.chr6 147033 6 - 593897 ----TGGCGA -s simHuman_chr6.simHuman.chr6 455807 6 + 601863 ----GGATTA -s simRat_chr6.simRat.chr6 480522 10 + 647215 AGGTAGAATA - -a -s simMouse_chr6.simMouse.chr6 470601 19 + 636262 AATATACAAATACGTACGG -s Anc0.Anc0refChr3 90915 18 + 222631 ACCATACAAATACATAC-A -s Anc1.Anc1refChr6 123863 18 + 197743 ACCATACAAATACATAC-A -s Anc2.Anc2refChr1 2122 18 + 142988 ACCACACAAATATATAC-A -s mr.mrrefChr3 26368 19 + 181027 AATATACAAATACATACGA -s simCow_chr6.simCow.chr6 455702 18 + 602619 ACCACACAAGTAGATTC-A -s simDog_chr6.simDog.chr6 147039 13 - 593897 A-----CAAATATATAC-A -s simHuman_chr6.simHuman.chr6 455813 18 + 601863 AGAATACAAAAACATAC-A -s simRat_chr6.simRat.chr6 480536 19 + 647215 AACATATAAATACATATGA - -a -s simMouse_chr6.simMouse.chr6 470620 1 + 636262 C -s Anc0.Anc0refChr3 90933 1 + 222631 C -s Anc1.Anc1refChr6 123881 1 + 197743 C -s Anc2.Anc2refChr1 2140 1 + 142988 T -s mr.mrrefChr3 26387 1 + 181027 C -s simCow_chr6.simCow.chr6 455721 1 + 602619 T -s simDog_chr6.simDog.chr6 147052 1 - 593897 T -s simHuman_chr6.simHuman.chr6 455831 1 + 601863 C -s simRat_chr6.simRat.chr6 480555 1 + 647215 C - -a -s simMouse_chr6.simMouse.chr6 470621 19 + 636262 TGAGCACTAATTAGTAGTA -s Anc0.Anc0refChr3 90934 19 + 222631 CGACCTCTAGTTAGTCATA -s Anc1.Anc1refChr6 123882 19 + 197743 CGACCTCTAGTTAGTCATA -s Anc2.Anc2refChr1 2141 19 + 142988 CGACCTCTAGTTAGTCATA -s mr.mrrefChr3 26388 19 + 181027 TGAGCACTAATTAGTAGTA -s simCow_chr6.simCow.chr6 455722 19 + 602619 CGACCTCGAGTTAGTTGAA -s simDog_chr6.simDog.chr6 147058 19 - 593897 TGACCCTTTGTTAGTCATA -s simHuman_chr6.simHuman.chr6 455832 19 + 601863 CAACCTCTAGTCAGCCATA -s simRat_chr6.simRat.chr6 480556 19 + 647215 TGGGCACTAATTAGTAGTA - -a -s simMouse_chr6.simMouse.chr6 470640 12 + 636262 TCAAATCAGATC -s Anc0.Anc0refChr3 90953 12 + 222631 CCACATCAAGTC -s Anc1.Anc1refChr6 123901 12 + 197743 CCACATCAAGTC -s Anc2.Anc2refChr1 2160 12 + 142988 CCACATCAAGTC -s mr.mrrefChr3 26407 12 + 181027 TCACATCAGATC -s simCow_chr6.simCow.chr6 455741 12 + 602619 TCATATCAAGTC -s simDog_chr6.simDog.chr6 147077 12 - 593897 CCACATCAAGTC -s simHuman_chr6.simHuman.chr6 455851 12 + 601863 CCGCATCAAGTC -s simRat_chr6.simRat.chr6 480593 12 + 647215 TTACATCTGATC - -a -s simMouse_chr6.simMouse.chr6 470652 43 + 636262 TAGGTACTAAGACTCAATTTAAGACCAGTGCTTTCATGACCAT -s Anc0.Anc0refChr3 90967 43 + 222631 TATGCACTAAATCTCAATTTATGGCCAGTGCTTTTATGACCAT -s Anc1.Anc1refChr6 123915 43 + 197743 TATGCACTAAATCTCAATTTATGGCCAGTGCTTTTATGACCAT -s Anc2.Anc2refChr1 2174 43 + 142988 TATGCACTAAATTTCAATTTATGGCGAGTGCCTTTATGACCAT -s mr.mrrefChr3 26419 43 + 181027 TAGGCACTAAAACTCAATTTATGACCAGTGCTTTTATGACCAT -s simCow_chr6.simCow.chr6 455755 39 + 602619 TA-GTACTAAATTTCAATTTATAG---GTGCCTTTATGAACAC -s simDog_chr6.simDog.chr6 147091 42 - 593897 TATACATTGAATTTCAATTTATGGCGAATACCTT-ACAACTTT -s simHuman_chr6.simHuman.chr6 455865 43 + 601863 TGTGCACCAAATCTCAATCTGTGGTCAGTGCTTTTATGACCAT -s simRat_chr6.simRat.chr6 480605 43 + 647215 TAGGCACAAAAACTCAATTTATGACTGACGCTTTTATGACCGT - -a -s simMouse_chr6.simMouse.chr6 470695 35 + 636262 AGCTAAGCCCAACTAAAAAAGGAAGTAGCAATGAA -s Anc0.Anc0refChr3 91017 35 + 222631 GCCTAAGTTGAGCTGACAAAGGAAGCAGCTATTAA -s Anc1.Anc1refChr6 123965 35 + 197743 GCCTAAGTTGAGCTGACAAAGGAAGCAGCTATTAA -s Anc2.Anc2refChr1 2224 35 + 142988 GCCTAAGTTGAGCCGACAAAGGAAGCAACTATTAA -s mr.mrrefChr3 26462 35 + 181027 AGCTAAGCCCAACTAAAAAAGGAAGTAGCAATGAA -s simCow_chr6.simCow.chr6 455800 35 + 602619 GACTAAGGTGAGTCAATAAAGAAACAAATAATTGG -s simDog_chr6.simDog.chr6 147140 35 - 593897 GCCTGAGTTGCACCGACATAGGAAGCAACTATTAA -s simHuman_chr6.simHuman.chr6 455920 35 + 601863 GCCCAAATTGAGCTGACAAAGGAAGCCGCCATCAA -s simRat_chr6.simRat.chr6 480648 35 + 647215 AGCTAAGCCCAACTAATAAAGGAAGTAGCAACGAA - -a -s simMouse_chr6.simMouse.chr6 470730 1 + 636262 A -s Anc0.Anc0refChr3 91052 1 + 222631 A -s Anc1.Anc1refChr6 124000 1 + 197743 A -s Anc2.Anc2refChr1 2259 1 + 142988 A -s mr.mrrefChr3 26497 1 + 181027 A -s simCow_chr6.simCow.chr6 455836 1 + 602619 A -s simDog_chr6.simDog.chr6 147175 1 - 593897 A -s simHuman_chr6.simHuman.chr6 455955 1 + 601863 A -s simRat_chr6.simRat.chr6 480683 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 470731 47 + 636262 AAATCAGATTAGCAGTAACAAACACGGCATTGAGACAACTGTCTTCA -s Anc0.Anc0refChr3 91053 38 + 222631 TA-----CTAAGCAGTACCA----CCAGGTTGAGACAACTGTATCCA -s Anc1.Anc1refChr6 124001 38 + 197743 TA-----CTAAGCAGTACCA----CCAGGTTGAGACAACTGTATCCA -s Anc2.Anc2refChr1 2260 38 + 142988 TA-----CTAAACAGTACAA----CCAGGTTGAGAGAACTATATCCA -s mr.mrrefChr3 26498 43 + 181027 AAATCAGCTTAGCAGTAACA----CCAGGTTGAGACAACTGTCTTCA -s simCow_chr6.simCow.chr6 455837 38 + 602619 TA-----CTAAACAGAACTA----CTAGGTTGAGAGAGCTATATCAA -s simDog_chr6.simDog.chr6 147183 38 - 593897 TA-----TTAAACAGTACAA----CCAGCTTGAGAGAACTATCTCCA -s simHuman_chr6.simHuman.chr6 455956 38 + 601863 TA-----CCAAGTATTACCA----CCAGGTTGAGACAACTGTATCCG -s simRat_chr6.simRat.chr6 480684 43 + 647215 AAATCAGCTTACCAGTAACA----CCAGGTTGAGACAACTATCTTCA - -a -s simMouse_chr6.simMouse.chr6 470778 28 + 636262 ACCTGGTTAGGTAGATGCAACAAGGGCC -s Anc0.Anc0refChr3 91091 28 + 222631 GCCTGGATATGTAGACAGGAGAGGAGCA -s Anc1.Anc1refChr6 124039 28 + 197743 GCCTGGATATGTAGACAGGAGAGGAGCA -s Anc2.Anc2refChr1 2298 28 + 142988 GCCTGGAGATGTAGACAGGAGAGGAGCA -s mr.mrrefChr3 26541 28 + 181027 ACCTGGTTAGGTAGACACAAGAAGGGCC -s simCow_chr6.simCow.chr6 455875 28 + 602619 GCCTGGAGATATAGACAGGAAAGGAGCA -s simDog_chr6.simDog.chr6 147229 28 - 593897 GCCTGGAGATGTAGACAGGAGAGGAGCA -s simHuman_chr6.simHuman.chr6 455994 24 + 601863 ----GGCTATGTAAACAGGAGAGGAGCA -s simRat_chr6.simRat.chr6 480727 28 + 647215 ACCTGGTGAGGTAGACATAAGGAGGGCC - -a -s simMouse_chr6.simMouse.chr6 470806 29 + 636262 TTTATTATGTTCTTCTCTCCACCCACAGA -s Anc0.Anc0refChr3 91128 17 + 222631 TGTAAT---------C-TC--TCCACGCA -s Anc1.Anc1refChr6 124076 26 + 197743 TGTAATAAGCTCTACC-TC--TCCACGCA -s Anc2.Anc2refChr1 2335 17 + 142988 TGTACT---------C-TC--TCCACGCA -s mr.mrrefChr3 26569 28 + 181027 TTTATTATGTTCTTCT-TCCACCCACAGA -s simCow_chr6.simCow.chr6 455912 16 + 602619 CATAC----------C-TC--TCCACGCA -s simDog_chr6.simDog.chr6 147266 6 - 593897 TGTACT----------------------- -s simHuman_chr6.simHuman.chr6 456027 26 + 601863 TGTAATAAGCTGTACC-TC--TCCAAGCA -s simRat_chr6.simRat.chr6 480755 28 + 647215 ATTATTATGTTCTTCT-TCCACCCACAGA - -a -s simMouse_chr6.simMouse.chr6 470835 44 + 636262 AAGCAGGAGTTATCTTACACTTGAGGTTTCACTTAGGAAGGTTT -s Anc0.Anc0refChr3 91145 44 + 222631 AAGCAGGGGTTATTTTACACTTAAGGATCCACCTAGGGAGGCTT -s Anc1.Anc1refChr6 124102 44 + 197743 AAGCAGGGGTTATTTTACACTTAAGGATCCACCTAGGGAGGCTT -s Anc2.Anc2refChr1 2352 44 + 142988 AAGCAGGGGTTATTTTACATTTAAGGATTCATCTATAGAGGCTA -s mr.mrrefChr3 26597 44 + 181027 AAGCAGGAGTTATCTTACACTTGAGGTTCCACTTAGGGAGGTTT -s simCow_chr6.simCow.chr6 455932 44 + 602619 AAGCAGGGGTTATTTTACATTTAAGGATTCATCTATAGAGGCTA -s simHuman_chr6.simHuman.chr6 456053 44 + 601863 AAGCGAAGAGTGTTTCACACCTAGGGATCCACCTAGGGATGCTT -s simRat_chr6.simRat.chr6 480783 33 + 647215 ATGC-----------TACACTTGTGGTTCCACTTAGGGAGGTTT - -a -s simMouse_chr6.simMouse.chr6 470879 40 + 636262 GTGGAAGATTGACTACAAGAGTGAGGGGCCGGCTGGTTGA -s Anc0.Anc0refChr3 91189 40 + 222631 GTGGGAGATTTATTACAGGGGCATAGAGCAGGCTTCTTCA -s Anc1.Anc1refChr6 124146 40 + 197743 GTGGGAGATTTATTACAGGGGCATAGAGCAGGCTTCTTCA -s Anc2.Anc2refChr1 2396 40 + 142988 GTGGGGAGTTCATTACAGGGGCATAGAGCGGGCTTCTTCA -s mr.mrrefChr3 26641 40 + 181027 GTGGAAGATTTACTACAAGGGTGAGGGGCAGGCTCGTTGA -s simCow_chr6.simCow.chr6 455977 40 + 602619 GTGGGGAGTTCACTGTGGGGGCATGGAGCGGACTTCATCA -s simDog_chr6.simDog.chr6 147272 28 - 593897 ------------TCACACGGTCATAGAGTGAGCTTTTTCA -s simHuman_chr6.simHuman.chr6 456097 40 + 601863 GTGGGAGATTTGTTACAGGGGCATAGAGCAGGCCTCCTCA -s simRat_chr6.simRat.chr6 480816 37 + 647215 GTGGAA---TTACTACAAGGGTGAGGGGTAGGTTCATTGA - -a -s simMouse_chr6.simMouse.chr6 470919 3 + 636262 GCT -s Anc0.Anc0refChr3 91229 3 + 222631 ATT -s Anc1.Anc1refChr6 124186 3 + 197743 ATT -s Anc2.Anc2refChr1 2447 3 + 142988 ATT -s mr.mrrefChr3 26681 3 + 181027 GCT -s simCow_chr6.simCow.chr6 456028 3 + 602619 ATT -s simDog_chr6.simDog.chr6 147311 3 - 593897 ATT -s simHuman_chr6.simHuman.chr6 456137 3 + 601863 ATT -s simRat_chr6.simRat.chr6 480853 3 + 647215 GCT - -a -s simMouse_chr6.simMouse.chr6 470922 13 + 636262 CAATTGTCATTCT -s Anc0.Anc0refChr3 91232 1 + 222631 C------------ -s Anc1.Anc1refChr6 124189 1 + 197743 C------------ -s Anc2.Anc2refChr1 2450 1 + 142988 C------------ -s mr.mrrefChr3 26684 1 + 181027 C------------ -s simCow_chr6.simCow.chr6 456034 1 + 602619 C------------ -s simDog_chr6.simDog.chr6 147314 1 - 593897 C------------ -s simHuman_chr6.simHuman.chr6 456140 1 + 601863 C------------ -s simRat_chr6.simRat.chr6 480856 1 + 647215 C------------ - -a -s simMouse_chr6.simMouse.chr6 470935 12 + 636262 TAGATGCAGAAT -s Anc0.Anc0refChr3 91234 12 + 222631 TAGATGCAGAGT -s Anc1.Anc1refChr6 124191 12 + 197743 TAGATGCAGAGT -s Anc2.Anc2refChr1 2452 12 + 142988 TAGATGCAGAGT -s mr.mrrefChr3 26685 12 + 181027 TAGATGCAGAAT -s simCow_chr6.simCow.chr6 456036 12 + 602619 TGGATGCAGGGT -s simDog_chr6.simDog.chr6 147316 12 - 593897 TAGATGCAGAGT -s simHuman_chr6.simHuman.chr6 456142 12 + 601863 TAGAGGCAGAGC -s simRat_chr6.simRat.chr6 480857 12 + 647215 AAGATGCAGTTT - -a -s simMouse_chr6.simMouse.chr6 470947 4 + 636262 TATG -s Anc0.Anc0refChr3 91246 4 + 222631 TATG -s Anc1.Anc1refChr6 124203 4 + 197743 TATG -s Anc2.Anc2refChr1 2464 4 + 142988 TATG -s mr.mrrefChr3 26697 4 + 181027 TATG -s simCow_chr6.simCow.chr6 456054 4 + 602619 TATG -s simDog_chr6.simDog.chr6 147328 4 - 593897 TATG -s simHuman_chr6.simHuman.chr6 456154 4 + 601863 TATG -s simRat_chr6.simRat.chr6 480869 4 + 647215 TATG - -a -s simMouse_chr6.simMouse.chr6 470951 4 + 636262 TAGG -s Anc0.Anc0refChr3 91250 4 + 222631 TAGC -s Anc1.Anc1refChr6 124207 4 + 197743 TAGC -s Anc2.Anc2refChr1 2470 4 + 142988 CATC -s mr.mrrefChr3 26701 4 + 181027 TAGG -s simCow_chr6.simCow.chr6 456060 4 + 602619 CATC -s simDog_chr6.simDog.chr6 147334 4 - 593897 CATC -s simHuman_chr6.simHuman.chr6 456158 4 + 601863 TGGC -s simRat_chr6.simRat.chr6 480873 4 + 647215 TAGG - -a -s simMouse_chr6.simMouse.chr6 470955 66 + 636262 GACTATTACTAAGGTAGAAGACAAAAGACATTCACTGCATGGCCTTAAAGACAGAAATCAATTTTG -s Anc0.Anc0refChr3 91254 59 + 222631 GTTTCTTCCAAGGGT--AA-----AAGGCTCTTACTGTATGCCCTTGAAGTCAGATGTTGATTTTG -s Anc1.Anc1refChr6 124211 60 + 197743 GTTTCTTCCAAGGGT-TAA-----AAGGCTCTTACTGTATGCCCTTGAAGTCAGATGTTGATTTTG -s Anc2.Anc2refChr1 2474 59 + 142988 GTTTCTGCCAAGGGT--AA-----AAGGCTCTTAATGTATGCCCTTGAAGTCAGATGTTGATCTTG -s mr.mrrefChr3 26705 61 + 181027 GACTATTACTAGGGTAGAA-----AAGACATTTACTGCATGGCCTTAAAGACAGATATCAATTTTG -s simCow_chr6.simCow.chr6 456066 58 + 602619 GTTTTTGCCAAGGTT--AA-----AAGGCTCTTTGTGTGTACA-TTGGAGTTGGATGTTGATCTTG -s simDog_chr6.simDog.chr6 147338 58 - 593897 ATTTCTGCCAAGGGT--AA-----AAGGCTCTTAATGTATGCCCTTGAAGTCAGA-ATTGATCTTG -s simHuman_chr6.simHuman.chr6 456162 57 + 601863 GTTCGTTTCAAG----TAA-----AAGGCCCTTGCCGTATGTCTTTGAAGCCAGATGTTGGTTTTG -s simRat_chr6.simRat.chr6 480877 61 + 647215 GACTATTACTAGGCTAGGA-----AAGCCATTTACTGCATCACCTTAGAGTAAGATATCCATTTTG - -a -s simMouse_chr6.simMouse.chr6 471021 15 + 636262 CCCCTGTATTTTCCT -s Anc0.Anc0refChr3 91324 15 + 222631 CCCTTGTATCTTTCT -s Anc1.Anc1refChr6 124282 15 + 197743 CCCTTGTATCTTTCT -s Anc2.Anc2refChr1 2544 15 + 142988 CCCTTGTATTTTTCT -s mr.mrrefChr3 26766 15 + 181027 CCCCTGTATCTTCCT -s simCow_chr6.simCow.chr6 456135 15 + 602619 CCCTTGTATTATTCT -s simDog_chr6.simDog.chr6 147407 15 - 593897 CCCCTGTATTTTTCT -s simHuman_chr6.simHuman.chr6 456230 15 + 601863 CCCTTGTATCTTTCT -s simRat_chr6.simRat.chr6 480938 15 + 647215 CCCCTTTACCTACTT - -a -s simMouse_chr6.simMouse.chr6 471036 47 + 636262 GTCTTGGCAGGTAATGACTCTCACATTCTTCACGAGTATGTTGTCCA -s Anc0.Anc0refChr3 91341 44 + 222631 AT--TGGCATATCATGACTGTTGTATTTTCCAGTAAGAT-TTTTACA -s Anc1.Anc1refChr6 124299 46 + 197743 ATCTTGGCATATCATGACTGTTGTATTTTCCAGTAAGAT-TTTTACA -s Anc2.Anc2refChr1 2561 44 + 142988 AT--TGGCATATCATAACTGTTGTATTTTCCCATAAGAT-TTTTATC -s mr.mrrefChr3 26781 47 + 181027 GTCTTGGCATGTAATGACTCTCACATTCTTCAGGAGTATGTTGTCCA -s simCow_chr6.simCow.chr6 456152 44 + 602619 AT--TGGGATGTCATAACTCTTGTATTTTCCCATAATAT-TTCTATT -s simDog_chr6.simDog.chr6 147422 41 - 593897 -----GTCAAATCATAGCTGTTGTATTTTCCCACAAGAT-TTTTATC -s simHuman_chr6.simHuman.chr6 456247 38 + 601863 ATCTTGGCATATCATGACCTCTGGCTTTTCCAGTAA---------CA -s simRat_chr6.simRat.chr6 480953 47 + 647215 GTCTTGGCATGTAATTACTCTCATATTCTTCAGGAGTCTGTTGACCG - -a -s simMouse_chr6.simMouse.chr6 471083 26 + 636262 GGAGACCTTAGTAAATCTTTGCTCAT -s Anc0.Anc0refChr3 91385 26 + 222631 GAAGCTCTTATTAAATCTTAGCTTAT -s Anc1.Anc1refChr6 124345 26 + 197743 GAAGCTCTTATTAAATCTTAGCTTAT -s Anc2.Anc2refChr1 2605 26 + 142988 GAAGCTCTTATTAAATCTTAGCTTAT -s mr.mrrefChr3 26828 26 + 181027 GGAGACCTTAGTAAATCTTTGCTCAT -s simCow_chr6.simCow.chr6 456198 26 + 602619 GAAGCTCTTAGAAGATCTTAGGTTGT -s simDog_chr6.simDog.chr6 147463 26 - 593897 GAAGCTCCTATTAATTCTCAGCTTAT -s simHuman_chr6.simHuman.chr6 456285 26 + 601863 GAAGCTCTTTCTAAAACTTAGCTTAT -s simRat_chr6.simRat.chr6 481000 26 + 647215 GGAGGCCTTATTAACTCTTCGCTCAT - -a -s simMouse_chr6.simMouse.chr6 471109 4 + 636262 TAGA -s Anc0.Anc0refChr3 91411 4 + 222631 TAAA -s Anc1.Anc1refChr6 124371 4 + 197743 TAAA -s Anc2.Anc2refChr1 2631 4 + 142988 TGAA -s mr.mrrefChr3 26854 4 + 181027 TAGA -s simCow_chr6.simCow.chr6 456224 4 + 602619 ATAA -s simDog_chr6.simDog.chr6 147490 4 - 593897 TGAA -s simHuman_chr6.simHuman.chr6 456311 4 + 601863 CAAA -s simRat_chr6.simRat.chr6 481026 4 + 647215 TAGA - -a -s simMouse_chr6.simMouse.chr6 471113 27 + 636262 TATACTAACCCTCATCTGCCATCACCA -s Anc0.Anc0refChr3 91415 27 + 222631 TCTGCTTACCCTCATGTGCCATCATCA -s Anc1.Anc1refChr6 124375 27 + 197743 TCTGCTTACCCTCATGTGCCATCATCA -s Anc2.Anc2refChr1 2635 27 + 142988 TCTGCTTATCCTCATGTGCCATCATCA -s mr.mrrefChr3 26858 27 + 181027 TATGCTAACCCTCATCTGCCATCACCA -s simCow_chr6.simCow.chr6 456228 27 + 602619 TCTGCTTATCCTCATTGGCTGTCACCA -s simDog_chr6.simDog.chr6 147494 27 - 593897 TCTGCTTATCTTCATGTGCCATCATCA -s simHuman_chr6.simHuman.chr6 456315 27 + 601863 TCTGCTTGCCCTGATGTGCCATCATCA -s simRat_chr6.simRat.chr6 481032 27 + 647215 TGTGCTAACCCTCAACTGCCATCCCCA - -a -s simMouse_chr6.simMouse.chr6 471140 33 + 636262 TTATTTAAGAACATTGGTCTATGAGTTTATGCT -s Anc0.Anc0refChr3 91442 33 + 222631 CCATTCAAGAGTATTGGTCTATGTGCTGATGAT -s Anc1.Anc1refChr6 124402 33 + 197743 CCATTCAAGAGTATTGGTCTATGTGCTGATGAT -s Anc2.Anc2refChr1 2662 33 + 142988 CCATTCAAGAGTATTGGTCTATGTGTTGATGAT -s mr.mrrefChr3 26885 33 + 181027 TTATTTAAGAACATTGGTCTATGAGCTTATGCT -s simCow_chr6.simCow.chr6 456255 17 + 602619 C----------------TCTATGTGATTATGAT -s simDog_chr6.simDog.chr6 147528 33 - 593897 CCATTCAAGAGTATTGGTCTATGTGTCGATGAT -s simHuman_chr6.simHuman.chr6 456342 33 + 601863 CCATTCAAGGGTATTGGTTTCAGTGCTGAAGAT -s simRat_chr6.simRat.chr6 481059 33 + 647215 TTGTTTAAAAACACTGGTCTATGAGCTTGTGGT - -a -s simMouse_chr6.simMouse.chr6 471173 9 + 636262 TAAGATGAA -s Anc0.Anc0refChr3 91475 9 + 222631 CAACAGGAC -s Anc1.Anc1refChr6 124435 9 + 197743 CAACAGGAC -s Anc2.Anc2refChr1 2695 9 + 142988 CAACAGGAT -s mr.mrrefChr3 26918 9 + 181027 TAAGAGGAC -s simCow_chr6.simCow.chr6 456272 9 + 602619 TAACAGGAT -s simDog_chr6.simDog.chr6 449803 9 + 593897 CATATGGAG -s simHuman_chr6.simHuman.chr6 456375 9 + 601863 CAACAGGAC -s simRat_chr6.simRat.chr6 481092 9 + 647215 TAAGAGGAC - -a -s simMouse_chr6.simMouse.chr6 471182 10 + 636262 CCCTGGCCGT -s Anc0.Anc0refChr3 91484 10 + 222631 CCCAAGCTGG -s Anc1.Anc1refChr6 124444 10 + 197743 CCCAAGCTGG -s Anc2.Anc2refChr1 2704 10 + 142988 CCCAAGCTGG -s mr.mrrefChr3 26927 10 + 181027 CCCTGGCTGT -s simCow_chr6.simCow.chr6 456281 10 + 602619 CCCAAGCTGG -s simDog_chr6.simDog.chr6 449812 10 + 593897 CCCAAGCTGG -s simHuman_chr6.simHuman.chr6 456386 10 + 601863 CCCAAGCTGG -s simRat_chr6.simRat.chr6 481101 10 + 647215 CCCTGGATGT - -a -s simMouse_chr6.simMouse.chr6 471192 5 + 636262 GTCCG -s Anc0.Anc0refChr3 91496 5 + 222631 GTCTG -s Anc1.Anc1refChr6 124456 5 + 197743 GTCTG -s Anc2.Anc2refChr1 2716 5 + 142988 GTCTG -s mr.mrrefChr3 26937 5 + 181027 GTCCG -s simCow_chr6.simCow.chr6 456293 5 + 602619 GTCTG -s simDog_chr6.simDog.chr6 449824 5 + 593897 GTCTG -s simHuman_chr6.simHuman.chr6 456398 5 + 601863 GTCTG -s simRat_chr6.simRat.chr6 481111 5 + 647215 GTCCA - -a -s simMouse_chr6.simMouse.chr6 471197 3 + 636262 CGT -s Anc0.Anc0refChr3 91501 3 + 222631 TGT -s Anc1.Anc1refChr6 124461 3 + 197743 TGT -s Anc2.Anc2refChr1 2721 3 + 142988 TGT -s mr.mrrefChr3 26942 3 + 181027 TGT -s simCow_chr6.simCow.chr6 456299 3 + 602619 TAT -s simDog_chr6.simDog.chr6 449829 3 + 593897 TGT -s simHuman_chr6.simHuman.chr6 456403 3 + 601863 TGT -s simRat_chr6.simRat.chr6 481116 3 + 647215 TGT - -a -s simMouse_chr6.simMouse.chr6 471200 29 + 636262 TCCATATTGTTTGGCTTTTGTCTGCATCC -s Anc0.Anc0refChr3 91505 29 + 222631 CTGGTATTGTTTGGCATTTTTTTGCAATT -s Anc1.Anc1refChr6 124465 29 + 197743 CTGGTATTGTTTGGCATTTTTTTGCAATT -s Anc2.Anc2refChr1 2725 29 + 142988 CTGGTATTCTTTGGCATTTTTTAGCAATT -s mr.mrrefChr3 26945 29 + 181027 TTGGTATTGTTTGGCTTTTGTCTGCATCC -s simCow_chr6.simCow.chr6 456303 27 + 602619 CTGGTATTCTCTGGCATTTCTTAGCAA-- -s simDog_chr6.simDog.chr6 449833 29 + 593897 TTTGTGTTCTTTGGCATCTTTTGGCAATT -s simHuman_chr6.simHuman.chr6 456407 28 + 601863 CTGGAACTGCTTGGCGTTT-TTTACAATT -s simRat_chr6.simRat.chr6 481119 29 + 647215 TTGGTATTGTTTAGCTTTTGTCACCAACC - -a -s simMouse_chr6.simMouse.chr6 471229 4 + 636262 ATCC -s Anc0.Anc0refChr3 91534 4 + 222631 GTCC -s Anc1.Anc1refChr6 124494 4 + 197743 GTCC -s Anc2.Anc2refChr1 2754 4 + 142988 GTCC -s mr.mrrefChr3 26974 4 + 181027 ATCC -s simDog_chr6.simDog.chr6 449863 4 + 593897 GTCC -s simHuman_chr6.simHuman.chr6 456435 4 + 601863 GTCT -s simRat_chr6.simRat.chr6 481148 4 + 647215 ATCC - -a -s simMouse_chr6.simMouse.chr6 471233 2 + 636262 TT -s Anc0.Anc0refChr3 91538 2 + 222631 TT -s Anc1.Anc1refChr6 124498 2 + 197743 TT -s Anc2.Anc2refChr1 2758 2 + 142988 TT -s mr.mrrefChr3 26978 2 + 181027 TT -s simDog_chr6.simDog.chr6 449867 2 + 593897 TT -s simHuman_chr6.simHuman.chr6 456443 2 + 601863 TA -s simRat_chr6.simRat.chr6 481152 2 + 647215 TC - -a -s simMouse_chr6.simMouse.chr6 471235 22 + 636262 GGCTAGCAGAGTTAGCAGCTAC -s Anc0.Anc0refChr3 91540 22 + 222631 AGCTAGCATAGTTAGTGGTTAC -s Anc1.Anc1refChr6 124500 22 + 197743 AGCTAGCATAGTTAGTGGTTAC -s Anc2.Anc2refChr1 2764 22 + 142988 AGCTAGTGTAATTAGTGTTTAC -s mr.mrrefChr3 26980 22 + 181027 AGCTAGCAGAGTTAGCAGCTAC -s simCow_chr6.simCow.chr6 456330 12 + 602619 ----------ATTAGTGCCTGC -s simDog_chr6.simDog.chr6 449873 22 + 593897 AGCTAGTGTAATTAGTGTTTAC -s simHuman_chr6.simHuman.chr6 456445 22 + 601863 AGCTAGCAAAGTTAGGGGTTAC -s simRat_chr6.simRat.chr6 481154 22 + 647215 AGCTAGCAGAGTTAGCAGCTAC - -a -s simMouse_chr6.simMouse.chr6 471257 46 + 636262 ATCGGCTGACAATCAAATCATTCCACATATTATTATCATCAATTCA -s Anc0.Anc0refChr3 91562 41 + 222631 ACAGACCCAC-----TGTCATTCCACCTGTTATTTTCAACAATCCA -s Anc1.Anc1refChr6 124522 41 + 197743 ACAGACCCAC-----TGTCATTCCACCTGTTATTTTCAACAATCCA -s Anc2.Anc2refChr1 2786 41 + 142988 ACAGACCCAC-----TGTCACTTCACCCATTATTTTCAAGTATCCA -s mr.mrrefChr3 27002 46 + 181027 ATAGGCTGACAATCAAATCATTCCACCTGTTATTATCATCAATTCA -s simCow_chr6.simCow.chr6 456342 36 + 602619 ACAGACCCAC-----TGTCACTTCACCCATTATTTTCA-----CTA -s simDog_chr6.simDog.chr6 449895 24 + 593897 ACA-----AC-----TACT------------ACCTTCAAGTATCCA -s simHuman_chr6.simHuman.chr6 456467 41 + 601863 ACAGACCCAT-----GGTCCTTCCACCTGTTATTTTTAGCAATCCA -s simRat_chr6.simRat.chr6 481184 46 + 647215 ATAGGCTAACAACCAAACCATTCCGACCGTTATCATCATTAATTCA - -a -s simMouse_chr6.simMouse.chr6 471303 16 + 636262 TAGAGATAATACAGGG -s Anc0.Anc0refChr3 91603 12 + 222631 TTGCAA----ACAGGG -s Anc1.Anc1refChr6 124563 12 + 197743 TTGCAA----ACAGGG -s Anc2.Anc2refChr1 2827 12 + 142988 TTGCAA----ACAGGG -s mr.mrrefChr3 27048 12 + 181027 TAGAGA----ACAGGG -s simCow_chr6.simCow.chr6 456378 12 + 602619 TAACAA----ACAGGG -s simDog_chr6.simDog.chr6 449922 12 + 593897 TTGTTT----GCTATG -s simHuman_chr6.simHuman.chr6 456508 12 + 601863 TTGCAA----ACAGGG -s simRat_chr6.simRat.chr6 481230 12 + 647215 TAGAGA----ACAGGG - -a -s simMouse_chr6.simMouse.chr6 471319 17 + 636262 TGGATGCTTGATTGGAA -s Anc0.Anc0refChr3 91616 6 + 222631 -----ACTT-----GA- -s Anc1.Anc1refChr6 124577 11 + 197743 AGGATACTT-----GA- -s Anc2.Anc2refChr1 2840 6 + 142988 -----ACTT-----GA- -s mr.mrrefChr3 27062 17 + 181027 AGGATACTTGATTGGAA -s simDog_chr6.simDog.chr6 449935 6 + 593897 -----ACTT-----GA- -s simHuman_chr6.simHuman.chr6 456522 11 + 601863 AGGATACTT-----GA- -s simRat_chr6.simRat.chr6 481244 17 + 647215 AGGATACTTGATTGGCA - -a -s simMouse_chr6.simMouse.chr6 471336 83 + 636262 GAAATGCTAACATTGCAAATTGGCATTGGAATTTGTCTAAATCTGCTTAGGGTATCTAGTTGAATAGCCCCCAGAAGGTGACC -s Anc0.Anc0refChr3 91622 54 + 222631 -----------------------CAATAGGAATGGT-----TCTACTTAGAGTATCTTGTG-AACAGCCTCCAGAGGATGACC -s Anc1.Anc1refChr6 124588 59 + 197743 -----------------------CAATAGGAATGGTGTAGATCTACTTAGAGTATCTTGTG-AACAGCCTCCAGAGGATGACC -s Anc2.Anc2refChr1 2846 54 + 142988 -----------------------CGAAAATAATGGC-----TCTACTTAGAGCATCTTGTG-AACAACCTCCAGGGGACAAGC -s mr.mrrefChr3 27079 83 + 181027 GAAATGCTAACATTGCAAATTGGCATTGGGATTTGTCTAAATCTGCTTAGAGTATCTAGTTGAACAGCCCCCAGAAGGTGACC -s simCow_chr6.simCow.chr6 456391 41 + 602619 -----------------------------------------TTTACTTAGAGCTTTTTGTG-AACAACCTTTAGTTGACAGGG -s simDog_chr6.simDog.chr6 449941 54 + 593897 -----------------------CGAAAATAATGGC-----TCTACTTAGAGCATCTTGTG-AACAACCTCCAGGGGACAAGC -s simHuman_chr6.simHuman.chr6 456533 59 + 601863 -----------------------CAGTAGGAGTAGTGTAGATCTACTTAGAGTAACTTGTC-AACAGCCTACAGAGGATGACC -s simRat_chr6.simRat.chr6 481263 83 + 647215 GTAGTGCAAACATTGCAAATTGGCGTTGGGATTTGTCTAAATCCGCTTAGAGTATCTAGTTGATCAGCCCTGGGAAGGTGACC - -a -s simMouse_chr6.simMouse.chr6 471419 2 + 636262 TA -s Anc0.Anc0refChr3 91677 2 + 222631 AA -s Anc1.Anc1refChr6 124648 2 + 197743 AA -s Anc2.Anc2refChr1 2901 2 + 142988 AG -s mr.mrrefChr3 27162 2 + 181027 AA -s simCow_chr6.simCow.chr6 456433 2 + 602619 AT -s simDog_chr6.simDog.chr6 449996 2 + 593897 AG -s simHuman_chr6.simHuman.chr6 456593 2 + 601863 AA -s simRat_chr6.simRat.chr6 481346 2 + 647215 AA - -a -s simMouse_chr6.simMouse.chr6 471421 41 + 636262 CATTGGAGAAAGCAGATAACACTCAATACAATAAAGCTGGG -s Anc0.Anc0refChr3 91680 41 + 222631 TTATGAAGAAGGCGGAGGGCtCTTGGTGTGATAGAGCTGGT -s Anc1.Anc1refChr6 124651 41 + 197743 TTATGAAGAAGGCGGAGGGCtCTTGGTGTGATAGAGCTGGT -s Anc2.Anc2refChr1 2904 41 + 142988 TTATAAACAAGGCGTAGGGCtCTTGGTGTGATAGAGCTGGT -s mr.mrrefChr3 27165 41 + 181027 CGTTGGAGAAAGCAGATAACACTCAATACAATAAAGCTGGG -s simCow_chr6.simCow.chr6 456436 41 + 602619 TTATAAACTAGGTGTAGGGCTTTTGGTGTGATGGAGCTGGC -s simDog_chr6.simDog.chr6 449999 40 + 593897 TTATAAACAAGGCATAGGGC-CTTGCTGAGACACAATTGGT -s simHuman_chr6.simHuman.chr6 456596 41 + 601863 Gaaggaagaaggcggagggctcttggtgtgatagagctggt -s simRat_chr6.simRat.chr6 481349 41 + 647215 TGTTGGAGAAAGCAGAAAACACTCAAGACACTAAAGCTGGG - -a -s simMouse_chr6.simMouse.chr6 471462 10 + 636262 GGATGGAGAC -s Anc0.Anc0refChr3 91721 9 + 222631 gat-tgagat -s Anc1.Anc1refChr6 124692 9 + 197743 gat-tgagat -s Anc2.Anc2refChr1 2945 9 + 142988 gat-tgagat -s mr.mrrefChr3 27206 9 + 181027 GGA-TGAGAT -s simCow_chr6.simCow.chr6 456501 9 + 602619 aat-caaaat -s simDog_chr6.simDog.chr6 450039 9 + 593897 GAT-TGAGAt -s simHuman_chr6.simHuman.chr6 456637 9 + 601863 gat-tgagat -s simRat_chr6.simRat.chr6 481390 9 + 647215 GGA-TGAGAT - -a -s simMouse_chr6.simMouse.chr6 471472 12 + 636262 GGACATACCATC -s Anc0.Anc0refChr3 91730 12 + 222631 ggataacccatc -s Anc1.Anc1refChr6 124701 12 + 197743 ggataacccatc -s Anc2.Anc2refChr1 2958 12 + 142988 gaataacacatc -s mr.mrrefChr3 27215 12 + 181027 GGACAAACCATC -s simCow_chr6.simCow.chr6 456514 12 + 602619 caacaatacaac -s simDog_chr6.simDog.chr6 450052 12 + 593897 gaatcacacgtc -s simHuman_chr6.simHuman.chr6 456646 12 + 601863 ggataacctatc -s simRat_chr6.simRat.chr6 481399 12 + 647215 GGACAAACCCTC - -a -s simMouse_chr6.simMouse.chr6 471484 2 + 636262 AT -s Anc0.Anc0refChr3 91746 2 + 222631 at -s Anc1.Anc1refChr6 124717 2 + 197743 at -s Anc2.Anc2refChr1 2975 2 + 142988 at -s mr.mrrefChr3 27227 2 + 181027 AT -s simCow_chr6.simCow.chr6 456531 2 + 602619 at -s simDog_chr6.simDog.chr6 450069 2 + 593897 gt -s simHuman_chr6.simHuman.chr6 456662 2 + 601863 at -s simRat_chr6.simRat.chr6 481411 2 + 647215 CT - -a -s simMouse_chr6.simMouse.chr6 471486 12 + 636262 CAGAGGGACCAA -s Anc0.Anc0refChr3 91748 12 + 222631 cacagtacccag -s Anc1.Anc1refChr6 124719 12 + 197743 cacagtacccag -s Anc2.Anc2refChr1 2986 12 + 142988 cacagtactgag -s mr.mrrefChr3 27229 12 + 181027 CAGAGGGACCAA -s simCow_chr6.simCow.chr6 456542 12 + 602619 cacagtactgag -s simDog_chr6.simDog.chr6 450080 12 + 593897 cacagaactgag -s simHuman_chr6.simHuman.chr6 456664 12 + 601863 catagtacccag -s simRat_chr6.simRat.chr6 481413 12 + 647215 CAGAGGGACCAA - -a -s simMouse_chr6.simMouse.chr6 471498 19 + 636262 GTTTCTCTGATTATACTGA -s Anc0.Anc0refChr3 91760 19 + 222631 tattaggtcatgacgctga -s Anc1.Anc1refChr6 124731 19 + 197743 TATTAGGTCATGACGCTGA -s Anc2.Anc2refChr1 2998 19 + 142988 tattaggtcatgacgcttg -s mr.mrrefChr3 27241 19 + 181027 TTTTCTCTGATTATGCTGA -s simCow_chr6.simCow.chr6 456557 19 + 602619 tattaggtcatgacccttg -s simDog_chr6.simDog.chr6 450092 19 + 593897 cattaggtcatgatgcttg -s simHuman_chr6.simHuman.chr6 456676 19 + 601863 TATTAGGTCAGGACGCTGA -s simRat_chr6.simRat.chr6 481425 19 + 647215 TTTTCTCTGATTATGCTGA - -a -s simMouse_chr6.simMouse.chr6 471517 9 + 636262 GCCAGGGTA -s Anc0.Anc0refChr3 91785 9 + 222631 GTTAGCCTG -s Anc1.Anc1refChr6 124756 9 + 197743 GTTAGCCTG -s Anc2.Anc2refChr1 3023 9 + 142988 GTTAGCCTG -s mr.mrrefChr3 27260 9 + 181027 GTTAGTGTA -s simCow_chr6.simCow.chr6 456582 9 + 602619 gTGAGCCTG -s simDog_chr6.simDog.chr6 450117 9 + 593897 GTTAGCCTG -s simHuman_chr6.simHuman.chr6 456701 9 + 601863 TCACGCCTG -s simRat_chr6.simRat.chr6 481444 9 + 647215 GTTGGTGTA - -a -s simMouse_chr6.simMouse.chr6 471526 8 + 636262 CATCCAGG -s Anc0.Anc0refChr3 91824 8 + 222631 CACCCAGA -s Anc1.Anc1refChr6 124795 8 + 197743 CACCCAGA -s Anc2.Anc2refChr1 3062 8 + 142988 CACCCAGA -s mr.mrrefChr3 27269 8 + 181027 CATCCAGA -s simCow_chr6.simCow.chr6 456621 8 + 602619 CGCCCAGA -s simDog_chr6.simDog.chr6 450156 8 + 593897 CACTCAGA -s simHuman_chr6.simHuman.chr6 456740 8 + 601863 CACCCAGA -s simRat_chr6.simRat.chr6 481453 8 + 647215 CTTCTAGA - -a -s simMouse_chr6.simMouse.chr6 471534 25 + 636262 TTTGAACTCTCTTAGAATCTCAAAT -s Anc0.Anc0refChr3 91869 24 + 222631 TTTGATCTCTCTTACAATCTCAA-T -s Anc1.Anc1refChr6 124840 25 + 197743 TTTGATCTCTCTTACAATCTCAAAT -s Anc2.Anc2refChr1 3107 24 + 142988 TTTGACCTCTCTTACAATCTCAA-T -s mr.mrrefChr3 27277 25 + 181027 TTTGATCTCTCTTAGAATCTCAAAT -s simCow_chr6.simCow.chr6 456668 24 + 602619 TTTGAACTCTCTTAGGGTCTCAA-T -s simDog_chr6.simDog.chr6 450201 24 + 593897 TTTGACCTCTCTTGCAATCTCAA-T -s simHuman_chr6.simHuman.chr6 456786 25 + 601863 TTTGTTCTCTCTTACAATCTCAATG -s simRat_chr6.simRat.chr6 481461 25 + 647215 TTTGATTTCTCTTCGAATCTCAAAT - -a -s simMouse_chr6.simMouse.chr6 471559 7 + 636262 AGCACAC -s Anc0.Anc0refChr3 91893 7 + 222631 GGCAAGT -s Anc1.Anc1refChr6 124865 7 + 197743 GGCAAGT -s Anc2.Anc2refChr1 3131 7 + 142988 GGCAAGT -s mr.mrrefChr3 27302 7 + 181027 GGCAAAT -s simCow_chr6.simCow.chr6 456693 7 + 602619 GGCCACT -s simDog_chr6.simDog.chr6 450225 7 + 593897 GGCAAGT -s simHuman_chr6.simHuman.chr6 456811 7 + 601863 GATAAGT -s simRat_chr6.simRat.chr6 481486 7 + 647215 GGCAAAT - -a -s simMouse_chr6.simMouse.chr6 471566 13 + 636262 TAGATAATCTTTT -s Anc0.Anc0refChr3 91902 13 + 222631 AAGACTATGTTGT -s Anc1.Anc1refChr6 124874 13 + 197743 AAGACTATGTTGT -s Anc2.Anc2refChr1 3140 13 + 142988 AAGACTATGTTGT -s mr.mrrefChr3 27311 13 + 181027 TAGACAATCTTTT -s simCow_chr6.simCow.chr6 456702 13 + 602619 TAAACTATGCTGT -s simDog_chr6.simDog.chr6 450234 13 + 593897 AAGACCATGTTGT -s simHuman_chr6.simHuman.chr6 456820 13 + 601863 AAGGCTATTTTGT -s simRat_chr6.simRat.chr6 481495 10 + 647215 TAGACAATCT--- - -a -s simMouse_chr6.simMouse.chr6 471579 1 + 636262 G -s Anc0.Anc0refChr3 91916 1 + 222631 A -s Anc1.Anc1refChr6 124888 1 + 197743 A -s Anc2.Anc2refChr1 3154 1 + 142988 A -s mr.mrrefChr3 27324 1 + 181027 G -s simCow_chr6.simCow.chr6 456716 1 + 602619 G -s simDog_chr6.simDog.chr6 450248 1 + 593897 A -s simHuman_chr6.simHuman.chr6 456834 1 + 601863 A - -a -s simMouse_chr6.simMouse.chr6 471580 50 + 636262 GATGCAATTTCTAGAGCATAGGTTCTAATCCATGCCAAAGGAGAGGCAAG -s Anc0.Anc0refChr3 91917 50 + 222631 AATGCAGTTTCCAGACCATATGTTGTAATTGGGGCTAATGGAGAGGAGAG -s Anc1.Anc1refChr6 124889 50 + 197743 AATGCAGTTTCCAGACCATATGTTGTAATTGGGGCTAATGGAGAGGAGAG -s Anc2.Anc2refChr1 3155 50 + 142988 ATTGCAGTTTCCAGACCATATGTTGTAATTGGGGCTAATGGAGAGGAGAG -s mr.mrrefChr3 27325 50 + 181027 GATGCAATTTCTAGAGCATAGGTTCTAATTCATGCCAATGGAGAGGCAAG -s simCow_chr6.simCow.chr6 456717 49 + 602619 CTT-CAGCTTCTAGTCCATATGTTCTAATTGAGGCTAATGGAGAGGAGGG -s simDog_chr6.simDog.chr6 450323 48 + 593897 ATTGCAGTTTCCAGAGCATATGTTGTAATTGG--CTAATGGAGAGGAGAG -s simHuman_chr6.simHuman.chr6 456835 50 + 601863 AATGTAGTTCCCAGACCATATGTTATAGTTTGGCCTAATGGAAAGGGGTG -s simRat_chr6.simRat.chr6 481505 26 + 647215 ------------------------CTAATTCATGCACATAGAGAGGCAAG - -a -s simMouse_chr6.simMouse.chr6 471630 20 + 636262 GATATATAACACTCATTTTA -s Anc0.Anc0refChr3 91970 20 + 222631 GATGTAGAACACTTATTTTA -s Anc1.Anc1refChr6 124942 20 + 197743 GATGTAGAACACTTATTTTA -s Anc2.Anc2refChr1 3208 20 + 142988 GATGTAGAACATTTATTTTA -s mr.mrrefChr3 27375 20 + 181027 GATGTATAACACTTATTTTA -s simCow_chr6.simCow.chr6 456769 20 + 602619 GATGTAGAAGATTTATCTGA -s simDog_chr6.simDog.chr6 450374 20 + 593897 TATGTGGAACATATATTTTA -s simHuman_chr6.simHuman.chr6 456888 20 + 601863 GATGTAGAGTACTTATTTTG -s simRat_chr6.simRat.chr6 481531 20 + 647215 GATGTATAACACTTATTTTA - -a -s simMouse_chr6.simMouse.chr6 471650 11 + 636262 AGGCATGCCTG -s Anc0.Anc0refChr3 91992 10 + 222631 AGG-ATGCTTG -s Anc1.Anc1refChr6 124964 10 + 197743 AGG-ATGCTTG -s Anc2.Anc2refChr1 3230 10 + 142988 GGG-ATGCTTG -s mr.mrrefChr3 27397 11 + 181027 AGGCATGCTTG -s simCow_chr6.simCow.chr6 456791 10 + 602619 GTG-ATGCTGG -s simDog_chr6.simDog.chr6 450396 10 + 593897 GGG-ATGCTTG -s simHuman_chr6.simHuman.chr6 456910 10 + 601863 AGG-ATGCTTG -s simRat_chr6.simRat.chr6 481553 11 + 647215 GGGCATGCTTG - -a -s simMouse_chr6.simMouse.chr6 471661 6 + 636262 CTACAG -s Anc0.Anc0refChr3 92004 6 + 222631 TTACAT -s Anc1.Anc1refChr6 124976 6 + 197743 TTACAT -s Anc2.Anc2refChr1 3242 6 + 142988 TTACAT -s mr.mrrefChr3 27408 6 + 181027 TTACAG -s simCow_chr6.simCow.chr6 456803 6 + 602619 TTACAT -s simDog_chr6.simDog.chr6 450408 6 + 593897 TTAAAT -s simHuman_chr6.simHuman.chr6 456922 6 + 601863 TTACAT -s simRat_chr6.simRat.chr6 481564 6 + 647215 TTACAG - -a -s simMouse_chr6.simMouse.chr6 471667 26 + 636262 ATAGCAAGAAACATTAGCCCTATGTG -s Anc0.Anc0refChr3 92010 26 + 222631 ATGCTAATAAACATTAGTTCCATGTG -s Anc1.Anc1refChr6 124982 26 + 197743 ATGCTAATAAACATTAGTTCCATGTG -s Anc2.Anc2refChr1 3248 26 + 142988 ATGCTAATTAACATTAGTTTCATGTG -s mr.mrrefChr3 27414 26 + 181027 ATAGCAAGAAACATTAGCCCTATGTG -s simCow_chr6.simCow.chr6 456809 26 + 602619 ATGCAAATGAGCATTAGTTTCCTGTG -s simDog_chr6.simDog.chr6 450414 22 + 593897 ATGCTAAGTAACATTAA----AAATC -s simHuman_chr6.simHuman.chr6 456928 26 + 601863 ATGCTAATAAACATTAGTTCCATGTG -s simRat_chr6.simRat.chr6 481571 26 + 647215 ATAGCAAGAAACATTAGCCCTATGTG - -a -s simMouse_chr6.simMouse.chr6 471693 4 + 636262 TTTA -s Anc0.Anc0refChr3 92040 2 + 222631 --AG -s Anc1.Anc1refChr6 125012 4 + 197743 TTAG -s Anc2.Anc2refChr1 3278 2 + 142988 --AG -s mr.mrrefChr3 27440 4 + 181027 TTTA -s simDog_chr6.simDog.chr6 450440 2 + 593897 --AG -s simHuman_chr6.simHuman.chr6 456959 4 + 601863 TTAG -s simRat_chr6.simRat.chr6 481597 4 + 647215 TTTA - -a -s simMouse_chr6.simMouse.chr6 471697 82 + 636262 TGGGGAAGCCTTCTGGACCATGCAAGGCTGAGGAGTAGACCACTAGATGGAATTGCTAGTATAAGAATTAAATAGATCGTCA -s Anc0.Anc0refChr3 92067 82 + 222631 GGGGCAACCCCTCTAGACCATTCAAGACTGTGGAAGGGACTGCCAGAAGAAATTACTAGTACAAGAATAAAATAGAGCAACA -s Anc1.Anc1refChr6 125041 82 + 197743 GGGGCAACCCCTCTAGACCATTCAAGACTGTGGAAGGGACTGCCAGAAGAAATTACTAGTACAAGAATAAAATAGAGCAACA -s Anc2.Anc2refChr1 3305 82 + 142988 GGGGCAACCCCTCCAGACCATTCAAGACTGTTGAAGCTGCTGCCAGAAGAAATTACTAGCACAAGTATAAAATAGTGCAACA -s mr.mrrefChr3 27469 82 + 181027 TGGGGAAGCCCTCTGGACCATGCAAGGCTGAGGAGTGGACCACTAGATGGAATTGCTAGTACAAGAATTAAATAGATCATCA -s simCow_chr6.simCow.chr6 456854 82 + 602619 GGGACAACACCTTCAGACCATTCAAGACTATAGAAGCTGCTCCCAGAAGGAATTACCAGCACAAGGATAAAATAGCACAACA -s simDog_chr6.simDog.chr6 450701 76 + 593897 GAGGCAACCCCTCCAGACCATCCAGGACTGTTG------CTGTCAGAAGAAATTACTGGCATGAGTATGAACTAGTGCAGCA -s simHuman_chr6.simHuman.chr6 456988 82 + 601863 AGGGTAACTCCTCTAGGTTACTCAAGACTGTGGAAAGGACTGCCAGAGCTGGGGAATAATGCAAGAATAAAATAGAGCAACA -s simRat_chr6.simRat.chr6 481626 82 + 647215 TGGGCAAGCCCTTTGGTCCATGCAAGGCTGAGGAGTGGACCACTAGATGGAATTGCCAGTACAAGAATTAAATAGATCATTA - -a -s simMouse_chr6.simMouse.chr6 471779 18 + 636262 TGATTGTAGCACTATAGA -s Anc0.Anc0refChr3 92161 18 + 222631 TGTTTATAGCACTAGCAA -s Anc1.Anc1refChr6 125135 18 + 197743 TGTTTATAGCACTAGCAA -s Anc2.Anc2refChr1 3399 18 + 142988 TGTTTATAGCACTAGCAA -s mr.mrrefChr3 27551 18 + 181027 TGATTGTAGCACTATAAA -s simCow_chr6.simCow.chr6 456947 18 + 602619 TGTTCACAGCACTAGTAT -s simDog_chr6.simDog.chr6 450789 18 + 593897 TGTTTATAGTACCCGCAA -s simHuman_chr6.simHuman.chr6 457082 18 + 601863 TATTTATAGCACTAGCAG -s simRat_chr6.simRat.chr6 481708 18 + 647215 TGATTGTAGCACTATGAA - -a -s simMouse_chr6.simMouse.chr6 471797 11 + 636262 AAAGGGTAAAT -s Anc0.Anc0refChr3 92179 11 + 222631 AAAAGAAAAGT -s Anc1.Anc1refChr6 125153 11 + 197743 AAAAGAAAAGT -s Anc2.Anc2refChr1 3417 11 + 142988 AAAAGAAAAGT -s mr.mrrefChr3 27569 11 + 181027 AAAGGGTAAAT -s simCow_chr6.simCow.chr6 456965 11 + 602619 AAAAGAAAAGT -s simDog_chr6.simDog.chr6 450807 11 + 593897 AAAATAAAAGT -s simHuman_chr6.simHuman.chr6 457100 11 + 601863 AAAAGAAAACC -s simRat_chr6.simRat.chr6 481730 11 + 647215 AAAGATTAAAT - -a -s simMouse_chr6.simMouse.chr6 471808 60 + 636262 CCTGCTCATGTCAATGACTAAAAGGAAAGACCAAGGATGTTCAAGTGAGAAAATAGGAAA -s Anc0.Anc0refChr3 92190 60 + 222631 CCTGCATAAAGAAATGGTTAAATGGAAAAACCAAGGATGTTCAACCAAGAAGACAAGTGA -s Anc1.Anc1refChr6 125164 60 + 197743 CCTGCATAAAGAAATGGTTAAATGGAAAAACCAAGGATGTTCAACCAAGAAGACAAGTGA -s Anc2.Anc2refChr1 3428 60 + 142988 CCTGCATAAAGAAATGGTTAAATGGAAAAACCAAGGATGTTCAACCAGGAAGACAAATGA -s mr.mrrefChr3 27580 60 + 181027 CCTGCTCATATCAATGATTAAAAGGAAAAACCAAGGATGTTCAAGTGAGAAAACAAGAAA -s simCow_chr6.simCow.chr6 456976 59 + 602619 GCTGAATAAAGGAAAGATTGAATGGAAACACCAAGGATGTT-AGCCAGGAAAATAAATGA -s simDog_chr6.simDog.chr6 450818 60 + 593897 CCTGCATAAAGAATTGGTTAAATGGAACAACTAAGGATGTTCAACCAGGAAGACAAATGA -s simHuman_chr6.simHuman.chr6 457111 57 + 601863 CCTGCATAAAAAAATGGTTAA---GAAAAACCTAGGAAGTTCAACCAAGAAGACAAGTGA -s simRat_chr6.simRat.chr6 481830 59 + 647215 ACTATGAATATCAAAGATTAAATGGAAAAAGCAAGGATGTTTAA-TCAGAAAACAAGAAA - -a -s simMouse_chr6.simMouse.chr6 471868 78 + 636262 ATGGATGATCTTACTAGTGAGGAGGTGTAAGTTATTCAATTAGCATCTATTGTCAGTTACATTAATGGTAAAGAAGCA -s Anc0.Anc0refChr3 92263 78 + 222631 GTAGATTATTCTACTAGCATGGAAGTGTAAATTATTCCATTAGCATCTGTGGTCAGCTACATCAAGGGTACACAAGCA -s Anc1.Anc1refChr6 125237 78 + 197743 GTAGATTATTCTACTAGCATGGAAGTGTAAATTATTCCATTAGCATCTGTGGTCAGCTACATCAAGGGTACACAAGCA -s Anc2.Anc2refChr1 3501 78 + 142988 GTAGATTATTATACTAGCATGGAAGTGTAAATTATTCCATTAGCATCTGTGAGCAGCTACACCAAGGGTACACAAGCA -s mr.mrrefChr3 27640 78 + 181027 ATGGATGATCCTACTAGTAAGGAGGTGTAAATTATTCAATTAGCATCTATGGTCAGTTACATTAATGGTACAGAAGCA -s simCow_chr6.simCow.chr6 457048 77 + 602619 ATAGATTTTTTTATTAGCATGGAAGTTTAGA-TGACCCCTTAGCATCTGTGAGCAGCTACACCAAGGGCACACAAGCA -s simDog_chr6.simDog.chr6 450891 71 + 593897 GCAGATTATTATACTAGCATGGAAGTGTAAATTATTCGAATAGTATCTGTG-------ACACCATGGGTACACATGTA -s simHuman_chr6.simHuman.chr6 457181 78 + 601863 GTAAATTATTCCACTAGCATGGAAGTATAAAATATTCCATTAGCATCTGTGGTCAGCTACATCAAGGGTACACAAGCA -s simRat_chr6.simRat.chr6 481889 78 + 647215 ATGGATCATCCTACTAGTAAGGAGGTGTAAAGTATTCAATTAGCATTTATGGTCAGTTACATTAATCGTACAGAAGCA - -a -s simMouse_chr6.simMouse.chr6 471946 3 + 636262 GGG -s Anc0.Anc0refChr3 92341 3 + 222631 AGG -s Anc1.Anc1refChr6 125315 3 + 197743 AGG -s Anc2.Anc2refChr1 3580 3 + 142988 AGG -s mr.mrrefChr3 27718 3 + 181027 GGG -s simCow_chr6.simCow.chr6 457126 3 + 602619 TAA -s simDog_chr6.simDog.chr6 450963 3 + 593897 AGG -s simHuman_chr6.simHuman.chr6 457259 3 + 601863 AGG -s simRat_chr6.simRat.chr6 481967 3 + 647215 TAG - -a -s simMouse_chr6.simMouse.chr6 471949 70 + 636262 GTCCTCAGATGCTTAATAATTTTGACTTTGAGCCATTCCAGATCTAACGTAACTCACTTACTACACTTCA -s Anc0.Anc0refChr3 92352 66 + 222631 ATACTAAGAAGCTTAATAATGTTAACCATGAGTTATTCCAGATCCAATGTAGCT----TATGACCCTAGG -s Anc1.Anc1refChr6 125326 66 + 197743 ATACTAAGAAGCTTAATAATGTTAACCATGAGTTATTCCAGATCCAATGTAGCT----TATGACCCTAGG -s Anc2.Anc2refChr1 3591 66 + 142988 ATACTAAGAAGCTTAATAATGTTAATCATGAGTTGTTCCAGATCCAATGTAGCT----TATGACCCTAGG -s mr.mrrefChr3 27721 66 + 181027 GTACTCAGATGCTTAATAATTTTGACCTTGAGCTATTCCAGATCTAATGTAACT----TACTACACTTCA -s simCow_chr6.simCow.chr6 457137 63 + 602619 ATACTAAGAAGATTACTAATGTCAATCATGAGTTGTTCCAGATTCAATGTAACT----TATG---CTAGA -s simDog_chr6.simDog.chr6 450974 66 + 593897 ATAATAAGAAGCTTAATAATGTTGATCATGAGTTGTTCCAGATCCAATGTAGCT----TATGACCCTAAG -s simHuman_chr6.simHuman.chr6 457270 66 + 601863 ATACAACAAAGCTTAATAAAGCGAACCATGAATTATTGCACATCCAATGTAGCG----TATGACCCTAGC -s simRat_chr6.simRat.chr6 481970 66 + 647215 GTACTCAGATGCTTAATAATTTTGACCTTGAGCTGTTCCCAATCTAGTGTAACA----TACTACACTTCA - -a -s simMouse_chr6.simMouse.chr6 472019 7 + 636262 CCCTGCC -s Anc0.Anc0refChr3 92418 7 + 222631 CCCTACC -s Anc1.Anc1refChr6 125392 7 + 197743 CCCTACC -s Anc2.Anc2refChr1 3657 7 + 142988 CCCTACC -s mr.mrrefChr3 27787 7 + 181027 CCCTGCC -s simCow_chr6.simCow.chr6 457200 7 + 602619 CCTTACC -s simDog_chr6.simDog.chr6 451040 7 + 593897 TTCTACC -s simHuman_chr6.simHuman.chr6 457354 7 + 601863 CCCTACC -s simRat_chr6.simRat.chr6 482036 7 + 647215 CCCTGCC - -a -s simMouse_chr6.simMouse.chr6 472026 23 + 636262 TTAGTGCATGGTCCTGGCTTGAG -s Anc0.Anc0refChr3 92429 23 + 222631 TTAGTGCATGATTGTGCCCTGAG -s Anc1.Anc1refChr6 125403 23 + 197743 TTAGTGCATGATTGTGCCCTGAG -s Anc2.Anc2refChr1 3668 23 + 142988 TTAGTGCATGATTGTGCCCTGAG -s mr.mrrefChr3 27794 23 + 181027 TTAGTGCATGGTCCTGGCCTGAG -s simCow_chr6.simCow.chr6 457211 23 + 602619 TTAGTGCCTGATTGTGCTCTGAG -s simDog_chr6.simDog.chr6 451051 23 + 593897 TTAGTGCATGATTGAGCCCTGAG -s simHuman_chr6.simHuman.chr6 457365 23 + 601863 TCAGTGCATGATTGTGCCCTGAG -s simRat_chr6.simRat.chr6 482043 23 + 647215 TTACTGCATGGTCCTGGCCTGAG - -a -s simMouse_chr6.simMouse.chr6 472049 49 + 636262 CTCTGATAACCTGGGTGGACAACTAGGCTCTGAGCTCTGATTACAGACA -s Anc0.Anc0refChr3 92454 48 + 222631 CTCTGACAAACTGGGTGGACACCTAGGCTCTGTACTCTACCTGCAGAC- -s Anc1.Anc1refChr6 125428 48 + 197743 CTCTGACAAACTGGGTGGACACCTAGGCTCTGTACTCTACCTGCAGAC- -s Anc2.Anc2refChr1 3693 48 + 142988 TTTTGACAAACTGGATGGACACCTAGGCTCTGTGCTCTACCTGCAGAC- -s mr.mrrefChr3 27817 49 + 181027 CTCTGATAACCTGGGTGGACAACTAGGCTCTGAACTCTGATTGCAGACA -s simCow_chr6.simCow.chr6 457236 47 + 602619 TTTAGACAACCTGGCTGGACAC-TAGGCCTTGTGCTCTGCCTGCAGGC- -s simDog_chr6.simDog.chr6 451076 48 + 593897 TTTTCACGAACTGAACGGGCACCTAGGCTCTGTGCTCTACCTACAGAC- -s simHuman_chr6.simHuman.chr6 457390 48 + 601863 CTCTGACAATCTGGGTGGAACGCTAGGCTCTGCACTCTACCTGTGGAC- -s simRat_chr6.simRat.chr6 482066 49 + 647215 CTTTGATAACCTGGGTGGACAACTAGGCTCTGAAATCTGATTGCAGACA - -a -s simMouse_chr6.simMouse.chr6 472098 35 + 636262 GCAGTTGCATGACTATGATGATCCTTGTACTCGGT -s mr.mrrefChr3 27866 32 + 181027 GCAGTTGCATGACTATGATGATCCTTGTACTC--- -s simRat_chr6.simRat.chr6 482123 30 + 647215 GCAGTTACATGATTATGATGATCCTTTCAT----- - -a -s simMouse_chr6.simMouse.chr6 472133 289 + 636262 TTGGCCAGACAAAGTCTTAATGTTTTTAAGGGGGAGTTATCGTCACTTTCTATTGTCTGGTGTCCTTCCAAAGCAAGCGACCAACAAAAACAGGTGACTAACTGCAGAATTGTACGATTATGACTCTGCTCATTTGGAGGACCATATCTAATGCAGGTACCAGCACCCCTAGCCACCCTATCCAAAACTGAGAAGTTCAAGGCTGGTGAGTGCTCTTATGCAATGCACCTCCTTGTTGATTGGAATCCATCATCTAATGTACCCCAGACTGAGAGCCAACTCAAATGCT -s mr.mrrefChr3 27898 287 + 181027 TTGGCCAGACAAAGTCTTAATGTTTTTA-GGGGGAGTTATCGTCACTTTCTATTGTCTGGTGTCCTTCCAA-GCAAGCGACCAACAAAAACAGGTGACTAACTGCAGAATTGTACGATTATGACTCTGCTCATTTGGAGGACCATATCTAATGCAGGTACCAGCACCCCTAGCCACCCTATCCAAAACTGAGAAGTTCAAGGCTGGTGAGTGCTCTTATGCAATGCACCTCCTTGTTGATTGGAATCCATCATCTAATGTACCCCAGACTGAGAGCCAACTCAAATGCT -s simRat_chr6.simRat.chr6 163578 287 - 647215 TTGGCCAGATAAAGTCTTAAAGTTTTTA-GGGGGAGTTACCTTCCCTTTCTATTATCTGGTGTCCTTTTGT-GCAAGCAACCAACAAAACCAGATGGCTAACTACAGAATTGTACTATTGTGACTCTGCTCGTTCGGAGGACAATTTCTATTTCAGGTACCAGTATCCCTAGCCACCCTATACAAAACTGAGAAGTTCAAGGCTGGTGAGTGCTCTTATGCGATGAGCCTCCATGTTGAGTGGAATCCATCATCTAATATACCCCAGACTAATAGCCAATTTAAATCGC - -a -s simMouse_chr6.simMouse.chr6 472422 99 + 636262 CTGCAATAGTTTATGTATGTGTTCCCTACACTCATAGCCACCTCAAAAGGTGGCAGCCACCCCTTACATATGTAAAAAGATCTAAGGGGCTTATATGGA -s Anc0.Anc0refChr3 92502 1 + 222631 --------------------------------------------------------------------------------------------------A -s Anc1.Anc1refChr6 125476 1 + 197743 --------------------------------------------------------------------------------------------------A -s Anc2.Anc2refChr1 3741 1 + 142988 --------------------------------------------------------------------------------------------------A -s mr.mrrefChr3 28185 99 + 181027 CTGCAATAGTTTATGTATGTGTTCCCTACACTCATAGCCACCTCAAAAGGTGGCAGCCACCCCTTACATATGTAAAAAGATCTAAGGGGCTTATATGGA -s simCow_chr6.simCow.chr6 457283 1 + 602619 --------------------------------------------------------------------------------------------------A -s simDog_chr6.simDog.chr6 451124 1 + 593897 --------------------------------------------------------------------------------------------------A -s simHuman_chr6.simHuman.chr6 457438 1 + 601863 --------------------------------------------------------------------------------------------------C -s simRat_chr6.simRat.chr6 163870 99 - 647215 CTGCAATAGTTTATGTATGTGTTCCATATACTAATAGCCACCACAAAAGGTTTCGACCCTCCCTTACATATATATGAAGATCCAAAGGGCTCACGTGGA - -a -s simMouse_chr6.simMouse.chr6 472521 12 + 636262 TTTCAAGCCTAC -s Anc0.Anc0refChr3 92503 12 + 222631 TAGCTAACCCAC -s Anc1.Anc1refChr6 125477 12 + 197743 TAGCTAACCCAC -s Anc2.Anc2refChr1 3742 12 + 142988 TAGCTCACCCAC -s mr.mrrefChr3 28284 12 + 181027 TTTCAAGCCTAC -s simCow_chr6.simCow.chr6 457285 9 + 602619 TAGC---ACCAC -s simDog_chr6.simDog.chr6 451125 12 + 593897 TAGCTCACCCAC -s simHuman_chr6.simHuman.chr6 457439 12 + 601863 TAGCTAACCCAC -s simRat_chr6.simRat.chr6 163969 12 - 647215 CCTCAAGCCTAC - -a -s simMouse_chr6.simMouse.chr6 472533 15 + 636262 TCATGTTTGTAGATT -s Anc0.Anc0refChr3 92515 14 + 222631 ACTTGTTTTT-AATT -s Anc1.Anc1refChr6 125489 14 + 197743 ACTTGTTTTT-AATT -s Anc2.Anc2refChr1 3754 14 + 142988 ACTTGTTTTT-AATT -s mr.mrrefChr3 28296 15 + 181027 TCATGTTTTTAGATT -s simCow_chr6.simCow.chr6 457294 14 + 602619 ACTTGTTTTT-AATT -s simDog_chr6.simDog.chr6 451144 14 + 593897 ACTTGTTTTT-AATT -s simHuman_chr6.simHuman.chr6 457451 14 + 601863 ACTTGGTTTT-TACC -s simRat_chr6.simRat.chr6 163981 15 - 647215 TCATGTTTTTAGATT - -a -s simMouse_chr6.simMouse.chr6 472548 5 + 636262 ATCTG -s Anc0.Anc0refChr3 92529 5 + 222631 AGCTG -s Anc1.Anc1refChr6 125503 5 + 197743 AGCTG -s Anc2.Anc2refChr1 3768 5 + 142988 TGCTA -s mr.mrrefChr3 28311 5 + 181027 ATCTG -s simDog_chr6.simDog.chr6 451159 5 + 593897 TGCTA -s simHuman_chr6.simHuman.chr6 457465 5 + 601863 ACCTG -s simRat_chr6.simRat.chr6 163996 5 - 647215 ATCTG - -a -s simMouse_chr6.simMouse.chr6 472553 3 + 636262 CTG -s Anc0.Anc0refChr3 92534 3 + 222631 CTG -s Anc1.Anc1refChr6 125508 3 + 197743 CTG -s Anc2.Anc2refChr1 3773 3 + 142988 CTG -s mr.mrrefChr3 28316 3 + 181027 CTG -s simDog_chr6.simDog.chr6 451164 3 + 593897 CTG -s simHuman_chr6.simHuman.chr6 457471 3 + 601863 CTG -s simRat_chr6.simRat.chr6 164001 3 - 647215 TAG - -a -s simMouse_chr6.simMouse.chr6 472556 13 + 636262 AGTGTTCTTGGCT -s Anc0.Anc0refChr3 92537 13 + 222631 AGTGTTTGTGGTG -s Anc1.Anc1refChr6 125511 13 + 197743 AGTGTTTGTGGTG -s Anc2.Anc2refChr1 3781 13 + 142988 AGTATTTGTGGTG -s mr.mrrefChr3 28319 13 + 181027 AGTGTTTTTGGCT -s simCow_chr6.simCow.chr6 457308 6 + 602619 ----TTTATG--- -s simDog_chr6.simDog.chr6 451172 13 + 593897 AGTATATGTAGTG -s simHuman_chr6.simHuman.chr6 457474 13 + 601863 AGTGTTTGTGGGG -s simRat_chr6.simRat.chr6 164004 13 - 647215 AGTGTTTTTGGCT - -a -s simMouse_chr6.simMouse.chr6 472569 16 + 636262 TGCACCTCTATCCTGG -s Anc0.Anc0refChr3 92550 15 + 222631 TACATTTG-ATCCTGG -s Anc1.Anc1refChr6 125524 15 + 197743 TACATTTG-ATCCTGG -s Anc2.Anc2refChr1 3794 15 + 142988 TACATTTG-TTCCTGA -s mr.mrrefChr3 28332 16 + 181027 TGCACCTGTATCCTGG -s simCow_chr6.simCow.chr6 457314 10 + 602619 -ACATT-----CCTGA -s simDog_chr6.simDog.chr6 451187 15 + 593897 TACATTTG-TTCCTGA -s simHuman_chr6.simHuman.chr6 457487 15 + 601863 TAGCTGTG-ATCTTGG -s simRat_chr6.simRat.chr6 164017 16 - 647215 TGCATCTGTATCCTGG - -a -s simMouse_chr6.simMouse.chr6 472585 14 + 636262 ATATCTGTTCCTGG -s Anc0.Anc0refChr3 92565 12 + 222631 ATGCCCATT-CT-G -s Anc1.Anc1refChr6 125539 12 + 197743 ATGCCCATT-CT-G -s Anc2.Anc2refChr1 3809 12 + 142988 ATGCCCATT-CT-G -s mr.mrrefChr3 28348 13 + 181027 ATATCTATT-CTGG -s simCow_chr6.simCow.chr6 457324 12 + 602619 CAGCTCATT-CT-G -s simDog_chr6.simDog.chr6 451202 8 + 593897 ATGGCTG------G -s simHuman_chr6.simHuman.chr6 457504 12 + 601863 ATGCCCATC-CT-G -s simRat_chr6.simRat.chr6 164033 13 - 647215 ATATCTATT-CTGG - -a -s simMouse_chr6.simMouse.chr6 472599 54 + 636262 ATGCCTGACATTGGAAAAGATGGGGACCATGGATGAATTAAATGCATAAAGTTG -s Anc0.Anc0refChr3 92577 53 + 222631 ATG-CTGAGGTTGGAAAAGACAGGGGCCTAGGAAGAAATAAATGTAGAAAGTTG -s Anc1.Anc1refChr6 125551 53 + 197743 ATG-CTGAGGTTGGAAAAGACAGGGGCCTAGGAAGAAATAAATGTAGAAAGTTG -s Anc2.Anc2refChr1 3821 53 + 142988 ATG-CTGAGGTTGGAAAAAACAGGAACCTAGGAAGAAATAAGTCCAGAAAGTTG -s mr.mrrefChr3 28361 54 + 181027 ATGCCTGACATTGGAAAAGATGGGGGCCATGGATGAATTAAATGTATAAAGTTG -s simCow_chr6.simCow.chr6 457337 53 + 602619 ATG-CTGAAGCTAGAAAAAATAGGAACCTTGGAAGAAACAGGTACAGAAAGTCG -s simDog_chr6.simDog.chr6 451210 53 + 593897 ATG-CTGAGATTGGAAAAAACAGGAACCTAGGAAGAAATAAGTCCAGAAAGCTC -s simHuman_chr6.simHuman.chr6 457516 44 + 601863 ATG-CTGATGTTGGGAGAGACAGGGGCCCAGG---------AGGTAGAAAGTTG -s simRat_chr6.simRat.chr6 164046 54 - 647215 GTGACTGACATTGGAAAAGATGGGGGTTGTGGATGAACTAAATGTAAAAAGTTG - -a -s simMouse_chr6.simMouse.chr6 472653 46 + 636262 ATGACACACTACCATTTAACAGTCTGGTGAGTAATCAATTAAAAGA -s Anc0.Anc0refChr3 92630 46 + 222631 AGGACACACTATCATGTTACATTCGGGCCACCAATTAATTAAAAAA -s Anc1.Anc1refChr6 125604 46 + 197743 AGGACACACTATCATGTTACATTCGGGCCACCAATTAATTAAAAAA -s Anc2.Anc2refChr1 3874 46 + 142988 AGGACACACTATCATGTTATATTAGGGCCACCAATTAATTAAAAAA -s mr.mrrefChr3 28415 46 + 181027 AGGACACACTATCATGTAACAGTCTGGTCAGTAATCAATTAAAAGA -s simCow_chr6.simCow.chr6 457391 45 + 602619 AGGATGCACCATCATGTTATATTTGGGACACCA-CTAATTAAAAAA -s simDog_chr6.simDog.chr6 451263 46 + 593897 CGAACACACTATCATGTTATCATAGGGCCACCAATAAGTCAAAAAA -s simHuman_chr6.simHuman.chr6 457560 46 + 601863 AGGACACACTATTATGTCACATTCGGGCCACCAGTTAATTAAAACA -s simRat_chr6.simRat.chr6 164100 43 - 647215 AGGACA---TATCATGTTACAGTTTGGGCAGTAATCAATTGAAAGA - -a -s simMouse_chr6.simMouse.chr6 472699 10 + 636262 CCAAACTCGG -s Anc0.Anc0refChr3 92678 10 + 222631 CCAGACTCTG -s Anc1.Anc1refChr6 125652 10 + 197743 CCAGACTCTG -s Anc2.Anc2refChr1 3922 10 + 142988 CCAGACTTTG -s mr.mrrefChr3 28463 10 + 181027 CCAAACTCGG -s simCow_chr6.simCow.chr6 457438 10 + 602619 CAAGTCTTTG -s simDog_chr6.simDog.chr6 451311 10 + 593897 CCAGACCTTG -s simHuman_chr6.simHuman.chr6 457608 10 + 601863 CCATAATCTG -s simRat_chr6.simRat.chr6 164145 10 - 647215 CCAAACTCGG - -a -s simMouse_chr6.simMouse.chr6 472709 5 + 636262 AAGCC -s Anc0.Anc0refChr3 92689 5 + 222631 AGGCT -s Anc1.Anc1refChr6 125663 5 + 197743 AGGCT -s Anc2.Anc2refChr1 3933 5 + 142988 AGGCT -s mr.mrrefChr3 28474 5 + 181027 AGGCT -s simCow_chr6.simCow.chr6 457449 5 + 602619 GGTct -s simDog_chr6.simDog.chr6 451322 5 + 593897 AGGCT -s simHuman_chr6.simHuman.chr6 457619 5 + 601863 AGACT -s simRat_chr6.simRat.chr6 164156 5 - 647215 AGGCT - -a -s simMouse_chr6.simMouse.chr6 472714 25 + 636262 CCAGACCAGGGGTACATTGAGTGCT -s Anc0.Anc0refChr3 92694 25 + 222631 GCTGACCAGGGGTACAACAAATGCC -s Anc1.Anc1refChr6 125668 25 + 197743 GCTGACCAGGGGTACAACAAATGCC -s Anc2.Anc2refChr1 3938 25 + 142988 GCTGACCAGGGGAACAACAAATCCC -s mr.mrrefChr3 28479 25 + 181027 CCAGACCAGGGGTACATTGAGTGCT -s simCow_chr6.simCow.chr6 457639 21 + 602619 gctgtgtaggggaacAC----TCCA -s simDog_chr6.simDog.chr6 451327 25 + 593897 CCAGACCAGGGAAACAACAAATCCC -s simHuman_chr6.simHuman.chr6 457624 25 + 601863 GCTAACCAGGGGTACAACAAATGCC -s simRat_chr6.simRat.chr6 164161 25 - 647215 CCAGACCTGGGATACATTGAGTGCT - -a -s simMouse_chr6.simMouse.chr6 472739 49 + 636262 CATGGATTGCAAATTCACAGTCAATAGTGAACATTGGCCACCAGTACGT -s Anc0.Anc0refChr3 92720 49 + 222631 CAGGGACTATAAATTCATAGATGATAGAGAGTATATGCTACCTGTGCAT -s Anc1.Anc1refChr6 125694 49 + 197743 CAGGGACTATAAATTCATAGATGATAGAGAGTATATGCTACCTGTGCAT -s Anc2.Anc2refChr1 3964 49 + 142988 CAGAGTCTATAAATACTTAGATGATAGAGAGTATATGCTACCTGTGCAT -s mr.mrrefChr3 28505 49 + 181027 CATGGATTGCAAATTCACAGTCAATAGTGAATATTGGCTACCAGTACAT -s simCow_chr6.simCow.chr6 457661 47 + 602619 CATTG--TGTAAATACTTATATGATCAAGTGTATTTGCAACCTGTGCAT -s simDog_chr6.simDog.chr6 451353 49 + 593897 TAGAGTCTAAAAATACTTAGATGACAGTGAGTAGATGTTATCTATGCAT -s simHuman_chr6.simHuman.chr6 457650 48 + 601863 CAGGGACTTTAAATTCAGAGATGAT-GAGATTATATGCTACCTGTGCAT -s simRat_chr6.simRat.chr6 164187 49 - 647215 CATGGATTACAAATTCACAGTCAATAGTGACTATTAGCTACTGGTACAT - -a -s simMouse_chr6.simMouse.chr6 472788 71 + 636262 TCTTAAAACATATCTAAGCTTAAACCTAATAGTCAGGATATTGCAACATAATGCCTGGAACTTTGCATGTC -s Anc0.Anc0refChr3 92769 68 + 222631 TCTCCAAAT--GTATAGGTTTAAGCACTATAATCAGGATATTGCAATGTAGTGCGTGTCACTTTGCAT-GC -s Anc1.Anc1refChr6 125743 68 + 197743 TCTCCAAAT--GTATAGGTTTAAGCACTATAATCAGGATATTGCAATGTAGTGCGTGTCACTTTGCAT-GC -s Anc2.Anc2refChr1 4014 68 + 142988 TCTCCAAAT--GTATAGGTTTAAGCACTATAATCAGGATATTGTAATGTAGCCTGTGTCACTTTGTAT-GC -s mr.mrrefChr3 28554 68 + 181027 TCTTAAAAC--ATCTAAGCTTAAACCTAATAGTCAGGATATTGCAATGTAGTGCCTGGAACTTTGCAT-TC -s simCow_chr6.simCow.chr6 457709 67 + 602619 AC-ATAATC--ATATAAACTTAAATACCTCAGTCAGGGTGTTGTAGATTAGCCTGTGTAGCTTTGGAT-GC -s simDog_chr6.simDog.chr6 451403 68 + 593897 TCTCCAAAT--GTATAGGTTTAAGCACTATAATCAGGATATTGTAATGTAGCCTGTGTCACTTGATAT-GC -s simHuman_chr6.simHuman.chr6 457698 31 + 601863 --------------------------------------GGTTGC-ATGTGGTGCACATCACTTTGCAT-CG -s simRat_chr6.simRat.chr6 164236 68 - 647215 TCTTTAAAC--ATCTAAGCTTAGCCCAAATAGTCAGGATATTGTAATGTAGTGCCTGGAAGTGTGCAT-TC - -a -s simMouse_chr6.simMouse.chr6 472859 1 + 636262 A -s Anc0.Anc0refChr3 92837 1 + 222631 A -s Anc1.Anc1refChr6 125811 1 + 197743 A -s Anc2.Anc2refChr1 4082 1 + 142988 A -s mr.mrrefChr3 28622 1 + 181027 A -s simCow_chr6.simCow.chr6 457777 1 + 602619 A -s simDog_chr6.simDog.chr6 451471 1 + 593897 A -s simHuman_chr6.simHuman.chr6 457729 1 + 601863 A -s simRat_chr6.simRat.chr6 164304 1 - 647215 A - -a -s simMouse_chr6.simMouse.chr6 472860 7 + 636262 ATTCCAT -s Anc0.Anc0refChr3 92840 7 + 222631 ATTCTAT -s Anc1.Anc1refChr6 125814 7 + 197743 ATTCTAT -s Anc2.Anc2refChr1 4085 7 + 142988 ATTCTAT -s mr.mrrefChr3 28623 7 + 181027 ATTCCAT -s simCow_chr6.simCow.chr6 457780 7 + 602619 ATCCTAT -s simDog_chr6.simDog.chr6 451474 7 + 593897 ACTCTAT -s simHuman_chr6.simHuman.chr6 457732 7 + 601863 ATTCTAT -s simRat_chr6.simRat.chr6 164305 7 - 647215 ATTCCAT - -a -s simMouse_chr6.simMouse.chr6 472867 53 + 636262 CCTATACTTCCACAGTACATCGGGGCGGGCTCGTATTGAATTGGAAGTTAGCA -s Anc0.Anc0refChr3 92847 41 + 222631 CCTTTATTCTCACAGCT------------CTGGAATTAAATTGAGAATCACTA -s Anc1.Anc1refChr6 125821 41 + 197743 CCTTTATTCTCACAGCT------------CTGGAATTAAATTGAGAATCACTA -s Anc2.Anc2refChr1 4092 41 + 142988 CCCTTACTCTCAAAGCT------------CCAGATCCAAATTGAGAATCACTA -s mr.mrrefChr3 28630 41 + 181027 CCTATATTCCCACAGTA------------CTGGAATTGAATTGGAAGTTAGCA -s simCow_chr6.simCow.chr6 457787 41 + 602619 TGATCACTCTCAAAACT------------CCAAACCCAGATTGAGAATCACTA -s simDog_chr6.simDog.chr6 451481 41 + 593897 CCCTTACTCTCAAAGCT------------CCAGATCCGAATTGAGAATGACTA -s simHuman_chr6.simHuman.chr6 457739 41 + 601863 CCTTGATTCATACAGGT------------CTGGAATTACATTGAGAATCACTA -s simRat_chr6.simRat.chr6 164313 41 - 647215 CCTGTATTCCCACAGTA------------TTGAAATCGAATTGCAAGTTAGCA - -a -s simMouse_chr6.simMouse.chr6 472920 10 + 636262 TTCTTTTCCT -s Anc0.Anc0refChr3 92888 9 + 222631 CCCTTTTCT- -s Anc1.Anc1refChr6 125862 10 + 197743 CCCTTTTCTG -s Anc2.Anc2refChr1 4133 9 + 142988 CCCTTTTCT- -s mr.mrrefChr3 28671 10 + 181027 TTCTTTTCCT -s simCow_chr6.simCow.chr6 457828 9 + 602619 CTCATTACT- -s simDog_chr6.simDog.chr6 451522 9 + 593897 CCCTTTTCT- -s simHuman_chr6.simHuman.chr6 457780 10 + 601863 CCCCCGTCTG -s simRat_chr6.simRat.chr6 164355 10 - 647215 TTCTTCCCCT - -a -s simMouse_chr6.simMouse.chr6 472930 15 + 636262 TGTTAGATTTGTCTG -s Anc0.Anc0refChr3 92899 15 + 222631 TGTTTGGTTTATCTG -s Anc1.Anc1refChr6 125875 15 + 197743 TGTTTGGTTTATCTG -s Anc2.Anc2refChr1 4144 15 + 142988 TGTTAGGTTTATCTG -s mr.mrrefChr3 28681 15 + 181027 TGTTTGGTTTGTCTG -s simCow_chr6.simCow.chr6 457839 15 + 602619 TGTCAGGTACATTGA -s simDog_chr6.simDog.chr6 451533 15 + 593897 TGTTAGGTTTACCTG -s simHuman_chr6.simHuman.chr6 457793 15 + 601863 TGTTTGGATTATCTG -s simRat_chr6.simRat.chr6 164365 15 - 647215 AGTTTGGTTTGTCTG - -a -s simMouse_chr6.simMouse.chr6 472945 24 + 636262 CTAGAAGAACTAGTACATCATGTT -s Anc0.Anc0refChr3 92915 24 + 222631 TTAGGAGGATTAGTATGTCATGTT -s Anc1.Anc1refChr6 125891 24 + 197743 TTAGGAGGATTAGTATGTCATGTT -s Anc2.Anc2refChr1 4160 24 + 142988 TTAGGAGGATTAGTATGTCATGTT -s mr.mrrefChr3 28696 24 + 181027 CTAGAAGGATTAGTACGTCATGTT -s simCow_chr6.simCow.chr6 457855 23 + 602619 TTAGAAGGATCAGT-TGTCATGTT -s simDog_chr6.simDog.chr6 451549 24 + 593897 TGAGGGGGGTTAGTATTTCATGTT -s simHuman_chr6.simHuman.chr6 457809 24 + 601863 TTAGGAGGATTAGTATGTCATGTT -s simRat_chr6.simRat.chr6 164380 24 - 647215 CTAGAAGGATTGGTACGTCATGTT - -a -s simMouse_chr6.simMouse.chr6 472969 77 + 636262 TTATCTTCTGCAATGGCAGTATAGCCGACCTGAAAACTGAGTTGCAAGCTCATGCATGGTTATTATGGGGCTTTCAA -s Anc0.Anc0refChr3 92959 77 + 222631 TTGTATTCTACAATGGCAGTGTAGCTCACTTGAAAAGTAAGGGACTAGCTAATACATGGTACCTATGGAGCCTTTTG -s Anc1.Anc1refChr6 125935 77 + 197743 TTGTATTCTACAATGGCAGTGTAGCTCACTTGAAAAGTAAGGGACTAGCTAATACATGGTACCTATGGAGCCTTTTG -s Anc2.Anc2refChr1 4204 77 + 142988 TTATATTCCACAATGGCAGTGTAGCTCACTTTAAAAGCAAGGGAGTAGCTAATACATGGTACCTGTGGAGCCTTTTG -s mr.mrrefChr3 28720 77 + 181027 TTGTCTTCTACAATGGCAGTGTAGCTGACCTGAAAACTAAGTTGCAAGCTCATGCATGGTTCTTATGGAGCTTTCTA -s simCow_chr6.simCow.chr6 457898 77 + 602619 CTATGTTCCACAATGGCAGTGTAGCTCGCTTATAAGGCAAGGGAGAAGCTCATACATGGTAACTGGGGAGCCTTCTG -s simDog_chr6.simDog.chr6 451593 77 + 593897 TTACATTCCACTATGGCAGTGTACCTCACATTAAAAGCAAGGGAGTAGCCAATACATGATACCTGTCAAGCCTTTTG -s simHuman_chr6.simHuman.chr6 457853 77 + 601863 TCGTAGTTTACAATGGTAGTGTAGTTTACTTGAAAAGTAAAGGACTAGCTTACACATGGTACCTATGGAGCCTTGTG -s simRat_chr6.simRat.chr6 164404 77 - 647215 TTGTGCTCCACAATGTGAGTGTAGCTCACCTGAAAATTAAGTTGCAAGCTCATGCATGGTTCTTATGGAGCTTTCTA - -a -s simMouse_chr6.simMouse.chr6 473046 9 + 636262 TGGTGTGAC -s Anc0.Anc0refChr3 93043 9 + 222631 TGGTGTGAC -s Anc1.Anc1refChr6 126019 9 + 197743 TGGTGTGAC -s Anc2.Anc2refChr1 4288 9 + 142988 TGGTGTGAC -s mr.mrrefChr3 28797 9 + 181027 TGGTGTGAC -s simCow_chr6.simCow.chr6 457982 9 + 602619 TGGTCTGGC -s simDog_chr6.simDog.chr6 451677 9 + 593897 TGATGTAAC -s simHuman_chr6.simHuman.chr6 457937 9 + 601863 TGGTGGGAC -s simRat_chr6.simRat.chr6 164481 9 - 647215 TGGTGTGAC - -a -s simMouse_chr6.simMouse.chr6 473055 15 + 636262 AGATCTAGAGGAACT -s Anc0.Anc0refChr3 93062 15 + 222631 AGATCTAAAGGAACT -s Anc1.Anc1refChr6 126038 15 + 197743 AGATCTAAAGGAACT -s Anc2.Anc2refChr1 4307 15 + 142988 AAATCTAAAGGAACT -s mr.mrrefChr3 28816 15 + 181027 AGATCTAGAGGAACT -s simCow_chr6.simCow.chr6 458001 15 + 602619 AAATCTAAAGGAACT -s simDog_chr6.simDog.chr6 451696 15 + 593897 AAGTCTAAAGGCAGT -s simHuman_chr6.simHuman.chr6 457956 15 + 601863 AGATTTAAAGGAACT -s simRat_chr6.simRat.chr6 164500 14 - 647215 AAATCTAGAGGAAC- - -a -s simMouse_chr6.simMouse.chr6 473070 63 + 636262 TATCTTATAAGTGAAGATAGTAGCTCTGACATGATGGATGTGGAATCCCTCTTAAGTATACAT -s Anc0.Anc0refChr3 93077 60 + 222631 TATTTTAAAAGTAAAGG-AATAGCTCAGACATGACAGCTAAGGAAC--CTCTTGAGGATACAG -s Anc1.Anc1refChr6 126053 60 + 197743 TATTTTAAAAGTAAAGG-AATAGCTCAGACATGACAGCTAAGGAAC--CTCTTGAGGATACAG -s Anc2.Anc2refChr1 4322 60 + 142988 TTATTTAAAAGCAAAGG-AATAGCTCAGACATGACAGCTAAGGGAC--CTTTTGAGGATACAG -s mr.mrrefChr3 28831 63 + 181027 TATCTTATAAGTGAAGATAGTAGCTCTGACATGATGGATGAGGAATCCCTCTTGAGTATACAG -s simCow_chr6.simCow.chr6 458016 60 + 602619 TAACTTAAAAACACAGG-AGCACCTCAGACAAGACACTTAAGGGAC--CTTTTGAGGGTACAG -s simDog_chr6.simDog.chr6 451711 50 + 593897 TTATTCAAAAGCAAAGG-AATAGCTCAGACATGGCAGCTA------------TGAGGATACAG -s simHuman_chr6.simHuman.chr6 457972 60 + 601863 TATTTTAAAAGTAAAGG-ACTAGCTCGGACTTGACAGCTAAGGAGG--CTCTTGAAGATACAG -s simRat_chr6.simRat.chr6 164514 61 - 647215 --TCTAATTAGTGAAGATAATAGCTCTGATGTGATCAATGAGGAATCCCTCTTGAGTATACAG - -a -s simMouse_chr6.simMouse.chr6 473133 101 + 636262 TGCCACCCAGCATGAAATCTCAAGGAACTCCAAAGACACCAGGAATCCCCACTTCACTGTCTTGAAATAGCTCACATAAAGGAAAGAGTCTTTTAAGAGAA -s Anc0.Anc0refChr3 93138 99 + 222631 TGCTACCTTGGAGGAAAGCTAGAGGAAGTCCTACCACA-TAGGAATTCCTACCTCACTGTCTTGACATAGCTCACATAAAGGAATGAGTCTTCT-GGAGAA -s Anc1.Anc1refChr6 126114 99 + 197743 TGCTACCTTGGAGGAAAGCTAGAGGAAGTCCTACCACA-TAGGAATTCCTACCTCACTGTCTTGACATAGCTCACATAAAGGAATGAGTCTTCT-GGAGAA -s Anc2.Anc2refChr1 4383 99 + 142988 TTCTACCTTGGAGGAAAGCTAGAGGAAGTCCTACCACA-TAGGAATTCCTGCCTTGTTGTCTTGACATAGCTCACATAAAGGAATGAGTCTTCT-GGAGAA -s mr.mrrefChr3 28894 100 + 181027 TGCCACCCAGGATGAAATCTCAAGGAACTCCAAAGACA-CAGGAATCCCCACCTCACTGTCTTGAAATAGCTCACATAAAGGAAAGAGTCTTTTAAGAGAA -s simCow_chr6.simCow.chr6 458077 98 + 602619 TACTACCCTA-AGGAAAGCTAGGGGAAGTCCTGCCACA-TAGGAATTCCTGACTTCTTGTTGCAACATAGCTTACATAAAGGACTGAGCCTTTT-GGAAAA -s simDog_chr6.simDog.chr6 451762 89 + 593897 TTCTACCTTGGAGGAAAGCACGAGGAAGTCCTACCACA-TA----------CCTTGTAATCTTGCCATAGTTCACATAAAAGAATGAATCTTCT-GGAGAA -s simHuman_chr6.simHuman.chr6 458033 99 + 601863 TGGTACCTTGGAGGAAACCTAGAGGGAGGCCCACCACA-TAGGGATTCCTACCTCACTGTCTTGACATGGCTCACATAAAGGAATGAGTGTTCT-GGATAA -s simRat_chr6.simRat.chr6 164575 100 - 647215 TGCCACCCAGGATGAAATCTCAAAGACCTCCAATGACA-CAGGAATCCCCACCTCACTGGCTTGAAATAGTTCACATAAAGGAAAGAGTCTTTCAAGAGAC - -a -s simMouse_chr6.simMouse.chr6 473234 2 + 636262 CT -s Anc0.Anc0refChr3 93237 2 + 222631 CT -s Anc1.Anc1refChr6 126213 2 + 197743 CT -s Anc2.Anc2refChr1 4482 2 + 142988 CT -s mr.mrrefChr3 28994 2 + 181027 CT -s simCow_chr6.simCow.chr6 458175 2 + 602619 CT -s simDog_chr6.simDog.chr6 451851 2 + 593897 CT -s simHuman_chr6.simHuman.chr6 458132 2 + 601863 CT -s simRat_chr6.simRat.chr6 164677 2 - 647215 CT - -a -s simMouse_chr6.simMouse.chr6 473236 17 + 636262 CCACTTATATGAGTTAA -s Anc0.Anc0refChr3 93244 17 + 222631 CAGCCCTTATGTGTCAA -s Anc1.Anc1refChr6 126220 17 + 197743 CAGCCCTTATGTGTCAA -s Anc2.Anc2refChr1 4489 17 + 142988 TAGCCCTTATGTGTCAG -s mr.mrrefChr3 28996 17 + 181027 CCACTTATATGAGTTAA -s simCow_chr6.simCow.chr6 458199 17 + 602619 GGGCCCTTATGTTTCAG -s simDog_chr6.simDog.chr6 451858 17 + 593897 TAGCCCTTCTGTGTCAG -s simHuman_chr6.simHuman.chr6 458139 17 + 601863 CTGCCCTTATGCAGCAA -s simRat_chr6.simRat.chr6 164679 17 - 647215 CATCTTATATGAGTTAA - -a -s simMouse_chr6.simMouse.chr6 473253 48 + 636262 GGTGATGTTTTAGGTGTCACCCCCTTAGGTGTCGCTTCTTTGACACTG -s Anc0.Anc0refChr3 93261 35 + 222631 GGTGATGGTTTAGGTGTAACTACCTAAGCT-------------CACTG -s Anc1.Anc1refChr6 126237 35 + 197743 GGTGATGGTTTAGGTGTAACTACCTAAGCT-------------CACTG -s Anc2.Anc2refChr1 4506 35 + 142988 GGTGATGGTTTAGGTGTAACCACCTAATCT-------------CACGG -s mr.mrrefChr3 29013 48 + 181027 GGTGATGTTTTAGGTGTCACTCCCTTAGGTGTCGCTTCTTTGACACTG -s simCow_chr6.simCow.chr6 458216 35 + 602619 GGTGCTGGGTTGATTGTAACCACCTAACCT-------------CACGG -s simDog_chr6.simDog.chr6 451875 35 + 593897 GGTGATAATTTAGGTGTAACCACCTAATCT-------------CATGG -s simHuman_chr6.simHuman.chr6 458156 35 + 601863 GGTGATGGTATAGGTGTGACTACCTAAGCT-------------TACTG -s simRat_chr6.simRat.chr6 164697 48 - 647215 GGTGAGGTTTTGGGTGTCACTCACTTGGGTGTCACTGCCTTGACACTG - -a -s simMouse_chr6.simMouse.chr6 473301 12 + 636262 TTCATAACACTT -s Anc0.Anc0refChr3 93296 12 + 222631 TCTGTGATGGTT -s Anc1.Anc1refChr6 126272 12 + 197743 TCTGTGATGGTT -s Anc2.Anc2refChr1 4541 12 + 142988 TCTGTGATGGTT -s mr.mrrefChr3 29061 12 + 181027 TTCATGACACTT -s simCow_chr6.simCow.chr6 458252 12 + 602619 TTTCTGATGGGT -s simDog_chr6.simDog.chr6 451910 12 + 593897 TCTGGGGTGGTT -s simHuman_chr6.simHuman.chr6 458191 12 + 601863 TCTGTGATGGTT -s simRat_chr6.simRat.chr6 164745 12 - 647215 TTCATGCCACTT - -a -s simMouse_chr6.simMouse.chr6 473313 50 + 636262 AGTATGATATATTCATATGGCTTGCCATCCCGATTATATGGTCGAATATG -s Anc0.Anc0refChr3 93308 50 + 222631 AATATGATCTATTCACATGACATGCCATCCCATGTATATGGTCAAGTTCA -s Anc1.Anc1refChr6 126284 50 + 197743 AATATGATCTATTCACATGACATGCCATCCCATGTATATGGTCAAGTTCA -s Anc2.Anc2refChr1 4553 50 + 142988 AATATGATCTATTCACATGACATGCCATCCCATGTATATGGTCAAGTTCA -s mr.mrrefChr3 29073 50 + 181027 AGTATGATATATTCATATGGCTTGCCATCCCGATTATATGGTCAAATTTG -s simCow_chr6.simCow.chr6 458264 50 + 602619 AATATGATCTATTCACATGACAAGCCATCCCATGTATGCTGCCAAGTTCA -s simDog_chr6.simDog.chr6 451923 50 + 593897 AGTATGGTTCATTTGCATGACATGCCATGCTATGTGTATGGTCAAGTTTA -s simHuman_chr6.simHuman.chr6 458203 50 + 601863 AACATTATCTATTCACATGATATGCCCTCCCATGTATCTAATCAAGTTCA -s simRat_chr6.simRat.chr6 164757 50 - 647215 AGTATGATATATTCATATGGCTTGCCATCCCGATTATATGGTCAACTTTG - -a -s simMouse_chr6.simMouse.chr6 473363 50 + 636262 AATAGAGCAGGGTTCGACCATGATATTGGATAGAACAGGATTTTCCAATA -s Anc0.Anc0refChr3 93358 44 + 222631 AATAGAGCTGGGGTAGACCATGACATGAGGTAGACCATGATCTC------ -s Anc1.Anc1refChr6 126334 44 + 197743 AATAGAGCTGGGGTAGACCATGACATGAGGTAGACCATGATCTC------ -s Anc2.Anc2refChr1 4603 44 + 142988 AATAGAGCTGGGGTAGAACATGACATGAGGTAGACCATGATCTC------ -s mr.mrrefChr3 29123 50 + 181027 AATAGAGCAGGGGTAGACCATGATATTGGGTAGAACAGGATTTTCCAATA -s simCow_chr6.simCow.chr6 458314 44 + 602619 AATAGAGCTGGGCTAGAACCTGACATAAGGCAGAACATGATCCC------ -s simDog_chr6.simDog.chr6 451973 43 + 593897 AATAAAGCTAGGGTGGAACATGATATGAAGTGGGCCATGAC-TC------ -s simHuman_chr6.simHuman.chr6 458253 44 + 601863 AATAGAGCGGGGGTAGACCATGACATCAGGTAAATCATGATATC------ -s simRat_chr6.simRat.chr6 164849 50 - 647215 AATAGAGCAGGGGTAGAATATGATATTGGGTATAATGGGCTTTTCCACTA - -a -s simMouse_chr6.simMouse.chr6 473413 7 + 636262 CAATACT -s Anc0.Anc0refChr3 93403 7 + 222631 CTATACT -s Anc1.Anc1refChr6 126379 7 + 197743 CTATACT -s Anc2.Anc2refChr1 4648 7 + 142988 CTATCTT -s mr.mrrefChr3 29174 7 + 181027 CAATACT -s simCow_chr6.simCow.chr6 458359 7 + 602619 CTATGTC -s simDog_chr6.simDog.chr6 452017 7 + 593897 CTATCTT -s simHuman_chr6.simHuman.chr6 458298 7 + 601863 CTATACT -s simRat_chr6.simRat.chr6 164900 7 - 647215 CAATACT - -a -s simMouse_chr6.simMouse.chr6 473420 4 + 636262 TCTG -s Anc0.Anc0refChr3 93410 4 + 222631 TCCT -s Anc1.Anc1refChr6 126386 4 + 197743 TCCT -s Anc2.Anc2refChr1 4659 4 + 142988 TTCT -s mr.mrrefChr3 29181 4 + 181027 TCTG -s simCow_chr6.simCow.chr6 458370 4 + 602619 TTCG -s simDog_chr6.simDog.chr6 452028 4 + 593897 CTCT -s simHuman_chr6.simHuman.chr6 458305 4 + 601863 TCCA -s simRat_chr6.simRat.chr6 164907 4 - 647215 TCTG - -a -s simMouse_chr6.simMouse.chr6 473424 17 + 636262 TCAAGCACCAGAGGTAT -s Anc0.Anc0refChr3 93414 17 + 222631 TCAAGCACCAGAAGAAT -s Anc1.Anc1refChr6 126390 17 + 197743 TCAAGCACCAGAAGAAT -s Anc2.Anc2refChr1 4663 17 + 142988 TCAAGCACCAGAAGAAT -s mr.mrrefChr3 29185 17 + 181027 TCAAGCACCAGAGGAAT -s simCow_chr6.simCow.chr6 458375 17 + 602619 TCAGGCACCAGATGAAT -s simDog_chr6.simDog.chr6 452032 17 + 593897 GCAAGCACCAGGAGAAT -s simHuman_chr6.simHuman.chr6 458309 17 + 601863 TTGAGCACCAGAAGAAT -s simRat_chr6.simRat.chr6 164911 17 - 647215 TCTAGCATCAGAGGAAT - -a -s simMouse_chr6.simMouse.chr6 473441 43 + 636262 ACAGATCAAGGTTGAGAAAGTATTGACATCTTTTTCTTGCTAC -s Anc0.Anc0refChr3 93431 42 + 222631 ATAGATTAAGGGTTAGAGAGTATTGATATTTTTTT-CTACTGC -s Anc1.Anc1refChr6 126407 42 + 197743 ATAGATTAAGGGTTAGAGAGTATTGATATTTTTTT-CTACTGC -s Anc2.Anc2refChr1 4680 42 + 142988 ATAGATTTAGGGTTAGAGAGTATTGATGTATTCTT-CTACTGC -s mr.mrrefChr3 29202 42 + 181027 ATAGATCAAGGTTGAGAAAGTATTGATATTTTTTT-TTGCTAC -s simCow_chr6.simCow.chr6 458392 42 + 602619 ATAGATTTAGGGTTAGAGAGTATTGATGTATTCTT-TGACTGC -s simDog_chr6.simDog.chr6 452056 21 + 593897 ATAGATTTAGGTTTAGA-----------------T-CTA---- -s simHuman_chr6.simHuman.chr6 458326 42 + 601863 ATGGATTAAGGGCTAGAGAGTATTGATAGTTTTTT-CTATTGC -s simRat_chr6.simRat.chr6 164928 42 - 647215 CTAGATCAAGGTTAAGACAGTATTGGTATTTTTCT-TTGCTAG - -a -s simMouse_chr6.simMouse.chr6 473484 7 + 636262 AGCTGTT -s Anc0.Anc0refChr3 93473 7 + 222631 AGTCGTC -s Anc1.Anc1refChr6 126449 7 + 197743 AGTCGTC -s Anc2.Anc2refChr1 4722 7 + 142988 AGTCGTC -s mr.mrrefChr3 29244 7 + 181027 AGCTGTT -s simCow_chr6.simCow.chr6 458438 7 + 602619 AGTCGTC -s simHuman_chr6.simHuman.chr6 458368 7 + 601863 AGTAGTC -s simRat_chr6.simRat.chr6 164970 7 - 647215 AGCTGTT - -a -s simMouse_chr6.simMouse.chr6 473491 18 + 636262 GAACATTTCTATGTGTTT -s Anc0.Anc0refChr3 93483 18 + 222631 CAGCATTTCTATGTGTTT -s Anc1.Anc1refChr6 126459 18 + 197743 CAGCATTTCTATGTGTTT -s Anc2.Anc2refChr1 4732 18 + 142988 CAGCATTTCTATGAGTTT -s mr.mrrefChr3 29251 18 + 181027 GAGCATTTCTATGTGTTT -s simCow_chr6.simCow.chr6 458448 12 + 602619 CA----TGCTA--ACTTT -s simDog_chr6.simDog.chr6 452077 16 + 593897 --GCATGTCTATGAGTTT -s simHuman_chr6.simHuman.chr6 458378 18 + 601863 CAGCATTTCTATTTGTTT -s simRat_chr6.simRat.chr6 164977 18 - 647215 GAGCACTTCTATGCATTT - -a -s simMouse_chr6.simMouse.chr6 473509 28 + 636262 TGGAATCTTGGGCAGATCACAAGCATAG -s Anc0.Anc0refChr3 93501 27 + 222631 TGGAATCTTGGTTAGCT-ATTAAAAGGG -s Anc1.Anc1refChr6 126477 28 + 197743 TGGAATCTTGGTTAGCTTATTAAAAGGG -s Anc2.Anc2refChr1 4765 27 + 142988 TAGAATCTTGGTTAGCT-ATTAAATGGG -s mr.mrrefChr3 29269 28 + 181027 TGGAATCTTGGGCAGATCACAAGAATAG -s simCow_chr6.simCow.chr6 458475 27 + 602619 TAGACTCTTGGTTGGCT-ATTAAATGGG -s simDog_chr6.simDog.chr6 452109 23 + 593897 TAGAATCTTGGCTA-----CGAAGTGAG -s simHuman_chr6.simHuman.chr6 458396 28 + 601863 TGGAGTGTTGGTTAGCTTATTAAAAGGG -s simRat_chr6.simRat.chr6 164995 28 - 647215 TGGAATTTTGGGCAGATCACAAGAAAAG - -a -s simMouse_chr6.simMouse.chr6 473537 11 + 636262 GTTTATTTGGA -s Anc0.Anc0refChr3 93541 11 + 222631 GTTTAATTGGG -s Anc1.Anc1refChr6 126518 11 + 197743 GTTTAATTGGG -s Anc2.Anc2refChr1 4805 11 + 142988 GTTTAATTAGG -s mr.mrrefChr3 29297 11 + 181027 GTTTATTTGGG -s simCow_chr6.simCow.chr6 458515 11 + 602619 GTTTTATTAGC -s simDog_chr6.simDog.chr6 452145 11 + 593897 GTTGAAGTAGG -s simHuman_chr6.simHuman.chr6 458437 11 + 601863 ATATCATTGGG -s simRat_chr6.simRat.chr6 165023 11 - 647215 GTTTACTTGGG - -a -s simMouse_chr6.simMouse.chr6 473548 6 + 636262 GTGAAT -s Anc0.Anc0refChr3 93554 6 + 222631 GGAATT -s Anc1.Anc1refChr6 126531 6 + 197743 GGAATT -s Anc2.Anc2refChr1 4818 6 + 142988 GGAATT -s mr.mrrefChr3 29308 6 + 181027 GTAAAT -s simCow_chr6.simCow.chr6 458528 6 + 602619 ATAATT -s simDog_chr6.simDog.chr6 452158 6 + 593897 GGAATT -s simHuman_chr6.simHuman.chr6 458450 6 + 601863 GGAACT -s simRat_chr6.simRat.chr6 165034 6 - 647215 GTAAAT - -a -s simMouse_chr6.simMouse.chr6 473554 29 + 636262 AAAGGCACTTCAAGATGAGTACTAGTTAA -s Anc0.Anc0refChr3 93613 24 + 222631 AAGATCCCTTTAAAATGGGTGCTG----- -s Anc1.Anc1refChr6 126590 29 + 197743 AAGATCCCTTTAAAATGGGTGCTGTTCAA -s Anc2.Anc2refChr1 4877 24 + 142988 AAGATCCCCTTAAAATGGGTGCTG----- -s mr.mrrefChr3 29314 29 + 181027 AAAGTCACTTTAAGATGAGTACTAGTTAA -s simCow_chr6.simCow.chr6 458589 24 + 602619 AAGATCCCCTTAGAATGTGTGCTG----- -s simDog_chr6.simDog.chr6 452221 24 + 593897 AAGATCCCCTTAAAATGGGTGCTG----- -s simHuman_chr6.simHuman.chr6 458509 29 + 601863 AAGAATTCTTTAAAATGGGCGCTGTTCAA -s simRat_chr6.simRat.chr6 165040 22 - 647215 AAGGTCGCTTTAAGATGTGTAC------- - -a -s simMouse_chr6.simMouse.chr6 473583 29 + 636262 GCTGCATCATCGGAATTGGTGGATGAGTA -s Anc0.Anc0refChr3 93637 25 + 222631 ----CACCATAAGAATTGCTGGATGCTTA -s Anc1.Anc1refChr6 126619 29 + 197743 GCCACACCATAAGAATTGCTGGATGCTTA -s Anc2.Anc2refChr1 4901 25 + 142988 ----CACCATAAGAATTACTGGGTGCTTA -s mr.mrrefChr3 29343 29 + 181027 GCTACATCATCGGAATTGGTGGATGAGTA -s simCow_chr6.simCow.chr6 458613 21 + 602619 ----CACCATATGGATGATTGGGCG---- -s simDog_chr6.simDog.chr6 452245 25 + 593897 ----CACCATGAGAATTACCAGGTGCTTA -s simHuman_chr6.simHuman.chr6 458545 29 + 601863 GCCATACCATAAGAATTGCTGGATGCTTA -s simRat_chr6.simRat.chr6 483650 27 + 647215 -CTACATTATCGGA-TTGGTGGATGAATA - -a -s simMouse_chr6.simMouse.chr6 473612 5 + 636262 TAATT -s Anc0.Anc0refChr3 93662 5 + 222631 TAAAT -s Anc1.Anc1refChr6 126648 5 + 197743 TAAAT -s Anc2.Anc2refChr1 4927 5 + 142988 TAAAT -s mr.mrrefChr3 29372 5 + 181027 TAATT -s simDog_chr6.simDog.chr6 452271 5 + 593897 TAAAT -s simHuman_chr6.simHuman.chr6 458574 5 + 601863 TAAAT -s simRat_chr6.simRat.chr6 483677 5 + 647215 TAATT - -a -s simMouse_chr6.simMouse.chr6 473617 6 + 636262 GCATCA -s Anc0.Anc0refChr3 93667 3 + 222631 GCA--- -s Anc1.Anc1refChr6 126653 6 + 197743 GCATCA -s Anc2.Anc2refChr1 4932 3 + 142988 ACC--- -s mr.mrrefChr3 29377 6 + 181027 GCATCA -s simDog_chr6.simDog.chr6 452276 3 + 593897 ACC--- -s simHuman_chr6.simHuman.chr6 458585 6 + 601863 GCATTA -s simRat_chr6.simRat.chr6 483682 6 + 647215 GCATCA - -a -s simMouse_chr6.simMouse.chr6 473623 29 + 636262 ACGGCATACAAGAAGTGACGTGGAGAATG -s Anc0.Anc0refChr3 93670 29 + 222631 AAAGCATAGTAGAAGTAGAGTGGATAACA -s Anc1.Anc1refChr6 126659 29 + 197743 AAAGCATAGTAGAAGTAGAGTGGATAACA -s Anc2.Anc2refChr1 4935 29 + 142988 AGAGTCTAGTAGAAGTAGAGATGATAATA -s mr.mrrefChr3 29383 29 + 181027 AAGGCATAGAAGAAGTAACGTGGAGAACG -s simCow_chr6.simCow.chr6 458634 27 + 602619 --AGTTTAGAAGAAGTAGAGGTGATAATG -s simDog_chr6.simDog.chr6 452279 28 + 593897 AGGATCTAGTGGAAGGAGAAATGATAA-A -s simHuman_chr6.simHuman.chr6 458618 29 + 601863 AAAGCATAGTAGAAGTAGAGTGGATAACA -s simRat_chr6.simRat.chr6 483688 28 + 647215 AAGGCATAGAAGAA-TAAGGTGGAGAACG - -a -s simMouse_chr6.simMouse.chr6 473652 4 + 636262 TTCG -s Anc0.Anc0refChr3 93700 4 + 222631 TTCA -s Anc1.Anc1refChr6 126689 4 + 197743 TTCA -s Anc2.Anc2refChr1 4965 4 + 142988 TTCA -s mr.mrrefChr3 29413 4 + 181027 TTCA -s simCow_chr6.simCow.chr6 458662 4 + 602619 TTCA -s simDog_chr6.simDog.chr6 452308 3 + 593897 TTC- -s simHuman_chr6.simHuman.chr6 458648 4 + 601863 TTCA -s simRat_chr6.simRat.chr6 483717 4 + 647215 TTCA - -a -s simMouse_chr6.simMouse.chr6 473656 31 + 636262 GCTCTTCATAACATGCTAGAGAGTTTTCCCA -s Anc0.Anc0refChr3 93706 31 + 222631 ACTTTTAATGTAATGCCAGAAAGTTTACCTC -s Anc1.Anc1refChr6 126695 31 + 197743 ACTTTTAATGTAATGCCAGAAAGTTTACCTC -s Anc2.Anc2refChr1 4971 31 + 142988 ACTTCTAATGTATTGCCATAAAGTTTTCCTT -s mr.mrrefChr3 29417 31 + 181027 GCTTTTCATGACATGCTAGAAAGTTTACCCC -s simCow_chr6.simCow.chr6 458668 3 + 602619 AGT---------------------------- -s simDog_chr6.simDog.chr6 452312 31 + 593897 ACTTCTAATGTATTGCCATAAAGTTTTCCTT -s simHuman_chr6.simHuman.chr6 458654 31 + 601863 ACTTTCAATGGAATGTGAGAAAGTTTACCTC -s simRat_chr6.simRat.chr6 483721 31 + 647215 GCTTTTCATGACATGCTAGAAAGGTTACCCC - -a -s simMouse_chr6.simMouse.chr6 473687 12 + 636262 CTGTCAAGAATC -s Anc0.Anc0refChr3 93737 11 + 222631 GC-TCGATGATT -s Anc1.Anc1refChr6 126726 11 + 197743 GC-TCGATGATT -s Anc2.Anc2refChr1 5002 11 + 142988 GC-TTGAAGATT -s mr.mrrefChr3 29448 12 + 181027 CTATCAATAATC -s simDog_chr6.simDog.chr6 452344 11 + 593897 GC-TTGAAGATT -s simHuman_chr6.simHuman.chr6 458685 11 + 601863 AA-TCGATGATT -s simRat_chr6.simRat.chr6 483752 12 + 647215 CTATTAATAATC - -a -s simMouse_chr6.simMouse.chr6 473699 70 + 636262 ACCAAGGTCAACAATCTTGACGACCAGGGGACCACTAGGAATCCTTACCGCTAGAGCCTATATCATGCAT -s Anc0.Anc0refChr3 93748 66 + 222631 GCCACTGTGAGTAATTTTGGTGA-AAAGGGACCACTAGGAGTCCTT---GATAGGAGTTATATCATCCAT -s Anc1.Anc1refChr6 126737 66 + 197743 GCCACTGTGAGTAATTTTGGTGA-AAAGGGACCACTAGGAGTCCTT---GATAGGAGTTATATCATCCAT -s Anc2.Anc2refChr1 5013 66 + 142988 GCCACTGTGAGTAATTTTGGTGA-AAAGGAACCACTAGGAGTCCTT---GATAGGAGTTATATCATCCAT -s mr.mrrefChr3 29460 70 + 181027 ACCAAGGTGAGTAATCTTGACGACCAGGGGACCACTAGGAATCCTTGCCGATAGAACTTATATCATGCAT -s simCow_chr6.simCow.chr6 458671 63 + 602619 ---ACTGTGAGTAATTTTGGTAA-AATAGAACCACTAGGACTCGTT---GAAAGGAGTTATTTCATCCAT -s simDog_chr6.simDog.chr6 452356 66 + 593897 GCCACTGTGAGTAACTTTGGTGA-AAAGGAACCACTAGGAGTCCTC---AATGGGGGTTATATCATCCAT -s simHuman_chr6.simHuman.chr6 458696 66 + 601863 GACACTGTGAGTAATTTTGGTGA-AAAGAGTCCACTAGGAGTCCTT---GACAGGAGTTAAATCAACCAT -s simRat_chr6.simRat.chr6 483764 70 + 647215 ACCAAGGCGAGTAATCTTGACGACCAGGGGACCTCTAGAAAACCTTGCTGATAGAACTTATATCATTCAT - -a -s simMouse_chr6.simMouse.chr6 473769 2 + 636262 AC -s Anc0.Anc0refChr3 93814 2 + 222631 AC -s Anc1.Anc1refChr6 126803 2 + 197743 AC -s Anc2.Anc2refChr1 5079 2 + 142988 AC -s mr.mrrefChr3 29530 2 + 181027 AC -s simCow_chr6.simCow.chr6 458734 2 + 602619 AC -s simDog_chr6.simDog.chr6 452422 2 + 593897 AC -s simHuman_chr6.simHuman.chr6 458762 2 + 601863 AC -s simRat_chr6.simRat.chr6 483838 2 + 647215 AC - -a -s simMouse_chr6.simMouse.chr6 473771 54 + 636262 TAAAGGCATGCAGATGTGTTGCCAGCTCTCAACCAAGAGTCAAGAGTCAATTTA -s Anc0.Anc0refChr3 93816 47 + 222631 TCAAGGCATACAGATGTGTTACCAGCTCTCTACCAAG-------AGGTAATTTA -s Anc1.Anc1refChr6 126805 47 + 197743 TCAAGGCATACAGATGTGTTACCAGCTCTCTACCAAG-------AGGTAATTTA -s Anc2.Anc2refChr1 5082 47 + 142988 TCAAGACATAAAGATGTGTTACCAGCTCTCTACCAAG-------AGGTAATATA -s mr.mrrefChr3 29532 54 + 181027 TAAAGGCATGCAGATGTGTTGCCAGCTCTCAACCAAGAGTCAAGAGTCAATTTA -s simCow_chr6.simCow.chr6 458737 47 + 602619 TCAAGCCAGAAAGATGTGCTTCCAGCTCTTTACCAAG-------AGGTAATGTA -s simDog_chr6.simDog.chr6 452425 47 + 593897 TCAAGACTTGAAGATGTGTTACCAGCTCACTACCAAG-------TCATAATATA -s simHuman_chr6.simHuman.chr6 458764 47 + 601863 TCAAGGCATACAGATGGGTACACAGCTCTCTGCCAAG-------AGGTAATTCA -s simRat_chr6.simRat.chr6 483840 54 + 647215 TAAAGGCATGCGGATGTGTTGCCAGCTCTCATTCAAGAGTCAAGCGTCCATTTA - -a -s simMouse_chr6.simMouse.chr6 473825 33 + 636262 ATCTGCATATTAATAAAGATGGTGTCCAGTGCT -s Anc0.Anc0refChr3 93863 33 + 222631 ATTTGCAACTTAACGAAGTTAGTACCCAATGGT -s Anc1.Anc1refChr6 126852 33 + 197743 ATTTGCAACTTAACGAAGTTAGTACCCAATGGT -s Anc2.Anc2refChr1 5132 33 + 142988 ATTTGCAACTTAACGAAGTTAGTACCCAATGGT -s mr.mrrefChr3 29586 33 + 181027 ATCTGCAGATTAATAAAGATGCTGTCCAGTGCT -s simCow_chr6.simCow.chr6 458787 33 + 602619 GCTCACACCTTAACAAGGTTAGTACCCAATGGT -s simDog_chr6.simDog.chr6 452475 33 + 593897 ATTTGTAACTTAACGAAGGTGGTGTCCAACGGT -s simHuman_chr6.simHuman.chr6 458811 26 + 601863 AT-------TTGAAGATGTTAGAACCCACTGTT -s simRat_chr6.simRat.chr6 483894 33 + 647215 ATATGTAGCTTAATAAAGTTGCTGTCCAGTGAT - -a -s simMouse_chr6.simMouse.chr6 473858 25 + 636262 CATGCAGTAGCTTTCTGCCTTGAAT -s Anc0.Anc0refChr3 93901 25 + 222631 CCTGCAGTAGCTTTCTGCCTCAAAC -s Anc1.Anc1refChr6 126890 25 + 197743 CCTGCAGTAGCTTTCTGCCTCAAAC -s Anc2.Anc2refChr1 5170 25 + 142988 CCTGCAGTAGTTTTCTGGCTCAAAC -s mr.mrrefChr3 29619 25 + 181027 CATGCAGTAGCTTTCTGCCTTGAAT -s simCow_chr6.simCow.chr6 458825 25 + 602619 CCTGCAGTAGTTTTCTGGCTCAAAC -s simHuman_chr6.simHuman.chr6 458842 25 + 601863 CCTGCAACAGCTCTCTTCCCCTAAC -s simRat_chr6.simRat.chr6 483927 25 + 647215 CATTCAGTAACTTTCTGCCTTGAAT - -a -s simMouse_chr6.simMouse.chr6 473883 39 + 636262 TATTCTGATGGCCATCCATCAATAGCTCTGATTACTTGA -s Anc0.Anc0refChr3 93926 39 + 222631 TATTTTGATGTTCATCCATCAATAAATCTGGTCACTTGA -s Anc1.Anc1refChr6 126915 39 + 197743 TATTTTGATGTTCATCCATCAATAAATCTGGTCACTTGA -s Anc2.Anc2refChr1 5195 39 + 142988 CACTTTGATGTTCATCCAACAATAAAGCTGGTTACTTGA -s mr.mrrefChr3 29644 39 + 181027 TATTCTGATGTCCATCCATCAATAACTCTGATCACTTGA -s simCow_chr6.simCow.chr6 458851 39 + 602619 CACTTTGATGTTCATCCAACAATAAAGCTGGTTACTTGA -s simHuman_chr6.simHuman.chr6 458867 39 + 601863 TATTTTAATGTTCCTCCATCAATAAATCTGGTCACTTGA -s simRat_chr6.simRat.chr6 483952 38 + 647215 TGT-CTGATGTCCATCCATTAATAACTCTAATCACTTGA - -a -s simMouse_chr6.simMouse.chr6 473922 22 + 636262 GAGCAGGACTGTCTACAGGTTG -s Anc0.Anc0refChr3 93965 18 + 222631 GATCAGAATTATCTACAT---- -s Anc1.Anc1refChr6 126954 22 + 197743 GATCAGAATTATCTACATTCTG -s Anc2.Anc2refChr1 5234 18 + 142988 GGTCTGAATGATGCACAT---- -s mr.mrrefChr3 29683 22 + 181027 GAGCAGGACTGTCTACAGGTTG -s simCow_chr6.simCow.chr6 458890 18 + 602619 GGTCTGAATGATGCACAT---- -s simHuman_chr6.simHuman.chr6 458910 22 + 601863 GATCAGAATTATCTGCATTCTG -s simRat_chr6.simRat.chr6 483990 22 + 647215 GAGCAGGACTGTCCACAGGTTG - -a -s simMouse_chr6.simMouse.chr6 473944 10 + 636262 TGCACCTGTG -s Anc0.Anc0refChr3 94036 10 + 222631 TGCACCTGCG -s Anc1.Anc1refChr6 127032 10 + 197743 TGCACCTGCG -s Anc2.Anc2refChr1 5305 10 + 142988 TGCACCTGCT -s mr.mrrefChr3 29705 10 + 181027 TGCACCTGTG -s simCow_chr6.simCow.chr6 458962 10 + 602619 TGCACACACA -s simDog_chr6.simDog.chr6 452525 10 + 593897 TGCACCTGCT -s simHuman_chr6.simHuman.chr6 458990 10 + 601863 TGCACTTGAG -s simRat_chr6.simRat.chr6 484012 10 + 647215 TACACCTCTG - -a -s simMouse_chr6.simMouse.chr6 473954 13 + 636262 TTAAAAGGTACTA -s Anc0.Anc0refChr3 94047 13 + 222631 TAGAATGGTGCCC -s Anc1.Anc1refChr6 127043 13 + 197743 TAGAATGGTGCCC -s Anc2.Anc2refChr1 5316 13 + 142988 TATAATTGTCCCC -s mr.mrrefChr3 29715 13 + 181027 TTGAAAGGTGCTA -s simCow_chr6.simCow.chr6 458973 13 + 602619 TTAAACTGTCCCT -s simDog_chr6.simDog.chr6 452536 13 + 593897 TATAATTGTCCCC -s simHuman_chr6.simHuman.chr6 459001 13 + 601863 TGGAAGGGTGCCC -s simRat_chr6.simRat.chr6 484022 13 + 647215 TTGAAAGGTGCTA - -a -s simMouse_chr6.simMouse.chr6 473967 33 + 636262 ACTGGACCTGGGTCCATATTCAGAAGAGATCCT -s Anc0.Anc0refChr3 94061 33 + 222631 ACTGAAACTGTGTCCATATTCAGAAGAGATGCC -s Anc1.Anc1refChr6 127057 33 + 197743 ACTGAAACTGTGTCCATATTCAGAAGAGATGCC -s Anc2.Anc2refChr1 5330 33 + 142988 ACTGAAACTGTGTCCATATTCAGAAGTGATGGC -s mr.mrrefChr3 29729 33 + 181027 ACTGGACCTGGGTCCATATTCAGAAGAGATCCT -s simCow_chr6.simCow.chr6 458987 33 + 602619 ACTGAAACTGTGTCCTTATTTAGAAGGGATGGC -s simDog_chr6.simDog.chr6 452550 24 + 593897 ACTG---------CCACATTCAGAAGTGATTGC -s simHuman_chr6.simHuman.chr6 459015 33 + 601863 CCTGAAAGTGTGTCAATATTCGGAAGAGATGCC -s simRat_chr6.simRat.chr6 484036 33 + 647215 ACTGGCCCTTAGTCCATATTCAGAAGAGATCCT - -a -s simMouse_chr6.simMouse.chr6 474000 5 + 636262 GCACC -s Anc0.Anc0refChr3 94094 5 + 222631 TCACC -s Anc1.Anc1refChr6 127090 5 + 197743 TCACC -s Anc2.Anc2refChr1 5363 5 + 142988 TCACT -s mr.mrrefChr3 29762 5 + 181027 GCACC -s simCow_chr6.simCow.chr6 459020 5 + 602619 TCAAT -s simDog_chr6.simDog.chr6 452574 5 + 593897 TCACT -s simHuman_chr6.simHuman.chr6 459048 5 + 601863 TCACC -s simRat_chr6.simRat.chr6 484070 5 + 647215 GTAAC - -a -s simMouse_chr6.simMouse.chr6 474005 38 + 636262 ATTGTCACTTCTTTGGGTCCATTTGGGTCCATGCCAGA -s Anc0.Anc0refChr3 94099 24 + 222631 TTTGTCACTTCTATGGGA--------------GGCACA -s Anc1.Anc1refChr6 127095 24 + 197743 TTTGTCACTTCTATGGGA--------------GGCACA -s Anc2.Anc2refChr1 5368 24 + 142988 TTTGTCACTTCTATAGGA--------------GGCACA -s mr.mrrefChr3 29767 24 + 181027 ATTGTCACTTCTTTGGGT--------------GCCAGA -s simCow_chr6.simCow.chr6 459025 24 + 602619 ATAGTCACTTCTATAGCA--------------GGCCCA -s simDog_chr6.simDog.chr6 452579 24 + 593897 TTTGCCACTTCTATAGGA--------------GGCACA -s simHuman_chr6.simHuman.chr6 459069 24 + 601863 TTTGTCACATCTATGGGA--------------GGCACA -s simRat_chr6.simRat.chr6 484075 9 + 647215 AAAATCAGT----------------------------- - -a -s simMouse_chr6.simMouse.chr6 474043 49 + 636262 TACCAAATTGAAACCTCTGTATTAGTATAGCATGTGCATTATTTATAAC -s Anc0.Anc0refChr3 94123 45 + 222631 AACTGAATTAAAACCTGTGTACTGATATAACATGTACACTATC----AC -s Anc1.Anc1refChr6 127119 49 + 197743 AACTGAATTAAAACCTGTGTACTGATATAACATGTACACTATCTATGAC -s Anc2.Anc2refChr1 5397 45 + 142988 AACTGAATTAAAACCTGTACACAGATATAACATGTACACTATC----AC -s mr.mrrefChr3 29791 49 + 181027 TACCAAATTGAAACCTCTGTATTAGTATAGCATGTGCATTATTTATAAC -s simCow_chr6.simCow.chr6 459054 44 + 602619 AACTGAATTAAAACCTGTACACAGATATAACATGCACACAATC----A- -s simDog_chr6.simDog.chr6 452608 45 + 593897 AACTGAATTAAAACCTGAACATAGATAAAACATGTACACTATC----AC -s simHuman_chr6.simHuman.chr6 459093 49 + 601863 AACTGAGTAAAAACCTGTGTACTGATATATTATATACACTATCTATGAC - -a -s simMouse_chr6.simMouse.chr6 474092 13 + 636262 AACAGCTCCTAAT -s Anc0.Anc0refChr3 94193 13 + 222631 AACAGTGTCTCAG -s Anc1.Anc1refChr6 127193 13 + 197743 AACAGTGTCTCAG -s Anc2.Anc2refChr1 5468 13 + 142988 AGCAGTGTCTCAG -s mr.mrrefChr3 29840 13 + 181027 AACAGCTCCTAAT -s simCow_chr6.simCow.chr6 459120 13 + 602619 AGCAGTGTCTCAG -s simDog_chr6.simDog.chr6 452680 13 + 593897 AGCAGTGTCTCAG -s simHuman_chr6.simHuman.chr6 459167 13 + 601863 AACAGTGTCACAG - -a -s simMouse_chr6.simMouse.chr6 474105 43 + 636262 GGCCCTACCTAGAAGGGGCAAAAGGCAAGGCAGGTTGAGGGAG -s Anc0.Anc0refChr3 94206 43 + 222631 TGACCTACCTAGAAGGGGCCAAAGGCAAGGCAGATTCAGGGAG -s Anc1.Anc1refChr6 127206 43 + 197743 TGACCTACCTAGAAGGGGCCAAAGGCAAGGCAGATTCAGGGAG -s Anc2.Anc2refChr1 5481 43 + 142988 TAACCTACCTAGAAGGGGCCAAATGCAAGGCAGATTCAAGAAA -s mr.mrrefChr3 29853 43 + 181027 GGCCCTACCTAGAAGGGGCAAAAGGCAAGGCAGATTGAGGGAG -s simCow_chr6.simCow.chr6 459133 43 + 602619 TAGCCTACTTACAAGGGGCCAAATGCAAGTAAGCTTCCAGAAA -s simDog_chr6.simDog.chr6 452695 37 + 593897 TAACCTACC-AGAAGGGGCCAAGTGCAAGGCAGATATA----- -s simHuman_chr6.simHuman.chr6 459180 43 + 601863 TGATCTACCTAGAAGGGGTCAAAGGCAAGGCAGATTCAGGGGG -s simRat_chr6.simRat.chr6 484084 42 + 647215 -GCCCTACGCAGAAGGGGCAAAATGCAAGGCAGATTGAGAGAG - -a -s simMouse_chr6.simMouse.chr6 474148 22 + 636262 CCTGACCTGTCATAATTGGCGC -s Anc0.Anc0refChr3 94249 22 + 222631 TCTAACTCCCCATAATGCTCTC -s Anc1.Anc1refChr6 127249 22 + 197743 TCTAACTCCCCATAATGCTCTC -s Anc2.Anc2refChr1 5524 22 + 142988 TCTAACTCCCCATAATGCTCTC -s mr.mrrefChr3 29896 22 + 181027 CCTGACTTGTCATAATTCGCGC -s simCow_chr6.simCow.chr6 459176 19 + 602619 TCTAACTCCCCATAATGC---C -s simDog_chr6.simDog.chr6 242827 22 - 593897 ACTGACTCCCCATATTGCTCTC -s simHuman_chr6.simHuman.chr6 459223 22 + 601863 TCTAACTCCCCGTAATGCACTC -s simRat_chr6.simRat.chr6 484126 22 + 647215 CTTGACTTTTCATAATCCGCGC - -a -s simMouse_chr6.simMouse.chr6 474170 13 + 636262 CTTACCAAAGGGC -s Anc0.Anc0refChr3 94272 12 + 222631 TTCTC-AGAGTGC -s Anc1.Anc1refChr6 127272 13 + 197743 TTCTCCAGAGTGC -s Anc2.Anc2refChr1 5547 12 + 142988 TTCTC-AGAGTGT -s mr.mrrefChr3 29918 13 + 181027 TTTTCCAAAGGGC -s simCow_chr6.simCow.chr6 459196 9 + 602619 TTCT----AGTGT -s simDog_chr6.simDog.chr6 242850 12 - 593897 ATTTC-AGAGTGT -s simHuman_chr6.simHuman.chr6 459246 13 + 601863 TTCTCCAGAGTGC -s simRat_chr6.simRat.chr6 484148 13 + 647215 TTTTCCACAGGGC - -a -s simMouse_chr6.simMouse.chr6 474183 75 + 636262 TCTCCAAAATGATGTTGGTCGAATCATCTATGTCGTGGGGTCTAGCTTCCTGGATAGAGGTCTAGCTTACTGGAT -s Anc0.Anc0refChr3 94287 48 + 222631 CTTCCATG--GGTGGTGACTAAATCATTTATGG------------------CAATATAATCT-AGCT------AT -s Anc1.Anc1refChr6 127288 49 + 197743 CTTCCATG--GGTGGTGACTAAATCATTTATGG------------------CAATATAATCTTAGCT------AT -s Anc2.Anc2refChr1 5562 48 + 142988 TTTCCAGG--GGTGGTGACTAAATCATTTATGG------------------CAGTGTAATCT-AACT------AT -s mr.mrrefChr3 29931 51 + 181027 CTTCCATGATGATGTTGGTCAAATCATTTATGT------------------GAATATAGGTCTAGCT------AT -s simCow_chr6.simCow.chr6 459208 48 + 602619 TTTCCAGA--TGTGGTGATTCAATCTTTTAAGG------------------CAGTGTAATCT-AACT------AT -s simDog_chr6.simDog.chr6 242865 48 - 593897 TTCCCAGG--GGTGGTGACTAAATCATCTATGG------------------CAGTGGTATCT-AACC------AT -s simHuman_chr6.simHuman.chr6 459262 49 + 601863 CTTCCATG--GGCAGTGACTACATCAGTTATCG------------------CAATATAATCTTAGCT------AT -s simRat_chr6.simRat.chr6 484161 43 + 647215 CTTCCGTGATGATGTT---CAAATCATTTTTGT------------------TAGTGT-GGTCTA----------T - -a -s simMouse_chr6.simMouse.chr6 474258 28 + 636262 AGAAAGTACGGTGCCCTTGTGTGAATTC -s Anc0.Anc0refChr3 94335 28 + 222631 AGAAGGCGCAGTGTCCTTGGGTGTACTC -s Anc1.Anc1refChr6 127337 28 + 197743 AGAAGGCGCAGTGTCCTTGGGTGTACTC -s Anc2.Anc2refChr1 5615 28 + 142988 AGAAGGCGCAGTGTCTTTGGATGTACTC -s mr.mrrefChr3 29982 28 + 181027 AGAAAGTACGGTGCCCTTGTGTGAATTC -s simCow_chr6.simCow.chr6 459261 28 + 602619 GGCAAGTGTAGCACCTTTGGTTGGCCTC -s simDog_chr6.simDog.chr6 242918 28 - 593897 AGAAGGCGCAGTGTCTTTTTATGTACTC -s simHuman_chr6.simHuman.chr6 459311 18 + 601863 GGAA----------TCTTGGGTGTACTC -s simRat_chr6.simRat.chr6 484204 28 + 647215 AGAAAGCGCAGTGCCCTGGTGTGAATTC - -a -s simMouse_chr6.simMouse.chr6 474286 9 + 636262 AAGTTACTT -s Anc0.Anc0refChr3 94364 9 + 222631 TAGTTACTT -s Anc1.Anc1refChr6 127366 9 + 197743 TAGTTACTT -s Anc2.Anc2refChr1 5644 9 + 142988 TAGTTACTT -s mr.mrrefChr3 30010 9 + 181027 AAGTTACTT -s simCow_chr6.simCow.chr6 459290 9 + 602619 TCGTTACAT -s simDog_chr6.simDog.chr6 242947 9 - 593897 CAGTTGCTT -s simHuman_chr6.simHuman.chr6 459330 9 + 601863 TAGTTACTT -s simRat_chr6.simRat.chr6 484232 9 + 647215 AAGTTACTT - -a -s simMouse_chr6.simMouse.chr6 474295 2 + 636262 GG -s Anc0.Anc0refChr3 94373 2 + 222631 GG -s Anc1.Anc1refChr6 127375 2 + 197743 GG -s Anc2.Anc2refChr1 5653 2 + 142988 GG -s mr.mrrefChr3 30019 2 + 181027 GG -s simCow_chr6.simCow.chr6 459347 2 + 602619 GG -s simDog_chr6.simDog.chr6 242956 2 - 593897 GG -s simHuman_chr6.simHuman.chr6 459339 2 + 601863 GG -s simRat_chr6.simRat.chr6 484241 2 + 647215 GG - -a -s simMouse_chr6.simMouse.chr6 474297 22 + 636262 AGGACTAGAAAATACATGATGC -s Anc0.Anc0refChr3 94375 17 + 222631 A---CTAGAATATACATTAT-- -s Anc1.Anc1refChr6 127377 17 + 197743 A---CTAGAATATACATTAT-- -s Anc2.Anc2refChr1 5658 17 + 142988 A---CTAGAATATACATTAT-- -s mr.mrrefChr3 30021 19 + 181027 A---CTAGAAAATACATGATGC -s simCow_chr6.simCow.chr6 459352 17 + 602619 A---CTAGAATATACATCAT-- -s simDog_chr6.simDog.chr6 242961 17 - 593897 A---CTAAAATATACATTAT-- -s simHuman_chr6.simHuman.chr6 459341 7 + 601863 T---CTAGAA------------ -s simRat_chr6.simRat.chr6 484243 19 + 647215 A---CTAGAAAGTACATCATGC - -a -s simMouse_chr6.simMouse.chr6 474319 6 + 636262 TGAAGC -s Anc0.Anc0refChr3 94392 6 + 222631 TGAAGC -s Anc1.Anc1refChr6 127394 6 + 197743 TGAAGC -s Anc2.Anc2refChr1 5675 6 + 142988 TGAAGC -s mr.mrrefChr3 30040 6 + 181027 TGAAGC -s simCow_chr6.simCow.chr6 459369 6 + 602619 TGAAGT -s simDog_chr6.simDog.chr6 242980 6 - 593897 TGAAGC -s simRat_chr6.simRat.chr6 484262 6 + 647215 TGAAGT - -a -s simMouse_chr6.simMouse.chr6 474325 1 + 636262 C -s Anc0.Anc0refChr3 94398 1 + 222631 C -s Anc1.Anc1refChr6 127400 1 + 197743 C -s Anc2.Anc2refChr1 5684 1 + 142988 C -s mr.mrrefChr3 30046 1 + 181027 C -s simCow_chr6.simCow.chr6 459378 1 + 602619 C -s simDog_chr6.simDog.chr6 242989 1 - 593897 C -s simRat_chr6.simRat.chr6 484268 1 + 647215 C - -a -s simMouse_chr6.simMouse.chr6 474326 10 + 636262 TGCCATTCAG -s Anc0.Anc0refChr3 94399 10 + 222631 GACCATTCAA -s Anc1.Anc1refChr6 127401 10 + 197743 GACCATTCAA -s Anc2.Anc2refChr1 5685 10 + 142988 GACCATTCAA -s mr.mrrefChr3 30047 10 + 181027 TGCCATTCAA -s simCow_chr6.simCow.chr6 459379 7 + 602619 ---CATTCAA -s simDog_chr6.simDog.chr6 242991 10 - 593897 GACCGTTCAA -s simHuman_chr6.simHuman.chr6 459348 10 + 601863 ACCCATTCAA -s simRat_chr6.simRat.chr6 484269 10 + 647215 TACTATTCAA - -a -s simMouse_chr6.simMouse.chr6 474336 17 + 636262 GGATTAATGATACCCAA -s Anc0.Anc0refChr3 94409 16 + 222631 AGATTAATAATGTCT-G -s Anc1.Anc1refChr6 127411 16 + 197743 AGATTAATAATGTCT-G -s Anc2.Anc2refChr1 5695 16 + 142988 AGATTAATGATGTCT-G -s mr.mrrefChr3 30057 17 + 181027 GGATTAATAATACCCAA -s simCow_chr6.simCow.chr6 459387 15 + 602619 AGATTAATGATGTCT-- -s simDog_chr6.simDog.chr6 243001 16 - 593897 AGATTAATGACGTTT-G -s simHuman_chr6.simHuman.chr6 459358 16 + 601863 AGACTAATAGTGTCT-G -s simRat_chr6.simRat.chr6 484279 17 + 647215 GGATGAGTAATACCCAT - -a -s simMouse_chr6.simMouse.chr6 474353 70 + 636262 AAAGGCACTCCTCTTATCCCTATGTATAAAAACAACCGCATGCATTACAACAATACAAAAGTATCAAAGA -s Anc0.Anc0refChr3 94425 51 + 222631 GAAAGCACTCCTCCACTTCCCATGTATA------------------ACAACAATACGAAATCATAAGA-A -s Anc1.Anc1refChr6 127427 51 + 197743 GAAAGCACTCCTCCACTTCCCATGTATA------------------ACAACAATACGAAATCATAAGA-A -s Anc2.Anc2refChr1 5711 51 + 142988 GAGAGCACTCCTGCACTTCCCATGTATA------------------ACAACAATAGGAATTCATAAGA-A -s mr.mrrefChr3 30074 70 + 181027 GAAGGCACTCCTCTTATCCCCATGTATAAAAACAACCGCATGCATTACAACAATACAAAAGTATCAGAGA -s simCow_chr6.simCow.chr6 459402 46 + 602619 -----CACTCCTACACTTCCCATGCCTA------------------GTAACAATAGGAATCTATAAGA-A -s simDog_chr6.simDog.chr6 243018 46 - 593897 GAGAGCATTCCTGCACTTCCCATGTATA------------------ACAACAGTAGGAATTCT------A -s simHuman_chr6.simHuman.chr6 459374 51 + 601863 GAAAGCACTCCTCCACTTCCCATGTACA------------------ACAACAATACGATATCATAAGA-A -s simRat_chr6.simRat.chr6 484296 70 + 647215 GAGGGCACTCCTCTCATCCCCATGGGTAAAAACAACCACATGCATTACAACAATACAAAAGTATCAGAGA - -a -s simMouse_chr6.simMouse.chr6 474423 3 + 636262 GAT -s Anc0.Anc0refChr3 94476 3 + 222631 GAC -s Anc1.Anc1refChr6 127478 3 + 197743 GAC -s Anc2.Anc2refChr1 5762 3 + 142988 GAC -s mr.mrrefChr3 30144 3 + 181027 GAT -s simCow_chr6.simCow.chr6 459449 3 + 602619 GAA -s simDog_chr6.simDog.chr6 243064 3 - 593897 GAC -s simHuman_chr6.simHuman.chr6 459425 3 + 601863 GAC -s simRat_chr6.simRat.chr6 484366 3 + 647215 GAT - -a -s simMouse_chr6.simMouse.chr6 474426 33 + 636262 GCATTTGAGAGGTTAGGGCACACACATTGCATA -s Anc0.Anc0refChr3 155989 33 + 222631 TTACTTCAAAAGTTAGGGCACACACATTGTGCA -s Anc1.Anc1refChr6 192163 33 + 197743 TTACTTCAAAAGTTAGGGCACACACATTGTGCA -s Anc2.Anc2refChr1 70197 33 + 142988 TTACTTCAAAAGTTAGGGCACACACATTGTGCA -s mr.mrrefChr3 104204 33 + 181027 TCACTCCAGAGGTTAGGGCACACACATTGCATA -s simCow_chr6.simCow.chr6 528446 25 + 602619 TTACTTCCAAAGTTAGGGTACA--------GCG -s simDog_chr6.simDog.chr6 517183 33 + 593897 TTACTTTAAAAACTGGGGCACACACATTGTGCA -s simHuman_chr6.simHuman.chr6 524133 33 + 601863 TTACTTCAAATGTTAGGGCACACATATTGTGCA -s simMouse_chr6.simMouse.chr6 554208 33 + 636262 TCACTCCAGAGGTTAGGGCACACACATTGCATA -s simRat_chr6.simRat.chr6 29355 33 - 647215 TCACTCCAGGGGTTCGGGCACACACATTGTGTA - -a -s simMouse_chr6.simMouse.chr6 474459 107 + 636262 AAATAAATGGTCTGGCAGGTGGCCTTGAAAGAATAGGCTCCAGTAATCAGGTTCATGTGGTTAGCAGCATCCCTAATCTCAAGGGAGGATATTCAAGTGGTGGAGCA -s Anc0.Anc0refChr3 156022 104 + 222631 AA-TAAATGGTGTGGCACATGGTCCAAAGAGAAAAAGCTACAGTAGTCAG--CACTGTCGTTAGCCGTTTCCCTAATCTCAAGGGAGTATATTCTATCTGTGGAGTC -s Anc1.Anc1refChr6 192196 106 + 197743 AA-TAAATGGTGTGGCACATGGTCCAAAGAGAAAAAGCTACAGTAGTCAGGACACTGTCGTTAGCCGTTTCCCTAATCTCAAGGGAGTATATTCTATCTGTGGAGTC -s Anc2.Anc2refChr1 70230 104 + 142988 AA-TAAATGGTGTGGCACATGGTCTAAAGAGAAAAAGCTACAGTAGTCAG--CACTGCCGTTCACCGTTTCCCTGATCTCAAGGGAGTATATTCTGTCTGTGGAGTC -s mr.mrrefChr3 104237 106 + 181027 AA-TAAATGGTCTGGCAGGTGGTCCTGAAAGAATAAGCTCCAGTAATCAGGTTCATGTGGTTAGCAGCATCCCTAATCTCAAGGGAGGATATTCAAGTGGTGGAGCA -s simCow_chr6.simCow.chr6 528471 104 + 602619 GC-TAACTGGTGTGGCATATGGCCTAAAGAGAATACGCTCCAATCTTCAG--CACTGCCATTGATCACCTATCTGATCTCAAGGGAGTATATTCTGTCTGGGGAATC -s simDog_chr6.simDog.chr6 517236 95 + 593897 AA-TAAATGGTGTGGCGCATGGTCTAAAGCGGAAAAGCTACAGTAGTCAG---------GTTCACGGTTTCCCTGATCTCAAGGGAACTTATTCTGTCTGTGGAG-- -s simHuman_chr6.simHuman.chr6 524166 106 + 601863 AA-TAAATGGTGTGAAACATGATCCAAAGAGAACAAACTAGAGTAGTCGGGACACTGTAGTCAGCCGTTTCCCTAATCTCAAGGGAGTAGATTCTATCTGTGGAGTC -s simMouse_chr6.simMouse.chr6 554241 100 + 636262 AA-TAAA------GGCAGGTGGTCCTGAAAGATTACGCTCCAGTAAACAGGTTCATGTGGTAAGCAGCATCCCTAATCTCAAGGGAGGATATTCAAGCAGTGGAGCA -s simRat_chr6.simRat.chr6 29388 106 - 647215 AA-TAAATGGTCTGGCAGGTGGTCCTGAAAGAATAAGCTGCAGTGCTCAGTTTCCTGTGGCTAGCAGTTTCCCTAATCTCAAGGGAGTATATTTAACTGGTGGAGCA - -a -s simMouse_chr6.simMouse.chr6 474566 5 + 636262 AGTAA -s Anc0.Anc0refChr3 156126 5 + 222631 AGTAA -s Anc1.Anc1refChr6 192302 5 + 197743 AGTAA -s Anc2.Anc2refChr1 70334 5 + 142988 AGTAT -s mr.mrrefChr3 104343 5 + 181027 AGTAA -s simCow_chr6.simCow.chr6 528600 5 + 602619 AGTAT -s simHuman_chr6.simHuman.chr6 524272 5 + 601863 AGTAA -s simMouse_chr6.simMouse.chr6 554341 5 + 636262 AGTAA -s simRat_chr6.simRat.chr6 29494 5 - 647215 TGTAA - -a -s simMouse_chr6.simMouse.chr6 474571 55 + 636262 CCATAAGTCTGCCATTGCTCTTGCTCTCAAACTCTGTGATTTATGAGTCCCCAAA -s Anc0.Anc0refChr3 156142 55 + 222631 CAAAGGGTCTCCCATTGCTCTTCCTCTCAAACTCCCTAATTTCTGGCTTCCCACA -s Anc1.Anc1refChr6 192318 55 + 197743 CAAAGGGTCTCCCATTGCTCTTCCTCTCAAACTCCCTAATTTCTGGCTTCCCACA -s Anc2.Anc2refChr1 70350 55 + 142988 CAAAGGGTCTCCCATTGCTCTTCCTCCCAGACTCCCTAATTACTGGCTTGCCACA -s mr.mrrefChr3 104348 55 + 181027 CCATAAGTCTGCCATTGCTCTTGCTCTCAAACTCTGTGATTTATGAGTCCCCAAA -s simCow_chr6.simCow.chr6 528626 55 + 602619 CAAGGGGTCTCCCAATGCTCTTTCTCCCACACTCCCTAATTACTGGCGTGCCTCA -s simDog_chr6.simDog.chr6 517341 50 + 593897 CAAAGGGTCTCCCATTGCTCTTCC-----GACTCCCAACTTACTGGCTTGCTACA -s simHuman_chr6.simHuman.chr6 524288 55 + 601863 CAAAGGGCGTCCCATTGCATGCACTCTGAAACTCCCTAATTTCTGGCTTCCCACA -s simMouse_chr6.simMouse.chr6 554346 52 + 636262 CCAT---TCTGCCATTGCTCTTGCTCTCAAACTCTGTGATTTATGAGTCCCCAAA -s simRat_chr6.simRat.chr6 29499 55 - 647215 CCTTAATTTTGCCAGTGCTCTTGCTCTCAAACTCTGTGATATATAAGTCCCCAAA - -a -s simMouse_chr6.simMouse.chr6 474626 10 + 636262 GCTGCTCATA -s Anc0.Anc0refChr3 156198 8 + 222631 G--GCCCACA -s Anc1.Anc1refChr6 192374 8 + 197743 G--GCCCACA -s Anc2.Anc2refChr1 70406 8 + 142988 T--CCCCACT -s mr.mrrefChr3 104404 10 + 181027 GCTGCTCATA -s simCow_chr6.simCow.chr6 528682 8 + 602619 A--ACCTATG -s simDog_chr6.simDog.chr6 517392 8 + 593897 T--CCCCACT -s simHuman_chr6.simHuman.chr6 524344 8 + 601863 G--GCCCACA -s simMouse_chr6.simMouse.chr6 554398 10 + 636262 GCTGCTCATA -s simRat_chr6.simRat.chr6 29555 10 - 647215 GCTGTTCATG - -a -s simMouse_chr6.simMouse.chr6 474636 5 + 636262 GTATA -s Anc0.Anc0refChr3 156231 5 + 222631 GTATA -s Anc1.Anc1refChr6 192407 5 + 197743 GTATA -s Anc2.Anc2refChr1 70439 5 + 142988 GTATA -s mr.mrrefChr3 104414 5 + 181027 GTATA -s simCow_chr6.simCow.chr6 528715 5 + 602619 TCATA -s simDog_chr6.simDog.chr6 517425 5 + 593897 GTATA -s simHuman_chr6.simHuman.chr6 524378 5 + 601863 GTATA -s simMouse_chr6.simMouse.chr6 554408 5 + 636262 GTATG -s simRat_chr6.simRat.chr6 29565 5 - 647215 GTATA - -a -s simMouse_chr6.simMouse.chr6 474641 25 + 636262 ACTAAATTCTAATGTCTATATCTAG -s Anc0.Anc0refChr3 156236 25 + 222631 ATCAAATTCTAAGATCTAGGTCAGG -s Anc1.Anc1refChr6 192412 25 + 197743 ATCAAATTCTAAGATCTAGGTCAGG -s Anc2.Anc2refChr1 70444 25 + 142988 ATCAAATTCTAAGATCCAGGTCAGG -s mr.mrrefChr3 104419 25 + 181027 ACTAAATTCTAATGTCTATATCTAG -s simCow_chr6.simCow.chr6 528723 25 + 602619 ATTAAATTCTAAGACTAAGGTCGGG -s simDog_chr6.simDog.chr6 517430 25 + 593897 ATCAAATTCAGAAATCCAAGTCATG -s simHuman_chr6.simHuman.chr6 524383 25 + 601863 ATCAAATTCTAAGATCTAGGTTAGG -s simMouse_chr6.simMouse.chr6 554413 25 + 636262 ACTAAATTCTAATGTCTATATCTAG -s simRat_chr6.simRat.chr6 29570 25 - 647215 GCTGAATTCTAATGTCCATATCTGG - -a -s simMouse_chr6.simMouse.chr6 474666 12 + 636262 AAATGGGTTGTA -s Anc0.Anc0refChr3 156261 10 + 222631 AGATGGG--GTA -s Anc1.Anc1refChr6 192437 12 + 197743 AGATGGGTTGTA -s Anc2.Anc2refChr1 70469 10 + 142988 AGATGGG--GCA -s mr.mrrefChr3 104444 12 + 181027 AAATGGGTTGTA -s simCow_chr6.simCow.chr6 528749 10 + 602619 AGATGGG--GCA -s simDog_chr6.simDog.chr6 517455 10 + 593897 GGTCAGG--GCA -s simHuman_chr6.simHuman.chr6 524408 12 + 601863 AGATGAGTTGTG -s simMouse_chr6.simMouse.chr6 554438 12 + 636262 AAATGGGTTGTG -s simRat_chr6.simRat.chr6 29595 12 - 647215 AAATAGGTTGCA - -a -s simMouse_chr6.simMouse.chr6 474678 57 + 636262 CCATTGTGACAATGACCCTGCCTTAATTACCGACCAGGGGGAAAAAGATGTAACTGT -s Anc0.Anc0refChr3 156271 44 + 222631 GCATGGTGAGAATGACCCTCTCTTAATTAACAACCAGGGCAAAA------------- -s Anc1.Anc1refChr6 192449 44 + 197743 GCATGGTGAGAATGACCCTCTCTTAATTAACAACCAGGGCAAAA------------- -s Anc2.Anc2refChr1 70479 44 + 142988 GCATGGTGAGAATGACCTTCTCTTAATTAACAACCTGGACAAAA------------- -s mr.mrrefChr3 104456 44 + 181027 CCATTGTGACAATGACCCTGCCTTAATTACCAACCAGGGGGAAA------------- -s simCow_chr6.simCow.chr6 528761 44 + 602619 GTATGGTGAGAATGACCTTCTCTTAATTAACAGCTTGGACAAAA------------- -s simDog_chr6.simDog.chr6 517465 44 + 593897 GCATGGTGAGAATGGCCTTCTGTTAATTAGCAAACTGGACCAAA------------- -s simHuman_chr6.simHuman.chr6 524420 44 + 601863 GCTTGGTGAGTATGATCCCCTCTTGATTAACGACAAGGGCAAAA------------- -s simMouse_chr6.simMouse.chr6 554450 44 + 636262 CCATTGTGACAATGACCCTGCCTTAATCACCAACCAGGGGAAAA------------- -s simRat_chr6.simRat.chr6 29615 44 - 647215 CCATGATGACAGTGACCCTACCTTAATTAATAACCACGGGGAAA------------- - -a -s simMouse_chr6.simMouse.chr6 474735 7 + 636262 GTATTTG -s Anc0.Anc0refChr3 94486 5 + 222631 GTATT-- -s Anc1.Anc1refChr6 127488 5 + 197743 GTATT-- -s Anc2.Anc2refChr1 5772 5 + 142988 GTATT-- -s mr.mrrefChr3 30154 7 + 181027 GTATTTG -s simCow_chr6.simCow.chr6 459459 5 + 602619 GTATG-- -s simDog_chr6.simDog.chr6 243074 5 - 593897 GTATT-- -s simHuman_chr6.simHuman.chr6 459435 5 + 601863 GTATT-- -s simRat_chr6.simRat.chr6 484376 7 + 647215 ATATTTA - -a -s simMouse_chr6.simMouse.chr6 474742 62 + 636262 CTTAATTATATAGGCCTGACAAGTCTTTTTGGACATAATAAAAGGATTGCAAATAATAACAT -s Anc0.Anc0refChr3 94491 62 + 222631 ACTAAATATAGAGGCCTGAAAAGTCTTTTTAGAAAGAATTGGAGGACTAGGAACATCAACAT -s Anc1.Anc1refChr6 127493 62 + 197743 ACTAAATATAGAGGCCTGAAAAGTCTTTTTAGAAAGAATTGGAGGACTAGGAACATCAACAT -s Anc2.Anc2refChr1 5778 62 + 142988 ACTAAACATCGAGGCCTGAAAAGTCTTTTTAGAAAGAATTGGAGGACTAGGAACATCAACAT -s mr.mrrefChr3 30161 62 + 181027 CTTAAATATAGAGGCCTGACAAGTCTTTTTGGACAGAATTGGAGGATTGCAAATAATAACAT -s simCow_chr6.simCow.chr6 459465 62 + 602619 ACTAAACATCCAGGTCTGATAAGTCTTTTTACTAAGAATTGGAGCGCTAGGACTATCAACAT -s simDog_chr6.simDog.chr6 243080 59 - 593897 ACTAAACATCGAGGCCCACA---TTTTTGTAGAAAGAATTAGGGGAATAGGAACGGCAACAT -s simHuman_chr6.simHuman.chr6 459440 62 + 601863 ACTAAATCTAGAGGCCTGAAAAGTCCTTTTCGAAAGAATTGGAGGACTAAGAACATCCAAAT -s simRat_chr6.simRat.chr6 484383 62 + 647215 CTTAAACATAGAGGCCTGACAAGCCTTTTTAGAGAGAAATGGACGATTGCAAATAATAACAT - -a -s simMouse_chr6.simMouse.chr6 474804 5 + 636262 TTCCC -s Anc0.Anc0refChr3 94574 5 + 222631 TTTGC -s Anc1.Anc1refChr6 127576 5 + 197743 TTTGC -s Anc2.Anc2refChr1 5861 5 + 142988 TTTGC -s mr.mrrefChr3 30223 5 + 181027 TTCCC -s simCow_chr6.simCow.chr6 459548 5 + 602619 TTTGC -s simDog_chr6.simDog.chr6 243160 5 - 593897 TTTGC -s simHuman_chr6.simHuman.chr6 459523 5 + 601863 TTTGC -s simRat_chr6.simRat.chr6 484445 5 + 647215 TTCCC - -a -s simMouse_chr6.simMouse.chr6 474809 17 + 636262 ATTTAGTATTGCAGCAA -s Anc0.Anc0refChr3 94640 17 + 222631 TTTTAACACTGCAGCTA -s Anc1.Anc1refChr6 127642 17 + 197743 TTTTAACACTGCAGCTA -s Anc2.Anc2refChr1 5927 17 + 142988 TCTTAACACTGCAGCTA -s mr.mrrefChr3 30279 17 + 181027 ATTTAGCATTGCAGCAA -s simCow_chr6.simCow.chr6 459613 17 + 602619 TCCTAATACTGCAGTTA -s simDog_chr6.simDog.chr6 243226 17 - 593897 TCTTAACACTGCAGCTG -s simHuman_chr6.simHuman.chr6 459589 17 + 601863 TTTTAACACTGCAGCTA -s simRat_chr6.simRat.chr6 484501 17 + 647215 ACTTAGCAATGCAGCAG - -a -s simMouse_chr6.simMouse.chr6 474826 20 + 636262 TCTAGTACTTCTATGTGACG -s Anc0.Anc0refChr3 94659 16 + 222631 TCCAGTAC----ATGTGGCA -s Anc1.Anc1refChr6 127661 16 + 197743 TCCAGTAC----ATGTGGCA -s Anc2.Anc2refChr1 5946 16 + 142988 TCCAGTGC----ATGTGGCA -s mr.mrrefChr3 30296 20 + 181027 TCTAGTACTTGTATGTGACA -s simCow_chr6.simCow.chr6 459632 16 + 602619 TCCAGTGC----ATGAGGCA -s simDog_chr6.simDog.chr6 243245 12 - 593897 TCCAGTGC----ATGT---- -s simHuman_chr6.simHuman.chr6 459608 16 + 601863 TCCAGTAA----ACATGGCA -s simRat_chr6.simRat.chr6 484518 20 + 647215 TCGAGTACTTGTAGGTGACA - -a -s simMouse_chr6.simMouse.chr6 474846 15 + 636262 GGTTGGAGTGACTCA -s Anc0.Anc0refChr3 94678 15 + 222631 GGTTGATAGGGATTA -s Anc1.Anc1refChr6 127680 15 + 197743 GGTTGATAGGGATTA -s Anc2.Anc2refChr1 5965 15 + 142988 GGTTAATAGGGATTA -s mr.mrrefChr3 30319 15 + 181027 GGTTGGAATGGCTCA -s simCow_chr6.simCow.chr6 459651 15 + 602619 GGTTAATATGGATTA -s simDog_chr6.simDog.chr6 452732 7 + 593897 --------GGGACTA -s simHuman_chr6.simHuman.chr6 459627 15 + 601863 GGTTGATAAGGATTA -s simRat_chr6.simRat.chr6 484541 15 + 647215 GGTTGGAATGGCTCA - -a -s simMouse_chr6.simMouse.chr6 474861 36 + 636262 CCCAACCACATACTCCTTGAATTGAGTTACTGGGTA -s Anc0.Anc0refChr3 94694 36 + 222631 CCTAACCCCAAGCTTCGTAAATTGAGTGAGTGGGTA -s Anc1.Anc1refChr6 127696 36 + 197743 CCTAACCCCAAGCTTCGTAAATTGAGTGAGTGGGTA -s Anc2.Anc2refChr1 5981 36 + 142988 CCTAACCCCAAGCTTTGCAAACTGAGTGAGTGGGTA -s mr.mrrefChr3 30334 36 + 181027 CCCAACCCCAAGCTCCTTGAATTGAGTGACTGGGTA -s simCow_chr6.simCow.chr6 459667 32 + 602619 CACAACCCCAATCTTGTAAAG----GTGAGTGAGTA -s simDog_chr6.simDog.chr6 452740 36 + 593897 TCTAGTCCCAAGCTTTGCAAACTGAGTGAAAGGGGA -s simHuman_chr6.simHuman.chr6 459643 36 + 601863 CCTAACCCGAAGTTTCGTAATTTGAGTGAGTGGGTA -s simRat_chr6.simRat.chr6 484556 36 + 647215 CCCAATCCCAAGCTCCCTGAATTGAGTGATTGGGTA - -a -s simMouse_chr6.simMouse.chr6 474897 3 + 636262 GTT -s Anc0.Anc0refChr3 94730 3 + 222631 GTT -s Anc1.Anc1refChr6 127732 3 + 197743 GTT -s Anc2.Anc2refChr1 6019 3 + 142988 GTT -s mr.mrrefChr3 30370 3 + 181027 GTT -s simCow_chr6.simCow.chr6 459700 2 + 602619 -TC -s simDog_chr6.simDog.chr6 452778 3 + 593897 GTT -s simHuman_chr6.simHuman.chr6 459688 3 + 601863 GTT -s simRat_chr6.simRat.chr6 484592 3 + 647215 GTT - -a -s simMouse_chr6.simMouse.chr6 474900 46 + 636262 TAGCAGGTTAACACCTTGGAAGTTAGTAAGCACAAGGGTGATGATT -s Anc0.Anc0refChr3 94733 46 + 222631 AAGCGGGTTCAAATCTTCAAGGTTCCTAAGCATAAAGTAAATGACT -s Anc1.Anc1refChr6 127735 46 + 197743 AAGCGGGTTCAAATCTTCAAGGTTCCTAAGCATAAAGTAAATGACT -s Anc2.Anc2refChr1 6022 46 + 142988 AAGTGGGTTCAAATCTTCAAAGTTCCTAAGCATAAAGTAAATGACT -s mr.mrrefChr3 30373 46 + 181027 TAGCAGGTTAACATCTTGAAGGTTAGTAAGCACAAAGGTGATGATT -s simCow_chr6.simCow.chr6 459702 46 + 602619 AAGTGGGGTCAAATCTTCAAAGTTTGTAAGCCCAAAGTAAAAGACT -s simDog_chr6.simDog.chr6 452781 46 + 593897 AGGTGGGTTCAGATCTTCAAAGTCCCTAAACATAAAGCAGGTTATT -s simHuman_chr6.simHuman.chr6 459698 46 + 601863 CAGCGGGTTCAAATCTTCAAGGTTCCTAAGCGTATAATAAATGACT -s simRat_chr6.simRat.chr6 484595 46 + 647215 TAGCAGGTTAACATCTAGAAGGTTAGCAAGCACAAAGGTGATGATT - -a -s simMouse_chr6.simMouse.chr6 474946 6 + 636262 GAGTCT -s Anc0.Anc0refChr3 94779 6 + 222631 GACTCT -s Anc1.Anc1refChr6 127781 6 + 197743 GACTCT -s Anc2.Anc2refChr1 6068 6 + 142988 GACTCT -s mr.mrrefChr3 30419 6 + 181027 GACTCT -s simCow_chr6.simCow.chr6 459748 6 + 602619 GACTCT -s simDog_chr6.simDog.chr6 452830 6 + 593897 AACTCC -s simHuman_chr6.simHuman.chr6 459744 6 + 601863 GACTCT -s simRat_chr6.simRat.chr6 484641 6 + 647215 GACTCT - -a -s simMouse_chr6.simMouse.chr6 474952 100 + 636262 TCAAGTATTGATTGATACAACAGCAAGGGGTTGCACAGTTCCAGCAGGTTTCCATGTCCAACACAAGGTATTGTAATCTGCTCTAAATTAGGAGCAACCC -s Anc0.Anc0refChr3 94785 89 + 222631 GCAAGTGTAGAATAATAGGACAGTGAGGGG----------CTAGAAGGTTTCGGTGTCCAGCACAAAGTACTGTAATCTTGTCTAAATTGGAAGCA-CAC -s Anc1.Anc1refChr6 127787 89 + 197743 GCAAGTGTAGAATAATAGGACAGTGAGGGG----------CTAGAAGGTTTCGGTGTCCAGCACAAAGTACTGTAATCTTGTCTAAATTGGAAGCA-CAC -s Anc2.Anc2refChr1 6074 89 + 142988 GAAACTGTAGCATAATAGCACAGTGTGCGG----------CTAGAAGGTCTCGGTGTCCAGCATAAAGTACTGTAATCTTGTCTAAACTGGAAGCA-CAC -s mr.mrrefChr3 30425 99 + 181027 TCAAGTGTTGATTGATAGGACAGCAAGGGGTTGCACAGTTCCAGCAGGTTTCCATGTCCAACACAAGGTATTGTAATCTTCTCTAAATTGGGAGCA-CCC -s simCow_chr6.simCow.chr6 459754 85 + 602619 G----TGTAGTATGATAGAACAGCAGGAGG----------TTAAAGCGTCTCGGTGTTGAGTATAAAGAATTGTAATCTTGTCTACACAGTAAGCA-TAC -s simDog_chr6.simDog.chr6 452844 87 + 593897 GAAACCATGGCGTAATGACTCGGTGTCCAG----------CCAGAAG--CGCAGTGCCCAGCATAAAGTACTGTAATCTTGCCTAAACTGGAAGCA-CAC -s simHuman_chr6.simHuman.chr6 459750 89 + 601863 GCAAGTGTAGAATAGTAGGACAGTGAGGGG----------CTAGAAGGTTTTGGTGTCCATAACAAAGTACTGTAATTTTATCTAAATTGGAAGCC-CAC -s simRat_chr6.simRat.chr6 484647 99 + 647215 TCAAGTGTCGATGGATAGGACAGCAAGGGGTTGCAAGGTTCCAGCAGGTTTCCATGTTCAACACAAGGTATTGTAATCCTCTCTAGATTGGGAGCA-CCC - -a -s simMouse_chr6.simMouse.chr6 475052 40 + 636262 ATGCATCACAGACTCAGCATTTTCAGCCAGCCCTACTATG -s Anc0.Anc0refChr3 94874 36 + 222631 ATGCATCCCAAACTCAGCATTTGCAGCC----ACACCCTC -s Anc1.Anc1refChr6 127876 36 + 197743 ATGCATCCCAAACTCAGCATTTGCAGCC----ACACCCTC -s Anc2.Anc2refChr1 6163 36 + 142988 ATGCATCCCAAACTCAGCATTTGCAGCA----ACTGCCTC -s mr.mrrefChr3 30524 36 + 181027 ATGCATCCCAGACTCAGCATTTTCAGCC----CTACTATG -s simCow_chr6.simCow.chr6 459840 36 + 602619 ATGCATCCCAAACTCAGCATTTGGAGTG----ACTACCTC -s simDog_chr6.simDog.chr6 452931 36 + 593897 ATGCATTCCAAACTCAGCATTTGCAGCA----ACTGCCTC -s simHuman_chr6.simHuman.chr6 459839 35 + 601863 ACATATCCCAAACTCAGCATTTGCAGCC----ACACCTT- -s simRat_chr6.simRat.chr6 484746 36 + 647215 ATGCATCCCTGACTCAGCATTTTCAGCC----CTACAATG - -a -s simMouse_chr6.simMouse.chr6 475092 33 + 636262 GCTGTAAGCTGGCTTTTTAAGCACAATTAATTT -s Anc0.Anc0refChr3 94910 24 + 222631 GTCATAAGAT--CTTTACAA-------TAACTC -s Anc1.Anc1refChr6 127912 24 + 197743 GTCATAAGAT--CTTTACAA-------TAACTC -s Anc2.Anc2refChr1 6199 24 + 142988 GTCATAAGAT--CTTTACAA-------TAACTC -s mr.mrrefChr3 30560 33 + 181027 GCTGTTAGCTGGCTTTTTAAGCACAATTAATCC -s simCow_chr6.simCow.chr6 459876 24 + 602619 TTCACAAGAT--CTTTACAT-------TAACTC -s simDog_chr6.simDog.chr6 452988 24 + 593897 GTCATAAGAT--CTTTACAA-------TAACTC -s simRat_chr6.simRat.chr6 484782 33 + 647215 GCTGTTAGCTTGCTTTTTAAGCACAATTAATCC - -a -s simMouse_chr6.simMouse.chr6 475125 18 + 636262 GAACGGCAAGACCCGACG -s Anc0.Anc0refChr3 94934 18 + 222631 AAATGAAGAGAGCCAACC -s Anc1.Anc1refChr6 127936 18 + 197743 AAATGAAGAGAGCCAACC -s Anc2.Anc2refChr1 6223 18 + 142988 AAATGAAGAGAGCCAACC -s mr.mrrefChr3 30593 18 + 181027 AAACGTTGAGACGCAACG -s simCow_chr6.simCow.chr6 459901 18 + 602619 AAATTGAGAGGGCCAACC -s simDog_chr6.simDog.chr6 453012 16 + 593897 AAATGAAGAGAGCCAA-- -s simHuman_chr6.simHuman.chr6 459874 8 + 601863 ----------AGCCCACC -s simRat_chr6.simRat.chr6 484815 18 + 647215 AAATGTTGAGACGCAACG - -a -s simMouse_chr6.simMouse.chr6 475143 3 + 636262 ATC -s Anc0.Anc0refChr3 94952 3 + 222631 ACC -s Anc1.Anc1refChr6 127954 3 + 197743 ACC -s Anc2.Anc2refChr1 6241 3 + 142988 ACC -s mr.mrrefChr3 30611 3 + 181027 ATC -s simCow_chr6.simCow.chr6 459919 2 + 602619 -CT -s simDog_chr6.simDog.chr6 453028 3 + 593897 ATC -s simHuman_chr6.simHuman.chr6 459883 3 + 601863 ACC -s simRat_chr6.simRat.chr6 484833 3 + 647215 ATC - -a -s simMouse_chr6.simMouse.chr6 475146 51 + 636262 ATTAGAAGACCTCCATGGGCCATCCGTTGTTCCAGACAAACAGTATTCTTA -s Anc0.Anc0refChr3 94958 51 + 222631 GTTTGAAAAGTATCATGGGCTGTTCAGTGTTATAGCCTAACAGTGTCCACA -s Anc1.Anc1refChr6 127960 51 + 197743 GTTTGAAAAGTATCATGGGCTGTTCAGTGTTATAGCCTAACAGTGTCCACA -s Anc2.Anc2refChr1 6247 51 + 142988 GCTTGAAAAGTATCGTGGGCTGCTCAGTGTTATAGCCTAACAGTGTCCACA -s mr.mrrefChr3 30614 51 + 181027 ATTAGAAGACCTTCATGGGCCATCCATTGTTATAGACAAACAGTGTTCATA -s simCow_chr6.simCow.chr6 459924 51 + 602619 GCTTGAAAAGCATTGTGGGCTGCCCAGTGTTATAGCCTAACAGTGTCCACA -s simDog_chr6.simDog.chr6 453034 51 + 593897 GCTTGAAAAGTATCGTGGGCTGCTCAGTGTTAAAGCCTAACAGTGTCCACA -s simHuman_chr6.simHuman.chr6 459889 51 + 601863 GTTTGAAAAGTATCATTGGCTGTTTAGTGTCATAGCCTAACAATGTCCACA -s simRat_chr6.simRat.chr6 484836 51 + 647215 CTTAGACGGCCTTCATGGGCCATCAATTGTTATAGACAAATAGTGTGCAAA - -a -s simMouse_chr6.simMouse.chr6 475197 12 + 636262 GAGTGATGGTGA -s Anc0.Anc0refChr3 95009 12 + 222631 GAGTGATAATGA -s Anc1.Anc1refChr6 128011 12 + 197743 GAGTGATAATGA -s Anc2.Anc2refChr1 6298 12 + 142988 GAGCGATAATAA -s mr.mrrefChr3 30665 12 + 181027 GAGTGATAGTGA -s simCow_chr6.simCow.chr6 459975 12 + 602619 GAGCGATCAGAA -s simCow_chr6.simCow.chr6 460224 10 + 602619 GAG--AGGATAC -s simDog_chr6.simDog.chr6 453085 10 + 593897 GAG--ATAATAA -s simHuman_chr6.simHuman.chr6 459940 12 + 601863 GAGTGATAATGA -s simRat_chr6.simRat.chr6 484887 12 + 647215 GAGTGATAGTGA - -a -s simMouse_chr6.simMouse.chr6 475209 2 + 636262 CA -s Anc0.Anc0refChr3 95035 2 + 222631 CA -s Anc1.Anc1refChr6 128037 2 + 197743 CA -s Anc2.Anc2refChr1 6324 2 + 142988 CA -s mr.mrrefChr3 30691 2 + 181027 CA -s simCow_chr6.simCow.chr6 460001 2 + 602619 CA -s simCow_chr6.simCow.chr6 460251 2 + 602619 CA -s simDog_chr6.simDog.chr6 453109 2 + 593897 CA -s simHuman_chr6.simHuman.chr6 459966 2 + 601863 CA -s simRat_chr6.simRat.chr6 484913 2 + 647215 TA - -a -s simMouse_chr6.simMouse.chr6 475211 25 + 636262 GCCTGAGTGGCCCACCTAATTCACA -s Anc0.Anc0refChr3 95037 25 + 222631 GCTTCAGTGGCCCACCTAATTCACA -s Anc1.Anc1refChr6 128039 25 + 197743 GCTTCAGTGGCCCACCTAATTCACA -s Anc2.Anc2refChr1 6326 25 + 142988 GCTTCAGTGGCCCACCTAATTCACA -s mr.mrrefChr3 30693 25 + 181027 GCCTGAGTGGCCCACCTAATTCACA -s simCow_chr6.simCow.chr6 460003 25 + 602619 GGTTCAGTGGCCCTCCTAGTTCACA -s simCow_chr6.simCow.chr6 460253 25 + 602619 GCTTCAGCGGCCCTCCTAATTCACA -s simDog_chr6.simDog.chr6 453112 25 + 593897 GCTTCAGTAGCTCACCTAATCAATG -s simHuman_chr6.simHuman.chr6 459968 25 + 601863 GCTTCAGTGGCCCACCAAATTTACA -s simRat_chr6.simRat.chr6 484915 25 + 647215 GCCTTAATGGCCCACCTAATTCATA - -a -s simMouse_chr6.simMouse.chr6 475236 3 + 636262 TCG -s Anc0.Anc0refChr3 95062 3 + 222631 TTG -s Anc1.Anc1refChr6 128064 3 + 197743 TTG -s Anc2.Anc2refChr1 6351 3 + 142988 TTG -s mr.mrrefChr3 30718 3 + 181027 TCG -s simCow_chr6.simCow.chr6 460046 3 + 602619 TTG -s simCow_chr6.simCow.chr6 460278 3 + 602619 TTG -s simDog_chr6.simDog.chr6 453137 3 + 593897 CTG -s simHuman_chr6.simHuman.chr6 459993 3 + 601863 TTG -s simRat_chr6.simRat.chr6 484940 3 + 647215 TAG - -a -s simMouse_chr6.simMouse.chr6 475239 411 + 636262 AGGGGCAAGCACTGTGGGACTGCTCCGTAAGCATTTTCGAGTTTAGAGCAATAGTGAAATTGGGAGGCAGCACATTTCCTGTGGAACCCGTCAACTGCATGGTCCTGCTACCCCTAACCCTGGAATCCACGTCTTGACCCATCAACACTACTATAAGTCTCGTGATGGGAGTTCGAACCATTTAACCCTTCCCCCAGAATCCACATCTTGGCCCATCAACACTACAATATAGTCTTGCGTTAAGAGTTCGAACCATTCGGACACAGTCCCGGAGCTACAGAACGTTTGAAGCGTCATTTCGGGACATAGCCTGTGCTCAGCACTCAAACCCCCGCAGAATCATAAATTCCAGAGTAGATTAACTTCCTTATTTACTATAAGTGACGAGATAGGATATCAGAATGATTCGGG -s Anc0.Anc0refChr3 95065 15 + 222631 AGGGG----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GAATGATT--GA -s Anc1.Anc1refChr6 128067 17 + 197743 AGGGG----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GAATGATTCAGA -s Anc2.Anc2refChr1 6359 15 + 142988 AGGCA----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CAGTGAAT--GA -s mr.mrrefChr3 30721 17 + 181027 AGGGG----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GAATGATTCGGG -s simCow_chr6.simCow.chr6 460054 15 + 602619 GGGTA----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TAGTAAAT--GA -s simCow_chr6.simCow.chr6 460286 15 + 602619 AGGCA----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CAGGGAAT--GA -s simDog_chr6.simDog.chr6 453142 13 + 593897 --GCA----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CAGTGAAT--GT -s simHuman_chr6.simHuman.chr6 459996 6 + 601863 AGG---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AGA -s simRat_chr6.simRat.chr6 484943 17 + 647215 ACAGT----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GTATGAGTTGGG - -a -s simMouse_chr6.simMouse.chr6 475650 5 + 636262 GTTAG -s Anc0.Anc0refChr3 95080 5 + 222631 GTCAG -s Anc1.Anc1refChr6 128084 5 + 197743 GTCAG -s Anc2.Anc2refChr1 6374 5 + 142988 TTCAG -s mr.mrrefChr3 30738 5 + 181027 GTTAG -s simCow_chr6.simCow.chr6 460301 5 + 602619 TATGG -s simDog_chr6.simDog.chr6 453155 5 + 593897 TTCAG -s simHuman_chr6.simHuman.chr6 460002 5 + 601863 GTCAG -s simRat_chr6.simRat.chr6 484960 5 + 647215 GTTAG - -a -s simMouse_chr6.simMouse.chr6 475655 12 + 636262 CATTCCTCCAAC -s Anc0.Anc0refChr3 95085 12 + 222631 AATTCCTACAGC -s Anc1.Anc1refChr6 128089 12 + 197743 AATTCCTACAGC -s Anc2.Anc2refChr1 6379 12 + 142988 AATTCCTACAGC -s mr.mrrefChr3 30743 12 + 181027 CATTCCTCCAGC -s simCow_chr6.simCow.chr6 460069 12 + 602619 AGTTCCTACAGC -s simCow_chr6.simCow.chr6 460306 12 + 602619 AACTCCTACACC -s simDog_chr6.simDog.chr6 453160 12 + 593897 AATTCCTGCAGC -s simHuman_chr6.simHuman.chr6 460007 12 + 601863 AGTTCCTACAGC -s simRat_chr6.simRat.chr6 484965 12 + 647215 GTTTCCTCCAGC - -a -s simMouse_chr6.simMouse.chr6 475667 1 + 636262 T -s Anc0.Anc0refChr3 95097 1 + 222631 T -s Anc1.Anc1refChr6 128101 1 + 197743 T -s Anc2.Anc2refChr1 6391 1 + 142988 T -s mr.mrrefChr3 30755 1 + 181027 T -s simCow_chr6.simCow.chr6 460318 1 + 602619 T -s simDog_chr6.simDog.chr6 453172 1 + 593897 T -s simHuman_chr6.simHuman.chr6 460019 1 + 601863 T -s simRat_chr6.simRat.chr6 484977 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 475668 7 + 636262 GTAGGCT -s Anc0.Anc0refChr3 95098 7 + 222631 GTAAGCT -s Anc1.Anc1refChr6 128102 7 + 197743 GTAAGCT -s Anc2.Anc2refChr1 6392 7 + 142988 ATAAGCT -s mr.mrrefChr3 30756 7 + 181027 GTAGGCT -s simCow_chr6.simCow.chr6 460081 7 + 602619 ATAAGTT -s simCow_chr6.simCow.chr6 460319 7 + 602619 AGTAGTT -s simDog_chr6.simDog.chr6 453173 7 + 593897 ATGACCT -s simHuman_chr6.simHuman.chr6 460020 7 + 601863 GTAAACT -s simRat_chr6.simRat.chr6 484978 7 + 647215 GTAGGTT - -a -s simMouse_chr6.simMouse.chr6 475675 11 + 636262 TGCACAAGTAA -s Anc0.Anc0refChr3 95105 11 + 222631 TGCACAAGTCA -s Anc1.Anc1refChr6 128109 11 + 197743 TGCACAAGTCA -s Anc2.Anc2refChr1 6399 11 + 142988 TGCACAAGTCA -s mr.mrrefChr3 30763 11 + 181027 TGCACAAGTAA -s simCow_chr6.simCow.chr6 460088 11 + 602619 TGCATAAGTCA -s simCow_chr6.simCow.chr6 460326 11 + 602619 TGCACAGGTCA -s simDog_chr6.simDog.chr6 453180 11 + 593897 TGCACCAACTA -s simHuman_chr6.simHuman.chr6 460027 11 + 601863 TGTACACGTCA -s simRat_chr6.simRat.chr6 484988 9 + 647215 TGCACAAGT-- - -a -s simMouse_chr6.simMouse.chr6 475686 14 + 636262 TAGAATGCATTGGA -s Anc0.Anc0refChr3 95116 14 + 222631 TGGAATGTGCTGAG -s Anc1.Anc1refChr6 128120 14 + 197743 TGGAATGTGCTGAG -s Anc2.Anc2refChr1 6410 14 + 142988 TGGGATGTGCTGAG -s mr.mrrefChr3 30774 14 + 181027 TAGAATGTGCTGGA -s simCow_chr6.simCow.chr6 460099 14 + 602619 GGGGATGTTCAGAG -s simCow_chr6.simCow.chr6 460337 12 + 602619 TGAACTGTGCTG-- -s simDog_chr6.simDog.chr6 453192 14 + 593897 TGGGATGTGATGAG -s simHuman_chr6.simHuman.chr6 460038 11 + 601863 AGGAATGTGCT--- -s simRat_chr6.simRat.chr6 484997 14 + 647215 CAGAATGTGCTGGA - -a -s simMouse_chr6.simMouse.chr6 475700 11 + 636262 TGATGTGTTAA -s Anc0.Anc0refChr3 95130 10 + 222631 TGGC-TGTTAC -s Anc1.Anc1refChr6 128134 10 + 197743 TGGC-TGTTAC -s Anc2.Anc2refChr1 6424 10 + 142988 TGGC-TGTTAC -s mr.mrrefChr3 30788 11 + 181027 TGATGTGTTAA -s simCow_chr6.simCow.chr6 460120 10 + 602619 TGGC-TGTTAC -s simCow_chr6.simCow.chr6 460349 8 + 602619 --GC-TATTAC -s simDog_chr6.simDog.chr6 453206 10 + 593897 TGGC-TGTTAG -s simRat_chr6.simRat.chr6 485011 11 + 647215 CGATATGCAGG - -a -s simMouse_chr6.simMouse.chr6 475711 15 + 636262 ATATTGCTACATTGG -s Anc0.Anc0refChr3 95140 15 + 222631 ACACTGCCATAGTGG -s Anc1.Anc1refChr6 128144 15 + 197743 ACACTGCCATAGTGG -s Anc2.Anc2refChr1 6435 15 + 142988 ACACTGCCATAGTGG -s mr.mrrefChr3 30799 15 + 181027 ATATTGCTACATTGG -s simCow_chr6.simCow.chr6 460131 15 + 602619 ACACTACAATAGCAG -s simCow_chr6.simCow.chr6 460358 15 + 602619 GCACTGCCACAGTGG -s simDog_chr6.simDog.chr6 453217 15 + 593897 ATGTTGTCATAGTGG -s simHuman_chr6.simHuman.chr6 460049 5 + 601863 ----------AGTGG -s simRat_chr6.simRat.chr6 485022 15 + 647215 ATATCACTACATTGG - -a -s simMouse_chr6.simMouse.chr6 475726 3 + 636262 AAT -s Anc0.Anc0refChr3 95169 3 + 222631 ATT -s Anc1.Anc1refChr6 128173 3 + 197743 ATT -s Anc2.Anc2refChr1 6466 3 + 142988 ATT -s mr.mrrefChr3 30814 3 + 181027 AAT -s simCow_chr6.simCow.chr6 460162 3 + 602619 ATT -s simCow_chr6.simCow.chr6 460389 3 + 602619 ATT -s simDog_chr6.simDog.chr6 453248 3 + 593897 AAC -s simHuman_chr6.simHuman.chr6 460068 3 + 601863 ATT -s simRat_chr6.simRat.chr6 485037 3 + 647215 AAT - -a -s simMouse_chr6.simMouse.chr6 475729 7 + 636262 GAGTCCT -s Anc0.Anc0refChr3 95172 7 + 222631 CAGTCCT -s Anc1.Anc1refChr6 128176 7 + 197743 CAGTCCT -s Anc2.Anc2refChr1 6469 7 + 142988 CAGCCCT -s mr.mrrefChr3 30817 7 + 181027 GAGTCCT -s simCow_chr6.simCow.chr6 460165 6 + 602619 CAGGCC- -s simCow_chr6.simCow.chr6 460392 6 + 602619 CAGCCC- -s simDog_chr6.simDog.chr6 453251 7 + 593897 CAACCCT -s simHuman_chr6.simHuman.chr6 460071 7 + 601863 CAGTTGT -s simRat_chr6.simRat.chr6 485044 7 + 647215 GAGCCCT - -a -s simMouse_chr6.simMouse.chr6 475736 1 + 636262 A -s Anc0.Anc0refChr3 95179 1 + 222631 A -s Anc1.Anc1refChr6 128183 1 + 197743 A -s Anc2.Anc2refChr1 6476 1 + 142988 A -s mr.mrrefChr3 30824 1 + 181027 A -s simCow_chr6.simCow.chr6 460398 1 + 602619 A -s simDog_chr6.simDog.chr6 453258 1 + 593897 A -s simHuman_chr6.simHuman.chr6 460078 1 + 601863 A -s simRat_chr6.simRat.chr6 485051 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 475737 18 + 636262 CCAGGAGGCTTTAAACAT -s Anc0.Anc0refChr3 95180 18 + 222631 CCAGGGTGAATTAAACAT -s Anc1.Anc1refChr6 128184 18 + 197743 CCAGGGTGAATTAAACAT -s Anc2.Anc2refChr1 6477 18 + 142988 CTAGGGTGAATTATGCAT -s mr.mrrefChr3 30825 18 + 181027 CCAGGGTGCTTTAAACAT -s simCow_chr6.simCow.chr6 460171 18 + 602619 CTAAAGTGAATTGTGCAT -s simCow_chr6.simCow.chr6 460399 18 + 602619 CCAGGATGAATTATGCAT -s simDog_chr6.simDog.chr6 453259 18 + 593897 CTAGGTTGAATTACGCAT -s simHuman_chr6.simHuman.chr6 460079 18 + 601863 CCAAGGTGGGTTAAACAT -s simRat_chr6.simRat.chr6 485052 18 + 647215 CCAGAGTGATTTGAACAT - -a -s simMouse_chr6.simMouse.chr6 475755 1 + 636262 C -s Anc0.Anc0refChr3 95198 1 + 222631 C -s Anc1.Anc1refChr6 128202 1 + 197743 C -s Anc2.Anc2refChr1 6495 1 + 142988 C -s mr.mrrefChr3 30843 1 + 181027 C -s simCow_chr6.simCow.chr6 460417 1 + 602619 A -s simDog_chr6.simDog.chr6 453277 1 + 593897 C -s simHuman_chr6.simHuman.chr6 460097 1 + 601863 C -s simRat_chr6.simRat.chr6 485070 1 + 647215 C - -a -s simMouse_chr6.simMouse.chr6 475756 49 + 636262 AAGACGCGTTGCCAGCAGCAAACCACCCATTCATTGGACATATGGGTAC -s Anc0.Anc0refChr3 95199 49 + 222631 AGGACCTGTTGCCAGCTGCAAACAGCCCAGTCATGTGACATTTGGGTAC -s Anc1.Anc1refChr6 128203 49 + 197743 AGGACCTGTTGCCAGCTGCAAACAGCCCAGTCATGTGACATTTGGGTAC -s Anc2.Anc2refChr1 6496 49 + 142988 AGGACCTGAGGCCAGCTGCAAACAGCCCAGTAATGTGATGTTTGGGTAC -s mr.mrrefChr3 30844 49 + 181027 AAGACGCGTTGCCAGCAGCAAACCACCCATTCATTGGACATTTGGGTAC -s simCow_chr6.simCow.chr6 460189 35 + 602619 AGGACCTGCAGCCTTTTCTTAACAGCCAAGT-ATGT------------- -s simCow_chr6.simCow.chr6 460418 19 + 602619 AGGACCAG---CCAGTCACAAA--------------------------- -s simDog_chr6.simDog.chr6 453278 49 + 593897 AGGACCCAAGTCCAGCTGCAAGCAGCCCAGTAATGTGATGTTTGGGTAC -s simHuman_chr6.simHuman.chr6 460098 49 + 601863 AGGACCTGTTGCCAGCTGCAAAGAGCACAGTCTTCTGACATTTGGATAC -s simRat_chr6.simRat.chr6 485071 49 + 647215 AAGACTGGTCACCAGCAGCAAACCACCCATTCATTGAACATTTGGGTAC - -a -s simMouse_chr6.simMouse.chr6 475805 25 + 636262 AGCAACTAGGAAGACTGACCAAGAC -s Anc0.Anc0refChr3 95255 15 + 222631 AGCTGCCAGGAAGCC---------- -s Anc1.Anc1refChr6 128259 17 + 197743 AGCTGCCAGGAAGCCTG-------- -s Anc2.Anc2refChr1 6552 15 + 142988 AACTGCCAGAAAGCC---------- -s mr.mrrefChr3 30893 25 + 181027 AGCAACCAGGAAGACTGACCAAGAC -s simCow_chr6.simCow.chr6 460437 9 + 602619 ------GGGAAAGCC---------- -s simDog_chr6.simDog.chr6 453334 15 + 593897 AACTGCCAGAGGGCC---------- -s simHuman_chr6.simHuman.chr6 460154 17 + 601863 AGCTGCCAGGAAGCCTG-------- -s simRat_chr6.simRat.chr6 485120 25 + 647215 AGCAACCAGAAAGACTGACCAAGAC - -a -s simMouse_chr6.simMouse.chr6 475830 38 + 636262 AACCGGTACATAGATATCCGTCCTATTTGGGTGTAAAA -s Anc0.Anc0refChr3 95270 30 + 222631 AACCAGTAGGTAGATGTG--------TTGGCTGTCAAA -s Anc1.Anc1refChr6 128276 30 + 197743 AACCAGTAGGTAGATGTG--------TTGGCTGTCAAA -s Anc2.Anc2refChr1 6567 30 + 142988 AACTAGTCGGTAGATGTG--------TTACCTGTCTGA -s mr.mrrefChr3 30918 38 + 181027 AACCAGTACATAGATATCCGTCCTATTTGGGTGTAAAA -s simCow_chr6.simCow.chr6 460446 30 + 602619 AACTAGTCGAGAGATATG--------TTACCTGTCTGA -s simDog_chr6.simDog.chr6 453349 27 + 593897 AACTA---GGTAGTTGTG--------TTACCTGTCTGA -s simHuman_chr6.simHuman.chr6 460171 30 + 601863 AACCAGTAGGTAGATGTG--------TTGGTTGGCAAA -s simRat_chr6.simRat.chr6 485147 38 + 647215 AACCAGTACATAAATATCCGTCCCGTCTGGGTGTAAAA - -a -s simMouse_chr6.simMouse.chr6 475868 3 + 636262 TGG -s Anc0.Anc0refChr3 95300 3 + 222631 TAG -s Anc1.Anc1refChr6 128306 3 + 197743 TAG -s Anc2.Anc2refChr1 6597 3 + 142988 TAG -s mr.mrrefChr3 30956 3 + 181027 TGG -s simCow_chr6.simCow.chr6 460484 3 + 602619 TAG -s simDog_chr6.simDog.chr6 453376 3 + 593897 TAG -s simHuman_chr6.simHuman.chr6 460201 3 + 601863 TAG -s simRat_chr6.simRat.chr6 485185 3 + 647215 TTG - -a -s simMouse_chr6.simMouse.chr6 475871 318 + 636262 AGCTAACAGCTTATCCTACGAGCAGTGGGACAGCCAGCCAAGGGAGGATGACAGATACCACTTCTTGTTGTCTGACACCCAAGGATCACTTGAGAGGGTAGTAATGTGCATCAGATCAAAATACTTGTCTGTCTAATTGGTATGTTATTTTTGTGTTGATGATGTACCTCCCAGAATCCAATGACTTTACAACCACTACCCCAATGTTCAAGAGGTTTTAAGCTGGTTACATGGTAATACTGTTTAGACTTCACACAGTGCCGTGTGAAAATTTCTAAAAAAAGGCAAACACGGCCCGGTAAACATGGCTAGTGCTTG -s Anc0.Anc0refChr3 95304 19 + 222631 AGGTTACAGGTTATCCTGC----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- -s Anc1.Anc1refChr6 128310 19 + 197743 AGGTTACAGGTTATCCTGC----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- -s Anc2.Anc2refChr1 6601 19 + 142988 AGGTTACAGGTTATCCTGC----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- -s mr.mrrefChr3 30959 109 + 181027 AGCTAACAGCTTATCCTACGAGCAGTGGG-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ACTGTTTAGACTTCACACAGTGCCGTGTGAAAATTTCTAAAAAAAGGCAAACACGGCCCGGTAAACATGGCTAGTGCTTG -s simCow_chr6.simCow.chr6 460488 19 + 602619 AAGTTGCAAGTCTCCCTGC----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- -s simDog_chr6.simDog.chr6 453380 19 + 593897 AGGTTACAGGTTATCCTGC----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- -s simHuman_chr6.simHuman.chr6 460206 19 + 601863 AGGTCACAGGTTATCCTGC----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- -s simRat_chr6.simRat.chr6 485188 109 + 647215 AGCTAACAGCTTATCCTATGAGCAATGGG-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ATTGTTTAGACTTCACATAGCGCCTTGTGCAAATCTCTAAAAAGAGGCAAACGTGGCCAGGTAAACATGGTTAGTGCTTA - -a -s simMouse_chr6.simMouse.chr6 476189 217 + 636262 GGCCATGTACACACAGTTAGTCCTTGGCGACGAGGCTACCCCCTTGACGAGAAGTCAAGCAATCTCCCTGCATGCATTGTCGATCCCCTGTTCAATTCACACATCCCTGCATACATTGTAGGTCCCCTGTCCTGACAGGTCCCTGCATACATTGTAGGTCCCCTGTCCAATTCATGCACTGTCAAGCACTGACAGGCATCTGGTTCATGTCTAGAAT -s mr.mrrefChr3 31068 166 + 181027 GGCCATGTACACACAGTTAGTCCTTGGCGACGAGGCTACC-------CGAGAAGTCAAGCAATCTCCCTGCATGCATTGTCGATCCCCTGTTCAATTCACACATCCCTG-------------------GTCCTGACAGGTCC------------------------CCAATTCATGCACTGTCAAGCAC-GACAGGCATCTGGTTCATGTCTAGAAT -s simRat_chr6.simRat.chr6 485317 166 + 647215 GATCATGTACAAGCAGTCAGTGCTTGGCTATGTGCCTGCC-------TGAGAAATCAAGCACTCCCCCTGCATACATTGTTTATCCCATGTCTGTTTCACACACGTCAA-------------------GTGATGACAGGTCC------------------------CCGATTCATGCACTGTCAAGTAA-GACAGGCACCTAGTTTGCATTCAGAAT - -a -s simMouse_chr6.simMouse.chr6 476406 56 + 636262 GCCTGCCCGCACTACAGTGGACAGTAACTCATTGTCTATTGGTGGGCATAGTGCTC -s mr.mrrefChr3 31234 56 + 181027 GCCTGCCCGCACTACAGTGGACAGTAACTCATTGTCTATTGGTGGGCATAGTGCTC -s simRat_chr6.simRat.chr6 485485 56 + 647215 GCCCGCCTACGCTACAGTAAACAATAACTGATTGCCTGTTGATGGACATAGTGTTC - -a -s simMouse_chr6.simMouse.chr6 476462 238 + 636262 AGTCACCTCTTTCAAACAAAAATAAAAGATTGGTTATTTTTAGCGTGTATGTTTCATTGGTAATATTTAGCATGTATGTTTCAAATCGAGTCTATGGATTGTGAATATTTAGAATTGGCAGGCAGGAATTTAAAATCAATTTGGCAGACACACGTACTGGCTTTAACATCAATTCAATAAGCCAACAAACCCTCCCTTCAACATCCCTGAATCTCTCAGAGAAGGACATTAATGTGTT -s Anc0.Anc0refChr3 95323 6 + 222631 ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ATGTG-T -s Anc1.Anc1refChr6 128329 6 + 197743 ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ATGTG-T -s Anc2.Anc2refChr1 6620 6 + 142988 ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ACCAG-T -s mr.mrrefChr3 31290 209 + 181027 AGTCACCTCTTTCAAACA-------------------TTTTAGCGTGTATGTTTCATTGGTAATATTTAGCATGTATGT---------AGTCTATGGATTGTGAATATTTAGAATTGGCAGGCAGGAATTTAAAATCAATTTGGCAGACACACGTACTGGCTTTAACATCAATTCAATAAGCCAACAAACCCTCCCTTCAACATCCCTGAATCTCTCAGAGAAGGACATTAATGTG-T -s simCow_chr6.simCow.chr6 460507 6 + 602619 ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ACAAG-T -s simDog_chr6.simDog.chr6 453399 6 + 593897 ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ACCAG-T -s simHuman_chr6.simHuman.chr6 460225 6 + 601863 ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ATGTG-T -s simRat_chr6.simRat.chr6 485542 209 + 647215 AGTAACTTCTTTCAAACA-------------------TTCAAACAAATATAAAGGATTGGTAATAATTAGCATCTGTGT---------ATTTTAGGCGTTGTGGACATTTAGAATTTGTGGGCAGGAATTTAAAATCAACTTGGCATACACACGTACTGGATTTAACATCAAATCAATAAGCCAACAAACCTTCCCTTCAACAGCCCTGAATCTCTCAGAGAAGGACATCAGCTTG-T - -a -s simMouse_chr6.simMouse.chr6 476700 46 + 636262 TCCCTCTGCATCAATATATGGCAACCCCATGTCCTCTGTCGAACTC -s Anc0.Anc0refChr3 95718 24 + 222631 -------ACATCAAT---------------GTCCTCTGTTTAACTC -s Anc1.Anc1refChr6 128724 36 + 197743 TTTCTGAACATCAATATATG----------GTCCTCTGTTTAACTC -s Anc2.Anc2refChr1 7032 24 + 142988 -------ACACCAAT---------------GTCCCCTGTTTAACTC -s mr.mrrefChr3 31499 36 + 181027 TCCCTCTGCATCAATATATG----------GTCCTCTGTCGAACTC -s simCow_chr6.simCow.chr6 460986 24 + 602619 -------ACACGCAT---------------GTCCCCTGTTAAACCC -s simDog_chr6.simDog.chr6 453800 24 + 593897 -------ACACCAAT---------------GTCCCCTGTTTAACTC -s simHuman_chr6.simHuman.chr6 460641 35 + 601863 TTTCTGAACATC-CTATATG----------ATGTTCTGTTCAACTC -s simRat_chr6.simRat.chr6 485751 36 + 647215 TCCCTCTGCAACACTCTATA----------GTCCTCTGTTAAACAC - -a -s simMouse_chr6.simMouse.chr6 476746 6 + 636262 ACAGAT -s Anc0.Anc0refChr3 95745 6 + 222631 ACAGAT -s Anc1.Anc1refChr6 128763 6 + 197743 ACAGAT -s Anc2.Anc2refChr1 7059 6 + 142988 ACAGAT -s mr.mrrefChr3 31535 6 + 181027 ACAGAT -s simCow_chr6.simCow.chr6 461013 6 + 602619 ACAGAT -s simDog_chr6.simDog.chr6 453827 6 + 593897 ACAGAT -s simHuman_chr6.simHuman.chr6 460679 6 + 601863 ACAGAT -s simRat_chr6.simRat.chr6 485787 6 + 647215 ACAAAT - -a -s simMouse_chr6.simMouse.chr6 476752 1 + 636262 G -s Anc0.Anc0refChr3 95758 1 + 222631 G -s Anc1.Anc1refChr6 128776 1 + 197743 G -s Anc2.Anc2refChr1 7072 1 + 142988 C -s mr.mrrefChr3 31541 1 + 181027 G -s simCow_chr6.simCow.chr6 461026 1 + 602619 C -s simHuman_chr6.simHuman.chr6 460692 1 + 601863 G -s simRat_chr6.simRat.chr6 485793 1 + 647215 G - -a -s simMouse_chr6.simMouse.chr6 476753 49 + 636262 AAGTTACTGCATGGTGTATCAAGGTTTAGTTTTGAGTCTAAGTGACCTG -s Anc0.Anc0refChr3 95759 43 + 222631 AAACTACTGCATGGTATACCAAGGTCTAG------GTGTAGCTGACCTG -s Anc1.Anc1refChr6 128777 43 + 197743 AAACTACTGCATGGTATACCAAGGTCTAG------GTGTAGCTGACCTG -s Anc2.Anc2refChr1 7073 43 + 142988 AAACTACTGCTTGGTATACCAAGGTCTGG------GTGTAGCTGACCTG -s mr.mrrefChr3 31542 49 + 181027 AAGTTACTGCATGGTGTATCAAGGTTTAGTTTTGAGTCTAAGTGACCTG -s simCow_chr6.simCow.chr6 461027 43 + 602619 AAACTATTGCTCAGTAGACCAAGGTCTGG------GTGTAGCTGACCTG -s simDog_chr6.simDog.chr6 453835 33 + 593897 CAACTACTGCTTGCTATACCAAGGTCTGG------GTTT---------- -s simHuman_chr6.simHuman.chr6 460693 43 + 601863 AAACTACTGAATGGTATGCCGCGGTCTAG------GTGTAGCTAACCTG -s simRat_chr6.simRat.chr6 485801 49 + 647215 AAGTTATCGCATGGTGTATCAAGGTTTAGTTTTGAGTGTAGGTGACCTG - -a -s simMouse_chr6.simMouse.chr6 476802 85 + 636262 ATTTCTATGCAAAGTGGTATTGCATCAAACTTGAGGATTGTCTATTGGAAATATACAAAGCCATAACATTCAGAAAAACCACATG -s Anc0.Anc0refChr3 95802 69 + 222631 ATTCCCATGCACAGTGGCACTTCATCAAACGTGA-TCTGACCCATTGCAGATGTATAAGG-TGGGACTT--------------TG -s Anc1.Anc1refChr6 128820 69 + 197743 ATTCCCATGCACAGTGGCACTTCATCAAACGTGA-TCTGACCCATTGCAGATGTATAAGG-TGGGACTT--------------TG -s Anc2.Anc2refChr1 7116 69 + 142988 ATTCCCATGCACAGTGGCACTTCATCAAACGTGA-TCTGACCCTTCACAGATGTATAGGG-TGGGACTT--------------TG -s mr.mrrefChr3 31591 70 + 181027 ATTTCTATGCAAAGTGGTATTGCATCAAACTTGAGGATTGTCTATTGGAAATATACAAAG-CATAACAT--------------TG -s simCow_chr6.simCow.chr6 461070 67 + 602619 ATTCCCATGCACAGTGTCACTTCATCAAAC-TGA-TCTGGCCCTT-ATAGACATACAGGG-TGGGACTT--------------TG -s simDog_chr6.simDog.chr6 453979 69 + 593897 ATTTCCATGCACAGTGGCACTTAATCAAACGCAA-TCTGACCCTTCACAGATGTATAGGG-TGGAACTT--------------TG -s simHuman_chr6.simHuman.chr6 460736 69 + 601863 ATCCCCATACACAATGGCACTTCATCAAACCTGA-TCCAACCCATTGAAGTTGTATGATG-TCGGACCT--------------TG -s simRat_chr6.simRat.chr6 485850 70 + 647215 ATCACTATGCAAAGTGGTATTTCATCAAACTTCAAGATTGTCTTTTGGAAATATACAAAG-CATAAGAT--------------TG - -a -s simMouse_chr6.simMouse.chr6 476887 12 + 636262 TCCACAATACTT -s Anc0.Anc0refChr3 95906 12 + 222631 tgcacaagacct -s Anc1.Anc1refChr6 128924 12 + 197743 tgcacaagacct -s Anc2.Anc2refChr1 7220 12 + 142988 tgcacaagacct -s mr.mrrefChr3 31661 12 + 181027 TCCACAATACTT -s simCow_chr6.simCow.chr6 461172 12 + 602619 tgcataagaccc -s simDog_chr6.simDog.chr6 454075 12 + 593897 TACACAAGACCT -s simHuman_chr6.simHuman.chr6 460840 12 + 601863 tgcacaagacct -s simRat_chr6.simRat.chr6 485920 12 + 647215 TACACAATACTT - -a -s simMouse_chr6.simMouse.chr6 476899 4 + 636262 TAAG -s Anc0.Anc0refChr3 95918 4 + 222631 taag -s Anc1.Anc1refChr6 128936 4 + 197743 taag -s Anc2.Anc2refChr1 7232 4 + 142988 tgat -s mr.mrrefChr3 31673 4 + 181027 TAAG -s simCow_chr6.simCow.chr6 461184 2 + 602619 --at -s simDog_chr6.simDog.chr6 454088 4 + 593897 TGAT -s simHuman_chr6.simHuman.chr6 460852 4 + 601863 taag -s simRat_chr6.simRat.chr6 485932 4 + 647215 TAAG - -a -s simMouse_chr6.simMouse.chr6 476903 8 + 636262 tcacttct -s Anc0.Anc0refChr3 95923 8 + 222631 tcatttct -s Anc1.Anc1refChr6 128941 8 + 197743 tcatttct -s Anc2.Anc2refChr1 7237 8 + 142988 tcctttct -s mr.mrrefChr3 31677 8 + 181027 tcacttct -s simCow_chr6.simCow.chr6 461187 8 + 602619 ttgctcct -s simDog_chr6.simDog.chr6 454093 8 + 593897 CCCTCTCT -s simHuman_chr6.simHuman.chr6 460857 8 + 601863 tcatttct -s simRat_chr6.simRat.chr6 485936 8 + 647215 TTACTCCT - -a -s simMouse_chr6.simMouse.chr6 476911 25 + 636262 cataggaaggatggcatctcccctg -s Anc0.Anc0refChr3 95931 22 + 222631 cataggaaggatggca---cctcta -s Anc1.Anc1refChr6 128949 22 + 197743 cataggaaggatggca---cctcta -s Anc2.Anc2refChr1 7245 22 + 142988 cataggaaggatggca---cctcta -s mr.mrrefChr3 31685 25 + 181027 cataggaaggatggcatctcccctg -s simCow_chr6.simCow.chr6 461195 20 + 602619 catagggaggatggca---cctc-- -s simDog_chr6.simDog.chr6 454102 22 + 593897 CACAGGAAGAATGGCA---CCTTTA -s simHuman_chr6.simHuman.chr6 460865 22 + 601863 cataagaaggatggca---cctcta -s simRat_chr6.simRat.chr6 485944 25 + 647215 TATAGGAAGAATGGCATCTCCCCTG - -a -s simMouse_chr6.simMouse.chr6 476936 34 + 636262 caactgtaacaatgaatgtacacactagaatggt -s Anc0.Anc0refChr3 95953 34 + 222631 ccactgtaacaatgaatataggcactggtttggc -s Anc1.Anc1refChr6 128971 34 + 197743 ccactgtaacaatgaatataggcactggtttggc -s Anc2.Anc2refChr1 7272 34 + 142988 ccactgtaacaatgaatataggcactggtttggc -s mr.mrrefChr3 31710 34 + 181027 caactgtaacaatgaatgtacacactagaatggt -s simCow_chr6.simCow.chr6 461220 34 + 602619 ccactgtaacattgaatataggcagtggtttggc -s simDog_chr6.simDog.chr6 454139 32 + 593897 CCACTGTAACAATGAA--TAGGCACTGGTTTGGC -s simHuman_chr6.simHuman.chr6 460887 34 + 601863 ccactctaacaatgaaaatatgcactgatttgag -s simRat_chr6.simRat.chr6 485969 34 + 647215 CAACTGTAACACTGAATGTACACACTAGTATGGG - -a -s simMouse_chr6.simMouse.chr6 476970 2 + 636262 ac -s Anc0.Anc0refChr3 95987 2 + 222631 ac -s Anc1.Anc1refChr6 129005 2 + 197743 ac -s Anc2.Anc2refChr1 7306 2 + 142988 cc -s mr.mrrefChr3 31744 2 + 181027 ac -s simCow_chr6.simCow.chr6 461254 2 + 602619 cc -s simDog_chr6.simDog.chr6 454171 2 + 593897 CT -s simHuman_chr6.simHuman.chr6 460921 2 + 601863 ac -s simRat_chr6.simRat.chr6 486010 2 + 647215 AC - -a -s simMouse_chr6.simMouse.chr6 476972 2 + 636262 ag -s Anc0.Anc0refChr3 95989 2 + 222631 ag -s Anc1.Anc1refChr6 129007 2 + 197743 ag -s Anc2.Anc2refChr1 7308 2 + 142988 ag -s mr.mrrefChr3 31746 2 + 181027 ag -s simCow_chr6.simCow.chr6 461257 2 + 602619 aa -s simDog_chr6.simDog.chr6 454173 2 + 593897 GG -s simHuman_chr6.simHuman.chr6 460923 2 + 601863 ag -s simRat_chr6.simRat.chr6 486012 2 + 647215 AG - -a -s simMouse_chr6.simMouse.chr6 476974 2 + 636262 gg -s Anc0.Anc0refChr3 95994 2 + 222631 gg -s Anc1.Anc1refChr6 129012 2 + 197743 gg -s Anc2.Anc2refChr1 7313 2 + 142988 gg -s mr.mrrefChr3 31748 2 + 181027 gg -s simCow_chr6.simCow.chr6 461262 2 + 602619 gg -s simDog_chr6.simDog.chr6 454178 2 + 593897 GG -s simHuman_chr6.simHuman.chr6 460928 2 + 601863 gg -s simRat_chr6.simRat.chr6 486014 2 + 647215 GG - -a -s simMouse_chr6.simMouse.chr6 476976 57 + 636262 aaaagcataacttctcaaactgagccatccacTGGCACACAGCTTATTGGAAGGAAC -s Anc0.Anc0refChr3 95996 45 + 222631 aaggggatagttcctctaactcagtcaccCACTGGCCCAGT--TTAT---------- -s Anc1.Anc1refChr6 129014 45 + 197743 aaggggatagttcctctaactcagtcaccCACTGGCCCAGT--TTAT---------- -s Anc2.Anc2refChr1 7315 45 + 142988 atggggatagttcctctaactcagtcaccCACTGGCCCAGT--CTAT---------- -s mr.mrrefChr3 31750 57 + 181027 aaaagcataacttctcaaactgagccatccacTGGCACACAGCTTATTGGAAGGAAC -s simCow_chr6.simCow.chr6 461264 38 + 602619 gtggggatagtccctctaactgagtcacccagttgccc------------------- -s simDog_chr6.simDog.chr6 454188 44 + 593897 ATGGGGATAGTTGCTCTAACTCAGTCAC-CACTGCCCCAGT--CTAT---------- -s simHuman_chr6.simHuman.chr6 460930 45 + 601863 aaggggatggttcctctaactaggtcacTTACTGGCCCAAG--TTAT---------- -s simRat_chr6.simRat.chr6 486016 57 + 647215 AAGAGCATAACTTCTCAAGCTGAGTCATCCACTGGCAAGTAGCTTACAGGAAGGCAC - -a -s simMouse_chr6.simMouse.chr6 477033 29 + 636262 AGGAGAAAGCATAGTACTAATGCTTCAGT -s Anc0.Anc0refChr3 96041 20 + 222631 ----GAAAAAATTGTACTAATGC-----T -s Anc1.Anc1refChr6 129059 20 + 197743 ----GAAAAAATTGTACTAATGC-----T -s Anc2.Anc2refChr1 7360 20 + 142988 ----GATAAAATTGTACTAATGG-----A -s mr.mrrefChr3 31807 24 + 181027 AGGAGAAAGCATAGTACTAATGC-----T -s simCow_chr6.simCow.chr6 464166 15 + 602619 ---------CATAGCAATACTGA-----G -s simDog_chr6.simDog.chr6 454232 20 + 593897 ----GATAAAATTGTACTGATGG-----A -s simHuman_chr6.simHuman.chr6 460975 20 + 601863 ----GCAAAAATTGTACTAATTC-----T -s simRat_chr6.simRat.chr6 486083 24 + 647215 AGAAGGAAGCATAGTACTAATTC-----T - -a -s simMouse_chr6.simMouse.chr6 477062 20 + 636262 TCACTCACCTACTAGTCCAC -s Anc0.Anc0refChr3 96067 20 + 222631 CTATTCACTTATAAATCCAC -s Anc1.Anc1refChr6 129085 20 + 197743 CTATTCACTTATAAATCCAC -s Anc2.Anc2refChr1 7386 20 + 142988 CTATTCACTTATAAATCCAC -s mr.mrrefChr3 31831 20 + 181027 TCACTCACCTACTAGTCCAC -s simCow_chr6.simCow.chr6 464187 20 + 602619 CTATTCACTTATAAAGCCAC -s simDog_chr6.simDog.chr6 454258 20 + 593897 GCAGCCACTTATTCATCCAC -s simHuman_chr6.simHuman.chr6 461001 20 + 601863 CTGTTCACTTATAAATGTAC -s simRat_chr6.simRat.chr6 486107 20 + 647215 TCATTCACCTATTCGTCCAC - -a -s simMouse_chr6.simMouse.chr6 477082 94 + 636262 ATTCAATTGTAGGTGCTCTGTGAGAATGCACACCCCCCCTCCCTGGAGGGCATGGTCTGAAGGCTTTAGAACCTTGAGTTATAATCCGGCCTGG -s Anc0.Anc0refChr3 96091 86 + 222631 ATTCAATTATAGGATCTC-GTGAGTATGCACA---CCCCTCCCTGAAGGCCATGGTTTAAAGGTTTTAGCTTCTGAAGCCATAAT---ACCT-G -s Anc1.Anc1refChr6 129109 86 + 197743 ATTCAATTATAGGATCTC-GTGAGTATGCACA---CCCCTCCCTGAAGGCCATGGTTTAAAGGTTTTAGCTTCTGAAGCCATAAT---ACCT-G -s Anc2.Anc2refChr1 7410 86 + 142988 ATTCAATTATAGGATCTT-GTGAGTATGCACA---GCCCTCCCTGAAGGCCATAGTTCAAAGGTCTTAGCTTCTGAAGCCATAAT---ACCT-G -s mr.mrrefChr3 31851 93 + 181027 ATTCAATTGTAGGTGCTCTGTGAGAATGCACACCCCCCCTCCCTGGAGGGCATGGTCTGAAGGCTTTAGAACCTTGAGTTATAATCCGGCCT-G -s simCow_chr6.simCow.chr6 464212 86 + 602619 ATTCAATTATAGGGCTTT-GTGAGTATGTGCA---ACCATTCCTGAAGGCCTTAGTCCAAAGGCCTTGGCTTCTGAGGCCATAAT---ACCT-G -s simDog_chr6.simDog.chr6 454282 85 + 593897 ATTCATTTACAGCATCCT-GTGAGTATTCACA---GCCCTCCCTGAAGGCCAT-GCTCAAAGGTCTTAGCTTCTATAGACATAAT---ACTG-G -s simHuman_chr6.simHuman.chr6 461025 86 + 601863 ATTCGATTATAGGAACTC-GTGTGTATGCACA---CCCCTCCCTGCAGGCTGTGGTTTTAAGGTTGTAGCTTCTGAAGCCATAAT---ACCT-G -s simRat_chr6.simRat.chr6 486127 93 + 647215 ATTCAATTGTAGGAGCTCTGTGAGTATGCACACCCCCCCTCCCTGCAAGGCATGGTCTGAATGGTTTAGACCCTGGAACCATAACCCAGCCT-G - -a -s simMouse_chr6.simMouse.chr6 477176 63 + 636262 TTATTGTGTACAGGCTGAATGGAGGACTAGTGATGGAGAATCTTTAAGTGCACAATTATATAC -s Anc0.Anc0refChr3 96177 63 + 222631 CTAGTGTATACAGGCTAATAGGGGATGTAGCAATGCAAAATTTTTAAAGGCACAATTATGTGC -s Anc1.Anc1refChr6 129195 63 + 197743 CTAGTGTATACAGGCTAATAGGGGATGTAGCAATGCAAAATTTTTAAAGGCACAATTATGTGC -s Anc2.Anc2refChr1 7496 63 + 142988 CTAGTGTAGACAGGCTAATAGGGGATGTAGCAATGCAAAACTTTGAAAGGCACAATTATGTGC -s mr.mrrefChr3 31944 63 + 181027 TTATTGTGTACAGGCTGAATGGAGGACTAGTGATGGAGAATCTTTAAGTGCACAATTATATAC -s simCow_chr6.simCow.chr6 464298 63 + 602619 CCAGTGCAGACAGACTAATAGGGGATGTAGCGATGCAAAACTGTGTTGGGCACAATTATGTCC -s simDog_chr6.simDog.chr6 454371 63 + 593897 CTAGTGTAGACAGGCTAATAGGGAATGTTGCAATTCAAAACTTTGAAATGCACAATTATTTGC -s simHuman_chr6.simHuman.chr6 461111 63 + 601863 CTAGTGAATACAGGCTAATAGCCGATGTAGCAATGTAAAATTTTTAATGGCTGAATTGTGTGC -s simRat_chr6.simRat.chr6 486220 63 + 647215 CTAGTGTGTAAAGGCTCATCAGAGGACTAGCGCTGGAAAATTTTTAAGAGCACAATTCTGTAC - -a -s simMouse_chr6.simMouse.chr6 477239 12 + 636262 TCAAAGTTTGAT -s Anc0.Anc0refChr3 96247 12 + 222631 TGAGTGTTTGAT -s Anc1.Anc1refChr6 129265 12 + 197743 TGAGTGTTTGAT -s Anc2.Anc2refChr1 7566 12 + 142988 TGAGTGTGTGAT -s mr.mrrefChr3 32007 12 + 181027 TCAAAGTTTGAT -s simCow_chr6.simCow.chr6 464368 12 + 602619 TGAGTGTGTTAT -s simDog_chr6.simDog.chr6 454441 12 + 593897 TATGTGTGCGAT -s simHuman_chr6.simHuman.chr6 461181 12 + 601863 TGACTGTTTGAT -s simRat_chr6.simRat.chr6 486283 12 + 647215 CCAAAGTTTGGT - -a -s simMouse_chr6.simMouse.chr6 477251 1 + 636262 A -s Anc0.Anc0refChr3 96259 1 + 222631 A -s Anc1.Anc1refChr6 129277 1 + 197743 A -s Anc2.Anc2refChr1 7578 1 + 142988 A -s mr.mrrefChr3 32019 1 + 181027 A -s simCow_chr6.simCow.chr6 464382 1 + 602619 T -s simDog_chr6.simDog.chr6 454453 1 + 593897 A -s simHuman_chr6.simHuman.chr6 461193 1 + 601863 A -s simRat_chr6.simRat.chr6 486295 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 477252 4 + 636262 AAGT -s Anc0.Anc0refChr3 96270 4 + 222631 ATGT -s Anc1.Anc1refChr6 129288 4 + 197743 ATGT -s Anc2.Anc2refChr1 7589 4 + 142988 ATTC -s mr.mrrefChr3 32020 4 + 181027 AAGT -s simCow_chr6.simCow.chr6 464393 4 + 602619 ATCC -s simDog_chr6.simDog.chr6 454464 4 + 593897 ATTC -s simHuman_chr6.simHuman.chr6 461204 4 + 601863 ATGT -s simRat_chr6.simRat.chr6 486296 4 + 647215 AAAT - -a -s simMouse_chr6.simMouse.chr6 477256 2 + 636262 CT -s Anc0.Anc0refChr3 96274 2 + 222631 CT -s Anc1.Anc1refChr6 129292 2 + 197743 CT -s Anc2.Anc2refChr1 7593 2 + 142988 CT -s mr.mrrefChr3 32024 2 + 181027 CT -s simCow_chr6.simCow.chr6 464397 2 + 602619 CA -s simDog_chr6.simDog.chr6 454468 2 + 593897 TT -s simHuman_chr6.simHuman.chr6 461208 2 + 601863 CT -s simRat_chr6.simRat.chr6 486314 2 + 647215 CT - -a -s simMouse_chr6.simMouse.chr6 477258 15 + 636262 ATAACCTGTTAGAGT -s Anc0.Anc0refChr3 96278 13 + 222631 AAACCCAGTCAGA-- -s Anc1.Anc1refChr6 129296 13 + 197743 AAACCCAGTCAGA-- -s Anc2.Anc2refChr1 7598 13 + 142988 AAACCCAGTCAGA-- -s mr.mrrefChr3 32026 15 + 181027 ATAACCTGTTAGAGT -s simCow_chr6.simCow.chr6 464403 12 + 602619 AAACCCACTCAG--- -s simDog_chr6.simDog.chr6 454473 13 + 593897 AAACCCGGTCAGA-- -s simHuman_chr6.simHuman.chr6 461212 13 + 601863 AAACCCAGTCAGA-- -s simRat_chr6.simRat.chr6 486316 15 + 647215 AAACCCTGTTAGAGT - -a -s simMouse_chr6.simMouse.chr6 477273 21 + 636262 TCAAAAGCACTCTCTCTGTCT -s Anc0.Anc0refChr3 96291 21 + 222631 TCAAAAACAATCTCTCTGTCT -s Anc1.Anc1refChr6 129309 21 + 197743 TCAAAAACAATCTCTCTGTCT -s Anc2.Anc2refChr1 7611 21 + 142988 TCAAAAACAATCTTACTGCCT -s mr.mrrefChr3 32041 21 + 181027 TCAAAAGCACTCTCTCTGTCT -s simCow_chr6.simCow.chr6 464415 17 + 602619 ----AAATAATTTTGCTGCCT -s simDog_chr6.simDog.chr6 454488 21 + 593897 TCAAGAACAATCATACTGCCT -s simHuman_chr6.simHuman.chr6 461225 21 + 601863 TAAAAAACAATCTCTCTGTCC -s simRat_chr6.simRat.chr6 486331 21 + 647215 TCAAAAGCCATCTCTCTGTCC - -a -s simMouse_chr6.simMouse.chr6 477294 2 + 636262 CA -s Anc0.Anc0refChr3 96312 2 + 222631 CA -s Anc1.Anc1refChr6 129330 2 + 197743 CA -s Anc2.Anc2refChr1 7632 2 + 142988 CA -s mr.mrrefChr3 32062 2 + 181027 CA -s simCow_chr6.simCow.chr6 464444 2 + 602619 CA -s simDog_chr6.simDog.chr6 454509 2 + 593897 CA -s simHuman_chr6.simHuman.chr6 461246 2 + 601863 AA -s simRat_chr6.simRat.chr6 486352 2 + 647215 CA - -a -s simMouse_chr6.simMouse.chr6 477296 28 + 636262 CCAGACTGTTCGAAGTTCGAGCTAATGC -s Anc0.Anc0refChr3 96314 27 + 222631 CCATCCCTTAC-AAGTTGGAGCTACTGC -s Anc1.Anc1refChr6 129332 27 + 197743 CCATCCCTTAC-AAGTTGGAGCTACTGC -s Anc2.Anc2refChr1 7635 27 + 142988 CCATCCCTTAC-AAGTTGGAGCTACTGC -s mr.mrrefChr3 32064 28 + 181027 CCAGACTGTTCGAAGTTCGAGCTAATGC -s simCow_chr6.simCow.chr6 464447 27 + 602619 CCATCCCTTAA-AAGTCGGGGCTATAGC -s simDog_chr6.simDog.chr6 454512 27 + 593897 CCATCCCTTGC-AAGTTGGAGCTACTGC -s simHuman_chr6.simHuman.chr6 461248 27 + 601863 CCATCCCTTAC-ACATTGGAGCTACTGC -s simRat_chr6.simRat.chr6 486354 28 + 647215 CCAGTCTGTTAGAAGTGGGAGCTAATGC - -a -s simMouse_chr6.simMouse.chr6 477324 14 + 636262 CATTATTAATACTT -s Anc0.Anc0refChr3 96345 14 + 222631 CATTGTTTATACTT -s Anc1.Anc1refChr6 129363 14 + 197743 CATTGTTTATACTT -s Anc2.Anc2refChr1 7666 14 + 142988 CATTGATTATACTT -s mr.mrrefChr3 32092 14 + 181027 CATTATTAATACTT -s simCow_chr6.simCow.chr6 464478 14 + 602619 CATTGATTATGCTT -s simDog_chr6.simDog.chr6 454542 11 + 593897 CACTGATTGTA--- -s simHuman_chr6.simHuman.chr6 461279 14 + 601863 CATTGTTTATACTT -s simRat_chr6.simRat.chr6 486382 14 + 647215 CATTCTTCATACTT - -a -s simMouse_chr6.simMouse.chr6 477338 9 + 636262 AATTCCCTT -s Anc0.Anc0refChr3 96369 9 + 222631 AGTTCCTTT -s Anc1.Anc1refChr6 129387 9 + 197743 AGTTCCTTT -s Anc2.Anc2refChr1 7690 9 + 142988 AGTTTTTTT -s mr.mrrefChr3 32106 9 + 181027 AATTCCCTT -s simCow_chr6.simCow.chr6 464502 9 + 602619 AGTCTTTTT -s simDog_chr6.simDog.chr6 454563 4 + 593897 AGGT----- -s simHuman_chr6.simHuman.chr6 461303 9 + 601863 AGTTCCTTT -s simRat_chr6.simRat.chr6 486396 9 + 647215 AATTCCCTT - -a -s simMouse_chr6.simMouse.chr6 477347 17 + 636262 TTGCTGGTTAAAAGGCA -s Anc0.Anc0refChr3 96378 17 + 222631 TTATTTGTTAAGAGGCA -s Anc1.Anc1refChr6 129396 17 + 197743 TTATTTGTTAAGAGGCA -s Anc2.Anc2refChr1 7699 17 + 142988 TTATTTGTTCAGAGGCA -s mr.mrrefChr3 32115 17 + 181027 TTGCTGGTTAAAAGGCA -s simCow_chr6.simCow.chr6 464512 17 + 602619 TTATTTGTTCAGAGGCA -s simHuman_chr6.simHuman.chr6 461312 17 + 601863 TTAATTGTAAAGAGACA -s simRat_chr6.simRat.chr6 486405 17 + 647215 TTACTTGTTAAAAGGCA - -a -s simMouse_chr6.simMouse.chr6 477364 389 + 636262 GGGCCTCCCAGCTTGTATGAAGGTGACTGGGGTCATTGGGAGGCACAATTGGATGCTATGTTTGTCTAGGAGTTCCGCTCAGTAGACAATCGGTCTGAATTGGAGTCGTTCAATTAAAAGACGTTATGGGATTGCTCATTTATGGGTATGACTAAGTGCACCGGATTGGGGAACTTAGCCAACAATATGTCAGACATTCTACTTAGGAGCTGGTACGAGCATCAGCTGGTACGAGCATCAGAATGGGGGCCCAAGACATTTATATGCCTCCAAGGTTTTCCGTTATGACCCCATAAGAAAACGTTTCGTTATAGGGGGCCATCCAGTTCAAACATTACCCAGGCGTGCGCGATAATTTAATTCCATGTGGTTCGGTAGGCGCCCAATCA -s Anc0.Anc0refChr3 96395 4 + 222631 GGGT------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- -s Anc1.Anc1refChr6 129413 15 + 197743 GGGTTTCCCAGCTTG-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- -s Anc2.Anc2refChr1 7716 4 + 142988 GGGT------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- -s mr.mrrefChr3 32132 20 + 181027 GGGCCTCCCAGCTTGTATGA--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- -s simCow_chr6.simCow.chr6 464529 3 + 602619 GGG-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- -s simDog_chr6.simDog.chr6 454567 1 + 593897 ---T------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- -s simHuman_chr6.simHuman.chr6 461329 15 + 601863 AGGTTTCCCAGCTTG-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- -s simRat_chr6.simRat.chr6 486424 20 + 647215 GGGCCTCCCAGCATTTATGG--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- - -a -s simMouse_chr6.simMouse.chr6 477753 77 + 636262 AACTATTGTAACTGTCTCAAACGAATGTAACTGTGGCGGGGTAACCTGAACTCAAATGATCTTTGCTGGACCAATCA -s Anc1.Anc1refChr6 129428 4 + 197743 -------------------------------------------------------------------------AACA -s mr.mrrefChr3 32152 77 + 181027 AACTATTGTAACTGTCTCAAACGAGTGTAACTGTGGCGGGGTAACCTGAACTCAAATAATCTTTGCCGGACCAAGCA -s simHuman_chr6.simHuman.chr6 461344 4 + 601863 -------------------------------------------------------------------------AACA -s simMouse_chr6.simMouse.chr6 477830 77 + 636262 AACCATTGTAACTGTCTCAAACAAGTGTAACTGTGGCAGGGTAACCTGAACTCACACAATCTTGGCCGTAGCAAGCA - -a -s simMouse_chr6.simMouse.chr6 477907 48 + 636262 GATTCATAGAACGATCCAACTCACATGAACGGGTTCAGCCCCCTGGCT -s Anc1.Anc1refChr6 129432 13 + 197743 -------------------------------GG----GTTCTCTGACT -s mr.mrrefChr3 32229 17 + 181027 -------------------------------GGTTCAGCCCCCTGGCT -s simHuman_chr6.simHuman.chr6 461348 13 + 601863 -------------------------------GG----GTTCTCTGACT -s simRat_chr6.simRat.chr6 486444 17 + 647215 -------------------------------GGTTCAGACCCCTGGCT - -a -s simMouse_chr6.simMouse.chr6 477955 6 + 636262 GTAAAG -s Anc0.Anc0refChr3 96399 4 + 222631 --ATAG -s Anc1.Anc1refChr6 129445 6 + 197743 GTATAG -s Anc2.Anc2refChr1 7720 4 + 142988 --GTAG -s mr.mrrefChr3 32246 6 + 181027 GTAAAG -s simDog_chr6.simDog.chr6 454568 4 + 593897 --GTAG -s simHuman_chr6.simHuman.chr6 461371 6 + 601863 GTATAG -s simRat_chr6.simRat.chr6 486461 6 + 647215 GTATAG - -a -s simMouse_chr6.simMouse.chr6 477961 11 + 636262 ATTTAACTGCT -s Anc0.Anc0refChr3 96406 11 + 222631 AGTTGACCGCT -s Anc1.Anc1refChr6 129454 11 + 197743 AGTTGACCGCT -s Anc2.Anc2refChr1 7727 11 + 142988 AGACGACCCCT -s mr.mrrefChr3 32252 11 + 181027 ATTTAACTGCT -s simDog_chr6.simDog.chr6 454575 11 + 593897 AGACGACCCCT -s simHuman_chr6.simHuman.chr6 461380 11 + 601863 AGTTGACAGCC -s simRat_chr6.simRat.chr6 486467 11 + 647215 AATTAGATGCT - -a -s simMouse_chr6.simMouse.chr6 477972 9 + 636262 GTGTGAGGT -s Anc0.Anc0refChr3 96417 9 + 222631 GTGTGATGT -s Anc1.Anc1refChr6 129465 9 + 197743 GTGTGATGT -s Anc2.Anc2refChr1 7738 9 + 142988 GAGTGATGT -s mr.mrrefChr3 32263 9 + 181027 GTGTGAGGT -s simDog_chr6.simDog.chr6 454588 9 + 593897 GAGTGATGT -s simHuman_chr6.simHuman.chr6 461391 9 + 601863 GTGTGATGT -s simRat_chr6.simRat.chr6 486478 9 + 647215 GTGTGATGT - -a -s simMouse_chr6.simMouse.chr6 477981 68 + 636262 TGTACATTGTGGCTATGACGACTTGGGCTGAAGAGAAGACCATTAGAATGTGTCCCCAGAAGTGTAAT -s Anc0.Anc0refChr3 96435 68 + 222631 TGTACATTGTCACTTTGACTACCCGGGTCACAAAGAAAACCATAAGAACATGACCTCAAAGGTGTAAT -s Anc1.Anc1refChr6 129483 68 + 197743 TGTACATTGTCACTTTGACTACCCGGGTCACAAAGAAAACCATAAGAACATGACCTCAAAGGTGTAAT -s Anc2.Anc2refChr1 7756 68 + 142988 TGTACATTGTCACTTTGGCTACCCGGGTCACAAAAAAAACCATAAAAACATGACCTCAAAGGCGTAAT -s mr.mrrefChr3 32272 68 + 181027 TGTACATTGTGGCTATGACGACTTGGGCTGAAGAGAAGACCATTAGAATGTGTCCCCAGAAGTGTAAT -s simCow_chr6.simCow.chr6 464532 21 + 602619 ---------------TGTCT-------------------------------GCCCTCAGAGGCCT-AT -s simDog_chr6.simDog.chr6 454606 68 + 593897 TGTACATTGTCACTTTGGCTACCCGGGTCACAAAAAAAACCATAAAAACATGACCTCAAAGGCGAAAT -s simHuman_chr6.simHuman.chr6 461409 68 + 601863 TATGCTTTGTCACTTTGATTCCCCAGGTCACAAAGAAAACCACAAGAGCAGGACCTCAAGGGTGTAAT -s simRat_chr6.simRat.chr6 486487 68 + 647215 TACACATTGTCGCTATGACAACTTGGGCCAAGAATAAGACCATTAGAGCCTGTCCCCAGAAGTGTAAT - -a -s simMouse_chr6.simMouse.chr6 478049 2 + 636262 TA -s Anc0.Anc0refChr3 96508 2 + 222631 TC -s Anc1.Anc1refChr6 129556 2 + 197743 TC -s Anc2.Anc2refChr1 7829 2 + 142988 TC -s mr.mrrefChr3 32340 2 + 181027 TA -s simCow_chr6.simCow.chr6 464558 2 + 602619 TC -s simDog_chr6.simDog.chr6 454679 2 + 593897 TG -s simHuman_chr6.simHuman.chr6 461482 2 + 601863 TC -s simRat_chr6.simRat.chr6 486555 2 + 647215 TA - -a -s simMouse_chr6.simMouse.chr6 478051 24 + 636262 AAGATTCCAGCTTTACTGCCTGAA -s Anc0.Anc0refChr3 96510 18 + 222631 AACATACC--T----CTACTTAAA -s Anc1.Anc1refChr6 129558 22 + 197743 AACATACC--TATTGCTACTTAAA -s Anc2.Anc2refChr1 7831 18 + 142988 AACAAAAC--T----CCACTTAAG -s mr.mrrefChr3 32342 24 + 181027 AAGATTCCAGCTTTACTGCCTGAA -s simCow_chr6.simCow.chr6 464560 16 + 602619 AACAA--T--T----CCACTTAAG -s simDog_chr6.simDog.chr6 454681 18 + 593897 AACAAAAC--T----TCACTTAAG -s simHuman_chr6.simHuman.chr6 461484 22 + 601863 AACATACC--TATTGCTACTTAAA -s simRat_chr6.simRat.chr6 486562 24 + 647215 AACATTCCAGCTTCACTACCTGAA - -a -s simMouse_chr6.simMouse.chr6 478075 56 + 636262 AGGGGCTGAGTACTATTGTGTGCACACCTATTATTGCCCCTGGGTTTAGGAAGGAT -s Anc0.Anc0refChr3 96531 24 + 222631 AGGCATTAAGTACTATTGTGTGCA-------------------------------- -s Anc1.Anc1refChr6 129583 32 + 197743 AGGCATTAAGTACTATTGTGTGCACATCTATT------------------------ -s Anc2.Anc2refChr1 7853 24 + 142988 AGGCATTAGGTACTATTGTGTGCA-------------------------------- -s mr.mrrefChr3 32366 56 + 181027 AGGGGCTGAGTACTATTGTGTGCACACCTATTATTGCCCCTGGGTTTAGGAAGGAT -s simCow_chr6.simCow.chr6 464580 8 + 602619 AGGCATCA------------------------------------------------ -s simDog_chr6.simDog.chr6 454703 24 + 593897 AGGCATTGGGTACTATTGTGTGCA-------------------------------- -s simHuman_chr6.simHuman.chr6 461509 32 + 601863 AGGCATTAAGTACTATTGAGTGCACATCTATT------------------------ -s simRat_chr6.simRat.chr6 486586 56 + 647215 AAGGGTTGAGTACTATTGTGTGAACACCTATTATTACCCCTGGGTTCAGGAAGCAT - -a -s simMouse_chr6.simMouse.chr6 478131 209 + 636262 ACATTGTGAAGGGAATACTAATGGATATAATAGGCAAGACAGGTGGAGAGAGATGATATGTGTGTCCCTCCTCTTGTTCATCAGGTTCATCAGACACCATTTTCGGATTTGATTGTAAAGTTAGGAGTACCAGCTAGCAATCACTGAGTGCATTCAATGCAGTGTTGCATCCAGTCTCCCAGACTGAGAGTGCCAGGGTGTCAAGAAAA -s Anc0.Anc0refChr3 96555 5 + 222631 ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AAAGA -s Anc1.Anc1refChr6 129615 20 + 197743 ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GACCTAGGGTGACCAAAAGA -s Anc2.Anc2refChr1 7877 5 + 142988 ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ATAGA -s mr.mrrefChr3 32422 162 + 181027 ACATTGTGAAGGGAATACTAAT--------------------------------------------CCTCCTCTTGTTCATCAGG--CATCAGACACC-TTTTCGGATTTGATTGTAAAGTTAGGAGTACCAGCTAGCAATCACTGAGTGCATTCAATGCAGTGTTGCATCCAGTCTCCCAGACTGAGAGTGCTAGGGTGTCAAAAAAA -s simDog_chr6.simDog.chr6 454727 5 + 593897 ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ATAGA -s simHuman_chr6.simHuman.chr6 461541 20 + 601863 ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GACCTAGGGTGACCAAAAGA -s simRat_chr6.simRat.chr6 486643 162 + 647215 ACGTTGTAATGAGAATATGAGT--------------------------------------------CCTCCACTTGTTCATTGGA--CACCATATGAC-TCTTCAAATTTGATCGTAGGGTGATAAGTACCAGCTAGCAATCACTGAATGCGTTGAATGCAGTGTCACATCCAGTCTTCCAGACTAGGAGTGCTGGGGTGTCAAAAAAA - -a -s simMouse_chr6.simMouse.chr6 478340 22 + 636262 ACCCTTAAAAGGCGTTCAGGCT -s Anc0.Anc0refChr3 96567 22 + 222631 ACGCTTGACAGTCATACAGACT -s Anc1.Anc1refChr6 129642 22 + 197743 ACGCTTGACAGTCATACAGACT -s Anc2.Anc2refChr1 7889 22 + 142988 AGGTTAGGCAGTCATACAGACT -s mr.mrrefChr3 32584 22 + 181027 ACCCTTAAAAGGCGTTCAGGCT -s simDog_chr6.simDog.chr6 454739 22 + 593897 AGGTTAGGCAGTCATACAGACT -s simHuman_chr6.simHuman.chr6 461568 22 + 601863 ACGCTTGATAGCCATACAGACT -s simRat_chr6.simRat.chr6 486805 22 + 647215 ACCATTAAAAGGTGTTCAACTG - -a -s simMouse_chr6.simMouse.chr6 478362 28 + 636262 GAGAGTGCTGGGGCATTAAGAAAAGCCT -s Anc0.Anc0refChr3 96595 28 + 222631 GAAAGCATTACATTTTAAAGAAACGACT -s Anc1.Anc1refChr6 129670 28 + 197743 GAAAGCATTACATTTTAAAGAAACGACT -s Anc2.Anc2refChr1 7917 28 + 142988 GAAAGCATCACATTCCAAACCAACCACA -s mr.mrrefChr3 32606 28 + 181027 GAGAGTGCTGGGTCTTTAAGAAAAGCCT -s simCow_chr6.simCow.chr6 464594 28 + 602619 GAAGGCATCACTTTGCAAACCAACAACA -s simDog_chr6.simDog.chr6 454767 28 + 593897 GTAAGCATCATATTCCAAACCAGCCACA -s simHuman_chr6.simHuman.chr6 461596 28 + 601863 GAAAGCATTACCTTTTGAAGAAACGACT -s simRat_chr6.simRat.chr6 486827 28 + 647215 GAGAGTGCCGGGTCTTTATGAAAAACCT - -a -s simMouse_chr6.simMouse.chr6 478390 7 + 636262 TAAGAAG -s Anc0.Anc0refChr3 96630 7 + 222631 CAGCAAG -s Anc1.Anc1refChr6 129705 7 + 197743 CAGCAAG -s Anc2.Anc2refChr1 7952 7 + 142988 CAGCAAG -s mr.mrrefChr3 32634 7 + 181027 TAAGAAG -s simCow_chr6.simCow.chr6 464629 7 + 602619 AAGCAAA -s simDog_chr6.simDog.chr6 454802 7 + 593897 CATCAGG -s simHuman_chr6.simHuman.chr6 461631 7 + 601863 CAGAAAG -s simRat_chr6.simRat.chr6 486855 7 + 647215 TAAGAAG - -a -s simMouse_chr6.simMouse.chr6 478397 12 + 636262 ATAAACACATGA -s Anc0.Anc0refChr3 96637 12 + 222631 TAAGACAGCTGA -s Anc1.Anc1refChr6 129712 12 + 197743 TAAGACAGCTGA -s Anc2.Anc2refChr1 7959 12 + 142988 TAAGATAGCTGG -s mr.mrrefChr3 32641 12 + 181027 ATAAACACATGA -s simCow_chr6.simCow.chr6 464636 12 + 602619 TAAGTTAGCTGG -s simDog_chr6.simDog.chr6 454810 12 + 593897 TTACATGGCTCG -s simHuman_chr6.simHuman.chr6 461638 12 + 601863 TAAGACAGGTGA -s simRat_chr6.simRat.chr6 486862 12 + 647215 ATAAAAACATGA - -a -s simMouse_chr6.simMouse.chr6 478409 14 + 636262 ATAGATTCACCATG -s Anc0.Anc0refChr3 96655 14 + 222631 AGAGTTTCACCATG -s Anc1.Anc1refChr6 129730 14 + 197743 AGAGTTTCACCATG -s Anc2.Anc2refChr1 7977 14 + 142988 AGAGTTTTACCATC -s mr.mrrefChr3 32653 14 + 181027 AGAGATTCACCATG -s simCow_chr6.simCow.chr6 464654 14 + 602619 AGAGATTTACCATA -s simDog_chr6.simDog.chr6 454828 14 + 593897 AATGTTTTATCGTC -s simHuman_chr6.simHuman.chr6 461656 14 + 601863 AGAGGTTCACCATG -s simRat_chr6.simRat.chr6 486874 14 + 647215 AGAGATTCACCATG - -a -s simMouse_chr6.simMouse.chr6 478423 10 + 636262 AGATGTAATT -s Anc0.Anc0refChr3 96670 10 + 222631 AGACATAGTT -s Anc1.Anc1refChr6 129745 10 + 197743 AGACATAGTT -s Anc2.Anc2refChr1 7992 10 + 142988 AGACATAGTT -s mr.mrrefChr3 32667 10 + 181027 AGACATAATT -s simCow_chr6.simCow.chr6 464669 10 + 602619 AAACTTAGGT -s simDog_chr6.simDog.chr6 454843 10 + 593897 AGAGATAGTT -s simHuman_chr6.simHuman.chr6 461671 10 + 601863 AGACATAGTT -s simRat_chr6.simRat.chr6 486888 10 + 647215 AGACATAATT - -a -s simMouse_chr6.simMouse.chr6 478433 35 + 636262 TTTCTCACCAAAGATCAGACTGCTAGAGCATGTGA -s Anc0.Anc0refChr3 96680 31 + 222631 TTT----CCAAATATCACACTGCTAGGGCATGGGC -s Anc1.Anc1refChr6 129755 35 + 197743 TTTTTTGCCAAATATCACACTGCTAGGGCATGGGC -s Anc2.Anc2refChr1 8002 31 + 142988 TCT----CCAAATATCACACTGCTAGGGCATGGAC -s mr.mrrefChr3 32677 35 + 181027 TTTCTTACCAAATATCAGACTGCTAGAGCATGGGA -s simCow_chr6.simCow.chr6 464683 31 + 602619 TCT----TAAAATATCACACTGCTTGTGCATGGTC -s simDog_chr6.simDog.chr6 454853 31 + 593897 TCT----CCAAAGATCACACTGCTAGGGCATGAAC -s simHuman_chr6.simHuman.chr6 461681 35 + 601863 TTTTTTGCCAAATGTCACACTGCCAGGACATGGGC -s simRat_chr6.simRat.chr6 486898 35 + 647215 TTACTTTCCAAATATCAGACTGCTAGTGCATGGGA - -a -s simMouse_chr6.simMouse.chr6 478468 16 + 636262 TAAGGAGACTCATCTT -s Anc0.Anc0refChr3 96712 16 + 222631 TAAAGAGATTATTTTT -s Anc1.Anc1refChr6 129791 16 + 197743 TAAAGAGATTATTTTT -s Anc2.Anc2refChr1 8034 16 + 142988 TAAAGAGATTATTTTT -s mr.mrrefChr3 32712 16 + 181027 TAAGGAGACTCATCTT -s simCow_chr6.simCow.chr6 464715 16 + 602619 TGAGGAGATTATCTAT -s simDog_chr6.simDog.chr6 454885 16 + 593897 TAAAGATATTATTTTT -s simHuman_chr6.simHuman.chr6 461717 16 + 601863 TAAATAGATTGTTTTT -s simRat_chr6.simRat.chr6 486933 16 + 647215 TAAGGAGACTCATCTT - -a -s simMouse_chr6.simMouse.chr6 478484 43 + 636262 AAAATGGACTGTGGACCATGGTTTTAACATGGTGCCAGTAGAT -s Anc0.Anc0refChr3 96728 34 + 222631 AA-ATGGG-----GACCATGGTTATGACA---TGCCAGCAGGT -s Anc1.Anc1refChr6 129807 39 + 197743 AA-ATGGGTAACAGACCATGGTTATGACA---TGCCAGCAGGT -s Anc2.Anc2refChr1 8050 34 + 142988 AA-ATGGG-----AACTATGGTTATGACA---TGCCAGCAGGT -s mr.mrrefChr3 32728 43 + 181027 AAAATGGACTGTAGACCATGGTTTTGACATGGTGCCAGTAGAT -s simCow_chr6.simCow.chr6 464735 34 + 602619 AA-ATGGC-----AACTATCATTATGACA---TGCTGGCAGGT -s simDog_chr6.simDog.chr6 454901 34 + 593897 AA-ATGGG-----AACTATGGTAATGACA---TGCCACCAGTT -s simHuman_chr6.simHuman.chr6 461733 39 + 601863 AA-TTGGGTAACAGACCATGGTTATGACA---TGCCAGCAAGT -s simRat_chr6.simRat.chr6 486949 42 + 647215 AA-GTACACTGTAGACCATGGTCTTGATGTGGTGCGAGTAGAT - -a -s simMouse_chr6.simMouse.chr6 478527 8 + 636262 ATCTCTAA -s Anc0.Anc0refChr3 96763 8 + 222631 ATCGCTAA -s Anc1.Anc1refChr6 129847 8 + 197743 ATCGCTAA -s Anc2.Anc2refChr1 8085 8 + 142988 ATCGCTAA -s mr.mrrefChr3 32771 8 + 181027 ATCTCTAA -s simCow_chr6.simCow.chr6 464770 8 + 602619 ATCGCTTA -s simDog_chr6.simDog.chr6 454936 6 + 593897 AT--TTAA -s simHuman_chr6.simHuman.chr6 461773 8 + 601863 ATGGCTGA -s simRat_chr6.simRat.chr6 486991 8 + 647215 ATCTCTAA - -a -s simMouse_chr6.simMouse.chr6 478535 135 + 636262 AGCCTCGTGCTTTTCCCCTTAATTGCAGGTCAGACCAGTAGGCTATTGAATGTGCTAATCAAGGCGAGTCAAGAATATTATTGGATAGACTAAGTTTGTTGTCCACACTACCTCATTATGCAGTGAGCTACCAAT -s Anc0.Anc0refChr3 96772 116 + 222631 AGCCTCATGTGTATCCTCTCAGTTACAGGTATGA------------------GGCCAATCAAGGCAAATCAACATTACTATTGGATAGACTAAGG-TATTCTAGACAGTACCTCCTTATGTATCAAGGTACCCAT -s Anc1.Anc1refChr6 129856 116 + 197743 AGCCTCATGTGTATCCTCTCAGTTACAGGTATGA------------------GGCCAATCAAGGCAAATCAACATTACTATTGGATAGACTAAGG-TATTCTAGACAGTACCTCCTTATGTATCAAGGTACCCAT -s Anc2.Anc2refChr1 8094 116 + 142988 AGCCTCATGTGCATCCTCTCAGTTACAGGTATGA------------------GGCCAATCAAGGCAAAGCAACATTACTATTGGATAGACCAAGG-TATTCTAGACAGAGCCTCCTTATGTAGCAAGGTACCCAT -s mr.mrrefChr3 32779 135 + 181027 AGCCTCGTGCATGTCCGCTTAATTGCAGGTGTGACCAGTAGGCTATTGAATGTGCTAATCAAGGCAAGTCAAGAATATTATTGGATAGACTAAGGTTGTTCTCCACACTACCTCATTATGCATCAAGCTACCAAT -s simCow_chr6.simCow.chr6 464779 116 + 602619 GGCCTCATATGAATTCTCCCACTTACAGGTGGGA------------------GGCCAATCAAGGCAAAGCAACATTATTATTGGATAGACCAAGG-TGATCTAGACAGAGCTGCCTTATGTGGCAAGGTACCCAT -s simDog_chr6.simDog.chr6 454943 116 + 593897 AGCCTCATGTGCATCCTCTCAGTTACAGGTATGA------------------GGCCAATCAAGGCAATGCAACACCCCTATTGGATAGACCAAGG-TATTCCCGACAGAGCCTCCCTGTGTAGAAAGGTACCCAT -s simHuman_chr6.simHuman.chr6 461782 83 + 601863 AGCTTCAGGTGT---------------------------------------------------GCAAATCAACATTAATATTAGGTAAACTAAGG-TATTCTAGATTGTACCTCCTTATGTATCAAGGTACCCAT -s simRat_chr6.simRat.chr6 486999 135 + 647215 AACCTCGTGCATGTCCGCTTAATTGCGGGTGTGACAAGTAGGCTATTGAATGTGCTAATCAAGGCAAGTTGAGAATATTGTTGGATAGACTAAGGTTGTTCTCCACACTACCTCGTGATGAATCAAGTTACCAAT - -a -s simMouse_chr6.simMouse.chr6 478670 37 + 636262 AATTATTTCAACCACTACACAACCCATGAGCTTTTGT -s Anc0.Anc0refChr3 96889 30 + 222631 AATCATTGCAACCAATA-------CATGACCCTTTAA -s Anc1.Anc1refChr6 129973 30 + 197743 AATCATTGCAACCAATA-------CATGACCCTTTAA -s Anc2.Anc2refChr1 8211 30 + 142988 AATCATAGCAACTAATA-------CATGACCCTTTAA -s mr.mrrefChr3 32914 37 + 181027 AATTATTTCAACCACTACACAACCCATGAGCTTTTGT -s simCow_chr6.simCow.chr6 464896 28 + 602619 AATCATAGCAATA--TA-------CATGACCAACTAA -s simDog_chr6.simDog.chr6 455060 30 + 593897 AATCATAGCACCTAATA-------CATGACCCTTTAA -s simHuman_chr6.simHuman.chr6 461866 30 + 601863 AATCGTTACAACCAGTC-------TGTGATCCTTTAA -s simRat_chr6.simRat.chr6 487134 37 + 647215 AATTATTGCATGCAATACACAACCCATGACCTTCTGT - -a -s simMouse_chr6.simMouse.chr6 478707 24 + 636262 TGGGGCCACACACACTGCATTTTG -s Anc0.Anc0refChr3 96919 21 + 222631 TAG---TTCATTCATGGCATTTAT -s Anc1.Anc1refChr6 130003 21 + 197743 TAG---TTCATTCATGGCATTTAT -s Anc2.Anc2refChr1 8245 21 + 142988 TAG---TTCATTCATGGCTTTTAT -s mr.mrrefChr3 32951 24 + 181027 TGGGGCTACACACACTGCATTTTG -s simCow_chr6.simCow.chr6 464928 21 + 602619 TAC---TTCATTTATAGCTTTCAT -s simDog_chr6.simDog.chr6 455094 21 + 593897 TAG---TTCATTCATGACTTTTAT -s simHuman_chr6.simHuman.chr6 461896 16 + 601863 TAG---TTCATTCATGGCA----- -s simRat_chr6.simRat.chr6 487171 24 + 647215 TGCGGCTACACACACTGCAATCTG - -a -s simMouse_chr6.simMouse.chr6 478731 16 + 636262 AAAAGTGTCTACAATT -s Anc0.Anc0refChr3 96940 16 + 222631 AGGGGCACATACATTG -s Anc1.Anc1refChr6 130024 16 + 197743 AGGGGCACATACATTG -s Anc2.Anc2refChr1 8266 16 + 142988 AGGGGCACATACATTG -s mr.mrrefChr3 32975 16 + 181027 AAAAGTGTCTACAATT -s simCow_chr6.simCow.chr6 464950 16 + 602619 AGGGCCATATACATTG -s simDog_chr6.simDog.chr6 455115 16 + 593897 AGGGGCACATACATTG -s simHuman_chr6.simHuman.chr6 461912 7 + 601863 ---------TATATCG -s simRat_chr6.simRat.chr6 487195 16 + 647215 AATGGGGTCTACAATT - -a -s simMouse_chr6.simMouse.chr6 478747 11 + 636262 GAATTTTTCTT -s Anc0.Anc0refChr3 96956 11 + 222631 GATCTTTTGTT -s Anc1.Anc1refChr6 130040 11 + 197743 GATCTTTTGTT -s Anc2.Anc2refChr1 8296 11 + 142988 GATCTTTAGTT -s mr.mrrefChr3 32991 11 + 181027 GAACTTTTCTT -s simCow_chr6.simCow.chr6 464980 11 + 602619 GATCTCTGCTT -s simDog_chr6.simDog.chr6 455145 11 + 593897 GATCTTTAGTT -s simHuman_chr6.simHuman.chr6 461919 11 + 601863 GGGCCGTTTCT -s simRat_chr6.simRat.chr6 487211 11 + 647215 GAACTTTTCTT - -a -s simMouse_chr6.simMouse.chr6 478758 28 + 636262 TGTTTAAGGTTGGATGCTGTTGAAATTG -s Anc0.Anc0refChr3 96967 24 + 222631 TCTTCAAGGTTGAAAGTTATT----TTG -s Anc1.Anc1refChr6 130051 24 + 197743 TCTTCAAGGTTGAAAGTTATT----TTG -s Anc2.Anc2refChr1 8312 24 + 142988 TCTTCAAGGTTGACAGTTATT----TTC -s mr.mrrefChr3 33002 28 + 181027 TGTTCAAGGTTGGATGCTGTTGAAATTG -s simCow_chr6.simCow.chr6 465000 23 + 602619 TCTTTTAGGTC-ATAATTACT----TTC -s simDog_chr6.simDog.chr6 455161 24 + 593897 TTTTCAAGATTGACAGTTATT----TTC -s simHuman_chr6.simHuman.chr6 461930 24 + 601863 TCTTCAAGGTTGAAAGTTATC----TTG -s simRat_chr6.simRat.chr6 487222 28 + 647215 TGTTCAAGGATGGATGCCGTTGAAATTG - -a -s simMouse_chr6.simMouse.chr6 478786 11 + 636262 AATGAATGTTT -s Anc0.Anc0refChr3 96992 11 + 222631 AATGAGTGTTT -s Anc1.Anc1refChr6 130076 11 + 197743 AATGAGTGTTT -s Anc2.Anc2refChr1 8337 11 + 142988 AATGAGTGTTT -s mr.mrrefChr3 33030 11 + 181027 AATGAGTGTTT -s simCow_chr6.simCow.chr6 465024 11 + 602619 TATGAGTGTTT -s simDog_chr6.simDog.chr6 455186 6 + 593897 A-----TGTTT -s simHuman_chr6.simHuman.chr6 461955 11 + 601863 AATAAGTGTAT -s simRat_chr6.simRat.chr6 487250 11 + 647215 AATGAGTATTT - -a -s simMouse_chr6.simMouse.chr6 478797 2 + 636262 CA -s Anc0.Anc0refChr3 97003 2 + 222631 CA -s Anc1.Anc1refChr6 130087 2 + 197743 CA -s Anc2.Anc2refChr1 8349 2 + 142988 AA -s mr.mrrefChr3 33041 2 + 181027 CA -s simCow_chr6.simCow.chr6 465036 2 + 602619 AA -s simDog_chr6.simDog.chr6 455193 2 + 593897 AA -s simHuman_chr6.simHuman.chr6 461966 2 + 601863 CA -s simRat_chr6.simRat.chr6 487261 2 + 647215 GA - -a -s simMouse_chr6.simMouse.chr6 478799 51 + 636262 GTGACATGCCACTATAAGTGTTACCATCAGTTTGGAGGGAGGTAGGTTTCT -s Anc0.Anc0refChr3 97007 50 + 222631 GGGACATGCCACTATGAGTGTTAGTATCAGCTTGGAGAACAG-AGGTTTCT -s Anc1.Anc1refChr6 130091 50 + 197743 GGGACATGCCACTATGAGTGTTAGTATCAGCTTGGAGAACAG-AGGTTTCT -s Anc2.Anc2refChr1 8353 50 + 142988 GGGACATGCCACTATGAGTGTTAGTATCAGCTTGGAGGACAG-AGGCTTCT -s mr.mrrefChr3 33043 51 + 181027 GTGACATGCCACTATAAGTGTTACCATCAGTTTGGAGAGAGGTAGGTTTCT -s simCow_chr6.simCow.chr6 465040 50 + 602619 AGGAGCTGCCCCTATGAGTGTTAGTATCAGTTTGTAGGACAG-AGGACTCT -s simDog_chr6.simDog.chr6 455197 50 + 593897 GAGACATGCCACTATGAGTGCTAGTATCAGCTTAGAGGACTG-AAGCTTCT -s simHuman_chr6.simHuman.chr6 461970 50 + 601863 GGGACATGTCACTATGAGTGTTAGTATCAACTTGGAGAACAG-AGGTTCCT -s simRat_chr6.simRat.chr6 487263 51 + 647215 GTGACATGCCACTATAAGTGTTACCATTAGTCTGGAGAGTGTTGGGTTTCT - -a -s simMouse_chr6.simMouse.chr6 478850 25 + 636262 ATCCATCCGACTGCCTTCAGATAGA -s Anc0.Anc0refChr3 97057 25 + 222631 AACCACATGATTGCCGTCAGGTGGG -s Anc1.Anc1refChr6 130141 25 + 197743 AACCACATGATTGCCGTCAGGTGGG -s Anc2.Anc2refChr1 8403 25 + 142988 AACTACATGATTGCGGTTAGGTGGG -s mr.mrrefChr3 33094 25 + 181027 ATCCACCCGACTGCCTTCAGATAGA -s simCow_chr6.simCow.chr6 465090 25 + 602619 AAGTACATGATTGCGGTTAGGTGGG -s simDog_chr6.simDog.chr6 455248 14 + 593897 AACTACATAATTCC----------- -s simHuman_chr6.simHuman.chr6 462020 25 + 601863 AACCACATGATTGCCCACAGGTGGG -s simRat_chr6.simRat.chr6 487314 10 + 647215 AGCCACCAGA--------------- - -a -s simMouse_chr6.simMouse.chr6 478875 14 + 636262 GGTAACTTTTCTAG -s Anc0.Anc0refChr3 97082 14 + 222631 GGTAACTGTTCTAG -s Anc1.Anc1refChr6 130166 14 + 197743 GGTAACTGTTCTAG -s Anc2.Anc2refChr1 8428 14 + 142988 GGTAACTGTTCTAG -s mr.mrrefChr3 33119 14 + 181027 GGTAACTTTTCTAG -s simCow_chr6.simCow.chr6 465117 14 + 602619 GGCAACTCTTCTAA -s simDog_chr6.simDog.chr6 455262 13 + 593897 -GTAACTGTTCTAG -s simHuman_chr6.simHuman.chr6 462045 14 + 601863 GGTAGCTGTTCTAG -s simRat_chr6.simRat.chr6 487324 6 + 647215 --------TTCTAG - -a -s simMouse_chr6.simMouse.chr6 478889 27 + 636262 GGCAGACACTACATTCACTTATCTTCA -s Anc0.Anc0refChr3 97107 27 + 222631 GGTAGTCACTTCATCCACTTATCTCCA -s Anc1.Anc1refChr6 130191 27 + 197743 GGTAGTCACTTCATCCACTTATCTCCA -s Anc2.Anc2refChr1 8453 27 + 142988 AGTAGTCACTTCACCCACTTATCTCAG -s mr.mrrefChr3 33133 27 + 181027 GGCAGACACTTCATTCACTTATCTTCA -s simCow_chr6.simCow.chr6 465142 27 + 602619 ATTAGTCACTTCACACATTTATGTCAG -s simDog_chr6.simDog.chr6 455286 27 + 593897 AGTAGTCACTTCACCCACTTGTCTCAA -s simHuman_chr6.simHuman.chr6 462070 27 + 601863 GGTAGTCTCTTCATCTACTTATCCACA -s simRat_chr6.simRat.chr6 487330 27 + 647215 GGCAGACCCTTTGTTCGCTTATCTGCA - -a -s simMouse_chr6.simMouse.chr6 478916 12 + 636262 CTCTACCTATGG -s Anc0.Anc0refChr3 97134 12 + 222631 CTCTACCTATGC -s Anc1.Anc1refChr6 130218 12 + 197743 CTCTACCTATGC -s Anc2.Anc2refChr1 8480 12 + 142988 CCCTACCTATGC -s mr.mrrefChr3 33160 12 + 181027 CTCTACCTATGG -s simCow_chr6.simCow.chr6 465169 12 + 602619 CCCTACCTATGC -s simDog_chr6.simDog.chr6 455313 12 + 593897 CCCTCCCTATGT -s simHuman_chr6.simHuman.chr6 462127 12 + 601863 CTCTACTTATGC -s simRat_chr6.simRat.chr6 487357 12 + 647215 CTCTACCTATGG - -a -s simMouse_chr6.simMouse.chr6 478928 31 + 636262 TATGTGAAAAATCAGCTCATAATCAAGAGTA -s Anc0.Anc0refChr3 97146 31 + 222631 TATGTGATACATTAGCTCATAATAAACAACA -s Anc1.Anc1refChr6 130230 31 + 197743 TATGTGATACATTAGCTCATAATAAACAACA -s Anc2.Anc2refChr1 8492 31 + 142988 TATCTGATACATTAGCGCATAATAAACAACA -s mr.mrrefChr3 33172 31 + 181027 TATGTGATAAATCAGCTCATAATCAAGAATA -s simCow_chr6.simCow.chr6 465182 31 + 602619 TGTTTGATACGTTTGCGCATAATAACAAGCA -s simDog_chr6.simDog.chr6 455325 31 + 593897 TAACTGATACATTAGCGCATAATTAACCATA -s simHuman_chr6.simHuman.chr6 462139 31 + 601863 TATGTGATACAGTAGCTCACAATAAACAACA -s simRat_chr6.simRat.chr6 487369 31 + 647215 TATGTGATAAATCAGCCCATAATCAAGAATA - -a -s simMouse_chr6.simMouse.chr6 478959 21 + 636262 AAAAGTGATGGAACACGCTTG -s Anc0.Anc0refChr3 97177 21 + 222631 AAATGCAATTAGACATGTTTA -s Anc1.Anc1refChr6 130261 21 + 197743 AAATGCAATTAGACATGTTTA -s Anc2.Anc2refChr1 8523 21 + 142988 AAATGCAATTAGACATGTTTA -s mr.mrrefChr3 33203 21 + 181027 AAAAGTAATTGAACACGCTTG -s simCow_chr6.simCow.chr6 465219 21 + 602619 AGAAGCAATTAGACGTGTTTA -s simDog_chr6.simDog.chr6 455356 21 + 593897 GAATGCAGATAGACATGTTTA -s simHuman_chr6.simHuman.chr6 462170 21 + 601863 AAATGCAATTAGACATGTTTA -s simRat_chr6.simRat.chr6 487400 21 + 647215 AAAAGTAATTGAACACACTTG - -a -s simMouse_chr6.simMouse.chr6 478980 70 + 636262 GAAGACAATGAGTGTCCCCAAATCCATTTGACTTGGCAGGCTAGCAAATTTGTGATCTAGTTTTCTTCTC -s Anc0.Anc0refChr3 97198 70 + 222631 GAGGCTAATGAGTCTCCCCAAATCTATTTCACTTGGCAGGCTTGCAAATTTGTGATCCAGTTTTCTTCTT -s Anc1.Anc1refChr6 130282 70 + 197743 GAGGCTAATGAGTCTCCCCAAATCTATTTCACTTGGCAGGCTTGCAAATTTGTGATCCAGTTTTCTTCTT -s Anc2.Anc2refChr1 8544 70 + 142988 GAGGCTAATGAGTCTCCCCAAATCTATTTCCCTTGGCAGGCTTGCAAATTTGGGATCCAGTTTTCTTCTT -s mr.mrrefChr3 33224 70 + 181027 GAAGACAATGAGTGTCCCCAAATCCATTTGACTTGGCAGGCTAGCAAATTTGTGATCTAGTTTTCTTCTT -s simCow_chr6.simCow.chr6 465240 70 + 602619 AAGGCTAGTGAGTGTCCTCAAATCTAGTTCCTTTGACAGGCTTGCAAATTTGCAATCCAGTTTTCTTCAT -s simDog_chr6.simDog.chr6 455377 70 + 593897 GAGGCCAACAAGTCCCCCCCAATCCATTGCCCTGGGCATGCTTGCTAATTCGGGATCCAGTTTCCTTCTT -s simHuman_chr6.simHuman.chr6 462191 70 + 601863 GTCCCTAATGAGTTTTCCCAAATCTATTTCACTTGGCAGGCTTGCAAACTTTTGAACCAGTTTTCCTCTT -s simRat_chr6.simRat.chr6 487435 70 + 647215 TAAGACAATGAGTGTCCCCAAATCCATTTTACTTGGGGGGCTCGCAAATTTGTGATCTGGTTTTCTTGTT - -a -s simMouse_chr6.simMouse.chr6 479050 39 + 636262 TGCCAGATTGTGATAGTGGTACAGGATGGCCATGGTATG -s Anc0.Anc0refChr3 97268 39 + 222631 TGTCAGGGTCTCACAATGGTATAAGATGATCAGGGAATG -s Anc1.Anc1refChr6 130352 39 + 197743 TGTCAGGGTCTCACAATGGTATAAGATGATCAGGGAATG -s Anc2.Anc2refChr1 8614 39 + 142988 AGTGAGGGTCTCACAAAACCATAAGATGATCAGGGAATG -s mr.mrrefChr3 33294 39 + 181027 TGCCAGATTGTGACAGTGGTACAGGATGGCCATGGTATG -s simCow_chr6.simCow.chr6 465310 37 + 602619 AGTTAGGGTCTCACCAACAGAT--GATGATCAGAGAATG -s simDog_chr6.simDog.chr6 455447 39 + 593897 AGGGAGGGTTTCACAAAACCATAAGATTATCGGGGAATG -s simHuman_chr6.simHuman.chr6 462278 39 + 601863 TGGCAGGGTCTCGCAATGGTATGAGATGATCAAGAAAGG -s simRat_chr6.simRat.chr6 487505 39 + 647215 TGCCAAATTGTGACAGAGGTACAGGATAGCCAGTGCATA - -a -s simMouse_chr6.simMouse.chr6 479089 20 + 636262 GCTCTGGGCTTTAGGGACTG -s Anc0.Anc0refChr3 97307 19 + 222631 G-TCTGGGCTCTAGGGCCTG -s Anc1.Anc1refChr6 130391 19 + 197743 G-TCTGGGCTCTAGGGCCTG -s Anc2.Anc2refChr1 8653 19 + 142988 G-TGTGGGCTCTAGGGCCTG -s mr.mrrefChr3 33333 20 + 181027 GCTCTGGGCTTTAGGGACTG -s simCow_chr6.simCow.chr6 465348 19 + 602619 G-TGTGAGCTCTAGGGCCTG -s simDog_chr6.simDog.chr6 455486 14 + 593897 -----AGGCTCT-AGACCTG -s simHuman_chr6.simHuman.chr6 462317 19 + 601863 G-TCTGGGCTCTCGGGCCTC -s simRat_chr6.simRat.chr6 487544 20 + 647215 GCTCTGAGCTTTAGGGACTG - -a -s simMouse_chr6.simMouse.chr6 479109 5 + 636262 TCTCA -s Anc0.Anc0refChr3 97327 5 + 222631 TACTA -s Anc1.Anc1refChr6 130411 5 + 197743 TACTA -s Anc2.Anc2refChr1 8673 5 + 142988 TACTG -s mr.mrrefChr3 33354 5 + 181027 TCTCA -s simCow_chr6.simCow.chr6 465368 5 + 602619 TTCGG -s simDog_chr6.simDog.chr6 455501 5 + 593897 TACTG -s simHuman_chr6.simHuman.chr6 462337 5 + 601863 TAATA -s simRat_chr6.simRat.chr6 487565 5 + 647215 TCCCA - -a -s simMouse_chr6.simMouse.chr6 479114 30 + 636262 TTTTCAACAGAAGAGGGTTGAAGGACTCTG -s Anc0.Anc0refChr3 97332 30 + 222631 CTTTTAACAAAAGAGGAGTGAAGACTTCTC -s Anc1.Anc1refChr6 130416 30 + 197743 CTTTTAACAAAAGAGGAGTGAAGACTTCTC -s Anc2.Anc2refChr1 8680 30 + 142988 CTCTTAACAAAAGAGGAGTGAAGACTCCTG -s mr.mrrefChr3 33359 30 + 181027 TTTTCAACAGAAGAGGGTTGAAGGATTCTC -s simCow_chr6.simCow.chr6 465375 29 + 602619 CTC-TAACAAAAGAGGAGTGAAGACCCCTG -s simDog_chr6.simDog.chr6 455508 26 + 593897 CTCT----AAAGGAGGAGTTAAGGCTCCTG -s simHuman_chr6.simHuman.chr6 462342 30 + 601863 CTTTTGACAAAAGAGGAGTGAGAACTTCAC -s simRat_chr6.simRat.chr6 487570 30 + 647215 TTCTCAAGAGGAGAGGGTTGAAGGATTCTC - -a -s simMouse_chr6.simMouse.chr6 479144 30 + 636262 CCATGCAATAACTCTGGATCAGTCTAAGAC -s Anc0.Anc0refChr3 97362 30 + 222631 CCACGGAACAGCACTGGATCCATCTAAGAC -s Anc1.Anc1refChr6 130446 30 + 197743 CCACGGAACAGCACTGGATCCATCTAAGAC -s Anc2.Anc2refChr1 8710 30 + 142988 CCACATAACAGCACTGGATTCAACTAATAT -s mr.mrrefChr3 33389 30 + 181027 CCATGGAATAACACTGGATCAATCTAAGAC -s simCow_chr6.simCow.chr6 465421 30 + 602619 CCACACAATAGTGCTTGATTCAATTCATAT -s simDog_chr6.simDog.chr6 455534 25 + 593897 CCACATGTC-GCACTGGATTCAACTA---- -s simHuman_chr6.simHuman.chr6 462372 30 + 601863 CCGCGGAACAGCACTGGATCCATCTAAGAC -s simRat_chr6.simRat.chr6 487600 30 + 647215 CCATGGAATACCACTGGACCAATCAACGAA - -a -s simMouse_chr6.simMouse.chr6 479174 127 + 636262 ATTTGGAATGTGCACTGGAGATGCTTCTGTCTTCACAAAAATGTAATTACAGCTTCTTATACAATGTCAATGTTAACTTGATCTGAATGCAGCTTTACCGCTATGCACATAAGGCGTGGGCAGAGAA -s Anc0.Anc0refChr3 97392 96 + 222631 ATTTCGAATCTGCACAGGAGATGTTAATGTTTTTGCAAAGATGAAATTACTGCTTC----------TCAATGCAGACTG---------------------CTATGTACATAAGTGGTAGGCAGGGCA -s Anc1.Anc1refChr6 130476 96 + 197743 ATTTCGAATCTGCACAGGAGATGTTAATGTTTTTGCAAAGATGAAATTACTGCTTC----------TCAATGCAGACTG---------------------CTATGTACATAAGTGGTAGGCAGGGCA -s Anc2.Anc2refChr1 8740 96 + 142988 ATTTCAAAACTGCACAGGAGATGGTAATGTTCTTGCAAAGATGACACCACTGCTCC----------TCAATGCAGACTG---------------------CTATGTACATAAGTGGTAGGCAGGGCA -s mr.mrrefChr3 33419 106 + 181027 ATTTGGAATGTGCACTGGAGATGTTAATGTCTTCACAAAAATGTAATTACAGCTTCTTATACAATGTCAATGTTAACTT---------------------CTATGCACATAAGGGGTGGGCAGAGAA -s simCow_chr6.simCow.chr6 465456 90 + 602619 ATTTCAAAACTGGACAGGAGATGGTA------TTGAAAAGATGAGACCACAGCTCC----------TCAATGCAGACCA---------------------CAATGTACATAGAAGGTAGGCAGGACA -s simDog_chr6.simDog.chr6 455559 83 + 593897 ---------CTGCACAGGACATGGTGATGTTCTAGCAAGGATGACA----TGCTCC----------TCATTGTACACTG---------------------CTATGTACCTAAGTGGTAGGCAGGGCA -s simHuman_chr6.simHuman.chr6 462402 96 + 601863 CTTTTGAATCTGCACAGGAGATGTTAATGTTTTTGCAAAGATGAAATTTCTGCTTC----------TCAATGCAGACTG---------------------CTATGTACACCTGTGGTAGGCAGGGCA -s simRat_chr6.simRat.chr6 487630 106 + 647215 AATTAGAATGTGCACTGGAGATGTTAATATCTTCATAAAAATGTAATTACAGCCTCTTACTCAATGTCAATGTCAATTT---------------------CTATGCACATAAGGGGTGGGTAGAGAA - -a -s simMouse_chr6.simMouse.chr6 479301 97 + 636262 TCCCAAATATAGACCATCTCTCTAGCCCCAATGCCCAGCTGCTGTAATGCACATAGAGGTCGTATTAAAGGAACATTTAAGAAGATACACACTTTTC -s Anc0.Anc0refChr3 97488 94 + 222631 TACAAAATATAAATCATCTTTTTTGCACCAATGCCAAGCTGCTGTAGT--ACACAGAGGTCCTACTAAAAGAACATTCAATCAGACTGACACCCTT- -s Anc1.Anc1refChr6 130572 95 + 197743 TACAAAATATAAATCATCTTTTTTGCACCAATGCCAAGCTGCTGTAGT--ACACAGAGGTCCTACTAAAAGAACATTCAATCAGACTGACACCCTTC -s Anc2.Anc2refChr1 8836 94 + 142988 TACAAAATATAAATCATTGTTTTTGCACCAATGCCAGGCTGCTGTAGT--ACACAGAGGTCCTATGAAAAGAACATTCAATCAGACTGACACCCTT- -s mr.mrrefChr3 33525 97 + 181027 TCCCAAATATAGACCATCTCTCTAGCCCCAATGCCAAGCTGCTGTAGTGCACACAGAGGTCGTACTAAAGGAACATTTAAGAAGATACACACTTTTC -s simCow_chr6.simCow.chr6 465546 93 + 602619 TACACAATATAAATCAG-GTTTTAGGACCAATGCCAGACTGCTGTAGT--AAACAGAGATCGTATCAAATGATCATTCAATGGAACAGACATCTTT- -s simDog_chr6.simDog.chr6 455643 94 + 593897 TACAAAATATAAATCATTGTTTTTGCACCAATGCCAGGCTGCTGTTGC--ACACAGAGGTCCTGTGAAAAGAACATTCAATCAGACTGACACCCTT- -s simHuman_chr6.simHuman.chr6 462498 80 + 601863 TACAAAATATAAATCATCTTTTTGGCTCCAATGCCAAGGTACTGTAGT--ACACAGAAGTCCTACTAAAACAAGATTCA---------------TTC -s simRat_chr6.simRat.chr6 487736 83 + 647215 TTCCAAATATAGACCATCTC--------------CAAGCTGCTATAGTGTACACAGAGGCCAAACTAAAGGAACATTTAAGAAGATACATATCTGTC - -a -s simMouse_chr6.simMouse.chr6 479398 16 + 636262 ATGCCCCTTACACTAG -s Anc0.Anc0refChr3 97582 16 + 222631 AAGCCCATTTTAGTAT -s Anc1.Anc1refChr6 130667 16 + 197743 AAGCCCATTTTAGTAT -s Anc2.Anc2refChr1 8930 16 + 142988 AAGTACATTTTAGTAT -s mr.mrrefChr3 33622 16 + 181027 AAGCCCCTTACACTAT -s simCow_chr6.simCow.chr6 465639 11 + 602619 -----CAATTTAGTAT -s simDog_chr6.simDog.chr6 455738 16 + 593897 AAGTACATTTTAGTAT -s simHuman_chr6.simHuman.chr6 462578 16 + 601863 AAGCCCGTTTTAGTAT -s simRat_chr6.simRat.chr6 487819 15 + 647215 AAGCCCCTTAC-CTAT - -a -s simMouse_chr6.simMouse.chr6 479414 12 + 636262 TTCATCTGAACC -s Anc0.Anc0refChr3 97611 12 + 222631 TTAGTCTGAATC -s Anc1.Anc1refChr6 130696 12 + 197743 TTAGTCTGAATC -s Anc2.Anc2refChr1 8959 12 + 142988 TTAGTCTGAATC -s mr.mrrefChr3 33638 12 + 181027 TTAGTCTGAATC -s simCow_chr6.simCow.chr6 465663 12 + 602619 TTGGTCTGAATC -s simDog_chr6.simDog.chr6 455767 12 + 593897 TTAGTCTGACTC -s simHuman_chr6.simHuman.chr6 462607 12 + 601863 TTAGTCTGAATC -s simRat_chr6.simRat.chr6 487834 12 + 647215 TTAGTCGGAATC - -a -s simMouse_chr6.simMouse.chr6 479426 66 + 636262 TGACTCTCTATTTATTGTCCAATGATGGTGGGCCCCCGATTTAGTGTCTGCTTATCGTATTCATGC -s Anc0.Anc0refChr3 97624 36 + 222631 TGATTGTATCTTTATTGTCCAATGATGGTG--------------------------G----CATCC -s Anc1.Anc1refChr6 130709 36 + 197743 TGATTGTATCTTTATTGTCCAATGATGGTG--------------------------G----CATCC -s Anc2.Anc2refChr1 8973 36 + 142988 TGACTGTATCCTTAACTTCCAATGATAGTG--------------------------G----CATCC -s mr.mrrefChr3 33650 62 + 181027 TGATTCTCTATTTATTGTCCAATGATGGTGGGCCCCCGATTTAGTGTCTGCTTATCG----CATGC -s simCow_chr6.simCow.chr6 465677 36 + 602619 TGACTGCCTTCTTAACTTCCAATGATAGTG--------------------------G----CATCC -s simDog_chr6.simDog.chr6 455781 10 + 593897 TTTCTGTATC-------------------------------------------------------- -s simHuman_chr6.simHuman.chr6 462620 36 + 601863 TGATTGTATCTTTATTGTTCAATGATGGTG--------------------------G----CATTC -s simRat_chr6.simRat.chr6 487846 57 + 647215 TGATTCTCAATTCGTTGCCCCATGGTGGTGGGCCCCCGATTTAACGTCTGCTTATTG--------- - -a -s simMouse_chr6.simMouse.chr6 479492 15 + 636262 AATTTCAGTCTTATT -s Anc0.Anc0refChr3 97660 15 + 222631 AATCTTAGTCTTATT -s Anc1.Anc1refChr6 130745 15 + 197743 AATCTTAGTCTTATT -s Anc2.Anc2refChr1 9009 15 + 142988 AATCTTAGTCTTATT -s mr.mrrefChr3 33712 15 + 181027 AATTTCAGTCTTATT -s mr.mrrefChr3 33934 15 + 181027 AAACTCACCTTTATT -s simCow_chr6.simCow.chr6 465713 15 + 602619 AATCTTAGTCTTATT -s simHuman_chr6.simHuman.chr6 462656 15 + 601863 AATTTTAGTCTTATT -s simMouse_chr6.simMouse.chr6 479721 15 + 636262 AAACTCACCTTTATT -s simRat_chr6.simRat.chr6 487995 15 + 647215 AAGCTCACTTTTATT - -a -s simMouse_chr6.simMouse.chr6 479507 7 + 636262 GGGTTTG -s Anc0.Anc0refChr3 97675 7 + 222631 GAATTTG -s Anc1.Anc1refChr6 130760 7 + 197743 GAATTTG -s Anc2.Anc2refChr1 9024 7 + 142988 GAATGTG -s mr.mrrefChr3 33727 7 + 181027 GGGTTTG -s mr.mrrefChr3 33951 7 + 181027 ATGGTGC -s simCow_chr6.simCow.chr6 465728 7 + 602619 GAATGTG -s simHuman_chr6.simHuman.chr6 462671 7 + 601863 GAATCTG -s simMouse_chr6.simMouse.chr6 479738 7 + 636262 ATGGTGC -s simRat_chr6.simRat.chr6 488012 7 + 647215 ATGATGC - -a -s simMouse_chr6.simMouse.chr6 479514 31 + 636262 ACATATTAGTGTCTCAAAGTATCGTTTGCAC -s Anc0.Anc0refChr3 97683 31 + 222631 ACATATTAGCTATTAGTAGCATGTTCTGAAC -s Anc1.Anc1refChr6 130768 31 + 197743 ACATATTAGCTATTAGTAGCATGTTCTGAAC -s Anc2.Anc2refChr1 9032 31 + 142988 ACATATTTCCTATTAGTAGCTTGTTCTGAAT -s mr.mrrefChr3 33734 31 + 181027 ACATATTAGTGTCTCAAAGTATCGTTTGCAC -s mr.mrrefChr3 33958 31 + 181027 CCATGTCCACTACTTATTGCAGATTCTGACC -s simCow_chr6.simCow.chr6 465736 31 + 602619 ACATATTTCCTATTAGTAGCTTGTTCTGAAT -s simHuman_chr6.simHuman.chr6 462679 31 + 601863 ACATATTAGCAGTTAGTAGCATTAGTTGCAC -s simMouse_chr6.simMouse.chr6 479745 31 + 636262 CCATGTCCACTACTTATTGCAGATTCTGACC -s simRat_chr6.simRat.chr6 488019 31 + 647215 CCATGTCCACAAATCATTGCAGATTCCAGCC - -a -s simMouse_chr6.simMouse.chr6 479545 7 + 636262 TTTAAAG -s Anc0.Anc0refChr3 97714 7 + 222631 TTCAAAG -s Anc1.Anc1refChr6 130799 7 + 197743 TTCAAAG -s Anc2.Anc2refChr1 9063 7 + 142988 TTCTAAG -s mr.mrrefChr3 33765 7 + 181027 TTTAAAG -s mr.mrrefChr3 33993 7 + 181027 TGCATAA -s simCow_chr6.simCow.chr6 465767 7 + 602619 TTCTAAG -s simHuman_chr6.simHuman.chr6 462710 7 + 601863 TGCAAAG -s simMouse_chr6.simMouse.chr6 479780 7 + 636262 TGCATAA -s simRat_chr6.simRat.chr6 488054 7 + 647215 TGCATAA - -a -s simMouse_chr6.simMouse.chr6 479552 15 + 636262 ATGTACCATGTGGCC -s Anc0.Anc0refChr3 97734 15 + 222631 GTGTACTATGTAGAC -s Anc1.Anc1refChr6 130819 15 + 197743 GTGTACTATGTAGAC -s Anc2.Anc2refChr1 9083 15 + 142988 GCGTACTATGTAGAC -s mr.mrrefChr3 33772 15 + 181027 ATGTACCATGTGGCC -s mr.mrrefChr3 34000 15 + 181027 GTCCACTAATCAAAC -s simCow_chr6.simCow.chr6 465788 15 + 602619 GCGTACTATGTGGTC -s simDog_chr6.simDog.chr6 455791 4 + 593897 -----------AGAG -s simHuman_chr6.simHuman.chr6 462730 15 + 601863 ATGTTCTATGTAGAC -s simMouse_chr6.simMouse.chr6 479787 15 + 636262 GTCCACTAATCAAAC -s simRat_chr6.simRat.chr6 488061 15 + 647215 GTCCCCTAATCAAAT - -a -s simMouse_chr6.simMouse.chr6 479567 12 + 636262 GATCAACTGGCA -s Anc0.Anc0refChr3 97749 12 + 222631 AAGCAACAGGTA -s Anc1.Anc1refChr6 130834 12 + 197743 AAGCAACAGGTA -s Anc2.Anc2refChr1 9098 12 + 142988 AAGCAACAGGTA -s mr.mrrefChr3 33787 12 + 181027 GATCAACTGGCA -s mr.mrrefChr3 34019 12 + 181027 GAAATACTGCCA -s simCow_chr6.simCow.chr6 465803 12 + 602619 AATTAACAGGCA -s simDog_chr6.simDog.chr6 455795 12 + 593897 AGGCACAGACTC -s simHuman_chr6.simHuman.chr6 462745 12 + 601863 AAGCAACAGGTA -s simMouse_chr6.simMouse.chr6 479806 12 + 636262 GAAATACTGCCA -s simRat_chr6.simRat.chr6 488080 12 + 647215 GAAGTACTGCCA - -a -s simMouse_chr6.simMouse.chr6 479579 25 + 636262 ACCACTGTGAGGCTTCTGCCTTTTT -s Anc0.Anc0refChr3 97762 25 + 222631 AAAGCTGTTGAGTTTCTGCCTCTTT -s Anc1.Anc1refChr6 130847 25 + 197743 AAAGCTGTTGAGTTTCTGCCTCTTT -s Anc2.Anc2refChr1 9111 25 + 142988 AAAGCTCTTGAGTTTCTGCCTCTTT -s mr.mrrefChr3 33799 25 + 181027 ACCACTGTGAGGCTTCTGCCTTTTT -s mr.mrrefChr3 34032 24 + 181027 AATGTTAGTGTGTCACTGTCTCTT- -s simCow_chr6.simCow.chr6 465816 25 + 602619 TACACTCTTGAGTCTCCGCCCCTTT -s simDog_chr6.simDog.chr6 455808 18 + 593897 AGAGC-------TTTTTGTCTGTTT -s simHuman_chr6.simHuman.chr6 462758 25 + 601863 AAGGCTGTGGAGTTTCTGCCACTTT -s simMouse_chr6.simMouse.chr6 479819 24 + 636262 AATGTTAGTGTGTCACTGTCTCTT- -s simRat_chr6.simRat.chr6 488093 24 + 647215 AATGTTAATGTGTCACTATATCTT- - -a -s simMouse_chr6.simMouse.chr6 479604 10 + 636262 GTCCCTATAC -s Anc0.Anc0refChr3 97787 10 + 222631 GTCCCTATAC -s Anc1.Anc1refChr6 130872 10 + 197743 GTCCCTATAC -s Anc2.Anc2refChr1 9136 10 + 142988 GTTCCTATGC -s mr.mrrefChr3 33824 10 + 181027 GTCCCTATAC -s simCow_chr6.simCow.chr6 465841 10 + 602619 GTTCCTATGC -s simDog_chr6.simDog.chr6 455935 10 + 593897 GTTCCAATGC -s simHuman_chr6.simHuman.chr6 462783 10 + 601863 GTCCCTATAC - -a -s simMouse_chr6.simMouse.chr6 479614 18 + 636262 ATCCACCATGTAATAGTT -s Anc0.Anc0refChr3 97811 18 + 222631 GTCCACTGTATCAGCATT -s Anc1.Anc1refChr6 130896 18 + 197743 GTCCACTGTATCAGCATT -s Anc2.Anc2refChr1 9160 18 + 142988 GTCCACTGTATCAGCATT -s mr.mrrefChr3 33834 18 + 181027 ATCCACCATGTAATAGTT -s simCow_chr6.simCow.chr6 465865 18 + 602619 GTCCACTGTATCAGCATT -s simDog_chr6.simDog.chr6 455959 18 + 593897 GTCCACGATATCAGCATT -s simHuman_chr6.simHuman.chr6 462807 18 + 601863 GTCCACTGTATCAGCATT -s simRat_chr6.simRat.chr6 487903 10 + 647215 --------CTTAATAGTT - -a -s simMouse_chr6.simMouse.chr6 479632 56 + 636262 CCCCGATCTCAGATTTATCATAACTACCACAACAAATAAATCCTACATACTGTCAG -s Anc0.Anc0refChr3 97829 15 + 222631 CTCCAATCTCAAACT----------------------------------------- -s Anc1.Anc1refChr6 130914 15 + 197743 CTCCAATCTCAAACT----------------------------------------- -s Anc2.Anc2refChr1 9178 15 + 142988 CTCCAACCTCAAACT----------------------------------------- -s mr.mrrefChr3 33852 56 + 181027 CCCCAATCTCAGACTTATCATAACTACCACAACAAATAAATCCTACATACTGTCAG -s simCow_chr6.simCow.chr6 465883 14 + 602619 CTCAAGCC-TGAACT----------------------------------------- -s simDog_chr6.simDog.chr6 455990 15 + 593897 ATCCAACCTCAAACT----------------------------------------- -s simHuman_chr6.simHuman.chr6 462825 15 + 601863 CTCCAATCTCAAACT----------------------------------------- -s simRat_chr6.simRat.chr6 487913 56 + 647215 CCCCAATCTCAGACTTATCATAACTACCACTGCAAATAAATCATATAGACTGTCGG - -a -s simMouse_chr6.simMouse.chr6 479688 5 + 636262 CAAGC -s Anc1.Anc1refChr6 130929 5 + 197743 CAATC -s mr.mrrefChr3 33908 5 + 181027 CAAGC -s mr.mrrefChr3 34056 5 + 181027 CAATC -s simMouse_chr6.simMouse.chr6 479843 5 + 636262 CAATC -s simRat_chr6.simRat.chr6 488117 5 + 647215 CGATC -s simRat_chr6.simRat.chr6 487969 5 + 647215 CAAGC - -a -s simMouse_chr6.simMouse.chr6 479693 28 + 636262 TCACTTTTGTTTCCTATACACTGTCAAC -s Anc0.Anc0refChr3 97844 2 + 222631 --------------------------TT -s Anc1.Anc1refChr6 130934 2 + 197743 --------------------------TT -s Anc2.Anc2refChr1 9193 2 + 142988 --------------------------TT -s mr.mrrefChr3 33913 21 + 181027 TCACTTTT-------ATACACTGTCAAC -s simCow_chr6.simCow.chr6 465897 2 + 602619 --------------------------TG -s simDog_chr6.simDog.chr6 456005 2 + 593897 --------------------------TT -s simHuman_chr6.simHuman.chr6 462840 2 + 601863 --------------------------TT -s simRat_chr6.simRat.chr6 487974 21 + 647215 TCACTTTT-------ATACATTGTCGGC - -a -s simMouse_chr6.simMouse.chr6 479736 2 + 636262 TC -s mr.mrrefChr3 33949 2 + 181027 TC -s simRat_chr6.simRat.chr6 488010 2 + 647215 TC - -a -s simMouse_chr6.simMouse.chr6 479776 4 + 636262 AAAG -s mr.mrrefChr3 33989 4 + 181027 AAAG -s simRat_chr6.simRat.chr6 488050 4 + 647215 AAAG - -a -s simMouse_chr6.simMouse.chr6 479802 4 + 636262 TTAA -s mr.mrrefChr3 34015 4 + 181027 TTAA -s simRat_chr6.simRat.chr6 488076 4 + 647215 TTAA - -a -s simMouse_chr6.simMouse.chr6 479818 1 + 636262 T -s Anc0.Anc0refChr3 97761 1 + 222631 A -s Anc1.Anc1refChr6 130846 1 + 197743 A -s Anc2.Anc2refChr1 9110 1 + 142988 A -s mr.mrrefChr3 34031 1 + 181027 T -s simCow_chr6.simCow.chr6 465815 1 + 602619 A -s simDog_chr6.simDog.chr6 455807 1 + 593897 A -s simHuman_chr6.simHuman.chr6 462757 1 + 601863 A -s simRat_chr6.simRat.chr6 488092 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 479848 95 + 636262 TGCACGTCTGGTAGATACATGTCATTCTTGACCTTGAGCAGTTGATGACTTTATGTATAAAAAGCTTTTACTGATTAATTGATTTTGCTGATTAG -s Anc0.Anc0refChr3 97850 56 + 222631 ---------------------------------------GATTGATGACTTTTGGTATAAGTAGTTTTTACTAATTATCTCAATTGGCTGACTAG -s Anc1.Anc1refChr6 130940 56 + 197743 ---------------------------------------GATTGATGACTTTTGGTATAAGTAGTTTTTACTAATTATCTCAATTGGCTGACTAG -s Anc2.Anc2refChr1 9199 56 + 142988 ---------------------------------------GATTGATTAATTTTGGTATGAGTAGTTTGTACTAACTATCTCAATTGGCTGACTAG -s mr.mrrefChr3 34061 95 + 181027 TGCACGTCTGGTAGATACATGTCATTCTTGACCTTGAGCAGTTGATGACTTTATGTATAAAAAGCTTTTACTGATTAATTGATTTTGCTGATTAG -s simCow_chr6.simCow.chr6 465903 55 + 602619 ---------------------------------------GATTGATTAATTTTGGTATGACCAGTTTGTACTAACTATACCAATTGACTGAC-AG -s simDog_chr6.simDog.chr6 456011 56 + 593897 ---------------------------------------GATCGATTAATTTAGGTCCGTGTAGTTTGTACTACCTATCTTAATTGGCTGACTAC -s simHuman_chr6.simHuman.chr6 462846 56 + 601863 ---------------------------------------GTTTGATGACTTTTGGTATAAGTGGTTTTTACTAATTAGCTCAATTGCCTGAGTAG -s simRat_chr6.simRat.chr6 488122 95 + 647215 TGGACCTTTGGCAGATATATGTCATTATTGACCTTGAACTGTTGATAACTTTATGTATGAAAGGCTTGTCCTGTTTAGTTGAATCTGCTGACTAG - -a -s simMouse_chr6.simMouse.chr6 479943 9 + 636262 TACAAAGTC -s Anc0.Anc0refChr3 97909 9 + 222631 TGCAAAATT -s Anc1.Anc1refChr6 130999 9 + 197743 TGCAAAATT -s Anc2.Anc2refChr1 9258 9 + 142988 TGCAAAATT -s mr.mrrefChr3 34156 9 + 181027 TACAAAGTC -s simCow_chr6.simCow.chr6 465961 9 + 602619 TGTAAAATT -s simDog_chr6.simDog.chr6 456070 9 + 593897 TGCTAAATC -s simHuman_chr6.simHuman.chr6 462905 9 + 601863 TCCAAATTT -s simRat_chr6.simRat.chr6 488217 9 + 647215 TACAAAGTC - -a -s simMouse_chr6.simMouse.chr6 479952 1 + 636262 A -s Anc0.Anc0refChr3 97918 1 + 222631 A -s Anc1.Anc1refChr6 131008 1 + 197743 A -s Anc2.Anc2refChr1 9267 1 + 142988 A -s mr.mrrefChr3 34165 1 + 181027 A -s simCow_chr6.simCow.chr6 465971 1 + 602619 C -s simDog_chr6.simDog.chr6 456081 1 + 593897 A -s simHuman_chr6.simHuman.chr6 462914 1 + 601863 A -s simRat_chr6.simRat.chr6 488226 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 479953 2 + 636262 TT -s Anc0.Anc0refChr3 97949 2 + 222631 TT -s Anc1.Anc1refChr6 131039 2 + 197743 TT -s Anc2.Anc2refChr1 9298 2 + 142988 TT -s mr.mrrefChr3 34166 2 + 181027 TT -s simCow_chr6.simCow.chr6 466002 2 + 602619 TT -s simDog_chr6.simDog.chr6 456112 2 + 593897 TT -s simHuman_chr6.simHuman.chr6 463233 2 + 601863 TT -s simRat_chr6.simRat.chr6 488227 2 + 647215 CT - -a -s simMouse_chr6.simMouse.chr6 479955 13 + 636262 GGCAGTTCTCTAA -s Anc0.Anc0refChr3 97951 13 + 222631 GGCAGTTCTCTAA -s Anc1.Anc1refChr6 131041 13 + 197743 GGCAGTTCTCTAA -s Anc2.Anc2refChr1 9300 13 + 142988 GGCAGTTCTCTTA -s mr.mrrefChr3 34168 13 + 181027 GGCAGTTCTCTAA -s simCow_chr6.simCow.chr6 466004 13 + 602619 GGCTGTTCTCTCA -s simDog_chr6.simDog.chr6 456118 13 + 593897 GGCAGTTTTCTTA -s simHuman_chr6.simHuman.chr6 463235 13 + 601863 GATGGGTCTCTAA -s simRat_chr6.simRat.chr6 488229 13 + 647215 GGCAGTTCCCTAA - -a -s simMouse_chr6.simMouse.chr6 479968 9 + 636262 CTTAAGACA -s Anc0.Anc0refChr3 97965 9 + 222631 CTTGAGACA -s Anc1.Anc1refChr6 131055 9 + 197743 CTTGAGACA -s Anc2.Anc2refChr1 9314 9 + 142988 CATGAGACA -s mr.mrrefChr3 34181 9 + 181027 CTTAAGACA -s simCow_chr6.simCow.chr6 466018 9 + 602619 CATGAGACA -s simDog_chr6.simDog.chr6 456132 9 + 593897 CATGAGACT -s simHuman_chr6.simHuman.chr6 463249 9 + 601863 CTTGAGACA -s simRat_chr6.simRat.chr6 488242 9 + 647215 CTTAAGACA - -a -s simMouse_chr6.simMouse.chr6 479977 22 + 636262 TTATGGGCTCAGGCCCCTTACA -s Anc0.Anc0refChr3 97974 22 + 222631 TTATAGGCTCAGGCCCCTTAAA -s Anc1.Anc1refChr6 131064 22 + 197743 TTATAGGCTCAGGCCCCTTAAA -s Anc2.Anc2refChr1 9323 22 + 142988 TTATAGGCTCAGACCACTTAAA -s mr.mrrefChr3 34190 22 + 181027 TTATGGGCTCAGGCCCCTTACA -s simCow_chr6.simCow.chr6 466038 22 + 602619 TTATAGGCTCAGACCACTTAAA -s simDog_chr6.simDog.chr6 456141 12 + 593897 CGATAACCTCTG---------- -s simHuman_chr6.simHuman.chr6 463258 22 + 601863 TTATAGGTTCAGGCCCCTTAAA -s simRat_chr6.simRat.chr6 488251 22 + 647215 TTATGGGCACAGGCCCCTTACA - -a -s simMouse_chr6.simMouse.chr6 479999 61 + 636262 ACCCATACTTGAAATAAACAGTTTTGACAGCAACTGTCTGAGTTGGAAGTTGCAAGCTCCT -s Anc0.Anc0refChr3 97996 58 + 222631 T-CAATTCTTGAACAAAACAGTTTAG--AACAATTAACCTAATTGGAAATCAGAAGGTCAT -s Anc1.Anc1refChr6 131086 58 + 197743 T-CAATTCTTGAACAAAACAGTTTAG--AACAATTAACCTAATTGGAAATCAGAAGGTCAT -s Anc2.Anc2refChr1 9345 58 + 142988 A-CAGTTCTTGAACAACATGTTTTAC--AATAATTAACCTGATTGGAGATCAGAAGGTCAT -s mr.mrrefChr3 34212 61 + 181027 TCCCATACTTGAAATAAACAGTTTTGACAGCAACTGTCCGAGTTGGAAATCGCAAGCTCCT -s simCow_chr6.simCow.chr6 466062 58 + 602619 A-CAGTTCTTGAACAACATGTTTTAC--AATAATTAACCTGATTGGAGATCAGAAGGTCAT -s simHuman_chr6.simHuman.chr6 463280 58 + 601863 T-CAAGTCTTGAATAAAACAGTTTAG--AACAATTACCCCAATTAGAAATCAGAAGATCAT -s simRat_chr6.simRat.chr6 488273 61 + 647215 TCTCGTACTTGAAATAAACAGTTTTGACTGCTACTGTCCGAGTTCAAAATCGTAAGCTCCT - -a -s simMouse_chr6.simMouse.chr6 480060 23 + 636262 TTTGTGCTGACCTTTGTGGTTGT -s Anc0.Anc0refChr3 98054 9 + 222631 TCTGT--------------TAAT -s Anc1.Anc1refChr6 131144 9 + 197743 TCTGT--------------TAAT -s Anc2.Anc2refChr1 9403 9 + 142988 TCTGT--------------TAAT -s mr.mrrefChr3 34273 23 + 181027 TTTGTGCTGACCTTTGTGGTTGT -s simCow_chr6.simCow.chr6 466132 9 + 602619 TCTGC--------------TGAT -s simDog_chr6.simDog.chr6 456153 6 + 593897 ---CT--------------GAGG -s simHuman_chr6.simHuman.chr6 463338 9 + 601863 TCTGT--------------TAAT -s simRat_chr6.simRat.chr6 488334 23 + 647215 TTTGTGCTGACCCTTGTGCATGT - -a -s simMouse_chr6.simMouse.chr6 480083 155 + 636262 GTGTGGGTTGTTACTTTCAATTAATTGGGTCTCCCAGTTCCCCATGCAATCCTAAAGCACCATGCTCCGTCTAAGCTCCCATCCCGTTCCAGTAAATAAGCAACCTTTGCAGATGCACTCTGAGACCCACCCCACTAAGATAGCCTACACCACTC -s Anc0.Anc0refChr3 98063 125 + 222631 GATTAGGTTGTCACTTTCAATT--ACAGGTCTCCTGG---CATAAGCAGTC-TA--------------GT--AAGCTCCCATCCTGTTCCACTAAACA--------TCATAGATGTGCTCTGAGACCCACCCCCCTAAGATAGTTAACACTACTC -s Anc1.Anc1refChr6 131153 127 + 197743 GATTAGGTTGTCACTTTCAATT--ACAGGTCTCCTGG---CATAAGCAGTC-TA--------------GTCTAAGCTCCCATCCTGTTCCACTAAACA--------TCATAGATGTGCTCTGAGACCCACCCCCCTAAGATAGTTAACACTACTC -s Anc2.Anc2refChr1 9412 125 + 142988 GATTAAATTGTCACTTTTAACT--ACAGGCATCTTGG---CATAATCAGAC-CA--------------AT--AAGCTCCCATCCTATTCCACTAAACA--------TCATAGATGTGCTCTGAGACCCACCCCCCTAAGATAGTTAGCACTACCC -s mr.mrrefChr3 34296 150 + 181027 GTGTGGGTTGTTACTTTCAATTAATCGGGTCTCCCGGT--CCCATGCAATC-TAAAGCACCATGCTCCGTCTAAGCTCCCATCCTGTTCCAGTAAACAAGCAAC--TCACAGATGCACTCTGAGACCCACCCCACTAAGATAGTCTACACCACTC -s simCow_chr6.simCow.chr6 466142 119 + 602619 GATTAAATTGTAACTTTTAACT--ACAGGCATCTTGG---CATAATCAGAC-CA--------------AT--------CCGTCCTATTCCACTAAGCA--------CCACAGATGTGCTCTGGGACCCACCCCCCTAAGATAGTGATCACCACGC -s simDog_chr6.simDog.chr6 456159 86 + 593897 GGTTAAATTGTCACCTTTA-----------------------------------------------------AAGCTCACATTC-ATTCTACTAAACA--------TCAT---TGCATTCTAAGACCCACTCTCCTAAG----TTAGCACTACCT -s simHuman_chr6.simHuman.chr6 463347 127 + 601863 GATTAGGCTGTCACTTCCAATT--CCTGGTCTCCGGG---CATGAGCAGTC-TA--------------GTCTAAGCTCCCATCCTGTTCCACTAAACA--------TCATGGATGTGCTCTGAGACCCACCGCCTTAAGATACTTAACACTACTC -s simRat_chr6.simRat.chr6 488357 150 + 647215 GTGTGGGTTGTAACTTTTACTTGATCAGGTCTCCCGTA--CCCATGCAATC-TAATGCAGCATGCTCAGTCTAAATTCCCGTCCTGTTCCAGTAAACAAGCCAC--TCACAGATACACACTGAGATGCACCCCACTGAGGTAGTCCACACCAGCC - -a -s simMouse_chr6.simMouse.chr6 480238 10 + 636262 AGCTTGCAGT -s Anc0.Anc0refChr3 98191 10 + 222631 AGCTTGTGGT -s Anc1.Anc1refChr6 131283 10 + 197743 AGCTTGTGGT -s Anc2.Anc2refChr1 9540 10 + 142988 ATCTTGTGGT -s mr.mrrefChr3 34446 10 + 181027 AGCTTGCAGT -s simCow_chr6.simCow.chr6 466264 10 + 602619 AATTTGTAGC -s simDog_chr6.simDog.chr6 456248 10 + 593897 ATCTTGTGGT -s simHuman_chr6.simHuman.chr6 463477 10 + 601863 AGGTTGTGGT -s simRat_chr6.simRat.chr6 488507 10 + 647215 AGCTTGCAGT - -a -s simMouse_chr6.simMouse.chr6 480248 44 + 636262 GGAGACTGTTGCTTAATGAACATAGGGGCCTACATAAGTTGGAT -s Anc0.Anc0refChr3 98201 37 + 222631 GGAGACTGTTCCT-AAGGGACATATTGGCTT------GTTGGAG -s Anc1.Anc1refChr6 131293 38 + 197743 GGAGACTGTTCCTTAAGGGACATATTGGCTT------GTTGGAG -s Anc2.Anc2refChr1 9550 37 + 142988 GAAGGCTGTTCCT-AAGGGACATATTGGCTT------GTTGGAG -s mr.mrrefChr3 34456 44 + 181027 GGAGACTGTTCCTTAATGAACATAGGGGCCTACATAAGTTGGAT -s simCow_chr6.simCow.chr6 466286 36 + 602619 AAGGGGTGCT-TT-AAGAGACATATTGGCTT------GTTGGAG -s simDog_chr6.simDog.chr6 456258 37 + 593897 GAAGGCTGTTCCT-TAGGGACATATTGGCTT------GTCGGAG -s simHuman_chr6.simHuman.chr6 463487 35 + 601863 GGAAACAGTTCCTTAAGGGACATATCGGCTT------GTTG--- -s simRat_chr6.simRat.chr6 488517 44 + 647215 GGAGACTGTTCCCTAATGAACATTGTGGTCTACATAAGTTGGAT - -a -s simMouse_chr6.simMouse.chr6 480292 5 + 636262 ACCAT -s Anc0.Anc0refChr3 98238 5 + 222631 GTCAA -s Anc1.Anc1refChr6 131331 5 + 197743 GTCAA -s Anc2.Anc2refChr1 9587 5 + 142988 GTCAA -s mr.mrrefChr3 34500 5 + 181027 ACCAT -s simCow_chr6.simCow.chr6 466322 5 + 602619 GTCAA -s simDog_chr6.simDog.chr6 456295 5 + 593897 GTCAA -s simRat_chr6.simRat.chr6 488565 5 + 647215 ACTAT - -a -s simMouse_chr6.simMouse.chr6 480297 27 + 636262 AGAGGCAACATTTGCCATGGTCAGACT -s Anc0.Anc0refChr3 98243 27 + 222631 AGAGGCGAAATTTGCCGTTGTTGGTCT -s Anc1.Anc1refChr6 131336 27 + 197743 AGAGGCGAAATTTGCCGTTGTTGGTCT -s Anc2.Anc2refChr1 9599 27 + 142988 AGGTGCGAAGTTTGCCGTTGTTGGTCT -s mr.mrrefChr3 34505 27 + 181027 AGAGGCAACATTTGCCATGGTCAGACT -s simCow_chr6.simCow.chr6 466334 24 + 602619 AGGGGCGTAGTTAGCCATTGT---TGT -s simDog_chr6.simDog.chr6 456307 27 + 593897 AGGTGCGAAGTTTGCCGTTGTTGGACG -s simHuman_chr6.simHuman.chr6 463522 26 + 601863 -AAGGTGATATTTGTAGTTGTAGGTCT -s simRat_chr6.simRat.chr6 488570 27 + 647215 AGAGGCAACATTTGCCATGGTCAGATT - -a -s simMouse_chr6.simMouse.chr6 480324 4 + 636262 TCAA -s Anc0.Anc0refChr3 98270 4 + 222631 CCTA -s Anc1.Anc1refChr6 131363 4 + 197743 CCTA -s Anc2.Anc2refChr1 9626 4 + 142988 CCTA -s mr.mrrefChr3 34532 4 + 181027 TCAA -s simCow_chr6.simCow.chr6 466358 4 + 602619 CTTA -s simDog_chr6.simDog.chr6 456344 4 + 593897 CCTA -s simHuman_chr6.simHuman.chr6 463548 4 + 601863 GCTA -s simRat_chr6.simRat.chr6 488597 2 + 647215 AC-- - -a -s simMouse_chr6.simMouse.chr6 480328 20 + 636262 TAAGCAGCTGGCACAGAAAC -s Anc0.Anc0refChr3 98275 20 + 222631 TAAACTGCTAGCTCAGAAAC -s Anc1.Anc1refChr6 131368 20 + 197743 TAAACTGCTAGCTCAGAAAC -s Anc2.Anc2refChr1 9631 20 + 142988 AAGACTGCTAGCTCAGAAAC -s mr.mrrefChr3 34536 20 + 181027 TAAGCAGCTGGCACAGAAAC -s simCow_chr6.simCow.chr6 466363 20 + 602619 GAGACAGCCAGCTCAGAAAC -s simDog_chr6.simDog.chr6 456349 17 + 593897 AAGACTGGTAGCTC---AAC -s simHuman_chr6.simHuman.chr6 463553 20 + 601863 TAAACTACTAGCTCGGAAAC - -a -s simMouse_chr6.simMouse.chr6 480348 118 + 636262 AGTTACTTCTCTGATCTCGTACCACATCCTGTTATTATACCACCCCCTACCAGTAATCTACTAGATCCAGGATTAGGGGGAATGCCCCAACCTCTTGACCCACGACATCTGTAATTTA -s Anc0.Anc0refChr3 98295 88 + 222631 AGCTAGGCCTCTGGTCTCCTACCCCATCTTGTTCTTGTGCCACCCCCAACCAATAGTCTAATAGAGAGAACTATAGGG------------------------------TAATAATTCA -s Anc1.Anc1refChr6 131388 115 + 197743 AGCTAGGCCTCTGGTCTCCTACCCCATCTTGTTCTTGTGCCACCCCCAACCAATAGTCTAATAGAGAGAACTATAGGGGGAATGCTTCAAGCTTTTGGCCCATG---TTAATAATTCA -s Anc2.Anc2refChr1 9651 88 + 142988 AGCTAGGCCTTTGGTCTCCTGCCCCATCTTGTTCTTGTGTCACCCCCAACCAATTGTCTGACAGAGAGAACTATAGGG------------------------------TGATGCTTCA -s mr.mrrefChr3 34556 118 + 181027 AGTTACTTCTCTGATCTCGTACCACATCCTGTTATTATACCACCCCCTACCAATAATCTACTAGAGCCAAGATTAGGGGGAATGCCCCAACCTCTTGACCCACGACATTTGTAATTTA -s simCow_chr6.simCow.chr6 466388 83 + 602619 AGCTAGGCCCT-----TCCTGGCCCAGCTTCCTCTGGAGTGACTCCTGACCAATGGTTTGACAGAGAGAACTATAGGG------------------------------TGGTACTTCA -s simDog_chr6.simDog.chr6 456366 81 + 593897 ATCTAGGTCTTTGGTCTCCTGCCCCATCTTGT--TTGTGTCACCCCCAACAAATTGTCT-----AGACAACCATAGGA------------------------------TGATGCTTTA -s simHuman_chr6.simHuman.chr6 463573 115 + 601863 AGCTATGCCTCAAGTGTCTTACCCCATCTTGTTCTTGTGCTACCCCCAGCCAATAGTCTAATGGAGAGAACTATGGGGGGGATGCTTCAAGCTTTTGGCCCATG---TTAACAACTCA -s simRat_chr6.simRat.chr6 488599 111 + 647215 -------ACTCTGATCTCATACCTCGTCCTGTTATTATACCACCCCCTACCAATAATCTACTAAAGCCAAGATTAGGGGGAATGCCCGAACCTCTTGACCCACAACATTGGTAATTTA - -a -s simMouse_chr6.simMouse.chr6 480466 190 + 636262 TGAAGGTAAGGTAAACATAGGTACATTATTGTGCATAGGAGGAACGCACGTTCACATCTGTATCTTCCCATGGCATAGTCTCTCTAACAAGCATCGCAGATCCATAGTCTCTATGCCCATAGGTCGGTCTTGTGGTTAATTTTAGCTGTACTTTGACATGTCAAGGGGTGTCTAGATTGCATGCCCGTGG -s Anc0.Anc0refChr3 98384 28 + 222631 TGAACAAAATGTTAACAATGAT------------------------------------------------------------------------------------------------------------------------------------------------------------------CCATGA -s Anc1.Anc1refChr6 131504 28 + 197743 TGAACAAAATGTTAACAATGAT------------------------------------------------------------------------------------------------------------------------------------------------------------------CCATGA -s Anc2.Anc2refChr1 9740 28 + 142988 TGAACAAAATTTTAACAATCAT------------------------------------------------------------------------------------------------------------------------------------------------------------------AAATGA -s mr.mrrefChr3 34674 181 + 181027 TGAACATAAGGTAAACATAGGTACATTATTGTGCATAGGAGGAACGCACGTTCACATCTGTATCTTCCCATGGCATAGTCTCTCTAACAAGCATCGCA-----ATAGTCTCTATGCCCATAGGTCGGTCTTGTGGTTAATT---GCTGTACTTTGACATGTCAAGGGGTG-CTAGATTGCATGCCCGTGG -s simCow_chr6.simCow.chr6 466472 28 + 602619 TGAACAAATCCCTATCAATCAT------------------------------------------------------------------------------------------------------------------------------------------------------------------AAATGA -s simDog_chr6.simDog.chr6 456448 17 + 593897 TGAACAAAATTTTAACA----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- -s simHuman_chr6.simHuman.chr6 463689 28 + 601863 TGAACAAAATGATAACAATGAT------------------------------------------------------------------------------------------------------------------------------------------------------------------CCTTGA -s simRat_chr6.simRat.chr6 488710 177 + 647215 TGAACATAAGGT----ATAAGTAAATTATCGTGTACAGGAGGAATGTGCATTCACACCCGTATCTTCCCATGGCATAGTCTCCCTAACAATCGTCGCA-----ATAGTCTTTAATCCCATGGGTCTGTCTTGTTTTAGAAT---GCTGCACTTTGACATGTTAAGGGGTG-CAAGATTTCATCCTCATGG - -a -s simMouse_chr6.simMouse.chr6 480656 19 + 636262 CAGACCATCTCAACCAAGG -s Anc0.Anc0refChr3 98412 11 + 222631 C--------TCAACCAAGG -s Anc1.Anc1refChr6 131532 19 + 197743 CACAATTTCTCAACCAAGG -s Anc2.Anc2refChr1 9768 11 + 142988 C--------TCAACCAAGG -s mr.mrrefChr3 34855 19 + 181027 CAGACCATCTCAACCAAGG -s simCow_chr6.simCow.chr6 466502 11 + 602619 C--------TCAACCAAAG -s simDog_chr6.simDog.chr6 456465 2 + 593897 -----------------GG -s simHuman_chr6.simHuman.chr6 463717 19 + 601863 CACAATTTCTGATCCCATG -s simRat_chr6.simRat.chr6 488887 19 + 647215 CAGACCATCTCAACCAAGG - -a -s simMouse_chr6.simMouse.chr6 480675 27 + 636262 CTTGCATGGTTGCATGGGAAACCACAC -s Anc0.Anc0refChr3 98433 25 + 222631 CTTGGCT--TTGTCTGGTAATTTATTT -s Anc1.Anc1refChr6 131561 25 + 197743 CTTGGCT--TTGTCTGGTAATTTATTT -s Anc2.Anc2refChr1 9789 25 + 142988 CATGGCT--TTGTCTGGTAGTTTATTT -s mr.mrrefChr3 34874 27 + 181027 CTTGCATGGTTGCATGGGAAACCACAC -s simCow_chr6.simCow.chr6 466523 25 + 602619 CATAGCT--TTGTATTCTAGTTTATTT -s simDog_chr6.simDog.chr6 456477 25 + 593897 CATGGCC--TTGTCTGGTAGTTTATTT -s simHuman_chr6.simHuman.chr6 463747 25 + 601863 CTTGGCT--TTGTCTCGCAATTAATTT -s simRat_chr6.simRat.chr6 488906 27 + 647215 CTTGCATGTTTACATGTGAAACCACAC - -a -s simMouse_chr6.simMouse.chr6 480702 12 + 636262 AGTAGGCTCTTG -s Anc0.Anc0refChr3 98460 12 + 222631 CGATGGCTCTTG -s Anc1.Anc1refChr6 131588 12 + 197743 CGATGGCTCTTG -s Anc2.Anc2refChr1 9816 12 + 142988 CAATGGCCCTTG -s mr.mrrefChr3 34901 12 + 181027 AGTAGGCTCTTG -s simCow_chr6.simCow.chr6 466550 12 + 602619 CAATGGCCCTTG -s simDog_chr6.simDog.chr6 456504 12 + 593897 CAACGGTCCTTG -s simHuman_chr6.simHuman.chr6 463774 12 + 601863 GGATGGCTCTTG -s simRat_chr6.simRat.chr6 488933 12 + 647215 GGGAGGCTCTTG - -a -s simMouse_chr6.simMouse.chr6 480714 11 + 636262 TTTAACTAAAG -s Anc0.Anc0refChr3 98473 11 + 222631 TGTTTCCAAAG -s Anc1.Anc1refChr6 131601 11 + 197743 TGTTTCCAAAG -s Anc2.Anc2refChr1 9829 11 + 142988 TGTTTTCAAAG -s mr.mrrefChr3 34913 11 + 181027 TTTAACTAAAG -s simCow_chr6.simCow.chr6 466563 11 + 602619 TCTTTTCAAAG -s simDog_chr6.simDog.chr6 456517 11 + 593897 TGTTCTCAAAG -s simHuman_chr6.simHuman.chr6 463787 11 + 601863 TATTTCCAGAG -s simRat_chr6.simRat.chr6 488945 11 + 647215 TTTCACTAAAG - -a -s simMouse_chr6.simMouse.chr6 480725 2 + 636262 TA -s Anc0.Anc0refChr3 98489 2 + 222631 TA -s Anc1.Anc1refChr6 131617 2 + 197743 TA -s Anc2.Anc2refChr1 9845 2 + 142988 TA -s mr.mrrefChr3 34924 2 + 181027 TA -s simCow_chr6.simCow.chr6 466579 2 + 602619 TA -s simDog_chr6.simDog.chr6 456533 2 + 593897 TA -s simHuman_chr6.simHuman.chr6 463803 2 + 601863 TA -s simRat_chr6.simRat.chr6 488956 2 + 647215 TA - -a -s simMouse_chr6.simMouse.chr6 480727 56 + 636262 GATTAACAATCTGCAAGGGGACTAAGATACATGAGATTGCATCAAGACTTCATTTA -s Anc0.Anc0refChr3 98491 56 + 222631 GTTTAATAACCCTCAAGCTGACCACAATACATGAGTTTGCATTCAGGAATCACTTA -s Anc1.Anc1refChr6 131619 56 + 197743 GTTTAATAACCCTCAAGCTGACCACAATACATGAGTTTGCATTCAGGAATCACTTA -s Anc2.Anc2refChr1 9847 56 + 142988 GTTTAATAGCCCTCAAGCTGACCACAATACATGAGTTTGAATTCAGGAATCACTAA -s mr.mrrefChr3 34926 56 + 181027 GATTAACAATCTGCAAGGGGACCAAGATACATGAGATTGCATTAAGACTTCATTTA -s simCow_chr6.simCow.chr6 466581 56 + 602619 ATTTGATAGCCCCCAAACTGCCCACAATACATGAATTTGTGTTCAGGCATAACTAA -s simDog_chr6.simDog.chr6 456536 56 + 593897 GTTTAATAGGTCTTGAGTGGACCAGAATACATGAGTCTGAATTCAGGAACCACTAA -s simHuman_chr6.simHuman.chr6 463805 55 + 601863 GTACAATAACCCTCAGGCTAA-CACAATGCATGAGTTTGCATTCAGGTGTCGCTTA -s simRat_chr6.simRat.chr6 488958 56 + 647215 GCTTAACAATCTACAAGGGGACCAAGATACATGAGCTTGCATTAAGACTTTATTTA - -a -s simMouse_chr6.simMouse.chr6 480783 25 + 636262 CTCACTGACTATAGTTTGGTATGAG -s Anc0.Anc0refChr3 98547 25 + 222631 CTCACTTAATATAGTCTGATATGAG -s Anc1.Anc1refChr6 131675 25 + 197743 CTCACTTAATATAGTCTGATATGAG -s Anc2.Anc2refChr1 9903 25 + 142988 CTCACTTAATATAGTCTGATATGAG -s mr.mrrefChr3 34982 25 + 181027 CTCACTGACTATAGTTTGATATGAG -s simCow_chr6.simCow.chr6 466638 25 + 602619 CTCACTTAATATAGTCTGTATTGAG -s simDog_chr6.simDog.chr6 456592 25 + 593897 CTCACTTTGTATAGACTGATATGAG -s simHuman_chr6.simHuman.chr6 463860 25 + 601863 CTTGCTTAATACAGTCGGATATGAT -s simRat_chr6.simRat.chr6 489014 25 + 647215 CTCACTGACTATGGTTTGATATAAG - -a -s simMouse_chr6.simMouse.chr6 480808 27 + 636262 CACCAATGCCAATGTCTGGAGTGTACT -s Anc0.Anc0refChr3 98572 5 + 222631 GACCA---------------------- -s Anc1.Anc1refChr6 131700 5 + 197743 GACCA---------------------- -s Anc2.Anc2refChr1 9928 5 + 142988 GACCA---------------------- -s mr.mrrefChr3 35007 27 + 181027 CACCAATGCCAATGTCTGGAGTGTACT -s simCow_chr6.simCow.chr6 466664 5 + 602619 GCTTA---------------------- -s simDog_chr6.simDog.chr6 456617 5 + 593897 GACCA---------------------- -s simHuman_chr6.simHuman.chr6 463885 5 + 601863 GACCA---------------------- -s simRat_chr6.simRat.chr6 489039 27 + 647215 AACCAATACCAATTCCTAGAGTGTATT - -a -s simMouse_chr6.simMouse.chr6 480835 35 + 636262 GGAAAGACGTGCGATGCACTGTCAATTTTCCAAGC -s Anc0.Anc0refChr3 98577 19 + 222631 ----------------CTCTCTCAAGAGACTGGAA -s Anc1.Anc1refChr6 131705 19 + 197743 ----------------CTCTCTCAAGAGACTGGAA -s Anc2.Anc2refChr1 9933 19 + 142988 ----------------CTCTCTCAGGAGACTGGAA -s mr.mrrefChr3 35034 35 + 181027 GGAAAGACGTGCGATGCACTGTCAATTTTCCAAGC -s simCow_chr6.simCow.chr6 466669 19 + 602619 ----------------CTCTCTCAGGAGACTAGAA -s simDog_chr6.simDog.chr6 456622 19 + 593897 ----------------TTCCTTCTGGAGACTGGAG -s simHuman_chr6.simHuman.chr6 463890 19 + 601863 ----------------CTCTCTCAACCAACTGGAA -s simRat_chr6.simRat.chr6 489072 35 + 647215 GGAAAGATGTGTGATGCACTGTCGATTTTCCAAGC - -a -s simMouse_chr6.simMouse.chr6 480870 5 + 636262 ATAGA -s Anc0.Anc0refChr3 98596 5 + 222631 ATAAC -s Anc1.Anc1refChr6 131724 5 + 197743 ATAAC -s Anc2.Anc2refChr1 9952 5 + 142988 ATGAC -s mr.mrrefChr3 35069 5 + 181027 ATAGA -s simCow_chr6.simCow.chr6 466688 5 + 602619 ATGAC -s simDog_chr6.simDog.chr6 456641 5 + 593897 ATGAC -s simHuman_chr6.simHuman.chr6 463909 5 + 601863 ACAAC -s simRat_chr6.simRat.chr6 489116 5 + 647215 ATAGT - -a -s simMouse_chr6.simMouse.chr6 480875 22 + 636262 GCTAAATAATGAGTTATAATGG -s Anc0.Anc0refChr3 98601 21 + 222631 ACTAGA-AATGAATTATACTGG -s Anc1.Anc1refChr6 131729 21 + 197743 ACTAGA-AATGAATTATACTGG -s Anc2.Anc2refChr1 9970 21 + 142988 ACTAGG-GATGAATTATCCTGG -s mr.mrrefChr3 35074 22 + 181027 GCTAAATAATGAGTTATACTGG -s simCow_chr6.simCow.chr6 466706 16 + 602619 ACTATG------ATAATCCTGG -s simDog_chr6.simDog.chr6 456659 21 + 593897 ACTAGG-GATGAATTATCATGG -s simHuman_chr6.simHuman.chr6 463914 21 + 601863 ATTAGA-AATGACCTATACTGG -s simRat_chr6.simRat.chr6 489121 22 + 647215 GCTAAATAATAAGATATACTGT - -a -s simMouse_chr6.simMouse.chr6 480897 14 + 636262 TACTCCACTTGAAT -s Anc0.Anc0refChr3 98637 14 + 222631 TATTCTACTGGAAA -s Anc1.Anc1refChr6 131765 14 + 197743 TATTCTACTGGAAA -s Anc2.Anc2refChr1 10006 14 + 142988 TATTCTACTGGAAA -s mr.mrrefChr3 35096 14 + 181027 TACTCTACTTGAAT -s simCow_chr6.simCow.chr6 466737 14 + 602619 TATTCTCCTGGAGA -s simDog_chr6.simDog.chr6 456695 14 + 593897 TATTCTACTGGAAA -s simHuman_chr6.simHuman.chr6 463950 14 + 601863 TATTTTACTGAAAA -s simRat_chr6.simRat.chr6 489143 14 + 647215 GACTCTGCTTGAAT - -a -s simMouse_chr6.simMouse.chr6 480911 40 + 636262 CAGCTAGGTCTCTTTCTGCCTGTCCTACCACCATATAGCA -s Anc0.Anc0refChr3 98651 40 + 222631 CAGCTAGATCTCTTTCTTCCATACCACCCACCTTGTAGCG -s Anc1.Anc1refChr6 131779 40 + 197743 CAGCTAGATCTCTTTCTTCCATACCACCCACCTTGTAGCG -s Anc2.Anc2refChr1 10020 40 + 142988 CAGCTAGATTACTTCCTTCCATACTGCCCACCTTGTAGCG -s mr.mrrefChr3 35110 40 + 181027 CAGCTAGGTCTCTTTCTGCCTGTCCAACCACCATATAGCA -s simCow_chr6.simCow.chr6 466751 39 + 602619 CAACT-GATTTCTTCCTTCCATACTGCCCACCTAGTAGCG -s simDog_chr6.simDog.chr6 456710 40 + 593897 CAGCTAGGTTACTTCCTTCCATACTGCCCACCGTGTAGCA -s simHuman_chr6.simHuman.chr6 463964 38 + 601863 CAGCTAGATCTA--TCTTCCATACCACCTGCCTTGAAGTG -s simRat_chr6.simRat.chr6 489157 40 + 647215 CAGCTAGGTTTGTTCCTACCTGGCCAACCAACACATAGCA - -a -s simMouse_chr6.simMouse.chr6 480951 56 + 636262 CTTTTTAGCATCTCATTGCCTTTGATTCCAACCTGTAACCAAGTACAGGATACTGA -s Anc0.Anc0refChr3 98691 54 + 222631 G--TTTAACATCACTTTGCCCTTGATTCCAATCTGAGGCTGGGTACAGGATACTGA -s Anc1.Anc1refChr6 131819 54 + 197743 G--TTTAACATCACTTTGCCCTTGATTCCAATCTGAGGCTGGGTACAGGATACTGA -s Anc2.Anc2refChr1 10060 54 + 142988 G--CTTAACATCACTTTGCCCTTGATTCAAATTTGAGGCTGGGTACAGGATAATGA -s mr.mrrefChr3 35150 56 + 181027 CTTTTTAGCATCACATTGCCTTTGATTCCAATCTGAAGCTGAGTACAGGATACTGA -s simCow_chr6.simCow.chr6 466790 54 + 602619 G--CCTAGTAGCATTTTGCTCTTGATTCAAATTCCTGACTGGGTTCAGGATATTGA -s simDog_chr6.simDog.chr6 456756 54 + 593897 G--CTCAACATCACTTTGCCCTTGATTCAGATTTGAGGCTGGGTACAGGATAATGA -s simHuman_chr6.simHuman.chr6 464002 54 + 601863 A--TTTAACATCACCTTGCCCTTGATTCCAATCTGAGGCTGGGCACAGGATACTGA -s simRat_chr6.simRat.chr6 489197 56 + 647215 GCTTTTAGCATAACATTGTCTTTGATTCCAGTCCAAAGCTGAGGACAGGACACTGA - -a -s simMouse_chr6.simMouse.chr6 481007 57 + 636262 ATATGATGATGGACAGATACCTCTAACAAGGTGGAGTTTCACACCTTATAAGTTAAG -s Anc0.Anc0refChr3 98745 57 + 222631 ATATCATGACGAACGGAAACCTCCTACATGTGGCAGTCTCATTTATGAGAGGTTGAA -s Anc1.Anc1refChr6 131873 57 + 197743 ATATCATGACGAACGGAAACCTCCTACATGTGGCAGTCTCATTTATGAGAGGTTGAA -s Anc2.Anc2refChr1 10114 57 + 142988 ATATCATGATAAACGGAAACCTCCTGCATGTTGCAGTCTCATTTATGAGAGGTTGAA -s mr.mrrefChr3 35206 57 + 181027 ATATGATGACGGACAGATACCTCTAACATGGGGGAGTTTCACTCCTTATAAGTTAAG -s simCow_chr6.simCow.chr6 466844 57 + 602619 ATATCATGATTAACGGGAACCTCCTGCATGTTGCAGTCTTGTTTATAAGAGGTTAAA -s simDog_chr6.simDog.chr6 456810 57 + 593897 ATATAATTATAAACAGAAATCTCCAGCATGTTGGTGTCTCATTTATGAGAGGTTGAA -s simHuman_chr6.simHuman.chr6 464056 57 + 601863 ACCTCATGACGAACGAAAACCTCCTACGTGTGGCAGTCTCATTTTCGACACCCTCCA -s simRat_chr6.simRat.chr6 489255 57 + 647215 ATATGATGACGGACAGATACCTCTAATATGGGGGAGTTTTACTCCTAGTAAGTTAAA - -a -s simMouse_chr6.simMouse.chr6 481064 37 + 636262 AAGATGCCACCTCTAGTTCTTGGATTAGCCAAAAATC -s Anc0.Anc0refChr3 98802 36 + 222631 AAGATGACACATACAGCCATTTGGTTAGGCAAAAA-C -s Anc1.Anc1refChr6 131930 36 + 197743 AAGATGACACATACAGCCATTTGGTTAGGCAAAAA-C -s Anc2.Anc2refChr1 10171 36 + 142988 AAGATGACACATACAGCCATTTGGTTAGGCCACAG-A -s mr.mrrefChr3 35263 36 + 181027 AAGATGCCACCTCCAGTCATTGGATTAGTCAAAAA-C -s simCow_chr6.simCow.chr6 466901 35 + 602619 AACCTGACAGACACAGTCATTGGGTTAGGCC-CAG-T -s simDog_chr6.simDog.chr6 456867 36 + 593897 AAGATGGCACATACAGCCATTTGATTAGGCCACAG-A -s simHuman_chr6.simHuman.chr6 464116 18 + 601863 AATATAACTCAT------------------AAAAA-C -s simRat_chr6.simRat.chr6 489312 36 + 647215 AAGATGCCACCTCCAGTCACTGGATTAGTCAAAAA-C - -a -s simMouse_chr6.simMouse.chr6 481101 52 + 636262 AAGGCACCCCCAACCAGGAGATGAAGCATGCCAGGCTAGTTAATGTGGCATA -s Anc0.Anc0refChr3 98838 32 + 222631 AATTCACCCTTACCAAGGA------------GTGGCGAGATAAG-------- -s Anc1.Anc1refChr6 131966 40 + 197743 AATTCACCCTTACCAAGGA------------GTGGCGAGATAAGTCGCCATA -s Anc2.Anc2refChr1 10212 32 + 142988 AATCCACCCTTGCCAAGGA------------GTGGAGGGACAAG-------- -s mr.mrrefChr3 35299 52 + 181027 AAGTCACCCTCACCCAGGAGATGAAGCATGCCAGGCTAGTTAATGTGGCATA -s simCow_chr6.simCow.chr6 466941 27 + 602619 AAGACACCCTTGTCAAGGG------------ATGGAGGG------------- -s simDog_chr6.simDog.chr6 456908 32 + 593897 AATCCACCCTTGCCAAGGA------------GTGGAGGGACAAG-------- -s simHuman_chr6.simHuman.chr6 464134 37 + 601863 A--TCTCTCT-ACCAAAGA------------TCGGCGATATGAGTCGCCATA -s simRat_chr6.simRat.chr6 489348 52 + 647215 AAGTCGCCCTCACCTTGGAAGTGAAGCATGCCAGGCTAGTTAATGTGGCATA - -a -s simMouse_chr6.simMouse.chr6 481153 5 + 636262 GTAAA -s Anc1.Anc1refChr6 132006 5 + 197743 GCAGA -s mr.mrrefChr3 35351 5 + 181027 GTAGA -s simHuman_chr6.simHuman.chr6 464172 5 + 601863 GCAGA -s simRat_chr6.simRat.chr6 489400 5 + 647215 GTAGA - -a -s simMouse_chr6.simMouse.chr6 481158 4 + 636262 TCCT -s mr.mrrefChr3 35469 4 + 181027 TCCT -s simRat_chr6.simRat.chr6 489528 4 + 647215 TGCT - -a -s simMouse_chr6.simMouse.chr6 481162 64 + 636262 CATTTGTCTCAGCTGGGATCTGAAGCCCAATAGCCTGAGAGAAATGCCTGAGGAATGCCTTGAG -s Anc0.Anc0refChr3 98942 51 + 222631 CATTCGTAT-ACTCCAGATCTGGGAGCCAATAGCCCGGGCA--GTGC----------CCCTGGC -s Anc1.Anc1refChr6 132127 51 + 197743 CATTCGTAT-ACTCCAGATCTGGGAGCCAATAGCCCGAGCA--GTGC----------CCCTGGC -s Anc2.Anc2refChr0 36258 47 + 56053 CATTCCTAT-AGTCCAGATCTGGGAGCCAAGAACCTGGGCA--TTGC----------CCT---- -s Anc2.Anc2refChr1 10316 51 + 142988 CATTTGTAT-ACTCCAGACCTTGGAGGCAATAGCCCGGGCA--GTGC----------CCCTGGC -s mr.mrrefChr3 35473 64 + 181027 CATTTGTCTCAGCTGGGATCTGGGGCCCAATAGCCTGAGAGACATGCCTGAGGAATGCCCTGAG -s simCow_chr6.simCow.chr6 467038 51 + 602619 CATTTGGAT-ACTCTAGACCTAGGGGTGAATAGGCCGGGTA--GTAC----------CCTTGGC -s simCow_chr6.simCow.chr6 42326 47 + 602619 GATTCGTAT-ACACCGGACCTGGGAGCCAATAGCCTAGGTA--GTAC----------CCT---- -s simDog_chr6.simDog.chr6 457011 51 + 593897 CATTTATAT-ACTCCGGACCTTGGAGGCAGTAACCTGGGCA--GTGA----------CCCCAGC -s simDog_chr6.simDog.chr6 37152 47 + 593897 CATTCCTAT-AGTCCAGATCTGGGAGCCAAGAACCTGGGCA--TTGC----------CCT---- -s simHuman_chr6.simHuman.chr6 464303 51 + 601863 TACTCGTTT-ACTACAGAACAGGGAGCCAATAGCCCAAGCA--GTCC----------CTCTGGC -s simRat_chr6.simRat.chr6 489532 64 + 647215 TATTTGTCTCAGTTGGGATCTGGGGCCCAATTGCCTGAGAGACATGCCTGAGACATGCCCTGAT - -a -s simMouse_chr6.simMouse.chr6 481226 10 + 636262 ATTAGCACAA -s Anc0.Anc0refChr3 98993 10 + 222631 ATTAGTGTGA -s Anc1.Anc1refChr6 132178 10 + 197743 ATTAGTGTGA -s Anc2.Anc2refChr0 36305 10 + 56053 ATTAGTGTGA -s Anc2.Anc2refChr1 10367 10 + 142988 ATTAGTGTGA -s mr.mrrefChr3 35537 10 + 181027 ATTAGCACAA -s simCow_chr6.simCow.chr6 467089 10 + 602619 ATTAGTGCAA -s simCow_chr6.simCow.chr6 42373 10 + 602619 ATTAGTGCAA -s simDog_chr6.simDog.chr6 457062 10 + 593897 ATTAATTTGA -s simDog_chr6.simDog.chr6 37203 10 + 593897 ATTAGTGTGA -s simHuman_chr6.simHuman.chr6 464354 10 + 601863 ATTGGTGTGA -s simRat_chr6.simRat.chr6 489596 10 + 647215 ATTAGCACAA - -a -s simMouse_chr6.simMouse.chr6 481236 10 + 636262 GGCATAAGGG -s Anc0.Anc0refChr3 99003 10 + 222631 GGTAGAGGGG -s Anc1.Anc1refChr6 132188 10 + 197743 GGTAGAGGGG -s Anc2.Anc2refChr0 36315 10 + 56053 GGTAGAGGGG -s Anc2.Anc2refChr1 10377 10 + 142988 GGTAGAGGGG -s mr.mrrefChr3 35547 10 + 181027 GGCATAAGGG -s simCow_chr6.simCow.chr6 467100 10 + 602619 GGTAACGGGG -s simCow_chr6.simCow.chr6 42383 10 + 602619 GGTAGAGGGG -s simDog_chr6.simDog.chr6 457072 10 + 593897 GGTAGAGGGG -s simDog_chr6.simDog.chr6 37213 10 + 593897 GGTAGAGGGG -s simHuman_chr6.simHuman.chr6 464364 10 + 601863 GGTAGAGGGA -s simRat_chr6.simRat.chr6 489606 10 + 647215 AGCATAAGGG - -a -s simMouse_chr6.simMouse.chr6 481246 28 + 636262 TATCCACCTCAGCTTTTTAGAGTGCTGG -s Anc0.Anc0refChr3 99014 28 + 222631 AATCCACCTCAGCTCTCCAGAGTGCTGG -s Anc1.Anc1refChr6 132199 28 + 197743 AATCCACCTCAGCTCTCCAGAGTGCTGG -s Anc2.Anc2refChr0 36326 28 + 56053 AATCCACCTCAGCTCTCTAGAGTGCTGG -s Anc2.Anc2refChr1 10388 28 + 142988 CATCCACCTCAGTTCTCCAGAGCACTGG -s mr.mrrefChr3 35557 28 + 181027 TATCCACCTCAGCTCTCTAGAGTGCTGG -s simCow_chr6.simCow.chr6 467111 28 + 602619 GATCCACCTCTGGTATCCAGAGCACTGG -s simCow_chr6.simCow.chr6 42394 28 + 602619 AATCCACCTCAGCTCCCTAGAGTGCTGG -s simDog_chr6.simDog.chr6 457088 28 + 593897 CAGCCCTCTTAGTTCTCTAGAGCAGCAA -s simDog_chr6.simDog.chr6 37224 28 + 593897 AATCCACCTCAGCTCTCTAGAGTGCTGG -s simHuman_chr6.simHuman.chr6 464375 28 + 601863 AATCCACCTCACCTCTCCAGAAAGCTGG -s simRat_chr6.simRat.chr6 489616 28 + 647215 CATTCACCTCAGCTCTCTAAAGTGCTAG - -a -s simMouse_chr6.simMouse.chr6 481274 14 + 636262 TAAATGGAGAACTA -s Anc0.Anc0refChr3 99042 14 + 222631 CAAATGATAGCCTA -s Anc1.Anc1refChr6 132227 14 + 197743 CAAATGATAGCCTA -s Anc2.Anc2refChr0 36354 14 + 56053 CAAATGATAGTCAA -s Anc2.Anc2refChr1 10416 14 + 142988 CAAATGATAGCCTA -s mr.mrrefChr3 35585 14 + 181027 CAAATGAAAGACTA -s simCow_chr6.simCow.chr6 467141 14 + 602619 CAAAAGGTAGCCTA -s simCow_chr6.simCow.chr6 42422 14 + 602619 CAAAAGATGGCCTA -s simDog_chr6.simDog.chr6 457116 14 + 593897 CAAATGATAGCCTA -s simDog_chr6.simDog.chr6 37252 14 + 593897 CAAATGATAGTCAA -s simHuman_chr6.simHuman.chr6 464403 14 + 601863 CAAATGATAGCCTA -s simRat_chr6.simRat.chr6 489644 14 + 647215 CAAATGAAAGACTA - -a -s simMouse_chr6.simMouse.chr6 481288 8 + 636262 AGTCCAAT -s Anc0.Anc0refChr3 99056 8 + 222631 ATGCCAGT -s Anc1.Anc1refChr6 132241 8 + 197743 ATGCCAGT -s Anc2.Anc2refChr0 36368 8 + 56053 GTACTTTG -s Anc2.Anc2refChr1 10430 8 + 142988 AGGCCAGT -s mr.mrrefChr3 35599 8 + 181027 AGTCCAGT -s simCow_chr6.simCow.chr6 467155 8 + 602619 AGGCCAGT -s simCow_chr6.simCow.chr6 42436 8 + 602619 ATACTTCG -s simDog_chr6.simDog.chr6 37266 8 + 593897 GTACTTTG -s simHuman_chr6.simHuman.chr6 464417 8 + 601863 ATGCAAGT -s simRat_chr6.simRat.chr6 489658 8 + 647215 AATCTCGT - -a -s simMouse_chr6.simMouse.chr6 481296 6 + 636262 GCATAT -s Anc0.Anc0refChr3 99064 6 + 222631 ACTCAT -s Anc1.Anc1refChr6 132249 6 + 197743 ACTCAT -s Anc2.Anc2refChr0 36376 4 + 56053 ACTT-- -s Anc2.Anc2refChr1 10438 6 + 142988 ATTCAG -s mr.mrrefChr3 35607 6 + 181027 ACATAT -s simCow_chr6.simCow.chr6 467163 6 + 602619 ATTCAG -s simCow_chr6.simCow.chr6 42445 4 + 602619 ACTT-- -s simDog_chr6.simDog.chr6 37274 4 + 593897 ACTT-- -s simHuman_chr6.simHuman.chr6 464425 6 + 601863 ACTCAT -s simRat_chr6.simRat.chr6 489666 6 + 647215 ACCTAT - -a -s simMouse_chr6.simMouse.chr6 481302 2 + 636262 AC -s Anc0.Anc0refChr3 99070 2 + 222631 GT -s Anc1.Anc1refChr6 132255 2 + 197743 GT -s Anc2.Anc2refChr1 10444 2 + 142988 GT -s mr.mrrefChr3 35613 2 + 181027 AT -s simCow_chr6.simCow.chr6 467169 2 + 602619 AT -s simDog_chr6.simDog.chr6 457130 2 + 593897 GA -s simHuman_chr6.simHuman.chr6 464431 2 + 601863 GT -s simRat_chr6.simRat.chr6 489672 2 + 647215 AT - -a -s simMouse_chr6.simMouse.chr6 481304 18 + 636262 ACACCCAAGTGGTGTCTC -s Anc0.Anc0refChr3 99072 17 + 222631 AACCGTGA-TGGAGTGCT -s Anc1.Anc1refChr6 132257 18 + 197743 AACCGTGAGTGGAGTGCT -s Anc2.Anc2refChr1 10446 17 + 142988 AACCCAGA-TGGAGTGCT -s mr.mrrefChr3 35615 18 + 181027 AAACGTGAGTGGTGTCTC -s simCow_chr6.simCow.chr6 467172 17 + 602619 AACCTAGA-TGGAGTGCT -s simDog_chr6.simDog.chr6 457132 17 + 593897 AATCCAGA-CAGAGTGCT -s simHuman_chr6.simHuman.chr6 464433 18 + 601863 AACCGTGAGTGGAGTGCT -s simRat_chr6.simRat.chr6 489674 18 + 647215 AAACGTGAATGGCATCTG - -a -s simMouse_chr6.simMouse.chr6 481322 2 + 636262 CT -s Anc0.Anc0refChr3 99089 2 + 222631 CT -s Anc1.Anc1refChr6 132275 2 + 197743 CT -s Anc2.Anc2refChr1 10463 2 + 142988 CT -s mr.mrrefChr3 35633 2 + 181027 CT -s simCow_chr6.simCow.chr6 467189 2 + 602619 CT -s simDog_chr6.simDog.chr6 457152 2 + 593897 TT -s simHuman_chr6.simHuman.chr6 464451 2 + 601863 CT -s simRat_chr6.simRat.chr6 489692 2 + 647215 AC - -a -s simMouse_chr6.simMouse.chr6 481324 49 + 636262 CCATAAGCCAATAGCCAGTATCAGGTTAGTCCAACACTTAAAAGCATAT -s Anc0.Anc0refChr3 99103 5 + 222631 CCA--------------------------------------------GT -s Anc1.Anc1refChr6 132289 5 + 197743 CCA--------------------------------------------GT -s Anc2.Anc2refChr1 10477 5 + 142988 CCA--------------------------------------------GT -s mr.mrrefChr3 35635 5 + 181027 CCA--------------------------------------------AT -s simCow_chr6.simCow.chr6 467202 2 + 602619 -----------------------------------------------GG -s simDog_chr6.simDog.chr6 457166 5 + 593897 CCA--------------------------------------------GT -s simHuman_chr6.simHuman.chr6 464465 5 + 601863 CTA--------------------------------------------GT -s simRat_chr6.simRat.chr6 489694 5 + 647215 CCA--------------------------------------------AT - -a -s simMouse_chr6.simMouse.chr6 481373 11 + 636262 TAGTACAGCCC -s Anc0.Anc0refChr3 99108 11 + 222631 CAGGTTAGCCT -s Anc1.Anc1refChr6 132294 11 + 197743 CAGGTTAGCCT -s Anc2.Anc2refChr1 10485 11 + 142988 CAGGTTAACCT -s mr.mrrefChr3 35640 11 + 181027 CAGTACAGCCC -s simCow_chr6.simCow.chr6 467207 11 + 602619 CACCTTAACCT -s simDog_chr6.simDog.chr6 457174 11 + 593897 CAGGTTAACCT -s simHuman_chr6.simHuman.chr6 464470 11 + 601863 CAGGTTAGCCT -s simRat_chr6.simRat.chr6 489699 11 + 647215 CAGTACAGCCA - -a -s simMouse_chr6.simMouse.chr6 481384 28 + 636262 ATTAAACCCTCTGTGGATGGCTTGAATA -s Anc0.Anc0refChr3 99154 27 + 222631 ACTCCATCTCCTATGGATTGCCTGAA-A -s Anc1.Anc1refChr6 132340 27 + 197743 ACTCCATCTCCTATGGATTGCCTGAA-A -s Anc2.Anc2refChr1 10531 27 + 142988 ACCCCATCTCCTATTGATTGCCTGAA-A -s mr.mrrefChr3 35651 28 + 181027 ATTAAACCTTCTGTGGATTGCTTGAATA -s simCow_chr6.simCow.chr6 467294 27 + 602619 ACCCCATTTACTTTAGATTGCCTTCA-G -s simDog_chr6.simDog.chr6 457219 27 + 593897 ACCCAACCTCCTATTGATTGCCTGAA-A -s simHuman_chr6.simHuman.chr6 464516 27 + 601863 ACTCCATCTCCCATGGATTTCCTGAG-A -s simRat_chr6.simRat.chr6 489710 24 + 647215 ATTAAACCTTC----ACTTGCTTGGACA - -a -s simMouse_chr6.simMouse.chr6 481412 8 + 636262 TTAAGACA -s Anc0.Anc0refChr3 99181 8 + 222631 TTAAGATA -s Anc1.Anc1refChr6 132367 8 + 197743 TTAAGATA -s Anc2.Anc2refChr1 10558 8 + 142988 TTAAGATG -s mr.mrrefChr3 35679 8 + 181027 TTAAGACA -s simCow_chr6.simCow.chr6 467321 8 + 602619 TTAATATG -s simDog_chr6.simDog.chr6 457246 8 + 593897 ATAAGATG -s simHuman_chr6.simHuman.chr6 464543 8 + 601863 TTAAGGTA -s simRat_chr6.simRat.chr6 489739 8 + 647215 TTAAGAAA - -a -s simMouse_chr6.simMouse.chr6 481420 7 + 636262 AGCCTCA -s Anc0.Anc0refChr3 99193 7 + 222631 ACCCTCA -s Anc1.Anc1refChr6 132379 7 + 197743 ACCCTCA -s Anc2.Anc2refChr1 10570 7 + 142988 ACCCTCA -s mr.mrrefChr3 35687 7 + 181027 AGCCTCA -s simCow_chr6.simCow.chr6 467333 7 + 602619 AACCTTC -s simDog_chr6.simDog.chr6 457258 7 + 593897 ACCATCA -s simHuman_chr6.simHuman.chr6 464555 7 + 601863 ATCCTCA -s simRat_chr6.simRat.chr6 489747 3 + 647215 AGT---- - -a -s simMouse_chr6.simMouse.chr6 481427 36 + 636262 CCACTAATCAGTTACCCTCAGGTCTGACCCGCATCC -s Anc0.Anc0refChr3 99200 35 + 222631 T-GCCAATCAGCTGCCTTCAGGTCCGCAATACACCC -s Anc1.Anc1refChr6 132386 35 + 197743 T-GCCAATCAGCTGCCTTCAGGTCCGCAATACACCC -s Anc2.Anc2refChr1 10578 35 + 142988 T-GCCAATCAGCTGCCTTCAGGTCCGCAATACACAC -s mr.mrrefChr3 35694 35 + 181027 C-ACTAATCAGTTACCCTCAGGTCTGACCCACATCC -s simCow_chr6.simCow.chr6 467341 35 + 602619 A-ACCAATCAGCTGCCTTTGGGTCTGCACAACGCAC -s simDog_chr6.simDog.chr6 457266 35 + 593897 T-GCTAATCAGCTACCTTCAGGTCCACAATACACAC -s simHuman_chr6.simHuman.chr6 464562 35 + 601863 T-GCCAAGCAGCTGCCTTCAGGTCCGCATTACACCT -s simRat_chr6.simRat.chr6 489750 30 + 647215 ------ATCAGTAATCCTCAGCTCTGACCCACATCC - -a -s simMouse_chr6.simMouse.chr6 481463 6 + 636262 TTGCTT -s Anc0.Anc0refChr3 99235 6 + 222631 TTTTTT -s Anc1.Anc1refChr6 132421 6 + 197743 TTTTTT -s Anc2.Anc2refChr1 10614 6 + 142988 CTTTTT -s mr.mrrefChr3 35729 6 + 181027 TTTCTT -s simCow_chr6.simCow.chr6 467377 6 + 602619 CTTTCT -s simDog_chr6.simDog.chr6 457302 6 + 593897 CTTCTT -s simHuman_chr6.simHuman.chr6 464597 6 + 601863 TTTTTT -s simRat_chr6.simRat.chr6 489780 6 + 647215 TTTCTT - -a -s simMouse_chr6.simMouse.chr6 481469 26 + 636262 GTATTGTTTACCAAGCTACACCCCAC -s Anc0.Anc0refChr3 99241 16 + 222631 G---TGTCTACCAAG-------CCAC -s Anc1.Anc1refChr6 132427 26 + 197743 GTACTGTCTACCAAGCCGCATCCCAC -s Anc2.Anc2refChr1 10620 16 + 142988 G---TGTCTACCAAG-------CCAG -s mr.mrrefChr3 35735 26 + 181027 GTATTGTTTACCAAGCTACATCCCAC -s simCow_chr6.simCow.chr6 467387 10 + 602619 G---TGACTTACA------------- -s simDog_chr6.simDog.chr6 457308 16 + 593897 G---TGTTTACCAAG-------CCAG -s simHuman_chr6.simHuman.chr6 464603 26 + 601863 CTACTGTCTCCCAGTCCGCATCACAC -s simRat_chr6.simRat.chr6 489786 26 + 647215 GTATTGTTTACCAAGCTACATTCCAC - -a -s simMouse_chr6.simMouse.chr6 481495 11 + 636262 ATCCCAGTGCT -s Anc0.Anc0refChr3 99257 11 + 222631 GTTCTAGTATT -s Anc1.Anc1refChr6 132453 11 + 197743 GTTCTAGTATT -s Anc2.Anc2refChr1 10636 11 + 142988 GCTCTAGTATT -s mr.mrrefChr3 35761 11 + 181027 ATTCCAGTGCT -s simCow_chr6.simCow.chr6 467397 9 + 602619 --TCTAGTATT -s simDog_chr6.simDog.chr6 457324 11 + 593897 GCTCTAGTATT -s simHuman_chr6.simHuman.chr6 464656 11 + 601863 GTTCTAGTATT -s simRat_chr6.simRat.chr6 489812 11 + 647215 ATTCCAGTGCT - -a -s simMouse_chr6.simMouse.chr6 481506 7 + 636262 TGCCGAT -s Anc0.Anc0refChr3 99268 7 + 222631 TGCCCCT -s Anc1.Anc1refChr6 132464 7 + 197743 TGCCCCT -s Anc2.Anc2refChr1 10647 7 + 142988 TGCCCCT -s mr.mrrefChr3 35772 7 + 181027 TGCCCAT -s mr.mrrefChr3 36515 7 + 181027 TGCCCCA -s simCow_chr6.simCow.chr6 467406 7 + 602619 TGCTCCT -s simDog_chr6.simDog.chr6 457335 7 + 593897 TGCCCCT -s simHuman_chr6.simHuman.chr6 464667 7 + 601863 TGTCCAT -s simMouse_chr6.simMouse.chr6 482305 7 + 636262 TGCCCCA -s simRat_chr6.simRat.chr6 490571 7 + 647215 TGCCCCA -s simRat_chr6.simRat.chr6 489823 7 + 647215 TGCCCAC - -a -s simMouse_chr6.simMouse.chr6 481513 13 + 636262 TAAGTCCACCATC -s Anc0.Anc0refChr3 99275 13 + 222631 TAATTTCACTATC -s Anc1.Anc1refChr6 132471 13 + 197743 TAATTTCACTATC -s Anc2.Anc2refChr1 10654 13 + 142988 TATTTTCGCTATG -s mr.mrrefChr3 35779 13 + 181027 TAAGTCCACCATC -s mr.mrrefChr3 36522 13 + 181027 TAATTTTATCACC -s simCow_chr6.simCow.chr6 467413 13 + 602619 CAATTTCCCTATC -s simDog_chr6.simDog.chr6 457342 13 + 593897 TATTGTCGTTAAG -s simHuman_chr6.simHuman.chr6 464674 13 + 601863 TCCTTTCACTATT -s simMouse_chr6.simMouse.chr6 482312 13 + 636262 TAATTTTATCACA -s simRat_chr6.simRat.chr6 490579 13 + 647215 TAATTTTATCACC -s simRat_chr6.simRat.chr6 489830 13 + 647215 TAAGTCCACCAGC - -a -s simMouse_chr6.simMouse.chr6 481526 44 + 636262 CATGGATATATATACTGATAGTAGAGAAATAACTGAGTTCAGTG -s Anc0.Anc0refChr3 99304 44 + 222631 CATTGAATGACATCTTGATAGTAGGAAAATTACTGAGTTGAGTG -s Anc1.Anc1refChr6 132500 44 + 197743 CATTGAATGACATCTTGATAGTAGGAAAATTACTGAGTTGAGTG -s Anc2.Anc2refChr1 10689 44 + 142988 CATTGAATGACATCTTGATAGTAAGAAAATTACTGAGTTGAGTT -s mr.mrrefChr3 35792 44 + 181027 CATGAATATATATACTGATAGTAGAGAAATAACTGAGTTCAGTG -s mr.mrrefChr3 36541 44 + 181027 CATCAAATGATATCATGCTAGTAGGAAAACTATTTAACAGACTG -s simCow_chr6.simCow.chr6 467451 39 + 602619 CATTGACTGTCATGATGAGAGTAAGGTAATTAC-----TGAGGT -s simDog_chr6.simDog.chr6 457377 44 + 593897 CATTGAATGACATCTTGGTAGTAAGAAAAGTACTGAGTAAAGTT -s simHuman_chr6.simHuman.chr6 464703 44 + 601863 CATTGAATGACATCTTGATAGTAGGAAAATTATTGTGTTGAGAG -s simMouse_chr6.simMouse.chr6 482331 44 + 636262 CATCAAATGATATCATGCTAGCAGGAAAACGACTTAACAGACTG -s simRat_chr6.simRat.chr6 490598 44 + 647215 CATCAAATGATATCATCCTATTAGGAAAACTATTTAACAGCCTG -s simRat_chr6.simRat.chr6 489843 44 + 647215 CATGAATATATATGTTAATAGTGGGAAAATTACCGAGTTTGCTG - -a -s simMouse_chr6.simMouse.chr6 481570 5 + 636262 CAAGA -s Anc0.Anc0refChr3 99348 5 + 222631 CAATA -s Anc1.Anc1refChr6 132544 5 + 197743 CAATA -s Anc2.Anc2refChr1 10733 5 + 142988 CAATA -s mr.mrrefChr3 35836 5 + 181027 CAAGA -s simCow_chr6.simCow.chr6 467490 5 + 602619 CAATG -s simDog_chr6.simDog.chr6 457421 5 + 593897 CAATA -s simRat_chr6.simRat.chr6 489887 5 + 647215 CAAGA - -a -s simMouse_chr6.simMouse.chr6 481575 1 + 636262 G -s Anc0.Anc0refChr3 99353 1 + 222631 G -s Anc1.Anc1refChr6 132549 1 + 197743 G -s Anc2.Anc2refChr1 10739 1 + 142988 G -s mr.mrrefChr3 35841 1 + 181027 G -s simCow_chr6.simCow.chr6 467496 1 + 602619 C -s simDog_chr6.simDog.chr6 457427 1 + 593897 G -s simRat_chr6.simRat.chr6 489892 1 + 647215 G - -a -s simMouse_chr6.simMouse.chr6 481576 3 + 636262 ACC -s Anc0.Anc0refChr3 99354 3 + 222631 AGC -s Anc1.Anc1refChr6 132550 3 + 197743 AGC -s Anc2.Anc2refChr1 10740 3 + 142988 AGC -s mr.mrrefChr3 35842 3 + 181027 ACC -s mr.mrrefChr3 36585 3 + 181027 AGC -s simCow_chr6.simCow.chr6 467497 3 + 602619 AGC -s simDog_chr6.simDog.chr6 457428 3 + 593897 AGC -s simHuman_chr6.simHuman.chr6 464747 3 + 601863 TGC -s simMouse_chr6.simMouse.chr6 482375 3 + 636262 AGC -s simRat_chr6.simRat.chr6 490642 3 + 647215 AGC -s simRat_chr6.simRat.chr6 489893 3 + 647215 ACG - -a -s simMouse_chr6.simMouse.chr6 481579 4 + 636262 CATG -s Anc0.Anc0refChr3 99357 4 + 222631 CATG -s Anc1.Anc1refChr6 132553 4 + 197743 CATG -s Anc2.Anc2refChr1 10747 4 + 142988 CATG -s mr.mrrefChr3 35845 4 + 181027 CATG -s mr.mrrefChr3 36588 4 + 181027 AATG -s simCow_chr6.simCow.chr6 467504 4 + 602619 CATG -s simDog_chr6.simDog.chr6 457435 4 + 593897 CATG -s simHuman_chr6.simHuman.chr6 464750 4 + 601863 GTGA -s simMouse_chr6.simMouse.chr6 482378 4 + 636262 AATG -s simRat_chr6.simRat.chr6 490645 4 + 647215 AATG -s simRat_chr6.simRat.chr6 489896 4 + 647215 CATG - -a -s simMouse_chr6.simMouse.chr6 481583 1 + 636262 C -s Anc0.Anc0refChr3 99361 1 + 222631 A -s Anc1.Anc1refChr6 132557 1 + 197743 A -s Anc2.Anc2refChr1 10751 1 + 142988 A -s mr.mrrefChr3 35849 1 + 181027 C -s simCow_chr6.simCow.chr6 467508 1 + 602619 A -s simDog_chr6.simDog.chr6 457439 1 + 593897 A -s simRat_chr6.simRat.chr6 489900 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 481584 31 + 636262 GTTTGATGTGGATCACGATAATAATACCTAA -s Anc0.Anc0refChr3 99362 31 + 222631 TTTTGATGTGGTTGACGATAATCATACCTAA -s Anc1.Anc1refChr6 132558 31 + 197743 TTTTGATGTGGTTGACGATAATCATACCTAA -s Anc2.Anc2refChr1 10752 31 + 142988 TTTTGATGTGGTTTACGATAATCATACCCAA -s mr.mrrefChr3 35850 31 + 181027 GTTTGATGTGGATCACGATAATAATACCTAA -s mr.mrrefChr3 36592 31 + 181027 TTTTGATTTGGTTGATGATAATTATACCTAA -s simCow_chr6.simCow.chr6 467509 31 + 602619 TTTTGGTTTGGTTTACGATAATCATACCCCT -s simDog_chr6.simDog.chr6 457440 26 + 593897 TTTTGATGTGGTTTCCAA-----GTATCCAA -s simHuman_chr6.simHuman.chr6 464754 31 + 601863 CTGTGATGTGGTTGATGATAATGATACCTGA -s simMouse_chr6.simMouse.chr6 482382 31 + 636262 TTTTGATTGGGTTGATGATAGTTATAACTAA -s simRat_chr6.simRat.chr6 490649 31 + 647215 TTATGATCTGGTTGATAATAATTATACCTAA -s simRat_chr6.simRat.chr6 489901 31 + 647215 ATTTGATGTGGTTAATGATAACAATACCTAA - -a -s simMouse_chr6.simMouse.chr6 481615 22 + 636262 TGGATAACGTGCAATCATTACA -s Anc0.Anc0refChr3 99403 22 + 222631 TAGTTAACATGCAATTATTAGG -s Anc1.Anc1refChr6 132599 22 + 197743 TAGTTAACATGCAATTATTAGG -s Anc2.Anc2refChr1 10793 22 + 142988 TAGTTAACATTCAATTGTGAGG -s mr.mrrefChr3 35881 22 + 181027 TGGATAACGTGCAATCATTACA -s mr.mrrefChr3 36623 22 + 181027 TGGTCAACATGAAATTATAGGG -s simCow_chr6.simCow.chr6 467550 22 + 602619 TGGTTAACATTCAATTATGGTG -s simDog_chr6.simDog.chr6 457476 22 + 593897 CAGTTAACATTCAATTGAGAGG -s simHuman_chr6.simHuman.chr6 464795 22 + 601863 TAGTTAGCATCCAATATGTGAG -s simMouse_chr6.simMouse.chr6 482413 22 + 636262 TGGTCAACATGAAATTATAGGG -s simRat_chr6.simRat.chr6 490680 22 + 647215 TGGTCAACATGAAATTATGGGG -s simRat_chr6.simRat.chr6 489932 22 + 647215 TGGATAACTTGCAATCATTAGA - -a -s simMouse_chr6.simMouse.chr6 481637 5 + 636262 TAAAA -s Anc0.Anc0refChr3 99425 5 + 222631 TAAAA -s Anc1.Anc1refChr6 132621 5 + 197743 TAAAA -s Anc2.Anc2refChr1 10815 5 + 142988 TAAGC -s mr.mrrefChr3 35903 5 + 181027 TAAAA -s mr.mrrefChr3 36645 5 + 181027 TAGAA -s simCow_chr6.simCow.chr6 467572 5 + 602619 TCAGC -s simDog_chr6.simDog.chr6 457498 5 + 593897 TAAGC -s simHuman_chr6.simHuman.chr6 464817 5 + 601863 GAAAA -s simMouse_chr6.simMouse.chr6 482435 5 + 636262 TAGAA -s simRat_chr6.simRat.chr6 490702 5 + 647215 TAGAA -s simRat_chr6.simRat.chr6 489955 5 + 647215 TAACA - -a -s simMouse_chr6.simMouse.chr6 481642 14 + 636262 ATTTATTAAGCTCT -s Anc0.Anc0refChr3 99436 14 + 222631 ATCTATAATGCTCT -s Anc1.Anc1refChr6 132632 14 + 197743 ATCTATAATGCTCT -s Anc2.Anc2refChr1 10826 14 + 142988 ATCTAGAATGCTCT -s mr.mrrefChr3 35908 14 + 181027 ATTTATTAAGCTCT -s mr.mrrefChr3 36650 14 + 181027 ATCTATAATGCTCT -s simCow_chr6.simCow.chr6 467583 14 + 602619 ATCTAATATGCTCT -s simDog_chr6.simDog.chr6 457509 14 + 593897 ATTTAGAATGCTCT -s simHuman_chr6.simHuman.chr6 464828 14 + 601863 ATCTACAATGCTCT -s simMouse_chr6.simMouse.chr6 482440 14 + 636262 ATCTATAATGCTCT -s simRat_chr6.simRat.chr6 490707 14 + 647215 ATCTATAATGCCCT -s simRat_chr6.simRat.chr6 489960 14 + 647215 ACCTATTATACTGG - -a -s simMouse_chr6.simMouse.chr6 481656 1 + 636262 T -s Anc0.Anc0refChr3 99450 1 + 222631 T -s Anc1.Anc1refChr6 132646 1 + 197743 T -s Anc2.Anc2refChr1 10840 1 + 142988 T -s mr.mrrefChr3 35922 1 + 181027 T -s mr.mrrefChr3 36664 1 + 181027 T -s simCow_chr6.simCow.chr6 467597 1 + 602619 C -s simDog_chr6.simDog.chr6 457523 1 + 593897 T -s simHuman_chr6.simHuman.chr6 464842 1 + 601863 T -s simMouse_chr6.simMouse.chr6 482454 1 + 636262 T -s simRat_chr6.simRat.chr6 489974 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 481657 13 + 636262 GTAGTAAGGGGCA -s Anc0.Anc0refChr3 99451 13 + 222631 GTAGAAAGGGGCA -s Anc1.Anc1refChr6 132647 13 + 197743 GTAGAAAGGGGCA -s Anc2.Anc2refChr1 10841 13 + 142988 GTAGAAAGGGGCA -s mr.mrrefChr3 35923 13 + 181027 GTAGTAAGGGGCA -s mr.mrrefChr3 36665 13 + 181027 GTAGAGCAGGGCA -s simCow_chr6.simCow.chr6 467598 4 + 602619 CTAG--------- -s simDog_chr6.simDog.chr6 457524 13 + 593897 GTAGAAAGGGGCA -s simHuman_chr6.simHuman.chr6 464843 13 + 601863 GTAGCAAGGGGCA -s simMouse_chr6.simMouse.chr6 482455 13 + 636262 ATAGAGCAGGGCA -s simRat_chr6.simRat.chr6 490721 13 + 647215 GCAGAGCAGGGCA -s simRat_chr6.simRat.chr6 489975 13 + 647215 GTAGCAAGGAGCA - -a -s simMouse_chr6.simMouse.chr6 481670 2 + 636262 CC -s mr.mrrefChr3 35936 2 + 181027 CC -s simRat_chr6.simRat.chr6 489988 2 + 647215 CC - -a -s simMouse_chr6.simMouse.chr6 481672 4 + 636262 TGCA -s Anc0.Anc0refChr3 99464 4 + 222631 CTGA -s Anc1.Anc1refChr6 132660 4 + 197743 CTGA -s Anc2.Anc2refChr1 10854 4 + 142988 CTGT -s mr.mrrefChr3 35938 4 + 181027 TGCA -s mr.mrrefChr3 36678 4 + 181027 TGGA -s simDog_chr6.simDog.chr6 457537 4 + 593897 CTGT -s simHuman_chr6.simHuman.chr6 464856 4 + 601863 CTGA -s simMouse_chr6.simMouse.chr6 482468 4 + 636262 TGGA -s simRat_chr6.simRat.chr6 490734 4 + 647215 TGGA -s simRat_chr6.simRat.chr6 489990 4 + 647215 TGCA - -a -s simMouse_chr6.simMouse.chr6 481676 13 + 636262 CAGATGTTGCCTT -s Anc0.Anc0refChr3 99480 13 + 222631 AGTATGTTGCCTT -s Anc1.Anc1refChr6 132676 13 + 197743 AGTATGTTGCCTT -s Anc2.Anc2refChr1 10870 13 + 142988 AGTATGTTGCCTT -s mr.mrrefChr3 35942 13 + 181027 CAGATGTTGCCTT -s mr.mrrefChr3 36694 13 + 181027 AGTATGTTGCCTT -s simCow_chr6.simCow.chr6 467602 11 + 602619 --TATGTCACCTT -s simDog_chr6.simDog.chr6 457553 13 + 593897 AGCATGTTGCCTT -s simHuman_chr6.simHuman.chr6 464872 13 + 601863 AATATCTTGCCTT -s simMouse_chr6.simMouse.chr6 482484 13 + 636262 AGTATGTAGCCCT -s simRat_chr6.simRat.chr6 490750 13 + 647215 AGTATGTTGTCTT -s simRat_chr6.simRat.chr6 489994 13 + 647215 AGGATGCTGCCTT - -a -s simMouse_chr6.simMouse.chr6 481689 2 + 636262 CT -s Anc0.Anc0refChr3 99493 2 + 222631 CT -s Anc1.Anc1refChr6 132689 2 + 197743 CT -s Anc2.Anc2refChr1 10883 2 + 142988 CT -s mr.mrrefChr3 35955 2 + 181027 CT -s mr.mrrefChr3 36707 2 + 181027 CT -s simCow_chr6.simCow.chr6 467613 2 + 602619 CT -s simDog_chr6.simDog.chr6 457566 2 + 593897 CT -s simHuman_chr6.simHuman.chr6 464885 2 + 601863 CT -s simMouse_chr6.simMouse.chr6 482497 2 + 636262 CT -s simRat_chr6.simRat.chr6 490007 2 + 647215 CT - -a -s simMouse_chr6.simMouse.chr6 481691 13 + 636262 CACTTAGTTGTCC -s Anc0.Anc0refChr3 99495 13 + 222631 TATTCAGCTGCCC -s Anc1.Anc1refChr6 132691 13 + 197743 TATTCAGCTGCCC -s Anc2.Anc2refChr1 10885 13 + 142988 TATTCAGCTACCC -s mr.mrrefChr3 35957 13 + 181027 CACTTAGTTGTCC -s mr.mrrefChr3 36709 13 + 181027 TATTCAGATGCCC -s simCow_chr6.simCow.chr6 467615 13 + 602619 TATTCAACTACCT -s simDog_chr6.simDog.chr6 457568 13 + 593897 GATACAGCTACCC -s simHuman_chr6.simHuman.chr6 464887 13 + 601863 TTTTCAGCTGCCC -s simMouse_chr6.simMouse.chr6 482499 13 + 636262 TATTCAGATGCCA -s simRat_chr6.simRat.chr6 490763 13 + 647215 TATTCGGATGCCC -s simRat_chr6.simRat.chr6 490009 13 + 647215 CATTCAGTTGTGA - -a -s simMouse_chr6.simMouse.chr6 481704 3 + 636262 TGC -s Anc0.Anc0refChr3 99508 3 + 222631 TAT -s Anc1.Anc1refChr6 132704 3 + 197743 TAT -s Anc2.Anc2refChr1 10898 3 + 142988 TAT -s mr.mrrefChr3 35970 3 + 181027 TGC -s mr.mrrefChr3 36722 3 + 181027 TGT -s simCow_chr6.simCow.chr6 467634 3 + 602619 TCT -s simDog_chr6.simDog.chr6 457581 3 + 593897 TAT -s simHuman_chr6.simHuman.chr6 464900 3 + 601863 TAT -s simMouse_chr6.simMouse.chr6 482512 3 + 636262 TGT -s simRat_chr6.simRat.chr6 490776 3 + 647215 TGT -s simRat_chr6.simRat.chr6 490022 3 + 647215 TGT - -a -s simMouse_chr6.simMouse.chr6 481707 3 + 636262 ATT -s Anc0.Anc0refChr3 99511 3 + 222631 GTC -s Anc1.Anc1refChr6 132707 3 + 197743 GTC -s Anc2.Anc2refChr1 10902 3 + 142988 GTC -s mr.mrrefChr3 35973 3 + 181027 ATT -s mr.mrrefChr3 36725 3 + 181027 GTC -s simCow_chr6.simCow.chr6 467638 3 + 602619 GTC -s simDog_chr6.simDog.chr6 457585 3 + 593897 GCC -s simHuman_chr6.simHuman.chr6 464903 3 + 601863 GTT -s simMouse_chr6.simMouse.chr6 482515 3 + 636262 ATC -s simRat_chr6.simRat.chr6 490779 3 + 647215 GTC -s simRat_chr6.simRat.chr6 490025 3 + 647215 GTT - -a -s simMouse_chr6.simMouse.chr6 481710 2 + 636262 AC -s Anc0.Anc0refChr3 99516 2 + 222631 AC -s Anc1.Anc1refChr6 132712 2 + 197743 AC -s Anc2.Anc2refChr1 10907 2 + 142988 AC -s mr.mrrefChr3 35976 2 + 181027 AC -s mr.mrrefChr3 36728 2 + 181027 TG -s simCow_chr6.simCow.chr6 467643 2 + 602619 GC -s simDog_chr6.simDog.chr6 457590 2 + 593897 AC -s simHuman_chr6.simHuman.chr6 464908 2 + 601863 AC -s simMouse_chr6.simMouse.chr6 482518 2 + 636262 TG -s simRat_chr6.simRat.chr6 490782 2 + 647215 AG -s simRat_chr6.simRat.chr6 490028 2 + 647215 AC - -a -s simMouse_chr6.simMouse.chr6 481712 6 + 636262 ATGTAT -s Anc0.Anc0refChr3 99518 6 + 222631 ATATTT -s Anc1.Anc1refChr6 132714 6 + 197743 ATATTT -s Anc2.Anc2refChr1 10909 6 + 142988 ATATTT -s mr.mrrefChr3 35978 6 + 181027 ATGTAT -s mr.mrrefChr3 36730 6 + 181027 AAATAT -s simCow_chr6.simCow.chr6 467646 6 + 602619 ATGGTT -s simDog_chr6.simDog.chr6 457592 6 + 593897 ATATAT -s simHuman_chr6.simHuman.chr6 464910 6 + 601863 ATCTTT -s simMouse_chr6.simMouse.chr6 482520 6 + 636262 AAATAC -s simRat_chr6.simRat.chr6 490784 6 + 647215 AAATAT -s simRat_chr6.simRat.chr6 490030 6 + 647215 ATGTAT - -a -s simMouse_chr6.simMouse.chr6 481718 4 + 636262 GATG -s Anc0.Anc0refChr3 99524 4 + 222631 GATG -s Anc1.Anc1refChr6 132720 4 + 197743 GATG -s Anc2.Anc2refChr1 10915 4 + 142988 GATG -s mr.mrrefChr3 35984 4 + 181027 GATG -s simCow_chr6.simCow.chr6 467652 4 + 602619 GACA -s simDog_chr6.simDog.chr6 457598 4 + 593897 GCTG -s simHuman_chr6.simHuman.chr6 464916 4 + 601863 AATG -s simRat_chr6.simRat.chr6 490036 4 + 647215 GATG - -a -s simMouse_chr6.simMouse.chr6 481722 30 + 636262 TTCTCCTTACAGATGAGTTGGATCAAAACC -s Anc0.Anc0refChr3 99528 30 + 222631 TTCTCCCAGCTGACAAACTGTATCAAAACT -s Anc1.Anc1refChr6 132724 30 + 197743 TTCTCCCAGCTGACAAACTGTATCAAAACT -s Anc2.Anc2refChr1 10919 30 + 142988 TTCTCTCAGCTGACAAACTGTATCAAAACT -s mr.mrrefChr3 35988 30 + 181027 TTCTCCTTACAGATGAGTTGGATCAAAACC -s mr.mrrefChr3 36736 30 + 181027 TTCTCCAATCAGATAAGCTGTATCTAAACT -s simCow_chr6.simCow.chr6 467656 30 + 602619 TTCTTTCACCTGACGAATTGTATCAAAAAT -s simDog_chr6.simDog.chr6 457602 30 + 593897 TTCTCTCAGCTGACAAACTGTATCAAAACT -s simHuman_chr6.simHuman.chr6 464920 30 + 601863 TCCTCCCAGCTGACAAACCTTATCAAGACT -s simMouse_chr6.simMouse.chr6 482526 30 + 636262 TTCTCCAATCAGATAAGCTGTATCTAAACT -s simRat_chr6.simRat.chr6 490790 30 + 647215 TTCTCCAATCAAATAAGCTGTATCTATACT -s simRat_chr6.simRat.chr6 490040 30 + 647215 TTCCCCTTACAGATGAGTTGGATCAAAGCC - -a -s simMouse_chr6.simMouse.chr6 481752 2 + 636262 TG -s Anc0.Anc0refChr3 99566 2 + 222631 TG -s Anc1.Anc1refChr6 132762 2 + 197743 TG -s Anc2.Anc2refChr1 10957 2 + 142988 TA -s mr.mrrefChr3 36018 2 + 181027 TG -s mr.mrrefChr3 36766 2 + 181027 TG -s simCow_chr6.simCow.chr6 467694 2 + 602619 TA -s simDog_chr6.simDog.chr6 457640 2 + 593897 TA -s simHuman_chr6.simHuman.chr6 464958 2 + 601863 TG -s simMouse_chr6.simMouse.chr6 482556 2 + 636262 TG -s simRat_chr6.simRat.chr6 490820 2 + 647215 TG -s simRat_chr6.simRat.chr6 490070 2 + 647215 TG - -a -s simMouse_chr6.simMouse.chr6 481754 20 + 636262 CACAAATGTACACTCAGTGG -s Anc0.Anc0refChr3 99572 8 + 222631 -----------C-TCAATGT -s Anc1.Anc1refChr6 132774 10 + 197743 C---------AC-TCAATGT -s Anc2.Anc2refChr1 10963 8 + 142988 -----------C-TCAATGA -s mr.mrrefChr3 36020 10 + 181027 C---------CA-TCAGTGG -s mr.mrrefChr3 36778 10 + 181027 C---------TC-TCATTGT -s simCow_chr6.simCow.chr6 467700 7 + 602619 -----------C-TCAATG- -s simDog_chr6.simDog.chr6 457646 8 + 593897 -----------C-TCAATAA -s simHuman_chr6.simHuman.chr6 464987 10 + 601863 C---------AC-TCAATGT -s simMouse_chr6.simMouse.chr6 482568 10 + 636262 C---------TC-TCATTGC -s simRat_chr6.simRat.chr6 490832 10 + 647215 C---------TC-TCAGTGT -s simRat_chr6.simRat.chr6 490072 10 + 647215 C---------CA-TCAGTGG - -a -s simMouse_chr6.simMouse.chr6 481774 9 + 636262 GTGCAAGAA -s Anc0.Anc0refChr3 99583 9 + 222631 GAGTGCAAA -s Anc1.Anc1refChr6 132787 9 + 197743 GAGTGCAAA -s Anc2.Anc2refChr1 10974 9 + 142988 AAGTGCAAG -s mr.mrrefChr3 36030 9 + 181027 GTGCAAGAA -s mr.mrrefChr3 36791 9 + 181027 GTGTACAAA -s simCow_chr6.simCow.chr6 467709 9 + 602619 AAGTGCAAG -s simDog_chr6.simDog.chr6 457657 9 + 593897 AAGTGCAAG -s simHuman_chr6.simHuman.chr6 465000 9 + 601863 GAGTGCGAA -s simMouse_chr6.simMouse.chr6 482581 9 + 636262 ATGTACAAA -s simRat_chr6.simRat.chr6 490845 9 + 647215 GTGCACAAG -s simRat_chr6.simRat.chr6 490082 9 + 647215 GTGCAAGAA - -a -s simMouse_chr6.simMouse.chr6 481783 20 + 636262 GAAACAACAAAGTAAGCACT -s Anc0.Anc0refChr3 99595 19 + 222631 A-AACAATAAAGCAATTACT -s Anc1.Anc1refChr6 132799 19 + 197743 A-AACAATAAAGCAATTACT -s Anc2.Anc2refChr1 10986 19 + 142988 A-AACAATAAAGCACTTACT -s mr.mrrefChr3 36039 19 + 181027 G-AACAACAAAGTAAGCACT -s mr.mrrefChr3 36803 19 + 181027 A-AACAATAAAGCAAATATT -s simCow_chr6.simCow.chr6 467721 19 + 602619 A-AACAATAAAACACTTACT -s simDog_chr6.simDog.chr6 457669 19 + 593897 A-AGCGATAAAGCGCGGACT -s simHuman_chr6.simHuman.chr6 465012 19 + 601863 A-AACAATAAAGCAATTATT -s simMouse_chr6.simMouse.chr6 482593 19 + 636262 A-AACAATAGAGCCAATACT -s simRat_chr6.simRat.chr6 490857 19 + 647215 A-AGCATTAAAGCAAATATT -s simRat_chr6.simRat.chr6 490091 19 + 647215 G-AACAATGAAGTAAGCACT - -a -s simMouse_chr6.simMouse.chr6 481803 1 + 636262 T -s Anc0.Anc0refChr3 99614 1 + 222631 T -s Anc1.Anc1refChr6 132818 1 + 197743 T -s Anc2.Anc2refChr1 11005 1 + 142988 T -s mr.mrrefChr3 36058 1 + 181027 T -s mr.mrrefChr3 36822 1 + 181027 T -s simCow_chr6.simCow.chr6 467740 1 + 602619 T -s simDog_chr6.simDog.chr6 457688 1 + 593897 T -s simHuman_chr6.simHuman.chr6 465034 1 + 601863 T -s simMouse_chr6.simMouse.chr6 482612 1 + 636262 T -s simRat_chr6.simRat.chr6 490876 1 + 647215 T -s simRat_chr6.simRat.chr6 490110 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 481804 14 + 636262 CTCTCCCAGATACT -s Anc0.Anc0refChr3 99615 14 + 222631 CTCTCCATGACACT -s Anc1.Anc1refChr6 132819 14 + 197743 CTCTCCATGACACT -s Anc2.Anc2refChr1 11006 14 + 142988 CTGTCCATGACACT -s mr.mrrefChr3 36059 14 + 181027 CTCTCCCAGATACT -s mr.mrrefChr3 36840 14 + 181027 CTCTCCGTAATACT -s simCow_chr6.simCow.chr6 467741 14 + 602619 CTCTCCATGAAACT -s simDog_chr6.simDog.chr6 457689 14 + 593897 CTGTCCATGACACT -s simHuman_chr6.simHuman.chr6 465035 14 + 601863 CTATCCTTGACATT -s simMouse_chr6.simMouse.chr6 482633 14 + 636262 CTCTCCGCAATACT -s simRat_chr6.simRat.chr6 490894 14 + 647215 CTCACTGTAATACT -s simRat_chr6.simRat.chr6 490111 14 + 647215 CTCTCCCAGACCTC - -a -s simMouse_chr6.simMouse.chr6 481818 1 + 636262 G -s mr.mrrefChr3 36073 1 + 181027 G -s simRat_chr6.simRat.chr6 490125 1 + 647215 G - -a -s simMouse_chr6.simMouse.chr6 481819 25 + 636262 CTTTACAATCAATCCAGCTGCTAAC -s Anc0.Anc0refChr3 99629 19 + 222631 C-TA-----CAATCCAGCCGCTAAC -s Anc1.Anc1refChr6 132833 24 + 197743 C-TACCAAGCAATCCAGCCGCTAAC -s Anc2.Anc2refChr1 11020 19 + 142988 C-TA-----TGACCCAGACGCTAAC -s mr.mrrefChr3 36074 24 + 181027 C-TTACAATCAATCCAGCTGCTAAC -s mr.mrrefChr3 36854 24 + 181027 C-TACTAAGTTTTCTAGCTGCTGAC -s simCow_chr6.simCow.chr6 467755 19 + 602619 C-TA-----TGAAGCAGTTGCTAAC -s simDog_chr6.simDog.chr6 457703 19 + 593897 C-TA-----TGACCCAGACGCTAAT -s simHuman_chr6.simHuman.chr6 465049 19 + 601863 C-TAC-----AATCCAGCCACTAAC -s simMouse_chr6.simMouse.chr6 482647 24 + 636262 C-TTCTAAGTTTTTTAGCTGCTGAC -s simRat_chr6.simRat.chr6 490908 24 + 647215 C-TACTAACTCTTCTAGCTTCTGAC -s simRat_chr6.simRat.chr6 490126 24 + 647215 C-TCACAATCAATTTAGCTGCTAAC - -a -s simMouse_chr6.simMouse.chr6 481844 5 + 636262 ATACT -s Anc0.Anc0refChr3 99648 3 + 222631 AT--G -s Anc1.Anc1refChr6 132857 3 + 197743 AT--G -s Anc2.Anc2refChr1 11039 3 + 142988 AT--G -s mr.mrrefChr3 36098 3 + 181027 AT--T -s mr.mrrefChr3 36878 3 + 181027 GT--G -s simCow_chr6.simCow.chr6 467774 3 + 602619 AC--A -s simDog_chr6.simDog.chr6 457722 3 + 593897 GT--G -s simHuman_chr6.simHuman.chr6 465068 3 + 601863 AT--G -s simMouse_chr6.simMouse.chr6 482671 3 + 636262 GT--G -s simRat_chr6.simRat.chr6 490150 3 + 647215 AT--T - -a -s simMouse_chr6.simMouse.chr6 481849 1 + 636262 C -s Anc0.Anc0refChr3 99651 1 + 222631 T -s Anc1.Anc1refChr6 132860 1 + 197743 T -s Anc2.Anc2refChr1 11042 1 + 142988 T -s mr.mrrefChr3 36101 1 + 181027 C -s mr.mrrefChr3 36881 1 + 181027 T -s simCow_chr6.simCow.chr6 467777 1 + 602619 T -s simDog_chr6.simDog.chr6 457725 1 + 593897 T -s simHuman_chr6.simHuman.chr6 465071 1 + 601863 T -s simMouse_chr6.simMouse.chr6 482674 1 + 636262 T -s simRat_chr6.simRat.chr6 490932 1 + 647215 T -s simRat_chr6.simRat.chr6 490153 1 + 647215 G - -a -s simMouse_chr6.simMouse.chr6 481850 1 + 636262 T -s Anc0.Anc0refChr3 99653 1 + 222631 G -s Anc1.Anc1refChr6 132862 1 + 197743 G -s Anc2.Anc2refChr1 11044 1 + 142988 G -s mr.mrrefChr3 36102 1 + 181027 T -s mr.mrrefChr3 36882 1 + 181027 T -s simCow_chr6.simCow.chr6 467779 1 + 602619 G -s simDog_chr6.simDog.chr6 457727 1 + 593897 G -s simHuman_chr6.simHuman.chr6 465073 1 + 601863 G -s simMouse_chr6.simMouse.chr6 482675 1 + 636262 T -s simRat_chr6.simRat.chr6 490933 1 + 647215 T -s simRat_chr6.simRat.chr6 490154 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 481851 26 + 636262 TAATGAAGTTGTGAGGATGTTAGATG -s Anc0.Anc0refChr3 99655 26 + 222631 TAATGAAGTTCTTAGGAGGGTAAACA -s Anc1.Anc1refChr6 132864 26 + 197743 TAATGAAGTTCTTAGGAGGGTAAACA -s Anc2.Anc2refChr1 11046 26 + 142988 TAATGAAGTTCTTATGAGGGTATACA -s mr.mrrefChr3 36103 26 + 181027 TAATGAAGTTGTGAGGATGTTAGATG -s mr.mrrefChr3 36884 26 + 181027 TTATGAGGTTTTCAAGTTGATAAACA -s simCow_chr6.simCow.chr6 467781 18 + 602619 TAATGAA--------GAGGGTATACA -s simDog_chr6.simDog.chr6 457729 21 + 593897 TAACCAAGTTCTTATGAGGAT----- -s simHuman_chr6.simHuman.chr6 465075 26 + 601863 TAATGAGGCTCTTAGGTGGGTAAACA -s simMouse_chr6.simMouse.chr6 482677 26 + 636262 TTACAAAGTTTTCAAGTTGAGATACA -s simRat_chr6.simRat.chr6 490935 26 + 647215 TTATGAGGTTTTCAAGTAGATAAAAA -s simRat_chr6.simRat.chr6 490155 26 + 647215 TAACGAAGTTTTGAGGATCTTAGATG - -a -s simMouse_chr6.simMouse.chr6 481877 6 + 636262 ATTATG -s mr.mrrefChr3 36129 6 + 181027 ATTATG -s simRat_chr6.simRat.chr6 490181 6 + 647215 ATTATG - -a -s simMouse_chr6.simMouse.chr6 481883 16 + 636262 TCACGGTGTTACATAC -s Anc0.Anc0refChr3 99681 16 + 222631 TCATGGAGTCACATGC -s Anc1.Anc1refChr6 132890 16 + 197743 TCATGGAGTCACATGC -s Anc2.Anc2refChr1 11072 16 + 142988 TCATGGAGTCACATGC -s mr.mrrefChr3 36135 16 + 181027 TCACGGTGTTACATAC -s mr.mrrefChr3 36910 16 + 181027 TCCTGGGGCTACATGC -s simCow_chr6.simCow.chr6 467799 15 + 602619 TCA-GGAATTACATGC -s simDog_chr6.simDog.chr6 457750 14 + 593897 --ATGGAGTCACATGC -s simHuman_chr6.simHuman.chr6 465101 16 + 601863 TCATGGCGTCGCATGT -s simMouse_chr6.simMouse.chr6 482703 16 + 636262 TCCTGGGGCTACATGC -s simRat_chr6.simRat.chr6 490961 16 + 647215 TCCTGGGGCTACATGC -s simRat_chr6.simRat.chr6 490187 16 + 647215 TCACAATGTTACACAC - -a -s simMouse_chr6.simMouse.chr6 481899 5 + 636262 TGCAC -s Anc0.Anc0refChr3 99697 5 + 222631 TGCAT -s Anc1.Anc1refChr6 132906 5 + 197743 TGCAT -s Anc2.Anc2refChr1 11090 5 + 142988 TGCAT -s mr.mrrefChr3 36151 5 + 181027 TGCAC -s mr.mrrefChr3 36926 5 + 181027 TGTAC -s simCow_chr6.simCow.chr6 467816 5 + 602619 TGCAT -s simDog_chr6.simDog.chr6 457766 5 + 593897 CACAT -s simHuman_chr6.simHuman.chr6 465117 5 + 601863 TGTCT -s simMouse_chr6.simMouse.chr6 482719 5 + 636262 TGTAC -s simRat_chr6.simRat.chr6 490977 5 + 647215 TGTAC -s simRat_chr6.simRat.chr6 490203 5 + 647215 TGCAC - -a -s simMouse_chr6.simMouse.chr6 481904 66 + 636262 ATAAGTTCAATATCTTGTCATGATAACCCCTATTTTGAGGCATCTATCCCCCTGAGCAGGAATGCT -s Anc0.Anc0refChr3 99702 18 + 222631 ATAATGTCAATATCTGGT------------------------------------------------ -s Anc1.Anc1refChr6 132911 19 + 197743 ATAATGTCAATATCTGGTC----------------------------------------------- -s Anc2.Anc2refChr1 11095 18 + 142988 GTAATGTCAATATCTGGT------------------------------------------------ -s mr.mrrefChr3 36156 66 + 181027 ATAAGTTCAATATCTTGTCATGATAACCCCTATTTTGAGGCATCTATCCCCCTGAGCAGGAATGCT -s simCow_chr6.simCow.chr6 467821 18 + 602619 GTAATGTCAGTATCTGGT------------------------------------------------ -s simDog_chr6.simDog.chr6 457771 18 + 593897 GTAGTGTCAATATCTGGT------------------------------------------------ -s simHuman_chr6.simHuman.chr6 465122 19 + 601863 AGAATCCCAATATCTGGTC----------------------------------------------- -s simRat_chr6.simRat.chr6 490208 66 + 647215 ATAATTTTACTAGCTTGTCCTGATAACTCCTGTTTTGAGGTCTCTATCCCCCTGACCAGGGCTGCT - -a -s simMouse_chr6.simMouse.chr6 481970 19 + 636262 GATGATTCAGTGGAGACTA -s mr.mrrefChr3 36222 19 + 181027 GATGATTCAGTGGAGACTA -s simRat_chr6.simRat.chr6 490276 19 + 647215 GATGATTCAGTGGGGACTA - -a -s simMouse_chr6.simMouse.chr6 481989 4 + 636262 TTGA -s Anc1.Anc1refChr6 132930 4 + 197743 TTGA -s mr.mrrefChr3 36241 4 + 181027 TTGA -s mr.mrrefChr3 36931 4 + 181027 TTGA -s simMouse_chr6.simMouse.chr6 482724 4 + 636262 TTGA -s simRat_chr6.simRat.chr6 490982 4 + 647215 TTGA -s simRat_chr6.simRat.chr6 490295 4 + 647215 TTGA - -a -s simMouse_chr6.simMouse.chr6 481993 43 + 636262 TGATTCAGTGGGTTTCAATACATGATTCCTGAATAGTTGGCAC -s Anc0.Anc0refChr3 99720 1 + 222631 ------------------------------------------C -s Anc1.Anc1refChr6 132934 43 + 197743 TGATGTAGTGGGTATTGTTGCAGGACTACTGATTAGTTGGCAC -s Anc2.Anc2refChr1 11113 1 + 142988 ------------------------------------------T -s mr.mrrefChr3 36245 43 + 181027 TGATTCAGTGGGTTTCAATACATGATTCCTGAATAGTTGGCAC -s mr.mrrefChr3 36938 43 + 181027 TGGTGTGGTGGGGACTGTAGGAGTACTACTGATTAGCTGGCAC -s simCow_chr6.simCow.chr6 467839 1 + 602619 ------------------------------------------T -s simDog_chr6.simDog.chr6 457789 1 + 593897 ------------------------------------------T -s simMouse_chr6.simMouse.chr6 482731 43 + 636262 TGGTGTGGTGGGGACTGTAGGAGTACTACTGATTAGCTGGCAC -s simRat_chr6.simRat.chr6 490989 43 + 647215 TGGTGTGGTGGGGACTGTAGGAGTAATATTGATTACCTGGCAC -s simRat_chr6.simRat.chr6 490299 43 + 647215 TAATTCAGTCGGTTTTAATACAAGATGCCTGGGTAGTTTGCAC - -a -s simMouse_chr6.simMouse.chr6 482036 13 + 636262 ACACTGCTGAATA -s Anc0.Anc0refChr3 99815 11 + 222631 --CACGTTGAATA -s Anc1.Anc1refChr6 133072 13 + 197743 ATCACGTTGAATA -s Anc2.Anc2refChr1 11210 11 + 142988 --CACATTGAATA -s mr.mrrefChr3 36288 13 + 181027 ACACTGCTGAATA -s mr.mrrefChr3 37130 13 + 181027 ATGATGTAGAATA -s simDog_chr6.simDog.chr6 457895 11 + 593897 --CACATTGAATA -s simHuman_chr6.simHuman.chr6 465235 13 + 601863 ATCACTTTGAATA -s simMouse_chr6.simMouse.chr6 482906 13 + 636262 ATGATGTAGCATA -s simRat_chr6.simRat.chr6 491194 13 + 647215 CTAATGTAGAATA -s simRat_chr6.simRat.chr6 490342 13 + 647215 CCACTGCCGAATA - -a -s simMouse_chr6.simMouse.chr6 482049 1 + 636262 A -s Anc0.Anc0refChr3 99826 1 + 222631 G -s Anc1.Anc1refChr6 133085 1 + 197743 G -s Anc2.Anc2refChr1 11221 1 + 142988 G -s mr.mrrefChr3 36301 1 + 181027 A -s mr.mrrefChr3 37143 1 + 181027 G -s simDog_chr6.simDog.chr6 457906 1 + 593897 G -s simHuman_chr6.simHuman.chr6 465248 1 + 601863 T -s simMouse_chr6.simMouse.chr6 482919 1 + 636262 G -s simRat_chr6.simRat.chr6 491207 1 + 647215 G -s simRat_chr6.simRat.chr6 490356 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 482050 22 + 636262 TAAGCGTGCTTTAATACACCAA -s Anc0.Anc0refChr3 99828 22 + 222631 TAACCGCACTTTAATAGGCCAA -s Anc1.Anc1refChr6 133087 22 + 197743 TAACCGCACTTTAATAGGCCAA -s Anc2.Anc2refChr1 11223 22 + 142988 TATCCGCACTTTAACAGGCCAA -s mr.mrrefChr3 36302 22 + 181027 TAAGCGTGCTTTAATACACCAA -s mr.mrrefChr3 37145 22 + 181027 TAATGACACTGTAATAAGTCAA -s simCow_chr6.simCow.chr6 467943 10 + 602619 ------------AACAGACCAT -s simDog_chr6.simDog.chr6 457908 22 + 593897 TATCCGCACTTTAACAGGCCAA -s simHuman_chr6.simHuman.chr6 465250 22 + 601863 TAAACTCACTTTAATGGGTCAA -s simMouse_chr6.simMouse.chr6 482921 22 + 636262 TAATGACACTGTAATAAGTCAA -s simRat_chr6.simRat.chr6 491209 22 + 647215 TAATGACCCTGTAATAAGTGAA -s simRat_chr6.simRat.chr6 490357 22 + 647215 TAAGCTCACTTTTAGAGACCAA - -a -s simMouse_chr6.simMouse.chr6 482072 2 + 636262 AA -s mr.mrrefChr3 36324 2 + 181027 AA -s simRat_chr6.simRat.chr6 490379 2 + 647215 AA - -a -s simMouse_chr6.simMouse.chr6 482074 3 + 636262 TGC -s Anc0.Anc0refChr3 99850 3 + 222631 TGC -s Anc1.Anc1refChr6 133109 3 + 197743 TGC -s Anc2.Anc2refChr1 11245 3 + 142988 TGC -s mr.mrrefChr3 36326 3 + 181027 TGC -s mr.mrrefChr3 37167 3 + 181027 TGC -s simCow_chr6.simCow.chr6 467953 3 + 602619 TGT -s simDog_chr6.simDog.chr6 457930 3 + 593897 TGC -s simHuman_chr6.simHuman.chr6 465272 3 + 601863 TGC -s simMouse_chr6.simMouse.chr6 482943 3 + 636262 TGT -s simRat_chr6.simRat.chr6 491231 3 + 647215 CAC -s simRat_chr6.simRat.chr6 490381 3 + 647215 TGC - -a -s simMouse_chr6.simMouse.chr6 482077 35 + 636262 ATTACCAGCAAGCATTATTTTTGGAGCTGGTCATG -s Anc0.Anc0refChr3 99853 35 + 222631 ATTATCATCAACCATCTTTATTGGAATTGGACATG -s Anc1.Anc1refChr6 133112 35 + 197743 ATTATCATCAACCATCTTTATTGGAATTGGACATG -s Anc2.Anc2refChr1 11248 35 + 142988 ATTATCAACAACCATCTCTATTGGAATTGAACATC -s mr.mrrefChr3 36329 35 + 181027 ATTACCAGCAAGCATTATTTTTGGAGCTGGTCATG -s mr.mrrefChr3 37170 35 + 181027 ATTATCATCAACTATGTTTATTAGAATTGGACATG -s simCow_chr6.simCow.chr6 467956 35 + 602619 ATTATCAACAACAATCTCTAATGGAATTGAACATC -s simDog_chr6.simDog.chr6 457933 35 + 593897 ATTATCGACGATCATCTCTATTGGAATTGAACAAC -s simHuman_chr6.simHuman.chr6 465275 34 + 601863 ATTATCATCAGCCAC-TTTATTGGAATTGGATATA -s simMouse_chr6.simMouse.chr6 482948 35 + 636262 ATTATCCTCAACTATGTCTATTAGAATTGGACATG -s simRat_chr6.simRat.chr6 491234 35 + 647215 ATTATCATCAACTATGTTTATTAGAACTCAACATG -s simRat_chr6.simRat.chr6 490384 35 + 647215 ATTACTAGTGAGCATTATTATTGAAGCTGGACATG - -a -s simMouse_chr6.simMouse.chr6 482112 1 + 636262 C -s Anc0.Anc0refChr3 99888 1 + 222631 G -s Anc1.Anc1refChr6 133147 1 + 197743 G -s Anc2.Anc2refChr1 11283 1 + 142988 A -s mr.mrrefChr3 36364 1 + 181027 C -s mr.mrrefChr3 37205 1 + 181027 G -s simCow_chr6.simCow.chr6 467991 1 + 602619 A -s simDog_chr6.simDog.chr6 457968 1 + 593897 A -s simHuman_chr6.simHuman.chr6 465309 1 + 601863 G -s simMouse_chr6.simMouse.chr6 482983 1 + 636262 G -s simRat_chr6.simRat.chr6 490419 1 + 647215 C - -a -s simMouse_chr6.simMouse.chr6 482113 1 + 636262 C -s Anc0.Anc0refChr3 99889 1 + 222631 C -s Anc1.Anc1refChr6 133148 1 + 197743 C -s Anc2.Anc2refChr1 11284 1 + 142988 C -s mr.mrrefChr3 36365 1 + 181027 C -s mr.mrrefChr3 37206 1 + 181027 T -s simCow_chr6.simCow.chr6 467992 1 + 602619 T -s simDog_chr6.simDog.chr6 457969 1 + 593897 C -s simHuman_chr6.simHuman.chr6 465310 1 + 601863 C -s simMouse_chr6.simMouse.chr6 482984 1 + 636262 T -s simRat_chr6.simRat.chr6 491269 1 + 647215 T -s simRat_chr6.simRat.chr6 490420 1 + 647215 C - -a -s simMouse_chr6.simMouse.chr6 482114 41 + 636262 TGATGGAGCTGGTCATGCCGGACTACCCCACTACTGAAGTC -s Anc0.Anc0refChr3 99890 3 + 222631 A-------------------GA------------------- -s Anc1.Anc1refChr6 133149 22 + 197743 A-------------------GACTCCCATGCCATTGAAGTA -s Anc2.Anc2refChr1 11285 3 + 142988 A-------------------GG------------------- -s mr.mrrefChr3 36366 22 + 181027 T-------------------GACTACCCCACTACTGAAGTC -s mr.mrrefChr3 37208 22 + 181027 T-------------------AACTCATATGCCATTGGGATA -s simCow_chr6.simCow.chr6 467993 3 + 602619 A-------------------AG------------------- -s simDog_chr6.simDog.chr6 457970 3 + 593897 A-------------------GG------------------- -s simHuman_chr6.simHuman.chr6 465311 3 + 601863 A-------------------GA------------------- -s simMouse_chr6.simMouse.chr6 482986 22 + 636262 T-------------------AACTCATATGCCATTGGGATA -s simRat_chr6.simRat.chr6 491271 22 + 647215 T-------------------AACTCCTCTGCCATCGGCATT -s simRat_chr6.simRat.chr6 490421 22 + 647215 T-------------------ATCTACTCCATAATTGAAGTC - -a -s simMouse_chr6.simMouse.chr6 482155 22 + 636262 GCTCCTAGGGCATTACCTGCAC -s Anc1.Anc1refChr6 133171 22 + 197743 GCTACTATGGCCTTACTTGCAC -s mr.mrrefChr3 36388 22 + 181027 GCTCCTAGGGCATTACCTGCAC -s mr.mrrefChr3 37230 22 + 181027 GCTACCATGCCCTTACTTGAAT -s simMouse_chr6.simMouse.chr6 483008 22 + 636262 GCTACCATGCCCTTACTTGAAT -s simRat_chr6.simRat.chr6 491299 22 + 647215 GCTACCACTCCAATACTTGAAT -s simRat_chr6.simRat.chr6 490443 22 + 647215 ACTACCAAGGTGTTACCTGCAC - -a -s simMouse_chr6.simMouse.chr6 482177 1 + 636262 C -s Anc0.Anc0refChr3 99904 1 + 222631 C -s Anc1.Anc1refChr6 133204 1 + 197743 C -s Anc2.Anc2refChr1 11299 1 + 142988 C -s mr.mrrefChr3 36410 1 + 181027 C -s mr.mrrefChr3 37265 1 + 181027 C -s simCow_chr6.simCow.chr6 468007 1 + 602619 C -s simDog_chr6.simDog.chr6 457984 1 + 593897 C -s simHuman_chr6.simHuman.chr6 465325 1 + 601863 C -s simMouse_chr6.simMouse.chr6 483043 1 + 636262 C -s simRat_chr6.simRat.chr6 491334 1 + 647215 T -s simRat_chr6.simRat.chr6 490465 1 + 647215 C - -a -s simMouse_chr6.simMouse.chr6 482178 27 + 636262 AACTAGCTACACATTATGTGCACCATA -s Anc0.Anc0refChr3 99905 21 + 222631 AAATATATAT------TGTATATACTC -s Anc1.Anc1refChr6 133205 21 + 197743 AAATATATAT------TGTATATACTC -s Anc2.Anc2refChr1 11300 21 + 142988 TAATATTTAT------TATATATATTC -s mr.mrrefChr3 36411 21 + 181027 AACTAGCTAC------TGTGCACCATA -s mr.mrrefChr3 37266 21 + 181027 AAATGTATAT------TGTATATACTC -s simCow_chr6.simCow.chr6 468008 20 + 602619 TAATATG-AT------TCTATATATCC -s simDog_chr6.simDog.chr6 457985 21 + 593897 TAATGTTTAT------TATATATATTC -s simHuman_chr6.simHuman.chr6 465327 21 + 601863 AAATATATAT------ATTATATACTC -s simMouse_chr6.simMouse.chr6 483044 21 + 636262 AAATGTATAT------TGTACATACGC -s simRat_chr6.simRat.chr6 491335 21 + 647215 AAAGGTATAC------TGTATGTACTC -s simRat_chr6.simRat.chr6 490466 21 + 647215 AACTAGCTAT------TGTGGCCCGTA - -a -s simMouse_chr6.simMouse.chr6 482205 5 + 636262 CCTGT -s Anc0.Anc0refChr3 99926 5 + 222631 CCATT -s Anc1.Anc1refChr6 133226 5 + 197743 CCATT -s Anc2.Anc2refChr1 11321 5 + 142988 CTATT -s mr.mrrefChr3 36432 5 + 181027 CCTGT -s mr.mrrefChr3 37287 5 + 181027 CCATT -s simCow_chr6.simCow.chr6 468028 5 + 602619 CTATT -s simDog_chr6.simDog.chr6 458006 5 + 593897 CTGTT -s simHuman_chr6.simHuman.chr6 465348 5 + 601863 CCATT -s simMouse_chr6.simMouse.chr6 483065 5 + 636262 CCAGT -s simRat_chr6.simRat.chr6 491391 5 + 647215 CCATT -s simRat_chr6.simRat.chr6 490487 5 + 647215 CTTGT - -a -s simMouse_chr6.simMouse.chr6 482210 3 + 636262 ATT -s Anc0.Anc0refChr3 99931 3 + 222631 GTT -s Anc1.Anc1refChr6 133231 3 + 197743 GTT -s Anc2.Anc2refChr1 11326 3 + 142988 GTC -s mr.mrrefChr3 36437 3 + 181027 ATT -s mr.mrrefChr3 37292 3 + 181027 GTT -s simCow_chr6.simCow.chr6 468033 3 + 602619 GCC -s simDog_chr6.simDog.chr6 458011 3 + 593897 GTC -s simHuman_chr6.simHuman.chr6 465353 3 + 601863 GTA -s simMouse_chr6.simMouse.chr6 483070 3 + 636262 GTT -s simRat_chr6.simRat.chr6 491396 3 + 647215 GTC -s simRat_chr6.simRat.chr6 490493 3 + 647215 ATT - -a -s simMouse_chr6.simMouse.chr6 482213 12 + 636262 CCATTGGTAAGC -s Anc0.Anc0refChr3 99937 12 + 222631 TCAGTGTTGAGC -s Anc1.Anc1refChr6 133237 12 + 197743 TCAGTGTTGAGC -s Anc2.Anc2refChr1 11332 12 + 142988 TCAGTGTTGGGC -s mr.mrrefChr3 36440 12 + 181027 CCATTGGTAAGC -s mr.mrrefChr3 37298 12 + 181027 TCAGTGCTGAGC -s simCow_chr6.simCow.chr6 468039 12 + 602619 CCAGTGCTGGGC -s simDog_chr6.simDog.chr6 458017 12 + 593897 TCAGTGTTGGGC -s simHuman_chr6.simHuman.chr6 465359 12 + 601863 TGAGTGTTAAGC -s simMouse_chr6.simMouse.chr6 483076 12 + 636262 TCAGTGCTGAGC -s simRat_chr6.simRat.chr6 491402 12 + 647215 TCAGTGCTGAGC -s simRat_chr6.simRat.chr6 490496 12 + 647215 CCACTGTTAAGC - -a -s simMouse_chr6.simMouse.chr6 482225 3 + 636262 CCA -s Anc0.Anc0refChr3 99949 3 + 222631 CAA -s Anc1.Anc1refChr6 133249 3 + 197743 CAA -s Anc2.Anc2refChr1 11344 3 + 142988 CAG -s mr.mrrefChr3 36452 3 + 181027 CCA -s mr.mrrefChr3 37310 3 + 181027 CAA -s simCow_chr6.simCow.chr6 468051 3 + 602619 CGA -s simDog_chr6.simDog.chr6 458029 3 + 593897 TAG -s simHuman_chr6.simHuman.chr6 465371 3 + 601863 CAC -s simMouse_chr6.simMouse.chr6 483088 3 + 636262 CAA -s simRat_chr6.simRat.chr6 490508 3 + 647215 CAA - -a -s simMouse_chr6.simMouse.chr6 482228 3 + 636262 TGT -s Anc0.Anc0refChr3 99954 2 + 222631 T-T -s Anc1.Anc1refChr6 133254 3 + 197743 TGT -s Anc2.Anc2refChr1 11349 2 + 142988 T-C -s mr.mrrefChr3 36455 3 + 181027 TGT -s mr.mrrefChr3 37315 3 + 181027 TGT -s simCow_chr6.simCow.chr6 468056 2 + 602619 T-T -s simDog_chr6.simDog.chr6 458034 2 + 593897 C-C -s simHuman_chr6.simHuman.chr6 465376 3 + 601863 TGG -s simMouse_chr6.simMouse.chr6 483093 3 + 636262 TGT -s simRat_chr6.simRat.chr6 490511 3 + 647215 TGT - -a -s simMouse_chr6.simMouse.chr6 482231 12 + 636262 GAAAAAATATTT -s Anc0.Anc0refChr3 99956 11 + 222631 GAAGTATAATT- -s Anc1.Anc1refChr6 133257 11 + 197743 GAAGTATAATT- -s Anc2.Anc2refChr1 11351 11 + 142988 GAAGTATAATT- -s mr.mrrefChr3 36458 12 + 181027 GAAAAAATATTT -s mr.mrrefChr3 37318 11 + 181027 GAACTGTTATT- -s simCow_chr6.simCow.chr6 468058 11 + 602619 GAAGTGTAATT- -s simDog_chr6.simDog.chr6 458036 11 + 593897 AAAGTATAACT- -s simHuman_chr6.simHuman.chr6 465379 11 + 601863 GAAGTATAATT- -s simMouse_chr6.simMouse.chr6 483097 11 + 636262 GAACTGTTATT- -s simRat_chr6.simRat.chr6 490514 12 + 647215 GAAAAAATAAAT - -a -s simMouse_chr6.simMouse.chr6 482243 8 + 636262 ATAGCTAA -s Anc0.Anc0refChr3 99967 3 + 222631 ATA----- -s Anc1.Anc1refChr6 133268 3 + 197743 ATA----- -s Anc2.Anc2refChr1 11362 3 + 142988 TAA----- -s mr.mrrefChr3 36470 8 + 181027 ATAGCTAA -s mr.mrrefChr3 37329 3 + 181027 ATA----- -s simCow_chr6.simCow.chr6 468074 3 + 602619 CAA----- -s simDog_chr6.simDog.chr6 458047 3 + 593897 TAA----- -s simHuman_chr6.simHuman.chr6 465390 3 + 601863 ATT----- -s simMouse_chr6.simMouse.chr6 483108 3 + 636262 ATA----- -s simRat_chr6.simRat.chr6 490526 8 + 647215 ATAGCTAA - -a -s simMouse_chr6.simMouse.chr6 482251 2 + 636262 AT -s Anc0.Anc0refChr3 99970 2 + 222631 AT -s Anc1.Anc1refChr6 133271 2 + 197743 AT -s Anc2.Anc2refChr1 11365 2 + 142988 AT -s mr.mrrefChr3 36478 2 + 181027 AT -s mr.mrrefChr3 37332 2 + 181027 AT -s simCow_chr6.simCow.chr6 468077 2 + 602619 GT -s simDog_chr6.simDog.chr6 458050 2 + 593897 AT -s simHuman_chr6.simHuman.chr6 465393 2 + 601863 AT -s simMouse_chr6.simMouse.chr6 483116 2 + 636262 AT -s simRat_chr6.simRat.chr6 490534 2 + 647215 AT - -a -s simMouse_chr6.simMouse.chr6 482253 5 + 636262 TCTTG -s Anc0.Anc0refChr3 99972 5 + 222631 TCATG -s Anc1.Anc1refChr6 133273 5 + 197743 TCATG -s Anc2.Anc2refChr1 11367 5 + 142988 TCAGG -s mr.mrrefChr3 36480 5 + 181027 TCTTG -s mr.mrrefChr3 37334 5 + 181027 TTGTA -s simCow_chr6.simCow.chr6 468079 5 + 602619 TCATG -s simDog_chr6.simDog.chr6 458052 5 + 593897 CCAGG -s simHuman_chr6.simHuman.chr6 465395 5 + 601863 TCACG -s simMouse_chr6.simMouse.chr6 483118 5 + 636262 TTGTA -s simRat_chr6.simRat.chr6 491414 5 + 647215 TTGTA -s simRat_chr6.simRat.chr6 490536 5 + 647215 TCTGG - -a -s simMouse_chr6.simMouse.chr6 482258 1 + 636262 G -s Anc0.Anc0refChr3 99977 1 + 222631 A -s Anc1.Anc1refChr6 133278 1 + 197743 A -s Anc2.Anc2refChr1 11372 1 + 142988 A -s mr.mrrefChr3 36485 1 + 181027 G -s mr.mrrefChr3 37339 1 + 181027 A -s simCow_chr6.simCow.chr6 468084 1 + 602619 A -s simDog_chr6.simDog.chr6 458057 1 + 593897 A -s simHuman_chr6.simHuman.chr6 465400 1 + 601863 A -s simMouse_chr6.simMouse.chr6 483123 1 + 636262 A -s simRat_chr6.simRat.chr6 490541 1 + 647215 G - -a -s simMouse_chr6.simMouse.chr6 482259 42 + 636262 ATTAGCAGACCACAATCCTGCACCATGGCTAGGCCACATCCA -s Anc0.Anc0refChr3 99978 25 + 222631 ATAGATGGGCCACAATCATGCA-----------------CCA -s Anc1.Anc1refChr6 133279 25 + 197743 ATAGATGGGCCACAATCATGCA-----------------CCA -s Anc2.Anc2refChr1 11373 25 + 142988 ATAGATGGGCCACAATCATGCA-----------------CCA -s mr.mrrefChr3 36486 25 + 181027 ATTAGCAGACCACAATCCTGCA-----------------CCA -s mr.mrrefChr3 37340 25 + 181027 GTAGATTGACCACAGTCATACA-----------------TCA -s simCow_chr6.simCow.chr6 468085 25 + 602619 ATAGATGGGCCACAATCATGCA-----------------CCA -s simDog_chr6.simDog.chr6 458058 25 + 593897 ATGGATGGGCCACAATCATGTG-----------------CCA -s simHuman_chr6.simHuman.chr6 465401 25 + 601863 ATAGATGGGCCACAATTTTACA-----------------CCA -s simMouse_chr6.simMouse.chr6 483124 25 + 636262 GTAGATTGACCACAGTCATACC-----------------TCA -s simRat_chr6.simRat.chr6 491419 25 + 647215 GTAGATAAACCACAGTCATACA-----------------TCG -s simRat_chr6.simRat.chr6 490542 25 + 647215 ATCACCAGACCACAATCTTGCA-----------------CCA - -a -s simMouse_chr6.simMouse.chr6 482301 3 + 636262 GTG -s mr.mrrefChr3 36511 3 + 181027 GTG -s simRat_chr6.simRat.chr6 490567 3 + 647215 ATA - -a -s simMouse_chr6.simMouse.chr6 482304 1 + 636262 T -s Anc0.Anc0refChr3 100003 1 + 222631 T -s Anc1.Anc1refChr6 133304 1 + 197743 T -s Anc2.Anc2refChr1 11398 1 + 142988 T -s mr.mrrefChr3 36514 1 + 181027 T -s mr.mrrefChr3 37365 1 + 181027 T -s simCow_chr6.simCow.chr6 468110 1 + 602619 T -s simDog_chr6.simDog.chr6 458083 1 + 593897 T -s simHuman_chr6.simHuman.chr6 465426 1 + 601863 C -s simMouse_chr6.simMouse.chr6 483149 1 + 636262 T -s simRat_chr6.simRat.chr6 491444 1 + 647215 T -s simRat_chr6.simRat.chr6 490570 1 + 647215 C - -a -s simMouse_chr6.simMouse.chr6 482325 1 + 636262 T -s Anc0.Anc0refChr3 99288 1 + 222631 T -s Anc1.Anc1refChr6 132484 1 + 197743 T -s Anc2.Anc2refChr1 10667 1 + 142988 T -s mr.mrrefChr3 36535 1 + 181027 T -s simCow_chr6.simCow.chr6 467426 1 + 602619 T -s simDog_chr6.simDog.chr6 457355 1 + 593897 T -s simHuman_chr6.simHuman.chr6 464687 1 + 601863 T -s simRat_chr6.simRat.chr6 490592 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 482326 2 + 636262 CC -s Anc0.Anc0refChr3 99299 2 + 222631 CT -s Anc1.Anc1refChr6 132495 2 + 197743 CT -s Anc2.Anc2refChr1 10678 2 + 142988 CT -s mr.mrrefChr3 36536 2 + 181027 CT -s simCow_chr6.simCow.chr6 467437 2 + 602619 CT -s simDog_chr6.simDog.chr6 457366 2 + 593897 CT -s simHuman_chr6.simHuman.chr6 464698 2 + 601863 TT -s simRat_chr6.simRat.chr6 490593 2 + 647215 CT - -a -s simMouse_chr6.simMouse.chr6 482328 2 + 636262 CT -s Anc0.Anc0refChr3 99301 2 + 222631 CT -s Anc1.Anc1refChr6 132497 2 + 197743 CT -s Anc2.Anc2refChr1 10680 2 + 142988 CT -s mr.mrrefChr3 36538 2 + 181027 CT -s simCow_chr6.simCow.chr6 467442 2 + 602619 CT -s simDog_chr6.simDog.chr6 457368 2 + 593897 CT -s simHuman_chr6.simHuman.chr6 464700 2 + 601863 GT -s simRat_chr6.simRat.chr6 490595 2 + 647215 CT - -a -s simMouse_chr6.simMouse.chr6 482330 1 + 636262 A -s Anc0.Anc0refChr3 99303 1 + 222631 A -s Anc1.Anc1refChr6 132499 1 + 197743 A -s Anc2.Anc2refChr1 10688 1 + 142988 C -s mr.mrrefChr3 36540 1 + 181027 A -s simCow_chr6.simCow.chr6 467450 1 + 602619 C -s simDog_chr6.simDog.chr6 457376 1 + 593897 C -s simHuman_chr6.simHuman.chr6 464702 1 + 601863 A -s simRat_chr6.simRat.chr6 490597 1 + 647215 C - -a -s simMouse_chr6.simMouse.chr6 482472 12 + 636262 ATGTTTTATTGT -s Anc0.Anc0refChr3 99468 12 + 222631 ATGTCTTCTGAT -s Anc1.Anc1refChr6 132664 12 + 197743 ATGTCTTCTGAT -s Anc2.Anc2refChr1 10858 12 + 142988 AAGCCTGCTGAT -s mr.mrrefChr3 36682 12 + 181027 ATGTCTTATTGT -s simDog_chr6.simDog.chr6 457541 12 + 593897 AAGCCTGCTGAT -s simHuman_chr6.simHuman.chr6 464860 12 + 601863 ATGTCTTTTGAT -s simRat_chr6.simRat.chr6 490738 12 + 647215 ATTTCTTATTGC - -a -s simMouse_chr6.simMouse.chr6 482558 9 + 636262 GTCACTGAA -s Anc0.Anc0refChr3 99568 4 + 222631 GACA----- -s Anc1.Anc1refChr6 132764 9 + 197743 GACACTCAA -s Anc2.Anc2refChr1 10959 4 + 142988 GACA----- -s mr.mrrefChr3 36768 9 + 181027 GTCACTGAA -s simCow_chr6.simCow.chr6 467696 4 + 602619 GACA----- -s simDog_chr6.simDog.chr6 457642 4 + 593897 GACA----- -s simHuman_chr6.simHuman.chr6 464960 9 + 601863 GACACTCAA -s simRat_chr6.simRat.chr6 490822 9 + 647215 GTCACCAAA - -a -s simMouse_chr6.simMouse.chr6 482567 1 + 636262 A -s Anc1.Anc1refChr6 132773 1 + 197743 A -s mr.mrrefChr3 36777 1 + 181027 A -s simHuman_chr6.simHuman.chr6 464986 1 + 601863 A -s simRat_chr6.simRat.chr6 490831 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 482578 3 + 636262 ACC -s Anc0.Anc0refChr3 99580 3 + 222631 ATC -s Anc1.Anc1refChr6 132784 3 + 197743 ATC -s Anc2.Anc2refChr1 10971 3 + 142988 ATC -s mr.mrrefChr3 36788 3 + 181027 ATC -s simCow_chr6.simCow.chr6 467707 2 + 602619 -CC -s simDog_chr6.simDog.chr6 457654 3 + 593897 ATC -s simHuman_chr6.simHuman.chr6 464997 3 + 601863 ATT -s simRat_chr6.simRat.chr6 490842 3 + 647215 GTC - -a -s simMouse_chr6.simMouse.chr6 482590 3 + 636262 TGG -s Anc0.Anc0refChr3 99592 3 + 222631 AAG -s Anc1.Anc1refChr6 132796 3 + 197743 AAG -s Anc2.Anc2refChr1 10983 3 + 142988 AAA -s mr.mrrefChr3 36800 3 + 181027 TGG -s simCow_chr6.simCow.chr6 467718 3 + 602619 GAA -s simDog_chr6.simDog.chr6 457666 3 + 593897 AAA -s simHuman_chr6.simHuman.chr6 465009 3 + 601863 AAG -s simRat_chr6.simRat.chr6 490854 3 + 647215 TGG - -a -s simMouse_chr6.simMouse.chr6 482613 20 + 636262 ATCAATAAAGCATGTACTTC -s mr.mrrefChr3 36823 17 + 181027 ATCAATAAAGCATGCAT--- -s simRat_chr6.simRat.chr6 490877 17 + 647215 ATCAATACAGCAAGCAT--- - -a -s simMouse_chr6.simMouse.chr6 482676 1 + 636262 G -s Anc0.Anc0refChr3 99654 1 + 222631 G -s Anc1.Anc1refChr6 132863 1 + 197743 G -s Anc2.Anc2refChr1 11045 1 + 142988 T -s mr.mrrefChr3 36883 1 + 181027 G -s simCow_chr6.simCow.chr6 467780 1 + 602619 T -s simDog_chr6.simDog.chr6 457728 1 + 593897 T -s simHuman_chr6.simHuman.chr6 465074 1 + 601863 G -s simRat_chr6.simRat.chr6 490934 1 + 647215 G - -a -s simMouse_chr6.simMouse.chr6 482728 3 + 636262 ACC -s mr.mrrefChr3 36935 3 + 181027 ACC -s simRat_chr6.simRat.chr6 490986 3 + 647215 GCC - -a -s simMouse_chr6.simMouse.chr6 482774 55 + 636262 TTAACCCAAGTGTCCAACTGTAAATTCAGCATGGTTTTGGGGATCTGAGTCTGAA -s Anc0.Anc0refChr3 99721 5 + 222631 --------------------------------------------------CTGGA -s Anc1.Anc1refChr6 132977 5 + 197743 --------------------------------------------------CTGGA -s Anc2.Anc2refChr1 11114 5 + 142988 --------------------------------------------------CTGGA -s mr.mrrefChr3 36981 55 + 181027 TTAACCCAAGTGTCCAACTGTAAATTCAGCATGGTTTTGGGGATCTGAGTCTGAA -s simCow_chr6.simCow.chr6 467840 5 + 602619 --------------------------------------------------GTGGA -s simDog_chr6.simDog.chr6 457790 5 + 593897 --------------------------------------------------CTGAA -s simHuman_chr6.simHuman.chr6 465141 5 + 601863 --------------------------------------------------CTGGA -s simRat_chr6.simRat.chr6 491032 55 + 647215 TTAACCCAAGTATCCAACTGTAAATTCAGCATGGAGTTACAGATCTGACTCTGAA - -a -s simMouse_chr6.simMouse.chr6 482829 12 + 636262 AACTGTCATTTC -s Anc0.Anc0refChr3 99726 12 + 222631 AACTCTTATTTC -s Anc1.Anc1refChr6 132982 12 + 197743 AACTCTTATTTC -s Anc2.Anc2refChr1 11119 12 + 142988 AACTCTTGTTTC -s mr.mrrefChr3 37036 12 + 181027 AACTGTTATTTC -s simCow_chr6.simCow.chr6 467845 12 + 602619 AAATCTTGTTTT -s simDog_chr6.simDog.chr6 457799 12 + 593897 AGCTCTTGTTTC -s simHuman_chr6.simHuman.chr6 465146 11 + 601863 AAGTTTTATC-C -s simRat_chr6.simRat.chr6 491087 12 + 647215 AGCTCTTGTTTG - -a -s simMouse_chr6.simMouse.chr6 482841 6 + 636262 AAAAGA -s Anc0.Anc0refChr3 99738 6 + 222631 AAAGGT -s Anc1.Anc1refChr6 132994 6 + 197743 AAAGGT -s Anc2.Anc2refChr1 11131 6 + 142988 AAAGGT -s mr.mrrefChr3 37048 6 + 181027 AAAAGT -s simCow_chr6.simCow.chr6 467857 6 + 602619 CAAGGT -s simDog_chr6.simDog.chr6 457813 6 + 593897 AAAGGT -s simHuman_chr6.simHuman.chr6 465157 6 + 601863 AAAGGT -s simRat_chr6.simRat.chr6 491099 6 + 647215 AAAAGT - -a -s simMouse_chr6.simMouse.chr6 482847 15 + 636262 CAACCTGTAAACTGG -s Anc0.Anc0refChr3 99761 14 + 222631 AATCCT-TGAGCCAG -s Anc1.Anc1refChr6 133017 14 + 197743 AATCCT-TGAGCCAG -s Anc2.Anc2refChr1 11154 14 + 142988 AATCCT-TGAGCCGG -s mr.mrrefChr3 37071 15 + 181027 CAACCTGTGAACTAG -s simCow_chr6.simCow.chr6 467882 14 + 602619 AATCCT-TGTGTCCT -s simDog_chr6.simDog.chr6 457839 14 + 593897 AACCCA-TGAGCCGG -s simHuman_chr6.simHuman.chr6 465180 14 + 601863 AATCCT-TGAGCGAG -s simRat_chr6.simRat.chr6 491123 15 + 647215 CAACCTGTGAACTAG - -a -s simMouse_chr6.simMouse.chr6 482862 4 + 636262 TGCG -s Anc0.Anc0refChr3 99775 4 + 222631 TGGG -s Anc1.Anc1refChr6 133031 4 + 197743 TGGG -s Anc2.Anc2refChr1 11170 4 + 142988 TGCC -s mr.mrrefChr3 37086 4 + 181027 TGGG -s simCow_chr6.simCow.chr6 467898 4 + 602619 TGCC -s simDog_chr6.simDog.chr6 457855 4 + 593897 TGCC -s simHuman_chr6.simHuman.chr6 465194 4 + 601863 TGGG -s simRat_chr6.simRat.chr6 491138 4 + 647215 TGGG - -a -s simMouse_chr6.simMouse.chr6 482866 3 + 636262 ATA -s Anc0.Anc0refChr3 99779 3 + 222631 CTT -s Anc1.Anc1refChr6 133035 3 + 197743 CTT -s Anc2.Anc2refChr1 11174 3 + 142988 CTT -s mr.mrrefChr3 37090 3 + 181027 ATA -s simCow_chr6.simCow.chr6 467912 3 + 602619 CTT -s simDog_chr6.simDog.chr6 457859 3 + 593897 CTT -s simHuman_chr6.simHuman.chr6 465198 3 + 601863 TTT -s simRat_chr6.simRat.chr6 491142 3 + 647215 ATA - -a -s simMouse_chr6.simMouse.chr6 482869 11 + 636262 AAATATGATAT -s Anc0.Anc0refChr3 99782 11 + 222631 CAATATGTGAT -s Anc1.Anc1refChr6 133038 11 + 197743 CAATATGTGAT -s Anc2.Anc2refChr1 11177 11 + 142988 CAATATCTGCT -s mr.mrrefChr3 37093 11 + 181027 AAATATGATAT -s simCow_chr6.simCow.chr6 467915 11 + 602619 ACATATCTGCT -s simDog_chr6.simDog.chr6 457862 11 + 593897 CAATGTCTGCT -s simHuman_chr6.simHuman.chr6 465201 11 + 601863 CAATATGTGAT -s simRat_chr6.simRat.chr6 491147 11 + 647215 AAATAAGATGT - -a -s simMouse_chr6.simMouse.chr6 482880 26 + 636262 GTATGAGGTGTCCCCTTTGTTCAGAG -s Anc0.Anc0refChr3 99793 22 + 222631 G-CTGAGGA---CTCATTGCACAGTG -s Anc1.Anc1refChr6 133049 23 + 197743 GTCTGAGGA---CTCATTGCACAGTG -s Anc2.Anc2refChr1 11188 22 + 142988 G-CTGAGTA---CTCATTGCACAGTG -s mr.mrrefChr3 37104 26 + 181027 GTATGAGGAGTCCCCTTTGTTCAGAG -s simCow_chr6.simCow.chr6 467926 17 + 602619 G-CTGAGTA---CTCATTACA----- -s simDog_chr6.simDog.chr6 457873 22 + 593897 G-CTGAGTA---TTCATTGCACAGTG -s simHuman_chr6.simHuman.chr6 465212 23 + 601863 GTCTGGGGA---CTCATTGCACAGTG -s simRat_chr6.simRat.chr6 491168 26 + 647215 GTATGAGGAGTCCCCTTTGTTCAGAG - -a -s simMouse_chr6.simMouse.chr6 482920 1 + 636262 C -s Anc0.Anc0refChr3 99827 1 + 222631 A -s Anc1.Anc1refChr6 133086 1 + 197743 A -s Anc2.Anc2refChr1 11222 1 + 142988 A -s mr.mrrefChr3 37144 1 + 181027 C -s simDog_chr6.simDog.chr6 457907 1 + 593897 A -s simHuman_chr6.simHuman.chr6 465249 1 + 601863 A -s simRat_chr6.simRat.chr6 491208 1 + 647215 C - -a -s simMouse_chr6.simMouse.chr6 482946 2 + 636262 TT - -a -s simMouse_chr6.simMouse.chr6 482985 1 + 636262 G -s mr.mrrefChr3 37207 1 + 181027 G -s simRat_chr6.simRat.chr6 491270 1 + 647215 G - -a -s simMouse_chr6.simMouse.chr6 483030 13 + 636262 AAAACAATGTACT -s Anc0.Anc0refChr3 99893 11 + 222631 --AACAATGTACT -s Anc1.Anc1refChr6 133193 11 + 197743 --AACAATGTACT -s Anc2.Anc2refChr1 11288 11 + 142988 --GACAATGTACT -s mr.mrrefChr3 37252 13 + 181027 AAAACAATGTACT -s simCow_chr6.simCow.chr6 467996 11 + 602619 --GATAATGTACT -s simDog_chr6.simDog.chr6 457973 11 + 593897 --GACAATGTACT -s simHuman_chr6.simHuman.chr6 465314 11 + 601863 --AACAATGTCCT -s simRat_chr6.simRat.chr6 491321 13 + 647215 AAAACAATGTACT - -a -s simMouse_chr6.simMouse.chr6 483073 3 + 636262 ATG -s Anc0.Anc0refChr3 99934 3 + 222631 ATT -s Anc1.Anc1refChr6 133234 3 + 197743 ATT -s Anc2.Anc2refChr1 11329 3 + 142988 ACT -s mr.mrrefChr3 37295 3 + 181027 ATG -s simCow_chr6.simCow.chr6 468036 3 + 602619 AGG -s simDog_chr6.simDog.chr6 458014 3 + 593897 ACT -s simHuman_chr6.simHuman.chr6 465356 3 + 601863 GTT -s simRat_chr6.simRat.chr6 491399 3 + 647215 ATG - -a -s simMouse_chr6.simMouse.chr6 483091 2 + 636262 AA -s Anc0.Anc0refChr3 99952 2 + 222631 TG -s Anc1.Anc1refChr6 133252 2 + 197743 TG -s Anc2.Anc2refChr1 11347 2 + 142988 TG -s mr.mrrefChr3 37313 2 + 181027 AA -s simCow_chr6.simCow.chr6 468054 2 + 602619 TG -s simDog_chr6.simDog.chr6 458032 2 + 593897 TG -s simHuman_chr6.simHuman.chr6 465374 2 + 601863 TG - -a -s simMouse_chr6.simMouse.chr6 483096 1 + 636262 T - -a -s simMouse_chr6.simMouse.chr6 483111 5 + 636262 GCCAA - -a -s simMouse_chr6.simMouse.chr6 483150 19 + 636262 TAAGAAACAAGATATATAG -s Anc0.Anc0refChr3 100004 19 + 222631 TAGGAAGCAAGATATATGG -s Anc1.Anc1refChr6 133305 19 + 197743 TAGGAAGCAAGATATATGG -s Anc2.Anc2refChr1 11399 19 + 142988 TAGGAAGCAAAATATATGG -s mr.mrrefChr3 37366 19 + 181027 TAAGAAGCAAGATATATAG -s simCow_chr6.simCow.chr6 468111 19 + 602619 TAAGACCCAACATATATGG -s simDog_chr6.simDog.chr6 458084 19 + 593897 TAGGAAGCAAAATATATGG -s simHuman_chr6.simHuman.chr6 465427 19 + 601863 TACGAAGCAAGGTATATGG -s simRat_chr6.simRat.chr6 491445 19 + 647215 TAAGAAGCAGTATATATAG - -a -s simMouse_chr6.simMouse.chr6 483169 5 + 636262 TGGGA -s Anc0.Anc0refChr3 100029 5 + 222631 TGGGA -s Anc1.Anc1refChr6 133330 5 + 197743 TGGGA -s Anc2.Anc2refChr1 11424 5 + 142988 TGGGA -s mr.mrrefChr3 37385 5 + 181027 TGGGA -s simCow_chr6.simCow.chr6 468136 5 + 602619 TGGGT -s simDog_chr6.simDog.chr6 458109 5 + 593897 TGGGA -s simHuman_chr6.simHuman.chr6 465452 5 + 601863 TGGGA -s simRat_chr6.simRat.chr6 491464 5 + 647215 TGTGA - -a -s simMouse_chr6.simMouse.chr6 483174 35 + 636262 GTGCCCCTAGGATGACTGATCTCAATGACTGATCT -s Anc0.Anc0refChr3 100047 23 + 222631 AAGCATCTATGATGACTGATCTC------------ -s Anc1.Anc1refChr6 133348 23 + 197743 AAGCATCTATGATGACTGATCTC------------ -s Anc2.Anc2refChr1 11442 23 + 142988 AAGCATCTATGATGACTGATCTC------------ -s mr.mrrefChr3 37403 35 + 181027 GTGCCCCTAGGATGACTGATCTCAATGACTGATCT -s simCow_chr6.simCow.chr6 468154 23 + 602619 AAGCATCTATGATGACTAATCTC------------ -s simDog_chr6.simDog.chr6 458127 23 + 593897 AAGCATCTGTGATGACTGATCTT------------ -s simHuman_chr6.simHuman.chr6 465469 23 + 601863 AGACATCTATGATGACCGATCTC------------ -s simRat_chr6.simRat.chr6 491482 35 + 647215 GTGCCCATAGAATGACTGATCTCGATGACTGGCCT - -a -s simMouse_chr6.simMouse.chr6 483209 31 + 636262 CTGACAAAAAAAGTATTAGGGTAGCAAAGTA -s Anc0.Anc0refChr3 100070 30 + 222631 CAATTAAAAAATG-ATTTAGTCAGCAAGGTG -s Anc1.Anc1refChr6 133371 30 + 197743 CAATTAAAAAATG-ATTTAGTCAGCAAGGTG -s Anc2.Anc2refChr1 11465 30 + 142988 TAATTAAAGAACG-ATTTATTCACCAAGATG -s mr.mrrefChr3 37438 31 + 181027 CTAATAAAAAATGTATTAGGGTAGCAAAGTG -s simCow_chr6.simCow.chr6 468177 30 + 602619 TAATTAAAGAACA-ATTCAATCTCCAAAATG -s simDog_chr6.simDog.chr6 458150 30 + 593897 TAATTAAAGAACG-TCTTATTCACCGAGATG -s simHuman_chr6.simHuman.chr6 465492 30 + 601863 CAATTAAAAAATG-ATTTAGTCAGCAAGGTG -s simRat_chr6.simRat.chr6 491518 31 + 647215 CTAATAAAAAATGTATTAGGATAGCAAAGTG - -a -s simMouse_chr6.simMouse.chr6 483240 18 + 636262 TTTGTATATAGGAAAGGT -s Anc0.Anc0refChr3 100104 18 + 222631 TTAATATGCAGTTAAGGC -s Anc1.Anc1refChr6 133405 18 + 197743 TTAATATGCAGTTAAGGC -s Anc2.Anc2refChr1 11499 18 + 142988 TTAATTTGCAGTTAAGGC -s mr.mrrefChr3 37469 18 + 181027 TTTGTATATAGGAAAGGT -s simCow_chr6.simCow.chr6 468211 13 + 602619 TTAATTTG-----ATAGC -s simDog_chr6.simDog.chr6 458184 18 + 593897 TTAATTCGCAGTTGAGGC -s simHuman_chr6.simHuman.chr6 465526 18 + 601863 TTAAGATGCAGTTAAGGC -s simRat_chr6.simRat.chr6 491549 17 + 647215 TTTGTAT-TAGGAAAGGT - -a -s simMouse_chr6.simMouse.chr6 483258 12 + 636262 TCTGTGCCCACT -s Anc0.Anc0refChr3 100122 12 + 222631 TCTGTGCACATT -s Anc1.Anc1refChr6 133423 12 + 197743 TCTGTGCACATT -s Anc2.Anc2refChr1 11517 12 + 142988 TCTGTGCACATT -s mr.mrrefChr3 37487 12 + 181027 TCTGTGCCCACT -s simCow_chr6.simCow.chr6 468224 12 + 602619 TTTGTGCACATT -s simDog_chr6.simDog.chr6 458203 12 + 593897 TCTGTGAACATT -s simHuman_chr6.simHuman.chr6 465544 12 + 601863 TCTGTGCTCATT -s simRat_chr6.simRat.chr6 491566 12 + 647215 TCTGTGCCCACT - -a -s simMouse_chr6.simMouse.chr6 483270 14 + 636262 CCTAAACAATACTC -s Anc0.Anc0refChr3 100134 2 + 222631 ------------TC -s Anc1.Anc1refChr6 133435 2 + 197743 ------------TC -s Anc2.Anc2refChr1 11529 2 + 142988 ------------TC -s mr.mrrefChr3 37499 14 + 181027 CCTAAACAATACTC -s simCow_chr6.simCow.chr6 468236 2 + 602619 ------------TC -s simDog_chr6.simDog.chr6 458215 2 + 593897 ------------TC -s simHuman_chr6.simHuman.chr6 465556 2 + 601863 ------------TC -s simRat_chr6.simRat.chr6 491579 14 + 647215 CCTAAACAATACTC - -a -s simMouse_chr6.simMouse.chr6 483284 24 + 636262 TCCATCATTGTTACGGGTTAGAAA -s Anc0.Anc0refChr3 100136 13 + 222631 TCAATCA----------A-ATAAA -s Anc1.Anc1refChr6 133437 13 + 197743 TCAATCA----------A-ATAAA -s Anc2.Anc2refChr1 11531 13 + 142988 CCAATTC----------A-AAGAA -s mr.mrrefChr3 37513 23 + 181027 TCCATCATTGTTACGGGT-ATAAA -s simCow_chr6.simCow.chr6 468240 13 + 602619 ACAATTC----------A-CAGAA -s simDog_chr6.simDog.chr6 458217 13 + 593897 CCAATTC----------A-AAGAA -s simHuman_chr6.simHuman.chr6 465558 13 + 601863 TCTATCA----------A-ATAAA -s simRat_chr6.simRat.chr6 491593 23 + 647215 TCCGTCATTGTGATGGGT-ATAAA - -a -s simMouse_chr6.simMouse.chr6 483308 28 + 636262 CATCCTTACAAGGAATACACTACATGTG -s Anc0.Anc0refChr3 100149 27 + 222631 CATCC-TGCTATGAATACTCAACAAGTG -s Anc1.Anc1refChr6 133450 27 + 197743 CATCC-TGCTATGAATACTCAACAAGTG -s Anc2.Anc2refChr1 11544 27 + 142988 GTCCC-TGCTATGAAGACTCAACAAGTG -s mr.mrrefChr3 37536 28 + 181027 CATCCTTACAAGGAATACACTACATGTG -s simCow_chr6.simCow.chr6 468255 27 + 602619 ATCCC-TGCTGTGAACACTCAGCAAGTG -s simDog_chr6.simDog.chr6 458230 27 + 593897 GTCCC-TGCTATGAAGACACAACAAGTG -s simHuman_chr6.simHuman.chr6 465571 27 + 601863 CATCC-TGCCATAAATACTCAACGAGTG -s simRat_chr6.simRat.chr6 491616 28 + 647215 CATCCTCACAAGGAACTCACTACATGTG - -a -s simMouse_chr6.simMouse.chr6 483336 135 + 636262 TTTGAGTTATTGGGGGACCGCTCCGTAAGCATTTTGGAGTTTAGAGCAATAGTGAAATCGGGAGGTATTCCTATGGAACGCGTCGACAGCATGGTCCTAACCCCGGAATCCACATCTCGTTTAGAGCAATAGGAT -s Anc0.Anc0refChr3 100177 16 + 222631 TTCAAGTAATTGGGG-----------------------------------------------------------------------------------------------------------------------T -s Anc1.Anc1refChr6 133478 16 + 197743 TTCAAGTAATTGGGG-----------------------------------------------------------------------------------------------------------------------T -s Anc2.Anc2refChr1 11572 16 + 142988 TTTGAGTAATTAGGG-----------------------------------------------------------------------------------------------------------------------T -s mr.mrrefChr3 37564 16 + 181027 TTCAAGTTATTGGGG-----------------------------------------------------------------------------------------------------------------------T -s simCow_chr6.simCow.chr6 468283 16 + 602619 TTTGAGCAATTAGGG-----------------------------------------------------------------------------------------------------------------------T -s simDog_chr6.simDog.chr6 458258 16 + 593897 TTTGAGTAATTAGGG-----------------------------------------------------------------------------------------------------------------------C -s simHuman_chr6.simHuman.chr6 465599 16 + 601863 TTCAAGTAACTGAGG-----------------------------------------------------------------------------------------------------------------------T -s simRat_chr6.simRat.chr6 491644 16 + 647215 TTCAAGTTATTGGGG-----------------------------------------------------------------------------------------------------------------------T - -a -s simMouse_chr6.simMouse.chr6 483471 3 + 636262 CTA -s Anc0.Anc0refChr3 100196 3 + 222631 TTA -s Anc1.Anc1refChr6 133497 3 + 197743 TTA -s Anc2.Anc2refChr1 11591 3 + 142988 TTA -s mr.mrrefChr3 37580 3 + 181027 CTA -s simCow_chr6.simCow.chr6 468302 3 + 602619 TTC -s simDog_chr6.simDog.chr6 458302 3 + 593897 TTA -s simHuman_chr6.simHuman.chr6 465618 3 + 601863 TTA -s simRat_chr6.simRat.chr6 491660 3 + 647215 CTA - -a -s simMouse_chr6.simMouse.chr6 483474 27 + 636262 AGCTCAGTGTGGGTCATGCTCTGGCAT -s Anc0.Anc0refChr3 100199 27 + 222631 AAATCATCTTGGGTCATGCTCTGGCAT -s Anc1.Anc1refChr6 133500 27 + 197743 AAATCATCTTGGGTCATGCTCTGGCAT -s Anc2.Anc2refChr1 11594 27 + 142988 AAATCATCTTGGGTCATGCTCTGGCAT -s mr.mrrefChr3 37583 27 + 181027 AACTCAGTGTGGGTCATGCTCTGGCAT -s simCow_chr6.simCow.chr6 468305 27 + 602619 AAATCATTTTGGGTCATACTCTGGCAC -s simDog_chr6.simDog.chr6 458308 27 + 593897 AAATCATCTCGGGTCATGCTCAGGTGT -s simHuman_chr6.simHuman.chr6 465621 27 + 601863 AAATCATCATGAGTTATGCTCTGGCAT -s simRat_chr6.simRat.chr6 491663 27 + 647215 AACCCAGTGTGGGTGATGCTCTGGCAT - -a -s simMouse_chr6.simMouse.chr6 483501 12 + 636262 TAACGTAGTAGT -s Anc0.Anc0refChr3 100226 12 + 222631 TAACCTAGTGGT -s Anc1.Anc1refChr6 133527 12 + 197743 TAACCTAGTGGT -s Anc2.Anc2refChr1 11621 12 + 142988 TAACCGAGTGGT -s mr.mrrefChr3 37610 12 + 181027 TAACGTAGTAGT -s simCow_chr6.simCow.chr6 468333 12 + 602619 TATCTGAGTGGT -s simDog_chr6.simDog.chr6 458335 12 + 593897 TAACCGAGTCGT -s simHuman_chr6.simHuman.chr6 465648 12 + 601863 TCATCTCGTGAT -s simRat_chr6.simRat.chr6 491690 12 + 647215 TAACGTAGTAGT - -a -s simMouse_chr6.simMouse.chr6 483513 6 + 636262 CAAAAT -s Anc0.Anc0refChr3 100238 5 + 222631 ACAAA- -s Anc1.Anc1refChr6 133539 5 + 197743 ACAAA- -s Anc2.Anc2refChr1 11633 5 + 142988 ACAAA- -s mr.mrrefChr3 37622 6 + 181027 CAAAAT -s simCow_chr6.simCow.chr6 468345 5 + 602619 ACAAA- -s simDog_chr6.simDog.chr6 458349 5 + 593897 AGAGC- -s simHuman_chr6.simHuman.chr6 465660 5 + 601863 ACAAA- -s simRat_chr6.simRat.chr6 491702 6 + 647215 CAAAAT - -a -s simMouse_chr6.simMouse.chr6 483519 56 + 636262 CAAGTGGGTGTGGATTGCCTGAGTATGACCTGAGTAGGAGAATTGCCTCATTGAAA -s Anc0.Anc0refChr3 100243 46 + 222631 CAAGTGGGTGTGGATTGTCTGGGCATGAATT----------ATTGCTTCATTGATA -s Anc1.Anc1refChr6 133544 46 + 197743 CAAGTGGGTGTGGATTGTCTGGGCATGAATT----------ATTGCTTCATTGATA -s Anc2.Anc2refChr1 11638 46 + 142988 CAAGTGGGTGTGGATTGCCTGGGCATGAATA----------ATTGCTTCATTGATA -s mr.mrrefChr3 37628 56 + 181027 CAAGTGGGTGTGGATTGTCTGAGTATGACCTGAGTAGGAGAATTGCCTCATTGAAA -s simCow_chr6.simCow.chr6 468352 46 + 602619 CAAGTGGATGTGGATTGCCTGGGCATGAATA----------ATCCCCTTAGTAATA -s simDog_chr6.simDog.chr6 458354 46 + 593897 CAAGTTGGTGTGAATTGCCTGGGGAGAAATA----------ATTGCTTCATTGATA -s simHuman_chr6.simHuman.chr6 465665 46 + 601863 CAAGTGGGTGTGGACTGTATGGGCATGAGTT----------ATTGCTTCATTGATG -s simRat_chr6.simRat.chr6 491708 56 + 647215 CAAGTAGGTGTGGATTGTGTGAGTAGGACCTCAGTCAGAGGATTGCCACATTGGAA - -a -s simMouse_chr6.simMouse.chr6 483575 9 + 636262 ACAATCGGG -s Anc0.Anc0refChr3 100299 6 + 222631 ---ATTGGG -s Anc1.Anc1refChr6 133600 6 + 197743 ---ATTGGG -s Anc2.Anc2refChr1 11694 6 + 142988 ---GTTGGG -s mr.mrrefChr3 37694 9 + 181027 ACAATCGGG -s simCow_chr6.simCow.chr6 468408 6 + 602619 ---GTTGGA -s simDog_chr6.simDog.chr6 458406 3 + 593897 ------GAG -s simHuman_chr6.simHuman.chr6 465721 6 + 601863 ---ATTGGG -s simRat_chr6.simRat.chr6 491778 9 + 647215 ACAGTGGGG - -a -s simMouse_chr6.simMouse.chr6 483584 24 + 636262 TGTTGGAGGTAATTAGTATCCTTT -s Anc0.Anc0refChr3 100305 24 + 222631 TGTTGGAGCTGACTGGTACTTTTT -s Anc1.Anc1refChr6 133606 24 + 197743 TGTTGGAGCTGACTGGTACTTTTT -s Anc2.Anc2refChr1 11700 24 + 142988 TGTTGGAGCTGACTAGTACTTTTT -s mr.mrrefChr3 37703 24 + 181027 TGTTGGAGGTAATTGGTATTCTTT -s simCow_chr6.simCow.chr6 468438 24 + 602619 TGCTGGAGCTGACTAGTACTTTTT -s simDog_chr6.simDog.chr6 458409 24 + 593897 CGTTGGAGCTGACTAGTACTTTTT -s simHuman_chr6.simHuman.chr6 465727 20 + 601863 TATTGGAGCTGAATGGTA----TT -s simRat_chr6.simRat.chr6 491787 24 + 647215 CGTTGGAGGTAATTGGTATTCTTT - -a -s simMouse_chr6.simMouse.chr6 483608 13 + 636262 GTTATTTGTTGAA -s Anc0.Anc0refChr3 100329 13 + 222631 GATACTTATTGAA -s Anc1.Anc1refChr6 133630 13 + 197743 GATACTTATTGAA -s Anc2.Anc2refChr1 11724 13 + 142988 GATACTTATTGAA -s mr.mrrefChr3 37727 13 + 181027 GTTATTTGTTGAA -s simCow_chr6.simCow.chr6 468462 13 + 602619 GATACTTATCGAA -s simDog_chr6.simDog.chr6 458433 13 + 593897 GATCCTTATTTAA -s simHuman_chr6.simHuman.chr6 465747 13 + 601863 GATACTTACTGAA -s simRat_chr6.simRat.chr6 491812 13 + 647215 GTTATTTGGTGAA - -a -s simMouse_chr6.simMouse.chr6 483621 1 + 636262 T -s Anc0.Anc0refChr3 100343 1 + 222631 T -s Anc1.Anc1refChr6 133644 1 + 197743 T -s Anc2.Anc2refChr1 11738 1 + 142988 T -s mr.mrrefChr3 37741 1 + 181027 T -s simCow_chr6.simCow.chr6 468476 1 + 602619 T -s simDog_chr6.simDog.chr6 458447 1 + 593897 T -s simHuman_chr6.simHuman.chr6 465761 1 + 601863 T -s simRat_chr6.simRat.chr6 491826 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 483622 11 + 636262 CTTGTTCACAT -s Anc0.Anc0refChr3 100344 10 + 222631 CTTGTACTGA- -s Anc1.Anc1refChr6 133645 10 + 197743 CTTGTACTGA- -s Anc2.Anc2refChr1 11739 10 + 142988 TTTGTACTGA- -s mr.mrrefChr3 37742 11 + 181027 CTTGTTCTCAT -s simCow_chr6.simCow.chr6 468477 10 + 602619 TTTATACTGA- -s simDog_chr6.simDog.chr6 458448 10 + 593897 TTTGTACAGA- -s simHuman_chr6.simHuman.chr6 465763 10 + 601863 CTTGTGCTTA- -s simRat_chr6.simRat.chr6 491827 11 + 647215 CTGGTACTCGT - -a -s simMouse_chr6.simMouse.chr6 483633 6 + 636262 TAATTG -s Anc0.Anc0refChr3 100357 6 + 222631 TGTTCA -s Anc1.Anc1refChr6 133658 6 + 197743 TGTTCA -s Anc2.Anc2refChr1 11752 6 + 142988 TGTCCA -s mr.mrrefChr3 37756 6 + 181027 TAATCA -s simCow_chr6.simCow.chr6 468493 6 + 602619 TGTCCA -s simDog_chr6.simDog.chr6 458461 6 + 593897 GGTCCA -s simHuman_chr6.simHuman.chr6 465776 6 + 601863 TGTTCA -s simRat_chr6.simRat.chr6 491841 6 + 647215 TAATCA - -a -s simMouse_chr6.simMouse.chr6 483639 12 + 636262 GTAAAAGACACC -s Anc0.Anc0refChr3 100363 12 + 222631 ATATAAGTGACC -s Anc1.Anc1refChr6 133664 12 + 197743 ATATAAGTGACC -s Anc2.Anc2refChr1 11759 12 + 142988 ATATAAGTGACC -s mr.mrrefChr3 37762 12 + 181027 GTATAAGACACC -s simCow_chr6.simCow.chr6 468500 12 + 602619 ATATAAGTAACC -s simDog_chr6.simDog.chr6 458468 12 + 593897 ATATAAGTGACC -s simHuman_chr6.simHuman.chr6 465782 12 + 601863 ATATAAGGGGCT -s simRat_chr6.simRat.chr6 491847 12 + 647215 GTATAAGACACC - -a -s simMouse_chr6.simMouse.chr6 483651 231 + 636262 TGGTATCTTGCCCCTTTATGCATATATAATGTCTCACCATCGGGGAGCCCCTAAAGCCTCCACCTGTGTTATTGCCAGTCGGCGTAGTTTAACAGTGTCACAAGCCCCTGATAGGAGACCAGCAGGAGAATTAAATTGGTCAGGTCCCGAAGGGTATAGTGTTGGCAGAGGTGGTTGTTGGAGGGCTACCTCAAGACACCCAGAGGCAGTTGCTGTGGGCCCTGACGAGCT -s Anc0.Anc0refChr3 100376 231 + 222631 TGGTGTTGTACACCTTCATTCATGTATGATGTCTCACCATCGGGGTGCTCCAAAGGCCTCCACATGTGTTATTGCCAGTCGGCGTAGTTTAACTGTGTCACAAGCCCCTGATCGGAGACCAGCAGGAGAATTAAATTGGTCAGGTCCTGAAGGGTATAGTGTAGGCAGAGGTGGTTGTTGGAGGGCCACCTCAAGACACCCAGAGGCAGTTGCTGTGGGTCCTGATGAGCT -s Anc1.Anc1refChr6 133677 231 + 197743 TGGTGTTGTACACCTTCATTCATGTATGATGTCTCACCATCGGGGTGCTCCAAAGGCCTCCACATGTGTTATTGCCAGTCGGCGTAGTTTAACTGTGTCACAAGCCCCTGATCGGAGACCAGCAGGAGAATTAAATTGGTCAGGTCCTGAAGGGTATAGTGTAGGCAGAGGTGGTTGTTGGAGGGCCACCTCAAGACACCCAGAGGCAGTTGCTGTGGGTCCTGATGAGCT -s Anc2.Anc2refChr1 11772 231 + 142988 TGGTGTTGTACACCTTCTTTCATGTATGATGTCTCACCATAGGGGTGCTCCAAAGGCCTCCACATGTGTTATTGCCAGTCGGCGTAGTTTAACTGTGTCACAAGCACCTGATCGGAGACCAGCAGGAGAATTAAATTGGTCAGGTCCTGAAGGGTATAGTGTTGGAAGAGGTGGTTGTTGGAGGGCCACCTCTAGACACCCAGAGGCAGTTGCTGTGGGTCCTGATGAGCT -s mr.mrrefChr3 37774 231 + 181027 TGGTGTCTTGCCCCTTTATGCATATATAATGTCTCACCATCGGGGAGCCCCTAAAGCCTCCACCTGTGTTATTGCCAGTCGGCGTAGTTTAACAGTGTCACAAGCCCCTGATAGGAGACCAGCAGGAGAATTAAATTGGTCAGGTCCCGAAGGGTATAGTGTAGGCAGAGGTGGTTGTTGGAGGGCTACCTCAAGACACCCAGAGGCAGTTGCTGTGGGTCCTGATGAGCT -s simCow_chr6.simCow.chr6 468513 223 + 602619 TGGTGTTGT--------CTTCACGTATGATGTCTCACCATAGGGGAGCTCCAAAAGCATCCACATGTGTCATTGCCAGCCGGCGTAGTTTAACTGTGTCACAAGCTCCTGATCAGAGGCCAGCAGGGGAATTAAATTGGTCAGGTCCTGAAGGGTATAGTGTTGGAAGAGGTGGTTGTTGGAGGGCTACCTCTAGACACCCTGAGGCAGTTGCTGTGGGTCCTGATGAGCT -s simDog_chr6.simDog.chr6 458481 229 + 593897 TGG--TTGTACACCTTCTTTCATACCTTATGTCTCACCATAGGGGTGCTCCAAAGGCCTCTACTTGTGTTATTGCCAGTCGGCGTAGTTTGACTGTGTCACAAGCACCTGACCGGAGACCAGCAGGAGAATTAAATTGGTCAAGTCCTGAAGGGTATAGTGTTGGAAGGGGTGGCTGTTGGAGGGCCACCTCTAGACACCCAGAGGCAGTCGCTGTGGGCCCTGATGAGCT -s simHuman_chr6.simHuman.chr6 465795 231 + 601863 TGATGTTGTACACTTTCATTCATGTATGATGTCTCACCATCGGGGGGCTCCAAAGGCCTCCACATGTGTTATCGCCAGTCGGCGTAGTTTAACTGTGTCACAAGCCCCTGATCGGAGACCAGCAGGAGAGTTAAATTGGTCAGGTCCTGAAGGGTATAGTGTAGGCAGAGGTGGTTGTTGGGGGGCCACCTCAAGAGATCCAGAGGCAGTTGCTGTGGGTCCTGATGAGCT -s simRat_chr6.simRat.chr6 491859 231 + 647215 TGGTGTATTGCCCCTTTATGCATATATAATGTCACACCATCGGGGAGCCCCTAAAGCCTCTACCTGTGTTATTGCCAGGCGGCGTAGTTTAACAGTGTCACAAGCACCTGATAGGAGACCAGCAGGAGAATTAAATTGGTCAGGTCCCGAAGGGTATAGTGTAGGCAGAGGTGGTTGTTGGAGGGCTACCTCACGACACCCGGAGGCAGTTGCAGTGGGTCCTGATGAGCT - -a -s simMouse_chr6.simMouse.chr6 483882 75 + 636262 ATTGTTTCTTGCACTTACAAGCCACTTTGTTGGTGCAGTAATTAGTCAATATCCTATCAAAATGCATGGGGTAAC -s Anc0.Anc0refChr3 100610 75 + 222631 ACTGTTTCTTGCACTTACAAGCCACTTTGTTGGTGCAGTAATTAGTCAATCTCCTGCCAATATACTTGGGGTGAT -s Anc1.Anc1refChr6 133911 75 + 197743 ACTGTTTCTTGCACTTACAAGCCACTTTGTTGGTGCAGTAATTAGTCAATCTCCTGCCAATATACTTGGGGTGAT -s Anc2.Anc2refChr1 12006 75 + 142988 ACTGTTTTTTGCACTTACAAGCCACTTTGTTGGTGCAGTAATTAGTCAATCTCCTGCCAATATACTTGGGGTGAT -s mr.mrrefChr3 38005 75 + 181027 ATTGTTTCTTGCACTTACAAGCCACTTTGTTGGTGCAGTAATTAGTCAATCTCCTACCAAAATGCATGGGGTAAC -s simCow_chr6.simCow.chr6 468739 75 + 602619 ACTTTTTTTTGCGCTTACAAGCCACTTCTTCGGTGCAGTAATTAGTCAATCTCCTGTCAATTTACTGTGGGTTAT -s simDog_chr6.simDog.chr6 458713 75 + 593897 ACTGTTTTTTGCACTTACAAGCCACTTTGTTGGTGCAGTAATTAGTCATTCTCCTTCCAATATACTTGGGGAGGT -s simHuman_chr6.simHuman.chr6 466029 75 + 601863 ACTATTTCTTGCACTTACGAGCCACTTTGTTGGAGCAGTAATTAGTCAATCTCCTGCCAATATACTTGGGGTGAT -s simRat_chr6.simRat.chr6 492090 75 + 647215 ATTGTTTCTTGCACTTACAAGTCACTTTGTTGGTGCAGTAATTAGTCATTCTCCTACCAAAAAGCACGGGGTAAC - -a -s simMouse_chr6.simMouse.chr6 483957 21 + 636262 ACTGGGGTTGGACCAACGCAG -s Anc0.Anc0refChr3 100685 21 + 222631 ACAGGTGTTGGATACACACAG -s Anc1.Anc1refChr6 133986 21 + 197743 ACAGGTGTTGGATACACACAG -s Anc2.Anc2refChr1 12081 21 + 142988 ACAGATGTTGGATACATGAAG -s mr.mrrefChr3 38080 21 + 181027 ACTGGGGTTGGACCAACACAG -s simCow_chr6.simCow.chr6 468817 21 + 602619 ATGAACGTCAGATACATGAAG -s simDog_chr6.simDog.chr6 458788 21 + 593897 GCAGATGTTGGACACATGAAG -s simHuman_chr6.simHuman.chr6 466104 21 + 601863 ACAGGTGGTGGATACACACGG -s simRat_chr6.simRat.chr6 492165 20 + 647215 AA-GGGTTCGGACCAACACAG - -a -s simMouse_chr6.simMouse.chr6 483978 2 + 636262 AA -s Anc0.Anc0refChr3 100706 2 + 222631 AA -s Anc1.Anc1refChr6 134007 2 + 197743 AA -s Anc2.Anc2refChr1 12102 2 + 142988 AA -s mr.mrrefChr3 38101 2 + 181027 AA -s simCow_chr6.simCow.chr6 468839 2 + 602619 AA -s simDog_chr6.simDog.chr6 458809 2 + 593897 AA -s simHuman_chr6.simHuman.chr6 466125 2 + 601863 AA -s simRat_chr6.simRat.chr6 492185 2 + 647215 AA - -a -s simMouse_chr6.simMouse.chr6 483980 24 + 636262 CAGAGTTTAAGTCTATATCCTACT -s Anc0.Anc0refChr3 100708 24 + 222631 TGGAGCCTAAGTCTGTCTCCTACC -s Anc1.Anc1refChr6 134009 24 + 197743 TGGAGCCTAAGTCTGTCTCCTACC -s Anc2.Anc2refChr1 12104 24 + 142988 TGGAGCCTAAATCTGTCTCCTACC -s mr.mrrefChr3 38103 24 + 181027 CAGAGTTTAAGTCTATCTCCTACT -s simCow_chr6.simCow.chr6 468841 22 + 602619 TG--GTCTAAATCCATGTCCTGCT -s simDog_chr6.simDog.chr6 458811 24 + 593897 TGGAGCCTAAATCTGTCTACTATC -s simHuman_chr6.simHuman.chr6 466127 24 + 601863 TGGAGCCTAAGTCTGTCTCCTACC -s simRat_chr6.simRat.chr6 492188 24 + 647215 CAGGGTTTAAGTCTATCTCTTACT - -a -s simMouse_chr6.simMouse.chr6 484004 7 + 636262 CTGCTAG -s Anc0.Anc0refChr3 100732 7 + 222631 CTTCTAG -s Anc1.Anc1refChr6 134033 7 + 197743 CTTCTAG -s Anc2.Anc2refChr1 12128 7 + 142988 CTTCTAG -s mr.mrrefChr3 38127 7 + 181027 CTGCTAG -s simCow_chr6.simCow.chr6 468863 7 + 602619 CTTCTTG -s simDog_chr6.simDog.chr6 458838 7 + 593897 CCTCTAG -s simHuman_chr6.simHuman.chr6 466151 7 + 601863 CTCCTAG -s simRat_chr6.simRat.chr6 492212 7 + 647215 CTGCTAG - -a -s simMouse_chr6.simMouse.chr6 484011 19 + 636262 CCCAATACTCCTCTTAATA -s Anc0.Anc0refChr3 100745 19 + 222631 ACCAATGCTCCTCTTAATA -s Anc1.Anc1refChr6 134046 19 + 197743 ACCAATGCTCCTCTTAATA -s Anc2.Anc2refChr1 12141 19 + 142988 ACTGATGCCCCTCTTAATA -s mr.mrrefChr3 38134 19 + 181027 CCCAATGCTCCTCTTAATA -s simCow_chr6.simCow.chr6 468876 19 + 602619 ACTGTTGCCTCTCTTCATA -s simDog_chr6.simDog.chr6 458851 19 + 593897 ACTGATACCCCTCTTAATA -s simHuman_chr6.simHuman.chr6 466164 19 + 601863 TCCAATGCTCCTCTTAATA -s simRat_chr6.simRat.chr6 492219 19 + 647215 GTGGATGCTCCTCTTAACA - -a -s simMouse_chr6.simMouse.chr6 484030 31 + 636262 CCATCACACCTAATATGGAATAGAAATAGGT -s Anc0.Anc0refChr3 100785 31 + 222631 CCATGACACTTGATATAGAAAAGGCATACCT -s Anc1.Anc1refChr6 134086 31 + 197743 CCATGACACTTGATATAGAAAAGGCATACCT -s Anc2.Anc2refChr1 12181 31 + 142988 CCATGACACTCAATACAGAAAAGCCATACCT -s mr.mrrefChr3 38153 31 + 181027 CCATGACACCTGATATGGAATAGGCATAGGT -s simCow_chr6.simCow.chr6 468916 16 + 602619 CCATG---------------AAGCCATACCT -s simDog_chr6.simDog.chr6 459004 31 + 593897 CCACGACACTCAATACAGAAGAACCATACCT -s simHuman_chr6.simHuman.chr6 466204 31 + 601863 CCATGACACTTGTTGTAGAAAAGGCCTAATT -s simRat_chr6.simRat.chr6 492238 31 + 647215 CCATGACACCTGATATGGAATAGGCATAGGT - -a -s simMouse_chr6.simMouse.chr6 484061 86 + 636262 ACCCCAAAAAGTGTTAGTATAAAATAGAATAATATGTTAACTAGGGTACATGCACACATGCAGCTCCTTCCTGATGACCCACCTGT -s Anc0.Anc0refChr3 100816 82 + 222631 ATCC-AAGACCTGTCACTATAGAATAGAATAATGTATTGGCTAGGGTACACGCACACAGGAGGTTCCTTGC---TGACCCACCTGA -s Anc1.Anc1refChr6 134117 85 + 197743 ATCC-AAGACCTGTCACTATAGAATAGAATAATGTATTGGCTAGGGTACACGCACACAGGAGGTTCCTTGCTGGTGACCCACCTGA -s Anc2.Anc2refChr1 12212 82 + 142988 ATTT-GAGGCCTGTCACTATAGAATAGAATAATGTATTGGCTAGGGTACATGCGTACAGGAGGTTGCTTGC---TGACCCACCTCA -s mr.mrrefChr3 38184 85 + 181027 ACCC-AAGAAGTGTTAGTATAAAATAGAATAATGTGTTAGCTAGGGTACACGCACACATGCAGTTCCTTCCTGGTGACCCACCTGT -s simCow_chr6.simCow.chr6 468933 62 + 602619 ATTT-GAGGCCTGTCACTATAGAATAGAATAATGTCTTGGCTAGGGTACATACGGATAGGAGG----------------------- -s simDog_chr6.simDog.chr6 459035 67 + 593897 A----------------TATAGAATAGAATAATGTATTAGCTAGGGTATATGCGTGCAGGATTTTGCTTGC---TGACCCACCTCA -s simHuman_chr6.simHuman.chr6 466235 85 + 601863 ATCC-AAGACCTGTCACTACAGAATAAAATGATGAAGAGGCTAGGGTACGCGCACACAGGAGGTTCCCTTCTGGTGACCCCCCTGG -s simRat_chr6.simRat.chr6 492269 85 + 647215 ACCC-AAGAAGTGTTAGTATAAAATACAATAATGTGTTAGGTTGGGTACACGCACACATGCAGTTCCTTCCTGGAGACCCACCTGT - -a -s simMouse_chr6.simMouse.chr6 484147 60 + 636262 ACCCAGATCTTGGCACCAGTATGTTCCACAACTTCTCAACTGCCCTACCCCTACCAATTA -s Anc0.Anc0refChr3 100898 58 + 222631 ACCCTGATCTTGGCACCAGAATGGTCCACAACTTCTTAACT--CCTTCCCCTGCCAACTA -s Anc1.Anc1refChr6 134202 58 + 197743 ACCCTGATCTTGGCACCAGAATGGTCCACAACTTCTTAACT--CCTTCCCCTGCCAACTA -s Anc2.Anc2refChr1 12294 58 + 142988 ATCCTGATCTTGGCACCAGAATGGTCCACAACTTCTTAACT--CCTTCACCTGCCAACTA -s mr.mrrefChr3 38269 60 + 181027 ACCCAGATCTTGGCACCAGTATGTTCCACAACTTCTCAACTGCCCTTCCCCTACCAATTA -s simCow_chr6.simCow.chr6 468995 55 + 602619 ---CGGATCTTGGCACCAGAATTGTCCACAACTTCTTAACT--CCTAAACCTGCTAAGGA -s simDog_chr6.simDog.chr6 459102 58 + 593897 ATCCTGATCTTGGCATTAGAATGGTCCACAACATACTAACT--CCTTCACCTGCCCGCTA -s simHuman_chr6.simHuman.chr6 466355 57 + 601863 ACCCTGATCCTGGCACCAGAATGGTCCACAATTTCTTAACG--CCTTCCTCCGCCAACT- -s simRat_chr6.simRat.chr6 492354 60 + 647215 ACCCGGATCTAGGCACCAGTATGTTCCACAACTTCTCAACTGCCCTTCCCCTACCAATTA - -a -s simMouse_chr6.simMouse.chr6 484207 22 + 636262 ATTAAGCAGGTTGTGTTTACGA -s Anc0.Anc0refChr3 100956 22 + 222631 ATTAAGTAGGCTGTGTATAAGA -s Anc1.Anc1refChr6 134260 22 + 197743 ATTAAGTAGGCTGTGTATAAGA -s Anc2.Anc2refChr1 12353 22 + 142988 ATTAAGTAGGCTGTGTATAAGA -s mr.mrrefChr3 38329 22 + 181027 ATTAAGCAGGTTGTGTTTACGA -s simCow_chr6.simCow.chr6 469051 21 + 602619 AT-AATTAGGCTGTGTAAAAGA -s simDog_chr6.simDog.chr6 459161 22 + 593897 ATTAGGTAGGCTGTGTATAAGA -s simHuman_chr6.simHuman.chr6 466412 22 + 601863 ATCAAGAAGGCTGTATATAGGA -s simRat_chr6.simRat.chr6 492414 22 + 647215 ATTAAGCAGGTTGTGTCTATGA - -a -s simMouse_chr6.simMouse.chr6 484229 2 + 636262 CA -s Anc0.Anc0refChr3 100983 2 + 222631 CA -s Anc1.Anc1refChr6 134287 2 + 197743 CA -s Anc2.Anc2refChr1 12380 2 + 142988 TA -s mr.mrrefChr3 38351 2 + 181027 CA -s simCow_chr6.simCow.chr6 469077 2 + 602619 TA -s simDog_chr6.simDog.chr6 459188 2 + 593897 TA -s simHuman_chr6.simHuman.chr6 466439 2 + 601863 CA -s simRat_chr6.simRat.chr6 492436 2 + 647215 CA - -a -s simMouse_chr6.simMouse.chr6 484231 5 + 636262 CAAAG -s Anc0.Anc0refChr3 100987 5 + 222631 TAAAA -s Anc1.Anc1refChr6 134291 5 + 197743 TAAAA -s Anc2.Anc2refChr1 12384 5 + 142988 TAAAA -s mr.mrrefChr3 38353 5 + 181027 TAAAG -s simCow_chr6.simCow.chr6 469081 5 + 602619 TAGAA -s simDog_chr6.simDog.chr6 459192 5 + 593897 TAAAA -s simHuman_chr6.simHuman.chr6 466443 5 + 601863 TAAAA -s simRat_chr6.simRat.chr6 492438 5 + 647215 TACAG - -a -s simMouse_chr6.simMouse.chr6 484236 17 + 636262 CTTTCCAAAGTTGGCAA -s Anc0.Anc0refChr3 100992 17 + 222631 CTTTCCAAAGGTGGCAC -s Anc1.Anc1refChr6 134296 17 + 197743 CTTTCCAAAGGTGGCAC -s Anc2.Anc2refChr1 12389 17 + 142988 CTTTCCAGTGGTGACAC -s mr.mrrefChr3 38358 17 + 181027 CTTTCCAAAGTTGGCAA -s simCow_chr6.simCow.chr6 469090 17 + 602619 CCATCCAGTGGTGACAG -s simDog_chr6.simDog.chr6 459197 17 + 593897 CTTGCAAGTGGTGACAC -s simHuman_chr6.simHuman.chr6 466448 17 + 601863 CTTTTCAAAGGTGGCAC -s simRat_chr6.simRat.chr6 492443 17 + 647215 CTTTCCTGAGTTGGCAA - -a -s simMouse_chr6.simMouse.chr6 484253 2 + 636262 TA -s Anc0.Anc0refChr3 101009 2 + 222631 TA -s Anc1.Anc1refChr6 134313 2 + 197743 TA -s Anc2.Anc2refChr1 12406 2 + 142988 TA -s mr.mrrefChr3 38375 2 + 181027 TA -s simCow_chr6.simCow.chr6 469107 2 + 602619 TA -s simDog_chr6.simDog.chr6 459215 2 + 593897 TA -s simHuman_chr6.simHuman.chr6 466465 2 + 601863 TA -s simRat_chr6.simRat.chr6 492460 2 + 647215 TA - -a -s simMouse_chr6.simMouse.chr6 484255 36 + 636262 ATGGGACTATGATTGATTCAGTGATTGGCATCTGTG -s Anc0.Anc0refChr3 101018 32 + 222631 ATGGGACTAAGATC----GAGTGATAAGCATCTGTG -s Anc1.Anc1refChr6 134322 32 + 197743 ATGGGACTAAGATC----GAGTGATAAGCATCTGTG -s Anc2.Anc2refChr1 12415 32 + 142988 GTGGGACTAAGATC----GAGTAATAAGCACCTGTG -s mr.mrrefChr3 38377 32 + 181027 ATGGGACTATGATT----CAGTGATTGGCATCTGTG -s simCow_chr6.simCow.chr6 469116 12 + 602619 GCGGGACTAAGA------------------------ -s simDog_chr6.simDog.chr6 459224 32 + 593897 GTGGGACTAAGATC----GAGTAATAAGCACCTGTG -s simHuman_chr6.simHuman.chr6 466474 32 + 601863 ATGGGAATAAGATC----AAGTGATGAGCATCTGTG -s simRat_chr6.simRat.chr6 492462 32 + 647215 ATGGGCCTATGATT----CCATGGTCGGCATCTGTG - -a -s simMouse_chr6.simMouse.chr6 484291 24 + 636262 TAGGCATCTGTCTTTTTGCAAGCG -s Anc0.Anc0refChr3 101050 11 + 222631 TC-------------TTGCAGGTG -s Anc1.Anc1refChr6 134354 11 + 197743 TC-------------TTGCAGGTG -s Anc2.Anc2refChr1 12447 11 + 142988 CC-------------TTACAGTTG -s mr.mrrefChr3 38409 24 + 181027 TAGGCATCTGTCTTTTTGCAGGTG -s simDog_chr6.simDog.chr6 459257 11 + 593897 CC-------------TTACAGTTG -s simHuman_chr6.simHuman.chr6 466506 11 + 601863 TG-------------TTGCAGGTG -s simRat_chr6.simRat.chr6 492494 24 + 647215 TAGGCATCGGTCTTTTTGCGGGTG - -a -s simMouse_chr6.simMouse.chr6 484315 31 + 636262 AACACTTTTCTATCATGTATGTGAGGGTCCT -s Anc0.Anc0refChr3 101064 31 + 222631 AAAACTTTTCTAGCATGGATGTGTAGGTATT -s Anc1.Anc1refChr6 134368 31 + 197743 AAAACTTTTCTAGCATGGATGTGTAGGTATT -s Anc2.Anc2refChr1 12461 31 + 142988 CAACCTTTTCTAGCGTGGTTGTGTAGGTATT -s mr.mrrefChr3 38433 31 + 181027 AACACTTTTCTATCATGGATGTGAGGGTCCT -s simDog_chr6.simDog.chr6 459271 31 + 593897 CAACCTTTTCTAGCGTGGTTGTGTAGGTATT -s simHuman_chr6.simHuman.chr6 466520 31 + 601863 AAGACTTTTCTTGCATGGATGTGTTCAGTTT -s simRat_chr6.simRat.chr6 492518 31 + 647215 AACACTTTTCTATCAAGGATGTGAGGGTCCT - -a -s simMouse_chr6.simMouse.chr6 484346 5 + 636262 TGCTG -s Anc0.Anc0refChr3 101095 5 + 222631 TGTTG -s Anc1.Anc1refChr6 134399 5 + 197743 TGTTG -s Anc2.Anc2refChr1 12492 5 + 142988 TGTTG -s mr.mrrefChr3 38464 5 + 181027 TGTTG -s simDog_chr6.simDog.chr6 459302 5 + 593897 TGTTG -s simHuman_chr6.simHuman.chr6 466551 5 + 601863 TGTTG -s simRat_chr6.simRat.chr6 492656 5 + 647215 TGTGG - -a -s simMouse_chr6.simMouse.chr6 484351 11 + 636262 AGAGACTTACA -s Anc0.Anc0refChr3 101104 11 + 222631 GCAGGACTACA -s Anc1.Anc1refChr6 134408 11 + 197743 GCAGGACTACA -s Anc2.Anc2refChr1 12501 11 + 142988 GCAGGATTACT -s mr.mrrefChr3 38469 11 + 181027 ATAGGCCTACA -s simCow_chr6.simCow.chr6 469128 11 + 602619 GCAGGCTTAAG -s simDog_chr6.simDog.chr6 459311 6 + 593897 -----ATTACT -s simHuman_chr6.simHuman.chr6 466562 11 + 601863 GCAAGACTACA -s simRat_chr6.simRat.chr6 492661 11 + 647215 ATAGGGCTACA - -a -s simMouse_chr6.simMouse.chr6 484362 29 + 636262 GAAATCCACAGAGTTGGCAAATATAATTG -s Anc0.Anc0refChr3 101116 19 + 222631 GAAAGT-----AGTGGG-----ATAAATG -s Anc1.Anc1refChr6 134420 19 + 197743 GAAAGT-----AGTGGG-----ATAAATG -s Anc2.Anc2refChr1 12513 19 + 142988 GAAAGT-----AGGGTG-----ATCCACG -s mr.mrrefChr3 38480 29 + 181027 GAAATTCACAGAGTTGGCAAATATAATTG -s simCow_chr6.simCow.chr6 469140 19 + 602619 GAAAGT-----AGCATG-----ATCCACT -s simDog_chr6.simDog.chr6 459318 19 + 593897 GAGAGT-----AGGGTG-----ATCCACG -s simHuman_chr6.simHuman.chr6 466574 19 + 601863 GAAAGT-----AGTGGG-----ATAAGTG -s simRat_chr6.simRat.chr6 492672 29 + 647215 GAAACTCACAGAGTTGGCAAATATAATTG - -a -s simMouse_chr6.simMouse.chr6 484391 15 + 636262 ACACAATTGGCATAC -s Anc0.Anc0refChr3 101136 13 + 222631 ACACAGTTGGCAT-- -s Anc1.Anc1refChr6 134440 13 + 197743 ACACAGTTGGCAT-- -s Anc2.Anc2refChr1 12533 13 + 142988 ACATGATTGGCAT-- -s mr.mrrefChr3 38509 15 + 181027 ACACAGTTGGCATAC -s simCow_chr6.simCow.chr6 469160 10 + 602619 AC--GACTGGT-T-- -s simDog_chr6.simDog.chr6 459338 13 + 593897 GAATGATTGGCAT-- -s simHuman_chr6.simHuman.chr6 466594 13 + 601863 ACACAGTTGGCAT-- -s simRat_chr6.simRat.chr6 492701 15 + 647215 ACATGGTTGGCACAC - -a -s simMouse_chr6.simMouse.chr6 484406 104 + 636262 ACCTATAGTGCTGTTGGGAGACCTTTACTAGTTGGGCATGCCCAGCATTGGTCTTGTGTTTAAAATTGTGATGAGCTGGTATTCTAATGCACTCTATATTGTTT -s Anc0.Anc0refChr3 101149 55 + 222631 ACTTATAATGCTGATAGA-------------------------------------------------AGGATAAACTGGTGTAATGATGAACAATATGTTATTT -s Anc1.Anc1refChr6 134453 102 + 197743 ACTTATAATGCTGATAGAGGGTCTTTAGTAGTCGAGCC--CTCAATAGTGGTCTGGTATCTATAATTAGGATAAACTGGTGTAATGATGAACAATATGTTATTT -s Anc2.Anc2refChr1 12546 55 + 142988 ACTTATGATGCTGATAGA-------------------------------------------------AGGATAAACTGGTGTAATGAGAAACAATATGTTATTT -s mr.mrrefChr3 38524 104 + 181027 ACCTATAGTGCTGTTGGGAGACCTTTACTAGTCGGGCATGCCCAACATTGGTCTTGTGTCTAAAATTGTGATGAGCTGGTATTATAATGCACACTATATTGTTT -s simCow_chr6.simCow.chr6 469170 52 + 602619 ATTT---ATGCTGGTACA-------------------------------------------------AGGATAAACTGGTGTAATGAACAACAATATGTTATTT -s simDog_chr6.simDog.chr6 459351 55 + 593897 ACTTATGGCACTGATAGA-------------------------------------------------AAGATAAACTGGTGTAATGAGAAATAATGTGTTATTT -s simHuman_chr6.simHuman.chr6 466607 102 + 601863 GCTTATAATGCTGATAGAGGGTCTTTAGTAGTCGAGCC--CTCAATAGTGGTCTGGTATCTATAATTAGGATTAACTGGTCTAATGATGAACAATATGTTATTT -s simRat_chr6.simRat.chr6 492718 104 + 647215 ACCTATAGTGCTGTTGGGAGCCATTTACAAGTCGGGCATGCCCAAAATTGGTTTTGTGTCTAAAATTGTGATGAGCCGGTATTATAATGCAGACTATATTGTTT - -a -s simMouse_chr6.simMouse.chr6 484510 7 + 636262 TGATGAG -s Anc0.Anc0refChr3 101212 7 + 222631 TGATTAA -s Anc1.Anc1refChr6 134563 7 + 197743 TGATTAA -s Anc2.Anc2refChr1 12609 7 + 142988 AGATTGA -s mr.mrrefChr3 38628 7 + 181027 TGATTAG -s simCow_chr6.simCow.chr6 469230 7 + 602619 AGATTGA -s simHuman_chr6.simHuman.chr6 466732 7 + 601863 TGATTAA -s simRat_chr6.simRat.chr6 492822 7 + 647215 TGATTAG - -a -s simMouse_chr6.simMouse.chr6 484517 73 + 636262 CAAAACCCTACTGGTTCTTTGCAACTACAGGGAGCTGTGCAGGTCTCTCAAACTAGTGTCAAGGGGTTTTCAA -s Anc0.Anc0refChr3 101229 69 + 222631 TAAAACTCTAATTGGTGTTCGCAATTGGTGGGAA----GTAGGACTTTTAAGCCAGCCTCAAGCTGTTTTCCA -s Anc1.Anc1refChr6 134580 71 + 197743 TAAAACTCTAATTGGTGTTCGCAATTGGTGGGAACT--GTAGGACTTTTAAGCCAGCCTCAAGCTGTTTTCCA -s Anc2.Anc2refChr1 12626 69 + 142988 TAAAACTCTAACTGGTGTTCACAATTGGTGAGAA----GTAGGGCTTTTAAGCCAGCCTCAAGCTGTTTTCCA -s mr.mrrefChr3 38635 73 + 181027 CAAAACCCTACTGGTTCTTTGCAACTACAGGGAGCTGTGCAGGACTCTCAAACCAGTGTCAAGGGGTTTTCCA -s simCow_chr6.simCow.chr6 469254 68 + 602619 TAAAACTCTAA-TGGTGTTCACAACTGGTGAAAA----GTAGGGCTTTTAAACTAGCCTTAAGCTGTATTCCA -s simDog_chr6.simDog.chr6 459415 63 + 593897 TAAAACTCTAACTGGTGTTCACAATTGATGAGAT----GTAGGGCTTTTAAGCCA-CTTCA-----TTTTCCA -s simHuman_chr6.simHuman.chr6 466749 65 + 601863 TAAAACTCTAATTGCTATTCGCAGGTGGTGGGAACT-----AGACT---AGGCCAGCCTCAAGCAGTTTTCCA -s simRat_chr6.simRat.chr6 492829 73 + 647215 CAAAAGCCTACTGGTTCTTTGCAACCACAGGAAGCTGTGCAGGACTCTCAAACCAGTGTCAAGTGGTTTTCCA - -a -s simMouse_chr6.simMouse.chr6 484590 20 + 636262 AGTGTTTTGCACATCATGAT -s Anc0.Anc0refChr3 101299 20 + 222631 AGTATTTTGCATATCCATAT -s Anc1.Anc1refChr6 134652 20 + 197743 AGTATTTTGCATATCCATAT -s Anc2.Anc2refChr1 12696 20 + 142988 AGCATTTTGCATATCCATAT -s mr.mrrefChr3 38708 20 + 181027 AGTGTTTTGCATATCCAGAT -s simCow_chr6.simCow.chr6 469323 20 + 602619 AGCATTTTCCATATCTATCT -s simDog_chr6.simDog.chr6 459479 20 + 593897 AGCATTTTGCATATCCATAT -s simHuman_chr6.simHuman.chr6 466815 20 + 601863 AATATTTTGCATGCCCATAT -s simRat_chr6.simRat.chr6 492902 20 + 647215 AGAGTTTTGCATATTCAAAT - -a -s simMouse_chr6.simMouse.chr6 484610 2 + 636262 GA -s Anc0.Anc0refChr3 101324 2 + 222631 GA -s Anc1.Anc1refChr6 134677 2 + 197743 GA -s Anc2.Anc2refChr1 12721 2 + 142988 GA -s mr.mrrefChr3 38728 2 + 181027 GA -s simCow_chr6.simCow.chr6 469348 2 + 602619 GA -s simDog_chr6.simDog.chr6 459504 2 + 593897 CG -s simHuman_chr6.simHuman.chr6 466840 2 + 601863 GA -s simRat_chr6.simRat.chr6 492922 2 + 647215 CA - -a -s simMouse_chr6.simMouse.chr6 484612 49 + 636262 ATTATGGAACAAAATGTCAAACATCCAACTCCCTATATTGTCTTAACAC -s Anc0.Anc0refChr3 101332 49 + 222631 ATTATGCACCAAAATGTAAAACTTCCAAATTCTTATATTGTCTTAACAC -s Anc1.Anc1refChr6 134685 49 + 197743 ATTATGCACCAAAATGTAAAACTTCCAAATTCTTATATTGTCTTAACAC -s Anc2.Anc2refChr1 12729 49 + 142988 ATCATGCACCAAAATATAAAACTTCCAAATTCTTATATTGTCTTAACAA -s mr.mrrefChr3 38735 49 + 181027 ATTATGGAACAAAATGTCAAACATCCAACTCCTTATATTGTCTTAACAC -s simCow_chr6.simCow.chr6 469356 49 + 602619 ATCCTGCACCAAAATATAAATCTTCCAAACTGTTATATTCTCCTAAGAA -s simDog_chr6.simDog.chr6 459512 43 + 593897 ATCATGGACCA------TAAACTTTCAGATTCTTATGTTGTCTTAACAA -s simHuman_chr6.simHuman.chr6 466848 49 + 601863 AGTATGCACCAAAATGTAAAACCTCCAAATTCTTATATTGTCTTAACAC -s simRat_chr6.simRat.chr6 492929 49 + 647215 ATTATGGAACAAAATATCATACATCCAACTCCTTATATTGTCTTGACAT - -a -s simMouse_chr6.simMouse.chr6 484661 27 + 636262 AAAAATGAAGTAAAAAACACAAGATAG -s Anc0.Anc0refChr3 101382 27 + 222631 AAAAATGAAATAAAAGCTACAACATTG -s Anc1.Anc1refChr6 134735 27 + 197743 AAAAATGAAATAAAAGCTACAACATTG -s Anc2.Anc2refChr1 12779 27 + 142988 AAAAATGAAATAAAAGCCACAGCATTG -s mr.mrrefChr3 38784 27 + 181027 AAAAATGAAATAAAAAATACAACATAG -s simCow_chr6.simCow.chr6 469406 27 + 602619 AAACATGAAATAAAAACCACTTCATTG -s simDog_chr6.simDog.chr6 459556 27 + 593897 AAAAGTGAAATAAAAGCCACAGCATTG -s simHuman_chr6.simHuman.chr6 466898 27 + 601863 AAAAATTAAACAAAAGCTGCAACATTG -s simRat_chr6.simRat.chr6 492978 27 + 647215 AAAAATGAAATAAAAAGTACAACATAG - -a -s simMouse_chr6.simMouse.chr6 484688 33 + 636262 CACAGGAATTATAATTCCCACTAGTGGTCCAAG -s Anc0.Anc0refChr3 101409 33 + 222631 CACAGAAATTATAATTGTTGCTGGTTTTTCAAG -s Anc1.Anc1refChr6 134762 33 + 197743 CACAGAAATTATAATTGTTGCTGGTTTTTCAAG -s Anc2.Anc2refChr1 12815 33 + 142988 TATAGAAACTATAATGGTTGCTGGTTTTTCAAG -s mr.mrrefChr3 38811 33 + 181027 CACAGGAATTATAATTCCCGCTAGTGTTCCAAG -s simCow_chr6.simCow.chr6 469442 33 + 602619 TGTAGAAACTGTAATGGTTGCTCGGTTTTTGAG -s simDog_chr6.simDog.chr6 459592 33 + 593897 TATAGAAACTATAATGGGTTCTGGTTTTTCAAG -s simHuman_chr6.simHuman.chr6 466925 33 + 601863 CACAGACATTATAATTGTTGCTGGATTTTCAAG -s simRat_chr6.simRat.chr6 493005 33 + 647215 CACAGGGATTATAATTCCAGCCAATGTTCCAAA - -a -s simMouse_chr6.simMouse.chr6 484721 4 + 636262 AGTT -s Anc0.Anc0refChr3 101444 4 + 222631 AGTT -s Anc1.Anc1refChr6 134797 4 + 197743 AGTT -s Anc2.Anc2refChr1 12850 4 + 142988 AGTC -s mr.mrrefChr3 38844 4 + 181027 AGTT -s simCow_chr6.simCow.chr6 469477 4 + 602619 AGTA -s simDog_chr6.simDog.chr6 459627 4 + 593897 AGTC -s simHuman_chr6.simHuman.chr6 466960 4 + 601863 AGTT -s simRat_chr6.simRat.chr6 493038 4 + 647215 AGTT - -a -s simMouse_chr6.simMouse.chr6 484725 8 + 636262 TGTGAAAT -s Anc0.Anc0refChr3 101448 8 + 222631 TTCCACTT -s Anc1.Anc1refChr6 134801 8 + 197743 TTCCACTT -s Anc2.Anc2refChr1 12854 8 + 142988 TTCCACTT -s mr.mrrefChr3 38848 8 + 181027 TGCGAATT -s simCow_chr6.simCow.chr6 469481 8 + 602619 TTGCACCT -s simDog_chr6.simDog.chr6 459631 8 + 593897 TTCCACTT -s simHuman_chr6.simHuman.chr6 466964 8 + 601863 TCCCATTC -s simRat_chr6.simRat.chr6 493043 8 + 647215 TGCGAATT - -a -s simMouse_chr6.simMouse.chr6 484733 7 + 636262 ACAGTGG -s Anc0.Anc0refChr3 101457 7 + 222631 ACAGTTG -s Anc1.Anc1refChr6 134810 7 + 197743 ACAGTTG -s Anc2.Anc2refChr1 12863 7 + 142988 ACAGTTG -s mr.mrrefChr3 38856 7 + 181027 ACAGTGG -s simCow_chr6.simCow.chr6 469490 3 + 602619 ACA---- -s simDog_chr6.simDog.chr6 459640 7 + 593897 ACAGTTG -s simHuman_chr6.simHuman.chr6 466973 7 + 601863 ACAGTTG -s simRat_chr6.simRat.chr6 493051 7 + 647215 ACAGTGG - -a -s simMouse_chr6.simMouse.chr6 484740 25 + 636262 CATTACACCTTGCGCACTATTTATA -s Anc0.Anc0refChr3 101464 23 + 222631 TGTTGCTCCCCAAGCACTATCTA-- -s Anc1.Anc1refChr6 134817 23 + 197743 TGTTGCTCCCCAAGCACTATCTA-- -s Anc2.Anc2refChr1 12870 23 + 142988 GGCTGCTCCCCAAGCATCTCCTA-- -s mr.mrrefChr3 38863 25 + 181027 TATTGCACCTTGCGCACTATTTATA -s simCow_chr6.simCow.chr6 469493 14 + 602619 ---------CCCATCACTATCTA-- -s simDog_chr6.simDog.chr6 459649 23 + 593897 GGCTGCTCCTCAAGCATCTCCTA-- -s simHuman_chr6.simHuman.chr6 466980 23 + 601863 TGTGGCTTCCCAAGCACTATATG-- -s simRat_chr6.simRat.chr6 493058 24 + 647215 TATTGC-CCTTGTGCACTATGTATA - -a -s simMouse_chr6.simMouse.chr6 484765 7 + 636262 CCATTTA -s Anc0.Anc0refChr3 101487 3 + 222631 ----TTA -s Anc1.Anc1refChr6 134840 3 + 197743 ----TTA -s Anc2.Anc2refChr1 12893 3 + 142988 ----TGA -s mr.mrrefChr3 38888 7 + 181027 CCATTTA -s simCow_chr6.simCow.chr6 469507 3 + 602619 ----TGA -s simDog_chr6.simDog.chr6 459672 3 + 593897 ----TGA -s simHuman_chr6.simHuman.chr6 467003 3 + 601863 ----TTA -s simRat_chr6.simRat.chr6 493084 7 + 647215 CTATTTA - -a -s simMouse_chr6.simMouse.chr6 484772 7 + 636262 AGGTTAA -s Anc0.Anc0refChr3 101490 7 + 222631 AACTAAA -s Anc1.Anc1refChr6 134843 7 + 197743 AACTAAA -s Anc2.Anc2refChr1 12901 7 + 142988 AACTAAA -s mr.mrrefChr3 38895 7 + 181027 AGGTTAA -s simCow_chr6.simCow.chr6 469515 7 + 602619 GAACAGA -s simDog_chr6.simDog.chr6 459680 7 + 593897 AACTAAA -s simHuman_chr6.simHuman.chr6 467006 7 + 601863 AACAAAA -s simRat_chr6.simRat.chr6 493091 7 + 647215 AGGTTAA - -a -s simMouse_chr6.simMouse.chr6 484779 10 + 636262 TTAACAAATT -s Anc0.Anc0refChr3 101497 10 + 222631 TGAAAATATC -s Anc1.Anc1refChr6 134850 10 + 197743 TGAAAATATC -s Anc2.Anc2refChr1 12908 10 + 142988 TGAAAATATC -s mr.mrrefChr3 38902 10 + 181027 TAAACAAATT -s simCow_chr6.simCow.chr6 469522 10 + 602619 TGAAAATGTT -s simDog_chr6.simDog.chr6 459687 10 + 593897 TGAAAATATC -s simHuman_chr6.simHuman.chr6 467013 1 + 601863 T--------- -s simRat_chr6.simRat.chr6 493100 10 + 647215 TAAACAAATT - -a -s simMouse_chr6.simMouse.chr6 484789 62 + 636262 AGAATTTGTGTCCCACAATTCTTGAAATGTTTTTATTTAAAAGTCACCTGTTACTATATCAA -s Anc0.Anc0refChr3 101507 56 + 222631 TGAAAATATATCCCACAACATTTGAAATGTTGCTATTTCAAAGTCAT------CTATGTGAA -s Anc1.Anc1refChr6 134860 56 + 197743 TGAAAATATATCCCACAACATTTGAAATGTTGCTATTTCAAAGTCAT------CTATGTGAA -s Anc2.Anc2refChr1 12918 56 + 142988 TGAAAATATATCCCACAACATTTGAAATGTTGCAATTTCAAAGTCAC------CCATGTGAA -s mr.mrrefChr3 38912 62 + 181027 AGAATTTATGTCCCACAATTCTTGAAATGTTTCTATTTAAAAGTCATCTGTTACTATATCAA -s simCow_chr6.simCow.chr6 469532 56 + 602619 TGAAAATATATCCCACAACATTTGAAATGTTCCAATCCATAAGTCAA------CCAAGTGAA -s simDog_chr6.simDog.chr6 459718 56 + 593897 TGAAAATATTTCCGGCAGTGTTTGAAATGCTGCAATTTCAAAGTCAC------CCATGTGCA -s simHuman_chr6.simHuman.chr6 467014 54 + 601863 --AAAACATATCCCACAACATTTGAATTGTGGCTATTTCAAGGTTGT------CTATGTGAA -s simRat_chr6.simRat.chr6 493110 62 + 647215 AGAATTTATGTCCCACAGTTCTTGAAATGTTTCTATTTAAAAGTCATCTGTTACTATTTAAA - -a -s simMouse_chr6.simMouse.chr6 484851 28 + 636262 ATTCCTTTAAAAGCTTCACTCTGCTTAA -s Anc0.Anc0refChr3 101566 28 + 222631 ATAGCTTTGAATCTCTCACTCTCGTTAA -s Anc1.Anc1refChr6 134919 28 + 197743 ATAGCTTTGAATCTCTCACTCTCGTTAA -s Anc2.Anc2refChr1 12977 28 + 142988 ATAGTTTTGAATCTCTCACTCTCGTCAA -s mr.mrrefChr3 38974 28 + 181027 ATTCCTTTAAAAGCTTCACTCTGCTTAA -s simCow_chr6.simCow.chr6 469591 28 + 602619 TTATTTTTGAATCTCTCACTCTGGTCAA -s simDog_chr6.simDog.chr6 459777 27 + 593897 ATAGTTCTGAATCTCTCGCTTTCATCA- -s simHuman_chr6.simHuman.chr6 467071 28 + 601863 ATAGCTTTGAATCTCTCACTCTAGTTGA -s simRat_chr6.simRat.chr6 493172 28 + 647215 ATTTCTCTATAAGCTTCACTCTGCTTAA - -a -s simMouse_chr6.simMouse.chr6 484879 29 + 636262 TGAATGGTTTTCAGTGATGTCCCAATCCT -s Anc0.Anc0refChr3 101597 29 + 222631 TAGATGGTTTTCTGTGATGCCCCAGTACC -s Anc1.Anc1refChr6 134950 29 + 197743 TAGATGGTTTTCTGTGATGCCCCAGTACC -s Anc2.Anc2refChr1 13008 29 + 142988 TAGACAGTTTTCTGTGACACCCCAGAACC -s mr.mrrefChr3 39002 29 + 181027 TGAATGGTTTTCAGTGATGTCCCAGTCCT -s simCow_chr6.simCow.chr6 469622 29 + 602619 TAGACCGTTTTCTGTGACACCCCAGAGCC -s simDog_chr6.simDog.chr6 459805 29 + 593897 TAGACAGTTATCTCAatcattccagaaca -s simHuman_chr6.simHuman.chr6 467102 29 + 601863 TAGATGGTTTTCTGTGATGCCCCCGTTCC -s simRat_chr6.simRat.chr6 493200 29 + 647215 TGAATGGCTTTCAGTACTGTCCCAGTCCT - -a -s simMouse_chr6.simMouse.chr6 484908 7 + 636262 ATTATGA -s Anc0.Anc0refChr3 101626 7 + 222631 GTTATGa -s Anc1.Anc1refChr6 134979 7 + 197743 GTTATGA -s Anc2.Anc2refChr1 13037 7 + 142988 GTTATGa -s mr.mrrefChr3 39031 7 + 181027 ATTATGA -s simCow_chr6.simCow.chr6 469651 7 + 602619 TTTATGA -s simDog_chr6.simDog.chr6 459835 7 + 593897 gttgata -s simHuman_chr6.simHuman.chr6 467131 7 + 601863 CTTATGA -s simRat_chr6.simRat.chr6 493229 7 + 647215 ATTATTA - -a -s simMouse_chr6.simMouse.chr6 484915 17 + 636262 ACAATGCTGATTACTTA -s Anc0.Anc0refChr3 101633 16 + 222631 acaATGCTCATCATTT- -s Anc1.Anc1refChr6 134986 16 + 197743 ACAATGCTCATCATTT- -s Anc2.Anc2refChr1 13158 16 + 142988 aaaATGTTCTTCGTTT- -s mr.mrrefChr3 39038 17 + 181027 ACAATGCTCATTATTTA -s simCow_chr6.simCow.chr6 469772 16 + 602619 aaaattttCGTTTTTT- -s simDog_chr6.simDog.chr6 459969 16 + 593897 aaaATGTTCTTCGTTT- -s simHuman_chr6.simHuman.chr6 467138 16 + 601863 ACACTACTCATCATTT- -s simRat_chr6.simRat.chr6 493236 17 + 647215 ACAATGCTCATTATTTA - -a -s simMouse_chr6.simMouse.chr6 484932 1 + 636262 G -s Anc0.Anc0refChr3 101649 1 + 222631 G -s Anc1.Anc1refChr6 135002 1 + 197743 G -s Anc2.Anc2refChr1 13174 1 + 142988 G -s mr.mrrefChr3 39055 1 + 181027 G -s simCow_chr6.simCow.chr6 469789 1 + 602619 G -s simDog_chr6.simDog.chr6 459985 1 + 593897 G -s simHuman_chr6.simHuman.chr6 467154 1 + 601863 G -s simRat_chr6.simRat.chr6 493253 1 + 647215 G - -a -s simMouse_chr6.simMouse.chr6 484933 11 + 636262 CAACGCATGTT -s Anc0.Anc0refChr3 101650 11 + 222631 CAACTCATGTT -s Anc1.Anc1refChr6 135003 11 + 197743 CAACTCATGTT -s Anc2.Anc2refChr1 13175 11 + 142988 CAACTCATGTT -s mr.mrrefChr3 39056 11 + 181027 CAACGCATGTT -s simCow_chr6.simCow.chr6 469790 11 + 602619 CAATCCATGTT -s simDog_chr6.simDog.chr6 459998 11 + 593897 CAACTCAGGTT -s simHuman_chr6.simHuman.chr6 467155 11 + 601863 CAACTCGTGTT -s simRat_chr6.simRat.chr6 493254 11 + 647215 CAATGCATGTT - -a -s simMouse_chr6.simMouse.chr6 484944 2 + 636262 AT -s Anc0.Anc0refChr3 101661 2 + 222631 AT -s Anc1.Anc1refChr6 135014 2 + 197743 AT -s Anc2.Anc2refChr1 13186 2 + 142988 AT -s mr.mrrefChr3 39067 2 + 181027 AT -s simCow_chr6.simCow.chr6 469801 2 + 602619 AT -s simDog_chr6.simDog.chr6 460016 2 + 593897 AT -s simHuman_chr6.simHuman.chr6 467166 2 + 601863 AT -s simRat_chr6.simRat.chr6 493265 2 + 647215 AG - -a -s simMouse_chr6.simMouse.chr6 484946 49 + 636262 CTGCCCTGTCAAGTGTTAGTCCATAGAGAGATTCGAGTTGGCCAGTTAG -s Anc0.Anc0refChr3 101663 49 + 222631 CTATCCTATCAGGTGTCAGTCCATAGAGGGAGTTGGGTTGGAAGGCTAC -s Anc1.Anc1refChr6 135016 49 + 197743 CTATCCTATCAGGTGTCAGTCCATAGAGGGAGTTGGGTTGGAAGGCTAC -s Anc2.Anc2refChr1 13188 49 + 142988 CTATCTTATCAGGTGTCAGTCCATGGAGGGAGTTAGGTCAGAAGGCTAC -s mr.mrrefChr3 39069 49 + 181027 CTGCCCTATCAAGTGTTAGTCCATAGAGAGATTCGAGTTGGAAGGTTAG -s simCow_chr6.simCow.chr6 469804 49 + 602619 CTATGTTTTCAGATGTTAGTACGTGGAGGGACTTAGGTCAGAAGGTTAC -s simDog_chr6.simDog.chr6 460018 49 + 593897 CTATCTTATCAGGTGTCAGGCCATGGAGGGAGTCAGGACACGAAGCTAC -s simHuman_chr6.simHuman.chr6 467168 49 + 601863 CTATCCTATCAGGTGTCAGTCCATACAGGGAATTGGATTGGAAGGCTAC -s simRat_chr6.simRat.chr6 493267 49 + 647215 CTGCCCTATCAAGTGTTAGTCCATAGAGAGATTCAAGTTGGAAGGTTAA - -a -s simMouse_chr6.simMouse.chr6 484995 6 + 636262 AACAAA -s Anc0.Anc0refChr3 101712 6 + 222631 AACAAA -s Anc1.Anc1refChr6 135065 6 + 197743 AACAAA -s Anc2.Anc2refChr1 13237 6 + 142988 AACAAA -s mr.mrrefChr3 39118 6 + 181027 AACAAA -s simCow_chr6.simCow.chr6 469854 6 + 602619 AACAAA -s simDog_chr6.simDog.chr6 460067 6 + 593897 AAGAAA -s simHuman_chr6.simHuman.chr6 467217 6 + 601863 AACAAA -s simRat_chr6.simRat.chr6 493316 6 + 647215 AACAAA - -a -s simMouse_chr6.simMouse.chr6 485001 14 + 636262 ATTTGTCAGTTTTT -s Anc0.Anc0refChr3 101721 14 + 222631 ATTTATCAGTTTTT -s Anc1.Anc1refChr6 135074 14 + 197743 ATTTATCAGTTTTT -s Anc2.Anc2refChr1 13246 14 + 142988 ATTTATCAGTTTTT -s mr.mrrefChr3 39127 14 + 181027 ATTTATCAGTTTTT -s simCow_chr6.simCow.chr6 469863 14 + 602619 ATCTATCAGTTTTC -s simDog_chr6.simDog.chr6 460076 14 + 593897 AGTGGTTAGCTTTT -s simHuman_chr6.simHuman.chr6 467226 14 + 601863 ATATATCCGTTTTT -s simRat_chr6.simRat.chr6 493325 14 + 647215 ATTTATCGGTTTTT - -a -s simMouse_chr6.simMouse.chr6 485015 28 + 636262 GGTTCTCCAGTATCTTTACTAATTAACC -s Anc0.Anc0refChr3 101735 28 + 222631 GGTTCTCCAGTAACTTCAATTATTTAAC -s Anc1.Anc1refChr6 135088 28 + 197743 GGTTCTCCAGTAACTTCAATTATTTAAC -s Anc2.Anc2refChr1 13260 28 + 142988 GGGTCTCCAGTAATTTCAATTACTTAAC -s mr.mrrefChr3 39141 28 + 181027 GGTTCTCCAGTATCTTCACTAATTAACC -s simCow_chr6.simCow.chr6 469877 28 + 602619 AGGCCTTCAGTAATCTCAAGTACTTGAC -s simDog_chr6.simDog.chr6 460092 28 + 593897 GGGTCACCAGAAATTTTAGTTACTTAAC -s simHuman_chr6.simHuman.chr6 467240 28 + 601863 GGTTCTCTAGTAACTTCAACTATACAGC -s simRat_chr6.simRat.chr6 493339 28 + 647215 GGTTCTCCAGTATTTTCACTAATTGACC - -a -s simMouse_chr6.simMouse.chr6 485043 4 + 636262 ACTA -s Anc0.Anc0refChr3 101763 4 + 222631 CCTG -s Anc1.Anc1refChr6 135116 4 + 197743 CCTG -s Anc2.Anc2refChr1 13288 4 + 142988 CCAG -s mr.mrrefChr3 39169 4 + 181027 ACTA -s simCow_chr6.simCow.chr6 469913 4 + 602619 CCAC -s simDog_chr6.simDog.chr6 460120 4 + 593897 CCAG -s simHuman_chr6.simHuman.chr6 467268 4 + 601863 CCTG -s simRat_chr6.simRat.chr6 493367 4 + 647215 ACTA - -a -s simMouse_chr6.simMouse.chr6 485047 19 + 636262 ACTGTGCTGACTAGTAAAC -s Anc0.Anc0refChr3 101767 10 + 222631 GCTC--------AGTAAA- -s Anc1.Anc1refChr6 135120 10 + 197743 GCTC--------AGTAAA- -s Anc2.Anc2refChr1 13296 10 + 142988 GTTC--------TGTAAA- -s mr.mrrefChr3 39173 19 + 181027 ACTGTGCTGACTAGTAAAC -s simCow_chr6.simCow.chr6 469921 10 + 602619 GTTT--------GGTAAG- -s simDog_chr6.simDog.chr6 460128 10 + 593897 GTCC--------TGTAAA- -s simHuman_chr6.simHuman.chr6 467272 9 + 601863 GCTA--------AGTGA-- -s simRat_chr6.simRat.chr6 493371 19 + 647215 ACTGCCCTGTCTTGTAAAC - -a -s simMouse_chr6.simMouse.chr6 485066 62 + 636262 CTATGATCCTGATTTGTTTTGCGATAGCAGACCTATTGTACTGAATCACTATTTATGCAGTT -s Anc0.Anc0refChr3 101777 62 + 222631 CTATGGTCCTGTTGTATTTTGGTAAAGCAGATCCATTGTAGTAATGTACTATTTTTGCAGGT -s Anc1.Anc1refChr6 135130 62 + 197743 CTATGGTCCTGTTGTATTTTGGTAAAGCAGATCCATTGTAGTAATGTACTATTTTTGCAGGT -s Anc2.Anc2refChr1 13306 62 + 142988 CTGTGGTCCTGTTGTATTTTGGTAAAGCAGATCCATTATTGCATTGTATTATTTTTGCAGGT -s mr.mrrefChr3 39192 62 + 181027 CTATGATCCTGATTTGTTTTGCGATAGCAGACCTATTGTACTGAATCACTATTTATGCAGTT -s simCow_chr6.simCow.chr6 469931 62 + 602619 CTGTGGTCCTGATGTATTTTGGATATGCAGATACATTATTGCATTGCATTATTTTTACAGGT -s simDog_chr6.simDog.chr6 460139 54 + 593897 CTGTGATCTTTTTGTATTTTGGTAAAGCAAATCC--------ATTGTATCATTTTTGCAGGT -s simHuman_chr6.simHuman.chr6 467281 55 + 601863 --ATGGTCCTGGTGTATTTTG-----GCAGATCCATTGTAATAATGTACTAATCTTGCAGGT -s simRat_chr6.simRat.chr6 493390 62 + 647215 CTATGATCCTGATTTGTTTTGCAAAAGCGGACCTATTGTTCTGAATCACTATTTATGCAGCT - -a -s simMouse_chr6.simMouse.chr6 485128 3 + 636262 ATC -s Anc0.Anc0refChr3 101842 3 + 222631 ATC -s Anc1.Anc1refChr6 135195 3 + 197743 ATC -s Anc2.Anc2refChr1 13371 3 + 142988 ATC -s mr.mrrefChr3 39257 3 + 181027 ATC -s simCow_chr6.simCow.chr6 469996 3 + 602619 ACC -s simDog_chr6.simDog.chr6 460196 3 + 593897 ATC -s simHuman_chr6.simHuman.chr6 467339 3 + 601863 ATC -s simRat_chr6.simRat.chr6 493455 3 + 647215 ATC - -a -s simMouse_chr6.simMouse.chr6 485131 2 + 636262 AC -s Anc0.Anc0refChr3 101845 1 + 222631 C- -s Anc1.Anc1refChr6 135198 2 + 197743 CC -s Anc2.Anc2refChr1 13374 1 + 142988 C- -s mr.mrrefChr3 39260 2 + 181027 AC -s simCow_chr6.simCow.chr6 470006 1 + 602619 C- -s simDog_chr6.simDog.chr6 460199 1 + 593897 C- -s simHuman_chr6.simHuman.chr6 467342 2 + 601863 CC -s simRat_chr6.simRat.chr6 493458 2 + 647215 AC - -a -s simMouse_chr6.simMouse.chr6 485133 34 + 636262 CCTGTCCTGTTCTGACTTGCATGCGTACAAACAT -s Anc0.Anc0refChr3 101846 23 + 222631 -----------CTGTCTTGTATGAATATTCACAC -s Anc1.Anc1refChr6 135204 34 + 197743 TCTGTCTTGTTCTGTCTTGTATGAATATTCACAC -s Anc2.Anc2refChr1 13375 23 + 142988 -----------CTGTCTTGTGAGAATATTCACAC -s mr.mrrefChr3 39266 34 + 181027 CCTGTCCTGTTCTGACTTGTATGCGTACAAACAC -s simCow_chr6.simCow.chr6 470007 23 + 602619 -----------CTGTCTTGTGCGAGTATTCACAC -s simDog_chr6.simDog.chr6 460200 23 + 593897 -----------CTATCTTGTGAGAATATTTACAC -s simHuman_chr6.simHuman.chr6 467349 34 + 601863 TCTGTCTTGTTCTGTCTTGTATGGATATTCACAC -s simRat_chr6.simRat.chr6 493464 34 + 647215 CCTGTCCTGTTCTGACTTGTGTGTGCACATACAC - -a -s simMouse_chr6.simMouse.chr6 485167 16 + 636262 TTTGCTAAGTATGAGT -s Anc0.Anc0refChr3 101871 16 + 222631 TTTGCTGAGTTTGAGT -s Anc1.Anc1refChr6 135240 16 + 197743 TTTGCTGAGTTTGAGT -s Anc2.Anc2refChr1 13400 16 + 142988 TTTTTTGAGTTTGAGT -s mr.mrrefChr3 39301 16 + 181027 TTTGCTAAGTATGAGT -s simCow_chr6.simCow.chr6 470032 15 + 602619 T-TAAGGAGTTTGAGT -s simDog_chr6.simDog.chr6 460225 16 + 593897 TTTTTTGAGTTTGAGT -s simHuman_chr6.simHuman.chr6 467385 16 + 601863 TCTGCTGAGTTTGAGT -s simRat_chr6.simRat.chr6 493499 16 + 647215 TTTGCTAAGTATGAGT - -a -s simMouse_chr6.simMouse.chr6 485183 5 + 636262 GCAAG -s Anc0.Anc0refChr3 101887 5 + 222631 GCAAG -s Anc1.Anc1refChr6 135256 5 + 197743 GCAAG -s Anc2.Anc2refChr1 13416 5 + 142988 GCAAG -s mr.mrrefChr3 39317 5 + 181027 GCAAG -s simCow_chr6.simCow.chr6 470047 5 + 602619 ACAAG -s simDog_chr6.simDog.chr6 460241 5 + 593897 GCAAG -s simHuman_chr6.simHuman.chr6 467401 5 + 601863 CCTAG -s simRat_chr6.simRat.chr6 493516 5 + 647215 GCGAG - -a -s simMouse_chr6.simMouse.chr6 485188 8 + 636262 CGATTGCC -s Anc0.Anc0refChr3 101892 8 + 222631 CTGCCGTC -s Anc1.Anc1refChr6 135261 8 + 197743 CTGCCGTC -s Anc2.Anc2refChr1 13421 8 + 142988 CTGCCGTC -s mr.mrrefChr3 39322 8 + 181027 CGATTGCC -s simCow_chr6.simCow.chr6 470052 8 + 602619 CTACTGTC -s simDog_chr6.simDog.chr6 460248 8 + 593897 CTGCCCCT -s simHuman_chr6.simHuman.chr6 467406 8 + 601863 CTTCCGTC -s simRat_chr6.simRat.chr6 493521 8 + 647215 CGATTGCC - -a -s simMouse_chr6.simMouse.chr6 485196 15 + 636262 CTAGACTCCTTGTCT -s Anc0.Anc0refChr3 101900 12 + 222631 G---CCTCCTTGTCT -s Anc1.Anc1refChr6 135269 12 + 197743 G---CCTCCTTGTCT -s Anc2.Anc2refChr1 13429 12 + 142988 G---CCTCCTTGTCT -s mr.mrrefChr3 39330 15 + 181027 CTAGACTCCTTGTCT -s simCow_chr6.simCow.chr6 470064 12 + 602619 G---CCCCCCTGTCA -s simDog_chr6.simDog.chr6 460256 12 + 593897 G---GCTCCTTGTCT -s simHuman_chr6.simHuman.chr6 467414 12 + 601863 T---CCTCCTTGTCT -s simRat_chr6.simRat.chr6 493529 15 + 647215 CAAGACTTCTTGTCT - -a -s simMouse_chr6.simMouse.chr6 485211 14 + 636262 AATATTTAAAAGAC -s Anc0.Anc0refChr3 101913 13 + 222631 AATATTTGAA-GAC -s Anc1.Anc1refChr6 135282 13 + 197743 AATATTTGAA-GAC -s Anc2.Anc2refChr1 13442 13 + 142988 AATATTTGAA-GAC -s mr.mrrefChr3 39345 13 + 181027 AATATTTGAA-GAC -s simCow_chr6.simCow.chr6 470077 13 + 602619 AACATTTGAA-AAC -s simDog_chr6.simDog.chr6 460269 13 + 593897 CATATTTAAA-GTG -s simHuman_chr6.simHuman.chr6 467427 13 + 601863 AATACTTGAA-GAC -s simRat_chr6.simRat.chr6 493544 13 + 647215 AATATTTGAA-GAC - -a -s simMouse_chr6.simMouse.chr6 485225 13 + 636262 ACAATGATTGATT -s Anc0.Anc0refChr3 101936 13 + 222631 AAAATGATTGATT -s Anc1.Anc1refChr6 135305 13 + 197743 AAAATGATTGATT -s Anc2.Anc2refChr1 13465 13 + 142988 AAAATGATTGATT -s mr.mrrefChr3 39358 13 + 181027 AAAATGATTGATT -s simCow_chr6.simCow.chr6 470100 13 + 602619 TAAATGATTCATT -s simDog_chr6.simDog.chr6 460292 13 + 593897 ATAATGATTGATT -s simHuman_chr6.simHuman.chr6 467450 13 + 601863 AAAATGGTTAATT -s simRat_chr6.simRat.chr6 493557 13 + 647215 AAAATAAGACGCT - -a -s simMouse_chr6.simMouse.chr6 485238 7 + 636262 AAGGTCA -s Anc0.Anc0refChr3 101954 7 + 222631 GAGGGAA -s Anc1.Anc1refChr6 135323 7 + 197743 GAGGGAA -s Anc2.Anc2refChr1 13483 7 + 142988 AAGGGAA -s mr.mrrefChr3 39371 7 + 181027 GAGGTCA -s simCow_chr6.simCow.chr6 470118 7 + 602619 AAGGGAA -s simDog_chr6.simDog.chr6 460310 7 + 593897 AAGGGAA -s simHuman_chr6.simHuman.chr6 467468 7 + 601863 GAGGAAG -s simRat_chr6.simRat.chr6 493570 7 + 647215 GAGGTCA - -a -s simMouse_chr6.simMouse.chr6 485245 3 + 636262 TCT -s Anc0.Anc0refChr3 101961 3 + 222631 TCT -s Anc1.Anc1refChr6 135330 3 + 197743 TCT -s Anc2.Anc2refChr1 13500 3 + 142988 TCT -s mr.mrrefChr3 39378 3 + 181027 TCT -s simCow_chr6.simCow.chr6 470129 3 + 602619 TCT -s simDog_chr6.simDog.chr6 460327 3 + 593897 TCT -s simHuman_chr6.simHuman.chr6 467475 3 + 601863 CCT -s simRat_chr6.simRat.chr6 493577 3 + 647215 TCT - -a -s simMouse_chr6.simMouse.chr6 485248 43 + 636262 AGAGATTGCCCCATTAATTTCATTCCCATATATAATTCTAAAG -s Anc0.Anc0refChr3 101964 43 + 222631 AGAGACTACCACATACAGCTAGGTCCCATGCATAAATCCTAAT -s Anc1.Anc1refChr6 135333 43 + 197743 AGAGACTACCACATACAGCTAGGTCCCATGCATAAATCCTAAT -s Anc2.Anc2refChr1 13503 43 + 142988 AGAGACTACCACATACAGCTAGGTCCCCTGCATAAATCCTAGT -s mr.mrrefChr3 39381 43 + 181027 AGAGACTGCCCCATTAATTTCGTTCCCATATATAATTCTAAAG -s simCow_chr6.simCow.chr6 470132 43 + 602619 AGATACAACCGCATATAGCTAGGTCCCCTATGTAAATCCTAGT -s simDog_chr6.simDog.chr6 460330 43 + 593897 AGAGACTACCATATACAGCCAGGTGCCCTGCATAAATCCTAGT -s simHuman_chr6.simHuman.chr6 467479 43 + 601863 AGAGACTACCACATACAGCTGGGTCCCATGCTTAAATCCTAAT -s simRat_chr6.simRat.chr6 493580 43 + 647215 AGAGACTGCCTCATTAATTTAGTTCACATATATAATTCTACGG - -a -s simMouse_chr6.simMouse.chr6 485291 8 + 636262 GTTCTCTT -s Anc0.Anc0refChr3 102007 8 + 222631 GCTCTCTT -s Anc1.Anc1refChr6 135376 8 + 197743 GCTCTCTT -s Anc2.Anc2refChr1 13547 8 + 142988 GCTCTCTT -s mr.mrrefChr3 39424 8 + 181027 GTTCTCTT -s simCow_chr6.simCow.chr6 470176 8 + 602619 CCTCCTGT -s simDog_chr6.simDog.chr6 460374 8 + 593897 GCACTCTG -s simHuman_chr6.simHuman.chr6 467522 8 + 601863 ACTCTCTT -s simRat_chr6.simRat.chr6 493623 8 + 647215 GTTCTCTT - -a -s simMouse_chr6.simMouse.chr6 485299 5 + 636262 CTCTC -s Anc0.Anc0refChr3 102018 5 + 222631 CTTGC -s Anc1.Anc1refChr6 135387 5 + 197743 CTTGC -s Anc2.Anc2refChr1 13558 5 + 142988 CTTGC -s mr.mrrefChr3 39432 5 + 181027 CTCTC -s simCow_chr6.simCow.chr6 470187 5 + 602619 CTTTC -s simDog_chr6.simDog.chr6 460385 5 + 593897 CTTGT -s simHuman_chr6.simHuman.chr6 467533 5 + 601863 CTTGC -s simRat_chr6.simRat.chr6 493631 5 + 647215 CGCTC - -a -s simMouse_chr6.simMouse.chr6 485304 3 + 636262 AGC -s Anc0.Anc0refChr3 102023 3 + 222631 AGT -s Anc1.Anc1refChr6 135392 3 + 197743 AGT -s Anc2.Anc2refChr1 13563 3 + 142988 ATT -s mr.mrrefChr3 39437 3 + 181027 AGC -s simCow_chr6.simCow.chr6 470192 3 + 602619 TTG -s simDog_chr6.simDog.chr6 460396 3 + 593897 ATT -s simHuman_chr6.simHuman.chr6 467538 3 + 601863 AGT -s simRat_chr6.simRat.chr6 493636 3 + 647215 AGA - -a -s simMouse_chr6.simMouse.chr6 485307 18 + 636262 ATATTTCACTCAAGGAAA -s Anc0.Anc0refChr3 102026 18 + 222631 CCATATTCCTCAAACAAA -s Anc1.Anc1refChr6 135395 18 + 197743 CCATATTCCTCAAACAAA -s Anc2.Anc2refChr1 13566 18 + 142988 CCATATTCCTCAAACAGA -s mr.mrrefChr3 39440 18 + 181027 ATATTTCACTCAAGGAAA -s simCow_chr6.simCow.chr6 470197 18 + 602619 CCGTGTTCCTCAAACAGC -s simDog_chr6.simDog.chr6 460399 8 + 593897 CCATATC----------A -s simHuman_chr6.simHuman.chr6 467541 18 + 601863 TCATATTTCTCAAACAAA -s simRat_chr6.simRat.chr6 493639 18 + 647215 GTATTTCACTTAAGGAAA - -a -s simMouse_chr6.simMouse.chr6 485325 10 + 636262 CGGAAACTGC -s Anc0.Anc0refChr3 102045 4 + 222631 C------TTC -s Anc1.Anc1refChr6 135414 4 + 197743 C------TTC -s Anc2.Anc2refChr1 13585 4 + 142988 C------TTC -s mr.mrrefChr3 39458 4 + 181027 C------TGC -s simCow_chr6.simCow.chr6 470216 3 + 602619 C------TT- -s simDog_chr6.simDog.chr6 460408 4 + 593897 C------TTC -s simHuman_chr6.simHuman.chr6 467560 4 + 601863 C------TTC -s simRat_chr6.simRat.chr6 493657 4 + 647215 C------TGC - -a -s simMouse_chr6.simMouse.chr6 485335 7 + 636262 ACACTAA -s Anc0.Anc0refChr3 102049 7 + 222631 ACAGTAT -s Anc1.Anc1refChr6 135418 7 + 197743 ACAGTAT -s Anc2.Anc2refChr1 13589 7 + 142988 ACACTAT -s mr.mrrefChr3 39462 7 + 181027 ACAGTAA -s simCow_chr6.simCow.chr6 470219 7 + 602619 ACACTAT -s simDog_chr6.simDog.chr6 460453 7 + 593897 ACTCTCC -s simHuman_chr6.simHuman.chr6 467564 7 + 601863 ACAGCAT -s simRat_chr6.simRat.chr6 493661 7 + 647215 ACAGTAA - -a -s simMouse_chr6.simMouse.chr6 485342 9 + 636262 AGGTTCTCA -s Anc0.Anc0refChr3 102056 9 + 222631 GTTCTGTCA -s Anc1.Anc1refChr6 135425 9 + 197743 GTTCTGTCA -s Anc2.Anc2refChr1 13596 9 + 142988 GTTCTGTCA -s mr.mrrefChr3 39469 9 + 181027 AGGTTCTCA -s simCow_chr6.simCow.chr6 470226 9 + 602619 GTTCTGTAA -s simDog_chr6.simDog.chr6 460460 9 + 593897 GTTCTGTCA -s simHuman_chr6.simHuman.chr6 467571 9 + 601863 GTTCTGTCA -s simRat_chr6.simRat.chr6 493677 9 + 647215 AAGTCTTCA - -a -s simMouse_chr6.simMouse.chr6 485351 9 + 636262 ACCAAACCT -s Anc0.Anc0refChr3 102068 9 + 222631 AGCTAGCCT -s Anc1.Anc1refChr6 135437 9 + 197743 AGCTAGCCT -s Anc2.Anc2refChr1 13611 9 + 142988 GGCTTGCCT -s mr.mrrefChr3 39478 9 + 181027 ACCAAACCT -s simCow_chr6.simCow.chr6 470241 5 + 602619 GGCTT---- -s simDog_chr6.simDog.chr6 460475 9 + 593897 GCCTTGCCT -s simHuman_chr6.simHuman.chr6 467583 9 + 601863 AGCTAGCCT -s simRat_chr6.simRat.chr6 493686 9 + 647215 ACCAAACCT - -a -s simMouse_chr6.simMouse.chr6 485360 9 + 636262 TTACACTAT -s Anc0.Anc0refChr3 102077 9 + 222631 TCACTCTGT -s Anc1.Anc1refChr6 135446 9 + 197743 TCACTCTGT -s Anc2.Anc2refChr1 13620 9 + 142988 TCACTCTGT -s mr.mrrefChr3 39487 9 + 181027 TTACACTAT -s simCow_chr6.simCow.chr6 470246 6 + 602619 ---TGCTGT -s simDog_chr6.simDog.chr6 460484 9 + 593897 TCACTCTGT -s simHuman_chr6.simHuman.chr6 467592 9 + 601863 TCACTCTGT -s simRat_chr6.simRat.chr6 493697 9 + 647215 TTACACCAT - -a -s simMouse_chr6.simMouse.chr6 485369 10 + 636262 GATCTGACAT -s Anc0.Anc0refChr3 102089 10 + 222631 GATCTGATTG -s Anc1.Anc1refChr6 135458 10 + 197743 GATCTGATTG -s Anc2.Anc2refChr1 13632 10 + 142988 GATCTGATTG -s mr.mrrefChr3 39496 10 + 181027 GATCTGATAT -s simCow_chr6.simCow.chr6 470256 10 + 602619 GATCAGGTCA -s simDog_chr6.simDog.chr6 460496 10 + 593897 GATCTGAGTG -s simHuman_chr6.simHuman.chr6 467604 10 + 601863 GATCCGATGG -s simRat_chr6.simRat.chr6 493706 10 + 647215 GATCTGATAT - -a -s simMouse_chr6.simMouse.chr6 485379 12 + 636262 TGCTTGCCTTTG -s Anc0.Anc0refChr3 102102 12 + 222631 TGCATGTAATAG -s Anc1.Anc1refChr6 135471 12 + 197743 TGCATGTAATAG -s Anc2.Anc2refChr1 13645 12 + 142988 TGCATGTAATAG -s mr.mrrefChr3 39506 12 + 181027 TGCTTGCCTTTG -s simCow_chr6.simCow.chr6 470269 12 + 602619 TGCAGGCAACGT -s simDog_chr6.simDog.chr6 460509 12 + 593897 TGCATATAATAG -s simHuman_chr6.simHuman.chr6 467617 12 + 601863 TGCAAGGAATAG -s simRat_chr6.simRat.chr6 493716 12 + 647215 TGCTTGCCTTTG - -a -s simMouse_chr6.simMouse.chr6 485391 13 + 636262 CTAGCAGTTGTCC -s Anc0.Anc0refChr3 102116 13 + 222631 CCTAAACTAGTCA -s Anc1.Anc1refChr6 135485 13 + 197743 CCTAAACTAGTCA -s Anc2.Anc2refChr1 13659 13 + 142988 ACTAATCTACTCA -s mr.mrrefChr3 39518 13 + 181027 CCTACAGTTGTCA -s simCow_chr6.simCow.chr6 470283 13 + 602619 TCTAATTTAATCA -s simDog_chr6.simDog.chr6 460523 13 + 593897 ACTAATCCACTTA -s simHuman_chr6.simHuman.chr6 467631 13 + 601863 CCTAAACTAGTCA -s simRat_chr6.simRat.chr6 493728 13 + 647215 CCTACAGTTGTCA - -a -s simMouse_chr6.simMouse.chr6 485404 18 + 636262 CTTCATGTAGATAACAAG -s Anc0.Anc0refChr3 102148 18 + 222631 TTTCATGAAGATAACAAA -s Anc1.Anc1refChr6 135517 18 + 197743 TTTCATGAAGATAACAAA -s Anc2.Anc2refChr1 13691 18 + 142988 TGTCATGAATATAATGAA -s mr.mrrefChr3 39531 18 + 181027 CTTCATGTAGATAACAAG -s simCow_chr6.simCow.chr6 470315 18 + 602619 TGTCATGAATATAATGAA -s simHuman_chr6.simHuman.chr6 467663 18 + 601863 GTTAATAAAGATAGCAAA -s simRat_chr6.simRat.chr6 493741 18 + 647215 CTTCATGTAGATAACAAG - -a -s simMouse_chr6.simMouse.chr6 485422 16 + 636262 TTGACCAGTACCAAAC -s Anc0.Anc0refChr3 102166 14 + 222631 TTGTCAAGTACCAA-- -s Anc1.Anc1refChr6 135535 14 + 197743 TTGTCAAGTACCAA-- -s Anc2.Anc2refChr1 13709 14 + 142988 TTGTCAAGTGCCAA-- -s mr.mrrefChr3 39549 16 + 181027 TTGACCAGTACCAAAC -s simCow_chr6.simCow.chr6 470333 14 + 602619 TTGTCAGATGCCAA-- -s simDog_chr6.simDog.chr6 460536 10 + 593897 ----CCAGTGCTGA-- -s simHuman_chr6.simHuman.chr6 467681 14 + 601863 TTGTCAAGTACCAA-- -s simRat_chr6.simRat.chr6 493764 16 + 647215 TTGACCAGTACCAAAC - -a -s simMouse_chr6.simMouse.chr6 485438 29 + 636262 CTGGTAAAGAGCACATCCTGGAAATGGAT -s Anc0.Anc0refChr3 102180 29 + 222631 TTGGTGAATAGCATATTTTGGAAATGGAG -s Anc1.Anc1refChr6 135549 29 + 197743 TTGGTGAATAGCATATTTTGGAAATGGAG -s Anc2.Anc2refChr1 13724 29 + 142988 TTGGTGAATAGCATATTTTGGAAATGGAG -s mr.mrrefChr3 39565 29 + 181027 CTGGTAAAGAGCACATCTTGGAAATGGAT -s simCow_chr6.simCow.chr6 470348 29 + 602619 TTGGTGAAGAACAAATTTTGCAAATGGAG -s simDog_chr6.simDog.chr6 460547 29 + 593897 TTGGTGGATAGCGTATATTGGAAATGGAG -s simHuman_chr6.simHuman.chr6 467695 29 + 601863 TTGGAGAATAGCATATTTAGGAAGTAGAG -s simRat_chr6.simRat.chr6 493780 29 + 647215 CTGGTAAAGAGCAGATCTTGGAAATGTAC - -a -s simMouse_chr6.simMouse.chr6 485467 2 + 636262 AG -s Anc0.Anc0refChr3 102209 1 + 222631 A- -s Anc1.Anc1refChr6 135578 1 + 197743 A- -s Anc2.Anc2refChr1 13753 1 + 142988 A- -s mr.mrrefChr3 39594 2 + 181027 AG -s simCow_chr6.simCow.chr6 470406 1 + 602619 A- -s simDog_chr6.simDog.chr6 460576 1 + 593897 A- -s simHuman_chr6.simHuman.chr6 467724 1 + 601863 A- -s simRat_chr6.simRat.chr6 493809 2 + 647215 AG - -a -s simMouse_chr6.simMouse.chr6 485469 104 + 636262 GGGTATCTTGGGATATACTGAGCAATATATACTGGTGGTCAAGTTAGTTAAGGTAAGTGAGTAAAGACATGGCAAGCCACCCCTATTTCCCATACTAGGGGGCA -s Anc0.Anc0refChr3 102210 42 + 222631 TGGTCTCCTCTGGCATACTGGGCATTATGTGTTGCCATGCAG-------------------------------------------------------------- -s Anc1.Anc1refChr6 135579 42 + 197743 TGGTCTCCTCTGGCATACTGGGCATTATGTGTTGCCATGCAG-------------------------------------------------------------- -s Anc2.Anc2refChr1 13754 42 + 142988 TGGTCTCCTCTGGCATACTGGGCATTATGTGTTGCCATGCAG-------------------------------------------------------------- -s mr.mrrefChr3 39596 102 + 181027 GGGTATCTTGGGGCATACTGAGCAATATATGTTGGTAGGCAGGTTAGTTAAGGTAAGTGAGTAAAGACATGGCAAGCCACCCCTAT--CCCATACTAGGGGGCA -s simCow_chr6.simCow.chr6 470407 42 + 602619 GGGTATCTTCTGGCATACTGGGCATTATATGTTGCCATGAAG-------------------------------------------------------------- -s simDog_chr6.simDog.chr6 460578 42 + 593897 TAGTCACCTCTGGGATTCTGCGCACTATGTGTTGTCATGCAG-------------------------------------------------------------- -s simHuman_chr6.simHuman.chr6 467725 42 + 601863 AGGTGTCCTCTGGCATATTGGATATTATGTGTTGCCATGCGG-------------------------------------------------------------- -s simRat_chr6.simRat.chr6 493811 102 + 647215 GGGTATCTTTGGGCATACTGAGCAATATATGTTAGTAGGCAGGTCAGTTAAGGTAAGTGAGTAAAGACATGGCAAGCCGTTCCTAT--CCTGTACTAGGCGTCA - -a -s simMouse_chr6.simMouse.chr6 485573 15 + 636262 TTAGGACCTGACCAC -s Anc0.Anc0refChr3 102252 8 + 222631 -------CTAGACCT -s Anc1.Anc1refChr6 135621 8 + 197743 -------CTAGACCT -s Anc2.Anc2refChr1 13796 8 + 142988 -------CTAGACCT -s mr.mrrefChr3 39698 15 + 181027 TTAGGACCTGGCCAC -s simCow_chr6.simCow.chr6 470449 8 + 602619 -------CTAAACCT -s simDog_chr6.simDog.chr6 460620 8 + 593897 -------CTAGACCT -s simHuman_chr6.simHuman.chr6 467767 8 + 601863 -------CTAGGCCT -s simRat_chr6.simRat.chr6 493921 15 + 647215 TAAGGACCAGGACGC - -a -s simMouse_chr6.simMouse.chr6 485588 40 + 636262 CCTGGTTGGCATTGAGAAGTATTGAATATGACAGCACAGA -s Anc0.Anc0refChr3 102260 40 + 222631 CCTGTCCAACAATAAGAAGCCTTGGATTCAACAACACAGA -s Anc1.Anc1refChr6 135629 40 + 197743 CCTGTCCAACAATAAGAAGCCTTGGATTCAACAACACAGA -s Anc2.Anc2refChr1 13804 40 + 142988 TCTGTCCAACAATAAGAAGCCTTGGAGTCAACAACATAGA -s mr.mrrefChr3 39713 40 + 181027 CCTGTTTGGCAATGAGAAGCCTTGAATATGACAACACAGA -s simCow_chr6.simCow.chr6 470457 29 + 602619 TCTGTCAAACGAT-AGGAGCCTTGAA----------TGGG -s simDog_chr6.simDog.chr6 460628 40 + 593897 TCTGTCCAACAATAAAAAGTCTTGGAGTCAACAACATAGA -s simHuman_chr6.simHuman.chr6 467775 40 + 601863 CCTGTCCAAAAATAAGAAGCCTTGGATGGAACAACACAGA -s simRat_chr6.simRat.chr6 493937 40 + 647215 CCTGTTTGGCAATGAGAAGCCTTGAATATGATAACACAGA - -a -s simMouse_chr6.simMouse.chr6 485628 66 + 636262 AACATTCAGTTCAAGATATAATCATCTTGCATGACAAGTGAAGTATAAAGATGTTTAAGGTACTGA -s Anc0.Anc0refChr3 102301 51 + 222631 AACATTCA-----------ATTCAACTTATGATAATGATCAGGAAG----CTGGGTGAAGTTGTGA -s Anc1.Anc1refChr6 135670 63 + 197743 AACATTCAGTCAAAGAAACATTCAACTTATGATAATGATCAGGAAGT---CTGGGTGAAGTTGTGA -s Anc2.Anc2refChr1 13845 51 + 142988 AACATTCA-----------ATTCAAGTTATGATAATGATCAGGAGG----CTGGGTGAAGTTGTGA -s mr.mrrefChr3 39753 66 + 181027 AACATTCAGTTCAAGATATAATCATCTTGCAAGACAAGTCAAGTAGTAAGATGTTTAAGGTACTGA -s simCow_chr6.simCow.chr6 470487 51 + 602619 AAGATTCA-----------GCTCAAGAGATAATAATGATCAGGAGA----CTTTTTGAAGTTGTTA -s simDog_chr6.simDog.chr6 460669 47 + 593897 AACATTCC-----------ATTCAAGTTATGATGATGTC----AGG----CTGGGCAAAGTTGTGA -s simHuman_chr6.simHuman.chr6 467816 63 + 601863 AACATTCAGCCAAAGAAACATTCAGCTAAGGATAACGATCATGAAGT---CTGGATGAAGTCATGA -s simRat_chr6.simRat.chr6 493977 66 + 647215 AACATTCAGTTTAAGATATAATGACCTTGCAAGACAAGTCGAGTAGTAAGATGTTTAATGTACTGA - -a -s simMouse_chr6.simMouse.chr6 485694 28 + 636262 GCATGCTGATCATCCTCAGTAGGCATAA -s Anc0.Anc0refChr3 102355 28 + 222631 ATTTTCTGATCACTCTCAGTAGCCGATA -s Anc1.Anc1refChr6 135736 28 + 197743 ATTTTCTGATCACTCTCAGTAGCCGATA -s Anc2.Anc2refChr1 13899 28 + 142988 ATTCTCTGATCACTCTCGGTAGCAGATA -s mr.mrrefChr3 39819 28 + 181027 GCATGCTGATCATTCTCAGTAGGCATAA -s simCow_chr6.simCow.chr6 470546 28 + 602619 ATTCTCTGATCACTCTCGGTAGCAGATA -s simDog_chr6.simDog.chr6 460719 1 + 593897 G--------------------------- -s simHuman_chr6.simHuman.chr6 467882 28 + 601863 ATGTTCTGATCACTTCCAGTAGCCTGTA -s simRat_chr6.simRat.chr6 494043 28 + 647215 GCATGCTGATCATTATCAGCAGAGATAA - -a -s simMouse_chr6.simMouse.chr6 485722 24 + 636262 CATCAATAGGAGACTAATGACATA -s Anc0.Anc0refChr3 102383 16 + 222631 CAGCA---GTAGATTT-----ATG -s Anc1.Anc1refChr6 135764 16 + 197743 CAGCA---GTAGATTT-----ATG -s Anc2.Anc2refChr1 13927 16 + 142988 CAGCA---GTAGATCT-----ATG -s mr.mrrefChr3 39847 24 + 181027 CATCAATAGGAGACTAATGACATA -s simCow_chr6.simCow.chr6 470577 16 + 602619 CAGCA---GTAGATCT-----ATG -s simHuman_chr6.simHuman.chr6 467910 16 + 601863 CAGCA---GCAGATTG-----ATG -s simRat_chr6.simRat.chr6 494071 24 + 647215 CATCAATAGGAGAATAATGACACA - -a -s simMouse_chr6.simMouse.chr6 485746 23 + 636262 GGCTTTCCACAACCCTCATACCA -s Anc0.Anc0refChr3 102399 23 + 222631 GACTTTCCACAGCCCTTACACCA -s Anc1.Anc1refChr6 135780 23 + 197743 GACTTTCCACAGCCCTTACACCA -s Anc2.Anc2refChr1 13943 23 + 142988 CACTCTCTACAGCCCCTACACCA -s mr.mrrefChr3 39871 23 + 181027 GACTTTCCACAACCCTCATACCA -s simCow_chr6.simCow.chr6 470593 23 + 602619 CACTCTCTACAGCCCCTACACCA -s simHuman_chr6.simHuman.chr6 467926 23 + 601863 GACTTGCCATAGCCCTTACAACA -s simRat_chr6.simRat.chr6 494097 23 + 647215 GAGTTTCCACAACTCTCATACCT - -a -s simMouse_chr6.simMouse.chr6 485769 10 + 636262 TCTCATGCTA -s Anc0.Anc0refChr3 102424 10 + 222631 TCTCATGCTA -s Anc1.Anc1refChr6 135805 10 + 197743 TCTCATGCTA -s Anc2.Anc2refChr1 13968 10 + 142988 TCTCATACTA -s mr.mrrefChr3 39896 10 + 181027 TCTCATGCTA -s simCow_chr6.simCow.chr6 470618 10 + 602619 TCTCATACTA -s simHuman_chr6.simHuman.chr6 467951 10 + 601863 TCTCATGCTA -s simRat_chr6.simRat.chr6 494122 9 + 647215 TC-AATGCCA - -a -s simMouse_chr6.simMouse.chr6 485779 36 + 636262 TGGCAGGTACTCAAGAACAAATGTTGCTATGGAAGT -s Anc0.Anc0refChr3 102434 32 + 222631 TAGCTGGTACTCAAATA----TGTAGCTGTGTAAAG -s Anc1.Anc1refChr6 135815 32 + 197743 TAGCTGGTACTCAAATA----TGTAGCTGTGTAAAG -s Anc2.Anc2refChr1 13978 32 + 142988 TAGATTGAACTCAAATT----CACAGCTGTATAGAG -s mr.mrrefChr3 39906 32 + 181027 TGGCAGGTACTCAAGAA----TGTTGCTGTGTAAAG -s simCow_chr6.simCow.chr6 470628 32 + 602619 TAGATTGAACTCAAATT----CACAGCTGTATAGAG -s simHuman_chr6.simHuman.chr6 467969 32 + 601863 TAGCTGGTACTCAAAGA----TGTAGCTGTGTAAAG -s simRat_chr6.simRat.chr6 494131 32 + 647215 TGGCAGGGACTCAAGAA----TGTTGCTGTGTCAAG - -a -s simMouse_chr6.simMouse.chr6 485815 58 + 636262 TAGAACAAGTGCCTTAGTGGTCAGATCAGTAGTTATTAATGCATTGCAGATATACTGC -s Anc0.Anc0refChr3 102471 57 + 222631 TGGGAAAA-TGTTTTATCAGTCAGATGAAAAGTTATTAAATCATTGCAAGAAGTCTGC -s Anc1.Anc1refChr6 135852 58 + 197743 TGGGAAAAGTGTTTTATCAGTCAGATGAAAAGTTATTAAATCATTGCAAGAAGTCTGC -s Anc2.Anc2refChr1 14015 57 + 142988 CGAGAGAA-TGTTTTATCAATCAGATGAAAAATTATCAAATCATTAGGAGATGTCTGC -s mr.mrrefChr3 39938 58 + 181027 TAGAACAAGTGCCTTAGTGGTCAGATCAATAGTTATTAATTCATTGCAGATATACTGC -s simCow_chr6.simCow.chr6 470667 57 + 602619 CGAGAGAA-TGTTTTATCAATCAGATGAAAAATTATCAAATCATTAGGAGATGTCTGC -s simHuman_chr6.simHuman.chr6 468006 58 + 601863 TGGGAAAAGTGTTTTCTCAGTCAGATAAAAAGTTATTGGGTCATTGCAAGAACTCTGC -s simRat_chr6.simRat.chr6 494163 55 + 647215 TAGAACAAGTGCCTTAGTGGTCGGATCAACAGTTATTAATTCATTGTGGATAT---GC - -a -s simMouse_chr6.simMouse.chr6 485873 11 + 636262 TTTGGATGTCT -s Anc0.Anc0refChr3 102544 11 + 222631 TTTATATGTCT -s Anc1.Anc1refChr6 135926 11 + 197743 TTTATATGTCT -s Anc2.Anc2refChr1 14088 11 + 142988 TTTATATGTCA -s mr.mrrefChr3 39996 11 + 181027 TTTGGATGTCT -s simCow_chr6.simCow.chr6 470740 11 + 602619 TTTAGATGCCA -s simDog_chr6.simDog.chr6 460720 10 + 593897 -TTATATTTCA -s simHuman_chr6.simHuman.chr6 468080 11 + 601863 TTTATATGTCT -s simRat_chr6.simRat.chr6 494218 11 + 647215 TTTGGATGTCT - -a -s simMouse_chr6.simMouse.chr6 485884 12 + 636262 GAGCTCTTTCAC -s Anc0.Anc0refChr3 102556 12 + 222631 GACCTCTTTTAT -s Anc1.Anc1refChr6 135938 12 + 197743 GACCTCTTTTAT -s Anc2.Anc2refChr1 14100 12 + 142988 GACCTCTTTTAT -s mr.mrrefChr3 40007 12 + 181027 GAGCTCTTTCAC -s simCow_chr6.simCow.chr6 470751 12 + 602619 GACCTCTTTCAT -s simDog_chr6.simDog.chr6 460731 6 + 593897 GA------GTAG -s simHuman_chr6.simHuman.chr6 468092 12 + 601863 GACCTCTTTTAT -s simRat_chr6.simRat.chr6 494229 12 + 647215 GAGCTCTTTCAC - -a -s simMouse_chr6.simMouse.chr6 485896 114 + 636262 AGGCCAGGGAGCCCTCCCAAGAAAAAAGCAGGGAATGAAACCTACCCTTAGAAGCCCAGGCCAAATGGTAGTGGGGACAGCCTCTCAGAGGGTGCCACTCTTTGGACCAGTACT -s Anc0.Anc0refChr3 102568 20 + 222631 AGGA-TGAGA-CCTGCCCAGG----G---------------------------------------------------------------------------------------- -s Anc1.Anc1refChr6 135950 25 + 197743 AGGA-TGAGATCCTGCCCAGGGAGAG---------------------------------------------------------------------------------------- -s Anc2.Anc2refChr1 14112 20 + 142988 AGAA-TGAGA-CCTGCCCAGG----G---------------------------------------------------------------------------------------- -s mr.mrrefChr3 40019 113 + 181027 AGGC-AGGGAGCCCTCCCAAGGAAAAAGCAGGGAATGAAACCTACCCTTAGAAGCCCAGGCCAAATGGTAGTGGGGACAGCCTCTCAGAGGGTGCCACTCTTTGGACCAGTACT -s simCow_chr6.simCow.chr6 470768 20 + 602619 AGAA-TGAGA-CCTGCCCAGC----A---------------------------------------------------------------------------------------- -s simDog_chr6.simDog.chr6 460737 20 + 593897 AGAA-TGAGA-TGTACCCAGG----G---------------------------------------------------------------------------------------- -s simHuman_chr6.simHuman.chr6 468104 20 + 601863 AGGT------TCCTGCCCATGGAGAG---------------------------------------------------------------------------------------- -s simRat_chr6.simRat.chr6 494241 113 + 647215 AGGC-AGGGAACCCTACCAAGGAAAAAGCAGGGAATGAGACCTACCCAGAGAAGCCCAGGCTGAACGGTAGTGGGGTTGGTCACTTGGGGGGTGCCACTCTTTGAACCAGTACC - -a -s simMouse_chr6.simMouse.chr6 486010 239 + 636262 AACCCAGTAtttcttcttaagtcagcaacatacagtctttcttgttatgtgattggtcagattgtagtgaaaatatctaaggacccctgagacaaggatggagtgaacttagccctggagcacaaccccacaggttggtgtactccattccaattcataAACATGGAAAGTTAGGCCCACAGCAACATGGAAGCTGCGCAGAGTCTTGGCTCAATGGTTAGTTTTCACAATATGTGTAG -s Anc0.Anc0refChr3 102588 40 + 222631 -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AGAGTTGTAGCTCAAAAGTTAGTTTGCAGGACATGTGCAG -s Anc1.Anc1refChr6 135975 40 + 197743 -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AGAGTTGTAGCTCAAAAGTTAGTTTGCAGGACATGTGCAG -s Anc2.Anc2refChr1 14132 40 + 142988 -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AGAGTTGTAGCTCAAAAGTTAGTTTGCAGGACATGTGCAG -s mr.mrrefChr3 40132 239 + 181027 AACCCAGTAtttcttcttaagtcagcaacatacagtctttcttgttatgtgattggtcagattgtagtgaaaatatctaaggacccctgagacaaggatggagtgaacttagccctggagcacaaccccacaggttggtgtactccattccaattcataAACATGGAAAGTTAGGCCCACAGCAACATGGAAGCTGCGCAGAGTCTTGGCTCAATGGTTAGTTTTCACAATATGTGTAG -s simCow_chr6.simCow.chr6 470788 40 + 602619 -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AGAGGTGTAGCTCAAGGGTGTGTGCTCGGAATATGTGCAG -s simDog_chr6.simDog.chr6 460757 40 + 593897 -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AGAGTTGTAGCTCAAAAGTTAGTTTGCAGGACATGTGCAG -s simHuman_chr6.simHuman.chr6 468124 4 + 601863 -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TCAG -s simRat_chr6.simRat.chr6 494360 239 + 647215 AACCCAGTAGTTcttcttaaggcaggatcatactgtctttcttgtgatgcaattggacacactgcagtgggaatatctaggggcccctaagaccaggacgaggcagacttagccctggagcacaaccccacaggttggtgtactccattccaatTCATGATCACGAAAAGTTAGGCCCATGTCAACATGGAAGCTGCACAGAGTCTTGGCTAGATGATTAGTTCTCGCAATATGCGTAG - -a -s simMouse_chr6.simMouse.chr6 486249 33 + 636262 AACTCATACAAGCCATAACAGAATAGATAACCC -s Anc0.Anc0refChr3 102628 32 + 222631 AACTCATAAG-TCTGTAACAGGATAGAATACCC -s Anc1.Anc1refChr6 136015 32 + 197743 AACTCATAAG-TCTGTAACAGGATAGAATACCC -s Anc2.Anc2refChr1 14172 32 + 142988 AACTCATAAG-TCTGTAACAGGAAACAATACCC -s mr.mrrefChr3 40371 32 + 181027 AACTCATACA-GCCATAACAGGATAGATTACCC -s simCow_chr6.simCow.chr6 470832 32 + 602619 AACTCATAAG-TCAGCAAAAGGAAATAATACCT -s simDog_chr6.simDog.chr6 460797 32 + 593897 TACTCATAAA-TCTCTAACGGGAAACACCACCC -s simHuman_chr6.simHuman.chr6 468128 32 + 601863 AATTCATAAG-TCTGTAACAGGATAGAATACCC -s simRat_chr6.simRat.chr6 494599 32 + 647215 AACTCATACA-GCCATTACAGGATAGATTACCA - -a -s simMouse_chr6.simMouse.chr6 486282 4 + 636262 CCAA -s Anc0.Anc0refChr3 102661 4 + 222631 CCAA -s Anc1.Anc1refChr6 136048 4 + 197743 CCAA -s Anc2.Anc2refChr1 14205 4 + 142988 CTGA -s mr.mrrefChr3 40403 4 + 181027 CCAA -s simCow_chr6.simCow.chr6 470865 4 + 602619 TTGA -s simDog_chr6.simDog.chr6 460830 4 + 593897 CTGA -s simHuman_chr6.simHuman.chr6 468161 4 + 601863 CCAA -s simRat_chr6.simRat.chr6 494631 4 + 647215 CCAA - -a -s simMouse_chr6.simMouse.chr6 486286 26 + 636262 GTCTCTGTCACCAGATAGCTACATTC -s Anc0.Anc0refChr3 102666 26 + 222631 GTCTTTATAACTGAATAGCTATATTC -s Anc1.Anc1refChr6 136053 26 + 197743 GTCTTTATAACTGAATAGCTATATTC -s Anc2.Anc2refChr1 14210 26 + 142988 GTCTTCATAACTGAATAGCTATATTC -s mr.mrrefChr3 40408 26 + 181027 GTCTCTGTCACCAGATAGCTATATTC -s simCow_chr6.simCow.chr6 470870 9 + 602619 GTCTTCTTA----------------- -s simDog_chr6.simDog.chr6 460835 26 + 593897 GTCTTCATAACTGAATAGCTATATTC -s simHuman_chr6.simHuman.chr6 468166 26 + 601863 CTCTTTATAATTGAATCGCTATATTC -s simRat_chr6.simRat.chr6 494636 26 + 647215 GCCTCTGTCACCAGTTAGCTATATTC - -a -s simMouse_chr6.simMouse.chr6 486312 93 + 636262 ACTTCCTAGAGAGTCATTATTTACCTCGTATTATGCCTGAGTTTAGGGGCCCCAATATAATCGACAGATCATTTGTAATAGATCACCGTATAG -s Anc0.Anc0refChr3 102692 92 + 222631 ACACCTACCCAG-CCATTATTTAGCTTGTTTCATGACTGCTTTTAGTGGCCATAGTATAGCACACCAATCATCTGTAGTAGAACACCTTGTAG -s Anc1.Anc1refChr6 136079 92 + 197743 ACACCTACCCAG-CCATTATTTAGCTTGTTTCATGACTGCTTTTAGTGGCCATAGTATAGCACACCAATCATCTGTAGTAGAACACCTTGTAG -s Anc2.Anc2refChr1 14236 92 + 142988 CCACCTACCCAG-CCATGATTTAGCTTATTTCAAGACTGCTTTTAGTGGCCATAGCATAGCACACCAATCTTCTGTAGTAGAACACCTTGTAG -s mr.mrrefChr3 40434 92 + 181027 ACTTCCTACAAA-TCATTATTTACCTCGTATTATGACTGAGTTTAGGGGCCCTAGTATAATAGACAAATCATTTGTAATAGATCACCTTATAG -s simCow_chr6.simCow.chr6 470879 73 + 602619 --------------------TTAGCTCATTTCAAGACCACTTTTAGTGGCCATAGCATAGCACACCAATCTTCTGTAATAGAACAGCTTAGAG -s simDog_chr6.simDog.chr6 460862 87 + 593897 CCACCTACCCAG-CCATGATTTTGTTT-----AAGACTGGTTTTAGTGGCCTTACCAGAGCACGCCAATTTTCTGTAGTTGAACACCTTGTAG -s simHuman_chr6.simHuman.chr6 468192 92 + 601863 ACACCTACCTAT-CTGGTATTTAACTTGTTACATGACTGCTTATTGTGGCCATAGTATAGCACACCAATCATCTGTATTAGAACACCTTGTAG -s simRat_chr6.simRat.chr6 494662 92 + 647215 ACTTCCTACAAA-GCATTATTTACCTCGTATTTTGACTGAGTTCAGGGGTCCTAGTATAATAGACAAATCACTTGTAGTTGATCATCTTATAG - -a -s simMouse_chr6.simMouse.chr6 486405 27 + 636262 GAGCCTCCAAGCTAGGGAGTTTAGGAC -s Anc0.Anc0refChr3 102806 27 + 222631 AGGCCTCTGAACTAGGTAGTTAAGGAC -s Anc1.Anc1refChr6 136193 27 + 197743 AGGCCTCTGAACTAGGTAGTTAAGGAC -s Anc2.Anc2refChr1 14358 27 + 142988 AGGCCTCTGAGCTAGGTAGTTAAGGAC -s mr.mrrefChr3 40548 27 + 181027 GAGCCTCCAAACTAGGGAGTTTAGGAC -s simCow_chr6.simCow.chr6 470980 27 + 602619 AGGCCTCCAAGCCAGGTAGTTAAGGAC -s simDog_chr6.simDog.chr6 460979 27 + 593897 GGTCCTCTGAGCTAGGTAGTTATGGAC -s simHuman_chr6.simHuman.chr6 468306 25 + 601863 AGGCCTC--GACTAGGTAGTGAAGGAC -s simRat_chr6.simRat.chr6 494781 27 + 647215 GAGCCTCCAAACTAGGAAGTTGAGGAC - -a -s simMouse_chr6.simMouse.chr6 486432 31 + 636262 TTTCGTAGCTTACTTCTACATGCATCGTAAA -s Anc0.Anc0refChr3 102834 31 + 222631 TGATTTAGCTTAGTCCTACATGCATCTCAAA -s Anc1.Anc1refChr6 136221 31 + 197743 TGATTTAGCTTAGTCCTACATGCATCTCAAA -s Anc2.Anc2refChr1 14386 31 + 142988 TGATTTAGCTTAGTCCTACATATATCTCAAA -s mr.mrrefChr3 40575 31 + 181027 TTTTTTAGCTTACTTCTACATGCATCTTAAA -s simCow_chr6.simCow.chr6 471008 13 + 602619 TGATTTATCTTGG------------------ -s simDog_chr6.simDog.chr6 461007 31 + 593897 TGATTTCGCTGATTCCTACATATATCTCAAA -s simHuman_chr6.simHuman.chr6 468332 31 + 601863 TGATTTAGCTTAGCCTCATGCGCATCTCAGA -s simRat_chr6.simRat.chr6 494808 31 + 647215 TTCTTTAGCTTACTTCTACATGCATCTTAAA - -a -s simMouse_chr6.simMouse.chr6 486463 42 + 636262 CACAACTGATGTAAAATGGCCATTAAGCAACAAATCATTCCA -s Anc0.Anc0refChr3 102868 36 + 222631 C---ATTTTTGTGAAGAGACCATTGGGCAACAAAATATT--- -s Anc1.Anc1refChr6 136255 42 + 197743 CAAAATTTTTGTGAAGAGACCATTGGGCAACAAAATATTCCA -s Anc2.Anc2refChr1 14420 36 + 142988 C---ATTTTTGTGAAGAGACCTTTGGGCAACAAAATATT--- -s mr.mrrefChr3 40609 42 + 181027 CACAATTGATGTAAAATGGCCATTAAGCAACAAATCATTCCA -s simCow_chr6.simCow.chr6 471021 20 + 602619 -------------------CCTTTGGGCAACAAAGAATT--- -s simDog_chr6.simDog.chr6 461041 36 + 593897 C---ATTTTTGTGAAGAGACCTTTGGGCAACAAAATATT--- -s simHuman_chr6.simHuman.chr6 468366 29 + 601863 TAAAATTTCTGTGAAGAGACCATTT-------------TCCA -s simRat_chr6.simRat.chr6 494842 42 + 647215 CACAATTGATTTAACATGGCCACTAAGGAACAAACCATTCCA - -a -s simMouse_chr6.simMouse.chr6 486505 115 + 636262 GCCATGGCTACATGTATAGTGAGCAGACCTACTCATCTTTGCTCTATCCTAGGAACCTTGTTTACAGTAGATACATGGCACATAGGTTCCATCGATTGCTATGTTTAGAATTTGA -s Anc0.Anc0refChr3 102904 107 + 222631 GCCATGGCTTCATGCATAGTGAACAGTACTACTCATCTATGCACAATCAT---GTCTCACATTACAGTAGACACATGAC----AGGTCCCA-TGATTAATATGTGGAGAATTTGG -s Anc1.Anc1refChr6 136297 108 + 197743 GCCATGGCTTCATGCATAGTGAACAGTACTACTCATCTATGCACAATCAT---GTCTCACATTACAGTAGACACATGAC----AGGTCCCATTGATTAATATGTGGAGAATTTGG -s Anc2.Anc2refChr1 14456 107 + 142988 GCCATGGCTTCATGCATAGTGAACGGTACTACTCATCTATACACAGTGAT---GTTTCACATCACACTGGACACAACAC----AGGTCCCA-TGATTAATGTGTGGAGAATTTGG -s mr.mrrefChr3 40651 115 + 181027 GCCATGGCTTCATGTATAGTGAGCAGTACTACTCATCTTTGCTCTATCCTAGGAACCCAGTTTACAGTAGATACATGGCACATAGGTTCCATTGATTGCTATGTTGAGAATTTGG -s simCow_chr6.simCow.chr6 471044 100 + 602619 GCCATGACTTGATGCATATTGAAGGGTGCTACTCATCTATATAC---GAT---TTATCTCATCACAGTAGACA----CC----AGGTCCAC-AGATTAATGTGTGGAGAATTTGG -s simDog_chr6.simDog.chr6 461077 107 + 593897 GCTATGGCTTCTCGCATAGTGAACGGTACTACTTGTCTATACACAGTGAT---GTTGTACATCACACTGGACACAACAC----AGGCCCCA-TAATTGATGTCAGGAGAATTAGG -s simHuman_chr6.simHuman.chr6 468395 108 + 601863 ACCATGGCATAATACTCAGTGACTAGTATTACTCACCTATGCACCATCAT---GCCTCACCTTATAGCAAACAGATGAC----AGGTCCTATTGATCAATATGTAGAGAATTTGG -s simRat_chr6.simRat.chr6 494884 115 + 647215 GCCATGGCTTTATGTATAATGATCAGTACTACTCTTCTTTGCTCTATCCTTGGAATACATTCTACAGTAGATACATGGCAGGTAGGTGCCATTGATTTCTATGTTGAGAATTTAG - -a -s simMouse_chr6.simMouse.chr6 486620 7 + 636262 TAGTGCT -s Anc0.Anc0refChr3 103011 7 + 222631 TAATGCT -s Anc1.Anc1refChr6 136405 7 + 197743 TAATGCT -s Anc2.Anc2refChr1 14566 7 + 142988 TAATGCC -s mr.mrrefChr3 40766 7 + 181027 TAGTGCT -s simCow_chr6.simCow.chr6 471147 6 + 602619 T-GTGCT -s simDog_chr6.simDog.chr6 461187 7 + 593897 TAATGCC -s simHuman_chr6.simHuman.chr6 468503 7 + 601863 TATAGTT -s simRat_chr6.simRat.chr6 494999 7 + 647215 TAGTGCC - -a -s simMouse_chr6.simMouse.chr6 486627 23 + 636262 ACTTACAATAGTACTATGTAGCA -s Anc0.Anc0refChr3 103018 23 + 222631 ACTTACAATAGTACTGAGTAGGA -s Anc1.Anc1refChr6 136412 23 + 197743 ACTTACAATAGTACTGAGTAGGA -s Anc2.Anc2refChr1 14573 23 + 142988 TGTTATAGTAGTACTGAGTAAGA -s mr.mrrefChr3 40773 23 + 181027 ACTTACAATAGTACTATGTAGGA -s simCow_chr6.simCow.chr6 471153 22 + 602619 TCTTATGGTA-TACTGAGTAAGA -s simDog_chr6.simDog.chr6 461194 23 + 593897 TGTTATAGTAGTACTGTTTAAAG -s simHuman_chr6.simHuman.chr6 468511 23 + 601863 ACTTACCATAGTACTGAGTGGGA -s simRat_chr6.simRat.chr6 495006 23 + 647215 ACTTACAATAGTACTATGTAGGA - -a -s simMouse_chr6.simMouse.chr6 486650 2 + 636262 TG -s Anc0.Anc0refChr3 103043 2 + 222631 TG -s Anc1.Anc1refChr6 136437 2 + 197743 TG -s Anc2.Anc2refChr1 14598 2 + 142988 AG -s mr.mrrefChr3 40796 2 + 181027 TG -s simCow_chr6.simCow.chr6 471177 2 + 602619 AA -s simDog_chr6.simDog.chr6 461219 2 + 593897 AG -s simHuman_chr6.simHuman.chr6 468536 2 + 601863 TG -s simRat_chr6.simRat.chr6 495029 2 + 647215 TG - -a -s simMouse_chr6.simMouse.chr6 486652 29 + 636262 AACTTCCTATCTTCATCTGAACATTTCCG -s Anc0.Anc0refChr3 103045 29 + 222631 AGCTTCATATCTTCATTTGAACACCAATG -s Anc1.Anc1refChr6 136439 29 + 197743 AGCTTCATATCTTCATTTGAACACCAATG -s Anc2.Anc2refChr1 14613 29 + 142988 AGCTTCATATCTTCATTTGAACACCAATG -s mr.mrrefChr3 40798 29 + 181027 AACTTCATATCTTCATCTGAACATTTCCG -s simCow_chr6.simCow.chr6 471192 29 + 602619 CGTTTGATATCTTAATCAGAACACCAACA -s simDog_chr6.simDog.chr6 461234 29 + 593897 AACTTCATAGCCACATTTGAACACCAATG -s simHuman_chr6.simHuman.chr6 468538 29 + 601863 AGCTTAATATCTTCTCTTGAACACCGATG -s simRat_chr6.simRat.chr6 495031 28 + 647215 A-CTTCATATCTTCATCTCAACATTACCA - -a -s simMouse_chr6.simMouse.chr6 486681 3 + 636262 GTG -s Anc0.Anc0refChr3 103074 3 + 222631 ATT -s Anc1.Anc1refChr6 136468 3 + 197743 ATT -s Anc2.Anc2refChr1 14648 3 + 142988 ATT -s mr.mrrefChr3 40827 3 + 181027 GTT -s simCow_chr6.simCow.chr6 471227 1 + 602619 A-- -s simDog_chr6.simDog.chr6 461269 3 + 593897 ATT -s simHuman_chr6.simHuman.chr6 468567 3 + 601863 ATT -s simRat_chr6.simRat.chr6 495059 3 + 647215 GTT - -a -s simMouse_chr6.simMouse.chr6 486684 50 + 636262 GGTTGGGATTCCTTCAAGTAGTAAAGAGTAACACCAGTTAATGTATAGGC -s Anc0.Anc0refChr3 103077 45 + 222631 A--TGTGGTTCCTTCTGGTAGTAAGGAGTAACACAAGTTAATATCTT--- -s Anc1.Anc1refChr6 136471 45 + 197743 A--TGTGGTTCCTTCTGGTAGTAAGGAGTAACACAAGTTAATATCTT--- -s Anc2.Anc2refChr1 14651 45 + 142988 A--TATGGTGCCTTCCGATAGGAAGGAGTAAGACAAGCTAATAGCTT--- -s mr.mrrefChr3 40830 50 + 181027 GGTTGGGATTCCTTCTGGTAGTAAAGAGTAACACCAGTTAATGTATTGGC -s simCow_chr6.simCow.chr6 471228 31 + 602619 ----------------GTTAGGACGGAGTAAAGCATGCTAATACCTT--- -s simDog_chr6.simDog.chr6 461273 45 + 593897 A--TATGGTGCCTTCCAATAGGAAGTAGTAAGACAAGCTAATAGCTT--- -s simHuman_chr6.simHuman.chr6 468570 45 + 601863 A--TGTGGTTCCTTATGGTAGTAAGGTGTAGCACAAGTTTATATCTT--- -s simRat_chr6.simRat.chr6 495062 50 + 647215 GGTTGGGATTCCTTCTGGTAGTAAAGAGTGAGATCAGTTAATGTATTGGC - -a -s simMouse_chr6.simMouse.chr6 486734 14 + 636262 CTAACACATCATCA -s Anc0.Anc0refChr3 103122 14 + 222631 TCTACACATCAATG -s Anc1.Anc1refChr6 136516 14 + 197743 TCTACACATCAATG -s Anc2.Anc2refChr1 14706 14 + 142988 TCTGCATAGCAATG -s mr.mrrefChr3 40880 14 + 181027 CTAACACATCATTG -s simCow_chr6.simCow.chr6 471269 14 + 602619 TCTTGCTAGCACTG -s simDog_chr6.simDog.chr6 461333 14 + 593897 TCTGCATGGCAATG -s simHuman_chr6.simHuman.chr6 468615 14 + 601863 TCTACACATTGATG -s simRat_chr6.simRat.chr6 495112 14 + 647215 CTAACATGTCAGTG - -a -s simMouse_chr6.simMouse.chr6 486748 70 + 636262 CTGCTATTGCGGTGGTTGGAGTTTGTTAGTGTCTGGAGTGAGTTAGGATGCGAAGTGTTTTGACCCATGT -s Anc0.Anc0refChr3 103136 36 + 222631 CTATTATTGTGGTGCTT----------------------------------GGAGTGCACTGGCCCATGT -s Anc1.Anc1refChr6 136530 68 + 197743 CTATTATTGTGGTGCTTGGACTGTGTTGGTGCTTGGAGTGCA--ATGGCCCGGAGTGCACTGGCCCATGT -s Anc2.Anc2refChr1 14720 36 + 142988 CTATTATTGTGGTGCTT----------------------------------GGAGTGCACTGGCCCATGT -s mr.mrrefChr3 40894 70 + 181027 CTGCTATTGTGGTGGTTGGAGTTTGTTGGTGTTTGGAGTGAGTTAGGGTGCGAAGTGTTTTGGCCCATGT -s simCow_chr6.simCow.chr6 471287 31 + 602619 CTGTGGTGGTGGTGCTT----------------------------------AGAGTGTGTTGGCC----- -s simDog_chr6.simDog.chr6 461347 36 + 593897 CTATTATTGTGGTACTT----------------------------------GGAGTGCACTGGCCCATGT -s simHuman_chr6.simHuman.chr6 468629 68 + 601863 CTATTATTGTGGAGCTTGGACTGTGTTGGTGCTTGGAGTGCA--ATGGCCCGGAGTGCAATGGCCCATGT -s simRat_chr6.simRat.chr6 495126 70 + 647215 CTGCTATTGTGGTGGTTGGATTTTGTTGGTAGTTGGAGTGTGTTTGGGTGCGAAGTGTTTTGGCCGATGT - -a -s simMouse_chr6.simMouse.chr6 486818 2 + 636262 AT -s Anc0.Anc0refChr3 103179 2 + 222631 AT -s Anc1.Anc1refChr6 136605 2 + 197743 AT -s Anc2.Anc2refChr1 14763 2 + 142988 AT -s mr.mrrefChr3 40971 2 + 181027 AT -s simCow_chr6.simCow.chr6 471323 2 + 602619 AT -s simDog_chr6.simDog.chr6 461390 2 + 593897 AT -s simHuman_chr6.simHuman.chr6 468704 2 + 601863 AT -s simRat_chr6.simRat.chr6 495203 2 + 647215 AT - -a -s simMouse_chr6.simMouse.chr6 486820 1 + 636262 G -s Anc0.Anc0refChr3 103181 1 + 222631 G -s Anc1.Anc1refChr6 136607 1 + 197743 G -s Anc2.Anc2refChr1 14765 1 + 142988 T -s mr.mrrefChr3 40973 1 + 181027 G -s simCow_chr6.simCow.chr6 471325 1 + 602619 T -s simDog_chr6.simDog.chr6 461397 1 + 593897 T -s simHuman_chr6.simHuman.chr6 468706 1 + 601863 G -s simRat_chr6.simRat.chr6 495205 1 + 647215 G - -a -s simMouse_chr6.simMouse.chr6 486821 23 + 636262 ATGTTATAGTTATTTGAGAACTT -s Anc0.Anc0refChr3 103183 23 + 222631 ATGCAATCCTTATTTGAAAACTC -s Anc1.Anc1refChr6 136609 23 + 197743 ATGCAATCCTTATTTGAAAACTC -s Anc2.Anc2refChr1 14767 23 + 142988 ATGCAGTCCCTATTTGAAAACTC -s mr.mrrefChr3 40974 23 + 181027 ATGTTATCGTTATTTGAGAACTC -s simCow_chr6.simCow.chr6 471327 23 + 602619 ATGCAGTACCTATTTAAAGACTC -s simDog_chr6.simDog.chr6 461399 23 + 593897 ATGCAGTCCCTATTTGACAACTC -s simHuman_chr6.simHuman.chr6 468708 23 + 601863 ATGCGATCCTAATTTGAAAACTC -s simRat_chr6.simRat.chr6 495206 23 + 647215 ATGTTATCATTATTTGCGAGCTC - -a -s simMouse_chr6.simMouse.chr6 486844 99 + 636262 GTATGACAGGAAGCAGGCCGTGGTGGATCGAAAATAAAGAAGGTAAAAAATATACAAACTCCGACGAACACCACCATTCAGGTATGATACATTCATATG -s Anc0.Anc0refChr3 103206 97 + 222631 ATATACTTGGAAGCAGGCCGTGGTGGATCAAAGATAAAGAAGATAAAGAATATACAAAGTCCAACCAACACTACCATTCAGGTAAGCTATA--CACATG -s Anc1.Anc1refChr6 136632 97 + 197743 ATATACTTGGAAGCAGGCCGTGGTGGATCAAAGATAAAGAAGATAAAGAATATACAAAGTCCAACCAACACTACCATTCAGGTAAGCTATA--CACATG -s Anc2.Anc2refChr1 14790 97 + 142988 ATATACTTGGAAGCAGGCCGTGGTGGATCAAAGATAAAAAAGATAAAGAATATACAAAGTCCAACCAACACTACCATTCAGGTAAGCTATA--TACATG -s mr.mrrefChr3 40997 99 + 181027 ATATGACAGGAAGCAGGCCGTGGTGGATCGAAAATAAAGAAGGTAAAGAATATACAAACTCCAACCAACACCACCATTCAGGTATGATACATTCACATG -s simCow_chr6.simCow.chr6 471366 93 + 602619 ATATACCTGAAATCAGGTCGTGGTGGATCAAGGATAAAAAAGATAAAGAATAAACAAAGTCCAACCAACACTACCATTCAGGTA----ATA--TACATG -s simDog_chr6.simDog.chr6 461422 97 + 593897 AAATATTTGGAAGCAGGCCGTGGTGGATCAAAGATAAAAAAAATAAAGAATATACAAAGTCCAACCAACACTACCATTCAGGTAAGCTACA--TACATG -s simHuman_chr6.simHuman.chr6 468731 97 + 601863 ATATACTTAGAAGCAGGCCGTGGTGGATCAAAGATGAAGAAGATCAAGAATATACAAAGTCCAACCAACACTACCATTCAGGTACACTATA--CACACG -s simRat_chr6.simRat.chr6 495229 99 + 647215 ATATGACAGGAAGCAGGCCGTGGTGGATCGAAAATAAAGAAGGTAAAGAATATACAAACTCCAACCAACACCACCATTCAGGTATGGTAGCTTCACATG - -a -s simMouse_chr6.simMouse.chr6 486943 47 + 636262 TTTAATATATTTGTACTTCACAGCCCATAGCTGTACAGCCCATTGTC -s Anc0.Anc0refChr3 103303 45 + 222631 ATTAATATATTTGTATT--ACATCTCATTACTGCACAGCCTATTGGA -s Anc1.Anc1refChr6 136729 45 + 197743 ATTAATATATTTGTATT--ACATCTCATTACTGCACAGCCTATTGGA -s Anc2.Anc2refChr1 14887 45 + 142988 ATTAGTATATTTGTATT--ACATCTCATTACTGCACAGCCTATTGGA -s mr.mrrefChr3 41096 45 + 181027 TTTAATATATTTGTACT--ACAGCCCATAGCTGTACAGCCCATTGTC -s simCow_chr6.simCow.chr6 471460 45 + 602619 ATAGCCATTTTTGTGTT--ACAGATCATTACTGCACAGCCTGTTGAA -s simDog_chr6.simDog.chr6 461519 45 + 593897 TCTAGTATATTTGTATT--ACATCTCATAACTGCACTGCCCATTGGA -s simHuman_chr6.simHuman.chr6 468828 45 + 601863 ATTAATATATTTGTATT--ATATCTTGATACTGGAGAGCTTAATGGA -s simRat_chr6.simRat.chr6 495328 4 + 647215 TCTA------------------------------------------- - -a -s simMouse_chr6.simMouse.chr6 486990 7 + 636262 TGACCAA -s Anc0.Anc0refChr3 103348 7 + 222631 TGGCCAG -s Anc1.Anc1refChr6 136774 7 + 197743 TGGCCAG -s Anc2.Anc2refChr1 14937 7 + 142988 TGGCCAG -s mr.mrrefChr3 41141 7 + 181027 TGACCAA -s simCow_chr6.simCow.chr6 471506 6 + 602619 -GGCCAA -s simDog_chr6.simDog.chr6 461569 7 + 593897 TGGCCAG -s simHuman_chr6.simHuman.chr6 468873 7 + 601863 TGGCCAG - -a -s simMouse_chr6.simMouse.chr6 486997 27 + 636262 CTTGGAATCTAAGTTTTTCCTTCTTTA -s Anc0.Anc0refChr3 103355 23 + 222631 CTTGAAATCTAATTTT----TTTTCTA -s Anc1.Anc1refChr6 136781 23 + 197743 CTTGAAATCTAATTTT----TTTTCTA -s Anc2.Anc2refChr1 14944 23 + 142988 CTTGAAACCTAATTTT----TTTTCTA -s mr.mrrefChr3 41148 27 + 181027 CTTGGAATCTAAGTTTTTCCTTCTTTA -s simCow_chr6.simCow.chr6 471512 19 + 602619 CTTGAAACCTAAT--------TTTCTA -s simDog_chr6.simDog.chr6 461576 23 + 593897 CTTGAAACCTAGTTTT----TTTTCTA -s simHuman_chr6.simHuman.chr6 468900 23 + 601863 CTTGAAATAGAACTTT----TTTTCTA -s simRat_chr6.simRat.chr6 495332 10 + 647215 -----------------CCCATCTTTA - -a -s simMouse_chr6.simMouse.chr6 487024 5 + 636262 GGGAC -s Anc0.Anc0refChr3 103378 5 + 222631 GGGAC -s Anc1.Anc1refChr6 136804 5 + 197743 GGGAC -s Anc2.Anc2refChr1 14967 5 + 142988 GGGAC -s mr.mrrefChr3 41175 5 + 181027 GGGAC -s simCow_chr6.simCow.chr6 471531 5 + 602619 GGGAC -s simDog_chr6.simDog.chr6 461601 5 + 593897 GAGAC -s simHuman_chr6.simHuman.chr6 468923 5 + 601863 GGGAC -s simRat_chr6.simRat.chr6 495342 5 + 647215 GGCAC - -a -s simMouse_chr6.simMouse.chr6 487029 36 + 636262 AGACAAGCCTTAGGGAAAACGTGAATGATGAGAGAG -s Anc0.Anc0refChr3 103383 34 + 222631 AGAAAAGCCTTGGGTAAAACCTCCATGATGAT--AG -s Anc1.Anc1refChr6 136809 36 + 197743 AGAAAAGCCTTGGGTAAAACCTCCATGATGATAGAG -s Anc2.Anc2refChr1 14973 34 + 142988 AGGAAAGCCTTGGGTAAAACCTGCATGATGAT--AG -s mr.mrrefChr3 41180 36 + 181027 AGACAAGCCTTAGGTAAAACCTCCATGATGAGAGAG -s simCow_chr6.simCow.chr6 471537 34 + 602619 GGGACAGTCTCGGGTAAAACTTGCTTCATGAT--AG -s simDog_chr6.simDog.chr6 461607 34 + 593897 AGGAAAGCCTTGGGTAGAACCCGCATGGTGAT--AG -s simHuman_chr6.simHuman.chr6 468928 35 + 601863 -GAGAATGCTTGGATAACACCTCCATGATGATAGAA -s simRat_chr6.simRat.chr6 495347 36 + 647215 AGAAAAGCTTTAGGTAAACCCTCCATGGTTAGAGAG - -a -s simMouse_chr6.simMouse.chr6 487065 22 + 636262 ACAAAAAGGAAGCAGTGTAAGC -s Anc0.Anc0refChr3 103417 17 + 222631 ATAAGAAGGC--CAGTG---GC -s Anc1.Anc1refChr6 136845 17 + 197743 ATAAGAAGGC--CAGTG---GC -s Anc2.Anc2refChr1 15007 17 + 142988 ATAAGAAGGC--CAGTG---GC -s mr.mrrefChr3 41216 20 + 181027 ACAAAAAGGAAGCAGTG--AGC -s simCow_chr6.simCow.chr6 471573 17 + 602619 TTAAGTAGGC--CAGAA---GT -s simDog_chr6.simDog.chr6 461641 17 + 593897 ATAAGAAGGC--CAGTG---GC -s simHuman_chr6.simHuman.chr6 468963 1 + 601863 A--------------------- -s simRat_chr6.simRat.chr6 495383 20 + 647215 ACAAAAAGGAAGCAGTG--AGT - -a -s simMouse_chr6.simMouse.chr6 487087 11 + 636262 ACTACTCTCTT -s Anc0.Anc0refChr3 103434 11 + 222631 AATACCCTTTT -s Anc1.Anc1refChr6 136862 11 + 197743 AATACCCTTTT -s Anc2.Anc2refChr1 15027 11 + 142988 AATACCCTTTT -s mr.mrrefChr3 41236 11 + 181027 ACTACTCTCTT -s simCow_chr6.simCow.chr6 471593 11 + 602619 AATACTCCTTA -s simDog_chr6.simDog.chr6 461661 11 + 593897 AATACCCTTTT -s simRat_chr6.simRat.chr6 495403 11 + 647215 ACTACTCTCTT - -a -s simMouse_chr6.simMouse.chr6 487098 8 + 636262 CCTGTTCA -s Anc0.Anc0refChr3 103445 8 + 222631 TCTGTTCA -s Anc1.Anc1refChr6 136873 8 + 197743 TCTGTTCA -s Anc2.Anc2refChr1 15039 8 + 142988 TCTGTTCA -s mr.mrrefChr3 41247 8 + 181027 CCTGTTCA -s simCow_chr6.simCow.chr6 471605 8 + 602619 CCTGTTCG -s simDog_chr6.simDog.chr6 461673 8 + 593897 TCTGTTCA -s simRat_chr6.simRat.chr6 495414 8 + 647215 CCTGTTAA - -a -s simMouse_chr6.simMouse.chr6 487106 47 + 636262 AGATTAGGGAGTATTTTAATCTTAGATAGGCCCTAGCATCTGCTTTT -s Anc0.Anc0refChr3 103453 47 + 222631 GCTCTAGAGGTTGACTCAATTGTAAGTAGGTCCTAGCACCCCTTTTT -s Anc1.Anc1refChr6 136881 47 + 197743 GCTCTAGAGGTTGACTCAATTGTAAGTAGGTCCTAGCACCCCTTTTT -s Anc2.Anc2refChr1 15047 47 + 142988 GCTCTAGAGGTTGACTCAATTGTAAGTAGGTCCTAGCACCCCTTTTT -s mr.mrrefChr3 41255 47 + 181027 AGATTAGGGAGTATTTTAATCTTAGATAGGCCCTAGCATCTGCTTTT -s simCow_chr6.simCow.chr6 471617 47 + 602619 GCATTAGGGATTGACTCAATTGTAAGCAGATCCTAGCACTTCCTTTT -s simDog_chr6.simDog.chr6 461681 47 + 593897 GCTCTAGAGGTTGACTCAATTGTAAGTAGGTCCTAGCACCCCTTTTT -s simRat_chr6.simRat.chr6 495422 47 + 647215 AGTTTAGGGAGTATTTTAATTCTAGGTAGGGCCTAGCACTTTCTTTT - -a -s simMouse_chr6.simMouse.chr6 487153 5 + 636262 TTAAA -s Anc0.Anc0refChr3 103500 5 + 222631 TTTTT -s Anc1.Anc1refChr6 136928 5 + 197743 TTTTT -s Anc2.Anc2refChr1 15094 5 + 142988 TTTTT -s mr.mrrefChr3 41302 5 + 181027 TTAAA -s simCow_chr6.simCow.chr6 471664 5 + 602619 TTATT -s simDog_chr6.simDog.chr6 461742 5 + 593897 TTTTT -s simRat_chr6.simRat.chr6 495469 5 + 647215 TTAAA - -a -s simMouse_chr6.simMouse.chr6 487158 33 + 636262 AACAATCTACCTCACTTCCCTGAGGAAAACCTA -s Anc0.Anc0refChr3 103505 33 + 222631 AAAAACTTGACTCACTCTCCTGGGGGTACCCTG -s Anc1.Anc1refChr6 136933 33 + 197743 AAAAACTTGACTCACTCTCCTGGGGGTACCCTG -s Anc2.Anc2refChr1 15099 33 + 142988 AAAAACTTGACTCACTCTCCTGGGGGTACCCTG -s mr.mrrefChr3 41307 33 + 181027 AACAATCTACCTCACTTCCCTGAGGAAAACCTA -s simCow_chr6.simCow.chr6 471669 33 + 602619 AAAAACTTTGCCCGCTACCCTGGGAGTATCCTT -s simDog_chr6.simDog.chr6 461751 33 + 593897 AAAAACTTGACTCACTCTCCTGGGGGTACCCTG -s simRat_chr6.simRat.chr6 495474 33 + 647215 AGCAATCTACCCCACTTCCCTGAGGATAACTTA - -a -s simMouse_chr6.simMouse.chr6 487191 60 + 636262 TAGCTGCTCTATCGTTGCGGATGAAGCTCTATTCTAAGAAGAAAATACCAGGCTTCATCC -s Anc0.Anc0refChr3 103538 23 + 222631 TTGATATTCC-------------AGGGCCCATTCTA------------------------ -s Anc1.Anc1refChr6 136966 23 + 197743 TTGATATTCC-------------AGGGCCCATTCTA------------------------ -s Anc2.Anc2refChr1 15132 23 + 142988 TTGATATTCC-------------AGGGCCCATTCTA------------------------ -s mr.mrrefChr3 41340 36 + 181027 TAGCTGCTCTATCGTTGCGGATGAAGCTCTATTCTA------------------------ -s simCow_chr6.simCow.chr6 471716 23 + 602619 TTGATATTCA-------------AAGCCCCACTTTA------------------------ -s simDog_chr6.simDog.chr6 461784 23 + 593897 TTGATATTCC-------------AGGGCCCATTCTA------------------------ -s simRat_chr6.simRat.chr6 495507 36 + 647215 AATGTGTTCTATTCTTGCAGATGAAGCTCTATCCTA------------------------ - -a -s simMouse_chr6.simMouse.chr6 487251 12 + 636262 TACACAATTACT -s Anc0.Anc0refChr3 103561 12 + 222631 TAGATAATTAGT -s Anc1.Anc1refChr6 136989 12 + 197743 TAGATAATTAGT -s Anc2.Anc2refChr1 15188 12 + 142988 TAGATAATTAGT -s mr.mrrefChr3 41376 12 + 181027 TACACAATTACT -s simCow_chr6.simCow.chr6 471772 12 + 602619 TAGATGGTTCAC -s simDog_chr6.simDog.chr6 461840 12 + 593897 TAGATAATTAGT -s simRat_chr6.simRat.chr6 495543 12 + 647215 TAGACAATTACT - -a -s simMouse_chr6.simMouse.chr6 487263 45 + 636262 TTCTTCACTTCACCGTCAGATAGCTCGAGACTCTAAAGTATTCTG -s Anc0.Anc0refChr3 103573 44 + 222631 TTTTTCACTGCT-TCTTGAATAGCTAGAGACTTCTAAGTCTTTTG -s Anc1.Anc1refChr6 137001 44 + 197743 TTTTTCACTGCT-TCTTGAATAGCTAGAGACTTCTAAGTCTTTTG -s Anc2.Anc2refChr1 15200 44 + 142988 TTTTTCACTGCT-TCTTGAATAGCTAGAGACTTCTAAGTCTTTTG -s mr.mrrefChr3 41388 44 + 181027 TTCTTCACTTCA-CGTCAGATAGCTCGAGACTCTAAAGTATTCTG -s simCow_chr6.simCow.chr6 471799 44 + 602619 TTTTTCTCTGCT-TCGTGGGTGGTTAGAGACTTCAGAGTGTTCTG -s simDog_chr6.simDog.chr6 461852 44 + 593897 TTTTTCACTGCT-TCTTGAATAGCTAGAGACTTCTAAGTCTTTTG -s simRat_chr6.simRat.chr6 495555 44 + 647215 TGCTTCACTTCA-TGTCGGATAGCTAGAGATTCCTAAGTGCTCTG - -a -s simMouse_chr6.simMouse.chr6 487308 53 + 636262 CACAATATGTATATAGACAAATCAAAGGGGTGAGATTTAGTGGACATAAACTA -s Anc0.Anc0refChr3 103617 52 + 222631 TACAACCCATATAATGGTCAAGCAAA-GGGTCAAATTGAGTGGACCTCATATA -s Anc1.Anc1refChr6 137045 52 + 197743 TACAACCCATATAATGGTCAAGCAAA-GGGTCAAATTGAGTGGACCTCATATA -s Anc2.Anc2refChr1 15248 52 + 142988 TACAACCCATATAATGGTCAAGCAAA-GGGTCAAATTGAGTGGACCTCATATA -s mr.mrrefChr3 41432 53 + 181027 CACAATATGTATATAGACAAATCAAAGGGGTGAGATTTAGTGGACATAAACTA -s simCow_chr6.simCow.chr6 471847 52 + 602619 TACAATACATATAATGGCCAAGTGAA-GAGTCAAATTAAGTGGACCTTGGCTA -s simDog_chr6.simDog.chr6 461900 52 + 593897 TACAACCCATATAATGGTCAAGCAAA-GGGTCAAATTGAGTGGACCTCATATA -s simRat_chr6.simRat.chr6 495599 53 + 647215 CACAATATGTATATAGACCAATCAGAGGGGTAAGATTTAGTGGACGTAAACTG - -a -s simMouse_chr6.simMouse.chr6 487361 5 + 636262 GGTAC -s Anc0.Anc0refChr3 103669 5 + 222631 AGCAC -s Anc1.Anc1refChr6 137097 5 + 197743 AGCAC -s Anc2.Anc2refChr1 15300 5 + 142988 AGCAC -s mr.mrrefChr3 41485 5 + 181027 GGTAC -s simCow_chr6.simCow.chr6 471899 5 + 602619 GGTAC -s simDog_chr6.simDog.chr6 461965 5 + 593897 AGCAC -s simRat_chr6.simRat.chr6 495652 5 + 647215 GGTAC - -a -s simMouse_chr6.simMouse.chr6 487366 277 + 636262 AACCTAGTACTACTGAGCTTACGTTGTTGTAGAACAAAATAAAATGGAACATTATGTTGTTTGCGGAGAAATATCAATAATACCTCTTTTACACACAATTTCTAACCCATTACCAATAGTCACTTGGGTGCCATTATTTCAGTCCACTATACATGGCCACTTCAAGATTATTCTAATAATGCATAATGCCTAGACCCAGGGCCCAGGGCATAGACCCCAACAATCATTCTCTTCATGGTGTGCTAGTCTGATAGATCCATGGAGCTTTGGTGTAATA -s Anc0.Anc0refChr3 103674 6 + 222631 aacc-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ta -s Anc1.Anc1refChr6 137102 9 + 197743 aacc----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TAATA -s Anc2.Anc2refChr1 15399 6 + 142988 aacc-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ta -s mr.mrrefChr3 41490 259 + 181027 AACCTAGTACTACTGAGCTTACGTTGTTGTAGAACAAAAT-AAATGGAACATTATGTTGTTTGCGGAGAAATAT-----ATACCTCTTTTACACACAATTTCTAACCC--TACCAATAGTCACTTGGGTGCC---ATTTCAGTCCACTATACATGGCCACTTCAAGATTATTCTAATAATGCATAATGCCTAGA-------CCCAGGGCATAGACCCCAACAATCATTCTCTTCATGGTGTGCTAGTCTGATAGATCCATGGAGCTTTGGTGTAATA -s simCow_chr6.simCow.chr6 472006 6 + 602619 gaac-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ta -s simDog_chr6.simDog.chr6 462095 6 + 593897 aacc-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ta -s simHuman_chr6.simHuman.chr6 468964 5 + 601863 --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TAATA -s simRat_chr6.simRat.chr6 495657 259 + 647215 AACCTAGTACTACTGAGGTTAAACTGCTGTGGAACAAAAT-AAATGCAACATTATGCAGTTTGCAGAGAAATGT-----ATACCTCTTTTATACACAACTTCTAACCC--TACCAATAGTCTCTTGTGTGCC---ATTTCAGTCCACTATGCATGGCTACTCCAAGATTGTTCTAATAACCCATAATGCCTAGA-------CCCAGGGCATAGATCCCATCAATCATTCTCTTCATGTTCTGTTAGCCTATTAGATCTACGGAGCTTTGGTGTCATA - -a -s simMouse_chr6.simMouse.chr6 487643 59 + 636262 TTTCCCACACCACTATATAGCATGCTCCCTTTATCTATGTGGGATGTTAAGTAAGTCTG -s Anc0.Anc0refChr3 103900 59 + 222631 TTTCAGCCAACAGTGTATATTGTGCTTTCCTTGTCTATGGAAGATATTAAGAAATTCTT -s Anc1.Anc1refChr6 137331 59 + 197743 TTTCAGCCAACAGTGTATATTGTGCTTTCCTTGTCTATGGAAGATATTAAGAAATTCTT -s Anc2.Anc2refChr1 15625 59 + 142988 TTTCAGCTAACAGTGTACATTGTGCTTTCCTGGTCTATGGAAAATATTAAAAAATTCTT -s mr.mrrefChr3 41749 59 + 181027 TTTCACACACCACTATATAGCATGCTCCCTTTGTCTATGTGAGATATTAAGTAAGTCTG -s simCow_chr6.simCow.chr6 472241 35 + 602619 ------------------------CTTTCCTGATCTGTGGAAAATATTGCAAAGTTCTT -s simDog_chr6.simDog.chr6 462321 59 + 593897 TTTCAGCTAACAGTGTACATTGTGCTCCCCTGGTCTAGGGAAAATATTAAAAAATTCTT -s simHuman_chr6.simHuman.chr6 469200 59 + 601863 TTTCAGCCAACAGTGTATATTGTACTTTCCTTGTCTATGGAAGATATTAAGCAATTCTT -s simRat_chr6.simRat.chr6 495916 59 + 647215 TTTCAAATACCACCATTTAGCATGCTCCCTTTGTCTATGTGAGATATTAGGTAAGCCTG - -a -s simMouse_chr6.simMouse.chr6 487702 37 + 636262 ATAAATACTACTCGGTTGGTTGTCTTTCGATTTGTCC -s Anc0.Anc0refChr3 103959 33 + 222631 ACAATTGCAAGT----TAGTTGACGTTCAATTTGACC -s Anc1.Anc1refChr6 137390 33 + 197743 ACAATTGCAAGT----TAGTTGACGTTCAATTTGACC -s Anc2.Anc2refChr1 15684 33 + 142988 ACAATTGCAAGT----GAGTTGGTGTTCAATTTGACC -s mr.mrrefChr3 41808 33 + 181027 ATAAATACTACT----TGGTTGACTTTCAATTTGTCC -s simCow_chr6.simCow.chr6 472277 26 + 602619 ACAATTGCAAGT----GAGTTG-------ATTTGTCG -s simDog_chr6.simDog.chr6 462380 33 + 593897 ATCATTGCAAGT----GAGTTGGTGTTCAATCTGACC -s simHuman_chr6.simHuman.chr6 469259 33 + 601863 ACAATTGCAGGT----TAGTTGACCTTCAATTTGACC -s simRat_chr6.simRat.chr6 495975 33 + 647215 ATAAATACTACT----TGGTTGACTTTCAATTTGGCC - -a -s simMouse_chr6.simMouse.chr6 487739 57 + 636262 CAAATCTCAATCTTTGTTTTTATTCATCTTACCAGTTCTTGGTTATCAGGAGCACCA -s Anc0.Anc0refChr3 103997 24 + 222631 TAAATCTAAAT-CTTGTTTTTATTC-------------------------------- -s Anc1.Anc1refChr6 137428 47 + 197743 TAAATCTAAATCCTTGTTTTTATTCATCTTAACAATTCC----------GACCACCA -s Anc2.Anc2refChr1 15722 24 + 142988 TAAATCTAAAT-CTCGATTTTATTC-------------------------------- -s mr.mrrefChr3 41841 53 + 181027 CAAATCTCAATCTTTGTTTTTATTCATCTTACCAGTTCTTGGT----AGGACCACCA -s simCow_chr6.simCow.chr6 472308 24 + 602619 CAAACTTACAT-CTCTGTTTTACTG-------------------------------- -s simDog_chr6.simDog.chr6 462418 24 + 593897 TAAATCTAAAT-CTCGATTTTATTC-------------------------------- -s simHuman_chr6.simHuman.chr6 469300 47 + 601863 TAAATCTAAATCCTTGTTTTTATTCATCTTAACAATTCC----------GACCACCA -s simRat_chr6.simRat.chr6 496008 53 + 647215 CAAATCTTAATCTTTGTTTTTATTCATCTTACCAGTTCTTGGT----ATGACCACCT - -a -s simMouse_chr6.simMouse.chr6 487796 7 + 636262 ACTGGTC -s Anc1.Anc1refChr6 137475 6 + 197743 A-TGGCC -s mr.mrrefChr3 41894 6 + 181027 A-TGGTC -s simHuman_chr6.simHuman.chr6 469361 6 + 601863 A-TGGCC -s simRat_chr6.simRat.chr6 496061 6 + 647215 A-TGGTA - -a -s simMouse_chr6.simMouse.chr6 487803 126 + 636262 AAGCCACAATGGATATGAATGTCTGAATCTCAGCAGGATACCAATACCTAACGGCAACAGTGGTAAGGCTAGATGACATATGTACTTTCATATGGAGTAATCAAAGAGAGTTTCCAGGAATCACTC -s Anc0.Anc0refChr3 104021 3 + 222631 ---------------------------------------------------------------------------------------------------------------------------GTC -s Anc1.Anc1refChr6 137481 124 + 197743 AGGCAATAACTGA-ATGAATACCTGAATCTCAATCAGATTCCACTGCCCAATATTCATTG-AGTCCATTGACACAACATACATACTTACCTCAGCTGTAATCAAAGAGGGCCTGTAGTAGTGAGTC -s Anc2.Anc2refChr1 15746 3 + 142988 ---------------------------------------------------------------------------------------------------------------------------GTC -s mr.mrrefChr3 41900 124 + 181027 AAGCCACAATGGA-ATGAATGTCTGAATCTCAGCAGGATACCAATACCTAACGGCAACAG-GGTAAGGCTAGATGACATATGTACTTTCATATGGAGTAATCAAAGAGAGTTTCCAGGAATCACTC -s simCow_chr6.simCow.chr6 472332 3 + 602619 ---------------------------------------------------------------------------------------------------------------------------ATC -s simDog_chr6.simDog.chr6 462442 3 + 593897 ---------------------------------------------------------------------------------------------------------------------------GTT -s simHuman_chr6.simHuman.chr6 469373 124 + 601863 AGGCAATAACTGA-ATGAATACCTGAATCTCAATCAGATTCCACTGCCCAATATTCATTG-AGTCCATTGACACAACATACATACTTACCTCAGCTGTAATCAAAGAGGGCCTGTAGTAGTGAGTC -s simRat_chr6.simRat.chr6 496067 11 + 647215 GAGTCACAATG------------------------------------------------------------------------------------------------------------------- - -a -s simMouse_chr6.simMouse.chr6 487929 10 + 636262 ACCCCCATCC -s Anc0.Anc0refChr3 104024 10 + 222631 ACTCCTATCC -s Anc1.Anc1refChr6 137605 10 + 197743 ACTCCTATCC -s Anc2.Anc2refChr1 15749 10 + 142988 ACTCCTATCG -s mr.mrrefChr3 42024 10 + 181027 ACCCCCATCC -s simCow_chr6.simCow.chr6 472337 10 + 602619 AATCCTATGA -s simDog_chr6.simDog.chr6 462445 10 + 593897 GCTGTAGTCG -s simHuman_chr6.simHuman.chr6 469497 10 + 601863 ACTCCTATCC - -a -s simMouse_chr6.simMouse.chr6 487939 5 + 636262 ATCAG -s Anc0.Anc0refChr3 104036 5 + 222631 AAGAG -s Anc1.Anc1refChr6 137617 5 + 197743 AAGAG -s Anc2.Anc2refChr1 15761 5 + 142988 AAGAC -s mr.mrrefChr3 42034 5 + 181027 ATCAG -s simCow_chr6.simCow.chr6 472349 5 + 602619 CTGAC -s simDog_chr6.simDog.chr6 462457 5 + 593897 AAGAC -s simHuman_chr6.simHuman.chr6 469509 5 + 601863 AATGG - -a -s simMouse_chr6.simMouse.chr6 487944 2 + 636262 AG -s Anc0.Anc0refChr3 104041 2 + 222631 AG -s Anc1.Anc1refChr6 137622 2 + 197743 AG -s Anc2.Anc2refChr1 15766 2 + 142988 CC -s mr.mrrefChr3 42039 2 + 181027 AG -s simCow_chr6.simCow.chr6 472367 2 + 602619 GC -s simDog_chr6.simDog.chr6 462462 2 + 593897 CC -s simHuman_chr6.simHuman.chr6 469514 2 + 601863 AG - -a -s simMouse_chr6.simMouse.chr6 487946 40 + 636262 TGTCTAATCTGCCCCCAGGACTCACGGGAGACAGACATAT -s Anc0.Anc0refChr3 104051 39 + 222631 TGACTAATCTGCTCC-AGGACTCAGGTGTGAGAGAAATAG -s Anc1.Anc1refChr6 137632 39 + 197743 TGACTAATCTGCTCC-AGGACTCAGGTGTGAGAGAAATAG -s Anc2.Anc2refChr1 15776 39 + 142988 TGATTAATCTGCTCC-AGGACTCAGGTGTGAGAGAATTTG -s mr.mrrefChr3 42041 39 + 181027 TGTCTAATCTGCCCC-AGGACTCACGGGAGACAGACATAT -s simCow_chr6.simCow.chr6 472377 38 + 602619 TTAGTAATCTTGT-C-AGGGCTCAGGTGTGGAAGAATTTG -s simDog_chr6.simDog.chr6 462472 39 + 593897 TGATTACTCTGCTCC-AAGACTCAGGTGTGAGAGAATTTG -s simHuman_chr6.simHuman.chr6 469524 39 + 601863 TGACAAATCTGCTCC-AGGACTCAGATGTGAGAGAAATAG - -a -s simMouse_chr6.simMouse.chr6 487986 5 + 636262 AGCAG -s Anc0.Anc0refChr3 104090 5 + 222631 AAGCG -s Anc1.Anc1refChr6 137671 5 + 197743 AAGCG -s Anc2.Anc2refChr1 15815 5 + 142988 AAGCA -s mr.mrrefChr3 42080 5 + 181027 AGCAG -s simCow_chr6.simCow.chr6 472416 5 + 602619 AAGCA -s simDog_chr6.simDog.chr6 462511 5 + 593897 AAGCA -s simHuman_chr6.simHuman.chr6 469563 5 + 601863 AAGTG - -a -s simMouse_chr6.simMouse.chr6 487991 1 + 636262 T -s Anc0.Anc0refChr3 104100 1 + 222631 T -s Anc1.Anc1refChr6 137681 1 + 197743 T -s Anc2.Anc2refChr1 15825 1 + 142988 T -s mr.mrrefChr3 42085 1 + 181027 T -s simCow_chr6.simCow.chr6 472436 1 + 602619 C -s simDog_chr6.simDog.chr6 462527 1 + 593897 T -s simHuman_chr6.simHuman.chr6 469573 1 + 601863 T - -a -s simMouse_chr6.simMouse.chr6 487992 14 + 636262 AATTTTCCAGACAA -s Anc0.Anc0refChr3 104101 14 + 222631 CATGCCCCACACCT -s Anc1.Anc1refChr6 137682 14 + 197743 CATGCCCCACACCT -s Anc2.Anc2refChr1 15826 14 + 142988 CATGCCCTACACCT -s mr.mrrefChr3 42086 14 + 181027 AATTTTCCAGACAA -s simCow_chr6.simCow.chr6 472437 14 + 602619 CAAACCCTACACTT -s simDog_chr6.simDog.chr6 462532 14 + 593897 CTTGCTCTACACCT -s simHuman_chr6.simHuman.chr6 469574 14 + 601863 CATCCCCCACACCT - -a -s simMouse_chr6.simMouse.chr6 488006 22 + 636262 GGCGATGTGCTGCAAGTGGAGG -s Anc0.Anc0refChr3 104115 16 + 222631 GTCAATGTGCTG------GAAG -s Anc1.Anc1refChr6 137696 16 + 197743 GTCAATGTGCTG------GAAG -s Anc2.Anc2refChr1 15840 16 + 142988 GTCAATGTGCTG------GAAG -s mr.mrrefChr3 42100 16 + 181027 GGCGATGTGCTG------GAGG -s simCow_chr6.simCow.chr6 472451 16 + 602619 ATCAATGTGCTG------GAAG -s simDog_chr6.simDog.chr6 462697 15 + 593897 GTCAATGTGC-A------GAAA -s simHuman_chr6.simHuman.chr6 469588 16 + 601863 GTCACTGTGCTG------GAAG - -a -s simMouse_chr6.simMouse.chr6 488028 8 + 636262 CTATCCTA -s Anc0.Anc0refChr3 104131 8 + 222631 CTATCCTA -s Anc1.Anc1refChr6 137712 8 + 197743 CTATCCTA -s Anc2.Anc2refChr1 15856 8 + 142988 CTATCCTA -s mr.mrrefChr3 42116 8 + 181027 CTATCCTA -s simCow_chr6.simCow.chr6 472468 8 + 602619 CTATCCTA -s simDog_chr6.simDog.chr6 462712 8 + 593897 TTATCCCA -s simHuman_chr6.simHuman.chr6 469604 8 + 601863 CTATCCTA - -a -s simMouse_chr6.simMouse.chr6 488036 16 + 636262 GTTGGAAGTCAAGTTT -s Anc0.Anc0refChr3 104148 10 + 222631 ATT-GTGA-----TTG -s Anc1.Anc1refChr6 137729 11 + 197743 ATTGGTGA-----TTG -s Anc2.Anc2refChr1 15873 10 + 142988 ATT-GTGA-----CTG -s mr.mrrefChr3 42124 16 + 181027 GTTGGAAATCAAGTTT -s simCow_chr6.simCow.chr6 472485 10 + 602619 GTT-GTGA-----CTG -s simDog_chr6.simDog.chr6 462730 10 + 593897 ATT-ATGA-----CTA -s simHuman_chr6.simHuman.chr6 469621 11 + 601863 ATTGGTGA-----TTG -s simRat_chr6.simRat.chr6 496078 14 + 647215 --TGGAAATCAAGTTT - -a -s simMouse_chr6.simMouse.chr6 488052 35 + 636262 TCATTAAAGTACCCACACTTACACTTCATAAGAAG -s Anc0.Anc0refChr3 104158 32 + 222631 TCACTCAAGTA-CCCCACTTAC--TTCAGGGGAAA -s Anc1.Anc1refChr6 137740 33 + 197743 TCACTCAAGTACCCCCACTTAC--TTCAGGGGAAA -s Anc2.Anc2refChr1 15887 32 + 142988 TCACTCAAGTA-CCCCATTTAC--TTCAGGGGAAA -s mr.mrrefChr3 42140 33 + 181027 TCATTAAAGTACCCACACTTAC--TTCAGAGGAAG -s simCow_chr6.simCow.chr6 472501 24 + 602619 TCACTAAAACG---------AC--TTCAGGGGAAA -s simDog_chr6.simDog.chr6 462744 24 + 593897 TGACTCAAGTA-CCCCATTTAC--ATC-------- -s simHuman_chr6.simHuman.chr6 469632 33 + 601863 TCACTCAAGTCTGCCCACTTAC--TTCAGGGGAAA -s simRat_chr6.simRat.chr6 496092 33 + 647215 TCATTAAAGTGCCCACACTTAC--TTCAGAGGGAG - -a -s simMouse_chr6.simMouse.chr6 488087 51 + 636262 GATACAGTCATGCAAAAGTGGAACCCTAAAGGAGAACCCTAAAGGAGACTG -s Anc0.Anc0refChr3 104191 23 + 222631 AATACAGTCAGCCACAGTTAC----------------------------CA -s Anc1.Anc1refChr6 137774 23 + 197743 AATACAGTCAGCCACAGTTAC----------------------------CA -s Anc2.Anc2refChr1 15920 23 + 142988 AATATAGCCAGCCACAGTTAC----------------------------CA -s mr.mrrefChr3 42173 32 + 181027 GATACAGTCATGCAAAAGTGGAACCCTAA-------------------CTA -s simCow_chr6.simCow.chr6 472526 23 + 602619 AATATAGCCAGCCACAGTTAC----------------------------CA -s simHuman_chr6.simHuman.chr6 469666 23 + 601863 AACACAGTCAGCCACAGTTCA----------------------------CA -s simRat_chr6.simRat.chr6 496125 32 + 647215 GATACAGTCATGTAAAAGCGGAACCCTAA-------------------CTA - -a -s simMouse_chr6.simMouse.chr6 488138 16 + 636262 TCAGGCAAAGGTGGAA -s Anc0.Anc0refChr3 104214 12 + 222631 TAAGACATTG--GG-- -s Anc1.Anc1refChr6 137797 12 + 197743 TAAGACATTG--GG-- -s Anc2.Anc2refChr1 15943 12 + 142988 TAATACATTG--GG-- -s mr.mrrefChr3 42205 14 + 181027 TCAGGCAAAGGTGG-- -s simCow_chr6.simCow.chr6 472550 12 + 602619 TAAAACATTG--GA-- -s simDog_chr6.simDog.chr6 462768 11 + 593897 -AATACATTG--GG-- -s simHuman_chr6.simHuman.chr6 469689 12 + 601863 TAAGACAGTG--GG-- -s simRat_chr6.simRat.chr6 496157 14 + 647215 TCAGGCAAAGGTGG-- - -a -s simMouse_chr6.simMouse.chr6 488154 75 + 636262 CCTAGCAGCCTAAAACCACAGTGACCTAGCCAACTCACAGTGACCTAGCCAGGGAGAATGGGAAATGGAAAAATC -s Anc0.Anc0refChr3 104226 63 + 222631 CCCAACAATCTAAGCTGACAGTGACCTAGTAATAT------------GGCAGGGGGTATGGGAAATGGAAAAATA -s Anc1.Anc1refChr6 137809 63 + 197743 CCCAACAATCTAAGCTGACAGTGACCTAGTAATAT------------GGCAGGGGGTATGGGAAATGGAAAAATA -s Anc2.Anc2refChr1 15955 63 + 142988 CCCAACAATCTAAGCTGACAGTGACCTAGTAGTAT------------GGCAGGGGGTAGGGGAAATAGGAAAATA -s mr.mrrefChr3 42219 75 + 181027 CCTAACAGCCTAAAATCACAGTGACCTAGCCAACTCACAGTGACCTAGCCAGGGAGAATGGGAAATGGAAAAATC -s simCow_chr6.simCow.chr6 472562 56 + 602619 CCTAACATTCTAAGCTGACAGTGACCTAGTAGTCT------------GCCAGGGGGTGAGGGAAAAAG------- -s simDog_chr6.simDog.chr6 462780 63 + 593897 CCCGACTATCCAATTTCACAGTGACTTGGTGGTAC------------AGCAGGGGGTAGGGGAAATAGGAAAATA -s simHuman_chr6.simHuman.chr6 469701 54 + 601863 CCCAACAATCTAAGCTGACAGTGGCCTAGTAATGT---------------------GTTGGGATATGGAAAGCCA -s simRat_chr6.simRat.chr6 496171 58 + 647215 CCTAACAGACCAAAATCACAGTGACCTAGCCAACTCACAGTGACCTAGCAAGGGAGAA----------------- - -a -s simMouse_chr6.simMouse.chr6 488229 18 + 636262 AACAAATGGAAAAATCAA -s Anc0.Anc0refChr3 104289 17 + 222631 AACTA-TAGAGAAATCAA -s Anc1.Anc1refChr6 137872 18 + 197743 AACTATTAGAGAAATCAA -s Anc2.Anc2refChr1 16023 17 + 142988 AACCG-TATAGAGATCAA -s mr.mrrefChr3 42294 18 + 181027 AACAAATGGAGAAATCAA -s simCow_chr6.simCow.chr6 472618 15 + 602619 --CCA-TATAGAGATCAA -s simDog_chr6.simDog.chr6 462848 17 + 593897 AACCG-TATAGAGATCAA -s simHuman_chr6.simHuman.chr6 469755 13 + 601863 AACTATTTGAGAA----- -s simRat_chr6.simRat.chr6 496229 13 + 647215 -----ATGGAGAAATTAG - -a -s simMouse_chr6.simMouse.chr6 488247 16 + 636262 CAACATGATGTGCAAT -s Anc0.Anc0refChr3 104306 16 + 222631 TAACATGATTTGCGGT -s Anc1.Anc1refChr6 137890 16 + 197743 TAACATGATTTGCGGT -s Anc2.Anc2refChr1 16056 16 + 142988 TAACTTCTGTAGTGGT -s mr.mrrefChr3 42312 16 + 181027 CAACATGATGTGCAAT -s simCow_chr6.simCow.chr6 472669 16 + 602619 CAACCTCTGCAGTTGT -s simDog_chr6.simDog.chr6 462881 16 + 593897 TAACTTCTGTAGTGGT -s simHuman_chr6.simHuman.chr6 469768 15 + 601863 -CACATGATCTGCTGT -s simRat_chr6.simRat.chr6 496242 16 + 647215 CAATATGATGTGCAAT - -a -s simMouse_chr6.simMouse.chr6 488263 74 + 636262 TCTCTATATACATGTACATGAGTACACGAGTCAGATCAAGTAAACAGTTGGTGTCCCTGCTTCATATTAGTGCA -s Anc0.Anc0refChr3 104322 60 + 222631 TCTATATAAACCAG--------------AGTCAAGTCAAATAAAAAGTTGATGTACCCACTTCCTTTTAGTATG -s Anc1.Anc1refChr6 137906 60 + 197743 TCTATATAAACCAG--------------AGTCAAGTCAAATAAAAAGTTGATGTACCCACTTCCTTTTAGTATG -s Anc2.Anc2refChr1 16072 60 + 142988 TCTATATAAACCAG--------------AATCAAGTCAAATAAAAAGTTGATGTACCCACTTTCTTTTAGTATG -s mr.mrrefChr3 42328 60 + 181027 TCTCTATATACATG--------------AGTCAGATCAAATAAACAGTTGATGTACCCGCTTCATATTAGTGCA -s simCow_chr6.simCow.chr6 472685 58 + 602619 --TGTACATACCAG--------------AAACAAGTCAGAGGAAAAGTGGGTGTACCCACTTTATTTGAGAATG -s simDog_chr6.simDog.chr6 462915 60 + 593897 TCAAAGTAAACAAG--------------GATCAAATCAAATAAAAAGTTGATGTACCCACTTTCCTTTAGTATT -s simHuman_chr6.simHuman.chr6 469783 60 + 601863 TCTTTATAAACCAG--------------AGTCAAGTCAAATAAAAAGATGATGAACCCCCTTCGTTTTAGCTTG -s simRat_chr6.simRat.chr6 496258 47 + 647215 TCTCCATATACATG--------------AGTCAGATCAAATAAACAGTTGATGTACCCACT------------- - -a -s simMouse_chr6.simMouse.chr6 488337 63 + 636262 AAAGTAAGAACACTGGCTACTCCTACAGATCTGCTGCATTGAATCACTGCAGGCTTAGGGTTA -s Anc0.Anc0refChr3 104402 34 + 222631 GAAGTAAG----------------------------CTTCCAATCACTGCATTCCTAGGGTT- -s Anc1.Anc1refChr6 137986 34 + 197743 GAAGTAAG----------------------------CTTCCAATCACTGCATTCCTAGGGTT- -s Anc2.Anc2refChr1 16152 34 + 142988 GAAGTAAC----------------------------ATTCCAATCACTGCATTCCTGGGGTT- -s mr.mrrefChr3 42388 34 + 181027 AAAGTAAG----------------------------CATTGAATCACTGCAGGCTTAGGGTT- -s simCow_chr6.simCow.chr6 472763 34 + 602619 TAAGTAAC----------------------------ATTCCAATCACTGCATTTCTGGGGTT- -s simDog_chr6.simDog.chr6 462995 34 + 593897 GAAGTAAC----------------------------AATCCAGTCACTGCTTTCTTGGGGTT- -s simHuman_chr6.simHuman.chr6 469863 34 + 601863 GAAGTAAG----------------------------CTTCCAATCACTGCATTGCTAGAGTT- - -a -s simMouse_chr6.simMouse.chr6 488400 3 + 636262 TAC -s Anc0.Anc0refChr3 104436 3 + 222631 TGC -s Anc1.Anc1refChr6 138020 3 + 197743 TGC -s Anc2.Anc2refChr1 16187 3 + 142988 TGC -s mr.mrrefChr3 42422 3 + 181027 TAC -s simCow_chr6.simCow.chr6 472798 3 + 602619 TGC -s simDog_chr6.simDog.chr6 463030 3 + 593897 TGC -s simHuman_chr6.simHuman.chr6 469897 3 + 601863 TGC - -a -s simMouse_chr6.simMouse.chr6 488403 57 + 636262 AGATTCATAAATTCTCATTCCCACCTTTAGAGAGACGAGAGACAAATCAAATGACAG -s Anc0.Anc0refChr3 104439 51 + 222631 AGCTTCATTAGTTCTCAGTCCCAC---TAGATGGATGAGAGACTT-T--GAGGATGG -s Anc1.Anc1refChr6 138023 53 + 197743 AGCTTCATTAGTTCTCAGTCCCAC---TAGATGGATGAGAGACTT-TGAGAGGATGG -s Anc2.Anc2refChr1 16190 51 + 142988 AGCTTCATTAGGTCTCAGTTCCAC---TAAATGGATGAGAGACTT-T--GAGGATGG -s mr.mrrefChr3 42425 53 + 181027 AGATTCATAAATTCTCATTCCCAC---TAGAGAGACGAGAGACAA-TCAAATGACAG -s simCow_chr6.simCow.chr6 472802 51 + 602619 AGCTTGATTAGGTCCTAGTACCAC---TAAATGGATGAGAGACTT-T--GAAGATGG -s simDog_chr6.simDog.chr6 463033 51 + 593897 AGCTTCAAGAAGTCTCAGTTCGAC---TAAATGGATGAGAGACTT-T--GAGGATGA -s simHuman_chr6.simHuman.chr6 469900 53 + 601863 AGCCACATTAGTTCTGAGCCCCAC---TAGATGTAAGAGAGACTT-TGAGAGGATGG - -a -s simMouse_chr6.simMouse.chr6 488460 25 + 636262 GCCCAGGAATGGTGAACTTCAAATA -s Anc0.Anc0refChr3 104493 25 + 222631 GCCCAGGAATGGTCAACCTCAAATA -s Anc1.Anc1refChr6 138079 25 + 197743 GCCCAGGAATGGTCAACCTCAAATA -s Anc2.Anc2refChr1 16244 25 + 142988 GCCCAGGAATCGTCAATCACAAATA -s mr.mrrefChr3 42478 25 + 181027 GCCCAGGAATGGTGAACTTCAAATA -s simCow_chr6.simCow.chr6 472856 25 + 602619 GCCCAGGAATAGTCAATCACAAATA -s simDog_chr6.simDog.chr6 463087 25 + 593897 GCCCAGGAATCGGCAATTACAAATA -s simHuman_chr6.simHuman.chr6 469956 25 + 601863 GCCCAGAGATGATCAACCTCAATTA -s simRat_chr6.simRat.chr6 496305 23 + 647215 --CCAGGAATAGTAAACTTCAAATA - -a -s simMouse_chr6.simMouse.chr6 488485 6 + 636262 GATATT -s Anc0.Anc0refChr3 104519 6 + 222631 GATATT -s Anc1.Anc1refChr6 138105 6 + 197743 GATATT -s Anc2.Anc2refChr1 16270 6 + 142988 GATATT -s mr.mrrefChr3 42503 6 + 181027 GATATT -s simCow_chr6.simCow.chr6 472882 6 + 602619 GATATC -s simDog_chr6.simDog.chr6 463113 6 + 593897 AACACT -s simHuman_chr6.simHuman.chr6 469982 6 + 601863 GATATT -s simRat_chr6.simRat.chr6 496328 6 + 647215 AATATT - -a -s simMouse_chr6.simMouse.chr6 488491 34 + 636262 CTTATGACACCCAGAACAGTGTTATAATGTTTAT -s Anc0.Anc0refChr3 104542 24 + 222631 TTTATGACAACCAGAACATTGTCA---------- -s Anc1.Anc1refChr6 138128 24 + 197743 TTTATGACAACCAGAACATTGTCA---------- -s Anc2.Anc2refChr1 16304 24 + 142988 TTTATGACAATCAGAACATTGTCA---------- -s mr.mrrefChr3 42509 34 + 181027 TTTATGACACCCAGAACATTGTTATAATGTTTAT -s simCow_chr6.simCow.chr6 472916 14 + 602619 TTTATGACCA----------ATCA---------- -s simDog_chr6.simDog.chr6 463158 24 + 593897 TTGATGACAATCAGAACATTGTCA---------- -s simHuman_chr6.simHuman.chr6 470005 24 + 601863 TTTGTGACAACCAGAACATTGTCA---------- -s simRat_chr6.simRat.chr6 496334 34 + 647215 TTTACGCCACCCAGAACATTGTTATAATATTTAT - -a -s simMouse_chr6.simMouse.chr6 488525 19 + 636262 AGAATTACTTCATACACCA -s Anc0.Anc0refChr3 104566 19 + 222631 AGTATCACCTCATACATCA -s Anc1.Anc1refChr6 138152 19 + 197743 AGTATCACCTCATACATCA -s Anc2.Anc2refChr1 16329 19 + 142988 AGTATCACCTCATACATCA -s mr.mrrefChr3 42543 19 + 181027 AGAATTACTTCATACACCA -s simCow_chr6.simCow.chr6 472931 19 + 602619 AGTATCGCCTCATACACCA -s simDog_chr6.simDog.chr6 463183 18 + 593897 AGTA-CACCTCATACATTG -s simHuman_chr6.simHuman.chr6 470029 19 + 601863 AGTATCACCTCATACATCA -s simRat_chr6.simRat.chr6 496368 19 + 647215 AGAGTTACTTCATATACCA - -a -s simMouse_chr6.simMouse.chr6 488544 17 + 636262 GTAAGAGTAAATGCTGT -s Anc0.Anc0refChr3 104625 17 + 222631 GTATGAGCAAGTACTGA -s Anc1.Anc1refChr6 138211 17 + 197743 GTATGAGCAAGTACTGA -s Anc2.Anc2refChr1 16388 17 + 142988 ACATGAGCAAGTACTAA -s mr.mrrefChr3 42562 17 + 181027 GTAAGAGTAAATACTGT -s simDog_chr6.simDog.chr6 463246 17 + 593897 ACATGAGCAAGTACTAA -s simHuman_chr6.simHuman.chr6 470088 17 + 601863 GTATTAGCAAGTACTGG -s simRat_chr6.simRat.chr6 496387 17 + 647215 ATAGGAGTAAATACTGT - -a -s simMouse_chr6.simMouse.chr6 488561 16 + 636262 CAGAAAAATATTCTTA -s Anc0.Anc0refChr3 104642 16 + 222631 GGGAACTTTCTGGTTA -s Anc1.Anc1refChr6 138228 16 + 197743 GGGAACTTTCTGGTTA -s Anc2.Anc2refChr1 16405 16 + 142988 GGGAACTTTCTGGGTA -s mr.mrrefChr3 42579 16 + 181027 AGGAAAAATATTCTTA -s simCow_chr6.simCow.chr6 472967 12 + 602619 ----ACTTTCTGGGTC -s simDog_chr6.simDog.chr6 463263 16 + 593897 GGGAACTTTCTGGGCA -s simHuman_chr6.simHuman.chr6 470106 16 + 601863 GGGAAGGTTCTGGTTA -s simRat_chr6.simRat.chr6 496404 6 + 647215 AGGAAA---------- - -a -s simMouse_chr6.simMouse.chr6 488577 23 + 636262 GATGTGTAGTCCCATGCAATTCT -s Anc0.Anc0refChr3 104659 23 + 222631 TATGCCTATTCCCATTCAATTGT -s Anc1.Anc1refChr6 138245 23 + 197743 TATGCCTATTCCCATTCAATTGT -s Anc2.Anc2refChr1 16422 23 + 142988 TATGCCTATTCCCATTCAATTGT -s mr.mrrefChr3 42595 23 + 181027 GATGTGTAGTCCCATTCAATTCT -s simCow_chr6.simCow.chr6 472980 23 + 602619 TACGCCTATTCCCATTAAAATAG -s simDog_chr6.simDog.chr6 463280 23 + 593897 TATGCCTATTCACATTCTATTGT -s simHuman_chr6.simHuman.chr6 470123 23 + 601863 TATTCCTATACCCATTCAAGTTT -s simRat_chr6.simRat.chr6 496410 21 + 647215 --CGTGTAGTCCCATTCAATTCT - -a -s simMouse_chr6.simMouse.chr6 488600 11 + 636262 AGGGGCACTTC -s Anc0.Anc0refChr3 104687 11 + 222631 GTTAGCATTTC -s Anc1.Anc1refChr6 138273 11 + 197743 GTTAGCATTTC -s Anc2.Anc2refChr1 16450 11 + 142988 GTTAGCATTTA -s mr.mrrefChr3 42618 11 + 181027 AGTGGCATTTC -s simCow_chr6.simCow.chr6 473008 11 + 602619 GTTGGCATTTA -s simDog_chr6.simDog.chr6 463308 9 + 593897 GCCA--ATTTA -s simHuman_chr6.simHuman.chr6 470151 11 + 601863 GTTAGCATTTC -s simRat_chr6.simRat.chr6 496431 11 + 647215 AGTGGCATTTC - -a -s simMouse_chr6.simMouse.chr6 488611 13 + 636262 TGGTCTTGCAGCT -s Anc0.Anc0refChr3 104698 13 + 222631 TGGTTTCACTGTT -s Anc1.Anc1refChr6 138284 13 + 197743 TGGTTTCACTGTT -s Anc2.Anc2refChr1 16461 13 + 142988 TTGTTTCACTATC -s mr.mrrefChr3 42629 13 + 181027 TGGTCTAGCAGCT -s simCow_chr6.simCow.chr6 473019 13 + 602619 CAGTTTCACTATC -s simDog_chr6.simDog.chr6 463317 13 + 593897 TTGTGTTACTATC -s simHuman_chr6.simHuman.chr6 470173 13 + 601863 TGGTTTCACTGTT -s simRat_chr6.simRat.chr6 496442 13 + 647215 GGATCTAGCAGCT - -a -s simMouse_chr6.simMouse.chr6 488624 26 + 636262 CTTGGCATTTGTAAGCAATCTCTGGC -s Anc0.Anc0refChr3 104712 26 + 222631 CCTGTTATTTATAAGGAGGCTCTGGT -s Anc1.Anc1refChr6 138298 26 + 197743 CCTGTTATTTATAAGGAGGCTCTGGT -s Anc2.Anc2refChr1 16475 26 + 142988 CCTGTTATTTATAAGGAGGCTCTGGT -s mr.mrrefChr3 42642 26 + 181027 CCTGGTATTTGTAAGCAAGCTCTGGC -s simCow_chr6.simCow.chr6 473033 26 + 602619 GCTCGTATTTATAAGGAGGCTCTAGT -s simDog_chr6.simDog.chr6 463331 26 + 593897 CTTGTTAGTTATAGGGGGGCTCTGGC -s simHuman_chr6.simHuman.chr6 470187 26 + 601863 CCTGTTATTTATAAGGAGGCTTTTGT -s simRat_chr6.simRat.chr6 496455 26 + 647215 CCTGGTATTTTTAAGCAAGCCCTGGC - -a -s simMouse_chr6.simMouse.chr6 488650 40 + 636262 CTCAGGTAACTATAGTATTTATTACATACCAGTATTAGAC -s Anc0.Anc0refChr3 104758 35 + 222631 CTCAGGTTACTATTGTATTCCTTAGGTACCACTAT----- -s Anc1.Anc1refChr6 138344 40 + 197743 CTCAGGTTACTATTGTATTCCTTAGGTACCACTATTAGAC -s Anc2.Anc2refChr1 16521 35 + 142988 CTCAAGTTACAAATGTATTCCTTAGGTACCACTAT----- -s mr.mrrefChr3 42668 40 + 181027 CTCAGGTAACTATAGTATTTATTACGTACCAGTATTAGAC -s simCow_chr6.simCow.chr6 473071 32 + 602619 GTCATGAGAC---TGTATTCCTTGGGCACCACTAT----- -s simDog_chr6.simDog.chr6 463377 35 + 593897 CTCCAGTTCCAAATGTATTCCTTAGGTCCCACTAT----- -s simHuman_chr6.simHuman.chr6 470233 40 + 601863 CTCAGGCTACTATTGAGTTCGTTAGGTACCACTATTAGAC -s simRat_chr6.simRat.chr6 496481 39 + 647215 CTCAGGTCATTACAGTATTTATTAAGT-CCAGTATTAGAC - -a -s simMouse_chr6.simMouse.chr6 488690 19 + 636262 AATGAGTTTAAGTTGCGCT -s Anc0.Anc0refChr3 104795 19 + 222631 AATGAGTTCAAGTTGCTCT -s Anc1.Anc1refChr6 138386 19 + 197743 AATGAGTTCAAGTTGCTCT -s Anc2.Anc2refChr1 16558 19 + 142988 AATGAGTTCAAGTTGCTCT -s mr.mrrefChr3 42708 19 + 181027 AATGAGTTCAAGTTGCGCT -s simCow_chr6.simCow.chr6 473105 19 + 602619 ACTGAGTTCAAGTTGCTCT -s simDog_chr6.simDog.chr6 463414 19 + 593897 GACTATTTGATATTGCCTT -s simHuman_chr6.simHuman.chr6 470275 19 + 601863 AATGCGTTCAAGTTGCTCC -s simRat_chr6.simRat.chr6 496520 19 + 647215 AATGAGTTCAAGTTGTACT - -a -s simMouse_chr6.simMouse.chr6 488709 9 + 636262 AGTGAGTGC -s Anc0.Anc0refChr3 104816 9 + 222631 AGCAAGTGC -s Anc1.Anc1refChr6 138407 9 + 197743 AGCAAGTGC -s Anc2.Anc2refChr1 16579 9 + 142988 AGCAAGTGC -s mr.mrrefChr3 42727 9 + 181027 AGTAAGTGC -s simCow_chr6.simCow.chr6 473126 8 + 602619 A-CAAGTAC -s simDog_chr6.simDog.chr6 463435 9 + 593897 AGCAAGTGC -s simHuman_chr6.simHuman.chr6 470296 9 + 601863 AGCAACTGC -s simRat_chr6.simRat.chr6 496539 9 + 647215 AGTAAATGC - -a -s simMouse_chr6.simMouse.chr6 488718 1 + 636262 C -s Anc0.Anc0refChr3 104825 1 + 222631 T -s Anc1.Anc1refChr6 138416 1 + 197743 T -s Anc2.Anc2refChr1 16645 1 + 142988 T -s mr.mrrefChr3 42736 1 + 181027 C -s simCow_chr6.simCow.chr6 473192 1 + 602619 T -s simDog_chr6.simDog.chr6 463502 1 + 593897 T -s simHuman_chr6.simHuman.chr6 470305 1 + 601863 T -s simRat_chr6.simRat.chr6 496548 1 + 647215 C - -a -s simMouse_chr6.simMouse.chr6 488719 13 + 636262 TTGGCATTTTACT -s Anc0.Anc0refChr3 104827 12 + 222631 TTGACACTTTA-G -s Anc1.Anc1refChr6 138418 12 + 197743 TTGACACTTTA-G -s Anc2.Anc2refChr1 16647 12 + 142988 TTAACACCTTA-G -s mr.mrrefChr3 42737 13 + 181027 TTGGCATTTTACT -s simCow_chr6.simCow.chr6 473194 1 + 602619 C------------ -s simDog_chr6.simDog.chr6 463504 12 + 593897 TTAACACCTTA-G -s simHuman_chr6.simHuman.chr6 470307 12 + 601863 TAGACACTTTA-G -s simRat_chr6.simRat.chr6 496549 13 + 647215 TTGGCATTTTATA - -a -s simMouse_chr6.simMouse.chr6 488732 12 + 636262 AGTTACCACTGC -s Anc0.Anc0refChr3 104839 8 + 222631 TGTT---ACTG- -s Anc1.Anc1refChr6 138430 11 + 197743 TGTTACCACTG- -s Anc2.Anc2refChr1 16659 8 + 142988 TGTT---AATG- -s mr.mrrefChr3 42750 12 + 181027 TGTTACCACTGC -s simDog_chr6.simDog.chr6 463517 8 + 593897 TGTT---AATG- -s simHuman_chr6.simHuman.chr6 470319 11 + 601863 TGTTACCACTA- -s simRat_chr6.simRat.chr6 496562 12 + 647215 TGTTTCCACTGC - -a -s simMouse_chr6.simMouse.chr6 488744 23 + 636262 TGGGTGGATAACAAGCGCCACCC -s Anc0.Anc0refChr3 104847 23 + 222631 TTGATTAAGAAGAACCGCCACAC -s Anc1.Anc1refChr6 138441 23 + 197743 TTGATTAAGAAGAACCGCCACAC -s Anc2.Anc2refChr1 16667 23 + 142988 TTGATTAAGAAGAACCACCACAA -s mr.mrrefChr3 42762 23 + 181027 TGGATGGATAACAAGCGCCACCC -s simCow_chr6.simCow.chr6 473195 17 + 602619 ---ATGAAG--TAACCACCAC-A -s simDog_chr6.simDog.chr6 463525 23 + 593897 TTGCTTACAAAGTACCATCACAA -s simHuman_chr6.simHuman.chr6 470330 23 + 601863 TCAATTAAGATGAACTGCCACAC -s simRat_chr6.simRat.chr6 496578 23 + 647215 TGGATAGATAGCAAGCACCACCC - -a -s simMouse_chr6.simMouse.chr6 488767 64 + 636262 TTGTAAGTTGTTTTAGTTTTTTTCTCTTAATGGATGGAGCGCTGGTGTTAAGTGCTTTGGATGT -s Anc0.Anc0refChr3 104870 51 + 222631 TAGCAAATTTTTTTACTTTTTT--GCGTAGTGGATGGGTCAC--------AGTGTTTTGGA--- -s Anc1.Anc1refChr6 138464 54 + 197743 TAGCAAATTTTTTTACTTTTTT--GCGTAGTGGATGGGTCAC--------AGTGTTTTGGATAA -s Anc2.Anc2refChr1 16690 51 + 142988 TAGCAAATTTTCTTACTTTTTT--GTGTAGTAGATGGGTCAC--------AGTGTTTTGGA--- -s mr.mrrefChr3 42785 62 + 181027 TTGTAAATTGTTTTAGTTTTTTTCTCTTAGTGGATGGAGCGCTGGTGT--AGTGCTTTGGATGT -s simCow_chr6.simCow.chr6 473212 51 + 602619 TAGCAAATTTTCTGACTTTTTT--GTGTACTAGATGAGTAAC--------AGTGTTTTGGG--- -s simDog_chr6.simDog.chr6 463548 51 + 593897 TAGCAAATTTTCCTACTTTTAT--ATGTAGCAGGTGGATCAC--------AATCTTTTGGA--- -s simHuman_chr6.simHuman.chr6 470353 54 + 601863 TAACAAACTTTTTTGATTTCTT--GCATAGTGCATGGGTCAC--------AGTGTTTTGGATAA -s simRat_chr6.simRat.chr6 496603 62 + 647215 TTGTAAATTGTTTTAGTTTTTTTCTCTTAGTGGATGGAGTGCTGGTGT--AGTGCTTTGGCTGT - -a -s simMouse_chr6.simMouse.chr6 488831 27 + 636262 CATGTTAATCCACTCCACCCTCCAAAG -s Anc0.Anc0refChr3 104921 22 + 222631 -----TAATCCACTCCACCTTTCAAGG -s Anc1.Anc1refChr6 138518 27 + 197743 CACATTAATCCACTCCACCTTTCAAGG -s Anc2.Anc2refChr1 16741 22 + 142988 -----TAATCCACTCCACCTTTCAAGG -s mr.mrrefChr3 42847 27 + 181027 CATGTTAATCCACTCCACCCTCCAAGG -s simCow_chr6.simCow.chr6 473263 22 + 602619 -----TGATCCACTCGACCTTTTAGGG -s simDog_chr6.simDog.chr6 463599 21 + 593897 -----TA-CGTACTCCACCTTTCAAGG -s simHuman_chr6.simHuman.chr6 470407 27 + 601863 CACATCAGTCCACTCCACTTTTCTAGG -s simRat_chr6.simRat.chr6 496670 27 + 647215 CATGTTAATCCACTCGACCCTGCAAGG - -a -s simMouse_chr6.simMouse.chr6 488858 1 + 636262 C -s Anc0.Anc0refChr3 104944 1 + 222631 C -s Anc1.Anc1refChr6 138546 1 + 197743 C -s Anc2.Anc2refChr1 16764 1 + 142988 C -s mr.mrrefChr3 42875 1 + 181027 C -s simCow_chr6.simCow.chr6 473286 1 + 602619 C -s simDog_chr6.simDog.chr6 463621 1 + 593897 C -s simHuman_chr6.simHuman.chr6 470435 1 + 601863 C -s simRat_chr6.simRat.chr6 496698 1 + 647215 C - -a -s simMouse_chr6.simMouse.chr6 488859 12 + 636262 AATATTGCAGTC -s Anc0.Anc0refChr3 104946 12 + 222631 AATACTTGAGTG -s Anc1.Anc1refChr6 138548 12 + 197743 AATACTTGAGTG -s Anc2.Anc2refChr1 16766 12 + 142988 AATACTTGAGTG -s mr.mrrefChr3 42876 12 + 181027 AATATTGCAGTC -s simCow_chr6.simCow.chr6 473288 12 + 602619 AATACTTCAGCC -s simDog_chr6.simDog.chr6 463623 12 + 593897 CATACTTGAGTG -s simHuman_chr6.simHuman.chr6 470437 12 + 601863 AAGACTTTAGTA -s simRat_chr6.simRat.chr6 496699 12 + 647215 AATATTGCAGTC - -a -s simMouse_chr6.simMouse.chr6 488871 11 + 636262 ACCTGGTTTCA -s Anc0.Anc0refChr3 104958 11 + 222631 ACCTGGGTTCA -s Anc1.Anc1refChr6 138560 11 + 197743 ACCTGGGTTCA -s Anc2.Anc2refChr1 16778 11 + 142988 ACCTGAGTTGA -s mr.mrrefChr3 42888 11 + 181027 ACCTGGTTTCA -s simCow_chr6.simCow.chr6 473300 2 + 602619 AC--------- -s simDog_chr6.simDog.chr6 463637 11 + 593897 ACCTGAGTTGA -s simHuman_chr6.simHuman.chr6 470449 11 + 601863 ACTTGGGATCA -s simRat_chr6.simRat.chr6 496711 11 + 647215 ACCTGATTTTG - -a -s simMouse_chr6.simMouse.chr6 488882 45 + 636262 CACACATGCTAGTGGCTGACTCCTAAATGGGCCGGTTCTTCAACC -s Anc0.Anc0refChr3 104969 44 + 222631 CACTAATATT-TTTGTTTCCTCCCAAACATGTTTGTTTTTTAATC -s Anc1.Anc1refChr6 138571 45 + 197743 CACTAATATTATTTGTTTCCTCCCAAACATGTTTGTTTTTTAATC -s Anc2.Anc2refChr1 16789 44 + 142988 CGCTAGTATT-TTTGTTTCTTCCCAGATATGTTTGTTTTTTAACC -s mr.mrrefChr3 42899 45 + 181027 CACACATGCTAGTGGTTTACTCCTAAACAGGCCTGTTCTTCAATC -s simCow_chr6.simCow.chr6 473302 42 + 602619 --CCAGTCTC-TTTGGTTCTTCCCAGAGATGTTTGGTTTTTAACC -s simDog_chr6.simDog.chr6 463648 44 + 593897 CGCTAGTATT-TTTGTTTCTTCCCAGATATGTTTGTTCTTTAACC -s simHuman_chr6.simHuman.chr6 470461 45 + 601863 CACTAATATTATTTGTTTCCTCCCAAACATGTTTGTTTTTTACTC -s simRat_chr6.simRat.chr6 496722 45 + 647215 CACACATGCTAGTGGTTTACTCCTAAACAGGCCTGTTCTTGAATC - -a -s simMouse_chr6.simMouse.chr6 488927 2 + 636262 AT -s Anc0.Anc0refChr3 105013 2 + 222631 AC -s Anc1.Anc1refChr6 138616 2 + 197743 AC -s Anc2.Anc2refChr1 16833 2 + 142988 AC -s mr.mrrefChr3 42944 2 + 181027 AT -s simCow_chr6.simCow.chr6 473345 2 + 602619 AC -s simDog_chr6.simDog.chr6 463692 2 + 593897 AT -s simHuman_chr6.simHuman.chr6 470506 2 + 601863 AC -s simRat_chr6.simRat.chr6 496767 2 + 647215 AT - -a -s simMouse_chr6.simMouse.chr6 488929 37 + 636262 TAGCTCTTGCAGCTTACTCCTGCAGCTTAAGCCTAGA -s Anc0.Anc0refChr3 105015 24 + 222631 TAGCTCTATCAGCTAA-------------AGGCCCTA -s Anc1.Anc1refChr6 138618 24 + 197743 TAGCTCTATCAGCTAA-------------AGGCCCTA -s Anc2.Anc2refChr1 16835 24 + 142988 GAGCTCTATCAGCTAA-------------AGGGCCTA -s mr.mrrefChr3 42946 24 + 181027 TAGCTCTTGCAGCTTA-------------AGCCCAGA -s simCow_chr6.simCow.chr6 473347 24 + 602619 AAGGTCTATCAGCTTA-------------AGGGTTGA -s simDog_chr6.simDog.chr6 463695 24 + 593897 GGGCTCTATCAGCTAA-------------AGGGCCTA -s simHuman_chr6.simHuman.chr6 470508 24 + 601863 TAGCTCTATCAGCTAA-------------GGACCCTA -s simRat_chr6.simRat.chr6 496769 24 + 647215 TAGCTCTTGCTGCGTA-------------AGGCCAGA - -a -s simMouse_chr6.simMouse.chr6 488966 6 + 636262 GTTCAG -s Anc0.Anc0refChr3 105039 6 + 222631 GATTGG -s Anc1.Anc1refChr6 138642 6 + 197743 GATTGG -s Anc2.Anc2refChr1 16859 6 + 142988 GATTGG -s mr.mrrefChr3 42970 6 + 181027 GTTTAG -s simCow_chr6.simCow.chr6 473371 6 + 602619 GACTGG -s simDog_chr6.simDog.chr6 463723 6 + 593897 GATGGG -s simHuman_chr6.simHuman.chr6 470532 6 + 601863 AATTGG -s simRat_chr6.simRat.chr6 496793 6 + 647215 GTTTAG - -a -s simMouse_chr6.simMouse.chr6 488972 21 + 636262 CTAATTTGAGATTGTACTCCT -s Anc0.Anc0refChr3 105047 20 + 222631 TTCATTTGAGATTGTGCTC-T -s Anc1.Anc1refChr6 138650 20 + 197743 TTCATTTGAGATTGTGCTC-T -s Anc2.Anc2refChr1 16873 20 + 142988 TTCAGTTGAGATTGTGCTC-T -s mr.mrrefChr3 42978 20 + 181027 CTCATTTGAGATTGTGCTC-T -s simCow_chr6.simCow.chr6 473385 16 + 602619 TTC---CAAGAGTGTG-TC-T -s simDog_chr6.simDog.chr6 463737 20 + 593897 TTCAGTTGCGGTTGTGCTC-T -s simHuman_chr6.simHuman.chr6 470540 20 + 601863 TGCATCTGAGATTGTGCTC-T -s simRat_chr6.simRat.chr6 496801 20 + 647215 CTCATTTGATATTGTGCTT-T - -a -s simMouse_chr6.simMouse.chr6 488993 5 + 636262 CAAAC -s Anc0.Anc0refChr3 105067 5 + 222631 CAGCC -s Anc1.Anc1refChr6 138670 5 + 197743 CAGCC -s Anc2.Anc2refChr1 16895 5 + 142988 CAGCC -s mr.mrrefChr3 42998 5 + 181027 CAAAC -s simCow_chr6.simCow.chr6 473403 5 + 602619 CAGCC -s simDog_chr6.simDog.chr6 463759 5 + 593897 CAGCC -s simRat_chr6.simRat.chr6 496821 5 + 647215 CAAAC - -a -s simMouse_chr6.simMouse.chr6 488998 77 + 636262 TCATATAAGGTTGAAGCTCATGTACACTGGGAGGCTCCATACTCTACATACTCTGCCTGTCTTATTATAGCCTGTTA -s Anc0.Anc0refChr3 105072 14 + 222631 TTCCATTATGTCA---------------------------------------------------------------A -s Anc1.Anc1refChr6 138675 14 + 197743 TTCCATTATGTCA---------------------------------------------------------------A -s Anc2.Anc2refChr1 16900 14 + 142988 TTCTACTGTGGCA---------------------------------------------------------------A -s mr.mrrefChr3 43003 68 + 181027 TCACATAAGGTCAAAGCTCATGTACACTGGGAGGCTCCATACTCTAC---------CTGTCTTATTATAGCCTGTTA -s simDog_chr6.simDog.chr6 463834 14 + 593897 TTCTACTGTGGCA---------------------------------------------------------------A -s simHuman_chr6.simHuman.chr6 470560 14 + 601863 TTCCATCAAGTCA---------------------------------------------------------------A -s simRat_chr6.simRat.chr6 496826 68 + 647215 TCACATAAGCTCAAAGCTCATGTACACTGGGAGGTTCCGTACTCTAC---------CTGTCTTATCATAGCCTGATT - -a -s simMouse_chr6.simMouse.chr6 489075 2 + 636262 AA -s Anc0.Anc0refChr3 105086 2 + 222631 AA -s Anc1.Anc1refChr6 138689 2 + 197743 AA -s Anc2.Anc2refChr1 16914 2 + 142988 AA -s mr.mrrefChr3 43071 2 + 181027 AA -s simDog_chr6.simDog.chr6 463848 2 + 593897 AA -s simHuman_chr6.simHuman.chr6 470574 2 + 601863 AA -s simRat_chr6.simRat.chr6 496898 2 + 647215 AA - -a -s simMouse_chr6.simMouse.chr6 489077 4 + 636262 GCAT -s Anc0.Anc0refChr3 105088 4 + 222631 GTAT -s Anc1.Anc1refChr6 138691 4 + 197743 GTAT -s Anc2.Anc2refChr1 16916 4 + 142988 GTTT -s mr.mrrefChr3 43073 4 + 181027 GCAT -s simDog_chr6.simDog.chr6 463853 4 + 593897 GTTT -s simHuman_chr6.simHuman.chr6 470576 4 + 601863 GGAT -s simRat_chr6.simRat.chr6 496900 4 + 647215 GCAT - -a -s simMouse_chr6.simMouse.chr6 489081 107 + 636262 ATTTATACTGTGACATGACTCTCTATTCAACATAGTTAAATTGTGTTTTTTCCTGGAGTGAGGCCAAGGTATAAGGTAGAGTATTTAAAGAACTGCATTTAAACTTG -s Anc0.Anc0refChr3 105093 92 + 222631 TCCTACAC----ACATG------TATTTTACA---TTAA-TTTTAATTATTTCTGGAGTGAAGCCAGGGTATAAGGGAAAGTATTT-ATGAGCTGCATTTAATCTTA -s Anc1.Anc1refChr6 138696 99 + 197743 TCCTACACTGTGACATG------TATTTTACATGGTTAA-TTTTAATTATTTCTGGAGTGAAGCCAGGGTATAAGGGAAAGTATTT-ATGAGCTGCATTTAATCTTA -s Anc2.Anc2refChr1 16921 92 + 142988 TCCTACAC----ATAGA------TAATTTACA---TTAT-TTTTCATTATTTCTGGAGTGAGGCCAGGGCATAAGGGAAAGTATTT-ATGAGCTACATTAAATCTTA -s mr.mrrefChr3 43078 106 + 181027 ATTTATACTGTGACATGACTCTCTATTCAACATAGTTAA-TTGTATTTTTTCCTGGAGTGAAGCCAGGGTATAAGGTAGAGTATTTAAAGAACTGCATTTAAACTTG -s simCow_chr6.simCow.chr6 473408 40 + 602619 ------------------------------------------------------------------GGGCATAAGGGAAAGTATTT-ATAAGCCACATTCTATCTTA -s simDog_chr6.simDog.chr6 463858 92 + 593897 TCCTACAC----ATAGA------TAATTTACA---TTAT-TTTTCATTATTTCTGGAGTGAGGCCAGGGCACAAGGGAAAGCATTT-GTGAGCTACATTAAATCTTA -s simHuman_chr6.simHuman.chr6 470581 99 + 601863 GCCTACACTGTGACATG------TGTTTGACATGGACAA-TTATAGTTCTTTCTGGGGTGAAGTGAGGGTGTAAGGGAATGTATTC-ATGAGTTGCACATAGCCTTA -s simRat_chr6.simRat.chr6 496905 106 + 647215 ATTGTTATTCTGACATGACGCCCTATTAAAGATAGGTAA-TCGTATTTATTCCTGGACTGAAGCCAGGGTATTAGGTAGAGTATTTAAAGAACTGCATTTAAACTTG - -a -s simMouse_chr6.simMouse.chr6 489188 6 + 636262 CAGATT -s Anc0.Anc0refChr3 105193 6 + 222631 CAGAAA -s Anc1.Anc1refChr6 138803 6 + 197743 CAGAAA -s Anc2.Anc2refChr1 17021 6 + 142988 CAGAAA -s mr.mrrefChr3 43192 6 + 181027 CAGATT -s simCow_chr6.simCow.chr6 473456 6 + 602619 TAGAAA -s simDog_chr6.simDog.chr6 463958 6 + 593897 CAGAAA -s simHuman_chr6.simHuman.chr6 470688 6 + 601863 CAGACA -s simRat_chr6.simRat.chr6 497019 6 + 647215 CAGATG - -a -s simMouse_chr6.simMouse.chr6 489194 17 + 636262 TTGTGGCATCGGGTGAA -s Anc0.Anc0refChr3 105204 16 + 222631 ATGCAAC-AGAGGCAAA -s Anc1.Anc1refChr6 138814 16 + 197743 ATGCAAC-AGAGGCAAA -s Anc2.Anc2refChr1 17032 16 + 142988 ATGCAAC-AGAGGCAAA -s mr.mrrefChr3 43203 16 + 181027 TTGTGAC-TGAGGCAAA -s simCow_chr6.simCow.chr6 473467 16 + 602619 TTACAAC-AAATACAAA -s simDog_chr6.simDog.chr6 463969 16 + 593897 ATGCTAC-CGAGGTAAA -s simHuman_chr6.simHuman.chr6 470699 16 + 601863 GTGCAAC-AGAGGCAAA -s simRat_chr6.simRat.chr6 497030 16 + 647215 TTGTGAA-TGAGACAAA - -a -s simMouse_chr6.simMouse.chr6 489211 5 + 636262 CTCTC -s Anc0.Anc0refChr3 105220 5 + 222631 CTCTC -s Anc1.Anc1refChr6 138830 5 + 197743 CTCTC -s Anc2.Anc2refChr1 17048 5 + 142988 CTCTC -s mr.mrrefChr3 43219 5 + 181027 CTCTC -s simCow_chr6.simCow.chr6 473483 5 + 602619 CTCTC -s simDog_chr6.simDog.chr6 463986 5 + 593897 CTCTC -s simHuman_chr6.simHuman.chr6 470715 5 + 601863 CGCTC -s simRat_chr6.simRat.chr6 497046 5 + 647215 CTCTC - -a -s simMouse_chr6.simMouse.chr6 489216 50 + 636262 CCCATGGGCACTAAGCTTCTATTGATTATCATGCCTCTATCTTATCTACT -s Anc0.Anc0refChr3 105227 47 + 222631 TCCGTTGTCACTGAACCTCTATCAATTGTAGT---TCCATCTTATCTAGT -s Anc1.Anc1refChr6 138837 47 + 197743 TCCGTTGTCACTGAACCTCTATCAATTGTAGT---TCCATCTTATCTAGT -s Anc2.Anc2refChr1 17055 47 + 142988 TCTGTTGTCACTGAACCTCTATCAGTTGTAGT---TCCATCTTATCTAGT -s mr.mrrefChr3 43224 50 + 181027 CCCATGGGCACTGAGCCTCTATTGATTGTCATGCCTCCATCTTATCTACT -s simCow_chr6.simCow.chr6 473490 47 + 602619 TCTGTTGATACCCACTCACTATTAGTTGTAGT---TCCACCCTAACTAGT -s simDog_chr6.simDog.chr6 463993 47 + 593897 TTTGGTGTCACTGGACTTCTATCAGTTGAGGT---TCCATCTTATCTAGT -s simHuman_chr6.simHuman.chr6 470722 47 + 601863 TCCGTTGTGACTGATCCTCAATCCATTGTAGT---TCCAGCTTATCTAGT -s simRat_chr6.simRat.chr6 497051 50 + 647215 CCCATGGGCACTGAGCCTCTACTGATTGTCATGCCTCCATCTTATCAACT - -a -s simMouse_chr6.simMouse.chr6 489266 18 + 636262 TCCTTCTCAAACCTTGCA -s Anc0.Anc0refChr3 105288 18 + 222631 TGCTTTTTGAACTGCATG -s Anc1.Anc1refChr6 138898 18 + 197743 TGCTTTTTGAACTGCATG -s Anc2.Anc2refChr1 17116 18 + 142988 TGTTTTTTGAACTGCATG -s mr.mrrefChr3 43274 18 + 181027 TGCTTTTCAAACTTTGTA -s simCow_chr6.simCow.chr6 473551 18 + 602619 TGTGTTTTGAACTGCATA -s simDog_chr6.simDog.chr6 464054 18 + 593897 CGTTTCTTGAACTGCATG -s simHuman_chr6.simHuman.chr6 470783 18 + 601863 TGCTTTTTGAATTGCATG -s simRat_chr6.simRat.chr6 497101 18 + 647215 TGCTTTTCAAACTTTGTA - -a -s simMouse_chr6.simMouse.chr6 489284 35 + 636262 GGTTTGCCCAGATATAGCAGGGAGATATGTTTAAA -s Anc0.Anc0refChr3 105306 35 + 222631 ATTTTCCCCAAATATAGCAGGGAGATATGGTTGAA -s Anc1.Anc1refChr6 138916 35 + 197743 ATTTTCCCCAAATATAGCAGGGAGATATGGTTGAA -s Anc2.Anc2refChr1 17134 35 + 142988 ATTTTCCCCAAATATAGGAAGGAGATATGGTTGAA -s mr.mrrefChr3 43292 35 + 181027 GGTTTGCCCAGATATAGCAGGGAGATATGTTTAAA -s simCow_chr6.simCow.chr6 473570 35 + 602619 ATTTTGCCCAAATATAGAAAGGAGATATGGTTGAA -s simDog_chr6.simDog.chr6 464072 35 + 593897 ATTTTCCCCAAGTAGATGCAGGAGATATGGTTGAA -s simHuman_chr6.simHuman.chr6 470801 34 + 601863 TATTTATGCAAATAT-GCAGGGAGATATGGTTTAA -s simRat_chr6.simRat.chr6 497119 34 + 647215 GGTTTGCC-ACATATAGCAGGGAGATATGTTTGAA - -a -s simMouse_chr6.simMouse.chr6 489319 3 + 636262 TGG -s Anc0.Anc0refChr3 105346 3 + 222631 TGG -s Anc1.Anc1refChr6 138956 3 + 197743 TGG -s Anc2.Anc2refChr1 17174 3 + 142988 TGA -s mr.mrrefChr3 43327 3 + 181027 TGG -s simCow_chr6.simCow.chr6 473610 3 + 602619 TGC -s simDog_chr6.simDog.chr6 464113 3 + 593897 TGA -s simHuman_chr6.simHuman.chr6 470840 3 + 601863 TGG -s simRat_chr6.simRat.chr6 497153 3 + 647215 TGG - -a -s simMouse_chr6.simMouse.chr6 489322 61 + 636262 CATTGTAGAGATAGTACCTCAACAGTGCCCACTCATTCAGGGGTTCGCTTATGCACTTGAG -s Anc0.Anc0refChr3 105350 61 + 222631 TATTGTAGAGATAGTCCCTCAACTGTGCTGGGTAATTCAGGGTTTAACTTATGCACTTGAG -s Anc1.Anc1refChr6 138960 61 + 197743 TATTGTAGAGATAGTCCCTCAACTGTGCTGGGTAATTCAGGGTTTAACTTATGCACTTGAG -s Anc2.Anc2refChr1 17178 61 + 142988 TATTGGAGAGAAGGTCCCTCAACTGTGCTGGGTAATTCAAGGTTTAACTTATGCACTTGAG -s mr.mrrefChr3 43331 61 + 181027 CATTGTAGAGATAGTACCTCAACAGTGCCCGCTCATTCAGGGTTTAGCTTATGCACTTGAG -s simCow_chr6.simCow.chr6 473614 61 + 602619 TGCTGATGAGAAGGTACCTTAACTGTGCTGGGTGATTTGAGCTGTAACCTACTCACTTGAG -s simDog_chr6.simDog.chr6 464117 58 + 593897 TATTGGAGAG--GGTCCCTCAACAGTGCTGTGTAATTCAAGGCTTAGCTTATGTACTTG-G -s simHuman_chr6.simHuman.chr6 470844 61 + 601863 GATTGTAGAGATAGTGTGTCAACTATGCTGGGTAATTCAGGGTTTAACTTGTGCACTTGAG -s simRat_chr6.simRat.chr6 497157 61 + 647215 TATTGTAGAGATAGTCCCTCACCAGTGCCCGTTCATTCAAGGTCTAGCTTATGCACTTCAG - -a -s simMouse_chr6.simMouse.chr6 489383 31 + 636262 GCTGTATTACATTTCTCCCTCTTGTACCTTC -s Anc0.Anc0refChr3 105411 28 + 222631 GCTGGATTACATCTCTACCTCTT---CTCTT -s Anc1.Anc1refChr6 139021 28 + 197743 GCTGGATTACATCTCTACCTCTT---CTCTT -s Anc2.Anc2refChr1 17239 28 + 142988 GCTGGATTACATCTCTACCTCTT---CTCTT -s mr.mrrefChr3 43392 31 + 181027 GCTGTATTACATTTCTCCCTCTTGTACCTTC -s simCow_chr6.simCow.chr6 473686 28 + 602619 GATATATTATGTCTCTACCTCTT---CTCTT -s simDog_chr6.simDog.chr6 464175 28 + 593897 GCCGGATTACATCTCTACCTCTT---CTCTT -s simHuman_chr6.simHuman.chr6 470905 28 + 601863 GCTGGATAACATCTCCACGTCTT---CAATT -s simRat_chr6.simRat.chr6 497218 30 + 647215 ACTGCATTAGATTTCTCC-TCTTGTCCCTTC - -a -s simMouse_chr6.simMouse.chr6 489414 17 + 636262 TTTCCAGTCACCAGCAG -s Anc0.Anc0refChr3 105441 16 + 222631 TT-CCAAGCACCAATAA -s Anc1.Anc1refChr6 139051 16 + 197743 TT-CCAAGCACCAATAA -s Anc2.Anc2refChr1 17269 16 + 142988 TT-CCAGGCGCCAGTAA -s mr.mrrefChr3 43425 16 + 181027 TT-CCAATCACCAACAA -s simCow_chr6.simCow.chr6 473716 16 + 602619 TT-CCGGGTGCCATTAA -s simDog_chr6.simDog.chr6 464205 16 + 593897 TT-CTAGGCGTCAGTGC -s simHuman_chr6.simHuman.chr6 470935 16 + 601863 TT-TCCAACACCAATAA -s simRat_chr6.simRat.chr6 497250 16 + 647215 TT-CCAATCACCAACAA - -a -s simMouse_chr6.simMouse.chr6 489431 15 + 636262 CCCCATTGCGTTTAT -s Anc0.Anc0refChr3 105471 15 + 222631 TCCGATTACTTTAAC -s Anc1.Anc1refChr6 139081 15 + 197743 TCCGATTACTTTAAC -s Anc2.Anc2refChr1 17299 15 + 142988 TCTGATTACTTTAAC -s mr.mrrefChr3 43441 15 + 181027 TCCCATTGCGTTTAT -s simCow_chr6.simCow.chr6 473746 15 + 602619 TCTAATTACTGAAAT -s simDog_chr6.simDog.chr6 464235 15 + 593897 TTTGATTACTTTGCC -s simHuman_chr6.simHuman.chr6 470965 15 + 601863 TCCGATTACTTTAAC -s simRat_chr6.simRat.chr6 497266 15 + 647215 TCAAATTGCGTTTAT - -a -s simMouse_chr6.simMouse.chr6 489446 5 + 636262 CACCC -s Anc0.Anc0refChr3 105486 5 + 222631 TAATG -s Anc1.Anc1refChr6 139096 5 + 197743 TAATG -s Anc2.Anc2refChr1 17314 5 + 142988 TAAGG -s mr.mrrefChr3 43456 5 + 181027 CAATC -s simCow_chr6.simCow.chr6 473761 3 + 602619 TGA-- -s simDog_chr6.simDog.chr6 464252 5 + 593897 TAAGG -s simHuman_chr6.simHuman.chr6 470980 5 + 601863 TAATG -s simRat_chr6.simRat.chr6 497281 5 + 647215 CAATC - -a -s simMouse_chr6.simMouse.chr6 489451 71 + 636262 AATCTTGTATCCTGATGACCAGGTGGCATCCAATAAATAAAAATTAAGTGACAACAGTATACCAGTTGCTA -s Anc0.Anc0refChr3 105491 61 + 222631 ACTTTTGTATACTGATCACCA-GTAGCACATAAT----AAATATGGAGTGCTAACAATACATCAGT----- -s Anc1.Anc1refChr6 139101 67 + 197743 ACTTTTGTATACTGATCACCA-GTAGCACATAATA---AAATATGGAGTGCTAACAATACATCAGTTATTC -s Anc2.Anc2refChr1 17319 61 + 142988 ACTTCTGTATACTGACCACCA-GTAGCTCACAAT----AAATTTGGAGTGCTAACAGTACATCAGT----- -s mr.mrrefChr3 43461 71 + 181027 AATCTTGTATCCTGATGACCAGGTAGCACATAATAAATAAAAATGGAGTGACAACAATACACCAGTTGCTA -s simCow_chr6.simCow.chr6 473764 59 + 602619 --TTGCGTGTACTGACCACTA-GTAGCCCACAAC----AAATGTATAGTGCTCACAGTACAGCGAT----- -s simDog_chr6.simDog.chr6 464262 61 + 593897 ACCTCTGTATATTAACCTCCA-GTAGCTCACAAT----AGATTTGGAGTGCTAACAGTATGTCAGT----- -s simHuman_chr6.simHuman.chr6 470985 67 + 601863 ATTTTTGTCTACTGATCACCA-GTAGCACATAATA---AAATATGGAGTGCTAACAATACATCAGTTATTC -s simRat_chr6.simRat.chr6 497286 71 + 647215 AATCTTGTATTCTGATGACCAAGTAGCACATAATAGATAAAAATGGAGTGACAACAATACACCAGTTGATA - -a -s simMouse_chr6.simMouse.chr6 489522 8 + 636262 TATGTTAT -s Anc0.Anc0refChr3 105552 8 + 222631 TATATTGT -s Anc1.Anc1refChr6 139168 8 + 197743 TATATTGT -s Anc2.Anc2refChr1 17380 8 + 142988 AATATTGG -s mr.mrrefChr3 43532 8 + 181027 TATGTTGT -s simCow_chr6.simCow.chr6 473824 8 + 602619 AATATTGC -s simDog_chr6.simDog.chr6 464323 8 + 593897 AACATTGG -s simHuman_chr6.simHuman.chr6 471052 8 + 601863 TATATCGT -s simRat_chr6.simRat.chr6 497357 8 + 647215 TATGTTGT - -a -s simMouse_chr6.simMouse.chr6 489530 5 + 636262 CTCTC -s Anc0.Anc0refChr3 105562 5 + 222631 CTGTT -s Anc1.Anc1refChr6 139178 5 + 197743 CTGTT -s Anc2.Anc2refChr1 17390 5 + 142988 CTGTT -s mr.mrrefChr3 43540 5 + 181027 CTCTC -s simCow_chr6.simCow.chr6 473834 5 + 602619 CTGTT -s simDog_chr6.simDog.chr6 464333 5 + 593897 CTGTT -s simHuman_chr6.simHuman.chr6 471062 5 + 601863 CTGTT -s simRat_chr6.simRat.chr6 497365 5 + 647215 CTCCC - -a -s simMouse_chr6.simMouse.chr6 489535 59 + 636262 GAATCTAGGTACTTCGGGGAAGGACTCTTGGGCGTTAACAGTCCTGGGACACACTATTA -s Anc0.Anc0refChr3 105567 59 + 222631 GAAGCTAGGTGCTTTGGAGAGGAATTATTGGGAGTTCAAGGTCCTGGGGACCCCTGTTA -s Anc1.Anc1refChr6 139183 59 + 197743 GAAGCTAGGTGCTTTGGAGAGGAATTATTGGGAGTTCAAGGTCCTGGGGACCCCTGTTA -s Anc2.Anc2refChr1 17395 59 + 142988 GCAGCTAGGTGCTCTGTGAAAGCAATATTGGGAGTTCGAGGTCCTAGGGACACCTGTTA -s mr.mrrefChr3 43545 59 + 181027 GAATCTAGGTACTTTGGGGAAGGACTCTTGGGAGTTCACAGTCCTGGGACACACTATTA -s simCow_chr6.simCow.chr6 473839 53 + 602619 GCATCTAGGTGCTACGTGAAAGTAATACCAGGAGT------TACTACGGACAACTGTTA -s simDog_chr6.simDog.chr6 464338 57 + 593897 GCAGCTTGGTGCTCTATGAAGGCAATATTGGGAGTTCGAGGTCATAGGGA--CCAGTTA -s simHuman_chr6.simHuman.chr6 471067 59 + 601863 GAAACTATGTGCTTTGGAGAGGAATATGGAGGAGTTCAAGGTCCTGGGGACCCCTGCTA -s simRat_chr6.simRat.chr6 497371 59 + 647215 GAATCTAGGTACTTTGTGGAAGGACTCTTGGGAGTCCGCAAGCCTGGAACGTGCTATTA - -a -s simMouse_chr6.simMouse.chr6 489594 6 + 636262 GATTCT -s Anc0.Anc0refChr3 105643 6 + 222631 AAATCC -s Anc1.Anc1refChr6 139259 6 + 197743 AAATCC -s Anc2.Anc2refChr1 17492 6 + 142988 AAATCC -s mr.mrrefChr3 43604 6 + 181027 GAATCT -s simCow_chr6.simCow.chr6 473931 6 + 602619 ATCACT -s simDog_chr6.simDog.chr6 464433 6 + 593897 AAATAC -s simHuman_chr6.simHuman.chr6 471143 6 + 601863 AAATCC -s simRat_chr6.simRat.chr6 497430 6 + 647215 GAATCT - -a -s simMouse_chr6.simMouse.chr6 489600 167 + 636262 GATTCACCCAGATAATACAGGAACAGCCTGAATCATTAGTCAAGGTCTTTGGCAGTAAGGCTATGCAATCAAAGGCAGAAGCGGTAATTGAAAATTTTGTTAAAAAGTTGGAAGAAAATTACAATCCAGAATGTGGAATTGGTTCATTCCATGACTCAGATCTAGTC -s Anc0.Anc0refChr3 105649 167 + 222631 TATTCACCCAGATTATACAGGAACAGCCTGAATCACTAGTCAAAGTCTTTGGCAGTAAGGCTATGCAAACTGAAGCAAAAGCTGTTATAGACAATTTTGTTAAAAAGTTGGAAGAAAATTACAATCCAGAGTGTGGAATTGGTGAGTTCCTTGATTCAACTTCTTTC -s Anc1.Anc1refChr6 139265 167 + 197743 TATTCACCCAGATTATACAGGAACAGCCTGAATCACTAGTCAAAGTCTTTGGCAGTAAGGCTATGCAAACTGAAGCAAAAGCTGTTATAGACAATTTTGTTAAAAAGTTGGAAGAAAATTACAATCCAGAGTGTGGAATTGGTGAGTTCCTTGATTCAACTTCTTTC -s Anc2.Anc2refChr1 17498 167 + 142988 TATTCACCCAGATTATACAGGAGCAGCCTGAATCACTAGTCAAAGTCTTTGGCAGTAAGGCTATGCAAACTGAAGCAAAAGCTGTTATAGACAATTTTGTTAAAAAGTTGGAAGAAAATTACAATCCAGAGTGTGGAATTGGTGAGTTCCTTGATTCAACTTCTTAC -s mr.mrrefChr3 43610 167 + 181027 GATTCACCCAGATTATACAGGAACAGCCTGAATCATTAGTCAAGGTCTTTGGCAGTAAGGCTATGCAATCTAAAGCAAAAGCGGTAATTGAAAATTTTGTTAAAAAGTTGGAAGAAAATTACAATCCAGAATGTGGAATTGGTGCATTCCATGACTCAGATCTAGTC -s simCow_chr6.simCow.chr6 473937 167 + 602619 TATTAACTGAGATTATACAAGAGCAGCCTGAGTCACTAGTCAAAGTCTTTGGCAGTAAAGCTATGCAAACTGAAGCAAAAGCCATTATAGACAATTTTGTTAAAAAGCTGGAAGAAAACTACAATCCAGAGTGTGGAATTGGTAACTGCCTTAACACAACTTCCTAT -s simDog_chr6.simDog.chr6 464441 167 + 593897 TACTCAACCAGATTATACAGGAGCAGCCAGAATCACTAGTCAAAGTCTTTGGCAGTATGGCTATGCAAACTGAGGCAAAAGCTGTTATAGACAATTTTGTTAAAAAGTTGGAAGAAAATTACAATCCAGAATGTGGAATTGGTGAGTTCCTTGATTCAATGTCTAAC -s simHuman_chr6.simHuman.chr6 471149 167 + 601863 TATTCGCCCAGATTATACAGGAACAACCTGAATCACTAGTCAAAGTCTTTGGCAGTAAGGCTAAGCAAACTGAAGCAAAAGCTGTTATAGACAATTTCATTAAAAAGTTGGAAGAAAATTACAATCCAGAGTGTGGAATTGGTGAGTTCCTTGAGTCAACTTCTTTC -s simRat_chr6.simRat.chr6 497436 167 + 647215 GATTCACCCAGATTATACAGGAACAGCCTGAATCATTAGTCAAGGTCTTTGGCAGTAAGGCTATGCAATCTAAAGCAAAAGCCATCATTGATAATTTTGTTAAAAAGTTGGAGGAAAATTACAATCCAGAATGTGGAATTGGTGCATTCCATGACTCATATCTAGTC - -a -s simMouse_chr6.simMouse.chr6 489767 85 + 636262 CAAAGGTTATGTCAGTGTAACAGGTTTGGATGTGAATTCTGGTATGAACACAAAGGGGACCACGTACCAAGTCTTACCGTACAAA -s Anc0.Anc0refChr3 105816 74 + 222631 CAGGGTTTATCTCAGTGTAAAGTGTTTGGTTGTAAATTTTGATCCCAACGTAAAGGGGAC-----------TGTTAGTGTACAAA -s Anc1.Anc1refChr6 139432 85 + 197743 CAGGGTTTATCTCAGTGTAAAGTGTTTGGTTGTAAATTTTGATCCCAACGTAAAGGGGACTATATCCCAAGTGTTAGTGTACAAA -s Anc2.Anc2refChr1 17671 74 + 142988 CAGGGTTTATCTCAGTGTAATGTGGTTGGTTGTAAATTTTGATCCCAATGTAAAGGGGAC-----------TGTTAGTGTACAAA -s mr.mrrefChr3 43777 85 + 181027 CAAAGGTTATGTCAGTGTAAAGGGTTTGGATGTGAATTCTGGTACCAACATAAAGGGGACTACATACCAAGTGTTACTGTACAAA -s simCow_chr6.simCow.chr6 474110 73 + 602619 CTAAGTTTATCTGAGTCTAATGTGCTTGGTT-TAAGTTTTGACCCTGGTATAATGGAGAC-----------TGTTAGTCTACAAT -s simDog_chr6.simDog.chr6 464614 74 + 593897 CAGGGTATAGCTCAGTGTAATGTGGTTGGTTGTAAATTTTGATCTCAATGTAAAGGGGAC-----------TGTTAGTGTAGGAA -s simHuman_chr6.simHuman.chr6 471316 85 + 601863 CAGTTCTTTTCTCAGTGTAAAGTGTTTGGTTGTAAACTTTGATCCCATCGTAAAGGGGAATATATCCCAAGTGTCGGTATACAGA -s simRat_chr6.simRat.chr6 497603 83 + 647215 CAAAGGTT-TGTCAGCATAAAGAGTTTGGGTGTGAATTCCGTTACCAAAATAAAGGG-ACTACAGACCAGGTGATACTGTAAAAA - -a -s simMouse_chr6.simMouse.chr6 489852 1 + 636262 T -s Anc0.Anc0refChr3 105893 1 + 222631 T -s Anc1.Anc1refChr6 139520 1 + 197743 T -s Anc2.Anc2refChr1 17748 1 + 142988 T -s mr.mrrefChr3 43862 1 + 181027 T -s simCow_chr6.simCow.chr6 474186 1 + 602619 T -s simDog_chr6.simDog.chr6 464691 1 + 593897 A -s simHuman_chr6.simHuman.chr6 471404 1 + 601863 T -s simRat_chr6.simRat.chr6 497686 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 489853 5 + 636262 TCATG -s Anc0.Anc0refChr3 105894 5 + 222631 TCCTG -s Anc1.Anc1refChr6 139521 5 + 197743 TCCTG -s Anc2.Anc2refChr1 17749 5 + 142988 TCCTA -s mr.mrrefChr3 43863 5 + 181027 TCATG -s simCow_chr6.simCow.chr6 474189 5 + 602619 TCCTA -s simDog_chr6.simDog.chr6 464692 5 + 593897 TATTA -s simHuman_chr6.simHuman.chr6 471405 5 + 601863 TCCTG -s simRat_chr6.simRat.chr6 497687 5 + 647215 TCATG - -a -s simMouse_chr6.simMouse.chr6 489858 25 + 636262 TGAATCAGTCTTGTGTCAACTGTCC -s Anc0.Anc0refChr3 105952 21 + 222631 GGAAACAGCTTTACATTTA----CT -s Anc1.Anc1refChr6 139579 21 + 197743 GGAAACAGCTTTACATTTA----CT -s Anc2.Anc2refChr1 17807 21 + 142988 GGAAACAGCTTTACATTTA----CT -s mr.mrrefChr3 43921 21 + 181027 TGAATCAGTGTTGTGTCAA----CC -s simCow_chr6.simCow.chr6 474247 21 + 602619 GGAAACAGCTTTATACCAA----CT -s simDog_chr6.simDog.chr6 464750 21 + 593897 GAGAACAGCATTACATTTA----CT -s simRat_chr6.simRat.chr6 497748 21 + 647215 TGAATCAGTGTTGTGTCAA----CC - -a -s simMouse_chr6.simMouse.chr6 489883 10 + 636262 TATTAATTCC -s Anc0.Anc0refChr3 105973 10 + 222631 TATAAACTCC -s Anc1.Anc1refChr6 139600 10 + 197743 TATAAACTCC -s Anc2.Anc2refChr1 17832 10 + 142988 TATAAACTCC -s mr.mrrefChr3 43942 10 + 181027 TATTAATTCC -s simCow_chr6.simCow.chr6 474272 10 + 602619 TATTGACTTC -s simDog_chr6.simDog.chr6 464775 10 + 593897 TATAAACTCC -s simRat_chr6.simRat.chr6 497769 10 + 647215 TATTTATTCC - -a -s simMouse_chr6.simMouse.chr6 489893 7 + 636262 ATTGGTG -s Anc0.Anc0refChr3 105983 4 + 222631 AGTG--- -s Anc1.Anc1refChr6 139610 4 + 197743 AGTG--- -s Anc2.Anc2refChr1 17842 4 + 142988 AGTG--- -s mr.mrrefChr3 43952 7 + 181027 ATTGGTG -s simCow_chr6.simCow.chr6 474282 4 + 602619 ATTG--- -s simDog_chr6.simDog.chr6 464786 4 + 593897 AGTG--- -s simRat_chr6.simRat.chr6 497779 7 + 647215 ATTGGTG - -a -s simMouse_chr6.simMouse.chr6 489900 45 + 636262 TAGTTACTTGAAAGCTCTGGTGCTTGCTTAATGCCACAATATCAT -s Anc0.Anc0refChr3 105987 5 + 222631 ----------------------------------------AGCAT -s Anc1.Anc1refChr6 139614 17 + 197743 ----------------------------TGGAGCTGTAACAGCAT -s Anc2.Anc2refChr1 17846 5 + 142988 ----------------------------------------AGAAC -s mr.mrrefChr3 43959 45 + 181027 TAGTTACTTGAAAGCTCCAGTGCTTGCTTAATGCCACAATATCAT -s simCow_chr6.simCow.chr6 474286 5 + 602619 ----------------------------------------GGAAA -s simDog_chr6.simDog.chr6 464790 5 + 593897 ----------------------------------------AGAAC -s simHuman_chr6.simHuman.chr6 471461 17 + 601863 ----------------------------TGGAGCTGTAACAGCTT -s simRat_chr6.simRat.chr6 497801 45 + 647215 TAGTTATCTAAAGGCTCCAGTGCTTGCTTAATGCCACAATATCAT - -a -s simMouse_chr6.simMouse.chr6 489945 4 + 636262 ACCT -s Anc0.Anc0refChr3 105992 4 + 222631 AGCT -s Anc1.Anc1refChr6 139631 4 + 197743 AGCT -s Anc2.Anc2refChr1 17851 4 + 142988 AGCT -s mr.mrrefChr3 44004 4 + 181027 ACCT -s simCow_chr6.simCow.chr6 474306 4 + 602619 AGCT -s simHuman_chr6.simHuman.chr6 471478 4 + 601863 AACT -s simRat_chr6.simRat.chr6 497846 4 + 647215 ACCT - -a -s simMouse_chr6.simMouse.chr6 490065 17 + 636262 TACAGCACACCAGGGAA -s Anc0.Anc0refChr3 105996 17 + 222631 TACAGAGCAGCAAGGAA -s Anc1.Anc1refChr6 139635 17 + 197743 TACAGAGCAGCAAGGAA -s Anc2.Anc2refChr1 17855 17 + 142988 TACAGAGCAGTAAGGAA -s mr.mrrefChr3 44008 17 + 181027 TACAGCACATCAGGGAA -s simCow_chr6.simCow.chr6 474310 17 + 602619 TACAGAGCAGTAAGGAA -s simHuman_chr6.simHuman.chr6 471482 17 + 601863 TAGAGAGCAGCAAGGAA -s simRat_chr6.simRat.chr6 497850 17 + 647215 TACAGAACATGAGGGAA - -a -s simMouse_chr6.simMouse.chr6 490082 14 + 636262 ATGATTGTTCACTA -s Anc0.Anc0refChr3 106035 13 + 222631 ATGA-TATACACTC -s Anc1.Anc1refChr6 139674 13 + 197743 ATGA-TATACACTC -s Anc2.Anc2refChr1 17894 13 + 142988 ATGA-CATATACTC -s mr.mrrefChr3 44025 14 + 181027 ATGATTATTCACTA -s simCow_chr6.simCow.chr6 474349 13 + 602619 ATGA-CATATACTA -s simDog_chr6.simDog.chr6 464798 13 + 593897 ATTA-CATATACTC -s simHuman_chr6.simHuman.chr6 471523 13 + 601863 ATGA-TATACACTC -s simRat_chr6.simRat.chr6 497867 14 + 647215 ATGATAATTCACCA - -a -s simMouse_chr6.simMouse.chr6 490096 24 + 636262 TATTACCTTATCAGAACCACTAAG -s Anc0.Anc0refChr3 106048 10 + 222631 TCTAATACT---A----------- -s Anc1.Anc1refChr6 139687 21 + 197743 TCTAATACT---AGTACTAGTAGG -s Anc2.Anc2refChr1 17907 10 + 142988 TCTAATACC---A----------- -s mr.mrrefChr3 44039 21 + 181027 TATTATCCT---AGAACCACTAAG -s simCow_chr6.simCow.chr6 474362 10 + 602619 TCTAATACC---A----------- -s simDog_chr6.simDog.chr6 464851 10 + 593897 TCTAATATC---A----------- -s simHuman_chr6.simHuman.chr6 471536 21 + 601863 TCTAATACT---AGTACTAGTAGG -s simRat_chr6.simRat.chr6 497881 20 + 647215 TATGATCCT----GAACCACTAAG - -a -s simMouse_chr6.simMouse.chr6 490120 26 + 636262 CAATCATATCTACAAGATGAGAATTA -s Anc0.Anc0refChr3 106058 26 + 222631 CGATCACATCTACAAGATGAAAATGA -s Anc1.Anc1refChr6 139708 26 + 197743 CGATCACATCTACAAGATGAAAATGA -s Anc2.Anc2refChr1 17917 26 + 142988 CGATCACATCCACTAGATGAAACTGA -s mr.mrrefChr3 44060 26 + 181027 CAATCACATCTACAAGATGAGAATTA -s simCow_chr6.simCow.chr6 474372 26 + 602619 CGATCTCGTTCACCAGACGAAAGTGA -s simDog_chr6.simDog.chr6 464861 26 + 593897 AGATCACATCCCCTAGATGAAACTGA -s simHuman_chr6.simHuman.chr6 471558 26 + 601863 CGATCCCATCTACAAGTTGAAAATGA -s simRat_chr6.simRat.chr6 497901 26 + 647215 TAATCTCATCTGCAGTATGACAATTA - -a -s simMouse_chr6.simMouse.chr6 490146 13 + 636262 TATATATGAGAGC -s Anc0.Anc0refChr3 106084 13 + 222631 TACATTTGAAGGC -s Anc1.Anc1refChr6 139734 13 + 197743 TACATTTGAAGGC -s Anc2.Anc2refChr1 17943 13 + 142988 TACACTTGAAGGC -s mr.mrrefChr3 44086 13 + 181027 TATATATGAGAGC -s simCow_chr6.simCow.chr6 474398 13 + 602619 TACACTTGAAGCA -s simDog_chr6.simDog.chr6 464887 13 + 593897 AACACCTGAAGGC -s simHuman_chr6.simHuman.chr6 471587 13 + 601863 TACATTTGAACGC -s simRat_chr6.simRat.chr6 497927 13 + 647215 TATATATGAGAGC - -a -s simMouse_chr6.simMouse.chr6 490159 4 + 636262 AATT -s Anc0.Anc0refChr3 106103 4 + 222631 AATT -s Anc1.Anc1refChr6 139753 4 + 197743 AATT -s Anc2.Anc2refChr1 17962 4 + 142988 AATT -s mr.mrrefChr3 44099 4 + 181027 AATT -s simCow_chr6.simCow.chr6 474417 4 + 602619 AATT -s simDog_chr6.simDog.chr6 464906 4 + 593897 AATA -s simHuman_chr6.simHuman.chr6 471606 4 + 601863 AATT -s simRat_chr6.simRat.chr6 497940 4 + 647215 AATT - -a -s simMouse_chr6.simMouse.chr6 490163 65 + 636262 GACATGGAGATCGTGAAGGTAAGGCTCTAACTTGTGTGGTCTGTATCAGTGCGTGGCTCAACTCA -s Anc0.Anc0refChr3 106125 65 + 222631 GCCATGGAGATCTGGAGGGTATGGCTCTATGCTGTGCAGTCTATATCAATTGGAGAACGGACCCA -s Anc1.Anc1refChr6 139775 65 + 197743 GCCATGGAGATCTGGAGGGTATGGCTCTATGCTGTGCAGTCTATATCAATTGGAGAACGGACCCA -s Anc2.Anc2refChr1 17984 65 + 142988 GCCATGGAGATCTGACGGGTATGGCTCTATGTGATGCAGTCTACATCAATTGGAGAACGGACCCA -s mr.mrrefChr3 44103 65 + 181027 GACATGGAGATCTGGAAGGTATGGCTCTAACCTGTGCAGTCTGTATCAATGGGTGGCTCAACTCA -s simCow_chr6.simCow.chr6 474439 65 + 602619 ACCATGGAGATCTGACGGGTATGGCTCTATGTGATGCAGTCTAAATCAATTGGTGAACGAACGCA -s simDog_chr6.simDog.chr6 464928 44 + 593897 GCTATGAA------------------TTATGTGATGCA---TACATTGATTGGAGAATAGACCCA -s simHuman_chr6.simHuman.chr6 471628 65 + 601863 GCCATGGAGATCTGGAGGGTATGACCCTATGCTGTGCAGTCTCTATCAATTGAGGAACGGACACA -s simRat_chr6.simRat.chr6 497944 62 + 647215 GACATGGAGATCTGGTAGGTGTGGCTCT---CTGTGCAGTCTGCATCAATGGGTGGCTCAATTCA - -a -s simMouse_chr6.simMouse.chr6 490228 1 + 636262 T -s Anc0.Anc0refChr3 106190 1 + 222631 T -s Anc1.Anc1refChr6 139840 1 + 197743 T -s Anc2.Anc2refChr1 18049 1 + 142988 T -s mr.mrrefChr3 44168 1 + 181027 T -s simCow_chr6.simCow.chr6 474504 1 + 602619 T -s simDog_chr6.simDog.chr6 464972 1 + 593897 T -s simHuman_chr6.simHuman.chr6 471693 1 + 601863 T -s simRat_chr6.simRat.chr6 498010 1 + 647215 G - -a -s simMouse_chr6.simMouse.chr6 490229 33 + 636262 CTTGACATGTTGAAGTTCTTACAGTGGTTCGTG -s Anc0.Anc0refChr3 106191 33 + 222631 CTTTACACTATGCAATTTTTGCACTGGAAGCTG -s Anc1.Anc1refChr6 139841 33 + 197743 CTTTACACTATGCAATTTTTGCACTGGAAGCTG -s Anc2.Anc2refChr1 18050 33 + 142988 CTTTACACTATGCAATTTTTGCACTGGAAGCTG -s mr.mrrefChr3 44169 33 + 181027 CTTGACATGATGAAGTTCTTACAGTGGTTCCTG -s simCow_chr6.simCow.chr6 474505 33 + 602619 CCTTACCCTATGCAATTTTTATACTGGAAGCTG -s simDog_chr6.simDog.chr6 464974 33 + 593897 CTTTACACTGTGTAATTTTTGCACTGAGAGTTG -s simHuman_chr6.simHuman.chr6 471694 33 + 601863 CTCTATGCTATGCAATTTTTGGATTGGAAGCTG -s simRat_chr6.simRat.chr6 498011 33 + 647215 CTTGACATGATGAGGTTCTTACAGTGGTGCCTA - -a -s simMouse_chr6.simMouse.chr6 490262 50 + 636262 GGGAGAAATAATGGAAAGGTGCAAAAGACCTCTGTAGTCCAAATAAATTG -s Anc0.Anc0refChr3 106224 49 + 222631 GGATTAAATAATGGAAAAGTGAAATAGATATCTGAAGTCC-AATAAACTG -s Anc1.Anc1refChr6 139874 49 + 197743 GGATTAAATAATGGAAAAGTGAAATAGATATCTGAAGTCC-AATAAACTG -s Anc2.Anc2refChr1 18084 49 + 142988 TGATTAAATAAGGGAAAACTGAGATAGGTATTTGAAGTTC-AATAAACTG -s mr.mrrefChr3 44202 49 + 181027 GGGAGAAATAATGGAAAGGTGCAATAGATATCTGTAGTCC-AATAAACTG -s simCow_chr6.simCow.chr6 474539 49 + 602619 TGTTTAAAAAAGGGAAGAATGTGATAGGTATTTGAAGTTC-TATCAACTG -s simDog_chr6.simDog.chr6 465008 49 + 593897 TGATTAAATAAGGGAAAACTGAGATAGGTAGTTGAGGTTC-ACAAAAGTG -s simHuman_chr6.simHuman.chr6 471727 49 + 601863 GGATTAAATAATGGAAAAGTGGAATAGATATCTGAAGTCC-CATAAACTA -s simRat_chr6.simRat.chr6 498044 49 + 647215 GGGAGAAATAATGGAAAGGTGTAATAGATATTTGTAGTCC-AATAAACTG - -a -s simMouse_chr6.simMouse.chr6 490312 2 + 636262 TC -s Anc0.Anc0refChr3 106273 2 + 222631 TC -s Anc1.Anc1refChr6 139923 2 + 197743 TC -s Anc2.Anc2refChr1 18133 2 + 142988 TC -s mr.mrrefChr3 44251 2 + 181027 TC -s simCow_chr6.simCow.chr6 474589 2 + 602619 TG -s simDog_chr6.simDog.chr6 465057 2 + 593897 TC -s simHuman_chr6.simHuman.chr6 471776 2 + 601863 TC -s simRat_chr6.simRat.chr6 498093 2 + 647215 TT - -a -s simMouse_chr6.simMouse.chr6 490314 10 + 636262 CTTGGTGCCA -s Anc0.Anc0refChr3 106540 10 + 222631 CTTGGTACCA -s Anc1.Anc1refChr6 140196 10 + 197743 CTTGGTACCA -s Anc2.Anc2refChr1 18400 10 + 142988 CTTGGTACCA -s mr.mrrefChr3 44511 10 + 181027 CTTGGTACCA -s simCow_chr6.simCow.chr6 474863 10 + 602619 TTATGTACCA -s simDog_chr6.simDog.chr6 465316 10 + 593897 CATGGTACCA -s simHuman_chr6.simHuman.chr6 472049 10 + 601863 CTTGGGACCA -s simRat_chr6.simRat.chr6 498386 10 + 647215 CTTGGCACCA - -a -s simMouse_chr6.simMouse.chr6 490324 72 + 636262 ATGCACTGGGAACCTCTTTTATCTTGCAGCCAAGAACTTACACATGTGCTGCATACCTTCTTACTTATATAT -s Anc0.Anc0refChr3 106550 67 + 222631 A-----TGACAACCAAAGTTGTCTTGTGACCAAGAATTTACACATGTAATGGGTACCTACTAATTTATGTAT -s Anc1.Anc1refChr6 140206 67 + 197743 A-----TGACAACCAAAGTTGTCTTGTGACCAAGAATTTACACATGTAATGGGTACCTACTAATTTATGTAT -s Anc2.Anc2refChr1 18410 67 + 142988 T-----TGACAACCAAAGTTGTCTTGTGACCAAGAATTTACACATGTAATGGGTACCTATTAATTGATGTAT -s mr.mrrefChr3 44521 72 + 181027 ATGCACTGGGAACCTCTTTTATCTTGCAGCCAAGAACTTACACATGTGCTGCATACCTACTTACTTATATAT -s simCow_chr6.simCow.chr6 474873 67 + 602619 T-----TGACAACAGAAGATGTCTTGTGACCAAGAGTTCACACATGTGATGGATACCTATTAAATGATGTAC -s simDog_chr6.simDog.chr6 465371 67 + 593897 T-----TGGCAACCAAATTAGTCTTGCGACCAAGAATTTACACATCTAATGGGTACCTATTGATTGATGTAT -s simHuman_chr6.simHuman.chr6 472059 67 + 601863 A-----TGATAACCCAAGTTGTTTTGTGACCAAGAATTTGCACATGTAATGGGTATCTACTAGTTTATGTAT -s simRat_chr6.simRat.chr6 498396 72 + 647215 ATGCACTGGGAACTTCTCTTATCTTGCAGCCAAGAACTTACACATGTGCTGCATACCTACTTACTTATATAT - -a -s simMouse_chr6.simMouse.chr6 490396 40 + 636262 CCCAGATAAGTTTATTATATATCCCCAACACACAGTGCAT -s Anc0.Anc0refChr3 106695 36 + 222631 TACAGACAGGAGTACTATCTATCCCCA----AGAGTGCGT -s Anc1.Anc1refChr6 140351 39 + 197743 TACAGACAGGAGTACTATCTATCCCCA-TGCAGAGTGCGT -s Anc2.Anc2refChr1 18555 36 + 142988 TACAGACAGGAGTACTATCTATCCCCA----AGAGTGCGT -s mr.mrrefChr3 44593 40 + 181027 CCCAGATAAGATTATTATATATCCCCAACACACAGTGCAT -s simCow_chr6.simCow.chr6 475013 36 + 602619 TACAGACAGGACTGCTATCTATCCCCA----AGAGTGCTT -s simDog_chr6.simDog.chr6 465500 36 + 593897 TACAGATAGGAGCATTATCTACCCCCA----AGATTGTGT -s simHuman_chr6.simHuman.chr6 472204 36 + 601863 TACAGACAGGAATTCTATCTATCC----TGCAGAGTGCCT -s simRat_chr6.simRat.chr6 498468 39 + 647215 CCCAGATAAGAGTATTATTTA-CCCCAAGACATGGTGCAT - -a -s simMouse_chr6.simMouse.chr6 490436 1 + 636262 C -s Anc0.Anc0refChr3 106731 1 + 222631 C -s Anc1.Anc1refChr6 140390 1 + 197743 C -s Anc2.Anc2refChr1 18592 1 + 142988 C -s mr.mrrefChr3 44633 1 + 181027 C -s simCow_chr6.simCow.chr6 475050 1 + 602619 C -s simDog_chr6.simDog.chr6 465537 1 + 593897 C -s simHuman_chr6.simHuman.chr6 472240 1 + 601863 C -s simRat_chr6.simRat.chr6 498507 1 + 647215 C - -a -s simMouse_chr6.simMouse.chr6 490437 1 + 636262 A -s Anc0.Anc0refChr3 106732 1 + 222631 A -s Anc1.Anc1refChr6 140391 1 + 197743 A -s Anc2.Anc2refChr1 18593 1 + 142988 A -s mr.mrrefChr3 44634 1 + 181027 A -s simCow_chr6.simCow.chr6 475054 1 + 602619 A -s simDog_chr6.simDog.chr6 465538 1 + 593897 A -s simHuman_chr6.simHuman.chr6 472241 1 + 601863 A -s simRat_chr6.simRat.chr6 498508 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 490438 11 + 636262 ATTAAGGATGG -s Anc0.Anc0refChr3 106741 6 + 222631 ATTAAG----- -s Anc1.Anc1refChr6 140400 11 + 197743 ATTAAGAAGGC -s Anc2.Anc2refChr1 18602 6 + 142988 ATCAAG----- -s mr.mrrefChr3 44635 11 + 181027 ATTAAGGATGC -s simCow_chr6.simCow.chr6 475063 6 + 602619 GTGAAT----- -s simDog_chr6.simDog.chr6 465547 6 + 593897 ATCGAG----- -s simHuman_chr6.simHuman.chr6 472250 11 + 601863 ATTAAGAAGGC -s simRat_chr6.simRat.chr6 498509 11 + 647215 ATCAAGTATGC - -a -s simMouse_chr6.simMouse.chr6 490449 35 + 636262 CTTATGAGGGACTTTGACAGAACTATCTCGGTGTG -s Anc0.Anc0refChr3 106747 30 + 222631 -----GAGGGACACAGACAGAGTTATCTAATTGAG -s Anc1.Anc1refChr6 140411 35 + 197743 CCAATGAGGGACACAGACAGAGTTATCTAATTGAG -s Anc2.Anc2refChr1 18608 30 + 142988 -----GAAGGACACAGACAGAGTTATCTAATTGCG -s mr.mrrefChr3 44646 35 + 181027 CCTATGAGGGACTTAGACAGAACTATCTCGGTGAG -s simCow_chr6.simCow.chr6 475069 30 + 602619 -----GAAGAACACAGACAGAGTTATCTAATTGTG -s simDog_chr6.simDog.chr6 465553 30 + 593897 -----GAAGGACACAGACAGAGTTATATAATTGCG -s simHuman_chr6.simHuman.chr6 472263 35 + 601863 CCAATGAGGGAAACAGACAGACTTATCTGATTGAG -s simRat_chr6.simRat.chr6 498520 35 + 647215 TCTATAAGGGACTTAGATAGAACTATCTAGGTGAG - -a -s simMouse_chr6.simMouse.chr6 490484 9 + 636262 ATCATTAGT -s Anc0.Anc0refChr3 106781 8 + 222631 ATCCTTA-T -s Anc1.Anc1refChr6 140450 9 + 197743 ATCCTTACT -s Anc2.Anc2refChr1 18642 8 + 142988 ATCCTTA-T -s mr.mrrefChr3 44681 9 + 181027 ATCATTAGT -s simCow_chr6.simCow.chr6 475103 8 + 602619 ATCCTTC-A -s simDog_chr6.simDog.chr6 465587 8 + 593897 ATCCTTA-T -s simHuman_chr6.simHuman.chr6 472302 9 + 601863 ATCCCTACT -s simRat_chr6.simRat.chr6 498555 9 + 647215 ATCATTAGT - -a -s simMouse_chr6.simMouse.chr6 490493 11 + 636262 GTTGAATGCCA -s Anc0.Anc0refChr3 106792 11 + 222631 GTTGAATGTTA -s Anc1.Anc1refChr6 140462 11 + 197743 GTTGAATGTTA -s Anc2.Anc2refChr1 18653 11 + 142988 GATGGATGTTA -s mr.mrrefChr3 44690 11 + 181027 GTTGAATGCCA -s simCow_chr6.simCow.chr6 475114 11 + 602619 TATGGATGTCG -s simDog_chr6.simDog.chr6 465598 6 + 593897 G-----TATTA -s simHuman_chr6.simHuman.chr6 472314 11 + 601863 GTTGATTGTAA -s simRat_chr6.simRat.chr6 498564 11 + 647215 GTTGAATGCCA - -a -s simMouse_chr6.simMouse.chr6 490504 27 + 636262 TGTTGCAGTACAATGGTGAGGTGACTG -s Anc0.Anc0refChr3 106807 27 + 222631 TGTGGGGGTATGATGATGAAGAGACTG -s Anc1.Anc1refChr6 140477 27 + 197743 TGTGGGGGTATGATGATGAAGAGACTG -s Anc2.Anc2refChr1 18677 27 + 142988 TGTGGGGGTATTATGATGAAGAGATTG -s mr.mrrefChr3 44701 27 + 181027 TGTTGCAGTACGATGGTGAGGTGACTG -s simCow_chr6.simCow.chr6 475138 26 + 602619 TGTGAGGGTATTATGATGATGAG-AGG -s simDog_chr6.simDog.chr6 465619 26 + 593897 TGTGGGGGTATTATGATAAA-AGATTG -s simHuman_chr6.simHuman.chr6 472329 25 + 601863 TGTGG--GTCTGATAAAGAAGAGACTG -s simRat_chr6.simRat.chr6 498575 27 + 647215 TGCTGCAGTACGATGGTGAGGTGACTG - -a -s simMouse_chr6.simMouse.chr6 490531 12 + 636262 ACTCAAATCTCA -s Anc0.Anc0refChr3 106834 12 + 222631 GCCCTGTTTTGA -s Anc1.Anc1refChr6 140504 12 + 197743 GCCCTGTTTTGA -s Anc2.Anc2refChr1 18704 12 + 142988 GCCCTGTTTTGA -s mr.mrrefChr3 44728 12 + 181027 GCTCAGATCTCA -s simCow_chr6.simCow.chr6 475164 12 + 602619 GTACTATGATGA -s simDog_chr6.simDog.chr6 465652 12 + 593897 GCCCTGTTTTAG -s simHuman_chr6.simHuman.chr6 472354 12 + 601863 GCCCTGTTTTGA -s simRat_chr6.simRat.chr6 498602 12 + 647215 GCTCAGATCTTG - -a -s simMouse_chr6.simMouse.chr6 490543 21 + 636262 AGCTGGTGTTATAGAGTGCAG -s Anc0.Anc0refChr3 106846 21 + 222631 GGCCAGTGGTATAGAGTACAG -s Anc1.Anc1refChr6 140516 21 + 197743 GGCCAGTGGTATAGAGTACAG -s Anc2.Anc2refChr1 18716 21 + 142988 GACCAGTGGTATAGAGTACAG -s mr.mrrefChr3 44740 21 + 181027 AGCCGGTGTTATAGAGTACAG -s simCow_chr6.simCow.chr6 475185 21 + 602619 GAACCGTGGTTTAAAGTACAG -s simDog_chr6.simDog.chr6 465664 21 + 593897 GACAAGTGGTATAGAGTACAG -s simHuman_chr6.simHuman.chr6 472366 21 + 601863 GGCCTGTGCTATAGAATATAA -s simRat_chr6.simRat.chr6 498614 21 + 647215 AGCCGGTGTTATAGAGTACAG - -a -s simMouse_chr6.simMouse.chr6 490564 5 + 636262 ACCAT -s Anc0.Anc0refChr3 106867 5 + 222631 ATCAC -s Anc1.Anc1refChr6 140537 5 + 197743 ATCAC -s Anc2.Anc2refChr1 18737 5 + 142988 ATCAC -s mr.mrrefChr3 44761 5 + 181027 ACCAC -s simCow_chr6.simCow.chr6 475208 5 + 602619 ATCAC -s simDog_chr6.simDog.chr6 465685 5 + 593897 ATTAC -s simHuman_chr6.simHuman.chr6 472387 5 + 601863 ATCAC -s simRat_chr6.simRat.chr6 498635 5 + 647215 ACCAC - -a -s simMouse_chr6.simMouse.chr6 490569 16 + 636262 GCCAAAGTAGACATTG -s Anc0.Anc0refChr3 106873 16 + 222631 ACAGCAGTAGACATTA -s Anc1.Anc1refChr6 140543 16 + 197743 ACAGCAGTAGACATTA -s Anc2.Anc2refChr1 18743 16 + 142988 ACAGCAGTAGACATTA -s mr.mrrefChr3 44767 16 + 181027 GCCGAAGTAGACATTG -s simCow_chr6.simCow.chr6 475214 16 + 602619 AAAGTAGTAGACATAA -s simDog_chr6.simDog.chr6 465691 16 + 593897 ACAGCAGTATACATTA -s simHuman_chr6.simHuman.chr6 472393 16 + 601863 ACAGCAGTAGACATTA -s simRat_chr6.simRat.chr6 498641 16 + 647215 GCTGGAGTAGGCATTG - -a -s simMouse_chr6.simMouse.chr6 490585 22 + 636262 GGTAATTTAAATTAGATGGTGT -s Anc0.Anc0refChr3 106897 22 + 222631 GGTAATTTAAAGTGGATGGTGT -s Anc1.Anc1refChr6 140567 22 + 197743 GGTAATTTAAAGTGGATGGTGT -s Anc2.Anc2refChr1 18767 22 + 142988 GGCAATTTCAAGTGGATGGTGT -s mr.mrrefChr3 44783 22 + 181027 GGTAATTTAAATTAGATGGTGT -s simCow_chr6.simCow.chr6 475238 16 + 602619 GAGGGTCTTAAGTG------GT -s simDog_chr6.simDog.chr6 465715 22 + 593897 GGCAATTTCAAGTGGATGGTGT -s simHuman_chr6.simHuman.chr6 472417 22 + 601863 GGTATTTTAAAGTGGAGGGTGT -s simRat_chr6.simRat.chr6 498657 22 + 647215 GGTAATTTAAATTAGATGGTAC - -a -s simMouse_chr6.simMouse.chr6 490607 39 + 636262 AAGTTGCCAGCAAGAGTTGCTACAAGATCTCATAAACTT -s Anc0.Anc0refChr3 106921 3 + 222631 AAG------------------------------------ -s Anc1.Anc1refChr6 140591 3 + 197743 AAG------------------------------------ -s Anc2.Anc2refChr1 18791 3 + 142988 AAG------------------------------------ -s mr.mrrefChr3 44805 39 + 181027 AAGTTGCCAGCAAGAGTTGCTACAAGATCTCATAAACTT -s simCow_chr6.simCow.chr6 475256 3 + 602619 AAA------------------------------------ -s simDog_chr6.simDog.chr6 465739 3 + 593897 AAG------------------------------------ -s simHuman_chr6.simHuman.chr6 472441 3 + 601863 AAG------------------------------------ -s simRat_chr6.simRat.chr6 498679 39 + 647215 ATGTGGCCAACAAAAGTTGCTTCAGGATCTCATAACATT - -a -s simMouse_chr6.simMouse.chr6 490646 32 + 636262 ACGCACCTTGACTGGATCCAGGAAAAACCCTG -s Anc0.Anc0refChr3 106924 32 + 222631 ATACAGCTTGACAGGGCCTAGTAAAATCCCCA -s Anc1.Anc1refChr6 140594 32 + 197743 ATACAGCTTGACAGGGCCTAGTAAAATCCCCA -s Anc2.Anc2refChr1 18797 32 + 142988 ATACAGCTTGACAGGGCCTAGTAATCTTACCA -s mr.mrrefChr3 44844 32 + 181027 ACACACCTTGACAGGATCCAGGAAAAACCCTG -s simCow_chr6.simCow.chr6 475262 26 + 602619 ATATTTATTGACAAGGCCTAGTCA------CA -s simDog_chr6.simDog.chr6 465745 32 + 593897 ATGCAGCTTGATAGAGCCTTGTAATCTTACCA -s simHuman_chr6.simHuman.chr6 472444 32 + 601863 AGACAGCTTGACAGGGCCTAGTAAAAGCCTCA -s simRat_chr6.simRat.chr6 498718 32 + 647215 AAATACCTTGACAAGATCCAGGAAAAACCCTG - -a -s simMouse_chr6.simMouse.chr6 490678 23 + 636262 ATCTCAACTCTATCCATTCTTCC -s Anc0.Anc0refChr3 106958 17 + 222631 TTTTAAGCTTTATACAT------ -s Anc1.Anc1refChr6 140628 17 + 197743 TTTTAAGCTTTATACAT------ -s Anc2.Anc2refChr1 18831 17 + 142988 TTTTAAGCTTTAAACAT------ -s mr.mrrefChr3 44878 17 + 181027 ATCTCAACTCTATCCAT------ -s simCow_chr6.simCow.chr6 475290 17 + 602619 TCTTAAGCTTTGAACAT------ -s simDog_chr6.simDog.chr6 465779 17 + 593897 CTCTTAGCTTTAAACAT------ -s simHuman_chr6.simHuman.chr6 472478 17 + 601863 TTTTAAGCTTTATACAT------ -s simRat_chr6.simRat.chr6 498752 17 + 647215 CTCTCGATTCTAGCCAT------ - -a -s simMouse_chr6.simMouse.chr6 490701 1 + 636262 T -s Anc0.Anc0refChr3 106978 1 + 222631 C -s Anc1.Anc1refChr6 140648 1 + 197743 C -s Anc2.Anc2refChr1 18851 1 + 142988 C -s mr.mrrefChr3 44895 1 + 181027 T -s simCow_chr6.simCow.chr6 475310 1 + 602619 C -s simHuman_chr6.simHuman.chr6 472498 1 + 601863 C -s simRat_chr6.simRat.chr6 498769 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 490702 44 + 636262 TTTCCTTTGAATTCAGTTCAACACCTCCCCATCACACTCAGGAC -s Anc0.Anc0refChr3 106979 43 + 222631 TTACCTATAAAATTAGTTCAATGCCCCACCAGGACATTGAGGA- -s Anc1.Anc1refChr6 140649 44 + 197743 TTACCTATAAAATTAGTTCAATGCCCCACCAGGACATTGAGGAC -s Anc2.Anc2refChr1 18852 43 + 142988 TTACCTATAAAATTTGTTCAATGCTCCACCTGGACAGTGAGGA- -s mr.mrrefChr3 44896 44 + 181027 TTTCCTTTGAATTCAGTTCAACACCTCCCCATCACATTCAGGAC -s simCow_chr6.simCow.chr6 475312 43 + 602619 TTGTCCATAAAATTGGTTCAATGCTCCACCTGGACACTGAGGA- -s simDog_chr6.simDog.chr6 465799 34 + 593897 -TACCTCTTAGTTTTAGTCATTTT--------GCCTGTGAGGA- -s simHuman_chr6.simHuman.chr6 472499 44 + 601863 TTACCTATAAAATTAGTTCAATGCCCTACCAGGACATTGAAGAC -s simRat_chr6.simRat.chr6 498770 44 + 647215 TTTCCTGTGAATTCAATTCTACACCTCCCTATCACATTCAGGAC - -a -s simMouse_chr6.simMouse.chr6 490746 2 + 636262 CA -s Anc0.Anc0refChr3 107022 2 + 222631 CA -s Anc1.Anc1refChr6 140693 2 + 197743 CA -s Anc2.Anc2refChr1 18895 2 + 142988 CA -s mr.mrrefChr3 44940 2 + 181027 CA -s simCow_chr6.simCow.chr6 475355 2 + 602619 TA -s simDog_chr6.simDog.chr6 465833 2 + 593897 CA -s simHuman_chr6.simHuman.chr6 472546 2 + 601863 CA -s simRat_chr6.simRat.chr6 498814 2 + 647215 CA - -a -s simMouse_chr6.simMouse.chr6 490748 10 + 636262 TTTCCTGAGG -s Anc0.Anc0refChr3 107025 10 + 222631 TTGGCTAGGG -s Anc1.Anc1refChr6 140696 10 + 197743 TTGGCTAGGG -s Anc2.Anc2refChr1 18898 10 + 142988 TTGGCTAGGG -s mr.mrrefChr3 44943 10 + 181027 TTTCCTGGGG -s simCow_chr6.simCow.chr6 475358 10 + 602619 TTGGCTAGGG -s simDog_chr6.simDog.chr6 465836 10 + 593897 TTGGCTAGGG -s simHuman_chr6.simHuman.chr6 472549 10 + 601863 TCGTCCAGGG -s simRat_chr6.simRat.chr6 498817 10 + 647215 TTTCCTGGGG - -a -s simMouse_chr6.simMouse.chr6 490758 3 + 636262 CTG -s Anc0.Anc0refChr3 107035 3 + 222631 CTA -s Anc1.Anc1refChr6 140706 3 + 197743 CTA -s Anc2.Anc2refChr1 18908 3 + 142988 CTA -s mr.mrrefChr3 44953 3 + 181027 CTG -s simCow_chr6.simCow.chr6 475368 3 + 602619 CTT -s simDog_chr6.simDog.chr6 465846 3 + 593897 CTA -s simHuman_chr6.simHuman.chr6 472560 3 + 601863 CTA -s simRat_chr6.simRat.chr6 498827 3 + 647215 CTG - -a -s simMouse_chr6.simMouse.chr6 490761 32 + 636262 GGTTCACAATGCCATATCCATATGTAACATAA -s Anc0.Anc0refChr3 107045 26 + 222631 AACTCACAATG------GCAAATGTGACATCT -s Anc1.Anc1refChr6 140716 26 + 197743 AACTCACAATG------GCAAATGTGACATCT -s Anc2.Anc2refChr1 18918 26 + 142988 AACTCAAAATG------GCAAATGTGACATCT -s mr.mrrefChr3 44956 26 + 181027 AGTTCACAATG------CCATATGTAACATAA -s simCow_chr6.simCow.chr6 475378 26 + 602619 GACTCAAAATG------GCGGATGTGACATCT -s simDog_chr6.simDog.chr6 465856 26 + 593897 AACTCAAAATG------GCAAATGTGACATCT -s simHuman_chr6.simHuman.chr6 472570 26 + 601863 ATCTCACAGTG------GTAACTGTGGCACCT -s simRat_chr6.simRat.chr6 498830 26 + 647215 AGTTGACAATG------CCATATGTAACACAA - -a -s simMouse_chr6.simMouse.chr6 490793 18 + 636262 CATAATATTAAGGGGTGC -s Anc0.Anc0refChr3 107071 5 + 222631 CATTA------------- -s Anc1.Anc1refChr6 140742 5 + 197743 CATTA------------- -s Anc2.Anc2refChr1 18947 5 + 142988 CATTA------------- -s mr.mrrefChr3 44982 18 + 181027 CATAATAGTAAGGGGTGC -s simCow_chr6.simCow.chr6 475407 5 + 602619 CATTA------------- -s simDog_chr6.simDog.chr6 465885 5 + 593897 TATTA------------- -s simHuman_chr6.simHuman.chr6 472596 5 + 601863 CATTA------------- -s simRat_chr6.simRat.chr6 498856 18 + 647215 CCTAATAGTAAGGGGTGC - -a -s simMouse_chr6.simMouse.chr6 490811 2 + 636262 CC -s mr.mrrefChr3 45000 2 + 181027 CC -s simRat_chr6.simRat.chr6 498923 2 + 647215 GC - -a -s simMouse_chr6.simMouse.chr6 490813 27 + 636262 CTTTCTCTAAGGGGTGCTCCTTCTTCT -s Anc0.Anc0refChr3 107076 21 + 222631 ------GTAAGGGGTAACCCTTTTGGT -s Anc1.Anc1refChr6 140747 21 + 197743 ------GTAAGGGGTAACCCTTTTGGT -s Anc2.Anc2refChr1 18952 21 + 142988 ------GTAAGGGGTAACCCTTTTGGG -s mr.mrrefChr3 45004 27 + 181027 CTTTCTGTAAGGGGTGCTCCTTTTTGT -s simCow_chr6.simCow.chr6 475412 19 + 602619 ------GTAAGGAGCAACCCTTTTA-- -s simDog_chr6.simDog.chr6 465890 21 + 593897 ------ATGAGGGGTGACCCTTTGGGG -s simHuman_chr6.simHuman.chr6 472601 21 + 601863 ------GTAAGGGATAAGCCTGTTGGT -s simRat_chr6.simRat.chr6 498927 27 + 647215 CTTTCTGTAAAGGGTGCCCTTTTTTGT - -a -s simMouse_chr6.simMouse.chr6 490840 42 + 636262 TGTACAACTAGTCACAAAATTGCCCCAAAAATTTATTTTAAC -s Anc0.Anc0refChr3 107097 40 + 222631 TGTAATACCAGCAACAAAGAAGGCCCAAAAA-TT-TTTTAAC -s Anc1.Anc1refChr6 140768 40 + 197743 TGTAATACCAGCAACAAAGAAGGCCCAAAAA-TT-TTTTAAC -s Anc2.Anc2refChr1 18973 40 + 142988 TGTAATACTGGCAGCAAAGAAGGCCCAAAAA-TT-TTTTAAC -s mr.mrrefChr3 45031 41 + 181027 TGTACAACCAGCCACAAAATTGGCCCAAAAA-TTATTTTAAC -s simCow_chr6.simCow.chr6 475431 37 + 602619 ---AAAACTGGCATCTCAGAAGGCCCATAAC-TT-TTTTAAC -s simDog_chr6.simDog.chr6 465912 40 + 593897 TGTAATACTGCTAGCAAAGAAGGCCCAAAAA-TT-TTTTAAC -s simHuman_chr6.simHuman.chr6 472622 40 + 601863 TGTAATACCAGCAACAAAGAAGGCCCAGAAA-TT-TCTTAAC -s simRat_chr6.simRat.chr6 498954 41 + 647215 TGTACCACCAACCATAAAATTGGCCCAAAAA-TTATTTCAAC - -a -s simMouse_chr6.simMouse.chr6 490882 16 + 636262 CTATAGTGCAAAGTGA -s Anc0.Anc0refChr3 107137 16 + 222631 ATATAGCTCAAGGAGT -s Anc1.Anc1refChr6 140808 16 + 197743 ATATAGCTCAAGGAGT -s Anc2.Anc2refChr1 19013 16 + 142988 ATATAGCTCAAGGAGT -s mr.mrrefChr3 45072 16 + 181027 CTATAGTGCAAAGTGT -s simCow_chr6.simCow.chr6 475468 16 + 602619 ATATAGCCCAATGAGC -s simDog_chr6.simDog.chr6 465954 16 + 593897 ATAGAGCTTGGGGAAT -s simHuman_chr6.simHuman.chr6 472662 16 + 601863 ATGTAGCTCAACGAGT -s simRat_chr6.simRat.chr6 498995 16 + 647215 CTATAGTGCAAGGTGT - -a -s simMouse_chr6.simMouse.chr6 490898 85 + 636262 CCCAGTATTTTGTCTTTTGGCTCATCAATTGGGATACAACTATAGCATAGGGAGTTCCAGTTTCTTGCCTCTGAATCCAGATATT -s Anc0.Anc0refChr3 107153 59 + 222631 CCCAATTTTTTGCCTTTGAGTTTAGCTATTGGGATCCAAATATAGCTTAAGTAGTCCCA-------------------------- -s Anc1.Anc1refChr6 140824 59 + 197743 CCCAATTTTTTGCCTTTGAGTTTAGCTATTGGGATCCAAATATAGCTTAAGTAGTCCCA-------------------------- -s Anc2.Anc2refChr1 19029 59 + 142988 CCCAATTTTTTGCCTTTGAGCTTAGCTATTGGGATCCAAATATAGGTTAAGTAGTCCCA-------------------------- -s mr.mrrefChr3 45088 80 + 181027 CCCAGTATTTTGTCTTTTAGTTCATCAATTGGGATACAACTATAGCATAGGGAGTTCCAGTTTCTTGCCTCTGAATCC-----TT -s simCow_chr6.simCow.chr6 475484 59 + 602619 CCCAATATTATGCCTTCGAGCTTAGCCACTGGGATCCAAATATAGGTTAAGTAGTCCCA-------------------------- -s simDog_chr6.simDog.chr6 465970 39 + 593897 TCCAGCTTTTTGCCTTTGTGCTCAGCTTTT------CAAACACAT---------------------------------------- -s simHuman_chr6.simHuman.chr6 472678 59 + 601863 CCCAATGCTTTGCGTTTGAGTTTGGCTATTGGGATGCAAATATAGCTTGAGAAGACCCA-------------------------- -s simRat_chr6.simRat.chr6 499037 80 + 647215 CCCAGTATTTTGTCTTTCAGTTCACCAATTGGGATACAACTATCGCGCAGGGAGTTCCAGGTTTTTGCCTCTGAATCC-----TT - -a -s simMouse_chr6.simMouse.chr6 490983 44 + 636262 AAGAGACACTTAAAAATATTCAAATGTATTGATGGCTAGTAGGG -s Anc0.Anc0refChr3 107212 41 + 222631 AATAAAGAGCGAGAAATGTTCACATATATGGATAGCTAGTA--- -s Anc1.Anc1refChr6 140883 41 + 197743 AATAAAGAGCGAGAAATGTTCACATATATGGATAGCTAGTA--- -s Anc2.Anc2refChr1 19088 41 + 142988 ACTGAAGAGCGAGTCATGCTCACATATATGGATAGCTAGTA--- -s mr.mrrefChr3 45168 44 + 181027 AAGAGACACTTAAAAATATTCACATGTATTGATGGCTAGTAGGG -s simCow_chr6.simCow.chr6 475576 41 + 602619 ACTGAAGAGAGAGTCATGACCACATATAAGGATATCTAGCA--- -s simDog_chr6.simDog.chr6 466009 39 + 593897 --TGAAGAGCCAGTCCCGCTCACATGCATTGATAGCTAGTA--- -s simHuman_chr6.simHuman.chr6 472737 41 + 601863 AATAAAGAGGGATAAATGTTCATATATATGGATAGCTAGTG--- -s simRat_chr6.simRat.chr6 499117 44 + 647215 AAGAGACACTTAAGCATATGCACGTGTATTGACGGCTAGTAGGG - -a -s simMouse_chr6.simMouse.chr6 491027 3 + 636262 GGG -s Anc0.Anc0refChr3 107253 3 + 222631 GGG -s Anc1.Anc1refChr6 140924 3 + 197743 GGG -s Anc2.Anc2refChr1 19129 3 + 142988 GGG -s mr.mrrefChr3 45212 3 + 181027 GGG -s simCow_chr6.simCow.chr6 475619 3 + 602619 GGG -s simDog_chr6.simDog.chr6 466048 3 + 593897 GGG -s simHuman_chr6.simHuman.chr6 472778 3 + 601863 GTG -s simRat_chr6.simRat.chr6 499161 3 + 647215 GGG - -a -s simMouse_chr6.simMouse.chr6 491030 44 + 636262 GCATGTTTAAAGCAGGAGGATGTGCTGCCAGGTGCTCAGTACTA -s Anc0.Anc0refChr3 107257 41 + 222631 ATAAGTTGAAAGGATAAAGA---GCTGACAACCATTCAGTAACA -s Anc1.Anc1refChr6 140928 41 + 197743 ATAAGTTGAAAGGATAAAGA---GCTGACAACCATTCAGTAACA -s Anc2.Anc2refChr1 19133 41 + 142988 ATTAGTTGAAAGGATACAGA---GCTGAGAACCATTTAGTAACA -s mr.mrrefChr3 45216 44 + 181027 GCATGTTTAAAGCAGGAGGATGTGTTGCCAGGTGTTCAGTACTA -s simCow_chr6.simCow.chr6 475623 41 + 602619 ATGAGTTGAAAAGGTACAGA---GCTGATAACCAGTGAGTACCA -s simDog_chr6.simDog.chr6 466052 41 + 593897 GGTACTTGAACGGAAACAGA---ACTGAGAACTGTTTATTAATA -s simHuman_chr6.simHuman.chr6 472782 41 + 601863 ATAAGTTGAAAGTATAAAAA---GCTGTCAACCATTCAGAAACA -s simRat_chr6.simRat.chr6 499165 44 + 647215 GCATGTTTAAAGCAGGAGGATGTGTTTCCAGGTGTTCAGTACTT - -a -s simMouse_chr6.simMouse.chr6 491074 9 + 636262 GCTTATGCA -s Anc0.Anc0refChr3 107298 9 + 222631 GTTCACCCA -s Anc1.Anc1refChr6 140969 9 + 197743 GTTCACCCA -s Anc2.Anc2refChr1 19174 9 + 142988 GTTCACCCA -s mr.mrrefChr3 45260 9 + 181027 GCTTATGCA -s simCow_chr6.simCow.chr6 475664 9 + 602619 GTTCACCCA -s simDog_chr6.simDog.chr6 466094 9 + 593897 GTTCACCCA -s simHuman_chr6.simHuman.chr6 472823 9 + 601863 TTTCAGCCA -s simRat_chr6.simRat.chr6 499209 9 + 647215 GCTTATGCA - -a -s simMouse_chr6.simMouse.chr6 491083 12 + 636262 TTATGCATGAAG -s Anc0.Anc0refChr3 107307 12 + 222631 TTATACATGAAA -s Anc1.Anc1refChr6 140978 12 + 197743 TTATACATGAAA -s Anc2.Anc2refChr1 19183 12 + 142988 TTATACATGAAA -s mr.mrrefChr3 45269 12 + 181027 TTATGCATGAAG -s simCow_chr6.simCow.chr6 475674 12 + 602619 TTATACATGAAA -s simDog_chr6.simDog.chr6 466103 12 + 593897 TTATACAAGAAG -s simHuman_chr6.simHuman.chr6 472832 12 + 601863 CTATACATGAAA -s simRat_chr6.simRat.chr6 499218 12 + 647215 TTATGCATGAAG - -a -s simMouse_chr6.simMouse.chr6 491095 4 + 636262 TACA -s Anc0.Anc0refChr3 107319 4 + 222631 TACA -s Anc1.Anc1refChr6 140990 4 + 197743 TACA -s Anc2.Anc2refChr1 19195 4 + 142988 TGCA -s mr.mrrefChr3 45281 4 + 181027 TACA -s simCow_chr6.simCow.chr6 475686 4 + 602619 TCCA -s simDog_chr6.simDog.chr6 466116 4 + 593897 TGCA -s simHuman_chr6.simHuman.chr6 472844 4 + 601863 TATT -s simRat_chr6.simRat.chr6 499230 4 + 647215 TACG - -a -s simMouse_chr6.simMouse.chr6 491099 30 + 636262 CTGGATATTGAGTACATATGAGTAGTGGCC -s Anc0.Anc0refChr3 107323 30 + 222631 CTGGATCCTGAGCCCATACCAATAGAGGCG -s Anc1.Anc1refChr6 140994 30 + 197743 CTGGATCCTGAGCCCATACCAATAGAGGCG -s Anc2.Anc2refChr1 19199 30 + 142988 CTAGATCCTGAGCCCATACCAATAGAGGCG -s mr.mrrefChr3 45285 30 + 181027 CTGGATCCTGAGTACATATGAATAGAGGCC -s simCow_chr6.simCow.chr6 475694 30 + 602619 CTAGATCCTGAGTCCATACCATTAGAGGTG -s simDog_chr6.simDog.chr6 466120 30 + 593897 CTAGATCCTGAGCCAATACCAATAGAGGCA -s simHuman_chr6.simHuman.chr6 472848 30 + 601863 CTGGTTCCTAAGAGCATACAAATAGAGACG -s simRat_chr6.simRat.chr6 499234 30 + 647215 CTGGATCCTGAGTACATGTGAATAGAGGCC - -a -s simMouse_chr6.simMouse.chr6 491129 12 + 636262 TTCGTGGAATGT -s Anc0.Anc0refChr3 107353 12 + 222631 AAGATGGAATGT -s Anc1.Anc1refChr6 141024 12 + 197743 AAGATGGAATGT -s Anc2.Anc2refChr1 19229 12 + 142988 AAGATGGAATAT -s mr.mrrefChr3 45315 12 + 181027 TTCGTGGAATGT -s simCow_chr6.simCow.chr6 475724 12 + 602619 AAGATGGAATTT -s simDog_chr6.simDog.chr6 466155 12 + 593897 AAGATGGAATAA -s simHuman_chr6.simHuman.chr6 472878 12 + 601863 AAGATGTAATGT -s simRat_chr6.simRat.chr6 499264 12 + 647215 TTCGTGGCATGT - -a -s simMouse_chr6.simMouse.chr6 491141 32 + 636262 CATTGGCATTAGAAAAATCACTTGTAGATTCC -s Anc0.Anc0refChr3 107365 26 + 222631 ------CACTAGAAATGTTACTTGCAGATTTC -s Anc1.Anc1refChr6 141036 26 + 197743 ------CACTAGAAATGTTACTTGCAGATTTC -s Anc2.Anc2refChr1 19241 26 + 142988 ------CACTAGAAATGTTACTTGCAGATTTC -s mr.mrrefChr3 45327 32 + 181027 CATTGGCATTAGAAAAATTACTTGCAGATTCC -s simCow_chr6.simCow.chr6 475736 23 + 602619 ---------TAGAACTGTTATTTGCAGATTTC -s simDog_chr6.simDog.chr6 466167 26 + 593897 ------CACTAGAAACTTTACTTGCAGATTTC -s simHuman_chr6.simHuman.chr6 472890 26 + 601863 ------CAATAGAAATGTTACTTGCAGATTTC -s simRat_chr6.simRat.chr6 499280 32 + 647215 CATTGGTATTAGAAAAATTACCTGCAGATTCC - -a -s simMouse_chr6.simMouse.chr6 491173 5 + 636262 CAGCC -s Anc0.Anc0refChr3 107391 5 + 222631 CAGCC -s Anc1.Anc1refChr6 141062 5 + 197743 CAGCC -s Anc2.Anc2refChr1 19267 5 + 142988 CAGCC -s Anc2.Anc2refChr2 22799 5 - 27695 CAGTC -s mr.mrrefChr3 45359 5 + 181027 CAGCC -s simCow_chr6.simCow.chr6 475759 5 + 602619 CAGCC -s simDog_chr6.simDog.chr6 493218 5 - 593897 CAGTC -s simDog_chr6.simDog.chr6 466193 5 + 593897 CAGCC -s simHuman_chr6.simHuman.chr6 472916 5 + 601863 CAGCC -s simRat_chr6.simRat.chr6 499312 5 + 647215 CAGCC - -a -s simMouse_chr6.simMouse.chr6 491190 1 + 636262 A -s Anc0.Anc0refChr3 107408 1 + 222631 A -s Anc1.Anc1refChr6 141079 1 + 197743 A -s Anc2.Anc2refChr1 19284 1 + 142988 A -s mr.mrrefChr3 45376 1 + 181027 A -s simCow_chr6.simCow.chr6 475788 1 + 602619 A -s simDog_chr6.simDog.chr6 466210 1 + 593897 A -s simHuman_chr6.simHuman.chr6 472933 1 + 601863 A -s simRat_chr6.simRat.chr6 499329 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 491199 2 + 636262 AA -s mr.mrrefChr3 45385 2 + 181027 AA -s simRat_chr6.simRat.chr6 499338 2 + 647215 GA - -a -s simMouse_chr6.simMouse.chr6 491201 3 + 636262 TGA -s Anc0.Anc0refChr3 107417 2 + 222631 -CA -s Anc1.Anc1refChr6 141088 3 + 197743 GCA -s Anc2.Anc2refChr1 19293 2 + 142988 -CA -s Anc2.Anc2refChr2 22824 2 - 27695 -CA -s mr.mrrefChr3 45387 3 + 181027 CGA -s simCow_chr6.simCow.chr6 475797 2 + 602619 -CA -s simDog_chr6.simDog.chr6 493243 2 - 593897 -CA -s simDog_chr6.simDog.chr6 466219 2 + 593897 -TA -s simHuman_chr6.simHuman.chr6 512285 3 - 601863 CCA -s simHuman_chr6.simHuman.chr6 472941 3 + 601863 GCA -s simRat_chr6.simRat.chr6 499340 3 + 647215 CGA - -a -s simMouse_chr6.simMouse.chr6 491287 1 + 636262 G -s Anc0.Anc0refChr3 107502 1 + 222631 G -s Anc1.Anc1refChr6 141174 1 + 197743 G -s Anc2.Anc2refChr1 19378 1 + 142988 G -s mr.mrrefChr3 45473 1 + 181027 G -s simCow_chr6.simCow.chr6 507312 1 - 602619 G -s simCow_chr6.simCow.chr6 475882 1 + 602619 G -s simDog_chr6.simDog.chr6 466304 1 + 593897 G -s simHuman_chr6.simHuman.chr6 512371 1 - 601863 G -s simHuman_chr6.simHuman.chr6 473027 1 + 601863 G -s simRat_chr6.simRat.chr6 499420 1 + 647215 G - -a -s simMouse_chr6.simMouse.chr6 491306 1 + 636262 G -s Anc0.Anc0refChr3 107521 1 + 222631 G -s Anc1.Anc1refChr6 141193 1 + 197743 G -s Anc2.Anc2refChr1 19397 1 + 142988 G -s mr.mrrefChr3 45492 1 + 181027 G -s simCow_chr6.simCow.chr6 507331 1 - 602619 G -s simCow_chr6.simCow.chr6 475901 1 + 602619 A -s simDog_chr6.simDog.chr6 466323 1 + 593897 G -s simHuman_chr6.simHuman.chr6 512390 1 - 601863 G -s simHuman_chr6.simHuman.chr6 473046 1 + 601863 G -s simRat_chr6.simRat.chr6 499439 1 + 647215 G - -a -s simMouse_chr6.simMouse.chr6 491330 5 + 636262 CCATG -s Anc0.Anc0refChr3 107547 5 + 222631 CCACA -s Anc1.Anc1refChr6 141219 5 + 197743 CCACA -s Anc2.Anc2refChr1 19423 5 + 142988 CCAAA -s mr.mrrefChr3 45516 5 + 181027 CCATG -s simCow_chr6.simCow.chr6 507357 5 - 602619 TCAAA -s simCow_chr6.simCow.chr6 475922 5 + 602619 CAAAA -s simDog_chr6.simDog.chr6 466348 5 + 593897 TCAAA -s simHuman_chr6.simHuman.chr6 512416 5 - 601863 CCACA -s simHuman_chr6.simHuman.chr6 473080 5 + 601863 CAACA -s simRat_chr6.simRat.chr6 499463 5 + 647215 CCATG - -a -s simMouse_chr6.simMouse.chr6 491345 1 + 636262 C -s Anc0.Anc0refChr3 107562 1 + 222631 C -s Anc1.Anc1refChr6 141234 1 + 197743 C -s Anc2.Anc2refChr1 19438 1 + 142988 C -s mr.mrrefChr3 45531 1 + 181027 C -s simCow_chr6.simCow.chr6 507372 1 - 602619 C -s simCow_chr6.simCow.chr6 475937 1 + 602619 C -s simDog_chr6.simDog.chr6 466363 1 + 593897 C -s simHuman_chr6.simHuman.chr6 512431 1 - 601863 C -s simHuman_chr6.simHuman.chr6 473095 1 + 601863 C -s simRat_chr6.simRat.chr6 499478 1 + 647215 C - -a -s simMouse_chr6.simMouse.chr6 491440 2 + 636262 TG -s Anc0.Anc0refChr3 107670 2 + 222631 AG -s Anc1.Anc1refChr6 141342 2 + 197743 AG -s Anc2.Anc2refChr1 19546 2 + 142988 AG -s mr.mrrefChr3 45626 2 + 181027 TG -s simCow_chr6.simCow.chr6 476048 2 + 602619 AG -s simDog_chr6.simDog.chr6 466471 2 + 593897 AG -s simHuman_chr6.simHuman.chr6 473203 2 + 601863 AG -s simRat_chr6.simRat.chr6 499573 2 + 647215 TG - -a -s simMouse_chr6.simMouse.chr6 491529 1 + 636262 C -s Anc0.Anc0refChr3 107845 1 + 222631 C -s Anc1.Anc1refChr6 141519 1 + 197743 C -s Anc2.Anc2refChr1 19715 1 + 142988 C -s Anc2.Anc2refChr2 23013 1 - 27695 T -s mr.mrrefChr3 45715 1 + 181027 C -s simCow_chr6.simCow.chr6 507641 1 - 602619 T -s simCow_chr6.simCow.chr6 476223 1 + 602619 C -s simHuman_chr6.simHuman.chr6 512716 1 - 601863 T -s simHuman_chr6.simHuman.chr6 473368 1 + 601863 C -s simRat_chr6.simRat.chr6 499662 1 + 647215 C - -a -s simMouse_chr6.simMouse.chr6 491548 2 + 636262 AC -s mr.mrrefChr3 45734 2 + 181027 AC -s simRat_chr6.simRat.chr6 499681 2 + 647215 AC - -a -s simMouse_chr6.simMouse.chr6 491574 6 + 636262 ATTGCT -s Anc0.Anc0refChr3 107890 6 + 222631 ATGGCT -s Anc1.Anc1refChr6 141564 6 + 197743 ATAGCT -s Anc2.Anc2refChr1 19759 6 + 142988 ATGGCC -s Anc2.Anc2refChr2 23058 6 - 27695 ATGGTG -s mr.mrrefChr3 45760 6 + 181027 ATTGCT -s simCow_chr6.simCow.chr6 507685 6 - 602619 AGGGTG -s simCow_chr6.simCow.chr6 476267 6 + 602619 ATGGCC -s simDog_chr6.simDog.chr6 493548 6 - 593897 ATGGTG -s simHuman_chr6.simHuman.chr6 512762 6 - 601863 ATAGTG -s simHuman_chr6.simHuman.chr6 473412 6 + 601863 ACAGAT -s simRat_chr6.simRat.chr6 499707 6 + 647215 ATTGCC - -a -s simMouse_chr6.simMouse.chr6 491590 2 + 636262 TA -s Anc0.Anc0refChr3 107907 2 + 222631 AA -s Anc1.Anc1refChr6 141581 2 + 197743 AA -s Anc2.Anc2refChr1 19776 2 + 142988 AA -s Anc2.Anc2refChr2 23075 2 - 27695 AA -s mr.mrrefChr3 45777 2 + 181027 TA -s simCow_chr6.simCow.chr6 507702 2 - 602619 AA -s simCow_chr6.simCow.chr6 476285 2 + 602619 AA -s simDog_chr6.simDog.chr6 493565 2 - 593897 AG -s simHuman_chr6.simHuman.chr6 512779 2 - 601863 AA -s simHuman_chr6.simHuman.chr6 473429 2 + 601863 AA - -a -s simMouse_chr6.simMouse.chr6 491606 27 + 636262 GTCAACCTGCTTGGTGTCTAGTGAAAC -s Anc0.Anc0refChr3 107925 25 + 222631 --CAACGTGCTTGGCTTTCAGCTAGTC -s Anc1.Anc1refChr6 141631 27 + 197743 GTCAACGTGCTTGGCTTTCAGCTAGTC -s Anc2.Anc2refChr1 19794 25 + 142988 --CAATGTGCTTGGCTATCAGTTAGTC -s mr.mrrefChr3 45793 27 + 181027 GTCAACCTGCTTGGTGTCTAGCGAAAC -s simCow_chr6.simCow.chr6 476303 25 + 602619 --CAATGTGCTTGGCTATCAGTTAGTC -s simHuman_chr6.simHuman.chr6 473445 27 + 601863 GACAACATGCTTGACATTAAGCTAGGC -s simRat_chr6.simRat.chr6 499734 26 + 647215 GTCAACCTGCTTGGTGTCCAGC-CAAC - -a -s simMouse_chr6.simMouse.chr6 491633 15 + 636262 AACCGGCAAATTCCA -s Anc0.Anc0refChr3 107950 15 + 222631 AATCAGCAAACTTCA -s Anc1.Anc1refChr6 141658 15 + 197743 AATCAGCAAACTTCA -s Anc2.Anc2refChr1 19819 15 + 142988 AATTTGCAAACTTCA -s mr.mrrefChr3 45820 15 + 181027 AACCAGCAAATTCCA -s simCow_chr6.simCow.chr6 476333 15 + 602619 AATTTGCAAACTTCA -s simHuman_chr6.simHuman.chr6 473472 15 + 601863 AATCAGCAGACTTCA -s simRat_chr6.simRat.chr6 499760 15 + 647215 AACCAGCCAATTCCA - -a -s simMouse_chr6.simMouse.chr6 491648 20 + 636262 ATGTGTGTGCTTTGTTTTGA -s Anc0.Anc0refChr3 107965 18 + 222631 ATGTGTG-GC-TTGTCTCAT -s Anc1.Anc1refChr6 141673 19 + 197743 ATGTGTGTGC-TTGTCTCAT -s Anc2.Anc2refChr1 19834 18 + 142988 ATGCATG-AC-TTGACCCAT -s mr.mrrefChr3 45835 20 + 181027 ATGTGTGTGCTTTGTTTTGA -s simCow_chr6.simCow.chr6 476349 18 + 602619 ATGCATG-AC-TTGACCCAT -s simHuman_chr6.simHuman.chr6 473487 19 + 601863 ATGTGTGTGC-TTGTCTCAT -s simRat_chr6.simRat.chr6 499775 20 + 647215 ATGTTTGTGCTTTGTTCTGA - -a -s simMouse_chr6.simMouse.chr6 491668 30 + 636262 TAGATTATAAGACACATATAATAACTTTCA -s Anc0.Anc0refChr3 107983 30 + 222631 TAGAATATACAACAAGTAAGATGATTTTCA -s Anc1.Anc1refChr6 141692 30 + 197743 TAGAATATACAACAAGTAAGATGATTTTCA -s Anc2.Anc2refChr1 19852 30 + 142988 TAAAATGCACAACAAGTAAAATGGTTATCA -s mr.mrrefChr3 45855 30 + 181027 TAGATTATAAAACAAGTATGATGATTTTCA -s simCow_chr6.simCow.chr6 476371 30 + 602619 TAAAATGCACAACAAGTAAAATGGTTATCA -s simHuman_chr6.simHuman.chr6 473506 30 + 601863 TAGAATATGCAACAAGTACGATGATTTTCA -s simRat_chr6.simRat.chr6 499795 30 + 647215 TAAATTATAGAACAAGTATGATGATTTTCA - -a -s simMouse_chr6.simMouse.chr6 491698 2 + 636262 TT -s Anc0.Anc0refChr3 108013 2 + 222631 TT -s Anc1.Anc1refChr6 141722 2 + 197743 TT -s Anc2.Anc2refChr1 19882 2 + 142988 TT -s mr.mrrefChr3 45885 2 + 181027 TT -s simCow_chr6.simCow.chr6 476401 2 + 602619 TT -s simHuman_chr6.simHuman.chr6 473537 2 + 601863 TT -s simRat_chr6.simRat.chr6 499825 2 + 647215 TT - -a -s simMouse_chr6.simMouse.chr6 491700 1 + 636262 T -s Anc0.Anc0refChr3 108236 1 + 222631 T -s Anc1.Anc1refChr6 141952 1 + 197743 T -s Anc2.Anc2refChr1 20117 1 + 142988 T -s mr.mrrefChr3 46096 1 + 181027 T -s simCow_chr6.simCow.chr6 476647 1 + 602619 G -s simDog_chr6.simDog.chr6 466842 1 + 593897 T -s simRat_chr6.simRat.chr6 500232 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 491701 46 + 636262 GAGAGACAGCTGAAGTCACTTGATTCTAGACCCTCACTTAATATCT -s Anc0.Anc0refChr3 108237 46 + 222631 GAGAGACAGCTGGAGACACTCCCTTGTAGGGCCCCACTTGGTTTCC -s Anc1.Anc1refChr6 141953 46 + 197743 GAGAGACAGCTGGAGACACTCCCTTGTAGGGCCCCACTTGGTTTCC -s Anc2.Anc2refChr1 20118 46 + 142988 GAGAGACAGCTGGAGACACTCCCTTGTAGGGCCCCACTTGGTTTCC -s mr.mrrefChr3 46098 46 + 181027 GAGAGACAGCTGGAGACACTTGATTCTAGACCCTCACTTGATTTCT -s simCow_chr6.simCow.chr6 476648 46 + 602619 GAGGGACAGCTGGAGACGCTCTTTTGTAAGGCCCTACTTAGTTACC -s simDog_chr6.simDog.chr6 466843 46 + 593897 GAGAGAGATATGGAGACACTCCCTTATAGGGCCCCATGTGGCTTCC -s simRat_chr6.simRat.chr6 500234 45 + 647215 -AGAGACAGCTGGAGACACTTGATTGTAGACCCTCACTTGATTTCT - -a -s simMouse_chr6.simMouse.chr6 491747 3 + 636262 CAG -s Anc0.Anc0refChr3 108284 3 + 222631 AAG -s Anc1.Anc1refChr6 142000 3 + 197743 AAG -s Anc2.Anc2refChr1 20165 3 + 142988 AAG -s mr.mrrefChr3 46145 3 + 181027 CAG -s simCow_chr6.simCow.chr6 476695 3 + 602619 AAA -s simDog_chr6.simDog.chr6 466890 3 + 593897 AAG -s simRat_chr6.simRat.chr6 500280 3 + 647215 CAG - -a -s simMouse_chr6.simMouse.chr6 491750 50 + 636262 GTTGTCACTTCCTACTTGTTTCAATATGGTAGCACTTGAGAATTGATGGT -s Anc0.Anc0refChr3 108287 48 + 222631 CATGTCACTTCTTACTCGTTGT--TATGGTATTACTTGGAAACTGATGGT -s Anc1.Anc1refChr6 142003 48 + 197743 CATGTCACTTCTTACTCGTTGT--TATGGTATTACTTGGAAACTGATGGT -s Anc2.Anc2refChr1 20169 48 + 142988 CATGTCACTTCTTACTCGTTGT--TATGGTATTACTTGGAAACTGATGGT -s mr.mrrefChr3 46148 50 + 181027 CATGTCACTTCCTACTCGTTTCAATATGGTAGTACTTGAGAATTGATGGT -s simCow_chr6.simCow.chr6 476699 48 + 602619 CATGATGCTCCTTACTTGTTGA--TACAGTAATACTTGGTGATTGATTGG -s simDog_chr6.simDog.chr6 466894 46 + 593897 CATGTCACTTCTTACTCGTAGT--TATGGCATTACTTGGACGCCT--GCA -s simRat_chr6.simRat.chr6 500283 50 + 647215 CATGTCACTTCCTACTCATTTCAATATGGTAGTGCTTGAGAATTGATGGT - -a -s simMouse_chr6.simMouse.chr6 491800 19 + 636262 ATGCCAATAGTATGTGAAG -s Anc0.Anc0refChr3 108335 19 + 222631 ATGCCAGTGGTTTCTCCAA -s Anc1.Anc1refChr6 142051 19 + 197743 ATGCCAGTGGTTTCTCCAA -s Anc2.Anc2refChr1 20256 19 + 142988 ATGCCAGTGGGTTCTCCAA -s mr.mrrefChr3 46198 19 + 181027 ATGCCAATAGTTTTTGAAA -s simCow_chr6.simCow.chr6 476798 18 + 602619 ATGCCACAGGGTTCGCCA- -s simDog_chr6.simDog.chr6 466982 19 + 593897 ATGCCAGGAGGTTTTTCAA -s simHuman_chr6.simHuman.chr6 473757 19 + 601863 ATGCCAGTGGTGTCCCCAG -s simRat_chr6.simRat.chr6 500333 19 + 647215 ATGCCGATAGTTTTTCGAA - -a -s simMouse_chr6.simMouse.chr6 491819 3 + 636262 CGA -s Anc0.Anc0refChr3 108354 3 + 222631 CGA -s Anc1.Anc1refChr6 142070 3 + 197743 CGA -s Anc2.Anc2refChr1 20275 3 + 142988 GGA -s mr.mrrefChr3 46217 3 + 181027 CGA -s simCow_chr6.simCow.chr6 476816 3 + 602619 GGA -s simDog_chr6.simDog.chr6 467001 3 + 593897 GGA -s simHuman_chr6.simHuman.chr6 473777 3 + 601863 CGT -s simRat_chr6.simRat.chr6 500352 3 + 647215 CGA - -a -s simMouse_chr6.simMouse.chr6 491822 32 + 636262 TTGGTTTGGAATGTCTGACCAGGCAAATGTTA -s Anc0.Anc0refChr3 108357 30 + 222631 TTGGGGAGGATTAGCTAGCT--GCAAATGCTG -s Anc1.Anc1refChr6 142073 32 + 197743 TTGGGGAGGATTAGCTAGCTAAGCAAATGCTG -s Anc2.Anc2refChr1 20280 30 + 142988 TTGGGGAGGATTAGCTAGCT--GCAAATGCTG -s mr.mrrefChr3 46220 32 + 181027 TTGGTTTGGATTGTCTGACTAGGCAAATGTTA -s simCow_chr6.simCow.chr6 476821 30 + 602619 TTGGGGAGGACTAGCTAACT--GCCAATGCTA -s simDog_chr6.simDog.chr6 467006 30 + 593897 TTGGGGTGGGTTAGCTAGCT--GCAGATATTG -s simHuman_chr6.simHuman.chr6 473780 30 + 601863 ATGGGAAAGATTAGCTAGCTAAT--AATGCTG -s simRat_chr6.simRat.chr6 500355 32 + 647215 TTGGTCTGGATTGTCTGATTAGGCAAATGCTA - -a -s simMouse_chr6.simMouse.chr6 491854 20 + 636262 TATGTGTCTGATGACCAGCT -s Anc0.Anc0refChr3 108390 18 + 222631 CATAAGCCAAAGGA--AGTT -s Anc1.Anc1refChr6 142108 18 + 197743 CATAAGCCAAAGGA--AGTT -s Anc2.Anc2refChr1 20313 18 + 142988 CATAAGCCAAAGGA--AGTT -s mr.mrrefChr3 46252 20 + 181027 TATGTGTCTGATGACCAGCT -s simCow_chr6.simCow.chr6 476854 17 + 602619 C-TGAGCCAAAGCA--AGTT -s simDog_chr6.simDog.chr6 467039 18 + 593897 CATAAGCCAATGGG--AGTT -s simHuman_chr6.simHuman.chr6 473813 18 + 601863 CATAAACTGAAGGA--AGTT -s simRat_chr6.simRat.chr6 500387 20 + 647215 TATGTGTCTGAAGACCAGCT - -a -s simMouse_chr6.simMouse.chr6 491874 1 + 636262 A -s Anc0.Anc0refChr3 108415 1 + 222631 A -s Anc1.Anc1refChr6 142133 1 + 197743 A -s Anc2.Anc2refChr1 20338 1 + 142988 A -s mr.mrrefChr3 46272 1 + 181027 A -s simCow_chr6.simCow.chr6 476878 1 + 602619 A -s simDog_chr6.simDog.chr6 467064 1 + 593897 A -s simHuman_chr6.simHuman.chr6 473838 1 + 601863 G -s simRat_chr6.simRat.chr6 500407 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 491875 16 + 636262 GCTAATCAGTTACTGG -s Anc0.Anc0refChr3 108416 16 + 222631 ACATGTTCGTTACTGA -s Anc1.Anc1refChr6 142134 16 + 197743 ACATGTTCGTTACTGA -s Anc2.Anc2refChr1 20341 16 + 142988 ACATGTTCGTTACTGA -s mr.mrrefChr3 46273 16 + 181027 ACTAATCAGTTACTGA -s simDog_chr6.simDog.chr6 467067 16 + 593897 AGATGTTCATTCTTGA -s simHuman_chr6.simHuman.chr6 473839 16 + 601863 ACATGTAGGTCACTGG -s simRat_chr6.simRat.chr6 500408 16 + 647215 ACTAATCAGTTACTGA - -a -s simMouse_chr6.simMouse.chr6 491891 6 + 636262 GATATG -s Anc0.Anc0refChr3 108432 6 + 222631 AATATA -s Anc1.Anc1refChr6 142150 6 + 197743 AATATA -s Anc2.Anc2refChr1 20357 6 + 142988 AATATA -s mr.mrrefChr3 46289 6 + 181027 GATATG -s simDog_chr6.simDog.chr6 467083 6 + 593897 AGTATA -s simHuman_chr6.simHuman.chr6 473856 6 + 601863 AATGCA -s simRat_chr6.simRat.chr6 500424 6 + 647215 GATATG - -a -s simMouse_chr6.simMouse.chr6 491897 8 + 636262 AACACATG -s Anc0.Anc0refChr3 108438 8 + 222631 AACACAGG -s Anc1.Anc1refChr6 142156 8 + 197743 AACACAGG -s Anc2.Anc2refChr1 20363 8 + 142988 AACACAGG -s mr.mrrefChr3 46295 8 + 181027 AACACATG -s simDog_chr6.simDog.chr6 467091 8 + 593897 ATCACAGG -s simHuman_chr6.simHuman.chr6 473862 8 + 601863 AACGCAGG -s simRat_chr6.simRat.chr6 500430 8 + 647215 AACACATG - -a -s simMouse_chr6.simMouse.chr6 491905 46 + 636262 GTAAATCTCAAGCTTGATCAATTTTTTTTATGAGATTGGATGTTAA -s Anc0.Anc0refChr3 108448 41 + 222631 GAAATTC-TTTCTCTAATCAA----TTTAGTGAGATTGGATTTTAA -s Anc1.Anc1refChr6 142166 41 + 197743 GAAATTC-TTTCTCTAATCAA----TTTAGTGAGATTGGATTTTAA -s Anc2.Anc2refChr1 20373 41 + 142988 GAAATTC-TTTCTCTAATCAA----TTTAGTGAGATTGGATTTTAA -s mr.mrrefChr3 46303 42 + 181027 GTAATTCACAAGCCTAATCAA----TTTTATGAGATTGGATGTTAA -s simDog_chr6.simDog.chr6 467101 41 + 593897 AAAGTTT-TTTCTCTAATCAA----TTTAGTGAGAGTGGATTTTAA -s simHuman_chr6.simHuman.chr6 473872 41 + 601863 GAAATTC-TTGTTCTAAATAA----TCTAGTGAGATCGCATTTTAA -s simRat_chr6.simRat.chr6 500438 41 + 647215 GCAATTCAC-AGCCTAATCAA----TTTTATGAGGTTGGATGTTAA - -a -s simMouse_chr6.simMouse.chr6 491951 3 + 636262 CAC -s Anc0.Anc0refChr3 108489 3 + 222631 TAC -s Anc1.Anc1refChr6 142207 3 + 197743 TAC -s Anc2.Anc2refChr1 20414 3 + 142988 TAC -s mr.mrrefChr3 46345 3 + 181027 CAC -s simDog_chr6.simDog.chr6 467142 3 + 593897 TAC -s simHuman_chr6.simHuman.chr6 473918 3 + 601863 AAC -s simRat_chr6.simRat.chr6 500479 3 + 647215 CAC - -a -s simMouse_chr6.simMouse.chr6 491954 45 + 636262 TCTAGGATGCTGTACATCTCATGAGCAGGGTATACTCCCTTTCTT -s Anc0.Anc0refChr3 108492 45 + 222631 GCTAAGATGGATAAGGTCTCATGAGCAGGGTATACTCCCTTCCTT -s Anc1.Anc1refChr6 142210 45 + 197743 GCTAAGATGGATAAGGTCTCATGAGCAGGGTATACTCCCTTCCTT -s Anc2.Anc2refChr1 20417 45 + 142988 GCTAAGATGGATAAGGTCTCATGAGCAGGGTATACTCCCTTCCTT -s mr.mrrefChr3 46348 45 + 181027 ACTAGGATGGAGAACGTCTCATGAGCAGGGTATACTCCCTTTCTT -s simDog_chr6.simDog.chr6 467190 45 + 593897 GCTAAGATGGATAAGGCCTCATGAGCAGGGTACACTCCCTTCCTT -s simHuman_chr6.simHuman.chr6 473921 38 + 601863 GCTAAGATAGATAAGGTC-------CAGGGTTTACTCCATTCATT -s simRat_chr6.simRat.chr6 500482 45 + 647215 ACTAGGATGGAGAACGTCTCATGAGCAGGGTATACCCCCTTTTCT - -a -s simMouse_chr6.simMouse.chr6 491999 8 + 636262 ATCCACCC -s Anc0.Anc0refChr3 108537 8 + 222631 AACTGCAC -s Anc1.Anc1refChr6 142255 8 + 197743 AACTGCAC -s Anc2.Anc2refChr1 20462 8 + 142988 AACTGCAC -s mr.mrrefChr3 46393 8 + 181027 ATCGACCC -s simDog_chr6.simDog.chr6 467235 8 + 593897 AACTGCAC -s simHuman_chr6.simHuman.chr6 473959 8 + 601863 AACTGCAT -s simRat_chr6.simRat.chr6 500529 8 + 647215 ATCGTCCA - -a -s simMouse_chr6.simMouse.chr6 492007 5 + 636262 ACAGG -s Anc0.Anc0refChr3 108546 5 + 222631 GCAGG -s Anc1.Anc1refChr6 142264 5 + 197743 GCAGG -s Anc2.Anc2refChr1 20471 5 + 142988 GCAGG -s mr.mrrefChr3 46401 5 + 181027 GCAGG -s simDog_chr6.simDog.chr6 467244 5 + 593897 GCAGG -s simHuman_chr6.simHuman.chr6 473968 5 + 601863 GCAGG -s simRat_chr6.simRat.chr6 500537 5 + 647215 GCAGT - -a -s simMouse_chr6.simMouse.chr6 492012 16 + 636262 TTCAGGGACCCAATGC -s Anc0.Anc0refChr3 108552 16 + 222631 TTTGGGGACCCAATGC -s Anc1.Anc1refChr6 142270 16 + 197743 TTTGGGGACCCAATGC -s Anc2.Anc2refChr1 20477 16 + 142988 TTTGGGGACCCAATGC -s mr.mrrefChr3 46406 16 + 181027 TTCAGGGACCCAATGC -s simDog_chr6.simDog.chr6 467250 16 + 593897 TTTGGGGACGCAATGC -s simHuman_chr6.simHuman.chr6 473974 16 + 601863 CTTGGGTACCTGATGC -s simRat_chr6.simRat.chr6 500542 16 + 647215 TTCAGGGACCCAATGC - -a -s simMouse_chr6.simMouse.chr6 492028 18 + 636262 TCATAAGAGACCATGGGC -s Anc0.Anc0refChr3 108568 4 + 222631 TGTT-------------- -s Anc1.Anc1refChr6 142286 4 + 197743 TGTT-------------- -s Anc2.Anc2refChr1 20493 4 + 142988 TGTT-------------- -s mr.mrrefChr3 46422 18 + 181027 TCATAAGAGACCATGGGC -s simDog_chr6.simDog.chr6 467269 4 + 593897 TGGT-------------- -s simHuman_chr6.simHuman.chr6 473990 4 + 601863 TATC-------------- -s simRat_chr6.simRat.chr6 500558 18 + 647215 TCATAAGGGGCCACCAGC - -a -s simMouse_chr6.simMouse.chr6 492046 200 + 636262 ATCCTTGTTAAGTCTGTTAATAGTAAGCACTTGCAATCAGACCAAATAATGGGTTTGCTTATGTATACCTGGTTGGCATCAACTTTTTAATTGACTCTTCCAATGGACTCTCTATTGTGTCTGGATCTTGAGGATTATTTTTGCCAACTTTGTGGGTGGACTAAGTACAAGAGGCGAGCACCCTATCTTGACCAGCTGGA -s Anc0.Anc0refChr3 108572 29 + 222631 -----------------------------------------------------------------------------------------------------------------------------------------------------------GTTATCTCAGTATG----------------CTTTGCCCTGCTGGA -s Anc1.Anc1refChr6 142290 45 + 197743 -----------------------------------------------------------------------------------------------------------------------------------------------------------GTTATCTCAGTATGAGAACATAGCACCTATCTTTGCCCTGCTGGA -s Anc2.Anc2refChr1 20497 29 + 142988 -----------------------------------------------------------------------------------------------------------------------------------------------------------TTTATATCAGGATG----------------CTTTGCCCTGCTGGA -s mr.mrrefChr3 46440 191 + 181027 ATCCTTGTTAAGTCTGTTAATAGTAAGCAC-----ATCAGACCAAATAATGGGTTTGCTTATGTATACCTGGTTGGCATCAACTTTTTAATTGACTCTTCCAATGGACTCTCTATTGTGTCTGGATCTTGAG----ATTTTTGCCAACTTTGTGGGTGGACTAAGTACAAGAGGCGAGCACCCTATCTTGACCAGCTGGA -s simCow_chr6.simCow.chr6 476879 10 + 602619 ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------A-TCTTGTAGA -s simDog_chr6.simDog.chr6 467273 29 + 593897 -----------------------------------------------------------------------------------------------------------------------------------------------------------TTTATATAAGGGTA----------------TTTTGCCTCCCTTGA -s simHuman_chr6.simHuman.chr6 473994 45 + 601863 -----------------------------------------------------------------------------------------------------------------------------------------------------------GTTATCTCAGTATGAGAACATAGCACCTATCTTTGCCCTGCTGGA -s simRat_chr6.simRat.chr6 500577 191 + 647215 ATCTTCGTCCAGTCTGTTAACAGTAAGCAT-----ACCGGACCAGATAATGGGTTCGCTTATGTATGCCTGGCTGGCATCAACTCTCTAATGTACTTTTACAATAGACTCTTTATTGTGTCTGGATCTTAAG----ATATTTGCTAATTTGGTGGGTGTATTAAGTACAGGAGGGGAACACCCTATCTTTAGCTGCTGGA - -a -s simMouse_chr6.simMouse.chr6 492246 24 + 636262 TCTGGCTCATGTCATGAACAGCTA -s Anc0.Anc0refChr3 108601 24 + 222631 TCTGGCTCATCTTATGAGCAGCTA -s Anc1.Anc1refChr6 142335 24 + 197743 TCTGGCTCATCTTATGAGCAGCTA -s Anc2.Anc2refChr1 20528 24 + 142988 TCTGACTCATCTTATGAGCATCTA -s mr.mrrefChr3 46631 24 + 181027 TCTGGCTCATGTCATGAACAGCTA -s simCow_chr6.simCow.chr6 476891 18 + 602619 TTAGACTCATCTT------ATCTA -s simDog_chr6.simDog.chr6 467304 24 + 593897 TCTGACTTTTCTGAAGAGCATCTA -s simHuman_chr6.simHuman.chr6 474039 24 + 601863 TCTGGCTCATCTTTTGAGCTGCTA -s simRat_chr6.simRat.chr6 500768 24 + 647215 TCTGGCTGATGTCATGAACAGCTA - -a -s simMouse_chr6.simMouse.chr6 492270 2 + 636262 GA -s Anc0.Anc0refChr3 108625 2 + 222631 GG -s Anc1.Anc1refChr6 142359 2 + 197743 GG -s Anc2.Anc2refChr1 20552 2 + 142988 GG -s mr.mrrefChr3 46655 2 + 181027 GA -s simCow_chr6.simCow.chr6 476909 2 + 602619 GG -s simDog_chr6.simDog.chr6 467328 2 + 593897 GG -s simHuman_chr6.simHuman.chr6 474063 2 + 601863 GG -s simRat_chr6.simRat.chr6 500793 2 + 647215 GG - -a -s simMouse_chr6.simMouse.chr6 492272 22 + 636262 AGACAACCAACCCCTGGATCCT -s Anc0.Anc0refChr3 108628 12 + 222631 AGATG----------AGATCAT -s Anc1.Anc1refChr6 142362 12 + 197743 AGATG----------AGATCAT -s Anc2.Anc2refChr1 20555 12 + 142988 AGATG----------AGATCAT -s mr.mrrefChr3 46657 12 + 181027 AGACA----------GGATCCT -s simCow_chr6.simCow.chr6 476912 12 + 602619 AGGTG----------AGAGCAT -s simDog_chr6.simDog.chr6 467331 12 + 593897 AGATG----------AGATCAT -s simHuman_chr6.simHuman.chr6 474066 12 + 601863 AGATG----------AGATCAT -s simRat_chr6.simRat.chr6 500795 12 + 647215 AGATA----------GGATCAT - -a -s simMouse_chr6.simMouse.chr6 492294 5 + 636262 CTTCC -s Anc0.Anc0refChr3 108678 5 + 222631 CTCCC -s Anc1.Anc1refChr6 142412 5 + 197743 CTCCC -s Anc2.Anc2refChr1 20605 5 + 142988 CCCCC -s mr.mrrefChr3 46669 5 + 181027 CTTCC -s simCow_chr6.simCow.chr6 476962 5 + 602619 GCCCC -s simDog_chr6.simDog.chr6 467381 5 + 593897 CCCTC -s simHuman_chr6.simHuman.chr6 474287 5 + 601863 CTCCC -s simRat_chr6.simRat.chr6 500807 5 + 647215 GTAAC - -a -s simMouse_chr6.simMouse.chr6 492299 6 + 636262 AGTGGA -s Anc0.Anc0refChr3 108683 6 + 222631 AATGAA -s Anc1.Anc1refChr6 142417 6 + 197743 AATGAA -s Anc2.Anc2refChr1 20610 6 + 142988 AATGAA -s mr.mrrefChr3 46674 6 + 181027 AGTGGA -s simCow_chr6.simCow.chr6 476968 6 + 602619 AATCAA -s simDog_chr6.simDog.chr6 467386 6 + 593897 AATGAA -s simHuman_chr6.simHuman.chr6 474292 5 + 601863 AA-GAA -s simRat_chr6.simRat.chr6 500812 6 + 647215 ATAACA - -a -s simMouse_chr6.simMouse.chr6 492305 2 + 636262 CA -s Anc0.Anc0refChr3 108689 2 + 222631 CA -s Anc1.Anc1refChr6 142423 2 + 197743 CA -s Anc2.Anc2refChr1 20616 2 + 142988 CA -s mr.mrrefChr3 46680 2 + 181027 CA -s simCow_chr6.simCow.chr6 476974 2 + 602619 CA -s simDog_chr6.simDog.chr6 467392 2 + 593897 CA -s simHuman_chr6.simHuman.chr6 474297 2 + 601863 CA -s simRat_chr6.simRat.chr6 500835 2 + 647215 CA - -a -s simMouse_chr6.simMouse.chr6 492307 7 + 636262 CCTAGGA -s Anc0.Anc0refChr3 108691 5 + 222631 TCAAT-- -s Anc1.Anc1refChr6 142425 5 + 197743 TCAAT-- -s Anc2.Anc2refChr1 20618 5 + 142988 TCAAT-- -s mr.mrrefChr3 46682 7 + 181027 CCAAGGA -s simCow_chr6.simCow.chr6 476986 5 + 602619 TCTGT-- -s simDog_chr6.simDog.chr6 467394 5 + 593897 TCAAT-- -s simHuman_chr6.simHuman.chr6 474299 5 + 601863 GCCAT-- -s simRat_chr6.simRat.chr6 500837 7 + 647215 CCAAGGA - -a -s simMouse_chr6.simMouse.chr6 492314 10 + 636262 TGTAAATGGG -s Anc0.Anc0refChr3 108696 10 + 222631 TTCAACTATG -s Anc1.Anc1refChr6 142430 10 + 197743 TTCAACTATG -s Anc2.Anc2refChr1 20625 10 + 142988 TTCAACTATG -s mr.mrrefChr3 46689 10 + 181027 CACAACTGTG -s simCow_chr6.simCow.chr6 476993 10 + 602619 TTCAACTATG -s simDog_chr6.simDog.chr6 467401 10 + 593897 TTCAACTGTG -s simHuman_chr6.simHuman.chr6 474304 10 + 601863 TTCAACTATG -s simRat_chr6.simRat.chr6 500844 10 + 647215 CACAACTGTG - -a -s simMouse_chr6.simMouse.chr6 492324 10 + 636262 TGAAAAAGCC -s Anc0.Anc0refChr3 108707 10 + 222631 TGAACAAGCC -s Anc1.Anc1refChr6 142441 10 + 197743 TGAACAAGCC -s Anc2.Anc2refChr1 20636 10 + 142988 TGAACAAGCC -s mr.mrrefChr3 46699 10 + 181027 TGAAAAAGCC -s simCow_chr6.simCow.chr6 477004 10 + 602619 TGAACAACCC -s simDog_chr6.simDog.chr6 467412 10 + 593897 TGAACAAGCC -s simHuman_chr6.simHuman.chr6 474315 10 + 601863 TGAACAAGCA -s simRat_chr6.simRat.chr6 500854 10 + 647215 TGAAAAAGCC - -a -s simMouse_chr6.simMouse.chr6 492334 52 + 636262 TTTAGTGGGAAATCTAAGACTCCATCCATAAGTCACGCTTGCAATGGGAGAT -s Anc0.Anc0refChr3 108717 47 + 222631 TTTA--GTGAGTTACAGTGAACC--CCATAAGTCATATTCATAATGA-AAAA -s Anc1.Anc1refChr6 142451 47 + 197743 TTTA--GTGAGTTACAGTGAACC--CCATAAGTCATATTCATAATGA-AAAA -s Anc2.Anc2refChr1 20646 47 + 142988 TTTA--ATGAGTTACACTGAACC--CCATAAGTCATATTCATGGTGA-AAAA -s mr.mrrefChr3 46709 51 + 181027 TTTAGTGGGAAATCTAGGACTCCATCCATAAGTCATGCTTGCAATGG-AGAA -s simCow_chr6.simCow.chr6 477014 47 + 602619 TGTA--ATGAGTTATGCTGGAGC--CAATAAGTCATATGCATGGTGA-AAGA -s simDog_chr6.simDog.chr6 467422 47 + 593897 TTTA--AGGAGTTACACTGAACC--CCATAAGTCATGTTCATGGTGA-AAAA -s simHuman_chr6.simHuman.chr6 474327 47 + 601863 TTTT--GTGAGTTTCAGTGTACC--CCATATGTTATATTCATAATGA-GAAA -s simRat_chr6.simRat.chr6 500864 51 + 647215 TTTGGTGGGAAATCTTGGACTCCATCCATAAGTCATCCTTGCAATAG-AGAA - -a -s simMouse_chr6.simMouse.chr6 492386 101 + 636262 GCATTTATAACCTGGAGCATCAAATAGGACTGACCCCTCAGGCAAAATTGTCAGAGACCTGCTATTGTAGTGAGACCTCAAGGAGACAAGTTTCATGATAG -s Anc0.Anc0refChr3 108764 101 + 222631 GCATTTATAACCTAGGGCCTAAAACAGACCTGACACCTCAGGCAAAATTGTCAGAGACATACTATTCTAGAGAGGTCTTAGGGAGACAAGTGCTATGACAA -s Anc1.Anc1refChr6 142498 101 + 197743 GCATTTATAACCTAGGGCCTAAAACAGACCTGACACCTCAGGCAAAATTGTCAGAGACATACTATTCTAGAGAGGTCTTAGGGAGACAAGTGCTATGACAA -s Anc2.Anc2refChr1 20694 101 + 142988 GCATTTATAAGCTAGGGCCTAACACAGACCTGACACCTCAGGCAAAATCATCAGAGACATACTATTCTAGAGAGGTCTTAGGGAGACAAGTGCTATGACAA -s mr.mrrefChr3 46760 101 + 181027 GCATTTATAACCTAGGGCATCAAATAGGACTGACCCCTCAGGCAAAATTGTCAGAGACATGCTATTGTAGTGAGGTCTTAAGGAGACAAGTGTCATGATAG -s simCow_chr6.simCow.chr6 477062 100 + 602619 GTATTTACAAACTAGGGCCTAATACA-ACCTGACACCTCAGTCAAAATCATTGGAGATACACCATTCTGTACAGATTTTAGGGAGACAAGTGCTATGGTAA -s simDog_chr6.simDog.chr6 467470 101 + 593897 GCATTTCTAAGCCAGGTCCTAACACAGTGCTGATACTACGGGCAAAATCACCAGTGACATACTATCCAAGAGAGGTCTAAGGGAGACAAGTGCCTTGACAA -s simHuman_chr6.simHuman.chr6 474374 101 + 601863 GCAGTTATAACCTAGGGCCTAGAACAGACCTGCCTCCTCAGGCAAAATTGTCAGAGGCATACTATTATACAGAGGTCTTAGGAAGACAAGTGCTATAACAA -s simRat_chr6.simRat.chr6 500915 99 + 647215 GCGTTTATAACCTATGGCTTCAAATAGGACTGACCTCTCTGGCAACATTAT--GAGACAAGCTATTGTAGGGAGGTCTTAAGCAAACAAATGTCATGATAC - -a -s simMouse_chr6.simMouse.chr6 492487 1 + 636262 C -s Anc0.Anc0refChr3 108865 1 + 222631 C -s Anc1.Anc1refChr6 142599 1 + 197743 C -s Anc2.Anc2refChr1 20797 1 + 142988 C -s mr.mrrefChr3 46861 1 + 181027 C -s simCow_chr6.simCow.chr6 477164 1 + 602619 T -s simDog_chr6.simDog.chr6 467573 1 + 593897 C -s simHuman_chr6.simHuman.chr6 474475 1 + 601863 C -s simRat_chr6.simRat.chr6 501014 1 + 647215 C - -a -s simMouse_chr6.simMouse.chr6 492488 77 + 636262 TTGTTGAATCATAAAGTTAAAGAATACTAGGTATGTGCATGATAACTGTGCTGGAAAACATCAGTGACATTACGCAA -s Anc0.Anc0refChr3 108873 77 + 222631 GTGTTGGATAGTAGAGTTAAGGAATACTAAGTATGTGCAAAATAACTGTGCTGGAAAACATCAGTGACTTAACATGA -s Anc1.Anc1refChr6 142607 77 + 197743 GTGTTGGATAGTAGAGTTAAGGAATACTAAGTATGTGCAAAATAACTGTGCTGGAAAACATCAGTGACTTAACATGA -s Anc2.Anc2refChr1 20805 77 + 142988 GTGTTTGATAGTAGAGTTAAGGAATACTAAGTATGTGCAAAATAACTGTGCTGGCAAACATTAGTGACTTAACATGA -s mr.mrrefChr3 46862 77 + 181027 TTGTTGAATCATAAAGTTAAAGAATACTAGGTATGTGCATAATAACTGTGCTGGAAAACATCAGTGACATTACGCAA -s simCow_chr6.simCow.chr6 477172 74 + 602619 GTGTTAGATAGTAGAGTTAAAGAATGCTAAGCATATGCA---CGACTGTACTGGTAGTCATTAGTAACTTTACCCGG -s simDog_chr6.simDog.chr6 467581 77 + 593897 GTGTTTGATGGTAGAGTTGAGGAATACTAAGTGTGTGGAAAATAACTGTGCTGACAAATATTAATGATTTAACATGA -s simHuman_chr6.simHuman.chr6 474483 77 + 601863 GTGTAGGATAGGTGAGTTAAGGAATACTAAGTATGTGCAAAATAACTGTGCTGGAAAGCATCAGTGACTTCACATCA -s simRat_chr6.simRat.chr6 501015 77 + 647215 TTGTTGAATCATAAAGATAGAGAACATTAGGTATGTGCACAATAACTGTGCTGGAAAACACCAATGACGTTATGCAA - -a -s simMouse_chr6.simMouse.chr6 492565 26 + 636262 ACCTGATTAGCCATACGCAGTTGTAA -s Anc0.Anc0refChr3 108952 16 + 222631 ACTTGGCTAGCCATAT---------- -s Anc1.Anc1refChr6 142686 16 + 197743 ACTTGGCTAGCCATAT---------- -s Anc2.Anc2refChr1 20884 16 + 142988 ACTTGGCTAGCCATAT---------- -s mr.mrrefChr3 46939 26 + 181027 ACTTGATTAGCCATATGCAGTTGTAA -s simCow_chr6.simCow.chr6 477248 16 + 602619 ACTTGGCTTGCCATAC---------- -s simDog_chr6.simDog.chr6 467660 16 + 593897 ACTTGGCTAGCCATAT---------- -s simHuman_chr6.simHuman.chr6 474562 16 + 601863 ACTTTGGTAGCCATAT---------- -s simRat_chr6.simRat.chr6 501092 26 + 647215 TCTTGATTAGTCATATGCAGATGTGG - -a -s simMouse_chr6.simMouse.chr6 492591 1 + 636262 G -s Anc0.Anc0refChr3 108968 1 + 222631 C -s Anc1.Anc1refChr6 142702 1 + 197743 C -s Anc2.Anc2refChr1 20905 1 + 142988 C -s mr.mrrefChr3 46965 1 + 181027 G -s simCow_chr6.simCow.chr6 477269 1 + 602619 C -s simDog_chr6.simDog.chr6 467681 1 + 593897 C -s simHuman_chr6.simHuman.chr6 474578 1 + 601863 C -s simRat_chr6.simRat.chr6 501118 1 + 647215 G - -a -s simMouse_chr6.simMouse.chr6 492592 38 + 636262 CATTGACGGCATTCCGCTCTGCTGCAATGATAGAGGTC -s Anc0.Anc0refChr3 108969 33 + 222631 CATTGTGGCCAG-----GCTTGTAGAACAATAGAGGGC -s Anc1.Anc1refChr6 142703 33 + 197743 CATTGTGGCCAG-----GCTTGTAGAACAATAGAGGGC -s Anc2.Anc2refChr1 20906 33 + 142988 CATTGTGGCCAG-----GCTTGTGGAACAATAGAGGGC -s mr.mrrefChr3 46966 33 + 181027 CATTGACGGCAG-----TCTGCTACAATGATAGAGGTC -s simCow_chr6.simCow.chr6 477279 33 + 602619 CAAGGTGGCCAG-----GCATCCGGAACAATAGAGGGG -s simDog_chr6.simDog.chr6 467682 33 + 593897 CATTGTGGGCAG-----GCTTGTGGTACCATAAAGGTC -s simHuman_chr6.simHuman.chr6 474579 33 + 601863 CTTTGTGGCCAG-----GCCTATAAAACAATAGAGGGC -s simRat_chr6.simRat.chr6 501119 33 + 647215 CATTGAAGGGAG-----TCTGCTACAATGATACTGGTC - -a -s simMouse_chr6.simMouse.chr6 492630 2 + 636262 TG -s Anc0.Anc0refChr3 109011 2 + 222631 TG -s Anc1.Anc1refChr6 142745 2 + 197743 TG -s Anc2.Anc2refChr1 20951 2 + 142988 TG -s mr.mrrefChr3 46999 2 + 181027 TG -s simCow_chr6.simCow.chr6 477324 2 + 602619 TT -s simDog_chr6.simDog.chr6 467727 2 + 593897 TG -s simHuman_chr6.simHuman.chr6 474621 2 + 601863 TG -s simRat_chr6.simRat.chr6 501152 2 + 647215 TG - -a -s simMouse_chr6.simMouse.chr6 492632 174 + 636262 TTAAAATGACTTTGGCTAGATCAATGATAGAGGTCTGTTACAATGACTTTGGCTAGATGGTTGAAACTTGGTGCATAGGTGGGCCGAGTAACAGAATTGCATGACTACGCCTAGAGCTTCTGCGTGGGCCTAGACCTTCTGCGTGGCTGCAAAAGATCAGTCTAGTCCTGTCCA -s Anc0.Anc0refChr3 109013 60 + 222631 ATTGCATGACTTTGCCAA--------------------------------------------GAAGATTGGTG--------------------------------------------------------CTATG--------------ACAAGAGTTAAACCTAGTCATGTTCA -s Anc1.Anc1refChr6 142747 60 + 197743 ATTGCATGACTTTGCCAA--------------------------------------------GAAGATTGGTG--------------------------------------------------------CTATG--------------ACAAGAGTTAAACCTAGTCATGTTCA -s Anc2.Anc2refChr1 20954 60 + 142988 ATTGCATCACTTTGCCAA--------------------------------------------GAAGATTGTTG--------------------------------------------------------CTGTG--------------ACAAGGGTTAAACCTGGTCAAGTTCA -s mr.mrrefChr3 47001 73 + 181027 TTAAAATGACTTTGGCTAGAT------------------------------------TGGTTGAAACTTGGTGCATA---------------------------------------------------CCTAGA--------------GCAAAAGATCAGTCTAGTCCTGTCCA -s simCow_chr6.simCow.chr6 477327 53 + 602619 ATTGCATCATCTTGTCAG--------------------------------------------GAAGACTGATG--------------------------------------------------------CTGTG--------------ACAAGGCCTAAACCTGATC------- -s simDog_chr6.simDog.chr6 467730 60 + 593897 ATTCCATCACTTTGCCAA--------------------------------------------GGAGATTGTTG--------------------------------------------------------TTGTG--------------ACATGGGTAAAACCTGGTCAAGTTCA -s simHuman_chr6.simHuman.chr6 474623 60 + 601863 ATTGCATGACGTTGCCAA--------------------------------------------AAAGATTGGTA--------------------------------------------------------CTATG--------------ACAAGAGTTAAACCTAGTCTTGTTCA -s simRat_chr6.simRat.chr6 501154 41 + 647215 TTAAAATAGTCTTGGCTAGAT------------------------------------TGGTTGAGACATAGTGCATA------------------------------------------------------------------------------------------------- - -a -s simMouse_chr6.simMouse.chr6 492806 9 + 636262 GCAACCATG -s Anc0.Anc0refChr3 109076 9 + 222631 GTAACAGTG -s Anc1.Anc1refChr6 142810 9 + 197743 GTAACAGTG -s Anc2.Anc2refChr1 21017 9 + 142988 GTAACAGTG -s mr.mrrefChr3 47074 9 + 181027 GCAACCATG -s simCow_chr6.simCow.chr6 477382 9 + 602619 GTAACTGTG -s simDog_chr6.simDog.chr6 467793 9 + 593897 GTAACAGTG -s simHuman_chr6.simHuman.chr6 474687 9 + 601863 GTAACAGTG - -a -s simMouse_chr6.simMouse.chr6 492815 6 + 636262 CATTTG -s Anc0.Anc0refChr3 109097 5 + 222631 -AATTG -s Anc1.Anc1refChr6 142831 6 + 197743 CAATTG -s Anc2.Anc2refChr1 21038 5 + 142988 -GATTG -s mr.mrrefChr3 47083 6 + 181027 CATTTG -s simCow_chr6.simCow.chr6 477403 5 + 602619 -GATTG -s simDog_chr6.simDog.chr6 467814 5 + 593897 -GATTG -s simHuman_chr6.simHuman.chr6 474708 6 + 601863 CAATTG - -a -s simMouse_chr6.simMouse.chr6 492821 24 + 636262 AGATCAAAATCCAGAGGAAAGGAT -s Anc0.Anc0refChr3 109106 24 + 222631 AGATCCAAATTTACAGGAAAGGAT -s Anc1.Anc1refChr6 142841 24 + 197743 AGATCCAAATTTACAGGAAAGGAT -s Anc2.Anc2refChr1 21047 24 + 142988 AGATTCATATTTACAGAAAAAGCT -s mr.mrrefChr3 47089 24 + 181027 AGATCAAAATCCAGAGGAAAGGAT -s simCow_chr6.simCow.chr6 477412 24 + 602619 AAATTCATCATTACAGAAAGAGCC -s simDog_chr6.simDog.chr6 467823 15 + 593897 AGA-----ATTTA----ATAAGCT -s simHuman_chr6.simHuman.chr6 474718 24 + 601863 AGATCCAAATTTACAGGAACGGAT - -a -s simMouse_chr6.simMouse.chr6 492933 3 + 636262 GTC -s Anc0.Anc0refChr3 109235 3 + 222631 GAC -s Anc1.Anc1refChr6 142975 3 + 197743 GAC -s Anc2.Anc2refChr1 21176 3 + 142988 GAC -s mr.mrrefChr3 47201 3 + 181027 GTC -s simCow_chr6.simCow.chr6 477531 3 + 602619 GAC -s simDog_chr6.simDog.chr6 467943 3 + 593897 GAC -s simHuman_chr6.simHuman.chr6 474854 3 + 601863 GAC - -a -s simMouse_chr6.simMouse.chr6 492936 60 + 636262 TTGATTTGATTGCCGAAGGATTTTTGATGTGGTCCCTAAAAGGTCTGATGAAAGTATAAT -s Anc0.Anc0refChr3 109238 55 + 222631 TCTTGTTGA-TTCAGAAGGAT---TGCTGTGGCCCCTAGAAGGTCTGGATAAACTGG-AT -s Anc1.Anc1refChr6 142978 55 + 197743 TCTTGTTGA-TTCAGAAGGAT---TGCTGTGGCCCCTAGAAGGTCTGGATAAACTGG-AT -s Anc2.Anc2refChr1 21206 55 + 142988 CCTTGTTCA-TTCAGAAGAAT---TGCTGTGGCCCCTAGAATGTCTGGATGAACTGG-AT -s mr.mrrefChr3 47204 57 + 181027 TTGATTTGATTGCCGAAGGAT---TGATGTGGCCCCTAAAAGGTCTGATGAAAGTATAAT -s simCow_chr6.simCow.chr6 477562 54 + 602619 CCTTATTTA-TTCAGAAGAAT---TGCTGTGGCACCTAGAACGGCTGG-TGAACTGG-AA -s simDog_chr6.simDog.chr6 467973 54 + 593897 CCTTGTTCA-TTCAGAAGAAT---TACTGTCACCCCAATGATGTC-ATATGAACTGG-AT -s simHuman_chr6.simHuman.chr6 474857 55 + 601863 TCATGCTGA-TACTGAAGGAT---TGCTATGGCCCCTAGAAGGTCTGGGTAAACTGA-AT -s simRat_chr6.simRat.chr6 501213 32 + 647215 ----------------------------CTGGCCCCTAAAAAGCCTGATAAAAGTATAAT - -a -s simMouse_chr6.simMouse.chr6 492996 1 + 636262 A -s Anc0.Anc0refChr3 109293 1 + 222631 T -s Anc1.Anc1refChr6 143033 1 + 197743 T -s Anc2.Anc2refChr1 21261 1 + 142988 T -s mr.mrrefChr3 47261 1 + 181027 A -s simDog_chr6.simDog.chr6 468027 1 + 593897 T -s simHuman_chr6.simHuman.chr6 474912 1 + 601863 T -s simRat_chr6.simRat.chr6 501246 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 492997 7 + 636262 CAGCCAG -s Anc0.Anc0refChr3 109294 7 + 222631 CTGACAG -s Anc1.Anc1refChr6 143034 7 + 197743 CTGACAG -s Anc2.Anc2refChr1 21266 7 + 142988 CTGACTT -s mr.mrrefChr3 47262 7 + 181027 CAGCCAG -s simCow_chr6.simCow.chr6 477620 7 + 602619 ATGCCTC -s simDog_chr6.simDog.chr6 468032 7 + 593897 CTGACTT -s simHuman_chr6.simHuman.chr6 474913 7 + 601863 CGGGGAG -s simRat_chr6.simRat.chr6 501247 7 + 647215 CAGCCAG - -a -s simMouse_chr6.simMouse.chr6 493004 36 + 636262 TGATAATATCAGATGGTGTAATGTCATGACAGCAGT -s Anc0.Anc0refChr3 109304 36 + 222631 TCATTATAACAGACAGTATAATATCATGCCAGCAGT -s Anc1.Anc1refChr6 143044 36 + 197743 TCATTATAACAGACAGTATAATATCATGCCAGCAGT -s Anc2.Anc2refChr1 21276 36 + 142988 TCATTGTAACAGACATTATAATATCATGCCAGCAGT -s mr.mrrefChr3 47269 36 + 181027 TGATAATAACAGACAGTGTAATGTCATGACAGCAGT -s simCow_chr6.simCow.chr6 477630 36 + 602619 TCATTGTAGCAGACATTGTAATATAATCCCAGAAGT -s simDog_chr6.simDog.chr6 468042 36 + 593897 TCATTGTAACCGACATTATAATATCATGCCAGCAGT -s simHuman_chr6.simHuman.chr6 474923 23 + 601863 TTATCATAACAGACAG-------------CAGCAGT -s simRat_chr6.simRat.chr6 501254 36 + 647215 TGATAATAATAGACAGTTTAATGTCATGACAGCAGA - -a -s simMouse_chr6.simMouse.chr6 493040 1 + 636262 A -s Anc0.Anc0refChr3 109340 1 + 222631 T -s Anc1.Anc1refChr6 143080 1 + 197743 T -s Anc2.Anc2refChr1 21312 1 + 142988 T -s mr.mrrefChr3 47305 1 + 181027 A -s simCow_chr6.simCow.chr6 477668 1 + 602619 T -s simDog_chr6.simDog.chr6 468078 1 + 593897 T -s simHuman_chr6.simHuman.chr6 474946 1 + 601863 T -s simRat_chr6.simRat.chr6 501290 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 493041 6 + 636262 CAAAAA -s Anc0.Anc0refChr3 109342 6 + 222631 CACAAA -s Anc1.Anc1refChr6 143082 6 + 197743 CACAAA -s Anc2.Anc2refChr1 21314 6 + 142988 CACAAA -s mr.mrrefChr3 47307 6 + 181027 CAAAAA -s simCow_chr6.simCow.chr6 477670 6 + 602619 CACAAA -s simDog_chr6.simDog.chr6 468080 6 + 593897 CACAAA -s simHuman_chr6.simHuman.chr6 474948 6 + 601863 CACAAA -s simRat_chr6.simRat.chr6 501292 6 + 647215 CAAAAA - -a -s simMouse_chr6.simMouse.chr6 493047 53 + 636262 TAATATGGATGGTTAAGAGTAGTGGGTACAGAATTGAAGGATGCAGCATAATA -s Anc0.Anc0refChr3 109351 53 + 222631 TAAAAAGAATGGTTAAGAGAAGAGGCTGGATATTTGAAAGATGTAACATAATC -s Anc1.Anc1refChr6 143091 53 + 197743 TAAAAAGAATGGTTAAGAGAAGAGGCTGGATATTTGAAAGATGTAACATAATC -s Anc2.Anc2refChr1 21323 53 + 142988 TAAAAAGAATGGCTAAGACAACAGGCTGGATATTTGAAAGATGTAACATAATC -s mr.mrrefChr3 47313 53 + 181027 TAATATGGATGGTTAAGAGTAGTGGGTACAGAATTGAAGGATGCAGCATAATA -s simCow_chr6.simCow.chr6 477679 47 + 602619 TAAAATACATCACTAAGCACGTAGGTT------TTGTTGGGTGCAACATCATC -s simDog_chr6.simDog.chr6 468089 53 + 593897 TACAAAGAATGGCTCAAACAACAGGCTGGATATTTGAAAGATGTAATACAATC -s simHuman_chr6.simHuman.chr6 474957 53 + 601863 TAAGAAGAGTGGTTAAGAGAAGAGGCTGGATATTTGAAAGATGTAACATAATT -s simRat_chr6.simRat.chr6 501298 46 + 647215 TAATATGGATGGTTAAGATTAGTGGGGAC------GAAGGATGCATTA-AATA - -a -s simMouse_chr6.simMouse.chr6 493100 19 + 636262 CAGAGGCCCTTGACATTGA -s Anc0.Anc0refChr3 109404 17 + 222631 C-AAGGC-AGTAATAAGTG -s Anc1.Anc1refChr6 143144 17 + 197743 C-AAGGC-AGTAATAAGTG -s Anc2.Anc2refChr1 21376 17 + 142988 A-AAGGC-AGTAATAAGTG -s mr.mrrefChr3 47366 19 + 181027 CAAAGGCCCTTGACATTGG -s simCow_chr6.simCow.chr6 477727 17 + 602619 A-AAGGC-AGTAATAAGTG -s simDog_chr6.simDog.chr6 468142 17 + 593897 A-AGAAC-AGTCATTAGTG -s simHuman_chr6.simHuman.chr6 475010 17 + 601863 C-AAGGC-AGTAATAAGTG -s simRat_chr6.simRat.chr6 501344 19 + 647215 CAAAGGCACCTGAAACTGG - -a -s simMouse_chr6.simMouse.chr6 493119 27 + 636262 ACCATTATTACTGTCGCTGACAACTTC -s Anc0.Anc0refChr3 109421 27 + 222631 ATCATCACTGCTGTCTCTGACAACTTT -s Anc1.Anc1refChr6 143161 27 + 197743 ATCATCACTGCTGTCTCTGACAACTTT -s Anc2.Anc2refChr1 21394 27 + 142988 ATCATTACTGCTGTCTCTGACAACTTT -s mr.mrrefChr3 47385 27 + 181027 ACCATCATTACTGTCGCTGACAACTTC -s simCow_chr6.simCow.chr6 477745 27 + 602619 ATCATTACTGCTGTCTCGGACAACCTT -s simDog_chr6.simDog.chr6 468160 27 + 593897 ATCATTACTGCTGTCTCTGACAACTTT -s simHuman_chr6.simHuman.chr6 475027 27 + 601863 ATCATCACTGCTGCCTCTGACCACTTT -s simRat_chr6.simRat.chr6 501363 27 + 647215 ACCGCCATTACTGTCGCTGACAACTTC - -a -s simMouse_chr6.simMouse.chr6 493146 62 + 636262 ATCTAGGCTTGATACTCCTCGCAACCCAATGGTAGAGCATTCAATAACTATGTTTGGCTTGG -s Anc0.Anc0refChr3 109448 46 + 222631 ATCTATGCTTGAG-CACTTCGTAACCCAAT----GGG-----------TATGTACAGGCTTG -s Anc1.Anc1refChr6 143188 50 + 197743 ATCTATGCTTGAG-CACTTCGTAACCCAATGGTGGGG-----------TATGTACAGGCTTG -s Anc2.Anc2refChr1 21421 46 + 142988 ATCTATACTTCAG-CATTTTCTAACCCAAT----GGA-----------TATTTACAGGCTTG -s mr.mrrefChr3 47412 62 + 181027 ATCTAGGCTTGATACTCTTCGCAACCCAATGGTAGAGCATTCAATAACTATGTTTGGCTTGG -s simCow_chr6.simCow.chr6 477772 45 + 602619 ATCTGC-CTCCAC-CAATTTCTAACCCAAT----GGA-----------TATTTACAGGCTTG -s simDog_chr6.simDog.chr6 468188 27 + 593897 ATCTATACTTCAG-CATTTTCTAACCCA---------------------------------- -s simHuman_chr6.simHuman.chr6 475054 50 + 601863 ATCTATGCTTGAG-CACTTCGTAACCTATGGGTGGGG-----------TATGTACAGGCTTG -s simRat_chr6.simRat.chr6 501390 62 + 647215 ATCAAGGCTTGATACTCTTTGCAACCCAATGGTAAAGCACTCAATAACCAAGTTGGGCTTGG - -a -s simMouse_chr6.simMouse.chr6 493208 21 + 636262 TTAACAGCACCCTAAGCTCCT -s Anc0.Anc0refChr3 109494 14 + 222631 TTCACACCACCTTC------- -s Anc1.Anc1refChr6 143238 18 + 197743 TTCACACCACCTTCAG---CT -s Anc2.Anc2refChr1 21467 14 + 142988 TTCACCTCACCTTC------- -s mr.mrrefChr3 47474 21 + 181027 TTAACACCACCCTAAGCTCCT -s simCow_chr6.simCow.chr6 477818 14 + 602619 TTCACCTCACCTTC------- -s simHuman_chr6.simHuman.chr6 475104 18 + 601863 TTCACACCACCTTCAG---CT -s simRat_chr6.simRat.chr6 501452 21 + 647215 CTAAGACCACCCTACGCTCCT - -a -s simMouse_chr6.simMouse.chr6 493229 11 + 636262 GATTAAATAGC -s Anc1.Anc1refChr6 143262 11 + 197743 GATTAATTAGC -s mr.mrrefChr3 47501 11 + 181027 GATTAATTAGC -s simHuman_chr6.simHuman.chr6 475128 11 + 601863 GATTAATTAGC -s simRat_chr6.simRat.chr6 501479 11 + 647215 GATTAATTAGC - -a -s simMouse_chr6.simMouse.chr6 493240 100 + 636262 TTTAGCCACTAGCAGACCAGCAGAGATTGGTCTTTTTTATTTTGGAACCCTTGCCCTTGGCTTGCACAGGTTGAGGAAGATGACAACCTTAACTTGATGC -s Anc0.Anc0refChr3 109508 84 + 222631 ----------------CCAGTAGGTTTTGGCCTTCTTTGTTTAGGAACCATAGCCATTGCCTTGGACTGGTTATGGAACATCACAGCCTCAATGCCACCA -s Anc1.Anc1refChr6 143273 96 + 197743 TTCAACCT---GCAG-CCAGTAGGTTTTGGCCTTCTTTGTTTAGGAACCATAGCCATTGCCTTGGACTGGTTATGGAACATCACAGCCTCAATGCCACCA -s Anc2.Anc2refChr1 21481 84 + 142988 ----------------TTAGTAGGTTTTGGCCTTCTCTGTTTAGGAACCATAGACATTGCCCTGGACTGGTTATGGTACATCATAGCCTCAATGCCACCA -s mr.mrrefChr3 47512 97 + 181027 TTTAGCCA---GCAGACCAGCAGAGATTGGTCTTTTTTATTTTGGAACCCTTGCCCTTGGCTTGCACAGGTTAAGGAAGATGACAACCTTAACTTGATGC -s simCow_chr6.simCow.chr6 477832 84 + 602619 ----------------TTAGTAGGTTTTGGCCTTCTCTGATCAGGAACCATAGACATTACTCTGGATTGGTTATGCTACATCAAAGCCTCAATCCCACCA -s simDog_chr6.simDog.chr6 468215 62 + 593897 --------------------------------------GTGTGGGAACCATAGATATTGTCCTGGGCTGGCTATGGTTCATCGTAGCCTTGATGCCTCCA -s simHuman_chr6.simHuman.chr6 475150 96 + 601863 TTCAACCT---GCAG-CCAGTAGGTTTCAACCTTGTTAGTTTAGGAGCCATAGCCAATGCCTTGGACCGCTTATGTAATGCCACAGCCTCAGTGCAACCA -s simRat_chr6.simRat.chr6 501490 55 + 647215 TTTAGCCA---GCAGAC------------------------------------------GCCTGCACTAGTTAAGGAAAATGACAACCTAAACTAGATGC - -a -s simMouse_chr6.simMouse.chr6 493340 7 + 636262 CTGTAAG -s Anc0.Anc0refChr3 109592 7 + 222631 CAGTGGG -s Anc1.Anc1refChr6 143369 7 + 197743 CAGTGGG -s Anc2.Anc2refChr1 21566 7 + 142988 CAATGGA -s mr.mrrefChr3 47609 7 + 181027 CTGTAAG -s simCow_chr6.simCow.chr6 477917 7 + 602619 CAATGCA -s simDog_chr6.simDog.chr6 468278 7 + 593897 CAAGGGA -s simHuman_chr6.simHuman.chr6 475246 7 + 601863 CAGTGTG -s simRat_chr6.simRat.chr6 501545 7 + 647215 CTGTAAG - -a -s simMouse_chr6.simMouse.chr6 493347 21 + 636262 TCCATCAAGTTCAGCAGCTTT -s Anc0.Anc0refChr3 109605 21 + 222631 CTTATAGGGTTGAACAGCTGT -s Anc1.Anc1refChr6 143382 21 + 197743 CTTATAGGGTTGAACAGCTGT -s Anc2.Anc2refChr1 21579 21 + 142988 CTTATAGGGTTGAACAGCTGT -s mr.mrrefChr3 47616 21 + 181027 TTCATCAAGTTCAGCAGCTTT -s simCow_chr6.simCow.chr6 477930 19 + 602619 TTTATACAGTTA--CAGCTGT -s simDog_chr6.simDog.chr6 468291 21 + 593897 CTTATAGGGATGAATAACTGC -s simHuman_chr6.simHuman.chr6 475259 21 + 601863 CTGATATGGTTGACCAGCTGT -s simRat_chr6.simRat.chr6 501552 21 + 647215 TTTAACAAGTTCAGCAGCTTT - -a -s simMouse_chr6.simMouse.chr6 493368 7 + 636262 GTGAAAT -s Anc0.Anc0refChr3 109626 7 + 222631 GTACAAT -s Anc1.Anc1refChr6 143403 7 + 197743 GTACAAT -s Anc2.Anc2refChr1 21600 7 + 142988 GTACAAT -s mr.mrrefChr3 47637 7 + 181027 GTGAAAT -s simCow_chr6.simCow.chr6 477949 7 + 602619 GTACAAT -s simDog_chr6.simDog.chr6 468331 7 + 593897 GTACATG -s simHuman_chr6.simHuman.chr6 475280 7 + 601863 GTATAAT -s simRat_chr6.simRat.chr6 501573 7 + 647215 GTGAAAT - -a -s simMouse_chr6.simMouse.chr6 493375 31 + 636262 TTGCACTACAGCCCCTAAGGCACCTATCCTT -s Anc0.Anc0refChr3 109633 14 + 222631 TTG---------TCTGATGG--------GTT -s Anc1.Anc1refChr6 143410 14 + 197743 TTG---------TCTGATGG--------GTT -s Anc2.Anc2refChr1 21607 14 + 142988 TTC---------TCTGATGG--------GTG -s mr.mrrefChr3 47644 14 + 181027 TTG---------CCCTAAGG--------CTT -s simCow_chr6.simCow.chr6 477960 14 + 602619 CTC---------TCTGATGG--------GTG -s simDog_chr6.simDog.chr6 468338 14 + 593897 TTC---------CCTAATGG--------GTG -s simHuman_chr6.simHuman.chr6 475287 14 + 601863 TTG---------TCAGATGA--------GTT -s simRat_chr6.simRat.chr6 501580 11 + 647215 ------------CCCTAAGG--------CTT - -a -s simMouse_chr6.simMouse.chr6 493406 28 + 636262 CATTAGAGGAAATGAAGGTGCTGGTGCT -s Anc0.Anc0refChr3 109821 23 + 222631 CAGTAGAGGAAATGAAGGTACTA----- -s Anc1.Anc1refChr6 143598 23 + 197743 CAGTAGAGGAAATGAAGGTACTA----- -s Anc2.Anc2refChr1 21815 23 + 142988 TAGTACGGGAAATGAAGGTACTA----- -s mr.mrrefChr3 47658 28 + 181027 CAGTAGAGGAAATGAAGGTGCTGGTGCT -s simCow_chr6.simCow.chr6 478151 10 + 602619 -------------GTAGGTACTA----- -s simDog_chr6.simDog.chr6 468545 23 + 593897 TAGTACGGGAAATGAAGGTACTA----- -s simHuman_chr6.simHuman.chr6 475481 23 + 601863 CAGTAGAGGATATGGAGGTACTA----- -s simRat_chr6.simRat.chr6 501591 28 + 647215 CAGTAGAGGAAATGAAGGTACTGGTGCT - -a -s simMouse_chr6.simMouse.chr6 493434 86 + 636262 ACTTGCCTGCACTTGTATGACATGGCCCCTCATAGCAGATCCTATGCCCTCTGGCCAGTATGTTGCTGGGGCTCGCCTATAGGTAC -s Anc0.Anc0refChr3 109844 11 + 222631 --T-------------------------------------------------------------------------CTATCAGCAC -s Anc1.Anc1refChr6 143621 11 + 197743 --T-------------------------------------------------------------------------CTATCAGCAC -s Anc2.Anc2refChr1 21838 11 + 142988 --C-------------------------------------------------------------------------CTTTCAGCAC -s mr.mrrefChr3 47686 13 + 181027 ACT-------------------------------------------------------------------------CTATAGGTAC -s simCow_chr6.simCow.chr6 478161 11 + 602619 --C-------------------------------------------------------------------------CTGTCAGCAG -s simDog_chr6.simDog.chr6 468568 11 + 593897 --C-------------------------------------------------------------------------CTTTCAGCAC -s simHuman_chr6.simHuman.chr6 475504 11 + 601863 --T-------------------------------------------------------------------------CTATTAGCAC -s simRat_chr6.simRat.chr6 501636 13 + 647215 ATT-------------------------------------------------------------------------CTACTGGTCC - -a -s simMouse_chr6.simMouse.chr6 493520 2 + 636262 CA -s Anc0.Anc0refChr3 109901 2 + 222631 CA -s Anc1.Anc1refChr6 143678 2 + 197743 CA -s Anc2.Anc2refChr1 21919 2 + 142988 CA -s mr.mrrefChr3 47699 2 + 181027 CA -s simCow_chr6.simCow.chr6 478242 2 + 602619 CA -s simDog_chr6.simDog.chr6 468656 2 + 593897 CA -s simHuman_chr6.simHuman.chr6 475561 2 + 601863 CA -s simRat_chr6.simRat.chr6 501649 2 + 647215 AA - -a -s simMouse_chr6.simMouse.chr6 493522 102 + 636262 CTTACAACATTTTTGTGAAAGAAGAGCTGTGTGCTGTGTCATTCAACCATAATGAAAAGAGATCCAAATGAATTGTTTCACCCTGTTATCATTGTTACCAAG -s Anc0.Anc0refChr3 109903 53 + 222631 CTTATAACATTTTTGT----GAAGA---------------------------------------------AAGAGTTGCACCATGCTATCAGTGAAAGCAAG -s Anc1.Anc1refChr6 143680 53 + 197743 CTTATAACATTTTTGT----GAAGA---------------------------------------------AAGAGTTGCACCATGCTATCAGTGAAAGCAAG -s Anc2.Anc2refChr1 21921 53 + 142988 CTTATAACATTTTTTT----GAAGA---------------------------------------------AAGAGTTGCACCATGCTATCGGCAAAAGCAAA -s mr.mrrefChr3 47701 97 + 181027 CTTACAACATTTTTGT----GAAGAGCTG-GTGCTGTGTCATTCAACCATAATGAAAAGAGATCCAAATGAATTGTTTCACCCTGTTATCATTGTTACCAAG -s simCow_chr6.simCow.chr6 478244 52 + 602619 CTTATACAATCTTTTT----GAAGA---------------------------------------------AA-CGTTGCACCATGCTACCTGCAACAACAAT -s simDog_chr6.simDog.chr6 468658 53 + 593897 CCTGCAACATTTTCTT----GGAGA---------------------------------------------AAGAGTTGCACCATATAATTGGCAAATGCAAA -s simHuman_chr6.simHuman.chr6 475563 53 + 601863 CTTATTACATTTTTGT----GAAAA---------------------------------------------AAGAGTTGCATCATGCTATCAATGAGATCAAG -s simRat_chr6.simRat.chr6 501656 97 + 647215 CATACCTCATCTTCTC----AAAGTCCTG-GGACTGGGAGGTCTAACAATAATGAAAAGAGATCCTAATGAATTGTTTCAACCTGTTGCCATTGTTTGCAGC - -a -s simMouse_chr6.simMouse.chr6 493624 1 + 636262 C -s Anc0.Anc0refChr3 110190 1 + 222631 C -s Anc1.Anc1refChr6 143967 1 + 197743 C -s Anc2.Anc2refChr1 22235 1 + 142988 C -s mr.mrrefChr3 47798 1 + 181027 C -s simDog_chr6.simDog.chr6 468987 1 + 593897 C -s simHuman_chr6.simHuman.chr6 475850 1 + 601863 C -s simRat_chr6.simRat.chr6 501753 1 + 647215 C - -a -s simMouse_chr6.simMouse.chr6 493625 21 + 636262 TGTGACCTCAGTGTAAGTTGC -s Anc0.Anc0refChr3 110192 21 + 222631 TGTTACCCTAGTGAAAGTATC -s Anc1.Anc1refChr6 143969 21 + 197743 TGTTACCCTAGTGAAAGTATC -s Anc2.Anc2refChr1 22237 21 + 142988 TGTTGCCCTGGTGAAAGTATC -s mr.mrrefChr3 47800 21 + 181027 TGTGACCTCAGTGTAAGTTTC -s simCow_chr6.simCow.chr6 478497 20 + 602619 -ATTGCCCTGGTGGAAGTAAC -s simDog_chr6.simDog.chr6 468989 21 + 593897 TGTTGCCCTGGTGAAAGTATC -s simHuman_chr6.simHuman.chr6 475852 21 + 601863 TGTTACCCTAGTGAAAGTATC -s simRat_chr6.simRat.chr6 501755 21 + 647215 TCTAACTTCAGTGTAAGTTTC - -a -s simMouse_chr6.simMouse.chr6 493646 22 + 636262 TGTCATAAGGATGAGTATCTTC -s Anc0.Anc0refChr3 110213 22 + 222631 AGTCATAAGTAAGAGGATCTTC -s Anc1.Anc1refChr6 143990 22 + 197743 AGTCATAAGTAAGAGGATCTTC -s Anc2.Anc2refChr1 22259 22 + 142988 AGTTATAAGTAAGAGGATCTTC -s mr.mrrefChr3 47821 22 + 181027 AGTCATAAGGATGAGTATCTTC -s simCow_chr6.simCow.chr6 478518 20 + 602619 ACTTATAAGTAATGG--TCTTC -s simDog_chr6.simDog.chr6 469011 22 + 593897 AGTTGTAAGTGAGAGGATTGTC -s simHuman_chr6.simHuman.chr6 475873 22 + 601863 AGTCATATGTAAGAGGACCTCC -s simRat_chr6.simRat.chr6 501776 22 + 647215 AGTCATAAGGATGGGTATCTTC - -a -s simMouse_chr6.simMouse.chr6 493668 103 + 636262 CCCCAGACCTACCACCAATCAAGAAAAACTTTTATAAGGAGTCCACTGCAATGAGCACCATGACAAAAGTGCAAGCAGATAGTTGGAAGTATATCTCCATCAC -s Anc0.Anc0refChr3 110239 103 + 222631 CCCCAGATCTGCCACCAATCAAGAAGAACTTTTATAAGGAGTCCACTGCAATGAGTACTATGACAAAAGTACAAGCAGATAGTTGGAGGTATATTCCCATCCT -s Anc1.Anc1refChr6 144016 103 + 197743 CCCCAGATCTGCCACCAATCAAGAAGAACTTTTATAAGGAGTCCACTGCAATGAGTACTATGACAAAAGTACAAGCAGATAGTTGGAGGTATATTCCCATCCT -s Anc2.Anc2refChr1 22285 103 + 142988 CCCCAGATCTGCCACCAATCAAGAAGAACTTTTATAAGGAGTCCACTGCAATGAGTACTATGACAAAAGTACAAGCAGATAGTTGGAGGTATGTTCCCATACT -s mr.mrrefChr3 47843 103 + 181027 CCCCAGACCTACCACCAATCAAGAAAAACTTTTATAAGGAGTCCACTGCAATGAGCACCATGACAAAAGTGCAAGCAGATAGTTGGAAGTATATCCCCATCCC -s simCow_chr6.simCow.chr6 478542 103 + 602619 CCCCAGATCTGCCACCAATCAAGAAGAACTTTTATAAGGAGTCCACTGCAATGAGCACTATGACAAAAGTACAAACAGATAGTTGGAGGTATGTTCCCACTCT -s simDog_chr6.simDog.chr6 469037 103 + 593897 CCTCAGATCTGCCACCAATCAAGAAGAACTTTTATAAGGAGTCAACTGCAATAAGTACCATGACAAAAGTACAAGCAGATAGTTGGAGGTATGTTCCCATACT -s simHuman_chr6.simHuman.chr6 475899 103 + 601863 CCCCAGGTCTTCCACCAATCAAGAAGAACTTTTATAAGCAGTCCACTGCAATGAGTACTATGACAAAAGTACAAGCAGACGGTTGGAGGTATATTCCCATCCT -s simRat_chr6.simRat.chr6 501798 103 + 647215 CCCAAGACCTACCACCAATCAAGAAAAACTTTTATAAGGAGTCCACTGCAATGAGCACCATGACAAAGGTGCAAGCAGATAGTTGGAAGTATACCCCCACTCC - -a -s simMouse_chr6.simMouse.chr6 493771 18 + 636262 ACCACAGAGGGAAACAGA -s Anc0.Anc0refChr3 110343 17 + 222631 A-CATAGACTGGAACAGA -s Anc1.Anc1refChr6 144120 18 + 197743 AGCATAGACTGGAACAGA -s Anc2.Anc2refChr1 22389 17 + 142988 A-CACAGACTGGAACAGA -s mr.mrrefChr3 47946 18 + 181027 ACCATAGAGGGAAACAGA -s simCow_chr6.simCow.chr6 478646 15 + 602619 A-CA--GACTGGAACATG -s simDog_chr6.simDog.chr6 469141 17 + 593897 A-CACAGACTGAAACAGA -s simHuman_chr6.simHuman.chr6 476003 18 + 601863 AGCATAGAATGGAACAGA -s simRat_chr6.simRat.chr6 501901 18 + 647215 ATCATAGGGGGAAAGAGA - -a -s simMouse_chr6.simMouse.chr6 493789 7 + 636262 AATACTG -s Anc0.Anc0refChr3 110369 7 + 222631 AACACTG -s Anc1.Anc1refChr6 144147 7 + 197743 AACACTG -s Anc2.Anc2refChr1 22416 7 + 142988 AACACTG -s mr.mrrefChr3 47964 7 + 181027 AATACTG -s simCow_chr6.simCow.chr6 478671 7 + 602619 AACACTG -s simDog_chr6.simDog.chr6 469168 7 + 593897 AACTGTG -s simHuman_chr6.simHuman.chr6 476030 7 + 601863 AACACCG -s simRat_chr6.simRat.chr6 501919 7 + 647215 AATAATG - -a -s simMouse_chr6.simMouse.chr6 493796 39 + 636262 TGCCACTGGACTGTGATAATGCATATGGACACATGTTAA -s Anc0.Anc0refChr3 110377 39 + 222631 TGGCACTGGCCTGTGAGAGTGTAAATGGAGATATGTCAA -s Anc1.Anc1refChr6 144155 39 + 197743 TGGCACTGGCCTGTGAGAGTGTAAATGGAGATATGTCAA -s Anc2.Anc2refChr1 22424 39 + 142988 AGGCACTAGCCTGTGAGAGTGTAAATGGAGATATGTCAA -s mr.mrrefChr3 47971 39 + 181027 TGCCACTGGACTGTGATAATGTATATGGACATATGTCAA -s simCow_chr6.simCow.chr6 478679 39 + 602619 CGGCACTAGCCTGTGAGAGTATAAATGGACATATGTCAA -s simDog_chr6.simDog.chr6 469176 39 + 593897 AGGCACTAGGCTGTTTGAGTGTAAATGGAGATATGTCAA -s simHuman_chr6.simHuman.chr6 476038 39 + 601863 TGGCACTGGCCTGTGAGAGTGTAAATGGCGATATGTCAA -s simRat_chr6.simRat.chr6 501926 39 + 647215 CGCCACTGGGCTGTGATAACCTATATGGATTTACGTCAA - -a -s simMouse_chr6.simMouse.chr6 493835 6 + 636262 GAGAAT -s Anc0.Anc0refChr3 110419 6 + 222631 GAGAAT -s Anc1.Anc1refChr6 144197 6 + 197743 GAGAAT -s Anc2.Anc2refChr1 22466 6 + 142988 GATAAT -s mr.mrrefChr3 48013 6 + 181027 GAGAAT -s simCow_chr6.simCow.chr6 478721 6 + 602619 GAGACT -s simCow_chr6.simCow.chr6 498698 6 + 602619 AATACT -s simDog_chr6.simDog.chr6 469218 6 + 593897 GATCAT -s simHuman_chr6.simHuman.chr6 476080 6 + 601863 GAGAAT -s simRat_chr6.simRat.chr6 501968 6 + 647215 GAGAAT - -a -s simMouse_chr6.simMouse.chr6 493841 1 + 636262 A -s Anc0.Anc0refChr3 110425 1 + 222631 G -s Anc1.Anc1refChr6 144203 1 + 197743 G -s Anc2.Anc2refChr1 22472 1 + 142988 G -s mr.mrrefChr3 48019 1 + 181027 A -s simCow_chr6.simCow.chr6 498704 1 + 602619 G -s simHuman_chr6.simHuman.chr6 476086 1 + 601863 G -s simRat_chr6.simRat.chr6 501974 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 493842 8 + 636262 ATGTTAAG -s Anc0.Anc0refChr3 110426 8 + 222631 ATACTCAG -s Anc1.Anc1refChr6 144204 8 + 197743 ATACTCAG -s Anc2.Anc2refChr1 22473 8 + 142988 AAACACAG -s mr.mrrefChr3 48020 8 + 181027 ATGTTAAG -s simCow_chr6.simCow.chr6 478734 8 + 602619 AAACATAG -s simCow_chr6.simCow.chr6 498705 8 + 602619 TAACTCAG -s simDog_chr6.simDog.chr6 469224 8 + 593897 AGACACAG -s simHuman_chr6.simHuman.chr6 476087 8 + 601863 ATACTTAG -s simRat_chr6.simRat.chr6 501975 8 + 647215 ATGTTAAG - -a -s simMouse_chr6.simMouse.chr6 493850 4 + 636262 TCAT -s Anc0.Anc0refChr3 110437 4 + 222631 TCAT -s Anc1.Anc1refChr6 144215 4 + 197743 TCAT -s Anc2.Anc2refChr1 22484 4 + 142988 TCAT -s mr.mrrefChr3 48028 4 + 181027 TCAT -s simCow_chr6.simCow.chr6 478744 4 + 602619 TTAT -s simCow_chr6.simCow.chr6 498723 4 + 602619 ACAT -s simDog_chr6.simDog.chr6 469234 4 + 593897 TCAT -s simHuman_chr6.simHuman.chr6 476098 4 + 601863 TCAT -s simRat_chr6.simRat.chr6 501983 4 + 647215 TCAT - -a -s simMouse_chr6.simMouse.chr6 493854 20 + 636262 AGCATCTGAGAATAATGTTA -s Anc0.Anc0refChr3 110446 20 + 222631 TGAACTGGAGAATGATGTTC -s Anc1.Anc1refChr6 144224 20 + 197743 TGAACTGGAGAATGATGTTC -s Anc2.Anc2refChr1 22494 20 + 142988 TCAACTGGACCATGATGTTC -s mr.mrrefChr3 48032 20 + 181027 AGCATCTGAGAATAATGTTA -s simCow_chr6.simCow.chr6 478754 20 + 602619 CCAACTGAACCATGATGTTC -s simCow_chr6.simCow.chr6 498732 20 + 602619 CAACCCTGAGAGTGGTGAGC -s simDog_chr6.simDog.chr6 469244 20 + 593897 TCTACTGGACCATGATGTTT -s simHuman_chr6.simHuman.chr6 476107 20 + 601863 TGAACTGGAGAATGATGGTC -s simRat_chr6.simRat.chr6 501987 10 + 647215 AGCATCTGGT---------- - -a -s simMouse_chr6.simMouse.chr6 493874 81 + 636262 AGTCATTGTAGCATCATGAAGGGAAGGAATTTAGGGTCAGCATCATGGATGGTCAATTGGAGCCTAATGTCTAGCACAGTA -s Anc0.Anc0refChr3 110466 20 + 222631 AGGCA---TAGCATCATACAGGG---------------------------------------------------------- -s Anc1.Anc1refChr6 144244 20 + 197743 AGGCA---TAGCATCATACAGGG---------------------------------------------------------- -s Anc2.Anc2refChr1 22514 20 + 142988 AGGCA---CAGCATCATACAGGG---------------------------------------------------------- -s mr.mrrefChr3 48052 78 + 181027 AGTCA---TAGCATCATGAAGGGATGGAGTTTAGGGTCAGCATCATGGATGGTCAATTGGAGCCTAATGTCTAGCACAGTA -s simCow_chr6.simCow.chr6 478806 20 + 602619 AGACA---CAGCCTCATGCAGGG---------------------------------------------------------- -s simCow_chr6.simCow.chr6 498752 11 + 602619 ATTCG---TGGAAT------------------------------------------------------------------- -s simDog_chr6.simDog.chr6 469264 19 + 593897 AGGCA---CTGTATCATA-ATGG---------------------------------------------------------- -s simHuman_chr6.simHuman.chr6 476127 20 + 601863 AGCCA---TAGCATCATAGAGGG---------------------------------------------------------- -s simRat_chr6.simRat.chr6 501997 61 + 647215 --------------------GGGATGGAGTTTAGGCTCAGCATCATGGATGGTCAACTGGAGCCTAATGTCTAGCACAAGA - -a -s simMouse_chr6.simMouse.chr6 493955 5 + 636262 tttgt -s Anc0.Anc0refChr3 110486 4 + 222631 -TTGT -s Anc1.Anc1refChr6 144264 4 + 197743 -TTGT -s Anc2.Anc2refChr1 22534 4 + 142988 -TTGT -s mr.mrrefChr3 48130 5 + 181027 tttgt -s simCow_chr6.simCow.chr6 478826 4 + 602619 -TCAT -s simDog_chr6.simDog.chr6 469283 4 + 593897 -TTGT -s simHuman_chr6.simHuman.chr6 476147 4 + 601863 -TTGT -s simRat_chr6.simRat.chr6 502062 5 + 647215 TCTGT - -a -s simMouse_chr6.simMouse.chr6 493960 47 + 636262 gtgtgtaaagtcacgatgttgggaccctttgaggggtattttgtata -s Anc0.Anc0refChr3 110494 33 + 222631 AGGTACATAGACACAAAATT--------------GGTATAATAATTC -s Anc1.Anc1refChr6 144272 33 + 197743 AGGTACATAGACACAAAATT--------------GGTATAATAATTC -s Anc2.Anc2refChr1 22542 33 + 142988 AGGTACATAGACACAAAATT--------------GGTATAATAATTC -s mr.mrrefChr3 48135 47 + 181027 gtgtgtaaagtcacgatgttgggaccctttgaggggtattttgtata -s simCow_chr6.simCow.chr6 478834 33 + 602619 AGGTACATAGACACAAAATT--------------GGTATAATAATTC -s simDog_chr6.simDog.chr6 469291 3 + 593897 TAG-------------------------------------------- -s simHuman_chr6.simHuman.chr6 476155 33 + 601863 AGGTACATAGACACCTAACT--------------GTTATGAAAATTC -s simRat_chr6.simRat.chr6 502067 47 + 647215 GTATATAAAGTCATGATGTTGGGCTCCTTTGGGGGGCATCTTATATA - -a -s simMouse_chr6.simMouse.chr6 494007 3 + 636262 acc -s Anc0.Anc0refChr3 110527 3 + 222631 ACC -s Anc1.Anc1refChr6 144305 3 + 197743 ACC -s Anc2.Anc2refChr1 22575 3 + 142988 ACC -s mr.mrrefChr3 48182 3 + 181027 acc -s simCow_chr6.simCow.chr6 478867 3 + 602619 ACC -s simHuman_chr6.simHuman.chr6 476188 3 + 601863 ACC -s simRat_chr6.simRat.chr6 502115 3 + 647215 ACC - -a -s simMouse_chr6.simMouse.chr6 494010 5 + 636262 tgcta -s Anc0.Anc0refChr3 110531 5 + 222631 TGGTA -s Anc1.Anc1refChr6 144309 5 + 197743 TGGTA -s Anc2.Anc2refChr1 22579 5 + 142988 TGGTA -s mr.mrrefChr3 48185 5 + 181027 tgcta -s simCow_chr6.simCow.chr6 478871 5 + 602619 TGGTA -s simHuman_chr6.simHuman.chr6 476194 5 + 601863 TGGTA -s simRat_chr6.simRat.chr6 502118 5 + 647215 TGCGA - -a -s simMouse_chr6.simMouse.chr6 494015 16 + 636262 aagttagttgctcccc -s Anc0.Anc0refChr3 110537 11 + 222631 TACCTAATTGC----- -s Anc1.Anc1refChr6 144315 11 + 197743 TACCTAATTGC----- -s Anc2.Anc2refChr1 22585 11 + 142988 TGCCTAATTGC----- -s mr.mrrefChr3 48190 16 + 181027 aagttagttgctcccc -s simCow_chr6.simCow.chr6 478877 11 + 602619 TGCCTAATTGC----- -s simHuman_chr6.simHuman.chr6 476200 11 + 601863 GACCTTATCTC----- -s simRat_chr6.simRat.chr6 502123 16 + 647215 GAGTGAGTTGCCCTCC - -a -s simMouse_chr6.simMouse.chr6 494031 18 + 636262 tcaagcatcaactgatgc -s mr.mrrefChr3 48206 18 + 181027 tcaagcatcaactgatgc -s simRat_chr6.simRat.chr6 502158 18 + 647215 TCCAGCATCAGCTGATGC - -a -s simMouse_chr6.simMouse.chr6 494049 371 + 636262 agcatcctAGACCTACCTACATGAATGAACAATGTATAGTGAAGGGTGATGACATATCTCATGCAATGTGAGACTCTGTTTGGTGAAATCCATCTTACTGCTCCAGTAAGGAAGAGGCCTAACAAGGGGGCTAAAGATTCCATGTGACCTCTGGTACATTGGACTGTCCAATAAATAAGGGTGGGATCTCATCCCCCCCGGACTGTTAGCTCAACTCACAGGGGGCCAGCTGCAATACCTGAAATACACAAGATAGATCAATGGATTGCAGCAGCTTGCAGTAGCTTGTGTGCACAAAATAGATTGATGGGCTGTGGATTCGAGGTTTTGTGTAGACAATATAACTCACCAGGGGCCTAAAATTTTTATGT -s Anc0.Anc0refChr3 110548 48 + 222631 -----------------------------CAATTATTATAGATGG----TCATATATCATTTGTAAGTAG----AAT----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TTTTGTAG -s Anc1.Anc1refChr6 144326 52 + 197743 -----------------------------CAATTATTATAGATGGAACATCATATATCATTTGTAAGTAG----AAT----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TTTTGTAG -s Anc2.Anc2refChr1 22596 48 + 142988 -----------------------------CCACTATCATAGATGG----TCATATATCATTTGTAAGTAG----AAT----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TTATGTAG -s mr.mrrefChr3 48224 85 + 181027 agcatcctAGACCTACCTACATGAATGAACAATGTATAGTGAAGGGTGATGACATATCTCATGCAATGTGAGACTCT----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TTTTATGT -s simCow_chr6.simCow.chr6 478888 48 + 602619 -----------------------------CCACTATCATAGATGG----TCATATATCATTTGTAAGTAG----AAT----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TTACATAG -s simCow_chr6.simCow.chr6 498763 8 + 602619 ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TTATGTAG -s simHuman_chr6.simHuman.chr6 476211 52 + 601863 -----------------------------CAATTATTATGGATGGAACAATGTTTATTGTTTGTAAATAG----CAT----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TTTAGTAG -s simRat_chr6.simRat.chr6 502177 85 + 647215 AGTATCCTAAACCTACCTACATGAATGAACAATGCATAGTGAAGAGTGATGACATGTCTGATGCAATATGAGACTCT----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TTTAAAGT - -a -s simMouse_chr6.simMouse.chr6 494420 4 + 636262 GAGT -s Anc0.Anc0refChr3 110596 4 + 222631 AAAT -s Anc1.Anc1refChr6 144378 4 + 197743 AAAT -s Anc2.Anc2refChr1 22644 4 + 142988 AAAT -s mr.mrrefChr3 48309 4 + 181027 AAGT -s simCow_chr6.simCow.chr6 478936 4 + 602619 ACAT -s simCow_chr6.simCow.chr6 498771 4 + 602619 AAAT -s simDog_chr6.simDog.chr6 469294 3 + 593897 -AAT -s simHuman_chr6.simHuman.chr6 476263 4 + 601863 AAAA -s simRat_chr6.simRat.chr6 502264 4 + 647215 AATG - -a -s simMouse_chr6.simMouse.chr6 494424 62 + 636262 AGGAGGGGGTGAGGACCTTAGTTCTGGATGTGGTAAAATAggagtggggggggaggagggaa -s Anc0.Anc0refChr3 110600 38 + 222631 ATGAGGGGATGAGGAACCTAGTTCTAGATGTATTAA------------------------AG -s Anc1.Anc1refChr6 144382 38 + 197743 ATGAGGGGATGAGGAACCTAGTTCTAGATGTATTAA------------------------AG -s Anc2.Anc2refChr1 22649 38 + 142988 ATGAGGGGATGAGGAACCTGGTTCTAGATCTATTAA------------------------AG -s mr.mrrefChr3 48313 62 + 181027 ATGAGGGGGTGAGGACCCTAGTTCTAGATGTGGTAAAATAggagtggggggggaggagggag -s simCow_chr6.simCow.chr6 478941 38 + 602619 ATGAGGGGATGAGGAACCTGGTTCTCGATCTATTAA------------------------TT -s simCow_chr6.simCow.chr6 498776 37 + 602619 AAATGGGCATGAGGTA-CTGGTTCTAGATCTATTAA------------------------AG -s simDog_chr6.simDog.chr6 469298 31 + 593897 ATGAAGGGGTGAGGCA-GTGGTTCTAGATCTA------------------------------ -s simHuman_chr6.simHuman.chr6 476267 38 + 601863 GTGAGGGTAGAAGGAACCTAGTTCTAGCTGGAATAA------------------------AG -s simRat_chr6.simRat.chr6 502268 62 + 647215 ATGAGGGGGTGAGGACCCTAGTTCTAGAGGTGGTAAAATAGGGGCagggggggaggagggag - -a -s simMouse_chr6.simMouse.chr6 494486 43 + 636262 gagtggggggggggtaggggagggAAGTAAAGGAGGTAAGGTT -s Anc0.Anc0refChr3 110638 33 + 222631 G-GTAGGGGGGGGGGAGGGGAAGGAAGTAAA---------GTT -s Anc1.Anc1refChr6 144420 33 + 197743 G-GTAGGGGGGGGGGAGGGGAAGGAAGTAAA---------GTT -s Anc2.Anc2refChr1 22693 33 + 142988 G-GTAGGGGGGGGGGGGGGGTAGGAAGTAAA---------GTT -s mr.mrrefChr3 48375 42 + 181027 g-gtgggggggggggaggggagggAAGTAAAGGAGGTAAGGTT -s simCow_chr6.simCow.chr6 478985 33 + 602619 G-GGAGGGGGGGGGGAGGGGTGGAAAGTAAG---------ATT -s simCow_chr6.simCow.chr6 498819 33 + 602619 G-GTAGGGGGGTGGGGGGGGCAGAAAGTAAA---------AGT -s simDog_chr6.simDog.chr6 469329 25 + 593897 ------GGGGGGGGGGGGGG---GGAGTAGT---------GTT -s simHuman_chr6.simHuman.chr6 476305 33 + 601863 G-AAAGGGGGGGGGGAGGGGAAAGAAGTAAA---------GTT -s simRat_chr6.simRat.chr6 502330 42 + 647215 g-gtgggggggagggaggggagggaggTAAAGGAGGTAAAGTT - -a -s simMouse_chr6.simMouse.chr6 494529 29 + 636262 TAAAGCATAACAGTGCTTAGTAAACAAAT -s Anc0.Anc0refChr3 110671 21 + 222631 TAAAGCATAACAGTGTTTT--------GT -s Anc1.Anc1refChr6 144453 29 + 197743 TAAAGCATAACAGTGTTTTGTATACTAGT -s Anc2.Anc2refChr1 22726 21 + 142988 TAAAGCATAACAGTGTTCT--------GT -s mr.mrrefChr3 48417 29 + 181027 TAAAGCATAACAGTGCTTTGTAAACAAAT -s simCow_chr6.simCow.chr6 479020 21 + 602619 TAAAGCTGAGCAGTATTTT--------GT -s simCow_chr6.simCow.chr6 498852 21 + 602619 TAATGCACTGCAGTGTTCT--------GT -s simDog_chr6.simDog.chr6 469354 21 + 593897 TACATCATAACAGTGTTCT--------GT -s simHuman_chr6.simHuman.chr6 476338 29 + 601863 TAACACATAACAGATTTTTGTATACTAGT -s simRat_chr6.simRat.chr6 502372 29 + 647215 TAAAGCATAATAGTGCTCTGTAAACAAAT - -a -s simMouse_chr6.simMouse.chr6 494558 42 + 636262 TTCACAAAATGGCATATTGCGCAAAGTTATGTAAATTGAATT -s Anc0.Anc0refChr3 110693 42 + 222631 CTCATATAATAGAGTATTGCCCCAAGCTTTAGAGTTTGAATT -s Anc1.Anc1refChr6 144483 42 + 197743 CTCATATAATAGAGTATTGCCCCAAGCTTTAGAGTTTGAATT -s Anc2.Anc2refChr1 22748 42 + 142988 CTCATATAATAGAGTATTGCCCCAAGCCTTAGAGTTTGAATT -s mr.mrrefChr3 48446 42 + 181027 TTCACAAAATAGCATATTGCCCCAAGTTTTATAAATTGAATT -s simCow_chr6.simCow.chr6 479042 42 + 602619 CTCATGTAAAAGGGCATGGCCCCTAGCCTCAGACCTTGAAAC -s simCow_chr6.simCow.chr6 498874 42 + 602619 CTCATGTAATAGAGTATGGCCCCAAGCCTTAGATATTGGATT -s simDog_chr6.simDog.chr6 469376 42 + 593897 CTCATATAATAGAGTATTACGCCAAGCCTTAGAGTTTGAATT -s simHuman_chr6.simHuman.chr6 476368 41 + 601863 CTCATATAATAGAGTATTGCCTCAAGCTTCA-AGGTTGAATT -s simRat_chr6.simRat.chr6 502401 41 + 647215 TTCACAAAATAGCACATTGCC-CAAGTTTTATGAATCGTATT - -a -s simMouse_chr6.simMouse.chr6 494600 57 + 636262 CTGTTATGGTTAGGCACAGATAAAGGCTCACATTGAGTTATGACTGGTTATGTTAAA -s Anc0.Anc0refChr3 110737 53 + 222631 CTGTTAAGGTCAGACACAAATAAGAGCGAAGATTGGGTCA----TAGTCATGTTAAA -s Anc1.Anc1refChr6 144527 53 + 197743 CTGTTAAGGTCAGACACAAATAAGAGCGAAGATTGGGTCA----TAGTCATGTTAAA -s Anc2.Anc2refChr1 22792 53 + 142988 CTGTTAAGGTCAGACACAAGTAAGAGGGAAGATTGGGTCA----TAGTCATGTTAAA -s mr.mrrefChr3 48488 57 + 181027 CTGTTATGGTTAGGCACAGATAAGGGCTCACATTGGGTCATGACTGGTTATGTTAAA -s simCow_chr6.simCow.chr6 479086 53 + 602619 CTGTAAAAGTCAGACGCAACTAAGAGGGAAGATTGCATCA----TAGTCATGCAACA -s simCow_chr6.simCow.chr6 498918 53 + 602619 CCATAAGGGTCAGGCACAGGTAAGAGGGGAGATTGTGTCA----TAGTCAATTTGAA -s simDog_chr6.simDog.chr6 469420 53 + 593897 CTGTTAAGGTCAGACACAAGTAAGAGGGAAGATTGGGTCC----TAGTCCTGGTAAG -s simHuman_chr6.simHuman.chr6 476411 51 + 601863 CTGATAAGGCCAAAAATAAATCAGAGCAAAAATCAGGTCA----TAGTCATGTTA-- -s simRat_chr6.simRat.chr6 502442 57 + 647215 CTGTTCTGGTTAGGCACAGATAAGGGCCCACATTGGCGCATTACTCACTATGCTAAA - -a -s simMouse_chr6.simMouse.chr6 494657 24 + 636262 GGTAGACTCATTTTTTCTTTGATT -s Anc0.Anc0refChr3 110790 24 + 222631 GGTAGACTGCGGCTTCTTTAATTT -s Anc1.Anc1refChr6 144580 24 + 197743 GGTAGACTGCGGCTTCTTTAATTT -s Anc2.Anc2refChr1 22850 24 + 142988 GGTAGACTGCGGCTTCTTTAATCT -s mr.mrrefChr3 48545 24 + 181027 GGTAGACTCATTTTTTCTTCAATT -s simCow_chr6.simCow.chr6 479144 23 + 602619 GGTAGACTGAGGCTGCTTCAA-CA -s simCow_chr6.simCow.chr6 498976 23 + 602619 GGTAGACTGCTGCTTCTTTGA-CA -s simDog_chr6.simDog.chr6 469478 16 + 593897 GCTAGGTTA--------TTAATCT -s simHuman_chr6.simHuman.chr6 476462 10 + 601863 --------------TCTTCAATTT -s simRat_chr6.simRat.chr6 502499 23 + 647215 GGTATACTCATTCTT-CTTCAATT - -a -s simMouse_chr6.simMouse.chr6 494681 14 + 636262 GGATTAAATATGGC -s Anc0.Anc0refChr3 110836 14 + 222631 GTCTCAGTTGCGGC -s Anc1.Anc1refChr6 144626 14 + 197743 GTCTCAGTTGCGGC -s Anc2.Anc2refChr1 22896 14 + 142988 GTCTCAGTTGCAGC -s mr.mrrefChr3 48591 14 + 181027 GGTTTAAATATGAC -s simCow_chr6.simCow.chr6 479189 14 + 602619 ATCCCAGTTGTGGC -s simCow_chr6.simCow.chr6 499021 14 + 602619 ATCTTAGTTGCAGC -s simDog_chr6.simDog.chr6 469516 14 + 593897 GTCTCAGTTACAGC -s simHuman_chr6.simHuman.chr6 476494 14 + 601863 GTCTCAGCTGCGGC -s simRat_chr6.simRat.chr6 502544 14 + 647215 GGTTTAAATATGAC - -a -s simMouse_chr6.simMouse.chr6 494695 4 + 636262 GAGA -s Anc0.Anc0refChr3 110850 4 + 222631 GAGA -s Anc1.Anc1refChr6 144640 4 + 197743 GAGA -s Anc2.Anc2refChr1 22910 4 + 142988 CAGA -s mr.mrrefChr3 48605 4 + 181027 GAGA -s simCow_chr6.simCow.chr6 479203 4 + 602619 CAGA -s simCow_chr6.simCow.chr6 499035 4 + 602619 CAGA -s simDog_chr6.simDog.chr6 469530 4 + 593897 TGGC -s simHuman_chr6.simHuman.chr6 476540 4 + 601863 GCAC -s simRat_chr6.simRat.chr6 502559 4 + 647215 GAGG - -a -s simMouse_chr6.simMouse.chr6 494699 17 + 636262 AGGTTTTTCATATCATT -s Anc0.Anc0refChr3 110854 17 + 222631 AGGTGTGTAGTATCATT -s Anc1.Anc1refChr6 144644 17 + 197743 AGGTGTGTAGTATCATT -s Anc2.Anc2refChr1 22915 17 + 142988 ATGAGTGTAGTATCATT -s mr.mrrefChr3 48609 17 + 181027 AGGTTTTTCATATCATT -s simCow_chr6.simCow.chr6 479208 17 + 602619 AAGAGTGTAGTATAAGT -s simCow_chr6.simCow.chr6 499040 17 + 602619 ATGAGTGTAGGATCAGA -s simDog_chr6.simDog.chr6 469535 17 + 593897 ATATGTGTAGTGTCATT -s simHuman_chr6.simHuman.chr6 476544 17 + 601863 AGGTGCGGAGTATCATT -s simRat_chr6.simRat.chr6 502563 17 + 647215 AGGCTTTTCATATCATT - -a -s simMouse_chr6.simMouse.chr6 494716 24 + 636262 TTTCATGCAAGTCAAAATGCTCAG -s Anc0.Anc0refChr3 110872 24 + 222631 CTTCATGCAACCTAAACCCCTCAG -s Anc1.Anc1refChr6 144662 24 + 197743 CTTCATGCAACCTAAACCCCTCAG -s Anc2.Anc2refChr1 22933 24 + 142988 CATCATGTACCCTAAACCCCCCAG -s mr.mrrefChr3 48626 24 + 181027 TTTCATGCAAGTCAAAATGCTCAG -s simCow_chr6.simCow.chr6 479226 23 + 602619 GATCATGTACCCTAAACCCG-CTC -s simCow_chr6.simCow.chr6 499058 23 + 602619 GACCTCGCACCTTAAACCCC-CAA -s simDog_chr6.simDog.chr6 469553 24 + 593897 CCTAATGTTGCCTAAACCCCCAAG -s simHuman_chr6.simHuman.chr6 476562 24 + 601863 CTGCGCGCAACCTAAATCCCTCTG -s simRat_chr6.simRat.chr6 502580 24 + 647215 TTTCATGCAAGTCAAAATGCTTAG - -a -s simMouse_chr6.simMouse.chr6 494740 85 + 636262 TTGGACAAGGTAATTTTTCTATTGGGGAATTTAATCATTATGATCTAACTTACTGTAAAGGCACGATCAGAGTTACTTTATCTAG -s Anc0.Anc0refChr3 110896 84 + 222631 TTGGGTGAGGTAGTTTTCCTATCATGGAGTTTAATAATTCTAATC-AAAATACTGGAACTGCGCAATCCCAGTTACTTCATCTAT -s Anc1.Anc1refChr6 144686 84 + 197743 TTGGGTGAGGTAGTTTTCCTATCATGGAGTTTAATAATTCTAATC-AAAATACTGGAACTGCGCAATCCCAGTTACTTCATCTAT -s Anc2.Anc2refChr1 22957 84 + 142988 TTGGGTGAGGTGGTTTTCCTATCATGGAGTTTAATAATTCTAATC-AAAATACTGGAACTGCGCCCCCCCAGTTACTTCATCTGT -s mr.mrrefChr3 48650 85 + 181027 TTGGACAAGGTAATTTTCCTATTGGGGAATTTAATAATTATGATCTAACTTACTGTAAAGGCACAATCAGAGTTACTTTATCTAG -s simCow_chr6.simCow.chr6 479249 75 + 602619 TTGCAGGAGGTAGTTTTCCTATCATGGAGTTTAGTAATTTGAATT-AAATTACTGGAACTGCTC---CCCAGTT------TCTTT -s simCow_chr6.simCow.chr6 499082 43 + 602619 TTTAGTGAGGTGGTTTCCCGATCATGGAATGTAACAATTCTAA------------------------------------------ -s simDog_chr6.simDog.chr6 469577 84 + 593897 TTGGGTGGGGTGGTTTTGATAACAAGGAGTTCGATAGTTCTAAAC-AAAATACTGGAACTGCGCCCCCCCAGCTACTTCAACTGT -s simHuman_chr6.simHuman.chr6 476586 74 + 601863 TTGGGTGAGATAGTTTACTCATC----------ATAATTCTAATC-AAAATACTGGAACAGCCCAATCCCAGTTACTTCATCGAA -s simRat_chr6.simRat.chr6 502604 85 + 647215 TTGGACAAGGTAATTTTCCTATTTTCAAATTTAATAGTAGTGATCTAACTTACTGTAAATGTACAAACGGAGTTACCTTGTCTCG - -a -s simMouse_chr6.simMouse.chr6 494825 32 + 636262 GGATTACATACTGTCAGACCCAGTTACTTTTA -s Anc0.Anc0refChr3 110980 31 + 222631 GGTATCCACATTGTCATATCCAGTTGCCTTT- -s Anc1.Anc1refChr6 144770 31 + 197743 GGTATCCACATTGTCATATCCAGTTGCCTTT- -s Anc2.Anc2refChr1 23041 31 + 142988 GGTAACCACATTGTCATATCCAGTTACCTTT- -s mr.mrrefChr3 48735 32 + 181027 GGATTACATACTGTCAGATCCAGTTGCCTTTA -s simCow_chr6.simCow.chr6 479324 31 + 602619 GGTACCCGCATTGTCATACCCAGTCACCTTT- -s simDog_chr6.simDog.chr6 469661 31 + 593897 GGTAACCACATTGTCATCTCCACTTACCTTT- -s simHuman_chr6.simHuman.chr6 476661 31 + 601863 GGGATCCACATTGTCATATCCAGATGCCTTT- -s simRat_chr6.simRat.chr6 502689 32 + 647215 GGATTACATACTGTCAGATCCAGTTGCCTCCA - -a -s simMouse_chr6.simMouse.chr6 494857 10 + 636262 ATATCTCTCC -s Anc0.Anc0refChr3 111011 10 + 222631 ATACCTCTCC -s Anc1.Anc1refChr6 144801 10 + 197743 ATACCTCTCC -s Anc2.Anc2refChr1 23072 10 + 142988 ATACCTGTCC -s mr.mrrefChr3 48767 10 + 181027 ATATCTCTCC -s simCow_chr6.simCow.chr6 479357 10 + 602619 GTAGCTTTCC -s simDog_chr6.simDog.chr6 469693 10 + 593897 ATACCTGTCC -s simHuman_chr6.simHuman.chr6 476692 10 + 601863 ATACCTCTCC -s simRat_chr6.simRat.chr6 502721 10 + 647215 ATATCTCTCC - -a -s simMouse_chr6.simMouse.chr6 494867 5 + 636262 ACAAG -s Anc0.Anc0refChr3 111028 5 + 222631 ACAAG -s Anc1.Anc1refChr6 144818 5 + 197743 ACAAG -s Anc2.Anc2refChr1 23089 5 + 142988 GCAAG -s mr.mrrefChr3 48777 5 + 181027 ACAAG -s simCow_chr6.simCow.chr6 479373 5 + 602619 GAAAG -s simDog_chr6.simDog.chr6 469710 5 + 593897 GCAGG -s simHuman_chr6.simHuman.chr6 476709 5 + 601863 ACAAG -s simRat_chr6.simRat.chr6 502731 5 + 647215 ACAAG - -a -s simMouse_chr6.simMouse.chr6 494872 8 + 636262 TTTCCTCC -s Anc0.Anc0refChr3 111037 8 + 222631 TTTGCTCC -s Anc1.Anc1refChr6 144827 8 + 197743 TTTGCTCC -s Anc2.Anc2refChr1 23098 8 + 142988 CCTGCATC -s mr.mrrefChr3 48782 8 + 181027 TTTCCTCC -s simCow_chr6.simCow.chr6 479382 5 + 602619 CCTGC--- -s simDog_chr6.simDog.chr6 469719 8 + 593897 CCTGCATC -s simHuman_chr6.simHuman.chr6 476718 8 + 601863 TTTTCTCC -s simRat_chr6.simRat.chr6 502736 7 + 647215 TTTG-TCC - -a -s simMouse_chr6.simMouse.chr6 494880 33 + 636262 ATAACTATAAACTGATTGTATAGGGTAATCAGC -s Anc0.Anc0refChr3 111047 33 + 222631 ATAACTATAAAATGATTGTAGCAGTTCCTCTGC -s Anc1.Anc1refChr6 144837 33 + 197743 ATAACTATAAAATGATTGTAGCAGTTCCTCTGC -s Anc2.Anc2refChr1 23108 33 + 142988 ATAACTATAAAATGATTGAAGCAGTTCCTCTGC -s mr.mrrefChr3 48790 33 + 181027 ATAACTATAAACTGATTGTATAGGGTAATCAGC -s simCow_chr6.simCow.chr6 479388 33 + 602619 ATAACCATAGAATGATTGAATCAATTCCACTGC -s simDog_chr6.simDog.chr6 469729 33 + 593897 ATCACTAAAAAATGGCAGAAGTAGTTCCTCTGC -s simHuman_chr6.simHuman.chr6 476728 28 + 601863 ATAACTGTAAAATGATTATAGCAGC-----TGC -s simRat_chr6.simRat.chr6 502743 20 + 647215 ATAATTATA-------------TGGCTAACAGC - -a -s simMouse_chr6.simMouse.chr6 494913 5 + 636262 AGCCT -s Anc0.Anc0refChr3 111085 5 + 222631 AGGCT -s Anc1.Anc1refChr6 144875 5 + 197743 AGGCT -s Anc2.Anc2refChr1 23146 5 + 142988 AGGCT -s mr.mrrefChr3 48828 5 + 181027 AGCCT -s simCow_chr6.simCow.chr6 479426 5 + 602619 AGACT -s simDog_chr6.simDog.chr6 469767 5 + 593897 AGGCT -s simHuman_chr6.simHuman.chr6 476761 5 + 601863 AATCT -s simRat_chr6.simRat.chr6 502768 5 + 647215 AGCCT - -a -s simMouse_chr6.simMouse.chr6 494918 222 + 636262 AATAATAAGAAAGTTATTTAATAGTGCTCTTTTAGTTTGGATGGCTTTTTAATTTAAAGGGAAGAAAATTTTAACTTAACATGGGATGACTTAAAGGATGGAGAAAAACATCCCTTGAACCCCTGTACTTTCGACGATGCTTCTCCATGTTATCATCCTGATGTTACCGAAAACATAAAGAAGCCCTTTCAGAAACCTATGCCAATTCATGTAAGATAACGT -s Anc0.Anc0refChr3 111109 214 + 222631 AAGAATAATTAAGTTGCTGGATGGTGTC--------CTGGGCATTTTTGGAAGTTAAAGGGAAGAAAATTTTAACTTAACATGGGATGACTTAAAGGATGGAGAAAAACGTCCCTCCAACCCCTGCACTTTTGATGATGCCTCTCCATGTTATCATCCTGATGTTATGGAAAACATCAAGAAGACTTTTCAGAAACCAACACCAATTCAGGTAAGATAGTGT -s Anc1.Anc1refChr6 144899 222 + 197743 AAGAATAATTAAGTTGCTGGATGGTGTCCCTTTGGTCTGGGCATTTTTGGAAGTTAAAGGGAAGAAAATTTTAACTTAACATGGGATGACTTAAAGGATGGAGAAAAACGTCCCTCCAACCCCTGCACTTTTGATGATGCCTCTCCATGTTATCATCCTGATGTTATGGAAAACATCAAGAAGACTTTTCAGAAACCAACACCAATTCAGGTAAGATAGTGT -s Anc2.Anc2refChr1 23170 214 + 142988 AAGAATAATTAAGTTGCTGGATGGTGTC--------CTGGGCATTTTTGGAAGTTAAAGGGAAGAAAATTTTAACTTAACTTGGGATGACTTAAAGGATGGGGAAAAACGTCCCTCCAACCCCTGCACTTTTGATGATGCCTCTCCATGTTATCATCCTGATGTTATGGAAAACATCAAGAAGACTTTTCAGAAACCAACACCAATTCAGGTAAGATAGTGT -s mr.mrrefChr3 48833 222 + 181027 AATAATAAGTAAGTTATTGGATAGTGCTCTTTTAGTCTGGATGTTTTTTTAATTTAAAGGGAAGAAAATTTTAACTTAACATGGGATGACTTAAAGGATGGAGAAAAACATCCCTCCAACCCCTGTACTTTCGACGATGCTTCTCCATGTTATCATCCTGATGTTACCGAAAACATCAAGAAGACCTTTCAGAAACCTACACCAATTCATGTAAGATAGTGT -s simCow_chr6.simCow.chr6 479450 214 + 602619 AAGAATAATTACATTGCTGTATGGTGCT--------CGGGGTGTTTTTTCGATTTAAAGGGAGGAAAATTTTAACTTGACCTGGGATGACTTAAAGGATGGGGAAAAACGGCCCTCCAACCCCTGCACTTTTGATGATGCCTCTCCATGTTACCACCCTGATGTTATGGAAAACATCAAAAAGACTTATCAGAAACCAACTCCAATTCAGGTAAGATAGTGT -s simDog_chr6.simDog.chr6 469791 214 + 593897 GAGAATAATTAAGTTACTGGATGGTGTC--------CTGGGCATTTTTGGAAGTTACAGGGAAGAAAATTTTAACTTAACTTGGGATGACCTAAAGGATGGGGAAAAGCGTCCCTCCAACCCGTGTACTTTTGACGATGCCTCTCCATGTTATCATCCTGATGTTATGGAAAACATCAAGAAAACTTTCCAGAAACCAACACCAATTCAGGTGAGATAGTGT -s simHuman_chr6.simHuman.chr6 476785 219 + 601863 AAGAATAATTAAGTTGCTGGATGGTGACCCTTTGGTCTGGGCATTATCCAAAATGAAAGGGAAGAAAATTTTAACTTAACATGGGATGACTTAAAAGATGGAGAAAAACGTCCCTCCAACCCCTGCACTTTTGATGATGCCTCTCCA---TATCATCCTGATGTTATGGAGAACATCAAGAAGACTTTTCAGAAACCAACACCAATTCAAGTAAGGTCGTGT -s simRat_chr6.simRat.chr6 502773 222 + 647215 AATAATAAGTAAGTTATTGGATAGCGCTCTCTTAGTCTGGATGTTTATGTAATTCAAAGGGAAGAAAATTTTAACTTAACATGGGATGACTTACAGGATGGAGAAAAACATCCCTCCAACCCCTGTACTTTCGACGATGCTTCTCCATGTTATCATCCTGATGTTACAGAAAACATCAAGAAGACCTTTCAGAAACCTACACCAATTCATGTAAGAGAGTGT - -a -s simMouse_chr6.simMouse.chr6 495140 23 + 636262 GATTGAACAATGGATGTAACACT -s Anc0.Anc0refChr3 111327 23 + 222631 CACTGCACACTGGATCTAACACT -s Anc1.Anc1refChr6 145125 23 + 197743 CACTGCACACTGGATCTAACACT -s Anc2.Anc2refChr1 23388 23 + 142988 CACTACACACTGGATCTAACATT -s mr.mrrefChr3 49055 23 + 181027 GACTGAACAATGGATGTAACACT -s simCow_chr6.simCow.chr6 479668 23 + 602619 GACTACACACTGGATCTAAAATT -s simDog_chr6.simDog.chr6 470009 23 + 593897 CACTACACATTGGATCTAACATT -s simHuman_chr6.simHuman.chr6 477008 20 + 601863 AACTGCACGCTGAATCTA---CT -s simRat_chr6.simRat.chr6 502995 23 + 647215 GACTGGACAATGGATATTACACT - -a -s simMouse_chr6.simMouse.chr6 495163 4 + 636262 GCTA -s Anc0.Anc0refChr3 111350 4 + 222631 GCTG -s Anc1.Anc1refChr6 145148 4 + 197743 GCTG -s Anc2.Anc2refChr1 23416 4 + 142988 GATT -s mr.mrrefChr3 49078 4 + 181027 GCTG -s simCow_chr6.simCow.chr6 479696 4 + 602619 GGTG -s simDog_chr6.simDog.chr6 470037 4 + 593897 GATT -s simHuman_chr6.simHuman.chr6 477028 4 + 601863 ACTG -s simRat_chr6.simRat.chr6 503018 4 + 647215 GCTG - -a -s simMouse_chr6.simMouse.chr6 495167 5 + 636262 GGTTT -s Anc0.Anc0refChr3 111354 5 + 222631 GGTTT -s Anc1.Anc1refChr6 145152 5 + 197743 GGTTT -s Anc2.Anc2refChr1 23420 5 + 142988 GGTTG -s mr.mrrefChr3 49082 5 + 181027 GGTTT -s simCow_chr6.simCow.chr6 479721 5 + 602619 GGCTG -s simDog_chr6.simDog.chr6 470041 5 + 593897 GGTTG -s simHuman_chr6.simHuman.chr6 477032 5 + 601863 GGTTT -s simRat_chr6.simRat.chr6 503022 5 + 647215 AGTTT - -a -s simMouse_chr6.simMouse.chr6 495172 2 + 636262 AT -s Anc0.Anc0refChr3 111359 2 + 222631 AT -s Anc1.Anc1refChr6 145157 2 + 197743 AT -s Anc2.Anc2refChr1 23425 2 + 142988 AT -s mr.mrrefChr3 49087 2 + 181027 AT -s simCow_chr6.simCow.chr6 479734 2 + 602619 AC -s simDog_chr6.simDog.chr6 470046 2 + 593897 AT -s simHuman_chr6.simHuman.chr6 477037 2 + 601863 AT -s simRat_chr6.simRat.chr6 503027 2 + 647215 AT - -a -s simMouse_chr6.simMouse.chr6 495174 34 + 636262 TGGGTTCAATGCGACCTCTCTTTAGAAAGAAGAT -s Anc0.Anc0refChr3 111361 27 + 222631 AGTGTTCAATGTGACCTCT-------AAGAAGAT -s Anc1.Anc1refChr6 145159 27 + 197743 AGTGTTCAATGTGACCTCT-------AAGAAGAT -s Anc2.Anc2refChr1 23427 27 + 142988 AGTGTTCAATATGACGTCT-------AGGAAGAT -s mr.mrrefChr3 49089 34 + 181027 TGGGTTCAATGCGACCTCTCTTTAGAAAGAAGAT -s simCow_chr6.simCow.chr6 479736 27 + 602619 AGTGTTCAGTATGACGTCT-------AGGAAGAT -s simDog_chr6.simDog.chr6 470049 18 + 593897 AGTGTTCAATATCA----------------AGAT -s simHuman_chr6.simHuman.chr6 477039 27 + 601863 AGTGTTCAATGTGACCCTT-------AAGGAGAT -s simRat_chr6.simRat.chr6 503029 34 + 647215 TGGATTCAACACGGCCTCTCTCTAGAGAGAAGAT - -a -s simMouse_chr6.simMouse.chr6 495208 6 + 636262 AACGTA -s Anc0.Anc0refChr3 111390 6 + 222631 AATGTG -s Anc1.Anc1refChr6 145188 6 + 197743 AATGTG -s Anc2.Anc2refChr1 23456 6 + 142988 AATGTG -s mr.mrrefChr3 49123 6 + 181027 AATGTA -s simCow_chr6.simCow.chr6 479765 6 + 602619 AATGAG -s simDog_chr6.simDog.chr6 470069 6 + 593897 ATTGTG -s simHuman_chr6.simHuman.chr6 477068 6 + 601863 AATGTG -s simRat_chr6.simRat.chr6 503063 6 + 647215 AATGTA - -a -s simMouse_chr6.simMouse.chr6 495214 11 + 636262 GGGGGGTGCTG -s Anc0.Anc0refChr3 111396 6 + 222631 GGG---TG--G -s Anc1.Anc1refChr6 145194 6 + 197743 GGG---TG--G -s Anc2.Anc2refChr1 23462 6 + 142988 GGG---TG--G -s mr.mrrefChr3 49129 8 + 181027 GGG---TGCTG -s simCow_chr6.simCow.chr6 479771 6 + 602619 GGG---TG--C -s simDog_chr6.simDog.chr6 470076 6 + 593897 GGG---CA--G -s simHuman_chr6.simHuman.chr6 477074 6 + 601863 GGG---TG--G -s simRat_chr6.simRat.chr6 503069 8 + 647215 GGG---TGCTG - -a -s simMouse_chr6.simMouse.chr6 495225 83 + 636262 CCTCTTCTTTTCTGGGACAGGAGGAACCGACCTTACCTGGATCAGTCTCTGGTTCACAGGTACTGTATTTGGGTACACTCATT -s Anc0.Anc0refChr3 111402 83 + 222631 CCTTTTCTTTTCTGGAACAGGAGGAACTGGTTTCACCTGGGTCAGTCTCCGTTGCACAGGTATAATATATAGGTACACTTATT -s Anc1.Anc1refChr6 145200 83 + 197743 CCTTTTCTTTTCTGGAACAGGAGGAACTGGTTTCACCTGGGTCAGTCTCCGTTGCACAGGTATAATATATAGGTACACTTATT -s Anc2.Anc2refChr1 23468 83 + 142988 CCTTTTCTTTTCTGGAACAGGAGGAACTGGTTTCACCTGGGTCAGTCTCCGTTTCACTGATATAATATATAGGTACACTTATT -s mr.mrrefChr3 49137 83 + 181027 CCTCTTCTTTTCTGGGACAGGAGGAACTGACCTTACCTGGGTCAGTCTCTGTTGCACAGGTATTGTATTTGGGTACACTCATT -s simCow_chr6.simCow.chr6 479781 83 + 602619 CCTTTTCCTTTGTGCGACATGAGCAACTGGTTTCGCCTGGGTCAGTTCCTGTTCCGCTCACATAATATATAGGCATACTTCTT -s simDog_chr6.simDog.chr6 470082 83 + 593897 CCTTTTCTTTTCTGGAACAGGAGGAGCTGGTTTCACCTGTGTCAGTCTCCGCTTCATTGATATAATATGTAGGTACGCTTATT -s simHuman_chr6.simHuman.chr6 477080 79 + 601863 CCTTTTCTTTCCT----CAATAGAAACTGGTTTCACCTGGGTCGGTCTTAATTGCACAGGTATAACATATAAGTGCACTTACT -s simRat_chr6.simRat.chr6 503077 83 + 647215 CCTCTTCTTTTCTGGGACAGGATGAACTGACCTTACCTGGGTCAGCCTCTGTTGCACAGGTATGGTATTTGGGTTCACTCATT - -a -s simMouse_chr6.simMouse.chr6 495308 18 + 636262 CACCCCTTCAGTTGGTTC -s Anc0.Anc0refChr3 111485 18 + 222631 CACCCTTTAGGATGTTCT -s Anc1.Anc1refChr6 145283 18 + 197743 CACCCTTTAGGATGTTCT -s Anc2.Anc2refChr1 23551 18 + 142988 CACCCTTTAGGATGTTCT -s mr.mrrefChr3 49220 18 + 181027 CACCCCTTCAGTTGTTCC -s simCow_chr6.simCow.chr6 479864 18 + 602619 CTCCCCTTAGCACGTTCT -s simDog_chr6.simDog.chr6 470168 18 + 593897 CACCCTTTAGGATCTTTT -s simHuman_chr6.simHuman.chr6 477159 18 + 601863 CACCCTTTAGGATGTTCT -s simRat_chr6.simRat.chr6 503160 18 + 647215 CACTCCTTCAGTTATTCC - -a -s simMouse_chr6.simMouse.chr6 495326 61 + 636262 TAGAGATAAAGTGACTCAATGCTCACTTCTGAGATACAGAGGTTTGATCATAACACAATCA -s Anc0.Anc0refChr3 111503 59 + 222631 --GAGATAAACAGATTCAATGATCACTTCTGAGACACACAGGTTCAATGATCACACAATGC -s Anc1.Anc1refChr6 145301 59 + 197743 --GAGATAAACAGATTCAATGATCACTTCTGAGACACACAGGTTCAATGATCACACAATGC -s Anc2.Anc2refChr1 23569 59 + 142988 --GAGATAAACAGATTTAGTCACCACTTCTGAAACACACAAGTCCAATGATCACACAATGC -s mr.mrrefChr3 49238 61 + 181027 TAGAGATAAAGTGACTCAATGCTCACTTCTGAGATACAGAGGTTTGATCATAACACAATGA -s simCow_chr6.simCow.chr6 479882 59 + 602619 --GAGGTAATCAGATTTAGTAGCTATTTCTGAAATACACAAGTCCAATGATCACACAATGC -s simDog_chr6.simDog.chr6 470186 53 + 593897 --GAGACAAACAGATTTAGTCACCCCTTCTTAAACACACA------ATGATCACACAATGC -s simHuman_chr6.simHuman.chr6 477177 59 + 601863 --GAGATTAACAGATTCAATGATCACTTCTGAGACACACAGATTCAATGATCAGACATTGC -s simRat_chr6.simRat.chr6 503179 61 + 647215 CAGAGATGGAGCGACTCAATGCTCACTTCTGAGATACGGAGGTTTGATCACAACATAACGA - -a -s simMouse_chr6.simMouse.chr6 495387 4 + 636262 ACAT -s Anc0.Anc0refChr3 111562 4 + 222631 ATAT -s Anc1.Anc1refChr6 145360 4 + 197743 ATAT -s Anc2.Anc2refChr1 23628 4 + 142988 ATAT -s mr.mrrefChr3 49299 4 + 181027 ACAT -s simCow_chr6.simCow.chr6 479963 4 + 602619 ACAT -s simDog_chr6.simDog.chr6 470239 4 + 593897 ATAT -s simHuman_chr6.simHuman.chr6 477236 4 + 601863 AAAT -s simRat_chr6.simRat.chr6 503240 4 + 647215 ACAT - -a -s simMouse_chr6.simMouse.chr6 495391 24 + 636262 CACCTAGGACAGAGTGACCTCATT -s Anc0.Anc0refChr3 111566 24 + 222631 CAGCTGGGACAAAGTGACCCCATT -s Anc1.Anc1refChr6 145364 24 + 197743 CAGCTGGGACAAAGTGACCCCATT -s Anc2.Anc2refChr1 23639 24 + 142988 CAGCTGGGACTGAGTGACCCCATT -s mr.mrrefChr3 49303 24 + 181027 CACCTAGGACAAAGTGACCTCATT -s simCow_chr6.simCow.chr6 479974 16 + 602619 CAGCTAGGACGG--------TATT -s simDog_chr6.simDog.chr6 470250 24 + 593897 CATCTGGGACTGAGTGACCCCATT -s simHuman_chr6.simHuman.chr6 477240 24 + 601863 CAGCTGGGACAAAGTGTCCCCATT -s simRat_chr6.simRat.chr6 503244 13 + 647215 TATCTAGGTCGAA----------- - -a -s simMouse_chr6.simMouse.chr6 495415 17 + 636262 CTAGGAGACAGTGTGTA -s Anc0.Anc0refChr3 111607 17 + 222631 CAAAGAAGTAGCTTATG -s Anc1.Anc1refChr6 145405 17 + 197743 CAAAGAAGTAGCTTATG -s Anc2.Anc2refChr1 23680 17 + 142988 CAAAAAAGTAGCTTATG -s mr.mrrefChr3 49327 17 + 181027 CTAGGAGATAGCGTGTA -s simCow_chr6.simCow.chr6 480006 17 + 602619 CTAATAATTGGCTTATG -s simDog_chr6.simDog.chr6 470291 17 + 593897 AAAAAAAGCAGCTTATG -s simHuman_chr6.simHuman.chr6 477281 17 + 601863 CAAAGAAGTAGCTTATG -s simRat_chr6.simRat.chr6 503257 9 + 647215 --------TAGCATGTT - -a -s simMouse_chr6.simMouse.chr6 495432 16 + 636262 CTGAGCAACGAAGTAC -s Anc0.Anc0refChr3 111624 15 + 222631 CTAACCAACATAGCA- -s Anc1.Anc1refChr6 145422 16 + 197743 CTAACCAACATAGCAC -s Anc2.Anc2refChr1 23697 15 + 142988 CTAACCAACATAGCA- -s mr.mrrefChr3 49344 16 + 181027 CTAAGCAACGAAGTAC -s simCow_chr6.simCow.chr6 480023 15 + 602619 CTAACCAACATATCA- -s simDog_chr6.simDog.chr6 470309 15 + 593897 CTAACAAACATAGCA- -s simHuman_chr6.simHuman.chr6 477298 16 + 601863 CCAACCAACATAGCAC -s simRat_chr6.simRat.chr6 503266 16 + 647215 CTAAGCAAAGAAATAC - -a -s simMouse_chr6.simMouse.chr6 495448 12 + 636262 AGGTTTTGGCCA -s Anc0.Anc0refChr3 111639 12 + 222631 AGGGTTAGGTAA -s Anc1.Anc1refChr6 145438 12 + 197743 AGGGTTAGGTAA -s Anc2.Anc2refChr1 23712 12 + 142988 AGGGTTAGGGGA -s mr.mrrefChr3 49360 12 + 181027 AGGGTTTGGTAA -s simCow_chr6.simCow.chr6 480039 12 + 602619 AGGGTTAGCAAA -s simDog_chr6.simDog.chr6 470324 12 + 593897 AGGGTTAGGGGA -s simHuman_chr6.simHuman.chr6 477314 12 + 601863 AGAGTTAAGTAA -s simRat_chr6.simRat.chr6 503282 12 + 647215 AGGGTTTGGTAA - -a -s simMouse_chr6.simMouse.chr6 495460 18 + 636262 AAATTCTGAGCACTGCCA -s Anc0.Anc0refChr3 111651 18 + 222631 AAACACTGAGCACTCCCA -s Anc1.Anc1refChr6 145450 18 + 197743 AAACACTGAGCACTCCCA -s Anc2.Anc2refChr1 23728 18 + 142988 AAACACTGAGCACTCCCA -s mr.mrrefChr3 49372 18 + 181027 AAATTCTGAGCACTGCCA -s simCow_chr6.simCow.chr6 480055 18 + 602619 GACCATTGAGCACTCCCA -s simDog_chr6.simDog.chr6 470340 18 + 593897 AAACACTGAGCACTCCCA -s simHuman_chr6.simHuman.chr6 477347 18 + 601863 AAACCCTGAGTACTCCTA -s simRat_chr6.simRat.chr6 503294 18 + 647215 AAATACTGAGCACTACCA - -a -s simMouse_chr6.simMouse.chr6 495478 13 + 636262 GGAGCTGTTCTAA -s Anc0.Anc0refChr3 111669 13 + 222631 GGAACTCTTCCAA -s Anc1.Anc1refChr6 145468 13 + 197743 GGAACTCTTCCAA -s Anc2.Anc2refChr1 23746 13 + 142988 GGGACTCTTCCAA -s mr.mrrefChr3 49390 13 + 181027 GGAACTGTTCTAA -s simCow_chr6.simCow.chr6 480073 13 + 602619 GGGACTCTTCCAA -s simDog_chr6.simDog.chr6 470358 13 + 593897 GGTACTGTTCCAA -s simHuman_chr6.simHuman.chr6 477366 13 + 601863 GGAACTCTTCCAA -s simRat_chr6.simRat.chr6 503312 13 + 647215 GGAACTGTTCTAA - -a -s simMouse_chr6.simMouse.chr6 495491 4 + 636262 TAAG -s Anc0.Anc0refChr3 111682 4 + 222631 TAAG -s Anc1.Anc1refChr6 145481 4 + 197743 TAAG -s Anc2.Anc2refChr1 23759 4 + 142988 TAAG -s mr.mrrefChr3 49403 4 + 181027 TAAG -s simCow_chr6.simCow.chr6 480086 4 + 602619 TATG -s simDog_chr6.simDog.chr6 470423 4 + 593897 TGAG -s simHuman_chr6.simHuman.chr6 477379 4 + 601863 TAAG -s simRat_chr6.simRat.chr6 503325 4 + 647215 TGCA - -a -s simMouse_chr6.simMouse.chr6 495495 10 + 636262 AGTGAAATTT -s Anc0.Anc0refChr3 111690 10 + 222631 AGCAAGATTT -s Anc1.Anc1refChr6 145489 10 + 197743 AGCAAGATTT -s Anc2.Anc2refChr1 23767 10 + 142988 AGCAAGATTT -s mr.mrrefChr3 49407 10 + 181027 AGCAAAATTT -s simCow_chr6.simCow.chr6 480094 10 + 602619 AGCAAGATCT -s simDog_chr6.simDog.chr6 470431 10 + 593897 GGCAAGATTT -s simHuman_chr6.simHuman.chr6 477387 10 + 601863 AGCAAGATTT -s simRat_chr6.simRat.chr6 503329 10 + 647215 AGCAAAGTTA - -a -s simMouse_chr6.simMouse.chr6 495505 126 + 636262 TTTTAGTCCCATGCGTGGCCACTATTGTATGGTATAGATCTGATAGGTGTAGCCCGTGCTGGCACAGGGAAGACGTTGTGCTATGTAATGCCCGGTCTCATTCACCTGGTGCTCCAGCCGAGGTTG -s Anc0.Anc0refChr3 111701 126 + 222631 TTTTAGTCACATGCCTGGCCACTATTGTATGGTATAGATCTGATAGGTGTGGCCCGTGCTGGCACAGGGAAGACTTTGTGCTACGTAATGCCCGGTCTCATTCACCTGGTGCTCCAACCCAGGTCA -s Anc1.Anc1refChr6 145500 126 + 197743 TTTTAGTCACATGCCTGGCCACTATTGTATGGTATAGATCTGATAGGTGTGGCCCGTGCTGGCACAGGGAAGACTTTGTGCTACGTAATGCCCGGTCTCATTCACCTGGTGCTCCAACCCAGGTCA -s Anc2.Anc2refChr1 23778 126 + 142988 TTTTAGTCACATGCCTGGCCACTATTGTATGGTATAGATCTGATAGGTGTGGCCCGGGCTGGCACAGGGAAGACTTTGTGCTACGTAATGCCCGGTCTCATACACCTGGTGCTCCAACCCAGGTCA -s mr.mrrefChr3 49417 126 + 181027 TTTTAGTCCCATGCGTGGCCACTATTGTATGGTATAGATCTGATAGGTGTAGCCCGTGCTGGCACAGGGAAGACGTTGTGCTATGTAATGCCCGGTCTCATTCACCTGGTGCTCCAGCCCAGGTCA -s simCow_chr6.simCow.chr6 480105 126 + 602619 CTTTAGTCACATGCCTGGCCACTATTGTATGGTATAGATCTGATAGGTGTGGCCCGGGCCGGCACAGGGAAGACTTTGTGTTATGTAACGCCCGGGCTCATACACCTGGTGCTCCAACCCAGGTCA -s simDog_chr6.simDog.chr6 470442 126 + 593897 TTTTAGTCACATGCCTGGCCTCTATTGTATGGTATAGATCTGATAGGTGTCGCCCAGGCTGGCACAGGGAAGACTTTGTGCTACGTAATGCCCGGTCTCATACACCTGGTGCTCCACCCCGGGTCA -s simHuman_chr6.simHuman.chr6 477398 126 + 601863 TTTTAGTCACATGCCTGGCCACTATTGTATGGTATAGATCTGATAGGTGTGGCCCGTGCTGGCACAGGTAAGACTTTGTGCTACGTAATGCCCGGTCTCATTCATCTGGTACTCCAACCCAGGTCA -s simRat_chr6.simRat.chr6 503339 126 + 647215 TTTTAGTCCCATGCGTGGCCACTATTGTATGGTATAGATCTGATAGGTGTAGCGCGAGCTGGCACAGGGAAGACATTGTGCTATGTAATGCCCGGTCTCATTCACCTGGTGCTCCAGCCCAGGTCA - -a -s simMouse_chr6.simMouse.chr6 495685 1 + 636262 T -s mr.mrrefChr3 49597 1 + 181027 T -s simRat_chr6.simRat.chr6 508002 1 + 647215 t - -a -s simMouse_chr6.simMouse.chr6 495731 1 + 636262 C -s Anc0.Anc0refChr3 111929 1 + 222631 C -s Anc1.Anc1refChr6 145728 1 + 197743 C -s Anc2.Anc2refChr1 24008 1 + 142988 C -s mr.mrrefChr3 49643 1 + 181027 C -s simCow_chr6.simCow.chr6 480439 1 + 602619 C -s simDog_chr6.simDog.chr6 470674 1 + 593897 C -s simHuman_chr6.simHuman.chr6 477626 1 + 601863 T -s simRat_chr6.simRat.chr6 508048 1 + 647215 C - -a -s simMouse_chr6.simMouse.chr6 495736 12 + 636262 TAATTTGCCTCC -s Anc0.Anc0refChr3 111935 12 + 222631 TAAATTGGTCCA -s Anc1.Anc1refChr6 145734 12 + 197743 TAAATTGGTCCA -s Anc2.Anc2refChr1 24014 12 + 142988 TAAATTGGTCCA -s mr.mrrefChr3 49649 12 + 181027 TAATTTGCTTCA -s simCow_chr6.simCow.chr6 480448 12 + 602619 TAAGTTGGTTCA -s simDog_chr6.simDog.chr6 470680 12 + 593897 GGAATTGGTCCA -s simHuman_chr6.simHuman.chr6 477632 12 + 601863 TAACTTTGTCCA -s simRat_chr6.simRat.chr6 193458 12 - 647215 TGGTTTGGTTCA -s simRat_chr6.simRat.chr6 508054 12 + 647215 TTATTTGCTTCA - -a -s simMouse_chr6.simMouse.chr6 495748 27 + 636262 CTGCAGATTCTTATGATGCTTACAATA -s Anc0.Anc0refChr3 111948 26 + 222631 CTGCAGAATGCTGC-ATACTGACAATA -s Anc1.Anc1refChr6 145747 26 + 197743 CTGCAGAATGCTGC-ATACTGACAATA -s Anc2.Anc2refChr1 24027 26 + 142988 CTGCAGAATGCTGC-ATACTGACAAAA -s mr.mrrefChr3 49661 27 + 181027 CTGCAGATTGTGATGATGCTTATAATA -s simCow_chr6.simCow.chr6 480461 26 + 602619 CTACAGCATGCTGC-ATGCTGACTAAA -s simDog_chr6.simDog.chr6 470693 26 + 593897 CTGCAGAAAACTAC-TTATTTACAAAA -s simHuman_chr6.simHuman.chr6 477645 26 + 601863 CTGCAGGATGCTGC-ATACTGGCAATA -s simRat_chr6.simRat.chr6 193470 27 - 647215 CTTCAGAGTGTGACAATAATTATAAGA -s simRat_chr6.simRat.chr6 508066 26 + 647215 -TGCAGATTATGATGGTGCTTATAATA - -a -s simMouse_chr6.simMouse.chr6 495775 1 + 636262 T -s Anc0.Anc0refChr3 111974 1 + 222631 T -s Anc1.Anc1refChr6 145773 1 + 197743 T -s Anc2.Anc2refChr1 24053 1 + 142988 T -s mr.mrrefChr3 49688 1 + 181027 T -s simCow_chr6.simCow.chr6 480487 1 + 602619 T -s simDog_chr6.simDog.chr6 470720 1 + 593897 C -s simHuman_chr6.simHuman.chr6 477671 1 + 601863 T -s simRat_chr6.simRat.chr6 193497 1 - 647215 T -s simRat_chr6.simRat.chr6 508092 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 495776 4 + 636262 GTTG -s Anc0.Anc0refChr3 111975 4 + 222631 GTAG -s Anc1.Anc1refChr6 145774 4 + 197743 GTAG -s Anc2.Anc2refChr1 24054 4 + 142988 GTAG -s mr.mrrefChr3 49689 4 + 181027 GTTG -s simCow_chr6.simCow.chr6 480488 4 + 602619 GTAG -s simDog_chr6.simDog.chr6 470721 4 + 593897 GTAG -s simHuman_chr6.simHuman.chr6 477672 4 + 601863 GTAG -s simRat_chr6.simRat.chr6 193498 4 - 647215 GTAA -s simRat_chr6.simRat.chr6 508098 4 + 647215 GTTG - -a -s simMouse_chr6.simMouse.chr6 495780 5 + 636262 TGTCT -s Anc0.Anc0refChr3 112004 5 + 222631 TGTCA -s Anc1.Anc1refChr6 145803 5 + 197743 TGTCA -s Anc2.Anc2refChr1 24083 5 + 142988 TGTCA -s mr.mrrefChr3 49708 5 + 181027 TGTCT -s simCow_chr6.simCow.chr6 480517 5 + 602619 TGTCA -s simDog_chr6.simDog.chr6 470750 5 + 593897 TGTCA -s simHuman_chr6.simHuman.chr6 477701 5 + 601863 TGTCG -s simRat_chr6.simRat.chr6 508102 5 + 647215 TGTCA - -a -s simMouse_chr6.simMouse.chr6 495785 35 + 636262 ACTCTTGACTCTAACCACCCAGTTTTGTAGTACTA -s Anc0.Anc0refChr3 112009 34 + 222631 TCTCTTGACCAATACCACCCAGTTTTGCAGTACT- -s Anc1.Anc1refChr6 145808 34 + 197743 TCTCTTGACCAATACCACCCAGTTTTGCAGTACT- -s Anc2.Anc2refChr1 24088 34 + 142988 TCTCTTGACCAATACCACCCAGTTTTGCAGTACT- -s mr.mrrefChr3 49713 35 + 181027 TCTCTTGACTAAAACCACCCAGTTTTGTAGTACTA -s simCow_chr6.simCow.chr6 480522 34 + 602619 TGTCTTTACCAATACCTTCCAGCTTTGCAGTACT- -s simDog_chr6.simDog.chr6 470755 34 + 593897 TCTCTTGACGAATACTACCCAGTTTTGCACTACC- -s simHuman_chr6.simHuman.chr6 477706 34 + 601863 TCTATTGTCCAATATCACCCAGTTTTGCAGTACT- -s simRat_chr6.simRat.chr6 193517 35 - 647215 TCTCTTGATCAAGGCCAAGCAGTTTTGAAGTACGA -s simRat_chr6.simRat.chr6 508107 35 + 647215 TCTCTTGACTAAAACCACTCAGTTTTGTAGTACTA - -a -s simMouse_chr6.simMouse.chr6 495820 46 + 636262 CTGTAGTGCACTACCTTGTTAGACTGCACTGAACCTATCATTAGTA -s Anc0.Anc0refChr3 112043 46 + 222631 CTGCAGTACACATTCTTGTGAGTCAGCATTAAACCTAACATTAGTA -s Anc1.Anc1refChr6 145842 46 + 197743 CTGCAGTACACATTCTTGTGAGTCAGCATTAAACCTAACATTAGTA -s Anc2.Anc2refChr1 24122 46 + 142988 CTGCAGTACACATTCTAATGACTCAGTATTAAACCTAACATTAGTA -s mr.mrrefChr3 49748 46 + 181027 CTGCAGTACACAACCTTGTTAGACTGCACTGAACCTATCATTAGTA -s simCow_chr6.simCow.chr6 480556 23 + 602619 C-----------------------AGTGTTAAACTTAATATTAGTA -s simDog_chr6.simDog.chr6 470790 44 + 593897 CTGCAGTACACATTCTAATGACTCAGTATTAAACC--ACATTAGTG -s simHuman_chr6.simHuman.chr6 477740 46 + 601863 CTGCAGTGCACATTCCTGTGAGTCAGCATTAAACCTAAGATTAGTA -s simRat_chr6.simRat.chr6 193552 46 - 647215 TTGCAGCACACAACCATGTGAAACTGTGTTGAACCTAACATTAGTA -s simRat_chr6.simRat.chr6 508142 46 + 647215 CTGCAGTACACAACCGTGTTAGACTGCACCGAACCTATCATTAGTA - -a -s simMouse_chr6.simMouse.chr6 495866 34 + 636262 CTATCATTAGTATATGACAATGACATGGGTTTAA -s Anc0.Anc0refChr3 112089 22 + 222631 C------------ATAACATTGACACAGGTTTGA -s Anc1.Anc1refChr6 145888 22 + 197743 C------------ATAACATTGACACAGGTTTGA -s Anc2.Anc2refChr1 24168 22 + 142988 C------------ATAACATCAACACAGGTTTGA -s mr.mrrefChr3 49794 22 + 181027 C------------ATGACAATGACACGGGTTTAA -s simCow_chr6.simCow.chr6 480579 22 + 602619 T------------GAAACATCAACACCGGTTTAC -s simDog_chr6.simDog.chr6 470852 22 + 593897 C------------ATAGTATCAATTCAGGTTTGA -s simHuman_chr6.simHuman.chr6 477786 22 + 601863 C------------ATAACATTGACACAGGTTTGA -s simRat_chr6.simRat.chr6 193598 22 - 647215 T------------GTAACAATGACACAGCTTTGA -s simRat_chr6.simRat.chr6 508188 22 + 647215 C------------AGGACAATGGCACGGGTTCAA - -a -s simMouse_chr6.simMouse.chr6 495900 4 + 636262 TTAA -s Anc0.Anc0refChr3 112111 4 + 222631 TCAA -s Anc1.Anc1refChr6 145910 4 + 197743 TCAA -s Anc2.Anc2refChr1 24190 4 + 142988 TCAA -s mr.mrrefChr3 49816 4 + 181027 TTAA -s simCow_chr6.simCow.chr6 480601 4 + 602619 TTGC -s simDog_chr6.simDog.chr6 470874 4 + 593897 TCAA -s simHuman_chr6.simHuman.chr6 477808 4 + 601863 TCAA -s simRat_chr6.simRat.chr6 193627 4 - 647215 CCAA -s simRat_chr6.simRat.chr6 508210 4 + 647215 TTAA - -a -s simMouse_chr6.simMouse.chr6 495933 1 + 636262 G -s Anc0.Anc0refChr3 112144 1 + 222631 G -s Anc1.Anc1refChr6 145943 1 + 197743 G -s Anc2.Anc2refChr1 24223 1 + 142988 G -s mr.mrrefChr3 49849 1 + 181027 G -s simCow_chr6.simCow.chr6 480634 1 + 602619 G -s simDog_chr6.simDog.chr6 470913 1 + 593897 G -s simHuman_chr6.simHuman.chr6 477841 1 + 601863 G -s simRat_chr6.simRat.chr6 508243 1 + 647215 G - -a -s simMouse_chr6.simMouse.chr6 495940 1 + 636262 A - -a -s simMouse_chr6.simMouse.chr6 496043 1 + 636262 C -s Anc0.Anc0refChr3 112263 1 + 222631 T -s Anc1.Anc1refChr6 146066 1 + 197743 T -s Anc2.Anc2refChr1 24342 1 + 142988 T -s mr.mrrefChr3 49969 1 + 181027 C -s simCow_chr6.simCow.chr6 480752 1 + 602619 T -s simHuman_chr6.simHuman.chr6 477965 1 + 601863 T -s simRat_chr6.simRat.chr6 508413 1 + 647215 C - -a -s simMouse_chr6.simMouse.chr6 496113 4 + 636262 CAAC -s Anc0.Anc0refChr3 112334 3 + 222631 CAA- -s Anc1.Anc1refChr6 146137 4 + 197743 CAAC -s Anc2.Anc2refChr1 24413 3 + 142988 CAA- -s mr.mrrefChr3 50039 4 + 181027 CAAC -s simCow_chr6.simCow.chr6 480838 3 + 602619 CAA- -s simHuman_chr6.simHuman.chr6 478036 4 + 601863 CAAC -s simRat_chr6.simRat.chr6 193846 4 - 647215 TGAC -s simRat_chr6.simRat.chr6 508489 4 + 647215 CAAC - -a -s simMouse_chr6.simMouse.chr6 496200 1 + 636262 A -s Anc0.Anc0refChr3 112504 1 + 222631 A -s Anc1.Anc1refChr6 146310 1 + 197743 A -s Anc2.Anc2refChr1 24583 1 + 142988 A -s mr.mrrefChr3 50205 1 + 181027 A -s simCow_chr6.simCow.chr6 481019 1 + 602619 A -s simHuman_chr6.simHuman.chr6 478209 1 + 601863 A -s simRat_chr6.simRat.chr6 508633 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 496246 13 + 636262 GTTACAGGTGTGC -s Anc0.Anc0refChr3 112550 13 + 222631 TCTGCAGGTGTGT -s Anc1.Anc1refChr6 146356 13 + 197743 TCTGCAGGTGTGT -s Anc2.Anc2refChr1 24629 13 + 142988 TCTGCAGGTGTGT -s mr.mrrefChr3 50251 13 + 181027 GTTACAGGTGTGC -s simCow_chr6.simCow.chr6 481066 13 + 602619 TCTGCAGGAATGT -s simDog_chr6.simDog.chr6 471019 13 + 593897 TCTGCAGGTGTGT -s simRat_chr6.simRat.chr6 508679 13 + 647215 GTTACAGGTGTCT - -a -s simMouse_chr6.simMouse.chr6 496297 1 + 636262 A -s Anc0.Anc0refChr3 112598 1 + 222631 A -s Anc1.Anc1refChr6 146404 1 + 197743 A -s Anc2.Anc2refChr1 24682 1 + 142988 A -s mr.mrrefChr3 50308 1 + 181027 A -s simDog_chr6.simDog.chr6 471072 1 + 593897 A -s simHuman_chr6.simHuman.chr6 478290 1 + 601863 A -s simRat_chr6.simRat.chr6 196991 1 - 647215 G -s simRat_chr6.simRat.chr6 508730 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 496349 4 + 636262 CCCC - -a -s simMouse_chr6.simMouse.chr6 496365 1 + 636262 C -s mr.mrrefChr3 50376 1 + 181027 C -s simRat_chr6.simRat.chr6 508794 1 + 647215 C - -a -s simMouse_chr6.simMouse.chr6 496373 7 + 636262 TTTAACT -s mr.mrrefChr3 50384 7 + 181027 TTTAACT -s simRat_chr6.simRat.chr6 508802 7 + 647215 TTTAACT - -a -s simMouse_chr6.simMouse.chr6 496433 1 + 636262 T -s Anc0.Anc0refChr3 112687 1 + 222631 T -s Anc1.Anc1refChr6 146495 1 + 197743 T -s Anc2.Anc2refChr1 24771 1 + 142988 T -s mr.mrrefChr3 50444 1 + 181027 T -s simCow_chr6.simCow.chr6 481198 1 + 602619 T -s simHuman_chr6.simHuman.chr6 478381 1 + 601863 T -s simRat_chr6.simRat.chr6 197119 1 - 647215 T -s simRat_chr6.simRat.chr6 508862 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 496434 12 + 636262 TGGGAACTAAAG -s Anc0.Anc0refChr3 112688 12 + 222631 CACGTACTAATA -s Anc1.Anc1refChr6 146496 12 + 197743 CACGTACTAATA -s Anc2.Anc2refChr1 24772 12 + 142988 CACGTTCTAATA -s mr.mrrefChr3 50445 12 + 181027 CAGGAACTAAAA -s simCow_chr6.simCow.chr6 481199 12 + 602619 CACGTTCTAATA -s simHuman_chr6.simHuman.chr6 478383 12 + 601863 CAAGTACTCATA -s simRat_chr6.simRat.chr6 197120 12 - 647215 CAAGAACCAAAA -s simRat_chr6.simRat.chr6 508863 12 + 647215 CTGGAATTAAAA - -a -s simMouse_chr6.simMouse.chr6 496452 47 + 636262 ATAGCTTAAGCTTAAGGGGTCAAAGGAACAGACCTAGTACCTTAGTC -s Anc0.Anc0refChr3 112706 47 + 222631 CTCTCTAAAGCTTAAGGGGTCAAAGGAACAGACCTAGCACTTTAGTC -s Anc1.Anc1refChr6 146514 47 + 197743 CTCTCTAAAGCTTAAGGGGTCAAAGGAACAGACCTAGCACTTTAGTC -s Anc2.Anc2refChr1 24790 47 + 142988 CTCCCTAAAGCTTAAGGGGTCAAAGGAACAGACCTAGCACTTTAGTC -s mr.mrrefChr3 50463 47 + 181027 CTATCTTAAGCTTAAGGGGTCAAAGGAATAGACCTAGTACCTTAGTC -s simCow_chr6.simCow.chr6 481217 47 + 602619 CTCACCAGAGCTTAAGGGGTCAAAGGAACAGGCCTAGCTCCTTAGTC -s simDog_chr6.simDog.chr6 471151 47 + 593897 CTCCCTAAAGCTTAAAGGGTCAAAGGAACAGACCTAGTACTTTAGTT -s simHuman_chr6.simHuman.chr6 478401 47 + 601863 CTCTCTGAAGCTTGAGGGGTCAAAGGAACAGACCTAGCACTTTAGTC -s simRat_chr6.simRat.chr6 197138 47 - 647215 CTTTCGCAAGCTTAACGAATCAAAGGAATAGACCTAGTACCTTAGTC -s simRat_chr6.simRat.chr6 509109 38 + 647215 CTACGTTAAGCTTAA---------GGGGTAGACCTAGAACCTTAGTC - -a -s simMouse_chr6.simMouse.chr6 496499 1 + 636262 C -s Anc0.Anc0refChr3 112753 1 + 222631 C -s Anc1.Anc1refChr6 146561 1 + 197743 C -s Anc2.Anc2refChr1 24837 1 + 142988 C -s mr.mrrefChr3 50510 1 + 181027 C -s simCow_chr6.simCow.chr6 481264 1 + 602619 T -s simDog_chr6.simDog.chr6 471198 1 + 593897 C -s simHuman_chr6.simHuman.chr6 478448 1 + 601863 C -s simRat_chr6.simRat.chr6 509147 1 + 647215 C - -a -s simMouse_chr6.simMouse.chr6 496500 29 + 636262 TGACACCTACACATGAGCTAGCAATTCAA -s Anc0.Anc0refChr3 112754 29 + 222631 TGACTCCTACACATGAGCTAGCAATTCAA -s Anc1.Anc1refChr6 146562 29 + 197743 TGACTCCTACACATGAGCTAGCAATTCAA -s Anc2.Anc2refChr1 24838 29 + 142988 TGACTCCTACCCATGAGCTAGCAATTCAA -s mr.mrrefChr3 50511 29 + 181027 TGACACCTACACATGAGCTAGCAATTCAA -s simCow_chr6.simCow.chr6 481265 23 + 602619 TGACCCCTAC------GCTAGCGATTCAA -s simDog_chr6.simDog.chr6 471199 29 + 593897 TGACTCCTACCCATGAGCTAGCAATTCAA -s simHuman_chr6.simHuman.chr6 478449 29 + 601863 TGACTCCTACACATGAGTTAGCAATTCAA -s simRat_chr6.simRat.chr6 197185 29 - 647215 TGATGCTTACAAATGAGCTTGCAATTAAA -s simRat_chr6.simRat.chr6 509148 29 + 647215 TGACACCTACACATGAGCTAGCAATTCAA - -a -s simMouse_chr6.simMouse.chr6 496529 17 + 636262 GTGGAAGAAGGTGACTG -s Anc0.Anc0refChr3 112783 17 + 222631 GTGGAAGAAGGAGACTG -s Anc1.Anc1refChr6 146591 17 + 197743 GTGGAAGAAGGAGACTG -s Anc2.Anc2refChr1 24867 17 + 142988 GTGGAAGAAGGAGACTG -s mr.mrrefChr3 50540 17 + 181027 GTGGAAGAAGGTGACTG -s simCow_chr6.simCow.chr6 481288 17 + 602619 GTGGAAGAAGGAGACTG -s simDog_chr6.simDog.chr6 471228 17 + 593897 GTGGAAGAAGGAGACTG -s simHuman_chr6.simHuman.chr6 478478 17 + 601863 GTGGAAGAAGGAGACTG -s simRat_chr6.simRat.chr6 197215 17 - 647215 GTGGAGGAAGACGGCTG -s simRat_chr6.simRat.chr6 509177 17 + 647215 GTGGAAGAAGGTGACTG - -a -s simMouse_chr6.simMouse.chr6 496546 41 + 636262 TTGTAAATATTTTCACAAAGGGCTCCAGAGGTGGATAGGTT -s Anc0.Anc0refChr3 112800 37 + 222631 TTGTAAATATTTTCACAAAGGACTCCAGAGG----TAGGTT -s Anc1.Anc1refChr6 146608 37 + 197743 TTGTAAATATTTTCACAAAGGACTCCAGAGG----TAGGTT -s Anc2.Anc2refChr1 24884 37 + 142988 TTGTAAATATTTTCATAAAGGACTCCAGAGG----TAGGTT -s mr.mrrefChr3 50557 41 + 181027 TTGTAAATATTTTCACAAAGGGCTCCAGAGGTGGATAGGTT -s simCow_chr6.simCow.chr6 481305 37 + 602619 TTGTAAATATTTTCATAAAGGACTTCAGAGG----TAGGTT -s simDog_chr6.simDog.chr6 471245 37 + 593897 TTGCAAATATTTTCATAGAGGGCTCCAGAGG----TAGGTT -s simHuman_chr6.simHuman.chr6 478495 37 + 601863 TTGTAAATATTTTCACAAAGGACTCCAGAGG----TAGGTT -s simRat_chr6.simRat.chr6 197254 41 - 647215 GTGGGAACTTTTTCTCAAAGGCGTCCAGAGGCAAATAGGTT -s simRat_chr6.simRat.chr6 509194 41 + 647215 TTGTAAATATTTTCACAAAGGGCTCCAGAGGTGGATAGGTT - -a -s simMouse_chr6.simMouse.chr6 496587 2 + 636262 AT -s Anc0.Anc0refChr3 112837 2 + 222631 AT -s Anc1.Anc1refChr6 146645 2 + 197743 AT -s Anc2.Anc2refChr1 24921 2 + 142988 AC -s mr.mrrefChr3 50598 2 + 181027 AT -s simCow_chr6.simCow.chr6 481342 2 + 602619 AC -s simDog_chr6.simDog.chr6 471282 2 + 593897 AC -s simHuman_chr6.simHuman.chr6 478532 2 + 601863 AT -s simRat_chr6.simRat.chr6 509235 2 + 647215 AT - -a -s simMouse_chr6.simMouse.chr6 496589 41 + 636262 TTGTTCTCTCCAGCATTACATGTACCATTGCAGTACTCTGA -s Anc0.Anc0refChr3 112839 41 + 222631 TTTTTCTCACTCCCATTACCTGTACCATTGTAGTCCTGTGA -s Anc1.Anc1refChr6 146647 41 + 197743 TTTTTCTCACTCCCATTACCTGTACCATTGTAGTCCTGTGA -s Anc2.Anc2refChr1 24923 41 + 142988 CTTTTCTCACTCCCATTACCTGTACCATTGTAGTCCTGTGA -s mr.mrrefChr3 50600 41 + 181027 TTGTTCTCTCCAGCATTACCTGTACCATTGTAGTACTCTGA -s simCow_chr6.simCow.chr6 481344 41 + 602619 CTTTTCTCACTTCCATTACTTGTACCATTATAGTCCAGTGA -s simDog_chr6.simDog.chr6 471284 41 + 593897 CTTTTCACCCTCCCATCACCTGTACCATAGTAACCCTGTGA -s simHuman_chr6.simHuman.chr6 478534 41 + 601863 TTTTTTTCACTCCAACTACCTGTACTATTGTAGTCCTGTAA -s simRat_chr6.simRat.chr6 197295 41 - 647215 CTGGTCTCTCAAGCATTACCTGTACCATTGTACTCCCCTGA -s simRat_chr6.simRat.chr6 509237 41 + 647215 TTGTTCTCTCGAGCATTACCTGTACCCTTTTAGTACTCTGT - -a -s simMouse_chr6.simMouse.chr6 496630 44 + 636262 TAATTAAGCCCTTTCATTCTTTACTTTTATTTTTTTGGGTGCAA -s Anc0.Anc0refChr3 112880 44 + 222631 TACTTTCCCTCTTTCAACCCTTATTTCTATTCTTTTGGGTACAG -s Anc1.Anc1refChr6 146688 44 + 197743 TACTTTCCCTCTTTCAACCCTTATTTCTATTCTTTTGGGTACAG -s Anc2.Anc2refChr1 24988 44 + 142988 TACTTTCCCTCTTTTCACCCTTATTTCTATTCTTCTGGGTAAAG -s mr.mrrefChr3 50641 44 + 181027 TAATTACGCCCTTTCATTCTTTACCTTTATTTTTTTGGGTACAA -s simCow_chr6.simCow.chr6 481409 42 + 602619 CGCTTACCCTCTTATCACC--TATTTCTAATCTTCTGGTTGAAG -s simDog_chr6.simDog.chr6 471353 42 + 593897 TACTTTCCCACTAT--GCCCTTATTTCTATTCTTCTGGGCAAAG -s simHuman_chr6.simHuman.chr6 478575 40 + 601863 TACTTCCCCTCTTTCAACCCTTGTTTCTG----TTTGCGTACAG -s simRat_chr6.simRat.chr6 197336 44 - 647215 TACTTCCTCTCTTTCATACTTTATCTTCTTTTTTTTAGGTACAA -s simRat_chr6.simRat.chr6 509278 44 + 647215 GAATTATGCCCTTTCATTCTTTACCTTTACTTTTTTGGGTACAA - -a -s simMouse_chr6.simMouse.chr6 496674 15 + 636262 ATCCACTCTCAGTTC -s Anc0.Anc0refChr3 112925 12 + 222631 TTCTCCTCTCAG--- -s Anc1.Anc1refChr6 146733 15 + 197743 TTCTCCTCTCAGCTT -s Anc2.Anc2refChr1 25033 12 + 142988 TTCTCCTCTAGG--- -s mr.mrrefChr3 50686 15 + 181027 TTCTCCTCTCAGTTC -s simCow_chr6.simCow.chr6 481452 12 + 602619 TTCTCCTATTGG--- -s simDog_chr6.simDog.chr6 471396 12 + 593897 TGCTCCTCTAGG--- -s simHuman_chr6.simHuman.chr6 478616 15 + 601863 TTCTCCTCTCAGCTT -s simRat_chr6.simRat.chr6 197381 15 - 647215 TTCTCCTATCAGTCC -s simRat_chr6.simRat.chr6 509322 15 + 647215 TTCTCCTCTTGGTTC - -a -s simMouse_chr6.simMouse.chr6 496689 3 + 636262 TAC -s Anc1.Anc1refChr6 146748 2 + 197743 TG- -s mr.mrrefChr3 50701 3 + 181027 TAC -s simHuman_chr6.simHuman.chr6 478631 2 + 601863 TG- -s simRat_chr6.simRat.chr6 509337 3 + 647215 TAC - -a -s simMouse_chr6.simMouse.chr6 496704 10 + 636262 CCTTGCTTCA - -a -s simMouse_chr6.simMouse.chr6 496720 3 + 636262 TTT -s Anc0.Anc0refChr3 112947 3 + 222631 CTT -s Anc1.Anc1refChr6 146768 3 + 197743 CTT -s Anc2.Anc2refChr1 25055 3 + 142988 CTT -s mr.mrrefChr3 50722 3 + 181027 CTT -s simCow_chr6.simCow.chr6 481474 3 + 602619 CTT -s simDog_chr6.simDog.chr6 471418 3 + 593897 CTT -s simRat_chr6.simRat.chr6 509358 3 + 647215 CTT - -a -s simMouse_chr6.simMouse.chr6 496799 1 + 636262 G -s Anc0.Anc0refChr3 113023 1 + 222631 A -s Anc1.Anc1refChr6 146849 1 + 197743 A -s Anc2.Anc2refChr1 25131 1 + 142988 A -s mr.mrrefChr3 50801 1 + 181027 G -s simCow_chr6.simCow.chr6 481552 1 + 602619 A -s simDog_chr6.simDog.chr6 471494 1 + 593897 A -s simHuman_chr6.simHuman.chr6 478703 1 + 601863 T -s simRat_chr6.simRat.chr6 509436 1 + 647215 G - -a -s simMouse_chr6.simMouse.chr6 496891 20 + 636262 TGAGGTCTGGCTCTTCGTAC -s Anc0.Anc0refChr3 113155 20 + 222631 TGAGGTCTTGCTTTTCCTGT -s Anc1.Anc1refChr6 146981 20 + 197743 TGAGGTCTTGCTTTTCCTGT -s Anc2.Anc2refChr1 25275 20 + 142988 TGAGAACTTGCTTCTTCTGT -s mr.mrrefChr3 50893 20 + 181027 TGAGGTCTGGCTCTTCGTAC -s simCow_chr6.simCow.chr6 481715 20 + 602619 TGATAACTTGCTTGTTTTGT -s simDog_chr6.simDog.chr6 471680 20 + 593897 TGAGAATTTGCTTCTTCTGT -s simHuman_chr6.simHuman.chr6 478834 20 + 601863 TGAGGTCTAGCTATTCCTGT -s simRat_chr6.simRat.chr6 509528 20 + 647215 TGAGGTCTGGCCCTTTGTAC - -a -s simMouse_chr6.simMouse.chr6 496977 2 + 636262 GT -s Anc0.Anc0refChr3 113241 2 + 222631 GT -s Anc1.Anc1refChr6 147067 2 + 197743 GT -s Anc2.Anc2refChr1 25361 2 + 142988 GT -s mr.mrrefChr3 50979 2 + 181027 GT -s simCow_chr6.simCow.chr6 481801 2 + 602619 GT -s simDog_chr6.simDog.chr6 471766 2 + 593897 GT -s simHuman_chr6.simHuman.chr6 478920 2 + 601863 GT -s simRat_chr6.simRat.chr6 509614 2 + 647215 GT - -a -s simMouse_chr6.simMouse.chr6 496979 1 + 636262 G -s Anc0.Anc0refChr3 113243 1 + 222631 G -s Anc1.Anc1refChr6 147069 1 + 197743 G -s Anc2.Anc2refChr1 25363 1 + 142988 G -s mr.mrrefChr3 50981 1 + 181027 G -s simCow_chr6.simCow.chr6 481803 1 + 602619 G -s simDog_chr6.simDog.chr6 471768 1 + 593897 G -s simHuman_chr6.simHuman.chr6 478922 1 + 601863 G -s simRat_chr6.simRat.chr6 449557 1 + 647215 A -s simRat_chr6.simRat.chr6 509616 1 + 647215 G - -a -s simMouse_chr6.simMouse.chr6 496981 71 + 636262 ATATTATAATTGTAACACCTGGCAGATTAAATGATTTGCAAATGAGTAACTTTGTTAATTTGAAGAATATA -s Anc0.Anc0refChr3 113245 71 + 222631 ATATTATAATTGTAACTCCTGGCAGATTAAATGATTTGCAAATGAGTAACTTTGTCAATTTGAAAAATATA -s Anc1.Anc1refChr6 147071 71 + 197743 ATATTATAATTGTAACTCCTGGCAGATTAAATGATTTGCAAATGAGTAACTTTGTCAATTTGAAAAATATA -s Anc2.Anc2refChr1 25365 71 + 142988 ATATTATAATTGTAACTCCTGGGAGATTAAATGATTTGCAAATGAGTAACTTTGTCAATCTGAAAAATATA -s mr.mrrefChr3 50983 71 + 181027 ATATTATAATTGTAACACCTGGCAGATTAAATGATTTGCAAATGAGTAACTTTGTTAATTTGAAGAATATA -s simCow_chr6.simCow.chr6 481805 71 + 602619 ATATTATAATTGTAACTCCTGGAAGGTTAAATGATTTGCAAATAAGTAACTTCGTCAATCTGAAAAATATA -s simDog_chr6.simDog.chr6 471770 71 + 593897 ATATTATAATCGTAAGTCCTGGGAGATTGAATGATTTGCAAATGAGTAACTTTGTCAATCTGAAAAATATA -s simHuman_chr6.simHuman.chr6 478924 71 + 601863 ATATTAAAATTGTAACGCTTGGCAGATTAAATGATTTGCAAATGAGTAACTTTGTCAACTTGAAAAATATT -s simRat_chr6.simRat.chr6 449559 71 + 647215 ATATTCAAATTGTGATACCTGGCAAATTAAATGATTTGCAGATGAGTAACTTTCTTAATTTGAAGAATATA -s simRat_chr6.simRat.chr6 509618 71 + 647215 ATATTATAATTGTAACACCTGGCAGACTAAATGATTTGCAAATGAGTAACTTTGTTAATTTGAAAAACATA - -a -s simMouse_chr6.simMouse.chr6 497052 17 + 636262 ACTTACTTGGTGTCAGG -s Anc0.Anc0refChr3 113316 17 + 222631 ACTTACTTGGTGACAGA -s Anc1.Anc1refChr6 147142 17 + 197743 ACTTACTTGGTGACAGA -s Anc2.Anc2refChr1 25436 17 + 142988 ACTTACTTGGTGACAGA -s mr.mrrefChr3 51054 17 + 181027 ACTTACTTGGTGTCAGG -s simCow_chr6.simCow.chr6 481876 17 + 602619 ACCTACTTGGTGACAGA -s simDog_chr6.simDog.chr6 471841 17 + 593897 ACTTATCTGGTGTCAGA -s simHuman_chr6.simHuman.chr6 478995 17 + 601863 ACTTACTTGGTGAGAGA -s simRat_chr6.simRat.chr6 449632 17 + 647215 CCTTACTTGGTGTGAAA -s simRat_chr6.simRat.chr6 509689 17 + 647215 ACTTATTTGGTTTCAGG - -a -s simMouse_chr6.simMouse.chr6 497069 1 + 636262 A -s Anc0.Anc0refChr3 113334 1 + 222631 G -s Anc1.Anc1refChr6 147160 1 + 197743 G -s Anc2.Anc2refChr1 25454 1 + 142988 G -s mr.mrrefChr3 51072 1 + 181027 C -s simCow_chr6.simCow.chr6 481894 1 + 602619 A -s simDog_chr6.simDog.chr6 471859 1 + 593897 G -s simHuman_chr6.simHuman.chr6 479013 1 + 601863 G -s simRat_chr6.simRat.chr6 449650 1 + 647215 C -s simRat_chr6.simRat.chr6 509706 1 + 647215 C - -a -s simMouse_chr6.simMouse.chr6 497070 7 + 636262 TATCGGA -s Anc0.Anc0refChr3 113335 7 + 222631 CATCAGG -s Anc1.Anc1refChr6 147161 7 + 197743 CATCAGG -s Anc2.Anc2refChr1 25455 7 + 142988 CATCAGG -s mr.mrrefChr3 51073 7 + 181027 TATCGGA -s simCow_chr6.simCow.chr6 481895 7 + 602619 GGTGAGC -s simDog_chr6.simDog.chr6 471863 7 + 593897 CACCAGG -s simHuman_chr6.simHuman.chr6 479014 7 + 601863 CATTAGG -s simRat_chr6.simRat.chr6 449651 7 + 647215 TATTGAA -s simRat_chr6.simRat.chr6 509707 7 + 647215 TATCGGA - -a -s simMouse_chr6.simMouse.chr6 497077 9 + 636262 GGTTATGTT -s Anc0.Anc0refChr3 113342 9 + 222631 GATTAGGTT -s Anc1.Anc1refChr6 147168 9 + 197743 GATTAGGTT -s Anc2.Anc2refChr1 25462 9 + 142988 CATTAGGTT -s mr.mrrefChr3 51080 9 + 181027 GGTTAGGTT -s simCow_chr6.simCow.chr6 481902 9 + 602619 CATTAGCTT -s simDog_chr6.simDog.chr6 471870 9 + 593897 CATTAAGTT -s simHuman_chr6.simHuman.chr6 479021 9 + 601863 GATTAGGTT -s simRat_chr6.simRat.chr6 449748 9 + 647215 GATTAGGTC -s simRat_chr6.simRat.chr6 509714 9 + 647215 GGTTAGGTT - -a -s simMouse_chr6.simMouse.chr6 497086 1 + 636262 A -s Anc0.Anc0refChr3 113351 1 + 222631 G -s Anc1.Anc1refChr6 147177 1 + 197743 G -s Anc2.Anc2refChr1 25471 1 + 142988 G -s mr.mrrefChr3 51089 1 + 181027 A -s simCow_chr6.simCow.chr6 481911 1 + 602619 A -s simDog_chr6.simDog.chr6 471879 1 + 593897 G -s simHuman_chr6.simHuman.chr6 479030 1 + 601863 G -s simRat_chr6.simRat.chr6 509723 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 497087 33 + 636262 TGATATCCTCAGAGTGAATGGCTGAGGGATGGT -s Anc0.Anc0refChr3 113352 33 + 222631 TGACATACTCAGTGTAACTGGTTAAGAGTAGGT -s Anc1.Anc1refChr6 147178 33 + 197743 TGACATACTCAGTGTAACTGGTTAAGAGTAGGT -s Anc2.Anc2refChr1 25472 33 + 142988 TGACATACTCAGTGTAACTGGTTAAGAGTAGGT -s mr.mrrefChr3 51090 33 + 181027 TCATATCCTCAGAGTGAATGGTTGAGGGTTGGT -s simCow_chr6.simCow.chr6 481912 33 + 602619 TTACGTCCTCACTGTACCTGTTTAAGTGAAGGT -s simDog_chr6.simDog.chr6 471880 33 + 593897 TGTTATACTCAGTGTTACTTGTTAAGAGTTGGT -s simHuman_chr6.simHuman.chr6 479031 31 + 601863 TGACATATGAAGTGTAACTGGTTAA--ATAGGT -s simRat_chr6.simRat.chr6 449757 33 + 647215 TCCTTGCTGCATGGTGTGCAGTTTAGTGTTAAT -s simRat_chr6.simRat.chr6 509724 33 + 647215 TCATATCCTCAGAGTGAATGGTTGAGGGTGGGT - -a -s simMouse_chr6.simMouse.chr6 497120 9 + 636262 TACCCACTG -s Anc0.Anc0refChr3 113386 9 + 222631 AACCCATTA -s Anc1.Anc1refChr6 147212 9 + 197743 AACCCATTA -s Anc2.Anc2refChr1 25506 9 + 142988 AACCCATTA -s mr.mrrefChr3 51123 9 + 181027 TACCCATTA -s simCow_chr6.simCow.chr6 481946 9 + 602619 TACCCACCA -s simDog_chr6.simDog.chr6 471914 9 + 593897 AACCCATTA -s simHuman_chr6.simHuman.chr6 479063 9 + 601863 CACCTGTGA -s simRat_chr6.simRat.chr6 449790 9 + 647215 AATACAACA -s simRat_chr6.simRat.chr6 509757 9 + 647215 TACCCATTA - -a -s simMouse_chr6.simMouse.chr6 497129 5 + 636262 GCTGG -s Anc0.Anc0refChr3 113395 5 + 222631 GCTGG -s Anc1.Anc1refChr6 147221 5 + 197743 GCTGG -s Anc2.Anc2refChr1 25515 5 + 142988 GCTGG -s mr.mrrefChr3 51132 5 + 181027 GTTGG -s simCow_chr6.simCow.chr6 481955 5 + 602619 GCTGG -s simDog_chr6.simDog.chr6 471923 5 + 593897 GCTAG -s simHuman_chr6.simHuman.chr6 479072 5 + 601863 GCTGG -s simRat_chr6.simRat.chr6 449800 4 + 647215 TTTG- -s simRat_chr6.simRat.chr6 509766 4 + 647215 GTTG- - -a -s simMouse_chr6.simMouse.chr6 497134 13 + 636262 CCATAGTAGCTGT -s Anc0.Anc0refChr3 113401 13 + 222631 CCATAGTAGCTGG -s Anc1.Anc1refChr6 147227 13 + 197743 CCATAGTAGCTGG -s Anc2.Anc2refChr1 25521 13 + 142988 CCATAGTAGCAGG -s mr.mrrefChr3 51137 13 + 181027 CCATAGTAGCTGT -s simCow_chr6.simCow.chr6 481961 13 + 602619 CTGTAGTAGTAGG -s simDog_chr6.simDog.chr6 471929 13 + 593897 CCATAGTAACAGG -s simHuman_chr6.simHuman.chr6 479078 13 + 601863 CCATACTAGCTGG -s simRat_chr6.simRat.chr6 449804 2 + 647215 -----------AT -s simRat_chr6.simRat.chr6 509770 2 + 647215 -----------GT - -a -s simMouse_chr6.simMouse.chr6 497147 6 + 636262 TTGATA -s Anc0.Anc0refChr3 113414 6 + 222631 TCAATA -s Anc1.Anc1refChr6 147240 6 + 197743 TCAATA -s Anc2.Anc2refChr1 25534 6 + 142988 TCAATA -s mr.mrrefChr3 51150 6 + 181027 TTAATA -s simCow_chr6.simCow.chr6 481975 6 + 602619 TCAATA -s simDog_chr6.simDog.chr6 471942 6 + 593897 TCAATA -s simHuman_chr6.simHuman.chr6 479091 6 + 601863 TAGATA -s simRat_chr6.simRat.chr6 449806 6 + 647215 ATAATA -s simRat_chr6.simRat.chr6 509772 6 + 647215 TTAATA - -a -s simMouse_chr6.simMouse.chr6 497153 9 + 636262 GGCTGTAAA -s Anc0.Anc0refChr3 113420 9 + 222631 GTCTGTTAA -s Anc1.Anc1refChr6 147246 9 + 197743 GTCTGTTAA -s Anc2.Anc2refChr1 25540 9 + 142988 GTCTGCTAA -s mr.mrrefChr3 51156 9 + 181027 GTCTGTTAA -s simCow_chr6.simCow.chr6 481981 9 + 602619 GTCTGGTGA -s simDog_chr6.simDog.chr6 471948 9 + 593897 GTCCGCTAA -s simHuman_chr6.simHuman.chr6 479097 9 + 601863 GTCTGTTAA -s simRat_chr6.simRat.chr6 509778 9 + 647215 GTCTGTTAA - -a -s simMouse_chr6.simMouse.chr6 497162 18 + 636262 GATAGGAATATAACGTGG -s Anc0.Anc0refChr3 113429 18 + 222631 GATAGGAAGATAAGACTG -s Anc1.Anc1refChr6 147255 18 + 197743 GATAGGAAGATAAGACTG -s Anc2.Anc2refChr1 25549 18 + 142988 GACAGGAAGATAAGACTG -s mr.mrrefChr3 51165 18 + 181027 GATAGGAATATAACGCTG -s simCow_chr6.simCow.chr6 481990 18 + 602619 GACAGGAAGATAAGACGT -s simDog_chr6.simDog.chr6 471957 18 + 593897 TACGGGAAGGTAAGACTG -s simHuman_chr6.simHuman.chr6 479106 18 + 601863 GGTAGTAAGATAATCCTG -s simRat_chr6.simRat.chr6 509798 18 + 647215 GATAGGAATATAACACTG - -a -s simMouse_chr6.simMouse.chr6 497180 3 + 636262 TCC -s Anc0.Anc0refChr3 113449 3 + 222631 TTC -s Anc1.Anc1refChr6 147275 3 + 197743 TTC -s Anc2.Anc2refChr1 25569 3 + 142988 ATC -s mr.mrrefChr3 51183 3 + 181027 TCC -s simCow_chr6.simCow.chr6 482010 3 + 602619 ATC -s simHuman_chr6.simHuman.chr6 479126 3 + 601863 TTC -s simRat_chr6.simRat.chr6 509816 3 + 647215 TCT - -a -s simMouse_chr6.simMouse.chr6 497183 21 + 636262 CTCAGCCCTATTGCTAACTCT -s Anc0.Anc0refChr3 113452 21 + 222631 ATCAGCCCTATGACTAAGTTT -s Anc1.Anc1refChr6 147278 21 + 197743 ATCAGCCCTATGACTAAGTTT -s Anc2.Anc2refChr1 25572 21 + 142988 ATCCACCCTAGGACTAAGTTA -s mr.mrrefChr3 51186 21 + 181027 CTCAGCCCTATTGCTAACTCT -s simCow_chr6.simCow.chr6 482013 21 + 602619 ATCCACCCTAGGTCTAATCTC -s simDog_chr6.simDog.chr6 471976 16 + 593897 -----CCCTAGGACTGAGTCA -s simHuman_chr6.simHuman.chr6 479129 21 + 601863 TGCAGCCCTATCACCAAGTTT -s simRat_chr6.simRat.chr6 509838 21 + 647215 CTCAGCCCTATTGCTAACTCT - -a -s simMouse_chr6.simMouse.chr6 497204 644 + 636262 GGGCCTTATAAGGCACTTCTAAAGTCAGAAGCCTGAACAAAGGAGACTCCTCATACATCTCATATTGTATCCCACTAGTTTACAGGTCATGTCATACTCAAGAGACAAAACTTTAGAAATGAGAGTTTTCAGAATTAGACCTGTAACTCCATGCCACCTCACGACAACTCAGCAGCACCTCATGGATGACATGAATGCATTCCTGTGTGATGGAAGTTAATGTAGACGGGAAACTAACTTGTACACCTGCAAAATGAATACACATTCTTACACAGTACCTTGTTGTACCATAAACCTCCCTACAGAGATTGGGCTTCATTATGTGAGTCAAGTTAAAGGTTGGACATTATGAAGCCCTTAATTTGAAGCTTCAGGCAATTTGAGGATTAGATAATACAACCAGAAaatgggcaaggtctctgattcactttgcacacgggagaaatggtacttcctgtacaacagcgcgaccgaacatgatgtcaggtcactgggtcagtacagacactgagggtggcgttccgcccacagactctactaccccactgctgggtgcccctgggttcttttttgaaggattCATAGTGGTAGTTTGAAGATATGGTCAATGTGAATAAAAGGCAGTGGTCATGTACACGTGATTA -s Anc0.Anc0refChr3 113473 17 + 222631 GGG--ATATAAGGCACTCC------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- -s Anc1.Anc1refChr6 147299 17 + 197743 GGG--ATATAAGGCACTCC------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- -s Anc2.Anc2refChr1 25593 17 + 142988 GGT--ATATAAGGCACTCC------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- -s mr.mrrefChr3 51207 585 + 181027 GGGCCATATAAGGCACTTCTAAAGTCAGAAGCCTGAACAAAGGAGACTCCTCATACA--TCATATTGTATCCCACTAGTTTACAGGT--TGTCATACTCAAGAGACAAAACTTTAGAAATGAGAGTTTTCAGAATTAGACCTGTAACTTCGTGCTACCTCACGACAACTCAGCAGCACCTCATGGATGACATGAATGCATTCCTGTGTGATGGAAGTTAATGTAGACGGGAAACTAACTTGTACACCTGCAAAATGAATACACATTCTTACACAGTACCTTGTTGTACCATAAACCTCCCTACAGAGATTGGGCTTCATTATGTGAGTCAAGTTAAAGGTTGGACATTATGAAGCCCTTAATTTGAAGCTTCAGGCAATTTGAGGATTAGATAATACAACCAGAAaatgggcaaggtctctgattcactttgcacacgggagaaatggtacttc------------------------------------------------------tgagggtggcgttccgcccacagactctactaccccactgctgggtgcccctgggttcttttttgaaggattCATAGTGGTAGTT-GAAGATATGGTCAATGTGAATAAAAGGCAGTGGTCATGTACACGTGATTA -s simCow_chr6.simCow.chr6 482038 17 + 602619 GGT--AGATAAGGTACTCC------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- -s simDog_chr6.simDog.chr6 471992 17 + 593897 GGT--ATATAAGGCACTTC------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- -s simHuman_chr6.simHuman.chr6 479150 17 + 601863 GGG--ATATAAGGCGCTCC------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- -s simRat_chr6.simRat.chr6 509859 585 + 647215 GGGCCATACAAGGCACTTCTAAAGTCAGCAGCCTGAGCATAGGTGACCCCTCGTACA--TCATATTGTAACCCACTAGTTTACAGGT--TGTCATACTCAAGAAACAGAGCTTTTGAGATGAGATTTTTTGGAATTGGATCTGTAACTTCGTGCTACCTCATGACAACTCAGCAGCTCCTCATGGATGACATGAATGCATTCCTGTGTGATGATAGTTGATATAGACAGGAAACTAACTTGTATACCTGCAAAATGTATACACTTTCTTACACATTACTTTGATGTTCCATAAACCTCCCTACAGAGATTGGGCTTCATTATGTGAGTCAAGTTAAAGGTTACTCATTATAAAGCCCTTAATTTGAAGCTTTAGGCAATGTGAGGATTAGATAACACAATCAAAAagtgggcaagacctctgattcactctgcacatgagaaagatgTTACGCC------------------------------------------------------TgagggtggcattccgcccacagagccacctaccccattgcttggtgtccctgggttctctttgAAGGGATCTATAGTGGTAGTT-GAAAATATGGTCAATGAGAATAAAAGACAGCGATCATGTACATGTGGTTA - -a -s simMouse_chr6.simMouse.chr6 497848 98 + 636262 GTGCTTGGCTATGAGCCTGCCCCGCTTGACAAGATGTCAACCGATCACAGAAGATGTCTGCCCACCTCATGGAAGAGGTTTGTCATGCATAGTTCCCC -s Anc0.Anc0refChr3 113490 5 + 222631 -------------------------------------------------------------------------------TT------CAT-------- -s Anc1.Anc1refChr6 147316 19 + 197743 -------------------------------------------------------------------------------TTGTCATGCATATGTCTCC -s Anc2.Anc2refChr1 25610 5 + 142988 -------------------------------------------------------------------------------TT------CAT-------- -s mr.mrrefChr3 51792 98 + 181027 GTGCTTGGCTATGAGCCTGCCCCGCTTGACAAGATGTCAACCGATCACAGAAGATGTCTGCCCACCTCATGGAAGAGGTTTGTCATGCATAGTTCCCC -s simCow_chr6.simCow.chr6 482055 5 + 602619 -------------------------------------------------------------------------------TT------CGT-------- -s simDog_chr6.simDog.chr6 472009 5 + 593897 -------------------------------------------------------------------------------TT------CAT-------- -s simHuman_chr6.simHuman.chr6 479167 19 + 601863 -------------------------------------------------------------------------------TTGTCATGTAAATGTCTCC -s simRat_chr6.simRat.chr6 510445 98 + 647215 ATGCTTGACTATGAGCCTGCCCTGCTTGATGAGACGTCAAGCAATCACAGAAGTTGTCTGCCCGCCTCATGCAAGAGGTTTATCCTGCATAACTCCCC - -a -s simMouse_chr6.simMouse.chr6 497946 36 + 636262 CTGCATGTTACTATTACTAGACCTTGCTGATGCCAC -s Anc0.Anc0refChr3 113670 36 + 222631 CCACAGTTTACCATTGCTACACCTTACTGACACCAC -s Anc1.Anc1refChr6 147510 36 + 197743 CCACAGTTTACCATTGCTACACCTTACTGACACCAC -s Anc2.Anc2refChr1 25795 36 + 142988 CCACAGTTTATCATTGCTACACCTTACTGACACCAC -s mr.mrrefChr3 51890 36 + 181027 CTGCATGTTACTATTACTAGACCTTACTGACGCCAC -s simCow_chr6.simCow.chr6 482272 36 + 602619 CCACAGTTTATTACTGCTAAACCCTTCTGAGACCAC -s simDog_chr6.simDog.chr6 472216 36 + 593897 CCACATTTTTTCATTGCAACATCTTACTGACACCAC -s simHuman_chr6.simHuman.chr6 479370 36 + 601863 CAACAGTTTACCACTGCTAAACGTTCCTGACACCAC -s simRat_chr6.simRat.chr6 510543 36 + 647215 CTGCATATTACTATTATTAGGCCTTACTAACGCCAC - -a -s simMouse_chr6.simMouse.chr6 497982 1 + 636262 T -s Anc0.Anc0refChr3 113706 1 + 222631 T -s Anc1.Anc1refChr6 147546 1 + 197743 T -s Anc2.Anc2refChr1 25831 1 + 142988 T -s mr.mrrefChr3 51926 1 + 181027 T -s simCow_chr6.simCow.chr6 482308 1 + 602619 T -s simDog_chr6.simDog.chr6 472252 1 + 593897 T -s simHuman_chr6.simHuman.chr6 479406 1 + 601863 C -s simRat_chr6.simRat.chr6 510580 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 497983 6 + 636262 AAAGGT -s Anc0.Anc0refChr3 113707 6 + 222631 AAGGTT -s Anc1.Anc1refChr6 147547 6 + 197743 AAGGTT -s Anc2.Anc2refChr1 25832 6 + 142988 AAGGGT -s mr.mrrefChr3 51927 6 + 181027 AAAGTT -s simCow_chr6.simCow.chr6 482309 6 + 602619 AAGGGC -s simDog_chr6.simDog.chr6 472253 6 + 593897 GAGGGT -s simHuman_chr6.simHuman.chr6 479411 6 + 601863 AAGGTT -s simRat_chr6.simRat.chr6 510581 6 + 647215 AGAGTT - -a -s simMouse_chr6.simMouse.chr6 497989 10 + 636262 TAATGTTCCA -s Anc0.Anc0refChr3 113713 8 + 222631 GAA--TTCTA -s Anc1.Anc1refChr6 147553 10 + 197743 GAATGTTCTA -s Anc2.Anc2refChr1 25838 8 + 142988 AGA--TTCAT -s mr.mrrefChr3 51933 10 + 181027 GAATGTTCTA -s simCow_chr6.simCow.chr6 482315 4 + 602619 AGC--T---- -s simDog_chr6.simDog.chr6 472261 8 + 593897 ATA--CTCAT -s simHuman_chr6.simHuman.chr6 479417 10 + 601863 GATTGTCCTA -s simRat_chr6.simRat.chr6 510587 10 + 647215 GAATGTTCTA - -a -s simMouse_chr6.simMouse.chr6 497999 24 + 636262 ACATACCTATACCCTCTTCTCTCC -s Anc0.Anc0refChr3 113721 24 + 222631 ACATACCTCTACTCTCTTCCCTTC -s Anc1.Anc1refChr6 147563 24 + 197743 ACATACCTCTACTCTCTTCCCTTC -s Anc2.Anc2refChr1 25846 24 + 142988 AAATACCTCTGCTCCCTTCCCTTC -s mr.mrrefChr3 51943 24 + 181027 ACATACCTATACTCTCTTCCCTCC -s simCow_chr6.simCow.chr6 482319 22 + 602619 --ATGCCTCTCCTCCCTTCCCTCC -s simDog_chr6.simDog.chr6 472269 24 + 593897 AAATACCTCTGCTCCCCTTCCCTC -s simHuman_chr6.simHuman.chr6 479486 24 + 601863 ACATACCTCTACTCTCTTCCCTTC -s simRat_chr6.simRat.chr6 510597 24 + 647215 ACATACCTATACTCTCTTCCCTCC - -a -s simMouse_chr6.simMouse.chr6 498023 25 + 636262 TACTAGAGTTATCAGTTCTGCAGAG -s Anc0.Anc0refChr3 113745 24 + 222631 TGCTAGATCTATCC-TTATGCAAAG -s Anc1.Anc1refChr6 147587 24 + 197743 TGCTAGATCTATCC-TTATGCAAAG -s Anc2.Anc2refChr1 25870 24 + 142988 TGCTAGATCTATCC-TTATGCAAAG -s mr.mrrefChr3 51967 25 + 181027 TACTAGAGTTATCAGTTATGCAGAG -s simCow_chr6.simCow.chr6 482341 24 + 602619 TGCTTCGTCTATCC-TTATGCAAGG -s simDog_chr6.simDog.chr6 472293 24 + 593897 TGCCAGATCTATCC-TTCTGCAAAA -s simHuman_chr6.simHuman.chr6 479512 24 + 601863 TGCTAGATCTATCC-TTATGCAAAG -s simRat_chr6.simRat.chr6 510621 23 + 647215 TACTGGAATTATTGGTCAT--AGAG - -a -s simMouse_chr6.simMouse.chr6 498048 75 + 636262 TTGCTTGGGACTCGACATTACCTTTATGCATCTGGATTGTTTAGTTCAGGTTCAGCCACAATGTTCGTTGTGAGT -s Anc0.Anc0refChr3 113769 69 + 222631 TGGCCTGTGACTACACATTACCCTTATGAATCTGGCTTGCTTATTTCT------GCCACAATGTCAGTTGTAAGT -s Anc1.Anc1refChr6 147611 69 + 197743 TGGCCTGTGACTACACATTACCCTTATGAATCTGGCTTGCTTATTTCT------GCCACAATGTCAGTTGTAAGT -s Anc2.Anc2refChr1 25894 69 + 142988 TGGCCTATGACTACACATTACCTTTATCAATCGGGCTTGCTTATCTCT------GCCACAATGTCAGTTGTAAGT -s mr.mrrefChr3 51992 69 + 181027 TTGCTTGGGACTCGACATTACCCTTATGCATCTGGCTTGTTTAGTTCA------GCCACAATGTTAGTTGTGAGT -s simCow_chr6.simCow.chr6 482366 66 + 602619 TGGCATATGTCTACTCATG---TTTTTCATTCAGGCTAGTTTGTCTCT------ACCACAATGTCTGTTGTAGGT -s simDog_chr6.simDog.chr6 472317 69 + 593897 TGGGCTATGACTACACATTACCTTTATCAATCGAGCTTGCTTATCTCT------GCCACAATGTCAGCTGTCAGT -s simHuman_chr6.simHuman.chr6 479536 65 + 601863 TAGCCTGTGAC----CAATACTCTTGTGAATCTGGCTTGCCTATTTCT------GCTGCAATGTCAGTTGTAAGA -s simRat_chr6.simRat.chr6 510644 69 + 647215 TTGCTTGGGATTGGACATTACCCTTATGCATCTGGCTTGTTTAGATCA------GCCACAGTGTTAGTTGTGAGT - -a -s simMouse_chr6.simMouse.chr6 498123 51 + 636262 ATTTAGGTGCATTATTCCTGGCTTGGGATCTGCAATTCTGTTAAGGCCTTA -s Anc0.Anc0refChr3 113838 51 + 222631 CATTAATTGCATTATTCCTGGTTAATGACCTACAATATTGTTAAGCTATAA -s Anc1.Anc1refChr6 147680 51 + 197743 CATTAATTGCATTATTCCTGGTTAATGACCTACAATATTGTTAAGCTATAA -s Anc2.Anc2refChr1 25963 51 + 142988 CATTAATTGCATTATTCCTGGTTAATGACCTACAACATTGATAAGCTATAG -s mr.mrrefChr3 52061 51 + 181027 ATTTAGGTGCATTATTCCTGGTTAAGGATCTGCAATTTTGTTAAGGTCTTA -s simCow_chr6.simCow.chr6 482432 51 + 602619 CATTAGTTGCATTATGCCTCGTTAATGATCCACAAAATTGATAAGCAATTC -s simDog_chr6.simDog.chr6 472387 51 + 593897 CACTAATTGCATTATTCCTGATTAATAACCTATAACATTGATAAACTATAG -s simHuman_chr6.simHuman.chr6 479601 50 + 601863 -ATTTATAGCTTTATTCCTTGTTAATGACCTACAATATTGTTAAGCTATGA -s simRat_chr6.simRat.chr6 510713 51 + 647215 ATTTAGGTGCACTAATCCTGGTTAAGGATCTGCAATTTTGTTAAGATCTTA - -a -s simMouse_chr6.simMouse.chr6 498174 56 + 636262 CTGTATGAGAGATATTTGAGGGTGCCAAGCACTGGGCCCCCAACGGACCTTTTGGC -s Anc0.Anc0refChr3 113894 56 + 222631 GTGTATGAGAGCTATTTGAGGGTACCAAGGCATGATCATCCATCTGACCATTTGAT -s Anc1.Anc1refChr6 147736 56 + 197743 GTGTATGAGAGCTATTTGAGGGTACCAAGGCATGATCATCCATCTGACCATTTGAT -s Anc2.Anc2refChr1 26019 56 + 142988 GTGTATGAGAGCTATTCGAGGGTACCAAGGCATGATCATCCATCTGACCACTTGAT -s mr.mrrefChr3 52112 56 + 181027 CTGTATGAGAGATATTTGAGGGTACCAAGCACTGAGCACCCATCGGACCTTTTGGC -s simCow_chr6.simCow.chr6 482488 55 + 602619 GTGTATGACAGCTAACCGAGGGTGCCACGACATGATTGTCCACCTGACCACT-GAT -s simDog_chr6.simDog.chr6 472443 55 + 593897 GTGT-TGAGAGTGCTTCAAGGGTACCAAGGCATGGTCATCCATCTCACCACTTGAT -s simHuman_chr6.simHuman.chr6 479656 56 + 601863 GTGTATGAGTGCTATTTGAGGGTACCAAGGGGTGATCATACATCAGATGGTCTGAT -s simRat_chr6.simRat.chr6 510764 43 + 647215 CTGTATG-------------GGTACCAACAACTGAGCACCCATTGAGCATTTTGGC - -a -s simMouse_chr6.simMouse.chr6 498230 44 + 636262 GGTGTAGAGACCATGGTGACTCTCTTGGGTGTGATGTGTGTTGT -s Anc0.Anc0refChr3 113951 43 + 222631 GGCATGTAGACCCTGGTGACTCTTCTGGTGATTGCATTTG-TGT -s Anc1.Anc1refChr6 147793 43 + 197743 GGCATGTAGACCCTGGTGACTCTTCTGGTGATTGCATTTG-TGT -s Anc2.Anc2refChr1 26076 43 + 142988 GGCATGTAGACCCTGGTGACTCTTCTGATGATTGCATTTG-TGT -s mr.mrrefChr3 52168 44 + 181027 GGTGTATAGACCATGGTGACTCTCTTGGGTGTGATGTGTGTTGT -s simCow_chr6.simCow.chr6 482544 43 + 602619 GGCATGTCAACCCTGCCAGCTCCTCTGATGATTGTGTTTG-TAT -s simDog_chr6.simDog.chr6 472499 43 + 593897 GGCATGTAGACCCTGGTGATTCTTCTGATGGCCACATCTG-TGT -s simHuman_chr6.simHuman.chr6 479713 43 + 601863 GGCATCTAGACCCTGGTGACACTTCTGGTAATTGCACTTG-TGT -s simRat_chr6.simRat.chr6 510807 44 + 647215 AGTGTGTAGACCATGATGATTCTCTTGGGTGCACTGTGTGTTGT - -a -s simMouse_chr6.simMouse.chr6 498274 27 + 636262 AATTTAAACAAATTTGAAGCTGGCTGA -s Anc0.Anc0refChr3 113994 27 + 222631 AATTTAAACAGATTTGAGTATAGCTAC -s Anc1.Anc1refChr6 147836 27 + 197743 AATTTAAACAGATTTGAGTATAGCTAC -s Anc2.Anc2refChr1 26124 27 + 142988 AATTTAAACAGATTTGAGTATACCTAT -s mr.mrrefChr3 52212 27 + 181027 AATTTAAACAAATTTGAAGCTAGCTGC -s simCow_chr6.simCow.chr6 482607 27 + 602619 GATTTAAATAGATTTGAGCATACCTAT -s simDog_chr6.simDog.chr6 472547 26 + 593897 AATTTAAACAGATTTGA-TATACCTGT -s simHuman_chr6.simHuman.chr6 479756 27 + 601863 AATTTAATCAGGTTTGAGTATAGCTAC -s simRat_chr6.simRat.chr6 510851 27 + 647215 AATTTATACAAATTTGAAACCAGCTGC - -a -s simMouse_chr6.simMouse.chr6 498301 64 + 636262 CTGTTCTCTTATTCAGGGCTGTTAATCTAAGTCTGACAATTAAAATTAGGACTAAATAGATGTC -s Anc0.Anc0refChr3 114024 64 + 222631 CTGTTCTCTTATTCAGGGCTCTCAGTTTAACTCTGACAATTAAAATAAGAACTGACTAGATGTC -s Anc1.Anc1refChr6 147866 64 + 197743 CTGTTCTCTTATTCAGGGCTCTCAGTTTAACTCTGACAATTAAAATAAGAACTGACTAGATGTC -s Anc2.Anc2refChr1 26154 64 + 142988 CTGTTCTCTTATTCAGGGCTCTCAGTTTAGCTTTGACAATTCAAATAAGAACTGGCTAGATGTC -s mr.mrrefChr3 52239 64 + 181027 CTGTTCTCTTATTCAGGGCTGTTAGTCTAAGTCTGACAATTAAAATTAGGACTAAATAGATGTC -s simCow_chr6.simCow.chr6 482637 64 + 602619 ATGTTCTCTTATTTGGCACTCTCAGCTTAGCTTTGGCAACTGAAGCAACAACTGGCTAGATCTC -s simDog_chr6.simDog.chr6 472576 63 + 593897 CTGTTCTCTTATTCAAGGCTCTCAGTTTG-CTTTGACAATTCGAATAAGAACTGGCTAGATGTC -s simHuman_chr6.simHuman.chr6 479786 64 + 601863 CGGTTGTCTTAGCCAGAGCTCTAAGTTTAACTCTGACAATTAAAATAAGACCTGACTAGATGTC -s simRat_chr6.simRat.chr6 510878 64 + 647215 CTGTTCTCTTATTCAGGGCTGTTAGTCTAAGTCTGACAATTAAAATTAGGACTAAATAGATGTT - -a -s simMouse_chr6.simMouse.chr6 498365 33 + 636262 TCTTCTAACTTTGATTTGTGAGATGACAAATTT -s Anc0.Anc0refChr3 114088 26 + 222631 TTGTCTAACTTTG----GGGAATTG---AATTT -s Anc1.Anc1refChr6 147930 29 + 197743 TTGTCTAACTTTG----GGGAATTGGCTAATTT -s Anc2.Anc2refChr1 26218 26 + 142988 TTGTCTAACTTTG----GGGAATTG---AATCT -s mr.mrrefChr3 52303 33 + 181027 TCTTCTAACTTTGATTTGGGAATTGACTAATTT -s simCow_chr6.simCow.chr6 482720 26 + 602619 TTGTCTAGCTTTG----GATAGTTG---AATCT -s simDog_chr6.simDog.chr6 472639 25 + 593897 TTGCC-AACATTG----GGGAATTG---AATCT -s simHuman_chr6.simHuman.chr6 479850 29 + 601863 TTGTCTAACTTTG----GGAAATTGGCTAACTT -s simRat_chr6.simRat.chr6 510942 33 + 647215 TCTTCTAACTTAGTTTTGGGGATTCACTAATTT - -a -s simMouse_chr6.simMouse.chr6 498398 2 + 636262 TT -s Anc0.Anc0refChr3 114114 2 + 222631 TA -s Anc1.Anc1refChr6 147959 2 + 197743 TA -s Anc2.Anc2refChr1 26244 2 + 142988 AA -s mr.mrrefChr3 52336 2 + 181027 TT -s simCow_chr6.simCow.chr6 482748 2 + 602619 AA -s simDog_chr6.simDog.chr6 472664 2 + 593897 AA -s simHuman_chr6.simHuman.chr6 479879 2 + 601863 TA -s simRat_chr6.simRat.chr6 510975 2 + 647215 TT - -a -s simMouse_chr6.simMouse.chr6 498400 17 + 636262 TGGAATTACCCTTGATC -s Anc0.Anc0refChr3 114116 14 + 222631 TAGGGTAGC---CAAGC -s Anc1.Anc1refChr6 147961 14 + 197743 TAGGGTAGC---CAAGC -s Anc2.Anc2refChr1 26246 14 + 142988 TAGGGTAGC---CAAGC -s mr.mrrefChr3 52338 17 + 181027 TGGGATTACACTTGATC -s simCow_chr6.simCow.chr6 482750 14 + 602619 TTTGCAAGC---CAAGC -s simDog_chr6.simDog.chr6 472666 14 + 593897 TAGGGTAGC---AAAAC -s simHuman_chr6.simHuman.chr6 479883 14 + 601863 GAGAGTAGC---CAAGC -s simRat_chr6.simRat.chr6 510977 17 + 647215 TGGGACTACACTTGATC - -a -s simMouse_chr6.simMouse.chr6 498417 10 + 636262 AGACTAGGTC -s Anc0.Anc0refChr3 114130 10 + 222631 TGGCAAGGTA -s Anc1.Anc1refChr6 147975 10 + 197743 TGGCAAGGTA -s Anc2.Anc2refChr1 26260 10 + 142988 TGGCACGGTA -s mr.mrrefChr3 52355 10 + 181027 AGGCTAGGTC -s simCow_chr6.simCow.chr6 482764 10 + 602619 TGGCACGGTA -s simDog_chr6.simDog.chr6 472680 10 + 593897 TAGCACGGTA -s simHuman_chr6.simHuman.chr6 479910 10 + 601863 TGGCAAGGTA -s simRat_chr6.simRat.chr6 510994 10 + 647215 AGGGCAGGCC - -a -s simMouse_chr6.simMouse.chr6 498427 3 + 636262 ATT -s Anc0.Anc0refChr3 114140 3 + 222631 ATT -s Anc1.Anc1refChr6 147985 3 + 197743 ATT -s Anc2.Anc2refChr1 26270 3 + 142988 ATT -s mr.mrrefChr3 52365 3 + 181027 ATT -s simCow_chr6.simCow.chr6 482774 3 + 602619 GCT -s simDog_chr6.simDog.chr6 472690 3 + 593897 ATT -s simHuman_chr6.simHuman.chr6 479920 3 + 601863 ATT -s simRat_chr6.simRat.chr6 511011 3 + 647215 ACT - -a -s simMouse_chr6.simMouse.chr6 498430 5 + 636262 ATGTT -s Anc0.Anc0refChr3 114143 5 + 222631 TTGTT -s Anc1.Anc1refChr6 147988 5 + 197743 TTGTT -s Anc2.Anc2refChr1 26273 5 + 142988 TTGTA -s mr.mrrefChr3 52368 5 + 181027 ATGTT -s simCow_chr6.simCow.chr6 482777 5 + 602619 ATGTC -s simDog_chr6.simDog.chr6 472696 5 + 593897 TCCTA -s simHuman_chr6.simHuman.chr6 479923 5 + 601863 CTGTT -s simRat_chr6.simRat.chr6 511014 5 + 647215 ACGTT - -a -s simMouse_chr6.simMouse.chr6 498435 10 + 636262 GACAGTCCAC -s Anc0.Anc0refChr3 114148 10 + 222631 GACAGTCAGT -s Anc1.Anc1refChr6 147993 10 + 197743 GACAGTCAGT -s Anc2.Anc2refChr1 26278 10 + 142988 GACAGTCAGT -s mr.mrrefChr3 52373 10 + 181027 GACAGTCAGT -s simCow_chr6.simCow.chr6 482782 10 + 602619 AACAATGAGT -s simDog_chr6.simDog.chr6 472701 10 + 593897 GACAGTCAGT -s simHuman_chr6.simHuman.chr6 479928 10 + 601863 GACAGTCAGT -s simRat_chr6.simRat.chr6 511023 10 + 647215 GACAGTCAGT - -a -s simMouse_chr6.simMouse.chr6 498445 12 + 636262 AGAAAGGTTGTA -s Anc0.Anc0refChr3 114158 12 + 222631 GGATAGGTTGAA -s Anc1.Anc1refChr6 148003 12 + 197743 GGATAGGTTGAA -s Anc2.Anc2refChr1 26288 12 + 142988 GGATAGGTTGAA -s mr.mrrefChr3 52383 12 + 181027 AGATAGGTTGTA -s simCow_chr6.simCow.chr6 482792 12 + 602619 GTATAGGTGAAA -s simDog_chr6.simDog.chr6 472712 12 + 593897 GGATGAGTTGAG -s simHuman_chr6.simHuman.chr6 479938 12 + 601863 TGATAGGGTGAA -s simRat_chr6.simRat.chr6 511033 12 + 647215 AGATAGATTGTA - -a -s simMouse_chr6.simMouse.chr6 498457 1 + 636262 T -s Anc0.Anc0refChr3 114170 1 + 222631 T -s Anc1.Anc1refChr6 148015 1 + 197743 T -s Anc2.Anc2refChr1 26300 1 + 142988 T -s mr.mrrefChr3 52395 1 + 181027 T -s simCow_chr6.simCow.chr6 482805 1 + 602619 T -s simDog_chr6.simDog.chr6 472724 1 + 593897 T -s simHuman_chr6.simHuman.chr6 479950 1 + 601863 T -s simRat_chr6.simRat.chr6 511045 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 498458 1 + 636262 T -s Anc0.Anc0refChr3 114171 1 + 222631 T -s Anc1.Anc1refChr6 148016 1 + 197743 T -s Anc2.Anc2refChr1 26315 1 + 142988 T -s mr.mrrefChr3 52396 1 + 181027 T -s simCow_chr6.simCow.chr6 482820 1 + 602619 T -s simDog_chr6.simDog.chr6 472739 1 + 593897 T -s simHuman_chr6.simHuman.chr6 479951 1 + 601863 T -s simRat_chr6.simRat.chr6 511046 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 498459 4 + 636262 GTTG -s Anc0.Anc0refChr3 114194 4 + 222631 GATG -s Anc1.Anc1refChr6 148039 4 + 197743 GATG -s Anc2.Anc2refChr1 26338 4 + 142988 GAAT -s mr.mrrefChr3 52397 4 + 181027 GTTG -s simCow_chr6.simCow.chr6 482843 4 + 602619 GGAT -s simDog_chr6.simDog.chr6 472762 4 + 593897 CAAT -s simHuman_chr6.simHuman.chr6 479976 4 + 601863 GATG -s simRat_chr6.simRat.chr6 511047 4 + 647215 GTTG - -a -s simMouse_chr6.simMouse.chr6 498463 7 + 636262 ATATGGG -s Anc0.Anc0refChr3 114198 7 + 222631 ATATGGT -s Anc1.Anc1refChr6 148043 7 + 197743 ATATGGT -s Anc2.Anc2refChr1 26342 7 + 142988 ATATGGT -s mr.mrrefChr3 52401 7 + 181027 ATATGGG -s simCow_chr6.simCow.chr6 482847 7 + 602619 ATATGGT -s simDog_chr6.simDog.chr6 472768 7 + 593897 ATATGGT -s simHuman_chr6.simHuman.chr6 479980 7 + 601863 ATATGCT -s simRat_chr6.simRat.chr6 511051 7 + 647215 ATATGGG - -a -s simMouse_chr6.simMouse.chr6 498470 19 + 636262 TTCTGGTGGAGGAGTCTAA -s Anc0.Anc0refChr3 114205 19 + 222631 TTGTGCTGGAGGAGTTTAA -s Anc1.Anc1refChr6 148050 19 + 197743 TTGTGCTGGAGGAGTTTAA -s Anc2.Anc2refChr1 26349 19 + 142988 TTGTGCTGGAGGAGTTTAA -s mr.mrrefChr3 52408 19 + 181027 TTCTGGTGGAGGAGTCTAA -s simCow_chr6.simCow.chr6 482854 19 + 602619 TTGTGCTGGAGGAGCTTAA -s simDog_chr6.simDog.chr6 472775 19 + 593897 TTGTGCTGGAGGAGTTTAA -s simHuman_chr6.simHuman.chr6 479996 19 + 601863 TTGTGTTGGAGGAGTTTAA -s simRat_chr6.simRat.chr6 511058 19 + 647215 TTCTGGTGGAGGAGACTAA - -a -s simMouse_chr6.simMouse.chr6 498489 5 + 636262 ACAAT -s Anc0.Anc0refChr3 114235 5 + 222631 ACAAC -s Anc1.Anc1refChr6 148080 5 + 197743 ACAAC -s Anc2.Anc2refChr1 26383 5 + 142988 ACAAC -s mr.mrrefChr3 52427 5 + 181027 ACAAC -s simCow_chr6.simCow.chr6 482888 5 + 602619 ACAAC -s simDog_chr6.simDog.chr6 472809 5 + 593897 ACAAC -s simHuman_chr6.simHuman.chr6 480026 5 + 601863 ATAAC -s simRat_chr6.simRat.chr6 511077 5 + 647215 GCAAC - -a -s simMouse_chr6.simMouse.chr6 498494 146 + 636262 TGAAAGGAGGTTTTGGATGACGCGAAAAGGATGTTAGAGATGGGTTATAAACCCCAAGTAATGAGGATTCTACTAGATGTATGTCCAGACAAACAAGCATTGATGACCAGGTTGGAAATCACAGACCAGCATTGACATGACCAGGT -s Anc0.Anc0refChr3 114255 144 + 222631 TCAAAGTAGGTTTTGGATGATGCTGAAAGGATGTTAGAGATGGGTTATAAACCCCAAATAATGAGGATTCTATTAGATGTATGCCCAGACAAACAGGCATTGATGACCAGGTTGGAAATTGCAAACAGGCATTG--ATGACCAGGT -s Anc1.Anc1refChr6 148100 144 + 197743 TCAAAGTAGGTTTTGGATGATGCTGAAAGGATGTTAGAGATGGGTTATAAACCCCAAATAATGAGGATTCTATTAGATGTATGCCCAGACAAACAGGCATTGATGACCAGGTTGGAAATTGCAAACAGGCATTG--ATGACCAGGT -s Anc2.Anc2refChr1 26403 144 + 142988 TCAAAGTAGGTTTTGGATGATGCTGAAAGGATGTTAGAAATGGGTTATAAGCCACAAATAATGAGGATTCTATTAGATGTATGCCCAGACAAACAGGCATTGATGACCAGGTTGGAAATTGCATACAGGTATTA--ATGACCAGGT -s mr.mrrefChr3 52432 146 + 181027 TCAAAGGAGGTTTTGGATGACGCGAAAAGGATGTTAGAGATGGGTTATAAACCCCAAGTAATGAGGATTCTATTAGATGTATGTCCAGACAAACAAGCATTGATGACCAGGTTGGAAATCACAAACAGGCATTGACATGACCAGGT -s simCow_chr6.simCow.chr6 482908 144 + 602619 TCAATGTAGGTCTTAGATGATGCTGAAAGGATGTTAGAAATGGGTTATAAGCCACAAATAATGAGGATTCTATTAGATGTATGCCCAGACAAACAGGCATTAATGACCAGGTTGGAATTTGCATACAGGTATTA--ATAACCAGGT -s simDog_chr6.simDog.chr6 472829 135 + 593897 TCAAAGTAGGTTTTGGATGATGCAGAAAGGATGTTAGAAATGGGGTATAAGCCACAGATAATGAGGATTCTATTAGATGTATGCCCAGACAAACAGGCATTGATGACCAGGTTGGAAATTG---------ATGA--CTGACCACAT -s simHuman_chr6.simHuman.chr6 480046 144 + 601863 TCAAAGTAGGTTTTGGATGATGCTGAAAGGATGTTAGAGATGGGTTATAAACCCCAAATAATGAGGATTCTATTGGATGTATGCCCAGACAAACAGGCGTTGATGACCAGGTTGGAAATTGCAAACAGGCATTG--ATGACCAGGT -s simRat_chr6.simRat.chr6 511082 146 + 647215 TCAAAGGAGGTCTTGGAGGACGCAAAAAGAATGTTAGAGATGGGTTACAAACCCCAAGTAATGAGGATTCTATTAGACGTATGTCCAGACAAGCAAGCATTGATGACCAGGTTGGAAATCACAAGCAGACATCAGGATGATCAGAC - -a -s simMouse_chr6.simMouse.chr6 498640 1 + 636262 T -s Anc0.Anc0refChr3 114417 1 + 222631 T -s Anc1.Anc1refChr6 148262 1 + 197743 T -s Anc2.Anc2refChr1 26565 1 + 142988 T -s mr.mrrefChr3 52578 1 + 181027 T -s simDog_chr6.simDog.chr6 472982 1 + 593897 T -s simHuman_chr6.simHuman.chr6 480282 1 + 601863 T -s simRat_chr6.simRat.chr6 511228 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 498641 76 + 636262 GGGAATTGCACTTCCCTAAGTGCTATGACACTATGAAGATCCTTTTGCTAGTCAGAAGGGTATGAAAGTGGGCTCT -s Anc0.Anc0refChr3 114418 74 + 222631 GGAAATTGCACTTTCCTAATCTATATGTC--TCTGAAAAGCCCTTACCAAGTCGGAGGGTTATGAAGGGGGGTTCT -s Anc1.Anc1refChr6 148263 74 + 197743 GGAAATTGCACTTTCCTAATCTATATGTC--TCTGAAAAGCCCTTACCAAGTCGGAGGGTTATGAAGGGGGGTTCT -s Anc2.Anc2refChr1 26566 74 + 142988 AGAAATTGCACTTTCTTAATCTATATGTC--TCTGAGAAGCCCTTACCAAGTCGGAGGGTTATGGTGTGGGGTTCT -s mr.mrrefChr3 52579 74 + 181027 GGGAATTGCACTTCCCTAAGTGCTATGAC--TATGAAGATCCTTTTGCTAGTCAGAAGGGTATGAAAGTGGGCTCT -s simCow_chr6.simCow.chr6 483056 64 + 602619 ----------CTCTTTTAAGCCATAAGTC--TCTTAGACGCCCTTATGAAATTGGAGGGTTATGCTGTGGGGTTCG -s simDog_chr6.simDog.chr6 472984 73 + 593897 AGAAATTGCACTTTCTTAATCTATCTGTG--TCTGAGAAGCCTTTTCCAAGTCAGAGGGT-ATGGTGTGGGGTTCT -s simHuman_chr6.simHuman.chr6 480283 74 + 601863 GGAAATTGCATTTTCCTAAACAATATATC--ACTGAAAGGCCCTTACCAAGTCGGAGGGTTATGAAGGGGGGTTCA -s simRat_chr6.simRat.chr6 511229 74 + 647215 GGGAATCGCACTTCCCTAACTGGTATGAC--TGTGAACATCCTTTTGCTAGTCAGAAGGGTATGAAAGTGGGCTCT - -a -s simMouse_chr6.simMouse.chr6 498717 4 + 636262 CTCT -s Anc0.Anc0refChr3 114492 4 + 222631 ATTT -s Anc1.Anc1refChr6 148337 4 + 197743 ATTT -s Anc2.Anc2refChr1 26640 4 + 142988 ATTT -s mr.mrrefChr3 52653 4 + 181027 CTCT -s simCow_chr6.simCow.chr6 483120 4 + 602619 ATTT -s simDog_chr6.simDog.chr6 473057 4 + 593897 ATCT -s simHuman_chr6.simHuman.chr6 480358 4 + 601863 ATTT -s simRat_chr6.simRat.chr6 511303 4 + 647215 CTCT - -a -s simMouse_chr6.simMouse.chr6 498721 10 + 636262 CTCGCCTTTT -s Anc0.Anc0refChr3 114496 10 + 222631 TTTGCATTTT -s Anc1.Anc1refChr6 148341 10 + 197743 TTTGCATTTT -s Anc2.Anc2refChr1 26644 10 + 142988 TTTGCATTTT -s mr.mrrefChr3 52657 10 + 181027 CTCGCCTTTT -s simCow_chr6.simCow.chr6 483128 10 + 602619 TTCCCCATCT -s simDog_chr6.simDog.chr6 473061 10 + 593897 CTTGCATTTT -s simHuman_chr6.simHuman.chr6 480362 10 + 601863 TCTGTGTTTT -s simRat_chr6.simRat.chr6 511307 10 + 647215 CTTGCCTTTT - -a -s simMouse_chr6.simMouse.chr6 498731 22 + 636262 GCTTTGTTGAGCGCAGTGTAAG -s Anc0.Anc0refChr3 114507 20 + 222631 TCTATGTTGAAA--AGTGTAAG -s Anc1.Anc1refChr6 148352 20 + 197743 TCTATGTTGAAA--AGTGTAAG -s Anc2.Anc2refChr1 26655 20 + 142988 TCTATGTTGAAA--AGTGTAAG -s mr.mrrefChr3 52667 20 + 181027 GCTTTGTTGAAA--AGTGTAAG -s simCow_chr6.simCow.chr6 483139 20 + 602619 TCTCTGTTGAAA--AGGATAAG -s simDog_chr6.simDog.chr6 473072 20 + 593897 TCTATGTTGACA--CGTGTAAT -s simHuman_chr6.simHuman.chr6 480373 17 + 601863 TCC---TTGAAA--AGCGTAAG -s simRat_chr6.simRat.chr6 511317 20 + 647215 GCTTTATTGAAA--AGTGTAAG - -a -s simMouse_chr6.simMouse.chr6 498753 6 + 636262 CAGGTC -s Anc0.Anc0refChr3 114527 6 + 222631 CAGGTT -s Anc1.Anc1refChr6 148372 6 + 197743 CAGGTT -s Anc2.Anc2refChr1 26675 6 + 142988 CATGTT -s mr.mrrefChr3 52687 6 + 181027 CAGGTC -s simCow_chr6.simCow.chr6 483159 6 + 602619 CATGTG -s simDog_chr6.simDog.chr6 473092 6 + 593897 CATGTT -s simHuman_chr6.simHuman.chr6 480390 6 + 601863 CAGGTT -s simMouse_chr6.simMouse.chr6 622335 6 + 636262 CAAGTC -s simRat_chr6.simRat.chr6 511337 6 + 647215 CAGGTT - -a -s simMouse_chr6.simMouse.chr6 498759 25 + 636262 GTTATAATCTCGAGTGCATAGTGAG -s Anc0.Anc0refChr3 114565 25 + 222631 GCTATATTTTTGAAGGTGTAATTAG -s Anc1.Anc1refChr6 148410 25 + 197743 GCTATATTTTTGAAGGTGTAATTAG -s Anc2.Anc2refChr1 26713 25 + 142988 GCTATATTTTTGAAGGTGTAATTGG -s mr.mrrefChr3 52725 25 + 181027 GTTATAATCTCGAGTGCATAGTGAG -s simCow_chr6.simCow.chr6 483197 25 + 602619 GTCATATTTCTGAAGGTGTAGCTGG -s simDog_chr6.simDog.chr6 473130 25 + 593897 GCTATATTTTTGAAACTGTGATTGG -s simHuman_chr6.simHuman.chr6 480428 25 + 601863 ACTATACTTTTGAAGGTGTAATCAG -s simMouse_chr6.simMouse.chr6 622341 25 + 636262 GTTATAATCTCGAGTGCATAGTGAG -s simRat_chr6.simRat.chr6 511375 25 + 647215 ATTATACTCTTGAAGGTATAGCGAG - -a -s simMouse_chr6.simMouse.chr6 498784 22 + 636262 ATAATGCAGAAATGGACCCCAT -s Anc0.Anc0refChr3 114590 22 + 222631 ATAATGGGGAAATGGGCCCCTT -s Anc1.Anc1refChr6 148435 22 + 197743 ATAATGGGGAAATGGGCCCCTT -s Anc2.Anc2refChr1 26738 22 + 142988 ATAATGGGGAAATGGGCCCCTA -s mr.mrrefChr3 52750 22 + 181027 ATAATGCAGAAATGGACCCCAT -s simCow_chr6.simCow.chr6 483222 22 + 602619 GTAATGAAGAAACTGACCTGTG -s simDog_chr6.simDog.chr6 473155 21 + 593897 ATAGT-GGAAAATGGGCCCCTA -s simHuman_chr6.simHuman.chr6 480453 22 + 601863 ATAATAGGGAAATGGCCCCTTT -s simMouse_chr6.simMouse.chr6 622366 22 + 636262 ATAATGCAGAAATGGACCCCAT -s simRat_chr6.simRat.chr6 511403 22 + 647215 ATAATGCAGAAATGGACCCCTT - -a -s simMouse_chr6.simMouse.chr6 498806 18 + 636262 CACCCATCAGACCAGATA -s Anc0.Anc0refChr3 114614 18 + 222631 CACCCATCAGCCCCCATA -s Anc1.Anc1refChr6 148459 18 + 197743 CACCCATCAGCCCCCATA -s Anc2.Anc2refChr1 26762 18 + 142988 CACCCCTCAACCCCCATA -s mr.mrrefChr3 52772 18 + 181027 CACCCATCAGACCAGATA -s simCow_chr6.simCow.chr6 483246 18 + 602619 CATCCCTCATCCCCCAGA -s simDog_chr6.simDog.chr6 473178 18 + 593897 CACCCCTCAACCCCCATA -s simHuman_chr6.simHuman.chr6 480477 18 + 601863 CGCCCATCGGGACCCATA -s simMouse_chr6.simMouse.chr6 622388 18 + 636262 CACCCATCAGACCAGATA -s simRat_chr6.simRat.chr6 511425 18 + 647215 CACCTATCAGACCAGATA - -a -s simMouse_chr6.simMouse.chr6 498824 8 + 636262 ACCCTAAA -s Anc0.Anc0refChr3 114635 8 + 222631 ACCCTAAA -s Anc1.Anc1refChr6 148480 8 + 197743 ACCCTAAA -s Anc2.Anc2refChr1 26783 8 + 142988 ACCCTAAC -s mr.mrrefChr3 52790 8 + 181027 ACCCTAAA -s simCow_chr6.simCow.chr6 483267 8 + 602619 ATCCTAAC -s simDog_chr6.simDog.chr6 473199 3 + 593897 ACC----- -s simHuman_chr6.simHuman.chr6 480498 8 + 601863 ACCCTAGA -s simMouse_chr6.simMouse.chr6 622406 8 + 636262 ACCCTAAA -s simRat_chr6.simRat.chr6 511443 8 + 647215 ATCCTAAA - -a -s simMouse_chr6.simMouse.chr6 498832 194 + 636262 CCCTTTCCAATTGGTGAATACTTTTCCACTATATTAAGGTGTCACTAATAGGTACACGTGCCAATATTCTATACTACCAGTAGGGATAAGGAAGGCAGGCAACCAATTGCCTTCTATTTGCACACTTGCTTACTGAGACCTGTAGTCCTTATTTAGATGATTCTCTCATGGGCTAGGGAGGTTGGCCCAGCCCT -s Anc0.Anc0refChr3 114643 5 + 222631 -CCTTT-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- -s Anc1.Anc1refChr6 148488 8 + 197743 -CCTTTCCA----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- -s Anc2.Anc2refChr1 26791 5 + 142988 -ACTTT-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- -s mr.mrrefChr3 52798 194 + 181027 CCCTTTCCAATTGGTGAATACTTTTCCACTATATTAAGGTGTCACTAATAGGTACACGTGCCAATATTCTATACTACCAGTAGGGATAAGGAAGGCAGGCAACCAATTGCCTTCTATTTGCACACTTGCTTACTGAGACCTGTAGTCCTTATTTAGATGATTCTCTCATGGGCTAGGGAGGTTGGCCCAGCCCT -s simCow_chr6.simCow.chr6 483275 5 + 602619 -ACTTT-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- -s simHuman_chr6.simHuman.chr6 480506 8 + 601863 -CCTTTCCA----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- -s simMouse_chr6.simMouse.chr6 622414 194 + 636262 CCCTTTCCAATTGGTGAATACTTTTCCACTATATTAAGGTGTCACTAATAGGTACACGTGCCAATATTCTATACTACCAGTAGGGATAAGGAAGGCAGGCAACCAATTGCCTTCTATTTGCACACTTGCTTACTGAGACCTGTAGTCCTTATTTAGATGATTCTCTCATGGGCTAGGGAGGTTGGCCCAGCCCT -s simRat_chr6.simRat.chr6 511454 194 + 647215 CCCTTTCCAATTGGTGAATACTTTTCCACTATTTTAAGGTGTCCCTAACAGGTATACATGCTAATGTTCTATATTACCTGTAGGGATAAGGAAGGCAGCCAACTAATTGCCTTCTACTGGCACACTTGCTTACTGACACCTGTAGTCCTTCTTTAGACGGTTCACCCATGGGGCAGGGAGATTGGGCCATCCCT - -a -s simMouse_chr6.simMouse.chr6 499026 9 + 636262 AACCCTTTC -s Anc0.Anc0refChr3 114648 1 + 222631 --------C -s Anc1.Anc1refChr6 148496 1 + 197743 --------C -s Anc2.Anc2refChr1 26796 1 + 142988 --------G -s mr.mrrefChr3 52992 9 + 181027 AACCCTTTC -s simCow_chr6.simCow.chr6 483280 1 + 602619 --------G -s simHuman_chr6.simHuman.chr6 480514 1 + 601863 --------C -s simMouse_chr6.simMouse.chr6 622608 7 + 636262 AAGGC--TC -s simRat_chr6.simRat.chr6 511649 9 + 647215 AACCCTTTC - -a -s simMouse_chr6.simMouse.chr6 499035 49 + 636262 GAACTGGTGAACACTCCTCCATTATCTTAAGACATATATTGTTTCACTT -s Anc0.Anc0refChr3 114649 49 + 222631 CAACTGATGCACACTTTGCCACTATCTTAAGATGTATATAGTTTCACTT -s Anc1.Anc1refChr6 148497 49 + 197743 CAACTGATGCACACTTTGCCACTATCTTAAGATGTATATAGTTTCACTT -s Anc2.Anc2refChr1 26797 49 + 142988 CAACTGATGCACATTTTGCTACTATCTTAAGTTGTGTATAGTTTCACTT -s mr.mrrefChr3 53001 49 + 181027 AAACTGGTGAACACTCCTCCATTATCTTAAGACATATATTGTTTCACTT -s simCow_chr6.simCow.chr6 483281 49 + 602619 CAACTGATGACCATTTTGCTATTATCTCAAATTGTGTATATTTTCACCT -s simDog_chr6.simDog.chr6 473627 44 + 593897 -----gatgcacattttgctacAATTTTAAGTTGTGTGTAGTTCCACTT -s simHuman_chr6.simHuman.chr6 480515 49 + 601863 CAACTGCTGGACACTTTGCCACTATCCTAAGATGGATATAGTTTCACTT -s simMouse_chr6.simMouse.chr6 622615 18 + 636262 AAAT-------AACTCCTAC-------TGATA----------------- -s simRat_chr6.simRat.chr6 511669 49 + 647215 CAACTGGTGAACACTTTTCCACTATCTTAAGCCATATTTGGTTTCAGTT - -a -s simMouse_chr6.simMouse.chr6 499084 19 + 636262 ATGCTATTGCCTATTGCAA -s Anc0.Anc0refChr3 114698 19 + 222631 ATGCTATTGACTATTGCTA -s Anc1.Anc1refChr6 148546 19 + 197743 ATGCTATTGACTATTGCTA -s Anc2.Anc2refChr1 26846 19 + 142988 ATACTGTTGACTATTGCTG -s mr.mrrefChr3 53050 19 + 181027 ATGCTATTGCCTATTGCAA -s simCow_chr6.simCow.chr6 483330 18 + 602619 CTACTGTTGACCATTGCT- -s simDog_chr6.simDog.chr6 473672 19 + 593897 ATACTGTTACCTATGGCTG -s simHuman_chr6.simHuman.chr6 480564 19 + 601863 ATGCTATTGACTATTGTCA -s simRat_chr6.simRat.chr6 511718 19 + 647215 ATACTATTGTCTATTGCAA - -a -s simMouse_chr6.simMouse.chr6 499103 14 + 636262 CTTTGTATGTACAG -s Anc0.Anc0refChr3 114721 14 + 222631 CTTTGTATGTACAG -s Anc1.Anc1refChr6 148569 14 + 197743 CTTTGTATGTACAG -s Anc2.Anc2refChr1 26869 14 + 142988 CTTTGTCTGTACAG -s mr.mrrefChr3 53073 14 + 181027 CTTTGTATGTACAG -s simCow_chr6.simCow.chr6 483352 14 + 602619 CTTTGTGTGTACAG -s simDog_chr6.simDog.chr6 473695 14 + 593897 CTTTTTCTGTACAG -s simHuman_chr6.simHuman.chr6 480587 14 + 601863 TTTTGTATGTATGG -s simRat_chr6.simRat.chr6 511741 14 + 647215 CTTTGTATCTACAG - -a -s simMouse_chr6.simMouse.chr6 499117 47 + 636262 CCAGTTAAGAACTCATTGCCAGGCAATGCGGATCTATGGAACTTTTC -s Anc0.Anc0refChr3 114735 46 + 222631 CTATTTAAGAACTAATTTTAGGGAGATGGGGACCTTTAAAACTTT-C -s Anc1.Anc1refChr6 148583 46 + 197743 CTATTTAAGAACTAATTTTAGGGAGATGGGGACCTTTAAAACTTT-C -s Anc2.Anc2refChr1 26883 46 + 142988 CTATTTAAGAACTAATTTTAGGGAGATGGGGACCTTTAAAAGTTT-C -s mr.mrrefChr3 53087 47 + 181027 CTAGTTAAGAACTAATTGCAGGGCAATGCGGATCTATGAAACTTTCC -s simCow_chr6.simCow.chr6 483366 46 + 602619 CCATTTAAAAACTAATTCTAGGGAGATGGAGACCTCTAAAAGTTT-T -s simDog_chr6.simDog.chr6 473717 46 + 593897 GTATTTATGGACTAATTTTAGGGAGGTGGGGACCTTTAAAAGTTT-C -s simHuman_chr6.simHuman.chr6 480601 46 + 601863 CTGTTTAAGAACTAATTATAGGGAGATGGGGACTTGTAAAACTTT-C -s simRat_chr6.simRat.chr6 511755 47 + 647215 TTAGTTAAGAACCAATTGCAGGGCAATGCTGTTCTCTGAGACTTTCC - -a -s simMouse_chr6.simMouse.chr6 499164 12 + 636262 TCCACTTCACAC -s Anc0.Anc0refChr3 114781 12 + 222631 TCCATTTAGCTC -s Anc1.Anc1refChr6 148629 12 + 197743 TCCATTTAGCTC -s Anc2.Anc2refChr1 26929 12 + 142988 CCCATTTAGCTC -s mr.mrrefChr3 53134 12 + 181027 TCCATTTCACAC -s simCow_chr6.simCow.chr6 483412 12 + 602619 CCCACTTAGCTC -s simDog_chr6.simDog.chr6 473764 12 + 593897 CCCATTTAGCTC -s simHuman_chr6.simHuman.chr6 480647 12 + 601863 TCCTGTGAGCTC -s simRat_chr6.simRat.chr6 511802 12 + 647215 CCCATTTGACAC - -a -s simMouse_chr6.simMouse.chr6 499176 15 + 636262 ACTGCCAGTATTTTA -s Anc0.Anc0refChr3 114793 15 + 222631 TTTATCATTGTTTTA -s Anc1.Anc1refChr6 148641 15 + 197743 TTTATCATTGTTTTA -s Anc2.Anc2refChr1 26941 15 + 142988 TTTATCATTGTTTCA -s mr.mrrefChr3 53146 15 + 181027 TCTGCCAGTGTTTTA -s simCow_chr6.simCow.chr6 483424 15 + 602619 TTTATCCTTATTCCA -s simDog_chr6.simDog.chr6 473776 15 + 593897 CCTATCATTGTTTCA -s simHuman_chr6.simHuman.chr6 480668 15 + 601863 TTTATCATAGTTTTA -s simRat_chr6.simRat.chr6 511814 15 + 647215 TCTGCCAGTGAGTTA - -a -s simMouse_chr6.simMouse.chr6 499191 77 + 636262 TCTCTTATTTGCAATAACCACATCCAGTTAATGAGTCAGTCTGTGACGACCACATAAAGTTGACACATGGTCATGGA -s Anc0.Anc0refChr3 114809 45 + 222631 TTTCTTGGTTGCGATGACTACATACAGTTA--------------------------------ACATACAGTCATGGA -s Anc1.Anc1refChr6 148657 66 + 197743 TTTCTTGGTTGCGATGACTACATACAGTTAACATATC-----------GTCATTTATAGTTCACATACAGTCATGGA -s Anc2.Anc2refChr1 26957 45 + 142988 TTTCTCGGTTGCGATGACTACATACAGTTA--------------------------------ACATACAGTCATGGA -s mr.mrrefChr3 53162 77 + 181027 TCTCTTATTTGCAATAACCACATCCAGTTAACAAGTCAGTCTGTGACGACCACATAAAGTTGACACATGGTCATGGA -s simCow_chr6.simCow.chr6 483440 45 + 602619 TGTCTCAGTTGCAATAATTACGTACTATTA--------------------------------CCAAACAGTCACCAA -s simDog_chr6.simDog.chr6 473792 45 + 593897 TTTCTCGGTTGTGATGACTGCATACAGTTA--------------------------------ATATGCAGTCATGGA -s simHuman_chr6.simHuman.chr6 480684 55 + 601863 TTTCTTTATTACGGTGGCTACACATAGTTCACATATC-----------GTCATTTATAGTTCACAT----------- -s simRat_chr6.simRat.chr6 511830 77 + 647215 TCTCTTATTAGCAATAACCACATCCAGTTTACAAGCCAGTCTGTGATGACTGGATAAAGCTAACACATTGTCATGGA - -a -s simMouse_chr6.simMouse.chr6 499268 7 + 636262 AATGAGG -s Anc0.Anc0refChr3 114854 7 + 222631 GATGAAG -s Anc1.Anc1refChr6 148723 7 + 197743 GATGAAG -s Anc2.Anc2refChr1 27002 7 + 142988 GATGAAG -s mr.mrrefChr3 53239 7 + 181027 AATGAGG -s simCow_chr6.simCow.chr6 483487 7 + 602619 GATGCAG -s simDog_chr6.simDog.chr6 473837 7 + 593897 GATGAAG -s simHuman_chr6.simHuman.chr6 480739 6 + 601863 -ATGGTC -s simRat_chr6.simRat.chr6 511907 7 + 647215 AATGAGG - -a -s simMouse_chr6.simMouse.chr6 499275 2 + 636262 AC -s Anc0.Anc0refChr3 114861 2 + 222631 AT -s Anc1.Anc1refChr6 148730 2 + 197743 AT -s Anc2.Anc2refChr1 27009 2 + 142988 AT -s mr.mrrefChr3 53246 2 + 181027 AC -s simCow_chr6.simCow.chr6 483502 2 + 602619 CT -s simDog_chr6.simDog.chr6 473844 2 + 593897 AT -s simHuman_chr6.simHuman.chr6 480745 2 + 601863 AT -s simRat_chr6.simRat.chr6 511914 2 + 647215 AG - -a -s simMouse_chr6.simMouse.chr6 499277 4 + 636262 AAAC -s Anc0.Anc0refChr3 114865 4 + 222631 AGAC -s Anc1.Anc1refChr6 148734 4 + 197743 AGAC -s Anc2.Anc2refChr1 27013 4 + 142988 AGCC -s mr.mrrefChr3 53248 4 + 181027 AAAC -s simCow_chr6.simCow.chr6 483506 4 + 602619 AGCC -s simDog_chr6.simDog.chr6 473848 4 + 593897 AGCC -s simHuman_chr6.simHuman.chr6 480749 4 + 601863 AGAT -s simRat_chr6.simRat.chr6 511916 4 + 647215 GAAG - -a -s simMouse_chr6.simMouse.chr6 499281 73 + 636262 CCCGCAATTCTAATACACTTCCAAGCTCGCAATTCTAATCCAAGCCCCTCAGGGATGGTATATGACACCCTCA -s Anc0.Anc0refChr3 114869 45 + 222631 ATAGCTACTC---TACACATTCA-------------------------TCAGGGATGGTGTATGACACCCTTA -s Anc1.Anc1refChr6 148738 45 + 197743 ATAGCTACTC---TACACATTCA-------------------------TCAGGGATGGTGTATGACACCCTTA -s Anc2.Anc2refChr1 27017 45 + 142988 ATAGCTACTA---TACACATTCA-------------------------TCAGGGACGGTGTATAACACCTTTA -s mr.mrrefChr3 53252 48 + 181027 CCCGCAATTCTAATACACTTCCA-------------------------TCAGGGATGGTATATGACACCCTCA -s simCow_chr6.simCow.chr6 483510 43 + 602619 --AGCTATTA---GACATCTTCA-------------------------TCAGGGACAGTGTATAACACCTTCA -s simDog_chr6.simDog.chr6 473853 43 + 593897 ATAGTTACTA---TACACATTCA-------------------------TCAGG--CGGCCCATAGCTACTATA -s simHuman_chr6.simHuman.chr6 480753 45 + 601863 ATAGCTACTC---CACGCATGCT-------------------------TTAGGGATGGTGTATGACACCCTTA -s simRat_chr6.simRat.chr6 511920 48 + 647215 CCCGCAATTCTAATCCACTTCCA-------------------------TCAGTGATGGTATTTGACACCCTCA - -a -s simMouse_chr6.simMouse.chr6 499354 5 + 636262 GCAAA -s Anc0.Anc0refChr3 114914 5 + 222631 GCAAG -s Anc1.Anc1refChr6 148783 5 + 197743 GCAAG -s Anc2.Anc2refChr1 27062 5 + 142988 GCAAG -s mr.mrrefChr3 53300 5 + 181027 GCAAG -s simCow_chr6.simCow.chr6 483553 5 + 602619 GGAAG -s simDog_chr6.simDog.chr6 473904 5 + 593897 TCAGG -s simHuman_chr6.simHuman.chr6 480798 5 + 601863 GCAAG -s simRat_chr6.simRat.chr6 511968 5 + 647215 TCAAG - -a -s simMouse_chr6.simMouse.chr6 499359 17 + 636262 TCTCATAGGTTAGCTCC -s Anc0.Anc0refChr3 114919 17 + 222631 TCACACAGGTTAGCTCA -s Anc1.Anc1refChr6 148788 17 + 197743 TCACACAGGTTAGCTCA -s Anc2.Anc2refChr1 27067 17 + 142988 TCACACAGGCTAGCTCA -s mr.mrrefChr3 53305 17 + 181027 TCACATAGGTTAGCTCA -s simCow_chr6.simCow.chr6 483558 17 + 602619 TCTCCCCAGGTAGCTCA -s simDog_chr6.simDog.chr6 473924 17 + 593897 TCACACAGGCTAACTGA -s simHuman_chr6.simHuman.chr6 480803 17 + 601863 TCACACAGGTTAGCCCA -s simRat_chr6.simRat.chr6 511973 17 + 647215 TCACATAGGTTAGCTTA - -a -s simMouse_chr6.simMouse.chr6 499376 20 + 636262 TTGGGCATATGCAGGGAAAA -s Anc0.Anc0refChr3 114936 20 + 222631 TTGGACAAATGAGGAGAATA -s Anc1.Anc1refChr6 148805 20 + 197743 TTGGACAAATGAGGAGAATA -s Anc2.Anc2refChr1 27084 20 + 142988 TTGGACAAATGAGGAGAATA -s mr.mrrefChr3 53322 20 + 181027 TTGGGCATATGCAGAGAAAA -s simCow_chr6.simCow.chr6 483575 20 + 602619 TTGGACAAATGAGAAGAATA -s simDog_chr6.simDog.chr6 473942 20 + 593897 TTGGCCAAAAGAGGAGAATA -s simHuman_chr6.simHuman.chr6 480820 20 + 601863 TTGGAAGAATAAGGAGAATA -s simRat_chr6.simRat.chr6 511990 20 + 647215 TTGGGCAGATGCTGAGAAGG - -a -s simMouse_chr6.simMouse.chr6 499396 30 + 636262 CAGATCTGATCAAACCCTGTCTTAGGGAGG -s Anc0.Anc0refChr3 114956 30 + 222631 CGGATCTGATCAAACTCCATCTTAGGCATG -s Anc1.Anc1refChr6 148825 30 + 197743 CGGATCTGATCAAACTCCATCTTAGGCATG -s Anc2.Anc2refChr1 27104 30 + 142988 CGGATCCGATCTAACTCCATCTTAGGCATG -s mr.mrrefChr3 53342 30 + 181027 CAGATCTGATCAAACCCTGTCTTAGGGAGG -s simCow_chr6.simCow.chr6 483596 30 + 602619 CGGATCCGATATAGGCTTATCTTAGGCAGG -s simDog_chr6.simDog.chr6 473962 30 + 593897 CAGATCCGGTCTAACTCCATCTAAGGCATG -s simHuman_chr6.simHuman.chr6 480840 30 + 601863 CGGATATGATTAAAATCCATCTTAGTCATG -s simRat_chr6.simRat.chr6 512010 30 + 647215 CAGATCTGATCATACCCTGTCTTAGGGAGG - -a -s simMouse_chr6.simMouse.chr6 499426 38 + 636262 AGGGTAAAATATTGTTGTAGCCACACCCTTTGTGGGAG -s Anc0.Anc0refChr3 114988 38 + 222631 ATGGTAAAACATCCCTGTAGTCACATCCTTTGGGGGAG -s Anc1.Anc1refChr6 148857 38 + 197743 ATGGTAAAACATCCCTGTAGTCACATCCTTTGGGGGAG -s Anc2.Anc2refChr1 27136 38 + 142988 ATGGTAAAACATCCCTGTAGCCACATCCCTTGGGGGAG -s mr.mrrefChr3 53372 38 + 181027 AGGGTAAAATATTCCTGTAGTCACACCCTTTGGGGGAG -s simCow_chr6.simCow.chr6 483628 22 + 602619 ATGGTACAACATACCTAC----------------GGAG -s simDog_chr6.simDog.chr6 473994 38 + 593897 AGAATGAAACATCCCTGTAGCCACATCCCTTGGGGGAG -s simHuman_chr6.simHuman.chr6 480872 38 + 601863 ATGGTAAAACATGCCTGTAGTCACATCATTTGGAAGGA -s simRat_chr6.simRat.chr6 512040 38 + 647215 AGGGTAAAATATCCCTGTGGTCAGACCCTTTGGGGGAG - -a -s simMouse_chr6.simMouse.chr6 499464 21 + 636262 TTGTTTCACTGCAATTGGAGG -s Anc0.Anc0refChr3 115026 21 + 222631 TTGTTTCACTGCAATTGGAGG -s Anc1.Anc1refChr6 148895 21 + 197743 TTGTTTCACTGCAATTGGAGG -s Anc2.Anc2refChr1 27175 21 + 142988 TGGGTTCACTGCAATTGGAGG -s mr.mrrefChr3 53410 21 + 181027 TTGTTTCACTGCAATTGGAGG -s simCow_chr6.simCow.chr6 483651 21 + 602619 TCGGTCCAATGCAATCGGAGA -s simDog_chr6.simDog.chr6 474033 21 + 593897 TGGGCTAACAGTAATTGGAGG -s simHuman_chr6.simHuman.chr6 480910 21 + 601863 TTATTTCACTGCAACTGGACG -s simRat_chr6.simRat.chr6 512078 20 + 647215 TTGTTTCACTGCATTTGGA-T - -a -s simMouse_chr6.simMouse.chr6 499485 37 + 636262 ACTATCTAAGTGGAGTCCTTCCTAAAACAAAACACAG -s Anc0.Anc0refChr3 115053 37 + 222631 ATTGTATAAGTAGAGTCCTGCCTCAAACAAAAAGATG -s Anc1.Anc1refChr6 148922 37 + 197743 ATTGTATAAGTAGAGTCCTGCCTCAAACAAAAAGATG -s Anc2.Anc2refChr1 27202 37 + 142988 ATTGTATAAGTAGAGTCCTGCCTCAAACAAAAAGATG -s mr.mrrefChr3 53431 37 + 181027 ATTGTCTAAGTGGAGTCCTTCCTAAAACAAAACGCAG -s simCow_chr6.simCow.chr6 483680 37 + 602619 ATTCTAGAAGTAGGGTCCTGCCTCAAACAGAACAATG -s simDog_chr6.simDog.chr6 474060 37 + 593897 ATTGTATAAGTAGAGTCCTGCCTCAAACTAAAAGGTG -s simHuman_chr6.simHuman.chr6 480937 37 + 601863 ATTGTTTTAGTAGAGTCCTGCCTCAAGTAAAAAGATG -s simRat_chr6.simRat.chr6 512098 37 + 647215 ATTGTCTAAGTGGAGTCCTCCCTAAAACAGAATGCAA - -a -s simMouse_chr6.simMouse.chr6 499522 29 + 636262 ATGCAAAAATGGACATAGGGTTACAATGG -s Anc0.Anc0refChr3 115090 29 + 222631 ATGCAAACATGGACCAGAGTTTATAATGA -s Anc1.Anc1refChr6 148959 29 + 197743 ATGCAAACATGGACCAGAGTTTATAATGA -s Anc2.Anc2refChr1 27239 29 + 142988 AAGCAAACATGGACCAGAGTTTATAATGA -s mr.mrrefChr3 53468 29 + 181027 ATGCAAAAATGGACATAGGGTTACAATGG -s simCow_chr6.simCow.chr6 483717 28 + 602619 AAGCAAACTTATA-CAGGGCTTATAATGA -s simDog_chr6.simDog.chr6 474097 29 + 593897 AAGCAGACATGGACCAGAGTTTATAATGG -s simHuman_chr6.simHuman.chr6 480974 29 + 601863 ATGCGAGCATTGACTGGAGTCTATAGTGA -s simMouse_chr6.simMouse.chr6 500909 29 + 636262 ATGCAAAAATGGACATAGGGTTACAATGG -s simRat_chr6.simRat.chr6 512135 29 + 647215 ATGCACAAATAGACATGAGGTTACAATGA - -a -s simMouse_chr6.simMouse.chr6 499551 11 + 636262 CACCAAATCAT -s Anc0.Anc0refChr3 115119 8 + 222631 CACCAAT---T -s Anc1.Anc1refChr6 148988 11 + 197743 CACCAATACAT -s Anc2.Anc2refChr1 27268 8 + 142988 TCCCTGT---T -s mr.mrrefChr3 53497 11 + 181027 CACCAAATCAT -s simCow_chr6.simCow.chr6 483745 8 + 602619 TCCCTGT---T -s simDog_chr6.simDog.chr6 474126 8 + 593897 TACCTGT---T -s simHuman_chr6.simHuman.chr6 481064 11 + 601863 CACAAATACAC -s simMouse_chr6.simMouse.chr6 500938 11 + 636262 CACCAAATCAT -s simRat_chr6.simRat.chr6 512164 11 + 647215 CACCGAATCGT - -a -s simMouse_chr6.simMouse.chr6 499562 41 + 636262 TTAATGTCTAACAATTAAATATGTCAGACTCTGTACCTATG -s Anc0.Anc0refChr3 115127 41 + 222631 TTAATGTCTACCTATTAAATCTATGAGACCCTATACTTATG -s Anc1.Anc1refChr6 148999 41 + 197743 TTAATGTCTACCTATTAAATCTATGAGACCCTATACTTATG -s Anc2.Anc2refChr1 27276 41 + 142988 TGAATGTCTACCTATTAAATCTATGAGACCCTATACTTATG -s mr.mrrefChr3 53508 41 + 181027 TTAATGTCTAACAATTAAATATGTCAGACTCTGTACCTATG -s simCow_chr6.simCow.chr6 483754 41 + 602619 TGAATGTCTAAATATTAAATCTATGAGTCCTTATACTTATG -s simDog_chr6.simDog.chr6 474134 41 + 593897 TGAATGTCTACCTATTAAATCTATGAGACCCTATACTTGTG -s simHuman_chr6.simHuman.chr6 481075 41 + 601863 TTTGTGTTTACTCATTAAATCTATAAGACCCTATACTTATG -s simMouse_chr6.simMouse.chr6 500949 41 + 636262 TTAATGTCTAACAATTAAATATGTCAGACTCTGTACCTATG -s simRat_chr6.simRat.chr6 512175 38 + 647215 TTAATGTCTAACTGTTAAATACATGAGACCCTGTACCT--- - -a -s simMouse_chr6.simMouse.chr6 499603 37 + 636262 GTCACTCATAAGAAGAGAGCCAAGTGTAAATTTTGAA -s Anc0.Anc0refChr3 115168 37 + 222631 GTCACTCTTTAGAGTAGAGGCATATCTTAATTTTGAA -s Anc1.Anc1refChr6 149040 37 + 197743 GTCACTCTTTAGAGTAGAGGCATATCTTAATTTTGAA -s Anc2.Anc2refChr1 27318 37 + 142988 GGCACCCTTTAGAGTAGAGGCATAACTTAATTTTGAA -s mr.mrrefChr3 53549 37 + 181027 GTCACTCATAAGAAGAGAGCCAAGTGTAAATTTTGAA -s simCow_chr6.simCow.chr6 483796 37 + 602619 GACATCCATTAGAGTAGAGGCATAACTTAATTTTGAA -s simDog_chr6.simDog.chr6 474176 22 + 593897 GGCACCCTTTAGAGTAGAGGCA--------------- -s simHuman_chr6.simHuman.chr6 481116 35 + 601863 TT--GTGTGCAGAGTAGGAGCATATATTAACTTTGAA -s simMouse_chr6.simMouse.chr6 500990 37 + 636262 GTCACTCATAAGAAGAGAGCCAAGTGTAAATTTTGAA -s simRat_chr6.simRat.chr6 512213 35 + 647215 --CACTCATAAGAAGAGAGCCAAGTGTAAATTTTGAA - -a -s simMouse_chr6.simMouse.chr6 499640 172 + 636262 GGACGCATTTTTGGCCACATACCCTGTGCCCTAGCACCTTACTGTACCAAATTTGTCTTTAAAAATGTGGCTATATTATTACTGGAATATCCTAGCTACGTGCTGACTTCTATTGTGCTTTAGTAAAGCTCTGGCTGCGGACACCTATCATGCTGAGTGGTTTAGTAAAGCT -s Anc0.Anc0refChr3 115205 82 + 222631 GGAGGCATTT------------------------------------------------TTAAAAACATGGT-------TTGTTCGAATGTCCTAG-----------------------------------CTGTCTGCTAACATCTACCATGCCAAATGGGTTAGTAAAGCT -s Anc1.Anc1refChr6 149077 82 + 197743 GGAGGCATTT------------------------------------------------TTAAAAACATGGT-------TTGTTCGAATGTCCTAG-----------------------------------CTGTCTGCTAACATCTACCATGCCAAATGGGTTAGTAAAGCT -s Anc2.Anc2refChr1 27355 82 + 142988 GGAGGCATCT------------------------------------------------TTAAACACATGGT-------CTGTTCGACTGTCCTAG-----------------------------------CTGTCTGCTAACATCTACCGTGCCAAATGGGTTAGTAAAGCT -s mr.mrrefChr3 53586 172 + 181027 GGACGCATTTTTGGCCACATACCCTGTGCCCTAGCACCTTACTGTACCAAATTTGTCTTTAAAAATGTGGTTATATTATTACTGGAATATCCTAGCTACGTGCTGACTTCTATTGTGCTTTAGTAAAGCTCTGGCTGCGGACACCTATCATGCTGAGTGGTTTAGTAAAGCT -s simCow_chr6.simCow.chr6 483833 81 + 602619 GGAGGCATCT-------------------------------------------------TAAATACATGGG-------CTGTTCCACCATCCTAG-----------------------------------CTGCCTGCTAACATGTACCGTGCCGGATGGGTTAGTAAAGCT -s simDog_chr6.simDog.chr6 474198 73 + 593897 ---------T------------------------------------------------TTAAACACGTGAT-------CTGTTCGACTGTCCTAG-----------------------------------CTGTCTACTAGCATCTCCTGTGTCAAATGGGTTAGTAAAGCT -s simHuman_chr6.simHuman.chr6 481151 82 + 601863 GGAGGCATTT------------------------------------------------CTAAAAACATGGT-------TTGGTCTGATGTCCTAG-----------------------------------CTGTCTGCTAAGATCTAGCATGCCAAATGGGTTAGTAAAGCT -s simMouse_chr6.simMouse.chr6 501027 172 + 636262 GGACGCTTTTTTGGCCACATACCCTGTGCCCTAGCACCTTACTGTACCAAATTTGTCTTTAAAAATGTGGTTATATTATTACTGGAATATCCTAGCTACGTGCTGACTTCTATTGTGCTTTAGTAAAGCTCTGGCTGCGGACACCTATCATGCTGAGTGGTTTAGTAAAGCT -s simRat_chr6.simRat.chr6 512281 163 + 647215 AGATGTATTTTTGATCAGATACAATGTGCCCTAGCACC---------CAGATGTGCCTTTAAAAATGTGGTTATATATTTACTGAACTGTTCTAGTTGGGTGCTGACATCTATCATAGTTTAGTAAAGCTCTGGCCACTGACACCTATCATGCTGAGTGGTTCAATAAAACT - -a -s simMouse_chr6.simMouse.chr6 499812 66 + 636262 TTTTGGAATAAATTTCATCATGTTACCTGCTAAGTTCGCCCTATGTCCACATGTACTAGTACAAAA -s Anc0.Anc0refChr3 115287 53 + 222631 TTGTTAGAC-AATTTAACCATGGTCACTGCATAG------------AAGCATGCACTAGTCCATGA -s Anc1.Anc1refChr6 149159 53 + 197743 TTGTTAGAC-AATTTAACCATGGTCACTGCATAG------------AAGCATGCACTAGTCCATGA -s Anc2.Anc2refChr1 27437 53 + 142988 ATGTTAGTC-AATTTAACCATGGTCACTGCATGC------------AAGGATGCACTAGTCCATGA -s mr.mrrefChr3 53758 66 + 181027 TTTTGGAATAAATTTCATCATGTTTCCTGCTAAGTTCGCCCTATGTCCACATGTACTAGTACAAAA -s simCow_chr6.simCow.chr6 483930 51 + 602619 CTGTTAGTC-AATTTAACTATGTTTGCTGCATGC------------AAG--TGCAGTCTTCCATGA -s simDog_chr6.simDog.chr6 474271 53 + 593897 ATGTTAGTA-AATTTAATCATGGTCACTGCATGC------------AAGGATGCACCAGTCCATGA -s simHuman_chr6.simHuman.chr6 481233 53 + 601863 TTGTCAGAC-AATCTAACCATGCTCTCTGCACAG------------AAGCATGCACTAGTCCATGA -s simMouse_chr6.simMouse.chr6 501199 66 + 636262 TTTTGGAATAAATTTCATCATGTTTCCTGCTAAGTTCGCCCTATGTCCACATGTACTAGTACAAAA -s simRat_chr6.simRat.chr6 512444 53 + 647215 TTT-GGAATAAATTTCATCATGTTTCCTGC------------ATGTCCACTTGTACTAGTCCATGA - -a -s simMouse_chr6.simMouse.chr6 499878 8 + 636262 ACAGACGT -s Anc0.Anc0refChr3 115354 8 + 222631 ACAGATCC -s Anc1.Anc1refChr6 149226 8 + 197743 ACAGATCC -s Anc2.Anc2refChr1 27504 8 + 142988 ATAGATCC -s mr.mrrefChr3 53824 8 + 181027 ACAGACCT -s simCow_chr6.simCow.chr6 483995 8 + 602619 CTAGATCT -s simDog_chr6.simDog.chr6 474338 8 + 593897 ATAGATCC -s simHuman_chr6.simHuman.chr6 481300 8 + 601863 ACAGATCC -s simMouse_chr6.simMouse.chr6 501265 8 + 636262 ACAGACCT -s simRat_chr6.simRat.chr6 512497 8 + 647215 ACATACCT - -a -s simMouse_chr6.simMouse.chr6 499886 7 + 636262 ATGAAAA -s Anc0.Anc0refChr3 115363 7 + 222631 AAAAAAA -s Anc1.Anc1refChr6 149235 7 + 197743 AAAAAAA -s Anc2.Anc2refChr1 27513 7 + 142988 AAAAAAA -s mr.mrrefChr3 53832 7 + 181027 ATGAAAA -s simCow_chr6.simCow.chr6 484004 7 + 602619 TGAAAAA -s simDog_chr6.simDog.chr6 474347 7 + 593897 AAAAAAA -s simHuman_chr6.simHuman.chr6 481309 7 + 601863 AAAAAAA -s simMouse_chr6.simMouse.chr6 501273 7 + 636262 ATGAAAA -s simRat_chr6.simRat.chr6 512505 7 + 647215 TTGAAAA - -a -s simMouse_chr6.simMouse.chr6 499893 33 + 636262 ATTGCAGACCATTCCAGTCAAGGAGAATCATTT -s Anc0.Anc0refChr3 115380 29 + 222631 ATTGCAGACCACTCCTTTGAAGAGAAA----TT -s Anc1.Anc1refChr6 149254 33 + 197743 ATTGCAGACCACTCCTTTGAAGAGAAATTGGTT -s Anc2.Anc2refChr1 27530 29 + 142988 ATTGCAGACCACTGCTTTGAAGAGAAA----TT -s mr.mrrefChr3 53851 33 + 181027 ATTGCAGACCATTCCAGTCAAGGAGAATCATTT -s simCow_chr6.simCow.chr6 484026 29 + 602619 ATTGCACACCACTGCTCTGGAGAGAAA----TT -s simDog_chr6.simDog.chr6 474364 29 + 593897 ATTGTAGACCCCTGCTTTGAAGAGGAA----TT -s simHuman_chr6.simHuman.chr6 481343 33 + 601863 ATTCCAGACCACTCCTATGAAGAGAAATTGGTT -s simMouse_chr6.simMouse.chr6 501280 33 + 636262 ATTGCAGACCATTCCAGTCAAGGAGAATCATTT -s simRat_chr6.simRat.chr6 512524 33 + 647215 GTTGCAGCCCACCCCAGCCAAGGAAAATCATTT - -a -s simMouse_chr6.simMouse.chr6 499926 92 + 636262 TTAAAGGAGTTAAAAATATACTTTGGTATTATTAAGATGATATGAGCAATACTTACCCTAGGACCCTGTTTGTGTGATTAGAATCCCATACT -s Anc0.Anc0refChr3 115410 36 + 222631 ACAAAATAGTTAAAAGTATACTCTGGTATC-TTTAGA------------------------------------------------------- -s Anc1.Anc1refChr6 149288 37 + 197743 ACAAAATAGTTAAAAGTATACTCTGGTATCTTTTAGA------------------------------------------------------- -s Anc2.Anc2refChr1 27560 36 + 142988 ACAAAATAGTTAAAAGTATACTCTGACATC-TTTAGA------------------------------------------------------- -s mr.mrrefChr3 53884 92 + 181027 TTAAAGGAGTTAAAAATATACTTTGGTATTATTAAGATGATATGAGCAATACTTACCCTAGGACCCTGTTTGTGTGATTAGAATCCCATACT -s simCow_chr6.simCow.chr6 484056 36 + 602619 ACACAATAGGTAGAAATATATGCTGACATC-TTTAGA------------------------------------------------------- -s simDog_chr6.simDog.chr6 474394 36 + 593897 ACCAAATTGTTAAGAGAATACTCACACATC-TTTAGA------------------------------------------------------- -s simHuman_chr6.simHuman.chr6 481382 37 + 601863 ACAAAATAGTTAAAAGTGTACACTGGTGTCCTTTTGA------------------------------------------------------- -s simMouse_chr6.simMouse.chr6 501313 92 + 636262 TTAAAGGAGTTAAAAATATACTTTGGTATTATTAAGATGATATGAGCAATACTTACCCTAGGACCCTGTTTGTGTGATTAGAATCCCATACT -s simRat_chr6.simRat.chr6 512557 92 + 647215 TCAAAGGAGTCAAAAATATACTCTGGTATTATTGAGATGATATAAGAAATGCCCACCCTAGGACCCTGTTTGTGTGATCAGAATCCCATACT - -a -s simMouse_chr6.simMouse.chr6 500018 304 + 636262 TAAAAGGTCTACCATTTGCAGATTTAAGGTAAGTGCCTAAGTTGAGACAGTatggctgttaaaaattagtctcccagctatccaattacttgatgtttgagcaaaatccttcagtgggctatgagtttgaacttgaccctttaggcccagagttcattattcaataaatgatactggaggaaccgggttatctgtccatcgagagtttaaatttgatactttttcttaaacacccgatgtgttttatactaagattaagaccatatgcaagcgcactaaagatgtaaattcttggtcctcaaag -s mr.mrrefChr3 53976 304 + 181027 TAAAAGGTCTACCATTTGCAGATTTAAGGTAAGTGCCTAAGTTGAGACAGTatggctgttaaaaattagtctcccagctatccaattacttgatgtttgagcaaaatccttcagtgggctatgagtttgaacttgaccctttaggcccagagttcattattcaataaatgatactggaggaaccgggttatctgtccatcaagagtttaaatttgatactttttcttaaacacccgatgtgttttatactaagattaagaccatatgcaagcggactaaagatgtaaattcttgttcctcaaag -s simMouse_chr6.simMouse.chr6 501405 304 + 636262 TAAAAGGTCTACCATTTGCAGATTTAAGGTAAGTGCCTAAGTTGAGACAGTatggctgttaaaaattagtctcccagctatccaattacttgatgtttgagcaaaatcctttagtgggctatgagtttgaacttgaccctttaggcccagagttcattattcaataaatgatactgggggaaccgggttatctgtccatcaatagtttaaatttgatactttttcttaaacacccgatgtgttttatactaagattaagaccatatgcaagcggactaaagatgtaaattcttgttcctcaaag -s simRat_chr6.simRat.chr6 512650 300 + 647215 GAAGACATCGACCATTTGCGGAGTTAAGGAAAGTGCCTAAGTCGAGACAACATGGCTGTTGAAGTTCAGTCTcccaactattcaattacttgatgtttaaggaaaatccttcagtgggctatgagtttgaacgtgaccctt-gggcccaaagtgcattatccaataaatgatgctggtggaactgg-ttatctatccaccaacagtttaaatttgctccttt--cttatacaccctatatgttttataccgagattaagaccatgtgcaagtggactaaagatgcgaattcttgttcctcaaag - -a -s simMouse_chr6.simMouse.chr6 500322 7 + 636262 agtaaaa -s mr.mrrefChr3 54280 7 + 181027 agtaaaa -s simMouse_chr6.simMouse.chr6 501709 7 + 636262 agtaaaa -s simRat_chr6.simRat.chr6 512952 7 + 647215 agtaaaa - -a -s simMouse_chr6.simMouse.chr6 500329 19 + 636262 ggacagaagaattgtctat -s mr.mrrefChr3 54287 19 + 181027 ggacagaagaattgtctat -s simMouse_chr6.simMouse.chr6 501716 19 + 636262 ggacagaagaattgtctat -s simRat_chr6.simRat.chr6 512999 19 + 647215 ggacagaagaattgcctac - -a -s simMouse_chr6.simMouse.chr6 500348 26 + 636262 cctgaagccgtcaaaatcaatggcag -s mr.mrrefChr3 54306 26 + 181027 cctgaagctgtcaaaatcaatggcag -s simMouse_chr6.simMouse.chr6 501735 26 + 636262 cctgaagctgtcaaaatcaatggcag -s simRat_chr6.simRat.chr6 513020 26 + 647215 actgaagatgccaaagtcaaaggcag - -a -s simMouse_chr6.simMouse.chr6 500374 75 + 636262 ttaaacccacaatccacaagaatgtgaatgtacacatttaaagacgccatgtaggttacaagaagagaagtctTG -s mr.mrrefChr3 54332 75 + 181027 ttaaacccacaatccacaagaatgtgaatgtacacatttaaagacgccatgtaggttacaagaagagaagtctTG -s simMouse_chr6.simMouse.chr6 501761 75 + 636262 ttaaacccacaatccacgagaatgtgaatgtacacatttaaagacgccatgtaggttacaagaagagaagtctTG -s simRat_chr6.simRat.chr6 513047 75 + 647215 ttcaacccataatccacaagaatgtgaatgtacacaatcaaagaggccatgtgtattacaagaagagaagtctTG - -a -s simMouse_chr6.simMouse.chr6 500449 88 + 636262 AAAGCATATTGTAAGATAAGATGTGCCCAGTGCCCAATTATCTTTTGGGTTTTAATCACTGTGATGGATGCGCTGTGACACTGGTCGC -s Anc0.Anc0refChr3 115446 56 + 222631 ----------GTAACATGACATGTGCCCAGTG-------ATCTTTTAGATTTTTATCAGTCTACTAGAT---------------TTAC -s Anc1.Anc1refChr6 149325 56 + 197743 ----------GTAACATGACATGTGCCCAGTG-------ATCTTTTAGATTTTTATCAGTCTACTAGAT---------------TTAC -s Anc2.Anc2refChr1 27596 56 + 142988 ----------TTAACATGACATGTGCCCAGTG-------ATCTTTTAGATTTTTGTCAGTCTACTAGAT---------------TTAC -s mr.mrrefChr3 54407 73 + 181027 AAAGCATATTGTAAGATAAGATGTGCCCAGTGCCCAATTATCTTTTGGGTTTTAATCACTGTGATGGAT---------------TCGC -s simCow_chr6.simCow.chr6 484092 49 + 602619 -----------TAGCATGAGATGTGGCCAGTG-------ATCTTTTAG------CTCCGTCTACTTGAT---------------TTAC -s simDog_chr6.simDog.chr6 474430 56 + 593897 ----------TTAACATGACATGTGCCCGGTC-------CTCTTTTACATTTTTGTCAGCCTACTAGGT---------------TTAC -s simHuman_chr6.simHuman.chr6 481419 56 + 601863 ----------GAAAAATGACATGTGTCCAGTG-------ATCTTTTAGATTTTTATCAGTCTACTAGAT---------------TTAT -s simMouse_chr6.simMouse.chr6 501836 73 + 636262 AAAGCATATTGTAAGATAAGATGTGCCCAGTGCCCAATTATCTTTTGGGTTTTAATCACTGTGATGGAT---------------TCGC -s simRat_chr6.simRat.chr6 513127 44 + 647215 AAAGCATATTGCAAGGTA------------TGCCCAGTCATCTTTTGGGGATT--------------------------------TGC - -a -s simMouse_chr6.simMouse.chr6 500537 41 + 636262 TGTGACACTGGTCTGAATGCATCTACCTCTGAGGAAACAAA -s Anc0.Anc0refChr3 115503 41 + 222631 TGTAGCACCAGTCTGTATGGTTCTACTTTCATGGAGAGAAA -s Anc1.Anc1refChr6 149382 41 + 197743 TGTAGCACCAGTCTGTATGGTTCTACTTTCATGGAGAGAAA -s Anc2.Anc2refChr1 27653 41 + 142988 TGTAGCACCAGTCTGTATGGTTCTACTTTCATGGGGAGAAA -s mr.mrrefChr3 54480 41 + 181027 TGTGACACTGGTCTGAATGCATCTACCTCTGAGGAAACAAA -s simCow_chr6.simCow.chr6 484142 39 + 602619 CGTAG-AGCAGTCTTTATGGTTCTA-TATCATGAGGGGAGA -s simDog_chr6.simDog.chr6 474487 41 + 593897 TACAGCACCAGTCTGTATGGTACTACTTTCATGGGGAGAAA -s simHuman_chr6.simHuman.chr6 481476 37 + 601863 TGTAGCACCAGT----ATGGTTCTACTTTCATGGAGAGAAA -s simMouse_chr6.simMouse.chr6 501909 41 + 636262 TGTGACACTGGTCTGAATGCATCTACCTCTGAGGAAACAAA -s simRat_chr6.simRat.chr6 513171 41 + 647215 TGTAACACCGATCTGACTGTTTCAACCTTTGTGGAAAAGAA - -a -s simMouse_chr6.simMouse.chr6 500578 42 + 636262 GTTATTGTTGCATAAATAGTTAATTGACCCTACTTTTTGACC -s Anc0.Anc0refChr3 115546 42 + 222631 GTTATTGCAACACAATTAGTTACTTGACTCCAGTTCTTGAGT -s Anc1.Anc1refChr6 149425 42 + 197743 GTTATTGCAACACAATTAGTTACTTGACTCCAGTTCTTGAGT -s Anc2.Anc2refChr1 27696 42 + 142988 AATATTGCAACACAATTAGTTACTTGACTCCAGTTCTTGAGT -s mr.mrrefChr3 54523 42 + 181027 GTTATTGTTGCATAAATAGTTAATTGACCCTACTTTTTGACC -s simCow_chr6.simCow.chr6 484183 42 + 602619 AATATTGCAACACAAACAGGAACTTGACCCCAGTTCTTGAGT -s simDog_chr6.simDog.chr6 474530 42 + 593897 AATGTTGCAACACACTTAGTTGCTTGATTCCATTTCTTGAGA -s simHuman_chr6.simHuman.chr6 481515 42 + 601863 GTTATTGCAACACGATTAGCTACTTGCCTCCAGTTCTTGGGT -s simMouse_chr6.simMouse.chr6 501950 42 + 636262 GTTATTGTTGCATAAATAGTTAATTGACCCTACTTTTTGACC -s simRat_chr6.simRat.chr6 513214 40 + 647215 GTTGTCATTGCACA--TCGTTAATTGACTCTAGTTTTTGAGC - -a -s simMouse_chr6.simMouse.chr6 500620 3 + 636262 CTA -s Anc0.Anc0refChr3 115588 3 + 222631 TTA -s Anc1.Anc1refChr6 149467 3 + 197743 TTA -s Anc2.Anc2refChr1 27738 3 + 142988 TTA -s mr.mrrefChr3 54565 3 + 181027 CTA -s simCow_chr6.simCow.chr6 484226 3 + 602619 TTA -s simDog_chr6.simDog.chr6 474572 3 + 593897 CTA -s simHuman_chr6.simHuman.chr6 481557 3 + 601863 TTA -s simMouse_chr6.simMouse.chr6 501992 3 + 636262 CTA -s simRat_chr6.simRat.chr6 513254 3 + 647215 TTA - -a -s simMouse_chr6.simMouse.chr6 500623 15 + 636262 GCCACCTTAGTTATC -s Anc0.Anc0refChr3 115591 15 + 222631 GCTACTTCAATTATC -s Anc1.Anc1refChr6 149470 15 + 197743 GCTACTTCAATTATC -s Anc2.Anc2refChr1 27741 15 + 142988 GCTACTTCAATTATC -s mr.mrrefChr3 54568 15 + 181027 GCTACCTTAGTTATC -s simCow_chr6.simCow.chr6 484230 15 + 602619 ACAACTGCAACTATC -s simDog_chr6.simDog.chr6 474575 15 + 593897 GCTACTTCAATCATC -s simHuman_chr6.simHuman.chr6 481560 13 + 601863 G--ACTTCCATTATC -s simMouse_chr6.simMouse.chr6 501995 15 + 636262 GCTACCTTGGTTATC -s simRat_chr6.simRat.chr6 513257 15 + 647215 GCTACCTTAGTTATT - -a -s simMouse_chr6.simMouse.chr6 500638 30 + 636262 CATAGCTTTTAATAGCATGAGTCAAGAATC -s Anc0.Anc0refChr3 115606 30 + 222631 AGTACCTCCTAATAGCATGAGTCAATACCC -s Anc1.Anc1refChr6 149485 30 + 197743 AGTACCTCCTAATAGCATGAGTCAATACCC -s Anc2.Anc2refChr1 27756 30 + 142988 AGTACCTCCTGATAGCATGAGTCAATACCC -s mr.mrrefChr3 54583 30 + 181027 CATAGCTTTTAATAGCATGAGTCAAGAATC -s simCow_chr6.simCow.chr6 484245 30 + 602619 TGTACCTCCTTATGGCATGAGTCAATAGCC -s simDog_chr6.simDog.chr6 474592 30 + 593897 AGTACCTCAAGATAGCAGGAGTCAATACCC -s simHuman_chr6.simHuman.chr6 481573 30 + 601863 GGTACCTCCTAGTAGCATAAATGAATACCC -s simMouse_chr6.simMouse.chr6 502010 30 + 636262 CATAGCTTTTAATAGCATGAGTCAAGAATC -s simRat_chr6.simRat.chr6 513272 30 + 647215 CATACCTTTCAATAGCATGAGTCAAGAACT - -a -s simMouse_chr6.simMouse.chr6 500668 35 + 636262 GGGGGTTATTTGGGATGGAAGTAGTTGGTTTCAGA -s Anc0.Anc0refChr3 115643 35 + 222631 GGGGTTTACTTGAGATGAAAGTAGTTGGTTTCAGA -s Anc1.Anc1refChr6 149522 35 + 197743 GGGGTTTACTTGAGATGAAAGTAGTTGGTTTCAGA -s Anc2.Anc2refChr1 27793 35 + 142988 GGGGTTTACTCGAGAGGAAAGTAGTCCGTTTCAGA -s mr.mrrefChr3 54613 35 + 181027 GGGGGTTATTTGGGATGGAAGTAGTTGGTTTCAGA -s simCow_chr6.simCow.chr6 484279 34 + 602619 GAGG-TTACTCAAGAGGAAAGTAATCCAATCCAGA -s simDog_chr6.simDog.chr6 474629 33 + 593897 GGGGTCTACCCGGGAGGAAAGTAGT--GTTTCAGG -s simHuman_chr6.simHuman.chr6 481618 34 + 601863 GTGGATTACTT-ACATGAAAGTGGTTGGTTTAAGA -s simMouse_chr6.simMouse.chr6 502040 35 + 636262 AGGGGTTATTTGGGATGGAAGTAGTTGGTTTCAGA -s simRat_chr6.simRat.chr6 513302 35 + 647215 GGGGGTTATTCAGGGTGAAAGTACTAGGTTTCTGA - -a -s simMouse_chr6.simMouse.chr6 500703 25 + 636262 TCCTATGGCAAAAAAGTAAGGTGTG -s Anc0.Anc0refChr3 115678 25 + 222631 TCTTACAGCAAAAAAGTAAGGGGTG -s Anc1.Anc1refChr6 149557 25 + 197743 TCTTACAGCAAAAAAGTAAGGGGTG -s Anc2.Anc2refChr1 27828 25 + 142988 TCTTACAGCAGAAAAGTAGGGGGTG -s mr.mrrefChr3 54648 25 + 181027 TCCTATGGCAAAAAAGTAAGGTGTG -s simCow_chr6.simCow.chr6 484314 25 + 602619 TCATAGGGCAGAAGAGTAGGGGGTG -s simDog_chr6.simDog.chr6 474662 25 + 593897 TCTTACAGCAGAAAAGTAGGGGGTG -s simHuman_chr6.simHuman.chr6 481652 25 + 601863 TCTTACAGCAAAACAGTAAGGGGTG -s simMouse_chr6.simMouse.chr6 502075 25 + 636262 TCCTATGGCAAAAAAGTAAGGTGTG -s simRat_chr6.simRat.chr6 513337 11 + 647215 TCCTAAGCCAA-------------- - -a -s simMouse_chr6.simMouse.chr6 500728 17 + 636262 GGAGCCGCAATGTATGT -s Anc0.Anc0refChr3 115703 17 + 222631 GAAGCTGCACTGTATGT -s Anc1.Anc1refChr6 149582 17 + 197743 GAAGCTGCACTGTATGT -s Anc2.Anc2refChr1 27853 17 + 142988 GAAACTGCACTGTATGT -s mr.mrrefChr3 54673 17 + 181027 GGAGCCGCAATGTATGT -s simCow_chr6.simCow.chr6 484339 17 + 602619 GAAACTGCATTGCATGT -s simDog_chr6.simDog.chr6 474689 12 + 593897 GAA-----ACTGTGACT -s simHuman_chr6.simHuman.chr6 481677 17 + 601863 GAAGCTGCACTGTATGT -s simMouse_chr6.simMouse.chr6 502100 17 + 636262 GGAGCCGCAATGTATGT - -a -s simMouse_chr6.simMouse.chr6 500745 50 + 636262 TAGGCGCCACCCAAATCTACCGTGTGCCACATACAGCATGACAACTATTG -s Anc0.Anc0refChr3 115720 24 + 222631 TACTT--------------------------TGCTGCAAAGCAATTATCA -s Anc1.Anc1refChr6 149599 38 + 197743 TACTTGGTGCCTAAATATA------------TGCTGCAAAGCAATTATCA -s Anc2.Anc2refChr1 27870 24 + 142988 TACTT--------------------------TGCTGCAAAGCAATTATCA -s mr.mrrefChr3 54690 50 + 181027 TAGGTGCCACCCAAATCTACCGTGTGCCACATACAGCATGACAACTATTG -s simCow_chr6.simCow.chr6 484383 24 + 602619 TACCT--------------------------TGCTGGGAAACCATTGTCA -s simDog_chr6.simDog.chr6 474701 24 + 593897 TACTT--------------------------TGCTGCAAAGCAATTATCA -s simHuman_chr6.simHuman.chr6 481694 19 + 601863 TACATGGTGCCTAAATATA------------------------------- -s simMouse_chr6.simMouse.chr6 502117 50 + 636262 TAGGTGCCACCCAAATCTACTGTGTGCCACATACAGCATGACAACTATTG -s simRat_chr6.simRat.chr6 513348 44 + 647215 ------TCGCCCAAGTCTGCCTTGTGTCACATGCTGCATGACAAGTATTG - -a -s simMouse_chr6.simMouse.chr6 500795 21 + 636262 AATAGCAACACAACTTCACCA -s Anc0.Anc0refChr3 115744 21 + 222631 AATATCCACACATTTCCACCA -s Anc1.Anc1refChr6 149637 21 + 197743 AATATCCACACATTTCCACCA -s Anc2.Anc2refChr1 27897 21 + 142988 AATATCCACACATTTCCACCA -s mr.mrrefChr3 54740 21 + 181027 AATAGCAACACAACTTCACCA -s simCow_chr6.simCow.chr6 484415 21 + 602619 AGCTTCCACACATCTCCAGCA -s simDog_chr6.simDog.chr6 474728 21 + 593897 AATATCCACACATTTCCACCA -s simMouse_chr6.simMouse.chr6 502167 21 + 636262 AATAGCAACACAACTTCACCA -s simRat_chr6.simRat.chr6 513392 21 + 647215 AATATCAACACATCTCCACCA - -a -s simMouse_chr6.simMouse.chr6 500816 25 + 636262 AGTCCACTGTGGGTCCAACAGAGTG -s Anc0.Anc0refChr3 115765 23 + 222631 AGTCAACTGTCAGTCAAATAAA--T -s Anc1.Anc1refChr6 149658 23 + 197743 AGTCAACTGTCAGTCAAATAAA--T -s Anc2.Anc2refChr1 27919 23 + 142988 AGTCAACTGTCAGTCAAATAAA--T -s mr.mrrefChr3 54761 25 + 181027 AGTCCACTGTGGGTCCAACAGAGTG -s simCow_chr6.simCow.chr6 484437 23 + 602619 AGTCAACTGTCAGTTAAATAGA--T -s simDog_chr6.simDog.chr6 474750 23 + 593897 AGTCAACTGTCAGTCAAATAAA--T -s simMouse_chr6.simMouse.chr6 502188 25 + 636262 AGTCCACTGTGGGTCCAACAGAGTG -s simRat_chr6.simRat.chr6 513414 25 + 647215 AGTCCACTGTGGGTTCACCACAGTG - -a -s simMouse_chr6.simMouse.chr6 500841 15 + 636262 TAATACTCCCCACAA -s Anc0.Anc0refChr3 115788 15 + 222631 TAATACTCATTCAAC -s Anc1.Anc1refChr6 149681 15 + 197743 TAATACTCATTCAAC -s Anc2.Anc2refChr1 27942 15 + 142988 TAATACTCATTCAAC -s mr.mrrefChr3 54786 15 + 181027 TAATACTCCCCACAA -s simCow_chr6.simCow.chr6 484460 15 + 602619 CAGTACTCCCTCAAC -s simDog_chr6.simDog.chr6 474774 15 + 593897 TAATACTCATTCAAC -s simMouse_chr6.simMouse.chr6 502213 15 + 636262 TAATACTCCCCACAA -s simRat_chr6.simRat.chr6 513439 15 + 647215 TAATACTCCCCGCAA - -a -s simMouse_chr6.simMouse.chr6 500856 19 + 636262 CAGTTTTAGGGACCATCCA -s Anc0.Anc0refChr3 115803 19 + 222631 GTATTTTAGATCTCTAACA -s Anc1.Anc1refChr6 149696 19 + 197743 GTATTTTAGATCTCTAACA -s Anc2.Anc2refChr1 27957 19 + 142988 GTATTTTAGATCTCTAACA -s mr.mrrefChr3 54801 19 + 181027 CAGTTTTAGGGACCATCCA -s simCow_chr6.simCow.chr6 484475 19 + 602619 ATGTGTTAGGTCTCCAACA -s simDog_chr6.simDog.chr6 474793 19 + 593897 GTATTTTAGATCTCTAACA -s simMouse_chr6.simMouse.chr6 502228 19 + 636262 CAGTTTTAGGGACCATCCA -s simRat_chr6.simRat.chr6 513454 19 + 647215 GAGTTTGAGAGACCATCCA - -a -s simMouse_chr6.simMouse.chr6 500875 15 + 636262 CTTTCAAGAGCAAAA -s Anc0.Anc0refChr3 115822 14 + 222631 CTCTCCAGTGC-AAA -s Anc1.Anc1refChr6 149715 14 + 197743 CTCTCCAGTGC-AAA -s Anc2.Anc2refChr1 27976 14 + 142988 CTCTCCAGTGC-AAA -s mr.mrrefChr3 54820 15 + 181027 CTTTCAAGTGCAAAA -s simCow_chr6.simCow.chr6 484495 14 + 602619 TTCTCCAGTGC-ATC -s simDog_chr6.simDog.chr6 474812 14 + 593897 CTCTCCAGTGC-AAA -s simMouse_chr6.simMouse.chr6 502247 15 + 636262 CTTTCAAGTGCAAAA -s simRat_chr6.simRat.chr6 513473 15 + 647215 CTTTCTAGTGCGAAA - -a -s simMouse_chr6.simMouse.chr6 500890 19 + 636262 TGTGGAAGGATGTCTCAAG -s Anc0.Anc0refChr3 115836 19 + 222631 TGTGGAATGCTGTCTCATT -s Anc1.Anc1refChr6 149729 19 + 197743 TGTGGAATGCTGTCTCATT -s Anc2.Anc2refChr1 27990 19 + 142988 TGTGGAATGCTGTCTCATT -s mr.mrrefChr3 54835 19 + 181027 TGTGGAAGGATGTCTCAAT -s simCow_chr6.simCow.chr6 484509 19 + 602619 TGAGGGATGATGTTGCATT -s simDog_chr6.simDog.chr6 474827 19 + 593897 TGTGGAATGCTGTCTCATT -s simMouse_chr6.simMouse.chr6 502262 19 + 636262 TGTGGAAGGATGTCTCAAT -s simRat_chr6.simRat.chr6 513488 19 + 647215 CGTGGAAGGATGTCTCAAT - -a -s simMouse_chr6.simMouse.chr6 502281 7 + 636262 ACCATCT -s Anc0.Anc0refChr3 115855 2 + 222631 AC----- -s Anc1.Anc1refChr6 149748 2 + 197743 AC----- -s Anc2.Anc2refChr1 28009 2 + 142988 AC----- -s mr.mrrefChr3 54854 7 + 181027 ACTGTCT -s simCow_chr6.simCow.chr6 484528 2 + 602619 AC----- -s simDog_chr6.simDog.chr6 474846 2 + 593897 AC----- -s simRat_chr6.simRat.chr6 513507 7 + 647215 ACTGTCT - -a -s simMouse_chr6.simMouse.chr6 502288 14 + 636262 TACCCTCTTCTCCC -s Anc0.Anc0refChr3 115857 13 + 222631 CACTCT-TTCCCCA -s Anc1.Anc1refChr6 149750 13 + 197743 CACTCT-TTCCCCA -s Anc2.Anc2refChr1 28011 13 + 142988 CACTCT-TTCCCCA -s mr.mrrefChr3 54861 13 + 181027 TACCCT-TTCTCCC -s simCow_chr6.simCow.chr6 484530 13 + 602619 TGCCTT-TCCTTCA -s simDog_chr6.simDog.chr6 474849 13 + 593897 CACTCT-TTCCCCA -s simRat_chr6.simRat.chr6 513514 13 + 647215 TACCCT-TCCTCTC - -a -s simMouse_chr6.simMouse.chr6 502302 9 + 636262 ATGAAAACA -s Anc0.Anc0refChr3 115870 6 + 222631 AGA---ACA -s Anc1.Anc1refChr6 149763 6 + 197743 AGA---ACA -s Anc2.Anc2refChr1 28029 6 + 142988 AGA---ACA -s mr.mrrefChr3 54874 6 + 181027 ATG---ACA -s simCow_chr6.simCow.chr6 484552 6 + 602619 AAT---ACA -s simDog_chr6.simDog.chr6 474867 6 + 593897 AGA---ACA -s simRat_chr6.simRat.chr6 513527 6 + 647215 ATG---ACA - -a -s simMouse_chr6.simMouse.chr6 502311 116 + 636262 TTTTTGTCCACCTCCATGTGCTATTAACTATGTCAGCACTTATCATCAGATACATACTTCTAGTGGAGTTATACTGGATTCTAATATTTATAGGGGAGTTTAATATTGCTAATTTC -s Anc0.Anc0refChr3 115876 89 + 222631 TTTTTGTCGACTT----------TAAAATATATAGGAAA--AATTTCTAACATAGAGTTGAAGGTGATTTCTGCTGGCCCCCTTG--GTACAGGAGA-------------AGTTTC -s Anc1.Anc1refChr6 149769 91 + 197743 TTTTTGTCGACTT----------TAAAATATATAGGAAA--AATTTCTAACATAGAGTTGAAGGTGATTTCTGCTGGCCCCCTTGGTGTACAGGAGA-------------AGTTTC -s Anc2.Anc2refChr1 28037 89 + 142988 TTTTTGTCGACTT----------TAAAATATATAGGAAA--AATTTCTAACATAGAGTTGAAGGTAATTTCTGCTGGCCCCCTTG--GTACAGGAGA-------------AGTTTC -s mr.mrrefChr3 54880 116 + 181027 TTTTTGTCCACCTCCATGTGCTATTAACTATGTCAGCACTTATCATCAGATACATACTTCTAGTGGAGTTATACTGGATTCTAATATTTATAGGGGAGTTTAATATTGCTAATTTC -s simCow_chr6.simCow.chr6 484560 89 + 602619 TTTTTGTGGACTT----------CAAAATGTATAGGAAC--AACATCTGCCATTGAGTGCACGGTAATTCCTGCCAGCCCCCTTG--GTACAGGACC-------------AGTTTC -s simDog_chr6.simDog.chr6 474875 89 + 593897 TTTTTGTCGACTT----------TAAAATATATAGGAAA--AATTTCTAACATAGAGTTGAAGGTAATTTCTGCTGGCTCCCTTG--GTACAGGAGA-------------AGTTTG -s simHuman_chr6.simHuman.chr6 481713 44 + 601863 ----------------------------------------------------------TAAGAGTGATTTCTG-TGGCCCCCTTGGTGTACAGGAGA-------------AGCTTC -s simRat_chr6.simRat.chr6 513533 116 + 647215 TTTTTGTCCACCTCTATGTGCTATCAGCTATGTCAGCACTTATCATCAGATACACACTCCTGGTGGAGTTATACTGTATTCTAATCTTTATGGGGGAGTTTAATATTGCTAATTCC - -a -s simMouse_chr6.simMouse.chr6 502427 18 + 636262 TATTGGCCCTGGGTGTGA -s Anc0.Anc0refChr3 115968 17 + 222631 CATTGG-GCTGAGTGTGA -s Anc1.Anc1refChr6 149863 17 + 197743 CATTGG-GCTGAGTGTGA -s Anc2.Anc2refChr1 28129 17 + 142988 CATTGG-GCTGAGTGTGA -s mr.mrrefChr3 54996 18 + 181027 TATTGGCCCTGAGTGTGA -s simCow_chr6.simCow.chr6 484652 17 + 602619 CATTGG-GTTGAATGTGA -s simDog_chr6.simDog.chr6 474967 17 + 593897 CATTGA-GCTAAGTGTGG -s simHuman_chr6.simHuman.chr6 481760 17 + 601863 CATTGG-GCTGATTGTGA -s simRat_chr6.simRat.chr6 513649 18 + 647215 TATTGGACCTGAGAGTGA - -a -s simMouse_chr6.simMouse.chr6 502445 5 + 636262 GTTCT -s Anc0.Anc0refChr3 115985 5 + 222631 TTTCT -s Anc1.Anc1refChr6 149880 5 + 197743 TTTCT -s Anc2.Anc2refChr1 28146 5 + 142988 TTCCT -s mr.mrrefChr3 55014 5 + 181027 TTTCT -s simCow_chr6.simCow.chr6 484669 5 + 602619 TTCGG -s simDog_chr6.simDog.chr6 474985 5 + 593897 TTCCT -s simHuman_chr6.simHuman.chr6 481777 5 + 601863 TTTCT -s simRat_chr6.simRat.chr6 513667 5 + 647215 TTTCT - -a -s simMouse_chr6.simMouse.chr6 502450 68 + 636262 CTGACCCCCTTGGTGCCCACTTAGTATGCTACTAAATAAAGAGGCTGAGAGACAGCTCAATGTGATTT -s Anc0.Anc0refChr3 115991 53 + 222631 CTGGCCCCCCCGGTGCTTACTAAAT---------------GAGGCTGAGAGACAGCTGGATATGATTC -s Anc1.Anc1refChr6 149886 53 + 197743 CTGGCCCCCCCGGTGCTTACTAAAT---------------GAGGCTGAGAGACAGCTGGATATGATTC -s Anc2.Anc2refChr1 28152 53 + 142988 CTGGTCCCCCCGGTGCTTACTAAAT---------------GAGGCTGAGGGTCAGCTGGATAAGATTC -s mr.mrrefChr3 55019 68 + 181027 CTGGCCCCCTTGGTGCCCACTTAGTATGCTACTAAATAAAGAGGCTGAGAGACAGCTCGATGTGATTT -s simCow_chr6.simCow.chr6 484675 39 + 602619 CTGGTCCTCTCGGTTCTTATTT---------------------------GGTCAAT--GATAAGATTC -s simDog_chr6.simDog.chr6 474991 50 + 593897 CTGG---CCCTGGTGCTTACTAAAT---------------GAGGCTGAGGGTCAGCTGGATAAAATTC -s simHuman_chr6.simHuman.chr6 481783 53 + 601863 CTGGCACCCCCAGTGCTTCCTGAAT---------------GAGACTGAGAGACAGCTGGATATGACTC -s simRat_chr6.simRat.chr6 513672 68 + 647215 CTGGCTCCCTTGGTGCCCACTTAGTATGCTACTAAATACATAGGCTGAGAGACAGCTCGATGAGATTT - -a -s simMouse_chr6.simMouse.chr6 502518 21 + 636262 GGCCCTCAATAAGTCTTCTTT -s Anc0.Anc0refChr3 116044 21 + 222631 ACACCTCAGTAAATCTCCTTT -s Anc1.Anc1refChr6 149939 21 + 197743 ACACCTCAGTAAATCTCCTTT -s Anc2.Anc2refChr1 28205 21 + 142988 ACACCTCAGGAAATCTCCTTT -s mr.mrrefChr3 55087 21 + 181027 GGACCTCAATAAGTCTTCTTT -s simCow_chr6.simCow.chr6 484714 21 + 602619 AAACTTTAAGAAATCTCCCTT -s simDog_chr6.simDog.chr6 475043 21 + 593897 CCACCTCAGGAGATCTCTTTT -s simHuman_chr6.simHuman.chr6 481836 21 + 601863 ATACCTCAGTAAATCTCCTTT -s simRat_chr6.simRat.chr6 513740 21 + 647215 GGACCTCAATAAGTCTTCTTT - -a -s simMouse_chr6.simMouse.chr6 502539 12 + 636262 GTTTGCATAGTC -s Anc0.Anc0refChr3 116066 12 + 222631 GTGTGCTCAGTG -s Anc1.Anc1refChr6 149961 12 + 197743 GTGTGCTCAGTG -s Anc2.Anc2refChr1 28227 12 + 142988 GTGTGCTCAGTG -s mr.mrrefChr3 55108 12 + 181027 GTTTGCATAGTC -s simCow_chr6.simCow.chr6 484736 10 + 602619 GTGTGCTCAG-- -s simDog_chr6.simDog.chr6 475065 12 + 593897 GTGCGCTAAGTG -s simHuman_chr6.simHuman.chr6 481858 12 + 601863 ATGTATTCAGTG -s simRat_chr6.simRat.chr6 513761 12 + 647215 GTTTGCATAGTC - -a -s simMouse_chr6.simMouse.chr6 502551 49 + 636262 GTTAATAACTCTCTCGTCACATTGTTGCCATCAGTATCCACCAGTAATC -s Anc0.Anc0refChr3 116078 41 + 222631 CTTCAGGACTCTCTCACCCCATTGCTGCTCAC--------CCAGTATTT -s Anc1.Anc1refChr6 149973 41 + 197743 CTTCAGGACTCTCTCACCCCATTGCTGCTCAC--------CCAGTATTT -s Anc2.Anc2refChr1 28239 41 + 142988 CTTCAGGACTCTCTCATCCCATTACTGCTCAC--------CTAGTATTT -s mr.mrrefChr3 55120 41 + 181027 GTTAATAACTCTCTCACCACATTGTTGCCATC--------CCAGTAATC -s simCow_chr6.simCow.chr6 484746 30 + 602619 -----------TCTCATCCCATTACTGCTCAT--------CTGGTATTG -s simDog_chr6.simDog.chr6 475089 41 + 593897 CTTCAGGACTCTCTCATCCCATTAATGTTCAC--------CTAGTATTT -s simHuman_chr6.simHuman.chr6 481870 41 + 601863 CTTCAGGACTCTCTCACCCTATTGCTGCTCAC--------CCAGTAGTT -s simRat_chr6.simRat.chr6 513773 41 + 647215 TCTAATAACTCTCCCACCACGTTGTTTCCACC--------CCAGTATTC - -a -s simMouse_chr6.simMouse.chr6 502600 9 + 636262 TATTGCAGC -s Anc0.Anc0refChr3 116147 9 + 222631 TCCTGCAAC -s Anc1.Anc1refChr6 150042 9 + 197743 TCCTGCAAC -s Anc2.Anc2refChr1 28308 9 + 142988 TCTTGCAAC -s mr.mrrefChr3 55161 9 + 181027 TACTGCAGC -s simCow_chr6.simCow.chr6 484804 9 + 602619 TCTTGCATC -s simDog_chr6.simDog.chr6 475158 9 + 593897 TCTTGTTAC -s simHuman_chr6.simHuman.chr6 481939 9 + 601863 TCCTGCAAC -s simRat_chr6.simRat.chr6 513814 9 + 647215 TGCTGCAGC - -a -s simMouse_chr6.simMouse.chr6 502609 4 + 636262 ATTG -s Anc0.Anc0refChr3 116172 4 + 222631 ATTG -s Anc1.Anc1refChr6 150067 4 + 197743 ATTG -s Anc2.Anc2refChr1 28334 4 + 142988 ATTG -s mr.mrrefChr3 55170 4 + 181027 ATTG -s simCow_chr6.simCow.chr6 484830 4 + 602619 ATTT -s simDog_chr6.simDog.chr6 475184 4 + 593897 ATTG -s simHuman_chr6.simHuman.chr6 481964 4 + 601863 ATGG -s simRat_chr6.simRat.chr6 513823 4 + 647215 ATTG - -a -s simMouse_chr6.simMouse.chr6 502613 18 + 636262 GGTAAATCTCGGTATGGA -s Anc0.Anc0refChr3 116176 18 + 222631 GGTACATGTTGATCTGGA -s Anc1.Anc1refChr6 150071 18 + 197743 GGTACATGTTGATCTGGA -s Anc2.Anc2refChr1 28385 18 + 142988 GGTACATGTTGATCTGGA -s mr.mrrefChr3 55174 18 + 181027 GGTAAATCTCGGTCTGGA -s simCow_chr6.simCow.chr6 484880 18 + 602619 GATACATGTTGATCTGGT -s simDog_chr6.simDog.chr6 475236 18 + 593897 GGTACATGTTGATCTGGA -s simHuman_chr6.simHuman.chr6 481968 18 + 601863 GATCCCTGTTGATCTAGA -s simRat_chr6.simRat.chr6 513827 18 + 647215 GGTAAATCTCGGTCTGGA - -a -s simMouse_chr6.simMouse.chr6 502631 77 + 636262 AGTGTCACAACTATTGGGATCCTAGTTAGAATGACTGGACGTTAACAGCTTCACCTGACTGTGCTTCACTGAGTTTG -s Anc0.Anc0refChr3 116194 76 + 222631 GGTGTCACAACAAATGGGATCAAGGTTAGGACCACTGAGTGTCCA-GGGCTAACCCAGGTGTGCTTTCCTGATTTTG -s Anc1.Anc1refChr6 150089 76 + 197743 GGTGTCACAACAAATGGGATCAAGGTTAGGACCACTGAGTGTCCA-GGGCTAACCCAGGTGTGCTTTCCTGATTTTG -s Anc2.Anc2refChr1 28403 76 + 142988 GGTGTCACAGCAAATGGGATCAAGGTTAGGACCACTGAGTGTCCA-GAGCTAACCCAGGTATGCTTTCCTGATTTTA -s mr.mrrefChr3 55192 77 + 181027 AGTGTCACAACTATTGGGATCATAGTTAGAATGACTGGATGTTAACAGCTTAACCTGACTGTGCTTTACTGAGTTTG -s simCow_chr6.simCow.chr6 484898 75 + 602619 GAGGTCACAGCAAATTGGATCAAGGTTAGGAACACTGAGTGTTCA-GAGCTAACCCGGGTATGCTTTCCTGCTTTC- -s simDog_chr6.simDog.chr6 475255 70 + 593897 GGTGTCACG------GCAAACAAGGTTAGGACCACTGAGTGTCCA-GAGCTAACCCAGGTAGGCTCTCCTAAATTTA -s simHuman_chr6.simHuman.chr6 481986 76 + 601863 TGTGTCACAATCTACGGGATCAGGGTTAGGACCACTGAGTGTACA-GGACTAACCCATGTGTGCTTTCCTGATTATG -s simRat_chr6.simRat.chr6 513845 77 + 647215 AGTATCACAACTATTAGGATCATAGTTAGAATGACTGGATGTTGATAGCTTACCATTACTGTGCTTTATCGAAGTTT - -a -s simMouse_chr6.simMouse.chr6 502708 21 + 636262 TATTTATTTATTCTCATCAAG -s Anc0.Anc0refChr3 116271 21 + 222631 TATTTATTTATTTGATTCCAG -s Anc1.Anc1refChr6 150166 21 + 197743 TATTTATTTATTTGATTCCAG -s Anc2.Anc2refChr1 28480 21 + 142988 TATTTATTTATTTGATTCCAG -s mr.mrrefChr3 55269 21 + 181027 TATTTATTTATTCAGATCAAG -s simCow_chr6.simCow.chr6 484974 21 + 602619 TGTCTAGTCGTTTGATTCCGG -s simDog_chr6.simDog.chr6 475326 21 + 593897 TATTTATTTATCTAATTCCAG -s simHuman_chr6.simHuman.chr6 482063 21 + 601863 TATTTATTTATTTGATTCCAG -s simRat_chr6.simRat.chr6 513922 21 + 647215 CTCCCATGGATACAGATTACC - -a -s simMouse_chr6.simMouse.chr6 502729 2 + 636262 GG -s Anc0.Anc0refChr3 116296 2 + 222631 GG -s Anc1.Anc1refChr6 150191 2 + 197743 GG -s Anc2.Anc2refChr1 28505 2 + 142988 GG -s mr.mrrefChr3 55290 2 + 181027 GG -s simCow_chr6.simCow.chr6 484999 2 + 602619 GG -s simDog_chr6.simDog.chr6 475351 2 + 593897 GG -s simHuman_chr6.simHuman.chr6 482088 2 + 601863 GG -s simRat_chr6.simRat.chr6 513943 2 + 647215 AG - -a -s simMouse_chr6.simMouse.chr6 502731 4 + 636262 CACC -s Anc0.Anc0refChr3 116298 4 + 222631 TTGC -s Anc1.Anc1refChr6 150193 4 + 197743 TTGC -s Anc2.Anc2refChr1 28546 4 + 142988 TTGC -s mr.mrrefChr3 55292 4 + 181027 TTTC -s simCow_chr6.simCow.chr6 485045 4 + 602619 TTGT -s simDog_chr6.simDog.chr6 475392 4 + 593897 TTGC -s simHuman_chr6.simHuman.chr6 482090 4 + 601863 TTGC -s simRat_chr6.simRat.chr6 513945 4 + 647215 TTTC - -a -s simMouse_chr6.simMouse.chr6 502735 68 + 636262 TAAGGGAATAGGTCTTGCCCTGGCTTGAGGAGCTAATTGAATTGTATTGTGGCACTTTAGATTGCTAG -s Anc0.Anc0refChr3 116308 57 + 222631 TA-----------CTTACCTTAGTTTGAGGGACTAATCAAATCTTATTTTGGCAGTTCAGATTGATGG -s Anc1.Anc1refChr6 150203 57 + 197743 TA-----------CTTACCTTAGTTTGAGGGACTAATCAAATCTTATTTTGGCAGTTCAGATTGATGG -s Anc2.Anc2refChr1 28556 57 + 142988 TA-----------CTTACCTTAGTTTGAGGGACTAATCAAGCCTTATTTTGGCAGTCCAGATTAATGG -s mr.mrrefChr3 55296 57 + 181027 CA-----------CTTACCCTGGCTTGAGGAGCTAATTGAATTGTATTGTGGCACTTTAGATTGCTAG -s simCow_chr6.simCow.chr6 485055 57 + 602619 CA-----------CTTACCTTGGTTTGAGTGACTAATCAGCCCTTATTGTGGCAGTGAAGATTCATGG -s simDog_chr6.simDog.chr6 475404 57 + 593897 TA-----------CTTACCGTAGTCTGAGGGCCGAGTTGAGCCTTATTTTGGCAAGCCAGATGAATTG -s simHuman_chr6.simHuman.chr6 482100 57 + 601863 GG-----------CTTACCTCAGTTTGAGGGACTAATCATATCTTATTATGGCAGTTGAGATTGACGG -s simRat_chr6.simRat.chr6 513949 57 + 647215 CA-----------CTTACCCTGGCTTGAGGAGCTAATTGAATTGTATCGTAGCACCTTAGATTGCTAG - -a -s simMouse_chr6.simMouse.chr6 502803 41 + 636262 AACTTCAAATAATCTGTCAAGACCAAGCTGGAAAAGGGAAG -s Anc0.Anc0refChr3 116365 41 + 222631 AACCTCAAAGGATCTACCAAGACAATACTTCTTAAAACAAG -s Anc1.Anc1refChr6 150260 41 + 197743 AACCTCAAAGGATCTACCAAGACAATACTTCTTAAAACAAG -s Anc2.Anc2refChr1 28620 41 + 142988 AACCTCAAAGGATCTACCAAGACAATTCTCCTTAAAACAAG -s mr.mrrefChr3 55353 41 + 181027 AACTTCAAAGAATCTGTCAAGACCATACTTGAAAAGGGAAG -s simCow_chr6.simCow.chr6 485119 38 + 602619 AACCTCACAGGATCTACCAAGACAC---TCCTTAGGATGCC -s simDog_chr6.simDog.chr6 475468 41 + 593897 AACTTCAAAGGATCTACCAAGACAATTCTCCTTAAAACAAG -s simHuman_chr6.simHuman.chr6 482157 41 + 601863 AACCTCAAAGGATCCACCAAGACTGTACTTATGAAATCAAG -s simRat_chr6.simRat.chr6 514006 41 + 647215 ATCTCCAAAGAATCTGTCAAGACCATACTTGAAAGGAGAGA - -a -s simMouse_chr6.simMouse.chr6 502844 8 + 636262 AGGGTGCT -s Anc0.Anc0refChr3 116408 8 + 222631 GCGGTGAA -s Anc1.Anc1refChr6 150303 8 + 197743 GCGGTGAA -s Anc2.Anc2refChr1 28663 8 + 142988 GCAATGAA -s mr.mrrefChr3 55394 8 + 181027 AGGGTGCA -s simCow_chr6.simCow.chr6 485159 5 + 602619 GCTAT--- -s simDog_chr6.simDog.chr6 475511 8 + 593897 ACAATGAA -s simHuman_chr6.simHuman.chr6 482200 8 + 601863 GAGGTCAA -s simRat_chr6.simRat.chr6 514047 8 + 647215 AGGGTGCA - -a -s simMouse_chr6.simMouse.chr6 502852 12 + 636262 GTATGCACCAAT -s Anc0.Anc0refChr3 116416 12 + 222631 GTAGTCATCAAG -s Anc1.Anc1refChr6 150311 12 + 197743 GTAGTCATCAAG -s Anc2.Anc2refChr1 28671 12 + 142988 GTAGTCATCACG -s mr.mrrefChr3 55402 12 + 181027 GTATGCACCAAT -s simCow_chr6.simCow.chr6 485164 5 + 602619 -------TCTCA -s simDog_chr6.simDog.chr6 475520 12 + 593897 GTAGTCATCACG -s simHuman_chr6.simHuman.chr6 482208 12 + 601863 GTACACATCAAG -s simRat_chr6.simRat.chr6 514055 12 + 647215 CTATGCACCGAT - -a -s simMouse_chr6.simMouse.chr6 502864 14 + 636262 CCATAGGTCAGTTA -s Anc0.Anc0refChr3 116428 14 + 222631 CCATAGCCCAATTT -s Anc1.Anc1refChr6 150323 14 + 197743 CCATAGCCCAATTT -s Anc2.Anc2refChr1 28683 14 + 142988 CCATAGCCCAATTT -s mr.mrrefChr3 55414 14 + 181027 CCATAAGTCAGTTA -s simCow_chr6.simCow.chr6 485169 14 + 602619 CCATAGCTCAATTT -s simDog_chr6.simDog.chr6 475544 14 + 593897 CCATAACCCAATTT -s simHuman_chr6.simHuman.chr6 482220 14 + 601863 CAATAGTCAGTTTT -s simRat_chr6.simRat.chr6 514067 14 + 647215 TCATAAGCAAATTA - -a -s simMouse_chr6.simMouse.chr6 502878 10 + 636262 ATGTATTTCT -s Anc0.Anc0refChr3 116442 9 + 222631 A-TTATATCC -s Anc1.Anc1refChr6 150337 9 + 197743 A-TTATATCC -s Anc2.Anc2refChr1 28697 9 + 142988 A-TTATATGC -s mr.mrrefChr3 55428 10 + 181027 ATGTATATCT -s simCow_chr6.simCow.chr6 485183 9 + 602619 A-TTATATGC -s simDog_chr6.simDog.chr6 475558 9 + 593897 A-TTACATGC -s simHuman_chr6.simHuman.chr6 482234 9 + 601863 A-TTATATCC -s simRat_chr6.simRat.chr6 514103 10 + 647215 ATGTATATCT - -a -s simMouse_chr6.simMouse.chr6 502888 87 + 636262 CATATAGAATACATGAATTCGCGAATGGAAGTCAAAAAATTAGGGGCAGTCCTGCACATCAAGGAATCCCACGAACTATGGGAACTA -s Anc0.Anc0refChr3 116451 71 + 222631 GCTGAAGAGTATCTGACTCTGGAAATGGAGGCTAATGAGTCAGG--------GGGGT--------CTCAAACAAACTATGGGAATTA -s Anc1.Anc1refChr6 150346 78 + 197743 GCTGAAGAGTATCTGACTCTGGAAATGGAGGCTAATGAGTCAGG--------GGGGTATC-AGGACTCAAACAAACTATGGGAATTA -s Anc2.Anc2refChr1 28711 71 + 142988 GCTGAAGAGTTTCCAACTTTGGAAATGGAGACTAATGAGTCAGG--------GCGGT--------CTCAAACAAACTTTGGGAATCA -s mr.mrrefChr3 55438 87 + 181027 CATATAGAATATATGACTCTGCAAATGGAAGTCAAAAAATTAGGGGCAGTCCTGCGCATCAAGGACTCCCACGAACTATGGGAACTA -s simCow_chr6.simCow.chr6 485197 70 + 602619 GCTGAAGAGTGTCCAACTTTGGAAACGGAAACTAATGAGTCAGG--------AAGGT--------C-CAAACAAATTCTGGGAATCA -s simDog_chr6.simDog.chr6 475572 66 + 593897 GTTGAAGAGCTTACAGCTTTGGAAGTGGAGAAT-----GTCAGG--------GCAGT--------CTCCAACAAACTTCAGGAATCA -s simHuman_chr6.simHuman.chr6 482243 78 + 601863 GCTCAAAAGTATCTGACTCTGTAAAGGGGGGCTAATTAGTAAGG--------CGGGTATC-AGGACTCAGACTAACTATGAGAAATA -s simRat_chr6.simRat.chr6 514113 87 + 647215 CTTGTAGAATATATGACTCTGCAAATGGAAGTCAAGAAATTAGGGGCAGTCCTGCGCATCAAGTACTCCCACAAACTATGGGAATTA - -a -s simMouse_chr6.simMouse.chr6 502975 13 + 636262 TGAGAGATGAGAG -s Anc0.Anc0refChr3 116523 11 + 222631 TGAGAAATGA--G -s Anc1.Anc1refChr6 150425 13 + 197743 TGAGAAATGAGGG -s Anc2.Anc2refChr1 28783 11 + 142988 TGAAAAATGA--G -s mr.mrrefChr3 55525 13 + 181027 TGAGAGATGAGAG -s simCow_chr6.simCow.chr6 485268 11 + 602619 TGACATATGC--G -s simDog_chr6.simDog.chr6 475639 11 + 593897 TGCAAAATGA--G -s simHuman_chr6.simHuman.chr6 482322 13 + 601863 TGAGAAATGAGGG -s simRat_chr6.simRat.chr6 514200 13 + 647215 CAGGAGATGAGAG - -a -s simMouse_chr6.simMouse.chr6 502988 39 + 636262 AAACAAGCCACATTGGTGACTACCTGAGCCTTATGGGAT -s Anc0.Anc0refChr3 116549 35 + 222631 AAACAAGCCACACTGCT---TACCTAATCATTACAGG-T -s Anc1.Anc1refChr6 150453 35 + 197743 AAACAAGCCACACTGCT---TACCTAATCATTACAGG-T -s Anc2.Anc2refChr1 28809 35 + 142988 AAACAGACCACACTGCT---TACCTAATCATTACAGG-A -s mr.mrrefChr3 55538 39 + 181027 AAACAAGCCACATTGGTGACTACCTGAGCCTTATAGGAT -s simCow_chr6.simCow.chr6 485295 35 + 602619 AAACAGACCATACTGTG---TACCTCATCCTCGCAGG-A -s simDog_chr6.simDog.chr6 475660 35 + 593897 AAACAGACCGCATTGCT---TCCCTAATCATTATATG-A -s simHuman_chr6.simHuman.chr6 482358 34 + 601863 AAGCAAGCCACACTGCT---TACCC-AATATTACAGG-T -s simRat_chr6.simRat.chr6 514213 39 + 647215 AAACAAGCCACATTGGTAACTACCTGAGCCTTATAGGAT - -a -s simMouse_chr6.simMouse.chr6 503027 6 + 636262 TTGATA -s Anc0.Anc0refChr3 116584 6 + 222631 TTAACA -s Anc1.Anc1refChr6 150488 6 + 197743 TTAACA -s Anc2.Anc2refChr1 28844 6 + 142988 TTAACA -s mr.mrrefChr3 55577 6 + 181027 TTGACA -s simCow_chr6.simCow.chr6 485330 6 + 602619 CTAACA -s simDog_chr6.simDog.chr6 475695 6 + 593897 TTGACA -s simHuman_chr6.simHuman.chr6 482392 6 + 601863 TCAACA -s simRat_chr6.simRat.chr6 514256 6 + 647215 TTTACA - -a -s simMouse_chr6.simMouse.chr6 503033 8 + 636262 GTTGTCAC -s Anc0.Anc0refChr3 116590 8 + 222631 GTTTTTTC -s Anc1.Anc1refChr6 150494 8 + 197743 GTTTTTTC -s Anc2.Anc2refChr1 28850 8 + 142988 GTTTTTTC -s mr.mrrefChr3 55583 8 + 181027 GTTGTCAC -s simCow_chr6.simCow.chr6 485336 8 + 602619 GTTGGTTC -s simDog_chr6.simDog.chr6 475701 5 + 593897 GTATT--- -s simHuman_chr6.simHuman.chr6 482398 8 + 601863 ATTATTTC -s simRat_chr6.simRat.chr6 514274 8 + 647215 GTTGTCAC - -a -s simMouse_chr6.simMouse.chr6 503041 44 + 636262 ACTTGGCTAAAGTTGGGATTGAACATGTCTTTAGGATTACAGTG -s Anc0.Anc0refChr3 116599 44 + 222631 ACTTGCCTAATTCATCGATGGAATGTGTCTTAGGAATTAAAGTG -s Anc1.Anc1refChr6 150503 44 + 197743 ACTTGCCTAATTCATCGATGGAATGTGTCTTAGGAATTAAAGTG -s Anc2.Anc2refChr1 28859 44 + 142988 ACTTGCCTGGTTCATCAATGGAATGTGCCTTCGGAATTAAATTG -s mr.mrrefChr3 55591 44 + 181027 ACTTGGCTAAAGTTGGGATTGAACATGTCTTAAGGATTACAGTG -s simCow_chr6.simCow.chr6 485356 44 + 602619 ACTTGCCTGGTTCATCAATGGAATGTGCCTTCGAAATTAAAATG -s simDog_chr6.simDog.chr6 475706 11 + 593897 ---------------------------------GAAATAAATTG -s simHuman_chr6.simHuman.chr6 482407 44 + 601863 ACTCGTCTAATTCATTGATCTAGTGTGTCTTAGGAATTGAAGTG -s simRat_chr6.simRat.chr6 514282 44 + 647215 ACTTGGCTAAAGTTAGGATTGAACACGTCTTAAGGATTACAATG - -a -s simMouse_chr6.simMouse.chr6 503085 56 + 636262 TCCGGTGCGACAACCCCAGTTGGCGCCCAAGGTATATTCCACAACTTGACCTACAT -s Anc0.Anc0refChr3 116643 21 + 222631 TTC-----------------------------------TCACAGGATGCACTACAT -s Anc1.Anc1refChr6 150547 21 + 197743 TTC-----------------------------------TCACAGGATGCACTACAT -s Anc2.Anc2refChr1 28903 21 + 142988 TTC-----------------------------------TCCCAGGATGCACTACAT -s mr.mrrefChr3 55635 21 + 181027 TCC-----------------------------------CCACAAGTTGACCTACAT -s simCow_chr6.simCow.chr6 485410 21 + 602619 TTC-----------------------------------TCCCAGAATGTGCTAGAT -s simDog_chr6.simDog.chr6 475717 21 + 593897 TTC-----------------------------------TCCTAGGATGCACTACAT -s simHuman_chr6.simHuman.chr6 482451 21 + 601863 TTA-----------------------------------TCACAGGATGGACTACAT -s simRat_chr6.simRat.chr6 514326 20 + 647215 TCC-----------------------------------CCACAAGTTGA-CTACAT - -a -s simMouse_chr6.simMouse.chr6 503141 2 + 636262 GC -s Anc0.Anc0refChr3 116664 2 + 222631 GC -s Anc1.Anc1refChr6 150568 2 + 197743 GC -s Anc2.Anc2refChr1 28926 2 + 142988 GC -s mr.mrrefChr3 55656 2 + 181027 GC -s simCow_chr6.simCow.chr6 485433 2 + 602619 GC -s simDog_chr6.simDog.chr6 475740 2 + 593897 GC -s simHuman_chr6.simHuman.chr6 482472 2 + 601863 GT -s simRat_chr6.simRat.chr6 514346 2 + 647215 GC - -a -s simMouse_chr6.simMouse.chr6 503143 20 + 636262 AGTGCATTTTGCAAAAGTGC -s Anc0.Anc0refChr3 116666 18 + 222631 ATTGCATTTTGTAGAA--TC -s Anc1.Anc1refChr6 150570 18 + 197743 ATTGCATTTTGTAGAA--TC -s Anc2.Anc2refChr1 28928 18 + 142988 ATGCCATTTTGTAGAA--TC -s mr.mrrefChr3 55658 18 + 181027 ATTGCATTTTGCCAAA--CC -s simCow_chr6.simCow.chr6 485435 18 + 602619 ATGCCACTTTGCAGAA--TC -s simDog_chr6.simDog.chr6 475742 18 + 593897 ATGCCATTTTGTAGAA--TC -s simHuman_chr6.simHuman.chr6 482477 8 + 601863 ATTGTAGT------------ -s simRat_chr6.simRat.chr6 514348 18 + 647215 ATTGCATTTTGCCAAA--CC - -a -s simMouse_chr6.simMouse.chr6 503163 21 + 636262 CAATTCTACTGAACAAGATAT -s Anc0.Anc0refChr3 116684 21 + 222631 CAGTTCTATTAAGCAGTACAT -s Anc1.Anc1refChr6 150588 21 + 197743 CAGTTCTATTAAGCAGTACAT -s Anc2.Anc2refChr1 28948 21 + 142988 CAGTTCTATTAAGGAGTACAT -s mr.mrrefChr3 55676 21 + 181027 CAATTCTACTGAACAAGATAT -s simCow_chr6.simCow.chr6 485455 21 + 602619 GAACCCTCTTTGAGAATACAT -s simDog_chr6.simDog.chr6 475762 21 + 593897 CAGTTCTATTAAGGAGTACAT -s simHuman_chr6.simHuman.chr6 482485 12 + 601863 ---------TAACCAGACAAT -s simRat_chr6.simRat.chr6 514366 21 + 647215 CAATTCTACTAAGCAAGATAT - -a -s simMouse_chr6.simMouse.chr6 503184 7 + 636262 CTCTTAG -s Anc0.Anc0refChr3 116721 7 + 222631 ACTCCAA -s Anc1.Anc1refChr6 150625 7 + 197743 ACTCCAA -s Anc2.Anc2refChr1 28985 7 + 142988 ACTCCAA -s mr.mrrefChr3 55713 7 + 181027 CTCTTAG -s simCow_chr6.simCow.chr6 485492 7 + 602619 ACTTCAA -s simDog_chr6.simDog.chr6 475799 7 + 593897 ACTCCAA -s simHuman_chr6.simHuman.chr6 482511 7 + 601863 AGTCCAA -s simRat_chr6.simRat.chr6 514481 7 + 647215 TTCTCGG - -a -s simMouse_chr6.simMouse.chr6 503191 21 + 636262 ACCTGACACCAGTGTTCCTCC -s Anc0.Anc0refChr3 116764 21 + 222631 TCCTGCTGCCAGTGTGCCACC -s Anc1.Anc1refChr6 150668 21 + 197743 TCCTGCTGCCAGTGTGCCACC -s Anc2.Anc2refChr1 29028 21 + 142988 TCAGCCTGCCAGTGTGCCACC -s mr.mrrefChr3 55720 21 + 181027 ACCTGACACCAGTGTTCCTCC -s simCow_chr6.simCow.chr6 485536 21 + 602619 TCTGCCCGCCAGTGTGCCGCC -s simDog_chr6.simDog.chr6 475842 21 + 593897 TTAGCCTGGCAGTGTACCACC -s simHuman_chr6.simHuman.chr6 482554 21 + 601863 CCCTGGTGCCAGTGTGCCACC -s simRat_chr6.simRat.chr6 514488 21 + 647215 ACTTGACACCAGTGTTCCTCC - -a -s simMouse_chr6.simMouse.chr6 503212 8 + 636262 TCAGTGTC -s Anc0.Anc0refChr3 116797 8 + 222631 TCAGTGTC -s Anc1.Anc1refChr6 150701 8 + 197743 TCAGTGTC -s Anc2.Anc2refChr1 29061 8 + 142988 TCAGTGTC -s mr.mrrefChr3 55741 8 + 181027 TCAGTGTC -s simCow_chr6.simCow.chr6 485569 8 + 602619 TCAGTGTC -s simDog_chr6.simDog.chr6 475875 8 + 593897 CCAGGGTC -s simHuman_chr6.simHuman.chr6 482587 8 + 601863 TCAGTGTC -s simRat_chr6.simRat.chr6 514509 8 + 647215 TCAGTGTC - -a -s simMouse_chr6.simMouse.chr6 503220 108 + 636262 TCACACAATCTTATTTAAAAAAGCCCATGATGGTTTATGTTGGGACTTTGGATCATATAGTCTAGGTGAAGGAATTTGTCTACTTCAGCTGTATACTTATTAGTTTTT -s Anc0.Anc0refChr3 116805 87 + 222631 T---ACAATCATATTTGAAAGAGCCCATGATGGTCT---------------ATCAGATAGTCTAGGTGACATAGTCTGCCTACTGCA--TGC-TGCCTATTATTTCTT -s Anc1.Anc1refChr6 150709 105 + 197743 T---ACAATCATATTTGAAAGAGCCCATGATGGTCTATGTTGGGACTTTGGATCAGATAGTCTAGGTGACATAGTCTGCCTACTGCAACTGCATGCCTATTATTTCTT -s Anc2.Anc2refChr1 29069 87 + 142988 C---ACAATCATATTTGAAAGAGCCCATGAAGGTCT---------------ATCAGATAGTCTAGATGACATAGTCTTCCTACTGCA--TGC-TGCCTATTATTTCCT -s mr.mrrefChr3 55749 108 + 181027 TCACACAATCTTATTTAAAAGAGCCCATGATGGTTTATGTTGGGACTTTGGATCATATAGTCTAGGTGAAGGAATTTGCCTACTTCAGCTGTATACCTATTAGTTTTT -s simCow_chr6.simCow.chr6 485580 84 + 602619 C---ACAATCATATTTGAAGGAGCCCATGAAGGTCT---------------ATCAGATAGTCTAAATGAGATAGTCTTCCTATTGCA------GGCCTATTATTTTCT -s simDog_chr6.simDog.chr6 475883 84 + 593897 C---ACAATCATATTTGAAAGAGCCCATGAAGGTCT---------------ATCAGATAGTCTAGATGACATAGTCTTCCTACTGCA--TGC-TGCCTA---TTTCCT -s simHuman_chr6.simHuman.chr6 482595 105 + 601863 T---ACAATCATATTTGAAAGGGCCCATAATGGTCTATGTTGGGACTTTGGAACAGATGGTCTAGGTTACATAGTCTGCCCACTGCAACTGCATGCCTATTGTTTCTT -s simRat_chr6.simRat.chr6 514517 108 + 647215 TCACACAATCTTATTTAAAAGAGCCCATGATGGTATATGTTGGGACTTTGGATCATATAGTGTAAGTGAAGGAATTTGCCTACTTGAGCTGTATACCTATTAGTTTTT - -a -s simMouse_chr6.simMouse.chr6 503328 32 + 636262 GTTTATTGTGTACTTTGGAGAATGTGGATTTC -s Anc0.Anc0refChr3 116894 20 + 222631 GATGATT------------CAATATGTATTGG -s Anc1.Anc1refChr6 150816 20 + 197743 GATGATT------------CAATATGTATTGG -s Anc2.Anc2refChr1 29158 20 + 142988 GATGATT------------CAATATGTATTGG -s mr.mrrefChr3 55857 32 + 181027 GTTTATTGTGTACTTTGGAGAATGTGGATTTC -s simCow_chr6.simCow.chr6 485666 20 + 602619 GAAGATT------------CAATATGTATTGG -s simDog_chr6.simDog.chr6 475969 20 + 593897 GATGATT------------CAACATGTACTGG -s simHuman_chr6.simHuman.chr6 482702 20 + 601863 GATGATT------------CAATCTATATTGG -s simRat_chr6.simRat.chr6 514625 28 + 647215 GTTTATTGTTATCTTTGGGGAATATTGA---- - -a -s simMouse_chr6.simMouse.chr6 503360 122 + 636262 TTTGGAAAATTTTAAACTTTCGTGAATCACTATCAGTAGTAGGTACCCATGGTCCACATCAGCTCACATGTATACGGAAATATATTCAAGGACTCCACCTAGTGGAGATCAGTTCCTAGGGT -s Anc0.Anc0refChr3 116914 85 + 222631 TTTGGAGAATTTTAAACTTTTAACAATCTCTATTAAAAGTGGGTACCCATTGTCCCTATCAGCCTGCATGT-------------------------------------TCAGGGCATGGACC -s Anc1.Anc1refChr6 150836 85 + 197743 TTTGGAGAATTTTAAACTTTTAACAATCTCTATTAAAAGTGGGTACCCATTGTCCCTATCAGCCTGCATGT-------------------------------------TCAGGGCATGGACC -s Anc2.Anc2refChr1 29182 85 + 142988 TTTGGAGAATTTTAAACTTTTAACAATCTCTATTAAAAGTGGGTACCCATTGTCCCTATCAGCCTGCATGT-------------------------------------ACAGGGCAGGGACC -s mr.mrrefChr3 55889 109 + 181027 TTTGGAAAATTTTAAACTTTTGAGAATCACTATCAGTAGTAGGTACCCATGGTCCACATCAGCCCACATGTA-------------TCAAGGACTCCACCTAGTGGAGATCAGTTCCTAGGGT -s simCow_chr6.simCow.chr6 485690 85 + 602619 TTTGGAGAGTTTTGAACTTTTACGAATCCCTATTAGAAGTGGATACCTATTGTCCCTATCAGCCTGCATGT-------------------------------------ATAGGGTAAGGACC -s simDog_chr6.simDog.chr6 475993 85 + 593897 TTTGGGAAACTTCAAATTTTTAACAATCTCTATTAAAAGTGGGTACCCATTGGCCCTATCAGCCTGCATGT-------------------------------------ACAGGGCGGTGACC -s simHuman_chr6.simHuman.chr6 482722 67 + 601863 TTTTGAGAATTTTAAACTTTTAACAATCTCT------------------TTGTCTCAATCAGCCGGGATGT-------------------------------------TCAGGGCATGGAAC -s simRat_chr6.simRat.chr6 514653 99 + 647215 ----------TTTAAATTTTTGAGAATCACTATCACAAGTAGGTACCCAAGGTCCACATCAGCCCACGTGTA-------------TCAAGGACTCCACCTAGAGAGAATTAGTTCCAAGGGT - -a -s simMouse_chr6.simMouse.chr6 503482 3 + 636262 ACT -s Anc0.Anc0refChr3 116999 3 + 222631 ACT -s Anc1.Anc1refChr6 150921 3 + 197743 ACT -s Anc2.Anc2refChr1 29267 3 + 142988 ACT -s mr.mrrefChr3 55998 3 + 181027 ACT -s simCow_chr6.simCow.chr6 485775 3 + 602619 AGT -s simDog_chr6.simDog.chr6 476078 3 + 593897 ACC -s simHuman_chr6.simHuman.chr6 482789 3 + 601863 ATT -s simRat_chr6.simRat.chr6 514756 3 + 647215 ACT - -a -s simMouse_chr6.simMouse.chr6 503485 18 + 636262 GTGCTCCCAGTGCTGATT -s Anc0.Anc0refChr3 117002 13 + 222631 A-----ACAATGCAGATT -s Anc1.Anc1refChr6 150924 13 + 197743 A-----ACAATGCAGATT -s Anc2.Anc2refChr1 29272 13 + 142988 A-----ACAATACAGATT -s mr.mrrefChr3 56001 18 + 181027 GTGCTCACAGTGCTGATT -s simCow_chr6.simCow.chr6 485780 13 + 602619 A-----ATAATTCAGATG -s simDog_chr6.simDog.chr6 476083 13 + 593897 A-----ACAGTATAGATT -s simHuman_chr6.simHuman.chr6 482792 13 + 601863 A-----ACAATGCAGATT -s simRat_chr6.simRat.chr6 514759 18 + 647215 GAGCTCACAGTGATGATT - -a -s simMouse_chr6.simMouse.chr6 503503 19 + 636262 AGCAGTTGATTGAACCCAT -s Anc0.Anc0refChr3 117015 15 + 222631 GGC----GGTTGAACCCAT -s Anc1.Anc1refChr6 150937 15 + 197743 GGC----GGTTGAACCCAT -s Anc2.Anc2refChr1 29285 15 + 142988 GGC----AGTTGAATCCAT -s mr.mrrefChr3 56019 19 + 181027 AGCAGTTGATTGAACCCAT -s simCow_chr6.simCow.chr6 485793 15 + 602619 GGC----AATTGAATCCAT -s simDog_chr6.simDog.chr6 476096 15 + 593897 GTC----AGTTGCATTCAT -s simHuman_chr6.simHuman.chr6 482805 15 + 601863 TGT----GGTTGAACCCAT -s simRat_chr6.simRat.chr6 514791 19 + 647215 AGCAGTTGATTGAACCCAT - -a -s simMouse_chr6.simMouse.chr6 503522 11 + 636262 ACTTCCAGTGG -s Anc0.Anc0refChr3 117033 11 + 222631 ACTCCCAGTGG -s Anc1.Anc1refChr6 150955 11 + 197743 ACTCCCAGTGG -s Anc2.Anc2refChr1 29303 11 + 142988 TCTCCCAGTGG -s mr.mrrefChr3 56038 11 + 181027 ACTTCCAGTGG -s simCow_chr6.simCow.chr6 485811 11 + 602619 GCTTACTGTGA -s simDog_chr6.simDog.chr6 476114 11 + 593897 TCTCCCAGTAG -s simHuman_chr6.simHuman.chr6 482823 11 + 601863 ACTCCAAGTGG -s simRat_chr6.simRat.chr6 514810 11 + 647215 ACTTCCAGTAG - -a -s simMouse_chr6.simMouse.chr6 503533 9 + 636262 GAGCATATA -s Anc0.Anc0refChr3 117051 9 + 222631 GTTCAAAAA -s Anc1.Anc1refChr6 150973 9 + 197743 GTTCAAAAA -s Anc2.Anc2refChr1 29335 9 + 142988 GTTCAAAAA -s mr.mrrefChr3 56049 9 + 181027 GAGCATATA -s simCow_chr6.simCow.chr6 485844 9 + 602619 GTGCAAAAC -s simDog_chr6.simDog.chr6 476146 9 + 593897 GTTCAAAAA -s simHuman_chr6.simHuman.chr6 482841 9 + 601863 GTACAAAAA -s simRat_chr6.simRat.chr6 514821 9 + 647215 GAGCATATA - -a -s simMouse_chr6.simMouse.chr6 503542 32 + 636262 GTGTGGATAATAAATAGATAGTGACAGGGGCT -s Anc0.Anc0refChr3 117060 27 + 222631 TCTTGACT-----GCCTAGACTGGCAGGGTTT -s Anc1.Anc1refChr6 150982 27 + 197743 TCTTGACT-----GCCTAGACTGGCAGGGTTT -s Anc2.Anc2refChr1 29349 27 + 142988 TCTTGACT-----GCCTAGACTGGCAGGGTTT -s mr.mrrefChr3 56058 32 + 181027 TTGTGAATAATAAACAGATAGTGACAGGGGCT -s simCow_chr6.simCow.chr6 485858 27 + 602619 TCTTGACT-----GCCTAGACTGGCAGGGTTT -s simDog_chr6.simDog.chr6 476160 27 + 593897 TCCTGACT-----GCCTAGACTGGCGGGGTTT -s simHuman_chr6.simHuman.chr6 482850 27 + 601863 TCTTGACT-----GCCTACGATGGCAGGGTTT -s simRat_chr6.simRat.chr6 514830 32 + 647215 TTGTGAATAATGAACAGATAGTGACAGGGGCT - -a -s simMouse_chr6.simMouse.chr6 503574 7 + 636262 TGGATCT -s Anc0.Anc0refChr3 117088 7 + 222631 GTGATCT -s Anc1.Anc1refChr6 151010 7 + 197743 GTGATCT -s Anc2.Anc2refChr1 29377 7 + 142988 GTGAATT -s mr.mrrefChr3 56091 7 + 181027 GGGATCT -s simCow_chr6.simCow.chr6 485886 7 + 602619 TTGGATC -s simDog_chr6.simDog.chr6 476188 7 + 593897 GTGAATT -s simHuman_chr6.simHuman.chr6 482878 7 + 601863 GAGATCT -s simRat_chr6.simRat.chr6 514864 7 + 647215 GGGATCC - -a -s simMouse_chr6.simMouse.chr6 503581 36 + 636262 CTCATATTACCTATCTCCCTCATGCAGAGACTGGAG -s Anc0.Anc0refChr3 117095 36 + 222631 CTCGTAATGCATGACTACCTCATGCACAGACTGGGG -s Anc1.Anc1refChr6 151017 36 + 197743 CTCGTAATGCATGACTACCTCATGCACAGACTGGGG -s Anc2.Anc2refChr1 29384 36 + 142988 CTCGTAATGCATGACTACTTCATGCACAGACTGGGG -s mr.mrrefChr3 56098 36 + 181027 CTCATATTACCTATCTCCCTCATGCACAGACTGGAG -s simCow_chr6.simCow.chr6 485894 34 + 602619 CTCATAATGCATGACTACTTCAGGCACAGACTGA-- -s simDog_chr6.simDog.chr6 476195 36 + 593897 CTTGCTGTGCATGACTACTTCATGCACAGGCCGGGG -s simHuman_chr6.simHuman.chr6 482885 36 + 601863 CTCTTAATGCATGGCTACCTCACGCACAGACTGGGG -s simRat_chr6.simRat.chr6 514871 36 + 647215 CTCATGCTATCTACCTCCCTCATGTACAGACTGGAG - -a -s simMouse_chr6.simMouse.chr6 503617 25 + 636262 CTCCATGAAACAATAACTTGACAAC -s Anc0.Anc0refChr3 117131 24 + 222631 CCTGACT-AACAGCAACTAGCTGGT -s Anc1.Anc1refChr6 151053 25 + 197743 CCTGACTGAACAGCAACTAGCTGGT -s Anc2.Anc2refChr1 29420 24 + 142988 ACTGACT-AAGAGCAAGTAGTTGGT -s mr.mrrefChr3 56134 25 + 181027 CTTCATGAAACAATAACTTGCCAAT -s simDog_chr6.simDog.chr6 476232 24 + 593897 ACTGACT-AAGAGCAAGTAGTTGGT -s simHuman_chr6.simHuman.chr6 482921 25 + 601863 CCTGACTGAACAGCAACTGGCTGGT -s simRat_chr6.simRat.chr6 514907 25 + 647215 CTTCATGAATCAATAACTTGCCAAT - -a -s simMouse_chr6.simMouse.chr6 503642 30 + 636262 GATGACTCTGGGTTATCTATGCATGCATAA -s Anc0.Anc0refChr3 117157 30 + 222631 GCTGACTCTGGGTTATCTTTGTATGTAATA -s Anc1.Anc1refChr6 151080 30 + 197743 GCTGACTCTGGGTTATCTTTGTATGTAATA -s Anc2.Anc2refChr1 29446 30 + 142988 GCAGGCTTTGGGTTATCTTTGTATATAATT -s mr.mrrefChr3 56161 30 + 181027 GATGACTCTGGGTTATCTATGCATGCATAA -s simDog_chr6.simDog.chr6 476258 30 + 593897 GCAGGCTTTGGGTTATCTTTGTATATAATT -s simHuman_chr6.simHuman.chr6 482949 30 + 601863 GTTGACTCTGGATTATCTTTGTATGTAGTA -s simRat_chr6.simRat.chr6 514934 30 + 647215 GACCACTCTGGGTTATCAAGGCATGCATAA - -a -s simMouse_chr6.simMouse.chr6 503672 167 + 636262 ACCTCCTCACTTACATATTCATTGCCATAGGTCAGTTATAACAATAAGAATGTGCATTTACTGCCATGCCAACTTCTAAACACCTGAATAAGAGTTATTTCGACAGACAAATTGGTAATTCCCCTAACAACCGAACATGAAGAATTTTTATGGACTGAATGCTAACT -s Anc0.Anc0refChr3 117189 148 + 222631 ACCAATTTCGTTGGACAGCCATTGACATAGGAGAGTTATAACAATAAGAATGTGCATTTGTTGGCATGCCTATTTCTACACACCTTAATGAGAGGTATTTTTACGGACAAATTGGTGATTCCTTTA------------GAAG----CTTCTACGCT---TTCCAGTT -s Anc1.Anc1refChr6 151112 148 + 197743 ACCAATTTCGTTGGACAGCCATTGACATAGGAGAGTTATAACAATAAGAATGTGCATTTGTTGGCATGCCTATTTCTACACACCTTAATGAGAGGTATTTTTACGGACAAATTGGTGATTCCTTTA------------GAAG----CTTCTACGCT---TTCCAGTT -s Anc2.Anc2refChr1 29478 148 + 142988 ACCAATTTCGTTGGACAGCCATTGACATAGAAGGGTCATAACCGTAAGAATGTGCATTTGCTGGCACACCTATTTCTACACTGCTTAATGAGAGGTATTTTTACGGACAAAATGGTGATACCTTTA------------AAAG----CTTCTATGCT---GTCCAGTT -s mr.mrrefChr3 56193 167 + 181027 ACCTATTTACTTACATATTCATTGCCATAGGTCAGTTATAACAATAAGAATGTGCATTTATTGCCATGCCAACTTCTAAACACCTGAATAAGAGGTATTTTGACAGACAAATTGGTAATTCCTCTAACAACCGAACATGAAGAATTCTTATACACTGAATACTAACT -s simCow_chr6.simCow.chr6 485928 71 + 602619 ----------------------------------------------------------------------------TGCACTTCTTAATGAAAGATATTTTTAGAGGATGAATGGTGACACCTTTA------------AAAG----CTTC-ATGCT---GTCCAGTT -s simDog_chr6.simDog.chr6 476290 148 + 593897 ACCAATTTCGTTGGACAGCCATTGACATAGAAGGGTCATAACCGTAAGAATGTGCATTTGCTGGCACACCTATTTCTATACTGCTGAATGAGGGGTAGGTTTACGGACAAAATAGTGATACCTTTA------------ACAG----CTTCTATGCT---GTCCAGTT -s simHuman_chr6.simHuman.chr6 482981 137 + 601863 ATTAATTTGTTTGGACAGACATTGACATGTGAGAGTTATAACAACAAGAACCTGCATTTGTTGGCATGGCTATTTTTACACACCTTAATGAGAGGTATTT-----------TTGTGGATTCCTTTA------------GAAG----CTTTCACGCT---TTCCAGTA -s simRat_chr6.simRat.chr6 514966 167 + 647215 ACCTATTTACTTACATATTCATCACCACAGGTCAGTTATAACAATGAGAATGTGCATTTATTGCCATGCCAACTTCTAAACAACTGAATAAGATGTACTTTGGCAGACTAAATGGTAATTCATAAAATGACCAAACATGAAGTATTCTTATACACTGAATACTAATT - -a -s simMouse_chr6.simMouse.chr6 503839 8 + 636262 TTGTAAAA -s Anc0.Anc0refChr3 117343 8 + 222631 ACTTAGAA -s Anc1.Anc1refChr6 151266 8 + 197743 ACTTAGAA -s Anc2.Anc2refChr1 29632 8 + 142988 ACTTAGAA -s mr.mrrefChr3 56366 8 + 181027 TTTTAAAA -s simCow_chr6.simCow.chr6 486005 8 + 602619 ACTTAGAA -s simDog_chr6.simDog.chr6 476444 8 + 593897 ACCTAGAA -s simHuman_chr6.simHuman.chr6 483124 8 + 601863 ACTCAGAA -s simRat_chr6.simRat.chr6 515141 8 + 647215 TTTTAAAA - -a -s simMouse_chr6.simMouse.chr6 503847 35 + 636262 TCTGCTCTGGATTGTAAGACTTAAAACAATAAAAC -s Anc0.Anc0refChr3 117351 20 + 222631 TTGGCCCC---TTCTA----TCAG--------AAT -s Anc1.Anc1refChr6 151274 24 + 197743 TTGGCCCC---TTCTAAGACTCAG--------AAT -s Anc2.Anc2refChr1 29640 20 + 142988 CTGGCCCC---TTCTA----CCTG--------TAT -s mr.mrrefChr3 56374 35 + 181027 TCTGCTCTGGATTGTAAGACTTAGAACAATAAAAC -s simCow_chr6.simCow.chr6 486017 20 + 602619 CTGGCCCC---TTCTA----CCTG--------CAT -s simDog_chr6.simDog.chr6 476452 20 + 593897 CTGGCCCC---TTCTG----CCTG--------TAT -s simHuman_chr6.simHuman.chr6 483132 21 + 601863 TACGT------TTATAAGACTCAG--------AAT -s simRat_chr6.simRat.chr6 515149 35 + 647215 TCTGCTCTGGATTGTAAGACTTAGAACGATAAAGC - -a -s simMouse_chr6.simMouse.chr6 503882 20 + 636262 AATTGTGTACACTGTACTGA -s Anc0.Anc0refChr3 117371 20 + 222631 ACTTGGTTAGACTGTAGTGA -s Anc1.Anc1refChr6 151298 20 + 197743 ACTTGGTTAGACTGTAGTGA -s Anc2.Anc2refChr1 29660 20 + 142988 CCTTGGTTAGACTGTAGTGA -s mr.mrrefChr3 56409 20 + 181027 AATTGTGTACACTGTAGTGA -s simCow_chr6.simCow.chr6 486047 17 + 602619 CTTTG---AGACTGTAGTGA -s simDog_chr6.simDog.chr6 476472 20 + 593897 CCTTGGTTGCACTTTAAGAA -s simHuman_chr6.simHuman.chr6 483153 20 + 601863 ACTTGCCCAGACTGTAGTGA -s simRat_chr6.simRat.chr6 515184 20 + 647215 TATTGTGTTCACTGTAGTGA - -a -s simMouse_chr6.simMouse.chr6 503902 27 + 636262 GAGGTGAATGCCATGAGTATTCAATTA -s Anc0.Anc0refChr3 117391 27 + 222631 AAAGTCAAGGCCAGGAATCTTCAATTT -s Anc1.Anc1refChr6 151318 27 + 197743 AAAGTCAAGGCCAGGAATCTTCAATTT -s Anc2.Anc2refChr1 29680 27 + 142988 AAAGTCAAGGCCAGGAATCTTCAATTT -s mr.mrrefChr3 56429 27 + 181027 GAGGTGAATGCCATGAGTATTCAATTA -s simCow_chr6.simCow.chr6 486064 27 + 602619 GAAGCCAAGGCTACGAATCTTCAATTT -s simDog_chr6.simDog.chr6 476498 27 + 593897 AAAGTCAAGGCCAGGGAGCTTCGATTT -s simHuman_chr6.simHuman.chr6 483173 27 + 601863 AAAGTTAAGGCCAGGAATCTTCAATTG -s simRat_chr6.simRat.chr6 515204 20 + 647215 GGGATGAATGTC-------TACAATTA - -a -s simMouse_chr6.simMouse.chr6 503929 14 + 636262 TGTGCTTGGGTTTC -s Anc0.Anc0refChr3 117419 14 + 222631 CATAGTAAAGTGTC -s Anc1.Anc1refChr6 151346 14 + 197743 CATAGTAAAGTGTC -s Anc2.Anc2refChr1 29708 14 + 142988 GATAGTAAAGTGTC -s mr.mrrefChr3 56456 14 + 181027 CATGCTAGGGTTTC -s simCow_chr6.simCow.chr6 486092 14 + 602619 GCTTGTGAAGAGTT -s simDog_chr6.simDog.chr6 476526 14 + 593897 GATAGTAAAGTGTC -s simHuman_chr6.simHuman.chr6 483201 14 + 601863 CATATTAAAGTGTC -s simRat_chr6.simRat.chr6 515224 14 + 647215 CATCCTAGGGTTTC - -a -s simMouse_chr6.simMouse.chr6 503943 4 + 636262 ATTC -s Anc0.Anc0refChr3 117436 4 + 222631 ATTC -s Anc1.Anc1refChr6 151363 4 + 197743 ATTC -s Anc2.Anc2refChr1 29725 4 + 142988 ATTC -s mr.mrrefChr3 56470 4 + 181027 ATTC -s simCow_chr6.simCow.chr6 486109 4 + 602619 ATTC -s simDog_chr6.simDog.chr6 476543 4 + 593897 ATTC -s simHuman_chr6.simHuman.chr6 483218 4 + 601863 ACTC -s simRat_chr6.simRat.chr6 515238 4 + 647215 ATTC - -a -s simMouse_chr6.simMouse.chr6 503947 20 + 636262 ATTTAATCAACTTGCGATGA -s Anc0.Anc0refChr3 117440 20 + 222631 ATTTAATCAACTTGTGATGA -s Anc1.Anc1refChr6 151367 20 + 197743 ATTTAATCAACTTGTGATGA -s Anc2.Anc2refChr1 29729 20 + 142988 ATTTAATCAACTTGTAATGA -s mr.mrrefChr3 56474 20 + 181027 ATTTAATCAACTTGCGATGA -s simCow_chr6.simCow.chr6 486113 20 + 602619 ATTTAAGCAACTTGTAAAGA -s simDog_chr6.simDog.chr6 476547 20 + 593897 ATTTAATCGACTTGCAATAA -s simHuman_chr6.simHuman.chr6 483222 20 + 601863 ATTTAAACAACTTGTGATGG -s simRat_chr6.simRat.chr6 515244 19 + 647215 ATTTAGTCCA-GTGCGGTGA - -a -s simMouse_chr6.simMouse.chr6 503967 3 + 636262 AAA -s Anc0.Anc0refChr3 117460 3 + 222631 AAA -s Anc1.Anc1refChr6 151387 3 + 197743 AAA -s Anc2.Anc2refChr1 29749 3 + 142988 AAA -s mr.mrrefChr3 56494 3 + 181027 AAA -s simCow_chr6.simCow.chr6 486164 3 + 602619 AAA -s simDog_chr6.simDog.chr6 476567 3 + 593897 AAA -s simHuman_chr6.simHuman.chr6 483242 3 + 601863 AAA -s simRat_chr6.simRat.chr6 515263 3 + 647215 AAA - -a -s simMouse_chr6.simMouse.chr6 503970 4 + 636262 CCAT -s Anc0.Anc0refChr3 117464 2 + 222631 --AT -s Anc1.Anc1refChr6 151391 2 + 197743 --AT -s Anc2.Anc2refChr1 29753 2 + 142988 --AT -s mr.mrrefChr3 56498 4 + 181027 CCAT -s simCow_chr6.simCow.chr6 486168 2 + 602619 --AT -s simDog_chr6.simDog.chr6 476571 2 + 593897 --AT -s simHuman_chr6.simHuman.chr6 483246 2 + 601863 --AT -s simRat_chr6.simRat.chr6 515267 4 + 647215 GCAT - -a -s simMouse_chr6.simMouse.chr6 503974 13 + 636262 CTCTTAGTTACTA -s Anc0.Anc0refChr3 117466 13 + 222631 CTCTTAGTTCATA -s Anc1.Anc1refChr6 151393 13 + 197743 CTCTTAGTTCATA -s Anc2.Anc2refChr1 29755 13 + 142988 CTCTTAGTTCACT -s mr.mrrefChr3 56502 13 + 181027 CTCTTAGTTACTA -s simCow_chr6.simCow.chr6 486170 13 + 602619 TTCTCCGTTCACT -s simDog_chr6.simDog.chr6 476579 13 + 593897 CTCTTAGTCCACT -s simHuman_chr6.simHuman.chr6 483248 13 + 601863 ATCTTAGTTTATA -s simRat_chr6.simRat.chr6 515271 13 + 647215 CTCTTGGTTACTA - -a -s simMouse_chr6.simMouse.chr6 503987 12 + 636262 TAGCTTGGTCTT -s Anc0.Anc0refChr3 117480 12 + 222631 TTACTTGGTCTT -s Anc1.Anc1refChr6 151407 12 + 197743 TTACTTGGTCTT -s Anc2.Anc2refChr1 29769 12 + 142988 TTACTTGTTCTT -s mr.mrrefChr3 56515 12 + 181027 TTGCTTGGTCTT -s simCow_chr6.simCow.chr6 486184 12 + 602619 TCACTTGTTCTT -s simDog_chr6.simDog.chr6 476593 6 + 593897 TTA------CTC -s simHuman_chr6.simHuman.chr6 483262 12 + 601863 TTACTTGGTCTT -s simRat_chr6.simRat.chr6 515284 12 + 647215 TTGCTTGGTCCC - -a -s simMouse_chr6.simMouse.chr6 503999 21 + 636262 ATTACACTCCTCATAGTTCCA -s Anc0.Anc0refChr3 117498 21 + 222631 ATTACACTGGTCATAGTAGTA -s Anc1.Anc1refChr6 151425 21 + 197743 ATTACACTGGTCATAGTAGTA -s Anc2.Anc2refChr1 29787 21 + 142988 ATTATACTGGTCATAGTAGTA -s mr.mrrefChr3 56527 21 + 181027 ATTACACTCCTCATAGTTCCA -s simCow_chr6.simCow.chr6 486202 20 + 602619 ATTAGCCTGGTCATCGTC-TG -s simDog_chr6.simDog.chr6 476605 21 + 593897 ATTATACTGCTCTTAATAGTA -s simHuman_chr6.simHuman.chr6 483280 21 + 601863 ATGACACTGGCCATAGCAGTA -s simRat_chr6.simRat.chr6 515296 21 + 647215 ATTACACTCCTCATAGTTCCA - -a -s simMouse_chr6.simMouse.chr6 504020 4 + 636262 TTAC -s Anc0.Anc0refChr3 117529 4 + 222631 TTAC -s Anc1.Anc1refChr6 151456 4 + 197743 TTAC -s Anc2.Anc2refChr1 29818 4 + 142988 CAAC -s mr.mrrefChr3 56548 4 + 181027 TTAC -s simCow_chr6.simCow.chr6 486232 4 + 602619 CCCT -s simDog_chr6.simDog.chr6 476636 4 + 593897 CAAC -s simHuman_chr6.simHuman.chr6 483311 4 + 601863 TTAC -s simRat_chr6.simRat.chr6 515317 4 + 647215 TTAC - -a -s simMouse_chr6.simMouse.chr6 504024 13 + 636262 TATCACCTTATGA -s Anc0.Anc0refChr3 117533 13 + 222631 TATCACCTGGTGA -s Anc1.Anc1refChr6 151460 13 + 197743 TATCACCTGGTGA -s Anc2.Anc2refChr1 29824 13 + 142988 TATCACCTGGTGA -s mr.mrrefChr3 56552 13 + 181027 TATCACCTTATGA -s simCow_chr6.simCow.chr6 486238 11 + 602619 TACCATCTG--GG -s simDog_chr6.simDog.chr6 476642 13 + 593897 TATCTCATGGTGA -s simHuman_chr6.simHuman.chr6 483315 13 + 601863 TATCACCTGGTGA -s simRat_chr6.simRat.chr6 515321 13 + 647215 TATCACCTTATGA - -a -s simMouse_chr6.simMouse.chr6 504037 73 + 636262 ACTCGTTGTAACATAAAGTTCAGTCATTTTGATTTTGTATAGTAATAAGTGATTTCCTGTGCTGCTTTATCAC -s Anc0.Anc0refChr3 117547 72 + 222631 ACTTA-TGTAGCGAAAAGTCCAGTCACTAGGTTTTTGTGCAATTCTGATTGATTTCCTGTACTGCTTTATTAA -s Anc1.Anc1refChr6 151474 73 + 197743 ACTTATTGTAGCGAAAAGTCCAGTCACTAGGTTTTTGTGCAATTCTGATTGATTTCCTGTACTGCTTTATTAA -s Anc2.Anc2refChr1 29838 72 + 142988 ACTTA-TATAGCAAAAAGTCCAGTCACTAGGTTTTTGTGCAATTCTGATTGATTTCCTGTACTGCTTTATTAA -s mr.mrrefChr3 56565 73 + 181027 ACTCATTGTAACGTAAAGTTCAGTCATTTTGATTTTGTATAATAATAAGTGATTTCCTGTGCTGCTTTATCAC -s simCow_chr6.simCow.chr6 486250 72 + 602619 ACTTT-TATAGCAAAAAGGCCAATCACTTAGTCTTTGTGCAATTGTGACTGATTTCCTGTACTGCTTTAGTAG -s simDog_chr6.simDog.chr6 476656 72 + 593897 ACTTA-AATAGCAAAAAGTCCAGTCACTAGTTTGTTATACAATCCAGATTGACTTTGTGTACTGGTTTATTAA -s simHuman_chr6.simHuman.chr6 483329 73 + 601863 ACTTATTGTGGCGGAAAGTCCAGTCTCTCGGTTTTTGTGCAATTCTGAATGATTTCCCGTACTGCTTTATTAA -s simRat_chr6.simRat.chr6 515334 71 + 647215 CCTCATTGTAACGTAAAGGTCAGTCA--TTGATTTTGTATAATAGTAAGTGATTTCCAGTGCTGCTTTAAAAC - -a -s simMouse_chr6.simMouse.chr6 504110 18 + 636262 CGTAGGGCCTTCAGGGGC -s Anc0.Anc0refChr3 117766 18 + 222631 TGTAGGGCCTGAAGAGGC -s Anc1.Anc1refChr6 151694 18 + 197743 TGTAGGGCCTGAAGAGGC -s Anc2.Anc2refChr1 30149 18 + 142988 TGTAGGGCCTGAAGGGGC -s mr.mrrefChr3 56638 18 + 181027 TGTAGGGCCTGCAGAGGC -s simCow_chr6.simCow.chr6 486527 18 + 602619 TGTAGGGACTAAAGGGGC -s simDog_chr6.simDog.chr6 476973 18 + 593897 TGTAAGGCGTGAAGGAGC -s simHuman_chr6.simHuman.chr6 483553 18 + 601863 TGTAGAGCCTGATGAGGC -s simRat_chr6.simRat.chr6 515405 18 + 647215 TGTAGGGCCGGCAGAGGC - -a -s simMouse_chr6.simMouse.chr6 504128 29 + 636262 CCGCCCTTACCCAGCAGTTTGGCGGAAGG -s Anc0.Anc0refChr3 117787 27 + 222631 CAGCTCTTCCGCAGAA--CTACTCAAAGT -s Anc1.Anc1refChr6 151715 27 + 197743 CAGCTCTTCCGCAGAA--CTACTCAAAGT -s Anc2.Anc2refChr1 30173 27 + 142988 CACCTATTCGGCAGAA--CTACTCAATGT -s mr.mrrefChr3 56656 29 + 181027 CCGCCCTTACCCAGCAGTCTGGCGGAAGT -s simCow_chr6.simCow.chr6 486551 27 + 602619 CACCTGTTCAGTAGTG--CTTCTCTATGT -s simDog_chr6.simDog.chr6 476997 26 + 593897 CCCATA-TCGGCGGAA--CGATTCAATGT -s simHuman_chr6.simHuman.chr6 483574 27 + 601863 CAGCTCTCCCACAGAA--CTACTCAAAGT -s simRat_chr6.simRat.chr6 515423 29 + 647215 CCATCTTTACCCAGCAGTCTGGCAGAAGT - -a -s simMouse_chr6.simMouse.chr6 504157 10 + 636262 ACTCACAGTG -s Anc0.Anc0refChr3 117814 10 + 222631 AGTTATAGGG -s Anc1.Anc1refChr6 151742 10 + 197743 AGTTATAGGG -s Anc2.Anc2refChr1 30201 10 + 142988 AGTTGTAGGG -s mr.mrrefChr3 56685 10 + 181027 ACTCACAGGG -s simCow_chr6.simCow.chr6 486579 10 + 602619 AGTTGGAGGG -s simDog_chr6.simDog.chr6 477024 10 + 593897 AGTTGTGGGG -s simHuman_chr6.simHuman.chr6 483601 10 + 601863 AGTTAAAGGG -s simRat_chr6.simRat.chr6 515452 10 + 647215 ACTCACAGGG - -a -s simMouse_chr6.simMouse.chr6 504167 5 + 636262 CCTAG -s Anc0.Anc0refChr3 117835 5 + 222631 CATAG -s Anc1.Anc1refChr6 151763 5 + 197743 CATAG -s Anc2.Anc2refChr1 30222 5 + 142988 CATAG -s mr.mrrefChr3 56695 5 + 181027 CCTAG -s simCow_chr6.simCow.chr6 486600 5 + 602619 CAAAG -s simDog_chr6.simDog.chr6 477045 5 + 593897 CATAG -s simHuman_chr6.simHuman.chr6 483622 5 + 601863 CATAG -s simRat_chr6.simRat.chr6 515462 5 + 647215 CCTAG - -a -s simMouse_chr6.simMouse.chr6 504172 51 + 636262 TCTTTCAACAAAATGTTGAAGAACCATGTAGGTGGGATTTGAATTAAATGT -s Anc0.Anc0refChr3 117840 51 + 222631 TTTTTCAATGAAATATTGAATAACAAGATAAGTGGGTTATAAGTTCAATGT -s Anc1.Anc1refChr6 151768 51 + 197743 TTTTTCAATGAAATATTGAATAACAAGATAAGTGGGTTATAAGTTCAATGT -s Anc2.Anc2refChr1 30227 51 + 142988 TTTTTCAATGAAATATTGAATAACAAGATAAGTGGGTTCTAAGTTCAATGT -s mr.mrrefChr3 56700 51 + 181027 TCTTTCAACAAAATGTTGAATAACAATGTAGGTGGGATATGAGTTAAATGT -s simCow_chr6.simCow.chr6 486607 51 + 602619 TTTTTCAATCAAATATGGAAAAATGAGATGAGTTGATTCTAAGTTAAATGT -s simDog_chr6.simDog.chr6 477050 51 + 593897 TTTTTCAATGAAATATTGAATAACAAGATAAGTGGGTTCTAACTCCAATTG -s simHuman_chr6.simHuman.chr6 483627 51 + 601863 TTTTTCAATGAAATATTGAGTAACAAGATAAGTGGGTTATAAGTTCAATGT -s simRat_chr6.simRat.chr6 515467 51 + 647215 TCTTTCAACAAAATGTTGAATAACAATGTAGGTGCGATATGAGTTAAATGT - -a -s simMouse_chr6.simMouse.chr6 504223 9 + 636262 CATTGAACG -s Anc0.Anc0refChr3 117891 9 + 222631 CATTGGACT -s Anc1.Anc1refChr6 151819 9 + 197743 CATTGGACT -s Anc2.Anc2refChr1 30278 9 + 142988 CATTGGACT -s mr.mrrefChr3 56751 9 + 181027 CATTGAACG -s simCow_chr6.simCow.chr6 486659 9 + 602619 CATTGGACT -s simDog_chr6.simDog.chr6 477101 9 + 593897 CATTGAACT -s simHuman_chr6.simHuman.chr6 483678 8 + 601863 CATG-GACT -s simRat_chr6.simRat.chr6 515518 9 + 647215 CATTGGACT - -a -s simMouse_chr6.simMouse.chr6 504232 219 + 636262 CACAGCACCCAAAGCCTCCCACGTGGAACCATACTTACAATCAATTTCTAGTCCATAAGTTCAGTGAAGCAAAATATAATCGTTACAACAGAAGAGGATAAATGGAGCCACATGCGTAATTCCCTTCAGAGTGTCTCATCTTCAGACAAAGTTATTGTCTTTGTGCCCCGAAGGACTTTGTAGAGAGACCATGTGGGGGCTGCATAAATTACTAGAGAG -s Anc0.Anc0refChr3 117900 219 + 222631 CATAGTACTTAGAGCCTACCATTTGGAACCTTGTTTGTAATCAGTTTGTAGTCTGTAAGTTCAGTGAAGCAAAATATAATTGTTACAACAGAGGAGGATAAATGGAGCCACATGCATAATTCCCTTCAGAGTGTCTCATCCTCAGACAAAGTTATTGTCTTTGTGCCCCGAAGGACTTTGTATAGACCCTCTTTGATGGTGGCAGAAACAAATAGAGAG -s Anc1.Anc1refChr6 151828 219 + 197743 CATAGTACTTAGAGCCTACCATTTGGAACCTTGTTTGTAATCAGTTTGTAGTCTGTAAGTTCAGTGAAGCAAAATATAATTGTTACAACAGAGGAGGATAAATGGAGCCACATGCATAATTCCCTTCAGAGTGTCTCATCCTCAGACAAAGTTATTGTCTTTGTGCCCCGAAGGACTTTGTATAGACCCTCTTTGATGGTGGCAGAAACAAATAGAGAG -s Anc2.Anc2refChr1 30287 219 + 142988 CATAGTACTTAGAACTTACCATTTGAAACCTTGTTTGTAATCCGTTTGTAGTCTGTAAGTTCAGTGAAGCAAAATATAATTGTTACAACAGAGGAGGATAAATGGAGCCACATGCATAATTCCCTTCAGAGTGTCTCATCCTCAGACAAAGTTATTGTCTTCCTGCCCCGAAGGACTTTGTATAGACCCTCTTTGATGGTGGCTGCAACAAATAGAGAG -s mr.mrrefChr3 56760 219 + 181027 CACAGCACCCAAAGCCTCCCACTTGGAACCATACTTGTAATCAATTTCTAGTCCATAAGTTCAGTGAAGCAAAATATAATTGTTACAACAGAAGAGGATAAATGGAGCCACATGCATAATTCCCTTCAGAGTGTCTCATCTTCAGACAAAGTTATTGTCTTTGTGCCCCGAAGGACTTTGTATAGAGACCATGTGAGGGCGGCAGAAACTAATAGAGAG -s simCow_chr6.simCow.chr6 486668 205 + 602619 CATAGTATTTA--------------AAACCTTGTTTGTAGTCTGTGAGTAGTCGGTAAGTTCGGTAAAGCAAAATATAATTGTTACAACAGAGGAGGATAAATGGAGCCACATGCATAATTCTCTACAGAGTGTCTCATCCTCAGACAAAGTTTTTGTCTTCCTGCCGCGAAGGACTCTGTATAGACCCTGATAGATGCTGGCTGCAACAAATAGACAG -s simDog_chr6.simDog.chr6 477110 219 + 593897 CATAGCACTTGGAACTTACCATTTGAAACCTTGTTCGTAATCCGTTTGTAGTCTGTAAGTTCAGTGAAGCAAAACATAATTGTTACAACAGAGGAGGATAAATGGAGCCACATGCATAATTCCCTTCAAAGCGTCTCATCCTCAGACAAAGTTATTGTCTTCCTGCCCCGAAGGACTTTGTATAGACCCTCTTTGGTGGTGGCTGCAACGAATAGAGAG -s simHuman_chr6.simHuman.chr6 483686 219 + 601863 GATAGTACTTAGAGCCAACTATTTGGAACCTTGTTTGTAATCAGTTTGTAGTCTGTAAGTGCAGTGAAGCAAAATATAATTGTTACAACGGAGGAGGATAAATGGAGCCACATGCATAATTCCCTTCAGAGTGTCTCATCCTCAGACAAAGTTATTGTCTTTGTGCCCCGAAGGACTTTGTGTAGACCCTCTTTGATGTTGGCAGAAACAAATGGAAAG -s simRat_chr6.simRat.chr6 515528 218 + 647215 CACAGCACCCAAAGCCGCCCACTTGGAACCCTACTTGTAATCAATTTCTAGTCCATAAGTTCAGTGAAGCAAAATATAATTGTTACAACAGAAGAGGATAAATGGAGCCACATGCATAATTCCCTTCAGAGTGTCTCATCTTCAGACAAAGTTATCGTCTTTGTGCCCCGAAGGACTTTGTATAGA-ACCATGTGAGGGCGGCAGAAACTAATAGAGAG - -a -s simMouse_chr6.simMouse.chr6 504451 192 + 636262 AAGCATTATTGACCCCCTGTAGGGAGACTTATCTGCCCAACTATTTACACAAACACTAAGTTGAAACTGTCTCCTGAGGTCATCAGGATGGACTACCTTTCCTACAGTGCAGATCAATTACCGAGTGATTTAATACTTGGAACCAACTCAGTAGCTTTGCAAGCAGATAAGGAGCAGCGGGATCAAGAAAAG -s Anc0.Anc0refChr3 118119 192 + 222631 AACCAGTATTGGCCCCCTGTGGGGAGACTTATATGCCCGACTATTTACACAAACACTAAGCTGAAACTGTCTCCTAAAGTCATCAGGATGGACTACCTTTCCTATAGTGCAGACCATTTACCAAGTGATTTAATACTTGGGACCAAGTCAGTAGCTTTGCAGGGAGATAAGGAACAGCGAGATCAAGAGAAG -s Anc1.Anc1refChr6 152047 192 + 197743 AACCAGTATTGGCCCCCTGTGGGGAGACTTATATGCCCGACTATTTACACAAACACTAAGCTGAAACTGTCTCCTAAAGTCATCAGGATGGACTACCTTTCCTATAGTGCAGACCATTTACCAAGTGATTTAATACTTGGGACCAAGTCAGTAGCTTTGCAGGGAGATAAGGAACAGCGAGATCAAGAGAAG -s Anc2.Anc2refChr1 30506 192 + 142988 TACCTGTATTGGCTTCCTGTGGGGAGAGTTATATGCCGGGCTATTTACACAAACACTAAGCTGAAACTGTCTCCTAAAGTCATCAGGATGGACTACCTTTCCTATAGTGCAGACCATTTACCAAGTGATTTAATACTTGGGACCAAGTCAGTAGCTCTGCAGGGGGATAAGGAACAACGAGATCAAGAGAAG -s mr.mrrefChr3 56979 192 + 181027 AAGCATTATTGACCCCCTGTAGGGAGACTTATCTGCCCAACTATTTACACAAACACTAAGTTGAAACTGTCTCCTGAAGTCATCAGGATGGACTACCTTTCCTACAGTGCAGATCAATTACCAAGTGATTTAATACTTGGAACCAACTCAGTAGCTTTGCAAGCAGATAAGGAACAGCGGGATCAAGAGAAG -s simCow_chr6.simCow.chr6 486873 192 + 602619 GACCTGTATTGGCTTCCTGTGGGGAGAGTTATATGCTGGGCTATTTCCACAAACACTAAGCTGAAACTATCCTCCAAAGGCATCAGGATGGACTACCTTTCCTATAGTGCAGACCATTTACCAAGTGATTTGATACTTGGGACCAAATCAGTAGCCCTGCAGGGGGATAAGGAACAACGAGATCAAGAGAAG -s simDog_chr6.simDog.chr6 477329 192 + 593897 TACCTATATTGGCTTCCTGTAAGGGGAGATGTACGCCGGGCTTTTTACACAAACAGTAAGTTGGAGCCGTCTCCTGAAGTCACCAGGATGGACTACCTTTCCTATAGTGCAGACCATTTACCAAGTGATTTAATACTTGGGACCAAGTCAGTAGCTCTGCAGGGGGATAAGGAACAACGAGATCAAGACAAG -s simHuman_chr6.simHuman.chr6 483905 192 + 601863 AAATAGTATTGGCCCCCTGTGGGGAGACTTATATGCCCGACTATTTACACAAACACTAAACTGAAACTTTCTCCTAGAGTCATCAGGATGGACTACCTTTCCTATAGTGCTGACCATTTACCAAGTGATTTAATTCTTGGGACCAAGTCAGTAGCTTTGCAGGGAGATAAGGAACAGCGAGATCAAGAGAAG -s simRat_chr6.simRat.chr6 515762 192 + 647215 AAGCATGATTGACCCTTTGTAGGGAGGCTTATCTGCCCAACTATTTACATGAACACTAAGTTGAAGCTGTCACCTGAAGTCATCAGGATGGACTACCTTTCCTACAGTGCAGATCAATTACCAAGTGATCTAATACTTGGTACCAACTCGGTAGCTTTGCAAGCAGATAAAGAACAGCAGGATCAAGAGAAG - -a -s simMouse_chr6.simMouse.chr6 504643 53 + 636262 CTGGAAAATTTTAAAACAGGTGTATTCTCAGATGACAGGTACGTTTTCTAGGT -s Anc0.Anc0refChr3 118314 43 + 222631 CTAGAGAATTTTAAAACAGGTGTGCACTCAG------GGTACC----TCAGGT -s Anc1.Anc1refChr6 152242 47 + 197743 CTAGAGAATTTTAAAACAGGTGTGCACTCAG------GGTACCTAGATCAGGT -s Anc2.Anc2refChr1 30701 43 + 142988 CTCGAGAATTTTAAAACAGGTGTGCAGTCAG------GTTACC----TCAGGT -s mr.mrrefChr3 57171 52 + 181027 CTAGAAAATTTTAAAACAGGTGTGTTCTCAGATG-CAGGTACGTATTCCAGGT -s simCow_chr6.simCow.chr6 487068 43 + 602619 CTTGAGAATTTTGAAACAGGTGTGCAGTCAG------ATCACC----TCAGGT -s simDog_chr6.simDog.chr6 477524 43 + 593897 CTCAAGAATTTTAAAACAGGTGTGCAGTCAG------GTTACC----CCAGGT -s simHuman_chr6.simHuman.chr6 484100 47 + 601863 CTAGAGAATTTTAAAACAGGTGTGCACTCAG------GGTACCTAGATCAGTG -s simRat_chr6.simRat.chr6 515954 52 + 647215 CTAGAAAATTTTAAAATGGGTCTGTTCTCAGATG-CAGACACGTATTCCAGGT - -a -s simMouse_chr6.simMouse.chr6 504696 8 + 636262 TGGGTGCC -s Anc0.Anc0refChr3 118357 8 + 222631 TGTATGCA -s Anc1.Anc1refChr6 152289 8 + 197743 TGTATGCA -s Anc2.Anc2refChr1 30748 8 + 142988 TCTAGGCA -s mr.mrrefChr3 57223 8 + 181027 TGGATGCC -s simCow_chr6.simCow.chr6 487115 8 + 602619 TTTAGGTG -s simDog_chr6.simDog.chr6 477571 8 + 593897 TCTAGGCA -s simHuman_chr6.simHuman.chr6 484147 6 + 601863 AGTATG-- -s simRat_chr6.simRat.chr6 516006 8 + 647215 TGCATGCG - -a -s simMouse_chr6.simMouse.chr6 504704 4 + 636262 TATT -s Anc0.Anc0refChr3 118365 4 + 222631 TGCA -s Anc1.Anc1refChr6 152297 4 + 197743 TGCA -s Anc2.Anc2refChr1 30757 4 + 142988 TGCA -s mr.mrrefChr3 57231 4 + 181027 TATT -s simCow_chr6.simCow.chr6 487126 4 + 602619 TGCA -s simDog_chr6.simDog.chr6 477580 4 + 593897 TGCA -s simRat_chr6.simRat.chr6 516014 4 + 647215 TATT - -a -s simMouse_chr6.simMouse.chr6 504708 17 + 636262 ACTACCTGCTGACCAAC -s Anc0.Anc0refChr3 118369 17 + 222631 ACTACCTGCTGATCAAT -s Anc1.Anc1refChr6 152301 17 + 197743 ACTACCTGCTGATCAAT -s Anc2.Anc2refChr1 30761 17 + 142988 ACTACCTGCTGATCAAT -s mr.mrrefChr3 57235 17 + 181027 ATTACCTGCTGATCAAC -s simCow_chr6.simCow.chr6 487134 17 + 602619 TTTGCCCACTGAGCGAT -s simDog_chr6.simDog.chr6 477584 17 + 593897 ACTACCTGCTGATCAAT -s simHuman_chr6.simHuman.chr6 484153 1 + 601863 ----------------G -s simRat_chr6.simRat.chr6 516018 17 + 647215 ATTACCTGCTGATCAAC - -a -s simMouse_chr6.simMouse.chr6 504725 24 + 636262 TGTTTCCATCCTATGAGCTGACCT -s Anc0.Anc0refChr3 118386 22 + 222631 TGTTTCTAACCTAT--GCTGACCT -s Anc1.Anc1refChr6 152318 24 + 197743 TGTTTCTAACCTATGGGCTGACCT -s Anc2.Anc2refChr1 30787 22 + 142988 TGTTTCTAAGCTCC--GCTGACTC -s mr.mrrefChr3 57252 24 + 181027 TGTTTCCATCCTATGAGCTGACCT -s simCow_chr6.simCow.chr6 487160 13 + 602619 TGTGT-----------GCTGATGC -s simDog_chr6.simDog.chr6 477610 22 + 593897 TGTTTCTAAGCTCC--ACTGACTC -s simHuman_chr6.simHuman.chr6 484154 23 + 601863 TGTTTATAACCTATGGTTTGA-CT -s simRat_chr6.simRat.chr6 516035 24 + 647215 TGTTTCCGTCCTATCAGATGACCT - -a -s simMouse_chr6.simMouse.chr6 504749 26 + 636262 GTTATGCATAGTCTAATCTTTCAGGA -s Anc0.Anc0refChr3 118410 26 + 222631 ATCATGCACAGTCTAATTTTTCAGGA -s Anc1.Anc1refChr6 152344 26 + 197743 ATCATGCACAGTCTAATTTTTCAGGA -s Anc2.Anc2refChr1 30811 26 + 142988 ATCATGCACAGTCTAATTTTTTAGGA -s mr.mrrefChr3 57278 26 + 181027 ATCATGCATAGTCTAATTTTTCAGGA -s simCow_chr6.simCow.chr6 487175 26 + 602619 ATCATGCACAGCCTAGCTTTCTAGGA -s simDog_chr6.simDog.chr6 477634 26 + 593897 ATAAGGCACATTATAATTTCTTAGGA -s simHuman_chr6.simHuman.chr6 484179 26 + 601863 ATCGTGCACCGTCTAATTTTTCAGGA -s simRat_chr6.simRat.chr6 516061 26 + 647215 ATCATGCATAGTCTAATTTTTCAGGA - -a -s simMouse_chr6.simMouse.chr6 504775 37 + 636262 GCAGTTCCCAAAGCAAATGAAACTGATGATTAATCAG -s Anc0.Anc0refChr3 118437 35 + 222631 TCA--TCCCAAAGAAAATCACATCATTGATTGCTAAG -s Anc1.Anc1refChr6 152371 37 + 197743 TCAGTTCCCAAAGAAAATCACATCATTGATTGCTAAG -s Anc2.Anc2refChr1 30838 35 + 142988 TCG--TCCCAAAGAAAATCACATCATTGATGGCTGAG -s mr.mrrefChr3 57304 37 + 181027 GCAGTTCCCAAAGCAAATGAAACCAATGATTGATAAG -s simCow_chr6.simCow.chr6 487202 35 + 602619 TAT--CCCCAAAAAAAATCACAACATTGATGGCTGAG -s simDog_chr6.simDog.chr6 477661 22 + 593897 TCG--TCCCCAAGAAAATCACATC------------- -s simHuman_chr6.simHuman.chr6 484206 37 + 601863 TTAGTCCACAGAGAAAAGCACATCATTGATTGTTAGG -s simRat_chr6.simRat.chr6 516087 37 + 647215 GCAGTTCCCAAAGCAAATTAGACCAACCATTGCTAAG - -a -s simMouse_chr6.simMouse.chr6 504812 18 + 636262 GAGATAAACTATGGTGAA -s Anc0.Anc0refChr3 118475 18 + 222631 AAAATAAGCTATGTTAAG -s Anc1.Anc1refChr6 152411 18 + 197743 AAAATAAGCTATGTTAAG -s Anc2.Anc2refChr1 30876 18 + 142988 AAAATAAGCAATGTTAAG -s mr.mrrefChr3 57341 18 + 181027 GAGATAAACTATGGTGAG -s simCow_chr6.simCow.chr6 487240 18 + 602619 AAGATAAGCAATGTCAAG -s simDog_chr6.simDog.chr6 477683 18 + 593897 AAAATAAGCAATGTTAAG -s simHuman_chr6.simHuman.chr6 484246 18 + 601863 AAAATAAGCTATGCTAAG -s simRat_chr6.simRat.chr6 516124 18 + 647215 GAGATAAACTATGTTGAG - -a -s simMouse_chr6.simMouse.chr6 504830 12 + 636262 GCTTTAGTATGG -s Anc0.Anc0refChr3 118494 12 + 222631 ACCTTACTATAT -s Anc1.Anc1refChr6 152430 12 + 197743 ACCTTACTATAT -s Anc2.Anc2refChr1 30895 12 + 142988 ACCTTACTATAT -s mr.mrrefChr3 57360 12 + 181027 GCTTTAGTATGG -s simCow_chr6.simCow.chr6 487259 12 + 602619 ACCTTACTATAT -s simDog_chr6.simDog.chr6 477702 12 + 593897 ACCTTACTATAT -s simHuman_chr6.simHuman.chr6 484265 12 + 601863 ACCTTATTATAC -s simRat_chr6.simRat.chr6 516143 12 + 647215 GCTATCGTATGG - -a -s simMouse_chr6.simMouse.chr6 504842 14 + 636262 GTCTAGTATCTCCC -s Anc0.Anc0refChr3 118506 13 + 222631 GCCTGG-ACCTCTC -s Anc1.Anc1refChr6 152442 14 + 197743 GCCTGGCACCTCTC -s Anc2.Anc2refChr1 30907 13 + 142988 GCCTGG-ACCTCTC -s mr.mrrefChr3 57372 14 + 181027 GTCTGGTATCTCCC -s simCow_chr6.simCow.chr6 487271 8 + 602619 GACTAG------TA -s simDog_chr6.simDog.chr6 477714 13 + 593897 GCTTGG-ACCTCTC -s simHuman_chr6.simHuman.chr6 484332 14 + 601863 GCCTGTCACCTCTC -s simRat_chr6.simRat.chr6 516155 14 + 647215 GTCTGGTATCTCCC - -a -s simMouse_chr6.simMouse.chr6 504856 22 + 636262 CAGCTTTAACCTGACTAAATAG -s Anc0.Anc0refChr3 118519 22 + 222631 CAGCTTTAACATGACTAACTTG -s Anc1.Anc1refChr6 152456 22 + 197743 CAGCTTTAACATGACTAACTTG -s Anc2.Anc2refChr1 30922 22 + 142988 CAGCTTTAACATGACTAACTTA -s mr.mrrefChr3 57386 22 + 181027 CAGCTTTAACCTGACTAAATAG -s simCow_chr6.simCow.chr6 487281 22 + 602619 CAGCCTTAACATGACTAACTTA -s simDog_chr6.simDog.chr6 477729 22 + 593897 CAGCTTCAACATGGCAGACTTA -s simHuman_chr6.simHuman.chr6 484346 21 + 601863 CA-CTTTAACATGACTACCTTG -s simRat_chr6.simRat.chr6 516169 22 + 647215 CAGCTTTAACCTGACTAGATAG - -a -s simMouse_chr6.simMouse.chr6 504878 23 + 636262 TTGATGTAGGCTTACCAATAGAT -s Anc0.Anc0refChr3 118542 23 + 222631 TTAATGTAAGCTTACTAATAGAT -s Anc1.Anc1refChr6 152479 23 + 197743 TTAATGTAAGCTTACTAATAGAT -s Anc2.Anc2refChr1 30945 23 + 142988 TTAATGTAAGCTTACTAAAGGAT -s mr.mrrefChr3 57408 23 + 181027 TTGATGTAGGCTTACTAATAGAT -s simCow_chr6.simCow.chr6 487304 23 + 602619 TTAATGTAAGCTTACTAAAGGAT -s simDog_chr6.simDog.chr6 477752 23 + 593897 TTAATATAACTTTACTAAAGGAC -s simHuman_chr6.simHuman.chr6 484368 23 + 601863 TTAATGTAAGCTTACTGATAGAT -s simRat_chr6.simRat.chr6 516191 23 + 647215 TTGATGTAGGCTTACTAATAGGT - -a -s simMouse_chr6.simMouse.chr6 504901 124 + 636262 ATGCATCGACAGTGTCCAACTATTTCTTCTAGGACAGGACAGAATCCTGGTTGCAGCTGATCTTGGCACTCGAGGTGTCCATGAGGTGTCTCACACTCATAATCTTGACTTTCCACGAAACATT -s Anc0.Anc0refChr3 118567 124 + 222631 ATGTATCAGCATTGACTGGCTATTTCCTCTAGGACAAGACAGAATTCTGGTTGCAGCTGATCTTGGCACTCGAGGGGTTCATGATGTATCTCACATTCATAATCTTGACTTTCCACGAAACATT -s Anc1.Anc1refChr6 152504 124 + 197743 ATGTATCAGCATTGACTGGCTATTTCCTCTAGGACAAGACAGAATTCTGGTTGCAGCTGATCTTGGCACTCGAGGGGTTCATGATGTATCTCACATTCATAATCTTGACTTTCCACGAAACATT -s Anc2.Anc2refChr1 30970 124 + 142988 ATGTATCAGCATTAACTGGCTATTTCCTCTAGGACAAGACAGAATTCTGGTTGCAGCTGATCTTGGCACCCGAGGGGTTCATGATGTATCTCACATTCATAATTTTGACTTTCCACGAAACATT -s mr.mrrefChr3 57431 124 + 181027 ATGTATCGACATTGTCTAACTATTTCTTCTAGGACAGGACAGAATCCTGGTTGCAGCTGATCTTGGCACTCGAGGTGTCCATGATGTGTCTCACATTCATAATCTTGACTTTCCACGAAACATT -s simCow_chr6.simCow.chr6 487329 124 + 602619 ATGTATCAGCATTATCTCACTCTTTCCCCGAGGACAAGACAGAATTCTGATTGCAGCTGATCTTGGCACAAGAGGGATTCATGATGTGTCTCACATTCATAATTTTGACTTTCCACGAAACATT -s simDog_chr6.simDog.chr6 477777 121 + 593897 ACGCATCGGCA---ACTGGCTATTTGCTGTAGGAGAAGACAGAATTCTGGTTGCAGCTGATCTTGGCACCCGAGGGGTCCATGATGTATCTCACATTCATAATTTTGATTTTCCTAGAAACATT -s simHuman_chr6.simHuman.chr6 484393 124 + 601863 ATGTATCAGCATTGACTGGCTATTTCCTCCAGGACAAGACAGAATTCTGGTGGCAGCTGATCTTGGCACTCGAGGCGTTCCTGATGTATCCCACATTCATAATCTTGACTTTCCACGAAACATT -s simRat_chr6.simRat.chr6 516214 124 + 647215 AAGTATCGACATTGTCTAACTACTTCTTCTAGGACAGGACAGAATGCTGGTTGTGGCTGATCTTGGGACTCGAGGTGTCCACGATGTGTCTCACATTCATAATCTTGACTTTCCACGAAACATT - -a -s simMouse_chr6.simMouse.chr6 505025 58 + 636262 GAGCATGTGCACCATGTAGTAGCAGGGAGAGCAGGGTAAGCTTGAATAGTAGGCCATC -s Anc0.Anc0refChr3 118694 57 + 222631 GAGCATGTGCACCGTGTAGTTGCAGGGAGAGCAGGGTAAGCATGAATGGTATGCCAT- -s Anc1.Anc1refChr6 152631 58 + 197743 GAGCATGTGCACCGTGTAGTTGCAGGGAGAGCAGGGTAAGCATGAATGGTATGCCATC -s Anc2.Anc2refChr1 31097 57 + 142988 GAGCATGTGCACCGTGTAGTCTCAGGGAGAGCAGGGTAGGCAAGGCTGAGATACCAC- -s mr.mrrefChr3 57555 58 + 181027 GAGCATGTGCACCATGTAGTTGCAGGGAGAGCAGGGTAAGCATGAATAGTAGGCCATC -s simCow_chr6.simCow.chr6 487456 38 + 602619 GAGCATGTGCACCGTGTAGTAACAGGGAGAGCAGGGTA-------------------- -s simDog_chr6.simDog.chr6 477901 57 + 593897 GAGCATGTGCACCGTGTAGTCTCAGGGAGAGCAGGGTAGGCAAGGCTGAGATACCAC- -s simHuman_chr6.simHuman.chr6 484520 58 + 601863 GAACATGCGCACCGTGTAGTTGCAGGGAGAGTGGGGTGAGCATGAATGGTATGCCATC -s simRat_chr6.simRat.chr6 516338 58 + 647215 GAGCATGTGCACCATGTAGTTGCAGGGAGAGCAGGGTAAGCATGAAAAGTAGGCCATC - -a -s simMouse_chr6.simMouse.chr6 505083 41 + 636262 GTTAGCTTTTCATACCTCTCACTGTAGACCACTATAATTGC -s Anc0.Anc0refChr3 118751 25 + 222631 --AAACTGTTCATG--------------CCACCATAATTGA -s Anc1.Anc1refChr6 152692 41 + 197743 GAAAACTGTTCATGCCTCTCTATGTATACCACCATAATTGA -s Anc2.Anc2refChr1 31154 25 + 142988 --ACACTGTTTATG--------------CCACCACAATTGA -s mr.mrrefChr3 57616 41 + 181027 GTTAGCTTTTCATACCTCTCACTGTAGACCACCATAATTGC -s simDog_chr6.simDog.chr6 477958 25 + 593897 --ACACTGTTTATG--------------CCACCACAATTGA -s simHuman_chr6.simHuman.chr6 484581 41 + 601863 GAAAACTGTTCATGCCTCTCTATGTATACCACCATGATTGA -s simRat_chr6.simRat.chr6 516399 41 + 647215 GTTAGCTTTTCATACCTCTCGCTGTAGGCCACCATAATTGT - -a -s simMouse_chr6.simMouse.chr6 505124 97 + 636262 CCTTCGTGAGTGTACTGCATACTCCTAGCTTACAAACTGAATTCCAGTTCCATTAGAATAAAATATCTTATCCATTTGAGTCCTAAATCTATGAATA -s Anc0.Anc0refChr3 118777 90 + 222631 TCTTCATGGGTTCACAGCTTACTCACAGCCTACAAACCAACTTCT-CTTCCGTCAGAA-AATGCATCTTA-----AGGATTTTCAACCCTAAGCATA -s Anc1.Anc1refChr6 152734 91 + 197743 TCTTCATGGGTTCACAGCTTACTCACAGCCTACAAACCAACTTCTGCTTCCGTCAGAA-AATGCATCTTA-----AGGATTTTCAACCCTAAGCATA -s Anc2.Anc2refChr1 31180 90 + 142988 TCTTCACAGGTTCACAGCTTGCTCACAGCCAGCAAACCAACTTCT-CTTCCGTCTGAC-AATGCATTTTA-----AGGATTTTACACCCTTAGCATA -s mr.mrrefChr3 57657 97 + 181027 CCTTCATGAGTGTACTGCATACTCACAGCTTACAAACTGAATTCCAGTTCCATCAGAATAAAATATCTTATCCATTGGAGTCCCAAATCTATGAATA -s simCow_chr6.simCow.chr6 487494 70 + 602619 -----ACAGCTTCACAGCCTG------------AAACCAACTTCA-CTTCCATCTGAC-AATGCA---TA-----AGAATTTTACACCCTTAGCATA -s simDog_chr6.simDog.chr6 477984 71 + 593897 TCTTCACAGGTTTACAGCTTGCTCACAGCCAGCAAACTAACTTCT-TTCCCGTCTGAC-ATTGAATTTTA-----AAG------------------- -s simHuman_chr6.simHuman.chr6 484623 91 + 601863 TTTTCATGGGTTCACAGTTTACTCACAGCCTATAAAGCAACTTCTGCTTCCCTCAGAA-AATGCATCATA-----AGGGTTTTCAATCCTACGCATA -s simRat_chr6.simRat.chr6 516440 97 + 647215 CCCTCATGAGTGTAGTGAATGCTCACAGCTTACAAACTGAATTCCAGTTCTATCAGAATAAATTATCTTATCCATTGGAGTCCCAAGTCTAAGAGTA - -a -s simMouse_chr6.simMouse.chr6 505221 22 + 636262 AATTATCAAACACAAGTTAAAA -s Anc0.Anc0refChr3 119067 8 + 222631 AATTATCA-------------- -s Anc1.Anc1refChr6 153025 22 + 197743 AATTATCAAACACAAGTTAGGA -s Anc2.Anc2refChr1 31480 8 + 142988 TTGTATCA-------------- -s mr.mrrefChr3 57754 22 + 181027 AATTATCAAACACAAGTTAGAA -s simDog_chr6.simDog.chr6 478449 8 + 593897 TTGTATCA-------------- -s simHuman_chr6.simHuman.chr6 484918 22 + 601863 AATTATAGCACACAAGTTAGGA -s simRat_chr6.simRat.chr6 516537 22 + 647215 AATGATCAAACACAAGTTAGAA - -a -s simMouse_chr6.simMouse.chr6 505243 11 + 636262 CTGTATGTGAT -s Anc0.Anc0refChr3 119075 7 + 222631 ----ATACCAT -s Anc1.Anc1refChr6 153047 11 + 197743 CTACATACCAT -s Anc2.Anc2refChr1 31488 7 + 142988 ----ATCCTAC -s mr.mrrefChr3 57776 11 + 181027 CTGTATGCCAT -s simCow_chr6.simCow.chr6 487774 1 + 602619 ----------C -s simDog_chr6.simDog.chr6 478457 7 + 593897 ----ATCCTAC -s simHuman_chr6.simHuman.chr6 484940 11 + 601863 CTACATACCAT -s simRat_chr6.simRat.chr6 516563 11 + 647215 CTGTATGCCAT - -a -s simMouse_chr6.simMouse.chr6 505254 1 + 636262 C -s Anc0.Anc0refChr3 119082 1 + 222631 T -s Anc1.Anc1refChr6 153058 1 + 197743 T -s Anc2.Anc2refChr1 31495 1 + 142988 T -s mr.mrrefChr3 57787 1 + 181027 T -s simCow_chr6.simCow.chr6 487775 1 + 602619 T -s simDog_chr6.simDog.chr6 478464 1 + 593897 T -s simHuman_chr6.simHuman.chr6 484953 1 + 601863 T -s simRat_chr6.simRat.chr6 516574 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 505255 13 + 636262 GTGTCTTGTGCCA -s Anc0.Anc0refChr3 119083 13 + 222631 GCCTCTTGTGCCT -s Anc1.Anc1refChr6 153059 13 + 197743 GCCTCTTGTGCCT -s Anc2.Anc2refChr1 31496 13 + 142988 GCCTCTTGTGCCT -s mr.mrrefChr3 57788 13 + 181027 GTCTCTTGTGCCA -s simCow_chr6.simCow.chr6 487776 13 + 602619 GCCTCTTGTACCT -s simDog_chr6.simDog.chr6 478466 13 + 593897 GCCTTCGGTGACT -s simHuman_chr6.simHuman.chr6 484954 13 + 601863 GCCTCTTGTGCCT -s simRat_chr6.simRat.chr6 516575 13 + 647215 GTCTCTTGTGCCA - -a -s simMouse_chr6.simMouse.chr6 505268 7 + 636262 CCTATTT -s Anc0.Anc0refChr3 119096 7 + 222631 TTCATTT -s Anc1.Anc1refChr6 153072 7 + 197743 TTCATTT -s Anc2.Anc2refChr1 31509 7 + 142988 TTCGTTG -s mr.mrrefChr3 57801 7 + 181027 CCTATTT -s simCow_chr6.simCow.chr6 487789 7 + 602619 TTCCTAC -s simDog_chr6.simDog.chr6 478480 7 + 593897 CGCGTTG -s simHuman_chr6.simHuman.chr6 484967 7 + 601863 TTCATTT -s simRat_chr6.simRat.chr6 516588 7 + 647215 CCTATTT - -a -s simMouse_chr6.simMouse.chr6 505275 99 + 636262 GTAAGAAGAACTGGTGTTTCTATTTTAACCACAATCAGAAATGATTGGAGAGTTGCCACTGAATTGATCAATATTCTTGAAAGAGCAAATCATGTGCAA -s Anc0.Anc0refChr3 119109 99 + 222631 TAAAGCAGGACTGGTGTTTCTATTTCAACTACAATCAGAAATGATTGGAGAGTTGCCACTGAATTGATCAATATTCTTGAAAGAGCAAATCATGTGCAA -s Anc1.Anc1refChr6 153085 99 + 197743 TAAAGCAGGACTGGTGTTTCTATTTCAACTACAATCAGAAATGATTGGAGAGTTGCCACTGAATTGATCAATATTCTTGAAAGAGCAAATCATGTGCAA -s Anc2.Anc2refChr1 31522 99 + 142988 TAAAGGAGGACTGGTGTTTCTATTTCAACTACAATCAGAAATGATTGGAGAGTTGACACTGAATTGATCAATATTCTTGAAAGAGCAAATCATGTGCAA -s mr.mrrefChr3 57808 99 + 181027 GTAAGCAGAACTGGTGTTTCTATTTTAACCACAATCAGAAATGATTGGAGAGTTGCCACTGAATTGATCAATATTCTTGAAAGAGCAAATCATGTGCAA -s simCow_chr6.simCow.chr6 487802 99 + 602619 TAAAGGAGGACTGGTGTTTCTATTTCAACTACAATCAGAAATGATTGGAGAGTTGACACTGAGTTGATCAATATTCTTGAAAGAGCTAATCATGTGGAA -s simDog_chr6.simDog.chr6 478493 96 + 593897 CAGAGGAGGACTGGTGTTTCTATATCAACTACAATCAGAAATGATTGGAGGGTTGACACTGAACTGTTCAATATTCTT---AGAGCAAATCATGTGCAA -s simHuman_chr6.simHuman.chr6 484980 99 + 601863 TAAAGCAGGACTGGTGTTTCTATTTCAACTACAATCAGAAATGATTGGAGAGTTGCCACCGAATCAATCAATATTCTCAAAAGAGCAAATCGTGTACAA -s simRat_chr6.simRat.chr6 516595 99 + 647215 GGAAGCAGCACTGGCGTTTCTATTTTAACCACAATCAGAAATGATTGGAGAGTTGCCACTGAATTGATCAATGTTCTTGAAAGAGCAAATCATGTGCAA - -a -s simMouse_chr6.simMouse.chr6 505374 114 + 636262 CAACCATCATTTCATGCACCCTGTTGGTTACACGAAAACTCCTGCTAATCCATTCAGGCAACTGCACCAGAAAAAGAGTATGGGATATACCAAGAGTGAAGGACATATCCATGG -s Anc0.Anc0refChr3 119214 108 + 222631 CATCCATCATTTTACTTGCACAATTAATTAGACTAAAATTCTTGCTAGC----TCAGGCAGCTGCATCAGCAATGGAATATGGGGTATACCAAGAGTGAAGAACACACCCA--G -s Anc1.Anc1refChr6 153190 109 + 197743 CATCCATCATTTTACTTGCACAATTAATTAGACTAAAATTCTTGCTAGCT---TCAGGCAGCTGCATCAGCAATGGAATATGGGGTATACCAAGAGTGAAGAACACACCCA--G -s Anc2.Anc2refChr1 31634 108 + 142988 CATCCATCATTTTACTTGCACAATTCATTAGACTAAAATCCTTGCTAGC----TCAGGCAGCTGCTTGAGCAATGAAATATGGGGTATACCAAGAGGGAAGAGCACACCCA--G -s mr.mrrefChr3 57907 114 + 181027 CAACCATCATTTCATGCACACTGTTAATTAGACGAAAACTCCTGCTAATTCATTCAGGCAACTGCACCAGAAAAGGAATATGGGATATACCAAGAGTGAAGGACATATCCATGG -s simCow_chr6.simCow.chr6 487914 104 + 602619 CAGCCATCATTTCATTTGCACAATACATCAAATTAGAATCCTTGCTAGT----TTAGCCCACTGCTTGAGCAATGAAATGTAATGTATAC----AGGGAAGAGCACACCCA--G -s simDog_chr6.simDog.chr6 478602 97 + 593897 CATCCAGCAATCTACTTGAACAACTCGTTAGACTAAAGTCCTTGCTAGC----TCAGGCAGCTTC-------GTG----ATGGGGTATACCAAGGGGGAAGAGCACACCAA--G -s simHuman_chr6.simHuman.chr6 485085 107 + 601863 CATCCATCATTTTTCTTGCACAATTAACTGGTCTAAGAGTCTTGCCAGCT-----AGGTAGCTGCAACAGCAATGGAACATGGGGGACACCAAGAGTGAAGAACACACCCA--G -s simRat_chr6.simRat.chr6 516694 113 + 647215 CAACCA-CATTTCATGCACACTGTTAATTAGACCAAAACTCCTGCTACTTCATTCAGGCAACTCCACCAGAAAAGGAATGTGCGATATACCTAGAGTGAATGACATATCCATGG - -a -s simMouse_chr6.simMouse.chr6 505488 2 + 636262 AG -s Anc0.Anc0refChr3 119322 2 + 222631 GG -s Anc1.Anc1refChr6 153299 2 + 197743 GG -s Anc2.Anc2refChr1 31742 2 + 142988 GT -s mr.mrrefChr3 58021 2 + 181027 AG -s simCow_chr6.simCow.chr6 488020 2 + 602619 GT -s simDog_chr6.simDog.chr6 478699 2 + 593897 GT -s simHuman_chr6.simHuman.chr6 485192 2 + 601863 GG -s simRat_chr6.simRat.chr6 516807 2 + 647215 AG - -a -s simMouse_chr6.simMouse.chr6 505490 23 + 636262 TTTGGTAATTCATAACGAGGTAT -s Anc0.Anc0refChr3 119324 18 + 222631 TCAGTC-----ATAACAAGGTAT -s Anc1.Anc1refChr6 153301 18 + 197743 TCAGTC-----ATAACAAGGTAT -s Anc2.Anc2refChr1 31747 18 + 142988 TTAGTC-----ATAACAAGGTAC -s mr.mrrefChr3 58023 18 + 181027 TCTGGT-----ATAACAAGGTAT -s simCow_chr6.simCow.chr6 488025 18 + 602619 GAAGTC-----ATAACAAGGTTC -s simDog_chr6.simDog.chr6 478704 18 + 593897 TTAGTC-----ATAACAAGGTAC -s simHuman_chr6.simHuman.chr6 485194 15 + 601863 TCAG--------TATTAGGGTAT -s simRat_chr6.simRat.chr6 516809 18 + 647215 TCTGGG-----ATAACAAGGTAT - -a -s simMouse_chr6.simMouse.chr6 505513 9 + 636262 CTGTTTGAG -s Anc0.Anc0refChr3 119386 9 + 222631 CCATGTGAG -s Anc1.Anc1refChr6 153363 9 + 197743 CCATGTGAG -s Anc2.Anc2refChr1 31809 9 + 142988 CCATGTGAG -s mr.mrrefChr3 58094 9 + 181027 CTGTTTGAG -s simCow_chr6.simCow.chr6 488087 9 + 602619 CCATACAAG -s simDog_chr6.simDog.chr6 478769 9 + 593897 CCAAGTGAA -s simHuman_chr6.simHuman.chr6 485253 9 + 601863 CCATGAGAG -s simRat_chr6.simRat.chr6 516880 9 + 647215 CTGTATGAG - -a -s simMouse_chr6.simMouse.chr6 505522 10 + 636262 CTTGTTTAAT -s Anc0.Anc0refChr3 119396 10 + 222631 CTTGTTTGGA -s Anc1.Anc1refChr6 153373 10 + 197743 CTTGTTTGGA -s Anc2.Anc2refChr1 31819 10 + 142988 CTTGTTTGGA -s mr.mrrefChr3 58103 10 + 181027 CTTGTTTAAT -s simCow_chr6.simCow.chr6 488097 10 + 602619 TTTTATAGGA -s simDog_chr6.simDog.chr6 478779 10 + 593897 CTTGTTTGGA -s simHuman_chr6.simHuman.chr6 485263 10 + 601863 CTTGTTTGGG -s simRat_chr6.simRat.chr6 516889 10 + 647215 CTTGTTTAAT - -a -s simMouse_chr6.simMouse.chr6 505532 36 + 636262 TGCTTCAGGCCCAAACTGTGAATTTAGCTTAAAGTA -s Anc0.Anc0refChr3 119406 8 + 222631 TAC-----------ACTGT----------------- -s Anc1.Anc1refChr6 153383 8 + 197743 TAC-----------ACTGT----------------- -s Anc2.Anc2refChr1 31829 8 + 142988 TAC-----------ACTTT----------------- -s mr.mrrefChr3 58113 34 + 181027 TGCTTCAGGCC--AACTGTGAATTTAGCTTAAAGTA -s simCow_chr6.simCow.chr6 488111 8 + 602619 TAC-----------ATATT----------------- -s simDog_chr6.simDog.chr6 478789 8 + 593897 TAC-----------ACTTG----------------- -s simHuman_chr6.simHuman.chr6 485273 8 + 601863 TAC-----------ACTGT----------------- -s simRat_chr6.simRat.chr6 516899 34 + 647215 TGTTTGAGGTC--AACTGTGCATTTAGTTTAAAGGG - -a -s simMouse_chr6.simMouse.chr6 505568 147 + 636262 CAGTTCTATGAACATGTAGGCGTTAACAGGACCTAAAACTTATTACCCCTTAGCAGGTAAGAATGCCCCTGGCAACTTCATATCTGAACAGCTATATTGACAACCTGCTCTTCATCACCTTTGACAAAAACTCATATCTCACAGAGC -s Anc0.Anc0refChr3 119414 4 + 222631 ----------------------------------------------------------------------------------------------------------------------------------------------AGTT- -s Anc1.Anc1refChr6 153391 4 + 197743 ----------------------------------------------------------------------------------------------------------------------------------------------AGTT- -s Anc2.Anc2refChr1 31837 4 + 142988 ----------------------------------------------------------------------------------------------------------------------------------------------AGTT- -s mr.mrrefChr3 58147 130 + 181027 CAGTTCTATGAACATGTAGGCGTTAACAGGA-CTAAAACTTATTACCCCTTAGCAGGTAAGAATGCCCCTGGCAACTTCATATCTGAACAGCTATATTGACAACCTGCTCTTC---------------AACTCATATCTCACAGAG- -s simCow_chr6.simCow.chr6 488119 4 + 602619 ----------------------------------------------------------------------------------------------------------------------------------------------GGTT- -s simDog_chr6.simDog.chr6 478797 4 + 593897 ----------------------------------------------------------------------------------------------------------------------------------------------AGTT- -s simHuman_chr6.simHuman.chr6 485281 4 + 601863 ----------------------------------------------------------------------------------------------------------------------------------------------AGTT- -s simRat_chr6.simRat.chr6 516934 130 + 647215 CAGTTCTCTGAACATGCAGGTGTTAATGGGA-CTAAAACTTATTACCCTTTAGCAGGCAAGAATACCCCTGGTGTCTTTGTATCTGAACAGCTATATTCACAACCTGCTCTGC---------------AACTCATATCTCACAGAG- - -a -s simMouse_chr6.simMouse.chr6 505715 22 + 636262 ACACAATCATAAGAAGTTGGTT -s Anc0.Anc0refChr3 119418 22 + 222631 AAACTACAATAAGAGGTTGGTC -s Anc1.Anc1refChr6 153395 22 + 197743 AAACTACAATAAGAGGTTGGTC -s Anc2.Anc2refChr1 31905 22 + 142988 AAACTACAACAAGAGGTTGGTT -s mr.mrrefChr3 58277 22 + 181027 ACACAATAATAAGAAGTTGGTC -s simCow_chr6.simCow.chr6 488188 10 + 602619 AAATCATAA------------T -s simDog_chr6.simDog.chr6 478867 22 + 593897 AAACTACAACAAGAGGTTGGTT -s simHuman_chr6.simHuman.chr6 485285 22 + 601863 GGACTACAATAAGAGGTTGGTC -s simRat_chr6.simRat.chr6 517064 22 + 647215 ACACAATACTAAGGATTGGGTC - -a -s simMouse_chr6.simMouse.chr6 505737 171 + 636262 TCCAGAGCATCCCAGAAGAGCTAGTTTCAATGGTTGAGATGCTAAAGGCACATCAACAGCGGACTGAGATGGAGAGAAAGATAGAGAGACCTCAAGGGAGGCCTAAGAAATTCCACCAGTTTTTTCAAGGAGGCAGGTGTGGTACCTCCAACTATATTATTGGCTTTTAGC -s Anc0.Anc0refChr3 119445 165 + 222631 T-CAGAGCATCCCAGAAGAGCTAGTTTCAATGGTTGAGATGCTAAAGGCACACCAACAGAGGAGAGAGATGGAGAGAAAAATGGAAAGACCTCAAGGAAGGCCTAAGAAATTCCACCAATTCTTTCAGGGAGGCAGGTGTGGAACCTCTAACTATG-----GGCTTTTAGG -s Anc1.Anc1refChr6 153422 165 + 197743 T-CAGAGCATCCCAGAAGAGCTAGTTTCAATGGTTGAGATGCTAAAGGCACACCAACAGAGGAGAGAGATGGAGAGAAAAATGGAAAGACCTCAAGGAAGGCCTAAGAAATTCCACCAATTCTTTCAGGGAGGCAGGTGTGGAACCTCTAACTATG-----GGCTTTTAGG -s Anc2.Anc2refChr1 31932 165 + 142988 T-CAGAGCATCCCAGAAGAGCTAGTTTCAATGGTTGAGATGCTAAAGGCACACCAACAGAGGAGAGAGATGGAGAGAAAAATGGAAAGACCTCAAGGAAGGCCTAAGAAATTCCATCAATTCTTTCAGGGAGGCAGGTGTGGAACATCTAACTATG-----GGCTATTAGG -s mr.mrrefChr3 58299 170 + 181027 T-CAGAGCATCCCAGAAGAGCTAGTTTCAATGGTTGAGATGCTAAAGGCACATCAACAGAGGAGTGAGATGGAGAGAAAGATGGAAAGACCTCAAGGGAGGCCTAAGAAATTCCACCAATTTTTTCAGGGAGGCAGGTGTGGTACCTCCAACTATATTATTGGCTTTTAGC -s simCow_chr6.simCow.chr6 488203 165 + 602619 T-CAGAGCATCCCGGAAGAGCTAGTTTCAATGGTAGAGATGCTGAAGGCACACCAACAGAGGAGGGAGATGGAGAGAAAAATGGAAAGACCTCAGGGAAGGCCAAAAAAGTTCCATCAGTTCTTTCAGGGAGGCAGGTGTGAGACATCGAACTATG-----GGCTATTAGG -s simDog_chr6.simDog.chr6 478894 164 + 593897 T-CAGAGCATCCCAGAAGAGCTAGTTTCAATGGTTGAGATGCTAAAGGCCCACCAACAGCGAAGAGCAATGGAGAGAAAAATGGAAAGACCCCAAGGAAGGCCTAAGAAATTCCATCAATTCTTTCAGGGAGGCAGGTGTGGAACACCTAGCGATG-----GGCTATTAG- -s simHuman_chr6.simHuman.chr6 485312 165 + 601863 T-CAGAGCATCCCAGAAGAGCTAGTTACGATGGTTGAGATGTTAAAGGCACACCAACAGAGGAGAGAGATGGAGAGAAAAATGGAAAGACCTCAAGGAAGGCCTAAGAAATACCACCAATTCTTTCAGGGAGGCAGGTGTGGAATCTCTAACTATG-----GGCTTTTAGG -s simRat_chr6.simRat.chr6 517086 170 + 647215 T-CAGAGCATCCCGGAAGAGCTAGTTTCAATGGTCGAGATGCTAAAGGCACATCAACAGAGGAGTGAGATGGAGAGAAAGATGGAAAGACCTCAAGGGAGGCCTAAGAAATTCCATCAATTTTTTCAGGGAGGCAGGTGTGGTACCTTCAACTACACTATTGGCTTTTAGC - -a -s simMouse_chr6.simMouse.chr6 505908 24 + 636262 TACAAAGCTGCTTACTCTAAATGC -s Anc0.Anc0refChr3 119610 24 + 222631 TACCAAACTGTTTACACTAGACAA -s Anc1.Anc1refChr6 153587 24 + 197743 TACCAAACTGTTTACACTAGACAA -s Anc2.Anc2refChr1 32097 24 + 142988 TACCAAACTGTTTACACTAGACAA -s mr.mrrefChr3 58469 24 + 181027 TACAAAACTGCTTACTCTAGATGC -s simCow_chr6.simCow.chr6 488399 24 + 602619 TACCAAACTGTTTATACTAGACAC -s simDog_chr6.simDog.chr6 479058 19 + 593897 -----AACTGGTTACACTAGACAA -s simHuman_chr6.simHuman.chr6 485477 24 + 601863 TACCAAACTGTTATCACTAGACAT -s simRat_chr6.simRat.chr6 517256 24 + 647215 TACAAAACTGCTCACTCAAGATGC - -a -s simMouse_chr6.simMouse.chr6 505932 33 + 636262 AAATGTCTTCAATTAGGTCCCATTACTTTGACT -s Anc0.Anc0refChr3 119640 20 + 222631 GAATGTTTT----------CAATTACTTTG--- -s Anc1.Anc1refChr6 153617 23 + 197743 GAATGTTTT----------CAATTACTTTGAAT -s Anc2.Anc2refChr1 32127 20 + 142988 GACAAGTTT----------CAATTACTTTG--- -s mr.mrrefChr3 58499 33 + 181027 AAATGTTTTCAATTAGTTCCCATTACTTTGACT -s simCow_chr6.simCow.chr6 488429 20 + 602619 GACAAGTTT----------CAATTGCTTTG--- -s simDog_chr6.simDog.chr6 479083 15 + 593897 GA-----TT----------CAATTACGTTG--- -s simHuman_chr6.simHuman.chr6 485507 23 + 601863 CAATGTTTT----------CAATTACTTTGAAT -s simRat_chr6.simRat.chr6 517286 33 + 647215 GAATGTTTTCAATTATTTTCAATTACTTTGGCT - -a -s simMouse_chr6.simMouse.chr6 505965 7 + 636262 AGTGTAC -s Anc0.Anc0refChr3 119660 7 + 222631 ACCATTC -s Anc1.Anc1refChr6 153640 7 + 197743 ACCATTC -s Anc2.Anc2refChr1 32147 7 + 142988 ACCATTG -s mr.mrrefChr3 58532 7 + 181027 AGTATAC -s simCow_chr6.simCow.chr6 488449 7 + 602619 ACCATTG -s simDog_chr6.simDog.chr6 479098 7 + 593897 GCCACTG -s simHuman_chr6.simHuman.chr6 485530 7 + 601863 ACCATGC -s simRat_chr6.simRat.chr6 517321 7 + 647215 AATATAC - -a -s simMouse_chr6.simMouse.chr6 505972 5 + 636262 AAGCA -s Anc0.Anc0refChr3 119667 5 + 222631 AACCA -s Anc1.Anc1refChr6 153647 5 + 197743 AACCA -s Anc2.Anc2refChr1 32154 5 + 142988 AACCA -s mr.mrrefChr3 58539 5 + 181027 AAGCA -s simCow_chr6.simCow.chr6 488456 5 + 602619 AGCCA -s simDog_chr6.simDog.chr6 479107 5 + 593897 AAGCC -s simHuman_chr6.simHuman.chr6 485537 5 + 601863 AACCA -s simRat_chr6.simRat.chr6 517328 5 + 647215 AAGCA - -a -s simMouse_chr6.simMouse.chr6 505977 11 + 636262 GCTGTTTCCAT -s Anc0.Anc0refChr3 119672 11 + 222631 ACTGTTCCCAC -s Anc1.Anc1refChr6 153652 11 + 197743 ACTGTTCCCAC -s Anc2.Anc2refChr1 32159 11 + 142988 ACTGTTCCCAC -s mr.mrrefChr3 58544 11 + 181027 ACTGTTCCCAT -s simCow_chr6.simCow.chr6 488463 11 + 602619 ACTGTCCCCAG -s simDog_chr6.simDog.chr6 479112 11 + 593897 ACTGTTCCCAC -s simHuman_chr6.simHuman.chr6 485542 11 + 601863 ACTGTTCATGC -s simRat_chr6.simRat.chr6 517333 11 + 647215 ACTGTTCCCAT - -a -s simMouse_chr6.simMouse.chr6 505988 3 + 636262 AGT -s Anc0.Anc0refChr3 119683 3 + 222631 CAT -s Anc1.Anc1refChr6 153663 3 + 197743 CAT -s Anc2.Anc2refChr1 32170 3 + 142988 CAT -s mr.mrrefChr3 58555 3 + 181027 CGT -s mr.mrrefChr3 58654 3 + 181027 TGT -s simCow_chr6.simCow.chr6 488474 3 + 602619 TAT -s simDog_chr6.simDog.chr6 479123 3 + 593897 CAT -s simHuman_chr6.simHuman.chr6 485553 3 + 601863 CAT -s simMouse_chr6.simMouse.chr6 506085 3 + 636262 TGT -s simRat_chr6.simRat.chr6 517443 3 + 647215 TGT -s simRat_chr6.simRat.chr6 517344 3 + 647215 CGT - -a -s simMouse_chr6.simMouse.chr6 505991 4 + 636262 TTAT -s Anc0.Anc0refChr3 119686 4 + 222631 TTAT -s Anc1.Anc1refChr6 153666 4 + 197743 TTAT -s Anc2.Anc2refChr1 32173 4 + 142988 TTAT -s mr.mrrefChr3 58558 4 + 181027 TTAT -s mr.mrrefChr3 58657 4 + 181027 AAAC -s simCow_chr6.simCow.chr6 488480 4 + 602619 TTAT -s simDog_chr6.simDog.chr6 479126 4 + 593897 TTAT -s simHuman_chr6.simHuman.chr6 485556 4 + 601863 TTAT -s simMouse_chr6.simMouse.chr6 506088 4 + 636262 AAAC -s simRat_chr6.simRat.chr6 517446 4 + 647215 AAAC -s simRat_chr6.simRat.chr6 517347 4 + 647215 TTAT - -a -s simMouse_chr6.simMouse.chr6 505995 1 + 636262 T -s mr.mrrefChr3 58562 1 + 181027 T -s simRat_chr6.simRat.chr6 517351 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 505996 30 + 636262 CAAAATTTTAGGGCTCTCAGGATGAACTGA -s Anc0.Anc0refChr3 119690 30 + 222631 CAAAATTTGGAGGTTTTCTGGAAACATTAA -s Anc1.Anc1refChr6 153670 30 + 197743 CAAAATTTGGAGGTTTTCTGGAAACATTAA -s Anc2.Anc2refChr1 32177 30 + 142988 CAATATTTGGAGGTCTTCTGGAAATGTTAA -s mr.mrrefChr3 58563 30 + 181027 CAAAATTTTAAGGCTCTCAGGATGCATTGA -s mr.mrrefChr3 58661 30 + 181027 CAACATTTCGGGGTTTTGTGGACTCACCAA -s simCow_chr6.simCow.chr6 488484 18 + 602619 CGCTATTTGGAAGTATTC------------ -s simDog_chr6.simDog.chr6 479130 30 + 593897 CAATATTTGGAGGTCATGTGGAAATGTTAA -s simHuman_chr6.simHuman.chr6 485560 30 + 601863 CAAAATCTGGAGGTTTTCTGGAAACATTAA -s simMouse_chr6.simMouse.chr6 506092 30 + 636262 CAACATTTCGGGGCTTTGTGGACTCACCAA -s simRat_chr6.simRat.chr6 517450 30 + 647215 CGACATTTTGGGGTTTTCTGGACTCACCAA -s simRat_chr6.simRat.chr6 517352 30 + 647215 CACAATTTCAAGACTCTCAGGATGCCTTGA - -a -s simMouse_chr6.simMouse.chr6 506026 5 + 636262 TGGCA -s Anc0.Anc0refChr3 119724 4 + 222631 TGGT- -s Anc1.Anc1refChr6 153704 5 + 197743 TGGTG -s Anc2.Anc2refChr1 32211 4 + 142988 TGGT- -s mr.mrrefChr3 58593 5 + 181027 TGGTG -s mr.mrrefChr3 58695 5 + 181027 TGATT -s simDog_chr6.simDog.chr6 479164 4 + 593897 TGGT- -s simHuman_chr6.simHuman.chr6 485594 5 + 601863 TGATG -s simMouse_chr6.simMouse.chr6 506126 5 + 636262 TGATG -s simRat_chr6.simRat.chr6 517484 5 + 647215 TGATT -s simRat_chr6.simRat.chr6 517382 5 + 647215 TGGTG - -a -s simMouse_chr6.simMouse.chr6 506031 15 + 636262 CCAAAAGGTGGGCCT -s Anc0.Anc0refChr3 119728 14 + 222631 -TAGAAGGCAGGCCT -s Anc1.Anc1refChr6 153709 15 + 197743 CTAGAAGGCAGGCCT -s Anc2.Anc2refChr1 32215 14 + 142988 -TAGAAGGCAGGCAT -s mr.mrrefChr3 58598 15 + 181027 CCAAAAGATGGGCCT -s mr.mrrefChr3 58703 15 + 181027 CCGAAAGGCAGGCCT -s simCow_chr6.simCow.chr6 488502 7 + 602619 --------CAGGTGT -s simDog_chr6.simDog.chr6 479168 14 + 593897 -TAGAAGGCAGGCAT -s simHuman_chr6.simHuman.chr6 485599 15 + 601863 CTAGAAGACAGGCCT -s simMouse_chr6.simMouse.chr6 506134 15 + 636262 CCGAAAGGCAGGCCT -s simRat_chr6.simRat.chr6 517492 15 + 647215 CCAAAAGGCAGGCTT -s simRat_chr6.simRat.chr6 517387 15 + 647215 CCAAAAGATGGGCCC - -a -s simMouse_chr6.simMouse.chr6 506046 39 + 636262 GTTGTTGATACTGAGATATCTTACTCTGGGAGATCTAGA -s Anc0.Anc0refChr3 119744 39 + 222631 TTACATGATGCTGAGATATCTTCTGTTGGAAAATGAATA -s Anc1.Anc1refChr6 153726 39 + 197743 TTACATGATGCTGAGATATCTTCTGTTGGAAAATGAATA -s Anc2.Anc2refChr1 32231 39 + 142988 TTACATGATGCTGATATATCTTCTGTTGGAACATGAATA -s mr.mrrefChr3 58615 39 + 181027 GTTCTTGATAATGAGATATCTTACTCTGGGAAATCTAGA -s mr.mrrefChr3 58720 39 + 181027 TCACATGATGCTGAGATATCTTATTCTGGGAGATGTAGA -s simCow_chr6.simCow.chr6 488511 39 + 602619 TTACATGATGCTGTAATAGCTTCTGTTGGAACATGAATA -s simDog_chr6.simDog.chr6 479184 39 + 593897 TTACATGATGCTGATATATCTTCTGTTGGAACATGAATA -s simHuman_chr6.simHuman.chr6 485616 39 + 601863 TTGCATGATAATGAGATATTTTCTGTTAGACAGTGAATA -s simMouse_chr6.simMouse.chr6 506151 39 + 636262 TCACTTGATGCTGAGATTTCTTATTCTGGGAGATGTAGA -s simRat_chr6.simRat.chr6 517509 39 + 647215 TGACATGATACTGAAATATCTTACTCTGGGAGATGTCAA -s simRat_chr6.simRat.chr6 517404 39 + 647215 ATTCCTGATAATGAAATATCTTACTCTGGGAAATCTTGA - -a -s simMouse_chr6.simMouse.chr6 506122 4 + 636262 TACT -s Anc0.Anc0refChr3 119720 4 + 222631 GAAT -s Anc1.Anc1refChr6 153700 4 + 197743 GAAT -s Anc2.Anc2refChr1 32207 4 + 142988 GAAT -s mr.mrrefChr3 58691 4 + 181027 GACT -s simDog_chr6.simDog.chr6 479160 4 + 593897 GAAT -s simHuman_chr6.simHuman.chr6 485590 4 + 601863 GATT -s simRat_chr6.simRat.chr6 517480 4 + 647215 GACT - -a -s simMouse_chr6.simMouse.chr6 506131 3 + 636262 AAT -s mr.mrrefChr3 58700 3 + 181027 AAT -s simRat_chr6.simRat.chr6 517489 3 + 647215 AAG - -a -s simMouse_chr6.simMouse.chr6 506149 2 + 636262 AT -s Anc0.Anc0refChr3 119742 2 + 222631 AT -s Anc1.Anc1refChr6 153724 2 + 197743 AT -s Anc2.Anc2refChr1 32229 2 + 142988 AT -s mr.mrrefChr3 58718 2 + 181027 AT -s mr.mrrefChr3 58613 2 + 181027 CT -s simCow_chr6.simCow.chr6 488509 2 + 602619 AT -s simDog_chr6.simDog.chr6 479182 2 + 593897 CT -s simHuman_chr6.simHuman.chr6 485614 2 + 601863 AT -s simRat_chr6.simRat.chr6 517402 2 + 647215 CT -s simRat_chr6.simRat.chr6 517507 2 + 647215 AT - -a -s simMouse_chr6.simMouse.chr6 506190 156 + 636262 TGTAAAAGCTCTACACAACGAAGGACTTTAGCGGTCCGCGACACATTCTGCTGGACTTTTAGGACGCGACTGTTGCATCGCCTATAGCAGGGTGAAAAATAATTGGGAACATATAATGGATAGGCCTTGGGAAGGTATAATGTGGAATAATCCTAC -s Anc0.Anc0refChr3 119783 75 + 222631 TGTAAGAGCTCTATACCATG-----CC----------------------------------------------------------------ATGATAAAAACCAGTGAGCAAAAAA---------CTTAGGAAGACATAA--T-GCATAATCCTAC -s Anc1.Anc1refChr6 153765 75 + 197743 TGTAAGAGCTCTATACCATG-----CC----------------------------------------------------------------ATGATAAAAACCAGTGAGCAAAAAA---------CTTAGGAAGACATAA--T-GCATAATCCTAC -s Anc2.Anc2refChr1 32270 75 + 142988 TGTAAGAGCTCTATACCATG-----CC----------------------------------------------------------------ACAATTAAAACCAGTGAGTAAAAAA---------CTTAGGAATACATAA--T-GCATAATCCTAG -s mr.mrrefChr3 58759 100 + 181027 TGTAAAAGCTCTACACAATGAAGGACCTTAGTGGT------------------------------------------------------GGGTGAAAAATAATTGTAAACATATAATGTATAAGCCTTGGGAAGGTATAA--TGGCATAATCCTAC -s simCow_chr6.simCow.chr6 488550 69 + 602619 TGTAAGAACTCTATACCATG-----CC----------------------------------------------------------------AC------AATCAGTGAGTAGAAAT---------CTTAGGACTAAATAA--T-GCATAATCCTAT -s simDog_chr6.simDog.chr6 479223 75 + 593897 TATAAGAGCTCTATACCATG-----CC----------------------------------------------------------------TCAATTAAAACCACTGAGTAAAAAA---------CCTTGGAATACATAA--T-GCATAATCCTGG -s simHuman_chr6.simHuman.chr6 485655 71 + 601863 TGTAAGAGCTCTATAC---------CC----------------------------------------------------------------ATGAGAAAAACCAGTGAGCAAAAAA---------CTCAGGAAGACATAA--T-ACATGATCCTAC -s simRat_chr6.simRat.chr6 517548 100 + 647215 TGTAAAAGCTCTAAACAATGAAAGACCTTAGTGGC------------------------------------------------------GGTTCAAAAATAATCATAAATATATGATGTATAAGCCTTGGGAAGGTATAA--TGGCATAGTCCTAC - -a -s simMouse_chr6.simMouse.chr6 506346 14 + 636262 ATACTAAGGCTATA -s Anc0.Anc0refChr3 119858 11 + 222631 ATACAAAGGCT--- -s Anc1.Anc1refChr6 153840 11 + 197743 ATACAAAGGCT--- -s Anc2.Anc2refChr1 32345 11 + 142988 GTACAAAGGCT--- -s mr.mrrefChr3 58859 14 + 181027 ATACTAAGGCTATA -s simCow_chr6.simCow.chr6 488688 11 + 602619 GTATAGGGGCT--- -s simDog_chr6.simDog.chr6 479298 11 + 593897 GTACTAAAACC--- -s simHuman_chr6.simHuman.chr6 485726 11 + 601863 ATTCACAGGTT--- -s simRat_chr6.simRat.chr6 517648 14 + 647215 ATGCTGAGGTTATA - -a -s simMouse_chr6.simMouse.chr6 506360 42 + 636262 TAACATAATGCCACTTGGCTTTTGATAAAGGTAGAGATAAGC -s Anc0.Anc0refChr3 119869 40 + 222631 --ACATAGTGATACTTGATCTTACATAAAGGCAAAGACAAGT -s Anc1.Anc1refChr6 153851 40 + 197743 --ACATAGTGATACTTGATCTTACATAAAGGCAAAGACAAGT -s Anc2.Anc2refChr1 32356 40 + 142988 --ACATAGTGATACCTGATCTTACATAAAGGCAAAGACAAGT -s mr.mrrefChr3 58873 42 + 181027 TAACATAATGCCACTTGGCTTTTGATAAAGGTAGAGACAAGC -s simCow_chr6.simCow.chr6 488699 38 + 602619 --ACATAGTGATGCCTGATCTTACATAAGGACCAAA--AAGT -s simDog_chr6.simDog.chr6 479309 40 + 593897 --ACATAGCGACACCAGATCTGACATAAAGGCAAAGACAAGT -s simHuman_chr6.simHuman.chr6 485737 40 + 601863 --ACATAGTGATACTTGATCTTCCATAAAGGCAAAGACTAGT -s simRat_chr6.simRat.chr6 517676 42 + 647215 TAACATAATTCCACTGGGCTATGAATAAAGGTAGAGACAAGC - -a -s simMouse_chr6.simMouse.chr6 506402 3 + 636262 GGT -s Anc0.Anc0refChr3 119918 3 + 222631 GAT -s Anc1.Anc1refChr6 153900 3 + 197743 GAT -s Anc2.Anc2refChr1 32405 3 + 142988 GAT -s mr.mrrefChr3 58915 3 + 181027 GGT -s simCow_chr6.simCow.chr6 488747 3 + 602619 GAT -s simDog_chr6.simDog.chr6 479358 3 + 593897 GAT -s simHuman_chr6.simHuman.chr6 485786 3 + 601863 GCT -s simRat_chr6.simRat.chr6 517718 3 + 647215 AGT - -a -s simMouse_chr6.simMouse.chr6 506405 32 + 636262 AACCCATAATACATAATGGGTATTTGGGAATC -s Anc0.Anc0refChr3 119921 32 + 222631 AACCCATTATAGTTACTGGTGCTTGGGAAGTA -s Anc1.Anc1refChr6 153903 32 + 197743 AACCCATTATAGTTACTGGTGCTTGGGAAGTA -s Anc2.Anc2refChr1 32419 32 + 142988 AACCCATTATAGTTACTGGTGCTTGGGAAGCA -s mr.mrrefChr3 58918 32 + 181027 AACCCATTATACATAATGGGTATTTGGAAATC -s simCow_chr6.simCow.chr6 488761 32 + 602619 AAGCCATTATAGTTATCGTTGCATGGGAAGCA -s simDog_chr6.simDog.chr6 479372 25 + 593897 AACCCATTATAATTACTGGTGTTGG------- -s simHuman_chr6.simHuman.chr6 485789 32 + 601863 AATCCATTATGGTCACTGGTACTTGGGAAGTA -s simRat_chr6.simRat.chr6 517721 32 + 647215 AATCCATTATACAAAATGGGTACTTGGAAATC - -a -s simMouse_chr6.simMouse.chr6 506437 10 + 636262 CAGGACCCAA -s Anc0.Anc0refChr3 119953 10 + 222631 TTAGATCTTA -s Anc1.Anc1refChr6 153935 10 + 197743 TTAGATCTTA -s Anc2.Anc2refChr1 32451 10 + 142988 TTAGATCTTA -s mr.mrrefChr3 58950 10 + 181027 TGGGACCCAA -s simCow_chr6.simCow.chr6 488799 10 + 602619 TTAGATTTTA -s simDog_chr6.simDog.chr6 479397 8 + 593897 --AAATCAAA -s simHuman_chr6.simHuman.chr6 485821 10 + 601863 TCAGATCTTA -s simRat_chr6.simRat.chr6 517753 10 + 647215 TGGGACCCTA - -a -s simMouse_chr6.simMouse.chr6 506447 8 + 636262 TGTAAAAT -s Anc0.Anc0refChr3 119963 8 + 222631 TGGATTCT -s Anc1.Anc1refChr6 153945 8 + 197743 TGGATTCT -s Anc2.Anc2refChr1 32461 8 + 142988 TGGATTCT -s mr.mrrefChr3 58960 8 + 181027 TGTAAAAT -s simCow_chr6.simCow.chr6 488813 8 + 602619 TGGATTCT -s simDog_chr6.simDog.chr6 479405 8 + 593897 TGGGTACT -s simHuman_chr6.simHuman.chr6 485831 8 + 601863 TGGACTCT -s simRat_chr6.simRat.chr6 517763 8 + 647215 TGCAAAAT - -a -s simMouse_chr6.simMouse.chr6 506455 70 + 636262 ACAATGTATAATCTTACATACTGAGACCACATTAATAACTGGTCAACTAGTCTTCCATTAGGGCAGAGGC -s Anc0.Anc0refChr3 119971 6 + 222631 GGAATG---------------------------------------------------------------- -s Anc1.Anc1refChr6 153953 6 + 197743 GGAATG---------------------------------------------------------------- -s Anc2.Anc2refChr1 32470 6 + 142988 GGAATG---------------------------------------------------------------- -s mr.mrrefChr3 58968 70 + 181027 ATAATGTATGATCCTACATACTGAGACCACATTAATAATTGGTCAACTAGTCTTCCATTAGGGCAGAGGC -s simCow_chr6.simCow.chr6 488872 6 + 602619 GGAATG---------------------------------------------------------------- -s simDog_chr6.simDog.chr6 479414 6 + 593897 GGAATG---------------------------------------------------------------- -s simHuman_chr6.simHuman.chr6 485839 6 + 601863 CAAATG---------------------------------------------------------------- -s simRat_chr6.simRat.chr6 517771 70 + 647215 ATAATGTATGAGCCTACATACTGAGAACACATTAAAAATTGGTCTACTAGTCTTCCTCTAGGGCAGAGGC - -a -s simMouse_chr6.simMouse.chr6 506525 46 + 636262 CGCAGTTTAACTACTTGTACAGGGTCATGAAATGGGTACCTTGAAG -s Anc0.Anc0refChr3 119977 1 + 222631 ---------------------------------------------G -s Anc1.Anc1refChr6 153959 1 + 197743 ---------------------------------------------G -s Anc2.Anc2refChr1 32476 1 + 142988 ---------------------------------------------G -s mr.mrrefChr3 59038 46 + 181027 CACATTTTAACTACTTGTACAGGGTCATGAAATGGGTACCTTGAAG -s simCow_chr6.simCow.chr6 488878 1 + 602619 ---------------------------------------------G -s simDog_chr6.simDog.chr6 479420 1 + 593897 ---------------------------------------------G -s simHuman_chr6.simHuman.chr6 485845 1 + 601863 ---------------------------------------------G -s simRat_chr6.simRat.chr6 517849 31 + 647215 CACATTTTAACTACTTG---------------TGGGTACCTTGACA - -a -s simMouse_chr6.simMouse.chr6 506571 23 + 636262 ACTTTGCTTGGAAGACCAATAAT -s Anc0.Anc0refChr3 119978 23 + 222631 ACTTTTTTTGGTACTGTAAAAAT -s Anc1.Anc1refChr6 153960 23 + 197743 ACTTTTTTTGGTACTGTAAAAAT -s Anc2.Anc2refChr1 32478 23 + 142988 ACTTCTTTACGTACTGTAAACAT -s mr.mrrefChr3 59084 23 + 181027 ACTTTGCTTGGAAGACCAATAAT -s simCow_chr6.simCow.chr6 488880 23 + 602619 GCTTCTTTATGTACTGTAAAGAT -s simDog_chr6.simDog.chr6 479422 23 + 593897 ACATCTTTACATACTGTAAACAT -s simHuman_chr6.simHuman.chr6 485846 23 + 601863 ATTTTTTTTGGGACTGTAAAAAT -s simRat_chr6.simRat.chr6 517880 23 + 647215 ACTGCGCATGGAAGACCAATATT - -a -s simMouse_chr6.simMouse.chr6 506594 44 + 636262 TTTTTGATTGTGCAGGTGCTTATCTTTCCCAGGTCACTGCTGAT -s Anc0.Anc0refChr3 120001 36 + 222631 TT--------TGAATGAACTTCTTTTTTCCACAGCACTGGTGAT -s Anc1.Anc1refChr6 153983 36 + 197743 TT--------TGAATGAACTTCTTTTTTCCACAGCACTGGTGAT -s Anc2.Anc2refChr1 32513 36 + 142988 TT--------TGAATGAACATCTTTTTTCCCCAGCACTGGTGAT -s mr.mrrefChr3 59107 44 + 181027 TTTTTGATTGTGCAGGTGCTTATCTTTTCCAGGGCACTGCTGAT -s simCow_chr6.simCow.chr6 488915 33 + 602619 TT--------TGAATGAATGGATTTTTT---AGGCACTGGTGAT -s simDog_chr6.simDog.chr6 479457 36 + 593897 TT--------TGGATGAACATCTTTTTTCCCCACCTCTGGTTAT -s simHuman_chr6.simHuman.chr6 485869 35 + 601863 TT--------TGAAAGAACTAGTTTTCTCCACAGCACTGGTGA- -s simRat_chr6.simRat.chr6 517903 44 + 647215 TTTTTCATTGCACAGGTGCTTATCTTTTCCAGGGCACTGCTGAT - -a -s simMouse_chr6.simMouse.chr6 506638 12 + 636262 GATAAAGATTCT -s Anc0.Anc0refChr3 120037 12 + 222631 GCTGGAGAAGCT -s Anc1.Anc1refChr6 154019 12 + 197743 GCTGGAGAAGCT -s Anc2.Anc2refChr1 32549 12 + 142988 GCTGGAGAAGCT -s mr.mrrefChr3 59151 12 + 181027 GATAAAGATTCT -s simCow_chr6.simCow.chr6 488948 12 + 602619 GTTGGGGAAGCG -s simDog_chr6.simDog.chr6 479495 12 + 593897 CCTGGAGAAGCT -s simHuman_chr6.simHuman.chr6 485904 1 + 601863 -----------T -s simRat_chr6.simRat.chr6 517947 12 + 647215 GATAAAGATTCT - -a -s simMouse_chr6.simMouse.chr6 506650 3 + 636262 TCT -s Anc0.Anc0refChr3 120049 3 + 222631 GCT -s Anc1.Anc1refChr6 154031 3 + 197743 GCT -s Anc2.Anc2refChr1 32563 3 + 142988 GCT -s mr.mrrefChr3 59163 3 + 181027 GCT -s simCow_chr6.simCow.chr6 488962 3 + 602619 ACT -s simDog_chr6.simDog.chr6 479509 3 + 593897 GCT -s simHuman_chr6.simHuman.chr6 485905 3 + 601863 GCT -s simRat_chr6.simRat.chr6 517959 3 + 647215 GCT - -a -s simMouse_chr6.simMouse.chr6 506653 34 + 636262 GTGTAATATTAGAATCATTCACCTATTAGTAGCT -s Anc0.Anc0refChr3 120053 34 + 222631 GCATAATGTCATAATAATTTTCCTATTGAGAACT -s Anc1.Anc1refChr6 154035 34 + 197743 GCATAATGTCATAATAATTTTCCTATTGAGAACT -s Anc2.Anc2refChr1 32567 34 + 142988 GCAAAATGTCATAATTGCTTTCCTATTGAGCATT -s mr.mrrefChr3 59167 34 + 181027 GTGTAATGTTAGAATAATTCACCTATTAGTAGCT -s simCow_chr6.simCow.chr6 488966 24 + 602619 GCAAAGTTCCATAATCACTTCCTT---------- -s simDog_chr6.simDog.chr6 479513 34 + 593897 GCAAAATGTCATAATTGCTTTCCTATTGAGCATT -s simHuman_chr6.simHuman.chr6 485909 26 + 601863 GCATAATG------TAATT--CCAATTGAGAACT -s simRat_chr6.simRat.chr6 517963 34 + 647215 GTGTAATGTTAGAATAACATGCCTATTAGTAGCT - -a -s simMouse_chr6.simMouse.chr6 506687 11 + 636262 TAGTAAAAAAT -s Anc0.Anc0refChr3 120088 11 + 222631 CAGTGAAAGAT -s Anc1.Anc1refChr6 154070 11 + 197743 CAGTGAAAGAT -s Anc2.Anc2refChr1 32602 11 + 142988 CAGTGACAGAT -s mr.mrrefChr3 59201 11 + 181027 CAGTAAAAAAT -s simCow_chr6.simCow.chr6 488990 10 + 602619 -AGTGATAGAT -s simDog_chr6.simDog.chr6 479548 11 + 593897 CAGTGACAGAT -s simHuman_chr6.simHuman.chr6 485936 11 + 601863 CATTGAAAGAT -s simRat_chr6.simRat.chr6 517997 11 + 647215 CAGAAAAAAAT - -a -s simMouse_chr6.simMouse.chr6 506698 16 + 636262 GTTTTGGTACTCCAGT -s Anc0.Anc0refChr3 120100 16 + 222631 GTTTCTAAACTCTCTT -s Anc1.Anc1refChr6 154082 16 + 197743 GTTTCTAAACTCTCTT -s Anc2.Anc2refChr1 32614 16 + 142988 GTTTCTAAACTCTCTT -s mr.mrrefChr3 59213 16 + 181027 GTTTTGGTACTCTAGT -s simCow_chr6.simCow.chr6 489001 16 + 602619 GTTACTACACTCTCCT -s simDog_chr6.simDog.chr6 479560 16 + 593897 GTTTCTAAGCTCTCTT -s simHuman_chr6.simHuman.chr6 485948 16 + 601863 ATTTCTAAACCCTCAT -s simRat_chr6.simRat.chr6 518009 16 + 647215 GTTTTGGTTCTCTTGT - -a -s simMouse_chr6.simMouse.chr6 506714 61 + 636262 AAGTCTGGAGACATGTGAGACATGCTGGATGTATGCTTACTCACTTACCCACAACATACTT -s Anc0.Anc0refChr3 120116 40 + 222631 AGGCCTGGAT--------------------GTATG-CTACTCAATTACCCTCAACATACTT -s Anc1.Anc1refChr6 154098 41 + 197743 AGGCCTGGAT--------------------GTATGCCTACTCAATTACCCTCAACATACTT -s Anc2.Anc2refChr1 32630 40 + 142988 AGGCCTGGAT--------------------GTATG-CTACTCAATTACCCTCAAAATACTT -s mr.mrrefChr3 59229 53 + 181027 AAGCCTGGAGACATGT--------CTGGATGTATGCTTACTCACTTACCCACAACATACTT -s simCow_chr6.simCow.chr6 489017 40 + 602619 AGGCCCGGAC--------------------ATATG-CTACTCAATTACCTTCAAAAGACTC -s simDog_chr6.simDog.chr6 479577 40 + 593897 AGGCCTGGAT--------------------GTATG-CTAGTCAAATTCCCTCAAAATACTT -s simHuman_chr6.simHuman.chr6 485964 41 + 601863 TGGCCTGGAA--------------------GCATGCCGACCCAATTATCCTCAACATCTTT -s simRat_chr6.simRat.chr6 518025 53 + 647215 GAGCCTGGATATATGT--------CTGGATGTATGCTTGCTCACCTACCCACAAGATACTT - -a -s simMouse_chr6.simMouse.chr6 506775 29 + 636262 CCCTCAAGAGTTAGCCAGTAGTTCAGCAT -s Anc0.Anc0refChr3 120164 25 + 222631 CACTATAATAACAGCCAGTGATTT----T -s Anc1.Anc1refChr6 154147 25 + 197743 CACTATAATAACAGCCAGTGATTT----T -s Anc2.Anc2refChr1 32683 25 + 142988 TATTATAATAACAGCAGGTGGTTT----T -s mr.mrrefChr3 59282 29 + 181027 CACTCAAGAGTTAGCCAGTAATTCAGCAT -s simCow_chr6.simCow.chr6 489071 25 + 602619 TAATATAATAACAGCTGATGGTTT----T -s simDog_chr6.simDog.chr6 479639 25 + 593897 TATTATAATAACAGCAGGTGGTGT----T -s simHuman_chr6.simHuman.chr6 486013 25 + 601863 CACTACAACAACAGCCAGTGATTT----T -s simRat_chr6.simRat.chr6 518078 22 + 647215 CACTCAAGTGT-------TAATTCAGCAT - -a -s simMouse_chr6.simMouse.chr6 506804 15 + 636262 TGAAAAGGAACCAGA -s Anc0.Anc0refChr3 120189 15 + 222631 CAAAAGCAGACCAGG -s Anc1.Anc1refChr6 154172 15 + 197743 CAAAAGCAGACCAGG -s Anc2.Anc2refChr1 32708 15 + 142988 CAAAAGCAGACCAGG -s mr.mrrefChr3 59311 15 + 181027 TGAAAACGAACCAGA -s simCow_chr6.simCow.chr6 489096 15 + 602619 GGATTAAGACCCAAG -s simDog_chr6.simDog.chr6 479665 15 + 593897 CACAAGCAGACCAGG -s simHuman_chr6.simHuman.chr6 486038 15 + 601863 CAAAAGCAGATCAGG -s simRat_chr6.simRat.chr6 518100 15 + 647215 TGAAAACGAACCAGG - -a -s simMouse_chr6.simMouse.chr6 506819 13 + 636262 GATCTCTTGTTGG -s Anc0.Anc0refChr3 120205 13 + 222631 TCTCTGTTTTTGG -s Anc1.Anc1refChr6 154188 13 + 197743 TCTCTGTTTTTGG -s Anc2.Anc2refChr1 32724 13 + 142988 TCTCTGTTTGTAG -s mr.mrrefChr3 59326 13 + 181027 GATCTCTTGTTGG -s simCow_chr6.simCow.chr6 489112 13 + 602619 TCTCTGTGTGTAG -s simDog_chr6.simDog.chr6 479681 13 + 593897 CCTCTGTTTGCAG -s simHuman_chr6.simHuman.chr6 486054 13 + 601863 TTTCTGTTTTTGG -s simRat_chr6.simRat.chr6 518115 13 + 647215 GCTTTCTTGTTGG - -a -s simMouse_chr6.simMouse.chr6 506832 1 + 636262 C -s Anc0.Anc0refChr3 120218 1 + 222631 C -s Anc1.Anc1refChr6 154201 1 + 197743 C -s Anc2.Anc2refChr1 32737 1 + 142988 C -s mr.mrrefChr3 59339 1 + 181027 C -s simCow_chr6.simCow.chr6 489125 1 + 602619 C -s simDog_chr6.simDog.chr6 479694 1 + 593897 C -s simHuman_chr6.simHuman.chr6 486067 1 + 601863 C -s simRat_chr6.simRat.chr6 518129 1 + 647215 C - -a -s simMouse_chr6.simMouse.chr6 506833 45 + 636262 TCAAACTGAAAAGAATATTCTGAAGCAGCTAAAATGCTAACATAT -s Anc0.Anc0refChr3 120219 44 + 222631 GCAAA-AAAACTTATTATTCTCAAGCTGCTAAAATGCTAACCTAT -s Anc1.Anc1refChr6 154202 44 + 197743 GCAAA-AAAACTTATTATTCTCAAGCTGCTAAAATGCTAACCTAT -s Anc2.Anc2refChr1 32745 44 + 142988 GCAAA-AAAACTTATTATTCTCAAGCTGCTAAAATGCTAACCTAC -s mr.mrrefChr3 59340 45 + 181027 TCAAACAGAAAAGAATATTCTGAAGCAGCTAAAATGCTAACATAT -s simCow_chr6.simCow.chr6 489135 44 + 602619 GAGAA-AAAACTTAGTATTCTCAGGTAGCTCAAATTCAATCCTAC -s simDog_chr6.simDog.chr6 479702 44 + 593897 GCAAA-AAAAAATATTATTCTCGAGCTGCTAAAATGCTAAGCTAC -s simHuman_chr6.simHuman.chr6 486068 44 + 601863 ACAAA-AAAACTTATTATTCTCAAACTTCTAAAATGCCAACCCGT -s simRat_chr6.simRat.chr6 518130 45 + 647215 TTAACCAGAAAAGAATATTCTGAAGCAGCTAAAATGCTAACATAT - -a -s simMouse_chr6.simMouse.chr6 506878 79 + 636262 TCAGGCAGAAAAAACAAAGATGCAGCATCAGCAAGTACCCCATGAGGGATTTATGTTTCCCCTGGTTGGTAATAATCCT -s Anc0.Anc0refChr3 120263 77 + 222631 TCAGGTAT-ATAAACAAAAA-CCATTAGTGCCTACTAGCCCAAAAGTAATTTGTGTTTGCATCAGTTAGTGATATTCCT -s Anc1.Anc1refChr6 154246 78 + 197743 TCAGGTAT-ATAAACAAAAATCCATTAGTGCCTACTAGCCCAAAAGTAATTTGTGTTTGCATCAGTTAGTGATATTCCT -s Anc2.Anc2refChr1 32789 77 + 142988 TCAGGTAT-ATAAACAAAAA-CCAGTAGTGCCTACTAGCCCAAAAGTGATTTGTGTTTGCATCAGTTAGTGATATTCCT -s mr.mrrefChr3 59385 79 + 181027 TCAGGCAGAAAAAACAAAGATCCATCAGTGGCTAGTACCCCATAAGGAATTTGTGTTTCCCCCAGTTGGTAATAATCCT -s simCow_chr6.simCow.chr6 489179 67 + 602619 TCAGGTGC-A-----------CCAGAAGTGCCTACTAGCCCAAAAGTGGTTTGTGTTTACGTTAGCTGGGGATATTCCT -s simDog_chr6.simDog.chr6 479746 73 + 593897 TGAGGTAT-ATAAACAAAAA-----TAGTGCCTACTAGTCCACAAGTGATTTAGGCTTGCACCAGTTAGTGATATGTCC -s simHuman_chr6.simHuman.chr6 486112 78 + 601863 TCAGGTAT-ATAAACAAGACTCCATTAGTGCCTACTAGCCCAAAAGTAATTTGTGTTTGCATCAGTTAGTTACATTCAT -s simRat_chr6.simRat.chr6 518182 79 + 647215 TCAGGCCGAAAAAACAAAGATCCATGAGTGGCTAGTAACCCACAAGGAATTTGTGTTTCCCCCAGTTGGTAATCATCCT - -a -s simMouse_chr6.simMouse.chr6 506957 45 + 636262 ATTGTGCAGAATTGAGGATAAAATCTTTTTGGCTTGGCTCAGTAA -s Anc0.Anc0refChr3 120342 44 + 222631 ATTGTGCAGAGTTAAGGATGATAT-CTATTTGCTTGGCTGATCAA -s Anc1.Anc1refChr6 154326 44 + 197743 ATTGTGCAGAGTTAAGGATGATAT-CTATTTGCTTGGCTGATCAA -s Anc2.Anc2refChr1 32868 44 + 142988 ATTGTGCAGAGTTAAGGATGATAT-CTATTTGCTTGGCCAATCAA -s mr.mrrefChr3 59464 44 + 181027 ATTGTGCAGAATTAAGGATAAAAT-TTTTTGGCTTGGCTGATCAA -s simCow_chr6.simCow.chr6 489248 44 + 602619 ATTGTGCAGAGTTAATGAGGATAT-CTTTTGGCTTGGCCAATCAA -s simDog_chr6.simDog.chr6 479821 44 + 593897 ATTGTGCAGAGTTGAGGATGATAT-CTATCTGTCTGGCCAATTAA -s simHuman_chr6.simHuman.chr6 486192 44 + 601863 ATTGTGCAGAGTTAGGGATGGTAT-CTCTTAGCTTGGCTGCTCAA -s simRat_chr6.simRat.chr6 518261 44 + 647215 ATTGTGCAGAATTAAGGATAACAT-TTTCTGGCTTGGCTGATCAA - -a -s simMouse_chr6.simMouse.chr6 507002 73 + 636262 CTGAGAAAGGCTTGCCATGTCAATATGAAATTGCATTATTCCTAATGTAAAGAAGGCCGGTATATCCAGACTT -s Anc0.Anc0refChr3 120424 73 + 222631 TTGAAAATGACTTGCAAAATCAGTATGGAATCATGTTATTCCTCATGTAAAGAAGGTTGACATATTCTGACTT -s Anc1.Anc1refChr6 154408 73 + 197743 TTGAAAATGACTTGCAAAATCAGTATGGAATCATGTTATTCCTCATGTAAAGAAGGTTGACATATTCTGACTT -s Anc2.Anc2refChr1 32951 73 + 142988 CTGAAAATGACTTGCAAAATCAGTATGGAATCATGTTATTCCTCATGTAAAGAAGGTTGACATATTCTGACTG -s mr.mrrefChr3 59508 73 + 181027 TTGAAAATGACTTGCCATGTCAGTATGGAATTGCATTATTCCTAATGTAAAGAAGGCTGGTATATCCAGACTT -s simCow_chr6.simCow.chr6 489332 73 + 602619 CTGAAAGTGATTTGCAAAATCAGTATGGAATTGTGTTATTCATCAGGTAACAAAGGTTGACACATTCTGACTG -s simDog_chr6.simDog.chr6 479904 72 + 593897 CTAAAAATGGCTTGC-AAGTCAATATGGAATCATGTCATTCCTCATGTAAAGAAGATAGACATATTCTGACTG -s simHuman_chr6.simHuman.chr6 486274 73 + 601863 TGGAAAATGACTTGCAAAATCAGTATGGAATCATGTTATACCTCATGTTAACAAGGATGACAGGATCTGACTT -s simRat_chr6.simRat.chr6 518305 73 + 647215 TTGAAAATGACTTGCTATGTCAGTATGGAATTGCATTATTCCTAATGTATAGTAGGCTGCTATATCCAGACTT - -a -s simMouse_chr6.simMouse.chr6 507075 28 + 636262 CCTCTGGTTCAATTTCACCAAGGAGAGA -s Anc0.Anc0refChr3 120504 24 + 222631 TCCTA----CAATTTCATCTAGAAGAGT -s Anc1.Anc1refChr6 154488 24 + 197743 TCCTA----CAATTTCATCTAGAAGAGT -s Anc2.Anc2refChr1 33031 24 + 142988 TCCTA----GATTACCATCTAGAAGAGT -s mr.mrrefChr3 59581 28 + 181027 TCTTTGGTTCAATTTCACCAAGGAGAGA -s simCow_chr6.simCow.chr6 489412 17 + 602619 ACCAA-----------ATCTTAATCAGG -s simDog_chr6.simDog.chr6 479983 24 + 593897 TCCTA----GATTACCATCAAGGAGCAT -s simHuman_chr6.simHuman.chr6 486354 24 + 601863 TCCTA----CAATTTGGTCTGGAAGAGT -s simRat_chr6.simRat.chr6 518378 28 + 647215 TCTTTGGCTTAATTCTACCAAGGAAAGA - -a -s simMouse_chr6.simMouse.chr6 507103 36 + 636262 GGTATTAGCAAAATTAGGGAGTCCTCTCTCATAGTT -s Anc0.Anc0refChr3 120528 36 + 222631 GAGAATAGTGCACTTAGACAATCGTTTCTCTTAGCT -s Anc1.Anc1refChr6 154512 36 + 197743 GAGAATAGTGCACTTAGACAATCGTTTCTCTTAGCT -s Anc2.Anc2refChr1 33055 36 + 142988 GAGATTAGTGCACATAGACAATCGTTTCTCTTAGCT -s mr.mrrefChr3 59609 36 + 181027 GGTAATAGCAAAATTAGGGAGTCCTCTCTCTTAGTT -s simCow_chr6.simCow.chr6 489429 36 + 602619 GGGATTAGTGCACATAGACAGTTCTTCCTCTTGGCC -s simDog_chr6.simDog.chr6 480007 35 + 593897 GAGATTA-TGCACATAGATAATCGTTTCTCTTAACT -s simHuman_chr6.simHuman.chr6 486378 36 + 601863 GAGAATAGTGTGCTTAGACAATCGTTTCTCTTAGCT -s simRat_chr6.simRat.chr6 518407 36 + 647215 GGTAATCTCAAAATTAGGTAGTTCTCCCTCTTAATT - -a -s simMouse_chr6.simMouse.chr6 507139 5 + 636262 GTATA -s Anc0.Anc0refChr3 120564 5 + 222631 GTATA -s Anc1.Anc1refChr6 154548 5 + 197743 GTATA -s Anc2.Anc2refChr1 33091 5 + 142988 GGATA -s mr.mrrefChr3 59645 5 + 181027 GTATA -s simCow_chr6.simCow.chr6 489465 5 + 602619 GAATA -s simDog_chr6.simDog.chr6 480042 5 + 593897 GGATA -s simHuman_chr6.simHuman.chr6 486424 5 + 601863 GTATA -s simRat_chr6.simRat.chr6 518443 5 + 647215 GTATA - -a -s simMouse_chr6.simMouse.chr6 507144 17 + 636262 AATACCACCAAATTGAA -s Anc0.Anc0refChr3 120570 16 + 222631 AGTACCACC-AATCCTA -s Anc1.Anc1refChr6 154554 16 + 197743 AGTACCACC-AATCCTA -s Anc2.Anc2refChr1 33097 16 + 142988 AGTACCCCC-AATCCTA -s mr.mrrefChr3 59650 17 + 181027 AGTACCACCAAATTGAA -s simCow_chr6.simCow.chr6 489471 16 + 602619 AGTACTCCC-AATCCTA -s simDog_chr6.simDog.chr6 480048 16 + 593897 AGTATCCCC-AGTCCTA -s simHuman_chr6.simHuman.chr6 486430 16 + 601863 AGTCCCACC-GATCCTA -s simRat_chr6.simRat.chr6 518448 17 + 647215 AGTACCACTAAATTAAA - -a -s simMouse_chr6.simMouse.chr6 507161 22 + 636262 TGAGGGTCAATCTATCTCCCAG -s Anc0.Anc0refChr3 120586 19 + 222631 TGAGGGTTAACCTATCTC---A -s Anc1.Anc1refChr6 154570 19 + 197743 TGAGGGTTAACCTATCTC---A -s Anc2.Anc2refChr1 33113 19 + 142988 TTAGGGTTAACCTATCTC---A -s mr.mrrefChr3 59667 22 + 181027 TGAGGGTCAATCTATCTCCCAG -s simCow_chr6.simCow.chr6 489487 17 + 602619 --AGAGTTAACCTATCTC---C -s simDog_chr6.simDog.chr6 480065 13 + 593897 TTGGGGTCAA------TC---A -s simHuman_chr6.simHuman.chr6 486446 19 + 601863 TGAGGGTTAACATTTCTC---A -s simRat_chr6.simRat.chr6 518465 22 + 647215 TGAGGGCCTATCTCTCTCCCAG - -a -s simMouse_chr6.simMouse.chr6 507183 7 + 636262 TTACATT -s Anc0.Anc0refChr3 120605 7 + 222631 TTACATG -s Anc1.Anc1refChr6 154589 7 + 197743 TTACATG -s Anc2.Anc2refChr1 33132 7 + 142988 TCACATG -s mr.mrrefChr3 59689 7 + 181027 TTACATT -s simCow_chr6.simCow.chr6 489509 4 + 602619 TCAC--- -s simDog_chr6.simDog.chr6 480078 7 + 593897 TCACATG -s simHuman_chr6.simHuman.chr6 486465 7 + 601863 TTACATG -s simRat_chr6.simRat.chr6 518487 7 + 647215 TTGCATT - -a -s simMouse_chr6.simMouse.chr6 507190 17 + 636262 CACGTGAAGCTATCAAA -s Anc0.Anc0refChr3 120612 11 + 222631 TTCATGCAGCT------ -s Anc1.Anc1refChr6 154596 11 + 197743 TTCATGCAGCT------ -s Anc2.Anc2refChr1 33267 11 + 142988 TTCAGGCAGCT------ -s mr.mrrefChr3 59696 17 + 181027 CACATGAAGCTATCAAA -s simCow_chr6.simCow.chr6 489696 11 + 602619 TTCATGCAACT------ -s simDog_chr6.simDog.chr6 480213 11 + 593897 TTCAGGCAGCT------ -s simHuman_chr6.simHuman.chr6 486472 11 + 601863 TTCATGCAACT------ -s simRat_chr6.simRat.chr6 518494 17 + 647215 CACATGAAGCTATAAAA - -a -s simMouse_chr6.simMouse.chr6 507207 90 + 636262 TATCCTCTCATCAAACGTAATGAAAGTTCACAGAACGTCACATGTCTTCCAGTACGTTAAGAAGTTGGTTTCTGTGAAGAGTCTGACTCC -s Anc0.Anc0refChr3 120623 49 + 222631 --------------------------TACCAAGTAGGTCACATGT-TTGTAATTCTTTAAGAAGCTGATTTCTGTG-------------- -s Anc1.Anc1refChr6 154607 50 + 197743 --------------------------TACCAAGTAGGTCACATGTATTGTAATTCTTTAAGAAGCTGATTTCTGTG-------------- -s Anc2.Anc2refChr1 33278 49 + 142988 --------------------------GACCAAGTAGGTAACATGT-TTGTAATTCTTTAAGAAGCTGATTTCTGTG-------------- -s mr.mrrefChr3 59713 90 + 181027 TATCCTCTCATCAAACGTAATGAAAGTTCACAGAACGTCACATGTCTTGCAATACTTTAAGAAGTTGGTTTCTGTGAAGAGTCTGACTCC -s simCow_chr6.simCow.chr6 489707 46 + 602619 --------------------------TACCAAGTGGGTAACAC---TTGTAATTAATTAAGAAAGTGATTTCTGT--------------- -s simDog_chr6.simDog.chr6 480224 49 + 593897 --------------------------GACCAAGTAGGTAACATGT-CAGCAATTCTGTAAGAAGCTTATTTCTGTG-------------- -s simHuman_chr6.simHuman.chr6 486483 50 + 601863 --------------------------TACCATGGAGGCCACATATATTGTAATTCTTTGAGAAGCTGATTTCTGTG-------------- -s simRat_chr6.simRat.chr6 518512 90 + 647215 TATCCTCTTGTCTAATTTCATGAGAGTTCACAGAAAGTCACATGTCTTGCAATACTTTAAGAAGTCGGATTTTGTGAACAGGCTGATTTC - -a -s simMouse_chr6.simMouse.chr6 507297 14 + 636262 CAAAAATGTTATGT -s Anc0.Anc0refChr3 120672 13 + 222631 CAAAAATGTAGCA- -s Anc1.Anc1refChr6 154657 13 + 197743 CAAAAATGTAGCA- -s Anc2.Anc2refChr1 33327 13 + 142988 TAAAAATGTAGCA- -s mr.mrrefChr3 59803 14 + 181027 CAAAAATGTTATGT -s simCow_chr6.simCow.chr6 489753 12 + 602619 -AAAAATGTAGAA- -s simDog_chr6.simDog.chr6 480274 13 + 593897 TAAAAACATAGCA- -s simHuman_chr6.simHuman.chr6 486533 13 + 601863 CAAAAATGTAGCA- -s simRat_chr6.simRat.chr6 518602 14 + 647215 CTAAAATGTTATGC - -a -s simMouse_chr6.simMouse.chr6 507311 5 + 636262 TGCAA -s Anc0.Anc0refChr3 120685 5 + 222631 TTCAG -s Anc1.Anc1refChr6 154670 5 + 197743 TTCAG -s Anc2.Anc2refChr1 33340 5 + 142988 TTCAG -s mr.mrrefChr3 59817 5 + 181027 TTCAA -s simCow_chr6.simCow.chr6 489768 5 + 602619 GTCAT -s simDog_chr6.simDog.chr6 480287 5 + 593897 TTGTG -s simHuman_chr6.simHuman.chr6 486546 5 + 601863 TTCAG -s simRat_chr6.simRat.chr6 518616 5 + 647215 TTCAA - -a -s simMouse_chr6.simMouse.chr6 507316 5 + 636262 GGAAG -s Anc0.Anc0refChr3 120690 5 + 222631 GGAAG -s Anc1.Anc1refChr6 154675 5 + 197743 GGAAG -s Anc2.Anc2refChr1 33345 5 + 142988 GGAAG -s mr.mrrefChr3 59822 5 + 181027 GGAAG -s simCow_chr6.simCow.chr6 489773 5 + 602619 GAGGT -s simDog_chr6.simDog.chr6 480293 5 + 593897 AGAAG -s simHuman_chr6.simHuman.chr6 486551 5 + 601863 GGAAG -s simRat_chr6.simRat.chr6 518621 5 + 647215 GCAGG - -a -s simMouse_chr6.simMouse.chr6 507321 12 + 636262 TTTCCTTTGGCC -s Anc0.Anc0refChr3 120695 10 + 222631 TCTCATTT--CC -s Anc1.Anc1refChr6 154680 12 + 197743 TCTCATTTGACC -s Anc2.Anc2refChr1 33350 10 + 142988 TTTCACTT--CT -s mr.mrrefChr3 59827 12 + 181027 TCTCCTTTGACC -s simCow_chr6.simCow.chr6 489778 10 + 602619 TTTGACTC--CT -s simDog_chr6.simDog.chr6 480302 10 + 593897 CTTCACTT--CT -s simHuman_chr6.simHuman.chr6 486556 12 + 601863 TCTCATTTGATC -s simRat_chr6.simRat.chr6 518626 12 + 647215 ACTCCTTTGACC - -a -s simMouse_chr6.simMouse.chr6 507333 79 + 636262 TATGGACTCTATAACACTGCTTGTCCCAAATTTCCATGCCATTAGAGTCCTTTGCTAAGGAAACAAGTGACACATTGGA -s Anc0.Anc0refChr3 120705 78 + 222631 TACAAACACTATTACACTGCTAATCCCAAATATGCATTCCATTGGATTCCTTTGC-AATGAGAGTAGTGACACTTTGGA -s Anc1.Anc1refChr6 154692 78 + 197743 TACAAACACTATTACACTGCTAATCCCAAATATGCATTCCATTGGATTCCTTTGC-AATGAGAGTAGTGACACTTTGGA -s Anc2.Anc2refChr1 33360 78 + 142988 TACAAACACTATTACTCTGCTAATCCCAAATATGCATTCCATCGGATTCCCTTGC-AATGAGAGTGGTGACACTTTGGA -s mr.mrrefChr3 59839 78 + 181027 TATGGACACTATAACACTGCTTGTCCCAAATTTCCATGCCATTAGATTCCTTTGC-AAGGAGACAAGTGACACATTGGA -s simCow_chr6.simCow.chr6 489788 78 + 602619 TACAAATACTATTACTCTGCTTGTCCGAAATATACATTCCATGGGATTCCCTCGC-AATGAGAGTGGTGACACTTTGGA -s simDog_chr6.simDog.chr6 480321 78 + 593897 CACTAACACTATTACTCTGCCAATCTCTAATGTGCATTCGGTCGGATTCCCTTGC-AATAAGAGTGGTGACACTTCGGA -s simHuman_chr6.simHuman.chr6 486568 75 + 601863 TACAAACACTATTACACTGCTCATCCCAAACATGCATTCCATTGGATTCCTT----AATGAGGGTAGTCACACTTTGAA -s simRat_chr6.simRat.chr6 518638 75 + 647215 TATGGGCACTATAACA---CTTTTCTCAAATTTTCACGCCATTAGGTTCCTTTGC-AAGGAGACAGGCGACACATTGGA - -a -s simMouse_chr6.simMouse.chr6 507412 40 + 636262 GCTCAGCCATATTTGTACACAATAGTCTATCTGTAACCCA -s Anc0.Anc0refChr3 120792 40 + 222631 AATCAGTCAAGTCTGTATGTACTAGTTGATTTGTAACCAG -s Anc1.Anc1refChr6 154779 40 + 197743 AATCAGTCAAGTCTGTATGTACTAGTTGATTTGTAACCAG -s Anc2.Anc2refChr1 33447 40 + 142988 AATCAGTCAAGTCTGCATGTACTAGTTGATTTGTAGCCAG -s mr.mrrefChr3 59926 40 + 181027 AATCAGCCATGTCTGTACACAATAGTCTATCTGTAACCCA -s simCow_chr6.simCow.chr6 489875 40 + 602619 AATCAGTCAAGTCTGCGTCTACTAGTCTATTTGTAGCCAG -s simDog_chr6.simDog.chr6 480408 40 + 593897 AATCAGTCAAGACAACATGTACTAGTTGATTTGTAGCCAA -s simHuman_chr6.simHuman.chr6 486652 40 + 601863 AATCAGTCAGGTCTGTATGTACTAATGGATTCATAACCAG -s simRat_chr6.simRat.chr6 518754 40 + 647215 AATCACCCAAGTCTGTACACAATAGTCTATCTGTAACCCA - -a -s simMouse_chr6.simMouse.chr6 507452 43 + 636262 GCCTCTGCGTCTATTATCCAAGGCTGCTTTTTATTGAAAGTTG -s Anc0.Anc0refChr3 120832 43 + 222631 GCCTATCAACCTGTCATCCGTGGCTTCTTTTTATTGAAACTCC -s Anc1.Anc1refChr6 154819 43 + 197743 GCCTATCAACCTGTCATCCGTGGCTTCTTTTTATTGAAACTCC -s Anc2.Anc2refChr1 33487 43 + 142988 GCCTATCAACCTGTTATTCGTGGCTTCTTTCTATTGAAACTCC -s mr.mrrefChr3 59966 43 + 181027 GCCTCTGCATCTATCATCCAAGGCTGCTTTTTATTGAAAGTTG -s simCow_chr6.simCow.chr6 489930 42 + 602619 GCCTATCAAAC-GTTGTTTGTGGCTTCTTTCTATTGAAACTCC -s simDog_chr6.simDog.chr6 480448 43 + 593897 GCCAATCAACCTATTATTCATGGCTTCTTTCTATTGAAACTCC -s simHuman_chr6.simHuman.chr6 486692 43 + 601863 GCCTATTAACCTGTCAACCGTGGCTTCTTTTTATTGAAACTCT -s simRat_chr6.simRat.chr6 518794 43 + 647215 ACCTCTGCATCTATCATCCAAGGCTGCTCTTTATTGAAAGTTG - -a -s simMouse_chr6.simMouse.chr6 507495 15 + 636262 CCCGTGGGATTAGGC -s Anc0.Anc0refChr3 120875 13 + 222631 CCTGCTGTATTAG-- -s Anc1.Anc1refChr6 154862 13 + 197743 CCTGCTGTATTAG-- -s Anc2.Anc2refChr1 33530 13 + 142988 CCTGCTGTATTAG-- -s mr.mrrefChr3 60009 14 + 181027 CCCGCTGGATTAG-C -s simCow_chr6.simCow.chr6 490167 13 + 602619 CCTGCTGTATTAG-- -s simDog_chr6.simDog.chr6 480491 13 + 593897 CCTGCTCTATTGG-- -s simHuman_chr6.simHuman.chr6 486735 13 + 601863 CCTGCTGTATTAG-- -s simRat_chr6.simRat.chr6 518837 11 + 647215 CCCGCTGGAC----C - -a -s simMouse_chr6.simMouse.chr6 507510 13 + 636262 ACCTTAATGTACT -s Anc0.Anc0refChr3 120888 13 + 222631 AGCTTAATGTTCT -s Anc1.Anc1refChr6 154875 13 + 197743 AGCTTAATGTTCT -s Anc2.Anc2refChr1 33545 13 + 142988 AGCTTTCTATTTT -s mr.mrrefChr3 60023 13 + 181027 ACCTTAATGTACT -s simCow_chr6.simCow.chr6 490182 6 + 602619 AGC-------CTT -s simDog_chr6.simDog.chr6 480506 13 + 593897 AGCTTTCTATTTT -s simHuman_chr6.simHuman.chr6 486748 13 + 601863 AGCTTAATGTTCT -s simRat_chr6.simRat.chr6 518848 13 + 647215 ACCTTAATGTGCT - -a -s simMouse_chr6.simMouse.chr6 507523 36 + 636262 TGTGATCTTTGGGAGGTTGTCAACTAGATTTATAGC -s Anc0.Anc0refChr3 120901 35 + 222631 TGTTTTGTTGGGATTGCTGT-AACTAGAGTAACACC -s Anc1.Anc1refChr6 154888 35 + 197743 TGTTTTGTTGGGATTGCTGT-AACTAGAGTAACACC -s Anc2.Anc2refChr1 33559 35 + 142988 TGTTTTGTTGGAATTACTGT-AACTAGAGAAACACT -s mr.mrrefChr3 60036 36 + 181027 TGTTATCTTGGGAAGGCTGTCAACTAGATTTACAGC -s simCow_chr6.simCow.chr6 490189 35 + 602619 GGTCTTGTTGGAATAATTGT-AACTAGAGGTACACT -s simDog_chr6.simDog.chr6 480520 35 + 593897 TACTTTGTTGGAATTACGGA-AACTAGAGAAGCACT -s simHuman_chr6.simHuman.chr6 486764 35 + 601863 TGTTCTGTTGGGAGTGCTGT-AACTAGAGTAACATC -s simRat_chr6.simRat.chr6 518861 36 + 647215 GGTTATCTTGAGAAGGCTGACAACTAAAAGTACAGC - -a -s simMouse_chr6.simMouse.chr6 507559 16 + 636262 AGCACATCAGCGGCAT -s Anc0.Anc0refChr3 120937 16 + 222631 GGCATACAGGCAGCAT -s Anc1.Anc1refChr6 154924 16 + 197743 GGCATACAGGCAGCAT -s Anc2.Anc2refChr1 33595 16 + 142988 GAGATACAGGCAGCGG -s mr.mrrefChr3 60072 16 + 181027 GGCACACCAGCAGCAT -s simCow_chr6.simCow.chr6 490225 16 + 602619 GATGTACCGGAAGTGC -s simDog_chr6.simDog.chr6 480556 16 + 593897 GAGATACAGGCAGCGG -s simHuman_chr6.simHuman.chr6 486800 16 + 601863 GGCATACAGGCAGCAT -s simRat_chr6.simRat.chr6 518897 16 + 647215 GGCACACCAGCAGCAT - -a -s simMouse_chr6.simMouse.chr6 507575 28 + 636262 TTTATACATGCATCACCATACAGCATGA -s Anc0.Anc0refChr3 120953 28 + 222631 TAGAAACATAGGTCAGCATACAGTTTGC -s Anc1.Anc1refChr6 154940 28 + 197743 TAGAAACATAGGTCAGCATACAGTTTGC -s Anc2.Anc2refChr1 33620 28 + 142988 TAGAATCATGGGTCAGCACACAGTTTGC -s mr.mrrefChr3 60088 28 + 181027 TAGATACATAGGTCAGCATACAGCATGA -s simCow_chr6.simCow.chr6 490250 21 + 602619 TAGAAACATGGATCAGTA-------TGT -s simDog_chr6.simDog.chr6 480581 28 + 593897 TAGAATCTTGGGTCACCACACAGTTGGC -s simHuman_chr6.simHuman.chr6 486816 28 + 601863 TAGTGATATAGGTTAGCTTACAGTCTGG -s simRat_chr6.simRat.chr6 518913 28 + 647215 TAGATACATAGGTCAGTGTACAGCATGA - -a -s simMouse_chr6.simMouse.chr6 507603 13 + 636262 TGCTGTTTAAGAA -s Anc0.Anc0refChr3 120984 13 + 222631 CTCCATTTAAGAC -s Anc1.Anc1refChr6 154971 13 + 197743 CTCCATTTAAGAC -s Anc2.Anc2refChr1 33651 13 + 142988 CTTCATTTAAGAC -s mr.mrrefChr3 60116 13 + 181027 TGCTGTTTAAGAA -s simCow_chr6.simCow.chr6 490274 13 + 602619 CTTCATTTAAGAA -s simDog_chr6.simDog.chr6 480612 12 + 593897 CT-AATCTAAGAC -s simHuman_chr6.simHuman.chr6 486847 13 + 601863 CTCCATTTAAGAC -s simRat_chr6.simRat.chr6 518941 13 + 647215 TGTTGTTGAAGAA - -a -s simMouse_chr6.simMouse.chr6 507616 35 + 636262 ATGCTGGGCCTAAAGGATACTGCAGCCACTCTGGG -s Anc0.Anc0refChr3 120997 35 + 222631 ATGTTTGGCCTAATGGATCTTGCAAATATCCAGGG -s Anc1.Anc1refChr6 154984 35 + 197743 ATGTTTGGCCTAATGGATCTTGCAAATATCCAGGG -s Anc2.Anc2refChr1 33664 35 + 142988 ATATTTGGCGTAATAGATCTTGCAAATATCCAGGG -s mr.mrrefChr3 60129 35 + 181027 ATGTTGGGCCTAAAGGATACTGCAGCCACTCTGGG -s simCow_chr6.simCow.chr6 490288 35 + 602619 ACATGTGGCAAAATAGATCATGCAAATACCCTGGG -s simDog_chr6.simDog.chr6 480624 32 + 593897 ATATTAGGCGTAATAA---TTGTGAATATCCAGGT -s simHuman_chr6.simHuman.chr6 486860 35 + 601863 ATGTTTGGCCTAATGGGTCGTGCACATATCCCGGG -s simRat_chr6.simRat.chr6 518954 35 + 647215 ATGTTGGGCCTAAAGGATACTGCAGCCACGCAGGG - -a -s simMouse_chr6.simMouse.chr6 507651 8 + 636262 TCCTAACT -s Anc0.Anc0refChr3 121032 8 + 222631 TCCTAGAT -s Anc1.Anc1refChr6 155019 8 + 197743 TCCTAGAT -s Anc2.Anc2refChr1 33699 8 + 142988 TCCTAGAT -s mr.mrrefChr3 60164 8 + 181027 TCCTAACT -s simCow_chr6.simCow.chr6 490326 8 + 602619 CCCTAGAT -s simDog_chr6.simDog.chr6 480656 8 + 593897 TCCTAGAT -s simHuman_chr6.simHuman.chr6 486895 8 + 601863 TCCTAGGT -s simRat_chr6.simRat.chr6 518989 8 + 647215 TCCTAACT - -a -s simMouse_chr6.simMouse.chr6 507659 11 + 636262 TATGTAAGGGC -s Anc0.Anc0refChr3 121040 9 + 222631 TGTGTAAGG-- -s Anc1.Anc1refChr6 155027 11 + 197743 TGTGTAAGGGT -s Anc2.Anc2refChr1 33707 9 + 142988 TGTGTGAGG-- -s mr.mrrefChr3 60172 11 + 181027 TATGTAAGGGT -s simCow_chr6.simCow.chr6 490334 9 + 602619 TGTGTAAGG-- -s simDog_chr6.simDog.chr6 480664 9 + 593897 TATGTGAGG-- -s simHuman_chr6.simHuman.chr6 486915 11 + 601863 TGTGTAAGAGT -s simRat_chr6.simRat.chr6 518997 11 + 647215 TATTTAAGGAT - -a -s simMouse_chr6.simMouse.chr6 507670 24 + 636262 AGAGTGTCTAAGGGTCCAAAAAAG -s Anc0.Anc0refChr3 121049 24 + 222631 AGAGTGTGTAAGGGGCCAAAGAAG -s Anc1.Anc1refChr6 155038 24 + 197743 AGAGTGTGTAAGGGGCCAAAGAAG -s Anc2.Anc2refChr1 33716 24 + 142988 AGAGTGTGTAAGGGGCCAAAGAAG -s mr.mrrefChr3 60183 24 + 181027 AGAGTGTCTAAGGGGCCAAAAAAG -s simCow_chr6.simCow.chr6 490345 24 + 602619 AGAGTGTATGAGGGGCCAAAGAAG -s simDog_chr6.simDog.chr6 480673 24 + 593897 AGAGTGTGTAAGAGGCAAAAGAAG -s simHuman_chr6.simHuman.chr6 486926 24 + 601863 AGAGTGTGGAAGGGGCCGGAGAAC -s simRat_chr6.simRat.chr6 519008 24 + 647215 AGAATGTCTATGAGGCCTAAAGAG - -a -s simMouse_chr6.simMouse.chr6 507694 6 + 636262 AAGTCC -s Anc0.Anc0refChr3 121073 6 + 222631 TAGGTC -s Anc1.Anc1refChr6 155062 6 + 197743 TAGGTC -s Anc2.Anc2refChr1 33740 6 + 142988 TGGGTT -s mr.mrrefChr3 60207 6 + 181027 TAGTCC -s simCow_chr6.simCow.chr6 490369 6 + 602619 TGCACT -s simDog_chr6.simDog.chr6 480697 6 + 593897 CGGGTT -s simHuman_chr6.simHuman.chr6 486955 6 + 601863 TAGGTC -s simRat_chr6.simRat.chr6 519032 6 + 647215 TAGTCC - -a -s simMouse_chr6.simMouse.chr6 507700 24 + 636262 CAAAAGAGCCTATACACACACGTA -s Anc0.Anc0refChr3 121088 16 + 222631 CGAAAGAT--------CAAAGGTC -s Anc1.Anc1refChr6 155077 24 + 197743 CGAAAGATCACGTACACAAAGGTC -s Anc2.Anc2refChr1 33755 16 + 142988 TGAAAGAT--------CAAAGGTC -s mr.mrrefChr3 60213 24 + 181027 CAAAAGAGCCTATACACACACGTA -s simCow_chr6.simCow.chr6 490383 14 + 602619 --CAAGAT--------CAAAGGTC -s simDog_chr6.simDog.chr6 480712 16 + 593897 TGAAAGAT--------CAAAGGTC -s simHuman_chr6.simHuman.chr6 486970 24 + 601863 CGAAAGATCACGTACACAAAGGTC -s simRat_chr6.simRat.chr6 519038 24 + 647215 CAAAAGAGCCTATACACACACATA - -a -s simMouse_chr6.simMouse.chr6 507724 80 + 636262 ATTTACAGAAGTCTAGCACGAAGCATTATGCAATGCTATATTTCACACTTCGAAATCTAAAGTGAATAGGGTGACTAAGA -s Anc0.Anc0refChr3 121104 79 + 222631 ATTTACAGAAGTTTAGGATCAAGCATTATGCAATATTAAATTTCACATCCTGAAATTT-GAGTTAATAGGGTGACTAGGA -s Anc1.Anc1refChr6 155101 80 + 197743 ATTTACAGAAGTTTAGGATCAAGCATTATGCAATATTAAATTTCACATCCTGAAATTTGGAGTTAATAGGGTGACTAGGA -s Anc2.Anc2refChr1 33771 79 + 142988 ATGTACAGAAGTTTAGGATCAAGCATTATGCAATATTAAATTTCACATCCTGAAATTC-GAGTTAATAGGGTGACTAGGA -s mr.mrrefChr3 60237 80 + 181027 ATTTACAGAAGTCTAGCACGAAGCATTATGCAATGCTATATTTCACACTTTGAAATCTAAAGTGAATAGGGTGACTAGGA -s simCow_chr6.simCow.chr6 490397 79 + 602619 ATGTACAGTCGATCAGCATGAAGCATTGTGCAATATTATATTACACATCCTGAAATTA-GAGTTAATAGGGTGACTAGGA -s simDog_chr6.simDog.chr6 480732 79 + 593897 ATGTACAGAAGTTTAGGGTCAAGCATTATGCAACATTAAATCTCACAACTTGTAATTC-AAGCTAATAGGGTGACTAGGA -s simHuman_chr6.simHuman.chr6 486994 78 + 601863 ATTTACAGAACTTATGTAGCGAACATTATGCAATAATAAATTTCACATCCTGAAGTTTGGAGTTA--AGGGTGACTAGGA -s simRat_chr6.simRat.chr6 519062 80 + 647215 GTTTACAGAAGTCTAGCATGAAGCATTATGCAATGCTATATTTCATACTTTGGAATCTAAAGTGAATAGGGTGAATAGGA - -a -s simMouse_chr6.simMouse.chr6 507804 24 + 636262 CAATGGACACAGGCATATATTAGT -s Anc0.Anc0refChr3 121183 24 + 222631 AAGTTGATACAGGTACATAAAAGT -s Anc1.Anc1refChr6 155181 24 + 197743 AAGTTGATACAGGTACATAAAAGT -s Anc2.Anc2refChr1 33850 24 + 142988 AAGTTGATACAGGTACATGAAAGT -s mr.mrrefChr3 60317 24 + 181027 CAATGGACACAGGCATATAATAGT -s simCow_chr6.simCow.chr6 490476 22 + 602619 AGGTTGATACAGGTACATGGAA-- -s simDog_chr6.simDog.chr6 480811 24 + 593897 AACTTGACACAAATACATGAAAGT -s simHuman_chr6.simHuman.chr6 487073 24 + 601863 AAGATGATAGAGGTACGTAAAAGT -s simRat_chr6.simRat.chr6 519142 24 + 647215 CTGTGGACCCGGGCAAATAATAAT - -a -s simMouse_chr6.simMouse.chr6 507828 29 + 636262 GCCAGAGAAATACCACCCCATAACAGATC -s Anc0.Anc0refChr3 121207 29 + 222631 GCCAAGGAAACACCACCCTGTGATGGATG -s Anc1.Anc1refChr6 155205 29 + 197743 GCCAAGGAAACACCACCCTGTGATGGATG -s Anc2.Anc2refChr1 33885 29 + 142988 GCCAAGGAAACACTACCCTGTGATGGATG -s mr.mrrefChr3 60341 29 + 181027 GCCAAAGAAATACCACCCCATAACAGATC -s simCow_chr6.simCow.chr6 490516 29 + 602619 GCAAAACAAACAGGACCCTGTGATGGATG -s simDog_chr6.simDog.chr6 480846 29 + 593897 GCCAAGGAAACACTATCTTGTGATGGATG -s simHuman_chr6.simHuman.chr6 487097 29 + 601863 ACCAAGGAGACACCACCCTCTTATGGATG -s simRat_chr6.simRat.chr6 519166 29 + 647215 GCCAAAGGAATACCACCACATAACAGATC - -a -s simMouse_chr6.simMouse.chr6 507857 11 + 636262 AGTTTACCTTG -s Anc0.Anc0refChr3 121236 11 + 222631 AGTCTATATTG -s Anc1.Anc1refChr6 155234 11 + 197743 AGTCTATATTG -s Anc2.Anc2refChr1 33914 11 + 142988 AGTCTATATTG -s mr.mrrefChr3 60370 11 + 181027 AGTCTATCTTG -s simCow_chr6.simCow.chr6 490557 11 + 602619 ACTGTAGATCC -s simDog_chr6.simDog.chr6 480875 11 + 593897 AGTCTATATTG -s simHuman_chr6.simHuman.chr6 487126 11 + 601863 AGTCTATATTG -s simRat_chr6.simRat.chr6 519195 11 + 647215 AGTCTATTTTG - -a -s simMouse_chr6.simMouse.chr6 507868 6 + 636262 TCCTTC -s Anc0.Anc0refChr3 121247 4 + 222631 TC--TA -s Anc1.Anc1refChr6 155245 4 + 197743 TC--TA -s Anc2.Anc2refChr1 33925 4 + 142988 TA--TA -s mr.mrrefChr3 60381 6 + 181027 TCCTTC -s simCow_chr6.simCow.chr6 490568 4 + 602619 TA--TA -s simDog_chr6.simDog.chr6 480895 4 + 593897 TA--TA -s simHuman_chr6.simHuman.chr6 487137 4 + 601863 TC--TG -s simRat_chr6.simRat.chr6 519206 6 + 647215 TCCTTC - -a -s simMouse_chr6.simMouse.chr6 507874 33 + 636262 ATACAAGTAAACTCTAATACATTCCAAGTGGGA -s Anc0.Anc0refChr3 121251 33 + 222631 ATATAACCAAGTTCTGATACATTCCAAGTGGGC -s Anc1.Anc1refChr6 155249 33 + 197743 ATATAACCAAGTTCTGATACATTCCAAGTGGGC -s Anc2.Anc2refChr1 33929 33 + 142988 ATATAACCATGTTCTGATACATTCAAAGTGGGC -s mr.mrrefChr3 60387 33 + 181027 ATACAAGTAAACTCTAATACATTCCAAGTGGGA -s simCow_chr6.simCow.chr6 490572 32 + 602619 CTATAACCAGGCT-TGGGACATTCTACGCGGAC -s simDog_chr6.simDog.chr6 480908 32 + 593897 ATATAACCGTGTTCTAATAGCTCCAAAGTGGG- -s simHuman_chr6.simHuman.chr6 487141 33 + 601863 GTATAACCAAGTTTTGTTGCATTCCAAGTGGTC -s simRat_chr6.simRat.chr6 519212 33 + 647215 ATACACATAAACTCTAATACTTTCCAAGTGGGA - -a -s simMouse_chr6.simMouse.chr6 507907 8 + 636262 CCATTATG -s Anc0.Anc0refChr3 121284 8 + 222631 CCATTATG -s Anc1.Anc1refChr6 155282 8 + 197743 CCATTATG -s Anc2.Anc2refChr1 33962 8 + 142988 CCATTATG -s mr.mrrefChr3 60420 8 + 181027 CCATTATG -s simCow_chr6.simCow.chr6 490617 8 + 602619 CCATTATG -s simHuman_chr6.simHuman.chr6 487174 8 + 601863 CCACGATG -s simRat_chr6.simRat.chr6 519245 8 + 647215 CCATTATG - -a -s simMouse_chr6.simMouse.chr6 507915 28 + 636262 GCCCTATTACCTGTACCCTTCTCTTGCA -s Anc0.Anc0refChr3 121302 26 + 222631 AACCTACCACCTGTACCCA--GTTTGCC -s Anc1.Anc1refChr6 155300 28 + 197743 AACCTACCACCTGTACCCATTGTTTGCC -s Anc2.Anc2refChr1 33980 26 + 142988 AATCAACCACCTTTACCCA--GTATGCC -s mr.mrrefChr3 60428 28 + 181027 ACCCTATTACCTGTACCCTTCTCTTGCA -s simCow_chr6.simCow.chr6 490648 26 + 602619 AATCAACCACCTTTACCCA--GTATGCC -s simHuman_chr6.simHuman.chr6 487192 28 + 601863 AACCTCCCACCTGTACCCATTGTTTGCT -s simRat_chr6.simRat.chr6 519253 28 + 647215 ACCATATTACCTGTACCCTTCTGTTCCA - -a -s simMouse_chr6.simMouse.chr6 507943 38 + 636262 TAAGCCCAGATTTTAAGCTATCAAGTCTGCAAAGTCAC -s Anc0.Anc0refChr3 121328 20 + 222631 TACACATAGATTTTAAGTT------------------G -s Anc1.Anc1refChr6 155328 20 + 197743 TACACATAGATTTTAAGTT------------------G -s Anc2.Anc2refChr1 34006 20 + 142988 TACACATGGATTTTAAGTT------------------G -s mr.mrrefChr3 60456 38 + 181027 TAAGCCCAGATTTTAAGCTATCAAGTCTGCAAAGTTAA -s simCow_chr6.simCow.chr6 490678 20 + 602619 TACACATGGATTTTAAGTT------------------G -s simHuman_chr6.simHuman.chr6 487220 20 + 601863 TACACATAGATTTTAAGTT------------------G -s simRat_chr6.simRat.chr6 519281 38 + 647215 TAAGCCCAGATTTTAAGCTATCAAGTCTGCAAAGTTAA - -a -s simMouse_chr6.simMouse.chr6 507981 21 + 636262 GGGGAAGACTTGTGGTACAAA -s Anc0.Anc0refChr3 121348 21 + 222631 AAGGAAGACCTGTGGTACAAA -s Anc1.Anc1refChr6 155348 21 + 197743 AAGGAAGACCTGTGGTACAAA -s Anc2.Anc2refChr1 34026 21 + 142988 AAGGACGACCTGGAGTACGAA -s mr.mrrefChr3 60494 21 + 181027 GGGGAAGACTTGTGGTACAAA -s simCow_chr6.simCow.chr6 490715 21 + 602619 AAGGACGACCTGGAGTACGAA -s simHuman_chr6.simHuman.chr6 487240 21 + 601863 ATGGAAGGCCTGTGGTACAAA -s simRat_chr6.simRat.chr6 519319 21 + 647215 GAAAAGGACATGCAGTACAAA - -a -s simMouse_chr6.simMouse.chr6 508002 7 + 636262 AGTTGAG -s Anc0.Anc0refChr3 121372 7 + 222631 AGTCGAA -s Anc1.Anc1refChr6 155372 7 + 197743 AGTCGAA -s Anc2.Anc2refChr1 34050 7 + 142988 AGTCCAA -s mr.mrrefChr3 60515 7 + 181027 AGTTGAG -s simCow_chr6.simCow.chr6 490739 7 + 602619 AGTCCAA -s simHuman_chr6.simHuman.chr6 487264 7 + 601863 AGTAGAA -s simRat_chr6.simRat.chr6 519340 7 + 647215 AGTTAAG - -a -s simMouse_chr6.simMouse.chr6 508009 11 + 636262 CCAGAATCTCC -s Anc0.Anc0refChr3 121379 7 + 222631 T-AACAG---T -s Anc1.Anc1refChr6 155379 10 + 197743 T-AACAGCTCT -s Anc2.Anc2refChr1 34057 7 + 142988 G-AACAG---T -s mr.mrrefChr3 60522 11 + 181027 TCAGAATCTCC -s simCow_chr6.simCow.chr6 490750 7 + 602619 G-AACAG---T -s simHuman_chr6.simHuman.chr6 487271 10 + 601863 T-AACAGCTCT -s simRat_chr6.simRat.chr6 519347 11 + 647215 TCAGAATCTCC - -a -s simMouse_chr6.simMouse.chr6 508020 20 + 636262 TGAAATGGTCAGGAGCTGAG -s Anc0.Anc0refChr3 121389 20 + 222631 TAAAAAGGGCATCAGCTTAG -s Anc1.Anc1refChr6 155392 20 + 197743 TAAAAAGGGCATCAGCTTAG -s Anc2.Anc2refChr1 34067 20 + 142988 TAATAAGGATGTCAGCCTAG -s mr.mrrefChr3 60533 20 + 181027 TGAAATGGGCAGGAGCTGAG -s simCow_chr6.simCow.chr6 490760 20 + 602619 TAATAAGGATGTCAGCCTAG -s simHuman_chr6.simHuman.chr6 487284 20 + 601863 TAAAAAGGGCACCAGTTTAG -s simRat_chr6.simRat.chr6 519358 20 + 647215 TGAAATGGGCATGAGGTGAG - -a -s simMouse_chr6.simMouse.chr6 508040 2 + 636262 CC -s Anc0.Anc0refChr3 121409 2 + 222631 CC -s Anc1.Anc1refChr6 155412 2 + 197743 CC -s Anc2.Anc2refChr1 34090 2 + 142988 CC -s mr.mrrefChr3 60553 2 + 181027 CC -s simCow_chr6.simCow.chr6 490783 2 + 602619 CC -s simHuman_chr6.simHuman.chr6 487304 2 + 601863 TA -s simRat_chr6.simRat.chr6 519378 2 + 647215 CC - -a -s simMouse_chr6.simMouse.chr6 508042 20 + 636262 CAATGTGGTCTTGACACCCT -s Anc0.Anc0refChr3 121411 20 + 222631 CAATGTGATCTTGACACCCT -s Anc1.Anc1refChr6 155414 20 + 197743 CAATGTGATCTTGACACCCT -s Anc2.Anc2refChr1 34092 20 + 142988 CAGTGTGGTTTTGACACCTT -s mr.mrrefChr3 60555 20 + 181027 CAATGTGATCTTGACACCCT -s simCow_chr6.simCow.chr6 490785 20 + 602619 CAGTGTGGTTTTGACACCTT -s simHuman_chr6.simHuman.chr6 487309 20 + 601863 CAATGTGATCTTGACACCCT -s simRat_chr6.simRat.chr6 519380 20 + 647215 AAAGGTGATCTTGACACCCT - -a -s simMouse_chr6.simMouse.chr6 508062 3 + 636262 GGA -s Anc0.Anc0refChr3 121431 3 + 222631 TGA -s Anc1.Anc1refChr6 155434 3 + 197743 TGA -s Anc2.Anc2refChr1 34112 3 + 142988 TGA -s mr.mrrefChr3 60575 3 + 181027 GGA -s simCow_chr6.simCow.chr6 490806 3 + 602619 TGA -s simHuman_chr6.simHuman.chr6 487329 3 + 601863 TGA -s simRat_chr6.simRat.chr6 519400 1 + 647215 G-- - -a -s simMouse_chr6.simMouse.chr6 508065 31 + 636262 GCCATAGCAACAAATAATTCATAGGAAGCTG -s Anc0.Anc0refChr3 121435 31 + 222631 GCCATAGCAAATAATGATTCATAGTAGGCTG -s Anc1.Anc1refChr6 155438 31 + 197743 GCCATAGCAAATAATGATTCATAGTAGGCTG -s Anc2.Anc2refChr1 34116 31 + 142988 CCTATAGGGAATAATGATTCCAAATTGGCTG -s mr.mrrefChr3 60578 31 + 181027 GCCATAGCAACAAATAATTCATAGGAGGCTG -s simCow_chr6.simCow.chr6 490810 31 + 602619 CCTATAGGGAATAATGATTCCAAATTGGCTG -s simHuman_chr6.simHuman.chr6 487333 31 + 601863 GCCATAGCAAGTAATGATGCATAGAAGGCTG -s simRat_chr6.simRat.chr6 519401 25 + 647215 ------GCAACAAATAATTCATAGGAGGTTG - -a -s simMouse_chr6.simMouse.chr6 508096 7 + 636262 TCAGACA -s Anc0.Anc0refChr3 121466 7 + 222631 GCGTTCC -s Anc1.Anc1refChr6 155469 7 + 197743 GCGTTCC -s Anc2.Anc2refChr1 34147 7 + 142988 GAGTTAC -s mr.mrrefChr3 60609 7 + 181027 TCAGACA -s simCow_chr6.simCow.chr6 490855 7 + 602619 GAGTTAC -s simHuman_chr6.simHuman.chr6 487364 7 + 601863 GCGTCCC -s simRat_chr6.simRat.chr6 519426 7 + 647215 TCTGGCA - -a -s simMouse_chr6.simMouse.chr6 508103 78 + 636262 GGGCATGTGTCACAGAGAGGCAGAATCTTGCTACTTATGACAGTTCCTGGTAGACCAAACAGAAAAATCAACTTCTGA -s Anc0.Anc0refChr3 121482 58 + 222631 GGAGATACATTTAGCAGAGGCAGAA-TTTGCTACTA-------------------CTAATAGAACAGTTATTTTCTGA -s Anc1.Anc1refChr6 155485 76 + 197743 GGAGATACATTTAGCAGAGGCAGAATTTTGCTACTAGTGATAATTTC--GTAGATCTAATAGAACAGTTATTTTCTGA -s Anc2.Anc2refChr1 34163 58 + 142988 GAAGTTACATTTAGCAGAGGTAAAA-TTTGCTGCTA-------------------CTAATTAAACAGTTATTTTGTTA -s mr.mrrefChr3 60616 76 + 181027 GGGCATATGTCACAGAGAGGCAGAATCTTGCTACTTATGACAATTCC--GTAGACCTAACAGAAAAATCAACTTCTGA -s simCow_chr6.simCow.chr6 490871 58 + 602619 GAAGTTACATTTAGCAGAGGTAAAA-TTTGCTGCTA-------------------CTAATTAAACAGTTATTTTGTTA -s simHuman_chr6.simHuman.chr6 487380 76 + 601863 GGATAAACATTTAGCAGGGGCAGAATTTTGCTACTAGTGATAATTTC--GTAGATCTAATAGACCAGTAATTTTCTGA -s simRat_chr6.simRat.chr6 519433 74 + 647215 GAGCATATGTCACAGAGA--GAAAATCTTGCTTATTTTGACAATTCC--GCAGACCTAACAAAAAAATCAACTTCTGA - -a -s simMouse_chr6.simMouse.chr6 508181 36 + 636262 GTTACTCATGATTGTCTGGGCTATTCAGGGGGCTAT -s Anc0.Anc0refChr3 121540 34 + 222631 CTTACTGATGATTGTCTAGCCTACTCA--GGGCTAT -s Anc1.Anc1refChr6 155561 34 + 197743 CTTACTGATGATTGTCTAGCCTACTCA--GGGCTAT -s Anc2.Anc2refChr1 34221 34 + 142988 CTCACTGATGATAGTCTAGCCAACTCA--GGGCTAT -s mr.mrrefChr3 60692 36 + 181027 GTTACTCATGATTGTCTGGGCTATTCAGGGGGCTAT -s simCow_chr6.simCow.chr6 490930 34 + 602619 CTCACTGATGATAGTCTAGCCAACTTA--CAGCTAT -s simDog_chr6.simDog.chr6 480940 9 + 593897 -------------------------CA--GGGCTAT -s simHuman_chr6.simHuman.chr6 487456 34 + 601863 CTTACTGATAATTGTCTAGCCTACCCA--GGGCTAT -s simRat_chr6.simRat.chr6 519507 36 + 647215 TTTACTCATGACTGTTTGGGCTATTCAGCGGGCTAT - -a -s simMouse_chr6.simMouse.chr6 508217 18 + 636262 AGTATGAACACATTTAAA -s Anc0.Anc0refChr3 121574 18 + 222631 GGTGCCAACATATTTGAG -s Anc1.Anc1refChr6 155595 18 + 197743 GGTGCCAACATATTTGAG -s Anc2.Anc2refChr1 34255 18 + 142988 GGTGCCAGCATATTTGAG -s mr.mrrefChr3 60728 18 + 181027 AGTATGAACACATTTAAA -s simCow_chr6.simCow.chr6 490965 18 + 602619 GGGGCCAGCATATTTGAG -s simDog_chr6.simDog.chr6 480949 18 + 593897 AGTGCCAGCATATTTGAG -s simHuman_chr6.simHuman.chr6 487490 18 + 601863 GGTGCCAACATATTTGAG -s simRat_chr6.simRat.chr6 519543 18 + 647215 AACAAAAAGACATTTAAA - -a -s simMouse_chr6.simMouse.chr6 508235 3 + 636262 GAT -s Anc0.Anc0refChr3 121592 3 + 222631 AAT -s Anc1.Anc1refChr6 155613 3 + 197743 AAT -s Anc2.Anc2refChr1 34273 3 + 142988 AAT -s mr.mrrefChr3 60746 3 + 181027 GAT -s simCow_chr6.simCow.chr6 490984 3 + 602619 AAA -s simDog_chr6.simDog.chr6 480967 3 + 593897 AAT -s simHuman_chr6.simHuman.chr6 487508 3 + 601863 CAT -s simRat_chr6.simRat.chr6 519561 3 + 647215 GAT - -a -s simMouse_chr6.simMouse.chr6 508238 21 + 636262 TTCAAAGAAGCACTAAGATCT -s Anc0.Anc0refChr3 121596 21 + 222631 CCCAAAGAGGATCTAAGATGT -s Anc1.Anc1refChr6 155617 21 + 197743 CCCAAAGAGGATCTAAGATGT -s Anc2.Anc2refChr1 34277 21 + 142988 CCCAAAGAGAATCTAAGATGT -s mr.mrrefChr3 60749 21 + 181027 TTCAAAGAAGCTCTAAGATCT -s simCow_chr6.simCow.chr6 490988 21 + 602619 CCCAAAGTGAATCTAAGATGT -s simDog_chr6.simDog.chr6 480971 21 + 593897 CTCAAAGAGAATCTAAGAAAT -s simHuman_chr6.simHuman.chr6 487512 21 + 601863 CCCGAAGAGGATCTGAGATGT -s simRat_chr6.simRat.chr6 519564 21 + 647215 TTCAAAAAAGCTCTAAGATCT - -a -s simMouse_chr6.simMouse.chr6 508259 11 + 636262 ATTTTTAGATC -s Anc0.Anc0refChr3 121621 11 + 222631 ATTTCTAAATG -s Anc1.Anc1refChr6 155642 11 + 197743 ATTTCTAAATG -s Anc2.Anc2refChr1 34302 11 + 142988 ATTTCTGAGGG -s mr.mrrefChr3 60774 11 + 181027 ATTTTTAGATC -s simCow_chr6.simCow.chr6 491013 11 + 602619 ATTTGTGAGGG -s simDog_chr6.simDog.chr6 480996 11 + 593897 AATTCTGAAGG -s simHuman_chr6.simHuman.chr6 487537 9 + 601863 A--TCTAAATG -s simRat_chr6.simRat.chr6 519589 11 + 647215 ATTCTTAGAGC - -a -s simMouse_chr6.simMouse.chr6 508270 11 + 636262 AGCCTTCTTCA -s Anc0.Anc0refChr3 121632 2 + 222631 A---------A -s Anc1.Anc1refChr6 155653 11 + 197743 AGATGTCCTCA -s Anc2.Anc2refChr1 34313 2 + 142988 A---------A -s mr.mrrefChr3 60785 11 + 181027 AGCCTTCTTCA -s simCow_chr6.simCow.chr6 491027 2 + 602619 A---------A -s simDog_chr6.simDog.chr6 481007 2 + 593897 A---------A -s simHuman_chr6.simHuman.chr6 487546 11 + 601863 AGATGTCCTCA -s simRat_chr6.simRat.chr6 519600 11 + 647215 AGCCTTCTTCC - -a -s simMouse_chr6.simMouse.chr6 508281 18 + 636262 AGGTTCAGACTGAGTCAG -s Anc0.Anc0refChr3 121689 15 + 222631 AAGTCCAGATTGAG---G -s Anc1.Anc1refChr6 155719 15 + 197743 AAGTCCAGATTGAG---G -s Anc2.Anc2refChr1 34370 15 + 142988 AAGTCCAAACTGAG---G -s mr.mrrefChr3 60796 18 + 181027 AAGTTCAGATTGAGTCAG -s simCow_chr6.simCow.chr6 491067 15 + 602619 AAGTCCAAACTGAG---T -s simDog_chr6.simDog.chr6 481071 15 + 593897 AAGTCCAAACTGAG---G -s simHuman_chr6.simHuman.chr6 487613 15 + 601863 AAGTCCAGGTTGAG---G -s simRat_chr6.simRat.chr6 519611 18 + 647215 AAGTTCAGATTAAGTTAG - -a -s simMouse_chr6.simMouse.chr6 508299 25 + 636262 TAAAAAGATGGAACAGTTTCCTGCC -s Anc0.Anc0refChr3 121704 23 + 222631 A--AAAGATGCAACAGATTCCTGCC -s Anc1.Anc1refChr6 155734 23 + 197743 A--AAAGATGCAACAGATTCCTGCC -s Anc2.Anc2refChr1 34385 23 + 142988 A--AAGCATGCAACACATTCCTGCC -s mr.mrrefChr3 60814 23 + 181027 T--AAAGATGGAACAGTTTCCTGCC -s simCow_chr6.simCow.chr6 491082 7 + 602619 G--AG----------------TGCC -s simDog_chr6.simDog.chr6 481091 23 + 593897 A--AAGCATGCAACACATTCCTGCC -s simHuman_chr6.simHuman.chr6 487628 23 + 601863 A--AAAGATACAACAGCCTCCTACC -s simRat_chr6.simRat.chr6 519629 23 + 647215 T--AAAGATGGAATAGTGTCCTGCC - -a -s simMouse_chr6.simMouse.chr6 508324 22 + 636262 CGAAAAGTTCAACCACTTGGCC -s Anc0.Anc0refChr3 121730 22 + 222631 CCAAAAGTTCAACCAATGGGCC -s Anc1.Anc1refChr6 155760 22 + 197743 CCAAAAGTTCAACCAATGGGCC -s Anc2.Anc2refChr1 34411 22 + 142988 GCAAAAGTTCAATCAATGGGTT -s mr.mrrefChr3 60837 22 + 181027 CCAAAAGTTCAACCACTTGGCC -s simCow_chr6.simCow.chr6 491092 21 + 602619 GTGAAAGCTCTATCAAT-TGTT -s simDog_chr6.simDog.chr6 481117 21 + 593897 -CAGAAGTTCAATCAATGGGTT -s simHuman_chr6.simHuman.chr6 487654 22 + 601863 CCAAGAGTGTAACCATTAGGCC -s simRat_chr6.simRat.chr6 519652 22 + 647215 ACAAAAGGACAACGGCTTGGCC - -a -s simMouse_chr6.simMouse.chr6 508346 38 + 636262 GGCATTACCACAACCAACCAGCACTACTAATAGAACTG -s Anc0.Anc0refChr3 121752 23 + 222631 GCTGTTACCACAACCACTTTG---------------TG -s Anc1.Anc1refChr6 155782 23 + 197743 GCTGTTACCACAACCACTTTG---------------TG -s Anc2.Anc2refChr1 34433 23 + 142988 GCTGTTACCACAACCACCTTG---------------TA -s mr.mrrefChr3 60859 38 + 181027 GGCATTACCACAACCAATCAGCACTACTAATAGAACTG -s simCow_chr6.simCow.chr6 491113 23 + 602619 GCTGATACCACAAGCACCCCA---------------TA -s simDog_chr6.simDog.chr6 481138 23 + 593897 GCCCTTAACACAACCATCTTG---------------TA -s simHuman_chr6.simHuman.chr6 487679 23 + 601863 GTTGTTGCCACAACCACTGTG---------------TG -s simRat_chr6.simRat.chr6 519674 38 + 647215 AGCATTACCACAACCAATCAATCCTACCAATAGACCTG - -a -s simMouse_chr6.simMouse.chr6 508384 4 + 636262 TTAG -s Anc0.Anc0refChr3 121775 4 + 222631 TTGA -s Anc1.Anc1refChr6 155805 4 + 197743 TTGA -s Anc2.Anc2refChr1 34456 4 + 142988 TTGA -s mr.mrrefChr3 60897 4 + 181027 TTAG -s simCow_chr6.simCow.chr6 491143 4 + 602619 TTGA -s simDog_chr6.simDog.chr6 481161 4 + 593897 CTGA -s simHuman_chr6.simHuman.chr6 487702 4 + 601863 TTGA -s simRat_chr6.simRat.chr6 519712 4 + 647215 CTAG - -a -s simMouse_chr6.simMouse.chr6 508388 46 + 636262 TGTTACACAAGTTGCTTGAAAAGCCAAGACAAGCTTGGTCCAAAGG -s Anc0.Anc0refChr3 121779 14 + 222631 TGTTA--------------------------------GGCAAAAGT -s Anc1.Anc1refChr6 155809 14 + 197743 TGTTA--------------------------------GGCAAAAGT -s Anc2.Anc2refChr1 34460 14 + 142988 TGTTT--------------------------------GGCAAAAGT -s mr.mrrefChr3 60901 14 + 181027 TGTTA--------------------------------GTCCAAAGG -s simCow_chr6.simCow.chr6 491147 14 + 602619 TGTTT--------------------------------GGTAAAATT -s simDog_chr6.simDog.chr6 481165 14 + 593897 TCTTT--------------------------------GGCAAAAGT -s simHuman_chr6.simHuman.chr6 487706 14 + 601863 TGTTA--------------------------------GACAAAAGT -s simRat_chr6.simRat.chr6 519721 14 + 647215 GATGA--------------------------------GTCCAAAGG - -a -s simMouse_chr6.simMouse.chr6 508434 1 + 636262 T -s Anc0.Anc0refChr3 121793 1 + 222631 T -s Anc1.Anc1refChr6 155823 1 + 197743 T -s Anc2.Anc2refChr1 34474 1 + 142988 T -s mr.mrrefChr3 60915 1 + 181027 T -s simCow_chr6.simCow.chr6 491162 1 + 602619 T -s simDog_chr6.simDog.chr6 481179 1 + 593897 T -s simHuman_chr6.simHuman.chr6 487720 1 + 601863 T -s simRat_chr6.simRat.chr6 519735 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 508435 4 + 636262 CTGC -s Anc0.Anc0refChr3 121794 4 + 222631 CAGC -s Anc1.Anc1refChr6 155824 4 + 197743 CAGC -s Anc2.Anc2refChr1 34477 4 + 142988 CAGC -s mr.mrrefChr3 60916 4 + 181027 CTGC -s simCow_chr6.simCow.chr6 491165 4 + 602619 CAGT -s simDog_chr6.simDog.chr6 481182 4 + 593897 CAGC -s simHuman_chr6.simHuman.chr6 487721 1 + 601863 C--- -s simRat_chr6.simRat.chr6 519736 4 + 647215 CTGC - -a -s simMouse_chr6.simMouse.chr6 508439 2 + 636262 TT -s Anc0.Anc0refChr3 121798 2 + 222631 TT -s Anc1.Anc1refChr6 155828 2 + 197743 TT -s Anc2.Anc2refChr1 34481 2 + 142988 TT -s mr.mrrefChr3 60920 2 + 181027 TT -s simCow_chr6.simCow.chr6 491172 2 + 602619 TT -s simDog_chr6.simDog.chr6 481186 2 + 593897 TT -s simRat_chr6.simRat.chr6 519740 2 + 647215 TT - -a -s simMouse_chr6.simMouse.chr6 508441 23 + 636262 CTTCCAATAAAATAATGATACTA -s Anc0.Anc0refChr3 121800 23 + 222631 TCTCCAAAAAAATAATGTTAACC -s Anc1.Anc1refChr6 155830 23 + 197743 TCTCCAAAAAAATAATGTTAACC -s Anc2.Anc2refChr1 34485 23 + 142988 TCTCCAAAAAAATCACATTAACC -s mr.mrrefChr3 60922 23 + 181027 CTTCCAATAAAATAATGATACTA -s simCow_chr6.simCow.chr6 491176 23 + 602619 TCTCCAAATAAAACACAATAACC -s simDog_chr6.simDog.chr6 481190 23 + 593897 TCTCCAAAAAAATCACATTAACC -s simHuman_chr6.simHuman.chr6 487722 6 + 601863 -----------ATAATG------ -s simRat_chr6.simRat.chr6 519742 23 + 647215 CTTCCAATAAAATAATGATACCA - -a -s simMouse_chr6.simMouse.chr6 508464 40 + 636262 TGTGGTGCCATTCCGAAGATTCACACCCCTCAACGCTTTG -s Anc0.Anc0refChr3 121823 39 + 222631 TGTGTTGACATTCAGAAAATTCA-ACCTCTAAAGATATTG -s Anc1.Anc1refChr6 155853 40 + 197743 TGTGTTGACATTCAGAAAATTCATACCTCTAAAGATATTG -s Anc2.Anc2refChr1 34508 39 + 142988 TGTGTTGACATTCAGAAAATTCA-AACTCTAAAGATATTG -s mr.mrrefChr3 60945 40 + 181027 TGTGGTGCCATTCAGAAGATTCACACCCCTCAACACTTTG -s simCow_chr6.simCow.chr6 491200 39 + 602619 TCAGTTGACATTCAGAATATTTA-TATCCTCAAGATATTG -s simDog_chr6.simDog.chr6 481213 39 + 593897 TGTGTTGACATTTAGAAAACTCA-AACTTTAAAGATATTG -s simHuman_chr6.simHuman.chr6 487728 34 + 601863 ------GACATACAGAAAATCCATACCTCTGAAGAGATTG -s simRat_chr6.simRat.chr6 519765 39 + 647215 TGTGGTGCCATTAAGAAGATTCACG-CCCTCAAAACTTTG - -a -s simMouse_chr6.simMouse.chr6 508504 5 + 636262 TTGCA -s Anc0.Anc0refChr3 121862 5 + 222631 TTACA -s Anc1.Anc1refChr6 155893 5 + 197743 TTACA -s Anc2.Anc2refChr1 34547 5 + 142988 TTACA -s mr.mrrefChr3 60985 5 + 181027 TTACA -s simCow_chr6.simCow.chr6 491239 5 + 602619 TCACA -s simDog_chr6.simDog.chr6 481252 5 + 593897 TTACA -s simHuman_chr6.simHuman.chr6 487763 5 + 601863 TTACA -s simRat_chr6.simRat.chr6 519804 5 + 647215 TTATA - -a -s simMouse_chr6.simMouse.chr6 508509 30 + 636262 CTACCCCGTGTCACATGGGATATATTTCGA -s Anc0.Anc0refChr3 121867 23 + 222631 CTGTCC----TTA---TGGCTATACTTGGA -s Anc1.Anc1refChr6 155898 23 + 197743 CTGTCC----TTA---TGGCTATACTTGGA -s Anc2.Anc2refChr1 34552 23 + 142988 CTGTAG----TTA---TGGCTCAATTTTGA -s mr.mrrefChr3 60990 30 + 181027 CTATCCCGTGTCACATTGGATATACTTGGA -s simCow_chr6.simCow.chr6 491244 23 + 602619 CTATAA----TTG---TGGCTCCATTAAGA -s simDog_chr6.simDog.chr6 481272 23 + 593897 CTGCAG----CTA---CACCCCACTTTTGA -s simHuman_chr6.simHuman.chr6 487768 23 + 601863 CTGTCC----TTA---TGGCTATACTTGGA -s simRat_chr6.simRat.chr6 519809 30 + 647215 CCATCCATTATCACATTGGATACACTTGGA - -a -s simMouse_chr6.simMouse.chr6 508539 10 + 636262 GCCATAGGTA -s Anc0.Anc0refChr3 121890 10 + 222631 GCCCTATGTA -s Anc1.Anc1refChr6 155921 10 + 197743 GCCCTATGTA -s Anc2.Anc2refChr1 34576 10 + 142988 GGCCTGTGCA -s mr.mrrefChr3 61020 10 + 181027 GCCATAGGTA -s simCow_chr6.simCow.chr6 491268 10 + 602619 GATCTGTGCA -s simDog_chr6.simDog.chr6 481296 10 + 593897 GGCCTGTACA -s simHuman_chr6.simHuman.chr6 487791 10 + 601863 GCCTTATGTA -s simRat_chr6.simRat.chr6 519839 10 + 647215 GCCATAGGTA - -a -s simMouse_chr6.simMouse.chr6 508549 1 + 636262 C -s Anc0.Anc0refChr3 121900 1 + 222631 T -s Anc1.Anc1refChr6 155931 1 + 197743 T -s Anc2.Anc2refChr1 34586 1 + 142988 T -s mr.mrrefChr3 61030 1 + 181027 C -s simCow_chr6.simCow.chr6 491279 1 + 602619 T -s simDog_chr6.simDog.chr6 481306 1 + 593897 T -s simHuman_chr6.simHuman.chr6 487801 1 + 601863 T -s simRat_chr6.simRat.chr6 519849 1 + 647215 C - -a -s simMouse_chr6.simMouse.chr6 508550 75 + 636262 TCCCATTTGAGTTGGTGTATCCATTGTTTCACAGGGCAGCATAAAGGGGAAGCAATTGATTTAGACTGTGGAACA -s Anc0.Anc0refChr3 121901 39 + 222631 T-----------------------------------CAGTACAAAGGAGGGCCAAAAAAGTGAG-CTTTTGAAGG -s Anc1.Anc1refChr6 155932 39 + 197743 T-----------------------------------CAGTACAAAGGAGGGCCAAAAAAGTGAG-CTTTTGAAGG -s Anc2.Anc2refChr1 34596 39 + 142988 T-----------------------------------CAGTACATAGGAGGGCTAAAAAGGTGAG-CTTTTGAAGG -s mr.mrrefChr3 61031 67 + 181027 TCCCAGTTGA--------ATCCATTGTTTCACAGGGCAGTATAAAGGGGAAGCAATTGATTGAGACTGTGGAACA -s simCow_chr6.simCow.chr6 491289 39 + 602619 G-----------------------------------CAGGACATAGGCGGGCTCAAAAGGTCTG-GGCTAAAAAG -s simDog_chr6.simDog.chr6 481316 39 + 593897 T-----------------------------------CAGTACATAGGAGGGCTAAAATGGTGAG-CTTGTGGAGT -s simHuman_chr6.simHuman.chr6 487802 39 + 601863 C-----------------------------------CAGTACAAAAGAGGGTCTAAAAAGTGAG-TTTTTGAAGG -s simRat_chr6.simRat.chr6 519850 67 + 647215 TCCCAGTTGA--------ATCCATTGTTTCATAGGGCAGTGTAAAGGGGAGGCATAAGATTGAGAGTGTGGAACC - -a -s simMouse_chr6.simMouse.chr6 508625 35 + 636262 CAGTGTCTTAGTACGAAATAAAAGATTGACACTCT -s Anc0.Anc0refChr3 121940 35 + 222631 CAATGTGTTCGTACTAAAGAAAACATTGCCACCTT -s Anc1.Anc1refChr6 155971 35 + 197743 CAATGTGTTCGTACTAAAGAAAACATTGCCACCTT -s Anc2.Anc2refChr1 34635 35 + 142988 CAATGTGTTCGTACTAAAGAAAACACTACCACCCT -s mr.mrrefChr3 61098 35 + 181027 CAGTGTCTTAGTACGAAATAAAAGATTGACACTTT -s simCow_chr6.simCow.chr6 491328 30 + 602619 --GTGTG---GTACTAAAGAAAACACCACCACCCT -s simDog_chr6.simDog.chr6 481356 35 + 593897 CAATGTGTTCGTACTAAAGGAAACACTACCACCCT -s simHuman_chr6.simHuman.chr6 487841 35 + 601863 CAATGTGTTGTTACTAGAAAAAACATTGCCACCTT -s simRat_chr6.simRat.chr6 519917 34 + 647215 TAGTGTCTTAATATGAAAGAAAAGATTGA-ACTTC - -a -s simMouse_chr6.simMouse.chr6 508660 39 + 636262 CTGGAACTCTAATTACAATGCATTTATACGGGACCCTTT -s Anc0.Anc0refChr3 121994 31 + 222631 --------CCAATTGCAAGGAGTTTAGATTGGACCCCTT -s Anc1.Anc1refChr6 156025 39 + 197743 CAGTTACTCCAATTGCAAGGAGTTTAGATTGGACCCCTT -s Anc2.Anc2refChr1 34689 31 + 142988 --------CCAATTGCAAGGAGTTGAGATTGGACCCCTT -s mr.mrrefChr3 61133 39 + 181027 CAGGAACTCTAATTACAATGCATTTATATGGGACCCTTT -s simCow_chr6.simCow.chr6 491377 31 + 602619 --------CTAATTGCAAGGGGTGGAGATTGGACCCCTT -s simDog_chr6.simDog.chr6 481410 31 + 593897 --------CCAATTGCAGGGAGTTGAGACTGAGTCCCTC -s simHuman_chr6.simHuman.chr6 487909 39 + 601863 CAGTTACTCCCATTGCAAGCAGTTTAGATTGGACCTCTT -s simRat_chr6.simRat.chr6 519951 39 + 647215 CAGGAACTCGAATTATAATGCAGTTATATGTGACCCTTT - -a -s simMouse_chr6.simMouse.chr6 508699 21 + 636262 AGAATATAGCTTTGTGTAACC -s Anc0.Anc0refChr3 122038 21 + 222631 ATAATGTAACGTTGAGTGAAT -s Anc1.Anc1refChr6 156077 21 + 197743 ATAATGTAACGTTGAGTGAAT -s Anc2.Anc2refChr1 34733 21 + 142988 GTGATGTAATGTTGAGTGGAT -s mr.mrrefChr3 61172 21 + 181027 AGAATGTAGCTTTGAGTAACC -s simCow_chr6.simCow.chr6 491433 16 + 602619 GTGAAGGAC-----AGAGGAT -s simDog_chr6.simDog.chr6 481454 20 + 593897 GTGATGTAATGTTGACTG-AT -s simHuman_chr6.simHuman.chr6 487961 21 + 601863 ATAGTGTAACCTTGAGTGAAT -s simRat_chr6.simRat.chr6 519990 21 + 647215 AGAATGTAGCTTTGAGTAACC - -a -s simMouse_chr6.simMouse.chr6 508720 7 + 636262 TAGGACA -s Anc0.Anc0refChr3 122059 7 + 222631 TAGGACA -s Anc1.Anc1refChr6 156098 7 + 197743 TAGGACA -s Anc2.Anc2refChr1 34754 7 + 142988 TAGGACA -s mr.mrrefChr3 61193 7 + 181027 TAGGACA -s simCow_chr6.simCow.chr6 491450 7 + 602619 TAGGTGA -s simDog_chr6.simDog.chr6 481474 7 + 593897 CGGGACA -s simHuman_chr6.simHuman.chr6 487982 7 + 601863 TAGGACA -s simRat_chr6.simRat.chr6 520011 7 + 647215 TGGGACA - -a -s simMouse_chr6.simMouse.chr6 508727 14 + 636262 GGTCTGCAAGGTAC -s Anc0.Anc0refChr3 122066 14 + 222631 GGTCTACAAGTTAA -s Anc1.Anc1refChr6 156105 14 + 197743 GGTCTACAAGTTAA -s Anc2.Anc2refChr1 34761 14 + 142988 GGTCTACAAAATAA -s mr.mrrefChr3 61200 14 + 181027 GGTCTGCAAGTTAC -s simCow_chr6.simCow.chr6 491457 14 + 602619 GGCCTGGCAAATAA -s simDog_chr6.simDog.chr6 481481 14 + 593897 GGTCTACAAAATAA -s simHuman_chr6.simHuman.chr6 487989 14 + 601863 GGTTTACAAGTTAT -s simRat_chr6.simRat.chr6 520019 14 + 647215 GGTCTGCAAGTTAC - -a -s simMouse_chr6.simMouse.chr6 508741 3 + 636262 TGG -s Anc0.Anc0refChr3 122080 3 + 222631 TTG -s Anc1.Anc1refChr6 156119 3 + 197743 TTG -s Anc2.Anc2refChr1 34775 3 + 142988 TTG -s mr.mrrefChr3 61214 3 + 181027 TGG -s simCow_chr6.simCow.chr6 491471 3 + 602619 CTG -s simDog_chr6.simDog.chr6 481497 3 + 593897 TAG -s simHuman_chr6.simHuman.chr6 488003 2 + 601863 -TG -s simRat_chr6.simRat.chr6 520033 3 + 647215 TGG - -a -s simMouse_chr6.simMouse.chr6 508744 16 + 636262 GGTTGCTTTACTGTTG -s Anc0.Anc0refChr3 122083 16 + 222631 AAGTGCTTTATAATCC -s Anc1.Anc1refChr6 156122 16 + 197743 AAGTGCTTTATAATCC -s Anc2.Anc2refChr1 34778 16 + 142988 AAGTACTTTATAATCC -s mr.mrrefChr3 61217 16 + 181027 GGTTGCTTTACTGTCC -s simCow_chr6.simCow.chr6 491477 16 + 602619 GAGTTCTTAATAATCC -s simDog_chr6.simDog.chr6 481500 16 + 593897 AAATAGTTTATAATCC -s simHuman_chr6.simHuman.chr6 488005 16 + 601863 AAGTGCTTTATCACCC -s simRat_chr6.simRat.chr6 520036 16 + 647215 CATTGCTTTACTGTCC - -a -s simMouse_chr6.simMouse.chr6 508760 20 + 636262 CTCAAGGTTCCTAATCTTTA -s Anc0.Anc0refChr3 122112 16 + 222631 CCCAAG----CTAAGGTGGT -s Anc1.Anc1refChr6 156151 16 + 197743 CCCAAG----CTAAGGTGGT -s Anc2.Anc2refChr1 34807 16 + 142988 CCCAAG----CTAGGGGGTT -s mr.mrrefChr3 61233 20 + 181027 CTCAAGGTTCCTAATCTTGA -s simCow_chr6.simCow.chr6 491506 16 + 602619 CCCAAC----CTTGGGAGTT -s simDog_chr6.simDog.chr6 481529 16 + 593897 CTTTAG----CTAGGGGGTT -s simHuman_chr6.simHuman.chr6 488034 16 + 601863 CCCAAG----CCAAGGTGGT -s simRat_chr6.simRat.chr6 520052 20 + 647215 CTCAAGATTCCTAATCTTGA - -a -s simMouse_chr6.simMouse.chr6 508780 31 + 636262 CTCTACAATTAACAAGTGTGGTCCTTGGAAA -s Anc0.Anc0refChr3 122128 31 + 222631 CTTTATGATTAACCAATGTGGTCCTTGGGAA -s Anc1.Anc1refChr6 156167 31 + 197743 CTTTATGATTAACCAATGTGGTCCTTGGGAA -s Anc2.Anc2refChr1 34823 31 + 142988 CTTTATGGTTAACCAATGTGCTCCTTAGGAC -s mr.mrrefChr3 61253 31 + 181027 CTTTACAATTAACAAGTGTGGTCCTTGGAAA -s simCow_chr6.simCow.chr6 491534 31 + 602619 CTTCATGGTTAACCAATGTGCTCCTTAGGAC -s simDog_chr6.simDog.chr6 481545 6 + 593897 TCTTAT------------------------- -s simHuman_chr6.simHuman.chr6 488050 31 + 601863 CTTTATGATTAACTAATGTGGTCCTTGGGGA -s simRat_chr6.simRat.chr6 520072 30 + 647215 CTTTACAATTAACAAGCGTGGTCC-TGGAAA - -a -s simMouse_chr6.simMouse.chr6 508811 12 + 636262 ATGTGTTTCCTT -s Anc0.Anc0refChr3 122209 12 + 222631 ATGCTTTTTCTT -s Anc1.Anc1refChr6 156248 12 + 197743 ATGCTTTTTCTT -s Anc2.Anc2refChr1 34904 12 + 142988 ATGCTTCTTCTT -s mr.mrrefChr3 61284 12 + 181027 ATGCGTTTCCTT -s simCow_chr6.simCow.chr6 491630 12 + 602619 ATGGTTCTTCTT -s simDog_chr6.simDog.chr6 481582 12 + 593897 ATGCGACTCCTT -s simHuman_chr6.simHuman.chr6 488133 12 + 601863 AAGCTTTTTCTT -s simRat_chr6.simRat.chr6 520102 12 + 647215 ATGCGTTTCCTT - -a -s simMouse_chr6.simMouse.chr6 508823 84 + 636262 CACGTTTTTACTACAGGAAAACTCTAGCAATGTTCCTGGTACTCAGGACAGGTTATATCACAACAGGGTTACTGTTCTAGTTAG -s Anc0.Anc0refChr3 122221 58 + 222631 --CATTTTTACTGCAGGGAAGCTTCTGAGATGTTCCTAGTACACAGGAC--------TCACACCA----------TCT------ -s Anc1.Anc1refChr6 156260 58 + 197743 --CATTTTTACTGCAGGGAAGCTTCTGAGATGTTCCTAGTACACAGGAC--------TCACACCA----------TCT------ -s Anc2.Anc2refChr1 34916 58 + 142988 --CATTTTTCCTGCAGGGTAGCTCCTGAGATGTTCCTAATACACAGGAC--------TCACACCA----------TCT------ -s mr.mrrefChr3 61296 84 + 181027 CACGTTTTTACTACAGGAAAACTTTAGCAATGTTCCTGGTACTCAGGACAGGTTATATCACAACAGGGTTACTGTTCTAGTTAG -s simCow_chr6.simCow.chr6 491642 58 + 602619 --CATTTTTCCAGCAAGGAAGCTCCTGAGACGTTACTAACATACAGGAC--------TCACACCA----------TCT------ -s simDog_chr6.simDog.chr6 481594 58 + 593897 --CGTTTTTCCTGCAGGGTAGTTCCTTAGATGTTCCTAATACACAGGAC--------CCAGACCA----------TCT------ -s simHuman_chr6.simHuman.chr6 488145 57 + 601863 --CATTTTTACTGCAGG-AAGCTTCTGAGATGTCCCTAGTACACAGGAC--------TCACACCA----------TCT------ -s simRat_chr6.simRat.chr6 520117 84 + 647215 CGTGTTTTTACTACAGGGAAACTTTAGCAATGCTCCTTGTACTCAGGACAGGTTGCATCACAACAGGGATCCTGTTCTAGTTAG - -a -s simMouse_chr6.simMouse.chr6 508907 2 + 636262 AG -s Anc0.Anc0refChr3 122279 2 + 222631 AT -s Anc1.Anc1refChr6 156318 2 + 197743 AT -s Anc2.Anc2refChr1 34975 2 + 142988 AT -s mr.mrrefChr3 61380 2 + 181027 AG -s simCow_chr6.simCow.chr6 491701 2 + 602619 AT -s simDog_chr6.simDog.chr6 481653 2 + 593897 AT -s simHuman_chr6.simHuman.chr6 488202 2 + 601863 AT -s simRat_chr6.simRat.chr6 520201 2 + 647215 AG - -a -s simMouse_chr6.simMouse.chr6 508909 8 + 636262 TATTCTGA -s Anc0.Anc0refChr3 122281 8 + 222631 TATTCTGA -s Anc1.Anc1refChr6 156320 8 + 197743 TATTCTGA -s Anc2.Anc2refChr1 34977 8 + 142988 TACCCTGA -s mr.mrrefChr3 61382 8 + 181027 TATTCTGA -s simCow_chr6.simCow.chr6 491707 8 + 602619 TACCCTGG -s simDog_chr6.simDog.chr6 481655 6 + 593897 TA--CTGA -s simHuman_chr6.simHuman.chr6 488204 8 + 601863 TATTCTGA -s simRat_chr6.simRat.chr6 520203 8 + 647215 TATTCTGA - -a -s simMouse_chr6.simMouse.chr6 508917 38 + 636262 CACTGTTGATACCATGGCCATCAATTGTGCTCAATCTA -s Anc0.Anc0refChr3 122289 36 + 222631 CAGTGTTTATTCCCTGATCATCAATTGTGTTCAG--TA -s Anc1.Anc1refChr6 156328 36 + 197743 CAGTGTTTATTCCCTGATCATCAATTGTGTTCAG--TA -s Anc2.Anc2refChr1 34985 36 + 142988 CAGTGTTTATTCCCTCATTATTGATAGTGTTCAG--TC -s mr.mrrefChr3 61390 38 + 181027 CACTGTTGATACCCTGGCCATCAATTGTGCTCAATCTA -s simCow_chr6.simCow.chr6 491715 36 + 602619 CACTGTTGATTTCCTCATTATTGATAGTGTTCAG--TC -s simDog_chr6.simDog.chr6 481662 15 + 593897 TAGGGTTTGTTCTCT----------------------- -s simHuman_chr6.simHuman.chr6 488212 36 + 601863 CAGTGTCAATTCCCTGATCATCAATTGTGTTCAG--TA -s simRat_chr6.simRat.chr6 520211 38 + 647215 TACTGTTGATACCCTGGCCATTAACTGTGCTCAATCTA - -a -s simMouse_chr6.simMouse.chr6 508955 32 + 636262 TCCAGCCATCATCCCTCAGAGGATACCTAGCC -s Anc0.Anc0refChr3 122325 30 + 222631 TCC--CCATCATCCCTGGGGGCATCCCTAGGT -s Anc1.Anc1refChr6 156364 30 + 197743 TCC--CCATCATCCCTGGGGGCATCCCTAGGT -s Anc2.Anc2refChr1 35021 30 + 142988 TAA--CTGTCATCCTGGGAGGCATCCCAAGGT -s mr.mrrefChr3 61428 32 + 181027 TCCAGCCATCATCCCTCGGAGGATACCTAGCC -s simCow_chr6.simCow.chr6 491751 30 + 602619 TAA--CTGTCATCCTGGGAGGCATCCCAAGGT -s simHuman_chr6.simHuman.chr6 488248 30 + 601863 CCC--CCATCATCCCTAGGGGCATCCCTAGGT -s simRat_chr6.simRat.chr6 520250 32 + 647215 TCCATCCATCATCACTTGGAGGATACCTAGCC - -a -s simMouse_chr6.simMouse.chr6 508987 6 + 636262 CAGGCC -s Anc0.Anc0refChr3 122355 6 + 222631 CAGGAC -s Anc1.Anc1refChr6 156394 6 + 197743 CAGGAC -s Anc2.Anc2refChr1 35051 6 + 142988 CCAGAC -s mr.mrrefChr3 61460 6 + 181027 CAGGCC -s simCow_chr6.simCow.chr6 491781 6 + 602619 CCAGAC -s simHuman_chr6.simHuman.chr6 488278 6 + 601863 CAGGAC -s simRat_chr6.simRat.chr6 520287 6 + 647215 CAGGCC - -a -s simMouse_chr6.simMouse.chr6 508993 18 + 636262 TATTAGGACTACAGATTG -s Anc0.Anc0refChr3 122364 18 + 222631 TACCAAGACTACAGATTG -s Anc1.Anc1refChr6 156403 18 + 197743 TACCAAGACTACAGATTG -s Anc2.Anc2refChr1 35060 18 + 142988 TACCCAGACTACAAATTG -s mr.mrrefChr3 61466 18 + 181027 TATTAGGACTACAGATTG -s simCow_chr6.simCow.chr6 491790 18 + 602619 TACCCAGACTACAAATTG -s simHuman_chr6.simHuman.chr6 488287 18 + 601863 TACCAAGTCCACAGATTC -s simRat_chr6.simRat.chr6 520293 18 + 647215 TATTAGGACTACAGGTTG - -a -s simMouse_chr6.simMouse.chr6 509011 5 + 636262 TGTTC -s Anc0.Anc0refChr3 122382 5 + 222631 TCATC -s Anc1.Anc1refChr6 156421 5 + 197743 TCATC -s Anc2.Anc2refChr1 35080 5 + 142988 TCACC -s mr.mrrefChr3 61484 5 + 181027 TGATC -s simCow_chr6.simCow.chr6 491810 5 + 602619 TCACC -s simHuman_chr6.simHuman.chr6 488305 5 + 601863 TCATC -s simRat_chr6.simRat.chr6 520311 5 + 647215 TGATC - -a -s simMouse_chr6.simMouse.chr6 509016 39 + 636262 CAATCTTACAAACTCCTCCATTTAGCTTTCATACAGACC -s Anc0.Anc0refChr3 122387 35 + 222631 CAATCT-GTACA---CACTGCTTAGCTGTTATACTGCCC -s Anc1.Anc1refChr6 156426 36 + 197743 CAATCTGGTACA---CACTGCTTAGCTGTTATACTGCCC -s Anc2.Anc2refChr1 35085 35 + 142988 TAATTT-GTACA---CACTGCTTAGCTGTTATACTGCCC -s mr.mrrefChr3 61489 36 + 181027 CAATCTTACACA---CTCCATTTAGCTTTCATACTGACC -s simCow_chr6.simCow.chr6 491815 35 + 602619 TAATTT-GTACA---CACTGCTTGGCTGTTATACTGCCC -s simDog_chr6.simDog.chr6 481677 29 + 593897 -------GCACG---CATTACTTAGCTGTTGTACCTTCC -s simHuman_chr6.simHuman.chr6 488366 36 + 601863 CAATCTGGTACA---CACTGCTTATCTATTATACTGCCC -s simRat_chr6.simRat.chr6 520316 36 + 647215 CAATCTTAAACA---CTCCAATTAGCTTTCATACTGATC - -a -s simMouse_chr6.simMouse.chr6 509055 37 + 636262 TTCTATCCATACATAGGCCTAAGGTATCAGGTAAGTC -s Anc0.Anc0refChr3 122422 37 + 222631 TGCTTCCCATACATAGACCTAGAGCTTCAGGCCAGCC -s Anc1.Anc1refChr6 156462 37 + 197743 TGCTTCCCATACATAGACCTAGAGCTTCAGGCCAGCC -s Anc2.Anc2refChr1 35120 37 + 142988 TGCTTCCCATATATAGACTGAGAGCTTCAGACCAGCC -s mr.mrrefChr3 61525 37 + 181027 TGCTATCCATACATAGGCCTAAGGCATCAGGTAAGTC -s simCow_chr6.simCow.chr6 491850 33 + 602619 TGCTGCCCATATATAGGC----ATCTTCAGACCAGCC -s simDog_chr6.simDog.chr6 481708 37 + 593897 TGCATCCCGTATATAGACTGAGGGCTTCAGACCAGTC -s simHuman_chr6.simHuman.chr6 488402 37 + 601863 TGCTTCCCACACATAGATCTAGAACTTCAGGCCAGCT -s simRat_chr6.simRat.chr6 520352 37 + 647215 TGCTATCAATACATAGGCCTAAGGCATCAGGTAACTC - -a -s simMouse_chr6.simMouse.chr6 509092 3 + 636262 CAG -s Anc0.Anc0refChr3 122467 3 + 222631 CAA -s Anc1.Anc1refChr6 156507 3 + 197743 CAA -s Anc2.Anc2refChr1 35165 3 + 142988 CAA -s mr.mrrefChr3 61562 3 + 181027 CAG -s simCow_chr6.simCow.chr6 491891 3 + 602619 CAA -s simDog_chr6.simDog.chr6 481753 3 + 593897 CAT -s simHuman_chr6.simHuman.chr6 488447 3 + 601863 CAA -s simRat_chr6.simRat.chr6 520389 3 + 647215 CAG - -a -s simMouse_chr6.simMouse.chr6 509095 25 + 636262 CCCCCATTACTGCCAGGGTAGATGG -s Anc0.Anc0refChr3 122477 25 + 222631 CCCCCATCTCTGCCAGGATGTATGG -s Anc1.Anc1refChr6 156517 25 + 197743 CCCCCATCTCTGCCAGGATGTATGG -s Anc2.Anc2refChr1 35175 25 + 142988 CCCCCATCTCTGCTAGGATGTATGG -s mr.mrrefChr3 61568 25 + 181027 CCCCCATTACTGCCAGGGTGGATGG -s simCow_chr6.simCow.chr6 491905 25 + 602619 CCGCAATCTCTAATAGGGTGTTTGG -s simDog_chr6.simDog.chr6 481759 25 + 593897 CCCCCATCCCTGCTACAATGTATAG -s simHuman_chr6.simHuman.chr6 488457 25 + 601863 CACCCATCTCTGCCAGGATGTATGG -s simRat_chr6.simRat.chr6 520395 25 + 647215 CCACCATTGCTGCCAGGGTGGATGG - -a -s simMouse_chr6.simMouse.chr6 509120 19 + 636262 TTCAATAGCATATGGAACA -s Anc0.Anc0refChr3 122502 19 + 222631 ATCAGTAACATATAGAACA -s Anc1.Anc1refChr6 156542 19 + 197743 ATCAGTAACATATAGAACA -s Anc2.Anc2refChr1 35200 19 + 142988 ATCAGTAATGTATAGAACA -s mr.mrrefChr3 61593 19 + 181027 TTCAATAACATATAGAACA -s simCow_chr6.simCow.chr6 491954 17 + 602619 ATGAGGA--GGATAAAACA -s simDog_chr6.simDog.chr6 481784 19 + 593897 AACAGTAATGTATAGGACA -s simHuman_chr6.simHuman.chr6 488482 19 + 601863 ATCAGTAACATATAGAACA -s simRat_chr6.simRat.chr6 520420 19 + 647215 TTCAATGACATGTAGGACA - -a -s simMouse_chr6.simMouse.chr6 509139 15 + 636262 GGACAGCTTATAGTA -s Anc0.Anc0refChr3 122529 12 + 222631 GGACAGTT--T-GTA -s Anc1.Anc1refChr6 156569 13 + 197743 GGACAGTT--TCGTA -s Anc2.Anc2refChr1 35227 12 + 142988 GGACAGTT--T-GTA -s mr.mrrefChr3 61612 15 + 181027 GGACAGCTTATAGTA -s simCow_chr6.simCow.chr6 491977 12 + 602619 GGACAGTT--G-ATA -s simDog_chr6.simDog.chr6 481811 12 + 593897 GAACAGTT--T-GTA -s simHuman_chr6.simHuman.chr6 488509 13 + 601863 GGACAGTT--TCGTA -s simRat_chr6.simRat.chr6 520439 15 + 647215 GGACAACTTATAGTA - -a -s simMouse_chr6.simMouse.chr6 509154 40 + 636262 ATGGGGATGCTAAAAAAAATCTAAGGACAGTCCTGAGCCA -s Anc0.Anc0refChr3 122541 40 + 222631 ATGGGGATGCTAAAAAAAATCTAAACAGGGTGCTAAGCCG -s Anc1.Anc1refChr6 156582 40 + 197743 ATGGGGATGCTAAAAAAAATCTAAACAGGGTGCTAAGCCG -s Anc2.Anc2refChr1 35239 40 + 142988 ATGGGGATGCTAAAACAAGCCTAAACAGGGTGCCAAGCAG -s mr.mrrefChr3 61627 40 + 181027 ATGGGGATGCTAAAAAAAATCTAAGGACAGTCCTGAGCCA -s simCow_chr6.simCow.chr6 491991 40 + 602619 ATGGGGATGCCAAAACAAGCCTAAACAGGGTGGCAAGCAG -s simDog_chr6.simDog.chr6 481823 36 + 593897 A----GATACTAAAACAAGCATAAACAGAGGGCCAAGAAG -s simHuman_chr6.simHuman.chr6 488522 40 + 601863 ATGAGGATGCTTAAAAAAATCTATACAGGGTTCTAAACCG -s simRat_chr6.simRat.chr6 520454 40 + 647215 ATGGGGATACTAAAAAAAACCTAAGGCCAGTCCTGAGCCT - -a -s simMouse_chr6.simMouse.chr6 509194 13 + 636262 GGAACCATAACTC -s Anc0.Anc0refChr3 122581 4 + 222631 GGA---------C -s Anc1.Anc1refChr6 156622 4 + 197743 GGA---------C -s Anc2.Anc2refChr1 35279 4 + 142988 AGA---------C -s mr.mrrefChr3 61667 4 + 181027 GGA---------C -s simCow_chr6.simCow.chr6 492031 4 + 602619 CGA---------C -s simDog_chr6.simDog.chr6 481905 4 + 593897 AGA---------C -s simHuman_chr6.simHuman.chr6 488562 4 + 601863 GGA---------C -s simRat_chr6.simRat.chr6 520494 1 + 647215 G------------ - -a -s simMouse_chr6.simMouse.chr6 509207 11 + 636262 ATTTTAATTCA -s Anc0.Anc0refChr3 122585 11 + 222631 AGTATAATCCA -s Anc1.Anc1refChr6 156626 11 + 197743 AGTATAATCCA -s Anc2.Anc2refChr1 35283 11 + 142988 AGTATAATCCA -s mr.mrrefChr3 61671 11 + 181027 ATTTTAATTCA -s simCow_chr6.simCow.chr6 492041 11 + 602619 AACATAATCCA -s simDog_chr6.simDog.chr6 481909 11 + 593897 AGTATGATCCA -s simHuman_chr6.simHuman.chr6 488566 11 + 601863 ACTACAATCCA -s simRat_chr6.simRat.chr6 520495 3 + 647215 --------TCA - -a -s simMouse_chr6.simMouse.chr6 509218 12 + 636262 TTTCAGGGCGTC -s Anc0.Anc0refChr3 122596 12 + 222631 GTTCAGAGTTCC -s Anc1.Anc1refChr6 156637 12 + 197743 GTTCAGAGTTCC -s Anc2.Anc2refChr1 35294 12 + 142988 GCTCAGAGTTCT -s mr.mrrefChr3 61682 12 + 181027 TTTCAGGGCGTC -s simCow_chr6.simCow.chr6 492054 12 + 602619 ACTCAGAGTTTG -s simDog_chr6.simDog.chr6 481920 12 + 593897 GCTCAGAGTCCT -s simHuman_chr6.simHuman.chr6 488577 12 + 601863 CTTCAGAGTTCC -s simRat_chr6.simRat.chr6 520498 12 + 647215 TTTCAGGGAGTG - -a -s simMouse_chr6.simMouse.chr6 509230 58 + 636262 AAGTTATAGGAGGCACAGTAATCTCTGGACTCAGAGAAGTAATCTGCCACCCAAGTAG -s Anc0.Anc0refChr3 122608 58 + 222631 CAGTTGCAGGAGGCACAGCACTCTCTGGTGCTAGAGAACTAATCTACCAGCTAACTAG -s Anc1.Anc1refChr6 156649 58 + 197743 CAGTTGCAGGAGGCACAGCACTCTCTGGTGCTAGAGAACTAATCTACCAGCTAACTAG -s Anc2.Anc2refChr1 35306 58 + 142988 CAGTTGCAGGAGGCACAGCACTTTCTGGTGCTAGGGAACTACGTTACCAGCTAGCTAG -s mr.mrrefChr3 61694 58 + 181027 AAGTTACAGGAGGCACAGTAATCTCTGGTGCCAGAGAAGTAATCTGCCACCTAAGTAG -s simCow_chr6.simCow.chr6 492066 56 + 602619 CAGTTACAGGAGGCAC--CATTATCTGGGGCTAGGACACTAATTTACCATCTAGGTGG -s simDog_chr6.simDog.chr6 481933 58 + 593897 TAGTTGCAGAAGGCACAGCACTTTCTGTTACTAGGGAACCACGTTACCAGCTAGCTAG -s simHuman_chr6.simHuman.chr6 488589 52 + 601863 CAGTTGCAGGAGGCACAGCGCTCACTGGTGCTAGAGAACTAATCG------TAACTAG -s simRat_chr6.simRat.chr6 520510 58 + 647215 AAGGTACAGGAGGCACTGTAATCTCTGGTGCCTGAGAAATAATCTGACACCTAGGGAG - -a -s simMouse_chr6.simMouse.chr6 509288 17 + 636262 ACTTGAGGTAGACTTCA -s Anc0.Anc0refChr3 122680 17 + 222631 ACTTTAGGTAAACTTCA -s Anc1.Anc1refChr6 156721 17 + 197743 ACTTTAGGTAAACTTCA -s Anc2.Anc2refChr1 35382 17 + 142988 CCTTTAGGTAAACTTCA -s mr.mrrefChr3 61752 17 + 181027 ACTTGAGGTAGACTTCA -s simCow_chr6.simCow.chr6 492140 17 + 602619 CCTTTAAGTAAACTTCA -s simDog_chr6.simDog.chr6 482009 17 + 593897 CCTTTAGGTAAACTCCA -s simHuman_chr6.simHuman.chr6 488655 17 + 601863 ACTTTAGGTAAACTTCA -s simRat_chr6.simRat.chr6 520568 17 + 647215 ACTTGAGGTAGACTTCA - -a -s simMouse_chr6.simMouse.chr6 509305 9 + 636262 AGGACATGT -s Anc0.Anc0refChr3 122697 9 + 222631 ATATTTTGT -s Anc1.Anc1refChr6 156738 9 + 197743 ATATTTTGT -s Anc2.Anc2refChr1 35399 9 + 142988 ATATTTTGT -s mr.mrrefChr3 61769 9 + 181027 AGGACATGT -s simDog_chr6.simDog.chr6 482031 9 + 593897 ATATTTTGT -s simHuman_chr6.simHuman.chr6 488672 9 + 601863 ATTTTTTGT -s simRat_chr6.simRat.chr6 520585 9 + 647215 AGGACATGT - -a -s simMouse_chr6.simMouse.chr6 509314 16 + 636262 GGTACCAGACTGTATA -s Anc0.Anc0refChr3 122715 16 + 222631 GTTACCAGACTGCATA -s Anc1.Anc1refChr6 156756 16 + 197743 GTTACCAGACTGCATA -s Anc2.Anc2refChr1 35417 16 + 142988 TTTACCAGCCCCCATA -s mr.mrrefChr3 61778 16 + 181027 GTTACCAGACTGTATA -s simDog_chr6.simDog.chr6 482050 16 + 593897 TTTACCAGCCCCCATA -s simHuman_chr6.simHuman.chr6 488690 16 + 601863 GTTACCAGACTGCATA -s simRat_chr6.simRat.chr6 520594 16 + 647215 GTTAAAAGACTGTACA - -a -s simMouse_chr6.simMouse.chr6 509330 1 + 636262 A -s Anc0.Anc0refChr3 122755 1 + 222631 C -s Anc1.Anc1refChr6 156796 1 + 197743 C -s Anc2.Anc2refChr1 35457 1 + 142988 T -s mr.mrrefChr3 61794 1 + 181027 C -s simDog_chr6.simDog.chr6 482094 1 + 593897 T -s simHuman_chr6.simHuman.chr6 488730 1 + 601863 C -s simRat_chr6.simRat.chr6 520610 1 + 647215 C - -a -s simMouse_chr6.simMouse.chr6 509331 24 + 636262 GGTTAGCCACTATCCCCGACCAAT -s Anc0.Anc0refChr3 122756 24 + 222631 GATTGGCGACTATCCACGACCAAG -s Anc1.Anc1refChr6 156797 24 + 197743 GATTGGCGACTATCCACGACCAAG -s Anc2.Anc2refChr1 35458 24 + 142988 GGCTGGTGACTATCCATGATAAGG -s mr.mrrefChr3 61795 24 + 181027 GATTAGCCACTATCCACGACCAAT -s simCow_chr6.simCow.chr6 492157 18 + 602619 ------TGACTATCCATGATAAGC -s simDog_chr6.simDog.chr6 482141 24 + 593897 GGCTGGTGACTATACATGATAAGG -s simHuman_chr6.simHuman.chr6 488731 24 + 601863 AATTGACGATCATCCACGACCAAG -s simRat_chr6.simRat.chr6 520611 24 + 647215 GATTAGCCACTATCCATGACCAAT - -a -s simMouse_chr6.simMouse.chr6 509355 24 + 636262 ACTTTCTAGCATTACCAGAAAGAG -s Anc0.Anc0refChr3 122780 24 + 222631 ACTTTCTAGCAGTAAGAAAAATAG -s Anc1.Anc1refChr6 156821 24 + 197743 ACTTTCTAGCAGTAAGAAAAATAG -s Anc2.Anc2refChr1 35484 24 + 142988 TCTTTCTAGCAGTCAGAACAATGT -s mr.mrrefChr3 61819 24 + 181027 ACTTTCTAGCAGTACCAGAAAGAG -s simCow_chr6.simCow.chr6 492177 22 + 602619 CCCTTTTAGCAGTCAGAATAAT-- -s simDog_chr6.simDog.chr6 482171 24 + 593897 TCTTTCTAGCGGTCCGAACAATGT -s simHuman_chr6.simHuman.chr6 488755 24 + 601863 ACGGTCTACCAGTAAGAAAAATAG -s simRat_chr6.simRat.chr6 520635 24 + 647215 ACTTTATAGGAGTACAAGAAAGAT - -a -s simMouse_chr6.simMouse.chr6 509379 54 + 636262 GGATTTTAAAGGATTGAGGGGTACAGATAGCACATTAATTCCTCAATCTATTAT -s Anc0.Anc0refChr3 122806 54 + 222631 AGATTTTTGGGGAATGAGGAACACAGATAGCACATTAAAACATCTATCTACTAT -s Anc1.Anc1refChr6 156847 54 + 197743 AGATTTTTGGGGAATGAGGAACACAGATAGCACATTAAAACATCTATCTACTAT -s Anc2.Anc2refChr1 35510 54 + 142988 AAATTTTTGGGGAATGAGAAACACAGATAGCACATTAGAACATCTATCTACTAT -s mr.mrrefChr3 61843 54 + 181027 GGATTTTAAAGGATTGAGGAATACAGATAGCACATTAATTCCTCAATCTATTAT -s simCow_chr6.simCow.chr6 492200 54 + 602619 AAATTTCTGAGGAATGGGAAAAACAGATAGCGCATTAGCACATCTATGTACTAT -s simDog_chr6.simDog.chr6 482196 41 + 593897 ----TTTTGGAGGAAGAAAAACA-------CACATT--AACATCTATCTACTAT -s simHuman_chr6.simHuman.chr6 488783 54 + 601863 AGATTTGTGGGGAATAAGGAACACAGATGGCACATTAAAACATCTATCCACTAT -s simRat_chr6.simRat.chr6 520659 54 + 647215 CGATTTAAAAGGATTGAGGAATACGGATAGCACATTAATTCCTCAAGCTATTAT - -a -s simMouse_chr6.simMouse.chr6 509433 24 + 636262 GGGAAATAAAACCCAGTTGATGAT -s Anc0.Anc0refChr3 122860 23 + 222631 GGAAGGCAAAAGTCAGTTAATG-T -s Anc1.Anc1refChr6 156901 23 + 197743 GGAAGGCAAAAGTCAGTTAATG-T -s Anc2.Anc2refChr1 35564 23 + 142988 GGAAGGCAAAAGTCAGTTAATG-G -s mr.mrrefChr3 61897 24 + 181027 GGGAAATAAAACCCAGTTGATGAT -s simCow_chr6.simCow.chr6 492255 23 + 602619 GGAAGGTGAGAGTCAGTTAATG-A -s simDog_chr6.simDog.chr6 482237 23 + 593897 GGAAGGCAAAAGTCAGTTAATG-G -s simHuman_chr6.simHuman.chr6 488837 23 + 601863 GGAAGGCAAAAGTCAGTTACTG-T -s simRat_chr6.simRat.chr6 520713 23 + 647215 GGG-AATAAAACCCAGTTGATGAC - -a -s simMouse_chr6.simMouse.chr6 509457 2 + 636262 GG -s Anc0.Anc0refChr3 122883 2 + 222631 AG -s Anc1.Anc1refChr6 156924 2 + 197743 AG -s Anc2.Anc2refChr1 35587 2 + 142988 AG -s mr.mrrefChr3 61921 2 + 181027 AG -s simCow_chr6.simCow.chr6 492306 2 + 602619 AG -s simDog_chr6.simDog.chr6 482260 2 + 593897 GG -s simHuman_chr6.simHuman.chr6 488860 2 + 601863 AG -s simRat_chr6.simRat.chr6 520736 2 + 647215 AG - -a -s simMouse_chr6.simMouse.chr6 509459 46 + 636262 AGAGTTGTAGGGCTCACCTCAGGGTGATTCAGGGATATAAGCAGCC -s Anc0.Anc0refChr3 122885 45 + 222631 AT-GTTGTAAGTATCACCTTAGTGTGATCCAGGTATATATGCAGTC -s Anc1.Anc1refChr6 156926 45 + 197743 AT-GTTGTAAGTATCACCTTAGTGTGATCCAGGTATATATGCAGTC -s Anc2.Anc2refChr1 35589 45 + 142988 GT-GTTGTAAGTATCACCTTTGTGTGATCCAGAAATACATGCGGTC -s mr.mrrefChr3 61923 46 + 181027 AGAGTTGTAGGGCTCACCTCAGGGTGATTCAGGTATATAAGCAGCC -s simCow_chr6.simCow.chr6 492308 39 + 602619 GT-GTTGTAATTAAGACCTTGGGGTAATCCAG------ATGCTGTC -s simDog_chr6.simDog.chr6 482264 45 + 593897 GA-GTTGTATGTATCACCTTTGTATGATCCAAAAATACATGCGGTC -s simHuman_chr6.simHuman.chr6 488862 45 + 601863 AT-ATTGTAAGTGTCACCTTAGTGTGATACAGGTATATTCCCAGTC -s simRat_chr6.simRat.chr6 520738 46 + 647215 AGAGTTGTAGGCATGACCTGAGGGTGATTCAGGTATACAAGCAGCC - -a -s simMouse_chr6.simMouse.chr6 509505 15 + 636262 CACCTAAACATATAA -s Anc0.Anc0refChr3 122930 15 + 222631 TACATAAACATGTAA -s Anc1.Anc1refChr6 156971 15 + 197743 TACATAAACATGTAA -s Anc2.Anc2refChr1 35634 15 + 142988 TATAGAAACATGTAT -s mr.mrrefChr3 61969 15 + 181027 TACATAAACATATAA -s simCow_chr6.simCow.chr6 492347 14 + 602619 TA-GGAATCATGTAT -s simDog_chr6.simDog.chr6 482309 15 + 593897 CATAGAAACACGTAT -s simHuman_chr6.simHuman.chr6 488907 15 + 601863 TACATAAACATGCAA -s simRat_chr6.simRat.chr6 520806 15 + 647215 TCCATAAACATATAA - -a -s simMouse_chr6.simMouse.chr6 509520 18 + 636262 CTTCTTGATTATGTCTTA -s Anc0.Anc0refChr3 122946 8 + 222631 CTTC-TG-----G----A -s Anc1.Anc1refChr6 156987 9 + 197743 CTTCTTG-----G----A -s Anc2.Anc2refChr1 35650 8 + 142988 CTTC-TG-----G----A -s mr.mrrefChr3 61984 13 + 181027 CTTCTTG-----GTCTTA -s simCow_chr6.simCow.chr6 492362 8 + 602619 CTTC-TG-----G----A -s simDog_chr6.simDog.chr6 482325 8 + 593897 CTTC-TG-----G----T -s simHuman_chr6.simHuman.chr6 488923 9 + 601863 CTTCTTG-----G----A -s simRat_chr6.simRat.chr6 520821 13 + 647215 CTTCTTG-----GTCTTA - -a -s simMouse_chr6.simMouse.chr6 509538 5 + 636262 TGCAA -s Anc0.Anc0refChr3 122954 5 + 222631 TGAAA -s Anc1.Anc1refChr6 156996 5 + 197743 TGAAA -s Anc2.Anc2refChr1 35658 5 + 142988 TCAAA -s mr.mrrefChr3 61997 5 + 181027 TGCAA -s simCow_chr6.simCow.chr6 492371 5 + 602619 TAAAG -s simDog_chr6.simDog.chr6 482333 5 + 593897 GCAAA -s simHuman_chr6.simHuman.chr6 488932 5 + 601863 TGAAA -s simRat_chr6.simRat.chr6 520834 5 + 647215 TGCAA - -a -s simMouse_chr6.simMouse.chr6 509543 8 + 636262 TAGCTGAA -s Anc0.Anc0refChr3 123074 8 + 222631 TAGCTGAA -s Anc1.Anc1refChr6 157116 8 + 197743 TAGCTGAA -s Anc2.Anc2refChr1 35813 8 + 142988 TGGCTCAA -s mr.mrrefChr3 62002 8 + 181027 TAGCTGAA -s simCow_chr6.simCow.chr6 492525 8 + 602619 TGGCTCAA -s simDog_chr6.simDog.chr6 482488 8 + 593897 TGGCTCAG -s simHuman_chr6.simHuman.chr6 489058 8 + 601863 TAGTTGAA -s simRat_chr6.simRat.chr6 520839 8 + 647215 TAGGTGAG - -a -s simMouse_chr6.simMouse.chr6 509551 24 + 636262 AAATAAAAAATTACTGGCAACTAC -s Anc0.Anc0refChr3 123086 24 + 222631 AGCTAAACAATTACTAGTGACAAT -s Anc1.Anc1refChr6 157128 24 + 197743 AGCTAAACAATTACTAGTGACAAT -s Anc2.Anc2refChr1 35825 24 + 142988 AGCTAAACAGTTACTAGTGACAAT -s mr.mrrefChr3 62010 24 + 181027 AAATAAAAAATTACTGGTGACAAC -s simCow_chr6.simCow.chr6 492534 24 + 602619 AGCTAGACATTTACTAGTTACAAT -s simDog_chr6.simDog.chr6 482547 24 + 593897 AATTAAACAGTTATTGGTGACAAT -s simHuman_chr6.simHuman.chr6 489070 24 + 601863 AGCTAAACAAATTCCAGTGACAAT -s simRat_chr6.simRat.chr6 520847 24 + 647215 ACATAAGAAATTACTGGTGACAAC - -a -s simMouse_chr6.simMouse.chr6 509575 13 + 636262 CACTTATGAGATG -s Anc0.Anc0refChr3 123110 13 + 222631 TAGGGATGAGATG -s Anc1.Anc1refChr6 157152 13 + 197743 TAGGGATGAGATG -s Anc2.Anc2refChr1 35849 13 + 142988 TTTGGATGGGACA -s mr.mrrefChr3 62034 13 + 181027 CAGTTATGAGATG -s simCow_chr6.simCow.chr6 492558 2 + 602619 TT----------- -s simDog_chr6.simDog.chr6 482583 13 + 593897 TTTGGATGGGACA -s simHuman_chr6.simHuman.chr6 489094 13 + 601863 TAGGGATGAGATG -s simRat_chr6.simRat.chr6 520871 13 + 647215 CAGTTTTGAGATG - -a -s simMouse_chr6.simMouse.chr6 509588 58 + 636262 TTAGCTCCGGGCATTATGGTGTACTATGGTGCACCCAGTTTGTGAAAAAGGATGAGAC -s Anc0.Anc0refChr3 123127 48 + 222631 TGAACTATAGGCATACTGATGA----------AAACGGTTTTTGAAGAATGATGTCAC -s Anc1.Anc1refChr6 157169 48 + 197743 TGAACTATAGGCATACTGATGA----------AAACGGTTTTTGAAGAATGATGTCAC -s Anc2.Anc2refChr1 35866 48 + 142988 TGAACTATAGGCATACTTAAGA----------AAATGGTTTTTGAAGAATGATGTCAT -s mr.mrrefChr3 62051 48 + 181027 TTAGCTCTGGGCATTATGGTGT----------ACCCAGTTTGTGAAGAAGGATGTAAC -s simCow_chr6.simCow.chr6 492560 38 + 602619 ----------GAATACTTAAGA----------AAATGATTTTTGAAGAAAGATGTCAT -s simDog_chr6.simDog.chr6 482600 48 + 593897 TGAACTATAGGCATACCTCAGT----------AGATGGTTTGTGAAGAATGATGTAAT -s simHuman_chr6.simHuman.chr6 489111 48 + 601863 TGATCTGTAGGTGGACTGATGA----------AAACGGTTTTTGGAGGATGATGGCAC -s simRat_chr6.simRat.chr6 520888 48 + 647215 TTAGCTCTGGGCATTATGGTGT----------ACCCAATTTGAAAAGAAGGATATAAC - -a -s simMouse_chr6.simMouse.chr6 509646 7 + 636262 TGTCCAA -s Anc0.Anc0refChr3 123186 7 + 222631 AGTCCAA -s Anc1.Anc1refChr6 157228 7 + 197743 AGTCCAA -s Anc2.Anc2refChr1 35925 7 + 142988 AGTCCCA -s mr.mrrefChr3 62110 7 + 181027 TGTCCAA -s simCow_chr6.simCow.chr6 492609 7 + 602619 AGTCCCA -s simDog_chr6.simDog.chr6 482659 6 + 593897 AGTCC-A -s simHuman_chr6.simHuman.chr6 489170 7 + 601863 AGTCCAA -s simRat_chr6.simRat.chr6 520947 7 + 647215 TGTCCAA - -a -s simMouse_chr6.simMouse.chr6 509653 14 + 636262 TTCATACCAGACAA -s Anc0.Anc0refChr3 123193 13 + 222631 CTCTTACCTAAC-A -s Anc1.Anc1refChr6 157235 13 + 197743 CTCTTACCTAAC-A -s Anc2.Anc2refChr1 35932 13 + 142988 CTCTTACCTAAC-A -s mr.mrrefChr3 62117 13 + 181027 TTCTTACCAGAC-A -s simCow_chr6.simCow.chr6 492618 13 + 602619 CTCTTATCTAAC-A -s simDog_chr6.simDog.chr6 482665 13 + 593897 CTCTTACCTAAC-A -s simHuman_chr6.simHuman.chr6 489177 13 + 601863 CTCTTACCCAAC-A -s simRat_chr6.simRat.chr6 520954 13 + 647215 TTCTTACTGGAC-A - -a -s simMouse_chr6.simMouse.chr6 509667 43 + 636262 AGTAGAGAGAGTAATACTTGGCTATTTCGGATCTACCTAGCCG -s Anc0.Anc0refChr3 123211 42 + 222631 AGTAGAG-GTAACATGATCGGCATTTCTAGATCTACTTAACTG -s Anc1.Anc1refChr6 157253 42 + 197743 AGTAGAG-GTAACATGATCGGCATTTCTAGATCTACTTAACTG -s Anc2.Anc2refChr1 35950 42 + 142988 AGTAGAG-GTAACATGATCAGCATTTCTAGATCTACTTAACTG -s mr.mrrefChr3 62130 43 + 181027 AGTAGAGAGTGACATACTTGGCAATTCCGGATCTACCTAGCCG -s simCow_chr6.simCow.chr6 492636 31 + 602619 ------------CATCATTAGTGTTTGCAGATCTACATAACTG -s simDog_chr6.simDog.chr6 482683 42 + 593897 AGTAGAG-GTAACATGATCAGCATTTCTAGATCTATTTAGCTG -s simHuman_chr6.simHuman.chr6 489195 42 + 601863 AGTGGAG-GCAACATGATCGGCATTTCTAGATCTACTTAACTG -s simRat_chr6.simRat.chr6 520967 43 + 647215 ACTAGAGAATGACATACTTGGCAATCCCTGACCTACCTAGCCA - -a -s simMouse_chr6.simMouse.chr6 509710 4 + 636262 GGTT -s Anc1.Anc1refChr6 157299 4 + 197743 GCTG -s mr.mrrefChr3 62173 4 + 181027 GCTG -s simHuman_chr6.simHuman.chr6 489241 4 + 601863 GCTG -s simRat_chr6.simRat.chr6 521010 4 + 647215 GCTG - -a -s simMouse_chr6.simMouse.chr6 509714 38 + 636262 GACACGCCTCGAAAGACAAATACCTAGATCAGTGATTG -s Anc0.Anc0refChr3 123257 38 + 222631 GACATACCTTGAAAGACAACTACCTAGCTCAGTGATTA -s Anc1.Anc1refChr6 157303 38 + 197743 GACATACCTTGAAAGACAACTACCTAGCTCAGTGATTA -s Anc2.Anc2refChr1 35996 38 + 142988 GACATACCCTAAAAGACAACTACCTAGCTCAGTGATTA -s mr.mrrefChr3 62177 38 + 181027 GACACACCTTGAAAGACAAATACCTAGCTCAGTGATTG -s simCow_chr6.simCow.chr6 492671 38 + 602619 GACATATCCCAAAAGACAAATACGTAGCTCAGTGGTTA -s simDog_chr6.simDog.chr6 482729 38 + 593897 GACATACCCTAAACGGCAACTACCTAGCTCAGTGATTG -s simHuman_chr6.simHuman.chr6 489249 38 + 601863 GATATTCCTTGAAAGACAACTACATAGCTTAGTGATTA -s simRat_chr6.simRat.chr6 521014 38 + 647215 GACACACTTTGAAAGACCAATACTTAGCTCAGTGATTG - -a -s simMouse_chr6.simMouse.chr6 509752 15 + 636262 AATATGATTGGAAAT -s Anc0.Anc0refChr3 123295 15 + 222631 AGTGTAATTGATCAT -s Anc1.Anc1refChr6 157341 15 + 197743 AGTGTAATTGATCAT -s Anc2.Anc2refChr1 36034 15 + 142988 AGTGTAATTGATCAT -s mr.mrrefChr3 62215 15 + 181027 AATATGATTGATAAT -s simCow_chr6.simCow.chr6 492727 15 + 602619 ATTGTAATTGAACAT -s simDog_chr6.simDog.chr6 482767 15 + 593897 AGTATAATAGATCAG -s simHuman_chr6.simHuman.chr6 489287 15 + 601863 AGTGTAATTGATCAT -s simRat_chr6.simRat.chr6 521052 15 + 647215 AATATGATTGATAAT - -a -s simMouse_chr6.simMouse.chr6 509767 86 + 636262 TGTTCTACTTCAATGCTGAATGTACTGGTCCCTGTGTTAATGTGACTAGACATACAGAGTCATGGATGAAAACAGAAAAGTAAATT -s Anc0.Anc0refChr3 123342 86 + 222631 TATTCAATCTGTAATCTCAGTGTACTGATCTCTGTGTCAATGGGACGAGATATCCAGATACATAGATGGACACAGAAGAATGATTT -s Anc1.Anc1refChr6 157388 86 + 197743 TATTCAATCTGTAATCTCAGTGTACTGATCTCTGTGTCAATGGGACGAGATATCCAGATACATAGATGGACACAGAAGAATGATTT -s Anc2.Anc2refChr1 36081 86 + 142988 TATTCAATCTGTAATCCCGGTGTACTGATCTCTGTGTCAATAGGATGAGATATCCCAATACAAAATTGGACACAGAAGAATGATTT -s mr.mrrefChr3 62230 86 + 181027 TGTTCTACCTCAATGCTGAATGTACTGGTCTCTGTGTTAATGTGACTAGACATACAGATACATGGATGAACACAGAAAAATAAATT -s simCow_chr6.simCow.chr6 492840 86 + 602619 AGGTCCATCTGTTATCACCCTGTACTGACCTCTGTGTCAATAGGATGAGACATCCCAATACAAACTCAGAATTTAAAGATAGATTT -s simDog_chr6.simDog.chr6 482814 86 + 593897 TATCTAAGCTGTAATGCTGGTCTACAGATCTTTGTGTCAATAGGATGAGATGTCCCAATACAAAATTGAACACAGAAAAATAACTT -s simHuman_chr6.simHuman.chr6 489334 86 + 601863 TATTCAATCTGTAATCTCAGTGTACTGATCTCTGTGTCAATGGGACCAGAGATGCAGATATCTAGATGGGCACAGGAGTATGATTT -s simRat_chr6.simRat.chr6 521067 86 + 647215 CGTACTACCTAAAGCCTGGATGTACTGGTCTGTGTACTAATGTGACTAGACATACAGATACATGGCTGAACACAGAAAAATAAATT - -a -s simMouse_chr6.simMouse.chr6 509853 7 + 636262 TGGTCAT -s Anc0.Anc0refChr3 123428 7 + 222631 TAGTAAC -s Anc1.Anc1refChr6 157474 7 + 197743 TAGTAAC -s Anc2.Anc2refChr1 36167 7 + 142988 TAGTAAC -s mr.mrrefChr3 62316 7 + 181027 TGGTCAT -s simCow_chr6.simCow.chr6 492928 7 + 602619 TAGTAAC -s simDog_chr6.simDog.chr6 482900 7 + 593897 TTGTAAC -s simHuman_chr6.simHuman.chr6 489420 7 + 601863 TAATAAC -s simRat_chr6.simRat.chr6 521153 7 + 647215 TGGTCAT - -a -s simMouse_chr6.simMouse.chr6 509860 1 + 636262 G -s Anc0.Anc0refChr3 123438 1 + 222631 C -s Anc1.Anc1refChr6 157484 1 + 197743 C -s Anc2.Anc2refChr1 36177 1 + 142988 C -s mr.mrrefChr3 62323 1 + 181027 C -s simCow_chr6.simCow.chr6 492938 1 + 602619 C -s simDog_chr6.simDog.chr6 482908 1 + 593897 C -s simHuman_chr6.simHuman.chr6 489430 1 + 601863 C -s simRat_chr6.simRat.chr6 521160 1 + 647215 C - -a -s simMouse_chr6.simMouse.chr6 509861 43 + 636262 CAAAGATGTATGGCTTTTAGAAGAAAACTAGTGGTAAGAAATC -s Anc0.Anc0refChr3 123439 43 + 222631 TAAACATGTATGGCTACTACAAAGAAATTAGTGGAAAAAGATT -s Anc1.Anc1refChr6 157485 43 + 197743 TAAACATGTATGGCTACTACAAAGAAATTAGTGGAAAAAGATT -s Anc2.Anc2refChr1 36178 43 + 142988 TAAACATCTATGGCTACTACAAAGAAATTAGTGGAAAAAGATT -s mr.mrrefChr3 62324 43 + 181027 CAAAGATGTATGGCTTTTAGAAAAAAACTAGTGGAAAGAAATC -s simCow_chr6.simCow.chr6 492975 43 + 602619 GAAACATCTATGGCTTCTACAAACTGATTAGTGGAAAAAGCGT -s simDog_chr6.simDog.chr6 482909 43 + 593897 TGAACATCTATGGCCAATACAAAGAAGTTAGTGCAAAAAGATT -s simHuman_chr6.simHuman.chr6 489431 43 + 601863 TAAACATGTATTGCTCCTACAAAGAAATTAGTTGAAACAGATT -s simRat_chr6.simRat.chr6 521161 39 + 647215 CAAATGTGTATGGCTTTTAGAAAAAGACTAGCGGAA----GTC - -a -s simMouse_chr6.simMouse.chr6 509904 38 + 636262 CAGATAAGGTTTCTGGTTCCACACCTTCCATGTTTGCA -s Anc0.Anc0refChr3 123482 35 + 222631 CAGACAAGGTTCCTAGGCCCA---CTTCTACATATTCA -s Anc1.Anc1refChr6 157528 35 + 197743 CAGACAAGGTTCCTAGGCCCA---CTTCTACATATTCA -s Anc2.Anc2refChr1 36221 35 + 142988 CAGACAAGGTTCCTAGGCCCT---CTTCTACATAGTTC -s mr.mrrefChr3 62367 38 + 181027 CAGATAAGGTTCCTGGGTCCACACCTTCCATGTTTGCA -s simCow_chr6.simCow.chr6 493023 35 + 602619 TAGACAAGGTTCCTAGCCCCT---CCTCGGCATAGTTC -s simDog_chr6.simDog.chr6 482952 31 + 593897 CAGATAAGGTTCCTAGGCCCT---CTGTTACATA---- -s simHuman_chr6.simHuman.chr6 489474 35 + 601863 CAGACACGGTTCCTAGACCCA---CTTCAACATGTCCA -s simRat_chr6.simRat.chr6 521200 38 + 647215 CAGATAAGGTTCCTGGGTCCACACCTTCCATGCTTGCA - -a -s simMouse_chr6.simMouse.chr6 509942 6 + 636262 TGAGTT -s Anc0.Anc0refChr3 123517 6 + 222631 TGAGCT -s Anc1.Anc1refChr6 157563 6 + 197743 TGAGCT -s Anc2.Anc2refChr1 36256 6 + 142988 TGAGCT -s mr.mrrefChr3 62405 6 + 181027 TGAGTT -s simCow_chr6.simCow.chr6 493058 6 + 602619 TGAGCT -s simHuman_chr6.simHuman.chr6 489509 6 + 601863 TGAGCT -s simRat_chr6.simRat.chr6 370153 6 - 647215 TGAATC -s simRat_chr6.simRat.chr6 521238 6 + 647215 TGAGTT - -a -s simMouse_chr6.simMouse.chr6 509948 1 + 636262 A -s Anc0.Anc0refChr3 123524 1 + 222631 A -s Anc1.Anc1refChr6 157570 1 + 197743 A -s Anc2.Anc2refChr1 36263 1 + 142988 A -s mr.mrrefChr3 62411 1 + 181027 A -s simCow_chr6.simCow.chr6 493065 1 + 602619 A -s simHuman_chr6.simHuman.chr6 489516 1 + 601863 A -s simRat_chr6.simRat.chr6 370159 1 - 647215 A -s simRat_chr6.simRat.chr6 521244 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 509949 3 + 636262 TAC -s Anc0.Anc0refChr3 123525 3 + 222631 TAC -s Anc1.Anc1refChr6 157571 3 + 197743 TAC -s Anc2.Anc2refChr1 36264 3 + 142988 TAG -s mr.mrrefChr3 62412 3 + 181027 TAC -s simCow_chr6.simCow.chr6 493066 3 + 602619 TAG -s simHuman_chr6.simHuman.chr6 489517 3 + 601863 TAC -s simRat_chr6.simRat.chr6 521245 3 + 647215 TAC - -a -s simMouse_chr6.simMouse.chr6 509952 4 + 636262 AAGA -s Anc0.Anc0refChr3 123528 4 + 222631 AAGA -s Anc1.Anc1refChr6 157574 4 + 197743 AAGA -s Anc2.Anc2refChr1 36267 4 + 142988 AAGA -s mr.mrrefChr3 62415 4 + 181027 AAGA -s simCow_chr6.simCow.chr6 493069 4 + 602619 AAGA -s simHuman_chr6.simHuman.chr6 489520 4 + 601863 AAGA -s simRat_chr6.simRat.chr6 370160 4 - 647215 AAAA -s simRat_chr6.simRat.chr6 521248 4 + 647215 AAGA - -a -s simMouse_chr6.simMouse.chr6 509956 9 + 636262 CATTTCTAC -s Anc0.Anc0refChr3 123534 9 + 222631 CACTTCTCA -s Anc1.Anc1refChr6 157580 9 + 197743 CACTTCTCA -s Anc2.Anc2refChr1 36273 9 + 142988 CACTCCTCA -s mr.mrrefChr3 62419 9 + 181027 CATTTCTAC -s simCow_chr6.simCow.chr6 493075 9 + 602619 CACTCCTCA -s simHuman_chr6.simHuman.chr6 489526 9 + 601863 CAGTTCTTT -s simRat_chr6.simRat.chr6 370164 9 - 647215 GTTCACTAC -s simRat_chr6.simRat.chr6 521252 9 + 647215 CATTTCTAC - -a -s simMouse_chr6.simMouse.chr6 509965 2 + 636262 TT -s Anc0.Anc0refChr3 123543 2 + 222631 TT -s Anc1.Anc1refChr6 157589 2 + 197743 TT -s Anc2.Anc2refChr1 36282 2 + 142988 TT -s mr.mrrefChr3 62428 2 + 181027 TT -s simCow_chr6.simCow.chr6 493084 2 + 602619 TT -s simDog_chr6.simDog.chr6 482983 2 + 593897 TT -s simHuman_chr6.simHuman.chr6 489535 2 + 601863 TT -s simRat_chr6.simRat.chr6 521261 2 + 647215 GT - -a -s simMouse_chr6.simMouse.chr6 509967 3 + 636262 TTA -s Anc0.Anc0refChr3 123545 3 + 222631 TCA -s Anc1.Anc1refChr6 157591 3 + 197743 TCA -s Anc2.Anc2refChr1 36284 3 + 142988 TCA -s mr.mrrefChr3 62430 3 + 181027 TTA -s simCow_chr6.simCow.chr6 493086 3 + 602619 TCA -s simDog_chr6.simDog.chr6 482985 3 + 593897 TCA -s simHuman_chr6.simHuman.chr6 489537 3 + 601863 TCA -s simRat_chr6.simRat.chr6 370173 3 - 647215 TCA -s simRat_chr6.simRat.chr6 521263 3 + 647215 TTA - -a -s simMouse_chr6.simMouse.chr6 509970 2 + 636262 AT -s Anc0.Anc0refChr3 123561 2 + 222631 AC -s Anc1.Anc1refChr6 157607 2 + 197743 AC -s Anc2.Anc2refChr1 36300 2 + 142988 AC -s mr.mrrefChr3 62433 2 + 181027 AT -s simCow_chr6.simCow.chr6 493102 2 + 602619 AC -s simDog_chr6.simDog.chr6 483001 2 + 593897 AC -s simHuman_chr6.simHuman.chr6 489553 2 + 601863 AC -s simRat_chr6.simRat.chr6 370176 2 - 647215 TC -s simRat_chr6.simRat.chr6 521266 2 + 647215 AT - -a -s simMouse_chr6.simMouse.chr6 509972 3 + 636262 AGG -s Anc0.Anc0refChr3 123563 3 + 222631 AGT -s Anc1.Anc1refChr6 157609 3 + 197743 AGT -s Anc2.Anc2refChr1 36313 3 + 142988 AGT -s mr.mrrefChr3 62435 3 + 181027 AGG -s simCow_chr6.simCow.chr6 493115 3 + 602619 AGT -s simDog_chr6.simDog.chr6 483015 3 + 593897 AGT -s simHuman_chr6.simHuman.chr6 489555 3 + 601863 AGT -s simRat_chr6.simRat.chr6 370178 3 - 647215 AGG -s simRat_chr6.simRat.chr6 521268 3 + 647215 AGG - -a -s simMouse_chr6.simMouse.chr6 509975 3 + 636262 CCA -s Anc0.Anc0refChr3 123566 3 + 222631 ACA -s Anc1.Anc1refChr6 157612 3 + 197743 ACA -s Anc2.Anc2refChr1 36316 3 + 142988 ACA -s mr.mrrefChr3 62438 3 + 181027 CCA -s simCow_chr6.simCow.chr6 493118 3 + 602619 ACA -s simDog_chr6.simDog.chr6 483018 2 + 593897 A-A -s simHuman_chr6.simHuman.chr6 489558 3 + 601863 ATA -s simRat_chr6.simRat.chr6 521271 3 + 647215 CTA - -a -s simMouse_chr6.simMouse.chr6 509978 1 + 636262 G -s Anc0.Anc0refChr3 123591 1 + 222631 G -s Anc1.Anc1refChr6 157637 1 + 197743 G -s Anc2.Anc2refChr1 36341 1 + 142988 G -s mr.mrrefChr3 62441 1 + 181027 G -s simCow_chr6.simCow.chr6 493143 1 + 602619 G -s simDog_chr6.simDog.chr6 483042 1 + 593897 G -s simHuman_chr6.simHuman.chr6 489583 1 + 601863 G -s simRat_chr6.simRat.chr6 521274 1 + 647215 G - -a -s simMouse_chr6.simMouse.chr6 509979 9 + 636262 TTGGTGATT -s Anc0.Anc0refChr3 123592 9 + 222631 TGGGGCCCT -s Anc1.Anc1refChr6 157638 9 + 197743 TGGGGCCCT -s Anc2.Anc2refChr1 36342 9 + 142988 GGTGCCCCT -s mr.mrrefChr3 62442 9 + 181027 TTGGGGATT -s simCow_chr6.simCow.chr6 493144 9 + 602619 GGCCCCCCT -s simDog_chr6.simDog.chr6 483043 9 + 593897 GGTGCCCCT -s simHuman_chr6.simHuman.chr6 489584 9 + 601863 TGGGGCCCT -s simRat_chr6.simRat.chr6 370181 9 - 647215 TTGGGAATA -s simRat_chr6.simRat.chr6 521275 9 + 647215 TTGGGGATT - -a -s simMouse_chr6.simMouse.chr6 509988 14 + 636262 AGTGGCCTGCCATA -s Anc0.Anc0refChr3 123629 14 + 222631 AATGAACTGTTCAA -s Anc1.Anc1refChr6 157675 14 + 197743 AATGAACTGTTCAA -s Anc2.Anc2refChr1 36379 14 + 142988 AATGAACTGTTCAA -s mr.mrrefChr3 62451 14 + 181027 AATGGCCTGCCAAA -s simCow_chr6.simCow.chr6 493176 14 + 602619 AATGAAATGTTCCC -s simDog_chr6.simDog.chr6 483080 14 + 593897 AAAGAACTGTTTAA -s simHuman_chr6.simHuman.chr6 489621 14 + 601863 AATAAACTGTTCAA -s simRat_chr6.simRat.chr6 370190 14 - 647215 TAAAGCCTACTGAG -s simRat_chr6.simRat.chr6 521284 14 + 647215 AATGGCCTGCCAAA - -a -s simMouse_chr6.simMouse.chr6 510002 1 + 636262 T -s Anc0.Anc0refChr3 123643 1 + 222631 T -s Anc1.Anc1refChr6 157689 1 + 197743 T -s Anc2.Anc2refChr1 36393 1 + 142988 T -s mr.mrrefChr3 62465 1 + 181027 T -s simCow_chr6.simCow.chr6 493190 1 + 602619 T -s simDog_chr6.simDog.chr6 483099 1 + 593897 T -s simHuman_chr6.simHuman.chr6 489635 1 + 601863 T -s simRat_chr6.simRat.chr6 370204 1 - 647215 T -s simRat_chr6.simRat.chr6 521298 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 510003 3 + 636262 TGG -s Anc0.Anc0refChr3 123665 3 + 222631 TGG -s Anc1.Anc1refChr6 157711 3 + 197743 TGG -s Anc2.Anc2refChr1 36415 3 + 142988 TGG -s mr.mrrefChr3 62466 3 + 181027 TGG -s simCow_chr6.simCow.chr6 493212 3 + 602619 TGG -s simDog_chr6.simDog.chr6 483111 1 + 593897 --A -s simHuman_chr6.simHuman.chr6 489657 3 + 601863 TGG -s simRat_chr6.simRat.chr6 370205 3 - 647215 AAG -s simRat_chr6.simRat.chr6 521299 3 + 647215 TGG - -a -s simMouse_chr6.simMouse.chr6 510006 41 + 636262 TTTTATAGCATGTATTACAGCATGGCTGTAGGAGTCCTAGT -s Anc0.Anc0refChr3 123668 41 + 222631 CCTTGTAACATGTGTTGCAGTATGGCTGTAGGAGTCCTGGT -s Anc1.Anc1refChr6 157714 41 + 197743 CCTTGTAACATGTGTTGCAGTATGGCTGTAGGAGTCCTGGT -s Anc2.Anc2refChr1 36418 41 + 142988 CCTTGCAACATGTGTTGCAGTGTGGCTGTAAGAGTCCTGGT -s mr.mrrefChr3 62469 41 + 181027 TTTTATAGCATGTGTTACAGCATGGCTGTAGGAGTCCTAGT -s simCow_chr6.simCow.chr6 493230 41 + 602619 CCTTGCACCACACGTTCCAGTGTGGCTGTACAAGTCCTGGT -s simDog_chr6.simDog.chr6 483112 41 + 593897 CCTTGCAACATGTGTTGCAGTGTGGCTGTGAGAGTCCTGGT -s simHuman_chr6.simHuman.chr6 489660 33 + 601863 CCTAGTG--------AGTAATATGGCTGTAGGAGTCCTGAT -s simRat_chr6.simRat.chr6 370208 41 - 647215 CCTTGCTACATGTGTTACAGTGTGGTTGTAAGAGTCTTGGT -s simRat_chr6.simRat.chr6 521302 41 + 647215 TTTTATAGCATGTCTCGCAGCATGGCTGCAGGACTCCTAGT - -a -s simMouse_chr6.simMouse.chr6 510047 9 + 636262 GCGCAGTGG -s Anc0.Anc0refChr3 123709 9 + 222631 GTCCAGTGG -s Anc1.Anc1refChr6 157755 9 + 197743 GTCCAGTGG -s Anc2.Anc2refChr1 36459 9 + 142988 GTCCAGTGA -s mr.mrrefChr3 62510 9 + 181027 GTGCAGTGG -s simCow_chr6.simCow.chr6 493274 9 + 602619 GTGCTGTGA -s simDog_chr6.simDog.chr6 483153 9 + 593897 GTCCAGTGA -s simHuman_chr6.simHuman.chr6 489693 9 + 601863 GTCCAGTGG -s simRat_chr6.simRat.chr6 370249 9 - 647215 GTGCAATTT -s simRat_chr6.simRat.chr6 521343 9 + 647215 GTCCGGTGG - -a -s simMouse_chr6.simMouse.chr6 510056 5 + 636262 ATCTC -s Anc0.Anc0refChr3 123719 5 + 222631 TTCCC -s Anc1.Anc1refChr6 157765 5 + 197743 TTCCC -s Anc2.Anc2refChr1 36469 5 + 142988 TTCCT -s mr.mrrefChr3 62519 5 + 181027 ATCTC -s simCow_chr6.simCow.chr6 493284 5 + 602619 TTCCT -s simDog_chr6.simDog.chr6 483163 5 + 593897 TTCCT -s simHuman_chr6.simHuman.chr6 489703 5 + 601863 GTCCC -s simRat_chr6.simRat.chr6 370258 5 - 647215 GCTCC -s simRat_chr6.simRat.chr6 521352 5 + 647215 ATCTC - -a -s simMouse_chr6.simMouse.chr6 510061 41 + 636262 TGTTTCTAAACTTGATGATATAAGTATCATCCCTGTTTCAT -s Anc0.Anc0refChr3 123726 41 + 222631 TTTTTCTACACTTGGTGATAGTATCATCCTCCTTGTTCCAT -s Anc1.Anc1refChr6 157772 41 + 197743 TTTTTCTACACTTGGTGATAGTATCATCCTCCTTGTTCCAT -s Anc2.Anc2refChr1 36476 41 + 142988 TTTTACTACACTTGGTGGTAGTATCGTCCTCCTTGTTCCAT -s mr.mrrefChr3 62524 41 + 181027 TGTTTCTAAACTTGATGATATAATTATCATCCTTGTTTCAT -s simCow_chr6.simCow.chr6 493291 41 + 602619 TTTTACTACACTTGGTGGTACAATCCCCCTCCTTATTCCAT -s simDog_chr6.simDog.chr6 483170 40 + 593897 CTTTACTACACTT-GTGGTAGTATTGTCCTCCTTGTTCGAT -s simHuman_chr6.simHuman.chr6 489710 41 + 601863 TTTTTCTACTCTTGGTGATAGTATCATCCTCCTTGGACCAT -s simRat_chr6.simRat.chr6 370263 41 - 647215 TCCTTCTACATTTGATGCTGGAATTATCCTTCTTGCTCCAT -s simRat_chr6.simRat.chr6 521357 41 + 647215 TGTTTCTAAACTTGATGATATAAATATCATCCTTGTTTCAT - -a -s simMouse_chr6.simMouse.chr6 510102 19 + 636262 CCTGGAACATGCCTGAGCT -s Anc0.Anc0refChr3 123770 19 + 222631 TGTGGGACATGGCTGAGCT -s Anc1.Anc1refChr6 157816 19 + 197743 TGTGGGACATGGCTGAGCT -s Anc2.Anc2refChr1 36520 19 + 142988 TGCAGGACATGGCTAAGCT -s mr.mrrefChr3 62568 19 + 181027 TCTGGAACATGCCTGAGCT -s simCow_chr6.simCow.chr6 493335 18 + 602619 T-CAGGATATGGCTAAGTT -s simDog_chr6.simDog.chr6 483213 19 + 593897 TGCAGGACATGGCTAAACT -s simHuman_chr6.simHuman.chr6 489754 19 + 601863 TGTGAGACATGACTGAGCT -s simRat_chr6.simRat.chr6 370307 19 - 647215 TGAATGATAGGGCTGACCT -s simRat_chr6.simRat.chr6 521401 19 + 647215 TCTGGAACATGCCTCAGCT - -a -s simMouse_chr6.simMouse.chr6 510121 15 + 636262 GGGTGGCGCATATAC -s Anc0.Anc0refChr3 123789 5 + 222631 TGGT----------T -s Anc1.Anc1refChr6 157835 15 + 197743 TGGTTGCCCACTCAT -s Anc2.Anc2refChr1 36539 5 + 142988 TGGC----------T -s mr.mrrefChr3 62587 15 + 181027 GGGTGGCGCATATAT -s simCow_chr6.simCow.chr6 493353 5 + 602619 TGGC----------G -s simDog_chr6.simDog.chr6 483232 5 + 593897 TGGC----------T -s simHuman_chr6.simHuman.chr6 489773 15 + 601863 CTGTTGCCCACTCAT -s simRat_chr6.simRat.chr6 370326 15 - 647215 TGGTGGTACGGTTAT -s simRat_chr6.simRat.chr6 521421 15 + 647215 GGGTGGCGCATGTAT - -a -s simMouse_chr6.simMouse.chr6 510136 7 + 636262 CATTCTT -s Anc0.Anc0refChr3 123794 7 + 222631 CCCTTTT -s Anc1.Anc1refChr6 157850 7 + 197743 CCCTTTT -s Anc2.Anc2refChr1 36544 7 + 142988 CCCTTCT -s mr.mrrefChr3 62602 7 + 181027 CATTCTT -s simCow_chr6.simCow.chr6 493364 7 + 602619 CCCGTCT -s simDog_chr6.simDog.chr6 483237 7 + 593897 TCCTTCT -s simHuman_chr6.simHuman.chr6 489788 7 + 601863 CCCTTTT -s simRat_chr6.simRat.chr6 370341 7 - 647215 TCTCCAT -s simRat_chr6.simRat.chr6 521436 7 + 647215 CATTCTT - -a -s simMouse_chr6.simMouse.chr6 510143 9 + 636262 TTTTTGAAT -s Anc0.Anc0refChr3 123802 9 + 222631 GCTCTGAAT -s Anc1.Anc1refChr6 157858 9 + 197743 GCTCTGAAT -s Anc2.Anc2refChr1 36552 9 + 142988 GCTCTGAAT -s mr.mrrefChr3 62609 9 + 181027 TTTTTGAAT -s simCow_chr6.simCow.chr6 493372 9 + 602619 GCTCTGAGT -s simDog_chr6.simDog.chr6 483245 9 + 593897 GCTTTGAAT -s simHuman_chr6.simHuman.chr6 489796 9 + 601863 GGTCTGAAC -s simRat_chr6.simRat.chr6 370348 9 - 647215 GCTCTGAAT -s simRat_chr6.simRat.chr6 521443 9 + 647215 TTTTTGGAT - -a -s simMouse_chr6.simMouse.chr6 510152 2 + 636262 AC -s Anc0.Anc0refChr3 123811 2 + 222631 AC -s Anc1.Anc1refChr6 157867 2 + 197743 AC -s Anc2.Anc2refChr1 36561 2 + 142988 AC -s mr.mrrefChr3 62618 2 + 181027 AC -s simCow_chr6.simCow.chr6 493381 2 + 602619 AC -s simDog_chr6.simDog.chr6 483254 2 + 593897 AC -s simHuman_chr6.simHuman.chr6 489808 2 + 601863 AC -s simRat_chr6.simRat.chr6 521452 2 + 647215 AC - -a -s simMouse_chr6.simMouse.chr6 510154 6 + 636262 ACATAT -s Anc0.Anc0refChr3 123813 6 + 222631 ACATAT -s Anc1.Anc1refChr6 157869 6 + 197743 ACATAT -s Anc2.Anc2refChr1 36563 6 + 142988 ACATAT -s mr.mrrefChr3 62620 6 + 181027 ACATAT -s simCow_chr6.simCow.chr6 493383 6 + 602619 TCATTT -s simDog_chr6.simDog.chr6 483256 6 + 593897 ACATAT -s simHuman_chr6.simHuman.chr6 489810 6 + 601863 ACATCT -s simRat_chr6.simRat.chr6 370357 6 - 647215 AGATAT -s simRat_chr6.simRat.chr6 521454 6 + 647215 ACATAT - -a -s simMouse_chr6.simMouse.chr6 510160 15 + 636262 ACAAGTTTGAGATCA -s Anc0.Anc0refChr3 123819 15 + 222631 ACATGACTGAGGTGG -s Anc1.Anc1refChr6 157875 15 + 197743 ACATGACTGAGGTGG -s Anc2.Anc2refChr1 36569 15 + 142988 ACATGACTAAGGTGG -s mr.mrrefChr3 62626 15 + 181027 ACAAGTCTGAGGTCA -s simCow_chr6.simCow.chr6 493553 15 + 602619 GGATGGCTACGGTGT -s simDog_chr6.simDog.chr6 483262 15 + 593897 ACATCACTAAGGTAG -s simHuman_chr6.simHuman.chr6 489816 15 + 601863 ACATGCCTGAGTTGG -s simRat_chr6.simRat.chr6 370363 15 - 647215 ACTTGGCTAGGGTAA -s simRat_chr6.simRat.chr6 521460 15 + 647215 ACAAATCTGAGGTCA - -a -s simMouse_chr6.simMouse.chr6 510175 14 + 636262 GCATCATAAGAAAC -s Anc0.Anc0refChr3 123836 14 + 222631 GCATCAGAGCAACC -s Anc1.Anc1refChr6 157892 14 + 197743 GCATCAGAGCAACC -s Anc2.Anc2refChr1 36586 14 + 142988 GCATCAGAGCAACC -s mr.mrrefChr3 62643 14 + 181027 GCATCATAAGAAAC -s simCow_chr6.simCow.chr6 493570 14 + 602619 GCATCAGAGTAACC -s simDog_chr6.simDog.chr6 483279 14 + 593897 GCATCAGAGCTACC -s simHuman_chr6.simHuman.chr6 489833 14 + 601863 ACATCAGAGCAACC -s simRat_chr6.simRat.chr6 370380 14 - 647215 GCATCAGAACAAAC -s simRat_chr6.simRat.chr6 521475 14 + 647215 GCATCATAAGAAAC - -a -s simMouse_chr6.simMouse.chr6 510189 6 + 636262 ACTTTA -s Anc0.Anc0refChr3 123850 6 + 222631 ACTTTA -s Anc1.Anc1refChr6 157906 6 + 197743 ACTTTA -s Anc2.Anc2refChr1 36600 6 + 142988 ACTTTA -s mr.mrrefChr3 62657 6 + 181027 ACTTTA -s simCow_chr6.simCow.chr6 493584 6 + 602619 ACTTTA -s simDog_chr6.simDog.chr6 483293 6 + 593897 ACTTTA -s simHuman_chr6.simHuman.chr6 489847 6 + 601863 ACTTTA -s simRat_chr6.simRat.chr6 521489 6 + 647215 ACTTTA - -a -s simMouse_chr6.simMouse.chr6 510195 8 + 636262 TGTCACAA -s Anc0.Anc0refChr3 123952 6 + 222631 GGT--CGA -s Anc1.Anc1refChr6 158008 6 + 197743 GGT--CGA -s Anc2.Anc2refChr1 36706 6 + 142988 GGC--CGA -s mr.mrrefChr3 62663 8 + 181027 TGTCACAA -s simCow_chr6.simCow.chr6 493687 6 + 602619 GCC--CAC -s simDog_chr6.simDog.chr6 483398 6 + 593897 GGC--CGA -s simHuman_chr6.simHuman.chr6 489956 6 + 601863 GGT--CCA -s simRat_chr6.simRat.chr6 521495 8 + 647215 TGTCACAA - -a -s simMouse_chr6.simMouse.chr6 510203 8 + 636262 GAAGTGAT -s Anc0.Anc0refChr3 123958 8 + 222631 CAGGTGAT -s Anc1.Anc1refChr6 158014 8 + 197743 CAGGTGAT -s Anc2.Anc2refChr1 36712 8 + 142988 CAGGTGAT -s mr.mrrefChr3 62671 8 + 181027 GAGGTGAT -s simCow_chr6.simCow.chr6 493693 7 + 602619 AAGGTGA- -s simDog_chr6.simDog.chr6 483404 8 + 593897 CAGGTGGT -s simHuman_chr6.simHuman.chr6 489962 8 + 601863 CAGGTGAT -s simRat_chr6.simRat.chr6 521541 8 + 647215 GGGGTGAT - -a -s simMouse_chr6.simMouse.chr6 510211 163 + 636262 TTTTGATTGCAGTATTCGGGCAACAAGGGTTCATGTGTAAGACTGTTTCTGCAAGACATAATTGTTCGCATGCCAGAAAATGTCATGGATTGTTTGGCATAACCTCACAAAAGCAGCCATCATTTCCTTAGAAGTGGGTTTGATAATTCATATGTAGACATAA -s Anc0.Anc0refChr3 123966 153 + 222631 TCTTAATTGCAGGATGTGGCCAAAAGGGGATTATGTATAAGACTGTATCTGATAAATATAATTGATGGCTTGGCAAAAAACATTATTGACTGCTTGGCCCAATCTAACAAAATCAGCCATCATTTCCTTAGAAGTGGGTTTGATAA----------GACATTC -s Anc1.Anc1refChr6 158022 153 + 197743 TCTTAATTGCAGGATGTGGCCAAAAGGGGATTATGTATAAGACTGTATCTGATAAATATAATTGATGGCTTGGCAAAAAACATTATTGACTGCTTGGCCCAATCTAACAAAATCAGCCATCATTTCCTTAGAAGTGGGTTTGATAA----------GACATTC -s Anc2.Anc2refChr1 36733 153 + 142988 TCTTAACTGCAGGATGTGGCCAAAAGGGTATTATGTATAAGACTGTATCTGATAAATATAATTGATGGCTTGGCAAAAAACATTATTGACCACTTGACCCAATCTAACAAAATCAGCCCTCGATTCCTTAAAAGTGGGTTTAATAA----------GTCATTC -s mr.mrrefChr3 62679 163 + 181027 TCTTAATTGCAGTATTCGGGCAAAAAGGGTTTATGTGTAAGACTGTTTCTGCAAGATATAATTGTTCGCTTGCCAGAAAATGTCATGGATTGTTTGGCATAACCTCACAAAATCAGCCATCATTTCCTTAGAAGTGGGTTTGATAATTCATATGTAGACATAC -s simCow_chr6.simCow.chr6 493713 147 + 602619 TCTTAACTGCAGGATGTGGCCAAGAGGGAATAATATATAAGACTGTATCTGATCAATATAATTGATGGCATGGCAAAAAATGTTATTGACCATTTGTCCCAATCTAACAGAATGAG------CTGCCTTAAAATTGGGTTTAATAG----------GTCATAC -s simDog_chr6.simDog.chr6 483426 153 + 593897 TCTTGACAACAAGAAGTGGCCAAAAGGGTATTATGTGTAAGATTGCATTTGATAGAGATAATTGATTGTTTGGCAAACAACATTATTGACCACCTGACCCAATCAGACAAAATCAACCCTCGAATCCTTAAAAGTGTGTTTAATAA----------GTCATTC -s simHuman_chr6.simHuman.chr6 489970 153 + 601863 TCTTAATTGCAGGGTGTAGCTAGAAGGGGATTATGTATAAGCCTGTGTCTGATAAATATAATGGATGGCTTAGCGAAAAACATTATTGGGTGCTTGGCCCGATGTAACAAGATCAGGCATCATTTCCTTAGAAGTGGGTTTGATAA----------GACATGC -s simRat_chr6.simRat.chr6 521549 162 + 647215 TCTCAATTGCAGCATTCGGGCAAAAAGGGTTTATGTGTAAGGCTGTTTCTGCAAGATCTAATTGTTTGCTTGCCAGAAAAAGTCATGGATTGTTTGGCATAGCTTCACCAAATGGGCCATC-TTTCCTTAGAAGTGTTTTTGATAATTCGTATGTAGACATAC - -a -s simMouse_chr6.simMouse.chr6 510374 6 + 636262 TCACTC -s Anc0.Anc0refChr3 124134 6 + 222631 TCTCTC -s Anc1.Anc1refChr6 158190 6 + 197743 TCTCTC -s Anc2.Anc2refChr1 36901 6 + 142988 TCTCTC -s mr.mrrefChr3 62857 6 + 181027 TCACTC -s simCow_chr6.simCow.chr6 493875 6 + 602619 TCTCTC -s simDog_chr6.simDog.chr6 483594 6 + 593897 TCTCAC -s simHuman_chr6.simHuman.chr6 490138 6 + 601863 TCTCTC -s simRat_chr6.simRat.chr6 521726 6 + 647215 TCACTC - -a -s simMouse_chr6.simMouse.chr6 510380 60 + 636262 TCGTCTAGTCTTCAATCTCTTGTCATCTACCTGCAATCCCTTATCCGTATGCACACGCTT -s Anc0.Anc0refChr3 124140 60 + 222631 TTGTCTAGTCTTTTGTTTCCTGTCCTCTTCCTGCAATCCCGTATCTTCCTGCACACACTT -s Anc1.Anc1refChr6 158196 60 + 197743 TTGTCTAGTCTTTTGTTTCCTGTCCTCTTCCTGCAATCCCGTATCTTCCTGCACACACTT -s Anc2.Anc2refChr1 36907 60 + 142988 TTGTCTAGTCTTTTGTTTTCTCTCCTCTTCCTGCAATCCCGTATTTTCCTGCACACACTT -s mr.mrrefChr3 62863 60 + 181027 TTGTCTAGTCTTCAGTCTCTTGTCATCTTCCTGCAATCCCTTATCCGCCTGCACACACTT -s simCow_chr6.simCow.chr6 493881 60 + 602619 TTGTCTAGTCTTATGTCTGCTCTCCTCTTCCTGCAATCCTGTATTTTCGTGCGCACACTT -s simDog_chr6.simDog.chr6 483605 60 + 593897 CTCTTTCGTCTTTTGTTTTCTCTCCACTTCCTGCAATCCCTTATTTTTCTGCACATGCTT -s simHuman_chr6.simHuman.chr6 490144 60 + 601863 TTGTCTAGTCTTTTGTTCCCTGTTGTCTTCCTGCAATCCCGTATCTCCCTGTACACATTT -s simRat_chr6.simRat.chr6 521732 60 + 647215 TTGTCTAGTTTCCAGTCTCTTGTGATCTTCCTGCAATCCCTTATCCTCCCGCGCACACTT - -a -s simMouse_chr6.simMouse.chr6 510440 16 + 636262 AACTTAAGTCCTTGTG -s Anc0.Anc0refChr3 124200 16 + 222631 AACTTAAGTCCCTGTG -s Anc1.Anc1refChr6 158256 16 + 197743 AACTTAAGTCCCTGTG -s Anc2.Anc2refChr1 36967 16 + 142988 AAATTAAATCCCCCTG -s mr.mrrefChr3 62923 16 + 181027 AACTTAAGTCCCTGTG -s simCow_chr6.simCow.chr6 493941 16 + 602619 AAGTAAAATCCCCCTG -s simDog_chr6.simDog.chr6 483665 16 + 593897 AAATTAAATCTGCCTT -s simHuman_chr6.simHuman.chr6 490204 16 + 601863 ACCTTAAGTCCCTGTG -s simRat_chr6.simRat.chr6 521797 16 + 647215 AACTTAAGTCCCTGTT - -a -s simMouse_chr6.simMouse.chr6 510456 19 + 636262 TGATGCTAAGGACATTTTG -s Anc0.Anc0refChr3 124217 19 + 222631 TGACTCTAAGGACTTGTTG -s Anc1.Anc1refChr6 158273 19 + 197743 TGACTCTAAGGACTTGTTG -s Anc2.Anc2refChr1 36984 19 + 142988 TGACTCTAAGGACTTGTTG -s mr.mrrefChr3 62939 19 + 181027 TGACGCTAAGGACATTTTG -s simCow_chr6.simCow.chr6 493958 19 + 602619 TGGCTCTAAGGACTTGTTG -s simDog_chr6.simDog.chr6 483682 19 + 593897 TGACTCTAAGGACTTGTTG -s simHuman_chr6.simHuman.chr6 490221 19 + 601863 TGACTCCAGGTACTTGTTG -s simRat_chr6.simRat.chr6 521813 19 + 647215 TGACATTAAGGACATATTG - -a -s simMouse_chr6.simMouse.chr6 510475 13 + 636262 CTATCAGCACAGT -s Anc0.Anc0refChr3 124236 13 + 222631 TTATCAACACAGT -s Anc1.Anc1refChr6 158292 13 + 197743 TTATCAACACAGT -s Anc2.Anc2refChr1 37003 13 + 142988 TTATCAACACTGT -s mr.mrrefChr3 62958 13 + 181027 TTATCAACACAGT -s simCow_chr6.simCow.chr6 493977 12 + 602619 TTATCAA-ATGGA -s simDog_chr6.simDog.chr6 483701 13 + 593897 TTATCAACACTGT -s simHuman_chr6.simHuman.chr6 490240 13 + 601863 TTATTAATACAGT -s simRat_chr6.simRat.chr6 521843 13 + 647215 TTATCAACACAGT - -a -s simMouse_chr6.simMouse.chr6 510488 9 + 636262 AGATAGATA -s Anc0.Anc0refChr3 124249 8 + 222631 ATATAGAT- -s Anc1.Anc1refChr6 158305 8 + 197743 ATATAGAT- -s Anc2.Anc2refChr1 37016 8 + 142988 ATATAGAT- -s mr.mrrefChr3 62971 9 + 181027 AGATAGATA -s simCow_chr6.simCow.chr6 493989 8 + 602619 ACATAGAT- -s simDog_chr6.simDog.chr6 483720 8 + 593897 ATATAAAT- -s simHuman_chr6.simHuman.chr6 490253 8 + 601863 GTCTAGAT- -s simRat_chr6.simRat.chr6 521856 9 + 647215 AGATAGATA - -a -s simMouse_chr6.simMouse.chr6 510497 29 + 636262 AATCAATTTAGTATGTAGCTTTACAGTCT -s Anc0.Anc0refChr3 124259 29 + 222631 AATCCCTTTGATATGTAGTCTCTCAGCCT -s Anc1.Anc1refChr6 158315 29 + 197743 AATCCCTTTGATATGTAGTCTCTCAGCCT -s Anc2.Anc2refChr1 37026 29 + 142988 AGTCCCTTAGATATGTAGTCTCTTGGCCT -s mr.mrrefChr3 62982 29 + 181027 AATCAATTTAATATGTAGCTTCTCAGTCT -s simCow_chr6.simCow.chr6 493999 29 + 602619 AGCCCCATAGATATGTAGTCTCTTGGCCC -s simDog_chr6.simDog.chr6 483730 29 + 593897 GGTCCCTGAGATATGTAGCCTTTTGGCCT -s simHuman_chr6.simHuman.chr6 490263 25 + 601863 AATCCTTTTGATATGCATTCTCTCA---- -s simRat_chr6.simRat.chr6 521869 29 + 647215 AATCACTTTAATATGTAGCTCCTCAGTCT - -a -s simMouse_chr6.simMouse.chr6 510526 41 + 636262 ATACAGTTGATGGTCCTGCAAGGGGCATGCCTCACTTAGCT -s Anc0.Anc0refChr3 124288 39 + 222631 GTTCTGTTAGTGAAACTGTGAGGGTCATGCTT--GTTGGTT -s Anc1.Anc1refChr6 158344 39 + 197743 GTTCTGTTAGTGAAACTGTGAGGGTCATGCTT--GTTGGTT -s Anc2.Anc2refChr1 37055 39 + 142988 GTTCTGTTAGTGAAACTGTGAGGGTCATGCTT--GTTGGTT -s mr.mrrefChr3 63011 41 + 181027 ATACAGTTGATGGTCCTGCAAGGGGCATGCCTCACTTAGCT -s simCow_chr6.simCow.chr6 494029 39 + 602619 ACTCTCCTAATGAAACTGTGCGGTGGATGCTT--GCTGATT -s simDog_chr6.simDog.chr6 483759 39 + 593897 GTTCTGTTAGTGAAACTGTGAGGGTCATGCTT--GTTGGTT -s simRat_chr6.simRat.chr6 521898 41 + 647215 ATACGGTTGATGGTACTGCAAAGAGCATGTCTTACTAAGCT - -a -s simMouse_chr6.simMouse.chr6 510567 41 + 636262 GGAGGTACTCTGATACACACTTGAAGACCTAAAGTCAAGCA -s Anc0.Anc0refChr3 124327 40 + 222631 GGAGGTACTTGGATACATACTGGAAGAGAT-AAGTCAAGCA -s Anc1.Anc1refChr6 158383 40 + 197743 GGAGGTACTTGGATACATACTGGAAGAGAT-AAGTCAAGCA -s Anc2.Anc2refChr1 37095 40 + 142988 GGAGGTAGTTGGATACATACTGGAAAAGAT-AAGTCAAGCA -s mr.mrrefChr3 63052 41 + 181027 GGAGGTACTCTGATACACACTTGAAGACCTAAAGTCAAGCA -s simCow_chr6.simCow.chr6 494069 40 + 602619 GGAGACATATGGATACATACAGGAAAAGAC-ATGTCAAGCA -s simDog_chr6.simDog.chr6 483799 40 + 593897 GGAGGTAGTTGGGTACATACTGGAAAAGAT-AAGTCAAGAA -s simHuman_chr6.simHuman.chr6 490288 36 + 601863 ----TCACTTGGATACATACCAGAAGAAGT-AAGCCACACA -s simRat_chr6.simRat.chr6 521939 41 + 647215 GGAGGTACTCTGACATGCACTTGAAGACATAAAGTCAAACA - -a -s simMouse_chr6.simMouse.chr6 510608 29 + 636262 TAGAGAGTGAATATCTAGCTGATCCCAAT -s Anc1.Anc1refChr6 158459 29 + 197743 CAGGTAGTGGTGATCAATCTATATTAGGC -s mr.mrrefChr3 63093 29 + 181027 TAGAGAGTGAATATCTAGCTGATCCCAAT -s simHuman_chr6.simHuman.chr6 490448 29 + 601863 CAGGTAGTGGTGATCAATCTATATTAGGC -s simRat_chr6.simRat.chr6 521980 29 + 647215 TAGAGAGTTAAGGTCTGGCTGAACTCAAT - -a -s simMouse_chr6.simMouse.chr6 510637 46 + 636262 AGCTTATCTACCAACACAGTGCAGTATAATACTTGGGTTTCCAGCG -s Anc1.Anc1refChr6 158488 30 + 197743 AGCTTAACTGGCCCTACGGTACA----------------TCCAGTG -s mr.mrrefChr3 63122 46 + 181027 AGCTTATCTACCAACACAGTGCAGTATAATACTTGGGTTTCCAGCG -s simHuman_chr6.simHuman.chr6 490477 30 + 601863 AGCTTAACTGGCCCTACGGTACA----------------TCCAGTG -s simRat_chr6.simRat.chr6 522020 46 + 647215 AGCTTATCTGTCAACACAGTGCTACATAATACTTGGACTTCCAGCA - -a -s simMouse_chr6.simMouse.chr6 510683 220 + 636262 CAAAAGATGCAACTTGCACTTAATCAAAGGCTGTCATGTATACACTGTAGTTTTGAAGTGTGGAACTGTTCTTTGGTGTTGCAAAATGGTGTTTGTCCCCAAAGATGGGCCCATTGTTGCCAATCCATGGTGAGAGCCTCAGTAAGTTGCACGTCTCTTTGCAAGTCTCTATGTATTCGATCACAAGTTCATAAGTATACTCCAATTAGCATTCTACACT -s Anc0.Anc0refChr3 124403 32 + 222631 -------------------------------TGTTATGCATACA-------------------------------------------------------------------------------------------------------------------------------------------------------------TCAATTAAGATCATACACT -s Anc1.Anc1refChr6 158518 44 + 197743 CA-------------------CATCAAAGACTGTTATGCATACA-------------------------------------------------------------------------------------------------------------------------------------------------------------TCAATTAAGATCATACACT -s Anc2.Anc2refChr1 37172 32 + 142988 -------------------------------TGTTATGCATACA-------------------------------------------------------------------------------------------------------------------------------------------------------------TCAATTAAGGTCACGCACT -s mr.mrrefChr3 63168 197 + 181027 CAAAAGATGCAACTTGCACT-AATCAAAGGCTGTCATGTATACACTGT-----TGAAGTGTGGAACTGTTCTTTGGTGTTGCAAAATGGTGTTTGTCCCCAAAGATGGGCCCATTGTTGCCAATCCATGGTGAGAGCCTCAGTAAGTTGCACGTCTCTTTG------------TATTCGATCACAAGTTCA-----ATACTCCAATTAGCATTATACACT -s simCow_chr6.simCow.chr6 494138 19 + 602619 ----------------------------------TATGCATATA-------------------------------------------------------------------------------------------------------------------------------------------------------------TCAATTAAA---------- -s simDog_chr6.simDog.chr6 483877 32 + 593897 -------------------------------TGTTATGCATACA-------------------------------------------------------------------------------------------------------------------------------------------------------------TCAATTAAGGTCACGCACT -s simHuman_chr6.simHuman.chr6 490507 44 + 601863 CA-------------------CATCAAAGACTGCTATACATCCA-------------------------------------------------------------------------------------------------------------------------------------------------------------TCAATTAAGACCATAAACT -s simRat_chr6.simRat.chr6 522067 197 + 647215 CAATAGATGAAACTTGCGCA-GATCAAGAGCTGTCGTGTATACACTGC-----CAGAGTGTGGAACTGTTCTTTGATGTTGTGAAATGGTGTTCATCCCCAAAGATAGGCCCTTTTTTGCCAATCCGTGAAGAGAGTCTCAGTAAGCTGCAAGTGTCTTTG------------TATTCCATCACAAGTTCG-----ATAATCCAATTAGAATTATACACT - -a -s simMouse_chr6.simMouse.chr6 510903 69 + 636262 TCTAGGGATAGATACATATCCAAGCTTCTCCCACTAACAAATGATAATCATTCCAATTAAACCATCTTA -s Anc0.Anc0refChr3 124436 67 + 222631 TCTAGGGAGTGGTAGATA-TCAAGCTCCTTCTGTTAACACCTGATGAACATTCCAAT-AAACCATCATA -s Anc1.Anc1refChr6 158563 67 + 197743 TCTAGGGAGTGGTAGATA-TCAAGCTCCTTCTGTTAACACCTGATGAACATTCCAAT-AAACCATCATA -s Anc2.Anc2refChr1 37205 67 + 142988 CCTAGGGAGTGGTAGATA-TCAGGTTCTTTCTGGTAACACCTGATGAACATTCCCAT-AAACCATCATA -s mr.mrrefChr3 63366 67 + 181027 TCTAGGGATAGATACATA-CCAAGCTTCTTCCATTAACAACTGATAAACATTCCAAT-AAACCATCTTA -s simCow_chr6.simCow.chr6 494157 23 + 602619 --------------------------------------------TAGACATTCTGAT-AA-CAATTATA -s simDog_chr6.simDog.chr6 483910 65 + 593897 CCTAGGGAGTGGTAGATA-TCAGGTTCTTTCTGGTAACACCTGATGAACATTCCCAT-GAACCATCA-- -s simHuman_chr6.simHuman.chr6 490552 67 + 601863 TCTTGGGAGTGGTGGATA-TCAAGCTCCTTCTGTTAATTCCTGATTAACATTCCAAT-AAGTCATCATG -s simRat_chr6.simRat.chr6 522265 67 + 647215 TCCAGGGAAGGATACATA-CCAAGCTTGTTCCATTAAAAACTGATAAACTTTCCAAT-AAACCATCTTA - -a -s simMouse_chr6.simMouse.chr6 510972 6 + 636262 AGGCAG -s Anc0.Anc0refChr3 124513 6 + 222631 AGGCAA -s Anc1.Anc1refChr6 158640 6 + 197743 AGGCAA -s Anc2.Anc2refChr1 37282 6 + 142988 AGGCAA -s mr.mrrefChr3 63433 6 + 181027 AGGCAG -s simCow_chr6.simCow.chr6 494190 6 + 602619 AGGCAA -s simHuman_chr6.simHuman.chr6 490629 6 + 601863 AGGCAA -s simRat_chr6.simRat.chr6 522332 6 + 647215 AGGCAG - -a -s simMouse_chr6.simMouse.chr6 510978 8 + 636262 GCTCAGTA -s Anc0.Anc0refChr3 124523 8 + 222631 GTTGAGTA -s Anc1.Anc1refChr6 158650 8 + 197743 GTTGAGTA -s Anc2.Anc2refChr1 37292 8 + 142988 GTTGAGTA -s mr.mrrefChr3 63443 8 + 181027 GCTCAGTA -s simCow_chr6.simCow.chr6 494200 8 + 602619 GTTGAGTA -s simHuman_chr6.simHuman.chr6 490639 8 + 601863 ATTGACCA -s simRat_chr6.simRat.chr6 522342 8 + 647215 GCTCAGTA - -a -s simMouse_chr6.simMouse.chr6 510986 5 + 636262 CTCTC -s Anc0.Anc0refChr3 124534 5 + 222631 CTGTC -s Anc1.Anc1refChr6 158661 5 + 197743 CTGTC -s Anc2.Anc2refChr1 37303 5 + 142988 ATGTC -s mr.mrrefChr3 63451 5 + 181027 CTCTC -s simCow_chr6.simCow.chr6 494211 5 + 602619 ATGTC -s simHuman_chr6.simHuman.chr6 490650 5 + 601863 CTATC -s simRat_chr6.simRat.chr6 522350 5 + 647215 CTCTC - -a -s simMouse_chr6.simMouse.chr6 510991 48 + 636262 TACATAATTTGTTGTAGGACAGTATAGTAAACACTAAAAAGCTCCCAC -s Anc0.Anc0refChr3 124539 43 + 222631 TAATTCATT----GCAGGACAATTTAGT-AACACTAAAAAGCCCCCAT -s Anc1.Anc1refChr6 158666 44 + 197743 TAATTCATT----GCAGGACAATTTAGTAAACACTAAAAAGCCCCCAT -s Anc2.Anc2refChr1 37308 43 + 142988 TAATTCATT----GCAGGACAATTGAGT-AACACTGAAAAGCCTCTAT -s mr.mrrefChr3 63456 44 + 181027 TACATAATT----GTAGGACAGTATAGTAAACACTAAAAAGCTCCCAC -s simCow_chr6.simCow.chr6 494229 43 + 602619 TAATTCATT----GCAGAACAATTGTGC-AACACTGAAAAGCCTCTGT -s simDog_chr6.simDog.chr6 483975 26 + 593897 GAATTTGCC----GCCAGGCAATTGAGT------------------AT -s simHuman_chr6.simHuman.chr6 490655 44 + 601863 TATTTCATT----GCAGTACAATTTAGTACACACTAAAAAGTACCCAT -s simRat_chr6.simRat.chr6 522355 44 + 647215 TACATGATT----GTAGGACAGCGTAGCAAACTCTAACTAGCCCCCAC - -a -s simMouse_chr6.simMouse.chr6 511039 72 + 636262 AAAGGATGCCAATCCTCTCGTTGGTTGGTCTGGCTAAGAAAGTGTTGAGTGTTGTTCTTGTACCCCATCATA -s Anc0.Anc0refChr3 124583 62 + 222631 AAAAGATCTCAATCCTCTAATTGGTTCATCCGGCCAAGAGAG----------TGTTATTGTACCCCATGGTG -s Anc1.Anc1refChr6 158711 62 + 197743 AAAAGATCTCAATCCTCTAATTGGTTCATCCGGCCAAGAGAG----------TGTTATTGTACCCCATGGTG -s Anc2.Anc2refChr1 37352 62 + 142988 AGAAGATCTAGATCCTCAAATTGGTTCATCCTGCCAAGAGAG----------TGTTATTGTACCCCATGGTG -s mr.mrrefChr3 63500 66 + 181027 AAAGGATGCCAATCCTCTCGTTGGTTGGTCTGGCTAAGAAAGTG------GTTGTTCTTGTACCCCATCATA -s simCow_chr6.simCow.chr6 494273 62 + 602619 AGAATATCTAGACCTCCCAATTGTCCACTCCTGCCAGGCGAG----------GGTTATGGTACCCCGTAGTC -s simDog_chr6.simDog.chr6 484002 62 + 593897 AGAAGATCTAGATCCTCAAATTGGTTCATCCTGCCAAAAGAG----------TGTTATTATACCCCATGGTG -s simHuman_chr6.simHuman.chr6 490700 54 + 601863 GAAAGATCTCAATCCTCTAACTG--------GGCCAAGAGAG----------TGTTATTGTACCCCAAGGTG -s simRat_chr6.simRat.chr6 522399 66 + 647215 AAAGGATGACAATCCTCTGGTTAGTTGGTCTTGATAAGAAAGTA------GGTGTTCTAGTACCCTATCACA - -a -s simMouse_chr6.simMouse.chr6 511111 4 + 636262 TTTT -s Anc0.Anc0refChr3 124645 4 + 222631 TTTT -s Anc1.Anc1refChr6 158773 4 + 197743 TTTT -s Anc2.Anc2refChr1 37414 4 + 142988 TTTT -s mr.mrrefChr3 63566 4 + 181027 TTTT -s simCow_chr6.simCow.chr6 494335 4 + 602619 CTTT -s simDog_chr6.simDog.chr6 484067 4 + 593897 TTTT -s simHuman_chr6.simHuman.chr6 490754 4 + 601863 TTTT -s simRat_chr6.simRat.chr6 522465 4 + 647215 TTTT - -a -s simMouse_chr6.simMouse.chr6 511115 32 + 636262 ATGAGTTTGTTGACCATGACCATACTTAAGAA -s Anc0.Anc0refChr3 124650 32 + 222631 AGGGTTCTATTACTTAGAAATGTACTTAAAAA -s Anc1.Anc1refChr6 158778 32 + 197743 AGGGTTCTATTACTTAGAAATGTACTTAAAAA -s Anc2.Anc2refChr1 37419 32 + 142988 AGGGTTCAATTACTTTGAAATGTACTTAAAAA -s mr.mrrefChr3 63571 32 + 181027 ATGATTTTGTTAACTATGAACATACTTAAGAA -s simCow_chr6.simCow.chr6 494340 32 + 602619 AGGATTCATTTACTTTTAAATGGACTTAAAGC -s simDog_chr6.simDog.chr6 484072 32 + 593897 GGAGTTTAATTACTTTGGAATGTATTTCAGAA -s simHuman_chr6.simHuman.chr6 490759 32 + 601863 AGGTTTCTATCACGTAGACATGTACCTACAAA -s simRat_chr6.simRat.chr6 522470 32 + 647215 ACAATTTTGTTAACTATGAACATACTTAAGAA - -a -s simMouse_chr6.simMouse.chr6 511147 16 + 636262 GCAAGGATGTGCATAA -s Anc0.Anc0refChr3 124685 16 + 222631 GCTATGATGTGCAGGA -s Anc1.Anc1refChr6 158813 16 + 197743 GCTATGATGTGCAGGA -s Anc2.Anc2refChr1 37454 16 + 142988 GCTATGATGTGCAGGA -s mr.mrrefChr3 63606 16 + 181027 GCAAGGATGTGCAGAA -s simCow_chr6.simCow.chr6 494375 16 + 602619 GCTATGATGTACAGCA -s simDog_chr6.simDog.chr6 484107 16 + 593897 ACTATGATGTGCAGGA -s simHuman_chr6.simHuman.chr6 490794 16 + 601863 GCCATGATCTGCAGGA -s simRat_chr6.simRat.chr6 522512 16 + 647215 GTAAGGATGTGCAGAA - -a -s simMouse_chr6.simMouse.chr6 511163 23 + 636262 AAAATACCTATTCGTTGGCGAAT -s Anc0.Anc0refChr3 124702 23 + 222631 AAAGTACCTAGTAATTGACTAAT -s Anc1.Anc1refChr6 158830 23 + 197743 AAAGTACCTAGTAATTGACTAAT -s Anc2.Anc2refChr1 37471 23 + 142988 TAAGTACCTAGTAATTGACTAAT -s mr.mrrefChr3 63622 23 + 181027 AAAATACCTAGTAATTGGCGAAT -s simCow_chr6.simCow.chr6 494392 23 + 602619 TAAGTCCCTAGTAATTGACTAAT -s simDog_chr6.simDog.chr6 484124 23 + 593897 TAAGTACCTAGTAGTTGTCTAAC -s simHuman_chr6.simHuman.chr6 490811 23 + 601863 ATAGTACCTAGCAATTGACAAAT -s simRat_chr6.simRat.chr6 522528 23 + 647215 AAAATATCTAGTAATTGGCCAAT - -a -s simMouse_chr6.simMouse.chr6 511186 7 + 636262 TCTGTTT -s Anc0.Anc0refChr3 124754 7 + 222631 ATGGTTC -s Anc1.Anc1refChr6 158882 7 + 197743 ATGGTTC -s Anc2.Anc2refChr1 37523 7 + 142988 ATGGTTC -s mr.mrrefChr3 63645 7 + 181027 TTTGTTC -s simCow_chr6.simCow.chr6 494444 7 + 602619 ATAGTCC -s simDog_chr6.simDog.chr6 484176 6 + 593897 ATG-CTC -s simHuman_chr6.simHuman.chr6 490863 7 + 601863 GTGATTC -s simRat_chr6.simRat.chr6 522551 7 + 647215 TTTGTTC - -a -s simMouse_chr6.simMouse.chr6 511193 8 + 636262 AAAATCCA -s Anc0.Anc0refChr3 124761 8 + 222631 ATATCCTA -s Anc1.Anc1refChr6 158889 8 + 197743 ATATCCTA -s Anc2.Anc2refChr1 37530 8 + 142988 ATATCCTA -s mr.mrrefChr3 63652 8 + 181027 ACAATCTA -s simCow_chr6.simCow.chr6 494454 8 + 602619 ATACCCTG -s simDog_chr6.simDog.chr6 484182 8 + 593897 AAATTCCA -s simHuman_chr6.simHuman.chr6 490870 8 + 601863 ATGTCCTC -s simRat_chr6.simRat.chr6 522558 8 + 647215 CCAAACTA - -a -s simMouse_chr6.simMouse.chr6 511201 16 + 636262 TTTACAAGCCATTAAT -s Anc0.Anc0refChr3 124818 15 + 222631 TTTAC-AGGTGTTTAT -s Anc1.Anc1refChr6 158946 15 + 197743 TTTAC-AGGTGTTTAT -s Anc2.Anc2refChr1 37589 15 + 142988 TTAAC-AGGTGTTTAT -s mr.mrrefChr3 63660 16 + 181027 TTTACAAGTCATTAAT -s simCow_chr6.simCow.chr6 494513 15 + 602619 TTAAC-AGGTGTTTTT -s simDog_chr6.simDog.chr6 484241 15 + 593897 TTAAC-AGATGTTTAC -s simHuman_chr6.simHuman.chr6 490927 15 + 601863 TTTAC-AGGTGTTTAT -s simRat_chr6.simRat.chr6 522566 15 + 647215 TTT-CAAGTCATTAAT - -a -s simMouse_chr6.simMouse.chr6 511217 6 + 636262 TGGATG -s Anc0.Anc0refChr3 124843 6 + 222631 TGTATA -s Anc1.Anc1refChr6 158971 6 + 197743 TGTATA -s Anc2.Anc2refChr1 37614 6 + 142988 CTTATA -s mr.mrrefChr3 63676 6 + 181027 TGGATG -s simCow_chr6.simCow.chr6 494538 6 + 602619 CTTACA -s simDog_chr6.simDog.chr6 484266 6 + 593897 CTTATA -s simHuman_chr6.simHuman.chr6 490952 6 + 601863 TGTATA -s simRat_chr6.simRat.chr6 522581 6 + 647215 TGGATG - -a -s simMouse_chr6.simMouse.chr6 511223 6 + 636262 TTTTGT -s Anc0.Anc0refChr3 124855 4 + 222631 TT--TT -s Anc1.Anc1refChr6 158983 6 + 197743 TTTATT -s Anc2.Anc2refChr1 37626 4 + 142988 TC--TT -s mr.mrrefChr3 63682 6 + 181027 TTTTAT -s simCow_chr6.simCow.chr6 494550 4 + 602619 TC--GT -s simDog_chr6.simDog.chr6 484278 4 + 593897 TC--TT -s simHuman_chr6.simHuman.chr6 490964 6 + 601863 TTTATT -s simRat_chr6.simRat.chr6 522587 6 + 647215 TTTTAT - -a -s simMouse_chr6.simMouse.chr6 511229 10 + 636262 ACTCTATTAA -s Anc0.Anc0refChr3 124860 10 + 222631 ATACTATCAA -s Anc1.Anc1refChr6 158990 10 + 197743 ATACTATCAA -s Anc2.Anc2refChr1 37631 10 + 142988 ATACTATCAA -s mr.mrrefChr3 63689 10 + 181027 ATTCTATTAA -s simCow_chr6.simCow.chr6 494555 10 + 602619 ATACTTTTAA -s simDog_chr6.simDog.chr6 484283 10 + 593897 ATACCACCAA -s simHuman_chr6.simHuman.chr6 490971 10 + 601863 ATACTATATA -s simRat_chr6.simRat.chr6 522594 10 + 647215 ATTCTACTAA - -a -s simMouse_chr6.simMouse.chr6 511239 12 + 636262 CCTGTTATCTTG -s Anc0.Anc0refChr3 124882 12 + 222631 CTTGCTATCTTG -s Anc1.Anc1refChr6 159012 12 + 197743 CTTGCTATCTTG -s Anc2.Anc2refChr1 37655 12 + 142988 CTTGCTATCTTG -s mr.mrrefChr3 63699 12 + 181027 CCTGTTATCTTG -s simCow_chr6.simCow.chr6 494579 12 + 602619 CCTGCAACCTTG -s simDog_chr6.simDog.chr6 484307 12 + 593897 CTTGCTATCTTA -s simHuman_chr6.simHuman.chr6 490993 12 + 601863 CTTACTATCTTG -s simRat_chr6.simRat.chr6 522604 12 + 647215 CCTGTTATCTCA - -a -s simMouse_chr6.simMouse.chr6 511251 18 + 636262 CCTCTGTTGGAAGGATAC -s Anc0.Anc0refChr3 124894 18 + 222631 CCCCAGTTTTAAAGAAAT -s Anc1.Anc1refChr6 159024 18 + 197743 CCCCAGTTTTAAAGAAAT -s Anc2.Anc2refChr1 37667 18 + 142988 TCCCAGTTTCAAAAAAAT -s mr.mrrefChr3 63711 18 + 181027 CCTCTGTTGTAAGGATAC -s simCow_chr6.simCow.chr6 494591 18 + 602619 GCCCAGTTTCAAGCAAAT -s simDog_chr6.simDog.chr6 484319 18 + 593897 TCCAAATTTCATAAAAAT -s simHuman_chr6.simHuman.chr6 491006 18 + 601863 CCCCAGTTCTAAAGCAAT -s simRat_chr6.simRat.chr6 522616 17 + 647215 TCTCT-TTGTGAGGATAC - -a -s simMouse_chr6.simMouse.chr6 511269 12 + 636262 ATAGGAACCCTC -s Anc0.Anc0refChr3 124914 12 + 222631 ATAGGAACTCTC -s Anc1.Anc1refChr6 159044 12 + 197743 ATAGGAACTCTC -s Anc2.Anc2refChr1 37687 12 + 142988 ATAGGAACTCCC -s mr.mrrefChr3 63731 12 + 181027 ATAGGAACCCTC -s simCow_chr6.simCow.chr6 494611 12 + 602619 ATAGGAATTCCC -s simDog_chr6.simDog.chr6 484339 12 + 593897 ATAGGAACTCCC -s simHuman_chr6.simHuman.chr6 491026 12 + 601863 ATAGGAGCTCTA -s simRat_chr6.simRat.chr6 522635 12 + 647215 CTAGGACCCCCC - -a -s simMouse_chr6.simMouse.chr6 511281 7 + 636262 CAGACTA -s Anc0.Anc0refChr3 124926 7 + 222631 CAGATTA -s Anc1.Anc1refChr6 159056 7 + 197743 CAGATTA -s Anc2.Anc2refChr1 37699 7 + 142988 CAGATTA -s mr.mrrefChr3 63743 7 + 181027 CAGACTA -s simCow_chr6.simCow.chr6 494623 7 + 602619 CAACTAA -s simDog_chr6.simDog.chr6 484351 7 + 593897 CAGATTA -s simHuman_chr6.simHuman.chr6 491038 7 + 601863 CAGATGA -s simRat_chr6.simRat.chr6 522649 7 + 647215 CAGACTA - -a -s simMouse_chr6.simMouse.chr6 511288 26 + 636262 GGAGCTATAAAATTCGAAATAAGCTG -s Anc0.Anc0refChr3 124933 26 + 222631 TATGCTATACAATCTAAAATAAGTTG -s Anc1.Anc1refChr6 159063 26 + 197743 TATGCTATACAATCTAAAATAAGTTG -s Anc2.Anc2refChr1 37706 26 + 142988 TATGCTGTACAATCTAAAATAAGTTG -s mr.mrrefChr3 63750 26 + 181027 GGAGCTATAAAATTTGAAATAAGCTG -s simCow_chr6.simCow.chr6 494630 25 + 602619 CA-GCTGAACAATCTATAATAAGTCA -s simDog_chr6.simDog.chr6 484359 23 + 593897 TATG---TACAATCTAAATTAAGTTG -s simHuman_chr6.simHuman.chr6 491045 26 + 601863 TATGCTATACAATCTAAAATTAGTTG -s simRat_chr6.simRat.chr6 522656 26 + 647215 GGAGCCTTAAAATTTGAAATAAGCTG - -a -s simMouse_chr6.simMouse.chr6 511314 5 + 636262 GCAAA -s Anc0.Anc0refChr3 124971 5 + 222631 GCAAC -s Anc1.Anc1refChr6 159101 5 + 197743 GCAAC -s Anc2.Anc2refChr1 37744 5 + 142988 GTAAC -s mr.mrrefChr3 63776 5 + 181027 GCAAA -s simCow_chr6.simCow.chr6 494667 5 + 602619 ATAAT -s simDog_chr6.simDog.chr6 484394 5 + 593897 GTAAC -s simHuman_chr6.simHuman.chr6 491083 5 + 601863 GCAAC -s simRat_chr6.simRat.chr6 522682 5 + 647215 TCAAA - -a -s simMouse_chr6.simMouse.chr6 511319 17 + 636262 AAGATACACCTCATGCT -s Anc0.Anc0refChr3 124976 17 + 222631 AGGATACCCCTAATACT -s Anc1.Anc1refChr6 159106 17 + 197743 AGGATACCCCTAATACT -s Anc2.Anc2refChr1 37749 17 + 142988 AGGATACCCCTAATACT -s mr.mrrefChr3 63781 17 + 181027 AAGATACACCTCATGCT -s simCow_chr6.simCow.chr6 494672 17 + 602619 AGGATACCCCTAATATT -s simDog_chr6.simDog.chr6 484400 17 + 593897 AGGATACCCTTAATACT -s simHuman_chr6.simHuman.chr6 491088 17 + 601863 AGAATACTCCTAAGCCT -s simRat_chr6.simRat.chr6 522687 17 + 647215 AAGATACACCTCATGCT - -a -s simMouse_chr6.simMouse.chr6 511336 50 + 636262 GTTCATAGAGAAGAATAACAATGAAGAACATGAAGTCTTCCTAACATAGA -s Anc0.Anc0refChr3 124993 50 + 222631 GTTTACTGAGAAGAATTACAATGAATAATATGGAGTCTTTCATATATAGA -s Anc1.Anc1refChr6 159123 50 + 197743 GTTTACTGAGAAGAATTACAATGAATAATATGGAGTCTTTCATATATAGA -s Anc2.Anc2refChr1 37766 50 + 142988 GTTTACTGAGAAGAATTACAATCAATAATATGGAGTCTTTCATATATTGA -s mr.mrrefChr3 63798 50 + 181027 GTTTATAGAGAAGAATAACAATGAATAACATGAAGTCTTTCTAACATAGA -s simCow_chr6.simCow.chr6 147220 50 - 602619 GTATACTGAGAAGAACTACAATCAATAAAAAAGAGTCTTTCATATATTAA -s simCow_chr6.simCow.chr6 494689 49 + 602619 ATATAC-GAGAAGATATGTAATCAATAATACAGAGTCCTTCATGTATCGA -s simDog_chr6.simDog.chr6 484417 50 + 593897 GTTTACTGAGAAGAATTACAATCAATAATATGGAGTCTTTCATATATTGA -s simHuman_chr6.simHuman.chr6 491105 50 + 601863 GTTTACTGATAAGAATTACAGTGAATAATATGGAGTCTTTAATATATAGG -s simRat_chr6.simRat.chr6 522704 45 + 647215 GTTT-----GAAGAATAACAATGAGTAACATGAAATCTCTCTAACATAGA - -a -s simMouse_chr6.simMouse.chr6 511386 39 + 636262 CTTGTAAGTTTATTGTATTGGAAAACATGTTTTTTCTTT -s Anc0.Anc0refChr3 125241 39 + 222631 CTTCTAAGTATATTGTATCAGATAATGTACCTTTTCTAC -s Anc1.Anc1refChr6 159371 39 + 197743 CTTCTAAGTATATTGTATCAGATAATGTACCTTTTCTAC -s Anc2.Anc2refChr1 38022 39 + 142988 CTTCTAAGCATATTGTATCAGACAATGTACCTTGTCTAC -s mr.mrrefChr3 63848 39 + 181027 CTTGTAAGTTTATTGTATCGGATAACATGTTTTTTCTTC -s simCow_chr6.simCow.chr6 147468 39 - 602619 CTTCTAAGAAAATTGAATCTGACAAAATACTCTGTCTCC -s simCow_chr6.simCow.chr6 495013 39 + 602619 CATCTAAGCGGATTGTATCAGACAACATACTTTGTCTCC -s simDog_chr6.simDog.chr6 484648 25 + 593897 ------AGCATATTGTTT-------TGTTTCTTCTATA- -s simHuman_chr6.simHuman.chr6 491409 39 + 601863 CTTCTAAGTATATTGTATCAGATAATGTACCTTTTCTAC -s simRat_chr6.simRat.chr6 522749 39 + 647215 CTTGTAAGTGTATTGTATCGGATAACATGTTTTTTCTTC - -a -s simMouse_chr6.simMouse.chr6 511425 12 + 636262 ATTCCTTTGATC -s Anc0.Anc0refChr3 125280 12 + 222631 ATTTCCTTGCTC -s Anc1.Anc1refChr6 159410 12 + 197743 ATTTCCTTGCTC -s Anc2.Anc2refChr1 38062 12 + 142988 ATTTCTTTGCTC -s mr.mrrefChr3 63887 12 + 181027 ATTCCCTTGATC -s simCow_chr6.simCow.chr6 147508 12 - 602619 ATTCCTTAATTC -s simCow_chr6.simCow.chr6 495053 12 + 602619 ATTTCTTTGTCC -s simDog_chr6.simDog.chr6 484673 9 + 593897 ---TCTTTGCTC -s simHuman_chr6.simHuman.chr6 491448 12 + 601863 AATTCCTCACTA -s simRat_chr6.simRat.chr6 522788 12 + 647215 ATTCCCTTGATC - -a -s simMouse_chr6.simMouse.chr6 511437 125 + 636262 ACGGATCCCTTCCTTCCTTTTTTGTATCCGACCAAAAGGACATACCACACCTCCCGACACCTTCAGGTAGTTCTTCTACTATGGGCATATATCTATCATTGGGACAACATCTGAGAATTTTGGTA -s Anc0.Anc0refChr3 125292 114 + 222631 ACCAGCCCTTCCCTTTCTTTCTTCTGCCACACCAAAAGGAAGTAC----------CACACCCTTAGGTTGTTTTTCCATTATTGTCATGTATCATTT-CCGGGACAACAACTGAGGAGCCTCAGA -s Anc1.Anc1refChr6 159422 114 + 197743 ACCAGCCCTTCCCTTTCTTTCTTCTGCCACACCAAAAGGAAGTAC----------CACACCCTTAGGTTGTTTTTCCATTATTGTCATGTATCATTT-CCGGGACAACAACTGAGGAGCCTCAGA -s Anc2.Anc2refChr1 38074 114 + 142988 ACCAGCCCTTCCCTTTCTTTCTCCTGCCACACCAGAAGGAAGCAC----------CACACCCTTAGGTTGTTTTTCCATTATTTTCATGTATCATTT-CCCTGACAACAACTGGGGAACCTCGGA -s mr.mrrefChr3 63899 125 + 181027 ACCAACCCCTTCCTTCCTTTTTTGTATCAGACCAAAAGGACATACCACACCTCCCCACACCTTCAGGTTGTTTTTCTATTATGGTCATGTATCAATCATTGGGACAACATCTGAGAAGTTTCATA -s simCow_chr6.simCow.chr6 495065 106 + 602619 ACTAGACCTTCCCTTTCTTTA------CACACCAGA-GGAGGCAC----------CACACACATAAGTTGTTTTTACAATATTATCGTGTATCATTT-CC-AAACAACAACTGGGGAACCTCGGA -s simDog_chr6.simDog.chr6 484682 107 + 593897 GCCAGCCCT-CCCTATCTTTCTCCTGCCACACCAGAAGGTAGCAC----------TGCACCCTTAGGTTGTTTTTCCATTGTTTTCATAT------T-CCCTGACAACAACTGGGGAACCCTGGA -s simHuman_chr6.simHuman.chr6 491460 113 + 601863 ACCAGCCCTTCCCTTTCTTTCTTCAGCCACACTAAAATGAAGTAC----------CACAGCCTTAGGTTT-TTTTTCATTATTGTCATGTATCATTT-CCGGGACAACACCTTAGGAGCCTCAGG -s simRat_chr6.simRat.chr6 522800 114 + 647215 ACCAACCCCTTCCTTCCTTTTTTGTATCAGAG----------TACCACACCTCCCCACACCTTCAGGTTGTTTTTCTATTACGGTCATGTATCAATCATTGGGACAACATCTGAG-AGTTTCATA - -a -s simMouse_chr6.simMouse.chr6 511562 10 + 636262 AGCTAACCCC -s Anc0.Anc0refChr3 125407 10 + 222631 AGCTGACCCC -s Anc1.Anc1refChr6 159537 10 + 197743 AGCTGACCCC -s Anc2.Anc2refChr1 38189 10 + 142988 AGCTGACCAT -s mr.mrrefChr3 64024 10 + 181027 AGCTAACCCC -s simCow_chr6.simCow.chr6 495172 10 + 602619 CGATGACCAT -s simDog_chr6.simDog.chr6 484790 10 + 593897 AGCTAACCAT -s simHuman_chr6.simHuman.chr6 491574 10 + 601863 AGCTGACCCC -s simRat_chr6.simRat.chr6 522914 10 + 647215 AGCTAACTCG - -a -s simMouse_chr6.simMouse.chr6 511572 5 + 636262 TTGGA -s Anc0.Anc0refChr3 125417 5 + 222631 TCAAA -s Anc1.Anc1refChr6 159547 5 + 197743 TCAAA -s Anc2.Anc2refChr1 38202 5 + 142988 ACAAA -s mr.mrrefChr3 64034 5 + 181027 TTGGA -s simCow_chr6.simCow.chr6 495185 5 + 602619 GCAAA -s simDog_chr6.simDog.chr6 484803 5 + 593897 ACATA -s simHuman_chr6.simHuman.chr6 491584 5 + 601863 TCAAA -s simRat_chr6.simRat.chr6 522924 5 + 647215 TAGGA - -a -s simMouse_chr6.simMouse.chr6 511577 64 + 636262 CATGGATGTTCCAGCAGGAATTCATGGACCCAATTTGCCGGAGCCACCATGGTTGCTAACTTTT -s Anc0.Anc0refChr3 125423 57 + 222631 CAGGGATGTCCCAGCATGAGCTTGTTGACCCAATTCACCAGAGCCAACACAGCTG-------GC -s Anc1.Anc1refChr6 159553 57 + 197743 CAGGGATGTCCCAGCATGAGCTTGTTGACCCAATTCACCAGAGCCAACACAGCTG-------GC -s Anc2.Anc2refChr1 38208 57 + 142988 CAGGGATGTCCCAGCATGAGCTTGTTGACCCAATTAGCCAGGGTCAACACAGCTG-------GC -s mr.mrrefChr3 64039 64 + 181027 CATGGATGTTCCAGCTGGAATCCATGAACCTAATTCACCAGAGCCAACATGGTTGCTAACTTGC -s simCow_chr6.simCow.chr6 495191 57 + 602619 CTGGGAGGAACCTGCATGAGTTTGTTGACCAAATTAGCCAGGGGCAACACATCTG-------GG -s simDog_chr6.simDog.chr6 484809 57 + 593897 CAGAAATGTCCCAGCCTAAGCTTGTTGACGCAATCAGCCAGGGTCAACATAGCTG-------GC -s simHuman_chr6.simHuman.chr6 491590 57 + 601863 CAGGGATATCCTAGCATGAGGTTGTTGACCCAATTCACCAGAACCAACACAGCTG-------GA -s simRat_chr6.simRat.chr6 522929 64 + 647215 CAAGGATGTTCCAGCTGGAATCCATGAACCTGATTCACCAGAGCCAACATGGTTGCTAACTTGC - -a -s simMouse_chr6.simMouse.chr6 511641 13 + 636262 TTGCTTGGAATGC -s Anc0.Anc0refChr3 125480 11 + 222631 CAGCCTAGA--GC -s Anc1.Anc1refChr6 159610 11 + 197743 CAGCCTAGA--GC -s Anc2.Anc2refChr1 38265 11 + 142988 CAGCCTAGA--GC -s mr.mrrefChr3 64103 13 + 181027 TTGCTTGGAATGC -s simCow_chr6.simCow.chr6 495248 10 + 602619 CAAC-TAGA--GC -s simDog_chr6.simDog.chr6 484867 5 + 593897 CTGCC-------- -s simHuman_chr6.simHuman.chr6 491647 11 + 601863 CAGCCTTGA--GC -s simRat_chr6.simRat.chr6 522993 11 + 647215 --ACTTGGAATGC - -a -s simMouse_chr6.simMouse.chr6 511654 2 + 636262 TT -s Anc0.Anc0refChr3 125491 2 + 222631 TT -s Anc1.Anc1refChr6 159621 2 + 197743 TT -s Anc2.Anc2refChr1 38287 2 + 142988 TT -s mr.mrrefChr3 64116 2 + 181027 TT -s simCow_chr6.simCow.chr6 495269 2 + 602619 TT -s simHuman_chr6.simHuman.chr6 491658 2 + 601863 TT -s simRat_chr6.simRat.chr6 523004 2 + 647215 TT - -a -s simMouse_chr6.simMouse.chr6 511656 14 + 636262 GCTCAAATTTACAG -s Anc0.Anc0refChr3 125493 14 + 222631 GCCCAAACTTACAG -s Anc1.Anc1refChr6 159623 14 + 197743 GCCCAAACTTACAG -s Anc2.Anc2refChr1 38289 14 + 142988 GCCCAAACTTACAG -s mr.mrrefChr3 64118 14 + 181027 GCTCAAATTTACAG -s simCow_chr6.simCow.chr6 495271 14 + 602619 GCCCAAACTTACAG -s simDog_chr6.simDog.chr6 484872 3 + 593897 -----------CAA -s simHuman_chr6.simHuman.chr6 491760 14 + 601863 ACCCAACCTTACAG -s simRat_chr6.simRat.chr6 523006 14 + 647215 GATCAAATTTACAG - -a -s simMouse_chr6.simMouse.chr6 511670 18 + 636262 CTATATGATAGTGGGATA -s Anc0.Anc0refChr3 125507 18 + 222631 CCATCTCATAGGGGGATA -s Anc1.Anc1refChr6 159637 18 + 197743 CCATCTCATAGGGGGATA -s Anc2.Anc2refChr1 38303 18 + 142988 CCATCTCAGAGGGGGACA -s mr.mrrefChr3 64132 18 + 181027 CCATATGATAGTGGGATA -s simCow_chr6.simCow.chr6 495286 18 + 602619 CCATCACAAAGTTGGACA -s simDog_chr6.simDog.chr6 484875 18 + 593897 ACGTCTCAGAGGGGAACA -s simHuman_chr6.simHuman.chr6 491774 18 + 601863 CCATCTCATAGAGTGATA -s simRat_chr6.simRat.chr6 523020 18 + 647215 CCTTATGATAGTGGGATA - -a -s simMouse_chr6.simMouse.chr6 511688 34 + 636262 TATTATAGCTGCCAGATAGGTGGAACTTAATACC -s Anc0.Anc0refChr3 125538 19 + 222631 ---------------AAAAATGGAACTCATTCTC -s Anc1.Anc1refChr6 159673 34 + 197743 TATTACTGTTGCAAGAAAAATGGAACTCATTCTC -s Anc2.Anc2refChr1 38334 19 + 142988 ---------------AAAAATGGAACTCATTCTC -s mr.mrrefChr3 64168 34 + 181027 TATTATGGCTGCAAGATAAGTGGAACTTAATCTC -s simCow_chr6.simCow.chr6 495317 19 + 602619 ---------------AAAAATAGGACTGATTCTC -s simDog_chr6.simDog.chr6 484907 19 + 593897 ---------------AAAAATGGAACTCTTTTTT -s simHuman_chr6.simHuman.chr6 491810 34 + 601863 TATTACTGTTGCAAGAAAAATGGAACTCATTCTC -s simRat_chr6.simRat.chr6 523056 34 + 647215 TACTATGGCTGCAAGATAAGTGGAACTAAATCTC - -a -s simMouse_chr6.simMouse.chr6 511722 15 + 636262 CGGTAACTCTGGCAT -s Anc0.Anc0refChr3 125557 12 + 222631 C---AACTATGGTAG -s Anc1.Anc1refChr6 159707 12 + 197743 C---AACTATGGTAG -s Anc2.Anc2refChr1 38353 12 + 142988 C---AACAATGGTAG -s mr.mrrefChr3 64202 15 + 181027 CAGTAACTCTGGCAG -s simCow_chr6.simCow.chr6 495336 12 + 602619 C---AATAACTGTAG -s simDog_chr6.simDog.chr6 484928 12 + 593897 T---AACAATGGTAG -s simHuman_chr6.simHuman.chr6 491844 12 + 601863 C---AACTATGGTGG -s simRat_chr6.simRat.chr6 523090 15 + 647215 CAGTAACTCTGGCAG - -a -s simMouse_chr6.simMouse.chr6 511737 6 + 636262 AAATAA -s Anc0.Anc0refChr3 125575 6 + 222631 AAGTAA -s Anc1.Anc1refChr6 159725 6 + 197743 AAGTAA -s Anc2.Anc2refChr1 38371 6 + 142988 GAGTAA -s mr.mrrefChr3 64223 6 + 181027 AAATAA -s simCow_chr6.simCow.chr6 495354 6 + 602619 GAATAA -s simDog_chr6.simDog.chr6 484946 6 + 593897 GAGTAA -s simHuman_chr6.simHuman.chr6 491862 6 + 601863 AAGTAA -s simRat_chr6.simRat.chr6 523111 6 + 647215 AAATAA - -a -s simMouse_chr6.simMouse.chr6 511743 6 + 636262 TTGTGA -s Anc0.Anc0refChr3 125581 6 + 222631 GTGTGC -s Anc1.Anc1refChr6 159731 6 + 197743 GTGTGC -s Anc2.Anc2refChr1 38377 6 + 142988 GTGTGC -s mr.mrrefChr3 64229 6 + 181027 TTGTGA -s simCow_chr6.simCow.chr6 495361 6 + 602619 GTGTAC -s simDog_chr6.simDog.chr6 484952 6 + 593897 GTGTGC -s simHuman_chr6.simHuman.chr6 491868 6 + 601863 ATGTGC -s simRat_chr6.simRat.chr6 523117 6 + 647215 TTGTGA - -a -s simMouse_chr6.simMouse.chr6 511749 30 + 636262 TGAAAAAGTGCAACCCACATTGTGTCTGGT -s Anc0.Anc0refChr3 125587 26 + 222631 TGGAAAAGTGTAACCCACA--GTGTC--GT -s Anc1.Anc1refChr6 159737 26 + 197743 TGGAAAAGTGTAACCCACA--GTGTC--GT -s Anc2.Anc2refChr1 38383 26 + 142988 TCGAAAAGTGTAACCCACA--GTGTC--GT -s mr.mrrefChr3 64235 30 + 181027 TGGAAAAGTGCAACCCACATTGTGTCTGGT -s simCow_chr6.simCow.chr6 495367 25 + 602619 CAGAAAAGTGCAACTCACA--GTGTT--G- -s simDog_chr6.simDog.chr6 485011 25 + 593897 TCGAAGAGTGTAACCCACA--ATA-C--GT -s simHuman_chr6.simHuman.chr6 491874 26 + 601863 TGGAAAAGTGTAACCCACA--GTGTC--GT -s simRat_chr6.simRat.chr6 523123 30 + 647215 TGGTAAAGTGCAAGCTACATTGTGTCTGGT - -a -s simMouse_chr6.simMouse.chr6 511779 15 + 636262 GACATAAAATGTGAC -s Anc0.Anc0refChr3 125613 15 + 222631 GGCCTAAGATCTAAC -s Anc1.Anc1refChr6 159763 15 + 197743 GGCCTAAGATCTAAC -s Anc2.Anc2refChr1 38414 15 + 142988 GGACTCAGATCTAAC -s mr.mrrefChr3 64265 15 + 181027 GGCATAAAATGTGAC -s simCow_chr6.simCow.chr6 495397 15 + 602619 GGTCTCAGATGTAAC -s simDog_chr6.simDog.chr6 485041 15 + 593897 GGACTCAGATCTGAC -s simHuman_chr6.simHuman.chr6 491900 15 + 601863 AGCTTACGATATAAC -s simRat_chr6.simRat.chr6 523153 15 + 647215 GGCATAGAATGTGAC - -a -s simMouse_chr6.simMouse.chr6 511794 9 + 636262 TAAACACCA -s Anc0.Anc0refChr3 125629 9 + 222631 AACACACCA -s Anc1.Anc1refChr6 159779 9 + 197743 AACACACCA -s Anc2.Anc2refChr1 38430 9 + 142988 AACACACCA -s mr.mrrefChr3 64281 9 + 181027 AACACACCA -s simCow_chr6.simCow.chr6 495413 9 + 602619 AAGACACCA -s simDog_chr6.simDog.chr6 485057 9 + 593897 GACACACCA -s simHuman_chr6.simHuman.chr6 491915 9 + 601863 AACACACCA -s simRat_chr6.simRat.chr6 523169 9 + 647215 AACACTCCA - -a -s simMouse_chr6.simMouse.chr6 511803 93 + 636262 GAGAATGGGCCTTTAGCAATAAAAAGCATTTTGACAAATAAATTACACACAATTCCTATTGTACAGCTGGACTATGTACAATATTTTTGGATT -s Anc0.Anc0refChr3 125648 86 + 222631 GAAATGTGGTTTTTAGCAAAAAAGAGAATTTGGACAGATACATTCCACACCA-TCCTATTGTACT----GACCATGAACAATCTTCTAGG--T -s Anc1.Anc1refChr6 159798 91 + 197743 GAAATGTGGTTTTTAGCAAAAAAGAGAATTTGGACAGATACATTCCACACCA-TCCTATTGTACTGAC-GACCATGAACAATCTTCTAGGGCT -s Anc2.Anc2refChr1 38449 86 + 142988 GAAATGTGGTTTTCAATAGAAAAGAGAATTTGGACAGATACATTCCACACCA-TCCTATTGTGCT----GACCATGAACAATCTCCTAGG--T -s mr.mrrefChr3 64290 93 + 181027 GAGAATGGGCCTTTAGCAAGAAAAAGCATTTTGACAAATAAATTACACACAATTCCTATTGTACAGACGGACCATGTACAATATTCTAGGATT -s simCow_chr6.simCow.chr6 495432 86 + 602619 GAAATCTGATACTCAATACAAAAGAGAATTTGGACAGATACCTTCCACACTG-GCCTACTGTGCT----GACCATGAACAATCTTAAGGG--T -s simDog_chr6.simDog.chr6 485076 82 + 593897 GAAGTGTGGTTTTCAATTGGAAAGAGAATTTGGACAGATACATTCC----CA-TCCTATTGTGCA----GACCATGAACAATCTCCTAGG--T -s simHuman_chr6.simHuman.chr6 491934 80 + 601863 AAAATATGGTTTTTAGCAAAAAAGAGAGTTTCGACAGAGACACTCCACACCA-TCCTTTTGTACTGAC--------CACAGGTTTC----GCT -s simRat_chr6.simRat.chr6 523178 93 + 647215 GAGAATGGGCCTTTAGCAAGAATAAGCATTTTAACAAATAAATTACACACAATTCCCATTGTACAGACGGACCATGTACAATATTCTAGGATT - -a -s simMouse_chr6.simMouse.chr6 511896 28 + 636262 CATTTTGTTCCCTCACAGTTCTCCATGA -s Anc0.Anc0refChr3 125734 28 + 222631 TCTTTTGTCCCTTAATGTCTCTCTACTT -s Anc1.Anc1refChr6 159889 28 + 197743 TCTTTTGTCCCTTAATGTCTCTCTACTT -s Anc2.Anc2refChr1 38535 28 + 142988 TGTTTTGTCCCTTCATGTCTCTCTACTT -s mr.mrrefChr3 64383 28 + 181027 TCTTTTGTCCCTTAATGTCTCTCCACGT -s simCow_chr6.simCow.chr6 495520 28 + 602619 TATCCTGTCGGTTTATGTGTCTCTACTT -s simDog_chr6.simDog.chr6 485158 28 + 593897 TGTTTTGTCCCTTCATGTCTCTCTACTT -s simHuman_chr6.simHuman.chr6 492014 15 + 601863 GCTTTGGCACTTGAA------------- -s simRat_chr6.simRat.chr6 523271 28 + 647215 TCTTTTGTCCCTTAATGTCTCTCCACCT - -a -s simMouse_chr6.simMouse.chr6 511924 70 + 636262 CTTGCCCCAGCGATCTCTACTGCTGGCAGATCACCATCTGGGGGGTGACATACATAAAGGATCTGCTAGT -s Anc0.Anc0refChr3 125762 30 + 222631 CTT----------------------------------------GATAACAAACCTGGAGGATCTGCTGTT -s Anc1.Anc1refChr6 159917 30 + 197743 CTT----------------------------------------GATAACAAACCTGGAGGATCTGCTGTT -s Anc2.Anc2refChr1 38568 30 + 142988 CTT----------------------------------------GATATCAAACCTGGAGATTCTACTGTT -s mr.mrrefChr3 64411 68 + 181027 CTTGCCCTAGCGATCC--ACTGCTGGCAGATCACCATCTGGGGGGTAACAAACATAAAGGATCTGCTGGT -s simCow_chr6.simCow.chr6 495553 30 + 602619 CCA----------------------------------------ATTATCAAACTTGAAGGATCTACTGTT -s simDog_chr6.simDog.chr6 485191 30 + 593897 CTT----------------------------------------GATATCAAACCTGGAGATTCTACAGCC -s simHuman_chr6.simHuman.chr6 492029 21 + 601863 ----------------------------------------------AACAAACCT---GGATCTGCTGTT -s simRat_chr6.simRat.chr6 523299 68 + 647215 CTTGTCCTAGCAACCC--ACTGCTAGCAGATCATCATCTGGGGGGTAACAAACATCAAGGATCTGCTGGT - -a -s simMouse_chr6.simMouse.chr6 511994 15 + 636262 GCAATCACAAGTATT -s Anc0.Anc0refChr3 125801 15 + 222631 GCAACCACAAATTTT -s Anc1.Anc1refChr6 159956 15 + 197743 GCAACCACAAATTTT -s Anc2.Anc2refChr1 38607 15 + 142988 GCAACCACAAATTTT -s mr.mrrefChr3 64479 15 + 181027 GCAATCACAAATTTT -s simCow_chr6.simCow.chr6 495592 15 + 602619 GCAACCACAAATGTT -s simDog_chr6.simDog.chr6 485284 15 + 593897 GTAACAATAAACTTT -s simHuman_chr6.simHuman.chr6 492059 15 + 601863 ACAACCACAAATTTT -s simRat_chr6.simRat.chr6 523367 15 + 647215 GCAATCACAAATTTT - -a -s simMouse_chr6.simMouse.chr6 512009 3 + 636262 GTG -s Anc0.Anc0refChr3 125820 3 + 222631 TTC -s Anc1.Anc1refChr6 159975 3 + 197743 TTC -s Anc2.Anc2refChr1 38637 3 + 142988 TGT -s mr.mrrefChr3 64494 3 + 181027 TTC -s simCow_chr6.simCow.chr6 495622 3 + 602619 CCT -s simDog_chr6.simDog.chr6 485314 3 + 593897 TGT -s simHuman_chr6.simHuman.chr6 492078 3 + 601863 TTC -s simRat_chr6.simRat.chr6 523382 3 + 647215 TTC - -a -s simMouse_chr6.simMouse.chr6 512012 24 + 636262 ATTTGTTAGTGTTTGAACGTAGGG -s Anc0.Anc0refChr3 125823 24 + 222631 GTTTGTTGGTGTTGGAACATAAGG -s Anc1.Anc1refChr6 159978 24 + 197743 GTTTGTTGGTGTTGGAACATAAGG -s Anc2.Anc2refChr1 38640 24 + 142988 GCTTGTTGGTGTTGGAACATGAGA -s mr.mrrefChr3 64497 24 + 181027 GTTTGTTAGTGTTTGAACATAGGG -s simCow_chr6.simCow.chr6 495625 17 + 602619 AAGTGTTGGTATT---ACAT---- -s simDog_chr6.simDog.chr6 485317 24 + 593897 GCTTGTTGGTGTTGGACCATGAGA -s simHuman_chr6.simHuman.chr6 492083 24 + 601863 GTTTATTGGTGTTGAAACATAAGG -s simRat_chr6.simRat.chr6 523385 24 + 647215 GTTTGGTAGTGTTTGAACATAGGG - -a -s simMouse_chr6.simMouse.chr6 512036 84 + 636262 CTAATGGTGCTTCTGCTTGTGATTCAATTCTTACTGTCATGATCTTATTGTGAAATCACACTCTCTGGTTGATATCAAGTCCCA -s Anc0.Anc0refChr3 125854 84 + 222631 GAATTGGCATTTATGCCTGTCATTCAATCCTTTCTGTCTTGGTTTTATTGTGAAAACACACTATGATATTAATTCCTACACTAG -s Anc1.Anc1refChr6 160009 84 + 197743 GAATTGGCATTTATGCCTGTCATTCAATCCTTTCTGTCTTGGTTTTATTGTGAAAACACACTATGATATTAATTCCTACACTAG -s Anc2.Anc2refChr1 38671 84 + 142988 GAATTGGCATTTATGCCTGTAATTCATTCCCTTCTGTCTTGGTTTTATTGTGAAAATACACTATGATATTAATTCCTACACTAG -s mr.mrrefChr3 64521 84 + 181027 GTAATGGTGCTTCTGCTTGTCATTCAATTCTTTCTGTCATGATCTTATTGTGAAATCACACTCTGTGGTTGATATCAAGTCCCA -s simCow_chr6.simCow.chr6 495642 72 + 602619 -TATCGGCCTTTATGTCTGTAGTTCACT-----TGGTCTTAGTTTAATTGTGAAAAT------TGATATTGATCCCTACACTGG -s simDog_chr6.simDog.chr6 485348 84 + 593897 GAACTGACATTTACGCCTCTAATGCATTCCCTTCTGTCTTGGTTTTATTGTGTAAATACACTATAATATTAATTCCTACACTAG -s simHuman_chr6.simHuman.chr6 492115 84 + 601863 GCATGAGCATTTGTCCCTGTCATTTAATCCTTTCTGTGTTGGTTTTATTGTGAAAACACACTATGATATTAATTCCCATGCTTG -s simRat_chr6.simRat.chr6 523409 84 + 647215 GTAATGGTGCATCTACTTGTCATTCAATTCTTTCTGTCAAGATCTTACTGTGAAATTGCACTCTGTGGTTGAAATCAACTCCCA - -a -s simMouse_chr6.simMouse.chr6 512120 12 + 636262 ACTTTAGACACT -s Anc0.Anc0refChr3 125938 12 + 222631 ACTTTAGGCACT -s Anc1.Anc1refChr6 160093 12 + 197743 ACTTTAGGCACT -s Anc2.Anc2refChr1 38755 12 + 142988 AAGTTTGGCATT -s mr.mrrefChr3 64605 12 + 181027 ACTTTAGACACT -s simCow_chr6.simCow.chr6 495714 12 + 602619 AATTCTGGCACT -s simDog_chr6.simDog.chr6 485432 12 + 593897 AGGTTTGGCATT -s simHuman_chr6.simHuman.chr6 492200 12 + 601863 ACTTGAGCCACT -s simRat_chr6.simRat.chr6 523493 12 + 647215 ACTTTAGACGCT - -a -s simMouse_chr6.simMouse.chr6 512132 57 + 636262 GGGCTGTGGAGAACATATAACGTGCATTCCTGGTTCTAACCTGCTATCTTTTGTATG -s Anc0.Anc0refChr3 125950 56 + 222631 GGGCTGTGGAGAACATATAACCTACACCCCCAGTTCT-CCCTGCAATCTTTTGTatg -s Anc1.Anc1refChr6 160105 56 + 197743 GGGCTGTGGAGAACATATAACCTACACCCCCAGTTCT-CCCTGCAATCTTTTGTatg -s Anc2.Anc2refChr1 38767 56 + 142988 GGGCTGTGGAGAACATTCAACCTACACCCCCAGTTCT-CCCTGCAATCTTTAGTatg -s mr.mrrefChr3 64617 57 + 181027 GGGCTGTGGAGAACATATAACGTGCATTCCTGGTTCTACCCTGCTATCTTTTGTATG -s simCow_chr6.simCow.chr6 495726 56 + 602619 AGACTGTGCAGAGCATTCAACCTACACCCCCAGTTCT-TCCTGTAATCTTTAGTatg -s simDog_chr6.simDog.chr6 485444 56 + 593897 GGGCTCTGGAGAACATTCAACCTGCACCCCTAGTTCC-CCCTGCAACCTTTACTATG -s simHuman_chr6.simHuman.chr6 492213 54 + 601863 GGGCTGTTGAGAAC--ATTACCTACACCCCCAGTTCT-CCCTGCAGTCTTTTGTatg -s simRat_chr6.simRat.chr6 523505 57 + 647215 GGGCTGTGGAGAACATATGATGTGCATGCCTGGTTATACCCTCCTATCTTTTGTATG - -a -s simMouse_chr6.simMouse.chr6 512189 26 + 636262 ATTCAAGCCTGGCCATAGGCTTATGT -s Anc0.Anc0refChr3 126066 26 + 222631 atttcaggcttgccataaggttgtgt -s Anc1.Anc1refChr6 160221 26 + 197743 atttcaggcttgccataaggttgtgt -s Anc2.Anc2refChr1 38883 26 + 142988 atttcaggcctgccataaggttgtgt -s mr.mrrefChr3 64674 26 + 181027 ATTCCAGCCTGGCCATAGGCTTATGT -s simCow_chr6.simCow.chr6 495850 26 + 602619 atttcagtcctgccataaggttgtgc -s simDog_chr6.simDog.chr6 485561 26 + 593897 ATTTCAGGCCTACCATAAGTTTAGGT -s simHuman_chr6.simHuman.chr6 492328 26 + 601863 atttcaggcttgccataaggaagtgt -s simRat_chr6.simRat.chr6 523562 26 + 647215 ATTCCAGCCCAGCCGTAGACTTATGT - -a -s simMouse_chr6.simMouse.chr6 512215 28 + 636262 CTTATTATCACTAGCTgatctggaagtc -s Anc0.Anc0refChr3 126144 27 + 222631 CCCCCTAGCACtTAC-gacctggaagtc -s Anc1.Anc1refChr6 160299 27 + 197743 CCCCCTAGCACtTAC-gacctggaagtc -s Anc2.Anc2refChr1 38961 27 + 142988 CCCCCTAGCACTTAT-GACctcgaagac -s mr.mrrefChr3 64752 28 + 181027 CTCCTTATCACtAGCTgatctggaagtc -s simCow_chr6.simCow.chr6 495903 27 + 602619 CCCCCTAGCACTTAT-GACCTCGAAGAC -s simDog_chr6.simDog.chr6 485640 18 + 593897 CCCCCTAACACTTAT-GAC--------- -s simHuman_chr6.simHuman.chr6 492406 27 + 601863 tcccctagcaatcac-gacctgaaagtg -s simRat_chr6.simRat.chr6 523641 27 + 647215 CGCCTTATCAC-AGCTGATGTGGAAGTC - -a -s simMouse_chr6.simMouse.chr6 512243 19 + 636262 ttcttaaaactgggcaagc -s Anc0.Anc0refChr3 126171 14 + 222631 t-----aaaattgggaacc -s Anc1.Anc1refChr6 160326 14 + 197743 t-----aaaattgggaacc -s Anc2.Anc2refChr1 38989 14 + 142988 t-----cacactgagatcc -s mr.mrrefChr3 64780 18 + 181027 t-cttaaaaattgggaagc -s simCow_chr6.simCow.chr6 495931 14 + 602619 T-----CACACTGAGATCC -s simHuman_chr6.simHuman.chr6 492433 14 + 601863 t-----aaaattcggtacc -s simRat_chr6.simRat.chr6 523668 18 + 647215 T-CTTAAAAATTGGGAAAC - -a -s simMouse_chr6.simMouse.chr6 512262 51 + 636262 caagacctattgagctgcactgtgtcatagtaaccaaactagaaaagggat -s Anc0.Anc0refChr3 126185 42 + 222631 c--------ttgagctatactgcatcctaat-accaaactagaagagagat -s Anc1.Anc1refChr6 160340 51 + 197743 caacccgtattgagctatactgcatcctaataaccaaactagaagagagat -s Anc2.Anc2refChr1 39003 42 + 142988 c--------ttgagctataccacatcctgat-accaaattacATGAGAGAT -s mr.mrrefChr3 64798 51 + 181027 caagacctattgagctgtactgtgtcatagtaaccaaactagaaaagggat -s simCow_chr6.simCow.chr6 495945 42 + 602619 C--------TTGAGCTATACCACATCCTGAT-ACCAAATTACATGAGAGAA -s simDog_chr6.simDog.chr6 485658 9 + 593897 ------------------------------------------ATGGAAGAT -s simHuman_chr6.simHuman.chr6 492450 48 + 601863 caacccgtattg---catattgcatcctaataactgaactagaagagtgat -s simRat_chr6.simRat.chr6 523686 51 + 647215 CAAgacctattgagctgtgctgtgccatagtaaccaaattagaaaagggat - -a -s simMouse_chr6.simMouse.chr6 512313 12 + 636262 atggattctagG -s Anc0.Anc0refChr3 126227 12 + 222631 atgaaatccaAG -s Anc1.Anc1refChr6 160391 12 + 197743 atgaaatccaAG -s Anc2.Anc2refChr1 39045 12 + 142988 ATGAAATCCAAG -s mr.mrrefChr3 64849 12 + 181027 atggaatctaGG -s simCow_chr6.simCow.chr6 495987 12 + 602619 ATGGAATCCAAG -s simDog_chr6.simDog.chr6 485721 12 + 593897 ATGAAATCCAAG -s simHuman_chr6.simHuman.chr6 492498 12 + 601863 atgtaatccaAG -s simRat_chr6.simRat.chr6 523737 12 + 647215 atggaatctaTG - -a -s simMouse_chr6.simMouse.chr6 512325 16 + 636262 TAGACAGTATTGAATC -s Anc0.Anc0refChr3 126259 16 + 222631 TCTGCAGCAGTGGTTC -s Anc1.Anc1refChr6 160423 16 + 197743 TCTGCAGCAGTGGTTC -s Anc2.Anc2refChr1 39079 16 + 142988 TCTGCAGCAGTGGTTG -s mr.mrrefChr3 64861 16 + 181027 TCGACAGTATTGAATC -s simCow_chr6.simCow.chr6 496122 16 + 602619 TCTGCAGTAATGATTG -s simDog_chr6.simDog.chr6 485755 16 + 593897 TGTGCAGCAGTAGTTG -s simHuman_chr6.simHuman.chr6 492530 16 + 601863 TCTGCCGCAGTGGTTC -s simRat_chr6.simRat.chr6 523749 16 + 647215 TCGACTGTATTGAATG - -a -s simMouse_chr6.simMouse.chr6 512341 7 + 636262 ATAGACT -s Anc0.Anc0refChr3 126278 7 + 222631 ACGAACT -s Anc1.Anc1refChr6 160442 7 + 197743 ACGAACT -s Anc2.Anc2refChr1 39098 7 + 142988 CCGAACT -s mr.mrrefChr3 64877 7 + 181027 ACAGACT -s simCow_chr6.simCow.chr6 496141 7 + 602619 TCAAACG -s simDog_chr6.simDog.chr6 485774 7 + 593897 CCGAAGT -s simHuman_chr6.simHuman.chr6 492549 7 + 601863 ACCAACC -s simRat_chr6.simRat.chr6 523765 7 + 647215 ACTGACT - -a -s simMouse_chr6.simMouse.chr6 512348 19 + 636262 TACAATTTATTATCGCTGT -s Anc0.Anc0refChr3 126288 6 + 222631 TACCAT------------- -s Anc1.Anc1refChr6 160452 19 + 197743 TACCATTGATGGCAACTGT -s Anc2.Anc2refChr1 39108 6 + 142988 TACCTT------------- -s mr.mrrefChr3 64887 19 + 181027 TACAATTGATTGTCACTGT -s simCow_chr6.simCow.chr6 496151 6 + 602619 TGCCTT------------- -s simDog_chr6.simDog.chr6 485784 6 + 593897 TACCTT------------- -s simHuman_chr6.simHuman.chr6 492559 19 + 601863 TACCATTGATGGCAACTGT -s simRat_chr6.simRat.chr6 523775 19 + 647215 TACTATTGATTGTCACTGT - -a -s simMouse_chr6.simMouse.chr6 512367 56 + 636262 GGGATGTCTGATGAGATCAGATAACAACTTTCAAGTGGAGTGGCTATTGCTGTAGG -s Anc1.Anc1refChr6 160489 49 + 197743 GGGATGTCACATGAGACCATGTAA-------GAGATGGGCTAGGTACTAAAGTGGA -s mr.mrrefChr3 64924 56 + 181027 GGGATGTCTGATGAGATCAGATAACAACTTTCAAGTGGAGTGGCTACTGCAGTAGG -s simHuman_chr6.simHuman.chr6 492603 49 + 601863 GGGATGTCACATGAGACCATGTAA-------GAGATGGGCTAGGTACTAAAGTGGA -s simRat_chr6.simRat.chr6 523812 56 + 647215 GGGATGTCTGATGAGATCAGATAACAACTTCCCAGTGAAGCGGCTACTGCAGTAGG - -a -s simMouse_chr6.simMouse.chr6 512423 49 + 636262 TTGGCTCTAGCAAACCTAAACAAGTTTCTCCCTAATGTATCAGAACACT -s Anc1.Anc1refChr6 160539 48 + 197743 TAGTGTATAGCAAAACCAAATAACCCTCTGCCAGGTCCATAGGCAAAC- -s mr.mrrefChr3 64981 49 + 181027 TTGTCTATAGCAAACCTAAACAAGTTTCTGCCTAATGTATCGGAACACT -s simHuman_chr6.simHuman.chr6 492653 48 + 601863 TAGTGTATAGCAAAACCAAATAACCCTCTGCCAGGTCCATAGGCAAAC- -s simRat_chr6.simRat.chr6 523869 49 + 647215 TTGTATATAGTAAACCTAAACTAGTTTCTGCCTAATGAATGGGTACACT - -a -s simMouse_chr6.simMouse.chr6 512472 85 + 636262 AATACCTCTATAACACTAAACTAAGATCAAGGTTCACTTGCTCGGCCTTTTTATTGGCCTTTAAACAATACTAAGTCTATCAAGT -s Anc0.Anc0refChr3 126302 61 + 222631 AACACCTTTATCATATTAAACCAAGCTCAATGTTCAC-------------TTATTGACCTT-----ACTATTAAGTGTA------ -s Anc1.Anc1refChr6 160595 61 + 197743 AACACCTTTATCATATTAAACCAAGCTCAATGTTCAC-------------TTATTGACCTT-----ACTATTAAGTGTA------ -s Anc2.Anc2refChr1 39122 61 + 142988 AACACCTTTATCATATTAAACCAAGCTCAATATTCAC-------------TTATTGACCTT-----CCTAATAAGTGTA------ -s mr.mrrefChr3 65030 85 + 181027 AATACCTCTATAACACTAAACTAAGATCAAGGTTCACTTGCTCGGCCTTTTTATTGGCCTTTAAACAATATTAAGTCTATCAAGT -s simCow_chr6.simCow.chr6 496165 60 + 602619 AACACCTTTATCACATTAAAACAAGCCCAAT-TTCAC-------------ACATCGAGCTT-----CCTAGTATGTGTA------ -s simDog_chr6.simDog.chr6 485798 60 + 593897 AACACCTTCATCGTATTAAACCAAGGT-AATATTCAC-------------TTATTGACCTT-----CCTAACGACTGTG------ -s simHuman_chr6.simHuman.chr6 492711 61 + 601863 AACACCTGTATCATATTGAATGAAGCTCAACGTTCAC-------------TTATTAACCTT-----ACTATTAAGTGTA------ -s simRat_chr6.simRat.chr6 523918 85 + 647215 AATACCTCCATAACACTAAACTAAGATCTAGGTTCACTTTCTTGGCCTTTTTATTGGCCCTTAAACAATGTTAAGTCTATCAAGT - -a -s simMouse_chr6.simMouse.chr6 512557 22 + 636262 GTGAAGTATTATTCCCCTGTGG -s Anc0.Anc0refChr3 126363 22 + 222631 GTAAAGTATTATTTCCCTGTGG -s Anc1.Anc1refChr6 160656 22 + 197743 GTAAAGTATTATTTCCCTGTGG -s Anc2.Anc2refChr1 39183 22 + 142988 GGAAAGTTTTATTTCCCTGTGG -s mr.mrrefChr3 65115 22 + 181027 GTGAAGTATTATTCCCCTGTGG -s simCow_chr6.simCow.chr6 496225 19 + 602619 ---AAGTTTTATTTGCTTATGG -s simDog_chr6.simDog.chr6 485897 22 + 593897 GGAAAGTTTTATTTCCCTGTGA -s simHuman_chr6.simHuman.chr6 492772 22 + 601863 GTAAAGTATTATTTCCCTGTGG -s simRat_chr6.simRat.chr6 524003 22 + 647215 GTGAAGTATTATTCCCCTGTGG - -a -s simMouse_chr6.simMouse.chr6 512579 7 + 636262 ACTTCAA -s Anc0.Anc0refChr3 126385 7 + 222631 ACCCTAA -s Anc1.Anc1refChr6 160678 7 + 197743 ACCCTAA -s Anc2.Anc2refChr1 39205 7 + 142988 GTCCTAA -s mr.mrrefChr3 65137 7 + 181027 ACTTCAA -s simCow_chr6.simCow.chr6 496244 7 + 602619 ACTCTAA -s simDog_chr6.simDog.chr6 485919 7 + 593897 GTCCTAA -s simHuman_chr6.simHuman.chr6 492816 7 + 601863 ACCCTAT -s simRat_chr6.simRat.chr6 524025 7 + 647215 ACTTCGA - -a -s simMouse_chr6.simMouse.chr6 512586 1 + 636262 C -s Anc0.Anc0refChr3 126392 1 + 222631 C -s Anc1.Anc1refChr6 160685 1 + 197743 C -s Anc2.Anc2refChr1 39226 1 + 142988 C -s mr.mrrefChr3 65144 1 + 181027 C -s simCow_chr6.simCow.chr6 496266 1 + 602619 C -s simDog_chr6.simDog.chr6 485940 1 + 593897 C -s simHuman_chr6.simHuman.chr6 492823 1 + 601863 C -s simRat_chr6.simRat.chr6 524032 1 + 647215 C - -a -s simMouse_chr6.simMouse.chr6 512587 35 + 636262 ACAACTAGGCACATCAAATAACGGAATTGTGGAAA -s Anc0.Anc0refChr3 126393 29 + 222631 ATAATGAGTAGCATCA------GACATTGCCAAAA -s Anc1.Anc1refChr6 160686 29 + 197743 ATAATGAGTAGCATCA------GACATTGCCAAAA -s Anc2.Anc2refChr1 39227 29 + 142988 ATTATGTGTAATGTCT------TACATCCCTGTGG -s mr.mrrefChr3 65145 35 + 181027 ATAACTAGGAGCATCAAATAACGGAATTGTCAAAA -s simCow_chr6.simCow.chr6 496270 29 + 602619 ATTATGTTTAAAGTTT------TATGTCCCTGTGG -s simDog_chr6.simDog.chr6 485941 29 + 593897 TATATGTGTAATGTCT------TACATCCCTGTGG -s simHuman_chr6.simHuman.chr6 492824 29 + 601863 ATAAAGAGAAGCATCA------GAGATTGGCAAAA -s simRat_chr6.simRat.chr6 524033 35 + 647215 ATAATTAGGAGCATCAAATAACTGTGTTGCCAAAA - -a -s simMouse_chr6.simMouse.chr6 512622 37 + 636262 GGTCCTTTTAGTATGTAATGCAGTCTAGAAATTTTGG -s Anc0.Anc0refChr3 126422 37 + 222631 GCCAGTTTTAGTATCTAAGGCATGCTAGAATTTGTAG -s Anc1.Anc1refChr6 160715 37 + 197743 GCCAGTTTTAGTATCTAAGGCATGCTAGAATTTGTAG -s Anc2.Anc2refChr1 39256 37 + 142988 GCCAGATTTAGTATCCAAGGCATGCCAGAATTTGTAG -s mr.mrrefChr3 65180 37 + 181027 GGTCCTTTTAGTATGTAATGCATTCTAGAATTTTTGG -s simCow_chr6.simCow.chr6 496339 37 + 602619 GCCATCTTTAGTAGCCAAGGCATGCCAGAATTTGTAG -s simDog_chr6.simDog.chr6 485970 36 + 593897 GCCTGAAT-AATATACAAGGCATGCCAGAACTTGTAG -s simHuman_chr6.simHuman.chr6 492853 37 + 601863 GCCAGTTTTAGTATCTAAGGCATGCTAGAATTTGTAG -s simRat_chr6.simRat.chr6 524068 37 + 647215 GGTCCTTTTATTATGTAAACCATCCTAGAATTTTTGG - -a -s simMouse_chr6.simMouse.chr6 512659 1 + 636262 G -s Anc0.Anc0refChr3 126459 1 + 222631 G -s Anc1.Anc1refChr6 160752 1 + 197743 G -s Anc2.Anc2refChr1 39293 1 + 142988 G -s mr.mrrefChr3 65217 1 + 181027 G -s simCow_chr6.simCow.chr6 496453 1 + 602619 G -s simDog_chr6.simDog.chr6 486006 1 + 593897 G -s simHuman_chr6.simHuman.chr6 492890 1 + 601863 G -s simRat_chr6.simRat.chr6 524105 1 + 647215 G - -a -s simMouse_chr6.simMouse.chr6 512660 25 + 636262 ACTAGGAGTAAACATGCCCTAGAGT -s Anc0.Anc0refChr3 126460 25 + 222631 ACTAGGAGGAAAAATGCCCTAGTGG -s Anc1.Anc1refChr6 160753 25 + 197743 ACTAGGAGGAAAAATGCCCTAGTGG -s Anc2.Anc2refChr1 39295 25 + 142988 ACTAGGAGGAAAAATGCCCTAGTGG -s mr.mrrefChr3 65218 25 + 181027 ACTAGGAGTAAACATGCCCTAGAGT -s simCow_chr6.simCow.chr6 496455 25 + 602619 ACTAGGAGGAAAAAAGGCTTAGTGT -s simDog_chr6.simDog.chr6 486008 25 + 593897 ACTAGGAGGAAAAATGCCCTAGTGG -s simRat_chr6.simRat.chr6 524106 25 + 647215 ACTAGGAATAAACATGCCCTAGAGT - -a -s simMouse_chr6.simMouse.chr6 512685 7 + 636262 ATCCCTT -s Anc0.Anc0refChr3 126485 4 + 222631 G---CAC -s Anc1.Anc1refChr6 160778 4 + 197743 G---CAC -s Anc2.Anc2refChr1 39320 4 + 142988 G---AAC -s mr.mrrefChr3 65243 7 + 181027 ATCCCTC -s simCow_chr6.simCow.chr6 496480 4 + 602619 G---CAC -s simDog_chr6.simDog.chr6 486034 4 + 593897 G---AAC -s simHuman_chr6.simHuman.chr6 492891 3 + 601863 ----CAC -s simRat_chr6.simRat.chr6 524131 7 + 647215 AACCCCC - -a -s simMouse_chr6.simMouse.chr6 512692 15 + 636262 ATTCATCCAAAATGT -s Anc0.Anc0refChr3 126491 14 + 222631 GGTTATAAAAGA-GT -s Anc1.Anc1refChr6 160785 14 + 197743 GGTTATAAAAGA-GT -s Anc2.Anc2refChr1 39326 14 + 142988 GGCCAAAAGAGA-AT -s mr.mrrefChr3 65253 15 + 181027 GTTTATACAAAATGT -s simCow_chr6.simCow.chr6 496486 14 + 602619 GTGCAAAAGAGC-AT -s simDog_chr6.simDog.chr6 486040 14 + 593897 GGCCAAATGAGA-AT -s simHuman_chr6.simHuman.chr6 492897 14 + 601863 GCTTATAAAAGA-GT -s simRat_chr6.simRat.chr6 524141 15 + 647215 GTATGTACAAAATGT - -a -s simMouse_chr6.simMouse.chr6 512707 101 + 636262 CTTAGGGTAGCCCTTGTACACCCCGAATAAGTGATTTGTGTACTTCAAATAACCCCCATGAGCGTTGAGATTCCCCATACATGTCTCTTGTCTAGAGTTAA -s Anc0.Anc0refChr3 126505 72 + 222631 ---------GCCCT--------------------TTTGTGTGGTCAGAACAACCCTCATGGGTTTTGAGAATCCCCATACATGTTTTCTGTCTACCATTAA -s Anc1.Anc1refChr6 160800 72 + 197743 ---------GCCCT--------------------TTTGTGTGGTCAGAACAACCCTCATGGGTTTTGAGAATCCCCATACATGTTTTCTGTCTACCATTAA -s Anc2.Anc2refChr1 39340 72 + 142988 ---------GCCCT--------------------TTTGTGTGGTCAGAACAACCCTCAAAGGTATTGAGAATCCCCATACATGTTTTCCGTCTACCATTAA -s mr.mrrefChr3 65269 100 + 181027 CTTAGGGTAGCCCT-GTACACCCCGAATAAGTGATTTGTGTACTTCAAATAACCCCCATGAGCTTTGAGATTCCCCATACATGTCTCTTGTCTAGAATTAA -s simCow_chr6.simCow.chr6 496500 72 + 602619 ---------GACCA--------------------CTTCTGTGCTCAAAATAACCCCCACAGGTATTGAGAATCCCCATACTTGTCTTCGGTCTACCATTAC -s simDog_chr6.simDog.chr6 486054 72 + 593897 ---------GCCCT--------------------TTTGTGTGGTCAGAACAACCCTCAAAGGTATTGAGAATCCCCAAGCATGTTTCCCTTCTAGCATTAA -s simHuman_chr6.simHuman.chr6 492912 48 + 601863 -----------------------------------------------------CCATTTGTGTTCTGAGAATCAGCATACATGCATTCTGTTTACCATTAA -s simRat_chr6.simRat.chr6 524157 100 + 647215 CTTAGGGTAGCCCA-GTTCACCCAGGATAGGTAATTTGTGTACTCCGAATAACCCCCATAAGGTTTGAGATTCCCAACACATGTCTCTTGTCTGGAATTAA - -a -s simMouse_chr6.simMouse.chr6 512808 24 + 636262 TAATTGACTGTTTTGATTGCCAGA -s Anc0.Anc0refChr3 126582 24 + 222631 CAGTTGAACGTCTAGATTATCAGG -s Anc1.Anc1refChr6 160877 24 + 197743 CAGTTGAACGTCTAGATTATCAGG -s Anc2.Anc2refChr1 39417 24 + 142988 CAGTTCAACATCTAGATTATCAGG -s mr.mrrefChr3 65369 24 + 181027 TAATTGACTGTCTAGATTGCCAGG -s simCow_chr6.simCow.chr6 496577 24 + 602619 CAATTCAACATCTTGATTATCAGG -s simDog_chr6.simDog.chr6 486131 24 + 593897 CAGTTCAACATCTAGATTAACAGG -s simHuman_chr6.simHuman.chr6 492965 24 + 601863 CAGTTGATCGTCTAGACTATCATG -s simRat_chr6.simRat.chr6 524257 20 + 647215 T----GGCTTGCTAGATTGCCAGG - -a -s simMouse_chr6.simMouse.chr6 512832 13 + 636262 ACTTCTGGTCTAG -s Anc0.Anc0refChr3 126608 13 + 222631 ACTTCTGGACTAG -s Anc1.Anc1refChr6 160903 13 + 197743 ACTTCTGGACTAG -s Anc2.Anc2refChr1 39443 13 + 142988 ACTTCTGGACTGG -s mr.mrrefChr3 65393 13 + 181027 ACTTCTGGTCTAG -s simCow_chr6.simCow.chr6 496603 13 + 602619 AATTCTGCCCTTG -s simDog_chr6.simDog.chr6 486157 13 + 593897 ACTTATTGATTGG -s simHuman_chr6.simHuman.chr6 492991 13 + 601863 ACTTCTGGGCTAG -s simRat_chr6.simRat.chr6 524277 11 + 647215 --TTCTGCTCTAA - -a -s simMouse_chr6.simMouse.chr6 512845 8 + 636262 ACAGGAAC -s Anc0.Anc0refChr3 126621 8 + 222631 ACAGGAAC -s Anc1.Anc1refChr6 160916 8 + 197743 ACAGGAAC -s Anc2.Anc2refChr1 39456 8 + 142988 ACAGGAAC -s mr.mrrefChr3 65406 8 + 181027 ACAGGAAC -s simCow_chr6.simCow.chr6 496616 8 + 602619 GCAGGAAT -s simDog_chr6.simDog.chr6 486176 8 + 593897 ACCGGAAC -s simHuman_chr6.simHuman.chr6 493004 8 + 601863 ACAGGAAC -s simRat_chr6.simRat.chr6 524288 8 + 647215 ACAAGAGC - -a -s simMouse_chr6.simMouse.chr6 512853 33 + 636262 AGTGTCGGCTATAATAGTTAACTGTCAAGATAG -s Anc0.Anc0refChr3 126650 33 + 222631 TGCCTTGGCTATTATAATTATTTGTCAAGATAT -s Anc1.Anc1refChr6 160945 33 + 197743 TGCCTTGGCTATTATAATTATTTGTCAAGATAT -s Anc2.Anc2refChr1 39485 33 + 142988 TGCCTTGGCTATTATAATTATTTGTCAAGATAT -s mr.mrrefChr3 65414 33 + 181027 TGTGTTGGCTATAATAGTTAACTGTCAAGATAG -s simCow_chr6.simCow.chr6 496645 33 + 602619 TACCTTGGCTATAATAATAATTTGTTGGGATCC -s simDog_chr6.simDog.chr6 486205 33 + 593897 TGCCTTGGCTATTATAATTCTTTGTCAACATAT -s simHuman_chr6.simHuman.chr6 493033 33 + 601863 TGCCCTGGCAGTCATACTTATTTGTCAAGATAT -s simRat_chr6.simRat.chr6 524296 33 + 647215 TGTGTTGATTATAATAGTTAACTGTCAAGATAG - -a -s simMouse_chr6.simMouse.chr6 512886 6 + 636262 CATGTC -s Anc0.Anc0refChr3 126683 6 + 222631 TATGTT -s Anc1.Anc1refChr6 160978 6 + 197743 TATGTT -s Anc2.Anc2refChr1 39518 6 + 142988 TATGTT -s mr.mrrefChr3 65447 6 + 181027 CATGTT -s simCow_chr6.simCow.chr6 496683 6 + 602619 TAGGTT -s simDog_chr6.simDog.chr6 486238 6 + 593897 TATGTT -s simHuman_chr6.simHuman.chr6 493066 6 + 601863 GATGTT -s simRat_chr6.simRat.chr6 524329 6 + 647215 CATGTT - -a -s simMouse_chr6.simMouse.chr6 512892 21 + 636262 AAATTCACATTTTTGCTATGC -s Anc0.Anc0refChr3 126689 21 + 222631 AAATTATCATGCTTGTTATGC -s Anc1.Anc1refChr6 160984 21 + 197743 AAATTATCATGCTTGTTATGC -s Anc2.Anc2refChr1 39524 21 + 142988 AAATTATCATGATTGTTATGC -s mr.mrrefChr3 65453 21 + 181027 AAATTCACATTCTTGTTATGC -s simCow_chr6.simCow.chr6 496689 21 + 602619 AAGTTATCATGTTTGTCATGC -s simDog_chr6.simDog.chr6 486244 21 + 593897 AAATTATTATGATTGTTATGC -s simHuman_chr6.simHuman.chr6 493072 21 + 601863 AAACCATCATGCTTTTTATGC -s simRat_chr6.simRat.chr6 524338 21 + 647215 AAATTCACAACCTTGTTATGC - -a -s simMouse_chr6.simMouse.chr6 512913 50 + 636262 ATAATTGGACTCAAATGTAAAAGGTGGGTATAGCTGATAGCAAACTTTAA -s Anc0.Anc0refChr3 126719 49 + 222631 ATAATTGCAACCTAACATACAAATGGAAAATAG-TCATAGCACGTTTGAA -s Anc1.Anc1refChr6 161014 50 + 197743 ATAATTGCAACCTAACATACAAATGGAAAATAGTTCATAGCACGTTTGAA -s Anc2.Anc2refChr1 39554 49 + 142988 ATAATTGCAACCTCACATACAAATGGAAAATAG-TCATAGAACGTCTGAA -s mr.mrrefChr3 65474 50 + 181027 ATAATTGCACCCAAATGTAAAAATTGAGTATAGCTGATAGCAAACTTGAA -s simCow_chr6.simCow.chr6 496719 49 + 602619 GTTATTGCCACATGACATACAAATGGAGAATTT-TCAGCGTGTGACTGAA -s simDog_chr6.simDog.chr6 486274 48 + 593897 ATAATTACA-CCTCAACTATGAATGGAAAATAG-TCATAGAACATCTGAA -s simHuman_chr6.simHuman.chr6 493102 50 + 601863 ATAATTGCAACCTAACATGCAAATGGAAAATACTGAATAGCACGTTTGAA -s simRat_chr6.simRat.chr6 524359 48 + 647215 ATAATGGCACCCAAATCTAAAAATAGAGTATA--TGATAGCAAACTTGAA - -a -s simMouse_chr6.simMouse.chr6 512963 26 + 636262 TATTAGATTTTACATTCTACCCCAGT -s Anc0.Anc0refChr3 126768 26 + 222631 CATTAGATTTTATACTCGACTCTACT -s Anc1.Anc1refChr6 161064 26 + 197743 CATTAGATTTTATACTCGACTCTACT -s Anc2.Anc2refChr1 39603 26 + 142988 CATTAGATCTTATACTCGACTCTACT -s mr.mrrefChr3 65524 26 + 181027 CATTAGATTTTACATTCTACCCTACT -s simCow_chr6.simCow.chr6 496768 26 + 602619 CATTAGATCTTATACTCGACTTTACT -s simDog_chr6.simDog.chr6 486322 18 + 593897 TATTAGATCTTAT--------CTACT -s simHuman_chr6.simHuman.chr6 493152 26 + 601863 CAGTAAACTTTATACTTAATACTACT -s simRat_chr6.simRat.chr6 524409 26 + 647215 CATTAGATTTTACATTCTACCCTACT - -a -s simMouse_chr6.simMouse.chr6 512989 10 + 636262 TTGGGATAGG -s Anc0.Anc0refChr3 126807 10 + 222631 TTCAAACAGG -s Anc1.Anc1refChr6 161103 10 + 197743 TTCAAACAGG -s Anc2.Anc2refChr1 39642 10 + 142988 TTTAAACAGG -s mr.mrrefChr3 65550 10 + 181027 TTCAAATAGG -s simCow_chr6.simCow.chr6 496809 10 + 602619 TTTAAACAGG -s simHuman_chr6.simHuman.chr6 493191 10 + 601863 TTCAAACAGG -s simRat_chr6.simRat.chr6 524435 10 + 647215 TTCAAATAGG - -a -s simMouse_chr6.simMouse.chr6 512999 30 + 636262 AAGGTATGTTATATGGCAGTGACTAAGGCC -s Anc0.Anc0refChr3 126817 27 + 222631 A---TTTGATAAATGGCAGTAACTAAGACC -s Anc1.Anc1refChr6 161113 27 + 197743 A---TTTGATAAATGGCAGTAACTAAGACC -s Anc2.Anc2refChr1 39652 27 + 142988 G---GTTGATCAATGGCTGTAAATAAGACC -s mr.mrrefChr3 65560 30 + 181027 AAGGTATGTTAAATGGCAGTGACTAAGACC -s simCow_chr6.simCow.chr6 496822 27 + 602619 G---GTTGATCAATGGCTGTAAATAAGACC -s simDog_chr6.simDog.chr6 486349 3 + 593897 ---------------------------ACC -s simHuman_chr6.simHuman.chr6 493201 27 + 601863 A---TCTGATAAATGGCAGCAGCTATAACC -s simRat_chr6.simRat.chr6 524445 30 + 647215 TAGGTATGTTAAATGGCAGTGACCAAGACC - -a -s simMouse_chr6.simMouse.chr6 513029 46 + 636262 CAGTATAAGTAGTAAGAGCAGCCTAACCATGATGTAGATTCTTAAA -s Anc0.Anc0refChr3 126845 46 + 222631 CAGTATAAGCAGTAGTAGCTGCCTTGCACTGATGTGTATTTTTAAA -s Anc1.Anc1refChr6 161141 46 + 197743 CAGTATAAGCAGTAGTAGCTGCCTTGCACTGATGTGTATTTTTAAA -s Anc2.Anc2refChr1 39680 46 + 142988 CAGTATAAGCAGTAGTAGTTGCCTTGCACTAATGTGTATTTTTAAA -s mr.mrrefChr3 65590 46 + 181027 CAGTATAAGTAGTAAGAGCAGCCTAACCATGATGTAGATTCTTAAA -s simCow_chr6.simCow.chr6 496850 46 + 602619 CAGTGTAAGTAATAGCAGTTGCCTTACACTAATGTGTATTTTTAAA -s simDog_chr6.simDog.chr6 486353 31 + 593897 CAGCATAAGCAGTAGTACTTGCCTTGTA---------------TAA -s simHuman_chr6.simHuman.chr6 493229 46 + 601863 CAGTATAAACATTAGTAGCTGCCTTCCAGTGATGTCAATTGTTAAA -s simRat_chr6.simRat.chr6 524475 46 + 647215 CAGTATAAGTAGTAAGAGCAGCCTAACCATGATGCAGATTATTAAA - -a -s simMouse_chr6.simMouse.chr6 513075 32 + 636262 TGCAAAGTGGTGAATATAACAACAGTATTGAT -s Anc0.Anc0refChr3 126905 31 + 222631 TGCAATGTAGTGAAAGTGACAAAAGTA-TGAT -s Anc1.Anc1refChr6 161201 32 + 197743 TGCAATGTAGTGAAAGTGACAAAAGTACTGAT -s Anc2.Anc2refChr1 39740 31 + 142988 TTAATCATAGTGAAAGTGACAAAAGTA-TGAG -s mr.mrrefChr3 65636 32 + 181027 TGCAATGTGGTGAATATGACAACAGTATTGAT -s simCow_chr6.simCow.chr6 496911 31 + 602619 TTAATCATAGTTAAAGTTAGAAAAGTA-GGAG -s simDog_chr6.simDog.chr6 486392 23 + 593897 --------AGTGAAAGTGACAAAAGTA-TGAG -s simHuman_chr6.simHuman.chr6 493289 30 + 601863 TGCAATGTAGTGTAGGTGATGAAAGCAC--AT -s simRat_chr6.simRat.chr6 524521 32 + 647215 AGCAATGTGGTGAACATGACAACAGTATTAAT - -a -s simMouse_chr6.simMouse.chr6 513107 23 + 636262 AGCAAGATAAGTATATCATTTGT -s Anc0.Anc0refChr3 126936 23 + 222631 GGCAAGATAAGTATATCAATTAT -s Anc1.Anc1refChr6 161233 23 + 197743 GGCAAGATAAGTATATCAATTAT -s Anc2.Anc2refChr1 39771 23 + 142988 GACATGATAAGTATACCAATTAT -s mr.mrrefChr3 65668 23 + 181027 GGCAAGATAAGTATATCATTTGT -s simCow_chr6.simCow.chr6 496942 23 + 602619 GCCATGATAAGTACACAAATTGT -s simDog_chr6.simDog.chr6 486415 23 + 593897 GACATAACAAGTATACCTATTAT -s simHuman_chr6.simHuman.chr6 493319 23 + 601863 GGCAAGATAAGTATATCAATTCT -s simRat_chr6.simRat.chr6 524555 23 + 647215 GGCAAGATAATTATATCATTTGT - -a -s simMouse_chr6.simMouse.chr6 513130 48 + 636262 CGATGATGTGGCCACTAATGACCATCCACACCACACCCATGGATAGGA -s Anc0.Anc0refChr3 126960 42 + 222631 TTGTGATGTGGCCAACAATGACCACCCACACT-----TTTGGAAAGG- -s Anc1.Anc1refChr6 161257 42 + 197743 TTGTGATGTGGCCAACAATGACCACCCACACT-----TTTGGAAAGG- -s Anc2.Anc2refChr1 39795 42 + 142988 TTGTGATATGGCCAACAATGACCACCTACACT-----TTTGGAAAGG- -s mr.mrrefChr3 65691 48 + 181027 CGATGATGTGGCCAATAATGACCATCCACACTACACCCATGGATAGGA -s simCow_chr6.simCow.chr6 496966 42 + 602619 TTGTGATATGGCCAACAAGGACCATTGATACT-----TCTGGACAGG- -s simDog_chr6.simDog.chr6 486439 42 + 593897 TTACCATATGGCCAACAATGACCACCTACACT-----TTAGGAAAGG- -s simHuman_chr6.simHuman.chr6 493343 42 + 601863 TTGTGATGTGGCCAACAATGACCACCCACACT-----TTTGGAGAGG- -s simRat_chr6.simRat.chr6 524578 48 + 647215 CGATGATGTGGCGAATAATGACCATCCGCACTACACCCATGGATAGGA - -a -s simMouse_chr6.simMouse.chr6 513178 1 + 636262 A -s Anc0.Anc0refChr3 127002 1 + 222631 A -s Anc1.Anc1refChr6 161299 1 + 197743 A -s Anc2.Anc2refChr1 39837 1 + 142988 A -s mr.mrrefChr3 65739 1 + 181027 A -s simCow_chr6.simCow.chr6 497008 1 + 602619 A -s simDog_chr6.simDog.chr6 486481 1 + 593897 A -s simHuman_chr6.simHuman.chr6 493385 1 + 601863 A -s simRat_chr6.simRat.chr6 524628 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 513179 2 + 636262 GA -s Anc0.Anc0refChr3 127003 2 + 222631 GA -s Anc1.Anc1refChr6 161300 2 + 197743 GA -s Anc2.Anc2refChr1 39838 2 + 142988 GA -s mr.mrrefChr3 65740 2 + 181027 GA -s simCow_chr6.simCow.chr6 497009 2 + 602619 GA -s simDog_chr6.simDog.chr6 486486 2 + 593897 GA -s simHuman_chr6.simHuman.chr6 493386 2 + 601863 GA -s simRat_chr6.simRat.chr6 524629 2 + 647215 GA - -a -s simMouse_chr6.simMouse.chr6 513181 25 + 636262 GGATAAGGAGCGAGTTTTCTGATTA -s Anc0.Anc0refChr3 127005 25 + 222631 GGACAAAGAGCTGGTTTTTTGCCTG -s Anc1.Anc1refChr6 161302 25 + 197743 GGACAAAGAGCTGGTTTTTTGCCTG -s Anc2.Anc2refChr1 39840 25 + 142988 GGACAAAGAGCTGGTTTTTTGCCTG -s mr.mrrefChr3 65742 25 + 181027 GGATAAGGAGCGGGTTTTCTGCTTA -s simCow_chr6.simCow.chr6 497014 25 + 602619 GGACAAAGATACAGTTTTTGTCCCC -s simDog_chr6.simDog.chr6 486488 24 + 593897 GG-AAAAGAGCTGGTTATGTGCCTG -s simHuman_chr6.simHuman.chr6 493388 25 + 601863 GGACCAAGAGCTGGTTTTTTGCCTG -s simRat_chr6.simRat.chr6 524631 25 + 647215 GGATAAGGAGCGGGTTTTCTGCTTA - -a -s simMouse_chr6.simMouse.chr6 513206 4 + 636262 AAGT -s Anc0.Anc0refChr3 127030 4 + 222631 AATA -s Anc1.Anc1refChr6 161327 4 + 197743 AATA -s Anc2.Anc2refChr1 39866 4 + 142988 AATA -s mr.mrrefChr3 65767 4 + 181027 AAGA -s simCow_chr6.simCow.chr6 497040 4 + 602619 AATA -s simDog_chr6.simDog.chr6 486513 4 + 593897 ATTA -s simHuman_chr6.simHuman.chr6 493413 4 + 601863 AATA -s simRat_chr6.simRat.chr6 524656 4 + 647215 AAGA - -a -s simMouse_chr6.simMouse.chr6 513210 3 + 636262 AAC -s Anc0.Anc0refChr3 127165 3 + 222631 AAT -s Anc1.Anc1refChr6 161462 3 + 197743 AAT -s Anc2.Anc2refChr1 40136 3 + 142988 ACA -s mr.mrrefChr3 65835 3 + 181027 AAT -s simCow_chr6.simCow.chr6 497314 3 + 602619 AAA -s simDog_chr6.simDog.chr6 486789 3 + 593897 ACA -s simHuman_chr6.simHuman.chr6 493548 3 + 601863 AAT -s simRat_chr6.simRat.chr6 524724 3 + 647215 AAT - -a -s simMouse_chr6.simMouse.chr6 513213 22 + 636262 TTGAAGGAGAACCTATACTTGA -s Anc0.Anc0refChr3 127168 20 + 222631 C--AAGGAGAACCTATACTTCA -s Anc1.Anc1refChr6 161465 20 + 197743 C--AAGGAGAACCTATACTTCA -s Anc2.Anc2refChr1 40139 20 + 142988 C--AAGGAGAACCTATACTTCA -s mr.mrrefChr3 65838 22 + 181027 TTGAAGGAGAACCTATACTTGA -s simCow_chr6.simCow.chr6 497317 7 + 602619 ---------------TACTTAG -s simDog_chr6.simDog.chr6 486805 20 + 593897 C--AAGGAGAACCTATACTTCA -s simHuman_chr6.simHuman.chr6 493551 16 + 601863 ------GAGAACCTATACTTTA -s simRat_chr6.simRat.chr6 524727 22 + 647215 TTTAAGGAGAACCTATACTCGA - -a -s simMouse_chr6.simMouse.chr6 513235 6 + 636262 TATGCT -s Anc0.Anc0refChr3 127189 3 + 222631 TAT--- -s Anc1.Anc1refChr6 161486 3 + 197743 TAT--- -s Anc2.Anc2refChr1 40160 3 + 142988 TAT--- -s mr.mrrefChr3 65860 6 + 181027 TATGCT -s simCow_chr6.simCow.chr6 497325 2 + 602619 TA---- -s simDog_chr6.simDog.chr6 486826 3 + 593897 TAT--- -s simHuman_chr6.simHuman.chr6 493568 3 + 601863 TAT--- -s simRat_chr6.simRat.chr6 524749 6 + 647215 TATGCT - -a -s simMouse_chr6.simMouse.chr6 513241 38 + 636262 TAATTGGTAACTAAGTCATAAATGCCTCAGTTCAAAAG -s Anc0.Anc0refChr3 127192 19 + 222631 --ATT--TACCTAAGGT---AAT------------TAG -s Anc1.Anc1refChr6 161489 24 + 197743 --ATTAGTACCTAAGGTACAAAT------------TAG -s Anc2.Anc2refChr1 40163 19 + 142988 --ATC--TACCGAAAGT---AAT------------TAG -s mr.mrrefChr3 65866 26 + 181027 TAATTGGTAACTAAGTCACAAAT------------AAG -s simCow_chr6.simCow.chr6 497327 14 + 602619 ---------CTGAAATT---GAT------------TAG -s simDog_chr6.simDog.chr6 486829 19 + 593897 --ATC--TACCGAAAGT---AAT------------TAG -s simHuman_chr6.simHuman.chr6 493571 24 + 601863 --ATTAGTAGCTAAGGTACAAAT------------TAG -s simRat_chr6.simRat.chr6 524756 26 + 647215 TAATTGGTAACTAAGTCACAAAT------------AGG - -a -s simMouse_chr6.simMouse.chr6 513279 6 + 636262 TGAATA -s Anc0.Anc0refChr3 127214 6 + 222631 TGAATG -s Anc1.Anc1refChr6 161516 6 + 197743 TGAATG -s Anc2.Anc2refChr1 40185 6 + 142988 CGAATG -s mr.mrrefChr3 65892 6 + 181027 TGAATA -s simCow_chr6.simCow.chr6 497344 6 + 602619 CGCATA -s simDog_chr6.simDog.chr6 486851 6 + 593897 CCAAGG -s simHuman_chr6.simHuman.chr6 493598 6 + 601863 TGAATG -s simRat_chr6.simRat.chr6 524782 6 + 647215 GGAATA - -a -s simMouse_chr6.simMouse.chr6 513285 1 + 636262 T -s Anc0.Anc0refChr3 127220 1 + 222631 C -s Anc1.Anc1refChr6 161522 1 + 197743 C -s Anc2.Anc2refChr1 40191 1 + 142988 C -s mr.mrrefChr3 65898 1 + 181027 T -s simCow_chr6.simCow.chr6 497357 1 + 602619 C -s simDog_chr6.simDog.chr6 486857 1 + 593897 C -s simHuman_chr6.simHuman.chr6 493604 1 + 601863 C -s simRat_chr6.simRat.chr6 524788 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 513286 7 + 636262 TACCCAT -s Anc0.Anc0refChr3 127221 7 + 222631 AATAGAT -s Anc1.Anc1refChr6 161523 7 + 197743 AATAGAT -s Anc2.Anc2refChr1 40198 7 + 142988 AATAAAT -s mr.mrrefChr3 65899 7 + 181027 TACCGAT -s simCow_chr6.simCow.chr6 497364 2 + 602619 CA----- -s simDog_chr6.simDog.chr6 486864 7 + 593897 AATAAAT -s simHuman_chr6.simHuman.chr6 493605 7 + 601863 AAGGGAT -s simRat_chr6.simRat.chr6 524789 7 + 647215 TAATGAT - -a -s simMouse_chr6.simMouse.chr6 513293 3 + 636262 GCA -s Anc0.Anc0refChr3 127232 3 + 222631 GAA -s Anc1.Anc1refChr6 161534 3 + 197743 GAA -s Anc2.Anc2refChr1 40209 3 + 142988 GAA -s mr.mrrefChr3 65906 3 + 181027 GCA -s simCow_chr6.simCow.chr6 497368 3 + 602619 GAA -s simDog_chr6.simDog.chr6 486875 3 + 593897 TAA -s simHuman_chr6.simHuman.chr6 493616 3 + 601863 GAA -s simRat_chr6.simRat.chr6 524796 3 + 647215 GTA - -a -s simMouse_chr6.simMouse.chr6 513296 3 + 636262 TGC -s Anc0.Anc0refChr3 127235 3 + 222631 TGC -s Anc1.Anc1refChr6 161537 3 + 197743 TGC -s Anc2.Anc2refChr1 40224 3 + 142988 TGC -s mr.mrrefChr3 65909 3 + 181027 TGC -s simDog_chr6.simDog.chr6 486891 3 + 593897 TGC -s simHuman_chr6.simHuman.chr6 493619 3 + 601863 TGC -s simRat_chr6.simRat.chr6 524799 3 + 647215 TGC - -a -s simMouse_chr6.simMouse.chr6 513299 21 + 636262 TGAGATGGGCAAGCAGTTAGA -s Anc0.Anc0refChr3 127239 21 + 222631 AGGGATGGAGGAGTAGTTAGA -s Anc1.Anc1refChr6 161541 21 + 197743 AGGGATGGAGGAGTAGTTAGA -s Anc2.Anc2refChr1 40228 21 + 142988 AGGGATGGAGGATTTGTTAGA -s mr.mrrefChr3 65912 21 + 181027 TGAGATGGACAAGCAGTTAGA -s simCow_chr6.simCow.chr6 497383 9 + 602619 ------------CTTGTTAAA -s simDog_chr6.simDog.chr6 486895 20 + 593897 AGGGATGGAGGATTTGTT-GC -s simHuman_chr6.simHuman.chr6 493623 21 + 601863 AGGGATCAAGGAGTAGTTAGA -s simRat_chr6.simRat.chr6 524802 20 + 647215 TAAGATGGACA-GCAGTTAGA - -a -s simMouse_chr6.simMouse.chr6 513320 66 + 636262 TACCATTATGCAATCTAAGGTAGGGGTACAAAGATAGGTAGTGGAATTTATGATCTATAGCAATAT -s Anc0.Anc0refChr3 127268 60 + 222631 TACCATCATGGAATTCA------TGGTAGAAAGATGGCTGGTGGAATCCACGATATAAAAATGACT -s Anc1.Anc1refChr6 161570 60 + 197743 TACCATCATGGAATTCA------TGGTAGAAAGATGGCTGGTGGAATCCACGATATAAAAATGACT -s Anc2.Anc2refChr1 40257 60 + 142988 TACCATCATGGAATTCA------TGGTAGATAGATGGCTGGTGGAATCCACGATATAAAAATGACT -s mr.mrrefChr3 65933 66 + 181027 TACCATTATGGAATCCAAGGTAGGGGTAGAAAGATAGGTGGTGGAATTTATGATCTATAAAAAACT -s simCow_chr6.simCow.chr6 497400 58 + 602619 TAGCATCATGT--CTTA------TGGTATAGAGATGGCTCATGGAATCCATGATATAAAGAGGACC -s simDog_chr6.simDog.chr6 486923 60 + 593897 TACCATTATGGAATCCA------TAGTAGTTAGATGGCTGGTGGCACCCACAGTATAAAAATGACT -s simHuman_chr6.simHuman.chr6 493652 60 + 601863 TACCATCAGGGAATTCA------TGGTAGAAAGATGGCTGGTGGAATGCACGATATAACAATGACT -s simRat_chr6.simRat.chr6 524822 66 + 647215 TACCATTATGGAATCCAAGGTAGAGGTAGAAAGATAGGTGGTGGATTTTGTGAGCTATAAAAAACT - -a -s simMouse_chr6.simMouse.chr6 513386 1 + 636262 A -s Anc0.Anc0refChr3 127334 1 + 222631 T -s Anc1.Anc1refChr6 161636 1 + 197743 T -s Anc2.Anc2refChr1 40323 1 + 142988 T -s mr.mrrefChr3 66005 1 + 181027 A -s simCow_chr6.simCow.chr6 497464 1 + 602619 A -s simDog_chr6.simDog.chr6 486989 1 + 593897 T -s simHuman_chr6.simHuman.chr6 493718 1 + 601863 T -s simRat_chr6.simRat.chr6 524894 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 513387 51 + 636262 CACCAGCATTTGAGTACTTAATTTCCCCCTCCAAAGAATTGGAGACTGCGC -s Anc0.Anc0refChr3 127335 40 + 222631 CACCAGCATTCAAGTACTTATTTTACACCTCTAAAGAA-T----------C -s Anc1.Anc1refChr6 161637 40 + 197743 CACCAGCATTCAAGTACTTATTTTACACCTCTAAAGAA-T----------C -s Anc2.Anc2refChr1 40325 40 + 142988 CACCAGCATTCAAGTACTTATTGTTCACCTCTTAAGAT-T----------T -s mr.mrrefChr3 66006 41 + 181027 CACCAGCATTTAAGTACTTAATTTACCCCTCCAAAGAATT----------C -s simCow_chr6.simCow.chr6 497466 40 + 602619 TAACAGTGTTTAAGTACTTATTGTTCACCTTTCCAGAT-T----------T -s simDog_chr6.simDog.chr6 486991 26 + 593897 CACCAGCATTC--------------CATCTCTTAAGAT-T----------T -s simHuman_chr6.simHuman.chr6 493719 40 + 601863 CAACCACATTCAGAGACATATTTTACACCTCTAAAGGA-T----------C -s simRat_chr6.simRat.chr6 524895 39 + 647215 CACCAGCATTTAAGC-CTTAATTTACCCGTCCAAAGAATT----------- - -a -s simMouse_chr6.simMouse.chr6 513438 16 + 636262 CAAAGAATTAGAGACT -s Anc0.Anc0refChr3 127375 6 + 222631 GAAAG----------T -s Anc1.Anc1refChr6 161677 16 + 197743 GAAAGAGATAAGGACT -s Anc2.Anc2refChr1 40365 6 + 142988 GAAAG----------T -s mr.mrrefChr3 66047 16 + 181027 CAAAGAATTAGAGACT -s simCow_chr6.simCow.chr6 497507 6 + 602619 GAAAC----------T -s simDog_chr6.simDog.chr6 487017 6 + 593897 GAAAG----------T -s simHuman_chr6.simHuman.chr6 493759 16 + 601863 TAAAGAGATAAGGACT -s simRat_chr6.simRat.chr6 524934 7 + 647215 ---------AGATGCT - -a -s simMouse_chr6.simMouse.chr6 513454 33 + 636262 GTTGAGTACAGTGTTAAGGATGCTGAAAGTAAT -s Anc0.Anc0refChr3 127386 33 + 222631 GTAGTGTCCAGTTTTAAAGATGCTGAAAGTAAT -s Anc1.Anc1refChr6 161698 33 + 197743 GTAGTGTCCAGTTTTAAAGATGCTGAAAGTAAT -s Anc2.Anc2refChr1 40376 33 + 142988 GTAGTGTCCAGTTGTAAAGATGCTGAAAGTAAT -s mr.mrrefChr3 66063 33 + 181027 GTAGAGTACAGTTTTAAGGATGCTGAAAGTAAT -s simCow_chr6.simCow.chr6 497518 33 + 602619 GTAGTGTCTAGTCCTAAACATGCTGCAAGTAAT -s simDog_chr6.simDog.chr6 487028 32 + 593897 GTAGCACCCAGTTGGAAAGACACTTAA-GTAAT -s simHuman_chr6.simHuman.chr6 493780 33 + 601863 GTAGTGTCCAGTTTTAAAGATGCTGAAAGTAAT -s simRat_chr6.simRat.chr6 524941 33 + 647215 GTAGAATACAGTTTTAAGGGTGCTGAAAGTAAT - -a -s simMouse_chr6.simMouse.chr6 513487 17 + 636262 TAGCAAAGGAAAGTGAA -s Anc0.Anc0refChr3 127421 17 + 222631 AAGAATAGGAAAGCAAA -s Anc1.Anc1refChr6 161733 17 + 197743 AAGAATAGGAAAGCAAA -s Anc2.Anc2refChr1 40411 17 + 142988 AAGAATAGGAAGGCAAA -s mr.mrrefChr3 66096 17 + 181027 AAGCAAAGGAAAGTGAA -s simCow_chr6.simCow.chr6 497553 17 + 602619 ATGATTAGGAAGTCAAA -s simDog_chr6.simDog.chr6 487062 17 + 593897 AAGCATACAAAGGAAAA -s simHuman_chr6.simHuman.chr6 493815 17 + 601863 AAGAATAGGTGAACAAA -s simRat_chr6.simRat.chr6 524974 17 + 647215 AAGCAAAGGAAAGTGAA - -a -s simMouse_chr6.simMouse.chr6 513504 17 + 636262 CCTGGATATAGGGGCTG -s Anc0.Anc0refChr3 127444 16 + 222631 CTTGGATGTA-GAGCTG -s Anc1.Anc1refChr6 161756 17 + 197743 CTTGGATGTAGGAGCTG -s Anc2.Anc2refChr1 40434 16 + 142988 CTTGTGTGTA-GAGCTG -s mr.mrrefChr3 66113 17 + 181027 CCTGGATATAGGGGCTG -s simCow_chr6.simCow.chr6 497576 11 + 602619 CT-----GTA-GAGATA -s simDog_chr6.simDog.chr6 487085 16 + 593897 CCTGTGTGTA-GAGCTG -s simHuman_chr6.simHuman.chr6 493838 17 + 601863 CTTGGATGTAGGAGCTG -s simRat_chr6.simRat.chr6 524991 17 + 647215 CCTGGATATAGGTGCTG - -a -s simMouse_chr6.simMouse.chr6 513521 88 + 636262 GGTTGATTTATGGTAAATATCTGATGAAAACAGTAGTTAGGTGCTAACGTGTGTTACTGTGGACCAAACCAGGGCACTATGACCTGAG -s Anc0.Anc0refChr3 127461 88 + 222631 TGTGGATCTAGGGTTTGGAATCTGTGGAGACAGGTTTTAAGTGTGAAAATGTGGTGCCATGGATCAAGCCAAGGCACTATTACCTGAG -s Anc1.Anc1refChr6 161774 88 + 197743 TGTGGATCTAGGGTTTGGAATCTGTGGAGACAGGTTTTAAGTGTGAAAATGTGGTGCCATGGATCAAGCCAAGGCACTATTACCTGAG -s Anc2.Anc2refChr1 40451 88 + 142988 TGTGGATCTAGGGTTTGGAATCTGTGGAGGCAGGTTTTAAGTGTGGAAATGTTGCGCCATGGATCAAGCCAAGGCACTACTGCTTGGG -s mr.mrrefChr3 66130 88 + 181027 GGTTGATCTAGGGTAAATATCTGATGAAAACAGTAGTTAGGTGCTAACGTGTGTTACTGTGGACCAAACCAGGGCACTATGACCTGAG -s simCow_chr6.simCow.chr6 497588 78 + 602619 TGTGGGTCCAGGGTTTATAATCTGTGCAGGCAGGTGTTACGTGTGGAAATGTTGCACCATGGATCAAGGCAGGGCCTC---------- -s simDog_chr6.simDog.chr6 487102 81 + 593897 TGTGTATCTGGGGTTTGGAATCGATGGAGGCTGGGTTTAAATGTGGGAATGCTGCGCCA-------AACCAAGGCACTACTGCTTGGG -s simHuman_chr6.simHuman.chr6 493856 88 + 601863 TGCAGCTCTAGGGTTTGGAAACTGTAGAGACAGGTTTTAAGTGTGAAAACATGGTGCCATGGATCAAGCCAAGGCACTATAACCTGAG -s simRat_chr6.simRat.chr6 525008 79 + 647215 GGTCGATCTAGGGTAAATATCTGATGAAAACAGTAGTTAGGTGCAAA--------ATTGTGGACTGAACTAGGGCACTAC-ACCTGAG - -a -s simMouse_chr6.simMouse.chr6 513609 14 + 636262 CTCCCAGACTAAGT -s Anc0.Anc0refChr3 127550 14 + 222631 CTATCTTTTTAAGT -s Anc1.Anc1refChr6 161863 14 + 197743 CTATCTTTTTAAGT -s Anc2.Anc2refChr1 40540 14 + 142988 CCTTTTTTTTTAGT -s mr.mrrefChr3 66218 14 + 181027 CTACCATACTAAGT -s simDog_chr6.simDog.chr6 487184 14 + 593897 CCTTTTTTTTTAGT -s simHuman_chr6.simHuman.chr6 493945 14 + 601863 CTATCTTTATAAGT -s simRat_chr6.simRat.chr6 525087 14 + 647215 CTACCATACTAAGT - -a -s simMouse_chr6.simMouse.chr6 513623 1 + 636262 T -s Anc0.Anc0refChr3 127568 1 + 222631 T -s Anc1.Anc1refChr6 161881 1 + 197743 T -s Anc2.Anc2refChr1 40558 1 + 142988 T -s mr.mrrefChr3 66232 1 + 181027 T -s simDog_chr6.simDog.chr6 487202 1 + 593897 T -s simHuman_chr6.simHuman.chr6 493963 1 + 601863 T -s simRat_chr6.simRat.chr6 525101 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 513624 23 + 636262 ACATGACTATTCAGGGTGGGGAA -s Anc0.Anc0refChr3 127659 23 + 222631 ATGGGGCAATTCAGGTTGGTACG -s Anc1.Anc1refChr6 161972 23 + 197743 ATGGGGCAATTCAGGTTGGTACG -s Anc2.Anc2refChr1 40649 23 + 142988 ATAGGGCAATTCTGGTTGGTACG -s mr.mrrefChr3 66321 23 + 181027 ATGTGACTATTCAGGGTGGGGAG -s simCow_chr6.simCow.chr6 497696 10 + 602619 TTAGGGCAGT------------- -s simDog_chr6.simDog.chr6 487299 23 + 593897 ATATGACAATTCTGGTTGGTACG -s simHuman_chr6.simHuman.chr6 494054 23 + 601863 ATGGGGCAATTTAGGTTGGTACG -s simRat_chr6.simRat.chr6 525288 23 + 647215 ATGTGACTATTCAGGGTGGGGAG - -a -s simMouse_chr6.simMouse.chr6 513647 1 + 636262 G -s Anc0.Anc0refChr3 127682 1 + 222631 A -s Anc1.Anc1refChr6 161995 1 + 197743 A -s Anc2.Anc2refChr1 40672 1 + 142988 A -s mr.mrrefChr3 66344 1 + 181027 G -s simDog_chr6.simDog.chr6 487323 1 + 593897 A -s simHuman_chr6.simHuman.chr6 494077 1 + 601863 A -s simRat_chr6.simRat.chr6 525311 1 + 647215 G - -a -s simMouse_chr6.simMouse.chr6 513648 28 + 636262 GTCAAAATGGACTAGATGTAACCTTAAC -s Anc0.Anc0refChr3 127700 28 + 222631 GTTAAAATGGACTGGATACAACATTCAC -s Anc1.Anc1refChr6 162013 28 + 197743 GTTAAAATGGACTGGATACAACATTCAC -s Anc2.Anc2refChr1 40690 28 + 142988 GTTAAACAGGACCGGAGACAACATTCAC -s mr.mrrefChr3 66345 28 + 181027 GTCAAAATGGACTAGATACAACCTTAAC -s simCow_chr6.simCow.chr6 497719 28 + 602619 GTTAAACAGGACCGGAGACAACATTCAC -s simHuman_chr6.simHuman.chr6 494095 28 + 601863 GTGAAAATGGCCTGGGTACAACGTCCAC -s simRat_chr6.simRat.chr6 525312 28 + 647215 GTCAAAATGGACTAGATACAACCTTAAC - -a -s simMouse_chr6.simMouse.chr6 513676 12 + 636262 TTTAAATATGAA -s Anc0.Anc0refChr3 127730 12 + 222631 TTTAAATATGAG -s Anc1.Anc1refChr6 162043 12 + 197743 TTTAAATATGAG -s Anc2.Anc2refChr1 40720 12 + 142988 TTTAAATATGAG -s mr.mrrefChr3 66373 12 + 181027 TTTAAATATGAA -s simCow_chr6.simCow.chr6 497749 12 + 602619 TTTAAATATGAG -s simHuman_chr6.simHuman.chr6 494125 12 + 601863 TTTAAATATGAG -s simRat_chr6.simRat.chr6 525340 12 + 647215 TTTAAATATGAA - -a -s simMouse_chr6.simMouse.chr6 513688 22 + 636262 CTGTCCTTGAGTGTATTTGAAA -s Anc0.Anc0refChr3 127743 11 + 222631 CTGTCCTTGAG----------- -s Anc1.Anc1refChr6 162056 11 + 197743 CTGTCCTTGAG----------- -s Anc2.Anc2refChr1 40733 11 + 142988 CTCTCCTTGAG----------- -s mr.mrrefChr3 66385 22 + 181027 CTGTCCTTGAGTGTATTTGAAA -s simCow_chr6.simCow.chr6 497762 11 + 602619 CTCTCCTTGAG----------- -s simHuman_chr6.simHuman.chr6 494138 11 + 601863 CTGACCTCTAG----------- -s simRat_chr6.simRat.chr6 525352 22 + 647215 TTGTCCTTGAGTGCATTTGAAA - -a -s simMouse_chr6.simMouse.chr6 513710 28 + 636262 CGTTTCATTCTCTCAGTGCCCTAATGAA -s Anc0.Anc0refChr3 127754 24 + 222631 AGGTGCTTACTCTCAG----CTTTTGAA -s Anc1.Anc1refChr6 162067 24 + 197743 AGGTGCTTACTCTCAG----CTTTTGAA -s Anc2.Anc2refChr1 40744 24 + 142988 AGGTGTTTACTTTCAG----AATTTGGA -s mr.mrrefChr3 66407 28 + 181027 CGTTTCATTCTCTCAGTGCCCTAATGAA -s simCow_chr6.simCow.chr6 497774 24 + 602619 AGGTGTTTACTTTCAG----AATTTGGA -s simHuman_chr6.simHuman.chr6 494149 24 + 601863 AGGTGCTCACTCTCAG----CTTTTAAA -s simRat_chr6.simRat.chr6 525374 28 + 647215 CACTTCATTCTGTCAGTGCTCTACCGAA - -a -s simMouse_chr6.simMouse.chr6 513738 9 + 636262 CAGAAAATC -s Anc0.Anc0refChr3 127778 9 + 222631 TATCAGATT -s Anc1.Anc1refChr6 162091 9 + 197743 TATCAGATT -s Anc2.Anc2refChr1 40768 9 + 142988 TATCAGGTT -s mr.mrrefChr3 66435 9 + 181027 CAGAAAATC -s simCow_chr6.simCow.chr6 497805 9 + 602619 TATCAGGTT -s simHuman_chr6.simHuman.chr6 494173 9 + 601863 TATCACATT -s simRat_chr6.simRat.chr6 525402 9 + 647215 CAGAAAATC - -a -s simMouse_chr6.simMouse.chr6 513747 109 + 636262 ACCTATCATGTGGAATAAACTCCCCACAAGGCAGCATGTATGCCTGTGTATGCCACCACTTGCTCAGAAATGGTGTCTTTATCAACCCCCCACTGATTGCTATGTAATT -s Anc0.Anc0refChr3 127787 45 + 222631 AC-TAT----------------------------AGAGTATTGTTGTG---------------------------------TCAATCAG--ACTGTCTGCTATGTAACA -s Anc1.Anc1refChr6 162100 45 + 197743 AC-TAT----------------------------AGAGTATTGTTGTG---------------------------------TCAATCAG--ACTGTCTGCTATGTAACA -s Anc2.Anc2refChr1 40777 45 + 142988 AC-AAT----------------------------AGAGTATTGTTTCA---------------------------------TCAATCAG--ACTGTCTGCTATGTAACA -s mr.mrrefChr3 66444 105 + 181027 AC-TATCATGTGGAATAAACTCCC-ACAAGGCAGCGTGTATGGCTGTGTATGCCACCACTTGCTCAGAAATGGTGTCTTTATCAACCCG--ACTGTTTGCTATGTAACT -s simCow_chr6.simCow.chr6 497921 43 + 602619 AC-AAT----------------------------AGATTATTGTTACA---------------------------------TCAATCAG--ACTGT--GCTATGCAACA -s simDog_chr6.simDog.chr6 487332 37 + 593897 ------------------------------------AGTGTAGTTTCA---------------------------------TCAATC-G--ATTGTCTGATTTATAACA -s simHuman_chr6.simHuman.chr6 494182 45 + 601863 AC-TAT----------------------------AGAGTATTGTTGTG---------------------------------TCAATCAG--ACTGTCTGCTATGTTACA -s simRat_chr6.simRat.chr6 525411 105 + 647215 AC-TATCATGTGGAATAAATTCCT-GCAAGGCAATGTGTATGGCTGTGTATGTCCCCACTTGCTGAGAAGTGGTGTCTTTAGCAACCTG--ACTGTTTGCTACGTAGCT - -a -s simMouse_chr6.simMouse.chr6 513856 59 + 636262 TGCTTTGTGTATAAACACTCAATATCCTTGGCATTCTGTAGTATGTCTTGGTTCATTTC -s Anc0.Anc0refChr3 127843 58 + 222631 TCCTTTGCATAC-TACACCCAATGACCCTGGTGGTATCCTATTTATCTTGGTTTCTTTA -s Anc1.Anc1refChr6 162156 58 + 197743 TCCTTTGCATAC-TACACCCAATGACCCTGGTGGTATCCTATTTATCTTGGTTTCTTTA -s Anc2.Anc2refChr1 40833 58 + 142988 CCCTTTGCATAC-TACACCCAATGAGCCTGGTGGTATCCTATTTATCTTGGTTTCATTA -s mr.mrrefChr3 66560 59 + 181027 TGCTTTGTGTATAAACACTCAATATCCTTGGTATTCTGTAGTATGTCTTGGTTCATTTC -s simCow_chr6.simCow.chr6 497975 58 + 602619 CTCTTTGCATAC-TACATTCAATAAACCTGGTGATATCTGATCCAACTTGGTTTCCTTA -s simDog_chr6.simDog.chr6 487380 58 + 593897 CCTTTTGCATAC-TACACCCACTGAGCCTGGTGGTATCCTATTTATTGGGGTTTCATTA -s simHuman_chr6.simHuman.chr6 494238 58 + 601863 TCCTTTGCATAC-CACACCCAATGACCCTGGTGGTTTCCTCTTTACCTTGGTTTCTCTT -s simRat_chr6.simRat.chr6 525527 58 + 647215 TGTTTTGTGTATAAACACTCAATATCCTTGGTATTCTGTAGTATGTCTTGGTTCACTT- - -a -s simMouse_chr6.simMouse.chr6 513915 12 + 636262 TTCGAATAGCTG -s Anc0.Anc0refChr3 127901 12 + 222631 TACTATTATCTA -s Anc1.Anc1refChr6 162214 12 + 197743 TACTATTATCTA -s Anc2.Anc2refChr1 40891 12 + 142988 AATTATTATCTA -s mr.mrrefChr3 66619 12 + 181027 TTCGAATAGCTG -s simCow_chr6.simCow.chr6 498036 12 + 602619 CGTTATTATCTG -s simDog_chr6.simDog.chr6 487438 12 + 593897 AATTATTATCTA -s simHuman_chr6.simHuman.chr6 494296 12 + 601863 TACTATGACCTA -s simRat_chr6.simRat.chr6 525585 1 + 647215 -----------G - -a -s simMouse_chr6.simMouse.chr6 513927 20 + 636262 CTCTGTTATATACCATCTCA -s Anc0.Anc0refChr3 127914 20 + 222631 CTCTGTTATGTACCATCCCC -s Anc1.Anc1refChr6 162227 20 + 197743 CTCTGTTATGTACCATCCCC -s Anc2.Anc2refChr1 40904 20 + 142988 CTCTGTTATGTACCATCCCC -s mr.mrrefChr3 66631 20 + 181027 CTCTGTTATATACCATCTCC -s simCow_chr6.simCow.chr6 498049 20 + 602619 ACCTGTTATGCACCATTCTC -s simDog_chr6.simDog.chr6 487451 18 + 593897 CTCTGTT--GTACCTTCCCC -s simHuman_chr6.simHuman.chr6 494309 20 + 601863 CTCTGCTATGTACCATCACC -s simRat_chr6.simRat.chr6 525586 20 + 647215 CTCTGTTATATACTATCTCC - -a -s simMouse_chr6.simMouse.chr6 513947 35 + 636262 AATATCTAATATGAATATAGTAGCATCTATGTGTT -s Anc0.Anc0refChr3 127944 33 + 222631 GAACACTAATATGGATATCACA--ATCTATTTATT -s Anc1.Anc1refChr6 162257 33 + 197743 GAACACTAATATGGATATCACA--ATCTATTTATT -s Anc2.Anc2refChr1 40934 33 + 142988 GAACACTAATATGGATATCACA--ATCTATTAATT -s mr.mrrefChr3 66661 35 + 181027 AAAATCTAATATGAATATAGTAGCATCTATGTGTT -s simCow_chr6.simCow.chr6 498079 33 + 602619 GAACATTAATATGGATAACAGG--ATCTATGAACT -s simDog_chr6.simDog.chr6 487479 33 + 593897 GAACACTAATATGCTTATCGCA--ACTTATTAATT -s simHuman_chr6.simHuman.chr6 494339 29 + 601863 GAAGCCTAATATGGATATCACA------ATCTATT -s simRat_chr6.simRat.chr6 525616 35 + 647215 AAAAATTAATATGAATATAGTAGCATCTATGTGTT - -a -s simMouse_chr6.simMouse.chr6 513982 33 + 636262 GTGCATATTATGTTGACTGTATGTATTAACATG -s Anc0.Anc0refChr3 127977 32 + 222631 ATGTATATTCTGTTGCCTATACG-GTTAACATA -s Anc1.Anc1refChr6 162290 32 + 197743 ATGTATATTCTGTTGCCTATACG-GTTAACATA -s Anc2.Anc2refChr1 40967 32 + 142988 ATGTATACTCTGTTGCCTATTCA-TTTAACATA -s mr.mrrefChr3 66696 33 + 181027 GTGCATATTATGTTGACTATATGTGTTAACATG -s simCow_chr6.simCow.chr6 498112 32 + 602619 GTGTATACTCTGTTGCCTATTCA-TTTGACATA -s simDog_chr6.simDog.chr6 487514 32 + 593897 ATGTATGCTCTATTGCCCATTCA-TTTAACATA -s simHuman_chr6.simHuman.chr6 494368 32 + 601863 ATGTATATTCTGTTGTCTATACG-GTTAGCATA -s simRat_chr6.simRat.chr6 525651 33 + 647215 GTGCATATTAGGTTGACTATATGTGTTAACATG - -a -s simMouse_chr6.simMouse.chr6 514015 123 + 636262 CCCAGCCTATGTCCCAACTAGGATCAAAGGATGGAGCCTTAATGAAAGGACCGCTAGAACCTTAATAAAGCCTTATTTGATAGAATAGGTATACCTGGCTTCCTATTTGCAGATAAATGAGTG -s Anc0.Anc0refChr3 128009 94 + 222631 CCATTCCCATGTCCAA--------------ATGGAGTCTAAGTAA----------AGAGCCTTTTTATAGCCTTATTTCATAGAAGAGATCTTACTGGCCT-CCATTTGCAGATAAC----TA -s Anc1.Anc1refChr6 162322 95 + 197743 CCATTCCCATGTCCAA--------------ATGGAGTCTAAGTAA----------AGAGCCTTTTTATAGCCTTATTTCATAGAAGAGATCTTACTGGCCTCCCATTTGCAGATAAC----TA -s Anc2.Anc2refChr1 40999 94 + 142988 CCATTCCCACGTCCAA--------------CTAGGGTCTAAGGAT----------TGAGCCTTTTTATAGTCTTGTTTCATAGAAGAAATCTTATTGGCCT-CCATTTGCAGATAAC----TA -s mr.mrrefChr3 66729 123 + 181027 CCCAGCCCATGTCCCAACTAGGATCAAAGGATGGAGCCTTAATGAAAGGACCGCTAGAGCCTTAATAAAGCCTTATTTGATAGAATAGGTATACCTGGCTTCCTATTTGCAGATAAATGAGTG -s simCow_chr6.simCow.chr6 498144 88 + 602619 CCATTCCCACGTCCGA--------------CTAAGATCAAAGGAT----------TGAGCCTTAATATAGTTTTGTTTCATGGAAGAAGTCTTATTGGCCG-CCAGTTGCAGA---------- -s simDog_chr6.simDog.chr6 487546 92 + 593897 CCATTCCCACATGCAA--------------CAAG-GACTAGG-AT----------TGAGCCTTTTTGCACTCCTGTTTTGTAGAACAAATCTTATTGGCCT-CCATTTGCAGATAAC----TA -s simHuman_chr6.simHuman.chr6 494400 95 + 601863 CCACTCCCATGTCCTA--------------ATGGAGTCTAAGTAA----------AGAGCCTTGGTATAGCCTCATTTCATCATTGAGATCTGACTGGCATCCCTTTTGCACATAAC----TA -s simRat_chr6.simRat.chr6 525689 118 + 647215 CCCAGCCCATGTCCCATCTAGGATCAAAGAATAGAGCCTTACTGAAGGGGCCGCTAGAGCCTTAATAAAGCCTTATTCGATAG-----GTATACCTGGCTTCCTATTTGCAGATAAATGAGTG - -a -s simMouse_chr6.simMouse.chr6 514138 26 + 636262 ATGGATCAACACCCCAGAGCCCTAGA -s Anc0.Anc0refChr3 128103 25 + 222631 ATAGGTCAATAGCTCAAAGCCC-AGA -s Anc1.Anc1refChr6 162417 25 + 197743 ATAGGTCAATAGCTCAAAGCCC-AGA -s Anc2.Anc2refChr1 41093 25 + 142988 CTAGGTCAATAGCTTGAAGCCC-AGA -s mr.mrrefChr3 66852 26 + 181027 ATGGGTCAACAGCCCAGAGCCCTAGA -s simCow_chr6.simCow.chr6 498232 9 + 602619 ----------------CAGCCC-AGA -s simDog_chr6.simDog.chr6 487638 25 + 593897 CTAGGTCAATAGCTTGAAGCCC-AGA -s simHuman_chr6.simHuman.chr6 494495 25 + 601863 ATAGGTTAATAGTTCATAGCCA-AGA -s simRat_chr6.simRat.chr6 525808 26 + 647215 AGGGGTCACCAGCCCAGAGCCCTAGA - -a -s simMouse_chr6.simMouse.chr6 514164 53 + 636262 CGATTAGCAGGTTAAAAAGGGGTATGATTAAAGACTTGTTCATTGATTTTGAC -s Anc0.Anc0refChr3 128130 52 + 222631 TGATTGTCAGGATAAGAAGGGGTATGA-TAATGACTTATTGATGCATTATGAC -s Anc1.Anc1refChr6 162444 52 + 197743 TGATTGTCAGGATAAGAAGGGGTATGA-TAATGACTTATTGATGCATTATGAC -s Anc2.Anc2refChr1 41120 52 + 142988 TGGTTGTTAGGATAAGAAGGGGTATGA-TTATGACTTAATGATGCATTATGAC -s mr.mrrefChr3 66880 53 + 181027 TGATTGGCAGGTAAGAAAGGGGTATGATTAAAGACTTGTTCATTGATTTTGAC -s simCow_chr6.simCow.chr6 498243 52 + 602619 TGGTTGTTAAGATGAGAAAGGGCATGA-TCATGAATTAATGATTCATTATGAC -s simDog_chr6.simDog.chr6 487665 51 + 593897 TGGCTGTTAGGGTAAGAAGGGGTATGA-ATATGACTGA-TCATGCATAGTGAC -s simHuman_chr6.simHuman.chr6 494522 52 + 601863 TGATTGTCAGGATAAGAAGGGGTATGA-TAAGTACTTCTTGATCTATTATGAC -s simRat_chr6.simRat.chr6 525836 53 + 647215 TGGTTGGAGGATAAGAAAAGGTAATGATTAAAGACTTGTTCATTGACTTTAAC - -a -s simMouse_chr6.simMouse.chr6 514217 8 + 636262 GAGAATAA -s Anc0.Anc0refChr3 128184 8 + 222631 CAGAATAA -s Anc1.Anc1refChr6 162498 8 + 197743 CAGAATAA -s Anc2.Anc2refChr1 41174 8 + 142988 CAGAATAA -s mr.mrrefChr3 66935 8 + 181027 GAGAATAA -s simCow_chr6.simCow.chr6 498297 8 + 602619 CAGAATAA -s simDog_chr6.simDog.chr6 487718 8 + 593897 TAGAATAA -s simHuman_chr6.simHuman.chr6 494576 5 + 601863 ---CACAA -s simRat_chr6.simRat.chr6 525891 8 + 647215 GAGAATAA - -a -s simMouse_chr6.simMouse.chr6 514225 26 + 636262 CACTCTAGGCAGACTTATAAATTGAT -s Anc0.Anc0refChr3 128193 26 + 222631 AATTCTAGGCACACTTATAAATTAAT -s Anc1.Anc1refChr6 162507 26 + 197743 AATTCTAGGCACACTTATAAATTAAT -s Anc2.Anc2refChr1 41183 26 + 142988 AATTCTAGGCACACTTACAAATTAAT -s mr.mrrefChr3 66944 26 + 181027 CACTCTAGGCAGACTTATAAATTGAT -s simCow_chr6.simCow.chr6 498306 26 + 602619 AATTCTAGGCACACTTACAAATTAAT -s simDog_chr6.simDog.chr6 487727 26 + 593897 AATTCTAGGCACAATTACAAATTAAT -s simHuman_chr6.simHuman.chr6 494582 25 + 601863 AATTCTAGGCACACGTATAAAGT-AC -s simRat_chr6.simRat.chr6 525900 26 + 647215 CACTCTAGGCAGACCTATAAATCAAT - -a -s simMouse_chr6.simMouse.chr6 514251 4 + 636262 ACTT -s Anc0.Anc0refChr3 128219 4 + 222631 ATCC -s Anc1.Anc1refChr6 162533 4 + 197743 ATCC -s Anc2.Anc2refChr1 41209 4 + 142988 ATCC -s mr.mrrefChr3 66970 4 + 181027 ATTT -s simCow_chr6.simCow.chr6 498341 4 + 602619 ATCC -s simDog_chr6.simDog.chr6 487753 4 + 593897 ATCC -s simHuman_chr6.simHuman.chr6 494607 4 + 601863 ATCC -s simRat_chr6.simRat.chr6 525926 4 + 647215 ATTT - -a -s simMouse_chr6.simMouse.chr6 514255 13 + 636262 ATTCTCACTATCA -s Anc0.Anc0refChr3 128223 10 + 222631 AGTCTTACCA--- -s Anc1.Anc1refChr6 162537 10 + 197743 AGTCTTACCA--- -s Anc2.Anc2refChr1 41215 10 + 142988 GATCTTACCA--- -s mr.mrrefChr3 66974 10 + 181027 AGTCTTACTA--- -s simCow_chr6.simCow.chr6 498347 10 + 602619 AGTTTTACCA--- -s simDog_chr6.simDog.chr6 487759 10 + 593897 GATCTTACCA--- -s simHuman_chr6.simHuman.chr6 494611 10 + 601863 AGGCTTACCA--- -s simRat_chr6.simRat.chr6 525930 10 + 647215 AGATTTGCTA--- - -a -s simMouse_chr6.simMouse.chr6 514268 9 + 636262 GGTACATGG -s Anc0.Anc0refChr3 93654 9 - 222631 GCTAAACAG -s Anc1.Anc1refChr6 34446 9 - 197743 GCTAAACAG -s Anc2.Anc2refChr1 101014 9 - 142988 GCTTAACAG -s mr.mrrefChr3 113616 9 - 181027 GCTACACAG -s simDog_chr6.simDog.chr6 105391 9 - 593897 GCTTAACAG -s simHuman_chr6.simHuman.chr6 106461 9 - 601863 GCTAAACAG -s simRat_chr6.simRat.chr6 120863 9 - 647215 GCTATACAG - -a -s simMouse_chr6.simMouse.chr6 514277 41 + 636262 TGTACACTATGACAGAGGGTATATTCCTCATATGACAATTG -s Anc0.Anc0refChr3 93663 41 - 222631 AGAAGACTATTCCAGAGCGTAGAGCTCTCATATGACAGTTG -s Anc1.Anc1refChr6 34455 41 - 197743 AGAAGACTATTCCAGAGCGTAGAGCTCTCATATGACAGTTG -s Anc2.Anc2refChr1 101023 41 - 142988 AGAAGACTATTTCAGCGCGAAGAGCTCTCATATGACAATTG -s mr.mrrefChr3 113625 41 - 181027 TGTACACTATGCCAGAGGGTAGATTCCTCATATGACAGTTG -s simCow_chr6.simCow.chr6 136542 33 + 602619 AGAAGATGGTT-------GAAGAGCTCTCATATG-CAATTG -s simCow_chr6.simCow.chr6 103430 33 - 602619 AGAAGATGGTT-------GAAGAGCTATCATATG-CAATTG -s simDog_chr6.simDog.chr6 105401 34 - 593897 AGAAAACTATTTCAGCGCCCAGA-------TATGACAATTG -s simHuman_chr6.simHuman.chr6 106470 41 - 601863 AGAAGACTACACCAGAGAGTAGAGCTCTCGTAGGACAGTTG -s simRat_chr6.simRat.chr6 120872 41 - 647215 TGTACGCTATGCCAGAGGGTGGATTCCTCATATGACAGTTG - -a -s simMouse_chr6.simMouse.chr6 514318 2 + 636262 AC -s Anc0.Anc0refChr3 93704 2 - 222631 GC -s Anc1.Anc1refChr6 34496 2 - 197743 GC -s Anc2.Anc2refChr1 101064 2 - 142988 GC -s mr.mrrefChr3 113666 2 - 181027 AC -s simCow_chr6.simCow.chr6 103463 2 - 602619 GC -s simDog_chr6.simDog.chr6 105435 2 - 593897 AC -s simHuman_chr6.simHuman.chr6 106511 2 - 601863 GC -s simRat_chr6.simRat.chr6 120913 2 - 647215 AC - -a -s simMouse_chr6.simMouse.chr6 514320 22 + 636262 TTTGACATTCTGAAGTTTAGTG -s Anc0.Anc0refChr3 93708 21 - 222631 TTGCACATGTGGAAGCCTAG-A -s Anc1.Anc1refChr6 34500 21 - 197743 TTGCACATGTGGAAGCCTAG-A -s Anc2.Anc2refChr1 101068 21 - 142988 TTGCACATGTGGAAGCCTAT-A -s mr.mrrefChr3 113668 22 - 181027 TTTCACATGTTGAAGCTTAGTG -s simCow_chr6.simCow.chr6 103467 21 - 602619 TTGCACATGTGGAAGCCTAC-A -s simDog_chr6.simDog.chr6 105439 21 - 593897 TTGCACATGTCCAAGCTTAT-A -s simHuman_chr6.simHuman.chr6 106515 21 - 601863 TTGCACACGTGGAAGCCTAG-A -s simRat_chr6.simRat.chr6 120915 22 - 647215 TTTCACATGTTGAAGCTTAGTG - -a -s simMouse_chr6.simMouse.chr6 514342 27 + 636262 CCGTAGACCTCCTACTGTTAATATCCT -s Anc0.Anc0refChr3 93729 26 - 222631 ACATATGCCTCC-ACTGTTAATGTACC -s Anc1.Anc1refChr6 34521 26 - 197743 ACATATGCCTCC-ACTGTTAATGTACC -s Anc2.Anc2refChr1 101092 26 - 142988 AAATATGACTCC-ATTGTTAATGAACC -s mr.mrrefChr3 113690 27 - 181027 CCATATGCCTCCTACTGTTAATATCCT -s simCow_chr6.simCow.chr6 103491 3 - 602619 ATA------------------------ -s simDog_chr6.simDog.chr6 105463 26 - 593897 AAATATGACTCC-ATTGTTAATGAACC -s simHuman_chr6.simHuman.chr6 106536 26 - 601863 ACATATGCTTCA-ACTGTTATTGTACC -s simRat_chr6.simRat.chr6 120937 18 - 647215 CTATATGCCTCCTACTGT--------- - -a -s simMouse_chr6.simMouse.chr6 514369 20 + 636262 TCGGTATTGAGCCACTGCGT -s Anc0.Anc0refChr3 93755 19 - 222631 TCTGTACTGAGCAT-TCCGT -s Anc1.Anc1refChr6 34547 19 - 197743 TCTGTACTGAGCAT-TCCGT -s Anc2.Anc2refChr1 101118 19 - 142988 TCTGCACTGCACAT-TCCTT -s mr.mrrefChr3 113717 20 - 181027 TCGGTATTGAGCCACTGCGT -s simDog_chr6.simDog.chr6 105532 19 - 593897 TCTGCACTGCACAT-TCCTT -s simHuman_chr6.simHuman.chr6 106562 19 - 601863 TCTGTACAGAGCTG-TACGT -s simRat_chr6.simRat.chr6 120955 14 - 647215 ------TTGAGACCTTGCAT - -a -s simMouse_chr6.simMouse.chr6 514389 8 + 636262 GTGACCTT -s Anc0.Anc0refChr3 93774 8 - 222631 GTAACATT -s Anc1.Anc1refChr6 34566 8 - 197743 GTAACATT -s Anc2.Anc2refChr1 101137 8 - 142988 GCAATACT -s mr.mrrefChr3 113737 8 - 181027 GTAACCTT -s simDog_chr6.simDog.chr6 105553 8 - 593897 GCAATACT -s simHuman_chr6.simHuman.chr6 106581 8 - 601863 GTAACATT -s simRat_chr6.simRat.chr6 120969 8 - 647215 GTAACCAT - -a -s simMouse_chr6.simMouse.chr6 514397 12 + 636262 CTATCCAGAGTA -s Anc0.Anc0refChr3 93784 11 - 222631 -TACTCAATGGG -s Anc1.Anc1refChr6 34576 12 - 197743 CTACTCAATGGG -s Anc2.Anc2refChr1 101147 11 - 142988 -TACTCGATGGG -s mr.mrrefChr3 113745 12 - 181027 CTATTCAGTGTA -s simDog_chr6.simDog.chr6 105563 11 - 593897 -TACTCGATGGG -s simHuman_chr6.simHuman.chr6 106593 12 - 601863 CCAATCAATGCG -s simRat_chr6.simRat.chr6 120977 12 - 647215 CTATTCAGTGTA - -a -s simMouse_chr6.simMouse.chr6 514409 178 + 636262 TCCTACATTACTTACCAAAGCAAGATGTAAGAAAGCTTGTGGGTGTACTCCCTAGATGTATCTTAACACTCTTTAGATAGATTGGCAAATCATTATATCAACAAATTAGCTGCAACTGCAGTTAGTGTCATAAAATCAAGTGATGGTGTCCCTGTCACTGTAGGCTTGGTGATCCTTC -s Anc0.Anc0refChr3 93796 39 - 222631 TTCTTCATTAGTTCCCGCAGCAAGACATAAGAA----------------------------------------------------------------------------------------------------------------------------------------TA---CTTA -s Anc1.Anc1refChr6 34589 39 - 197743 TTCTTCATTAGTTCCCGCAGCAAGACATAAGAA----------------------------------------------------------------------------------------------------------------------------------------TA---CTTA -s Anc2.Anc2refChr1 101159 39 - 142988 TTTCCCATTAGTTCCCGCAACAAGACATAAGAA----------------------------------------------------------------------------------------------------------------------------------------TG---TCTC -s mr.mrrefChr3 113758 170 - 181027 TCCTTCATTAGTTCCCACAGCAAGATGTAAGAAAGCTTGTGGGTGTACTCCCTAGATGTATCTTAACACTCTTTAGATAGATTGGCAAATCATTATATCAACAAATTAGCTGCAACTGCAGTTAGTGTCATAAAATCAAGTGATGGTGTCCC-----CTGTAGGCTTGGTA---CTTA -s simDog_chr6.simDog.chr6 105575 39 - 593897 TTTCCCATTAGTTCCCGCAACAAGACATAAGAA----------------------------------------------------------------------------------------------------------------------------------------TG---TCTC -s simHuman_chr6.simHuman.chr6 106606 39 - 601863 TTCTTTATTAGTTCCCTCAGCAAGACTTAAGAA----------------------------------------------------------------------------------------------------------------------------------------TA---CTTA -s simRat_chr6.simRat.chr6 120990 170 - 647215 TCCTTCATTAGTTCCCACAGCAAGATGTAAGAATGTTTTCAGGTATACTCCCTATATGTATATTAATACTCTTTAGATGGGTTGGCAACATCTTATATCAGCAAATTAGCTGCAACTGCAGTTAGTATCAGAAAATCAAATGACAGTGTCCC-----CTGCAGGCTTGGCA---TTTA - -a -s simMouse_chr6.simMouse.chr6 514587 42 + 636262 TCAGTTACTTACCCTACACACATATCAAGAAGAAAGCACTGG -s Anc0.Anc0refChr3 94279 39 - 222631 TGAATTACTTTC---CCCCTCACATCTAGAAGAAGGTACTGG -s Anc1.Anc1refChr6 35072 39 - 197743 TGAATTACTTTC---CCCCTCACATCTAGAAGAAGGTACTGG -s Anc2.Anc2refChr1 101643 39 - 142988 TGAATTACTTAC---CCCCTCACATCTAGAAGAAGGTACTGG -s mr.mrrefChr3 113928 39 - 181027 TCAGTTACTTTC---ACACACACATCAAGAAGAAAGCACTGG -s simCow_chr6.simCow.chr6 104145 39 - 602619 TGAATTAATGAC---CTCCTAACATCCAGAAGAGGGCACAGG -s simDog_chr6.simDog.chr6 106007 39 - 593897 TCAATTGCCTAC---CCCCTCACATTTAGAAGAAAATACTGG -s simHuman_chr6.simHuman.chr6 107093 39 - 601863 TGAATTACTTTT---CCTCTCACATCTAGAAGAAGGTACTGG -s simRat_chr6.simRat.chr6 121160 39 - 647215 TCAGTTACTTTC---GCACACACATCCAGAATGAAGCACTGG - -a -s simMouse_chr6.simMouse.chr6 514629 47 + 636262 AAAAATCTGAGGTGATGATGTTGAGTCTCTAGGAGAGATAATAGCGG -s Anc0.Anc0refChr3 94323 35 - 222631 AAAAATCTGATGTGGTGATCTTGAA-CTTT-----------TAGTGT -s Anc1.Anc1refChr6 35116 39 - 197743 AAAAATCTGATGTGGTGATCTTGAA-CTTTAG-------AATAGTGT -s Anc2.Anc2refChr1 101687 35 - 142988 AAAAATCTGATGTGGTGATCTTGAA-CTTT-----------CAGGGT -s mr.mrrefChr3 113967 47 - 181027 AAAAATCTGATGTGATGATGTTGAGTCTCTAGGAGAGATAATAGTGG -s simCow_chr6.simCow.chr6 104189 34 - 602619 AAAAATCTGAT-TGGTGATCTTGAA-CATT-----------CAGGGT -s simDog_chr6.simDog.chr6 106051 35 - 593897 AAAAATCTCAGGTGGTGATCTAGAA-CTTT-----------CAGGGG -s simHuman_chr6.simHuman.chr6 107137 39 - 601863 AAAAATCTGATGTGGCGATCTTGAA-CTTTAG-------AATAGTGT -s simRat_chr6.simRat.chr6 121199 47 - 647215 AAAAATCTGATATGATGATGTTGAGTCTCTAGGAGCGATAATAGTGG - -a -s simMouse_chr6.simMouse.chr6 514676 8 + 636262 CAATGGCA -s Anc0.Anc0refChr3 94358 8 - 222631 CAATAGCA -s Anc1.Anc1refChr6 35155 8 - 197743 CAATAGCA -s Anc2.Anc2refChr1 101722 8 - 142988 CAATAGTA -s mr.mrrefChr3 114014 8 - 181027 CAATGGCA -s simCow_chr6.simCow.chr6 104223 8 - 602619 CAATAGTA -s simDog_chr6.simDog.chr6 106087 8 - 593897 TGATAGTA -s simHuman_chr6.simHuman.chr6 107176 8 - 601863 CAATAGCT -s simRat_chr6.simRat.chr6 121246 8 - 647215 CAATGGCA - -a -s simMouse_chr6.simMouse.chr6 514684 10 + 636262 TGACTCACAC -s Anc0.Anc0refChr3 94366 10 - 222631 TGTCTCACCC -s Anc1.Anc1refChr6 35163 10 - 197743 TGTCTCACCC -s Anc2.Anc2refChr1 101731 10 - 142988 TGTCTCACCC -s mr.mrrefChr3 114022 10 - 181027 TGACTCACAC -s simCow_chr6.simCow.chr6 104232 10 - 602619 CATTTCACCA -s simDog_chr6.simDog.chr6 106096 10 - 593897 TGTCTCACAC -s simHuman_chr6.simHuman.chr6 107184 7 - 601863 ---CTCACCC -s simRat_chr6.simRat.chr6 121254 10 - 647215 TCACTCGGAT - -a -s simMouse_chr6.simMouse.chr6 514694 11 + 636262 AGCCACACTGA -s Anc0.Anc0refChr3 94388 10 - 222631 -GCCACCCAGA -s Anc1.Anc1refChr6 35185 11 - 197743 AGCCACCCAGA -s Anc2.Anc2refChr1 101753 10 - 142988 -GCCAATTAGA -s mr.mrrefChr3 114032 11 - 181027 AGCCACCCTGA -s simCow_chr6.simCow.chr6 104254 8 - 602619 -G--AATTAGC -s simDog_chr6.simDog.chr6 106118 10 - 593897 -GCCCATTAAA -s simHuman_chr6.simHuman.chr6 107231 11 - 601863 AGCCACCCAGA -s simRat_chr6.simRat.chr6 121264 11 - 647215 AGCCATCCTGA - -a -s simMouse_chr6.simMouse.chr6 514705 1 + 636262 C -s Anc0.Anc0refChr3 128977 1 + 222631 C -s Anc1.Anc1refChr6 163297 1 + 197743 C -s Anc2.Anc2refChr1 41974 1 + 142988 T -s mr.mrrefChr3 67411 1 + 181027 C -s simDog_chr6.simDog.chr6 488506 1 + 593897 T -s simHuman_chr6.simHuman.chr6 495402 1 + 601863 C -s simRat_chr6.simRat.chr6 526355 1 + 647215 C - -a -s simMouse_chr6.simMouse.chr6 514706 6 + 636262 AATGCA -s Anc0.Anc0refChr3 128978 6 + 222631 AATGCA -s Anc1.Anc1refChr6 163298 6 + 197743 AATGCA -s Anc2.Anc2refChr1 41975 6 + 142988 AATGCA -s mr.mrrefChr3 67412 6 + 181027 AATGCA -s simCow_chr6.simCow.chr6 466077 6 - 602619 AATGCA -s simCow_chr6.simCow.chr6 499189 6 + 602619 AATGCA -s simDog_chr6.simDog.chr6 488507 6 + 593897 AATATA -s simHuman_chr6.simHuman.chr6 495403 6 + 601863 AATGCA -s simRat_chr6.simRat.chr6 526356 6 + 647215 AATGCA - -a -s simMouse_chr6.simMouse.chr6 514712 20 + 636262 ACTAAGTCCTGGTGGCTACA -s Anc0.Anc0refChr3 128988 20 + 222631 ACTAAGTCCTGGGGACCAGG -s Anc1.Anc1refChr6 163308 20 + 197743 ACTAAGTCCTGGGGACCAGG -s Anc2.Anc2refChr1 41985 20 + 142988 ACTAAGCCCTGGGAACCAGG -s mr.mrrefChr3 67418 20 + 181027 ACTAAGTCCTGGTGACTACA -s simCow_chr6.simCow.chr6 466087 20 - 602619 GCTTAGCCCTGGGAACTACA -s simCow_chr6.simCow.chr6 499199 20 + 602619 ACTTAGCCCTGGGAACTAGG -s simDog_chr6.simDog.chr6 488517 20 + 593897 ACTAAGGCCTGGGAACCAGG -s simHuman_chr6.simHuman.chr6 495414 20 + 601863 AATAAGTCCTGGGGACCAGG -s simRat_chr6.simRat.chr6 526362 14 + 647215 ACTAAGTC------ACTACA - -a -s simMouse_chr6.simMouse.chr6 514732 66 + 636262 TGGGGTGGTAATTTAGATCTAGGGTCTTCATACTCTTGCCTTCCAAGATTGACTTGACCATTATCA -s Anc0.Anc0refChr3 129008 58 + 222631 CAGGACAATAATATAGCTCTAGGGTGCTAACACTCTTACCTTACAGACATGCCT--------GTCA -s Anc1.Anc1refChr6 163328 58 + 197743 CAGGACAATAATATAGCTCTAGGGTGCTAACACTCTTACCTTACAGACATGCCT--------GTCA -s Anc2.Anc2refChr1 42005 58 + 142988 CAGGACAATAATATAGCTCTAGGGTGCTAACACTCTCACCTTAAAGACATGCCT--------GTCA -s mr.mrrefChr3 67438 58 + 181027 CAGGATAGTAATATAGATCTAGGGTGTTCATACTCTTGCCTTCCAAGATTGACT--------ATCA -s simCow_chr6.simCow.chr6 466107 58 - 602619 CAAGATAATACTTTAACTCCAGGGTGCTAACACTCTCACCTTAAAGACATGCCT--------GTTA -s simCow_chr6.simCow.chr6 499219 58 + 602619 CAAGATAATACTATAACTCTAGGGTGCTAACACTCTCACCTTAAAGACATGCCT--------GTTA -s simDog_chr6.simDog.chr6 488539 57 + 593897 CAGGCCAGTAATATAGGTCGATGGTGCTAA-ACTCTCACCTTAAAAACATAGCT--------GTCA -s simHuman_chr6.simHuman.chr6 495434 44 + 601863 CAGGACAATAATATAGCTCTAAGGTGCCAACACTCTTCAGCTAC---------------------- -s simRat_chr6.simRat.chr6 526376 58 + 647215 CAGGATAGTAATATAGATCTAGGACGTTCATACTTTTGCCTTCCAAGAATGACC--------ATTG - -a -s simMouse_chr6.simMouse.chr6 514798 17 + 636262 CCCAGGGAAACTTTACC -s Anc0.Anc0refChr3 129066 17 + 222631 TACCAAGAAACTCTATT -s Anc1.Anc1refChr6 163386 17 + 197743 TACCAAGAAACTCTATT -s Anc2.Anc2refChr1 42065 17 + 142988 TACCAAGAAACTCTATT -s mr.mrrefChr3 67496 17 + 181027 CCCAGGGAAACTCTACC -s simCow_chr6.simCow.chr6 466167 17 - 602619 TACCAAGAAAATCTATT -s simCow_chr6.simCow.chr6 499279 17 + 602619 TACCAAGAAAATCTATT -s simDog_chr6.simDog.chr6 488598 17 + 593897 TACCAAGAAACTTTATT -s simHuman_chr6.simHuman.chr6 495478 13 + 601863 ----AAGGCACTCTATT -s simRat_chr6.simRat.chr6 526434 17 + 647215 CCCAGGGAAACTCTACC - -a -s simMouse_chr6.simMouse.chr6 514815 19 + 636262 CAACTACAACTCTTGTAGT -s Anc0.Anc0refChr3 129083 19 + 222631 TAGTCCCCAGTCTTGTAAT -s Anc1.Anc1refChr6 163403 19 + 197743 TAGTCCCCAGTCTTGTAAT -s Anc2.Anc2refChr1 42086 19 + 142988 TATTCCCCAGTCTTGTAAT -s mr.mrrefChr3 67513 19 + 181027 CAGTTACAACTCTTGTAAT -s simCow_chr6.simCow.chr6 466188 19 - 602619 TATTCCCCCATCATGTGAA -s simCow_chr6.simCow.chr6 499300 19 + 602619 TGTTCCCCCGTCATGTGAA -s simDog_chr6.simDog.chr6 488617 17 + 593897 --CTTCCCAGTCTTGTAAT -s simHuman_chr6.simHuman.chr6 495491 19 + 601863 TAGTCCCTAGTCTTGTAAT -s simRat_chr6.simRat.chr6 526451 19 + 647215 CAGTTGCAACTCTTGTAAA - -a -s simMouse_chr6.simMouse.chr6 514834 66 + 636262 TCCACTCTTGTAGTTCAGACAGGCTTGACTCCAGGATCTAAGCTAACTGTGGAAAGTTAATATGTT -s Anc0.Anc0refChr3 129105 52 + 222631 CC--------------AGACAGACTTGTCTTCAGGGTCTAACCTAGCTGCAAAAAGTAAACATGAT -s Anc1.Anc1refChr6 163425 52 + 197743 CC--------------AGACAGACTTGTCTTCAGGGTCTAACCTAGCTGCAAAAAGTAAACATGAT -s Anc2.Anc2refChr1 42108 52 + 142988 CC--------------AGACAGACTTGTCTTCAGGGTCTAACCTAGCAGCAAAAAGTAAATATGAC -s mr.mrrefChr3 67532 52 + 181027 TC--------------AGACAGGCTTGACTCCAGGGTCTAAGCTAACTGCAGAAAGTTAACATGTT -s simCow_chr6.simCow.chr6 466213 52 - 602619 TC--------------AGACAGACTAGTCTTCACAGTCTCACCTAGAAGCAAACAGTAAATACGAC -s simCow_chr6.simCow.chr6 499322 51 + 602619 AT--------------CT-CAGACTGGTCTTCACAGTCTAACCTAGAAGCAAACAGTAAATATGAC -s simDog_chr6.simDog.chr6 488637 52 + 593897 CC--------------AGACAGACTTGGCTTCAGGGTGGAACTTACCAGCAAAAAGTATATATGGT -s simHuman_chr6.simHuman.chr6 495513 52 + 601863 CC--------------AGACAGACTTGTCTGCAGGGTCTAACCTAGCTGCAAAAAGTAAACAGGAT -s simRat_chr6.simRat.chr6 526470 52 + 647215 TC--------------AGACAGGATTGACTCCAGGGTCTAGGGCAACTGCAGAGAGTTAACATGTT - -a -s simMouse_chr6.simMouse.chr6 514900 24 + 636262 TAAACACTTGGGATGATTGCCTAA -s Anc0.Anc0refChr3 129157 24 + 222631 TAAACGGATGGGATTATTGCCTGC -s Anc1.Anc1refChr6 163477 24 + 197743 TAAACGGATGGGATTATTGCCTGC -s Anc2.Anc2refChr1 42161 24 + 142988 TAAACGGATGGGATTATTGCCTGC -s mr.mrrefChr3 67584 24 + 181027 TAAACACTTGGGATGATTGCCTAA -s simCow_chr6.simCow.chr6 466266 24 - 602619 TAAACAGATGGGATTTTTGCCTGC -s simCow_chr6.simCow.chr6 499374 24 + 602619 TAAACAGATGGGATTTTTGCCTGC -s simDog_chr6.simDog.chr6 488689 24 + 593897 TTAATGGGTGGGATGATTGCCTCA -s simHuman_chr6.simHuman.chr6 495565 15 + 601863 TAC---------ATCATTGCCTGG -s simRat_chr6.simRat.chr6 526522 24 + 647215 TAAACACTTGTGATGATTGCCTAA - -a -s simMouse_chr6.simMouse.chr6 514924 7 + 636262 TGTATTT -s Anc0.Anc0refChr3 129182 7 + 222631 TGTATTT -s Anc1.Anc1refChr6 163502 7 + 197743 TGTATTT -s Anc2.Anc2refChr1 42186 7 + 142988 TGTATTT -s mr.mrrefChr3 67608 7 + 181027 TGTATTT -s simCow_chr6.simCow.chr6 466291 7 - 602619 TGTATTT -s simCow_chr6.simCow.chr6 499399 7 + 602619 TGTATTT -s simDog_chr6.simDog.chr6 488714 7 + 593897 TGTATTT -s simHuman_chr6.simHuman.chr6 495581 7 + 601863 TGTATTT -s simRat_chr6.simRat.chr6 526546 7 + 647215 TACATTT - -a -s simMouse_chr6.simMouse.chr6 514931 12 + 636262 CTTGCAGACCCT -s Anc0.Anc0refChr3 129189 11 + 222631 TA-ACAGACCAC -s Anc1.Anc1refChr6 163509 11 + 197743 TA-ACAGACCAC -s Anc2.Anc2refChr1 42194 11 + 142988 TA-ACATACCAC -s mr.mrrefChr3 67615 12 + 181027 CATGCAGACCAT -s simCow_chr6.simCow.chr6 466299 11 - 602619 TA-ACATATCAC -s simCow_chr6.simCow.chr6 499407 11 + 602619 TA-ACATATCAC -s simDog_chr6.simDog.chr6 488722 11 + 593897 TA-ACATACCAG -s simHuman_chr6.simHuman.chr6 495588 11 + 601863 TA-ACAGACCAC -s simRat_chr6.simRat.chr6 526553 12 + 647215 CATGCATATCAT - -a -s simMouse_chr6.simMouse.chr6 514943 30 + 636262 AAAAGAGCATGCTCGCCCTGTGGCATCATC -s Anc0.Anc0refChr3 129200 30 + 222631 AAAAGAGTGTTGTGACTTGGTAACATCATA -s Anc1.Anc1refChr6 163520 30 + 197743 AAAAGAGTGTTGTGACTTGGTAACATCATA -s Anc2.Anc2refChr1 42212 30 + 142988 AAAAGAGTGTTGTGACTTGGTAACATTATA -s mr.mrrefChr3 67627 30 + 181027 AAAAGAGCATGCTCGCCCTGTGGCATCATC -s simCow_chr6.simCow.chr6 466317 30 - 602619 AAAAAAGTGTTGTGACTTGGTAACATTATG -s simCow_chr6.simCow.chr6 499425 30 + 602619 AAAAGAGTGTTGTGACTTTGTAACATTATA -s simDog_chr6.simDog.chr6 488733 30 + 593897 AAAATAGTGTTTGGACTTGGTAACATTGTA -s simHuman_chr6.simHuman.chr6 495599 13 + 601863 AAAAGAGT-----------------TCATA -s simRat_chr6.simRat.chr6 526565 30 + 647215 AAAAGAGCATGCTAGCCCTGTAGCATTATC - -a -s simMouse_chr6.simMouse.chr6 514973 43 + 636262 GAAAGATTGCCCACTGGCAAGTGTTGCTGCAGCGGGTTGGACT -s Anc0.Anc0refChr3 129231 43 + 222631 GCAAGGTTGTCCAGTTGCAAGGATTACTGCATCAGGTTCTATT -s Anc1.Anc1refChr6 163551 43 + 197743 GCAAGGTTGTCCAGTTGCAAGGATTACTGCATCAGGTTCTATT -s Anc2.Anc2refChr1 42243 43 + 142988 GCAAGGCTGTCCAGTTGCAAGGATTACTGCATCAGGTGCTATT -s mr.mrrefChr3 67658 43 + 181027 GAAAGGTTGCCCACTTGCAAGTGTTGCTGCATCAGGTTGGACT -s simCow_chr6.simCow.chr6 466348 43 - 602619 GCAAGGCAGCCTAGTTACAAGGAAGACTGCACCAGGTGCTGTT -s simCow_chr6.simCow.chr6 499456 43 + 602619 GCAAGGTAGTCCAGTCACAAGGATTACTGCACCAGGTGCTGTT -s simDog_chr6.simDog.chr6 488764 43 + 593897 GTAAGACTGTCCAATTGCAAGAATCACTGCATCAGGTGCCATT -s simHuman_chr6.simHuman.chr6 495613 43 + 601863 GGAAGGTTGTCCAGCTGCAAGCATTACTGCATCAGGTTCAATT -s simRat_chr6.simRat.chr6 526596 43 + 647215 GAAAGGTTGCCCACTTGCAAATGTTGCTGCATCAGGTTGGACT - -a -s simMouse_chr6.simMouse.chr6 515016 4 + 636262 AGCA -s Anc0.Anc0refChr3 129274 4 + 222631 AGCA -s Anc1.Anc1refChr6 163594 4 + 197743 AGCA -s Anc2.Anc2refChr1 42286 4 + 142988 AGCA -s mr.mrrefChr3 67701 4 + 181027 AGCA -s simCow_chr6.simCow.chr6 499499 4 + 602619 CACA -s simDog_chr6.simDog.chr6 488807 4 + 593897 AGCA -s simHuman_chr6.simHuman.chr6 495656 4 + 601863 AGCA -s simRat_chr6.simRat.chr6 526639 4 + 647215 AGCA - -a -s simMouse_chr6.simMouse.chr6 515020 1 + 636262 T -s Anc0.Anc0refChr3 129286 1 + 222631 T -s Anc1.Anc1refChr6 163606 1 + 197743 T -s Anc2.Anc2refChr1 42298 1 + 142988 T -s mr.mrrefChr3 67713 1 + 181027 T -s simCow_chr6.simCow.chr6 499511 1 + 602619 T -s simDog_chr6.simDog.chr6 488819 1 + 593897 T -s simHuman_chr6.simHuman.chr6 495668 1 + 601863 T -s simRat_chr6.simRat.chr6 526651 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 515021 87 + 636262 TGTGGTAGGTCAGAAATGCAGATAGTGCTACATCAGGGCGGACTAGCATGATGACATTGTGGGAAATCAGAAATGCAGCTAGTGACT -s Anc0.Anc0refChr3 129288 38 + 222631 TATGGGAAGTCGGAAAT-CAACATGATCTATTT----------------------------------------TGGAG--------T -s Anc1.Anc1refChr6 163608 46 + 197743 TATGGGAAGTCGGAAAT-CAACATGATCTATTT----------------------------------------TGGAGCTTGCAATT -s Anc2.Anc2refChr1 42300 38 + 142988 TATGGGAAGTCGTAGAT-TAAAATGATCTGTTT----------------------------------------GGGAG--------T -s mr.mrrefChr3 67714 87 + 181027 TGTGGTAGGTCAGAAATGCAGCTAGTGCTACATCAGGGCGGACTAGCATGATGACATTGTGGGAAATCAGAAATGCAGCTAGTAACT -s simCow_chr6.simCow.chr6 499513 37 + 602619 TATGG-AAGTCGTAGAT-TAAAATGATCTGTTT----------------------------------------GGGAG--------T -s simDog_chr6.simDog.chr6 488821 12 + 593897 GATGGGAAGTCA--------------------------------------------------------------------------- -s simHuman_chr6.simHuman.chr6 495670 46 + 601863 TATGGAAAGTTGGTAAT-CAACGGGAATTATTT----------------------------------------TGAAGCTTGCAATT -s simRat_chr6.simRat.chr6 526652 87 + 647215 TGTGGTAGGTCAGAAATGCAGCTAGTGCTGCATCAGATTAGACTAGCATGGTGACATTGAGGGAAGTCAGAAATGCAGCTAGTAACT - -a -s simMouse_chr6.simMouse.chr6 515108 88 + 636262 AATGAGTAATTTGAGAATACTATCAGGGAGCTTCAAATAGATGAAGAAATCAGGGAGATGCAAATAGATCAAGAAGTGGAAGAAGTGT -s Anc0.Anc0refChr3 129328 16 + 222631 AATGAGTTGTTTGGGA------------------------------------------------------------------------ -s Anc1.Anc1refChr6 163656 16 + 197743 AATGAGTTGTTTGGGA------------------------------------------------------------------------ -s Anc2.Anc2refChr1 42340 16 + 142988 AATGAGTTGTTTGGGA------------------------------------------------------------------------ -s mr.mrrefChr3 67801 51 + 181027 AATGAGTTGTTTGGGAATACTATCAGGGAGCTTCAAATAG-------------------------------------GGAAGAAGTGT -s simCow_chr6.simCow.chr6 499552 16 + 602619 AATGAGTTGTTTGGGA------------------------------------------------------------------------ -s simHuman_chr6.simHuman.chr6 495718 16 + 601863 AATGAGATGTTTGGGA------------------------------------------------------------------------ -s simRat_chr6.simRat.chr6 526739 51 + 647215 AGTGAGTTGTTTGGGAATGCTATCAGGGAGTTGCAAGTGG-------------------------------------TGAAGAAGTGT - -a -s simMouse_chr6.simMouse.chr6 515196 25 + 636262 AAGGATCTTGCAATTATCGGACCAT -s Anc0.Anc0refChr3 129344 25 + 222631 GAGGATCGAGCAATCATCAGGCTAT -s Anc1.Anc1refChr6 163672 25 + 197743 GAGGATCGAGCAATCATCAGGCTAT -s Anc2.Anc2refChr1 42356 25 + 142988 GAGGATCGAGCATATATCGTGCTAT -s mr.mrrefChr3 67852 25 + 181027 AAGGATCTAGCAATCATCAGACCAT -s simCow_chr6.simCow.chr6 499607 25 + 602619 GAGGATCGAGCATATATCGTGCTAT -s simHuman_chr6.simHuman.chr6 495734 25 + 601863 GAGGATCAAGCAATCATCAGGCTAC -s simRat_chr6.simRat.chr6 526790 25 + 647215 AAGAATCCAGCAATCATCAGATCAT - -a -s simMouse_chr6.simMouse.chr6 515221 5 + 636262 TTGAA -s Anc0.Anc0refChr3 129370 5 + 222631 TTGAG -s Anc1.Anc1refChr6 163698 5 + 197743 TTGAG -s Anc2.Anc2refChr1 42382 5 + 142988 CTGAG -s mr.mrrefChr3 67878 5 + 181027 TTGAA -s simCow_chr6.simCow.chr6 499633 5 + 602619 CTGAG -s simHuman_chr6.simHuman.chr6 495760 5 + 601863 TTGAG -s simRat_chr6.simRat.chr6 526816 5 + 647215 TTGAA - -a -s simMouse_chr6.simMouse.chr6 515226 56 + 636262 TTGTATCTAAAAGGCAAAAGGTGGGTGCAGTGTACAGACTGGTTCAGATTGACCAG -s Anc0.Anc0refChr3 129376 56 + 222631 TTGCATCGAAAAGACAAGAGTTGGGTGCACTGTACAGACAGAGTCAGTTTGACAAG -s Anc1.Anc1refChr6 163704 56 + 197743 TTGCATCGAAAAGACAAGAGTTGGGTGCACTGTACAGACAGAGTCAGTTTGACAAG -s Anc2.Anc2refChr1 42388 56 + 142988 TAGCATTGAGAACAGACGAGTTGGGGGCACTGTACAGATAGAGCCAGTTTGACAAG -s mr.mrrefChr3 67883 56 + 181027 TTGTATCTAAAAGGCAAAAGGTGGGTGCAGTGTACAGACTGATTCAGTTTGACAAG -s simCow_chr6.simCow.chr6 499639 56 + 602619 TAGCATTGAGAACAGACGAGTTGGGGGCGCTGTACAGAAAGAGCCAGTTTGACAAG -s simDog_chr6.simDog.chr6 488833 28 + 593897 --------------------------GCACTGTCCAGAT--AGCCAGTTTGATAAG -s simHuman_chr6.simHuman.chr6 495766 56 + 601863 TTGCATCAAAAAGACAAGAGTAGAATGCACTGTACAGACAGAGTCAGTTTGACATG -s simRat_chr6.simRat.chr6 526821 56 + 647215 TTATATCTAAAAGGCAAAGGGTGGGTGCAGTGTACAGACTGATCCAGTTTGATAAG - -a -s simMouse_chr6.simMouse.chr6 515282 21 + 636262 CCACAGTAAAGAAATAGATAA -s Anc0.Anc0refChr3 129432 21 + 222631 CCATACTAGTGTGATCTGTGA -s Anc1.Anc1refChr6 163760 21 + 197743 CCATACTAGTGTGATCTGTGA -s Anc2.Anc2refChr1 42444 21 + 142988 CCCTACTAGTGTGATCTGTGA -s mr.mrrefChr3 67939 21 + 181027 CCATAGTAAAGAAATCGATGA -s simCow_chr6.simCow.chr6 499695 21 + 602619 CCCTACTAGTGTGATCTGTAA -s simDog_chr6.simDog.chr6 488861 21 + 593897 CTCTACTAGTGTGATCTGTGG -s simHuman_chr6.simHuman.chr6 495823 21 + 601863 CCATACTAGTGGGATCTGTGA -s simRat_chr6.simRat.chr6 526877 21 + 647215 CCATAGTAAAGAAATCGATGA - -a -s simMouse_chr6.simMouse.chr6 515303 17 + 636262 CACCTGTCAAAGTAAGG -s Anc0.Anc0refChr3 129454 17 + 222631 CACCCATCAAAGTAAAA -s Anc1.Anc1refChr6 163782 17 + 197743 CACCCATCAAAGTAAAA -s Anc2.Anc2refChr1 42466 17 + 142988 CACCCATCCAAGTAGAA -s mr.mrrefChr3 67960 17 + 181027 CACCTGTCAAAGTAAAG -s simCow_chr6.simCow.chr6 499717 17 + 602619 CACTCATCCAGGTAGAA -s simDog_chr6.simDog.chr6 488883 17 + 593897 CTCCAATCCTAGTAGAA -s simHuman_chr6.simHuman.chr6 495845 17 + 601863 CACCCATCAAAGTAAAA -s simRat_chr6.simRat.chr6 526898 17 + 647215 CACCTGTCCAAGTAAAG - -a -s simMouse_chr6.simMouse.chr6 515320 12 + 636262 TGGATCTATCAG -s Anc0.Anc0refChr3 129471 2 + 222631 TG---------- -s Anc1.Anc1refChr6 163799 12 + 197743 TGAACAGCTCAG -s Anc2.Anc2refChr1 42483 2 + 142988 TG---------- -s mr.mrrefChr3 67977 12 + 181027 TGAATCGATCAG -s simCow_chr6.simCow.chr6 466391 2 - 602619 TG---------- -s simCow_chr6.simCow.chr6 499734 2 + 602619 TG---------- -s simDog_chr6.simDog.chr6 488900 2 + 593897 TG---------- -s simHuman_chr6.simHuman.chr6 495862 12 + 601863 TAAACAGCTCAG -s simRat_chr6.simRat.chr6 526915 12 + 647215 TGAATCGACAAG - -a -s simMouse_chr6.simMouse.chr6 515332 22 + 636262 GAGAAACACTGTTATTCTGTTA -s Anc0.Anc0refChr3 129473 10 + 222631 ------------TTTTCTGTGA -s Anc1.Anc1refChr6 163811 22 + 197743 GATTACCAGGCCTTTTCTGTGA -s Anc2.Anc2refChr1 42485 10 + 142988 ------------TTTTCAGTGA -s mr.mrrefChr3 67989 22 + 181027 GAGAAACACTGTTATTCTGTTA -s simCow_chr6.simCow.chr6 466393 10 - 602619 ------------ATCCCAACCA -s simCow_chr6.simCow.chr6 499736 10 + 602619 ------------ATTTCAATGA -s simDog_chr6.simDog.chr6 488902 8 + 593897 ------------TCTT--GTGA -s simHuman_chr6.simHuman.chr6 495879 22 + 601863 GATTACCAGGCCTGTATTGTGA -s simRat_chr6.simRat.chr6 526927 22 + 647215 GGGAAACACTGTTATTCTGTCA - -a -s simMouse_chr6.simMouse.chr6 515354 1 + 636262 G -s Anc0.Anc0refChr3 129483 1 + 222631 C -s Anc1.Anc1refChr6 163833 1 + 197743 C -s Anc2.Anc2refChr1 42495 1 + 142988 C -s mr.mrrefChr3 68011 1 + 181027 G -s simCow_chr6.simCow.chr6 466403 1 - 602619 C -s simCow_chr6.simCow.chr6 499747 1 + 602619 T -s simDog_chr6.simDog.chr6 488910 1 + 593897 G -s simHuman_chr6.simHuman.chr6 495901 1 + 601863 C -s simRat_chr6.simRat.chr6 526949 1 + 647215 G - -a -s simMouse_chr6.simMouse.chr6 515355 8 + 636262 TAAGGATA -s Anc0.Anc0refChr3 129484 8 + 222631 CAAGGATA -s Anc1.Anc1refChr6 163834 8 + 197743 CAAGGATA -s Anc2.Anc2refChr1 42496 8 + 142988 CAAGGATA -s mr.mrrefChr3 68012 8 + 181027 TAAGGATA -s simCow_chr6.simCow.chr6 499748 8 + 602619 CAAGGATG -s simDog_chr6.simDog.chr6 488911 8 + 593897 AAAGGATA -s simHuman_chr6.simHuman.chr6 495902 8 + 601863 CAAGGATA -s simRat_chr6.simRat.chr6 526950 8 + 647215 TAAGGACA - -a -s simMouse_chr6.simMouse.chr6 515363 7 + 636262 ACATCTA -s Anc0.Anc0refChr3 129492 7 + 222631 TCAGGTA -s Anc1.Anc1refChr6 163842 7 + 197743 TCAGGTA -s Anc2.Anc2refChr1 42504 7 + 142988 TTAGGTA -s mr.mrrefChr3 68020 7 + 181027 ACATCTA -s simCow_chr6.simCow.chr6 466404 1 - 602619 T------ -s simCow_chr6.simCow.chr6 499756 1 + 602619 T------ -s simDog_chr6.simDog.chr6 488919 7 + 593897 TTAGGTA -s simHuman_chr6.simHuman.chr6 495910 7 + 601863 TCAGGTA -s simRat_chr6.simRat.chr6 526958 7 + 647215 ATATCTA - -a -s simMouse_chr6.simMouse.chr6 515370 44 + 636262 GTGTCTTAAGATCAAAAGTTGGGAGCACATGTGCAGAACAATTT -s Anc0.Anc0refChr3 129499 43 + 222631 GTATCTTCAAATTAGATA-GGGGAGCAACTATGCAGAACAAGTT -s Anc1.Anc1refChr6 163849 43 + 197743 GTATCTTCAAATTAGATA-GGGGAGCAACTATGCAGAACAAGTT -s Anc2.Anc2refChr1 42511 43 + 142988 GTATCTTCAAATTAGATA-GGGGATCAACCATGCAGAACAAGTT -s mr.mrrefChr3 68027 44 + 181027 GTGTCTTAAGATCAAAAATTGGGAGCACATGTGCAGAACAAGTT -s simCow_chr6.simCow.chr6 240251 43 + 602619 GTGTCTTCAGATTAAATA-TGGGAACATTCATACAGAACAAGTT -s simDog_chr6.simDog.chr6 488926 42 + 593897 GTATCTTCCAATTAGATA-GG-GATAAACCATGCAGACCAAGTT -s simHuman_chr6.simHuman.chr6 495917 43 + 601863 GTATCTTTACATTAGATA-AGTGAGCAACTAAGCAGAACTAGTT -s simRat_chr6.simRat.chr6 526965 44 + 647215 GTGTCTTAAGATCAACAATGGGGAGCACATGTGCAGAACAAGTT - -a -s simMouse_chr6.simMouse.chr6 515414 12 + 636262 CTGGCTCTCAAG -s Anc0.Anc0refChr3 129542 10 + 222631 CTGTCCCTCA-- -s Anc1.Anc1refChr6 163892 12 + 197743 CTGTCCCTCAAG -s Anc2.Anc2refChr1 42554 10 + 142988 TTGTCCCTCA-- -s mr.mrrefChr3 68071 12 + 181027 CTGTCTCTCAAG -s simCow_chr6.simCow.chr6 240294 10 + 602619 TTGGCCCTCA-- -s simDog_chr6.simDog.chr6 488968 10 + 593897 TTGTCCCTCA-- -s simHuman_chr6.simHuman.chr6 495961 12 + 601863 CTGTCCCTCAAG -s simRat_chr6.simRat.chr6 527009 12 + 647215 CTGTCTCTCAAG - -a -s simMouse_chr6.simMouse.chr6 515426 4 + 636262 CAGG -s Anc0.Anc0refChr3 129552 3 + 222631 -AGA -s Anc1.Anc1refChr6 163904 4 + 197743 CAGA -s Anc2.Anc2refChr1 42564 3 + 142988 -AAG -s mr.mrrefChr3 68083 4 + 181027 CAGA -s simCow_chr6.simCow.chr6 240304 3 + 602619 -AAG -s simDog_chr6.simDog.chr6 488978 3 + 593897 -AAA -s simHuman_chr6.simHuman.chr6 495986 4 + 601863 CAGA -s simRat_chr6.simRat.chr6 527021 4 + 647215 CAGA - -a -s simMouse_chr6.simMouse.chr6 515430 47 + 636262 TATGTTCCACCAGAATTCAGTGTGGCGCCAGCACCATATAAGAGAGT -s Anc0.Anc0refChr3 129555 47 + 222631 TATATTTCATCAGAACCAAGCATGGTGGTAGCATCATAGAAGAGGAA -s Anc1.Anc1refChr6 163908 47 + 197743 TATATTTCATCAGAACCAAGCATGGTGGTAGCATCATAGAAGAGGAA -s Anc2.Anc2refChr1 42567 47 + 142988 TGTATTTCATTAGAACCAAGCATGGTGGTAGCATCATAGAAGAGGAA -s mr.mrrefChr3 68087 47 + 181027 TATGTTCCATCAGAATTAAGTGTGGCGCCAGCATCATATAAGAGAGT -s simCow_chr6.simCow.chr6 240307 47 + 602619 TGGATTTCATGGGAGCCAAGCATAGTGGCGGCGCCATGTAAGAGGAA -s simDog_chr6.simDog.chr6 488981 45 + 593897 TATATTTCATTAGAATCAAGCATGGTGGTAGCAT-ACAGGAG-GGAA -s simHuman_chr6.simHuman.chr6 495992 47 + 601863 CATTTCACATCAGAACCAAACATGGTGGTAACATCATAAAAGAGGTA -s simRat_chr6.simRat.chr6 527025 47 + 647215 TATGTTCCGTCAGGATTAAGTGTGCCGCGAGCATCATCTTAGAGAAT - -a -s simMouse_chr6.simMouse.chr6 515477 26 + 636262 TACAGCATTCAACTAGTGCACAAACA -s Anc0.Anc0refChr3 129606 26 + 222631 TACAGGACTCCACTGCTCCACAAAGC -s Anc1.Anc1refChr6 163959 26 + 197743 TACAGGACTCCACTGCTCCACAAAGC -s Anc2.Anc2refChr1 42618 26 + 142988 TACAGGACTCCACTGCTCCACAAAGC -s mr.mrrefChr3 68138 26 + 181027 TACAGCATTCAACTAGTGCACAAAGA -s simCow_chr6.simCow.chr6 240358 26 + 602619 TACAGGACTTAACTGCTCCACAAAGC -s simDog_chr6.simDog.chr6 489030 26 + 593897 TATGGGACTCCATTGCCCCAGGAAGC -s simHuman_chr6.simHuman.chr6 496043 26 + 601863 TACAGGGATCCGCTGCTTCACAAAGC -s simRat_chr6.simRat.chr6 527076 26 + 647215 TACAGCATTCAACTAGTCCACAAAGA - -a -s simMouse_chr6.simMouse.chr6 515503 11 + 636262 TGAACATCTAC -s Anc0.Anc0refChr3 129632 11 + 222631 TGAGCATGTTC -s Anc1.Anc1refChr6 163985 11 + 197743 TGAGCATGTTC -s Anc2.Anc2refChr1 42652 11 + 142988 TGACCATGTTC -s mr.mrrefChr3 68164 11 + 181027 TGAGCATCTAC -s simCow_chr6.simCow.chr6 240392 11 + 602619 TGCCCGTGTTC -s simDog_chr6.simDog.chr6 489064 11 + 593897 TGACCATGTTC -s simHuman_chr6.simHuman.chr6 496069 11 + 601863 TCAGCCTGTTC -s simRat_chr6.simRat.chr6 527102 11 + 647215 TGAGCAACTAC - -a -s simMouse_chr6.simMouse.chr6 515514 11 + 636262 CTTTTGTGATC -s Anc0.Anc0refChr3 129643 11 + 222631 CTTTTGTGAAC -s Anc1.Anc1refChr6 163996 11 + 197743 CTTTTGTGAAC -s Anc2.Anc2refChr1 42663 11 + 142988 CTTTTGTGAAC -s mr.mrrefChr3 68175 11 + 181027 CTTTTGTGATC -s simCow_chr6.simCow.chr6 240403 11 + 602619 CTTTTGAGACC -s simDog_chr6.simDog.chr6 489077 11 + 593897 CTTTTGTGAAC -s simHuman_chr6.simHuman.chr6 496080 11 + 601863 CTTTTATGAAC -s simRat_chr6.simRat.chr6 527113 11 + 647215 CTTTTGTGATC - -a -s simMouse_chr6.simMouse.chr6 515525 74 + 636262 ACCTGGCAGTTATTGTCTGATATATAACATAGCCCTTAGTTGTTTGCCTCATTTAGATTCCCTTCAGATCCTGT -s Anc0.Anc0refChr3 129654 61 + 222631 ACCCATTTATTGTAATCTGATATATAC-----ACCTTACTTGTTTACCTTATTTAGATCACC--------ATGT -s Anc1.Anc1refChr6 164007 61 + 197743 ACCCATTTATTGTAATCTGATATATAC-----ACCTTACTTGTTTACCTTATTTAGATCACC--------ATGT -s Anc2.Anc2refChr1 42692 61 + 142988 ACCCATTTATTGTAATTTGATATATAC-----ACCTTACTTGTTTAGCTTATGTAGATCGCC--------ATGT -s mr.mrrefChr3 68186 72 + 181027 ACCTGGCTATTATTGTCTGATATATAA--TAGCCCTTAGTTGTTTGCCTCATTTAGATTACCTTCAGATCCTGT -s simCow_chr6.simCow.chr6 240432 60 + 602619 ATCTGTTTATTATAATGTGATGTATAC-----ACCTTAC-TGCTTAACTTATGTAGTTTGTC--------ATGC -s simDog_chr6.simDog.chr6 489106 61 + 593897 ACCCATCTATTGTAACTTGATATATGC-----ACCTTACTGGTTTAGCTTATGTAGATCGCA--------ATGT -s simHuman_chr6.simHuman.chr6 496091 61 + 601863 ACCCATTTATTGTCATCTGAGATATAC-----ACCTTATTTGTTTACCTTATTTAGATCACC--------ATGT -s simRat_chr6.simRat.chr6 527124 72 + 647215 ACCTGGCTATTATTGTCCGATATATAA--TAGCCCTTAGTTGTTCGTCTCATTTAGATTACCTTCAAATCCTGT - -a -s simMouse_chr6.simMouse.chr6 515599 47 + 636262 GGTATCTCAAACTATAAGATCCATGTTACAGAAACCGGATTGTTATA -s Anc0.Anc0refChr3 129715 28 + 222631 G--------CTCTATGGAA--------TCCC-GACTGGAT--TCTTA -s Anc1.Anc1refChr6 164068 34 + 197743 GGC-CC-CACTCTATGGAA--------TCCC-GACTGGAT--TCTTA -s Anc2.Anc2refChr1 42753 28 + 142988 G--------CCCTATGGAA--------TCCA-GATTAGAT--TCTAA -s mr.mrrefChr3 68258 38 + 181027 GGTATC-CAAACTATAAAA--------ACACAAACCGGATTGTCATA -s simCow_chr6.simCow.chr6 240519 28 + 602619 A--------CCCTATGGAA--------GCAT-GTTTAGAG--TATAA -s simDog_chr6.simDog.chr6 489167 28 + 593897 G--------CCCTATATAA--------TTCA-GATTAGAT--TCTAA -s simHuman_chr6.simHuman.chr6 496152 34 + 601863 GGC-CC-CACTTTATGGAA--------TCTC-GACTGGAT--TCTTA -s simRat_chr6.simRat.chr6 527196 38 + 647215 GCAATA-CAAGCTATAAAG--------ATACAAATAGGAATATCATA - -a -s simMouse_chr6.simMouse.chr6 515646 48 + 636262 GAGTGGAATCAAATTGATGCACCAACCAGATTCTACATTAATTATACG -s Anc0.Anc0refChr3 129743 34 + 222631 AAGTGGAATCCAATCAATGTACCAA--------------AATAATACC -s Anc1.Anc1refChr6 164102 34 + 197743 AAGTGGAATCCAATCAATGTACCAA--------------AATAATACC -s Anc2.Anc2refChr1 42816 34 + 142988 AAGTGGAAACCAATCAAGGTACAAT--------------AACAATACC -s mr.mrrefChr3 68296 47 + 181027 AAGTGGAATCAAATTGATGCACCAACCAGAT-CTACATTAATTATACG -s simCow_chr6.simCow.chr6 240577 34 + 602619 TGGGAGAGCCAGATCAAGGTACAAT--------------AGCAATACC -s simDog_chr6.simDog.chr6 489230 34 + 593897 AAGTGGAAACCAATCAAGGTACAAT--------------AACAATACC -s simHuman_chr6.simHuman.chr6 496186 34 + 601863 AAGTTACATCTAACCAATGTACCAA--------------AATAATACC -s simRat_chr6.simRat.chr6 527234 47 + 647215 AAGTCGAATCAAATTGATGCATCAACTAGAT-CTACACTAATTATATA - -a -s simMouse_chr6.simMouse.chr6 515694 20 + 636262 ATGGTCTTCTTTTAACCAAT -s Anc0.Anc0refChr3 129777 9 + 222631 A----TTTCTGTT------- -s Anc1.Anc1refChr6 164136 20 + 197743 ATGGTTTTCTGTTATGCGTT -s Anc2.Anc2refChr1 42850 9 + 142988 A----TTCCTGAT------- -s mr.mrrefChr3 68343 20 + 181027 ATGGTCTTCTTTTAACCAAT -s simCow_chr6.simCow.chr6 240624 9 + 602619 A----TTCCGGAT------- -s simDog_chr6.simDog.chr6 489264 9 + 593897 A----TTCCTGAT------- -s simHuman_chr6.simHuman.chr6 496220 20 + 601863 ATGGTTTTCTATTATGCGTT -s simRat_chr6.simRat.chr6 527281 20 + 647215 ATAGTCTTCTTTTAACCAAT - -a -s simMouse_chr6.simMouse.chr6 515714 14 + 636262 ATCTATATTCAGAC -s Anc0.Anc0refChr3 129786 11 + 222631 ---TGTATTCAGGC -s Anc1.Anc1refChr6 164156 14 + 197743 ATCTGTATTCAGGC -s Anc2.Anc2refChr1 42859 11 + 142988 ---TGTGTTCAGGC -s mr.mrrefChr3 68363 14 + 181027 ATCTGTATTCAGAC -s simCow_chr6.simCow.chr6 240634 11 + 602619 ---TGTGTTCATGC -s simDog_chr6.simDog.chr6 489273 11 + 593897 ---TGTGTTCAGGC -s simHuman_chr6.simHuman.chr6 496284 14 + 601863 ATCTGTATTCAAGT -s simRat_chr6.simRat.chr6 527301 14 + 647215 ATCTGTATTCGGAC - -a -s simMouse_chr6.simMouse.chr6 515728 7 + 636262 GAGCCTG -s Anc0.Anc0refChr3 129801 7 + 222631 ATGCCTG -s Anc1.Anc1refChr6 164174 7 + 197743 ATGCCTG -s Anc2.Anc2refChr1 42874 7 + 142988 ATGCCTG -s mr.mrrefChr3 68381 7 + 181027 GTGCCTG -s simCow_chr6.simCow.chr6 240646 2 + 602619 -----TG -s simDog_chr6.simDog.chr6 489288 7 + 593897 ATGCCTG -s simHuman_chr6.simHuman.chr6 496302 7 + 601863 ATGCCTG -s simRat_chr6.simRat.chr6 527319 7 + 647215 GTGCCTG - -a -s simMouse_chr6.simMouse.chr6 515735 12 + 636262 TTACTTAAGGAT -s Anc0.Anc0refChr3 129815 12 + 222631 TTGCTGGAGGAT -s Anc1.Anc1refChr6 164188 12 + 197743 TTGCTGGAGGAT -s Anc2.Anc2refChr1 42888 12 + 142988 TTGCTGGAGGAT -s mr.mrrefChr3 68388 12 + 181027 TTACTTGAGGAT -s simCow_chr6.simCow.chr6 240654 12 + 602619 TTGCTGGAGGAT -s simDog_chr6.simDog.chr6 489311 12 + 593897 TTGCTGAAGGAT -s simHuman_chr6.simHuman.chr6 496316 12 + 601863 TTGCTAGAGGAT -s simRat_chr6.simRat.chr6 527326 12 + 647215 TTTCTTGAGGAT - -a -s simMouse_chr6.simMouse.chr6 515747 33 + 636262 CTAGGAGTGGAATAGACAGTCATCGCATAAGAG -s Anc0.Anc0refChr3 129827 21 + 222631 CTAGGCCGGGAATAGGCAGTC------------ -s Anc1.Anc1refChr6 164200 33 + 197743 CTAGGCCGGGAATAGGCAGTCATCTGACTTGTG -s Anc2.Anc2refChr1 42900 21 + 142988 CTAGACCGGGAATAGGCAGTC------------ -s mr.mrrefChr3 68400 33 + 181027 CTAGGAGTGGAATAGGCAGTCATCGCATAAGTG -s simCow_chr6.simCow.chr6 240666 21 + 602619 GTAGAACTGCAATGGGCAGTT------------ -s simDog_chr6.simDog.chr6 489324 21 + 593897 CTCGACTGCGAGTAAGCAGGC------------ -s simHuman_chr6.simHuman.chr6 496328 33 + 601863 ATAGGCCAGGAAGAGGCAGTCATCTGACTTGTG -s simRat_chr6.simRat.chr6 527338 33 + 647215 CTAGGAGTGGGGTAGGCAGTCATCACATAAGTG - -a -s simMouse_chr6.simMouse.chr6 515780 3 + 636262 ACT -s Anc0.Anc0refChr3 129848 3 + 222631 ACT -s Anc1.Anc1refChr6 164233 3 + 197743 ACT -s Anc2.Anc2refChr1 42921 3 + 142988 ACT -s mr.mrrefChr3 68433 3 + 181027 ACT -s simCow_chr6.simCow.chr6 240693 3 + 602619 AAT -s simDog_chr6.simDog.chr6 489348 3 + 593897 ACT -s simHuman_chr6.simHuman.chr6 496361 3 + 601863 AGT -s simRat_chr6.simRat.chr6 527371 3 + 647215 GCC - -a -s simMouse_chr6.simMouse.chr6 515783 28 + 636262 TTACAGGTAACTCAAATTTTATCCATAA -s Anc0.Anc0refChr3 129851 28 + 222631 TTCAGAGTAACTCACATTCTATCCGTCA -s Anc1.Anc1refChr6 164236 28 + 197743 TTCAGAGTAACTCACATTCTATCCGTCA -s Anc2.Anc2refChr1 42924 28 + 142988 TTCAGAGTAACTTACATTCTATCTGTCA -s mr.mrrefChr3 68436 28 + 181027 TTACGGGTAACTCAAATTTTATCCATAA -s simCow_chr6.simCow.chr6 240699 28 + 602619 TTCAGAGTAACTCACATGCTAAATCCTA -s simDog_chr6.simDog.chr6 489351 28 + 593897 TTCAGAGTAACTTACATTCTATCTGTCA -s simHuman_chr6.simHuman.chr6 496364 28 + 601863 TTCAGAGTAACTCATATTGCAACCGTTA -s simRat_chr6.simRat.chr6 527374 28 + 647215 TTACGGATAACTCCCATTTTAGCTTTAA - -a -s simMouse_chr6.simMouse.chr6 515811 13 + 636262 TCCTGCTTCATTG -s Anc0.Anc0refChr3 129879 4 + 222631 TCCT--------- -s Anc1.Anc1refChr6 164264 10 + 197743 TCCT---ACATTG -s Anc2.Anc2refChr1 42952 4 + 142988 TCCT--------- -s mr.mrrefChr3 68464 13 + 181027 TCCTGCTTCATTG -s simCow_chr6.simCow.chr6 240729 4 + 602619 TCAT--------- -s simDog_chr6.simDog.chr6 489379 4 + 593897 TCCT--------- -s simHuman_chr6.simHuman.chr6 496392 6 + 601863 -------ACATTG -s simRat_chr6.simRat.chr6 527402 13 + 647215 TCCAGTTTCATTG - -a -s simMouse_chr6.simMouse.chr6 515824 12 + 636262 AGAACGTTTCTA -s Anc0.Anc0refChr3 129883 12 + 222631 AGAACATTTCTA -s Anc1.Anc1refChr6 164274 12 + 197743 AGAACATTTCTA -s Anc2.Anc2refChr1 42956 12 + 142988 AGAACATTTCCA -s mr.mrrefChr3 68477 12 + 181027 AGAACATTTCTA -s simCow_chr6.simCow.chr6 499757 5 + 602619 -------TTCTA -s simDog_chr6.simDog.chr6 489392 12 + 593897 AGAACATTTCCG -s simHuman_chr6.simHuman.chr6 496398 11 + 601863 -GAACAATTTTA -s simRat_chr6.simRat.chr6 527415 12 + 647215 AGAACATTTCTA - -a -s simMouse_chr6.simMouse.chr6 515836 239 + 636262 TACCCAATGCAACTATAATTCAAGAGAACTGAGAAGTTATACTGCTTTTAGACATGTGTAGCACCAAAGCATCCTGTTGTGTTCTTAAGATGGCTGGACTCTTTTTTCTGCTCCTGCTAATTTATACATCAAAAGTACCACAAAGAGTTGGGATCAATTAAGTATTACAGAATCCATTGAGGCTTCAGCACTGTTAACAGCTTGTTTGGACCTCTCATATTCATTATACCAGGTTGCCA -s Anc0.Anc0refChr3 129900 16 + 222631 -ACTCAAAGTGACTCTG------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ -s Anc1.Anc1refChr6 164291 17 + 197743 CACTCAAAGTGACTCTG------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ -s Anc2.Anc2refChr1 42973 16 + 142988 -ACTCAAAGTGACTCTG------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ -s mr.mrrefChr3 68489 231 + 181027 TACCCAAAGCGACTATAATTCAAGAGAACTGAGAAGTTATACTGCTTTTAGACATGTGTAGCACCAAAGCATCCTGTTGTGTTCTTAAGATGGCTGGACTCTTTTTTCTGCTCCTGCTAATTTATACATCAAAAGTACCACAAAGAGTTGGGATCAATTAAGTATTACAGAATCCATTGAGGCTTCAGCACTGTTAACAGCTT--------CTCTCATATTCATTATACCAGGTTGCCA -s simCow_chr6.simCow.chr6 499767 16 + 602619 -CTTCAAATTGACACTG------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ -s simDog_chr6.simDog.chr6 489409 16 + 593897 -ACTCAAAGTGACTTTT------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ -s simHuman_chr6.simHuman.chr6 496414 17 + 601863 CACTCAAAATGACCCTG------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ -s simRat_chr6.simRat.chr6 527427 231 + 647215 TACCCAAAGCGACTATAATTCAAGAGAACTGAGAAGTTACACTGCTTTTAGACATGTCTAGCATCAACACATCATCTTGTGTTCTTAAGATGGCTGGACTGTTTTGCCTGCTCCTGCTAATTTATACATCAAAAGTACCACAAAGAGTTGGGATCAACTAAGTCTTACAGGATCCACTGAGGCTTCAGCATTGTTAACTACTT--------CTGTTGTATTCTTTACACCAGGTTGCCA - -a -s simMouse_chr6.simMouse.chr6 516075 315 + 636262 GTAACAGCAGGGTAGGGTTACATGTTCATTTCGTTAGAGAGGAGTCCATTCAACTGGGTCTAGTTCAAGATTGAGCTGGTAATAACCTCACTCTGCTTTATTGCCCAAAGGACTGCTGTATGGCACTGCTATATACTACCCATAGAAGCTATTTCTCTTTATCATCTTGGCTGACTATCTACTTTCACACTTATAGCCAAGCCGTTCTACTCATCAGAATATTATCCATGTAAATGGGTTATACATCAATTGCCTCACTCTAGATGTTTAGTCACTGTGGGCTACCCCACAGGTTCACACCACGAGACTAGGCAG -s mr.mrrefChr3 68720 292 + 181027 GTAACAGCAGGGTA------CATGTTCATTTCGTTAGAGAGGAGTCCATTCAACTGGGTCTAGTTCAAGATTGAGCTGGTAATAACCTCACTCTGCTTTATTGCCCAAA--------------CACTGCTATATACTACCCATAGAAGCTATTTCTCTTTATCATCTTGGCTGACTATCTACTTTCACACTTATAGCCAAGC---TCTACTCATCAGAATATTATCCATGTAAATGGGTTATACATCAATTGCCTCACTCTAGATGTTTAGTCACTGTGGGCTACCCCACAGGTTCACACCACGAGACTAGCCAG -s simRat_chr6.simRat.chr6 527666 292 + 647215 GTAACAGCAGAGTA------CATGTTCAGTACATGAGAGAGGAGTCCATTCAACTGGGTCTAGTTCAAGAATGAGATGATAATAACCTCACTCTGCTCTATTGCCCAAA--------------TACTGCTGTAGGCTTCCTAAAGGGGCTGTTTTTTCTTGTCATCTTTGGTGACTATCTATTTTCATGTTTACAGCCATTC---TCTAATCATCAGAATATTACGCATGCAAATTGGTTATATGCCAATTTCCTCACTCCAGATGTTTAATCAATGTGGGCTGCTCCATCGGCTCATACCAAGAGTCTAGCCAG - -a -s simMouse_chr6.simMouse.chr6 516390 15 + 636262 TCAGTCTAATTTTCA -s mr.mrrefChr3 69013 11 + 181027 TCAGT--AATTT--A -s simRat_chr6.simRat.chr6 527959 11 + 647215 TCAGT--AATCG--A - -a -s simMouse_chr6.simMouse.chr6 516418 75 + 636262 AGGATAGGTGGTCGTCTGCGAAGCAATCACCATTGGCTGCATTTCTCCCCTGCTAGTGCTGCTAATAGTCTCAAT - -a -s simMouse_chr6.simMouse.chr6 516512 1 + 636262 A -s Anc0.Anc0refChr0 13107 1 + 26507 A -s Anc1.Anc1refChr6 13430 1 + 197743 A -s Anc2.Anc2refChr17 6442 1 + 28526 C -s mr.mrrefChr3 69058 1 + 181027 A -s simCow_chr6.simCow.chr6 322021 1 + 602619 C -s simDog_chr6.simDog.chr6 313856 1 + 593897 C -s simHuman_chr6.simHuman.chr6 333591 1 + 601863 A -s simRat_chr6.simRat.chr6 528003 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 516548 2 + 636262 CA -s Anc0.Anc0refChr0 13154 2 + 26507 CA -s Anc1.Anc1refChr6 13477 2 + 197743 CA -s Anc2.Anc2refChr17 6490 2 + 28526 CA -s mr.mrrefChr3 69094 2 + 181027 CA -s simCow_chr6.simCow.chr6 322069 2 + 602619 GA -s simDog_chr6.simDog.chr6 313904 2 + 593897 CA -s simRat_chr6.simRat.chr6 528031 2 + 647215 CA - -a -s simMouse_chr6.simMouse.chr6 516561 1 + 636262 T -s Anc0.Anc0refChr0 13167 1 + 26507 C -s Anc1.Anc1refChr6 13490 1 + 197743 C -s Anc2.Anc2refChr17 6507 1 + 28526 G -s mr.mrrefChr3 69107 1 + 181027 T -s mr.mrrefChr5 197116 1 + 294540 C -s simCow_chr6.simCow.chr6 322098 1 + 602619 G -s simDog_chr6.simDog.chr6 313921 1 + 593897 G -s simHuman_chr6.simHuman.chr6 333649 1 + 601863 C -s simRat_chr6.simRat.chr6 341206 1 + 647215 C -s simRat_chr6.simRat.chr6 528044 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 516571 19 + 636262 GAGGTGACCATCAGTCAGC -s mr.mrrefChr3 69117 19 + 181027 GAGGTGACCATCAGTCAGC -s simRat_chr6.simRat.chr6 528054 19 + 647215 AAGGTGACCGCCAGTCAGC - -a -s simMouse_chr6.simMouse.chr6 516629 74 + 636262 AGCTACAGAGACCCTGAACCATGCGCGTTACTGTAATGAACATGTTAATCTATAACTGTGAACCACTGGCCACC - -a -s simMouse_chr6.simMouse.chr6 516714 1 + 636262 T -s mr.mrrefChr3 69344 1 + 181027 T -s simRat_chr6.simRat.chr6 528287 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 516796 37 + 636262 CATGTTCCATGTGGTTTCCACTAGTTCATACAGGGCC -s mr.mrrefChr3 69427 35 + 181027 CATGTTC-ATGTGGTTTC-ACTAGTTCATACAGGGCC -s simRat_chr6.simRat.chr6 528370 35 + 647215 CACGTTC-ATGTGGTTTC-ACTAGTTCATACAGGGCT - -a -s simMouse_chr6.simMouse.chr6 516833 81 + 636262 CTAACACCATTTGAGCTATGGGGCTAAGAGTTAAGTCCATTGCCTCAGCATATTAACACTTATCTCAGGCTTGGCAGACTG -s mr.mrrefChr3 69462 81 + 181027 CTAACACCATTTGAGCTATGGGGCTAAGAGTTAAGTCCATTGCCTCAGCATATTAACACTTATCTCAGGCTTGGCAGACTG -s simRat_chr6.simRat.chr6 528421 81 + 647215 CTGACATCATTTGAGCTATGGGGCTAAGAGTTAAGTCCATTACCTCGGCATATTAATCCTTACCTCACCTCTGGCAGACTG - -a -s simMouse_chr6.simMouse.chr6 516914 864 + 636262 ACTCAGGGTCCATTCTCAGTACCATCAACTATAATATATGAGGCTGTAGTGATCTCTTGGCCTGATAAAACAGCCTGACATATGGACGCCTGCAAAAGGCTAGCAGTGCCTATATTGTAACCATCAGTAGTATGGCATGTGTGTGGTGGTAATCTACATTGTTTGGAACTTGATACCATCTTCAGGTTGTCAGGTCTACCACGGTACTGCTCACCTCAATGCTATCAGGATGCCCATTCGTCTGTTTATTATCTTGACATGGATATCCCCTCTTCAGGGAAGTGGAGAATTAGTGACACAGATAGTATAACATTATATATAGTAACCAGGCCGGGTTATCCCCTTATCTATTGGAGATGACTGATTCTTCTGCTGTCTTTCCCTGAAGTTAATACTGTCATAAGCTATAATAAAAGGCAAATGTGGCCATGTACACACGGCTAGTGCTTGGCTATGAGCCTGGCCATGTACTCATGGTTAGTGCTTTGCTATCAGCCTACCTTGCTTGATGAGATGTCAAGCAATCACAGGAAGAGTCTGTCTTCCTCACACAAAAGGTTTGTCATGCCTAGTTCCCCACCTCTTTGTGTGCACCTGCACTTTGATTCAGCTATGTAGTAATAGCTTGACATACAAAGGGAGATTTATTTTGGTTTTGCTGTGCCTATTAATGTCATTTACTAATTTGGTAATCCCCCAGTACCCCTTATCTACCAGAAATAGGTGATGCTCCTGCTGCCTGCACCTGGAGTTAACATCATCATTTCTTTCTGTATACCTTACGCACTAGCTTGCCATATGAAGGGGGGCTGACTTTAGATTTGCTGTGCTCGTTAAATGTAATTTGCTATTTCCCCAGTGTAT -s mr.mrrefChr3 69543 489 + 181027 ACTCAGGGTCCATTCTCAGTACCATCAACTATAATATATGAGGCTGTAGTGATCTCTTGGCCTGATAAAACAGCCTGACATATGGACGCCTGCAAAAGGCTAGCAGTGCCTATATTGTAACCATCAGTAGTATGGCATGTGTGTGGTGG-AATCTACATTGTTTGGAACTTGATACCATCTTCAGGTTGTCAGGTCTACCACGGTACTGCTCACCTCAATGCTATCAGGATGCCCATTCGTCTGTTTATTATCTTGACATGGATATCCCCTCTTCAGGGAAGTGGAGAATTAGTGACACAGATAGTATAACATTATATATAGTAACCAGGCCGGGTT-TCCCCTTATCTATTGGAGATGACTGATTCTTCTGCTGTCTTTCCCTGAAGTTAA------------CTATAATAAAAGGCAA-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ACGCACTAGCTTGCCATATGAAGGGGGGCTGACTTTAGATTTGCTGTGCTCGTTAAATGTAATTTGCTATTTCCCCAGTGTAT -s simRat_chr6.simRat.chr6 528507 489 + 647215 ACTCAATGTCCATTCTCAGTACCATTATCTATAATGTAGGAGGCTGTGGTGATCTCTTGGCCTGATAAAACAGCCTGACATATGGACACTTTCAAAAGGCTAGCAATGTCTATATTGTAACCATCAGTCATATGTAAAGTGTGTGGTGA-GATCTACATTGTAAAGCACTTGATACCATCTCCAGGTTGTCAGGTTGACCACAGTACTGCTGGCCTCATTGTTGTTACCACACCCATGTGTCTGTTTATTATCTTAACATGGATCTCCCATCCTCAGGGAGGAAGAGAGTTAGTGACAGAGATAGCTTATCATCATATGTAGTCACCAGGCTGGTCT-TCCCCTTATCTAGTAGAGATAAATGATGCTTCTGCTGCCTGCCCCTGAAGTTAA------------CTATAATAAAAGGCAA-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AAGCAATAGCTTGGCATATGAAGGGGGACTGACTTCAGATCTGCTATGCCCGTTAAATGTGATATGCTAATTCCCCAGCATAT - -a -s simMouse_chr6.simMouse.chr6 517778 4 + 636262 TCCA -s mr.mrrefChr3 70032 4 + 181027 TCCA -s simRat_chr6.simRat.chr6 529023 4 + 647215 CCCA - -a -s simMouse_chr6.simMouse.chr6 517782 207 + 636262 ATTGATAGTCCAATGTCTTGTAGCTTAGTTCACtcagtgtattccatacagctcttctaggtcagttcacaagggtgtgacttcatgtcatcctgggggttgtgcaaacaactttggaatttgtatacaaaGATCTAGAATGTGAGACACAGTCTGCATGATCATATATCAAGGGCTTATTCCTATCTTGCCAATTGCCTAGTACAG -s mr.mrrefChr3 70036 207 + 181027 ATTGATAGTCCAATGTCTTGTAGCTTAGTTCACtcagtgtattccatacagctcttctaggtcagttcacaagggtgtgacttcatgtcatcctgggggttgtgcaaacaactttggaatttgtatacaaaGATCTAGAATGTGAGACACAGTCTGATTGGTCACATTTCAAGGGCTTATTCCTATCTTGCCAATTGCCTAGTACAA -s simRat_chr6.simRat.chr6 529031 206 + 647215 ATTGATCGTCCAATGTTTTGTAGCTCAGTTCACtcaatgtaatccatgtagctcttctaggtcggttcacaggggtgtgacttcaagttatgctgggggtggcgtcaacaactttggaatttatatacaaaGATCTAAAATGTGAGACAC-GTCTGATTGGTTACATTTCAAGGGCTTACTCCTACCTTGCCAATTACCTAGTACAA - -a -s simMouse_chr6.simMouse.chr6 517989 99 + 636262 TAGCTTAAGGAACGAATATACCATGGACATGTGGTGGGCCCTGTGAGGGGGAGAACATCAATGTCTAAAATATCCACCTGGCTTGTGATGTATACATGA -s mr.mrrefChr3 70246 99 + 181027 TAGCTTAAGGAACGAATATACCATGGCCATGGGATGGGCCCAGTGAGGGGGAGAACATCAGTGTCTAAAATATCCACCTGGCATGTGATGTATACATGA -s simRat_chr6.simRat.chr6 529240 99 + 647215 TAGCTCAAGGAACGAATATACCATGGCCATGGGATGACCCCAATGAGGGGGAGAGCGTCAGTGTCTAAGATATCCACCTGGCATGTGATGTATACATGA - -a -s simMouse_chr6.simMouse.chr6 518088 89 + 636262 GCATATGAGAAGATGCTGACCTGTGACAAAGGGGAGCCCATCTCTCTCACTATCCAAATAAGCTTGTATGCTGTACGTGCTTCCCTCCT -s Anc0.Anc0refChr3 130030 15 + 222631 --------------------------------------------------------------------------AAGACCTCCCTTTCT -s Anc1.Anc1refChr6 164422 15 + 197743 --------------------------------------------------------------------------AAGACCTCCCTTTCT -s Anc2.Anc2refChr1 43120 15 + 142988 --------------------------------------------------------------------------AAGACCTCCCTTTCT -s mr.mrrefChr3 70479 86 + 181027 ACATATGAGAAGATTTTGACC---GACAAAGGGGAGCCCATCTCTCTCACTATCCAAATAAGCTTGTATGCTGTACGTGCTTCCCTCCT -s simCow_chr6.simCow.chr6 499925 15 + 602619 --------------------------------------------------------------------------AAGACCCTCTTTTCT -s simDog_chr6.simDog.chr6 489552 14 + 593897 --------------------------------------------------------------------------GAGACCTCCC-CTCT -s simHuman_chr6.simHuman.chr6 496546 15 + 601863 --------------------------------------------------------------------------AGGACCTCCCTTTCT -s simRat_chr6.simRat.chr6 529483 86 + 647215 ACGTATGAGAAGATTTTGACC---GACAAAGGGTAGCCCATCTTACGCACTATCCAAATAAGCTTGTATGTTGTATGTGCTTCCACCCT - -a -s simMouse_chr6.simMouse.chr6 518177 8 + 636262 ACACTCCA -s Anc0.Anc0refChr3 130046 8 + 222631 AAGGTCCT -s Anc1.Anc1refChr6 164438 8 + 197743 AAGGTCCT -s Anc2.Anc2refChr1 43136 8 + 142988 AAGGTTCT -s mr.mrrefChr3 70565 8 + 181027 AAACTCCA -s simCow_chr6.simCow.chr6 499941 8 + 602619 AAGATTCT -s simDog_chr6.simDog.chr6 489567 8 + 593897 AAGGTTCT -s simHuman_chr6.simHuman.chr6 496562 8 + 601863 GAGGTCCT -s simRat_chr6.simRat.chr6 529571 8 + 647215 AAACTCAA - -a -s simMouse_chr6.simMouse.chr6 518185 28 + 636262 CAAGTTATATATGCAAGCACTGAAATCC -s Anc0.Anc0refChr3 130054 28 + 222631 AGGATTGTACAGGCAAACACTAAGATCC -s Anc1.Anc1refChr6 164446 28 + 197743 AGGATTGTACAGGCAAACACTAAGATCC -s Anc2.Anc2refChr1 43145 28 + 142988 AGGATTGTGCAGGCAAACACTAAGATCC -s mr.mrrefChr3 70573 28 + 181027 CAAGTTATACATGCAAGCACTGAAATCC -s simCow_chr6.simCow.chr6 499950 26 + 602619 AGGATTGTGCAGGCAA--AGTAAGATGC -s simDog_chr6.simDog.chr6 489576 28 + 593897 AGGATTGTGTAGGCGCACCCTGATATCC -s simHuman_chr6.simHuman.chr6 496570 28 + 601863 AGGATTGTACAGGCAAACACTAAGATCC -s simRat_chr6.simRat.chr6 529579 26 + 647215 CAAGT--TACATGCAAGCACCGAAATCC - -a -s simMouse_chr6.simMouse.chr6 518213 17 + 636262 CATATCCCATACACCAG -s Anc0.Anc0refChr3 130082 10 + 222631 CATA-------CACAAG -s Anc1.Anc1refChr6 164474 10 + 197743 CATA-------CACAAG -s Anc2.Anc2refChr1 43183 10 + 142988 CATA-------CACAAG -s mr.mrrefChr3 70601 17 + 181027 CATATCCCATACACCAG -s simCow_chr6.simCow.chr6 499986 10 + 602619 CACA-------CACAAA -s simDog_chr6.simDog.chr6 489614 10 + 593897 CATG-------TGCTAG -s simHuman_chr6.simHuman.chr6 496598 10 + 601863 CATA-------CACAAG -s simRat_chr6.simRat.chr6 529605 17 + 647215 CATAGCCTATACACCAG - -a -s simMouse_chr6.simMouse.chr6 518230 5 + 636262 GCTCA -s Anc0.Anc0refChr3 130094 5 + 222631 GCCCC -s Anc1.Anc1refChr6 164486 5 + 197743 GCCCC -s Anc2.Anc2refChr1 43195 5 + 142988 GCCCC -s mr.mrrefChr3 70620 5 + 181027 GCTCA -s simCow_chr6.simCow.chr6 499998 5 + 602619 GTCCC -s simDog_chr6.simDog.chr6 489626 5 + 593897 ACCCC -s simHuman_chr6.simHuman.chr6 496610 5 + 601863 GCACT -s simRat_chr6.simRat.chr6 529624 5 + 647215 GCTCA - -a -s simMouse_chr6.simMouse.chr6 518235 17 + 636262 TTTGGATCTAGCTGGCC -s Anc0.Anc0refChr3 130104 17 + 222631 TCTGGATCTAGCTGGCC -s Anc1.Anc1refChr6 164496 17 + 197743 TCTGGATCTAGCTGGCC -s Anc2.Anc2refChr1 43205 17 + 142988 TCTGGATTTAGCTGGCC -s mr.mrrefChr3 70625 17 + 181027 TTTGGATCTAGCTGGCC -s simCow_chr6.simCow.chr6 500008 9 + 602619 TCTG---TGAGC----- -s simDog_chr6.simDog.chr6 489636 17 + 593897 TCTGGATTTAGCTGGCC -s simHuman_chr6.simHuman.chr6 496620 17 + 601863 TCTAGATCTGGCTGGCC -s simRat_chr6.simRat.chr6 529629 17 + 647215 TTTGGATCTAGCCGGCC - -a -s simMouse_chr6.simMouse.chr6 518252 51 + 636262 ATGGAGGTAGTCTCAGAGTAGACTACAAGAGTGCTACCTGTAACAGCAACA -s Anc0.Anc0refChr3 130127 51 + 222631 ATCAAGGTAATGTCATAGTAGACTGCAGAAGTACTAGATGTGATAGCAACA -s Anc1.Anc1refChr6 164519 51 + 197743 ATCAAGGTAATGTCATAGTAGACTGCAGAAGTACTAGATGTGATAGCAACA -s Anc2.Anc2refChr1 43228 51 + 142988 ATCAGGGTAATGTCATAGCCGACTGCAGAAGTACTAGATGTGATAGCAACA -s mr.mrrefChr3 70642 51 + 181027 ATGGAGGTAATCTCAGAGTAGACTACAAGAGTGCTAGATGTAACAGCAACA -s simCow_chr6.simCow.chr6 500017 32 + 602619 -------------CATAGC------CAGAAGTACTAGATGTGATAGCAACA -s simDog_chr6.simDog.chr6 489659 51 + 593897 ATCAGGGTAATGTCATAGCCGACTGCAGAAGTACTACATGTGTTAGGAACA -s simHuman_chr6.simHuman.chr6 496643 51 + 601863 ATCAAGGTAATGTCACAGTAAACTGCAGAAGTACTAGATGTGATAGCAACA -s simRat_chr6.simRat.chr6 529646 51 + 647215 ATTGGGGTAATTTCAGAGCCGACTATGAGGGTGCTAGATGTAACAGCAACA - -a -s simMouse_chr6.simMouse.chr6 518303 11 + 636262 AATGGGGTATT -s Anc0.Anc0refChr3 130178 7 + 222631 AACGG----GT -s Anc1.Anc1refChr6 164570 7 + 197743 AACGG----GT -s Anc2.Anc2refChr1 43280 7 + 142988 AACGG----GT -s mr.mrrefChr3 70693 7 + 181027 AATGG----TT -s simCow_chr6.simCow.chr6 500050 7 + 602619 AATCG----GT -s simDog_chr6.simDog.chr6 489711 7 + 593897 GACGG----GT -s simRat_chr6.simRat.chr6 529697 7 + 647215 AACGG----TT - -a -s simMouse_chr6.simMouse.chr6 518314 7 + 636262 GTAATAA -s Anc0.Anc0refChr3 130185 7 + 222631 GTAATAA -s Anc1.Anc1refChr6 164577 7 + 197743 GTAATAA -s Anc2.Anc2refChr1 43289 7 + 142988 GTAATAT -s mr.mrrefChr3 70700 7 + 181027 GTAATAA -s simCow_chr6.simCow.chr6 500059 7 + 602619 GTAATGC -s simDog_chr6.simDog.chr6 489720 7 + 593897 GTAATAT -s simHuman_chr6.simHuman.chr6 496694 6 + 601863 -TAATAA -s simRat_chr6.simRat.chr6 529704 7 + 647215 GTAATAA - -a -s simMouse_chr6.simMouse.chr6 518321 2 + 636262 TT -s Anc0.Anc0refChr3 130199 2 + 222631 TT -s Anc1.Anc1refChr6 164591 2 + 197743 TT -s Anc2.Anc2refChr1 43316 2 + 142988 TT -s mr.mrrefChr3 70707 2 + 181027 TT -s simCow_chr6.simCow.chr6 500087 2 + 602619 TT -s simDog_chr6.simDog.chr6 489747 2 + 593897 TT -s simHuman_chr6.simHuman.chr6 496707 2 + 601863 TT -s simRat_chr6.simRat.chr6 529711 2 + 647215 TT - -a -s simMouse_chr6.simMouse.chr6 518323 8 + 636262 AACCATCG -s Anc0.Anc0refChr3 130201 8 + 222631 CACCTTAT -s Anc1.Anc1refChr6 164593 8 + 197743 CACCTTAT -s Anc2.Anc2refChr1 43318 8 + 142988 CACTTTAT -s mr.mrrefChr3 70709 8 + 181027 AACCATCT -s simCow_chr6.simCow.chr6 500094 8 + 602619 CTCTTTAT -s simDog_chr6.simDog.chr6 489749 8 + 593897 CACTGTAT -s simHuman_chr6.simHuman.chr6 496709 8 + 601863 TACCTTAT -s simRat_chr6.simRat.chr6 529713 8 + 647215 AACCACTT - -a -s simMouse_chr6.simMouse.chr6 518331 28 + 636262 TGTATTCCAAAATGTATATTGGACTAGA -s Anc0.Anc0refChr3 130209 27 + 222631 TGAGTTCTGAA-TGCCAACTGGACTATA -s Anc1.Anc1refChr6 164601 27 + 197743 TGAGTTCTGAA-TGCCAACTGGACTATA -s Anc2.Anc2refChr1 43326 27 + 142988 TGAGGTCTGAA-TGCCAACTGGACTATA -s mr.mrrefChr3 70717 28 + 181027 TGTATTCTGAAATGTATATTGGACTATA -s simCow_chr6.simCow.chr6 500153 27 + 602619 TGAGGCGTGAA-TACCAACTGGACTATA -s simDog_chr6.simDog.chr6 489757 27 + 593897 TCAGGTCTAAA-TGCCAACTGCATTACA -s simHuman_chr6.simHuman.chr6 496717 27 + 601863 TGATTTCTGAA-TGCCAACTAGACTATA -s simRat_chr6.simRat.chr6 529721 28 + 647215 TTTATTCTGAGATGTATATAGGACTATA - -a -s simMouse_chr6.simMouse.chr6 518359 93 + 636262 TAGCTGGTATATTTATTTGTATTTATTCTCAGCATCCTTGAAGCAGCTTAGATACGAGCCACCTGGCACAGTGCAAGCTTATAAGCCTATAAT -s Anc0.Anc0refChr3 130242 76 + 222631 CAAATGGTATAGTTCTTTATATTAATTCTAACTGTCCTTGTAGCTGT-TGAATACAAGCATCCTGACATATTGCAAT---------------- -s Anc1.Anc1refChr6 164634 92 + 197743 CAAATGGTATAGTTCTTTATATTAATTCTAACTGTCCTTGTAGCTGT-TGAATACAAGCATCCTGACATATTGCAATCTTACAAGCCCATAAT -s Anc2.Anc2refChr1 43359 76 + 142988 CAAATGGTATAGTCCTTTATATTAAGTCTAACTGTCCTTGTAGCTGT-TGAATACAGGCATCTTAACATATTGCAAT---------------- -s mr.mrrefChr3 70745 92 + 181027 TAACTGGTATATTTATTTGTATTTATTCTCACTATCCTTGAAGCAGC-TAGATACAAGCCACCTGGCACAGTGCAAGCTTACAAGCCTATAAT -s simCow_chr6.simCow.chr6 500186 63 + 602619 CAAATGGTATGG---TTTATA-TAACTCTAACTGTCCTTGAGGCTGT-TGAAGACAG---------CAAATTGTAAT---------------- -s simDog_chr6.simDog.chr6 489790 76 + 593897 CAAATGGTATAGTCCTTTATATTATGTCTAGCTGTCCTTGTAGCTGT-AGGATACAGGCATCTTAACATGTAGCAAT---------------- -s simHuman_chr6.simHuman.chr6 496750 92 + 601863 CAAGTGGTAAAGTTCTTTATATTAATACTAACTGTCCTTGGAGCTGT-TGAGTACAAGCATCCTGACCTATTGCAACCTTACAAGCCCATAAT -s simRat_chr6.simRat.chr6 529749 92 + 647215 TAACTGGTATATTTATTTGTATTTAATCTCACTATCCTTGAAGCAGC-CAGATACAAGCCACCTGGCACAGTGCAATCTTACGAGCCTCTAAT - -a -s simMouse_chr6.simMouse.chr6 518452 23 + 636262 GTTCAGACTTGGGGATTAATTAA -s Anc1.Anc1refChr6 164726 21 + 197743 gtttgcagttggctat--attaa -s mr.mrrefChr3 70837 23 + 181027 GTTCGGACTTGGGGATTAATTAA -s simHuman_chr6.simHuman.chr6 496942 21 + 601863 gtttgcagttggctat--attaa -s simRat_chr6.simRat.chr6 529841 23 + 647215 GTTCGGGCTTGGGGATTAATTAA - -a -s simMouse_chr6.simMouse.chr6 518475 8 + 636262 CCTGTTAT -s Anc1.Anc1refChr6 164747 8 + 197743 tctgttgc -s mr.mrrefChr3 70860 8 + 181027 CCTGTTAC -s simHuman_chr6.simHuman.chr6 496965 8 + 601863 tctgttgc -s simRat_chr6.simRat.chr6 529864 8 + 647215 CCTATTAC - -a -s simMouse_chr6.simMouse.chr6 518483 12 + 636262 CATCAAACACCC -s Anc0.Anc0refChr3 130318 7 + 222631 -----AACGCCC -s Anc1.Anc1refChr6 164755 12 + 197743 catgaAACGCCC -s Anc2.Anc2refChr1 43435 7 + 142988 -----AATGTCC -s mr.mrrefChr3 70868 12 + 181027 CATCAAACACCC -s simCow_chr6.simCow.chr6 500249 7 + 602619 -----AATGTCC -s simDog_chr6.simDog.chr6 489866 7 + 593897 -----AATGTTC -s simHuman_chr6.simHuman.chr6 496985 12 + 601863 catgaggccCCC -s simRat_chr6.simRat.chr6 529872 12 + 647215 CGTCAAACACCC - -a -s simMouse_chr6.simMouse.chr6 518495 37 + 636262 TGTGTTAGGCGGAGAAGGTGCTTGAGTGTGACGAGAT -s Anc0.Anc0refChr3 130328 12 + 222631 TCTCTTAGG-------------------------AAT -s Anc1.Anc1refChr6 164770 12 + 197743 TCTCTTAGG-------------------------AAT -s Anc2.Anc2refChr1 43445 12 + 142988 TCTCCTAGG-------------------------ATT -s mr.mrrefChr3 70880 12 + 181027 TGTCTTAGG-------------------------GAT -s simCow_chr6.simCow.chr6 500259 12 + 602619 TCTTCTAGG-------------------------ATC -s simDog_chr6.simDog.chr6 489876 12 + 593897 TCTCCTAGG-------------------------ATT -s simHuman_chr6.simHuman.chr6 497000 12 + 601863 TCTCTTGGG-------------------------AAT -s simRat_chr6.simRat.chr6 529884 12 + 647215 TGTCTTAGG-------------------------GAT - -a -s simMouse_chr6.simMouse.chr6 518532 15 + 636262 GTGACCTGTCGTAGT -s Anc0.Anc0refChr3 130346 15 + 222631 ATTACCTCTCTTAGT -s Anc1.Anc1refChr6 164788 15 + 197743 ATTACCTCTCTTAGT -s Anc2.Anc2refChr1 43463 15 + 142988 ATTACCTCTCTTAGT -s mr.mrrefChr3 70892 15 + 181027 GTGACCTGTCTTAGT -s simCow_chr6.simCow.chr6 500282 15 + 602619 ATTACCTGTTTTAAT -s simDog_chr6.simDog.chr6 489894 11 + 593897 A----CTCTCATAGG -s simHuman_chr6.simHuman.chr6 497018 15 + 601863 ATCACCTATCTTGGT -s simRat_chr6.simRat.chr6 529896 14 + 647215 GTGACCTGTCTTAG- - -a -s simMouse_chr6.simMouse.chr6 518547 3 + 636262 TTA -s Anc0.Anc0refChr3 130363 3 + 222631 TTA -s Anc1.Anc1refChr6 164805 3 + 197743 TTA -s Anc2.Anc2refChr1 43480 3 + 142988 TTA -s mr.mrrefChr3 70907 3 + 181027 TTA -s simCow_chr6.simCow.chr6 500299 3 + 602619 TTA -s simDog_chr6.simDog.chr6 489907 3 + 593897 TTA -s simHuman_chr6.simHuman.chr6 497035 3 + 601863 TTA -s simRat_chr6.simRat.chr6 529910 1 + 647215 --A - -a -s simMouse_chr6.simMouse.chr6 518550 2 + 636262 TA -s Anc0.Anc0refChr3 130366 2 + 222631 CA -s Anc1.Anc1refChr6 164808 2 + 197743 CA -s Anc2.Anc2refChr1 43483 2 + 142988 CA -s mr.mrrefChr3 70910 2 + 181027 TA -s simCow_chr6.simCow.chr6 500302 2 + 602619 CA -s simDog_chr6.simDog.chr6 489914 2 + 593897 CA -s simHuman_chr6.simHuman.chr6 497038 2 + 601863 CA -s simRat_chr6.simRat.chr6 529911 2 + 647215 TA - -a -s simMouse_chr6.simMouse.chr6 518552 13 + 636262 AAATTTTACAGTA -s Anc0.Anc0refChr3 130368 12 + 222631 AAATTA-ACAGTT -s Anc1.Anc1refChr6 164810 12 + 197743 AAATTA-ACAGTT -s Anc2.Anc2refChr1 43485 12 + 142988 AAATCA-CCAGTT -s mr.mrrefChr3 70912 13 + 181027 AAATTTTACAGTA -s simCow_chr6.simCow.chr6 500304 9 + 602619 A---CA-CCTGTT -s simDog_chr6.simDog.chr6 489917 12 + 593897 AAATCA-CCAGTC -s simHuman_chr6.simHuman.chr6 497040 12 + 601863 GAATTA-ACAGTT -s simRat_chr6.simRat.chr6 529913 13 + 647215 AAATCTCGCAATA - -a -s simMouse_chr6.simMouse.chr6 518565 14 + 636262 TTCAAGTGGCTTGT -s Anc0.Anc0refChr3 130380 14 + 222631 CTCAAGTAACGTGA -s Anc1.Anc1refChr6 164822 14 + 197743 CTCAAGTAACGTGA -s Anc2.Anc2refChr1 43497 14 + 142988 CTCAAGTAATGTGA -s mr.mrrefChr3 70925 14 + 181027 TTCAAGTGGCTTGT -s simCow_chr6.simCow.chr6 500313 14 + 602619 CTCAGGTGGTATCA -s simDog_chr6.simDog.chr6 489932 14 + 593897 CTCAAGTAATGTGA -s simHuman_chr6.simHuman.chr6 497052 14 + 601863 CTCAAGTAACCTGA -s simRat_chr6.simRat.chr6 529926 14 + 647215 TTCCAGTGGCTTGT - -a -s simMouse_chr6.simMouse.chr6 518579 13 + 636262 TAAGCCGTCATGA -s Anc0.Anc0refChr3 130394 13 + 222631 TAAACAGCAATGA -s Anc1.Anc1refChr6 164836 13 + 197743 TAAACAGCAATGA -s Anc2.Anc2refChr1 43511 13 + 142988 TGAACACCAATGA -s mr.mrrefChr3 70939 13 + 181027 TAAGCCGCCATGA -s simCow_chr6.simCow.chr6 500329 13 + 602619 TCAACACCAATGA -s simDog_chr6.simDog.chr6 489946 5 + 593897 TGAAC-------- -s simHuman_chr6.simHuman.chr6 497066 13 + 601863 GAAACTGCAATGA -s simRat_chr6.simRat.chr6 529940 13 + 647215 TAAGCCACGATGA - -a -s simMouse_chr6.simMouse.chr6 518592 66 + 636262 TTCTTCCCATTGTTAAGTCACATTGGCCCACCAATGCACATTCTTTATGGTATTGTTCTGTGTGAG -s Anc0.Anc0refChr3 130410 65 + 222631 TTGTTGTCAATGCTAAGCCACCTTGACCTAACAATTCA-ATCCTTTATGATGTTGTTCTGTATGCC -s Anc1.Anc1refChr6 164852 66 + 197743 TTGTTGTCAATGCTAAGCCACCTTGACCTAACAATTCATATCCTTTATGATGTTGTTCTGTATGCC -s Anc2.Anc2refChr1 43527 65 + 142988 CTATTGTCAATGCTAACCCCCCTTGACTTAATAATTCA-ATCCTTTATCATGTTGTTCTGTATGCC -s mr.mrrefChr3 70952 66 + 181027 TTGTTCCCAATGCTAAGTCACATTGGCCCACCAATGCATATTCTTTATGGTATTGTTCTGTGTGAG -s simCow_chr6.simCow.chr6 500345 65 + 602619 CTATTGGCAATGCTGGCCCCCATTGACTTCATAATTTG-ATTCTTTACAGCGTTGTACTGTATGAC -s simDog_chr6.simDog.chr6 489951 57 + 593897 -----ATTAATGCTAACCCCCCTTGACTTAATACCTCA-ATCCTTTATCATGTTGTTCTG---ACC -s simHuman_chr6.simHuman.chr6 497082 66 + 601863 TTGTTGTCAATGCCAAGCCACCTTGACCTAACAATTCATGTCCATTATGATGTTGCTCTGTATGGC -s simRat_chr6.simRat.chr6 529953 66 + 647215 TTGTTACCAATGCTAAGTCTCGTTTGCCCACCAATCCATATTCTCTATGGTATTGTTCTGTGTAAG - -a -s simMouse_chr6.simMouse.chr6 518658 52 + 636262 ATCACTAGAGATGTAAACCGACAACAGAATGGTTGGATTGTCTCTTCAACGA -s Anc0.Anc0refChr3 130475 49 + 222631 ATCATA---GATGTTAACCCACAAAAGAATGGTTGGATTGCCTTTGCATCAA -s Anc1.Anc1refChr6 164918 49 + 197743 ATCATA---GATGTTAACCCACAAAAGAATGGTTGGATTGCCTTTGCATCAA -s Anc2.Anc2refChr1 43592 49 + 142988 ATTACA---GATGCTAGCCCACAAAAGAATGGTTGGATTGCCTTTGCATCAA -s mr.mrrefChr3 71018 52 + 181027 ATCATTAGAGATGTAAACCCACAACAGAATGGTTGGATTGTCTCTTCAACGA -s simCow_chr6.simCow.chr6 500413 49 + 602619 ATTACA---GATTCTACCCCACAAAAGAGTAGTTAGATTGCCTCTATATCAA -s simDog_chr6.simDog.chr6 490008 48 + 593897 ATTACA---GACG-TAGCCCACAAAAGAATGGTTGGATTGCCTTTGCATCAA -s simHuman_chr6.simHuman.chr6 497148 49 + 601863 ATCATC---AATGTTCACCCACAAAAGAATGGTTGAATTGCCTTTGCACCAA -s simRat_chr6.simRat.chr6 530019 52 + 647215 ATCATTGGAGATGTAAACCCACCACAGAATGGTTGCATGGTCCCTTCAGTGA - -a -s simMouse_chr6.simMouse.chr6 518710 15 + 636262 TGCTACAAAGGGATA -s Anc0.Anc0refChr3 130524 15 + 222631 TGCTACAAAGGGAGA -s Anc1.Anc1refChr6 164967 15 + 197743 TGCTACAAAGGGAGA -s Anc2.Anc2refChr1 43641 15 + 142988 TGCTACAAAGGGAGA -s mr.mrrefChr3 71070 15 + 181027 TGCTACAAAGGGAAA -s simCow_chr6.simCow.chr6 500464 15 + 602619 TGCTACAAAAGGAGA -s simDog_chr6.simDog.chr6 490056 15 + 593897 TGCTACGAAGAGAGA -s simHuman_chr6.simHuman.chr6 497197 15 + 601863 GCCTACAAAGGGAGA -s simRat_chr6.simRat.chr6 530071 15 + 647215 TGCTACCAGGGGAAT - -a -s simMouse_chr6.simMouse.chr6 518725 13 + 636262 TGGTATGTATGAA -s Anc0.Anc0refChr3 130540 13 + 222631 TGTTACCTATGCA -s Anc1.Anc1refChr6 164983 13 + 197743 TGTTACCTATGCA -s Anc2.Anc2refChr1 43657 13 + 142988 TGTTACCCATCCG -s mr.mrrefChr3 71085 13 + 181027 TGGTATGTATGAA -s simCow_chr6.simCow.chr6 500480 13 + 602619 TGATACCCCTCTG -s simDog_chr6.simDog.chr6 490072 13 + 593897 CGTTGCCCATCCG -s simHuman_chr6.simHuman.chr6 497213 13 + 601863 TGTTACTTATGCA -s simRat_chr6.simRat.chr6 530086 13 + 647215 TGGTATGTATGAA - -a -s simMouse_chr6.simMouse.chr6 518738 12 + 636262 ATCTGTGAGGCT -s Anc0.Anc0refChr3 130553 12 + 222631 ATCAGTGGGGAC -s Anc1.Anc1refChr6 164996 12 + 197743 ATCAGTGGGGAC -s Anc2.Anc2refChr1 43670 12 + 142988 ATCAGTGGGGAC -s mr.mrrefChr3 71098 12 + 181027 ATCTGTGAGGCT -s simCow_chr6.simCow.chr6 500493 12 + 602619 ATTTGTGAGGAC -s simDog_chr6.simDog.chr6 490103 12 + 593897 ATCAATGGGGAC -s simHuman_chr6.simHuman.chr6 497226 12 + 601863 ACCGGTGGGGAC -s simRat_chr6.simRat.chr6 530099 12 + 647215 ATCTGTGATGCT - -a -s simMouse_chr6.simMouse.chr6 518750 38 + 636262 AGCAGGCATACCAAAAGATAGTTAGCTCAATGTGTCAA -s Anc0.Anc0refChr3 130565 31 + 222631 TGTAGACATATCAAATGAT-------TCATTGGGTTGG -s Anc1.Anc1refChr6 165008 31 + 197743 TGTAGACATATCAAATGAT-------TCATTGGGTTGG -s Anc2.Anc2refChr1 43682 31 + 142988 TGTAGACATATCAAATGAT-------TCATTGGGTTGG -s mr.mrrefChr3 71110 38 + 181027 AGCAGGCATACCAAAAGATAGTTAGCTCAATGTGTTGA -s simCow_chr6.simCow.chr6 500505 31 + 602619 TTCAGACATATGAAATGAT-------TCATTGGGCTAG -s simDog_chr6.simDog.chr6 490115 31 + 593897 AGTGGACATATCATAAGGT-------TCAATGGGTTGG -s simHuman_chr6.simHuman.chr6 497238 31 + 601863 TGTAGACATATCAAATGAT-------TCATTGGGTTGG -s simRat_chr6.simRat.chr6 530114 38 + 647215 AGCAGGCATACTATAAGATAGTTAGCTCAATGTGTTGA - -a -s simMouse_chr6.simMouse.chr6 518788 31 + 636262 GAAATCAGATAATAGAGGATCACCAACACTT -s Anc0.Anc0refChr3 130605 30 + 222631 TAAGG-AAATAAAAGAGGCTCACCAACCCCC -s Anc1.Anc1refChr6 165048 30 + 197743 TAAGG-AAATAAAAGAGGCTCACCAACCCCC -s Anc2.Anc2refChr1 43722 30 + 142988 TGAGG-AAATAAAAGAGGCTCACCAACCCCC -s mr.mrrefChr3 71148 30 + 181027 TAAAT-AGATAATAGAGGATCACCAACACTT -s simCow_chr6.simCow.chr6 500560 30 + 602619 TGAGG-AAATAAGAGAGGCTCACCAATCTCC -s simDog_chr6.simDog.chr6 490155 30 + 593897 TGAGG-CAAAAAAAGAGACTCACCAACCCCC -s simHuman_chr6.simHuman.chr6 497278 30 + 601863 TAAGG-AAGTAACAGAGGCTCACCAACCCCC -s simRat_chr6.simRat.chr6 530152 25 + 647215 TAAAT-AGATAATAGATGATCACCAA----- - -a -s simMouse_chr6.simMouse.chr6 518819 6 + 636262 GATTGC -s Anc0.Anc0refChr3 130636 6 + 222631 GATTGC -s Anc1.Anc1refChr6 165079 6 + 197743 GATTGC -s Anc2.Anc2refChr1 43753 6 + 142988 GATTTC -s mr.mrrefChr3 71178 6 + 181027 GATTGC -s simCow_chr6.simCow.chr6 500591 6 + 602619 GATTTC -s simDog_chr6.simDog.chr6 490186 6 + 593897 GATTTC -s simHuman_chr6.simHuman.chr6 497309 6 + 601863 GATAGC -s simRat_chr6.simRat.chr6 530177 3 + 647215 ---TCC - -a -s simMouse_chr6.simMouse.chr6 518825 1 + 636262 T -s Anc0.Anc0refChr3 130644 1 + 222631 G -s Anc1.Anc1refChr6 165087 1 + 197743 G -s Anc2.Anc2refChr1 43761 1 + 142988 G -s mr.mrrefChr3 71184 1 + 181027 G -s simCow_chr6.simCow.chr6 500599 1 + 602619 G -s simDog_chr6.simDog.chr6 490194 1 + 593897 A -s simHuman_chr6.simHuman.chr6 497317 1 + 601863 G -s simRat_chr6.simRat.chr6 530180 1 + 647215 G - -a -s simMouse_chr6.simMouse.chr6 518826 4 + 636262 TATA -s Anc0.Anc0refChr3 130645 4 + 222631 TACA -s Anc1.Anc1refChr6 165088 4 + 197743 TACA -s Anc2.Anc2refChr1 43762 4 + 142988 TCCA -s mr.mrrefChr3 71185 4 + 181027 TACA -s simCow_chr6.simCow.chr6 500601 4 + 602619 TTCA -s simDog_chr6.simDog.chr6 490195 4 + 593897 TCCA -s simHuman_chr6.simHuman.chr6 497318 4 + 601863 TACG -s simRat_chr6.simRat.chr6 530181 4 + 647215 TACA - -a -s simMouse_chr6.simMouse.chr6 518830 50 + 636262 TAACTGATCAACGAATACGAGCTTAAGTCACCTTTATGCTCAACACCTAG -s Anc0.Anc0refChr3 130650 50 + 222631 TAATTCCTCATCCAACACTAGCTTAAGGAACCTTTATGCTCAACACCTAG -s Anc1.Anc1refChr6 165093 50 + 197743 TAATTCCTCATCCAACACTAGCTTAAGGAACCTTTATGCTCAACACCTAG -s Anc2.Anc2refChr1 43767 50 + 142988 TAATTCCTCATCCAACACTAGCTTAAGGAACCTCTATGCTCAACACCTAG -s mr.mrrefChr3 71190 50 + 181027 TAATTGATCAACGAATACGAGCTTAAGTCACCTTTATGCTCAACACCTAG -s simCow_chr6.simCow.chr6 500606 49 + 602619 TAATTCCTCATCC-ACACTGGGTCAAGGTACCTCTACCCTCATTGCCTAA -s simDog_chr6.simDog.chr6 490200 44 + 593897 TAAATCCCCATACA--ACTAGCCTGAGGA----CTATGCTCAACACCTAG -s simHuman_chr6.simHuman.chr6 497323 50 + 601863 AAATCCCTCATCCAACACTAGCTTAAGGAACCTTTAAACACAACACCTAG -s simRat_chr6.simRat.chr6 530186 50 + 647215 TAATGGATCAACGAATACGAGTTTGAGTCACGTTTATGCTCAACACCTAG - -a -s simMouse_chr6.simMouse.chr6 518880 1 + 636262 C -s Anc0.Anc0refChr3 130703 1 + 222631 T -s Anc1.Anc1refChr6 165146 1 + 197743 T -s Anc2.Anc2refChr1 43820 1 + 142988 T -s mr.mrrefChr3 71243 1 + 181027 T -s simCow_chr6.simCow.chr6 500658 1 + 602619 T -s simDog_chr6.simDog.chr6 490247 1 + 593897 T -s simHuman_chr6.simHuman.chr6 497376 1 + 601863 T -s simRat_chr6.simRat.chr6 530239 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 518881 49 + 636262 CTCAGTATTGTTTGCTAAGAAGAGAGTCAACATGGTATATCCCCACTTA -s Anc0.Anc0refChr3 130710 40 + 222631 CCCAGTACTGTCTGATAAGAAGAGATT---------ATATGTTCACTTA -s Anc1.Anc1refChr6 165153 40 + 197743 CCCAGTACTGTCTGATAAGAAGAGATT---------ATATGTTCACTTA -s Anc2.Anc2refChr1 43827 40 + 142988 CCCAGTACTGTCTGATAAGATGAGATT---------ATATGTTCACTTA -s mr.mrrefChr3 71244 49 + 181027 CTCAGTATTGTTTGCTAAGAAGAGAGTCAACATGGTATATCCCCACTTA -s simCow_chr6.simCow.chr6 500665 40 + 602619 TGCAGTATTGTCTGATAAGATGAGATT---------ATATGTTTACTTA -s simDog_chr6.simDog.chr6 490254 40 + 593897 CCCAGTGCTGTCTGATAAGATGATGTT---------ATATGTTCACTTA -s simHuman_chr6.simHuman.chr6 497383 38 + 601863 CCCAGGACTGTCTGGTT-GCAGAGATT---------ATATGTTC-CCTA -s simRat_chr6.simRat.chr6 530240 49 + 647215 CTCAGTATTGTATGCTAAGAAGAGGGTTTAAAGGGTATATCTCCACTCA - -a -s simMouse_chr6.simMouse.chr6 518930 2 + 636262 CC -s Anc0.Anc0refChr3 130750 2 + 222631 CA -s Anc1.Anc1refChr6 165193 2 + 197743 CA -s Anc2.Anc2refChr1 43867 2 + 142988 GA -s mr.mrrefChr3 71293 2 + 181027 CC -s simCow_chr6.simCow.chr6 500707 2 + 602619 GA -s simDog_chr6.simDog.chr6 490294 2 + 593897 GA -s simHuman_chr6.simHuman.chr6 497421 2 + 601863 CT -s simRat_chr6.simRat.chr6 530289 2 + 647215 CC - -a -s simMouse_chr6.simMouse.chr6 518932 1 + 636262 A -s Anc0.Anc0refChr3 130752 1 + 222631 A -s Anc1.Anc1refChr6 165195 1 + 197743 A -s Anc2.Anc2refChr1 43869 1 + 142988 A -s mr.mrrefChr3 71295 1 + 181027 A -s simCow_chr6.simCow.chr6 500709 1 + 602619 A -s simDog_chr6.simDog.chr6 490296 1 + 593897 A -s simHuman_chr6.simHuman.chr6 497425 1 + 601863 A -s simRat_chr6.simRat.chr6 530291 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 518933 41 + 636262 AACCCTCCAGGTTGTTTAAGCTAGGTTGCCAGGGTCAGGAA -s Anc0.Anc0refChr3 130753 15 + 222631 AGTCCT--------------------------GGAAAGCAA -s Anc1.Anc1refChr6 165196 15 + 197743 AGTCCT--------------------------GGAAAGCAA -s Anc2.Anc2refChr1 43870 15 + 142988 AGTCCT--------------------------GGAAGGCAA -s mr.mrrefChr3 71296 41 + 181027 AACCCTCCAGGTTGTTTAAGCTAGGTTGCCAGGGTCAGGAA -s simCow_chr6.simCow.chr6 500710 15 + 602619 AGTCCT--------------------------GGAAGGCAA -s simDog_chr6.simDog.chr6 490297 15 + 593897 AATCCT--------------------------AGAAGGCAA -s simHuman_chr6.simHuman.chr6 497426 15 + 601863 AGTCCT--------------------------GAAAAGCAA -s simRat_chr6.simRat.chr6 530295 41 + 647215 AACCCTCGAGGTTATCTAAAGTAGGTTGCCAGGGTCAGGAA - -a -s simMouse_chr6.simMouse.chr6 518974 31 + 636262 TTCCCTAGAGAGTCTTATAAGGACCTGGCAT -s Anc0.Anc0refChr3 130768 25 + 222631 TTACCCCTGGACTTATCT------ATGGTAA -s Anc1.Anc1refChr6 165211 25 + 197743 TTACCCCTGGACTTATCT------ATGGTAA -s Anc2.Anc2refChr1 43885 25 + 142988 GTACCCCTGGACTTATCT------AAGGTAA -s mr.mrrefChr3 71337 31 + 181027 TTCCCTACAGAGTCTTATAAGGACCTGGTAT -s simCow_chr6.simCow.chr6 500729 25 + 602619 GTACCCCTGGATTTACCT------AAAGTGA -s simDog_chr6.simDog.chr6 490312 25 + 593897 GTACCCCTGGACTTATCT------AAGTTAA -s simHuman_chr6.simHuman.chr6 497441 25 + 601863 TTACCCCTTACCTTATCT------TTGGTAA -s simRat_chr6.simRat.chr6 530336 31 + 647215 TTCCCTACAGAGTCTCATAAGGATCTGGTAT - -a -s simMouse_chr6.simMouse.chr6 519005 41 + 636262 CCAAGTCCATTGTGTTCACCTACTTCAATCCATAGTTTCTA -s Anc0.Anc0refChr3 130803 41 + 222631 CCCAGGTGGTTTTATGTACCTACATCAATCCACAATTCCTA -s Anc1.Anc1refChr6 165246 41 + 197743 CCCAGGTGGTTTTATGTACCTACATCAATCCACAATTCCTA -s Anc2.Anc2refChr1 43920 41 + 142988 CCCAGGTGGTTTTATGTACCGACATCAATCCACAATTCATA -s mr.mrrefChr3 71385 41 + 181027 CCAAGTTCATTGTGTTCACCTACTTCAATCCACAGTTTCTA -s simCow_chr6.simCow.chr6 500764 41 + 602619 CCCAGGTAGTTTTATGTACCAACATCAATCCATGACTCATA -s simDog_chr6.simDog.chr6 490347 38 + 593897 CTCAGGTGGTTTTATGTACCGGTGTTGATCCACAGTTC--- -s simHuman_chr6.simHuman.chr6 497476 41 + 601863 CCTGGGTGGTTTTTTGTATCTACATCAATCCACAATTCCTA -s simRat_chr6.simRat.chr6 530384 41 + 647215 CCAAGTTCATCATGTTCACCTATTTCAATCCACAGTTTCTA - -a -s simMouse_chr6.simMouse.chr6 519046 65 + 636262 GGCCGTAGCAATAACCCACCATGCAATGTTTGCCGAGAAGCCGAAGGGCACAAAAATGTATTTGG -s Anc0.Anc0refChr3 130844 52 + 222631 GGCAATAGCAATAACCCACCATGTGTTGCATGCCAA-------------ACCATAATGTATTCCA -s Anc1.Anc1refChr6 165287 52 + 197743 GGCAATAGCAATAACCCACCATGTGTTGCATGCCAA-------------ACCATAATGTATTCCA -s Anc2.Anc2refChr1 43961 52 + 142988 GGCAATAGCAATAACCCACGATGTGTTGCATGCCAA-------------ACCATGCTGTATTCCA -s mr.mrrefChr3 71426 63 + 181027 GGCCATAGCAATAACCCACCATGCAATGTTTGCCAAGAAGCCG--GGGCACAAAAATGTATTTGG -s simCow_chr6.simCow.chr6 500806 48 + 602619 GGCAATAGCAATAACCCACTATGTGTTGCATGCCAT-------------CCCAT----TATTCCA -s simDog_chr6.simDog.chr6 490385 34 + 593897 ------------------CGATGTGTTGCATGCCAA-------------ACCATGCTGTATTCCA -s simHuman_chr6.simHuman.chr6 497517 52 + 601863 CATGACAGTAATAACCCGCCATAAGTTACATAACAA-------------ACCCTAATGTATTACA -s simRat_chr6.simRat.chr6 530425 63 + 647215 GGCTATAGCAACGACCATCCATGCACTGTTTGCTAAGAAGCCG--GGGCACAAAAACATAATTGG - -a -s simMouse_chr6.simMouse.chr6 519111 2 + 636262 GA -s Anc0.Anc0refChr3 130896 2 + 222631 GA -s Anc1.Anc1refChr6 165339 2 + 197743 GA -s Anc2.Anc2refChr1 44013 2 + 142988 GA -s mr.mrrefChr3 71489 2 + 181027 GA -s simCow_chr6.simCow.chr6 500855 2 + 602619 GA -s simDog_chr6.simDog.chr6 490419 2 + 593897 GA -s simHuman_chr6.simHuman.chr6 497569 2 + 601863 GA -s simRat_chr6.simRat.chr6 530488 2 + 647215 GA - -a -s simMouse_chr6.simMouse.chr6 519113 4 + 636262 TTTG -s Anc0.Anc0refChr3 130898 2 + 222631 TT-- -s Anc1.Anc1refChr6 165341 2 + 197743 TT-- -s Anc2.Anc2refChr1 44016 2 + 142988 TC-- -s mr.mrrefChr3 71491 4 + 181027 TTTG -s simCow_chr6.simCow.chr6 500858 2 + 602619 CC-- -s simDog_chr6.simDog.chr6 490422 2 + 593897 TC-- -s simHuman_chr6.simHuman.chr6 497571 2 + 601863 TT-- -s simRat_chr6.simRat.chr6 530490 4 + 647215 TTTG - -a -s simMouse_chr6.simMouse.chr6 519117 112 + 636262 CTGGCAAAAAACATGCTCATAACAAAAGAAAGGCAGGTGACACATAAAAACTATAAAAGTGTTAGAGTATGAAGAGATTTTTTGTTACCCCCTTTGGACGACTTATGCAAAT -s Anc0.Anc0refChr3 130900 49 + 222631 ----------------------------------------------------------ACTTTAGAGTCTAAAGAGATTTTTTGTTCCC----TT-GATGGCTTATGCAAAT -s Anc1.Anc1refChr6 165343 53 + 197743 ----------------------------------------------------------ACTTTAGAGTCTAAAGAGATTTTTTGTTCCCCCCTTT-GATGGCTTATGCAAAT -s Anc2.Anc2refChr1 44018 49 + 142988 ----------------------------------------------------------ACTTTAGAGTCTAAAGAGATTTTTTATTCCC----TT-TTTGGTTTATGCAAAT -s mr.mrrefChr3 71495 94 + 181027 CTGGCAAAAAACATGCTCATAACA----AAAGGCAGGTGACACAT-------------GTGTTAGAGTATGAAGAGATTTTTTGTTACCCCCTTT-GACGACTTATGCAAAT -s simCow_chr6.simCow.chr6 500860 48 + 602619 ----------------------------------------------------------ACTTTAGAGTC-AAAGAGATTTTTTATTCCC----CT-ATTAGTTTATGCATAT -s simDog_chr6.simDog.chr6 490424 49 + 593897 ----------------------------------------------------------ACTTTAGAGTCTCAAGAGATTTTTTATTCCC----TT-TTTGGTTTATGCAAAT -s simHuman_chr6.simHuman.chr6 497573 53 + 601863 ----------------------------------------------------------ACTCTAGAGTCTAGAGAGATTTTTTGTTCCCCCCTTT-GATGGCTTCTGAACAT -s simRat_chr6.simRat.chr6 530499 78 + 647215 CTGGCAAAAAACATGCTCATGACA----AAGGGCAGGTGACACAT-----------------------------AGATTTTTTGTTAACCCCTTT-GACGACTTATGCAAAT - -a -s simMouse_chr6.simMouse.chr6 519229 10 + 636262 GATAACAGGA -s Anc0.Anc0refChr3 130949 10 + 222631 GAAAACAGGA -s Anc1.Anc1refChr6 165396 10 + 197743 GAAAACAGGA -s Anc2.Anc2refChr1 44067 10 + 142988 GAAAACAGGA -s mr.mrrefChr3 71589 10 + 181027 GATAACAGGA -s simCow_chr6.simCow.chr6 500909 10 + 602619 GAAAACAGGA -s simDog_chr6.simDog.chr6 490473 10 + 593897 GAAAACAGGA -s simHuman_chr6.simHuman.chr6 497626 10 + 601863 AGAAACAGGA -s simRat_chr6.simRat.chr6 530577 10 + 647215 GATACCAGAA - -a -s simMouse_chr6.simMouse.chr6 519239 34 + 636262 TTATGTCTGAATTTAAACAAATATGTGACACAGC -s Anc0.Anc0refChr3 130959 10 + 222631 CCATGACTGA------------------------ -s Anc1.Anc1refChr6 165406 10 + 197743 CCATGACTGA------------------------ -s Anc2.Anc2refChr1 44078 10 + 142988 CCATAAATTG------------------------ -s mr.mrrefChr3 71599 34 + 181027 TTATGTCTGAATTTAAACAAATATGTGACACAGC -s simCow_chr6.simCow.chr6 500922 9 + 602619 TTATAAATT------------------------- -s simDog_chr6.simDog.chr6 490484 10 + 593897 CCATAAATTG------------------------ -s simHuman_chr6.simHuman.chr6 497636 10 + 601863 CCACGACTGA------------------------ -s simRat_chr6.simRat.chr6 530587 34 + 647215 TTTTGCCTTAGTCTCAACGAAAGCCACCCACAAC - -a -s simMouse_chr6.simMouse.chr6 519273 42 + 636262 ATCGACATGCTGTATATTTTTTATTTTTCAACAGAACTATCT -s Anc0.Anc0refChr3 130969 14 + 222631 ----------------------------CTGCAGTACTGTCA -s Anc1.Anc1refChr6 165416 14 + 197743 ----------------------------CTGCAGTACTGTCA -s Anc2.Anc2refChr1 44088 14 + 142988 ----------------------------CTACAGTACTGTCA -s mr.mrrefChr3 71633 40 + 181027 ATCGACAT--TGTATATTTTTTATTTTTCTGCAGAACTATCT -s simCow_chr6.simCow.chr6 500931 14 + 602619 ----------------------------CTACAATACTGTCA -s simDog_chr6.simDog.chr6 490494 14 + 593897 ----------------------------CTACAGTACTATCT -s simHuman_chr6.simHuman.chr6 497646 14 + 601863 ----------------------------CTGCAGTATAGTTA -s simRat_chr6.simRat.chr6 530622 40 + 647215 ATAGACAT--TGTATATTTTTGATTTTTCTGCAGAACTATCT - -a -s simMouse_chr6.simMouse.chr6 519315 14 + 636262 GTTGATGACATAAC -s Anc0.Anc0refChr3 130990 14 + 222631 GTCACCTACACTAC -s Anc1.Anc1refChr6 165437 14 + 197743 GTCACCTACACTAC -s Anc2.Anc2refChr1 44109 14 + 142988 GTCACCTACTCTAC -s mr.mrrefChr3 71673 14 + 181027 GTTGATGACATAAC -s simCow_chr6.simCow.chr6 500949 14 + 602619 GTCACTTACCCTAC -s simDog_chr6.simDog.chr6 490515 14 + 593897 GTCACCTACTCTGC -s simHuman_chr6.simHuman.chr6 497667 14 + 601863 GTCACATACACTAC -s simRat_chr6.simRat.chr6 530662 14 + 647215 GTTGATGACATAAC - -a -s simMouse_chr6.simMouse.chr6 519329 18 + 636262 TGCTTTAATTCAGCCATA -s Anc0.Anc0refChr3 131004 3 + 222631 CC---------------A -s Anc1.Anc1refChr6 165451 3 + 197743 CC---------------A -s Anc2.Anc2refChr1 44125 3 + 142988 CC---------------A -s mr.mrrefChr3 71687 17 + 181027 TGCTTTAA-TCAGCCATA -s simCow_chr6.simCow.chr6 500965 3 + 602619 CC---------------A -s simDog_chr6.simDog.chr6 490531 3 + 593897 CC---------------A -s simHuman_chr6.simHuman.chr6 497681 3 + 601863 CA---------------A -s simRat_chr6.simRat.chr6 530676 17 + 647215 TGCTTCAA-TCAGTCATA - -a -s simMouse_chr6.simMouse.chr6 519347 71 + 636262 TGCACCAGGATCACCATGTACTGTGATTTCTGTATCTCTTCTTCTCACAAAGGAAATTAGTCAACAATGGA -s Anc0.Anc0refChr3 131007 50 + 222631 TGGACCAGGGCCA-------------------TATCTCC-AT-CACACAGAGGAAATTGGTCAGCAATGGA -s Anc1.Anc1refChr6 165454 51 + 197743 TGGACCAGGGCCA-------------------TATCTCCAAT-CACACAGAGGAAATTGGTCAGCAATGGA -s Anc2.Anc2refChr1 44128 50 + 142988 TGGACCAAGGGTG-------------------TATCTCC-AT-CATACTGAGGAAATTGGTCAGCAATGGG -s mr.mrrefChr3 71704 71 + 181027 TGCACCAGGACCACCATGTACTGTGATTTCTGTATCTCTTCTTCTCACAGAGGAAATTAGTCAGCAATGGA -s simCow_chr6.simCow.chr6 500968 50 + 602619 TGGACCAAGGGTG-------------------TATCTCC-AC-CATACTGATAAAACTGGTCAGCAGTGGG -s simDog_chr6.simDog.chr6 490534 50 + 593897 TGTACTAAGGGTG-------------------TATCTCT-GT-AATACTGAGGAAATTGGTCACCAAAGGG -s simHuman_chr6.simHuman.chr6 497684 51 + 601863 TAGACCAGGGCCA-------------------TATCTCCAAT-CACACAGAGGAAATTGGCCAGCAATGGA -s simRat_chr6.simRat.chr6 530702 71 + 647215 TGCACCAGGACCACCATGTGCTCTGATTTCTGTATCTCTGCTTTGCACAGGGGAAATTAGTCAGCAATGGA - -a -s simMouse_chr6.simMouse.chr6 519418 15 + 636262 GTAGGGTGATGGTTT -s Anc0.Anc0refChr3 131080 15 + 222631 GTAAGGTGATGGTTT -s Anc1.Anc1refChr6 165528 15 + 197743 GTAAGGTGATGGTTT -s Anc2.Anc2refChr1 44205 15 + 142988 GTGAGGTGATGGTTT -s mr.mrrefChr3 71775 15 + 181027 GTAGGGTGATGGTTT -s simCow_chr6.simCow.chr6 501047 15 + 602619 GTGAGGCTATGGTTT -s simDog_chr6.simDog.chr6 490611 15 + 593897 ATGAGGTGATGGATT -s simHuman_chr6.simHuman.chr6 497758 15 + 601863 GTAAGGTGATGGTTT -s simRat_chr6.simRat.chr6 530773 15 + 647215 GTAGGGTGATGGTTT - -a -s simMouse_chr6.simMouse.chr6 519433 48 + 636262 TAGTAAGCTAGTCCAAAAAACATTTCCCTGTGAATCATTCTCATGATC -s Anc0.Anc0refChr3 131095 48 + 222631 GAGTAAGCTAGTCCAAAGAACATTTCCCCATGAATTAATCTCAAAGTA -s Anc1.Anc1refChr6 165543 48 + 197743 GAGTAAGCTAGTCCAAAGAACATTTCCCCATGAATTAATCTCAAAGTA -s Anc2.Anc2refChr1 44220 48 + 142988 GAGTAAGCTAGTCCAAAGAACATTCTCCCATGAATTAACCTCAAAGTA -s mr.mrrefChr3 71790 48 + 181027 TAGTAAGCTAGTCCAAAAAACATTTCCCTGTGAATCAATCTCATGATA -s simCow_chr6.simCow.chr6 501063 48 + 602619 GAGAAAGTTAGTCCAAAGAACTTCCTGCCATGAATTGACCTTGAAGTA -s simDog_chr6.simDog.chr6 490626 45 + 593897 GAGTAAGCTAGTCCAAAGAATATTCTCCC---AATCACCCTCAAAGCA -s simHuman_chr6.simHuman.chr6 497773 48 + 601863 CAGTAAGCTAGTCCAAAGGACATTTCCCCATGAATTAATCTCACAGTA -s simRat_chr6.simRat.chr6 530788 48 + 647215 TAGTAAGCTAGACCAAAAAACATTTCCCTGTGAATCAATCTCGTGATA - -a -s simMouse_chr6.simMouse.chr6 519481 44 + 636262 ATGCCAGCCAGATCTAGAGTGTTTAGTTGTCTTGTCGCAGCCAA -s Anc0.Anc0refChr3 131175 44 + 222631 TCATCATCTAAATCTTGAGTTCTCAATCATTTAGTCCCTGCTAA -s Anc1.Anc1refChr6 165624 44 + 197743 TCATCATCTAAATCTTGAGTTCTCAATCATTTAGTCCCTGCTAA -s Anc2.Anc2refChr1 44300 44 + 142988 TCATCATCTGAATCTTGAGTTCTCAATCATTTAGTCCCTGTTAA -s mr.mrrefChr3 71866 44 + 181027 ACACCAGCCAGATCTTGAGTGTTTAGTTGTCTAGTCGCAGCCAA -s simCow_chr6.simCow.chr6 501143 44 + 602619 TCATCATCAGAATCTTGAGTTCTCAGTCACTTAGTCCCTGTTAA -s simDog_chr6.simDog.chr6 490704 44 + 593897 TCATCATCTGAATCTTGAGTTCTCAATCTTCTAGTCCCTGTAGA -s simHuman_chr6.simHuman.chr6 497854 44 + 601863 TCATCATCTAAATCTTGAGTTCTCAATCATTTAGTCCCTGCTAA -s simRat_chr6.simRat.chr6 530864 44 + 647215 CCACTAGCGAGATCTTGAGTGGTTGGTTGTCTACTCTTGGCCAA - -a -s simMouse_chr6.simMouse.chr6 519525 14 + 636262 GGCACCTTTGAGTT -s Anc0.Anc0refChr3 131221 13 + 222631 -ACAGCATTGAATT -s Anc1.Anc1refChr6 165670 14 + 197743 TACAGCATTGAATT -s Anc2.Anc2refChr1 44346 13 + 142988 -ACAGCATTGGACT -s mr.mrrefChr3 71910 14 + 181027 GGCACCATTGAGTT -s simCow_chr6.simCow.chr6 501188 13 + 602619 -ACACCACTGGACT -s simDog_chr6.simDog.chr6 490750 13 + 593897 -ACAGTATTGGACT -s simHuman_chr6.simHuman.chr6 497905 14 + 601863 TACATCATTGAATT -s simRat_chr6.simRat.chr6 530908 14 + 647215 ATTACCATTAAGTT - -a -s simMouse_chr6.simMouse.chr6 519539 9 + 636262 TAATAGTCA -s Anc0.Anc0refChr3 131234 9 + 222631 TGGTAGCCT -s Anc1.Anc1refChr6 165684 9 + 197743 TGGTAGCCT -s Anc2.Anc2refChr1 44359 9 + 142988 TAGTAACCT -s mr.mrrefChr3 71924 9 + 181027 TGATAGTCA -s simCow_chr6.simCow.chr6 501203 9 + 602619 TAGTAACCT -s simDog_chr6.simDog.chr6 490763 9 + 593897 TAGTAACCT -s simHuman_chr6.simHuman.chr6 497919 9 + 601863 TGGTAGCCT -s simRat_chr6.simRat.chr6 530922 9 + 647215 TGATAGTAA - -a -s simMouse_chr6.simMouse.chr6 519548 6 + 636262 AGTTTT -s Anc0.Anc0refChr3 131243 5 + 222631 G-TTTT -s Anc1.Anc1refChr6 165693 6 + 197743 GTTTTT -s Anc2.Anc2refChr1 44368 5 + 142988 G-TTTT -s mr.mrrefChr3 71933 6 + 181027 AGTTTT -s simCow_chr6.simCow.chr6 501213 5 + 602619 G-TTTT -s simDog_chr6.simDog.chr6 490772 5 + 593897 G-CTTT -s simHuman_chr6.simHuman.chr6 497928 6 + 601863 GTTTTT -s simRat_chr6.simRat.chr6 530931 6 + 647215 AGTTTT - -a -s simMouse_chr6.simMouse.chr6 519554 9 + 636262 GTAACTGTC -s Anc0.Anc0refChr3 131248 9 + 222631 GTAACTGTC -s Anc1.Anc1refChr6 165699 9 + 197743 GTAACTGTC -s Anc2.Anc2refChr1 44373 9 + 142988 GTAATTGTC -s mr.mrrefChr3 71939 9 + 181027 GTAACTGTC -s simCow_chr6.simCow.chr6 501218 9 + 602619 GTAATTGTC -s simDog_chr6.simDog.chr6 490777 9 + 593897 GTTATTGGC -s simHuman_chr6.simHuman.chr6 497935 9 + 601863 GTAACTGTC -s simRat_chr6.simRat.chr6 530937 9 + 647215 GTCACTGCC - -a -s simMouse_chr6.simMouse.chr6 519563 8 + 636262 CTGGGGTT -s Anc0.Anc0refChr3 131263 8 + 222631 CTGGGGTC -s Anc1.Anc1refChr6 165714 8 + 197743 CTGGGGTC -s Anc2.Anc2refChr1 44388 8 + 142988 CTGGGATC -s mr.mrrefChr3 71948 8 + 181027 CTGGGGTT -s simCow_chr6.simCow.chr6 501233 8 + 602619 CTGGGATC -s simDog_chr6.simDog.chr6 490792 8 + 593897 CTGAGATC -s simHuman_chr6.simHuman.chr6 497950 8 + 601863 CTGGGGTC -s simRat_chr6.simRat.chr6 530946 8 + 647215 CTGGGGTT - -a -s simMouse_chr6.simMouse.chr6 519571 13 + 636262 TAATTGAATCCAG -s Anc0.Anc0refChr3 131317 13 + 222631 CAACTTAATAACA -s Anc1.Anc1refChr6 165768 13 + 197743 CAACTTAATAACA -s Anc2.Anc2refChr1 44442 13 + 142988 CAACTTAATAACA -s mr.mrrefChr3 71956 13 + 181027 TAATTGAATCCAG -s simCow_chr6.simCow.chr6 501288 13 + 602619 CAACTTAATACAA -s simDog_chr6.simDog.chr6 490847 13 + 593897 CAACCTGATAACA -s simHuman_chr6.simHuman.chr6 498004 13 + 601863 CAACTTAATTACA -s simRat_chr6.simRat.chr6 530954 13 + 647215 TAATTGAACCCTG - -a -s simMouse_chr6.simMouse.chr6 519584 20 + 636262 CATAGACTACTATGATGTGG -s Anc0.Anc0refChr3 131330 20 + 222631 CTTATACCAGTATGATGTGA -s Anc1.Anc1refChr6 165781 20 + 197743 CTTATACCAGTATGATGTGA -s Anc2.Anc2refChr1 44455 20 + 142988 CTTATACCAGTATGATGTGA -s mr.mrrefChr3 71969 20 + 181027 CATAGACTACTATGATGTGG -s simCow_chr6.simCow.chr6 501301 20 + 602619 CTTATACCAATATAATCTGG -s simDog_chr6.simDog.chr6 490860 20 + 593897 CTTATATCAGTATGATGTGA -s simHuman_chr6.simHuman.chr6 498019 20 + 601863 TGTATACCAGTATGTTGTGA -s simRat_chr6.simRat.chr6 530967 20 + 647215 CATAGGCTACTATGATAAGG - -a -s simMouse_chr6.simMouse.chr6 519604 12 + 636262 AGAAGTTAGTGA -s Anc0.Anc0refChr3 131350 12 + 222631 AAAGGTTAGTGA -s Anc1.Anc1refChr6 165801 12 + 197743 AAAGGTTAGTGA -s Anc2.Anc2refChr1 44475 12 + 142988 AAAGGTTTGTGA -s mr.mrrefChr3 71989 12 + 181027 AGAAGTTAGTGA -s simCow_chr6.simCow.chr6 501321 12 + 602619 AACGGGTGCTTA -s simDog_chr6.simDog.chr6 490881 11 + 593897 GGAGGTTTGTG- -s simHuman_chr6.simHuman.chr6 498039 12 + 601863 AAAGGTTAGTGA -s simRat_chr6.simRat.chr6 530987 12 + 647215 AGAAGTTAGTGA - -a -s simMouse_chr6.simMouse.chr6 519616 6 + 636262 ACTTGT -s Anc0.Anc0refChr3 131365 6 + 222631 ATTTGC -s Anc1.Anc1refChr6 165816 6 + 197743 ATTTGC -s Anc2.Anc2refChr1 44490 6 + 142988 ATTTCC -s mr.mrrefChr3 72001 6 + 181027 ACTTGT -s simCow_chr6.simCow.chr6 501337 6 + 602619 ATTTCC -s simHuman_chr6.simHuman.chr6 498054 6 + 601863 ATTTGG -s simRat_chr6.simRat.chr6 530999 6 + 647215 ACTTGT - -a -s simMouse_chr6.simMouse.chr6 519622 2 + 636262 AT -s Anc0.Anc0refChr3 131371 2 + 222631 AT -s Anc1.Anc1refChr6 165822 2 + 197743 AT -s Anc2.Anc2refChr1 44496 2 + 142988 CC -s mr.mrrefChr3 72007 2 + 181027 AT -s simCow_chr6.simCow.chr6 501343 2 + 602619 CC -s simHuman_chr6.simHuman.chr6 498119 2 + 601863 AT -s simRat_chr6.simRat.chr6 531005 2 + 647215 TC - -a -s simMouse_chr6.simMouse.chr6 519624 84 + 636262 ATCTTGCCTAGCCATTATTAGGTAATATAGCCCTTGTGAATCAGGTACAGTGATTTTATGCCGGCCTTGGCACCATCAaataga -s Anc0.Anc0refChr3 131373 67 + 222631 ATC--ACCTAGCTATTATTAGGTAATATC-CCCTTGT-AATTTGGTGTAGTGAGTTCATTCTAGCCATGGA------------- -s Anc1.Anc1refChr6 165824 67 + 197743 ATC--ACCTAGCTATTATTAGGTAATATC-CCCTTGT-AATTTGGTGTAGTGAGTTCATTCTAGCCATGGA------------- -s Anc2.Anc2refChr1 44499 67 + 142988 ATC--ACCTATCTGTTGTTAGGGAATATC-CCCTTAT-AGTTTGGTGTAGTGAGTTCATTCTAGCCATGGA------------- -s mr.mrrefChr3 72009 83 + 181027 ATCTTGCCTAGCCATTATTAGGTAATATA-CCCTTGTGAATCAGGTACAGTGATTTTATGCCGGCCTTGGCACCATCAaataga -s simCow_chr6.simCow.chr6 501346 67 + 602619 ATC--ACCTATCTGGTGTTAGGGAATATC-CCCTTAT-AGATTGGGGGAGTGACCCCATTCTAGCTATGGA------------- -s simDog_chr6.simDog.chr6 490892 59 + 593897 ----------TCCGTTGTTAGGGATTTTC-CCCTTAT-AGTTTGATGTAGTGAGTTCATTCTATCCGTGGA------------- -s simHuman_chr6.simHuman.chr6 498121 67 + 601863 ATC--ACTTAGATATCATTAGGTGATATC-CCCTTGT-AATTTGGTGTAGTGAATTCACTCTAGCCATGGA------------- -s simRat_chr6.simRat.chr6 531007 83 + 647215 ATCTTGCCTAACCATTATTAGGTAATATA-CCCTTATGAATCAGGTATAGTGATTTTATGCTGGCCATTGAACCATCAAATAGA - -a -s simMouse_chr6.simMouse.chr6 519768 4 + 636262 tcgt -s mr.mrrefChr3 72152 4 + 181027 tcgt -s simRat_chr6.simRat.chr6 531165 4 + 647215 tcat - -a -s simMouse_chr6.simMouse.chr6 519806 22 + 636262 GCAACAGAGGTGAAGCAGTTGA - -a -s simMouse_chr6.simMouse.chr6 519854 35 + 636262 CAGTCTGCCCACTATAATTTCCCACACCCCACAAC -s mr.mrrefChr3 72216 35 + 181027 CAGTCTGCCCACTATAATTTCCCACACCCCACAAC -s simRat_chr6.simRat.chr6 531229 35 + 647215 AGGTCTGCCCACTATAAGTTCCCACACCTTTCTAC - -a -s simMouse_chr6.simMouse.chr6 519892 1 + 636262 T -s mr.mrrefChr3 72254 1 + 181027 T -s simRat_chr6.simRat.chr6 531267 1 + 647215 C - -a -s simMouse_chr6.simMouse.chr6 519939 2 + 636262 AA -s Anc1.Anc1refChr6 166060 2 + 197743 GA -s mr.mrrefChr3 72301 2 + 181027 AA -s mr.mrrefChr5 61289 2 - 294540 GA -s simRat_chr6.simRat.chr6 268176 2 - 647215 CA -s simRat_chr6.simRat.chr6 452850 2 + 647215 GA -s simRat_chr6.simRat.chr6 531315 2 + 647215 AA - -a -s simMouse_chr6.simMouse.chr6 519942 29 + 636262 ATATGAGAAGGACAGTACAGAAACCTATC -s mr.mrrefChr3 72304 29 + 181027 ATATGAGAAGGACAGTACAGAAACCTATC -s simRat_chr6.simRat.chr6 531318 29 + 647215 ATATAAGAAGGATGTTTCAGAAGCCTAAT - -a -s simMouse_chr6.simMouse.chr6 520057 7 + 636262 AACAAAC - -a -s simMouse_chr6.simMouse.chr6 520229 2 + 636262 TC -s mr.mrrefChr3 72584 2 + 181027 TC -s simRat_chr6.simRat.chr6 531657 2 + 647215 TA - -a -s simMouse_chr6.simMouse.chr6 520253 18 + 636262 GATTCAGTTTTTTCATCA -s Anc0.Anc0refChr3 131442 8 + 222631 -----AGTGATAC----- -s Anc1.Anc1refChr6 166338 13 + 197743 -----AGTGATACCATCA -s Anc2.Anc2refChr1 44568 8 + 142988 -----AATGATAC----- -s mr.mrrefChr3 72608 17 + 181027 GA-TCAGTTTTTCCATCA -s simCow_chr6.simCow.chr6 501415 8 + 602619 -----AATGATAC----- -s simDog_chr6.simDog.chr6 490953 5 + 593897 --------GATAC----- -s simHuman_chr6.simHuman.chr6 498190 13 + 601863 -----AGTGATACCATCA -s simRat_chr6.simRat.chr6 531684 17 + 647215 GA-TCAGTTTCTCCATCA - -a -s simMouse_chr6.simMouse.chr6 520271 24 + 636262 ACAAGACACTTTACCACTAAATCT -s Anc0.Anc0refChr3 131452 18 + 222631 ACTAGTCTTC------ATGAGTCT -s Anc1.Anc1refChr6 166353 18 + 197743 ACTAGTCTTC------ATGAGTCT -s Anc2.Anc2refChr1 44578 18 + 142988 ACTAGTCTCC------ATGAGTAT -s mr.mrrefChr3 72625 24 + 181027 ACCAGACATCTTACCACTAAATCT -s simCow_chr6.simCow.chr6 501425 17 + 602619 ACTAGTC-CC------ATGAATAC -s simDog_chr6.simDog.chr6 490960 18 + 593897 ACTAGTCTCA------ATGAGTAT -s simHuman_chr6.simHuman.chr6 498207 18 + 601863 ACTAGTCTTC------ATGAGTCT -s simRat_chr6.simRat.chr6 531701 24 + 647215 AACAGGCATCTTACAACCGAATCT - -a -s simMouse_chr6.simMouse.chr6 520295 33 + 636262 AACGTGTTACCTGTTGCCTTAATCACACCACAG -s Anc0.Anc0refChr3 131470 31 + 222631 TA-GTCCTACCCTTTGCCT-AATCACATCACAG -s Anc1.Anc1refChr6 166371 31 + 197743 TA-GTCCTACCCTTTGCCT-AATCACATCACAG -s Anc2.Anc2refChr1 44596 31 + 142988 TA-GTCCTACCCTTTGCCT-AATCACATCATAG -s mr.mrrefChr3 72649 32 + 181027 AATGTGTTACCTGTTGCCT-AATCACATTACAG -s simCow_chr6.simCow.chr6 501442 25 + 602619 AA-GTCCTACTCTTAGCTC-AATCATA------ -s simDog_chr6.simDog.chr6 490978 31 + 593897 TA-GACCTACCCTTTGCCT-AATCACATCATAG -s simHuman_chr6.simHuman.chr6 498225 30 + 601863 TA-GTCCTACCCTTTGCCT-AGTC-CATCACAG -s simRat_chr6.simRat.chr6 531726 32 + 647215 AATGTGTTACCTGTTGTCT-AATCACATTACAG - -a -s simMouse_chr6.simMouse.chr6 520328 36 + 636262 CGTTACAGATGGTTCTCTCTTTGCGCTGACCTACTG -s Anc0.Anc0refChr3 131501 36 + 222631 TATGATAGATGGTTTTCTCTTTGAGATGATTTCCTT -s Anc1.Anc1refChr6 166402 36 + 197743 TATGATAGATGGTTTTCTCTTTGAGATGATTTCCTT -s Anc2.Anc2refChr1 44632 36 + 142988 TATGATAGATGGTTTTCTCGTTGAGATGATTTCCTT -s mr.mrrefChr3 72681 36 + 181027 TGTTACAGATGGTTCTCTCTTTGAGCTGACCTACTG -s simCow_chr6.simCow.chr6 501467 28 + 602619 --------ATGGTTTTCTCATTGAGGTGGTGTCCTT -s simDog_chr6.simDog.chr6 491014 35 + 593897 TATGATAGATGGTTTTTCCGTTGAGATGATTT-TGG -s simHuman_chr6.simHuman.chr6 498255 36 + 601863 GATGATACATGGTTTTCTATCTGAGATCATTTCCTT -s simRat_chr6.simRat.chr6 531758 36 + 647215 TGTTACAGACGGTTCTCTCTTTGAGCTGACCTACTG - -a -s simMouse_chr6.simMouse.chr6 520364 2 + 636262 CT -s Anc0.Anc0refChr3 131537 2 + 222631 CT -s Anc1.Anc1refChr6 166438 2 + 197743 CT -s Anc2.Anc2refChr1 44668 2 + 142988 CT -s mr.mrrefChr3 72717 2 + 181027 CT -s simCow_chr6.simCow.chr6 501495 2 + 602619 CT -s simDog_chr6.simDog.chr6 491049 2 + 593897 CT -s simHuman_chr6.simHuman.chr6 498335 2 + 601863 CT -s simRat_chr6.simRat.chr6 531794 2 + 647215 CT - -a -s simMouse_chr6.simMouse.chr6 520366 25 + 636262 CATTATTATACTCAATACCACTCAT -s Anc0.Anc0refChr3 131539 25 + 222631 CATTATTATACTCAATACCACTCAT -s Anc1.Anc1refChr6 166440 25 + 197743 CATTATTATACTCAATACCACTCAT -s Anc2.Anc2refChr1 44670 25 + 142988 CACTGTTATACTCAATACCACTCAT -s mr.mrrefChr3 72719 25 + 181027 CATTATTATACTCAATACCACTCAT -s simCow_chr6.simCow.chr6 501509 25 + 602619 TACTGTTATACTCAACACTACCCAT -s simDog_chr6.simDog.chr6 491051 19 + 593897 CACTGTTAT------TGCCACTCAT -s simHuman_chr6.simHuman.chr6 498337 25 + 601863 CATTATTATACTCAAGACCACTCAT -s simRat_chr6.simRat.chr6 531796 25 + 647215 CATTATTATACTGAATACTACTCAT - -a -s simMouse_chr6.simMouse.chr6 520391 20 + 636262 GCTGATGGAAATCACTAGTT -s Anc0.Anc0refChr3 131564 20 + 222631 GATTAGAGAAATCACTAGTC -s Anc1.Anc1refChr6 166465 20 + 197743 GATTAGAGAAATCACTAGTC -s Anc2.Anc2refChr1 44695 20 + 142988 GATTAGAGAAATCACTAGTC -s mr.mrrefChr3 72744 20 + 181027 GCTGATAGAAATCACTAGTC -s simCow_chr6.simCow.chr6 501536 20 + 602619 GATTAGAGAAATCACTAGTC -s simDog_chr6.simDog.chr6 491070 20 + 593897 GATTAGAGAAATCGCTAGTC -s simHuman_chr6.simHuman.chr6 498362 20 + 601863 GAGAAGAGAAATCACTAGTC -s simRat_chr6.simRat.chr6 531821 20 + 647215 GCTGATAGAAATCATTAGTC - -a -s simMouse_chr6.simMouse.chr6 520411 82 + 636262 GTGAGTGGTGCATTTGGGTCATAAGGTATGTTACTATGCTTGCTATGTAGTATGTAACCTGGCCTTGTGTTTCTCCTGTGTC -s Anc0.Anc0refChr3 131598 81 + 222631 ATGGGTGGTGCGTATAGGCCAGAAAGTATTTTACTATACCTGCTATCCACTAT-TAATGTATCCTGGTGTATCACTTGTGTC -s Anc1.Anc1refChr6 166499 81 + 197743 ATGGGTGGTGCGTATAGGCCAGAAAGTATTTTACTATACCTGCTATCCACTAT-TAATGTATCCTGGTGTATCACTTGTGTC -s Anc2.Anc2refChr1 44729 81 + 142988 ATGGATGGTGCGTATAGGCTAGAAAGTATTTTACTATACCTGCTATCCACTAT-TAATGTATCCTGGTGTATCACTAGTGTC -s mr.mrrefChr3 72778 81 + 181027 GTGAGTGGTGCATTTGGGCCATAAGGTATGTTACTATGCTTGCTATGTAGTAT-TAATGTAGCCTTGTGTTTCTCCTGTGTC -s simCow_chr6.simCow.chr6 501571 73 + 602619 ATGGATGGTGCGTATGGGC------GTATTTTACTATTCCTGCTATCCACTGT-TA--GTCTCCTGGTGTAACACTAGTGCC -s simDog_chr6.simDog.chr6 491104 80 + 593897 ATGGATGGTGCATATAGGCTAGAAAGTACTTCACTATAGCTGCTATCGATTAT-TAATATATCCT-GGGTATCACTAATGTC -s simHuman_chr6.simHuman.chr6 498396 80 + 601863 ATGGGTGGTGTGTATAGGCCAGAAAGT-TTTTACTATACCTGCTGTCCACTAT-TAGTGTATCCTCGTTTGTCACTTGTGTC -s simRat_chr6.simRat.chr6 531855 81 + 647215 GTGAGTGGTACACTTGGGCCATAAGGTATCTTCCTATGCTTGCTATTTAGTAT-TAATGCACCCTGGTGTTTCTCCTGTGTC - -a -s simMouse_chr6.simMouse.chr6 520493 60 + 636262 TAATTAACTGACAGAATTTCCACTCAGTTAGATACGAACCCAGCCACTTCAAATGTCAAG -s Anc0.Anc0refChr3 131680 40 + 222631 TAGTTACTTGACAGATGTTCCAATCAGTTAA--------------------AATGTGAGG -s Anc1.Anc1refChr6 166581 40 + 197743 TAGTTACTTGACAGATGTTCCAATCAGTTAA--------------------AATGTGAGG -s Anc2.Anc2refChr1 44811 40 + 142988 TAGTTACTTGACATATGTTCCAATGACTTAA--------------------AATGTGAGG -s mr.mrrefChr3 72859 60 + 181027 TAGTTACCTGACAGAATTTCCACTCAGTTAAATACGAACCCAGCCACTTCAAATGTCAAG -s simCow_chr6.simCow.chr6 501645 40 + 602619 AAGTTACTTGACATATGTTCCAATGACTCAA--------------------CATGTGACG -s simDog_chr6.simDog.chr6 491185 40 + 593897 TAGTTATTAAACATACGTTCCAATGACTTAA--------------------AATGTGAGG -s simHuman_chr6.simHuman.chr6 498477 40 + 601863 TAGTTACTTGATAGATGCTCCAATCAGTTAA--------------------AATGTGAGG -s simRat_chr6.simRat.chr6 531936 60 + 647215 TAGTTACCCGAAAGAGTTTCCATTCAGTTAAATATGTATCCAGCCACTTCAAATGTAAAG - -a -s simMouse_chr6.simMouse.chr6 520553 12 + 636262 AGACAGTAGTAC -s Anc0.Anc0refChr3 131721 12 + 222631 TGACAGTTATAT -s Anc1.Anc1refChr6 166622 12 + 197743 TGACAGTTATAT -s Anc2.Anc2refChr1 44852 12 + 142988 TGCCAGTTATGT -s mr.mrrefChr3 72919 12 + 181027 TGACAGTAGTAC -s simCow_chr6.simCow.chr6 501686 12 + 602619 TGCCAGCTATGT -s simDog_chr6.simDog.chr6 491226 12 + 593897 TGCCAGTTATGT -s simHuman_chr6.simHuman.chr6 498518 12 + 601863 TGACAGTTACAT -s simRat_chr6.simRat.chr6 531996 12 + 647215 TGACAGTAGTAT - -a -s simMouse_chr6.simMouse.chr6 520565 5 + 636262 AGGGA -s Anc0.Anc0refChr3 131733 5 + 222631 AGTGA -s Anc1.Anc1refChr6 166634 5 + 197743 AGTGA -s Anc2.Anc2refChr1 44864 5 + 142988 AGTGA -s mr.mrrefChr3 72931 5 + 181027 AGGGA -s simCow_chr6.simCow.chr6 501698 5 + 602619 AGTGA -s simDog_chr6.simDog.chr6 491238 5 + 593897 AGTGA -s simHuman_chr6.simHuman.chr6 498530 5 + 601863 GTTGA -s simRat_chr6.simRat.chr6 532011 5 + 647215 AGAGA - -a -s simMouse_chr6.simMouse.chr6 520570 24 + 636262 CATGTGGTATGAGAGCCGTGCAGC -s Anc0.Anc0refChr3 131745 10 + 222631 CA-TTACTATG------------- -s Anc1.Anc1refChr6 166646 10 + 197743 CA-TTACTATG------------- -s Anc2.Anc2refChr1 44876 10 + 142988 CA-TTACCATG------------- -s mr.mrrefChr3 72936 10 + 181027 CA-GTGGTATG------------- -s simCow_chr6.simCow.chr6 501711 10 + 602619 CA-TTGCCATG------------- -s simDog_chr6.simDog.chr6 491250 10 + 593897 CA-TTACCATG------------- -s simHuman_chr6.simHuman.chr6 498550 10 + 601863 CA-TCAATGTG------------- -s simRat_chr6.simRat.chr6 532016 10 + 647215 CA-GTAGTATA------------- - -a -s simMouse_chr6.simMouse.chr6 520594 34 + 636262 AGGATCTAACCATAGTGTTGTCAGAGGATTTAAC -s Anc0.Anc0refChr3 131755 34 + 222631 GGGCTTGAACCACCATGTGCTGGGAGGAGTCAAC -s Anc1.Anc1refChr6 166656 34 + 197743 GGGCTTGAACCACCATGTGCTGGGAGGAGTCAAC -s Anc2.Anc2refChr1 44890 34 + 142988 GGGCTTGAACCACCATGTGCTGGGAGGAGTCATC -s mr.mrrefChr3 72946 34 + 181027 AGGATCTAACCATAGTGTTGTCAGAGGATTGAAC -s simCow_chr6.simCow.chr6 501725 34 + 602619 GGGCTCGAACTGTCATATGCTAGGAGGGGTCAGT -s simDog_chr6.simDog.chr6 491264 34 + 593897 GGGCTTGAACCACCATGTGCTGGGAGGAGTCATC -s simHuman_chr6.simHuman.chr6 498560 3 + 601863 -------------------------------GAC -s simRat_chr6.simRat.chr6 532026 34 + 647215 GGGGTCTAACCATAGTGTTGTCGGAGGGTTGAAC - -a -s simMouse_chr6.simMouse.chr6 520628 87 + 636262 TTCACCATGGAGAGTAGCTTATACCATGATGAAATCTAGCTCTAATATGTTGTTCTTGCGGTTCCTCTGAGAGGCCTGCCCCTCTCA -s Anc0.Anc0refChr3 131789 80 + 222631 CTCACCATTGAGAGTAGCTCATACCAGTAGGAAGTCTTACTTTAATACCTTGTTCTTTTAGTCCCTCAGAGAG-------CCTCTCA -s Anc1.Anc1refChr6 166690 80 + 197743 CTCACCATTGAGAGTAGCTCATACCAGTAGGAAGTCTTACTTTAATACCTTGTTCTTTTAGTCCCTCAGAGAG-------CCTCTCA -s Anc2.Anc2refChr1 44924 80 + 142988 CTCACCATTGAGAGTAGCCCATACCAGTAGGAAGTGTTACTTTAATACCTTGCTCTTTTAGTCCCTCATAGAG-------TCTCTCA -s mr.mrrefChr3 72980 87 + 181027 TTCACCATTGAGAGTAGCTTATACCATGATGAAATCTTGCTTTAATATGTTGTTCTTGCAGTTCCTCTGAGAGGCCTGCCCCTCTCA -s simCow_chr6.simCow.chr6 501768 80 + 602619 TCCACCATTAAAAGTAGCCCATACCGATATGAAGTGTTGCTTTCATAACTTGCTCCTTTAGTTCCTCAAAGAG-------TCTCTCA -s simDog_chr6.simDog.chr6 491298 76 + 593897 CTCATCCTTGAGAGTGGCCCATACCAGTAGGATGTGGCATGTTAAGACCTTGCTCTTTTAGTCTCTCCTAA-----------TCTCA -s simHuman_chr6.simHuman.chr6 498563 74 + 601863 CTAACCATTCAGAATAGCTCATACCAGTAAGAAGTCTTACTTTTATACTTTGT------AGTCCCTCAGAGAG-------CCTCTCA -s simRat_chr6.simRat.chr6 532060 86 + 647215 GTTATCCGTGAGAGTAGCTGATATCATGATGAAATCTTGCCTTAATATGTTGCTCTTGCAGTTCCTCG-AGGGACCTGCCCCTCCCA - -a -s simMouse_chr6.simMouse.chr6 520715 5 + 636262 GGCAA -s Anc0.Anc0refChr3 131869 1 + 222631 T---- -s Anc1.Anc1refChr6 166770 5 + 197743 TGAAA -s Anc2.Anc2refChr1 45004 1 + 142988 T---- -s mr.mrrefChr3 73067 5 + 181027 GGCAA -s simCow_chr6.simCow.chr6 501850 1 + 602619 T---- -s simDog_chr6.simDog.chr6 491374 1 + 593897 T---- -s simHuman_chr6.simHuman.chr6 498637 5 + 601863 CGAAA -s simRat_chr6.simRat.chr6 532146 5 + 647215 GGGAA - -a -s simMouse_chr6.simMouse.chr6 520720 106 + 636262 TTATCAAATATACCATGCATTAGGTTCTCCCCAAATAGCAACTTAATGGTCAACTATACAGGGCCATGTAGTACCTGGATGCTAGATTATGTAAAGGGATGCTGCC -s Anc0.Anc0refChr3 131870 43 + 222631 ------A------------------------------------------------------GGCCATGGAGTACCCAGATGCTAGATAATAT-AAG--ATGAAGCC -s Anc1.Anc1refChr6 166775 50 + 197743 TTACCAA------------------------------------------------------GGCCATGGAGTACCCAGATGCTAGATAATATAAAG--ATGAAGCC -s Anc2.Anc2refChr1 45005 43 + 142988 ------A------------------------------------------------------AGCCATGGAGTACCCAGATGCTAGATAACAT-AAG--ATGAAACC -s mr.mrrefChr3 73072 104 + 181027 TTACCAAATATACCATGCATTAGGT--TCCCCAAATAGCAACTTAATGGTCAACTATACAGGGCCATGTAGTACCTGGATGCTAGATTATGTAAAGGGATGCTGCC -s simCow_chr6.simCow.chr6 501851 43 + 602619 ------A------------------------------------------------------CTTCATGGAGTGTTCAGATGCGAGATAGCAT-AAG--ATGAAATT -s simDog_chr6.simDog.chr6 491375 43 + 593897 ------A------------------------------------------------------AGCCATGGAGTACCTAGATGCTAGGTAACAT-AAG--ATGAAACC -s simHuman_chr6.simHuman.chr6 498643 50 + 601863 TTACCAA------------------------------------------------------GGCCATGGAGTACCCAGATGGTAGATAATATACAG--ATGAAGCC -s simRat_chr6.simRat.chr6 532151 104 + 647215 TTACCAAATGTCCGATGGATGGGAT--TCCCCAAATAGCAACTTAATGGTCAACTATACAGGGCCATGTACTACCTGGAGGCTAGATTACGTAAGGAGATGCTGCC - -a -s simMouse_chr6.simMouse.chr6 520826 20 + 636262 TTGGCTAAAGGAACAAGAGT -s Anc0.Anc0refChr3 131913 20 + 222631 TTGACTAAAAAAACAAGGGA -s Anc1.Anc1refChr6 166825 20 + 197743 TTGACTAAAAAAACAAGGGA -s Anc2.Anc2refChr1 45048 20 + 142988 TTGACTACAAAAACAAGGGA -s mr.mrrefChr3 73176 20 + 181027 TTGGCTAAAGAAACAAGAGT -s simCow_chr6.simCow.chr6 501900 20 + 602619 TTGGCTACAAAAACGAACGA -s simDog_chr6.simDog.chr6 491418 20 + 593897 TTGAGTACGATATCAAGGGA -s simHuman_chr6.simHuman.chr6 498693 20 + 601863 TTGACTAAAAAAACACGGAA -s simRat_chr6.simRat.chr6 532255 20 + 647215 TTGGCTAAAGAAATAAGAGG - -a -s simMouse_chr6.simMouse.chr6 520846 16 + 636262 GACCTAAACAGTATAT -s Anc0.Anc0refChr3 131933 16 + 222631 GATTGACACAGTACAT -s Anc1.Anc1refChr6 166845 16 + 197743 GATTGACACAGTACAT -s Anc2.Anc2refChr1 45068 16 + 142988 GATTGACACAGAACAT -s mr.mrrefChr3 73196 16 + 181027 GACTTACACAGTATAT -s simCow_chr6.simCow.chr6 501920 16 + 602619 GATTAACACAGCATAT -s simDog_chr6.simDog.chr6 491438 16 + 593897 GATTGACACAGAACAT -s simHuman_chr6.simHuman.chr6 498713 15 + 601863 GA-TGACACAGTACAT -s simRat_chr6.simRat.chr6 532276 16 + 647215 GATTTACACAGTATGA - -a -s simMouse_chr6.simMouse.chr6 520862 10 + 636262 AAATACACAG -s Anc0.Anc0refChr3 131949 10 + 222631 AAACATACAC -s Anc1.Anc1refChr6 166861 10 + 197743 AAACATACAC -s Anc2.Anc2refChr1 45084 10 + 142988 AGACATACAC -s mr.mrrefChr3 73212 10 + 181027 AAATACACAG -s simCow_chr6.simCow.chr6 501936 10 + 602619 AGGCATACAC -s simDog_chr6.simDog.chr6 491454 10 + 593897 AGACATACAC -s simHuman_chr6.simHuman.chr6 498729 10 + 601863 AACCAGGCAC -s simRat_chr6.simRat.chr6 532292 10 + 647215 AAATACACAG - -a -s simMouse_chr6.simMouse.chr6 520872 10 + 636262 GCACCTGGTG -s Anc0.Anc0refChr3 131962 10 + 222631 GCACCTGAGT -s Anc1.Anc1refChr6 166874 10 + 197743 GCACCTGAGT -s Anc2.Anc2refChr1 45097 10 + 142988 GCACCTGAGT -s mr.mrrefChr3 73225 10 + 181027 GCACCTGGTG -s simCow_chr6.simCow.chr6 501949 10 + 602619 GCACCTGAAT -s simDog_chr6.simDog.chr6 491467 10 + 593897 GCACCTGAGT -s simHuman_chr6.simHuman.chr6 498742 10 + 601863 GCACCTGAGT -s simRat_chr6.simRat.chr6 532305 10 + 647215 GCACCTGGTG - -a -s simMouse_chr6.simMouse.chr6 520882 49 + 636262 AGCAGCAGAACGGACAGATATACAGCTGTAGGCATCAGACAGCACACAG -s Anc0.Anc0refChr3 131972 49 + 222631 AGCAGCAGAATAGATAGATACAGGGCTGCAGGCATTGGGCTACTGGGAG -s Anc1.Anc1refChr6 166884 49 + 197743 AGCAGCAGAATAGATAGATACAGGGCTGCAGGCATTGGGCTACTGGGAG -s Anc2.Anc2refChr1 45108 49 + 142988 AGCAACAGAATAGATAAATACAGGGCTACAGGCATTGGGCTACTGAGAG -s mr.mrrefChr3 73235 49 + 181027 AGCAGCAGAACAGACAGATACACAGCTGCAGGCATTAGACTGCACGCAG -s simCow_chr6.simCow.chr6 501960 49 + 602619 AACAACAGAATAGATAAACACAGGTCTACAGGCACGGGGCTACTCAGAG -s simDog_chr6.simDog.chr6 491478 49 + 593897 AGCAACAGGGTAGATGAATACAGGGCTACAGGCATTGGGCTACTGAGAG -s simHuman_chr6.simHuman.chr6 498752 47 + 601863 A--AGCAGAATAGTTAGATCCAGGACTGCAGACATTCGGCTACTTGGAG -s simRat_chr6.simRat.chr6 532315 49 + 647215 AGCAGCAGAACAGACAGGGACACAGCTGCAGGCATTGGACTGCCCGCAG - -a -s simMouse_chr6.simMouse.chr6 520931 28 + 636262 GTATCTAACACTGGCGTTTAGGGAATCT -s Anc0.Anc0refChr3 132022 28 + 222631 GCATGTAACGCTGGCATATAAGAAATTT -s Anc1.Anc1refChr6 166934 28 + 197743 GCATGTAACGCTGGCATATAAGAAATTT -s Anc2.Anc2refChr1 45158 28 + 142988 GCATGTAACGCTGGCATATAAGAAATTT -s mr.mrrefChr3 73284 28 + 181027 GTATCTAACACTGGCATATAGGGAATCT -s simCow_chr6.simCow.chr6 502010 26 + 602619 -TATTTAA-GATGGCATATAAAAAATAT -s simDog_chr6.simDog.chr6 491528 28 + 593897 GCATGTAACACTGGCTTATAAGAAATTT -s simHuman_chr6.simHuman.chr6 498800 28 + 601863 GCATATAACGCTAGCATATAAGAAATTG -s simRat_chr6.simRat.chr6 532364 27 + 647215 GTATTTAACACTGA-ATATCGAGAACCT - -a -s simMouse_chr6.simMouse.chr6 520959 13 + 636262 TGAGGACTCTAAG -s Anc0.Anc0refChr3 132050 13 + 222631 CAAGGACTTCAGA -s Anc1.Anc1refChr6 166962 13 + 197743 CAAGGACTTCAGA -s Anc2.Anc2refChr1 45186 13 + 142988 CAAAGAATTCAGA -s mr.mrrefChr3 73312 13 + 181027 CAAGGACTTTAGA -s simCow_chr6.simCow.chr6 502038 13 + 602619 CAGAGAATTAAAA -s simDog_chr6.simDog.chr6 491556 13 + 593897 CAAAGAATTCAGA -s simHuman_chr6.simHuman.chr6 498828 13 + 601863 CAAGGACCTCAGA -s simRat_chr6.simRat.chr6 532391 13 + 647215 CAAGGACTTTAGA - -a -s simMouse_chr6.simMouse.chr6 520972 9 + 636262 AAGAGTCTT -s Anc0.Anc0refChr3 132074 9 + 222631 AAGAGTTTC -s Anc1.Anc1refChr6 166986 9 + 197743 AAGAGTTTC -s Anc2.Anc2refChr1 45210 9 + 142988 AAGAGTTTC -s mr.mrrefChr3 73336 9 + 181027 AAGAGTCTC -s simCow_chr6.simCow.chr6 502060 9 + 602619 AAGAGCTTT -s simDog_chr6.simDog.chr6 491580 9 + 593897 AAGTGTATC -s simHuman_chr6.simHuman.chr6 498852 9 + 601863 AAGAGTTTC -s simRat_chr6.simRat.chr6 532415 9 + 647215 AAGGGGCTC - -a -s simMouse_chr6.simMouse.chr6 520981 3 + 636262 CCA -s Anc0.Anc0refChr3 132083 3 + 222631 CCT -s Anc1.Anc1refChr6 166995 3 + 197743 CCT -s Anc2.Anc2refChr1 45220 3 + 142988 TCT -s mr.mrrefChr3 73345 3 + 181027 CCA -s simCow_chr6.simCow.chr6 502070 3 + 602619 TCA -s simDog_chr6.simDog.chr6 491590 3 + 593897 TAT -s simHuman_chr6.simHuman.chr6 498861 3 + 601863 CCC -s simRat_chr6.simRat.chr6 532424 3 + 647215 CCA - -a -s simMouse_chr6.simMouse.chr6 520984 31 + 636262 AAAATGGTGGCAACTGGTGTGGTCTTTAGTA -s Anc0.Anc0refChr3 132094 31 + 222631 GCATTGTTGGCAACTAGAGAGGTTGCTAACA -s Anc1.Anc1refChr6 167006 31 + 197743 GCATTGTTGGCAACTAGAGAGGTTGCTAACA -s Anc2.Anc2refChr1 45231 31 + 142988 GCATTGTTGACAACAAGAGAGGTTGCTAACA -s mr.mrrefChr3 73348 31 + 181027 AAAATGGTGGCAACTAGAGTGGTCTTTAATA -s simCow_chr6.simCow.chr6 502081 31 + 602619 TCATTGCTGACAGCCAGAAAGGTTGCTAACA -s simDog_chr6.simDog.chr6 491601 22 + 593897 GCATTGTTGACAACAAGAGGGG--------- -s simHuman_chr6.simHuman.chr6 498872 31 + 601863 GGACCGTTGGCAACTAGAGAGGTTGCTAAAA -s simRat_chr6.simRat.chr6 532427 31 + 647215 AAAATGGCGGCAGCTAGAGTGGTCATTAATA - -a -s simMouse_chr6.simMouse.chr6 521015 5 + 636262 AGAGG -s Anc0.Anc0refChr3 132125 5 + 222631 TAGGG -s Anc1.Anc1refChr6 167037 5 + 197743 TAGGG -s Anc2.Anc2refChr1 45262 5 + 142988 TAGGG -s mr.mrrefChr3 73379 5 + 181027 TGAGG -s simCow_chr6.simCow.chr6 502112 5 + 602619 TAGGG -s simDog_chr6.simDog.chr6 491623 4 + 593897 -AGGG -s simHuman_chr6.simHuman.chr6 498904 5 + 601863 TTGGG -s simRat_chr6.simRat.chr6 532458 5 + 647215 TCAGG - -a -s simMouse_chr6.simMouse.chr6 521020 14 + 636262 CATGTAAGGCTTTA -s Anc0.Anc0refChr3 132130 14 + 222631 CATGTAAGGTTTTA -s Anc1.Anc1refChr6 167042 14 + 197743 CATGTAAGGTTTTA -s Anc2.Anc2refChr1 45268 14 + 142988 CATGTAAGGTTTTG -s mr.mrrefChr3 73384 14 + 181027 CATGTAAGGTTTTA -s simCow_chr6.simCow.chr6 502118 4 + 602619 CATG---------- -s simDog_chr6.simDog.chr6 491628 14 + 593897 CATGTAAGGTTTTG -s simHuman_chr6.simHuman.chr6 498909 14 + 601863 CACGTAATGTTTTA -s simRat_chr6.simRat.chr6 532463 14 + 647215 CATGTAAGGTTTCA - -a -s simMouse_chr6.simMouse.chr6 521034 71 + 636262 GGAAATAGGTGAAATGTGGCCTTGGCACTGTAATGCTTTGTTGGCCTCAATTGAATTAATTGTCTGCTCAT -s Anc0.Anc0refChr3 132144 71 + 222631 CGAAATAGGTGAAATGCGGTCTCATCACTGTAATGCTTTTTTGGCCTCAATTCAATCCAGTGCATGCTCAT -s Anc1.Anc1refChr6 167056 71 + 197743 CGAAATAGGTGAAATGCGGTCTCATCACTGTAATGCTTTTTTGGCCTCAATTCAATCCAGTGCATGCTCAT -s Anc2.Anc2refChr1 45282 71 + 142988 CGAAATAGGTGAAATGCGGTCTCATCACTGTAATGCATGGTTGGCCTCAATTCAATCCAGTGCACGCTTAT -s mr.mrrefChr3 73398 71 + 181027 GGAAATAGGTGAAATGCGGCCTTGTCACTGTAATGCTTTTTTGGCCTCAATTGAATTAATTGTATGCTCAT -s simCow_chr6.simCow.chr6 502122 61 + 602619 ----------GAAGTGCAGTCTCATTATTGTAATGCATGCTTGGGCTAAATTCAACCCAGCGCAGGAGTAT -s simDog_chr6.simDog.chr6 491642 71 + 593897 CGAAATAGGTGAAATGCGGCCTCATCACTGTGCTGTATGGTTGGCCTCAACTCAATCCAGTGTACGCTTGC -s simHuman_chr6.simHuman.chr6 498924 71 + 601863 AAAAATAGGCCATATGCGGTGTCATAAATGTAATGCTGTTTTGACGCCAATTCAATCTGGTGCATGCTCAT -s simRat_chr6.simRat.chr6 532477 71 + 647215 GGAAACAGGTGAAATGCAGCCTTGTCACAATAATGCATCTTTGGCCTCAATTAAATTAATTGTATGCTCAT - -a -s simMouse_chr6.simMouse.chr6 521105 113 + 636262 TGGATAGAAGTCTTGTAACTTGAGAACTGGGGACTGGAGGTCGGCGCTAAGTTATGATCCTGCTAAATCAGATGCCACAAGAGGTTAAAGTCCATTGAGCCTCATGGTGAAAG -s Anc0.Anc0refChr3 132216 73 + 222631 TGGATAGAGGTGCTGCAACTTGAGAGGTGGAGA-------TTGATGCTAAGTTGTGATCCCACT-AATCTGGTGGCAGAGT-------------------------------- -s Anc1.Anc1refChr6 167128 74 + 197743 TGGATAGAGGTGCTGCAACTTGAGAGGTGGAGA-------TTGATGCTAAGTTGTGATCCCACTAAATCTGGTGGCAGAGT-------------------------------- -s Anc2.Anc2refChr1 45354 73 + 142988 TAGATAAAGGTGCAGCAACTTGAGAGGTGGAGA-------TTCATGCTAAGTTGTAATCACACT-GATTTGGTAGCAGTGT-------------------------------- -s mr.mrrefChr3 73469 113 + 181027 TGGATAGAAGTCTTGCAACTTGAGAACTGGAGACTGGAGGTTGGTGCTAAGTTATGATCCTGCTAAATCAGATGGCACAGGAGGTTAAAGTCCATTGAGCCTCATGGTGAAAG -s simCow_chr6.simCow.chr6 502184 67 + 602619 TAGATAAAG------CAACTTGAGAGGAGGAGA-------TTTGTGCTAAGTTGTAGTTGCACT-GATTCGGTAGTAGGGT-------------------------------- -s simDog_chr6.simDog.chr6 491714 73 + 593897 AAGGTAAAGGTGCAGGAACTTGAGAGGTGGAGA-------TTCATGTTAAGTCGTAATCACTCT-GATTTGGTAGCAGTGT-------------------------------- -s simHuman_chr6.simHuman.chr6 498996 74 + 601863 TGCATAGAGGAGCTTCAACTTGAGAGGTGGAGA-------TTGCTGCTAAGTTGTGATCCCACTAAATCTGGTGGCAGAGT-------------------------------- -s simRat_chr6.simRat.chr6 532548 113 + 647215 TGGATAGAAGTCTTGCAACTTGAGAACTAGAGACTGGAGCTTGGTGCTAAGTTTTGATCCTGCTAAGTCAGATGGCACAGGAGGTTAAAGTCCACCGAGCATGATGATGAAAG - -a -s simMouse_chr6.simMouse.chr6 521218 16 + 636262 GGCAAAGTCTATAATG -s Anc0.Anc0refChr3 132289 16 + 222631 GTTGAAGTAGATATTG -s Anc1.Anc1refChr6 167202 16 + 197743 GTTGAAGTAGATATTG -s Anc2.Anc2refChr1 45428 16 + 142988 GTTGAAGTAGATATTG -s mr.mrrefChr3 73582 16 + 181027 GTTAAAGTCTATAATG -s simCow_chr6.simCow.chr6 502252 16 + 602619 GTTGAGGTACATATCG -s simDog_chr6.simDog.chr6 491788 16 + 593897 GTTGAAGTAGGTATTG -s simHuman_chr6.simHuman.chr6 499070 16 + 601863 GTTGAAGTAGATAGTG -s simRat_chr6.simRat.chr6 532661 16 + 647215 GTTAAAGTCTATAATG - -a -s simMouse_chr6.simMouse.chr6 521234 26 + 636262 AAAAATAAAGATAAGGGAGACCCATA -s Anc0.Anc0refChr3 132305 26 + 222631 AAGAATAAAGAGAAGGGAGACCCTTA -s Anc1.Anc1refChr6 167218 26 + 197743 AAGAATAAAGAGAAGGGAGACCCTTA -s Anc2.Anc2refChr1 45444 26 + 142988 AAGAATAGATGGAAGCGAGACCCTTT -s mr.mrrefChr3 73598 26 + 181027 AAAAATAAAGATAAGGGAGACCCATA -s simCow_chr6.simCow.chr6 502268 21 + 602619 -GGAATATAT----GAGAGACCCTTT -s simDog_chr6.simDog.chr6 491804 26 + 593897 AAGCATAGATGGAAGCGAGACCCTTT -s simHuman_chr6.simHuman.chr6 499087 26 + 601863 AAGAATAAAGAGAAGGGAGTCCCTTA -s simRat_chr6.simRat.chr6 532677 26 + 647215 AAAAATAAAGACAAGGGAGACCCATA - -a -s simMouse_chr6.simMouse.chr6 521260 41 + 636262 TGGTTTGTTGGTATGGAAGATCTGGTAGCTGAGTAGGGGGC -s Anc0.Anc0refChr3 132332 41 + 222631 TGTTTCATTTCCCCAGAAGATACAGTAGGAGAAGAGGAGGC -s Anc1.Anc1refChr6 167245 41 + 197743 TGTTTCATTTCCCCAGAAGATACAGTAGGAGAAGAGGAGGC -s Anc2.Anc2refChr1 45471 41 + 142988 TGTTTCATTTCCCCAGACGATACAGTAAGAGAAGAGGAGGC -s mr.mrrefChr3 73624 41 + 181027 TGGTTTGTTGGTATGGAAGATATGGTAGGTGAGTAGGAGGC -s simCow_chr6.simCow.chr6 502290 41 + 602619 TATTTCATTTTGCCAGACGATACAGTAAGATTAGAGGAGGC -s simDog_chr6.simDog.chr6 491831 41 + 593897 TGTTTCATCTCCCCAGACGACACTGTAAGAGAAGAGGAGGC -s simHuman_chr6.simHuman.chr6 499114 41 + 601863 TGTTTCATTTCACCAGAAGATACAGTAGGAGAACTGGAGGC -s simRat_chr6.simRat.chr6 532703 41 + 647215 TGGTTTGTCAGTATGGAAGATATGGTAAGTGAGTAGGAGGC - -a -s simMouse_chr6.simMouse.chr6 521301 58 + 636262 CCATACACTTTATCCCCCCACAGAGTACAGGGCAGAACTGTTGTTATTATATCTTGTG -s Anc0.Anc0refChr3 132373 58 + 222631 CCATACAGCTTATCCCCCCATAGGATACAGTGCAAAACCGGGGTTGTCAAATTTTGTG -s Anc1.Anc1refChr6 167286 58 + 197743 CCATACAGCTTATCCCCCCATAGGATACAGTGCAAAACCGGGGTTGTCAAATTTTGTG -s Anc2.Anc2refChr1 45512 58 + 142988 ATTAATAGCTTATCCCCCCATAGGATACAGTGCAAAACCAGGGTTGTCAAATTTTGTG -s mr.mrrefChr3 73665 58 + 181027 CCATACACTTTATCCCCCCACAGAATACAGGGCAAAACTGTTGTTATTATATTTTGTG -s simCow_chr6.simCow.chr6 502331 58 + 602619 GGGGATACCTTATCCCCCCAGAGGATACAGTGTAAGACCAGCGTTATCAAACTTCGTG -s simDog_chr6.simDog.chr6 491873 58 + 593897 ATTAATAGCTTATCCCCCTATAGGATACAGTGCAAAGACAGGGTTGTCAAATTTTGTG -s simHuman_chr6.simHuman.chr6 499155 58 + 601863 CCATACATCTTATCCCCCCAAAGGATACAGTACAAAACCGGGGTTGTCAAATTCTGTG -s simRat_chr6.simRat.chr6 532744 56 + 647215 CCATACACTCTATCCCCCCACAGAATACAGGGCAAAACTGTTGT--TTATATTTTGTG - -a -s simMouse_chr6.simMouse.chr6 521359 2 + 636262 GT -s Anc0.Anc0refChr3 132431 2 + 222631 GG -s Anc1.Anc1refChr6 167344 2 + 197743 GG -s Anc2.Anc2refChr1 45570 2 + 142988 GT -s mr.mrrefChr3 73723 2 + 181027 GG -s simCow_chr6.simCow.chr6 502426 2 + 602619 GT -s simDog_chr6.simDog.chr6 491931 2 + 593897 GT -s simHuman_chr6.simHuman.chr6 499213 2 + 601863 GG -s simRat_chr6.simRat.chr6 532800 2 + 647215 GG - -a -s simMouse_chr6.simMouse.chr6 521361 10 + 636262 TCATAAATAG -s Anc0.Anc0refChr3 132433 10 + 222631 TCACCAATGC -s Anc1.Anc1refChr6 167346 10 + 197743 TCACCAATGC -s Anc2.Anc2refChr1 45572 10 + 142988 TTATCAACAC -s mr.mrrefChr3 73725 10 + 181027 TCACAAATGG -s simCow_chr6.simCow.chr6 502428 10 + 602619 ATATCAACCC -s simDog_chr6.simDog.chr6 491933 10 + 593897 TTATCAACAC -s simHuman_chr6.simHuman.chr6 499219 10 + 601863 TCACCAATGT -s simRat_chr6.simRat.chr6 532802 10 + 647215 TCGCAAATGC - -a -s simMouse_chr6.simMouse.chr6 521371 6 + 636262 AGCATA -s Anc0.Anc0refChr3 132443 6 + 222631 AGCTTA -s Anc1.Anc1refChr6 167356 6 + 197743 AGCTTA -s Anc2.Anc2refChr1 45582 6 + 142988 AGCTTG -s mr.mrrefChr3 73735 6 + 181027 AGCATA -s simCow_chr6.simCow.chr6 502444 6 + 602619 AGCTTG -s simDog_chr6.simDog.chr6 491943 6 + 593897 ATCTTG -s simHuman_chr6.simHuman.chr6 499229 6 + 601863 AGCTTA -s simRat_chr6.simRat.chr6 532812 6 + 647215 AGCATA - -a -s simMouse_chr6.simMouse.chr6 521377 72 + 636262 AAAGACACTTGTACAAGTGAACACCAGTCCCTATCAGCATGCACAAAACAAAATGACAAGGTCATTTCAAGT -s Anc0.Anc0refChr3 132465 72 + 222631 AGAGATACAGATGCATGTGAACACCTATACCTTGCATCAAGCATCTGACAAAATGACAAGGTCATTTTAAGC -s Anc1.Anc1refChr6 167378 72 + 197743 AGAGATACAGATGCATGTGAACACCTATACCTTGCATCAAGCATCTGACAAAATGACAAGGTCATTTTAAGC -s Anc2.Anc2refChr1 45604 72 + 142988 AGAAATACAGAGGCATGTGGCCACCTATACCCTGCATCAAGCATCTGACAAAATGACAAGGTCATTTTCAGC -s mr.mrrefChr3 73741 72 + 181027 AAAGACACTTGTACAAGTGAACACCAGTACCTATCAGCATGCACATGACAAAATGACAAGGTCATTTTAAGT -s simCow_chr6.simCow.chr6 502466 69 + 602619 AGAAAA---GAAGAAGGTGGCCACCTACACCCTGCATCAAGCAAATGACAAATTGACAAGGCTGTTCTCAGC -s simDog_chr6.simDog.chr6 491965 72 + 593897 ACAAATACAGAGGCATGTGGCCACCTATGCCCTGCATTGAGTGTCTGACAAAATGACGAGGTCATTTTCAGC -s simHuman_chr6.simHuman.chr6 499251 72 + 601863 AGAGATGCAGATTCCTGTGAACACCTCTACCTGGCATCAAGCAGCTGAAAAAATGACAAGGTCATTTTAAGC -s simRat_chr6.simRat.chr6 532818 72 + 647215 AAAGACACTTGTACAAGTGAACACCAGTACCTATCAGCATGCACATGACAAAATGACAAGGTCATTTTAAGT - -a -s simMouse_chr6.simMouse.chr6 521449 35 + 636262 CTAACTAAATAAATATGGTATTTGTCTCAAAGGTA -s Anc0.Anc0refChr3 132538 35 + 222631 CTAGTCAGACAAATGTGGTGTTTCTCTCAGAGCAA -s Anc1.Anc1refChr6 167451 35 + 197743 CTAGTCAGACAAATGTGGTGTTTCTCTCAGAGCAA -s Anc2.Anc2refChr1 45677 35 + 142988 CTAGTCAGACAGATGTGGTGTTTCTCTCAGAGCAA -s mr.mrrefChr3 73814 35 + 181027 CTAACTAAACAAATATGGTATTTGTCTCAAAGGTA -s simCow_chr6.simCow.chr6 502536 35 + 602619 ATAGTCAGAGACATCTGGCATTTCCCTAAGAGCAG -s simDog_chr6.simDog.chr6 492038 35 + 593897 CAAGTCAGACAGATGTTGTGTTTTTCTCTGAGCAA -s simHuman_chr6.simHuman.chr6 499324 35 + 601863 TTAGTCAGACAAATGTGGTGCCTCTCTCAGAGCAA -s simRat_chr6.simRat.chr6 532891 35 + 647215 CTAACAAAACAAATATGGTATTTGTCTCAAAGGCA - -a -s simMouse_chr6.simMouse.chr6 521484 8 + 636262 CAATGTGG -s Anc0.Anc0refChr3 132575 8 + 222631 CAATGTAG -s Anc1.Anc1refChr6 167488 8 + 197743 CAATGTAG -s Anc2.Anc2refChr1 45714 8 + 142988 CAATGTAA -s mr.mrrefChr3 73849 8 + 181027 CAATGTGG -s simCow_chr6.simCow.chr6 502573 8 + 602619 CAATCTTA -s simDog_chr6.simDog.chr6 492075 8 + 593897 CAATGTAA -s simHuman_chr6.simHuman.chr6 499361 8 + 601863 CAATGTAG -s simRat_chr6.simRat.chr6 532926 7 + 647215 C-ATGTTG - -a -s simMouse_chr6.simMouse.chr6 521492 10 + 636262 TGGTATGTGG -s Anc0.Anc0refChr3 132592 10 + 222631 TGGTATCTTG -s Anc1.Anc1refChr6 167505 10 + 197743 TGGTATCTTG -s Anc2.Anc2refChr1 45731 10 + 142988 TGGTATCTTG -s mr.mrrefChr3 73857 10 + 181027 TGGTATCTGG -s simCow_chr6.simCow.chr6 502590 10 + 602619 TGGTACCCTG -s simDog_chr6.simDog.chr6 492092 10 + 593897 TGGTATCTTG -s simHuman_chr6.simHuman.chr6 499378 10 + 601863 TGGTATCTTG -s simRat_chr6.simRat.chr6 532933 10 + 647215 TGGTATCTGA - -a -s simMouse_chr6.simMouse.chr6 521502 362 + 636262 CTTTATCACAGCATAAACTATGACTGGTGCAAGTTAGTTATTAGCCGGGGGGACATGTACATAACATATTGAGTTGTGGGGAGGGGTCATAGCCAAACACTAACCGTATGTACATGGCTGTGTTTGCCTTTTTTTGAAGATTTGCACGAGCCACTGTGTGTAGAAGTATAAGTAGTGTTAAAGGTTATTAGTCTGGGGGACACTAGATCACCCTTGTTTCTTTTGTTTGGGGTACACTATATCTCCCTGTTTCTTGTGTTACTCCCATAAATCAAAATGGAGGACTGAGATAGATTCCACTGAACAGGAGGTGCCTCACATAAAACCCGTTTCCTACCCTTGTCTTTACTCCAAGTGCTGCT -s Anc0.Anc0refChr3 132602 20 + 222631 CATTAGCACA------------------------TACCTAT------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GTT -s Anc1.Anc1refChr6 167515 20 + 197743 CATTAGCACA------------------------TACCTAT------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GTT -s Anc2.Anc2refChr1 45741 20 + 142988 CATTAGCACT------------------------TACCTAT------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CCT -s mr.mrrefChr3 73867 69 + 181027 CATTATCACAGCATAAACTATGACTGGTGCAAGTTAGTTATTAGCCGGGGGGACATGTACATA-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GCTGTT -s simCow_chr6.simCow.chr6 502600 20 + 602619 CATTTTCACT------------------------CACCTAT------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CCT -s simDog_chr6.simDog.chr6 492108 20 + 593897 AATTAGCACT------------------------TACCTGT------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CCT -s simHuman_chr6.simHuman.chr6 499388 20 + 601863 CATTAGCACA------------------------TGCCTAT------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GTT -s simRat_chr6.simRat.chr6 532943 69 + 647215 CATTATCACAGCATAATCTATGACTGGTGTGAGCTCGTTATCAGCCACAGGGACGTGTATATA-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GTTGTT - -a -s simMouse_chr6.simMouse.chr6 521864 4 + 636262 CCAA -s Anc0.Anc0refChr3 132622 4 + 222631 CCAG -s Anc1.Anc1refChr6 167535 4 + 197743 CCAG -s Anc2.Anc2refChr1 45761 4 + 142988 CCAG -s mr.mrrefChr3 73936 4 + 181027 CCAA -s simCow_chr6.simCow.chr6 502646 4 + 602619 CCCG -s simDog_chr6.simDog.chr6 492128 4 + 593897 CTAG -s simHuman_chr6.simHuman.chr6 499408 4 + 601863 CCAG -s simRat_chr6.simRat.chr6 533012 4 + 647215 CCAA - -a -s simMouse_chr6.simMouse.chr6 521868 73 + 636262 GTGCCTACAGCCTACACAATTGAGTATAAAGAGGCTGTTATAAAAGTGCTTATAGCTCATATCCCCTCAATTT -s Anc0.Anc0refChr3 132626 46 + 222631 GTGC-------TAACATAA------ACAAGGAAACT------------C-TATGGCTCATCTCCCAT-GGTGC -s Anc1.Anc1refChr6 167539 53 + 197743 GTGC-------TAACATAAAAAAGTACAAGGAAACT------------CTTATGGCTCATCTCCCAT-GGTGC -s Anc2.Anc2refChr1 45766 46 + 142988 GTTC-------TATCATAA------ACAAGGAAGCT------------C-TATGACTCATCTCCGAT-GGTGC -s mr.mrrefChr3 73940 66 + 181027 GTGC-------CTACACAAATAAGTATAAGGAGACTGTTATAAAAGTGCTTATAGCTCATATCCCCTCAATTT -s simCow_chr6.simCow.chr6 502651 46 + 602619 GTAC-------CCTCTTGA------AGATAGAATCG------------G-TTCGATTCATATACGAG-AGAAC -s simDog_chr6.simDog.chr6 492133 46 + 593897 GTTC-------TATCACAG------ACAAGGAAGCT------------C-TATGACTCATCTCTGTT-GGTGC -s simHuman_chr6.simHuman.chr6 499412 53 + 601863 GTGC-------TGACATAAAAAAGTACAAGGAAACT------------CATATGGCTCATCTCCCAT-GCTGC -s simRat_chr6.simRat.chr6 533016 66 + 647215 GTGC-------CTACACAAACACGTATGAGGAGATTGTTCTAAAAGTGCTTATAGCTCATGACCCCTCAATTT - -a -s simMouse_chr6.simMouse.chr6 521941 43 + 636262 ACAACACTGAACCAGAGTTGTCCAAATAGTGCTTCTCTCGGCG -s Anc0.Anc0refChr3 132672 43 + 222631 ATAATGCAAAACTTGGGCTATGAAAGACGTGGGTCTCTAGGCA -s Anc1.Anc1refChr6 167592 43 + 197743 ATAATGCAAAACTTGGGCTATGAAAGACGTGGGTCTCTAGGCA -s Anc2.Anc2refChr1 45812 43 + 142988 ATAATGCAAAACTTGGGCTATGAAAGACGTGGGGCTCTAGGCA -s mr.mrrefChr3 74006 43 + 181027 ACAACACAGAACCAGAGTTGTCCAAATAGTGGTTCTCTAGGCA -s simCow_chr6.simCow.chr6 502711 43 + 602619 ATGACGCAAAACTTGGGCTATAAAAATAGTGGGACTCTAGGTA -s simDog_chr6.simDog.chr6 492179 43 + 593897 ATAATGCAAAGCTTGGGCTGTGAAAGACATGGAGCTCTATGCG -s simHuman_chr6.simHuman.chr6 499465 43 + 601863 AGAATGCAAAACTTGGGCTATGAAAGATGTGGGTCTCTAGGCA -s simRat_chr6.simRat.chr6 533082 43 + 647215 ACAACACAGAACCAGAGTTGTCCAAATAGTGGTTCTCTAGGCA - -a -s simMouse_chr6.simMouse.chr6 521984 25 + 636262 TGGCTCAACTAAATAAGGGCTTAAT -s Anc0.Anc0refChr3 132715 25 + 222631 TAAGTTAAATAAATAAAGACTGAAT -s Anc1.Anc1refChr6 167635 25 + 197743 TAAGTTAAATAAATAAAGACTGAAT -s Anc2.Anc2refChr1 45855 25 + 142988 TAAGTTAAATAATTAAAGACTGACT -s mr.mrrefChr3 74049 25 + 181027 TGGCTTAAATAAATAAGGGCTTAAT -s simCow_chr6.simCow.chr6 502765 23 + 602619 TAGGTTAGATAATTAAAGACTGA-- -s simDog_chr6.simDog.chr6 492222 24 + 593897 -AAGTTAAATAATTGAAGACTGACT -s simHuman_chr6.simHuman.chr6 499508 25 + 601863 TATGTTAAATAAATAAAGAAAGAAT -s simRat_chr6.simRat.chr6 533125 25 + 647215 TGGTTTAAATAAATAAGGGCTTAAT - -a -s simMouse_chr6.simMouse.chr6 522009 9 + 636262 AATTGGACG -s Anc0.Anc0refChr3 132744 9 + 222631 ATGTAGACA -s Anc1.Anc1refChr6 167664 9 + 197743 ATGTAGACA -s Anc2.Anc2refChr1 45884 9 + 142988 ATGTATTCA -s mr.mrrefChr3 74074 9 + 181027 AATTGGACA -s simCow_chr6.simCow.chr6 502792 9 + 602619 ATGTACGGA -s simDog_chr6.simDog.chr6 492250 8 + 593897 ATTT-TTCA -s simHuman_chr6.simHuman.chr6 499537 9 + 601863 ATGTAGACA -s simRat_chr6.simRat.chr6 533150 9 + 647215 AATTGGACA - -a -s simMouse_chr6.simMouse.chr6 522018 5 + 636262 ATTAA -s Anc0.Anc0refChr3 132762 5 + 222631 ATAAT -s Anc1.Anc1refChr6 167682 5 + 197743 ATAAT -s Anc2.Anc2refChr1 45902 5 + 142988 ATAAT -s mr.mrrefChr3 74083 5 + 181027 ATAAA -s simCow_chr6.simCow.chr6 502810 5 + 602619 ATAAT -s simDog_chr6.simDog.chr6 492267 5 + 593897 AAAAT -s simHuman_chr6.simHuman.chr6 499555 5 + 601863 ATAAT -s simRat_chr6.simRat.chr6 533159 5 + 647215 ATAAA - -a -s simMouse_chr6.simMouse.chr6 522023 1 + 636262 G -s Anc0.Anc0refChr3 132767 1 + 222631 A -s Anc1.Anc1refChr6 167687 1 + 197743 A -s Anc2.Anc2refChr1 45907 1 + 142988 A -s mr.mrrefChr3 74088 1 + 181027 G -s simCow_chr6.simCow.chr6 502828 1 + 602619 A -s simDog_chr6.simDog.chr6 492272 1 + 593897 G -s simHuman_chr6.simHuman.chr6 499560 1 + 601863 A -s simRat_chr6.simRat.chr6 533164 1 + 647215 G - -a -s simMouse_chr6.simMouse.chr6 522024 9 + 636262 TTCATATAG -s Anc0.Anc0refChr3 132768 9 + 222631 TTCACATAG -s Anc1.Anc1refChr6 167688 9 + 197743 TTCACATAG -s Anc2.Anc2refChr1 45918 9 + 142988 TTCACAAAG -s mr.mrrefChr3 74089 9 + 181027 TTCACATAG -s simCow_chr6.simCow.chr6 502839 9 + 602619 TCCAAACAG -s simDog_chr6.simDog.chr6 492283 9 + 593897 TTCCCAATT -s simHuman_chr6.simHuman.chr6 499561 9 + 601863 CTCACATAG -s simRat_chr6.simRat.chr6 533165 9 + 647215 TTCACTTAG - -a -s simMouse_chr6.simMouse.chr6 522033 54 + 636262 AGTGGCAGATTTGTTCCAAATTTAATGTAAACCATCTAAGGTGGACCCCTGACC -s Anc0.Anc0refChr3 132777 32 + 222631 A----------------------GGTGTAAATGATCTAGGCTGTATCCCTGATC -s Anc1.Anc1refChr6 167697 32 + 197743 A----------------------GGTGTAAATGATCTAGGCTGTATCCCTGATC -s Anc2.Anc2refChr1 45927 32 + 142988 A----------------------GGTGTAAATGATTTAGGCTGTATCCCTGATC -s mr.mrrefChr3 74098 54 + 181027 AGTGGCAGATTTGTTCCAAATTTAGTGTAAATCATCTAGGGTGGACCCCTGACC -s simCow_chr6.simCow.chr6 502857 31 + 602619 A----------------------AATGTAAATGATA-AGGCTGTATCCATTATC -s simDog_chr6.simDog.chr6 492292 32 + 593897 A----------------------GGTGTAAACGATTTAAGCTGTACCCCTGATC -s simHuman_chr6.simHuman.chr6 499570 32 + 601863 A----------------------GGTGTAAATGATCTAGGCAGTATCCCAGATC -s simRat_chr6.simRat.chr6 533174 54 + 647215 AGTGACAGACTAGTTCCAAATTTAGTGTAAATCATCTAGGGGGGACCCCTGGCC - -a -s simMouse_chr6.simMouse.chr6 522087 8 + 636262 TGATTGGA -s Anc0.Anc0refChr3 132812 8 + 222631 TGGTATGC -s Anc1.Anc1refChr6 167732 8 + 197743 TGGTATGC -s Anc2.Anc2refChr1 45964 8 + 142988 TGGTATGC -s mr.mrrefChr3 74152 8 + 181027 TGGTTGGA -s simCow_chr6.simCow.chr6 502893 8 + 602619 TGGTATGT -s simDog_chr6.simDog.chr6 492329 8 + 593897 TGGCACCC -s simHuman_chr6.simHuman.chr6 499605 8 + 601863 TGCTGTGC -s simRat_chr6.simRat.chr6 533228 8 + 647215 TGGCTGGC - -a -s simMouse_chr6.simMouse.chr6 522095 31 + 636262 GAAGGGAAAAGTTCAACGCCTCATGACTACA -s Anc0.Anc0refChr3 132821 30 + 222631 GAA-GGCAAAGATCGCTGCCCCATGACTAAA -s Anc1.Anc1refChr6 167741 31 + 197743 GAATGGCAAAGATCGCTGCCCCATGACTAAA -s Anc2.Anc2refChr1 45973 30 + 142988 GAA-AGCAAAGATCGCTGCCCCATGACTAAA -s mr.mrrefChr3 74160 31 + 181027 GAATGGCAAAGATCAATGCCCCATGACTACA -s simCow_chr6.simCow.chr6 502902 30 + 602619 GGA-AGGACAGATCACTGACAAATGACTAAA -s simDog_chr6.simDog.chr6 492338 30 + 593897 GAA-AGCGAAGATTGCTGCCCCATGACAAAA -s simHuman_chr6.simHuman.chr6 499614 31 + 601863 GCATGACAAAGATCGTTGCCCCATGATTAAA -s simRat_chr6.simRat.chr6 533241 31 + 647215 GAATGGCAAAGATTAATGCCCCATGACTACA - -a -s simMouse_chr6.simMouse.chr6 522126 101 + 636262 TGTAAATATCTGACACTTATGTTTACACAATAGCCTGTTCACACAATAGCCTGTTCAAGATTTCTTCTTCAGTTAATGTGATGGTTGGGAACAACATGTTA -s Anc0.Anc0refChr3 132851 41 + 222631 TGTA------------------------------------------------------------TTCTTCAGTTAGTGCTATGGTGGGGGTCAATGAGTTA -s Anc1.Anc1refChr6 167772 41 + 197743 TGTA------------------------------------------------------------TTCTTCAGTTAGTGCTATGGTGGGGGTCAATGAGTTA -s Anc2.Anc2refChr1 46003 41 + 142988 TGTA------------------------------------------------------------TTCTTCAGTTAGTGCTATTGTGGGGGTCAATGAGTTA -s mr.mrrefChr3 74191 85 + 181027 TGTAAATATCTGACACTTATGTTT----------------ACACAATAGCCTGTTCAAGATTTCTTCTTCAGTTAATGTGATGGTTGGGAACAACATGTTA -s simCow_chr6.simCow.chr6 502932 41 + 602619 TACA------------------------------------------------------------TTTTTTAGTTAATGCTATCATGGAGGCAAATGAGTTC -s simDog_chr6.simDog.chr6 492378 41 + 593897 TGTA------------------------------------------------------------TTCTTCGGTTAGTGCTATTGTGGGGGTCAATGTGTTA -s simHuman_chr6.simHuman.chr6 499645 41 + 601863 TGTA------------------------------------------------------------TTCTTCAGTTCGTGCTGTGGTGGGGGTCAATGAGTTA -s simRat_chr6.simRat.chr6 533272 85 + 647215 TGTAAATATTTGACACTTATATTT----------------ACTCAATAGTCTGATCAAGATGTCTTCTTCAGGTAATGTGATGGTTGGGTACAACATGTGA - -a -s simMouse_chr6.simMouse.chr6 522227 19 + 636262 GTTTTGATGAAAATCTGGT -s Anc0.Anc0refChr3 132893 19 + 222631 ATTATGTTCAACATCTGGT -s Anc1.Anc1refChr6 167814 19 + 197743 ATTATGTTCAACATCTGGT -s Anc2.Anc2refChr1 46045 19 + 142988 ACTATGTTCAACATCTTGT -s mr.mrrefChr3 74276 19 + 181027 GTTTTGATGAACATCTGGT -s simCow_chr6.simCow.chr6 502974 19 + 602619 GCTATATTAAACACCCTGT -s simDog_chr6.simDog.chr6 492420 19 + 593897 ACTATGTTCAACATCTTGT -s simHuman_chr6.simHuman.chr6 499687 19 + 601863 ATCATGTTCAACGACTGGT -s simRat_chr6.simRat.chr6 533357 19 + 647215 GCTTTGATGAACATCTAGT - -a -s simMouse_chr6.simMouse.chr6 522246 7 + 636262 GCGGTTG -s Anc0.Anc0refChr3 132912 4 + 222631 G---TCT -s Anc1.Anc1refChr6 167833 4 + 197743 G---TCT -s Anc2.Anc2refChr1 46064 4 + 142988 G---TCT -s mr.mrrefChr3 74295 7 + 181027 GCGGTTG -s simCow_chr6.simCow.chr6 503002 4 + 602619 G---CCT -s simDog_chr6.simDog.chr6 492439 4 + 593897 G---TCT -s simHuman_chr6.simHuman.chr6 499706 4 + 601863 G---TCT -s simRat_chr6.simRat.chr6 533376 7 + 647215 GCGGTTG - -a -s simMouse_chr6.simMouse.chr6 522253 36 + 636262 TTGTAGCCTGGATGGAACCAAGGCAATAAAAGAAGT -s Anc0.Anc0refChr3 132916 34 + 222631 TTGCATCCTGGAAGAACC--AAAAATTAGATGAAAT -s Anc1.Anc1refChr6 167837 36 + 197743 TTGCATCCTGGAAGAACCCAAAAAATTAGATGAAAT -s Anc2.Anc2refChr1 46091 34 + 142988 TTGCATCCTGGAAGAACC--AAAGGCTAGCTGAAAA -s mr.mrrefChr3 74302 36 + 181027 TTGTAGCCTGGATGGAACCAAGAAATTAAAAGAAGT -s simCow_chr6.simCow.chr6 503047 24 + 602619 TGGCAACCCAGCAGAATC--ACAG----------AA -s simDog_chr6.simDog.chr6 492466 34 + 593897 CTGTGTCCTGGAAGAACC--AAAGGCTAGCTGAAGA -s simHuman_chr6.simHuman.chr6 499710 36 + 601863 TTACATCCTGGAAGAACCCAAAAAATTAGATGAAAT -s simRat_chr6.simRat.chr6 533383 36 + 647215 TTGTAGCCTGGATTGTACCAAGAAATTAAAAGAAGT - -a -s simMouse_chr6.simMouse.chr6 522289 12 + 636262 GAAGAAGCCTTA -s Anc0.Anc0refChr3 132951 12 + 222631 GAAAAATATTAA -s Anc1.Anc1refChr6 167874 12 + 197743 GAAAAATATTAA -s Anc2.Anc2refChr1 46126 12 + 142988 GAAAAATCTTAA -s mr.mrrefChr3 74339 12 + 181027 GAAGAAAACTTA -s simCow_chr6.simCow.chr6 503072 11 + 602619 GAAAAATCTT-A -s simDog_chr6.simDog.chr6 492501 12 + 593897 AAAAAATCTTAA -s simHuman_chr6.simHuman.chr6 499747 12 + 601863 GAAAAATATGAA -s simRat_chr6.simRat.chr6 533420 12 + 647215 AAAGAAAACTTA - -a -s simMouse_chr6.simMouse.chr6 522301 69 + 636262 ACTGCACATGAGGGAAAGACATCCTTGTTCTTCTGAGAACAGTATTGATATGATTGGCAATTGTATATA -s Anc0.Anc0refChr3 132963 53 + 222631 ACTGCTCATAAGGGAGACAC-----TGTTCCTCTGAGGGCAGCAGCAATATG-----------TCTTTG -s Anc1.Anc1refChr6 167886 55 + 197743 ACTGCTCATAAGGGAGACACAG---TGTTCCTCTGAGGGCAGCAGCAATATG-----------TCTTTG -s Anc2.Anc2refChr1 46138 53 + 142988 ACTGCTCATAAGAGAGACAC-----TATTCCTCTGAGGGCAACAGCAATATG-----------ACTTTG -s mr.mrrefChr3 74351 69 + 181027 ACTGCACATGAGGGAAAGACATCCTTGTTCTTCTGAGAACAGTATTGATATGATTGGCAATTGTATTTA -s simCow_chr6.simCow.chr6 503083 53 + 602619 ACTGCTCATAAGAGAGACTC-----CATTACCCTGGGGGCAACAGCAATAAG-----------AATTAC -s simDog_chr6.simDog.chr6 492513 53 + 593897 ACTGCTCATCAGAGAGACAC-----TATTCCTCTGAGGACAACAGCAATATG-----------ACTTTG -s simHuman_chr6.simHuman.chr6 499761 55 + 601863 ACTGCTCATAAGGGAGACACAG---TGTTCCTCTGAGGGCCGAAGCCATACA-----------TCTTTG -s simRat_chr6.simRat.chr6 533432 69 + 647215 ACTGCACATGAGGGGAAGACATCATTGTTCTTCTGAGAACTGTATTGATTTCATTGGCAGGTGTACTTA - -a -s simMouse_chr6.simMouse.chr6 522370 38 + 636262 ACATGACCTCACAAGTAAGCTGAATCCCAAGTCTAAAC -s Anc0.Anc0refChr3 133024 34 + 222631 ACATTACCT--CCATTAAGCTGCATCCCAAGTACCA-- -s Anc1.Anc1refChr6 167949 36 + 197743 ACATTACCTCACCATTAAGCTGCATCCCAAGTACCA-- -s Anc2.Anc2refChr1 46199 34 + 142988 GCATTACCC--CCATTAAGCTGCATCCCAAGTAACA-- -s mr.mrrefChr3 74428 38 + 181027 ACATGACCTCACAAGTAAGCTGAATCCCAAGTCCAAAC -s simCow_chr6.simCow.chr6 503144 30 + 602619 GC----CCA--CCAATAAGTTGCATCCTCAGTAACA-- -s simDog_chr6.simDog.chr6 492573 34 + 593897 GTATTACCC--CTGTTAAGCTGCATCCCAAGTAACA-- -s simHuman_chr6.simHuman.chr6 499824 34 + 601863 ACATTACCTCACCACTAAGCT--ATCCCAAGTACCA-- -s simRat_chr6.simRat.chr6 533509 38 + 647215 ACATGACCTCACAAGTAAGCTGTATCCTAAGTCCAAGC - -a -s simMouse_chr6.simMouse.chr6 522408 81 + 636262 AGAAACAGTGTATCTAGGTGAGTCTAAGAAGAAACAGTGTATCTAGGTGCAACATGCATTCAATCAATAAGACAAATGCTA -s Anc0.Anc0refChr3 133058 53 + 222631 ---------TCACT---------------ATAAAGAGTATGTGTAAGTACAATATGCATACCATCAATA----ACATGTAA -s Anc1.Anc1refChr6 167985 53 + 197743 ---------TCACT---------------ATAAAGAGTATGTGTAAGTACAATATGCATACCATCAATA----ACATGTAA -s Anc2.Anc2refChr1 46233 53 + 142988 ---------TCACA---------------GCAAAGAGTATATGTAAGTACAATATGCATACCATCAATT----ACATGAAA -s mr.mrrefChr3 74466 62 + 181027 AGAAACAGAGCACT---------------ATAAACAGTGTGTGTAGGTGCAACATGCATTCAATCAATA----AAATGTTA -s simCow_chr6.simCow.chr6 503174 53 + 602619 ---------TCACA---------------GCAAAGAGTATATGTAAGTACAATAAGCTTCCCATCGATC----ACACGAAC -s simDog_chr6.simDog.chr6 492607 46 + 593897 ---------TCACA---------------GCAAAGAGT-------AGTACAATATGCAGACCATCAATT----GCATGAAA -s simHuman_chr6.simHuman.chr6 499858 53 + 601863 ---------TCACT---------------ATAAAGAGTATGTGTAAGCAGAATCTACATACTGCTAGTA----ACATATAA -s simRat_chr6.simRat.chr6 533550 61 + 647215 ATAAACAAACCACT---------------ATAAACAGTGTGTGTAGGTGCAACATGCACTC-ATCAATA----AAATGTTA - -a -s simMouse_chr6.simMouse.chr6 522489 3 + 636262 GTA -s Anc0.Anc0refChr3 133111 3 + 222631 GTA -s Anc1.Anc1refChr6 168038 3 + 197743 GTA -s Anc2.Anc2refChr1 46286 3 + 142988 ATG -s mr.mrrefChr3 74528 3 + 181027 GTA -s simCow_chr6.simCow.chr6 503227 3 + 602619 ATG -s simDog_chr6.simDog.chr6 492653 3 + 593897 ATG -s simHuman_chr6.simHuman.chr6 499938 3 + 601863 GTA -s simRat_chr6.simRat.chr6 533611 3 + 647215 GTA - -a -s simMouse_chr6.simMouse.chr6 522492 49 + 636262 GGCAGATGACTCTAATCAACTAGCTAATCTTTACAATGTCATACCTAAG -s Anc0.Anc0refChr3 133114 49 + 222631 GACAATTGGGGCTAATCAACTAGTTAACTTTTCCAACCCCATACCTAAG -s Anc1.Anc1refChr6 168041 49 + 197743 GACAATTGGGGCTAATCAACTAGTTAACTTTTCCAACCCCATACCTAAG -s Anc2.Anc2refChr1 46294 49 + 142988 GACAATTGGGGCTACTCAACTAGTTAACTTTTCCAGCCCCATACCTGAG -s mr.mrrefChr3 74531 49 + 181027 GACAGATGAGGCTAATCAACTAGCTAACCTTTACAATGTCATACCTAAG -s simCow_chr6.simCow.chr6 503235 49 + 602619 CACAGCCGAGACTACTCAACTGGTTAACCTTTCTAGCCCTATATGTGTA -s simDog_chr6.simDog.chr6 492661 49 + 593897 GACAATTGGGGCTACTCAACCAGTTAACTTCTCCAGCCCCATACCTGAG -s simHuman_chr6.simHuman.chr6 499941 49 + 601863 CACAAGTGCGGCTAATCAAATAGTTAACTTTCTCAACCCCATTCCTATA -s simRat_chr6.simRat.chr6 533614 49 + 647215 GATAGCTGAGGCTAATCAACTAGCTAACCTTTACAATGTCATACCTGAG - -a -s simMouse_chr6.simMouse.chr6 522541 3 + 636262 TGC -s Anc0.Anc0refChr3 133163 3 + 222631 TGT -s Anc1.Anc1refChr6 168090 3 + 197743 TGT -s Anc2.Anc2refChr1 46346 3 + 142988 TGT -s mr.mrrefChr3 74580 3 + 181027 TGC -s simCow_chr6.simCow.chr6 503287 3 + 602619 TGC -s simDog_chr6.simDog.chr6 492713 3 + 593897 TGT -s simHuman_chr6.simHuman.chr6 499990 3 + 601863 TGT -s simRat_chr6.simRat.chr6 533663 3 + 647215 TGC - -a -s simMouse_chr6.simMouse.chr6 522544 22 + 636262 GAGTGGGAACAAACATACAGGA -s Anc0.Anc0refChr3 133166 21 + 222631 GGGTGGGAACAAT-GTACGAGA -s Anc1.Anc1refChr6 168093 22 + 197743 GGGTGGGAACAATGGTACGAGA -s Anc2.Anc2refChr1 46349 21 + 142988 GGGTGGGAACAAT-GTACGAGA -s mr.mrrefChr3 74583 22 + 181027 GAGTGGGAACAAACATACAGGA -s simCow_chr6.simCow.chr6 503298 21 + 602619 AAGTGGGAACACT-GCATGAGA -s simDog_chr6.simDog.chr6 492716 20 + 593897 GGGCAGGAACAAT-GTACG-TA -s simHuman_chr6.simHuman.chr6 499993 22 + 601863 GGGTGGGATTAATGGTACGAGA -s simRat_chr6.simRat.chr6 533666 22 + 647215 GAGTGGAAACCAACATACAGGA - -a -s simMouse_chr6.simMouse.chr6 522566 20 + 636262 TTTTGGCCATAATTGCACCA -s Anc0.Anc0refChr3 133187 20 + 222631 TTTTGTCCACATTTGTGCCA -s Anc1.Anc1refChr6 168115 20 + 197743 TTTTGTCCACATTTGTGCCA -s Anc2.Anc2refChr1 46370 20 + 142988 TTTTGTCCACATTTGTAGCA -s mr.mrrefChr3 74605 20 + 181027 TTTTGTCCATAATTGTGCCA -s simCow_chr6.simCow.chr6 503339 20 + 602619 TTTTGTCCACATTTGTAGCA -s simDog_chr6.simDog.chr6 492736 20 + 593897 TTTTAACCACATTTGTAGCA -s simHuman_chr6.simHuman.chr6 500015 20 + 601863 TTTTGTCCACATTTGTGCCA -s simRat_chr6.simRat.chr6 533688 20 + 647215 TTTTCTCCATAGTTGTGCCA - -a -s simMouse_chr6.simMouse.chr6 522586 12 + 636262 GATACCTAAATC -s Anc0.Anc0refChr3 133210 12 + 222631 GATATCTACATT -s Anc1.Anc1refChr6 168138 12 + 197743 GATATCTACATT -s Anc2.Anc2refChr1 46393 12 + 142988 GATATCTACATT -s mr.mrrefChr3 74625 12 + 181027 GATACCTAAATC -s simCow_chr6.simCow.chr6 503362 12 + 602619 GGTATCAACATT -s simDog_chr6.simDog.chr6 492759 12 + 593897 GATGTCTACATT -s simHuman_chr6.simHuman.chr6 500038 12 + 601863 GATATCTACATG -s simRat_chr6.simRat.chr6 533708 12 + 647215 GATACCTAAATC - -a -s simMouse_chr6.simMouse.chr6 522598 36 + 636262 AGTGGCATTTTATCTGCCTACTTCCCTTGCACTCTC -s Anc0.Anc0refChr3 133222 36 + 222631 AGTGGCATTTTATCTGCCTACCTACCTAGCCTTCTC -s Anc1.Anc1refChr6 168150 36 + 197743 AGTGGCATTTTATCTGCCTACCTACCTAGCCTTCTC -s Anc2.Anc2refChr1 46406 36 + 142988 AGTGGGATTTTATCTGCTTACCCACTTATCCTTCTG -s mr.mrrefChr3 74637 36 + 181027 AGTGGCATTTTATCTGCCTACTTCCCTTGCACTCTC -s simCow_chr6.simCow.chr6 503374 30 + 602619 ------ATTTGATCTGCTTACCCACTTATCACTCCT -s simDog_chr6.simDog.chr6 492772 28 + 593897 AGTGGGATTTTCTCTT--------CTAATCCTCCTG -s simHuman_chr6.simHuman.chr6 500050 36 + 601863 AGTGGCAGTTTATCTGTCTACCTACCTAGCCTTCTC -s simRat_chr6.simRat.chr6 533720 36 + 647215 AGTGGCACTTTATCTGCCTACTTCTCTTGCACTCTC - -a -s simMouse_chr6.simMouse.chr6 522634 400 + 636262 CTACTTTCCTTGGGGCTTACTAGCACGATCACATCATTGCAGCACACATCCAAAGGGGGATCAACTCCCATGTGTTATATGGCATATTAGAAGGGGCCAGCAAAAACTGAAATGGACGGGTGTGCAAATCTTTGATACAATGTAAGTCTATGACTCATGAGTACGTAGAGCTGACGGGTCGAGATGTGGATTCCGGGGTTAGGTCCATGCTGTCGACGCGTTCCATAGGAATACCTCCCGATTTCACTATTGCTCTAAACGAGATGTGGATTCCGGGGTTAGGACCATGCTGTCGACGCGTTCCATAGGAATACCTCCCGATTTCACTATTGCTCTAAACTCCAAAATGCTTACGGAGCGGTCCCTGGAAATTGGTTATTATTGCTATTGGATATACTCA -s Anc0.Anc0refChr3 133258 139 + 222631 CCACTTTCCTCAGAGCTTACCCGCAC---CACAGCAAAACAGTACATAT------AAGGATAGATTATCATGTTTTATATGGCATAA-------------------------------------------------ACAAGGTGAGTCCATGACTTATGAATA---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TTGGAAATTGACTATTACTGC--TTAGACTTACTCA -s Anc1.Anc1refChr6 168186 141 + 197743 CCACTTTCCTCAGAGCTTACCCGCAC---CACAGCAAAACAGTACATAT------AAGGATAGATTATCATGTTTTATATGGCATAA-------------------------------------------------ACAAGGTGAGTCCATGACTTATGAATA---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TTGGAAATTGACTATTACTGCTATTAGACTTACTCA -s Anc2.Anc2refChr1 46442 139 + 142988 TCACTTTCCTCAGAGGTTACCCGCAC---CACAGCAAAAAAGTACATAT------AAGGACAGATTATCATGTTTTATATGGCATAA-------------------------------------------------ACAAGGTGAGTCCATGACTTATGAATG---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TTGGAAATTGACTATTGCTGC--CTAAACTTACTCA -s mr.mrrefChr3 74673 198 + 181027 CTACTTTCCTTGGGGCTTACTAGCACGACCACATCATTGCAGCACACATCCAAATGGGGATCAACTCCCATGTGTTATATGGCATATTAGAAGGGG-CAGCAAAAACTGAAATGGACGGGTGTGCAAATCTTTGATACAATGTAAGTCTATGACTCATGAGTA---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CTGGAAATTGGTTATTATTGCTATTGGATATACTCA -s simCow_chr6.simCow.chr6 503404 126 + 602619 CCAGTTTTCTCAGGGGTTACCTGCAC---CATAACAATGAAGTACATAT------AAGG--------TCATGCTCTCTATGGCATAA-------------------------------------------------ACAAGGTGAGTCCTTGTCTTAAGGATC---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TTGGAAATCTACTATTGCTG-------ACTTACTTA -s simDog_chr6.simDog.chr6 492800 135 + 593897 TCACTTTCATTGGAGGTTTCCCGCAC---CACAGTATAA--GCATATGT------AAGGACAGATTATCATGTTTTATATAGCATAA-------------------------------------------------AC--AGTGAGCCCATAACTTATGAATG---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CCAGAGATTGGCTATTGCTGC--CTAAACTTACTCA -s simHuman_chr6.simHuman.chr6 500087 141 + 601863 CAACTTTCCCCAGAGCTTACCCGCGC---TACAGCAACACTGTACATAT------AAGGATGGATCATCATGTTTCATATGGCATAA-------------------------------------------------ACCAGATGAGTCCGTGAATAATGAATA---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TTGGAAATTGACTATTAATGATATTAGACCTACTCA -s simRat_chr6.simRat.chr6 533756 198 + 647215 CTACTTTCCTTGGGCCTTAATAGAACCACCACATCGTTGCAGCACGCATCCAAATGGGGATCAACTCCCATGTGTTAGATGGCATGTCAAAAGAAG-TGGCAAAAACAGAAAGAGATGGGCGTGCAAATCTTCGATACAATGTAAGTATATGACTCATGAGTA---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CTGTAAATTGGTGATTATTGCTATTGGATATACTCA - -a -s simMouse_chr6.simMouse.chr6 523034 75 + 636262 CAGTTAATTCTTTCTTGCGCAGGGCTATTCACACACTCGTTTGCCAAAAGGAATGACCATTTACTACTTACCTTG -s Anc0.Anc0refChr3 133397 75 + 222631 CAGGTTGGTCTTTCTTGGTCAGGGCTATTCCCATACCCACTTGCCTATAAAAATGGCTATTTAATAGTTATCCTC -s Anc1.Anc1refChr6 168327 75 + 197743 CAGGTTGGTCTTTCTTGGTCAGGGCTATTCCCATACCCACTTGCCTATAAAAATGGCTATTTAATAGTTATCCTC -s Anc2.Anc2refChr1 46581 75 + 142988 CAGGTTGGCCTTTCTTGTTCAGGGCTATTCCCATACCGGGTTGCCTATAAAAATGGCTATTTAATAGTTATCCTC -s mr.mrrefChr3 74871 75 + 181027 CAGTTAGTTCTTTCTTGGGCAGGGCTATTCACACACTCACTTGCCAAAAGGAATGACCATTTACTACTTACCTTC -s simCow_chr6.simCow.chr6 503530 75 + 602619 CATGTAGGCCCTTCTTGTTTGGGCCTATTCCCATACCGGGTTGCCTATAAAAATGGCTATTTAACAGTTATCCTC -s simDog_chr6.simDog.chr6 492935 63 + 593897 AAGGTTGGCCTTCCTTGTTCACAGCCATTCCTAT------------ATAAGATTGGCTATCTAATGGTTACCCTC -s simHuman_chr6.simHuman.chr6 500239 75 + 601863 CAGGTGGGTCTTTCTTGGTCAGGGCTATTCCCATACCCACTTGCCCATACAAATGCCAAATTAATAGTTATCCCC -s simRat_chr6.simRat.chr6 533954 75 + 647215 CAGTTAGTTCTTTCTTGGGCATTTCCATTCACACACTCACTTGCCAACAGGAATGACTATTCACTATTTACCTTC - -a -s simMouse_chr6.simMouse.chr6 523109 15 + 636262 CACCTAACCCATGAG -s Anc0.Anc0refChr3 133472 15 + 222631 CACCTAGCCTATTAA -s Anc1.Anc1refChr6 168402 15 + 197743 CACCTAGCCTATTAA -s Anc2.Anc2refChr1 46656 15 + 142988 CACCTAGCCTGTTAA -s mr.mrrefChr3 74946 15 + 181027 CACCTAACCCATGAA -s simCow_chr6.simCow.chr6 503607 15 + 602619 CACCCAGCCTGTTAA -s simDog_chr6.simDog.chr6 492998 15 + 593897 CACCTAGTCTGCCAA -s simHuman_chr6.simHuman.chr6 500314 15 + 601863 CTCCTGGCCTATTAA -s simRat_chr6.simRat.chr6 534029 14 + 647215 CA-CTAACCCATGAA - -a -s simMouse_chr6.simMouse.chr6 523124 33 + 636262 TAATGAGATAACAACCCTGCATTGGTACAAGAC -s Anc0.Anc0refChr3 133523 32 + 222631 TAAA-AAATACCCACCCTGCATTGGTAGAAAAA -s Anc1.Anc1refChr6 168453 33 + 197743 TAAATAAATACCCACCCTGCATTGGTAGAAAAA -s Anc2.Anc2refChr1 46707 32 + 142988 TAAA-ACATGCCCACTATGCATTGGTAGAAAAA -s mr.mrrefChr3 74961 33 + 181027 TAATTAAATAACAACCCTGCATTGGTACAAGAC -s simCow_chr6.simCow.chr6 503658 32 + 602619 TAAA-ACATGCCCACTATGCATCAGTAGAAAAT -s simDog_chr6.simDog.chr6 493048 16 + 593897 -----------------TGCATTGGTAGAAGAA -s simHuman_chr6.simHuman.chr6 500365 33 + 601863 TAAATAACTATCCACCCTGCATTGGTAGGAATG -s simRat_chr6.simRat.chr6 534043 33 + 647215 TAGTTAAATCACAGCTGTACATTGGTACAAGAC - -a -s simMouse_chr6.simMouse.chr6 523157 53 + 636262 AATATCCATGAGAAGCCCTGAATGGCACAAGTGTCCCCATCATCAATGAATCA -s Anc0.Anc0refChr3 133555 53 + 222631 AATGTCCCCGAGAAGCTCTGAACTACACAAGAGGCCCTATCATCAACAAATTT -s Anc1.Anc1refChr6 168486 53 + 197743 AATGTCCCCGAGAAGCTCTGAACTACACAAGAGGCCCTATCATCAACAAATTT -s Anc2.Anc2refChr1 46739 53 + 142988 AATGTCCCCAAGAAGCTCTGAACTACACAAGAGGCCCTACCATCAACAAATTT -s mr.mrrefChr3 74994 53 + 181027 AATATCCATGAGAAGCTCTGAATGGCACAAGTGGCCCTATCATCAATAAATCA -s simCow_chr6.simCow.chr6 503690 53 + 602619 AGAGTTCCCATGCAGCTCAGGACTACACAAGAGGCCCTACCATGAACAAATTT -s simDog_chr6.simDog.chr6 493064 53 + 593897 AATGCCCCCAAGAAGCTCTGAACTACACAAGAGACACTACCATCAACAAATTT -s simHuman_chr6.simHuman.chr6 500398 52 + 601863 A-CTTCTCAGAGAAGCTCTGAACTACACAAGAGGCCCTATCATCAAGAAATTT -s simRat_chr6.simRat.chr6 534119 53 + 647215 AATGTCCATGAGAAGCTCTGCATGGCACAAGTGGCCCTATCATCAACAAATCA - -a -s simMouse_chr6.simMouse.chr6 523210 10 + 636262 GTTACCCTGA -s Anc0.Anc0refChr3 133610 10 + 222631 GTTTCCCTAA -s Anc1.Anc1refChr6 168541 10 + 197743 GTTTCCCTAA -s Anc2.Anc2refChr1 46794 10 + 142988 GGTTCTGTAG -s mr.mrrefChr3 75049 10 + 181027 GTTTCCCTGA -s simCow_chr6.simCow.chr6 503745 10 + 602619 GGTTCTGTAG -s simHuman_chr6.simHuman.chr6 500452 10 + 601863 ATTTCCCGAA -s simRat_chr6.simRat.chr6 534174 10 + 647215 GTTTCCCTGA - -a -s simMouse_chr6.simMouse.chr6 523220 5 + 636262 CTGTC -s Anc0.Anc0refChr3 133620 5 + 222631 CTGTT -s Anc1.Anc1refChr6 168551 5 + 197743 CTGTT -s Anc2.Anc2refChr1 46804 5 + 142988 CTGTT -s mr.mrrefChr3 75059 5 + 181027 CTGTC -s simCow_chr6.simCow.chr6 503755 5 + 602619 CTGTT -s simHuman_chr6.simHuman.chr6 500462 5 + 601863 CCGTT -s simRat_chr6.simRat.chr6 534185 5 + 647215 CTGTC - -a -s simMouse_chr6.simMouse.chr6 523225 49 + 636262 AGAATACTGTACCGATCACATTACATCAGGACACAATTTTTATTTTACT -s Anc0.Anc0refChr3 133625 49 + 222631 AGAGTATTGTACTGTTTACATTCCATCAGGGGACAATTTTTCTTGTTCC -s Anc1.Anc1refChr6 168556 49 + 197743 AGAGTATTGTACTGTTTACATTCCATCAGGGGACAATTTTTCTTGTTCC -s Anc2.Anc2refChr1 46809 49 + 142988 AGAGTATTGTACTGTTTACATTCCATCAGGGGACAATTTTTCTTGTTCC -s mr.mrrefChr3 75064 49 + 181027 AGAATATTGTACTGATCACATTACATCAGGACACAATTTTTATTTTACT -s simCow_chr6.simCow.chr6 503774 44 + 602619 AGAGTATTGTACCGTTTATATTCCATTAGTGGACAACCTTCC-----CT -s simDog_chr6.simDog.chr6 493119 47 + 593897 --AGTATTATACTGTTTACATTCTATCAGGGGACAATTTTTCTTGTTCC -s simHuman_chr6.simHuman.chr6 500467 49 + 601863 AGAGTATTGGACTGTTTACATTCCATCAGGTGACAATTTTACTTCTTGC -s simRat_chr6.simRat.chr6 534190 48 + 647215 AGAATATTGTACTGAGCACACTACATCAGGACACAATTTTTA-TTTACT - -a -s simMouse_chr6.simMouse.chr6 523274 27 + 636262 GTCAGCAGCAACCAGGGGATAATTGCG -s Anc0.Anc0refChr3 133674 27 + 222631 GTCAGGAGGGACTAGGGGATAACTGGG -s Anc1.Anc1refChr6 168605 27 + 197743 GTCAGGAGGGACTAGGGGATAACTGGG -s Anc2.Anc2refChr1 46858 27 + 142988 GTCAGGAGGGGCTAGGGGATAACTGGG -s mr.mrrefChr3 75113 27 + 181027 GTCAGCAGCAACTAGGGGATAATTGCG -s simCow_chr6.simCow.chr6 503818 27 + 602619 GTCAGGAGGAGCTTGGGGATAACTGGA -s simDog_chr6.simDog.chr6 493167 27 + 593897 ATCAGGGGTGGCTAGGGGATGCCTGGG -s simHuman_chr6.simHuman.chr6 500516 27 + 601863 GTCAGGAGGCATTAGGGGATAACTGGG -s simRat_chr6.simRat.chr6 534238 27 + 647215 GGCAGCAGTAACTGGGAGATAATCACA - -a -s simMouse_chr6.simMouse.chr6 523301 9 + 636262 TTTAGTCTC -s Anc0.Anc0refChr3 133701 9 + 222631 CCTAGTTTC -s Anc1.Anc1refChr6 168632 9 + 197743 CCTAGTTTC -s Anc2.Anc2refChr1 46885 9 + 142988 CCTAATTTC -s mr.mrrefChr3 75140 9 + 181027 TTTAGTTTC -s simCow_chr6.simCow.chr6 503845 9 + 602619 CCCGATCTC -s simDog_chr6.simDog.chr6 493195 9 + 593897 CCTAATTTC -s simHuman_chr6.simHuman.chr6 500543 9 + 601863 CCTAGTTTC -s simRat_chr6.simRat.chr6 534265 9 + 647215 TTTAGTTTC - -a -s simMouse_chr6.simMouse.chr6 523310 1 + 636262 C -s Anc0.Anc0refChr3 133712 1 + 222631 C -s Anc1.Anc1refChr6 168643 1 + 197743 C -s Anc2.Anc2refChr1 46896 1 + 142988 C -s mr.mrrefChr3 75149 1 + 181027 C -s simCow_chr6.simCow.chr6 503856 1 + 602619 C -s simDog_chr6.simDog.chr6 493206 1 + 593897 C -s simHuman_chr6.simHuman.chr6 500554 1 + 601863 C -s simRat_chr6.simRat.chr6 534274 1 + 647215 C - -a -s simMouse_chr6.simMouse.chr6 523311 3 + 636262 CTA -s Anc0.Anc0refChr3 133713 3 + 222631 TTA -s Anc1.Anc1refChr6 168644 3 + 197743 TTA -s Anc2.Anc2refChr1 46897 3 + 142988 TTA -s mr.mrrefChr3 75150 3 + 181027 CTA -s simCow_chr6.simCow.chr6 503857 3 + 602619 TTA -s simDog_chr6.simDog.chr6 493208 3 + 593897 TTT -s simHuman_chr6.simHuman.chr6 500555 3 + 601863 TTA -s simRat_chr6.simRat.chr6 534275 3 + 647215 CTG - -a -s simMouse_chr6.simMouse.chr6 523314 24 + 636262 CTTAGAAATGTAGTGTCTTAAACA -s Anc0.Anc0refChr3 133716 23 + 222631 CTGCGAAAAGAA-TGTCCCAAACA -s Anc1.Anc1refChr6 168647 23 + 197743 CTGCGAAAAGAA-TGTCCCAAACA -s Anc2.Anc2refChr1 46900 23 + 142988 CTGCAAAAAAAG-TGTCCCAAACA -s mr.mrrefChr3 75153 24 + 181027 CTTAGAAATGAAGTGTCTTGAACA -s simCow_chr6.simCow.chr6 503861 23 + 602619 CTGCAGGGATAG-TGTCCCAAACA -s simDog_chr6.simDog.chr6 493211 23 + 593897 ATGGAAAAAAAG-TGTCTCAAACA -s simHuman_chr6.simHuman.chr6 500558 23 + 601863 CTACGAACAGAA-TGTCCCAAATA -s simRat_chr6.simRat.chr6 534278 24 + 647215 CTTAGAATTGAATTGTCTTGAACT - -a -s simMouse_chr6.simMouse.chr6 523338 12 + 636262 GGTGCATCGTAC -s Anc0.Anc0refChr3 133768 11 + 222631 GGTGTAT-AGCG -s Anc1.Anc1refChr6 168699 11 + 197743 GGTGTAT-AGCG -s Anc2.Anc2refChr1 46968 11 + 142988 GATGTAT-AGCG -s mr.mrrefChr3 75177 11 + 181027 GGTGCAT-GTAC -s simCow_chr6.simCow.chr6 503964 11 + 602619 AATGTCT-AGCG -s simDog_chr6.simDog.chr6 493278 11 + 593897 GATGCAT-ACCG -s simHuman_chr6.simHuman.chr6 500610 11 + 601863 GGTGTTG-AGTA -s simRat_chr6.simRat.chr6 534302 11 + 647215 GGCACAT-GTAC - -a -s simMouse_chr6.simMouse.chr6 523350 3 + 636262 CCT -s Anc0.Anc0refChr3 133779 3 + 222631 TCC -s Anc1.Anc1refChr6 168710 3 + 197743 TCC -s Anc2.Anc2refChr1 46979 3 + 142988 TCC -s mr.mrrefChr3 75188 3 + 181027 CCT -s simCow_chr6.simCow.chr6 503975 3 + 602619 TCC -s simDog_chr6.simDog.chr6 493293 3 + 593897 TCA -s simHuman_chr6.simHuman.chr6 500621 3 + 601863 TCC -s simRat_chr6.simRat.chr6 534313 3 + 647215 CCT - -a -s simMouse_chr6.simMouse.chr6 523353 4 + 636262 CTAG -s Anc0.Anc0refChr3 133782 4 + 222631 TTAG -s Anc1.Anc1refChr6 168713 4 + 197743 TTAG -s Anc2.Anc2refChr1 46982 4 + 142988 TTCG -s mr.mrrefChr3 75191 4 + 181027 CTAG -s simCow_chr6.simCow.chr6 503988 4 + 602619 TTTG -s simDog_chr6.simDog.chr6 493296 4 + 593897 TTCT -s simHuman_chr6.simHuman.chr6 500624 4 + 601863 TTAG -s simRat_chr6.simRat.chr6 534316 4 + 647215 CTAG - -a -s simMouse_chr6.simMouse.chr6 523357 1 + 636262 A -s Anc0.Anc0refChr3 133793 1 + 222631 A -s Anc1.Anc1refChr6 168724 1 + 197743 A -s Anc2.Anc2refChr1 46993 1 + 142988 A -s mr.mrrefChr3 75202 1 + 181027 A -s simCow_chr6.simCow.chr6 503999 1 + 602619 A -s simDog_chr6.simDog.chr6 493307 1 + 593897 A -s simHuman_chr6.simHuman.chr6 500635 1 + 601863 A -s simRat_chr6.simRat.chr6 534327 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 523358 7 + 636262 TGGTGAA -s Anc0.Anc0refChr3 133808 7 + 222631 TGGTGAA -s Anc1.Anc1refChr6 168739 7 + 197743 TGGTGAA -s Anc2.Anc2refChr1 47008 7 + 142988 TGGTGAA -s mr.mrrefChr3 75203 7 + 181027 TGGTGAA -s simCow_chr6.simCow.chr6 504014 7 + 602619 GGGTGAA -s simDog_chr6.simDog.chr6 493321 7 + 593897 TGGTGAA -s simHuman_chr6.simHuman.chr6 500650 7 + 601863 TGGTGAA -s simRat_chr6.simRat.chr6 534328 7 + 647215 TGATGAA - -a -s simMouse_chr6.simMouse.chr6 523365 75 + 636262 ATCAAGTACAAAAGGAATGTATCATCTGAACTAGTTTATTGTTTCTCCGTTGAGATTCACACTTAAGATCCACCT -s Anc0.Anc0refChr3 133817 72 + 222631 ATCCAGCACAGGAAAAA-GTTTCAGTTGAACTAGTTTAGTCTTTC--TCTTCAGATTTACACATAAGATCCACCT -s Anc1.Anc1refChr6 168748 72 + 197743 ATCCAGCACAGGAAAAA-GTTTCAGTTGAACTAGTTTAGTCTTTC--TCTTCAGATTTACACATAAGATCCACCT -s Anc2.Anc2refChr1 47017 72 + 142988 ATCTAGCAAAGGAAAAA-GTTTCAGTTGAACTAGTTTAGTCTCTC--TCTTCAGATTTGCACATAAGATCCACCT -s mr.mrrefChr3 75210 75 + 181027 ATCCAGTACAAAAGGAATGTATCATCTGAACTAGTTTATTGTTTCTCCGTTGAGATTCACACTTAAGATCCACCT -s simCow_chr6.simCow.chr6 504023 72 + 602619 ATCTAGCAGAGGGGAAA-CTTTCAGTTCAACTAATTTGGCTGCTC--TGCTCAAATTTGCACATAAGATCCACCC -s simDog_chr6.simDog.chr6 493330 70 + 593897 ATCTAGCAAAGGAAC-A-GTTTCAGTTGAACTTGATTAGTCTCTC--TCTGCAGATTTGCACA-AAGAACCACCT -s simHuman_chr6.simHuman.chr6 500659 72 + 601863 ATCCAGCACGGGAAAGA-GTTTCAGTCAAACTAGTTCAGTCTTTC--TCTTCAGTCTTACACATAAGATCCACCT -s simRat_chr6.simRat.chr6 534335 72 + 647215 ATCCAGTACAAAAGGAATGTATCATCTGAGCTATTTTATTGCTTCTCTGTTGAGATTCACACTTAAGATCCG--- - -a -s simMouse_chr6.simMouse.chr6 523440 56 + 636262 GACCTGAGGTGATCTCCATCTGCAGTGTGCTTTTTCTGGGGTTATGCCTACTAATC -s Anc0.Anc0refChr3 133889 50 + 222631 GGTCTTAGA------CCATCCAGTGTGTCCTTTTTCTGGGGTTATGTGTTTTAATT -s Anc1.Anc1refChr6 168820 50 + 197743 GGTCTTAGA------CCATCCAGTGTGTCCTTTTTCTGGGGTTATGTGTTTTAATT -s Anc2.Anc2refChr1 47090 50 + 142988 GGTCTTAGA------CCACCCAGTGTGTCCTTTTTCTGGGGTTATGTGTTTTAATT -s mr.mrrefChr3 75285 56 + 181027 GACCTTAGGTGATCTCCATCTGCAGTGTGCTTTTTCTGGGGTTATGCCTACTAATT -s simCow_chr6.simCow.chr6 504096 49 + 602619 GCTTTTTGA------CCACCCAGTGTGTCCTTTCTCTAGGG-TATGTGTTTTAATT -s simDog_chr6.simDog.chr6 493401 50 + 593897 GGTCTTATG------CCACCCAGTGTGTCATTTTTCTGGCGTTGTGTGTTTTAATT -s simHuman_chr6.simHuman.chr6 500731 50 + 601863 GTTCTTGGA------CCATCCAGGGTATTCTTTTCCTGGGGTTATGTTCTTTAAAT -s simRat_chr6.simRat.chr6 534407 54 + 647215 --CCTTAGGTGATCTTCATCTGCAGTGTGCTTTTTCTGGGGTTATACCTACTAATT - -a -s simMouse_chr6.simMouse.chr6 523496 7 + 636262 CAATGCA -s Anc0.Anc0refChr3 133939 7 + 222631 CAATGCA -s Anc1.Anc1refChr6 168870 7 + 197743 CAATGCA -s Anc2.Anc2refChr1 47140 7 + 142988 CAATGCA -s mr.mrrefChr3 75341 7 + 181027 CAATGCA -s simCow_chr6.simCow.chr6 504145 7 + 602619 CAATGCA -s simDog_chr6.simDog.chr6 493452 7 + 593897 CAATGCA -s simHuman_chr6.simHuman.chr6 500781 7 + 601863 CAATGCA -s simRat_chr6.simRat.chr6 534461 7 + 647215 GAATGCA - -a -s simMouse_chr6.simMouse.chr6 523503 5 + 636262 TCCTT -s Anc0.Anc0refChr3 133947 5 + 222631 TCCTT -s Anc1.Anc1refChr6 168878 5 + 197743 TCCTT -s Anc2.Anc2refChr1 47148 5 + 142988 TCCTT -s mr.mrrefChr3 75348 5 + 181027 TCCTT -s simCow_chr6.simCow.chr6 504153 5 + 602619 TTCCC -s simDog_chr6.simDog.chr6 493460 5 + 593897 ACCTT -s simHuman_chr6.simHuman.chr6 500789 5 + 601863 TCCTT -s simRat_chr6.simRat.chr6 534468 5 + 647215 TCCTT - -a -s simMouse_chr6.simMouse.chr6 523508 57 + 636262 TGATGATACATGCAGAGGGTATGCAGAGGGTAAATGCCCATGCCTTTTGTTACTAGA -s Anc0.Anc0refChr3 133967 46 + 222631 TAATGATACAA----------T-CGTAGGGTTATTGCCTGTGCAACTCGTTACGAGA -s Anc1.Anc1refChr6 168898 46 + 197743 TAATGATACAA----------T-CGTAGGGTTATTGCCTGTGCAACTCGTTACGAGA -s Anc2.Anc2refChr1 47168 46 + 142988 TAATGATACAA----------T-CATAGAATTATTGCCTGTGCAATTTGTCACGAGA -s mr.mrrefChr3 75353 47 + 181027 TGATGATACAT----------TGCGGAGGGTAAATGCCCATGCCACTCGTTACTAGA -s simCow_chr6.simCow.chr6 504173 44 + 602619 TGATAATACAA----------T-CAAAGAATTATga--tgcaaaatctgagacaaaa -s simDog_chr6.simDog.chr6 493480 46 + 593897 TAATGATACAA----------T-CATAGAATTATTGCCTGTGCTATTTGTCACGAGA -s simHuman_chr6.simHuman.chr6 500809 46 + 601863 TAATGATACAC----------T-TGCAGGGTCATTGCCTTTGCAACTCGTTAACAGA -s simRat_chr6.simRat.chr6 534473 47 + 647215 TGATGATACAT----------TGCGGAGGGTAAATGCCCATGCCACTCGTTACTAGA - -a -s simMouse_chr6.simMouse.chr6 523565 26 + 636262 CTACCCTGAGCCTTTCTTTGGTCCTT -s Anc0.Anc0refChr3 134013 22 + 222631 CAACCCCAAG----TAATTGGCCCTT -s Anc1.Anc1refChr6 168944 26 + 197743 CAACCCCAAGTTTTTAATTGGCCCTT -s Anc2.Anc2refChr1 47214 22 + 142988 TAACCCCAAG----TAAATGGCCCTT -s mr.mrrefChr3 75400 26 + 181027 CTACCCTAAGCTTTTCTTTGGTCCTT -s simCow_chr6.simCow.chr6 504226 22 + 602619 taaccaggaa----tgagttaccctt -s simDog_chr6.simDog.chr6 493526 22 + 593897 TAACCCCAAG----CAAATGGCCCTT -s simHuman_chr6.simHuman.chr6 500855 26 + 601863 CCACCCCAAGTTTTTTATTGGCCCTT -s simRat_chr6.simRat.chr6 534520 26 + 647215 CTACCCTATGCTTTTCTTTGGTCCTT - -a -s simMouse_chr6.simMouse.chr6 523591 9 + 636262 TAGTATTAT -s Anc0.Anc0refChr3 134035 9 + 222631 TAGTATGAC -s Anc1.Anc1refChr6 168970 9 + 197743 TAGTATGAC -s Anc2.Anc2refChr1 47236 9 + 142988 TATGATGAC -s mr.mrrefChr3 75426 9 + 181027 TAGTATTAC -s simCow_chr6.simCow.chr6 504254 9 + 602619 tgtgctagc -s simDog_chr6.simDog.chr6 493548 9 + 593897 TATGATGAC -s simHuman_chr6.simHuman.chr6 500881 9 + 601863 TAGTATCAC -s simRat_chr6.simRat.chr6 534546 9 + 647215 TAGTATTAC - -a -s simMouse_chr6.simMouse.chr6 523600 29 + 636262 CTAACTATATTGCTTTGTGACAGAGTTTT -s Anc0.Anc0refChr3 134044 26 + 222631 TTGCTTATttggc---gtcaCAAAACTTT -s Anc1.Anc1refChr6 168979 29 + 197743 TTGCTTATTTGGCTTAGTCACAAAACTTT -s Anc2.Anc2refChr1 47246 26 + 142988 TTGCTTATtgggc---accaGAAAACTTT -s mr.mrrefChr3 75435 29 + 181027 TTAACTATATTGCTTTGTGACAAAGTTTT -s simCow_chr6.simCow.chr6 504264 26 + 602619 ctgaatagtgggc---accaGAAAATTTT -s simDog_chr6.simDog.chr6 493558 15 + 593897 TTGCTTAT--------------AAACTCT -s simHuman_chr6.simHuman.chr6 500890 29 + 601863 TTGCTTATGTAGCTTAGTCACAAACCTTC -s simRat_chr6.simRat.chr6 534555 28 + 647215 TT-ACTATATCGCTTTGAGACAAAGTTTT - -a -s simMouse_chr6.simMouse.chr6 523629 20 + 636262 GACATTAGACCATTATAGGG -s Anc0.Anc0refChr3 134074 20 + 222631 GACACTAGGCTCTTATAAGG -s Anc1.Anc1refChr6 169012 20 + 197743 GACACTAGGCTCTTATAAGG -s Anc2.Anc2refChr1 47276 20 + 142988 GACACTACGCTCTTATAAGT -s mr.mrrefChr3 75464 20 + 181027 GACATTAGACTATTATAGGG -s simCow_chr6.simCow.chr6 504294 19 + 602619 AAAATTCTGC-CTTGGAAGA -s simDog_chr6.simDog.chr6 493577 20 + 593897 GACACTACACTCTTATAAGT -s simHuman_chr6.simHuman.chr6 500923 20 + 601863 GATGCTAGGCTCATATAAGG -s simRat_chr6.simRat.chr6 534583 19 + 647215 AACA-TAGACTATTATATGG - -a -s simMouse_chr6.simMouse.chr6 523649 75 + 636262 AGCAGTCCTCATTGTTTTGCAAGTGGAGTAGATTACTGTAGGACATCCAGATAGGTTTTGGTGCTGTTTTTTGCT -s Anc0.Anc0refChr3 134094 21 + 222631 A------------------------------------------------------TTTTGGTGCAATTCCTTGCT -s Anc1.Anc1refChr6 169032 21 + 197743 A------------------------------------------------------TTTTGGTGCAATTCCTTGCT -s Anc2.Anc2refChr1 47296 21 + 142988 A------------------------------------------------------TTTTGGTGCAAGTCCTTGCT -s mr.mrrefChr3 75484 21 + 181027 A------------------------------------------------------TTTTGGTGCCATTTTTTGCT -s simCow_chr6.simCow.chr6 504325 21 + 602619 A------------------------------------------------------TCTTTGTGCAATGCCTCACT -s simDog_chr6.simDog.chr6 493597 21 + 593897 C------------------------------------------------------ATATGGTGCAAGTCCTTGCT -s simHuman_chr6.simHuman.chr6 500943 20 + 601863 A------------------------------------------------------TATTGGTGC-ATTGCCTGCT -s simRat_chr6.simRat.chr6 534602 21 + 647215 A------------------------------------------------------TTTTGGTGCCATTCTTTGCT - -a -s simMouse_chr6.simMouse.chr6 523724 19 + 636262 TCAGACTACTGTGCTAACT -s Anc0.Anc0refChr3 134116 19 + 222631 TCAGACTACCACTCTAACT -s Anc1.Anc1refChr6 169054 19 + 197743 TCAGACTACCACTCTAACT -s Anc2.Anc2refChr1 47318 19 + 142988 TCAGACTACCACTCTAACT -s mr.mrrefChr3 75505 19 + 181027 TCAGACTACCATGCTAACT -s simCow_chr6.simCow.chr6 504347 19 + 602619 TCAGACAACCACTGTAACC -s simDog_chr6.simDog.chr6 493619 19 + 593897 TCTGACTACCACCCTACCT -s simHuman_chr6.simHuman.chr6 500964 19 + 601863 TCAGACTACCACTCTGACT -s simRat_chr6.simRat.chr6 534623 19 + 647215 TCAGACTACCATGCTAATT - -a -s simMouse_chr6.simMouse.chr6 523743 45 + 636262 GGACATGAGGACTGGCTGGAATCTAGGCCATTCCAGTAATGGTGT -s Anc0.Anc0refChr3 134135 45 + 222631 GAATGTGAAGACTGCCTAGAATGTAGGCCATACCAGGAATGCTGT -s Anc1.Anc1refChr6 169073 45 + 197743 GAATGTGAAGACTGCCTAGAATGTAGGCCATACCAGGAATGCTGT -s Anc2.Anc2refChr1 47340 45 + 142988 GAATGTGAAGACTACCTAGAATGTAGGCCATACCAGGAATGCTGT -s mr.mrrefChr3 75524 45 + 181027 GGACATGAGGACTGGCTGGAATCTAGGCCATTCCAGTAATGGTGT -s simCow_chr6.simCow.chr6 504369 45 + 602619 GGATGTAAGGACTAGCTTCAATATAGGCCATGCCAGGAACGCTGT -s simDog_chr6.simDog.chr6 493641 45 + 593897 GAATGTGAAGACTACCTAGAGTGTAGGCCATACCAGGAATGCTGT -s simHuman_chr6.simHuman.chr6 500983 33 + 601863 ------------TGTTTAGAATGGACGCCATACCAAGAATGCTAT -s simRat_chr6.simRat.chr6 534642 45 + 647215 GGACATGAGGACTGGCTGCAGTCTAGGCCATTCCAGCAATGGTGT - -a -s simMouse_chr6.simMouse.chr6 523788 5 + 636262 GCTTG -s Anc0.Anc0refChr3 134180 4 + 222631 A-TTC -s Anc1.Anc1refChr6 169118 4 + 197743 A-TTC -s Anc2.Anc2refChr1 47385 4 + 142988 A-TTC -s mr.mrrefChr3 75569 5 + 181027 GCTTG -s simCow_chr6.simCow.chr6 504415 4 + 602619 A-TTC -s simDog_chr6.simDog.chr6 493686 4 + 593897 G-TTC -s simHuman_chr6.simHuman.chr6 501016 4 + 601863 A-TTC -s simRat_chr6.simRat.chr6 534687 5 + 647215 GCTTG - -a -s simMouse_chr6.simMouse.chr6 523793 12 + 636262 TCCATGTGTGTG -s Anc0.Anc0refChr3 134184 12 + 222631 TGCATATGTGAG -s Anc1.Anc1refChr6 169122 12 + 197743 TGCATATGTGAG -s Anc2.Anc2refChr1 47389 12 + 142988 TGCACATGTGAA -s mr.mrrefChr3 75574 12 + 181027 TCCATGTGTGAG -s simCow_chr6.simCow.chr6 504419 12 + 602619 TGCACACATGAA -s simDog_chr6.simDog.chr6 493691 12 + 593897 TGCACATGTGAA -s simHuman_chr6.simHuman.chr6 501020 12 + 601863 TGCATATGTGAG -s simRat_chr6.simRat.chr6 534692 12 + 647215 TCCATGTGTGAA - -a -s simMouse_chr6.simMouse.chr6 523805 23 + 636262 CTCTAATGTGCAGCAGACCACAA -s Anc0.Anc0refChr3 134197 23 + 222631 CTCTTATGCATAGAGGGCCACAA -s Anc1.Anc1refChr6 169135 23 + 197743 CTCTTATGCATAGAGGGCCACAA -s Anc2.Anc2refChr1 47402 23 + 142988 CTCTACTGCATAGAGGGCTACAA -s mr.mrrefChr3 75586 23 + 181027 CTCTTATGTGCAGCAGACCACAA -s simCow_chr6.simCow.chr6 504432 22 + 602619 CTTT-CTGCATAGAGGGTTACAT -s simDog_chr6.simDog.chr6 493704 23 + 593897 CTCTACTGCATAGGGGACTCTAA -s simHuman_chr6.simHuman.chr6 501033 23 + 601863 CTCTTATGCATAGATGGCCACAA -s simRat_chr6.simRat.chr6 534704 10 + 647215 CTTCTA-------------ACAA - -a -s simMouse_chr6.simMouse.chr6 523828 24 + 636262 ATTCATGAGAAGTAGTCTTTCTAG -s Anc0.Anc0refChr3 134220 23 + 222631 ATT-ATGAGAAATAGTCTTTTCAT -s Anc1.Anc1refChr6 169158 23 + 197743 ATT-ATGAGAAATAGTCTTTTCAT -s Anc2.Anc2refChr1 47425 23 + 142988 TGC-ATGAGAAATAGTCTTTTCAT -s mr.mrrefChr3 75609 24 + 181027 ATTCATGAGAAATAGTCTTTCCAG -s simCow_chr6.simCow.chr6 504455 23 + 602619 CAG-ATGGGGAATAGTTTTGCCAA -s simDog_chr6.simDog.chr6 493727 23 + 593897 TGC-ATAAGAAATAGTCTTTTCGT -s simHuman_chr6.simHuman.chr6 501056 23 + 601863 ATT-AAGAAAAATAGTCTTTTCAT -s simRat_chr6.simRat.chr6 534714 24 + 647215 ATTCATGTGAAATAGCCTTTCCAG - -a -s simMouse_chr6.simMouse.chr6 523852 10 + 636262 AGCCATTTTG -s Anc0.Anc0refChr3 134244 10 + 222631 AGCCATGTTG -s Anc1.Anc1refChr6 169182 10 + 197743 AGCCATGTTG -s Anc2.Anc2refChr1 47449 10 + 142988 AGACATGTGG -s mr.mrrefChr3 75633 10 + 181027 AGCCATTTTG -s simCow_chr6.simCow.chr6 504479 10 + 602619 AGATGTATGG -s simDog_chr6.simDog.chr6 493751 10 + 593897 AGACATGTGG -s simHuman_chr6.simHuman.chr6 501080 10 + 601863 AGCCATGTTG -s simRat_chr6.simRat.chr6 534738 10 + 647215 ATCCATTTTG - -a -s simMouse_chr6.simMouse.chr6 523862 67 + 636262 CCACTTATACATCAACCCAGTCCTCTAAATCGATTCCCAATGCAGATGAAATATCAAGGGCAATGCT -s Anc0.Anc0refChr3 134257 65 + 222631 ATACGTATACATGAACCAGGTTCCTCTAAGTGATTCTTAGTACAGAGCAATGATC--GGGCAATGAT -s Anc1.Anc1refChr6 169195 67 + 197743 ATACGTATACATGAACCAGGTTCCTCTAAGTGATTCTTAGTACAGAGCAATGATCCTGGGCAATGAT -s Anc2.Anc2refChr1 47462 65 + 142988 ATACGTATACATGAACCAGTTTCCTCTAAGTAGTTCTTCGTACAGAGCAATGATC--GGGCAATGAT -s mr.mrrefChr3 75643 67 + 181027 CTACTTATACATGAACCCGGTTCTCTAAATTGATTCCCAATGCAGATGAAATATCAAGGGCAATGCT -s simCow_chr6.simCow.chr6 504492 64 + 602619 ATACGTATTCATGAACCGGCTTCCTCTAAACAGTT-TGCATACAGAGCAAGGATG--AGATCATTAG -s simDog_chr6.simDog.chr6 493764 65 + 593897 TAACGTATACATGAACCAGTTCCACCTAAGTAGTTCCTCGTACAGAGTAATGATC--GGGCAATGAT -s simHuman_chr6.simHuman.chr6 501093 67 + 601863 ATAACTATACATGAACCAGGCTCCTGTAAGTGATTCTTAGTACAGACCAATGATCCTGAGAGATGGT -s simRat_chr6.simRat.chr6 534748 67 + 647215 CTACTCATTCATGAACCTGGTTCTCCAGATTGATTCCCAATGCAGAGGAAGTATCAAGGGCAATGCT - -a -s simMouse_chr6.simMouse.chr6 523929 11 + 636262 CAGTTCTAAAG -s Anc0.Anc0refChr3 134322 11 + 222631 CTGACCTGGAG -s Anc1.Anc1refChr6 169262 11 + 197743 CTGACCTGGAG -s Anc2.Anc2refChr1 47527 11 + 142988 CTGACCTGGAG -s mr.mrrefChr3 75710 11 + 181027 CAGTTCTAGAG -s simCow_chr6.simCow.chr6 504590 11 + 602619 CTCACATGGAG -s simDog_chr6.simDog.chr6 493829 11 + 593897 CCGTCCTAGGT -s simHuman_chr6.simHuman.chr6 501160 11 + 601863 CTGACCTGGAG -s simRat_chr6.simRat.chr6 534815 11 + 647215 CAGTTCTAGAG - -a -s simMouse_chr6.simMouse.chr6 523940 13 + 636262 CAAATGTGTAGCA -s Anc0.Anc0refChr3 134333 13 + 222631 CAAGTGTGGAACC -s Anc1.Anc1refChr6 169273 13 + 197743 CAAGTGTGGAACC -s Anc2.Anc2refChr1 47538 13 + 142988 CAAGTGTGGAACC -s mr.mrrefChr3 75721 13 + 181027 CAAATGTGTAACA -s simCow_chr6.simCow.chr6 504607 13 + 602619 CGAGTACAGACAC -s simDog_chr6.simDog.chr6 493840 11 + 593897 CAA--GTGGAACC -s simHuman_chr6.simHuman.chr6 501171 13 + 601863 CAGGTGTGGAACC -s simRat_chr6.simRat.chr6 534826 13 + 647215 CAAATGTGTAACA - -a -s simMouse_chr6.simMouse.chr6 523953 5 + 636262 TTCAT -s Anc0.Anc0refChr3 134346 5 + 222631 TTCAT -s Anc1.Anc1refChr6 169286 5 + 197743 TTCAT -s Anc2.Anc2refChr1 47552 5 + 142988 TTCAT -s mr.mrrefChr3 75734 5 + 181027 TTCAT -s simCow_chr6.simCow.chr6 504621 5 + 602619 TTCAT -s simDog_chr6.simDog.chr6 493852 5 + 593897 TTCAT -s simHuman_chr6.simHuman.chr6 501184 5 + 601863 TTCAT -s simRat_chr6.simRat.chr6 534839 5 + 647215 TTTGT - -a -s simMouse_chr6.simMouse.chr6 523958 12 + 636262 AGGTTTATAGTT -s Anc0.Anc0refChr3 134361 12 + 222631 AGGCATATAGTT -s Anc1.Anc1refChr6 169301 12 + 197743 AGGCATATAGTT -s Anc2.Anc2refChr1 47567 12 + 142988 AGGCATATAGGT -s mr.mrrefChr3 75739 12 + 181027 AGGTTTATAGTT -s simCow_chr6.simCow.chr6 504636 3 + 602619 AGA--------- -s simDog_chr6.simDog.chr6 493867 12 + 593897 GGGCATATAGGT -s simHuman_chr6.simHuman.chr6 501199 12 + 601863 AGGCATATAGTT -s simRat_chr6.simRat.chr6 534844 11 + 647215 AGGTTTATAA-T - -a -s simMouse_chr6.simMouse.chr6 523970 1 + 636262 T -s Anc0.Anc0refChr3 134373 1 + 222631 T -s Anc1.Anc1refChr6 169313 1 + 197743 T -s Anc2.Anc2refChr1 47579 1 + 142988 T -s mr.mrrefChr3 75751 1 + 181027 T -s simCow_chr6.simCow.chr6 504639 1 + 602619 T -s simDog_chr6.simDog.chr6 493931 1 + 593897 T -s simHuman_chr6.simHuman.chr6 501211 1 + 601863 T -s simRat_chr6.simRat.chr6 534855 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 523971 43 + 636262 TCTGTTCCCACATCCATAGTGCCAGACCATCCGACTTCCAGCC -s Anc0.Anc0refChr3 134374 43 + 222631 TCTGGTCTTACCTCTTAAATGCCAGAACATCCCATTTCTAGCC -s Anc1.Anc1refChr6 169314 43 + 197743 TCTGGTCTTACCTCTTAAATGCCAGAACATCCCATTTCTAGCC -s Anc2.Anc2refChr1 47600 43 + 142988 TCTGGTCTTACCTCTTAAATGCCAACACCTCCCATTTCTAGCC -s mr.mrrefChr3 75752 43 + 181027 TCTGTTCCTACATCCTTAGTGCCAGACCATCCGACTTCCAGCC -s simCow_chr6.simCow.chr6 504660 43 + 602619 TCTGGCCTTACCTCCTGAGTGCCAACACCTCCCACTTCTGGCC -s simDog_chr6.simDog.chr6 493952 30 + 593897 TGTGGTCTTACCTCTTAGATG-------------TTTCTAGCC -s simHuman_chr6.simHuman.chr6 501212 43 + 601863 TCCGATCTTACTTCTTAAATGCTAGAACATCTTATTTCTAGCC -s simRat_chr6.simRat.chr6 534856 43 + 647215 TCTGTTCCTAAATACTTAGTGCCAGTCCATCCAACTACCAGCC - -a -s simMouse_chr6.simMouse.chr6 524014 73 + 636262 GACCAACCACCCTTCGACAAGCTGCCATGGCCCAAGTCTTAAAGTGTTGTCATCACAAACATGACAGGGCGCA -s Anc0.Anc0refChr3 134422 57 + 222631 GATCC---GCCCTTCCATTAGCTCCCATTGCCC-AATCTTAAAGTGTGGT----------ATGG--GTGCTCA -s Anc1.Anc1refChr6 169362 70 + 197743 GATCC---GCCCTTCCATTAGCTCCCATTGCCCAAATCTTAAAGTGTGGTCATTACAGACATGGCAGTGCTCA -s Anc2.Anc2refChr1 47648 57 + 142988 GATGC---ATCCTTCTATTACCTCCTATTGCCC-GATCTTAACGTGTGGT----------ATGG--GTGCTCA -s mr.mrrefChr3 75800 70 + 181027 GACCA---GCCCTTCCACAAGCTGCCATGGCCCAAATCTTAAAGTGTTGTCATTACAAACATGACAGGGCGCA -s simCow_chr6.simCow.chr6 504708 50 + 602619 GATGC---ATCCTTCTGTTACCCACTTTGGCAT-GATCTTAAGGTGT-------------------GTGCTTG -s simDog_chr6.simDog.chr6 493983 46 + 593897 ---------TCCTTCTATTACCTCCTATTGCCC----CCAAACCTATGGT----------ATGG----GCCCA -s simHuman_chr6.simHuman.chr6 501260 70 + 601863 GATCC---GCCCTTCCATTAGCTCCCATCACCCATATCTTAAAGTGTGGTCATTACAGACATGGCAGTGCTCA -s simRat_chr6.simRat.chr6 534904 67 + 647215 GACCA---GTCCTTCCACAGGCTGCC---GCCCAAATCTTAAGGTTTTGTCATTACAAACATGACAGGGCCCA - -a -s simMouse_chr6.simMouse.chr6 524087 16 + 636262 GCCGTCTAGGAGGTCG -s Anc0.Anc0refChr3 134480 16 + 222631 GCAGTTTAGGAGGTCA -s Anc1.Anc1refChr6 169433 16 + 197743 GCAGTTTAGGAGGTCA -s Anc2.Anc2refChr1 47706 16 + 142988 ACAGTTTAGGAGTTCA -s mr.mrrefChr3 75870 16 + 181027 GCCGTCTAGGAGGTCG -s simCow_chr6.simCow.chr6 504759 16 + 602619 ACAGGTTAGGAGTTCA -s simDog_chr6.simDog.chr6 494030 16 + 593897 ACAGTTTAGAAGTTCA -s simHuman_chr6.simHuman.chr6 501331 16 + 601863 GCAGTTTAGGAGGTCA -s simRat_chr6.simRat.chr6 534971 16 + 647215 CCCGTCTAGGAGGTTG - -a -s simMouse_chr6.simMouse.chr6 524103 3 + 636262 AGA -s Anc0.Anc0refChr3 134496 3 + 222631 AGC -s Anc1.Anc1refChr6 169449 3 + 197743 AGC -s Anc2.Anc2refChr1 47722 3 + 142988 AAC -s mr.mrrefChr3 75886 3 + 181027 AGA -s simCow_chr6.simCow.chr6 504775 3 + 602619 ACC -s simDog_chr6.simDog.chr6 494047 3 + 593897 AAC -s simHuman_chr6.simHuman.chr6 501347 3 + 601863 AGG -s simRat_chr6.simRat.chr6 534987 3 + 647215 AAA - -a -s simMouse_chr6.simMouse.chr6 524106 124 + 636262 GTTGTGAGGGCGTACACTAATGACTCACACTAATGAAAGCATTATAGATTACTTCTGTGTGGAGCATGGCCTTGTGTTATCTTCCAAGCACCATTCCTGCTAGCTGTGAGTTGACACACTGGGC -s Anc0.Anc0refChr3 134499 124 + 222631 GTGGCTGGGGCATGCACTAATGACTCACATTCATGAAAGCATTTTAGATTACCTGCATATGGAGCAAAGCATAATGTCATCTTCCAAGCACCATTCCTGCCAGGTGTGAACCAACACATTGGGT -s Anc1.Anc1refChr6 169452 124 + 197743 GTGGCTGGGGCATGCACTAATGACTCACATTCATGAAAGCATTTTAGATTACCTGCATATGGAGCAAAGCATAATGTCATCTTCCAAGCACCATTCCTGCCAGGTGTGAACCAACACATTGGGT -s Anc2.Anc2refChr1 47725 124 + 142988 TTGTCTGGGGCATGCACTAATGACTCACATTCATGAAAGCATTTTAGATTACCTGCATATGGAGCAAAGTATAATGTCATCTTCCAAGCACCATTCCTGCCAAGTGTGTACCAACACATTGGCT -s mr.mrrefChr3 75889 124 + 181027 GTTGTGAGGGCGTACACTAATGACTCACACTCATGAAAGCATTATAGATTACTTGTGTATGGAGCATGGCCTTGTGTTATCTTCCAAGCACCATTCCTGCCAGGTGTGAATTGACACACTGGGC -s simCow_chr6.simCow.chr6 504779 123 + 602619 TTGTTGGGGGCATGCACTAATGAGCCACATTCATGTAATCATTATAGATTACCTGCATATAG-GCATAATATACTGTCATCTCTCAAGCACCATTCCTGCCAAGTGTGTACCCACAGATTGGCT -s simDog_chr6.simDog.chr6 494050 123 + 593897 TTGTCTGGGGCACACGATAATGCCTCACATTCATGAAAGCATTTTACATTACCTGCGTATGGAGCAAAGTATGATGTGATC-TCCAAGCAACATTCCTGCCAAGTGTGTACCAACACATTGGCT -s simHuman_chr6.simHuman.chr6 501350 124 + 601863 GTGGCAGGAGCATGCACTAATGACTCGCATTCATGAAAGCATCTTAGATTACCTGCATATGGAGCCAAGCAGATTGTCACCTTCCAAGCACCATTCCTGCCAGGTGTGAACCAACACATTGGGT -s simRat_chr6.simRat.chr6 534990 124 + 647215 GCTGTGAGGGTGTACACTAATGACTCACACTCATGAAAGCATTATAGAATACTTGTGCATGGAGCATGTCCACCTATTATCTTCCAAGCACCATTTCTGCCAAGTATGAATTGACATACTAGCC - -a -s simMouse_chr6.simMouse.chr6 524230 6 + 636262 AGCCCC -s Anc0.Anc0refChr3 134686 6 + 222631 AGCCAC -s Anc1.Anc1refChr6 169639 6 + 197743 AGCCAC -s Anc2.Anc2refChr1 47925 6 + 142988 AGCCAC -s mr.mrrefChr3 76013 6 + 181027 AGCCAC -s simCow_chr6.simCow.chr6 504980 6 + 602619 AGCCAC -s simDog_chr6.simDog.chr6 494249 6 + 593897 AACCTT -s simHuman_chr6.simHuman.chr6 501538 6 + 601863 AGCCAC -s simRat_chr6.simRat.chr6 535114 6 + 647215 ATTCAC - -a -s simMouse_chr6.simMouse.chr6 524236 49 + 636262 ATCCTGGTCTGAAGTAAAAAAGAGCCATATAAAAGAGAGTTATGGGGAA -s Anc0.Anc0refChr3 134692 49 + 222631 TTCATGGTCTGAAGTGAAGAGATACAAGACAAAATAAAGTCACGGGGAC -s Anc1.Anc1refChr6 169645 49 + 197743 TTCATGGTCTGAAGTGAAGAGATACAAGACAAAATAAAGTCACGGGGAC -s Anc2.Anc2refChr1 47931 49 + 142988 TTCAAGGTCAGAAGTGAGGAGATTCAAGACAAAGTAAAGTCACAGCAAC -s mr.mrrefChr3 76019 49 + 181027 ATCCTGGTCTGAAGTGAAAAGGTACCATATAAAAGAAAGTTATGGGGAC -s simCow_chr6.simCow.chr6 504986 30 + 602619 TTCAAGGTCAGAAGTG-------------------AAAGTCACAGAAAC -s simDog_chr6.simDog.chr6 494255 37 + 593897 CC------------GGAGGAGATTCAAGACAAAGTCAAGTCACAGCAAC -s simHuman_chr6.simHuman.chr6 501544 49 + 601863 TTCTTGGCCTAAAGTGAAGAGATACTAGACAAAATAAAGTCACGGGGAC -s simRat_chr6.simRat.chr6 535178 42 + 647215 ATCCTG-------GGGACCAGGTACAGTAATGGAAGAAATTATGGGGAC - -a -s simMouse_chr6.simMouse.chr6 524285 5 + 636262 GCATT -s Anc0.Anc0refChr3 134741 5 + 222631 AAATT -s Anc1.Anc1refChr6 169694 5 + 197743 AAATT -s Anc2.Anc2refChr1 47981 5 + 142988 AAATT -s mr.mrrefChr3 76068 5 + 181027 ACATT -s simCow_chr6.simCow.chr6 505017 5 + 602619 AAATT -s simDog_chr6.simDog.chr6 494293 5 + 593897 AAATT -s simHuman_chr6.simHuman.chr6 501593 5 + 601863 AAATT -s simRat_chr6.simRat.chr6 535220 5 + 647215 ACATT - -a -s simMouse_chr6.simMouse.chr6 524290 45 + 636262 CTCCATAGTATCAATGGGGTAATCATAGTCTTAGGAATTCCAAAT -s Anc0.Anc0refChr3 134746 45 + 222631 CTCTAATACATCAAGAGGATAATCATAGCCTTAGGAATACCAGAC -s Anc1.Anc1refChr6 169699 45 + 197743 CTCTAATACATCAAGAGGATAATCATAGCCTTAGGAATACCAGAC -s Anc2.Anc2refChr1 47986 45 + 142988 CTCTGATACATCTAGGGAATAATCATAGCCTCGGGAATACCAGAC -s mr.mrrefChr3 76073 45 + 181027 CTCCATAGTATCAATAGGGTAATCATAGTCTTAGGAATTCCAAAT -s simCow_chr6.simCow.chr6 505022 44 + 602619 CTCTGTAGCATCTGGTGCATAAGTGTAGTCTC-ATAGTACCAAAC -s simDog_chr6.simDog.chr6 494298 44 + 593897 CTCC-ATACATCTAGGGAATAATCATAGCCTCGGGAATGTCGGAC -s simHuman_chr6.simHuman.chr6 501604 45 + 601863 ATCTAACACATCAAGAGGCTAATCATAGCCTTAGGAATACCACAC -s simRat_chr6.simRat.chr6 535225 45 + 647215 CTTGATAGTGCCAACAGGGTAACCATAGTCTTAGGAACTCCATAT - -a -s simMouse_chr6.simMouse.chr6 524335 50 + 636262 TGTATCAAATTTTGACACAGTAAGCAGACACCTTCACATGTTAGAGGACA -s Anc0.Anc0refChr3 134792 34 + 222631 TGTATCAAATTTTAACACTGTT-----GTGCCTTA-----------TTTA -s Anc1.Anc1refChr6 169745 39 + 197743 TGTATCAAATTTTAACACTGTTAAGGCGTGCCTTA-----------TTTA -s Anc2.Anc2refChr1 48032 34 + 142988 TATATCAAATTGTAAAACTGTT-----GTGCAGTA-----------TTTA -s mr.mrrefChr3 76118 50 + 181027 TGTATCAAATTTTGACACAGTAAGCGGACACCTTCACATGTTAGAGGACA -s simCow_chr6.simCow.chr6 505067 34 + 602619 TATATCAAATTGTAAAACTGTT-----GTGCAGTA-----------TGTA -s simDog_chr6.simDog.chr6 494342 3 + 593897 -----------------------------------------------TTG -s simHuman_chr6.simHuman.chr6 501650 39 + 601863 TGTATCGAATTTTAACACTGTTAAGGCGTGCCTTT-----------TTTA -s simRat_chr6.simRat.chr6 535270 50 + 647215 TGTAACAACTTTTGACACAGTAAGAGGACACCTTCACATGTCAGAGGACA - -a -s simMouse_chr6.simMouse.chr6 524385 47 + 636262 CAGACACAGCAATGGTGGTGTCTTGGATCTCTGATGTGTTGTAATTC -s Anc0.Anc0refChr3 134839 47 + 222631 CAGATGCAGCAATGGTGGTGTCTTGGATCGTCAACATGTTGTAGTGC -s Anc1.Anc1refChr6 169797 47 + 197743 CAGATGCAGCAATGGTGGTGTCTTGGATCGTCAACATGTTGTAGTGC -s Anc2.Anc2refChr1 48079 47 + 142988 CAGATGCAGCAATGGTAGTGTCTTGGATCGTCAACATGTTGTAGTGC -s mr.mrrefChr3 76181 47 + 181027 CAGATGCAGCAATGGTGGTGTCTTGGATCTTCAATGTGTTGTAATGC -s simCow_chr6.simCow.chr6 505113 46 + 602619 CAGATGCAA-AATGGAAGTGTCTTGGATCTTCAATGTGTTGTAGTGT -s simDog_chr6.simDog.chr6 494358 47 + 593897 CTGGTGCAGCCATGGTAGTGTCTTGGATTGTAAACATGTTATAGTGC -s simHuman_chr6.simHuman.chr6 501702 47 + 601863 CAGATGCAGCAATGGTGGTGTCTTGGATCCTCAACATGTCGGAGTGC -s simRat_chr6.simRat.chr6 535337 47 + 647215 CAAATGCAGCAATGGTGGTGTCTTGGATCTTCAATGTGTTGTAATGC - -a -s simMouse_chr6.simMouse.chr6 524432 9 + 636262 AGAAGTGAA -s Anc0.Anc0refChr3 134886 9 + 222631 AGAAGTGAA -s Anc1.Anc1refChr6 169844 9 + 197743 AGAAGTGAA -s Anc2.Anc2refChr1 48126 9 + 142988 AGAAGTGAA -s mr.mrrefChr3 76228 9 + 181027 AGAAGTGAA -s simCow_chr6.simCow.chr6 505162 9 + 602619 GGGAGTGAA -s simDog_chr6.simDog.chr6 494405 9 + 593897 AGAAGCGAA -s simHuman_chr6.simHuman.chr6 501749 9 + 601863 AGAAGTGGA -s simRat_chr6.simRat.chr6 535384 9 + 647215 AGAAGTGAA - -a -s simMouse_chr6.simMouse.chr6 524441 3 + 636262 TAA -s Anc0.Anc0refChr3 134895 3 + 222631 TGA -s Anc1.Anc1refChr6 169853 3 + 197743 TGA -s Anc2.Anc2refChr1 48135 3 + 142988 CCA -s mr.mrrefChr3 76237 3 + 181027 TGA -s simCow_chr6.simCow.chr6 505171 3 + 602619 CCC -s simDog_chr6.simDog.chr6 494414 3 + 593897 CCA -s simHuman_chr6.simHuman.chr6 501760 3 + 601863 TGA -s simRat_chr6.simRat.chr6 535393 3 + 647215 TGA - -a -s simMouse_chr6.simMouse.chr6 524444 45 + 636262 TGAGATATGGATGCATGCACTTACCTCAAGCCTATCTTGGATGGT -s Anc0.Anc0refChr3 134898 45 + 222631 TAAGATGTGGATCCATGCAAATATTTTAACCCTACCTTGGATGAT -s Anc1.Anc1refChr6 169856 45 + 197743 TAAGATGTGGATCCATGCAAATATTTTAACCCTACCTTGGATGAT -s Anc2.Anc2refChr1 48138 45 + 142988 AAAGATGTGGATCCATGTAAATATTTTAACCCTACCTTGGATGAT -s mr.mrrefChr3 76240 45 + 181027 TGAGATATGGATGCATGCACATACTTCAAGCCTATCTTGGATGGT -s simCow_chr6.simCow.chr6 505174 45 + 602619 ACACAAGTGGGTACATATAAACAATTTAACCCTATGTTAGATGAT -s simDog_chr6.simDog.chr6 494417 45 + 593897 AAAGATGTGGATCCATGTGAATATTTTAACCCTACCTTGGATGAT -s simHuman_chr6.simHuman.chr6 501766 43 + 601863 TAAAATGTGGATCCATGCAAATATTTGAACCCTACCTTGGATG-- -s simRat_chr6.simRat.chr6 535396 44 + 647215 TCAGATATAG-TATGTGTGCATACTTCAATCCTATCTTGGATGGT - -a -s simMouse_chr6.simMouse.chr6 524489 21 + 636262 AAAATTTGTGAAACTTAACAG -s Anc0.Anc0refChr3 134943 20 + 222631 CTA-TTTGTGAAACTTATTGG -s Anc1.Anc1refChr6 169901 20 + 197743 CTA-TTTGTGAAACTTATTGG -s Anc2.Anc2refChr1 48183 20 + 142988 CTA-TTTGTGAAACTTGTTGG -s mr.mrrefChr3 76285 21 + 181027 AAAATTTGTGAAACTTAACAG -s simCow_chr6.simCow.chr6 505220 20 + 602619 ATC-TTTGAGAAACTTGTTGG -s simDog_chr6.simDog.chr6 494462 20 + 593897 CTA-TTTATGAAACTTGTTGG -s simHuman_chr6.simHuman.chr6 501809 16 + 601863 -----TTGTAAAACTTAGGTG -s simRat_chr6.simRat.chr6 535440 21 + 647215 ACGATTTGTGGGACTTAACAG - -a -s simMouse_chr6.simMouse.chr6 524510 9 + 636262 TATCTATTG -s Anc0.Anc0refChr3 134964 9 + 222631 CTTCTATTG -s Anc1.Anc1refChr6 169922 9 + 197743 CTTCTATTG -s Anc2.Anc2refChr1 48204 9 + 142988 TTTCTATTG -s mr.mrrefChr3 76306 9 + 181027 CTTCTATTG -s simCow_chr6.simCow.chr6 505241 9 + 602619 TTGCTATTG -s simDog_chr6.simDog.chr6 494483 9 + 593897 TTTCTAGTG -s simHuman_chr6.simHuman.chr6 501826 9 + 601863 CTTCTATTG -s simRat_chr6.simRat.chr6 535461 9 + 647215 CTTCTATTG - -a -s simMouse_chr6.simMouse.chr6 524519 51 + 636262 ACTGGAAGGAGAAAACTATTATAATTCTTTATAGCTACACTTGCATCACAA -s Anc0.Anc0refChr3 134974 40 + 222631 GCTAGAGGGAACAAA-----ATAA------ATAGTAATATTTCCATTATAG -s Anc1.Anc1refChr6 169932 43 + 197743 GCTAGAGGGAACAAA-T-TTATAA------ATAGTAATATTTCCATTATAG -s Anc2.Anc2refChr1 48214 40 + 142988 GTTAGAGGGAACAGA-----ATAA------GTATTAATATTTCCATTATAG -s mr.mrrefChr3 76315 50 + 181027 ACTGGAAGGAAAAAA-TATTATAATTCTTTATAGCTACATTTGCATCACAG -s simCow_chr6.simCow.chr6 505251 40 + 602619 GTTAGAGGGAATGTA-----ATCG------GTATAAATATTTCCGTCACAG -s simDog_chr6.simDog.chr6 494493 40 + 593897 GTTCATGGGAACAGA-----ATAA------GTATTAATATTTCTATTATAG -s simHuman_chr6.simHuman.chr6 501836 43 + 601863 GCTAGAGGGAACAAA-T-TTATAA------ATTGTACTATTTACATTATAG -s simRat_chr6.simRat.chr6 535470 50 + 647215 ACTTGAAGGAAGAAG-TATTATAATTCTTTATGGCTACATTTGCAGCACAG - -a -s simMouse_chr6.simMouse.chr6 524570 35 + 636262 TTACAGGTGAGGTGATACATCAGCAGTTGGATAAT -s Anc0.Anc0refChr3 135014 35 + 222631 TTAAAGAGGAGGTGATACAATTGAAGTTGGACAAC -s Anc1.Anc1refChr6 169975 35 + 197743 TTAAAGAGGAGGTGATACAATTGAAGTTGGACAAC -s Anc2.Anc2refChr1 48254 35 + 142988 TGAAAGAGGAGGTGATACAATTGAAGTTGGGCAAC -s mr.mrrefChr3 76365 35 + 181027 TTACAGGTGAGGTGATACATTAGCAGTTGGACAAT -s simCow_chr6.simCow.chr6 505291 32 + 602619 -CAAGGAGGAGGTGATGCAATTGAAGTTGGCTG-- -s simDog_chr6.simDog.chr6 494533 35 + 593897 TGAAAGAGGGGATGATACAATTGAGGTTGCGCAAC -s simHuman_chr6.simHuman.chr6 501880 35 + 601863 TTAAAGAGGATGTGATACAATTAAAGTTGGACAAC -s simRat_chr6.simRat.chr6 535520 35 + 647215 TTACAGGTGAGGTGATACATTAGCAATTGGACAAT - -a -s simMouse_chr6.simMouse.chr6 524605 26 + 636262 GATGAAAGAGTTCATTGGGTTTAAGA -s Anc0.Anc0refChr3 135050 26 + 222631 GCTGGAAAAGTCTACTTGGTTCAACA -s Anc1.Anc1refChr6 170011 26 + 197743 GCTGGAAAAGTCTACTTGGTTCAACA -s Anc2.Anc2refChr1 48290 26 + 142988 ACTGGAAAAGTCTACTTAGTTCAACA -s mr.mrrefChr3 76400 26 + 181027 GATGAAAGAGTCTATTGGGTTTAAGA -s simCow_chr6.simCow.chr6 505324 26 + 602619 ACTGGAAAGGTCCACTTAGTTCAACA -s simDog_chr6.simDog.chr6 494569 24 + 593897 ATTGGAAAAGTCTACCT-GTTCAA-A -s simHuman_chr6.simHuman.chr6 501916 26 + 601863 GCCGGAAAAACCTACTTGGTTCAACA -s simRat_chr6.simRat.chr6 535555 26 + 647215 GTTGAAAGAGTCTATTGGGTTTAAAA - -a -s simMouse_chr6.simMouse.chr6 524631 9 + 636262 CAATCAATT -s Anc0.Anc0refChr3 135086 6 + 222631 ---TCAGTT -s Anc1.Anc1refChr6 170047 6 + 197743 ---TCAGTT -s Anc2.Anc2refChr1 48327 6 + 142988 ---TTAGTT -s mr.mrrefChr3 76436 9 + 181027 CAATCAATT -s simCow_chr6.simCow.chr6 505361 6 + 602619 ---TTAGTT -s simDog_chr6.simDog.chr6 494604 6 + 593897 ---TTAGTT -s simHuman_chr6.simHuman.chr6 501952 6 + 601863 ---TCAGTT -s simRat_chr6.simRat.chr6 535593 9 + 647215 CAATCTATT - -a -s simMouse_chr6.simMouse.chr6 524640 1 + 636262 C -s Anc0.Anc0refChr3 135092 1 + 222631 A -s Anc1.Anc1refChr6 170053 1 + 197743 A -s Anc2.Anc2refChr1 48333 1 + 142988 A -s mr.mrrefChr3 76445 1 + 181027 C -s simCow_chr6.simCow.chr6 505368 1 + 602619 A -s simDog_chr6.simDog.chr6 494610 1 + 593897 A -s simHuman_chr6.simHuman.chr6 501958 1 + 601863 G -s simRat_chr6.simRat.chr6 535602 1 + 647215 C - -a -s simMouse_chr6.simMouse.chr6 524641 5 + 636262 TGATA -s Anc0.Anc0refChr3 135093 5 + 222631 TCTGA -s Anc1.Anc1refChr6 170054 5 + 197743 TCTGA -s Anc2.Anc2refChr1 48360 5 + 142988 TCTGC -s mr.mrrefChr3 76446 5 + 181027 TGATA -s simCow_chr6.simCow.chr6 505396 5 + 602619 TCCTC -s simDog_chr6.simDog.chr6 494642 5 + 593897 TCTGC -s simHuman_chr6.simHuman.chr6 501959 5 + 601863 TCTAA -s simRat_chr6.simRat.chr6 535603 5 + 647215 TGATA - -a -s simMouse_chr6.simMouse.chr6 524646 17 + 636262 TTAATAATAAGCCAGTT -s Anc0.Anc0refChr3 135098 11 + 222631 TCAATAA------AGTA -s Anc1.Anc1refChr6 170059 11 + 197743 TCAATAA------AGTA -s Anc2.Anc2refChr1 48365 11 + 142988 TTGATAA------AGTA -s mr.mrrefChr3 76451 17 + 181027 TCAATAATATGCCAGTT -s simCow_chr6.simCow.chr6 505403 11 + 602619 TTGATAA------ACCA -s simDog_chr6.simDog.chr6 494647 11 + 593897 TTGATAA------AGTA -s simHuman_chr6.simHuman.chr6 501964 11 + 601863 TCAATGA------AGTA -s simRat_chr6.simRat.chr6 535608 17 + 647215 TCTATAATATGCTAGTC - -a -s simMouse_chr6.simMouse.chr6 524663 41 + 636262 TTGTCCCTTGGAGATTTTCTATCTGTCCTTAACATTAGATT -s Anc0.Anc0refChr3 135109 41 + 222631 CTGCCCTGTGGAGGTCTTCTATCTGCTCTTAACATGAAATC -s Anc1.Anc1refChr6 170070 41 + 197743 CTGCCCTGTGGAGGTCTTCTATCTGCTCTTAACATGAAATC -s Anc2.Anc2refChr1 48382 41 + 142988 CTGCCCTGTGGAGGTCATCTGTGTGCTCTTAACATGAAATC -s mr.mrrefChr3 76468 41 + 181027 TTGTCCCTTGGAGATTTTCTATCTGTCCTTAACATTAGATT -s simCow_chr6.simCow.chr6 505421 41 + 602619 CTCCCCTGTGGAGAACATCTGTCTGTTCTTTACATCAAATC -s simDog_chr6.simDog.chr6 494664 41 + 593897 CTGCCCTGTGGAGGTCATCTGTGTGCTCTTAACATGAGATT -s simHuman_chr6.simHuman.chr6 501975 23 + 601863 CTGCCTTGTGGAGGTCTTCAATC------------------ -s simRat_chr6.simRat.chr6 535625 41 + 647215 TTGTCCATTGGAGATTTTCTATCTGTCCTTAACATTAGATT - -a -s simMouse_chr6.simMouse.chr6 524704 13 + 636262 CCTTAATAACACC -s Anc0.Anc0refChr3 135150 13 + 222631 CTTTCGCTAATCC -s Anc1.Anc1refChr6 170111 13 + 197743 CTTTCGCTAATCC -s Anc2.Anc2refChr1 48423 13 + 142988 CTTTCCCTGATCC -s mr.mrrefChr3 76509 13 + 181027 CCTTAGTTAATCC -s simCow_chr6.simCow.chr6 505481 13 + 602619 CTTTCACTGAGCT -s simDog_chr6.simDog.chr6 494705 13 + 593897 CATTCCCTGATCC -s simHuman_chr6.simHuman.chr6 501998 13 + 601863 CTTTCGCTAATCC -s simRat_chr6.simRat.chr6 535666 13 + 647215 CCTTAGTTAATCC - -a -s simMouse_chr6.simMouse.chr6 524717 3 + 636262 TAT -s Anc0.Anc0refChr3 135165 3 + 222631 GAT -s Anc1.Anc1refChr6 170126 3 + 197743 GAT -s Anc2.Anc2refChr1 48438 3 + 142988 GAT -s mr.mrrefChr3 76524 3 + 181027 TAT -s simCow_chr6.simCow.chr6 505496 3 + 602619 TAT -s simDog_chr6.simDog.chr6 494720 3 + 593897 GGT -s simHuman_chr6.simHuman.chr6 502013 3 + 601863 CAT -s simRat_chr6.simRat.chr6 535681 3 + 647215 TAT - -a -s simMouse_chr6.simMouse.chr6 524720 1 + 636262 T -s Anc0.Anc0refChr3 135168 1 + 222631 T -s Anc1.Anc1refChr6 170129 1 + 197743 T -s Anc2.Anc2refChr1 48445 1 + 142988 C -s mr.mrrefChr3 76527 1 + 181027 T -s simCow_chr6.simCow.chr6 505503 1 + 602619 C -s simDog_chr6.simDog.chr6 494727 1 + 593897 C -s simHuman_chr6.simHuman.chr6 502016 1 + 601863 T -s simRat_chr6.simRat.chr6 535684 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 524721 2 + 636262 GA -s Anc0.Anc0refChr3 135169 2 + 222631 GA -s Anc1.Anc1refChr6 170130 2 + 197743 GA -s Anc2.Anc2refChr1 48446 2 + 142988 GC -s mr.mrrefChr3 76528 2 + 181027 GA -s simCow_chr6.simCow.chr6 505504 2 + 602619 TC -s simDog_chr6.simDog.chr6 494729 2 + 593897 GC -s simHuman_chr6.simHuman.chr6 502017 2 + 601863 GA -s simRat_chr6.simRat.chr6 535685 2 + 647215 GA - -a -s simMouse_chr6.simMouse.chr6 524723 12 + 636262 ACACATCTGCAC -s Anc0.Anc0refChr3 135184 12 + 222631 GCTCATCAGCAC -s Anc1.Anc1refChr6 170145 12 + 197743 GCTCATCAGCAC -s Anc2.Anc2refChr1 48461 12 + 142988 GCTCATCAGCAC -s mr.mrrefChr3 76543 12 + 181027 ACTCATCAGCAC -s simCow_chr6.simCow.chr6 505519 12 + 602619 GCTCATCAGCAC -s simDog_chr6.simDog.chr6 494744 12 + 593897 GCTCATCAGCAC -s simHuman_chr6.simHuman.chr6 502031 12 + 601863 GCTCATCAACAC -s simRat_chr6.simRat.chr6 535705 12 + 647215 ACTCATTAGTAC - -a -s simMouse_chr6.simMouse.chr6 524735 4 + 636262 AAAG -s Anc0.Anc0refChr3 135196 4 + 222631 AAGG -s Anc1.Anc1refChr6 170157 4 + 197743 AAGG -s Anc2.Anc2refChr1 48473 4 + 142988 AAGG -s mr.mrrefChr3 76555 4 + 181027 AAAG -s simCow_chr6.simCow.chr6 505531 4 + 602619 AAAC -s simDog_chr6.simDog.chr6 494757 4 + 593897 AAGG -s simHuman_chr6.simHuman.chr6 502043 4 + 601863 AATT -s simRat_chr6.simRat.chr6 535717 4 + 647215 AAAG - -a -s simMouse_chr6.simMouse.chr6 524739 6 + 636262 AATAAA -s Anc0.Anc0refChr3 135201 6 + 222631 AATAAA -s Anc1.Anc1refChr6 170162 6 + 197743 AATAAA -s Anc2.Anc2refChr1 48478 6 + 142988 AATGAA -s mr.mrrefChr3 76559 6 + 181027 AATAAA -s simCow_chr6.simCow.chr6 505536 6 + 602619 AATGAA -s simDog_chr6.simDog.chr6 494762 6 + 593897 ATCGAA -s simHuman_chr6.simHuman.chr6 502048 6 + 601863 AATAAA -s simRat_chr6.simRat.chr6 535721 6 + 647215 AATAAA - -a -s simMouse_chr6.simMouse.chr6 524745 143 + 636262 GAACTTAGATGGATACTATGCCTTATCAATAAAAGTTGTTGGGGACCATGTTAGAAAACCAGTGTTAGGCTGGAGTCCTCAAGAAGACTGGTCACTCAACTTGAGCCTTGTGTGGCCTCCAATCTCAGTTCAAATTTGAGCTA -s Anc0.Anc0refChr3 135214 91 + 222631 AAACTTCAATGGATATAATGCCTTATAGATACAACTAGTTAGG----------------CAGGGTTAGACTA------------------------------------GGGGTGGCACCCAACCTCAGTTTGCACTTGGGCTA -s Anc1.Anc1refChr6 170175 127 + 197743 AAACTTCAATGGATATAATGCCTTATAGATACAACTAGTTAGG----------------CAGGGTTAGACTAGGGTCATTGTGAAGGCTGGGCACTCTGCTGAAGCCTGGGGTGGCACCCAACCTCAGTTTGCACTTGGGCTA -s Anc2.Anc2refChr1 48492 91 + 142988 AAACTTCAATGAATATAATGCCTTATAGATACAACTAGTTAGG----------------CAGGGTTAGACTA------------------------------------GGGGTAGCACCCAACCTCTGCTTGCACTTGGGCTA -s mr.mrrefChr3 76568 143 + 181027 AAACTTAAATGGATACTATGCCTTATCAATAAAAGTTGTTAGGGACCATGTTAGAAAACCAGTGTTAGGCTGGAGTCCTTAAGAAGGCTGGTCACTCAACTGGAGCCTTGGGTGGCCTCCAATCTCAGTTCAAATTTGAGCTA -s simCow_chr6.simCow.chr6 505555 91 + 602619 AAACTTCAATGAATGTAATGCCTTATAGATACAACTAGTTAGG----------------CAGGGTTCGACTA------------------------------------GGGGTAGCACCCAACCTCTGCTTACACTTGGCTTA -s simDog_chr6.simDog.chr6 494776 90 + 593897 AAACTTCAATGAATATAATGTCTTA-AGATACAGCAAGTTGGG----------------CAGCGTTAGACTA------------------------------------TGGATAGCACCCTACCTCTGCTTGCACTTGGGCTA -s simHuman_chr6.simHuman.chr6 502061 127 + 601863 AAACTTCAATGGATATAATGCCTTATAGATACAACTAGTTAGG----------------CAGGGTTGGACTAGGGTCATTGTGAAGGCTGGGCACTCTGCTGAAGCCTGGGGTGGCACGTAACGTTAGTTTGCACTTGGGCTA -s simRat_chr6.simRat.chr6 535730 143 + 647215 AAACTTAAATGGATACTATGCCTTATCAATTAAAGTTGTCAGGGACCATGGTAGCAAACCAGTGTTAGGCTGGAGACCTTAAGAAGGCTGGTCACTCAACTGTAGCCTCGGGTGACCTCAAATTCCAGTTCAGGTTTGAGCTA - -a -s simMouse_chr6.simMouse.chr6 524888 35 + 636262 CTGGATGGATTAATAGTTTGCTGTAGACAGTGAAG -s Anc0.Anc0refChr3 135305 33 + 222631 CAGGATAAATGAAAAGTTTGCCATAGATAG-GAA- -s Anc1.Anc1refChr6 170302 34 + 197743 CAGGATAAATGAAAAGTTTGCCATAGATAG-GAAG -s Anc2.Anc2refChr1 48583 33 + 142988 CAGGATAAATGAAAAGATTGCCATAGATAA-GAA- -s mr.mrrefChr3 76711 35 + 181027 CTGGATGGATTAATAGTTTGCTGTAGACAGTGAAG -s simCow_chr6.simCow.chr6 505646 31 + 602619 CAG--TAAATGAAAAGCTTGCCATAGATCA-AAG- -s simDog_chr6.simDog.chr6 494866 32 + 593897 GAGGATAAATGAAAAGAT-GCCATTGATAA-GCA- -s simHuman_chr6.simHuman.chr6 502196 34 + 601863 CAAGATAAATGAAAAATTAGCCACAGATAG-GAAG -s simRat_chr6.simRat.chr6 535873 34 + 647215 TTGGTTGTATTAATAGTTTACTGTAGACATTTAA- - -a -s simMouse_chr6.simMouse.chr6 524923 17 + 636262 GAGCCATAATACTGGGA -s Anc0.Anc0refChr3 135344 17 + 222631 AAGTCTTAAAACTGAGA -s Anc1.Anc1refChr6 170342 17 + 197743 AAGTCTTAAAACTGAGA -s Anc2.Anc2refChr1 48622 17 + 142988 AAGTTTTAAAACTGAGA -s mr.mrrefChr3 76746 17 + 181027 GAGCCATAATACTAGGA -s simCow_chr6.simCow.chr6 505683 17 + 602619 AAGTTTTGAAGATGAGA -s simDog_chr6.simDog.chr6 494904 17 + 593897 aagttttaaaactgaga -s simHuman_chr6.simHuman.chr6 502236 17 + 601863 AAGTCTGAAAACTGAGA -s simRat_chr6.simRat.chr6 535907 17 + 647215 GAGCCATAATACTAGGA - -a -s simMouse_chr6.simMouse.chr6 524940 14 + 636262 CTGCCCTGCACTGT -s Anc0.Anc0refChr3 135361 12 + 222631 -TCCCTTGAGCTG- -s Anc1.Anc1refChr6 170359 13 + 197743 -TCCCTTGAGCTGT -s Anc2.Anc2refChr1 48639 12 + 142988 -CCCCTTGAGCTG- -s mr.mrrefChr3 76763 14 + 181027 CTGCCATGCACTGT -s simCow_chr6.simCow.chr6 505700 12 + 602619 -ATCACTGAGCTG- -s simDog_chr6.simDog.chr6 494921 12 + 593897 -ccccttgagcta- -s simHuman_chr6.simHuman.chr6 502253 13 + 601863 -TCCCTTGAGCTGT -s simRat_chr6.simRat.chr6 535925 14 + 647215 CTGCCACACACTGT - -a -s simMouse_chr6.simMouse.chr6 524954 30 + 636262 AGCACATCCTGCATACCTGAGCTAGAAAAG -s Anc0.Anc0refChr3 135373 29 + 222631 atcgcatcctaataatcagacta-gaagag -s Anc1.Anc1refChr6 170372 29 + 197743 ATCgcatcctaataatcagacta-gaagag -s Anc2.Anc2refChr1 48651 29 + 142988 atggcatcctaataatcagacta-gaagag -s mr.mrrefChr3 76777 29 + 181027 AGCACATCCTGCATACCTGAGCT-GAAAAG -s simCow_chr6.simCow.chr6 505713 29 + 602619 GTGGCACCCTCATAGCCAAGCTA-GAACAG -s simDog_chr6.simDog.chr6 494933 29 + 593897 atggcatcctaataatcagacta-gaagag -s simHuman_chr6.simHuman.chr6 502266 3 + 601863 ATC--------------------------- -s simRat_chr6.simRat.chr6 535939 29 + 647215 ATCACATCCAGCGTACCTGAGCC-GAAAAG - -a -s simMouse_chr6.simMouse.chr6 524984 14 + 636262 CAACATGAATTCCA -s Anc0.Anc0refChr3 135402 14 + 222631 cAATAtggATTCCA -s Anc1.Anc1refChr6 170401 14 + 197743 cAATATGGATTCCA -s Anc2.Anc2refChr1 48683 14 + 142988 cAATAtggATTCCA -s mr.mrrefChr3 76806 14 + 181027 CAACATGAATTCCA -s simCow_chr6.simCow.chr6 505745 11 + 602619 TAATA---ACTCCA -s simDog_chr6.simDog.chr6 495045 14 + 593897 caatatggattcta -s simHuman_chr6.simHuman.chr6 502269 9 + 601863 -----TGGGATCCA -s simRat_chr6.simRat.chr6 535968 14 + 647215 CAACATGAATTCCA - -a -s simMouse_chr6.simMouse.chr6 524998 4 + 636262 CCCC -s Anc0.Anc0refChr3 135416 4 + 222631 ACCT -s Anc1.Anc1refChr6 170415 4 + 197743 ACCT -s Anc2.Anc2refChr1 48697 4 + 142988 ACCT -s mr.mrrefChr3 76820 4 + 181027 CCCC -s simCow_chr6.simCow.chr6 505760 4 + 602619 TCCT -s simDog_chr6.simDog.chr6 495059 4 + 593897 acct -s simHuman_chr6.simHuman.chr6 502278 4 + 601863 AGCT -s simRat_chr6.simRat.chr6 535982 4 + 647215 CCCC - -a -s simMouse_chr6.simMouse.chr6 525002 40 + 636262 ACAGGGAGTGTAGTGAGTAAATAGCCTAGTAATGGGGTGA -s Anc0.Anc0refChr3 135423 40 + 222631 ACAGGTAGTATGGCAAGTCAGAAGGGTAACCATGGTCTGT -s Anc1.Anc1refChr6 170422 40 + 197743 ACAGGTAGTATGGCAAGTCAGAAGGGTAACCATGGTCTGT -s Anc2.Anc2refChr1 48704 40 + 142988 ACAGGTAGTATGGCAAGTCAGAAGGGTAACCATGGTCTGT -s mr.mrrefChr3 76824 40 + 181027 ACAGGGAGTGTAGTGAGTAAATAGCCTAGTAATGGGCTGT -s simCow_chr6.simCow.chr6 505767 39 + 602619 ACAGGTGGTATGGCAACTCAGGGGGATAACCATGGT-TGT -s simDog_chr6.simDog.chr6 495066 40 + 593897 TTGGGTAGTGTGGCAAGTCAGAAGGGTAACTATGGTCTGT -s simHuman_chr6.simHuman.chr6 502285 40 + 601863 ACAGGCAGTATGGCAAGTCGGAAGGGTAACCATAGTCCGT -s simRat_chr6.simRat.chr6 535986 40 + 647215 ACAGAGGGTTTATTGGTTAAATAGCCTAGTAATTGGCTGT - -a -s simMouse_chr6.simMouse.chr6 525042 12 + 636262 TTCTGTGATCAA -s Anc0.Anc0refChr3 135463 12 + 222631 TTTAGTGATCAA -s Anc1.Anc1refChr6 170462 12 + 197743 TTTAGTGATCAA -s Anc2.Anc2refChr1 48755 12 + 142988 TTTAGAAATCAA -s mr.mrrefChr3 76864 12 + 181027 TTCTGTGATCAA -s simCow_chr6.simCow.chr6 505817 12 + 602619 TTTAGAAATCAA -s simDog_chr6.simDog.chr6 495117 12 + 593897 TTTAGAAATCAA -s simHuman_chr6.simHuman.chr6 502325 8 + 601863 TTGCGTGA---- -s simRat_chr6.simRat.chr6 536026 12 + 647215 TTCTGTGATTGA - -a -s simMouse_chr6.simMouse.chr6 525054 7 + 636262 CATCATG -s Anc0.Anc0refChr3 135475 7 + 222631 TATCATG -s Anc1.Anc1refChr6 170474 7 + 197743 TATCATG -s Anc2.Anc2refChr1 48776 7 + 142988 TATCATG -s mr.mrrefChr3 76876 7 + 181027 CATCATG -s simCow_chr6.simCow.chr6 505838 7 + 602619 TATCATA -s simDog_chr6.simDog.chr6 495138 7 + 593897 TATCATG -s simRat_chr6.simRat.chr6 536038 7 + 647215 CATTATG - -a -s simMouse_chr6.simMouse.chr6 525061 29 + 636262 TTCCCCTAATGCTACTTCCCATGAAGTCA -s Anc0.Anc0refChr3 135482 29 + 222631 TTGGCCTGACACCACTTCTCAAGGAGTCA -s Anc1.Anc1refChr6 170481 29 + 197743 TTGGCCTGACACCACTTCTCAAGGAGTCA -s Anc2.Anc2refChr1 48784 29 + 142988 TTGGCCTGGCACCACTTCTCAAGGAGTCA -s mr.mrrefChr3 76883 29 + 181027 TTCCCCTGATACTACTTCCCAAGGAGTCA -s simCow_chr6.simCow.chr6 505846 28 + 602619 TT-CCCTGGCACCACTTCTCAAGGAGTCC -s simDog_chr6.simDog.chr6 495146 29 + 593897 TTGGCCTGGCACCACTTCTCAAGGAATTA -s simHuman_chr6.simHuman.chr6 502333 25 + 601863 ----ACAGACACCACTTTTTAAGGAGTCA -s simRat_chr6.simRat.chr6 536045 29 + 647215 TTTCCCTGATACTAATTCCCAAAGAGTCA - -a -s simMouse_chr6.simMouse.chr6 525090 8 + 636262 CTCTGTCA -s Anc0.Anc0refChr3 135511 8 + 222631 CTCAGAGT -s Anc1.Anc1refChr6 170510 8 + 197743 CTCAGAGT -s Anc2.Anc2refChr1 48813 8 + 142988 CTCAGAGT -s mr.mrrefChr3 76912 8 + 181027 CTCTGTCA -s simCow_chr6.simCow.chr6 505874 8 + 602619 CTCAGAGT -s simDog_chr6.simDog.chr6 495224 8 + 593897 CTCAGAGT -s simHuman_chr6.simHuman.chr6 502358 8 + 601863 CTCAGAGT -s simRat_chr6.simRat.chr6 536074 8 + 647215 CTCTATAA - -a -s simMouse_chr6.simMouse.chr6 525098 2 + 636262 TG -s Anc0.Anc0refChr3 135519 2 + 222631 TG -s Anc1.Anc1refChr6 170518 2 + 197743 TG -s Anc2.Anc2refChr1 48821 2 + 142988 TG -s mr.mrrefChr3 76920 2 + 181027 TG -s simCow_chr6.simCow.chr6 505882 2 + 602619 TG -s simDog_chr6.simDog.chr6 495232 2 + 593897 TG -s simHuman_chr6.simHuman.chr6 502368 2 + 601863 GA -s simRat_chr6.simRat.chr6 536082 2 + 647215 TG - -a -s simMouse_chr6.simMouse.chr6 525100 30 + 636262 ATGCATACCATTATCTGGTAGTTAAATACT -s Anc0.Anc0refChr3 135521 27 + 222631 ATG---AACTATACCCAATAGTTGGATACC -s Anc1.Anc1refChr6 170520 27 + 197743 ATG---AACTATACCCAATAGTTGGATACC -s Anc2.Anc2refChr1 48824 27 + 142988 ATG---AACTATACCCACTAGTTGGGTGCC -s mr.mrrefChr3 76922 28 + 181027 ATG--TACCATTACCTGATAGTTAAATACT -s simCow_chr6.simCow.chr6 505885 27 + 602619 ATG---AACTATACCCACTAGTTGGGCGCC -s simDog_chr6.simDog.chr6 495235 27 + 593897 ATG---AACTATACCCTCTAGTTAGGTGCC -s simHuman_chr6.simHuman.chr6 502370 27 + 601863 ATG---GAACAAACCCAATAGTTGGATACC -s simRat_chr6.simRat.chr6 536084 28 + 647215 ATG--TACCATTACCTGATAGTTAAATACT - -a -s simMouse_chr6.simMouse.chr6 525130 72 + 636262 ACCAGTTCACTGAAAAACCCAATAGTTGTGTGCCAACTGTTCACTAAGCCGTTACAGGTGAGTTAGAGCCCT -s Anc0.Anc0refChr3 135548 72 + 222631 ACCAGTTCACTGAAATACCCAATGATTGGGTGCCACCTGTTCACTAAATTTCTACAGCTGTCTTTGAGCTCT -s Anc1.Anc1refChr6 170547 72 + 197743 ACCAGTTCACTGAAATACCCAATGATTGGGTGCCACCTGTTCACTAAATTTCTACAGCTGTCTTTGAGCTCT -s Anc2.Anc2refChr1 48851 72 + 142988 ACCAGTTCACTAAAATACCCAATGATTGGGTGCCACCTGTGCACTAAATTTCTACAGCTGTCTTTGAGCTCT -s mr.mrrefChr3 76950 72 + 181027 ACCAGTTCACTGAAAAACCCAATAGTTGTGTGCCAACTGTTCACTAAGCTGTTACAGGTGAGTTAGAGCCCT -s simCow_chr6.simCow.chr6 505913 72 + 602619 ACCAGTTCGCTCAAAGAGCCAACCGTTGGGAGCCCAATGTGCACCAAATTTCTACAGCTGTCTTTGAACTCT -s simDog_chr6.simDog.chr6 495262 72 + 593897 ACCAGTTCATTAGCATACCCAATGATTGGGTGCCACCTGTGCACTAAACTTCTACAGCTGTCTTTGAGCCCG -s simHuman_chr6.simHuman.chr6 502397 68 + 601863 ACCAGTTCTCTGAAATACCCAATGATTGGGTGCCACCAATTCACTGAATT----CAGCTGGCTTTGAGCTCT -s simRat_chr6.simRat.chr6 536112 72 + 647215 ACCAGTTCATGGAAAACCCCAATAGTTGTGTGCCAACTGTCCATTAAGCTGTTACAGGTGAGTTATAGCCCT - -a -s simMouse_chr6.simMouse.chr6 525202 28 + 636262 ATCTCCCTTTACTGGACTGTACACTCGG -s Anc0.Anc0refChr3 135621 23 + 222631 ATGTCCCTTTACTG-----TACCCTTAG -s Anc1.Anc1refChr6 170620 23 + 197743 ATGTCCCTTTACTG-----TACCCTTAG -s Anc2.Anc2refChr1 48924 23 + 142988 ATGTCCCTTTACTG-----TACCCTTAG -s mr.mrrefChr3 77022 28 + 181027 ATCTCCCTTTACTGGACTGTACCCTTGG -s simCow_chr6.simCow.chr6 505986 23 + 602619 ATGTCACACTACTG-----TAGCCTTAG -s simDog_chr6.simDog.chr6 495335 23 + 593897 ATGTCCGTTTACTG-----TACCCTTAG -s simHuman_chr6.simHuman.chr6 502466 23 + 601863 AGGTCCCTTCAGTG-----CACCCTTAG -s simRat_chr6.simRat.chr6 536184 28 + 647215 ACCTCCCTTTACTGGACTATACCCATGG - -a -s simMouse_chr6.simMouse.chr6 525230 19 + 636262 ATGGGTAAAGATCAATAGA -s Anc0.Anc0refChr3 135645 19 + 222631 ACATACCAGTATTGGCAGG -s Anc1.Anc1refChr6 170644 19 + 197743 ACATACCAGTATTGGCAGG -s Anc2.Anc2refChr1 48948 19 + 142988 ACATACCAGTGTTGGCATT -s mr.mrrefChr3 77051 19 + 181027 ATAGGCAAGGATCAATAGG -s simCow_chr6.simCow.chr6 506010 18 + 602619 ACAT-CCAGTGTTGGCACT -s simDog_chr6.simDog.chr6 495359 18 + 593897 TCATA-GAGTGTTGGCTTT -s simHuman_chr6.simHuman.chr6 502490 19 + 601863 ACATACCAGCATTGGCAGG -s simRat_chr6.simRat.chr6 536213 19 + 647215 AAAAGCAAGGATCAATAGG - -a -s simMouse_chr6.simMouse.chr6 525249 3 + 636262 AAG -s Anc0.Anc0refChr3 135668 3 + 222631 CAG -s Anc1.Anc1refChr6 170667 3 + 197743 CAG -s Anc2.Anc2refChr1 48971 3 + 142988 CAG -s mr.mrrefChr3 77070 3 + 181027 AAG -s simCow_chr6.simCow.chr6 506032 3 + 602619 CAC -s simDog_chr6.simDog.chr6 495381 3 + 593897 CAG -s simHuman_chr6.simHuman.chr6 502513 3 + 601863 CAG -s simRat_chr6.simRat.chr6 536232 3 + 647215 AAG - -a -s simMouse_chr6.simMouse.chr6 525252 8 + 636262 CTCTGGAT -s Anc0.Anc0refChr3 135673 8 + 222631 CTTTCAAC -s Anc1.Anc1refChr6 170672 8 + 197743 CTTTCAAC -s Anc2.Anc2refChr1 48976 8 + 142988 CTTTCAAC -s mr.mrrefChr3 77073 8 + 181027 CTCTGGAT -s simCow_chr6.simCow.chr6 506037 8 + 602619 CTTTCAAA -s simDog_chr6.simDog.chr6 495386 8 + 593897 ATATCAAC -s simHuman_chr6.simHuman.chr6 502518 8 + 601863 CTTTCAAC -s simRat_chr6.simRat.chr6 536235 7 + 647215 CTCTGGG- - -a -s simMouse_chr6.simMouse.chr6 525260 6 + 636262 CAGTAC -s Anc0.Anc0refChr3 135681 6 + 222631 CAGAGC -s Anc1.Anc1refChr6 170680 6 + 197743 CAGAGC -s Anc2.Anc2refChr1 48988 6 + 142988 CAGAGA -s mr.mrrefChr3 77081 6 + 181027 CAGTAC -s simCow_chr6.simCow.chr6 506049 6 + 602619 CAGAGA -s simDog_chr6.simDog.chr6 495398 6 + 593897 CAGAGA -s simHuman_chr6.simHuman.chr6 502526 6 + 601863 CAAAGC -s simRat_chr6.simRat.chr6 536242 5 + 647215 -AGTAC - -a -s simMouse_chr6.simMouse.chr6 525266 15 + 636262 TATTTATATGTTGAG -s Anc0.Anc0refChr3 135688 15 + 222631 AAGTTATATGTTTAG -s Anc1.Anc1refChr6 170687 15 + 197743 AAGTTATATGTTTAG -s Anc2.Anc2refChr1 48995 15 + 142988 AAGTGTTCTGGCTAG -s mr.mrrefChr3 77087 15 + 181027 TATTTATATGTTGAG -s simCow_chr6.simCow.chr6 506056 15 + 602619 TAATGTTCTGGCTAC -s simDog_chr6.simDog.chr6 495405 15 + 593897 AAGTGTTCTGGCTAG -s simHuman_chr6.simHuman.chr6 502533 12 + 601863 CACTTATATGTT--- -s simRat_chr6.simRat.chr6 536247 15 + 647215 TATTGATATGTTGGG - -a -s simMouse_chr6.simMouse.chr6 525281 45 + 636262 GGTAGAGGACAAGTGCACAGATGACAGGTGCACTCAGGGAGGCCA -s Anc0.Anc0refChr3 135710 29 + 222631 ATCAGAAGGTGAGTGCACTGA----------------GGGAGATC -s Anc1.Anc1refChr6 170709 29 + 197743 ATCAGAAGGTGAGTGCACTGA----------------GGGAGATC -s Anc2.Anc2refChr1 49017 29 + 142988 ATCAGAAGGTGAGTGCCCTGA----------------GGGAGATC -s mr.mrrefChr3 77109 45 + 181027 ATCAGAGGATAAGTGCACAGATGACAGGTGCACTCAGGGAGGCTA -s simCow_chr6.simCow.chr6 506078 29 + 602619 CTCAGCTGCTCAGTGCGCTGA----------------GGGAGATT -s simDog_chr6.simDog.chr6 495427 29 + 593897 ATCAGAAGGTGAATGCCCCGA----------------GGCAGATC -s simHuman_chr6.simHuman.chr6 502552 29 + 601863 ATCAAAAGGTGAGTGCACTGA----------------GGGAGATC -s simRat_chr6.simRat.chr6 536272 45 + 647215 ATCAGAGGATAAGTGCACAGTGGACAGGTGCACTCAGGGAGGCTA - -a -s simMouse_chr6.simMouse.chr6 525326 3 + 636262 TAA -s Anc0.Anc0refChr3 135762 2 + 222631 -TA -s Anc1.Anc1refChr6 170764 3 + 197743 TTA -s Anc2.Anc2refChr1 49069 2 + 142988 -TA -s mr.mrrefChr3 77180 3 + 181027 TAA -s simCow_chr6.simCow.chr6 506130 2 + 602619 -TA -s simDog_chr6.simDog.chr6 495479 2 + 593897 -TA -s simHuman_chr6.simHuman.chr6 502607 3 + 601863 TGA -s simRat_chr6.simRat.chr6 536378 3 + 647215 TAA - -a -s simMouse_chr6.simMouse.chr6 525329 110 + 636262 GTTAATAAAAGAGTAATTAGTGAACAAAGAGTGGCATATGTCTTGAAGAATTGTTTCCTTGAAGAACGATCAGAGAACTACCACATACAGCAGCAAAACTTTTGGAATTG -s Anc0.Anc0refChr3 135764 94 + 222631 TT-------AAAGAACATGGTGAAAAATAAAGAACATGG----TGAAAAATCATTTCCCTGTGGGGTGATCAGA--ACTACCACATACAGCA---AGACTTTTAGAGTTG -s Anc1.Anc1refChr6 170767 96 + 197743 TT-------AAAGAACATGGTGAAAAATAAAGAACATGG----TGAAAAATCATTTCCCTGTGGGGTGATCAGAGCACTACCACATACAGCA---AGACTTTTAGAGTTG -s Anc2.Anc2refChr1 49071 94 + 142988 TT-------AAAAAACATGGTGAAAAATAAAGAACATGG----TGAAGAATCATTTCCCCATGGGGTGATCACA--ACTACCACATATAGCA---AAACTTTTAGAGTTA -s mr.mrrefChr3 77183 110 + 181027 GTGAATAAAAGAGAACATAGTGAACAAAGAGGGGCATATGTCTTGAAAAATTGTTTCCCTGAAGGACGATCAGAGAACTACCACATACAGCAGCAAGACTTTTGGAATTG -s simCow_chr6.simCow.chr6 506138 82 + 602619 TT-------GAGAACCATGGTGAAAAATAGAGCAC-TGG----TGAACAATCATATCCCCAGG-------------ACTACCACATATAGAA---AAACTTTTAGAGGTA -s simDog_chr6.simDog.chr6 495481 92 + 593897 TT-------AAAAAATTTAGTGAAAATTTAAGAAAATAG----TGAAGAATCATTTCCCCATGGGGTGATCACA----TACCACATATAGCA---AAACTTTTAGAATTA -s simHuman_chr6.simHuman.chr6 502610 96 + 601863 TT-------AAAGAACATGGTGAAAAATAAAGAACATGG----TGATAGATCATTTCCCTGTGGGGTGATCAGAGCACCACCACATACAGCA---AGACTTTTTGAGTTG -s simRat_chr6.simRat.chr6 536381 110 + 647215 GTGAATAAAAGAGAACATAGTGAACAGAGAGGGGAATATGTATTGAAAAATTGTTGCCCTGAAGGACAATCAGAGAATTACCACATACAGTAGCAAGACTTTTGGAATTG - -a -s simMouse_chr6.simMouse.chr6 525439 14 + 636262 TTATTCAACCACCC -s Anc0.Anc0refChr3 135865 14 + 222631 TTATGTAACCACCC -s Anc1.Anc1refChr6 170870 14 + 197743 TTATGTAACCACCC -s Anc2.Anc2refChr1 49172 14 + 142988 TTATGTAGTCACCC -s mr.mrrefChr3 77300 14 + 181027 TTATGCAACCACCC -s simCow_chr6.simCow.chr6 506227 14 + 602619 TTATGTAGTCAACC -s simDog_chr6.simDog.chr6 495580 14 + 593897 TTATGTAGTCACCC -s simHuman_chr6.simHuman.chr6 502713 14 + 601863 TTACGTAACCACCC -s simRat_chr6.simRat.chr6 536498 14 + 647215 TTATGCAACCACTC - -a -s simMouse_chr6.simMouse.chr6 525453 6 + 636262 TGCTGC -s Anc0.Anc0refChr3 135879 6 + 222631 TGCCGC -s Anc1.Anc1refChr6 170884 6 + 197743 TGCCGC -s Anc2.Anc2refChr1 49186 6 + 142988 TGCCAT -s mr.mrrefChr3 77314 6 + 181027 TGCTGC -s simCow_chr6.simCow.chr6 506247 6 + 602619 GGCCAT -s simDog_chr6.simDog.chr6 495594 6 + 593897 TATCAT -s simHuman_chr6.simHuman.chr6 502727 6 + 601863 TGCCGC -s simRat_chr6.simRat.chr6 536512 6 + 647215 TGCTGC - -a -s simMouse_chr6.simMouse.chr6 525459 65 + 636262 CTCTTGGGGCCTTCTTTTCTAATCAGAGTAATGATTTGGTGTAAGGGTCTACACCCTTAGATAAA -s Anc0.Anc0refChr3 135885 65 + 222631 CTATAGGGTCCTGCTGATCTAATCAAAGCCATGACTTGGGCCAGGTGTCTACACTCCAAGAAAAA -s Anc1.Anc1refChr6 170890 65 + 197743 CTATAGGGTCCTGCTGATCTAATCAAAGCCATGACTTGGGCCAGGTGTCTACACTCCAAGAAAAA -s Anc2.Anc2refChr1 49192 65 + 142988 CTATGGGGTCCTGCTGATCTAATTGAAGCCATGACTTGCACCAGGTGTCTACACTCCAAGGAAAA -s mr.mrrefChr3 77320 65 + 181027 CTCTAGGGGCCTTCTTTTCTAATCAGAGTAATGACTTGGGGTAAGGGTCTACACCCTTAGAAAAA -s simCow_chr6.simCow.chr6 506253 62 + 602619 CCCTGGGTGCCTGCTGATCTAATTGAAGCCATGACTTGCACCAGG---CTACACTCCTACGGATA -s simDog_chr6.simDog.chr6 495600 44 + 593897 CTATGGGGTCCT---------------------ACTTGCATCAGATGTCTACACTCCAGGGAAAG -s simHuman_chr6.simHuman.chr6 502734 65 + 601863 CTACAGAGACCTATTGCTCTAATCAAAGCCATGACTTGGGCCAGGTTTCTACACTCCAAGAAAAA -s simRat_chr6.simRat.chr6 536518 65 + 647215 CTCTAGGGGCCCTCTTTTCTAATCAGAGTAATGACAAGGGGTAAGGGTCTGCACCATTAGAAAAA - -a -s simMouse_chr6.simMouse.chr6 525524 56 + 636262 TCCAGAGGAGGTTGGTGAAATGTACAAAAAATTACCTCCAAAGAAGGACGGTGAAA -s Anc0.Anc0refChr3 135969 25 + 222631 -------------------------------TTACCTCCAAAGGGGGACAGTCAAA -s Anc1.Anc1refChr6 170974 25 + 197743 -------------------------------TTACCTCCAAAGGGGGACAGTCAAA -s Anc2.Anc2refChr1 49276 25 + 142988 -------------------------------TTACCTCTAAAGGAGGATAGTCAAA -s mr.mrrefChr3 77404 55 + 181027 TCCAGAGGAGGTTGGTGAAATGTAC-AAAAATTACCTCCAAAGAGGGACGGTGAAA -s simCow_chr6.simCow.chr6 506334 25 + 602619 -------------------------------TTACCTCTAAAGGAGGATAGTCAAA -s simDog_chr6.simDog.chr6 495663 25 + 593897 -------------------------------TCACCTCTAGAGGAGGATAGTCAAA -s simHuman_chr6.simHuman.chr6 502818 25 + 601863 -------------------------------CTACCTCCAAAGTGGGACAGTTAAA -s simRat_chr6.simRat.chr6 536606 54 + 647215 TCCAAAGGAGGATGGTGAAATGTAC-GAAAATTACCTCCACAG-GGGAGGGTGAGA - -a -s simMouse_chr6.simMouse.chr6 525580 14 + 636262 ACAGATCAATGTCA -s Anc0.Anc0refChr3 135997 14 + 222631 ACAGATCAATGTGA -s Anc1.Anc1refChr6 171002 14 + 197743 ACAGATCAATGTGA -s Anc2.Anc2refChr1 49304 14 + 142988 AAAGATCAATGTGT -s mr.mrrefChr3 77462 14 + 181027 ACAGATCAATGTCA -s simCow_chr6.simCow.chr6 506362 14 + 602619 AAAGGTCAAAGTGT -s simDog_chr6.simDog.chr6 495691 14 + 593897 AAAGATTGATGTGT -s simHuman_chr6.simHuman.chr6 502846 14 + 601863 ACAGATCAATGTGA -s simRat_chr6.simRat.chr6 536663 14 + 647215 ACAGATCAATGTCA - -a -s simMouse_chr6.simMouse.chr6 525594 5 + 636262 TGCCT -s Anc0.Anc0refChr3 136011 5 + 222631 TACCG -s Anc1.Anc1refChr6 171016 5 + 197743 TACCG -s Anc2.Anc2refChr1 49318 5 + 142988 TGATG -s mr.mrrefChr3 77476 5 + 181027 TACCT -s simCow_chr6.simCow.chr6 506376 3 + 602619 TGA-- -s simDog_chr6.simDog.chr6 495705 5 + 593897 TGATG -s simHuman_chr6.simHuman.chr6 502860 5 + 601863 TACCA -s simRat_chr6.simRat.chr6 536697 5 + 647215 TACCT - -a -s simMouse_chr6.simMouse.chr6 525599 32 + 636262 ATATCCATAGTTGTTTAAAATTTTGACTGTCT -s Anc0.Anc0refChr3 136018 32 + 222631 ATAACCATAGCTGTTTATGGCCTTAACTGTCT -s Anc1.Anc1refChr6 171023 32 + 197743 ATAACCATAGCTGTTTATGGCCTTAACTGTCT -s Anc2.Anc2refChr1 49325 32 + 142988 ATAACCATAACTGTTTATGGCTTGAACTGTCT -s mr.mrrefChr3 77481 32 + 181027 ATATCCATAGTTGTTTAAGATCTTGACTGTCT -s simCow_chr6.simCow.chr6 506381 32 + 602619 ATAACCATAATTGTTTATGGCTTCAACTTTCT -s simDog_chr6.simDog.chr6 495712 32 + 593897 ATAACCATAACTGTTTATAACTTGTACTGTCT -s simHuman_chr6.simHuman.chr6 502867 32 + 601863 ATAACCATAGGTGTTTATGGCCTTAACTGTTG -s simRat_chr6.simRat.chr6 536702 32 + 647215 ACATCCATAGTTGTTTAAGATCTTGACTCTCT - -a -s simMouse_chr6.simMouse.chr6 525631 63 + 636262 TGCCTACCAAAAACGACACACAGATACTTGTCTAGATTAGGGCCCTGCAGAACAATAACTTGT -s Anc0.Anc0refChr3 136050 63 + 222631 TACCTACCAAAAACTACACACAGATACCTGTCTAGATTAAGGCCCTGCTGGCCAATAACTAGT -s Anc1.Anc1refChr6 171055 63 + 197743 TACCTACCAAAAACTACACACAGATACCTGTCTAGATTAAGGCCCTGCTGGCCAATAACTAGT -s Anc2.Anc2refChr1 49357 63 + 142988 CACCTACCAAAAACTACACACAGATACCTGTCTGGATCAAGGCCCTGCTGGCCAGTAACTAGT -s mr.mrrefChr3 77513 63 + 181027 TGCCTACCAAAAACTACACACAGATACTTGTCTAGATTAGGGCCCTGCAGGACAATAACTTGT -s simCow_chr6.simCow.chr6 506426 57 + 602619 CACCTACCAAAAACTACACAAAGATATCTGTTCGGGGCAAAG-CCTGCTGG-----AAATATT -s simDog_chr6.simDog.chr6 495744 63 + 593897 CACCTACCAAAAACTGCACACAGATACCTGTCTGGATCAGGGCCCTGCTGGCCAGTAGCTAGT -s simHuman_chr6.simHuman.chr6 502899 59 + 601863 TACCTACCAAAGACTACACACAGATACCTGTCTAGATTAAGGACCTGCTGGCCAACAAA---- -s simRat_chr6.simRat.chr6 536734 63 + 647215 TGCCTACCAAAAAATACACACAGATACTTGTCTAGATTAGGGCCTTGCAGGACAATAACTTGC - -a -s simMouse_chr6.simMouse.chr6 525694 47 + 636262 GAGTAATGCCATTCTGTGGTCACTGCCTTCCTGTCTCAGAAGAGTTG -s Anc0.Anc0refChr3 136113 42 + 222631 GCTTAATGTCCTTCTGCAAGCAC---CTTCCTTCCTCAGATAAAT-- -s Anc1.Anc1refChr6 171118 42 + 197743 GCTTAATGTCCTTCTGCAAGCAC---CTTCCTTCCTCAGATAAAT-- -s Anc2.Anc2refChr1 49422 42 + 142988 GCTTGATGCTCTTCTGCAAGCAC---CTTCTTTCCTCAGACAAAT-- -s mr.mrrefChr3 77576 45 + 181027 GAGTAATGTCATTCTGTGGTCACTGCCTTCCTATCTCAGTTGAGT-- -s simCow_chr6.simCow.chr6 506485 42 + 602619 GCTTGATCCTATTCTGCAAAAAC---CTTCTTTTCTTAAGCAAAT-- -s simDog_chr6.simDog.chr6 495809 41 + 593897 GCTT-ATGCTCTTCTGCAAGCAC---CTTCTTTCCTCAGACAAAT-- -s simHuman_chr6.simHuman.chr6 502958 25 + 601863 GCTTAATGTC------------------TCC--ACTCAGATAAAT-- -s simRat_chr6.simRat.chr6 536797 45 + 647215 GAGTAATGTCCTTCTGTGTGTACTGCCTTCCTATTTGAGTTGAGT-- - -a -s simMouse_chr6.simMouse.chr6 525741 35 + 636262 GGGCAATAAGGGTAGGAGGTGAATAAAGTGTTTGA -s Anc0.Anc0refChr3 136157 35 + 222631 GGGCAGTAAGGGTAGGAGGTGACCAAAATTTTTGA -s Anc1.Anc1refChr6 171162 35 + 197743 GGGCAGTAAGGGTAGGAGGTGACCAAAATTTTTGA -s Anc2.Anc2refChr1 49466 35 + 142988 GGGCAGTAAGGGTAAGAGGTGACCACAAATTTTGA -s mr.mrrefChr3 77621 35 + 181027 GGGCAATAAGGGTAGGAGGTGAATAAAATTTTTGA -s simCow_chr6.simCow.chr6 506529 34 + 602619 GGGCAGCAAGGGTAAGTGGGAACCAG-AGTTTCGA -s simDog_chr6.simDog.chr6 495852 35 + 593897 GGGCAGTGAGGGTAAGAAGTGACCACAAAATTTGA -s simHuman_chr6.simHuman.chr6 502985 35 + 601863 GGGGAGTAAGGGTAGGAGGTGACCAAAATTGCAGA -s simRat_chr6.simRat.chr6 536842 35 + 647215 GGGCAATAAGAGTAAGAGGTAAATACAACTTTGAG - -a -s simMouse_chr6.simMouse.chr6 525776 23 + 636262 ATAAAACTCTAGATTGACACTTA -s Anc0.Anc0refChr3 136192 23 + 222631 AGAAAACTGTAGGCTGACATTCA -s Anc1.Anc1refChr6 171197 23 + 197743 AGAAAACTGTAGGCTGACATTCA -s Anc2.Anc2refChr1 49502 23 + 142988 AGAAAACTGTGGGCTGACATTCA -s mr.mrrefChr3 77656 23 + 181027 ATAAAACTCTAGGTTGACACTCA -s simCow_chr6.simCow.chr6 506564 23 + 602619 GGGAAACTGTGGGCTGACATTCA -s simDog_chr6.simDog.chr6 495888 23 + 593897 AAAATACTGTGGGTTGACATTCA -s simHuman_chr6.simHuman.chr6 503020 23 + 601863 GGAAAACTGTAGGCTGACCTTCA -s simRat_chr6.simRat.chr6 536877 23 + 647215 ATAAAACACTAGGTCAACACTCA - -a -s simMouse_chr6.simMouse.chr6 525799 1 + 636262 T -s Anc0.Anc0refChr3 136215 1 + 222631 T -s Anc1.Anc1refChr6 171220 1 + 197743 T -s Anc2.Anc2refChr1 49525 1 + 142988 T -s mr.mrrefChr3 77679 1 + 181027 T -s simCow_chr6.simCow.chr6 506588 1 + 602619 T -s simDog_chr6.simDog.chr6 495911 1 + 593897 C -s simHuman_chr6.simHuman.chr6 503043 1 + 601863 T -s simRat_chr6.simRat.chr6 536900 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 525800 3 + 636262 CAG -s Anc0.Anc0refChr3 136217 3 + 222631 CTG -s Anc1.Anc1refChr6 171222 3 + 197743 CTG -s Anc2.Anc2refChr1 49527 3 + 142988 CTG -s mr.mrrefChr3 77680 3 + 181027 CAG -s simCow_chr6.simCow.chr6 506590 3 + 602619 CTG -s simDog_chr6.simDog.chr6 495913 3 + 593897 CTC -s simHuman_chr6.simHuman.chr6 503045 3 + 601863 CTG -s simRat_chr6.simRat.chr6 536901 3 + 647215 CAG - -a -s simMouse_chr6.simMouse.chr6 525803 8 + 636262 GCGTTGCG -s Anc0.Anc0refChr3 136257 7 + 222631 -GATTGCA -s Anc1.Anc1refChr6 171262 7 + 197743 -GATTGCA -s Anc2.Anc2refChr1 49567 7 + 142988 -GATTGTG -s mr.mrrefChr3 77720 8 + 181027 GCATTGCA -s simCow_chr6.simCow.chr6 506630 7 + 602619 -GATTGTG -s simHuman_chr6.simHuman.chr6 503085 7 + 601863 -GATCGCA -s simRat_chr6.simRat.chr6 536941 8 + 647215 GCATTACA - -a -s simMouse_chr6.simMouse.chr6 525811 30 + 636262 TTGGCTAATCAAAGAAATGAGTAACTGCAT -s Anc0.Anc0refChr3 136264 30 + 222631 TTTGTTAGACAAAGAGGAGGCTACTTATGT -s Anc1.Anc1refChr6 171269 30 + 197743 TTTGTTAGACAAAGAGGAGGCTACTTATGT -s Anc2.Anc2refChr1 49582 30 + 142988 TTTGTTAGACAAAAAAGAGGCTACTTATGT -s mr.mrrefChr3 77728 30 + 181027 TTGGCTAATCAAAGAGATGAGTAACTATAT -s simCow_chr6.simCow.chr6 506666 30 + 602619 TTAGTTAAAGGAAGGAGAGGTTACGTATGA -s simDog_chr6.simDog.chr6 495944 30 + 593897 TTTGTTAGACAAAAAAGAGGCTACTTATGT -s simHuman_chr6.simHuman.chr6 503092 18 + 601863 T------------GAGGGGGCTACTTATGT -s simRat_chr6.simRat.chr6 536949 30 + 647215 TTGGCTAATCAAAGAGATGAAAAACTATAT - -a -s simMouse_chr6.simMouse.chr6 525841 59 + 636262 ATGGCATAGATCAACTCTATCTTCCACAACAAATAAGCAGCCTTTTAGTGGTGTGTTGT -s Anc0.Anc0refChr3 136295 56 + 222631 ATGATTTAGCACAACTCTATCTTTCACAAC---AGAGCAGCTATTTAATGGTGTGCTAG -s Anc1.Anc1refChr6 171300 59 + 197743 ATGATTTAGCACAACTCTATCTTTCACAACAAGAGAGCAGCTATTTAATGGTGTGCTAG -s Anc2.Anc2refChr1 49613 56 + 142988 ATGATTTAGCACAACTCTATCTTTAACAAC---AGAGCAGCTATTTAATGGTGTACTAG -s mr.mrrefChr3 77758 59 + 181027 ATGGTATAGATCAACTCTATCTTCCACAACAAATAAGCAGCCTTTTAATGGTGTGCTGT -s simCow_chr6.simCow.chr6 506697 56 + 602619 ATGATTTAGAACAACACCATCTTTAACAAC---AGGGAAGCTATTTCATAGTGTATGAG -s simDog_chr6.simDog.chr6 495975 55 + 593897 ATGA-TCAGCACAACTCTATCTTTAACAAC---ATAGCGGCTATTTAATGGCGTACTAG -s simHuman_chr6.simHuman.chr6 503111 59 + 601863 ATGATTTTGCACAACTCTATCTTTCCCAACAAGGGAGCAGCTATTCAAGGGTCTGCTAG -s simRat_chr6.simRat.chr6 536979 59 + 647215 ATGGTATAAATCAACTCTTTCTTCCACAACAAATAAGCCGCCTTTTAATGGTATGCTGT - -a -s simMouse_chr6.simMouse.chr6 525900 91 + 636262 AATCTTTTGTTCTCATTGCCATCTGTTATCATTTGATCTGCAGCATATTTTGAGAAACACTTAAAGGTCTGTAGAACAGGAAGGACCACAT -s Anc0.Anc0refChr3 136353 90 + 222631 AATC-TTTGTTCAGATGGCTACCTGATATCATTTAACCTGCAGCATATCCCAAGAGATGGTTAAAGGTCTCCGAAACAGGAAGGACCAGAT -s Anc1.Anc1refChr6 171361 91 + 197743 AATCTTTTGTTCAGATGGCTACCTGATATCATTTAACCTGCAGCATATCCCAAGAGATGGTTAAAGGTCTCCGAAACAGGAAGGACCAGAT -s Anc2.Anc2refChr1 49671 90 + 142988 AATC-TGTGTTCAGATGGCTACTTAATATCAGTTAACCTGCAGCATATCCCAAGAGATGGTTAAAGGTTTCCGAAGCAGGACGGACCAGAT -s mr.mrrefChr3 77819 91 + 181027 AATCTTTTGTTCTCATTGCCATCTGTTATCATTTAATCTGCAGCATATCTCAAGAAACAGTTAAAGGTCTGCAGAACAGGAAGGACCACAT -s simCow_chr6.simCow.chr6 506755 90 + 602619 AATT-TATATGCAGATGGTTATTTAATATCAATTAACTGGCGGCATACCTCGAGAGGTGGTTTAAGATGTCTGAGGCAGGAGGGCCCATAT -s simDog_chr6.simDog.chr6 496033 88 + 593897 AACC-TGTGTTGAAATAGCTACTTAATATCAGTTGACCTACA-CATATCCCAAGAGATGGTTAAAGGTTGCC-AAGCAGGACGGACCAGAT -s simHuman_chr6.simHuman.chr6 503172 89 + 601863 AATCTTTT--TCAGTTGGCTAACTGATTTCGTTTAGCCTGCATCATATCCCATGAGATGGTTAAAGGTCTCCTAAACAAGAAGGACCAAAG -s simRat_chr6.simRat.chr6 537040 91 + 647215 AATCTGTTGTTCTCATTGCCATCTGTTGTCATTTAATCTGCAGCCTATCTCAAGAACCTGTTAGAGGTCTGCAGAGCAGGAAGGACAACAT - -a -s simMouse_chr6.simMouse.chr6 525991 21 + 636262 ATGTTTTTTCTTTATTGCCCT -s Anc0.Anc0refChr3 136443 21 + 222631 GTGTTTTTTCTTTATGACCCT -s Anc1.Anc1refChr6 171452 21 + 197743 GTGTTTTTTCTTTATGACCCT -s Anc2.Anc2refChr1 49761 21 + 142988 GTGTTTTTTCTTTATGAGCCT -s mr.mrrefChr3 77910 21 + 181027 GTGTTTTTTCTTTATTACCCT -s simCow_chr6.simCow.chr6 506876 21 + 602619 CTGCTTTTGCTTTATGAGCCT -s simDog_chr6.simDog.chr6 496121 21 + 593897 GTGTTTTTTCTTTGGGAGCCT -s simHuman_chr6.simHuman.chr6 503261 20 + 601863 GTGTTTTTT-GTTATAACCCT -s simRat_chr6.simRat.chr6 537131 21 + 647215 GTGTTTTTTCCTTATCACCCT - -a -s simMouse_chr6.simMouse.chr6 526012 101 + 636262 ACCTTGTTGACATGACCCTCAAATGATTAACGATTTCTGCAATCATAACACCAATTTACCTCACTCCTGGTGAACCAATGGGCCCTTGAGTTTATATGGTT -s Anc0.Anc0refChr3 136464 98 + 222631 ATCTTATTGACATGA---TCAAATGATTAAAGTTCACCACAATCCCAACACCAGTTTCCCTAACTCACAGCTAACAGATGCACCTTTAAGCTTTTATAGTT -s Anc1.Anc1refChr6 171473 98 + 197743 ATCTTATTGACATGA---TCAAATGATTAAAGTTCACCACAATCCCAACACCAGTTTCCCTAACTCACAGCTAACAGATGCACCTTTAAGCTTTTATAGTT -s Anc2.Anc2refChr1 49782 98 + 142988 ATCTTTCTGACATGA---TCAAATGATTAAAGTTCACCACAATCCCAACACCAGTTTCCCCAACCCACAGTTAACAGATGCACCTTTAAGCTCTAGCAGTT -s mr.mrrefChr3 77931 101 + 181027 ACCTTATTGACATGACCCTCAAATGATTAAAGATTTCTGCAATCATAACACCAGTTTACCTCACTCCTAGCTAACCAATGGGCCCTTGAGTTTATATGGTT -s simCow_chr6.simCow.chr6 506897 98 + 602619 GTATTTCTGACCTGC---TCAAATGATTAAAGATCCCCACAATGCCAACACCAATTTCCCCAACCCACAGTTAACATATGCACCTTTAAGCTCTAGCAGTT -s simDog_chr6.simDog.chr6 496142 87 + 593897 ATCTTTCTGACATGA---TCAA---ATTAAAGTGCACCACAATCCCAACACCAGTTTCCCCAATCGAAAATTGACAGATGCACCTTTAAGC--------AT -s simHuman_chr6.simHuman.chr6 503281 98 + 601863 ATCTTATTGACATGA---TCAAATGATTAAAGTTCACCAAAATCCCAATACCAGTATCCCTAACTCACAGCTAACAGGTGCACCTGTAAGCTTGTATAGTT -s simRat_chr6.simRat.chr6 537164 101 + 647215 ACCTTATTGGCATGACCCTCTAATGATCAAAGATTTCTGGAATCATAACACCAGTTTACCTCACTCCGAACTAACCACTGGGTGCTTGAGTTTATATGGTT - -a -s simMouse_chr6.simMouse.chr6 526113 34 + 636262 ATGTGTACATCCCAAAGCTAAGAATTGTCTGGTT -s Anc0.Anc0refChr3 136569 34 + 222631 ATGTTTCCTTCCCAAAGCTATGAACTGTCAGGTG -s Anc1.Anc1refChr6 171578 34 + 197743 ATGTTTCCTTCCCAAAGCTATGAACTGTCAGGTG -s Anc2.Anc2refChr1 49887 34 + 142988 ATGTTTCCTTCCCAAAGCTATGAACTGTCAGGTG -s mr.mrrefChr3 78032 34 + 181027 ATGTGTACATCCCAAAGCTAAGAATTGTCAGGTG -s simCow_chr6.simCow.chr6 507024 34 + 602619 ATGTTTCCTTCCCAAAGCTATGAACTTTCAGATC -s simDog_chr6.simDog.chr6 496236 33 + 593897 A-GTTTTCTTCGCAAAGCTATGAACTGTCAGGTG -s simHuman_chr6.simHuman.chr6 503386 34 + 601863 ATGTTTCCTCCCCAAAGCTATGAACTGTGAGGTG -s simRat_chr6.simRat.chr6 537265 34 + 647215 ATGTGTAGATCCCTAAGCTAAGAATTGTTAGATG - -a -s simMouse_chr6.simMouse.chr6 526147 12 + 636262 ATAACAACCCAA -s Anc0.Anc0refChr3 136603 12 + 222631 TTAAAAAACCAA -s Anc1.Anc1refChr6 171612 12 + 197743 TTAAAAAACCAA -s Anc2.Anc2refChr1 49921 12 + 142988 TTAAAAAACCAA -s mr.mrrefChr3 78066 12 + 181027 TTAAGAACCCAA -s simCow_chr6.simCow.chr6 507058 12 + 602619 CTAAAAAACTAA -s simDog_chr6.simDog.chr6 496271 12 + 593897 TTGAAAAACCAA -s simHuman_chr6.simHuman.chr6 503420 12 + 601863 TTAAAGCACCAA -s simRat_chr6.simRat.chr6 537299 12 + 647215 TTAGGAACCCAA - -a -s simMouse_chr6.simMouse.chr6 526159 18 + 636262 GATATAGTCTCTCAGTAT -s Anc0.Anc0refChr3 136615 18 + 222631 GATATAATTCCTTGGTAG -s Anc1.Anc1refChr6 171624 18 + 197743 GATATAATTCCTTGGTAG -s Anc2.Anc2refChr1 49933 18 + 142988 GATATAATTCCTTGGTAG -s mr.mrrefChr3 78078 18 + 181027 GATATAGTTTCTCAGTAT -s simCow_chr6.simCow.chr6 507070 18 + 602619 CACATCATTTCTTGGTTG -s simDog_chr6.simDog.chr6 496283 18 + 593897 GATTTAATTCCTTGGTAG -s simHuman_chr6.simHuman.chr6 503433 18 + 601863 AATATAATTCCTTGGTAG -s simRat_chr6.simRat.chr6 537311 18 + 647215 GATATAGTTTCTCAGTAT - -a -s simMouse_chr6.simMouse.chr6 526177 18 + 636262 TTGTTTTCAATACGGCTA -s Anc0.Anc0refChr3 136633 18 + 222631 TTGTTTTCAGTAGGTGTA -s Anc1.Anc1refChr6 171642 18 + 197743 TTGTTTTCAGTAGGTGTA -s Anc2.Anc2refChr1 49951 18 + 142988 TTGTTTTCAGTAGGTGTG -s mr.mrrefChr3 78096 18 + 181027 TTGTTTTCAATACGTCTA -s simCow_chr6.simCow.chr6 507088 18 + 602619 TTGTTTTCAGTAGGTGTG -s simDog_chr6.simDog.chr6 496303 18 + 593897 TTGTTTTCTGTAGGAGTG -s simHuman_chr6.simHuman.chr6 503451 18 + 601863 CTGTTTTAAGTAGGTGTA -s simRat_chr6.simRat.chr6 537329 18 + 647215 TTGTTTTCAATACGTCTG - -a -s simMouse_chr6.simMouse.chr6 526195 5 + 636262 AACCC -s Anc0.Anc0refChr3 136659 5 + 222631 ATCTC -s Anc1.Anc1refChr6 171668 5 + 197743 ATCTC -s Anc2.Anc2refChr1 49977 5 + 142988 ATCTC -s mr.mrrefChr3 78122 5 + 181027 AACCC -s simCow_chr6.simCow.chr6 507114 5 + 602619 ACATC -s simDog_chr6.simDog.chr6 496329 5 + 593897 GTCTC -s simHuman_chr6.simHuman.chr6 503481 5 + 601863 ATCTC -s simRat_chr6.simRat.chr6 537355 5 + 647215 AACCC - -a -s simMouse_chr6.simMouse.chr6 526200 25 + 636262 TACCTTCCTCTTATTTATCCACTTG -s Anc0.Anc0refChr3 136664 25 + 222631 TACCTTCCTCTCACTTATCCACTTG -s Anc1.Anc1refChr6 171673 25 + 197743 TACCTTCCTCTCACTTATCCACTTG -s Anc2.Anc2refChr1 49984 25 + 142988 TACCTTCCTCTCACTTATCCACTTG -s mr.mrrefChr3 78127 25 + 181027 TACCTTCCTCTTATTTATCCACTTG -s simCow_chr6.simCow.chr6 507119 25 + 602619 TACCTTCCTCTCATTTATCGACTTG -s simDog_chr6.simDog.chr6 496336 12 + 593897 -------------CTTATCCACTTG -s simHuman_chr6.simHuman.chr6 503486 25 + 601863 TACCTTCCTCTCTCTTATCCACTTG -s simRat_chr6.simRat.chr6 537360 24 + 647215 T-CCTTCCTCTTATTTATCCACCTG - -a -s simMouse_chr6.simMouse.chr6 526225 17 + 636262 TCTTTCTGACATCTGAA -s Anc0.Anc0refChr3 136689 17 + 222631 TCTATCTGACAACTGAA -s Anc1.Anc1refChr6 171698 17 + 197743 TCTATCTGACAACTGAA -s Anc2.Anc2refChr1 50009 17 + 142988 TCTATCTGACAACTGAA -s mr.mrrefChr3 78152 17 + 181027 TCTATCTGACATCTGAA -s simCow_chr6.simCow.chr6 507144 17 + 602619 TCTATCTGACCATTGAA -s simDog_chr6.simDog.chr6 496419 17 + 593897 TCTATCTGACAACTAAA -s simHuman_chr6.simHuman.chr6 503511 17 + 601863 TCTATCTGACAACGGAA -s simRat_chr6.simRat.chr6 537384 17 + 647215 TCTATCCGACCTCTGAA - -a -s simMouse_chr6.simMouse.chr6 526242 1 + 636262 A -s Anc0.Anc0refChr3 136707 1 + 222631 A -s Anc1.Anc1refChr6 171716 1 + 197743 A -s Anc2.Anc2refChr1 50027 1 + 142988 A -s mr.mrrefChr3 78169 1 + 181027 A -s simCow_chr6.simCow.chr6 507162 1 + 602619 G -s simDog_chr6.simDog.chr6 496437 1 + 593897 A -s simHuman_chr6.simHuman.chr6 503529 1 + 601863 A -s simRat_chr6.simRat.chr6 537401 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 526243 23 + 636262 CACCTGAAGCTAGAAGCCAACTG -s Anc0.Anc0refChr3 136715 23 + 222631 CATCCAAAGCTAGAAAGCAATTA -s Anc1.Anc1refChr6 171724 23 + 197743 CATCCAAAGCTAGAAAGCAATTA -s Anc2.Anc2refChr1 50035 23 + 142988 CATGCAAAGCTAGAAAGCAATTA -s mr.mrrefChr3 78177 23 + 181027 CATCTAAAGCTAGAAGGCAATTG -s simCow_chr6.simCow.chr6 507170 22 + 602619 -ATTCGAAAATAGGAAGCGATTA -s simDog_chr6.simDog.chr6 496445 23 + 593897 CCTGCAAAGCTAGAAAGCAATTA -s simHuman_chr6.simHuman.chr6 503537 23 + 601863 CATCCATAGCTAGAAAGCAATTA -s simRat_chr6.simRat.chr6 537409 23 + 647215 CATCTAAAGCTAAAAGGCGATTG - -a -s simMouse_chr6.simMouse.chr6 526266 18 + 636262 GAGGAGAGCAATACTAGA -s Anc0.Anc0refChr3 136739 18 + 222631 GAAGAAAACAATAATAGA -s Anc1.Anc1refChr6 171748 18 + 197743 GAAGAAAACAATAATAGA -s Anc2.Anc2refChr1 50059 18 + 142988 GAAGAAAACAATAATAGA -s mr.mrrefChr3 78200 18 + 181027 GAGGAGAGCAATAATAGA -s simCow_chr6.simCow.chr6 507193 18 + 602619 GGAGAAGACAATAATAGA -s simDog_chr6.simDog.chr6 496469 10 + 593897 GAAGAAAGCA-------- -s simHuman_chr6.simHuman.chr6 503561 18 + 601863 GAAGAAAACAATAATAGA -s simRat_chr6.simRat.chr6 537432 18 + 647215 GAGGAGAGCAATAATAGA - -a -s simMouse_chr6.simMouse.chr6 526284 4 + 636262 CCTC -s Anc0.Anc0refChr3 136757 4 + 222631 TGTG -s Anc1.Anc1refChr6 171766 4 + 197743 TGTG -s Anc2.Anc2refChr1 50077 4 + 142988 TGTG -s mr.mrrefChr3 78218 4 + 181027 CCTC -s simCow_chr6.simCow.chr6 507243 4 + 602619 TGTG -s simDog_chr6.simDog.chr6 496479 3 + 593897 -GTG -s simHuman_chr6.simHuman.chr6 503579 4 + 601863 TGTG -s simRat_chr6.simRat.chr6 537450 4 + 647215 CCTC - -a -s simMouse_chr6.simMouse.chr6 526288 10 + 636262 TATCAATCTA -s Anc0.Anc0refChr3 136763 7 + 222631 TGTA---CTA -s Anc1.Anc1refChr6 171772 10 + 197743 TGTAAATCTA -s Anc2.Anc2refChr1 50083 7 + 142988 TGTA---CTA -s mr.mrrefChr3 78222 10 + 181027 TGTCAATCTA -s simCow_chr6.simCow.chr6 507249 7 + 602619 TGTA---CTA -s simDog_chr6.simDog.chr6 496484 7 + 593897 TGTA---CTA -s simHuman_chr6.simHuman.chr6 503585 10 + 601863 TGTAAATCTA -s simRat_chr6.simRat.chr6 537454 10 + 647215 TGTCAAGCTA - -a -s simMouse_chr6.simMouse.chr6 526298 77 + 636262 GTCATGGAATAATAATTGTGGCTGTGCTAATCCCAGGTTGTCTCCACCCATGAAGTGCACAGAAGAACACCTAAGTA -s Anc0.Anc0refChr3 136770 57 + 222631 -----GGAATGA-----GC----------ATCTCCCATTGTCTTAACCCAGCAAGTGCACAGAAAAACACCTTAGTA -s Anc1.Anc1refChr6 171782 62 + 197743 GTCACGGAATGA-----GC----------ATCTCCCATTGTCTTAACCCAGCAAGTGCACAGAAAAACACCTTAGTA -s Anc2.Anc2refChr1 50090 57 + 142988 -----AGACGCA-----GC----------ATCTCCCATTGTCTTAGCCAGGCAAGTGCATAAAAAAATACCTTAGTA -s mr.mrrefChr3 78232 67 + 181027 GTCATGGAATGATAATTGT----------ATCCCAGATTGTCTCCACCCATGAAGTGCACAGAAGAACACCTAAGTA -s simCow_chr6.simCow.chr6 507256 57 + 602619 -----AGATGCA-----GT----------GTCTCCCATTCTCTTAGCCCATGAAATGCGTAAAAAAATCCTTTAGTA -s simDog_chr6.simDog.chr6 496491 57 + 593897 -----AGACGCA-----CC----------ATCTCCTAATGTCTCAGCCAGGCATGTGCATAAAAAGATACCTTAGTA -s simHuman_chr6.simHuman.chr6 503601 62 + 601863 GTCACGGAATGA-----GC----------CTCGCTCATTGTGTTGAGCCAGACAGTGCACAGAACACCACCTTAGTA -s simRat_chr6.simRat.chr6 537464 66 + 647215 GTCATGGAATGATAATTGT----------ATCCCGGATTG-CTCCACCCATGAAGTGCATAGAAGAACAGCTAAATA - -a -s simMouse_chr6.simMouse.chr6 526375 22 + 636262 TTAGGAGAAAGGATTAAAGCAG -s Anc0.Anc0refChr3 136829 22 + 222631 TTAAAAGAAGAGATTAAGTCAG -s Anc1.Anc1refChr6 171846 22 + 197743 TTAAAAGAAGAGATTAAGTCAG -s Anc2.Anc2refChr1 50149 22 + 142988 TTAAAAGAAAAGATTAAGTCAG -s mr.mrrefChr3 78299 22 + 181027 TTAAGAGAAGAGATTAAAGCAG -s simCow_chr6.simCow.chr6 507315 22 + 602619 TCAAAGGAAAAAATTAATGCAG -s simDog_chr6.simDog.chr6 496548 18 + 593897 CTAAGA----AGATTAAGTCAG -s simHuman_chr6.simHuman.chr6 503665 22 + 601863 TTAAAAGAAGAGATTAAGCCAG -s simRat_chr6.simRat.chr6 537530 22 + 647215 TTAAGTGAAGAGATTAAAGCAG - -a -s simMouse_chr6.simMouse.chr6 526397 23 + 636262 GCTAAAGTCATAGACGGTCTCGG -s Anc0.Anc0refChr3 136858 18 + 222631 GCTAGATTAATAGGGGGT----- -s Anc1.Anc1refChr6 171875 23 + 197743 GCTAGATTAATAGGGGGTGTTGG -s Anc2.Anc2refChr1 50178 18 + 142988 GTTAGATTAATAGGGGGT----- -s mr.mrrefChr3 78321 23 + 181027 GCTAAAGTCATAGGGGGTCTTGG -s simCow_chr6.simCow.chr6 507344 16 + 602619 GTTAGATTAATAGGGG------- -s simDog_chr6.simDog.chr6 496572 9 + 593897 ---------AAAGGGGGT----- -s simHuman_chr6.simHuman.chr6 503695 23 + 601863 GCCAGATTGATAGGGGGTGTTGG -s simRat_chr6.simRat.chr6 537552 23 + 647215 ACTAAGGTAATAGGGGGTCTTGG - -a -s simMouse_chr6.simMouse.chr6 526420 34 + 636262 CGGATCAACAGGGTGTTAATGACAGCTATGTGTA -s Anc0.Anc0refChr3 136876 6 + 222631 ----------------------------TGAGAG -s Anc1.Anc1refChr6 171898 16 + 197743 ------------------GAGAAGGCTCTGAGAG -s Anc2.Anc2refChr1 50196 6 + 142988 ----------------------------TGACAG -s mr.mrrefChr3 78344 34 + 181027 CGGATCAACAGGGTGTTAATGACAGCTATGTGTG -s simDog_chr6.simDog.chr6 496581 6 + 593897 ----------------------------TGACAG -s simHuman_chr6.simHuman.chr6 503718 16 + 601863 ------------------GAGAAGGCTCTGAGAG -s simRat_chr6.simRat.chr6 537576 34 + 647215 TGGATCAACAGGGTGTTATTGACAGCTATGTGTG - -a -s simMouse_chr6.simMouse.chr6 526454 17 + 636262 GTACATGGTGCTAGAAG -s Anc0.Anc0refChr3 136882 12 + 222631 CTAGCAGGTTCT----- -s Anc1.Anc1refChr6 171914 17 + 197743 CTAGCAGGTTCTATAGA -s Anc2.Anc2refChr1 50202 12 + 142988 CTGGCAGTTTTT----- -s mr.mrrefChr3 78378 17 + 181027 GTAGATGGTGCTAGAAA -s simDog_chr6.simDog.chr6 496588 12 + 593897 CTGGCAGTTTTT----- -s simHuman_chr6.simHuman.chr6 503734 17 + 601863 CTAGCAGGTTCTATAGA -s simRat_chr6.simRat.chr6 537610 17 + 647215 GTAGATGGTAGTAGAAA - -a -s simMouse_chr6.simMouse.chr6 526471 145 + 636262 GGCAAGTCGTCCACGTCCATTCATGTGCCAAAGAGACCGTCAGTCTCGTCGAGTTCACTGACATTGTCTACAACATTTGGCTAGCCTGCAGCCTATCATGTGCCAAAGAACCCTCATTGGCCAGCCTGCAGCCTGTCATGTGCCA -s Anc0.Anc0refChr3 136894 15 + 222631 -----------------CATTCA-----------------------------------------------------------------------------------------------------------------AAGAGGCCA -s Anc1.Anc1refChr6 171931 26 + 197743 TGTTAGT------TAGCCATTCA-----------------------------------------------------------------------------------------------------------------AAGAGGCCA -s Anc2.Anc2refChr1 50214 15 + 142988 -----------------CATCCA-----------------------------------------------------------------------------------------------------------------AAGAGGCCA -s mr.mrrefChr3 78395 48 + 181027 TGCTAGT------CATCCATTCATGTGCCA-------------------------------------------------------------------------------------------CAGCCTGCAGCCTGTCATGTGCCA -s simDog_chr6.simDog.chr6 496600 15 + 593897 -----------------CATCCA-----------------------------------------------------------------------------------------------------------------AAGAGGCCA -s simHuman_chr6.simHuman.chr6 503756 26 + 601863 TGTTAGT------TAGCCATTCA-----------------------------------------------------------------------------------------------------------------AAAAGACCA -s simRat_chr6.simRat.chr6 537627 48 + 647215 TGCTAGT------CATTCATTCATGTGCCA-------------------------------------------------------------------------------------------TAGCCTGCAGCCTTTCATGTGCCA - -a -s simMouse_chr6.simMouse.chr6 526616 4 + 636262 AAGA -s Anc0.Anc0refChr3 136909 4 + 222631 AGGA -s Anc1.Anc1refChr6 171957 4 + 197743 AGGA -s Anc2.Anc2refChr1 50229 4 + 142988 AGGA -s mr.mrrefChr3 78443 4 + 181027 AAGA -s simDog_chr6.simDog.chr6 496616 4 + 593897 AGGA -s simHuman_chr6.simHuman.chr6 503782 4 + 601863 AGGA -s simRat_chr6.simRat.chr6 537675 4 + 647215 AAGA - -a -s simMouse_chr6.simMouse.chr6 526620 22 + 636262 ACCCTCACTCTTGGAGACTTCA -s Anc0.Anc0refChr3 136914 22 + 222631 ACCATCAGTGTCGGAGACTTGA -s Anc1.Anc1refChr6 171962 22 + 197743 ACCATCAGTGTCGGAGACTTGA -s Anc2.Anc2refChr1 50234 22 + 142988 ACCAATGTTGGTCGAGACTTGA -s mr.mrrefChr3 78448 22 + 181027 ACCCTCAGTCTCGGAGACTTGA -s simCow_chr6.simCow.chr6 507360 5 + 602619 -----------------GGTGG -s simDog_chr6.simDog.chr6 496621 22 + 593897 ACCAATGTTGGTCGAGACTTGA -s simHuman_chr6.simHuman.chr6 503787 22 + 601863 ACCATCAGTATCGGGAACTTGA -s simRat_chr6.simRat.chr6 537680 22 + 647215 ACCTTCGGTCTCGGAGACACGG - -a -s simMouse_chr6.simMouse.chr6 526642 17 + 636262 ACAACATCTACAGCATA -s Anc0.Anc0refChr3 136936 10 + 222631 A-------TGCTGACAT -s Anc1.Anc1refChr6 171984 10 + 197743 A-------TGCTGACAT -s Anc2.Anc2refChr1 50256 10 + 142988 A-------TGATGACAT -s mr.mrrefChr3 78470 17 + 181027 ACAACATCTACAGCATA -s simCow_chr6.simCow.chr6 507366 9 + 602619 A-------TAGTGTCA- -s simDog_chr6.simDog.chr6 496643 10 + 593897 C-------TGATAACAT -s simHuman_chr6.simHuman.chr6 503809 10 + 601863 A-------TGCTGACGT -s simRat_chr6.simRat.chr6 537702 17 + 647215 ACAACATCGACAACATA - -a -s simMouse_chr6.simMouse.chr6 526659 60 + 636262 TGACTGGCCTGTGGCCTTTCTGCTGCAGAAATCAAGCAGTATAAGCAGTATGCCAACTGA -s Anc0.Anc0refChr3 136946 59 + 222631 TGGCTAGCCTATAGCCCTTCTTATGGGAAAATCAAACAGCATAGGCAGTAGATGGGCTG- -s Anc1.Anc1refChr6 171994 60 + 197743 TGGCTAGCCTATAGCCCTTCTTATGGGAAAATCAAACAGCATAGGCAGTAGATGGGCTGT -s Anc2.Anc2refChr1 50266 59 + 142988 TGGCCACTGTATGGCCCATCTTATGGGAAATTCAAACAGCATAGGCAGTAGATGGGCTG- -s mr.mrrefChr3 78487 60 + 181027 TGACTAGCCTGTAGCCTTTCTGCTGCAGAAATCAAACAGCATAGGCAGTATGTGAACTGA -s simCow_chr6.simCow.chr6 507375 46 + 602619 -GAAAAATGTCTGTGCTATC------------CAAACAGTGTAGGGAGTAGATGGGTGG- -s simDog_chr6.simDog.chr6 496654 59 + 593897 TGGCCACTGTATGGCCCATGTTATGGGAAATTCAAACAGCAGAGCCAGTACACGGGCTG- -s simHuman_chr6.simHuman.chr6 503819 60 + 601863 TGGTTAGCCTATAGCCCTTCTTATGGGAAAATCAAACAGCCTAGGCAGCAGATGGGCTGG -s simRat_chr6.simRat.chr6 537719 60 + 647215 TGACTAGCCTGCAGCCTTTCTGCACCAGAAATCAGACAGCAGAGGCAGTAAGTGAACTGA - -a -s simMouse_chr6.simMouse.chr6 526719 15 + 636262 AAGTCCCCTCAGGTT -s Anc0.Anc0refChr3 137009 13 + 222631 --CTCCCCTCGGGTT -s Anc1.Anc1refChr6 172201 15 + 197743 ACCTCCCCTCGGGTT -s Anc2.Anc2refChr1 50329 13 + 142988 --CTCCTCAGGGGTT -s mr.mrrefChr3 78547 15 + 181027 AAGTCCCCTCAGGTT -s simCow_chr6.simCow.chr6 507428 13 + 602619 --CTCCTCAGGGGTT -s simDog_chr6.simDog.chr6 496717 13 + 593897 --CTCCTCAGGGGTT -s simHuman_chr6.simHuman.chr6 504050 13 + 601863 --CTCGCCTCGGGTT -s simRat_chr6.simRat.chr6 537779 15 + 647215 AAGTCCCCTCATGTT - -a -s simMouse_chr6.simMouse.chr6 526734 8 + 636262 ATATCTCA -s Anc0.Anc0refChr3 137027 8 + 222631 GTATCTTA -s Anc1.Anc1refChr6 172221 8 + 197743 GTATCTTA -s Anc2.Anc2refChr1 50347 8 + 142988 GTATCTTA -s mr.mrrefChr3 78562 8 + 181027 ATATCTCA -s simCow_chr6.simCow.chr6 507446 8 + 602619 GTATGTTA -s simDog_chr6.simDog.chr6 496735 8 + 593897 GTATCTTC -s simHuman_chr6.simHuman.chr6 504068 8 + 601863 GTATCTTA -s simRat_chr6.simRat.chr6 537794 8 + 647215 ATATCTCA - -a -s simMouse_chr6.simMouse.chr6 526742 44 + 636262 CAAGGTAACCACACAAGAGAGACTAGAAGACAAATTGATTCTAC -s Anc0.Anc0refChr3 137035 43 + 222631 CAAGGTAG-CACTTAAAACAGACAAGAGGATAGGTTGATTCCAT -s Anc1.Anc1refChr6 172229 43 + 197743 CAAGGTAG-CACTTAAAACAGACAAGAGGATAGGTTGATTCCAT -s Anc2.Anc2refChr1 50355 43 + 142988 CAAGGGAG-CACTTAAAACAGACAAGAGGATAGGTTGATTCCAT -s mr.mrrefChr3 78570 43 + 181027 CAAGGTAA-CACACAAGAGAGACTAGAAGACAAATTGATTCTAT -s simCow_chr6.simCow.chr6 507454 42 + 602619 CGACAAAA-CACTCAAAATAGACAAGAGGATAGGT-GATTTCAT -s simDog_chr6.simDog.chr6 496746 43 + 593897 CACGGGAG-CGCTTAAAACAGACAGGAGAATAGGTTGATTCTAT -s simHuman_chr6.simHuman.chr6 504076 43 + 601863 CAAGGTAT-CACTTAAAAAAAACAAGAGGGAAGGTTGTTTCCGT -s simRat_chr6.simRat.chr6 537802 42 + 647215 CAACGTAG-CACACAAGAGAGA-TAGAAGACAAACTGATCCTAT - -a -s simMouse_chr6.simMouse.chr6 526786 17 + 636262 ATCACTCATTTTCTCTA -s Anc0.Anc0refChr3 137078 12 + 222631 TTCACTCATTTT----- -s Anc1.Anc1refChr6 172272 17 + 197743 TTCACTCATTTTCTCTT -s Anc2.Anc2refChr1 50398 12 + 142988 TTCACTCATTTT----- -s mr.mrrefChr3 78613 17 + 181027 ATCACTCATTTTCTCTA -s simCow_chr6.simCow.chr6 507496 12 + 602619 TGCACTCATTTT----- -s simDog_chr6.simDog.chr6 496790 12 + 593897 TTCATTCATTTT----- -s simHuman_chr6.simHuman.chr6 504119 17 + 601863 TCCACTCATTTTCTCTT -s simRat_chr6.simRat.chr6 537844 17 + 647215 ATCACTCATCCTCTCTA - -a -s simMouse_chr6.simMouse.chr6 526803 4 + 636262 CTCC -s Anc0.Anc0refChr3 137090 4 + 222631 CTCT -s Anc1.Anc1refChr6 172289 4 + 197743 CTCT -s Anc2.Anc2refChr1 50410 4 + 142988 CTTG -s mr.mrrefChr3 78630 4 + 181027 CTCT -s simCow_chr6.simCow.chr6 507508 1 + 602619 C--- -s simDog_chr6.simDog.chr6 496802 4 + 593897 TTTG -s simHuman_chr6.simHuman.chr6 504144 4 + 601863 CTCT -s simRat_chr6.simRat.chr6 537861 4 + 647215 CTCT - -a -s simMouse_chr6.simMouse.chr6 526807 24 + 636262 GGGTTCCTCTACAGAAAATAGTAA -s Anc0.Anc0refChr3 137100 24 + 222631 GGTTTCCCCTCCAGTAAGTAGTCA -s Anc1.Anc1refChr6 172299 24 + 197743 GGTTTCCCCTCCAGTAAGTAGTCA -s Anc2.Anc2refChr1 50420 24 + 142988 GGTTTCCCCTCCAATAAGTAGTCA -s mr.mrrefChr3 78634 24 + 181027 GGGTTCCTCTACAGAAAATAGTAA -s simCow_chr6.simCow.chr6 507509 21 + 602619 ---TTCCCCTTCAATAAACCCTCA -s simDog_chr6.simDog.chr6 496812 24 + 593897 GGTCTCCCCTCCAATAAGTAGTAA -s simHuman_chr6.simHuman.chr6 504163 24 + 601863 GGTTTTCCCTGCAGTTATTAGTCA -s simRat_chr6.simRat.chr6 537865 24 + 647215 GGGTTCCTCTACAGAAGATAGCAA - -a -s simMouse_chr6.simMouse.chr6 526831 15 + 636262 GCAGCAATACTTAGG -s Anc0.Anc0refChr3 137124 15 + 222631 GCAGGAATAGTTAGG -s Anc1.Anc1refChr6 172323 15 + 197743 GCAGGAATAGTTAGG -s Anc2.Anc2refChr1 50444 15 + 142988 GCAGGAATAGTTAGG -s mr.mrrefChr3 78658 15 + 181027 GCAGCAATACTTAGG -s simCow_chr6.simCow.chr6 507530 15 + 602619 GCAGGAACAGATAGG -s simDog_chr6.simDog.chr6 496836 15 + 593897 GAAGGAATAGTTAGG -s simHuman_chr6.simHuman.chr6 504192 15 + 601863 GCAGGAGTAGTTAGG -s simRat_chr6.simRat.chr6 537889 15 + 647215 GCAGCAATACTTGGG - -a -s simMouse_chr6.simMouse.chr6 526846 13 + 636262 TCCAATGTTTGCT -s Anc0.Anc0refChr3 137139 13 + 222631 TCCAATAATAACA -s Anc1.Anc1refChr6 172338 13 + 197743 TCCAATAATAACA -s Anc2.Anc2refChr1 50460 13 + 142988 CCCAATAATAGCA -s mr.mrrefChr3 78673 13 + 181027 TCCAATGTTTACT -s simCow_chr6.simCow.chr6 507546 13 + 602619 CTCAATAATACCC -s simDog_chr6.simDog.chr6 496852 13 + 593897 CCCAATAATTGCA -s simHuman_chr6.simHuman.chr6 504207 13 + 601863 TCCAATAATAACA -s simRat_chr6.simRat.chr6 537904 13 + 647215 TATGATGTTTACC - -a -s simMouse_chr6.simMouse.chr6 526859 1 + 636262 C -s Anc0.Anc0refChr3 137155 1 + 222631 C -s Anc1.Anc1refChr6 172354 1 + 197743 C -s Anc2.Anc2refChr1 50476 1 + 142988 C -s mr.mrrefChr3 78689 1 + 181027 C -s simCow_chr6.simCow.chr6 507562 1 + 602619 C -s simDog_chr6.simDog.chr6 496870 1 + 593897 C -s simHuman_chr6.simHuman.chr6 504223 1 + 601863 C -s simRat_chr6.simRat.chr6 537920 1 + 647215 C - -a -s simMouse_chr6.simMouse.chr6 526860 13 + 636262 CTGGACAACAGAA -s Anc0.Anc0refChr3 137156 13 + 222631 CTCTCCAACAGAA -s Anc1.Anc1refChr6 172355 13 + 197743 CTCTCCAACAGAA -s Anc2.Anc2refChr1 50477 13 + 142988 CTCTCCAACAGCA -s mr.mrrefChr3 78690 13 + 181027 CTGGACAACAGAA -s simCow_chr6.simCow.chr6 507564 9 + 602619 CACTGCTAC---- -s simDog_chr6.simDog.chr6 496871 13 + 593897 CTCCCCAACAGCA -s simHuman_chr6.simHuman.chr6 504224 13 + 601863 CTCTCCAACAGAA -s simRat_chr6.simRat.chr6 537921 13 + 647215 TTGGCCAACAGAA - -a -s simMouse_chr6.simMouse.chr6 526873 17 + 636262 ACCCAACTATTCACTAT -s Anc0.Anc0refChr3 137169 17 + 222631 ACTTAACTATCAAGTAT -s Anc1.Anc1refChr6 172368 17 + 197743 ACTTAACTATCAAGTAT -s Anc2.Anc2refChr1 50490 17 + 142988 ACTTAACTACCAAGTAT -s mr.mrrefChr3 78703 17 + 181027 ACCCAACTATCCACTAT -s simCow_chr6.simCow.chr6 507573 16 + 602619 -CTGAAGCACCTAGTAT -s simDog_chr6.simDog.chr6 496884 17 + 593897 ACTTAACTACCAAATAT -s simHuman_chr6.simHuman.chr6 504242 17 + 601863 ACAAAATTATCAAGTGG -s simRat_chr6.simRat.chr6 537934 17 + 647215 ACCCCACTATCCACTAT - -a -s simMouse_chr6.simMouse.chr6 526890 4 + 636262 CCCT -s Anc0.Anc0refChr3 137186 3 + 222631 C-TT -s Anc1.Anc1refChr6 172385 3 + 197743 C-TT -s Anc2.Anc2refChr1 50507 3 + 142988 C-CT -s mr.mrrefChr3 78720 4 + 181027 CCTT -s simCow_chr6.simCow.chr6 507590 3 + 602619 C-CT -s simDog_chr6.simDog.chr6 496901 3 + 593897 C-CT -s simHuman_chr6.simHuman.chr6 504259 3 + 601863 C-TT -s simRat_chr6.simRat.chr6 537951 4 + 647215 TCTT - -a -s simMouse_chr6.simMouse.chr6 526894 11 + 636262 TTATCTGGGTT -s Anc0.Anc0refChr3 137189 11 + 222631 CCATCTGGGCT -s Anc1.Anc1refChr6 172388 11 + 197743 CCATCTGGGCT -s Anc2.Anc2refChr1 50510 11 + 142988 CCATCTGGACT -s mr.mrrefChr3 78724 11 + 181027 TTATCTGGGTT -s simCow_chr6.simCow.chr6 507593 11 + 602619 CCTTCTGGACT -s simDog_chr6.simDog.chr6 496905 11 + 593897 CTATCTAGACT -s simHuman_chr6.simHuman.chr6 504262 11 + 601863 CCATCTGGGCG -s simRat_chr6.simRat.chr6 537955 11 + 647215 TTATCTGGGTT - -a -s simMouse_chr6.simMouse.chr6 526905 3 + 636262 GCA -s Anc0.Anc0refChr3 137209 3 + 222631 GCA -s Anc1.Anc1refChr6 172408 3 + 197743 GCA -s Anc2.Anc2refChr1 50535 3 + 142988 GCA -s mr.mrrefChr3 78735 3 + 181027 GCA -s simCow_chr6.simCow.chr6 507623 3 + 602619 GAG -s simDog_chr6.simDog.chr6 496930 3 + 593897 GCA -s simHuman_chr6.simHuman.chr6 504282 3 + 601863 GCA -s simRat_chr6.simRat.chr6 537966 3 + 647215 GTA - -a -s simMouse_chr6.simMouse.chr6 526908 12 + 636262 ACTCAGTTTCCC -s Anc0.Anc0refChr3 137218 12 + 222631 ACTCAGATTTTC -s Anc1.Anc1refChr6 172417 12 + 197743 ACTCAGATTTTC -s Anc2.Anc2refChr1 50544 12 + 142988 ACTCAGATTTTC -s mr.mrrefChr3 78738 12 + 181027 ACTCAGTTTCCC -s simCow_chr6.simCow.chr6 507632 12 + 602619 AGTCCAATGTTT -s simDog_chr6.simDog.chr6 496941 12 + 593897 ACTCAGATTTTC -s simHuman_chr6.simHuman.chr6 504291 12 + 601863 ACTCAGATTTTC -s simRat_chr6.simRat.chr6 537969 12 + 647215 ACTCAGTTTCCC - -a -s simMouse_chr6.simMouse.chr6 526920 8 + 636262 TAATATTC -s Anc0.Anc0refChr3 137230 6 + 222631 AAATA--C -s Anc1.Anc1refChr6 172429 6 + 197743 AAATA--C -s Anc2.Anc2refChr1 50556 6 + 142988 AAATA--C -s mr.mrrefChr3 78750 6 + 181027 TAATA--C -s simCow_chr6.simCow.chr6 507648 6 + 602619 GAGTA--C -s simDog_chr6.simDog.chr6 496953 6 + 593897 AAATA--C -s simHuman_chr6.simHuman.chr6 504303 5 + 601863 ACATA--- -s simRat_chr6.simRat.chr6 537981 4 + 647215 TAA----C - -a -s simMouse_chr6.simMouse.chr6 526928 26 + 636262 ACTTTTGTCTAGTTTGGAATAAGTCA -s Anc0.Anc0refChr3 137236 26 + 222631 ACTTTTGTTAGGTTTGGAATAAGTAA -s Anc1.Anc1refChr6 172435 26 + 197743 ACTTTTGTTAGGTTTGGAATAAGTAA -s Anc2.Anc2refChr1 50564 26 + 142988 AGATTTGTTAGGTATGGAATAAGTAA -s mr.mrrefChr3 78756 26 + 181027 ACTTTTGTTTAGTTTGGAATAAGTCA -s simCow_chr6.simCow.chr6 507656 26 + 602619 AGATGTGTAAGGTATGGAATAAGTAA -s simDog_chr6.simDog.chr6 496961 26 + 593897 AGATTTGTTAAGTATGGTATAGGTAA -s simHuman_chr6.simHuman.chr6 504308 26 + 601863 ACTTTTGTTAGGTTTGGAACAAGTTA -s simRat_chr6.simRat.chr6 537985 26 + 647215 ACTTCTGTTCAGTTTAGAATCAGTCA - -a -s simMouse_chr6.simMouse.chr6 526954 38 + 636262 CATTGATCAACTGGGACCCTAATGTCATGACTTAAGTC -s Anc0.Anc0refChr3 137262 15 + 222631 C-----------------TTACTGTCATGAC------C -s Anc1.Anc1refChr6 172461 21 + 197743 C-----------------TTACTGTCATGACCTCATCC -s Anc2.Anc2refChr1 50590 15 + 142988 C-----------------TCACTTTCATGAC------C -s mr.mrrefChr3 78782 38 + 181027 CATTGATCAACTGGGACCCTAATGTCATGACTTCAGTC -s simCow_chr6.simCow.chr6 507695 15 + 602619 C-----------------TCACTTTCATGAC------C -s simHuman_chr6.simHuman.chr6 504334 21 + 601863 C-----------------TTATTGTCTTGACCTCATCC -s simRat_chr6.simRat.chr6 538011 38 + 647215 CATTGCTCAACTGCCACCCTAATGTCACGGCTTCAGTC - -a -s simMouse_chr6.simMouse.chr6 526992 8 + 636262 CTGCCACC -s Anc0.Anc0refChr3 137289 8 + 222631 CTGCCACA -s Anc1.Anc1refChr6 172494 8 + 197743 CTGCCACA -s Anc2.Anc2refChr1 50617 8 + 142988 CTGTCACA -s mr.mrrefChr3 78820 8 + 181027 CTGCCACC -s simCow_chr6.simCow.chr6 507722 8 + 602619 CTGTCATA -s simDog_chr6.simDog.chr6 496998 8 + 593897 CTGTCACA -s simHuman_chr6.simHuman.chr6 504367 8 + 601863 CTGCCACA -s simRat_chr6.simRat.chr6 538049 8 + 647215 CTTCCACT - -a -s simMouse_chr6.simMouse.chr6 527000 28 + 636262 ACGATTCTGACTAGGAAGATGTATTGTG -s Anc0.Anc0refChr3 137297 15 + 222631 ACAA---TATTCTGAAAG---------- -s Anc1.Anc1refChr6 172502 27 + 197743 ACAATCCTATTCTGAAAGATGT-TTTTG -s Anc2.Anc2refChr1 50625 15 + 142988 ACAG---TATCCTGAAAG---------- -s mr.mrrefChr3 78828 28 + 181027 ACAATCCTGTTTTGAAAGATGTATTGTG -s simCow_chr6.simCow.chr6 507731 15 + 602619 ACAC---TATCCTGTAAT---------- -s simDog_chr6.simDog.chr6 497006 15 + 593897 ACAG---TATCCCAAAAG---------- -s simHuman_chr6.simHuman.chr6 504375 27 + 601863 ACAACCCTATTCTGAAAGATGT-TTTTG -s simRat_chr6.simRat.chr6 538057 25 + 647215 ACAATCCCGTTTTGAAAGATGTACT--- - -a -s simMouse_chr6.simMouse.chr6 527064 1 + 636262 T -s Anc0.Anc0refChr3 137340 1 + 222631 C -s Anc1.Anc1refChr6 172565 1 + 197743 C -s Anc2.Anc2refChr1 50668 1 + 142988 C -s mr.mrrefChr3 78892 1 + 181027 C -s simCow_chr6.simCow.chr6 507773 1 + 602619 C -s simDog_chr6.simDog.chr6 497049 1 + 593897 C -s simHuman_chr6.simHuman.chr6 504438 1 + 601863 C -s simRat_chr6.simRat.chr6 538114 1 + 647215 C - -a -s simMouse_chr6.simMouse.chr6 527206 29 + 636262 CATGAAAACTTTTTAACTAATCATATGCA -s Anc0.Anc0refChr3 137478 8 + 222631 CATGAA---------------------CA -s Anc1.Anc1refChr6 172714 28 + 197743 CATGAAAGCT-CTCGACTGATTGTACCCA -s Anc2.Anc2refChr1 50806 8 + 142988 CATGAA---------------------CA -s mr.mrrefChr3 79034 29 + 181027 CATGAAAACTTCTTAACTAATCATACGCA -s simCow_chr6.simCow.chr6 507930 8 + 602619 CATGAC---------------------CA -s simDog_chr6.simDog.chr6 497191 8 + 593897 CATGGA---------------------CA -s simHuman_chr6.simHuman.chr6 504583 28 + 601863 CATGAAAGCT-CTCGACTGATTGTACCCA -s simRat_chr6.simRat.chr6 538241 26 + 647215 CATGAAAACTTCTTCACTAATCATAC--- - -a -s simMouse_chr6.simMouse.chr6 527235 32 + 636262 GAGATGACACTGTAACCTCAACAAGTTGCAGA -s Anc0.Anc0refChr3 137489 32 + 222631 GAGATGACATCGTATCCTTAAACAGTTGCAGA -s Anc1.Anc1refChr6 172745 32 + 197743 GAGATGACATCGTATCCTTAAACAGTTGCAGA -s Anc2.Anc2refChr1 50817 32 + 142988 GAGATGACATCATATCCTTAAACAGTTGAAGA -s mr.mrrefChr3 79063 32 + 181027 GAGATGACACTGTAACCTCAACAAGTTGCAGA -s simCow_chr6.simCow.chr6 507941 32 + 602619 GAGATGACATCATATCCTTAAACCATTGAAGG -s simDog_chr6.simDog.chr6 497203 32 + 593897 AAAATGATACCATATGCTTAAACAGTTGAAGA -s simHuman_chr6.simHuman.chr6 504614 32 + 601863 GAGATGACATCGTTTCTGTAAACAGCTGCAGA - -a -s simMouse_chr6.simMouse.chr6 527267 1 + 636262 C -s Anc0.Anc0refChr3 137521 1 + 222631 T -s Anc1.Anc1refChr6 172777 1 + 197743 T -s Anc2.Anc2refChr1 50849 1 + 142988 T -s mr.mrrefChr3 79095 1 + 181027 C -s simCow_chr6.simCow.chr6 507979 1 + 602619 T -s simDog_chr6.simDog.chr6 497235 1 + 593897 T -s simHuman_chr6.simHuman.chr6 504646 1 + 601863 T - -a -s simMouse_chr6.simMouse.chr6 527268 23 + 636262 TCGCTGAGGCGTCAGTAGAAATT -s Anc0.Anc0refChr3 137525 23 + 222631 CTGCTGAGATGTCAGTAGAGATT -s Anc1.Anc1refChr6 172781 23 + 197743 CTGCTGAGATGTCAGTAGAGATT -s Anc2.Anc2refChr1 50853 23 + 142988 CTGCTGAGATGTCCGTAGAGATT -s mr.mrrefChr3 79096 23 + 181027 TCGCTGAGGCGTCAGTAGAAATT -s simCow_chr6.simCow.chr6 507983 22 + 602619 ATGCTGAGATG-CTGTAGGGATT -s simDog_chr6.simDog.chr6 497239 23 + 593897 CTGCTGAGATGTCCATAGAGACT -s simHuman_chr6.simHuman.chr6 504650 23 + 601863 CTACTGAGATGTCAGTAGAGGTT -s simRat_chr6.simRat.chr6 538267 3 + 647215 --------------------ATT - -a -s simMouse_chr6.simMouse.chr6 527291 14 + 636262 TAGAACAACTCACC -s Anc0.Anc0refChr3 137573 13 + 222631 TACAACAATTC-CA -s Anc1.Anc1refChr6 172829 13 + 197743 TACAACAATTC-CA -s Anc2.Anc2refChr1 50901 13 + 142988 TACAACAATTC-CA -s mr.mrrefChr3 79119 14 + 181027 TACAACAATTCACC -s simCow_chr6.simCow.chr6 508032 13 + 602619 TACAACAACTC-CA -s simDog_chr6.simDog.chr6 497286 13 + 593897 TATAACAATTG-CA -s simHuman_chr6.simHuman.chr6 504698 13 + 601863 TACATCATTTC-CA -s simRat_chr6.simRat.chr6 538270 14 + 647215 TACAACAATTCACC - -a -s simMouse_chr6.simMouse.chr6 527305 5 + 636262 CTGTG -s Anc0.Anc0refChr3 137586 5 + 222631 TTGTG -s Anc1.Anc1refChr6 172842 5 + 197743 TTGTG -s Anc2.Anc2refChr1 50915 5 + 142988 TTGTG -s mr.mrrefChr3 79133 5 + 181027 CTGTG -s simCow_chr6.simCow.chr6 508046 1 + 602619 T---- -s simDog_chr6.simDog.chr6 497300 5 + 593897 TTGTG -s simHuman_chr6.simHuman.chr6 504711 5 + 601863 TTGTG -s simRat_chr6.simRat.chr6 538284 5 + 647215 CTGGG - -a -s simMouse_chr6.simMouse.chr6 527310 19 + 636262 TAACTAACTCAAGTCTATT -s Anc0.Anc0refChr3 137591 19 + 222631 TGACTAACTCAAGTCCTTT -s Anc1.Anc1refChr6 172847 19 + 197743 TGACTAACTCAAGTCCTTT -s Anc2.Anc2refChr1 50920 19 + 142988 TGACTAGCTCAAATCCTAT -s mr.mrrefChr3 79138 19 + 181027 TAACTAACTCAAGTCTATT -s simDog_chr6.simDog.chr6 497305 19 + 593897 TGACTAGCTCAAATCCTAT -s simHuman_chr6.simHuman.chr6 504716 19 + 601863 AGACTAACTCAAGTCCTTT -s simRat_chr6.simRat.chr6 538292 19 + 647215 TAACTAACTCAGGTCTATT - -a -s simMouse_chr6.simMouse.chr6 527329 22 + 636262 GCTCCCCTGTGAAATTAATTGT -s Anc0.Anc0refChr3 137610 22 + 222631 CCTCTCCTGTGGAATTAATTAC -s Anc1.Anc1refChr6 172866 22 + 197743 CCTCTCCTGTGGAATTAATTAC -s Anc2.Anc2refChr1 50939 22 + 142988 CCTCTCCTGTGGAATTAATCAC -s mr.mrrefChr3 79157 22 + 181027 GCTCCCCTGTGGAATTAATTGT -s simCow_chr6.simCow.chr6 508047 13 + 602619 ---------TCGAATTAATCAT -s simDog_chr6.simDog.chr6 497345 22 + 593897 CCTCTCCTGTGGAACTAATCAC -s simHuman_chr6.simHuman.chr6 504735 22 + 601863 TCTCATCTGTGGAATAAATTAC -s simRat_chr6.simRat.chr6 538311 22 + 647215 GCTCCCCTGTGGAGTTAATTGT - -a -s simMouse_chr6.simMouse.chr6 527351 5 + 636262 TATGA -s Anc0.Anc0refChr3 137632 5 + 222631 ATTGA -s Anc1.Anc1refChr6 172888 5 + 197743 ATTGA -s Anc2.Anc2refChr1 50961 5 + 142988 ATTGA -s mr.mrrefChr3 79179 5 + 181027 TATGA -s simCow_chr6.simCow.chr6 508060 5 + 602619 ATTGA -s simDog_chr6.simDog.chr6 497383 5 + 593897 ATTGT -s simHuman_chr6.simHuman.chr6 504757 5 + 601863 CCTGA -s simRat_chr6.simRat.chr6 538333 5 + 647215 GATGA - -a -s simMouse_chr6.simMouse.chr6 527356 29 + 636262 AACCATTTGAGCATCTATTTATCTGATGT -s Anc0.Anc0refChr3 137652 29 + 222631 AACCCTTTGAGCATCTATTTTTCTTATGT -s Anc1.Anc1refChr6 172908 29 + 197743 AACCCTTTGAGCATCTATTTTTCTTATGT -s Anc2.Anc2refChr1 50981 29 + 142988 AACCCTTTAAGCATCTGTTTTTCTTATGT -s mr.mrrefChr3 79184 29 + 181027 AACCATTTGAGCATCTATTTATCTGATGT -s simCow_chr6.simCow.chr6 508080 29 + 602619 AACCTCTGAGTCTTCTGTTTTTCTGATGT -s simDog_chr6.simDog.chr6 497438 29 + 593897 GACCCTATAAGCATGTGTATTTCTTATGT -s simHuman_chr6.simHuman.chr6 504777 29 + 601863 AACCCTTTGAACATCTATTTTTTTTGTGT -s simRat_chr6.simRat.chr6 538338 29 + 647215 AACCATTTGAGCATCTATTTATCTGATGT - -a -s simMouse_chr6.simMouse.chr6 527385 32 + 636262 CTGGGACGTAAGCAACATGGACATGGATATGT -s mr.mrrefChr3 79267 32 + 181027 CTGGGACGTAAGCAACATGGACATGGATATGT -s simRat_chr6.simRat.chr6 538423 32 + 647215 TTGGGATGTAAGCAACCTGGACATGGGTATGT - -a -s simMouse_chr6.simMouse.chr6 527417 97 + 636262 AATTTTGTTCTGAATAaaagggctcaccaccacttgtagttgcagtccaaatcctagaactctttactaacccctgagtgcttgcaaccaaaaagtc -s mr.mrrefChr3 79299 97 + 181027 AATTTTGTTCTGAAtaaaagggctcaccaccacttgtagttgcagtccaaatcctagaactctttactaacccctgagtgcttgcaaccaaaaagtc -s simRat_chr6.simRat.chr6 538457 97 + 647215 GATTTTGTTCTGAAtaaatgagttcaacaccacttgtagtcgcagtccaaatcctaaaactatttactaacccccgaatgcttgcgaccgaaaagtc - -a -s simMouse_chr6.simMouse.chr6 527514 183 + 636262 acacaactccttgaaatgttttttgacatgttatttacatatggtccctaagctgggaTGAATAGCGAATGGCCCACACTAATACTGCCCCTTTTCTCTATGGTTAATCTATTCTGTCCACATTAAGTCTTTCAATCTTTCAGCTGGGACTCCTAAAGTCCGGTTACTGGTCTGGTGGTCATG -s mr.mrrefChr3 79396 174 + 181027 acacaactccttgaaatgttttttgacatgttatttacatatggtccctaagctgggatgAATAGCGAATGGCCCACACTAATACTGCCCCTTTTCTCTATGGTTAATCTATTCTGTCCACATTAAG--------TCTTTCAGCTGGGACTCCTAAAGT-CGGTTACTGGTCTGGTGGTCAtg -s simRat_chr6.simRat.chr6 538556 174 + 647215 ttaaaaccccttggaatgttttttgacatgtcattcacatatggtccataagcagggaccAATAGCAAATTGCCCACTCGAATACATCCTCCTTTCTCTATGGTTAATTTATTCTGTCCACATTAAG--------ACTTTTAGCTGGCCCTCCTTGAGT-TGGCTACTGGTTTGGGGGTCAtg - -a -s simMouse_chr6.simMouse.chr6 527697 18 + 636262 AATTACACCGTTGTCAAT -s mr.mrrefChr3 79570 18 + 181027 aattacaccgttgtcaat -s simRat_chr6.simRat.chr6 538731 18 + 647215 aattaaacccttgtcaac - -a -s simMouse_chr6.simMouse.chr6 527715 19 + 636262 AGGGATCCAGCAAAGGAAG -s mr.mrrefChr3 79588 19 + 181027 agggatccagcaaaggaag -s simRat_chr6.simRat.chr6 538767 19 + 647215 tgggatccagcaaaggacg - -a -s simMouse_chr6.simMouse.chr6 527734 46 + 636262 AGTCACATGGAATCCCCAGAAAACTTCTGTTCAGTGATATGTAATT -s Anc0.Anc0refChr3 137723 39 + 222631 -----CATGGGGGAACCAGAATATGCCTTGCC--TGGCATGTCATA -s Anc1.Anc1refChr6 172979 39 + 197743 -----CATGGGGGAACCAGAATATGCCTTGCC--TGGCATGTCATA -s Anc2.Anc2refChr1 51052 39 + 142988 -----CATGGGGGAACCAGAATATGCCTTGCC--TGGCATGTCACA -s mr.mrrefChr3 79607 46 + 181027 agtcacatggaatccccagAAAACTTCTGTTCAGTGATATGTAATT -s simCow_chr6.simCow.chr6 508151 38 + 602619 -----CATG-GGACACCAGATTATGCCTTGCC--TGGCATGTCACA -s simDog_chr6.simDog.chr6 497509 33 + 593897 -----CATGGTGGAACCAGAATATGCCTTGCC--TGGCAT------ -s simHuman_chr6.simHuman.chr6 504848 39 + 601863 -----CATGAGGGAACCAGAATATGCCGACCC--TGGCATATCATG -s simRat_chr6.simRat.chr6 538787 46 + 647215 agtcacatggaatccctagGCACCTTCTGTGCAGTGATATGTAATT - -a -s simMouse_chr6.simMouse.chr6 527780 27 + 636262 ACTAGGGGCTTATACAGCTGTTGGCAT -s Anc0.Anc0refChr3 137762 25 + 222631 ACTAAGGACT--TGCAGCTGTTGACAA -s Anc1.Anc1refChr6 173018 27 + 197743 ACTAAGGACTTGTGCAGCTGTTGACAA -s Anc2.Anc2refChr1 51091 25 + 142988 ACTTAGGACT--TGCAGCTGTTGACGA -s mr.mrrefChr3 79653 27 + 181027 ACTAGGGGCTTATGCAGCTGTTGACAT -s simCow_chr6.simCow.chr6 508191 25 + 602619 ACTTAGGACT--TGCAGCTGTTGACGA -s simHuman_chr6.simHuman.chr6 504887 27 + 601863 GGTAAGGACTTGTGCAGCTGTTGACAA -s simRat_chr6.simRat.chr6 538833 27 + 647215 ACTAGGGGCCTATGCGGCTGCTGACAT - -a -s simMouse_chr6.simMouse.chr6 527807 4 + 636262 GTGC -s Anc0.Anc0refChr3 137787 4 + 222631 GCCC -s Anc1.Anc1refChr6 173045 4 + 197743 GCCC -s Anc2.Anc2refChr1 51116 4 + 142988 GCCC -s mr.mrrefChr3 79680 4 + 181027 GTGC -s simCow_chr6.simCow.chr6 508216 4 + 602619 GCCC -s simHuman_chr6.simHuman.chr6 504915 4 + 601863 GCCC -s simRat_chr6.simRat.chr6 538860 4 + 647215 GTGC - -a -s simMouse_chr6.simMouse.chr6 527811 19 + 636262 ATATCTACCTGTGCATATC -s Anc0.Anc0refChr3 137791 8 + 222631 ATAT-----------TAGC -s Anc1.Anc1refChr6 173049 8 + 197743 ATAT-----------TAGC -s Anc2.Anc2refChr1 51121 8 + 142988 ACAT-----------CAGG -s mr.mrrefChr3 79684 19 + 181027 ATATCTACCTGTGCATATC -s simCow_chr6.simCow.chr6 508221 8 + 602619 ACAT-----------CAGG -s simHuman_chr6.simHuman.chr6 504919 8 + 601863 ATAT-----------TAGC -s simRat_chr6.simRat.chr6 538864 19 + 647215 ATATCTACCTGTGCATATC - -a -s simMouse_chr6.simMouse.chr6 527830 16 + 636262 AAACAACACTTTCTCA -s Anc0.Anc0refChr3 137913 16 + 222631 AAAAAACACTGCCACA -s Anc1.Anc1refChr6 173175 16 + 197743 AAAAAACACTGCCACA -s Anc2.Anc2refChr1 51243 16 + 142988 AAAAAATACTGCCACA -s mr.mrrefChr3 79805 16 + 181027 AAACAACACTTTCTCA -s simCow_chr6.simCow.chr6 508400 16 + 602619 AAAAAATACTGCCACA -s simHuman_chr6.simHuman.chr6 505049 16 + 601863 AAAAAACACTGACCCA -s simRat_chr6.simRat.chr6 538985 16 + 647215 AAACAACACTTTCTCA - -a -s simMouse_chr6.simMouse.chr6 527846 29 + 636262 TGTTGGGAGGAGAAAATCTTCTACAACTA -s Anc0.Anc0refChr3 137931 26 + 222631 TGT---GGGTACTGAACCTTCTACAAATG -s Anc1.Anc1refChr6 173193 29 + 197743 TGTGGGGGGTACTGAACCTTCTACAAATG -s Anc2.Anc2refChr1 51261 26 + 142988 TGT---GGGTACAGAACCTTCTACAAATG -s mr.mrrefChr3 79821 29 + 181027 TGTTGGGAGGAGTAAATCTTCTACAACTA -s simCow_chr6.simCow.chr6 508418 16 + 602619 TGT---GG----------TTCTACAAATG -s simDog_chr6.simDog.chr6 497542 21 + 593897 --------GTACAGAACCTTCCACAAGTA -s simHuman_chr6.simHuman.chr6 505067 29 + 601863 TGTGGGGGGTACTGAACCTCTTACATATG -s simRat_chr6.simRat.chr6 539001 29 + 647215 TGTTGGGAGAAGTAGGTCTTCTAGAACTA - -a -s simMouse_chr6.simMouse.chr6 527875 38 + 636262 CAAATATATTAATGCCTCCTTTGCGTTTTGAATGGTCT -s Anc0.Anc0refChr3 137960 31 + 222631 ------TTGTAATGCCTACCTTGCA-TTTGGATGGTTT -s Anc1.Anc1refChr6 173225 38 + 197743 CAAATATTGTAATGCCTACCTTGCATTTTGGATGGTTT -s Anc2.Anc2refChr1 51290 31 + 142988 ------TTGTAATGCCTAACTTGCA-TTTGGATGGTTT -s mr.mrrefChr3 79850 38 + 181027 CAAATATATTAATGCCTACTTTGCATTTTGAATGGTCT -s simCow_chr6.simCow.chr6 508437 31 + 602619 ------TTGTAATGTTTATCTAGCA-TTTGGATGGTTT -s simDog_chr6.simDog.chr6 497566 31 + 593897 ------TTGTTATGCCTAACTTGCG-CTTGGATGGTTT -s simHuman_chr6.simHuman.chr6 505103 38 + 601863 CAAATATCGCAATGCCTACCTTGCATTTTGGGTGGTTT -s simRat_chr6.simRat.chr6 539030 34 + 647215 CAAATA----AATGTCTACTTTGCATTTTGAATAGTAT - -a -s simMouse_chr6.simMouse.chr6 527913 13 + 636262 GAGGTCACTATTT -s Anc0.Anc0refChr3 137993 13 + 222631 GAACTCACTACTT -s Anc1.Anc1refChr6 173265 13 + 197743 GAACTCACTACTT -s Anc2.Anc2refChr1 51323 13 + 142988 GAACTCACTACTT -s mr.mrrefChr3 79888 13 + 181027 GAGGTCACTATTT -s simCow_chr6.simCow.chr6 508470 13 + 602619 GAACTAATGACTG -s simDog_chr6.simDog.chr6 497599 13 + 593897 GAACTCACTACTT -s simHuman_chr6.simHuman.chr6 505143 13 + 601863 TGCCTCACCACTT -s simRat_chr6.simRat.chr6 539064 3 + 647215 GAG---------- - -a -s simMouse_chr6.simMouse.chr6 527926 3 + 636262 CAG -s Anc0.Anc0refChr3 138009 3 + 222631 CAG -s Anc1.Anc1refChr6 173281 3 + 197743 CAG -s Anc2.Anc2refChr1 51339 3 + 142988 CAG -s mr.mrrefChr3 79901 3 + 181027 CAG -s simCow_chr6.simCow.chr6 508486 3 + 602619 TGG -s simDog_chr6.simDog.chr6 497615 3 + 593897 CAG -s simHuman_chr6.simHuman.chr6 505159 3 + 601863 CAA - -a -s simMouse_chr6.simMouse.chr6 527929 25 + 636262 TGGTGAGAGCTAGGGATAACTAACT -s Anc0.Anc0refChr3 138012 23 + 222631 TTGT--GAATTAGGGATAGACAACT -s Anc1.Anc1refChr6 173284 23 + 197743 TTGT--GAATTAGGGATAGACAACT -s Anc2.Anc2refChr1 51342 23 + 142988 TTGT--GAATTAGGGATAGACGACT -s mr.mrrefChr3 79904 23 + 181027 TGGT--GAGCTAGGGATAACTAACT -s simCow_chr6.simCow.chr6 508491 23 + 602619 TTGT--GCATTAGGGATAGACGACT -s simDog_chr6.simDog.chr6 497618 11 + 593897 TTGT--GAACTTG------------ -s simHuman_chr6.simHuman.chr6 505162 23 + 601863 TTGT--AAATTAGGGATAGACAGCT - -a -s simMouse_chr6.simMouse.chr6 527954 34 + 636262 AAGCTCCCTTTTCACTTGGCTTCAGCAGACGTTT -s Anc0.Anc0refChr3 138038 34 + 222631 AAATTCCCTTGTCTCATGGCTTTGGCAGAGGTTC -s Anc1.Anc1refChr6 173310 34 + 197743 AAATTCCCTTGTCTCATGGCTTTGGCAGAGGTTC -s Anc2.Anc2refChr1 51368 34 + 142988 AAATTCCCTTGTCACATGGCTTTGGCAGAGGCTC -s mr.mrrefChr3 79927 34 + 181027 AAGCTCCCTTGTCTCTTGGCTTCAGCAGACGTTT -s simCow_chr6.simCow.chr6 508517 34 + 602619 AAATTCCCTTGTCACATGGCTTTATCGAAGGCTC -s simDog_chr6.simDog.chr6 497629 22 + 593897 ------------CACATGGCTTTGGCAGAGGCTC -s simHuman_chr6.simHuman.chr6 505188 34 + 601863 AAATTTCCTTGTCTCATGATTTTGGCAGAGGTCC -s simRat_chr6.simRat.chr6 539067 23 + 647215 -----CTCTTGTCTCTTG------GCAAACGTTA - -a -s simMouse_chr6.simMouse.chr6 527988 5 + 636262 ATGTC -s Anc0.Anc0refChr3 138077 5 + 222631 TTGTC -s Anc1.Anc1refChr6 173349 5 + 197743 TTGTC -s Anc2.Anc2refChr1 51407 5 + 142988 TTGTC -s mr.mrrefChr3 79961 5 + 181027 ATGTC -s simCow_chr6.simCow.chr6 508556 5 + 602619 TTGTC -s simDog_chr6.simDog.chr6 497656 5 + 593897 TTGTC -s simHuman_chr6.simHuman.chr6 505227 5 + 601863 TTATC -s simRat_chr6.simRat.chr6 539090 5 + 647215 ATGTC - -a -s simMouse_chr6.simMouse.chr6 527993 26 + 636262 ACTTATCTATCATTACATCTGATATC -s Anc0.Anc0refChr3 138082 26 + 222631 ATTTGTCTTTCATTCCATCTTATGTT -s Anc1.Anc1refChr6 173354 26 + 197743 ATTTGTCTTTCATTCCATCTTATGTT -s Anc2.Anc2refChr1 51412 26 + 142988 ATTTGTCTTTCATTCCATCTTATGTT -s mr.mrrefChr3 79966 26 + 181027 ATTTATCTATCATTACATCTGATATC -s simCow_chr6.simCow.chr6 508561 26 + 602619 ATGTGTCTTTCATTCCACCCTATGTT -s simDog_chr6.simDog.chr6 497670 26 + 593897 CTTTGTCTTTCATTCCATTTTATGTT -s simHuman_chr6.simHuman.chr6 505232 26 + 601863 ATTTGTCTTTTGTTCCCTCTTATGTT -s simRat_chr6.simRat.chr6 539095 26 + 647215 ATTTATTGATCATTACATCTGATATC - -a -s simMouse_chr6.simMouse.chr6 528019 1 + 636262 C -s Anc0.Anc0refChr3 138126 1 + 222631 A -s Anc1.Anc1refChr6 173398 1 + 197743 A -s Anc2.Anc2refChr1 51456 1 + 142988 A -s mr.mrrefChr3 80010 1 + 181027 C -s simCow_chr6.simCow.chr6 508606 1 + 602619 A -s simDog_chr6.simDog.chr6 497714 1 + 593897 G -s simHuman_chr6.simHuman.chr6 505276 1 + 601863 A -s simRat_chr6.simRat.chr6 539139 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 528020 102 + 636262 TGCACTGAGCTAACCAACAGGTGATCCAGATCAAGGGAGAAGCCACATATGCAAAGCACAATCTTGTATTGGCTTGTCAGGCTGGAGATTGTATTCACCCTA -s Anc0.Anc0refChr3 138129 102 + 222631 GAGGCTAAGCTAACCAGGGTGTGGTCCAGGTCAAGGGAGAATCCAGACATGCAGCGTGCAATTCTTTATGCTTTTATCATGGTATGGCTTGTATTCACCCTA -s Anc1.Anc1refChr6 173401 102 + 197743 GAGGCTAAGCTAACCAGGGTGTGGTCCAGGTCAAGGGAGAATCCAGACATGCAGCGTGCAATTCTTTATGCTTTTATCATGGTATGGCTTGTATTCACCCTA -s Anc2.Anc2refChr1 51459 102 + 142988 GAGGTTAAGCTAACAAGGGGGTGGACCAAGTCAAGGAAGAATCCAGACATGTAGCGTGCAATTCTTTATGCTTTTATCATGGTATGGCTTGTATTGACACTA -s mr.mrrefChr3 80011 102 + 181027 TGCACTGAGCTAACCAACATGTGGTCCAGATCAAGGGAGAAGCCACATATGCAAAGCACAATTCTGTATTGGTTTGTCAGGCTAGAGATTGTATTCACCCTA -s simCow_chr6.simCow.chr6 508609 101 + 602619 GAGGTTAAGCGAACAAGTGGGTAGACCAAG-CAAGGAAGGACCCACACAAGTTGGGCACCATTCTTTATGCTTTGATCATGGTATGGTTTGTACTAAGACTG -s simDog_chr6.simDog.chr6 497717 102 + 593897 GGGATTAAGCTAACAAGGGGTTGGACCAAGTCAGGAAAGAATCTAGACATGTAACATGCAATTCTTTATGTTTTTATCACGTTATAGCTTGTATTGACACTA -s simHuman_chr6.simHuman.chr6 505279 99 + 601863 GAGGCGAAACTAACCATGGTGTGGTCCAGGTCAAGGGAAAATCCATACATGCAGTGTCCAATTCCTTATGCTTTTATCATGGTATGGCTTGTATTCTCC--- -s simRat_chr6.simRat.chr6 539140 101 + 647215 CGCACTTAGCTAACAAACATATGGTCCAGCTCAAGGAAGAAGCCGCATATGCAACACACAATTCTCTATC-GTTGGCCAAGCTAGAGATTGTACTTCTCCAA - -a -s simMouse_chr6.simMouse.chr6 528122 63 + 636262 CTTGATTAACATCCTTAATCTATTGGTGTGTAACACTACTTAGAATTTACACAGCGCCTTGTG -s Anc0.Anc0refChr3 138231 30 + 222631 CTCGATGAACACCCCTAATCC---------------------------------CTTTTTGTG -s Anc1.Anc1refChr6 173503 30 + 197743 CTCGATGAACACCCCTAATCC---------------------------------CTTTTTGTG -s Anc2.Anc2refChr1 51563 30 + 142988 CTCGGTGAATGCCCCTAATCC---------------------------------CTTGGTGTG -s mr.mrrefChr3 80113 33 + 181027 CTTGATTAACATCCTTAATCCAT------------------------------GCGTTTTGTG -s simCow_chr6.simCow.chr6 508712 30 + 602619 CCCTGTGAATGCCCCTAATCC---------------------------------CCTGGTGTA -s simDog_chr6.simDog.chr6 497821 30 + 593897 CTCGGTGCATGCCCCCAATCC---------------------------------CTTGGTGTG -s simHuman_chr6.simHuman.chr6 505378 26 + 601863 ----ATGAACACCCCTACTAC---------------------------------CTTTTGAGA -s simRat_chr6.simRat.chr6 539241 33 + 647215 CTTGATCAACATCCTTAATCCAT------------------------------GAGTTGTGTG - -a -s simMouse_chr6.simMouse.chr6 528185 11 + 636262 GATATTGACTA -s Anc0.Anc0refChr3 138261 11 + 222631 GATATTGACTA -s Anc1.Anc1refChr6 173533 11 + 197743 GATATTGACTA -s Anc2.Anc2refChr1 51594 11 + 142988 GATATTGACTA -s mr.mrrefChr3 80146 11 + 181027 GATATTGACTA -s simCow_chr6.simCow.chr6 508743 11 + 602619 GATGTCGGTTA -s simDog_chr6.simDog.chr6 497852 11 + 593897 GATATTGACTA -s simHuman_chr6.simHuman.chr6 505404 9 + 601863 GATACTGGT-- -s simRat_chr6.simRat.chr6 539274 11 + 647215 GATATTGAGTA - -a -s simMouse_chr6.simMouse.chr6 528196 27 + 636262 CCACAAAGGAGTGACTGTGAGAACTAT -s Anc0.Anc0refChr3 138272 27 + 222631 CCCCAAAAGAGTGACTGTGAGAACAAT -s Anc1.Anc1refChr6 173544 27 + 197743 CCCCAAAAGAGTGACTGTGAGAACAAT -s Anc2.Anc2refChr1 51605 27 + 142988 CCCTTAGAGAGATACTGTGAGAACAAT -s mr.mrrefChr3 80157 27 + 181027 CCACAAAGGAGTGACTGTGAGAACTAT -s simCow_chr6.simCow.chr6 508754 25 + 602619 CCCTTCG-GAAATGC-GTGAGAACAAT -s simDog_chr6.simDog.chr6 497863 27 + 593897 CCCTTAAAGAGATACTGTGAGACCAAT -s simHuman_chr6.simHuman.chr6 505413 12 + 601863 ---CAGAAGAGTGA------------G -s simRat_chr6.simRat.chr6 539286 27 + 647215 CCACAAAGGAGTGACTGTAAGAACTAT - -a -s simMouse_chr6.simMouse.chr6 528223 12 + 636262 ATTAAACTATTC -s Anc0.Anc0refChr3 138299 12 + 222631 GTTATAGTATTC -s Anc1.Anc1refChr6 173571 12 + 197743 GTTATAGTATTC -s Anc2.Anc2refChr1 51635 12 + 142988 GTTATAGTATTT -s mr.mrrefChr3 80184 12 + 181027 GTTAAACTATTC -s simCow_chr6.simCow.chr6 508782 12 + 602619 GTTAGAACATTT -s simDog_chr6.simDog.chr6 497893 12 + 593897 GCTATGGTTCAT -s simHuman_chr6.simHuman.chr6 505425 12 + 601863 GTTATAGTATTC -s simRat_chr6.simRat.chr6 539313 12 + 647215 GACAAACTACTC - -a -s simMouse_chr6.simMouse.chr6 528235 64 + 636262 ACCCTTGTTCATGTGTTCTAACTGGTCGGTGCCTACCCTGGATTTTAATTCTGACCAGAGATAC -s Anc0.Anc0refChr3 138311 55 + 222631 TTGG-TGTTCATGTGTTGT--CTGGTTTGTGTCGACCC---A-TCTGGTT--GCCCAGATAGGT -s Anc1.Anc1refChr6 173583 59 + 197743 TTGGCTGTTCATGTGTTGTAACTGGTTTGTGTCGACCC---ATTCTGGTT--GCCCAGATAGGT -s Anc2.Anc2refChr1 51647 55 + 142988 TTGG-TGTTTACCTCTGGT--CTGGTTTATGCCGAGCT---A-TCTGGTT--ACCCAGATAGGT -s mr.mrrefChr3 80196 64 + 181027 ATCCTTGTTCATGTGTTCTAACTGGTTGGTGTCTACCCTGGATTTTAATTCTGACCAGATATAC -s simCow_chr6.simCow.chr6 508840 53 + 602619 GTGG-TGTCTACATCTGTT--CCTGATTCTGCCGTACA---A-GTT--CT--ACCCAGGTATAT -s simDog_chr6.simDog.chr6 497905 48 + 593897 TTGG-TGTTTACCTCTGGT--CTGGTTTATGCCTAGAT---A-TCTGGT---------ACAGGT -s simHuman_chr6.simHuman.chr6 505437 59 + 601863 TTGGCTGTTCATGAGTTTTAACTGGTTAGTGTCGACCC---ACTCTGCTT--GCCCAGATAGGT -s simRat_chr6.simRat.chr6 539325 63 + 647215 ATACTTGTTCATGTGTTCTAA-TGGTTGATGTCTACCCTGGATTTTAATTCTGACCAACTATAC - -a -s simMouse_chr6.simMouse.chr6 528299 29 + 636262 CCTACAAGAAGCCAGATAGGTAGCATTTA -s Anc0.Anc0refChr3 138366 29 + 222631 GGTACAGGAAGGCAGATAGGAAGCGTTTA -s Anc1.Anc1refChr6 173642 29 + 197743 GGTACAGGAAGGCAGATAGGAAGCGTTTA -s Anc2.Anc2refChr1 51702 29 + 142988 GGTACAGGAAGGCGGATAGGAAGCGTTTA -s mr.mrrefChr3 80260 29 + 181027 CCTACAAGAAGCCAGATAGGTAGCATTTA -s simCow_chr6.simCow.chr6 508893 29 + 602619 AGTACAGGAAGGCGGATGGGAAGCGTTTA -s simDog_chr6.simDog.chr6 497960 29 + 593897 GGTACGGGAAGATGAATAGGAAGCATTTA -s simHuman_chr6.simHuman.chr6 505496 29 + 601863 GTTACATGAAGGCAGATAGGAAGCGTTTA -s simRat_chr6.simRat.chr6 539388 29 + 647215 CCTACAAGAAGCCAGATAGGGGGCACTTA - -a -s simMouse_chr6.simMouse.chr6 528328 54 + 636262 TGATTTAGGTTACAATCATGAATATAAAATACAGTAGCTTCTGGTACCAGCTAT -s Anc0.Anc0refChr3 138404 53 + 222631 TGATCTAGGTTACAATCATGAGCATAAA-TACAACAGCCATTTGTACTTGCTAT -s Anc1.Anc1refChr6 173680 53 + 197743 TGATCTAGGTTACAATCATGAGCATAAA-TACAACAGCCATTTGTACTTGCTAT -s Anc2.Anc2refChr1 51740 53 + 142988 TGGTCTAGGTTACAATCATGAGCATAAA-TACAACAGCCATTTGTACTTGCTAT -s mr.mrrefChr3 80289 54 + 181027 TGATTTAGGTTACAATCATGAATATAAAATACAGTAGCTTTTGGTACCAGCTAT -s simCow_chr6.simCow.chr6 508931 53 + 602619 TGCACTAGGTTACAATCGTTAGCATAAA-TATAACAGCCATGTGCACTTGCTAT -s simDog_chr6.simDog.chr6 497998 50 + 593897 TGGTCCAGGCTGTAACCATGAGCATAAA-TACAACAGCCATTTGTA---GCTAT -s simHuman_chr6.simHuman.chr6 505541 53 + 601863 TAATCTAGGTTACAATCATGAGCATAAA-TAGAACAGCCATTTGTACTTGCTAT -s simRat_chr6.simRat.chr6 539417 54 + 647215 TGATTTAGGTCACAATCATGAATTTAAAATTCAGTAGCTTTTAGTACCAGCTAT - -a -s simMouse_chr6.simMouse.chr6 528382 10 + 636262 TAGTAACCGT -s Anc0.Anc0refChr3 138458 10 + 222631 CAGTAGCAGC -s Anc1.Anc1refChr6 173734 10 + 197743 CAGTAGCAGC -s Anc2.Anc2refChr1 51794 10 + 142988 GAGTAGCAGC -s mr.mrrefChr3 80343 10 + 181027 CAGTAACCGT -s simCow_chr6.simCow.chr6 508985 10 + 602619 GAGTTACAAC -s simDog_chr6.simDog.chr6 498049 10 + 593897 GAGCAGGTGC -s simHuman_chr6.simHuman.chr6 505595 10 + 601863 CAGTACCAGC -s simRat_chr6.simRat.chr6 539471 10 + 647215 CAGTAACTAT - -a -s simMouse_chr6.simMouse.chr6 528392 58 + 636262 GAAAACAGATGCTGTACATTCACTAAGTCCGGGCTGGAAGCACATGAATGATAAAGAA -s Anc0.Anc0refChr3 138468 20 + 222631 AAAAA--------------------------------------GTGAATTGAAAAAGA -s Anc1.Anc1refChr6 173744 20 + 197743 AAAAA--------------------------------------GTGAATTGAAAAAGA -s Anc2.Anc2refChr1 51804 20 + 142988 AAAAA--------------------------------------GGAAATTGAAAAAGA -s mr.mrrefChr3 80353 58 + 181027 GAAAACAGATGCTGTACATTCACTAAGTCCGGGCTGGAAGCACATGAATGATAAAGAA -s simCow_chr6.simCow.chr6 508995 20 + 602619 AAAAA--------------------------------------GGAAATTGAAAAAGA -s simDog_chr6.simDog.chr6 498060 20 + 593897 GGAAA--------------------------------------GGAGATTGATAAGGA -s simHuman_chr6.simHuman.chr6 505605 20 + 601863 AAAAA--------------------------------------GTGAATTGAAAAAGA -s simRat_chr6.simRat.chr6 539481 58 + 647215 GAAAATAGATGACATCCATTCACTATGTCCTGGCTGGAATCACCTGGATGATAAAGAA - -a -s simMouse_chr6.simMouse.chr6 528450 17 + 636262 CTTTCTGAATTACTCCC -s Anc0.Anc0refChr3 138488 17 + 222631 CTTCATGGCTTACTCCC -s Anc1.Anc1refChr6 173764 17 + 197743 CTTCATGGCTTACTCCC -s Anc2.Anc2refChr1 51825 17 + 142988 CTTCATGGCTTACTCCC -s mr.mrrefChr3 80411 17 + 181027 CTTTCTGAATTACTCCC -s simCow_chr6.simCow.chr6 509016 17 + 602619 GCTCATCGCTTACTCCC -s simDog_chr6.simDog.chr6 498081 17 + 593897 CTTCATGGGTCACATCC -s simHuman_chr6.simHuman.chr6 505625 17 + 601863 TTTCGTGGCTTACTCCC -s simRat_chr6.simRat.chr6 539539 17 + 647215 CTTTCCTAATTACTCCC - -a -s simMouse_chr6.simMouse.chr6 528467 38 + 636262 ATATAAAATTTCATCAGTAGACTATGGCACTGTGGCTT -s Anc0.Anc0refChr3 138507 36 + 222631 --ATAAAAGGTCACCAGCAGACTATGGCAAAGCTGTAT -s Anc1.Anc1refChr6 173783 38 + 197743 ATATAAAAGGTCACCAGCAGACTATGGCAAAGCTGTAT -s Anc2.Anc2refChr1 51844 36 + 142988 --ATAGAAGGTCACCAGGAAACTATGGCAATGCTGTAT -s mr.mrrefChr3 80430 38 + 181027 ATATAAAATTTCATCAGCAGACTATGGCAAAGTGGCTT -s simCow_chr6.simCow.chr6 509035 35 + 602619 --ATA-AAGGTCACTAGTAAACTATGGGAATGCTGCAG -s simDog_chr6.simDog.chr6 498100 36 + 593897 --ATAGAGGCCCACCAGGAAGCAATAGCGATGCTGTCT -s simHuman_chr6.simHuman.chr6 505644 38 + 601863 ATATAATAGGTCACCAGCAGACTATGGCAAAGCTGTAT -s simRat_chr6.simRat.chr6 539558 38 + 647215 ATATAAGTTTTCGTCAGCAGACTATGGCAAAGTGGCTT - -a -s simMouse_chr6.simMouse.chr6 528505 39 + 636262 AATTCTTTTTAAGGTATAGGCCTCCACCATGGCTGATGA -s Anc0.Anc0refChr3 138544 39 + 222631 AGTTCTTGTTTAGGCATTGCTCCCTACCTGAACTGGTGA -s Anc1.Anc1refChr6 173822 39 + 197743 AGTTCTTGTTTAGGCATTGCTCCCTACCTGAACTGGTGA -s Anc2.Anc2refChr1 51881 39 + 142988 AGTTCTTGTTTAAGCATTGCTCCCAACCTGAACTGGTGA -s mr.mrrefChr3 80469 39 + 181027 AATTCTTTTTAAGGCATAGGCCTCTACCATGGCTGATGA -s simCow_chr6.simCow.chr6 509071 38 + 602619 AGTTCTTTTTTATGCATTGCTCCC-ACCTGATCTGGTGA -s simDog_chr6.simDog.chr6 498137 39 + 593897 AGTTCCTGTTTAAGCATGGCTCCCAATCTGAACTGGTGA -s simHuman_chr6.simHuman.chr6 505683 28 + 601863 GGTTCTTCTTTAGGCATTGCTCCCTACC----------- -s simRat_chr6.simRat.chr6 539597 39 + 647215 AATTCTCTTTAAGGCATAGGCCTCTACCATGGCTGATGA - -a -s simMouse_chr6.simMouse.chr6 528544 23 + 636262 GCTGTGTTCTTATCTCCTTGTTC -s Anc0.Anc0refChr3 138583 23 + 222631 GTTGTGTTTTGATCTCCTTGTTT -s Anc1.Anc1refChr6 173861 23 + 197743 GTTGTGTTTTGATCTCCTTGTTT -s Anc2.Anc2refChr1 51920 23 + 142988 GCTGTGTTTTGATCTCCTTGTCT -s mr.mrrefChr3 80508 23 + 181027 GTTGTGTTCTGATCTCCTTGTTC -s simCow_chr6.simCow.chr6 509111 22 + 602619 GTTGTGTTTTTATCTTCTTG-CT -s simDog_chr6.simDog.chr6 498176 23 + 593897 GCTGTGCTTTGATCTCCTTGTCC -s simHuman_chr6.simHuman.chr6 505711 22 + 601863 -TTGTGTTTTGATCTCCTTGTTT -s simRat_chr6.simRat.chr6 539636 23 + 647215 GTTGTGTTCTGATCTCCTTGTTC - -a -s simMouse_chr6.simMouse.chr6 528567 28 + 636262 TATTGACCCTGTGATGTTGACAGTAAAC -s Anc0.Anc0refChr3 138613 26 + 222631 CTTGGAACCTGTGCCTTGGAAAGTA--C -s Anc1.Anc1refChr6 173891 26 + 197743 CTTGGAACCTGTGCCTTGGAAAGTA--C -s Anc2.Anc2refChr1 51950 26 + 142988 CTTGTAACCTGTGCCCTGGAAGGCA--C -s mr.mrrefChr3 80531 28 + 181027 TATTGACCCTGTGATTTTGACAGTAAAC -s simCow_chr6.simCow.chr6 509140 1 + 602619 T--------------------------- -s simDog_chr6.simDog.chr6 498206 26 + 593897 CTTGTAACCTGTGCCCTGGAAGGCA--C -s simHuman_chr6.simHuman.chr6 505740 26 + 601863 CTTGGAACCTCTGCCTGGGAGAGTG--C -s simRat_chr6.simRat.chr6 539659 28 + 647215 TATTGACCCTGTGGTTTTGACAGTAAAC - -a -s simMouse_chr6.simMouse.chr6 528595 27 + 636262 CAATGCATCACATGGGCTAATGACGAA -s Anc0.Anc0refChr3 138639 25 + 222631 TAGAGCATCACATATG--AATGATGAA -s Anc1.Anc1refChr6 173917 27 + 197743 TAGAGCATCACATATGCTAATGATGAA -s Anc2.Anc2refChr1 51976 25 + 142988 CAGATCACCACAGATG--GATGATGGA -s mr.mrrefChr3 80559 27 + 181027 TAGAGCATCACATGGGCTAATGACGAA -s simCow_chr6.simCow.chr6 509141 13 + 602619 ------------GATG--GCTGATGGA -s simDog_chr6.simDog.chr6 498233 25 + 593897 CAGATCACCACAGATG--GATGATGGA -s simHuman_chr6.simHuman.chr6 505766 27 + 601863 TAGAGCATCACATATGCTAATGATTAA -s simRat_chr6.simRat.chr6 539687 27 + 647215 TGGAGCATCACATTGACTAACAAAGAA - -a -s simMouse_chr6.simMouse.chr6 528622 30 + 636262 TCATAGCATAGGAATACTGCATCCTTCAGG -s Anc0.Anc0refChr3 138664 30 + 222631 TCACCGTGTAGTGATACCCTAAGCTTCAGG -s Anc1.Anc1refChr6 173944 30 + 197743 TCACCGTGTAGTGATACCCTAAGCTTCAGG -s Anc2.Anc2refChr1 52002 30 + 142988 TCACCATGTAGTGATACCCTAAGCTTCAGG -s mr.mrrefChr3 80586 30 + 181027 TCACAGCATAGGAATACTGCAACCTTCAGG -s simCow_chr6.simCow.chr6 509157 30 + 602619 TTACCACATAATGATACCCTAATCATCAGG -s simDog_chr6.simDog.chr6 498259 30 + 593897 TCACTATGTAGTGATACCTTAAGCTCCACG -s simHuman_chr6.simHuman.chr6 505793 30 + 601863 TCACCGTGTAGTGATTCCCTAAGCTTCAGG -s simRat_chr6.simRat.chr6 539714 30 + 647215 TCACGTCATGTGAATACTGCAACGTTCAGG - -a -s simMouse_chr6.simMouse.chr6 528652 20 + 636262 GTTAATATTAGTCTAGTCAA -s Anc0.Anc0refChr3 138694 20 + 222631 GGTAATGCCAGTGTACTCAA -s Anc1.Anc1refChr6 173974 20 + 197743 GGTAATGCCAGTGTACTCAA -s Anc2.Anc2refChr1 52032 20 + 142988 GGTAATGCCAGCGTGCTCAA -s mr.mrrefChr3 80616 20 + 181027 GTTAATATTAGTCTAGTCAA -s simCow_chr6.simCow.chr6 509187 20 + 602619 GGTAATGCTAGAGTGCTCAA -s simDog_chr6.simDog.chr6 498294 12 + 593897 GGCAGTTCCAGC-------- -s simHuman_chr6.simHuman.chr6 505823 20 + 601863 GGTAATGCCAGTGTACTCAA -s simRat_chr6.simRat.chr6 539744 20 + 647215 GTTAATATTAGCCTAGTCAA - -a -s simMouse_chr6.simMouse.chr6 528672 4 + 636262 TCGG -s Anc0.Anc0refChr3 138714 1 + 222631 C--- -s Anc1.Anc1refChr6 173994 1 + 197743 C--- -s Anc2.Anc2refChr1 52052 1 + 142988 C--- -s mr.mrrefChr3 80636 4 + 181027 TCGG -s simCow_chr6.simCow.chr6 509270 1 + 602619 C--- -s simDog_chr6.simDog.chr6 498306 1 + 593897 T--- -s simHuman_chr6.simHuman.chr6 505843 1 + 601863 C--- -s simRat_chr6.simRat.chr6 539764 4 + 647215 TCAG - -a -s simMouse_chr6.simMouse.chr6 528676 1 + 636262 T -s Anc1.Anc1refChr6 173995 1 + 197743 T -s mr.mrrefChr3 80640 1 + 181027 T -s mr.mrrefChr3 80986 1 + 181027 T -s simMouse_chr6.simMouse.chr6 529032 1 + 636262 T -s simRat_chr6.simRat.chr6 540134 1 + 647215 T -s simRat_chr6.simRat.chr6 539768 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 528677 35 + 636262 ACCAATTATGGTATCTCTGACTGTCATTTGCCAGA -s Anc0.Anc0refChr3 138715 7 + 222631 -------ATAGCAT--------------------- -s Anc1.Anc1refChr6 173996 28 + 197743 -------ATAGCATGTTTGACCTTCCTTTGCCAGA -s Anc2.Anc2refChr1 52053 7 + 142988 -------ATAGCTT--------------------- -s mr.mrrefChr3 80641 35 + 181027 ACCAATTATGGTATCTCTGACTGTCATTTGCCAGA -s simCow_chr6.simCow.chr6 509271 7 + 602619 -------ATGGCCT--------------------- -s simDog_chr6.simDog.chr6 498307 7 + 593897 -------ACAGCTT--------------------- -s simHuman_chr6.simHuman.chr6 505844 28 + 601863 -------ATAGCATGTTTGACCTTCCTTTGCCAGA -s simRat_chr6.simRat.chr6 539769 35 + 647215 ACCAATTATGGTATCTCCGACTGTCACTTGCCACA - -a -s simMouse_chr6.simMouse.chr6 528712 3 + 636262 CAG -s Anc0.Anc0refChr3 138724 3 + 222631 CAG -s Anc1.Anc1refChr6 174026 3 + 197743 CAG -s Anc2.Anc2refChr1 52062 3 + 142988 CAG -s mr.mrrefChr3 80676 3 + 181027 CAG -s simCow_chr6.simCow.chr6 509280 3 + 602619 TAG -s simDog_chr6.simDog.chr6 498316 3 + 593897 CAG -s simHuman_chr6.simHuman.chr6 505874 3 + 601863 CGG -s simRat_chr6.simRat.chr6 539804 3 + 647215 CAG - -a -s simMouse_chr6.simMouse.chr6 528715 41 + 636262 TTCCAAGTAGGCTGTAACCTTTCTGCATACACTACTACAAG -s Anc0.Anc0refChr3 138727 41 + 222631 TTCCAACTAAGCTGTGACCTATCTGCATACCCTACCTCAAG -s Anc1.Anc1refChr6 174029 41 + 197743 TTCCAACTAAGCTGTGACCTATCTGCATACCCTACCTCAAG -s Anc2.Anc2refChr1 52065 41 + 142988 TTCCACCTAAGCTGTGACCTATCTACGTACCCTACCTCAAG -s mr.mrrefChr3 80679 41 + 181027 TTCCAAGTAGGCTGTAACCTATCTGCATACACTACCACAAG -s mr.mrrefChr3 80987 41 + 181027 TTCCAAGAAAGCGGAAACCTAACTGCATATGTTACCTCAAG -s simCow_chr6.simCow.chr6 509283 41 + 602619 CTCCACCTATGCTGTGACCAATCCCTTTATGCTACCTGAAC -s simDog_chr6.simDog.chr6 498319 41 + 593897 TTCCACCTAAGCTGTGACCTGTCTACGTACCCTATCTCAAG -s simHuman_chr6.simHuman.chr6 505877 41 + 601863 TTCCAACAAAGCCATGACCTATCTGCATACCTTACCTCAAG -s simMouse_chr6.simMouse.chr6 529033 41 + 636262 TTCCAAGAAAGCGGAAACCTAACTGCATATGTTACCTCAAG -s simRat_chr6.simRat.chr6 540138 41 + 647215 TTCCCAGAAAGCACAAACCTATGTGCTTATGTTACCTCAAG -s simRat_chr6.simRat.chr6 539807 41 + 647215 TTCCAAGTAGGCTGTAACCTATCAGCATACACTAACACAAG - -a -s simMouse_chr6.simMouse.chr6 528756 1 + 636262 A -s Anc0.Anc0refChr3 138768 1 + 222631 A -s Anc1.Anc1refChr6 174070 1 + 197743 A -s Anc2.Anc2refChr1 52106 1 + 142988 A -s mr.mrrefChr3 80720 1 + 181027 A -s mr.mrrefChr3 81028 1 + 181027 A -s simCow_chr6.simCow.chr6 509324 1 + 602619 A -s simDog_chr6.simDog.chr6 498360 1 + 593897 A -s simHuman_chr6.simHuman.chr6 505918 1 + 601863 A -s simMouse_chr6.simMouse.chr6 529074 1 + 636262 A -s simRat_chr6.simRat.chr6 540183 1 + 647215 A -s simRat_chr6.simRat.chr6 539848 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 528757 4 + 636262 GGAA -s Anc0.Anc0refChr3 138769 4 + 222631 GGTA -s Anc1.Anc1refChr6 174071 4 + 197743 GGTA -s Anc2.Anc2refChr1 52107 4 + 142988 GATA -s mr.mrrefChr3 80721 4 + 181027 GGAA -s simCow_chr6.simCow.chr6 509325 4 + 602619 GATA -s simDog_chr6.simDog.chr6 498361 4 + 593897 AATA -s simHuman_chr6.simHuman.chr6 505919 4 + 601863 GGTA -s simRat_chr6.simRat.chr6 539849 4 + 647215 GGAA - -a -s simMouse_chr6.simMouse.chr6 528761 19 + 636262 TACTTGTCTGCACTCCCTT -s Anc0.Anc0refChr3 138773 19 + 222631 TACTTGTTGCCACCCCTTC -s Anc1.Anc1refChr6 174075 19 + 197743 TACTTGTTGCCACCCCTTC -s Anc2.Anc2refChr1 52111 19 + 142988 TACTTGTTGCCACCACTTC -s mr.mrrefChr3 80725 19 + 181027 TACTTGTTTGCACTCCTTT -s mr.mrrefChr3 81029 19 + 181027 TAATTGTATGCACCCCCTC -s simCow_chr6.simCow.chr6 509329 19 + 602619 TACTTGTTGCCACCACATC -s simDog_chr6.simDog.chr6 498365 19 + 593897 TACTTGTTGCCACCACTTT -s simHuman_chr6.simHuman.chr6 505923 19 + 601863 TATTTGTTGCCACGCCTTC -s simMouse_chr6.simMouse.chr6 529075 19 + 636262 TAATTGTATGCACCCCCTC -s simRat_chr6.simRat.chr6 540184 19 + 647215 TAATTGTCTGCACCCCCTC -s simRat_chr6.simRat.chr6 539853 19 + 647215 TACTTGTTTGCACCCCTTT - -a -s simMouse_chr6.simMouse.chr6 528780 9 + 636262 ACGGCTAAT -s Anc0.Anc0refChr3 138793 9 + 222631 TCAGCGATA -s Anc1.Anc1refChr6 174095 9 + 197743 TCAGCGATA -s Anc2.Anc2refChr1 52131 9 + 142988 TCAGCGCTA -s mr.mrrefChr3 80745 9 + 181027 ACAGCTAAT -s mr.mrrefChr3 81049 9 + 181027 ACAGCTAAA -s simCow_chr6.simCow.chr6 509349 9 + 602619 TCAGCGCTA -s simDog_chr6.simDog.chr6 498385 9 + 593897 CTTGCCCTA -s simHuman_chr6.simHuman.chr6 505943 9 + 601863 TCATCGATA -s simMouse_chr6.simMouse.chr6 529095 9 + 636262 ACAGCTAAA -s simRat_chr6.simRat.chr6 540204 9 + 647215 ACAGCTAGA -s simRat_chr6.simRat.chr6 539873 9 + 647215 ACAGCTAGT - -a -s simMouse_chr6.simMouse.chr6 528789 17 + 636262 GCACAATGTACAACTTG -s Anc0.Anc0refChr3 138803 10 + 222631 C-------TAAGATATG -s Anc1.Anc1refChr6 174105 17 + 197743 CCACATTGTAAGATATG -s Anc2.Anc2refChr1 52141 10 + 142988 C-------TAAGATATG -s mr.mrrefChr3 80754 17 + 181027 GCACAATGTATGACTTG -s mr.mrrefChr3 81059 17 + 181027 GGAGATTGGGAAACTTG -s simCow_chr6.simCow.chr6 509359 10 + 602619 G-------TTGGATATG -s simDog_chr6.simDog.chr6 498395 10 + 593897 C-------TAAGATGCA -s simHuman_chr6.simHuman.chr6 505953 10 + 601863 C-------TATGATATG -s simMouse_chr6.simMouse.chr6 529105 17 + 636262 GGAGATTGGGAAACTTG -s simRat_chr6.simRat.chr6 540214 17 + 647215 GGAGATTGGGAAACTTT -s simRat_chr6.simRat.chr6 539882 16 + 647215 GCACGATGCATGACTT- - -a -s simMouse_chr6.simMouse.chr6 528806 7 + 636262 ACCACAA -s Anc0.Anc0refChr3 138813 5 + 222631 TCGAC-- -s Anc1.Anc1refChr6 174122 7 + 197743 TCGACAA -s Anc2.Anc2refChr1 52151 5 + 142988 TTGAC-- -s mr.mrrefChr3 80771 7 + 181027 ACGACAA -s mr.mrrefChr3 81076 7 + 181027 ACCACAA -s simCow_chr6.simCow.chr6 509369 3 + 602619 TTA---- -s simDog_chr6.simDog.chr6 498406 5 + 593897 TTGAC-- -s simHuman_chr6.simHuman.chr6 505963 6 + 601863 TCGACA- -s simMouse_chr6.simMouse.chr6 529122 7 + 636262 ACCACAA -s simRat_chr6.simRat.chr6 540231 7 + 647215 ACCACAA -s simRat_chr6.simRat.chr6 539898 7 + 647215 ACGAGGA - -a -s simMouse_chr6.simMouse.chr6 528813 20 + 636262 GTCAGGTTTAATGCTTGGGT -s Anc1.Anc1refChr6 174129 11 + 197743 GTCAG---------ATTTGT -s mr.mrrefChr3 80778 11 + 181027 GTCAG---------TTTGGT -s mr.mrrefChr3 81088 11 + 181027 GTCAA---------ATGCGT -s simHuman_chr6.simHuman.chr6 505969 4 + 601863 ----------------TTGT -s simMouse_chr6.simMouse.chr6 529134 11 + 636262 GTCAA---------ATGCGT -s simRat_chr6.simRat.chr6 540243 11 + 647215 GTCAA---------ATGTGT -s simRat_chr6.simRat.chr6 539905 11 + 647215 ATCTG---------TCTGAT - -a -s simMouse_chr6.simMouse.chr6 528833 1 + 636262 C -s Anc1.Anc1refChr6 174140 1 + 197743 C -s mr.mrrefChr3 80789 1 + 181027 C -s mr.mrrefChr3 81099 1 + 181027 G -s simHuman_chr6.simHuman.chr6 505973 1 + 601863 C -s simMouse_chr6.simMouse.chr6 529145 1 + 636262 G -s simRat_chr6.simRat.chr6 540256 1 + 647215 G -s simRat_chr6.simRat.chr6 539916 1 + 647215 C - -a -s simMouse_chr6.simMouse.chr6 528834 6 + 636262 AATAAG -s Anc1.Anc1refChr6 174141 6 + 197743 AATGAC -s mr.mrrefChr3 80790 6 + 181027 AATAAG -s mr.mrrefChr3 81102 6 + 181027 AACGAG -s simHuman_chr6.simHuman.chr6 505974 6 + 601863 AATGAC -s simMouse_chr6.simMouse.chr6 529148 6 + 636262 AACGAG -s simRat_chr6.simRat.chr6 540259 6 + 647215 AAGAAG -s simRat_chr6.simRat.chr6 539917 6 + 647215 TATATG - -a -s simMouse_chr6.simMouse.chr6 528840 5 + 636262 ATCTG -s Anc1.Anc1refChr6 174147 5 + 197743 GTCTG -s mr.mrrefChr3 80796 5 + 181027 ATCTG -s mr.mrrefChr3 81108 5 + 181027 GTCTG -s simMouse_chr6.simMouse.chr6 529154 5 + 636262 GTCTG -s simRat_chr6.simRat.chr6 540265 5 + 647215 GTCCG -s simRat_chr6.simRat.chr6 539928 5 + 647215 GTCTG - -a -s simMouse_chr6.simMouse.chr6 528845 2 + 636262 AC -s Anc0.Anc0refChr3 138818 1 + 222631 -C -s Anc1.Anc1refChr6 174152 2 + 197743 AC -s Anc2.Anc2refChr1 52156 1 + 142988 -C -s mr.mrrefChr3 80801 2 + 181027 AC -s mr.mrrefChr3 81113 2 + 181027 AC -s simDog_chr6.simDog.chr6 498411 1 + 593897 -C -s simMouse_chr6.simMouse.chr6 529159 2 + 636262 AC -s simRat_chr6.simRat.chr6 540288 2 + 647215 AC -s simRat_chr6.simRat.chr6 539933 2 + 647215 AC - -a -s simMouse_chr6.simMouse.chr6 528847 22 + 636262 ATATGACCCGGATTGTTAAGCT -s Anc0.Anc0refChr3 138819 16 + 222631 A--TGAC----ATTGTCAAACT -s Anc1.Anc1refChr6 174154 20 + 197743 A--TGACCTGGATTGTCAAACT -s Anc2.Anc2refChr1 52157 16 + 142988 T--TGAC----ACTGTCAAACT -s mr.mrrefChr3 80803 20 + 181027 A--TGACCCGGATTGTTAAGCT -s mr.mrrefChr3 81129 20 + 181027 C--TGACCTTGATTGTCAAACT -s simCow_chr6.simCow.chr6 509372 14 + 602619 ----GAC----ACTATCAAACT -s simDog_chr6.simDog.chr6 498412 14 + 593897 T--T--C----ACTGTCAAGTT -s simHuman_chr6.simHuman.chr6 505980 11 + 601863 -----------ATTGACCAACT -s simMouse_chr6.simMouse.chr6 529175 20 + 636262 C--TGACCTTGATTGTCAAACT -s simRat_chr6.simRat.chr6 540304 20 + 647215 C--TGACTTTGATTGTCAAACT -s simRat_chr6.simRat.chr6 539935 18 + 647215 A----ATCCGGATCAGTAATAT - -a -s simMouse_chr6.simMouse.chr6 528869 10 + 636262 GTTTCATTTA -s Anc0.Anc0refChr3 138835 10 + 222631 GTTCCATATA -s Anc1.Anc1refChr6 174174 10 + 197743 GTTCCATATA -s Anc2.Anc2refChr1 52173 10 + 142988 GTTCCATATA -s mr.mrrefChr3 80823 10 + 181027 GTTTCATTTA -s mr.mrrefChr3 81149 10 + 181027 GTTCCAAATA -s simCow_chr6.simCow.chr6 509386 10 + 602619 GTTCCATGTA -s simDog_chr6.simDog.chr6 498426 10 + 593897 GTCCCATATA -s simHuman_chr6.simHuman.chr6 505991 10 + 601863 TTTCCATAGA -s simMouse_chr6.simMouse.chr6 529195 10 + 636262 GTTCCAAATA -s simRat_chr6.simRat.chr6 540324 10 + 647215 GTTCCAAACA -s simRat_chr6.simRat.chr6 539966 10 + 647215 ATCTCATTCA - -a -s simMouse_chr6.simMouse.chr6 528879 6 + 636262 CATCAG -s Anc0.Anc0refChr3 138845 6 + 222631 AATCAC -s Anc1.Anc1refChr6 174184 6 + 197743 AATCAC -s Anc2.Anc2refChr1 52183 6 + 142988 GACCAC -s mr.mrrefChr3 80833 6 + 181027 CATCAG -s mr.mrrefChr3 81159 6 + 181027 AATCAC -s simCow_chr6.simCow.chr6 509396 6 + 602619 GACCCT -s simDog_chr6.simDog.chr6 498436 6 + 593897 GACCAC -s simHuman_chr6.simHuman.chr6 506001 6 + 601863 AATCAC -s simMouse_chr6.simMouse.chr6 529205 6 + 636262 AATCAC -s simRat_chr6.simRat.chr6 540334 6 + 647215 AATGAC -s simRat_chr6.simRat.chr6 539979 6 + 647215 CATTAA - -a -s simMouse_chr6.simMouse.chr6 528885 3 + 636262 ACA -s Anc0.Anc0refChr3 138851 3 + 222631 ACA -s Anc1.Anc1refChr6 174190 3 + 197743 ACA -s Anc2.Anc2refChr1 52195 3 + 142988 ACA -s mr.mrrefChr3 80839 3 + 181027 ACA -s mr.mrrefChr3 81165 3 + 181027 ACA -s simCow_chr6.simCow.chr6 509408 3 + 602619 ACA -s simDog_chr6.simDog.chr6 498448 1 + 593897 A-- -s simHuman_chr6.simHuman.chr6 506007 3 + 601863 ACA -s simMouse_chr6.simMouse.chr6 529211 3 + 636262 ACA -s simRat_chr6.simRat.chr6 540340 3 + 647215 ACA -s simRat_chr6.simRat.chr6 539985 2 + 647215 AC- - -a -s simMouse_chr6.simMouse.chr6 528888 10 + 636262 GATTCCTTGT -s Anc0.Anc0refChr3 138859 10 + 222631 GATTTCTTGT -s Anc1.Anc1refChr6 174198 10 + 197743 GATTTCTTGT -s Anc2.Anc2refChr1 52203 10 + 142988 GATTTCTTGT -s mr.mrrefChr3 80842 10 + 181027 GATTCCTTGT -s mr.mrrefChr3 81168 10 + 181027 GATCCCTTGT -s simCow_chr6.simCow.chr6 509416 10 + 602619 GATTTCTTGT -s simDog_chr6.simDog.chr6 498451 10 + 593897 GATTTCTTGT -s simHuman_chr6.simHuman.chr6 506015 10 + 601863 GATTTCTTGT -s simMouse_chr6.simMouse.chr6 529214 10 + 636262 GATCCCTTGT -s simRat_chr6.simRat.chr6 540343 10 + 647215 GATCCCTTGT -s simRat_chr6.simRat.chr6 539987 9 + 647215 -CTGGCTTGT - -a -s simMouse_chr6.simMouse.chr6 528898 11 + 636262 CTGAAAACCTT -s Anc0.Anc0refChr3 138869 11 + 222631 CTGAACACCTT -s Anc1.Anc1refChr6 174208 11 + 197743 CTGAACACCTT -s Anc2.Anc2refChr1 52213 11 + 142988 CTGAGCACCTT -s mr.mrrefChr3 80852 11 + 181027 CTGAATACCTT -s mr.mrrefChr3 81178 11 + 181027 CTGTACATCTT -s simCow_chr6.simCow.chr6 509426 11 + 602619 CTGAGCACCAT -s simDog_chr6.simDog.chr6 498461 10 + 593897 CTGAGCACCT- -s simHuman_chr6.simHuman.chr6 506025 11 + 601863 CTGAACACCGT -s simMouse_chr6.simMouse.chr6 529224 11 + 636262 CTGTACATCTT -s simRat_chr6.simRat.chr6 540353 11 + 647215 CTGTAGGTCTT -s simRat_chr6.simRat.chr6 540000 11 + 647215 CTGAATGCCTT - -a -s simMouse_chr6.simMouse.chr6 528909 38 + 636262 AATCTGCATAGTTAATTCTATGGATGAAAGACAAAAGG -s Anc0.Anc0refChr3 138893 38 + 222631 GATCTATATAGTTATGTGTATTGATAAGAGAGAGAAGG -s Anc1.Anc1refChr6 174232 38 + 197743 GATCTATATAGTTATGTGTATTGATAAGAGAGAGAAGG -s Anc2.Anc2refChr1 52237 38 + 142988 GATTTATCTAGTTATTTGTATTGATAAGTGAGAGAAAG -s mr.mrrefChr3 80863 38 + 181027 GATCTACATAGTTAAGTCTATGGATGAAAGACAGAAGG -s mr.mrrefChr3 81207 38 + 181027 GCTCTACATAGTTAAGTGTATTAATCAAGGGCAGCAGG -s simCow_chr6.simCow.chr6 509450 38 + 602619 GATTTATCTAGTTACTTGTAATAACAAATGAGTGAAAG -s simDog_chr6.simDog.chr6 498483 38 + 593897 GATTTATCTAGTTATTTGTATTGATAAGTGACAAAAAG -s simHuman_chr6.simHuman.chr6 506049 38 + 601863 GATCTATATAGTTATGTGTATTTGTAAGAGAGAGAAGG -s simMouse_chr6.simMouse.chr6 529253 38 + 636262 GCTCTACATAGTTAAGTGTATTAATCAAGGGCAGCAGG -s simRat_chr6.simRat.chr6 540382 38 + 647215 GCTCTACATAGTTAAGTGTCTTAATCAAAGGCAGAATG -s simRat_chr6.simRat.chr6 540011 38 + 647215 GATCCACACAGTTAAGTCTATGAATGAAAGACAGAAGG - -a -s simMouse_chr6.simMouse.chr6 528947 1 + 636262 A -s Anc0.Anc0refChr3 138931 1 + 222631 G -s Anc1.Anc1refChr6 174270 1 + 197743 G -s Anc2.Anc2refChr1 52275 1 + 142988 G -s mr.mrrefChr3 80901 1 + 181027 A -s simCow_chr6.simCow.chr6 509488 1 + 602619 G -s simDog_chr6.simDog.chr6 498521 1 + 593897 G -s simHuman_chr6.simHuman.chr6 506087 1 + 601863 G -s simRat_chr6.simRat.chr6 540049 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 528948 14 + 636262 TGAAGCTTTCACAC -s Anc0.Anc0refChr3 138933 14 + 222631 TAATGCTGTCATGT -s Anc1.Anc1refChr6 174272 14 + 197743 TAATGCTGTCATGT -s Anc2.Anc2refChr1 52277 14 + 142988 TAATGATGTCATGT -s mr.mrrefChr3 80902 14 + 181027 TGAAGCTTTCATGC -s simDog_chr6.simDog.chr6 498523 14 + 593897 TAATGATGTCATGT -s simHuman_chr6.simHuman.chr6 506089 14 + 601863 TAATGCTCACATGT -s simRat_chr6.simRat.chr6 540050 14 + 647215 TGAACCTTTCATGC - -a -s simMouse_chr6.simMouse.chr6 528962 15 + 636262 CTACTGCCTTTGTGG -s Anc0.Anc0refChr3 138947 15 + 222631 CTACAGCCTTTACGG -s Anc1.Anc1refChr6 174286 15 + 197743 CTACAGCCTTTACGG -s Anc2.Anc2refChr1 52291 15 + 142988 CTACAGCCTTTACGG -s mr.mrrefChr3 80916 15 + 181027 CTACAGCCTTTGTGG -s mr.mrrefChr3 81245 15 + 181027 CTGCAGCTTTCATGT -s simCow_chr6.simCow.chr6 509489 15 + 602619 TTCCAGTCTGTATGG -s simDog_chr6.simDog.chr6 498537 15 + 593897 CTACAGCCTTTACGG -s simHuman_chr6.simHuman.chr6 506103 15 + 601863 CTGCAGCCTTTACGT -s simMouse_chr6.simMouse.chr6 529291 15 + 636262 CTGCAGCTTTCATGT -s simRat_chr6.simRat.chr6 540420 15 + 647215 ATGCAACTTTCATGT -s simRat_chr6.simRat.chr6 540064 15 + 647215 CTACAGCCTTTTTGG - -a -s simMouse_chr6.simMouse.chr6 528977 2 + 636262 TT -s Anc0.Anc0refChr3 138962 2 + 222631 TT -s Anc1.Anc1refChr6 174301 2 + 197743 TT -s Anc2.Anc2refChr1 52308 2 + 142988 TT -s mr.mrrefChr3 80931 2 + 181027 TT -s mr.mrrefChr3 81260 2 + 181027 CT -s simCow_chr6.simCow.chr6 509506 2 + 602619 TT -s simDog_chr6.simDog.chr6 498554 2 + 593897 TT -s simHuman_chr6.simHuman.chr6 506118 2 + 601863 TT -s simMouse_chr6.simMouse.chr6 529306 2 + 636262 CT -s simRat_chr6.simRat.chr6 540435 2 + 647215 CT -s simRat_chr6.simRat.chr6 540079 2 + 647215 GT - -a -s simMouse_chr6.simMouse.chr6 528979 9 + 636262 TAAGATAAG -s mr.mrrefChr3 80933 9 + 181027 TAAGATAAG -s simRat_chr6.simRat.chr6 540081 9 + 647215 TAAGATAAG - -a -s simMouse_chr6.simMouse.chr6 528988 1 + 636262 A -s Anc0.Anc0refChr3 138964 1 + 222631 A -s Anc1.Anc1refChr6 174303 1 + 197743 A -s Anc2.Anc2refChr1 52310 1 + 142988 A -s mr.mrrefChr3 80942 1 + 181027 A -s mr.mrrefChr3 81262 1 + 181027 A -s simCow_chr6.simCow.chr6 509508 1 + 602619 A -s simDog_chr6.simDog.chr6 498556 1 + 593897 A -s simHuman_chr6.simHuman.chr6 506120 1 + 601863 A -s simMouse_chr6.simMouse.chr6 529308 1 + 636262 A -s simRat_chr6.simRat.chr6 540437 1 + 647215 A -s simRat_chr6.simRat.chr6 540090 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 528989 6 + 636262 TATCCT -s Anc0.Anc0refChr3 138968 6 + 222631 TATCCT -s Anc1.Anc1refChr6 174307 6 + 197743 TATCCT -s Anc2.Anc2refChr1 52314 6 + 142988 TATCCT -s mr.mrrefChr3 80943 6 + 181027 TATCCT -s mr.mrrefChr3 81263 6 + 181027 TAGCCT -s simCow_chr6.simCow.chr6 509512 6 + 602619 TATCCT -s simDog_chr6.simDog.chr6 498560 6 + 593897 TATCAT -s simHuman_chr6.simHuman.chr6 506124 6 + 601863 TATCCT -s simMouse_chr6.simMouse.chr6 529309 6 + 636262 TAGCCT -s simRat_chr6.simRat.chr6 540438 6 + 647215 TAGCCT -s simRat_chr6.simRat.chr6 540091 6 + 647215 TATCCT - -a -s simMouse_chr6.simMouse.chr6 528995 2 + 636262 TG -s Anc0.Anc0refChr3 138974 2 + 222631 TG -s Anc1.Anc1refChr6 174313 2 + 197743 TG -s Anc2.Anc2refChr1 52320 2 + 142988 TG -s mr.mrrefChr3 80949 2 + 181027 TG -s mr.mrrefChr3 81272 2 + 181027 TG -s simCow_chr6.simCow.chr6 509518 2 + 602619 TA -s simDog_chr6.simDog.chr6 498566 2 + 593897 GG -s simHuman_chr6.simHuman.chr6 506130 2 + 601863 TG -s simMouse_chr6.simMouse.chr6 529318 2 + 636262 TG -s simRat_chr6.simRat.chr6 540447 2 + 647215 TG -s simRat_chr6.simRat.chr6 540097 2 + 647215 TG - -a -s simMouse_chr6.simMouse.chr6 528997 3 + 636262 GCT -s Anc0.Anc0refChr3 138976 3 + 222631 GCC -s Anc1.Anc1refChr6 174315 3 + 197743 GCC -s Anc2.Anc2refChr1 52322 3 + 142988 GCC -s mr.mrrefChr3 80951 3 + 181027 GCT -s mr.mrrefChr3 81274 3 + 181027 TCT -s simCow_chr6.simCow.chr6 509520 3 + 602619 GTC -s simDog_chr6.simDog.chr6 498568 3 + 593897 GCC -s simHuman_chr6.simHuman.chr6 506132 3 + 601863 GCC -s simMouse_chr6.simMouse.chr6 529320 3 + 636262 TCT -s simRat_chr6.simRat.chr6 540504 3 + 647215 TCT -s simRat_chr6.simRat.chr6 540099 3 + 647215 GCT - -a -s simMouse_chr6.simMouse.chr6 529000 19 + 636262 AATAGAGCCACTCATAGTG -s Anc0.Anc0refChr3 138979 19 + 222631 AATAGAGCTGCTTTTAGTG -s Anc1.Anc1refChr6 174318 19 + 197743 AATAGAGCTGCTTTTAGTG -s Anc2.Anc2refChr1 52325 19 + 142988 AATAGAGCTGGTTTTAGTC -s mr.mrrefChr3 80954 19 + 181027 AATAGAGCCACTCATAGTG -s simCow_chr6.simCow.chr6 509523 19 + 602619 CATAAAGGTGGCTTTAGTA -s simDog_chr6.simDog.chr6 498571 19 + 593897 AATAGAGCCGGTTTTAGTC -s simHuman_chr6.simHuman.chr6 506135 19 + 601863 TATAGAGCTGCTTGTAGTG -s simRat_chr6.simRat.chr6 540102 19 + 647215 AATAGAGCCACTCATAGTC - -a -s simMouse_chr6.simMouse.chr6 529019 4 + 636262 CTTA -s Anc0.Anc0refChr3 138998 4 + 222631 CTTA -s Anc1.Anc1refChr6 174337 4 + 197743 CTTA -s Anc2.Anc2refChr1 52344 4 + 142988 ATTA -s mr.mrrefChr3 80973 4 + 181027 CTTA -s mr.mrrefChr3 81277 4 + 181027 CCTA -s simCow_chr6.simCow.chr6 509542 4 + 602619 ACTA -s simDog_chr6.simDog.chr6 498590 4 + 593897 ATTA -s simHuman_chr6.simHuman.chr6 506154 4 + 601863 TTTA -s simMouse_chr6.simMouse.chr6 529323 4 + 636262 CCTA -s simRat_chr6.simRat.chr6 540507 4 + 647215 CCTA -s simRat_chr6.simRat.chr6 540121 4 + 647215 CTTA - -a -s simMouse_chr6.simMouse.chr6 529023 9 + 636262 CTTTATCAG -s Anc0.Anc0refChr3 139002 9 + 222631 TTTTATCAG -s Anc1.Anc1refChr6 174341 9 + 197743 TTTTATCAG -s Anc2.Anc2refChr1 52348 9 + 142988 TTATATTAG -s mr.mrrefChr3 80977 9 + 181027 CTTTATCAG -s mr.mrrefChr3 81281 9 + 181027 TTTTATCAG -s simCow_chr6.simCow.chr6 509546 8 + 602619 CCATATTA- -s simDog_chr6.simDog.chr6 498596 9 + 593897 TTATATTAG -s simHuman_chr6.simHuman.chr6 506158 9 + 601863 TTTTATCGG -s simMouse_chr6.simMouse.chr6 529327 9 + 636262 TTTTATCAG -s simRat_chr6.simRat.chr6 540511 9 + 647215 TTTTATCAG -s simRat_chr6.simRat.chr6 540125 9 + 647215 TGTTATCAG - -a -s simMouse_chr6.simMouse.chr6 529094 1 + 636262 A -s Anc0.Anc0refChr3 138792 1 + 222631 A -s Anc1.Anc1refChr6 174094 1 + 197743 A -s Anc2.Anc2refChr1 52130 1 + 142988 A -s mr.mrrefChr3 81048 1 + 181027 A -s mr.mrrefChr3 80744 1 + 181027 A -s simCow_chr6.simCow.chr6 509348 1 + 602619 A -s simDog_chr6.simDog.chr6 498384 1 + 593897 G -s simHuman_chr6.simHuman.chr6 505942 1 + 601863 A -s simRat_chr6.simRat.chr6 539872 1 + 647215 A -s simRat_chr6.simRat.chr6 540203 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 529104 1 + 636262 A -s Anc0.Anc0refChr3 138802 1 + 222631 A -s Anc1.Anc1refChr6 174104 1 + 197743 A -s Anc2.Anc2refChr1 52140 1 + 142988 G -s mr.mrrefChr3 81058 1 + 181027 A -s simCow_chr6.simCow.chr6 509358 1 + 602619 G -s simDog_chr6.simDog.chr6 498394 1 + 593897 G -s simHuman_chr6.simHuman.chr6 505952 1 + 601863 A -s simRat_chr6.simRat.chr6 540213 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 529129 5 + 636262 TTAAT -s mr.mrrefChr3 81083 5 + 181027 TTAAT -s simRat_chr6.simRat.chr6 540238 5 + 647215 TTCAT - -a -s simMouse_chr6.simMouse.chr6 529146 2 + 636262 GG -s mr.mrrefChr3 81100 2 + 181027 GG -s simRat_chr6.simRat.chr6 540257 2 + 647215 GG - -a -s simMouse_chr6.simMouse.chr6 529161 14 + 636262 TGGTAAGGATATGA -s mr.mrrefChr3 81115 14 + 181027 TGGTAAGGATATGA -s simRat_chr6.simRat.chr6 540290 14 + 647215 TGGTAAGGATATGG - -a -s simMouse_chr6.simMouse.chr6 529235 18 + 636262 ACCTTGCTTTTCGCAAAT -s Anc0.Anc0refChr3 138880 13 + 222631 ACCTC---TCTAGCAG-- -s Anc1.Anc1refChr6 174219 13 + 197743 ACCTC---TCTAGCAG-- -s Anc2.Anc2refChr1 52224 13 + 142988 ACCTC---TCTAAGAG-- -s mr.mrrefChr3 81189 18 + 181027 ACCTTGCTTTTCGCAAAT -s simCow_chr6.simCow.chr6 509437 13 + 602619 ACCTC---ACTAAGAG-- -s simDog_chr6.simDog.chr6 498471 12 + 593897 -CCTC---TCCAAGAA-- -s simHuman_chr6.simHuman.chr6 506036 13 + 601863 ACCTC---TGTAGCAG-- -s simRat_chr6.simRat.chr6 540364 18 + 647215 ACTCTACCTTTGGCAGAT - -a -s simMouse_chr6.simMouse.chr6 529315 3 + 636262 GTA -s mr.mrrefChr3 81269 3 + 181027 GTA -s simRat_chr6.simRat.chr6 540444 3 + 647215 TCA - -a -s simMouse_chr6.simMouse.chr6 529336 39 + 636262 TATATCTTCTAGGGTTCATCACAACTGTTGCGGGACTCT -s Anc0.Anc0refChr3 139011 39 + 222631 TATATCTCCTGTGCTTCATCCTAAATCTTGGAGGCATTA -s Anc1.Anc1refChr6 174350 39 + 197743 TATATCTCCTGTGCTTCATCCTAAATCTTGGAGGCATTA -s Anc2.Anc2refChr1 52357 39 + 142988 TATATCTCCTGTGCTTCATCCTAAATCTTGGAGACATTA -s mr.mrrefChr3 81290 39 + 181027 TATATCTTCTAGGGTTCATCACAAATGTTGCAGGACTCT -s simCow_chr6.simCow.chr6 509554 33 + 602619 TATATCTCCTATGCTTCATCCTACA------AGACATTA -s simDog_chr6.simDog.chr6 498605 39 + 593897 TATATCTCCTGTGCTTCATCCTAAATCTTGGAGACATTA -s simHuman_chr6.simHuman.chr6 506167 38 + 601863 TATATCT-CTGTGCTTTGGCCTATATCTTGGAGGCATTA -s simRat_chr6.simRat.chr6 540520 39 + 647215 TATGTCTCCTAGGGTTCATCACAAATATTGCAGAACTTT - -a -s simMouse_chr6.simMouse.chr6 529375 19 + 636262 GCATCCCGTCTACATACTT -s Anc0.Anc0refChr3 139050 14 + 222631 GTATCCCCTCTACA----- -s Anc1.Anc1refChr6 174389 19 + 197743 GTATCCCCTCTACACCCTT -s Anc2.Anc2refChr1 52396 14 + 142988 GTATCCTCTCTATA----- -s mr.mrrefChr3 81329 19 + 181027 GCATCCCGTCTACACACTT -s simCow_chr6.simCow.chr6 509587 14 + 602619 GTATCCTCTCTATG----- -s simDog_chr6.simDog.chr6 498644 14 + 593897 GTATCCTCTCTATA----- -s simHuman_chr6.simHuman.chr6 506206 19 + 601863 GGATCCCCTCCACACCCTT -s simRat_chr6.simRat.chr6 540559 19 + 647215 GTATCCCGTCTACACACCT - -a -s simMouse_chr6.simMouse.chr6 529394 46 + 636262 GAATACACTTGCTGTATGCTTAGGAAACGCCTAATATAAAATCACT -s Anc0.Anc0refChr3 139129 46 + 222631 AAACCCTCCTGCTGCATACCAGGTAAACACTTATAATAGAATTACA -s Anc1.Anc1refChr6 174480 46 + 197743 AAACCCTCCTGCTGCATACCAGGTAAACACTTATAATAGAATTACA -s Anc2.Anc2refChr1 52477 46 + 142988 AAACCCTCCTGCTACATACTAGCTAAACACTTATAATAGAATTACA -s mr.mrrefChr3 81363 46 + 181027 GAATACACTTGCTGTATGCCTAGGAAACGCTTAATATAAAATCACT -s simCow_chr6.simCow.chr6 509651 46 + 602619 GAATCCTCCTGCTCTATGCTAGCTGGACACTTATAATAGAATTACA -s simDog_chr6.simDog.chr6 498737 46 + 593897 AAACCCTTCTGCCACACACTAGCCAAACACTTATTATTGAATTATA -s simHuman_chr6.simHuman.chr6 506298 46 + 601863 AAGCCCTCCTGCTGCATTCCGGGTAAACACTTATAATAGAATTACA -s simRat_chr6.simRat.chr6 540593 46 + 647215 GAATACACTTGCTGTGTGCCTAGGAAATGCTTAACATAAAAGCACT - -a -s simMouse_chr6.simMouse.chr6 529440 15 + 636262 CACGTAAGTACCTGG -s Anc0.Anc0refChr3 139178 15 + 222631 CATGAAATTTCATGG -s Anc1.Anc1refChr6 174529 15 + 197743 CATGAAATTTCATGG -s Anc2.Anc2refChr1 52526 15 + 142988 CATGAAGTTTCATGG -s mr.mrrefChr3 81409 15 + 181027 CATGTAAGTACATGG -s simCow_chr6.simCow.chr6 509700 14 + 602619 GGTG-AGTTTGATAG -s simDog_chr6.simDog.chr6 498786 15 + 593897 CATGAAGTTTCATGG -s simHuman_chr6.simHuman.chr6 506347 15 + 601863 CATGAAATCTCATGG -s simRat_chr6.simRat.chr6 540639 15 + 647215 CATGGAAGTACATGG - -a -s simMouse_chr6.simMouse.chr6 529455 39 + 636262 GTCTGAAGTGCAGGAACAGGCACCCAGCGCACACTTAAC -s Anc0.Anc0refChr3 139196 39 + 222631 ATGTGAAGTGGGGGAACAGGAACCCAGCCCACATTTAAC -s Anc1.Anc1refChr6 174547 39 + 197743 ATGTGAAGTGGGGGAACAGGAACCCAGCCCACATTTAAC -s Anc2.Anc2refChr1 52544 39 + 142988 ATGTGAAGTGGGGGAGCAGGAACCCAGCCCACATTTATC -s mr.mrrefChr3 81424 39 + 181027 GTCTGAAGTGGGGGAACAGGCACCCAGCGCACACTTAAC -s simCow_chr6.simCow.chr6 509717 39 + 602619 ATGTGGGCTGTGGGAGCAGGAACCCATCCTACACTTGCC -s simDog_chr6.simDog.chr6 498804 39 + 593897 ATGTGAAGTGGAGGAGCAGGAACCCAGCTCACATTTATT -s simHuman_chr6.simHuman.chr6 506365 39 + 601863 ACAGGAAGTGGGGGAACTGCAACCCTGCCCACATTTAAC -s simRat_chr6.simRat.chr6 540654 39 + 647215 GTCTGAAGTAGGGGGACAGGCACTCAGTGCACACTTAAC - -a -s simMouse_chr6.simMouse.chr6 529494 20 + 636262 CTTTTGCACTTAAAGTTCTC -s Anc0.Anc0refChr3 139235 20 + 222631 TTTATGCACTTAAAATATTC -s Anc1.Anc1refChr6 174586 20 + 197743 TTTATGCACTTAAAATATTC -s Anc2.Anc2refChr1 52583 20 + 142988 TTTATGCACTTAAAATATTT -s mr.mrrefChr3 81463 20 + 181027 CTTTTGCACTTAAAGTTCTC -s simCow_chr6.simCow.chr6 509756 20 + 602619 TTTCTGCCCTTAAAAAATTT -s simDog_chr6.simDog.chr6 498847 20 + 593897 TCTATGCACTTAAAATATTT -s simHuman_chr6.simHuman.chr6 506404 20 + 601863 TTTATGTTCTTAAAATATTC -s simRat_chr6.simRat.chr6 540693 20 + 647215 CTTTTGCACTCAGTGTTCTT - -a -s simMouse_chr6.simMouse.chr6 529514 3 + 636262 TGC -s Anc0.Anc0refChr3 139256 3 + 222631 TGA -s Anc1.Anc1refChr6 174607 3 + 197743 TGA -s Anc2.Anc2refChr1 52604 3 + 142988 TGA -s mr.mrrefChr3 81484 3 + 181027 TGC -s simCow_chr6.simCow.chr6 509777 3 + 602619 TGA -s simDog_chr6.simDog.chr6 498868 3 + 593897 TGA -s simHuman_chr6.simHuman.chr6 506425 3 + 601863 TAA -s simRat_chr6.simRat.chr6 540714 3 + 647215 TGC - -a -s simMouse_chr6.simMouse.chr6 529517 24 + 636262 CCTTTATGACTAAGAATTAATAAT -s Anc0.Anc0refChr3 139260 24 + 222631 CCTTTATAACTAAGAATCCAGAAT -s Anc1.Anc1refChr6 174611 24 + 197743 CCTTTATAACTAAGAATCCAGAAT -s Anc2.Anc2refChr1 52608 24 + 142988 CCTTTATAATTAAGAATCCAGAAT -s mr.mrrefChr3 81487 24 + 181027 CCTTTATGACTAAGAATTAATAAT -s simCow_chr6.simCow.chr6 509781 22 + 602619 CATTTATAATTA--AAGCCTGAAT -s simDog_chr6.simDog.chr6 498872 24 + 593897 CCTTTAGAATTAAGTGTCCAGAAT -s simHuman_chr6.simHuman.chr6 506429 24 + 601863 CTTTTATAGCTAAGAATCTAGAAT -s simRat_chr6.simRat.chr6 540717 24 + 647215 ACATTATGACCAAGAATTAATAAT - -a -s simMouse_chr6.simMouse.chr6 529541 21 + 636262 TGAAAGTGTGCTGCCACCCAA -s Anc0.Anc0refChr3 139284 21 + 222631 TGATGATGTGCTGCCAGCCAA -s Anc1.Anc1refChr6 174635 21 + 197743 TGATGATGTGCTGCCAGCCAA -s Anc2.Anc2refChr1 52632 21 + 142988 TGATGATGTGCTGCCAGCCAA -s mr.mrrefChr3 81511 21 + 181027 TGAAAGTGTGCTGCCACCCAA -s simCow_chr6.simCow.chr6 509803 21 + 602619 TGATGATGTGCTGCCAGCCAA -s simDog_chr6.simDog.chr6 498897 21 + 593897 CTATGATGTGCTGTCACCCAA -s simHuman_chr6.simHuman.chr6 506453 21 + 601863 TGACGATGTGCTGCCAGCCAA -s simRat_chr6.simRat.chr6 540741 21 + 647215 TGATAGTGTGCTGCCACCCAA - -a -s simMouse_chr6.simMouse.chr6 529562 43 + 636262 TAACACAAGACTCATATAGAATGGCATGGACAGATGAACAGTT -s Anc0.Anc0refChr3 139310 43 + 222631 TAATGCAAAACTCATATAGAATGTTATTGAGAGATGGACAGCT -s Anc1.Anc1refChr6 174661 43 + 197743 TAATGCAAAACTCATATAGAATGTTATTGAGAGATGGACAGCT -s Anc2.Anc2refChr1 52661 43 + 142988 TACTGCAAAACTCATATAGAATGTTATTGAGAGATGGACAGCT -s mr.mrrefChr3 81532 43 + 181027 TAATACAAGACTCATATAGAATGGTATTGACAGATGAACAGTT -s simCow_chr6.simCow.chr6 509832 43 + 602619 TACTGCAAAACTCATATAGAGTGTTATTGAGTGATGAACAGCT -s simDog_chr6.simDog.chr6 498926 43 + 593897 TACAGTAAAACTCATATAGAATGTTATTGTGAGATGGACAGCC -s simHuman_chr6.simHuman.chr6 506479 43 + 601863 TAATTCAAAACTCATATAGAATGTTATTGAGAGATGGACAGCT -s simRat_chr6.simRat.chr6 540762 43 + 647215 TAATACAAGACTTATATAGACTGGTATTGACAGATGAACACTT - -a -s simMouse_chr6.simMouse.chr6 529605 4 + 636262 TATA -s Anc0.Anc0refChr3 139353 4 + 222631 TATA -s Anc1.Anc1refChr6 174704 4 + 197743 TATA -s Anc2.Anc2refChr1 52704 4 + 142988 TATA -s mr.mrrefChr3 81575 4 + 181027 TATA -s simCow_chr6.simCow.chr6 509902 4 + 602619 TATA -s simDog_chr6.simDog.chr6 498971 4 + 593897 TGTA -s simHuman_chr6.simHuman.chr6 506522 4 + 601863 TATA -s simRat_chr6.simRat.chr6 540805 4 + 647215 TATA - -a -s simMouse_chr6.simMouse.chr6 529609 1 + 636262 C -s Anc0.Anc0refChr3 139358 1 + 222631 C -s Anc1.Anc1refChr6 174709 1 + 197743 C -s Anc2.Anc2refChr1 52709 1 + 142988 C -s mr.mrrefChr3 81579 1 + 181027 C -s simCow_chr6.simCow.chr6 509907 1 + 602619 T -s simDog_chr6.simDog.chr6 498976 1 + 593897 C -s simHuman_chr6.simHuman.chr6 506527 1 + 601863 C -s simRat_chr6.simRat.chr6 540809 1 + 647215 C - -a -s simMouse_chr6.simMouse.chr6 529610 16 + 636262 CTTGCTGATTTTTCCT -s Anc0.Anc0refChr3 139361 16 + 222631 CTCCCTGATTCTTCCT -s Anc1.Anc1refChr6 174712 16 + 197743 CTCCCTGATTCTTCCT -s Anc2.Anc2refChr1 52712 16 + 142988 TTCCCTGATTCTTCCT -s mr.mrrefChr3 81582 16 + 181027 CTCGCTGATTTTTCCT -s simCow_chr6.simCow.chr6 509910 16 + 602619 TTCCCTGATTTTACCT -s simDog_chr6.simDog.chr6 498979 16 + 593897 TTCCTTGATCCTTCCT -s simHuman_chr6.simHuman.chr6 506530 16 + 601863 CTCCCTAATTGTTCCT -s simRat_chr6.simRat.chr6 540812 16 + 647215 CTCTCTGATTTTTCCT - -a -s simMouse_chr6.simMouse.chr6 529626 69 + 636262 GTTTGAACAACATTACAACAAGGATGAGGCTACTCATGATGACCATCCACAACATCAATAACCAGAGAT -s Anc0.Anc0refChr3 139383 69 + 222631 GATTGAAGAACTTCACTCCAAGGACATGACTACTCATGATGGCCATTCACAAATTCAAAGTCCAGACAT -s Anc1.Anc1refChr6 174734 69 + 197743 GATTGAAGAACTTCACTCCAAGGACATGACTACTCATGATGGCCATTCACAAATTCAAAGTCCAGACAT -s Anc2.Anc2refChr1 52734 69 + 142988 GATTGAAGAACTTCACTCCAAGGACATGACTACTCATGATGGCCATCCACAAATTCAAAGTCCAGACAT -s mr.mrrefChr3 81604 69 + 181027 GTTTGAAGAACATTACAACAAGGATGAGGCTACTCATGATGACCATTCACAACTTCAATATCCAGAGAT -s simCow_chr6.simCow.chr6 509932 65 + 602619 GATAGAAGAACAGCACTCCAAGCATGTGGCTACTCATGATGGCCATCCTCAAATTAAAAG----GGCAT -s simDog_chr6.simDog.chr6 499001 69 + 593897 GATTGAAGAACTTCACTCTAAAGACATGACTAATCATGATGGCCATCCACAAATTCAAGCTCCAGACAT -s simHuman_chr6.simHuman.chr6 506552 64 + 601863 GATGGAAGAATTC-----CAAGAACATGCCCACTCATGATGGCCATTCACAAATTCAAAGTCTAGATAT -s simRat_chr6.simRat.chr6 540834 68 + 647215 GTTTGAAGAACCTTACAACAAGGATGAGACT-CTCATGAAGACCCTTCACAACTACAATATCCAGAGAT - -a -s simMouse_chr6.simMouse.chr6 529695 7 + 636262 CCAAAGT -s Anc0.Anc0refChr3 139453 6 + 222631 CCAAAG- -s Anc1.Anc1refChr6 174804 7 + 197743 CCAAAGT -s Anc2.Anc2refChr1 52840 6 + 142988 CCGAGG- -s mr.mrrefChr3 81674 7 + 181027 CCAAAGT -s simCow_chr6.simCow.chr6 510031 6 + 602619 CCAAAG- -s simDog_chr6.simDog.chr6 499111 6 + 593897 CCGAGG- -s simHuman_chr6.simHuman.chr6 506617 7 + 601863 CTAAAGT -s simRat_chr6.simRat.chr6 540903 7 + 647215 CCGAAGT - -a -s simMouse_chr6.simMouse.chr6 529702 36 + 636262 AGGAAAAAGCTATTGAAGTGAGTGGGGTTAAATGGC -s Anc0.Anc0refChr3 139459 36 + 222631 AGGAGATGACTATGGAAGTGAGCTGGGTTACACAGC -s Anc1.Anc1refChr6 174811 36 + 197743 AGGAGATGACTATGGAAGTGAGCTGGGTTACACAGC -s Anc2.Anc2refChr1 52846 36 + 142988 AGGAGATGACTATGGAAGTAAGCTAGGTTAGACAGC -s mr.mrrefChr3 81681 36 + 181027 AGGAAATAGCTATTGAAGTGAGCGGGGTTACACAGC -s simCow_chr6.simCow.chr6 510038 36 + 602619 GGGGGATGACCATGGAAGTTAGCCAGGTTATTAAGC -s simDog_chr6.simDog.chr6 499117 36 + 593897 AGGACATGGCTCTGGAAGCAAACTAGGTTAGACATC -s simHuman_chr6.simHuman.chr6 506624 36 + 601863 CAGAGATGACTATGGAAGTGGGCTGGATTACACAGC -s simRat_chr6.simRat.chr6 540910 36 + 647215 GGGGAATAGCTATTGAAGTGAGCGGGGTTACACAGC - -a -s simMouse_chr6.simMouse.chr6 529738 4 + 636262 AGGA -s Anc0.Anc0refChr3 139495 4 + 222631 AGGA -s Anc1.Anc1refChr6 174847 4 + 197743 AGGA -s Anc2.Anc2refChr1 52882 4 + 142988 AGGG -s mr.mrrefChr3 81717 4 + 181027 AGGA -s simCow_chr6.simCow.chr6 510084 4 + 602619 AGTG -s simDog_chr6.simDog.chr6 499153 4 + 593897 AGGG -s simHuman_chr6.simHuman.chr6 506660 4 + 601863 AGGA -s simRat_chr6.simRat.chr6 540946 4 + 647215 AGGC - -a -s simMouse_chr6.simMouse.chr6 529742 66 + 636262 CTTAATGTTATTGAGATTTTGAACAGCACCTCATACAAAGCTCCAATAAAAGGGCAAAAGTGGCCA -s Anc0.Anc0refChr3 139499 2 + 222631 TC---------------------------------------------------------------- -s Anc1.Anc1refChr6 174851 2 + 197743 TC---------------------------------------------------------------- -s Anc2.Anc2refChr1 52900 2 + 142988 TC---------------------------------------------------------------- -s mr.mrrefChr3 81721 64 + 181027 CTTAATG--ATTGAGATTTTGAACAGCACCTCATACAAAGCTCCAATAAAAGGGCAAAAGTGGCCA -s simCow_chr6.simCow.chr6 510102 2 + 602619 TC---------------------------------------------------------------- -s simDog_chr6.simDog.chr6 499171 2 + 593897 TT---------------------------------------------------------------- -s simHuman_chr6.simHuman.chr6 506664 2 + 601863 TC---------------------------------------------------------------- -s simRat_chr6.simRat.chr6 540950 64 + 647215 CTTAATG--ATTGAGATTTTGAACAGCACCTCATAGAAAGCTCTGATGAAAGGGAAAAAGTGGCCA - -a -s simMouse_chr6.simMouse.chr6 529808 50 + 636262 GATGCATGTGGGTAGGATTCAACGGATGAGCCTGCCGGCGTCATGCACTG -s mr.mrrefChr3 81785 50 + 181027 GATGTGTGTGGTTAGGATTCGGCGGATGAGCCTGCCGGCGTCATGCACTG -s simRat_chr6.simRat.chr6 541016 50 + 647215 GGTGTGTGTGGTTAGGATTTGGCTACTGAGCCTGCCTGCGTCATGCACTG - -a -s simMouse_chr6.simMouse.chr6 529858 38 + 636262 TAGGTGATGACAGGTTCATCATATAGTGCAAAATCAGG -s mr.mrrefChr3 81835 38 + 181027 TAGGTGATGACAGGTTCATCATATAGTGCAAAATCAGG -s simRat_chr6.simRat.chr6 541067 38 + 647215 TAAGTGATCACAGGTTGGTCATACAGTGCAAAATCAGG - -a -s simMouse_chr6.simMouse.chr6 529896 152 + 636262 GAAAGTCTTGAAGCTGGGTCCCTGTATACATAGTGCCTTGCAATCTTGCAACTGGTCCCTATGAGTTATCCATTGGTCTGGGGGACATGAGGCTGAACTCTAATTAATTGAACTGAACCAGTCATGGATTTCGGTGAACAAAGGGGGAATGG -s Anc0.Anc0refChr3 139501 9 + 222631 ---------------------------------------------------------------------------------------------------------------------------------------------GGCAG--TTGG -s Anc1.Anc1refChr6 174853 11 + 197743 ---------------------------------------------------------------------------------------------------------------------------------------------GGCAGGATTGG -s Anc2.Anc2refChr1 52902 9 + 142988 ---------------------------------------------------------------------------------------------------------------------------------------------GGCAG--TTGC -s mr.mrrefChr3 81873 151 + 181027 GAAAGTCTTGAAGCTGGGTCCCTGTATACATAGTGCCTTGCAATCTTGCAACTGG-CCCTATGAGTTATCCATTGGTCTGGGGGACATGAGGCTGAACTCTAATTAATTGAACTGAACCAGTCATGGATTTCGGTGAACAAAGGGGGAATGG -s simCow_chr6.simCow.chr6 510105 9 + 602619 ---------------------------------------------------------------------------------------------------------------------------------------------GGCAG--TTGC -s simDog_chr6.simDog.chr6 499173 9 + 593897 ---------------------------------------------------------------------------------------------------------------------------------------------GTCAT--TTGC -s simHuman_chr6.simHuman.chr6 506666 11 + 601863 ---------------------------------------------------------------------------------------------------------------------------------------------GGCAGGATTGG -s simRat_chr6.simRat.chr6 541128 151 + 647215 GACAGTCCTAAGGCAGGGTCCCTGTATACCTAGTACCTTGCAATCTTGCAACTGA-ACCTATGAGTTATCCATTGGTCTGGGGGACATGTGGCCGAACCCTAATTAATCGAACTGAACCAGTCATGGATTCCAGTGAACAAAGGGGGAATGG - -a -s simMouse_chr6.simMouse.chr6 530048 36 + 636262 AACAATTGTGGTGAACACACATTTAGTACCCTGGGT -s Anc0.Anc0refChr3 139562 23 + 222631 ATCGAT--CGGTGATCA---ATTTA--------GTG -s Anc1.Anc1refChr6 174916 28 + 197743 ATCGATGACGGTGATCACAGATTTA--------GTG -s Anc2.Anc2refChr1 52963 23 + 142988 ATTGAT--CAGTGATCA---ATTTA--------GTG -s mr.mrrefChr3 82024 28 + 181027 AACAATTATGGTGAACACACATTTA--------GGT -s simCow_chr6.simCow.chr6 510172 8 + 602619 --------------------ATGCA--------GTT -s simDog_chr6.simDog.chr6 499254 23 + 593897 ATTGAT--CAGTGATCA---ATTTA--------GTG -s simHuman_chr6.simHuman.chr6 506732 28 + 601863 ATCGATGACGGTGATCACAGATTTA--------GCG -s simRat_chr6.simRat.chr6 541279 28 + 647215 GGCAATCATGCTGAATACATATTTA--------GGT - -a -s simMouse_chr6.simMouse.chr6 530084 66 + 636262 TGTGCAGGTCACCTCACTGGTGCTTACTTACAAATTAATCCCCCAGATTTGTAAGGTGAGTTAGGC -s Anc0.Anc0refChr3 139585 57 + 222631 TGAATTTCTGGATCCACCA----CTACCTAGCAATTGGCCACCCACATTTGTAAG-----TCAGGG -s Anc1.Anc1refChr6 174944 57 + 197743 TGAATTTCTGGATCCACCA----CTACCTAGCAATTGGCCACCCACATTTGTAAG-----TCAGGG -s Anc2.Anc2refChr1 52986 57 + 142988 TGAATTTCTGGATCAACCA----CTACCTAGCAACTGGCCACCCGCATTTGAAAG-----TCCTGG -s mr.mrrefChr3 82052 66 + 181027 TGTGCAGCTCACCTCACTGGTGCTTACTTACAAATTAACCACCCAGATTTGTAAGGTGAGTCAGGC -s simCow_chr6.simCow.chr6 510180 55 + 602619 TGAACTCCTTGAT-AATCA----TGATCTAG-ATCTCGCATCCCGAGTTTGGCTG-----TAGTGG -s simDog_chr6.simDog.chr6 499280 55 + 593897 TGAATATCAGGATCAACTA----CTACCTAGCAACTGGCCATCCGCATTTGAAAG-----TCC--T -s simHuman_chr6.simHuman.chr6 506760 57 + 601863 TGAATTTCTGGATCCACCA----CCACCTAGGAATTGGCCACCCACATTTGTAAG-----TCAGGG -s simRat_chr6.simRat.chr6 541307 65 + 647215 TGTGCAGCTCACCTCACTGGTGCTTACTTACAAA-TAACCACTCAGATTTGTAAGGTGAGTCAGAC - -a -s simMouse_chr6.simMouse.chr6 530150 16 + 636262 TTTAGAAGATCATGTG -s Anc0.Anc0refChr3 139642 15 + 222631 TTTGAAAG-TCATATG -s Anc1.Anc1refChr6 175001 15 + 197743 TTTGAAAG-TCATATG -s Anc2.Anc2refChr1 53043 15 + 142988 TTTGCAAG-TCATATG -s mr.mrrefChr3 82118 16 + 181027 TTTGAAAGATCATGTG -s simCow_chr6.simCow.chr6 510236 15 + 602619 TTTGGAAG-CCATATC -s simDog_chr6.simDog.chr6 499335 15 + 593897 TATGCAAG-TCATATG -s simHuman_chr6.simHuman.chr6 506817 15 + 601863 TTTGAAAG-TCATCTG -s simRat_chr6.simRat.chr6 541372 16 + 647215 TTTGAAAGGTTATGTG - -a -s simMouse_chr6.simMouse.chr6 530166 1 + 636262 A -s Anc0.Anc0refChr3 139657 1 + 222631 A -s Anc1.Anc1refChr6 175016 1 + 197743 A -s Anc2.Anc2refChr1 53058 1 + 142988 A -s mr.mrrefChr3 82134 1 + 181027 A -s simCow_chr6.simCow.chr6 510251 1 + 602619 A -s simDog_chr6.simDog.chr6 499352 1 + 593897 A -s simHuman_chr6.simHuman.chr6 506832 1 + 601863 A -s simRat_chr6.simRat.chr6 541388 1 + 647215 G - -a -s simMouse_chr6.simMouse.chr6 530167 6 + 636262 TTTAAG -s Anc0.Anc0refChr3 139658 6 + 222631 AGTAAA -s Anc1.Anc1refChr6 175017 6 + 197743 AGTAAA -s Anc2.Anc2refChr1 53059 6 + 142988 AGTAAA -s mr.mrrefChr3 82135 6 + 181027 TTTAAG -s simCow_chr6.simCow.chr6 510252 4 + 602619 A--AAA -s simDog_chr6.simDog.chr6 499353 6 + 593897 GGTAAG -s simHuman_chr6.simHuman.chr6 506833 6 + 601863 AATAAA -s simRat_chr6.simRat.chr6 541395 6 + 647215 TCTGGG - -a -s simMouse_chr6.simMouse.chr6 530173 29 + 636262 GAGATTTGGAGCTAGATTGCTCCTAAACC -s Anc0.Anc0refChr3 139666 29 + 222631 TGGATTTGGAGCTAGATTGGTCTGGAATC -s Anc1.Anc1refChr6 175025 29 + 197743 TGGATTTGGAGCTAGATTGGTCTGGAATC -s Anc2.Anc2refChr1 53067 29 + 142988 TGGATTTGGAGTTAGATTGGTCTGGAATC -s mr.mrrefChr3 82141 29 + 181027 TAGATTTGGAGCTAGATTGCTCTTAAACC -s simCow_chr6.simCow.chr6 510258 29 + 602619 TGGGTTTGGAGTCAGATTGGTCTGGAATC -s simDog_chr6.simDog.chr6 499361 29 + 593897 TGGATTTGGAGTTAGATTGGTTGGAAATC -s simHuman_chr6.simHuman.chr6 506841 29 + 601863 TGGATTTGGAGCTAGATTGGTCTGGAGTC -s simRat_chr6.simRat.chr6 541401 29 + 647215 TAGATTTGGAGTTAGATCACTCTTAAACC - -a -s simMouse_chr6.simMouse.chr6 530202 236 + 636262 AGTTTGCCTTGAATATAAACTTCATATCCACTAATATCCACTCAGCATGTCTCAAAAGACATTCATGTACTTACTTACTATGTTATCATAAGCACATGCATAACATGATTTCTTAATTGTTCCCCAAGCTGCGGGGGACTTTTCGGTTTTCTCCCCATCTCAAGTTTTGACCAAAAGGGGGGGTAGCAGGTTTGATGATAGTCCTTTGGTGCATTTTGCTTTTTGCAGTCTCTAGT -s Anc0.Anc0refChr3 139719 158 + 222631 AGTGTGGCTCAAACCCAACATCTATACCTCCTATTACCAACACAGCATGTTTGAATAGGCATGCAGGTAC---CTTACTAAGCTATGATAGGCACATGCATAACATGAATTCTCA---------------------------------------------------------------------------TTTGGTAATAGTTCTGTGGCACATCTTGATTTTTGCAGTCTCTAGT -s Anc1.Anc1refChr6 175078 158 + 197743 AGTGTGGCTCAAACCCAACATCTATACCTCCTATTACCAACACAGCATGTTTGAATAGGCATGCAGGTAC---CTTACTAAGCTATGATAGGCACATGCATAACATGAATTCTCA---------------------------------------------------------------------------TTTGGTAATAGTTCTGTGGCACATCTTGATTTTTGCAGTCTCTAGT -s Anc2.Anc2refChr1 53120 158 + 142988 AGTGTGGCCCAAACCCAACATCTATACCTCCTATTACCAACACAGCATGTTTGAATAGGCATGCAGGTAC---CCTACTAAGCTATGATAGGCACATGCATAACATGAATTCTCA---------------------------------------------------------------------------TTTGGTAATAGTTCTATGTCACATCTTGATTTCTGTAGTCTCTAGT -s mr.mrrefChr3 82170 162 + 181027 AGTTTGCCTTAAACATAAACTCCATATCCCCTAATATCCACTCAGCATGTCTCAAAAGACATGCATGTACTTACTTACTATGTTATCATAGGCACATGCATAACATGATTTCTCA--------------------------------------------------------------------------GTTTGATAATAGTTCTGTGGTGCATTTTGATTTTTGCAGTCTCTAGT -s simCow_chr6.simCow.chr6 510312 150 + 602619 AATGTGGCCCAAACCC-ATGTATCTATCTCCTATTACCCACACAGCATGTTTGAATAGGCGTGCAGGTAC---TCTACTAGATAATAGTAGGCACGTGAATGGCATGAATTCTCA---------------------------------------------------------------------------TTTGGTAATAATTAT------CATC-TGATTTCTGTAGGCTCTAGT -s simDog_chr6.simDog.chr6 499414 156 + 593897 AG--TAGCCCAAACTTAACATCTATACCTTTTATCACCAACACAGCATGTTTGAATAGGCATGGAGGTGC---CCTACTAAGCTATGATATGCACATGCATAACATGAATTATCA---------------------------------------------------------------------------ACTAGTAATAGTTCTATGTCATATCTTGGGTTCTGTAGTCCCTAGT -s simHuman_chr6.simHuman.chr6 506894 157 + 601863 AGTCTGGATCAAACCCAACATCTATACCTCCTACTACCAACACAGCATGTTTGGGTAGGCATGCAAGTAC---CTTACTAAGGTACGATAGGCATA-GCATAACTTGAATACTCA---------------------------------------------------------------------------TTTGGTAGTAGTTCTGTGGCACATCTTAATTTTTCCAGTCTCTAGT -s simRat_chr6.simRat.chr6 541430 162 + 647215 AGTTTGCCCTAAACATATACTCCACATCCCCTAGTGTCCACCCAGCATATCTCTAAAGACATGTATGTACTTAGTGACTATGTTATCCTGGGTACATGGTTAACATGATTTCTCA--------------------------------------------------------------------------GTTAGATAATAGTTATGTGGTGTATTTTGATTTTTGCAGTCGCTAGT - -a -s simMouse_chr6.simMouse.chr6 530438 2 + 636262 TG -s Anc0.Anc0refChr3 139877 2 + 222631 CA -s Anc1.Anc1refChr6 175236 2 + 197743 CA -s Anc2.Anc2refChr1 53278 2 + 142988 CA -s mr.mrrefChr3 82332 2 + 181027 TA -s simCow_chr6.simCow.chr6 510497 2 + 602619 CA -s simDog_chr6.simDog.chr6 499570 2 + 593897 CA -s simHuman_chr6.simHuman.chr6 507051 2 + 601863 CA -s simRat_chr6.simRat.chr6 541592 2 + 647215 TA - -a -s simMouse_chr6.simMouse.chr6 530440 2 + 636262 GT -s Anc0.Anc0refChr3 139880 2 + 222631 GC -s Anc1.Anc1refChr6 175239 2 + 197743 GC -s Anc2.Anc2refChr1 53281 2 + 142988 GC -s mr.mrrefChr3 82334 2 + 181027 GT -s simCow_chr6.simCow.chr6 510500 2 + 602619 AC -s simDog_chr6.simDog.chr6 499573 2 + 593897 GC -s simHuman_chr6.simHuman.chr6 507054 2 + 601863 GC -s simRat_chr6.simRat.chr6 541594 2 + 647215 GT - -a -s simMouse_chr6.simMouse.chr6 530442 19 + 636262 GATAAACCAGCTGATCTAC -s Anc0.Anc0refChr3 139889 19 + 222631 GACAGACTGGCTGATACAC -s Anc1.Anc1refChr6 175248 19 + 197743 GACAGACTGGCTGATACAC -s Anc2.Anc2refChr1 53290 19 + 142988 TACAGACTAGCTGATACAC -s mr.mrrefChr3 82343 19 + 181027 GATAAACTGGCTGATCTAC -s simCow_chr6.simCow.chr6 510509 19 + 602619 AACAGACTCACTGATGCAC -s simDog_chr6.simDog.chr6 499582 19 + 593897 TACAGACTAGCTGATATAC -s simHuman_chr6.simHuman.chr6 507063 19 + 601863 GACAGATTGGCTGATACAC -s simRat_chr6.simRat.chr6 541603 19 + 647215 AATGAACTGGCTGATCTAC - -a -s simMouse_chr6.simMouse.chr6 530461 78 + 636262 CATTCTGGTCAAAGTTAGAGTTGGAAACATAGAAACTGGGCTAAGCTGCGAGTGGTGCTGGATGAAGTTTATTGTCAG -s Anc0.Anc0refChr3 139908 78 + 222631 CACTCTGGTTAATGTTTAAGCTGGAAACATGGAAACTGGGCTAAGGTACATGTAGGGCTGAAAATGATGTCTTTTGAG -s Anc1.Anc1refChr6 175267 78 + 197743 CACTCTGGTTAATGTTTAAGCTGGAAACATGGAAACTGGGCTAAGGTACATGTAGGGCTGAAAATGATGTCTTTTGAG -s Anc2.Anc2refChr1 53309 78 + 142988 CACTGTGCTTAATGTTTAAGCTGGAAGCATGGAAACTGGGCTAGGGTACATTTAGGGCTGAAAATGATGTCCATTGAG -s mr.mrrefChr3 82362 78 + 181027 CATTCTGGTCAAAGTTAGAGTTGGAAACATAGAAACTGGGCTAAGCTGCAAGTGGTGCTGGATATAGTTTATTGTCAG -s simCow_chr6.simCow.chr6 510528 76 + 602619 CACTTT--TTGAAGTTTCAGCTGGAAGCATGAAAACTGAGCCAGTTTACATCTATGGGTGAGAAAGATGTCCATTGAG -s simDog_chr6.simDog.chr6 499603 78 + 593897 CGCTGTGCTTAATGTTTAAGCTGGAAGCATGGAAACTGGACTAGGGAGCATTTAGGGCTGAAAATGCTATCCACTGAG -s simHuman_chr6.simHuman.chr6 507082 78 + 601863 TACTCTGGTAAAGGTCTAAGCTGGAAACATGGAAACTGGGCTAAGGTACATGTAGGGCTGAAAATGATGTCTTTTGAG -s simRat_chr6.simRat.chr6 541622 78 + 647215 CATCCTGTACAAAGTTAGAGTTGAAAACATAGAAACTGGGCTAACCTGCAAGTGGTGCTGGACATAGTTTATTGTCAG - -a -s simMouse_chr6.simMouse.chr6 530539 36 + 636262 AAGCATGGGTATATGCAACATTAAGTTCACTCCTCC -s Anc0.Anc0refChr3 139993 29 + 222631 GAGCATGGGTATATCCACTGTCATCTT--TT----- -s Anc1.Anc1refChr6 175352 34 + 197743 GAGCATGGGTATATCCACTGTCATCTT--TTTCTGC -s Anc2.Anc2refChr1 53394 29 + 142988 GAGCATGTTTATATCCACTGTCCTCTT--TT----- -s mr.mrrefChr3 82440 36 + 181027 AAGCATGGGTATATGCAACATTAAGTTCATTCCTCC -s simCow_chr6.simCow.chr6 510611 29 + 602619 GAGGATGACTGTAACCACTGTCCTCTT--TT----- -s simDog_chr6.simDog.chr6 499688 29 + 593897 GAGCATGTTTATATCCATCGCCCTCTG--AT----- -s simHuman_chr6.simHuman.chr6 507167 34 + 601863 GAGCATGGGCATATCCTCTGTCATCTT--TTTCTGC -s simRat_chr6.simRat.chr6 541700 36 + 647215 AGGCATGGGTCTAGGCCACATTAAGTTCATTCCTCC - -a -s simMouse_chr6.simMouse.chr6 530575 2 + 636262 CT -s Anc0.Anc0refChr3 140022 1 + 222631 -T -s Anc1.Anc1refChr6 175386 2 + 197743 CT -s Anc2.Anc2refChr1 53423 1 + 142988 -T -s mr.mrrefChr3 82476 2 + 181027 CT -s simCow_chr6.simCow.chr6 510640 1 + 602619 -T -s simDog_chr6.simDog.chr6 499717 1 + 593897 -T -s simHuman_chr6.simHuman.chr6 507205 2 + 601863 CT -s simRat_chr6.simRat.chr6 541736 2 + 647215 CT - -a -s simMouse_chr6.simMouse.chr6 530577 101 + 636262 TTGTAGGTCTTAGGTTGTTTCTATGTTGAACCGTGTGGGGGATGTAGGACGCAGACTCAACAAGTAACGCAGTTGATGTTATTGGGAGGAGCCACATTAAA -s Anc0.Anc0refChr3 140023 58 + 222631 CTGTAAGTCTGAAGCTCCCTACATGTTGTG-------------------------------------------TGGTGTTGCTGGGAGGAGCCACAATGAA -s Anc1.Anc1refChr6 175388 58 + 197743 CTGTAAGTCTGAAGCTCCCTACATGTTGTG-------------------------------------------TGGTGTTGCTGGGAGGAGCCACAATGAA -s Anc2.Anc2refChr1 53424 58 + 142988 CTGTAAGACTGAAGCTCCCAATATGTTATG-------------------------------------------TGGTGTTGCTGGGAAGAGCCACAATGAA -s mr.mrrefChr3 82478 58 + 181027 CTGTAGGTCTTAAGTTGTCTCCATGTTGTG-------------------------------------------TGGTGTTACTGGGAGGAGCCACATTAAA -s simCow_chr6.simCow.chr6 510641 58 + 602619 CTGTAAGACTGCAGCTCCCCATATGTTATG-------------------------------------------CAGTGTTGATGACAAGAACCACAGTGAA -s simDog_chr6.simDog.chr6 499718 58 + 593897 CTGTAAGACTAAGGTGCCCAATATGTCATG-------------------------------------------TGGTGTTGCTGGGAAGAGCCAAAATGAA -s simHuman_chr6.simHuman.chr6 507210 58 + 601863 CTGTAAGTCTGAAGCTTCCTACATGTTGTG-------------------------------------------TGGTGTAGCGGGGAGGAGCCACAATGAA -s simRat_chr6.simRat.chr6 541738 58 + 647215 CTGTAGGTCTTAAGTTGACTCCATGTTGTG-------------------------------------------TAGTGTTACTGGGAAGAGCCATATCAAA - -a -s simMouse_chr6.simMouse.chr6 530678 41 + 636262 TGCAGTATTGAATATGATTTTCCAGAGAACAAGGATGTCAG -s Anc0.Anc0refChr3 140087 41 + 222631 TTCAGTAGTGAATATTAACTCCCAGAGAAAAAGAACCTCAA -s Anc1.Anc1refChr6 175452 41 + 197743 TTCAGTAGTGAATATTAACTCCCAGAGAAAAAGAACCTCAA -s Anc2.Anc2refChr1 53488 41 + 142988 TTCAGTAGTGCATATTGACTCCCAGAGAAAAAGAACTTCAA -s mr.mrrefChr3 82536 41 + 181027 TGCAGTAGTGAATATGATTTTCCAGAGAACAAGAACCTCAG -s simCow_chr6.simCow.chr6 510705 39 + 602619 GGCAGTAGTGCATATTGCCTCCCAGAGTAAAAGAACGTC-- -s simDog_chr6.simDog.chr6 499782 40 + 593897 TTCAATAGTGCTTATT-ACCCCCAGAGAAAAAGAACTTTAA -s simHuman_chr6.simHuman.chr6 507274 41 + 601863 TTCAGTAGTGAATATCAACTCCCAGAGAAGAAGAACCTCAA -s simRat_chr6.simRat.chr6 541796 41 + 647215 TGTAGAAGCAAATATGATTTTTCAGAGAACAAGATCCTCAG - -a -s simMouse_chr6.simMouse.chr6 530719 3 + 636262 CCA -s Anc0.Anc0refChr3 140128 3 + 222631 TAG -s Anc1.Anc1refChr6 175493 3 + 197743 TAG -s Anc2.Anc2refChr1 53529 3 + 142988 CAG -s mr.mrrefChr3 82577 3 + 181027 TCA -s simDog_chr6.simDog.chr6 499823 3 + 593897 CAG -s simHuman_chr6.simHuman.chr6 507315 3 + 601863 TGG -s simRat_chr6.simRat.chr6 541837 3 + 647215 TCA - -a -s simMouse_chr6.simMouse.chr6 530722 48 + 636262 GTATCCTTATTCTTAATGTGAGTCTACCAAATTCAGACATATTCAAAT -s Anc0.Anc0refChr3 140131 46 + 222631 ATATTCT-ATTCTTCAGCTGGGTGTACTAAAATCTGACACATTCAAA- -s Anc1.Anc1refChr6 175496 46 + 197743 ATATTCT-ATTCTTCAGCTGGGTGTACTAAAATCTGACACATTCAAA- -s Anc2.Anc2refChr1 53532 46 + 142988 ATACTCT-CTTCTTCAGCTGGGTGTACTAAAATCTGACACATTCAAA- -s mr.mrrefChr3 82580 48 + 181027 GTATCCTTATTCTTAATGTGAGTCTACCAAATTCTGACATATTCAAAT -s simCow_chr6.simCow.chr6 510744 42 + 602619 -TGCTCT-CTTCTTCAGCTCGGTGTACAAAAATC---CATGTTCAGA- -s simDog_chr6.simDog.chr6 499826 32 + 593897 ATA---------------TGGGTCTACTAAAATCTGACACATTCAAA- -s simHuman_chr6.simHuman.chr6 507318 37 + 601863 ATATTCT-ATCCATCAGCTGTATGTAGTAAAATCTGAC---------- -s simRat_chr6.simRat.chr6 541841 48 + 647215 GTATCCTTATTCTTAATGTGAGTTTACCAAATTCTGACAGATTCAAAT - -a -s simMouse_chr6.simMouse.chr6 530770 73 + 636262 CCACATCTGAAGCTCCATTATAAGAAGACTGCGTCTGAGTTATGGCCTAGAAATACTGGCCAGAGTCGTTAAC -s Anc0.Anc0refChr3 140177 22 + 222631 CCATAGCTGAAACTG----------------------------------------------A-----ATTAAT -s Anc1.Anc1refChr6 175542 27 + 197743 CCATAGCTGAAACTG----------------------------------------------AAAACCATTAAT -s Anc2.Anc2refChr1 53578 22 + 142988 CCATAGCTGAAACTG----------------------------------------------A-----CTTAAT -s mr.mrrefChr3 82628 73 + 181027 CCACATCTGAAACTCCATTATAAGAAGACTGCGTCTGAGTTATGGCCTAGAAATACTGGCCAGAGTCATTAAC -s simCow_chr6.simCow.chr6 510786 22 + 602619 CCATAGCTGAAACAG----------------------------------------------C-----CATTAA -s simDog_chr6.simDog.chr6 499859 22 + 593897 CCATAGCTGATACTG----------------------------------------------A-----CTTAGT -s simHuman_chr6.simHuman.chr6 507355 26 + 601863 -CGTGGCTGAAACTG----------------------------------------------AAAACCATTAAT -s simRat_chr6.simRat.chr6 541889 73 + 647215 CCACATCTAAAACTCCGTGATAAGAAGTCAGCATCCAAGTTGTGGCCTAGGAATACTTGCCAGCGTAACGGAC - -a -s simMouse_chr6.simMouse.chr6 530843 15 + 636262 TTGCATTTGTAGGTG -s Anc0.Anc0refChr3 140199 14 + 222631 TTTCATCTGCA-GTG -s Anc1.Anc1refChr6 175569 15 + 197743 TTTCATCTGCAGGTG -s Anc2.Anc2refChr1 53600 14 + 142988 TTTCATATGCA-GTG -s mr.mrrefChr3 82701 15 + 181027 TTGCATCTGTAGGTG -s simCow_chr6.simCow.chr6 510808 14 + 602619 TTTCACATGCA-TTG -s simDog_chr6.simDog.chr6 499883 14 + 593897 TTTCATATGCA-GTG -s simHuman_chr6.simHuman.chr6 507381 15 + 601863 TTTCATCTGCAGGCG -s simRat_chr6.simRat.chr6 541962 15 + 647215 TTGCATCCGTAGGTG - -a -s simMouse_chr6.simMouse.chr6 530858 4 + 636262 TGGG -s Anc0.Anc0refChr3 140213 4 + 222631 TGGG -s Anc1.Anc1refChr6 175584 4 + 197743 TGGG -s Anc2.Anc2refChr1 53614 4 + 142988 ACGG -s mr.mrrefChr3 82716 4 + 181027 TGGG -s simCow_chr6.simCow.chr6 510822 4 + 602619 AAGG -s simDog_chr6.simDog.chr6 499897 4 + 593897 ACAC -s simHuman_chr6.simHuman.chr6 507399 4 + 601863 TGGG -s simRat_chr6.simRat.chr6 541977 4 + 647215 TGAC - -a -s simMouse_chr6.simMouse.chr6 530862 16 + 636262 AAATCTTCCTTTCATA -s Anc0.Anc0refChr3 140217 16 + 222631 GAATCTTCCCTTCAGA -s Anc1.Anc1refChr6 175588 16 + 197743 GAATCTTCCCTTCAGA -s Anc2.Anc2refChr1 53618 16 + 142988 GAATTGTCCCTTCAGA -s mr.mrrefChr3 82720 16 + 181027 AAATCTTCCTTTCATA -s simCow_chr6.simCow.chr6 510826 16 + 602619 GGAAGCTTCCTTCAGA -s simDog_chr6.simDog.chr6 499902 16 + 593897 GAATTGTCCTTCCAGA -s simHuman_chr6.simHuman.chr6 507403 16 + 601863 GATTCTTCCCTTCAGA -s simRat_chr6.simRat.chr6 541981 16 + 647215 AAATTTTCCTTTCATA - -a -s simMouse_chr6.simMouse.chr6 530878 22 + 636262 TAGTCACTGTATGCCTAACTCC -s Anc0.Anc0refChr3 140233 22 + 222631 CAGACATTGTATGTTTATCTTT -s Anc1.Anc1refChr6 175604 22 + 197743 CAGACATTGTATGTTTATCTTT -s Anc2.Anc2refChr1 53634 22 + 142988 CAGACATTGTATGTTAATCTTT -s mr.mrrefChr3 82736 22 + 181027 TAGTCACTGTATGCCTAACTCC -s simCow_chr6.simCow.chr6 510842 21 + 602619 CAGACATCATATGTTCATCTT- -s simDog_chr6.simDog.chr6 499918 22 + 593897 CAGACATTGTATGTTAATCTCT -s simHuman_chr6.simHuman.chr6 507419 22 + 601863 AAGATATTGTATGTTTTTCCTT -s simRat_chr6.simRat.chr6 541998 22 + 647215 TAGTCACTGTATGCCTAACCCC - -a -s simMouse_chr6.simMouse.chr6 530900 29 + 636262 ATTTTCATTCCTTTTAGCACCACCCAGAT -s Anc0.Anc0refChr3 140255 29 + 222631 ATTTCCATGTTTTCTAATGTCACCCTTAT -s Anc1.Anc1refChr6 175626 29 + 197743 ATTTCCATGTTTTCTAATGTCACCCTTAT -s Anc2.Anc2refChr1 53656 29 + 142988 CTTTCCATGTTTTCTAATGTTACCCTTGT -s mr.mrrefChr3 82758 29 + 181027 ATTTTCATTCCTTTTAGCATCACCCTTAT -s simCow_chr6.simCow.chr6 510863 22 + 602619 -------CGTTTTCTAGTGTTACCCTTTT -s simDog_chr6.simDog.chr6 499940 29 + 593897 CTTTCCATGTTTTCGAATGTTGCCCCTGA -s simHuman_chr6.simHuman.chr6 507442 29 + 601863 ATTTCTATGTTTTCTAATGTCACCATTAT -s simRat_chr6.simRat.chr6 542020 29 + 647215 ATTTTCATTCCTTTTAGCATTACCTTTAT - -a -s simMouse_chr6.simMouse.chr6 530929 15 + 636262 TTGGTGTTCACCTTT -s Anc0.Anc0refChr3 140286 15 + 222631 TTGGTGTTTTCCCTT -s Anc1.Anc1refChr6 175657 15 + 197743 TTGGTGTTTTCCCTT -s Anc2.Anc2refChr1 53687 15 + 142988 TTAAAGTTTTCCCTT -s mr.mrrefChr3 82787 15 + 181027 TTGGTGTTCACCTTT -s simCow_chr6.simCow.chr6 510887 15 + 602619 TTAAAGCTTTCCCTT -s simDog_chr6.simDog.chr6 499971 15 + 593897 TTAAAATTTTTCCTT -s simHuman_chr6.simHuman.chr6 507473 15 + 601863 TTGGTGTTTTCCCTT -s simRat_chr6.simRat.chr6 542049 15 + 647215 TTGATGTTCGCCTTT - -a -s simMouse_chr6.simMouse.chr6 530944 12 + 636262 GGAAAACTGCAG -s Anc0.Anc0refChr3 140303 8 + 222631 GACAGAC----A -s Anc1.Anc1refChr6 175674 8 + 197743 GACAGAC----A -s Anc2.Anc2refChr1 53704 8 + 142988 GACAGAC----A -s mr.mrrefChr3 82804 12 + 181027 GGAAAACTGCAG -s simCow_chr6.simCow.chr6 510904 8 + 602619 GACACAC----A -s simDog_chr6.simDog.chr6 499988 8 + 593897 GACAGTC----A -s simHuman_chr6.simHuman.chr6 507490 8 + 601863 GACAGAC----A -s simRat_chr6.simRat.chr6 542066 12 + 647215 GGAAAATTGCAT - -a -s simMouse_chr6.simMouse.chr6 530956 43 + 636262 CATATCCAAGTTCCCAAAGGTCACCTGTAAACTGCATCATATC -s Anc0.Anc0refChr3 140311 5 + 222631 TGTA--------------------------------------C -s Anc1.Anc1refChr6 175682 5 + 197743 TGTA--------------------------------------C -s Anc2.Anc2refChr1 53713 5 + 142988 TGTA--------------------------------------T -s mr.mrrefChr3 82816 5 + 181027 CATA--------------------------------------C -s simCow_chr6.simCow.chr6 510913 5 + 602619 TATA--------------------------------------T -s simDog_chr6.simDog.chr6 499997 5 + 593897 TGTA--------------------------------------T -s simHuman_chr6.simHuman.chr6 507498 5 + 601863 TGTA--------------------------------------C -s simRat_chr6.simRat.chr6 542078 5 + 647215 CATA--------------------------------------A - -a -s simMouse_chr6.simMouse.chr6 530999 15 + 636262 CAAGTTCCCAAAGGT -s Anc0.Anc0refChr3 140319 15 + 222631 CAAGTTCTCTAGTGG -s Anc1.Anc1refChr6 175690 15 + 197743 CAAGTTCTCTAGTGG -s Anc2.Anc2refChr1 53728 15 + 142988 CAGGTACTCTAATGA -s mr.mrrefChr3 82821 15 + 181027 CAAGTTCTCAAGGGG -s simCow_chr6.simCow.chr6 510928 12 + 602619 ---GTACACTAATGA -s simDog_chr6.simDog.chr6 500017 14 + 593897 CAGGTACTCTA-TGA -s simHuman_chr6.simHuman.chr6 507506 15 + 601863 CGAGTTCTCTAGTGG -s simRat_chr6.simRat.chr6 542083 15 + 647215 TAAGTCCTTGAGCGG - -a -s simMouse_chr6.simMouse.chr6 531020 633 + 636262 TGGTTatacagaaagactttcaatgttggtgcatgacctaggaatggtaaatttccctgttgtcgagaacagtcaatacagggtgtcagctaaaaacaatagatggcaccaagtgacaacaaataccctaccttacttctcctcttcaacttttgtttctaactatcactaaccctatcctttcgctacaaactttgtccataaagtgcgcttagagaagttggggacttgatcccttaacaaaggcaaagatttgtgcccatttgtcctgggcactttgatcactacggatgggtagaaattctgctggaagagattatgaccagtgcctaaaagaggaggcaaaggaagagtttatgaccagctctataagaggaccagccctataagaggagcaaagcaaaagttctgttggatgggatcgtcttgctgctggacctgacaggcactctgaacacatacaatgagatgcctaatagggtctttgattgattaccaatcccacccaccgcacactagccttgagcaaaatttgcaagaccccaaggacccctggatattggaatacatagaaggcctcccccctgctcagagggccagaagtgcaggcatattagtccttataaaagtcgt -s mr.mrrefChr3 82842 90 + 181027 TGGTTatacagaaagactttcaatgttggtgcatgacctaggaatggtaaatttccct-------agaacagtcaatacag--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------tccttataaaagtcgt -s simRat_chr6.simRat.chr6 542104 90 + 647215 TGGTTacacagaagaaccctcaaggttggtgcatgatttaggagcggtaaatctccct-------aaaagattcagtacag--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ccttgataagattgat - -a -s simMouse_chr6.simMouse.chr6 531653 7 + 636262 actgaat -s mr.mrrefChr3 82932 7 + 181027 actgaat -s simRat_chr6.simRat.chr6 542749 7 + 647215 actgcat - -a -s simMouse_chr6.simMouse.chr6 531660 6 + 636262 ctgttc -s mr.mrrefChr3 82939 6 + 181027 ctgttc -s simRat_chr6.simRat.chr6 542759 6 + 647215 ctgttc - -a -s simMouse_chr6.simMouse.chr6 531666 379 + 636262 agtgggtggatgctctagatcatgtcaaatgaaaacaaactccagttcttacataaggagtatgaacttgataaatatggtcactctcactcactgagtgaagatgtgcaggtagcacttcctaccgacagaatagggaatgacaaacttcaattttcgctcacgcttagaataaagtaccacttagctggagtgaatctcaatgtagcttacagagtaggagctgtgatctattgtaccaagctctctatttaaagtgatctgtggcatctggggtagacacaaaaaaataactgaaattactactctgtctacaccgattaaagcttgaaactaaagtcctctacctgatgcttttcagcttgatattcatcacatt -s mr.mrrefChr3 82945 361 + 181027 agtgggtggatgctctagatcatgtcaaatgaaaacaaactccagttcttacataaggagtatgaacttgataaatatggtcactc------actgagtgaagatgtgcaggtagcacttcctaccgacagaatagggaatgacaaacttcaattttcgct------tagaataaagtaccacttagctggagtgaatctcaatgtagcttacagagtaggagctgtgatctattgtaccaagctctctatttaaagtgatctgtggcatctggggtagacacaaaaa-----ctgaaattactactctgtctacaccg-ttaaagcttgaaactaaagtcctctacctgatgcttttcagcttgatattcatcacatt -s simRat_chr6.simRat.chr6 542774 361 + 647215 AGAgggtggacaatctacatcatgtcgaatgaaaacaaactacagttcttacatgaggaggatgaacttgataaatatggtcactc------aataagtaaaggtgagcaggtagtacttcctacccacgaaacagagtatgacaaactaggttttttgct------tagaataaagtgccacttagctggagtgaatcttaatatatcttacacagtgggagatgtgctccaatgtactaagctctctatccagagtgatctgccacatctagggtaaacacaaaaa-----ctgaaattactactccatctacactg-ttaaagcttgaaactaaagccctctaccttttgcttttcaccttaatattcatcacatt - -a -s simMouse_chr6.simMouse.chr6 532045 70 + 636262 gcagttcctcacaaggttaagcttgctctgtgttactagctcttttagccattcgatatcacatgctggg -s mr.mrrefChr3 83306 70 + 181027 gcagttcctcacaaggttaagcttgctctgtgttactagctcttttagccattcgatatcacatgctggg -s simRat_chr6.simRat.chr6 543137 70 + 647215 gcagttcctcacaaggttaagcttgttctgtgttactagctcttttagccactacatatcagatgttgga - -a -s simMouse_chr6.simMouse.chr6 532115 19 + 636262 attgacctttgataggccc -s mr.mrrefChr3 83376 19 + 181027 attgacctttgataggccc -s simRat_chr6.simRat.chr6 543237 19 + 647215 attgattgatgataggccc - -a -s simMouse_chr6.simMouse.chr6 532134 314 + 636262 ttcatcttgcattagtgcctggccaacgagataggtaaataagaggaatacaatcttggggagagaaatcagatgcctatacttctctagtaataccacagtggttgcagtgtgtattgttggtaagcccgatgtctctttttttgggggagaaagcaagatcatcaggtgatgggaaacctgttgaaccgtatgatgcttatcacactgaccctgtcacagcatgttatcttcatcatgacaccgcatgtccaaaacgttatttgaaatataacacccaccaacaggcagagaaattgctggaaatgtgagtc -s mr.mrrefChr3 83395 214 + 181027 ttcatcttgcattagtgcctggccaacgagataggtaaataagaggaatacaatcttggggagagaaatcagatgcctatacttctctagtaataccacagtggttgcagtgtgtattgttg----------------------------------------------------------------------------------------------------catgttatcttcatcatgacaccgcatgtccaaaacgttatttgaaatataacacccaccaacaggcagagaaattgctggaaatgtgagtc -s simRat_chr6.simRat.chr6 543257 214 + 647215 tttatctcgtattagtgtctgaccaacaagatagggaaataagagaaatgcaattgcggggagagaagtcgcttggctatagttcgttggtgctaccatggtggttgctgtgtgtattgttg----------------------------------------------------------------------------------------------------catgttatcctaatcatgacactgcatgtccaaaacattatttgaaatataacacccaccaacaggcagagaaatggctggatatgtgagtc - -a -s simMouse_chr6.simMouse.chr6 532448 50 + 636262 agaacgctcaaatatgactgtgtatcacagagaggtataataccatagta -s mr.mrrefChr3 83609 37 + 181027 agaacgctcaaatatgactgtgtat-------------aataccatagta -s simRat_chr6.simRat.chr6 543476 37 + 647215 agaatgcttgaatgtgaatgtgttt-------------gataccattgta - -a -s simMouse_chr6.simMouse.chr6 532498 560 + 636262 tatgaataccttttccaaccgtgttgctaggaaggagaagatggagaataaagatagatacctctaatgttgagacagagtggaattaaacaaacaaaccttctgttgtgactgaggctggattagtagaagtgctgtaaggataacttccatatccagaacacagcgggcagcatggaactagtgtctgatggttcttctgggatacttggtgatgggaaaggctataacaaacatgaaacatgctgtttaacatgcagttttgggtggaaaagataagtactcgctgtctctctttttccaaggagtaacacccatcccatcggtaagtcagttgcggggtgttcacttgaagtgttaaaactcctacaacaatggcattatgaagaacggactaaagatgttggccctccccacagctaggtgcacccacccaacagccacactcagtgcatctgtctgacagtggtgcaatatgggaagaatacacagtagttaataaaatgggcagggaattggaaaggaggctatgggtggcagtactgtcagctggggacgtt -s mr.mrrefChr3 83646 313 + 181027 tatgaataccttttccaacc---ttgctaggaaggagaagatggagaataaagatagatacctctaatgttgagacagagtggaattaaacaaacaaaccttctgttgtgactgaggctggattagtaga-gtgctgtaaggataacttccatatccagaacacagcgggcagcatggaactagtgtctgatggttcttctgggatactt-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ccctccccacagctaggtgcacccaccca----------------------------------------------gaatacacagtagttaataaaatgggcagggaattggaaaggaggctatgggtggcagtactgtcagctggggacgtt -s simRat_chr6.simRat.chr6 543515 313 + 647215 taagcataccttttccaacc---ttactaggaaggagaagaaggaaaaaagagatagttacctctgatgttgaagcagaatggaattaaacaaagacaccctctgttgtgattgaagctggattagtgga-gttctgtagggataacttcaatatcctgaacacagctggcagcatggaactggtgtctgacgtttcttctgagaccctt-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ctctccccacagataggtgcacccactca----------------------------------------------gaatacacagtagttaataaaaagggcagggaattggaaaggagggtttgggttgcagtagtgtcagctggggacatt - -a -s simMouse_chr6.simMouse.chr6 533058 25 + 636262 gctggaccacatctgaaatatccag -s mr.mrrefChr3 83959 25 + 181027 gctggaccacatctgaaatatccag -s simRat_chr6.simRat.chr6 543859 25 + 647215 gctggacttcatctaaaacatccag - -a -s simMouse_chr6.simMouse.chr6 533083 51 + 636262 tgagaacatggaaccatcaggtatggagataatgagtagccattaggctat -s mr.mrrefChr3 83984 50 + 181027 tgagaacatggaaccatcaggtatggagataatgagtagc-attaggctat -s simRat_chr6.simRat.chr6 543885 50 + 647215 tgagcacattgactgaccagatatggaaacaatgaggaaa-attaggctat - -a -s simMouse_chr6.simMouse.chr6 533134 102 + 636262 acatttatactacactggaccgacttaaggtgtcaatttactagaatccaagagcacaaaatttttttcaaccgcaaaagtgattcttgggcttaggctccc -s mr.mrrefChr3 84034 102 + 181027 acatttatactacactggaccgacttaaggtgtcaatttactagaatccaagagcacaaaatttttttcaaccgcaaaagtgattcttgggcttaggctccc -s simRat_chr6.simRat.chr6 543937 102 + 647215 acattcatatcacactggaccatcttaaggtgtcaattcactagaagccaagaacacaatattatttgaaggcacacaagtgattcatgggcttaggttttt - -a -s simMouse_chr6.simMouse.chr6 533236 50 + 636262 gtaccctgtattgaaataacagataaaaaccacttttttccagagacagg -s mr.mrrefChr3 84136 50 + 181027 gtaccctgtattgaaataacagataaaaaccacttttttccagagacagg -s simRat_chr6.simRat.chr6 544144 50 + 647215 gagccttcttttcaaatatcagatgaagaccatttttttccaaagacagg - -a -s simMouse_chr6.simMouse.chr6 533286 403 + 636262 attagatccatggcatagccctccctataatagctagcacatgaactgcttacacaaggtgactctctctgaagtgcaccgttgacacatgagccccggactcaggtgtctattttggcttctgaactgttggcacctgaaatgcaacctggcaaacaactgacacaggacctacttaatgacgatgcaagcaacagcatacctgagcaccctaactgtgtgagtgtatcttagttttgtctcagtttttgagcccaacgggctatgggcttggggatcagctgtacatggagacacatcactttgaaatacacgtccatgactcaaatcaacaactatctacccacccgcctacatgcggatcgtgttttgcctgcatccatatcaacaggatggtatacca -s mr.mrrefChr3 84186 392 + 181027 attagatccatggcatagccctccctataatagctagcacatgaactgcttacacaaggtgactctctctgaagtgcaccgttgacacatgagccccggactcaggtgtctattttggcttctgaactgttggcacctgaaatgcaacctggcaaacaactgacacaggacctacttaatgacgatgcaagcaacagcatacctgagcaccctaactgtgtgagtgt-----------gtctcagtttttgagcccaacgggctatgggcttggggatcagctgtacatggagacacatcactttgaaatacacgtccatgactcaaatcaacaactatctacccacccgcctacatgcggatcgtgttttgcctgcatccatatcaacaggatggtatacca -s simRat_chr6.simRat.chr6 544199 392 + 647215 atcaaatcagtggcatagccctcccgatcatacctaacatttgaaccactcactcaaggtaactctatctggagtgcactgttagcacatgaactgctgactcaggtgcctattttggttttcggactgttggagcctggaatgccacttggctaacaactgacacaggacctacctaacgaggatgctagcaacagcgttcctgagcaccctaattttgcgagagt-----------gcctgagtatttgagcccagtgggctatgggcttggggctcagctgtacctggagacacatcacttcgaaatacacatccataactcaaatcaacaactatccaccaacccccctacatgtggatcatattttgcctgcatccatatcaacaggatggtatatca - -a -s simMouse_chr6.simMouse.chr6 533689 9 + 636262 cacagcaga -s mr.mrrefChr3 84578 9 + 181027 cacagcaga -s simRat_chr6.simRat.chr6 544593 9 + 647215 cagagcagt - -a -s simMouse_chr6.simMouse.chr6 533698 115 + 636262 tagatttgacatcggacggagaatacttgcttacaaatgtgctggggggataatacttacttatgtcgccagagagatgagcctacacattggagaaaaacacaggatgcgaatg -s mr.mrrefChr3 84587 112 + 181027 tagatttgacatcggacggagaatacttgcttacaaatgtgctggggggataatacttacttatgtcgccagagagatgagcctacacattggagaaaaacacaggatg---atg -s simRat_chr6.simRat.chr6 544605 112 + 647215 ttggtttgacatcggacggagaacacttgcatacaactgtggtggggtgataatactcacttatgtcgccatagagatgagagaacacaattgaaagaaatgcaagatg---acg - -a -s simMouse_chr6.simMouse.chr6 533813 90 + 636262 gtatgttgggagtacatgggagcctccacaaggcacccgactaagagcggatcaaatactaattcactgtggtggtggagatgaactgca -s mr.mrrefChr3 84699 90 + 181027 gtatgttgggagtacatgggagcctccacaaggcacccgactaagagcggatcaaatactaattcactgtggtggtggagatgaactgca -s simRat_chr6.simRat.chr6 544719 90 + 647215 atacgttgggaggacatgggagcccccacaaggccctgaactaagtgcagatggaatactcgttcactgtggtggtggacatgaactgca - -a -s simMouse_chr6.simMouse.chr6 533903 343 + 636262 tgactggatattcccaaatagcaaatagtcccgagccaataatgactgtgggcccacacattatgatgtagcactcactggttataaagactcacatacccagatccgacttatcacactcatggttaccaacaaactgtggatttacccatcatgctgcagcactcattggctcattttatcacggctatgggagtcccccaactgaggctcagtacagcacataagatttgtagagcgaccatgatggtagaagaaatggctccccttcgtatgggtaacctctttagaaaggtttaatatactttgcgaaaggaatcatctaagaagaataacattgttg -s mr.mrrefChr3 84789 152 + 181027 tgactggata-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------gtcccccaactgaggctcagtacagcacataagatttgtagag------tgatggtagaagaaatggctccccttcgtatgggtaacctctttagaaaggtttaatatactttgcgaaaggaatcatctaagaagaataacattgttg -s simRat_chr6.simRat.chr6 544812 152 + 647215 tggctggata-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------gttccaagactgaggctcagtagagcacataaaattagtagag------tgatggtggaagaagtgcctccccttcatatgggtaacctctttagaaaggtttagtatactttgcctaaagaatcatctaaaaagactagcattgttg - -a -s simMouse_chr6.simMouse.chr6 534246 137 + 636262 acaatatggtgagtatactaatgctgagtcattctgtgcttaggggcatagtggatacgcatgcttgacatcaactctgccatcaaacggagtcatttcagtgcctgtgacatagtggcctaactatttccctatta -s mr.mrrefChr3 84941 133 + 181027 acaatatggtgagtatactaatgctgagtcattctgtgcttaggggcatagtggatacgc----ttgacatcaactctgccatcaaacggagtcatttcagtgcctgtgacatagtggcctaactatttccctatta -s simRat_chr6.simRat.chr6 544965 133 + 647215 agattatggcaattagactaatgctgagtcattctgtgcttaggggcatagtggatacac----ttgacatcaactctgctatcaaacagagttattttaatgcccgaggcataatggtctaactatttccttatta - -a -s simMouse_chr6.simMouse.chr6 534383 130 + 636262 cgttgctttgaatagcttggaagggtggtctttccctttatgacttgttagctggctaggtgtacctctattaggaactgtattgatggaagattgtctcagccctatcattgagaaaggccttaggcat -s mr.mrrefChr3 85074 130 + 181027 cgttgctttgaatagcttggaagggtggtctttccctttatgacttgttagctggctaggtgtacctctattaggaactgtattgatggaagattgtctcagccctatcattgagaaaggccttaggcat -s simRat_chr6.simRat.chr6 545124 130 + 647215 cattgcttgggatagctaggaagggtggtctttccccctatgccttgtcatctggcctggtgtactctgataagggaatatactgacggaagattctctgagccctatcattgtaaaaggccttagacat - -a -s simMouse_chr6.simMouse.chr6 534513 7 + 636262 agccttc -s mr.mrrefChr3 85204 7 + 181027 agccttc -s simRat_chr6.simRat.chr6 545258 7 + 647215 acccttc - -a -s simMouse_chr6.simMouse.chr6 534520 10 + 636262 actggagctt -s mr.mrrefChr3 85211 10 + 181027 actggagctt -s simRat_chr6.simRat.chr6 545266 10 + 647215 actggaattt - -a -s simMouse_chr6.simMouse.chr6 534530 6 + 636262 ccatca -s mr.mrrefChr3 85221 6 + 181027 ccatca -s simRat_chr6.simRat.chr6 545296 6 + 647215 ccgtca - -a -s simMouse_chr6.simMouse.chr6 534536 132 + 636262 tccacatgaaggtctttctaatagttaaatagagacccgacgctgtccactagaagcagtgtcctgcagacacagagttactataaaaatggtgacctctgatattgtctttatggtggactgtaaggctca -s mr.mrrefChr3 85227 131 + 181027 tccacatgaaggtctttctaatagttaaatagagacccgacgctgtccactagaagcagtgtcctgcagacacagagttactataaaaatg-tgacctctgatattgtctttatggtggactgtaaggctca -s simRat_chr6.simRat.chr6 545303 131 + 647215 tccataccaaggtctttcttatagttaagtagagagccagggttgtcaaccagaagcagtgtcctgcagacacagggttactatgaaaatg-tgacttctgatattgccatttcggttgactgtaaggctca - -a -s simMouse_chr6.simMouse.chr6 534668 327 + 636262 tattccccagtaactgcattcggcacttgaactgtaacttgacaggctgttcttttatagtcgatgcctcccagattgtagtgtgacacagggcattttgctttcaggcaatggaccggatgagggtcaactaactaccacctgccacttcgctatgggggtcagatgaggtgagtaatacatgtgcttgggttggatccaactatggtaaccaatctggcttggatgattagcaatgctccgagtggagtgacagaatggtaattgggaaggaacgccaccacaccccagtagatcggtcatcaatgttatgaagatagtggttcc -s mr.mrrefChr3 85358 302 + 181027 tattccccagtaactgcattcggcacttgaactgtaacttgacaggctgttcttttatagtcg---cctcccagattgtagtgtgacacagggcattttgctttcaggcaatggaccggatgagggtcaactaactaccacctgccacttcgctatgggggtcagatgaggtgagtaatacatgtgcttgggttggatccaactatggtaaccaatctggcttggatgattagcaatgctc----------------------attgggaaggaacgccaccacaccccagtagatcggtcatcaatgttatgaagatagtggttcc -s simRat_chr6.simRat.chr6 545441 302 + 647215 taatccccactaactgcgtatggcacttgaactgtaatgtgacaggctgttctattatagtca---cccctcagattgtaaggaaacacagggcattttgcttttaggctatggctaggatcgaagtcaactaactatcaccagccacttcataatgggggtcaaatgaggtgagtaatataccttcatgggttggatccaattatggtaactaatcttgctgggatgatcagcaatgcac----------------------attggcaaagaacgccaccacaccccagcagcttggtcaccaatgttctgaagatagtggttca - -a -s simMouse_chr6.simMouse.chr6 534995 43 + 636262 ataggccatcaatcttgacaccttgcaaggtgtcaaaatctaa -s mr.mrrefChr3 85660 43 + 181027 ataggccatcaatcttgacaccttgcaaggtgtcaaaatctaa -s simRat_chr6.simRat.chr6 545752 43 + 647215 ataggtcatcaatcttgacaccttgcaaggtctgggaatctag - -a -s simMouse_chr6.simMouse.chr6 535038 190 + 636262 cttgtgcaattggacaagtattttcgtcccaagcccaacacaggctacagtagtgcaccaccctatccttgctcggatgatatctggcgtcacttccaaggttggctgtcaacatagattgagagacagtaggagacagtgtttacgaacggacatcactggaaaagaccctcttggtgttttgttctta -s mr.mrrefChr3 85703 174 + 181027 cttgtgcaattggacaagtattttcgtcccaagcccaacacaggctacagtagtgcaccaccctatccttgctcggatgatatctgg---------------tggctgtcaacatagattgaga-acagtaggagacagtgtttacgaacggacatcactggaaaagaccctcttggtgttttgttctta -s simRat_chr6.simRat.chr6 545809 174 + 647215 cttgtgcaattggacaagtatttttgtcccaagcccaacacaggctacagtagtgcctcaccccatcctaactgggatgatatctgg---------------gggCTGTCAACGTATGTTGAGA-ACAGTGAAAGACAGTgtttgcgagcagacatcgctggaaaagatcttcttagcagtttgttctta - -a -s simMouse_chr6.simMouse.chr6 535228 57 + 636262 actgtactcctcaccttgcttggaagatgactcctccaaacccaaataacacctgaa -s mr.mrrefChr3 85877 56 + 181027 actgtactcctcaccttgcttggaag-tgactcctccaaacccaaataacacctgaa -s simRat_chr6.simRat.chr6 545996 56 + 647215 attgtacgtcttaccttgcttggaag-tgactactacagatccaaataacacctgag - -a -s simMouse_chr6.simMouse.chr6 535285 26 + 636262 aagcacttcagtccccctgagaatga -s mr.mrrefChr3 85933 20 + 181027 aagcact------cccctgagaatga -s simRat_chr6.simRat.chr6 546053 20 + 647215 aagcact------cccctgacaatga - -a -s simMouse_chr6.simMouse.chr6 535311 378 + 636262 agctggtgaagctgacagagttcaaaggtctatggatatccctaggtattgagatcggatagtaccagaacatcaatgggtgggcttagcttcaccatgcaagcttggattgggagcaattgctatgcatgtactggcctaagccaggaggtgtaatagaagtggacaatcggatatagcatatcacatgaatgttttagccttggctgcaggaaggttgcaactacaagcagtgccgattctactaggatgggacccagaccctggtgggatgtactgcatgttgactctctaacataataagacataataagaacacgtgggaaaatgagatatgtacaggcttgacagtcctatttcccgaatcacatagaccaa -s mr.mrrefChr3 85953 359 + 181027 agctggtgaagctgacagagttcaaaggtctatggatatccctaggtattgagatcggatagtaccagaacatcaatgggtgggcttagcttcaccatgcaagcttggattgggagcaattgctatgcatgtactggcctaagccaggaggtgtaatagaagtggacaatcggatatagcatatcacatgaatgttttagccttggctgcagga-ggttgcaactacaagcagtgccgattctactaggatgggacccagaccctggtgggatgtactgcatgttg-ctctctaacataataaga----------acacgtgggaaaatgagatatgta-------gacagtcctatttcccgaatcacatagaccaa -s simRat_chr6.simRat.chr6 546078 359 + 647215 agcacataaagctgatagagttcaaaggtctatggatatccctaggtattgggattgggtactaccaaaacatcaatgggtgggcttagattcaccaggcaagcttggaatgggaacaattgctatgcatgtacaggcctaagtctgggtgtgtaatgcaagtggacaatcggatatagcatatttcacaaacgtctgagccttggctgcagga-ggttgcccatacaagcagtgctgaatctactagggtgagacccggaccctggttggaagtactgcatggtg-ctctccaacataataaga----------acacctgaggaaatgagatgtgta-------gacagtcctatttcctgaattgcgtagaccaa - -a -s simMouse_chr6.simMouse.chr6 535689 137 + 636262 gattccaaccttttcaacagacagtctgagtcatccatcttgcttcctgcaaaaagtgacttgattcaataaatcagttgaccaactatctccttgtactcacatccctaatgtatctggagattcacccaacaaga -s mr.mrrefChr3 86312 137 + 181027 gattccaaccttttcaacagacagtctgagtcatccatcttgcttcctgcaaaaagtgacttgattcaataaatcagttgaccaactatctccttgtactcacatccctaatgtatctggagattcacccaacaaga -s simRat_chr6.simRat.chr6 546446 137 + 647215 ggttccagccttttccgcagacaatctggatcatccatcttgtttcatgaagaaagtgactttattcaataaatcagttgtccaactatctacttgtactcacatcactaatgtcactggagagtcatcccacagga - -a -s simMouse_chr6.simMouse.chr6 535826 29 + 636262 ttatttggaaaccctgcacatatcacatg -s mr.mrrefChr3 86449 29 + 181027 ttatttggaaaccctgcacatatcacatg -s simRat_chr6.simRat.chr6 546584 29 + 647215 ttatttggtggcgctccacaaatgtcaca - -a -s simMouse_chr6.simMouse.chr6 535855 140 + 636262 ttggttgtaactggataaggacttgcacccttattttgctcgccattccctcttcctcttcataaacacttcacaaatacccaagtacctgtacatgcataggaatcacttagatatcgccaattcattcaggaccataa -s mr.mrrefChr3 86478 139 + 181027 ttggttgtaactggataaggacttgcacccttattttgctcgccattccctcttcctcttcataaacacttcacaaatacccaagtacctgtacat-cataggaatcacttagatatcgccaattcattcaggaccataa -s simRat_chr6.simRat.chr6 546663 139 + 647215 ttgtctctaactggataaggacttgcacccttgttttgcttgccattcctttttcctctttataaacactttgcaaatgccaaagaaattgtacat-catatgaattactgagatatcatcaatttatccgggaccaaaa - -a -s simMouse_chr6.simMouse.chr6 535995 350 + 636262 atggattaatgccatatatttcaaccagcagttgattataagctattcctataactcagccgaagggtatcatcagtcacttggatacaatgagccaaatagcattgggagaacaggctaactctggataagattttggctggcactggcggtacatatttcatgctgaggggaaatcaccatctgcacatccagaagaacacagttccaaatggaactattagaaagacattgcaaggacctataatgctggctatggagtcggtggtaaacacaggtaccgatgatcctttctcggggtggtcagagggctggtttggccactcgaagggctccatagctctggtacC -s mr.mrrefChr3 86617 336 + 181027 atggattaatgccatatatttcaaccagcagttgattataagctattcctataactcagccgaagggtatcatcagtcacttggatacaatgagc-aaatagcattgggagaacaggctaactctggataagattttggctggcactggcggtacatatttcatgctgaggggaaatca--atctgcacatccagaagaa----gttccaaatggaactattagaaagacattgcaaggacctataatgctggctatggagtcggtggtaaacacaggtaccgatgatcctttctcggggtggtc-------tggtttggccactcgaagggctccatagctctggtacc -s simRat_chr6.simRat.chr6 546803 336 + 647215 atggattaattcgatatatttcagtcagcagtggattatgagctattcatgtaactcagccgaagggtatcatcagatacttggatacaatgagc-agataggattgggtgaacaggataactctggataaaattttggctgacactggcagtacatgtttcatgctaggagtacatca--atctgtacatccaaaagaa----gctccaaattgaactattaaaaagacattgcagggatttatagtgctggccatggtgttggtggtaaacacaggtatagatggtcctttcttggggtggtt-------tggtttggccactcgaaggggtccatggctctggaact - -a -s simMouse_chr6.simMouse.chr6 536579 16 + 636262 tgatcattgttcccaa -s mr.mrrefChr3 87190 16 + 181027 tgatcattgttcccaa -s simRat_chr6.simRat.chr6 547384 16 + 647215 caaacattgtttccaa - -a -s simMouse_chr6.simMouse.chr6 536595 104 + 636262 aacatacagaaggcagctgttggattccatgccatcccctgtatgcagagtctggcccagaggtacctgtaacagaacagcaatgaaaactaagtagatgtctg -s mr.mrrefChr3 87206 94 + 181027 aacatacagaaggcagctgttggattccatgccatc-------tgcagagtctggcccagaggtacctgtaa---aacagcaatgaaaactaagtagatgtctg -s simRat_chr6.simRat.chr6 547401 94 + 647215 aacgcacagagggcagctgtcagattttgccccatc-------tgcagagtctggcccagaggtaattgtaa---gacagcaaggaaaactaagcagatgtcca - -a -s simMouse_chr6.simMouse.chr6 536699 137 + 636262 atgctttccaactgaacaatttgctgtttctagaaacaaagctgaattcacacttaaatgaggatgagagtaaatgcattttagacgccttgaacatcaaaaggtcctaaatagaaatgagaaaaatgacaacaaat -s mr.mrrefChr3 87300 136 + 181027 atgctttccaactgaacaatttgctgtttctagaaacaaagctgaattcacacttaaatgaggatgagagtaaatgcattttagacgccttgaacatcaaaaggtcctaaatagaaatgagaaaaa-gacaacaaat -s simRat_chr6.simRat.chr6 547502 136 + 647215 atgatttgcaactgaataatttgctggttctagaagcaaggctgagttcacacttaaatgaggatgcgagtaattgctttctagacactttgaacatcaaaaggtcctatatagaaataagacaaa-ggtaccaaat - -a -s simMouse_chr6.simMouse.chr6 536836 22 + 636262 aattagcagttatgtagaaatg -s mr.mrrefChr3 87436 22 + 181027 aattagcagttatgtagaaatg -s simRat_chr6.simRat.chr6 547683 22 + 647215 TGTTTACATTTCTACAGAACTG - -a -s simMouse_chr6.simMouse.chr6 536858 283 + 636262 taatcacacacatctggtctctacagccaagTCCGTCACAACTGTTCTATGAATCTGAGTGCTATAGCTAAGACGTGTAAGTCATAAGTTGGATTACCTTGCTACAGGTATTAATGCAAGTTGGATTTACTGAATCACCTCAGATTAAAGGATCACACACACTTGGATAGCTTTGGAGCAGAATTGTAATTAATAATTGTAGGGCTTCATTACAAAGTGTGGCACCATTTCTTGGCTCAAATGAAAAACCCTGCACTAGCAAATCACTTCAGGAATAGAATTT -s mr.mrrefChr3 87458 58 + 181027 taatcacacacatctg-----tacagccaagTCCGTC----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AGCAAATCACTTCAGGAATAGAATTT -s simRat_chr6.simRat.chr6 547709 58 + 647215 TAATTACTTGCTGCTA-----TACAGCAAGGTTCCTC----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AGCAAATCACTTCAGGAATAGAATTT - -a -s simMouse_chr6.simMouse.chr6 537141 5 + 636262 CCCTG -s mr.mrrefChr3 87516 5 + 181027 CCCTG -s simRat_chr6.simRat.chr6 547771 5 + 647215 CCCTG - -a -s simMouse_chr6.simMouse.chr6 537146 87 + 636262 TCTGATTCATGTAACCATTCCCTTAACGAAATGTCGGAGATATCGTAGATTTTGGCCCCCATTCTGATGAAAGCAACCAGTTCCTAT -s mr.mrrefChr3 87521 87 + 181027 TCTGATTCATGTAACCATTCCCTTAACGAAATGTCGGAGATATCGTAGATTTTGGCCCCCATTCTGATGAAAGCAACCAGTTCCTAT -s simRat_chr6.simRat.chr6 547777 87 + 647215 TCTGATTCATGTCACGATTCCCTTGATGAAATGTCAGAGGTATGGTAGACTTGGGCCCCCATTCTGGTTTAAGTAACCAGTTCGTAC - -a -s simMouse_chr6.simMouse.chr6 537233 89 + 636262 AATAGAATGTCACCTGCTCTCCTTGGAACACCATGGCCACAGATTGAGATCCTGTAAATGAGCTAGAGAAGTATAACCAGTCCAACTAG -s Anc0.Anc0refChr3 140348 21 + 222631 --------------------------------------------------------------------GAGTTTAATCAGCCCAACTAA -s Anc1.Anc1refChr6 175719 21 + 197743 --------------------------------------------------------------------GAGTTTAATCAGCCCAACTAA -s Anc2.Anc2refChr1 53757 21 + 142988 --------------------------------------------------------------------GAATTTAATCAGCCCAACTAA -s mr.mrrefChr3 87608 87 + 181027 AATAGAATGTCACCTGCTCTCCTTGGAACACCATGGCCACAGATTGAGAT--TGTAAATGAGCTAGAGAAGTATAATCAGCCCAACTAA -s simCow_chr6.simCow.chr6 510954 21 + 602619 --------------------------------------------------------------------AAATTTAATCAACCCAGTTAA -s simDog_chr6.simDog.chr6 500045 14 + 593897 --------------------------------------------------------------------GAA-------AGCCCAACTAA -s simHuman_chr6.simHuman.chr6 507535 21 + 601863 --------------------------------------------------------------------GAGTTTAATCTGCCCAACTAA -s simRat_chr6.simRat.chr6 547865 87 + 647215 AATAAAATGTCCCATGACCTCCTTGGATTGCCAGGGCTAAGGATCAAGAG--TGTATGGGAGCTAGAGAAGTGTAATCAGCCCAGCCAA - -a -s simMouse_chr6.simMouse.chr6 537322 2 + 636262 CT -s Anc0.Anc0refChr3 140369 2 + 222631 TT -s Anc1.Anc1refChr6 175740 2 + 197743 TT -s Anc2.Anc2refChr1 53778 2 + 142988 TT -s mr.mrrefChr3 87695 2 + 181027 TT -s simCow_chr6.simCow.chr6 510976 2 + 602619 TT -s simDog_chr6.simDog.chr6 500059 2 + 593897 TT -s simHuman_chr6.simHuman.chr6 507556 2 + 601863 TT -s simRat_chr6.simRat.chr6 547952 2 + 647215 TT - -a -s simMouse_chr6.simMouse.chr6 537324 3 + 636262 TTA -s Anc1.Anc1refChr6 175743 3 + 197743 TTA -s mr.mrrefChr3 87697 3 + 181027 TTA -s simHuman_chr6.simHuman.chr6 507559 3 + 601863 TTA -s simRat_chr6.simRat.chr6 547954 3 + 647215 TTA - -a -s simMouse_chr6.simMouse.chr6 537327 18 + 636262 TGATGCCCAACAGGCTTG -s Anc0.Anc0refChr3 140377 18 + 222631 TGATACCCTACAGGCTCA -s Anc1.Anc1refChr6 175754 18 + 197743 TGATACCCTACAGGCTCA -s Anc2.Anc2refChr1 53786 18 + 142988 TGATACCTTACATGCTCA -s mr.mrrefChr3 87707 18 + 181027 TGATGCCCAACAGGCTTG -s simCow_chr6.simCow.chr6 510984 18 + 602619 TGATACCTTAGGAGCTCA -s simDog_chr6.simDog.chr6 500067 18 + 593897 TGCTACCTCACATGTCCA -s simHuman_chr6.simHuman.chr6 507572 18 + 601863 TGATACCCTACAGGCTCT -s simRat_chr6.simRat.chr6 547964 18 + 647215 TAATGCCCAACAGGCTAG - -a -s simMouse_chr6.simMouse.chr6 537345 9 + 636262 CATAAGTTT -s Anc0.Anc0refChr3 140395 9 + 222631 CATTAATGC -s Anc1.Anc1refChr6 175772 9 + 197743 CATTAATGC -s Anc2.Anc2refChr1 53804 9 + 142988 CATTAATGC -s mr.mrrefChr3 87725 9 + 181027 CATAAGTTT -s simCow_chr6.simCow.chr6 511002 9 + 602619 CATTGATGC -s simDog_chr6.simDog.chr6 500094 9 + 593897 CATTAACAC -s simHuman_chr6.simHuman.chr6 507590 9 + 601863 CGTTAATGC -s simRat_chr6.simRat.chr6 547982 9 + 647215 CATAAGTTT - -a -s simMouse_chr6.simMouse.chr6 537354 20 + 636262 ATACATGCTGCTAGTATGCA -s Anc0.Anc0refChr3 140404 20 + 222631 ATGCTTTGTGCTAATATACA -s Anc1.Anc1refChr6 175781 20 + 197743 ATGCTTTGTGCTAATATACA -s Anc2.Anc2refChr1 53813 20 + 142988 ATGCTTTGTGCTGATATACA -s mr.mrrefChr3 87734 20 + 181027 ATACTTGCTGCTAGTATGCA -s simCow_chr6.simCow.chr6 511015 20 + 602619 ATGCTTTCTGCTAAAACACA -s simDog_chr6.simDog.chr6 500103 20 + 593897 ATGCTTGGTGCTGATATACA -s simHuman_chr6.simHuman.chr6 507599 16 + 601863 ATGCTTTGTGCTAATA---- -s simRat_chr6.simRat.chr6 547991 20 + 647215 ATACTTGCTGCTAGTATGCA - -a -s simMouse_chr6.simMouse.chr6 537374 2 + 636262 GG -s Anc0.Anc0refChr3 140424 2 + 222631 AG -s Anc1.Anc1refChr6 175801 2 + 197743 AG -s Anc2.Anc2refChr1 53833 2 + 142988 AG -s mr.mrrefChr3 87754 2 + 181027 GG -s simCow_chr6.simCow.chr6 511035 2 + 602619 AG -s simDog_chr6.simDog.chr6 500125 2 + 593897 AG -s simRat_chr6.simRat.chr6 548011 2 + 647215 GG - -a -s simMouse_chr6.simMouse.chr6 537376 35 + 636262 TCCAAATCCAAGGAACTGTGTTGTTGATACAATGT -s Anc0.Anc0refChr3 140426 35 + 222631 TCTAAATCTTAGGTAATATTTTGTTGATATGATGC -s Anc1.Anc1refChr6 175803 35 + 197743 TCTAAATCTTAGGTAATATTTTGTTGATATGATGC -s Anc2.Anc2refChr1 53841 35 + 142988 TCTAAATCTTAGGTAATATTCTGTTGATATGATGC -s mr.mrrefChr3 87756 35 + 181027 TCCAAATCTTAGGAACTGTGTTGTTGATACAATGC -s simCow_chr6.simCow.chr6 511043 34 + 602619 TCCAAATCTTAGGTGATGTT-TGTTGATACAATGC -s simDog_chr6.simDog.chr6 500133 35 + 593897 TCTAAACCTTGCACAAAATTCTGTTGATATGATGC -s simHuman_chr6.simHuman.chr6 507615 27 + 601863 --------TTAGGTCATTTTTTGTTGATATGATGC -s simRat_chr6.simRat.chr6 548013 35 + 647215 TCCAAATCTTAGGAACTGTCTTGTTGATACATTGC - -a -s simMouse_chr6.simMouse.chr6 537411 7 + 636262 GCCACTT -s Anc0.Anc0refChr3 140461 7 + 222631 ACCAGTT -s Anc1.Anc1refChr6 175838 7 + 197743 ACCAGTT -s Anc2.Anc2refChr1 53876 7 + 142988 ACCAGTC -s mr.mrrefChr3 87791 7 + 181027 GCCACTT -s simCow_chr6.simCow.chr6 511077 7 + 602619 ACCAATC -s simDog_chr6.simDog.chr6 500168 7 + 593897 ACCAGTC -s simHuman_chr6.simHuman.chr6 507642 7 + 601863 ACCAGTT -s simRat_chr6.simRat.chr6 548078 7 + 647215 GCCACTT - -a -s simMouse_chr6.simMouse.chr6 537418 11 + 636262 TATGCCCACAG -s Anc0.Anc0refChr3 140469 11 + 222631 CATGCGCACAG -s Anc1.Anc1refChr6 175846 11 + 197743 CATGCGCACAG -s Anc2.Anc2refChr1 53884 11 + 142988 CATGTGGACAG -s mr.mrrefChr3 87798 11 + 181027 CATGCCCACAG -s simCow_chr6.simCow.chr6 511085 11 + 602619 CTTCTATAAAA -s simDog_chr6.simDog.chr6 500176 11 + 593897 CATGTGGACAG -s simHuman_chr6.simHuman.chr6 507650 11 + 601863 CATGCTCACAG -s simRat_chr6.simRat.chr6 548085 11 + 647215 CATCCCTACAG - -a -s simMouse_chr6.simMouse.chr6 537429 6 + 636262 AATGTA -s Anc0.Anc0refChr3 140480 6 + 222631 AATCTA -s Anc1.Anc1refChr6 175857 6 + 197743 AATCTA -s Anc2.Anc2refChr1 53895 6 + 142988 AATCTA -s mr.mrrefChr3 87809 6 + 181027 AATGTA -s simCow_chr6.simCow.chr6 511101 6 + 602619 AATGTA -s simDog_chr6.simDog.chr6 500187 6 + 593897 ATTCAC -s simHuman_chr6.simHuman.chr6 507661 6 + 601863 AACATA -s simRat_chr6.simRat.chr6 548096 6 + 647215 AATGTA - -a -s simMouse_chr6.simMouse.chr6 537435 61 + 636262 TCTCACCACTGGGATTGGCATGACTCACTGTATGATCAACTATCCATCGGTATTGATCACT -s Anc0.Anc0refChr3 140487 61 + 222631 CCTGGTCACAGGGATCGACATAACTCACTGTAGGACCAGCAATCCACCAGTCGTGATCACT -s Anc1.Anc1refChr6 175864 61 + 197743 CCTGGTCACAGGGATCGACATAACTCACTGTAGGACCAGCAATCCACCAGTCGTGATCACT -s Anc2.Anc2refChr1 53902 61 + 142988 CCTGGTCACAGGGATCAACATAATTCACTGTAGGACCAGCAATCCACCAGTCGTGAACACT -s mr.mrrefChr3 87815 61 + 181027 TCTCACCACTGGGATTGGCATGACTCACTGTATGATCAACTATCCATCAGTATTGATCACT -s simCow_chr6.simCow.chr6 511108 61 + 602619 CCTGGTCACAGGCATCAACATAATTCTCTGTAGGACTAACAATCCACCAATAGTGAACACT -s simDog_chr6.simDog.chr6 500194 61 + 593897 CCTGGTCACAGGGATCAACATAATACACTGTTTGACCAGCAATCCAGCAGTCGTGAACACT -s simHuman_chr6.simHuman.chr6 507668 55 + 601863 CCTGGTCACAGGGTTCGACATAACTTACTGTAGGACCA------CACCAGTGGTAATTACT -s simRat_chr6.simRat.chr6 548102 61 + 647215 TTTCACGACTGGGATTGGCATTACTCACTGTATGATCTACAATGCATCACTATTGATCACT - -a -s simMouse_chr6.simMouse.chr6 537496 67 + 636262 GCTTGTCCTGGCAATATTTCAAGCAGAAGCCACTAGTATAAGGTTCTACCCAGAGGATCAGAAACAC -s Anc0.Anc0refChr3 140548 67 + 222631 GCTTGTCCTAGCACTATTTCCAGCAAAGGCTAGCATTATAAGACTCTACCTAGGGAATCATGCACAC -s Anc1.Anc1refChr6 175925 67 + 197743 GCTTGTCCTAGCACTATTTCCAGCAAAGGCTAGCATTATAAGACTCTACCTAGGGAATCATGCACAC -s Anc2.Anc2refChr1 53963 67 + 142988 GCTTGTCCTGGCACTAGTTCCAGCCAAGGCTAGCATTATAAGACTCTACCCAGGAAATCATGCAAAC -s mr.mrrefChr3 87876 67 + 181027 GCTTGTCCTAGCAATATTTCAAGCAGAAGCCAGTAGTATAAGGTTCTACCTAGAGGATCATAAACAC -s simCow_chr6.simCow.chr6 511169 67 + 602619 GCTTGTCTTGGCACAAGTTCCAGCCAAGGCTAGCATTATAAGACTCTACTCAGGTAACCCTGCAAAC -s simDog_chr6.simDog.chr6 500257 67 + 593897 GCTTGTCCTGGCACTAGTTACACCCAAGGCTAGCATTATAAGTCTCTATCCGGAAAATCATGCAAAC -s simHuman_chr6.simHuman.chr6 507723 67 + 601863 GCTTGTCCTAGCAGTTTTTCCAGCAAAGGCTAGCATTATAAGAGTCTACCTAGGGTATCATGCTCAC -s simRat_chr6.simRat.chr6 548163 61 + 647215 GCTTTTCCTAGCAATATTTCAAACAGAAGCCAGTAGTATAAGGTTCTACCTGGAGGATCAT------ - -a -s simMouse_chr6.simMouse.chr6 537563 18 + 636262 ATCTTCCCTACTACTTTG -s Anc0.Anc0refChr3 140616 18 + 222631 ATTTACCCTAGTTTTTTG -s Anc1.Anc1refChr6 175993 18 + 197743 ATTTACCCTAGTTTTTTG -s Anc2.Anc2refChr1 54031 18 + 142988 ATTTACCCTAGTTTTTTG -s mr.mrrefChr3 87943 18 + 181027 ATCTTCCCTACTACTTTG -s simCow_chr6.simCow.chr6 511237 18 + 602619 TTTTACCCTAGTTTATGC -s simDog_chr6.simDog.chr6 500325 18 + 593897 ACCTACCCTAGTTTTTTG -s simHuman_chr6.simHuman.chr6 507791 18 + 601863 ATTTACCCTGGCTTTTTG -s simRat_chr6.simRat.chr6 548224 5 + 647215 -------------CTTTG - -a -s simMouse_chr6.simMouse.chr6 537581 15 + 636262 CTCCCACTCTAGACA -s Anc0.Anc0refChr3 140635 15 + 222631 CTCTCCCTCAAAACA -s Anc1.Anc1refChr6 176012 15 + 197743 CTCTCCCTCAAAACA -s Anc2.Anc2refChr1 54050 15 + 142988 CTCTCCCTCAAAACA -s mr.mrrefChr3 87961 15 + 181027 CTCCCCCTCTAGACA -s simCow_chr6.simCow.chr6 511256 15 + 602619 CTCTCCCTCAAAACA -s simHuman_chr6.simHuman.chr6 507810 15 + 601863 CTCACCCTCCATCCA -s simRat_chr6.simRat.chr6 548229 15 + 647215 CTCGCCCTCTAGACA - -a -s simMouse_chr6.simMouse.chr6 537596 1 + 636262 A -s Anc0.Anc0refChr3 140650 1 + 222631 A -s Anc1.Anc1refChr6 176027 1 + 197743 A -s Anc2.Anc2refChr1 54065 1 + 142988 A -s mr.mrrefChr3 87976 1 + 181027 A -s simDog_chr6.simDog.chr6 500344 1 + 593897 A -s simHuman_chr6.simHuman.chr6 507833 1 + 601863 A -s simRat_chr6.simRat.chr6 548244 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 537597 13 + 636262 AGCTTATTTGTAA -s Anc0.Anc0refChr3 140651 13 + 222631 AACTAATTTAGAG -s Anc1.Anc1refChr6 176028 13 + 197743 AACTAATTTAGAG -s Anc2.Anc2refChr1 54067 13 + 142988 AACTAATTTAGAG -s mr.mrrefChr3 87977 13 + 181027 AGCTTATTTGTAA -s simCow_chr6.simCow.chr6 511272 13 + 602619 AACTCATTTTAAG -s simDog_chr6.simDog.chr6 500346 13 + 593897 AATTAATTTAGAG -s simHuman_chr6.simHuman.chr6 507834 13 + 601863 AACTAATCTACAG -s simRat_chr6.simRat.chr6 548245 13 + 647215 GGCTTCTTTGTAA - -a -s simMouse_chr6.simMouse.chr6 537610 16 + 636262 GATTGCCCTAACTATG -s Anc0.Anc0refChr3 140665 15 + 222631 CA-TGCCCTGCCCTTG -s Anc1.Anc1refChr6 176042 16 + 197743 CACTGCCCTGCCCTTG -s Anc2.Anc2refChr1 54081 15 + 142988 CA-TGCCCTGCCCTTG -s mr.mrrefChr3 87990 16 + 181027 CATTGCCCTAACCATG -s simCow_chr6.simCow.chr6 511286 15 + 602619 AA-TACCCTGCCCTCA -s simDog_chr6.simDog.chr6 500360 15 + 593897 CA-TGCCCTGCCCTTG -s simHuman_chr6.simHuman.chr6 507848 16 + 601863 CACTGCCCCGCCCTGG -s simRat_chr6.simRat.chr6 548258 16 + 647215 CATGACCCTAACCATC - -a -s simMouse_chr6.simMouse.chr6 537626 25 + 636262 ACCTACAATCCAAGCTTGTATATAG -s Anc0.Anc0refChr3 140680 25 + 222631 ACCTATCACCCAAGCTTGTATATAG -s Anc1.Anc1refChr6 176058 25 + 197743 ACCTATCACCCAAGCTTGTATATAG -s Anc2.Anc2refChr1 54096 25 + 142988 ACCTATCACCCAAGCTTGTATATAG -s mr.mrrefChr3 88006 25 + 181027 ACCTACAATCCAAGCTTGTATATAG -s simCow_chr6.simCow.chr6 511326 25 + 602619 ACGTATCATCCAAGTATGTATATAG -s simDog_chr6.simDog.chr6 500375 24 + 593897 AGCCATC-CTCAAGCTTGTGTGTAG -s simHuman_chr6.simHuman.chr6 507864 25 + 601863 ACCTATCACCCCAGCTTGTATATAG -s simRat_chr6.simRat.chr6 548274 25 + 647215 GCCTACAATCCAAGCTTGTATATAG - -a -s simMouse_chr6.simMouse.chr6 537651 13 + 636262 TTGATAGCTCTTG -s Anc0.Anc0refChr3 140705 13 + 222631 ATGATAGCTCCTG -s Anc1.Anc1refChr6 176083 13 + 197743 ATGATAGCTCCTG -s Anc2.Anc2refChr1 54121 13 + 142988 ATCATAGCTCCTG -s mr.mrrefChr3 88031 13 + 181027 TTGATAGCTCTTG -s simCow_chr6.simCow.chr6 511352 13 + 602619 ATAATAGCTCCTG -s simDog_chr6.simDog.chr6 500399 4 + 593897 TTCA--------- -s simHuman_chr6.simHuman.chr6 507889 13 + 601863 ATGAGAGCTCCTG -s simRat_chr6.simRat.chr6 548299 13 + 647215 CTGATAGCTCTTG - -a -s simMouse_chr6.simMouse.chr6 537664 23 + 636262 GCCTATTACCTGGGTGCTGTTAT -s Anc0.Anc0refChr3 140719 23 + 222631 GCTTGTTGCCTGGGTTTTGATAT -s Anc1.Anc1refChr6 176097 23 + 197743 GCTTGTTGCCTGGGTTTTGATAT -s Anc2.Anc2refChr1 54135 23 + 142988 GCTTGTTGCCTGGGTTTTGATAT -s mr.mrrefChr3 88044 23 + 181027 GCTTATTACCTGGGTGCTGATAT -s simCow_chr6.simCow.chr6 511366 23 + 602619 TCATGTTGCCTGGGTTTTGATAC -s simDog_chr6.simDog.chr6 500404 23 + 593897 GCTTATTGCCTGCGTTTCAATAT -s simHuman_chr6.simHuman.chr6 507903 23 + 601863 GCTTGTGGCATGGGTTTTGATAT -s simRat_chr6.simRat.chr6 548312 23 + 647215 GCTTATTACCTGGGTGATGATAT - -a -s simMouse_chr6.simMouse.chr6 537687 2 + 636262 GA -s Anc0.Anc0refChr3 140747 2 + 222631 GA -s Anc1.Anc1refChr6 176125 2 + 197743 GA -s Anc2.Anc2refChr1 54163 2 + 142988 GA -s mr.mrrefChr3 88067 2 + 181027 GA -s simCow_chr6.simCow.chr6 511394 2 + 602619 GT -s simDog_chr6.simDog.chr6 500432 2 + 593897 GA -s simHuman_chr6.simHuman.chr6 507931 2 + 601863 GA -s simRat_chr6.simRat.chr6 548335 2 + 647215 GA - -a -s simMouse_chr6.simMouse.chr6 537689 18 + 636262 GCTCAACATTGGGGCCCA -s Anc0.Anc0refChr3 140749 18 + 222631 GCTCAGCACTGGAATTCA -s Anc1.Anc1refChr6 176127 18 + 197743 GCTCAGCACTGGAATTCA -s Anc2.Anc2refChr1 54166 18 + 142988 GCTCAGCACTGGAATTCA -s mr.mrrefChr3 88069 18 + 181027 GCTCAACACTGGGGCTCA -s simCow_chr6.simCow.chr6 511397 18 + 602619 GCTCAGCACTGGAATTCA -s simDog_chr6.simDog.chr6 500435 18 + 593897 GCCCAGCACTGGAATTCA -s simHuman_chr6.simHuman.chr6 507933 18 + 601863 GCTCAGCACTGGAATTCA -s simRat_chr6.simRat.chr6 548337 18 + 647215 GCTCACCACTGGGGCTCA - -a -s simMouse_chr6.simMouse.chr6 537707 10 + 636262 AACCTTAATT -s Anc0.Anc0refChr3 140768 10 + 222631 AATCTTCATT -s Anc1.Anc1refChr6 176146 10 + 197743 AATCTTCATT -s Anc2.Anc2refChr1 54185 10 + 142988 AATCTTCTTT -s mr.mrrefChr3 88087 10 + 181027 AACCTTAATT -s simCow_chr6.simCow.chr6 511416 10 + 602619 GATGTTCGTT -s simDog_chr6.simDog.chr6 500454 10 + 593897 AATCTTCTTT -s simHuman_chr6.simHuman.chr6 507952 10 + 601863 TGACTTCATT -s simRat_chr6.simRat.chr6 548355 10 + 647215 AACCTTTATT - -a -s simMouse_chr6.simMouse.chr6 537717 39 + 636262 TACCAACCCACACCGCCACCTTTACTTATTGCCTTAACA -s Anc0.Anc0refChr3 140778 39 + 222631 TACCAGCCCACCCCATCACCTTTGCCCAATGCTTCAAGA -s Anc1.Anc1refChr6 176156 39 + 197743 TACCAGCCCACCCCATCACCTTTGCCCAATGCTTCAAGA -s Anc2.Anc2refChr1 54195 39 + 142988 CACCAGCCCACCCCATCCCCTTTGCCCAATACTTCAAGG -s mr.mrrefChr3 88097 39 + 181027 TACCAACCCACCCCACCACCTTTACTTATTGCTTTAACA -s simCow_chr6.simCow.chr6 511426 39 + 602619 AACTACCACACCACATCGCCTTTGCCTTATACTTCAAGG -s simDog_chr6.simDog.chr6 500464 39 + 593897 CACCAGCCCATCCCATTCCCTCTGCCCAATACTCCAAAG -s simHuman_chr6.simHuman.chr6 507962 39 + 601863 TACCAGCCCACCCCATCACCTTTGCCCAATGCTTCTAGA -s simRat_chr6.simRat.chr6 548366 39 + 647215 TACAATCCCACCCCACCACCTTTACTTATTGGTTTCACA - -a -s simMouse_chr6.simMouse.chr6 537756 5 + 636262 CACTA -s Anc0.Anc0refChr3 140819 5 + 222631 CACTA -s Anc1.Anc1refChr6 176197 5 + 197743 CACTA -s Anc2.Anc2refChr1 54236 5 + 142988 CACTA -s mr.mrrefChr3 88136 5 + 181027 CACTA -s simCow_chr6.simCow.chr6 511467 5 + 602619 CTCTG -s simDog_chr6.simDog.chr6 500505 5 + 593897 CACTA -s simHuman_chr6.simHuman.chr6 508003 5 + 601863 CACTA -s simRat_chr6.simRat.chr6 548405 5 + 647215 CACTA - -a -s simMouse_chr6.simMouse.chr6 537761 8 + 636262 GAACGAAT -s Anc0.Anc0refChr3 140824 8 + 222631 GCAACAAG -s Anc1.Anc1refChr6 176202 8 + 197743 GCAACAAG -s Anc2.Anc2refChr1 54241 8 + 142988 GCAACAAG -s mr.mrrefChr3 88141 8 + 181027 GAACGAAT -s simCow_chr6.simCow.chr6 511472 8 + 602619 CCAGCAAG -s simDog_chr6.simDog.chr6 500754 8 + 593897 GCAACAAG -s simHuman_chr6.simHuman.chr6 508008 8 + 601863 GCAACAAG -s simRat_chr6.simRat.chr6 548410 8 + 647215 CAAGGAAT - -a -s simMouse_chr6.simMouse.chr6 537769 41 + 636262 CCTCGTGTATCCGAATTTATTGTTTAGTAAATTTGACTATG -s Anc0.Anc0refChr3 140832 40 + 222631 CTTCGTGTCT-CAAATTTATTGTTTAGTGAATTCAACTTTG -s Anc1.Anc1refChr6 176210 41 + 197743 CTTCGTGTCTCCAAATTTATTGTTTAGTGAATTCAACTTTG -s Anc2.Anc2refChr1 54250 40 + 142988 CTTGGTGTCT-CAAATTCATTGTTTAGGGTGTTCATTATTG -s mr.mrrefChr3 88149 41 + 181027 CCTCGTGTATCCAAATTTATTGTTTAGTAAATTCAACTATG -s simCow_chr6.simCow.chr6 511481 34 + 602619 CTGGGTGTCT-CAAATTGATTGTTTAGGGTGTTCA------ -s simDog_chr6.simDog.chr6 500763 34 + 593897 CTTGGTGTTT-CAAATTCATCGTTTA------TCCTTATTG -s simHuman_chr6.simHuman.chr6 508016 41 + 601863 CTTCATGTCTCAATATTTATTGTTTAGTGAATTCAACTCTG -s simRat_chr6.simRat.chr6 548418 41 + 647215 CCTTGCGTATCCAAATTTGTTGTTTAGTAGATTCAACTTTG - -a -s simMouse_chr6.simMouse.chr6 537810 2 + 636262 GT -s Anc0.Anc0refChr3 140876 2 + 222631 GT -s Anc1.Anc1refChr6 176255 2 + 197743 GT -s Anc2.Anc2refChr1 54294 2 + 142988 GT -s mr.mrrefChr3 88190 2 + 181027 GT -s simDog_chr6.simDog.chr6 500801 2 + 593897 GT -s simHuman_chr6.simHuman.chr6 508065 2 + 601863 GT -s simRat_chr6.simRat.chr6 548459 2 + 647215 GT - -a -s simMouse_chr6.simMouse.chr6 537812 5 + 636262 TACTG -s Anc0.Anc0refChr3 140878 5 + 222631 TGCTT -s Anc1.Anc1refChr6 176257 5 + 197743 TGCTT -s Anc2.Anc2refChr1 54296 5 + 142988 TGACT -s mr.mrrefChr3 88192 5 + 181027 TACTT -s simDog_chr6.simDog.chr6 500803 5 + 593897 TGACT -s simHuman_chr6.simHuman.chr6 508067 5 + 601863 TGCTT -s simRat_chr6.simRat.chr6 548463 5 + 647215 CACTT - -a -s simMouse_chr6.simMouse.chr6 537817 19 + 636262 AGAGGCTTACTGTGCATGC -s Anc0.Anc0refChr3 140883 19 + 222631 ACACTTGTGCTTTGCACAC -s Anc1.Anc1refChr6 176262 19 + 197743 ACACTTGTGCTTTGCACAC -s Anc2.Anc2refChr1 54301 19 + 142988 ACACTTGTGCTTTGCACAC -s mr.mrrefChr3 88197 19 + 181027 AGACTTGTACTGTGCATGC -s simCow_chr6.simCow.chr6 511515 19 + 602619 ATACTTGTGCTTTGCAATC -s simDog_chr6.simDog.chr6 500812 19 + 593897 ACACTTGTGCTTTACACAC -s simHuman_chr6.simHuman.chr6 508072 19 + 601863 ACACTTGTGCTTTGCACAC -s simRat_chr6.simRat.chr6 548468 19 + 647215 ATACTTGTCCTGTGCATGC - -a -s simMouse_chr6.simMouse.chr6 537836 7 + 636262 AGTGTGC -s Anc0.Anc0refChr3 140902 7 + 222631 TGTGGGA -s Anc1.Anc1refChr6 176281 7 + 197743 TGTGGGA -s Anc2.Anc2refChr1 54320 7 + 142988 TGTTGGA -s mr.mrrefChr3 88216 7 + 181027 AGTGGGC -s simCow_chr6.simCow.chr6 511534 6 + 602619 TG-TGGA -s simDog_chr6.simDog.chr6 500839 7 + 593897 TTTTGGA -s simHuman_chr6.simHuman.chr6 508091 7 + 601863 TGTGGGA -s simRat_chr6.simRat.chr6 548487 7 + 647215 AGTGGGC - -a -s simMouse_chr6.simMouse.chr6 537843 13 + 636262 TGGTTCAGGCCAT -s Anc0.Anc0refChr3 140910 13 + 222631 CTTTTCGGACCAT -s Anc1.Anc1refChr6 176289 13 + 197743 CTTTTCGGACCAT -s Anc2.Anc2refChr1 54328 13 + 142988 ATTTTTGGACCAT -s mr.mrrefChr3 88223 13 + 181027 CGGTTCAGGCCAT -s simCow_chr6.simCow.chr6 511541 13 + 602619 ATTTTTAGACCAT -s simDog_chr6.simDog.chr6 500847 11 + 593897 --TTTTGGACCAT -s simHuman_chr6.simHuman.chr6 508099 13 + 601863 CTTTTCTGACTAT -s simRat_chr6.simRat.chr6 548494 13 + 647215 CAGTTCAGGCCAT - -a -s simMouse_chr6.simMouse.chr6 537856 30 + 636262 AATTCTACTGTACATTACTACTATTTAAGA -s Anc0.Anc0refChr3 140923 30 + 222631 AATGCTAGAGTCCACAAATTTCATCAGAAA -s Anc1.Anc1refChr6 176302 30 + 197743 AATGCTAGAGTCCACAAATTTCATCAGAAA -s Anc2.Anc2refChr1 54341 30 + 142988 AATGCTAGAGTCCACAAATTTCATCAAAAA -s mr.mrrefChr3 88236 30 + 181027 AATTCTACTGTACATAACTATCATTAGAAA -s simCow_chr6.simCow.chr6 511555 30 + 602619 AATGCTAGAGTCCACAAATTTCATCAAAAA -s simDog_chr6.simDog.chr6 500858 30 + 593897 AATGCTAGAGCCCAAGAGTTCCATCAACAA -s simHuman_chr6.simHuman.chr6 508112 30 + 601863 AATGCTAGAATCCACAGATTTCTTCAGAAA -s simRat_chr6.simRat.chr6 548507 30 + 647215 GGTTCTACTGTACATAACTATCATTAGAAA - -a -s simMouse_chr6.simMouse.chr6 537886 17 + 636262 CCTTAATGTTATAGGAC -s Anc0.Anc0refChr3 140970 17 + 222631 TCCTATCAGAGTAGTAC -s Anc1.Anc1refChr6 176349 17 + 197743 TCCTATCAGAGTAGTAC -s Anc2.Anc2refChr1 54391 17 + 142988 TCCTGTCAGAGTGGTAC -s mr.mrrefChr3 88266 17 + 181027 CCCTAATGTAATAGGAC -s simCow_chr6.simCow.chr6 511597 16 + 602619 -TCTTTCAGAGTGGGAC -s simDog_chr6.simDog.chr6 500909 17 + 593897 TCCTGTCAGAGTGGTAT -s simHuman_chr6.simHuman.chr6 508159 17 + 601863 TCCTACCAGAGTAATAC -s simRat_chr6.simRat.chr6 548537 17 + 647215 CCCTAATGTAATAGGAC - -a -s simMouse_chr6.simMouse.chr6 537903 24 + 636262 ATGCTGATCCTCAGATACCTACAC -s Anc0.Anc0refChr3 140987 23 + 222631 AGACCTCTCCTCAGACTCCTGTA- -s Anc1.Anc1refChr6 176366 23 + 197743 AGACCTCTCCTCAGACTCCTGTA- -s Anc2.Anc2refChr1 54408 23 + 142988 AGACCTCACTTCAGACTACTGTT- -s mr.mrrefChr3 88283 24 + 181027 ATGCTGATCCTCAGATACCTGCAC -s simCow_chr6.simCow.chr6 511613 23 + 602619 AGACCTCACTTCACATTACTGTG- -s simDog_chr6.simDog.chr6 500927 23 + 593897 GGACCTCACTTCAGCCTACTGTT- -s simHuman_chr6.simHuman.chr6 508176 23 + 601863 AGACATCTCCTCGGACTCCTGTA- -s simRat_chr6.simRat.chr6 548554 24 + 647215 ATGCTGACCCTCAGATACCTGGAC - -a -s simMouse_chr6.simMouse.chr6 537927 8 + 636262 AAATCCAA -s Anc0.Anc0refChr3 141010 4 + 222631 ----CTAA -s Anc1.Anc1refChr6 176389 4 + 197743 ----CTAA -s Anc2.Anc2refChr1 54431 4 + 142988 ----CTAA -s mr.mrrefChr3 88307 8 + 181027 AAATCCAA -s simCow_chr6.simCow.chr6 511636 4 + 602619 ----CTCA -s simDog_chr6.simDog.chr6 500950 4 + 593897 ----CTAA -s simHuman_chr6.simHuman.chr6 508199 4 + 601863 ----CTAA -s simRat_chr6.simRat.chr6 548581 8 + 647215 AAATTCAA - -a -s simMouse_chr6.simMouse.chr6 537935 57 + 636262 TCCTGATTGCAGTTTTGAAAACTCTTGGCCAATCGTGTCGTATAGATACAGCCTACC -s Anc0.Anc0refChr3 141014 57 + 222631 TCCTGCTAGCAGTGTTGTAGCCATTTGGCCCTTCTTAATGTATAGATACACCATGGC -s Anc1.Anc1refChr6 176393 57 + 197743 TCCTGCTAGCAGTGTTGTAGCCATTTGGCCCTTCTTAATGTATAGATACACCATGGC -s Anc2.Anc2refChr1 54435 57 + 142988 TGCTGCTAGCAGTGTTGAAGCCATTTGGCCCTTCTTAATGTATAAATACACCATGGC -s mr.mrrefChr3 88315 57 + 181027 TCCTGATTGCAGTTTTGTAAACTCTTGGCCAATCGTGTTGTATAGATACACCCTACC -s simCow_chr6.simCow.chr6 511646 57 + 602619 TTCTGCTTGCAGTATGGAAGCCATTTGGTGTTTTTTGATGAATAAGTACATCACGGC -s simDog_chr6.simDog.chr6 500954 56 + 593897 TGCTGCTAACAGTGTTGAACCCATTTGGCCCTTCTTAACGTAT-AACACACCATGGT -s simHuman_chr6.simHuman.chr6 508203 57 + 601863 CCTTGTTAGCAGTGTTGTAGCCATGTGGCCCTTCTTAATGTATGGATACACCATGGC -s simRat_chr6.simRat.chr6 548589 57 + 647215 TCCTGATTGCAGTTTTGTAAACTCTTGGCCAATCCTGTTGTATAGATGCACCCTACC - -a -s simMouse_chr6.simMouse.chr6 537992 7 + 636262 TTTGTGA -s Anc0.Anc0refChr3 141108 7 + 222631 TTTATGA -s Anc1.Anc1refChr6 176487 7 + 197743 TTTATGA -s Anc2.Anc2refChr1 54529 7 + 142988 TTTATGA -s mr.mrrefChr3 88372 7 + 181027 TTTGTGA -s simCow_chr6.simCow.chr6 511740 7 + 602619 TTTATGC -s simDog_chr6.simDog.chr6 501047 7 + 593897 TTTATGA -s simHuman_chr6.simHuman.chr6 508297 7 + 601863 TTTATGC -s simRat_chr6.simRat.chr6 548646 7 + 647215 TTTGTGA - -a -s simMouse_chr6.simMouse.chr6 537999 3 + 636262 TAC -s Anc0.Anc0refChr3 141115 3 + 222631 TAC -s Anc1.Anc1refChr6 176494 3 + 197743 TAC -s Anc2.Anc2refChr1 54553 3 + 142988 TGA -s mr.mrrefChr3 88379 3 + 181027 TAC -s simCow_chr6.simCow.chr6 511764 3 + 602619 TGG -s simDog_chr6.simDog.chr6 501071 3 + 593897 TGA -s simHuman_chr6.simHuman.chr6 508304 3 + 601863 CAC -s simRat_chr6.simRat.chr6 548653 3 + 647215 TAC - -a -s simMouse_chr6.simMouse.chr6 538002 37 + 636262 AGCCACTGTCTGGTGATTTATAGCTCAGGCATTAGAA -s Anc0.Anc0refChr3 141118 36 + 222631 AGCCACTGTCTGGTGGGTTATAATTTAGGA-CTGGAA -s Anc1.Anc1refChr6 176497 36 + 197743 AGCCACTGTCTGGTGGGTTATAATTTAGGA-CTGGAA -s Anc2.Anc2refChr1 54556 36 + 142988 AGCCACTGTCTGGAGGGTTATAATTTAATA-CTCGAG -s mr.mrrefChr3 88382 37 + 181027 AGCCACTGTCTGGTGATTTATAGCTCAGGCACTGGAA -s simCow_chr6.simCow.chr6 511770 36 + 602619 AGCCACTGTCTGGAGGGTCATAACTTCAAA-TTCGAG -s simDog_chr6.simDog.chr6 501074 36 + 593897 AGCCACTGTCTTGAGGGTTGGAATTCAATA-CTCAAG -s simHuman_chr6.simHuman.chr6 508307 34 + 601863 TG--ACTATCTGGTGGGTTATCATCTAGGA-CTGGAA -s simRat_chr6.simRat.chr6 548656 37 + 647215 AGCCACTTTCTGGTGATTTGTAGCTCAGACACTGGAA - -a -s simMouse_chr6.simMouse.chr6 538039 6 + 636262 GATTTT -s Anc0.Anc0refChr3 141154 6 + 222631 GTTTTG -s Anc1.Anc1refChr6 176533 6 + 197743 GTTTTG -s Anc2.Anc2refChr1 54593 6 + 142988 GTTTTG -s mr.mrrefChr3 88419 6 + 181027 GATTTT -s simCow_chr6.simCow.chr6 511807 6 + 602619 GTTTTG -s simDog_chr6.simDog.chr6 501111 6 + 593897 GTTTAG -s simHuman_chr6.simHuman.chr6 508341 6 + 601863 GTTTTG -s simRat_chr6.simRat.chr6 548693 6 + 647215 GGTTTT - -a -s simMouse_chr6.simMouse.chr6 538045 20 + 636262 AAGGCCTGTCTGTCACTCCA -s Anc0.Anc0refChr3 141160 20 + 222631 GAAGTCCATCTGTTGCTCTA -s Anc1.Anc1refChr6 176539 20 + 197743 GAAGTCCATCTGTTGCTCTA -s Anc2.Anc2refChr1 54599 20 + 142988 GAAGTTCACCTGTTGCTCTA -s mr.mrrefChr3 88425 20 + 181027 AAGGCCTGTCTGTCACTCTA -s simCow_chr6.simCow.chr6 511814 20 + 602619 GCAGTTCACCCATTGCTCCA -s simDog_chr6.simDog.chr6 501117 20 + 593897 AAAATTCACCTGTTGCTCTG -s simHuman_chr6.simHuman.chr6 508347 20 + 601863 GTAGTCCATCTGTTGCTCTA -s simRat_chr6.simRat.chr6 548699 20 + 647215 AAGGCCTGTGTTTCACTCTG - -a -s simMouse_chr6.simMouse.chr6 538065 13 + 636262 GGACCTCCGAAGT -s Anc0.Anc0refChr3 141180 11 + 222631 GA--TCCCAGAAA -s Anc1.Anc1refChr6 176559 11 + 197743 GA--TCCCAGAAA -s Anc2.Anc2refChr1 54620 11 + 142988 GA--TCCCAGAAA -s mr.mrrefChr3 88445 13 + 181027 GGACTCCCGGAGT -s simCow_chr6.simCow.chr6 511835 11 + 602619 GA--TCCCAGAAC -s simDog_chr6.simDog.chr6 501138 11 + 593897 GA--TCCTAGGAA -s simHuman_chr6.simHuman.chr6 508367 11 + 601863 GA--TCCCAGAAA -s simRat_chr6.simRat.chr6 548719 13 + 647215 GGACTCCCGGAGT - -a -s simMouse_chr6.simMouse.chr6 538078 71 + 636262 GTCCCTGTATTAGCATGGAGCCTTTGAGCAGGCAGCGAACATCACTGGCAGACACCTTTGACATTTTTTCA -s Anc0.Anc0refChr3 141191 71 + 222631 ACCCCTGTCTTAGCACAGAGCCTTTGAGCAGGGAGCAAACACCACTGGCAGGCACCTTTCACATTTATTCA -s Anc1.Anc1refChr6 176570 71 + 197743 ACCCCTGTCTTAGCACAGAGCCTTTGAGCAGGGAGCAAACACCACTGGCAGGCACCTTTCACATTTATTCA -s Anc2.Anc2refChr1 54631 71 + 142988 ACCCCTGTCTTAGCACAGAGCCTTTCAGCAGGGAGCAAACACCACCGGCAGGCACCTTTCACATTTATTCA -s mr.mrrefChr3 88458 71 + 181027 GTCCCTGTATTAGCATGGAGCCTTTGAGCAGGCAGCGAACATCACTGGCAGGCACCTTTGACATTTTTTCA -s simCow_chr6.simCow.chr6 511846 71 + 602619 GCGCCTGTCTTAGCACAGAGCCATTACACAGGGACAAAACACCACCTGAAGGCACCTTTCACATTGGTTCA -s simDog_chr6.simDog.chr6 501153 71 + 593897 ACCCCAGTTTTAACACAAAGCCTTACAGCAGAGAGCCAACACCACCGGCGGGCATGTTTGATATTTATTCA -s simHuman_chr6.simHuman.chr6 508378 71 + 601863 ACCCCTGTCTTAGCACAGGGCCTTTGAGCAAGGAGCAAACACCACTGGCAGGCACCTTTCACTTTTATTCG -s simRat_chr6.simRat.chr6 548732 70 + 647215 GTCCCCGTTTTCGCATGGAGTCATTGAGCGGGCAGAGAACATCATCGGCAGGCACC-TTGACATTTCTCCC - -a -s simMouse_chr6.simMouse.chr6 538149 14 + 636262 TGCAGGGGTTTCAC -s Anc0.Anc0refChr3 141263 14 + 222631 ACCGTGGGTTTCAC -s Anc1.Anc1refChr6 176642 14 + 197743 ACCGTGGGTTTCAC -s Anc2.Anc2refChr1 54703 14 + 142988 ACCGAGGATTTCAC -s mr.mrrefChr3 88529 14 + 181027 AGCATGGGTTTCAC -s simCow_chr6.simCow.chr6 511918 14 + 602619 ACCAAGGATTTTAA -s simDog_chr6.simDog.chr6 501225 14 + 593897 ACCGAGGATTTCAC -s simHuman_chr6.simHuman.chr6 508450 14 + 601863 AACCTGGGTTTCAC -s simRat_chr6.simRat.chr6 548802 14 + 647215 AGCGTGGGTTGCAC - -a -s simMouse_chr6.simMouse.chr6 538163 36 + 636262 TGGCTCACCTGAAAGTCAAGGATGTCTTCAAGTAGT -s Anc0.Anc0refChr3 141290 36 + 222631 TGGGAGACCTGAAAGTTAAGTATGTCATCAACTATA -s Anc1.Anc1refChr6 176669 36 + 197743 TGGGAGACCTGAAAGTTAAGTATGTCATCAACTATA -s Anc2.Anc2refChr1 54730 36 + 142988 TGTGAGACCTGGAGATTAAGTTTGTCATCAACTATA -s mr.mrrefChr3 88543 36 + 181027 TGGCAGACCTGAAAGTTAAGGATGTCTTCAAGTAGT -s simCow_chr6.simCow.chr6 511945 33 + 602619 TGTGAGACCATGAGAGGGAGTGTCACATCAACT--- -s simDog_chr6.simDog.chr6 501248 33 + 593897 ---GAAACCTGGAGATTAAGTTTGTCATTAACTATA -s simHuman_chr6.simHuman.chr6 508477 36 + 601863 TGGGAGACATAAAAGCTAAGTATGTCATCAAAGATA -s simRat_chr6.simRat.chr6 548816 36 + 647215 TAGCAGACCTGAGACTTAAGCATGTCCCCAAGTAGT - -a -s simMouse_chr6.simMouse.chr6 538199 28 + 636262 ATAGCACAGGAGTTTCATCTGTATAGAT -s Anc0.Anc0refChr3 141326 28 + 222631 ATAGCACAGGAGTCTCCCCCAAACAAAG -s Anc1.Anc1refChr6 176705 28 + 197743 ATAGCACAGGAGTCTCCCCCAAACAAAG -s Anc2.Anc2refChr1 54766 28 + 142988 ATAGCACAGCAGTCCCCCCCAAACAATG -s mr.mrrefChr3 88579 28 + 181027 ATAGCACAGGAGTTTCCTCTGTATAGAT -s simCow_chr6.simCow.chr6 511978 20 + 602619 ATAGAATAGCAGTCCCCCCC-------- -s simDog_chr6.simDog.chr6 501293 27 + 593897 ATAGCACAACAGTCC-CCTCAAACAATG -s simHuman_chr6.simHuman.chr6 508513 28 + 601863 ATAGCACAGGAGACTCCCCCAGACAAAG -s simRat_chr6.simRat.chr6 548852 28 + 647215 GTAGCACAGGAGTTTTCTCTGTATAGAT - -a -s simMouse_chr6.simMouse.chr6 538227 2 + 636262 GT -s Anc0.Anc0refChr3 141362 2 + 222631 GA -s Anc1.Anc1refChr6 176741 2 + 197743 GA -s Anc2.Anc2refChr1 54802 2 + 142988 GA -s mr.mrrefChr3 88607 2 + 181027 GT -s simCow_chr6.simCow.chr6 512005 2 + 602619 GA -s simDog_chr6.simDog.chr6 501328 2 + 593897 GT -s simHuman_chr6.simHuman.chr6 508549 2 + 601863 GA -s simRat_chr6.simRat.chr6 548880 2 + 647215 GG - -a -s simMouse_chr6.simMouse.chr6 538229 12 + 636262 CAGAGTTTGACT -s Anc0.Anc0refChr3 141364 12 + 222631 CAGATTTTGACC -s Anc1.Anc1refChr6 176743 12 + 197743 CAGATTTTGACC -s Anc2.Anc2refChr1 54804 12 + 142988 CAGATTTTGACC -s mr.mrrefChr3 88609 12 + 181027 CAGAGTTTGACT -s simCow_chr6.simCow.chr6 512010 12 + 602619 CAGATTTTGACA -s simDog_chr6.simDog.chr6 501330 12 + 593897 TGGATTTTGACC -s simHuman_chr6.simHuman.chr6 508551 12 + 601863 CAGATTTTGGCC -s simRat_chr6.simRat.chr6 548882 12 + 647215 TAGGGTTTGACT - -a -s simMouse_chr6.simMouse.chr6 538241 3 + 636262 GTC -s Anc0.Anc0refChr3 141381 3 + 222631 GTC -s Anc1.Anc1refChr6 176760 3 + 197743 GTC -s Anc2.Anc2refChr1 54821 3 + 142988 ATC -s mr.mrrefChr3 88621 3 + 181027 GTC -s simCow_chr6.simCow.chr6 512027 3 + 602619 TTC -s simDog_chr6.simDog.chr6 501347 3 + 593897 ATC -s simHuman_chr6.simHuman.chr6 508568 3 + 601863 GTC -s simRat_chr6.simRat.chr6 548894 3 + 647215 GAC - -a -s simMouse_chr6.simMouse.chr6 538244 55 + 636262 CAATACAGTGCATATCCACCCCTTGAACAAATACATGCCTTATGTGTGCTCAGCA -s Anc0.Anc0refChr3 141384 51 + 222631 CTTAACAGTGCTTATCTACCTTTTAAAC----ACATACCTAATGTGTGCACAGCA -s Anc1.Anc1refChr6 176763 51 + 197743 CTTAACAGTGCTTATCTACCTTTTAAAC----ACATACCTAATGTGTGCACAGCA -s Anc2.Anc2refChr1 54824 51 + 142988 CTTAACAGTGCTTAACTACCTTTTAACT----ACATATCTAAAGTGTGCACAGCA -s mr.mrrefChr3 88624 51 + 181027 CAAAACAGTGCATATCCACCCCTTGAAC----ACATGCCTTATGTGTGCTCAGCA -s simCow_chr6.simCow.chr6 512030 51 + 602619 CTTAAGGGTGTGTACCTGCTGTATAACT----ACATGTCTATAGCATGCACAGCA -s simDog_chr6.simDog.chr6 501355 46 + 593897 CTTAACAATGCTTAACTACCTTTTAACT----ACATATCTAA--TGTGCAAA--- -s simHuman_chr6.simHuman.chr6 508571 51 + 601863 GTGAGCAGTGCTTATCTACATTTTAAAC----ACATACCTAATGTGTGCACAGCA -s simRat_chr6.simRat.chr6 548897 17 + 647215 CACAACGGTGCCTA--------------------------------------GCA - -a -s simMouse_chr6.simMouse.chr6 538299 32 + 636262 GTATGTTGGATCCCAGTTAGGCATTTAGGGTT -s Anc0.Anc0refChr3 141437 18 + 222631 GTATGTTGGAT-TCAGTTA------------- -s Anc1.Anc1refChr6 176816 18 + 197743 GTATGTTGGAT-TCAGTTA------------- -s Anc2.Anc2refChr1 54877 18 + 142988 GTATGTTGGAT-TCAGTCA------------- -s mr.mrrefChr3 88677 31 + 181027 GTATGTTGGAT-CCAGTTAGGCATTTAGGGTT -s simCow_chr6.simCow.chr6 512083 14 + 602619 GTATGTCAGAT-TCA----------------- -s simDog_chr6.simDog.chr6 501401 18 + 593897 GTATGTTGTAT-TCAGTCA------------- -s simHuman_chr6.simHuman.chr6 508624 18 + 601863 GTATGTTGGAA-TCAGATA------------- -s simRat_chr6.simRat.chr6 548916 31 + 647215 GTATGTCGGAT-ACAGTTATGCATGTAGGGTT - -a -s simMouse_chr6.simMouse.chr6 538331 18 + 636262 GCCATTTAGGTGTTGGAC -s Anc0.Anc0refChr3 141455 18 + 222631 GCCATTTCGGTATTAGAC -s Anc1.Anc1refChr6 176834 18 + 197743 GCCATTTCGGTATTAGAC -s Anc2.Anc2refChr1 54895 18 + 142988 GCCACTCCGGTATTAGAA -s mr.mrrefChr3 88708 18 + 181027 GCCATTTAGGTGTTGGAC -s simCow_chr6.simCow.chr6 512097 4 + 602619 --------------AGAG -s simDog_chr6.simDog.chr6 501419 18 + 593897 GCCACTCCGGTATTAGAA -s simHuman_chr6.simHuman.chr6 508642 18 + 601863 GTCATTTTGGTATTAGAC -s simRat_chr6.simRat.chr6 548948 18 + 647215 GCCATGTAGGTGTTGGAC - -a -s simMouse_chr6.simMouse.chr6 538349 17 + 636262 ATTTGTAAAACTTCATA -s Anc0.Anc0refChr3 141473 15 + 222631 ATTCCTAATTTTTAA-- -s Anc1.Anc1refChr6 176852 15 + 197743 ATTCCTAATTTTTAA-- -s Anc2.Anc2refChr1 54913 15 + 142988 ATTCCTAATTTTTAA-- -s mr.mrrefChr3 88726 17 + 181027 ATTTGTAAAATTTAATA -s simCow_chr6.simCow.chr6 512101 5 + 602619 ----------TGTAT-- -s simDog_chr6.simDog.chr6 501437 15 + 593897 ATTCCTAATTCTTAA-- -s simHuman_chr6.simHuman.chr6 508660 15 + 601863 ATTCATAATCTTGAA-- -s simRat_chr6.simRat.chr6 550506 17 + 647215 atTTGTAAAATTTAATA - -a -s simMouse_chr6.simMouse.chr6 538366 110 + 636262 GCATTAGCCGGTCCTATACATAAGAGTTAACACCACAAAGGCACCAATCCTTATGTTCATACCGGTCCTATACATAAGAGTTAACACCACAAAGGCACCAAACCTTATGT -s Anc0.Anc0refChr3 141488 55 + 222631 -CTTTAGCCTGTCACTCACCTAAAGGTTAACACCACTAGGGTACCAAT------------------------------------------------------CATTCTGT -s Anc1.Anc1refChr6 176867 55 + 197743 -CTTTAGCCTGTCACTCACCTAAAGGTTAACACCACTAGGGTACCAAT------------------------------------------------------CATTCTGT -s Anc2.Anc2refChr1 54928 55 + 142988 -CTTTAGCCTGCCACTCACCTAAAGGATAGCACCGCTAGGGTACCAAT------------------------------------------------------CATTCTGT -s mr.mrrefChr3 88743 56 + 181027 GCATTAGCCTGTCCCATACATAAAAGTTAACACCACAAAGGCACCAAT------------------------------------------------------CATTATGT -s simCow_chr6.simCow.chr6 512106 55 + 602619 -CTACAGCCTGCCACTCACCTAAAGTATTGCACCTCTATGGTACCAAT------------------------------------------------------CACTCTGT -s simDog_chr6.simDog.chr6 501452 43 + 593897 -CTTTAGTCTG-------CTTAAAGGATAGCACCGTTAGGGTACC-----------------------------------------------------------TTCTGT -s simHuman_chr6.simHuman.chr6 508675 55 + 601863 -CTCTAACCTGTTACCCACCTAAAGATTAACAGCACTACGGTACCAAT------------------------------------------------------CATTCTGT -s simRat_chr6.simRat.chr6 550525 56 + 647215 GCATTAGCCTGTCCCATACATAAAAGTTAATACCACAAAAGCACCAAT------------------------------------------------------CATTATGT - -a -s simMouse_chr6.simMouse.chr6 538476 65 + 636262 TCATAGAGATCTGGTCTTTTCTAGCTACACACTCGACTCTCTCCTGTGTAGTCTCGCCCCTGTGC -s Anc0.Anc0refChr3 141549 65 + 222631 ACACAGATATATGTTCTTTTAATGATCCACATTCCACACTCTTCTATGTAGCCTTGCACCATTAA -s Anc1.Anc1refChr6 176928 65 + 197743 ACACAGATATATGTTCTTTTAATGATCCACATTCCACACTCTTCTATGTAGCCTTGCACCATTAA -s Anc2.Anc2refChr1 54989 65 + 142988 ACACAAATATATGTTCTTTTAATGATCAACATTCCACACTTTTCCATGTAGTCTTACAACATCAA -s mr.mrrefChr3 88799 65 + 181027 TCATAGAGATCTGGTCTTTTCAAGCTACACACTCGACTCTCTCCTGTGTAGCCTCGCCCCTGTGC -s simCow_chr6.simCow.chr6 512167 56 + 602619 GCACAAATATCTATTCTTTTCATGATCTAAAGTCCACAC---------TAGTCTTACAACATCAA -s simDog_chr6.simDog.chr6 501501 58 + 593897 ACACAAATGTATGTTCTGTTAATGATCAACATTCCACACTTTTCCATGTAGTCTTAA-------A -s simHuman_chr6.simHuman.chr6 508742 65 + 601863 ACACAGATATTTGTTCTTTTTATGATCCACATTCCACACTCTACTATGTTGCTTTGCACCAATAA -s simRat_chr6.simRat.chr6 550581 41 + 647215 TCATAGAGATCTTGTCTTTTCAAGCTACACA-----------CCTGTGTAGC------------- - -a -s simMouse_chr6.simMouse.chr6 538541 5 + 636262 AGAAT -s Anc0.Anc0refChr3 141614 5 + 222631 ATAAT -s Anc1.Anc1refChr6 176993 5 + 197743 ATAAT -s Anc2.Anc2refChr1 55054 5 + 142988 ATAAT -s mr.mrrefChr3 88864 5 + 181027 AGAAT -s simCow_chr6.simCow.chr6 512225 5 + 602619 ATAAT -s simDog_chr6.simDog.chr6 501559 5 + 593897 ATAGT -s simHuman_chr6.simHuman.chr6 508807 5 + 601863 ATAAT - -a -s simMouse_chr6.simMouse.chr6 538546 1 + 636262 A -s Anc0.Anc0refChr3 141619 1 + 222631 A -s Anc1.Anc1refChr6 176998 1 + 197743 A -s Anc2.Anc2refChr1 55059 1 + 142988 A -s mr.mrrefChr3 88869 1 + 181027 A -s simCow_chr6.simCow.chr6 512231 1 + 602619 A -s simDog_chr6.simDog.chr6 501564 1 + 593897 A -s simHuman_chr6.simHuman.chr6 508812 1 + 601863 A - -a -s simMouse_chr6.simMouse.chr6 538547 7 + 636262 GCATAAT -s Anc0.Anc0refChr3 141632 7 + 222631 GAATAGT -s Anc1.Anc1refChr6 177011 7 + 197743 GAATAGT -s Anc2.Anc2refChr1 55072 7 + 142988 GAATAGC -s mr.mrrefChr3 88870 7 + 181027 GCATAAT -s simCow_chr6.simCow.chr6 512244 7 + 602619 AAATAGC -s simDog_chr6.simDog.chr6 501577 6 + 593897 GAACA-C -s simHuman_chr6.simHuman.chr6 508825 7 + 601863 GAATAGT - -a -s simMouse_chr6.simMouse.chr6 538554 33 + 636262 AGCTCCAATATGCAGGTGCTCAAAACTTGGGTG -s Anc0.Anc0refChr3 141641 33 + 222631 AACCACAATAGGCAGGTGACTAAAACTGGAGTG -s Anc1.Anc1refChr6 177020 33 + 197743 AACCACAATAGGCAGGTGACTAAAACTGGAGTG -s Anc2.Anc2refChr1 55081 33 + 142988 AACCACAATGGGCAGGTCACTAAAAGTGGAGTG -s mr.mrrefChr3 88877 33 + 181027 AGCTCCAATATGCAGGTGCTCAAAACTTGGGTG -s simCow_chr6.simCow.chr6 512253 32 + 602619 AACC-CAATGGTCAGGTGATTAAAAGTGGGGTG -s simDog_chr6.simDog.chr6 501585 33 + 593897 AACGACAATGGGGAGGTCACTAAAAGCCGAGTA -s simHuman_chr6.simHuman.chr6 508834 30 + 601863 ATCCACAACAGGCAGGTG---AAATCTGGAGTG -s simRat_chr6.simRat.chr6 550622 23 + 647215 ----------TCCAAGTGCTTAAAACTCAGGTG - -a -s simMouse_chr6.simMouse.chr6 538587 66 + 636262 CCTTGAGCTACTTATAAACCATAGGCAGGCCATAGCATGTTTATTTCCTAAGTGGGCATCTTGTTT -s Anc0.Anc0refChr3 141678 66 + 222631 CCTTCAGACATTTGTAAACCACCACCACCCCTTGGCATGGATATCTACTGAGTGGACATCTACTTT -s Anc1.Anc1refChr6 177057 66 + 197743 CCTTCAGACATTTGTAAACCACCACCACCCCTTGGCATGGATATCTACTGAGTGGACATCTACTTT -s Anc2.Anc2refChr1 55118 66 + 142988 CCTTCAGACATTTGTAGACCACCACCACCCCTTGGCATGGATATCTACTGTGTGGACATGTACTTT -s mr.mrrefChr3 88910 66 + 181027 CCTTGAGCCACTTATAAACCATAGGCAGGCCATAGCATGGTTATTTCCTAAGTGGACATCTTGTTT -s simCow_chr6.simCow.chr6 512289 66 + 602619 CATTCAGACACTTGTTGACAACCACCAGACCTGAGCATAGATATGTACTGGGTGGACATATAGCTT -s simDog_chr6.simDog.chr6 501625 66 + 593897 CCTTCAGACATTTGTAGACCACCACCACCCCCTGGCATGGATATCTGCCATATGAACATGTGCTTT -s simHuman_chr6.simHuman.chr6 508868 66 + 601863 CTTTCAGACATGTGTAAACCACCATCACTCCTTGGCATGGATAACTAGTGAGTGGACATCTAATTT -s simRat_chr6.simRat.chr6 550645 66 + 647215 CCCTAAGCCACTTATGAACCATTGGCAGGCCATAGCATGGTTATTTCCTAAGTGGACATCTCGTTT - -a -s simMouse_chr6.simMouse.chr6 538653 35 + 636262 TAAAACCAAGCTGATTTGCCATCTGCAGAGGGGTG -s Anc0.Anc0refChr3 141745 33 + 222631 GCTGGCCAATCTCATTTGCCATATG--GAACTGTG -s Anc1.Anc1refChr6 177124 33 + 197743 GCTGGCCAATCTCATTTGCCATATG--GAACTGTG -s Anc2.Anc2refChr1 55185 33 + 142988 GCTGGCCAATCTCGTTTGCCAAATG--GAACTGCG -s mr.mrrefChr3 88977 35 + 181027 TAAAACCAAGCTGATTTGCCATCTGCAGAGGGGTG -s simCow_chr6.simCow.chr6 512355 11 + 602619 --TTGCCAATTTC---------------------- -s simDog_chr6.simDog.chr6 501692 33 + 593897 GCTGGCCTTACTCGTTTGCCAAATG--GAACTGCG -s simHuman_chr6.simHuman.chr6 508935 33 + 601863 GCTGGGCAATCTTATTTGCCATTTG--GAATTGTG -s simRat_chr6.simRat.chr6 550712 35 + 647215 TGAAATGAAGCTGACTTGCCATCTGCAAAGGGGCC - -a -s simMouse_chr6.simMouse.chr6 538688 3 + 636262 TTA -s Anc0.Anc0refChr3 141778 3 + 222631 TTA -s Anc1.Anc1refChr6 177157 3 + 197743 TTA -s Anc2.Anc2refChr1 55218 3 + 142988 TTA -s mr.mrrefChr3 89012 3 + 181027 TTA -s simDog_chr6.simDog.chr6 501726 3 + 593897 TTA -s simHuman_chr6.simHuman.chr6 508968 3 + 601863 TTA -s simRat_chr6.simRat.chr6 550747 3 + 647215 TTA - -a -s simMouse_chr6.simMouse.chr6 538691 10 + 636262 AATCTATGCG -s Anc0.Anc0refChr3 141782 10 + 222631 AATCTATTCC -s Anc1.Anc1refChr6 177161 10 + 197743 AATCTATTCC -s Anc2.Anc2refChr1 55222 10 + 142988 AATCTTATCC -s mr.mrrefChr3 89015 10 + 181027 AATCTATGCG -s simDog_chr6.simDog.chr6 501730 10 + 593897 AATCTTATCC -s simHuman_chr6.simHuman.chr6 508972 10 + 601863 AATCTATCTC -s simRat_chr6.simRat.chr6 550750 10 + 647215 AATCTGTGCA - -a -s simMouse_chr6.simMouse.chr6 538701 34 + 636262 TCAATGGTCTTATATTGCTGCTATAATTTTTCTG -s Anc0.Anc0refChr3 141792 24 + 222631 ATGTGGATCTTTTATGG----------TTTTATG -s Anc1.Anc1refChr6 177171 24 + 197743 ATGTGGATCTTTTATGG----------TTTTATG -s Anc2.Anc2refChr1 55232 24 + 142988 ATGTGGATTTTTTGTGG----------TCTTATG -s mr.mrrefChr3 89025 34 + 181027 TCAATGGTCTTATATTGCTGCTATAATTTTTCTG -s simDog_chr6.simDog.chr6 501740 24 + 593897 ATGTGGATTTTTTGTGG----------TCTTATG -s simHuman_chr6.simHuman.chr6 508982 24 + 601863 ATGTCGATCTTTTATGG----------TTTTATG -s simRat_chr6.simRat.chr6 550772 34 + 647215 TCAAGGGTGTTATATTGCCGCTATAATTTTTTTA - -a -s simMouse_chr6.simMouse.chr6 538735 2 + 636262 GC -s Anc0.Anc0refChr3 141816 2 + 222631 TC -s Anc1.Anc1refChr6 177195 2 + 197743 TC -s Anc2.Anc2refChr1 55258 2 + 142988 TC -s mr.mrrefChr3 89059 2 + 181027 GC -s simDog_chr6.simDog.chr6 501766 2 + 593897 TC -s simRat_chr6.simRat.chr6 550806 2 + 647215 GC - -a -s simMouse_chr6.simMouse.chr6 538737 67 + 636262 CAATTTGGGCTGTATGTGGTCCTATGTACATACTTACTCCACAGACTTAACTATGCTACCCTGTCCA -s Anc0.Anc0refChr3 141818 56 + 222631 TAATTTGGGTTGTATATGGCCCTATTTTCATACT------ACAGCCATAATTATGCTGCCAT----- -s Anc1.Anc1refChr6 177197 61 + 197743 TAATTTGGGTTGTATATGGCCCTATTTTCATACT------ACAGCCATAATTATGCTGCCATACCCA -s Anc2.Anc2refChr1 55260 56 + 142988 TAACTTGGGTTGTATATGGCCCTATTTTCATACT------ACAGCCATAATTATGCTGCCAT----- -s mr.mrrefChr3 89061 67 + 181027 CAATTTGGGTTGTATGTGGTCCTATGTACATACTTACTCCACAGACTTAACTATGCTACCCTGTCCA -s simCow_chr6.simCow.chr6 512366 56 + 602619 TCACTCAGGTTGTATATGACCCCATTTCCAAACT------ACAGCCATAATTATGCTGCCAT----- -s simDog_chr6.simDog.chr6 501786 56 + 593897 TAACTTGGGTTGTATATAGCCCTATTTTCATACT------TCGGCTATAATTCTGCTGCCAT----- -s simHuman_chr6.simHuman.chr6 509006 58 + 601863 ---TTTTGGTTGTATATGGCCCTATATTCATAGT------ACAGCCATAATTATTCTGCCATACCCA -s simRat_chr6.simRat.chr6 550808 66 + 647215 CCAATTCGGTTGTATGTCGTCCTGTGTACATACTTACACCACAGACTTGA-TATGCCACCCTGTTCA - -a -s simMouse_chr6.simMouse.chr6 538804 8 + 636262 CTTACTTA -s Anc1.Anc1refChr6 177258 8 + 197743 CTTTCTTA -s mr.mrrefChr3 89128 8 + 181027 CTTACTTA -s simHuman_chr6.simHuman.chr6 509065 8 + 601863 CTTTCTTA -s simRat_chr6.simRat.chr6 550874 8 + 647215 CTTACTTA - -a -s simMouse_chr6.simMouse.chr6 538812 25 + 636262 ACAGAAGGGTATCATTGCCTTGATT -s Anc0.Anc0refChr3 141888 25 + 222631 ATAGAAAGGTATCATCGCCTGGATC -s Anc1.Anc1refChr6 177280 25 + 197743 ATAGAAAGGTATCATCGCCTGGATC -s Anc2.Anc2refChr1 55330 25 + 142988 ATAGAGAGGTATCATCACCTGGATC -s mr.mrrefChr3 89136 25 + 181027 ACAGAAGGGTATCATTGCCTTGATT -s simCow_chr6.simCow.chr6 512437 25 + 602619 ATAGAGAGGTATCATCACCTGGATC -s simDog_chr6.simDog.chr6 501856 24 + 593897 GTAG-GAGGTATCATCACCTGGATC -s simHuman_chr6.simHuman.chr6 509112 25 + 601863 ATAGAAAGGTATCATCGCCTGTATC -s simRat_chr6.simRat.chr6 550882 25 + 647215 ACAGAAGGGTATCATAACCTGGATT - -a -s simMouse_chr6.simMouse.chr6 538837 3 + 636262 ATT -s Anc0.Anc0refChr3 142074 3 + 222631 ATT -s Anc1.Anc1refChr6 177466 3 + 197743 ATT -s Anc2.Anc2refChr1 55525 3 + 142988 CTT -s mr.mrrefChr3 89161 3 + 181027 ATT -s simCow_chr6.simCow.chr6 512627 3 + 602619 CTT -s simDog_chr6.simDog.chr6 502050 3 + 593897 CAT -s simHuman_chr6.simHuman.chr6 509300 3 + 601863 ATT -s simRat_chr6.simRat.chr6 550907 3 + 647215 ATT - -a -s simMouse_chr6.simMouse.chr6 538840 37 + 636262 AACTAATCCATACACAAGTCATTATATGCCCCAATTT -s Anc0.Anc0refChr3 142077 32 + 222631 GACTAATACATTTACTAGTCATCATATGTC-----TT -s Anc1.Anc1refChr6 177469 32 + 197743 GACTAATACATTTACTAGTCATCATATGTC-----TT -s Anc2.Anc2refChr1 55528 32 + 142988 GACTAGTACATTTACTAATCATCGTATGTC-----TT -s mr.mrrefChr3 89164 37 + 181027 AACTAATACATACACTAGTCATTATATGCCTCAATTT -s simCow_chr6.simCow.chr6 512630 27 + 602619 AGGTACTACATTTATTAATTACCTTAT---------- -s simDog_chr6.simDog.chr6 502053 32 + 593897 GACCAGTACATTTACTAACCATTGTCTGTC-----TT -s simHuman_chr6.simHuman.chr6 509303 32 + 601863 GCCTCATACATTTAATAGTCATCATATGTC-----TT -s simRat_chr6.simRat.chr6 550913 37 + 647215 ACCTAATACATAAACTAGTTATTATATGCCTCCATTT - -a -s simMouse_chr6.simMouse.chr6 538877 77 + 636262 ACATAGATTTTAGCCTGGGCATGGAAAAGTCTGTAGTGGACTCCTGGATGCCTTGTGCCAACATACTACATGCCAGA -s Anc0.Anc0refChr3 142109 68 + 222631 ACATAGATGTTAACCTAGACTTGGGAAAGTCTGCAACGGACTCCTGGATGACTTGC---------CTACCTGCCTGA -s Anc1.Anc1refChr6 177501 68 + 197743 ACATAGATGTTAACCTAGACTTGGGAAAGTCTGCAACGGACTCCTGGATGACTTGC---------CTACCTGCCTGA -s Anc2.Anc2refChr1 55560 68 + 142988 ACATAGGTGTTAACCCAGACTTGGGAAAGTGTGCAACGGACTCGTGGATGACTTGC---------CTACCTGCCTGA -s mr.mrrefChr3 89201 77 + 181027 ACATAGATTTTAGCCTAGACATGGAAAAGTCTGTAGTGGACTCCTGGATGACTTGTGCCAACATACTACATGCCAGA -s simCow_chr6.simCow.chr6 512657 62 + 602619 ------GTGTTAACCCAGAATTGGGAAAGTTGACTACAGACTCATGGATGCCTAGC---------CTACCTACCTGA -s simDog_chr6.simDog.chr6 502089 68 + 593897 ACATAGGTGTTAACCCAGACTTGGGAAAGTGTGCAGTGGACTCGTGGATGACTTGT---------CTACTTGCCTGA -s simHuman_chr6.simHuman.chr6 509335 68 + 601863 ACACAGATGTTACCCTAAACTCGGGAACGTCTGCAACGGACACCTGCATGATTTGC---------CTACCTGCCTGT -s simRat_chr6.simRat.chr6 550950 69 + 647215 TCATAGTTTTTAGCCTAGACATGGA-------GTAATGGACT-CTGGATGACTTGTGCCTACATACTACATGCCAGA - -a -s simMouse_chr6.simMouse.chr6 538954 25 + 636262 TTCATATAAAAATGGTCTCCGTGTC -s Anc0.Anc0refChr3 142177 24 + 222631 TTTT-TTAAAGAGGGTCTCCGTGTC -s Anc1.Anc1refChr6 177569 24 + 197743 TTTT-TTAAAGAGGGTCTCCGTGTC -s Anc2.Anc2refChr1 55628 24 + 142988 TTTT-TCAAAGAGGGTCTCCGTGTC -s mr.mrrefChr3 89278 24 + 181027 TTCA-ATAAAGATGGTCTCCGTGTC -s simCow_chr6.simCow.chr6 512720 24 + 602619 TTTT-TCAAAGCGGGTCTCCGTGTC -s simDog_chr6.simDog.chr6 502157 24 + 593897 TCCT-GCAAAGAGGGTCTCCGTGTC -s simHuman_chr6.simHuman.chr6 509403 24 + 601863 ATTT-TTAGAGAGGGCCTCCGTGTG -s simRat_chr6.simRat.chr6 551019 24 + 647215 TTCA-ATAAAGATGATCTCCGTGTT - -a -s simMouse_chr6.simMouse.chr6 538979 45 + 636262 ATATGATAAAACGAGCCAAATATTGACAATCTACAGGTTTATGTT -s Anc0.Anc0refChr3 142201 45 + 222631 ATCTGCTTAGATAAGCCAACTCCAAACAATCAATAGTATGATGTT -s Anc1.Anc1refChr6 177593 45 + 197743 ATCTGCTTAGATAAGCCAACTCCAAACAATCAATAGTATGATGTT -s Anc2.Anc2refChr1 55652 45 + 142988 ATCTTCTTAGATAAGCCAGCTCCAAACAAGCAATAGTATGATGTT -s mr.mrrefChr3 89302 45 + 181027 ATATGATAAAACGAGCCAAATATAGACAATCAATAGGTTTATGTT -s simCow_chr6.simCow.chr6 512746 35 + 602619 GTCATCTGAGATAAGCTATCTATAACC----------ATGAGGTT -s simDog_chr6.simDog.chr6 502181 44 + 593897 ATCTTCTTAGATA-GCCTGCTCCAAAAAAGCAATAGTATGATGTT -s simHuman_chr6.simHuman.chr6 509427 45 + 601863 ATCTGCTTAGATAAGCCAACTGGAAACAATCAATTGCATGATGTT -s simRat_chr6.simRat.chr6 551043 39 + 647215 ACATGATAAAACGAGCCGAATATAGACAATCAATAGGTT------ - -a -s simMouse_chr6.simMouse.chr6 539024 13 + 636262 ACTATATGGTATA -s Anc0.Anc0refChr3 142247 13 + 222631 ATTACATGGTCTA -s Anc1.Anc1refChr6 177639 13 + 197743 ATTACATGGTCTA -s Anc2.Anc2refChr1 55698 13 + 142988 ATTACGTGCTCTA -s mr.mrrefChr3 89347 13 + 181027 ACTATATGGTATA -s simCow_chr6.simCow.chr6 512782 11 + 602619 AATA--TGTTCCA -s simDog_chr6.simDog.chr6 502226 13 + 593897 TTTACGTGCTCTA -s simHuman_chr6.simHuman.chr6 509473 13 + 601863 ATTGAATCGTCTA - -a -s simMouse_chr6.simMouse.chr6 539037 112 + 636262 CTACCAATGAATTGAACTTAATTAGTTGGTGTTCATTACATTAAAAGGCATAATAAGCGGATGTCACTGCCAACTACTGGTGCGTTATTGATCTGCAACAAAAACCATAGCA -s Anc0.Anc0refChr3 142263 42 + 222631 GTATCAATAAATTCAATTTAATTTTGTTGTGTTTTTTGT----------------------------------------------------------------------GAA -s Anc1.Anc1refChr6 177655 42 + 197743 GTATCAATAAATTCAATTTAATTTTGTTGTGTTTTTTGT----------------------------------------------------------------------GAA -s Anc2.Anc2refChr1 55714 42 + 142988 GTATCATTAAATTCATTTTAATTTTGTTGTGTTTTTTGT----------------------------------------------------------------------GAA -s mr.mrrefChr3 89360 46 + 181027 CTACCAATGAATTGAATTTAATTAGTTTGTGTTCATTACAC------------------------------------------------------------------TAGCA -s simCow_chr6.simCow.chr6 512796 42 + 602619 ATATCAGTAAATTTGTTCTAATTTTGTTGTGTTTTTTGT----------------------------------------------------------------------GAA -s simDog_chr6.simDog.chr6 502242 42 + 593897 GTGTCATTGAATTCATTTTAATTTTTTTGTGTTTTTTGT----------------------------------------------------------------------GAA -s simHuman_chr6.simHuman.chr6 509489 42 + 601863 TCATCAATAAACTCAATTTAATTTTGTTGTGTTTCTTGT----------------------------------------------------------------------GAA -s simRat_chr6.simRat.chr6 551082 43 + 647215 ---CCAATGAATTGAATTTAATTAGGTTGTGTTCATTACAC------------------------------------------------------------------TAGCA - -a -s simMouse_chr6.simMouse.chr6 539149 3 + 636262 AAC -s Anc0.Anc0refChr3 142305 3 + 222631 TTC -s Anc1.Anc1refChr6 177697 3 + 197743 TTC -s Anc2.Anc2refChr1 55765 3 + 142988 TTC -s mr.mrrefChr3 89406 3 + 181027 AAC -s simCow_chr6.simCow.chr6 512847 3 + 602619 GTC -s simDog_chr6.simDog.chr6 502293 3 + 593897 TTC -s simHuman_chr6.simHuman.chr6 509531 3 + 601863 TCC -s simRat_chr6.simRat.chr6 551125 3 + 647215 ACC - -a -s simMouse_chr6.simMouse.chr6 539152 50 + 636262 CGAAAAATAGTGCAATATACTAGACCTGGAACCACGAGTTTCTATACATC -s Anc0.Anc0refChr3 142308 47 + 222631 CTAGAGACAATATGATGCACTAAGCCTGGGACCACAATTTACTATG---C -s Anc1.Anc1refChr6 177700 50 + 197743 CTAGAGACAATATGATGCACTAAGCCTGGGACCACAATTTACTATGCATC -s Anc2.Anc2refChr1 55768 47 + 142988 CTAGAGACAATATGATGCAAGAAGCCTGGGACCTCAATTTACTATG---C -s mr.mrrefChr3 89409 50 + 181027 CGAAAAACAGTGCAATATACTAGACCTGGAACCACAAGTTACTATACATC -s simCow_chr6.simCow.chr6 512866 47 + 602619 CTAGAAACCATATGATGCTAGAAACCTGGGAGCCAGATTTACTATG---T -s simDog_chr6.simDog.chr6 502296 47 + 593897 CTGGAGACAATATGATGCAAGAAGCCTGGGACCTCAATTTACTATA---C -s simHuman_chr6.simHuman.chr6 509534 50 + 601863 CCAGGGGCAATATGATGCACTGTGCCTGGGACCACAATTTACTATGCATC -s simRat_chr6.simRat.chr6 551128 50 + 647215 CCATAAACTGTGCAATATAGTCGACCTGGAACCACAAGTTACTATACATC - -a -s simMouse_chr6.simMouse.chr6 539202 140 + 636262 AAATAATTTGTTCTGTTTCTCTTAGGCCTCGCTCAACATTTTGTTATGTGGCAACATAATAATTGAGCCCAATTGAGTTGGTGGGTCCACTAAGCCACCAGACAGGCCAGACAGCTGCAGCCTGTGTTCTAGGTATAGTA -s Anc0.Anc0refChr3 142362 102 + 222631 AAGTAATTCATCCTGTGTCTCACAGTCTT----------------------C-ACCTAATGCTTGAGCCAAATTCAATCACTGAGTTTACTAAGCAGCCAG------------GCTGTAGCC-AAGCCatagg--tagca -s Anc1.Anc1refChr6 177757 102 + 197743 AAGTAATTCATCCTGTGTCTCACAGTCTT----------------------C-ACCTAATGCTTGAGCCAAATTCAATCACTGAGTTTACTAAGCAGCCAG------------GCTGTAGCC-AAGCCatagg--tagca -s Anc2.Anc2refChr1 55822 102 + 142988 AAGTAATTCAGCCTGTGTCTCACAGTTTT----------------------T-GCCTAATGCTTGAGCCAAATTCAATCACTGAGTTTACTAAGCAGCCAG------------GCTGTAGCC-AAGCCataga--tagca -s mr.mrrefChr3 89459 117 + 181027 AAATAATTCGTTCTGTTTCTCTCAGGCCT----------------------CAACATAATAATTGAGCCAAATTGAGTTGGTGGGTCTACTAAGCCACCAGACAGGCCAGACAGCTGCAGCC-GAGTTCTAGGTATAGTA -s simCow_chr6.simCow.chr6 512920 102 + 602619 AAGTAATTCACCCTCTGTCTCACAATGCT----------------------T-GCATAATGCTTAAGCGAAATTCAGTCACTGGGTTTGCTAAATAGCCAA------------GCTGTAGCC-AAGCCaaaga--tagca -s simDog_chr6.simDog.chr6 502350 102 + 593897 AGGTACTTCGGCCTGTGTCTCTCAGCTTT----------------------T-GCCTAGTGCTTGAGCCAAATTCAATCACTGAGTTTACTAAGCAGCCAG------------ACTGTAGTC-AAGCCGTAGA--TAACA -s simHuman_chr6.simHuman.chr6 509591 78 + 601863 AAGTaaatcatcccgtgtctcacattctt----------------------c-acctaacgcatga------------------------taagcagccag------------gatgtagct-aagccatagg--tagca -s simRat_chr6.simRat.chr6 551178 108 + 647215 AATTAATTCATTCTGTTTCTCTCAAGTCT----------------------CCACATAATAATTGAGACACATTGAGTTCTTGTGTCTACTAAGCCA---------CCAGGCTGCTGCAGCA-GAGTTGTAGGTATTGTa - -a -s simMouse_chr6.simMouse.chr6 539342 18 + 636262 ATATGCAAAGACAGCAAT -s Anc0.Anc0refChr3 142464 18 + 222631 ctatgcaaaggtttcaat -s Anc1.Anc1refChr6 177859 18 + 197743 ctatgcaaaggtttcaat -s Anc2.Anc2refChr1 55924 18 + 142988 ctatgcaaaggtttcaat -s mr.mrrefChr3 89576 18 + 181027 ATATGcaaagacagcaat -s simCow_chr6.simCow.chr6 513022 18 + 602619 acatgcaaaggcttcaat -s simDog_chr6.simDog.chr6 502457 18 + 593897 CTAGCCATAGATAACAAT -s simHuman_chr6.simHuman.chr6 509669 18 + 601863 ctgtgcaaaggattcaat -s simRat_chr6.simRat.chr6 551286 18 + 647215 atacacaaaggaagcaat - -a -s simMouse_chr6.simMouse.chr6 539360 10 + 636262 ATTTGATAAC -s Anc0.Anc0refChr3 142482 10 + 222631 cttaaacaac -s Anc1.Anc1refChr6 177877 10 + 197743 cttaaacaac -s Anc2.Anc2refChr1 55942 10 + 142988 cttaaacaat -s mr.mrrefChr3 89594 10 + 181027 atttgataac -s simCow_chr6.simCow.chr6 513040 7 + 602619 att---caat -s simDog_chr6.simDog.chr6 502486 10 + 593897 ctcaaacaat -s simHuman_chr6.simHuman.chr6 509687 10 + 601863 cttcaacaac -s simRat_chr6.simRat.chr6 551304 10 + 647215 attcatcaac - -a -s simMouse_chr6.simMouse.chr6 539370 37 + 636262 ATGCCAGAGTATTTGGTGTCCTATCTGCTAGGAGCAA -s Anc0.Anc0refChr3 142494 37 + 222631 gtgctggagtaattggtgttctatctgccaggagctg -s Anc1.Anc1refChr6 177889 37 + 197743 gtgctggagtaattggtgttctatctgccaggagctg -s Anc2.Anc2refChr1 55954 37 + 142988 gtgctggagtaattggtgctctatctaccaggagctg -s mr.mrrefChr3 89606 37 + 181027 gtgccagagtatttggtgtcctatctgttaggagctA -s simCow_chr6.simCow.chr6 513049 37 + 602619 gtactgaagtaattggagctccatcttccaggagctg -s simDog_chr6.simDog.chr6 502498 37 + 593897 gtgctggaataattagtgctctatctatcaggagctg -s simHuman_chr6.simHuman.chr6 509699 37 + 601863 gtgctggagtaattggtgttctatctgcacggagttg -s simRat_chr6.simRat.chr6 551316 37 + 647215 gtgccagagtatttggtatcctatctcttgagagctA - -a -s simMouse_chr6.simMouse.chr6 539407 87 + 636262 GACTAAAATGAGCTGCATGGCACCCCTGGCCCTCTCAGTAATTGATCTAGAGGAGTAATATGGACTCCACCAGACAAGGAACTACAT -s Anc0.Anc0refChr3 142531 46 + 222631 a---------agct------caaccct---tttctcac-------tcc----------------ttacaccaaaattaaaaccagat -s Anc1.Anc1refChr6 177926 46 + 197743 a---------agct------caaccct---tttctcac-------tcc----------------ttacaccaaaattaaaaccagat -s Anc2.Anc2refChr1 55991 46 + 142988 a---------aact------caaccct---tttctcac-------tcc----------------ttacaccaaaattaaaaccagat -s mr.mrrefChr3 89643 80 + 181027 AACTAAAATGAGCTGCATGGCACCCCTGGCCCTCTCAG-------TCTAGAGGAGTAATATGGACTCCACCAGACAAGGAACTACAT -s simCow_chr6.simCow.chr6 513086 46 + 602619 a---------tact------caaccac---tatctcac-------tcc----------------tctcagtgagattaaaaccggat -s simDog_chr6.simDog.chr6 502536 46 + 593897 a---------aact------caaccct---tttctcat-------gcc----------------ttacaccaaaggtaaaaccagac -s simHuman_chr6.simHuman.chr6 509736 46 + 601863 a---------agct------caaccct---tttttcac-------tcc----------------ttacatcaaaattaacacaagat -s simRat_chr6.simRat.chr6 551353 80 + 647215 AACTAAAATGAGTTGCATGGCATCCCTGGCCCTCTCAG-------TCTAGAGGGGTAAGATGGACTCCACCAGACAAGGAAGTACAT - -a -s simMouse_chr6.simMouse.chr6 539494 4 + 636262 TGTG -s Anc0.Anc0refChr3 142580 4 + 222631 cgtg -s Anc1.Anc1refChr6 177975 4 + 197743 cgtg -s Anc2.Anc2refChr1 56040 4 + 142988 tgtg -s mr.mrrefChr3 89723 4 + 181027 CGTG -s simCow_chr6.simCow.chr6 513135 4 + 602619 agtg -s simDog_chr6.simDog.chr6 502585 4 + 593897 tgtg -s simHuman_chr6.simHuman.chr6 509785 4 + 601863 cgtg -s simRat_chr6.simRat.chr6 551433 4 + 647215 CATT - -a -s simMouse_chr6.simMouse.chr6 539498 1 + 636262 T -s Anc0.Anc0refChr3 142587 1 + 222631 t -s Anc1.Anc1refChr6 177982 1 + 197743 t -s Anc2.Anc2refChr1 56047 1 + 142988 t -s mr.mrrefChr3 89727 1 + 181027 T -s simCow_chr6.simCow.chr6 513142 1 + 602619 t -s simDog_chr6.simDog.chr6 502592 1 + 593897 t -s simHuman_chr6.simHuman.chr6 509792 1 + 601863 t -s simRat_chr6.simRat.chr6 551437 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 539499 89 + 636262 GGAATTCTGCCCTACTCCTCATTCCTACTCctttcagctaccaaagtgtgttccagaggattatttgggtcacagaattcaatattctg -s Anc0.Anc0refChr3 142588 67 + 222631 gga--------------------tctaa-actctcggctaccaaggagtgttctaga-gataatgtaggcaacaagattcaagatactg -s Anc1.Anc1refChr6 177983 68 + 197743 gga--------------------tctaa-actctcggctaccaaggagtgttctagaggataatgtaggcaacaagattcaagatactg -s Anc2.Anc2refChr1 56050 67 + 142988 gaa--------------------tctaa-actctgggctatcaaggagtattctaga-gataatgtaggcaacaagattcaagatactg -s mr.mrrefChr3 89728 89 + 181027 GGAATTCTACCCTACTCCTCATTCCTAATCctttcagctgccaaagtgtgttccagaggattatttgggtcacaggattcaatattctg -s simCow_chr6.simCow.chr6 513145 66 + 602619 gca--------------------tccaa-actcttgggtagcatggagcactctaaa-gataatgtagacaacaacatttaaaatact- -s simDog_chr6.simDog.chr6 502595 67 + 593897 gag--------------------tctaa-actctgggctgtcaaggagtattctaga-gataatatagggaaaaagattcaagctactg -s simHuman_chr6.simHuman.chr6 509793 68 + 601863 gga--------------------tctaa-actctcggctactagggagtgttctagaggataatgtaggcaccttgattcaagacactg -s simRat_chr6.simRat.chr6 551438 89 + 647215 GGCATTCCACCCAACTCCCCATTCCTAATCctgtcagctgccaaagtctgttccagaggattatttgggtcacatgactcaatattctg - -a -s simMouse_chr6.simMouse.chr6 539588 29 + 636262 cattaaaatgacttgcaagcttgagacac -s Anc0.Anc0refChr3 142656 29 + 222631 cactaaaaagacttgtaagctcaagacac -s Anc1.Anc1refChr6 178052 29 + 197743 cactaaaaagacttgtaagctcaagacac -s Anc2.Anc2refChr1 56118 29 + 142988 cactgaaaagactgttaagctcaagacac -s mr.mrrefChr3 89818 29 + 181027 cattaaaatgacttgcaagcttgagacac -s simCow_chr6.simCow.chr6 513212 28 + 602619 cactgaaaaca-tgttaagctaaagacat -s simDog_chr6.simDog.chr6 502663 29 + 593897 caatgaaaagactgttaagctcaagacac -s simHuman_chr6.simHuman.chr6 509862 29 + 601863 cactacaaagacttgtaagctcaagatac -s simRat_chr6.simRat.chr6 551528 29 + 647215 cattaagatgtcttgcaagtttgtgacac - -a -s simMouse_chr6.simMouse.chr6 539617 11 + 636262 caaggaaggta -s Anc0.Anc0refChr3 142685 11 + 222631 caaagaaggta -s Anc1.Anc1refChr6 178081 11 + 197743 caaagaaggta -s Anc2.Anc2refChr1 56147 11 + 142988 caaagaaggta -s mr.mrrefChr3 89847 11 + 181027 caaggaaggta -s simCow_chr6.simCow.chr6 513241 11 + 602619 aaaagaaggta -s simDog_chr6.simDog.chr6 502692 11 + 593897 caaggaaggca -s simHuman_chr6.simHuman.chr6 509891 11 + 601863 caaagaaggta -s simRat_chr6.simRat.chr6 551557 11 + 647215 caaagaaggga - -a -s simMouse_chr6.simMouse.chr6 539628 19 + 636262 gaggaaactgaagctcagt -s Anc0.Anc0refChr3 142696 18 + 222631 gt-gaaactaagggttggt -s Anc1.Anc1refChr6 178092 18 + 197743 gt-gaaactaagggttggt -s Anc2.Anc2refChr1 56158 18 + 142988 gt-gaaactaagggttggt -s mr.mrrefChr3 89858 18 + 181027 ga-gaaactgaggcttggt -s simCow_chr6.simCow.chr6 513252 18 + 602619 gt-gaaaccaaggattagt -s simDog_chr6.simDog.chr6 502703 18 + 593897 gt-gaaactaagggttgGC -s simHuman_chr6.simHuman.chr6 509905 18 + 601863 gg-tgaatgacgttgtgat -s simRat_chr6.simRat.chr6 551568 18 + 647215 ga-gaaactgaggcttggt - -a -s simMouse_chr6.simMouse.chr6 539647 14 + 636262 ctaccacatgggga -s Anc0.Anc0refChr3 142715 14 + 222631 ttattcgattgagg -s Anc1.Anc1refChr6 178111 14 + 197743 ttattcgattgagg -s Anc2.Anc2refChr1 56177 14 + 142988 ttattcgattgagg -s mr.mrrefChr3 89876 14 + 181027 ctacaagatgggga -s simCow_chr6.simCow.chr6 513286 14 + 602619 ttatcaggttgcag -s simDog_chr6.simDog.chr6 502722 13 + 593897 CTATTCAAGCAAG- -s simHuman_chr6.simHuman.chr6 509924 14 + 601863 ttattggattgagg -s simRat_chr6.simRat.chr6 551586 14 + 647215 ctacaagatgggga - -a -s simMouse_chr6.simMouse.chr6 539661 37 + 636262 tactaCAGTTAACTGCAAACCTACACAATATGTAATG -s Anc0.Anc0refChr3 142761 37 + 222631 tactacagccaactgcaaacctacaaaatatttgctg -s Anc1.Anc1refChr6 178157 37 + 197743 tactacagccaactgcaaacctacaaaatatttgctg -s Anc2.Anc2refChr1 56223 37 + 142988 ttctacagccaactgtaaacttacaaaagatttgctg -s mr.mrrefChr3 89890 37 + 181027 tactacagTTAACTGcAAACCTACACAATATGTAATG -s simCow_chr6.simCow.chr6 513332 35 + 602619 ttctacagccaacgataaac--atcagaaatttgctg -s simDog_chr6.simDog.chr6 502735 25 + 593897 -----------ATTGTGAGATTacagatgagtt-cag -s simHuman_chr6.simHuman.chr6 509970 37 + 601863 taatatagccaactgcaaacctacaaaatatttgctg -s simRat_chr6.simRat.chr6 551600 36 + 647215 tactaccaCCAACTG-AAACCTACACAATATGTACTA - -a -s simMouse_chr6.simMouse.chr6 539698 6 + 636262 TATTCA -s Anc0.Anc0refChr3 142799 4 + 222631 --tgca -s Anc1.Anc1refChr6 178195 6 + 197743 tatgca -s Anc2.Anc2refChr1 56261 4 + 142988 --tgca -s mr.mrrefChr3 89927 6 + 181027 TATTCA -s simCow_chr6.simCow.chr6 513368 4 + 602619 --ttta -s simDog_chr6.simDog.chr6 502761 4 + 593897 --tgca -s simHuman_chr6.simHuman.chr6 510009 6 + 601863 tatgca -s simRat_chr6.simRat.chr6 551636 6 + 647215 TATTCA - -a -s simMouse_chr6.simMouse.chr6 539704 2 + 636262 TC -s Anc0.Anc0refChr3 142804 2 + 222631 cc -s Anc1.Anc1refChr6 178202 2 + 197743 cc -s Anc2.Anc2refChr1 56266 2 + 142988 cc -s mr.mrrefChr3 89933 2 + 181027 TC -s simCow_chr6.simCow.chr6 513373 2 + 602619 tc -s simDog_chr6.simDog.chr6 502766 2 + 593897 ct -s simHuman_chr6.simHuman.chr6 510016 2 + 601863 cc -s simRat_chr6.simRat.chr6 551642 2 + 647215 TC - -a -s simMouse_chr6.simMouse.chr6 539706 6 + 636262 ATAAGA -s Anc0.Anc0refChr3 142806 6 + 222631 aaagga -s Anc1.Anc1refChr6 178204 6 + 197743 aaagga -s Anc2.Anc2refChr1 56268 6 + 142988 aaagga -s mr.mrrefChr3 89935 6 + 181027 ATAAGA -s simCow_chr6.simCow.chr6 513380 6 + 602619 aaaaga -s simDog_chr6.simDog.chr6 502768 6 + 593897 taggga -s simHuman_chr6.simHuman.chr6 510018 6 + 601863 aaagga -s simRat_chr6.simRat.chr6 551644 6 + 647215 ATAAGA - -a -s simMouse_chr6.simMouse.chr6 539712 18 + 636262 AGGCTAGCCTCATGGAAT -s Anc0.Anc0refChr3 142812 18 + 222631 aggctaacctcctaggcc -s Anc1.Anc1refChr6 178210 18 + 197743 aggctaacctcctaggcc -s Anc2.Anc2refChr1 56274 18 + 142988 aggctaaccttctaggcc -s mr.mrrefChr3 89941 18 + 181027 AGGCTAGCCTCATGGAAT -s simCow_chr6.simCow.chr6 513386 18 + 602619 ggactagccttctgggcc -s simDog_chr6.simDog.chr6 502780 18 + 593897 aggagaaccataaatgct -s simHuman_chr6.simHuman.chr6 510024 18 + 601863 aggctaacctcctaggtc -s simRat_chr6.simRat.chr6 551650 18 + 647215 AGGCTAACCACATGGAAT - -a -s simMouse_chr6.simMouse.chr6 539730 7 + 636262 AATATAC -s Anc0.Anc0refChr3 142830 1 + 222631 ------c -s Anc1.Anc1refChr6 178228 1 + 197743 ------c -s Anc2.Anc2refChr1 56292 1 + 142988 ------c -s mr.mrrefChr3 89959 7 + 181027 AATATAC -s simCow_chr6.simCow.chr6 513404 1 + 602619 ------c -s simDog_chr6.simDog.chr6 502798 1 + 593897 ------c -s simHuman_chr6.simHuman.chr6 510042 1 + 601863 ------c -s simRat_chr6.simRat.chr6 551672 7 + 647215 AACATAT - -a -s simMouse_chr6.simMouse.chr6 539737 5 + 636262 AAAAC -s Anc0.Anc0refChr3 142831 5 + 222631 ataac -s Anc1.Anc1refChr6 178229 5 + 197743 ataac -s Anc2.Anc2refChr1 56293 5 + 142988 gtgac -s mr.mrrefChr3 89966 5 + 181027 AAAAC -s simCow_chr6.simCow.chr6 513585 5 + 602619 gtgat -s simDog_chr6.simDog.chr6 502799 5 + 593897 gtgac -s simHuman_chr6.simHuman.chr6 510043 5 + 601863 acaac -s simRat_chr6.simRat.chr6 551679 5 + 647215 GAAAC - -a -s simMouse_chr6.simMouse.chr6 539742 4 + 636262 TAAC -s Anc0.Anc0refChr3 142837 4 + 222631 taac -s Anc1.Anc1refChr6 178235 4 + 197743 taac -s Anc2.Anc2refChr1 56299 4 + 142988 caac -s mr.mrrefChr3 89971 4 + 181027 TAAC -s simCow_chr6.simCow.chr6 513591 4 + 602619 cacc -s simDog_chr6.simDog.chr6 502805 4 + 593897 caac -s simHuman_chr6.simHuman.chr6 510049 4 + 601863 ttac -s simRat_chr6.simRat.chr6 551684 4 + 647215 TAAC - -a -s simMouse_chr6.simMouse.chr6 539746 20 + 636262 AATGGGCAAAGAATGTGAAT -s Anc0.Anc0refChr3 142841 16 + 222631 accg----agggaggaagac -s Anc1.Anc1refChr6 178239 16 + 197743 accg----agggaggaagac -s Anc2.Anc2refChr1 56311 16 + 142988 acct----agagaggaagac -s mr.mrrefChr3 89975 20 + 181027 AATGGGCAAAGAATGTGAAT -s simCow_chr6.simCow.chr6 513603 7 + 602619 ccc-------------accc -s simDog_chr6.simDog.chr6 502817 16 + 593897 acct----agagaggaagac -s simHuman_chr6.simHuman.chr6 510053 16 + 601863 acgg----atggaagaagac -s simRat_chr6.simRat.chr6 551688 20 + 647215 AATGGGCAAGGAATGTGAAT - -a -s simMouse_chr6.simMouse.chr6 539766 5 + 636262 AGGTG -s Anc0.Anc0refChr3 142857 5 + 222631 acgtg -s Anc1.Anc1refChr6 178255 5 + 197743 ACGTG -s Anc2.Anc2refChr1 56327 5 + 142988 ccaac -s mr.mrrefChr3 89995 5 + 181027 AGGTG -s simCow_chr6.simCow.chr6 513610 5 + 602619 acacc -s simDog_chr6.simDog.chr6 502833 5 + 593897 ccaac -s simHuman_chr6.simHuman.chr6 510081 5 + 601863 ATGTG -s simRat_chr6.simRat.chr6 551708 5 + 647215 AGGTG - -a -s simMouse_chr6.simMouse.chr6 539771 17 + 636262 CTAGGGAAGATATCCCT -s Anc0.Anc0refChr3 142862 17 + 222631 ctagagaggaagaccat -s Anc1.Anc1refChr6 178260 17 + 197743 CTagagaggaagaccat -s Anc2.Anc2refChr1 56332 17 + 142988 ctagagaggaagaccat -s mr.mrrefChr3 90000 17 + 181027 CTAGGGAAGATATCCCT -s simCow_chr6.simCow.chr6 513615 17 + 602619 ctacggaggaaaaccat -s simDog_chr6.simDog.chr6 502838 17 + 593897 ctagagaggaagaccat -s simHuman_chr6.simHuman.chr6 510086 14 + 601863 CT---gagaaagaccat -s simRat_chr6.simRat.chr6 551718 17 + 647215 CTAGGGAGGATATCCCT - -a -s simMouse_chr6.simMouse.chr6 539788 14 + 636262 TAAGGATATACTAG -s Anc0.Anc0refChr3 142881 14 + 222631 tgaggaaatgctgg -s Anc1.Anc1refChr6 178279 14 + 197743 tgaggaaatgctgg -s Anc2.Anc2refChr1 56351 14 + 142988 tgaggaaatgctgg -s mr.mrrefChr3 90017 14 + 181027 TAAGGATATACTAG -s simCow_chr6.simCow.chr6 513634 14 + 602619 tcaggaaatactgg -s simDog_chr6.simDog.chr6 502857 14 + 593897 tgaggaaatgctgg -s simHuman_chr6.simHuman.chr6 510102 14 + 601863 ttacaaaatgctgg -s simRat_chr6.simRat.chr6 551735 14 + 647215 CAAGAATAGACTTG - -a -s simMouse_chr6.simMouse.chr6 539802 13 + 636262 TGCATAGCCCACT -s Anc0.Anc0refChr3 142895 13 + 222631 tgagatatccact -s Anc1.Anc1refChr6 178293 13 + 197743 tgagatatccact -s Anc2.Anc2refChr1 56365 13 + 142988 tgagatatcctct -s mr.mrrefChr3 90031 13 + 181027 TGCATAGCCCACT -s simCow_chr6.simCow.chr6 513648 13 + 602619 tgagaactccccc -s simDog_chr6.simDog.chr6 502872 13 + 593897 ttgaatatcctct -s simHuman_chr6.simHuman.chr6 510116 13 + 601863 tgagacagccatt -s simRat_chr6.simRat.chr6 551749 13 + 647215 CACATTGCCTGCT - -a -s simMouse_chr6.simMouse.chr6 539815 46 + 636262 TTAGTGGCTGCGTTTTAACTGACATAGAGAAGGATTATAAACACTA -s Anc0.Anc0refChr3 142908 34 + 222631 caa-----tttgttttaag-----aagtgagtgaatatag--ccta -s Anc1.Anc1refChr6 178306 34 + 197743 caa-----tttgttttaag-----aagtgagtgaatatag--ccta -s Anc2.Anc2refChr1 56378 34 + 142988 caa-----tttgtttcaag-----aagtgagtgaatatag--ccta -s mr.mrrefChr3 90044 46 + 181027 TTAGTGGCTGCGTTTTAACTGACATAGAGAAGGATTATAAACACTA -s simCow_chr6.simCow.chr6 513662 34 + 602619 caa-----tgtgtttggag-----aagtgagtggatatag--tcta -s simDog_chr6.simDog.chr6 502885 34 + 593897 caa-----tttgtttcaag-----cagtgcgtgaatatag--ccta -s simHuman_chr6.simHuman.chr6 510129 34 + 601863 caa-----tctattttaat-----aagtgagtgaatacag--ccta -s simRat_chr6.simRat.chr6 551762 46 + 647215 TTAATGGTTGTGGTTTAACCGACTTAGAAGAGGACTATAACCACTA - -a -s simMouse_chr6.simMouse.chr6 539861 5 + 636262 ATAAC -s Anc0.Anc0refChr3 142947 5 + 222631 atagc -s Anc1.Anc1refChr6 178345 5 + 197743 atagc -s Anc2.Anc2refChr1 56417 5 + 142988 ctagc -s mr.mrrefChr3 90090 5 + 181027 ATAAC -s simCow_chr6.simCow.chr6 513700 5 + 602619 ctagc -s simDog_chr6.simDog.chr6 502924 5 + 593897 ctagc -s simHuman_chr6.simHuman.chr6 510168 5 + 601863 agagc -s simRat_chr6.simRat.chr6 551808 5 + 647215 ATAAC - -a -s simMouse_chr6.simMouse.chr6 539866 137 + 636262 ATAACTAATCAACCCCAAGGGAGACAGTAGTTAGTTTAGGTTAGGTTCAGACAGCCTGAGTCAATAGAGCTTAAGCTGAGTCAATGCATGCAGGTGGGCAGCTGTCCAAATTAAAATATAAATGAAACAAGAGTGAG -s Anc0.Anc0refChr3 142967 61 + 222631 gtcactgactaaatctaagggaggggcttgt---------------------------------------------------------------------at-------gtcaacacatagaggaaacaaaagtcag -s Anc1.Anc1refChr6 178365 61 + 197743 gtcactgactaaatctaagggaggggcttgt---------------------------------------------------------------------at-------gtcaacacatagaggaaacaaaagtcag -s Anc2.Anc2refChr1 56438 61 + 142988 gccactgactaaatctaagggaggggcttgt---------------------------------------------------------------------at-------gtcaacacatagaggaaatgaaagtcag -s mr.mrrefChr3 90095 67 + 181027 ATAACTAATCAACCCCAAGGGAGACAGTAGT---------------------------------------------------------------------GCTGTCC-AATTAAAATATAAATGAAACAAGAGTGAG -s simCow_chr6.simCow.chr6 513721 61 + 602619 gccactggctaaatcttagggagggacttat---------------------------------------------------------------------at-------gtcaacacatacaggaaatggaagtcag -s simDog_chr6.simDog.chr6 502945 61 + 593897 gctactgactatatctaggggaggggtttgt---------------------------------------------------------------------ac-------atcaacacatagaggaaatgaaactcag -s simHuman_chr6.simHuman.chr6 510188 61 + 601863 gtcactgactcaagctgagggaggggcttgt---------------------------------------------------------------------at-------gtgaacacatataggatacaatagtaag -s simRat_chr6.simRat.chr6 551813 67 + 647215 ATAACTAATCAACCCCAAGGGAGACGGTAGT---------------------------------------------------------------------GCTGAGC-AATTAAAATATAAAAGAAATAAGGGTGAA - -a -s simMouse_chr6.simMouse.chr6 540003 4 + 636262 ACCT -s Anc0.Anc0refChr3 143028 4 + 222631 acct -s Anc1.Anc1refChr6 178426 4 + 197743 acct -s Anc2.Anc2refChr1 56499 4 + 142988 actt -s mr.mrrefChr3 90162 4 + 181027 ACCT -s simCow_chr6.simCow.chr6 513782 4 + 602619 acat -s simDog_chr6.simDog.chr6 503006 4 + 593897 actt -s simHuman_chr6.simHuman.chr6 510257 4 + 601863 acct -s simRat_chr6.simRat.chr6 551880 4 + 647215 ACCC - -a -s simMouse_chr6.simMouse.chr6 540007 20 + 636262 TAAATCAGTTCTATGGAGTG -s Anc0.Anc0refChr3 143033 19 + 222631 ttcatcagaggaatggtga- -s Anc1.Anc1refChr6 178431 20 + 197743 ttcatcagaggaatggtgag -s Anc2.Anc2refChr1 56504 19 + 142988 ttcctcagaggaatggtga- -s mr.mrrefChr3 90166 20 + 181027 TAAATCAGTTCTATggagtg -s simCow_chr6.simCow.chr6 513787 15 + 602619 aacct----ggaaaggtga- -s simDog_chr6.simDog.chr6 503011 17 + 593897 tt--tcagaggcatggtga- -s simHuman_chr6.simHuman.chr6 510262 20 + 601863 ttcattaaaggaatggtgag -s simRat_chr6.simRat.chr6 551884 20 + 647215 TAACTCAGTTCTATgaaatg - -a -s simMouse_chr6.simMouse.chr6 540027 11 + 636262 GTCATTAGAAT -s Anc0.Anc0refChr3 143052 11 + 222631 gtaattaaact -s Anc1.Anc1refChr6 178451 11 + 197743 gtaattaaact -s Anc2.Anc2refChr1 56523 11 + 142988 gtaattaaact -s mr.mrrefChr3 90186 11 + 181027 gtcattagaat -s simCow_chr6.simCow.chr6 513802 11 + 602619 gtaattaaata -s simDog_chr6.simDog.chr6 503028 11 + 593897 gtaattaaact -s simHuman_chr6.simHuman.chr6 510297 11 + 601863 gtaattaaact -s simRat_chr6.simRat.chr6 551904 11 + 647215 gtcattagact - -a -s simMouse_chr6.simMouse.chr6 540038 20 + 636262 ACTTCAGAGTAAAAATGAGA -s Anc0.Anc0refChr3 143063 20 + 222631 cctttagagcaaaaatgaga -s Anc1.Anc1refChr6 178462 20 + 197743 cctttagagcaaaaatgaga -s Anc2.Anc2refChr1 56534 20 + 142988 cctttggagcaaacatgaga -s mr.mrrefChr3 90197 20 + 181027 acttcagagtaaaaatgaga -s simCow_chr6.simCow.chr6 513813 20 + 602619 cctttggagcaaacatgaga -s simDog_chr6.simDog.chr6 503039 20 + 593897 tctttggagcaaacatgaaa -s simHuman_chr6.simHuman.chr6 510316 20 + 601863 gctttagagcgaaagcgaga -s simRat_chr6.simRat.chr6 551915 20 + 647215 acttcagagtaaaagtgaga - -a -s simMouse_chr6.simMouse.chr6 540058 5 + 636262 CATTT -s Anc0.Anc0refChr3 143083 5 + 222631 ctgtt -s Anc1.Anc1refChr6 178482 5 + 197743 ctgtt -s Anc2.Anc2refChr1 56557 5 + 142988 ctgtt -s mr.mrrefChr3 90217 5 + 181027 cattt -s simCow_chr6.simCow.chr6 513836 5 + 602619 ctgta -s simDog_chr6.simDog.chr6 503062 5 + 593897 ctgtt -s simHuman_chr6.simHuman.chr6 510336 5 + 601863 ccatt -s simRat_chr6.simRat.chr6 551962 5 + 647215 aattt - -a -s simMouse_chr6.simMouse.chr6 540063 3 + 636262 TTG -s Anc0.Anc0refChr3 143101 3 + 222631 ttg -s Anc1.Anc1refChr6 178500 3 + 197743 ttg -s Anc2.Anc2refChr1 56585 3 + 142988 ttg -s mr.mrrefChr3 90222 3 + 181027 ttg -s simCow_chr6.simCow.chr6 513864 3 + 602619 ttg -s simDog_chr6.simDog.chr6 503090 3 + 593897 ttg -s simHuman_chr6.simHuman.chr6 510354 3 + 601863 ttg -s simRat_chr6.simRat.chr6 551967 3 + 647215 tcg - -a -s simMouse_chr6.simMouse.chr6 540066 6 + 636262 AGAAAA -s Anc0.Anc0refChr3 143125 6 + 222631 agggaa -s Anc1.Anc1refChr6 178524 6 + 197743 agggaa -s Anc2.Anc2refChr1 56611 6 + 142988 agggaa -s mr.mrrefChr3 90225 6 + 181027 agaaaa -s simCow_chr6.simCow.chr6 513890 6 + 602619 ggggaa -s simDog_chr6.simDog.chr6 503116 6 + 593897 agggaa -s simHuman_chr6.simHuman.chr6 510379 6 + 601863 agtgca -s simRat_chr6.simRat.chr6 551970 6 + 647215 agaaac - -a -s simMouse_chr6.simMouse.chr6 540072 2 + 636262 TT -s Anc0.Anc0refChr3 143131 2 + 222631 tt -s Anc1.Anc1refChr6 178530 2 + 197743 tt -s Anc2.Anc2refChr1 56617 2 + 142988 gg -s mr.mrrefChr3 90231 2 + 181027 tt -s simCow_chr6.simCow.chr6 513896 2 + 602619 gg -s simDog_chr6.simDog.chr6 503122 2 + 593897 gg -s simHuman_chr6.simHuman.chr6 510385 2 + 601863 tt -s simRat_chr6.simRat.chr6 551977 2 + 647215 tt - -a -s simMouse_chr6.simMouse.chr6 540074 4 + 636262 GAGA -s Anc0.Anc0refChr3 143136 4 + 222631 gtcc -s Anc1.Anc1refChr6 178535 4 + 197743 gtcc -s Anc2.Anc2refChr1 56622 4 + 142988 gtcc -s mr.mrrefChr3 90233 4 + 181027 gaga -s simCow_chr6.simCow.chr6 513901 4 + 602619 gtcc -s simDog_chr6.simDog.chr6 503127 4 + 593897 gtcc -s simHuman_chr6.simHuman.chr6 510390 4 + 601863 gtac -s simRat_chr6.simRat.chr6 551979 4 + 647215 aaga - -a -s simMouse_chr6.simMouse.chr6 540078 32 + 636262 ATAATAAAAGCCTTGAGGTTTGATGCAAGTGT -s Anc0.Anc0refChr3 143140 32 + 222631 ataattagagcctctaggtctcagactagcct -s Anc1.Anc1refChr6 178539 32 + 197743 ataattagagcctctaggtctcagactagcct -s Anc2.Anc2refChr1 56628 32 + 142988 atagttagaacgtctaggtctcagactagcct -s mr.mrrefChr3 90237 32 + 181027 ataataAAAGCCTTGAGGTTTGATGCAAGTGT -s simCow_chr6.simCow.chr6 513907 32 + 602619 gtagttaaaacctctatgtatgagacaattct -s simDog_chr6.simDog.chr6 503133 32 + 593897 atagttagaacgtctaggtctcagactagcct -s simHuman_chr6.simHuman.chr6 510394 18 + 601863 ataattggagactctagg-------------- -s simRat_chr6.simRat.chr6 551983 32 + 647215 agaataAAAGCTTTGAGGTTTGATACAATTGT - -a -s simMouse_chr6.simMouse.chr6 540110 20 + 636262 TCAAAAAACAAAAAAATAGA -s Anc0.Anc0refChr3 143172 17 + 222631 ctgaag---ataagaattga -s Anc1.Anc1refChr6 178571 17 + 197743 ctgaag---ataagaattga -s Anc2.Anc2refChr1 56660 17 + 142988 ctgaag---ttaagaattgg -s mr.mrrefChr3 90269 20 + 181027 TCAAAAAACAAAAAAATAGA -s simCow_chr6.simCow.chr6 513939 17 + 602619 ttgcag---ttaaggattgg -s simDog_chr6.simDog.chr6 503165 17 + 593897 ctgaag---ttaagaattgg -s simHuman_chr6.simHuman.chr6 510412 11 + 601863 ---------aggagtatgca -s simRat_chr6.simRat.chr6 552017 20 + 647215 TGTCAAAATAAAAGAATAGA - -a -s simMouse_chr6.simMouse.chr6 540130 44 + 636262 GGTGAAGGATCCACAGTCTAAGAATGGATTCGAAGATGAGACAT -s Anc0.Anc0refChr3 143189 43 + 222631 ggtgaaggatccacaatccaagaatagattcgaagttaaga-at -s Anc1.Anc1refChr6 178588 44 + 197743 ggtgaaggatccacaatccaagaatagattcgaagttaagatat -s Anc2.Anc2refChr1 56677 43 + 142988 ggcaaaggatccacaaaccaagaataagttcgaagttaaga-ag -s mr.mrrefChr3 90289 44 + 181027 GGTGAAGGATCCACAGTCTAAGAATGGATTCGAAGATGAGACAT -s simCow_chr6.simCow.chr6 513957 2 + 602619 gg------------------------------------------ -s simDog_chr6.simDog.chr6 503182 43 + 593897 ggcaaaggatccacaaaccaagaataagttcgaagttaaga-ag -s simHuman_chr6.simHuman.chr6 510423 44 + 601863 ggtgcagcacttacattccggtgacagattcaaaggtatgatgt -s simRat_chr6.simRat.chr6 552037 44 + 647215 AGTGAAGGATCCACAGTCTAAGAATGGATTCAAAGATGAGATGT - -a -s simMouse_chr6.simMouse.chr6 540174 90 + 636262 GCCAATGCAGAGCTCACTTAGTTAaatgtgatccacctagtgaattgaaaagcaagacctgggaaaatgaaaagaagctttcatatccac -s Anc0.Anc0refChr3 143232 78 + 222631 g-aagtgaagcacttactaagtttaatgtaat-cacctagtcaatttaagggccatagctaggaacttgta---------ttgt-tctac -s Anc1.Anc1refChr6 178632 88 + 197743 g-aagtgaagcacttactaagtttaatgtaatgcacctagtcaatttaagggccatagctaggaacttgtaatgaagtatttgt-tctac -s Anc2.Anc2refChr1 56720 78 + 142988 g-aagtgaagcacttgctaaatttaatgtaat-tgcctagtcaatttaaggcccatagctaggagCTTGTA---------TTGT-TCTGG -s mr.mrrefChr3 90333 89 + 181027 G-CAATGCAGAGCTCACTTAGTTAaatgtgatccacctagtgaattgaaaagcaagacctgggaaaatgaaaagaagctttcatatccac -s simCow_chr6.simCow.chr6 83447 48 - 602619 -----------------------------AGC-TGATTAGT--ATTTCAAGCTCATAACTGGGAGCTCATA---------TTGC-TCTGG -s simDog_chr6.simDog.chr6 503225 78 + 593897 g-aagtgaagcacttgctaaatttaatgtaat-tgcctattcaattcaagccccatagccaggagCCTGTA---------TTGT-TGTTG -s simHuman_chr6.simHuman.chr6 510468 87 + 601863 g-aaggaaagcacttactcagtttaatgtaatgcacctagtcaatttaacggcgataggt-agaagttgcaatgaagtatttgt-tcaac -s simRat_chr6.simRat.chr6 552081 89 + 647215 G-TGATGCAGTGCTCAATTAGTTTAATGTGATCCAGCAAGTCAATTCAAAACCCAGATCTGGGAAATTGAAAAGAAGTTGTCATATCCAG - -a -s simMouse_chr6.simMouse.chr6 540264 13 + 636262 taagataattcca -s Anc0.Anc0refChr3 143310 13 + 222631 taagtgcactcca -s Anc1.Anc1refChr6 178720 13 + 197743 taagtgcactcca -s Anc2.Anc2refChr1 56798 13 + 142988 TAAGTGCACTACA -s mr.mrrefChr3 90422 13 + 181027 taagataattcca -s simCow_chr6.simCow.chr6 83495 13 - 602619 TAAGCGCACTACA -s simDog_chr6.simDog.chr6 503303 13 + 593897 TAAGTGCACTAAA -s simHuman_chr6.simHuman.chr6 510589 13 + 601863 taagtgcactcca -s simRat_chr6.simRat.chr6 552170 13 + 647215 TAAGATAATTCCA - -a -s simMouse_chr6.simMouse.chr6 540277 8 + 636262 agaagcat -s Anc0.Anc0refChr3 143325 8 + 222631 aaaaacat -s Anc1.Anc1refChr6 178735 8 + 197743 aaaaacat -s Anc2.Anc2refChr1 56813 8 + 142988 Aaaaacat -s mr.mrrefChr3 90435 8 + 181027 agaagcat -s simCow_chr6.simCow.chr6 83510 8 - 602619 GGAAACAT -s simDog_chr6.simDog.chr6 503318 8 + 593897 Aaaaacat -s simHuman_chr6.simHuman.chr6 510604 8 + 601863 aaaaagat -s simRat_chr6.simRat.chr6 552183 8 + 647215 AGAAACAT - -a -s simMouse_chr6.simMouse.chr6 540285 5 + 636262 gccag -s Anc0.Anc0refChr3 143333 5 + 222631 gccgg -s Anc1.Anc1refChr6 178743 5 + 197743 gccgg -s Anc2.Anc2refChr1 56821 5 + 142988 tctgg -s mr.mrrefChr3 90443 5 + 181027 gccag -s simCow_chr6.simCow.chr6 83518 5 - 602619 TTTGG -s simDog_chr6.simDog.chr6 503326 5 + 593897 tctgg -s simHuman_chr6.simHuman.chr6 510648 5 + 601863 gccgg -s simRat_chr6.simRat.chr6 552191 5 + 647215 GCCAG - -a -s simMouse_chr6.simMouse.chr6 540290 1 + 636262 g -s Anc0.Anc0refChr3 143338 1 + 222631 g -s Anc1.Anc1refChr6 178748 1 + 197743 g -s Anc2.Anc2refChr1 56826 1 + 142988 g -s mr.mrrefChr3 90448 1 + 181027 g -s simCow_chr6.simCow.chr6 83534 1 - 602619 A -s simDog_chr6.simDog.chr6 503331 1 + 593897 g -s simHuman_chr6.simHuman.chr6 510653 1 + 601863 c -s simRat_chr6.simRat.chr6 552196 1 + 647215 G - -a -s simMouse_chr6.simMouse.chr6 540291 46 + 636262 cagtaggaatactccatgcagttaaagacctgttggaaactgttcc -s Anc0.Anc0refChr3 143339 46 + 222631 cagtaggaatactccatggatttctagacctgctgcaaattgttct -s Anc1.Anc1refChr6 178749 46 + 197743 cagtaggaatactccatggatttctagacctgctgcaaattgttct -s Anc2.Anc2refChr1 56829 46 + 142988 cagtcagaatactccatggattcctagacctgctgcaaattgttct -s mr.mrrefChr3 90449 46 + 181027 cagtaggaatactccatgcagttaaagacctgttggaaactgttcc -s simCow_chr6.simCow.chr6 83537 46 - 602619 CAGTCAGAATATGccctggagtccgagacatgctgcacatcattct -s simDog_chr6.simDog.chr6 503334 46 + 593897 cagtcagaatactccatggattcctagacctgctgcaaactgtttt -s simHuman_chr6.simHuman.chr6 510654 46 + 601863 cagtaggaatacttcatagcattctagacgtgctgcaaattgttct -s simRat_chr6.simRat.chr6 552197 46 + 647215 cagtaggcatactccatgtagttaaggtcctgttggaaactgttcc - -a -s simMouse_chr6.simMouse.chr6 540337 19 + 636262 catcaaatttacaactctt -s Anc0.Anc0refChr3 143385 19 + 222631 catctaattaaaggagatt -s Anc1.Anc1refChr6 178795 19 + 197743 catctaattaaaggagatt -s Anc2.Anc2refChr1 56875 19 + 142988 catctaattaaaggagatt -s mr.mrrefChr3 90495 19 + 181027 catcaaatttacaactctt -s simCow_chr6.simCow.chr6 83583 19 - 602619 aatctaattagaagaaatt -s simDog_chr6.simDog.chr6 503386 19 + 593897 catctaattaaaggagatt -s simHuman_chr6.simHuman.chr6 510700 19 + 601863 catctaatcaaagcagatt -s simRat_chr6.simRat.chr6 552243 19 + 647215 caacaaatttacaacctta - -a -s simMouse_chr6.simMouse.chr6 540356 55 + 636262 aagaaggggtcacttgtttgacagatcacatacttcctgtgcattcaccacaaat -s Anc0.Anc0refChr3 143405 55 + 222631 aagaaggggtcacatttttgacaggtcacatacttgttgtgcatgcaccacacat -s Anc1.Anc1refChr6 178815 55 + 197743 aagaaggggtcacatttttgacaggtcacatacttgttgtgcatgcaccacacat -s Anc2.Anc2refChr1 56895 55 + 142988 aaaaaggggtcacatttttgacaggtcacatacttgttgtgcatgcaccacacat -s mr.mrrefChr3 90514 55 + 181027 aagaaggggtcacttgtttgacagatcacatacttcctgtgcattcaccacaaat -s simCow_chr6.simCow.chr6 83603 55 - 602619 aataaagggtcacatttttgagggatcactcacttgttgagcctgtaccaaacat -s simDog_chr6.simDog.chr6 503406 55 + 593897 aaaagggggtcacatttttaacaggtcacatacttgttgtgcatgcaccacaaat -s simHuman_chr6.simHuman.chr6 510720 55 + 601863 aagaaggggtgaccttcttgattggtcacatacttattctgcatgcaccacacat -s simRat_chr6.simRat.chr6 552262 55 + 647215 aagaaggggtcacttgtttgacaggttgcatacttcttgtgcattcaccacaagt - -a -s simMouse_chr6.simMouse.chr6 540411 26 + 636262 CTCAAATTGAGCACAGTTTCAAAACA -s Anc0.Anc0refChr3 143460 22 + 222631 ----acttgtgaagcagtttaaaaca -s Anc1.Anc1refChr6 178870 22 + 197743 ----acttgtgaagcagtttaaaaca -s Anc2.Anc2refChr1 56950 22 + 142988 ----acttgtgaggcagtttaaaaca -s mr.mrrefChr3 90569 26 + 181027 ctcaaattgagcacagtttcaaaaca -s simCow_chr6.simCow.chr6 83658 21 - 602619 ----acgtgtgaggt-gtttaacaca -s simDog_chr6.simDog.chr6 503461 22 + 593897 ----atttatgaggcagtttaaaaca -s simHuman_chr6.simHuman.chr6 510775 22 + 601863 ----gcttgcaaagcagtagaaaaca -s simRat_chr6.simRat.chr6 552328 26 + 647215 cttaaattgatcccagttacaaaaca - -a -s simMouse_chr6.simMouse.chr6 540437 35 + 636262 TATAGAACATATTGTAGCACTACATTTAACCCCTT -s Anc0.Anc0refChr3 143490 35 + 222631 tacaaaaCGTATTGTGGCACCACATTCAACCCCTT -s Anc1.Anc1refChr6 178900 35 + 197743 tacaaaaCGTATTGTGGCACCACATTCAACCCCTT -s Anc2.Anc2refChr1 56980 35 + 142988 tacaagtCGTATTGTGCCACCACATTCAACCCCTT -s mr.mrrefChr3 90595 35 + 181027 taTAGAACATATTGTAGCACTACATTTAACCCCTT -s simCow_chr6.simCow.chr6 83687 35 - 602619 tgcaggTCGTAATGCTTCACTACATTCCACCCTTT -s simDog_chr6.simDog.chr6 503491 35 + 593897 gacaagtcataTTGTGCCACCACATGCAACCCCCG -s simHuman_chr6.simHuman.chr6 510805 35 + 601863 tacaaaaTGAATTGTCGCACCACATTGAACCCCTT -s simRat_chr6.simRat.chr6 552354 35 + 647215 taTAGAACATACTGTGGCACCACACTTAACCTCTT - -a -s simMouse_chr6.simMouse.chr6 540472 9 + 636262 TTCATATTT -s Anc0.Anc0refChr3 143526 8 + 222631 TTG-TATTT -s Anc1.Anc1refChr6 178936 8 + 197743 TTG-TATTT -s Anc2.Anc2refChr1 57016 8 + 142988 TTG-TATTT -s mr.mrrefChr3 90630 8 + 181027 TTC-TATTT -s simCow_chr6.simCow.chr6 83723 8 - 602619 TGG-TATTT -s simDog_chr6.simDog.chr6 503527 8 + 593897 TTG-AGTTT -s simHuman_chr6.simHuman.chr6 510841 8 + 601863 TTG-TATTT -s simRat_chr6.simRat.chr6 552389 8 + 647215 TTC-TATTT - -a -s simMouse_chr6.simMouse.chr6 540481 9 + 636262 TTAGATGTC -s Anc0.Anc0refChr3 143541 9 + 222631 TTAGCTTTC -s Anc1.Anc1refChr6 178951 9 + 197743 TTAGCTTTC -s Anc2.Anc2refChr1 57031 9 + 142988 TTAGCTTTC -s mr.mrrefChr3 90638 9 + 181027 TTAGATGTC -s simCow_chr6.simCow.chr6 83738 9 - 602619 TTAGCTTTC -s simDog_chr6.simDog.chr6 503542 9 + 593897 TTAGCTTTC -s simHuman_chr6.simHuman.chr6 510856 9 + 601863 TTAGTTTTC -s simRat_chr6.simRat.chr6 552397 9 + 647215 TTAGATGTC - -a -s simMouse_chr6.simMouse.chr6 540490 3 + 636262 AAT -s Anc0.Anc0refChr3 143550 3 + 222631 AAT -s Anc1.Anc1refChr6 178960 3 + 197743 AAT -s Anc2.Anc2refChr1 57041 3 + 142988 AAT -s mr.mrrefChr3 90647 3 + 181027 AAT -s simCow_chr6.simCow.chr6 83748 3 - 602619 AAT -s simDog_chr6.simDog.chr6 503552 3 + 593897 AAT -s simHuman_chr6.simHuman.chr6 510865 3 + 601863 AGT -s simRat_chr6.simRat.chr6 552406 3 + 647215 AAT - -a -s simMouse_chr6.simMouse.chr6 540493 4 + 636262 TATG -s Anc0.Anc0refChr3 143569 4 + 222631 TTTG -s Anc1.Anc1refChr6 178979 4 + 197743 TTTG -s Anc2.Anc2refChr1 57060 4 + 142988 TTTG -s mr.mrrefChr3 90650 4 + 181027 TATG -s simCow_chr6.simCow.chr6 83767 4 - 602619 TCTG -s simDog_chr6.simDog.chr6 503571 4 + 593897 GTTG -s simHuman_chr6.simHuman.chr6 510884 4 + 601863 TTTG -s simRat_chr6.simRat.chr6 552409 4 + 647215 TATG - -a -s simMouse_chr6.simMouse.chr6 540497 7 + 636262 TGATACT -s Anc0.Anc0refChr3 143573 7 + 222631 TAAAGCT -s Anc1.Anc1refChr6 178983 7 + 197743 TAAAGCT -s Anc2.Anc2refChr1 57065 7 + 142988 TAAAGCT -s mr.mrrefChr3 90654 7 + 181027 TGATACT -s simCow_chr6.simCow.chr6 83772 7 - 602619 TAGAGCT -s simDog_chr6.simDog.chr6 503576 7 + 593897 TAAAGCT -s simHuman_chr6.simHuman.chr6 510888 7 + 601863 TAACGCT -s simRat_chr6.simRat.chr6 552413 7 + 647215 TGATACT - -a -s simMouse_chr6.simMouse.chr6 540504 14 + 636262 TATCAAGGGGCAAT -s Anc0.Anc0refChr3 143584 14 + 222631 TGTGGAGGTACTAT -s Anc1.Anc1refChr6 178994 14 + 197743 TGTGGAGGTACTAT -s Anc2.Anc2refChr1 57076 14 + 142988 TGTGGAGGTAATGT -s mr.mrrefChr3 90661 14 + 181027 TATCAAGGGGCAAT -s simCow_chr6.simCow.chr6 83783 14 - 602619 TGGGGAAGTATTAT -s simDog_chr6.simDog.chr6 503587 14 + 593897 TGTCAAGGTAATGT -s simHuman_chr6.simHuman.chr6 510899 14 + 601863 TGTGGAGGAACTAT -s simRat_chr6.simRat.chr6 552420 14 + 647215 TGTGGAGGGGCAAT - -a -s simMouse_chr6.simMouse.chr6 540518 21 + 636262 TGGGGTAGAAAGAGGGGTGTT -s Anc0.Anc0refChr3 143600 21 + 222631 TCCAGTTGAAAGAGGGGTGTT -s Anc1.Anc1refChr6 179010 21 + 197743 TCCAGTTGAAAGAGGGGTGTT -s Anc2.Anc2refChr1 57137 21 + 142988 TCCAATTGAAAGAAATGTGTT -s mr.mrrefChr3 90675 21 + 181027 TGGGGTAGAAAGAGGGGTGTT -s simCow_chr6.simCow.chr6 83844 21 - 602619 TCCAGGTAAAAGGGGAATGTT -s simDog_chr6.simDog.chr6 503650 21 + 593897 TCCAATTGAAAGAAATGTGTT -s simHuman_chr6.simHuman.chr6 510915 21 + 601863 TCTAGTTGAAAGAGGGGCTCT -s simRat_chr6.simRat.chr6 552434 21 + 647215 TATGGTGGTAGGAGGGATGTT - -a -s simMouse_chr6.simMouse.chr6 540539 26 + 636262 CAACTGATAAGCAGCCCTCTAGCTGC -s Anc0.Anc0refChr3 143623 22 + 222631 CAAC--ATA--CACCACTCTAACTGC -s Anc1.Anc1refChr6 179033 22 + 197743 CAAC--ATA--CACCACTCTAACTGC -s Anc2.Anc2refChr1 57162 22 + 142988 TAAC--AGA--CACCAACATAACTGA -s mr.mrrefChr3 90696 24 + 181027 CAACTGATA--CAGCCCTCTAGCTGC -s simCow_chr6.simCow.chr6 83869 22 - 602619 TAAC--AGT--CACCAACCTATCTGA -s simDog_chr6.simDog.chr6 503675 22 + 593897 TAAC--AGA--CACCAACATAACTGA -s simHuman_chr6.simHuman.chr6 510938 22 + 601863 CAAC--ATA--CACCACTCTATCTGC -s simRat_chr6.simRat.chr6 552455 24 + 647215 CAACTGACA--CAGCCACCTACCTGC - -a -s simMouse_chr6.simMouse.chr6 540565 22 + 636262 TCTGCCTCTTAGTCAATGTTAA -s Anc0.Anc0refChr3 143646 16 + 222631 T---CCCAGTGGACA---TTAG -s Anc1.Anc1refChr6 179056 19 + 197743 TCTGCCCAGTGGACA---TTAG -s Anc2.Anc2refChr1 57185 16 + 142988 T---GCCAGTGGACA---TTAG -s mr.mrrefChr3 90720 19 + 181027 TCTGCCTCTTAGTCA---TTAA -s simCow_chr6.simCow.chr6 83892 16 - 602619 A---CCCAGTTTCTG---TTAG -s simDog_chr6.simDog.chr6 503698 16 + 593897 T---GCCAGTGGACA---TTAG -s simHuman_chr6.simHuman.chr6 510961 7 + 601863 TCTGCTC--------------- -s simRat_chr6.simRat.chr6 552479 19 + 647215 TCTGACTCTCAGTCA---TTAA - -a -s simMouse_chr6.simMouse.chr6 540587 13 + 636262 TCAATGTTAGCTT -s Anc0.Anc0refChr3 143662 5 + 222631 T--------GCTT -s Anc1.Anc1refChr6 179075 5 + 197743 T--------GCTT -s Anc2.Anc2refChr1 57201 5 + 142988 T--------GCTT -s mr.mrrefChr3 90739 13 + 181027 TCAATGTTAGCTT -s simCow_chr6.simCow.chr6 83908 5 - 602619 T--------ACTT -s simDog_chr6.simDog.chr6 503716 5 + 593897 T--------GCTT -s simRat_chr6.simRat.chr6 552498 13 + 647215 TCAGTGTTAGCTT - -a -s simMouse_chr6.simMouse.chr6 540600 8 + 636262 CTTCCATT -s Anc0.Anc0refChr3 143667 8 + 222631 CTTTCTGA -s Anc1.Anc1refChr6 179080 8 + 197743 CTTTCTGA -s Anc2.Anc2refChr1 57209 8 + 142988 CTTTCTGA -s mr.mrrefChr3 90752 8 + 181027 CTTCCATT -s simCow_chr6.simCow.chr6 83916 8 - 602619 CTTTCTGG -s simDog_chr6.simDog.chr6 503724 8 + 593897 CTTTCTGA -s simRat_chr6.simRat.chr6 552511 8 + 647215 CTTCCATT - -a -s simMouse_chr6.simMouse.chr6 540608 27 + 636262 CTACCTACCTTGACTCAGAGTGGTAAG -s Anc0.Anc0refChr3 143675 27 + 222631 GTATCTGCTTTCCTTCAGAGTGGGAAG -s Anc1.Anc1refChr6 179088 27 + 197743 GTATCTGCTTTCCTTCAGAGTGGGAAG -s Anc2.Anc2refChr1 57217 27 + 142988 GTATCTGCTTTCCTTCAGAGTGGGAAG -s mr.mrrefChr3 90760 27 + 181027 CTACCTACCTTGACTCAGAGTGGTAAG -s simCow_chr6.simCow.chr6 83927 27 - 602619 GTCTCTACCTTACGTCAGAGTGGAAAG -s simDog_chr6.simDog.chr6 503732 27 + 593897 GTATCTGCTTTCCTTCAGAGTGGGAAG -s simRat_chr6.simRat.chr6 552519 27 + 647215 GCACCTACCTTGACTCAGAGTGGTAAG - -a -s simMouse_chr6.simMouse.chr6 540635 6 + 636262 GCAAAC -s Anc0.Anc0refChr3 143702 6 + 222631 ACAAGC -s Anc1.Anc1refChr6 179115 6 + 197743 ACAAGC -s Anc2.Anc2refChr1 57244 6 + 142988 ACAAGC -s mr.mrrefChr3 90787 6 + 181027 GCAAAC -s simCow_chr6.simCow.chr6 83954 6 - 602619 ACGAAC -s simDog_chr6.simDog.chr6 503760 6 + 593897 ACAAGC -s simRat_chr6.simRat.chr6 552546 6 + 647215 GCAATC - -a -s simMouse_chr6.simMouse.chr6 540641 2 + 636262 TT -s Anc0.Anc0refChr3 143708 2 + 222631 TT -s Anc1.Anc1refChr6 179121 2 + 197743 TT -s Anc2.Anc2refChr1 57251 2 + 142988 TT -s mr.mrrefChr3 90793 2 + 181027 TT -s simCow_chr6.simCow.chr6 83961 2 - 602619 TA -s simDog_chr6.simDog.chr6 503767 2 + 593897 TT -s simRat_chr6.simRat.chr6 552552 2 + 647215 TT - -a -s simMouse_chr6.simMouse.chr6 540643 10 + 636262 CATTAGACTG -s Anc0.Anc0refChr3 143710 10 + 222631 CATTACTGTG -s Anc1.Anc1refChr6 179123 10 + 197743 CATTACTGTG -s Anc2.Anc2refChr1 57253 10 + 142988 CATTACTGTG -s mr.mrrefChr3 90795 10 + 181027 CATTAGACTG -s simCow_chr6.simCow.chr6 83963 10 - 602619 CATTACTGGG -s simDog_chr6.simDog.chr6 503770 10 + 593897 CATTACTGTG -s simRat_chr6.simRat.chr6 552554 10 + 647215 CATCAGCCTG - -a -s simMouse_chr6.simMouse.chr6 540653 9 + 636262 ATTAGTTAT -s Anc0.Anc0refChr3 143720 9 + 222631 CTTAATGAC -s Anc1.Anc1refChr6 179133 9 + 197743 CTTAATGAC -s Anc2.Anc2refChr1 57263 9 + 142988 CTTAATGAC -s mr.mrrefChr3 90805 9 + 181027 ATTAGTTAT -s simCow_chr6.simCow.chr6 83974 9 - 602619 CTGATTGAC -s simDog_chr6.simDog.chr6 503780 9 + 593897 CTTAATGAC -s simRat_chr6.simRat.chr6 552564 9 + 647215 ATTAATTAT - -a -s simMouse_chr6.simMouse.chr6 540662 2 + 636262 GC -s Anc0.Anc0refChr3 143729 2 + 222631 GT -s Anc1.Anc1refChr6 179142 2 + 197743 GT -s Anc2.Anc2refChr1 57274 2 + 142988 GT -s mr.mrrefChr3 90814 2 + 181027 GC -s simCow_chr6.simCow.chr6 83985 2 - 602619 AT -s simDog_chr6.simDog.chr6 503791 2 + 593897 GT -s simRat_chr6.simRat.chr6 552573 2 + 647215 GT - -a -s simMouse_chr6.simMouse.chr6 540664 10 + 636262 CCTCAGAGCC -s Anc0.Anc0refChr3 143731 10 + 222631 CGTCACAACA -s Anc1.Anc1refChr6 179144 10 + 197743 CGTCACAACA -s Anc2.Anc2refChr1 57276 10 + 142988 CGTCACAACA -s mr.mrrefChr3 90816 10 + 181027 CCTCAGAGCC -s simCow_chr6.simCow.chr6 83987 10 - 602619 TGTCTCAAAA -s simDog_chr6.simDog.chr6 503797 10 + 593897 CGTCACAACA -s simRat_chr6.simRat.chr6 552575 10 + 647215 CCTCAAAGCA - -a -s simMouse_chr6.simMouse.chr6 540674 20 + 636262 TTCATCCCTGGTAAAATAAG -s Anc0.Anc0refChr3 143741 20 + 222631 TTCAGCCCTGCTAGAATAGG -s Anc1.Anc1refChr6 179154 20 + 197743 TTCAGCCCTGCTAGAATAGG -s Anc2.Anc2refChr1 57307 20 + 142988 TTCAGCCCTGCTAGAATAGG -s mr.mrrefChr3 90826 20 + 181027 TTCATCCCTGGTAAAATAAG -s simCow_chr6.simCow.chr6 84018 20 - 602619 TTCATCCTTACTAGAAAAGA -s simDog_chr6.simDog.chr6 503829 20 + 593897 TTCAGCCCTGCTAGAATAGG -s simRat_chr6.simRat.chr6 552585 20 + 647215 TTCATCCCTGGTGAAATAAC - -a -s simMouse_chr6.simMouse.chr6 540694 33 + 636262 GGGAAATGAGTAGAAGTGATAGCCCTCATCAAA -s Anc0.Anc0refChr3 143761 9 + 222631 G--------------------GCCCTAAT---- -s Anc1.Anc1refChr6 179174 9 + 197743 G--------------------GCCCTAAT---- -s Anc2.Anc2refChr1 57327 9 + 142988 G--------------------GCCCTAAT---- -s mr.mrrefChr3 90846 29 + 181027 GGGAAATGAGTAGAAGTGATAGCCCTCAT---- -s simCow_chr6.simCow.chr6 84050 9 - 602619 G--------------------GTTCCAGT---- -s simDog_chr6.simDog.chr6 503849 9 + 593897 G--------------------GCCCTAAT---- -s simRat_chr6.simRat.chr6 552605 29 + 647215 AGGGAATGAGTGGAAGCAATAGCCCTAGT---- - -a -s simMouse_chr6.simMouse.chr6 540727 7 + 636262 CAAATTT -s Anc0.Anc0refChr3 143770 7 + 222631 CAACTGT -s Anc1.Anc1refChr6 179183 7 + 197743 CAACTGT -s Anc2.Anc2refChr1 57338 7 + 142988 CAACTGT -s mr.mrrefChr3 90875 7 + 181027 CAAATTT -s simCow_chr6.simCow.chr6 84061 7 - 602619 GAGCTGT -s simDog_chr6.simDog.chr6 503860 7 + 593897 CAACTGT -s simRat_chr6.simRat.chr6 552634 7 + 647215 CAAATTT - -a -s simMouse_chr6.simMouse.chr6 540734 35 + 636262 TGTCTCTTAAGTATTTCTGTGTGCTTCTAGCTCCT -s Anc0.Anc0refChr3 143777 35 + 222631 TGCACTTTAATTATTTTTGTGTGCTCCTAACTCCT -s Anc1.Anc1refChr6 179190 35 + 197743 TGCACTTTAATTATTTTTGTGTGCTCCTAACTCCT -s Anc2.Anc2refChr1 57359 35 + 142988 TGCACTTTAATTGTTGTTGTGTGCTCCTAACTCAT -s mr.mrrefChr3 90882 35 + 181027 TGTCTCTTAATTATTTTTGTGTGCTTCTAGCTCCT -s simCow_chr6.simCow.chr6 84082 31 - 602619 CGCAT----AGTGCAAATATGTGCCCCTAACTTAG -s simDog_chr6.simDog.chr6 503881 35 + 593897 TGCTCTTTAATTGTTGTTGTGTGATCCTAACTCAT -s simHuman_chr6.simHuman.chr6 510968 25 + 601863 ----------TAATTTTTGTGTGCTACTAACTCCT -s simRat_chr6.simRat.chr6 552641 35 + 647215 TGCCTCTTGATTATTTTTATGTGCTTCTAGCTCGT - -a -s simMouse_chr6.simMouse.chr6 540769 17 + 636262 CAAACCCTGAGCTGCTC -s Anc0.Anc0refChr3 143812 17 + 222631 TAAACCCTTAGATGTGC -s Anc1.Anc1refChr6 179225 17 + 197743 TAAACCCTTAGATGTGC -s Anc2.Anc2refChr1 57394 17 + 142988 TAAACCCTTAGACGTGC -s mr.mrrefChr3 90917 17 + 181027 TAAACCCTTAGCTGCTC -s simCow_chr6.simCow.chr6 84113 17 - 602619 TAAGACCTTAGACATGC -s simDog_chr6.simDog.chr6 503918 15 + 593897 TAAACCCCTAG--GTGC -s simHuman_chr6.simHuman.chr6 510993 17 + 601863 TAATCCCTTAGATGTCC -s simRat_chr6.simRat.chr6 552676 17 + 647215 TAAACCCTTGGCTGGTC - -a -s simMouse_chr6.simMouse.chr6 540786 125 + 636262 TAGTCTTGATAGGGCCCCAGTGCATGCTGTGTAGGTCATGGTGGCTATCGGGTGTTGACATTAGTGTAGGTCATGGTGGCTATCGGGTGTTGACATTACTTAGTGAATCTTTCTGTTTTAAGGCA -s Anc0.Anc0refChr3 143829 88 + 222631 AAATCTTGACATGGCCCTAGTGCTTCCTG-----------------------------------CTTAGGTAATG--GGATATCAGGCATTGATATTACATAGTGAATCTTGCTGTTTTACTGTA -s Anc1.Anc1refChr6 179242 88 + 197743 AAATCTTGACATGGCCCTAGTGCTTCCTG-----------------------------------CTTAGGTAATG--GGATATCAGGCATTGATATTACATAGTGAATCTTGCTGTTTTACTGTA -s Anc2.Anc2refChr1 57411 88 + 142988 AAATCTTGTCATGACCTTGGTGTTTCCTG-----------------------------------CTTAGGTAATG--GGATATCAGGCATTGATATTACATAGCCAATCTTGCTGTTTTACTGTA -s mr.mrrefChr3 90934 90 + 181027 TAGTCTTGATAGGGCCCCAGTGCATGCTG-----------------------------------TGTAGGTAATGGTGGCTATCGGGTGTTGACATTACTTAGTGAATCTTTCTGTTTTAATGCA -s simCow_chr6.simCow.chr6 84130 81 - 602619 AAATCTTGGCAT-------GTGTTTCCTG-----------------------------------CTTAGGTAGCA--GCATATCAGGTATTGAGATTACATAGCCAATCTGGCTGTTTTACTGTA -s simDog_chr6.simDog.chr6 503933 87 + 593897 TGATCTTGTCATGACCTTGACATTTACTA-----------------------------------CTTAGGGAATG--GGATATCAGGCGTTGATATTACATGGCCAATCTTGCTGTTTTTCT-TG -s simHuman_chr6.simHuman.chr6 511012 88 + 601863 AAATCTTGACATGGCCCTAGTGCCTCCTG-----------------------------------CTTAGGTAATG--GGATATCAGGCATTGATATTACATAGTGAATCTTGCTGTCTTACTGTA -s simRat_chr6.simRat.chr6 552693 79 + 647215 TAGTCTTGA-----------TGCATACTG-----------------------------------TATAGGTAATGGAGGCTATCGGGTGTTGACATTGCTTAGTGAATCTTTATGTTTTAATGCA - -a -s simMouse_chr6.simMouse.chr6 540911 12 + 636262 GAGAAAATCAGC -s Anc0.Anc0refChr3 143917 12 + 222631 GAGAAAATCAAC -s Anc1.Anc1refChr6 179330 12 + 197743 GAGAAAATCAAC -s Anc2.Anc2refChr1 57499 12 + 142988 GACATCATCAAC -s mr.mrrefChr3 91024 12 + 181027 GAGAAAATTAGC -s simCow_chr6.simCow.chr6 84211 12 - 602619 GTGATTATCAAC -s simDog_chr6.simDog.chr6 504020 12 + 593897 CACATCATCCAC -s simHuman_chr6.simHuman.chr6 511123 12 + 601863 GAGAAAACCAAC -s simRat_chr6.simRat.chr6 552772 12 + 647215 GAAAAAATTAGC - -a -s simMouse_chr6.simMouse.chr6 540923 5 + 636262 TACTT -s Anc0.Anc0refChr3 143952 5 + 222631 TGCTC -s Anc1.Anc1refChr6 179365 5 + 197743 TGCTC -s Anc2.Anc2refChr1 57534 5 + 142988 TGCCC -s mr.mrrefChr3 91036 5 + 181027 TATTT -s simCow_chr6.simCow.chr6 84242 5 - 602619 TCTCC -s simDog_chr6.simDog.chr6 504053 5 + 593897 TGCCC -s simHuman_chr6.simHuman.chr6 511158 5 + 601863 TGCTC -s simRat_chr6.simRat.chr6 552784 5 + 647215 GATTC - -a -s simMouse_chr6.simMouse.chr6 540928 38 + 636262 ACTGATGTTCTGATGTGTGAATTGCAACTCACACTATA -s Anc0.Anc0refChr3 143957 28 + 222631 TCTG----------GGGTGTGTAGGAGCACACAATATA -s Anc1.Anc1refChr6 179370 28 + 197743 TCTG----------GGGTGTGTAGGAGCACACAATATA -s Anc2.Anc2refChr1 57539 28 + 142988 TCTG----------GGGTGTGTAGGAGCAGACAACATA -s mr.mrrefChr3 91041 28 + 181027 ACTG----------TTGTGAATTGCAACTCACACTATA -s simCow_chr6.simCow.chr6 84249 28 - 602619 GCTG----------GGAAGTGTAGGAGCATACAAAGTA -s simDog_chr6.simDog.chr6 504058 28 + 593897 TCTG----------GGGTGTGTAGGAAAAGTCGACATA -s simHuman_chr6.simHuman.chr6 511163 28 + 601863 TCCG----------GGGTGTGTAGTAGCACACAATATA -s simRat_chr6.simRat.chr6 552789 28 + 647215 ACTG----------TTGTGAATTGCCACTCACACTATA - -a -s simMouse_chr6.simMouse.chr6 540966 18 + 636262 TCAAGCGAAATAAAAATA -s Anc0.Anc0refChr3 144014 18 + 222631 TCAATAGCAGAAATATTA -s Anc1.Anc1refChr6 179427 18 + 197743 TCAATAGCAGAAATATTA -s Anc2.Anc2refChr1 57596 18 + 142988 TCAATAACAGAAATATGA -s mr.mrrefChr3 91069 18 + 181027 TCAAGCGAAATAAAAATA -s simCow_chr6.simCow.chr6 84309 18 - 602619 TCAATACCACAAATACCA -s simDog_chr6.simDog.chr6 504115 18 + 593897 TCAATAACAGAGCTATGA -s simHuman_chr6.simHuman.chr6 511221 18 + 601863 TCAATAGGAGAAATATTA -s simRat_chr6.simRat.chr6 552817 18 + 647215 TCAAGCACCATAAAAATA - -a -s simMouse_chr6.simMouse.chr6 540984 46 + 636262 ATAATCATCAACTCCACAAATAGCTTGGTAGTATATTAAATAGCTT -s Anc0.Anc0refChr3 144072 26 + 222631 ATAATCACCATC-----------------ATCA---CAAGTCGCTT -s Anc1.Anc1refChr6 179485 26 + 197743 ATAATCACCATC-----------------ATCA---CAAGTCGCTT -s Anc2.Anc2refChr1 57654 26 + 142988 ATAATTGCCATC-----------------ATCA---GAAGTCGCTT -s mr.mrrefChr3 91087 26 + 181027 ATAATCATCAAC-----------------AGTA---CAAATAGCTT -s simCow_chr6.simCow.chr6 84371 23 - 602619 ATAGTTGCCGTC-----------------AACA---GAAGCC---T -s simDog_chr6.simDog.chr6 504173 26 + 593897 GTGATTGCCACC-----------------ATCT---GAAGTAGCTT -s simHuman_chr6.simHuman.chr6 511279 26 + 601863 ATAATCACCATC-----------------ATCA---CTAGTCGTTT -s simRat_chr6.simRat.chr6 552835 26 + 647215 ATAATCATCAAC-----------------AGTA---CAAATAGCGT - -a -s simMouse_chr6.simMouse.chr6 541030 44 + 636262 GGTAGTATATTCCTGATAACACTACCACCTGCCCTCTATATAGC -s Anc0.Anc0refChr3 144098 44 + 222631 GGTTAAACATCCCAGATAGCTTTGCTACCTGCCCTCTGTGTAGC -s Anc1.Anc1refChr6 179511 44 + 197743 GGTTAAACATCCCAGATAGCTTTGCTACCTGCCCTCTGTGTAGC -s Anc2.Anc2refChr1 57680 44 + 142988 GGTTAAACATTCCACATAGCTTTGCTACCTGCCCTCTGTGTAGC -s mr.mrrefChr3 91113 44 + 181027 GGTAGTATATCCCTGATAACACTACCACCTGCCCTCTGTATAGC -s simCow_chr6.simCow.chr6 84394 44 - 602619 GTTTAAAAATGATGTGTAGTTTTGCTACCTGACCTCCGTGTCGC -s simDog_chr6.simDog.chr6 504200 44 + 593897 GGCTAAACACTCCACATAGCTTTGCTACCTGCCCTCTGTGTAGA -s simHuman_chr6.simHuman.chr6 511305 44 + 601863 GGTTAAACATCCCAGTTAGCTTTGCTACCTGCCCTTTGTCTAGC -s simRat_chr6.simRat.chr6 552861 44 + 647215 GGTAGTATATCCCTGATAACACTACCACCTGCCCTCTGTATAGT - -a -s simMouse_chr6.simMouse.chr6 541074 6 + 636262 ACAAAT -s Anc0.Anc0refChr3 144145 6 + 222631 GCAAAG -s Anc1.Anc1refChr6 179558 6 + 197743 GCAAAG -s Anc2.Anc2refChr1 57727 6 + 142988 GCAAAG -s mr.mrrefChr3 91157 6 + 181027 ACAAAT -s simCow_chr6.simCow.chr6 84441 6 - 602619 GCAAAG -s simDog_chr6.simDog.chr6 504247 5 + 593897 GC-AAG -s simHuman_chr6.simHuman.chr6 511352 6 + 601863 GCAAAG -s simRat_chr6.simRat.chr6 552905 6 + 647215 ACACAT - -a -s simMouse_chr6.simMouse.chr6 541080 13 + 636262 TCTACACCTGTTC -s Anc0.Anc0refChr3 144153 13 + 222631 TCTACTCCTGTGC -s Anc1.Anc1refChr6 179566 13 + 197743 TCTACTCCTGTGC -s Anc2.Anc2refChr1 57735 13 + 142988 TCTACTCCTGTGC -s mr.mrrefChr3 91163 13 + 181027 TCTACACCTGTTC -s simCow_chr6.simCow.chr6 84449 13 - 602619 TCTACTCCCATGC -s simDog_chr6.simDog.chr6 504254 13 + 593897 TCTACTCCTGCAT -s simHuman_chr6.simHuman.chr6 511360 13 + 601863 TCCACTCCTGTGC -s simRat_chr6.simRat.chr6 552911 13 + 647215 TCTACACCTGTTC - -a -s simMouse_chr6.simMouse.chr6 541093 23 + 636262 ATATTTCTTAGTGATTCATTTGT -s Anc0.Anc0refChr3 144167 23 + 222631 ATATTTCTTAGCAATTCATTCTT -s Anc1.Anc1refChr6 179580 23 + 197743 ATATTTCTTAGCAATTCATTCTT -s Anc2.Anc2refChr1 57749 23 + 142988 ACATCTCTTAGCAATTCTTTCTT -s mr.mrrefChr3 91176 23 + 181027 ATATTTCTTAGTGATTCATTTGT -s simCow_chr6.simCow.chr6 84463 23 - 602619 AGATCTCTTAGCAATTCTTTCCT -s simDog_chr6.simDog.chr6 504268 23 + 593897 ACATCTCCCAGCAATTCTTTCTT -s simHuman_chr6.simHuman.chr6 511374 23 + 601863 ATATTTCTTAGCAATTCATTCTT -s simRat_chr6.simRat.chr6 552924 23 + 647215 ATATGTCTTAGTGATTCATTTGT - -a -s simMouse_chr6.simMouse.chr6 541116 4 + 636262 CTCT -s Anc0.Anc0refChr3 144190 4 + 222631 TCCT -s Anc1.Anc1refChr6 179603 4 + 197743 TCCT -s Anc2.Anc2refChr1 57772 4 + 142988 TCCT -s mr.mrrefChr3 91199 4 + 181027 CTCT -s simCow_chr6.simCow.chr6 84486 4 - 602619 TTCT -s simDog_chr6.simDog.chr6 504292 4 + 593897 CCCT -s simHuman_chr6.simHuman.chr6 511397 4 + 601863 TCCT -s simRat_chr6.simRat.chr6 552947 4 + 647215 CTCT - -a -s simMouse_chr6.simMouse.chr6 541120 103 + 636262 TATAGAGTGATGTGAGGTATATGGGGGAATCTTCAATTCCAGTACTGATATATGGGGGAATCTTCAATTCCAGTACTGATTAGGGCTTGGGCAGCCATGATAT -s Anc0.Anc0refChr3 144194 72 + 222631 CATAGACTGATGTGAGG-------------------------------TATATGCAGGAATCTCCTATTCCAGTATTGTTTGCGGCTTGGGCAGCCATGGTAT -s Anc1.Anc1refChr6 179607 72 + 197743 CATAGACTGATGTGAGG-------------------------------TATATGCAGGAATCTCCTATTCCAGTATTGTTTGCGGCTTGGGCAGCCATGGTAT -s Anc2.Anc2refChr1 57776 72 + 142988 CACAGGGTGGCATAAGG-------------------------------TATATGCAGGAAACTCCTATTCTGGTATTGTTTGCGGCTTGTGCAGCCATGGTAC -s mr.mrrefChr3 91203 72 + 181027 CATAGACTGATGTGAGG-------------------------------TATATGGAGGAATCTCCAATTCCAGTACTGATTAGGGCTTGGGCAGCCATGATAT -s simCow_chr6.simCow.chr6 84495 72 - 602619 CACATGATAGCATAAGG-------------------------------TTTATGCAGGAAACTCCAATCCTGGTACTGTTTGTGGCCTGAGCAAACATGATAC -s simDog_chr6.simDog.chr6 504296 65 + 593897 CACAGGGTGGCATA-----------------------------------ATATGCAGTAG---ACTATTCTGATATTGTCTGCGGCTTGTGCGGCCATGGTAC -s simHuman_chr6.simHuman.chr6 511401 72 + 601863 CATAGACTCATGTGAGG-------------------------------CATATGCAGGAATCCCCCATTCCAGTAGTGTTTGCGGCTTGGGAAGCCATGTTAT -s simRat_chr6.simRat.chr6 552951 71 + 647215 CATGGACCGA-GTGAGT-------------------------------TATATGGAGGAATCTCCATTTCCAGTACTGATTAGGGCTAGGGCAGCCATGATAT - -a -s simMouse_chr6.simMouse.chr6 541223 11 + 636262 TTAGGAGATAA -s Anc0.Anc0refChr3 144276 11 + 222631 TCAGGAGTTAA -s Anc1.Anc1refChr6 179689 11 + 197743 TCAGGAGTTAA -s Anc2.Anc2refChr1 57858 11 + 142988 TCAGGAGTTAA -s mr.mrrefChr3 91275 11 + 181027 TTAGGAGATAA -s simCow_chr6.simCow.chr6 84577 11 - 602619 TCAGGAGTTAA -s simDog_chr6.simDog.chr6 504371 11 + 593897 TCGAGGGTTAA -s simHuman_chr6.simHuman.chr6 511484 11 + 601863 TCAGGAGTTAA -s simRat_chr6.simRat.chr6 553022 11 + 647215 TTAGGAGATAA - -a -s simMouse_chr6.simMouse.chr6 541234 107 + 636262 TTTGCTATGATTCGCTGTTGATCAACTTGTTGTTGGCTCACGAAAAGTTGTGGCCCCAAATTAGATTGAGTAGGGATTTGTAACCTCAGATATGGCTTGTGAAGGGC -s Anc0.Anc0refChr3 144287 106 + 222631 CCC-CCAAGATTCACAACTGATTTGCTTGTCATAGGCTCATATAAAGTTGTGACACCAAGTTAGATTGACTTTAGATTCATAAGCACAAATATGGCCAGCTGAGGAG -s Anc1.Anc1refChr6 179700 107 + 197743 CCCGCCAAGATTCACAACTGATTTGCTTGTCATAGGCTCATATAAAGTTGTGACACCAAGTTAGATTGACTTTAGATTCATAAGCACAAATATGGCCAGCTGAGGAG -s Anc2.Anc2refChr1 57869 106 + 142988 CCC-CCAAGATTCCCAACTGATTTGCGTGTCATAGGCTCATATAAAGTTGTGATACCAAGTTAGATTGACTTTAGATTCATAAGCACAAATATAGACAGCTGAGGAG -s mr.mrrefChr3 91286 107 + 181027 TCTGCTATGATTCACTGTTGATCTACTTGTCATTGGCTCACAAAAAGTTGTGGCCCCAAGTTAGATTGAGTAGGGATTTGTAACCTCAGATATGGCTTGTGAAGGGC -s simCow_chr6.simCow.chr6 84589 105 - 602619 CCC-CCAAGATTTCCAACTTATTTGTGGGCCGTAGGCTCATCTAAACTTGCAATAGCAAGTTAGATTGACTTTAGATTCATAAGCAT-GATATAGTCAGCTGACGAG -s simDog_chr6.simDog.chr6 504382 104 + 593897 CCC-CCAAGACTCCCAACTGATTTGCGTGTCATAGTCTCATATTAAGTTGTGATACCAAGCTAGATTGACTTTAGATTGATAAGCACAAATATAGACAGCTGAGG-- -s simHuman_chr6.simHuman.chr6 511500 105 + 601863 GCCGCCAAAATTCACCACTGATTTTCTTGTCA--GGCTCATATAAAGTTGTGACGCCAAGTTAGATTGACTTTAGATTCACATGTGCAAATAAGGCCAGCTGAGGAG -s simRat_chr6.simRat.chr6 553033 107 + 647215 TCTGCTATGATTTACTGTTGATCTATTTGTCATTGGCTCACAAAAAGTTGCAGCCCCAAGTTAAATTGAGTAGGGATTTGTAACCTCAGACGTGGCATTTGAAAGGC - -a -s simMouse_chr6.simMouse.chr6 541341 24 + 636262 ACACATCTTATCTAATATAATTCC -s Anc0.Anc0refChr3 144393 24 + 222631 GTACACTTAAACTGATATGACTCT -s Anc1.Anc1refChr6 179807 24 + 197743 GTACACTTAAACTGATATGACTCT -s Anc2.Anc2refChr1 57975 24 + 142988 GTACACTCAAACTGATATGACTTT -s mr.mrrefChr3 91393 24 + 181027 ACACACCTTAACTAATATGACTCC -s simCow_chr6.simCow.chr6 84696 24 - 602619 GTACACTCAAACTGATATGCCTTT -s simDog_chr6.simDog.chr6 504486 20 + 593897 ----ACTCAAAATGGTATGACTTT -s simHuman_chr6.simHuman.chr6 511605 24 + 601863 GTACACTTAAACTGATATGACTCT -s simRat_chr6.simRat.chr6 553140 24 + 647215 ACATACCCGAACTAATATGACTCC - -a -s simMouse_chr6.simMouse.chr6 541365 16 + 636262 ACTCGCATCCATATTC -s Anc0.Anc0refChr3 144417 16 + 222631 GGTCACAGGTATATTC -s Anc1.Anc1refChr6 179831 16 + 197743 GGTCACAGGTATATTC -s Anc2.Anc2refChr1 57999 16 + 142988 GGTCACAGGTATATTC -s mr.mrrefChr3 91417 16 + 181027 ACTCGCATACATATTC -s simCow_chr6.simCow.chr6 84721 6 - 602619 GGTCAC---------- -s simDog_chr6.simDog.chr6 504506 16 + 593897 AGTCACAGGTATATTC -s simHuman_chr6.simHuman.chr6 511629 16 + 601863 GGTCACAGGTGTTTTC -s simRat_chr6.simRat.chr6 553165 16 + 647215 ACTTGCACACATATTC - -a -s simMouse_chr6.simMouse.chr6 541381 119 + 636262 TAACTAGGCCTGCTTTAAGCTAAGTACTGTCCTGTGGGGACCACCCTTTACTTACCCCCCCCCCAAATTGAGAAAATAATAAAAGGACTACTTTAAAGTGGGAGATGGAATTAGTTGAA -s Anc0.Anc0refChr3 144448 43 + 222631 TAACTGTCCCTGCCTTAAGC-AACTGTTGT-CC--------------------------------------------------------------AAGAGGAACAT------------A -s Anc1.Anc1refChr6 179862 43 + 197743 TAACTGTCCCTGCCTTAAGC-AACTGTTGT-CC--------------------------------------------------------------AAGAGGAACAT------------A -s Anc2.Anc2refChr1 58030 43 + 142988 TAACTGTCCCTGCCTTGAGC-AACTGTTGT-CC--------------------------------------------------------------ACGAGGAACAT------------C -s mr.mrrefChr3 91433 63 + 181027 TAACTGTGCCTGCCTTAAGCTAACTACTGT-CTGTG-------------------------------------------------------TTTAAAGTGGGAGATGGAATTAGTTGAA -s simCow_chr6.simCow.chr6 84731 43 - 602619 CAACTGCCCCTGCCTTCAGC-CACTATTGT-CC--------------------------------------------------------------GTGAAGAACAT------------T -s simDog_chr6.simDog.chr6 504537 43 + 593897 TGACTGTCCCTACCTTGGGC-AACTGTTAT-CA--------------------------------------------------------------ACGAGGAACAC------------C -s simHuman_chr6.simHuman.chr6 511661 43 + 601863 TAACTGTCCCTGGCTCAAGC-AACTGTTGT-CC--------------------------------------------------------------AAGAGGAACAT------------A -s simRat_chr6.simRat.chr6 553181 63 + 647215 TAACTGTGCCTGCCTTAAGCGAACTACTGT-CTGTG-------------------------------------------------------TTTAGAGTGGGAGATGGAATTAGTTGAG - -a -s simMouse_chr6.simMouse.chr6 541500 1 + 636262 T -s Anc0.Anc0refChr3 144491 1 + 222631 T -s Anc1.Anc1refChr6 179905 1 + 197743 T -s Anc2.Anc2refChr1 58135 1 + 142988 T -s mr.mrrefChr3 91496 1 + 181027 T -s simCow_chr6.simCow.chr6 84836 1 - 602619 T -s simDog_chr6.simDog.chr6 504642 1 + 593897 T -s simHuman_chr6.simHuman.chr6 511704 1 + 601863 T -s simRat_chr6.simRat.chr6 553244 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 541501 15 + 636262 TACAAAAAATGAGAG -s Anc0.Anc0refChr3 144492 15 + 222631 TTCCAAAAGTTAGGG -s Anc1.Anc1refChr6 179906 15 + 197743 TTCCAAAAGTTAGGG -s Anc2.Anc2refChr1 58136 15 + 142988 TTCCAAAAGTTAGGG -s mr.mrrefChr3 91497 15 + 181027 TTCAAAAAGTGAGAG -s simCow_chr6.simCow.chr6 84837 7 - 602619 --------GTTAGGG -s simDog_chr6.simDog.chr6 504651 15 + 593897 TTCCAAAAGGTAGAG -s simHuman_chr6.simHuman.chr6 511705 15 + 601863 TTCCAAAGGTTAGGG -s simRat_chr6.simRat.chr6 553245 15 + 647215 TTCAAGAAGCGAGAG - -a -s simMouse_chr6.simMouse.chr6 541516 70 + 636262 CCTTACTATGATAGCCTTACCTGGGCCGTGAATAAAGTGACCCCTTAAGCCAAAGGGCACCTAGCGCATA -s Anc0.Anc0refChr3 144507 62 + 222631 TCTTACTATGGTA--CTCACCTGGCACCTGAATAAACTGACCCTTTAAGCTACCAGGACCCCAA------ -s Anc1.Anc1refChr6 179921 64 + 197743 TCTTACTATGGTAGCCTCACCTGGCACCTGAATAAACTGACCCTTTAAGCTACCAGGACCCCAA------ -s Anc2.Anc2refChr1 58151 62 + 142988 TCTTACTTTGATA--CTCACCTGGCACCTGAATAAACTGACCCTTTAAGTTACCAGGACCCCAA------ -s mr.mrrefChr3 91512 70 + 181027 CCTTACTATGGTAGCCTTACCTGGGCCGTGAATAAAGTGACCCCTTAAGCCACAGGGCACCTAGCGCATA -s simCow_chr6.simCow.chr6 84844 56 - 602619 TCTTAGTTTGATA--CTCACCGGGCATCTGGATA-----ACCTTTTAAGTTA-CAGGACCCCCA------ -s simDog_chr6.simDog.chr6 504666 62 + 593897 TCTAACTTTGATA--CTTACCTGGCACCTGAATAAACTGACCCTTTAGGTTACCAGGATCCCAG------ -s simHuman_chr6.simHuman.chr6 511720 64 + 601863 TCTTATTATGGTAGCATCACCTGGCACCTGAATAAACTGATCCGTTAAGCTACCTGGACCACAA------ -s simRat_chr6.simRat.chr6 553261 70 + 647215 CTTTGCTAGGGTAGCCTTACTTGGGCCATGAATAAAGTGACACTTTAAGCCACAGGGGACCTAGCACATG - -a -s simMouse_chr6.simMouse.chr6 541586 95 + 636262 TGAGTGGGGTGAGTAATTAATCACCTGCAGTCCGCTACCACCCTAAAACTGCCTATAACTAAATTCACCCCAGCCCAATGTTGAACTAAGACTGA -s Anc0.Anc0refChr3 144569 94 + 222631 TGCGTGGGATGAGTAATTGATCACCTGCCTTGCACTA-CACCATGACATACCCTATATCTAAATTTACCCCAGACCATTGTTAGCCTAGGAATAA -s Anc1.Anc1refChr6 179985 95 + 197743 TGCGTGGGATGAGTAATTGATCACCTGCCTTGCACTACCACCATGACATACCCTATATCTAAATTTACCCCAGACCATTGTTAGCCTAGGAATAA -s Anc2.Anc2refChr1 58213 94 + 142988 TACATGGGATAAGTAATTGATCACCTGCCTTGCACTA-CACCATGACATACCCTATATTTAAGTTTACCCCAGACCAATGTTAGCCTAGGAATAA -s mr.mrrefChr3 91582 95 + 181027 TGAGTGGGGTGAGTAATTAATCACCTGCAGTCCACTACCACCCTAACATTGCCTATAACTAAATTCACCCCAGCCCATTGTTGGACTAGGACTGA -s simCow_chr6.simCow.chr6 84900 42 - 602619 CACATATGAT-----------------------------------------------------TTTACCCCAGATCAATGTTAGCCTACGATTGA -s simDog_chr6.simDog.chr6 504734 90 + 593897 TACATGGGGTAAGTAATTGATCACCTGCCTTGCACTA-CACCATGACATACCCTATATTTAAGATTA----AGACTAATGTTAGCCCAGGAATAT -s simHuman_chr6.simHuman.chr6 511784 95 + 601863 TGTGTGGGATGAGTAATTGATCACCTGCCTTGCACTACCACCATGACATATCCTATAGCTGCATTTACCCCAGGCCATACTTAGCCTAGGAATAA -s simRat_chr6.simRat.chr6 553331 95 + 647215 TGATTGGGTTGAATCATTAATCACCTGCAGTCCACTACCACCCTAACATTGCCTATAACTAAATTCACCACAGACCATTGTTTGACTAGGACTGA - -a -s simMouse_chr6.simMouse.chr6 541681 41 + 636262 TGGGCATTATGGGATGTACTGTAATCTCTGTAACTCACTAT -s Anc0.Anc0refChr3 144676 31 + 222631 AGAGCCTAATGGGAGGATCTATCA----------TCACCAT -s Anc1.Anc1refChr6 180093 31 + 197743 AGAGCCTAATGGGAGGATCTATCA----------TCACCAT -s Anc2.Anc2refChr1 58320 31 + 142988 AGAGCCTAATGGGAGGATTCATCA----------TCACCAT -s mr.mrrefChr3 91677 31 + 181027 AGGGCATTATGGGATGTACTGTAA----------TCACTAT -s simCow_chr6.simCow.chr6 84956 31 - 602619 CGTGCCTAATGGGAGAATTCATCA----------TCACCAT -s simDog_chr6.simDog.chr6 504836 31 + 593897 AGAGCATATGTGGAGGATTCATCA----------TCACCAT -s simHuman_chr6.simHuman.chr6 511892 31 + 601863 AGAGCCTAATGGGAGGACCTTTCA----------TGACCAA -s simRat_chr6.simRat.chr6 553426 31 + 647215 AGGGCATTATGGGATGTACTATAA----------TCACTAT - -a -s simMouse_chr6.simMouse.chr6 541722 2 + 636262 AC -s Anc0.Anc0refChr3 144707 2 + 222631 AC -s Anc1.Anc1refChr6 180124 2 + 197743 AC -s Anc2.Anc2refChr1 58351 2 + 142988 AC -s mr.mrrefChr3 91708 2 + 181027 AC -s simCow_chr6.simCow.chr6 84987 2 - 602619 AC -s simDog_chr6.simDog.chr6 504867 2 + 593897 AC -s simHuman_chr6.simHuman.chr6 252384 2 + 601863 AT -s simHuman_chr6.simHuman.chr6 511923 2 + 601863 AC -s simRat_chr6.simRat.chr6 553457 2 + 647215 AC - -a -s simMouse_chr6.simMouse.chr6 541724 35 + 636262 CGGGGCCAAGGTGAGGTTACATGTAAATGTCTCAA -s Anc0.Anc0refChr3 144709 35 + 222631 CATGATGGGGGTGAAGTTACAAATAACTATTTCAA -s Anc1.Anc1refChr6 180126 35 + 197743 CATGATGGGGGTGAAGTTACAAATAACTATTTCAA -s Anc2.Anc2refChr1 58353 35 + 142988 CATGATGGGGGTGAAGTTGCAAATAACTATTTCAA -s mr.mrrefChr3 91710 35 + 181027 CAGGGCCAAGGTGAGGTTACATGTAAATGTCTCAA -s simCow_chr6.simCow.chr6 84989 35 - 602619 CACGATGGGGGTGAAGTTGCACATAACTGTCTCAA -s simDog_chr6.simDog.chr6 504869 35 + 593897 CATGATGGTGGTGAAATTGCAACCAACCATTTCAA -s simHuman_chr6.simHuman.chr6 511925 35 + 601863 TATGATGGGGGTGAAGTTACAAATAACTATTTCAA -s simRat_chr6.simRat.chr6 553459 17 + 647215 CAGGGC------------------AAATGTCTCAA - -a -s simMouse_chr6.simMouse.chr6 541759 46 + 636262 TATTTGTTTTGGTCCACAATTTCCCGTTATTAGCATGGAATCGAAC -s Anc0.Anc0refChr3 144744 35 + 222631 TATTTGATGTGGCCC----TTGCCCCTCATT-------AATTGAAC -s Anc1.Anc1refChr6 180161 46 + 197743 TATTTGATGTGGCCCACTATTGCCCCTCATTAGCATGGAATTGAAC -s Anc2.Anc2refChr1 58388 35 + 142988 TATTTGATGTATCAC----TTGCTCCTCATT-------GAGTGAAC -s mr.mrrefChr3 91745 46 + 181027 TATTTGATGTGGTCCACAATTTCCCCTTATTAGCATGGAATTGAAC -s simCow_chr6.simCow.chr6 85024 35 - 602619 GACCTGATGTATCAC----TTGCTCCTCATT-------GAGTGAAC -s simDog_chr6.simDog.chr6 504907 10 + 593897 TTTTTAATAT------------------------------------ -s simHuman_chr6.simHuman.chr6 511960 46 + 601863 TATTTGATGTGGCCCACTATTACCCCTCATTAGCATGGAATTGAAC -s simRat_chr6.simRat.chr6 553476 46 + 647215 TATTTGATGTGGTCTACAATTGCCCCTTATTAGTATGAAATTGAAC - -a -s simMouse_chr6.simMouse.chr6 541805 37 + 636262 TTTTTTTGTCTCCTGTTTGCAGGCTTATAACCATCCT -s Anc0.Anc0refChr3 144786 14 + 222631 TTGATATA-----------------------TGTCCT -s Anc1.Anc1refChr6 180214 14 + 197743 TTGATATA-----------------------TGTCCT -s Anc2.Anc2refChr1 58430 14 + 142988 TAGATATA-----------------------TGCCTT -s mr.mrrefChr3 91791 14 + 181027 TTTTTTTG-----------------------CATCCT -s simCow_chr6.simCow.chr6 85066 14 - 602619 TAGATATA-----------------------TGCCTT -s simHuman_chr6.simHuman.chr6 512013 14 + 601863 TTGATATA-----------------------TGTCCT -s simRat_chr6.simRat.chr6 553522 14 + 647215 TTTCTTTG-----------------------CACTGT - -a -s simMouse_chr6.simMouse.chr6 541842 27 + 636262 GTTTGCTGGCTTTTAACCATCCACCAG -s Anc0.Anc0refChr3 144803 25 + 222631 GCTAGCAGGC--TTAACCTTCAACCAG -s Anc1.Anc1refChr6 180231 27 + 197743 GCTAGCAGGCTTTTAACCTTCAACCAG -s Anc2.Anc2refChr1 58447 25 + 142988 GCCAGCAGGC--TTAACCTTCAACCAG -s mr.mrrefChr3 91805 27 + 181027 GCTTGCAGGCTTTTAACCATCCACCAG -s simCow_chr6.simCow.chr6 85083 25 - 602619 GCCAGCAGGC--TTAACCTTCAACCAG -s simHuman_chr6.simHuman.chr6 512030 27 + 601863 GCTAGCAGGCTTTTACCTTTCAACCAG -s simRat_chr6.simRat.chr6 553536 27 + 647215 GCATGCAGGCTTTTAACCATCCACCAG - -a -s simMouse_chr6.simMouse.chr6 541869 3 + 636262 GAA -s Anc0.Anc0refChr3 144829 3 + 222631 GGA -s Anc1.Anc1refChr6 180259 3 + 197743 GGA -s Anc2.Anc2refChr1 58473 3 + 142988 AGA -s mr.mrrefChr3 91832 3 + 181027 GAA -s simCow_chr6.simCow.chr6 85109 3 - 602619 AGA -s simHuman_chr6.simHuman.chr6 512058 3 + 601863 GGA -s simRat_chr6.simRat.chr6 553563 3 + 647215 GAA - -a -s simMouse_chr6.simMouse.chr6 541872 9 + 636262 ATGTAGGTC -s Anc0.Anc0refChr3 144832 9 + 222631 TCATAGGTT -s Anc1.Anc1refChr6 180262 9 + 197743 TCATAGGTT -s Anc2.Anc2refChr1 58476 9 + 142988 TCCAAGGGT -s mr.mrrefChr3 91835 9 + 181027 ACATAGGTC -s simCow_chr6.simCow.chr6 85112 9 - 602619 TCCAAGGGT -s simHuman_chr6.simHuman.chr6 252386 9 + 601863 ACATCGgtt -s simHuman_chr6.simHuman.chr6 512061 9 + 601863 TCATAGGTT -s simRat_chr6.simRat.chr6 553566 9 + 647215 ACATAGGTC - -a -s simMouse_chr6.simMouse.chr6 541881 1 + 636262 T -s Anc0.Anc0refChr3 144842 1 + 222631 T -s Anc1.Anc1refChr6 180272 1 + 197743 T -s Anc2.Anc2refChr1 58486 1 + 142988 C -s mr.mrrefChr3 91844 1 + 181027 T -s simCow_chr6.simCow.chr6 85122 1 - 602619 C -s simHuman_chr6.simHuman.chr6 252396 1 + 601863 t -s simHuman_chr6.simHuman.chr6 512178 1 + 601863 T -s simRat_chr6.simRat.chr6 553575 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 541882 7 + 636262 ATGGTGT -s Anc0.Anc0refChr3 144843 2 + 222631 AT----- -s Anc1.Anc1refChr6 180273 7 + 197743 ATGGTAT -s Anc2.Anc2refChr1 58487 2 + 142988 AT----- -s mr.mrrefChr3 91845 7 + 181027 ATGGTAT -s simCow_chr6.simCow.chr6 85123 2 - 602619 AT----- -s simHuman_chr6.simHuman.chr6 252397 7 + 601863 atgggat -s simHuman_chr6.simHuman.chr6 512179 7 + 601863 ATGGGAT -s simRat_chr6.simRat.chr6 553725 7 + 647215 GTGGTAT - -a -s simMouse_chr6.simMouse.chr6 541889 69 + 636262 CAGCCCCAGTTGTAAGAAATGATCTTGGTTGGGCTTCACCAAGTCATCTGGTTACTAATTTTGATCATC -s Anc0.Anc0refChr3 144849 67 + 222631 TGGCTCTAGTTGCTTGATAAGGTCCTGATTAGACACTACCCTGCCACCTGGTTCC--TTTTTGAACATC -s Anc1.Anc1refChr6 180324 69 + 197743 TGGCTCTAGTTGCTTGATAAGGTCCTGATTAGACACTACCCTGCCACCTGGTTCCTATTTTTGAACATC -s Anc2.Anc2refChr1 58493 67 + 142988 TGGCTCTAGTTGCTTGATGAGGTCCTGATTAGAGCCTACCCTGCCACCTGGTTCC--TTTTTGAACATC -s mr.mrrefChr3 91852 69 + 181027 TGGCTCTAGTTGCAAGATATGATCTTGGTTAGACTTTACCATGTCATCTGGTTACTATTTTTGATCATC -s simCow_chr6.simCow.chr6 85129 67 - 602619 TGGCTCTAGTCACTTAATCAGTCCTGTATTGGATGCTACCCTGCCACCTGATTCC--TTTTTGAACACC -s simDog_chr6.simDog.chr6 504917 67 + 593897 TGGCTCTAGTTGCCTGATGGGGTCCTGACTAGAGCCTACCCTGGCACCTGGTTCC--TTTATGAACATC -s simHuman_chr6.simHuman.chr6 252448 69 + 601863 TGGCTCTAGTTGCTTGATAAGGTCCTGATTAGACACTACCCTGCAACCTGGGTACTATTTTTGAACTTC -s simHuman_chr6.simHuman.chr6 512230 69 + 601863 TGGCTCTAGTTGCTTGATAAGGTCCTGATTAGACACTACCCTGCAATCTGGGTCCTATTTTTGATCTTC -s simRat_chr6.simRat.chr6 553732 69 + 647215 TGGCTCTAAGTGCAAGATACAATCTTGGTTAGACTTTACCATGACGTCTGGTTACTATTTTTGATCATC - -a -s simMouse_chr6.simMouse.chr6 541958 50 + 636262 ATCTAGGGGCATGCACACATCAACTCCTGTCTGGAGACAGGGGTTGCAGA -s Anc0.Anc0refChr3 144920 47 + 222631 ATTGAGGGGCCTGTACACA---GCTCCTGCTTGGAGACAGAGTTGGAAGA -s Anc1.Anc1refChr6 180397 47 + 197743 ATTGAGGGGCCTGTACACA---GCTCCTGCTTGGAGACAGAGTTGGAAGA -s Anc2.Anc2refChr1 58564 47 + 142988 ATTGAGGGGCCAGGACACA---GCTGTTGCTTGGAGGTAGAGCTGGAAGA -s mr.mrrefChr3 91921 50 + 181027 ATCTAGGGGCATGTACACATCAACTCCTGCCTGGAGACAGAGGTTGAAGA -s simCow_chr6.simCow.chr6 85198 40 - 602619 -------TGCCAGGACACA---GCTGTTGCTTGGAGGTAGGGCTGGGAGA -s simDog_chr6.simDog.chr6 504988 21 + 593897 ATTGAGGGG-----------------------------AGAGCTGGAAGA -s simHuman_chr6.simHuman.chr6 252521 47 + 601863 ACTGAGGGGCCTGTGCACA---GTTCCTGCTTGGAGACAAAGTGGGAAGA -s simHuman_chr6.simHuman.chr6 512303 47 + 601863 ACTGAGAGGCCTGTGCACA---GCTCCTGCTTGGAGACAAAGTGGGAAGA -s simRat_chr6.simRat.chr6 553801 50 + 647215 ATCTAGGGGCATGTACACAACAACTCCTGCCTGGAGACAGAGATTGAAGA - -a -s simMouse_chr6.simMouse.chr6 542008 6 + 636262 CTAGAC -s Anc0.Anc0refChr3 144967 6 + 222631 ATAGAC -s Anc1.Anc1refChr6 180444 6 + 197743 ATAGAC -s Anc2.Anc2refChr1 58611 6 + 142988 ATAGAC -s mr.mrrefChr3 91971 6 + 181027 ATAGAC -s simCow_chr6.simCow.chr6 85238 6 - 602619 AAAGAC -s simDog_chr6.simDog.chr6 505011 6 + 593897 ATAGAC -s simHuman_chr6.simHuman.chr6 252568 6 + 601863 ATAGGC -s simHuman_chr6.simHuman.chr6 512350 6 + 601863 ATAGGC -s simRat_chr6.simRat.chr6 553851 6 + 647215 ATAAAT - -a -s simMouse_chr6.simMouse.chr6 542014 8 + 636262 ATAAAAGC -s Anc0.Anc0refChr3 144973 7 + 222631 ATAGCAT- -s Anc1.Anc1refChr6 180450 8 + 197743 ATAGCATC -s Anc2.Anc2refChr1 58627 7 + 142988 CCAGCAT- -s mr.mrrefChr3 91977 8 + 181027 ATAACAGC -s simCow_chr6.simCow.chr6 85254 7 - 602619 CCAGCAT- -s simDog_chr6.simDog.chr6 505027 7 + 593897 CCAGCAT- -s simHuman_chr6.simHuman.chr6 252574 8 + 601863 ATAGCATC -s simHuman_chr6.simHuman.chr6 512356 8 + 601863 AAAGCATC -s simRat_chr6.simRat.chr6 553857 8 + 647215 ATAACAGC - -a -s simMouse_chr6.simMouse.chr6 542022 31 + 636262 AGGagaaagtccatttcagccataagcttgc -s Anc0.Anc0refChr3 144981 31 + 222631 AGgagaaatctcatttctaccataaggttgt -s Anc1.Anc1refChr6 180459 31 + 197743 AGgagaaatctcatttctaccataaggttgt -s Anc2.Anc2refChr1 58635 31 + 142988 AGGagaaatctcatttccaccataaggttgt -s mr.mrrefChr3 91985 31 + 181027 AGGagaaatcccatttcagccataagcttgt -s simCow_chr6.simCow.chr6 85262 31 - 602619 AGGagagatttcatttccatgataaggttgt -s simDog_chr6.simDog.chr6 505035 31 + 593897 AGGTGAAGTCTCAGCTCCACCACAAAGTTGT -s simHuman_chr6.simHuman.chr6 252583 31 + 601863 AGaagaaatctcttttctactataaggttgt -s simHuman_chr6.simHuman.chr6 512365 31 + 601863 AGaagaaatcccttttctactataaggttgt -s simRat_chr6.simRat.chr6 553865 31 + 647215 AGGagaaatcccatttcagccataagcttgt - -a -s simMouse_chr6.simMouse.chr6 542053 7 + 636262 tccctct -s Anc0.Anc0refChr3 145025 7 + 222631 tccccct -s Anc1.Anc1refChr6 180503 7 + 197743 tccccct -s Anc2.Anc2refChr1 58681 7 + 142988 tcccacc -s mr.mrrefChr3 92016 7 + 181027 tccctct -s simCow_chr6.simCow.chr6 85304 7 - 602619 tcccacc -s simDog_chr6.simDog.chr6 505081 2 + 593897 TC----- -s simHuman_chr6.simHuman.chr6 252627 7 + 601863 tccccgt -s simHuman_chr6.simHuman.chr6 512409 7 + 601863 tccccgt -s simRat_chr6.simRat.chr6 553896 7 + 647215 tccctct - -a -s simMouse_chr6.simMouse.chr6 542060 37 + 636262 cagcattctgactatttaaagagttcagtagtacctg -s Anc0.Anc0refChr3 145035 37 + 222631 ctgcattctgtctacttaaagagttcaatagtgcctg -s Anc1.Anc1refChr6 180513 37 + 197743 ctgcattctgtctacttaaagagttcaatagtgcctg -s Anc2.Anc2refChr1 58691 37 + 142988 ctgcattctgtctacttagagagttcaatagtgcttg -s mr.mrrefChr3 92026 37 + 181027 cagcattctgactatttaaagagttcagtagtacctg -s simCow_chr6.simCow.chr6 85314 37 - 602619 atgcattctgtctacatcgggagttcaatgacttggg -s simDog_chr6.simDog.chr6 505083 37 + 593897 ctgcattttgattatttagagagtccaagagtgcttg -s simHuman_chr6.simHuman.chr6 252637 37 + 601863 ctgcattctgtcgacttaaagagttcattagtgcctg -s simHuman_chr6.simHuman.chr6 512419 37 + 601863 ctgcattctgtctacttaaagagttcaatagtgcctg -s simRat_chr6.simRat.chr6 553906 37 + 647215 cagctttctgactatttaaagagttctgtggtacttg - -a -s simMouse_chr6.simMouse.chr6 542097 18 + 636262 gtgggcatatgctaggtt -s Anc0.Anc0refChr3 145076 18 + 222631 gtgcacatattctaaatt -s Anc1.Anc1refChr6 180554 18 + 197743 gtgcacatattctaaatt -s Anc2.Anc2refChr1 58732 18 + 142988 gtgtacatatcctaaatt -s mr.mrrefChr3 92067 18 + 181027 gtgggcatatgctaagtt -s simCow_chr6.simCow.chr6 85355 18 - 602619 gtatacacatcttaaatt -s simDog_chr6.simDog.chr6 505124 18 + 593897 gtgttcatttcctaaatt -s simHuman_chr6.simHuman.chr6 252678 18 + 601863 atgcatatattctaaatt -s simHuman_chr6.simHuman.chr6 512460 18 + 601863 gtgcatatattctaaatt -s simRat_chr6.simRat.chr6 553947 18 + 647215 gtggtcatatgctaagtt - -a -s simMouse_chr6.simMouse.chr6 542115 49 + 636262 actgtccttgcaacctgaaaactctcagatctaaaagctggaaccccta -s Anc0.Anc0refChr3 145113 36 + 222631 g-----ctcgcaacctgaaag-tcttaaaactgggagcccgc------- -s Anc1.Anc1refChr6 180591 36 + 197743 g-----ctcgcaacctgaaag-tcttaaaactgggagcccgc------- -s Anc2.Anc2refChr1 58769 36 + 142988 g-----ctcacagcctgaaag-tcttaaaactgggacccctc------- -s mr.mrrefChr3 92099 49 + 181027 gctgtcctcgcaacctgaaaactctcagatctaaaagctggaaccccta -s simCow_chr6.simCow.chr6 85392 34 - 602619 a-----ttcac--catgcaag-tcttaaaagtaggacctccc------- -s simDog_chr6.simDog.chr6 505157 36 + 593897 g-----ctcacagcctgagag-tctcaaaactgcatcccctt------- -s simHuman_chr6.simHuman.chr6 252715 36 + 601863 g-----ctcgcaacctgaacg-tctcaacactgggagcccGC------- -s simHuman_chr6.simHuman.chr6 512497 36 + 601863 g-----ctcgcaacctgaacg-tcttaacactgggagcccgc------- -s simRat_chr6.simRat.chr6 553979 49 + 647215 GCTGTCCTCACTACTGGAATATTCTACGATCCAAAAGTTATAACCCCTA - -a -s simMouse_chr6.simMouse.chr6 542164 7 + 636262 aggtgGT -s Anc0.Anc0refChr3 145149 7 + 222631 aggatgt -s Anc1.Anc1refChr6 180627 7 + 197743 aggatgt -s Anc2.Anc2refChr1 58805 7 + 142988 ggaatat -s mr.mrrefChr3 92148 7 + 181027 aggtgGT -s simCow_chr6.simCow.chr6 85426 7 - 602619 gTTACAT -s simDog_chr6.simDog.chr6 505193 7 + 593897 ggactat -s simHuman_chr6.simHuman.chr6 512533 7 + 601863 aggatgt -s simRat_chr6.simRat.chr6 554028 7 + 647215 AGGTGGT - -a -s simMouse_chr6.simMouse.chr6 542171 59 + 636262 AACACGTGTGGCTAGTCGCATTGTAAAACTGGAGCCCACCAAGCTGTGTGTCTTGCAAA -s Anc0.Anc0refChr3 145156 56 + 222631 atcacatc---ctaatcgcattatgaaactggggcccctcaagctgtgttacacACAAA -s Anc1.Anc1refChr6 180634 56 + 197743 atcacatc---ctaatcgcattatgaaactggggcccctcaagCTGTGttACACACAAA -s Anc2.Anc2refChr1 58812 56 + 142988 atcacacc---ttaattgcattctgaaactgggccccctcaagctgtgttgcacACAAA -s mr.mrrefChr3 92155 59 + 181027 ATCACATGTGGCTAGTCgCATTATAAAACTGGAGCCCACCAAGCTGTGTGACTTGCAAA -s simCow_chr6.simCow.chr6 86015 56 - 602619 ATCACACC---TTAGTTGCATTCtgaaactgggacccctccagctgtgttgcacacaaA -s simDog_chr6.simDog.chr6 505200 56 + 593897 atcaaacc---taaactgcattctgaaactgggccccctcaagctgtgttgcacACAAA -s simHuman_chr6.simHuman.chr6 512540 54 + 601863 attgcatt---ctaatcacatcattaaactggggccccacaagCACAC--ACACACAAA -s simRat_chr6.simRat.chr6 554035 58 + 647215 ATCATATGTAGCTAGTC-CATTATAAAACTGGAGCCTGCCATGCTGTGTGACCAGCAAA - -a -s simMouse_chr6.simMouse.chr6 542230 70 + 636262 TGGATGGTTTCTGAAGCATTGTCTCACTGGGATGTTGACAGCTCCTGGAGAATTGTTCACATCACTTAAG -s Anc0.Anc0refChr3 145221 62 + 222631 TGAAAAGTTTCACAAGCATAGTAACACTGA-----TGTCAGC---AAGAGACTTGTATACATTGCTTAAG -s Anc1.Anc1refChr6 180699 62 + 197743 TGAAAAGTTTCACAAGCATAGTAACACTGA-----TGTCAGC---AAGAGACTTGTATACATTGCTTAAG -s Anc2.Anc2refChr1 58877 62 + 142988 TGAAAAGTATCACAAGCATAATAACACTGA-----TGTTACC---CAGAGACTTGTATGCATTACTTAAG -s mr.mrrefChr3 92223 70 + 181027 TGGATGGTTTCTGAAGCATTGTCACACTGGGATGTTGACAGCTCCAGGAGACTTGTTCACATTGCTTAAG -s simCow_chr6.simCow.chr6 86080 62 - 602619 GGAAAAGTATCACAACCATAATAACACTGA-----CATTACT---GACAAACTTGTATGAATTACTTAAG -s simDog_chr6.simDog.chr6 505265 56 + 593897 TGAGAAGTATTACAAGCAGAATAATGCTGC-----TGTTACC---CAGAGACTTGTATGCATCA------ -s simHuman_chr6.simHuman.chr6 512603 62 + 601863 AGAAAAATTTCACAAGTGTAGTAACACTGA-----TGTCAGC---AAGAGACTTGAAAACATTGCTTAAG -s simRat_chr6.simRat.chr6 554102 70 + 647215 TGGATGGTTTCTGAAGCATTGTCACACTGGCATGTTCATAGTTCCAGGAGACTCGTTCACATTGCTTTAG - -a -s simMouse_chr6.simMouse.chr6 542300 7 + 636262 TGGCAGC -s Anc0.Anc0refChr3 145283 2 + 222631 T-----C -s Anc1.Anc1refChr6 180761 7 + 197743 TGGTAGC -s Anc2.Anc2refChr1 58939 2 + 142988 T-----C -s mr.mrrefChr3 92293 7 + 181027 TGGCAGC -s simCow_chr6.simCow.chr6 86142 2 - 602619 T-----C -s simDog_chr6.simDog.chr6 87333 2 - 593897 T-----C -s simHuman_chr6.simHuman.chr6 512665 6 + 601863 -GGTAGG -s simRat_chr6.simRat.chr6 554172 7 + 647215 TGGCTGC - -a -s simMouse_chr6.simMouse.chr6 542307 12 + 636262 CACACAAAAAGG -s Anc0.Anc0refChr3 145285 11 + 222631 TAGATGAAA-GT -s Anc1.Anc1refChr6 180768 11 + 197743 TAGATGAAA-GT -s Anc2.Anc2refChr1 58941 11 + 142988 TAGATGAAA-AT -s mr.mrrefChr3 92300 12 + 181027 CACACAAAAAGG -s simCow_chr6.simCow.chr6 86145 11 - 602619 CAGCTGCAA-AT -s simDog_chr6.simDog.chr6 87335 11 - 593897 TAGATGAAA-AT -s simHuman_chr6.simHuman.chr6 512671 11 + 601863 TAGGTGAGA-GT -s simRat_chr6.simRat.chr6 554179 12 + 647215 CACACAAAAAGG - -a -s simMouse_chr6.simMouse.chr6 542319 21 + 636262 CTAGCCTTCAGATAGGCACTA -s Anc0.Anc0refChr3 145296 21 + 222631 CAAGCCTCCAGATTTGCTTAT -s Anc1.Anc1refChr6 180779 21 + 197743 CAAGCCTCCAGATTTGCTTAT -s Anc2.Anc2refChr1 58952 21 + 142988 CAAGCCTCCAGATTTGCTTAT -s mr.mrrefChr3 92312 21 + 181027 TTAGCCTTTAGATAGGCACTA -s simCow_chr6.simCow.chr6 86157 21 - 602619 CCAGCCTCTGGATTTGCTTAT -s simDog_chr6.simDog.chr6 87346 21 - 593897 CAAGCCTCCAGATTTGCTTAG -s simHuman_chr6.simHuman.chr6 512682 21 + 601863 CAAACCTCCAGATTTGCTTAT -s simRat_chr6.simRat.chr6 554191 21 + 647215 TTAACCTTTTGATAGGCGCTA - -a -s simMouse_chr6.simMouse.chr6 542340 6 + 636262 TACAAC -s Anc0.Anc0refChr3 145317 6 + 222631 TAGGAC -s Anc1.Anc1refChr6 180800 6 + 197743 TAGGAC -s Anc2.Anc2refChr1 58973 6 + 142988 TAGAAC -s mr.mrrefChr3 92333 6 + 181027 TACGAC -s simCow_chr6.simCow.chr6 86179 6 - 602619 TAGAAG -s simDog_chr6.simDog.chr6 87367 6 - 593897 TAGAAC -s simHuman_chr6.simHuman.chr6 512703 6 + 601863 GTGGAT -s simRat_chr6.simRat.chr6 554213 6 + 647215 TATGAG - -a -s simMouse_chr6.simMouse.chr6 542346 137 + 636262 TAGAGCTACTGTTATTCATACATTCAGCATTCGCCCTATTGCTGTTAGTCCTAGGGTATTCCCTCCAACTAATTTCAGGCCGATGTGGTAAATTGGATAAACACTATTACTAAGGTACATTCATGTGTTTGATATAA -s Anc0.Anc0refChr3 145330 129 + 222631 CAG------TGTTATCCATATATTC-ACATTTGCCTTGTTGCTATTAGCCCTTAGCT-TTCACTGCACCTAATTGTAGCCAGATGTAGTAAATTAGATGGACATTATTGGTAAGGTACATCCATATGTGTGATATAA -s Anc1.Anc1refChr6 180813 136 + 197743 CAGTGTTGCTGTTATCCATATATTCAACATTTGCCTTGTTGCTATTAGCCCTTAGCT-TTCACTGCACCTAATTGTAGCCAGATGTAGTAAATTAGATGGACATTATTGGTAAGGTACATCCATATGTGTGATATAA -s Anc2.Anc2refChr1 58986 129 + 142988 CAG------TGTTATCCATATATCC-ACATTTGCCTTGTTGTTATTAGCCCCTAGCT-TTCACTGCACCTAATTGTAGCTAGATGTAGTAAATAAGATGGGGCTTATCTGTAAGGTACTTATATACATGTGATATAA -s mr.mrrefChr3 92339 136 + 181027 TAGAGCTACTGTTATTCATATATTCAGCATTTGCCCTATTGCTGTTAGCCCTAGGGT-TTCCCTCCACCTAATTTCAGCCCGATGTGGTAAATTGGATAAACACTATTGGTAAGGTACATCCATGTGTTTGATATAA -s simCow_chr6.simCow.chr6 86192 126 - 602619 CAA------TGTTACCCATATA----ACATTTGCCTTGTTATCATGAGCCCCTAGCT-TACACTTCACCTAATTGTAGCTAGATGCAGTAAATAAGATGGGGCTTATCTGTAAGGTACTTATATACATGTGATATAA -s simDog_chr6.simDog.chr6 87380 83 - 593897 CAG------TATTATCCATATATCC-ACATCTGCCTTGTTGTTATTAGCCCCTTGCT-TTTGCTGCATGTAATTATAGCTAGATGTAGTAA---------------------------------------------- -s simHuman_chr6.simHuman.chr6 512720 136 + 601863 CAGTGTTGCTGTTATGAATATATTCAACATTTGCCTTGTGGCTATAAGCTCTTATCT-TTCACTGCACCTAATTGTAACCAGATGTAGGGACCTAGATTGACATTATTGGTAAGGTGCATCCATATGTGTGATATAA -s simRat_chr6.simRat.chr6 554219 124 + 647215 TAGAGCTAGTGTTATTTATATATTCAGCATTTGCCCTATTGCTGTTAGCCCTAGGTT-TTCCCTCCACCTAA---CAGCCGGGTGTGG---------CAAACACTATTGGCAAGGTACATCCTTGTGTTTAATATAG - -a -s simMouse_chr6.simMouse.chr6 542483 62 + 636262 CCATGAAAGCAATCATTTAGTGTTTCTGTACTCACTAATTCCAGTAATCCTTCTCTAACAGT -s Anc0.Anc0refChr3 145459 60 + 222631 TCATGAGAACAATCAGATAGTG--TATGTAGCCTCTTAATCCTGTCATCCTTCACTAATGGC -s Anc1.Anc1refChr6 180949 62 + 197743 TCATGAGAACAATCAGATAGTGTTTATGTAGCCTCTTAATCCTGTCATCCTTCACTAATGGC -s Anc2.Anc2refChr1 59115 60 + 142988 TCATGAGAACAGTAAGATAGTG--TATGTAGCCTCTTTACCCTGACTACCTTTATTAAAGTC -s mr.mrrefChr3 92475 62 + 181027 CCATGAAAGCAATCATTTAGTGTTTCTGTACTCACTAAATCCAGTCATCCTTCACTAATGGT -s simCow_chr6.simCow.chr6 86318 60 - 602619 TCATGAGAACAGTAAGATAGTG--TATGTAGCCTCTTTACCCTGACTACCTTTATTAAAGTT -s simDog_chr6.simDog.chr6 87463 4 - 593897 ----------------------------------------------------------AGTC -s simHuman_chr6.simHuman.chr6 512856 62 + 601863 TCTTGAGAACAATCAACTAGTGCTTATGTGGCCTCTCAATACTGTCATTCTTCACTAATGGC -s simRat_chr6.simRat.chr6 554344 50 + 647215 CCATGAAAGCAATTGTTCAGTG------------CTAAATCCAATCATCCTTCACGAATGAT - -a -s simMouse_chr6.simMouse.chr6 542545 4 + 636262 ACTT -s Anc0.Anc0refChr3 145519 4 + 222631 ACTT -s Anc1.Anc1refChr6 181011 4 + 197743 ACTT -s Anc2.Anc2refChr1 59176 4 + 142988 ACCA -s mr.mrrefChr3 92537 4 + 181027 ACTT -s simCow_chr6.simCow.chr6 86379 4 - 602619 CTGT -s simDog_chr6.simDog.chr6 87468 4 - 593897 ACCA -s simHuman_chr6.simHuman.chr6 512918 4 + 601863 ACTT -s simRat_chr6.simRat.chr6 554394 4 + 647215 ACTT - -a -s simMouse_chr6.simMouse.chr6 542549 140 + 636262 CCATGGTTCATTGGAAGGATTTACCACACCAGAGGGAATTACAAAGACCTGACAGTATTATATCTCAACTTAAGCCCCTTGGGAGGTGTCAAAAAAGTGCGCCATATTCACATGCAGAAATCTGGTGTCTCAGGCACCAT -s Anc0.Anc0refChr3 145523 124 + 222631 CTATTGTTCAATTGGAGGAAT--CTACACCAGAAGAAATTACACAAAAAC--CTGTCTTATACTTTCAATAAAGCCCCTTGAGAGGC------------TGCCACATTCATGTGCAGAAATCTGGTCTCTTTGGTATTGT -s Anc1.Anc1refChr6 181015 136 + 197743 CTATTGTTCAATTGGAGGAAT--CTACACCAGAAGAAATTACACAAAAAC--CTGTCTTATACTTTCAATAAAGCCCCTTGAGAGGCATTGAGGAACTGTGCCACATTCATGTGCAGAAATCTGGTCTCTTTGGTATTGT -s Anc2.Anc2refChr1 59180 124 + 142988 CTATTGTTCAATTGGAGGAAT--CTACATCAGAATAAATTACACAAAAAC--CCATCTTATACTTTTAATTTAGCTCCTTGATGAGC------------TGCCACATTTACATGCAGAAGTCTGGCCTCTTTGGTATTGT -s mr.mrrefChr3 92541 140 + 181027 CCATGGTTCATTGGGAGGATTTACCACACCAGAGGGAATTACACAGACCCGACTGTATTATATCTCCACTAAAGCCCCTTGGGAGGTGTCAAAGAAGTGTGCCATATTCATGTGCAGAAATCTGGTGTCTCAGGTACCAT -s simCow_chr6.simCow.chr6 86383 71 - 602619 CTATTG----------GGAAC--CCTCAT-AGAACAAATTACACAAAAAC--CCTTGAACTAC------------------------------------------------------AATCCTGGACTCTTTGGTAGTGC -s simDog_chr6.simDog.chr6 87472 124 - 593897 CCACTGTTCAATTGGAGCAAT--TTACTTCAGAATAAACTACACTAAAAG--CCATCTTATATTTTTAATTTAGCTCCTTGATGAGC------------TGCCACATTTACATGCAGAAGTATGGCCTCTTTGGTATTGT -s simHuman_chr6.simHuman.chr6 512938 135 + 601863 CTATTGTTCAAATAGAGGAAT--CTACACCAGATG-AATTACACAAAAAC--CTGTCTTATACTTTCATTAAAGCCCCTTCAGAGGCATTGAGGAACTGTGCCACATTCATGTGAAGAAAACTGGTCCCTTTGGTAATGT -s simRat_chr6.simRat.chr6 554398 138 + 647215 CCATGGTTCATCGGGAGGACTTACCACACCAGAGGGAATTACACAGACCCAACTTTATTATATCTACACTAAAGCTCTTTGGGAGGTGTCAAAGAATTGTGCCATATTCATGTGCAGGAA--TGGTGTCTCGGGTGCCAG - -a -s simMouse_chr6.simMouse.chr6 542689 2 + 636262 TG -s Anc0.Anc0refChr3 145647 2 + 222631 TA -s Anc1.Anc1refChr6 181151 2 + 197743 TA -s Anc2.Anc2refChr1 59304 2 + 142988 CA -s mr.mrrefChr3 92681 2 + 181027 TG -s simCow_chr6.simCow.chr6 86454 2 - 602619 GA -s simDog_chr6.simDog.chr6 87603 2 - 593897 CA -s simHuman_chr6.simHuman.chr6 513073 2 + 601863 TA -s simRat_chr6.simRat.chr6 554536 2 + 647215 TG - -a -s simMouse_chr6.simMouse.chr6 542691 5 + 636262 AGATC -s Anc0.Anc0refChr3 145652 5 + 222631 AGATC -s Anc1.Anc1refChr6 181156 5 + 197743 AGATC -s Anc2.Anc2refChr1 59309 5 + 142988 AGATC -s mr.mrrefChr3 92683 5 + 181027 AGATC -s simCow_chr6.simCow.chr6 86459 5 - 602619 AGAGC -s simDog_chr6.simDog.chr6 87608 5 - 593897 AGATC -s simHuman_chr6.simHuman.chr6 513078 5 + 601863 AGATC -s simRat_chr6.simRat.chr6 554538 5 + 647215 AGATC - -a -s simMouse_chr6.simMouse.chr6 542696 6 + 636262 GCTCAA -s Anc0.Anc0refChr3 145658 6 + 222631 GGTCAA -s Anc1.Anc1refChr6 181162 6 + 197743 GGTCAA -s Anc2.Anc2refChr1 59315 6 + 142988 GGTCAG -s mr.mrrefChr3 92688 6 + 181027 GCTCAA -s simCow_chr6.simCow.chr6 86465 6 - 602619 GAACAG -s simDog_chr6.simDog.chr6 87614 6 - 593897 GGTCAG -s simHuman_chr6.simHuman.chr6 513084 6 + 601863 GGTCAA -s simRat_chr6.simRat.chr6 554543 6 + 647215 ACTCAA - -a -s simMouse_chr6.simMouse.chr6 542702 16 + 636262 CAGGTCCTAGGGCGGG -s Anc0.Anc0refChr3 145673 15 + 222631 CAGGTGCCAGGGCA-G -s Anc1.Anc1refChr6 181177 16 + 197743 CAGGTGCCAGGGCAGG -s Anc2.Anc2refChr1 59330 15 + 142988 CAGGTGCCAGGGCA-G -s mr.mrrefChr3 92694 16 + 181027 CAGGTGCCAGGGCAGG -s simCow_chr6.simCow.chr6 86473 8 - 602619 CAGGTGCC-------- -s simDog_chr6.simDog.chr6 87629 15 - 593897 TGAGTGCCAGGGCA-G -s simHuman_chr6.simHuman.chr6 513099 16 + 601863 CAGGTGCCAGTGCACG -s simRat_chr6.simRat.chr6 554549 16 + 647215 TGGGTGCCAGGGCAGG - -a -s simMouse_chr6.simMouse.chr6 542718 20 + 636262 GTGAATCATCTATAAGTTTA -s Anc0.Anc0refChr3 145690 20 + 222631 GTGAATCAGCTATAGGTTTA -s Anc1.Anc1refChr6 181195 20 + 197743 GTGAATCAGCTATAGGTTTA -s Anc2.Anc2refChr1 59347 20 + 142988 GTGATTCAGCTATAGGTTTA -s mr.mrrefChr3 92710 20 + 181027 GTGAATCATCTATAAGTTTA -s simCow_chr6.simCow.chr6 86483 20 - 602619 GGGGTTCAGTTATAGATTTT -s simDog_chr6.simDog.chr6 87646 20 - 593897 GTGATTCGGCTATAGGTTTA -s simHuman_chr6.simHuman.chr6 513119 20 + 601863 GTGAATCAGCTATAGGCTTA -s simRat_chr6.simRat.chr6 554565 18 + 647215 GTGAATCAACTAT--GTTTA - -a -s simMouse_chr6.simMouse.chr6 542738 11 + 636262 GACCTATCTTA -s Anc0.Anc0refChr3 145719 11 + 222631 TATCTGACTCA -s Anc1.Anc1refChr6 181224 11 + 197743 TATCTGACTCA -s Anc2.Anc2refChr1 59376 11 + 142988 TATTTGACTCA -s mr.mrrefChr3 92739 11 + 181027 GACCTAACTCA -s simCow_chr6.simCow.chr6 86512 11 - 602619 TATTTGACTCA -s simDog_chr6.simDog.chr6 87675 10 - 593897 TATTTAACT-G -s simHuman_chr6.simHuman.chr6 513148 11 + 601863 TATCTGATTCA -s simRat_chr6.simRat.chr6 554592 11 + 647215 GACCTAACTCA - -a -s simMouse_chr6.simMouse.chr6 542749 46 + 636262 TTGGATGTGTGGGTGAGCTTTTGCCTATTGAGACATAGTCTATATA -s Anc0.Anc0refChr3 145733 46 + 222631 TTGGGTTCGTGGGTGCATGTTTGCATATTGAAACATAGTATGTATA -s Anc1.Anc1refChr6 181238 46 + 197743 TTGGGTTCGTGGGTGCATGTTTGCATATTGAAACATAGTATGTATA -s Anc2.Anc2refChr1 59390 46 + 142988 TTGGGATCCTGGGTGCATGTTTGCATATTGAAATATAATATGTATA -s mr.mrrefChr3 92750 46 + 181027 TTGGATGTGTGGGTGAGCTTTTGCCTATTGAAACATAGTATATATA -s simCow_chr6.simCow.chr6 86526 46 - 602619 TTGGGATCCGGGGTGCATGTTTTCGTATTGAAATATAATATGTATA -s simDog_chr6.simDog.chr6 87688 46 - 593897 TAGGGATCCTGGGTTCATGTTTGCATATTGAAATATAATGTGTATA -s simHuman_chr6.simHuman.chr6 513162 46 + 601863 TTCAGTTCGTGGGTGCATGTTCGCATAATGAAACATAGTATGTATA -s simRat_chr6.simRat.chr6 554603 46 + 647215 TTGGATGTATAGGCGTGCATTTGCCTATTGAAACATAGTATATATA - -a -s simMouse_chr6.simMouse.chr6 542795 48 + 636262 CACAGGCACAAGTTATTAGCCAGGGCAAAACTTGCCAGATAATTATAT -s Anc0.Anc0refChr3 145779 48 + 222631 CACAGTCACAACTTATTGGCCAGGACATAACTTGCCATATATTTACAT -s Anc1.Anc1refChr6 181284 48 + 197743 CACAGTCACAACTTATTGGCCAGGACATAACTTGCCATATATTTACAT -s Anc2.Anc2refChr1 59436 48 + 142988 CACAGTCACAACTTATTGGCCAAGACATAAATCACCATATATTTACTT -s mr.mrrefChr3 92796 48 + 181027 CACAGGCACAAGTTATTAGCCAGGACAAAACTTGCCAGATATTTATAT -s simCow_chr6.simCow.chr6 86618 48 - 602619 CACAGCCACAATTTATTGTCCAAGACATAAATCACCATATATTTACTT -s simDog_chr6.simDog.chr6 87734 41 - 593897 CACAGTCAGAACTTATTAGCTGAGACATGAATCAATAT-------CTT -s simHuman_chr6.simHuman.chr6 513208 48 + 601863 GACAATCACAACCTATTGGCCAGGACATAACTTGCCATACATTTACAT -s simRat_chr6.simRat.chr6 554649 47 + 647215 CATAGGCACAAGTTA-TAGCCGGTACAGAACTTGCCACATATTTATAT - -a -s simMouse_chr6.simMouse.chr6 542843 31 + 636262 CATGCAAAACCATATATTTACATGGAACATG -s Anc0.Anc0refChr3 145831 12 + 222631 CATTGAAAAAAA------------------- -s Anc1.Anc1refChr6 181336 12 + 197743 CATTGAAAAAAA------------------- -s Anc2.Anc2refChr1 59488 12 + 142988 CATTGAAAAAAA------------------- -s mr.mrrefChr3 92848 31 + 181027 CATGCAAAACCATATATTTACATGGAACATG -s simCow_chr6.simCow.chr6 86670 12 - 602619 CATAGAAACAAA------------------- -s simDog_chr6.simDog.chr6 87779 12 - 593897 CATTGATAAACA------------------- -s simHuman_chr6.simHuman.chr6 513260 12 + 601863 CATTGGAATAAA------------------- -s simRat_chr6.simRat.chr6 554700 31 + 647215 CATGCAAAACCATATATTTACATAGAACCTG - -a -s simMouse_chr6.simMouse.chr6 542874 48 + 636262 AAACATAGGAGAATGAGTTACTGGGAAGTTGGGATACTGGAAATCTAG -s Anc0.Anc0refChr3 145843 39 + 222631 ---------AGTAGGAGTTACTTGGAAGTCAGGAAATTGGAAGTGTAG -s Anc1.Anc1refChr6 181348 39 + 197743 ---------AGTAGGAGTTACTTGGAAGTCAGGAAATTGGAAGTGTAG -s Anc2.Anc2refChr1 59500 39 + 142988 ---------AGTAGGCGTTACTTGGGTGACATAAAGTTGGAAGTGTAG -s mr.mrrefChr3 92879 48 + 181027 AAACATAGGAGAATGAGTTACTGGGAAGTTGGGATACTGGAAATCTAG -s simCow_chr6.simCow.chr6 86682 18 - 602619 ---------AGT---------------------TAGTTGGAAGTGTAG -s simDog_chr6.simDog.chr6 87791 39 - 593897 ---------AGTAGGCGTTACTTGGGTGACATAAAGCTGGAAGCGGAG -s simHuman_chr6.simHuman.chr6 513272 39 + 601863 ---------AGTAGGAGTTACTAGGAAATCTGGAGATTGGAAGTGTAG -s simRat_chr6.simRat.chr6 554735 48 + 647215 AAAAGTAGGAGAATGAGTTATAGGGAAGATGGGATACTGGGAATCTAG - -a -s simMouse_chr6.simMouse.chr6 542922 6 + 636262 TTTCCA -s Anc0.Anc0refChr3 145895 6 + 222631 TATCCA -s Anc1.Anc1refChr6 181400 6 + 197743 TATCCA -s Anc2.Anc2refChr1 59552 6 + 142988 TATCTA -s mr.mrrefChr3 92927 6 + 181027 TATCCA -s simCow_chr6.simCow.chr6 86713 6 - 602619 TATCTA -s simDog_chr6.simDog.chr6 87843 3 - 593897 ---CTA -s simHuman_chr6.simHuman.chr6 513324 6 + 601863 TATCCT -s simRat_chr6.simRat.chr6 554783 6 + 647215 TATCCA - -a -s simMouse_chr6.simMouse.chr6 542928 5 + 636262 TAATA -s Anc0.Anc0refChr3 145911 4 + 222631 TGAT- -s Anc1.Anc1refChr6 181416 5 + 197743 TGATA -s Anc2.Anc2refChr1 59568 4 + 142988 TGAT- -s mr.mrrefChr3 92943 5 + 181027 TAATA -s simDog_chr6.simDog.chr6 87856 4 - 593897 TGAT- -s simHuman_chr6.simHuman.chr6 513340 5 + 601863 TGATA -s simRat_chr6.simRat.chr6 554799 5 + 647215 TAATA - -a -s simMouse_chr6.simMouse.chr6 542933 35 + 636262 TTCATAAGATCAAGAAGGTTAATGTCTGGCAGATC -s Anc0.Anc0refChr3 145915 9 + 222631 -TTATAA-------------------------GTC -s Anc1.Anc1refChr6 181421 25 + 197743 CTTATAAGAT----------AATGTATGGTGTGTC -s Anc2.Anc2refChr1 59572 9 + 142988 -CTATAA-------------------------GTC -s mr.mrrefChr3 92948 35 + 181027 TTCATAAGATCAAGAAGGTTAATGTCTGGTGGATC -s simDog_chr6.simDog.chr6 87860 9 - 593897 -CTATAA-------------------------GTC -s simHuman_chr6.simHuman.chr6 513345 25 + 601863 CTTACAAGAT----------AATGTATGGTGTGTT -s simRat_chr6.simRat.chr6 554809 35 + 647215 TTCATGAGATCATTAAGGTTAATGTCTGATGGATC - -a -s simMouse_chr6.simMouse.chr6 542968 23 + 636262 CATATGTGGCATGTTAATTCCTA -s Anc0.Anc0refChr3 145924 23 + 222631 AATATATGGTATGTGAGTTTCAA -s Anc1.Anc1refChr6 181446 23 + 197743 AATATATGGTATGTGAGTTTCAA -s Anc2.Anc2refChr1 59581 23 + 142988 AATACATGGTATGTGAGTTTCAA -s mr.mrrefChr3 92983 23 + 181027 CATATATGGCATGTTAGTTCCAA -s simDog_chr6.simDog.chr6 87869 23 - 593897 AATACATGGTATGTGAGTTTCAA -s simHuman_chr6.simHuman.chr6 513370 23 + 601863 AATATATGGTGTGTGAGTTTCAA -s simRat_chr6.simRat.chr6 554848 23 + 647215 CATATATGGCATGTTAGTTCCAA - -a -s simMouse_chr6.simMouse.chr6 542991 16 + 636262 TTCAAAGGATGTAAGA -s Anc0.Anc0refChr3 145948 16 + 222631 GTCTAGGGATGTAAGA -s Anc1.Anc1refChr6 181470 16 + 197743 GTCTAGGGATGTAAGA -s Anc2.Anc2refChr1 59605 16 + 142988 GTCTAGGGATATAAGA -s mr.mrrefChr3 93006 16 + 181027 TTCAAAGGATGTAAGA -s simCow_chr6.simCow.chr6 86722 13 - 602619 ---TGAGGATATAAGA -s simDog_chr6.simDog.chr6 87893 16 - 593897 GTCTAGGGATACAAAA -s simHuman_chr6.simHuman.chr6 513394 16 + 601863 CTCTAGGCACGTAAGA -s simRat_chr6.simRat.chr6 554871 16 + 647215 TTCACAGGATATAAGA - -a -s simMouse_chr6.simMouse.chr6 543007 18 + 636262 CAGAGACATGGTCAACAG -s Anc0.Anc0refChr3 145971 18 + 222631 CAAAGACACATTCACCAG -s Anc1.Anc1refChr6 181493 18 + 197743 CAAAGACACATTCACCAG -s Anc2.Anc2refChr1 59628 18 + 142988 CAAAATCACATTCACCAG -s mr.mrrefChr3 93029 18 + 181027 CAGAGACACAGTCAACAG -s simCow_chr6.simCow.chr6 86740 12 - 602619 ------CACAATCACCAG -s simDog_chr6.simDog.chr6 87916 18 - 593897 CAAAATCACATTCACCAG -s simHuman_chr6.simHuman.chr6 513417 18 + 601863 CAAAGACACATTCATCAG -s simRat_chr6.simRat.chr6 554898 18 + 647215 CAGAGACACAGTCAACAA - -a -s simMouse_chr6.simMouse.chr6 543025 19 + 636262 TATTGTCAGTTGGACTAAT -s Anc0.Anc0refChr3 145989 19 + 222631 TGTCGTAGGTTGGACTCAT -s Anc1.Anc1refChr6 181511 19 + 197743 TGTCGTAGGTTGGACTCAT -s Anc2.Anc2refChr1 59646 19 + 142988 TGTCGTAGGTTGGACTCAT -s mr.mrrefChr3 93047 19 + 181027 TATTGTCAGTTGGACTAAT -s simCow_chr6.simCow.chr6 86752 19 - 602619 TGTTGTGGGTTGAACTCGT -s simDog_chr6.simDog.chr6 87934 19 - 593897 TGTCGTAGGTTGGACTTAT -s simHuman_chr6.simHuman.chr6 513435 15 + 601863 TGT----GGTTGGACGCAT -s simRat_chr6.simRat.chr6 554986 19 + 647215 TATTGTCAGCTGGACTGAT - -a -s simMouse_chr6.simMouse.chr6 543044 14 + 636262 TTGTAGTTCATTTT -s Anc0.Anc0refChr3 146008 14 + 222631 TTGTAGTTCAGTTT -s Anc1.Anc1refChr6 181530 14 + 197743 TTGTAGTTCAGTTT -s Anc2.Anc2refChr1 59665 14 + 142988 TCGTAGTTCAGTTT -s mr.mrrefChr3 93066 14 + 181027 TTGTAGTTCATTTT -s simCow_chr6.simCow.chr6 86799 13 - 602619 TCGTAGTTCAGTT- -s simDog_chr6.simDog.chr6 87953 14 - 593897 TCGCAGTTCAGTTT -s simHuman_chr6.simHuman.chr6 513450 14 + 601863 TTGTAGTTCAGTTT -s simRat_chr6.simRat.chr6 555005 13 + 647215 TGGTAGTTC-TTCT - -a -s simMouse_chr6.simMouse.chr6 543058 8 + 636262 AATAACAA -s Anc0.Anc0refChr3 146022 8 + 222631 AATAACAA -s Anc1.Anc1refChr6 181544 8 + 197743 AATAACAA -s Anc2.Anc2refChr1 59680 8 + 142988 AATTACAA -s mr.mrrefChr3 93080 8 + 181027 AATAACAA -s simCow_chr6.simCow.chr6 86813 8 - 602619 AAGTATAA -s simDog_chr6.simDog.chr6 87967 7 - 593897 -GTTACAA -s simHuman_chr6.simHuman.chr6 513464 8 + 601863 AATAACAA -s simRat_chr6.simRat.chr6 555018 8 + 647215 AATAGCAA - -a -s simMouse_chr6.simMouse.chr6 543066 36 + 636262 TCAACAAAGCAATACCTCAAGCTGTTACTATGAGTA -s Anc0.Anc0refChr3 146030 36 + 222631 CTAGTAAAGCAATACCTCAAGCTGTTACCAAGAGTA -s Anc1.Anc1refChr6 181552 36 + 197743 CTAGTAAAGCAATACCTCAAGCTGTTACCAAGAGTA -s Anc2.Anc2refChr1 59688 36 + 142988 CTAGTAAAGCAATACCACAAGCTGGTACCAAAAGTA -s mr.mrrefChr3 93088 36 + 181027 TTAACAAAGCAATACCTCAAGCTGTTACTATGAGTA -s simCow_chr6.simCow.chr6 86821 35 - 602619 CTA-TAAAGGAAGACCACAACCTGGTACCAAAAGTA -s simDog_chr6.simDog.chr6 87974 22 - 593897 CCAGTAAAGCAATACCACAAGC-------------- -s simHuman_chr6.simHuman.chr6 513478 36 + 601863 CTAGTAAAGCAATTCCTCAAGCTATTACCAAGAGAA -s simRat_chr6.simRat.chr6 555026 36 + 647215 TTAACAAAGCAATATCTCAAGCTGTTACTATGAGTA - -a -s simMouse_chr6.simMouse.chr6 543102 72 + 636262 TGCAAAAGCCGATAGAGGTATTATATGTAAGAGATAAACTTGCTTGAGAACACTTTAGTGGTGCTACATAAA -s Anc0.Anc0refChr3 146066 69 + 222631 TGCAAAAGCCTTTAGAGGTACTATATATAA---ACCCACTTACTTTGGAAAACTTTAGTGGTGCTACATACA -s Anc1.Anc1refChr6 181588 69 + 197743 TGCAAAAGCCTTTAGAGGTACTATATATAA---ACCCACTTACTTTGGAAAACTTTAGTGGTGCTACATACA -s Anc2.Anc2refChr1 59724 69 + 142988 TACAGAAGCCTTTATACGTGCTATATATAA---ACCCACTTACTTTGAAAAACTTTAGTGGTGCTACATACA -s mr.mrrefChr3 93124 72 + 181027 TGCAAAAGCCGATAGAGGTATTATATGTAAGAGATACACTTACTTTAGAACACTTTAGTGGTGCTACATAAA -s simCow_chr6.simCow.chr6 86856 59 - 602619 TAAAGAAGCTT---------CAATATATAA---ACCCACCC-TTTCGAAAAACTCTAGTGGAGCTACATACA -s simDog_chr6.simDog.chr6 87996 67 - 593897 --CAGAAGCCTTTATACGTGCTATATATAA---ATATACTTACTTTGAAAAACCTTAGTGGTGCTACATACA -s simHuman_chr6.simHuman.chr6 513514 69 + 601863 TGCAAGAACCTTCAGAGGTACTACGCATAA---ACCCACTTACTTTGGAAAACTTTAGTGGTGCTACACACA -s simRat_chr6.simRat.chr6 555071 72 + 647215 TGCAAAAGCCGATAGAGGTCTTATATGTAAGAGTTACACTTACTTTTGAACACTTTAGTGGTGCTACAGAAG - -a -s simMouse_chr6.simMouse.chr6 543174 3 + 636262 AAC -s Anc0.Anc0refChr3 146135 3 + 222631 AAC -s Anc1.Anc1refChr6 181657 3 + 197743 AAC -s Anc2.Anc2refChr1 59793 3 + 142988 AAC -s mr.mrrefChr3 93196 3 + 181027 AAC -s simCow_chr6.simCow.chr6 86922 3 - 602619 AAC -s simDog_chr6.simDog.chr6 88063 3 - 593897 AAC -s simHuman_chr6.simHuman.chr6 513583 3 + 601863 AAC -s simRat_chr6.simRat.chr6 555143 3 + 647215 AAC - -a -s simMouse_chr6.simMouse.chr6 543177 77 + 636262 CCACTGTGATGAATCTAACAGGGAGGAAAGGACCGCTCCGTAAGCACTTTTGAAGTGGCACCTGAGGGGTGTAAATA -s Anc0.Anc0refChr3 146144 44 + 222631 CCTATGTGAAGA---TAACAAGGAGGGA----------------------------GGTAACTCT--TAAGCCAATA -s Anc1.Anc1refChr6 181666 44 + 197743 CCTATGTGAAGA---TAACAAGGAGGGA----------------------------GGTAACTCT--TAAGCCAATA -s Anc2.Anc2refChr1 59802 44 + 142988 CCTATGTGAAGC---TAACTAGGAGGGT----------------------------GGTAACTCT--TAAGCCAATA -s mr.mrrefChr3 93205 49 + 181027 CCACTGTGATGAATCTAACAAGGAGGAA----------------------------GGCACCTGTGGTGTGTAAATA -s simCow_chr6.simCow.chr6 86929 44 - 602619 CTTATGTGAAGC---TAAGGAGGAGAAT----------------------------GGTACCTCT--TAAGTCAATA -s simDog_chr6.simDog.chr6 88072 43 - 593897 CCTATGT-GAGC---CAACTTGGAAGGT----------------------------GGTAACTCT--TAAGCCAATC -s simHuman_chr6.simHuman.chr6 513592 44 + 601863 CCTATGTAAAGA---TAACAAGGAGGTA----------------------------GGTATTTCT--TAAGGTAATA -s simRat_chr6.simRat.chr6 555152 49 + 647215 TCACTGTGATGAATCTAACAATGAGGAA----------------------------GGCACATGTGGTGTGTAAATA - -a -s simMouse_chr6.simMouse.chr6 543254 56 + 636262 TTCCTAGTTGCCTCAAGGTCTCTTCTTGAGTGATTTTGTGTTGTAGTTAATTCCAT -s Anc0.Anc0refChr3 146188 56 + 222631 TCCCTAGTTCCTTTAGAATCTTTCCTTGACTTTTTTTACGTCATGTTTGATTCCAT -s Anc1.Anc1refChr6 181710 56 + 197743 TCCCTAGTTCCTTTAGAATCTTTCCTTGACTTTTTTTACGTCATGTTTGATTCCAT -s Anc2.Anc2refChr1 59846 56 + 142988 TCCCTAGTCCCTTTAGAATCTTTCCTTGACTTTTTTTACGTCATGTTTGATTCCAC -s mr.mrrefChr3 93254 56 + 181027 TTCCTAGTTGCCTCAGGATCTCTTCTTGACTGATTTTGTGTCGTATTTAATTCCAT -s simCow_chr6.simCow.chr6 87009 56 - 602619 TCCCTAGTCCCTTTAGATTCTTTCCTTGAGTTTGTTTACATCATGTTTGATCCTAC -s simDog_chr6.simDog.chr6 88115 56 - 593897 GCCCTAGACCCTTCAGAAACTTTCCTTGACTTTTTTTACGTTACATTTGATTCCAC -s simHuman_chr6.simHuman.chr6 513636 56 + 601863 TCCCCAGTTCTTTTAGAATATTTCCTTGACATTTTTTACTTCATGTTTGATTCCAT -s simRat_chr6.simRat.chr6 555201 55 + 647215 TTCCTAATTGCCTCAGGATCTCTTCTCAACTAATTTTGTGTCGTATTT-ATTCAAC - -a -s simMouse_chr6.simMouse.chr6 543310 14 + 636262 GGAGGTTGTAGTGG -s Anc0.Anc0refChr3 146245 14 + 222631 GGAGGTTGTAGTAG -s Anc1.Anc1refChr6 181767 14 + 197743 GGAGGTTGTAGTAG -s Anc2.Anc2refChr1 59903 14 + 142988 GAAGGTTCTAGTAG -s mr.mrrefChr3 93310 14 + 181027 GGAGGTTGTAGTGG -s simCow_chr6.simCow.chr6 87066 14 - 602619 GAAAATTATAGTAG -s simDog_chr6.simDog.chr6 88172 14 - 593897 GAAGGTTCTAGAAG -s simHuman_chr6.simHuman.chr6 513693 14 + 601863 GGAGGTTGTAGTAG -s simRat_chr6.simRat.chr6 555256 14 + 647215 AGAAGTTGTAGTGG - -a -s simMouse_chr6.simMouse.chr6 543324 59 + 636262 GTGTGCAGCCACCCACATTCTAGACTTTTCCTTCACTGGTAAATAAGTTACGAAGAATA -s Anc0.Anc0refChr3 146259 58 + 222631 -TATGTGAACAGCCACAATTTAAACTTCTACTTCATCGATGTGTAAGTTGCTAAAAATA -s Anc1.Anc1refChr6 181781 58 + 197743 -TATGTGAACAGCCACAATTTAAACTTCTACTTCATCGATGTGTAAGTTGCTAAAAATA -s Anc2.Anc2refChr1 59917 58 + 142988 -TATGTGAACAGTCATAATTTAAACTTCTACTTCATGGATGTGTAAGTTGCTAAAAATA -s mr.mrrefChr3 93324 59 + 181027 GTGTGTGGACACCCACATTCTAGACTTTTCCTTCACCGGTAAATAAGTTACTAAAAATA -s simCow_chr6.simCow.chr6 87080 58 - 602619 -TATGTGATCAGTGAAATTTTAAACTTCTCCTTCATTGATGTATTAGTTGCTAAGAATG -s simDog_chr6.simDog.chr6 88186 55 - 593897 -TATGTGAACAGTCCTAATCTAAACTTCTACTTCATGGATGTGTAATGTAC---AAATA -s simHuman_chr6.simHuman.chr6 513707 58 + 601863 -TATGTGAACAGCCACAGTTTAAACTTCTTCTTCATCGATGTGTAGGTGGCTAAAGATA -s simRat_chr6.simRat.chr6 555271 59 + 647215 GTGGTTGGACATCCACGTTGTACACTTTTCCTTCACCGGTAAATAAGTTACTAAAAATA - -a -s simMouse_chr6.simMouse.chr6 543383 80 + 636262 TGCAATGGCCTCCTTGTAAAGGATGGATCACTTCTCCTAATAGTTCACATGACTACTTTGATCATTTTGAATTTGAACTC -s Anc0.Anc0refChr3 146317 69 + 222631 TGAAATGGTCTTCCTATAAAGGATGGACCACTACTCGTTATATG--ACA-GA-----TCTCCTATTATGAA---AAGCTC -s Anc1.Anc1refChr6 181839 74 + 197743 TGAAATGGTCTTCCTATAAAGGATGGACCACTACTCGTTATATG--ACA-GACTCGTTCTCCTATTATGAA---AAGCTC -s Anc2.Anc2refChr1 59975 69 + 142988 TGAAATGGTCTTCCTATAAAGGAAGGACCACTACTTGTTAAATG--TCA-AA-----TCTCCTATCAAGAA---AAGCTC -s mr.mrrefChr3 93383 78 + 181027 TGCAATGGTCTCCTTATAAAGGATGGATCACTTCTCCTAATAGT--ACATGACTACTTTGACCATTTTGAATTTGAGCTC -s simCow_chr6.simCow.chr6 87139 69 - 602619 TGAAGTGGTCATTCTTTAAAGGAGAGACTACTGCCTGTTAAGTT--TAA-AT-----CCTCCCACCAAGAA---AAGAGC -s simDog_chr6.simDog.chr6 88241 69 - 593897 TGAAATGGCCTTCCTATAAAAAAAGAACCACTACTTGCTAAATG--TCA-AA-----TCTCTTATCAAGAA---AAGCTC -s simHuman_chr6.simHuman.chr6 513765 73 + 601863 TGAAATGGTCTTCCCATAAAGGATGGAACACT-CTCATGATATG--AGA-GGCTCGTTCTCCTAATATGAA---AAGCTC -s simRat_chr6.simRat.chr6 555330 78 + 647215 TGCGATGGTCCCCTTATAAAGGATGGATTGCTTCCCCTAGTAGT--ACATGACCACTTTGACCATTTTGAATTTGAGCTC - -a -s simMouse_chr6.simMouse.chr6 543463 48 + 636262 CTACATGCCTGTTTTCATTATTATGATTTTAAGCTTTGGGTGGGAGCC -s Anc0.Anc0refChr3 146393 25 + 222631 TTACATGCTTATTTTGAT--------TTTTGA---------------C -s Anc1.Anc1refChr6 181920 33 + 197743 TTACATGCTTATTTTGATTATTTCGATTTTGA---------------C -s Anc2.Anc2refChr1 60051 25 + 142988 TTACATGCTTATTTTGAT--------TTTAAG---------------C -s mr.mrrefChr3 93461 48 + 181027 CTACATGCCTGTTTTCATTATTATGATTTTGAGCTTTGGGTGGGAGCC -s simCow_chr6.simCow.chr6 87215 25 - 602619 TTACATGCCCACTTTGAT--------TTTGAG---------------C -s simDog_chr6.simDog.chr6 88317 25 - 593897 TAATATGCTTATTTTGAT--------TTTAAG---------------C -s simHuman_chr6.simHuman.chr6 513845 33 + 601863 TTACATGCTTATTTTGATTATTTCGATTTTGA---------------C -s simRat_chr6.simRat.chr6 555408 48 + 647215 CTACATGCCTGGTTTCAGCATTATGATTTTGAGCTTTGAGTGGCAGCT - -a -s simMouse_chr6.simMouse.chr6 543511 4 + 636262 TTAC -s Anc0.Anc0refChr3 146418 4 + 222631 TTGA -s Anc1.Anc1refChr6 181953 4 + 197743 TTGA -s Anc2.Anc2refChr1 60076 4 + 142988 TTGA -s mr.mrrefChr3 93509 4 + 181027 TTAC -s simCow_chr6.simCow.chr6 87241 4 - 602619 TTGA -s simDog_chr6.simDog.chr6 88342 4 - 593897 TTCA -s simHuman_chr6.simHuman.chr6 513878 4 + 601863 TTGA -s simRat_chr6.simRat.chr6 555456 4 + 647215 TTAC - -a -s simMouse_chr6.simMouse.chr6 543515 67 + 636262 TGGCAACCTCCTCAAGGTCTTGGTCCTGGTTGTCAGGGATCAGAATTTGGTCCAACTAGTGTGGTTC -s Anc0.Anc0refChr3 146422 65 + 222631 TGTAACCAT--TCTAGGTTTTGATCTTGGTTGACTGGTATCTGGGTTTGGTGTAATTAGTAAGGTTT -s Anc1.Anc1refChr6 181957 65 + 197743 TGTAACCAT--TCTAGGTTTTGATCTTGGTTGACTGGTATCTGGGTTTGGTGTAATTAGTAAGGTTT -s Anc2.Anc2refChr1 60082 65 + 142988 GGTAACCAT--GTTAGGTTTTGATCTTGGCTAACTGGTATCTGGGTTTGGTGTAATCAGTAAGGTTT -s mr.mrrefChr3 93513 65 + 181027 TGGCAACCT--TCAAGGTCTTGATCCTGGTTGTCAGGGATCAGAATTTGGTCTAATTAGTATGGTTC -s simCow_chr6.simCow.chr6 87251 65 - 602619 AGTAATCAT--CTTAGGTTTTGATCTTGGCCAACTGGGGTCTGGGTTTAGTGCAATCAGTACGGTTC -s simDog_chr6.simDog.chr6 88348 65 - 593897 GGTAACCAT--GTTTGGCTTTGTTCCTGGCTAACTGGTATTTGGGCTTGGTGTGATCAGTAAGGTTT -s simHuman_chr6.simHuman.chr6 513882 65 + 601863 TGCAACCAA--TCCAGGTTCTGATCTAGGTTGACTGGAATCTGGGTTTGGTATAATTAGTAAGGTTT -s simRat_chr6.simRat.chr6 555460 65 + 647215 TGGCAACCT--TCAAGGTCTTGATCCTGGTTGCCAGGGATCAGAATTTGATCTAATCAGAATGGTTC - -a -s simMouse_chr6.simMouse.chr6 543582 21 + 636262 AAAGAAAGTCAGTCAAACCAT -s Anc0.Anc0refChr3 146487 21 + 222631 GAAATTAGTCAACCTAACCAC -s Anc1.Anc1refChr6 182022 21 + 197743 GAAATTAGTCAACCTAACCAC -s Anc2.Anc2refChr1 60147 21 + 142988 GAAATTAGTCAACCTACCCAC -s mr.mrrefChr3 93578 21 + 181027 AAAATAAGTCAGCCTAACCAT -s simCow_chr6.simCow.chr6 87319 21 - 602619 AAAATAAGTCAACCTATCAAC -s simDog_chr6.simDog.chr6 88413 17 - 593897 GAGATTAGTC----TACCCAC -s simHuman_chr6.simHuman.chr6 513947 21 + 601863 GAAATGAGTCAACCTAACGAC -s simRat_chr6.simRat.chr6 555525 21 + 647215 AAAATAAGTCAGCCTCACCAT - -a -s simMouse_chr6.simMouse.chr6 543603 56 + 636262 GGTGTGTCATTATCCTTAGACTGGCACACGACACACATCATCCTAAATAGCCGAAT -s Anc0.Anc0refChr3 146686 52 + 222631 GGTG----GTTACACTTAATGTAGCACAAGACACACATCATAATAAGTAGCCTAGC -s Anc1.Anc1refChr6 182221 52 + 197743 GGTG----GTTACACTTAATGTAGCACAAGACACACATCATAATAAGTAGCCTAGC -s Anc2.Anc2refChr1 60346 52 + 142988 TGTA----GTTACACCTAATGTAACGCCAGGCGCAGATCATAATAAGTAGCTTAAG -s mr.mrrefChr3 93754 56 + 181027 GGTGTGTCATTATCCTTAGAGTGGCACACGACACACATCATCATAAGTAGCCGAGC -s simCow_chr6.simCow.chr6 87593 52 - 602619 TGTA----GTTACACCTAATGTAACGCCAGGCGCAGATCATAATAAGTAGCTTAAG -s simHuman_chr6.simHuman.chr6 514146 52 + 601863 GTTG----GTTGCGTTTAAGGTAGCACATGACACACACCATGATAAGTAACCTCGC -s simRat_chr6.simRat.chr6 555711 56 + 647215 GGTGTGTCATTATCCTTAGAGTGGCACACGACACACATCATCATAAGTAGACAAGC - -a -s simMouse_chr6.simMouse.chr6 543659 1 + 636262 C -s Anc0.Anc0refChr3 146739 1 + 222631 G -s Anc1.Anc1refChr6 182274 1 + 197743 G -s Anc2.Anc2refChr1 60399 1 + 142988 G -s mr.mrrefChr3 93810 1 + 181027 C -s simCow_chr6.simCow.chr6 87646 1 - 602619 G -s simHuman_chr6.simHuman.chr6 514199 1 + 601863 G -s simRat_chr6.simRat.chr6 555767 1 + 647215 C - -a -s simMouse_chr6.simMouse.chr6 543660 9 + 636262 TTCATTATG -s Anc1.Anc1refChr6 182342 9 + 197743 TTCACTAGG -s mr.mrrefChr3 93877 9 + 181027 TTCATTATG -s simHuman_chr6.simHuman.chr6 514267 9 + 601863 TTCACTAGG -s simRat_chr6.simRat.chr6 555847 9 + 647215 GTTATTATG - -a -s simMouse_chr6.simMouse.chr6 543669 17 + 636262 TAAAGTCAATCTTTCAC -s Anc0.Anc0refChr3 146783 4 + 222631 -------------TCAC -s Anc1.Anc1refChr6 182351 17 + 197743 CTGAGGAAATCTTTCAC -s Anc2.Anc2refChr1 60443 4 + 142988 -------------TCAC -s mr.mrrefChr3 93886 17 + 181027 CAAAGTCAATCTTTCAC -s simCow_chr6.simCow.chr6 87690 4 - 602619 -------------TCAC -s simHuman_chr6.simHuman.chr6 514278 17 + 601863 CTGAGGAAATCTTCCAC -s simRat_chr6.simRat.chr6 555856 17 + 647215 CATGGTCAATCTTTCAC - -a -s simMouse_chr6.simMouse.chr6 543686 3 + 636262 ATT -s Anc0.Anc0refChr3 146787 3 + 222631 GTT -s Anc1.Anc1refChr6 182368 3 + 197743 GTT -s Anc2.Anc2refChr1 60447 3 + 142988 ATT -s mr.mrrefChr3 93903 3 + 181027 GTT -s simCow_chr6.simCow.chr6 87694 3 - 602619 ATT -s simHuman_chr6.simHuman.chr6 514297 3 + 601863 GTT -s simRat_chr6.simRat.chr6 555873 3 + 647215 GTC - -a -s simMouse_chr6.simMouse.chr6 543689 23 + 636262 AACAGCAAATTGTTGCCTATAAT -s Anc0.Anc0refChr3 146790 22 + 222631 AA-AGTAAGCTGTCACCTGCAAC -s Anc1.Anc1refChr6 182371 22 + 197743 AA-AGTAAGCTGTCACCTGCAAC -s Anc2.Anc2refChr1 60452 22 + 142988 AA-AGTAAGCTGTCACCAGCAAC -s mr.mrrefChr3 93906 23 + 181027 AACAGCAAATTGTTGCCTATAAT -s simCow_chr6.simCow.chr6 87699 20 - 602619 GA-AACAAGTT--CACCAACAAC -s simDog_chr6.simDog.chr6 506591 22 + 593897 AT-AGTAATCTGTACCTAGCAAC -s simHuman_chr6.simHuman.chr6 514300 22 + 601863 AA-AGTAAGCTATCACCTGCAAC -s simRat_chr6.simRat.chr6 555876 23 + 647215 AACGGCAAATTCTTGCCTATAAT - -a -s simMouse_chr6.simMouse.chr6 543712 29 + 636262 ATATCTGGGACTACAAGCGACACATTGAT -s Anc0.Anc0refChr3 146812 13 + 222631 ATATCTGGGACTA---------------- -s Anc1.Anc1refChr6 182393 13 + 197743 ATATCTGGGACTA---------------- -s Anc2.Anc2refChr1 60474 13 + 142988 ATATCTGGGACTA---------------- -s mr.mrrefChr3 93929 29 + 181027 ATATCTGGGACTACAAGCGACACATTGAT -s simCow_chr6.simCow.chr6 87719 13 - 602619 ATAACTGGGACTA---------------- -s simDog_chr6.simDog.chr6 506636 13 + 593897 ATATCTGGATCGA---------------- -s simHuman_chr6.simHuman.chr6 514322 13 + 601863 ATATCTGGGACTA---------------- -s simRat_chr6.simRat.chr6 555899 29 + 647215 ATATCTGGGACTTCAAGCAAAACGTTGAT - -a -s simMouse_chr6.simMouse.chr6 543741 44 + 636262 TCCCCTGGTAAATATATTTAGAAGTATGAACCCCTCAAGGCTAG -s Anc0.Anc0refChr3 146825 1 + 222631 -------------------------------------------G -s Anc1.Anc1refChr6 182406 1 + 197743 -------------------------------------------G -s Anc2.Anc2refChr1 60487 1 + 142988 -------------------------------------------G -s mr.mrrefChr3 93958 44 + 181027 TCCCCTGGTAAATATATTTAGAAGTATGAACCCCTCAAGGCTAG -s simCow_chr6.simCow.chr6 87732 1 - 602619 -------------------------------------------G -s simDog_chr6.simDog.chr6 506649 1 + 593897 -------------------------------------------G -s simHuman_chr6.simHuman.chr6 514335 1 + 601863 -------------------------------------------G -s simRat_chr6.simRat.chr6 555930 44 + 647215 TCCCCTGGTGAATATTTACGGAAGTATGAACCCCTAAATGATAG - -a -s simMouse_chr6.simMouse.chr6 543785 4 + 636262 CATG -s Anc0.Anc0refChr3 146826 4 + 222631 CAGG -s Anc1.Anc1refChr6 182407 4 + 197743 CAGG -s Anc2.Anc2refChr1 60488 4 + 142988 CAGG -s mr.mrrefChr3 94002 4 + 181027 CATG -s simCow_chr6.simCow.chr6 87733 4 - 602619 CAGG -s simDog_chr6.simDog.chr6 506650 4 + 593897 CAGG -s simHuman_chr6.simHuman.chr6 514336 4 + 601863 CAGG -s simRat_chr6.simRat.chr6 555975 4 + 647215 CATG - -a -s simMouse_chr6.simMouse.chr6 543789 4 + 636262 CAAC -s Anc0.Anc0refChr3 146830 4 + 222631 CAAG -s Anc1.Anc1refChr6 182411 4 + 197743 CAAG -s Anc2.Anc2refChr1 60508 4 + 142988 CAAG -s mr.mrrefChr3 94006 4 + 181027 CAAC -s simCow_chr6.simCow.chr6 87755 4 - 602619 CAAG -s simDog_chr6.simDog.chr6 506670 4 + 593897 CAAG -s simHuman_chr6.simHuman.chr6 514340 4 + 601863 TAAT -s simRat_chr6.simRat.chr6 555979 4 + 647215 CAAC - -a -s simMouse_chr6.simMouse.chr6 543793 19 + 636262 TATGCTTGCAGTCTCCAAA -s Anc0.Anc0refChr3 146836 19 + 222631 AATCCTTTCAGTCTCCAAA -s Anc1.Anc1refChr6 182417 19 + 197743 AATCCTTTCAGTCTCCAAA -s Anc2.Anc2refChr1 60514 19 + 142988 AATCCTTTTAGTTGTCAAA -s mr.mrrefChr3 94010 19 + 181027 TATCCTTGCAGTCTCCAAA -s simCow_chr6.simCow.chr6 87761 18 - 602619 AAGCCT-TTAGTGGTCAAA -s simDog_chr6.simDog.chr6 506676 19 + 593897 AATCTTTCTAGTTGTCAAA -s simHuman_chr6.simHuman.chr6 514346 19 + 601863 CATCCTTTCGGTCTCCAAA -s simRat_chr6.simRat.chr6 555983 19 + 647215 TATCCTTGCAGTCTCCGGA - -a -s simMouse_chr6.simMouse.chr6 543812 5 + 636262 CAAAG -s Anc1.Anc1refChr6 182443 5 + 197743 CTAGG -s mr.mrrefChr3 94036 5 + 181027 CTAGG -s simHuman_chr6.simHuman.chr6 514372 5 + 601863 CTAGG -s simRat_chr6.simRat.chr6 556009 5 + 647215 CTAGG - -a -s simMouse_chr6.simMouse.chr6 543817 5 + 636262 ACCAC -s Anc1.Anc1refChr6 182448 5 + 197743 ACTCC -s mr.mrrefChr3 94041 5 + 181027 ACCCC -s simHuman_chr6.simHuman.chr6 514377 5 + 601863 ACTCC -s simRat_chr6.simRat.chr6 556026 5 + 647215 ACCCC - -a -s simMouse_chr6.simMouse.chr6 543822 79 + 636262 TCTGGCTGTGTGGAGACCGATACATTGATAGGATTCAACCACCGGCAGCACATTACTATGGATTAACTTGCTGCCACCC -s Anc0.Anc0refChr3 146856 64 + 222631 -------TTG--------GGCACCCTGATAGGGTCCAACCACCAGCAGAACATTTGTGAAGAAGACCTTTGATCCACAA -s Anc1.Anc1refChr6 182453 71 + 197743 TCCCGTTTTG--------GGCACCCTGATAGGGTCCAACCACCAGCAGAACATTTGTGAAGAAGACCTTTGATCCACAA -s Anc2.Anc2refChr1 60534 64 + 142988 -------TTT--------GGCATCCTGATAGGGTCCAACCAGCAGCAAAACATTTGTGAAGAAGACCTTTGATTCACAA -s mr.mrrefChr3 94046 79 + 181027 TCTGGCTGTGTGGAGACCGACACATTGATAGGATCCAACCACCGGCAGCACATTACTGTGGATTAACTTGCTGCCACAC -s simCow_chr6.simCow.chr6 87780 57 - 602619 -------TTT--------GGTATCCTTATAGTGTCAAACCAGCAGCCAAACATTTGTAAATAAGACC-------CACAA -s simDog_chr6.simDog.chr6 506696 64 + 593897 -------TTT--------GGCATCCTGATGGGGTTCAACCTGCGGCAAAACATTTATGAAGAAGACCTTTGATTCACAA -s simHuman_chr6.simHuman.chr6 514393 71 + 601863 TCCCGTTTTG--------GGCACCATGATAGGGTCCGACCACCAGCAGAATGTTTGTGAAAAAGACCTCTGACCCACAA -s simRat_chr6.simRat.chr6 556031 79 + 647215 CTTGGCCATGTGGAAACTGACACATTGCTAAGATCCAACCACCTGCAGCACATTAATGTGGATTAACATGCTGCCGCAC - -a -s simMouse_chr6.simMouse.chr6 543901 9 + 636262 AGGGGAGTG -s Anc0.Anc0refChr3 146920 9 + 222631 TTGGAGGGG -s Anc1.Anc1refChr6 182524 9 + 197743 TTGGAGGGG -s Anc2.Anc2refChr1 60598 9 + 142988 TTGGAGGGG -s mr.mrrefChr3 94125 9 + 181027 AGGGGAGTG -s simCow_chr6.simCow.chr6 87838 9 - 602619 TTAGAGGGG -s simDog_chr6.simDog.chr6 506760 9 + 593897 TTGGAGGGG -s simHuman_chr6.simHuman.chr6 514464 9 + 601863 TAGGAGGGG -s simRat_chr6.simRat.chr6 556110 9 + 647215 GGGGGAGTG - -a -s simMouse_chr6.simMouse.chr6 543910 4 + 636262 TGGA -s Anc0.Anc0refChr3 146934 4 + 222631 TGAA -s Anc1.Anc1refChr6 182538 4 + 197743 TGAA -s Anc2.Anc2refChr1 60612 4 + 142988 TGAA -s mr.mrrefChr3 94134 4 + 181027 TGGA -s simCow_chr6.simCow.chr6 87852 4 - 602619 TGAA -s simHuman_chr6.simHuman.chr6 514478 4 + 601863 TGTA -s simRat_chr6.simRat.chr6 556119 4 + 647215 TGGA - -a -s simMouse_chr6.simMouse.chr6 543914 3 + 636262 AGA -s Anc0.Anc0refChr3 146938 3 + 222631 AGA -s Anc1.Anc1refChr6 182542 3 + 197743 AGA -s Anc2.Anc2refChr1 60616 3 + 142988 AGA -s mr.mrrefChr3 94138 3 + 181027 AGA -s simCow_chr6.simCow.chr6 87859 3 - 602619 AGA -s simHuman_chr6.simHuman.chr6 514482 3 + 601863 AGA -s simRat_chr6.simRat.chr6 556123 3 + 647215 AAA - -a -s simMouse_chr6.simMouse.chr6 543917 14 + 636262 GGTGGATACTTGTT -s Anc0.Anc0refChr3 146957 14 + 222631 GGTGGATACTTGTT -s Anc1.Anc1refChr6 182561 14 + 197743 GGTGGATACTTGTT -s Anc2.Anc2refChr1 60635 14 + 142988 GGTGCATGTTTTTT -s mr.mrrefChr3 94141 14 + 181027 GGTGGATACTTGTT -s simCow_chr6.simCow.chr6 87878 14 - 602619 AGTGTACTGTTGTT -s simDog_chr6.simDog.chr6 506785 14 + 593897 GGTGCATGTCTTTT -s simHuman_chr6.simHuman.chr6 514501 14 + 601863 GGTGGATACTTGTT -s simRat_chr6.simRat.chr6 556126 14 + 647215 TGTGGATACTTATT - -a -s simMouse_chr6.simMouse.chr6 543931 1 + 636262 A -s Anc0.Anc0refChr3 146971 1 + 222631 A -s Anc1.Anc1refChr6 182575 1 + 197743 A -s Anc2.Anc2refChr1 60649 1 + 142988 A -s mr.mrrefChr3 94155 1 + 181027 A -s simCow_chr6.simCow.chr6 87892 1 - 602619 G -s simDog_chr6.simDog.chr6 506799 1 + 593897 A -s simHuman_chr6.simHuman.chr6 514516 1 + 601863 A -s simRat_chr6.simRat.chr6 556140 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 543932 21 + 636262 ACCTACTGACCGCTGCAGCAC -s Anc0.Anc0refChr3 146972 21 + 222631 ACCTACTTACCGCTCCCTCAC -s Anc1.Anc1refChr6 182576 21 + 197743 ACCTACTTACCGCTCCCTCAC -s Anc2.Anc2refChr1 60650 21 + 142988 CCCTACTTACCACACCCTCAC -s mr.mrrefChr3 94156 21 + 181027 ACCTACTGACCGCTGCAGCAC -s simCow_chr6.simCow.chr6 87893 21 - 602619 CCCCACTTACCACCCCATCAC -s simDog_chr6.simDog.chr6 506800 21 + 593897 CCCTACTTACCACACCCTCAC -s simHuman_chr6.simHuman.chr6 514517 21 + 601863 AGCTACTTACTGCTCCCTCAC -s simRat_chr6.simRat.chr6 556142 21 + 647215 CCCTACTGACCACTGTAGCAT - -a -s simMouse_chr6.simMouse.chr6 543953 14 + 636262 ATGAGGAGGGCTTG -s Anc0.Anc0refChr3 146993 14 + 222631 ACAAGAAAGGGCTG -s Anc1.Anc1refChr6 182597 14 + 197743 ACAAGAAAGGGCTG -s Anc2.Anc2refChr1 60671 14 + 142988 ACAAGAAAGGGCTG -s mr.mrrefChr3 94177 14 + 181027 ATGAGGAGGGCTTG -s simCow_chr6.simCow.chr6 87988 14 - 602619 ACATAAAAGGGGTG -s simDog_chr6.simDog.chr6 506821 14 + 593897 AGGAGAAAGGGCTG -s simHuman_chr6.simHuman.chr6 514538 14 + 601863 ACAAGAAAGGGATG -s simRat_chr6.simRat.chr6 556163 14 + 647215 GTGAAGAGGGCTTG - -a -s simMouse_chr6.simMouse.chr6 543967 37 + 636262 AACCAATGAAAGATCAGACCACCACACATTTTTGTAC -s Anc0.Anc0refChr3 147010 33 + 222631 AACCAACAAAAGATCAAACCACCCCACATTTCT---- -s Anc1.Anc1refChr6 182615 37 + 197743 AACCAACAAAAGATCAAACCACCCCACATTTCTGTAC -s Anc2.Anc2refChr1 60688 33 + 142988 AACCAACAAAGGATTAAACCACACCACACCTCT---- -s mr.mrrefChr3 94191 37 + 181027 AACCAATGAAAGATCAGACCACCACACATTTCTGTAC -s simCow_chr6.simCow.chr6 88005 27 - 602619 AACAAACA------TAAACCACTACAAACCTTT---- -s simDog_chr6.simDog.chr6 506838 33 + 593897 AACCAACAAAGGATTAAACCACACCACACCTCT---- -s simHuman_chr6.simHuman.chr6 514556 37 + 601863 AACCAACAAAAAATCAAACCACCCCGCCTTTCTGTAC -s simRat_chr6.simRat.chr6 556177 37 + 647215 AACCAATGAAAGTTCAGATTACCACACATTTCTGTAC - -a -s simMouse_chr6.simMouse.chr6 544004 14 + 636262 ATGAACTGAAGGAG -s Anc0.Anc0refChr3 147043 14 + 222631 CTGTACAGAGAAAG -s Anc1.Anc1refChr6 182652 14 + 197743 CTGTACAGAGAAAG -s Anc2.Anc2refChr1 60721 14 + 142988 CTTTATAGAGAAAG -s mr.mrrefChr3 94228 14 + 181027 ATGAACCGAAGGAG -s simCow_chr6.simCow.chr6 88032 14 - 602619 GCTGATAGGGAAAA -s simDog_chr6.simDog.chr6 506871 14 + 593897 CTTTATAGAGAAAG -s simHuman_chr6.simHuman.chr6 514594 14 + 601863 CTGTACAGAGAAAG -s simRat_chr6.simRat.chr6 556214 14 + 647215 ATGAACCGAAGGAG - -a -s simMouse_chr6.simMouse.chr6 544018 15 + 636262 AGAACATGTGGCCAA -s Anc0.Anc0refChr3 147062 6 + 222631 G---------GCCAG -s Anc1.Anc1refChr6 182671 6 + 197743 G---------GCCAG -s Anc2.Anc2refChr1 60740 6 + 142988 G---------GCCAG -s mr.mrrefChr3 94242 6 + 181027 A---------CCCAA -s simCow_chr6.simCow.chr6 88051 6 - 602619 G---------GCCAG -s simDog_chr6.simDog.chr6 506890 6 + 593897 G---------GCTAG -s simHuman_chr6.simHuman.chr6 514613 6 + 601863 G---------GCCTG -s simRat_chr6.simRat.chr6 556228 6 + 647215 A---------CCCAG - -a -s simMouse_chr6.simMouse.chr6 544033 4 + 636262 GAGC -s Anc0.Anc0refChr3 147068 4 + 222631 GGGC -s Anc1.Anc1refChr6 182677 4 + 197743 GGGC -s Anc2.Anc2refChr1 60746 4 + 142988 GGGC -s mr.mrrefChr3 94248 4 + 181027 GGGC -s simCow_chr6.simCow.chr6 88191 4 - 602619 GGAG -s simDog_chr6.simDog.chr6 506896 4 + 593897 GGGC -s simHuman_chr6.simHuman.chr6 514619 4 + 601863 GAGC -s simRat_chr6.simRat.chr6 556234 4 + 647215 GGGC - -a -s simMouse_chr6.simMouse.chr6 544037 16 + 636262 TAGAACTGGAGTCCCC -s Anc0.Anc0refChr3 147072 16 + 222631 TGGATGTAGAGTACCC -s Anc1.Anc1refChr6 182681 16 + 197743 TGGATGTAGAGTACCC -s Anc2.Anc2refChr1 60750 16 + 142988 TGGATGTAGAGTACCC -s mr.mrrefChr3 94252 16 + 181027 TAGAACTGGAGTCCCC -s simCow_chr6.simCow.chr6 88195 16 - 602619 TACATGTAGTGTACTC -s simDog_chr6.simDog.chr6 506902 16 + 593897 TGGATCATGAGTCCCC -s simHuman_chr6.simHuman.chr6 514623 16 + 601863 TGGATGTAGAATACCC -s simRat_chr6.simRat.chr6 556238 14 + 647215 TAGAAC--GGGTCCCC - -a -s simMouse_chr6.simMouse.chr6 544053 55 + 636262 ATGGGACAGGGATAGCAGTTGGACAGTGATCTGATCTAGGTTCTCTTGTTTTGGA -s Anc0.Anc0refChr3 147114 54 + 222631 ACAGGGAAGGGATGTCAGTTGGTCGATGGTCTAATCTAGTTTCTATTATTG-TAA -s Anc1.Anc1refChr6 182723 54 + 197743 ACAGGGAAGGGATGTCAGTTGGTCGATGGTCTAATCTAGTTTCTATTATTG-TAA -s Anc2.Anc2refChr1 60792 54 + 142988 GCAGTGAAGGGATGTCAGTTGGCTGATGGTCTAATCTAGTTTCTATTATTG-TAA -s mr.mrrefChr3 94268 55 + 181027 ATAGGGAAGGGATAGCAGTTGGTCAGTGATCTGATCTAGGTTCTCTTGTTTTGAA -s simCow_chr6.simCow.chr6 88237 51 - 602619 GCA--GAAGGGATGTAAGTTAGCTGCTGGCATGATCT-GCTTGTATTGTTG-TAA -s simDog_chr6.simDog.chr6 506940 53 + 593897 -TAGTGAAGGGATGTCAGTTGGCTGATGGTCTAATCTAGTTTCCAGTATTG-TAA -s simHuman_chr6.simHuman.chr6 514665 54 + 601863 ACAAGGAAGGGATGTCAGTTGGTCGTTGGTCTAATCTAGTTTCTGTTATTG-AAA -s simRat_chr6.simRat.chr6 556252 55 + 647215 ATAGCGAAGGGATAACAGTTGGTGAGTGATCTGATCTAGGTTCTATTGTTTTTAA - -a -s simMouse_chr6.simMouse.chr6 544108 29 + 636262 CATAAAATGGCACATCCCGTCTTGTCATG -s Anc0.Anc0refChr3 147168 27 + 222631 CATACAACAGCACA--CTCTTTTGTCATG -s Anc1.Anc1refChr6 182777 27 + 197743 CATACAACAGCACA--CTCTTTTGTCATG -s Anc2.Anc2refChr1 60846 27 + 142988 CATACGACAGCATA--CTCTTTTGTCATG -s mr.mrrefChr3 94323 29 + 181027 CATAAAATGGCACATCCCCTCTTGTCATG -s simCow_chr6.simCow.chr6 88289 27 - 602619 TATTCCACAGCATA--CTATTTTGTCATG -s simDog_chr6.simDog.chr6 506993 26 + 593897 CATACGACAG-ATA--CTCTTCTGCCATA -s simHuman_chr6.simHuman.chr6 514719 27 + 601863 CGTACAACAGCACA--CTCTTTTGTTGTG -s simRat_chr6.simRat.chr6 556307 26 + 647215 C---AAATGACATATCTCCTCTTGTCAAG - -a -s simMouse_chr6.simMouse.chr6 544137 6 + 636262 CCACCA -s Anc0.Anc0refChr3 147196 6 + 222631 TCATGA -s Anc1.Anc1refChr6 182805 6 + 197743 TCATGA -s Anc2.Anc2refChr1 60874 6 + 142988 TCATGA -s mr.mrrefChr3 94352 6 + 181027 TCATCA -s simCow_chr6.simCow.chr6 88317 6 - 602619 TCATGA -s simDog_chr6.simDog.chr6 507020 6 + 593897 TCATAA -s simHuman_chr6.simHuman.chr6 514747 6 + 601863 TCATGA -s simRat_chr6.simRat.chr6 556333 6 + 647215 TCATCA - -a -s simMouse_chr6.simMouse.chr6 544143 13 + 636262 TGTCACCATCATA -s Anc0.Anc0refChr3 147203 13 + 222631 TGTCATCTTCATG -s Anc1.Anc1refChr6 182812 13 + 197743 TGTCATCTTCATG -s Anc2.Anc2refChr1 60881 13 + 142988 TGTCATCTTCATG -s mr.mrrefChr3 94358 13 + 181027 TGTCACCATCATA -s simCow_chr6.simCow.chr6 88324 13 - 602619 TGTCATTTCCATA -s simDog_chr6.simDog.chr6 507027 13 + 593897 TGCCATCTTCATG -s simHuman_chr6.simHuman.chr6 514754 13 + 601863 TGTCATCTTCATG -s simRat_chr6.simRat.chr6 556339 13 + 647215 TGGCACCATCATA - -a -s simMouse_chr6.simMouse.chr6 544156 11 + 636262 CTTACTAAAGC -s Anc0.Anc0refChr3 147216 11 + 222631 ATTGCTAATGC -s Anc1.Anc1refChr6 182825 11 + 197743 ATTGCTAATGC -s Anc2.Anc2refChr1 60897 11 + 142988 ATTGCTAATGC -s mr.mrrefChr3 94371 11 + 181027 ATTACTAATGC -s simCow_chr6.simCow.chr6 88340 11 - 602619 ATTGCACATGC -s simDog_chr6.simDog.chr6 507043 11 + 593897 ATTACTAATGA -s simHuman_chr6.simHuman.chr6 514767 11 + 601863 ATTGCTAATAC -s simRat_chr6.simRat.chr6 556352 11 + 647215 ATTACTAATGC - -a -s simMouse_chr6.simMouse.chr6 544167 31 + 636262 CTACTTCTATAAATATCCGACAGGATTGTAT -s Anc0.Anc0refChr3 147231 31 + 222631 CTACTTCTATTAATATACCACAGAATTATGT -s Anc1.Anc1refChr6 182840 31 + 197743 CTACTTCTATTAATATACCACAGAATTATGT -s Anc2.Anc2refChr1 60912 31 + 142988 CTATTTCTATTAATATATCACAGAATTATGT -s mr.mrrefChr3 94382 31 + 181027 CTACTTCTATAAATATCCCACAGGATTGTAT -s simCow_chr6.simCow.chr6 88355 31 - 602619 CTATTTATATTAAAATATCACAGAATCATAT -s simDog_chr6.simDog.chr6 507058 22 + 593897 TTATTTCTATAAATATA---------TATGT -s simHuman_chr6.simHuman.chr6 514782 31 + 601863 CTACTTCTATTAATATACCACGGAATTATGT -s simRat_chr6.simRat.chr6 556363 31 + 647215 CTACTTCTATAAATATCCCACAGGATTGTAT - -a -s simMouse_chr6.simMouse.chr6 544198 10 + 636262 TTCTCCATGA -s Anc0.Anc0refChr3 147262 9 + 222631 CTACCCA-AC -s Anc1.Anc1refChr6 182871 9 + 197743 CTACCCA-AC -s Anc2.Anc2refChr1 60943 9 + 142988 CTACCCA-AC -s mr.mrrefChr3 94413 10 + 181027 TTCTCCATGA -s simCow_chr6.simCow.chr6 88388 9 - 602619 CTACACA-AC -s simDog_chr6.simDog.chr6 507080 9 + 593897 TTACCCA-AC -s simHuman_chr6.simHuman.chr6 514813 2 + 601863 CT-------- -s simRat_chr6.simRat.chr6 556394 10 + 647215 TTCTACATAA - -a -s simMouse_chr6.simMouse.chr6 544208 8 + 636262 CCTCTTAT -s Anc0.Anc0refChr3 147271 8 + 222631 TCTCCTTT -s Anc1.Anc1refChr6 182880 8 + 197743 TCTCCTTT -s Anc2.Anc2refChr1 60952 8 + 142988 TCTCCTTT -s mr.mrrefChr3 94423 8 + 181027 CCTCTTAT -s simCow_chr6.simCow.chr6 88397 8 - 602619 TCTTCTCT -s simDog_chr6.simDog.chr6 507125 8 + 593897 TCTCCTTT -s simRat_chr6.simRat.chr6 556404 8 + 647215 ATTCTTAT - -a -s simMouse_chr6.simMouse.chr6 544216 50 + 636262 TTTTTCAAGAAACCTTACCTAAGAACATCTCACATCCCAAACTCTGAATT -s Anc0.Anc0refChr3 147279 48 + 222631 TTTCT-AA-AAACCTAACCTAAGAGCATCTCACAACATACATTCTGGATG -s Anc1.Anc1refChr6 182888 48 + 197743 TTTCT-AA-AAACCTAACCTAAGAGCATCTCACAACATACATTCTGGATG -s Anc2.Anc2refChr1 60960 48 + 142988 TTTCT-AA-AAATCTAACCTAAGAGCTTCTCATAACATACATTCGGGACG -s mr.mrrefChr3 94431 49 + 181027 TTTTT-AAGAAACCTTACCTAAGAACATCTCACATCCCAAATTCTGAATG -s simCow_chr6.simCow.chr6 88407 47 - 602619 TATCT-AA-AAGTCTAACCTAA-AGCTTCTCACACCCTACATTCAAGACG -s simDog_chr6.simDog.chr6 507133 46 + 593897 TTTCT-AA-AAATCTGACTTAAGAGCTTCTCATAACATACATTCGGGA-- -s simHuman_chr6.simHuman.chr6 514815 36 + 601863 ---------GCACCCAACCTAAGAGCATCTCACAC-----CTGCTGGATG -s simRat_chr6.simRat.chr6 556412 49 + 647215 TTTTT-AAGAAACCTTACCTAGGATCATCTCACATCCCAAATTCTGACTG - -a -s simMouse_chr6.simMouse.chr6 544266 39 + 636262 CTGATGTGAGGGTGGGCTACACAAGCACCGCTCCATCAT -s Anc0.Anc0refChr3 147331 32 + 222631 TCACCGTGATTGTT-----CATGAGGACCATTCCGT--T -s Anc1.Anc1refChr6 182940 39 + 197743 TCACCGTGATTGTTGGCTCCATGAGGACCATTCCGTCAT -s Anc2.Anc2refChr1 61012 32 + 142988 CCACCGTGATTGTT-----CATGAGGACCAATCCGT--T -s mr.mrrefChr3 94484 39 + 181027 TTGCTGTGAGGGTGGGCTACACAAGCACCATTCCATCAT -s simCow_chr6.simCow.chr6 88458 32 - 602619 CCACCGTGATTGTT-----CATGAGGACCAATCCGT--T -s simHuman_chr6.simHuman.chr6 514855 39 + 601863 TCACCCTGCATATTGGCTCCATGCGGACTATTCCTTCAT -s simRat_chr6.simRat.chr6 556465 36 + 647215 TTGCTGTAATGGTGGACCTCACA---ACCATTCCATCAT - -a -s simMouse_chr6.simMouse.chr6 544305 33 + 636262 CTGGTACAAGTGTTTCCCTTTTGAGCTAACTTG -s Anc0.Anc0refChr3 147372 26 + 222631 CTGGTA-------TTCCCTTTTAAGCCAAATCA -s Anc1.Anc1refChr6 182988 33 + 197743 CTGGTACAACTGTTTCCCTTTTAAGCCAAATCA -s Anc2.Anc2refChr1 61053 26 + 142988 GTGATA-------TTCCCTTTTAAGCCAAATCA -s mr.mrrefChr3 94523 33 + 181027 CTGGTACAAGTGTTTCCCTTTTGAGCTAAATTG -s simCow_chr6.simCow.chr6 88499 24 - 602619 GTGAT---------TCCTTTTTAAGCCAAATCA -s simDog_chr6.simDog.chr6 507179 21 + 593897 -----A-------TTCCCTTTTAAGCCAAATTA -s simHuman_chr6.simHuman.chr6 514903 33 + 601863 CTGGTTCAACTGTCTCCCTTCTAAGCCAAATCA -s simRat_chr6.simRat.chr6 556501 33 + 647215 CTGGTATGAGTGCTTCCCTTTTGAGCTAAATTG - -a -s simMouse_chr6.simMouse.chr6 544338 35 + 636262 TTGAGTTACAGTCACTTGGGTGAAACGCGAGTTAT -s Anc0.Anc0refChr3 147398 28 + 222631 TC--ACTTCGGCG--TCAAATGCAAATCAG---AT -s Anc1.Anc1refChr6 183021 28 + 197743 TC--ACTTCGGCG--TCAAATGCAAATCAG---AT -s Anc2.Anc2refChr1 61082 28 + 142988 TC--ACTTGGGCT--TGAAATACTAATCAG---GT -s mr.mrrefChr3 94556 35 + 181027 TTGAATTACAGTGACTCAGGTGAAAAGCAAGTTAT -s simCow_chr6.simCow.chr6 88526 23 - 602619 CC--ACTTAAGCT--TGAAATATTAAT-------- -s simDog_chr6.simDog.chr6 507203 28 + 593897 TC--ACTTGGGCT--TGAAATACTAATCAG---GT -s simHuman_chr6.simHuman.chr6 514936 28 + 601863 TC--ACTTCGGCG--TCAAATGCAAATCAG---AT -s simRat_chr6.simRat.chr6 556534 35 + 647215 TTGAATTACAGTGACTCAGGTGAAAAGCAAGTAAT - -a -s simMouse_chr6.simMouse.chr6 544373 60 + 636262 AGGGGATAGCTATGTGGTTAAAAGGTGCGCCCTAGTTGATCCCCACTATCAACAAAAAAA -s Anc0.Anc0refChr3 147426 54 + 222631 AGGGGAGAGCTATGGGGTTAAAAAGTGTACTCT----GAT--ACATATTTTCCATCAACA -s Anc1.Anc1refChr6 183049 54 + 197743 AGGGGAGAGCTATGGGGTTAAAAAGTGTACTCT----GAT--ACATATTTTCCATCAACA -s Anc2.Anc2refChr1 61110 54 + 142988 AGGGGAGAGCTACAAGGTTAAAAAGTGTAGTCT----CAT--ACATATCTTCCATCAACA -s mr.mrrefChr3 94591 58 + 181027 AGGGGATAGCTATGGGGTTAAAAGGTGTACCCTAGTAGAT--CCACTATCAACAGAAAAA -s simCow_chr6.simCow.chr6 519172 54 + 602619 AGGGGAGAGCTACAAGATTAAAGTATGTAGGCT----CAT--GCATATCTTTCATCAATA -s simDog_chr6.simDog.chr6 507231 54 + 593897 AGGGGAGAGCTACAATGTGAGAAAGTGCAGTCT----CAT--ACGTAACTTCAATCAACA -s simHuman_chr6.simHuman.chr6 514964 54 + 601863 AGGGGAAAACTATGGGGTTAAAAAGTGTACTCA----GAT--ACATATTTTCCATCGATG -s simRat_chr6.simRat.chr6 556569 58 + 647215 AGGGGATAGCTATAGAGTTAAAAGTGGTACCCTAGTAGAT--TCAATATCAACAGAAAAA - -a -s simMouse_chr6.simMouse.chr6 544433 16 + 636262 ACTAATAAATAATGAT -s Anc0.Anc0refChr3 147480 16 + 222631 ACTAATAAATAATGAT -s Anc1.Anc1refChr6 183103 16 + 197743 ACTAATAAATAATGAT -s Anc2.Anc2refChr1 61181 16 + 142988 ACTAGTAAATAATGAT -s mr.mrrefChr3 94649 16 + 181027 ACTAATAAATAATGAT -s simCow_chr6.simCow.chr6 519243 16 + 602619 ACTAGTAAACAGCAAT -s simDog_chr6.simDog.chr6 507302 16 + 593897 ACTAGTAAATAATGGT -s simHuman_chr6.simHuman.chr6 515018 14 + 601863 AGTAATA--CAATGAT -s simRat_chr6.simRat.chr6 556627 16 + 647215 ACTCTTAAATAATGAT - -a -s simMouse_chr6.simMouse.chr6 544449 39 + 636262 CAACAGTGCATTCTTGCTTTAGAGGGACTATCATTGTTA -s Anc0.Anc0refChr3 147500 36 + 222631 TTTGCATGCATACTTGG---AGGGAGAAACACATCTTTA -s Anc1.Anc1refChr6 183123 36 + 197743 TTTGCATGCATACTTGG---AGGGAGAAACACATCTTTA -s Anc2.Anc2refChr1 61201 36 + 142988 TTTGCATACATACTTGG---AGGGAGAAACACATCTTCA -s mr.mrrefChr3 94669 39 + 181027 CAACAATGCATTCTTGCTTTAGAGGGACTCTCATTTTTA -s simCow_chr6.simCow.chr6 519263 36 + 602619 TTTGCATACACAATTGG---AGGGAGAAACACATCTGCA -s simDog_chr6.simDog.chr6 507322 35 + 593897 GTTTCATACATACTTAG---AGGGAGAAACACTTC-TCA -s simHuman_chr6.simHuman.chr6 515036 36 + 601863 TTTGCACGCATACTTGA---AGGGAGAAACCCATCTTTA -s simRat_chr6.simRat.chr6 556647 39 + 647215 CAACAATGCGTCCTTGGTTTAGAGGGACTCTCATTTCTA - -a -s simMouse_chr6.simMouse.chr6 544488 42 + 636262 CACCTCCACACGATTTCCCATTCACTGGGTATCTTTATTTTT -s Anc0.Anc0refChr3 147537 41 + 222631 TACCTC-ACACTGTGCCCTGTTCACTGTACATGTTTTTTTTC -s Anc1.Anc1refChr6 183160 42 + 197743 TACCTCAACACTGTGCCCTGTTCACTGTACATGTTTTTTTTC -s Anc2.Anc2refChr1 61238 41 + 142988 TACCTC-ACACTGTGCCCTATTCACCGTACGTGCTGTTTTTC -s mr.mrrefChr3 94709 42 + 181027 CACCTCCACACGGTTCCCTGTTCACTGGGTATGTTTATTTTT -s simCow_chr6.simCow.chr6 519300 39 + 602619 TACCTC-A-ACTATGCCCTATTCACAGTACTCACT-TTTTTC -s simDog_chr6.simDog.chr6 507358 41 + 593897 TGCCTC-ACACTGTGCCCTATTCACCGTATGTGCTGTGTTTC -s simHuman_chr6.simHuman.chr6 515073 42 + 601863 TACTTAAACACTGTACCCTGTGCACTGTACATGTGTTTTTTC -s simRat_chr6.simRat.chr6 556687 42 + 647215 CACCTCCACATAGTTCCCTGTTCACTGGGTATGTTCATTTTT - -a -s simMouse_chr6.simMouse.chr6 544530 1 + 636262 A -s Anc0.Anc0refChr3 147579 1 + 222631 A -s Anc1.Anc1refChr6 183203 1 + 197743 A -s Anc2.Anc2refChr1 61280 1 + 142988 A -s mr.mrrefChr3 94752 1 + 181027 A -s simCow_chr6.simCow.chr6 519340 1 + 602619 A -s simDog_chr6.simDog.chr6 507400 1 + 593897 A -s simHuman_chr6.simHuman.chr6 515116 1 + 601863 A -s simRat_chr6.simRat.chr6 556730 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 544531 25 + 636262 TGTATCTTGGCCACAATTAGGAACA -s Anc0.Anc0refChr3 147580 21 + 222631 TAA--CAATGGG--AAGTAATGATC -s Anc1.Anc1refChr6 183204 23 + 197743 TAA--CAATGGGATAAGTAATGATC -s Anc2.Anc2refChr1 61281 21 + 142988 TAA--CAATGGG--AAGTAATGATC -s mr.mrrefChr3 94753 25 + 181027 TAAATCATGGCCATAAGTAGGAATA -s simCow_chr6.simCow.chr6 519341 16 + 602619 TGA--ATATGGT--AGGTAA----- -s simDog_chr6.simDog.chr6 507402 21 + 593897 TAG--CAATGGG--AAGTAATGATC -s simHuman_chr6.simHuman.chr6 515117 23 + 601863 TAA--CACTGGAATAAGTAATGTTC -s simRat_chr6.simRat.chr6 556731 25 + 647215 CAAATCATAGCCATAAGTAGGAATA - -a -s simMouse_chr6.simMouse.chr6 544556 27 + 636262 GCAACTGTGTACATCCAAACTTGTACA -s Anc0.Anc0refChr3 147604 27 + 222631 TCTATTCTGCACATCCACACTTGCAGG -s Anc1.Anc1refChr6 183230 27 + 197743 TCTATTCTGCACATCCACACTTGCAGG -s Anc2.Anc2refChr1 61305 27 + 142988 TCTCTTCTGCACATCCACACTTGCAGG -s mr.mrrefChr3 94778 27 + 181027 GCAACTGTGTACATCCAAACTTGTACG -s simCow_chr6.simCow.chr6 519360 24 + 602619 TCTCTTCTGCA---ATGCACTTGTGTG -s simDog_chr6.simDog.chr6 507426 19 + 593897 TC-------TGCATCCA-AATTACAGA -s simHuman_chr6.simHuman.chr6 515143 27 + 601863 TCCATCCTGCACATCCACACTTGCAGG -s simRat_chr6.simRat.chr6 556756 27 + 647215 ACAACTATGTACATCCAAATTTGTATG - -a -s simMouse_chr6.simMouse.chr6 544583 235 + 636262 AGAGTGTTTCATTTTTCTCTGGGTAATTGGGCCTGATCAGATATGGCCATCTGTCCTAACCAATTGGCTGAATCGGTGTGTAAGACAAGGTAGCTATGCATAAGCATTGATATTTAGCTGTGAGCTTTCACTTTGGGTGAGCCCATGTATGGACACATCTCTGTTCCCGTACTAGAAATAAAATTAATTCCTTTGCAAGTTTGGTAACTCCAATACAAGCTATATTCAATAATTA -s Anc0.Anc0refChr3 147632 32 + 222631 AGAGTATTCCATTTTCTTCTAACTAATTGGAT----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- -s Anc1.Anc1refChr6 183258 32 + 197743 AGAGTATTCCATTTTCTTCTAACTAATTGGAT----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- -s Anc2.Anc2refChr1 61333 32 + 142988 AGAGCATTCCATTTTCTTCTAACTGATTGGAT----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- -s mr.mrrefChr3 94805 235 + 181027 AGAGTGTTTCATTTTCCTCTGAGTAATTGGGCCTGATCAGATATGGCCATCTGTCCTAACCAATTGGCTGAATCGGTGTGTAAGACAAGGTAGCTATGCATAAGCATTGATATTTAGCTGTGAGCTTTCACTTTGGGTGAGCCCATGTATGGACACATCTCTGTTCCCGTACTAGAAATAAAATTAATTCCTTTGCAAGTTTGGTAACTCCAATACAAGCTATATTCaataatta -s simCow_chr6.simCow.chr6 519385 31 + 602619 AAACCCTTCTATTTTCTGCTAACTGATT-GTT----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- -s simDog_chr6.simDog.chr6 507446 32 + 593897 AGAGCATTCCATTTTTTTCTAACTGATTGGAT----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- -s simHuman_chr6.simHuman.chr6 515171 31 + 601863 TGAGTATTGCATTTTCTTCTAA-CAATTGGAT----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- -s simRat_chr6.simRat.chr6 556783 235 + 647215 ACAGTGTTTCATTTTCCTTTGAGTAATTGGACCTGATTTGATATCCCCGTCTGTCCTAACCAATTGGCTGAATCTGTGTGCAAGACAAGGTGACTAGGCATAAGGATTGATATTTAGCTGTGAGCCTGCACTTTGGGCGGGCCATTGTATATAAACATCGCTGTTCCTGTACTAGAAATAAAATCAATTCCTTTGTAAGCATAGTAAATCAATTCCTAGCTACATTCaataatta - -a -s simMouse_chr6.simMouse.chr6 544818 19 + 636262 TTTGATTAATCGTCCAAAC -s Anc0.Anc0refChr3 147664 7 + 222631 ------------TCTAAGG -s Anc1.Anc1refChr6 183290 7 + 197743 ------------TCTAAGG -s Anc2.Anc2refChr1 61365 7 + 142988 ------------TTTAAGG -s mr.mrrefChr3 95040 19 + 181027 tttgattaatcgTCCAAAC -s simCow_chr6.simCow.chr6 519416 7 + 602619 ------------TTAAAGC -s simDog_chr6.simDog.chr6 507478 7 + 593897 ------------TTTGAGG -s simHuman_chr6.simHuman.chr6 515202 7 + 601863 ------------TCTAAGA -s simRat_chr6.simRat.chr6 557025 19 + 647215 ttttattaattatCCAAAC - -a -s simMouse_chr6.simMouse.chr6 544837 82 + 636262 TAATGAGTGAATACAGTGAAATAACTGAGTCCTCAGAGATGGAAAGTCTGGACCCGACCACCAAGTGTGAAAAACTATCTGA -s Anc0.Anc0refChr3 147671 82 + 222631 TGATGAATGGATACAGTGTAATAATAGGATCCTCATAGATGGAAAGTCTGAACCCCACCACCTCGTCTGAAAAACCATCTGG -s Anc1.Anc1refChr6 183297 82 + 197743 TGATGAATGGATACAGTGTAATAATAGGATCCTCATAGATGGAAAGTCTGAACCCCACCACCTCGTCTGAAAAACCATCTGG -s Anc2.Anc2refChr1 61372 82 + 142988 TGATGAATGGATACAGTGTTATAATAGGATTCTCATAGATGGAAAGTCTGAAACACACCACCTCGTCTGAAAAACCATCTTG -s mr.mrrefChr3 95059 82 + 181027 TAATGAGTGGATACAGTGAAATAACAGAATCCTCAGAGATGGAAAGTCTGAACCCGACCACCTAGTGTGAAAAACTATCTGA -s simCow_chr6.simCow.chr6 519423 73 + 602619 TAATGAATGGATACATTGTGATAATGGGACACGCAAAGATGGACAGTCTG---------GCCTCGTCTGCAAAACCCTCTCA -s simDog_chr6.simDog.chr6 507486 82 + 593897 TGATGAATGGATATAGTGATATAATAGGATTCTCATATATGGAAAGTCTGAAACACACCACCTGGTCTGAAATACCATCTTG -s simHuman_chr6.simHuman.chr6 515209 82 + 601863 TGGAGAATGGATTCAGTGTAATAATAGGATCCTCATAGAAGGATAGTCTGAACCCAACCACGTCATCTGAGAAACCATCTGG -s simRat_chr6.simRat.chr6 557044 82 + 647215 CAATCAGTGGACACAGTGAAATAACAGAATCCTCAGAGATGGAAAGTCTGAACCCGATCACCTGGAGTGAAAAACTATCTGA - -a -s simMouse_chr6.simMouse.chr6 544919 3 + 636262 TGC -s Anc0.Anc0refChr3 147753 3 + 222631 AGT -s Anc1.Anc1refChr6 183379 3 + 197743 AGT -s Anc2.Anc2refChr1 61459 3 + 142988 TAT -s mr.mrrefChr3 95141 3 + 181027 AGC -s simCow_chr6.simCow.chr6 519501 2 + 602619 CA- -s simDog_chr6.simDog.chr6 507573 3 + 593897 TAT -s simHuman_chr6.simHuman.chr6 515291 3 + 601863 AGT -s simRat_chr6.simRat.chr6 557126 3 + 647215 AGC - -a -s simMouse_chr6.simMouse.chr6 544922 20 + 636262 CAAGATGCTAAGGTGTTGGA -s Anc0.Anc0refChr3 147769 20 + 222631 AACGATGATGAGGTACTGGT -s Anc1.Anc1refChr6 183395 20 + 197743 AACGATGATGAGGTACTGGT -s Anc2.Anc2refChr1 61475 20 + 142988 AACAATGATGAGGTACTGGT -s mr.mrrefChr3 95144 20 + 181027 CAAGGTGCTAAGGTGTTGGA -s simCow_chr6.simCow.chr6 519510 20 + 602619 AACAATGATGTGGAACTGAT -s simDog_chr6.simDog.chr6 507591 20 + 593897 AATAGTGATGATGTACTGGT -s simHuman_chr6.simHuman.chr6 515307 20 + 601863 TACGACCATGAGGTACTGCT -s simRat_chr6.simRat.chr6 557129 20 + 647215 CAGGGTGCTAAGGTGTTGGA - -a -s simMouse_chr6.simMouse.chr6 544942 50 + 636262 TACCAGAATCAGAATTGAAGAGCCCTTCCATCTGCAGGCAGGTTACATTA -s Anc0.Anc0refChr3 147792 50 + 222631 CAACAGTATTAGGAGTGATGAGCCCTTTCAACAGCAAGCAGGTTATATTG -s Anc1.Anc1refChr6 183418 50 + 197743 CAACAGTATTAGGAGTGATGAGCCCTTTCAACAGCAAGCAGGTTATATTG -s Anc2.Anc2refChr1 61498 50 + 142988 CAACTGTATTAGGAGTGATGAGCCATTTCAACAGCAAGCAGGTTATATTG -s mr.mrrefChr3 95164 50 + 181027 CACCAGAATCAGAATTGAAGAGCCCTTTCATCTGCAGGCAGGTTACATTG -s simCow_chr6.simCow.chr6 519533 50 + 602619 CAACTGTATTTGGAGTAATGAGCCATGTCAACAGCAAGGGGGTTATATTG -s simDog_chr6.simDog.chr6 507614 50 + 593897 CAATTGTATTAGGAGTGATGAGACATTTCAACAACAAACAAGTCATATTG -s simHuman_chr6.simHuman.chr6 515330 50 + 601863 CAACAGTATTAGGAATGATGGGCCCCCTCAACCGCAAGCAGGTTGTATTG -s simRat_chr6.simRat.chr6 557149 50 + 647215 CACCAGAATCCGAATTGAAGAGCCCTTTCATCTGCAGGCAGGTTACATTG - -a -s simMouse_chr6.simMouse.chr6 544992 58 + 636262 TTCAATATGGGGCACCCCAAAAAAACAGTCACACAATGATAAGTAACAAAGTGGGTTT -s Anc0.Anc0refChr3 147847 51 + 222631 TTAAATATAACGCATACATAAAAAACGCT--TACAATGAGTAATAACAAAGTA----- -s Anc1.Anc1refChr6 183473 51 + 197743 TTAAATATAACGCATACATAAAAAACGCT--TACAATGAGTAATAACAAAGTA----- -s Anc2.Anc2refChr1 61553 51 + 142988 TTAAATATAACCCATACAGAAAAAACGCT--TACAATGAGTAATAACAAAGTA----- -s mr.mrrefChr3 95214 56 + 181027 TTCAATATAGGGCACCCCTAAAAAACAGT--CACAATGATAAGTAACAAAGTGGGTTT -s simCow_chr6.simCow.chr6 519588 45 + 602619 TTAAATATAACCCATAGAGAAAAAACAGT--TACAAT--GTAATAACAG--------- -s simDog_chr6.simDog.chr6 507669 51 + 593897 TTAAAAATAACCCAGACAGAAAAAACGCT--AGCAATGAGTAACAACAAAGTA----- -s simHuman_chr6.simHuman.chr6 515385 51 + 601863 TTAGATATAAAGTATACATAAAGACTGTT--TACGATGAGTATTAACGAAGTA----- -s simRat_chr6.simRat.chr6 557212 56 + 647215 TTCAATATAGGGCACCCCTAAAAAACAGT--CACAATGATAAGTAGCAAAGTGGGTTT - -a -s simMouse_chr6.simMouse.chr6 545050 97 + 636262 GCCTACCTTTTGAAACCTTTGAAGTGTAATTAACTTCTTATCTTAGGTGGAATTCAATATGTGATCAAGTTGAAATGCATTTGCTTTTGGTTACCAA -s Anc0.Anc0refChr3 147898 72 + 222631 ACTTAACTTTAGGAACCTATGATG-GTAAT-----------------------TCAATCTGTGAT-GTGGTGAAATGCATTTTCTTCTGAATATCAA -s Anc1.Anc1refChr6 183524 73 + 197743 ACTTAACTTTAGGAACCTATGATGTGTAAT-----------------------TCAATCTGTGAT-GTGGTGAAATGCATTTTCTTCTGAATATCAA -s Anc2.Anc2refChr1 61604 72 + 142988 ATTTAACTGCAGGGCCCTATAATG-GTAAT-----------------------TCAATCTGTTAT-GTGGTGAAATGCATTGTCTTCTGAATATAAC -s mr.mrrefChr3 95270 97 + 181027 ACCTACCTTTTGAAACCTTTGAAGTGTAATTAACTTCTTATCTTAGGTGGAATTCAATCTGTGATCAAGTTGAAATGCATTTGCTTCTGGTTACCAA -s simCow_chr6.simCow.chr6 519633 46 + 602619 ---------------------------AAT-----------------------TCAATCTGATAT-GTGGTAAAATGCATTGCCTTCTGAATACAAT -s simDog_chr6.simDog.chr6 507725 72 + 593897 ATTTAACTGCAGGGCCCTATAATG-GTACT-----------------------ACAATCTATTAT-ATAGTGAAATGCATTGTCTTCTGAATATAAC -s simHuman_chr6.simHuman.chr6 515436 73 + 601863 ACTTAGCTTTGCGAACCTCCGGTGTGTAAT-----------------------TCAATCTGTGAT-GTGGTGAAATGCATTTACCTCTGAATTACTA -s simRat_chr6.simRat.chr6 557268 97 + 647215 ATCTACCTTTAGAAACCTTTGAAGTGTACTTAAGTTCTTACTTTATGTGGAATCCAATCTGCGATAAAGTTGAAGTGAATTTCCTTCTGGGTACAAA - -a -s simMouse_chr6.simMouse.chr6 545147 38 + 636262 AACATATAATCTTGTGAGATTCAGAGTTCTTTTGAATC -s Anc0.Anc0refChr3 147970 38 + 222631 AACATATCATCTTAAGAGATTTAGGGTTGCTTTTACTC -s Anc1.Anc1refChr6 183597 38 + 197743 AACATATCATCTTAAGAGATTTAGGGTTGCTTTTACTC -s Anc2.Anc2refChr1 61676 38 + 142988 AGCATATCATCTTAAGAAATTTAGGTTTGCTTTTACTT -s mr.mrrefChr3 95367 38 + 181027 AACATATAATCTTGTGAGATTTAGGGTTCCTTTGAATC -s simCow_chr6.simCow.chr6 519703 35 + 602619 GGCATATTATCTTAAAAAATTGAGATCTGTATTTA--- -s simDog_chr6.simDog.chr6 507797 38 + 593897 AGCAAATCATCTTAAGAAATTTAGGTTTGCTTTTACTT -s simHuman_chr6.simHuman.chr6 515509 38 + 601863 AACATGTCATCTTAAGCGATTTAAGGTTGCTTTTGCTC -s simRat_chr6.simRat.chr6 557365 36 + 647215 AAC--ATAAACTTGTGAGTTTTATGGTTCCTTCGAATC - -a -s simMouse_chr6.simMouse.chr6 545185 51 + 636262 TGCATTCAACTGAGGATCAACACCAAACCAGGATAGAGTTGGGACAAAACT -s Anc0.Anc0refChr3 148008 47 + 222631 T----TCAATAGAGGATTGAGAATTACCTAGACCAGGGTTGAGACAAAATC -s Anc1.Anc1refChr6 183635 47 + 197743 T----TCAATAGAGGATTGAGAATTACCTAGACCAGGGTTGAGACAAAATC -s Anc2.Anc2refChr1 61715 47 + 142988 T----TCAATAGAGGATTGAGAAGTACCTAGACCAGGGTTGAGATATAATC -s mr.mrrefChr3 95405 51 + 181027 TGCATTCAACTGAGGATTAACAATTAACTAGGATAGAGTTGGGACAAAACT -s simCow_chr6.simCow.chr6 519739 47 + 602619 T----TCAACTAAGGATTGACAGGTACCTAGATCAGGGTTGAGATACAACC -s simDog_chr6.simDog.chr6 507838 47 + 593897 T----CCAATAGAGGATTGAGAAGTACCTGGACCAAGGTTGAGATGTAATC -s simHuman_chr6.simHuman.chr6 515547 47 + 601863 T----TCCATGGAGAATTGAGAATTGCCTAGACCAGGGATGAGACAAAGTC -s simRat_chr6.simRat.chr6 557401 51 + 647215 TCCATGCAACTGAGGATTAACAATTAGCTAGGATAGAGTTAGGACAAAACT - -a -s simMouse_chr6.simMouse.chr6 545236 21 + 636262 GCCAAGGGGATCAGAGAACCT -s Anc0.Anc0refChr3 148058 13 + 222631 ACCCT-GGGA-------GCAT -s Anc1.Anc1refChr6 183685 14 + 197743 ACCCTGGGGA-------GCAT -s Anc2.Anc2refChr1 61765 13 + 142988 ACCCT-GGGA-------TCAT -s mr.mrrefChr3 95456 21 + 181027 GCCATGGGGATCAGAGAGCCT -s simCow_chr6.simCow.chr6 519789 13 + 602619 GTCCT-GAGA-------TCAT -s simDog_chr6.simDog.chr6 507888 13 + 593897 ACCCT-GGCA-------TCAT -s simHuman_chr6.simHuman.chr6 515597 14 + 601863 TCCCTGTGGA-------GTAT -s simRat_chr6.simRat.chr6 557452 21 + 647215 GCCGTGGTGATCAGGGAGCCC - -a -s simMouse_chr6.simMouse.chr6 545257 4 + 636262 CCAG -s Anc0.Anc0refChr3 148071 4 + 222631 CCTG -s Anc1.Anc1refChr6 183699 4 + 197743 CCTG -s Anc2.Anc2refChr1 61778 4 + 142988 CCTG -s mr.mrrefChr3 95477 4 + 181027 CCAG -s simCow_chr6.simCow.chr6 519809 4 + 602619 TCAC -s simDog_chr6.simDog.chr6 507901 4 + 593897 CATG -s simHuman_chr6.simHuman.chr6 515611 4 + 601863 CCTG -s simRat_chr6.simRat.chr6 557473 4 + 647215 CCAG - -a -s simMouse_chr6.simMouse.chr6 545261 20 + 636262 AAATAAAGTTGTTGTGTGAT -s Anc0.Anc0refChr3 148075 20 + 222631 AAATGAATTTGTTGCATTGT -s Anc1.Anc1refChr6 183703 20 + 197743 AAATGAATTTGTTGCATTGT -s Anc2.Anc2refChr1 61782 20 + 142988 AAATGAGTTTGTTGCATTGT -s mr.mrrefChr3 95481 20 + 181027 AAATAAATTTGTTGTGTGAT -s simCow_chr6.simCow.chr6 519813 20 + 602619 AAAAGAGTCTGTGGCAATGT -s simDog_chr6.simDog.chr6 508203 20 + 593897 AAATGAGTTTGTTGCATTGT -s simHuman_chr6.simHuman.chr6 515615 20 + 601863 AAACGGATTTGTTGCATTGT -s simRat_chr6.simRat.chr6 557477 20 + 647215 AAATATATCCGTTGTGTGAT - -a -s simMouse_chr6.simMouse.chr6 545281 26 + 636262 AAGCAAACCTGTGAGATTCAGAAAGA -s Anc0.Anc0refChr3 148104 18 + 222631 --------CTGTGAGATTCAGAAAAG -s Anc1.Anc1refChr6 183733 24 + 197743 AGTCAA--CTGTGAGATTCAGAAAAG -s Anc2.Anc2refChr1 61811 18 + 142988 --------CTGTAAGATTCAGCAATA -s mr.mrrefChr3 95501 26 + 181027 AAGCAAACCTGTGAGATTCAGAAAAG -s simCow_chr6.simCow.chr6 519842 18 + 602619 --------CTGTGAGATTCAGTAATA -s simDog_chr6.simDog.chr6 508232 18 + 593897 --------CTGTAAGATTCAGCAATA -s simHuman_chr6.simHuman.chr6 515645 24 + 601863 AGTCAA--CTTTGAGAGCCCCAAGAG -s simRat_chr6.simRat.chr6 557497 26 + 647215 GGGCAAACCTGTGAGGTTCAGAAAAG - -a -s simMouse_chr6.simMouse.chr6 545307 21 + 636262 CACAACTGTTAGAAGGGCAGT -s Anc0.Anc0refChr3 148125 21 + 222631 CACAATTGGTAGCAAAGAGGT -s Anc1.Anc1refChr6 183760 21 + 197743 CACAATTGGTAGCAAAGAGGT -s Anc2.Anc2refChr1 61832 21 + 142988 TACTATCGGACACAAAGGGGT -s mr.mrrefChr3 95527 21 + 181027 CACAACTGTTAGAAGGGAAGT -s simCow_chr6.simCow.chr6 519864 21 + 602619 TAATAAACTATTCAACTGGGT -s simDog_chr6.simDog.chr6 508253 21 + 593897 TACTATCGGACACAAAGGGGT -s simHuman_chr6.simHuman.chr6 515672 18 + 601863 CACAGTTTATAGCAAAGA--- -s simRat_chr6.simRat.chr6 557523 21 + 647215 CCCAACTATTAAAAGGGAAGT - -a -s simMouse_chr6.simMouse.chr6 545328 13 + 636262 GAAAAGCAACATA -s Anc0.Anc0refChr3 148146 13 + 222631 GAAACATAGCATT -s Anc1.Anc1refChr6 183781 13 + 197743 GAAACATAGCATT -s Anc2.Anc2refChr1 61861 13 + 142988 GAAACATACCATT -s mr.mrrefChr3 95548 13 + 181027 GAAAAGCAGCATA -s simCow_chr6.simCow.chr6 519893 13 + 602619 GGAACATATCATT -s simDog_chr6.simDog.chr6 508282 13 + 593897 GAAACATACAATT -s simHuman_chr6.simHuman.chr6 515690 7 + 601863 ------TAGCTTT -s simRat_chr6.simRat.chr6 557544 13 + 647215 GAAAAGCAGCATA - -a -s simMouse_chr6.simMouse.chr6 545341 8 + 636262 CCAATTGA -s Anc0.Anc0refChr3 148159 6 + 222631 T--ATTGA -s Anc1.Anc1refChr6 183794 6 + 197743 T--ATTGA -s Anc2.Anc2refChr1 61874 6 + 142988 T--ATTGA -s mr.mrrefChr3 95561 8 + 181027 CCAATTGA -s simCow_chr6.simCow.chr6 519906 6 + 602619 T--ATTGA -s simDog_chr6.simDog.chr6 508295 6 + 593897 C--ATCGA -s simHuman_chr6.simHuman.chr6 515697 6 + 601863 T--ATTGA -s simRat_chr6.simRat.chr6 557559 8 + 647215 CCAATTAA - -a -s simMouse_chr6.simMouse.chr6 545349 11 + 636262 ATCGACACTGA -s Anc0.Anc0refChr3 148168 11 + 222631 ATTGATACTGA -s Anc1.Anc1refChr6 183803 11 + 197743 ATTGATACTGA -s Anc2.Anc2refChr1 61883 11 + 142988 ATTGATACTTA -s mr.mrrefChr3 95569 11 + 181027 ATTGATACTGA -s simCow_chr6.simCow.chr6 519915 11 + 602619 ATTGATAATAA -s simDog_chr6.simDog.chr6 508304 11 + 593897 ACTGACACTTA -s simHuman_chr6.simHuman.chr6 515706 11 + 601863 ATTGATACTGA -s simRat_chr6.simRat.chr6 557567 11 + 647215 TTTGATACTGA - -a -s simMouse_chr6.simMouse.chr6 545360 5 + 636262 TTACT -s Anc0.Anc0refChr3 148179 5 + 222631 TAACA -s Anc1.Anc1refChr6 183814 5 + 197743 TAACA -s Anc2.Anc2refChr1 61894 5 + 142988 TAACA -s mr.mrrefChr3 95580 5 + 181027 TAACT -s simCow_chr6.simCow.chr6 519932 5 + 602619 TAGCA -s simDog_chr6.simDog.chr6 508315 5 + 593897 TAATG -s simHuman_chr6.simHuman.chr6 515717 5 + 601863 TAACA -s simRat_chr6.simRat.chr6 557578 5 + 647215 TAATT - -a -s simMouse_chr6.simMouse.chr6 545365 8 + 636262 TGTTAAGT -s Anc0.Anc0refChr3 148188 8 + 222631 TGTTAAAT -s Anc1.Anc1refChr6 183823 8 + 197743 TGTTAAAT -s Anc2.Anc2refChr1 61905 8 + 142988 TGTTAAAT -s mr.mrrefChr3 95585 8 + 181027 TGTTAAGT -s simCow_chr6.simCow.chr6 519943 8 + 602619 TGCTCAAT -s simDog_chr6.simDog.chr6 508326 8 + 593897 TGTTAACT -s simHuman_chr6.simHuman.chr6 515726 8 + 601863 TAATAAAT -s simRat_chr6.simRat.chr6 557588 8 + 647215 TGTTAAGT - -a -s simMouse_chr6.simMouse.chr6 545373 22 + 636262 TTCCCTGAGTGTGTGATTGCAT -s Anc0.Anc0refChr3 148196 22 + 222631 TTATCTAAGTGCTTGATAGTGG -s Anc1.Anc1refChr6 183831 22 + 197743 TTATCTAAGTGCTTGATAGTGG -s Anc2.Anc2refChr1 61913 22 + 142988 CTATCTAAATGCTTAGTAGTGG -s mr.mrrefChr3 95593 22 + 181027 TTACCTGAGTGTGTGATTGCAT -s simCow_chr6.simCow.chr6 519951 20 + 602619 C--CCTAAATGCTTATAAGGGG -s simDog_chr6.simDog.chr6 508334 22 + 593897 CTATCTAAATGTTTAGTAGTGG -s simHuman_chr6.simHuman.chr6 515735 22 + 601863 TTATCTAAGTGCTTGATAGTGG -s simRat_chr6.simRat.chr6 557596 21 + 647215 TTACCT-AGTGTGTGATTGCAT - -a -s simMouse_chr6.simMouse.chr6 545395 1 + 636262 G -s Anc0.Anc0refChr3 148218 1 + 222631 G -s Anc1.Anc1refChr6 183853 1 + 197743 G -s Anc2.Anc2refChr1 61935 1 + 142988 G -s mr.mrrefChr3 95615 1 + 181027 G -s simCow_chr6.simCow.chr6 519985 1 + 602619 G -s simDog_chr6.simDog.chr6 508356 1 + 593897 G -s simHuman_chr6.simHuman.chr6 515757 1 + 601863 G -s simRat_chr6.simRat.chr6 557617 1 + 647215 G - -a -s simMouse_chr6.simMouse.chr6 545396 2 + 636262 GT -s Anc0.Anc0refChr3 148219 2 + 222631 GT -s Anc1.Anc1refChr6 183854 2 + 197743 GT -s Anc2.Anc2refChr1 61936 2 + 142988 GT -s mr.mrrefChr3 95616 2 + 181027 GT -s simCow_chr6.simCow.chr6 519986 2 + 602619 GT -s simDog_chr6.simDog.chr6 508361 2 + 593897 GT -s simHuman_chr6.simHuman.chr6 515758 2 + 601863 TT -s simRat_chr6.simRat.chr6 557618 2 + 647215 GT - -a -s simMouse_chr6.simMouse.chr6 545398 10 + 636262 TGGCTCAGTC -s Anc0.Anc0refChr3 148246 10 + 222631 TGGCTTAGAT -s Anc1.Anc1refChr6 183881 10 + 197743 TGGCTTAGAT -s Anc2.Anc2refChr1 61980 10 + 142988 TGACTTAGAT -s mr.mrrefChr3 95618 10 + 181027 TGGCTCAGTC -s simCow_chr6.simCow.chr6 520030 10 + 602619 TGACTTTGAT -s simDog_chr6.simDog.chr6 508408 10 + 593897 CAACTTAAAT -s simHuman_chr6.simHuman.chr6 515785 10 + 601863 TGGCTTAGAT -s simRat_chr6.simRat.chr6 557620 10 + 647215 TGGCTCAGTC - -a -s simMouse_chr6.simMouse.chr6 545408 10 + 636262 ACTTTCCTGA -s Anc0.Anc0refChr3 148256 10 + 222631 TGTCACCTGA -s Anc1.Anc1refChr6 183891 10 + 197743 TGTCACCTGA -s Anc2.Anc2refChr1 61990 10 + 142988 TGTCACCTGA -s mr.mrrefChr3 95628 10 + 181027 ACTTTCCTGA -s simCow_chr6.simCow.chr6 520040 6 + 602619 TGGCAT---- -s simDog_chr6.simDog.chr6 508418 10 + 593897 TGTCACCTGA -s simDog_chr6.simDog.chr6 85067 6 - 593897 T----CCTTG -s simHuman_chr6.simHuman.chr6 515795 10 + 601863 TGTCACCTGA -s simRat_chr6.simRat.chr6 557630 10 + 647215 ACTTGCCTAA - -a -s simMouse_chr6.simMouse.chr6 545418 5 + 636262 GGAGT -s Anc0.Anc0refChr3 148277 5 + 222631 GGAGT -s Anc1.Anc1refChr6 183912 5 + 197743 GGAGT -s Anc2.Anc2refChr1 62011 5 + 142988 TCATC -s mr.mrrefChr3 95638 5 + 181027 GGAGT -s simCow_chr6.simCow.chr6 520049 5 + 602619 TCATT -s simDog_chr6.simDog.chr6 508439 5 + 593897 TCATC -s simDog_chr6.simDog.chr6 85082 5 - 593897 TCATC -s simHuman_chr6.simHuman.chr6 515816 5 + 601863 GGAGT -s simRat_chr6.simRat.chr6 557640 5 + 647215 GGAGT - -a -s simMouse_chr6.simMouse.chr6 545423 13 + 636262 CCAACACTACTAG -s Anc0.Anc0refChr3 148293 13 + 222631 CCATGACTACTAG -s Anc1.Anc1refChr6 183928 13 + 197743 CCATGACTACTAG -s Anc2.Anc2refChr1 62027 13 + 142988 CTATGACTACTAG -s mr.mrrefChr3 95643 13 + 181027 CCAACACTACTAG -s simCow_chr6.simCow.chr6 520062 7 + 602619 -----ACAAACA- -s simDog_chr6.simDog.chr6 508455 13 + 593897 CTATGACTACTAG -s simDog_chr6.simDog.chr6 85098 13 - 593897 CTATGACTACTAG -s simHuman_chr6.simHuman.chr6 515832 13 + 601863 CCATTGCTACTAA -s simRat_chr6.simRat.chr6 557645 13 + 647215 CCAACACTACTAG - -a -s simMouse_chr6.simMouse.chr6 545436 1 + 636262 T -s Anc0.Anc0refChr3 148306 1 + 222631 T -s Anc1.Anc1refChr6 183941 1 + 197743 T -s Anc2.Anc2refChr1 62042 1 + 142988 T -s mr.mrrefChr3 95656 1 + 181027 T -s simDog_chr6.simDog.chr6 508470 1 + 593897 T -s simDog_chr6.simDog.chr6 85113 1 - 593897 T -s simHuman_chr6.simHuman.chr6 515845 1 + 601863 T -s simRat_chr6.simRat.chr6 557658 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 545437 62 + 636262 TGCAAGATTGGGCTGCAACAGAATGTGACTGTGCAAGCAATAATATGAGAGTCCTACACCAC -s Anc0.Anc0refChr3 148330 45 + 222631 TGCAAGACTGTGCTGCAA-----------------AGGAATGATGTGATAGTCCTAAACTAC -s Anc1.Anc1refChr6 183965 45 + 197743 TGCAAGACTGTGCTGCAA-----------------AGGAATGATGTGATAGTCCTAAACTAC -s Anc2.Anc2refChr1 62066 45 + 142988 TGCAGAACTGTGCAGCAA-----------------AAGAATGATGTGATAGTCCTAAGCTAT -s mr.mrrefChr3 95657 62 + 181027 TGCAAGATTGGGCTGCAACAGAATGTGACTGTGCAAGCAATAATGTGAGAGTCCTAAACCAC -s simCow_chr6.simCow.chr6 520088 45 + 602619 TGCAAGACTGTGCTGCCA-----------------AAGAATTATGTGACAGTCCTAAACTAT -s simDog_chr6.simDog.chr6 508494 45 + 593897 TGCAGAACTGTGCAGCAA-----------------AAGAATGATGTGATAGTCCTAAGCTAT -s simDog_chr6.simDog.chr6 85137 45 - 593897 TGCAGAACTGTGCAGCAA-----------------AAGAATGATGTGATAGTCCTAAGCTAT -s simHuman_chr6.simHuman.chr6 515869 45 + 601863 TGCAAGCCTACCCTACAA-----------------AGGAATCCAGTGATAGTCATAAACTAC -s simRat_chr6.simRat.chr6 557659 62 + 647215 TGCAAGATTGGGCTGCAACAGAATGTGACTGTGCAAACAATAATGTGAGAATCCTGAACCAC - -a -s simMouse_chr6.simMouse.chr6 545499 7 + 636262 AGCTTGG -s Anc0.Anc0refChr3 148375 7 + 222631 AGCTTGC -s Anc1.Anc1refChr6 184010 7 + 197743 AGCTTGC -s Anc2.Anc2refChr1 62111 7 + 142988 GGGTTGC -s mr.mrrefChr3 95719 7 + 181027 AGCTTGG -s simCow_chr6.simCow.chr6 520133 7 + 602619 AGTTTGC -s simDog_chr6.simDog.chr6 508539 7 + 593897 GGGTTGC -s simDog_chr6.simDog.chr6 85182 7 - 593897 GCGTTGC -s simHuman_chr6.simHuman.chr6 515914 7 + 601863 AGCTTGT -s simRat_chr6.simRat.chr6 557722 7 + 647215 AGCTTGG - -a -s simMouse_chr6.simMouse.chr6 545506 30 + 636262 CATGTATACATTGAGGTGCAAGGCCGGCAA -s Anc0.Anc0refChr3 148382 29 + 222631 CATGTATACACCCAGGTTTGATTCAGGC-A -s Anc1.Anc1refChr6 184017 30 + 197743 CATGTATACACCCAGGTTTGATTCAGGCAA -s Anc2.Anc2refChr1 62118 29 + 142988 TGTGTACACACCCAGGGTTGATTCAGAC-A -s mr.mrrefChr3 95726 30 + 181027 CATGTATACACCGAGGTGTGATGCAGGCAA -s simCow_chr6.simCow.chr6 520144 29 + 602619 CATATATACACCCAGGTATAATTCAGGC-A -s simDog_chr6.simDog.chr6 508546 29 + 593897 TGTGTACACACCCAGGGTTGATCCAGAC-A -s simDog_chr6.simDog.chr6 85189 29 - 593897 TGTGTACACACCCAGGGTTGATTCAGAC-A -s simHuman_chr6.simHuman.chr6 515921 30 + 601863 CATTTATACACCCGGATATGATTCAGGTGA -s simRat_chr6.simRat.chr6 557729 30 + 647215 CATGTATACACCGAGGTGTGATGCAGGCAA - -a -s simMouse_chr6.simMouse.chr6 545536 14 + 636262 TTTTGCACGATAGA -s Anc0.Anc0refChr3 148411 14 + 222631 CTATGCAGGATAGA -s Anc1.Anc1refChr6 184047 14 + 197743 CTATGCAGGATAGA -s Anc2.Anc2refChr1 62147 14 + 142988 CCATGCAGGATAGA -s mr.mrrefChr3 95756 14 + 181027 TTTTGCAGGATAGA -s simCow_chr6.simCow.chr6 520173 14 + 602619 CCAGGCAGGATGGA -s simDog_chr6.simDog.chr6 508575 14 + 593897 CCATGCAGGATAGA -s simDog_chr6.simDog.chr6 85218 14 - 593897 CCATGCAGGATAGA -s simHuman_chr6.simHuman.chr6 515951 14 + 601863 CTAAGTAGGATAGA -s simRat_chr6.simRat.chr6 557760 14 + 647215 TTTTGCAGGATAGA - -a -s simMouse_chr6.simMouse.chr6 545550 46 + 636262 TTTTAAAGCAGAAAAGAGAGCTTGAACATGTTTGAGGATGCAATAA -s Anc0.Anc0refChr3 148425 46 + 222631 TCTCAAAGCAGAAAACAGAGATAGAACATGTTTGAGCAGGCAATGA -s Anc1.Anc1refChr6 184061 46 + 197743 TCTCAAAGCAGAAAACAGAGATAGAACATGTTTGAGCAGGCAATGA -s Anc2.Anc2refChr1 62163 46 + 142988 TCTCAAAGCTGAAAACAGATATAGAACCTGTTTGAGCAGGCAGGGA -s mr.mrrefChr3 95770 46 + 181027 TTTTAAAGCAGAAAACAGAGCTTGAACATGTTTGAGGATGCAATGA -s simCow_chr6.simCow.chr6 520189 44 + 602619 TT--AAAACTGAAAACATGAATGGAGCATGCTTGAGCAGGCAGGGA -s simDog_chr6.simDog.chr6 508591 39 + 593897 TCTCAAAGCTGAAAATGGATATAGAACCTATT--AGCATGC----- -s simDog_chr6.simDog.chr6 85234 33 - 593897 TCTCAAAGCTGAAAACAGATATAGAACCTGTT--A----------- -s simHuman_chr6.simHuman.chr6 515965 46 + 601863 TGTCAAAGCAGAGAACAGAGATAGAACATGTTTGAGCGGGCAATGA -s simRat_chr6.simRat.chr6 557774 45 + 647215 TTTTAAAGCAGAAAACAGAGCTTGAGCATGTTTGAGGATGC-ATGA - -a -s simMouse_chr6.simMouse.chr6 545596 26 + 636262 CTGTGCAGTATACTAGCATGCTGGGA -s Anc0.Anc0refChr3 148471 26 + 222631 CTGTGCAATGCACTAGCATGCTGGGA -s Anc1.Anc1refChr6 184107 26 + 197743 CTGTGCAATGCACTAGCATGCTGGGA -s Anc2.Anc2refChr1 62209 26 + 142988 CTGTGCAATGCACTAGCATGCTGGGG -s mr.mrrefChr3 95816 26 + 181027 CTGTGCAGTATACTAGCATGCTGGGA -s simCow_chr6.simCow.chr6 520233 26 + 602619 CTTTGCAATGCACTAGCATGCTGGGG -s simDog_chr6.simDog.chr6 508830 26 + 593897 TTGTGCAATGCACTAGCATGCTGGGG -s simHuman_chr6.simHuman.chr6 516011 26 + 601863 CTGTTTAACGCACTAGTATGCTGGTA -s simRat_chr6.simRat.chr6 557819 21 + 647215 CTGTCC-----ACTAGCATGCTGGGA - -a -s simMouse_chr6.simMouse.chr6 545622 9 + 636262 GTATGGGAC -s Anc0.Anc0refChr3 148497 9 + 222631 GCATAGGGT -s Anc1.Anc1refChr6 184133 9 + 197743 GCATAGGGT -s Anc2.Anc2refChr1 62235 9 + 142988 GCATAGGGT -s mr.mrrefChr3 95842 9 + 181027 GTATGGGAC -s simCow_chr6.simCow.chr6 520259 9 + 602619 ACATAGGGT -s simDog_chr6.simDog.chr6 508856 9 + 593897 GCATGGGGT -s simHuman_chr6.simHuman.chr6 7963 9 + 601863 GCAGAGAGT -s simHuman_chr6.simHuman.chr6 516037 9 + 601863 GCAAAGAGT -s simRat_chr6.simRat.chr6 557840 9 + 647215 GTATGGGAC - -a -s simMouse_chr6.simMouse.chr6 545631 14 + 636262 AGTGTGTCAGACTA -s Anc0.Anc0refChr3 148508 14 + 222631 AGTGTGTCAGACTG -s Anc1.Anc1refChr6 184144 14 + 197743 AGTGTGTCAGACTG -s Anc2.Anc2refChr1 62246 14 + 142988 ACTGTGTCAGACTG -s mr.mrrefChr3 95851 14 + 181027 AGTGTGTCAGACTA -s simCow_chr6.simCow.chr6 520270 6 + 602619 AT--------GCAG -s simDog_chr6.simDog.chr6 508867 14 + 593897 ACTGTGTCAGACTG -s simHuman_chr6.simHuman.chr6 7974 14 + 601863 AGTTAGTTGGACCG -s simHuman_chr6.simHuman.chr6 516048 14 + 601863 AGTGAGTTGGACTG -s simRat_chr6.simRat.chr6 557849 14 + 647215 AGTGTGTCAGACTA - -a -s simMouse_chr6.simMouse.chr6 545645 43 + 636262 AGGCTTTGGCAGCATTGCTCTTAGTCAGCATAGACTAGTGAGA -s Anc0.Anc0refChr3 148522 12 + 222631 AGTC-------------------------------AAGTGAGA -s Anc1.Anc1refChr6 184158 43 + 197743 AGTCACGGGCAGCAGTGTATTTATTTAGCGTAGCTAAGTGAGA -s Anc2.Anc2refChr1 62260 12 + 142988 AGAC-------------------------------AAGTGAGA -s mr.mrrefChr3 95865 43 + 181027 AGGCTCTGGCAGCATTGTTCTTAGTCAGCATAGCCTAGTGAGA -s simCow_chr6.simCow.chr6 520276 12 + 602619 AGCC-------------------------------AGGTTAGA -s simDog_chr6.simDog.chr6 508921 12 + 593897 AGAC-------------------------------AAGTGAGA -s simHuman_chr6.simHuman.chr6 7988 43 + 601863 AGTCATGGGCAGCAGTCTATTTATTTAGTGTAGCTAAGTGAGA -s simHuman_chr6.simHuman.chr6 516062 41 + 601863 AGTCACGGGCAGCAGTGTATTTATTTAGCGCAGCTAAGTGA-- -s simRat_chr6.simRat.chr6 557863 43 + 647215 AGGCTCTGACAGAATTGTTCTTTGTCAGCATAGCCTAGTGAGA - -a -s simMouse_chr6.simMouse.chr6 545688 24 + 636262 ATTGCTAAGTCATGACAATAGTGC -s Anc0.Anc0refChr3 148534 21 + 222631 A---CCAAGATATGGCAATAATGC -s Anc1.Anc1refChr6 184201 24 + 197743 ATTGCCAAGATATGGCAATAATGC -s Anc2.Anc2refChr1 62272 21 + 142988 A---CCAAGATATGTCAATAACAC -s mr.mrrefChr3 95908 24 + 181027 ATTGCTAAGTCATGACAATAGTGC -s simCow_chr6.simCow.chr6 520291 21 + 602619 A---CCAACACATGCCAATCACAT -s simDog_chr6.simDog.chr6 508933 21 + 593897 A---CCAAGATATGTCAATAACAC -s simHuman_chr6.simHuman.chr6 8031 24 + 601863 ATTGCCAAGAAATAGCAACAATGC -s simHuman_chr6.simHuman.chr6 516103 19 + 601863 -----TAAGAGATAGCAACAATGC -s simRat_chr6.simRat.chr6 557906 24 + 647215 ATTGCTAAGTCACGACAATAGATC - -a -s simMouse_chr6.simMouse.chr6 545712 12 + 636262 CAATGTTTGATT -s Anc0.Anc0refChr3 148557 12 + 222631 CAAAGTGAGCTT -s Anc1.Anc1refChr6 184227 12 + 197743 CAAAGTGAGCTT -s Anc2.Anc2refChr1 62295 12 + 142988 CAAAGTGAGCTT -s mr.mrrefChr3 95932 12 + 181027 CAATGTTAGCTT -s simCow_chr6.simCow.chr6 520314 12 + 602619 CAAGGTGAGCTT -s simDog_chr6.simDog.chr6 508956 12 + 593897 CAAAGCAAGCTT -s simHuman_chr6.simHuman.chr6 8057 12 + 601863 CAAAGTGAGCTT -s simHuman_chr6.simHuman.chr6 516124 11 + 601863 CAA-GTGAGCTT -s simRat_chr6.simRat.chr6 557930 12 + 647215 CAATGTTAGCTT - -a -s simMouse_chr6.simMouse.chr6 545724 19 + 636262 CAGGCAAGCTATAATACAG -s Anc0.Anc0refChr3 148570 14 + 222631 CAGCTAAGCTATAG----- -s Anc1.Anc1refChr6 184240 19 + 197743 CAGCTAAGCTATAGTAGAA -s Anc2.Anc2refChr1 62308 14 + 142988 CAGCTAAACTTTAG----- -s mr.mrrefChr3 95944 19 + 181027 CAGGCAAGCTATAATACAG -s simCow_chr6.simCow.chr6 520327 14 + 602619 CATTCACACTTTAA----- -s simDog_chr6.simDog.chr6 508969 14 + 593897 TAGCTAAACTTTAG----- -s simHuman_chr6.simHuman.chr6 8070 19 + 601863 CAGCTAAGCTAGAATAGAA -s simHuman_chr6.simHuman.chr6 516136 19 + 601863 CAGCTAAGCTAGAGCCGAA -s simRat_chr6.simRat.chr6 557942 19 + 647215 CAGTCCAGCTATAATATGA - -a -s simMouse_chr6.simMouse.chr6 545743 26 + 636262 ATAGTGAAGAACATTGCACAGGAACA -s Anc0.Anc0refChr3 148592 26 + 222631 ATTATGAAGTACATTGCACAGACAGA -s Anc1.Anc1refChr6 184267 26 + 197743 ATTATGAAGTACATTGCACAGACAGA -s Anc2.Anc2refChr1 62330 26 + 142988 ATTATGAAGTACATTACACGGACAGA -s mr.mrrefChr3 95963 26 + 181027 ATAGTGAAGTACATTGCACAGGAACA -s simCow_chr6.simCow.chr6 520349 26 + 602619 ATTATGAAGTACATTAGATAGACATC -s simDog_chr6.simDog.chr6 508991 26 + 593897 ATTATGAAGTGCATTACACGGACAGA -s simHuman_chr6.simHuman.chr6 8093 26 + 601863 ATTATGAAGTACAATGCACAGACATA -s simHuman_chr6.simHuman.chr6 516163 16 + 601863 ATTATGAAGTACAATG---------- -s simRat_chr6.simRat.chr6 557961 26 + 647215 TAAGTAAAGTAGACTGCACAGGAACA - -a -s simMouse_chr6.simMouse.chr6 545769 51 + 636262 AGCCGAATATATGTGGATAACAGGCTCCCAGGTACCGTTGGTCTGGAATTA -s Anc0.Anc0refChr3 148627 51 + 222631 AGTTGAACCGAAATGGAAAACAGTCTTACAAATATAATTGGCTCGGAATTG -s Anc1.Anc1refChr6 184302 51 + 197743 AGTTGAACCGAAATGGAAAACAGTCTTACAAATATAATTGGCTCGGAATTG -s Anc2.Anc2refChr1 62365 51 + 142988 AATTGAACTGAAATAGAAAACTGTCTTACAAATATAATTGGCTCGGAATTG -s mr.mrrefChr3 95989 51 + 181027 AGTCGAACATATGTGGATAACAGGCTCCCAGGTACAGTTGGCCTGGAATTA -s simCow_chr6.simCow.chr6 520384 51 + 602619 AATTGAATAGAAATAGAAAACTGTCTGCCAGATAAGATTGGCTTGGAATTA -s simDog_chr6.simDog.chr6 509026 51 + 593897 AATCGAACTAAAATAGAAAACTGTCTTACAAATATAATTGGCTCGGAATTG -s simHuman_chr6.simHuman.chr6 8128 22 + 601863 AGTTGAGCCGAAATGGAAAACA----------------------------- -s simHuman_chr6.simHuman.chr6 516179 22 + 601863 AGTTGAACCGAAATGGAATACG----------------------------- -s simRat_chr6.simRat.chr6 557996 51 + 647215 AGTCAAACATACTAGGATAACAGGCTCCCAGATACAGTTGGCCTGGAATTG - -a -s simMouse_chr6.simMouse.chr6 545820 7 + 636262 GATTAAT -s Anc0.Anc0refChr3 148678 7 + 222631 TACTAGT -s Anc1.Anc1refChr6 184353 7 + 197743 TACTAGT -s Anc2.Anc2refChr1 62416 7 + 142988 TACTAGT -s mr.mrrefChr3 96040 7 + 181027 GATTAAT -s simCow_chr6.simCow.chr6 520435 7 + 602619 CACCATT -s simDog_chr6.simDog.chr6 509081 7 + 593897 TACTAGT -s simRat_chr6.simRat.chr6 558047 7 + 647215 GAGTAAC - -a -s simMouse_chr6.simMouse.chr6 545827 20 + 636262 GAGACCCAATATTTTGAGTG -s Anc0.Anc0refChr3 148690 17 + 222631 GGGAC---ATATTACAGGTG -s Anc1.Anc1refChr6 184365 17 + 197743 GGGAC---ATATTACAGGTG -s Anc2.Anc2refChr1 62496 17 + 142988 GGGAC---ATATTACAGGTG -s mr.mrrefChr3 96047 20 + 181027 GAGACCCAATATTTTGAGTG -s simCow_chr6.simCow.chr6 520515 14 + 602619 T---C---ATTTTTCAGGTG -s simDog_chr6.simDog.chr6 509161 17 + 593897 AGGAC---ATATAACAGGTG -s simHuman_chr6.simHuman.chr6 8155 16 + 601863 GGGAT---ATATT-CAGGTG -s simHuman_chr6.simHuman.chr6 516206 16 + 601863 GGGAT---ATGTT-CAGGTG -s simRat_chr6.simRat.chr6 558054 20 + 647215 TACACCCAATATTTTGGGTG - -a -s simMouse_chr6.simMouse.chr6 545847 9 + 636262 CTAAGATTA -s Anc0.Anc0refChr3 148711 9 + 222631 ATAACATAA -s Anc1.Anc1refChr6 184386 9 + 197743 ATAACATAA -s Anc2.Anc2refChr1 62517 9 + 142988 ATAACATAA -s mr.mrrefChr3 96067 9 + 181027 CTAAGATTA -s simCow_chr6.simCow.chr6 520533 9 + 602619 AAAACGTAA -s simDog_chr6.simDog.chr6 509182 9 + 593897 ATAAGATGA -s simHuman_chr6.simHuman.chr6 8175 9 + 601863 ATAACACAA -s simHuman_chr6.simHuman.chr6 516226 9 + 601863 ATAACACAA -s simRat_chr6.simRat.chr6 558074 9 + 647215 CTAGGATCA - -a -s simMouse_chr6.simMouse.chr6 545856 92 + 636262 CCTGGTCAGTTAGCCAGTATAACACAGATGTTTTTCAAGTGATACACGTTCATTAGCGACGTTTCTGACCATAATGCACCACTAGTAGGGAG -s Anc0.Anc0refChr3 148720 92 + 222631 CATGGACAGTTTGCTAATGTTACACAGACACATTACTAGTGTTACATAATCCATAGTGAAAGTTCTCACCATGATGTGCCACTAGTAGGGAG -s Anc1.Anc1refChr6 184395 92 + 197743 CATGGACAGTTTGCTAATGTTACACAGACACATTACTAGTGTTACATAATCCATAGTGAAAGTTCTCACCATGATGTGCCACTAGTAGGGAG -s Anc2.Anc2refChr1 62526 92 + 142988 CATGGACAATTTGCTAATGTTACACAGACAAATTGCTAGTGTTACACAATCCATAGTGTAAGTTCTCACCATGATGTGCCACTAGTAGGCAG -s mr.mrrefChr3 96076 92 + 181027 CCTGGTCAGTTAGCCAGTATAACACAGATGTTTTTCAAGTGATACATGTTCATTAGCGACATTTCTGACCATAATGCACCACTAGTAGGGAG -s simCow_chr6.simCow.chr6 520556 83 + 602619 CATTGAGAACCTCGTAGTGTAGTATAGACAAATTGATAGTGTTACACAGTCTATAGTGTAAGTTCTCAACAAGGTGTGCC---------CAG -s simDog_chr6.simDog.chr6 509191 92 + 593897 TTTGGACAATTTGCTAATGTTACACAGACAAATTGCTAGTGTCATGCAATCCATAATGTAAGTTCTCACTATGATGTGCCACTAGTGGGCAG -s simHuman_chr6.simHuman.chr6 8184 90 + 601863 CATGGACAGTTTGCT--TGTTACACAGACACATTATTGGTGTTACATAATCCACAGTGAAAGGTCTCACCATGATGTGCAGCTAGTAGGGTG -s simHuman_chr6.simHuman.chr6 516235 90 + 601863 CATGGACAGGTTGCT--TGTTACACAGACACTTCACTGGTGTTACATAATTTATAGTGAAAGGTCTCACCATGGTGCGCAACTAGTAGGGCG -s simRat_chr6.simRat.chr6 558083 92 + 647215 CCTGGTCGGTTAGTCAGTATGACACAGATGTTTTTCAAGTGGTACATGTTCATTAGCAACATTTCCGACTGTAATGCACTACCAGTAGGGAG - -a -s simMouse_chr6.simMouse.chr6 545948 14 + 636262 ATTAGAATGGAGTT -s Anc0.Anc0refChr3 148815 14 + 222631 ATAAGAAGGCAGTC -s Anc1.Anc1refChr6 184490 14 + 197743 ATAAGAAGGCAGTC -s Anc2.Anc2refChr1 62621 14 + 142988 ATAAGAAGACAGTC -s mr.mrrefChr3 96171 14 + 181027 ATTAGAATGGAGTT -s simCow_chr6.simCow.chr6 520642 14 + 602619 ATCAGAAGCCAGAC -s simDog_chr6.simDog.chr6 509286 14 + 593897 ATAAGAATACAGTC -s simHuman_chr6.simHuman.chr6 516328 14 + 601863 ATAAGTAGGTAGTC -s simRat_chr6.simRat.chr6 558178 11 + 647215 ATTAGAATAGA--- - -a -s simMouse_chr6.simMouse.chr6 545962 30 + 636262 CATCAGTATCTTAGCTACAGCGAAGCGATC -s Anc0.Anc0refChr3 148943 29 + 222631 CAGCTGCATATTGGCTACTG-GGAGTGGTC -s Anc1.Anc1refChr6 184618 29 + 197743 CAGCTGCATATTGGCTACTG-GGAGTGGTC -s Anc2.Anc2refChr1 62768 29 + 142988 CAGCTGCATATTGGTTACTG-AGAGTGGTT -s mr.mrrefChr3 96185 30 + 181027 CATCAGTATCTTAGCTACAGCGAAGCGATC -s simCow_chr6.simCow.chr6 520788 27 + 602619 --GCTGCGTATTGGTTCCTG-AGAGTGGTT -s simDog_chr6.simDog.chr6 509434 29 + 593897 CAGCTGCACATTGATTACTG-AGAATGAGT -s simHuman_chr6.simHuman.chr6 516457 29 + 601863 CAGCCGCATGTTGGCTACTG-GGTGTGGTC -s simRat_chr6.simRat.chr6 20785 10 - 647215 --------------------CACAGGAATC - -a -s simMouse_chr6.simMouse.chr6 545992 27 + 636262 AAGATACCAAACTTGCCCTGATTAAAA -s Anc0.Anc0refChr3 148972 27 + 222631 ACAACACCAAACTTGTCCTGATTCAAG -s Anc1.Anc1refChr6 184647 27 + 197743 ACAACACCAAACTTGTCCTGATTCAAG -s Anc2.Anc2refChr1 62797 27 + 142988 ACAACACCAAACTTGTCCCAATTCAAG -s mr.mrrefChr3 96215 27 + 181027 AAGATACCAAACTTGCCCTGATTAAAA -s simCow_chr6.simCow.chr6 520816 26 + 602619 AAAACACCAAACTTGTCCCAACT-AAG -s simDog_chr6.simDog.chr6 509463 27 + 593897 GCACCACCAAACTTGTCCCAATTCAAG -s simHuman_chr6.simHuman.chr6 516486 26 + 601863 ACAACACCAAGCCTGGCCTG-TTGAAG -s simRat_chr6.simRat.chr6 20795 27 - 647215 AGGATACCAAGCTTGTCTAGATTAATA - -a -s simMouse_chr6.simMouse.chr6 546019 19 + 636262 TTAACTTCAGAGGGTGGCA -s Anc0.Anc0refChr3 148999 19 + 222631 CCAACATTGTAAGGTGACA -s Anc1.Anc1refChr6 184674 19 + 197743 CCAACATTGTAAGGTGACA -s Anc2.Anc2refChr1 62824 19 + 142988 CCAACATTGTAAGGTGACA -s mr.mrrefChr3 96242 19 + 181027 TTAACTTCAGAGGGTGGCA -s simCow_chr6.simCow.chr6 520842 19 + 602619 TCAACTTTGTAGGGTGACA -s simDog_chr6.simDog.chr6 509490 19 + 593897 CCAACACTGTAAGGTGACA -s simHuman_chr6.simHuman.chr6 516512 19 + 601863 CCAACATTGTAAGGTGACA -s simRat_chr6.simRat.chr6 20828 19 - 647215 TAGATTTGAGCAGGTGGCA - -a -s simMouse_chr6.simMouse.chr6 546038 13 + 636262 TTACAGTATCATG -s Anc0.Anc0refChr3 149018 13 + 222631 TTATAATGTCTTG -s Anc1.Anc1refChr6 184693 13 + 197743 TTATAATGTCTTG -s Anc2.Anc2refChr1 62843 13 + 142988 TTATAATGTCTTG -s mr.mrrefChr3 96261 13 + 181027 TTACAGTATCATG -s simCow_chr6.simCow.chr6 520861 13 + 602619 CTATAGTGTCTTA -s simDog_chr6.simDog.chr6 509509 13 + 593897 TTATGATGTCTTG -s simHuman_chr6.simHuman.chr6 516531 12 + 601863 TTATAATCTTGT- -s simRat_chr6.simRat.chr6 20850 13 - 647215 TAAATTTGTCAAG - -a -s simMouse_chr6.simMouse.chr6 546051 1 + 636262 A -s Anc0.Anc0refChr3 149031 1 + 222631 A -s Anc1.Anc1refChr6 184706 1 + 197743 A -s Anc2.Anc2refChr1 62856 1 + 142988 A -s mr.mrrefChr3 96274 1 + 181027 A -s simCow_chr6.simCow.chr6 520874 1 + 602619 A -s simDog_chr6.simDog.chr6 509523 1 + 593897 A -s simRat_chr6.simRat.chr6 20863 1 - 647215 A - -a -s simMouse_chr6.simMouse.chr6 546052 11 + 636262 GTCACTTGTAT -s Anc0.Anc0refChr3 149032 4 + 222631 -CCAC------ -s Anc1.Anc1refChr6 184707 4 + 197743 -CCAC------ -s Anc2.Anc2refChr1 62857 4 + 142988 -CCAC------ -s mr.mrrefChr3 96275 5 + 181027 GTCAC------ -s simCow_chr6.simCow.chr6 520875 4 + 602619 -GAAC------ -s simDog_chr6.simDog.chr6 509524 4 + 593897 -CCAC------ -s simRat_chr6.simRat.chr6 20866 5 - 647215 GTCTC------ - -a -s simMouse_chr6.simMouse.chr6 546063 5 + 636262 ACTAT -s Anc0.Anc0refChr3 149036 5 + 222631 ACTAT -s Anc1.Anc1refChr6 184711 5 + 197743 ACTAT -s Anc2.Anc2refChr1 62865 5 + 142988 ACTAT -s mr.mrrefChr3 96280 5 + 181027 ACTAT -s simCow_chr6.simCow.chr6 520883 5 + 602619 ACTAT -s simDog_chr6.simDog.chr6 509532 5 + 593897 ACTAT -s simHuman_chr6.simHuman.chr6 516543 5 + 601863 ACTAT -s simRat_chr6.simRat.chr6 20871 5 - 647215 ACCAT - -a -s simMouse_chr6.simMouse.chr6 546068 17 + 636262 AGTGATTATTTACCCAC -s Anc0.Anc0refChr3 149041 7 + 222631 AGTCCTT---------- -s Anc1.Anc1refChr6 184716 7 + 197743 AGTCCTT---------- -s Anc2.Anc2refChr1 62870 7 + 142988 ATTCCTT---------- -s mr.mrrefChr3 96285 15 + 181027 AGTGATTAT--ACCCAC -s simCow_chr6.simCow.chr6 520888 7 + 602619 ATTCCCT---------- -s simDog_chr6.simDog.chr6 509537 7 + 593897 ATTCCTT---------- -s simHuman_chr6.simHuman.chr6 516548 7 + 601863 AGTCCTT---------- -s simRat_chr6.simRat.chr6 20879 15 - 647215 AGTGGGTGC--AAACAC - -a -s simMouse_chr6.simMouse.chr6 546085 20 + 636262 TAGAGCTAGCTAAAAAAAAA -s Anc0.Anc0refChr3 149179 18 + 222631 TAAAACTAGCCAAAACAA-- -s Anc1.Anc1refChr6 184854 20 + 197743 TAAAACTAGCCAAAACAAAA -s Anc2.Anc2refChr1 63010 18 + 142988 TAAAACTAGCCAAAACAA-- -s mr.mrrefChr3 96300 20 + 181027 TAGAGCTAGCTAAAAAAAAA -s simCow_chr6.simCow.chr6 521149 18 + 602619 TAAAACCAGCCAAATCAA-- -s simDog_chr6.simDog.chr6 509687 18 + 593897 TAGAACTAGTCAAAAACA-- -s simHuman_chr6.simHuman.chr6 516806 20 + 601863 TAAAACTAGCCATAACAAAA -s simRat_chr6.simRat.chr6 20894 20 - 647215 TAGAGCTAGCTGAAAAAAAA - -a -s simMouse_chr6.simMouse.chr6 546105 28 + 636262 GCTATAGTGGCAAACGCCTTTGTTGAAA -s Anc0.Anc0refChr3 149197 6 + 222631 -CTATGG--------------------- -s Anc1.Anc1refChr6 184874 7 + 197743 GCTATGG--------------------- -s Anc2.Anc2refChr1 63028 6 + 142988 -CTATGA--------------------- -s mr.mrrefChr3 96320 7 + 181027 GCTATAG--------------------- -s simCow_chr6.simCow.chr6 521172 6 + 602619 -CTATAA--------------------- -s simDog_chr6.simDog.chr6 509705 6 + 593897 -CCATGA--------------------- -s simHuman_chr6.simHuman.chr6 516906 7 + 601863 GATATGG--------------------- -s simRat_chr6.simRat.chr6 20914 7 - 647215 GCTATAA--------------------- - -a -s simMouse_chr6.simMouse.chr6 546133 95 + 636262 AGACCAAGTGAGTGCTACTGGGAGATGTGAGTTGCCTTTACTCTCTTATCAGAAATAGAGCCATGGGAGGGCTATTGGGTATCTGCGGCAGTGGC -s Anc0.Anc0refChr3 149203 7 + 222631 TGAGCAA---------------------------------------------------------------------------------------- -s Anc1.Anc1refChr6 184881 7 + 197743 TGAGCAA---------------------------------------------------------------------------------------- -s Anc2.Anc2refChr1 63034 7 + 142988 TGAGCAA---------------------------------------------------------------------------------------- -s mr.mrrefChr3 96327 95 + 181027 AGACCAAGTGAGTGCTACTGGGAGATGTGAGTTGCCTTTACTCTCTTATCAGAAATAGAGCCATGGGAGGGCTATTGGGTATCTGCGGCAGTGGC -s simCow_chr6.simCow.chr6 521178 7 + 602619 TGAGCAA---------------------------------------------------------------------------------------- -s simDog_chr6.simDog.chr6 509711 7 + 593897 TGCGCAA---------------------------------------------------------------------------------------- -s simHuman_chr6.simHuman.chr6 516913 7 + 601863 TGAGCAA---------------------------------------------------------------------------------------- -s simRat_chr6.simRat.chr6 626188 95 + 647215 AGACTAGATGTGTTCTACTGGGAGATGTGAGTTGCCTTTACTCTCCTATCAGAAATAGAGCCATGGGAAGGCTGCTGGATATTGGCGGATATGGC - -a -s simMouse_chr6.simMouse.chr6 546228 2 + 636262 TT -s mr.mrrefChr3 96422 2 + 181027 TT -s simRat_chr6.simRat.chr6 21134 2 - 647215 TT -s simRat_chr6.simRat.chr6 21027 2 - 647215 TT - -a -s simMouse_chr6.simMouse.chr6 546230 66 + 636262 GCTAGTTGCATGGCCTCTGGCCAATAAGTGAGCAACAATCGAGTAAAGTTAATTAATGAGAATAAC -s mr.mrrefChr3 96434 66 + 181027 GCTTGTAGCATGCCCTCTGGCCAGTAAGCAAGCAACAATAAAGTGGAGTCAATTAATGAGAATAAC -s simRat_chr6.simRat.chr6 21146 66 - 647215 GCTTGTAGCATGCCCTCTGGTCAGTAAGCAAGCAACAATAAAGTGGAGTCAATTAATGAGAATAAC -s simRat_chr6.simRat.chr6 21039 66 - 647215 GGTTGTAGCATGCCCTCTGGCCAGTAAGCAAGCAACAATAAAGTGGAGTCAATTAATGAGAATAAC - -a -s simMouse_chr6.simMouse.chr6 546296 98 + 636262 TGTGTAATGCCTGTGTATTGTGGATGGTTCTCTTAGGTTGGCCAGTCTTCTACAACAGTTTGGATGCCTCTGACCAGGGGCTTTCTGATTTCTGACCA -s mr.mrrefChr3 96512 95 + 181027 TGTGTACTGCCTGTGTATTGTGGATGGTTCTCTTAGGTTGGCCAGTCTTCTACAACAGTTTGGATGCCTCTGACCAGGGGCTTT---ATTTCTGACCA -s simRat_chr6.simRat.chr6 21224 95 - 647215 TGTGTACTGCCTGTGTATTGTGGATAATACTCATAGGTAGGCCAGTCGTCTACAACGGTTTGGACCCCTATGACTAGGGGCCCT---ATTTCATGCTA -s simRat_chr6.simRat.chr6 21117 16 - 647215 TGTGTACTGCCTGTGT---------------------------------------------------------------------------------- - -a -s simMouse_chr6.simMouse.chr6 546394 41 + 636262 GGGGACTGTATTACTAATAATTGGGTCTCAACAAGCAGCAA -s mr.mrrefChr3 96607 41 + 181027 GGGGACTGTATTACTAATAATTGGGTCTCAACAAGCAGCAA -s simRat_chr6.simRat.chr6 21324 41 - 647215 AGTGGTCAGATTACCAATAATTAGGTCTCAACAATCACCAA - -a -s simMouse_chr6.simMouse.chr6 546435 46 + 636262 CGTCAAAGAAGTTGGCAGTGGGTCATTTGAAACTTATGCAGTAGCA -s mr.mrrefChr3 96648 46 + 181027 CGTCAAAGAAGTTGGCAGTGGGTCATTTGAAACTTATGCAGTAGCA -s simRat_chr6.simRat.chr6 21374 46 - 647215 CGTTAAAGAGGTTGGCATTGATTCATTTGAAAGCTTTGCATTAGGA - -a -s simMouse_chr6.simMouse.chr6 546481 14 + 636262 ATGAGTCAACAGAA -s mr.mrrefChr3 96694 14 + 181027 ATGAGTCAACAGAA -s simRat_chr6.simRat.chr6 21421 14 - 647215 ATGACTCAACAGAA - -a -s simMouse_chr6.simMouse.chr6 546495 270 + 636262 TGCTCAAGGAATTGGAGCCTCTTAGTTGCCCTTTCTACTCCACCCAGTCCACCCAATCTGCTGCTTGAAAACTTGATTCTACATCCTTGAAAAGGCTTGCTTTAAGTTTTTCATTTGCCCCCCATCTTATGATCTTAGACACGTTTTCCTCCCACCTGTCTGTACAGGAGGTCTTACAAAAAACTCCATGTGAATGTCTTGTCAAAGTTTTGCCTTAGGACCTCAGGGAAATTGATCTCTGAGTGTGAGTGTGATGTTTCGTTAGATTAG -s Anc0.Anc0refChr3 149210 38 + 222631 ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ACCCC--TAAAATTGATCCATGAGAATG-----------TTGTTAAATTAA -s Anc1.Anc1refChr6 184888 38 + 197743 ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ACCCC--TAAAATTGATCCATGAGAATG-----------TTGTTAAATTAA -s Anc2.Anc2refChr1 63041 38 + 142988 ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ACCCC--TAAAACTGATTCATGAGAATG-----------TTGTTAAATTAA -s mr.mrrefChr3 96708 263 + 181027 TGCTCAAGGAATTGGAGCCTCTTAGTTGCCCTTTCTACTCCACCCAGTCCACCCAATCTGCTGCTTGAAAACTTGATTCTACATCCTTGAAAAGGCTT----TAAGTTTTTCATTTGCCCCCCATCTTATGATCTTAGACACGTTTTCCTCCCACCTGTCTGTACAGGAGGTCTTACAAAAAACTCCATG--AATGTCTTGTCAAAGTTTTGCCT-AGGACCTCAGGGAAATTGATCTCTGAGTGTGAGTGTGATGTTTTGTTAGATTAG -s simCow_chr6.simCow.chr6 521185 38 + 602619 ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ACCCC--ATAAAGATACTTATGAGATTG-----------GGGTTAGATTAA -s simDog_chr6.simDog.chr6 509718 36 + 593897 -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CCT--TAAAACTGATTCATGAGAATG-----------TTGTTAAATTAA -s simHuman_chr6.simHuman.chr6 516920 38 + 601863 ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ACCCC--CAAAATTAATCCACGAGAATG-----------TTGTGAAATCAA -s simRat_chr6.simRat.chr6 21438 263 - 647215 TGCTCAAGGGACTGGAGTGCCTTAGGTGCCCTTTCTAGTCCACCTGGGCCACCGAAACTGCTGCTCAAAAACTTGAATCTACATCTTTGAGAAAGCTT----TAAGTTTTCCATCTGACCCTCGCCATATGATCTTTGACAGGTTTTCCTTCCACCGGTCTGTAAAGGAGCTCTTACAGAAAAGTCCAGG--AAAGTATTGTCAAAGTTTTGCAT-AGGACCTCAGGGAAATTGATCTCTGAGAGTTAGTGCTATGTTTTGTTAGATTAG - -a -s simMouse_chr6.simMouse.chr6 546765 18 + 636262 TTTAGGGTAGTTGAAAAT -s Anc0.Anc0refChr3 149288 18 + 222631 TTTGAGGCAGGCCTAAAT -s Anc1.Anc1refChr6 184966 18 + 197743 TTTGAGGCAGGCCTAAAT -s Anc2.Anc2refChr1 63119 18 + 142988 TTTGAGGCAGGCCTAAAC -s mr.mrrefChr3 96971 18 + 181027 TTTGGGGCAGTTGAAAAT -s simCow_chr6.simCow.chr6 521264 17 + 602619 -TTGAGGCAAGCCTAAGC -s simDog_chr6.simDog.chr6 509780 17 + 593897 TTTGAGGCAGGCCTGAA- -s simHuman_chr6.simHuman.chr6 517011 18 + 601863 TTTGAGGCAGGCATAAAT -s simRat_chr6.simRat.chr6 21701 9 - 647215 TTTGGGGCA--------- - -a -s simMouse_chr6.simMouse.chr6 546783 42 + 636262 GAAAGGGCTTGCCCAGCTTATTTATTTCATATCTTTCAATTC -s Anc0.Anc0refChr3 149309 28 + 222631 GAAAGGGCCTACCCAGC--------------TCTTTCAGCTC -s Anc1.Anc1refChr6 184987 41 + 197743 GAAAGGGCCTACCCAGCTGGCT-GTTCCATTTCTTTCAGCTC -s Anc2.Anc2refChr1 63140 28 + 142988 GAAAGTGCCTACCCAGC--------------GCTTCCAGCTC -s mr.mrrefChr3 96989 42 + 181027 GAAAGGGCCTGCCCAGCTTATTTATTTCATATCTTTCAATTC -s simCow_chr6.simCow.chr6 521284 22 + 602619 GAAAGTGTTTACCTAGC--------------ACTTC------ -s simDog_chr6.simDog.chr6 509797 21 + 593897 -------CCAACCCATC--------------GCTTCCAGCTC -s simHuman_chr6.simHuman.chr6 517032 41 + 601863 GAGGGGGCCTACCCTGCTGGCT-GTTCCATTTCATTCAGCTC -s simRat_chr6.simRat.chr6 21710 39 - 647215 ---AGTGTCTGCCCAGCATATTTATTTCATATCTTTTGATTC - -a -s simMouse_chr6.simMouse.chr6 546825 9 + 636262 TTTGGGTTA -s Anc0.Anc0refChr3 149348 9 + 222631 TTAAAGTTA -s Anc1.Anc1refChr6 185039 9 + 197743 TTAAAGTTA -s Anc2.Anc2refChr1 63179 9 + 142988 TTAAAGTTA -s mr.mrrefChr3 97031 9 + 181027 TTTGGGTTA -s simCow_chr6.simCow.chr6 521310 9 + 602619 TTCATGTTA -s simDog_chr6.simDog.chr6 509833 9 + 593897 TTAGAGTCA -s simHuman_chr6.simHuman.chr6 517084 9 + 601863 TTGAAGTTA -s simRat_chr6.simRat.chr6 21749 9 - 647215 TTTGGGTTA - -a -s simMouse_chr6.simMouse.chr6 546834 8 + 636262 AGAAACTT -s Anc0.Anc0refChr3 149383 8 + 222631 AGAAAATT -s Anc1.Anc1refChr6 185074 8 + 197743 AGAAAATT -s Anc2.Anc2refChr1 63214 8 + 142988 AGGAAATT -s mr.mrrefChr3 97040 8 + 181027 AGAAACTT -s simCow_chr6.simCow.chr6 521341 8 + 602619 AGGAATTT -s simDog_chr6.simDog.chr6 509877 8 + 593897 AGGAAATT -s simHuman_chr6.simHuman.chr6 517119 8 + 601863 AGAAAATG -s simRat_chr6.simRat.chr6 21758 8 - 647215 AGGAACTT - -a -s simMouse_chr6.simMouse.chr6 546842 21 + 636262 AATCATTAACCACTAAGAGGT -s Anc0.Anc0refChr3 149391 21 + 222631 AAGCATTAACCACTAAGAAGT -s Anc1.Anc1refChr6 185082 21 + 197743 AAGCATTAACCACTAAGAAGT -s Anc2.Anc2refChr1 63222 21 + 142988 AATCATTAACCACTAACAAGT -s mr.mrrefChr3 97048 21 + 181027 AAGCATTAACCACTAAGAGGT -s simCow_chr6.simCow.chr6 521349 17 + 602619 CTTCATTAACCAC----AAGT -s simDog_chr6.simDog.chr6 509885 21 + 593897 AATCATTAAATACTAACATGT -s simHuman_chr6.simHuman.chr6 517127 21 + 601863 AAGCATTAACCATTAAGCAGT -s simRat_chr6.simRat.chr6 21787 21 - 647215 AAGTGCTAACCACTCAGAGGT - -a -s simMouse_chr6.simMouse.chr6 546863 34 + 636262 AAAGTGGTAAAACCAGTGTTTTGAGGAAAGCAAT -s Anc0.Anc0refChr3 149417 34 + 222631 AAAGATGTAGAACCAACATTTGGATGCAAGCAAC -s Anc1.Anc1refChr6 185108 34 + 197743 AAAGATGTAGAACCAACATTTGGATGCAAGCAAC -s Anc2.Anc2refChr1 63248 34 + 142988 AAATATGTGGAGCCAACATTTGGATGCAAGCAAC -s mr.mrrefChr3 97069 34 + 181027 AAAGTGGTAAAACCAGTGTTTTGAGGAAAGCAAT -s simCow_chr6.simCow.chr6 521371 34 + 602619 AATTATGTGGAGCCAACACTTGGATGCAAGAACC -s simDog_chr6.simDog.chr6 509911 34 + 593897 AAATATGTGGGGCTAACATTTGGATGAAAGCAAT -s simHuman_chr6.simHuman.chr6 517153 34 + 601863 AAAGATGTAGAACCAACTTTTGGATGCAAGCAAC -s simRat_chr6.simRat.chr6 21808 34 - 647215 AAAGTGATAAAACCAGTGTTTTGAGGAAAGCGAT - -a -s simMouse_chr6.simMouse.chr6 546897 19 + 636262 GTCACTAGGAAATATAATG -s Anc0.Anc0refChr3 149451 19 + 222631 TTTACTAGGAAGAATAATG -s Anc1.Anc1refChr6 185142 19 + 197743 TTTACTAGGAAGAATAATG -s Anc2.Anc2refChr1 63283 19 + 142988 TTTACTAGGAAGAATAATG -s mr.mrrefChr3 97103 19 + 181027 GTTACTAGGAAATATAATG -s simCow_chr6.simCow.chr6 521406 19 + 602619 CTTACTAGGAAGAAGAATG -s simDog_chr6.simDog.chr6 509946 19 + 593897 TTTGCTCGGAAGGATAATG -s simHuman_chr6.simHuman.chr6 517187 19 + 601863 ATTACTAGGAGCAACTATG -s simRat_chr6.simRat.chr6 21842 19 - 647215 GTTATTAGATAACATAATG - -a -s simMouse_chr6.simMouse.chr6 546916 14 + 636262 GATAAGAGACAACC -s Anc0.Anc0refChr3 149471 14 + 222631 GATAAAAGATCACT -s Anc1.Anc1refChr6 185162 14 + 197743 GATAAAAGATCACT -s Anc2.Anc2refChr1 63303 14 + 142988 GATAAAAGATCACT -s mr.mrrefChr3 97123 14 + 181027 GATAAAAGACAACC -s simCow_chr6.simCow.chr6 521426 13 + 602619 GA-AAAAGATCACC -s simDog_chr6.simDog.chr6 509966 14 + 593897 GATAAGAGATCACT -s simHuman_chr6.simHuman.chr6 517207 14 + 601863 GACAAAGGATCGCT -s simRat_chr6.simRat.chr6 21862 14 - 647215 GATAAAAGACAACC - -a -s simMouse_chr6.simMouse.chr6 546930 14 + 636262 TTTATATTTCTTGT -s Anc0.Anc0refChr3 149485 14 + 222631 TTTTTATTTGTTTG -s Anc1.Anc1refChr6 185176 14 + 197743 TTTTTATTTGTTTG -s Anc2.Anc2refChr1 63317 14 + 142988 TTTTTATTTGTTTG -s mr.mrrefChr3 97137 14 + 181027 TTTATATTTCTTGT -s simCow_chr6.simCow.chr6 521439 14 + 602619 TCTTTATTTGTTTG -s simDog_chr6.simDog.chr6 509980 14 + 593897 TTTTTATTTAATTG -s simHuman_chr6.simHuman.chr6 517221 14 + 601863 TGTTTATTTGTTTG -s simRat_chr6.simRat.chr6 21883 14 - 647215 TTTATATCTCTTGT - -a -s simMouse_chr6.simMouse.chr6 546944 48 + 636262 CTTGTATACCAGCTACATATTCTTAAATGTTCTGACTGGCATTGGGGG -s Anc0.Anc0refChr3 149499 48 + 222631 CTTCTATACCAGCTAAGTATTCTAAAATGTTCAGACTGCCACTGGGGG -s Anc1.Anc1refChr6 185190 48 + 197743 CTTCTATACCAGCTAAGTATTCTAAAATGTTCAGACTGCCACTGGGGG -s Anc2.Anc2refChr1 63332 48 + 142988 CTTCTAAACCAGCTAAGTATTCTAAGATGTTAAGACTGCCACTGGGGG -s mr.mrrefChr3 97151 48 + 181027 CTTGTATACCAGCTACATATTCTAAAATGTTCTGACTGGCATTGGGGG -s simCow_chr6.simCow.chr6 521454 48 + 602619 CTTCTAGACAACCTAAGTATTCTAAGATGTTAAGACTGGCACTGGGGA -s simDog_chr6.simDog.chr6 509995 48 + 593897 CTTCTAACCCAGCTAGGGATTCTGAGTTGTTAAGACTGCCTCTGGGGG -s simHuman_chr6.simHuman.chr6 517235 48 + 601863 CTTCTATACCAGGTAAGTATTCTAAAATGTCCAGACTGTCACTGGGGA -s simRat_chr6.simRat.chr6 21897 45 - 647215 CTTGGATACCAGCTCCATATTCTAAAATGTTCTG---GGCATTGGGGG - -a -s simMouse_chr6.simMouse.chr6 546992 25 + 636262 CCTTCTTGAGGTACCACAAAAAAAA -s Anc0.Anc0refChr3 149547 17 + 222631 CCTATTAAGTGAATAT--------A -s Anc1.Anc1refChr6 185238 17 + 197743 CCTATTAAGTGAATAT--------A -s Anc2.Anc2refChr1 63398 17 + 142988 CACATTAAGTTAATAT--------A -s mr.mrrefChr3 97199 17 + 181027 CCTTCTTGAGGTACCT--------A -s simCow_chr6.simCow.chr6 521521 12 + 602619 CA-----AGTTAACGT--------A -s simDog_chr6.simDog.chr6 510061 17 + 593897 CACATTAAGTTAATAT--------A -s simHuman_chr6.simHuman.chr6 517283 16 + 601863 CCTATTAATTGAATAT--------- -s simRat_chr6.simRat.chr6 21942 17 - 647215 CCCTCTTGAGGTACCT--------A - -a -s simMouse_chr6.simMouse.chr6 547017 26 + 636262 ACATCCCTTGGTGCAAAATCAATACG -s Anc0.Anc0refChr3 149564 26 + 222631 ACGTCCCTTGTGGGAAAGGCTATAGG -s Anc1.Anc1refChr6 185255 26 + 197743 ACGTCCCTTGTGGGAAAGGCTATAGG -s Anc2.Anc2refChr1 63418 26 + 142988 ACGTCCCTGGTGGGGAAGGCTATAGG -s mr.mrrefChr3 97216 26 + 181027 ACATCCCTTGTTGCAAAATCAATACG -s simCow_chr6.simCow.chr6 521536 24 + 602619 ATATCCCTAG--GGGAAGGCTATATA -s simDog_chr6.simDog.chr6 510081 26 + 593897 ACGTCCCTGGTGCGGAAGGCTATAGG -s simHuman_chr6.simHuman.chr6 517299 23 + 601863 ---TCCCTTGTCGGAAAGGCTATAAG -s simRat_chr6.simRat.chr6 21959 26 - 647215 ACATCCCTTGTTGTAAAATCAATATG - -a -s simMouse_chr6.simMouse.chr6 547043 1 + 636262 G -s Anc0.Anc0refChr3 149590 1 + 222631 G -s Anc1.Anc1refChr6 185281 1 + 197743 G -s Anc2.Anc2refChr1 63444 1 + 142988 G -s mr.mrrefChr3 97242 1 + 181027 G -s simCow_chr6.simCow.chr6 521560 1 + 602619 G -s simDog_chr6.simDog.chr6 510107 1 + 593897 G -s simHuman_chr6.simHuman.chr6 517329 1 + 601863 G -s simRat_chr6.simRat.chr6 21985 1 - 647215 G - -a -s simMouse_chr6.simMouse.chr6 547044 29 + 636262 CTAATGATACCGTAAACTCATTACCATTT -s Anc0.Anc0refChr3 149591 29 + 222631 TTGGTAATACAGTCAACCTATTACCACCA -s Anc1.Anc1refChr6 185282 29 + 197743 TTGGTAATACAGTCAACCTATTACCACCA -s Anc2.Anc2refChr1 63446 29 + 142988 TTGGTAATATAGTCAACCTATCACCACCC -s mr.mrrefChr3 97243 29 + 181027 CTGGTGATACAGTAAACCCATTACCATTA -s simCow_chr6.simCow.chr6 521562 28 + 602619 C-AGCACTATAGTCAACTTATCACCACCC -s simDog_chr6.simDog.chr6 510109 19 + 593897 TTGATCATATAGTCAATCT---------- -s simHuman_chr6.simHuman.chr6 517330 29 + 601863 TTGGTAATACAGTCAACCTACTACCACCA -s simRat_chr6.simRat.chr6 21986 29 - 647215 CTGGTGATACAGTATACCCATTACCATTA - -a -s simMouse_chr6.simMouse.chr6 547073 11 + 636262 GTAGTGACAAA -s Anc0.Anc0refChr3 149620 11 + 222631 GTTCTCCCAAC -s Anc1.Anc1refChr6 185311 11 + 197743 GTTCTCCCAAC -s Anc2.Anc2refChr1 63475 11 + 142988 ATTCTCCTAAC -s mr.mrrefChr3 97272 11 + 181027 GTAGTGCCAAA -s simCow_chr6.simCow.chr6 521593 11 + 602619 ATTCTCCTAAC -s simHuman_chr6.simHuman.chr6 517359 11 + 601863 GTGCGCCCAGC -s simRat_chr6.simRat.chr6 22015 10 - 647215 GTAT-GCCAAA - -a -s simMouse_chr6.simMouse.chr6 547084 5 + 636262 CTCCT -s Anc0.Anc0refChr3 149631 5 + 222631 CTCCC -s Anc1.Anc1refChr6 185322 5 + 197743 CTCCC -s Anc2.Anc2refChr1 63486 5 + 142988 TTCCC -s mr.mrrefChr3 97283 5 + 181027 CTCCT -s simCow_chr6.simCow.chr6 521607 5 + 602619 TTCCC -s simHuman_chr6.simHuman.chr6 517370 5 + 601863 CTCCC -s simRat_chr6.simRat.chr6 22025 5 - 647215 TTCCT - -a -s simMouse_chr6.simMouse.chr6 547089 20 + 636262 CCTGCCCTGGTCTAGTATGC -s Anc0.Anc0refChr3 149636 17 + 222631 CCTACTCTGCTCTTGTA--- -s Anc1.Anc1refChr6 185327 17 + 197743 CCTACTCTGCTCTTGTA--- -s Anc2.Anc2refChr1 63491 17 + 142988 CCTACTCTGCTCTTGGA--- -s mr.mrrefChr3 97288 20 + 181027 CCTGCCCTGGTCTAGTATGC -s simCow_chr6.simCow.chr6 521634 17 + 602619 CCTACTCCACTCTTGGA--- -s simDog_chr6.simDog.chr6 510128 9 + 593897 ----CTCTGCTCT------- -s simHuman_chr6.simHuman.chr6 517375 17 + 601863 TCTACGCTGCTCTTGTG--- -s simRat_chr6.simRat.chr6 22030 20 - 647215 CCTGCCCTGGTGTACTATGC - -a -s simMouse_chr6.simMouse.chr6 547109 83 + 636262 CTGTATAAATAGCAGTAATACATAAAGGATACTTCTGCCAATGTCAGTGTCTGTCACTGCTTGACACATTATATGTGTGTGCA -s Anc0.Anc0refChr3 149653 83 + 222631 CAGTGTATACAGTGGCAGTACATACCAGATACTTTTGTCAGTGTAATAGTCTTTCACAACTTGCTGCATTATATGCATGAGCA -s Anc1.Anc1refChr6 185344 83 + 197743 CAGTGTATACAGTGGCAGTACATACCAGATACTTTTGTCAGTGTAATAGTCTTTCACAACTTGCTGCATTATATGCATGAGCA -s Anc2.Anc2refChr1 63508 83 + 142988 CAGGGGATACAGTGGCAGTACATACCATATACTTTTGTCAGTGTACTAGTCTTTCACAACTTGCTGCATTATATGCATGAGCA -s mr.mrrefChr3 97308 83 + 181027 CTGTATAAATAGTAGTAGTACATAACAGATACTTTTGTCAATGTCAGTGTCTGTCACTGCTTGACACATTATATGTGTGTGCA -s simCow_chr6.simCow.chr6 521654 83 + 602619 CAGGAGATACAGTGGCAATACATACCATATCCTTTGATTAGCGTACTAGTCTTCCACAACTTGCTGCATTAAATGCCTGAGCA -s simDog_chr6.simDog.chr6 510137 81 + 593897 --GGGGAAGCAGTGGCAGGACATACCATTTACTTTTGTCAGTCTACGGGTCTTTCACAACTTGCTGTACTATATGCATGAGCA -s simHuman_chr6.simHuman.chr6 517392 83 + 601863 CAGTGTATACAGTGGCAGTACATGTCAGATACTTTTCTCAGTGATATAGTCTTTCACAACTTGGTGCATTATATACATGCACA -s simRat_chr6.simRat.chr6 22050 83 - 647215 CTGTATACATAGTAGTAGTACATAACAGATACTTTTGTCAATGTCAGGGTCTATCACTGCTGGCCACATTATAAGTGTGTGCA - -a -s simMouse_chr6.simMouse.chr6 547192 1 + 636262 G -s Anc0.Anc0refChr3 149736 1 + 222631 G -s Anc1.Anc1refChr6 185427 1 + 197743 G -s Anc2.Anc2refChr1 63598 1 + 142988 G -s mr.mrrefChr3 97391 1 + 181027 G -s simCow_chr6.simCow.chr6 521744 1 + 602619 G -s simDog_chr6.simDog.chr6 510225 1 + 593897 G -s simHuman_chr6.simHuman.chr6 517475 1 + 601863 G -s simRat_chr6.simRat.chr6 22133 1 - 647215 G - -a -s simMouse_chr6.simMouse.chr6 547193 116 + 636262 TGCCCTCAGCAGCCATTATGCCACGTATGTTTAGCCTAATATTGTAAACCCTTCTGATTTGTATTAACCATCAGTGGCCGTTTTTCATTTGCCGCCTTTTTTTGTGTAATGAGACT -s Anc0.Anc0refChr3 149761 103 + 222631 TGTACACAGAACCCATTAAGCTACATTGGTTGAGCATAGTAGTGTAAACTCCTCTGGTTGGCATTTACCATCAGTGGT-GTTTTTCATTAGTCACCTTTTTTT------------T -s Anc1.Anc1refChr6 185452 104 + 197743 TGTACACAGAACCCATTAAGCTACATTGGTTGAGCATAGTAGTGTAAACTCCTCTGGTTGGCATTTACCATCAGTGGTGGTTTTTCATTAGTCACCTTTTTTT------------T -s Anc2.Anc2refChr1 63623 103 + 142988 TGTATACAGAACCCATTGAGCTACATTGGTTGAAGATAGCAGTGAAAACTTCTCTAACTGGCACATTCCATCAGTGGT-GCTTGTAATTAGTCAGCTTTTTTT------------T -s mr.mrrefChr3 97392 116 + 181027 TGCCCTCAGCAGCCATTATGCCACATTGGTTTAGCCTAATATTGTAAACCCTTCTGGTTTGTATTAACCATCAGTGGCCGTTTTTCATTTGCCGCCTTTTTTTGTGTATTGATAGT -s simCow_chr6.simCow.chr6 521777 103 + 602619 CGCATGTAGAACCCATTGTGCCACACTGCTTGAAGATAGCAGTGAAAACTTCTCTAACTGGCACATTCCATCAGTGGT-GCTTGTAATTAGTCCACTTTTTTT------------T -s simDog_chr6.simDog.chr6 510243 49 + 593897 TTTATACAAGACCCACTGAGCTGTATAGGCTG-------------------------------------------------------TAAGTCAGCTTTTTTT------------T -s simHuman_chr6.simHuman.chr6 517500 104 + 601863 TGTACCCAGAACCCATCACTATACATTGGTTGGGCATAGTACTGTAAACACCTCTGGTTGGCATTTACTATTAGTGGTGGTTATTCATTAGTCACGTTTATAG------------C -s simRat_chr6.simRat.chr6 22134 115 - 647215 TGCTCTCAGCAGCCATTATGCCACATTGGTTTAGCCTAAT-TTCTAAACCCGTCTGGTTTGTATTAACCATCAGTGGCTAATTTTCACTTGCTGCCTTTTTTTTTGCATTGGTAGT - -a -s simMouse_chr6.simMouse.chr6 547309 17 + 636262 TAGTGGAATGTATTGTT -s Anc0.Anc0refChr3 149864 17 + 222631 TAGCAGAACTGATAGTC -s Anc1.Anc1refChr6 185556 17 + 197743 TAGCAGAACTGATAGTC -s Anc2.Anc2refChr1 63726 17 + 142988 TGTCAAAGCTGATAGTC -s mr.mrrefChr3 97508 17 + 181027 TAGCGGAATTTATTGTT -s simCow_chr6.simCow.chr6 521881 17 + 602619 TTTTGATTTTGATAGTT -s simDog_chr6.simDog.chr6 510292 17 + 593897 TGTCAAAGCTGATAGTC -s simHuman_chr6.simHuman.chr6 517604 17 + 601863 TAGCAGAAGTGATGGTC -s simRat_chr6.simRat.chr6 22249 17 - 647215 TAGCGGTACTTATTGTT - -a -s simMouse_chr6.simMouse.chr6 547326 120 + 636262 CTATTGGCCGCAGGTCAGCGAAATAAAATCCCAGTGGCTGCTGGTTAGCAGAAGAAAGTTGACTTGGTTAATGAGTTGTAGCTGCTGGGCCACAGGCAAGGGAGGCATGACCATACTTGG -s Anc0.Anc0refChr3 149881 62 + 222631 CCAATAGCTGTAGATCAGCAGAATAGAAGCAC----GCTGGAGTCAAACAGGTGACAG---ACTCGGG---------------------------------------------------A -s Anc1.Anc1refChr6 185573 62 + 197743 CCAATAGCTGTAGATCAGCAGAATAGAAGCAC----GCTGGAGTCAAACAGGTGACAG---ACTCGGG---------------------------------------------------A -s Anc2.Anc2refChr1 63743 62 + 142988 CCAATAGCTGTAGATCAGCAGAATAGAAGCAG----ACTGGGGTCAAACAGGTGACAG---ACTCGGG---------------------------------------------------A -s mr.mrrefChr3 97525 69 + 181027 CCATTAGCCGCAGGTCAGCGAAATAAAATCCCAGTGGCTGCAGGTTAGCAGAAGAAAGTTGACTCGGT---------------------------------------------------G -s simCow_chr6.simCow.chr6 521909 62 + 602619 CCAATAGCTGTAGGTCAGCAGAATAAAAGCTG----ATTGGGGTTAAACAGGTGACAG---ACTCAGG---------------------------------------------------A -s simDog_chr6.simDog.chr6 510309 57 + 593897 CTGATGGCTGTAAA---GCTGAATGGAGTCAG----ACAGG--TCAAACAGGTGGGAG---ACTTGGG---------------------------------------------------A -s simHuman_chr6.simHuman.chr6 517621 62 + 601863 CCAATAGCTGTGGATCAGCAGAATACAAGCGC----GCTGGAGTCAAACAGGTAACAG---ACTCTGG---------------------------------------------------A -s simRat_chr6.simRat.chr6 22266 69 - 647215 CCAGTAGCCGAAGGTCAGCGAAATAAAATCCCAGTGGCTGCAGGTCAGCAGAAGAAAGTAGACTCGGT---------------------------------------------------T - -a -s simMouse_chr6.simMouse.chr6 547446 69 + 636262 CCGAGTGGGCACAGCTAAAAGGTCTTTATCTAACTTTTGTGTTTCAAAGCTTGGGAGCTATGCTTGCCC -s Anc0.Anc0refChr3 149950 39 + 222631 T------------------------------CAGGTTCACATTTCTCTGCTTGGGAGCTGTGCTTGCCC -s Anc1.Anc1refChr6 185642 39 + 197743 T------------------------------CAGGTTCACATTTCTCTGCTTGGGAGCTGTGCTTGCCC -s Anc2.Anc2refChr1 63812 39 + 142988 T------------------------------CAGGTTCACATTTCTCTGCTTGGGAGCTGTGCTTGCCC -s mr.mrrefChr3 97594 39 + 181027 T------------------------------AAGTTTTGTATTTCTAAGCTTGGGAGCTATGCTTGCCC -s simCow_chr6.simCow.chr6 521976 39 + 602619 A------------------------------CAGGTTCATGTTTCTCAGCTTGGGAGCTGTCATTGCCC -s simDog_chr6.simDog.chr6 510373 39 + 593897 T------------------------------CAGGTTCACATTTCTCTGCTTGGCAGCTGTGCTTGCCA -s simHuman_chr6.simHuman.chr6 517690 39 + 601863 T------------------------------CAGGTTCACATTTCTCTGCTTGGGAGCTGTACTTGCCC -s simRat_chr6.simRat.chr6 22335 39 - 647215 T------------------------------AAGTTTTGTATTTCTTAGCGCGGGAGCTATTCTTGCCC - -a -s simMouse_chr6.simMouse.chr6 547515 1 + 636262 A -s Anc0.Anc0refChr3 149989 1 + 222631 A -s Anc1.Anc1refChr6 185681 1 + 197743 A -s Anc2.Anc2refChr1 63855 1 + 142988 A -s mr.mrrefChr3 97633 1 + 181027 A -s simDog_chr6.simDog.chr6 510416 1 + 593897 A -s simHuman_chr6.simHuman.chr6 517729 1 + 601863 A -s simRat_chr6.simRat.chr6 22374 1 - 647215 A - -a -s simMouse_chr6.simMouse.chr6 547516 36 + 636262 ATTTAAAGTTGTGTGGAGATTCTATTGATGCTAACC -s Anc0.Anc0refChr3 149990 36 + 222631 ATTTGAATTTATGTGGAGACTGCATTGATGTAAACA -s Anc1.Anc1refChr6 185682 36 + 197743 ATTTGAATTTATGTGGAGACTGCATTGATGTAAACA -s Anc2.Anc2refChr1 63856 36 + 142988 ATTTAAATTTGTGTGGAGACTGCATTGATATAAACA -s mr.mrrefChr3 97634 36 + 181027 ATTTGAATTTATGTGGAGATTCCATTGATGCTAACC -s simCow_chr6.simCow.chr6 522016 36 + 602619 ATTTAAATTTGTGTGGGAACTGCATTGACATAAACA -s simDog_chr6.simDog.chr6 510417 36 + 593897 ATTTAAATTTGTGGGGAGACTGCATTAATATAAACA -s simHuman_chr6.simHuman.chr6 517754 36 + 601863 ATTTGAATTTATGTGGAGAATGCAATGATGAAATCA -s simRat_chr6.simRat.chr6 22375 33 - 647215 ATTTGAATTTATGTGGAGATTCCATTGATGCTA--- - -a -s simMouse_chr6.simMouse.chr6 547552 29 + 636262 AGGAAACCTTAGAAGGAGCCTTAATGGCC -s Anc0.Anc0refChr3 150026 29 + 222631 GGAAAACCTTAGTAGGAGCCTTGCTGGCC -s Anc1.Anc1refChr6 185718 29 + 197743 GGAAAACCTTAGTAGGAGCCTTGCTGGCC -s Anc2.Anc2refChr1 63892 29 + 142988 GGAAAACCTTAGTTGGAACCTTGCTGGCC -s mr.mrrefChr3 97670 29 + 181027 AGGAAACCTTAGAAGGAGCCTTAATGGCC -s simCow_chr6.simCow.chr6 522053 29 + 602619 GAAAAACCTTAGTGGGAATGTTGCTGGCC -s simDog_chr6.simDog.chr6 510453 29 + 593897 GGAAAACCTTATTTGGCACCTTACTGGCT -s simHuman_chr6.simHuman.chr6 517790 29 + 601863 GGAAGACCTTAGCAGGAGCCCTGCTGGCC -s simRat_chr6.simRat.chr6 22408 3 - 647215 --------------------------GCC - -a -s simMouse_chr6.simMouse.chr6 547581 12 + 636262 ACAACACTGCAA -s Anc0.Anc0refChr3 150055 11 + 222631 ACAACACCTC-A -s Anc1.Anc1refChr6 185747 12 + 197743 ACAACACCTCAA -s Anc2.Anc2refChr1 63923 11 + 142988 AAAATGCCTC-A -s mr.mrrefChr3 97699 12 + 181027 ACAACACCTCAA -s simCow_chr6.simCow.chr6 522084 11 + 602619 AAGATGCCTC-A -s simDog_chr6.simDog.chr6 510484 11 + 593897 AAAATGCCTC-A -s simHuman_chr6.simHuman.chr6 517819 12 + 601863 ACAACACCTCAA -s simRat_chr6.simRat.chr6 22411 12 - 647215 ACAACACCTCAA - -a -s simMouse_chr6.simMouse.chr6 547593 18 + 636262 TCAACTCTAAAACCAAAT -s Anc0.Anc0refChr3 150066 13 + 222631 TCAACCCTAAAAC----- -s Anc1.Anc1refChr6 185759 13 + 197743 TCAACCCTAAAAC----- -s Anc2.Anc2refChr1 63934 13 + 142988 TAAACCCTAAAAC----- -s mr.mrrefChr3 97711 18 + 181027 TCAACTCTAAAACCAAAT -s simCow_chr6.simCow.chr6 522096 13 + 602619 TAACCTCTAAAAC----- -s simDog_chr6.simDog.chr6 510495 13 + 593897 TAAACCCTAAAAC----- -s simHuman_chr6.simHuman.chr6 517831 5 + 601863 TCAAC------------- -s simRat_chr6.simRat.chr6 22423 18 - 647215 TCAACTCTAAAACTGAAT - -a -s simMouse_chr6.simMouse.chr6 547611 16 + 636262 TCATCATTGATGGGTC -s Anc0.Anc0refChr3 150079 11 + 222631 TCATCACTGG-----C -s Anc1.Anc1refChr6 185772 11 + 197743 TCATCACTGG-----C -s Anc2.Anc2refChr1 63947 11 + 142988 TCATCACTGG-----C -s mr.mrrefChr3 97729 16 + 181027 TCATCATTGATGGGTC -s simCow_chr6.simCow.chr6 522109 10 + 602619 -CATCATTGA-----C -s simDog_chr6.simDog.chr6 510513 11 + 593897 TCATCACTGG-----T -s simHuman_chr6.simHuman.chr6 517836 6 + 601863 -----ACTGG-----C -s simRat_chr6.simRat.chr6 22441 16 - 647215 TCATCATTGATGGGTC - -a -s simMouse_chr6.simMouse.chr6 547627 27 + 636262 TTGCTGATGTTAGGTTTTATGATGTTG -s Anc0.Anc0refChr3 150090 20 + 222631 TTTC-------AGTTTTTATGATGTTG -s Anc1.Anc1refChr6 185783 20 + 197743 TTTC-------AGTTTTTATGATGTTG -s Anc2.Anc2refChr1 63962 20 + 142988 TTTT-------AGTTTTTATGATATTG -s mr.mrrefChr3 97745 27 + 181027 TTTCTGATGTTAGGTTTTATGATGTTG -s simCow_chr6.simCow.chr6 522124 20 + 602619 TTTT-------AGTTTTTATGACACTG -s simDog_chr6.simDog.chr6 510528 20 + 593897 TTTT-------AGCTTATATAATATTG -s simHuman_chr6.simHuman.chr6 517842 20 + 601863 TTTC-------AGTTCTTATGATGTTG -s simRat_chr6.simRat.chr6 22457 27 - 647215 TTTCTGGTGTTGAGTTTTATGATGTTG - -a -s simMouse_chr6.simMouse.chr6 547654 19 + 636262 CTCATGAATTTTTGTGAGT -s Anc0.Anc0refChr3 150110 19 + 222631 CATGTGATTTTGTGTGAGC -s Anc1.Anc1refChr6 185803 19 + 197743 CATGTGATTTTGTGTGAGC -s Anc2.Anc2refChr1 63982 19 + 142988 CATGTGATTTTGTGTGTGC -s mr.mrrefChr3 97772 19 + 181027 CTCATGATTTTTTGTGAGC -s simCow_chr6.simCow.chr6 522144 11 + 602619 CATATGATTTT-------- -s simDog_chr6.simDog.chr6 510548 19 + 593897 CATGTGATTTTGTGTGTGC -s simHuman_chr6.simHuman.chr6 517862 19 + 601863 CATGTGATTTTATGTGAGC -s simRat_chr6.simRat.chr6 22485 19 - 647215 CGCATGATTTTTTGTGAGC - -a -s simMouse_chr6.simMouse.chr6 547673 9 + 636262 TCAACCTCA -s Anc0.Anc0refChr3 150130 9 + 222631 TCAACCTCA -s Anc1.Anc1refChr6 185823 9 + 197743 TCAACCTCA -s Anc2.Anc2refChr1 64002 9 + 142988 TCATCCTCA -s mr.mrrefChr3 97792 9 + 181027 TCAACCTCA -s simCow_chr6.simCow.chr6 522155 4 + 602619 ---TCCT-- -s simDog_chr6.simDog.chr6 510568 9 + 593897 TCATCCTCA -s simHuman_chr6.simHuman.chr6 517882 9 + 601863 TCAACCTCA -s simRat_chr6.simRat.chr6 22505 9 - 647215 TCAACCTCA - -a -s simMouse_chr6.simMouse.chr6 547682 17 + 636262 TGCATAACACATTGGTT -s Anc0.Anc0refChr3 150139 17 + 222631 TGGGTTTAGGATTGATT -s Anc1.Anc1refChr6 185832 17 + 197743 TGGGTTTAGGATTGATT -s Anc2.Anc2refChr1 64012 17 + 142988 TGGGTTTAGGATTGATT -s mr.mrrefChr3 97801 17 + 181027 TGGGTAACACATTGATT -s simCow_chr6.simCow.chr6 522159 17 + 602619 TGGGTTTAGGATTGGTT -s simDog_chr6.simDog.chr6 510579 17 + 593897 TGGGTTTAGGGTTGATT -s simHuman_chr6.simHuman.chr6 517891 17 + 601863 AGGGTTTGGGATTGAGT -s simRat_chr6.simRat.chr6 22514 17 - 647215 TGGGTGAAACATTGATT - -a -s simMouse_chr6.simMouse.chr6 547699 14 + 636262 GCATGCAGAGCTTG -s Anc0.Anc0refChr3 150156 14 + 222631 GCATGCAGAGCTTG -s Anc1.Anc1refChr6 185849 14 + 197743 GCATGCAGAGCTTG -s Anc2.Anc2refChr1 64029 14 + 142988 GCATGTAGAGCTTG -s mr.mrrefChr3 97818 14 + 181027 GCATGCAGAGCTTG -s simCow_chr6.simCow.chr6 522176 14 + 602619 GCATGAAGAGCATG -s simDog_chr6.simDog.chr6 510596 14 + 593897 GCATATAGAGCTTC -s simHuman_chr6.simHuman.chr6 517918 14 + 601863 GCATGCAGAGCTTG -s simRat_chr6.simRat.chr6 22531 14 - 647215 GCATGCAGAGCTTG - -a -s simMouse_chr6.simMouse.chr6 547713 23 + 636262 GCCAGAATTAGAACGCTTGTTTT -s Anc0.Anc0refChr3 150170 20 + 222631 TGCAGGGTTAAAACCCTT---TC -s Anc1.Anc1refChr6 185863 20 + 197743 TGCAGGGTTAAAACCCTT---TC -s Anc2.Anc2refChr1 64043 20 + 142988 TGCAGGGCTAAAACCCTT---TC -s mr.mrrefChr3 97832 23 + 181027 GCCAGAATTAGAACGCTTGTTTT -s simCow_chr6.simCow.chr6 522190 12 + 602619 TACAGGGCTTAA----------- -s simDog_chr6.simDog.chr6 510610 20 + 593897 TGCAGAGCTAACACCCTT---TC -s simHuman_chr6.simHuman.chr6 517935 20 + 601863 AGCAGGGTTAAAACCCTC---TC -s simRat_chr6.simRat.chr6 22545 23 - 647215 GCCAAAATTAGAACACTTGTTTT - -a -s simMouse_chr6.simMouse.chr6 547736 14 + 636262 GTACAATCCACTGT -s Anc0.Anc0refChr3 150190 13 + 222631 GT-CAATTCTTTCT -s Anc1.Anc1refChr6 185883 13 + 197743 GT-CAATTCTTTCT -s Anc2.Anc2refChr1 64063 13 + 142988 GC-CAATTCTTTCT -s mr.mrrefChr3 97855 14 + 181027 GTACAATCCACTCT -s simCow_chr6.simCow.chr6 522202 8 + 602619 ------TTCTTTGT -s simDog_chr6.simDog.chr6 510631 13 + 593897 GC-CAAATCTCTCT -s simHuman_chr6.simHuman.chr6 517955 13 + 601863 GT-CAGTTCTTTCT -s simRat_chr6.simRat.chr6 22568 14 - 647215 GTACCATCCACTCT - -a -s simMouse_chr6.simMouse.chr6 547750 54 + 636262 ACATTCATTTTGAGGGAACTGAGCCTTACTATTGTCCACTAAACATAATTAGCC -s Anc0.Anc0refChr3 150203 53 + 222631 CTATTTATTTTGA-AGAATTGAGCCTTCCTATTCTGGTTTCAACATAACTTACT -s Anc1.Anc1refChr6 185896 53 + 197743 CTATTTATTTTGA-AGAATTGAGCCTTCCTATTCTGGTTTCAACATAACTTACT -s Anc2.Anc2refChr1 64076 53 + 142988 CTATTTGTTTTGA-AGAATTGAGCCTTCCAATTCTGGTTTCAACATAACTTACT -s mr.mrrefChr3 97869 54 + 181027 ACATTCATTTTGAGAGAATTGAGCCTTACTATTCTCCATTAAACATAATTAGCC -s simCow_chr6.simCow.chr6 522211 53 + 602619 CAATTTGTTTTGA-AGCATTGGGACTTCCCATTCTGATCTAGATGTAATTTACA -s simDog_chr6.simDog.chr6 510644 53 + 593897 TTTTTTGTTTTGA-AGAATTGAACCTTTCAATTCTGGTTTCAACATAACTTACT -s simHuman_chr6.simHuman.chr6 517968 53 + 601863 CTATTTATTTTCA-AGAATTGAGCTTCCCTATTCTTGTTCGCACATAGGGTATG -s simRat_chr6.simRat.chr6 22582 52 - 647215 ACATTCATTTTGAGAGAATCTAG--TAGCTATTCTCCATTAAATATAATTAGCT - -a -s simMouse_chr6.simMouse.chr6 547804 24 + 636262 CAACCTTATTAAACAGCAGCCTGT -s Anc0.Anc0refChr3 150259 23 + 222631 CATCCCCATTAGACAG-AGCCTCC -s Anc1.Anc1refChr6 185952 23 + 197743 CATCCCCATTAGACAG-AGCCTCC -s Anc2.Anc2refChr1 64132 23 + 142988 CATCCCCATTAGACAG-AGCCTCC -s mr.mrrefChr3 97926 24 + 181027 CAACCTTATTAAACAGCAGCCTGT -s simCow_chr6.simCow.chr6 522267 23 + 602619 CAGTCCTAATAGACAG-AGCCTCC -s simDog_chr6.simDog.chr6 510700 22 + 593897 GATCCTC-TGAGAAAG-AGCCTCT -s simHuman_chr6.simHuman.chr6 518024 23 + 601863 CACCTCCATTAGACAG-ACCCTCC -s simRat_chr6.simRat.chr6 22637 24 - 647215 CAACCTTACTAAACAGCAGCCTAT - -a -s simMouse_chr6.simMouse.chr6 547828 1 + 636262 A -s Anc0.Anc0refChr3 150282 1 + 222631 G -s Anc1.Anc1refChr6 185975 1 + 197743 G -s Anc2.Anc2refChr1 64155 1 + 142988 G -s mr.mrrefChr3 97950 1 + 181027 G -s simCow_chr6.simCow.chr6 522290 1 + 602619 A -s simDog_chr6.simDog.chr6 510722 1 + 593897 G -s simHuman_chr6.simHuman.chr6 518049 1 + 601863 G -s simRat_chr6.simRat.chr6 22661 1 - 647215 G - -a -s simMouse_chr6.simMouse.chr6 547829 20 + 636262 CACTGTCTTATACATGTATT -s Anc0.Anc0refChr3 150283 20 + 222631 CGCTGTATTGTATATGTATT -s Anc1.Anc1refChr6 185976 20 + 197743 CGCTGTATTGTATATGTATT -s Anc2.Anc2refChr1 64158 20 + 142988 AGCTGTATTGTATATGTATT -s mr.mrrefChr3 97951 20 + 181027 CACTGTCTTATACATGTATT -s simCow_chr6.simCow.chr6 522293 19 + 602619 AG-TGTACAGTATATGGATT -s simDog_chr6.simDog.chr6 510723 19 + 593897 -GCGGCGTTATATATGTATT -s simHuman_chr6.simHuman.chr6 518050 20 + 601863 CGCTGTAATGTATATGTATT -s simRat_chr6.simRat.chr6 22662 20 - 647215 CACTGTCTCATAGATGTACT - -a -s simMouse_chr6.simMouse.chr6 547849 10 + 636262 TAGGTGCCAC -s Anc0.Anc0refChr3 150304 10 + 222631 TTGGTGCCAT -s Anc1.Anc1refChr6 185997 10 + 197743 TTGGTGCCAT -s Anc2.Anc2refChr1 64179 10 + 142988 TTGGTGCAAT -s mr.mrrefChr3 97972 10 + 181027 TAGGTGCCAC -s simCow_chr6.simCow.chr6 522313 10 + 602619 TTGGTGTTTT -s simDog_chr6.simDog.chr6 510743 10 + 593897 TTGGTGCAAT -s simHuman_chr6.simHuman.chr6 518071 10 + 601863 TTGGTCCCAT -s simRat_chr6.simRat.chr6 22683 10 - 647215 TAGGTGCTAC - -a -s simMouse_chr6.simMouse.chr6 547859 2 + 636262 AT -s Anc0.Anc0refChr3 150315 2 + 222631 AT -s Anc1.Anc1refChr6 186008 2 + 197743 AT -s Anc2.Anc2refChr1 64190 2 + 142988 AT -s mr.mrrefChr3 97982 2 + 181027 AT -s simCow_chr6.simCow.chr6 522324 2 + 602619 GC -s simDog_chr6.simDog.chr6 510754 2 + 593897 AT -s simHuman_chr6.simHuman.chr6 518082 2 + 601863 AT -s simRat_chr6.simRat.chr6 22693 2 - 647215 AC - -a -s simMouse_chr6.simMouse.chr6 547861 1 + 636262 C -s Anc0.Anc0refChr3 150317 1 + 222631 C -s Anc1.Anc1refChr6 186010 1 + 197743 C -s Anc2.Anc2refChr1 64192 1 + 142988 C -s mr.mrrefChr3 97984 1 + 181027 C -s simCow_chr6.simCow.chr6 522326 1 + 602619 C -s simDog_chr6.simDog.chr6 510758 1 + 593897 C -s simHuman_chr6.simHuman.chr6 518084 1 + 601863 C -s simRat_chr6.simRat.chr6 22695 1 - 647215 C - -a -s simMouse_chr6.simMouse.chr6 547862 1 + 636262 A -s Anc0.Anc0refChr3 150318 1 + 222631 A -s Anc1.Anc1refChr6 186011 1 + 197743 A -s Anc2.Anc2refChr1 64194 1 + 142988 A -s mr.mrrefChr3 97985 1 + 181027 A -s simCow_chr6.simCow.chr6 522328 1 + 602619 A -s simDog_chr6.simDog.chr6 510760 1 + 593897 A -s simHuman_chr6.simHuman.chr6 518085 1 + 601863 A -s simRat_chr6.simRat.chr6 22696 1 - 647215 A - -a -s simMouse_chr6.simMouse.chr6 547863 21 + 636262 TTTGCGGGTAACCCTTATTGT -s Anc0.Anc0refChr3 150319 12 + 222631 TGATCCAGTTAT--------- -s Anc1.Anc1refChr6 186012 12 + 197743 TGATCCAGTTAT--------- -s Anc2.Anc2refChr1 64195 12 + 142988 TGATCCAAATAT--------- -s mr.mrrefChr3 97986 12 + 181027 TTAGCCAGTAAC--------- -s simCow_chr6.simCow.chr6 522329 8 + 602619 TGAACCAA------------- -s simDog_chr6.simDog.chr6 510761 12 + 593897 TGATCCAAATAT--------- -s simHuman_chr6.simHuman.chr6 518088 12 + 601863 TGATCCAGTTAT--------- -s simRat_chr6.simRat.chr6 22697 12 - 647215 TTAGCCAGTAAC--------- - -a -s simMouse_chr6.simMouse.chr6 547884 3 + 636262 CTA -s Anc0.Anc0refChr3 150331 3 + 222631 TTA -s Anc1.Anc1refChr6 186024 3 + 197743 TTA -s Anc2.Anc2refChr1 64207 3 + 142988 CTA -s mr.mrrefChr3 97998 3 + 181027 TTA -s simDog_chr6.simDog.chr6 510775 3 + 593897 CTA -s simHuman_chr6.simHuman.chr6 518100 3 + 601863 TTA -s simRat_chr6.simRat.chr6 22709 3 - 647215 TTA - -a -s simMouse_chr6.simMouse.chr6 547887 4 + 636262 CCGG -s Anc0.Anc0refChr3 150334 3 + 222631 CCA- -s Anc1.Anc1refChr6 186027 3 + 197743 CCA- -s Anc2.Anc2refChr1 64210 3 + 142988 CCA- -s mr.mrrefChr3 98001 4 + 181027 CCAG -s simDog_chr6.simDog.chr6 510778 3 + 593897 CCA- -s simHuman_chr6.simHuman.chr6 518103 3 + 601863 CCA- -s simRat_chr6.simRat.chr6 22720 4 - 647215 CCAG - -a -s simMouse_chr6.simMouse.chr6 547891 41 + 636262 TGTTAATGATATTGCCACGTGGTATCCTGATATCACACACA -s Anc0.Anc0refChr3 150337 34 + 222631 TACTATTGGTATAGCCA-------TAGCAATATCACAACTA -s Anc1.Anc1refChr6 186030 34 + 197743 TACTATTGGTATAGCCA-------TAGCAATATCACAACTA -s Anc2.Anc2refChr1 64213 34 + 142988 TACTATTGGCATAGCCA-------TAGCAATATCACAACTA -s mr.mrrefChr3 98005 41 + 181027 TGTTAATGATATTGCCACGTGGTATCCTGATATCACACATA -s simCow_chr6.simCow.chr6 522337 29 + 602619 --TTATTGGCATAGCCA-------TA-CAAT--CATAGCCA -s simDog_chr6.simDog.chr6 510782 34 + 593897 TACTATTGGCATAGCCA-------CAGCAATATCACAACTA -s simHuman_chr6.simHuman.chr6 518106 34 + 601863 TACTATTAGTGCAACCA-------TAGCAATACCTCAACTA -s simRat_chr6.simRat.chr6 22724 40 - 647215 TGTTAGTGATATAGCCAGGTGA-ATCATGATATCACACATA - -a -s simMouse_chr6.simMouse.chr6 547932 7 + 636262 CCACACT -s Anc0.Anc0refChr3 150372 7 + 222631 CCACATT -s Anc1.Anc1refChr6 186065 7 + 197743 CCACATT -s Anc2.Anc2refChr1 64248 7 + 142988 CCACATT -s mr.mrrefChr3 98046 7 + 181027 CCACACT -s simCow_chr6.simCow.chr6 522367 7 + 602619 CCACGTA -s simDog_chr6.simDog.chr6 510817 7 + 593897 CCACATT -s simHuman_chr6.simHuman.chr6 518141 2 + 601863 CC----- -s simRat_chr6.simRat.chr6 22764 7 - 647215 CCACACC - -a -s simMouse_chr6.simMouse.chr6 547939 20 + 636262 GCACACCTGAATGGCAATAA -s Anc0.Anc0refChr3 150384 20 + 222631 GCATATCTGAATCGGCTCAA -s Anc1.Anc1refChr6 186077 20 + 197743 GCATATCTGAATCGGCTCAA -s Anc2.Anc2refChr1 64260 20 + 142988 TCATATCTGAATCAGCTCAA -s mr.mrrefChr3 98053 20 + 181027 GCATACCTGAATGGCAACAA -s simCow_chr6.simCow.chr6 522379 20 + 602619 ACATATCTGAATCAGCTCAC -s simDog_chr6.simDog.chr6 510829 20 + 593897 TCATATTTGAATCAGATCAA -s simHuman_chr6.simHuman.chr6 518148 20 + 601863 GCATATCTGAATTGGCTCAA -s simRat_chr6.simRat.chr6 22771 20 - 647215 ACATACCTGAATGGCAACAC - -a -s simMouse_chr6.simMouse.chr6 547959 5 + 636262 AGATC -s Anc0.Anc0refChr3 150409 5 + 222631 AGACC -s Anc1.Anc1refChr6 186102 5 + 197743 AGACC -s Anc2.Anc2refChr1 64285 5 + 142988 AGACC -s mr.mrrefChr3 98073 5 + 181027 AGATC -s simCow_chr6.simCow.chr6 522404 4 + 602619 AG-CA -s simDog_chr6.simDog.chr6 510854 5 + 593897 AGAAC -s simHuman_chr6.simHuman.chr6 518173 5 + 601863 AGACC -s simRat_chr6.simRat.chr6 22791 5 - 647215 AGATC - -a -s simMouse_chr6.simMouse.chr6 547964 29 + 636262 CCCACCCTCCAGAACATTTAAGCCAGTGG -s Anc0.Anc0refChr3 150414 29 + 222631 CCCAACCCCCTGTGCATTTAAGCCAGGGG -s Anc1.Anc1refChr6 186107 29 + 197743 CCCAACCCCCTGTGCATTTAAGCCAGGGG -s Anc2.Anc2refChr1 64290 29 + 142988 CCCAACCCCCTGTGCATTTAAGCCAGGGG -s mr.mrrefChr3 98078 29 + 181027 CCCACCCTCCAGAGCATTTAAGCCAGGGG -s simCow_chr6.simCow.chr6 522408 28 + 602619 CCCAACCCTCTATGC-TTTAAGCCAGGGG -s simDog_chr6.simDog.chr6 510863 29 + 593897 CCCATCCCCCTGAACATTTAAGCCAGGGG -s simHuman_chr6.simHuman.chr6 518178 29 + 601863 CCCAACCCCCTGTGCATCTAAGCCAGGGG -s simRat_chr6.simRat.chr6 22796 29 - 647215 ACAACTCTCGAGAGCATTTCAGCCGGGGG - -a -s simMouse_chr6.simMouse.chr6 547993 9 + 636262 GGCCTGGAC -s Anc0.Anc0refChr3 150445 9 + 222631 AGCATGGAT -s Anc1.Anc1refChr6 186138 9 + 197743 AGCATGGAT -s Anc2.Anc2refChr1 64321 9 + 142988 AGCATGGAT -s mr.mrrefChr3 98107 9 + 181027 GGCCTGGAC -s simCow_chr6.simCow.chr6 522438 9 + 602619 AGTACAGAT -s simDog_chr6.simDog.chr6 510894 9 + 593897 AGCATGGAT -s simHuman_chr6.simHuman.chr6 518209 9 + 601863 AGCATGGAT -s simRat_chr6.simRat.chr6 22825 9 - 647215 GGCCTGGTA - -a -s simMouse_chr6.simMouse.chr6 548002 6 + 636262 TGGAGG -s Anc0.Anc0refChr3 150454 6 + 222631 TTAGGA -s Anc1.Anc1refChr6 186147 6 + 197743 TTAGGA -s Anc2.Anc2refChr1 64330 6 + 142988 TTTGTT -s mr.mrrefChr3 98116 6 + 181027 TGAAGA -s simDog_chr6.simDog.chr6 510904 6 + 593897 TTTGTT -s simHuman_chr6.simHuman.chr6 518218 6 + 601863 TTAGGA -s simRat_chr6.simRat.chr6 22834 6 - 647215 TCAAGA - -a -s simMouse_chr6.simMouse.chr6 548008 5 + 636262 ATTAA -s Anc0.Anc0refChr3 150476 5 + 222631 TATAA -s Anc1.Anc1refChr6 186169 5 + 197743 TATAA -s Anc2.Anc2refChr1 64352 5 + 142988 TATAA -s mr.mrrefChr3 98122 5 + 181027 ATTAA -s simCow_chr6.simCow.chr6 522461 5 + 602619 CTCAT -s simDog_chr6.simDog.chr6 82158 5 - 593897 TATAA -s simHuman_chr6.simHuman.chr6 518240 5 + 601863 TGAAA -s simRat_chr6.simRat.chr6 22840 5 - 647215 ATTGA - -a -s simMouse_chr6.simMouse.chr6 548013 22 + 636262 GCACTTCAGGCTCACTGATTAT -s Anc0.Anc0refChr3 150481 22 + 222631 GAACTTCAGGCTTACTAATTAT -s Anc1.Anc1refChr6 186174 22 + 197743 GAACTTCAGGCTTACTAATTAT -s Anc2.Anc2refChr1 64357 22 + 142988 GACCTTCAGGCATACTAATTTT -s mr.mrrefChr3 98127 22 + 181027 GCACTTCAGGCTCACTGATTAT -s simCow_chr6.simCow.chr6 522466 22 + 602619 GACCCTCAAACCTACTAATTTT -s simDog_chr6.simDog.chr6 82163 22 - 593897 GCCCTCCAGGCATACTAACTTT -s simHuman_chr6.simHuman.chr6 518245 22 + 601863 GAACTTCAGGCTTACTAATTAT -s simRat_chr6.simRat.chr6 22870 22 - 647215 GTGCTTCAGGCTATCAGATTAT - -a -s simMouse_chr6.simMouse.chr6 548035 20 + 636262 TTAGGCTTGATTGATTATAT -s Anc0.Anc0refChr3 150509 20 + 222631 TTAAACTGGACTAATCATAC -s Anc1.Anc1refChr6 186202 20 + 197743 TTAAACTGGACTAATCATAC -s Anc2.Anc2refChr1 64385 20 + 142988 TTAAACTGGACTAATCATAC -s mr.mrrefChr3 98149 20 + 181027 TTAGACTTGATTAATCATAT -s simCow_chr6.simCow.chr6 522495 17 + 602619 TTAAACTGGACTAACCA--- -s simDog_chr6.simDog.chr6 82191 20 - 593897 TTAAACTACATTAATTATAC -s simHuman_chr6.simHuman.chr6 518273 20 + 601863 TTAAATTGGACTAATCATAC -s simRat_chr6.simRat.chr6 22892 20 - 647215 TCACACTTGATCAATCATAT - -a -s simMouse_chr6.simMouse.chr6 548055 7 + 636262 CCATCTG -s Anc0.Anc0refChr3 150573 7 + 222631 CCTTATG -s Anc1.Anc1refChr6 186266 7 + 197743 CCTTATG -s Anc2.Anc2refChr1 64449 7 + 142988 CCTTATG -s mr.mrrefChr3 98169 7 + 181027 CCATCTG -s simCow_chr6.simCow.chr6 522535 5 + 602619 CCTTA-- -s simDog_chr6.simDog.chr6 82309 7 - 593897 CCTTATG -s simHuman_chr6.simHuman.chr6 83310 7 - 601863 CCTTATG -s simRat_chr6.simRat.chr6 22912 7 - 647215 CCATATG - -a -s simMouse_chr6.simMouse.chr6 548062 17 + 636262 CAGTAAGCCAAATAACC -s Anc0.Anc0refChr3 150584 17 + 222631 CACAAGGCCCAACAGCC -s Anc1.Anc1refChr6 186277 17 + 197743 CACAAGGCCCAACAGCC -s Anc2.Anc2refChr1 64460 17 + 142988 CACAAGGCCCAACAGCC -s mr.mrrefChr3 98176 17 + 181027 CAGTAAGCCAAATAACC -s simCow_chr6.simCow.chr6 522544 15 + 602619 CACAAGGTTCATCA--C -s simDog_chr6.simDog.chr6 82319 17 - 593897 TACGGGGCCCAACAGCC -s simHuman_chr6.simHuman.chr6 83321 17 - 601863 CACAAGAACCACCAGCC -s simRat_chr6.simRat.chr6 22919 17 - 647215 CAGTAAATCAGATAACC - -a -s simMouse_chr6.simMouse.chr6 548079 19 + 636262 AAACTGCTCAATTGGCTGT -s Anc0.Anc0refChr3 150603 19 + 222631 AAGTGGTAGTAGCGACCGT -s Anc1.Anc1refChr6 186296 19 + 197743 AAGTGGTAGTAGCGACCGT -s Anc2.Anc2refChr1 64479 19 + 142988 AAGTGGTAGTAGCGACCGT -s mr.mrrefChr3 98193 19 + 181027 AAACTGCTCAATTGGCTGT -s simCow_chr6.simCow.chr6 522561 19 + 602619 AAATGGTAGTAGCGACCGA -s simDog_chr6.simDog.chr6 82338 19 - 593897 AAGTGATAGTAGCGATCGT -s simHuman_chr6.simHuman.chr6 83340 19 - 601863 AAGTAGTAGTCGAGACCGT -s simRat_chr6.simRat.chr6 22936 19 - 647215 AAACTGCTCAATTGGATGT - -a -s simMouse_chr6.simMouse.chr6 548098 14 + 636262 TTATTTACGTCCTG -s Anc0.Anc0refChr3 150622 14 + 222631 TTGATGTAGTCCTG -s Anc1.Anc1refChr6 186315 14 + 197743 TTGATGTAGTCCTG -s Anc2.Anc2refChr1 64498 14 + 142988 CTGATGTAGTCCTG -s mr.mrrefChr3 98212 14 + 181027 TTATTTACGTCCTG -s simCow_chr6.simCow.chr6 522580 14 + 602619 GTGATTTAGTCATG -s simDog_chr6.simDog.chr6 82357 14 - 593897 CTGATGTAGTCCTG -s simHuman_chr6.simHuman.chr6 83359 14 - 601863 TTGATCTATGCCTT -s simRat_chr6.simRat.chr6 22956 14 - 647215 TTATCTACGTCCCG - -a -s simMouse_chr6.simMouse.chr6 548112 24 + 636262 GGGTTCATGGCTAACTGCAATGCT -s Anc0.Anc0refChr3 150638 24 + 222631 GGCTTCGCAGCTAACTAGGTCGCT -s Anc1.Anc1refChr6 186331 24 + 197743 GGCTTCGCAGCTAACTAGGTCGCT -s Anc2.Anc2refChr1 64514 24 + 142988 GGCTTCGCAGCTAACTAGGTCGCT -s mr.mrrefChr3 98226 24 + 181027 GGGTTCATGGCTAACTGCAATGCT -s simCow_chr6.simCow.chr6 522596 24 + 602619 GGCTTCGCCGCTAACTAGATTGCT -s simDog_chr6.simDog.chr6 82373 24 - 593897 GGCTTCGCAGCTCACGAAGTCCCC -s simHuman_chr6.simHuman.chr6 83375 20 - 601863 GGCCTCGCAACTAACTA----GCT -s simRat_chr6.simRat.chr6 22970 24 - 647215 GGGTTCGCGGCTAAGTACAATGCT - -a -s simMouse_chr6.simMouse.chr6 548136 19 + 636262 CCAACATACCCCATTTTAA -s Anc0.Anc0refChr3 150674 19 + 222631 TAAACACGTTCCATTTTAA -s Anc1.Anc1refChr6 186367 19 + 197743 TAAACACGTTCCATTTTAA -s Anc2.Anc2refChr1 64551 19 + 142988 TAAACACGTTCCATTTTAA -s mr.mrrefChr3 98262 19 + 181027 CCAACATGCCCCATTTTAA -s simCow_chr6.simCow.chr6 522633 19 + 602619 TAAACACGTCCCATTGTAA -s simDog_chr6.simDog.chr6 82418 19 - 593897 GAAACATGTTCCATTTTAA -s simHuman_chr6.simHuman.chr6 83413 19 - 601863 TACACACATTCCATTTTAA -s simRat_chr6.simRat.chr6 23006 19 - 647215 TGAGCATGCCCCATTTTAA - -a -s simMouse_chr6.simMouse.chr6 548155 8 + 636262 CCCACAGT -s Anc0.Anc0refChr3 150696 8 + 222631 CAAACAGT -s Anc1.Anc1refChr6 186389 8 + 197743 CAAACAGT -s Anc2.Anc2refChr1 64573 8 + 142988 CAAACAGT -s mr.mrrefChr3 98284 8 + 181027 CCCACAGT -s simCow_chr6.simCow.chr6 522655 8 + 602619 CAAATAGT -s simDog_chr6.simDog.chr6 82440 8 - 593897 CAAACAGT -s simHuman_chr6.simHuman.chr6 83435 8 - 601863 CAAGCAGC -s simRat_chr6.simRat.chr6 23028 8 - 647215 CCCACAGT - -a -s simMouse_chr6.simMouse.chr6 548163 16 + 636262 TTACAAGCTCGAGTCC -s Anc0.Anc0refChr3 150705 16 + 222631 TTACAAGTTCGAGTGC -s Anc1.Anc1refChr6 186398 16 + 197743 TTACAAGTTCGAGTGC -s Anc2.Anc2refChr1 64582 16 + 142988 TTACAAGTTCGAGTGC -s mr.mrrefChr3 98292 16 + 181027 TTACAAGCTCGAGTCC -s simCow_chr6.simCow.chr6 522664 16 + 602619 TTACAGGCTCGAGTGA -s simDog_chr6.simDog.chr6 82449 16 - 593897 TTACAAGTCCGAGTGC -s simHuman_chr6.simHuman.chr6 83444 16 - 601863 TTACAAGTTCGAGTGC -s simRat_chr6.simRat.chr6 23036 14 - 647215 TTA--AGCTCGAGTCA - -a -s simMouse_chr6.simMouse.chr6 548179 2 + 636262 TC -s Anc0.Anc0refChr3 150723 2 + 222631 CT -s Anc1.Anc1refChr6 186416 2 + 197743 CT -s Anc2.Anc2refChr1 64600 2 + 142988 CT -s mr.mrrefChr3 98308 2 + 181027 TA -s simCow_chr6.simCow.chr6 522682 2 + 602619 CC -s simDog_chr6.simDog.chr6 82467 2 - 593897 CT -s simHuman_chr6.simHuman.chr6 83462 2 - 601863 CT -s simRat_chr6.simRat.chr6 23050 2 - 647215 TA - -a -s simMouse_chr6.simMouse.chr6 548181 14 + 636262 AACCCGGGAGTTAT -s Anc0.Anc0refChr3 150725 14 + 222631 AACACCAGAGTTAT -s Anc1.Anc1refChr6 186418 14 + 197743 AACACCAGAGTTAT -s Anc2.Anc2refChr1 64603 14 + 142988 AACACCAGAGTTAT -s mr.mrrefChr3 98310 14 + 181027 AACCCGGGAGTTAT -s simCow_chr6.simCow.chr6 522685 13 + 602619 AGAA-CAAAATTAG -s simDog_chr6.simDog.chr6 82470 14 - 593897 AACACCAGAGTTAT -s simHuman_chr6.simHuman.chr6 83464 14 - 601863 AACACCAGAGTTGT -s simRat_chr6.simRat.chr6 23052 14 - 647215 AACCCAGGAGTTAT - -a -s simMouse_chr6.simMouse.chr6 548195 5 + 636262 AAGGG -s Anc0.Anc0refChr3 150752 2 + 222631 AA--- -s Anc1.Anc1refChr6 186445 5 + 197743 AAGGG -s Anc2.Anc2refChr1 64630 2 + 142988 AA--- -s mr.mrrefChr3 98337 5 + 181027 AAGGG -s simCow_chr6.simCow.chr6 522711 2 + 602619 AA--- -s simDog_chr6.simDog.chr6 82497 2 - 593897 AA--- -s simHuman_chr6.simHuman.chr6 83491 5 - 601863 AAGGG -s simRat_chr6.simRat.chr6 23085 5 - 647215 AAGGC - -a -s simMouse_chr6.simMouse.chr6 548200 31 + 636262 GAAAACCAGCTTAGTTTTAACTTCAAGTAAC -s Anc0.Anc0refChr3 150754 28 + 222631 GGGAGACAAC---GGTTTAACTTCAAGTAAC -s Anc1.Anc1refChr6 186450 28 + 197743 GGGAGACAAC---GGTTTAACTTCAAGTAAC -s Anc2.Anc2refChr1 64632 28 + 142988 GGGAGACAAC---GGTTTAACTTCAAGTAAC -s mr.mrrefChr3 98342 31 + 181027 GAGAACCAACTTAGTTTTAACTTCAAGTAAC -s simCow_chr6.simCow.chr6 522713 28 + 602619 AGGAGACAAC---GGTTTAACTTCAAGTACC -s simDog_chr6.simDog.chr6 82499 28 - 593897 GAGAGACAAC---GGTTCAACTTCATGTAAC -s simHuman_chr6.simHuman.chr6 83501 28 - 601863 GGGAGACACC---GGTTTAAATCCAAGCCGC -s simRat_chr6.simRat.chr6 23090 31 - 647215 GAGAACCAACTTAGTTTTATCTTCAAGTAGC - -a -s simMouse_chr6.simMouse.chr6 548231 24 + 636262 AACCTGCCCCCCCCAAGTCAGCCT -s Anc0.Anc0refChr3 150782 24 + 222631 AATCTACCACCCCCCGGTCAGCCT -s Anc1.Anc1refChr6 186478 24 + 197743 AATCTACCACCCCCCGGTCAGCCT -s Anc2.Anc2refChr1 64660 24 + 142988 AATCTACCACCCCCCGGTCAGCCT -s mr.mrrefChr3 98373 24 + 181027 AACCTGTCACCCCCAAGTCAGCCT -s simCow_chr6.simCow.chr6 522741 24 + 602619 AATCTGCCACCCCCCGGTCAGCCT -s simDog_chr6.simDog.chr6 82527 24 - 593897 AACCTATCACCCCCCGGTAAACCT -s simHuman_chr6.simHuman.chr6 83529 24 - 601863 AATCTCCCACCTCCCGGTCAGCCT -s simRat_chr6.simRat.chr6 23122 24 - 647215 AACCTGTCAGCCCCAAGTCGGCCT - -a -s simMouse_chr6.simMouse.chr6 548255 10 + 636262 GGTTGATACC -s Anc0.Anc0refChr3 150814 8 + 222631 GGTTGATG-- -s Anc1.Anc1refChr6 186510 8 + 197743 GGTTGATG-- -s Anc2.Anc2refChr1 64692 8 + 142988 GGTTGTTG-- -s mr.mrrefChr3 98397 10 + 181027 GGTTGATACC -s simCow_chr6.simCow.chr6 522775 2 + 602619 ------CT-- -s simDog_chr6.simDog.chr6 82559 8 - 593897 GGTTGTTG-- -s simHuman_chr6.simHuman.chr6 83561 8 - 601863 GATTGATG-- -s simRat_chr6.simRat.chr6 23146 10 - 647215 GGTTGATACC - -a -s simMouse_chr6.simMouse.chr6 548265 16 + 636262 CCCCCTACGAGGAACC -s Anc0.Anc0refChr3 150836 16 + 222631 CCCCCTGCGAGGTCTC -s Anc1.Anc1refChr6 186532 16 + 197743 CCCCCTGCGAGGTCTC -s Anc2.Anc2refChr1 64715 16 + 142988 CCCCCTGCGAGGTCTC -s mr.mrrefChr3 98407 16 + 181027 CCCCCTGCGAGGAATC -s simCow_chr6.simCow.chr6 522792 16 + 602619 AACCCTGAGAGGTCTC -s simDog_chr6.simDog.chr6 82582 16 - 593897 CCCCTTGCGAAGTCTC -s simHuman_chr6.simHuman.chr6 518625 16 + 601863 TCCCCTGCGAGGTCTC -s simRat_chr6.simRat.chr6 23156 16 - 647215 CCCCCTGTGAGGAATT - -a -s simMouse_chr6.simMouse.chr6 548281 6 + 636262 ACTAAC -s Anc0.Anc0refChr3 150857 6 + 222631 AGTAAC -s Anc1.Anc1refChr6 186553 6 + 197743 AGTAAC -s Anc2.Anc2refChr1 64736 6 + 142988 AGTAAC -s mr.mrrefChr3 98423 6 + 181027 ACTAAC -s simCow_chr6.simCow.chr6 522812 6 + 602619 AGTGAC -s simDog_chr6.simDog.chr6 82603 6 - 593897 AGTAAG -s simHuman_chr6.simHuman.chr6 518646 6 + 601863 AGTAAC -s simRat_chr6.simRat.chr6 23172 6 - 647215 ACTGAC - -a -s simMouse_chr6.simMouse.chr6 548287 94 + 636262 CAGCCGCTCTGCAGACACGATATGGGGACGTCTCATGTGCCGTCGTCGAAGACGCAACGCGGGGTGGGTATGTTCGTGCGGCGTTGGGCAATAC -s Anc0.Anc0refChr3 150863 93 + 222631 CGGCCGTTCTGTAGATACGATGTCGGGACGACCCAGATGTCGTCGTTTCAGACTGAATGAGGGGTGGGTACGTTCGCGCGGGGCTAAGCAAA-C -s Anc1.Anc1refChr6 186559 93 + 197743 CGGCCGTTCTGTAGATACGATGTCGGGACGACCCAGATGTCGTCGTTTCAGACTGAATGAGGGGTGGGTACGTTCGCGCGGGGCTAAGCAAA-C -s Anc2.Anc2refChr1 64742 93 + 142988 CGGCCGTTGTGTAGATACGATGTCGGGACGACCCGGAGATCGTCGCTTCAGACTGAATGAGGGGTGGGTACGTTCGCGCGGGGCTAAGCAAA-C -s mr.mrrefChr3 98429 94 + 181027 CAGCCGCTCTGCAGACACGATATGGGGACGTCTCATGTGCCGTCGTCGCAGACGCAATGCGGGGTGGGTATGTTCGCGCGGCGTTGGGCAATAC -s simCow_chr6.simCow.chr6 522819 89 + 602619 CGGCCGTCATGTAGATACGATGTCAGAACGAGCCCAAGATCGTCGC----GACTCAATGAGGGGTGGGAACGTACGCGCGGGGCTAAGCAAA-C -s simDog_chr6.simDog.chr6 82609 90 - 593897 CGGC---TGTGTAGATACGATATCGGGACGACCCGGAGATCGTCGCTTCAGACTGAATGAGGGGTGGGTACGTTCGCGTGGGGTTAAGCACA-C -s simHuman_chr6.simHuman.chr6 518652 92 + 601863 CGGCAGTTCTGTATATACGATGTCGGGACGGCCCAGATGGCCTCGTTTCAGTTTGAGTGAGGGGTAG-TACGTTCTCGCGAGGCTAAAGAAC-C -s simRat_chr6.simRat.chr6 23178 94 - 647215 CGGCCGCTCTGCAGTCACGATAAGGGGACGTTTCATGTGCCGTCGTCGCAGACGTAGTGCGGGGTGGGTATGATCGCGCGGCGTTGGGCAATAC - -a -s simMouse_chr6.simMouse.chr6 548381 66 + 636262 GCCCCATCGCTTATTGATTGAGCTCAATATCATCTCTCAGCTCCACAGTCTCCAGCTCCATTGTTT -s Anc0.Anc0refChr3 150956 65 + 222631 GCACCGTCGCTTGTTGATTTAGCTCAATATCATCTCTGAG-CCCATGGTCTCTGTCTCCATTGTTT -s Anc1.Anc1refChr6 186652 65 + 197743 GCACCGTCGCTTGTTGATTTAGCTCAATATCATCTCTGAG-CCCATGGTCTCTGTCTCCATTGTTT -s Anc2.Anc2refChr1 64835 65 + 142988 GCACCGTCGCTTGTTGATTTAGCTCAATATCATCTCTGAG-CCCATGGTCTCTGTTTCCATTGCCC -s mr.mrrefChr3 98523 66 + 181027 GCCCCATCGCTTATTGATTGAGCTCAATATCATCTCTGAGCTCCATGGTCTCCAGCTCCATTGTTT -s simCow_chr6.simCow.chr6 522908 65 + 602619 GCCGCATCGCTTGTTGATCTATCTCACTATCAGCTGTAAG-CCCATGGTCTCTGTACCCGTTGCCC -s simDog_chr6.simDog.chr6 82699 64 - 593897 GCACCGTCGCTTGATGATTTCGCTCAACAACATCTCAGAG-CCCGTGGTCTCTGTTTCCATTGCC- -s simHuman_chr6.simHuman.chr6 518744 65 + 601863 GCGTCGGCGCTTGTCAATTTAGCTCAATATCATTTCTGAG-GCCATGGTCTCTGTCTCCACTGTTT -s simRat_chr6.simRat.chr6 23293 66 - 647215 GACCCACCGCTTATTGATTGAGCTAAATATCATCTCTGAGCTCCATGGTCTCCACCTCCACTGTTT - -a -s simMouse_chr6.simMouse.chr6 548447 1 + 636262 T -s Anc0.Anc0refChr3 151023 1 + 222631 T -s Anc1.Anc1refChr6 186719 1 + 197743 T -s Anc2.Anc2refChr1 64902 1 + 142988 A -s mr.mrrefChr3 98589 1 + 181027 T -s simCow_chr6.simCow.chr6 522975 1 + 602619 G -s simDog_chr6.simDog.chr6 82765 1 - 593897 A -s simHuman_chr6.simHuman.chr6 518811 1 + 601863 T -s simRat_chr6.simRat.chr6 23359 1 - 647215 T - -a -s simMouse_chr6.simMouse.chr6 548448 12 + 636262 CCCTGTGACAAG -s Anc0.Anc0refChr3 151024 12 + 222631 CCCTCCAGTGAG -s Anc1.Anc1refChr6 186720 12 + 197743 CCCTCCAGTGAG -s Anc2.Anc2refChr1 64903 12 + 142988 CCCCCCAGTGAG -s mr.mrrefChr3 98590 12 + 181027 CCCTGCAACAAG -s simCow_chr6.simCow.chr6 522976 12 + 602619 GCCCCTAGTGAG -s simDog_chr6.simDog.chr6 82766 12 - 593897 CACCCCAGTGAG -s simHuman_chr6.simHuman.chr6 518812 12 + 601863 CCCTCCAGTGAG -s simRat_chr6.simRat.chr6 23362 12 - 647215 CCCTGCAACAAG - -a -s simMouse_chr6.simMouse.chr6 548460 55 + 636262 TACCACTATGGGCATTATCCTGTTCCATTGTGCAATGCAAGCATTATGTAAAACT -s Anc0.Anc0refChr3 151037 47 + 222631 TACCA--------ACAATTCTGTTCCATTGTACACTGCAAACAATGTGTACAGCG -s Anc1.Anc1refChr6 186733 47 + 197743 TACCA--------ACAATTCTGTTCCATTGTACACTGCAAACAATGTGTACAGCG -s Anc2.Anc2refChr1 64916 47 + 142988 TACCA--------ACAATTCTGTTCCATTGTACACTGCAAACAATGTGTACAGCG -s mr.mrrefChr3 98602 55 + 181027 TACCACTGTGGGCATTATCCTGTTCCATTGTACAATGCAAACATTATGTAAAACT -s simCow_chr6.simCow.chr6 522989 47 + 602619 TACCA--------ACAATTCTGTTCCATTGTACACTGCAAAGATTGTGTACAGCG -s simDog_chr6.simDog.chr6 82779 38 - 593897 TACCT--------ATAATTTCTTGCCATTATACACTGGAAACAAGA--------- -s simHuman_chr6.simHuman.chr6 518825 47 + 601863 TACCA--------ACAATTCTGTTTCATTGCACACTGCAAACACTGTGTATTGCA -s simRat_chr6.simRat.chr6 23374 55 - 647215 TACCACTGTGGGCATTATCCTGTTCCATTGTACCTTGCAAACATTATGTATAACT - -a -s simMouse_chr6.simMouse.chr6 548515 13 + 636262 GGTTTGAGTGGGA -s Anc0.Anc0refChr3 151084 13 + 222631 AGTTTGCGTGGGA -s Anc1.Anc1refChr6 186780 13 + 197743 AGTTTGCGTGGGA -s Anc2.Anc2refChr1 64963 13 + 142988 AGCTAGCTTGGGA -s mr.mrrefChr3 98657 13 + 181027 GGTTTGAGTGGGG -s simCow_chr6.simCow.chr6 523039 13 + 602619 AGCTAGCTTGGGA -s simHuman_chr6.simHuman.chr6 518872 13 + 601863 AGTCTGGGTGATA -s simRat_chr6.simRat.chr6 23429 13 - 647215 GGTTTGGGTTGGG - -a -s simMouse_chr6.simMouse.chr6 548528 2 + 636262 AG -s Anc0.Anc0refChr3 151099 2 + 222631 AG -s Anc1.Anc1refChr6 186795 2 + 197743 AG -s Anc2.Anc2refChr1 64978 2 + 142988 AG -s mr.mrrefChr3 98670 2 + 181027 AG -s simCow_chr6.simCow.chr6 523054 2 + 602619 AG -s simDog_chr6.simDog.chr6 82818 2 - 593897 AG -s simHuman_chr6.simHuman.chr6 518887 2 + 601863 AG -s simRat_chr6.simRat.chr6 23442 2 - 647215 AG - -a -s simMouse_chr6.simMouse.chr6 548530 29 + 636262 CTCAACATACAAGGTCTTCCTTCACATTA -s Anc0.Anc0refChr3 151101 29 + 222631 CTCAACATACAAGATCTCCTGATATACCA -s Anc1.Anc1refChr6 186797 29 + 197743 CTCAACATACAAGATCTCCTGATATACCA -s Anc2.Anc2refChr1 64980 29 + 142988 CTCAACATATAAGATCTCCTGATATACCA -s mr.mrrefChr3 98672 29 + 181027 CTCAACATACAAGGTCTCCCTTCACATCA -s simCow_chr6.simCow.chr6 523058 29 + 602619 CGTGACATATAAGGTCTCCTCATCTACCA -s simDog_chr6.simDog.chr6 82820 29 - 593897 CTCAACATATAAGATCTCCTGGGACACCA -s simHuman_chr6.simHuman.chr6 518889 29 + 601863 CTCAACATACAAGCTCTCCTAATGTACCA -s simRat_chr6.simRat.chr6 23444 29 - 647215 CTCAACATACAAGGTCTCCCCACATATCA - -a -s simMouse_chr6.simMouse.chr6 548559 9 + 636262 TAAACAATG -s Anc0.Anc0refChr3 151130 9 + 222631 CAAATAATG -s Anc1.Anc1refChr6 186826 9 + 197743 CAAATAATG -s Anc2.Anc2refChr1 65009 9 + 142988 CAAATAATG -s mr.mrrefChr3 98701 9 + 181027 TAAACAATG -s simCow_chr6.simCow.chr6 523089 9 + 602619 CAAACAATG -s simDog_chr6.simDog.chr6 82849 9 - 593897 TAAATAATG -s simHuman_chr6.simHuman.chr6 518918 9 + 601863 CAAGTAATG -s simRat_chr6.simRat.chr6 23473 9 - 647215 TAAACACTG - -a -s simMouse_chr6.simMouse.chr6 548568 16 + 636262 ACCAAGGTTTATACTA -s Anc0.Anc0refChr3 151141 16 + 222631 ACCAAGGTTTATACCA -s Anc1.Anc1refChr6 186837 16 + 197743 ACCAAGGTTTATACCA -s Anc2.Anc2refChr1 65020 16 + 142988 ACCAAGATTTAAACCA -s mr.mrrefChr3 98710 16 + 181027 ACCAAGGTTTATACTA -s simCow_chr6.simCow.chr6 523100 16 + 602619 ACTGAGATTTGGACCA -s simDog_chr6.simDog.chr6 82860 16 - 593897 ACCAAGATGTAAATCA -s simHuman_chr6.simHuman.chr6 518929 16 + 601863 GCCAAGGTTTATACCA -s simRat_chr6.simRat.chr6 23482 16 - 647215 TCCAAGGTTTATACAA - -a -s simMouse_chr6.simMouse.chr6 548584 21 + 636262 GACACAATATGAAGGTTGGAG -s Anc0.Anc0refChr3 151163 5 + 222631 GATAT---------------- -s Anc1.Anc1refChr6 186859 5 + 197743 GATAT---------------- -s Anc2.Anc2refChr1 65042 5 + 142988 GATAT---------------- -s mr.mrrefChr3 98726 5 + 181027 GACAT---------------- -s simCow_chr6.simCow.chr6 523122 5 + 602619 GATGT---------------- -s simDog_chr6.simDog.chr6 82882 5 - 593897 AATAT---------------- -s simHuman_chr6.simHuman.chr6 518951 5 + 601863 GATAT---------------- -s simRat_chr6.simRat.chr6 23498 5 - 647215 TACAT---------------- - -a -s simMouse_chr6.simMouse.chr6 548605 17 + 636262 CTTATCCTACTCCACAC -s Anc0.Anc0refChr3 151170 8 + 222631 GAT---------CATAT -s Anc1.Anc1refChr6 186866 17 + 197743 GATATCCAACCCCATAT -s Anc2.Anc2refChr1 65049 8 + 142988 GAT---------CATGT -s mr.mrrefChr3 98731 17 + 181027 CTTATCCTACTCCACAC -s simCow_chr6.simCow.chr6 523129 1 + 602619 C---------------- -s simDog_chr6.simDog.chr6 82889 8 - 593897 GAT---------CATGT -s simHuman_chr6.simHuman.chr6 518958 17 + 601863 ACTATCCAACCCCATAT -s simRat_chr6.simRat.chr6 23503 17 - 647215 CCTATCCTACTCCACAT - -a -s simMouse_chr6.simMouse.chr6 548622 7 + 636262 GCTTCAT -s Anc0.Anc0refChr3 151195 7 + 222631 CCCTCAT -s Anc1.Anc1refChr6 186900 7 + 197743 CCCTCAT -s Anc2.Anc2refChr1 65077 7 + 142988 CCCTCAT -s mr.mrrefChr3 98748 7 + 181027 GCTTCAT -s simCow_chr6.simCow.chr6 523139 7 + 602619 CCCTCAT -s simDog_chr6.simDog.chr6 82917 7 - 593897 CCCTCAT -s simHuman_chr6.simHuman.chr6 518992 7 + 601863 CCCACAT -s simRat_chr6.simRat.chr6 23520 7 - 647215 GGTTCAT - -a -s simMouse_chr6.simMouse.chr6 548629 68 + 636262 AACACTAATATGCACTGACCACATGGATCCTATCTGTGGGCATACATGGCGCAGCAAAGAAGCTTTCA -s Anc0.Anc0refChr3 151211 52 + 222631 AACACTAACACACACTGCAAACATGG----------TGTGTATCCA-GCTTGGGCAAAGAGG-----A -s Anc1.Anc1refChr6 186916 57 + 197743 AACACTAACACACACTGCAAACATGG----------TGTGTATCCA-GCTTGGGCAAAGAGGAGTCAA -s Anc2.Anc2refChr1 65093 52 + 142988 AACACTATCACACATTGCAAATTTGG----------TGTGTATCCA-GCTTGGATAAAGAGG-----G -s mr.mrrefChr3 98755 67 + 181027 AACACTAATATGCACTGACCACATGGATCCTATCTGTGGGCATACA-GGCGCAGCAAAGAAGCTTTCA -s simCow_chr6.simCow.chr6 523155 40 + 602619 AACATCACCATA------------GG----------TGCATATCTG-GCATTGAGAAGAGGG-----C -s simDog_chr6.simDog.chr6 82933 52 - 593897 AACGCTATCACACATTGCAAATTTGG----------TGTGTTTCCA-GCTTGGATAAAGAGG-----G -s simHuman_chr6.simHuman.chr6 519008 52 + 601863 AACAATAA-----ACTGCAGACATGG----------TGTGTATCAA-GCTAGGGCAAAGAGGAGTCAA -s simRat_chr6.simRat.chr6 23527 67 - 647215 AACACTAGTCCAGACTGAAAAAATGGATCCTATCTGTGGGCATACA-GGCTCAGCAAGGAAGATTTCT - -a -s simMouse_chr6.simMouse.chr6 548697 1 + 636262 T -s Anc0.Anc0refChr3 151263 1 + 222631 C -s Anc1.Anc1refChr6 186973 1 + 197743 C -s Anc2.Anc2refChr1 65145 1 + 142988 C -s mr.mrrefChr3 98822 1 + 181027 T -s simCow_chr6.simCow.chr6 523209 1 + 602619 C -s simDog_chr6.simDog.chr6 511841 1 + 593897 T -s simHuman_chr6.simHuman.chr6 519060 1 + 601863 C -s simRat_chr6.simRat.chr6 23594 1 - 647215 T - -a -s simMouse_chr6.simMouse.chr6 548698 24 + 636262 TCCCACTATACCACAAAAAAATGC -s Anc0.Anc0refChr3 151264 24 + 222631 TCCTGTTATACCACACAACAATGT -s Anc1.Anc1refChr6 186974 24 + 197743 TCCTGTTATACCACACAACAATGT -s Anc2.Anc2refChr1 65146 24 + 142988 TCCTGTTATACCACACAACAATGT -s mr.mrrefChr3 98823 24 + 181027 TCCCACTATACCACAAAAAAATGC -s simCow_chr6.simCow.chr6 523210 24 + 602619 TCCTGTTATACCACATGACAATGC -s simDog_chr6.simDog.chr6 511842 24 + 593897 TCCTGTTAAACCACACAACAATGT -s simHuman_chr6.simHuman.chr6 519071 17 + 601863 TCCTGTTATACCACAGA------- -s simRat_chr6.simRat.chr6 23595 24 - 647215 TCTCATTACACCACACAAAAATGC - -a -s simMouse_chr6.simMouse.chr6 548722 7 + 636262 ATTTTTC -s Anc0.Anc0refChr3 151288 7 + 222631 ATTTATA -s Anc1.Anc1refChr6 186998 7 + 197743 ATTTATA -s Anc2.Anc2refChr1 65177 7 + 142988 ATTTATA -s mr.mrrefChr3 98847 7 + 181027 ATTTTTC -s simCow_chr6.simCow.chr6 523241 7 + 602619 ATTTTCA -s simDog_chr6.simDog.chr6 511873 7 + 593897 ATTTATA -s simRat_chr6.simRat.chr6 23619 7 - 647215 TGTTTTC - -a -s simMouse_chr6.simMouse.chr6 548729 38 + 636262 TATGTGATGCAGGTTATTCAGCCAAGGATATCTCTTCC -s Anc0.Anc0refChr3 151295 38 + 222631 TGTGTGATATAGGTTATCTACTAATGCAAATCTCCTCC -s Anc1.Anc1refChr6 187005 38 + 197743 TGTGTGATATAGGTTATCTACTAATGCAAATCTCCTCC -s Anc2.Anc2refChr1 65189 38 + 142988 TGTGTGATATAGGTTATCTACTAATGCAAATCTCCTCC -s mr.mrrefChr3 98854 38 + 181027 TATGTGATGCAGGTTATTCAGCCAAGGATATCTCTTCC -s simCow_chr6.simCow.chr6 523253 38 + 602619 TACATGATATAGGTTATCCTGCAATGCAAGTCTATTAC -s simDog_chr6.simDog.chr6 511885 38 + 593897 TGTGTGATATAGGTTATCTACTAATGCAAATCTCCTCC -s simRat_chr6.simRat.chr6 23626 38 - 647215 TATATGATATGGGTTTTCCAGCCATGGCTGTCTCTTCC - -a -s simMouse_chr6.simMouse.chr6 548767 6 + 636262 TATCTA -s Anc0.Anc0refChr3 151333 6 + 222631 TCTCTA -s Anc1.Anc1refChr6 187043 6 + 197743 TCTCTA -s Anc2.Anc2refChr1 65250 6 + 142988 TCTCTA -s mr.mrrefChr3 98892 6 + 181027 TATCTA -s simCow_chr6.simCow.chr6 523314 6 + 602619 TCTCTA -s simDog_chr6.simDog.chr6 511946 6 + 593897 TCTCTA -s simRat_chr6.simRat.chr6 23664 6 - 647215 TATCTA - -a -s simMouse_chr6.simMouse.chr6 548773 37 + 636262 TTGTTAGAATGGGAGAGGACTGACCTTTTCTGTGTTG -s Anc0.Anc0refChr3 151339 34 + 222631 TTCTCAGGAAGTCAGAGAATCTGCCT---CAGTGTTG -s Anc1.Anc1refChr6 187049 34 + 197743 TTCTCAGGAAGTCAGAGAATCTGCCT---CAGTGTTG -s Anc2.Anc2refChr1 65256 34 + 142988 TTCTCAGGAAGTCAGAGAATCTGCCT---CAGTGTTG -s mr.mrrefChr3 98898 37 + 181027 TTGTTAGAATGGGAGAGGACTGACCTTTTCTGTGTTG -s simCow_chr6.simCow.chr6 523320 34 + 602619 TTCTCAGGAACTCAGATAATCTGCTT---CAGTGCTG -s simDog_chr6.simDog.chr6 511952 34 + 593897 TTCTCAGGAAGTCAGAGAATCTGCCT---CAGTGTTG -s simRat_chr6.simRat.chr6 23693 37 - 647215 TTGTTGGAATGAGGGATAGCTGACCTGTTCTGAGTTG - -a -s simMouse_chr6.simMouse.chr6 548810 12 + 636262 CAAAATAGGCAT -s Anc0.Anc0refChr3 151373 10 + 222631 CAA--TCACCAT -s Anc1.Anc1refChr6 187083 10 + 197743 CAA--TCACCAT -s Anc2.Anc2refChr1 65290 10 + 142988 CAA--TCACCAT -s mr.mrrefChr3 98935 12 + 181027 CAAAATAGGCAT -s simCow_chr6.simCow.chr6 523354 10 + 602619 CGA--CGACCAT -s simDog_chr6.simDog.chr6 511988 10 + 593897 CAA--TCACCAT -s simRat_chr6.simRat.chr6 23730 12 - 647215 CATAATAGGCAT - -a -s simMouse_chr6.simMouse.chr6 548822 3 + 636262 ATT -s Anc0.Anc0refChr3 151383 3 + 222631 ATG -s Anc1.Anc1refChr6 187093 3 + 197743 ATG -s Anc2.Anc2refChr1 65302 3 + 142988 ATG -s mr.mrrefChr3 98947 3 + 181027 ATT -s simCow_chr6.simCow.chr6 523366 3 + 602619 TTA -s simDog_chr6.simDog.chr6 512000 3 + 593897 ATG -s simRat_chr6.simRat.chr6 23742 3 - 647215 ATT - -a -s simMouse_chr6.simMouse.chr6 548825 2 + 636262 AA -s Anc0.Anc0refChr3 151386 2 + 222631 AA -s Anc1.Anc1refChr6 187096 2 + 197743 AA -s Anc2.Anc2refChr1 65305 2 + 142988 AA -s mr.mrrefChr3 98950 2 + 181027 AA -s simCow_chr6.simCow.chr6 523369 2 + 602619 AG -s simDog_chr6.simDog.chr6 512003 2 + 593897 AA -s simRat_chr6.simRat.chr6 23753 2 - 647215 AC - -a -s simMouse_chr6.simMouse.chr6 548827 25 + 636262 TTATCTACCCAATAGCATTTGTGTT -s Anc0.Anc0refChr3 151388 24 + 222631 TT-TGTACCTAAAGGCAGTTGCAAT -s Anc1.Anc1refChr6 187098 24 + 197743 TT-TGTACCTAAAGGCAGTTGCAAT -s Anc2.Anc2refChr1 65307 24 + 142988 TT-TGTACCTAAAGGCAGTTGCAAT -s mr.mrrefChr3 98952 25 + 181027 TTATCTACCCAATAGCATTTGTGTT -s simCow_chr6.simCow.chr6 523372 24 + 602619 TT-TATCCCTAAAAACACTCACATT -s simDog_chr6.simDog.chr6 512005 24 + 593897 TT-TGTACCTAAAGGCAGTTGCAAT -s simRat_chr6.simRat.chr6 23755 25 - 647215 TTATCTACCCAATAGCATTTGCGTT - -a -s simMouse_chr6.simMouse.chr6 548852 21 + 636262 ACAGGGCATATAAAGTTCAAG -s Anc0.Anc0refChr3 151412 21 + 222631 ATTGGATGCATGGATTTTCAG -s Anc1.Anc1refChr6 187122 21 + 197743 ATTGGATGCATGGATTTTCAG -s Anc2.Anc2refChr1 65336 21 + 142988 ATTGGATGCATGGATTTTCAG -s mr.mrrefChr3 98977 21 + 181027 ACAGGGCATATAAAGTTCAAG -s simCow_chr6.simCow.chr6 523401 21 + 602619 ATGGGATGCATGAATTTTAAG -s simDog_chr6.simDog.chr6 512034 21 + 593897 ATTGGATGCATGGATTTTCAG -s simRat_chr6.simRat.chr6 23780 21 - 647215 ACAGGGCATATAAATCTCAAG - -a -s simMouse_chr6.simMouse.chr6 548873 16 + 636262 TGTCTCCTAGTCCCTG -s Anc0.Anc0refChr3 151433 14 + 222631 TGCCCCC--ATCCCTG -s Anc1.Anc1refChr6 187143 14 + 197743 TGCCCCC--ATCCCTG -s Anc2.Anc2refChr1 65357 14 + 142988 TGCCCCC--ATCCCTG -s mr.mrrefChr3 98998 16 + 181027 TGTCTCCTAGTCCCTG -s simCow_chr6.simCow.chr6 523422 14 + 602619 TATGCCA--GGGTCTG -s simDog_chr6.simDog.chr6 512068 14 + 593897 TGCCCCC--ATCCCTG -s simRat_chr6.simRat.chr6 23801 16 - 647215 TAACTTCTAGTCCTTG - -a -s simMouse_chr6.simMouse.chr6 548889 5 + 636262 ATCCA -s Anc0.Anc0refChr3 151447 5 + 222631 ACCCA -s Anc1.Anc1refChr6 187157 5 + 197743 ACCCA -s Anc2.Anc2refChr1 65371 5 + 142988 ACCCA -s mr.mrrefChr3 99014 5 + 181027 ATCCA -s simCow_chr6.simCow.chr6 523436 5 + 602619 ACCCA -s simDog_chr6.simDog.chr6 512082 5 + 593897 ACCCA -s simRat_chr6.simRat.chr6 23818 5 - 647215 ATCCA - -a -s simMouse_chr6.simMouse.chr6 548894 45 + 636262 GCGTGAGATGGATGCACTAAAAGAGAGACATCAACCATCATGGGA -s Anc0.Anc0refChr3 151452 45 + 222631 GCCTGATATGGGCCTGCCAAAAGGTGGACATTGAGCACAAAGGAA -s Anc1.Anc1refChr6 187162 45 + 197743 GCCTGATATGGGCCTGCCAAAAGGTGGACATTGAGCACAAAGGAA -s Anc2.Anc2refChr1 65376 45 + 142988 GCCTGATATGGGCCTGCCAAAAGGTGGACATTGAGCACAAAGGAA -s mr.mrrefChr3 99019 45 + 181027 GCGTGAGATGGATGCACTAAAAGAGAGACATCAACCATCATGGGA -s simCow_chr6.simCow.chr6 523441 45 + 602619 GCATGATATACGTATTCTAACAAGTGGATGTCGAGCACCCAGGAA -s simDog_chr6.simDog.chr6 512089 45 + 593897 GCCTGATATGGGCCTGCCAAAAGGTGGACATTGAGCACAAAGGAA -s simRat_chr6.simRat.chr6 23823 45 - 647215 GCATGAAGTGGATGCGCTAAAAGAGAGACATCAAGCATTTTGGGA - -a -s simMouse_chr6.simMouse.chr6 548939 6 + 636262 CATAAT -s Anc0.Anc0refChr3 151497 5 + 222631 GATAA- -s Anc1.Anc1refChr6 187207 5 + 197743 GATAA- -s Anc2.Anc2refChr1 65421 5 + 142988 GATAA- -s mr.mrrefChr3 99064 6 + 181027 CATAAT -s simCow_chr6.simCow.chr6 523486 5 + 602619 GATAG- -s simDog_chr6.simDog.chr6 512134 5 + 593897 GATAA- -s simRat_chr6.simRat.chr6 23871 6 - 647215 CGTAAT - -a -s simMouse_chr6.simMouse.chr6 548945 17 + 636262 CAACCAGGCAGAAATGT -s Anc0.Anc0refChr3 151502 17 + 222631 CAATGAGGTGTAAATTC -s Anc1.Anc1refChr6 187212 17 + 197743 CAATGAGGTGTAAATTC -s Anc2.Anc2refChr1 65426 17 + 142988 CAATGAGGTGTAAATTC -s mr.mrrefChr3 99070 17 + 181027 CAACCAGGCAGAAATGT -s simCow_chr6.simCow.chr6 523491 17 + 602619 CCATCAAGTATAAATTT -s simDog_chr6.simDog.chr6 512141 17 + 593897 CAATGAGGTGTAAATTC -s simRat_chr6.simRat.chr6 23877 17 - 647215 CAACCAGGCAGAAATGT - -a -s simMouse_chr6.simMouse.chr6 548962 34 + 636262 GGTACCAGCTGAGAGCCTTTGCCCGAAGAGCTAT -s Anc0.Anc0refChr3 151519 32 + 222631 GTTTTCAGACAAG--CTCTGGCCCAAAAAGATAT -s Anc1.Anc1refChr6 187229 32 + 197743 GTTTTCAGACAAG--CTCTGGCCCAAAAAGATAT -s Anc2.Anc2refChr1 65445 32 + 142988 GTTTTCAGACAAG--CTCTGGCCCAAAAAGAGAT -s mr.mrrefChr3 99087 34 + 181027 GGTACCAGCTGAGAGCCTTTGCCCAAAGAGCTAT -s simCow_chr6.simCow.chr6 523510 32 + 602619 GATCTCAAACAAG--CCCTTGTCCAGAAAGAAAT -s simDog_chr6.simDog.chr6 512160 32 + 593897 GTTTTCAGACAAG--CTCTGGCCCAAAAGGAGAT -s simHuman_chr6.simHuman.chr6 519088 13 + 601863 ---------------------CCCAAAAAGATAT -s simRat_chr6.simRat.chr6 23894 34 - 647215 AGTACCAGCCAAGAGCCCTTGTCCAAATAGGTAT - -a -s simMouse_chr6.simMouse.chr6 548996 42 + 636262 GATGTGCTACTAGGTATGAGAGACTGGTCTAATGATAGCCAG -s Anc0.Anc0refChr3 151552 42 + 222631 GATGTGCTACTAAGTTTGAGATGTCAAGCTAATAATAACCAG -s Anc1.Anc1refChr6 187262 42 + 197743 GATGTGCTACTAAGTTTGAGATGTCAAGCTAATAATAACCAG -s Anc2.Anc2refChr1 65478 42 + 142988 CATGAACTACTAAGCTAGAGATGTCAAGCTAATAATAATCAA -s mr.mrrefChr3 99122 42 + 181027 GATGTGCTACTAGGTATGAGAGGCTGGTCTAATGATAACCAG -s simCow_chr6.simCow.chr6 523543 42 + 602619 CATACACTACTAAGCTGGAGATGTCAATCCGATAATAAATAA -s simDog_chr6.simDog.chr6 512193 42 + 593897 CATGAACTAACAAACCAGAAATGCTAAGCTAATAATAGTCAA -s simHuman_chr6.simHuman.chr6 519102 42 + 601863 GATGTGCTACTAAGTTTGAGAAGTCAACCTAATAGTCACCAG -s simRat_chr6.simRat.chr6 23929 40 - 647215 GATGTGCT-CTAGGTATTTGGGGCTGGT-TATTGATAACCAG - -a -s simMouse_chr6.simMouse.chr6 549038 54 + 636262 AATGTCCTTGCCAGCGGGTGAACACAATTATTTGGCCGTTTGCACAATCATTTG -s Anc0.Anc0refChr3 151594 38 + 222631 GGTGTCCCTGCCAGCGTTGGTACACACTTATTT-----------CACTA----- -s Anc1.Anc1refChr6 187304 43 + 197743 GGTGTCCCTGCCAGCGTTGGTACACACTTATTT-----------CACTAATTTG -s Anc2.Anc2refChr1 65520 38 + 142988 GGTGGCCCTGCCAGCGTTGATACCAACTTATTT-----------CACTA----- -s mr.mrrefChr3 99164 54 + 181027 AATGTCCCTGCCAGCGGGTGTACACAATTATTTGGCCGTTTGCACAATCATTTG -s simCow_chr6.simCow.chr6 523589 38 + 602619 GGTGGCTCTGCCAGTGTTGATACTTACTTTTTT-----------CACTA----- -s simDog_chr6.simDog.chr6 512235 32 + 593897 GGTGGCCGTGCCAGCTTTGATACCAATTTATT---------------------- -s simHuman_chr6.simHuman.chr6 519144 43 + 601863 TGTGTTCCTGCCAGCGATGGTGCACACTGATTA-----------CACTGATTTG -s simRat_chr6.simRat.chr6 23969 54 - 647215 AACGTCCCTCCCAGCGGGTGTACACAATCGTTCGGCCGTTTACATAATTATTTG - -a -s simMouse_chr6.simMouse.chr6 549092 28 + 636262 TGTAAGCCTGCATCCCGTGAGTGTTGAA -s Anc0.Anc0refChr3 151635 27 + 222631 AGCAAG-CGGCATCCCGTGGGTGTTGGG -s Anc1.Anc1refChr6 187356 28 + 197743 AGCAAGCCGGCATCCCGTGGGTGTTGGG -s Anc2.Anc2refChr1 65561 27 + 142988 AACAAG-CGGAATCCCGTGGATATTGGG -s mr.mrrefChr3 99226 28 + 181027 TGTAAGCCTGCATCCCGTGAGTGTTGAA -s simCow_chr6.simCow.chr6 523630 27 + 602619 AACAAG-CGGAATCCCGTGGATATTGCT -s simDog_chr6.simDog.chr6 512267 4 + 593897 ------------------------TGGG -s simHuman_chr6.simHuman.chr6 519196 28 + 601863 AGCAAGCCGGCATCCCTTGGGTGTTGGG -s simRat_chr6.simRat.chr6 24031 28 - 647215 TGTAAGCCTGCGTCCCGTGAGTGTTGAA - -a -s simMouse_chr6.simMouse.chr6 549120 40 + 636262 TCTAGAGGTGAGCGCGGGGCGAATATACTCTCCTTTCTGC -s Anc0.Anc0refChr3 151662 35 + 222631 CTTGGTGGTGAT-----GGCGATTGTCCTCCCCTGTTTGA -s Anc1.Anc1refChr6 187384 35 + 197743 CTTGGTGGTGAT-----GGCGATTGTCCTCCCCTGTTTGA -s Anc2.Anc2refChr1 65588 35 + 142988 CTTGGTAGTGAT-----GGCGATTGTCCTCCCCTGCTTAA -s mr.mrrefChr3 99254 40 + 181027 TTTGGAGGTGAGCGCGGGGCGAATATACTCTCCTTTCTGC -s simCow_chr6.simCow.chr6 523657 35 + 602619 CTTGGTAGCGAT-----GGTTATTGTCCGCCCCTGCTCAA -s simDog_chr6.simDog.chr6 512273 35 + 593897 CTTGGTAGTGGT-----GGCGATTGTTCTCCACTGCTTGG -s simHuman_chr6.simHuman.chr6 519224 35 + 601863 CTCGGGGGTAAT-----GGCGATTGTCCTCCCCTCTATGT -s simRat_chr6.simRat.chr6 24059 40 - 647215 TTTGGAAGTGAGCGCGGGGCGAATATACCCTCGTTTCTGC - -a -s simMouse_chr6.simMouse.chr6 549160 13 + 636262 GTTGGAGGCTTCT -s Anc0.Anc0refChr3 151697 11 + 222631 ATTGGAGGCTT-- -s Anc1.Anc1refChr6 187419 11 + 197743 ATTGGAGGCTT-- -s Anc2.Anc2refChr1 65623 11 + 142988 ATTGGAGGCTT-- -s mr.mrrefChr3 99294 13 + 181027 GTTGGAGGCTTCT -s simCow_chr6.simCow.chr6 523692 11 + 602619 ATTGTAGGCTT-- -s simDog_chr6.simDog.chr6 512308 11 + 593897 ATTGGAGCCTT-- -s simHuman_chr6.simHuman.chr6 519304 11 + 601863 ATTGGAGGTTT-- -s simRat_chr6.simRat.chr6 24099 7 - 647215 AT------CTTCT - -a -s simMouse_chr6.simMouse.chr6 549173 52 + 636262 TACAGGATGAGCGGCTGTTTATTTCACGGGACAGTCAGAACTATTCGATTCT -s Anc0.Anc0refChr3 151708 39 + 222631 -ACACGCAGAAGG-----------CACGAGTCTACGAAAGCTGTT-GATTCT -s Anc1.Anc1refChr6 187430 39 + 197743 -ACACGCAGAAGG-----------CACGAGTCTACGAAAGCTGTT-GATTCT -s Anc2.Anc2refChr1 65634 39 + 142988 -ACACGCAGAAGT-----------CCCGAGTCTACGAAAGTTGTT-GATTTA -s mr.mrrefChr3 99307 52 + 181027 TACAGGAAGAGTGGCTGTTTATTTCACGGGACAGTCAGAGCTATTCGATTCT -s simCow_chr6.simCow.chr6 523703 27 + 602619 -ATACGC-----------------------TCTACGAAAGTTGTT-GATTTC -s simDog_chr6.simDog.chr6 512319 31 + 593897 -ACACGGAGAAGT-----------CCCGAG--------AATTGTT-GATGTA -s simHuman_chr6.simHuman.chr6 519315 36 + 601863 -ACACGCAGAACG-----------CAGAAGTCTAAGGAAGCTG----ATTCT -s simRat_chr6.simRat.chr6 24107 52 - 647215 TGCAGGAAGAATGGCTGTTTATTTCACGGGACAGTCAGAGCTATTGGATTCC - -a -s simMouse_chr6.simMouse.chr6 549225 5 + 636262 GACCC -s Anc0.Anc0refChr3 151749 5 + 222631 GGCCC -s Anc1.Anc1refChr6 187471 5 + 197743 GGCCC -s Anc2.Anc2refChr1 65675 5 + 142988 GGACC -s mr.mrrefChr3 99359 5 + 181027 GACCC -s simCow_chr6.simCow.chr6 523732 5 + 602619 GCACC -s simDog_chr6.simDog.chr6 512352 5 + 593897 GGACC -s simHuman_chr6.simHuman.chr6 519353 5 + 601863 GGCCC -s simRat_chr6.simRat.chr6 24159 5 - 647215 GACGC - -a -s simMouse_chr6.simMouse.chr6 549230 24 + 636262 AGTAAGAACTATTATATTCTGACT -s Anc0.Anc0refChr3 151754 24 + 222631 AGTCATAACCACTGGATCTTGACT -s Anc1.Anc1refChr6 187476 24 + 197743 AGTCATAACCACTGGATCTTGACT -s Anc2.Anc2refChr1 65680 24 + 142988 AGTCATAACCACTGGATCTTGATT -s mr.mrrefChr3 99364 24 + 181027 AGTAAGAACTATTGGATTCTGACT -s simCow_chr6.simCow.chr6 523737 24 + 602619 AATCACAACCACTGGATCCCGATC -s simDog_chr6.simDog.chr6 512357 24 + 593897 AGTCTTAACCACTAGGTCTTTATT -s simHuman_chr6.simHuman.chr6 519359 24 + 601863 AGTGATAATCACTGGATCTTGACT -s simRat_chr6.simRat.chr6 24164 24 - 647215 AGTCAAAACTATTGGATTCCGACT - -a -s simMouse_chr6.simMouse.chr6 549254 21 + 636262 TACCCCTGGATCCGTATTTAA -s Anc0.Anc0refChr3 151778 21 + 222631 TACCACTGGATCCTGACTTGA -s Anc1.Anc1refChr6 187500 21 + 197743 TACCACTGGATCCTGACTTGA -s Anc2.Anc2refChr1 65704 21 + 142988 TACCACTGGATCCTGACTTGA -s mr.mrrefChr3 99388 21 + 181027 TACCACTGGATCCGTATTTAA -s simCow_chr6.simCow.chr6 523761 21 + 602619 TACTACTGGATCCTGACGAGA -s simDog_chr6.simDog.chr6 512381 21 + 593897 TACCACTCAATGCTGACTTCA -s simHuman_chr6.simHuman.chr6 519383 21 + 601863 TACCATTGGATCCTGACTTGA -s simRat_chr6.simRat.chr6 24228 21 - 647215 TACCACTGGATCCGTATTTAA - -a -s simMouse_chr6.simMouse.chr6 549275 4 + 636262 GTCG -s Anc0.Anc0refChr3 151799 4 + 222631 GTAG -s Anc1.Anc1refChr6 187521 4 + 197743 GTAG -s Anc2.Anc2refChr1 65725 4 + 142988 GTAC -s mr.mrrefChr3 99409 4 + 181027 GTCG -s simCow_chr6.simCow.chr6 523782 4 + 602619 GGAC -s simDog_chr6.simDog.chr6 512402 4 + 593897 GTAC -s simHuman_chr6.simHuman.chr6 519404 4 + 601863 GTAG -s simRat_chr6.simRat.chr6 24251 4 - 647215 GTCG - -a -s simMouse_chr6.simMouse.chr6 549279 15 + 636262 TGTAACCGCGGGAAT -s Anc0.Anc0refChr3 151805 15 + 222631 CATAGCCGCTGGATC -s Anc1.Anc1refChr6 187527 15 + 197743 CATAGCCGCTGGATC -s Anc2.Anc2refChr1 65731 15 + 142988 CATAGCGGCTGGATC -s mr.mrrefChr3 99413 15 + 181027 CATAACCGCTGGAAC -s simCow_chr6.simCow.chr6 523788 15 + 602619 TATAGTGATTGGATC -s simDog_chr6.simDog.chr6 512408 15 + 593897 CATAGCGGCTGGATC -s simHuman_chr6.simHuman.chr6 519410 15 + 601863 CATAGCCGCTAGATC -s simRat_chr6.simRat.chr6 24255 15 - 647215 CAGAACCGCTGGGAC - -a -s simMouse_chr6.simMouse.chr6 549294 12 + 636262 GACTTAAATAAG -s Anc0.Anc0refChr3 151822 12 + 222631 GACTTAAGCAAG -s Anc1.Anc1refChr6 187544 12 + 197743 GACTTAAGCAAG -s Anc2.Anc2refChr1 65748 12 + 142988 GACTTAAGCAAG -s mr.mrrefChr3 99428 12 + 181027 GACTTAAATAAG -s simCow_chr6.simCow.chr6 523805 12 + 602619 GGCTTAAGCGAG -s simDog_chr6.simDog.chr6 512425 12 + 593897 GACTTACGCAAG -s simHuman_chr6.simHuman.chr6 519427 12 + 601863 GTTTTAAGCAAG -s simRat_chr6.simRat.chr6 24270 12 - 647215 GACTTAAATGTG - -a -s simMouse_chr6.simMouse.chr6 549306 17 + 636262 AGCAACGTCGCTCTATT -s Anc0.Anc0refChr3 151836 17 + 222631 ACCAACGGTGATCCATT -s Anc1.Anc1refChr6 187558 17 + 197743 ACCAACGGTGATCCATT -s Anc2.Anc2refChr1 65762 17 + 142988 ACCAACGGTGATCCTTT -s mr.mrrefChr3 99440 17 + 181027 AGCAACGTCGCTCTATT -s simCow_chr6.simCow.chr6 523819 17 + 602619 GGCATAGGCGATCTATT -s simDog_chr6.simDog.chr6 512439 17 + 593897 ACCAACGGTGATCCTTC -s simHuman_chr6.simHuman.chr6 519441 17 + 601863 ACCACCGGTGATCCATT -s simRat_chr6.simRat.chr6 24282 17 - 647215 AGCAACGTCGTTCTATT - -a -s simMouse_chr6.simMouse.chr6 549323 7 + 636262 CGTCCGT -s Anc0.Anc0refChr3 151853 7 + 222631 CGCCCCT -s Anc1.Anc1refChr6 187575 7 + 197743 CGCCCCT -s Anc2.Anc2refChr1 65779 7 + 142988 CGCCCCT -s mr.mrrefChr3 99457 7 + 181027 CGTCCGT -s simCow_chr6.simCow.chr6 523836 7 + 602619 CGCCCCT -s simDog_chr6.simDog.chr6 512456 7 + 593897 CGCGCCT -s simHuman_chr6.simHuman.chr6 519459 7 + 601863 CACCCCT -s simRat_chr6.simRat.chr6 24299 7 - 647215 CGTCCGT - -a -s simMouse_chr6.simMouse.chr6 549330 8 + 636262 TAAGGTTA -s Anc0.Anc0refChr3 151861 8 + 222631 TTGGGTGT -s Anc1.Anc1refChr6 187583 8 + 197743 TTGGGTGT -s Anc2.Anc2refChr1 65787 8 + 142988 TTGGGTGT -s mr.mrrefChr3 99464 8 + 181027 TAAGGTTA -s simCow_chr6.simCow.chr6 523844 8 + 602619 TCGGGTGT -s simDog_chr6.simDog.chr6 512464 8 + 593897 TTGGGTGA -s simHuman_chr6.simHuman.chr6 519467 8 + 601863 CTGGGTGT -s simRat_chr6.simRat.chr6 24306 8 - 647215 TAAGGTTA - -a -s simMouse_chr6.simMouse.chr6 549338 7 + 636262 AAGAGCG -s Anc0.Anc0refChr3 151869 7 + 222631 AAGAGCA -s Anc1.Anc1refChr6 187591 7 + 197743 AAGAGCA -s Anc2.Anc2refChr1 65795 7 + 142988 AAGAGCA -s mr.mrrefChr3 99472 7 + 181027 AAGAGCG -s simCow_chr6.simCow.chr6 523853 7 + 602619 AAGAGCA -s simDog_chr6.simDog.chr6 512472 7 + 593897 CAGAGCG -s simHuman_chr6.simHuman.chr6 519475 7 + 601863 AAGAGCA -s simRat_chr6.simRat.chr6 24314 7 - 647215 AAGAACG - -a -s simMouse_chr6.simMouse.chr6 549345 24 + 636262 CTGCTGGGAAAGGGGAACTGTAAA -s Anc0.Anc0refChr3 151876 23 + 222631 CTGCTGG-CAGGGGGATCTGTAAG -s Anc1.Anc1refChr6 187598 23 + 197743 CTGCTGG-CAGGGGGATCTGTAAG -s Anc2.Anc2refChr1 65802 23 + 142988 CTGTTGG-CAGAGGGATCTGTAAG -s mr.mrrefChr3 99479 24 + 181027 CTGCTGGGAAAGGGGATCTGTAAA -s simCow_chr6.simCow.chr6 523860 23 + 602619 CTGTTGG-GAGAGGGAACTATAAG -s simDog_chr6.simDog.chr6 512479 23 + 593897 CTGTAGG-CAGAAGGATCTGTAAG -s simHuman_chr6.simHuman.chr6 519482 23 + 601863 CTGCTAG-CGGGGGGATCCGTAAG -s simRat_chr6.simRat.chr6 24322 24 - 647215 CTGCTGGGAAAGGGGATCTGCAAA - -a -s simMouse_chr6.simMouse.chr6 549369 34 + 636262 GGATGCTCAGTAAAGGTTATGCCGACATTAGCTT -s Anc0.Anc0refChr3 151899 34 + 222631 GAAGGCTCGCTAAATATTATGCCCATATTAGCTT -s Anc1.Anc1refChr6 187621 34 + 197743 GAAGGCTCGCTAAATATTATGCCCATATTAGCTT -s Anc2.Anc2refChr1 65825 34 + 142988 GAAGGCTCGCTTAATATTATTCCCATATTAGCTT -s mr.mrrefChr3 99503 34 + 181027 GGATGCTCAGTAAAGGTTATGCCCACATTAGCTT -s simCow_chr6.simCow.chr6 523895 34 + 602619 GAAGGCTCGCTTGATATTATTCCCATATTAGATT -s simDog_chr6.simDog.chr6 512502 34 + 593897 GAAGGCCCGTTTAAAATTATTCCCATGTTAGCTT -s simHuman_chr6.simHuman.chr6 519505 34 + 601863 GCAGGCTGGCTAAATCTTATGTCCCTAGTAGCTT -s simRat_chr6.simRat.chr6 24346 34 - 647215 GGCTGCTCAGTAAAGGTTATGCCCACGTTAGGTT - -a -s simMouse_chr6.simMouse.chr6 549403 20 + 636262 ACGTCGCTGCAGGAAGAGAT -s Anc0.Anc0refChr3 151934 20 + 222631 ATCCCACTAAAGCATGAGAT -s Anc1.Anc1refChr6 187656 20 + 197743 ATCCCACTAAAGCATGAGAT -s Anc2.Anc2refChr1 65860 20 + 142988 ATCCCACTAATGCATGAGAT -s mr.mrrefChr3 99537 20 + 181027 ATGTCACTGCAGGAAGAGAT -s simCow_chr6.simCow.chr6 523930 20 + 602619 GTCCCACTACTTCCTCAGAT -s simDog_chr6.simDog.chr6 512537 20 + 593897 ATCCCACTAATGCATGAGCT -s simHuman_chr6.simHuman.chr6 519540 20 + 601863 ATCCCACTTTAGCACGAGAT -s simRat_chr6.simRat.chr6 24380 20 - 647215 ATGTCACTGCAGGAAGAAAT - -a -s simMouse_chr6.simMouse.chr6 549423 66 + 636262 ATGGACTACACCCCCTTTCTTGGTCCTGTGTCATCCTACAAATTTTCCTGGGTCATTTGAAACCAT -s Anc0.Anc0refChr3 151954 26 + 222631 C----------------------------------------ATCTTCCTAGGTCATCTGAAACCCT -s Anc1.Anc1refChr6 187676 26 + 197743 C----------------------------------------ATCTTCCTAGGTCATCTGAAACCCT -s Anc2.Anc2refChr1 65888 26 + 142988 C----------------------------------------CTCTTCTTAAGCCATCTGAAACCCT -s mr.mrrefChr3 99557 65 + 181027 ATGGACTACACCCC-TTTCTTGGTCCTGTGTCATCCTACAAATTTTCCTAGGTCATTTGAAACCAT -s simCow_chr6.simCow.chr6 523963 26 + 602619 C----------------------------------------CGCTTCTTATGCCGTCTGAAACCCT -s simDog_chr6.simDog.chr6 512565 26 + 593897 C----------------------------------------CTCTTCTTAAGCCATCTGAAACCAT -s simHuman_chr6.simHuman.chr6 519560 26 + 601863 T----------------------------------------AACCGCCTAGATCATATGAAATCCT -s simRat_chr6.simRat.chr6 24400 65 - 647215 ATGGACAACACCCC-TTTCTTGGTCATGTCTCATCCTACAAGTTTTCCTAGGTCATTTGAAACCAT - -a -s simMouse_chr6.simMouse.chr6 549489 18 + 636262 GCACTCATGCTATAAATT -s Anc0.Anc0refChr3 151980 18 + 222631 GCAATTATGCAATTAGCT -s Anc1.Anc1refChr6 187702 18 + 197743 GCAATTATGCAATTAGCT -s Anc2.Anc2refChr1 65914 18 + 142988 GCAATTATGCAATTAGCA -s mr.mrrefChr3 99622 18 + 181027 GCACTCATGCAATAAATT -s simCow_chr6.simCow.chr6 523997 18 + 602619 ACACTCATGGAATTAGCA -s simDog_chr6.simDog.chr6 512591 18 + 593897 GCAATTATGCAATTAGCA -s simHuman_chr6.simHuman.chr6 519586 18 + 601863 GCAATTATGCAATTAGCT -s simRat_chr6.simRat.chr6 24465 18 - 647215 GCATTCGTGCAATAAATT - -a -s simMouse_chr6.simMouse.chr6 549507 21 + 636262 AGCTGCTTGACATCAGAAGAC -s Anc0.Anc0refChr3 152005 18 + 222631 AGCGGCTTGA---CACAAAAC -s Anc1.Anc1refChr6 187727 21 + 197743 AGCGGCTTGACACCACAAAAC -s Anc2.Anc2refChr1 65939 18 + 142988 GGTGGCTTGG---CACAAAAC -s mr.mrrefChr3 99640 21 + 181027 AGCTGCTTGACATCACAAGAC -s simCow_chr6.simCow.chr6 524022 13 + 602619 GGTGGCT--------CAAAAC -s simDog_chr6.simDog.chr6 512616 18 + 593897 GGTGGCTTGG---CACAAAAT -s simHuman_chr6.simHuman.chr6 519611 21 + 601863 AGCAGCTTGATACCACAAAAC -s simRat_chr6.simRat.chr6 24483 21 - 647215 AGCTGCTTGACATCACAAGAG - -a -s simMouse_chr6.simMouse.chr6 549528 44 + 636262 TCATTGAGCTGACCAAAGACTGGTCTCGGCTCTACGTCTAATAC -s Anc0.Anc0refChr3 152023 43 + 222631 TCATTAAGCTG-GCAAAGACTGTTCTCGGCCATGCGTCTAATCA -s Anc1.Anc1refChr6 187748 44 + 197743 TCATTAAGCTGAGCAAAGACTGTTCTCGGCCATGCGTCTAATCA -s Anc2.Anc2refChr1 65957 43 + 142988 TCAATAAGCTG-GCAAAGACTGTTCTCGGCCATGCGTCTAATCA -s mr.mrrefChr3 99661 44 + 181027 TCATTGAGCTGACCAAAGACTGGTCTCGGCTCTACGTCTAATAC -s simCow_chr6.simCow.chr6 524035 39 + 602619 TCAGTAAGCTG-GCAAAGACTGGTCTCGGCCAT----CTACTCC -s simDog_chr6.simDog.chr6 512634 43 + 593897 TCTATCAGCTG-GTGCTGACTGTTCTCGGCCATGCGTCTAATCA -s simHuman_chr6.simHuman.chr6 519632 44 + 601863 TCATTAAGCTGAGCAAAGACTGAGCTCAGCCATGTGTTTAATCA -s simRat_chr6.simRat.chr6 24506 44 - 647215 TCATTGAGCTGACCAAAGACTGGTCTCGGCTGGACGTCTAATAC - -a -s simMouse_chr6.simMouse.chr6 549572 49 + 636262 CACCAGTGTGTGTGAGCACACAGTTGATAGCTTAGACAGTCAACTTAAA -s Anc0.Anc0refChr3 152068 45 + 222631 CCCAACCATGTGTGCACACATACTTGATAGTCTAG----TCAAGTTAAG -s Anc1.Anc1refChr6 187794 45 + 197743 CCCAACCATGTGTGCACACATACTTGATAGTCTAG----TCAAGTTAAG -s Anc2.Anc2refChr1 66002 45 + 142988 CCCAACCATGTGCACACACATACTTGATAGTCAAG----TTAAGTTAAG -s mr.mrrefChr3 99705 49 + 181027 CACCAGTGTGTGTGAGCACACAGTTGATAGCTTAGACAGTCAAGTTAAA -s simCow_chr6.simCow.chr6 524076 45 + 602619 CCCAACCATGTGCACACACATACTTGATAACTAAG----TTACATTAAG -s simDog_chr6.simDog.chr6 512679 45 + 593897 CCAAACCGTGTCCACACACATCCTTGATAGTCAGG----TTAAGTTAGC -s simHuman_chr6.simHuman.chr6 519678 44 + 601863 CCCAACCATGTGTGCACTCATA-CTGATAGTCTAG----TCAAGTTAAG -s simRat_chr6.simRat.chr6 24550 49 - 647215 CTCCAGTGTTTGTGAACACACAGTGGATAGCTTAGACAGTCAAGTCAAA - -a -s simMouse_chr6.simMouse.chr6 549621 128 + 636262 CCCTCACCGTAGTACAGAGATTGAGAGACATGAGTCTTAAGCTCTTGAGTGGAAAGAGGTTATAAACTTGTTATAGCTAGGGGCTGCTTTTATCCATCCAGAAGAGTAGCTGGTGGTAATTTCCATCT -s Anc0.Anc0refChr3 152113 127 + 222631 CCCTCACTGTAATACAGAGATTGAGAATAATGAGCTGTAAGGTTTT-AGTGGTGTGAGGTGTTAAAAACTTCATAGCTACCGAAAGCTATTATCCATCTATAAAGGTAGCTGGTTGTACTTTTCATGT -s Anc1.Anc1refChr6 187839 128 + 197743 CCCTCACTGTAATACAGAGATTGAGAATAATGAGCTGTAAGGTTTTAAGTGGTGTGAGGTGTTAAAAACTTCATAGCTACCGAAAGCTATTATCCATCTATAAAGGTAGCTGGTTGTACTTTTCATGT -s Anc2.Anc2refChr1 66047 127 + 142988 CCCCCACTGTAATACAGAGATTGAGAAGAATGAGTTGTAAAGTTTT-AGTGGTGTGAGGTGTTAAAAACTTCATAGCTAGCAAAAGCTATTATCCATCTATACAGGTAGCTGGTTGTGCTTTGCATGT -s mr.mrrefChr3 99754 128 + 181027 CCCTCACTGTAGTACAGAGATTGAGAGTCATGAGCCTTAAGCTCTTGAGTGGAAAGAGGTTATAAACTTGTCATAGCTACGGGCTGCTATTATCCATCTAGAAAAGTAGCTGGTGGTAATTTTCATGT -s simCow_chr6.simCow.chr6 524121 127 + 602619 CCCCCACTGCCATACAGAGGTTGAGAGGAATGAGTTGTAAAGTTTT-AGGGGAGTGAGGTGTTAAAATGTTCATAGCTAGGACAAGCTATTACCCATCCATAGAGGTAGCTTGATGTGCTTTGCATGT -s simDog_chr6.simDog.chr6 512724 119 + 593897 TCCCCACTGTAATACAGAGATTGAAAAGAATGAGTTGTAAAGTTTT-AGTGGTGTGAGGTGTTAGAAACTTCATAGCTAGCAAAAGCTATTATCCATCTTTTCT---AGCCGGTTGTGC-----ATGT -s simHuman_chr6.simHuman.chr6 519722 123 + 601863 CCCTCACTATACTACAGAGATTGAGATTAATGAGCTGTAAGGTTTGATGT-----GAGGTGTTAAAAACTTCATAGCTACCGAAAGCTATTGTCCATCTATAAAGGTAGCTAGTTGTACTTTTCGTGT -s simRat_chr6.simRat.chr6 24617 128 - 647215 CACTCACTGCAATACAGAGAGTGAGAGTCATGGGCGTTAAGCTCTTGAATGTAGAGAGGTTATAAACTTGTCATAGCTACGGGCTGCTATTATCCATATAGAAAAGTAGCGGATGGTAATTTTCATGT - -a -s simMouse_chr6.simMouse.chr6 549749 22 + 636262 CCATAGTGTAAATGAGGGATAA -s Anc0.Anc0refChr3 152241 22 + 222631 CCATAGTGTACAGGAGGGAAAA -s Anc1.Anc1refChr6 187968 22 + 197743 CCATAGTGTACAGGAGGGAAAA -s Anc2.Anc2refChr1 66175 22 + 142988 CCATAGTGTACAGGGGGGAAAG -s mr.mrrefChr3 99882 22 + 181027 CCATAGTGTAAATGAGGGATAA -s simCow_chr6.simCow.chr6 524249 12 + 602619 CCATAGTGTACA---------- -s simDog_chr6.simDog.chr6 512844 22 + 593897 CCATAGTCTATTGGGGGGAAAG -s simHuman_chr6.simHuman.chr6 519846 22 + 601863 CTATAGTGTGCAGGAGGGAAAA -s simRat_chr6.simRat.chr6 24745 22 - 647215 CCATAGTGTATACGAGGGATAA - -a -s simMouse_chr6.simMouse.chr6 549771 30 + 636262 TAGTGCTACAACCCCTGGCAGGGGAGTTTG -s Anc0.Anc0refChr3 152264 30 + 222631 TAGTGCTACATCCTTTGACAAGGGAGAGAA -s Anc1.Anc1refChr6 187991 30 + 197743 TAGTGCTACATCCTTTGACAAGGGAGAGAA -s Anc2.Anc2refChr1 66198 30 + 142988 TAGTGCTACATCCTTTGTTAAGGGAGAGAA -s mr.mrrefChr3 99904 30 + 181027 TAGTGCTACAACCCCTGACAGGGGAGTTTA -s simCow_chr6.simCow.chr6 524261 21 + 602619 ---------ACACCTTGTTAGGGGAAAGAA -s simDog_chr6.simDog.chr6 512867 30 + 593897 TAGTGCTACATCCTTTGTTGAAGGAGAGAA -s simHuman_chr6.simHuman.chr6 519869 30 + 601863 CAATGCCACATCCTTTGACAAGGGAGAGAA -s simRat_chr6.simRat.chr6 24767 30 - 647215 TAGTGCTTCAACCCCCGACAGAGGAGTATA - -a -s simMouse_chr6.simMouse.chr6 549801 26 + 636262 AAAGAGCTCTCACCTGTAACTAGAAT -s Anc0.Anc0refChr3 152299 26 + 222631 GATGAACTCTTACCTGTAGCTACACT -s Anc1.Anc1refChr6 188026 26 + 197743 GATGAACTCTTACCTGTAGCTACACT -s Anc2.Anc2refChr1 66233 26 + 142988 GATGAACTCTTACATGTAGGTACACT -s mr.mrrefChr3 99934 26 + 181027 AAAGAGCTCTTACCTGTAGCTAGAAT -s simCow_chr6.simCow.chr6 524287 26 + 602619 AATGAACTCCTACATGTAGTTACACT -s simDog_chr6.simDog.chr6 512902 26 + 593897 GATGAACTCTTACACGTACGTTCACT -s simHuman_chr6.simHuman.chr6 519904 26 + 601863 GATGAACACTTACCTGTGGCTACACT -s simRat_chr6.simRat.chr6 24797 26 - 647215 AAGGAGCTCTTACCTGCAGCTAGAAT - -a -s simMouse_chr6.simMouse.chr6 549827 12 + 636262 ACTGCTCATTGA -s Anc0.Anc0refChr3 152327 12 + 222631 ACTCCTTATTGC -s Anc1.Anc1refChr6 188054 12 + 197743 ACTCCTTATTGC -s Anc2.Anc2refChr1 66261 12 + 142988 ACACCATACTGC -s mr.mrrefChr3 99960 12 + 181027 ACTGCTCATTGA -s simCow_chr6.simCow.chr6 524315 12 + 602619 GCACCGTACTGA -s simDog_chr6.simDog.chr6 512930 12 + 593897 ACACCATACTGC -s simHuman_chr6.simHuman.chr6 519932 12 + 601863 ACTTCTTATTGG -s simRat_chr6.simRat.chr6 24823 12 - 647215 ACTGCTCATTGA - -a -s simMouse_chr6.simMouse.chr6 549839 2 + 636262 TA -s Anc0.Anc0refChr3 152339 2 + 222631 TA -s Anc1.Anc1refChr6 188066 2 + 197743 TA -s Anc2.Anc2refChr1 66274 2 + 142988 TA -s mr.mrrefChr3 99972 2 + 181027 TA -s simCow_chr6.simCow.chr6 524328 2 + 602619 TC -s simDog_chr6.simDog.chr6 512943 2 + 593897 TA -s simHuman_chr6.simHuman.chr6 519944 2 + 601863 TA -s simRat_chr6.simRat.chr6 24835 2 - 647215 CA - -a -s simMouse_chr6.simMouse.chr6 549841 16 + 636262 AAACACTGCTGTAGTG -s Anc0.Anc0refChr3 152348 11 + 222631 AGACCTTACTG----- -s Anc1.Anc1refChr6 188075 11 + 197743 AGACCTTACTG----- -s Anc2.Anc2refChr1 66283 11 + 142988 AGACCTTACTG----- -s mr.mrrefChr3 99974 11 + 181027 AGACACTACTG----- -s simCow_chr6.simCow.chr6 524337 11 + 602619 GGACCTTCCTG----- -s simDog_chr6.simDog.chr6 512952 11 + 593897 AGACCTTACTG----- -s simHuman_chr6.simHuman.chr6 519953 11 + 601863 AGACCTTACTG----- -s simRat_chr6.simRat.chr6 24837 11 - 647215 AGACACCACTG----- - -a -s simMouse_chr6.simMouse.chr6 549857 10 + 636262 CTGGACTTGG -s Anc0.Anc0refChr3 152359 10 + 222631 CTGTGAGAAG -s Anc1.Anc1refChr6 188086 10 + 197743 CTGTGAGAAG -s Anc2.Anc2refChr1 66297 10 + 142988 CTTTGAGAAG -s mr.mrrefChr3 99985 10 + 181027 CTGGAATTAG -s simCow_chr6.simCow.chr6 524361 10 + 602619 CCCTGAGAGG -s simDog_chr6.simDog.chr6 512966 10 + 593897 CTTTGAGAAG -s simHuman_chr6.simHuman.chr6 519964 10 + 601863 TTGAGAGAAG -s simRat_chr6.simRat.chr6 24848 10 - 647215 CTAGAATTAG - -a -s simMouse_chr6.simMouse.chr6 549867 3 + 636262 AGA -s Anc0.Anc0refChr3 152375 3 + 222631 ATA -s Anc1.Anc1refChr6 188102 3 + 197743 ATA -s Anc2.Anc2refChr1 66313 3 + 142988 ATA -s mr.mrrefChr3 99995 3 + 181027 AGA -s simCow_chr6.simCow.chr6 524377 3 + 602619 GTA -s simDog_chr6.simDog.chr6 512982 3 + 593897 ATA -s simHuman_chr6.simHuman.chr6 519980 3 + 601863 ATG -s simRat_chr6.simRat.chr6 24858 3 - 647215 AGA - -a -s simMouse_chr6.simMouse.chr6 549870 106 + 636262 CACAGTAACTGACCCGGGATATGGATCGGTATTCTCCTAAATCTTAATTAGCTGTCATACCTGTATCTCTGTATGAGCCACCTGCGTGTGGAGTTGAGATTATTGA -s Anc0.Anc0refChr3 152378 29 + 222631 CACAGTAACAGGCACAGG-----------------------------------------------------------------------------GAGAATAATGT -s Anc1.Anc1refChr6 188105 29 + 197743 CACAGTAACAGGCACAGG-----------------------------------------------------------------------------GAGAATAATGT -s Anc2.Anc2refChr1 66316 29 + 142988 CACAGTAACAGGCACAGC-----------------------------------------------------------------------------GAGAATAATAT -s mr.mrrefChr3 99998 79 + 181027 CACAGTAACTGACCCAGGATATGGATCGGTATTCTCCTAAATCTT-----------------------CTGTATGAGCCACCTGCGTGTGG----GAGATTATTGA -s simCow_chr6.simCow.chr6 524380 29 + 602619 GATGGTAACAGGCAGAGT-----------------------------------------------------------------------------GAGAATATGAT -s simDog_chr6.simDog.chr6 512987 29 + 593897 CACAGTAGCTGGCACAGC-----------------------------------------------------------------------------AAGAATGATAT -s simHuman_chr6.simHuman.chr6 519983 29 + 601863 CACAGTAACAGGCACAGG-----------------------------------------------------------------------------GAGAATACTGG -s simRat_chr6.simRat.chr6 24861 70 - 647215 CACAGTGACTGACGCAGGATATGTATTGGTATTCTCCTAAATCTT-----------------------CTGTATGAGCTACCTGCTTGTGG-------------GA - -a -s simMouse_chr6.simMouse.chr6 549976 35 + 636262 ACTGTACTTCACAATCTGATAAACCCCCGGTGTTT -s Anc0.Anc0refChr3 152407 35 + 222631 ACTTTACTTCATGAAGTGGTAAACCCCTGGTGTTT -s Anc1.Anc1refChr6 188134 35 + 197743 ACTTTACTTCATGAAGTGGTAAACCCCTGGTGTTT -s Anc2.Anc2refChr1 66345 35 + 142988 ACTTTACGTAATGAAGTGGTAAACCCCTGGTGTTT -s mr.mrrefChr3 100077 35 + 181027 ACTGTACTTCACAATCTGGTAAACCCCCGGTGTTT -s simCow_chr6.simCow.chr6 524412 34 + 602619 ACTTTACCTTATGAAGTGGTAAACCCTTGGTTTT- -s simDog_chr6.simDog.chr6 513016 35 + 593897 ACTTTACGTAATAAAGTGATAAACCCCTGGTGTTT -s simHuman_chr6.simHuman.chr6 520012 35 + 601863 ACTTCACTTCGTGAAGTGGTAAACCCCTGGTGTTT -s simRat_chr6.simRat.chr6 24931 35 - 647215 ACTGTACTTCACAATCTGGTAATCCCCCGGTGTTT - -a -s simMouse_chr6.simMouse.chr6 550011 14 + 636262 TGGAAGAAAAATCT -s Anc0.Anc0refChr3 152442 14 + 222631 CGGGAAGAGAATCT -s Anc1.Anc1refChr6 188169 14 + 197743 CGGGAAGAGAATCT -s Anc2.Anc2refChr1 66380 14 + 142988 CGGGAAGAGAACCT -s mr.mrrefChr3 100112 14 + 181027 TGGAAGAAAAATCT -s simCow_chr6.simCow.chr6 524446 12 + 602619 --GGAAGAGAACCT -s simDog_chr6.simDog.chr6 513051 8 + 593897 CG------GAACCT -s simHuman_chr6.simHuman.chr6 520060 14 + 601863 CGAGAAGAGAATCT -s simRat_chr6.simRat.chr6 24966 13 - 647215 TGGAAGAAAA-TCT - -a -s simMouse_chr6.simMouse.chr6 550025 1 + 636262 G -s Anc0.Anc0refChr3 152456 1 + 222631 G -s Anc1.Anc1refChr6 188183 1 + 197743 G -s Anc2.Anc2refChr1 66394 1 + 142988 A -s mr.mrrefChr3 100126 1 + 181027 G -s simCow_chr6.simCow.chr6 524458 1 + 602619 A -s simDog_chr6.simDog.chr6 513059 1 + 593897 A -s simHuman_chr6.simHuman.chr6 520074 1 + 601863 G -s simRat_chr6.simRat.chr6 25021 1 - 647215 G - -a -s simMouse_chr6.simMouse.chr6 550026 50 + 636262 GTATAAAAGGAGAATTGTATATTTGAAGCACCATAGTATGAAATGAAAAC -s Anc0.Anc0refChr3 152499 31 + 222631 GTGTAGAAC-------------------GACAATAGTATGACTCCAAAAT -s Anc1.Anc1refChr6 188226 50 + 197743 GTGTAGAACGTCAATAATATGAAAGAAGGACAATAGTATGACTCCAAAAT -s Anc2.Anc2refChr1 66437 31 + 142988 GTGTAGAAC-------------------GACTATAGTATAACTCCAAAAT -s mr.mrrefChr3 100127 50 + 181027 GTATAAAAGGAGAATAGTATAATTGAAGGACAATAGTATGAAACCAAAAC -s simCow_chr6.simCow.chr6 524474 4 + 602619 ----------------------------------------------AAAT -s simDog_chr6.simDog.chr6 513102 31 + 593897 GTGTAGAAC-------------------GACTATAGTATAACTCCAGAAT -s simHuman_chr6.simHuman.chr6 520123 50 + 601863 GTGGAGAAAGTCAATAATATGAAAGAAGGACAACAGTATGAGTCCAAAAT -s simRat_chr6.simRat.chr6 25022 50 - 647215 ATATAAAAGGAGAATATTATAACTGAAGGACAATAGTATGAAACCAAAAC - -a -s simMouse_chr6.simMouse.chr6 550076 30 + 636262 CTCTACACCTTGGTACAAATTGAGGAATTG -s Anc0.Anc0refChr3 152534 29 + 222631 CTGTGCATCATGAGACAAATTGAGGAATT- -s Anc1.Anc1refChr6 188280 30 + 197743 CTGTGCATCATGAGACAAATTGAGGAATTA -s Anc2.Anc2refChr1 66472 29 + 142988 CAGTGCATCATGAGACAAATTGAGGAATT- -s mr.mrrefChr3 100177 30 + 181027 CTCTGCATCTTGGTACAAATTGAGGAATTG -s simCow_chr6.simCow.chr6 524482 29 + 602619 CAGTATAGTATGAGTCAAAGTGAGGAGAC- -s simDog_chr6.simDog.chr6 513137 29 + 593897 CAGTGCATCATGAAACAAATTGGGGAATT- -s simHuman_chr6.simHuman.chr6 520177 30 + 601863 CTATGCATCATGAGGCAAATTGAGGAATTA -s simRat_chr6.simRat.chr6 25072 30 - 647215 CTCTGCATCTTGGTACAAATTGAGGAATTG - -a -s simMouse_chr6.simMouse.chr6 550106 9 + 636262 TGTTGAATC -s Anc0.Anc0refChr3 152563 4 + 222631 -----TTTC -s Anc1.Anc1refChr6 188310 7 + 197743 T--TGTTTC -s Anc2.Anc2refChr1 66501 4 + 142988 -----TTCT -s mr.mrrefChr3 100207 7 + 181027 T--TGAATC -s simCow_chr6.simCow.chr6 524511 4 + 602619 -----TTAT -s simDog_chr6.simDog.chr6 513166 4 + 593897 -----TTCT -s simHuman_chr6.simHuman.chr6 520211 7 + 601863 T--TGTTTC -s simRat_chr6.simRat.chr6 25102 7 - 647215 T--TGGATA - -a -s simMouse_chr6.simMouse.chr6 550115 10 + 636262 TAGCCTTGGC -s Anc0.Anc0refChr3 152572 9 + 222631 TAGGCTTG-T -s Anc1.Anc1refChr6 188322 9 + 197743 TAGGCTTG-T -s Anc2.Anc2refChr1 66511 9 + 142988 TAAGCTTG-T -s mr.mrrefChr3 100214 10 + 181027 TAGCCTTGGC -s simCow_chr6.simCow.chr6 524521 9 + 602619 TAAACTGG-T -s simDog_chr6.simDog.chr6 513176 9 + 593897 TAAGCTTG-T -s simHuman_chr6.simHuman.chr6 520223 9 + 601863 TGGGCTTG-T -s simRat_chr6.simRat.chr6 25109 10 - 647215 TAGCCTTGGC - -a -s simMouse_chr6.simMouse.chr6 550125 51 + 636262 CATAATCATTTTGAATTAGGTAATCCCTCAGTCATGTGTTGCTAACAGATA -s Anc0.Anc0refChr3 152581 38 + 222631 AATGA-------------TGTGATCCCTCATACATCTGTTTCTGAAAGATA -s Anc1.Anc1refChr6 188331 38 + 197743 AATGA-------------TGTGATCCCTCATACATCTGTTTCTGAAAGATA -s Anc2.Anc2refChr1 66534 38 + 142988 AATGA-------------TGTGATCCCTCATACATCTGTTTCTGAAAGACT -s mr.mrrefChr3 100224 38 + 181027 CATAA-------------GGTAATCCCTCAGTCATGTGTTGCTAACAGATA -s simCow_chr6.simCow.chr6 524544 36 + 602619 AATGA-------------TGCCATCCT--ATATATATGTTTCTGACAAATA -s simDog_chr6.simDog.chr6 513199 38 + 593897 AATGA-------------TGTGATCCCTCATACATCTGTTTCTGAACGACT -s simHuman_chr6.simHuman.chr6 520232 38 + 601863 AATGA-------------CCTGATCTCTCATACAGCTGTGTCAGAAAGATA -s simRat_chr6.simRat.chr6 25119 38 - 647215 TATAA-------------GGTAATCCCTCAGACATGTGTTCCTAACAGATA - -a -s simMouse_chr6.simMouse.chr6 550176 3 + 636262 GAG -s Anc0.Anc0refChr3 152619 3 + 222631 GAA -s Anc1.Anc1refChr6 188369 3 + 197743 GAA -s Anc2.Anc2refChr1 66572 3 + 142988 GAA -s mr.mrrefChr3 100262 3 + 181027 GAG -s simCow_chr6.simCow.chr6 524580 3 + 602619 GAA -s simDog_chr6.simDog.chr6 513237 3 + 593897 GAA -s simHuman_chr6.simHuman.chr6 520270 2 + 601863 GA- -s simRat_chr6.simRat.chr6 25165 3 - 647215 GGA - -a -s simMouse_chr6.simMouse.chr6 550179 34 + 636262 AAATCAAATAATATACCTGTGTGTACAGTTCCCA -s Anc0.Anc0refChr3 152622 32 + 222631 AATTCAGA-AATATTCATGTGAGAGCAGTCACC- -s Anc1.Anc1refChr6 188372 33 + 197743 AATTCAGA-AATATTCATGTGAGAGCAGTCACCA -s Anc2.Anc2refChr1 66581 32 + 142988 AATTCAGA-AACATTCATGTGAGAGCAGTCACC- -s mr.mrrefChr3 100265 34 + 181027 AAATCAAATAATATACCTGTGTGTACAGTTCCCA -s simCow_chr6.simCow.chr6 524589 32 + 602619 GATACTGT-AGCATTCATGTAAGAAGAGCCACC- -s simDog_chr6.simDog.chr6 513246 32 + 593897 AATTCAGA-AATGTTTCTGTGAGAGCAGTCACC- -s simHuman_chr6.simHuman.chr6 520272 12 + 601863 -----------TAT-----------CAGTCACCA -s simRat_chr6.simRat.chr6 25168 34 - 647215 AAATCAAGTAATATTCCTATGTGTACAGGTACCA - -a -s simMouse_chr6.simMouse.chr6 550213 54 + 636262 GCTCATGCCCTTCCTGCCCACAGCCCCCTTTTTGTGTACATATTATCAGTACAG -s Anc0.Anc0refChr3 152654 34 + 222631 -------CCACCCATACCCTCAGTCCTCTCTTTGCATACCT------------- -s Anc1.Anc1refChr6 188405 35 + 197743 G------CCACCCATACCCTCAGTCCTCTCTTTGCATACCT------------- -s Anc2.Anc2refChr1 66613 34 + 142988 -------CCACCCATACCCTCAGTCCTCTCTTTGCATACCT------------- -s mr.mrrefChr3 100299 54 + 181027 GCTCATGCCCTTCCTGCCCACAGCCCCCTTTTTGTGTACATATTATCAGTACAG -s simCow_chr6.simCow.chr6 524621 34 + 602619 -------ACACACATGCCCTCAGTTCCCTTTCTGCATACCA------------- -s simDog_chr6.simDog.chr6 513278 34 + 593897 -------CCACCCATACCCTCAGTCCTCTCTTTGCATACCT------------- -s simHuman_chr6.simHuman.chr6 520284 1 + 601863 G----------------------------------------------------- -s simRat_chr6.simRat.chr6 25203 54 - 647215 GCTCATGCCCTTCCGGCCCACAGCCCCCTTCTTGTGTACATATTATCAGTACAA - -a -s simMouse_chr6.simMouse.chr6 550267 2 + 636262 CT -s Anc0.Anc0refChr3 152688 2 + 222631 TA -s Anc1.Anc1refChr6 188440 2 + 197743 TA -s Anc2.Anc2refChr1 66647 2 + 142988 TA -s mr.mrrefChr3 100353 2 + 181027 CT -s simCow_chr6.simCow.chr6 524655 2 + 602619 TA -s simDog_chr6.simDog.chr6 513325 2 + 593897 TA -s simRat_chr6.simRat.chr6 25257 2 - 647215 CT - -a -s simMouse_chr6.simMouse.chr6 550269 32 + 636262 GAGCAACTGACTCAAATGACCTAGCTACTGAC -s Anc0.Anc0refChr3 152690 30 + 222631 AAGTAACTGACTCAA--GGTAAACCCACTTAC -s Anc1.Anc1refChr6 188442 32 + 197743 AAGTAACTGACTCAAATGGTAAACCCACTTAC -s Anc2.Anc2refChr1 66649 30 + 142988 AAGTAGTTGTGTCCA--GGTAAGCCCACTTAC -s mr.mrrefChr3 100355 32 + 181027 GAGCAACTGACTCAAATGACCTAGCTACTGAC -s simCow_chr6.simCow.chr6 524657 28 + 602619 GAGCAGGTGAGTCCA--GGGTAGGTC--TTAC -s simDog_chr6.simDog.chr6 513327 27 + 593897 AAGTAGTTGTGTCCA--GGTAAGCCCACT--- -s simHuman_chr6.simHuman.chr6 520285 27 + 601863 -----ACCCACTCACATGTTAGACCCACTCAC -s simRat_chr6.simRat.chr6 25272 32 - 647215 GAGTAACTGACTCAAATGACCTATCTACTGAC - -a -s simMouse_chr6.simMouse.chr6 550301 78 + 636262 CCATGGACCAATCACCAAGGCAAGAGCTACATTAAAGCAAAATCACAGTACCCGATGTCTTATTTATGATTTCAGTAC -s Anc0.Anc0refChr3 152743 34 + 222631 CCAGAACCCACT------------------------------------TAT--------TGATTTTTGATTTCCGCAC -s Anc1.Anc1refChr6 188497 34 + 197743 CCAGAACCCACT------------------------------------TAT--------TGATTTTTGATTTCCGCAC -s Anc2.Anc2refChr1 66702 34 + 142988 TCAGAACCCACT------------------------------------TAT--------TGATTTTTAATTTCCACAC -s mr.mrrefChr3 100387 38 + 181027 CCATGGACCAATC--------------------------------CAGTAC--------TTATTTATGATTTCAGTAC -s simCow_chr6.simCow.chr6 524708 34 + 602619 ACTGGACCCACT------------------------------------TAT--------TGATTTTTAATTTCCACAC -s simDog_chr6.simDog.chr6 513375 7 + 593897 TCAGAGC----------------------------------------------------------------------- -s simHuman_chr6.simHuman.chr6 520335 34 + 601863 CCAAAACTGAGT------------------------------------TTT--------AGATTCTTGATTACTGCAC -s simRat_chr6.simRat.chr6 25304 38 - 647215 CCATAGACCAATC--------------------------------TAGTAT--------TTATTTTTGATTACAGCAC - -a -s simMouse_chr6.simMouse.chr6 550379 6 + 636262 TAACTG -s Anc1.Anc1refChr6 188543 6 + 197743 TGACTG -s mr.mrrefChr3 100425 6 + 181027 TAACTG -s simHuman_chr6.simHuman.chr6 520405 6 + 601863 TGACTG -s simRat_chr6.simRat.chr6 25342 6 - 647215 TAACGG - -a -s simMouse_chr6.simMouse.chr6 550385 56 + 636262 CTGGCAAATAAAACAGAGGTACACCAATGGGGATGGAATTGATCCAATTGATTGCC -s Anc0.Anc0refChr3 152789 26 + 222631 ----------------------------AAAGGAGGAAGCGATCCAAT--GTTGGA -s Anc1.Anc1refChr6 188549 56 + 197743 CTGCCAGAAAAAAAGGGGAGCCTTTAACAAAGGAGGAAGCGATCCAATAAGTTGGA -s Anc2.Anc2refChr1 66748 26 + 142988 ----------------------------AAAGGAGGAAGCGATCTGGT--GTTGGA -s mr.mrrefChr3 100431 56 + 181027 CTGGCAAATAAAACAGAGGTACACCAATGGGGATGGAATTGATCCAATTGATTGCC -s simCow_chr6.simCow.chr6 524754 22 + 602619 --------------------------------GAGAAGGCTAGTGGGT--GCAGTA -s simDog_chr6.simDog.chr6 513382 26 + 593897 ----------------------------AAAGGAAGAAGTGATCTGGT--GTTAGG -s simHuman_chr6.simHuman.chr6 520413 56 + 601863 CTGCCAGAAAAAAAGGGGAGCCTTTAACAAAGGGGGAAACGATCCAATAAGTTGGA -s simRat_chr6.simRat.chr6 25348 56 - 647215 CTGTCAAATAAAACAGAGATTCGTCAACGGGGGTGGAATTGATTCGATTGATTGCT - -a -s simMouse_chr6.simMouse.chr6 550441 5 + 636262 GTTAG -s Anc0.Anc0refChr3 152815 5 + 222631 GTTAG -s Anc1.Anc1refChr6 188605 5 + 197743 GTTAG -s Anc2.Anc2refChr1 66774 5 + 142988 GTTAG -s mr.mrrefChr3 100487 5 + 181027 GTTAG -s simCow_chr6.simCow.chr6 524776 5 + 602619 TATAG -s simDog_chr6.simDog.chr6 513411 5 + 593897 GTCGG -s simHuman_chr6.simHuman.chr6 520469 5 + 601863 GTTAG -s simRat_chr6.simRat.chr6 25404 5 - 647215 GTTAG - -a -s simMouse_chr6.simMouse.chr6 550446 3 + 636262 CAT -s Anc0.Anc0refChr3 152821 3 + 222631 CAT -s Anc1.Anc1refChr6 188611 3 + 197743 CAT -s Anc2.Anc2refChr1 66780 3 + 142988 CAT -s mr.mrrefChr3 100492 3 + 181027 CAT -s simCow_chr6.simCow.chr6 524782 3 + 602619 TGT -s simDog_chr6.simDog.chr6 513417 3 + 593897 CAT -s simHuman_chr6.simHuman.chr6 520475 3 + 601863 CAT -s simRat_chr6.simRat.chr6 25410 3 - 647215 CAT - -a -s simMouse_chr6.simMouse.chr6 550449 27 + 636262 ACATATATGGAACCTATACCATAAGAG -s Anc0.Anc0refChr3 152824 27 + 222631 AGGTAAGTAGAACCTATGCCACAAGAG -s Anc1.Anc1refChr6 188614 27 + 197743 AGGTAAGTAGAACCTATGCCACAAGAG -s Anc2.Anc2refChr1 66783 27 + 142988 AGGTAAGAAGAAACTATGCTACAAGAG -s mr.mrrefChr3 100495 27 + 181027 ACATATATGGAACCTATACCATAAGAG -s simCow_chr6.simCow.chr6 524786 27 + 602619 AGATAAGAAGAAGATTTGTGAACAAAG -s simDog_chr6.simDog.chr6 513420 27 + 593897 GGGCAAGAAGAAACCATGCTTCAAGAA -s simHuman_chr6.simHuman.chr6 520478 27 + 601863 AGGTAAGTAGAACCTATGCCACAAGAG -s simRat_chr6.simRat.chr6 25413 27 - 647215 GCATATATGGAACCTACACCATAAGAA - -a -s simMouse_chr6.simMouse.chr6 550476 8 + 636262 ATGAGCAT -s Anc0.Anc0refChr3 152854 8 + 222631 AGAAGGAT -s Anc1.Anc1refChr6 188644 8 + 197743 AGAAGGAT -s Anc2.Anc2refChr1 66813 8 + 142988 AGAAGGAT -s mr.mrrefChr3 100522 8 + 181027 ATGAGCAT -s simCow_chr6.simCow.chr6 524816 8 + 602619 AAAGTGAT -s simDog_chr6.simDog.chr6 513450 8 + 593897 AGAAGGAC -s simHuman_chr6.simHuman.chr6 520508 8 + 601863 AGAAGGAT -s simRat_chr6.simRat.chr6 25440 8 - 647215 ATGAGCAT - -a -s simMouse_chr6.simMouse.chr6 550484 4 + 636262 TAAA -s Anc0.Anc0refChr3 152862 4 + 222631 TAGA -s Anc1.Anc1refChr6 188652 4 + 197743 TAGA -s Anc2.Anc2refChr1 66821 4 + 142988 TAGA -s mr.mrrefChr3 100530 4 + 181027 TAAA -s simCow_chr6.simCow.chr6 524848 4 + 602619 TAGG -s simDog_chr6.simDog.chr6 513458 4 + 593897 TAGA -s simHuman_chr6.simHuman.chr6 520516 4 + 601863 TAGA -s simRat_chr6.simRat.chr6 25448 4 - 647215 TAAA - -a -s simMouse_chr6.simMouse.chr6 550488 8 + 636262 CCTCAGCA -s Anc0.Anc0refChr3 152866 8 + 222631 CCTCAGCA -s Anc1.Anc1refChr6 188656 8 + 197743 CCTCAGCA -s Anc2.Anc2refChr1 66870 8 + 142988 CCTCAGCA -s mr.mrrefChr3 100534 8 + 181027 CCTCAGCA -s simCow_chr6.simCow.chr6 524897 8 + 602619 CCTAAACA -s simDog_chr6.simDog.chr6 513508 8 + 593897 CCTCAGAA -s simHuman_chr6.simHuman.chr6 520520 8 + 601863 CCTCAGCT -s simRat_chr6.simRat.chr6 25452 8 - 647215 CCCCAGCA - -a -s simMouse_chr6.simMouse.chr6 550496 11 + 636262 AGCATACCAGC -s Anc0.Anc0refChr3 152875 10 + 222631 G-TGTATCAGC -s Anc1.Anc1refChr6 188665 10 + 197743 G-TGTATCAGC -s Anc2.Anc2refChr1 66879 10 + 142988 G-TGTATCAGG -s mr.mrrefChr3 100542 10 + 181027 A-CATACCAGC -s simCow_chr6.simCow.chr6 524906 9 + 602619 G-TGAATT-GG -s simDog_chr6.simDog.chr6 513517 10 + 593897 G-TGTACCAGG -s simHuman_chr6.simHuman.chr6 520529 10 + 601863 G-TCTATCATC -s simRat_chr6.simRat.chr6 25460 10 - 647215 A-CGTATCAGT - -a -s simMouse_chr6.simMouse.chr6 550507 26 + 636262 CTTAGCATTGTTGTTCATACATACTG -s Anc0.Anc0refChr3 152886 26 + 222631 CTTTGGATTGTTCTTCAAATTTCTTG -s Anc1.Anc1refChr6 188676 26 + 197743 CTTTGGATTGTTCTTCAAATTTCTTG -s Anc2.Anc2refChr1 66890 26 + 142988 CTTTGGATTGTTCTTCAAATTTCTTT -s mr.mrrefChr3 100552 26 + 181027 CTTAGCATTGTTGTTCATACATACTG -s simCow_chr6.simCow.chr6 524916 26 + 602619 GTTTGGATTGCTGTTGACATATCTTT -s simDog_chr6.simDog.chr6 513528 26 + 593897 CTCTAGATTGTGCTTCAAGTTTCTCT -s simHuman_chr6.simHuman.chr6 520540 26 + 601863 CTTCGGATTGTTTTTCAAATTTCTTG -s simRat_chr6.simRat.chr6 25470 26 - 647215 TTTAGCATTGTTGTTCATACATACTG - -a -s simMouse_chr6.simMouse.chr6 550533 54 + 636262 TCCTAAAGGGCCCCCTATGATCAACAGTAACTTGTAGTTATCATACCCAAGTGA -s Anc0.Anc0refChr3 152913 54 + 222631 TCCTAAAAGTCCCCCTATCATCATCAGCAATTTTTTGTCCACACACCCAAGTGA -s Anc1.Anc1refChr6 188703 54 + 197743 TCCTAAAAGTCCCCCTATCATCATCAGCAATTTTTTGTCCACACACCCAAGTGA -s Anc2.Anc2refChr1 66917 54 + 142988 TCCTGGTAGTTCCCCTATCATCTTCAGCAATCTTTTGTCCACACACCCAAGTGA -s mr.mrrefChr3 100578 54 + 181027 TCCTAAAGGGCCCCCTATGATCAACAGTAACTTGTAGTTATCATACCCAAGTGA -s simCow_chr6.simCow.chr6 524943 54 + 602619 TCCTGGCAGCTCCCCTATGATCTTCAGCAATGAATTGTCCACACACACACATGA -s simDog_chr6.simDog.chr6 513555 53 + 593897 TCCTGGTAGTTCCCCTATCATCTTCAGCAATCTTG-GTCCACCCAGCCAAGTGA -s simHuman_chr6.simHuman.chr6 520567 54 + 601863 TCCAAAAAGTCCCCCTATAACCATCATCAGTTTTTTGGCCACACGCCCAAGTGA -s simRat_chr6.simRat.chr6 25496 54 - 647215 TCCTAAAGGGCCCCCTATGATCAACGGTAACTTGTAGTCATCATACCCAAGTGA - -a -s simMouse_chr6.simMouse.chr6 550587 7 + 636262 AAGGGCC -s Anc0.Anc0refChr3 152975 7 + 222631 ATTTGTG -s Anc1.Anc1refChr6 188765 7 + 197743 ATTTGTG -s Anc2.Anc2refChr1 66979 7 + 142988 ATTTGTG -s mr.mrrefChr3 100632 7 + 181027 AAGGGCC -s simCow_chr6.simCow.chr6 525005 7 + 602619 CTTTTTG -s simDog_chr6.simDog.chr6 513616 7 + 593897 ATTTGTA -s simHuman_chr6.simHuman.chr6 520629 7 + 601863 ACCTGTG -s simRat_chr6.simRat.chr6 25550 7 - 647215 ATAGGCC - -a -s simMouse_chr6.simMouse.chr6 550594 5 + 636262 ATTGG -s Anc0.Anc0refChr3 152982 5 + 222631 ACTGG -s Anc1.Anc1refChr6 188772 5 + 197743 ACTGG -s Anc2.Anc2refChr1 66992 5 + 142988 ACTGA -s mr.mrrefChr3 100639 5 + 181027 ATTGG -s simCow_chr6.simCow.chr6 525018 5 + 602619 CCTTA -s simDog_chr6.simDog.chr6 513629 5 + 593897 ACTGA -s simHuman_chr6.simHuman.chr6 520636 5 + 601863 ACTTG -s simRat_chr6.simRat.chr6 25557 5 - 647215 ACTGG - -a -s simMouse_chr6.simMouse.chr6 550599 33 + 636262 CACCCAAGGTCCACAAAAGTAACAGTTTGTAAC -s Anc0.Anc0refChr3 152993 33 + 222631 CACCCAGAGTCGGCAAGGGCAAGTTTTTGTAAC -s Anc1.Anc1refChr6 188783 33 + 197743 CACCCAGAGTCGGCAAGGGCAAGTTTTTGTAAC -s Anc2.Anc2refChr1 67003 33 + 142988 CACCCAGAGTCGGCAAGGGCAAGTTTTTGTAAC -s mr.mrrefChr3 100644 33 + 181027 CACCCAAGGTCCACAAAAGTAACAGTTTGTAAC -s simCow_chr6.simCow.chr6 525029 33 + 602619 CACCCAGAGTCAGCAACGGCGAATTTTTGCAAC -s simDog_chr6.simDog.chr6 513640 33 + 593897 CACCCAGAGTCGGCAAGGGTAAGTTGTTGTAAC -s simHuman_chr6.simHuman.chr6 520647 33 + 601863 CACCCAGAGTTGGGAAGGGCAAGTTTATGTAAC -s simRat_chr6.simRat.chr6 25562 33 - 647215 CACCAAAGGCCCACAAAGGTAAGAGTTTAGAAC - -a -s simMouse_chr6.simMouse.chr6 550632 38 + 636262 CACGCTAGAAGGCAGCTTATAGCCATCTACACATTTCT -s Anc0.Anc0refChr3 153026 35 + 222631 CACAC---AAGGCAGCCTATGGCCTTCTCTGCATTTCT -s Anc1.Anc1refChr6 188816 35 + 197743 CACAC---AAGGCAGCCTATGGCCTTCTCTGCATTTCT -s Anc2.Anc2refChr1 67036 35 + 142988 CACAT---AATGCAGCCTATGGCCTTCTCTGCATTTCT -s mr.mrrefChr3 100677 38 + 181027 CACGCTAGAAGGCAGCTTATAGCCATCTACACATTTCT -s simCow_chr6.simCow.chr6 525065 35 + 602619 CACAG---AATGCAGCCTATGGCCCTCTCTGCATTTCT -s simDog_chr6.simDog.chr6 513673 34 + 593897 CACAT---GATGCAGCCTGTGGC-TTCTCTGTGTTTCT -s simHuman_chr6.simHuman.chr6 520680 35 + 601863 CACAC---AAGGGATCCTATGGCCTTCTCTGCATTTCT -s simRat_chr6.simRat.chr6 25595 38 - 647215 CACATTAGCAGGCAGTCTATGACCTTCTAAACATTTCT - -a -s simMouse_chr6.simMouse.chr6 550670 5 + 636262 TCTTA -s Anc0.Anc0refChr3 153069 5 + 222631 TCTTC -s Anc1.Anc1refChr6 188859 5 + 197743 TCTTC -s Anc2.Anc2refChr1 67079 5 + 142988 TCTTC -s mr.mrrefChr3 100715 5 + 181027 TCTTA -s simCow_chr6.simCow.chr6 525108 5 + 602619 TCATC -s simDog_chr6.simDog.chr6 513715 5 + 593897 ACTTC -s simHuman_chr6.simHuman.chr6 520726 5 + 601863 TCTTC -s simRat_chr6.simRat.chr6 25633 5 - 647215 TCTTC - -a -s simMouse_chr6.simMouse.chr6 550675 51 + 636262 AATCCCAGTGGCACTCTTCTTCTCCTTTTCTTTTCTCTTAGTTCTTTTCTC -s Anc0.Anc0refChr3 153076 49 + 222631 AATCCCATGACCTCTCTTCTCT--CTTTTCTTTTTTCCTATTTCTTTTCTC -s Anc1.Anc1refChr6 188866 49 + 197743 AATCCCATGACCTCTCTTCTCT--CTTTTCTTTTTTCCTATTTCTTTTCTC -s Anc2.Anc2refChr1 67086 49 + 142988 AATCCCATGACCTCTGTTATCT--TCTTTCTTTTTTCCTATTTCTTTTCTC -s mr.mrrefChr3 100720 51 + 181027 AATCCCAGTGGCACTCTTCTTCTCCTTTTCTTTTCTCTTAGTTCTTTTCTC -s simCow_chr6.simCow.chr6 525115 49 + 602619 AACCCCATGACCTCTGTTATCT--TCTTTCCTTTTTCCCATTTCTTTTCTC -s simDog_chr6.simDog.chr6 513722 49 + 593897 GATGACATGACCCCTGCTATCT--TCTTCCTTTTTTCCTATTTCTTTTCTT -s simHuman_chr6.simHuman.chr6 520733 49 + 601863 AATCCCATGACATCTCTTCTCT--CTTTTCTTTTTTCCTCTTTCTTTTCTC -s simRat_chr6.simRat.chr6 25638 51 - 647215 AATTCCAGTACCTCTCTTCTTCTCCCTTTCTTTTCTCCTAGTCCTTTTCTC - -a -s simMouse_chr6.simMouse.chr6 550726 2 + 636262 AC -s Anc0.Anc0refChr3 153125 2 + 222631 AC -s Anc1.Anc1refChr6 188915 2 + 197743 AC -s Anc2.Anc2refChr1 67135 2 + 142988 AC -s mr.mrrefChr3 100771 2 + 181027 AC -s simCow_chr6.simCow.chr6 525168 2 + 602619 AT -s simDog_chr6.simDog.chr6 513771 2 + 593897 AC -s simHuman_chr6.simHuman.chr6 520782 2 + 601863 AC -s simRat_chr6.simRat.chr6 25689 2 - 647215 AC - -a -s simMouse_chr6.simMouse.chr6 550728 5 + 636262 AACTA -s Anc0.Anc0refChr3 153128 5 + 222631 AACTA -s Anc1.Anc1refChr6 188918 5 + 197743 AACTA -s Anc2.Anc2refChr1 67138 5 + 142988 AACTA -s mr.mrrefChr3 100773 5 + 181027 AACTA -s simCow_chr6.simCow.chr6 525171 5 + 602619 AACAA -s simDog_chr6.simDog.chr6 513774 5 + 593897 AACTA -s simHuman_chr6.simHuman.chr6 520785 5 + 601863 AACTA -s simRat_chr6.simRat.chr6 25691 5 - 647215 AACTA - -a -s simMouse_chr6.simMouse.chr6 550733 64 + 636262 TAAACATTTCAGATTGAAAAGAGTAAGGGAGAGTGTACTGCAGACACACAAGAAATTGTCTATC -s Anc0.Anc0refChr3 153146 40 + 222631 TAAACACTTCAGATTGAG--------GGGGAGGGGTACTGTTGATCC----------------C -s Anc1.Anc1refChr6 188936 40 + 197743 TAAACACTTCAGATTGAG--------GGGGAGGGGTACTGTTGATCC----------------C -s Anc2.Anc2refChr1 67156 40 + 142988 TAAACACTTCAGTTTGAG--------GGGGAGGGGTACTGTTGGTCC----------------A -s mr.mrrefChr3 100778 48 + 181027 TAAACATTTCAGATTGAAAAGAGTAAGGGAGAGTGTACTGCAGACAC----------------C -s simCow_chr6.simCow.chr6 525189 40 + 602619 TAAACACTTCAGTTTGAA--------GGGCAGGGCTACTGTTGGTCC----------------A -s simDog_chr6.simDog.chr6 513792 32 + 593897 TAATCAT--------GAG--------GGAGGGAGGTCCTGTTGGCCC----------------A -s simHuman_chr6.simHuman.chr6 520803 40 + 601863 TAGACACTTCAGAGCAAG--------GGGGAGGAGTAACATTGATCC----------------C -s simRat_chr6.simRat.chr6 25696 48 - 647215 TAAACACTCTAGAGCGAGAAGAGTAAAGAAGGTTGTACTGTGGACAC----------------C - -a -s simMouse_chr6.simMouse.chr6 550797 48 + 636262 ATTTTGGAAGTTGACAACTGATAAGATGGTGCTGATAACTGATATGAT -s Anc1.Anc1refChr6 188987 40 + 197743 ATTTCAGAAATTGGTAA----TAAAA--GTGAGGACAA--GATAAGTC -s mr.mrrefChr3 100826 48 + 181027 ATTTTGGAAGTTGACAACTGATAAGATGGTGCTGATAACTGATATGAT -s simHuman_chr6.simHuman.chr6 520859 40 + 601863 ATTTCAGAAATTGGTAA----TAAAA--GTGAGGACAA--GATAAGTC -s simRat_chr6.simRat.chr6 25744 48 - 647215 ACTTTTGAAGTTCATAACTGATAAGATGGTGCTGATAACTAGTATGAT - -a -s simMouse_chr6.simMouse.chr6 550845 29 + 636262 GGTGTAGCCTGGGGAAGAGCAACCTCCCA -s Anc0.Anc0refChr3 153197 10 + 222631 -------------------CTACCTCCCA -s Anc1.Anc1refChr6 189027 29 + 197743 ACTTTAGCTCCCATGAGAGCTACCTCCCA -s Anc2.Anc2refChr1 67207 10 + 142988 -------------------CTACCTCCCA -s mr.mrrefChr3 100874 29 + 181027 GGTGTAGCCTGGGGAAGAGCAACCTCCCA -s simCow_chr6.simCow.chr6 525240 10 + 602619 -------------------CTACCTCCCC -s simDog_chr6.simDog.chr6 513835 10 + 593897 -------------------CTACCTCCCA -s simHuman_chr6.simHuman.chr6 520902 29 + 601863 ACTTTAGCTCCCATGAGAGCTGCTTCCTA -s simRat_chr6.simRat.chr6 25792 29 - 647215 GGTGTAGCCCAGGGAAGAGCAGCCTCCCA - -a -s simMouse_chr6.simMouse.chr6 550874 65 + 636262 CATCCAGTAATGTTAGCCCAGCCTTCCTAGGGCAAGAATATGAGGGAATAAACACAGTTTCTGTA -s Anc0.Anc0refChr3 153209 65 + 222631 CATGCAGTAATGTTAGCGCAACTTTCCTAGGGCAGGAAGAGGAGGGTTTAAACATAATTTCTCTG -s Anc1.Anc1refChr6 189058 65 + 197743 CATGCAGTAATGTTAGCGCAACTTTCCTAGGGCAGGAAGAGGAGGGTTTAAACATAATTTCTCTG -s Anc2.Anc2refChr1 67219 65 + 142988 CATGCAGTAATGTTAGCGCAACTTTCATTGGGCAGGAAGAGGAGGGTTTAAACATAATTTCTCTG -s mr.mrrefChr3 100903 65 + 181027 CATCCAGTAATGTTAGCCCAGCCTTCCTAGGGCAAGAATATGAGGGAATAAACACAGTTTCTGTA -s simCow_chr6.simCow.chr6 525252 64 + 602619 CATGCAGTACTCTTAGCTCAATTGTCATTGGGCAAGAATAGGAGGGCGGAAACATAACTTCT-TG -s simDog_chr6.simDog.chr6 513847 65 + 593897 CATAGAGTAATGTTAGTGCAACTTCCATTGGGCAGGAAGATGAGGATTTGAACGTAATTTCTCTG -s simHuman_chr6.simHuman.chr6 520933 65 + 601863 CATGCAGTAATGTTAGCACAACTATTCAAGGGGATCAGGGGGGGGGTCCAAACATAATTTTTCTG -s simRat_chr6.simRat.chr6 25821 65 - 647215 CATGCAGTGATGTTAGCCCAGCTTTCCTAGGGCAAGAATATGAGGGGACTGATACAATTTCTCTA - -a -s simMouse_chr6.simMouse.chr6 550939 9 + 636262 GTTCAGTGT -s Anc0.Anc0refChr3 153274 9 + 222631 GTTCCCTGT -s Anc1.Anc1refChr6 189123 9 + 197743 GTTCCCTGT -s Anc2.Anc2refChr1 67284 9 + 142988 ATTCCCTGT -s mr.mrrefChr3 100968 9 + 181027 GTTCAGTGT -s simCow_chr6.simCow.chr6 525316 9 + 602619 ATGCACAGG -s simDog_chr6.simDog.chr6 513918 9 + 593897 ATTCCATGT -s simHuman_chr6.simHuman.chr6 520998 9 + 601863 GTTCTCTGT -s simRat_chr6.simRat.chr6 25886 9 - 647215 GTTCAGTAT - -a -s simMouse_chr6.simMouse.chr6 550948 24 + 636262 CTGTGATAAGTAAAAGTATCATGT -s Anc0.Anc0refChr3 153283 13 + 222631 TTAATGTAATTCA----------- -s Anc1.Anc1refChr6 189132 13 + 197743 TTAATGTAATTCA----------- -s Anc2.Anc2refChr1 67293 13 + 142988 TTAATGTAATTCA----------- -s mr.mrrefChr3 100977 24 + 181027 CTGTGATAAGTAAAAGTATCATGT -s simCow_chr6.simCow.chr6 525325 13 + 602619 TTAATGCAATTCA----------- -s simDog_chr6.simDog.chr6 513936 13 + 593897 TTTATGTAATTCA----------- -s simHuman_chr6.simHuman.chr6 521007 13 + 601863 TCAATCTAATTCA----------- -s simRat_chr6.simRat.chr6 25895 24 - 647215 CTGTGATAAGTAAAAGTATCCTAG - -a -s simMouse_chr6.simMouse.chr6 550972 25 + 636262 TCCTACAGTTTTGTCTTAATTGATT -s Anc0.Anc0refChr3 153296 11 + 222631 --------------CCTGCTTGATT -s Anc1.Anc1refChr6 189145 11 + 197743 --------------CCTGCTTGATT -s Anc2.Anc2refChr1 67306 11 + 142988 --------------GCTGCTTTAAT -s mr.mrrefChr3 101001 25 + 181027 TCCTACAGTTTTGTCTTAATTGATT -s simCow_chr6.simCow.chr6 525338 11 + 602619 --------------ACTGCTCTAAT -s simDog_chr6.simDog.chr6 513949 11 + 593897 --------------GTTACTTTAAT -s simHuman_chr6.simHuman.chr6 521020 11 + 601863 --------------CCTGCCTGATT -s simRat_chr6.simRat.chr6 25924 25 - 647215 TTCTGCCATTTTGCCTTAATTGATT - -a -s simMouse_chr6.simMouse.chr6 550997 10 + 636262 GTGCTAATAT -s Anc0.Anc0refChr3 153308 10 + 222631 GTGTGAATAT -s Anc1.Anc1refChr6 189157 10 + 197743 GTGTGAATAT -s Anc2.Anc2refChr1 67318 10 + 142988 GTGTGAATAT -s mr.mrrefChr3 101026 10 + 181027 GTGCTAATAT -s simCow_chr6.simCow.chr6 525350 10 + 602619 GTGTGAATAT -s simDog_chr6.simDog.chr6 513961 10 + 593897 ATATTAATAT -s simHuman_chr6.simHuman.chr6 521032 10 + 601863 GTGTGGATAT -s simRat_chr6.simRat.chr6 25949 10 - 647215 GTGCTAATAT - -a -s simMouse_chr6.simMouse.chr6 551007 20 + 636262 ATTACAGGGAAGTCAAGCTT -s Anc0.Anc0refChr3 153336 20 + 222631 ATTATAGGGACAACGAGCTA -s Anc1.Anc1refChr6 189185 20 + 197743 ATTATAGGGACAACGAGCTA -s Anc2.Anc2refChr1 67346 20 + 142988 ATTATAGGGACAACGATCTA -s mr.mrrefChr3 101036 20 + 181027 ATTACAGGGAAGTCAAGCTT -s simCow_chr6.simCow.chr6 525378 20 + 602619 ATTACAGGTACAACAATCTA -s simDog_chr6.simDog.chr6 513989 20 + 593897 ATTATAGGGACAACGATCTA -s simHuman_chr6.simHuman.chr6 521060 20 + 601863 ATTATAGGGACAAGGAGCTG -s simRat_chr6.simRat.chr6 25959 20 - 647215 ATTACAGGGATGTCAAGCTC - -a -s simMouse_chr6.simMouse.chr6 551027 38 + 636262 TTTCTCATCCTAATGTTACTTTTTAACTATGAGATGAA -s Anc0.Anc0refChr3 153356 38 + 222631 TATCTCATCCTGGTTTCATTTTTTAATTAGGAGATGGA -s Anc1.Anc1refChr6 189205 38 + 197743 TATCTCATCCTGGTTTCATTTTTTAATTAGGAGATGGA -s Anc2.Anc2refChr1 67366 38 + 142988 TAACTCATCCTGGTTTCATTTTTTAATTAGGAGATGGA -s mr.mrrefChr3 101056 38 + 181027 TTTCTCATCCTAATGTTACTTTTTAACTATGAGATGAA -s simCow_chr6.simCow.chr6 525405 38 + 602619 TAACTTATCCTGGTTGCGTTTTTAAATTAGGACATGAA -s simDog_chr6.simDog.chr6 514009 38 + 593897 CAACCCATCCTGGTTTCATTTGTTAATTAGGAGATGGA -s simHuman_chr6.simHuman.chr6 521080 38 + 601863 TGTGTCATCCTCGTTTCATTTTTTAATTAGGGGATATA -s simRat_chr6.simRat.chr6 25979 38 - 647215 TTTCTCATCCCAGTGTGGATTCTTAACTAGGAGATGAA - -a -s simMouse_chr6.simMouse.chr6 551065 13 + 636262 ACTCAGGTGATTA -s Anc0.Anc0refChr3 153396 8 + 222631 ACTTTGG-----A -s Anc1.Anc1refChr6 189245 8 + 197743 ACTTTGG-----A -s Anc2.Anc2refChr1 67406 8 + 142988 AATTTTA-----A -s mr.mrrefChr3 101094 13 + 181027 ACTCAGGTGATTA -s simCow_chr6.simCow.chr6 525445 6 + 602619 ATTTTT------- -s simDog_chr6.simDog.chr6 514049 8 + 593897 GATTTTA-----A -s simHuman_chr6.simHuman.chr6 521120 8 + 601863 ACTTTGG-----A -s simRat_chr6.simRat.chr6 26017 13 - 647215 ACTCAGGTGATTA - -a -s simMouse_chr6.simMouse.chr6 551078 5 + 636262 CTGAG -s Anc0.Anc0refChr3 153404 5 + 222631 CTGAG -s Anc1.Anc1refChr6 189253 5 + 197743 CTGAG -s Anc2.Anc2refChr1 67414 5 + 142988 CTAAG -s mr.mrrefChr3 101107 5 + 181027 CTGAG -s simDog_chr6.simDog.chr6 514066 5 + 593897 CTAAG -s simHuman_chr6.simHuman.chr6 521128 5 + 601863 CTGAG -s simRat_chr6.simRat.chr6 26030 5 - 647215 CTGAG - -a -s simMouse_chr6.simMouse.chr6 551083 42 + 636262 AATGAAGTATGTACTTAATCAACATATCTTGCATCCATTCTT -s Anc0.Anc0refChr3 153413 26 + 222631 ATTGAAGT------CAAACCAATCTATCTGGC---------- -s Anc1.Anc1refChr6 189262 42 + 197743 ATTGAAGTATGTACCAAACCAATCTATCTGGCATCTTTCTTT -s Anc2.Anc2refChr1 67423 26 + 142988 ATTAAAGG------CAAACCAATCTATCTGGC---------- -s mr.mrrefChr3 101112 42 + 181027 AATGAAGTATGTACTTAATCAACATATCTTGCATCCATTCTT -s simCow_chr6.simCow.chr6 525451 25 + 602619 -TCAACGC------CAAACCAATCTATCTGGC---------- -s simDog_chr6.simDog.chr6 514075 26 + 593897 AATAAAGG------CAGACCAGTCCATCTGGT---------- -s simHuman_chr6.simHuman.chr6 521137 42 + 601863 ATTGAAGTATGTACCAATCCAATCTATCTGGCATCTTTCTTT -s simRat_chr6.simRat.chr6 26039 42 - 647215 AATGAGGTATGTACTTAATCAATGCATCTTGCATCCATTCTT - -a -s simMouse_chr6.simMouse.chr6 551125 17 + 636262 CCACCAAAGTTAACCTC -s Anc1.Anc1refChr6 189304 17 + 197743 CCACTGAACTGAACCTG -s mr.mrrefChr3 101154 17 + 181027 CCACCAAAGTTAACCTC -s simHuman_chr6.simHuman.chr6 521180 17 + 601863 CCACTGAACTGAACCTG -s simRat_chr6.simRat.chr6 26081 17 - 647215 CCACCAAAGTTAACCTC - -a -s simMouse_chr6.simMouse.chr6 551142 51 + 636262 ATCATCTTCAAGTCAGGGTGAACAGTAGTAACAGGTGGCTGGGCTGCAAGG -s Anc1.Anc1refChr6 189321 45 + 197743 ATCATTTTCAAGTCAATAAGAACAAGAACAA------GCTGGGCAGCAGGG -s mr.mrrefChr3 101171 51 + 181027 ATCATCTTCAAGTCAGGGTGAACAGTAGTAACAGGTGGCTGGGCTGCAAGG -s simHuman_chr6.simHuman.chr6 521197 45 + 601863 ATCATTTTCAAGTCAATAAGAACAAGAACAA------GCTGGGCAGCAGGG -s simRat_chr6.simRat.chr6 26101 51 - 647215 ATTATCTTTAAGTCAAGGTGAACAGTAGTAACAGGTGGCTGGGTTGAGGAA - -a -s simMouse_chr6.simMouse.chr6 551193 27 + 636262 TAGTGTAACACTTAATGGATGACAAAC -s Anc0.Anc0refChr3 153439 22 + 222631 -----TAGCAGTTAATGGATGGCAACA -s Anc1.Anc1refChr6 189366 27 + 197743 TCCTGTAGCAGTTAATGGATGGCAACA -s Anc2.Anc2refChr1 67449 22 + 142988 -----TAGCAGTTAATGGATGGCAGCA -s mr.mrrefChr3 101222 27 + 181027 TAGTGTAACACTTAATGGATGACAAAC -s simCow_chr6.simCow.chr6 525476 22 + 602619 -----CAGAAATAGATTGATGGCATTC -s simDog_chr6.simDog.chr6 514101 22 + 593897 -----TAGCAGTTAATGGATGGAAGCA -s simHuman_chr6.simHuman.chr6 521246 27 + 601863 TCCTGTAGCATATAATGGACAGCAACT -s simRat_chr6.simRat.chr6 26152 27 - 647215 TAGTGTAACACTCAATGGACAGCAAAT - -a -s simMouse_chr6.simMouse.chr6 551220 27 + 636262 GTTTAGGTATGTTTAGATAGGGGCACA -s Anc0.Anc0refChr3 153464 27 + 222631 GTTAAGGTATGACTAAAAAGGGGCACA -s Anc1.Anc1refChr6 189396 27 + 197743 GTTAAGGTATGACTAAAAAGGGGCACA -s Anc2.Anc2refChr1 67474 27 + 142988 GTTAAGGTATGACTAAAAAGGGGCACA -s mr.mrrefChr3 101249 27 + 181027 GTTTAGGTATGTTTAGATAGGGGCACA -s simCow_chr6.simCow.chr6 525501 24 + 602619 TTCAAGGAATGA---AAAAGGAGCACA -s simDog_chr6.simDog.chr6 514126 27 + 593897 GATGAGGTATTGCTAAAAACGGGCACA -s simHuman_chr6.simHuman.chr6 521276 27 + 601863 GTTAAGGTATGACTAAAAAGGGACACA -s simRat_chr6.simRat.chr6 26179 27 - 647215 GTCTAGGTATGTTTAGATTGGGGTACA - -a -s simMouse_chr6.simMouse.chr6 551247 74 + 636262 TGGAATTAGGGTTGTTTGTCTAAAAGTGCATACGTACATCAACTTATGGGTACCCTATCAAAAATCAAGGCAAT -s Anc0.Anc0refChr3 153493 38 + 222631 TC-TATTTAGGATGTTTGTCTAGAAG-----ACAGGCAT------------------------------GACAC -s Anc1.Anc1refChr6 189425 39 + 197743 TCATATTTAGGATGTTTGTCTAGAAG-----ACAGGCAT------------------------------GACAC -s Anc2.Anc2refChr1 67503 38 + 142988 TC-TAATTAGGATGTTTGTCTAGAAG-----ACAGGCAT------------------------------GACAC -s mr.mrrefChr3 101276 73 + 181027 TGGAATTAGGGTTGTTTGTCTAAAAGTGCATACGTACATCAACTTATGG-TACCCTATCAAAAATCAAGGCAAT -s simCow_chr6.simCow.chr6 525527 36 + 602619 TC-TGAATAGGATGTTTGT--GGAGT-----ACATGCAT------------------------------GACAC -s simDog_chr6.simDog.chr6 514155 38 + 593897 TC-TAATTAGGACCTTGGTCTAGAAG-----ACAGGAAT------------------------------GACAC -s simHuman_chr6.simHuman.chr6 521305 39 + 601863 TTATATTTAGGGTGTTTGTCTAGAAG-----ACAGGCAT------------------------------GACAC -s simRat_chr6.simRat.chr6 26206 73 - 647215 TGGAATTAGGGTTGTTTCTCTAAAAATGCATACATACATCAGCTTGTGG-TACCCTACCAAAAATCAAGGAAGT - -a -s simMouse_chr6.simMouse.chr6 551321 11 + 636262 TATTTTTGAAG -s Anc0.Anc0refChr3 153531 11 + 222631 CATTGTTGATG -s Anc1.Anc1refChr6 189464 11 + 197743 CATTGTTGATG -s Anc2.Anc2refChr1 67562 11 + 142988 CATTGTTGATA -s mr.mrrefChr3 101349 11 + 181027 TATTTTTGAAG -s simCow_chr6.simCow.chr6 525584 11 + 602619 CATTGATGATA -s simDog_chr6.simDog.chr6 514214 11 + 593897 CATTGTTGATA -s simHuman_chr6.simHuman.chr6 521344 11 + 601863 CACTCCAGCCG -s simRat_chr6.simRat.chr6 26279 11 - 647215 TATTTTTCAAG - -a -s simMouse_chr6.simMouse.chr6 551332 1 + 636262 T -s Anc0.Anc0refChr3 153542 1 + 222631 G -s Anc1.Anc1refChr6 189475 1 + 197743 G -s Anc2.Anc2refChr1 67638 1 + 142988 G -s mr.mrrefChr3 101360 1 + 181027 T -s simCow_chr6.simCow.chr6 525669 1 + 602619 G -s simDog_chr6.simDog.chr6 514475 1 + 593897 G -s simHuman_chr6.simHuman.chr6 521355 1 + 601863 G -s simRat_chr6.simRat.chr6 26290 1 - 647215 C - -a -s simMouse_chr6.simMouse.chr6 551333 120 + 636262 ATGACATAGCAAACCTCACAGGTTACTATGCCTTATTGATTTTTCAAACTCACATGTAGTTGCAATGTGAGAGATCACGTGCTAGTGCCATCAGTGATATTCAGTGCAAGCAATTACTTG -s Anc0.Anc0refChr3 153543 11 + 222631 CTGAAAT-------------------------------------------------------------------------------------------------------------TATA -s Anc1.Anc1refChr6 189476 11 + 197743 CTGAAAT-------------------------------------------------------------------------------------------------------------TATA -s Anc2.Anc2refChr1 67639 11 + 142988 CTGAAAC-------------------------------------------------------------------------------------------------------------TATA -s mr.mrrefChr3 101361 106 + 181027 ATGACATAGCAAACCTCACAGGTTACTATGCCTTATTGATTTTTCAAACTCACAT---------ATGTGAGAGATCA--TGCTAGT--CATCAGTGATATTCA-TACAAGCAATTATTTA -s simCow_chr6.simCow.chr6 525887 11 + 602619 CTTAACC-------------------------------------------------------------------------------------------------------------AAGA -s simDog_chr6.simDog.chr6 514476 11 + 593897 TAGAAAC-------------------------------------------------------------------------------------------------------------TATG -s simHuman_chr6.simHuman.chr6 521356 11 + 601863 CTGAAAT-------------------------------------------------------------------------------------------------------------TATA -s simRat_chr6.simRat.chr6 26291 105 - 647215 ATAACATAGCAAACCTTGCAGGTTACAATGCCTTATCGATTCTTTGAACTTACAT---------ATGTAAGAAATTA--TGCTAAT--CATCAGTGATATTGA-TACAAGCAAT-ATTTA - -a -s simMouse_chr6.simMouse.chr6 551453 1 + 636262 A -s Anc0.Anc0refChr3 153554 1 + 222631 C -s Anc1.Anc1refChr6 189487 1 + 197743 C -s Anc2.Anc2refChr1 67650 1 + 142988 C -s mr.mrrefChr3 101467 1 + 181027 A -s simCow_chr6.simCow.chr6 525899 1 + 602619 C -s simDog_chr6.simDog.chr6 514487 1 + 593897 T -s simHuman_chr6.simHuman.chr6 521367 1 + 601863 C -s simRat_chr6.simRat.chr6 26396 1 - 647215 A - -a -s simMouse_chr6.simMouse.chr6 551454 70 + 636262 TGCTATGATAAAAGTGCAGGTGAACTTAAGTGCTTCACCCAGTTATGGTTAGTGGCCCCCTCTGTCCTTT -s Anc0.Anc0refChr3 153555 70 + 222631 TGGTAAGTTAGAAGTGCAGTTGAAATTAACTGATTCACCCATTTATGGTTAGTGGCCTCCTATATCAATT -s Anc1.Anc1refChr6 189488 70 + 197743 TGGTAAGTTAGAAGTGCAGTTGAAATTAACTGATTCACCCATTTATGGTTAGTGGCCTCCTATATCAATT -s Anc2.Anc2refChr1 67651 70 + 142988 TTGTAAGTTAGAAGTGTAGTTGAGATTAACTTATTCATCCATTTATGGTTAGTGGCCTCCTATATCAATT -s mr.mrrefChr3 101468 70 + 181027 TGCTATGATAGAAGTGCAGGTGAACTTAACTGCTTCACCCAGTTATGGTTAGTGGCCTCCTCTGTCCTTT -s simCow_chr6.simCow.chr6 525900 67 + 602619 TTGTAATT---ATGGGGAGTTGAGATTAACTCATTCATCCATTTGTGGTTAGTGGCCACCTAAATCAATT -s simDog_chr6.simDog.chr6 514489 70 + 593897 TTGCAAGTTAGAAGTGTAGTTAAGATTAACTTTTTCTTCCATTTATGGCTAGTGACGTACTATTTCAATC -s simHuman_chr6.simHuman.chr6 521368 70 + 601863 TGGTAAGGTAGAAGTGCAGTTGAAATTAACTGATTGACCCATTCATGGTTAGTGGCCTCCTATATCAATT -s simRat_chr6.simRat.chr6 26397 70 - 647215 TGCTAGGATAGAAGTGCAGGTGAACTTAACTGCTTCATCCAGTTGTGGTCAGTGGTCTCCTCTGTCCGTT - -a -s simMouse_chr6.simMouse.chr6 551524 51 + 636262 GAAGTCAGTGCTTGGCTGTGCTTGCCCCATGTGGCCATGTACACACTGCGA -s Anc0.Anc0refChr3 153628 6 + 222631 GAAGT---------------------------------------------A -s Anc1.Anc1refChr6 189561 6 + 197743 GAAGT---------------------------------------------A -s Anc2.Anc2refChr1 67724 6 + 142988 GAAGT---------------------------------------------G -s mr.mrrefChr3 101541 6 + 181027 GAAGT---------------------------------------------A -s simCow_chr6.simCow.chr6 525970 6 + 602619 GAAGT---------------------------------------------G -s simDog_chr6.simDog.chr6 514562 6 + 593897 GAAGT---------------------------------------------G -s simHuman_chr6.simHuman.chr6 521441 6 + 601863 GAAGT---------------------------------------------A -s simRat_chr6.simRat.chr6 26470 6 - 647215 GAGGT---------------------------------------------G - -a -s simMouse_chr6.simMouse.chr6 551575 2 + 636262 GT -s Anc0.Anc0refChr3 153634 2 + 222631 AC -s Anc1.Anc1refChr6 189567 2 + 197743 AC -s Anc2.Anc2refChr1 67730 2 + 142988 GC -s mr.mrrefChr3 101547 2 + 181027 AC -s simCow_chr6.simCow.chr6 525976 2 + 602619 GG -s simDog_chr6.simDog.chr6 514568 2 + 593897 GC -s simHuman_chr6.simHuman.chr6 521447 2 + 601863 AC -s simRat_chr6.simRat.chr6 26478 2 - 647215 AC - -a -s simMouse_chr6.simMouse.chr6 551577 4 + 636262 CTGT -s Anc0.Anc0refChr3 153636 4 + 222631 CTGT -s Anc1.Anc1refChr6 189569 4 + 197743 CTGT -s Anc2.Anc2refChr1 67734 4 + 142988 CTGT -s mr.mrrefChr3 101549 4 + 181027 CTGT -s simCow_chr6.simCow.chr6 525980 4 + 602619 CGGT -s simDog_chr6.simDog.chr6 514572 4 + 593897 CTGT -s simHuman_chr6.simHuman.chr6 521449 4 + 601863 CTGT -s simRat_chr6.simRat.chr6 26480 4 - 647215 TTAT - -a -s simMouse_chr6.simMouse.chr6 551581 5 + 636262 CTCGC -s Anc0.Anc0refChr3 153644 5 + 222631 CTCTT -s Anc1.Anc1refChr6 189577 5 + 197743 CTCTT -s Anc2.Anc2refChr1 67742 5 + 142988 CTCTT -s mr.mrrefChr3 101557 5 + 181027 CTCGT -s simCow_chr6.simCow.chr6 525988 5 + 602619 CTCTT -s simDog_chr6.simDog.chr6 514582 5 + 593897 CTCTT -s simHuman_chr6.simHuman.chr6 521457 5 + 601863 CTCCT -s simRat_chr6.simRat.chr6 26488 5 - 647215 CTTGT - -a -s simMouse_chr6.simMouse.chr6 551586 2 + 636262 AT -s Anc0.Anc0refChr3 153649 2 + 222631 CT -s Anc1.Anc1refChr6 189582 2 + 197743 CT -s Anc2.Anc2refChr1 67747 2 + 142988 CT -s mr.mrrefChr3 101562 2 + 181027 AT -s simCow_chr6.simCow.chr6 525993 2 + 602619 AG -s simDog_chr6.simDog.chr6 514587 2 + 593897 CT -s simHuman_chr6.simHuman.chr6 521462 2 + 601863 CT -s simRat_chr6.simRat.chr6 26498 2 - 647215 AG - -a -s simMouse_chr6.simMouse.chr6 551588 13 + 636262 GACCAGGTTGCTT -s Anc0.Anc0refChr3 153651 13 + 222631 AAGCAGGTTGCCT -s Anc1.Anc1refChr6 189584 13 + 197743 AAGCAGGTTGCCT -s Anc2.Anc2refChr1 67749 13 + 142988 AAATAGGTTGCCT -s mr.mrrefChr3 101564 13 + 181027 AAGCAGGTTGCTT -s simCow_chr6.simCow.chr6 525995 13 + 602619 ATAGACGTCTATT -s simDog_chr6.simDog.chr6 514590 13 + 593897 AAATGGGTTGCCT -s simHuman_chr6.simHuman.chr6 521464 12 + 601863 AAGCAAGTT-CCA -s simRat_chr6.simRat.chr6 26500 13 - 647215 AGGTGGCTTGCTT - -a -s simMouse_chr6.simMouse.chr6 551601 72 + 636262 CACACTTGAGTTGCCATTTGCCTGCCCACTTAATTCACTGAAGGGATATTATTGGCAGATGCATGCTGTGAT -s Anc0.Anc0refChr3 153664 41 + 222631 CACTCATCAGTTGCTGCTGGCCTACATACTTAGTTCACTGC------------------------------- -s Anc1.Anc1refChr6 189597 72 + 197743 CACTCATCAGTTGCTGCTGGCCTACATACTTAGTTCACTGCTGGGCTGGTATTAGTAGAAACTTGTCTAGGT -s Anc2.Anc2refChr1 67766 41 + 142988 CCCTCATCAGTTGCTGCTGGCCTACATACTTAGTTCTCTTC------------------------------- -s mr.mrrefChr3 101577 72 + 181027 CACACTTGAGTTGCCATTTGCCTACCCACTTAATTCACTGAAGGGATATTATTGGCAGATGCATGTCGTGAT -s simCow_chr6.simCow.chr6 526012 41 + 602619 TCTTCATCACTTGCGGTTGGCATAAAAACTAAATTCCCTTC------------------------------- -s simDog_chr6.simDog.chr6 514607 41 + 593897 CCCTCATCAGTTGCTGCTGGCCTACATACTTAGTTCTCTTC------------------------------- -s simHuman_chr6.simHuman.chr6 521476 72 + 601863 CACTCATCATCTGCTGGGGGCCTACATACTTATTTCACTGCTGGGCTGGTATTAGTAGAAACTTGTCTAGGT -s simRat_chr6.simRat.chr6 26513 72 - 647215 CTCGCTTGAGTTACCATTAGCCTACCCCCTCAACTCACTGAAGGATTAATATCGGCAGATGCATGTCGTGAT - -a -s simMouse_chr6.simMouse.chr6 551673 152 + 636262 GGTCCAGCATGGTCTATATAATGATTTCCTTCAACTACACATCTGCCATACCCATGCTTGGGTTCCAATGCTCAGCCCCAGAGGAATTTGGAAAAACCTTACATCCTAGGTGAGTGCCCGCCACAAGCTGGGTGCTGCAACAGGGAAAGCCT -s Anc1.Anc1refChr6 189669 88 + 197743 AGTTGAGCATT-------------TTTGATTTTACTAC--------------------------TAAATTCATGGGACTGGAGGAA-------------------------AAGTCCCTGCCAGAAATTGAGTGCCGCTTTAGGGAGATCCT -s mr.mrrefChr3 101649 152 + 181027 GGTCCAGCATGGTCTATATAATGATTTGATTCAACTACACATCTGCCATACCCATGCTTGGGTTCCAATGCTTGGGCCCAGAGGAATTTGGAAAAACCTTACATCCTAGGTGAGTGCCCGCCACAAGCTGGGTGCTGCAACAGGGAAAGCCT -s simHuman_chr6.simHuman.chr6 521558 88 + 601863 AGTTGAGCATT-------------TTTGATTTTACTAC--------------------------TAAATTCATGGGACTGGAGGAA-------------------------AAGTCCCTGCCAGAAATTGAGTGCCGCTTTAGGGAGATCCT -s simRat_chr6.simRat.chr6 26585 151 - 647215 GGGCCAGCACAGTCTTTATAAAGATTTGATTCAATTACACATCTGCCATACCCATGCTTGGGTTCCGAAGCTTGGGCCGAGAAGAATTTGGAAAAATCTTACATCCTAGCTGAGTGCCCACTACAAGCTGGGTGCTGCAACAGGGTA-GCCT - -a -s simMouse_chr6.simMouse.chr6 551825 11 + 636262 ACCAACCCAGC -s Anc0.Anc0refChr3 153705 2 + 222631 ---------AC -s Anc1.Anc1refChr6 189757 11 + 197743 GCCAAGACAAC -s Anc2.Anc2refChr1 67807 2 + 142988 ---------AC -s mr.mrrefChr3 101801 11 + 181027 GCCAAGCCAGC -s simCow_chr6.simCow.chr6 526053 2 + 602619 ---------AC -s simDog_chr6.simDog.chr6 514648 2 + 593897 ---------AC -s simHuman_chr6.simHuman.chr6 521647 11 + 601863 GCCAAGACAAC -s simRat_chr6.simRat.chr6 26736 11 - 647215 GCCAAGCCAGC - -a -s simMouse_chr6.simMouse.chr6 551836 13 + 636262 CTAGACTAATCTA -s Anc0.Anc0refChr3 153707 12 + 222631 CTA-ACTAATCTA -s Anc1.Anc1refChr6 189768 12 + 197743 CTA-ACTAATCTA -s Anc2.Anc2refChr1 67809 12 + 142988 CTC-ATTAATATA -s mr.mrrefChr3 101812 13 + 181027 CTAGACTAATCTA -s simCow_chr6.simCow.chr6 526060 12 + 602619 CCC-TTCACTTCA -s simDog_chr6.simDog.chr6 514650 12 + 593897 TTC-AGTAATATA -s simHuman_chr6.simHuman.chr6 521658 12 + 601863 ATA-ACTAATCTA -s simRat_chr6.simRat.chr6 26747 13 - 647215 CTAAACTAACCTG - -a -s simMouse_chr6.simMouse.chr6 551849 13 + 636262 GACTTAAGACACA -s Anc0.Anc0refChr3 153719 13 + 222631 GGATTACCAAACA -s Anc1.Anc1refChr6 189780 13 + 197743 GGATTACCAAACA -s Anc2.Anc2refChr1 67821 13 + 142988 GAATTACCTAACA -s mr.mrrefChr3 101825 13 + 181027 GGCTTACGAAACA -s simCow_chr6.simCow.chr6 526072 9 + 602619 GTAATACTT---- -s simDog_chr6.simDog.chr6 514672 13 + 593897 GAATTACCTAACA -s simHuman_chr6.simHuman.chr6 521670 13 + 601863 GGATAACAAAACA -s simRat_chr6.simRat.chr6 26760 13 - 647215 AGCTTACGAAACA - -a -s simMouse_chr6.simMouse.chr6 551862 1 + 636262 C -s Anc0.Anc0refChr3 153744 1 + 222631 C -s Anc1.Anc1refChr6 189805 1 + 197743 C -s Anc2.Anc2refChr1 67846 1 + 142988 C -s mr.mrrefChr3 101838 1 + 181027 C -s simCow_chr6.simCow.chr6 526088 1 + 602619 C -s simDog_chr6.simDog.chr6 514697 1 + 593897 C -s simHuman_chr6.simHuman.chr6 521695 1 + 601863 C -s simRat_chr6.simRat.chr6 26773 1 - 647215 C - -a -s simMouse_chr6.simMouse.chr6 551863 6 + 636262 AATAAC -s Anc0.Anc0refChr3 153745 6 + 222631 AATAAA -s Anc1.Anc1refChr6 189806 6 + 197743 AATAAA -s Anc2.Anc2refChr1 67852 6 + 142988 AAAATA -s mr.mrrefChr3 101839 6 + 181027 AATAAC -s simCow_chr6.simCow.chr6 526094 6 + 602619 AATCCA -s simDog_chr6.simDog.chr6 514703 6 + 593897 ATAATA -s simHuman_chr6.simHuman.chr6 521696 6 + 601863 AATAAA -s simRat_chr6.simRat.chr6 26774 6 - 647215 AATAAC - -a -s simMouse_chr6.simMouse.chr6 551869 2 + 636262 CA -s Anc0.Anc0refChr3 153751 2 + 222631 CA -s Anc1.Anc1refChr6 189812 2 + 197743 CA -s Anc2.Anc2refChr1 67858 2 + 142988 CA -s mr.mrrefChr3 101845 2 + 181027 CA -s simCow_chr6.simCow.chr6 526100 2 + 602619 AA -s simDog_chr6.simDog.chr6 514709 2 + 593897 CA -s simHuman_chr6.simHuman.chr6 521711 2 + 601863 CA -s simRat_chr6.simRat.chr6 26780 2 - 647215 CA - -a -s simMouse_chr6.simMouse.chr6 551871 20 + 636262 TGTTAAAATGCCGTCTAACT -s Anc0.Anc0refChr3 153754 18 + 222631 TGTGACAAT--TACCTCCTT -s Anc1.Anc1refChr6 189815 18 + 197743 TGTGACAAT--TACCTCCTT -s Anc2.Anc2refChr1 67861 18 + 142988 GGTTACAAT--CACCACCTT -s mr.mrrefChr3 101848 20 + 181027 TGTTAAAATGCCACCTCACT -s simCow_chr6.simCow.chr6 526103 18 + 602619 GGTTACTTC--CTGTGCTTT -s simDog_chr6.simDog.chr6 514712 14 + 593897 GG----AAT--CACCACCTT -s simHuman_chr6.simHuman.chr6 521714 18 + 601863 TGTGACAAT--TACCTCCTT -s simRat_chr6.simRat.chr6 26783 20 - 647215 TGTTAAGGTGCCACCTCACT - -a -s simMouse_chr6.simMouse.chr6 551891 14 + 636262 GTTCTAGATGTACA -s Anc0.Anc0refChr3 153772 14 + 222631 AATCTAGGATAACA -s Anc1.Anc1refChr6 189833 14 + 197743 AATCTAGGATAACA -s Anc2.Anc2refChr1 67890 14 + 142988 ACTAGGGGACTACA -s mr.mrrefChr3 101868 14 + 181027 GTTCTAGATGTACA -s simCow_chr6.simCow.chr6 526132 14 + 602619 ACTACAGGGCTAAA -s simDog_chr6.simDog.chr6 514737 14 + 593897 ACTAGGGGACTACA -s simHuman_chr6.simHuman.chr6 521732 14 + 601863 AATCTAGGATAACA -s simRat_chr6.simRat.chr6 26803 14 - 647215 GTTCTAGATGGACA - -a -s simMouse_chr6.simMouse.chr6 551905 9 + 636262 ACCTAATAG -s Anc0.Anc0refChr3 153786 9 + 222631 AAACAATTA -s Anc1.Anc1refChr6 189847 9 + 197743 AAACAATTA -s Anc2.Anc2refChr1 67904 9 + 142988 CAACAATAA -s mr.mrrefChr3 101882 9 + 181027 ACCTAATAG -s simCow_chr6.simCow.chr6 526152 9 + 602619 CAAAAATAA -s simDog_chr6.simDog.chr6 514751 9 + 593897 CAACAATAA -s simHuman_chr6.simHuman.chr6 521746 9 + 601863 AAACAATTA -s simRat_chr6.simRat.chr6 26817 9 - 647215 ACCTAATAG - -a -s simMouse_chr6.simMouse.chr6 551914 6 + 636262 AAGAGA -s Anc0.Anc0refChr3 153795 6 + 222631 ACATCA -s Anc1.Anc1refChr6 189856 6 + 197743 ACATCA -s Anc2.Anc2refChr1 67918 6 + 142988 ACATTA -s mr.mrrefChr3 101891 6 + 181027 AAAAGA -s simCow_chr6.simCow.chr6 526166 6 + 602619 CCATTG -s simDog_chr6.simDog.chr6 514765 6 + 593897 ACATTA -s simHuman_chr6.simHuman.chr6 521755 6 + 601863 ACATCA -s simRat_chr6.simRat.chr6 26826 6 - 647215 AAAAGA - -a -s simMouse_chr6.simMouse.chr6 551920 2 + 636262 AG -s Anc0.Anc0refChr3 153801 2 + 222631 AT -s Anc1.Anc1refChr6 189862 2 + 197743 AT -s Anc2.Anc2refChr1 67928 2 + 142988 AC -s mr.mrrefChr3 101897 2 + 181027 AG -s simCow_chr6.simCow.chr6 526176 2 + 602619 AC -s simDog_chr6.simDog.chr6 514775 2 + 593897 AC -s simHuman_chr6.simHuman.chr6 521761 2 + 601863 AT -s simRat_chr6.simRat.chr6 26832 2 - 647215 AG - -a -s simMouse_chr6.simMouse.chr6 551922 16 + 636262 CACCACTGACAATACT -s Anc0.Anc0refChr3 153868 16 + 222631 GACCAGCAGCAAAACA -s Anc1.Anc1refChr6 189934 16 + 197743 GACCAGCAGCAAAACA -s Anc2.Anc2refChr1 68015 16 + 142988 GCCCAGCAGTAAAATA -s mr.mrrefChr3 101899 16 + 181027 CACCACTGACAAAACT -s simCow_chr6.simCow.chr6 526263 16 + 602619 TACTAGCAGGAAAACA -s simDog_chr6.simDog.chr6 270432 16 - 593897 GCCCACCAGAAAAATA -s simDog_chr6.simDog.chr6 514908 16 + 593897 GCCCAGCAGTAAAATA -s simHuman_chr6.simHuman.chr6 521837 16 + 601863 TACCAGCATCAAAACA -s simRat_chr6.simRat.chr6 26834 16 - 647215 CACCACTGACAAAACT - -a -s simMouse_chr6.simMouse.chr6 551938 10 + 636262 TCCCCTACTT -s Anc0.Anc0refChr3 153884 10 + 222631 TCCCCTACAT -s Anc1.Anc1refChr6 189950 10 + 197743 TCCCCTACAT -s Anc2.Anc2refChr1 68031 10 + 142988 CCCCCTACAT -s mr.mrrefChr3 101915 10 + 181027 TCCCCTACTT -s simCow_chr6.simCow.chr6 526279 8 + 602619 CCCCCTAC-- -s simDog_chr6.simDog.chr6 270448 10 - 593897 CCCCCCACAT -s simDog_chr6.simDog.chr6 514924 10 + 593897 CCCCCTACAC -s simHuman_chr6.simHuman.chr6 521853 10 + 601863 TACCTTACAT -s simRat_chr6.simRat.chr6 26863 10 - 647215 TCCACTACTG - -a -s simMouse_chr6.simMouse.chr6 551948 4 + 636262 GCAT -s Anc0.Anc0refChr3 153894 4 + 222631 GGCT -s Anc1.Anc1refChr6 189960 4 + 197743 GGCT -s Anc2.Anc2refChr1 68041 4 + 142988 AGCT -s mr.mrrefChr3 101925 4 + 181027 GCAT -s simDog_chr6.simDog.chr6 514934 4 + 593897 AGCT -s simHuman_chr6.simHuman.chr6 521863 4 + 601863 GGTC -s simRat_chr6.simRat.chr6 26873 4 - 647215 ACAT - -a -s simMouse_chr6.simMouse.chr6 551952 44 + 636262 TTATAAGTACTAGCACCATAGTTTTTTCAGCTTTATAAGGTCAA -s Anc0.Anc0refChr3 153898 39 + 222631 GTATGA--ACTACCACCATAGCTTTCTCTGGGTTATA---TGCA -s Anc1.Anc1refChr6 189964 41 + 197743 GTATGAGTACTACCACCATAGCTTTCTCTGGGTTATA---TGCA -s Anc2.Anc2refChr1 68045 39 + 142988 GTATAA--ACTACCACCATAGCTTTCTCTGGGTTATA---AGCA -s mr.mrrefChr3 101929 41 + 181027 TTATGAGTACTAGCACCATAGCTTTCTCAGCTTTATA---TCAA -s simCow_chr6.simCow.chr6 526287 35 + 602619 ----GA--ACTACTACCATAGCTTTTTCTGAGTTATA---AGCA -s simDog_chr6.simDog.chr6 270458 39 - 593897 GTATAA--ACTACCACCATAGCGTTCTCTGGGTTATA---AGCA -s simDog_chr6.simDog.chr6 514938 39 + 593897 GTATAA--ACTACCACCATAGCTTTCTCTGGGTCATA---AGCA -s simHuman_chr6.simHuman.chr6 521867 41 + 601863 GTATGAGTACTACCACCTTAGCTTTCTCTGACTTATA---TGCA -s simRat_chr6.simRat.chr6 26877 41 - 647215 TTGTGAGTACTAGCACCATAGCTTTCTCAGCTTTATA---TCAA - -a -s simMouse_chr6.simMouse.chr6 551996 24 + 636262 ATCACTGTAAGGGTTCCTATCTGG -s Anc0.Anc0refChr3 153937 24 + 222631 ATCACTGTAAGATATTCCATCTGg -s Anc1.Anc1refChr6 190005 24 + 197743 ATCACTGTAAGATATTCCATCTGG -s Anc2.Anc2refChr1 68088 24 + 142988 ATCACTTACAGATGTTCCATCTTg -s mr.mrrefChr3 101970 24 + 181027 ATCACCGTAAGGGATCCTATCTGG -s simCow_chr6.simCow.chr6 526326 22 + 602619 ATCTCTCAAAGATCTTCCATCT-- -s simDog_chr6.simDog.chr6 270501 24 - 593897 ATCACTTACTGATGTTCCATCTTg -s simDog_chr6.simDog.chr6 514981 22 + 593897 ATCACTTACAGATGTTCCATCT-- -s simHuman_chr6.simHuman.chr6 521967 23 + 601863 GCCTCGGTAAAA-ATTCAACCTGG -s simRat_chr6.simRat.chr6 26918 24 - 647215 ACCACCGAAAGGGATCCTATCTTG - -a -s simMouse_chr6.simMouse.chr6 552020 10 + 636262 TTAGCACTGG -s Anc0.Anc0refChr3 153965 10 + 222631 TGGGGACTGG -s Anc1.Anc1refChr6 190033 10 + 197743 TGGGGACTGG -s Anc2.Anc2refChr1 68116 10 + 142988 TGGGGACTGG -s mr.mrrefChr3 101994 10 + 181027 TTAGCACTGG -s simCow_chr6.simCow.chr6 526350 10 + 602619 TGTGGACTGG -s simDog_chr6.simDog.chr6 515005 10 + 593897 TGGGGACTGG -s simHuman_chr6.simHuman.chr6 521996 10 + 601863 TGGGGACTGG -s simRat_chr6.simRat.chr6 26942 10 - 647215 TTAGCACTGG - -a -s simMouse_chr6.simMouse.chr6 552030 10 + 636262 CACCAATTAT -s Anc0.Anc0refChr3 153976 10 + 222631 CATCTATTAT -s Anc1.Anc1refChr6 190044 10 + 197743 CATCTATTAT -s Anc2.Anc2refChr1 68127 10 + 142988 CATCTATTAT -s mr.mrrefChr3 102004 10 + 181027 CATCTATTAT -s simCow_chr6.simCow.chr6 526361 10 + 602619 GATCTATTAT -s simDog_chr6.simDog.chr6 515016 10 + 593897 CATCTATTAT -s simHuman_chr6.simHuman.chr6 522007 10 + 601863 CATCTATTAC -s simRat_chr6.simRat.chr6 26952 10 - 647215 CATCTATTAT - -a -s simMouse_chr6.simMouse.chr6 552040 14 + 636262 GAAGGTAAAACAGA -s Anc0.Anc0refChr3 153987 14 + 222631 GAAGGTAAAAGGGA -s Anc1.Anc1refChr6 190055 14 + 197743 GAAGGTAAAAGGGA -s Anc2.Anc2refChr1 68138 14 + 142988 GATGGTAAAAGGCA -s mr.mrrefChr3 102014 14 + 181027 GAAGGTAAAACAGA -s simCow_chr6.simCow.chr6 526377 12 + 602619 GGTGGTTAAAGA-- -s simDog_chr6.simDog.chr6 515027 14 + 593897 GATGGTAAAAGGCA -s simHuman_chr6.simHuman.chr6 522018 14 + 601863 GAAGGTAAAAGGGA -s simRat_chr6.simRat.chr6 26962 14 - 647215 CAAAGTAAAACAGA - -a -s simMouse_chr6.simMouse.chr6 552054 21 + 636262 GGAAAAGTCTTCTATCAGACC -s Anc0.Anc0refChr3 154001 20 + 222631 AGAAA-GTCTCCAGTCAGTCC -s Anc1.Anc1refChr6 190069 20 + 197743 AGAAA-GTCTCCAGTCAGTCC -s Anc2.Anc2refChr1 68152 20 + 142988 AGAAA-ATCTCCAGTCAGTCC -s mr.mrrefChr3 102028 21 + 181027 GGAAAAGTCTTCAATCAGACC -s simCow_chr6.simCow.chr6 526389 9 + 602619 ------------AGCCAATCC -s simDog_chr6.simDog.chr6 515048 20 + 593897 AGAAA-ATCTCCAGTCAGTTT -s simHuman_chr6.simHuman.chr6 522032 20 + 601863 TGAAA-GTTTGCAGTCAGTCC -s simRat_chr6.simRat.chr6 26976 21 - 647215 GGAAAAGTCTTCAATCAGACC - -a -s simMouse_chr6.simMouse.chr6 552075 2 + 636262 CA -s Anc0.Anc0refChr3 154022 2 + 222631 TA -s Anc1.Anc1refChr6 190090 2 + 197743 TA -s Anc2.Anc2refChr1 68173 2 + 142988 TA -s mr.mrrefChr3 102049 2 + 181027 CA -s simCow_chr6.simCow.chr6 526399 2 + 602619 TA -s simDog_chr6.simDog.chr6 515069 2 + 593897 TA -s simHuman_chr6.simHuman.chr6 522053 2 + 601863 TA -s simRat_chr6.simRat.chr6 26997 2 - 647215 CA - -a -s simMouse_chr6.simMouse.chr6 552077 25 + 636262 GCAGTTCTGAGCTTGATAAAGTTGA -s Anc0.Anc0refChr3 154038 23 + 222631 GGAGTCAAGA--CTGCTAAAGAAGT -s Anc1.Anc1refChr6 190106 23 + 197743 GGAGTCAAGA--CTGCTAAAGAAGT -s Anc2.Anc2refChr1 68189 23 + 142988 GGAGTCAAGA--CCACTAAAAAAGT -s mr.mrrefChr3 102065 25 + 181027 GCAGTCATGAGCTTGATAAAGTTGA -s simCow_chr6.simCow.chr6 526415 23 + 602619 GGAGTCAAGG--CCACTGAGAAAGT -s simDog_chr6.simDog.chr6 515085 23 + 593897 GGAGTGAAGA--CCACTAAAAAAGT -s simHuman_chr6.simHuman.chr6 522069 23 + 601863 GGGGTCAAGA--CTGCTAAAGAGGT -s simRat_chr6.simRat.chr6 27013 25 - 647215 GCAGTCATGAGCTGGATAAAGTTGA - -a -s simMouse_chr6.simMouse.chr6 552102 17 + 636262 GCAGATACAACTGCTGA -s Anc0.Anc0refChr3 154061 17 + 222631 GTGGATGCAGCTGTTGG -s Anc1.Anc1refChr6 190129 17 + 197743 GTGGATGCAGCTGTTGG -s Anc2.Anc2refChr1 68219 17 + 142988 ATGGATGCAGCTGTCAG -s mr.mrrefChr3 102090 17 + 181027 GCAGATACAACTGTTGA -s simCow_chr6.simCow.chr6 526446 17 + 602619 ACAGCTGCAGCTGTCAG -s simDog_chr6.simDog.chr6 515115 17 + 593897 ATGGATGCAGCTAACAG -s simHuman_chr6.simHuman.chr6 522092 12 + 601863 G-----GCAGCAGTTGG -s simRat_chr6.simRat.chr6 27038 17 - 647215 GAAGATACAACTGTTGA - -a -s simMouse_chr6.simMouse.chr6 552119 12 + 636262 GATTGCAACATG -s Anc0.Anc0refChr3 154078 12 + 222631 GATTGGGACACA -s Anc1.Anc1refChr6 190146 12 + 197743 GATTGGGACACA -s Anc2.Anc2refChr1 68236 12 + 142988 GATTGGGACACA -s mr.mrrefChr3 102107 12 + 181027 GATTGCGACATG -s simCow_chr6.simCow.chr6 526467 12 + 602619 GGATGGAACACA -s simDog_chr6.simDog.chr6 515132 12 + 593897 GATTGGGATACA -s simHuman_chr6.simHuman.chr6 522104 12 + 601863 GATTGAGACAAA -s simRat_chr6.simRat.chr6 27055 12 - 647215 GATTGTGACATG - -a -s simMouse_chr6.simMouse.chr6 552131 20 + 636262 TAGCACTTAGGATTATTTAT -s Anc0.Anc0refChr3 154090 16 + 222631 CAGCTGTTAGGATTAT---- -s Anc1.Anc1refChr6 190158 16 + 197743 CAGCTGTTAGGATTAT---- -s Anc2.Anc2refChr1 68248 16 + 142988 CAGCTGTTAGGATTAT---- -s mr.mrrefChr3 102119 16 + 181027 CAGCACTTAGGATTAT---- -s simCow_chr6.simCow.chr6 526480 16 + 602619 TAGCAGCTAGGATTAT---- -s simDog_chr6.simDog.chr6 515144 16 + 593897 CTGCTGTTAGGAATAT---- -s simHuman_chr6.simHuman.chr6 522116 16 + 601863 CAGCTGTTAGGCTCTT---- -s simRat_chr6.simRat.chr6 27067 16 - 647215 CAACACTTAGGATTAT---- - -a -s simMouse_chr6.simMouse.chr6 552151 16 + 636262 AATCAGAGTATATTCT -s Anc0.Anc0refChr3 154106 16 + 222631 GGTGAGAGCAGAAACT -s Anc1.Anc1refChr6 190174 16 + 197743 GGTGAGAGCAGAAACT -s Anc2.Anc2refChr1 68264 16 + 142988 GGTGTAAGCAGAAAAT -s mr.mrrefChr3 102135 16 + 181027 AATCAGAGTATATTCT -s simCow_chr6.simCow.chr6 526496 16 + 602619 GGTGCAAGCACAGAAT -s simDog_chr6.simDog.chr6 515164 16 + 593897 GGTTTAAGAAGAAAAT -s simHuman_chr6.simHuman.chr6 522132 15 + 601863 GGTGAGAGCAGAG-CT -s simRat_chr6.simRat.chr6 27083 16 - 647215 ACACAGAGGATATTGT - -a -s simMouse_chr6.simMouse.chr6 552167 3 + 636262 CAG -s Anc0.Anc0refChr3 154123 3 + 222631 CAG -s Anc1.Anc1refChr6 190191 3 + 197743 CAG -s Anc2.Anc2refChr1 68281 3 + 142988 TTG -s mr.mrrefChr3 102152 3 + 181027 CAG -s simCow_chr6.simCow.chr6 526513 3 + 602619 TTG -s simDog_chr6.simDog.chr6 515181 3 + 593897 TTG -s simHuman_chr6.simHuman.chr6 522148 3 + 601863 CAG -s simRat_chr6.simRat.chr6 27100 3 - 647215 CAG - -a -s simMouse_chr6.simMouse.chr6 552170 14 + 636262 CACCCCGCTTGGGG -s Anc0.Anc0refChr3 154130 14 + 222631 CCTCTCTAATAGGA -s Anc1.Anc1refChr6 190198 14 + 197743 CCTCTCTAATAGGA -s Anc2.Anc2refChr1 68288 14 + 142988 CCTCTCTTATAGGA -s mr.mrrefChr3 102155 14 + 181027 CACCCCGATTGGGG -s simCow_chr6.simCow.chr6 526520 14 + 602619 CTTCTCTTACAGGG -s simDog_chr6.simDog.chr6 515188 14 + 593897 CCTCTCTTATAGGA -s simHuman_chr6.simHuman.chr6 522155 14 + 601863 CCTCTCTAGTAAGA -s simRat_chr6.simRat.chr6 27103 14 - 647215 CTCCCCCATTGGAG - -a -s simMouse_chr6.simMouse.chr6 552184 14 + 636262 ACAAATATAGAACA -s Anc0.Anc0refChr3 154144 14 + 222631 ACAAATACAGTACA -s Anc1.Anc1refChr6 190212 14 + 197743 ACAAATACAGTACA -s Anc2.Anc2refChr1 68302 14 + 142988 ACAAATACAGTACA -s mr.mrrefChr3 102169 14 + 181027 ACAAATACAGAACA -s simCow_chr6.simCow.chr6 526534 14 + 602619 ACAAGTACAGTACA -s simDog_chr6.simDog.chr6 515241 14 + 593897 ACAAATGCATCACA -s simHuman_chr6.simHuman.chr6 522169 14 + 601863 ACGAATACAGTACA -s simRat_chr6.simRat.chr6 27117 14 - 647215 ACACATACAGCACA - -a -s simMouse_chr6.simMouse.chr6 552198 17 + 636262 ATAGTGTCCTGAATCAG -s Anc0.Anc0refChr3 154158 17 + 222631 ATGGTGCCCTGAGCCAA -s Anc1.Anc1refChr6 190226 17 + 197743 ATGGTGCCCTGAGCCAA -s Anc2.Anc2refChr1 68316 17 + 142988 ATGGTGCCCTAAGCAAA -s mr.mrrefChr3 102183 17 + 181027 ATAGTGTCCTGAGCCAG -s simCow_chr6.simCow.chr6 526549 17 + 602619 GTGGTGCCCCAAGGTAG -s simDog_chr6.simDog.chr6 515255 17 + 593897 ACGGTGCCCTAAGCAAA -s simHuman_chr6.simHuman.chr6 522183 17 + 601863 ATGGTGACCTGAGCCAA -s simRat_chr6.simRat.chr6 27131 17 - 647215 ACAGCGTCCTGAGCCAG - -a -s simMouse_chr6.simMouse.chr6 552215 18 + 636262 CTGATGGTTAGGACAGAG -s Anc0.Anc0refChr3 154175 18 + 222631 CCAGTGGTTGGGACAGGG -s Anc1.Anc1refChr6 190243 18 + 197743 CCAGTGGTTGGGACAGGG -s Anc2.Anc2refChr1 68333 18 + 142988 CCAGTGGTTGGGACAGGG -s mr.mrrefChr3 102200 18 + 181027 CTGATGGTTAGGACAGAG -s simCow_chr6.simCow.chr6 526566 18 + 602619 CCAATGATTGAGCCAGTG -s simDog_chr6.simDog.chr6 515273 18 + 593897 CCAGTGGCTAGGACAGGG -s simHuman_chr6.simHuman.chr6 522200 18 + 601863 CCAGTGGTCGGGACAGGG -s simRat_chr6.simRat.chr6 27148 18 - 647215 CTGATGGTTAGGACAGAG - -a -s simMouse_chr6.simMouse.chr6 552233 5 + 636262 AGACC -s Anc0.Anc0refChr3 154193 5 + 222631 AGACC -s Anc1.Anc1refChr6 190261 5 + 197743 AGACC -s Anc2.Anc2refChr1 68351 5 + 142988 AGACC -s mr.mrrefChr3 102218 5 + 181027 AGACC -s simCow_chr6.simCow.chr6 526585 5 + 602619 AAACC -s simDog_chr6.simDog.chr6 515291 5 + 593897 GGACC -s simHuman_chr6.simHuman.chr6 522218 5 + 601863 AGACC -s simRat_chr6.simRat.chr6 27166 5 - 647215 AAACC - -a -s simMouse_chr6.simMouse.chr6 552238 25 + 636262 AAGAAATAACTGAATGGGATATGCT -s Anc0.Anc0refChr3 154199 25 + 222631 AACATATAACTGACTGGGATATGTA -s Anc1.Anc1refChr6 190267 25 + 197743 AACATATAACTGACTGGGATATGTA -s Anc2.Anc2refChr1 68357 25 + 142988 AACATATAACTGACTGGGATATGTA -s mr.mrrefChr3 102223 25 + 181027 AAGAAATAACTGAATGGGATATGTT -s simCow_chr6.simCow.chr6 526591 25 + 602619 AACATATAGTTGGCTGGGATGCGTT -s simDog_chr6.simDog.chr6 515297 25 + 593897 AACGTATAACTGACTGCGATATGTA -s simHuman_chr6.simHuman.chr6 522224 25 + 601863 AACATATAACCGACTGGGATATGTG -s simRat_chr6.simRat.chr6 27171 24 - 647215 AATAAATA-CTGAATGCGATGTGTT - -a -s simMouse_chr6.simMouse.chr6 552263 27 + 636262 GTAAGTAGCCCTATCATACGGTGTTTT -s Anc0.Anc0refChr3 154224 27 + 222631 TTAGTTACCCTTATCATATGGCTTTCT -s Anc1.Anc1refChr6 190292 27 + 197743 TTAGTTACCCTTATCATATGGCTTTCT -s Anc2.Anc2refChr1 68382 27 + 142988 TTAGTTACCCTTATCATATGGTTTTCT -s mr.mrrefChr3 102248 27 + 181027 GTAAGTAGCCCTATCATATGGCTTTTT -s simCow_chr6.simCow.chr6 526616 27 + 602619 TTAGTTAGTACTAACATATGGTTTTTT -s simDog_chr6.simDog.chr6 515322 27 + 593897 TTAGCTACCCTCATCATACGGTTTTCT -s simHuman_chr6.simHuman.chr6 522249 27 + 601863 TTAGTAAACTATATCATATGGCTTTCT -s simRat_chr6.simRat.chr6 27196 27 - 647215 GTAAGTAGGCCTATCATATTGCTTTTT - -a -s simMouse_chr6.simMouse.chr6 552290 26 + 636262 CAGGATTTAGTAGTCTTCACAGAGGC -s Anc0.Anc0refChr3 154251 23 + 222631 CA--ATTT-GCAGTCTTCACACAGGC -s Anc1.Anc1refChr6 190319 25 + 197743 CAAGATTT-GCAGTCTTCACACAGGC -s Anc2.Anc2refChr1 68409 23 + 142988 CA--ATTT-GCAGTCATCACACAGGC -s mr.mrrefChr3 102275 26 + 181027 CAGGATTTAGCAGTCTTCACAGAGGC -s simCow_chr6.simCow.chr6 526643 18 + 602619 CA--------CAATCATGACACAGGT -s simDog_chr6.simDog.chr6 515349 23 + 593897 CA--ATTT-GCAGTCATCACAGAGGC -s simHuman_chr6.simHuman.chr6 522281 25 + 601863 CAAGTTTT-GCAGTCTTCACACAGGC -s simRat_chr6.simRat.chr6 27223 26 - 647215 CAGAATTTAGCAGTCTTCACAGAGGC - -a -s simMouse_chr6.simMouse.chr6 552316 3 + 636262 TGT -s Anc0.Anc0refChr3 154277 3 + 222631 TAT -s Anc1.Anc1refChr6 190347 3 + 197743 TAT -s Anc2.Anc2refChr1 68435 3 + 142988 TAT -s mr.mrrefChr3 102301 3 + 181027 TGT -s simCow_chr6.simCow.chr6 526664 3 + 602619 TAT -s simDog_chr6.simDog.chr6 515375 3 + 593897 TGT -s simHuman_chr6.simHuman.chr6 522309 3 + 601863 TAT -s simRat_chr6.simRat.chr6 27249 3 - 647215 TGT - -a -s simMouse_chr6.simMouse.chr6 552319 46 + 636262 ATTTGCTGAGGACATTATGAGATACTCTAGAATGAATCCATTATGA -s Anc0.Anc0refChr3 154282 38 + 222631 A-TTGGTTAGAACATTATGAGAGAGTCTAGAATGAATAC------- -s Anc1.Anc1refChr6 190352 39 + 197743 ATTTGGTTAGAACATTATGAGAGAGTCTAGAATGAATAC------- -s Anc2.Anc2refChr1 68440 38 + 142988 A-TTGGTTGGAATATTATGAGAGAGTCTAGAATGAATAC------- -s mr.mrrefChr3 102306 46 + 181027 ATTTGCTGAGGACATTATGAGATACTCTAGAATGAATCCATTATGA -s simCow_chr6.simCow.chr6 526669 35 + 602619 A-CTGGTT---ATATGATGGGATATGCTAGAATGAACAC------- -s simDog_chr6.simDog.chr6 515380 38 + 593897 A-TTGGCTGGAATATTATGAGAGAGTCTAGAATGATTAC------- -s simHuman_chr6.simHuman.chr6 522314 39 + 601863 GTTTGGTTAGAACATTATGAGAGAGCCTTCAGTGAATAC------- -s simRat_chr6.simRat.chr6 27254 46 - 647215 ATTTGTTGAGGACATCAGGAGATACTCTAGAATGAGTCCATTATGA - -a -s simMouse_chr6.simMouse.chr6 552365 5 + 636262 TAGCC -s Anc0.Anc0refChr3 154320 5 + 222631 TGGGC -s Anc1.Anc1refChr6 190391 5 + 197743 TGGGC -s Anc2.Anc2refChr1 68478 5 + 142988 TTGGC -s mr.mrrefChr3 102352 5 + 181027 TGGCC -s simCow_chr6.simCow.chr6 526707 5 + 602619 TTGAC -s simDog_chr6.simDog.chr6 515418 5 + 593897 TTGGT -s simHuman_chr6.simHuman.chr6 522353 5 + 601863 TGGGC -s simRat_chr6.simRat.chr6 27300 5 - 647215 TGGCC - -a -s simMouse_chr6.simMouse.chr6 552370 48 + 636262 AATGAGGTAAAGGGCTAATGAACCAAAGAGAGGGATCATAGGCCATTC -s Anc0.Anc0refChr3 154325 36 + 222631 A------------GCTAATGGAGAAAAGACATGGATCATAGGCCCTTC -s Anc1.Anc1refChr6 190396 36 + 197743 A------------GCTAATGGAGAAAAGACATGGATCATAGGCCCTTC -s Anc2.Anc2refChr1 68483 36 + 142988 A------------GCTAATGGAGAAAGGACATGGAACATAGGCCCTTC -s mr.mrrefChr3 102357 48 + 181027 AATGAGGTAAAGGGCTAATGAACCAAAGACATGGATCATAGGCCATTC -s simCow_chr6.simCow.chr6 526712 33 + 602619 A------------GCTAATGGAGAA---AAATGGAGCATAAGCCCTTC -s simDog_chr6.simDog.chr6 515480 36 + 593897 A------------GCTAATGGAGAAAGGACATGGAACATGGGCCCTTC -s simHuman_chr6.simHuman.chr6 522358 36 + 601863 A------------GCTAATGGCATAAAGACATGGATCCTAGGCCTTTC -s simRat_chr6.simRat.chr6 27305 48 - 647215 AATGAAGTAAAGGGCTAATGAACCAAAGACATGGATCATAGGCCATTC - -a -s simMouse_chr6.simMouse.chr6 552418 35 + 636262 AGGGAATATGACATTCTGTGAGGGAAGAGTGCTTA -s Anc0.Anc0refChr3 154362 35 + 222631 GGGGAATGTAACTTTCTGTGAGGGAAGAGTGCCTA -s Anc1.Anc1refChr6 190433 35 + 197743 GGGGAATGTAACTTTCTGTGAGGGAAGAGTGCCTA -s Anc2.Anc2refChr1 68520 35 + 142988 GGGATATGTAACTTTCTGTGAGGGAAGAGTCCCTG -s mr.mrrefChr3 102405 35 + 181027 GGGGAATATGACATTCTGTGAGGGAAGAGTGCTTA -s simCow_chr6.simCow.chr6 526746 34 + 602619 GGGT-ATGCAACTTTCTGTGAGGGACAAGCACCTT -s simDog_chr6.simDog.chr6 515517 35 + 593897 ACGATGCGTCACTTTCTGTGGGGTGAGACTCACTG -s simHuman_chr6.simHuman.chr6 522395 35 + 601863 GGGGAATGTAACCTTCTGTTAGGGATGAGTGCCTA -s simRat_chr6.simRat.chr6 27353 35 - 647215 GGGGAATATGACATTCTGTGAGGGAAGTGTGCTTA - -a -s simMouse_chr6.simMouse.chr6 552453 1 + 636262 A -s Anc0.Anc0refChr3 154398 1 + 222631 A -s Anc1.Anc1refChr6 190469 1 + 197743 A -s Anc2.Anc2refChr1 68556 1 + 142988 A -s mr.mrrefChr3 102441 1 + 181027 A -s simCow_chr6.simCow.chr6 526781 1 + 602619 A -s simDog_chr6.simDog.chr6 515553 1 + 593897 A -s simHuman_chr6.simHuman.chr6 522431 1 + 601863 A -s simRat_chr6.simRat.chr6 27389 1 - 647215 A - -a -s simMouse_chr6.simMouse.chr6 552454 11 + 636262 ATCCAAAAACA -s Anc0.Anc0refChr3 154399 9 + 222631 ATTGAAAA--A -s Anc1.Anc1refChr6 190470 11 + 197743 ATTGAAAAACA -s Anc2.Anc2refChr1 68557 9 + 142988 ATTGAAAA--A -s mr.mrrefChr3 102442 11 + 181027 ATTCAAAAACA -s simCow_chr6.simCow.chr6 526782 9 + 602619 ACTGAAAA--A -s simDog_chr6.simDog.chr6 515570 9 + 593897 GTTGGAAA--T -s simHuman_chr6.simHuman.chr6 522432 11 + 601863 ATTGAAAAACA -s simRat_chr6.simRat.chr6 27390 11 - 647215 ATTCAAAGACA - -a -s simMouse_chr6.simMouse.chr6 552465 11 + 636262 AGATGAGTCTA -s Anc0.Anc0refChr3 154408 11 + 222631 AGAGGTATCTA -s Anc1.Anc1refChr6 190481 11 + 197743 AGAGGTATCTA -s Anc2.Anc2refChr1 68566 11 + 142988 AGAGGTATCTA -s mr.mrrefChr3 102453 11 + 181027 AGATGAATCTA -s simCow_chr6.simCow.chr6 526791 11 + 602619 AGAGGTATCTA -s simDog_chr6.simDog.chr6 515579 11 + 593897 TTGGGTGACTA -s simHuman_chr6.simHuman.chr6 522443 11 + 601863 AGAGGTATCTA -s simRat_chr6.simRat.chr6 27499 11 - 647215 AGGTTAATTTA - -a -s simMouse_chr6.simMouse.chr6 552476 7 + 636262 TGCTTAA -s Anc0.Anc0refChr3 154419 5 + 222631 AGAAT-- -s Anc1.Anc1refChr6 190492 7 + 197743 AGAATGA -s Anc2.Anc2refChr1 68577 5 + 142988 AGAAT-- -s mr.mrrefChr3 102464 7 + 181027 TGCTTAA -s simCow_chr6.simCow.chr6 526802 5 + 602619 AGAAT-- -s simDog_chr6.simDog.chr6 515603 5 + 593897 GATAT-- -s simHuman_chr6.simHuman.chr6 522454 7 + 601863 AGAATGA -s simRat_chr6.simRat.chr6 27510 7 - 647215 TGCTTAA - -a -s simMouse_chr6.simMouse.chr6 552483 12 + 636262 CTGCCACTCTGA -s Anc0.Anc0refChr3 154436 12 + 222631 ATGCCACTATGA -s Anc1.Anc1refChr6 190511 12 + 197743 ATGCCACTATGA -s Anc2.Anc2refChr1 68594 12 + 142988 ATGCCACCATGA -s mr.mrrefChr3 102471 12 + 181027 ATGCCACTCTGA -s simCow_chr6.simCow.chr6 526821 12 + 602619 CTGAAACCATGC -s simDog_chr6.simDog.chr6 515625 12 + 593897 ATGCCTCCATGA -s simHuman_chr6.simHuman.chr6 522473 12 + 601863 ATACCACTGTGA -s simRat_chr6.simRat.chr6 27517 12 - 647215 ATGCCATTCTGA - -a -s simMouse_chr6.simMouse.chr6 552495 24 + 636262 TTTTAATAGACATATTGTCTGGTT -s Anc0.Anc0refChr3 154448 18 + 222631 CTTTCATAAACATATTGT------ -s Anc1.Anc1refChr6 190523 18 + 197743 CTTTCATAAACATATTGT------ -s Anc2.Anc2refChr1 68607 18 + 142988 CTTTCATCAACATATTGT------ -s mr.mrrefChr3 102483 24 + 181027 TTTTAATAGACATATTGTCTGGTT -s simCow_chr6.simCow.chr6 526834 18 + 602619 TTTTTACTAACATCTTGT------ -s simDog_chr6.simDog.chr6 515638 18 + 593897 CTTTCATCAAGATATTGT------ -s simHuman_chr6.simHuman.chr6 522485 18 + 601863 CTTTGATAAGCAGATTGT------ -s simRat_chr6.simRat.chr6 27529 24 - 647215 TTTTAATAGACACTTTGTCTGGTT - -a -s simMouse_chr6.simMouse.chr6 552519 45 + 636262 AATCTCAAGAAACGCATGTACCAAAGTCATTAGTAGGATTAGGTC -s Anc0.Anc0refChr3 154466 8 + 222631 ----------------------------------ATGATTA---C -s Anc1.Anc1refChr6 190541 23 + 197743 AATC--------------------AGTC--TGGAATGATTAGCCC -s Anc2.Anc2refChr1 68625 8 + 142988 ----------------------------------ATGACTA---T -s mr.mrrefChr3 102507 44 + 181027 AATCTCAAGAA-CGCATGTACCAAAGTCATTAGTAGGATTAGGTC -s simCow_chr6.simCow.chr6 526852 8 + 602619 ----------------------------------ATGCCTA---A -s simDog_chr6.simDog.chr6 515656 8 + 593897 ----------------------------------ATGACTG---T -s simHuman_chr6.simHuman.chr6 522503 23 + 601863 AATC--------------------AGTC--TGGAATGTTCAGCCC -s simRat_chr6.simRat.chr6 27557 44 - 647215 AATCCCAAGAG-CGCATGCACCAAAGTCATTAGTAGGACTAGGTC - -a -s simMouse_chr6.simMouse.chr6 552564 5 + 636262 AATGC -s Anc0.Anc0refChr3 154474 5 + 222631 AATGC -s Anc1.Anc1refChr6 190564 5 + 197743 AATGC -s Anc2.Anc2refChr1 68633 5 + 142988 AATGC -s mr.mrrefChr3 102551 5 + 181027 AATGC -s simCow_chr6.simCow.chr6 526860 5 + 602619 TATGC -s simDog_chr6.simDog.chr6 515664 5 + 593897 AACGC -s simHuman_chr6.simHuman.chr6 522532 5 + 601863 AATGC -s simRat_chr6.simRat.chr6 27601 5 - 647215 AAAGC - -a -s simMouse_chr6.simMouse.chr6 552569 17 + 636262 AAGCGTTCTATATATGA -s Anc0.Anc0refChr3 154479 12 + 222631 AAACTTCTA-----TCA -s Anc1.Anc1refChr6 190569 17 + 197743 AAACTTCTAGGTTGTCA -s Anc2.Anc2refChr1 68638 12 + 142988 AAACTTCTA-----TCA -s mr.mrrefChr3 102556 17 + 181027 AAGCGTTCTATATATGA -s simCow_chr6.simCow.chr6 526865 12 + 602619 AAACTTCTA-----GGA -s simDog_chr6.simDog.chr6 515669 12 + 593897 AAACTGACA-----TCA -s simHuman_chr6.simHuman.chr6 522537 17 + 601863 AATTTTCTAGGTTGTAA -s simRat_chr6.simRat.chr6 27615 17 - 647215 AAGCATTCTATCTATGA - -a -s simMouse_chr6.simMouse.chr6 552586 60 + 636262 GATGCTGAGCTACAGAGCCTCAATTTTAAAGCTTGGCTTTCATGATAGAAGTAAAAACAG -s Anc0.Anc0refChr3 154492 60 + 222631 GATTCTGAGCTACAAAGCCTCAATCATAAAGCTGTGCTTTAGTGAGGGAGTTATAAACAG -s Anc1.Anc1refChr6 190587 60 + 197743 GATTCTGAGCTACAAAGCCTCAATCATAAAGCTGTGCTTTAGTGAGGGAGTTATAAACAG -s Anc2.Anc2refChr1 68651 60 + 142988 GATTCTGAGTTACAAACCCTCAATCATAAAGCTGTGCTTTAGTGAGGGTGTTATGGACAG -s mr.mrrefChr3 102574 60 + 181027 GATGCTGAGCTACAGAGCCTCAATTTTAAAGCTTGGCTTTCATGATGGAAGTAAAAACAG -s simCow_chr6.simCow.chr6 526878 59 + 602619 TTT-CTGAGTTACAAACCCTAAACCATTACGTAGTGCTTTAGTGAGGGTGTTACTAAAAG -s simDog_chr6.simDog.chr6 515682 59 + 593897 GATTCCG-ATGACTAACTCTCAATTATAAAGCTGTGCTTTAGTGGGGCTGTTATGGACAG -s simHuman_chr6.simHuman.chr6 522555 59 + 601863 GATTCTGAGCTACAAAGCCACAATCATAGAGCCATGCATTAGTAAGGGAG-TATAAAGAG -s simRat_chr6.simRat.chr6 27633 60 - 647215 GATGCTAAGCTACAGACCCTCTATTTTAAAGCTTGGCTTTCATGATGGTAGTAAAAACAG - -a -s simMouse_chr6.simMouse.chr6 552646 3 + 636262 CCT -s Anc0.Anc0refChr3 154552 3 + 222631 ACT -s Anc1.Anc1refChr6 190647 3 + 197743 ACT -s Anc2.Anc2refChr1 68711 3 + 142988 ACT -s mr.mrrefChr3 102634 3 + 181027 CCT -s simCow_chr6.simCow.chr6 526937 3 + 602619 GCT -s simDog_chr6.simDog.chr6 515741 3 + 593897 ACT -s simHuman_chr6.simHuman.chr6 522616 3 + 601863 AGC -s simRat_chr6.simRat.chr6 27693 3 - 647215 CCT - -a -s simMouse_chr6.simMouse.chr6 552649 77 + 636262 TTCCCACTTATACATGTTCTGGTAGGGATTTCAACTTCAACTGCTGTACTTTTTCTTTAAGGCATGCACATCTTTTG -s Anc0.Anc0refChr3 154556 66 + 222631 TTCCCCCTTGTACATGTGCAGGTAGGAATTTTAACTTCCA---------TATTTTTTTAAGGCATGCC--TCTTTCA -s Anc1.Anc1refChr6 190651 66 + 197743 TTCCCCCTTGTACATGTGCAGGTAGGAATTTTAACTTCCA---------TATTTTTTTAAGGCATGCC--TCTTTCA -s Anc2.Anc2refChr1 68715 66 + 142988 TTCCACCTTGTACATGTGCAGGTAGGAATTTTAAGTTTCA---------TATTTTTTTAAGGCATGCC--TCATTCA -s mr.mrrefChr3 102637 77 + 181027 TTCCCACTTATACATGTGCTGGTAGGAATTTCAACTTCAACTGCTGTACTTTTTTTTTAAGGCATGCACATCTTTTG -s simCow_chr6.simCow.chr6 526941 66 + 602619 GCCCACTTTCTACATGTGCAGGTAGGTATTTTAAGTTTCA---------TATTTTTTTAAGGCATGCC--TCATTCA -s simDog_chr6.simDog.chr6 515745 63 + 593897 TTC---CTTGTACATGTGTAGCTAGGAATTTTGAGTTTCA---------TATTTTTGTAAGACATGCC--TCATCCA -s simHuman_chr6.simHuman.chr6 522620 66 + 601863 TTCCCTCTTGTACACGTGCAGGTAGGAATTTTAACTTCCA---------TGCTTTTTTAGGGCATGCC--TCTTTCA -s simRat_chr6.simRat.chr6 27696 77 - 647215 TTCCCGCTTATACATGTGCTGGTAGGAATTTCAACTTTAACTGCTGTACTTTTCTTTTGAGGCATCCACATCTTTTG - -a -s simMouse_chr6.simMouse.chr6 552726 18 + 636262 CTGGGGTCAGAGAGGCAC -s Anc0.Anc0refChr3 154623 18 + 222631 CCGGGGACAAAATGGCAC -s Anc1.Anc1refChr6 190718 18 + 197743 CCGGGGACAAAATGGCAC -s Anc2.Anc2refChr1 68782 18 + 142988 CCGGGGACAAAATGGCAC -s mr.mrrefChr3 102715 18 + 181027 CTGGGGACAGAGAGGCAC -s simCow_chr6.simCow.chr6 527008 18 + 602619 CCAAGGACAAAATGACAC -s simDog_chr6.simDog.chr6 515809 18 + 593897 CTGGGGACAGAGCGGCCC -s simHuman_chr6.simHuman.chr6 522687 18 + 601863 CCGGGGACAATATGGCAC -s simRat_chr6.simRat.chr6 27774 18 - 647215 CTGACGACAGAGAGGCAC - -a -s simMouse_chr6.simMouse.chr6 552744 10 + 636262 TACGCTAACA -s Anc0.Anc0refChr3 154641 9 + 222631 TGCCCTGGT- -s Anc1.Anc1refChr6 190736 10 + 197743 TGCCCTGGTG -s Anc2.Anc2refChr1 68800 9 + 142988 TGCCCTGGT- -s mr.mrrefChr3 102733 10 + 181027 TACCCTAACA -s simCow_chr6.simCow.chr6 527028 9 + 602619 CGCCCTGGT- -s simDog_chr6.simDog.chr6 515827 9 + 593897 TGCCCTGTT- -s simHuman_chr6.simHuman.chr6 522705 10 + 601863 TGCCGTGGTG -s simRat_chr6.simRat.chr6 27792 10 - 647215 CACCCTAACA - -a -s simMouse_chr6.simMouse.chr6 552754 30 + 636262 TATGAACTCGTCCACTTGTAAGCTAGGGTG -s Anc0.Anc0refChr3 154651 27 + 222631 TATCCTCTCTCTCACTGATAAGC---TGTG -s Anc1.Anc1refChr6 190747 30 + 197743 TATCCTCTCTCTCACTGATAAGCTAGTGTG -s Anc2.Anc2refChr1 68810 27 + 142988 TATCCTCTCTCTCACTGATAAGC---TGTG -s mr.mrrefChr3 102743 30 + 181027 TATGAACTCGCTCACTTGTAAGCTAGGGTG -s simCow_chr6.simCow.chr6 527038 26 + 602619 TA-ACTCTCTCTCACTGATATGT---AGTG -s simDog_chr6.simDog.chr6 515837 27 + 593897 TATCCTCTCTCTCACTGATAAGC---TGTG -s simHuman_chr6.simHuman.chr6 522718 30 + 601863 TATTCTTTCTCTCACTAATAGACTAGTTTG -s simRat_chr6.simRat.chr6 27802 30 - 647215 TATGTACTCACTCACTTGTAAGCTAGCGCG - -a -s simMouse_chr6.simMouse.chr6 552784 21 + 636262 ACAAAACAATCTGCCCTCTTA -s Anc0.Anc0refChr3 154678 20 + 222631 A-AAAAGGATCCTCTCTCTTA -s Anc1.Anc1refChr6 190777 20 + 197743 A-AAAAGGATCCTCTCTCTTA -s Anc2.Anc2refChr1 68837 20 + 142988 C-AAAAGGATCCTTTCTCTTA -s mr.mrrefChr3 102773 21 + 181027 ACAAAACAATCTGCCCTCTTA -s simCow_chr6.simCow.chr6 527067 20 + 602619 C-AAAAGGATTGTTTCTCCTA -s simDog_chr6.simDog.chr6 515864 19 + 593897 C-AACA-AATCCTTTCTCTTA -s simHuman_chr6.simHuman.chr6 522748 20 + 601863 A-AAAAGGATCCTCTCTCTTA -s simRat_chr6.simRat.chr6 27832 21 - 647215 ACAAAACAATCTGGACTCTTA - -a -s simMouse_chr6.simMouse.chr6 552805 25 + 636262 AATGTGATTTTATGATTATGTTACT -s Anc0.Anc0refChr3 154698 24 + 222631 AACAT-ATTTCATAATTCCATTACT -s Anc1.Anc1refChr6 190797 24 + 197743 AACAT-ATTTCATAATTCCATTACT -s Anc2.Anc2refChr1 68857 24 + 142988 AACAT-ATTTCACAATTCCATTACT -s mr.mrrefChr3 102794 25 + 181027 AATGTGATTTTATAATTACGTTACT -s simCow_chr6.simCow.chr6 527088 24 + 602619 CATAT-ATGTCAGAATTCCATTGCT -s simDog_chr6.simDog.chr6 515883 24 + 593897 AACAT-ATTTCACAATTCCATTACT -s simHuman_chr6.simHuman.chr6 522768 24 + 601863 GACAT-ATTTCATAATTTCCATACT -s simRat_chr6.simRat.chr6 27853 21 - 647215 AATCTGTTC----AATTACTTTACT - -a -s simMouse_chr6.simMouse.chr6 552830 7 + 636262 CCCTGCC -s Anc0.Anc0refChr3 154726 7 + 222631 CTTTGCC -s Anc1.Anc1refChr6 190825 7 + 197743 CTTTGCC -s Anc2.Anc2refChr1 68885 7 + 142988 CTTTGCC -s mr.mrrefChr3 102819 7 + 181027 CTCTGCC -s simCow_chr6.simCow.chr6 527116 7 + 602619 CTTTGCA -s simDog_chr6.simDog.chr6 515911 7 + 593897 CTTTGCC -s simHuman_chr6.simHuman.chr6 522800 7 + 601863 CTTTGCC -s simRat_chr6.simRat.chr6 27874 7 - 647215 CTCTGCC - -a -s simMouse_chr6.simMouse.chr6 552837 32 + 636262 TAGAAGTGACGTTACAGGCTGCATGAATAAGA -s Anc0.Anc0refChr3 154733 32 + 222631 TTGATGTGGTATTTCAAACTGCTTGAATCAAA -s Anc1.Anc1refChr6 190832 32 + 197743 TTGATGTGGTATTTCAAACTGCTTGAATCAAA -s Anc2.Anc2refChr1 68892 32 + 142988 TTGATCTGGTATTTAAAACTGCTAGAATCAAA -s mr.mrrefChr3 102826 32 + 181027 TAGAAGTGACATTACAGGCTGCTTGAATAAGA -s simCow_chr6.simCow.chr6 527127 32 + 602619 TTGATCTAGTTTTTTAAACTGCTAGAACATAA -s simDog_chr6.simDog.chr6 515918 32 + 593897 GTGATCTGGGATTTAAAACTGCTATAATCAAA -s simHuman_chr6.simHuman.chr6 522807 32 + 601863 TTGAGGTGGTATCGCAAACTACTTGAATGGAA -s simRat_chr6.simRat.chr6 27881 30 - 647215 CAGAAGTGACAT--CAGGCTGCTTGAATAAGA - -a -s simMouse_chr6.simMouse.chr6 552869 56 + 636262 AACTCCCTGTCTGGGTCTGTGCCTAGTCAATTGTGATCCTCCATAGAAATCCGGTT -s Anc0.Anc0refChr3 154765 56 + 222631 AGCATCGCATGTGGGCCTGTACCTATTCAATTGTGGGCCTCCACAGAAGTCCAGTG -s Anc1.Anc1refChr6 190864 56 + 197743 AGCATCGCATGTGGGCCTGTACCTATTCAATTGTGGGCCTCCACAGAAGTCCAGTG -s Anc2.Anc2refChr1 68924 56 + 142988 AGCATCGCATGTGGGCCTATACCTATTCTATTGTGGGCTCCCACAGAAGTCTGGTG -s mr.mrrefChr3 102858 56 + 181027 AACTCCCTGTCTGGGTCTGTGCCTAGTCAATTGTGATCCTCCATAGAAATCCAGTT -s simCow_chr6.simCow.chr6 527164 51 + 602619 AGCAACGTGTGTGGGTCC-----TATCCTATTGTGCACTCCCACAGAAGTCTGGTG -s simDog_chr6.simDog.chr6 515950 48 + 593897 AGCATCCCATGTGGGCCTATACCTATT--------GGCTCCCGCAGAAGTTTGGTG -s simHuman_chr6.simHuman.chr6 522839 50 + 601863 AGCATC------GAGCCTGTACCTATTTAATTGCGTGCCTCCACAGAAGTCCAGTG -s simRat_chr6.simRat.chr6 27911 56 - 647215 AAATCCCTGTGTGGGTCTGTGCCTAGTCCATTGTGATCCTCCATAGAAATCCAGTT - -a -s simMouse_chr6.simMouse.chr6 552925 56 + 636262 GTGAATATGCTTGGGCACCAAACTCTCCCTCTTGTACTGAGAGAGCTGACATTAGT -s Anc0.Anc0refChr3 154830 28 + 222631 GTGGATATGCTTGGGCACCATACCCACA---------------------------- -s Anc1.Anc1refChr6 190929 56 + 197743 GTGGATATGCTTGGGCACCATACCCACATTGATGTATTAAGATGACTGGTGGCAGT -s Anc2.Anc2refChr1 68989 28 + 142988 GTGGATATGCTTGGGCAACATAACCACA---------------------------- -s mr.mrrefChr3 102914 56 + 181027 GTGGATATGCTTGGGCACCAAACTCTCATTGTTGTACTGAGAGAACTGACATCAGT -s simCow_chr6.simCow.chr6 527224 28 + 602619 GCTGATATGCTTGCGCAGCATAACCACA---------------------------- -s simDog_chr6.simDog.chr6 516007 28 + 593897 GTGGGTAAGTCTGGGCAAGATAAACACA---------------------------- -s simHuman_chr6.simHuman.chr6 522898 56 + 601863 GTGGATGTGCTTGGGCGCCATACCCACATTGATGTATTAAGATGACTGGTGGCAGT -s simRat_chr6.simRat.chr6 27967 56 - 647215 GTGGATATTCTTGGGCACCAAACTCTCATTGTTGTACTGAGAGAACTGACATCAGT - -a -s simMouse_chr6.simMouse.chr6 552981 108 + 636262 TGATGATAGATTTATTATAGAGGGCTCTGAGTACTCCCTCATATAGTTATTTGTTTATGGGGGCTATGGGCAATAGGCCCCTGGACAAACTCTTGGAATAAGATAAGC -s Anc0.Anc0refChr3 154858 71 + 222631 ---------------------------TAAATAGCCCCTTACATAGTTATTTGT---------CTCTGGGCTATAAGCCC-TGGACAAATTATTGGAATAAGCTCAGC -s Anc1.Anc1refChr6 190985 98 + 197743 TGGAGTTAAACTTAGCAACAACGGCTCTAAATAGCCCCTTACATAGTTATTTGT---------CTCTGGGCTATAAGCCC-TGGACAAATTATTGGAATAAGCTCAGC -s Anc2.Anc2refChr1 69017 71 + 142988 ---------------------------TGAATAGCCCCTTACATAGTTATTTGT---------CTCTGGGTTATAAGCCC-CGGACAAATTATTGGAATAAGCTCTGC -s mr.mrrefChr3 102970 107 + 181027 TGAAGATAGATTTATTATAGAGGGCTCTAAGTACTCCCTCATATAGTTATTTGTTTATGGGGGCTATGGGCAATAGGCCC-TGGACAAACTCTTGGAATAAGATAAGC -s simCow_chr6.simCow.chr6 527252 57 + 602619 ---------------------------TT--------------TAGCTATTTGT---------CTCTTTGGTACAAGCCC-GGGACAAAATATTGGAATAAGCTCTGC -s simDog_chr6.simDog.chr6 516035 71 + 593897 ---------------------------TGAATAGCCCCTTACATGGTTATTTGT---------CTCTGGGTTATAGGCCT-CGGACAACTTATTGAATTACGCACTGC -s simHuman_chr6.simHuman.chr6 522958 98 + 601863 TGGAGTTAAACTTAGCAACAACGGCTCTAAATAGCCCCTTACATAGTAATTTGT---------CTCTGGGCTATAAGCCC-TGTACAAATTACTGGAACAAGCTCAGC -s simRat_chr6.simRat.chr6 28023 107 - 647215 TAAAGACAGATTTAATATAGAGGGCTCTAGGTACTCCCTAATGTAGTTATTTATTTATAGGGGCTATGGGCAATGGGCCC-TGGACAAACTCTTGGAGTAAGATAAGC - -a -s simMouse_chr6.simMouse.chr6 553089 30 + 636262 GCCAGACTCTTTAATAGCACCAAGTTTTTG -s Anc0.Anc0refChr3 154930 30 + 222631 GCTGGACTCTATAATTCCACCATGTCTTTG -s Anc1.Anc1refChr6 191084 30 + 197743 GCTGGACTCTATAATTCCACCATGTCTTTG -s Anc2.Anc2refChr1 69089 30 + 142988 GCTGGACTCTATAATTCCACCGTGTCTTTA -s mr.mrrefChr3 103078 30 + 181027 GCCAGACTCTATAATAGCACCAAGTTTTTG -s simCow_chr6.simCow.chr6 527310 30 + 602619 GCTGGACTCTATAATGCCACTGCATCTTTA -s simDog_chr6.simDog.chr6 516107 30 + 593897 GCTGGACCCTATAATTTCACCGTGTCTTTA -s simHuman_chr6.simHuman.chr6 523057 30 + 601863 GCTGGACTCTATAATTCCACCAGGTCTTTG -s simRat_chr6.simRat.chr6 28131 30 - 647215 GCCAGACCCTATAATAGTAGCAAGTTTTTG - -a -s simMouse_chr6.simMouse.chr6 553119 32 + 636262 ATGTTTGTGAGAAGGAAAGGCCCAAATTCAAG -s Anc0.Anc0refChr3 154961 32 + 222631 ATGTTTGTAAGAAGGAAAAGTCAAAATTTGAG -s Anc1.Anc1refChr6 191115 32 + 197743 ATGTTTGTAAGAAGGAAAAGTCAAAATTTGAG -s Anc2.Anc2refChr1 69120 32 + 142988 ATGTTTGTAAGAAGGAAAAATCCAGCTTTGAG -s mr.mrrefChr3 103108 32 + 181027 ATGTTTGTGAGAAGGAAAGGCCAAAATTCAAG -s simCow_chr6.simCow.chr6 527341 32 + 602619 ATGTTTGTAAGAAGGAAAAATCTAGCCTTGAG -s simDog_chr6.simDog.chr6 516138 32 + 593897 ATGTTCGTAAGAAGGAAAAACACAGCTTTGAG -s simHuman_chr6.simHuman.chr6 523088 32 + 601863 ATGTTTGTAAGAAGGAAAAGTCAAAATTTGTG -s simRat_chr6.simRat.chr6 28161 32 - 647215 ATGTTTGTGAGAAGGAAAGGCCAAACTTCAAG - -a -s simMouse_chr6.simMouse.chr6 553151 2 + 636262 TT -s Anc0.Anc0refChr3 155020 2 + 222631 TT -s Anc1.Anc1refChr6 191174 2 + 197743 TT -s Anc2.Anc2refChr1 69179 2 + 142988 TT -s mr.mrrefChr3 103140 2 + 181027 TT -s simCow_chr6.simCow.chr6 527397 2 + 602619 TT -s simDog_chr6.simDog.chr6 516197 2 + 593897 TT -s simHuman_chr6.simHuman.chr6 523147 2 + 601863 TT -s simRat_chr6.simRat.chr6 28193 2 - 647215 TT - -a -s simMouse_chr6.simMouse.chr6 553153 18 + 636262 TCATTGTTGAGTTTGCAA -s Anc0.Anc0refChr3 155025 18 + 222631 TGTTAGTTGAGTTTGTAG -s Anc1.Anc1refChr6 191179 18 + 197743 TGTTAGTTGAGTTTGTAG -s Anc2.Anc2refChr1 69184 18 + 142988 GGTCAGTAGTGTTTGTAG -s mr.mrrefChr3 103145 18 + 181027 TCATTGTTGAGTTTGTAA -s simCow_chr6.simCow.chr6 527402 18 + 602619 CGTGTGTAGCATTTGTAG -s simDog_chr6.simDog.chr6 516202 18 + 593897 GGTCAGTAGTGTTTGTAG -s simHuman_chr6.simHuman.chr6 523152 18 + 601863 TATTAGTTGATTTTGTAG -s simRat_chr6.simRat.chr6 28198 16 - 647215 TCATTGTTGAGTTTGT-- - -a -s simMouse_chr6.simMouse.chr6 553171 16 + 636262 GTTTCTCCCCATCACT -s Anc0.Anc0refChr3 155047 10 + 222631 GTGCATCCCC------ -s Anc1.Anc1refChr6 191201 16 + 197743 GTGCATCCCCCCTACT -s Anc2.Anc2refChr1 69206 10 + 142988 GTGCATCCCC------ -s mr.mrrefChr3 103163 16 + 181027 GTTTCTCCCCATCACT -s simCow_chr6.simCow.chr6 527424 10 + 602619 GTGCATTCTC------ -s simDog_chr6.simDog.chr6 516224 10 + 593897 GTGTATCCCC------ -s simHuman_chr6.simHuman.chr6 523174 16 + 601863 GTCCATCCCCCCTACT -s simRat_chr6.simRat.chr6 28214 11 - 647215 -----TCCCCATCATT - -a -s simMouse_chr6.simMouse.chr6 553187 49 + 636262 CTTATTATAATGTTGACCCCATATGGGGACGCATATCTTAAATGCCTAC -s Anc0.Anc0refChr3 155057 49 + 222631 CTTACTAAAACGTTGACCCTGTTTGAAGGAGCCTATTTTAGATGCCTGC -s Anc1.Anc1refChr6 191217 49 + 197743 CTTACTAAAACGTTGACCCTGTTTGAAGGAGCCTATTTTAGATGCCTGC -s Anc2.Anc2refChr1 69216 49 + 142988 CTTACAAAAACGTTGACCCTGTTTGAAGGAACCTATTTTAGATGCCTGC -s mr.mrrefChr3 103179 49 + 181027 CTTACTATAATGTTGACCCCATATGGGGACGCATATCTTAAATGCCTAC -s simCow_chr6.simCow.chr6 527434 49 + 602619 TTAACCAAAACATTGATCCTATTTGAAGATACCTATTTTAAATGCCTGC -s simDog_chr6.simDog.chr6 516234 49 + 593897 CTTACAAAAACGTTGACCCTGTTTCAAGGAACCTATTTTAGATGCTTGC -s simHuman_chr6.simHuman.chr6 523220 49 + 601863 CCTACTAAAACGTTGACCCTGTGTGAAGGGGCCTAATTTAGGTGCCTGT -s simRat_chr6.simRat.chr6 28225 49 - 647215 CTTACTATTATGTTGACTCCATATGGGGATGCGTATCTTAAATGCCTAC - -a -s simMouse_chr6.simMouse.chr6 553236 22 + 636262 TGTTAGGTTAAAATAAACATCA -s Anc0.Anc0refChr3 155106 17 + 222631 TGTTA-----AAATAAATATCA -s Anc1.Anc1refChr6 191266 17 + 197743 TGTTA-----AAATAAATATCA -s Anc2.Anc2refChr1 69265 17 + 142988 TGTTA-----ATATGAATATCA -s mr.mrrefChr3 103228 22 + 181027 TGTTAGGTTAAAATAAACATCA -s simCow_chr6.simCow.chr6 527499 16 + 602619 TGTTA-----ATATGAATAT-A -s simDog_chr6.simDog.chr6 516283 17 + 593897 TGTTG-----ATAAGGATATCA -s simHuman_chr6.simHuman.chr6 523269 17 + 601863 TGTTA-----AAATAAATATCA -s simRat_chr6.simRat.chr6 28274 22 - 647215 TGTTATGTTAAAATAAACACCA - -a -s simMouse_chr6.simMouse.chr6 553258 39 + 636262 TGACAGCACCTTATCTAATGCCGGTCTCACATGACCCTT -s Anc0.Anc0refChr3 155140 39 + 222631 TGTGAGCACCTTATCAAACACTGGCTTCACATGGTCCTT -s Anc1.Anc1refChr6 191300 39 + 197743 TGTGAGCACCTTATCAAACACTGGCTTCACATGGTCCTT -s Anc2.Anc2refChr1 69299 39 + 142988 TGTGAGCACCTTATCAAACACTGGCGTCACATGGTCCCT -s mr.mrrefChr3 103250 39 + 181027 TGAGAGCACCTTATCTAATGCTGGTTTCACATGACCCTT -s simCow_chr6.simCow.chr6 527539 39 + 602619 TATGAGTGCCTTACCTGACAGTGGAATGACATGGTCCCT -s simDog_chr6.simDog.chr6 516311 34 + 593897 TGTGAGCACCTTATCAAACACTATCGTCACATAG----- -s simHuman_chr6.simHuman.chr6 523303 39 + 601863 TGTGAGCACCTTATCAAACACTGGCTTCATGTGGTCCTT -s simRat_chr6.simRat.chr6 28296 39 - 647215 TGGGAGCACCTTATCTAATGCTGGTTTCACATGACCCTT - -a -s simMouse_chr6.simMouse.chr6 553297 18 + 636262 GTCGGCCTTGAGTCATCT -s Anc0.Anc0refChr3 155180 18 + 222631 CTTGGCCTCTATTCATCT -s Anc1.Anc1refChr6 191340 18 + 197743 CTTGGCCTCTATTCATCT -s Anc2.Anc2refChr1 69339 18 + 142988 CTTGCCCTCTATTCACCT -s mr.mrrefChr3 103289 18 + 181027 GTCGGCCTTGAGTCATCT -s simCow_chr6.simCow.chr6 527579 18 + 602619 CTTGCCCCCTTGTCACCT -s simDog_chr6.simDog.chr6 516345 12 + 593897 ------CTTTATTCACCT -s simHuman_chr6.simHuman.chr6 523343 18 + 601863 CTGGGCCTCTATTCATCT -s simRat_chr6.simRat.chr6 28335 18 - 647215 GTAGGCCTTGAGTCCTCT - -a -s simMouse_chr6.simMouse.chr6 553315 3 + 636262 CTT -s Anc0.Anc0refChr3 155198 3 + 222631 TTT -s Anc1.Anc1refChr6 191358 3 + 197743 TTT -s Anc2.Anc2refChr1 69357 3 + 142988 TTT -s mr.mrrefChr3 103307 3 + 181027 CTT -s simCow_chr6.simCow.chr6 527598 3 + 602619 TTT -s simDog_chr6.simDog.chr6 516357 3 + 593897 TTT -s simHuman_chr6.simHuman.chr6 523361 3 + 601863 TTT -s simRat_chr6.simRat.chr6 28353 3 - 647215 CTT - -a -s simMouse_chr6.simMouse.chr6 553318 58 + 636262 ATCCAGGCTAATCCCCATATGATGTTCCTAATGGGAATGCTTTGGTGCAGCTATGCTT -s Anc0.Anc0refChr3 155202 47 + 222631 ATCCAAACTAATACCTATGTGAGGTGT----TGGACATTCCCAG-------TGGACTT -s Anc1.Anc1refChr6 191362 47 + 197743 ATCCAAACTAATACCTATGTGAGGTGT----TGGACATTCCCAG-------TGGACTT -s Anc2.Anc2refChr1 69361 47 + 142988 ATACAAAATAATACCTATGTGAGGTGT----TAGACATTCCCAG-------TGGATTT -s mr.mrrefChr3 103311 58 + 181027 ATCCAAGCTAATACCCATGTGATGTGCCTAATGGGAATGCTTTGGTGCAGCTATGCTT -s simCow_chr6.simCow.chr6 527602 47 + 602619 ATACAAAGTAATGCCCATATGAGGTGT----TAGCCATTCCAAG-------TGTATTT -s simDog_chr6.simDog.chr6 516361 45 + 593897 ACACAAAATAATACCTATGTGAGGTGC------AACATTTCCCA-------TGGATTT -s simHuman_chr6.simHuman.chr6 523365 47 + 601863 ATCCAAACTAATACCGATGTGTGGTGT----TGGAGATTCCCAG-------TGAACTT -s simRat_chr6.simRat.chr6 28357 58 - 647215 ATCCAAGCTAACACCCATGTGATGTGCCTAATGGGATTGCTGTGGTGCAACTGTGCTT - -a -s simMouse_chr6.simMouse.chr6 553376 57 + 636262 CTGTGTATGAATATAAGATTAATAACTTAACGACATGTCTGATTTCGCCCCTCAGCA -s Anc0.Anc0refChr3 155249 42 + 222631 AT-------AATACAGGATT-------TAAT-GCATGTCTGATCTAACCCCTGAGCA -s Anc1.Anc1refChr6 191409 43 + 197743 AT-------AATACAGGATT-------TAATGGCATGTCTGATCTAACCCCTGAGCA -s Anc2.Anc2refChr1 69408 42 + 142988 AC-------AATATAGGATT-------CAAT-GCATGTCAGACCTAACCCCTGGGCA -s mr.mrrefChr3 103369 57 + 181027 CTGTGTATGAATACAGGATTAATAACTTAATGACATGTCTGATTTAGCCCCTCAGCA -s simCow_chr6.simCow.chr6 527649 42 + 602619 AC-------AATATAGGATT-------CAAT-GCATGTCAGACCTAACCCCTGGGCA -s simDog_chr6.simDog.chr6 516406 12 + 593897 AC-------AATGTAGGAT-------------------------------------- -s simHuman_chr6.simHuman.chr6 523412 43 + 601863 TT-------AATACAGGATT-------TAATGGCATGTGTGATCTAACCCCTTAGCA -s simRat_chr6.simRat.chr6 28416 57 - 647215 CAGTGCATAAATACAGGATTAGTGATTCAATGACATGTCTGATTTAGCCCCTCAGCA - -a -s simMouse_chr6.simMouse.chr6 553433 41 + 636262 GAGATCAATAATCTCATAAAGTGAAGGTAATAATGGCAGTC -s Anc0.Anc0refChr3 155291 39 + 222631 GAGATCAATAATATCATAAAGCTAAGAAAGTG--GGCAACC -s Anc1.Anc1refChr6 191452 39 + 197743 GAGATCAATAATATCATAAAGCTAAGAAAGTG--GGCAACC -s Anc2.Anc2refChr1 69450 39 + 142988 GAGAATGATAATATCATAGAGCTGAGAATGTG--GACAACC -s mr.mrrefChr3 103426 39 + 181027 GAGATCAATAATCTCATAAAGTGAAGGTAATA--GGCAGTC -s simCow_chr6.simCow.chr6 527691 39 + 602619 GAGAATGATAATAACATAGTTCTGAGAGTGTG--GCCTACC -s simDog_chr6.simDog.chr6 516418 31 + 593897 --------TAATCTCATAGAGCTGAGAATGTG--GACAGCC -s simHuman_chr6.simHuman.chr6 523455 39 + 601863 GGGATCAATAATATAATAAAGCTAAGAAAGTG--GGCAACC -s simRat_chr6.simRat.chr6 28481 37 - 647215 GAGACCAATAATCTCATAAACGGAAGGTAA----GGCAGTC - -a -s simMouse_chr6.simMouse.chr6 553474 87 + 636262 CCCCCTGTCTATTGTGTCAGAAGGATCAAGGAAAGATTTAGGTGCCAATATAAGTACCTGAATGTTGGGTTTGACTTCATCTAATGT -s Anc0.Anc0refChr3 155330 87 + 222631 CCTCCTGTATATTGTATTGGATGCCTTTAGGCCAGATTTAGGTGCAGATATAAGCACCTGACAGTTGGGCATGACTTCATCTAAAGC -s Anc1.Anc1refChr6 191491 87 + 197743 CCTCCTGTATATTGTATTGGATGCCTTTAGGCCAGATTTAGGTGCAGATATAAGCACCTGACAGTTGGGCATGACTTCATCTAAAGC -s Anc2.Anc2refChr1 69524 87 + 142988 CCTCCTGTCTATTATATTGGATGCCTTTAGGCCAGATTTAGATGCAGATATAAGCACCTGACAGTTGGGCATGACTTCATCTAAAGC -s mr.mrrefChr3 103465 87 + 181027 CCTCCTGTATATTGTATCAGAAGGATCAAGGAAAGATTTAGGTGCCAATATAAGTACCTGAATGTTGGGCTTGACTTCATCTAATGT -s simCow_chr6.simCow.chr6 527765 86 + 602619 CTTCCTGTCTATTATATCAGAAACCTTTAGGCCAGATTTAGATGTGAATATAAGCACCTGGCAGGTGGGCATAACTTCATCTAAA-C -s simDog_chr6.simDog.chr6 516485 87 + 593897 CCTCCTGTCTATCATATTGGATGCCTTTAGGCCAGATTTAGATGCAGGTATAAACACCAAACAGTTGGGCATGACTTCATCTAAAGC -s simHuman_chr6.simHuman.chr6 523494 87 + 601863 CCTCCTGTATATTGTATTTGAGGCCTTGCGGCCGGATTTATGGGCAGATATAAGCGCCTGACAGTTGGGCAGGACTTCATCTAAAGC -s simRat_chr6.simRat.chr6 28518 87 - 647215 CTTTCCGTATATTGTATCAGAAGGATCAGGGAAAGATTTACAAGCCAATATAAGTATCTGAATGTTGGGCTTGACTTCATATAATGT - -a -s simMouse_chr6.simMouse.chr6 553561 41 + 636262 GACCACTGGAGGACCAGGATAGAGGATGGAGGGCTGGCAAT -s Anc0.Anc0refChr3 155420 40 + 222631 AGTAACTGGAGGACCAACCTAGTATATGGAGGA-TGGGAAC -s Anc1.Anc1refChr6 191581 41 + 197743 AGTAACTGGAGGACCAACCTAGTATATGGAGGAGTGGGAAC -s Anc2.Anc2refChr1 69614 40 + 142988 AGTAACTAGAGGACCAACCTAGTATATGGGGGA-TGGGACC -s mr.mrrefChr3 103552 41 + 181027 GACCACTGGAGGACCAGCATAGTGGATGGAGGGCTGGCAAT -s simCow_chr6.simCow.chr6 527854 37 + 602619 ACTAACT---GGACGGAGGTAGGATATGGGGGA-TGGGACC -s simDog_chr6.simDog.chr6 516575 39 + 593897 AGTAAC-AGAACCCCAACCCAGTATCTGGGGGA-TGGGACA -s simHuman_chr6.simHuman.chr6 523584 41 + 601863 AGTAACTGGAGGACCAACCTAGTATAAGGAAGAGTGAGAAC -s simRat_chr6.simRat.chr6 28605 41 - 647215 GACCACTGGAGGACCAGCTCAGTGGATGGGTGGCTGGACAT - -a -s simMouse_chr6.simMouse.chr6 553602 32 + 636262 CAGAGCAAATTAAACTTGGGATAACTTATTCA -s Anc0.Anc0refChr3 155460 24 + 222631 GGGAACAGCCTAAACTTGTGATAA-------- -s Anc1.Anc1refChr6 191622 24 + 197743 GGGAACAGCCTAAACTTGTGATAA-------- -s Anc2.Anc2refChr1 69654 24 + 142988 GGGAACAGCCTAAACTTGTGATAA-------- -s mr.mrrefChr3 103593 32 + 181027 CAGAGCAAATTAAACTTGGGATAACTTATTCA -s simCow_chr6.simCow.chr6 527892 24 + 602619 GGGAACAGGCTAAACTTGTGATAA-------- -s simDog_chr6.simDog.chr6 516614 24 + 593897 AAGAAGAGCCTCAACTTGTGATAC-------- -s simHuman_chr6.simHuman.chr6 523625 24 + 601863 GGGAACAGCCTAAAGTTGTAAGAA-------- -s simRat_chr6.simRat.chr6 28646 32 - 647215 CTGAGCAAATTCAACTTGGGCTAACTTATTCC - -a -s simMouse_chr6.simMouse.chr6 553634 13 + 636262 TCCAGTTCAATTC -s Anc0.Anc0refChr3 155484 9 + 222631 ----ATATAATTA -s Anc1.Anc1refChr6 191646 9 + 197743 ----ATATAATTA -s Anc2.Anc2refChr1 69678 9 + 142988 ----ATATAATTA -s mr.mrrefChr3 103625 13 + 181027 TCCAGTTCAATTA -s simCow_chr6.simCow.chr6 527916 9 + 602619 ----ATATAATTA -s simDog_chr6.simDog.chr6 516638 9 + 593897 ----CTATGATTA -s simHuman_chr6.simHuman.chr6 523649 9 + 601863 ----ATATAATTA -s simRat_chr6.simRat.chr6 28787 13 - 647215 TCCAGTTCAATTA -s simRat_chr6.simRat.chr6 28678 13 - 647215 TCCAGTTCAATTA - -a -s simMouse_chr6.simMouse.chr6 553647 77 + 636262 TGGCGGGGATAAGGAGTCCATGCCGCTGCAATTTTGGGCAAAGCCATCTTGCTCAACCAGTTATACAAATAAGGGAA -s Anc0.Anc0refChr3 155494 15 + 222631 TG---------------CCATTCCACTA-----------------------------------------------AT -s Anc1.Anc1refChr6 191656 15 + 197743 TG---------------CCATTCCACTA-----------------------------------------------AT -s Anc2.Anc2refChr1 69688 15 + 142988 TG---------------CTGTTTCACTA-----------------------------------------------AT -s mr.mrrefChr3 103639 77 + 181027 TGGCGGGGATAAGGGGTCCATGCCACTACAGTTTTGGGCAAAGCCATCTTACTCAGCCAGTTATATAAATAAGGGAA -s simCow_chr6.simCow.chr6 527926 15 + 602619 TG---------------ATGTGTCACTG-----------------------------------------------AT -s simDog_chr6.simDog.chr6 516648 15 + 593897 TG---------------CTGTTTAACCA-----------------------------------------------AT -s simHuman_chr6.simHuman.chr6 523659 13 + 601863 TA---------------CCATTCCACTA------------------------------------------------- -s simRat_chr6.simRat.chr6 28801 77 - 647215 GGGTGGGGGTAAGGGGTCCATGCCACTAGAGCTTTGGGCAAAGCCATCTTACTCAGCCAGTTATATAGATAAGAGAA -s simRat_chr6.simRat.chr6 28692 77 - 647215 TGGCAGGGCTAAGTGGTCCATGCCACTACAGTTTAGGGCAAAGCCATCATACTCAGCCAGTTATATAAATAAGGGAA - -a -s simMouse_chr6.simMouse.chr6 553724 45 + 636262 GGGAACTTAGTAATCAATCATAATAGGACTGCATACAGTTAATTA -s Anc0.Anc0refChr3 155509 45 + 222631 GGGAATTTGATAATCAGTCATGAGAGTATTGTGTATTGTTAATTT -s Anc1.Anc1refChr6 191671 45 + 197743 GGGAATTTGATAATCAGTCATGAGAGTATTGTGTATTGTTAATTT -s Anc2.Anc2refChr1 69703 45 + 142988 GGGAATTTGATAATCAGTCATGAGAGTATTGTGTATTGTTGATTT -s mr.mrrefChr3 103716 45 + 181027 GGGAACTTAGTAATCAACCATAATAGGACTGCATATAGTTAATTA -s simCow_chr6.simCow.chr6 527957 45 + 602619 TGGAACCTGATAATCAGTCATACTAGGATTGTGTATTGCTGATTT -s simDog_chr6.simDog.chr6 516663 45 + 593897 GGGAATTTGATAATCAGTCATGAGAGTATTGTGTATTGTTGATTC -s simHuman_chr6.simHuman.chr6 523672 15 + 601863 ------------------------------ATTTATTGTTATTTT -s simRat_chr6.simRat.chr6 28878 43 - 647215 GAGAACTTAGTAATCAACCATAATAGGACTACATATGG--AATTA -s simRat_chr6.simRat.chr6 28769 18 - 647215 GGGAACCTAGTACTCAAC--------------------------- - -a -s simMouse_chr6.simMouse.chr6 553769 8 + 636262 GGAGCCTT -s Anc0.Anc0refChr3 155554 8 + 222631 TGACCTTT -s Anc1.Anc1refChr6 191716 8 + 197743 TGACCTTT -s Anc2.Anc2refChr1 69749 8 + 142988 TAACCTTT -s mr.mrrefChr3 103761 8 + 181027 TGAGCCTT -s simCow_chr6.simCow.chr6 528003 8 + 602619 TAACCTTT -s simDog_chr6.simDog.chr6 516709 8 + 593897 TAACCTTT -s simHuman_chr6.simHuman.chr6 523687 8 + 601863 TGACCATC -s simRat_chr6.simRat.chr6 28921 8 - 647215 TGAGCCTT - -a -s simMouse_chr6.simMouse.chr6 553777 12 + 636262 TGATATGCATGG -s Anc0.Anc0refChr3 155565 12 + 222631 GTATATGCATGG -s Anc1.Anc1refChr6 191727 12 + 197743 GTATATGCATGG -s Anc2.Anc2refChr1 69760 12 + 142988 GTACATGCATGT -s mr.mrrefChr3 103769 12 + 181027 TGATATGCATGG -s simCow_chr6.simCow.chr6 528014 12 + 602619 ATACTTGCATGT -s simDog_chr6.simDog.chr6 516720 12 + 593897 GTACATGCATGT -s simHuman_chr6.simHuman.chr6 523698 12 + 601863 GTATAGGCATGG -s simRat_chr6.simRat.chr6 28929 12 - 647215 TGATATGCATGG - -a -s simMouse_chr6.simMouse.chr6 553789 29 + 636262 ATGTACAATACCCTGATTTCATAGTGTAG -s Anc0.Anc0refChr3 155577 29 + 222631 ATGTATAATACCCTGATTCCATAATCCAT -s Anc1.Anc1refChr6 191739 29 + 197743 ATGTATAATACCCTGATTCCATAATCCAT -s Anc2.Anc2refChr1 69772 29 + 142988 ATGCAAAATACCCTGATTCCATAATCCAT -s mr.mrrefChr3 103781 29 + 181027 ATGTATAATACCCTGATTTCATAGTGTAG -s simCow_chr6.simCow.chr6 528026 26 + 602619 ATGCAGAATACTCAGATTCCATAATC--- -s simDog_chr6.simDog.chr6 516732 29 + 593897 ATACAAAACGGCCTGATTTCATAATCCAT -s simHuman_chr6.simHuman.chr6 523713 28 + 601863 ATGT-TAATACCCTTGTTCCATAATCCAA -s simRat_chr6.simRat.chr6 28941 29 - 647215 ATGTATTCTACCCTGATTTTATAGTGTAG - -a -s simMouse_chr6.simMouse.chr6 553818 17 + 636262 TGATTTTATAACCCGGC -s Anc0.Anc0refChr3 155610 17 + 222631 TGATTTTATACTCGAGC -s Anc1.Anc1refChr6 191772 17 + 197743 TGATTTTATACTCGAGC -s Anc2.Anc2refChr1 69805 17 + 142988 TTATTTTATACTCGAAC -s mr.mrrefChr3 103810 17 + 181027 TGATTTTATACCCCGGC -s simCow_chr6.simCow.chr6 528052 16 + 602619 -AATTTTATACTCCAAC -s simDog_chr6.simDog.chr6 516765 17 + 593897 TTATCTTACACTTGAAC -s simHuman_chr6.simHuman.chr6 523745 17 + 601863 TGATTTCATACTCAAGC -s simRat_chr6.simRat.chr6 28970 17 - 647215 TGATTTTATACCCTGGC - -a -s simMouse_chr6.simMouse.chr6 553835 15 + 636262 TTTATATTATACCGC -s Anc0.Anc0refChr3 155627 5 + 222631 GCTGC---------- -s Anc1.Anc1refChr6 191789 5 + 197743 GCTGC---------- -s Anc2.Anc2refChr1 69828 5 + 142988 GCTGC---------- -s mr.mrrefChr3 103827 15 + 181027 TTTACATTATACCGC -s simCow_chr6.simCow.chr6 528074 2 + 602619 ---GC---------- -s simDog_chr6.simDog.chr6 516798 5 + 593897 GCTGT---------- -s simHuman_chr6.simHuman.chr6 523762 5 + 601863 GCTGC---------- -s simRat_chr6.simRat.chr6 28987 15 - 647215 TTTACACTATACCTT - -a -s simMouse_chr6.simMouse.chr6 553850 32 + 636262 CGTGCCTTCTCTCTATTTCTGTTTTGTAAGAA -s Anc0.Anc0refChr3 155632 27 + 222631 ----TCTTCTCTCT-TTTTTGTTTGGTAAGAA -s Anc1.Anc1refChr6 191794 28 + 197743 ----TCTTCTCTCTATTTTTGTTTGGTAAGAA -s Anc2.Anc2refChr1 69833 27 + 142988 ----TCCCCTCTCT-CTTTTGTTTGGTAAGAA -s mr.mrrefChr3 103842 32 + 181027 CGTGCCTTCTCTCTATTTCTGTTTTGTAAGAA -s simCow_chr6.simCow.chr6 528076 26 + 602619 ----TCCCCTCTCT-GATTTGTTTGGTAAG-A -s simDog_chr6.simDog.chr6 516803 27 + 593897 ----CCCCCTCTCT-CTGTCGTTAAGTAAGAA -s simHuman_chr6.simHuman.chr6 523767 26 + 601863 ----TCTTCTCTCTATTTTT--TTGGTGAGCA -s simRat_chr6.simRat.chr6 29005 32 - 647215 TACTCCTTCTCTCTATTTCTGTTTTGTAAGAA - -a -s simMouse_chr6.simMouse.chr6 553882 11 + 636262 ATTTACTATCC -s Anc0.Anc0refChr3 155660 7 + 222631 TTT----ATAC -s Anc1.Anc1refChr6 191823 7 + 197743 TTT----ATAC -s Anc2.Anc2refChr1 69861 7 + 142988 TTT----ATAC -s mr.mrrefChr3 103875 11 + 181027 ATTTATTATCC -s simCow_chr6.simCow.chr6 528103 7 + 602619 TTT----ATAC -s simDog_chr6.simDog.chr6 516831 7 + 593897 TTT----ATCT -s simHuman_chr6.simHuman.chr6 523794 7 + 601863 CTT----ATAC -s simRat_chr6.simRat.chr6 29038 11 - 647215 GTTTATTATCC - -a -s simMouse_chr6.simMouse.chr6 553893 34 + 636262 AATTATTTACTTTTTGATTGAGTGTGACACCCTG -s Anc0.Anc0refChr3 155667 18 + 222631 A----------------TTGAGTGTGGGACGTTG -s Anc1.Anc1refChr6 191830 18 + 197743 A----------------TTGAGTGTGGGACGTTG -s Anc2.Anc2refChr1 69868 18 + 142988 A----------------TCTAGTGGGGGTCGTTG -s mr.mrrefChr3 103886 34 + 181027 AATTATTTGATTTTTGATTGGGTATGACACCCTG -s simCow_chr6.simCow.chr6 528110 9 + 602619 A-------------------------GATCCTTG -s simDog_chr6.simDog.chr6 516853 18 + 593897 A----------------TCTAGTGGGGGTCGTTG -s simHuman_chr6.simHuman.chr6 523801 18 + 601863 A----------------TTGAGTGTTGGACATCG -s simRat_chr6.simRat.chr6 29049 34 - 647215 AATTATTTGATTTTTGATTGGGTATGTAACCCTG - -a -s simMouse_chr6.simMouse.chr6 553927 65 + 636262 TCCCCCCCTGGTCCTCTTATAATTCTTCTCAAGTGTGCAGGTTTGGTGGTAATGTTACACTACTA -s Anc0.Anc0refChr3 155685 65 + 222631 TCCCTCCCTTTTCCTATTATAATTCTTATCAAATGTACTGGTTTGATGGCAATGTAAATCTATCA -s Anc1.Anc1refChr6 191848 65 + 197743 TCCCTCCCTTTTCCTATTATAATTCTTATCAAATGTACTGGTTTGATGGCAATGTAAATCTATCA -s Anc2.Anc2refChr1 69886 65 + 142988 TCCCTCCCTTTTCCTATTATACTTCTAAGCAAATGTACTAGTTTGATGGCAATGCAAATCTATCA -s mr.mrrefChr3 103920 65 + 181027 TCCCCCCCTGGTCCTCTTATAATTCTTCTCAAGTGTGCAGGTTTGGTGGCAATGTTACACTATTA -s simCow_chr6.simCow.chr6 528119 65 + 602619 TCCCTCCCTTCTCCTCTTATAGTGGCAACCAAATCTACTAGTTTGATGGCAATGCAAAACTATTA -s simDog_chr6.simDog.chr6 516871 63 + 593897 TCCCTCCCTCTTCCTATTATACTTCTAAGCGAATGTGCTAATTTGATGGGCATT--GATAAATCA -s simHuman_chr6.simHuman.chr6 523824 65 + 601863 CCCCTCCCTTTGCCTTCTATAATTCTTATCAACTGTACTGGTTTGATGGCAATGTAAATCTATCA -s simRat_chr6.simRat.chr6 29083 64 - 647215 TCCCCCTTTGGTCCTCTTATAATTCTTCTCAAGTGTGCAAGTTTG-TGGCTATGTTACACTTTTA - -a -s simMouse_chr6.simMouse.chr6 553992 9 + 636262 CCACTATAT -s Anc0.Anc0refChr3 155752 9 + 222631 CCACTATGT -s Anc1.Anc1refChr6 191915 9 + 197743 CCACTATGT -s Anc2.Anc2refChr1 69953 9 + 142988 CCACTATGT -s mr.mrrefChr3 103985 9 + 181027 CCACTATAT -s simCow_chr6.simCow.chr6 528186 9 + 602619 CCACTATGT -s simDog_chr6.simDog.chr6 516936 9 + 593897 TCACTATGT -s simHuman_chr6.simHuman.chr6 523891 9 + 601863 CCACTATGT -s simRat_chr6.simRat.chr6 29147 9 - 647215 CCATTATAT - -a -s simMouse_chr6.simMouse.chr6 554001 46 + 636262 TTACAATGAGTAACAGATTTCTTTGCACCCTTGGGACAGAGTATCA -s Anc0.Anc0refChr3 155763 34 + 222631 TTACA--GAGT---------TTTTGCACCCATGAT-CAGGGAAAAA -s Anc1.Anc1refChr6 191926 45 + 197743 TTACAATGAGTAACAGATTCTTTTGCACCCATGAT-CAGGGAAAAA -s Anc2.Anc2refChr1 69964 34 + 142988 TTACA--GAAT---------TTTTACACCCATGAT-CGGGGAAAAA -s mr.mrrefChr3 103994 45 + 181027 TTACAATGAGTAACAGATTCCTTTGCACCCTTGGG-CAGAGTATCA -s simCow_chr6.simCow.chr6 528197 34 + 602619 TTACA--TAAA---------TAATAGACCTTTTAT-TGGGGAAAAA -s simDog_chr6.simDog.chr6 516947 34 + 593897 TAACA--GATT---------TTTTACACCCACGAT-CGGGGAAAAA -s simHuman_chr6.simHuman.chr6 523902 45 + 601863 TTACAATGAGTAACAGATTCTTTTGCACCCATAAT-CAGGAAAAAA -s simRat_chr6.simRat.chr6 29156 33 - 647215 TTACAGTGGGTAACAGTTTCCTTA-------------AGAGTATTA - -a -s simMouse_chr6.simMouse.chr6 554047 46 + 636262 GCGCTATAGACACTGGGCTTACAGACACCTGTAGAATAGGATTCTG -s Anc0.Anc0refChr3 155797 45 + 222631 ATGCCATAAACTCCGGGATTACAGACGTTTG-AGAGTAGGATTCTG -s Anc1.Anc1refChr6 191971 45 + 197743 ATGCCATAAACTCCGGGATTACAGACGTTTG-AGAGTAGGATTCTG -s Anc2.Anc2refChr1 70004 45 + 142988 ATGCCAAAAACTCCAGGATTACAGATGTTTG-TAAGATAGGTTCTG -s mr.mrrefChr3 104039 46 + 181027 GTGCTATAAACACTGGGCTTACAGACATCTGTAGAATAGGATTCTG -s simCow_chr6.simCow.chr6 528237 45 + 602619 ATTCCATAAACTCCAGGATCACAGATTTTAG-TAAAATAGGTTCTG -s simDog_chr6.simDog.chr6 516987 45 + 593897 ATGCCAAAAACTCCAGGATTACAGATGTCTG-TAAGATAGGTTCTG -s simHuman_chr6.simHuman.chr6 523947 40 + 601863 ATGCAATAA-----GAAATTACAGACGTTTT-AGAGTAGAATCCTG -s simRat_chr6.simRat.chr6 29189 46 - 647215 GTTCCATAAACACCGGGGTAACAGACATCTGTAGAATAGGATTCTC - -a -s simMouse_chr6.simMouse.chr6 554093 15 + 636262 GAAAAAAGCGAAGGA -s Anc0.Anc0refChr3 155850 15 + 222631 GAAAAAAGTGAAGGA -s Anc1.Anc1refChr6 192024 15 + 197743 GAAAAAAGTGAAGGA -s Anc2.Anc2refChr1 70057 15 + 142988 GCAAAAAGTGAAGGA -s mr.mrrefChr3 104085 15 + 181027 GAAAAAAGTGAAGGA -s simCow_chr6.simCow.chr6 528290 15 + 602619 GCAAAAAGTGCAGGA -s simDog_chr6.simDog.chr6 517040 15 + 593897 CCAAAAAGTCAAGGA -s simHuman_chr6.simHuman.chr6 523995 15 + 601863 GAAAAAAGTGAAGGA -s simRat_chr6.simRat.chr6 29235 15 - 647215 GTAAAGAGTGAAGGA - -a -s simMouse_chr6.simMouse.chr6 554108 9 + 636262 ACACAATGC -s Anc0.Anc0refChr3 155870 9 + 222631 ACACCATGC -s Anc1.Anc1refChr6 192044 9 + 197743 ACACCATGC -s Anc2.Anc2refChr1 70077 9 + 142988 ACACCATGC -s mr.mrrefChr3 104100 9 + 181027 ACACAATGC -s simCow_chr6.simCow.chr6 528310 9 + 602619 ACACTGTAT -s simDog_chr6.simDog.chr6 517060 9 + 593897 ACACCATGC -s simHuman_chr6.simHuman.chr6 524019 9 + 601863 ACAACATGC -s simRat_chr6.simRat.chr6 29250 9 - 647215 ACATAATGC - -a -s simMouse_chr6.simMouse.chr6 554117 9 + 636262 CAGTGTTAA -s Anc0.Anc0refChr3 155880 9 + 222631 CAGAGTTAA -s Anc1.Anc1refChr6 192054 9 + 197743 CAGAGTTAA -s Anc2.Anc2refChr1 70087 9 + 142988 CAGAGTTAA -s mr.mrrefChr3 104109 9 + 181027 CAGAGTTAA -s simCow_chr6.simCow.chr6 528320 9 + 602619 CAGAGTTAC -s simDog_chr6.simDog.chr6 517070 9 + 593897 TAGAGTTAA -s simHuman_chr6.simHuman.chr6 524029 9 + 601863 CAGAGTCAA -s simRat_chr6.simRat.chr6 29259 9 - 647215 CAGAGTTAA - -a -s simMouse_chr6.simMouse.chr6 554126 12 + 636262 GCCATATCATAT -s Anc0.Anc0refChr3 155893 12 + 222631 GCCATATTATAA -s Anc1.Anc1refChr6 192067 12 + 197743 GCCATATTATAA -s Anc2.Anc2refChr1 70100 12 + 142988 GCCATATTATAA -s mr.mrrefChr3 104122 12 + 181027 GCCATATCATAT -s simCow_chr6.simCow.chr6 528333 12 + 602619 GCCATATTATAA -s simDog_chr6.simDog.chr6 517083 11 + 593897 GCC-TATACTAA -s simHuman_chr6.simHuman.chr6 524042 12 + 601863 GTCATATTATAG -s simRat_chr6.simRat.chr6 29272 12 - 647215 GCCATTTCATAT - -a -s simMouse_chr6.simMouse.chr6 554138 5 + 636262 TCTTC -s Anc0.Anc0refChr3 155905 5 + 222631 ACGTT -s Anc1.Anc1refChr6 192079 5 + 197743 ACGTT -s Anc2.Anc2refChr1 70112 5 + 142988 ACGTT -s mr.mrrefChr3 104134 5 + 181027 TCTTT -s simCow_chr6.simCow.chr6 528345 5 + 602619 ATGTT -s simDog_chr6.simDog.chr6 517094 5 + 593897 ACGTT -s simHuman_chr6.simHuman.chr6 524054 5 + 601863 ACATT -s simRat_chr6.simRat.chr6 29285 5 - 647215 TCTTT - -a -s simMouse_chr6.simMouse.chr6 554143 35 + 636262 ATTTGTATGAAGAGTCCACACTTCATCTCAAAAAA -s Anc0.Anc0refChr3 155924 35 + 222631 GCTAGCATGTAAAATCTACACTTCTTCTAAAAGAA -s Anc1.Anc1refChr6 192098 35 + 197743 GCTAGCATGTAAAATCTACACTTCTTCTAAAAGAA -s Anc2.Anc2refChr1 70132 35 + 142988 GCCAGCATGTAAAATCTACACTTCTTCTAAAAGAA -s mr.mrrefChr3 104139 35 + 181027 GTTTGTATGAAGAGTCCACACTTCATCTCAAAAAA -s simCow_chr6.simCow.chr6 528381 35 + 602619 CTCACTATGTAAAATCTGCACTTCTTCTAAAGAGA -s simDog_chr6.simDog.chr6 517114 35 + 593897 GCCAGCATGTAAAACATACACTTCTTCTAAAAGAA -s simHuman_chr6.simHuman.chr6 524073 32 + 601863 GCTAGCATGTAAAATCTACACTTGTTCTAAAA--- -s simRat_chr6.simRat.chr6 29290 35 - 647215 GTTTGGATGAAGAGTCCAAACTTCATCTCAAAAAA - -a -s simMouse_chr6.simMouse.chr6 554178 15 + 636262 TTTTAGAATGTCCAT -s Anc0.Anc0refChr3 155959 15 + 222631 TTTTGGAATGTGCAT -s Anc1.Anc1refChr6 192133 15 + 197743 TTTTGGAATGTGCAT -s Anc2.Anc2refChr1 70167 15 + 142988 TTTTGGAATGTGCAT -s mr.mrrefChr3 104174 15 + 181027 TTTTAGAATGTGCAT -s simCow_chr6.simCow.chr6 528416 15 + 602619 TTTTGGAATGTGCAT -s simDog_chr6.simDog.chr6 517152 15 + 593897 TTTTAAATTCTGTGT -s simHuman_chr6.simHuman.chr6 524105 14 + 601863 -TTTGGAATGTGCAT -s simRat_chr6.simRat.chr6 29325 15 - 647215 TTTTAGAATGTGCAT - -a -s simMouse_chr6.simMouse.chr6 554193 15 + 636262 ATAGATACTTTTTCA -s Anc0.Anc0refChr3 155974 15 + 222631 ATATATACCTTTCCA -s Anc1.Anc1refChr6 192148 15 + 197743 ATATATACCTTTCCA -s Anc2.Anc2refChr1 70182 15 + 142988 ATATATACCTTTCCA -s mr.mrrefChr3 104189 15 + 181027 ATAGATACTTTTTCA -s simCow_chr6.simCow.chr6 528431 15 + 602619 ATATATACCTTACCA -s simDog_chr6.simDog.chr6 517168 15 + 593897 AAATAGACCTTTCCA -s simHuman_chr6.simHuman.chr6 524119 14 + 601863 ATA-ATACCTTTCTG -s simRat_chr6.simRat.chr6 29340 15 - 647215 ACAGATACTTTTTCA - -a -s simMouse_chr6.simMouse.chr6 554494 53 + 636262 AAGATGTAACTGTGCATATCGAGGTATAATTCTTGAGTTAATTCCTTGCAACG -s Anc0.Anc0refChr3 156315 41 + 222631 AAGATGTAC------------AGGGATAATCTGTTTGTTAATTCCTTGCAATA -s Anc1.Anc1refChr6 192493 41 + 197743 AAGATGTAC------------AGGGATAATCTGTTTGTTAATTCCTTGCAATA -s Anc2.Anc2refChr1 70523 41 + 142988 AAGATGTAC------------AGCGGTAAACTGTTTGTTAATTCCTTGCAACA -s mr.mrrefChr3 104500 53 + 181027 AAGATGTACCTGTGCATATCGAGGTATAATTCTTGAGTTAATTCCTTGCAATG -s simCow_chr6.simCow.chr6 528805 37 + 602619 AGGATGTAC------------AGTGGT----TGTTTGTCAACTCTTTGCAGCA -s simDog_chr6.simDog.chr6 517509 41 + 593897 AAGATCTAC------------AGCAGTAAACTGTTTGTTAATTCCTTGTAACA -s simHuman_chr6.simHuman.chr6 524464 41 + 601863 AAGATGTAC------------AGGGATAATCAGGTTGTTGATTCCTTGCAATA -s simRat_chr6.simRat.chr6 29659 53 - 647215 AAGATGTACCTGTGCACATCAAGGTATGGTTTCTGAGGTAATCCCCTACAATG - -a -s simMouse_chr6.simMouse.chr6 554547 62 + 636262 GGTGATGACAATCTTAGCCTATCCAAGAATTAGTGTGGTTTACATGTGACCTAAAACCCACA -s Anc0.Anc0refChr3 156356 55 + 222631 CGTGGTGACACCCTCTGCC--TACCCGAATTGGG-----TAATGTGTGGCCTAATACGCTTG -s Anc1.Anc1refChr6 192534 57 + 197743 CGTGGTGACACCCTCTGCCTATACCCGAATTGGG-----TAATGTGTGGCCTAATACGCTTG -s Anc2.Anc2refChr1 70564 55 + 142988 CGTGGTGACACCCTCTGCC--TACCCAAAGTGGG-----TAATGTGTGGCCTAATATGCTTG -s mr.mrrefChr3 104553 62 + 181027 GGTGATGACAACCTCAGCCTATCCAAGAATTAGTGTGGTTTACATGTGACCTAAAACCCTCA -s simCow_chr6.simCow.chr6 528842 55 + 602619 GGTGGTGGCACCCTCTGCC--TACCCAAACTGGG-----TAATGTGTGGCCTAATATGCTTG -s simDog_chr6.simDog.chr6 517552 54 + 593897 CTTGGTGACACCCACTGCC--CACCCAAAGTGGG-----TAATGTGGGGCCT-ATATGCTCA -s simHuman_chr6.simHuman.chr6 524505 55 + 601863 TGTGGTAACACCCTCT--CTGTACCCGAATTCGG-----TAATGCGTGGCCTAATACACTTG -s simRat_chr6.simRat.chr6 29712 61 - 647215 GG-GATGACAGCCTCAGTCTACCCAACAATTAGTGTGGTTTGCATGTGACCTAAAATCCTCA - -a -s simMouse_chr6.simMouse.chr6 554609 43 + 636262 GAGACTTCAAATTGCCTCCCCCTTTTCTGGGAGTTCCTGTACC -s Anc0.Anc0refChr3 156411 43 + 222631 GCTGTTCCCAATTGCCTACCTCTTTTCCAGGAGTTCCTGTATA -s Anc1.Anc1refChr6 192591 43 + 197743 GCTGTTCCCAATTGCCTACCTCTTTTCCAGGAGTTCCTGTATA -s Anc2.Anc2refChr1 70619 43 + 142988 GCTGTTCCCAATTGCCTACCTCTTTTCCAGGAGTTCCTGCATA -s mr.mrrefChr3 104615 43 + 181027 GAGACTTCAAATTGCCTCCCCCTTTTCTGGGAGTTCCTGTATC -s simCow_chr6.simCow.chr6 528898 43 + 602619 CCCGTTCCCAGTCACCTACCACTTTTCCAGGAGTTCCTGCATA -s simDog_chr6.simDog.chr6 517606 43 + 593897 GCTGTTCCCAATTGCCCGCCTTTTCTCCAGGAGTTGCTGCGCA -s simHuman_chr6.simHuman.chr6 524560 43 + 601863 GCTGTTCTGGATTGCCTACCTCTTTTCCAGGAGCTCCTGTATA -s simRat_chr6.simRat.chr6 29773 43 - 647215 GACACTTCAAATTTCCTCCCCCTTTTGTGGGAGTTCCTGTATG - -a -s simMouse_chr6.simMouse.chr6 554652 9 + 636262 GTTGATACT -s Anc0.Anc0refChr3 156454 9 + 222631 GTTGAAACT -s Anc1.Anc1refChr6 192634 9 + 197743 GTTGAAACT -s Anc2.Anc2refChr1 70662 9 + 142988 GTTGAAACT -s mr.mrrefChr3 104658 9 + 181027 GTTGATACT -s simCow_chr6.simCow.chr6 528942 9 + 602619 GTTGAAACT -s simDog_chr6.simDog.chr6 517649 9 + 593897 GTTGAAACT -s simHuman_chr6.simHuman.chr6 524603 9 + 601863 GTTGACACT -s simRat_chr6.simRat.chr6 29816 9 - 647215 GTTGAGACT - -a -s simMouse_chr6.simMouse.chr6 554661 2 + 636262 AA -s Anc0.Anc0refChr3 156463 2 + 222631 AA -s Anc1.Anc1refChr6 192643 2 + 197743 AA -s Anc2.Anc2refChr1 70671 2 + 142988 AA -s mr.mrrefChr3 104667 2 + 181027 AA -s simCow_chr6.simCow.chr6 528951 2 + 602619 AA -s simDog_chr6.simDog.chr6 517659 2 + 593897 AA -s simHuman_chr6.simHuman.chr6 524612 2 + 601863 GA -s simRat_chr6.simRat.chr6 29825 2 - 647215 AA - -a -s simMouse_chr6.simMouse.chr6 554663 4 + 636262 AACA -s Anc0.Anc0refChr3 156466 4 + 222631 GACA -s Anc1.Anc1refChr6 192646 4 + 197743 GACA -s Anc2.Anc2refChr1 70674 4 + 142988 GACA -s mr.mrrefChr3 104669 4 + 181027 AACA -s simCow_chr6.simCow.chr6 528954 4 + 602619 GACA -s simDog_chr6.simDog.chr6 517662 4 + 593897 GACA -s simHuman_chr6.simHuman.chr6 524615 4 + 601863 GACA -s simRat_chr6.simRat.chr6 29827 4 - 647215 AACA - -a -s simMouse_chr6.simMouse.chr6 554667 8 + 636262 AGATGAAT -s Anc0.Anc0refChr3 156470 8 + 222631 AGCTTCTC -s Anc1.Anc1refChr6 192650 8 + 197743 AGCTTCTC -s Anc2.Anc2refChr1 70699 8 + 142988 AGCTTCTC -s mr.mrrefChr3 104673 8 + 181027 AGCTGAAC -s simCow_chr6.simCow.chr6 528979 8 + 602619 AGCTTCTC -s simDog_chr6.simDog.chr6 517690 8 + 593897 AGCTTCTC -s simHuman_chr6.simHuman.chr6 524619 8 + 601863 AGCTTCCC -s simRat_chr6.simRat.chr6 29831 8 - 647215 AGCTGAAC - -a -s simMouse_chr6.simMouse.chr6 554675 11 + 636262 AATCATTTAGT -s Anc0.Anc0refChr3 156479 11 + 222631 AATCAGAGAGT -s Anc1.Anc1refChr6 192659 11 + 197743 AATCAGAGAGT -s Anc2.Anc2refChr1 70708 11 + 142988 AACCAGAGAGT -s mr.mrrefChr3 104681 11 + 181027 AATCATTTAGT -s simCow_chr6.simCow.chr6 528988 11 + 602619 AACCAGGGAGT -s simDog_chr6.simDog.chr6 517699 11 + 593897 AACCAGAGAGT -s simHuman_chr6.simHuman.chr6 524628 11 + 601863 AATCAGAGAGT -s simRat_chr6.simRat.chr6 29839 11 - 647215 AATTATTTAGT - -a -s simMouse_chr6.simMouse.chr6 554686 115 + 636262 AGAGAGGCCCTGGGAAGGTGGCCTCCTTACTAAGAAACTTGCTCAATGACTAAGGTCTGAGGTTTGAATCCTTTTGTCAAGGATTAGTACATATTTCGAGTATGAGTTTTGCTAG -s Anc0.Anc0refChr3 156633 98 + 222631 AGGGTGAGCCCACACAAGTGGCCTCCTTATTAAGCACCTTGCTCAATGATTGGGTT-------CTGAATTCCT--GTCAAGAATGAATACATGTTT------TAAGTCTTGTT-- -s Anc1.Anc1refChr6 192813 106 + 197743 AGGGTGAGCCCACACAAGTGGCCTCCTTATTAAGCACCTTGCTCAATGATTGGGTT-------CTGAATTCCT--GTCAAGAATGAATACATGTTTGGAGTATAAGTCTTGTTAA -s Anc2.Anc2refChr1 70875 98 + 142988 AGGGTGAGCCCACACAATTGGCTGCCTTATTAAGCACCTTGCTCAATGATTGGGTT-------CTGAATCCCT--GTCAAGAATGAATACATGTTT------TAAGTCTTGGT-- -s mr.mrrefChr3 104692 108 + 181027 AGAGAGGCCCTGGGAAGGTGGCCTCCTTACTAAGAAACTTGCTCAATGACTGAGGT-------TTGAATTCTTTTGTCAAGGATTAATACATATTTCGAGTATGAGTCTTGTTAG -s simCow_chr6.simCow.chr6 529162 98 + 602619 AGGGTGGGCCCACACAACTGGCTGCCTTATTAAGCACCTTGCCCAATGATTGGGTT-------TTGTATCCTT--GTAAGGAATGAATACATGAGC------TAAGTCTTGGT-- -s simDog_chr6.simDog.chr6 517870 96 + 593897 A-GGTGAGCCTACACAATTGGCTGCCTCATTAAGTAGGTTGCTCAATGATGAGGTT-------CTGAATCCCT--GTCAAG-ACAAATACATGTTT------TAAGTCTTGGT-- -s simHuman_chr6.simHuman.chr6 524782 106 + 601863 AGGGTGATCCCACACAAGTGGCCTTCTTATTAAGCACCTTGCTCAATGATTGGGTT-------CTGAATTCCA--GTCCAGAATGAAAACATGTTTGGAGTATAAGCCTTGTTAA -s simRat_chr6.simRat.chr6 29850 75 - 647215 A---------------------------------AAACTTGCTCAATGGCTGAGGT-------TTGAATTCTTTTGTCAAGGATTAATATATATTTCTAGTATGAGGCTTGTTAG - -a -s simMouse_chr6.simMouse.chr6 554801 49 + 636262 GTTGAAAGAAGAAAGGATGCTGGACTGAAAATCTGATCAACTGGTCTCC -s Anc0.Anc0refChr3 156731 49 + 222631 GAAGAATGAAAAAAGGATGCTGGACTGGAGACATGATCGACTAGCTCCC -s Anc1.Anc1refChr6 192919 49 + 197743 GAAGAATGAAAAAAGGATGCTGGACTGGAGACATGATCGACTAGCTCCC -s Anc2.Anc2refChr1 70973 49 + 142988 GAAGAATGAAAAAAGGATGCTGGACTGGATACATGATCGACTAGCTCCC -s mr.mrrefChr3 104800 49 + 181027 GTTGAATGAAGAAAGGATGCTGGACTGAAGATCTGATCAACTGGTCTCC -s simCow_chr6.simCow.chr6 529260 49 + 602619 GGAGAATTATAAAAGGATGCTGGACTGTGAACATGAATAACCACCTCCC -s simDog_chr6.simDog.chr6 517966 48 + 593897 GAAGAATGAAAAAAGGATGCTGGACTGGATACATGATCGGCTAGTT-TC -s simHuman_chr6.simHuman.chr6 524904 48 + 601863 GGGGAATGAATAAAGGATGATCAGCTGGAG-CATAATCTACTAGCTGCC -s simRat_chr6.simRat.chr6 29925 48 - 647215 GTTGAATGA-GAAAGGATGCTGGACTGAAGGTCTGATAAATTGGTTTCC - -a -s simMouse_chr6.simMouse.chr6 554850 8 + 636262 AACCAAGA -s Anc0.Anc0refChr3 156791 8 + 222631 AACCAGGA -s Anc1.Anc1refChr6 192979 8 + 197743 AACCAGGA -s Anc2.Anc2refChr1 71033 8 + 142988 AACCAGGA -s mr.mrrefChr3 104849 8 + 181027 AACCAAGA -s simCow_chr6.simCow.chr6 529320 8 + 602619 AACCAGGA -s simDog_chr6.simDog.chr6 518025 8 + 593897 GACCAAGA -s simHuman_chr6.simHuman.chr6 524963 8 + 601863 AACCAGGA -s simRat_chr6.simRat.chr6 29973 8 - 647215 AAACAAGA - -a -s simMouse_chr6.simMouse.chr6 554858 33 + 636262 TTGGTGATGCTCGAGGAATATTTGCACCTAGAT -s Anc0.Anc0refChr3 156799 33 + 222631 TTGAGGATGCTGGAGGACTGTTTGCATCTGGAT -s Anc1.Anc1refChr6 192987 33 + 197743 TTGAGGATGCTGGAGGACTGTTTGCATCTGGAT -s Anc2.Anc2refChr1 71041 33 + 142988 TTGAGGATGCTGAAGGGATGTTTGCATCTGGAG -s mr.mrrefChr3 104857 33 + 181027 TTGGTGATGCTGGAGGACTATTTGCACCTAGAT -s simCow_chr6.simCow.chr6 529328 33 + 602619 TTGAGGATGCCGAAGGGATGTATGCATCTGGAG -s simDog_chr6.simDog.chr6 518034 27 + 593897 TTGAGGTTGCTGAAG------TTGCATCTAGAG -s simHuman_chr6.simHuman.chr6 524971 33 + 601863 TTGAGGATGCTGGAGGACTGTTAGCATCTGGAT -s simRat_chr6.simRat.chr6 29981 33 - 647215 TTGGTGATGCTGGAGGACTATTTGGACCTAGGT - -a -s simMouse_chr6.simMouse.chr6 554891 16 + 636262 AGCTTAGAATTTAGGG -s Anc0.Anc0refChr3 156832 16 + 222631 AGTATAGATCTGGGGG -s Anc1.Anc1refChr6 193020 16 + 197743 AGTATAGATCTGGGGG -s Anc2.Anc2refChr1 71074 16 + 142988 ACTATACATCTGGGGG -s mr.mrrefChr3 104890 16 + 181027 AGCTTAGATTTTAGGG -s simCow_chr6.simCow.chr6 529361 16 + 602619 ACTAAACATCAGGGGT -s simDog_chr6.simDog.chr6 518061 16 + 593897 ACTATTCTTCTGGGAG -s simHuman_chr6.simHuman.chr6 525004 16 + 601863 AGTGTAGATCCGGGGG -s simRat_chr6.simRat.chr6 30015 16 - 647215 AGCTTTAATTTTAGGG - -a -s simMouse_chr6.simMouse.chr6 554907 12 + 636262 CTATAAGCACAA -s Anc0.Anc0refChr3 156849 11 + 222631 CTAGAAGTATA- -s Anc1.Anc1refChr6 193037 11 + 197743 CTAGAAGTATA- -s Anc2.Anc2refChr1 71091 11 + 142988 CTAGAAGTGTA- -s mr.mrrefChr3 104906 12 + 181027 CTATAAGCATAA -s simCow_chr6.simCow.chr6 529378 11 + 602619 CTAGAAGTTTA- -s simDog_chr6.simDog.chr6 518078 11 + 593897 TTAGAAGAGTA- -s simHuman_chr6.simHuman.chr6 525021 11 + 601863 CAAGAAGTATA- -s simRat_chr6.simRat.chr6 30031 12 - 647215 TTACAAGCATAA - -a -s simMouse_chr6.simMouse.chr6 554919 5 + 636262 TTTGT -s Anc0.Anc0refChr3 156860 5 + 222631 TGTGT -s Anc1.Anc1refChr6 193048 5 + 197743 TGTGT -s Anc2.Anc2refChr1 71102 5 + 142988 TGTGT -s mr.mrrefChr3 104918 5 + 181027 TTTGT -s simCow_chr6.simCow.chr6 529390 5 + 602619 TGTGG -s simDog_chr6.simDog.chr6 518089 3 + 593897 --TGT -s simHuman_chr6.simHuman.chr6 525032 5 + 601863 TGTGT -s simRat_chr6.simRat.chr6 30043 5 - 647215 TTTGT - -a -s simMouse_chr6.simMouse.chr6 554924 10 + 636262 TTAAAATGTG -s Anc0.Anc0refChr3 156865 10 + 222631 TTAATATGTT -s Anc1.Anc1refChr6 193053 10 + 197743 TTAATATGTT -s Anc2.Anc2refChr1 71107 10 + 142988 TTAGTATGTT -s mr.mrrefChr3 104923 10 + 181027 TTAAAATGTG -s simCow_chr6.simCow.chr6 529395 10 + 602619 TTGGTGTGTT -s simDog_chr6.simDog.chr6 518092 10 + 593897 TCAGTATGTT -s simHuman_chr6.simHuman.chr6 525037 10 + 601863 TTAATATGTA -s simRat_chr6.simRat.chr6 30057 10 - 647215 TTAGAATGTT - -a -s simMouse_chr6.simMouse.chr6 554934 30 + 636262 GTGGTCCTGGATGCACTGTATCTTTGCAAC -s Anc0.Anc0refChr3 156876 30 + 222631 ATTGTGTTGAATGCACTGGAAATTTGCAAC -s Anc1.Anc1refChr6 193064 30 + 197743 ATTGTGTTGAATGCACTGGAAATTTGCAAC -s Anc2.Anc2refChr1 71118 30 + 142988 ATTGTGTTGAATGCACTGGAAATTTGGAAC -s mr.mrrefChr3 104934 30 + 181027 GTGGTCCTGGATGCACTGTATCTTTGCAAC -s simCow_chr6.simCow.chr6 529406 29 + 602619 A-TGTGTTGAATGTACTGGAGATCTGGAAC -s simDog_chr6.simDog.chr6 518103 30 + 593897 ATGGGGTTGAATGCACTGGAAATTTGGAAC -s simHuman_chr6.simHuman.chr6 525048 30 + 601863 ATTATGTTGAATACAATGGAAATTTGCAAC -s simRat_chr6.simRat.chr6 30068 30 - 647215 GTGGTCCTGGATGGACTGTACGTTTGCAAA - -a -s simMouse_chr6.simMouse.chr6 554964 5 + 636262 TCTAT -s Anc0.Anc0refChr3 156906 5 + 222631 TCTAT -s Anc1.Anc1refChr6 193094 5 + 197743 TCTAT -s Anc2.Anc2refChr1 71148 5 + 142988 TCTAT -s mr.mrrefChr3 104964 5 + 181027 TCTAT -s simCow_chr6.simCow.chr6 529435 5 + 602619 TCTAT -s simDog_chr6.simDog.chr6 518137 5 + 593897 TTTAT -s simHuman_chr6.simHuman.chr6 525078 5 + 601863 TCTAT -s simRat_chr6.simRat.chr6 30098 5 - 647215 TCTAT - -a -s simMouse_chr6.simMouse.chr6 554969 44 + 636262 TCTAGAGCTCTTAAAGCACAACCAGGCCTCTACAAATGCACGTG -s Anc0.Anc0refChr3 156942 44 + 222631 CCAATAGCCTTTAAAGTGTCACTAGGGTTCTAACAGCTTCCATG -s Anc1.Anc1refChr6 193130 44 + 197743 CCAATAGCCTTTAAAGTGTCACTAGGGTTCTAACAGCTTCCATG -s Anc2.Anc2refChr1 71184 44 + 142988 CCAATAGCCTTTAAAGTGTCACTAGAGTTCTAACAGCTTCCATG -s mr.mrrefChr3 104969 44 + 181027 TCTAGAGCCCTTAAAGTACAACCAGGCCTCTACAAATGCACGTG -s simCow_chr6.simCow.chr6 529471 43 + 602619 CCAAGAG-CTTTAAACTGTCATTAGGCCTCTAACAACTTCCATG -s simDog_chr6.simDog.chr6 518173 44 + 593897 CCAATAGCCTTTGGGGTGACACTAGAGTGCTAACAGCTTCCATA -s simHuman_chr6.simHuman.chr6 525114 43 + 601863 CCAATGGCCTTTAAAGTGTCACTATGT-TCCAACAGCTTCATTG -s simRat_chr6.simRat.chr6 30103 44 - 647215 TCTACAGCCCTTAAAGTACAACAGGGCCTCTACAAGTGCACATA - -a -s simMouse_chr6.simMouse.chr6 555013 20 + 636262 ATTGTAGGGCACCAGCAATT -s Anc0.Anc0refChr3 156986 20 + 222631 ATTGGAAGGGACAAGCAAAC -s Anc1.Anc1refChr6 193174 20 + 197743 ATTGGAAGGGACAAGCAAAC -s Anc2.Anc2refChr1 71228 20 + 142988 ACTGGAAGGGACAAGCCAAC -s mr.mrrefChr3 105013 20 + 181027 ATTGTAAGGCACCAGCAATT -s simCow_chr6.simCow.chr6 529514 18 + 602619 CCCGGAAGATATAAG--AAC -s simDog_chr6.simDog.chr6 518225 20 + 593897 ACTAGAAGGGACCAGCCAAC -s simHuman_chr6.simHuman.chr6 525157 20 + 601863 ATTGGAAGGAAAAAGCAAAC -s simRat_chr6.simRat.chr6 30147 20 - 647215 ATTGTAAGGCACTAGCAATT - -a -s simMouse_chr6.simMouse.chr6 555033 9 + 636262 GCTGGTGTT -s Anc0.Anc0refChr3 157011 9 + 222631 GCTGGTGGG -s Anc1.Anc1refChr6 193199 9 + 197743 GCTGGTGGG -s Anc2.Anc2refChr1 71253 9 + 142988 GCTGGTGGG -s mr.mrrefChr3 105033 9 + 181027 GCTGGTGTG -s simCow_chr6.simCow.chr6 529537 9 + 602619 GCAGGCGGG -s simDog_chr6.simDog.chr6 518250 9 + 593897 GCTGCTGGG -s simHuman_chr6.simHuman.chr6 525182 9 + 601863 GCTGGTGGG -s simRat_chr6.simRat.chr6 30167 9 - 647215 GCTGTTGTG - -a -s simMouse_chr6.simMouse.chr6 555042 13 + 636262 GAATAAATGTGCA -s Anc0.Anc0refChr3 157020 12 + 222631 GAA-AAAGATGCA -s Anc1.Anc1refChr6 193208 12 + 197743 GAA-AAAGATGCA -s Anc2.Anc2refChr1 71262 12 + 142988 GAA-AGAGATGCA -s mr.mrrefChr3 105042 13 + 181027 GAATAAATGTGCA -s simCow_chr6.simCow.chr6 529546 11 + 602619 G-A-ATAGATGCA -s simDog_chr6.simDog.chr6 518267 12 + 593897 GAA-AGAGATGCA -s simHuman_chr6.simHuman.chr6 525191 12 + 601863 GAA-AAAGATGCA -s simRat_chr6.simRat.chr6 30176 12 - 647215 GAATAGATGTGC- - -a -s simMouse_chr6.simMouse.chr6 555055 45 + 636262 GCATTCTAGTAAACCTTTATTGATTACAAAGCAAGCATATATGGT -s Anc0.Anc0refChr3 157035 43 + 222631 GCATTGCACTTCACCT--ATTTATTCGAAATAAAGCTTATATAGC -s Anc1.Anc1refChr6 193223 43 + 197743 GCATTGCACTTCACCT--ATTTATTCGAAATAAAGCTTATATAGC -s Anc2.Anc2refChr1 71277 43 + 142988 GGATTGCACCTCACCT--AGTTATCCGAAATAAAGCTTATTTAGC -s mr.mrrefChr3 105055 45 + 181027 GCATTCCAGTAAACCTTTATTGATTACAAAGCAAGCATATATGGT -s simCow_chr6.simCow.chr6 529560 43 + 602619 GGAGTGCACCTCACCT--TGCTATCAGAAATAAAGCTTATCTAGC -s simDog_chr6.simDog.chr6 518282 40 + 593897 GGATTGCACC---ACT--AGTTATCCGAAATAAAGTTTACTTAGC -s simHuman_chr6.simHuman.chr6 525206 43 + 601863 GCATTGCAATTGACCT--ATTTATTGGAAATAAAGCTCGTATAGC -s simRat_chr6.simRat.chr6 30188 44 - 647215 -CATGCCACTAAAACTTTATTGGTTACAAAGCAAGCATACATGGT - -a -s simMouse_chr6.simMouse.chr6 555100 3 + 636262 TGT -s Anc0.Anc0refChr3 157078 3 + 222631 TGT -s Anc1.Anc1refChr6 193266 3 + 197743 TGT -s Anc2.Anc2refChr1 71320 3 + 142988 AGA -s mr.mrrefChr3 105100 3 + 181027 TGT -s simCow_chr6.simCow.chr6 529604 3 + 602619 AGA -s simDog_chr6.simDog.chr6 518322 3 + 593897 AGA -s simHuman_chr6.simHuman.chr6 525249 3 + 601863 TAT -s simRat_chr6.simRat.chr6 30232 3 - 647215 TGT - -a -s simMouse_chr6.simMouse.chr6 555103 9 + 636262 CCTCAATGG -s Anc0.Anc0refChr3 157081 9 + 222631 CCTCAATGC -s Anc1.Anc1refChr6 193269 9 + 197743 CCTCAATGC -s Anc2.Anc2refChr1 71323 9 + 142988 GCTCAATGC -s mr.mrrefChr3 105103 9 + 181027 CCTCAATGC -s simCow_chr6.simCow.chr6 529607 9 + 602619 GCCCAATGC -s simDog_chr6.simDog.chr6 518325 9 + 593897 GCTCAATGT -s simHuman_chr6.simHuman.chr6 525254 9 + 601863 CATTAAAGC -s simRat_chr6.simRat.chr6 30235 9 - 647215 CCTCAATGC - -a -s simMouse_chr6.simMouse.chr6 555112 39 + 636262 AACTCTCGTGCATAGCGAACTTTCCTTCAAACATTAGCA -s Anc0.Anc0refChr3 157090 28 + 222631 A-----------TAGTAGACTTTGAATTAAATCTTAGCA -s Anc1.Anc1refChr6 193278 39 + 197743 AGAACCCATGCCTAGTAGACTTTGAATTAAATCTTAGCA -s Anc2.Anc2refChr1 71332 28 + 142988 G-----------TAGTTGACTTTGAATTAAATCTTAGCA -s mr.mrrefChr3 105112 39 + 181027 AGCTCTCATGCATAGCAAACTTTCCTTCAAATATTAGCA -s simCow_chr6.simCow.chr6 529616 28 + 602619 A-----------TATTTGAGTTTGAACTAGATCATAGTA -s simDog_chr6.simDog.chr6 518334 23 + 593897 G-----------TAGTTGACC-----TTAAATCTTAGCA -s simHuman_chr6.simHuman.chr6 525272 39 + 601863 AGAACCCATGCCAAGTAGACTTTTAATTCAATCTTAGCA -s simRat_chr6.simRat.chr6 30244 33 - 647215 AGTTCTCATGCATAGCAAA------TTCAACTATTAGCA - -a -s simMouse_chr6.simMouse.chr6 555151 12 + 636262 ACTCTCAGCCCA -s Anc0.Anc0refChr3 157118 12 + 222631 AGTCAGGACCCA -s Anc1.Anc1refChr6 193317 12 + 197743 AGTCAGGACCCA -s Anc2.Anc2refChr1 71360 12 + 142988 AGTCAGGACCCA -s mr.mrrefChr3 105151 12 + 181027 ACTCTCGGCCCA -s simCow_chr6.simCow.chr6 529650 12 + 602619 AGTCAGGACCAA -s simDog_chr6.simDog.chr6 518357 5 + 593897 -------GCCCA -s simHuman_chr6.simHuman.chr6 525311 12 + 601863 AGTCAGGACACA -s simRat_chr6.simRat.chr6 30277 12 - 647215 ACTCTCGGCCCA - -a -s simMouse_chr6.simMouse.chr6 555163 47 + 636262 TCTGGAACTAATGGGCTCATTTTGGACTAATCGTGGTACTTCCTGAA -s Anc0.Anc0refChr3 157130 28 + 222631 TTTGG-------------------GACTAATGCTGTTCCTTTTTGAG -s Anc1.Anc1refChr6 193329 28 + 197743 TTTGG-------------------GACTAATGCTGTTCCTTTTTGAG -s Anc2.Anc2refChr1 71372 28 + 142988 TTTTG-------------------GACTAACGCTGTTCCTTTTTGAG -s mr.mrrefChr3 105163 47 + 181027 TTTGGAACTAATGGGCTCATTTTGGACTAATGGTGGTACTTCCTGAA -s simCow_chr6.simCow.chr6 529662 28 + 602619 TTTTG-------------------AATAAACACTGTTTCTTATTGAG -s simDog_chr6.simDog.chr6 518362 28 + 593897 TTTTG-------------------GACTAACGCTGTTCCTTTTTGAG -s simHuman_chr6.simHuman.chr6 525323 28 + 601863 TTTGG-------------------GACTAATGCTCTTCTGTTTTGGG -s simRat_chr6.simRat.chr6 30308 47 - 647215 TTTTGACCTCATGGGCCCAGTTTGGACTAATGGTGGTGCTTCCTGAA - -a -s simMouse_chr6.simMouse.chr6 555210 14 + 636262 TGTTTCCTGTTTAA -s Anc0.Anc0refChr3 157159 14 + 222631 TTTTACCTGTTTAA -s Anc1.Anc1refChr6 193358 14 + 197743 TTTTACCTGTTTAA -s Anc2.Anc2refChr1 71401 14 + 142988 TTTTACCTGTTTAA -s mr.mrrefChr3 105210 14 + 181027 TGTTTCCTGTTTAA -s simCow_chr6.simCow.chr6 529691 14 + 602619 TTTTCCCTGTTTGA -s simDog_chr6.simDog.chr6 518391 14 + 593897 TTTTACCTGTATAA -s simHuman_chr6.simHuman.chr6 525352 14 + 601863 TTTTGCCTGTTTAA -s simRat_chr6.simRat.chr6 30355 14 - 647215 TATTTCCTGTTTAA - -a -s simMouse_chr6.simMouse.chr6 555224 7 + 636262 CAAGGGT -s Anc0.Anc0refChr3 157173 6 + 222631 -AAGGGA -s Anc1.Anc1refChr6 193372 7 + 197743 CAAGGGA -s Anc2.Anc2refChr1 71415 6 + 142988 -GAGGGA -s mr.mrrefChr3 105224 7 + 181027 CAAGGGT -s simCow_chr6.simCow.chr6 529705 6 + 602619 -CGAGGA -s simDog_chr6.simDog.chr6 518405 6 + 593897 -GAGGGA -s simHuman_chr6.simHuman.chr6 525367 7 + 601863 CAAGTGA -s simRat_chr6.simRat.chr6 30369 7 - 647215 CATGGGT - -a -s simMouse_chr6.simMouse.chr6 555231 36 + 636262 CCCCATTGGGACCCATAGCGTAGAGCAACGCACCAT -s Anc0.Anc0refChr3 157179 36 + 222631 TCCTATTGTGACCCATAGCATTGAGCAATGCACTGT -s Anc1.Anc1refChr6 193379 36 + 197743 TCCTATTGTGACCCATAGCATTGAGCAATGCACTGT -s Anc2.Anc2refChr1 71421 36 + 142988 TCCTATTGTGACCCATAGCATTGAGCAATGCACTGC -s mr.mrrefChr3 105231 36 + 181027 CCCTATTGGGACCCATAGCGTAGAGCAATGCACTGT -s simCow_chr6.simCow.chr6 529711 35 + 602619 TCCTATTGTGACCCATAGCGTTG-GTGATGCACTGC -s simCow_chr6.simCow.chr6 529952 35 + 602619 AGTTTTTTTGACCCATAGCATTG-GCGATGCACTGC -s simDog_chr6.simDog.chr6 518411 36 + 593897 TCCTATTGTGACTTATATCATTGAGCAATGGACTGC -s simHuman_chr6.simHuman.chr6 525374 36 + 601863 TCCTACTGTGACCCATAGCATTGAGCAATGCACTGT -s simRat_chr6.simRat.chr6 30376 36 - 647215 CCCTATTGGGACCCGTAGTGTAGAGCAATGCACTGT - -a -s simMouse_chr6.simMouse.chr6 555267 80 + 636262 AACCAATTTTCATGTATTGCAATGCATACCCCCAGCACATGAAGTATGGGGAGGAGAAGGATGCCTGACCAGTATTTGTT -s Anc0.Anc0refChr3 157220 79 + 222631 ATTCAATTCATGAGTTTAGCAATTTATTCCCCC-GTACATTAAGTACTGGCAAGAGAAGAATTCCTGACCAGGATTTGTT -s Anc1.Anc1refChr6 193420 80 + 197743 ATTCAATTCATGAGTTTAGCAATTTATTCCCCCAGTACATTAAGTACTGGCAAGAGAAGAATTCCTGACCAGGATTTGTT -s Anc2.Anc2refChr1 71462 79 + 142988 ATTCAATTCATGATTTTAGCAATTTATTCCCCC-GTACCTCAAGTACTGGCAAGAGGAGAATTCCTGACCCAGATTTGTT -s mr.mrrefChr3 105267 80 + 181027 AACCAATTTTCAAGTATTGCAATGCATTCCCCCAGCACATTAAGTATGGGGAGGAGAAGAATTCCTGACCAGTATTTGTT -s simCow_chr6.simCow.chr6 529751 61 + 602619 ACGCAGTTCGAG---TTAGCAATTTATTCCCC---------------TGGCAAGAGGAGAATCCC-GACCCAGATTTGTT -s simCow_chr6.simCow.chr6 529992 61 + 602619 ACGCGGTTCGAG---TTAGCAATTTACTCCCC---------------TGGCAAGAGGAGAATCCC-GACCCAGATTTGTT -s simDog_chr6.simDog.chr6 518452 79 + 593897 ATTCAATCCATGATTCTAGCTAATCATTCCCCC-GTACCTCAAGTACGGGCAAGAGGGGAATTCCTGACACTGATTTGTT -s simHuman_chr6.simHuman.chr6 525415 80 + 601863 ATTCAATTCATGAGTTTAGCAATCTGTTTCCCCAGTGCATTAAGTACTGGTGAGAGAAGAATTCCTGACCAGAAATTGTT -s simRat_chr6.simRat.chr6 30412 80 - 647215 AACCAGTTTTCAAGTATTGCAATGCATTCCCCCAGCACATTAAGTATGGGCAGTAGAGGAATTCCTGACCAGTATTTGTT - -a -s simMouse_chr6.simMouse.chr6 555347 45 + 636262 TGTCTTTAATGATGATTCTATTGTTCTGGCACTATGCTTACTATA -s Anc0.Anc0refChr3 157299 45 + 222631 TGTTGTTAAAGATGTTTTTACTGTTGTGGCACTGAGTCTGCTAGG -s Anc1.Anc1refChr6 193500 45 + 197743 TGTTGTTAAAGATGTTTTTACTGTTGTGGCACTGAGTCTGCTAGG -s Anc2.Anc2refChr1 71542 45 + 142988 TGTTGTTACAGATGTTTTCACTGTTGTGGCACTGATTCTGCTTGG -s mr.mrrefChr3 105347 45 + 181027 TGTTTTTAATGATGATTTTATTGTTCTGGCACTATGCTTACTATA -s simCow_chr6.simCow.chr6 529813 43 + 602619 GGTTGTTACAGATGTTTTCACTGTGGTGTCACTGATTTTGA--GG -s simCow_chr6.simCow.chr6 530054 43 + 602619 GGTTGTTACAGATGTTTTCACTGTGGTGTCACTGATTTTGA--GG -s simDog_chr6.simDog.chr6 518532 37 + 593897 TGTTGGTA--------TTCACTGCTGTGGCACTGATTCTGCTTGG -s simHuman_chr6.simHuman.chr6 525495 45 + 601863 ATGTGTTAAAGAGGTTTTTACTGTTGCAGCACTGAGTCTGCTAAG -s simRat_chr6.simRat.chr6 30492 45 - 647215 TGTTATTAACGATGATTTTATTGTTCTGGCACTATGCTTACTATA - -a -s simMouse_chr6.simMouse.chr6 555392 7 + 636262 ACATCTA -s Anc0.Anc0refChr3 157344 7 + 222631 ACATCTA -s Anc1.Anc1refChr6 193545 7 + 197743 ACATCTA -s Anc2.Anc2refChr1 71587 7 + 142988 ACATCTA -s mr.mrrefChr3 105392 7 + 181027 ACATCTA -s simCow_chr6.simCow.chr6 529856 7 + 602619 ATATCAA -s simCow_chr6.simCow.chr6 530097 7 + 602619 ATATCAA -s simDog_chr6.simDog.chr6 518569 7 + 593897 ACATCTA -s simHuman_chr6.simHuman.chr6 525547 7 + 601863 ACATCTA -s simRat_chr6.simRat.chr6 30537 7 - 647215 ACATCTA - -a -s simMouse_chr6.simMouse.chr6 555399 2 + 636262 CT -s Anc0.Anc0refChr3 157351 2 + 222631 CC -s Anc1.Anc1refChr6 193552 2 + 197743 CC -s Anc2.Anc2refChr1 71594 2 + 142988 CC -s mr.mrrefChr3 105399 2 + 181027 CT -s simCow_chr6.simCow.chr6 529863 2 + 602619 CC -s simCow_chr6.simCow.chr6 530104 2 + 602619 CC -s simDog_chr6.simDog.chr6 518582 2 + 593897 CC -s simHuman_chr6.simHuman.chr6 525554 2 + 601863 CC -s simRat_chr6.simRat.chr6 30544 2 - 647215 CT - -a -s simMouse_chr6.simMouse.chr6 555401 6 + 636262 AACCCT -s Anc0.Anc0refChr3 157354 6 + 222631 AACCCT -s Anc1.Anc1refChr6 193555 6 + 197743 AACCCT -s Anc2.Anc2refChr1 71597 6 + 142988 AACCCT -s mr.mrrefChr3 105402 6 + 181027 AACCCT -s simCow_chr6.simCow.chr6 529866 6 + 602619 AACCCT -s simCow_chr6.simCow.chr6 530107 6 + 602619 AACCCT -s simDog_chr6.simDog.chr6 518585 6 + 593897 ATCCCT -s simHuman_chr6.simHuman.chr6 525557 6 + 601863 AACCTT -s simRat_chr6.simRat.chr6 30547 6 - 647215 AACCCT - -a -s simMouse_chr6.simMouse.chr6 555407 4 + 636262 CATG -s Anc0.Anc0refChr3 157360 4 + 222631 CATA -s Anc1.Anc1refChr6 193561 4 + 197743 CATA -s Anc2.Anc2refChr1 71606 4 + 142988 CATA -s mr.mrrefChr3 105408 4 + 181027 CATG -s simCow_chr6.simCow.chr6 529875 4 + 602619 TATA -s simCow_chr6.simCow.chr6 530116 4 + 602619 TATA -s simDog_chr6.simDog.chr6 518595 4 + 593897 CATG -s simHuman_chr6.simHuman.chr6 525563 4 + 601863 CATC -s simRat_chr6.simRat.chr6 30553 4 - 647215 CATG - -a -s simMouse_chr6.simMouse.chr6 555411 21 + 636262 CCCATAGCTGGCGAGTGTACC -s Anc0.Anc0refChr3 157368 21 + 222631 GGGATTGAAAAAGTGGTTACC -s Anc1.Anc1refChr6 193569 21 + 197743 GGGATTGAAAAAGTGGTTACC -s Anc2.Anc2refChr1 71614 21 + 142988 GGGATTGAAAAAGTGGTCACC -s mr.mrrefChr3 105416 21 + 181027 CCCATAGCTGGCGAGGGTACC -s simCow_chr6.simCow.chr6 529883 21 + 602619 GGGATTGAGATAATGGTCGCC -s simCow_chr6.simCow.chr6 530124 21 + 602619 GGGATTGAGATAATGGTCACC -s simDog_chr6.simDog.chr6 518603 21 + 593897 GCAATTGAAAAAGTGGACACC -s simHuman_chr6.simHuman.chr6 525571 21 + 601863 GGGATTAAAAAAGTGGTTACC -s simRat_chr6.simRat.chr6 30562 21 - 647215 CCCATAGCTGGCAAGGGTACC - -a -s simMouse_chr6.simMouse.chr6 555432 23 + 636262 ATATATCAGTCAGGTTTCATCTA -s Anc0.Anc0refChr3 157397 23 + 222631 GTATATCAGTTATGTTTATTTTA -s Anc1.Anc1refChr6 193598 23 + 197743 GTATATCAGTTATGTTTATTTTA -s Anc2.Anc2refChr1 71643 23 + 142988 GTATATCACTTATATTGATCTTG -s mr.mrrefChr3 105437 23 + 181027 ATATATCAGTCAGGTTTCATCTA -s simCow_chr6.simCow.chr6 529912 23 + 602619 GTATATTACTCATATTGACCTTG -s simCow_chr6.simCow.chr6 530153 23 + 602619 GTATATTACTCATATTGACCTTG -s simDog_chr6.simDog.chr6 518632 23 + 593897 GTATGTCACTTGCATTGATATTG -s simHuman_chr6.simHuman.chr6 525600 23 + 601863 GTATATCAGTTATGTTTGTTTTA -s simRat_chr6.simRat.chr6 30583 11 - 647215 ATAC--------GGTTTTA---- - -a -s simMouse_chr6.simMouse.chr6 555455 9 + 636262 GTGTAGGTT -s Anc0.Anc0refChr3 157427 9 + 222631 GTGTTGGCT -s Anc1.Anc1refChr6 193628 9 + 197743 GTGTTGGCT -s Anc2.Anc2refChr1 71673 9 + 142988 ATGTTGGCT -s mr.mrrefChr3 105460 9 + 181027 GTGTAGGTT -s simCow_chr6.simCow.chr6 529942 7 + 602619 AA--TGGCT -s simCow_chr6.simCow.chr6 530183 7 + 602619 AA--TGGCT -s simDog_chr6.simDog.chr6 518662 9 + 593897 TTGTTGGCT -s simHuman_chr6.simHuman.chr6 525630 9 + 601863 GTCTTGGCT - -a -s simMouse_chr6.simMouse.chr6 555464 25 + 636262 CTGTTTTCCTACAGCTAGCAGGCGA -s Anc0.Anc0refChr3 157441 25 + 222631 TTTTTTCCCTGCTGCTGGCAGAGAA -s Anc1.Anc1refChr6 193642 25 + 197743 TTTTTTCCCTGCTGCTGGCAGAGAA -s Anc2.Anc2refChr1 71687 25 + 142988 TTTTTTCCCTGCTGCCGACAGAGAG -s mr.mrrefChr3 105469 25 + 181027 CTGTTTTCCTACTGCTAGCAGGCAA -s simCow_chr6.simCow.chr6 530195 25 + 602619 TTTTTTCCCTGCTGCCAACAGCAAG -s simDog_chr6.simDog.chr6 518676 25 + 593897 TTTTTCTCCTGCTGCCGACAGAGAG -s simHuman_chr6.simHuman.chr6 525644 25 + 601863 TTTTTTCCTTGCTGCTGGCAGAGAA -s simRat_chr6.simRat.chr6 30594 25 - 647215 CTGTTTTCCGACTGCCAGCAGGAAA - -a -s simMouse_chr6.simMouse.chr6 555489 23 + 636262 GAATAGCCAAGATCATCATTCGT -s Anc0.Anc0refChr3 157466 23 + 222631 AGATAGCCAAGAACATCCCTCAT -s Anc1.Anc1refChr6 193667 23 + 197743 AGATAGCCAAGAACATCCCTCAT -s Anc2.Anc2refChr1 71712 23 + 142988 CGATAGCCAAGAACACCCCTCAC -s mr.mrrefChr3 105494 23 + 181027 AAATAGCCAAGATCATCATTCAT -s simCow_chr6.simCow.chr6 530220 23 + 602619 CAATAGCCAACAAGACCCTTCAC -s simDog_chr6.simDog.chr6 518701 23 + 593897 CGACGGCCACGAACACCCCTCAC -s simHuman_chr6.simHuman.chr6 525670 23 + 601863 AGATAGCTGAGAACATCCCTCAT -s simRat_chr6.simRat.chr6 30619 23 - 647215 AAATAGCCAAGATCATCATTGAT - -a -s simMouse_chr6.simMouse.chr6 555512 10 + 636262 GAGTATGCTG -s Anc0.Anc0refChr3 157489 10 + 222631 AAGCAAGTGA -s Anc1.Anc1refChr6 193690 10 + 197743 AAGCAAGTGA -s Anc2.Anc2refChr1 71735 10 + 142988 AGACAAGTGA -s mr.mrrefChr3 105517 10 + 181027 GAGTAAGCTG -s simCow_chr6.simCow.chr6 530263 10 + 602619 AGACAAGTTA -s simDog_chr6.simDog.chr6 518724 10 + 593897 AGACCGCTGA -s simHuman_chr6.simHuman.chr6 525693 10 + 601863 AAGCAAGTGA -s simRat_chr6.simRat.chr6 30642 10 - 647215 GACTAAGCTG - -a -s simMouse_chr6.simMouse.chr6 555522 1 + 636262 C -s Anc0.Anc0refChr3 157507 1 + 222631 C -s Anc1.Anc1refChr6 193708 1 + 197743 C -s Anc2.Anc2refChr1 71753 1 + 142988 C -s mr.mrrefChr3 105527 1 + 181027 C -s simCow_chr6.simCow.chr6 530279 1 + 602619 C -s simDog_chr6.simDog.chr6 518742 1 + 593897 C -s simHuman_chr6.simHuman.chr6 525711 1 + 601863 C -s simRat_chr6.simRat.chr6 30652 1 - 647215 C - -a -s simMouse_chr6.simMouse.chr6 555523 11 + 636262 CATGTTGGCTA -s Anc0.Anc0refChr3 157508 11 + 222631 CATATTTGCGA -s Anc1.Anc1refChr6 193709 11 + 197743 CATATTTGCGA -s Anc2.Anc2refChr1 71756 11 + 142988 CATATTTGTGA -s mr.mrrefChr3 105528 11 + 181027 CATGTTGGCTA -s simCow_chr6.simCow.chr6 530282 11 + 602619 TGTATTTGTGA -s simDog_chr6.simDog.chr6 518745 11 + 593897 CATATTTATGA -s simHuman_chr6.simHuman.chr6 525712 11 + 601863 CTTCATTGCGA -s simRat_chr6.simRat.chr6 30653 11 - 647215 CATGTTGGCTA - -a -s simMouse_chr6.simMouse.chr6 555534 6 + 636262 ATGAGA -s Anc0.Anc0refChr3 157519 6 + 222631 ATGAAA -s Anc1.Anc1refChr6 193720 6 + 197743 ATGAAA -s Anc2.Anc2refChr1 71816 6 + 142988 ATGAAT -s mr.mrrefChr3 105539 6 + 181027 ATGAGA -s simCow_chr6.simCow.chr6 530342 6 + 602619 CTAAAT -s simDog_chr6.simDog.chr6 518805 6 + 593897 ATGAAT -s simHuman_chr6.simHuman.chr6 525723 6 + 601863 GTGAAA - -a -s simMouse_chr6.simMouse.chr6 555540 8 + 636262 ACTACTAA -s Anc0.Anc0refChr3 157541 8 + 222631 AGTACTGC -s Anc1.Anc1refChr6 193742 8 + 197743 AGTACTGC -s Anc2.Anc2refChr1 71841 8 + 142988 TGTACTGC -s mr.mrrefChr3 105545 8 + 181027 ACTACTGA -s simCow_chr6.simCow.chr6 530367 8 + 602619 TGTACTGC -s simDog_chr6.simDog.chr6 518830 8 + 593897 TGTACTAC -s simHuman_chr6.simHuman.chr6 525745 8 + 601863 AGTACTGT -s simRat_chr6.simRat.chr6 30664 4 - 647215 ----CTGA - -a -s simMouse_chr6.simMouse.chr6 555548 13 + 636262 GAAAAATTCACAC -s Anc0.Anc0refChr3 157553 13 + 222631 GAAGACTCTACCC -s Anc1.Anc1refChr6 193754 13 + 197743 GAAGACTCTACCC -s Anc2.Anc2refChr1 71853 13 + 142988 GAAGACTCTACCC -s mr.mrrefChr3 105553 13 + 181027 GAAAACTTCACAC -s simCow_chr6.simCow.chr6 530379 13 + 602619 GAAGACTCTACCC -s simDog_chr6.simDog.chr6 518842 13 + 593897 GAGAATTCTATCC -s simHuman_chr6.simHuman.chr6 525757 13 + 601863 GAAGACTCTACCC -s simRat_chr6.simRat.chr6 30668 13 - 647215 GTAAACTTCATGC - -a -s simMouse_chr6.simMouse.chr6 555561 16 + 636262 TTAGAAAAAGCAGTCT -s Anc0.Anc0refChr3 157567 16 + 222631 TGAGAACAAGCCATCT -s Anc1.Anc1refChr6 193768 16 + 197743 TGAGAACAAGCCATCT -s Anc2.Anc2refChr1 71867 16 + 142988 TGAGAACAAGCCATCT -s mr.mrrefChr3 105567 16 + 181027 TTAGAAAAAGCAGTCT -s simCow_chr6.simCow.chr6 530393 16 + 602619 TGAGGACAAGCCATCT -s simDog_chr6.simDog.chr6 518856 16 + 593897 TGAAAACAAGCCATCT -s simHuman_chr6.simHuman.chr6 525771 16 + 601863 TGAGAACAAGCCATCT -s simRat_chr6.simRat.chr6 30682 16 - 647215 TTAGAAAAAGCAGTTT - -a -s simMouse_chr6.simMouse.chr6 555577 20 + 636262 GTAGGTTGCATTTTTGAAAG -s Anc0.Anc0refChr3 157584 20 + 222631 GTAGGTTGTATTTTTATAAG -s Anc1.Anc1refChr6 193785 20 + 197743 GTAGGTTGTATTTTTATAAG -s Anc2.Anc2refChr1 71884 20 + 142988 CTAGGTTGTATGTTTATTTG -s mr.mrrefChr3 105583 20 + 181027 GTAGGTTGTATTTTTGAAAG -s simCow_chr6.simCow.chr6 530410 17 + 602619 TTAGC---TAGGTGTGTCTG -s simDog_chr6.simDog.chr6 518873 20 + 593897 CTAGGTTGTATGTTTATTTG -s simHuman_chr6.simHuman.chr6 525788 20 + 601863 GTAGATTGTATTTTTATAAG -s simRat_chr6.simRat.chr6 30698 18 - 647215 GTAGCTTGTATTTT--AAAG - -a -s simMouse_chr6.simMouse.chr6 555597 34 + 636262 TCATTTGTAGGGCAGTCCCTCATTTTAATGTGAC -s Anc0.Anc0refChr3 157604 27 + 222631 TGGGTTGTAGGGCAGCCTCTCATTTTG------- -s Anc1.Anc1refChr6 193805 27 + 197743 TGGGTTGTAGGGCAGCCTCTCATTTTG------- -s Anc2.Anc2refChr1 71904 27 + 142988 TGGGTTGTAGGGCAGCCTCTCATTTTG------- -s mr.mrrefChr3 105603 34 + 181027 TGGTTTGTAGGGCAGTCCCTCATTTTAATGTGAC -s simCow_chr6.simCow.chr6 530431 27 + 602619 TGGGTTTTAGGGTAGTCTCTCAATTTG------- -s simDog_chr6.simDog.chr6 518893 27 + 593897 TGAATAGTAGAGCAGCCTCTCATTTTG------- -s simHuman_chr6.simHuman.chr6 525808 27 + 601863 TGGGTTGTAGGGCAGCCTCTCATTTTG------- -s simRat_chr6.simRat.chr6 30716 34 - 647215 TGGTTTGTAGCGCAGTCCCTCATTTTAAGGTGAC - -a -s simMouse_chr6.simMouse.chr6 555631 25 + 636262 TTGAGTAACCTCAAACTCTATGCCC -s Anc0.Anc0refChr3 157631 11 + 222631 -----------CAAAC---ATGCCC -s Anc1.Anc1refChr6 193832 11 + 197743 -----------CAAAC---ATGCCC -s Anc2.Anc2refChr1 71965 11 + 142988 -----------CAAAG---ATACCG -s mr.mrrefChr3 105638 25 + 181027 TTGAGTAACCTCAAACTCTATGCCC -s simCow_chr6.simCow.chr6 530494 11 + 602619 -----------CAAAG---ATACCT -s simDog_chr6.simDog.chr6 518954 11 + 593897 -----------CAAAG---CTACCG -s simHuman_chr6.simHuman.chr6 525835 11 + 601863 -----------CAAAC---ATGCCC -s simRat_chr6.simRat.chr6 30751 25 - 647215 TTGAGTTTCCTCAAACCTTATGCCC - -a -s simMouse_chr6.simMouse.chr6 555656 16 + 636262 ACTGTTGTGTGCTGAA -s Anc0.Anc0refChr3 157648 16 + 222631 AATGTTGCATCCAAAA -s Anc1.Anc1refChr6 193849 16 + 197743 AATGTTGCATCCAAAA -s Anc2.Anc2refChr1 71982 16 + 142988 GATATTGCATCCAAAA -s mr.mrrefChr3 105663 16 + 181027 ACTGTTGTGTGCTGAA -s simCow_chr6.simCow.chr6 530511 16 + 602619 TAGATTGCATTCAAAA -s simDog_chr6.simDog.chr6 518971 16 + 593897 GCTATTGCATCCAAAA -s simHuman_chr6.simHuman.chr6 525852 11 + 601863 AATGCTGCATC----- -s simRat_chr6.simRat.chr6 30776 16 - 647215 ACTCTTGTCTGCTGAA - -a -s simMouse_chr6.simMouse.chr6 555672 2 + 636262 CT -s Anc0.Anc0refChr3 157664 2 + 222631 CT -s Anc1.Anc1refChr6 193865 2 + 197743 CT -s Anc2.Anc2refChr1 72011 2 + 142988 CT -s mr.mrrefChr3 105679 2 + 181027 CT -s simCow_chr6.simCow.chr6 530540 2 + 602619 CT -s simDog_chr6.simDog.chr6 519000 2 + 593897 CT -s simRat_chr6.simRat.chr6 30792 2 - 647215 CT - -a -s simMouse_chr6.simMouse.chr6 555674 12 + 636262 GGCCAACAATCC -s Anc0.Anc0refChr3 157666 12 + 222631 GTCTAATTATCG -s Anc1.Anc1refChr6 193867 12 + 197743 GTCTAATTATCG -s Anc2.Anc2refChr1 72016 12 + 142988 GTCTAATTATCG -s mr.mrrefChr3 105681 12 + 181027 GGCCAACAATCC -s simCow_chr6.simCow.chr6 530545 12 + 602619 GTCTAGTTATCG -s simDog_chr6.simDog.chr6 519005 12 + 593897 GTCTAACTATTG -s simRat_chr6.simRat.chr6 30794 12 - 647215 GGCCAGCAATCC - -a -s simMouse_chr6.simMouse.chr6 555686 2 + 636262 TT -s Anc0.Anc0refChr3 157678 2 + 222631 TT -s Anc1.Anc1refChr6 193879 2 + 197743 TT -s Anc2.Anc2refChr1 72028 2 + 142988 TT -s mr.mrrefChr3 105693 2 + 181027 TT -s simCow_chr6.simCow.chr6 530600 2 + 602619 TC -s simDog_chr6.simDog.chr6 519017 2 + 593897 TT -s simRat_chr6.simRat.chr6 30806 2 - 647215 TC - -a -s simMouse_chr6.simMouse.chr6 555688 31 + 636262 GCATCTAAAAGACCCCCTACCCTCCCATATA -s Anc0.Anc0refChr3 157680 31 + 222631 CCATCCAGAAGATCTGGTTACCTCCCAAATC -s Anc1.Anc1refChr6 193881 31 + 197743 CCATCCAGAAGATCTGGTTACCTCCCAAATC -s Anc2.Anc2refChr1 72032 31 + 142988 CCATCCAGAAGATCTGGTTACCTCCCAAATC -s mr.mrrefChr3 105695 31 + 181027 GCATCTAAAAGACCCCCTACCCTCCCATATA -s simCow_chr6.simCow.chr6 530604 31 + 602619 CCATCCAAAGGATTTGCTTACCTCCCAAATC -s simDog_chr6.simDog.chr6 519021 31 + 593897 CCATCCAGAAGATCTGGTTACTTCCCATTTC -s simHuman_chr6.simHuman.chr6 526008 9 + 601863 ----------------------TCCAAAATC -s simRat_chr6.simRat.chr6 30808 31 - 647215 GCATCTAAAAGACCAACTTCCCTCCTATGTA - -a -s simMouse_chr6.simMouse.chr6 555719 1 + 636262 A -s Anc0.Anc0refChr3 157712 1 + 222631 A -s Anc1.Anc1refChr6 193913 1 + 197743 A -s Anc2.Anc2refChr1 72064 1 + 142988 A -s mr.mrrefChr3 105726 1 + 181027 A -s simCow_chr6.simCow.chr6 530636 1 + 602619 A -s simDog_chr6.simDog.chr6 519053 1 + 593897 G -s simHuman_chr6.simHuman.chr6 526018 1 + 601863 A -s simRat_chr6.simRat.chr6 30839 1 - 647215 A - -a -s simMouse_chr6.simMouse.chr6 555720 52 + 636262 TTGGATAATTCTCTATGTCCTTGAGGAAAAAACAACCATGTTATGCTCTGAA -s Anc0.Anc0refChr3 157713 49 + 222631 TTGGATCATTCTTTATATCCTTGAGAAAAAGATCACC---TGATACCTTGCA -s Anc1.Anc1refChr6 193914 49 + 197743 TTGGATCATTCTTTATATCCTTGAGAAAAAGATCACC---TGATACCTTGCA -s Anc2.Anc2refChr1 72069 49 + 142988 TTGGATCATTCTTTGTATTCTTGAGAAAAAGATCAAA---TGATACCTTGCA -s mr.mrrefChr3 105727 52 + 181027 TTGGATAATTCTCTATGTCCTTGAGGAAAAAATAACCATGTTATACTTTGAA -s simCow_chr6.simCow.chr6 530641 26 + 602619 TTGGATCATTCTCTGTATTCTTGACA-------------------------- -s simDog_chr6.simDog.chr6 519058 49 + 593897 TTGGATTGTTCTTTGTGTTCTTAAGGAAAAGATCAAA---TGATACCTTGCA -s simHuman_chr6.simHuman.chr6 526019 49 + 601863 GAGAATCATTCTTTATATCCTTGAGAGAAAGATGACC---TGATATGTGGCA -s simRat_chr6.simRat.chr6 30840 52 - 647215 TTGGATAATTCTCTATGTCCTTGAGGAAAAAATAACCATGTTATACTTTGAA - -a -s simMouse_chr6.simMouse.chr6 555772 32 + 636262 ACACAATACACCAGCTCTATATCTTGGAAAAA -s Anc0.Anc0refChr3 157762 32 + 222631 ACATACTATACCAACACTATATCCTGGTAAAA -s Anc1.Anc1refChr6 193963 32 + 197743 ACATACTATACCAACACTATATCCTGGTAAAA -s Anc2.Anc2refChr1 72126 32 + 142988 ACATACTATAACAACACTATATCCAGATAATA -s mr.mrrefChr3 105779 32 + 181027 ACATAATATACCAGCTCTATATCTTGGTAAAA -s simCow_chr6.simCow.chr6 530675 32 + 602619 ACATACTCTAACAACACTATATCCAGATAATA -s simDog_chr6.simDog.chr6 519116 32 + 593897 ACAGACGATAACAACTCTACATCCAGAATATA -s simHuman_chr6.simHuman.chr6 526068 32 + 601863 ACATGCTATACAAACACTATATGCTGGTAAAA -s simRat_chr6.simRat.chr6 30892 32 - 647215 ACATATTATACCGGCTCTATATCTTGATAAAA - -a -s simMouse_chr6.simMouse.chr6 555804 6 + 636262 GCATTG -s Anc0.Anc0refChr3 157794 6 + 222631 GCATTG -s Anc1.Anc1refChr6 193995 6 + 197743 GCATTG -s Anc2.Anc2refChr1 72158 6 + 142988 GCATTG -s mr.mrrefChr3 105811 6 + 181027 GCATTG -s simCow_chr6.simCow.chr6 530707 6 + 602619 GCTTCG -s simDog_chr6.simDog.chr6 519148 6 + 593897 GCATTG -s simHuman_chr6.simHuman.chr6 525867 6 + 601863 AGATTG -s simHuman_chr6.simHuman.chr6 526100 6 + 601863 GCATTG -s simRat_chr6.simRat.chr6 30924 6 - 647215 GCATTG - -a -s simMouse_chr6.simMouse.chr6 555810 28 + 636262 CGTGAATTTGCCTAATCCCCATGAGCAC -s Anc0.Anc0refChr3 157801 28 + 222631 TATAAATTCAGCTAATCACAATGAGCAC -s Anc1.Anc1refChr6 194002 28 + 197743 TATAAATTCAGCTAATCACAATGAGCAC -s Anc2.Anc2refChr1 72165 28 + 142988 AATAAATTCAGCTAATCACAATGAGCAC -s mr.mrrefChr3 105817 28 + 181027 CGTGAATTTGCCTAATCCCCATGAGCAC -s simCow_chr6.simCow.chr6 530714 27 + 602619 AATAAATTCAGCT-CTCACAATGAGCAC -s simDog_chr6.simDog.chr6 519162 28 + 593897 AATAGATTTGGCTAATGACAATGAGCAC -s simHuman_chr6.simHuman.chr6 525874 28 + 601863 TATAAATTTGGATCATCACAATGAGCAC -s simHuman_chr6.simHuman.chr6 526107 28 + 601863 TGTAAATGCAGCCCATCGCAATGAGCAC -s simRat_chr6.simRat.chr6 30930 28 - 647215 CATTAATTTGCCTACTCCCCATGAGCAC - -a -s simMouse_chr6.simMouse.chr6 555838 69 + 636262 TCTTGTACCAAGACTAAAAACATTGAAATTGTCTCAGGTCAAGATTATTTGTGTACCAGGGCTAAAAAC -s Anc0.Anc0refChr3 157830 19 + 222631 T--------------------------------------------------TGTACCAGGGCTAAAAAC -s Anc1.Anc1refChr6 194031 19 + 197743 T--------------------------------------------------TGTACCAGGGCTAAAAAC -s Anc2.Anc2refChr1 72194 19 + 142988 C--------------------------------------------------TGTACCAGGGCTAAACAA -s mr.mrrefChr3 105845 68 + 181027 TCTTGTACCAAGACTAAAAACATTGAAACTGTCTCAGGTCAAGATTATT-GTGTACCAGGGCTAAAAAC -s simCow_chr6.simCow.chr6 530742 19 + 602619 C--------------------------------------------------TGTTTCAGGGCTAAACAC -s simDog_chr6.simDog.chr6 519191 19 + 593897 C--------------------------------------------------AATACCAGGGCTAAGCAA -s simHuman_chr6.simHuman.chr6 525903 19 + 601863 T--------------------------------------------------TGTACCAGGGCTAAAAAC -s simHuman_chr6.simHuman.chr6 526135 19 + 601863 T--------------------------------------------------TGTACCAGTGCTAAAAAC -s simRat_chr6.simRat.chr6 30958 68 - 647215 TCTTGTACCAAGACTATAAACACTGAAACTGTCTCAGGTTAAGGTTATT-GTGCACCAGGGCTAAAGAC - -a -s simMouse_chr6.simMouse.chr6 555907 10 + 636262 CCTAAGTCTG -s Anc0.Anc0refChr3 157849 10 + 222631 AATGAATCTG -s Anc1.Anc1refChr6 194050 10 + 197743 AATGAATCTG -s Anc2.Anc2refChr1 72213 10 + 142988 AATGAATCTT -s mr.mrrefChr3 105913 10 + 181027 CCTAAGTCTG -s simCow_chr6.simCow.chr6 530761 10 + 602619 GATGAATCTT -s simDog_chr6.simDog.chr6 519210 10 + 593897 AATGAATCCG -s simHuman_chr6.simHuman.chr6 525922 10 + 601863 AATCAATCTG -s simHuman_chr6.simHuman.chr6 526155 10 + 601863 AATGAATCTG -s simRat_chr6.simRat.chr6 31026 10 - 647215 CCCAAGTATG - -a -s simMouse_chr6.simMouse.chr6 555917 67 + 636262 TTTTAGGTTGAATTTGTTTTAAAGAATATAATAATTGTATAGCAGGCCAATCTACGACAGTTCAATG -s Anc0.Anc0refChr3 157859 66 + 222631 TTACAGGTTAAAGTT-TTGGGAAGAATATACTAGTTGCAAAGCAGGCCAATCTATGACAGTTTACTG -s Anc1.Anc1refChr6 194060 67 + 197743 TTACAGGTTAAAGTTGTTGGGAAGAATATACTAGTTGCAAAGCAGGCCAATCTATGACAGTTTACTG -s Anc2.Anc2refChr1 72223 66 + 142988 TTGCAGGTTAAAGTT-TTGGGAAGAATATACTAGTTGCAAATCAGGCCAATCTATGACCGTTTACTG -s mr.mrrefChr3 105923 67 + 181027 TTTTAGGTTAAATTTGTTGTAAAGAATATAATAATTGTATAGCAGGCCAATCTATGACAGTTCAATG -s simCow_chr6.simCow.chr6 530771 61 + 602619 TTCCAGGTT--AGGC-TGGTGAAGAGTATTCTAGTTGCAAATCAGGCCAA---ATGACCATCTACCA -s simDog_chr6.simDog.chr6 519220 65 + 593897 TGGCAGGTTAAAGTT-TTGGAAAGAAGATACAAGTTCCAAATCAGCCCAATCTATGA-CGTTTACTG -s simHuman_chr6.simHuman.chr6 525932 67 + 601863 TTACAGGTTAAAGTTGTAGGAAAGAATCTACTAGTTGCAAAGCAGGCCAACCTATGACAGTTTACCA -s simHuman_chr6.simHuman.chr6 526166 67 + 601863 TTACAGGTTAAAGTTGTTGAGAAGAATCTACTAGTTGCAAACCAGGCCAATCTATGACAGTGTCCTG -s simRat_chr6.simRat.chr6 31036 66 - 647215 TTTTAGGTTAAATTTGATGGAAAGAAT-CAGTAATGGTGCAGTGGGCCAATCTATGACAGATCAATG - -a -s simMouse_chr6.simMouse.chr6 555984 5 + 636262 CATAT -s Anc0.Anc0refChr3 157927 5 + 222631 GAATA -s Anc1.Anc1refChr6 194129 5 + 197743 GAATA -s Anc2.Anc2refChr1 72291 5 + 142988 GAATA -s mr.mrrefChr3 105990 5 + 181027 CATAA -s simCow_chr6.simCow.chr6 530834 5 + 602619 GAATA -s simDog_chr6.simDog.chr6 519287 5 + 593897 ATATA -s simHuman_chr6.simHuman.chr6 526001 5 + 601863 CATTA -s simHuman_chr6.simHuman.chr6 526235 5 + 601863 GAATA -s simRat_chr6.simRat.chr6 31102 5 - 647215 CAAAA - -a -s simMouse_chr6.simMouse.chr6 555989 1 + 636262 T -s Anc0.Anc0refChr3 157932 1 + 222631 C -s Anc1.Anc1refChr6 194134 1 + 197743 C -s Anc2.Anc2refChr1 72297 1 + 142988 C -s mr.mrrefChr3 105995 1 + 181027 T -s simCow_chr6.simCow.chr6 530840 1 + 602619 C -s simDog_chr6.simDog.chr6 519293 1 + 593897 C -s simHuman_chr6.simHuman.chr6 526006 1 + 601863 C -s simHuman_chr6.simHuman.chr6 526240 1 + 601863 C -s simRat_chr6.simRat.chr6 31107 1 - 647215 T - -a -s simMouse_chr6.simMouse.chr6 555990 2 + 636262 TG -s Anc0.Anc0refChr3 157933 2 + 222631 TG -s Anc1.Anc1refChr6 194135 2 + 197743 TG -s Anc2.Anc2refChr1 72298 2 + 142988 TG -s mr.mrrefChr3 105996 2 + 181027 TG -s simCow_chr6.simCow.chr6 530841 2 + 602619 TG -s simDog_chr6.simDog.chr6 519294 2 + 593897 CA -s simHuman_chr6.simHuman.chr6 526241 2 + 601863 TG -s simRat_chr6.simRat.chr6 31108 2 - 647215 TG - -a -s simMouse_chr6.simMouse.chr6 555992 17 + 636262 TTGGCTTAGCTTTAAGA -s Anc0.Anc0refChr3 157935 13 + 222631 TGGATT----TTAAGGG -s Anc1.Anc1refChr6 194137 13 + 197743 TGGATT----TTAAGGG -s Anc2.Anc2refChr1 72303 13 + 142988 TGGATT----TTAAGGG -s mr.mrrefChr3 105998 17 + 181027 TTGACTTAGCTTTAAGG -s simCow_chr6.simCow.chr6 530846 13 + 602619 TGGATT----TGAAGGG -s simDog_chr6.simDog.chr6 519299 13 + 593897 CGGATT----GTAAGGG -s simHuman_chr6.simHuman.chr6 526243 13 + 601863 TGGATT----TTGAGGG -s simRat_chr6.simRat.chr6 31110 17 - 647215 GTGACTTAGCTTTAAAG - -a -s simMouse_chr6.simMouse.chr6 556009 1 + 636262 T -s Anc0.Anc0refChr3 157948 1 + 222631 T -s Anc1.Anc1refChr6 194150 1 + 197743 T -s Anc2.Anc2refChr1 72316 1 + 142988 T -s mr.mrrefChr3 106015 1 + 181027 T -s simCow_chr6.simCow.chr6 530859 1 + 602619 A -s simDog_chr6.simDog.chr6 519312 1 + 593897 T -s simHuman_chr6.simHuman.chr6 526007 1 + 601863 C -s simHuman_chr6.simHuman.chr6 526256 1 + 601863 T -s simRat_chr6.simRat.chr6 31127 1 - 647215 T - -a -s simMouse_chr6.simMouse.chr6 556010 11 + 636262 TCTATCACACT -s Anc0.Anc0refChr3 157949 11 + 222631 TCTACCACTCT -s Anc1.Anc1refChr6 194151 11 + 197743 TCTACCACTCT -s Anc2.Anc2refChr1 72317 11 + 142988 TCTACCACTCC -s mr.mrrefChr3 106016 11 + 181027 TCTATCACACT -s simCow_chr6.simCow.chr6 530860 9 + 602619 TCTACCA--CC -s simDog_chr6.simDog.chr6 519313 9 + 593897 TCTACGACT-- -s simHuman_chr6.simHuman.chr6 526257 11 + 601863 TCTACCACTCT -s simRat_chr6.simRat.chr6 31128 11 - 647215 TCTATCACATA - -a -s simMouse_chr6.simMouse.chr6 556021 97 + 636262 GTCTTCTACATTTGGTAACTGTATCATGAGCAACACCCATTTTGTGACTGTATCAGCTTAGGATTTGGCTTTCCCTCAACTGATGAACTCAAACAAT -s Anc0.Anc0refChr3 157962 64 + 222631 GACTTCTAGATGT-GTAACTGTATTGTTAGTCACACTCAT---------------------GATTTAGAGTTCCTTCAGCTGGTGA----------- -s Anc1.Anc1refChr6 194164 65 + 197743 GACTTCTAGATGTGGTAACTGTATTGTTAGTCACACTCAT---------------------GATTTAGAGTTCCTTCAGCTGGTGA----------- -s Anc2.Anc2refChr1 72330 64 + 142988 GACATCTAGGTGT-GTAACTGTATTGTTAGTCAGACTTGT---------------------GATTTAGAGTTCCTTCAGCTGGTGA----------- -s mr.mrrefChr3 106027 93 + 181027 GTCTTCTACATTTGGTAACTGTATCATGAGCAACACCCATTTTGTGACTGTAT----TTAGGATTTAGCTTTCCCTCAACTGATGAACTCAAACAAT -s simCow_chr6.simCow.chr6 530871 60 + 602619 GACATATAGGT-T-GGAACTGTATTGTTAGTCAGGCTT------------------------ATTAAGACCTCCCTTGGCTGGTGA----------- -s simDog_chr6.simDog.chr6 519322 60 + 593897 -ACATCCAGGTGT-GTAACTGTATTATTAGTCAGACTTGT---------------------GATTTAGAGTTCCTCCAGCTGG-------------- -s simHuman_chr6.simHuman.chr6 526270 65 + 601863 GACTTCTAGATGTGGTAGCTGTATTGTTAGTCACACTCAC---------------------GGTTTAGAATTCCATCATCTGGTTA----------- -s simRat_chr6.simRat.chr6 31139 93 - 647215 CTCTTCTACATCTGGAAACCGTATCATGAGCAACACCCATTTTGTGACTGTAT----TTAAGATTTAGCTTTCGCTCAGCTGATGTACTCAAACAAA - -a -s simMouse_chr6.simMouse.chr6 556118 93 + 636262 GCTTTAACTGATCAAACAAGCAACTTAGAGAGTACAATTAGTTACTCTCTGCAATCTCAAGAATTTTGAAATTTGGAACAATTAAACAAGTAG -s Anc0.Anc0refChr3 158026 45 + 222631 TCTTTAGCTAGTCAAACAAGTAAATTAAGGAGCACAATTAA------------------------------------------------GTAA -s Anc1.Anc1refChr6 194229 45 + 197743 TCTTTAGCTAGTCAAACAAGTAAATTAAGGAGCACAATTAA------------------------------------------------GTAA -s Anc2.Anc2refChr1 72394 45 + 142988 TCTATAGCCAGTCACACAAGTAAATTAAGGAGCACAATTAA------------------------------------------------GTAA -s mr.mrrefChr3 106120 88 + 181027 GCTTTAACTGGTCAAACAAGCAAATTAAAGAGTACAATTAGTTACTCTCTGCAATCTCAAG-----TGAAATTTGGAACAATTAAACAAGTAG -s simCow_chr6.simCow.chr6 530941 45 + 602619 TCTATAGCCAGTCACACAAGCAAACTAAAGAGTACAATTAA------------------------------------------------GTAA -s simDog_chr6.simDog.chr6 519382 27 + 593897 ------------------AATAAATTAAGGAGCACAATTAA------------------------------------------------GTTG -s simHuman_chr6.simHuman.chr6 526335 45 + 601863 TCTTCACCTAGATAAACAAGTAGATTAAGGTGGAGAATTAT------------------------------------------------GTAA -s simRat_chr6.simRat.chr6 31232 88 - 647215 ACCTTAGCTGGTCAAACAAGCAAATTAAAGAGTACAATTACTTACTCCCTGCAATCTAAAG-----TTAAATTCAGAACAATTGAATAAGTAG - -a -s simMouse_chr6.simMouse.chr6 556211 46 + 636262 TAGATAAGCCATCAGATTAAATTATGAATAGTTGCACAATCTGGAA -s Anc0.Anc0refChr3 158071 38 + 222631 TAGCCAAGATCTCAGGTTAAATTATGAATA--------ATCTGCAA -s Anc1.Anc1refChr6 194274 38 + 197743 TAGCCAAGATCTCAGGTTAAATTATGAATA--------ATCTGCAA -s Anc2.Anc2refChr1 72439 38 + 142988 TAGCCAAGATCTCAGGTTAAATTATGAATA--------ATCTGAAA -s mr.mrrefChr3 106208 46 + 181027 TAGCTAAGCCATCAGATTAAATTATGAATAGTTGCACAATCTGCAA -s simCow_chr6.simCow.chr6 530987 35 + 602619 TAGCCAAGAACTCAGGGTAAATT---CATA--------ATCTGTAA -s simDog_chr6.simDog.chr6 519409 38 + 593897 TAGCCAAGTTCTCAGGTTAGATTATGAACA--------ATCTGAAA -s simHuman_chr6.simHuman.chr6 526380 38 + 601863 TACCCAAGATCTCAGGTTAAATTATAAATG--------ATCTGCAA -s simRat_chr6.simRat.chr6 31320 46 - 647215 CAGCTAAGCCATCAGATTAAATTATGCAAATTTGCACAATCTGCAA - -a -s simMouse_chr6.simMouse.chr6 556257 42 + 636262 TCTTGATCATGAGTTCCTAATCACATTACACAGGACCAAGCA -s Anc0.Anc0refChr3 158109 42 + 222631 TCCTGATCATCAGTTCCTAATCACATTACACAGTACCAAGTG -s Anc1.Anc1refChr6 194312 42 + 197743 TCCTGATCATCAGTTCCTAATCACATTACACAGTACCAAGTG -s Anc2.Anc2refChr1 72480 42 + 142988 TCCTGATCATCAGTTCCTAATCACATTACACAGTACCAAGTG -s mr.mrrefChr3 106254 42 + 181027 TCTTGATCATCAGTTCCTAATCACATTACACAGGACCAAGCA -s simCow_chr6.simCow.chr6 531025 40 + 602619 GCCTGAT--TCTGCCCCTAATCACATTACACCATACCAAGTG -s simDog_chr6.simDog.chr6 519450 42 + 593897 TCCTGATCACCAGTTCCTAATCACATTACACAGTACCAAGTG -s simHuman_chr6.simHuman.chr6 526418 42 + 601863 TCCGAATTGTCAGTTCCTAATCACATTACACAGTGCCAAGTG -s simRat_chr6.simRat.chr6 31366 42 - 647215 TCTTGAACACCAGTTTGTAATCACATTACATAGGACCAAGCA - -a -s simMouse_chr6.simMouse.chr6 556299 12 + 636262 TTATTCTTTTAT -s Anc0.Anc0refChr3 158154 12 + 222631 CTTTTCTTTCAT -s Anc1.Anc1refChr6 194357 12 + 197743 CTTTTCTTTCAT -s Anc2.Anc2refChr1 72525 12 + 142988 CTTTTCTTTCAT -s mr.mrrefChr3 106296 12 + 181027 CTATTCTTTTAT -s simCow_chr6.simCow.chr6 531068 12 + 602619 CTTCTCTTTCTT -s simDog_chr6.simDog.chr6 519495 12 + 593897 CTTTTCTTTCAT -s simHuman_chr6.simHuman.chr6 526463 12 + 601863 CTTTTCTTTCAT -s simRat_chr6.simRat.chr6 31408 12 - 647215 CTATTCTTCTAT - -a -s simMouse_chr6.simMouse.chr6 556311 18 + 636262 GGCAAAGGCTCCGACTAA -s Anc0.Anc0refChr3 158167 18 + 222631 GGCCAAGGCATTGAATAA -s Anc1.Anc1refChr6 194370 18 + 197743 GGCCAAGGCATTGAATAA -s Anc2.Anc2refChr1 72538 18 + 142988 GGCCAAGGCACTGAATAA -s mr.mrrefChr3 106308 18 + 181027 GGCAAAGGCTTCGACTAA -s simCow_chr6.simCow.chr6 531081 18 + 602619 GGCCAAGGCACTGACTAA -s simDog_chr6.simDog.chr6 519508 13 + 593897 GGCT-----GCTGAATAA -s simHuman_chr6.simHuman.chr6 526476 18 + 601863 GGACAAGGCATTGATTGA -s simRat_chr6.simRat.chr6 31420 18 - 647215 GGCAAAGGTTTCAACTAA - -a -s simMouse_chr6.simMouse.chr6 556329 81 + 636262 TCACCCTGTGTAAACTTAAATGAATCCACCCAGCCCCCAGTAGAAGAGTGGGATACGTTTAGTGTTGACTCTGTTGGTACA -s Anc0.Anc0refChr3 158185 78 + 222631 ATTGCCTGTGCATACTTAAATGAATCCAGTCAATCTCAGGTGAAAGAGAGAGA---GTTCAGTGTTGGCTCTGTTGGCATG -s Anc1.Anc1refChr6 194388 78 + 197743 ATTGCCTGTGCATACTTAAATGAATCCAGTCAATCTCAGGTGAAAGAGAGAGA---GTTCAGTGTTGGCTCTGTTGGCATG -s Anc2.Anc2refChr1 72560 78 + 142988 ATTGCCAGTGCATACTTACATGAATCCAGTCCATCTCAGGTGAAAGAGAGAGA---GTTGAGTGTTGGCTCTGTTGGCATG -s mr.mrrefChr3 106326 81 + 181027 TCACCCTGTGTAAACTTAAATGAATCCACCCAACCCCCAGTAGAAGAGTGGGATAAGTTCAGTGTTGGCTCTGTTGGTACA -s simCow_chr6.simCow.chr6 531103 78 + 602619 ATTGCCAGCTCACACCTACATGCATCCAGTCCATCTGGATTGAAAGAGAGAGA---GTTGAGTGTTGGCTCTGTTGGTATG -s simDog_chr6.simDog.chr6 519525 72 + 593897 ATTGCCAGTGCATAGTTACATAAATCCAG------TCAGGTGACTGAGAGAGA---GTTGAGTGTTATCTCTGTTGGCATG -s simHuman_chr6.simHuman.chr6 526494 78 + 601863 ATTGCCTGTGCATACTTAATTGAATCCAGGCAATCTCATATGAAAGAGGGAGA---ATTCAATGTTGGCTCCGTTGGCATG -s simRat_chr6.simRat.chr6 31438 52 - 647215 -------------------ATG-------CCAAGCCCCAGTAGA---GTGAGATAAGTTCAGTGTTGGCTCTGTTGGTACA - -a -s simMouse_chr6.simMouse.chr6 556410 12 + 636262 CCTGTCTCCTTT -s Anc0.Anc0refChr3 158270 12 + 222631 CCTGCCTCCTTA -s Anc1.Anc1refChr6 194473 12 + 197743 CCTGCCTCCTTA -s Anc2.Anc2refChr1 72645 12 + 142988 CCTACCTCCTTA -s mr.mrrefChr3 106407 12 + 181027 CCTGTCTCCTTT -s simCow_chr6.simCow.chr6 531188 12 + 602619 CCTACTTCCTTC -s simDog_chr6.simDog.chr6 519604 12 + 593897 CTTACCTCCTTA -s simHuman_chr6.simHuman.chr6 526579 12 + 601863 CCTGCCTCCTTA -s simRat_chr6.simRat.chr6 31490 12 - 647215 CCTGTCTTCTTT - -a -s simMouse_chr6.simMouse.chr6 556422 89 + 636262 AAGTTAGTGCTCTAGGGTCTCATGTAGTAGATGCCACTGAACTACATCTTCATCTTGTTCAATATAAAAGTTTATTAGGGTGCCGTATT -s Anc0.Anc0refChr3 158285 80 + 222631 ACTCCAGTGTTCTAGGGGCCCATATTGTGGGTTCTACTCAACTACATACC------ATTCAACTTAAAAGCCTATTAGGG---CATGCT -s Anc1.Anc1refChr6 194488 83 + 197743 ACTCCAGTGTTCTAGGGGCCCATATTGTGGGTTCTACTCAACTACATACC------ATTCAACTTAAAAGCCTATTAGGGTAACATGCT -s Anc2.Anc2refChr1 72660 80 + 142988 TCTCCCGTGTTCTAGGGGCCCATATTGTGGATTCTACTCAACTACATACC------ATTTAACTTAAAAACCAATTAGGG---CATGCT -s mr.mrrefChr3 106419 83 + 181027 AAGTTAGTGTTCTAGGGGCTCATATAGTAGGTGCCACTGAACTACATCTT------GTTCAATTTAAAAGTTTATTAGGGTGCCGTATT -s simCow_chr6.simCow.chr6 531203 79 + 602619 TCTCCCGTGTTCTAGGGGCCTGTATTGT-GATGCTACTCAACTGTGTACC------ATTGAACTCAAAAATCCATTAGGA---TGTGAT -s simDog_chr6.simDog.chr6 519619 80 + 593897 TCTTGCGTGCTCTAGGGGCCCATATTGTGGATTCTACTCAACTACATACC------ATTTAACTTATGAACCAATTAGGG---CATGCT -s simHuman_chr6.simHuman.chr6 526594 77 + 601863 ACTCCAGTGTACTAGGGGCCCATATGCTGGGTACTACTCAGCTACATACC------ATTCAACTTAAAAGGCTGTTAGGATAA------ -s simRat_chr6.simRat.chr6 31502 83 - 647215 AAATTAGTATTCTAGGGGCTCATATAGTAGGAGCCACTGAACTACATCTT------GTTCAATTTAAAAATTTCTTGGGCTGCACTATT - -a -s simMouse_chr6.simMouse.chr6 556511 114 + 636262 GAGTGGTTTAATGTTTAGTTCAGTAATCAAATCTGTGCTAGGCAAACCTGGGTCTAATGATAGGCCATTTCAACATAAGCACAGTAAGATCAAGTTAGCACTATACCACTGATA -s Anc0.Anc0refChr3 158365 112 + 222631 TTGAGGTTCA-T-TTTGGTCCAGTAGTTGGATTTGTTCTTGGCAATCCAGTGCCCAGCAATCTGCCATTTTAACATGAGCAGAGCAGTGATAAGTCAGCACTATATCACTGAAA -s Anc1.Anc1refChr6 194571 112 + 197743 TTGAGGTTCA-T-TTTGGTCCAGTAGTTGGATTTGTTCTTGGCAATCCAGTGCCCAGCAATCTGCCATTTTAACATGAGCAGAGCAGTGATAAGTCAGCACTATATCACTGAAA -s Anc2.Anc2refChr1 72740 112 + 142988 TTGAGGTTCA-T-TTTGGTCCAGTAGACAGATTTGTTCTTGGCAATCCAGTGCCCAGCAATCTGCCATTATAACATGAGCAGAGCAGTGATAAATCAGCACTATATCACTGAAA -s mr.mrrefChr3 106502 113 + 181027 GAGTGGTTTA-TGTTTGGTTCAGTAATTGAATCTGTGCTAGGCAAACCTGGGTCTAACAATAGGCCATTTCAACATAAGCACAGCAAGATCAAGTCAGCACTATATCACTGAAA -s simCow_chr6.simCow.chr6 531282 105 + 602619 TTGAGGCTAA-T-TTTGGTGCAGTAGACAGATTTGTTCTTGGCAACCCAGTGCCCAGCAAT-TGCCATTACAACATGAGCACAGCAGTA------CAGCACTATACCACTGAAA -s simDog_chr6.simDog.chr6 519700 112 + 593897 TTGAGGTTCA-T-TTTGGTCCAGTAGACAGATTTGTTCTTGGCAATCTAGTGCCTAGCAAACTGCCATCATGACTTGCACAGAGCAGTGATAAATTAGTAACATATTGCCGGCA -s simHuman_chr6.simHuman.chr6 526671 99 + 601863 ---------------TGATCCAATATTTGGATTTGTCCTTAGCAATCCAGTGCCCAGCAATGTGCCATTTTAATATGAGCAATGCATTGATAAGTCATCACTGGATCACTGAAA -s simRat_chr6.simRat.chr6 31585 110 - 647215 GAGTGGTGCA-TGTTTGGTTCAGTAACTGAATCTATACTA--CAAACCTGAG-CTAACAATAAGCCATTTCAACCTAAATACAGCGAGCTCAAGTCAGCACTATATCACTGAAA - -a -s simMouse_chr6.simMouse.chr6 556625 20 + 636262 GTCCTACAAAGTGTTTATGT -s Anc0.Anc0refChr3 158484 20 + 222631 TCCTCCTATAGTGTTCACTT -s Anc1.Anc1refChr6 194690 20 + 197743 TCCTCCTATAGTGTTCACTT -s Anc2.Anc2refChr1 72859 20 + 142988 TCCCCCTATAGTGGTCACTC -s mr.mrrefChr3 106622 20 + 181027 GTCTTATATAGTGTTTATGT -s simCow_chr6.simCow.chr6 531394 20 + 602619 TCCCACTATAGTGGTCAATC -s simDog_chr6.simDog.chr6 519893 20 + 593897 TCCCCCTATGGTGGTCACTC -s simHuman_chr6.simHuman.chr6 526777 20 + 601863 TGCTGCTTTAGTGTTCACTT -s simRat_chr6.simRat.chr6 31702 20 - 647215 ATCTTATGTAGCATTTATGA - -a -s simMouse_chr6.simMouse.chr6 556645 34 + 636262 TGAAATCAGATTGCGATTGTAGTTTTCACTTCTT -s Anc0.Anc0refChr3 158505 34 + 222631 TGAAATAACATTGCCCCTATAGTGTTCACTTCTG -s Anc1.Anc1refChr6 194711 34 + 197743 TGAAATAACATTGCCCCTATAGTGTTCACTTCTG -s Anc2.Anc2refChr1 72880 34 + 142988 TGAAATAGCATTACCCCTATAGTGTTCACTTCTG -s mr.mrrefChr3 106642 34 + 181027 TGAAATCAGATTGCGACTGTAGTTTTCACTTCTT -s simCow_chr6.simCow.chr6 531415 33 + 602619 TGAAATAC-AGTCGCACTATAGTGTTCACTTCTG -s simDog_chr6.simDog.chr6 519914 34 + 593897 TGAAGTAGCATTACCCCTATAGAGTTCACTTCAG -s simHuman_chr6.simHuman.chr6 526798 34 + 601863 TGAAATAACCTTGCCCCTATAGTGTTCACTTATG -s simRat_chr6.simRat.chr6 31722 34 - 647215 TGGAGTCAGATTGCAACTGTAATTTTCACTTCTT - -a -s simMouse_chr6.simMouse.chr6 556679 38 + 636262 TACAACACAACGAAACTCCTAGATTGTCTGGCACATGC -s Anc0.Anc0refChr3 158542 35 + 222631 TTCAA---CACCAAACTCCTAGTTTGTCTTGCGGCAAC -s Anc1.Anc1refChr6 194748 35 + 197743 TTCAA---CACCAAACTCCTAGTTTGTCTTGCGGCAAC -s Anc2.Anc2refChr1 72917 35 + 142988 TTCCA---CACCAAACTCCTAGTTTGTCTTGTGGCAAC -s mr.mrrefChr3 106676 35 + 181027 TTCAA---AACGAAACTCCTAGATTGTCTGGCACATAC -s simCow_chr6.simCow.chr6 531451 35 + 602619 TTCCA---CACCAAACTCCTAGTTTGTCTTGTGGCAAC -s simDog_chr6.simDog.chr6 519951 9 + 593897 TTCCA---TACC-------------------------- -s simHuman_chr6.simHuman.chr6 526835 35 + 601863 TTCAA---CACTAAACTCCTAGTTTCTCTTACTTGAAC -s simRat_chr6.simRat.chr6 31756 35 - 647215 TTCAA---AACAAAGCTTCTAGATTGTCTGGCACATAC - -a -s simMouse_chr6.simMouse.chr6 556717 3 + 636262 TTT -s Anc0.Anc0refChr3 158582 3 + 222631 TTG -s Anc1.Anc1refChr6 194788 3 + 197743 TTG -s Anc2.Anc2refChr1 72957 3 + 142988 TTG -s mr.mrrefChr3 106711 3 + 181027 TTT -s simCow_chr6.simCow.chr6 531491 3 + 602619 TTG -s simHuman_chr6.simHuman.chr6 526875 3 + 601863 TTG -s simRat_chr6.simRat.chr6 31791 3 - 647215 TTT - -a -s simMouse_chr6.simMouse.chr6 556720 1 + 636262 C -s Anc0.Anc0refChr3 158585 1 + 222631 C -s Anc1.Anc1refChr6 194791 1 + 197743 C -s Anc2.Anc2refChr1 72960 1 + 142988 C -s mr.mrrefChr3 106714 1 + 181027 C -s simCow_chr6.simCow.chr6 531496 1 + 602619 C -s simHuman_chr6.simHuman.chr6 526878 1 + 601863 C -s simRat_chr6.simRat.chr6 31794 1 - 647215 C - -a -s simMouse_chr6.simMouse.chr6 556721 17 + 636262 TTTGACAAGTTCAACAA -s Anc0.Anc0refChr3 158588 17 + 222631 TTCGACAAGTTCAACAA -s Anc1.Anc1refChr6 194794 17 + 197743 TTCGACAAGTTCAACAA -s Anc2.Anc2refChr1 72963 17 + 142988 TTCAACAAGTTCACCAA -s mr.mrrefChr3 106715 17 + 181027 TTTGACAAGTTCAACAA -s simCow_chr6.simCow.chr6 531499 17 + 602619 TTCAACAAGTTCACCAA -s simHuman_chr6.simHuman.chr6 526881 17 + 601863 TTCGACAAGTTCAACAA -s simRat_chr6.simRat.chr6 31795 17 - 647215 TTTGACAAGTTCAACTA - -a -s simMouse_chr6.simMouse.chr6 556738 28 + 636262 ATTAGGAACTCAAACACCTGATCCTTAC -s Anc0.Anc0refChr3 158605 28 + 222631 GGTAGGAACTCTAACATCTGAATCTTCC -s Anc1.Anc1refChr6 194811 28 + 197743 GGTAGGAACTCTAACATCTGAATCTTCC -s Anc2.Anc2refChr1 72980 28 + 142988 GGTCCAAATTCTAACATCTAAATCACCC -s mr.mrrefChr3 106732 28 + 181027 ATTAGGAACTCAAACACCTGATCCTTAC -s simCow_chr6.simCow.chr6 531516 28 + 602619 GGTCCAAATTCTAACATCTAAATCACCC -s simHuman_chr6.simHuman.chr6 526899 28 + 601863 GGTAGGAACTTCAACATGTGAATCTTGT -s simRat_chr6.simRat.chr6 31812 28 - 647215 ATTAGGAATTCAAACACCTGATCCTTAC - -a -s simMouse_chr6.simMouse.chr6 556766 13 + 636262 TTGCTTTAGTACC -s Anc0.Anc0refChr3 158634 11 + 222631 AGGCC--GTTACC -s Anc1.Anc1refChr6 194840 13 + 197743 AGGCCCAGTTACC -s Anc2.Anc2refChr1 73009 11 + 142988 AGGCC--GTTACC -s mr.mrrefChr3 106761 13 + 181027 TGGCCTTAGTACC -s simCow_chr6.simCow.chr6 531545 11 + 602619 AGGCC--GTTACC -s simHuman_chr6.simHuman.chr6 526928 13 + 601863 GGGCCCAGTTGCC -s simRat_chr6.simRat.chr6 31841 13 - 647215 TGGCCTTAGTACC - -a -s simMouse_chr6.simMouse.chr6 556779 14 + 636262 CTCTGTTACCCATT -s Anc0.Anc0refChr3 158645 14 + 222631 CATTGTTGCCCATT -s Anc1.Anc1refChr6 194853 14 + 197743 CATTGTTGCCCATT -s Anc2.Anc2refChr1 73020 14 + 142988 CATTGCTGCCCATT -s mr.mrrefChr3 106774 14 + 181027 CACTGTTACCCATT -s simCow_chr6.simCow.chr6 531559 14 + 602619 CATTGCTGCCCGTT -s simDog_chr6.simDog.chr6 519960 9 + 593897 -----CTACCCATT -s simHuman_chr6.simHuman.chr6 526941 14 + 601863 TATTGTTGCCCATT -s simRat_chr6.simRat.chr6 31854 14 - 647215 CACTGTTATCCATT - -a -s simMouse_chr6.simMouse.chr6 556793 29 + 636262 CATAGCTTGCTATTGCAACTTGCCACCAT -s Anc0.Anc0refChr3 158659 25 + 222631 CATGGCTTACTATTGTAACTAGCC----T -s Anc1.Anc1refChr6 194867 25 + 197743 CATGGCTTACTATTGTAACTAGCC----T -s Anc2.Anc2refChr1 73034 25 + 142988 CATGGCTTACTATTGTAACTAGCC----T -s mr.mrrefChr3 106788 29 + 181027 CATGGCTTGCTATTGCAACTTGCCACCAT -s simCow_chr6.simCow.chr6 531573 25 + 602619 CATGGATTACTAGTACAACTAGCC----T -s simDog_chr6.simDog.chr6 519969 25 + 593897 CATGACTTACTATTGTATCTAGCC----C -s simHuman_chr6.simHuman.chr6 526955 25 + 601863 GATGGCTTACTGTTGTTACTAGCC----T -s simRat_chr6.simRat.chr6 31869 29 - 647215 CATGGCTTGCTATTGCAACTTGTCACCAA - -a -s simMouse_chr6.simMouse.chr6 556822 14 + 636262 ACTGTTGATTTCCA -s Anc0.Anc0refChr3 158684 6 + 222631 ACC--------CTA -s Anc1.Anc1refChr6 194892 6 + 197743 ACC--------CTA -s Anc2.Anc2refChr1 73059 6 + 142988 ACC--------CTA -s mr.mrrefChr3 106817 14 + 181027 ACCGTTGATTTCCA -s simCow_chr6.simCow.chr6 531598 6 + 602619 ACC--------CTA -s simDog_chr6.simDog.chr6 519994 6 + 593897 ACC--------ATA -s simHuman_chr6.simHuman.chr6 526980 6 + 601863 ACC--------CTA -s simRat_chr6.simRat.chr6 31901 14 - 647215 ACCGCAGATTTCCA - -a -s simMouse_chr6.simMouse.chr6 556836 5 + 636262 ACTGC -s Anc0.Anc0refChr3 158690 5 + 222631 ATTCC -s Anc1.Anc1refChr6 194898 5 + 197743 ATTCC -s Anc2.Anc2refChr1 73065 5 + 142988 ATTCC -s mr.mrrefChr3 106831 5 + 181027 ACTGC -s simCow_chr6.simCow.chr6 531604 5 + 602619 ATCTC -s simDog_chr6.simDog.chr6 520000 5 + 593897 ATTCC -s simHuman_chr6.simHuman.chr6 526986 2 + 601863 AT--- -s simRat_chr6.simRat.chr6 31986 5 - 647215 ACTGC - -a -s simMouse_chr6.simMouse.chr6 556841 27 + 636262 TTGGCTGTAGATGGTACGAGTATATAA -s Anc0.Anc0refChr3 158695 27 + 222631 TTGGCTGTAAATGGCATGATTATATGT -s Anc1.Anc1refChr6 194903 27 + 197743 TTGGCTGTAAATGGCATGATTATATGT -s Anc2.Anc2refChr1 73095 27 + 142988 TTGGCTGTAAATGGCCTGATTATAGGT -s mr.mrrefChr3 106836 27 + 181027 TTGGCTGTAGATGGTACGATTATATAA -s simCow_chr6.simCow.chr6 531634 27 + 602619 TTGGGTGTAAATGGCTTAACTGCACGT -s simDog_chr6.simDog.chr6 520030 27 + 593897 TTGGCTGTAAATCACCTGGTTATAGGT -s simHuman_chr6.simHuman.chr6 526988 24 + 601863 ---ACTGTAAATGGCATGATTATATGT -s simRat_chr6.simRat.chr6 31991 27 - 647215 TTGGCTGTAGATGGTACGATTATATAA - -a -s simMouse_chr6.simMouse.chr6 556868 34 + 636262 TTGTGTATGTTATTTAGCAGACAAAGAGTTATCA -s Anc0.Anc0refChr3 158738 20 + 222631 T--------------AACAGATACAGAGTAATCA -s Anc1.Anc1refChr6 194946 20 + 197743 T--------------AACAGATACAGAGTAATCA -s Anc2.Anc2refChr1 73138 20 + 142988 T--------------AACAGATACAGAGTAACCA -s mr.mrrefChr3 106863 20 + 181027 T--------------AGCAGACAAAGAGTTATCA -s simCow_chr6.simCow.chr6 531678 20 + 602619 C--------------AACAGATACAGAGTGAGCT -s simDog_chr6.simDog.chr6 520073 20 + 593897 T--------------AACAGACACAGAGTAACCA -s simHuman_chr6.simHuman.chr6 527028 20 + 601863 T--------------AACAGATCCAGAGTCTTCA -s simRat_chr6.simRat.chr6 32018 20 - 647215 T--------------AGCAGACAAAGAGTTATCA - -a -s simMouse_chr6.simMouse.chr6 556902 12 + 636262 AGTACAATGTAG -s Anc0.Anc0refChr3 158760 10 + 222631 AGAACCATGT-- -s Anc1.Anc1refChr6 194968 12 + 197743 AGAACCATGTAG -s Anc2.Anc2refChr1 73160 10 + 142988 AGAATAACGT-- -s mr.mrrefChr3 106883 12 + 181027 AGTACCATGTAG -s simCow_chr6.simCow.chr6 531700 10 + 602619 AAAAGAATGT-- -s simDog_chr6.simDog.chr6 520095 10 + 593897 TGAATAACGT-- -s simHuman_chr6.simHuman.chr6 527050 12 + 601863 AGAACCATACAT -s simRat_chr6.simRat.chr6 32038 12 - 647215 AGTACCATATGG - -a -s simMouse_chr6.simMouse.chr6 556914 40 + 636262 ACCTTAACTCATACAACTGGGACTATTGTTACACTGGATA -s Anc0.Anc0refChr3 158770 40 + 222631 GGCTAAACCCAAAAAATTGAGGATATTGTCAGAATGGATA -s Anc1.Anc1refChr6 194980 40 + 197743 GGCTAAACCCAAAAAATTGAGGATATTGTCAGAATGGATA -s Anc2.Anc2refChr1 73170 40 + 142988 GGCCAAACACAAAAAATTAAGGATATTGTCAGAATGAATA -s mr.mrrefChr3 106895 40 + 181027 AGCTTAACCCATACAATTGGGACTATTGTTACAATGGATA -s simCow_chr6.simCow.chr6 531710 39 + 602619 GGCCAAACACAAACAATTCAGGATTTTGTCACAA-GAATA -s simDog_chr6.simDog.chr6 520105 37 + 593897 GGCC---CACGAAAAATTAAGGGTATTGTCAGAATGAATA -s simHuman_chr6.simHuman.chr6 527163 40 + 601863 GGCTGAACCCAAAAAATTGAGGATATTGTCATAATGGACA -s simRat_chr6.simRat.chr6 32050 40 - 647215 AGCTTAACCCTTGCAATTGGGACTATTGTTACAATGGATT - -a -s simMouse_chr6.simMouse.chr6 556954 18 + 636262 TGGAACCACCAAATTGCC -s Anc0.Anc0refChr3 158811 18 + 222631 TGGCACAACCAGATTGCA -s Anc1.Anc1refChr6 195021 18 + 197743 TGGCACAACCAGATTGCA -s Anc2.Anc2refChr1 73211 18 + 142988 TGGCACAACCAGATTGCA -s mr.mrrefChr3 106935 18 + 181027 TGGAACAACCAAATTGCC -s simCow_chr6.simCow.chr6 531750 18 + 602619 TGGCACAACCAGATTGCA -s simDog_chr6.simDog.chr6 520143 18 + 593897 TGGCACAACCAGATTGCA -s simHuman_chr6.simHuman.chr6 527204 18 + 601863 TGGCACAGCCTGATTGCA -s simRat_chr6.simRat.chr6 32090 18 - 647215 TGGGACACCCAAATTGCC - -a -s simMouse_chr6.simMouse.chr6 556972 88 + 636262 AATGGGCTGTTGATAAAATAGGAGAGAACATGGAGGGGGTCTTCTGCCTATCACAGTTAAGGAGGAGGGTATGCATTTGAGACAAAAC -s Anc0.Anc0refChr3 158829 86 + 222631 AATGGTTGTGTAGTAAGGAAGGAGGAAACATGATGGGGG-CTTTTGGCTTTTGCAGTTAAAGTG-AGGCCATGGATTTGAGAAGGAAC -s Anc1.Anc1refChr6 195039 87 + 197743 AATGGTTGTGTAGTAAGGAAGGAGGAAACATGATGGGGG-CTTTTGGCTTTTGCAGTTAAAGTGCAGGCCATGGATTTGAGAAGGAAC -s Anc2.Anc2refChr1 73229 86 + 142988 AATGGTTGTGTAGTGAGGAAGGAGGAAATGTGATGGGGG-CTTTTGGCTTTTGCAGTTAAAGTG-AGGCCATGGATTTGAGAAGGAAC -s mr.mrrefChr3 106953 87 + 181027 AATGGGCTGTTGGTAAAATAGGAGAGAACATGGAGGGGG-CTTTTGCCTTTTACAGTTAAGGAGGAGGGCATGCATTTGAGACAAAAC -s simCow_chr6.simCow.chr6 531783 85 + 602619 AATGAGTGTGTATT-AGGAAGGAGGAAATGTGATGGGGC-CTGTTAGCTTATGCACCTAATGTG-AGGCCATATATTTGAGAAGGAAC -s simDog_chr6.simDog.chr6 520161 85 + 593897 AGTGGTTCAGTAGTGAGG-CGGAGGGAATGCAATGGGGG-CCTTTGGCTTTTATTGTTAAAGTG-AGGCCATGGGATTGAGAAGGAAC -s simHuman_chr6.simHuman.chr6 527222 87 + 601863 AATGGATGTGTAGTAAGGAAGGAGGACACATGATGGGGG-CTTTTGTCTTTTGCAGTTGAAGTGCAGGCCATGGATTTGAGTAGGAAC -s simRat_chr6.simRat.chr6 32108 84 - 647215 AATGGGCTGTTGGTAAAATGGGAGAGAACATGGAGGGGG-CTTTTGCCTTTTACAGTTAATGAAGAGGGC---CATTTGAGACCAAAC - -a -s simMouse_chr6.simMouse.chr6 557060 8 + 636262 ATTGGTGG -s Anc0.Anc0refChr3 158916 8 + 222631 ACAACTTT -s Anc1.Anc1refChr6 195127 8 + 197743 ACAACTTT -s Anc2.Anc2refChr1 73316 8 + 142988 ACAACTTT -s mr.mrrefChr3 107041 8 + 181027 ATTGGTGC -s simCow_chr6.simCow.chr6 531869 8 + 602619 TCAACTTG -s simDog_chr6.simDog.chr6 520247 8 + 593897 ACAACTTT -s simHuman_chr6.simHuman.chr6 527310 8 + 601863 ACAACTTT -s simRat_chr6.simRat.chr6 32193 8 - 647215 ACTGGTGC - -a -s simMouse_chr6.simMouse.chr6 557068 17 + 636262 AATTTCTCAAAATAAAC -s Anc0.Anc0refChr3 158927 17 + 222631 ACTTTCTCAAAATACCA -s Anc1.Anc1refChr6 195138 17 + 197743 ACTTTCTCAAAATACCA -s Anc2.Anc2refChr1 73327 17 + 142988 ACTCTCTCAAAATACCA -s mr.mrrefChr3 107049 17 + 181027 AATTTCTCAAAATAAAA -s simCow_chr6.simCow.chr6 531880 17 + 602619 ACTCTCTTAAAATACCA -s simDog_chr6.simDog.chr6 520258 17 + 593897 ACTCTCTCAAATTACCA -s simHuman_chr6.simHuman.chr6 527321 17 + 601863 ACCTTCACAAAATACTA -s simRat_chr6.simRat.chr6 32201 17 - 647215 AATTTCTCAAAATAAAA - -a -s simMouse_chr6.simMouse.chr6 557085 3 + 636262 TCC -s Anc0.Anc0refChr3 158944 3 + 222631 TGC -s Anc1.Anc1refChr6 195155 3 + 197743 TGC -s Anc2.Anc2refChr1 73344 3 + 142988 TGT -s mr.mrrefChr3 107066 3 + 181027 TCC -s simCow_chr6.simCow.chr6 531912 3 + 602619 TGT -s simDog_chr6.simDog.chr6 520275 3 + 593897 TGT -s simHuman_chr6.simHuman.chr6 527338 3 + 601863 TGC -s simRat_chr6.simRat.chr6 32218 3 - 647215 TCC - -a -s simMouse_chr6.simMouse.chr6 557088 12 + 636262 TGGATAACCACA -s Anc0.Anc0refChr3 158958 12 + 222631 CACATAACCATG -s Anc1.Anc1refChr6 195169 12 + 197743 CACATAACCATG -s Anc2.Anc2refChr1 73358 12 + 142988 CACATAACCATG -s mr.mrrefChr3 107069 12 + 181027 TGGATAACCACA -s simCow_chr6.simCow.chr6 531926 12 + 602619 TACAAAGCTAGG -s simDog_chr6.simDog.chr6 520289 12 + 593897 CACATAACCCTC -s simHuman_chr6.simHuman.chr6 527352 12 + 601863 CACACAACCATG -s simRat_chr6.simRat.chr6 32221 12 - 647215 TGGATGACCAAA - -a -s simMouse_chr6.simMouse.chr6 557100 5 + 636262 GATTG -s Anc0.Anc0refChr3 158986 5 + 222631 GAGTG -s Anc1.Anc1refChr6 195197 5 + 197743 GAGTG -s Anc2.Anc2refChr1 73386 5 + 142988 GAGTG -s mr.mrrefChr3 107081 5 + 181027 GATTG -s simCow_chr6.simCow.chr6 531952 5 + 602619 GGGTG -s simDog_chr6.simDog.chr6 520317 5 + 593897 AAGTG -s simHuman_chr6.simHuman.chr6 527380 5 + 601863 GTGTG -s simRat_chr6.simRat.chr6 32233 5 - 647215 GATTG - -a -s simMouse_chr6.simMouse.chr6 557105 13 + 636262 GGTTTTAACAAAG -s Anc0.Anc0refChr3 158991 8 + 222631 AGT-----CATGC -s Anc1.Anc1refChr6 195202 8 + 197743 AGT-----CATGC -s Anc2.Anc2refChr1 73391 8 + 142988 AGT-----CATGC -s mr.mrrefChr3 107086 13 + 181027 GGTTCTAACAAAG -s simCow_chr6.simCow.chr6 531957 5 + 602619 AGT-----CA--- -s simDog_chr6.simDog.chr6 520325 8 + 593897 AGT-----CATGC -s simHuman_chr6.simHuman.chr6 527385 8 + 601863 AGT-----CATGC -s simRat_chr6.simRat.chr6 32238 13 - 647215 GGTTCTAACAGAG - -a -s simMouse_chr6.simMouse.chr6 557118 29 + 636262 ATCATTATGACTGGCCCCATGGAAGGGCA -s Anc0.Anc0refChr3 158999 29 + 222631 ACTATTATGACAGGCCCCAAGGAAAGCCG -s Anc1.Anc1refChr6 195210 29 + 197743 ACTATTATGACAGGCCCCAAGGAAAGCCG -s Anc2.Anc2refChr1 73399 29 + 142988 ACTATTATGTCAGTCCCCAAGGAAAGCCG -s mr.mrrefChr3 107099 29 + 181027 ATCATCATGACTGGCCCCATGGAAGGGCA -s simCow_chr6.simCow.chr6 531962 29 + 602619 ACTATTATGTCAGACCCCAAGCCAAGTCA -s simDog_chr6.simDog.chr6 520333 24 + 593897 -----CTTGTCAGTCCCTAAGGAAAGCCG -s simHuman_chr6.simHuman.chr6 527396 23 + 601863 ACTATTATGACAGGCCCCCGGGA------ -s simRat_chr6.simRat.chr6 32251 29 - 647215 ATCATCATGACTGGCCCCATGGAAGGGCA - -a -s simMouse_chr6.simMouse.chr6 557147 52 + 636262 GGATAACTGATGCTCATATAGGGAAACAGTAAAGCGGATTTTCAAATAACAC -s Anc0.Anc0refChr3 159028 18 + 222631 A------TGATGCTCATATAG----------------------------AAT -s Anc1.Anc1refChr6 195239 18 + 197743 A------TGATGCTCATATAG----------------------------AAT -s Anc2.Anc2refChr1 73428 18 + 142988 A------TGATGCTCATATAG----------------------------AGT -s mr.mrrefChr3 107128 52 + 181027 GGATGACTGATGCTCATATAGGGAAACAGTAAAGCGGATTTTCAAATAAAAT -s simCow_chr6.simCow.chr6 531991 18 + 602619 G------TGATGCTCATATAG----------------------------AGT -s simDog_chr6.simDog.chr6 520360 18 + 593897 A------AGATGCTCATATAG----------------------------AGT -s simHuman_chr6.simHuman.chr6 527419 17 + 601863 -------TGACTTTCATATAG----------------------------AAT -s simRat_chr6.simRat.chr6 32280 52 - 647215 GGATGACTGATGCTCAGATCGGGAAACAATTAAGCCGATTCTCAAATAAAAT - -a -s simMouse_chr6.simMouse.chr6 557199 12 + 636262 CCTACCCACATA -s Anc0.Anc0refChr3 159048 10 + 222631 CATACC--CATA -s Anc1.Anc1refChr6 195259 12 + 197743 CATACCCACATA -s Anc2.Anc2refChr1 73448 10 + 142988 TATGCC--CATA -s mr.mrrefChr3 107182 12 + 181027 CATACCCACATA -s simCow_chr6.simCow.chr6 532011 10 + 602619 TCCTCC--CTTA -s simDog_chr6.simDog.chr6 520380 10 + 593897 TATGCC--CATA -s simHuman_chr6.simHuman.chr6 527438 12 + 601863 CATACCCACATA -s simRat_chr6.simRat.chr6 32334 12 - 647215 CATACCCACATA - -a -s simMouse_chr6.simMouse.chr6 557211 34 + 636262 CCATGTTAAAATAGAGGGCCCCATTAGATCTCAT -s Anc0.Anc0refChr3 159059 34 + 222631 TCACATTAAAATAGAGAGCCCCAGTAGCTCTTAT -s Anc1.Anc1refChr6 195272 34 + 197743 TCACATTAAAATAGAGAGCCCCAGTAGCTCTTAT -s Anc2.Anc2refChr1 73459 34 + 142988 TCACATTAAAATGGAGAGGCCCAGTAGCTCTTAC -s mr.mrrefChr3 107194 34 + 181027 CCATGTTAAAATAGAGGGCCCCATTAGATCTCAT -s simCow_chr6.simCow.chr6 532022 33 + 602619 CTACATTCAAATGGAGAGGCCCAATAGTTCTTA- -s simDog_chr6.simDog.chr6 520391 34 + 593897 TCACATTAAATTGGAGAGGCTCAGTAGCTCTGAC -s simHuman_chr6.simHuman.chr6 527451 34 + 601863 TCACATTAAAAGAGAGAGCCCCAGTAGCTCTTAT -s simRat_chr6.simRat.chr6 32346 34 - 647215 CCATCTCAAAATGGAGGGACCCACTAGATCTCAC - -a -s simMouse_chr6.simMouse.chr6 557245 8 + 636262 CAGAGTTC -s Anc0.Anc0refChr3 159094 8 + 222631 CAGAGTTC -s Anc1.Anc1refChr6 195307 8 + 197743 CAGAGTTC -s Anc2.Anc2refChr1 73494 8 + 142988 CAGAGTTC -s mr.mrrefChr3 107228 8 + 181027 CAGAGTTC -s simCow_chr6.simCow.chr6 532055 8 + 602619 CAGAGTCT -s simDog_chr6.simDog.chr6 520426 8 + 593897 CAGAGTTC -s simHuman_chr6.simHuman.chr6 527486 8 + 601863 CAAAGTTC -s simRat_chr6.simRat.chr6 32380 8 - 647215 CAGAGTTC - -a -s simMouse_chr6.simMouse.chr6 557253 39 + 636262 TTACAACAATCACCCTCTAATCAAGTTTTGTAGTGTGAC -s Anc0.Anc0refChr3 159128 22 + 222631 T---------------CTAATC-AGTTTTGTGGAG-GAC -s Anc1.Anc1refChr6 195341 38 + 197743 TTACCACAATCCCCCCCTAATCAAGTTTTGTGGAG-GAC -s Anc2.Anc2refChr1 73548 22 + 142988 T---------------CTGATC-AGTTTTGTGAAT-TGT -s mr.mrrefChr3 107236 39 + 181027 TTACCACAATCACCCTCTAATCAAGTTTTGTAGTGTGAC -s simCow_chr6.simCow.chr6 532106 22 + 602619 T---------------CTGCTC-AGTCATGTGAAT-TGT -s simDog_chr6.simDog.chr6 520479 22 + 593897 T---------------CTGATC-AGTTTTGTGAAT-TGT -s simHuman_chr6.simHuman.chr6 527520 36 + 601863 TTACCACAATCCCCCCAGAA--AAGTTTTGTGGAG-GAC -s simRat_chr6.simRat.chr6 32388 39 - 647215 TTACCACAATCACCCTCTGATCAAGTTTTGTTGCGTGAC - -a -s simMouse_chr6.simMouse.chr6 557292 8 + 636262 ACCATTTT -s Anc0.Anc0refChr3 159150 8 + 222631 ACCATTTA -s Anc1.Anc1refChr6 195379 8 + 197743 ACCATTTA -s Anc2.Anc2refChr1 73570 8 + 142988 ACCATTTA -s mr.mrrefChr3 107275 8 + 181027 ACCATTTT -s simCow_chr6.simCow.chr6 532130 8 + 602619 ACCACCCA -s simDog_chr6.simDog.chr6 520501 7 + 593897 AC-ATTTT -s simHuman_chr6.simHuman.chr6 527556 8 + 601863 ACTATTTA -s simRat_chr6.simRat.chr6 32427 8 - 647215 ACCAGTTT - -a -s simMouse_chr6.simMouse.chr6 557300 27 + 636262 CTTCTAGGAGATGCATTTCTTGCTTTA -s Anc0.Anc0refChr3 159158 25 + 222631 A--CCAGGAGATGCATTTCTTGATTTA -s Anc1.Anc1refChr6 195387 25 + 197743 A--CCAGGAGATGCATTTCTTGATTTA -s Anc2.Anc2refChr1 73580 25 + 142988 A--CCAGGAGATGCATTTCTTGATTTC -s mr.mrrefChr3 107283 27 + 181027 CTTCTAGGAGATGCATTTCTTGCTTTA -s simCow_chr6.simCow.chr6 532140 25 + 602619 A--CCAGGAGATACAATTCTTGATTTT -s simDog_chr6.simDog.chr6 520510 25 + 593897 A--GTAGGAGATGCATTTATTGATTTC -s simHuman_chr6.simHuman.chr6 527564 25 + 601863 A--CCAGGAGATGCATTTCTTGATTCA -s simRat_chr6.simRat.chr6 32435 27 - 647215 CTTCTGGGAGATGCAGTTCTTGCTTTA - -a -s simMouse_chr6.simMouse.chr6 557327 82 + 636262 AACCAAGTATCTGTAAAATTGCAAGCTACAGAAGTTCAAATAAGCATAGTTGCACGAAGTGATTAAGGTGTCAGATATTATA -s Anc0.Anc0refChr3 159183 82 + 222631 ATCCAAGTATCTATCAAGTTATAATCTACAGAAATTCTCATAAGCATAGCTGCATAAAGTTATTAAGGTGTGTAATATTATA -s Anc1.Anc1refChr6 195412 82 + 197743 ATCCAAGTATCTATCAAGTTATAATCTACAGAAATTCTCATAAGCATAGCTGCATAAAGTTATTAAGGTGTGTAATATTATA -s Anc2.Anc2refChr1 73605 82 + 142988 ATCCAAGTATCTATCAAGTTATAATCTACAGAAACTCTCATAAGCATAGCTGCATAAAGTGACAAAGGCTTTTAATATTATA -s mr.mrrefChr3 107310 82 + 181027 AACCAAGTATCTGTAAAATTGCAATCTACAGAAGTTCAAATAAGCATAGCTGCACAAAGTTATTAAGGTGTGAAATATTATA -s simCow_chr6.simCow.chr6 532166 72 + 602619 ATCTGACTATCTATCAAGTTATA--CTACAGAAAATCTCACAACTATAGCTGACTAAA------AAGGCT--TAATATTATA -s simDog_chr6.simDog.chr6 520535 82 + 593897 ATCCAAGGATCTCTCAAGTTATAATCTACAGAGACTCTCATAAGCATAGCTGCACAAAGTGACAAAGGCTTTAAATATTATG -s simHuman_chr6.simHuman.chr6 527589 82 + 601863 TTCCAAGTATCTATCAAGTTATAATCTACTGAAATTCTGATATGCATGGCTGGGTACAGTTATTAAGGTGTGTAATATTATA -s simRat_chr6.simRat.chr6 32462 82 - 647215 GACCAAGTATCTCTGAAATTGCAATCTACAGAAGTTCAAGTAAGCATAGCCGCACAAAGTTATTAAGGTGTGAAATATTATA - -a -s simMouse_chr6.simMouse.chr6 557409 138 + 636262 CTAGATACTAATTATGCCGCCATGCAGATGTCTACATTTGTTAAGCCTTGATCCGCAAAAACCAGCAGCCTCACGACACTGGGTTACATCAAAGCCAGAATGAAATCCTACCCAACCAATGTATTGGAATGAAAAAGA -s Anc0.Anc0refChr3 159281 133 + 222631 CCAGATATTATTTTTGCCG---TGCACATCTTTACATTCATTAGGC-TTGGTCTGCAAAAATCAGCAGCATCATGAAGCTGACTTACATCAAAGCCAGAATGGCAATCCA-CCAACCGATGTATTGACATGAGATACA -s Anc1.Anc1refChr6 195510 134 + 197743 CCAGATATTATTTTTGCCG---TGCACATCTTTACATTCATTAGGC-TTGGTCTGCAAAAATCAGCAGCATCATGAAGCTGACTTACATCAAAGCCAGAATGGCAATCCACCCAACCGATGTATTGACATGAGATACA -s Anc2.Anc2refChr1 73703 133 + 142988 CCAGATATTATTTTAGCCG---TGCACATCTTTACATTCACTAGGC-TTGGTCTGCAAAAATCAGGAACAACATGGAACTCACTTACATCAAAGCCAGAATGGCAATCCA-CCAACCGTTTTATTGACATGAGATACA -s mr.mrrefChr3 107392 138 + 181027 CCAGATACTAATTATGCCGCCATGCAGATGTCTACATTTGTTAAGCCTTGATCCGCAAAAACCAGCAGCCTCATGACGCTGGGTTACATCAAAGCCAGAATGAAATCCTACCCAACCAATGTATTGGAATGAGAAAGA -s simCow_chr6.simCow.chr6 532254 90 + 602619 CCAGGCATTATTTTGGCCG---TGCAGAATTTTACATGCACTAGGT-GTAGTCTGCA---ACTAGGAACAACATGGAACTCACTTACAGCAAAGCCA----------------------------------------- -s simDog_chr6.simDog.chr6 520633 133 + 593897 CCAAATATAACTTCAGTCA---CATGCATCTTTACATTCACTAAGC-TTGGTCTGCAAAAATCGTGAACAACATGGAACTCACCTACATCAAAGCCTGAATGGCAATCCA-CCAACCGTTTTATTGACATGAGATACA -s simHuman_chr6.simHuman.chr6 527687 133 + 601863 CCAGATATTATTCTTGCCG---TGCAAATCCTTACATTCATTAGGC-TTGCTCTACTAACATCAGCAGCATCATGA-GATGACTTACACAAAAGCCAGAACGGGCATCCACCCAACTGATGTATTGATATGAGATACA -s simRat_chr6.simRat.chr6 32611 138 - 647215 CCAGATACTACTTATGCCGCCATGTAGATGTCCATATTTGTTAAGCCTTAATCCGCAAAAACCAGCAGCCTCATGACGCTGGGTTACATCAAAGCCAGGATGAAATACTACCCAACCAATGTCTTGGGATGAGGAAGA - -a -s simMouse_chr6.simMouse.chr6 557547 7 + 636262 AAGTACC -s Anc0.Anc0refChr3 159414 6 + 222631 TA-TACT -s Anc1.Anc1refChr6 195644 6 + 197743 TA-TACT -s Anc2.Anc2refChr1 73836 6 + 142988 TA-CATT -s mr.mrrefChr3 107530 6 + 181027 AA-TACT -s simDog_chr6.simDog.chr6 520769 6 + 593897 TA-CATT -s simHuman_chr6.simHuman.chr6 527820 6 + 601863 TA-TACT -s simRat_chr6.simRat.chr6 32749 4 - 647215 AA---CT - -a -s simMouse_chr6.simMouse.chr6 557554 16 + 636262 TTTATGAGCTACTATG -s Anc0.Anc0refChr3 159423 16 + 222631 TGTATGAACAACTCTG -s Anc1.Anc1refChr6 195653 16 + 197743 TGTATGAACAACTCTG -s Anc2.Anc2refChr1 73845 16 + 142988 TGTATGAACAACACTG -s mr.mrrefChr3 107536 16 + 181027 TTTATGAGCTACTATG -s simDog_chr6.simDog.chr6 520778 16 + 593897 TGTATGAACAACACTG -s simHuman_chr6.simHuman.chr6 527829 16 + 601863 TGTGTGAACAACTCTG -s simRat_chr6.simRat.chr6 32753 16 - 647215 TTTATAAGCTATTATT - -a -s simMouse_chr6.simMouse.chr6 557570 13 + 636262 TGAGCATAAGGGT -s Anc0.Anc0refChr3 159442 13 + 222631 TAACCACAAGGGT -s Anc1.Anc1refChr6 195672 13 + 197743 TAACCACAAGGGT -s Anc2.Anc2refChr1 73864 13 + 142988 TACCCACAAAGGT -s mr.mrrefChr3 107552 13 + 181027 TGAGCATAAGGGT -s simCow_chr6.simCow.chr6 532344 2 + 602619 -----------GT -s simDog_chr6.simDog.chr6 520797 13 + 593897 TACCCACAAAGGT -s simHuman_chr6.simHuman.chr6 527848 13 + 601863 TAACCAGGAGGGT -s simRat_chr6.simRat.chr6 32769 13 - 647215 TGAGCATAAGGGT - -a -s simMouse_chr6.simMouse.chr6 557583 19 + 636262 GCCCCTTGTGTAGTTTTCT -s Anc0.Anc0refChr3 159455 14 + 222631 GCCCC-----TAGTGTTAT -s Anc1.Anc1refChr6 195685 19 + 197743 GCCCCTTGTGTAGTGTTAT -s Anc2.Anc2refChr1 73877 14 + 142988 TGCCC-----TGGTGTTAT -s mr.mrrefChr3 107565 19 + 181027 GCCCCTTGTGTAGTTTTCT -s simCow_chr6.simCow.chr6 532352 14 + 602619 TGCCC-----TCGTGTTTT -s simDog_chr6.simDog.chr6 520810 14 + 593897 TGGCC-----TGGTGTCAT -s simHuman_chr6.simHuman.chr6 527861 19 + 601863 GCCCCCTGTTCAGTGTTGT -s simRat_chr6.simRat.chr6 32782 19 - 647215 GCCCCTTGTGTAGTTTTCT - -a -s simMouse_chr6.simMouse.chr6 557602 48 + 636262 GGTCCGAAGAACTCTTAATGGTCATCTCTGAAGATCATGGTCCTCCTC -s Anc0.Anc0refChr3 159487 33 + 222631 --TCTGAAGATCTATAAATG-------------ATTATGGCCCACTCC -s Anc1.Anc1refChr6 195722 33 + 197743 --TCTGAAGATCTATAAATG-------------ATTATGGCCCACTCC -s Anc2.Anc2refChr1 73909 33 + 142988 --TCTTAAGATCTATAAATG-------------TCTATGGCCCACTAC -s mr.mrrefChr3 107603 48 + 181027 GGTCCGAAGATCTCTTAATGGTCATCTCTGAAGATCATGGTCCTCCCC -s simCow_chr6.simCow.chr6 532379 33 + 602619 --TCTTAAGATCTGTAAATC-------------TGCATGACCCACTAC -s simDog_chr6.simDog.chr6 520842 33 + 593897 --TCTTAAGATATACTGATG-------------TCTATGGCCCACTAT -s simHuman_chr6.simHuman.chr6 527898 33 + 601863 --TCTGGAGATCTATAAATG-------------ATAATGGCCCACTCC -s simRat_chr6.simRat.chr6 32832 48 - 647215 GGTCCAAAGATTTCTTAATGGTCATCTCTGAAGATCACGGAGCTCCCC - -a -s simMouse_chr6.simMouse.chr6 557650 10 + 636262 ATCAGAAGGC -s Anc0.Anc0refChr3 159522 10 + 222631 ACCAGAAGGT -s Anc1.Anc1refChr6 195757 10 + 197743 ACCAGAAGGT -s Anc2.Anc2refChr1 73944 10 + 142988 ACTAGAAGGT -s mr.mrrefChr3 107653 10 + 181027 ATCAGAAGGC -s simCow_chr6.simCow.chr6 532414 10 + 602619 ACTAGGAGTT -s simDog_chr6.simDog.chr6 520877 10 + 593897 ACTAGAAGGC -s simHuman_chr6.simHuman.chr6 527933 10 + 601863 ACCAAAAGGT -s simRat_chr6.simRat.chr6 32882 10 - 647215 GTCAGAAGGC - -a -s simMouse_chr6.simMouse.chr6 557660 8 + 636262 GATACCAG -s Anc0.Anc0refChr3 159532 8 + 222631 GAGACCTG -s Anc1.Anc1refChr6 195767 8 + 197743 GAGACCTG -s Anc2.Anc2refChr1 73954 8 + 142988 GAGACCTG -s mr.mrrefChr3 107663 8 + 181027 GAGACCAG -s simCow_chr6.simCow.chr6 532681 8 + 602619 GAGACCTG -s simDog_chr6.simDog.chr6 520887 8 + 593897 GAGACCTG -s simHuman_chr6.simHuman.chr6 527943 8 + 601863 GAGACCTG -s simRat_chr6.simRat.chr6 32892 8 - 647215 GAGACCGG - -a -s simMouse_chr6.simMouse.chr6 557668 121 + 636262 TTCCTTAACTATTGTAGGCTATCAATGAGTCTTATTGTAACTGAAGACGGCCAATATAATAATACTAAGATAGTCCTTTGGATGGGTTTACTTGTGCTTATGCCTAAGGATAATGATTGAG -s Anc0.Anc0refChr3 159540 120 + 222631 TTACTGAAGTATTGCAGGCTATTAGTGAGTCATAT-GGTACTGAGAACAGCCAATGCAATAGTGCTAAAGTAGTCCTGTAGGCGGGCTTACTTGCGTTTGGGCCTACGGAAAATAGTTGGG -s Anc1.Anc1refChr6 195775 120 + 197743 TTACTGAAGTATTGCAGGCTATTAGTGAGTCATAT-GGTACTGAGAACAGCCAATGCAATAGTGCTAAAGTAGTCCTGTAGGCGGGCTTACTTGCGTTTGGGCCTACGGAAAATAGTTGGG -s Anc2.Anc2refChr1 73962 120 + 142988 TTACTGAAGTATTGCAGGCTATTAGTAAGTTATAT-TGTACTGAGAACATCCAATGCAATAGTGCTGAAGTAGTTGTGTAGGCAGGCTTACTTGCTTTCAGGCTTACGGAAAATAGTTGGG -s mr.mrrefChr3 107671 120 + 181027 TTCCTTAACTATTGCAGGCTATCAATGAGTCTTAT-GTAACTGAAGACAGCCAATGCAATAGTACTAAGATAGTCCTGTGGATGGGTTTACTTGTGCTTGTGCCTAAGGATAATAATTGAG -s simCow_chr6.simCow.chr6 532689 120 + 602619 TTACTGAAATATTGCAGGCTATCGGTAAGTTATAT-TGTACTGAGAACAACCAATGTAATAGTGCTGAAGTAGTTATGTAGACAGGCTTATTTGTCTTCAGGCTTACAGACAATAGGTAGG -s simDog_chr6.simDog.chr6 520903 109 + 593897 TTCCTGAAGTATTGCAAGCTACTAGTAGTTTATAT-TGTGGTGAGAACATCCAATGCAACAGTGC-----TAGTTGTGTAGGCAGGCTTACTTGCTTTCAG------GGAAAACAATTGAG -s simHuman_chr6.simHuman.chr6 527951 120 + 601863 TTACTCAAGTATTGCAGGCTATTAGTGAGTCATAT-GACACTAAGAACAGCCAATGCAATAGTGCTAGAGTAGTCCTGTTGCCGGGCTTACTTGCGTTTGGGCCTATGAAAAATAGTTGGG -s simRat_chr6.simRat.chr6 32900 118 - 647215 TTCCTTCACTATTGCAGGGTATCAATGAATCTTA--GTAACTGAAGACAACCAATGCAA-AGTACTAAGATAGGCCTGTGGATGGGTTTGCCCGTGCTTGAGCCTAAGGACAACAATTGAG - -a -s simMouse_chr6.simMouse.chr6 557789 78 + 636262 AGGGGGATTAATAAGGATCAGAGCCTACAAGTTACAGGGTGCTGACAGTGAGCCTAGGTTTGATTTCTATTAGTACAC -s Anc0.Anc0refChr3 159660 52 + 222631 ACAGGGATTCA-GAGGAGCCTGGCATACAAGTTTCAAAGTGCAGTTAGTGAGC------------------------- -s Anc1.Anc1refChr6 195895 52 + 197743 ACAGGGATTCA-GAGGAGCCTGGCATACAAGTTTCAAAGTGCAGTTAGTGAGC------------------------- -s Anc2.Anc2refChr1 74082 52 + 142988 ACAGGGATTCT-GAGGAGCCTGGCATACAAGTTTCAAAGTGTAGTTAATGAGC------------------------- -s mr.mrrefChr3 107791 78 + 181027 AGGGGGATTAATGAGGATCAGAGCCTACAAGTTACAGGGTGCTGACAGTGAGCCTAGGTTTGATTTCTATTAGTACAC -s simCow_chr6.simCow.chr6 532809 21 + 602619 ACAGGGATTCT-GAGGAGCCTG-------------------------------------------------------- -s simDog_chr6.simDog.chr6 521012 52 + 593897 ACAGGGATTCT-GAAGAGCCAGGCATACAAGTTTCAAAGTGTAGTTAATGAGC------------------------- -s simHuman_chr6.simHuman.chr6 528072 52 + 601863 ACAGGGACTCA-GAGGAGCCTGGCTTGCAAGTATCAAAGCGCAGTAAGTGAGC------------------------- -s simRat_chr6.simRat.chr6 33018 78 - 647215 AGGGGGATTAATGAGGATCTGAGCCTATAAGTTACAGGGTGCTGGCAATGAGCCTAGGTATGGTTTCTATTAGTACAC - -a -s simMouse_chr6.simMouse.chr6 557867 52 + 636262 CGCTTGCCCCACATATTAATCTATGTTGAGCCTCAGAGGCTTGCATGTGCAC -s mr.mrrefChr3 107869 46 + 181027 CGCTTGCCCCACATATTAATCTATGTTG-GCCTCAGAGG-----ATGTGCAC -s simRat_chr6.simRat.chr6 33102 46 - 647215 CCCTTGCCCCACATGTTAATCTATGTAG-GCTTCAGAGG-----ATGTGCAG - -a -s simMouse_chr6.simMouse.chr6 557919 19 + 636262 ACAGTCTTAATATCTGTAC -s mr.mrrefChr3 107915 19 + 181027 ACAGTCTTAATATCTGTAC -s simRat_chr6.simRat.chr6 33150 19 - 647215 ACAATCTTTATAGCTCAAC - -a -s simMouse_chr6.simMouse.chr6 557938 198 + 636262 TGTCCTATCATTACCCCAGTGAATATCATGGAACCCTGAGGTATCTCTGATATGGATATCATGTGATAGACAGCATCCCCCTCGTTTTATAGGGTAAAATGTGTTGGGCCCTGGTATCTCTGATATGGATATCATGTGATAGACAGCGTCCCACTCGTTTTATAGGGTAAAATGTGTTGGGCCCTTCTCCAGATGTCT -s mr.mrrefChr3 107934 124 + 181027 TGTCCTATCATTACCCCAGTGAATATCATGGAACCCTGAGGTATCTCTGATATGGATATCATGTGATAGACAGCATCCC-------------------------------------------------------------------------ACTCGTTTTATAGGGTAAAATGTGTTGGGCCCTTCTCCAGATG-CT -s simRat_chr6.simRat.chr6 33170 124 - 647215 TATCCTATCATTACCCCAGTGAACATCATGGTACCCTGAAGTATCTCAGATATGAATATCATGTGAAACACAGCATCCC-------------------------------------------------------------------------ACTTGTTTTATGGCGTGAAATGTGTTGGGTCCTCCTACGGGTG-CC - -a -s simMouse_chr6.simMouse.chr6 558141 7 + 636262 TTGGTTG -s mr.mrrefChr3 108063 7 + 181027 TTGGTTG -s simRat_chr6.simRat.chr6 33299 7 - 647215 TTGCTTG - -a -s simMouse_chr6.simMouse.chr6 558221 1 + 636262 T - -a -s simMouse_chr6.simMouse.chr6 558347 62 + 636262 CCTGGACTTGCCTTAAAGGTACTTCACCAATGCAATAGTGAATAGGCCAAATGTTTGATCAC -s mr.mrrefChr3 108268 45 + 181027 CCTGGACTTGCCTTAAAGGTACTT-----------------ATAGGCCAAATGTTTGATCAC -s simRat_chr6.simRat.chr6 33505 45 - 647215 CCTGGACTTGCCTTAAAGGTACTT-----------------ATAAGCCAAATGTTGGATATC - -a -s simMouse_chr6.simMouse.chr6 558409 115 + 636262 ATTGATGAGGTTACAGGGTTTCAGAGGCATGATTGAAAGCCTGAGTTACAACCCTGGGGCAACACAATATGTGTACTCTCTACTCTCTTCAATTTCTGAGGTAGTCAGGATCATA -s Anc0.Anc0refChr3 159712 7 + 222631 ------------------------------------------------------------------------------------------------------------GAACATA -s Anc1.Anc1refChr6 195947 7 + 197743 ------------------------------------------------------------------------------------------------------------GAACATA -s Anc2.Anc2refChr1 74134 7 + 142988 ------------------------------------------------------------------------------------------------------------TAACATA -s mr.mrrefChr3 108313 96 + 181027 ATTGATGAGGTTACAGGGTTTCAGAGGCA------------TGAGTTACAACCCTGGGGCAACACAATATGTGTAC-------TCTCTTCAATTTCTGAGGTAGTCAGGATCATA -s simCow_chr6.simCow.chr6 532830 7 + 602619 ------------------------------------------------------------------------------------------------------------CAACATA -s simDog_chr6.simDog.chr6 521064 7 + 593897 ------------------------------------------------------------------------------------------------------------TAACATA -s simHuman_chr6.simHuman.chr6 528124 7 + 601863 ------------------------------------------------------------------------------------------------------------GAACATA -s simRat_chr6.simRat.chr6 33553 96 - 647215 ATTTATCAGGCTACAGCGATACAGAGACA------------TGAGTTGCAACCTTGGGGCAGCACAATATCTGAAC-------TGTCTCCAATTTCTGAGGTAGTCAGGATCATA - -a -s simMouse_chr6.simMouse.chr6 558524 21 + 636262 TATAACACATAGGGAGTGCAA -s Anc0.Anc0refChr3 159804 21 + 222631 TACAACATGCAGGGGGTGTCA -s Anc1.Anc1refChr6 196039 21 + 197743 TACAACATGCAGGGGGTGTCA -s Anc2.Anc2refChr1 74395 21 + 142988 TACTACTTGCAGGGGGGGTCA -s mr.mrrefChr3 108409 21 + 181027 TATAACACATAGGGAGTGCAA -s simCow_chr6.simCow.chr6 533130 20 + 602619 TACTAC-TGTGCAGGGGCTCA -s simDog_chr6.simDog.chr6 521339 21 + 593897 TACTGCTGACAGGGGGGGCCA -s simHuman_chr6.simHuman.chr6 528221 21 + 601863 TACAACATGCAGGGGGTGTGA -s simRat_chr6.simRat.chr6 33649 21 - 647215 TATAACACATAGTGAGTGCAG - -a -s simMouse_chr6.simMouse.chr6 558545 22 + 636262 TGCAGGACCTTCCCTGGTACAT -s Anc0.Anc0refChr3 159825 21 + 222631 TGCAG-ACTCTTTCAGGTTCAG -s Anc1.Anc1refChr6 196060 21 + 197743 TGCAG-ACTCTTTCAGGTTCAG -s Anc2.Anc2refChr1 74416 21 + 142988 TGTAG-ACTCTTTCAGGTTCAG -s mr.mrrefChr3 108430 22 + 181027 TGCAGGACCTTCCCTGGTACAT -s simCow_chr6.simCow.chr6 533151 21 + 602619 TGAAG-CCTCTTTCAGGTTCAG -s simDog_chr6.simDog.chr6 521360 19 + 593897 ATT---ACTCTTTCAGGTTCAG -s simHuman_chr6.simHuman.chr6 528242 21 + 601863 TGCAG-ACTCTTTCAGGTTCAA -s simRat_chr6.simRat.chr6 33670 22 - 647215 TGCAGGACCTTCCCTGGTAAAT - -a -s simMouse_chr6.simMouse.chr6 558567 14 + 636262 GTTAATTATATATA -s Anc0.Anc0refChr3 159846 14 + 222631 GTTGGCTATGTATA -s Anc1.Anc1refChr6 196081 14 + 197743 GTTGGCTATGTATA -s Anc2.Anc2refChr1 74437 14 + 142988 ATTGGCTATGTATA -s mr.mrrefChr3 108452 14 + 181027 GTTGGTTATATATA -s simCow_chr6.simCow.chr6 533173 14 + 602619 TTTTGCTATGCATA -s simDog_chr6.simDog.chr6 521379 14 + 593897 ATTGGCAATGTATC -s simHuman_chr6.simHuman.chr6 528263 14 + 601863 GTTGGCTATGTATA -s simRat_chr6.simRat.chr6 33692 14 - 647215 GTAGGTTATATATA - -a -s simMouse_chr6.simMouse.chr6 558581 58 + 636262 AGACTATTCACATAGTGCACATCAAGGCAAGCAACATTTAATAGTGCCTGGTAGCTTC -s Anc0.Anc0refChr3 159860 57 + 222631 AGATTATTCATATAGTGTATATCAGAGTAAGGAACATATTACAATGC-TGGTAGCTTC -s Anc1.Anc1refChr6 196095 57 + 197743 AGATTATTCATATAGTGTATATCAGAGTAAGGAACATATTACAATGC-TGGTAGCTTC -s Anc2.Anc2refChr1 74451 57 + 142988 AGACTATTCATCTCGTGTATATCAGAGTAAGGAACATATTACAATGC-TGCTAGCTTC -s mr.mrrefChr3 108466 58 + 181027 AGATTATTCACATAGTGCACATCAAGGTAAGCAACATTTAATAATGCCTGGTAGCTTC -s simCow_chr6.simCow.chr6 533187 56 + 602619 GGACTATTCACTTCGTGTATATCAAAGTCAGGAACATATTGC-ATAC-TGCTAGTTTC -s simDog_chr6.simDog.chr6 521393 57 + 593897 AGGCTACTTATCTCGTGTATAGCGGAGTAAGGAACATGTTATAATGC-TTCTAGCTTC -s simHuman_chr6.simHuman.chr6 528277 57 + 601863 ATATTATTCATATAGTGTATATCATAGTAAGTAACATATTACAATGC-TGGTAGCTTC -s simRat_chr6.simRat.chr6 33708 58 - 647215 AGGTTATACTCATAGTGCACATCAATGTAAGCAACATTTAATAATGCCTGGAAGCTTC - -a -s simMouse_chr6.simMouse.chr6 558639 77 + 636262 CCAATAAACTGGTAGGGGCTTTAGCATGTTGTAAAATTGGGAAAGAGACATTAGAACTGTTCCAATTATAAACTTGT -s Anc0.Anc0refChr3 159918 77 + 222631 CCAACAAACTGGTAGGGGCCTCAGCATGTTTTAATATTAGAAAATAAATAGCTGAACTGTTTCAATTACAAACTTGT -s Anc1.Anc1refChr6 196153 77 + 197743 CCAACAAACTGGTAGGGGCCTCAGCATGTTTTAATATTAGAAAATAAATAGCTGAACTGTTTCAATTACAAACTTGT -s Anc2.Anc2refChr1 74509 77 + 142988 CCGACAAACTGGTAGAGGCCTCACCATGTTTTACTATTAGAAAGTAAATAGCTGAACTGTTTAAGGTACAAACTTGT -s mr.mrrefChr3 108525 77 + 181027 CCAATAAACTGGTAGGGGCTTTAGCATGTTGTAAAATTGGGAAATAGATAGTTGAACTGTTCCAATTATAAACTTGT -s simCow_chr6.simCow.chr6 533245 69 + 602619 CCGACCAACTGGGAGTGACCTCAACATGCTTTACTCTTAAAAGGTAAATAGCTGAGCTGT--------CAAACTTGT -s simDog_chr6.simDog.chr6 521451 74 + 593897 CCGA-AAACTGGTAGAGGCCTCACAATGTTCTACTACCAGAAAGTCAATGGCTGAACTTTTTAAGGTACA--CTTGT -s simHuman_chr6.simHuman.chr6 528335 77 + 601863 CCAACAAACTCGTAGGGCCCTCAGCATATTTCAAGATTAGAAAATATATAGCTAAAATGTTTCAATTGCAACCTTGT -s simRat_chr6.simRat.chr6 33767 77 - 647215 CCAATAAACTGGTAGGGGCTTTAGCATGTCGTAAAATTGGGAAATAGATAGTTGAACTTTTCCAATTATAAATTTGT - -a -s simMouse_chr6.simMouse.chr6 558716 34 + 636262 TCACAATTGCTTTCTCATTTCTTCCACTTAACCA -s Anc0.Anc0refChr3 159997 33 + 222631 -CACAATTGCAATTTCATTCTTTCTGATTAACTT -s Anc1.Anc1refChr6 196232 33 + 197743 -CACAATTGCAATTTCATTCTTTCTGATTAACTT -s Anc2.Anc2refChr1 74588 33 + 142988 -CACAGTTGCAATTTCATTCTTTGTGATTAACTT -s mr.mrrefChr3 108604 34 + 181027 TCACAATTGCTATCTCATTTCTTCCACTTAACCA -s simCow_chr6.simCow.chr6 533316 32 + 602619 -TCCAGGTGCAATTTCATTCTTTGTGTTTAAC-T -s simDog_chr6.simDog.chr6 521527 33 + 593897 -CACAGTTGCAATTTCATTCCTTGTGATCAACTT -s simHuman_chr6.simHuman.chr6 528414 33 + 601863 -CACAATTGCAATTTCATTCTTTCTGATTAACTT -s simRat_chr6.simRat.chr6 33846 34 - 647215 TCACAATTGCTATCTCATTTCTTTCACTTAAGCA - -a -s simMouse_chr6.simMouse.chr6 558750 33 + 636262 GCTACTTTTTCTCTGGTTGATCTAATAGCAAGG -s Anc0.Anc0refChr3 160030 33 + 222631 TCTCCTCTTTTTGTGGTTGATTTAATATAATGA -s Anc1.Anc1refChr6 196265 33 + 197743 TCTCCTCTTTTTGTGGTTGATTTAATATAATGA -s Anc2.Anc2refChr1 74621 33 + 142988 TCTCCTCTTTTTGTAGTTGATTTAATATAATGA -s mr.mrrefChr3 108638 33 + 181027 GCTACTTTTTCTCTGGTTGATTTAATAGCAAGG -s simCow_chr6.simCow.chr6 533348 33 + 602619 CCTACCTTTTCTGAAGTTGATTTAATATGGTTG -s simDog_chr6.simDog.chr6 521561 33 + 593897 TTTCCTCTTTTTATAGCTGATTTAATCTAATGA -s simHuman_chr6.simHuman.chr6 528447 33 + 601863 TCTTCTCTTTTTGTGATTGACTTAATATAATGA -s simRat_chr6.simRat.chr6 33880 33 - 647215 GCTACTTTTCCTCTGTTTGATTAAATAGCAAGG - -a -s simMouse_chr6.simMouse.chr6 558783 2 + 636262 GA -s Anc0.Anc0refChr3 160063 2 + 222631 GA -s Anc1.Anc1refChr6 196298 2 + 197743 GA -s Anc2.Anc2refChr1 74654 2 + 142988 GA -s mr.mrrefChr3 108671 2 + 181027 GA -s simCow_chr6.simCow.chr6 533423 2 + 602619 GA -s simDog_chr6.simDog.chr6 521594 2 + 593897 TA -s simHuman_chr6.simHuman.chr6 528480 2 + 601863 GA -s simRat_chr6.simRat.chr6 33913 2 - 647215 GA - -a -s simMouse_chr6.simMouse.chr6 558785 27 + 636262 ATATGTTGTTCCAAACAACTGTTCTAC -s Anc0.Anc0refChr3 160072 27 + 222631 ATTTGTCCCTTTTAATAACTTATCCAT -s Anc1.Anc1refChr6 196307 27 + 197743 ATTTGTCCCTTTTAATAACTTATCCAT -s Anc2.Anc2refChr1 74663 27 + 142988 ATTTGTCCCTTTTAATAGCCTATCCAT -s mr.mrrefChr3 108673 27 + 181027 ATTTGTTCTTCCAAACAACTGTTCTAT -s simCow_chr6.simCow.chr6 533432 27 + 602619 ATTTTTCCCTTTTAATGGTCTATCCAT -s simDog_chr6.simDog.chr6 521603 27 + 593897 GTTTGTCCCTTATAATAGCCTTTCCAT -s simHuman_chr6.simHuman.chr6 528489 27 + 601863 ATTTGTCCCTATTAATAACTTATCCGT -s simRat_chr6.simRat.chr6 33915 27 - 647215 ATTTGTTCTTCCAAACAACTGTTCTAT - -a -s simMouse_chr6.simMouse.chr6 558812 11 + 636262 TGGCCTACTTA -s Anc0.Anc0refChr3 160101 11 + 222631 TGACCTCCTCA -s Anc1.Anc1refChr6 196336 11 + 197743 TGACCTCCTCA -s Anc2.Anc2refChr1 74692 11 + 142988 TGACCTCCTCA -s mr.mrrefChr3 108702 11 + 181027 TGACCTACTCA -s simCow_chr6.simCow.chr6 533461 11 + 602619 TGACGTCCTCA -s simDog_chr6.simDog.chr6 521632 11 + 593897 TGACCTCTTTA -s simHuman_chr6.simHuman.chr6 528518 11 + 601863 TGATTTCCTCA -s simRat_chr6.simRat.chr6 33944 11 - 647215 TGACCTACTCA - -a -s simMouse_chr6.simMouse.chr6 558823 24 + 636262 GCTGTGTAACACATTAATTGTTGG -s Anc0.Anc0refChr3 160112 24 + 222631 GCAATCTATCACATTGATTTTTGG -s Anc1.Anc1refChr6 196347 24 + 197743 GCAATCTATCACATTGATTTTTGG -s Anc2.Anc2refChr1 74704 24 + 142988 GTAATCTATCACATAGATTTCTGG -s mr.mrrefChr3 108713 24 + 181027 GCTGTGTAACACATTAATTGTTGG -s simCow_chr6.simCow.chr6 533473 24 + 602619 GTAATCTATCACATCAATTTCTGG -s simDog_chr6.simDog.chr6 521644 24 + 593897 GTAGTCCAACACACAGATCCCCAG -s simHuman_chr6.simHuman.chr6 528529 24 + 601863 GCAATCTATCACATTGATTTTTGG -s simRat_chr6.simRat.chr6 33955 24 - 647215 ACTGTGTAGCACAGTAATTGTTGG - -a -s simMouse_chr6.simMouse.chr6 558847 42 + 636262 CTTGGTCAACTTAGGCAGTCCTTTTTCACCTTGGTGCCTTTA -s Anc0.Anc0refChr3 160176 39 + 222631 CCTCTACAGGTTAGGCAGTTCTTTTTCACCTTAGTCACC--- -s Anc1.Anc1refChr6 196411 42 + 197743 CCTCTACAGGTTAGGCAGTTCTTTTTCACCTTAGTCACCTTA -s Anc2.Anc2refChr1 74768 39 + 142988 CCTCTACAGGTTAGGCAGTTTTTTTCCACCTTAGTCATC--- -s mr.mrrefChr3 108737 42 + 181027 CTTGGTCAACTTAGGCAGTCCTTTTTCACCTTGGTCCCCTTA -s simCow_chr6.simCow.chr6 533541 31 + 602619 GCTCTACAGGTTTCGCAGTCTTTTTCTGCCT----------- -s simDog_chr6.simDog.chr6 521708 39 + 593897 CCTCAACAGTTTAGGCAGTTTCTCTCCAACTTAGTCATC--- -s simHuman_chr6.simHuman.chr6 528594 42 + 601863 CCTCTGCAGGTTAGACAGTTCTCTCTCACCTTAGTCACCTTA -s simRat_chr6.simRat.chr6 33979 33 - 647215 CTTG---------GGCAGTCCTTTTTCACCTTGGTCGCCTTA - -a -s simMouse_chr6.simMouse.chr6 558889 19 + 636262 ATCTCTGCCTTTACCCATG -s Anc0.Anc0refChr3 160238 19 + 222631 ATCTTTGCCTCTATTCATG -s Anc1.Anc1refChr6 196500 19 + 197743 ATCTTTGCCTCTATTCATG -s Anc2.Anc2refChr1 74830 19 + 142988 CTCTTTGCCTCTATTCTTG -s mr.mrrefChr3 108826 19 + 181027 ATCTCTGCCTTTACCCATG -s simCow_chr6.simCow.chr6 533572 14 + 602619 CTCTCTGCCTCTGT----- -s simDog_chr6.simDog.chr6 521770 19 + 593897 CTCTTCGCCTCTACTCTTG -s simHuman_chr6.simHuman.chr6 528697 19 + 601863 ACCCGTGCCTATATTCATG -s simRat_chr6.simRat.chr6 34059 19 - 647215 GTCTCTGCCTTTACCCATG - -a -s simMouse_chr6.simMouse.chr6 558908 60 + 636262 TGCTCTGGGACAAGTTTTAATATTTATGATCCCACAGTATTTATGATCCTGTCGTCGTGG -s Anc0.Anc0refChr3 160260 44 + 222631 TGCT-TGGCACA----TACATGTTGACAATCCTG----AT-------ACTGTTGCTGTGG -s Anc1.Anc1refChr6 196522 46 + 197743 TGCTCTGGCACA---GTACATGTTGACAATCCTG----AT-------ACTGTTGCTGTGG -s Anc2.Anc2refChr1 74852 44 + 142988 TGGT-TGGCACA----TACATGTTGGCAATCCTG----AT-------ACTGCTGCTGTGG -s mr.mrrefChr3 108845 53 + 181027 TGCTCTGGGACAAGTTTTAATATTTATGATCCCGTAGTAT-------CCTGTCGTCGTGG -s simCow_chr6.simCow.chr6 533586 33 + 602619 ----------------AACATTTTGTCAATCATG----AT-------ACAGCAGCTTTGA -s simDog_chr6.simDog.chr6 521792 44 + 593897 TGGT-TGGCACA----TACATGTTAGCAATCCTG----GT-------ACTGCTGATGTGG -s simHuman_chr6.simHuman.chr6 528719 44 + 601863 TGCTCAGGCA-----GTACGTGTTGACAATCCTG----AT-------ACTGTTGCTGTGG -s simRat_chr6.simRat.chr6 34078 53 - 647215 TGCTCTCGGACAGGTTTTAATATTTATGATCCCGTAGTCG-------CCCGTAGTCGCGG - -a -s simMouse_chr6.simMouse.chr6 558968 31 + 636262 ACAATAGATTATAGGCCCAAACCAAAGCAAC -s Anc0.Anc0refChr3 160318 31 + 222631 ACAACAGATTGTAGGGCCAGACCACATCATC -s Anc1.Anc1refChr6 196582 31 + 197743 ACAACAGATTGTAGGGCCAGACCACATCATC -s Anc2.Anc2refChr1 74910 31 + 142988 ACAACAGATTGTAGGGCCAGACCACATCATC -s mr.mrrefChr3 108898 31 + 181027 ACAATAGATTATAGGCCCAGACCAAAGCAAC -s simCow_chr6.simCow.chr6 533633 31 + 602619 ACAGCAGATTGTAAGGCCAGACCACTTTATC -s simDog_chr6.simDog.chr6 521849 31 + 593897 ACAACACATTGTAGGGTCAGACCACATCATC -s simHuman_chr6.simHuman.chr6 528777 31 + 601863 ACAACAGATTGTAGGGCCAGGCCACATCATC -s simRat_chr6.simRat.chr6 34131 31 - 647215 ACAATAGATTATAGGCCCAGACCAAAGCAAC - -a -s simMouse_chr6.simMouse.chr6 558999 6 + 636262 TATCTA -s Anc0.Anc0refChr3 160349 6 + 222631 TGTCTG -s Anc1.Anc1refChr6 196613 6 + 197743 TGTCTG -s Anc2.Anc2refChr1 74951 6 + 142988 TGTCTG -s mr.mrrefChr3 108929 6 + 181027 TGTCTA -s simCow_chr6.simCow.chr6 533674 6 + 602619 CGTTTG -s simDog_chr6.simDog.chr6 521890 6 + 593897 TGTCTG -s simHuman_chr6.simHuman.chr6 528808 2 + 601863 TG---- -s simRat_chr6.simRat.chr6 34162 6 - 647215 CGCCTA - -a -s simMouse_chr6.simMouse.chr6 559005 8 + 636262 CTGAAATG -s Anc0.Anc0refChr3 160355 8 + 222631 CTAAAATG -s Anc1.Anc1refChr6 196619 8 + 197743 CTAAAATG -s Anc2.Anc2refChr1 74964 8 + 142988 CTAAAATG -s mr.mrrefChr3 108935 8 + 181027 CTGAAATG -s simCow_chr6.simCow.chr6 533687 8 + 602619 CTAAAATG -s simDog_chr6.simDog.chr6 521903 8 + 593897 CTAAAATG -s simRat_chr6.simRat.chr6 34168 8 - 647215 TTGAAATG - -a -s simMouse_chr6.simMouse.chr6 559013 16 + 636262 TACCCATTAGATACTC -s Anc0.Anc0refChr3 160363 16 + 222631 TACCCACTAGATATAC -s Anc1.Anc1refChr6 196627 16 + 197743 TACCCACTAGATATAC -s Anc2.Anc2refChr1 74972 16 + 142988 TACCCACTAGATATAC -s mr.mrrefChr3 108943 16 + 181027 TACCCATTAGATACTC -s simCow_chr6.simCow.chr6 533695 16 + 602619 TACCTACTAGATATTA -s simDog_chr6.simDog.chr6 521911 16 + 593897 TACCCACTAGATATAC -s simRat_chr6.simRat.chr6 34179 16 - 647215 TACCCATCAGATACTC - -a -s simMouse_chr6.simMouse.chr6 559029 74 + 636262 TAATCAGTGACAGTTCAACCCACGTCTTCCAAGGCAGTGGATGGGGGCCAATAAACTCTCTTAGCTTCAGAGGT -s Anc0.Anc0refChr3 160379 74 + 222631 TGGCCGGTGCTAGTACAACAAATATCTCCCAAGTCAGAGGACATGGGCCACTTCACTCTCTTAGTTTCAAGGCC -s Anc1.Anc1refChr6 196643 74 + 197743 TGGCCGGTGCTAGTACAACAAATATCTCCCAAGTCAGAGGACATGGGCCACTTCACTCTCTTAGTTTCAAGGCC -s Anc2.Anc2refChr1 74995 74 + 142988 TGGCCGGTGCTAGTACAACAAATATCTCCCAAGTCAGAGGACATGGGCCACTTCACACTTGTAGTTTCAAGGCC -s mr.mrrefChr3 108959 74 + 181027 TAATCAGTGACAGTTCAACCCATATCTCCCAAGGCAGTGGACAGGGGCCACTAAACTCTCTTAGCTTCAGAGCC -s simCow_chr6.simCow.chr6 533718 73 + 602619 TGACTGCTGACGTTACAACAAATGCCTCTCAAATCAGAGGACATCGA-GACTAAGCACTTATCGTTTCAAGGCC -s simDog_chr6.simDog.chr6 521934 74 + 593897 TGGCCGGTGCTAGTACAACAAATATCTCCCAAGTTAGAGGAAATGGGCCACTTCACACTTGTAGTCTCAAGGCC -s simHuman_chr6.simHuman.chr6 528810 53 + 601863 ---------------------ATATCTCCCAAGTCAAAGGACATGGGCCACTTCACTCCCTTAGTTTCAAGGCC -s simRat_chr6.simRat.chr6 34195 73 - 647215 TAATCAATGACAGTTCAACCCATAAATCCCAAGGCAGTGGACAGGGGCCACTAAAATCTCTCAGCAC-AGAGCC - -a -s simMouse_chr6.simMouse.chr6 559103 3 + 636262 TCA -s Anc0.Anc0refChr3 160453 3 + 222631 ACA -s Anc1.Anc1refChr6 196717 3 + 197743 ACA -s Anc2.Anc2refChr1 75070 3 + 142988 ACA -s mr.mrrefChr3 109033 3 + 181027 TCA -s simCow_chr6.simCow.chr6 533792 3 + 602619 ACA -s simDog_chr6.simDog.chr6 522009 3 + 593897 ACA -s simHuman_chr6.simHuman.chr6 528863 3 + 601863 ACA -s simRat_chr6.simRat.chr6 34268 3 - 647215 TCA - -a -s simMouse_chr6.simMouse.chr6 559106 42 + 636262 AATGAGTAGGTCCTGTTGTGGTTGCAGGACTCATACACTGTG -s Anc0.Anc0refChr3 160458 41 + 222631 AATGAGATTGTCTTGCTGTGGTTGCAGG-GTCACACACCGTG -s Anc1.Anc1refChr6 196722 41 + 197743 AATGAGATTGTCTTGCTGTGGTTGCAGG-GTCACACACCGTG -s Anc2.Anc2refChr1 75075 41 + 142988 AATGAAATTGTCTGGCTGTGGTTGCAGG-GTCACACACCATG -s mr.mrrefChr3 109036 42 + 181027 AATGAGTAGGTCTTGTTGTGGTTGCAGGAGTCATACACTGTG -s simCow_chr6.simCow.chr6 533797 41 + 602619 AATGAAATTGTCTGGCTAGGGTTTAAGG-GTCACACACTATG -s simDog_chr6.simDog.chr6 522014 41 + 593897 AACGAAGTTGTCTGGCTGTGGTTGCAAG-GTCACACACCATG -s simHuman_chr6.simHuman.chr6 528868 41 + 601863 AATGAGATTGTCTTGCTGTGGTTGTGGG-GTTACACATAGTG -s simRat_chr6.simRat.chr6 34271 42 - 647215 AATGAGTAGGTCTTGTTGTGGTTGCAGGCGCCATACACCACG - -a -s simMouse_chr6.simMouse.chr6 559148 9 + 636262 GCCCTAATA -s Anc0.Anc0refChr3 160499 9 + 222631 GAGCTAATG -s Anc1.Anc1refChr6 196763 9 + 197743 GAGCTAATG -s Anc2.Anc2refChr1 75116 9 + 142988 CAGCTAATG -s mr.mrrefChr3 109078 9 + 181027 GCCCTAATG -s simCow_chr6.simCow.chr6 533838 9 + 602619 CAGGTAATG -s simDog_chr6.simDog.chr6 522055 9 + 593897 CAGCTAATG -s simHuman_chr6.simHuman.chr6 528911 9 + 601863 GAGCTAAAG -s simRat_chr6.simRat.chr6 34313 9 - 647215 GCTCTAATG - -a -s simMouse_chr6.simMouse.chr6 559157 62 + 636262 ACCATGCACTTTGGGGAGTGACTACTATTAATCTTTGATTCCGTGGCACTGATCTAGGGCTA -s Anc0.Anc0refChr3 160508 59 + 222631 ACCATACACTTTA---AGTAACGACTATTACTTTTTAATTCAGTGGCACTAATCTAGAGCTA -s Anc1.Anc1refChr6 196772 59 + 197743 ACCATACACTTTA---AGTAACGACTATTACTTTTTAATTCAGTGGCACTAATCTAGAGCTA -s Anc2.Anc2refChr1 75125 59 + 142988 ACCATACACTTGA---AGTAATGACTATTACTTTTTAATTCAGTGGCACTAATCTAGAGCTA -s mr.mrrefChr3 109087 62 + 181027 ACCATGCACTTTGGGGAGTGACTACTATTAATCTTTGATTCAGTGGCACTAATCTAGAGCTA -s simCow_chr6.simCow.chr6 533847 59 + 602619 ACCATACAATTGA---AGTAATTGCTAGAACCTTTTAATTCAGTGGCATTAATCTAGGGTTA -s simDog_chr6.simDog.chr6 522065 59 + 593897 ATCGTGCACTTGA---AGTAATGACTATTACTTTTTAATTCAGTGGCACTAGTCTAGAGCTA -s simHuman_chr6.simHuman.chr6 528920 59 + 601863 ACCATACACTTTA---AGTAACAACTATTACTTTTTAATGCAATGGCACAAATCTAGAGCTA -s simRat_chr6.simRat.chr6 34322 62 - 647215 AACATGCACCTTGGGGAGTGACTACTATGAATCTTTGACTCAGTGGTACTAATCTAGAGCTA - -a -s simMouse_chr6.simMouse.chr6 559219 8 + 636262 AATAAGGC -s Anc0.Anc0refChr3 160567 8 + 222631 AACTAAGC -s Anc1.Anc1refChr6 196831 8 + 197743 AACTAAGC -s Anc2.Anc2refChr1 75184 8 + 142988 AACTAAGC -s mr.mrrefChr3 109149 8 + 181027 AATTAGGC -s simCow_chr6.simCow.chr6 533906 8 + 602619 AACTAAGC -s simDog_chr6.simDog.chr6 522129 8 + 593897 AACTAAGC -s simHuman_chr6.simHuman.chr6 528979 8 + 601863 AACTGAGC -s simRat_chr6.simRat.chr6 34384 8 - 647215 AATTTGGC - -a -s simMouse_chr6.simMouse.chr6 559227 9 + 636262 TTAAAAACC -s Anc0.Anc0refChr3 160575 9 + 222631 ATAGAAACT -s Anc1.Anc1refChr6 196839 9 + 197743 ATAGAAACT -s Anc2.Anc2refChr1 75193 9 + 142988 ATAGAAACT -s mr.mrrefChr3 109157 9 + 181027 TTAAAAACC -s simCow_chr6.simCow.chr6 533915 9 + 602619 ACAGAAACC -s simDog_chr6.simDog.chr6 522142 9 + 593897 ATAGAAAGT -s simHuman_chr6.simHuman.chr6 528987 9 + 601863 ATAGAGACT -s simRat_chr6.simRat.chr6 34392 9 - 647215 TTAAAAACC - -a -s simMouse_chr6.simMouse.chr6 559236 15 + 636262 CATATCTGCTTCTCT -s Anc0.Anc0refChr3 160599 15 + 222631 AAGATCTGCTTCTCC -s Anc1.Anc1refChr6 196863 15 + 197743 AAGATCTGCTTCTCC -s Anc2.Anc2refChr1 75217 15 + 142988 AAGATCTGCTTCTCC -s mr.mrrefChr3 109181 15 + 181027 AATATCTGCTTCTCT -s simCow_chr6.simCow.chr6 533939 15 + 602619 AGGGTCTGCTTCTCT -s simDog_chr6.simDog.chr6 522166 15 + 593897 AAGATCTGCTTCTCC -s simHuman_chr6.simHuman.chr6 529011 15 + 601863 AAGATCCACTTCTCC -s simRat_chr6.simRat.chr6 34416 15 - 647215 AATATCTGCTTTTCT - -a -s simMouse_chr6.simMouse.chr6 559251 5 + 636262 CTCTT -s Anc0.Anc0refChr3 160614 5 + 222631 CTCTA -s Anc1.Anc1refChr6 196878 5 + 197743 CTCTA -s Anc2.Anc2refChr1 75232 5 + 142988 CTCTA -s mr.mrrefChr3 109196 5 + 181027 CTCTT -s simCow_chr6.simCow.chr6 533954 5 + 602619 CTCTA -s simDog_chr6.simDog.chr6 522182 5 + 593897 CTCTA -s simHuman_chr6.simHuman.chr6 529026 5 + 601863 CTCCA -s simRat_chr6.simRat.chr6 34431 5 - 647215 CTCTT - -a -s simMouse_chr6.simMouse.chr6 559256 17 + 636262 TCCTATGTTAGGTAATG -s Anc0.Anc0refChr3 160620 15 + 222631 TCTCAAGTTAAG--ATG -s Anc1.Anc1refChr6 196884 15 + 197743 TCTCAAGTTAAG--ATG -s Anc2.Anc2refChr1 75238 15 + 142988 TCTCAAGTTAAG--ATG -s mr.mrrefChr3 109201 17 + 181027 TCCTATGTTAGGTAATG -s simCow_chr6.simCow.chr6 533960 15 + 602619 TCTTAAGTTAAG--ATG -s simDog_chr6.simDog.chr6 522188 15 + 593897 TTTCAAGTTAAG--ATG -s simHuman_chr6.simHuman.chr6 529032 15 + 601863 TCTCAAGTTAAG--ATG -s simRat_chr6.simRat.chr6 34436 17 - 647215 TGCTATGTTAGGTAATG - -a -s simMouse_chr6.simMouse.chr6 559273 14 + 636262 TTGATGCCACTGGA -s Anc0.Anc0refChr3 160638 14 + 222631 TGGAGGACAGTGGA -s Anc1.Anc1refChr6 196902 14 + 197743 TGGAGGACAGTGGA -s Anc2.Anc2refChr1 75256 14 + 142988 TGGAGGACAGTGGA -s mr.mrrefChr3 109218 14 + 181027 TTGATGCCACAGGA -s simCow_chr6.simCow.chr6 533978 14 + 602619 TTGTGGACAGTCAA -s simDog_chr6.simDog.chr6 522206 14 + 593897 CGGAGGACACTGGA -s simHuman_chr6.simHuman.chr6 529050 14 + 601863 TAGGGGACAGTGCA -s simRat_chr6.simRat.chr6 34453 14 - 647215 TTGATGCCACAGGA - -a -s simMouse_chr6.simMouse.chr6 559287 5 + 636262 GACTA -s Anc0.Anc0refChr3 160652 5 + 222631 TATTA -s Anc1.Anc1refChr6 196916 5 + 197743 TATTA -s Anc2.Anc2refChr1 75270 5 + 142988 TATTA -s mr.mrrefChr3 109232 5 + 181027 GACTA -s simCow_chr6.simCow.chr6 533995 5 + 602619 TATTA -s simDog_chr6.simDog.chr6 522220 5 + 593897 CAGTA -s simHuman_chr6.simHuman.chr6 529064 5 + 601863 TATTA -s simRat_chr6.simRat.chr6 34467 5 - 647215 GACTA - -a -s simMouse_chr6.simMouse.chr6 559292 13 + 636262 TTACCTAGCACTC -s Anc0.Anc0refChr3 160657 9 + 222631 T---CTAA-GCTT -s Anc1.Anc1refChr6 196921 9 + 197743 T---CTAA-GCTT -s Anc2.Anc2refChr1 75275 9 + 142988 T---CCAA-GCTT -s mr.mrrefChr3 109237 13 + 181027 TTACCTAGCACTC -s simCow_chr6.simCow.chr6 534000 9 + 602619 T---TCTA-GCTT -s simDog_chr6.simDog.chr6 522227 9 + 593897 T---CCAA-GTTT -s simHuman_chr6.simHuman.chr6 529069 9 + 601863 T---CTAA-GCTT -s simRat_chr6.simRat.chr6 34472 13 - 647215 TTGCCTAGCACTC - -a -s simMouse_chr6.simMouse.chr6 559305 8 + 636262 TGCAATTA -s Anc0.Anc0refChr3 160667 7 + 222631 GG-ACTCT -s Anc1.Anc1refChr6 196931 7 + 197743 GG-ACTCT -s Anc2.Anc2refChr1 75285 7 + 142988 GG-ACTCT -s mr.mrrefChr3 109251 8 + 181027 TGCAATTA -s simCow_chr6.simCow.chr6 534010 7 + 602619 GG-GCTCT -s simDog_chr6.simDog.chr6 522237 7 + 593897 GG-ACACT -s simHuman_chr6.simHuman.chr6 529079 7 + 601863 AG-ACTCT -s simRat_chr6.simRat.chr6 34486 8 - 647215 TGCAATTA - -a -s simMouse_chr6.simMouse.chr6 559313 31 + 636262 AGTGTGCCCAAATCTCCTGAATCATATAAAC -s Anc0.Anc0refChr3 160674 29 + 222631 AGTATGACCATATCTCCTGCATTATAGA--T -s Anc1.Anc1refChr6 196938 29 + 197743 AGTATGACCATATCTCCTGCATTATAGA--T -s Anc2.Anc2refChr1 75299 29 + 142988 AGCATGACCATATCTCCTGCACTATAGA--T -s mr.mrrefChr3 109259 31 + 181027 AGTGTGACCAAATCTCCTGAATTATAGAAAT -s simCow_chr6.simCow.chr6 534024 29 + 602619 AGCATGACCATACCTCCTGCACTATAGG--T -s simDog_chr6.simDog.chr6 522251 27 + 593897 AGCATGACCATATCTCCTGCA--ATATA--T -s simHuman_chr6.simHuman.chr6 529086 28 + 601863 AGTCTAAA-ATATCTCCTGCATTATAGA--T -s simRat_chr6.simRat.chr6 34494 31 - 647215 AGTGGGACCAAGTCTCCTGAATTATAGAAAT - -a -s simMouse_chr6.simMouse.chr6 559344 55 + 636262 TCACTTCCATTCAGTAAACTGTACAGAATAGAAATAAAGGTAGATTTACACAGAA -s Anc0.Anc0refChr3 160703 55 + 222631 TCACTTCAATTCAATAAGTTAAACAGATCAGTAATAAAAGAACAATTACACAGAG -s Anc1.Anc1refChr6 196967 55 + 197743 TCACTTCAATTCAATAAGTTAAACAGATCAGTAATAAAAGAACAATTACACAGAG -s Anc2.Anc2refChr1 75328 55 + 142988 TCACTTCAATTCAATAAGTTAAACAGATCAGTAATAAAAGAACAATCACACAGAG -s mr.mrrefChr3 109290 55 + 181027 TCACTTCCATTCAGTAAACTGTACAGAATAGAAATAAAGGTAGATTTACACAGAA -s simCow_chr6.simCow.chr6 534058 55 + 602619 TCACTTCAATTCAATAAGTTAAACAGATCAGTAAGAAATAACCAATCACACAAAG -s simDog_chr6.simDog.chr6 522278 54 + 593897 TCATTTCAATTCAATAAATTAAAGAGATTAGTAATTA-AGAACAATCACACAGAG -s simHuman_chr6.simHuman.chr6 529114 55 + 601863 TCACTTCAACTCAATAAGTTAAACAGGTCAGCAATAAAAGAATAATTACCCAGAT -s simRat_chr6.simRat.chr6 34525 55 - 647215 TCACCTCCTTTCAGTAAACTGTACAGAATAAAAATAAAGGTAGGTTTACACAGAA - -a -s simMouse_chr6.simMouse.chr6 559399 4 + 636262 GGAA -s Anc0.Anc0refChr3 160759 4 + 222631 GAAA -s Anc1.Anc1refChr6 197023 4 + 197743 GAAA -s Anc2.Anc2refChr1 75384 4 + 142988 GAAA -s mr.mrrefChr3 109345 4 + 181027 GGAA -s simCow_chr6.simCow.chr6 534114 4 + 602619 GACA -s simDog_chr6.simDog.chr6 522333 4 + 593897 GAAG -s simHuman_chr6.simHuman.chr6 529170 4 + 601863 AAAA -s simRat_chr6.simRat.chr6 34580 4 - 647215 GGAA - -a -s simMouse_chr6.simMouse.chr6 559403 32 + 636262 TCAGGAAATGAATCGGTCGGACCTAGGCGATG -s Anc0.Anc0refChr3 160763 31 + 222631 ACCAGAAATGACACGATCAGACCAGG-AGATG -s Anc1.Anc1refChr6 197027 31 + 197743 ACCAGAAATGACACGATCAGACCAGG-AGATG -s Anc2.Anc2refChr1 75388 31 + 142988 ACCAGAAATGGCGAGATCAGACCAGG-AGATG -s mr.mrrefChr3 109349 31 + 181027 TCAGGAAATGAAACGGTCGGACCTAG-CGATG -s simCow_chr6.simCow.chr6 534118 27 + 602619 CTTAGGAAT----AGATCACAACAGG-ACATG -s simDog_chr6.simDog.chr6 522337 31 + 593897 ACCAGAGATGGCGAGATCAGACAAGG-AGATG -s simHuman_chr6.simHuman.chr6 529175 31 + 601863 CCGAAAAATGACACGATCAGACCAGG-AAGTT -s simRat_chr6.simRat.chr6 34584 31 - 647215 TCAGGGAATGAAACGGCCGGACCTAG-CGATG - -a -s simMouse_chr6.simMouse.chr6 559435 6 + 636262 TTCCGG -s Anc0.Anc0refChr3 160800 6 + 222631 ATCCGG -s Anc1.Anc1refChr6 197064 6 + 197743 ATCCGG -s Anc2.Anc2refChr1 75425 6 + 142988 ATCCGG -s mr.mrrefChr3 109380 6 + 181027 TTCCGG -s simCow_chr6.simCow.chr6 534151 6 + 602619 ATCCGG -s simDog_chr6.simDog.chr6 522374 5 + 593897 AT-CGG -s simHuman_chr6.simHuman.chr6 529212 6 + 601863 ATCCGG -s simRat_chr6.simRat.chr6 34615 6 - 647215 GTCCGG - -a -s simMouse_chr6.simMouse.chr6 559466 5 + 636262 AAGCA -s Anc0.Anc0refChr3 160831 5 + 222631 ATCCG -s Anc1.Anc1refChr6 197095 5 + 197743 ATCCG -s Anc2.Anc2refChr1 75456 5 + 142988 ATCCG -s mr.mrrefChr3 109411 5 + 181027 AAGCA -s simCow_chr6.simCow.chr6 534182 5 + 602619 ATCCG -s simDog_chr6.simDog.chr6 522404 5 + 593897 ATCCG -s simHuman_chr6.simHuman.chr6 529243 5 + 601863 ATCCG -s simRat_chr6.simRat.chr6 34646 5 - 647215 AAGCA - -a -s simMouse_chr6.simMouse.chr6 559668 1 + 636262 C -s mr.mrrefChr3 109621 1 + 181027 C -s simRat_chr6.simRat.chr6 34856 1 - 647215 C - -a -s simMouse_chr6.simMouse.chr6 559782 1 + 636262 T -s Anc0.Anc0refChr3 161148 1 + 222631 T -s Anc1.Anc1refChr6 197444 1 + 197743 T -s Anc2.Anc2refChr1 75773 1 + 142988 T -s mr.mrrefChr3 109735 1 + 181027 T -s simCow_chr6.simCow.chr6 534492 1 + 602619 G -s simDog_chr6.simDog.chr6 522720 1 + 593897 T -s simHuman_chr6.simHuman.chr6 529586 1 + 601863 T -s simRat_chr6.simRat.chr6 34970 1 - 647215 T - -a -s simMouse_chr6.simMouse.chr6 559799 4 + 636262 ATTC -s Anc0.Anc0refChr3 161173 4 + 222631 ATTC -s Anc1.Anc1refChr6 197472 4 + 197743 ATTC -s Anc2.Anc2refChr1 75798 4 + 142988 ATTC -s mr.mrrefChr3 109752 4 + 181027 ATTC -s simCow_chr6.simCow.chr6 534517 4 + 602619 ATGC -s simDog_chr6.simDog.chr6 522745 4 + 593897 ATTC -s simHuman_chr6.simHuman.chr6 529689 4 + 601863 ATCC -s simRat_chr6.simRat.chr6 34987 4 - 647215 AATC - -a -s simMouse_chr6.simMouse.chr6 559828 60 + 636262 TTTACAAAAGGTGTATGCCAGGGGGACTACTAGGGCTTAATAAATGGAAGCCTGCCCATG -s mr.mrrefChr3 109781 60 + 181027 TTTACCAAAGGTGGATGCCAGGGGGACAACTAGGGCTTAATAAATGGAAGCCTGCCCATG -s simRat_chr6.simRat.chr6 35016 60 - 647215 TTTGCCAAAGGTGGATGCCAGGGGGGCAACTAGGGCTGAATAAATGCAAGCCTGCCCATG - -a -s simMouse_chr6.simMouse.chr6 559923 7 + 636262 TGCTCAG -s Anc0.Anc0refChr3 161234 7 + 222631 CTTTAAG -s Anc1.Anc1refChr6 197538 7 + 197743 CTTTAAG -s Anc2.Anc2refChr1 75859 7 + 142988 CTTCAAG -s mr.mrrefChr3 109881 7 + 181027 CGCTCAG -s simCow_chr6.simCow.chr6 534576 7 + 602619 CTTCAAG -s simDog_chr6.simDog.chr6 522781 7 + 593897 CCTCAAG -s simHuman_chr6.simHuman.chr6 529755 7 + 601863 CTTTAAG -s simRat_chr6.simRat.chr6 35116 7 - 647215 CGCTCAG - -a -s simMouse_chr6.simMouse.chr6 559955 2 + 636262 GC - -a -s simMouse_chr6.simMouse.chr6 559999 12 + 636262 GGTTGTTTTAAC -s Anc0.Anc0refChr3 161307 11 + 222631 GGTTACTTCA-C -s Anc1.Anc1refChr6 197614 12 + 197743 GGTTACTTCACC -s Anc2.Anc2refChr1 75932 11 + 142988 GGTTACTTCA-C -s mr.mrrefChr3 109955 12 + 181027 GGTTATTTCAAC -s simCow_chr6.simCow.chr6 534640 11 + 602619 GGTTACTTCA-C -s simDog_chr6.simDog.chr6 522857 11 + 593897 GGTTAATTCA-C -s simHuman_chr6.simHuman.chr6 529828 12 + 601863 GGTTACTTCACA -s simRat_chr6.simRat.chr6 35190 12 - 647215 GATTATTTCAAC - -a -s simMouse_chr6.simMouse.chr6 560011 31 + 636262 AGTATGTGATACCTATTCTATCTTCCGTGGT -s Anc0.Anc0refChr3 161318 24 + 222631 ATTGGTTGATACATATTCTATCTT------- -s Anc1.Anc1refChr6 197626 24 + 197743 ATTGGTTGATACATATTCTATCTT------- -s Anc2.Anc2refChr1 75943 24 + 142988 ATTGGTTGATACATATTCTATCTT------- -s mr.mrrefChr3 109967 31 + 181027 ATTATGTGATACATATTCTATCTTCCGTGGT -s simCow_chr6.simCow.chr6 534651 22 + 602619 ATTGATTGATACATAT--TATCTT------- -s simDog_chr6.simDog.chr6 522868 24 + 593897 ATTGGTTGATACATATTCTATATT------- -s simHuman_chr6.simHuman.chr6 529847 24 + 601863 ATTGGTTGATACATATTCTATCTT------- -s simRat_chr6.simRat.chr6 35202 31 - 647215 ATTATGCGATACACATTCTATCTTCCAAGTT - -a -s simMouse_chr6.simMouse.chr6 560042 10 + 636262 CCAAGCATTA -s mr.mrrefChr3 109998 10 + 181027 CCAAGCATTA -s simRat_chr6.simRat.chr6 35237 10 - 647215 CCAAGTTCCA - -a -s simMouse_chr6.simMouse.chr6 560052 12 + 636262 GCATTCACTTTA -s mr.mrrefChr3 110008 12 + 181027 GCATTCACTTTA -s simRat_chr6.simRat.chr6 35248 12 - 647215 GCCTTCACTTTA - -a -s simMouse_chr6.simMouse.chr6 560064 27 + 636262 TGAGTATTGTCAATATATGTAATGAGG -s Anc0.Anc0refChr3 161342 9 + 222631 ------------------ATAATAAGG -s Anc1.Anc1refChr6 197650 9 + 197743 ------------------ATAATAAGG -s Anc2.Anc2refChr1 75967 9 + 142988 ------------------ATAATAAGG -s mr.mrrefChr3 110020 27 + 181027 TGAGTATTGTCAATATATGTAATGAGG -s simCow_chr6.simCow.chr6 534673 9 + 602619 ------------------ATAACAAGG -s simDog_chr6.simDog.chr6 522892 9 + 593897 ------------------ATATTAAGG -s simHuman_chr6.simHuman.chr6 529871 9 + 601863 ------------------ATAATAAAG -s simRat_chr6.simRat.chr6 35273 27 - 647215 TGATTATTGTCAATATATGTAATGGGG - -a -s simMouse_chr6.simMouse.chr6 560172 12 + 636262 AAACTGTAATTC -s Anc0.Anc0refChr3 161434 12 + 222631 AATCTGTAATCT -s Anc1.Anc1refChr1 0 12 + 69767 AATCTGTAATCT -s Anc2.Anc2refChr1 76060 12 + 142988 AATCTTTAATCT -s mr.mrrefChr3 110129 12 + 181027 AAACTGTAATTC -s simCow_chr6.simCow.chr6 534744 11 + 602619 AATCTTAAATC- -s simDog_chr6.simDog.chr6 522981 8 + 593897 CA----TATTCT -s simHuman_chr6.simHuman.chr6 529965 12 + 601863 AAGCTGTAACCT -s simRat_chr6.simRat.chr6 35382 12 - 647215 AAACTGTAATTC - -a -s simMouse_chr6.simMouse.chr6 560184 13 + 636262 TTCTTGGGAACTA -s Anc0.Anc0refChr3 161449 13 + 222631 TCCTTGGGAAGTA -s Anc1.Anc1refChr1 15 13 + 69767 TCCTTGGGAAGTA -s Anc2.Anc2refChr1 76075 13 + 142988 ACCCTGGGAAGAA -s mr.mrrefChr3 110141 13 + 181027 TTCTTGGGAAGTA -s simCow_chr6.simCow.chr6 534755 5 + 602619 --------AAGAA -s simDog_chr6.simDog.chr6 522992 13 + 593897 ACCCTGGGAATAA -s simHuman_chr6.simHuman.chr6 529980 13 + 601863 TCCTTGGGAAGTA -s simRat_chr6.simRat.chr6 35394 13 - 647215 TTCTTGGGAAGTA - -a -s simMouse_chr6.simMouse.chr6 560197 19 + 636262 CTGCAGCTGGGATGATGGG -s Anc0.Anc0refChr3 161476 19 + 222631 CTGAGACTGAGGTCATGGG -s Anc1.Anc1refChr1 42 19 + 69767 CTGAGACTGAGGTCATGGG -s Anc2.Anc2refChr1 76104 19 + 142988 CTGAGACTGAGGTCATGGG -s mr.mrrefChr3 110154 19 + 181027 CTGCAACTGGGATCATGGG -s simCow_chr6.simCow.chr6 534772 19 + 602619 CTGATACTGAGGTCAAGGA -s simDog_chr6.simDog.chr6 523026 19 + 593897 CTGAGACTGAGGTCATGGG -s simHuman_chr6.simHuman.chr6 530007 19 + 601863 ATGGGTCTGAGGTCGTGGG -s simRat_chr6.simRat.chr6 35407 19 - 647215 CTGCGACTGGGATCACGGG - -a -s simMouse_chr6.simMouse.chr6 560216 11 + 636262 TTTGCTACAGA -s Anc0.Anc0refChr3 161497 9 + 222631 --TGTCACAGA -s Anc1.Anc1refChr1 63 9 + 69767 --TGTCACAGA -s Anc2.Anc2refChr1 76125 9 + 142988 --TGCCACAGA -s mr.mrrefChr3 110177 11 + 181027 TTTGTCACAGA -s simCow_chr6.simCow.chr6 534793 9 + 602619 --TGCCACAGA -s simDog_chr6.simDog.chr6 523047 9 + 593897 --TGCCACAGA -s simHuman_chr6.simHuman.chr6 530028 9 + 601863 --TGTCACAGA -s simRat_chr6.simRat.chr6 35431 11 - 647215 TTTGTCACACA - -a -s simMouse_chr6.simMouse.chr6 560227 51 + 636262 CTTGACATCTAATGCACTTTGCTCATGAACTCACTACAATCTGTAGCTAAG -s Anc0.Anc0refChr3 161506 43 + 222631 CCG--------ATGCACATTGCTCCTGAACTCACAACAATCTACAGCTCAG -s Anc1.Anc1refChr1 72 43 + 69767 CCG--------ATGCACATTGCTCCTGAACTCACAACAATCTACAGCTCAG -s Anc2.Anc2refChr1 76134 43 + 142988 CCG--------ATGCACAATGCTACTGAACTCACAACAATCTACAACTCAG -s mr.mrrefChr3 110188 51 + 181027 CTTGACATCTAATGCACTTTGCTCATGAACTCACTACAATCTGCAGCTAAG -s simCow_chr6.simCow.chr6 534826 43 + 602619 CCG--------ATGCACACTGCTTTTGAACTCACCACAATCTACAACTCAT -s simDog_chr6.simDog.chr6 523056 37 + 593897 --------------CTTGATGCTACTAAACTCACACCAAACTGCAACTCAG -s simHuman_chr6.simHuman.chr6 530037 43 + 601863 TCC--------ATGCACATTCCTCCTGAACCCATGACAATCTACAGCTCAG -s simRat_chr6.simRat.chr6 35442 51 - 647215 CTTGACATCTAATGCTGTTTGCTCATGAACTCACCACAACCTGCAACTAAG - -a -s simMouse_chr6.simMouse.chr6 560278 55 + 636262 TCAGCATCTAATGCACTTTGCTCATGAACTCACTACAATCTGTAGCTAAGTCAGA -s Anc0.Anc0refChr3 161550 5 + 222631 TAA--------------------------------------------------GA -s Anc1.Anc1refChr1 116 5 + 69767 TAA--------------------------------------------------GA -s Anc2.Anc2refChr1 76178 5 + 142988 CAA--------------------------------------------------AA -s mr.mrrefChr3 110239 5 + 181027 TCA--------------------------------------------------GA -s simCow_chr6.simCow.chr6 534870 5 + 602619 CAA--------------------------------------------------AA -s simDog_chr6.simDog.chr6 523094 5 + 593897 CAG--------------------------------------------------AA -s simHuman_chr6.simHuman.chr6 530081 5 + 601863 TAA--------------------------------------------------GA -s simRat_chr6.simRat.chr6 35493 5 - 647215 TCA--------------------------------------------------GA - -a -s simMouse_chr6.simMouse.chr6 560333 17 + 636262 CTATCAAATAAACTTAC -s Anc0.Anc0refChr3 161555 16 + 222631 CTACCTAAGAAACTTG- -s Anc1.Anc1refChr1 121 16 + 69767 CTACCTAAGAAACTTG- -s Anc2.Anc2refChr1 76183 16 + 142988 CTGCCTAAGAAACTTG- -s mr.mrrefChr3 110244 17 + 181027 CTATCAAATAAACTTAC -s simCow_chr6.simCow.chr6 534876 16 + 602619 CTGCCTGAGAAACTTG- -s simDog_chr6.simDog.chr6 523099 16 + 593897 CTGCCTAAGGAACTTG- -s simHuman_chr6.simHuman.chr6 530086 11 + 601863 CTACCTAAGAA------ -s simRat_chr6.simRat.chr6 35498 17 - 647215 CCATCAAATAAACTTAC - -a -s simMouse_chr6.simMouse.chr6 560350 69 + 636262 TTTGGGTGATGGTCCGGGCCCTACAATACAAGTTCTACACCACCATTAGGAGCTAGTTGTAGTATTATG -s Anc0.Anc0refChr3 161571 67 + 222631 TTGGGACAATGGCCCAGGTGTGACAATACTAGTGTTACACTACGATTTGAACCTCGTTG--ACCTTCAG -s Anc1.Anc1refChr1 137 67 + 69767 TTGGGACAATGGCCCAGGTGTGACAATACTAGTGTTACACTACGATTTGAACCTCGTTG--ACCTTCAG -s Anc2.Anc2refChr1 76199 67 + 142988 TTGGGACAACGGCCCAGCTGTGAGAATACTAGTGTTACACTGCGATGTGTGCCTCGTCA--ACCTTCAG -s mr.mrrefChr3 110261 69 + 181027 TTTGGGTGATGGCCCGGGTCTTACAATACAAGTTCTACACCACCATTAGAAGCTAGTTGTAGTCTTAAG -s simCow_chr6.simCow.chr6 534893 67 + 602619 TTGGGACAACGGCCCAGACGTTGGAATACTAGTGTTACACTGTGATGTGGGCCTGATCA--ACCTTCAG -s simDog_chr6.simDog.chr6 523115 66 + 593897 TTTGGACAA-GGACCAGCTGTGAGAGTACTAGTGTTACACTGCCATGTGTGCCTCGTCA--ACCTTCAG -s simHuman_chr6.simHuman.chr6 530097 66 + 601863 TTGGTACAGTGGCTCAGGTGTCACAATACTAGCGTTACACTACGATTTGAA-CCGGTTG--ACCTTCAA -s simRat_chr6.simRat.chr6 35515 69 - 647215 TTTGGGTGATAGCCCGGGTCTTACAATACAAGTTGTACACCACCAATAGAAGCTAGTTGTAGGCTGAAG - -a -s simMouse_chr6.simMouse.chr6 560419 9 + 636262 TCAAAATGA -s Anc0.Anc0refChr3 161638 9 + 222631 TGTAATAAG -s Anc1.Anc1refChr1 204 9 + 69767 TGTAATAAG -s Anc2.Anc2refChr1 76266 9 + 142988 TGTAATAAG -s mr.mrrefChr3 110330 9 + 181027 TCTAAATGA -s simCow_chr6.simCow.chr6 534960 9 + 602619 TGTAGTAAG -s simDog_chr6.simDog.chr6 523181 9 + 593897 TGGAACAGG -s simHuman_chr6.simHuman.chr6 530165 9 + 601863 TGTAATAAG -s simRat_chr6.simRat.chr6 35584 9 - 647215 TCTAAATAA - -a -s simMouse_chr6.simMouse.chr6 560428 15 + 636262 CAGGTGAGGCAATTT -s Anc0.Anc0refChr3 161656 14 + 222631 -AGGTAAAGCAACTT -s Anc1.Anc1refChr1 223 15 + 69767 CAGGTAAAGCAACTT -s Anc2.Anc2refChr1 76284 14 + 142988 -AGGTAAAGCAACTT -s mr.mrrefChr3 110349 15 + 181027 CAGGTGAGGCAATTT -s simCow_chr6.simCow.chr6 534988 14 + 602619 -AGGTAGAGGAAGTT -s simDog_chr6.simDog.chr6 523250 14 + 593897 -AGGTGAAGCTACTT -s simHuman_chr6.simHuman.chr6 530183 13 + 601863 --AGTAAAGTAACTT -s simRat_chr6.simRat.chr6 35603 15 - 647215 CAGGCGAGGCAATTT - -a -s simMouse_chr6.simMouse.chr6 560443 38 + 636262 TGAGGGACACCACTACAATTGTGTATGCAAGGTGTAGT -s Anc0.Anc0refChr3 161675 38 + 222631 TAAGAGACACCACTACAATTGTGTTCTCAATTTGCAgC -s Anc1.Anc1refChr1 243 38 + 69767 TAAGAGACACCACTACAATTGTGTTCTCAATTTGCAgC -s Anc2.Anc2refChr1 76303 38 + 142988 TATGAAACACCATTACCTTTGTGTTCTGGTTTTGCAgC -s mr.mrrefChr3 110369 38 + 181027 TGAGGGACACCACTACAATTGTGTATGCAAGGTGTAGC -s simCow_chr6.simCow.chr6 535007 37 + 602619 TATGAAGAACCATACCTGTTGCTTTCTTGCTTTGCA-C -s simDog_chr6.simDog.chr6 523269 38 + 593897 AATGAAACACCATTACCTTAGTGATCTGGTCTTACAGC -s simHuman_chr6.simHuman.chr6 530201 38 + 601863 TAACAGACACCACTATAACTGTGTTCTCAATATGcagc -s simRat_chr6.simRat.chr6 35623 38 - 647215 TGAGGGACACCACTACAATTCTGTATGCAAGGTGTAGC - -a -s simMouse_chr6.simMouse.chr6 560481 6 + 636262 GTACAA -s Anc0.Anc0refChr3 161714 6 + 222631 ACACAA -s Anc1.Anc1refChr1 282 6 + 69767 ACACAA -s Anc2.Anc2refChr1 76342 6 + 142988 ACACAA -s mr.mrrefChr3 110408 6 + 181027 GTACAA -s simCow_chr6.simCow.chr6 535045 6 + 602619 GCCCAA -s simDog_chr6.simDog.chr6 523308 6 + 593897 AGATGA -s simHuman_chr6.simHuman.chr6 530240 6 + 601863 acacaa -s simRat_chr6.simRat.chr6 35662 6 - 647215 GTACAA - -a -s simMouse_chr6.simMouse.chr6 560487 8 + 636262 AAAATTCG -s Anc0.Anc0refChr3 161735 8 + 222631 aaAATTTG -s Anc1.Anc1refChr1 303 8 + 69767 aaAATTTG -s Anc2.Anc2refChr1 76363 8 + 142988 aaAATTGC -s mr.mrrefChr3 110414 8 + 181027 AAAATTTG -s simCow_chr6.simCow.chr6 535066 6 + 602619 --AGTTGA -s simDog_chr6.simDog.chr6 523330 8 + 593897 AAAACAGC -s simHuman_chr6.simHuman.chr6 530261 8 + 601863 gaaatttg -s simRat_chr6.simRat.chr6 35668 8 - 647215 AAAATTTG - -a -s simMouse_chr6.simMouse.chr6 560495 7 + 636262 AGTTCAA -s Anc0.Anc0refChr3 161747 7 + 222631 GGTGCAA -s Anc1.Anc1refChr1 315 7 + 69767 GGTGCAA -s Anc2.Anc2refChr1 76375 7 + 142988 GGTGCAA -s mr.mrrefChr3 110422 7 + 181027 AGTGCAA -s simCow_chr6.simCow.chr6 535076 7 + 602619 GGTTCAA -s simDog_chr6.simDog.chr6 523342 7 + 593897 AGTGCAA -s simHuman_chr6.simHuman.chr6 530273 7 + 601863 ggtgcaa -s simRat_chr6.simRat.chr6 35676 7 - 647215 AGTGCCA - -a -s simMouse_chr6.simMouse.chr6 560502 7 + 636262 GGAGAAG -s Anc0.Anc0refChr3 161755 7 + 222631 GAAGAAG -s Anc1.Anc1refChr1 323 7 + 69767 GAAGAAG -s Anc2.Anc2refChr1 76383 7 + 142988 GAAGAAG -s mr.mrrefChr3 110429 7 + 181027 GGAGAAG -s simCow_chr6.simCow.chr6 535084 7 + 602619 AAAAAAA -s simDog_chr6.simDog.chr6 523350 7 + 593897 GAAGAAG -s simHuman_chr6.simHuman.chr6 530281 7 + 601863 gaagaag -s simRat_chr6.simRat.chr6 35683 7 - 647215 GGAGAAG - -a -s simMouse_chr6.simMouse.chr6 560509 8 + 636262 GAGCAACA -s Anc0.Anc0refChr3 161762 8 + 222631 GAATAATG -s Anc1.Anc1refChr1 330 8 + 69767 GAATAATG -s Anc2.Anc2refChr1 76390 8 + 142988 GAATAATG -s mr.mrrefChr3 110436 8 + 181027 GAGTAACA -s simCow_chr6.simCow.chr6 535120 8 + 602619 GAATAGTG -s simDog_chr6.simDog.chr6 523357 8 + 593897 GAATAAGG -s simHuman_chr6.simHuman.chr6 530288 8 + 601863 gaataatg -s simRat_chr6.simRat.chr6 35690 8 - 647215 GAGTAACA - -a -s simMouse_chr6.simMouse.chr6 560517 6 + 636262 TAATAT -s Anc0.Anc0refChr3 161774 6 + 222631 TAACAG -s Anc1.Anc1refChr1 342 6 + 69767 TAACAG -s Anc2.Anc2refChr1 76402 6 + 142988 TAACAG -s mr.mrrefChr3 110448 6 + 181027 TAATAT -s simCow_chr6.simCow.chr6 535132 6 + 602619 TAACAG -s simDog_chr6.simDog.chr6 523369 6 + 593897 TACCAG -s simHuman_chr6.simHuman.chr6 530300 6 + 601863 taacaG -s simRat_chr6.simRat.chr6 35702 6 - 647215 TAATAT - -a -s simMouse_chr6.simMouse.chr6 560523 2 + 636262 TG -s Anc0.Anc0refChr3 161791 2 + 222631 TG -s Anc1.Anc1refChr1 359 2 + 69767 TG -s Anc2.Anc2refChr1 76419 2 + 142988 TG -s mr.mrrefChr3 110465 2 + 181027 TG -s simCow_chr6.simCow.chr6 535149 2 + 602619 TG -s simDog_chr6.simDog.chr6 523386 2 + 593897 TG -s simHuman_chr6.simHuman.chr6 530317 2 + 601863 TG -s simRat_chr6.simRat.chr6 35719 2 - 647215 TG - -a -s simMouse_chr6.simMouse.chr6 560525 11 + 636262 GCACGTGTTGT -s Anc0.Anc0refChr3 161793 11 + 222631 GCAGGTTCTGT -s Anc1.Anc1refChr1 361 11 + 69767 GCAGGTTCTGT -s Anc2.Anc2refChr1 76421 11 + 142988 GCAGGTTCTAT -s mr.mrrefChr3 110467 11 + 181027 GCAGGTGTTGT -s simCow_chr6.simCow.chr6 535155 10 + 602619 GCA-ATCATCT -s simDog_chr6.simDog.chr6 523388 11 + 593897 GCAGGTTCTAC -s simHuman_chr6.simHuman.chr6 530319 11 + 601863 GTAGGTTCTGT -s simRat_chr6.simRat.chr6 35721 11 - 647215 GCAGGAGTTGT - -a -s simMouse_chr6.simMouse.chr6 560536 28 + 636262 CAGTACTCTGAAGTGTACCAGCAATAAG -s Anc0.Anc0refChr3 161804 18 + 222631 CAGTAC----------ACTTGCAATAGG -s Anc1.Anc1refChr1 372 18 + 69767 CAGTAC----------ACTTGCAATAGG -s Anc2.Anc2refChr1 76432 18 + 142988 AAGGAC----------ACTTGCAATAAG -s mr.mrrefChr3 110478 28 + 181027 CAGTACTCTGAAGTGTACTAGCAATAGG -s simCow_chr6.simCow.chr6 535165 18 + 602619 AAGGAC----------ACTTGCAATAAG -s simDog_chr6.simDog.chr6 523408 18 + 593897 AAGGGT----------ACTTGCAATAAG -s simHuman_chr6.simHuman.chr6 530330 18 + 601863 CAGTAC----------ACTCGCAATAGG -s simRat_chr6.simRat.chr6 35732 28 - 647215 CAGTACTCTGACATGTACTATCAATAGG - -a -s simMouse_chr6.simMouse.chr6 560564 17 + 636262 CCCGATTCCCTTGCATG -s Anc0.Anc0refChr3 161823 17 + 222631 TCCTATTTCATTGCATG -s Anc1.Anc1refChr1 391 17 + 69767 TCCTATTTCATTGCATG -s Anc2.Anc2refChr1 76451 17 + 142988 TCCTATTTCATCCCATG -s mr.mrrefChr3 110506 17 + 181027 CCCGATTCCCTTGCATG -s simCow_chr6.simCow.chr6 535184 17 + 602619 TTCTATTTCCCCCCGTG -s simDog_chr6.simDog.chr6 523427 17 + 593897 TCCTATCTCATCCCATG -s simHuman_chr6.simHuman.chr6 530349 17 + 601863 TCCCGTTTCGTTGCATA -s simRat_chr6.simRat.chr6 35760 17 - 647215 CCCTATTCCCTTGCATG - -a -s simMouse_chr6.simMouse.chr6 560581 23 + 636262 TTTAATAAATGGCTCCTCAAACA -s Anc0.Anc0refChr3 161841 23 + 222631 TTTTATATAGGGTTCCTCAAACA -s Anc1.Anc1refChr1 409 23 + 69767 TTTTATATAGGGTTCCTCAAACA -s Anc2.Anc2refChr1 76469 23 + 142988 TTTTATGTAGGGTTCCACAAACA -s mr.mrrefChr3 110523 23 + 181027 TTTAATATATGGCTCCTCAAACA -s simCow_chr6.simCow.chr6 535202 23 + 602619 CTTAATGTATGGTGCCCCAGACA -s simDog_chr6.simDog.chr6 523445 23 + 593897 TTTTATGTAGGGTTCCACAAGCA -s simHuman_chr6.simHuman.chr6 530367 23 + 601863 TTTGATATAGGGTTCCTTGAACA -s simRat_chr6.simRat.chr6 35777 23 - 647215 TTTAATATATGGCTCCTCAGACA - -a -s simMouse_chr6.simMouse.chr6 560604 6 + 636262 AGCCAA -s Anc0.Anc0refChr3 161864 6 + 222631 AATCAA -s Anc1.Anc1refChr1 432 6 + 69767 AATCAA -s Anc2.Anc2refChr1 76492 6 + 142988 AATCAA -s mr.mrrefChr3 110546 6 + 181027 AACCAA -s simCow_chr6.simCow.chr6 535225 6 + 602619 ACTCAA -s simDog_chr6.simDog.chr6 523468 6 + 593897 AATCAA -s simHuman_chr6.simHuman.chr6 530390 6 + 601863 AATGAA -s simRat_chr6.simRat.chr6 35801 6 - 647215 AAGCAG - -a -s simMouse_chr6.simMouse.chr6 560610 65 + 636262 GAGACGGACCTCATTTATATTGCATTTGCCTGTTGTATGCTATGCCATTCTCATCAGCTCGAGCT -s Anc0.Anc0refChr3 161877 55 + 222631 AGGAGT---------TATTGTGCACTTGGCTGTCTCA-GTTATGCCCTTCCTGTCATCTTGGGTC -s Anc1.Anc1refChr1 445 64 + 69767 AGGAGTGAGCATATTTATTGTGCACTTGGCTGTCTCA-GTTATGCCCTTCCTGTCATCTTGGGTC -s Anc2.Anc2refChr1 76505 55 + 142988 ATGAGT---------TACTGTGCACTTGGCTGTCTCA-GTTATTCACTTCCTGTCATTATGGATC -s mr.mrrefChr3 110552 65 + 181027 GGGACGGACCTTATTTATATTGCATTTGCCTGTTGTATGTTATGCCATTCTTATCAGCTTGAGTC -s simCow_chr6.simCow.chr6 535240 55 + 602619 CTGATT---------TACTCTTCACTTGACTGTCTCC-GTTATTCCATTCCTGTCATGGTGGTTT -s simDog_chr6.simDog.chr6 523481 55 + 593897 ATGAGT---------TGCCGTGCACTTGGCTATCCCA-GTTATTCACTTCCTTTCCTTATGAATC -s simHuman_chr6.simHuman.chr6 530403 63 + 601863 AGAAGTGAGCATCTTTATTGTGCACCTGTCTGTCTCA-GTTATGAC-TTCCTGTCATCTTGGGTC -s simRat_chr6.simRat.chr6 35807 63 - 647215 GGGATAGACCTTACTTAT--TACATTTGCCTGCTGTTCATTGTGCCATCCTTATCAACTTGAGTC - -a -s simMouse_chr6.simMouse.chr6 560675 7 + 636262 TGGGTAC -s Anc0.Anc0refChr3 161932 1 + 222631 C------ -s Anc1.Anc1refChr1 509 1 + 69767 C------ -s Anc2.Anc2refChr1 76560 1 + 142988 C------ -s mr.mrrefChr3 110617 7 + 181027 TGGGTAC -s simCow_chr6.simCow.chr6 535353 1 + 602619 C------ -s simDog_chr6.simDog.chr6 523536 1 + 593897 C------ -s simHuman_chr6.simHuman.chr6 530466 1 + 601863 C------ -s simRat_chr6.simRat.chr6 35870 7 - 647215 TGGGTAC - -a -s simMouse_chr6.simMouse.chr6 560682 29 + 636262 ATCTCAATGCCACCACAAAGAGATCCAAC -s Anc0.Anc0refChr3 161933 28 + 222631 -CATCTACACCATCGTCTATGGATCTAAC -s Anc1.Anc1refChr1 510 28 + 69767 -CATCTACACCATCGTCTATGGATCTAAC -s Anc2.Anc2refChr1 76561 28 + 142988 -CATCTACACCATCGTCTATTGGTCTAAG -s mr.mrrefChr3 110624 29 + 181027 ATCTCAATGCCACCACCAAGGGATCCAAC -s simCow_chr6.simCow.chr6 535354 28 + 602619 -TACCTACATCATTGTCTATTGGCCTAAA -s simDog_chr6.simDog.chr6 523537 28 + 593897 -CATCTACACAATCATCTATTGGTCTAAG -s simHuman_chr6.simHuman.chr6 530467 28 + 601863 -CATCGGCACCATCGTCTATGGATCAAGC -s simRat_chr6.simRat.chr6 35878 29 - 647215 ATCTCAATCCCACCACCAAGGGATCCAAC - -a -s simMouse_chr6.simMouse.chr6 560711 10 + 636262 CTAAATTATA -s Anc0.Anc0refChr3 161963 10 + 222631 CTAGCTTATA -s Anc1.Anc1refChr1 540 10 + 69767 CTAGCTTATA -s Anc2.Anc2refChr1 76591 10 + 142988 CTAGCTTATA -s mr.mrrefChr3 110653 10 + 181027 CTAAATTATA -s simCow_chr6.simCow.chr6 535384 10 + 602619 CCAGCTGATA -s simDog_chr6.simDog.chr6 523567 10 + 593897 CTAGCTTACC -s simHuman_chr6.simHuman.chr6 530497 10 + 601863 CTGGCTTATA -s simRat_chr6.simRat.chr6 35907 10 - 647215 CTAAATTATG - -a -s simMouse_chr6.simMouse.chr6 560721 28 + 636262 TCTGGGACGAGTTTCCAGAAAGAAACCT -s Anc0.Anc0refChr3 161973 28 + 222631 TCTGGTATGAATTACAAGTAAGCCCCCT -s Anc1.Anc1refChr1 550 28 + 69767 TCTGGTATGAATTACAAGTAAGCCCCCT -s Anc2.Anc2refChr1 76601 28 + 142988 TCTGGTATGAATTACAATTAAGCCCCCT -s mr.mrrefChr3 110663 28 + 181027 TCTGGGATGAGTTTCCAGTAAGAAACCT -s simCow_chr6.simCow.chr6 535394 28 + 602619 TCTGGTGTGAATTACAGTTCAGCCCCCT -s simDog_chr6.simDog.chr6 523614 20 + 593897 TCTGGCATGAATTTCAATTA-------- -s simHuman_chr6.simHuman.chr6 530507 28 + 601863 CCTGGTATAATTTATAAGTAGGGCTCCT -s simRat_chr6.simRat.chr6 35917 28 - 647215 GCTGGGATGAGTATCCAGTAAGAAACCT - -a -s simMouse_chr6.simMouse.chr6 560749 60 + 636262 CTCCATTGGTTGAGCTTTGTCTTTCCACACTGACTATGGTGAGCATGCTCTAATTAACAC -s Anc0.Anc0refChr3 162001 32 + 222631 C-ACTTTAGCTAAGCTCCTTCTTTCTGTGCTG---------------------------C -s Anc1.Anc1refChr1 578 32 + 69767 C-ACTTTAGCTAAGCTCCTTCTTTCTGTGCTG---------------------------C -s Anc2.Anc2refChr1 76629 32 + 142988 C-ACTTTAGCTAAGATACTTCTTCCTGTGCTG---------------------------C -s mr.mrrefChr3 110691 60 + 181027 CTCCTTTAGTTGAGCTCTGTCTTTCCATGCTGAGTATGGTGAGCATGCTCTAATTAACAC -s simCow_chr6.simCow.chr6 535423 32 + 602619 C-ACTTTAGCTAGGATATTTCTTCCTGTGCTG---------------------------T -s simDog_chr6.simDog.chr6 523634 22 + 593897 -----------AAGATACTTCCTCCTGTGCTG---------------------------C -s simHuman_chr6.simHuman.chr6 530535 32 + 601863 C-ACTTTAGCTTAGCTCCTCCTTTCTGTGCTG---------------------------C -s simRat_chr6.simRat.chr6 35945 60 - 647215 CTTCTTTAGTTGAGCTCTGTCTTTCCATGCTGAGCATGGCGAGCATACCCTAATTAACGC - -a -s simMouse_chr6.simMouse.chr6 560809 7 + 636262 ACTCACC -s Anc0.Anc0refChr3 162033 7 + 222631 CCTTACC -s Anc1.Anc1refChr1 610 7 + 69767 CCTTACC -s Anc2.Anc2refChr1 76661 7 + 142988 CCTTACT -s mr.mrrefChr3 110751 7 + 181027 ACTCACC -s simCow_chr6.simCow.chr6 535461 7 + 602619 CCTTATT -s simDog_chr6.simDog.chr6 523656 7 + 593897 CCTTGCT -s simHuman_chr6.simHuman.chr6 530567 7 + 601863 CCTTACC -s simRat_chr6.simRat.chr6 36005 7 - 647215 ACTCTCC - -a -s simMouse_chr6.simMouse.chr6 560816 26 + 636262 TTATTGCTAGGTACCCTGCATGTTGC -s Anc0.Anc0refChr3 162154 26 + 222631 TTGTTGCTAGGTACCCTCTGTTTGGC -s Anc1.Anc1refChr1 731 26 + 69767 TTGTTGCTAGGTACCCTCTGTTTGGC -s Anc2.Anc2refChr1 76792 26 + 142988 TTGTTGCTAGGTGCCCTCTGTTTGGC -s mr.mrrefChr3 110758 26 + 181027 TTATTGCTAGGTACCCTGCATGTTGC -s simCow_chr6.simCow.chr6 535607 26 + 602619 CTGTTGCTAAGTGCTCTTTGGTTGGC -s simDog_chr6.simDog.chr6 523787 26 + 593897 TTGTTGCTAGATGCCCTCTGTTTGGC -s simHuman_chr6.simHuman.chr6 530688 26 + 601863 TTGTTGTTCGGTACCCTCTGTTAGGC -s simRat_chr6.simRat.chr6 36012 26 - 647215 TTATTGCTAGGTACCCTACAAGTTGC - -a -s simMouse_chr6.simMouse.chr6 560842 4 + 636262 ATTG -s Anc0.Anc0refChr3 162180 4 + 222631 ATGA -s Anc1.Anc1refChr1 757 4 + 69767 ATGA -s Anc2.Anc2refChr1 76823 4 + 142988 ATGA -s mr.mrrefChr3 110784 4 + 181027 ATTG -s simCow_chr6.simCow.chr6 535638 4 + 602619 ATGA -s simDog_chr6.simDog.chr6 523818 4 + 593897 ATGA -s simHuman_chr6.simHuman.chr6 530714 4 + 601863 ATGA -s simRat_chr6.simRat.chr6 36038 4 - 647215 ATTG - -a -s simMouse_chr6.simMouse.chr6 560846 15 + 636262 CATGGAAGGTTTAAT -s Anc0.Anc0refChr3 162189 14 + 222631 CAA-GAATGATTAAC -s Anc1.Anc1refChr1 766 14 + 69767 CAA-GAATGATTAAC -s Anc2.Anc2refChr1 76832 14 + 142988 CAA-GAATGATTAAC -s mr.mrrefChr3 110788 14 + 181027 CAT-GAAGGTTTAAT -s simCow_chr6.simCow.chr6 535647 14 + 602619 CAA-GACTGATTAAC -s simDog_chr6.simDog.chr6 523827 14 + 593897 CAA-GAATGGTTAAC -s simHuman_chr6.simHuman.chr6 530723 14 + 601863 CAA-GAATGACTACA -s simRat_chr6.simRat.chr6 36042 14 - 647215 GAT-GAAGTTTTAAT - -a -s simMouse_chr6.simMouse.chr6 560861 8 + 636262 TGTCTTAC -s Anc0.Anc0refChr3 162203 8 + 222631 TATCTTAC -s Anc1.Anc1refChr1 780 8 + 69767 TATCTTAC -s Anc2.Anc2refChr1 76846 8 + 142988 AATGTTAC -s mr.mrrefChr3 110802 8 + 181027 TGTCTTAC -s simCow_chr6.simCow.chr6 535661 8 + 602619 AATGTCAC -s simDog_chr6.simDog.chr6 523841 8 + 593897 ATTGTTAC -s simHuman_chr6.simHuman.chr6 530737 8 + 601863 TACCTTAC -s simRat_chr6.simRat.chr6 36067 8 - 647215 TGTCTTAC - -a -s simMouse_chr6.simMouse.chr6 560869 11 + 636262 ATTAACTCAGG -s Anc0.Anc0refChr3 162211 10 + 222631 AATAGCT-AGG -s Anc1.Anc1refChr1 788 10 + 69767 AATAGCT-AGG -s Anc2.Anc2refChr1 76854 10 + 142988 AATAGCT-AGG -s mr.mrrefChr3 110810 11 + 181027 ATTAACTCAGG -s simCow_chr6.simCow.chr6 535669 10 + 602619 TCTAGCT-GGA -s simDog_chr6.simDog.chr6 523849 10 + 593897 AATAGCT-AAG -s simHuman_chr6.simHuman.chr6 530745 10 + 601863 ATTAGCT-AGG -s simHuman_chr6.simHuman.chr6 530969 10 + 601863 AATAGTT-AGG -s simRat_chr6.simRat.chr6 36075 11 - 647215 ATTAACTCAGG - -a -s simMouse_chr6.simMouse.chr6 560880 1 + 636262 C -s Anc0.Anc0refChr3 162221 1 + 222631 T -s Anc1.Anc1refChr1 798 1 + 69767 T -s Anc2.Anc2refChr1 76864 1 + 142988 T -s mr.mrrefChr3 110821 1 + 181027 C -s simCow_chr6.simCow.chr6 535781 1 + 602619 T -s simDog_chr6.simDog.chr6 523859 1 + 593897 T -s simHuman_chr6.simHuman.chr6 530755 1 + 601863 T -s simHuman_chr6.simHuman.chr6 530979 1 + 601863 T -s simRat_chr6.simRat.chr6 36086 1 - 647215 C - -a -s simMouse_chr6.simMouse.chr6 560881 15 + 636262 AGGGTTGCAAATAAT -s Anc0.Anc0refChr3 162222 12 + 222631 ---GTCGCAAATATA -s Anc1.Anc1refChr1 799 15 + 69767 AGAGTCGCAAATATA -s Anc2.Anc2refChr1 76865 12 + 142988 ---GACGTAAATCTA -s mr.mrrefChr3 110822 15 + 181027 AGGGTTGCAAATATT -s simCow_chr6.simCow.chr6 535782 12 + 602619 ---TAGGTAAATCAA -s simDog_chr6.simDog.chr6 523860 12 + 593897 ---GAAGTAAATCTA -s simHuman_chr6.simHuman.chr6 530756 15 + 601863 AGAGTCACAAATATG -s simHuman_chr6.simHuman.chr6 530988 15 + 601863 AGAGTCGCAAATATA -s simRat_chr6.simRat.chr6 36087 15 - 647215 AGGGTTGCAAATATT - -a -s simMouse_chr6.simMouse.chr6 560896 10 + 636262 GATGAGATCA -s Anc0.Anc0refChr3 162234 9 + 222631 GATGAGATC- -s Anc1.Anc1refChr1 814 9 + 69767 GATGAGATC- -s Anc2.Anc2refChr1 76877 9 + 142988 GATGAGATC- -s mr.mrrefChr3 110837 10 + 181027 GATGAGATCA -s simCow_chr6.simCow.chr6 535794 9 + 602619 GATGAGATC- -s simDog_chr6.simDog.chr6 523872 9 + 593897 GATGAGATC- -s simHuman_chr6.simHuman.chr6 530776 9 + 601863 GGCTTGATC- -s simHuman_chr6.simHuman.chr6 531003 9 + 601863 TATGAGATC- -s simRat_chr6.simRat.chr6 36102 10 - 647215 GATGAGATTA - -a -s simMouse_chr6.simMouse.chr6 560906 33 + 636262 TGTGCCCAAATATAGGGTATATTCCTTGAAGAA -s Anc0.Anc0refChr3 162243 16 + 222631 -----------------TGTGTGCCTTTGAGAA -s Anc1.Anc1refChr1 823 16 + 69767 -----------------TGTGTGCCTTTGAGAA -s Anc2.Anc2refChr1 76886 16 + 142988 -----------------TGTGTGCCTTTGAGAA -s mr.mrrefChr3 110847 33 + 181027 TGTGCCCAAATATAGGGTATATTCCTTGAAGAA -s simCow_chr6.simCow.chr6 535803 16 + 602619 -----------------AGCATACCTCTGAGAA -s simDog_chr6.simDog.chr6 523881 16 + 593897 -----------------TGGGAGTCTTTGAGAA -s simHuman_chr6.simHuman.chr6 530785 16 + 601863 -----------------TGTGTGCCTTTGAGAA -s simHuman_chr6.simHuman.chr6 531012 13 + 601863 -----------------TGTATT---TTGAGAA -s simRat_chr6.simRat.chr6 36113 33 - 647215 TGTGCCCAAATATGGGGTATGTTCCTTCGAGAA - -a -s simMouse_chr6.simMouse.chr6 560939 1 + 636262 C -s Anc0.Anc0refChr3 162259 1 + 222631 C -s Anc1.Anc1refChr1 839 1 + 69767 C -s Anc2.Anc2refChr1 76902 1 + 142988 C -s mr.mrrefChr3 110880 1 + 181027 C -s simCow_chr6.simCow.chr6 535819 1 + 602619 C -s simDog_chr6.simDog.chr6 523897 1 + 593897 C -s simHuman_chr6.simHuman.chr6 531025 1 + 601863 C -s simRat_chr6.simRat.chr6 36146 1 - 647215 C - -a -s simMouse_chr6.simMouse.chr6 560940 15 + 636262 ATAGCCTGTCTTATG -s Anc0.Anc0refChr3 162263 15 + 222631 ATCACCTATCTCACA -s Anc1.Anc1refChr1 843 15 + 69767 ATCACCTATCTCACA -s Anc2.Anc2refChr1 76906 15 + 142988 ATCACCTATCTCACA -s mr.mrrefChr3 110881 15 + 181027 ATAGCCTGTCTTATG -s simCow_chr6.simCow.chr6 535823 15 + 602619 ATCACCTATTTCATA -s simDog_chr6.simDog.chr6 523901 15 + 593897 GTCATCTTTCTCACT -s simHuman_chr6.simHuman.chr6 530801 15 + 601863 ATCACCTATATCACA -s simHuman_chr6.simHuman.chr6 531029 15 + 601863 ATCACCTATCAGACA -s simRat_chr6.simRat.chr6 36147 15 - 647215 ATACGCTGTCTCATG - -a -s simMouse_chr6.simMouse.chr6 560955 67 + 636262 GAAGACTGTCTTCAGGGTGATATTTGAACCTACGCAGAAATGAAGGATAATTAAATAGTCTCGATAA -s Anc0.Anc0refChr3 162278 67 + 222631 AAAAACCTTCTTAAGAATAGTATGAGAGCCTACAAAGAAACTCAGGATAGTCAAAGAACCACTGCAG -s Anc1.Anc1refChr1 858 67 + 69767 AAAAACCTTCTTAAGAATAGTATGAGAGCCTACAAAGAAACTCAGGATAGTCAAAGAACCACTGCAG -s Anc2.Anc2refChr1 76921 67 + 142988 AAAAACCTTCTCAAGAATAGTATGAGAGCCTACAAAGAAACTCAGGATAGTCAAAGAACCACTGCAG -s mr.mrrefChr3 110896 67 + 181027 AAAGACTGTCTTCAGGGTGATATTTGAACCTACACAGAAATGAAGGATAATTAAAGAATCTCTATAA -s simCow_chr6.simCow.chr6 535853 67 + 602619 TAAAATCCTCTCTAGAACAATATTAGAGTCTAGAAAGAAAATTAGGAAAGTCAAAAAACTACTGCAA -s simDog_chr6.simDog.chr6 523916 63 + 593897 AAAAACCTTCTCAAGAATAGTATGACAGCCTGCAAAGAAACTCATGGTATTCCAAGAACCACC---- -s simHuman_chr6.simHuman.chr6 530816 67 + 601863 AAAAACGTTCTTAAGAATAATATTAGAGACTACAAAGGAACTCAGGATAGTCAATAAACCACTACAG -s simHuman_chr6.simHuman.chr6 531044 67 + 601863 AGAAACCTTCCTAAGAATAGTATGAGAGCCTACAAGGAAACTCAGGATGGCCAAAGAACTACTGCAG -s simRat_chr6.simRat.chr6 36162 67 - 647215 AAAGACTGTCTTCAGGGTGATATTTGAACCTACACAGAAATGAAGGATAATTAAGGAATCTCTATAA - -a -s simMouse_chr6.simMouse.chr6 561022 23 + 636262 CAAACGATTGTTAATACATTCTC -s Anc0.Anc0refChr3 162361 23 + 222631 CCCAAGACCACTAATACTTCTTC -s Anc1.Anc1refChr1 941 23 + 69767 CCCAAGACCACTAATACTTCTTC -s Anc2.Anc2refChr1 77004 23 + 142988 CCCAGGACCACTAATACTTCTTC -s mr.mrrefChr3 110974 23 + 181027 CAAACGATCGTTAATACATACTC -s simCow_chr6.simCow.chr6 535936 16 + 602619 ---AG----ACTAATACTTATTC -s simDog_chr6.simDog.chr6 523984 23 + 593897 CCAAGGACCACCAATACTACTTC -s simHuman_chr6.simHuman.chr6 530899 23 + 601863 CCCAAGACCACTGATAGTTTTTC -s simHuman_chr6.simHuman.chr6 531127 16 + 601863 CCCAAGACCACTGATA------- -s simRat_chr6.simRat.chr6 36240 23 - 647215 CAAATGATCGTTAATACATACTC - -a -s simMouse_chr6.simMouse.chr6 561045 24 + 636262 TCTATTGTTCAACTTACTCAGCTC -s Anc0.Anc0refChr3 162399 24 + 222631 TCTGTTGCCTACTTGACATGTCTT -s Anc1.Anc1refChr1 979 24 + 69767 TCTGTTGCCTACTTGACATGTCTT -s Anc2.Anc2refChr1 77042 24 + 142988 TCTGTTGCCTACTTGACATGTCTT -s mr.mrrefChr3 111000 24 + 181027 TCTATTGTTCAACTTACCCAGCTC -s simCow_chr6.simCow.chr6 535968 24 + 602619 TCTGTTACCTACTTGACATGTCTC -s simDog_chr6.simDog.chr6 524019 24 + 593897 TCTGTTGCCTACTTGACATGTTTA -s simHuman_chr6.simHuman.chr6 530937 24 + 601863 TCCAATGCCAACTCGACATGTCTT -s simHuman_chr6.simHuman.chr6 531145 24 + 601863 TCTGAAGCCTACTTGACATGTCTT -s simRat_chr6.simRat.chr6 36266 24 - 647215 TATATTGTTTAACTTGCCCACCTC - -a -s simMouse_chr6.simMouse.chr6 561069 6 + 636262 TAGTTT -s Anc0.Anc0refChr3 162433 6 + 222631 TAGCTA -s Anc1.Anc1refChr1 1013 6 + 69767 TAGCTA -s Anc2.Anc2refChr1 77076 6 + 142988 TAGCTA -s mr.mrrefChr3 111024 6 + 181027 TAGTTT -s simCow_chr6.simCow.chr6 536001 6 + 602619 TAGCCA -s simDog_chr6.simDog.chr6 524053 6 + 593897 CAGCTG -s simHuman_chr6.simHuman.chr6 531179 6 + 601863 TAGCTA -s simRat_chr6.simRat.chr6 36290 6 - 647215 TAGTTT - -a -s simMouse_chr6.simMouse.chr6 561075 13 + 636262 GGCACTTCTTAAC -s Anc0.Anc0refChr3 162448 13 + 222631 GGCACTTTTAAAT -s Anc1.Anc1refChr1 1028 13 + 69767 GGCACTTTTAAAT -s Anc2.Anc2refChr1 77092 13 + 142988 GGCACTTTTAAAT -s mr.mrrefChr3 111030 13 + 181027 GGCACTTCTTAAT -s simCow_chr6.simCow.chr6 536017 13 + 602619 GGCACTTCTTGAT -s simDog_chr6.simDog.chr6 524069 11 + 593897 TGCACTCTTAA-- -s simHuman_chr6.simHuman.chr6 531194 13 + 601863 GGCACTTTTCAAT -s simRat_chr6.simRat.chr6 36296 13 - 647215 GGCACTTCTTAAT - -a -s simMouse_chr6.simMouse.chr6 561088 9 + 636262 GGACAATAC -s Anc0.Anc0refChr3 162462 9 + 222631 CGCCAATAC -s Anc1.Anc1refChr1 1042 9 + 69767 CGCCAATAC -s Anc2.Anc2refChr1 77106 9 + 142988 CACCAATGC -s mr.mrrefChr3 111043 9 + 181027 GGACAATAC -s simCow_chr6.simCow.chr6 536031 9 + 602619 CACCAATGC -s simHuman_chr6.simHuman.chr6 531208 9 + 601863 CGCCAATAA -s simRat_chr6.simRat.chr6 36309 9 - 647215 TGACAATTT - -a -s simMouse_chr6.simMouse.chr6 561097 12 + 636262 GGTACCATCCCA -s Anc0.Anc0refChr3 162471 12 + 222631 GGAACTATCTTA -s Anc1.Anc1refChr1 1051 12 + 69767 GGAACTATCTTA -s Anc2.Anc2refChr1 77115 12 + 142988 GGAACTATCCTA -s mr.mrrefChr3 111052 12 + 181027 GGTACCATCTCA -s simCow_chr6.simCow.chr6 536057 12 + 602619 GGAACTATCCTA -s simHuman_chr6.simHuman.chr6 531217 12 + 601863 GGAACTATCTTA -s simRat_chr6.simRat.chr6 36318 12 - 647215 GGTACCATCTCC - -a -s simMouse_chr6.simMouse.chr6 561109 30 + 636262 CCCCAAGCCCCCCACGTGGCTATCACCTGT -s Anc0.Anc0refChr3 162483 30 + 222631 CCCCAGGCCCCCTAAGTAACTGTTGCCTGT -s Anc1.Anc1refChr1 1063 30 + 69767 CCCCAGGCCCCCTAAGTAACTGTTGCCTGT -s Anc2.Anc2refChr1 77127 30 + 142988 CCTCAGGCCCCCTAAGTAACGGTTGCCTGT -s mr.mrrefChr3 111064 30 + 181027 CCCCAAGCCCCCCACGTAGCTATCACCTGT -s simCow_chr6.simCow.chr6 536071 30 + 602619 CCACAGGCCCCCTAAGTAACAGTTGCCTGT -s simDog_chr6.simDog.chr6 524080 28 + 593897 --TCATGCCCCCTAAGTAACGGTTGCCTGT -s simHuman_chr6.simHuman.chr6 531229 30 + 601863 CCCCAGGCCCCCTAAGTAAATGTTGCCTGT -s simRat_chr6.simRat.chr6 36330 30 - 647215 CCCCAAGCCCCCCACATAGCTATCACCTGT - -a -s simMouse_chr6.simMouse.chr6 561139 27 + 636262 AGCTGAGCTGAGTATCTACCTCCTTGT -s Anc0.Anc0refChr3 162513 22 + 222631 AG----A-TGTCTATCTAGCTCTTAGT -s Anc1.Anc1refChr1 1093 22 + 69767 AG----A-TGTCTATCTAGCTCTTAGT -s Anc2.Anc2refChr1 77157 22 + 142988 AG----A-TGTATACCTAGCTCTTAGT -s mr.mrrefChr3 111094 26 + 181027 AGCTGAG-TGTCTATCTACCTCCTAGT -s simCow_chr6.simCow.chr6 536102 22 + 602619 AG----A-TGTATCCCTAGCTCTTAGC -s simDog_chr6.simDog.chr6 524108 22 + 593897 CA----A-TGTATACCTAGCTCTTGAT -s simHuman_chr6.simHuman.chr6 531259 22 + 601863 AG----A-TGTCCATCTAGCTCTCAGT -s simRat_chr6.simRat.chr6 36360 26 - 647215 GTCTGAG-TATCTATCTATCTCCTATT - -a -s simMouse_chr6.simMouse.chr6 561166 28 + 636262 TCACATAACAGGATACCAAAGTGGACCT -s Anc0.Anc0refChr3 162535 18 + 222631 TTATATGGCAGGAT----------ACCT -s Anc1.Anc1refChr1 1115 18 + 69767 TTATATGGCAGGAT----------ACCT -s Anc2.Anc2refChr1 77184 18 + 142988 TTATATGGCAGGAT----------TCAT -s mr.mrrefChr3 111120 28 + 181027 TCACATAACAGGATACCAAAGTGGACCT -s simCow_chr6.simCow.chr6 536129 16 + 602619 TTATAGGGCAGGAT----------T--T -s simDog_chr6.simDog.chr6 524135 18 + 593897 TTGTATGGCAGGAT----------TCAC -s simHuman_chr6.simHuman.chr6 531281 18 + 601863 TTATATGGTAGGAT----------ACCT -s simRat_chr6.simRat.chr6 36386 28 - 647215 TCACATCACAGGATACCAAAGTGAAACT - -a -s simMouse_chr6.simMouse.chr6 561194 20 + 636262 GGAGTGGACCTGGAATCATT -s Anc0.Anc0refChr3 162553 20 + 222631 AGAGTGGTCCTGAGTTCATT -s Anc1.Anc1refChr1 1133 20 + 69767 AGAGTGGTCCTGAGTTCATT -s Anc2.Anc2refChr1 77202 20 + 142988 AGAGTGGTCCTGAGTTCATT -s mr.mrrefChr3 111148 20 + 181027 GGAGTGGACCTGGGATCATT -s simCow_chr6.simCow.chr6 536145 20 + 602619 AGAGTAGACCTGGGTTCATT -s simDog_chr6.simDog.chr6 524153 20 + 593897 AGAGTGGTCCTGAGTTCATT -s simHuman_chr6.simHuman.chr6 531299 9 + 601863 AGGGTC-----------ATG -s simRat_chr6.simRat.chr6 36417 20 - 647215 GGAGTGGACCTGGGTTCATT - -a -s simMouse_chr6.simMouse.chr6 561214 4 + 636262 CTCC -s Anc0.Anc0refChr3 162573 2 + 222631 CT-- -s Anc1.Anc1refChr1 1153 4 + 69767 CTGC -s Anc2.Anc2refChr1 77222 2 + 142988 CT-- -s mr.mrrefChr3 111168 4 + 181027 CTCC -s simCow_chr6.simCow.chr6 536168 2 + 602619 CC-- -s simDog_chr6.simDog.chr6 524173 2 + 593897 CT-- -s simHuman_chr6.simHuman.chr6 531308 4 + 601863 CTGC -s simRat_chr6.simRat.chr6 36437 4 - 647215 CTTC - -a -s simMouse_chr6.simMouse.chr6 561218 48 + 636262 AAATCTGTAGCTGACCCTGATGCCAGAGGCTTTCCCCATGCTGGAGTG -s Anc0.Anc0refChr3 162575 47 + 222631 -AATCCATAGCTGACCCTCATGCTAGGAGCTGACCTCATGCTAGAATG -s Anc1.Anc1refChr1 1157 48 + 69767 AAATCCATAGCTGACCCTCATGCTAGGAGCTGACCTCATGCTAGAATG -s Anc2.Anc2refChr1 77224 47 + 142988 -AATCCAGAGCTGACTCTCACGCTAGGAGTTGACCTCATGCTAGAATG -s mr.mrrefChr3 111172 48 + 181027 AAATCCATAGCTGACCCTCATGCCAGAGGCTTTCCTCATGCTGGAGTG -s simCow_chr6.simCow.chr6 536170 47 + 602619 -AATCCAGAAGCGACTCTCACGCTACGAGTCCACATGATGCTAGGATG -s simDog_chr6.simDog.chr6 524175 43 + 593897 -GATCCAGAGCTGACTCTTA---TAGAAATTGACCTC-TGCTAGAATG -s simHuman_chr6.simHuman.chr6 531312 48 + 601863 AAATCCATAGCTGATCCTCATGCTGGGAGCTGACCTCTTGCTAGAATG -s simRat_chr6.simRat.chr6 36444 48 - 647215 AAATCCATAGCTGACCCTCATGCCAGAGGCTTTCCTCATGCTGGAGTG - -a -s simMouse_chr6.simMouse.chr6 561266 7 + 636262 CAGAATA -s Anc0.Anc0refChr3 162629 7 + 222631 CAGAACA -s Anc1.Anc1refChr1 1212 7 + 69767 CAGAACA -s Anc2.Anc2refChr1 77278 7 + 142988 CAGAACA -s mr.mrrefChr3 111227 7 + 181027 CAGAATA -s simCow_chr6.simCow.chr6 536224 7 + 602619 TAGAACA -s simDog_chr6.simDog.chr6 524225 7 + 593897 CAGAACA -s simHuman_chr6.simHuman.chr6 531367 7 + 601863 CAGAACA -s simRat_chr6.simRat.chr6 36499 7 - 647215 CAGAATA - -a -s simMouse_chr6.simMouse.chr6 561273 57 + 636262 TTGTTAACATCATCAGTCATTCTTAGAAACAATTAGAAGAAGAACTTGCCTCTAAGT -s Anc0.Anc0refChr3 162636 57 + 222631 TCCTTCACACCACCTATCATTCTTAAGAACAATTAGCAGGAGAACTTGCCCAAAACT -s Anc1.Anc1refChr1 1219 57 + 69767 TCCTTCACACCACCTATCATTCTTAAGAACAATTAGCAGGAGAACTTGCCCAAAACT -s Anc2.Anc2refChr1 77285 57 + 142988 ACCTTCACACCACTTATCATTCTTAAGAACTATTAGCAGGATAACTTGCCCAAAACT -s mr.mrrefChr3 111234 57 + 181027 TTGTTAACATCATCAGTCATTCTTAGAAACAATTAGAAGAAGAACTTGCCTATAAGT -s simCow_chr6.simCow.chr6 536231 57 + 602619 ACCTACCCACCACTTCCCATTATTCAGAATTACGAACAGGAAAACTTGCCTGAAACT -s simDog_chr6.simDog.chr6 524232 56 + 593897 -CCTTCACACCACTTATCATTCTTAAGAACTATTAGCAGGATGACTTCCCCAAAACT -s simHuman_chr6.simHuman.chr6 531374 57 + 601863 TCCTCCACACCACCTATCATTCTTGACAACAATTAGCAGGAGAACTTGCCCAAAACT -s simRat_chr6.simRat.chr6 36507 57 - 647215 TTGTTAATATCATCGCTTGTTTTTAGAAACACTTTGAAGAAGAACTTGCCTATAAGT - -a -s simMouse_chr6.simMouse.chr6 561330 26 + 636262 TATATGGCACGCAGCAGTTTATTCTT -s Anc0.Anc0refChr3 162693 26 + 222631 TGTATTGCAAGCAACAGTTTATGTAT -s Anc1.Anc1refChr1 1276 26 + 69767 TGTATTGCAAGCAACAGTTTATGTAT -s Anc2.Anc2refChr1 77342 26 + 142988 TGTGTTGCAAGCAACAGTTTATGTAT -s mr.mrrefChr3 111291 26 + 181027 TATATGGCACGCAGCAGTTTATTCTT -s simCow_chr6.simCow.chr6 536299 26 + 602619 TGTCTTGCAAGCAATAATTCATGTGT -s simDog_chr6.simDog.chr6 524288 26 + 593897 GGTGTTTCACACAGCAGCTTATGTAT -s simHuman_chr6.simHuman.chr6 531431 26 + 601863 TGTATTGCAAGCAACAGTTTATGTAT -s simRat_chr6.simRat.chr6 36564 26 - 647215 TATATGGCACGCAGCAATTTATCCTT - -a -s simMouse_chr6.simMouse.chr6 561356 8 + 636262 GGCCTATG -s Anc0.Anc0refChr3 162719 8 + 222631 GGCCTATG -s Anc1.Anc1refChr1 1302 8 + 69767 GGCCTATG -s Anc2.Anc2refChr1 77368 8 + 142988 GGCCTATG -s mr.mrrefChr3 111317 8 + 181027 GGCCTATG -s simCow_chr6.simCow.chr6 536325 8 + 602619 GGCCTATA -s simDog_chr6.simDog.chr6 524314 8 + 593897 GGCCTATG -s simHuman_chr6.simHuman.chr6 531457 8 + 601863 GGCCTGTG -s simRat_chr6.simRat.chr6 36641 8 - 647215 GGCCTATG - -a -s simMouse_chr6.simMouse.chr6 561364 21 + 636262 GAAGAATGAGTACATACACAA -s Anc0.Anc0refChr3 162727 16 + 222631 GAAGAACATGTATA-----AA -s Anc1.Anc1refChr1 1310 16 + 69767 GAAGAACATGTATA-----AA -s Anc2.Anc2refChr1 77377 16 + 142988 GAAGAACATGTATA-----TA -s mr.mrrefChr3 111325 21 + 181027 GAAGAATGAGTACATACACAA -s simCow_chr6.simCow.chr6 536334 14 + 602619 --AGGACATATATA-----TC -s simDog_chr6.simDog.chr6 524323 16 + 593897 GAAGAACATGTATA-----TA -s simHuman_chr6.simHuman.chr6 531465 16 + 601863 GATGAACATGTATA-----AA -s simRat_chr6.simRat.chr6 36649 21 - 647215 GAAGAATGAATACATACACAA - -a -s simMouse_chr6.simMouse.chr6 561385 22 + 636262 TTTTTCATATGTTATAATTATG -s Anc0.Anc0refChr3 162743 20 + 222631 TCTATCAGATGT-ATAGGTAT- -s Anc1.Anc1refChr1 1326 21 + 69767 TCTATCAGATGT-ATAGGTATG -s Anc2.Anc2refChr1 77393 20 + 142988 TCTATCAGTTGT-ATAGGTAT- -s mr.mrrefChr3 111346 21 + 181027 TCTTTCATATGT-GTAATTATG -s simCow_chr6.simCow.chr6 536348 20 + 602619 TCTACCGGCTGT-ACAGCTAT- -s simDog_chr6.simDog.chr6 524339 20 + 593897 TCTATCAGTTGT-ATAGGTAT- -s simHuman_chr6.simHuman.chr6 531481 13 + 601863 TCTATCACATG---------TG -s simRat_chr6.simRat.chr6 36671 21 - 647215 TCTTTCATATGT-GTAATTATG - -a -s simMouse_chr6.simMouse.chr6 561407 10 + 636262 TGCAATTCTT -s Anc0.Anc0refChr3 162763 10 + 222631 CGCAATCCTT -s Anc1.Anc1refChr1 1347 10 + 69767 CGCAATCCTT -s Anc2.Anc2refChr1 77413 10 + 142988 CGCAGTCCTT -s mr.mrrefChr3 111367 10 + 181027 TGCAATTCTT -s simCow_chr6.simCow.chr6 536368 6 + 602619 ----GTCTTT -s simDog_chr6.simDog.chr6 524360 10 + 593897 CGCAGTCCTT -s simHuman_chr6.simHuman.chr6 531494 10 + 601863 AGCAATCGTC -s simRat_chr6.simRat.chr6 36692 10 - 647215 TGCAATGCTT - -a -s simMouse_chr6.simMouse.chr6 561417 30 + 636262 GACTGATATTCTAAGTTTTATTGAATGAGT -s Anc0.Anc0refChr3 162773 30 + 222631 GATGGTGTTACCAAGTATGATTGTATGATT -s Anc1.Anc1refChr1 1357 30 + 69767 GATGGTGTTACCAAGTATGATTGTATGATT -s Anc2.Anc2refChr1 77432 30 + 142988 GATGGTGTTACCAAGTATGATTGTATGGTT -s mr.mrrefChr3 111377 30 + 181027 GACTGATATTCTAAGTTTTATTGAATGAGT -s simCow_chr6.simCow.chr6 536383 29 + 602619 GACAGTGTTACCGAGTTT-ATTGTATGGTT -s simDog_chr6.simDog.chr6 524379 30 + 593897 GATGGTGTTACCAATTATGATTGTATGGTC -s simHuman_chr6.simHuman.chr6 531504 30 + 601863 AATGGTGTTACCAAGTCTGGTTTTACGACT -s simRat_chr6.simRat.chr6 36702 26 - 647215 GA----TATTCTAAGTTTTATTGAGTGAGT - -a -s simMouse_chr6.simMouse.chr6 561447 10 + 636262 AGAACATGGT -s Anc0.Anc0refChr3 162804 10 + 222631 TCAACTTGGT -s Anc1.Anc1refChr1 1388 10 + 69767 TCAACTTGGT -s Anc2.Anc2refChr1 77463 10 + 142988 TCAACTTGGT -s mr.mrrefChr3 111408 10 + 181027 AGAACTTGGT -s simCow_chr6.simCow.chr6 536413 10 + 602619 GGAACTTGGC -s simDog_chr6.simDog.chr6 524410 10 + 593897 TCAACTTGGT -s simHuman_chr6.simHuman.chr6 531535 10 + 601863 CAAACTTGAT -s simRat_chr6.simRat.chr6 36729 10 - 647215 AGAATTTGGT - -a -s simMouse_chr6.simMouse.chr6 561457 15 + 636262 TAAACTGTGGTAATT -s Anc0.Anc0refChr3 162815 15 + 222631 TCAACAGGGATGATT -s Anc1.Anc1refChr1 1399 15 + 69767 TCAACAGGGATGATT -s Anc2.Anc2refChr1 77474 15 + 142988 TCAACAGGGATGGTT -s mr.mrrefChr3 111418 15 + 181027 TAAACTGTGGTGATT -s simCow_chr6.simCow.chr6 536424 15 + 602619 TCAAGAGGGATAGTT -s simDog_chr6.simDog.chr6 524421 15 + 593897 CCAACAGGGATGGTT -s simHuman_chr6.simHuman.chr6 531546 15 + 601863 TCAATAGGGATGATG -s simRat_chr6.simRat.chr6 36739 15 - 647215 TAAACTGTAGTGATT - -a -s simMouse_chr6.simMouse.chr6 561472 20 + 636262 GCTATTACTGTGGGCTTATC -s Anc0.Anc0refChr3 162830 20 + 222631 GGTATGATTGGGAACTTGAC -s Anc1.Anc1refChr1 1414 20 + 69767 GGTATGATTGGGAACTTGAC -s Anc2.Anc2refChr1 77489 20 + 142988 GGTATGATTGGGAACTTGAT -s mr.mrrefChr3 111433 20 + 181027 GGTATGACTGTGGACTTATC -s simCow_chr6.simCow.chr6 536449 20 + 602619 GGTATGACTCGGAACTTGAT -s simDog_chr6.simDog.chr6 524436 20 + 593897 GGTATGATTGGAAACTTCAT -s simHuman_chr6.simHuman.chr6 531561 20 + 601863 GGTGTGATTTGGAACTAGGC -s simRat_chr6.simRat.chr6 36754 20 - 647215 GGTATGACGGTGTACTTATT - -a -s simMouse_chr6.simMouse.chr6 561492 36 + 636262 TCAACAGGGATGAATCTGAAGCAATGGACTATATCA -s Anc0.Anc0refChr3 162851 28 + 222631 TCAACAGGGGTGAATCTGAAGTC--------TTTCA -s Anc1.Anc1refChr1 1435 28 + 69767 TCAACAGGGGTGAATCTGAAGTC--------TTTCA -s Anc2.Anc2refChr1 77510 28 + 142988 TCAACAGGTGTGAATCTGAAATC--------TTTCA -s mr.mrrefChr3 111454 36 + 181027 TCAACAGGGATGAATCTGAAGCCATGGACTATATCA -s simCow_chr6.simCow.chr6 536470 28 + 602619 TTAACAGAAGTGAATCTGAAATC--------CTTCA -s simDog_chr6.simDog.chr6 524457 28 + 593897 TCAATAGGTATGAACCTGAAATC--------TTCTA -s simHuman_chr6.simHuman.chr6 531582 28 + 601863 TGATCAGGGGTGAATCTAAAGTC--------TTTCA -s simRat_chr6.simRat.chr6 36775 36 - 647215 TCAACAGGGACAAATCTGAAACCATGGAGTATCTCA - -a -s simMouse_chr6.simMouse.chr6 561528 4 + 636262 ACAT -s Anc0.Anc0refChr3 162937 4 + 222631 ATCT -s Anc1.Anc1refChr1 1521 4 + 69767 ATCT -s Anc2.Anc2refChr1 77596 4 + 142988 ATCC -s mr.mrrefChr3 111490 4 + 181027 ACAT -s simCow_chr6.simCow.chr6 536557 4 + 602619 ATCC -s simHuman_chr6.simHuman.chr6 531668 4 + 601863 ATCT -s simRat_chr6.simRat.chr6 36811 4 - 647215 ACAT - -a -s simMouse_chr6.simMouse.chr6 561532 20 + 636262 GCACTTTGTGACCAGGTGTA -s Anc0.Anc0refChr3 162941 19 + 222631 AAACTTTTTAATTAAGTAT- -s Anc1.Anc1refChr1 1525 19 + 69767 AAACTTTTTAATTAAGTAT- -s Anc2.Anc2refChr1 77600 19 + 142988 AAACACTTAAATTTAGTAT- -s mr.mrrefChr3 111494 20 + 181027 GCACTTTGTGACCAGGTGTA -s simCow_chr6.simCow.chr6 536561 19 + 602619 AAACACTTAAATTTAGTAT- -s simHuman_chr6.simHuman.chr6 531672 19 + 601863 ATACTTCTTCAATAAGTAT- -s simRat_chr6.simRat.chr6 36816 20 - 647215 GCACTTTGTGACCAGTTGTA - -a -s simMouse_chr6.simMouse.chr6 561552 50 + 636262 TCAATATGGGATTCTTGTGTATTAGTATTTGCAGACAAGCTTGTACTTTG -s Anc0.Anc0refChr3 162960 46 + 222631 TCTATATTAGGATCCTTTGTAATGGTCATTGGAGACAA---TG-ACTCTG -s Anc1.Anc1refChr1 1544 46 + 69767 TCTATATTAGGATCCTTTGTAATGGTCATTGGAGACAA---TG-ACTCTG -s Anc2.Anc2refChr1 77619 46 + 142988 ACTATATTAAGACCCTTTGCCATGGTCAGTGGAGACAA---TG-ACCCTG -s mr.mrrefChr3 111514 50 + 181027 TCAATATGGGATTCTTGTGTATTAGTATTTGCAGACAAGCTTGTACTTTG -s simCow_chr6.simCow.chr6 536581 45 + 602619 ACTATATGATGTCCCTTTGCCATGGTCACTGGAGACAA---C--ATCCTG -s simDog_chr6.simDog.chr6 524511 37 + 593897 ----TACTCAGACACC-----ACAGTGAGTGGAGACAA---TG-ACCCTA -s simHuman_chr6.simHuman.chr6 531691 46 + 601863 TCTATATTAGGATCCTTTGTAATGGTCATTGGAGTCAA---TG-ACTCTG -s simRat_chr6.simRat.chr6 36836 43 - 647215 GCAATTTGGAATTCT-GTGTATTTGTAT------ACAAGCCTGTACTTTA - -a -s simMouse_chr6.simMouse.chr6 561602 24 + 636262 GACCATAAATCCAAGATTCACCCT -s Anc0.Anc0refChr3 163008 24 + 222631 GAAAGTGAGTACAAATGCCGTCTT -s Anc1.Anc1refChr1 1592 24 + 69767 GAAAGTGAGTACAAATGCCGTCTT -s Anc2.Anc2refChr1 77667 24 + 142988 AAAAGTGAGCACGAATGCTGTCTT -s mr.mrrefChr3 111564 24 + 181027 GACCATAAATCCAAGATTCACCCT -s simCow_chr6.simCow.chr6 536628 24 + 602619 AAAAGTAAGCAGGAATCCTGTATA -s simDog_chr6.simDog.chr6 524550 24 + 593897 AAAGTTGAGCACGCATGCTGCCTT -s simHuman_chr6.simHuman.chr6 531739 24 + 601863 GAAAGTGAGTACAACTGCCGTCTT -s simRat_chr6.simRat.chr6 36879 22 - 647215 GACTATAGATGCTAGATTCAC--T - -a -s simMouse_chr6.simMouse.chr6 561626 6 + 636262 TACCTT -s Anc0.Anc0refChr3 163035 6 + 222631 TGAATT -s Anc1.Anc1refChr1 1619 6 + 69767 TGAATT -s Anc2.Anc2refChr1 77694 6 + 142988 TAAATT -s mr.mrrefChr3 111588 6 + 181027 TGACTT -s simCow_chr6.simCow.chr6 536655 6 + 602619 TACATT -s simDog_chr6.simDog.chr6 524577 6 + 593897 TAAATT -s simHuman_chr6.simHuman.chr6 531766 6 + 601863 TGAATT -s simRat_chr6.simRat.chr6 36901 6 - 647215 TGACCT - -a -s simMouse_chr6.simMouse.chr6 561632 47 + 636262 GTGGTTGATGCACTTGCCACTTCATATTATTTGGCTGTCAGGTATAT -s Anc0.Anc0refChr3 163066 45 + 222631 ATGGTTGATGCACTTGCCACT--ATATTATTAGGCTGTGGGATGTAT -s Anc1.Anc1refChr1 1650 47 + 69767 ATGGTTGATGCACTTGCCACTTAATATTATTAGGCTGTGGGATGTAT -s Anc2.Anc2refChr1 77725 45 + 142988 ATGGTTGATGCAGTTACCGCT--GTACTATTAGGGTGTGGGATGTAT -s mr.mrrefChr3 111594 47 + 181027 GTGGTTGATGCACTTGCCACTTAATATTATTTGGCTGTCAGGTGTAT -s simCow_chr6.simCow.chr6 536686 45 + 602619 ATGGTTGATGCAGTTACCGCT--GTACTATTTGGTTGTGAGATGTAT -s simDog_chr6.simDog.chr6 524601 19 + 593897 ----------------------------ACTAGGGTGTGGGAAGCAT -s simHuman_chr6.simHuman.chr6 531797 47 + 601863 ATGATGGATGCACTCGCCACTTAATATCATTGAGCTTTGGAATGTGT -s simRat_chr6.simRat.chr6 36907 47 - 647215 GTGGTTGATACACTTACCACTGAATATTATTTGGCCGTCAGGTGTAT - -a -s simMouse_chr6.simMouse.chr6 561679 13 + 636262 TGTCCTGAAATGA -s Anc0.Anc0refChr3 163111 13 + 222631 TGTCCAGAAATGA -s Anc1.Anc1refChr1 1697 13 + 69767 TGTCCAGAAATGA -s Anc2.Anc2refChr1 77770 13 + 142988 TGTCCAGAAATGA -s mr.mrrefChr3 111641 13 + 181027 TGTCCTGAAATGA -s simCow_chr6.simCow.chr6 536739 13 + 602619 TGTCCAGAAATGA -s simDog_chr6.simDog.chr6 524620 13 + 593897 TGTCCATAAACGA -s simHuman_chr6.simHuman.chr6 531844 13 + 601863 TGCCCAGAAATAA -s simRat_chr6.simRat.chr6 36954 13 - 647215 TGTCCTGGGATGA - -a -s simMouse_chr6.simMouse.chr6 561692 57 + 636262 TGGCTTATAGCGGCTAGAAAAATGTGAAATAGCTGGTGACAGATACAATTTCCTTTA -s Anc0.Anc0refChr3 163124 57 + 222631 TGGCTTATAGCAGCTAGAAGCATGTGACGTATCTAGTGACACATACAGCTTCCCTTA -s Anc1.Anc1refChr1 1710 57 + 69767 TGGCTTATAGCAGCTAGAAGCATGTGACGTATCTAGTGACACATACAGCTTCCCTTA -s Anc2.Anc2refChr1 77783 57 + 142988 TGGCTTATAGCAGCTAGAAGCATGCAACGTTTCTAGTTACACATACAGCTTGCCTTA -s mr.mrrefChr3 111654 57 + 181027 TGGCTTATAGCAGCTAGAAAAATGTGACATATCTGGTGACAGATACAATTTCCTTTA -s simCow_chr6.simCow.chr6 536752 57 + 602619 TGGCTTATAACAGGTAGAAGCATGCAACATCTCTAGTTACCTGTACAGCTTGTTTTA -s simDog_chr6.simDog.chr6 524633 56 + 593897 TGGCTTCTTGCTGCTAAAAACATGCAACGTTACTAGTTACACATACAGCTT-CCTTA -s simHuman_chr6.simHuman.chr6 531858 57 + 601863 TGGCTTATAGCAGTTAGGAGCATGTGTCGGATCTAGAGACACATTCAGCTTCCCCTA -s simRat_chr6.simRat.chr6 36967 57 - 647215 TGGCTTATAGCAGCTAGTAAAATGTGGCATATCTTGTGACAGATACAATTTGTTTTA - -a -s simMouse_chr6.simMouse.chr6 561749 6 + 636262 ACAACT -s Anc0.Anc0refChr3 163181 6 + 222631 ACAGTT -s Anc1.Anc1refChr1 1767 6 + 69767 ACAGTT -s Anc2.Anc2refChr1 77840 6 + 142988 TCAGTT -s mr.mrrefChr3 111711 6 + 181027 ACAATT -s simCow_chr6.simCow.chr6 536809 6 + 602619 TCAATT -s simDog_chr6.simDog.chr6 524689 6 + 593897 TTGGTT -s simHuman_chr6.simHuman.chr6 531935 6 + 601863 ACAGTT -s simRat_chr6.simRat.chr6 37024 6 - 647215 ACAATT - -a -s simMouse_chr6.simMouse.chr6 561755 7 + 636262 CAATATG -s Anc0.Anc0refChr3 163187 1 + 222631 ------G -s Anc1.Anc1refChr1 1773 7 + 69767 CAATGTG -s Anc2.Anc2refChr1 77846 1 + 142988 ------G -s mr.mrrefChr3 111717 7 + 181027 CAATATG -s simCow_chr6.simCow.chr6 536815 1 + 602619 ------G -s simDog_chr6.simDog.chr6 524695 1 + 593897 ------G -s simHuman_chr6.simHuman.chr6 531942 7 + 601863 CAATGTA -s simRat_chr6.simRat.chr6 37030 7 - 647215 CAATATG - -a -s simMouse_chr6.simMouse.chr6 561762 46 + 636262 ATTTTTATACAGTTTGAAGAACGTTTCTCACTGAACTGCCAATCAT -s Anc0.Anc0refChr3 163188 46 + 222631 AGTTATCCGCAGTTCAAAGAAAGTAGCCCACTGAACTGACAATCAC -s Anc1.Anc1refChr1 1780 46 + 69767 AGTTATCCGCAGTTCAAAGAAAGTAGCCCACTGAACTGACAATCAC -s Anc2.Anc2refChr1 77847 46 + 142988 AGTTATCCGCAGTTCAAAGAAAGAAGCCCAATGAACTGACAATTAC -s mr.mrrefChr3 111724 46 + 181027 ATTTTTATACAGTTCAAAGAAAGTTTCTCACTGAACTGCCAATCAT -s simCow_chr6.simCow.chr6 536823 46 + 602619 AGTTATCCACTGTTTAAATAAAGCAGCCCAATGAACTGCCAATTAC -s simDog_chr6.simDog.chr6 524696 46 + 593897 AGTTATCTGCAATTCAAAGAAAGAAGCCCAAGGAACTTACAGTTAC -s simHuman_chr6.simHuman.chr6 531949 46 + 601863 AGTTATTCGCAGTTCCAAGAAAGTAGCCCACTGAGCTGTCAATCTC -s simRat_chr6.simRat.chr6 37037 44 - 647215 ATTTTTATACAGTTCAAAGAGAGCTACTCACTGA--TACCAATCAT - -a -s simMouse_chr6.simMouse.chr6 561808 47 + 636262 AACAACCAAAGAGAGTTGTATTAGCAAGCAATCTATTGCTTATGTGT -s Anc0.Anc0refChr3 163272 47 + 222631 GACAACCAAAGATAGTTGCATGAGGGGGCAATCTATTGTGTATGAGT -s Anc1.Anc1refChr1 1864 47 + 69767 GACAACCAAAGATAGTTGCATGAGGGGGCAATCTATTGTGTATGAGT -s Anc2.Anc2refChr1 77931 47 + 142988 GATAACCAAAGATAGTTGCATGAGGGGGCAATCTATTGTGTATGAGT -s mr.mrrefChr3 111770 47 + 181027 ACCAACCAAAAAGAGTTGTATTAGCAAGCAATCTATTGTTTATGAGT -s simCow_chr6.simCow.chr6 536890 47 + 602619 AATAACCAAAAATAGTTGCATGAGGGGGGAATCTACTGTATATGAGA -s simDog_chr6.simDog.chr6 524780 47 + 593897 GATAACCAACGATAAGTGCATGAGGGGACAATCTATTGTGTGAGAGT -s simHuman_chr6.simHuman.chr6 532041 47 + 601863 GACAACCGAATATAGTTGCAAGAGGGTGCAATGTATTGGGTATGAGT -s simRat_chr6.simRat.chr6 37081 47 - 647215 ACCAACCAAAAAGAGTTGTATTTGCCAGCAATCTATTGTTAATCAGT - -a -s simMouse_chr6.simMouse.chr6 561855 6 + 636262 GCTGAG -s Anc0.Anc0refChr3 163319 6 + 222631 GCCAAG -s Anc1.Anc1refChr1 1911 6 + 69767 GCCAAG -s Anc2.Anc2refChr1 77978 6 + 142988 GCCAAG -s mr.mrrefChr3 111817 6 + 181027 GCCGAG -s simCow_chr6.simCow.chr6 536941 6 + 602619 GCCGAA -s simDog_chr6.simDog.chr6 524827 6 + 593897 GCCAAG -s simHuman_chr6.simHuman.chr6 532088 6 + 601863 GCCAAG -s simRat_chr6.simRat.chr6 37128 6 - 647215 GCCGAA - -a -s simMouse_chr6.simMouse.chr6 561861 34 + 636262 GAATTATTATGAGTTTAATTACACATTGAGGCCC -s Anc0.Anc0refChr3 163325 34 + 222631 GAATTATTGTGAATTTAATTTTGCATTGAGGCCC -s Anc1.Anc1refChr1 1917 34 + 69767 GAATTATTGTGAATTTAATTTTGCATTGAGGCCC -s Anc2.Anc2refChr1 77984 34 + 142988 GAATTAATGTGAGTTTAATTTTGCATTGAGGCCC -s mr.mrrefChr3 111823 34 + 181027 GAATTATTATGAATTTAATTACACATTGAGGCCC -s simCow_chr6.simCow.chr6 536950 34 + 602619 GAATTAATGTGAGTTTCATTTCAGATTGAGGCCC -s simDog_chr6.simDog.chr6 524833 34 + 593897 AACTTAATGCGAGATTAATTTTGCATTGAGGCCC -s simHuman_chr6.simHuman.chr6 532094 15 + 601863 GAATTGTTGTGAATT------------------- -s simRat_chr6.simRat.chr6 37134 34 - 647215 GAATTATTATGAATTTAATTATGCATTGAGTCCC - -a -s simMouse_chr6.simMouse.chr6 561895 46 + 636262 TGGGAGTCTTGAGACCACACAAGAGGCATGTGGTTAGTACATATAA -s Anc0.Anc0refChr3 163359 10 + 222631 TGGATGCCTT------------------------------------ -s Anc1.Anc1refChr1 1951 10 + 69767 TGGATGCCTT------------------------------------ -s Anc2.Anc2refChr1 78036 10 + 142988 TGGATGCCTT------------------------------------ -s mr.mrrefChr3 111857 44 + 181027 TGGGAGTCTTGAGACCACACAAGAGGCATGTGGT--GTACATATAA -s simCow_chr6.simCow.chr6 537002 10 + 602619 CAGGCACCAT------------------------------------ -s simDog_chr6.simDog.chr6 524885 10 + 593897 TGGATGCCTT------------------------------------ -s simRat_chr6.simRat.chr6 37168 44 - 647215 TGGGAGCCTTGGGACAATGCAAGAGGCATGTGGT--ATACATAAAA - -a -s simMouse_chr6.simMouse.chr6 561941 132 + 636262 CTTAAAACTGCAGCCCTCCGATTTATTTTGACTCTAGAAACATTGCAGCTGGTGCCCCTTGAATTGGCCATTGATTTGGAGGGCAAGAGTGCTGTTACACCTTCATCAGCTGAGTTGGGGCATTGAGGTGAT -s mr.mrrefChr3 111901 128 + 181027 CTTAAAACTGCAGCCCTCCGATTTATTTTGACTCTAGAAACATTGCAGCTGGTGCCCCTTGAATTGGCCATTGATTTGGAGGGCAAGAGTGCTGTTACACCTTCATCAGCTGAGTTGGGG----GAGGTGAT -s simRat_chr6.simRat.chr6 37213 128 - 647215 CTTGTAATTGCAGGCCTCTGATTTATTTTGTGTCCAGAAATATTGCAGCTGGTGCCCTTTGAGTTGGCCATCAATTTGGAGGACTTGAGTGCTGTCATACCTTCACCAACTGAAATGGGG----GGAGTGAG - -a -s simMouse_chr6.simMouse.chr6 562073 75 + 636262 TCAACCTGCTCAGGACACGCAGAATCGGTCTGAGACCCACGCAGAATCGGTCTGAGACCCCACAAGAGACATGTT -s mr.mrrefChr3 112029 53 + 181027 TCAACCTGCTCAGGACACGCAGAATCGGTCTGAGACCC----------------------CACAAGAGACATGTT -s simRat_chr6.simRat.chr6 37347 53 - 647215 TCAACCTAGTCAGGACACACAGAACCAGTCCGAGACCC----------------------CACAAGTGGCACATT - -a -s simMouse_chr6.simMouse.chr6 562148 52 + 636262 GTATTTTTTGTCCATCTATATTGCGGCTGGTGCCCTCTAAGTTGGCCATCAG -s mr.mrrefChr3 112082 52 + 181027 GTATTTTTTGTCCATCTATATTGCGGCTGGTGCCCTCTAAGTTGGCCATCAG -s simRat_chr6.simRat.chr6 37401 52 - 647215 GTATTTTTTGTCCATCTATATTGCAGCTGGTGCCCTCTGAATTGGCAATTGG - -a -s simMouse_chr6.simMouse.chr6 562200 15 + 636262 AGGACATGAGGTTGC -s mr.mrrefChr3 112134 15 + 181027 AGGACATGAGGTTGC -s simRat_chr6.simRat.chr6 37455 15 - 647215 AGGACATGAGGTTGC - -a -s simMouse_chr6.simMouse.chr6 562215 24 + 636262 GCCTTCATCAACCAAGCTGGGGGG -s mr.mrrefChr3 112149 24 + 181027 GCCTTCATCAACCAAGCTGGGGGG -s simRat_chr6.simRat.chr6 37473 24 - 647215 GCCTTCATCAACCAAGCTGGGGGA - -a -s simMouse_chr6.simMouse.chr6 562239 83 + 636262 ACACATGGGACTCCTAGCCCCCTTGTCAATGGAACTGGAGCAGTTAGATAGATTCACCAAACAGGGAGCCCACATTCCATGTG -s mr.mrrefChr3 112173 82 + 181027 ACACATGGGACTCCTAGCCCCCTTGTCAATGGAACTGGAGCAGTTAGATAGATTCACCAA-CAGGGAGCCCACATTCCATGTG -s simRat_chr6.simRat.chr6 37522 82 - 647215 ACACATGGAACCCCTGGCCCCCTTTTGAATGGAACCGGAACAGTTTTATGAATTTGCCAA-CAAGGAAGCCGCTTTGAATGTG - -a -s simMouse_chr6.simMouse.chr6 562322 45 + 636262 CTAGCATCACAGGATCTAAGGAACCATGGAATTATAAATCAGTAT -s Anc0.Anc0refChr3 163369 17 + 222631 ----------------------------GAATTTTCAATCACTAT -s Anc1.Anc1refChr1 1961 17 + 69767 ----------------------------GAATTTTCAATCACTAT -s Anc2.Anc2refChr1 78046 17 + 142988 ----------------------------GAATTTTCAATAACTAT -s mr.mrrefChr3 112255 45 + 181027 CTAGCATCACAGGATCTAAGGAACCATGGAATTATAAATCAGTAT -s simCow_chr6.simCow.chr6 537012 12 + 602619 ----------------------------GAGTT-----CGACTAT -s simDog_chr6.simDog.chr6 524895 17 + 593897 ----------------------------GAATTTTCAATAACTAT -s simHuman_chr6.simHuman.chr6 532109 13 + 601863 ----------------------------GAACTTCCAATCA---- -s simRat_chr6.simRat.chr6 37618 45 - 647215 CCAGCCTCACAGGGTCGAAGGAACCATGAAATTGTAAATCACTAT - -a -s simMouse_chr6.simMouse.chr6 562367 87 + 636262 GGAATGGACAGCTTAGCATTAGCAAGTCATATGCTTGTGGCATCATATCCCCAAAACAGTACATAACAGTCTGACCCATGCAACATG -s Anc0.Anc0refChr3 163386 45 + 222631 GGAATGAGCAGCT------TATCAACTCTTATGCTTGTGGCATCATATCCA------------------------------------ -s Anc1.Anc1refChr1 1978 45 + 69767 GGAATGAGCAGCT------TATCAACTCTTATGCTTGTGGCATCATATCCA------------------------------------ -s Anc2.Anc2refChr1 78067 45 + 142988 GGAATGAGCAGCT------TATCAACTCTTATGCTTGTGGCATCATATTCA------------------------------------ -s mr.mrrefChr3 112300 87 + 181027 GGAATGGGCAGCTTAGCATTAGCAAGTCATATGCTTGTGGCATCATATCCCCAAAACAGTACATAACAGTCTGACCCATGCAACATG -s simCow_chr6.simCow.chr6 537028 43 + 602619 AGACT-AGCAGCT------T-TTAACTCTTATGCTTGTGGCATCACATGCA------------------------------------ -s simDog_chr6.simDog.chr6 524916 45 + 593897 GGAATGAGCAGCT------GATCAACTCTTATTCTTGTGGTGTCATACTCA------------------------------------ -s simHuman_chr6.simHuman.chr6 532122 44 + 601863 -GAATGCGCAGCT------TATCAACTCTTATGCTTGTGGCATCATATCCA------------------------------------ -s simRat_chr6.simRat.chr6 37663 87 - 647215 GGAATGGGCACCTTAGCATTAACAAATCATATGCTTGTGTCATCATATCCCCAAAACAGTACACAACAGTCTGACCCATGCAACAAG - -a -s simMouse_chr6.simMouse.chr6 562454 10 + 636262 CATGTTTCTG -s Anc0.Anc0refChr3 163431 1 + 222631 ---------G -s Anc1.Anc1refChr1 2023 1 + 69767 ---------G -s Anc2.Anc2refChr1 78112 1 + 142988 ---------G -s mr.mrrefChr3 112387 10 + 181027 CATGTTTCTG -s simCow_chr6.simCow.chr6 537071 1 + 602619 ---------G -s simDog_chr6.simDog.chr6 524961 1 + 593897 ---------G -s simHuman_chr6.simHuman.chr6 532166 1 + 601863 ---------G -s simRat_chr6.simRat.chr6 37754 10 - 647215 CATATTTGTG - -a -s simMouse_chr6.simMouse.chr6 562464 10 + 636262 CATACAATGT -s Anc0.Anc0refChr3 163432 10 + 222631 CATACAATGT -s Anc1.Anc1refChr1 2024 10 + 69767 CATACAATGT -s Anc2.Anc2refChr1 78122 10 + 142988 CATACAATGT -s mr.mrrefChr3 112397 10 + 181027 CATACAATGT -s simCow_chr6.simCow.chr6 537081 10 + 602619 CATAAAATGT -s simDog_chr6.simDog.chr6 524971 10 + 593897 CCTACAATAC -s simHuman_chr6.simHuman.chr6 532167 10 + 601863 CATACAGTGT -s simRat_chr6.simRat.chr6 37764 10 - 647215 CATACAATGT - -a -s simMouse_chr6.simMouse.chr6 562474 2 + 636262 GC -s Anc0.Anc0refChr3 163443 2 + 222631 GC -s Anc1.Anc1refChr1 2035 2 + 69767 GC -s Anc2.Anc2refChr1 78133 2 + 142988 GC -s mr.mrrefChr3 112407 2 + 181027 GC -s simCow_chr6.simCow.chr6 537092 2 + 602619 AC -s simDog_chr6.simDog.chr6 524982 2 + 593897 GC -s simHuman_chr6.simHuman.chr6 532178 2 + 601863 GC -s simRat_chr6.simRat.chr6 37774 2 - 647215 GC - -a -s simMouse_chr6.simMouse.chr6 562476 1 + 636262 A -s Anc0.Anc0refChr3 163445 1 + 222631 A -s Anc1.Anc1refChr1 2037 1 + 69767 A -s Anc2.Anc2refChr1 78136 1 + 142988 A -s mr.mrrefChr3 112409 1 + 181027 A -s simCow_chr6.simCow.chr6 537095 1 + 602619 A -s simDog_chr6.simDog.chr6 524985 1 + 593897 A -s simHuman_chr6.simHuman.chr6 532180 1 + 601863 A -s simRat_chr6.simRat.chr6 37776 1 - 647215 A - -a -s simMouse_chr6.simMouse.chr6 562477 41 + 636262 AAATCAAGTAGCAGTGGAAATCTAACACTAGACTTGACTTC -s Anc0.Anc0refChr3 163457 37 + 222631 AATTCAAATAGCATGGGAA--TTAAC--TAAACCTAACTTC -s Anc1.Anc1refChr1 2049 39 + 69767 AATTCAAATAGCATGGGAA--TTAACACTAAACCTAACTTC -s Anc2.Anc2refChr1 78148 37 + 142988 AATCCAAATAGCATGGGAA--TTAAC--TAAACCTAACTTT -s mr.mrrefChr3 112410 41 + 181027 AAATCAAGTAGCAGTGGAAATTTAACACTAGACTTGACTTC -s simCow_chr6.simCow.chr6 537107 36 + 602619 AATCCAAATAGCATGGGAA--TTCAC--TTAACCTAA-TTT -s simDog_chr6.simDog.chr6 524997 31 + 593897 AA------CGGCATGGGAA--TTAAC--TACACCTAACTTT -s simHuman_chr6.simHuman.chr6 532192 39 + 601863 AATTCAATTATCATGGGAA--TTAACACTAAACCTAACTCC -s simRat_chr6.simRat.chr6 37777 41 - 647215 AAATCAAGTAGCACTGGAAATTTAACACTAGATTTGACTTC - -a -s simMouse_chr6.simMouse.chr6 562518 11 + 636262 CATCAAAGAAT -s Anc0.Anc0refChr3 163495 11 + 222631 CATAAAAAAAT -s Anc1.Anc1refChr1 2089 11 + 69767 CATAAAAAAAT -s Anc2.Anc2refChr1 78186 11 + 142988 CATAAAAAAAT -s mr.mrrefChr3 112451 11 + 181027 CATCAAAGAAT -s simCow_chr6.simCow.chr6 537144 11 + 602619 CATAAAAGAAT -s simDog_chr6.simDog.chr6 525029 11 + 593897 CATAAAAAAAT -s simHuman_chr6.simHuman.chr6 532232 11 + 601863 CATAAAAAAAT -s simRat_chr6.simRat.chr6 37818 11 - 647215 CATCAAAGAAA - -a -s simMouse_chr6.simMouse.chr6 562529 38 + 636262 TGGGTTGTTTTCCCTTGTTATTATTATGCAGCAGGGGA -s Anc0.Anc0refChr3 163506 31 + 222631 CGATTGTATTTTCAT-GTTGATATTATGCA------GG -s Anc1.Anc1refChr1 2100 32 + 69767 CGATTGTATTTTCATTGTTGATATTATGCA------GG -s Anc2.Anc2refChr1 78197 31 + 142988 TGATTGTATTTTCAT-GTTGATATTATGCA------GG -s mr.mrrefChr3 112462 38 + 181027 CGGGTTGTTTTTCCTTGTTATTATTATGCAGCAGGGGA -s simCow_chr6.simCow.chr6 537155 30 + 602619 AGATTGTTCTTTCA--ATTGATTTTATGCA------GG -s simDog_chr6.simDog.chr6 525043 31 + 593897 TGATTGTATTGTCAT-GTTGATATTATACA------GG -s simHuman_chr6.simHuman.chr6 532243 29 + 601863 CGATTGTCTTTTCATGGTTGGTATTATGT--------- -s simRat_chr6.simRat.chr6 37829 38 - 647215 CGGGTTCATTTTCCTTGTTAATATTATGCAGCAGGGGG - -a -s simMouse_chr6.simMouse.chr6 562567 23 + 636262 CTCAGCTCAACAATTGGTAAAAG -s Anc0.Anc0refChr3 163537 23 + 222631 CTCAATTAAACAATTGCTAAAAG -s Anc1.Anc1refChr1 2132 23 + 69767 CTCAATTAAACAATTGCTAAAAG -s Anc2.Anc2refChr1 78228 23 + 142988 CTCAATTAAACAATTGCCAAAAG -s mr.mrrefChr3 112500 23 + 181027 CTCAGTTCAACAATTGGTAAAAG -s simCow_chr6.simCow.chr6 537185 23 + 602619 GTCAATTAGACCATTGCCAAAAG -s simDog_chr6.simDog.chr6 525074 23 + 593897 CTCAATCAAACAATTGCCAAAAG -s simHuman_chr6.simHuman.chr6 532272 18 + 601863 -----TTGAACAATTGCTAAAAG -s simRat_chr6.simRat.chr6 37868 23 - 647215 CTCAGTTTAATGATTGGTGAAAG - -a -s simMouse_chr6.simMouse.chr6 562590 54 + 636262 CCTGTTCTGAATGACTCCCTTTAATATGCCAACAGCCTTGAGACTTAGGTGTCT -s Anc0.Anc0refChr3 163560 53 + 222631 TCTATTT-GAACTACTCCCACCAATGTGCCAACAGACTAGAGACTTAGGTGTCT -s Anc1.Anc1refChr1 2155 54 + 69767 TCTATTTTGAACTACTCCCACCAATGTGCCAACAGACTAGAGACTTAGGTGTCT -s Anc2.Anc2refChr1 78251 53 + 142988 TCCATTT-GAATTACTCCCACCTATGTGCCAACAGACTAGAGACTTAGGTGTCT -s mr.mrrefChr3 112523 54 + 181027 CCTGTTCTGAACGACTCCCTCTAATGTGCCAACAGCCTTGAGACTTAGGTGTCT -s simCow_chr6.simCow.chr6 537208 53 + 602619 TCCATTT-GAATGACTCCCATTCATGTACCAATAGACTAGAGACTTGGGAGTCT -s simDog_chr6.simDog.chr6 525097 50 + 593897 TCTGCTT-GAATTTCTCCAACCTATGTG---ACGGACTGGAGACTTAGGTGTCT -s simHuman_chr6.simHuman.chr6 532309 54 + 601863 TCTATTTTGAACCACTCCCACCAATGTGGCAGCAGACTAGTGACTTTGGTGTCT -s simRat_chr6.simRat.chr6 37891 54 - 647215 CCTGTTCTGAACGACTCCCTCTGATGTGCCAACCGCCTTGAGACTTAGGTGTCT - -a -s simMouse_chr6.simMouse.chr6 562644 19 + 636262 CTGTCTAATGGGCATTCTG -s Anc0.Anc0refChr3 163613 19 + 222631 CTCCCTAAAGAACACTGTA -s Anc1.Anc1refChr1 2209 19 + 69767 CTCCCTAAAGAACACTGTA -s Anc2.Anc2refChr1 78304 19 + 142988 CTCCCTAAAGAACACTGTA -s mr.mrrefChr3 112577 19 + 181027 CTGTCTAAAGGGCATTCTG -s simCow_chr6.simCow.chr6 537261 19 + 602619 TTTCCTAAAGAACACTGTA -s simDog_chr6.simDog.chr6 525159 19 + 593897 CTCCCCAAAGTACGCTGTA -s simHuman_chr6.simHuman.chr6 532363 19 + 601863 CTACCTAAAGAACACTGTA -s simRat_chr6.simRat.chr6 37945 19 - 647215 CTCTCTAAAGGGCATCCTG - -a -s simMouse_chr6.simMouse.chr6 562663 25 + 636262 TGCTGCTAGAAGAGGCAACCCAAAA -s Anc0.Anc0refChr3 163632 25 + 222631 CTATGCAAAAAGAGGCAACCCATAA -s Anc1.Anc1refChr1 2228 25 + 69767 CTATGCAAAAAGAGGCAACCCATAA -s Anc2.Anc2refChr1 78333 25 + 142988 CTATGCAAAAAGAGGCACCCCATAA -s mr.mrrefChr3 112596 25 + 181027 TTCTGCTAGAAGAGGCAACCCAAAA -s simCow_chr6.simCow.chr6 537290 25 + 602619 CTGGGCAAAAGGAGGCAGCTGATAA -s simDog_chr6.simDog.chr6 525188 25 + 593897 CTATGCAAAAAGAGGCACCCCATAA -s simHuman_chr6.simHuman.chr6 532382 25 + 601863 CTATGCAAAAAGGGTCAACACAGCA -s simRat_chr6.simRat.chr6 37964 25 - 647215 TTCTGGTAGATGAAGCAACCCAAAA - -a -s simMouse_chr6.simMouse.chr6 562688 4 + 636262 TTAT -s Anc0.Anc0refChr3 163657 4 + 222631 TCAT -s Anc1.Anc1refChr1 2253 4 + 69767 TCAT -s Anc2.Anc2refChr1 78358 4 + 142988 TCAT -s mr.mrrefChr3 112621 4 + 181027 TTAT -s simCow_chr6.simCow.chr6 537318 4 + 602619 TTAT -s simDog_chr6.simDog.chr6 525213 4 + 593897 TCAT -s simHuman_chr6.simHuman.chr6 532407 4 + 601863 TCAT -s simRat_chr6.simRat.chr6 37989 4 - 647215 TTAT - -a -s simMouse_chr6.simMouse.chr6 562692 116 + 636262 ACCTAAGACGTATAATCGCCAGGGCAATAAGTTGGTCAGGTATTAAGAGACATCTAATCGTGTTCCTACCGCTGTAAAAGCGGACACCTACACCTACTATAATGAAACTACATAAT -s Anc0.Anc0refChr3 163661 55 + 222631 A-TTAAGACTGAAAATTTTCAGGGAAA-----------------------------------------------------------CCTGGA-CTACTATCATGAAACTACATAAT -s Anc1.Anc1refChr1 2257 55 + 69767 A-TTAAGACTGAAAATTTTCAGGGAAA-----------------------------------------------------------CCTGGA-CTACTATCATGAAACTACATAAT -s Anc2.Anc2refChr1 78362 55 + 142988 A-GGAAGACTGAAAATTTTCAGGGAAA-----------------------------------------------------------CCTGGA-CTACTATCATGAAACTACATAAT -s mr.mrrefChr3 112625 57 + 181027 ACTTAAGACTTATAATCTCCAGGGCAA-----------------------------------------------------------CCTACACCTACTATCATGAAACTACATAAT -s simCow_chr6.simCow.chr6 537322 55 + 602619 A-AGAAGACTTAAAATTTTCAGGGAAA-----------------------------------------------------------CCTGGA-CTACTATCACAAAAGTATATAAT -s simDog_chr6.simDog.chr6 525218 52 + 593897 A-GGAAGACTGATAATCTTCAGGGA--------------------------------------------------------------CCGGA-CTACTATCATGAAACTACATTAG -s simHuman_chr6.simHuman.chr6 532411 55 + 601863 A-TTAAGACTCAAAATTTTCAGGGAAA-----------------------------------------------------------CCTGTA-CTACTATCATGAAACTACAAAAT -s simRat_chr6.simRat.chr6 37993 57 - 647215 CCTTAAGACTGACAATCTCCAGGGTGT-----------------------------------------------------------CCTACGCCTACCATCATGAAACTACATAAT - -a -s simMouse_chr6.simMouse.chr6 562808 18 + 636262 TTCTTCAAGGAAAACATC -s Anc0.Anc0refChr3 163722 17 + 222631 TCCTCCAAGG-AAACATG -s Anc1.Anc1refChr1 2318 17 + 69767 TCCTCCAAGG-AAACATG -s Anc2.Anc2refChr1 78423 17 + 142988 TCCTCCAAGG-AAACATG -s mr.mrrefChr3 112682 18 + 181027 TTCTCCAAGGAAAACATC -s simCow_chr6.simCow.chr6 537383 17 + 602619 TCCTCCACGG-AAGTGTG -s simDog_chr6.simDog.chr6 525276 17 + 593897 TCCTCCCAGA-AAACATG -s simHuman_chr6.simHuman.chr6 532472 17 + 601863 TCCTCCAAAG-AAACACG -s simRat_chr6.simRat.chr6 38050 18 - 647215 TGCTCCAAGGAAGACATC - -a -s simMouse_chr6.simMouse.chr6 562826 31 + 636262 AAATCATTCATCATTCTCTTCTCAACATCCC -s Anc0.Anc0refChr3 163739 31 + 222631 AAATCATATGTTATTcCCTCTTCAatgtact -s Anc1.Anc1refChr1 2335 31 + 69767 AAATCATATGTTATTcCCTCTTCAatgtact -s Anc2.Anc2refChr1 78440 31 + 142988 AAATCATATGTTATTcCCTCTTCActgtact -s mr.mrrefChr3 112700 31 + 181027 AAATCATTCATCATTCTCTTCTCAACGTCCC -s simCow_chr6.simCow.chr6 537400 30 + 602619 AAATCATATGTTATT-CCTCTGCTCTGTACT -s simDog_chr6.simDog.chr6 525293 24 + 593897 AAATCATATGTTATTCCATCTTCA------- -s simHuman_chr6.simHuman.chr6 532489 31 + 601863 AAATCATGGCttaccccctcttcaaagtgct -s simRat_chr6.simRat.chr6 38086 31 - 647215 AAAACATTCATCATTCTCTTCTCAATGTCCC - -a -s simMouse_chr6.simMouse.chr6 562857 20 + 636262 ATAGGATTGTACTGCTGACA -s Anc0.Anc0refChr3 163797 20 + 222631 ataaggttgtgttgctgaca -s Anc1.Anc1refChr1 2393 20 + 69767 ataaggttgtgttgctgaca -s Anc2.Anc2refChr1 78498 20 + 142988 ataaagttgtgtcactgaca -s mr.mrrefChr3 112731 20 + 181027 ATAGGGTTGTACTGCTGACA -s simCow_chr6.simCow.chr6 537456 20 + 602619 ataacatagtgccactgaca -s simDog_chr6.simDog.chr6 525344 20 + 593897 AGAAAGTTGTATCACTGACA -s simHuman_chr6.simHuman.chr6 532547 20 + 601863 gtaaggttgtggtgctggca -s simRat_chr6.simRat.chr6 38117 20 - 647215 ACAGGGTAGTACTACTGATA - -a -s simMouse_chr6.simMouse.chr6 562877 11 + 636262 ATCTACTTTCC -s Anc0.Anc0refChr3 163821 11 + 222631 tccctctttac -s Anc1.Anc1refChr1 2417 11 + 69767 tccctctttac -s Anc2.Anc2refChr1 78522 11 + 142988 tccctcttcac -s mr.mrrefChr3 112751 11 + 181027 ATCTACTTTAC -s simCow_chr6.simCow.chr6 537480 11 + 602619 tccctcttcac -s simDog_chr6.simDog.chr6 525372 11 + 593897 TGCCTCTTCac -s simHuman_chr6.simHuman.chr6 532571 11 + 601863 tccctctttat -s simRat_chr6.simRat.chr6 38137 11 - 647215 ATCTATTTTAC - -a -s simMouse_chr6.simMouse.chr6 562888 1 + 636262 C -s Anc0.Anc0refChr3 163838 1 + 222631 t -s Anc1.Anc1refChr1 2434 1 + 69767 t -s Anc2.Anc2refChr1 78539 1 + 142988 t -s mr.mrrefChr3 112762 1 + 181027 C -s simCow_chr6.simCow.chr6 537516 1 + 602619 t -s simDog_chr6.simDog.chr6 525387 1 + 593897 t -s simHuman_chr6.simHuman.chr6 532588 1 + 601863 t -s simRat_chr6.simRat.chr6 38148 1 - 647215 C - -a -s simMouse_chr6.simMouse.chr6 562889 17 + 636262 TGATACCCAAGATCTAT -s Anc0.Anc0refChr3 163839 17 + 222631 tcacaacctaaagttat -s Anc1.Anc1refChr1 2435 17 + 69767 tcacaacctaaagttat -s Anc2.Anc2refChr1 78547 17 + 142988 tcacgacctaaagttct -s mr.mrrefChr3 112763 17 + 181027 TCATACCCAAAATCTAT -s simCow_chr6.simCow.chr6 537524 17 + 602619 ttatgacctgaaaagct -s simDog_chr6.simDog.chr6 525396 17 + 593897 tcacgacctaaagttct -s simHuman_chr6.simHuman.chr6 532589 17 + 601863 tcacatcctaaacttat -s simRat_chr6.simRat.chr6 38149 17 - 647215 TCATACCCAAAAACTAT - -a -s simMouse_chr6.simMouse.chr6 562906 13 + 636262 CTACCAATGCTCA -s Anc0.Anc0refChr3 163856 13 + 222631 ctaccagtgcgca -s Anc1.Anc1refChr1 2452 13 + 69767 ctaccagtgcgca -s Anc2.Anc2refChr1 78596 13 + 142988 ctaatagcaagca -s mr.mrrefChr3 112780 13 + 181027 CTACCAATGCTCA -s simCow_chr6.simCow.chr6 537573 13 + 602619 ctaattgaaagca -s simDog_chr6.simDog.chr6 525445 13 + 593897 ctaatagcaagca -s simHuman_chr6.simHuman.chr6 532606 13 + 601863 ttgccagtgcaca -s simRat_chr6.simRat.chr6 38166 13 - 647215 CCACCAATGCTGA - -a -s simMouse_chr6.simMouse.chr6 562919 19 + 636262 GAACCTGACAGTCCCCCTT -s Anc0.Anc0refChr3 163869 9 + 222631 aaa----------agactt -s Anc1.Anc1refChr1 2465 9 + 69767 aaa----------agactt -s Anc2.Anc2refChr1 78609 9 + 142988 aaa----------agtctt -s mr.mrrefChr3 112793 19 + 181027 GAACCTGACAGTCACACTT -s simCow_chr6.simCow.chr6 537589 9 + 602619 aaa----------agtctt -s simDog_chr6.simDog.chr6 525458 9 + 593897 aaa----------agtctt -s simHuman_chr6.simHuman.chr6 532619 9 + 601863 cag----------agactt -s simRat_chr6.simRat.chr6 38179 19 - 647215 GAACCTGTCAGTCACACTC - -a -s simMouse_chr6.simMouse.chr6 562938 29 + 636262 GAACTGGCTCTAATTGCATGCTGAAATTC -s Anc0.Anc0refChr3 163879 22 + 222631 aaactgggacc-------cgttgagctat -s Anc1.Anc1refChr1 2475 22 + 69767 aaactgggacc-------cgttgagctat -s Anc2.Anc2refChr1 78619 22 + 142988 aaacttggacc-------ccttgagctat -s mr.mrrefChr3 112812 29 + 181027 AAACTGGCTCTAATTTCATGCTGAAATTC -s simCow_chr6.simCow.chr6 537599 22 + 602619 tagtcaggacc-------ccttggtctgt -s simDog_chr6.simDog.chr6 525468 22 + 593897 aaacttagacc-------cctcaagctat -s simHuman_chr6.simHuman.chr6 532629 22 + 601863 aaactgggacc-------cgttgagctct -s simRat_chr6.simRat.chr6 38198 29 - 647215 AAACTGGCTCTAATTTCATGCTGAAATTC - -a -s simMouse_chr6.simMouse.chr6 562967 36 + 636262 TGAAACTGGGAGTATGTAACCAGACTAAAGACTTAA -s Anc0.Anc0refChr3 163902 31 + 222631 ttgcacc-----cttataaccaaactagaagggttg -s Anc1.Anc1refChr1 2498 31 + 69767 ttgcacc-----cttataaccaaactagaagggttg -s Anc2.Anc2refChr1 78642 31 + 142988 ttgcacc-----cttataaccaaactagaagggttg -s mr.mrrefChr3 112842 36 + 181027 TGAAACTGGGAGTATATAACCAGACTAAAAACGTAA -s simCow_chr6.simCow.chr6 537622 29 + 602619 ttgaacc-----tgcataa--aaactagagggattg -s simDog_chr6.simDog.chr6 525491 30 + 593897 ttgca-c-----cttctagccaaacttgaaaagttg -s simHuman_chr6.simHuman.chr6 532652 31 + 601863 tcgcacc-----cttataaccaaactagaagggttg -s simRat_chr6.simRat.chr6 38228 36 - 647215 TGAATCTGGGAGTGTATAACCAGACTAAAAACGTAA - -a -s simMouse_chr6.simMouse.chr6 563003 12 + 636262 CAGATAACAAAA -s Anc0.Anc0refChr3 163958 12 + 222631 CCACTATCAGCA -s Anc1.Anc1refChr1 2554 12 + 69767 CCACTATCAGCA -s Anc2.Anc2refChr1 78699 12 + 142988 TCACTATCAGCA -s mr.mrrefChr3 112899 12 + 181027 CAGATATCAAAA -s simCow_chr6.simCow.chr6 537677 12 + 602619 ACCCTGTCAGCA -s simDog_chr6.simDog.chr6 525547 12 + 593897 TCACTATCAGCA -s simHuman_chr6.simHuman.chr6 532708 12 + 601863 CCTCTATCAGTA -s simRat_chr6.simRat.chr6 38286 12 - 647215 TTGATATCAAAG - -a -s simMouse_chr6.simMouse.chr6 563015 48 + 636262 CTCTGACTTTGGTCCCCAGGACAATTATCTTCAATAAATTAGCTTACT -s Anc0.Anc0refChr3 163970 48 + 222631 CTTTTATTTTGATCCCCAGCACAATCATCTTTACCTAATTAGCTTGCT -s Anc1.Anc1refChr1 2566 48 + 69767 CTTTTATTTTGATCCCCAGCACAATCATCTTTACCTAATTAGCTTGCT -s Anc2.Anc2refChr1 78711 48 + 142988 CTTTTATTTTGATCCCCAGCACAATCATCTTTACCTACTTAAATAGCT -s mr.mrrefChr3 112911 48 + 181027 CTCTGATTTTGGTCCCCAGGACAATCATCTTCACTAAATTAGCTTACT -s simCow_chr6.simCow.chr6 537691 44 + 602619 TTTTTATTATGATCCCCTGCACAATCATCTTTAC----TCAAATAGCT -s simDog_chr6.simDog.chr6 525559 37 + 593897 CTCTTACTTTGATCCCGAG-----------TTACCTACTTAAATAGCT -s simHuman_chr6.simHuman.chr6 532720 48 + 601863 CTTTTATTTTGATCCCCAGCACAATCAGCTTTACCTAATTAGCTTGCT -s simRat_chr6.simRat.chr6 38298 48 - 647215 CTCTGATTATGGTCCCCAGGCCAATCATCTTCACTAAATTAGCTTAGT - -a -s simMouse_chr6.simMouse.chr6 563063 1 + 636262 G -s Anc0.Anc0refChr3 164018 1 + 222631 G -s Anc1.Anc1refChr1 2614 1 + 69767 G -s Anc2.Anc2refChr1 78767 1 + 142988 A -s mr.mrrefChr3 112959 1 + 181027 G -s simCow_chr6.simCow.chr6 537743 1 + 602619 A -s simDog_chr6.simDog.chr6 525604 1 + 593897 A -s simHuman_chr6.simHuman.chr6 532768 1 + 601863 G -s simRat_chr6.simRat.chr6 38346 1 - 647215 G - -a -s simMouse_chr6.simMouse.chr6 563064 22 + 636262 GTCGTAACCCATCTGGCTATCA -s Anc0.Anc0refChr3 164019 21 + 222631 GTAGCAATC-GTCTAACTATGG -s Anc1.Anc1refChr1 2615 21 + 69767 GTAGCAATC-GTCTAACTATGG -s Anc2.Anc2refChr1 78768 21 + 142988 GTAGCAATT-GTTTAACTATGG -s mr.mrrefChr3 112960 21 + 181027 GTCGTAATC-ATCTGACTATCA -s simCow_chr6.simCow.chr6 537752 21 + 602619 GTACCAATT-GTTTAACTATGG -s simDog_chr6.simDog.chr6 525605 21 + 593897 GTAGCAATT-GTTCAACTATGG -s simHuman_chr6.simHuman.chr6 532769 21 + 601863 GTGGCAATC-GCCTAACTATAG -s simRat_chr6.simRat.chr6 38347 21 - 647215 GTAGTAATC-ATCTGACTATCA - -a -s simMouse_chr6.simMouse.chr6 563086 26 + 636262 GATCTAACCCCCCTAGTGTAAAGTAA -s Anc0.Anc0refChr3 164046 26 + 222631 GGTCTGGCCTCTCTTGTATTAACTCA -s Anc1.Anc1refChr1 2642 26 + 69767 GGTCTGGCCTCTCTTGTATTAACTCA -s Anc2.Anc2refChr1 78795 26 + 142988 AGTCTGGCCTCTCTTGTAATAACTCA -s mr.mrrefChr3 112981 26 + 181027 GATCTGACCTCTCTAGTGTAAAGTAA -s simCow_chr6.simCow.chr6 537778 26 + 602619 AGTTAAACCTCTCTTGTAATAAGTTA -s simDog_chr6.simDog.chr6 525632 26 + 593897 AGTCTGGCCTCTCTTGTAATAACTCA -s simHuman_chr6.simHuman.chr6 532796 26 + 601863 GGTCTGGCCTCTGTTGTATCAATTCA -s simRat_chr6.simRat.chr6 38368 26 - 647215 GATCTGACCTCTCTAGTGTTCACTGA - -a -s simMouse_chr6.simMouse.chr6 563112 6 + 636262 GAGATT -s Anc0.Anc0refChr3 164081 6 + 222631 GGTATT -s Anc1.Anc1refChr1 2677 6 + 69767 GGTATT -s Anc2.Anc2refChr1 78830 6 + 142988 GGTATT -s mr.mrrefChr3 113007 6 + 181027 GAGATT -s simDog_chr6.simDog.chr6 525667 6 + 593897 GGTATT -s simHuman_chr6.simHuman.chr6 532832 6 + 601863 AGTATT -s simRat_chr6.simRat.chr6 38394 6 - 647215 GAGATA - -a -s simMouse_chr6.simMouse.chr6 563118 12 + 636262 GAGTAACACTCG -s Anc0.Anc0refChr3 164090 8 + 222631 GAGAAACC---- -s Anc1.Anc1refChr1 2686 12 + 69767 GAGAAACCCTCG -s Anc2.Anc2refChr1 78839 8 + 142988 GAGAACCC---- -s mr.mrrefChr3 113013 12 + 181027 GAGTAACACTCG -s simDog_chr6.simDog.chr6 525676 8 + 593897 GAGAACCC---- -s simHuman_chr6.simHuman.chr6 532841 12 + 601863 GAGAAACTCTCG -s simRat_chr6.simRat.chr6 38400 12 - 647215 GAGTAACACTAA - -a -s simMouse_chr6.simMouse.chr6 563130 16 + 636262 ACTAACAGACCTGTGG -s Anc0.Anc0refChr3 164098 14 + 222631 AATAGCAGA-CA-TAG -s Anc1.Anc1refChr1 2698 14 + 69767 AATAGCAGA-CA-TAG -s Anc2.Anc2refChr1 78847 14 + 142988 AAAAGAAGC-CA-AAG -s mr.mrrefChr3 113025 15 + 181027 ACTTACAGACCT-TAG -s simDog_chr6.simDog.chr6 525684 14 + 593897 AAAAGAAGC-CA-AAG -s simHuman_chr6.simHuman.chr6 532858 14 + 601863 AATGGCAGA-CA-TAG -s simRat_chr6.simRat.chr6 38412 15 - 647215 CCCTAATCTTCT-TAG - -a -s simMouse_chr6.simMouse.chr6 563146 35 + 636262 TCTACAAGGAGTGATGTTCTCAGGGAGCTCTTATT -s Anc0.Anc0refChr3 164112 33 + 222631 TCTGCAAGGAGTAATGTTGCCCTGGAACTC--ACT -s Anc1.Anc1refChr1 2712 33 + 69767 TCTGCAAGGAGTAATGTTGCCCTGGAACTC--ACT -s Anc2.Anc2refChr1 78861 33 + 142988 TTTGCAAGGTGTAATGTCGCCCTGGAACTC--ACT -s mr.mrrefChr3 113040 35 + 181027 TCTACAAGGAGTAATGTTCTCAGGGAACTCTTATT -s simDog_chr6.simDog.chr6 525705 33 + 593897 TTTGCAAGGTGTAATGTCGCCCTGGAACTC--ACT -s simHuman_chr6.simHuman.chr6 532872 33 + 601863 TCTGCAAGGAGTAATCTTGCCCTGGAACCC--ACC -s simRat_chr6.simRat.chr6 38427 34 - 647215 TCTA-AAGGAGCAGTTTTCTCAGGGAACTCTTATT - -a -s simMouse_chr6.simMouse.chr6 563181 1 + 636262 G -s Anc0.Anc0refChr3 164145 1 + 222631 A -s Anc1.Anc1refChr1 2745 1 + 69767 A -s Anc2.Anc2refChr1 78894 1 + 142988 A -s mr.mrrefChr3 113075 1 + 181027 A -s simDog_chr6.simDog.chr6 525741 1 + 593897 A -s simHuman_chr6.simHuman.chr6 532905 1 + 601863 A -s simRat_chr6.simRat.chr6 38461 1 - 647215 A - -a -s simMouse_chr6.simMouse.chr6 563182 71 + 636262 ATGCTGACACATAGCATCTAAGATGTGCAATAGGAGTATAAGAAATTTTCTGGCTCATGATCATCTTAATC -s Anc0.Anc0refChr3 164171 65 + 222631 ATT-CAACA-----CCCCTAAGATGTGCAATAGGAGTATAAGAAATTTTCTGGCTCAAGATAATCTTAATC -s Anc1.Anc1refChr1 2771 65 + 69767 ATT-CAACA-----CCCCTAAGATGTGCAATAGGAGTATAAGAAATTTTCTGGCTCAAGATAATCTTAATC -s Anc2.Anc2refChr1 78920 65 + 142988 ATT-CAATT-----ACCATAAGATATGTGATAGGAGTATAAGAATTTGTCTGTCTTAGGGTAATCTTAATC -s mr.mrrefChr3 113093 70 + 181027 ATG-TGACACATAGCATCTAAGATGTGCAATAGGAGTATAAGAAATTTTCTGGCTCAAGATCATCTTAATC -s simDog_chr6.simDog.chr6 525767 65 + 593897 ATT-CAATT-----ACCATAAGATATGTGATAGGAGTATAAGAATTTGTCTGTCTTAGGGTAATCTTAATC -s simHuman_chr6.simHuman.chr6 532931 65 + 601863 ATT-CAACA-----CCGCTAACATGTGCAATAAGAGTATATGATATTTTCTGGCTCAAGATGAACTTAATC -s simRat_chr6.simRat.chr6 38479 70 - 647215 ATG-TGACACGTAGCATCCAAGATGTGCAATAGGAGTATAAGAAATTTTCTGGTTTAAGATCATCTTAATC - -a -s simMouse_chr6.simMouse.chr6 563253 9 + 636262 TAACTCAAA -s Anc0.Anc0refChr3 164238 9 + 222631 TAACTCCTA -s Anc1.Anc1refChr1 2838 9 + 69767 TAACTCCTA -s Anc2.Anc2refChr1 78987 9 + 142988 TAACTCCTA -s mr.mrrefChr3 113163 9 + 181027 TAACTCCAA -s simDog_chr6.simDog.chr6 525834 9 + 593897 TAACTCCTA -s simHuman_chr6.simHuman.chr6 532998 9 + 601863 TAACTCCCA -s simRat_chr6.simRat.chr6 38549 9 - 647215 TAACTTCAA - -a -s simMouse_chr6.simMouse.chr6 563262 34 + 636262 GATTAAACGTAACAGGGGGCAGAAATTATGTGCA -s Anc0.Anc0refChr3 164247 27 + 222631 GA-------TAGCAGGGGGCAGAAAGTAGGTACC -s Anc1.Anc1refChr1 2847 27 + 69767 GA-------TAGCAGGGGGCAGAAAGTAGGTACC -s Anc2.Anc2refChr1 78996 27 + 142988 CA-------TAGCAGGGGACAGAAAGTAGGTATC -s mr.mrrefChr3 113172 34 + 181027 GATTAAACGTAACAGGGGGCAGAAATTATGTACC -s simCow_chr6.simCow.chr6 537804 22 + 602619 ------------CACTGGACAGAAAATAGGTATT -s simDog_chr6.simDog.chr6 525850 26 + 593897 CA-------TAGTGGGAGACACAAAGCAGGTA-C -s simHuman_chr6.simHuman.chr6 533007 27 + 601863 GA-------TGGCAGGGGGCAGAAAGTAGGAACC -s simRat_chr6.simRat.chr6 38558 34 - 647215 GCCTAAACGTAACAGGGGGCAGAAATTATGTACC - -a -s simMouse_chr6.simMouse.chr6 563296 45 + 636262 GGACCATTCTAGGGGGACAGTTGTTTTTGGGTGGCTCACAAGGGG -s Anc0.Anc0refChr3 164279 5 + 222631 AGTTC---------------------------------------- -s Anc1.Anc1refChr1 2879 5 + 69767 AGTTC---------------------------------------- -s Anc2.Anc2refChr1 79028 5 + 142988 GGTTC---------------------------------------- -s mr.mrrefChr3 113206 45 + 181027 AGTTCATTCTAGGGGGACAGTTGTTTTTGGGTGGCTCACAAGGGG -s simCow_chr6.simCow.chr6 537831 5 + 602619 GGTAC---------------------------------------- -s simDog_chr6.simDog.chr6 525881 5 + 593897 GATTT---------------------------------------- -s simHuman_chr6.simHuman.chr6 533039 5 + 601863 AGTTC---------------------------------------- -s simRat_chr6.simRat.chr6 38592 45 - 647215 AGTTCATTCTAGGGGGACAGTTGTTTTTGTGTGGCTCATAAGGAA - -a -s simMouse_chr6.simMouse.chr6 563341 80 + 636262 GTGTATGACATTCTTGAATTCCTTAGCCCCGCCAGGTTGATCTTAGTAAGATCCCCCTCAATGGTAATAATTTCAGGGGC -s Anc0.Anc0refChr3 164284 72 + 222631 -----CCACAT-CTTGAATTCCTCAGTTCCACCAGGGTGTTCTTTGTAAGACGCTCCACAGTGGTAAGAATTT--GGGGT -s Anc1.Anc1refChr1 2884 72 + 69767 -----CCACAT-CTTGAATTCCTCAGTTCCACCAGGGTGTTCTTTGTAAGACGCTCCACAGTGGTAAGAATTT--GGGGT -s Anc2.Anc2refChr1 79046 72 + 142988 -----CCCCAT-CTTGAATTCCTCAGTTCTGCCAGGGTATTCTTTGTAAGACGCTGCACAATGGTAAGCATTG--GGGGT -s mr.mrrefChr3 113251 79 + 181027 GTGTACCACAT-CTTGAATTCCTTAGCCCCACCAGGTTGTTCTTAGTAAGATCCCCCTCAGTGGTAATAATTTCAGGGGC -s simCow_chr6.simCow.chr6 537850 72 + 602619 -----CTGCAT-CTTGAATTTCTCAGTTCTGCGAGGGTTTGCTTTGTGAGAAGATTCAGTATGATAAGTATTG--GGCTT -s simDog_chr6.simDog.chr6 525899 72 + 593897 -----CCCCAT-CTTAAATTCCACTGTTCTGCCAGGGTATTCTTTGTAACACGCTGCACAATGGTAAGCATTG--GGGGT -s simHuman_chr6.simHuman.chr6 533044 70 + 601863 -----CCACAT-TTTGAATTCCTCAG--TCACCAGGGTGTTCTTTGTAAGAGGCTCCCCAGTGGTAGGAATTT--GGAGT -s simRat_chr6.simRat.chr6 38640 73 - 647215 GTGTACCACAT-CTTGAATTCCCTAACCACACCAGGTTGTTCTTCGTAGGATCCCC---TGC---AATAATTTCAGGGTC - -a -s simMouse_chr6.simMouse.chr6 563421 147 + 636262 TCCTACAAGTTCTCTCAAGTTGCGGCACTGTTTTTCATATTTTATGTCAGATGGGTCTGTGGGAAGGCAATTAGCAAATACTGGCAAATGTTGATCACAACTCTAGCCAGACCCTTGCAATAGCGTGCAGCTCTGTAAGACAGTTCC -s Anc0.Anc0refChr3 164356 81 + 222631 TTCCAAAAGTCTTCCAAAG-TGGGGCACTGTTCTCAAGACATTACATCAAAGGGGTTTCTGGGGAGG-----------------------------------------------------------------CTGCAAGACAGTTCC -s Anc1.Anc1refChr1 2956 81 + 69767 TTCCAAAAGTCTTCCAAAG-TGGGGCACTGTTCTCAAGACATTACATCAAAGGGGTTTCTGGGGAGG-----------------------------------------------------------------CTGCAAGACAGTTCC -s Anc2.Anc2refChr1 79118 81 + 142988 TTCTAAAAGTCTTCCAAAG-TGGGGCACTGTTCTCTCGACATTACATCAAAGGGGTTTCTGGGGGGG-----------------------------------------------------------------CTGCAAGACAATTCC -s mr.mrrefChr3 113330 147 + 181027 TTCCACAAGTTCTCTCAAGTTGTGGCACTGTTTTTAATACTTTACATCAGATGGGTCTGTGGGGAGGCAATTAGCAAATACTGGCAAATGTTGATCACAACTCTAGCCAGACCCTTGCAATAGCGTGCAGCTCTGTAAGACAGTTCC -s simCow_chr6.simCow.chr6 537922 80 + 602619 TTCT-AGACTCTTCAAAAG-TGGGGCATTGTTCTCCTGACATTGCCTCCAAGGGGTTCCTGGGGGAG-----------------------------------------------------------------CTGCAAGAAAATTCC -s simDog_chr6.simDog.chr6 525972 78 + 593897 TTCTAAAAGTCTGCCAAGG-TTG---GCTGTTCTATCCACATTACACCAGTGGGGTTTCTGGGGGGG-----------------------------------------------------------------CTGCAGGACAATTTG -s simHuman_chr6.simHuman.chr6 533114 81 + 601863 TTCCAAAAGTCGTCCGAAG-TGGTGTACCGTTCACAAGACCTTACATAAAAGGGGTTTTTGCAGAGG-----------------------------------------------------------------CTGCAAGACAGTTCC -s simRat_chr6.simRat.chr6 38713 147 - 647215 TTCCACAAGTTTTCTCAAGCTATGGCAATGTTTTTAATACTTTACATCAGATGGGTCTGTGGGGAGGCAATTAGCAAATACTGGCAAATGCTGGTGGCAACTCTAGCCAGACCATTGAATTAGCGTCCAGCTCTGTAATACTGTTCC - -a -s simMouse_chr6.simMouse.chr6 563568 37 + 636262 ATTTCATGCTGCAAATAAAATGGGAGCATGGATCAAA -s Anc0.Anc0refChr3 164439 36 + 222631 ATT-CATGGTGCTGATATAAAAGGCCCATGGTTCAAG -s Anc1.Anc1refChr1 3039 36 + 69767 ATT-CATGGTGCTGATATAAAAGGCCCATGGTTCAAG -s Anc2.Anc2refChr1 79201 36 + 142988 TTT-CATGGTGCTGATATAAAAGACCCATAGTCTAAG -s mr.mrrefChr3 113477 36 + 181027 ATT-CATGCTGCAGATAAAATGGGACCATGGATCAAA -s simCow_chr6.simCow.chr6 538004 23 + 602619 TTT-CACATTGTTGATATAA----CCCA--------- -s simDog_chr6.simDog.chr6 526051 36 + 593897 TTT-CATGGTGCTGATATATAAGAGCCATAGTCTAAG -s simHuman_chr6.simHuman.chr6 533197 36 + 601863 ATT-CATGATGCTGATATAAGAGGCCTATGGTTCAAG -s simRat_chr6.simRat.chr6 38860 36 - 647215 ATT-CATGCTGCAGATAAAATGGGACGATGGATCCAA - -a -s simMouse_chr6.simMouse.chr6 563605 9 + 636262 CTGGGAGAA -s Anc0.Anc0refChr3 164478 8 + 222631 C-GGGAGGT -s Anc1.Anc1refChr1 3078 9 + 69767 CTGGGAGGT -s Anc2.Anc2refChr1 79240 8 + 142988 C-AGGAAGT -s mr.mrrefChr3 113513 9 + 181027 CTGGGAGAA -s simCow_chr6.simCow.chr6 538027 7 + 602619 --AGGAAGT -s simDog_chr6.simDog.chr6 526090 8 + 593897 C-AGGAAGT -s simHuman_chr6.simHuman.chr6 533236 9 + 601863 CTGGGGGGT -s simRat_chr6.simRat.chr6 38896 9 - 647215 CTGGGAAAA - -a -s simMouse_chr6.simMouse.chr6 563614 7 + 636262 CCTGTAA -s Anc0.Anc0refChr3 164486 5 + 222631 CCTGC-- -s Anc1.Anc1refChr1 3087 5 + 69767 CCTGC-- -s Anc2.Anc2refChr1 79248 5 + 142988 CCAGC-- -s mr.mrrefChr3 113522 7 + 181027 CCTGTAA -s simCow_chr6.simCow.chr6 538035 5 + 602619 CTAGC-- -s simDog_chr6.simDog.chr6 526098 5 + 593897 CCAGC-- -s simHuman_chr6.simHuman.chr6 533245 5 + 601863 CGTGC-- -s simRat_chr6.simRat.chr6 38905 7 - 647215 CCTGTAA - -a -s simMouse_chr6.simMouse.chr6 563621 8 + 636262 GATAGTAC -s Anc0.Anc0refChr3 58001 8 - 222631 GTTGGCAC -s Anc1.Anc1refChr1 66536 8 - 69767 GTTGGCAC -s Anc2.Anc2refChr1 63589 8 - 142988 GTTGGCAC -s mr.mrrefChr3 113529 8 + 181027 GATAGTAC -s simCow_chr6.simCow.chr6 64459 8 - 602619 GTTGGCAC -s simDog_chr6.simDog.chr6 67663 3 - 593897 GTT----- -s simHuman_chr6.simHuman.chr6 68478 8 - 601863 GTTTGCGC -s simRat_chr6.simRat.chr6 38912 8 - 647215 CACAGTAC - -a -s simMouse_chr6.simMouse.chr6 563629 23 + 636262 AGATGTGTGTGGAAGGGTCTTAT -s Anc0.Anc0refChr3 58012 21 - 222631 AGAGGTTTATGGAAGGGT--TCT -s Anc1.Anc1refChr1 66547 21 - 69767 AGAGGTTTATGGAAGGGT--TCT -s Anc2.Anc2refChr1 63600 21 - 142988 AGGGGCTTATGGAAGGGT--TCT -s mr.mrrefChr3 113537 23 + 181027 AGATGTTTATGGAAGGGTCTTAT -s simCow_chr6.simCow.chr6 64470 21 - 602619 AGGGGCTTATGGAAGGGT--CCT -s simDog_chr6.simDog.chr6 67666 11 - 593897 ----------GGAAGGGG--TCT -s simHuman_chr6.simHuman.chr6 68489 21 - 601863 AGAGGTTTATGAAAGGGT--TCT -s simRat_chr6.simRat.chr6 38920 23 - 647215 GAATGTTTATGGAAAGGTATAAT - -a -s simMouse_chr6.simMouse.chr6 563652 28 + 636262 AGTAACTACTACCTCTGCTAGTTCCAGA -s Anc0.Anc0refChr3 58033 28 - 222631 ACTTATTACAACCTATCCTAGTTGTAGA -s Anc1.Anc1refChr1 66568 28 - 69767 ACTTATTACAACCTATCCTAGTTGTAGA -s Anc2.Anc2refChr1 63621 28 - 142988 ACTTATTACAACCTATCCTAGTTGTAGA -s mr.mrrefChr3 113560 28 + 181027 AGTTACTACTACCTCTGCTAGTTCCAGA -s simCow_chr6.simCow.chr6 64491 16 - 602619 A------------TCCCCTAGTTGGACA -s simDog_chr6.simDog.chr6 67680 28 - 593897 ACTTATTACAACCTATCCTCATTATAGA -s simHuman_chr6.simHuman.chr6 68510 28 - 601863 GCTTATTATCACCTGTCCTAGTTGAAGA -s simRat_chr6.simRat.chr6 38943 28 - 647215 AATTAACACTACCTCTGTTAGTTCCAGA - -a -s simMouse_chr6.simMouse.chr6 563680 88 + 636262 TAATACCTCATGTGAAGGGAGCCTATGTCCTCTATGCCTGCAAAAGAAATCTAAGGGTGGATTTTTCCAGGATGTGATTAGACTACTG -s Anc0.Anc0refChr3 58061 73 - 222631 AAATATCTGATGTGAACGGAACCGATGTACTCTTTGCCTGCAAAAGGAATCCAAGAATG-ATGTTTTTGGGCTG-------------- -s Anc1.Anc1refChr1 66596 73 - 69767 AAATATCTGATGTGAACGGAACCGATGTACTCTTTGCCTGCAAAAGGAATCCAAGAATG-ATGTTTTTGGGCTG-------------- -s Anc2.Anc2refChr1 63649 73 - 142988 AAATATCTGATGTGAACAGAACTGATGTACTCTTTTCCTGCAAAAGGAATCCAAGAATA-ATGTTTGTGGGCTG-------------- -s mr.mrrefChr3 113588 88 + 181027 TAATACCTCATGTGAAGGGAGCCTATGTCCTCTATGCCTGCAAAAGAAATCTAAGAGTGGATTTTTTCAGGATGAGATTGGACTACTG -s simCow_chr6.simCow.chr6 64507 59 - 602619 AAATATGTGATGTGACCAGAACTTATGTACTATCTTTCTGCAAAA---------------ATATATATAGGATG-------------- -s simDog_chr6.simDog.chr6 67708 73 - 593897 AAATATCTCATATGGACAGAATTGATGTACTCTTATCCTGCAAGAGGAATCCAAGAATA-ATGTTTGTGGGCTG-------------- -s simHuman_chr6.simHuman.chr6 68538 69 - 601863 GAATAGCTGATGTGAACGGAACCAATGTACTTTTTGCCTGCAAAAGGAACCCGAGAATG-ATCCTTTTGG------------------ -s simRat_chr6.simRat.chr6 38972 88 - 647215 TAATACCTCATGTCAAGGGAGCTTATGTCCTCTAGGCCTTCAAAAGAAATCTAAGAGTAGATATTCTTAGGATGAGATTGGAGTACTG - -a -s simMouse_chr6.simMouse.chr6 563768 4 + 636262 CTTG -s Anc0.Anc0refChr3 164647 4 + 222631 CTTG -s Anc1.Anc1refChr1 3248 4 + 69767 CTTG -s Anc2.Anc2refChr1 79416 4 + 142988 CTCA -s mr.mrrefChr3 113676 4 + 181027 CTTG -s simCow_chr6.simCow.chr6 538177 4 + 602619 CTCA -s simDog_chr6.simDog.chr6 526251 4 + 593897 CTCA -s simHuman_chr6.simHuman.chr6 533402 4 + 601863 CATG -s simRat_chr6.simRat.chr6 39060 4 - 647215 CTTG - -a -s simMouse_chr6.simMouse.chr6 563772 5 + 636262 AAGAA -s Anc0.Anc0refChr3 164651 4 + 222631 AAGA- -s Anc1.Anc1refChr1 3252 4 + 69767 AAGA- -s Anc2.Anc2refChr1 79420 4 + 142988 CAGA- -s mr.mrrefChr3 113680 5 + 181027 AAGAA -s simCow_chr6.simCow.chr6 538189 4 + 602619 CAGA- -s simDog_chr6.simDog.chr6 526255 4 + 593897 CAGA- -s simHuman_chr6.simHuman.chr6 533406 4 + 601863 AAGA- -s simRat_chr6.simRat.chr6 39064 5 - 647215 AAGAA - -a -s simMouse_chr6.simMouse.chr6 563777 16 + 636262 CCTCTCAGTCTCACAG -s Anc0.Anc0refChr3 164655 16 + 222631 TTTTTAAATCTTAAAG -s Anc1.Anc1refChr1 3256 16 + 69767 TTTTTAAATCTTAAAG -s Anc2.Anc2refChr1 79424 16 + 142988 TTTTAAAATCTTAAAG -s mr.mrrefChr3 113685 16 + 181027 CCTCTAAGTCTCACAG -s simCow_chr6.simCow.chr6 538193 16 + 602619 TCCTAAAATCCTAAAG -s simDog_chr6.simDog.chr6 526262 16 + 593897 TTTTAAAATCTTAATG -s simHuman_chr6.simHuman.chr6 533410 16 + 601863 TTTTTAAATCTTGGAG -s simRat_chr6.simRat.chr6 39069 16 - 647215 CCTCTAAGTCTCACAG - -a -s simMouse_chr6.simMouse.chr6 563793 2 + 636262 AT -s Anc0.Anc0refChr3 164754 2 + 222631 AT -s Anc1.Anc1refChr1 3355 2 + 69767 AT -s Anc2.Anc2refChr1 79526 2 + 142988 AT -s mr.mrrefChr3 113701 2 + 181027 AT -s simCow_chr6.simCow.chr6 538295 2 + 602619 AT -s simDog_chr6.simDog.chr6 526364 2 + 593897 GA -s simHuman_chr6.simHuman.chr6 533509 2 + 601863 AT -s simRat_chr6.simRat.chr6 39085 2 - 647215 AT - -a -s simMouse_chr6.simMouse.chr6 563795 14 + 636262 GTTAACAGTTGGAC -s Anc0.Anc0refChr3 164756 14 + 222631 GTTAGCAGTTGGAT -s Anc1.Anc1refChr1 3357 14 + 69767 GTTAGCAGTTGGAT -s Anc2.Anc2refChr1 79528 14 + 142988 GTTGGCAGTTGGAT -s mr.mrrefChr3 113703 14 + 181027 GTTAACAGTTGGAT -s simCow_chr6.simCow.chr6 538297 11 + 602619 GCTG---GTTGTAT -s simDog_chr6.simDog.chr6 526372 14 + 593897 GTCGGCAATTGGAT -s simHuman_chr6.simHuman.chr6 533511 14 + 601863 GTTAGCAGTTGGAT -s simRat_chr6.simRat.chr6 39087 14 - 647215 GTTAACAGTTCAAT - -a -s simMouse_chr6.simMouse.chr6 563809 36 + 636262 ATTTCCTATGGCAGGTATAGTGCCAAGAATGTTTGG -s Anc0.Anc0refChr3 164770 36 + 222631 ATTATCTCTGGCAGGCATAGTGCAAAGATTGTTTGG -s Anc1.Anc1refChr1 3371 36 + 69767 ATTATCTCTGGCAGGCATAGTGCAAAGATTGTTTGG -s Anc2.Anc2refChr1 79544 36 + 142988 ATTATCTCTAGCAGGCATAGTGCACAGATTGTTTGG -s mr.mrrefChr3 113717 36 + 181027 ATTTCCTATGGCAGGCATAGTGCCAAGAATGTTTGG -s simCow_chr6.simCow.chr6 538310 36 + 602619 GTTATCTCTAGCAGGCATAGTACATAGAATGTTTTG -s simDog_chr6.simDog.chr6 526388 36 + 593897 ATTATCTCTAGCAGGCATGGTGCACAGATTGTTTGG -s simHuman_chr6.simHuman.chr6 533525 36 + 601863 ATTGTCACTGGCAAGCATAGTGTGAGGACTGTTTGG -s simRat_chr6.simRat.chr6 39101 34 - 647215 ATTTCCTATGGCAGGCATAGTGCCAAGGATTATT-- - -a -s simMouse_chr6.simMouse.chr6 563845 6 + 636262 TATCCA -s Anc0.Anc0refChr3 164809 6 + 222631 CTTCCA -s Anc1.Anc1refChr1 3410 6 + 69767 CTTCCA -s Anc2.Anc2refChr1 79583 6 + 142988 CTTCCA -s mr.mrrefChr3 113753 6 + 181027 TATCCA -s simCow_chr6.simCow.chr6 538349 6 + 602619 CTTTTA -s simDog_chr6.simDog.chr6 526427 6 + 593897 CTTCCA -s simHuman_chr6.simHuman.chr6 533564 6 + 601863 CGTCCG -s simRat_chr6.simRat.chr6 39135 3 - 647215 ---CAA - -a -s simMouse_chr6.simMouse.chr6 563851 3 + 636262 CTA -s Anc0.Anc0refChr3 164816 3 + 222631 CTA -s Anc1.Anc1refChr1 3417 3 + 69767 CTA -s Anc2.Anc2refChr1 79590 3 + 142988 CCA -s mr.mrrefChr3 113759 3 + 181027 CTA -s simCow_chr6.simCow.chr6 538356 3 + 602619 CCA -s simDog_chr6.simDog.chr6 526434 3 + 593897 CCA -s simHuman_chr6.simHuman.chr6 533571 3 + 601863 CTA -s simRat_chr6.simRat.chr6 39138 3 - 647215 CTA - -a -s simMouse_chr6.simMouse.chr6 563854 1 + 636262 C -s Anc0.Anc0refChr3 164819 1 + 222631 C -s Anc1.Anc1refChr1 3420 1 + 69767 C -s Anc2.Anc2refChr1 79593 1 + 142988 C -s mr.mrrefChr3 113762 1 + 181027 C -s simCow_chr6.simCow.chr6 538362 1 + 602619 G -s simDog_chr6.simDog.chr6 526437 1 + 593897 C -s simHuman_chr6.simHuman.chr6 533574 1 + 601863 C -s simRat_chr6.simRat.chr6 39141 1 - 647215 C - -a -s simMouse_chr6.simMouse.chr6 563855 44 + 636262 TTCCAAACTCTGTTTAACTCTGAAGTTGAATTATGACAAGGATG -s Anc0.Anc0refChr3 164820 44 + 222631 TTCTGACCCCTGTTCCACTCTGAGGTTGGATCTTGACAGGGATG -s Anc1.Anc1refChr1 3421 44 + 69767 TTCTGACCCCTGTTCCACTCTGAGGTTGGATCTTGACAGGGATG -s Anc2.Anc2refChr1 79594 44 + 142988 TTCTGACCCCTGTTCCACTCTGAGGTTGGATCTTGACAGGGATG -s mr.mrrefChr3 113763 44 + 181027 TTCCAAACTCTGTTTAACTCTGAAGTTGAATTATGACAAGGATG -s simCow_chr6.simCow.chr6 538363 39 + 602619 TTCCAACCCCTGTTCCACTCTGTGGTTGGATCATCACA-----G -s simDog_chr6.simDog.chr6 526455 43 + 593897 CTCTGAACCCTGTCCCACTCTGAAGTTGGATTTTGATAGGGAT- -s simHuman_chr6.simHuman.chr6 533575 44 + 601863 TTAGGGCCCCTGTTCCACTCTGAGGTTGGATCGTGACAGGGATG -s simRat_chr6.simRat.chr6 39142 44 - 647215 TTCTAAACTCTGTTTAACTTTGAAGTTGAATTATGACAATGGTG - -a -s simMouse_chr6.simMouse.chr6 563899 62 + 636262 GTGCTTCGTCATGATCTACTTGCACATAGTGTGTATAGACTTATGGCGGTCTAAAGGGGCCA -s Anc0.Anc0refChr3 164880 58 + 222631 GTGCTTTG----CACCTACTGATGTTTAGTTTATATAGACTTGTGGAGGGCTAGAAGAACCA -s Anc1.Anc1refChr1 3482 58 + 69767 GTGCTTTG----CACCTACTGATGTTTAGTTTATATAGACTTGTGGAGGGCTAGAAGAACCA -s Anc2.Anc2refChr1 79654 58 + 142988 GTGGTTGA----CACCTACTGATGTTTAGTTTATATAGACTTGTAGAGGGTTAGAAGAACCA -s mr.mrrefChr3 113807 62 + 181027 GTGCTTTGTCATGATCTACTTGCGCATAGTTTATATAGACTTATGGCGGGCTAAAGGGGCCA -s simCow_chr6.simCow.chr6 538418 57 + 602619 GTGGTTGA----CACCTACTCATGTTTAG-TTATATAGACTTGTAGATGATTAGAAGAACCA -s simDog_chr6.simDog.chr6 526504 58 + 593897 GTGGTCGA----CACCTATTGATGTTTAGTTTATGCAGACCTGTAGAGGGTTATAAGAACCG -s simHuman_chr6.simHuman.chr6 533642 58 + 601863 GTGCTTTG----TGCCTACTGATGTTCAGTTTATATAACCTTGCGGAGTGCAAGAAGAAACA -s simRat_chr6.simRat.chr6 39186 59 - 647215 GTGCTTTGGGATGATCTACTTGAGCATAGTTTATATAGACTTATGGCAGGCTATAG---CTG - -a -s simMouse_chr6.simMouse.chr6 563961 50 + 636262 ACTTATTATCAAGCTGTTTTTTGTGACCATTCTCCAGTCACACTGCCAAT -s Anc0.Anc0refChr3 164938 50 + 222631 ACTTATTATTCAACTGTTCCTGGTGATCCTTCTTCTTTTACACTTTCAAT -s Anc1.Anc1refChr1 3540 50 + 69767 ACTTATTATTCAACTGTTCCTGGTGATCCTTCTTCTTTTACACTTTCAAT -s Anc2.Anc2refChr1 79714 50 + 142988 ACTTATTATTCAACTGGTCCTGGTGATCCTTCTTCTTTTACACTTTCAAT -s mr.mrrefChr3 113869 50 + 181027 ACTTATTATCAAGCTGTTTTTTGTGACCATTCTCCTTTTACACTTCCAAT -s simCow_chr6.simCow.chr6 538477 50 + 602619 ACTTATTATTCAAATGATCTTGGTGAGCCTTCTTCTTTTACACTTTTAAT -s simDog_chr6.simDog.chr6 526564 50 + 593897 ACTTATCATTCAACTGGTCCTTATCATCCTTTTTCTTTTACACATGCAAT -s simHuman_chr6.simHuman.chr6 533700 50 + 601863 ACTTATTATTCAACTGTTCCTGGTGATCCTTCTTTTTTTACATTTTCAAT -s simRat_chr6.simRat.chr6 39245 50 - 647215 ACTTATTATCAAGCTGTTTTATGTAACCATTCTCCTTCTACACTTCCAAT - -a -s simMouse_chr6.simMouse.chr6 564011 12 + 636262 CCGCCCAGAACC -s Anc0.Anc0refChr3 164994 12 + 222631 TTGCCTGGAATC -s Anc1.Anc1refChr1 3596 12 + 69767 TTGCCTGGAATC -s Anc2.Anc2refChr1 79770 12 + 142988 TTGCCTGGAATC -s mr.mrrefChr3 113919 12 + 181027 CCGCCCAGAACC -s simCow_chr6.simCow.chr6 538533 12 + 602619 TTGCCTTGGATC -s simDog_chr6.simDog.chr6 526620 12 + 593897 TCGCCTGGAATC -s simHuman_chr6.simHuman.chr6 533760 12 + 601863 TTGCCTGGAATC -s simRat_chr6.simRat.chr6 39295 12 - 647215 CAGCCCAGAACC - -a -s simMouse_chr6.simMouse.chr6 564023 43 + 636262 CTTCAAACAGTTTTGTCTGAGCTATGAAGGAGTGGTAATGTCA -s Anc0.Anc0refChr3 165009 32 + 222631 CTTTGTAAGGTTCTCTCTGAGCT-----------GTAGTGTCC -s Anc1.Anc1refChr1 3611 32 + 69767 CTTTGTAAGGTTCTCTCTGAGCT-----------GTAGTGTCC -s Anc2.Anc2refChr1 79785 32 + 142988 CTTTGTAAGGTTCTCTCTGAGCT-----------ATAGTATCC -s mr.mrrefChr3 113931 43 + 181027 CTTTAAAAAGTTTTGTCTGAGCTATGAAGGAGTGGTAATGTCA -s simCow_chr6.simCow.chr6 538548 27 + 602619 CTGTGTAAAG-----TCTGAGCC-----------ATAGTATCA -s simDog_chr6.simDog.chr6 526635 32 + 593897 CTTTGTAAGGTTCTCTATGAGCT-----------ATAGTAACC -s simHuman_chr6.simHuman.chr6 533775 32 + 601863 CTCTGTAAGGTTGTTTCTGAGCT-----------GTAGTGTCC -s simRat_chr6.simRat.chr6 39307 43 - 647215 CTTTAGAAAGTCTTGTCTGAACTATAAAGGAGGGGTAATGTCA - -a -s simMouse_chr6.simMouse.chr6 564066 19 + 636262 TCTTACGTCACAGTCGTTA -s Anc0.Anc0refChr3 165041 16 + 222631 TCTTGCAT---GGTCCTTG -s Anc1.Anc1refChr1 3643 16 + 69767 TCTTGCAT---GGTCCTTG -s Anc2.Anc2refChr1 79817 16 + 142988 TCTTGCAT---GGTCCTTG -s mr.mrrefChr3 113974 19 + 181027 TCTTACATCACAGTCCTTA -s simCow_chr6.simCow.chr6 538575 16 + 602619 TCTTGTAT---GAGCCTTA -s simDog_chr6.simDog.chr6 526693 16 + 593897 TCGTGCAT---GGTCCTTG -s simHuman_chr6.simHuman.chr6 533807 16 + 601863 TATTGCAT---GGACCTTC -s simRat_chr6.simRat.chr6 39350 19 - 647215 TCTTACATCACAGTCCATA - -a -s simMouse_chr6.simMouse.chr6 564085 87 + 636262 CATGCTAGTCCAGGAACTTCAGGGAAACCACCCCAGAGGAGTATGTGGTCTAGCATAGCTTCAGCCGAAGTGACATGAAGTCACAGT -s Anc0.Anc0refChr3 165057 85 + 222631 CATGCTAACCCAGGAGCTTTA-GGAAACCAATTAGGAGGAGTGCATAGTTTGGCAAAGGTTTCACC-AAGTGAAATAAAATTACGGG -s Anc1.Anc1refChr1 3659 85 + 69767 CATGCTAACCCAGGAGCTTTA-GGAAACCAATTAGGAGGAGTGCATAGTTTGGCAAAGGTTTCACC-AAGTGAAATAAAATTACGGG -s Anc2.Anc2refChr1 79834 85 + 142988 CATGCTAACCCAGAAGCCTTA-GGAAACAAATTAGGAGGAAGGCATAGTCTGGCAAAGGTTTCACC-AAATGGAATAAAATTAAGGG -s mr.mrrefChr3 113993 86 + 181027 CATGCTAGCCCAGGAACTTCAGGGAAACCACCCCAGAGGAGTATGTGGTTTGGCAAAGGTTCAACC-AAGTGACATGAAATCACAGT -s simCow_chr6.simCow.chr6 538592 75 + 602619 TATGCCAAGCC---------A-GGTGACAAATA-GGTGGGAGGCATGGTCTGGCAAAGGTTTCACC-AAAGGGATTAAAATTGAGGG -s simDog_chr6.simDog.chr6 526710 85 + 593897 CATGCTAACCCAGAAGCCTTA-GGAAACAAATTAGGATGAAGGTACAGTCTGGCAGGGGTTTCACC-GGATGGAATAAAATGAAGGG -s simHuman_chr6.simHuman.chr6 533823 85 + 601863 TAGGCTCACCCGAGAGCTTTA-GGAAACCAATTTGGAGGAGTGCCTAGTTTGGCAAAGGGTTCACC-AAGTGAAATAAGATTACGGG -s simRat_chr6.simRat.chr6 39369 86 - 647215 CATACTAGCCCAGGAACTGCCTAGAAACCACCCCAGAGGAGTTAGTGGATTGGCAAAGGTGCTACC-AAGTGACATGAAATCACAGT - -a -s simMouse_chr6.simMouse.chr6 564172 66 + 636262 AGCTGCTGGCAGGGCACGACTTGAAGCAAATTGCAAATAAAGGAAATACATGATAAGCTCATTCAA -s Anc0.Anc0refChr3 165143 50 + 222631 AGCTGCAGGTAGACAGTAGCTTGAATCAAATAGTA----------------GCTCAACTCTTGCAA -s Anc1.Anc1refChr1 3745 50 + 69767 AGCTGCAGGTAGACAGTAGCTTGAATCAAATAGTA----------------GCTCAACTCTTGCAA -s Anc2.Anc2refChr1 79920 50 + 142988 AGCTGCAGGTAGACAGTAGCTTAAATTAGACAGTA----------------GCTCACCTCTTGCAA -s mr.mrrefChr3 114079 66 + 181027 AGCTGCTGGTAGGGCGCAACTTGAAGCAAATTGCAAATAAAGGAAATACATGATAAACTCATTCAA -s simCow_chr6.simCow.chr6 538668 49 + 602619 AGTTGTGAGTAAACAGTAG-GTAAAGTGTACAGTA----------------GCTCACATCTTTCAA -s simDog_chr6.simDog.chr6 526796 50 + 593897 AGCTGCAGGTAGACCGTAGCTTAAATTAGACAGAA----------------GCTCACCTCTTGCAA -s simHuman_chr6.simHuman.chr6 533909 50 + 601863 AGGTGCAGGTATACAGTAGCTTGAAACAAATAGTA----------------GCTCAACTTTTCCAG -s simRat_chr6.simRat.chr6 39455 66 - 647215 AGCTGCTGGTAGGGTGCAACTTGTAGCAAGTTGCAAATAAAGCAAATATACAATTAACTCATTCAA - -a -s simMouse_chr6.simMouse.chr6 564238 11 + 636262 CATGGAGGATA -s Anc0.Anc0refChr3 165197 11 + 222631 CATAGAAGATT -s Anc1.Anc1refChr1 3799 11 + 69767 CATAGAAGATT -s Anc2.Anc2refChr1 79974 11 + 142988 CTTAAAAGATT -s mr.mrrefChr3 114145 11 + 181027 CATGGAGGATA -s simCow_chr6.simCow.chr6 538721 11 + 602619 ATTAAAAGATT -s simDog_chr6.simDog.chr6 526850 11 + 593897 CTTAAAAGATT -s simHuman_chr6.simHuman.chr6 533963 11 + 601863 CATAGAAGATC -s simRat_chr6.simRat.chr6 39521 11 - 647215 CCTGGAGGATA - -a -s simMouse_chr6.simMouse.chr6 564249 32 + 636262 AAGTTGTAGACAATAAGCTGTACTAACTCTTA -s Anc0.Anc0refChr3 165213 32 + 222631 GAGTTGCAGACAGTAATCTGTACTATCGCTTT -s Anc1.Anc1refChr1 3815 32 + 69767 GAGTTGCAGACAGTAATCTGTACTATCGCTTT -s Anc2.Anc2refChr1 79990 32 + 142988 GAGTTTCAGACAGTAATCTGTACTATCGCTTT -s mr.mrrefChr3 114156 32 + 181027 AAGTTGTAGACAATAAGCTGTACTAACTCTTA -s simCow_chr6.simCow.chr6 538737 31 + 602619 TAGACACAGACAGT-ATCTGAACTATCACTTT -s simDog_chr6.simDog.chr6 526866 32 + 593897 GAGTTTCAGACAGTAATCTGTACGATCGTATT -s simHuman_chr6.simHuman.chr6 533979 32 + 601863 GAGTTGCAAACAGTAATCTGTAACTGCCCCTT -s simRat_chr6.simRat.chr6 39532 32 - 647215 ATGTTATAGACAAAAAACTGGACTAACTCTTA - -a -s simMouse_chr6.simMouse.chr6 564281 1 + 636262 T -s Anc0.Anc0refChr3 165245 1 + 222631 T -s Anc1.Anc1refChr1 3847 1 + 69767 T -s Anc2.Anc2refChr1 80022 1 + 142988 T -s mr.mrrefChr3 114188 1 + 181027 T -s simCow_chr6.simCow.chr6 538768 1 + 602619 T -s simDog_chr6.simDog.chr6 526898 1 + 593897 T -s simHuman_chr6.simHuman.chr6 534063 1 + 601863 T -s simRat_chr6.simRat.chr6 39564 1 - 647215 T - -a -s simMouse_chr6.simMouse.chr6 564282 10 + 636262 TATATTAACA -s Anc0.Anc0refChr3 165247 10 + 222631 TATATTAGCA -s Anc1.Anc1refChr1 3849 10 + 69767 TATATTAGCA -s Anc2.Anc2refChr1 80024 10 + 142988 TATATTAGCA -s mr.mrrefChr3 114189 10 + 181027 TATATTAACA -s simCow_chr6.simCow.chr6 538770 10 + 602619 TATATTAGGA -s simDog_chr6.simDog.chr6 526900 10 + 593897 TATATCAGCA -s simHuman_chr6.simHuman.chr6 534065 10 + 601863 TAGATTGGCA -s simRat_chr6.simRat.chr6 39565 10 - 647215 TACATTAACA - -a -s simMouse_chr6.simMouse.chr6 564292 10 + 636262 TTTCTCATAT -s Anc0.Anc0refChr3 165261 10 + 222631 TCTCTCATAT -s Anc1.Anc1refChr1 3863 10 + 69767 TCTCTCATAT -s Anc2.Anc2refChr1 80038 10 + 142988 TCTCTCATAT -s mr.mrrefChr3 114203 10 + 181027 TTTCTCATAT -s simCow_chr6.simCow.chr6 538784 10 + 602619 TCTCTCATAC -s simDog_chr6.simDog.chr6 526914 10 + 593897 CCTCTCATAT -s simHuman_chr6.simHuman.chr6 534079 10 + 601863 TCTCTCATAC -s simRat_chr6.simRat.chr6 39579 10 - 647215 TTTCTCATAT - -a -s simMouse_chr6.simMouse.chr6 564302 239 + 636262 CAATTATATTAATGATGGCCAGATTCATGTCATGTAATCCCTCTTTTGGTGGTATTGGAAAGGGACATCTAATGAGAGAAGTGGATGCACTGGATGGGTTGTGTTCTCATATCTGTGACCAGTCTGGTGCCCTTTATAAAGTATTGAACCGTCGTAAGGGACCTGATGTGGTGGGGGGGTTGCGGGCACAGATTGATAGAAAACTTTACAAGCAGAACATGCAAGTAACAAATATAAAG -s Anc0.Anc0refChr3 165271 235 + 222631 TATTTAT----ATAATGTTCAGCTTCATGTCATGTAATCCCTCCTTTGGTGGCATTGGCAAAGGGCATCTAATGCGAGAAGTAGATGCACTGGATGGGCTGTGTTCTCACATCTGTGACCAGTCTGGTGCACTTTATAAAGTATTGAACCGTCGTAAGGGACCTGATGTGGTGTGGGGGTTGCGGGCACAGATTGATAGGAAACTTTATAAGCAAAACATGCAGGTAACAGATGTAAAG -s Anc1.Anc1refChr1 3873 235 + 69767 TATTTAT----ATAATGTTCAGCTTCATGTCATGTAATCCCTCCTTTGGTGGCATTGGCAAAGGGCATCTAATGCGAGAAGTAGATGCACTGGATGGGCTGTGTTCTCACATCTGTGACCAGTCTGGTGCACTTTATAAAGTATTGAACCGTCGTAAGGGACCTGATGTGGTGTGGGGGTTGCGGGCACAGATTGATAGGAAACTTTATAAGCAAAACATGCAGGTAACAGATGTAAAG -s Anc2.Anc2refChr1 80052 235 + 142988 TATATGT----ATAATTTTCAGCTTTATGTCATGTAATCCCTCCTTTGGTGGCATTGGCAAGGGGCATCTAATGCGAGAAGTAGATGCACTGGATGGGCTGTGTTCTCACATCTGTGACCAGTCTGGTGCACTTTATAAAGTATTGAACCGTCGTAAGGGACCTGATGTGGTGTGGGGGTTGCGGGCACAGATTGACAGGAAACTTTATAAGCAAAACATGCAGGTAACAGATGTGAAG -s mr.mrrefChr3 114213 239 + 181027 TATTTATATTAATAATGGCCAGATTCATGTCATGTAATCCCTCCTTTGGTGGCATTGGAAAAGGACATCTAATGCGAGAAGTAGATGCACTGGATGGGTTGTGTTCTCATATCTGTGACCAGTCTGGTGCCCTTTATAAAGTATTGAACCGTCGTAAGGGACCTGATGTGGTGGGGGGGTTGCGGGCACAGATTGATAGAAAACTTTATAAGCAGAACATGCAAGTAACAAATATAAAG -s simCow_chr6.simCow.chr6 538798 235 + 602619 CATATCT----ATAATTTTCAGCTTTATGTCATGTAATCCCTCTTTTGGTGGCATTGGCAAGGGGCATTTAATGCGAGAAGTAGATGCACTGGACGGCCTGTGTTCTCACATCTGTGACCAGTCTGGTGAACTTTATAAAGTACTGAACCGTCGTAAGGGACCTGATGTGGTGTGGGGGTTGCGGGCACAGATTGACAGGAAACTTTATAAGCAAAACATGCAAGTAGCAGATGCCAAG -s simDog_chr6.simDog.chr6 526928 235 + 593897 TATACGC----ATATTTTTCAGCTTTATGTCATGTAATCCCTCCTTTGGTGGCATTGGCAAGGGGCATCTAATGCGGGAAGTAGATGCACTGGATGGGCTGTGTTCGCACATCTGTGACCAGTCTGGTGCACTTTATAAAGTATTAAACCGACGTAAGGGACCTGATGTTGTGTGGGGGTTGCGGGCACAGATTGACAGGAAACTGTATAAACAAAACATGCAGGTAATAGATGTGGAG -s simHuman_chr6.simHuman.chr6 534089 235 + 601863 TATTTAT----ATAATGCACAGCTTCATGTCATGTAATCCCTCCTTTGGTGGCATCGGCAAAGGGCATCTAATGCGAGAAGTAGATGCACTGGATGGGCTGTGCTCTCACATCTGTGACCAGTCTGGTGCACTTTATAAAGTATTGAACCGTCGTAAGGGACCTGATGTGGTGTGGGGGTTGCGGGCACAGATTGATAGGAAACTTTATAAGCAAAACATGCAGGTAACAGATGTAAAG -s simRat_chr6.simRat.chr6 39589 239 - 647215 TATTTGTTTTAATAATGACCAGATTCATGTCATGTAATCCCTCCTTTGGGGGCATTGGAAAAGGACATCTAATGCGAGAAGTAGATGCACTGGATGGGTTGTGTTCTCATATCTGTGACCAGTCTGGTGCTCTTTATAAAGTCCTGAACCATCGTAGGGGGCCTGACGTGGTGGGGGGGCTGCGGGCACAGATCGATAGAAAGCTTTATAAGCAGAACATGCAAGTTACAAATATAAAG - -a -s simMouse_chr6.simMouse.chr6 564541 28 + 636262 CATTATTGTAGCAGCCCCGAGTATTGAA -s Anc0.Anc0refChr3 165506 28 + 222631 GGTTGTTATAACTGAACCCAACATTAAA -s Anc1.Anc1refChr1 4108 28 + 69767 GGTTGTTATAACTGAACCCAACATTAAA -s Anc2.Anc2refChr1 80287 28 + 142988 GGTAGTTATAACTGAACCCAACATTAAA -s mr.mrrefChr3 114452 28 + 181027 CGTTATTGTAGCAGACCCGAGCATTGAA -s simCow_chr6.simCow.chr6 539040 28 + 602619 GGTAGTCACAGCTGACCCCAACATTACA -s simDog_chr6.simDog.chr6 527163 28 + 593897 GATAGTTATAACTTAACCCAACATTGAC -s simHuman_chr6.simHuman.chr6 534324 28 + 601863 GGCTGTGATAACTGAGCCTAACATTAAA -s simRat_chr6.simRat.chr6 39828 28 - 647215 CGTTATTGTAGCAGATCCCAGCATTGCA - -a -s simMouse_chr6.simMouse.chr6 564569 11 + 636262 TTTCTGGATGT -s Anc0.Anc0refChr3 165534 11 + 222631 TTCCCAGATGT -s Anc1.Anc1refChr1 4136 11 + 69767 TTCCCAGATGT -s Anc2.Anc2refChr1 80315 11 + 142988 TTCCCAGATGT -s mr.mrrefChr3 114480 11 + 181027 TTCCTAGATGT -s simCow_chr6.simCow.chr6 539068 11 + 602619 TACCTAGATGT -s simCow_chr6.simCow.chr6 580160 11 + 602619 TGTTCAGATGT -s simDog_chr6.simDog.chr6 527191 11 + 593897 TTCCCAGATAT -s simHuman_chr6.simHuman.chr6 534352 11 + 601863 TTCCCAGATGC -s simRat_chr6.simRat.chr6 39856 11 - 647215 TTCCTAACTGT - -a -s simMouse_chr6.simMouse.chr6 564580 142 + 636262 AAGTGTAGTCTCCCCATGGAGAAAGAGATATTAAACACACCATTGTTGACAGTCCAAGAAGGTGCAGTTGAAGAGCTTACTCTCCCTGAACCAGAGCCTGAACACACTGGTGAATGTCATGTCAGTGGTGTTGTCTTAGGTC -s Anc0.Anc0refChr3 165545 142 + 222631 AAATATAGACTCCACATTGAGAAAGAGATATTAAACACACCATTATTGTCAGTCCAGGAAGGAGCAGTTGAGGATCTTACTCTTCCTGAACCAGAGCCTGAACACACTGGTGAATGTCATGTCAGTGGCGTTGTCTTAGGTT -s Anc1.Anc1refChr1 4147 142 + 69767 AAATATAGACTCCACATTGAGAAAGAGATATTAAACACACCATTATTGTCAGTCCAGGAAGGAGCAGTTGAGGATCTTACTCTTCCTGAACCAGAGCCTGAACACACTGGTGAATGTCATGTCAGTGGCGTTGTCTTAGGTT -s Anc2.Anc2refChr1 80326 142 + 142988 AAAGATAGACTCCCCATTGAGAAAGAGATATTAAATACACCATTATTGTCAGTCCAGGAAGGAGCAGTTGAGGATCTTACTCTTCCTGAACCAGAGCCTGAACACACTGGTGAATGTCATGTCAGTGGCGTTGTCTTAGGTT -s mr.mrrefChr3 114491 142 + 181027 AAGTGTAGACTCCACATTGAGAAAGAGATATTAAACACACCATTGTTGACAGTCCAAGAAGGAGCAGTTGAAGAGCTTACTCTCCCTGAACCAGAGCCTGAACACACTGGTGAATGTCATGTCAGTGGTGTTGTCTTAGGTT -s simCow_chr6.simCow.chr6 539079 142 + 602619 AAAGATAAACTCCCCATTGAGAAAGAGATATTAAATACACCCTTATTGTCAGTCCAGGAAGGAGCAGTTGAGGATCTCACTCTTCCTGAACCAGAGCCTGAACACACTGGTGAATGTCATGTCAGTGGCATTGTCTTAGGTT -s simCow_chr6.simCow.chr6 580171 140 + 602619 AAAGATAGACTCCCCA--GAGAGAGAGATATTAAATACACCCTTATTGTCAGTTCAGGAAGGAGCAGTTGAGGATCTGCCTCCTCCTGAACCAGAGCCTGAACACACTGGTGAATGTCATGACAGTGGCGTTGTCCTAGGTT -s simDog_chr6.simDog.chr6 527202 142 + 593897 AACTATAGACTCCCCATTGAGAAAGAAATATTAAATACACCATTATTGACAGTCCAGGAAGGAGCAGTTGAAGATCTTACCCTTCCCGAACCAGAGCCTGAACACACTGGTGAGTGTCATGTCAGTGGTGTTGTCTTAGGTT -s simHuman_chr6.simHuman.chr6 534364 142 + 601863 AAATATAGAGTCCACATTGAGAAAGAGATATTAAACACACCATTATTGGCGGTCCAGGAAGGAGCAGTTGAGGATTTTACTCTACCTGAACCAGAGCCCGAACACACTGGTGAATGTCATGTCCGTGGCGTTGTCTTAGGTT -s simRat_chr6.simRat.chr6 39867 142 - 647215 AAGTGTAGACTCCAGATTGAGAAAGAGATATTAAATACGCCATTGTTGACAGTTCAAGAAGGAGCAGTTGAAGAGCTTACTCTCCCTGAACCAGAGCCTGAACACACTGGTGAATGTCATGTCAGTGGTGTTGTCTTAGGTT - -a -s simMouse_chr6.simMouse.chr6 564722 29 + 636262 TGTACTTAAAACTTGTGATATATGATACT -s Anc0.Anc0refChr3 165687 29 + 222631 TGTATTTAAAACCTGTGATATACAATACT -s Anc1.Anc1refChr1 4289 29 + 69767 TGTATTTAAAACCTGTGATATACAATACT -s Anc2.Anc2refChr1 80471 29 + 142988 TGTATTTAAAACCTGTGATATACAATACT -s mr.mrrefChr3 114633 29 + 181027 TGTATTTAAAACCTGTGATATATGATACT -s simCow_chr6.simCow.chr6 539224 29 + 602619 TGTACTTAAAACTTGTGATATATGTTACT -s simCow_chr6.simCow.chr6 580314 19 + 602619 TGTACTTAAAACCTGTGAT---------- -s simDog_chr6.simDog.chr6 527344 17 + 593897 GGTATTTATA------------CAATACT -s simHuman_chr6.simHuman.chr6 534506 29 + 601863 TGTATTTACCATCTGTGATGTTCAATACT -s simRat_chr6.simRat.chr6 40009 29 - 647215 TGTATTTAAAACCTGTGATACATGATACT - -a -s simMouse_chr6.simMouse.chr6 564751 3 + 636262 CCA -s Anc0.Anc0refChr3 165719 3 + 222631 CTA -s Anc1.Anc1refChr1 4321 3 + 69767 CTA -s Anc2.Anc2refChr1 80503 3 + 142988 CTA -s mr.mrrefChr3 114662 3 + 181027 CCA -s simCow_chr6.simCow.chr6 539256 3 + 602619 CTT -s simDog_chr6.simDog.chr6 527364 3 + 593897 CTA -s simHuman_chr6.simHuman.chr6 534538 3 + 601863 CTA -s simRat_chr6.simRat.chr6 40038 3 - 647215 CCA - -a -s simMouse_chr6.simMouse.chr6 564754 7 + 636262 AGATGGT -s Anc0.Anc0refChr3 165722 6 + 222631 AGAT-AT -s Anc1.Anc1refChr1 4324 6 + 69767 AGAT-AT -s Anc2.Anc2refChr1 80506 6 + 142988 AGAT-AT -s mr.mrrefChr3 114665 7 + 181027 AGATGGT -s simCow_chr6.simCow.chr6 539259 6 + 602619 AGAT-AT -s simCow_chr6.simCow.chr6 580333 4 + 602619 --AT-AT -s simDog_chr6.simDog.chr6 527369 6 + 593897 AGAT-AT -s simHuman_chr6.simHuman.chr6 534541 6 + 601863 AGAT-AT -s simRat_chr6.simRat.chr6 40041 7 - 647215 AGATGGT - -a -s simMouse_chr6.simMouse.chr6 564761 16 + 636262 GTGCACAGATTATCTC -s Anc0.Anc0refChr3 165731 13 + 222631 ATG---AGTTTATCTT -s Anc1.Anc1refChr1 4333 13 + 69767 ATG---AGTTTATCTT -s Anc2.Anc2refChr1 80515 13 + 142988 ATG---AGTTCCTCTT -s mr.mrrefChr3 114675 16 + 181027 GTGCACAGATTATCTC -s simCow_chr6.simCow.chr6 539268 12 + 602619 GTG---AGTTCCTC-T -s simCow_chr6.simCow.chr6 580340 8 + 602619 ATT---GGTTC----- -s simDog_chr6.simDog.chr6 527378 13 + 593897 ATG---AGTTCCCCTT -s simHuman_chr6.simHuman.chr6 534550 13 + 601863 ATG---AGTTTATCTT -s simRat_chr6.simRat.chr6 40051 16 - 647215 GTTCACAGATTATCTC - -a -s simMouse_chr6.simMouse.chr6 564777 42 + 636262 TCCAAGTTGGTCCAGTACAGGCTTACAGGGAAAGTGATTTCT -s Anc0.Anc0refChr3 165747 38 + 222631 TCCA----GGTTCAGTACAGGTTCACAGGAAAAGTAACTTCT -s Anc1.Anc1refChr1 4349 38 + 69767 TCCA----GGTTCAGTACAGGTTCACAGGAAAAGTAACTTCT -s Anc2.Anc2refChr1 80531 38 + 142988 TCCA----GGTTTGGGATGGGTTCACAGGAAAGATAACTTCT -s mr.mrrefChr3 114691 42 + 181027 TCCAAGTTGGTTCAGTACAGGCTCACAGGGAAAGTGATTTCT -s simCow_chr6.simCow.chr6 539282 27 + 602619 TCCA----GGTT-----------TACAGGGAATATAACTTCT -s simDog_chr6.simDog.chr6 527394 38 + 593897 TCCA----GGTTTGGGATGGGTTCGCAGGAAAGATAACTTCT -s simHuman_chr6.simHuman.chr6 534566 38 + 601863 TCCA----GGTTCAATCCAGGTGCATGGGAAAAGTAACCTCT -s simRat_chr6.simRat.chr6 40067 42 - 647215 TCCAAGTTGGTTTGCTACAGGCTCACCAGGAAAGTGATTTGT - -a -s simMouse_chr6.simMouse.chr6 564819 16 + 636262 AGGTGAAACCCCCCGA -s Anc0.Anc0refChr3 165786 16 + 222631 ACTTGATACCCTCTCA -s Anc1.Anc1refChr1 4388 16 + 69767 ACTTGATACCCTCTCA -s Anc2.Anc2refChr1 80570 16 + 142988 ATTTGATACCCTCTCA -s mr.mrrefChr3 114733 16 + 181027 ACGTGAAACCCCCCGA -s simCow_chr6.simCow.chr6 539310 16 + 602619 ATTTGATTCCCTCTCA -s simDog_chr6.simDog.chr6 527433 16 + 593897 ATTTGATACCTTCTCA -s simHuman_chr6.simHuman.chr6 534605 16 + 601863 ACATGATACACTCTCA -s simRat_chr6.simRat.chr6 40109 16 - 647215 ACGTGAAACCCCCCGG - -a -s simMouse_chr6.simMouse.chr6 564835 2 + 636262 CT -s Anc0.Anc0refChr3 165802 2 + 222631 CT -s Anc1.Anc1refChr1 4404 2 + 69767 CT -s Anc2.Anc2refChr1 80586 2 + 142988 CT -s mr.mrrefChr3 114749 2 + 181027 CT -s simCow_chr6.simCow.chr6 539326 2 + 602619 CT -s simDog_chr6.simDog.chr6 527449 2 + 593897 CT -s simHuman_chr6.simHuman.chr6 534621 2 + 601863 CT -s simRat_chr6.simRat.chr6 40128 2 - 647215 TT - -a -s simMouse_chr6.simMouse.chr6 564837 17 + 636262 GGTGGCTACAAAATACC -s Anc0.Anc0refChr3 165804 17 + 222631 GGTGACTGCTAAACACT -s Anc1.Anc1refChr1 4406 17 + 69767 GGTGACTGCTAAACACT -s Anc2.Anc2refChr1 80588 17 + 142988 GGTGACTGCTAAACACT -s mr.mrrefChr3 114751 17 + 181027 GGTGACTACAAAACACC -s simCow_chr6.simCow.chr6 539328 17 + 602619 GGTAACTGCTAAACACT -s simDog_chr6.simDog.chr6 527452 15 + 593897 GGTGAT--CTAAACACT -s simHuman_chr6.simHuman.chr6 534623 17 + 601863 GGTGACTGCTGGACACT -s simRat_chr6.simRat.chr6 40130 17 - 647215 GGTGACTACACAACACC - -a -s simMouse_chr6.simMouse.chr6 564854 4 + 636262 ATGA -s Anc0.Anc0refChr3 165826 4 + 222631 CTGA -s Anc1.Anc1refChr1 4428 4 + 69767 CTGA -s Anc2.Anc2refChr1 80610 4 + 142988 CCTT -s mr.mrrefChr3 114768 4 + 181027 ATGA -s simCow_chr6.simCow.chr6 539350 4 + 602619 CCTT -s simDog_chr6.simDog.chr6 527472 4 + 593897 CCTT -s simHuman_chr6.simHuman.chr6 534645 4 + 601863 CTGA -s simRat_chr6.simRat.chr6 40147 4 - 647215 ATGA - -a -s simMouse_chr6.simMouse.chr6 564858 13 + 636262 CTTTTGCGATAAA -s Anc0.Anc0refChr3 165831 12 + 222631 CTTTACACATCA- -s Anc1.Anc1refChr1 4433 12 + 69767 CTTTACACATCA- -s Anc2.Anc2refChr1 80615 12 + 142988 CTTTACACATCA- -s mr.mrrefChr3 114773 12 + 181027 CTTTTGCGATAA- -s simCow_chr6.simCow.chr6 539355 12 + 602619 CTTTACACATCT- -s simDog_chr6.simDog.chr6 527477 12 + 593897 CTTTATACATCA- -s simHuman_chr6.simHuman.chr6 534650 12 + 601863 CCTTACACATCA- -s simRat_chr6.simRat.chr6 40152 12 - 647215 CTTTTGAGATAA- - -a -s simMouse_chr6.simMouse.chr6 564871 14 + 636262 CTTTTATTTTCTTG -s Anc0.Anc0refChr3 165843 11 + 222631 CTTGTGTTTT---C -s Anc1.Anc1refChr1 4445 11 + 69767 CTTGTGTTTT---C -s Anc2.Anc2refChr1 80647 11 + 142988 CTTGTGTTTT---C -s mr.mrrefChr3 114785 11 + 181027 CTTTTATTTT---G -s simCow_chr6.simCow.chr6 539401 11 + 602619 CTTGTGTTTT---T -s simDog_chr6.simDog.chr6 527509 11 + 593897 CTTGTGTTTT---C -s simRat_chr6.simRat.chr6 40164 11 - 647215 CTTTTGTTTT---G - -a -s simMouse_chr6.simMouse.chr6 564885 22 + 636262 TATTGCCCTCTTGCTCCGATAC -s Anc0.Anc0refChr3 165854 22 + 222631 TGTTGCCCTGTTGCACCCTCAC -s Anc1.Anc1refChr1 4456 22 + 69767 TGTTGCCCTGTTGCACCCTCAC -s Anc2.Anc2refChr1 80661 22 + 142988 TGTTGCCCTGTTGCACCCTCAC -s mr.mrrefChr3 114796 22 + 181027 TATTGCCCTCTTGCTCCATCAC -s simCow_chr6.simCow.chr6 539415 22 + 602619 TGTAGCCTTGTTCGACCCTCAC -s simDog_chr6.simDog.chr6 527523 22 + 593897 TGTTGCCCTGTTGCACCCTCAC -s simRat_chr6.simRat.chr6 40175 22 - 647215 TGTTGCCCTCTTGCTCCATCAC - -a -s simMouse_chr6.simMouse.chr6 564907 33 + 636262 CATCTCCTACGGTTCTCAGCTCTGGCGGACATC -s Anc0.Anc0refChr3 165876 29 + 222631 AACCTCATTTTTAGTTTAGCTCTGGCT----TC -s Anc1.Anc1refChr1 4478 32 + 69767 AACCTCATTTTTAGTTTAGCTCTGGCT-ACATC -s Anc2.Anc2refChr1 80683 29 + 142988 AACCTCATTTTTAGTTTAGCTCTGGCT----CC -s mr.mrrefChr3 114818 33 + 181027 CATCTCATACGGTTCTCAGCTCTGGCGGACATC -s simCow_chr6.simCow.chr6 539437 29 + 602619 AGCTATATCTTGATTTGAGCTCTGGCT----TC -s simDog_chr6.simDog.chr6 527545 29 + 593897 AACCTCATTTTTAGTTTAGCTCTGGCT----CC -s simHuman_chr6.simHuman.chr6 534662 5 + 601863 ----------------------------ACATC -s simRat_chr6.simRat.chr6 40202 33 - 647215 CATCTCATCCGGTTCTCATCTCTGGTTGACACC - -a -s simMouse_chr6.simMouse.chr6 564940 19 + 636262 ATAGATGGTAAATTGTTAT -s Anc0.Anc0refChr3 165905 19 + 222631 ATCCATTGTAGAAAGTAAC -s Anc1.Anc1refChr1 4510 19 + 69767 ATCCATTGTAGAAAGTAAC -s Anc2.Anc2refChr1 80712 19 + 142988 ATCCATTGTGGAAAATAGC -s mr.mrrefChr3 114851 19 + 181027 ATAGATGGTAAATTGTTAT -s simCow_chr6.simCow.chr6 539466 14 + 602619 ACAAATGGCTGTA-----C -s simDog_chr6.simDog.chr6 527574 19 + 593897 ATCCATTGTGGATAATAGC -s simHuman_chr6.simHuman.chr6 534670 19 + 601863 ATGTAAAGTAGAAAGTAAC -s simRat_chr6.simRat.chr6 40235 19 - 647215 ATAAATGATAAATTGTCAT - -a -s simMouse_chr6.simMouse.chr6 564959 11 + 636262 ATATATCTACA -s Anc0.Anc0refChr3 165924 11 + 222631 CTGTATCTATT -s Anc1.Anc1refChr1 4529 11 + 69767 CTGTATCTATT -s Anc2.Anc2refChr1 80731 11 + 142988 CTGTATCTATT -s mr.mrrefChr3 114870 11 + 181027 ATATATCTACA -s simCow_chr6.simCow.chr6 539480 7 + 602619 CTGTACC---- -s simDog_chr6.simDog.chr6 527593 11 + 593897 CTGTATTTATT -s simHuman_chr6.simHuman.chr6 534689 11 + 601863 CTGTATCTTTT -s simRat_chr6.simRat.chr6 40255 11 - 647215 ATATATCTACA - -a -s simMouse_chr6.simMouse.chr6 564970 26 + 636262 ATACAGCTTACAAGACAAAGCAAGAT -s Anc0.Anc0refChr3 165935 25 + 222631 GCACAGCTTATTAGATGATGCACG-C -s Anc1.Anc1refChr1 4540 25 + 69767 GCACAGCTTATTAGATGATGCACG-C -s Anc2.Anc2refChr1 80742 25 + 142988 GCGCAGCTTAGTGGCTGATGCACA-C -s mr.mrrefChr3 114881 26 + 181027 ATACAGCTTATAAGATAAAGCAAGAT -s simDog_chr6.simDog.chr6 527611 25 + 593897 GCGCAGCTTAGTGGCTGATGCACA-C -s simHuman_chr6.simHuman.chr6 534700 25 + 601863 GCATAATCTATTAGATGATGCACG-C -s simRat_chr6.simRat.chr6 40266 26 - 647215 ATACAGCTTATAAGATAAAGCAAGAT - -a -s simMouse_chr6.simMouse.chr6 564996 81 + 636262 GCTTTCCACGCACACAAGAGATAAGTCTGTTAATGAACCCATAACCTGTTTTTATGATGCTCTCATCTACTCATAGTAATC -s Anc0.Anc0refChr3 165960 81 + 222631 ACTGTTCACCCACTCAAAAGATATATCTGTTAATGAACTACTAGCCTATGTTAATGATGCCCTCTTCTACTCAAAATAATA -s Anc1.Anc1refChr1 4565 81 + 69767 ACTGTTCACCCACTCAAAAGATATATCTGTTAATGAACTACTAGCCTATGTTAATGATGCCCTCTTCTACTCAAAATAATA -s Anc2.Anc2refChr1 80767 81 + 142988 ATAGTTCACCCAATTGAAGGATATATCTGTTAATGAACTACTAGCCAATGTTAATGATGCCCTCTTCTACTCAAAACATTA -s mr.mrrefChr3 114907 81 + 181027 GCTTTCCACGCACTCAAAAGATAAGTCTGTTAATGAACCCATAACCTGTTTTTATGATGCTCTCATCTACTCAAAGTAATC -s simCow_chr6.simCow.chr6 539487 75 + 602619 ------CACAAGATTGAAGGACAGGTCTGTTAATGAACTGCTAGCCAATGTTAATGGTGCCCTCTTCTACTCAGAACATTA -s simDog_chr6.simDog.chr6 527637 81 + 593897 ATAGTTCGCCCAATTGAAGAATGTATCTGTTAATGAACTACTCGCCACTGTTAATGATGCTGTCTTCTACCCAAAACATTA -s simHuman_chr6.simHuman.chr6 534725 81 + 601863 ACTGTTCACCCTCTCAAAAGATACATCCGTTAATGAACTACTAGACTATGTTCATGATGCCCTTCTCTGCTCGAAATGATA -s simRat_chr6.simRat.chr6 40292 81 - 647215 GCTTCCTACACACTCAAAAGATGGGTCTGTTAATGAACCCATAACCTGTTTTTATGATGCTATCATCTACTCAAAGTTAAC - -a -s simMouse_chr6.simMouse.chr6 565077 20 + 636262 CCCACATGCTACTCCTTAGC -s Anc0.Anc0refChr3 166048 20 + 222631 CCTGCAGACTCTTCTTTAGC -s Anc1.Anc1refChr1 4653 20 + 69767 CCTGCAGACTCTTCTTTAGC -s Anc2.Anc2refChr1 80855 20 + 142988 CCTGCGGACTCTCTTTTAGC -s mr.mrrefChr3 114988 20 + 181027 CCCGCATGCTCCTCCTTAGC -s simCow_chr6.simCow.chr6 539569 20 + 602619 CCTGCGGACTCTCTTTTAGC -s simDog_chr6.simDog.chr6 527724 3 + 593897 CCT----------------- -s simHuman_chr6.simHuman.chr6 534813 20 + 601863 CCTGCAGTTTCTTCTTTAGC -s simRat_chr6.simRat.chr6 40373 20 - 647215 CCGGCATGCTCCTCCTTAGC - -a -s simMouse_chr6.simMouse.chr6 565097 39 + 636262 CTGCAAACAACCCAGGACAGTGATCCTACAGACATTTAA -s Anc0.Anc0refChr3 166068 39 + 222631 CTGACATCAACTAAGGACAGAATTCCAAAACACATTGAA -s Anc1.Anc1refChr1 4673 39 + 69767 CTGACATCAACTAAGGACAGAATTCCAAAACACATTGAA -s Anc2.Anc2refChr1 80875 39 + 142988 CTGACATCAACTAAGGACTGAATTCCAAAACACATTGAG -s mr.mrrefChr3 115008 39 + 181027 CTGCAAACAACCCAGGACAGTGATCCAACAGACATTTAA -s simCow_chr6.simCow.chr6 539589 39 + 602619 CTGACATCAACTAAGGACTGAATTCCAAAACACATTGAG -s simHuman_chr6.simHuman.chr6 534833 39 + 601863 CTGACGTCGATTAAGGGCAGAATTCCAAAATGCATTGAA -s simRat_chr6.simRat.chr6 40400 39 - 647215 CTCCAAACAACCCAGGACAGTGATCCAACCCATATTTAA - -a -s simMouse_chr6.simMouse.chr6 565136 43 + 636262 GAAGAAGCGTCTAGTGTTATAAACCTAGCAATATAGGGATCCA -s Anc0.Anc0refChr3 166107 40 + 222631 CCAAAGAAGTGTAG---GTTTAATCTAGCAATCCAAGGATTCA -s Anc1.Anc1refChr1 4712 40 + 69767 CCAAAGAAGTGTAG---GTTTAATCTAGCAATCCAAGGATTCA -s Anc2.Anc2refChr1 80914 40 + 142988 CCAAAGAATTGTAT---GTTTAATGTAGCAATCCAAGGATTCA -s mr.mrrefChr3 115047 43 + 181027 GAAGAAGCGTCTAGTGTTATAAACCTAGCAATCTAGGGATCCA -s simCow_chr6.simCow.chr6 539628 38 + 602619 CCAA-GAATTGTAT---GTTTAATGTAGTGATCCATGGATT-A -s simDog_chr6.simDog.chr6 527727 38 + 593897 --CAAGAATTGTAT---ATTTAATGTAGCAATCCAAGGACTCA -s simHuman_chr6.simHuman.chr6 534872 40 + 601863 CCAAAGAAGTGTAG---GCTTAATCTAGCAATCCAAGAATTCA -s simRat_chr6.simRat.chr6 40440 43 - 647215 GAAGAAGTGTCTGGTACTATAAACCTACCAATCTACAGATCCA - -a -s simMouse_chr6.simMouse.chr6 565179 32 + 636262 ACATACTCATAGGCAGATGGGACACTCATGTG -s Anc0.Anc0refChr3 166150 22 + 222631 ACACAGTCACAGGCAGTTGT----------TG -s Anc1.Anc1refChr1 4755 22 + 69767 ACACAGTCACAGGCAGTTGT----------TG -s Anc2.Anc2refChr1 80957 22 + 142988 ACACAGTCACAGGCAGTTGT----------TG -s mr.mrrefChr3 115090 32 + 181027 ACATACTCACAGGCAGATGGGACACTCATGTG -s simCow_chr6.simCow.chr6 539669 22 + 602619 ACATAGTCACAGGCAATTGT----------TG -s simDog_chr6.simDog.chr6 527768 22 + 593897 ACACAGTCATAGGTGGTTGT----------TG -s simHuman_chr6.simHuman.chr6 534915 22 + 601863 ACACAATCACAGGCAGCTAA----------TT -s simRat_chr6.simRat.chr6 40483 32 - 647215 ACATACTCACAGGTAGATTGGACACTCCTGAG - -a -s simMouse_chr6.simMouse.chr6 565211 5 + 636262 AAGAT -s Anc0.Anc0refChr3 166172 5 + 222631 CACAT -s Anc1.Anc1refChr1 4777 5 + 69767 CACAT -s Anc2.Anc2refChr1 80987 5 + 142988 CACAT -s mr.mrrefChr3 115122 5 + 181027 AAGAT -s simCow_chr6.simCow.chr6 539699 5 + 602619 TTTAT -s simDog_chr6.simDog.chr6 527798 5 + 593897 CACAT -s simHuman_chr6.simHuman.chr6 534937 5 + 601863 GTTGT -s simRat_chr6.simRat.chr6 40515 5 - 647215 AAGAT - -a -s simMouse_chr6.simMouse.chr6 565216 2 + 636262 TG -s Anc0.Anc0refChr3 166177 2 + 222631 TC -s Anc1.Anc1refChr1 4782 2 + 69767 TC -s Anc2.Anc2refChr1 80992 2 + 142988 TC -s mr.mrrefChr3 115127 2 + 181027 TG -s simCow_chr6.simCow.chr6 539704 2 + 602619 TT -s simDog_chr6.simDog.chr6 527805 2 + 593897 TC -s simHuman_chr6.simHuman.chr6 534942 2 + 601863 TT -s simRat_chr6.simRat.chr6 40520 2 - 647215 TG - -a -s simMouse_chr6.simMouse.chr6 565218 17 + 636262 CTTGGTTTGCTATACAA -s Anc0.Anc0refChr3 166179 17 + 222631 CTCAGTTTGCTGCACAA -s Anc1.Anc1refChr1 4784 17 + 69767 CTCAGTTTGCTGCACAA -s Anc2.Anc2refChr1 80994 17 + 142988 CTCAGTTTGCTGCACAA -s mr.mrrefChr3 115129 17 + 181027 CTCAGTTTGCTGTACAA -s simCow_chr6.simCow.chr6 539706 17 + 602619 CTCAGTGTGCTGCACAA -s simDog_chr6.simDog.chr6 527807 17 + 593897 CTCAGTTTGTTGCACAG -s simHuman_chr6.simHuman.chr6 534944 17 + 601863 CTCAGTTTGCTGCACAA -s simRat_chr6.simRat.chr6 40535 14 - 647215 CCCAGTTTGCTGTA--- - -a -s simMouse_chr6.simMouse.chr6 565235 27 + 636262 TACAAGGGATTTGTATGGGGTGACATG -s Anc0.Anc0refChr3 166197 27 + 222631 GGAAAGGAAATTTTATGAGGTGACCTG -s Anc1.Anc1refChr1 4802 27 + 69767 GGAAAGGAAATTTTATGAGGTGACCTG -s Anc2.Anc2refChr1 81012 27 + 142988 GGAAAGGAAATTTTATAAGGTGATCTG -s mr.mrrefChr3 115146 27 + 181027 TACAAGGAATTTGTATGGGGTGACCTG -s simCow_chr6.simCow.chr6 539724 27 + 602619 GGAAAGGAAATTTTATAAGGTGATCTG -s simDog_chr6.simDog.chr6 527825 27 + 593897 GGTAAGGAAATTTTATAAGGTGATCTG -s simHuman_chr6.simHuman.chr6 534962 27 + 601863 GGAAAGGAAATTTTATGAAGTGACCTG -s simRat_chr6.simRat.chr6 40549 22 - 647215 -----GGAATCTGTATGGGGTGACCTG - -a -s simMouse_chr6.simMouse.chr6 565262 29 + 636262 AAGAGAAATCTGGCCAAGCACTATACTAT -s Anc0.Anc0refChr3 166225 28 + 222631 AAGAGAAAAATGGACAA-TGGTATACTCT -s Anc1.Anc1refChr1 4830 28 + 69767 AAGAGAAAAATGGACAA-TGGTATACTCT -s Anc2.Anc2refChr1 81040 28 + 142988 AAGAGAAAAATGGACAA-TGGTGTACACT -s mr.mrrefChr3 115173 29 + 181027 AAGAGAAATCTGGCCAAGTGCTATACTAT -s simCow_chr6.simCow.chr6 539752 26 + 602619 AAAATAAAAATGGACAA-TGAT--ACACT -s simDog_chr6.simDog.chr6 527853 28 + 593897 AAGAGAAAAACAGGCGA-TGGTGTACACT -s simHuman_chr6.simHuman.chr6 534990 28 + 601863 AAGAGAAAAATGAACAA-TGTCACATTCT -s simRat_chr6.simRat.chr6 40571 29 - 647215 AAGAGAATTCTGGCCAAGTGCTATACTAT - -a -s simMouse_chr6.simMouse.chr6 565291 25 + 636262 AGAACTGAATATGATATATTAGGGT -s Anc0.Anc0refChr3 166253 25 + 222631 AGAATGAACTATGATATGTTGGGGT -s Anc1.Anc1refChr1 4858 25 + 69767 AGAATGAACTATGATATGTTGGGGT -s Anc2.Anc2refChr1 81071 25 + 142988 AGAATGAACTACAGTATGTTGGGGT -s mr.mrrefChr3 115202 25 + 181027 AGAACTGAATATGATATATTAGGGT -s simCow_chr6.simCow.chr6 539781 25 + 602619 AGGACAAACTGCAGTATGTTGCGCC -s simDog_chr6.simDog.chr6 527884 25 + 593897 AGAATGAATTACAGTATGTTGGGGT -s simHuman_chr6.simHuman.chr6 535018 25 + 601863 AGAATGAACTATGATATGTTGAGGT -s simRat_chr6.simRat.chr6 40600 25 - 647215 AGAACTGAATATGATATAGTAGGGC - -a -s simMouse_chr6.simMouse.chr6 565316 69 + 636262 ATAATGGAGGCACTCCCATTAAAATACCCATGAAATGTTTAGCAGTCTAAAGGAGCCTGTAAGGTACCA -s Anc0.Anc0refChr3 166278 69 + 222631 ATTATGGAGTGGCTCCTCTTGAAATACCTATGAAATGTTTAGCAATATAAAGGGAACGATAAAGTACCC -s Anc1.Anc1refChr1 4883 69 + 69767 ATTATGGAGTGGCTCCTCTTGAAATACCTATGAAATGTTTAGCAATATAAAGGGAACGATAAAGTACCC -s Anc2.Anc2refChr1 81096 69 + 142988 ATTATGGAGTGGCTCCTCTGGAAATACCTATGAAATGTTTGGCAATATAAAGGGAACCATAAAGTACCC -s mr.mrrefChr3 115227 69 + 181027 ATAATGGAGTCACTCCTATTAAAATACCCATGAAATGTTTAGCAGTCTAAAGGAAACGGTAAGGTACCA -s simCow_chr6.simCow.chr6 539808 69 + 602619 ATAATTGAATGGCCCCTCTGGAAATACCTATGGGATGCTTGGCAACATAAAGGGCACCATAAAGTACCA -s simDog_chr6.simDog.chr6 527909 69 + 593897 ATTATGGAGTGGTTCCTCTGGGAGCACCTCTGAAATGTATGGCAATATAAAGAGAACCGTAAAGTATCC -s simHuman_chr6.simHuman.chr6 535043 68 + 601863 ATTGTGGACT-GCTACTCCTCAAATACCAATGAAATGTTTAGCAATAAAGAAGGAACGATAATATACTG -s simRat_chr6.simRat.chr6 40625 69 - 647215 AGAATGGAGTCACCCCTGTTAAAATACCCATGAAATGCTTAGCACTCTAAAGGAAACGGTAAGGTACCA - -a -s simMouse_chr6.simMouse.chr6 565385 2 + 636262 TA -s Anc0.Anc0refChr3 166347 2 + 222631 TA -s Anc1.Anc1refChr1 4952 2 + 69767 TA -s Anc2.Anc2refChr1 81165 2 + 142988 TA -s mr.mrrefChr3 115296 2 + 181027 TA -s simCow_chr6.simCow.chr6 539878 2 + 602619 TA -s simDog_chr6.simDog.chr6 527978 2 + 593897 CA -s simHuman_chr6.simHuman.chr6 535111 2 + 601863 TA -s simRat_chr6.simRat.chr6 40694 2 - 647215 TA - -a -s simMouse_chr6.simMouse.chr6 565387 34 + 636262 TAGTAGAATCTTTTGTTGAATAAGTGAAGCACAG -s Anc0.Anc0refChr3 166349 31 + 222631 TAATAGTTTGTTTTATTGTATAAATGAATCA--- -s Anc1.Anc1refChr1 4954 31 + 69767 TAATAGTTTGTTTTATTGTATAAATGAATCA--- -s Anc2.Anc2refChr1 81174 31 + 142988 TGATAGTTTGTTTTATTGTATAAATGAATCA--- -s mr.mrrefChr3 115298 34 + 181027 TAGTAGAATCTTTTGTTGAATAAGTGAAGCACAG -s simCow_chr6.simCow.chr6 539887 31 + 602619 AGCTAGTTTGTTTTATTGCATAAATGAATCA--- -s simDog_chr6.simDog.chr6 527987 31 + 593897 TGATAGTTTATTCCATTGTCTAAATGAATCA--- -s simHuman_chr6.simHuman.chr6 535113 31 + 601863 AAATAGTTTGGTTTATTGTATAATTAAATCA--- -s simRat_chr6.simRat.chr6 40696 34 - 647215 TAGTATAATCTATCGTTGAATAAATGGGGCACAA - -a -s simMouse_chr6.simMouse.chr6 565421 19 + 636262 ATACTACCTCTCCTGATAA -s Anc0.Anc0refChr3 166380 17 + 222631 ATATG--CGCTCCTTATAA -s Anc1.Anc1refChr1 4985 17 + 69767 ATATG--CGCTCCTTATAA -s Anc2.Anc2refChr1 81210 17 + 142988 ATATG--CGCTCTTTATGA -s mr.mrrefChr3 115332 19 + 181027 ATATTACCTCTCCTGATAA -s simCow_chr6.simCow.chr6 539923 9 + 602619 ATAT------TCTT----A -s simDog_chr6.simDog.chr6 528023 17 + 593897 ATATG--CGCTCTTTATGA -s simHuman_chr6.simHuman.chr6 535144 17 + 601863 ATATG--CCCTCCTTATAA -s simRat_chr6.simRat.chr6 40730 19 - 647215 ATATTACCTCTCCTGATAA - -a -s simMouse_chr6.simMouse.chr6 565440 13 + 636262 AAATCAAGCATAC -s Anc0.Anc0refChr3 166397 13 + 222631 AAATCAATCCTAC -s Anc1.Anc1refChr1 5002 13 + 69767 AAATCAATCCTAC -s Anc2.Anc2refChr1 81227 13 + 142988 AAATCTATCCTAG -s mr.mrrefChr3 115351 13 + 181027 AAATCAATCATAC -s simCow_chr6.simCow.chr6 539932 12 + 602619 AAAACTATC-TAG -s simDog_chr6.simDog.chr6 528040 13 + 593897 AAATCTATCCTAG -s simHuman_chr6.simHuman.chr6 535167 13 + 601863 AAATCAAACCTAC -s simRat_chr6.simRat.chr6 40749 13 - 647215 GAATCAATCATAC - -a -s simMouse_chr6.simMouse.chr6 565453 12 + 636262 TAAACATTAGAG -s Anc0.Anc0refChr3 166411 10 + 222631 TCAACATGCA-- -s Anc1.Anc1refChr1 5016 12 + 69767 TCAACATGCAGC -s Anc2.Anc2refChr1 81241 10 + 142988 TCAACATGCA-- -s mr.mrrefChr3 115364 12 + 181027 TAAACATTAGAG -s simCow_chr6.simCow.chr6 539945 10 + 602619 GCAACATGTA-- -s simDog_chr6.simDog.chr6 528054 10 + 593897 TCAACATGCA-- -s simHuman_chr6.simHuman.chr6 535181 12 + 601863 TTAACATGCAGC -s simRat_chr6.simRat.chr6 40762 12 - 647215 TAAACATTAGCG - -a -s simMouse_chr6.simMouse.chr6 565465 15 + 636262 GATGAAGGTTGTGGG -s Anc0.Anc0refChr3 166421 1 + 222631 ---A----------- -s Anc1.Anc1refChr1 5028 4 + 69767 AATA----------- -s Anc2.Anc2refChr1 81251 1 + 142988 ---C----------- -s mr.mrrefChr3 115376 15 + 181027 GATGAAGGTTGTGGG -s simCow_chr6.simCow.chr6 539955 1 + 602619 ---C----------- -s simDog_chr6.simDog.chr6 528064 1 + 593897 ---C----------- -s simHuman_chr6.simHuman.chr6 535193 4 + 601863 AATA----------- -s simRat_chr6.simRat.chr6 40782 15 - 647215 GATGAAGGTTGTGGG - -a -s simMouse_chr6.simMouse.chr6 565480 126 + 636262 ACTGGGTATTATCTGAGAAATCTGAGTTAATCAGCCACCCAAAACAAAACCACTTATAATTAGTGATAGTGCGCGTAAGGTATTTGCTAGGGGTTGCTCTAGAGGTTCAACCAACTGAAGATCTTG -s Anc0.Anc0refChr3 166422 28 + 222631 --TGGG------------------------------------------------------------------------------------------------ATGTTTGGGCAACCAGAGATCTTG -s Anc1.Anc1refChr1 5032 93 + 69767 --TGGGTAGTATTCGTGAAATATCAGATAGTTAGACCCCCAAAACGAAGCCACCTATAAT-------------------------------AGTCACTCTAAATGTTTGGGCAACCAGAGATCTTG -s Anc2.Anc2refChr1 81252 28 + 142988 --TGGG------------------------------------------------------------------------------------------------ATGTTTGGGCATCCAGAGATCTTG -s mr.mrrefChr3 115391 95 + 181027 ACTGGGTATTATCTGAGAAATCTGAGTTAATTAGCCACCCAAAACAAAACCACTTATAAT-------------------------------GGTTGCTCTAAAGGTTCAACCAACTGAAGATCTTG -s simCow_chr6.simCow.chr6 539956 27 + 602619 --CTAA------------------------------------------------------------------------------------------------ATGTTCAGACA-CCAGGAATCTCA -s simDog_chr6.simDog.chr6 528065 28 + 593897 --TGGG------------------------------------------------------------------------------------------------GTGTTTGGGCTTCCACAGTTCTTG -s simHuman_chr6.simHuman.chr6 535197 93 + 601863 --TGGGTAGTATTCGTGAAATATCAGATAGTTAGACCCCCAAAACGAAGCCACCTATAAT-------------------------------AGTCACTCTAAATGTTTGGGCAACCAGAGACCTTG -s simRat_chr6.simRat.chr6 40798 95 - 647215 AACAGGTAATAGCGAAGAGATCTGAGCTAATTAGCCAACCAAAACAAAACCACTTGTAAT-------------------------------GGTTGCTCTAAACGTTCAACCAACTGAAGATCTTG - -a -s simMouse_chr6.simMouse.chr6 565606 4 + 636262 GGAT -s Anc0.Anc0refChr3 166450 3 + 222631 G-AT -s Anc1.Anc1refChr1 5125 4 + 69767 GGAT -s Anc2.Anc2refChr1 81280 3 + 142988 G-AT -s mr.mrrefChr3 115486 4 + 181027 GGAT -s simCow_chr6.simCow.chr6 539983 3 + 602619 G-AT -s simDog_chr6.simDog.chr6 528093 3 + 593897 G-AC -s simHuman_chr6.simHuman.chr6 535301 4 + 601863 GGAA -s simRat_chr6.simRat.chr6 40893 4 - 647215 GGAT - -a -s simMouse_chr6.simMouse.chr6 565610 10 + 636262 TAGACCTTAA -s Anc0.Anc0refChr3 166453 10 + 222631 TTGACCTTAA -s Anc1.Anc1refChr1 5129 10 + 69767 TTGACCTTAA -s Anc2.Anc2refChr1 81283 10 + 142988 TTGACCTTAA -s mr.mrrefChr3 115490 10 + 181027 TAGACCTTAA -s simCow_chr6.simCow.chr6 539988 10 + 602619 TCAACTATAA -s simDog_chr6.simDog.chr6 528096 10 + 593897 CTGACCTTAA -s simHuman_chr6.simHuman.chr6 535305 10 + 601863 TTGACCTTAA -s simRat_chr6.simRat.chr6 40897 10 - 647215 TAGACCTCAA - -a -s simMouse_chr6.simMouse.chr6 565620 4 + 636262 TGCC -s Anc0.Anc0refChr3 166463 1 + 222631 C--- -s Anc1.Anc1refChr1 5139 4 + 69767 CACC -s Anc2.Anc2refChr1 81293 1 + 142988 C--- -s mr.mrrefChr3 115500 4 + 181027 TGCC -s simCow_chr6.simCow.chr6 539998 1 + 602619 C--- -s simDog_chr6.simDog.chr6 528106 1 + 593897 C--- -s simHuman_chr6.simHuman.chr6 535316 4 + 601863 CACC -s simRat_chr6.simRat.chr6 40907 4 - 647215 TGCC - -a -s simMouse_chr6.simMouse.chr6 565624 67 + 636262 TGATCCTGGATCATAATCACCTTGGTATCTCAATTCAATGCCTGTCAGGTGGGGTGTCGAGGGGTAT -s Anc0.Anc0refChr3 166464 67 + 222631 TGCTTTTAGATTCTGATCACTTTGCTGGCTCAGATCCTTGCTTGTCAGCTGGGTTATCAGGGGGTAT -s Anc1.Anc1refChr1 5143 67 + 69767 TGCTTTTAGATTCTGATCACTTTGCTGGCTCAGATCCTTGCTTGTCAGCTGGGTTATCAGGGGGTAT -s Anc2.Anc2refChr1 81294 67 + 142988 TGCTTTTAGATTCTGATCACTTTGCTGGCTCAGATCCTTGCTTGTCAGCTGGGTCATCTGGGGGTAT -s mr.mrrefChr3 115504 67 + 181027 TGATCCTAGATCATAATCACCTTGGTGTCTCAGTTCAATGCCTGTCAGGTGGGGTGTCAAGGGGTAT -s simCow_chr6.simCow.chr6 540002 58 + 602619 TGCCTTTAGTTTTTGATCACTTTGCTGACAT-----CTTGCTTGTCAGCG----CATCCAGGGGTAT -s simDog_chr6.simDog.chr6 528107 67 + 593897 AGTTTCTAGATTCTGATCACTTTGCTAGCTCAGATCCTTGCCTGTCAGATGGGTCATCTGGGGGTAC -s simHuman_chr6.simHuman.chr6 535320 67 + 601863 TGCTGTTAGATTGTGATCACTTTGTGGGATCAGATCCTTGCTTGTCAGCTTGGTTATCAGGAGGTAT -s simRat_chr6.simRat.chr6 40911 67 - 647215 TGATCCTAGACCATAATCACCTTGGTGTTTCAGTTCAATGCCTGTCAGGTGGGGTGTCAAGGGGTCT - -a -s simMouse_chr6.simMouse.chr6 565691 11 + 636262 CCACATAGAGT -s Anc0.Anc0refChr3 166532 11 + 222631 ACACAAACAGA -s Anc1.Anc1refChr1 5211 11 + 69767 ACACAAACAGA -s Anc2.Anc2refChr1 81362 11 + 142988 ACACGAACACA -s mr.mrrefChr3 115571 11 + 181027 CCACATACAGT -s simCow_chr6.simCow.chr6 540061 11 + 602619 ATATGAACAAG -s simDog_chr6.simDog.chr6 528175 11 + 593897 ACACGAACACA -s simHuman_chr6.simHuman.chr6 535388 11 + 601863 ACACAAACGGA -s simRat_chr6.simRat.chr6 40978 11 - 647215 CCGCATACAGG - -a -s simMouse_chr6.simMouse.chr6 565702 43 + 636262 ATGTAAGGTAAAAGGACTTTTGGTGGGAGAGGGTTTTCTTTGT -s Anc0.Anc0refChr3 166543 40 + 222631 ATGTAAGGTAAAGGGACTCT---TGGATAAGGCTTTTTATTGT -s Anc1.Anc1refChr1 5222 40 + 69767 ATGTAAGGTAAAGGGACTCT---TGGATAAGGCTTTTTATTGT -s Anc2.Anc2refChr1 81373 40 + 142988 ATGCAAGGTAAAGGGATCAT---TAGATAAGGCTTTTTATTGT -s mr.mrrefChr3 115582 43 + 181027 ATGTAAGGTAAAGGGACTCTTGGTGGGAGAGGCTTTTCTTTGT -s simCow_chr6.simCow.chr6 540541 40 + 602619 ATGGAAGGTAAAGGGGTAAT---TAGATGGGGCTTCTTCTTAT -s simDog_chr6.simDog.chr6 528186 40 + 593897 ATGCCAGGTAAAGGCATCAT---CAGATAAGGCTTTTAATTGT -s simHuman_chr6.simHuman.chr6 535399 40 + 601863 ATGTATTGACAAGGGACTCT---TGGACAAGGCCGTTTGTTCT -s simRat_chr6.simRat.chr6 40989 43 - 647215 ATATAAGGTAACGAGACTCCTGGTGTGAGAGGCTTTTCATTGT - -a -s simMouse_chr6.simMouse.chr6 565745 73 + 636262 CATACTTATGGTTCATTCAGCTTGAAAGTTACTTTTCATGTCCTACATTCATCAGATGTCCTCCACTAGCTAA -s Anc0.Anc0refChr3 166583 70 + 222631 CGTATCTATGGTTTA---GGTGGAACAATTACCTTTCACTTTTTACCTGCATCAGAAGCCATCCATTAGCCGA -s Anc1.Anc1refChr1 5262 70 + 69767 CGTATCTATGGTTTA---GGTGGAACAATTACCTTTCACTTTTTACCTGCATCAGAAGCCATCCATTAGCCGA -s Anc2.Anc2refChr1 81413 70 + 142988 CGTGTCTATGGTTTA---GGTGGAACAATTACCCTTCACTCTTTATCTGCATCAGAATCCATACATTAGCCGA -s mr.mrrefChr3 115625 73 + 181027 CATACTTATGGTTCATTCAGCTGAAAAATTACTTTTCATGTCCTACATTCATCAGATGTCATCCATTAGCTAA -s simCow_chr6.simCow.chr6 540594 69 + 602619 CGTGTCTATGGTTTG---GTTGGAACAATTACTGTTCACTCTTTATCTACATCAGAACC-ATGCACTAGTCAA -s simDog_chr6.simDog.chr6 528226 70 + 593897 CATGTCTATGGTTTA---GGTAGAACAACTACCCTTCATTCTTTATCTGCGTTATAATCCAAACATTAACTGA -s simHuman_chr6.simHuman.chr6 535439 70 + 601863 CGCATCTATGGTTTA---GGTGGAATAATTACATTTCACTTTTTACCTGCACCAGAAGCGATCCATTAGCCCA -s simRat_chr6.simRat.chr6 41032 73 - 647215 CATACTTATGATTCATTTAGCTGAAAAATTACTTTTCATGTCCTACATTTATCAAATGGCATCCATTAACTGA - -a -s simMouse_chr6.simMouse.chr6 565818 13 + 636262 TGTGACCATGATG -s Anc0.Anc0refChr3 166653 13 + 222631 TATGCCTATGATA -s Anc1.Anc1refChr1 5332 13 + 69767 TATGCCTATGATA -s Anc2.Anc2refChr1 81483 13 + 142988 TATGCCTATGATA -s mr.mrrefChr3 115698 13 + 181027 TGTGGCCATGATG -s simCow_chr6.simCow.chr6 540663 13 + 602619 TGTGCCTATGATA -s simDog_chr6.simDog.chr6 528296 13 + 593897 CAGATCAATGATA -s simHuman_chr6.simHuman.chr6 535531 13 + 601863 TATGCCTGTGATA -s simRat_chr6.simRat.chr6 41105 13 - 647215 TGTGGCCATGATG - -a -s simMouse_chr6.simMouse.chr6 565831 1 + 636262 G -s Anc0.Anc0refChr3 166666 1 + 222631 G -s Anc1.Anc1refChr1 5345 1 + 69767 G -s Anc2.Anc2refChr1 81496 1 + 142988 G -s mr.mrrefChr3 115711 1 + 181027 G -s simCow_chr6.simCow.chr6 540678 1 + 602619 g -s simDog_chr6.simDog.chr6 528309 1 + 593897 G -s simHuman_chr6.simHuman.chr6 535544 1 + 601863 G -s simRat_chr6.simRat.chr6 41118 1 - 647215 G - -a -s simMouse_chr6.simMouse.chr6 565832 4 + 636262 CCAA -s Anc0.Anc0refChr3 166668 4 + 222631 CcAA -s Anc1.Anc1refChr1 5347 4 + 69767 CCAA -s Anc2.Anc2refChr1 81498 4 + 142988 CcAA -s mr.mrrefChr3 115712 4 + 181027 CCAA -s simCow_chr6.simCow.chr6 540680 4 + 602619 ccaa -s simDog_chr6.simDog.chr6 528311 3 + 593897 C-AA -s simHuman_chr6.simHuman.chr6 535546 4 + 601863 CCAA -s simRat_chr6.simRat.chr6 41119 4 - 647215 CCAA - -a -s simMouse_chr6.simMouse.chr6 565836 15 + 636262 CCAAACTCTGTTTTT -s Anc0.Anc0refChr3 166674 15 + 222631 TTGTACTCTgttttt -s Anc1.Anc1refChr1 5353 15 + 69767 TTGTACTCTgttttt -s Anc2.Anc2refChr1 81504 15 + 142988 TTGTATTCTgtcttt -s mr.mrrefChr3 115718 15 + 181027 TCAAACTCTGTTTTT -s simCow_chr6.simCow.chr6 540686 12 + 602619 gtgaattct---tct -s simDog_chr6.simDog.chr6 528316 15 + 593897 TTGTATTCTGTCTTT -s simHuman_chr6.simHuman.chr6 535552 15 + 601863 TTGGACTATgttttt -s simRat_chr6.simRat.chr6 41125 15 - 647215 TCAAACTCTGTTGTG - -a -s simMouse_chr6.simMouse.chr6 565851 64 + 636262 ACAAATTTAGCCAGATGAAATAAGATCctattgtgaatggttaggaaaaaatgctcaaagagtc -s Anc0.Anc0refChr3 166691 63 + 222631 acaaaattaacgaaatg-aacaagccgctgttgagaatggtaaagaaaaaatgcagaaaaaatc -s Anc1.Anc1refChr1 5370 63 + 69767 acaaaattaacgaaatg-aacaagccgctgttgagaatggtaaagaaaaaatgcagaaaaaatc -s Anc2.Anc2refChr1 81521 63 + 142988 acaaaattaatgaaatg-accaagctgctgttgagactagcaaagaaaaaatgaagagagaatc -s mr.mrrefChr3 115735 64 + 181027 acaaatttaaccagatgaaataagcccctgttgtgaatggttaggaaaaaatgctcaaaaagtc -s simCow_chr6.simCow.chr6 540700 63 + 602619 acaaaatcaataaaatg-accaagctgctgttgagactagcaaagaaaaaatgaagagagaatc -s simDog_chr6.simDog.chr6 528333 16 + 593897 GCAAAactgctgatat------------------------------------------------ -s simHuman_chr6.simHuman.chr6 535569 63 + 601863 acaaaattaactaaatg-aacacgcctctgctgagcatggtaaaggaaaaccacagaaaaaatc -s simRat_chr6.simRat.chr6 41142 64 - 647215 acaaattcaacaagatgacataagcccctgttggaagtcattaggaaataatgctaaaaaagtc - -a -s simMouse_chr6.simMouse.chr6 565915 10 + 636262 tcttggggaa -s Anc0.Anc0refChr3 166760 10 + 222631 tcatgttgag -s Anc1.Anc1refChr1 5439 10 + 69767 tcatgttgag -s Anc2.Anc2refChr1 81590 10 + 142988 tcatgttgag -s mr.mrrefChr3 115799 10 + 181027 tcttggggaa -s simCow_chr6.simCow.chr6 540769 10 + 602619 tcatgttgag -s simHuman_chr6.simHuman.chr6 535638 10 + 601863 tcatattggg -s simRat_chr6.simRat.chr6 41206 10 - 647215 tcttggggaa - -a -s simMouse_chr6.simMouse.chr6 565925 57 + 636262 tcatccatagcacataaccactgaatctgctcttgttcaaatctgttgcaggaagta -s Anc0.Anc0refChr3 166770 54 + 222631 tcatccgtgggacataacgactgaccctgctgccattcaaatgagtacta---agtg -s Anc1.Anc1refChr1 5449 57 + 69767 tcatccgtgggacataacgactgaccctgctgccattcaaatgagtactattaagtg -s Anc2.Anc2refChr1 81600 54 + 142988 tcatttgtgggacgtaatgactgaccctgctgccatccagatgaggacta---agtg -s mr.mrrefChr3 115809 57 + 181027 tcatccatagcacataaccactgaatctgctcttgttcaaatctgttgcaggaagta -s simCow_chr6.simCow.chr6 540782 54 + 602619 tcatttgtgggacgtaatgactgaccctgctgccatccagatgaggacta---agtg -s simHuman_chr6.simHuman.chr6 535648 57 + 601863 tcatccgtcgaacataacaactgaccctgctgccatttaaataagtattattaagtg -s simRat_chr6.simRat.chr6 41216 50 - 647215 tcatccatagcatataaccacggaatctgcttttgttcaaatctg-------aagta - -a -s simMouse_chr6.simMouse.chr6 565982 2 + 636262 ca -s Anc0.Anc0refChr3 166848 2 + 222631 ca -s Anc1.Anc1refChr1 5530 2 + 69767 ca -s Anc2.Anc2refChr1 81678 2 + 142988 cc -s mr.mrrefChr3 115879 2 + 181027 ca -s simCow_chr6.simCow.chr6 540860 2 + 602619 CC -s simHuman_chr6.simHuman.chr6 535729 2 + 601863 ta -s simRat_chr6.simRat.chr6 41279 2 - 647215 ca - -a -s simMouse_chr6.simMouse.chr6 565984 8 + 636262 acccacct -s Anc0.Anc0refChr3 166864 8 + 222631 atcaacct -s Anc1.Anc1refChr1 5546 8 + 69767 atcaacct -s Anc2.Anc2refChr1 81694 8 + 142988 gtaaactt -s mr.mrrefChr3 115881 8 + 181027 accaacct -s simCow_chr6.simCow.chr6 540881 8 + 602619 GTAAACTT -s simHuman_chr6.simHuman.chr6 535747 8 + 601863 atcaacct -s simRat_chr6.simRat.chr6 41281 8 - 647215 aacaacct - -a -s simMouse_chr6.simMouse.chr6 565992 4 + 636262 cttt -s Anc0.Anc0refChr3 166872 4 + 222631 cttc -s Anc1.Anc1refChr1 5554 4 + 69767 cttc -s Anc2.Anc2refChr1 81702 4 + 142988 tgtc -s mr.mrrefChr3 115889 4 + 181027 cttt -s simCow_chr6.simCow.chr6 540893 4 + 602619 TGTC -s simHuman_chr6.simHuman.chr6 535755 4 + 601863 cttc -s simRat_chr6.simRat.chr6 41289 4 - 647215 cttt - -a -s simMouse_chr6.simMouse.chr6 565996 20 + 636262 ctggcaagatatggaactca -s Anc0.Anc0refChr3 166877 20 + 222631 gcatctagaaatctaactca -s Anc1.Anc1refChr1 5559 20 + 69767 gcatctagaaatctaactca -s Anc2.Anc2refChr1 81707 20 + 142988 gcattttgaaatcgagccta -s mr.mrrefChr3 115893 20 + 181027 gtggcaagatatgtaactca -s simCow_chr6.simCow.chr6 540898 20 + 602619 GCATTTTGAAATCGAGCCTA -s simHuman_chr6.simHuman.chr6 535760 20 + 601863 gcatccagaagtttaactca -s simRat_chr6.simRat.chr6 41293 20 - 647215 gtggcaagatatgtaactca - -a -s simMouse_chr6.simMouse.chr6 566016 69 + 636262 gataaagtagagcctttacattgtttaaccatatctattgttctccccacatcaactcaacaaagaaga -s Anc0.Anc0refChr3 166897 20 + 222631 gttaaaattgactcttt-----------------------------------------t--------ga -s Anc1.Anc1refChr1 5579 20 + 69767 gttaaaattgactcttt-----------------------------------------t--------ga -s Anc2.Anc2refChr1 81727 20 + 142988 gtcaaaattgactcttt-----------------------------------------t--------ga -s mr.mrrefChr3 115913 61 + 181027 gttaaagtagagcctttacattgtttaaccatatctattgttctccccacatcaactca--------ga -s simCow_chr6.simCow.chr6 540933 20 + 602619 GTCAAAattgactcttt-----------------------------------------t--------ga -s simHuman_chr6.simHuman.chr6 535780 20 + 601863 gttgaaattgactcttt-----------------------------------------t--------ga -s simRat_chr6.simRat.chr6 41313 59 - 647215 gttaaagtagagcctttacattgtttaaccatatatattgtcctcgccacatcaactca---------- - -a -s simMouse_chr6.simMouse.chr6 566085 51 + 636262 tcgactcaacaaagaagctatggtgtcacaggggttgaattctaactggac -s Anc0.Anc0refChr3 166917 38 + 222631 tcaa-tcaacaaagaagctatagtgtc------------ttttagatagac -s Anc1.Anc1refChr1 5599 47 + 69767 tcaactcaacaaagaagctatagtgtcataggaat----ttttagatagac -s Anc2.Anc2refChr1 81747 38 + 142988 tcaa-tcagtaaggaaggcacagtgtc------------tttgagatagac -s mr.mrrefChr3 115974 51 + 181027 tcgactcaacaaagaagctatggtgtcacaggggttgaattctaaatagac -s simCow_chr6.simCow.chr6 540968 38 + 602619 tcaa-tcagtaaggaaggcacagtgtc------------tttgagatagac -s simHuman_chr6.simHuman.chr6 535800 47 + 601863 tcaactcaacaaagaagctatagtgtcataggaat----ctttagatagac -s simRat_chr6.simRat.chr6 41372 43 - 647215 --------acaaagaagctatgctgtcacaagggttgaatcctaaatagac - -a -s simMouse_chr6.simMouse.chr6 566136 2 + 636262 cc -s Anc0.Anc0refChr3 166955 2 + 222631 cc -s Anc1.Anc1refChr1 5646 2 + 69767 cc -s Anc2.Anc2refChr1 81785 2 + 142988 cc -s mr.mrrefChr3 116025 2 + 181027 cc -s simCow_chr6.simCow.chr6 541007 2 + 602619 cc -s simHuman_chr6.simHuman.chr6 535847 2 + 601863 cc -s simRat_chr6.simRat.chr6 41415 2 - 647215 cc - -a -s simMouse_chr6.simMouse.chr6 566138 6 + 636262 tcaatg -s Anc0.Anc0refChr3 166958 6 + 222631 tcattg -s Anc1.Anc1refChr1 5649 6 + 69767 tcattg -s Anc2.Anc2refChr1 81788 6 + 142988 taattg -s mr.mrrefChr3 116027 6 + 181027 tcaatg -s simCow_chr6.simCow.chr6 541010 6 + 602619 taattg -s simHuman_chr6.simHuman.chr6 535850 6 + 601863 tcattg -s simRat_chr6.simRat.chr6 41417 6 - 647215 tcaatg - -a -s simMouse_chr6.simMouse.chr6 566144 6 + 636262 ccccaa -s Anc0.Anc0refChr3 166964 6 + 222631 gcccca -s Anc1.Anc1refChr1 5655 6 + 69767 gcccca -s Anc2.Anc2refChr1 81794 6 + 142988 gcgaca -s mr.mrrefChr3 116033 6 + 181027 ccccaa -s simCow_chr6.simCow.chr6 541018 6 + 602619 gcgaca -s simHuman_chr6.simHuman.chr6 535856 6 + 601863 gcccca -s simRat_chr6.simRat.chr6 41423 6 - 647215 ccccaa - -a -s simMouse_chr6.simMouse.chr6 566150 63 + 636262 caaaagtcactcatcgacaagcagacatagagattacagggtctactgacgcaagctccactg -s Anc0.Anc0refChr3 166972 59 + 222631 taaaagtctattattaacaagctgatgaagaaattacctggtttactgacaca----ccatag -s Anc1.Anc1refChr1 5663 59 + 69767 taaaagtctattattaacaagctgatgaagaaattacctggtttactgacaca----ccatag -s Anc2.Anc2refChr1 81802 59 + 142988 taaaagtctaatattatcaagctgatgaaacaattacctggtttactgaaaca----ggataa -s mr.mrrefChr3 116039 63 + 181027 caaaagtcactcatcaacaagcagacaaagagattacagggtctactgacacaagctccactg -s simCow_chr6.simCow.chr6 541026 47 + 602619 taaaagtctaatattatcaagctgatgaaacaattacctggtttTCT---------------- -s simDog_chr6.simDog.chr6 528349 16 + 593897 -------------------------------------------tacagaaaca----ggataa -s simHuman_chr6.simHuman.chr6 535864 59 + 601863 gaaaagtccgttattaacaagctggtgaagaaatttgttggcttactgacaca----ccatgg -s simRat_chr6.simRat.chr6 41429 59 - 647215 ctaaaatta----tcaacaagcagacaaagagattacagggtctactgacataagctccactg - -a -s simMouse_chr6.simMouse.chr6 566213 26 + 636262 acacacagtaaaacagaggagttgga -s Anc0.Anc0refChr3 167031 11 + 222631 a---------------aagagttggt -s Anc1.Anc1refChr1 5722 11 + 69767 a---------------aagagttggt -s Anc2.Anc2refChr1 81861 11 + 142988 a---------------aagagttagt -s mr.mrrefChr3 116102 26 + 181027 acacacagtaaaacagaagagttgga -s simDog_chr6.simDog.chr6 528366 11 + 593897 a---------------aagagttagt -s simHuman_chr6.simHuman.chr6 535923 11 + 601863 a---------------aagaggtggt -s simRat_chr6.simRat.chr6 41488 26 - 647215 acacgcactaaaacagaagagttgga - -a -s simMouse_chr6.simMouse.chr6 566239 9 + 636262 accatttct -s Anc0.Anc0refChr3 167042 9 + 222631 accctttct -s Anc1.Anc1refChr1 5733 9 + 69767 accctttct -s Anc2.Anc2refChr1 81872 9 + 142988 actcattct -s mr.mrrefChr3 116128 9 + 181027 accatttct -s simDog_chr6.simDog.chr6 528392 9 + 593897 actcattct -s simHuman_chr6.simHuman.chr6 535934 9 + 601863 accgtttct -s simRat_chr6.simRat.chr6 41514 9 - 647215 atcatttct - -a -s simMouse_chr6.simMouse.chr6 566248 39 + 636262 gcacaaaccacaatccattcaggttggctccattctata -s Anc0.Anc0refChr3 167051 39 + 222631 gcacaaattacaatccattgaaaatggaggaattctatt -s Anc1.Anc1refChr1 5742 39 + 69767 gcacaaattacaatccattgaaaatggaggaattctatt -s Anc2.Anc2refChr1 81881 39 + 142988 gcacaaattacggtcgattgaaactgaaggaattctgtt -s mr.mrrefChr3 116137 39 + 181027 gcacaaaccacaatccattgaagatggctcaattctata -s simDog_chr6.simDog.chr6 528402 39 + 593897 gcacaaattacggtcgattgaaactgaaggaattctgtt -s simHuman_chr6.simHuman.chr6 535943 39 + 601863 gcaggagttacaatccattgaaaagggaggaattttatc -s simRat_chr6.simRat.chr6 41523 37 - 647215 gcacaaaccacaatc--ttgaagatgaCTCAATCCTATA - -a -s simMouse_chr6.simMouse.chr6 566287 9 + 636262 tgcactgaa -s Anc0.Anc0refChr3 167090 9 + 222631 tgtatcgaa -s Anc1.Anc1refChr1 5781 9 + 69767 tgtatcgaa -s Anc2.Anc2refChr1 81920 9 + 142988 tgtatcgta -s mr.mrrefChr3 116176 9 + 181027 tgcactgaa -s simDog_chr6.simDog.chr6 528458 9 + 593897 tgtatcgta -s simHuman_chr6.simHuman.chr6 535982 9 + 601863 tgtatggaa -s simRat_chr6.simRat.chr6 41560 9 - 647215 TGCACTGAA - -a -s simMouse_chr6.simMouse.chr6 566296 3 + 636262 acc -s Anc0.Anc0refChr3 167099 3 + 222631 atc -s Anc1.Anc1refChr1 5790 3 + 69767 atc -s Anc2.Anc2refChr1 81929 3 + 142988 att -s mr.mrrefChr3 116185 3 + 181027 acc -s simDog_chr6.simDog.chr6 528471 3 + 593897 att -s simHuman_chr6.simHuman.chr6 535991 3 + 601863 atc -s simRat_chr6.simRat.chr6 41569 3 - 647215 ACC - -a -s simMouse_chr6.simMouse.chr6 566299 9 + 636262 tgtaaagca -s Anc0.Anc0refChr3 167104 9 + 222631 aattgagca -s Anc1.Anc1refChr1 5795 9 + 69767 aattgagca -s Anc2.Anc2refChr1 81934 9 + 142988 agttgggca -s mr.mrrefChr3 116190 9 + 181027 tataaagca -s simDog_chr6.simDog.chr6 528476 9 + 593897 agttgggca -s simHuman_chr6.simHuman.chr6 535996 9 + 601863 aattgagga -s simRat_chr6.simRat.chr6 41574 9 - 647215 TATAAAGCA - -a -s simMouse_chr6.simMouse.chr6 566308 30 + 636262 agtgagaggagaatacggattgcaaggcat -s Anc0.Anc0refChr3 167120 29 + 222631 aatgagaaaagaagacggaag-caagacct -s Anc1.Anc1refChr1 5811 30 + 69767 aatgagaaaagaagacggaaggcaagacct -s Anc2.Anc2refChr1 81950 29 + 142988 aatgggaagagaagacggaag-caagacct -s mr.mrrefChr3 116199 30 + 181027 aatgagagaagaatacggaatgcaaggcat -s simDog_chr6.simDog.chr6 528492 29 + 593897 aatgggaagagaagacggaag-caagacct -s simHuman_chr6.simHuman.chr6 536012 30 + 601863 aatgagacaagaagagtgaaggcaagacct -s simRat_chr6.simRat.chr6 41583 29 - 647215 AATGAGAGAGGAATACAGAAT-CAAGGCAT - -a -s simMouse_chr6.simMouse.chr6 566338 19 + 636262 gtttttgccaatgtcaaat -s Anc0.Anc0refChr3 167149 18 + 222631 gtatttt-caatgtcacat -s Anc1.Anc1refChr1 5841 18 + 69767 gtatttt-caatgtcacat -s Anc2.Anc2refChr1 81979 18 + 142988 gtatctt-caacatcacat -s mr.mrrefChr3 116229 19 + 181027 gttttttccaatgtcaaat -s simDog_chr6.simDog.chr6 528522 18 + 593897 gtatctt-caacatcacat -s simHuman_chr6.simHuman.chr6 536042 18 + 601863 gtatttt-caatgtcacaa -s simRat_chr6.simRat.chr6 41612 19 - 647215 GTTTTTTCTCATGTCAGAT - -a -s simMouse_chr6.simMouse.chr6 566357 110 + 636262 gctggaggtctgtgatcagtgtactagacatcatgtgctggacatttgcaatcagaacactagtcaactgaataattcattagaaagcccatctactatgaaccagtata -s Anc0.Anc0refChr3 167167 71 + 222631 gctggagatctgtgaacagagtact------cgcccactg-------------------------aaactattaatagatcagaaagatcatatactatgaa-------- -s Anc1.Anc1refChr1 5859 79 + 69767 gctggagatctgtgaacagagtact------cgcccactg-------------------------aaactattaatagatcagaaagatcatatactatgaaccaataca -s Anc2.Anc2refChr1 81997 71 + 142988 gctggaaatctgtgaacagagtact------agccaatcc-------------------------aaactattaatagatctgaaagatcaaatactatgag-------- -s mr.mrrefChr3 116248 110 + 181027 gctggagatctgtgatcagtgtactagacatcatgcactggacatttgcaatcagaacactagtcaactgaataattgattagaaagcccatctactatgaaccagtata -s simDog_chr6.simDog.chr6 528540 71 + 593897 gctggaaatctgtgaacagagtact------agccaatcc-------------------------aaactattaatagatctgaaagatcaaatactatgag-------- -s simHuman_chr6.simHuman.chr6 536060 79 + 601863 gacagagatctgtggacacaatact------ctcccactg-------------------------aaactatgaacagatcagaaagttcatatatagtgaaccaataca -s simRat_chr6.simRat.chr6 41687 110 - 647215 ACTGGACATCTGTGACCAGGGTGCCTGACACTAAGCACTGGACATTTGCGATCGGAGTGCTAACCAATTGAATAATTGATTAGAAAACCCATCCACTATGAATTAGTATA - -a -s simMouse_chr6.simMouse.chr6 566467 8 + 636262 taagatgt -s Anc0.Anc0refChr3 167239 8 + 222631 caagatat -s Anc1.Anc1refChr1 5939 8 + 69767 caagatat -s Anc2.Anc2refChr1 82069 8 + 142988 caagttat -s mr.mrrefChr3 116358 8 + 181027 taagatgt -s simDog_chr6.simDog.chr6 528612 8 + 593897 caagttat -s simHuman_chr6.simHuman.chr6 536142 8 + 601863 caagattt -s simRat_chr6.simRat.chr6 41797 8 - 647215 Taagatgt - -a -s simMouse_chr6.simMouse.chr6 566475 12 + 636262 gtggaactatat -s Anc0.Anc0refChr3 167247 12 + 222631 ctggacctataa -s Anc1.Anc1refChr1 5947 12 + 69767 ctggacctataa -s Anc2.Anc2refChr1 82077 12 + 142988 ctgaacatataa -s mr.mrrefChr3 116366 12 + 181027 gtggaactataa -s simDog_chr6.simDog.chr6 528620 12 + 593897 ctgaacatataa -s simHuman_chr6.simHuman.chr6 536151 12 + 601863 ccagacctataa -s simRat_chr6.simRat.chr6 41805 12 - 647215 gtggaactgtaa - -a -s simMouse_chr6.simMouse.chr6 566487 10 + 636262 gttatgtaat -s Anc0.Anc0refChr3 167261 10 + 222631 gtcatgcaac -s Anc1.Anc1refChr1 5961 10 + 69767 gtcatgcaac -s Anc2.Anc2refChr1 82091 10 + 142988 ctcatgcaac -s mr.mrrefChr3 116378 10 + 181027 gttatgtaac -s simDog_chr6.simDog.chr6 528634 10 + 593897 ctcatgcaac -s simHuman_chr6.simHuman.chr6 536165 10 + 601863 gtaatacaac -s simRat_chr6.simRat.chr6 41817 10 - 647215 gttatgtaac - -a -s simMouse_chr6.simMouse.chr6 566497 11 + 636262 tattaacgtaa -s Anc0.Anc0refChr3 167272 11 + 222631 tgttaactgaa -s Anc1.Anc1refChr1 5972 11 + 69767 tgttaactgaa -s Anc2.Anc2refChr1 82102 11 + 142988 tgttaattgaa -s mr.mrrefChr3 116389 11 + 181027 tattaactgaa -s simDog_chr6.simDog.chr6 528645 11 + 593897 tgttaattgaa -s simHuman_chr6.simHuman.chr6 536176 11 + 601863 tgttaactgga -s simRat_chr6.simRat.chr6 41828 11 - 647215 tattaactgaa - -a -s simMouse_chr6.simMouse.chr6 566508 27 + 636262 ccatcatgaatcacacaatattactgt -s Anc0.Anc0refChr3 167283 17 + 222631 c----------catgtgatattattgt -s Anc1.Anc1refChr1 5983 17 + 69767 c----------catgtgatattattgt -s Anc2.Anc2refChr1 82113 17 + 142988 t----------catgtgatattattgt -s mr.mrrefChr3 116400 27 + 181027 ccatcatgaatcacatgatattattgt -s simDog_chr6.simDog.chr6 528669 17 + 593897 t----------catgtgatattattgt -s simHuman_chr6.simHuman.chr6 536187 17 + 601863 c----------catgtgatattgttgt -s simRat_chr6.simRat.chr6 41839 27 - 647215 ccatcatgaatcacatgatattattgt - -a -s simMouse_chr6.simMouse.chr6 566535 8 + 636262 gaggacac -s Anc0.Anc0refChr3 167300 8 + 222631 gaggacaa -s Anc1.Anc1refChr1 6000 8 + 69767 gaggacaa -s Anc2.Anc2refChr1 82130 8 + 142988 ggggaaaa -s mr.mrrefChr3 116427 8 + 181027 gaggacac -s simDog_chr6.simDog.chr6 528691 8 + 593897 ggggaaaa -s simHuman_chr6.simHuman.chr6 536204 8 + 601863 gaggacaa -s simRat_chr6.simRat.chr6 41866 8 - 647215 gaggacac - -a -s simMouse_chr6.simMouse.chr6 566543 20 + 636262 attgaatacaccaggccagt -s Anc0.Anc0refChr3 167315 20 + 222631 attgaataaactgggcagga -s Anc1.Anc1refChr1 6015 20 + 69767 attgaataaactgggcagga -s Anc2.Anc2refChr1 82145 20 + 142988 attcaataaactgggcagga -s mr.mrrefChr3 116435 20 + 181027 attgaatacaccaggccagt -s simDog_chr6.simDog.chr6 528706 20 + 593897 attcaataaactgggcagga -s simHuman_chr6.simHuman.chr6 536219 20 + 601863 attgaataaactgggaagga -s simRat_chr6.simRat.chr6 41874 20 - 647215 attggatacaccaggccagt - -a -s simMouse_chr6.simMouse.chr6 566563 3 + 636262 tta -s Anc0.Anc0refChr3 167335 3 + 222631 tta -s Anc1.Anc1refChr1 6035 3 + 69767 tta -s Anc2.Anc2refChr1 82165 3 + 142988 tta -s mr.mrrefChr3 116455 3 + 181027 tta -s simDog_chr6.simDog.chr6 528727 3 + 593897 tta -s simHuman_chr6.simHuman.chr6 536239 3 + 601863 tta -s simRat_chr6.simRat.chr6 41894 3 - 647215 tta - -a -s simMouse_chr6.simMouse.chr6 566566 16 + 636262 catgttaagaatcctg -s Anc0.Anc0refChr3 167338 16 + 222631 gatactaacaatcctg -s Anc1.Anc1refChr1 6038 16 + 69767 gatactaacaatcctg -s Anc2.Anc2refChr1 82168 16 + 142988 gacactaacaggcctg -s mr.mrrefChr3 116458 16 + 181027 catattaagaatcctg -s simDog_chr6.simDog.chr6 528733 16 + 593897 gacactaacaggcctg -s simHuman_chr6.simHuman.chr6 536242 16 + 601863 gatacaaacaatccgg -s simRat_chr6.simRat.chr6 41897 16 - 647215 catattaagattcctg - -a -s simMouse_chr6.simMouse.chr6 566582 23 + 636262 aactgagggatattaccgatatt -s Anc0.Anc0refChr3 167361 23 + 222631 aattgagggaaattaccaatgtt -s Anc1.Anc1refChr1 6061 23 + 69767 aattgagggaaattaccaatgtt -s Anc2.Anc2refChr1 82191 23 + 142988 aattgaggggaattacctatgtt -s mr.mrrefChr3 116474 23 + 181027 aactgagggaaattaccaatgtt -s simDog_chr6.simDog.chr6 528756 23 + 593897 aattgaggggaattacctatgtt -s simHuman_chr6.simHuman.chr6 536265 23 + 601863 atttgagggaaatcataaatgtt -s simRat_chr6.simRat.chr6 41913 23 - 647215 agatgagggaaattaccaacgtt - -a -s simMouse_chr6.simMouse.chr6 566605 25 + 636262 gtttgggtgattaaagaataagcaa -s Anc0.Anc0refChr3 167384 9 + 222631 gttaggat----------------a -s Anc1.Anc1refChr1 6084 9 + 69767 gttaggat----------------a -s Anc2.Anc2refChr1 82214 9 + 142988 gttaggac----------------g -s mr.mrrefChr3 116497 25 + 181027 gtttgggtgattaaagaataagcaa -s simDog_chr6.simDog.chr6 528787 9 + 593897 gttaggac----------------g -s simHuman_chr6.simHuman.chr6 536288 9 + 601863 gttaggat----------------a -s simRat_chr6.simRat.chr6 41936 25 - 647215 gtgtgggtgtttaaagaatgataaa - -a -s simMouse_chr6.simMouse.chr6 566630 2 + 636262 ga -s Anc0.Anc0refChr3 167393 2 + 222631 ga -s Anc1.Anc1refChr1 6093 2 + 69767 ga -s Anc2.Anc2refChr1 82223 2 + 142988 ga -s mr.mrrefChr3 116522 2 + 181027 ga -s simDog_chr6.simDog.chr6 528800 2 + 593897 ga -s simHuman_chr6.simHuman.chr6 536297 2 + 601863 aa -s simRat_chr6.simRat.chr6 41961 2 - 647215 ga - -a -s simMouse_chr6.simMouse.chr6 566632 20 + 636262 catccaatctcatagtcaga -s Anc0.Anc0refChr3 167395 18 + 222631 catccaatctcatagt--ga -s Anc1.Anc1refChr1 6095 18 + 69767 catccaatctcatagt--ga -s Anc2.Anc2refChr1 82225 18 + 142988 catccaatcttatagg--ga -s mr.mrrefChr3 116524 20 + 181027 catccaatctcatagtcaga -s simDog_chr6.simDog.chr6 528802 18 + 593897 catccaatcttatagg--ga -s simHuman_chr6.simHuman.chr6 536299 18 + 601863 tgtccagtctcatagt--ga -s simRat_chr6.simRat.chr6 41972 20 - 647215 caaccaatctcatagtcaga - -a -s simMouse_chr6.simMouse.chr6 566652 24 + 636262 taatggataaagacctgtagcatg -s Anc0.Anc0refChr3 167413 24 + 222631 taatggatgaagacctggggtatt -s Anc1.Anc1refChr1 6113 24 + 69767 taatggatgaagacctggggtatt -s Anc2.Anc2refChr1 82243 24 + 142988 tattagctggagacctggggtatt -s mr.mrrefChr3 116544 24 + 181027 taatggataaagacctgtagcatg -s simDog_chr6.simDog.chr6 528822 24 + 593897 tattagctggagacctggggtatt -s simHuman_chr6.simHuman.chr6 536317 24 + 601863 caatggatgaagacctgaggtact -s simRat_chr6.simRat.chr6 41992 24 - 647215 taatggataaagacctgtagcatg - -a -s simMouse_chr6.simMouse.chr6 566676 24 + 636262 tcccaagatgggcacaagaatgaa -s Anc0.Anc0refChr3 167437 23 + 222631 cccttaaa-gggcacaagaaagca -s Anc1.Anc1refChr1 6137 23 + 69767 cccttaaa-gggcacaagaaagca -s Anc2.Anc2refChr1 82267 23 + 142988 ctcttaaa-gggctcaagcaagca -s mr.mrrefChr3 116568 24 + 181027 tcctaagatgggcacaagaatgaa -s simDog_chr6.simDog.chr6 528847 23 + 593897 ctcttaaa-gggctcaagcaagca -s simHuman_chr6.simHuman.chr6 536341 23 + 601863 cccttcaa-gggcacaaaaaggca -s simRat_chr6.simRat.chr6 42016 24 - 647215 tcctgagatgggaacaagaaTGAA - -a -s simMouse_chr6.simMouse.chr6 566700 12 + 636262 ggaaacaaaata -s Anc0.Anc0refChr3 167545 12 + 222631 ggaaaaaaaaga -s Anc1.Anc1refChr1 6245 12 + 69767 ggaaaaaaaaga -s Anc2.Anc2refChr1 82375 12 + 142988 gggcgaacaaga -s mr.mrrefChr3 116592 12 + 181027 ggaaacaaaata -s simDog_chr6.simDog.chr6 528966 12 + 593897 gggcgaacaaga -s simHuman_chr6.simHuman.chr6 536449 12 + 601863 ggaaaataaaga -s simRat_chr6.simRat.chr6 42040 12 - 647215 GGAAACAAAATC - -a -s simMouse_chr6.simMouse.chr6 566712 53 + 636262 tcttccacgttctcagatgatatgatgctctacctaggaaaccctGGCATGGA -s Anc0.Anc0refChr3 167557 52 + 222631 t-atccacattctcagatgacatgatactctaccttgggaaccctagtatggc -s Anc1.Anc1refChr1 6257 52 + 69767 t-atccacattctcagatgacatgatactctaccttgggaaccctagtatggc -s Anc2.Anc2refChr1 82387 52 + 142988 t-attcatatttgcaagtgacaacacactctacctctggaaccctagtgcggc -s mr.mrrefChr3 116604 52 + 181027 t-ttccacgttctcagatgatatgatgctctaccttggaaaccctAGCATGGC -s simDog_chr6.simDog.chr6 528986 52 + 593897 t-attcatatttgcaagtgacaacacactctacctctggaaccctagtgcggc -s simHuman_chr6.simHuman.chr6 536461 52 + 601863 t-gtccacatcctcagatgacatgatattctaccttgggaaccctagtatggc -s simRat_chr6.simRat.chr6 42052 26 - 647215 ---------------------------CTCTACCTTGGAAACTCTAGCATGGC - -a -s simMouse_chr6.simMouse.chr6 566765 17 + 636262 AAGTTGAGCACAGCTAG -s Anc0.Anc0refChr3 167616 17 + 222631 aacttagtcacagtgat -s Anc1.Anc1refChr1 6316 17 + 69767 aacttagtcacagtgat -s Anc2.Anc2refChr1 82446 17 + 142988 aactaactcacactgat -s mr.mrrefChr3 116656 17 + 181027 AAGTTGGGCACAGCTAG -s simCow_chr6.simCow.chr6 541073 6 + 602619 -----------ACataa -s simDog_chr6.simDog.chr6 529045 17 + 593897 aactaactcacactgat -s simHuman_chr6.simHuman.chr6 536520 17 + 601863 aaattagtcaaagtgat -s simRat_chr6.simRat.chr6 42078 17 - 647215 AAGCAGGGCACTGCTAG - -a -s simMouse_chr6.simMouse.chr6 566782 41 + 636262 CCTGGATGTAATTGAGAGGTACGAGAACAATAGGTAGGTAa -s Anc0.Anc0refChr3 167633 36 + 222631 cccagatgttctt-----gtacaagaataatcagcaaatca -s Anc1.Anc1refChr1 6333 36 + 69767 cccagatgttctt-----gtacaagaataatcagcaaatca -s Anc2.Anc2refChr1 82507 36 + 142988 cccagatgttctt-----gtacaaaaataatcagcaaatca -s mr.mrrefChr3 116673 41 + 181027 CCTAGATGTAATTGAGAGGTACGAGAACAATAGGTaGGTAa -s simCow_chr6.simCow.chr6 541124 36 + 602619 accaaacattctt-----gtacaactataatcagcaaatca -s simDog_chr6.simDog.chr6 529106 36 + 593897 cccagatgtcctt-----gtacaaaaataatcagcaaatta -s simHuman_chr6.simHuman.chr6 536537 36 + 601863 cccagatgatctt-----gtacaagaataatcagcaaatca -s simRat_chr6.simRat.chr6 42095 40 - 647215 CCTAGATATAATTAAGAGGTATGAGAACTAGAGGT-GGTAA - -a -s simMouse_chr6.simMouse.chr6 566823 20 + 636262 tactaaagaaacacccactg -s Anc0.Anc0refChr3 168343 19 + 222631 tactaa-gaaaaaaccacct -s Anc1.Anc1refChr1 7043 19 + 69767 tactaa-gaaaaaaccacct -s Anc2.Anc2refChr1 83442 19 + 142988 tgcaaa-gaaaagaccaact -s mr.mrrefChr3 116714 19 + 181027 tactaa-gaaacacccaccg -s simCow_chr6.simCow.chr6 542055 19 + 602619 ttcaaa-aataagaggaacg -s simDog_chr6.simDog.chr6 530081 19 + 593897 tgtaga-gaaaagaccaact -s simHuman_chr6.simHuman.chr6 537325 19 + 601863 tactat-gagaaaaccacca -s simRat_chr6.simRat.chr6 42135 19 - 647215 CACCAA-GAAACACCCACCG - -a -s simMouse_chr6.simMouse.chr6 566843 174 + 636262 gtaatactaaagaaacacccacctacagtttaggtaggaagatcatagttgggaaaggctaaagagacagctactccacccaattttatttttctcagtaggcacctccagcctcatcttaggcagggagacccttagggaatggagcaaaagtgggccctcaactcaaattaa -s Anc0.Anc0refChr3 168517 98 + 222631 gaaatgctaatgagacacccactcacagcctagg-------------------------tagggagacacccactcaactcaa-tttattt------------------------------------------------ga-ggaaggtaaagtgagcccccaactcaatct-a -s Anc1.Anc1refChr1 7217 163 + 69767 gaaatgctaatgagacacccactcacagcctaggg---------ataattaggaaaggctagggagacacccactcaactcaa-tttattttcctaagtgagtgagtacagacccatcttagaaagggaggcccatagcga-ggaaggtaaagtgagcccccaactcaatctta -s Anc2.Anc2refChr1 83618 98 + 142988 gaaatgctaatgagacacccactcacagcctagg-------------------------cagggagacacccactcaactcaa-tctattt------------------------------------------------ga-ggaaggtaaggtgagccaccaactcaatcc-a -s mr.mrrefChr3 116733 173 + 181027 gtaatactaaagaaacacccacctacagtttaggtaggaagatcatagttgggaaaggctaaagagacagccactccactcaattttatttttctcagtaggcacctccagcctcatcttaggcagggagacccttagcga-tgaagcaaaagtgggccctcaactcaaattaa -s simCow_chr6.simCow.chr6 542114 94 + 602619 gaaatgcagatgagaaacacactcacaacctaga-------------------------gaggagg----TTTGTCAATGCCA-AGAAAGT------------------------------------------------GA-GGAAGCAAAGGTGAGCCACCAACTCATTCC-A -s simDog_chr6.simDog.chr6 530263 98 + 593897 gagatgctaatgagacacctactcatagcctgtg-------------------------caaggagacacccactccactcaa-tctattt------------------------------------------------ga-gaaaggtaaggtgagccaccaacccaatcc-a -s simHuman_chr6.simHuman.chr6 537499 163 + 601863 gaaatgttaatgaggcacccattcgcagcctaggg---------ataattaggaaaggctagggagacacccacccaactcaa-tttattttcctaagtgagtgagtacagacccatcttagaaagggaggcccatagcga-ggaagtgatagtgaggccacagcttaatctta -s simRat_chr6.simRat.chr6 42154 172 - 647215 GTTATACTGAAGAAacacccacctacagtttaggtaggaagatcatggttggaaaaggctaaagagacagccactccacttaattttatttttctcagtaggcacctccaaccttatcttaggcagag-gaccctcagcga-tgaagcaaaagtgggccctcaactcaaattaa - -a -s simMouse_chr6.simMouse.chr6 567017 41 + 636262 gggaTGAATTCAGTTTTACCCACAAAAAGGAAACAAAAGTT -s Anc0.Anc0refChr3 168615 31 + 222631 gggaggagctcatgtttacccacataaa----------gtg -s Anc1.Anc1refChr1 7380 39 + 69767 gggaggagctcatgtttacccacataaa--aaatgaaagtg -s Anc2.Anc2refChr1 83716 31 + 142988 gggaggagcttttgttaacccaaatgag----------gtg -s mr.mrrefChr3 116906 41 + 181027 gggaTGAATTCAGttttacccACAAAAAGGAAACGAAAGTT -s simCow_chr6.simCow.chr6 542210 27 + 602619 GGGAGGAACTATTGTT----CCAAGGGC----------ACG -s simDog_chr6.simDog.chr6 530361 31 + 593897 aaaaggggtttttggtaacctaaatgag----------gtg -s simHuman_chr6.simHuman.chr6 537662 39 + 601863 gggaggagctcatatttaaacccataaa--aaatgaaagtg -s simRat_chr6.simRat.chr6 42326 33 - 647215 gggaTGAATTCAC--------ACAAAAAGGAAACGAAAGTT - -a -s simMouse_chr6.simMouse.chr6 567058 69 + 636262 AGAATGGTTCATATCTAGCAGCAAAATAGGAGTGAGAGTGAAACACACATCCAGTTGAACAGAGTGGCG -s Anc0.Anc0refChr3 168666 58 + 222631 agaacggttcatatctaggagcaaa-----------agtaaaacacccatccagttcaaaggagtagct -s Anc1.Anc1refChr1 7439 58 + 69767 agaacggttcatatctaggagcaaa-----------agtaaaacacccatccagttcaaaggagtagct -s Anc2.Anc2refChr1 83767 58 + 142988 ggaacggttcatatctaggagtgga-----------agtaaaacacccatccgattcaaagggatgggt -s mr.mrrefChr3 116947 69 + 181027 AGAATGGTTCATATCTAGCAGCAAAAtaggagtgagagtgaaacacccatccagttgaacagagtagct -s simCow_chr6.simCow.chr6 542315 36 + 602619 GGAACGGTTCATGTATAGGTGTGGC-----------AGTGAAACACC---------------------- -s simDog_chr6.simDog.chr6 530409 58 + 593897 ggaatggttcatatctgggagtgga-----------agcaaaacacccatccgattcaaagggatgggt -s simHuman_chr6.simHuman.chr6 537721 58 + 601863 agaacacttcatttcaaggagcaaa-----------agtaagactcccatccagtttaaaggagcagct -s simRat_chr6.simRat.chr6 42359 69 - 647215 AGAATGGTTTATGTCTGGCAGCAAAAtaggagcgagagtgaaacacccatccaattgaacagagtagct - -a -s simMouse_chr6.simMouse.chr6 567127 1 + 636262 C -s Anc0.Anc0refChr3 168724 1 + 222631 c -s Anc1.Anc1refChr1 7497 1 + 69767 c -s Anc2.Anc2refChr1 83825 1 + 142988 t -s mr.mrrefChr3 117016 1 + 181027 c -s simDog_chr6.simDog.chr6 530468 1 + 593897 t -s simHuman_chr6.simHuman.chr6 537779 1 + 601863 c -s simRat_chr6.simRat.chr6 42428 1 - 647215 c - -a -s simMouse_chr6.simMouse.chr6 567128 23 + 636262 TTGCAGCCCTTAAGAAGATATCA -s Anc0.Anc0refChr3 168729 23 + 222631 ttacagaccttaagaagagtatt -s Anc1.Anc1refChr1 7502 23 + 69767 ttacagaccttaagaagagtatt -s Anc2.Anc2refChr1 83830 23 + 142988 tgacagaccttaagaagagtatt -s mr.mrrefChr3 117017 23 + 181027 ttgcagaccttaagaagatatca -s simDog_chr6.simDog.chr6 530473 23 + 593897 tgacagaccttaagaagagtatt -s simHuman_chr6.simHuman.chr6 537784 23 + 601863 ttacagacctgaataagtgtaat -s simRat_chr6.simRat.chr6 42429 23 - 647215 ttgcagaccttaagaagatatca - -a -s simMouse_chr6.simMouse.chr6 567151 18 + 636262 AGGGCTAGTACTCAGACC -s Anc0.Anc0refChr3 168752 18 + 222631 agggcttgtactcaaacc -s Anc1.Anc1refChr1 7525 18 + 69767 agggcttgtactcaaacc -s Anc2.Anc2refChr1 83853 18 + 142988 agggcttgtactcaaacc -s mr.mrrefChr3 117040 18 + 181027 agggCTagtacTCAGACC -s simCow_chr6.simCow.chr6 542351 5 + 602619 -------------AAACC -s simDog_chr6.simDog.chr6 530498 18 + 593897 agggcttgtactcaaacc -s simHuman_chr6.simHuman.chr6 537807 18 + 601863 agggcttgtactcaaact -s simRat_chr6.simRat.chr6 42452 13 - 647215 agggCT-----TCAGACC - -a -s simMouse_chr6.simMouse.chr6 567169 29 + 636262 TTAGATCTAAGGGGAAGTATTTAAGTAAA -s Anc0.Anc0refChr3 168770 29 + 222631 ccatgtctaagaggagtcttttaagttga -s Anc1.Anc1refChr1 7543 29 + 69767 ccatgtctaagaggagtcttttaagttga -s Anc2.Anc2refChr1 83871 29 + 142988 ccttgtctaagaggagtctttgaagttga -s mr.mrrefChr3 117058 29 + 181027 CTAGATCTAAGGGGAAGTATTTAAGTAAA -s simCow_chr6.simCow.chr6 542356 29 + 602619 TCTTGTCTAAGAGGAGCCTTTGAGATTTA -s simDog_chr6.simDog.chr6 530516 16 + 593897 ct-------------gtctttgaagttga -s simHuman_chr6.simHuman.chr6 537829 29 + 601863 ccaactctaagaggagtcttttaagttga -s simRat_chr6.simRat.chr6 42465 29 - 647215 CTATATCTGAGGGGGAGTATTTAAGTAAA - -a -s simMouse_chr6.simMouse.chr6 567198 37 + 636262 ACCTCCACAGAATGGTTCTCATGTGAAGTAATGATGG -s Anc0.Anc0refChr3 168819 36 + 222631 actatctagga-cagtttacaagttaagaagtgaaag -s Anc1.Anc1refChr1 7592 37 + 69767 actatctaggaacagtttacaagttaagaagtgaaag -s Anc2.Anc2refChr1 83920 36 + 142988 tccatctagga-cagttttggagttcacaagtagaag -s mr.mrrefChr3 117107 37 + 181027 ACTTCCACAGAATGGTTCACATGTGAAGAAATGATGG -s simDog_chr6.simDog.chr6 530555 36 + 593897 tccatctagga-cagttttggagttcacaagtagaag -s simHuman_chr6.simHuman.chr6 537878 37 + 601863 actgtctaggaacagtttacaagttaagaagtgaaag -s simRat_chr6.simRat.chr6 42514 37 - 647215 ACTCCCACAGAGTGGTTCACATACGAAGAAATAATGG - -a -s simMouse_chr6.simMouse.chr6 567235 96 + 636262 AGAAGCACCTTACTTTAGAGGTTAAAGTTTATCATGCTATGGCTGATTGGCCTCATTAGCCTTGTGTAATCTCCTCAATCAATTATAGTGGACAAT -s Anc0.Anc0refChr3 168855 44 + 222631 tgaa--ccc------------------------------------------------agtataatgtaatctacctagtcaatttgagg--accat -s Anc1.Anc1refChr1 7629 50 + 69767 tgaa--cccttac------------------------------------------ctagtataatgtaatctacctagtcaatttgagg--accat -s Anc2.Anc2refChr1 83956 44 + 142988 ttaa--ctc------------------------------------------------agtataatgtaatccaactagttaatatgagg--accat -s mr.mrrefChr3 117144 86 + 181027 AGAAGCACCTTACTTTAG----------TTATCATGCTATGGCTGATTGGCCTCATTAGTCTAGTGTAATCTCCTTAATCAATTATAGTGGaCAAT -s simDog_chr6.simDog.chr6 530591 44 + 593897 ttaa--ctc------------------------------------------------agtataatgtaatccaactagttaatatgagg--accat -s simHuman_chr6.simHuman.chr6 537915 50 + 601863 tgaa--cccttac------------------------------------------ctggtttaatgtaatctgcctagtcaacttgagc--accat -s simRat_chr6.simRat.chr6 42552 85 - 647215 AGAAACATGTTGCTTTAG----------TTATCACGCCATGGCTGCTTGGTCTTGTTAGTGTAGTGTAATTTCCTTAATCAATTATAGTGG-CAAT - -a -s simMouse_chr6.simMouse.chr6 567331 18 + 636262 AGCGAGGAAATAGGTACA -s Anc0.Anc0refChr3 168899 13 + 222631 agc-----agtgggtatg -s Anc1.Anc1refChr1 7679 13 + 69767 agc-----agtgggtatg -s Anc2.Anc2refChr1 84000 13 + 142988 gga-----agtgggtatg -s mr.mrrefChr3 117230 18 + 181027 AGCGAGGAAATAGGTATG -s simDog_chr6.simDog.chr6 530641 13 + 593897 gga-----agtgggtatg -s simHuman_chr6.simHuman.chr6 537965 13 + 601863 agc-----agtggatatg -s simRat_chr6.simRat.chr6 42637 18 - 647215 AGCGACAAAATAGGTATG - -a -s simMouse_chr6.simMouse.chr6 567349 43 + 636262 AAGCACTCATTCGGCTAAGGGGAGAGGGTTGTGTTTCAAAATG -s Anc0.Anc0refChr3 168912 43 + 222631 aaggactcattcagctaactggagaggcttgtatttaaaaatg -s Anc1.Anc1refChr1 7692 43 + 69767 aaggactcattcagctaactggagaggcttgtatttaaaaatg -s Anc2.Anc2refChr1 84013 43 + 142988 aaggactcattcatcttactggagatgcttgtattgaaaaatg -s mr.mrrefChr3 117248 43 + 181027 AAGCACTCATTCAGCTaaggggaGAGGGTTGTGTTTCAAAATG -s simCow_chr6.simCow.chr6 542392 10 + 602619 ---------------------------------CTAAAAAACA -s simDog_chr6.simDog.chr6 530654 43 + 593897 aaggactcattcatcttactggagatgcttgtattgaaaaatg -s simHuman_chr6.simHuman.chr6 537979 43 + 601863 agggactcagtcagctaacaggagaggcttgtatctaagaatg -s simRat_chr6.simRat.chr6 42655 36 - 647215 AAGTACTCATTCAGCA-------GTCAATCATGGTTCACAATA - -a -s simMouse_chr6.simMouse.chr6 567392 36 + 636262 TTCCAGCAAAAAGATACAAACATTCTATTCTTCATA -s Anc0.Anc0refChr3 168955 32 + 222631 ttccagtaagagaata-ccacg-actaa-attc-tg -s Anc1.Anc1refChr1 7735 33 + 69767 ttccagtaagagaata-ccacg-actaatattc-tg -s Anc2.Anc2refChr1 84056 32 + 142988 ttccagtaagggaata-ccacg-actaa-acac-tg -s mr.mrrefChr3 117291 34 + 181027 TTCCAGCAAGAAAATA-ACACGTTCTATTCTTC-TG -s simCow_chr6.simCow.chr6 542402 25 + 602619 TTCTGATAAG--------CATG-ATTGT-GCAA-TC -s simDog_chr6.simDog.chr6 530697 32 + 593897 ttccagtaagggaata-ctact-actaa-acac-tg -s simHuman_chr6.simHuman.chr6 538022 33 + 601863 ttccagtaagagaata-ccacg-acaaatattc-tg -s simRat_chr6.simRat.chr6 42697 34 - 647215 CTCTATAAAGTCATGG-ACGCGTTTCATTCTTC-TG - -a -s simMouse_chr6.simMouse.chr6 567428 3 + 636262 GTG -s Anc0.Anc0refChr3 168987 3 + 222631 gtg -s Anc1.Anc1refChr1 7768 3 + 69767 gtg -s Anc2.Anc2refChr1 84088 3 + 142988 atg -s mr.mrrefChr3 117325 3 + 181027 GTG -s simCow_chr6.simCow.chr6 542427 3 + 602619 ATA -s simDog_chr6.simDog.chr6 530735 3 + 593897 atg -s simHuman_chr6.simHuman.chr6 538055 3 + 601863 gtg -s simRat_chr6.simRat.chr6 42731 3 - 647215 GTT - -a -s simMouse_chr6.simMouse.chr6 567431 29 + 636262 CCCAATAATGTGACTCCATAAAATCACAC -s Anc0.Anc0refChr3 168993 28 + 222631 cacaataggactcctccatggagcc-tag -s Anc1.Anc1refChr1 7774 28 + 69767 cacaataggactcctccatggagcc-tag -s Anc2.Anc2refChr1 84094 28 + 142988 cacaataggactcctccatggagcc-taa -s mr.mrrefChr3 117328 29 + 181027 CCCAATAATACTACTCCATAAAGTCATAG -s simCow_chr6.simCow.chr6 542433 28 + 602619 cataataggttttcttcacatagtc-caa -s simDog_chr6.simDog.chr6 530741 28 + 593897 cacaatagtactccaccatggagcc-taa -s simHuman_chr6.simHuman.chr6 538061 28 + 601863 cacagcaggactcctccatggagcc-tcg -s simRat_chr6.simRat.chr6 42734 29 - 647215 TACAATAATACTACTCCATAAAGTCATGG - -a -s simMouse_chr6.simMouse.chr6 567460 55 + 636262 AAGTGTTTCATATTCTTCTTTTATGAGTCAAAAAGACTAAGAAACAGGTTCCCTT -s Anc0.Anc0refChr3 169021 55 + 222631 acctgcttcatattgttcttgtctaagtaaagaagattaaagaaggggtttcctt -s Anc1.Anc1refChr1 7802 55 + 69767 acctgcttcatattgttcttgtctaagtaaagaagattaaagaaggggtttcctt -s Anc2.Anc2refChr1 84122 55 + 142988 acctgcttcaaattgttcttgtctaagtaaagaagattaaagaaggggtctcctt -s mr.mrrefChr3 117357 55 + 181027 ACGTGTTTCATatTCTTCTTTTATGAGTCAAAAAGACTAAGAAACAGGTTCCCTT -s simCow_chr6.simCow.chr6 542462 55 + 602619 gcctgctgcaaattgttttcatctaagtaaggaagattaagggagggatctcctt -s simDog_chr6.simDog.chr6 530769 55 + 593897 acctagttcaaattgttcttgtctaagtaaagaaggttaaagaaggggtctcctt -s simHuman_chr6.simHuman.chr6 538089 55 + 601863 acctgcttcatattgttcctgtgtaagtgaaggagatgagagaaggtgctacctt -s simRat_chr6.simRat.chr6 42763 53 - 647215 ACGCGTTTCAT--TCTTCTTATCTGAGTAAAAAAGACTAAGAAATAGATTCCCTG - -a -s simMouse_chr6.simMouse.chr6 567515 6 + 636262 TGTGAT -s Anc0.Anc0refChr3 169076 6 + 222631 tgtgat -s Anc1.Anc1refChr1 7857 6 + 69767 tgtgat -s Anc2.Anc2refChr1 84177 6 + 142988 tgtgat -s mr.mrrefChr3 117412 6 + 181027 TGTGAT -s simCow_chr6.simCow.chr6 542517 6 + 602619 tgtggt -s simDog_chr6.simDog.chr6 530829 6 + 593897 tgcaat -s simHuman_chr6.simHuman.chr6 538144 6 + 601863 tgtgat -s simRat_chr6.simRat.chr6 42816 6 - 647215 TGTGAT - -a -s simMouse_chr6.simMouse.chr6 567521 19 + 636262 TAGACATAAGTAACCCCCC -s Anc0.Anc0refChr3 169130 17 + 222631 CATACAAGGCGAGCTCT-- -s Anc1.Anc1refChr1 7911 19 + 69767 CATACAAGGCGAGCTCTCC -s Anc2.Anc2refChr1 84253 17 + 142988 CATACCAGGCGAGCTCT-- -s mr.mrrefChr3 117418 19 + 181027 TAGACATAAGTAACCCCCC -s simCow_chr6.simCow.chr6 542593 17 + 602619 cacacCAGGCTAGCTCC-- -s simDog_chr6.simDog.chr6 530905 17 + 593897 CATACCAAGTGAGCTCT-- -s simHuman_chr6.simHuman.chr6 538211 19 + 601863 CAAACAAGGCCAGCTCTCC -s simRat_chr6.simRat.chr6 42822 19 - 647215 TAGGCATAAGTAACCCCCC - -a -s simMouse_chr6.simMouse.chr6 567540 49 + 636262 TTTTCCAACATCCAGCCACCTCAGAAAAATTCTCAGAAAAAAACCATCA -s Anc0.Anc0refChr3 169161 46 + 222631 TTTTTTAACATACAGCCACCTAAGAAGAATCCTC---GAAAAAATATCA -s Anc1.Anc1refChr1 7944 46 + 69767 TTTTTTAACATACAGCCACCTAAGAAGAATCCTC---GAAAAAATATCA -s Anc2.Anc2refChr1 84284 46 + 142988 TTTTTTAACATACAGCCACCTAAGAAGAATCCCC---GAAGAAATATTA -s mr.mrrefChr3 117437 49 + 181027 TTTTTCAACATCCAGCCACCTCAGAAGAATTCTCAGAAAAAAACCATCA -s simCow_chr6.simCow.chr6 542624 46 + 602619 TTTTTTAGCATACAGCCACCTAGGAAGAATCCCC---AGAGAAAGATTA -s simDog_chr6.simDog.chr6 530936 45 + 593897 TTTTTTAACCTACAGTCCCCTAAGAACAATCCCC---GAAGAT-TATTA -s simHuman_chr6.simHuman.chr6 538244 46 + 601863 TTTTTTATCATATAGCCAACTTAAAGGAATCCTG---GAAAAAATATCA -s simRat_chr6.simRat.chr6 42841 46 - 647215 TTTTT---CGTCCAGCCACCTCAGAAGAATTCTCACAAGGAAACCATTA - -a -s simMouse_chr6.simMouse.chr6 567589 15 + 636262 ATTTGTGACTCAACT -s Anc0.Anc0refChr3 169207 6 + 222631 ATGTGT--------- -s Anc1.Anc1refChr1 7990 6 + 69767 ATGTGT--------- -s Anc2.Anc2refChr1 84330 6 + 142988 ATGTGT--------- -s mr.mrrefChr3 117486 6 + 181027 ATTTGT--------- -s simCow_chr6.simCow.chr6 542681 6 + 602619 ATGTGT--------- -s simDog_chr6.simDog.chr6 530981 6 + 593897 ATGTGT--------- -s simHuman_chr6.simHuman.chr6 538290 6 + 601863 ACATGT--------- -s simRat_chr6.simRat.chr6 42887 6 - 647215 TTTTGT--------- - -a -s simMouse_chr6.simMouse.chr6 567604 27 + 636262 CATTTATCATTTGAATAAGGCCTAGTA -s Anc0.Anc0refChr3 169217 21 + 222631 CAGTTATCATTTGAATATGTC------ -s Anc1.Anc1refChr1 8000 21 + 69767 CAGTTATCATTTGAATATGTC------ -s Anc2.Anc2refChr1 84340 21 + 142988 CAGTTATTGTTTGAAGCTGTC------ -s mr.mrrefChr3 117492 21 + 181027 CAGTTATCATTTGAATAAGGC------ -s simCow_chr6.simCow.chr6 542691 21 + 602619 CAGTTATTGTTTGCAGTTGTC------ -s simDog_chr6.simDog.chr6 530991 19 + 593897 CAGTTA--GTTTGAAGCTGTC------ -s simHuman_chr6.simHuman.chr6 538300 21 + 601863 CAGTTATCATTTGAATATGTC------ -s simRat_chr6.simRat.chr6 42893 12 - 647215 CAGTTATCACTC--------------- - -a -s simMouse_chr6.simMouse.chr6 567631 7 + 636262 TGTTAGT -s Anc0.Anc0refChr3 169238 7 + 222631 TGTTAGA -s Anc1.Anc1refChr1 8021 7 + 69767 TGTTAGA -s Anc2.Anc2refChr1 84367 7 + 142988 TGTTAGA -s mr.mrrefChr3 117513 7 + 181027 TGTTAGT -s simCow_chr6.simCow.chr6 542718 7 + 602619 AGTTCGA -s simDog_chr6.simDog.chr6 531016 7 + 593897 TGTTAGA -s simHuman_chr6.simHuman.chr6 538321 7 + 601863 TGTTGGA -s simRat_chr6.simRat.chr6 42905 5 - 647215 --TTAGT - -a -s simMouse_chr6.simMouse.chr6 567638 14 + 636262 CGAACATAAGGATC -s Anc0.Anc0refChr3 169245 14 + 222631 CAGACATCAGGATC -s Anc1.Anc1refChr1 8028 14 + 69767 CAGACATCAGGATC -s Anc2.Anc2refChr1 84374 14 + 142988 CAGACATCAGGATC -s mr.mrrefChr3 117520 14 + 181027 CAAACATCAGGATC -s simCow_chr6.simCow.chr6 542725 14 + 602619 CAAACATCAGGGTT -s simDog_chr6.simDog.chr6 531023 14 + 593897 CAGAGATCAGGATC -s simHuman_chr6.simHuman.chr6 538329 9 + 601863 CAGACATCA----- -s simRat_chr6.simRat.chr6 42910 14 - 647215 CAAGCATCAGTATC - -a -s simMouse_chr6.simMouse.chr6 567652 7 + 636262 CACCCCA -s Anc0.Anc0refChr3 169259 7 + 222631 AATTCCA -s Anc1.Anc1refChr1 8042 7 + 69767 AATTCCA -s Anc2.Anc2refChr1 84389 7 + 142988 AATTCCA -s mr.mrrefChr3 117534 7 + 181027 CACCCCA -s simCow_chr6.simCow.chr6 542740 7 + 602619 GATTTCA -s simDog_chr6.simDog.chr6 531038 7 + 593897 AATTCCA -s simRat_chr6.simRat.chr6 42924 7 - 647215 CACCCCA - -a -s simMouse_chr6.simMouse.chr6 567659 8 + 636262 TATGACCA -s Anc0.Anc0refChr3 169266 8 + 222631 TATAACCA -s Anc1.Anc1refChr1 8049 8 + 69767 TATAACCA -s Anc2.Anc2refChr1 84396 8 + 142988 TATAACCA -s mr.mrrefChr3 117541 8 + 181027 TATGACCA -s simCow_chr6.simCow.chr6 542747 8 + 602619 CATGGCCA -s simDog_chr6.simDog.chr6 531046 8 + 593897 TATAACCA -s simHuman_chr6.simHuman.chr6 538338 5 + 601863 ---ATTTA -s simRat_chr6.simRat.chr6 42931 8 - 647215 TATGACCA - -a -s simMouse_chr6.simMouse.chr6 567667 14 + 636262 CTCTATATGCCCTG -s Anc0.Anc0refChr3 169274 9 + 222631 C-----TTGTCCTG -s Anc1.Anc1refChr1 8057 9 + 69767 C-----TTGTCCTG -s Anc2.Anc2refChr1 84404 9 + 142988 C-----TTGTCATG -s mr.mrrefChr3 117549 14 + 181027 CTCTATTTGCCCTG -s simCow_chr6.simCow.chr6 542760 9 + 602619 C-----TTGTCTTC -s simDog_chr6.simDog.chr6 531054 9 + 593897 C-----TCAACATG -s simHuman_chr6.simHuman.chr6 538343 9 + 601863 T-----TTGTCCTG -s simRat_chr6.simRat.chr6 42939 14 - 647215 CTCTATTTTCCTTT - -a -s simMouse_chr6.simMouse.chr6 567681 21 + 636262 CCCAATGAAATGTTGTGAGAT -s Anc0.Anc0refChr3 169283 21 + 222631 CCTTGTGAAATGCTGAGACTT -s Anc1.Anc1refChr1 8066 21 + 69767 CCTTGTGAAATGCTGAGACTT -s Anc2.Anc2refChr1 84413 21 + 142988 CCTTGTGAAATGCTGAGACTT -s mr.mrrefChr3 117563 21 + 181027 CCCTATGAAATGTTGTGAGAT -s simCow_chr6.simCow.chr6 542769 21 + 602619 CCTTGTGAAGTGCTGAGACTT -s simDog_chr6.simDog.chr6 531066 21 + 593897 CCATATGAAATGCTGAGACTT -s simHuman_chr6.simHuman.chr6 538352 21 + 601863 CCTTGTGTAATGCTGAGACTT -s simRat_chr6.simRat.chr6 42953 21 - 647215 CCCTATGAAATGTTGTGAGAT - -a -s simMouse_chr6.simMouse.chr6 567702 13 + 636262 ATGGAGTGTGGAA -s Anc0.Anc0refChr3 169310 12 + 222631 A-GGTGTATGGAA -s Anc1.Anc1refChr1 8093 13 + 69767 ATGGTGTATGGAA -s Anc2.Anc2refChr1 84440 12 + 142988 G-GGTGTATGGAA -s mr.mrrefChr3 117584 13 + 181027 ATGGTGTATGGAA -s simCow_chr6.simCow.chr6 542796 12 + 602619 T-GGTATATGGAA -s simDog_chr6.simDog.chr6 531093 12 + 593897 G-GGTGTATGGAA -s simHuman_chr6.simHuman.chr6 538379 13 + 601863 ATGGTGTATTGAA -s simRat_chr6.simRat.chr6 42974 13 - 647215 ACAGTGGATGGAA - -a -s simMouse_chr6.simMouse.chr6 567715 2 + 636262 TA -s Anc0.Anc0refChr3 169329 2 + 222631 TG -s Anc1.Anc1refChr1 8113 2 + 69767 TG -s Anc2.Anc2refChr1 84459 2 + 142988 TG -s mr.mrrefChr3 117597 2 + 181027 TG -s simCow_chr6.simCow.chr6 542815 2 + 602619 TG -s simDog_chr6.simDog.chr6 531112 2 + 593897 TA -s simHuman_chr6.simHuman.chr6 538399 2 + 601863 TG -s simRat_chr6.simRat.chr6 42987 2 - 647215 TG - -a -s simMouse_chr6.simMouse.chr6 567717 42 + 636262 TGAGTTCTAGGGAAGGGCGAACAAGGGCCCATAGGGATCAAG -s Anc0.Anc0refChr3 169331 37 + 222631 TGAGTTCC-----AGGGCCATCAGGGGCCCATGGCTGGACAG -s Anc1.Anc1refChr1 8115 37 + 69767 TGAGTTCC-----AGGGCCATCAGGGGCCCATGGCTGGACAG -s Anc2.Anc2refChr1 84461 37 + 142988 TGGCTTCC-----AGGGCCATCAGGAGCCCATGGCTGGACAG -s mr.mrrefChr3 117599 42 + 181027 TGAGTTCTAGGGAAGGGCGATCAAGGGCCCATAGGAATCAAG -s simCow_chr6.simCow.chr6 542817 37 + 602619 TAGCTTCC-----AAGGCCATCAGGAGCCCATAGCTGGACAC -s simDog_chr6.simDog.chr6 531115 36 + 593897 TGGCCCCC-----AGGGCCATCTGGAGCCCA-GGCTGGACAG -s simHuman_chr6.simHuman.chr6 538401 37 + 601863 TGAGTTGC-----AGTGCTGTCAGGGGTCCATGGCTGAACAG -s simRat_chr6.simRat.chr6 42989 42 - 647215 TAGGTTCTAGGGAATGGCCATCAAGAGCCCATAGGAATCAAG - -a -s simMouse_chr6.simMouse.chr6 567759 32 + 636262 CATGTAGAAGCCTGAGAGTAATAACATTTCAA -s Anc0.Anc0refChr3 169372 32 + 222631 CATGTGGGATCCTGAGAAGAATCATAACATGA -s Anc1.Anc1refChr1 8156 32 + 69767 CATGTGGGATCCTGAGAAGAATCATAACATGA -s Anc2.Anc2refChr1 84502 32 + 142988 TATGTGGGATCTTGAGAAGAATCATAACATGA -s mr.mrrefChr3 117641 32 + 181027 CATGTGGAATCCTGAGAGTAATCATATTTCAA -s simCow_chr6.simCow.chr6 542858 31 + 602619 AATGTGGGGTATTG-GAGGCAAAATAACATGA -s simDog_chr6.simDog.chr6 531155 32 + 593897 TGTGTGGGATCTTGACAAGAATCATAACATGA -s simHuman_chr6.simHuman.chr6 538442 32 + 601863 CAAGTGGGATGCCGAGAAGAATCATAACATGA -s simRat_chr6.simRat.chr6 43031 32 - 647215 CATGTGGAATCCTGGGAGTAACCATATTTCAA - -a -s simMouse_chr6.simMouse.chr6 567791 6 + 636262 GGGATA -s Anc0.Anc0refChr3 169404 6 + 222631 GGAATA -s Anc1.Anc1refChr1 8188 6 + 69767 GGAATA -s Anc2.Anc2refChr1 84534 6 + 142988 GGAATA -s mr.mrrefChr3 117673 6 + 181027 GGGATA -s simCow_chr6.simCow.chr6 542946 6 + 602619 GGAATA -s simDog_chr6.simDog.chr6 531187 6 + 593897 GGATTA -s simHuman_chr6.simHuman.chr6 538474 6 + 601863 GGAATA -s simRat_chr6.simRat.chr6 43063 6 - 647215 GGGATG - -a -s simMouse_chr6.simMouse.chr6 567797 3 + 636262 GCT -s Anc0.Anc0refChr3 169410 3 + 222631 GCT -s Anc1.Anc1refChr1 8194 3 + 69767 GCT -s Anc2.Anc2refChr1 84568 3 + 142988 GCC -s mr.mrrefChr3 117679 3 + 181027 GCT -s simCow_chr6.simCow.chr6 542979 3 + 602619 ACC -s simDog_chr6.simDog.chr6 531221 3 + 593897 GCC -s simHuman_chr6.simHuman.chr6 538480 3 + 601863 GCT -s simRat_chr6.simRat.chr6 43069 3 - 647215 GCT - -a -s simMouse_chr6.simMouse.chr6 567800 7 + 636262 GTCAAGG -s Anc0.Anc0refChr3 169413 7 + 222631 TTAGTAG -s Anc1.Anc1refChr1 8197 7 + 69767 TTAGTAG -s Anc2.Anc2refChr1 84571 7 + 142988 TTAGTAG -s mr.mrrefChr3 117682 7 + 181027 GTCAAGG -s simCow_chr6.simCow.chr6 542982 6 + 602619 -TAGTGG -s simDog_chr6.simDog.chr6 531225 7 + 593897 TTAGTAG -s simHuman_chr6.simHuman.chr6 538483 7 + 601863 TTAGTTG -s simRat_chr6.simRat.chr6 43072 7 - 647215 CTCAAAG - -a -s simMouse_chr6.simMouse.chr6 567807 2 + 636262 AT -s Anc0.Anc0refChr3 169421 2 + 222631 AT -s Anc1.Anc1refChr1 8205 2 + 69767 AT -s Anc2.Anc2refChr1 84579 2 + 142988 AT -s mr.mrrefChr3 117690 2 + 181027 AT -s simCow_chr6.simCow.chr6 542989 2 + 602619 AT -s simDog_chr6.simDog.chr6 531233 2 + 593897 AT -s simHuman_chr6.simHuman.chr6 538491 2 + 601863 AG -s simRat_chr6.simRat.chr6 43080 2 - 647215 AT - -a -s simMouse_chr6.simMouse.chr6 567809 25 + 636262 TTATTTTTTGACTAACCCCTCATCA -s Anc0.Anc0refChr3 169424 25 + 222631 TTATTGACTTGCTAACCCCTCATCA -s Anc1.Anc1refChr1 8208 25 + 69767 TTATTGACTTGCTAACCCCTCATCA -s Anc2.Anc2refChr1 84582 25 + 142988 TTACTGATTTGCTAACCCCCCATCA -s mr.mrrefChr3 117692 25 + 181027 TTATTTTCTGACTAACCCCTCATCA -s simCow_chr6.simCow.chr6 542992 22 + 602619 TG---GAATTACAAACCCCCCATCA -s simDog_chr6.simDog.chr6 531236 25 + 593897 TTACTGGTTTGCTAAACCCCCATCA -s simHuman_chr6.simHuman.chr6 538494 25 + 601863 CTATTGACTTGCTAACCCCTTATCA -s simRat_chr6.simRat.chr6 43082 25 - 647215 TTGTTTCCTCACTAACCCCTCATCG - -a -s simMouse_chr6.simMouse.chr6 567834 49 + 636262 TGCCAACCTATTGTCCTTGCTTGTCTGATGTCTGTATTCTTGATTGTAA -s Anc0.Anc0refChr3 169449 17 + 222631 TGATGACCTGTCCTTCT-------------------------------- -s Anc1.Anc1refChr1 8233 49 + 69767 TGATGACCTGTCCTTCTATTTTGTCTAATGTCAATATTCTCAATTGTAA -s Anc2.Anc2refChr1 84607 17 + 142988 TGATGACCTGTCCCACT-------------------------------- -s mr.mrrefChr3 117717 49 + 181027 TGCCAACCTATTGTTCTTGCTTGTCTGATGTCTGTATTCTTGATTGTAA -s simCow_chr6.simCow.chr6 543014 17 + 602619 TGCTGACCTGTCCCACT-------------------------------- -s simDog_chr6.simDog.chr6 531262 17 + 593897 TGATGACCTGTCCCACT-------------------------------- -s simHuman_chr6.simHuman.chr6 538519 49 + 601863 TGTTGATCTGTGATTCTATTTTGTCTAATGTCAATATTCTCAATTGTAA -s simRat_chr6.simRat.chr6 43107 49 - 647215 CGCCAACCCACTGTTCTTGCTTGTCTGATGTCTTTATTCCTGATTGTAA - -a -s simMouse_chr6.simMouse.chr6 567883 2 + 636262 AT -s Anc1.Anc1refChr1 8282 2 + 69767 AT -s mr.mrrefChr3 117766 2 + 181027 AT -s simHuman_chr6.simHuman.chr6 538586 2 + 601863 AT -s simRat_chr6.simRat.chr6 43156 2 - 647215 AT - -a -s simMouse_chr6.simMouse.chr6 567885 4 + 636262 CTGT -s Anc0.Anc0refChr3 169466 3 + 222631 -CAT -s Anc1.Anc1refChr1 8284 4 + 69767 CCAT -s Anc2.Anc2refChr1 84624 3 + 142988 -CAT -s mr.mrrefChr3 117768 4 + 181027 CCAT -s simCow_chr6.simCow.chr6 543031 3 + 602619 -CAT -s simDog_chr6.simDog.chr6 531279 3 + 593897 -CAT -s simHuman_chr6.simHuman.chr6 538589 4 + 601863 CCAT -s simRat_chr6.simRat.chr6 43158 4 - 647215 CCAA - -a -s simMouse_chr6.simMouse.chr6 567889 52 + 636262 CTCTCCTGGCTTATCCAGTGTTTACACCAATAAAATGTGAGACTGAAAGGAA -s Anc0.Anc0refChr3 169469 52 + 222631 CACTCCCGACTTACCCAATGCCTACACAAATAAACTATGGTACTGAGAGGAA -s Anc1.Anc1refChr1 8288 52 + 69767 CACTCCCGACTTACCCAATGCCTACACAAATAAACTATGGTACTGAGAGGAA -s Anc2.Anc2refChr1 84627 52 + 142988 CACACGCGACTTACCCAATGCCTACAAAAATGAACTACGGTACTGAGAGGGA -s mr.mrrefChr3 117772 52 + 181027 CTCTCCTGGCTTATCCAGTGTTTACACCAATAAAATGTGGGACTGAAAGGAA -s simCow_chr6.simCow.chr6 543042 52 + 602619 AAGACTGGACTAACCCAATGCCTACATAAATGACCTAGGGTACTGAGAGGGA -s simDog_chr6.simDog.chr6 531282 52 + 593897 CTCACGCGACTTACCCAATGTCTTCAAAAATGAACTACGGTACTGAGAGCGA -s simHuman_chr6.simHuman.chr6 538593 52 + 601863 CATTCCCAATTTGCCCAATGCGTACACTAACAGACTATGGTACTGAGAGGAA -s simRat_chr6.simRat.chr6 43162 52 - 647215 CTCTCTTGGCTTATCCGGTGTTTACACCAATAAAGCGTGGGACTGAAAGGTA - -a -s simMouse_chr6.simMouse.chr6 567941 41 + 636262 TGTTAGAATTCAGTAGAACCAAGGGTTAAGGCAGCTGCATG -s Anc0.Anc0refChr3 169521 39 + 222631 TGATAGGATTCATTAG--TCAAGGGTCAAGGGAGCTGCATG -s Anc1.Anc1refChr1 8340 41 + 69767 TGATAGGATTCATTAGCTTCAAGGGTCAAGGGAGCTGCATG -s Anc2.Anc2refChr1 84679 39 + 142988 TGATAGCATCCATTAG--TCAAGGGTCAAGGGAGCTGCATG -s mr.mrrefChr3 117824 41 + 181027 TGTTAGGATTCAGTAGAACCAAGGGTTAAGGCAGCTGCATG -s simCow_chr6.simCow.chr6 543101 31 + 602619 TGATAGCATCCATCAG-------GATCAAGCG---TGCATG -s simDog_chr6.simDog.chr6 531334 39 + 593897 TGATTGCATCCATTAG--TCAAGGGTCAAGGGAGCTGCATG -s simHuman_chr6.simHuman.chr6 538645 40 + 601863 TGGTAAGA-TCGTTGGCTGCAAGTGTCATAGTCGCTGCATG -s simRat_chr6.simRat.chr6 43214 41 - 647215 TTATATGCCTCAGTAGAACCTAGGGTTAAGACAGCTGCCTG - -a -s simMouse_chr6.simMouse.chr6 567982 4 + 636262 TTAT -s Anc0.Anc0refChr3 169562 4 + 222631 ACAC -s Anc1.Anc1refChr1 8383 4 + 69767 ACAC -s Anc2.Anc2refChr1 84720 4 + 142988 ACAC -s mr.mrrefChr3 117865 4 + 181027 TTAT -s simCow_chr6.simCow.chr6 543134 4 + 602619 ACAC -s simDog_chr6.simDog.chr6 531375 4 + 593897 ACAC -s simHuman_chr6.simHuman.chr6 538687 4 + 601863 CCCC -s simRat_chr6.simRat.chr6 43255 4 - 647215 TTAT - -a -s simMouse_chr6.simMouse.chr6 567986 18 + 636262 TTTTGTGCATGGTGGGAT -s Anc0.Anc0refChr3 169566 18 + 222631 TTTTGAGAGTTGTTGGAG -s Anc1.Anc1refChr1 8387 18 + 69767 TTTTGAGAGTTGTTGGAG -s Anc2.Anc2refChr1 84724 18 + 142988 TTTTGAGAGTTGTTGGTG -s mr.mrrefChr3 117869 18 + 181027 TTTTGTGCATGGTGGGAT -s simCow_chr6.simCow.chr6 543138 18 + 602619 TTTTGAGAGTTGTTGGTG -s simDog_chr6.simDog.chr6 531379 13 + 593897 TTTTGAGGTTTGT----- -s simHuman_chr6.simHuman.chr6 538691 18 + 601863 TTTCGAGAGTAGTTGGAA -s simRat_chr6.simRat.chr6 43260 18 - 647215 TTTTTGGCATGGTGGGAT - -a -s simMouse_chr6.simMouse.chr6 568004 10 + 636262 TATTGGATCT -s Anc0.Anc0refChr3 169585 10 + 222631 CATTGGATCT -s Anc1.Anc1refChr1 8406 10 + 69767 CATTGGATCT -s Anc2.Anc2refChr1 84743 10 + 142988 TGTTGGATCT -s mr.mrrefChr3 117888 10 + 181027 CATTGGATCT -s simCow_chr6.simCow.chr6 543157 10 + 602619 TGTTGGATAT -s simDog_chr6.simDog.chr6 531393 10 + 593897 TGTTGGATCT -s simHuman_chr6.simHuman.chr6 538710 10 + 601863 CAATGGATCT -s simRat_chr6.simRat.chr6 43279 10 - 647215 CACTGTATCT - -a -s simMouse_chr6.simMouse.chr6 568014 68 + 636262 GCCCTTACCTACCAGACCAACACCTATTGATAGGAACTGTAAACAGCTCACAGACCTCGTGTAATATC -s Anc0.Anc0refChr3 169595 68 + 222631 GCCCTTTCCCACAGGACTAAAGCCTATCGATATAAACTGTCAACATATCGCAGACCATTGGTTATATC -s Anc1.Anc1refChr1 8416 68 + 69767 GCCCTTTCCCACAGGACTAAAGCCTATCGATATAAACTGTCAACATATCGCAGACCATTGGTTATATC -s Anc2.Anc2refChr1 84753 68 + 142988 GCCCTTTCCCACAGGACTAAAGCCTATCGCTATAAACTTTCAGCATATCGCAGACGATTGGTTATATC -s mr.mrrefChr3 117898 68 + 181027 GCCCTTACCTACCAGACCAACACCTATTGATAGGAACTGTAAACATCTCACAGACCACTTGTAATATC -s simCow_chr6.simCow.chr6 543233 62 + 602619 GCCCTTTCCCACGGGGCTAAAGCCTATCACCATGAACTCTCAGCATCCCACAGACAATGT------TC -s simDog_chr6.simDog.chr6 531403 68 + 593897 GCCCTTTCCCACAGGATTAAAGCCTATTGCTATAAACTTGTAGTGTATTGCAGATGATTGGTTATATC -s simHuman_chr6.simHuman.chr6 538720 68 + 601863 GGCCTCTCCCACAGGACAAAAGCCTACCGATATAGATTGTCAACATATCGCAGACCATTCGCCATATC -s simRat_chr6.simRat.chr6 43289 56 - 647215 GCCCTTA------------ATACCTATTGATAGGAACTGTAAACATCTCACAGACCACTTTTAATATC - -a -s simMouse_chr6.simMouse.chr6 568082 93 + 636262 TAATGATCAGACTAAAGAATGTAATACTCTGTAGCATCTTGTCTGGGTACTGGGCACCAGTGCTGCTCTTGTTACCCTCCCATTAAGAAATGT -s Anc0.Anc0refChr3 169666 87 + 222631 TAATAATCACACTAAAGCAAACAATACTTTGTA------TTTATGGATATATTGCATCAGTGCTGTTCCTGCTACTCTCCCATTGAATAATAT -s Anc1.Anc1refChr1 8487 87 + 69767 TAATAATCACACTAAAGCAAACAATACTTTGTA------TTTATGGATATATTGCATCAGTGCTGTTCCTGCTACTCTCCCATTGAATAATAT -s Anc2.Anc2refChr1 84824 87 + 142988 TAATAATCACACTAAAGCAAACAATACTTTGTA------TTTAGAGATATATTGCATCAGTACTGTTCCTGCTACTCTCCCCTTGAATGATAT -s mr.mrrefChr3 117966 93 + 181027 TAATGATCAGACTAAAGAATATAATACTCTGTAGCATCTTGTCTGGGTACTGTGCACCAGTGCTGCTCTTGTTACCCTCCCATTAAGTAATGT -s simCow_chr6.simCow.chr6 543298 86 + 602619 TAATAATC-TACTAAAGCAAGCAACACTTTGTA------CTTAGAGATATCCTGAATCAGCAGTGTTCTGGCTACTCTCCCTTTGAATCATAT -s simDog_chr6.simDog.chr6 531474 80 + 593897 TAACGACCACACTAAAGCAAACAATTCGCTGTA------TC-------ATATTGCATCAGTACTGTTCCTGGCACTTTCCCCTGGTATGATAT -s simHuman_chr6.simHuman.chr6 538791 87 + 601863 TAATAATCAAACTAAAGCAGACGATACTTTTTA------TTTATGGATATATTACATCAGTGCTGTTTCTGCTACTCTCCCATTGAATAATAT -s simRat_chr6.simRat.chr6 43345 93 - 647215 TAACGCTCATACTAAAGAACATAATACTCTGTAGCATCTTGTTTGGGTACCATGCACCAGTGCTGCTCTGGTTACCCTCCCATTAAGTAATGT - -a -s simMouse_chr6.simMouse.chr6 568175 33 + 636262 GTCCACATTCCAAATTGGATGTAGTTTTGTATG -s Anc0.Anc0refChr3 169764 33 + 222631 GTTCACAGTCCAAATTTGATGCGCTATCTCTTT -s Anc1.Anc1refChr1 8585 33 + 69767 GTTCACAGTCCAAATTTGATGCGCTATCTCTTT -s Anc2.Anc2refChr1 84922 33 + 142988 GTTCACAGTCCAAATTTGATGCGCTATCTCTTT -s mr.mrrefChr3 118059 33 + 181027 GTCCACATTCCAAATTGGATGTAGTTTTGTATG -s simCow_chr6.simCow.chr6 543395 33 + 602619 GTTCATAGTTTAGATTCAATCGGCTATCTCTTT -s simDog_chr6.simDog.chr6 531565 33 + 593897 GTACACAGTCCAAATTTGATGCGCTATCTCTTT -s simHuman_chr6.simHuman.chr6 538889 19 + 601863 GTTCACAGTCCAAATTCAA-------------- -s simRat_chr6.simRat.chr6 43438 33 - 647215 GCCCACATTCCAAATTTGATGTACTTTTGTATG - -a -s simMouse_chr6.simMouse.chr6 568208 18 + 636262 GGTGATCTGAATTATTTA -s Anc0.Anc0refChr3 169797 18 + 222631 GATTATCTGACTTATCCA -s Anc1.Anc1refChr1 8618 18 + 69767 GATTATCTGACTTATCCA -s Anc2.Anc2refChr1 84955 18 + 142988 GATTATCTGACTTATCCA -s mr.mrrefChr3 118092 18 + 181027 GGTGATCTGAATTATTTA -s simCow_chr6.simCow.chr6 543429 18 + 602619 GGTGATCAGTCTTAATCC -s simDog_chr6.simDog.chr6 531598 18 + 593897 GATTATCTGACTTATCCA -s simRat_chr6.simRat.chr6 43471 18 - 647215 GGTGATCTGAATTATTCA - -a -s simMouse_chr6.simMouse.chr6 568226 11 + 636262 GTTTACAATTG -s Anc0.Anc0refChr3 169815 11 + 222631 ATTTACATTCA -s Anc1.Anc1refChr1 8636 11 + 69767 ATTTACATTCA -s Anc2.Anc2refChr1 84975 11 + 142988 ATTTACATTCA -s mr.mrrefChr3 118110 11 + 181027 GTTTACAGTTG -s simCow_chr6.simCow.chr6 543449 11 + 602619 AGTCAAATTTA -s simDog_chr6.simDog.chr6 531618 11 + 593897 ATTTACATTCA -s simRat_chr6.simRat.chr6 43489 11 - 647215 GTTTACAGTTG - -a -s simMouse_chr6.simMouse.chr6 568237 3 + 636262 GAA -s Anc0.Anc0refChr3 169826 3 + 222631 GAA -s Anc1.Anc1refChr1 8647 3 + 69767 GAA -s Anc2.Anc2refChr1 84994 3 + 142988 GAA -s mr.mrrefChr3 118121 3 + 181027 GAA -s simCow_chr6.simCow.chr6 543468 3 + 602619 GAA -s simDog_chr6.simDog.chr6 531637 3 + 593897 GAA -s simHuman_chr6.simHuman.chr6 538908 3 + 601863 GAA -s simRat_chr6.simRat.chr6 43500 3 - 647215 GAA - -a -s simMouse_chr6.simMouse.chr6 568240 30 + 636262 AATAGTGCTGATGGGGGCCTACCATTTTGT -s Anc0.Anc0refChr3 169829 25 + 222631 AA-----CTACACGGGGCCTATCATTTTGC -s Anc1.Anc1refChr1 8650 25 + 69767 AA-----CTACACGGGGCCTATCATTTTGC -s Anc2.Anc2refChr1 84997 25 + 142988 AA-----CTACACAAGGCCTATCACTTTGC -s mr.mrrefChr3 118124 30 + 181027 AATAGTGCTGATGGGGGCCTACCATTTTGC -s simCow_chr6.simCow.chr6 543472 25 + 602619 AA-----CTATGCAAGTCCTGACACCTCAC -s simDog_chr6.simDog.chr6 531640 25 + 593897 TA-----CTACATAAGGCCTATCACTCTGT -s simHuman_chr6.simHuman.chr6 538911 25 + 601863 AA-----CTACACGGGGGCTAGCATTTTGC -s simRat_chr6.simRat.chr6 43503 30 - 647215 GACAGTGCTGGTGGGGGCTTACCATTTTGC - -a -s simMouse_chr6.simMouse.chr6 568270 22 + 636262 ACCTGGAGTGTTTCCGACAGTG -s Anc0.Anc0refChr3 169855 22 + 222631 ACCTGTAATGTTTCCAACAGTG -s Anc1.Anc1refChr1 8676 22 + 69767 ACCTGTAATGTTTCCAACAGTG -s Anc2.Anc2refChr1 85023 22 + 142988 ACTTGTAATATTTCCAACAGTG -s mr.mrrefChr3 118154 22 + 181027 ACCTGGAATGTTTCCAACAGTG -s simCow_chr6.simCow.chr6 543498 22 + 602619 ACTTGTAATATTTCCAACACTG -s simDog_chr6.simDog.chr6 531666 22 + 593897 ACTTGCAATATAGCCAACAGTG -s simHuman_chr6.simHuman.chr6 538937 22 + 601863 ACCTGTAATGTTTCCAACAGTG -s simRat_chr6.simRat.chr6 43533 22 - 647215 ACCTGGGATGTTTCTAACAGTG - -a -s simMouse_chr6.simMouse.chr6 568292 44 + 636262 TTCAGTCCAGTGTGATAAGTGTCATACTAATTTCTAAGCTCCCA -s Anc0.Anc0refChr3 169877 44 + 222631 TTCAATCTGGTGTGATGAGTGCCATCCAAATTCTTAAGTTCCCA -s Anc1.Anc1refChr1 8698 44 + 69767 TTCAATCTGGTGTGATGAGTGCCATCCAAATTCTTAAGTTCCCA -s Anc2.Anc2refChr1 85045 44 + 142988 TTCAACATGGTGTGATGAGTGCCATCCACACTCTTAAGTTCCCA -s mr.mrrefChr3 118176 44 + 181027 TTCAGTCCAGTGTGATAAGTGTCATCCTAATTTCTAAGCTCCCA -s simCow_chr6.simCow.chr6 543520 40 + 602619 TACA----GGTATGATGGGTGCCTTCCACCCTCTTAAGTTCCCA -s simDog_chr6.simDog.chr6 531688 44 + 593897 TTCAACATGTTGTGATGAGTGCCACCCACACTCTTAAGTTCCTA -s simHuman_chr6.simHuman.chr6 538960 44 + 601863 TTCAATCTGGTGTGATGAGTGCCATCTGAATTATTAAGTGCTCA -s simRat_chr6.simRat.chr6 43555 44 - 647215 TTCAGTCCAGTGTGATAACTGTCATCCTCATTTCTAAGCTCCCA - -a -s simMouse_chr6.simMouse.chr6 568336 176 + 636262 GTGTTATTACAGTTAGACTTCTCCAATGAAATAGGTCAATGACAATTAACAAATGTATAATAACATTGAGGTCAGTAGAATAACTGGAAAAACAGCAGTGAGGTTGTTTACAGATATCTTGTGATGCACCTCCTGTACAAGAGAGCCAACAGCACACCTAAACTTACAGAATTCTA -s Anc0.Anc0refChr3 169923 146 + 222631 ATGCTCCTATGGGTAGAGT-CTATGATAGAGTAGGTGGATACCCATTAGTAAACATATAATCACATTAAGGTAGGTAGGGTGACTGGAATAATAA------------------AAATCA------GCATCACCAGGATAAGAGCAGCACCAGGA-----AAACTTGTTGAATTCTG -s Anc1.Anc1refChr1 8744 166 + 69767 ATGCTCCTATGGGTAGAGTTCTATGATAGAGTAGGTGGATACCCATTAGTAAACATATAATCACATTAAGGTAGGTAGGGTGACTGGAATAATAATGGTAGGG-CGGCTGCAAAAATCATG----GCATCACCAGGATAAGAGCAGCACCAGGA-----AAACTTGTTGAATTCTG -s Anc2.Anc2refChr1 85091 146 + 142988 ATGCCCCTATGGGTATAGA-CTATGATAGAGTAGGTGGATACCCATTAGTAAACATATAATCACATTAAGGTAGGTAGGGTGACTGGAATGATAA------------------AAATCA------GCATCACCAGGATAAGAGCAGCACCAGGA-----AAACTTGTTGAATTCTG -s mr.mrrefChr3 118220 176 + 181027 GTGTTATTACAGTTAGAGTTCTCCAATGGAATAGGTGGATGCCAATTAATAAATGTATAATCACATTGAGGTCAGTAGAATAACTGGAAAAACAGCAGTAAGGTTGGTTACAGATATCTTGTGATGCACCTCCTGTACAAGAGCACCAACAGCACACCTAAACTTGCAGAATTCTG -s simCow_chr6.simCow.chr6 543560 142 + 602619 GTGCCCCTATGGGTATAGA-CTATGATAGAGTAGGTGGATACCCATTAGTAGACATATAATCATATTAAGGTCAGCAGGGTGACAGTAATGTCAA------------------AA----------GCATCACCAGGATAAGAGAAGCACCAGGA-----TAACTTGCTGAATTCTG -s simDog_chr6.simDog.chr6 531734 89 + 593897 AC-------------------------------------------------ATCATATAATCACCTTGAGGTAGGTAGGGTCACTAGACTGATAA------------------AAATCA---------------GGATAAGTGCAGTACTAGGA-----AAACTTGTTGAATTCTG -s simHuman_chr6.simHuman.chr6 539006 165 + 601863 ATGCTCCTATGGGTAGTGTTCAAGCACAGACTAGGTGGATACCCATGAGTAAACAGATAATCACAAT-AGGTAGGTAGGGCGGCTGCAATAATCATGGTAGGG-CGGCTGCAATAATCATG----GCAGCACCAGGATAACAGCAGCATCAGGA-----AAACTTGGTTAATTCTG -s simRat_chr6.simRat.chr6 43599 176 - 647215 GTGTTATTACAGCTAGAGTTCTCCAATGGAGTAGGTGGATGCCAGTTAATGAATGTGTAAGCACATTGAGGTCAGTAGAATAACTGGAACAACAGCAGCAAGGTTGGTGACAGATCTCTTGTGATTCACCTCCTGCACGAGGACATCAACAGCAAACCTAAACCTGCAGAATACTG - -a -s simMouse_chr6.simMouse.chr6 568512 1 + 636262 T -s Anc0.Anc0refChr3 170071 1 + 222631 C -s Anc1.Anc1refChr1 8912 1 + 69767 C -s Anc2.Anc2refChr1 85239 1 + 142988 C -s mr.mrrefChr3 118396 1 + 181027 T -s simCow_chr6.simCow.chr6 543704 1 + 602619 C -s simDog_chr6.simDog.chr6 531825 1 + 593897 C -s simHuman_chr6.simHuman.chr6 539173 1 + 601863 C -s simRat_chr6.simRat.chr6 43775 1 - 647215 T - -a -s simMouse_chr6.simMouse.chr6 568513 4 + 636262 GGAC -s Anc0.Anc0refChr3 170072 4 + 222631 TAAA -s Anc1.Anc1refChr1 8913 4 + 69767 TAAA -s Anc2.Anc2refChr1 85240 4 + 142988 TAAA -s mr.mrrefChr3 118397 4 + 181027 GGAC -s simCow_chr6.simCow.chr6 543705 4 + 602619 TAAA -s simDog_chr6.simDog.chr6 531827 4 + 593897 TAAA -s simHuman_chr6.simHuman.chr6 539174 4 + 601863 TAAA -s simRat_chr6.simRat.chr6 43776 4 - 647215 GGAC - -a -s simMouse_chr6.simMouse.chr6 568517 17 + 636262 AACCATCCCGTTTTTCG -s Anc0.Anc0refChr3 170076 16 + 222631 TACTATCCC-TTTTTCT -s Anc1.Anc1refChr1 8917 16 + 69767 TACTATCCC-TTTTTCT -s Anc2.Anc2refChr1 85244 16 + 142988 TACTATTAC-TTTTTCT -s mr.mrrefChr3 118401 17 + 181027 AACCATCCCGTTTTTCG -s simCow_chr6.simCow.chr6 543710 11 + 602619 TGCT------TTTTTCT -s simDog_chr6.simDog.chr6 531831 16 + 593897 TACTATTAC-TTCTCTT -s simHuman_chr6.simHuman.chr6 539178 16 + 601863 TACGATCCC-CTTTTCT -s simRat_chr6.simRat.chr6 43780 17 - 647215 GACCATCCCGTTTTTCG - -a -s simMouse_chr6.simMouse.chr6 568534 1 + 636262 T -s Anc0.Anc0refChr3 170092 1 + 222631 T -s Anc1.Anc1refChr1 8933 1 + 69767 T -s Anc2.Anc2refChr1 85260 1 + 142988 T -s mr.mrrefChr3 118418 1 + 181027 T -s simCow_chr6.simCow.chr6 543723 1 + 602619 T -s simDog_chr6.simDog.chr6 531847 1 + 593897 T -s simHuman_chr6.simHuman.chr6 539194 1 + 601863 T -s simRat_chr6.simRat.chr6 43797 1 - 647215 T - -a -s simMouse_chr6.simMouse.chr6 568535 6 + 636262 TTCCTG -s Anc0.Anc0refChr3 170093 6 + 222631 CTCCCA -s Anc1.Anc1refChr1 8934 6 + 69767 CTCCCA -s Anc2.Anc2refChr1 85261 6 + 142988 CTCCCA -s mr.mrrefChr3 118419 6 + 181027 TTCCCA -s simCow_chr6.simCow.chr6 543724 6 + 602619 CTCCCT -s simDog_chr6.simDog.chr6 531848 6 + 593897 GTACCA -s simHuman_chr6.simHuman.chr6 539195 6 + 601863 CTCCCA -s simRat_chr6.simRat.chr6 43799 6 - 647215 TTCCCA - -a -s simMouse_chr6.simMouse.chr6 568541 10 + 636262 TTATTAAAGA -s Anc0.Anc0refChr3 170105 10 + 222631 TCATTAATTT -s Anc1.Anc1refChr1 8946 10 + 69767 TCATTAATTT -s Anc2.Anc2refChr1 85273 10 + 142988 TCATTAATTT -s mr.mrrefChr3 118425 10 + 181027 TTATTAAAGA -s simCow_chr6.simCow.chr6 543735 6 + 602619 ----TAACCT -s simDog_chr6.simDog.chr6 531860 10 + 593897 TCATTAATTA -s simHuman_chr6.simHuman.chr6 539207 10 + 601863 TCATTACTTT -s simRat_chr6.simRat.chr6 43805 10 - 647215 TTGTTAGAGA - -a -s simMouse_chr6.simMouse.chr6 568551 36 + 636262 CCGAAGACTGTTAATTGCAGTAACATCTGCTCTGGT -s Anc0.Anc0refChr3 170117 36 + 222631 CTAAAAACCCTTGATTGCAGTAGCATTTGTTCTGGT -s Anc1.Anc1refChr1 8958 36 + 69767 CTAAAAACCCTTGATTGCAGTAGCATTTGTTCTGGT -s Anc2.Anc2refChr1 85285 36 + 142988 CTAAAAACCCTTGCTTGCAGTAGCATTCAATCTGGT -s mr.mrrefChr3 118437 36 + 181027 CCAAAAACTGTTAATTGCAGTAACATCTGTTCTGGT -s simDog_chr6.simDog.chr6 531872 36 + 593897 CTAAAAACCCTTGCTTGCAGTAGCATTCAATCTGGT -s simHuman_chr6.simHuman.chr6 539219 36 + 601863 CTAAAAGCGCTTGATTGCAATATCATTTGTTCTGAT -s simRat_chr6.simRat.chr6 43817 36 - 647215 CCAAAAACCTTTAAGTGCAGTAACATCTGTTCCGGT - -a -s simMouse_chr6.simMouse.chr6 568587 51 + 636262 CTAGATGAATGCCTCATCACCAGCCTCCACAAGAAATGACATCTGCATCTG -s Anc0.Anc0refChr3 170153 45 + 222631 CTAGATTCATGCCTCATGTTCAGCCTGTACAAAAAATGACATCTG------ -s Anc1.Anc1refChr1 8994 45 + 69767 CTAGATTCATGCCTCATGTTCAGCCTGTACAAAAAATGACATCTG------ -s Anc2.Anc2refChr1 85336 45 + 142988 CTACATTCATGCCTCATGTTCAGCCTGTACAAAATATGACAACTG------ -s mr.mrrefChr3 118473 45 + 181027 CTAGATGAATGCCTCATCACCAGCCTCCACAAGAAATGACATCTG------ -s simCow_chr6.simCow.chr6 543757 45 + 602619 CTACATTCAAGCCTCATGTTAAGCGTGTACAAAAGTTCACAACTG------ -s simDog_chr6.simDog.chr6 532043 45 + 593897 CTACATTCATGTCTCATATGCAGCCTGTACAAAATATGACAACCG------ -s simHuman_chr6.simHuman.chr6 539255 45 + 601863 GTAGATTTATGCCTCAAGTTCAGCCTGTATAAAAAGTGACATCTG------ -s simRat_chr6.simRat.chr6 43853 45 - 647215 CTAGATGAATGCCTCATCACTAGCCTCCACAAGAAATGAGATCTG------ - -a -s simMouse_chr6.simMouse.chr6 568638 27 + 636262 TGCAGGTATCTGGTTGGGGGGAACTGG -s Anc0.Anc0refChr3 170199 26 + 222631 TGCAAGCGTA-GGTTTGGGGGAGCTGG -s Anc1.Anc1refChr1 9040 26 + 69767 TGCAAGCGTA-GGTTTGGGGGAGCTGG -s Anc2.Anc2refChr1 85382 26 + 142988 TGTGAGTGTA-GGTTTGGGGGAGCTGG -s mr.mrrefChr3 118518 27 + 181027 TGCAAGCATCTGGTTGGGGGGAACTGG -s simCow_chr6.simCow.chr6 543803 26 + 602619 GGTGAGTGTA-GGTCTGGGGCACCTGA -s simDog_chr6.simDog.chr6 532089 26 + 593897 TGTGAGTGTA-GGTTTGGGAGAGCTTG -s simHuman_chr6.simHuman.chr6 539301 26 + 601863 TGCAAGCGGA-GGTTTGGGGGAGCTGG -s simRat_chr6.simRat.chr6 43898 27 - 647215 TGCAAGCATCTTGCTGGGGGGAACTGG - -a -s simMouse_chr6.simMouse.chr6 568665 2 + 636262 GA -s Anc0.Anc0refChr3 170228 2 + 222631 GA -s Anc1.Anc1refChr1 9069 2 + 69767 GA -s Anc2.Anc2refChr1 85411 2 + 142988 GA -s mr.mrrefChr3 118545 2 + 181027 GA -s simCow_chr6.simCow.chr6 543832 2 + 602619 TA -s simDog_chr6.simDog.chr6 532118 2 + 593897 GA -s simHuman_chr6.simHuman.chr6 539330 2 + 601863 GC -s simRat_chr6.simRat.chr6 43925 2 - 647215 GA - -a -s simMouse_chr6.simMouse.chr6 568667 2 + 636262 CT -s Anc0.Anc0refChr3 170230 2 + 222631 CT -s Anc1.Anc1refChr1 9071 2 + 69767 CT -s Anc2.Anc2refChr1 85413 2 + 142988 CC -s mr.mrrefChr3 118547 2 + 181027 CT -s simCow_chr6.simCow.chr6 543834 2 + 602619 GC -s simDog_chr6.simDog.chr6 532120 2 + 593897 CC -s simHuman_chr6.simHuman.chr6 539332 2 + 601863 TT -s simRat_chr6.simRat.chr6 43931 2 - 647215 CT - -a -s simMouse_chr6.simMouse.chr6 568669 12 + 636262 ACCCCAATGCTT -s Anc0.Anc0refChr3 170232 12 + 222631 GGAGGAGGAGAT -s Anc1.Anc1refChr1 9073 12 + 69767 GGAGGAGGAGAT -s Anc2.Anc2refChr1 85423 12 + 142988 GGAGGAGGAGAT -s mr.mrrefChr3 118549 12 + 181027 ACCCCAATGCTT -s simCow_chr6.simCow.chr6 543844 4 + 602619 GGAG-------- -s simDog_chr6.simDog.chr6 532130 12 + 593897 GGAGGAGGAGAT -s simHuman_chr6.simHuman.chr6 539334 12 + 601863 GGAGGAGAAGAT -s simRat_chr6.simRat.chr6 43933 12 - 647215 ACCCTGCTGCTT - -a -s simMouse_chr6.simMouse.chr6 568681 38 + 636262 AAGACTAATTTATCTAGAATGCTAATAGACGCCTGATG -s Anc0.Anc0refChr3 170244 36 + 222631 AAGACTAATAT--CTATATTGCTAATAGACAACTGATG -s Anc1.Anc1refChr1 9085 38 + 69767 AAGACTAATATATCTATATTGCTAATAGACAACTGATG -s Anc2.Anc2refChr1 85435 36 + 142988 GAGACTAATAT--CTATATTGCTAATAGACAACTGGCG -s mr.mrrefChr3 118561 38 + 181027 AAGACTAATTTATCTAGAATGCTAATAGACACCTGATG -s simCow_chr6.simCow.chr6 543848 33 + 602619 ---ACTAATAT--CTGTTTTGCTGATAGACAACTGGCG -s simDog_chr6.simDog.chr6 532143 36 + 593897 GAGACTAATAT--CTATATTGCTAAAAGACAACAGGCA -s simHuman_chr6.simHuman.chr6 539346 31 + 601863 AAGACTAGTAT-------GTGCTAATAGACAACTGATG -s simRat_chr6.simRat.chr6 43945 36 - 647215 AAGACTAATTTTTCTAGAATGCT--TAGACACCTGATG - -a -s simMouse_chr6.simMouse.chr6 568719 10 + 636262 TGCTTCAATG -s Anc0.Anc0refChr3 170283 10 + 222631 TGCTTCAATG -s Anc1.Anc1refChr1 9126 10 + 69767 TGCTTCAATG -s Anc2.Anc2refChr1 85474 10 + 142988 TGCTTGAATG -s mr.mrrefChr3 118599 10 + 181027 TGCTTCAATG -s simCow_chr6.simCow.chr6 543884 10 + 602619 TGCTTGGATG -s simDog_chr6.simDog.chr6 532182 10 + 593897 TGCTTGAATT -s simHuman_chr6.simHuman.chr6 539380 10 + 601863 TGCTTCAATG -s simRat_chr6.simRat.chr6 43981 10 - 647215 TGCTTCAATG - -a -s simMouse_chr6.simMouse.chr6 568729 7 + 636262 ATAAATC -s Anc0.Anc0refChr3 170293 7 + 222631 ATTAATG -s Anc1.Anc1refChr1 9136 7 + 69767 ATTAATG -s Anc2.Anc2refChr1 85484 7 + 142988 TTTGATG -s mr.mrrefChr3 118609 7 + 181027 ATTAATC -s simCow_chr6.simCow.chr6 543894 7 + 602619 TTTTATT -s simDog_chr6.simDog.chr6 532199 7 + 593897 TTTGAGG -s simHuman_chr6.simHuman.chr6 539390 7 + 601863 ATTAATG -s simRat_chr6.simRat.chr6 43991 7 - 647215 ATTAATC - -a -s simMouse_chr6.simMouse.chr6 568736 8 + 636262 ATGGTGAG -s Anc0.Anc0refChr3 170300 8 + 222631 ATTGTGCT -s Anc1.Anc1refChr1 9143 8 + 69767 ATTGTGCT -s Anc2.Anc2refChr1 85491 8 + 142988 ATTGTGCT -s mr.mrrefChr3 118616 8 + 181027 ATTGTGAG -s simCow_chr6.simCow.chr6 543902 8 + 602619 GTTGTGAT -s simDog_chr6.simDog.chr6 532206 8 + 593897 ATTATGCA -s simHuman_chr6.simHuman.chr6 539397 8 + 601863 ATTGTGCT -s simRat_chr6.simRat.chr6 43998 8 - 647215 ATTGTGAG - -a -s simMouse_chr6.simMouse.chr6 568744 57 + 636262 AGGTAAGAATTCTTTTTTTGTTTCATCAGAGATTAAGGAGCTATTGGTTTAGGATTG -s Anc0.Anc0refChr3 170308 57 + 222631 AGGTAGTAGCTCTTTTTTTGTTTGATCTGAGATTTGTCAGAAGTTGGTTTAGGATTG -s Anc1.Anc1refChr1 9151 57 + 69767 AGGTAGTAGCTCTTTTTTTGTTTGATCTGAGATTTGTCAGAAGTTGGTTTAGGATTG -s Anc2.Anc2refChr1 85503 57 + 142988 AGCTAGTAGCTCTTTTTTTGTTTGATGGGGGATTTGTCAGAAGTTGGTCAAGGATTG -s mr.mrrefChr3 118624 57 + 181027 AGGTAAGAATTCTTTTTTTGTTTGATCTGAGATTAAGGAGCTATTGGTTTAGGATTG -s simCow_chr6.simCow.chr6 543914 57 + 602619 CACTAGTAGCTCATCATTTGCTTGACTGGCGATTAGTCATAAGTTGGTCAACGACTG -s simDog_chr6.simDog.chr6 532218 57 + 593897 AGCTACTAGCTTTTTTTTTATACAATGGGGGATTTGTCAGAAGTCGGTCAGGGTTTG -s simHuman_chr6.simHuman.chr6 539405 54 + 601863 AGGT---AGCTCTTTTTTTGGTTGATCTGAGATATGTCAGAAGTTGGTTTAGGATTG -s simRat_chr6.simRat.chr6 44006 57 - 647215 AGGTAAGAATTCTTTTTTTGTTTGATCTGAGATTCAGGAGGTATTGGTTTAGTACTG - -a -s simMouse_chr6.simMouse.chr6 568801 2 + 636262 CC -s Anc0.Anc0refChr3 170615 2 + 222631 CT -s Anc1.Anc1refChr1 9458 2 + 69767 CT -s Anc2.Anc2refChr1 85819 2 + 142988 CT -s mr.mrrefChr3 118681 2 + 181027 CC -s simCow_chr6.simCow.chr6 544216 2 + 602619 CT -s simDog_chr6.simDog.chr6 532534 2 + 593897 CT -s simHuman_chr6.simHuman.chr6 539734 2 + 601863 CT -s simRat_chr6.simRat.chr6 44063 2 - 647215 CC - -a -s simMouse_chr6.simMouse.chr6 568803 6 + 636262 AGAGCG -s Anc0.Anc0refChr3 170619 6 + 222631 aagttg -s Anc1.Anc1refChr1 9462 6 + 69767 AAGTTG -s Anc2.Anc2refChr1 85823 6 + 142988 aaggtg -s mr.mrrefChr3 118685 6 + 181027 AAATTG -s simCow_chr6.simCow.chr6 544220 6 + 602619 aaggtg -s simHuman_chr6.simHuman.chr6 539738 6 + 601863 AAGTTG -s simRat_chr6.simRat.chr6 44067 6 - 647215 AAATTG - -a -s simMouse_chr6.simMouse.chr6 568809 17 + 636262 GTTTCACGTTTACTTAC -s Anc0.Anc0refChr3 170632 15 + 222631 atttcacttttgctt-- -s Anc1.Anc1refChr1 9475 17 + 69767 ATTTCACTTTTGCTTGC -s Anc2.Anc2refChr1 85836 15 + 142988 atttcacttttgctt-- -s mr.mrrefChr3 118691 17 + 181027 GTTTCACTTTTGCTTAC -s simCow_chr6.simCow.chr6 544233 15 + 602619 atttcacttttgctt-- -s simHuman_chr6.simHuman.chr6 539751 17 + 601863 ATTTAACTTTTGCATGC -s simRat_chr6.simRat.chr6 44073 17 - 647215 GTTTCATTTTTGCTTGA - -a -s simMouse_chr6.simMouse.chr6 568826 17 + 636262 TATGGGCGTCTCCTTTG -s Anc0.Anc0refChr3 170648 16 + 222631 tattaggggctcccgt- -s Anc1.Anc1refChr1 9493 16 + 69767 TATTAGGGGCTCCCGT- -s Anc2.Anc2refChr1 85852 16 + 142988 tactatgggtttccgc- -s mr.mrrefChr3 118708 17 + 181027 TATGGGCGTCTCCTTTG -s simCow_chr6.simCow.chr6 544249 16 + 602619 tactatgggtttccgc- -s simHuman_chr6.simHuman.chr6 539769 16 + 601863 TATCAGGGGCCCCCCT- -s simRat_chr6.simRat.chr6 44090 17 - 647215 TTTGCGTGTCTCCTTTG - -a -s simMouse_chr6.simMouse.chr6 568843 8 + 636262 GTAGAGTT -s Anc0.Anc0refChr3 170664 8 + 222631 gtagacta -s Anc1.Anc1refChr1 9509 8 + 69767 GTAGACTA -s Anc2.Anc2refChr1 85868 8 + 142988 gtagacaa -s mr.mrrefChr3 118725 8 + 181027 GTAGAGTT -s simCow_chr6.simCow.chr6 544270 8 + 602619 gtagacaa -s simHuman_chr6.simHuman.chr6 539785 8 + 601863 GTAGACTA -s simRat_chr6.simRat.chr6 44107 8 - 647215 GTAGAGTT - -a -s simMouse_chr6.simMouse.chr6 568851 25 + 636262 GGTCAGGGTCTTGTCTTTCTATTAA -s Anc0.Anc0refChr3 170672 25 + 222631 ggtgggggcagtgttttctcattaa -s Anc1.Anc1refChr1 9517 25 + 69767 GGTGGGGGCAGTGTTTTCTCattaa -s Anc2.Anc2refChr1 85876 25 + 142988 ggtggaggcagtgttctctcactaa -s mr.mrrefChr3 118733 25 + 181027 GGTCAGGGTCTTGTCTTCCTATTAA -s simCow_chr6.simCow.chr6 544278 25 + 602619 ggtggaggcagtgttctctcactaa -s simHuman_chr6.simHuman.chr6 539793 25 + 601863 GGTTGGAGCAGTGTTTTCTGattaa -s simRat_chr6.simRat.chr6 44116 25 - 647215 GGTCAAGGTCTTGTCTTCCTATTAA - -a -s simMouse_chr6.simMouse.chr6 568876 65 + 636262 GATGAAATTCTTTCCATGTTTCCTCACAATGTGAATGCCAGGAGAATGCGCCTCAATAACCTTTG -s Anc0.Anc0refChr3 170707 60 + 222631 gaggaaatactttacatgattcttcacaatgtaaatgtcaaaagaatgcccattcatga-----g -s Anc1.Anc1refChr1 9552 60 + 69767 gaggaaatactttacatgattcttcacaatgtaaatgtcaaaagaatgcccattcatga-----g -s Anc2.Anc2refChr1 85911 60 + 142988 gagaaaataatatgcatgattcttcacaatgtaaatatcaagagagtgcccattcatga-----g -s mr.mrrefChr3 118758 65 + 181027 GATGAAATTCTTTACATGTTTCTTCACAATGTGAATGTCAGAAGAATGCGCCTCCATAACCTTTG -s simCow_chr6.simCow.chr6 544313 60 + 602619 gagaaaataatatgcatgattcttcacaatgtaaatatcaagagagtgcccattcatga-----g -s simHuman_chr6.simHuman.chr6 539828 60 + 601863 gagggagtactttacaagattcttgacaaattaaatgtcataaggatgccctttcatga-----g -s simRat_chr6.simRat.chr6 44141 65 - 647215 GATGAAATTCTTTACATGTTTCTTCACAATGTGAATGTCACAAGAATGTAGCTCCATAACCTTTG - -a -s simMouse_chr6.simMouse.chr6 568941 8 + 636262 ATGGTTTT -s Anc0.Anc0refChr3 170767 8 + 222631 ccggtttt -s Anc1.Anc1refChr1 9612 8 + 69767 ccggtttt -s Anc2.Anc2refChr1 85971 8 + 142988 cccgtttt -s mr.mrrefChr3 118823 8 + 181027 CTGGTTTT -s simCow_chr6.simCow.chr6 544378 8 + 602619 cccgtttt -s simHuman_chr6.simHuman.chr6 539888 8 + 601863 ccgatctt -s simRat_chr6.simRat.chr6 44206 8 - 647215 CAGTTTTT - -a -s simMouse_chr6.simMouse.chr6 568949 9 + 636262 TTATTTTTG -s Anc0.Anc0refChr3 170775 9 + 222631 ttaattatg -s Anc1.Anc1refChr1 9620 9 + 69767 ttaattatg -s Anc2.Anc2refChr1 85979 9 + 142988 ctaactatg -s mr.mrrefChr3 118831 9 + 181027 TTATTTTTG -s simCow_chr6.simCow.chr6 544386 9 + 602619 ctaactatg -s simHuman_chr6.simHuman.chr6 539896 9 + 601863 ttaattgtg -s simRat_chr6.simRat.chr6 44230 9 - 647215 TTATTTTTG - -a -s simMouse_chr6.simMouse.chr6 568958 77 + 636262 TTTTGGACAACCTACAACCTCCTTCTGTAACTGAGTAAAATCAACAGAGTATGATCGTGATGGATATATGAAAGCAG -s Anc0.Anc0refChr3 170785 56 + 222631 ttttggtccacc-------tctttctgtatcagcgtaagatca--------------ttgtggatccaggaaactag -s Anc1.Anc1refChr1 9630 56 + 69767 ttttggtccacc-------tctttctgtatcagcgtaagatca--------------ttgtggatccaggaaactag -s Anc2.Anc2refChr1 85989 56 + 142988 ttgtgctccacc-------tctttgtgcttcagcataagatca--------------ttgtggacccaggaaactaa -s mr.mrrefChr3 118840 68 + 181027 TTTTGGACAACC-------TCCTTCTGTAACAGAGTAAGATCAACAG--TATGATCGTGATGGATATATGAAAGTAG -s simCow_chr6.simCow.chr6 544396 56 + 602619 ttgtgctccacc-------tctttgtgcttcagcataagatca--------------ttgtggacccaggaaactaa -s simHuman_chr6.simHuman.chr6 539906 56 + 601863 ttttggtccacc-------tctttctgtaccagtgtaagttca--------------ttgcggatccagtagactag -s simRat_chr6.simRat.chr6 44239 68 - 647215 TATTGGATGAGC-------TCCTTCTTTAATAGAGTGAGATCAACAG--TATGATCATGATGGATATATGAAAGTAG - -a -s simMouse_chr6.simMouse.chr6 569035 14 + 636262 GCCTTCTATCAGCT -s Anc0.Anc0refChr3 170841 10 + 222631 -ccttctctca--- -s Anc1.Anc1refChr1 9686 14 + 69767 gccttctctcagct -s Anc2.Anc2refChr1 86045 10 + 142988 -ccctctctca--- -s mr.mrrefChr3 118908 14 + 181027 GCCTTCTATCAGCT -s simCow_chr6.simCow.chr6 544452 10 + 602619 -ccctctctca--- -s simHuman_chr6.simHuman.chr6 539963 14 + 601863 gcctactctcagct -s simRat_chr6.simRat.chr6 44307 14 - 647215 GCCTTCTATCAGCT - -a -s simMouse_chr6.simMouse.chr6 569049 12 + 636262 AATGAGAGATGA -s Anc0.Anc0refChr3 170851 11 + 222631 -atcagaagcaa -s Anc1.Anc1refChr1 9700 12 + 69767 aatcagaagcaa -s Anc2.Anc2refChr1 86055 11 + 142988 -atcagacgcaa -s mr.mrrefChr3 118922 12 + 181027 AATGAGAAATGA -s simCow_chr6.simCow.chr6 544462 11 + 602619 -atcagacgcaa -s simHuman_chr6.simHuman.chr6 539978 12 + 601863 gataagaagcca -s simRat_chr6.simRat.chr6 44321 12 - 647215 AATGAGAAATGA - -a -s simMouse_chr6.simMouse.chr6 569061 3 + 636262 GTG -s Anc0.Anc0refChr3 170862 3 + 222631 ata -s Anc1.Anc1refChr1 9712 3 + 69767 ata -s Anc2.Anc2refChr1 86066 3 + 142988 ata -s mr.mrrefChr3 118934 3 + 181027 GTA -s simCow_chr6.simCow.chr6 544473 3 + 602619 ata -s simHuman_chr6.simHuman.chr6 539990 3 + 601863 ata -s simRat_chr6.simRat.chr6 44340 3 - 647215 GTA - -a -s simMouse_chr6.simMouse.chr6 569064 17 + 636262 TAGTCTTCCAAACTGTA -s Anc0.Anc0refChr3 170865 17 + 222631 ttttcttccaaactgta -s Anc1.Anc1refChr1 9715 17 + 69767 tTTTCTTCCAAACtgta -s Anc2.Anc2refChr1 86069 17 + 142988 ttttcttccaaatagaa -s mr.mrrefChr3 118937 17 + 181027 TAGTCTTCCAAACTGTA -s simCow_chr6.simCow.chr6 544480 17 + 602619 ttttcttccaaatagaa -s simHuman_chr6.simHuman.chr6 539993 17 + 601863 tTCTCTTCCTAACtgta -s simRat_chr6.simRat.chr6 44343 17 - 647215 TCATCTTTCAAACTGTA - -a -s simMouse_chr6.simMouse.chr6 569081 83 + 636262 GCACATAGGGGAGTGTATCGATAAACTATAACTCTACTGACACACACAAGGCATTTAACCTAATATTTTTGTGCCATCATTCA -s Anc0.Anc0refChr3 170883 68 + 222631 gctcatagtggactgta-------gcaatagctcctc--------ataaggcctttaacttaataatttcccactatcactca -s Anc1.Anc1refChr1 9733 83 + 69767 gctcatagtggactgtaatagccagcaatagctcctctgacccacataaggcctttaacttaataatttcccactatcactca -s Anc2.Anc2refChr1 86087 68 + 142988 actcatgatgggctgta-------gcaatagctcctt--------gtaaggcctttaacttaataatttcccactatcactca -s mr.mrrefChr3 118954 83 + 181027 GCACATAGGGGAGTGTATCAACAAACTATAGCTCCACTGACACACACAAGGCATTTAACCTAATATTTTTGTGCCATCATTCA -s simCow_chr6.simCow.chr6 544498 68 + 602619 actcatgatgggctgta-------gcaatagctcctt--------gtaaggcctttaacttaataatttcccactatcactca -s simHuman_chr6.simHuman.chr6 540011 83 + 601863 gctcacagtgcactctaatagccatcaaaagctcctctgacccacataaggcctttatcttaatcatttcacactatcactca -s simRat_chr6.simRat.chr6 44360 83 - 647215 ACCGATAGGTGAGCGTATCAACAAACTATAGCTCCACTGACACACACATGGCATTTAACCTCATATGTTTGTGCCATCATTCA - -a -s simMouse_chr6.simMouse.chr6 569164 38 + 636262 TTGACTAGCTGCAACTATGTTTGGTGCTGTTGACACAA -s Anc0.Anc0refChr3 170951 2 + 222631 AT------------------------------------ -s Anc1.Anc1refChr1 9816 2 + 69767 AT------------------------------------ -s Anc2.Anc2refChr1 86155 2 + 142988 AT------------------------------------ -s mr.mrrefChr3 119037 36 + 181027 TTGACTAGCTGCAACTATGTTTGGTGTT--TGACACAA -s simCow_chr6.simCow.chr6 544577 2 + 602619 AT------------------------------------ -s simHuman_chr6.simHuman.chr6 540094 2 + 601863 AT------------------------------------ -s simRat_chr6.simRat.chr6 44443 36 - 647215 TTGACAAGCGGACAATGTGTTTGGTGTT--TGACACAG - -a -s simMouse_chr6.simMouse.chr6 569202 10 + 636262 AGTCCCTCCA -s Anc0.Anc0refChr3 170953 2 + 222631 --------CA -s Anc1.Anc1refChr1 9818 2 + 69767 --------CA -s Anc2.Anc2refChr1 86157 2 + 142988 --------CA -s mr.mrrefChr3 119073 10 + 181027 AGTCCCTCCA -s simCow_chr6.simCow.chr6 544579 2 + 602619 --------CA -s simHuman_chr6.simHuman.chr6 540096 2 + 601863 --------CA -s simRat_chr6.simRat.chr6 44480 10 - 647215 ACTACCTCCA - -a -s simMouse_chr6.simMouse.chr6 569212 14 + 636262 TTGCTAGGATCCTG -s Anc0.Anc0refChr3 170955 14 + 222631 CAGTGAGCATCATG -s Anc1.Anc1refChr1 9820 14 + 69767 CAGTGAGCATCATG -s Anc2.Anc2refChr1 86159 14 + 142988 CAGTGAGCATTATG -s mr.mrrefChr3 119083 14 + 181027 TTGCTAGGATCCTG -s simCow_chr6.simCow.chr6 544590 14 + 602619 CAGTGAGCATTATG -s simHuman_chr6.simHuman.chr6 540098 14 + 601863 CAGTGGGTATCGGA -s simRat_chr6.simRat.chr6 44490 14 - 647215 TTGCTAAGATCCTG - -a -s simMouse_chr6.simMouse.chr6 569226 37 + 636262 GGTGTTCTTGCTGGGAACATTATTCTTGCAAAAAATT -s Anc0.Anc0refChr3 170969 25 + 222631 GGT----GTGCTGGCAACATC--------CAGTAGAT -s Anc1.Anc1refChr1 9834 33 + 69767 GGT----GTGCTGGCAACATCTAACGTGGCAGTAGAT -s Anc2.Anc2refChr1 86173 25 + 142988 GGT----GTGTTGGCAACTCC--------CAATAGAT -s mr.mrrefChr3 119097 37 + 181027 GGTGTTCTTGCTGGGAACATTATTCTTGCAAGAAATT -s simCow_chr6.simCow.chr6 544607 25 + 602619 GGT----GTGTTGGCAACTCC--------CAATAGAT -s simHuman_chr6.simHuman.chr6 540112 33 + 601863 AGT----CCGCAGGCGACATCTAACGTGGCAGTGGGT -s simRat_chr6.simRat.chr6 44504 37 - 647215 GGTGTTCTTGCCTGGAACATTATTCTAGCATGGAATT - -a -s simMouse_chr6.simMouse.chr6 569263 20 + 636262 CTATAGCTGCCCCAAGAGGG -s Anc0.Anc0refChr3 170994 12 + 222631 CTATAAGAG--------GGA -s Anc1.Anc1refChr1 9867 12 + 69767 CTATAAGAG--------GGA -s Anc2.Anc2refChr1 86198 12 + 142988 CTACAAGAG--------TGA -s mr.mrrefChr3 119134 20 + 181027 CTATAGCTGCCCCAAGAGGG -s simCow_chr6.simCow.chr6 544636 12 + 602619 CTACAAGAG--------TGA -s simHuman_chr6.simHuman.chr6 540145 12 + 601863 CTATATTAG--------GGA -s simRat_chr6.simRat.chr6 44541 20 - 647215 CTATAGCTACCTAAAGAGAG - -a -s simMouse_chr6.simMouse.chr6 569283 52 + 636262 CCCTAAGGTAGAGCACATGTAGGTGCTTGATCTTAATATTGTAAAAATGATG -s Anc0.Anc0refChr3 171006 43 + 222631 CACTTGTATAGTGACCATGt---------ttttaagtgtcttaaacatgaag -s Anc1.Anc1refChr1 9879 43 + 69767 CACTTGTATAGTGACCATGt---------ttttaagtgtcttaaacatgaag -s Anc2.Anc2refChr1 86210 43 + 142988 CACTTGTATATTTACCCTTg---------tcttaggtgtcttaaacatgaag -s mr.mrrefChr3 119154 52 + 181027 CCCTAAGGTAGAGCACATGTAGGTGCTTGATTTTAATATTTTAAAAATGATG -s simCow_chr6.simCow.chr6 544652 38 + 602619 CACTT-TAAATTCAAC-------------tctttggtgtcctcaatccgcag -s simDog_chr6.simDog.chr6 532536 38 + 593897 -----GATTATTTACCCTTG---------tcttaggtgtctcaaccataaag -s simHuman_chr6.simHuman.chr6 540157 43 + 601863 TTCTTGTATAGTGACCATGt---------ttttcagtgtcttgaacatgagg -s simRat_chr6.simRat.chr6 44561 52 - 647215 CCCTAAGGTAGAGCACATATAGGTACTTGAATGTAAGATTTAAAAAATGGAG - -a -s simMouse_chr6.simMouse.chr6 569335 23 + 636262 TGAACATATGTGACATCATGTGC -s Anc0.Anc0refChr3 171052 23 + 222631 tcttcattgctggcatcctggat -s Anc1.Anc1refChr1 9925 23 + 69767 tcttcattgctggcatcctggat -s Anc2.Anc2refChr1 86256 23 + 142988 ccttcattgctagtgtcctggat -s mr.mrrefChr3 119206 23 + 181027 TGAACATATGTGACATCATGTGC -s simCow_chr6.simCow.chr6 544693 23 + 602619 cctctgttgccagtgtcctggat -s simDog_chr6.simDog.chr6 532577 23 + 593897 ccttcattgctagtgtcctggat -s simHuman_chr6.simHuman.chr6 540203 23 + 601863 tcttcatgacagccatcctggat -s simRat_chr6.simRat.chr6 44613 23 - 647215 TGAACACATTCGACATCATGTGC - -a -s simMouse_chr6.simMouse.chr6 569358 9 + 636262 AATTAGCAT -s Anc0.Anc0refChr3 171075 9 + 222631 attctgtcc -s Anc1.Anc1refChr1 9948 9 + 69767 attctgtcc -s Anc2.Anc2refChr1 86279 9 + 142988 attctttcc -s mr.mrrefChr3 119229 9 + 181027 AATTAGCAC -s simCow_chr6.simCow.chr6 544716 9 + 602619 attctttcc -s simDog_chr6.simDog.chr6 532600 9 + 593897 gttcttttc -s simHuman_chr6.simHuman.chr6 540226 9 + 601863 attctgtcc -s simRat_chr6.simRat.chr6 44642 9 - 647215 ACTTAGCAC - -a -s simMouse_chr6.simMouse.chr6 569367 85 + 636262 GCAGGATCTTTCAATATCTTGACCCTCTATACTGGTTCACATTTACTTAGATCCCTGATCCATCTGCACTTATTCTCAGCATTGA -s Anc0.Anc0refChr3 171086 82 + 222631 gaacatctttccaatatcttgacactctttagaggttgaga---acttagatcccaaatccgtctgcacttggtatcagctttgg -s Anc1.Anc1refChr1 9959 82 + 69767 gaacatctttccaatatcttgacactctttagaggttgaga---acttagatcccaaatccgtctgcacttggtatcagctttgg -s Anc2.Anc2refChr1 86290 82 + 142988 gaacatcttgctaatatcttcacactctttagagactggga---gattagttcccaaatctgtcaggacttggtattagctttgg -s mr.mrrefChr3 119238 85 + 181027 GCAGAACCTTTCAATatcttgacactctttagtggttcagatttacttagatccctgatccatctgcacttagtctcagctttga -s simCow_chr6.simCow.chr6 544727 73 + 602619 gaacatcttgctaatatcttcacactctttagagactggga---gaa--gttccctaatttgtaaggacttggt-------ctgg -s simDog_chr6.simDog.chr6 532611 60 + 593897 gaacat---------------------gttagag-ctggga---gattaattcccaaatctgtcaggacttggtattagctttgg -s simHuman_chr6.simHuman.chr6 540237 80 + 601863 gaacatctttccaacatcttgacactctttagaggttgaga---acttagatcc--aatccgtctgcacttggtttcagctttgg -s simRat_chr6.simRat.chr6 44651 85 - 647215 GCAGAACCTCACCATatcttgacactctttagtggttcagaatcacttagatccctgattcatctgcacttagtctcagctttga - -a -s simMouse_chr6.simMouse.chr6 569452 7 + 636262 GCTTCCT -s Anc0.Anc0refChr3 171196 7 + 222631 gctccta -s Anc1.Anc1refChr1 10070 7 + 69767 gctccta -s Anc2.Anc2refChr1 86419 7 + 142988 gctccta -s mr.mrrefChr3 119352 7 + 181027 gcttctt -s simCow_chr6.simCow.chr6 544839 7 + 602619 gctccga -s simDog_chr6.simDog.chr6 532721 7 + 593897 gccccta -s simHuman_chr6.simHuman.chr6 540347 7 + 601863 gctccta -s simRat_chr6.simRat.chr6 44765 7 - 647215 gcctctt - -a -s simMouse_chr6.simMouse.chr6 569459 16 + 636262 GTTGATGGATGTCTAA -s Anc0.Anc0refChr3 171203 16 + 222631 gccgatagatgtccaa -s Anc1.Anc1refChr1 10077 16 + 69767 gccgatagatgtccaa -s Anc2.Anc2refChr1 86426 16 + 142988 gccaatagatggccaa -s mr.mrrefChr3 119359 16 + 181027 gttgatggatgtccaa -s simCow_chr6.simCow.chr6 544846 16 + 602619 gttaatagatggccga -s simDog_chr6.simDog.chr6 532729 16 + 593897 gccaatagatggccaa -s simHuman_chr6.simHuman.chr6 540354 16 + 601863 gaaggtagatgtccaa -s simRat_chr6.simRat.chr6 44772 16 - 647215 gttgatggatgtccaa - -a -s simMouse_chr6.simMouse.chr6 569475 21 + 636262 TTTCGATGTCACTTCCTGCGG -s Anc0.Anc0refChr3 171222 21 + 222631 ttccaatgctacttgctgagt -s Anc1.Anc1refChr1 10097 21 + 69767 ttccaatgctacttgctgagt -s Anc2.Anc2refChr1 86445 21 + 142988 atctagtgctacttgttgagt -s mr.mrrefChr3 119375 21 + 181027 tttcaatgtcacttcctgcgg -s simCow_chr6.simCow.chr6 544865 21 + 602619 gtctggtgccacttgttgaat -s simDog_chr6.simDog.chr6 532748 21 + 593897 atctagtgctacttgttgagt -s simHuman_chr6.simHuman.chr6 540374 21 + 601863 ttccaatgcaacttgctgagt -s simRat_chr6.simRat.chr6 44788 21 - 647215 tttcactgtcacttcttgggg - -a -s simMouse_chr6.simMouse.chr6 569496 12 + 636262 AGTGACTATTAG -s Anc0.Anc0refChr3 171243 12 + 222631 agtgactactgg -s Anc1.Anc1refChr1 10118 12 + 69767 agtgactactgg -s Anc2.Anc2refChr1 86466 12 + 142988 attgactcctgg -s mr.mrrefChr3 119396 12 + 181027 agtgactattag -s simCow_chr6.simCow.chr6 544886 12 + 602619 attaactcctgg -s simDog_chr6.simDog.chr6 532771 12 + 593897 attgaccccctg -s simHuman_chr6.simHuman.chr6 540395 12 + 601863 agtgactactgg -s simRat_chr6.simRat.chr6 44809 12 - 647215 agtgactattaa - -a -s simMouse_chr6.simMouse.chr6 569508 24 + 636262 CAATTCTCTTAGCCTTCTCCCTGA -s Anc0.Anc0refChr3 171262 24 + 222631 ggtttctctctgggttctctctga -s Anc1.Anc1refChr1 10137 24 + 69767 ggtttctctctgggttctctctga -s Anc2.Anc2refChr1 86485 24 + 142988 ggtttctctctgggttccctctga -s mr.mrrefChr3 119408 24 + 181027 caattctcttagccttctccctga -s simCow_chr6.simCow.chr6 544905 14 + 602619 ggcttctctctagg---------- -s simDog_chr6.simDog.chr6 532790 24 + 593897 ggtttctcactgggttccctctga -s simHuman_chr6.simHuman.chr6 540414 24 + 601863 tgtttctctctggtttctctctga -s simRat_chr6.simRat.chr6 44821 24 - 647215 caattctcttagtcttctccctgg - -a -s simMouse_chr6.simMouse.chr6 569532 32 + 636262 ACAATGAAGGATAGAACGATCAatgaaagata -s Anc0.Anc0refChr3 171286 22 + 222631 -caattgaggatagaataat---------ata -s Anc1.Anc1refChr1 10161 23 + 69767 acaattgaggatagaataat---------ata -s Anc2.Anc2refChr1 86509 22 + 142988 -caattgaggatagaataat---------ata -s mr.mrrefChr3 119432 32 + 181027 acaatgaaggatagaacgatcaatgaaagata -s simCow_chr6.simCow.chr6 544919 22 + 602619 -caatgggggacagaataat---------tta -s simDog_chr6.simDog.chr6 532815 22 + 593897 -caattgaggatagaataat---------ata -s simHuman_chr6.simHuman.chr6 540441 6 + 601863 acaata-------------------------- -s simRat_chr6.simRat.chr6 44845 32 - 647215 acaatgaaggatagaacagtcaatgaaggata - -a -s simMouse_chr6.simMouse.chr6 569564 33 + 636262 gaacaatccagttcgctgagaagtaaacagaag -s Anc0.Anc0refChr3 171308 22 + 222631 gaa-----------gctaagagataaacctgat -s Anc1.Anc1refChr1 10184 22 + 69767 gaa-----------gctaagagataaacctgat -s Anc2.Anc2refChr1 86531 22 + 142988 gaa-----------gctaagagataaacctgat -s mr.mrrefChr3 119464 33 + 181027 gaacaatccagttcgctgagaagtaaacagaag -s simCow_chr6.simCow.chr6 544942 22 + 602619 gaa-----------tctaataaataaaaacaat -s simDog_chr6.simDog.chr6 532837 22 + 593897 gaa-----------gctaagagttaaacctgat -s simRat_chr6.simRat.chr6 44877 33 - 647215 gaacaatccagtttactgagaagtaaacagaag - -a -s simMouse_chr6.simMouse.chr6 569597 3 + 636262 tct -s Anc0.Anc0refChr3 171330 3 + 222631 tct -s Anc1.Anc1refChr1 10206 3 + 69767 tct -s Anc2.Anc2refChr1 86560 3 + 142988 tct -s mr.mrrefChr3 119497 3 + 181027 tct -s simCow_chr6.simCow.chr6 544971 3 + 602619 tct -s simDog_chr6.simDog.chr6 532866 3 + 593897 tct -s simHuman_chr6.simHuman.chr6 540447 2 + 601863 -ct -s simRat_chr6.simRat.chr6 44910 3 - 647215 tct - -a -s simMouse_chr6.simMouse.chr6 569600 23 + 636262 gacaagcccactttcttaccagg -s Anc0.Anc0refChr3 171334 23 + 222631 gacaagtccattttattgccagg -s Anc1.Anc1refChr1 10210 23 + 69767 gacaagtccattttattgccagg -s Anc2.Anc2refChr1 86564 23 + 142988 gacaagtccatttcattgccagg -s mr.mrrefChr3 119501 23 + 181027 gacaagcccactttcttgccagg -s simCow_chr6.simCow.chr6 544975 22 + 602619 gacatgtccattt-attgccagg -s simDog_chr6.simDog.chr6 532870 23 + 593897 gacaaatccatttcattgccagg -s simHuman_chr6.simHuman.chr6 540450 20 + 601863 gacaagtccattttattgcc--- -s simRat_chr6.simRat.chr6 44914 23 - 647215 aacaagcccactttcttgccggg - -a -s simMouse_chr6.simMouse.chr6 569623 1 + 636262 t -s Anc0.Anc0refChr3 171357 1 + 222631 t -s Anc1.Anc1refChr1 10233 1 + 69767 t -s Anc2.Anc2refChr1 86590 1 + 142988 t -s mr.mrrefChr3 119524 1 + 181027 t -s simCow_chr6.simCow.chr6 545000 1 + 602619 t -s simDog_chr6.simDog.chr6 532896 1 + 593897 t -s simHuman_chr6.simHuman.chr6 540470 1 + 601863 t -s simRat_chr6.simRat.chr6 44937 1 - 647215 t - -a -s simMouse_chr6.simMouse.chr6 569624 13 + 636262 atagtttctgacc -s Anc0.Anc0refChr3 171358 12 + 222631 gtggtttctg-tt -s Anc1.Anc1refChr1 10234 13 + 69767 gtggtttctgatt -s Anc2.Anc2refChr1 86591 12 + 142988 gtggtttctg-tt -s mr.mrrefChr3 119525 13 + 181027 atggtttctgacc -s simCow_chr6.simCow.chr6 545001 12 + 602619 gcagtttctg-tt -s simDog_chr6.simDog.chr6 532897 12 + 593897 gtggtttctg-tt -s simHuman_chr6.simHuman.chr6 540471 11 + 601863 gtggattctga-- -s simRat_chr6.simRat.chr6 44941 13 - 647215 atggtgtctgatc - -a -s simMouse_chr6.simMouse.chr6 569637 28 + 636262 tcctggtaccagcataTTGGGTTTAATG -s Anc0.Anc0refChr3 171370 28 + 222631 tcccagtaccagtataaccagtataatg -s Anc1.Anc1refChr1 10247 28 + 69767 tcccagtaccagtataaccagtataatg -s Anc2.Anc2refChr1 86603 28 + 142988 tcccagtaccagtataaccactacaatg -s mr.mrrefChr3 119538 28 + 181027 tcctggtaccagcatattgggtttaatg -s simCow_chr6.simCow.chr6 545014 28 + 602619 tccttgtaccagtataacctataaaacg -s simDog_chr6.simDog.chr6 532909 28 + 593897 tcccagtaccagtataacaactgcaatc -s simHuman_chr6.simHuman.chr6 540482 22 + 601863 ------taccagtataaccagtataatg -s simRat_chr6.simRat.chr6 44954 28 - 647215 tcctggtaccagcacattgggtttaatg - -a -s simMouse_chr6.simMouse.chr6 569665 13 + 636262 CTGCTTCGGTCCC -s Anc0.Anc0refChr3 171398 13 + 222631 ttgttttggtcat -s Anc1.Anc1refChr1 10275 13 + 69767 ttgttttggtcat -s Anc2.Anc2refChr1 86631 13 + 142988 ttgttttggtcat -s mr.mrrefChr3 119566 13 + 181027 ctgttttggtccc -s simCow_chr6.simCow.chr6 545046 13 + 602619 ttgtcctggccaa -s simDog_chr6.simDog.chr6 532937 13 + 593897 atgttttggtcat -s simHuman_chr6.simHuman.chr6 540504 13 + 601863 ttattttggtcat -s simRat_chr6.simRat.chr6 44982 13 - 647215 ctcttttggttgc - -a -s simMouse_chr6.simMouse.chr6 569678 34 + 636262 ATTTACTCATAATATTTCCAAAAAACCAGGTAGT -s Anc0.Anc0refChr3 171411 33 + 222631 agttgctcatagtagaacc-aaaaaccaggtagt -s Anc1.Anc1refChr1 10288 33 + 69767 agttgctcatagtagaacc-aaaaaccaggtagt -s Anc2.Anc2refChr1 86647 33 + 142988 agttgctcgtagtagaaca-aaaaagcagatagt -s mr.mrrefChr3 119579 34 + 181027 atttactcATAATATATCCAAAAAACCAGGTAGT -s simCow_chr6.simCow.chr6 545062 33 + 602619 agttggtcacagtaaaaca-aaaaatcacatagt -s simDog_chr6.simDog.chr6 532953 33 + 593897 agttgctcgtagtagaaca-aaatagcagatagt -s simHuman_chr6.simHuman.chr6 540517 28 + 601863 a-----gcaaagtagaacc-agaaaccaggtggt -s simRat_chr6.simRat.chr6 44995 34 - 647215 atttgctcATAATATATCCGAAAAACCAGGTAGT - -a -s simMouse_chr6.simMouse.chr6 569712 14 + 636262 TCAAATAGAATTAG -s Anc0.Anc0refChr3 171459 14 + 222631 cAGAATTGATTTTG -s Anc1.Anc1refChr1 10336 14 + 69767 cAGAATTGATTTTG -s Anc2.Anc2refChr1 86695 14 + 142988 cAGAATTCATTTTG -s mr.mrrefChr3 119618 14 + 181027 TCGAATTGAATTAG -s simCow_chr6.simCow.chr6 545110 14 + 602619 cAGAATTTATTTTG -s simDog_chr6.simDog.chr6 533001 14 + 593897 cAGAATTCATTTTG -s simHuman_chr6.simHuman.chr6 540560 14 + 601863 cAGAATTGATTTTG -s simRat_chr6.simRat.chr6 45034 14 - 647215 TTGAATTGAATTAG - -a -s simMouse_chr6.simMouse.chr6 569726 17 + 636262 TGCTCCCTGCACAAACT -s Anc0.Anc0refChr3 171478 17 + 222631 TGCTCCCTACACAAACT -s Anc1.Anc1refChr1 10355 17 + 69767 TGCTCCCTACACAAACT -s Anc2.Anc2refChr1 86714 17 + 142988 TGCCCCCTACACAAACT -s mr.mrrefChr3 119632 17 + 181027 TGCTCCCTGCACTGACT -s simCow_chr6.simCow.chr6 545129 17 + 602619 TGCACCTTTCACAAACT -s simDog_chr6.simDog.chr6 533020 17 + 593897 CGCCCCCTACACAAACT -s simHuman_chr6.simHuman.chr6 540579 7 + 601863 TGCTCCG---------- -s simRat_chr6.simRat.chr6 45048 17 - 647215 TGCTCCCTGCACTGACT - -a -s simMouse_chr6.simMouse.chr6 569743 9 + 636262 AATCAGCAT -s Anc0.Anc0refChr3 171495 9 + 222631 AAGCAGCAT -s Anc1.Anc1refChr1 10372 9 + 69767 AAGCAGCAT -s Anc2.Anc2refChr1 86731 9 + 142988 AAGCAGCAT -s mr.mrrefChr3 119649 9 + 181027 AATCAGCAT -s simCow_chr6.simCow.chr6 545147 9 + 602619 GACCAGCAT -s simDog_chr6.simDog.chr6 533037 9 + 593897 AAGCAGCAT -s simHuman_chr6.simHuman.chr6 540586 5 + 601863 ----AGCAT -s simRat_chr6.simRat.chr6 45065 9 - 647215 AATCAGCAT - -a -s simMouse_chr6.simMouse.chr6 569752 22 + 636262 TGGACAGGGACATAACCAAAGT -s Anc0.Anc0refChr3 171510 22 + 222631 TTAAGTGGGTCATCCCCAAAGT -s Anc1.Anc1refChr1 10387 22 + 69767 TTAAGTGGGTCATCCCCAAAGT -s Anc2.Anc2refChr1 86746 22 + 142988 TTAAGTGGGTCATCCCCAAAGT -s mr.mrrefChr3 119658 22 + 181027 TGGAGAGGGACATAACCAAAGT -s simCow_chr6.simCow.chr6 545162 22 + 602619 TCAAGTGGGTTATCCCCAAAGT -s simDog_chr6.simDog.chr6 533052 22 + 593897 TTAAGTGGGTCATCCCCAGAGT -s simHuman_chr6.simHuman.chr6 540597 22 + 601863 CAAAGTGAGTCATTTCCAAAGT -s simRat_chr6.simRat.chr6 45074 22 - 647215 TCGAGAGGGACCTCCCTAAAGA - -a -s simMouse_chr6.simMouse.chr6 569774 7 + 636262 GAGTGCT -s Anc0.Anc0refChr3 171532 7 + 222631 GGGTGCT -s Anc1.Anc1refChr1 10409 7 + 69767 GGGTGCT -s Anc2.Anc2refChr1 86768 7 + 142988 GGGTGCT -s mr.mrrefChr3 119680 7 + 181027 GGGTGCT -s simCow_chr6.simCow.chr6 545184 7 + 602619 GGGTACT -s simDog_chr6.simDog.chr6 533075 7 + 593897 GGGTGCT -s simHuman_chr6.simHuman.chr6 540619 7 + 601863 GGGTGCT -s simRat_chr6.simRat.chr6 45096 7 - 647215 GGGTGCT - -a -s simMouse_chr6.simMouse.chr6 569781 10 + 636262 CACAGGATCT -s Anc0.Anc0refChr3 171543 10 + 222631 CACAGAAACT -s Anc1.Anc1refChr1 10420 10 + 69767 CACAGAAACT -s Anc2.Anc2refChr1 86779 10 + 142988 CACAGAAACC -s mr.mrrefChr3 119687 10 + 181027 CACAGAATCT -s simCow_chr6.simCow.chr6 545195 10 + 602619 CACAGAAACC -s simDog_chr6.simDog.chr6 533086 10 + 593897 CAGAGAAACC -s simHuman_chr6.simHuman.chr6 540630 10 + 601863 CACAGAACCT -s simRat_chr6.simRat.chr6 45103 10 - 647215 CATAGAAGCT - -a -s simMouse_chr6.simMouse.chr6 569791 48 + 636262 GCTACTGCTAACACAACACAACTAATAATCAAGTTGAAATGTGTCAAA -s Anc0.Anc0refChr3 171553 22 + 222631 GCTACACCTA------------------------TCAACTGTAT--AG -s Anc1.Anc1refChr1 10430 22 + 69767 GCTACACCTA------------------------TCAACTGTAT--AG -s Anc2.Anc2refChr1 86789 22 + 142988 GCTACACCTA------------------------TCAACCATAT--AG -s mr.mrrefChr3 119697 43 + 181027 GCTACTCCTAACACAACA-----AATAATCAAGTTCAAATGTATCAAA -s simCow_chr6.simCow.chr6 545206 22 + 602619 GCTACACCTA------------------------CCAACCATAT--TG -s simDog_chr6.simDog.chr6 533096 22 + 593897 GCTCCATCTA------------------------TCAACCATCT--AG -s simHuman_chr6.simHuman.chr6 540640 22 + 601863 GCTATGCCTA------------------------TCAACTGTAT--AG -s simRat_chr6.simRat.chr6 45113 43 - 647215 GCTTCTCCTAACACAACA-----AGTAACCTAGTTCAAATGTATCAAA - -a -s simMouse_chr6.simMouse.chr6 569839 27 + 636262 TACTATTGTGTTTGTGTGTATCCGTGT -s Anc0.Anc0refChr3 171575 25 + 222631 TGATGTAA--TTTGAGTGTATCTGTGT -s Anc1.Anc1refChr1 10452 25 + 69767 TGATGTAA--TTTGAGTGTATCTGTGT -s Anc2.Anc2refChr1 86811 25 + 142988 TGATGTAG--TTTGAGTGTATCTGTGT -s mr.mrrefChr3 119740 27 + 181027 TACTATAATGTTTGTGTGTATCTGTGT -s simCow_chr6.simCow.chr6 545228 25 + 602619 TGATGTCG--TTGGAGTGTATCTGTGT -s simDog_chr6.simDog.chr6 533119 25 + 593897 TGATGCAG--TTTGGGTGTATCTGCGT -s simHuman_chr6.simHuman.chr6 540662 25 + 601863 CGATGTAA--TTTGAGTGTATCTGTGT -s simRat_chr6.simRat.chr6 45156 27 - 647215 TATTATAATATTTGTGTGTATCTGTGC - -a -s simMouse_chr6.simMouse.chr6 569866 43 + 636262 CATAGGGTTTTGGCAATGTTGATTCACTTACTGTTGTACTACT -s Anc0.Anc0refChr3 171606 43 + 222631 TGCAGAGTTTCAGATATGTTGATTCACTTTCTGTTGTACACTT -s Anc1.Anc1refChr1 10483 43 + 69767 TGCAGAGTTTCAGATATGTTGATTCACTTTCTGTTGTACACTT -s Anc2.Anc2refChr1 86842 43 + 142988 TGCAGAGTTTCAGATACATTAATTCTCTTTATGCTGTACACTT -s mr.mrrefChr3 119767 43 + 181027 CATAGGGTTTCGGAAATGTTGATTCACTTACTGTTGTACTATT -s simCow_chr6.simCow.chr6 545259 43 + 602619 TGTGGAGTTTTAGATACACTAATTCTCATTATGCTGTACACTT -s simDog_chr6.simDog.chr6 533146 43 + 593897 TGCAGAATTTCAAGTACATCAATTCTCTCTATGCTGTACACTT -s simHuman_chr6.simHuman.chr6 540693 43 + 601863 TGCATAGTTTCAGAGATGTTGATTCACTTTCTGTTGTACACTT -s simRat_chr6.simRat.chr6 45183 43 - 647215 CATAGGGTTACGGAAATGTTGATTTGCTGACTGTTGTACTATT - -a -s simMouse_chr6.simMouse.chr6 569909 28 + 636262 CCCTTAATAACCCAAGCCCTAGATAATA -s Anc0.Anc0refChr3 171649 28 + 222631 CCTTTAACAGCCCAAGCCCTAAATAATA -s Anc1.Anc1refChr1 10526 28 + 69767 CCTTTAACAGCCCAAGCCCTAAATAATA -s Anc2.Anc2refChr1 86887 28 + 142988 CCTATAACAGTCCAAGCCCTGAATGACA -s mr.mrrefChr3 119810 28 + 181027 CCTTTAATAACCCAAGCCCTAGATAATA -s simCow_chr6.simCow.chr6 545304 23 + 602619 CCTACAACAG-----GCCCTGAATGACA -s simDog_chr6.simDog.chr6 533191 24 + 593897 CCTATAGCAGTCCAAGCACTGAAT---- -s simHuman_chr6.simHuman.chr6 540736 26 + 601863 --TTTAACAGCCCAAGCCCAAAATAATA -s simRat_chr6.simRat.chr6 45226 28 - 647215 CCTTTAATTATCCTGGTCCTATATTATA - -a -s simMouse_chr6.simMouse.chr6 569937 33 + 636262 ACCTCAACAACTAGCAAGCATAGACGGCTGAAT -s Anc0.Anc0refChr3 171678 33 + 222631 ACCTCAACAACTGTCAATAATAAATTGCTAATT -s Anc1.Anc1refChr1 10555 33 + 69767 ACCTCAACAACTGTCAATAATAAATTGCTAATT -s Anc2.Anc2refChr1 86916 33 + 142988 ACCTCAATTACTGTCAATAATAAATTGCAAATT -s mr.mrrefChr3 119838 33 + 181027 ACCTCAACAACTAGCAAGCATAAACGGCTGAAT -s simCow_chr6.simCow.chr6 545328 33 + 602619 ACCACAATTATGGTCAGTGGTAAACTGCCAATT -s simDog_chr6.simDog.chr6 533215 31 + 593897 --CTCAGTTACTGTTAATAACAAATTGTAAAGT -s simHuman_chr6.simHuman.chr6 540763 33 + 601863 ACCTCAACAACTGTCATTTATGAATTGCTAATC -s simRat_chr6.simRat.chr6 45254 32 - 647215 AC-TCAACAAATAGCAAACGTAAACGGCTGAAT - -a -s simMouse_chr6.simMouse.chr6 569970 25 + 636262 TTTGCCTAAGTCATTTTGGCCATCC -s Anc0.Anc0refChr3 171713 25 + 222631 TTTGCATAAGTCATTTGGGTCGTCT -s Anc1.Anc1refChr1 10590 25 + 69767 TTTGCATAAGTCATTTGGGTCGTCT -s Anc2.Anc2refChr1 86951 25 + 142988 GTTGCATCAGTCATTTGGGTAGTCT -s mr.mrrefChr3 119873 25 + 181027 TTTGCCTAAGTCATTTTGGCCATCT -s simCow_chr6.simCow.chr6 545362 23 + 602619 -TTTCAT-AGTCTTTTGGGCTATTT -s simDog_chr6.simDog.chr6 533248 25 + 593897 GTAGCATCAGTCATTTAGGTAGTCT -s simHuman_chr6.simHuman.chr6 540798 25 + 601863 TTTGCATAAGTCATTTGGGTCGTCT -s simRat_chr6.simRat.chr6 45288 25 - 647215 TTAGCCTAAGTCATTTTGGCTATTT - -a -s simMouse_chr6.simMouse.chr6 569995 49 + 636262 CAGGAAGACTAGCTTTTAGTCATAAAGTGTGGTAGTTCTGTATTGACCT -s Anc0.Anc0refChr3 171738 34 + 222631 TATGAAGGTTACCTTTGG---------C------ACTCCTTATTGACCT -s Anc1.Anc1refChr1 10615 43 + 69767 TATGAAGGTTACCTTTGGTGCTAAAAGC------ACTCCTTATTGACCT -s Anc2.Anc2refChr1 86987 34 + 142988 TGTGAGTGTGGCCTTTGG---------C------ACTCCTTATTGAGCT -s mr.mrrefChr3 119898 49 + 181027 CATGAAGATTAGCTTTTGGTCATAAAGTGTGGTAATTCTGTATTGACCT -s simCow_chr6.simCow.chr6 545409 34 + 602619 AGTGATAGTAGCCTTTGG---------C------ACTCCTTATTGATCT -s simDog_chr6.simDog.chr6 533284 34 + 593897 TGTGGGTGTGGCTTTTGG---------C------ATTCTTTATAATGCT -s simHuman_chr6.simHuman.chr6 540823 43 + 601863 TATGAAGGTTACCTTTGGTGCTAAAAGC------ACTCCATAATGACCA -s simRat_chr6.simRat.chr6 45313 49 - 647215 CATGAAGATTAGCTTTTGGTCATAAAGTGTGGTAATTCTGTATTGACTT - -a -s simMouse_chr6.simMouse.chr6 570044 6 + 636262 CAGAAG -s Anc0.Anc0refChr3 171787 6 + 222631 CAGCAG -s Anc1.Anc1refChr1 10673 6 + 69767 CAGCAG -s Anc2.Anc2refChr1 87036 6 + 142988 TAGCAG -s mr.mrrefChr3 119947 6 + 181027 CAGAAG -s simCow_chr6.simCow.chr6 545462 6 + 602619 TAGCAG -s simDog_chr6.simDog.chr6 533333 6 + 593897 TTGCAG -s simHuman_chr6.simHuman.chr6 540881 6 + 601863 CAGCAG -s simRat_chr6.simRat.chr6 45362 6 - 647215 CAGAAG - -a -s simMouse_chr6.simMouse.chr6 570050 70 + 636262 CTATCTGGTTCAGTGTAGTTATTAGGTCATGGTCAATTGTAAGTTACAAGTTTCTACTAATAGAAGTCCT -s Anc0.Anc0refChr3 171809 70 + 222631 CTATCTGGTTCAGTGTAATTATCAGGTCATTGTCAACTGGAAATTTCAAGTTTCTGCTAATTGAGTGCCT -s Anc1.Anc1refChr1 10695 70 + 69767 CTATCTGGTTCAGTGTAATTATCAGGTCATTGTCAACTGGAAATTTCAAGTTTCTGCTAATTGAGTGCCT -s Anc2.Anc2refChr1 87058 70 + 142988 GTATCTGGTCCAGTGTAATTATCAGGTCATTGTCAACTGGAAATTTCAAGTTTCTGCTAATTGAGTGCCT -s mr.mrrefChr3 119953 70 + 181027 CTATCTGGTTCAGTGTAATTATTAGGTCATTGTCAACTGTAAGTTACAAGTTTCTACTAATAGAAGTCCT -s simCow_chr6.simCow.chr6 545484 70 + 602619 TTATTGGGTCCAGTGTAATTATCAGGTCATTGTCAACTGAAAATTTCAAGTTTATGCAAATTGAATTCCT -s simDog_chr6.simDog.chr6 533354 70 + 593897 GTATCTGGTCCAGTGTAATTATCAGGTCATCGTCAAGCAGAAATGTCAAGTTTCTGCTAGTTGAGTGCCT -s simHuman_chr6.simHuman.chr6 540903 70 + 601863 CTATCTTGTTTAGTGTAATTAACAGGTCATTGTCAACTGGGAATTTCAAGTTTCTGCTAAACATGTACCT -s simRat_chr6.simRat.chr6 45368 70 - 647215 CTACCTGGTTCATAGTGACTACTAGGTCATTGTCAACTGTAAGTTAAACATTTGTACTAATTGAGGTGCT - -a -s simMouse_chr6.simMouse.chr6 570120 18 + 636262 TTGAATATCTATTGTCAT -s Anc0.Anc0refChr3 171890 15 + 222631 TTGAGTATACATTG---T -s Anc1.Anc1refChr1 10776 15 + 69767 TTGAGTATACATTG---T -s Anc2.Anc2refChr1 87139 15 + 142988 CGGAGAGTACATTG---T -s mr.mrrefChr3 120023 18 + 181027 TTGTGTATCTATTGTCAT -s simCow_chr6.simCow.chr6 545560 6 + 602619 ---------CATAC---T -s simDog_chr6.simDog.chr6 533435 15 + 593897 CGGAGAGTACATTG---T -s simHuman_chr6.simHuman.chr6 540984 15 + 601863 TTAGGTATTCAATG---T -s simRat_chr6.simRat.chr6 45438 18 - 647215 TTGTGTATCTATTGTCAT - -a -s simMouse_chr6.simMouse.chr6 570138 23 + 636262 TAAAAAGTGAGTGTCAACAAAAT -s Anc0.Anc0refChr3 171905 23 + 222631 TAAAAAGTTAATGTCAAAGAAAT -s Anc1.Anc1refChr1 10791 23 + 69767 TAAAAAGTTAATGTCAAAGAAAT -s Anc2.Anc2refChr1 87154 23 + 142988 TAAAAAGTTAATGTCAAAGAAAT -s mr.mrrefChr3 120041 23 + 181027 TAAAAAGTGAGTGTCAACGAAAT -s simCow_chr6.simCow.chr6 545566 23 + 602619 CAAAAAGTTAATGCTAAAGAAAT -s simDog_chr6.simDog.chr6 533453 23 + 593897 TAAAAACTTAATGTCAAAGAAAT -s simHuman_chr6.simHuman.chr6 540999 23 + 601863 TAAAAAGTTATTGTAAAAGAAAT -s simRat_chr6.simRat.chr6 45456 15 - 647215 TAAAAAG--------AAGGAAAT - -a -s simMouse_chr6.simMouse.chr6 570161 12 + 636262 AATTTAAATATT -s Anc0.Anc0refChr3 171931 12 + 222631 AATCTAAAGATT -s Anc1.Anc1refChr1 10817 12 + 69767 AATCTAAAGATT -s Anc2.Anc2refChr1 87180 12 + 142988 AATCTAAAGATT -s mr.mrrefChr3 120064 12 + 181027 AATTTAAATATT -s simCow_chr6.simCow.chr6 545592 12 + 602619 ACTCTATAGGTT -s simDog_chr6.simDog.chr6 533479 12 + 593897 AATCTAAAGATT -s simHuman_chr6.simHuman.chr6 541026 12 + 601863 AATCTAACAATT -s simRat_chr6.simRat.chr6 45471 12 - 647215 AATTTGAATATT - -a -s simMouse_chr6.simMouse.chr6 570173 52 + 636262 CGGGATTACCACAAAAACTACCTTGACCTTTACTACATTTTGCATGGACAAC -s Anc0.Anc0refChr3 171949 52 + 222631 TGGGATTACCATGAAAAGTACTTTTGCCTTCGCTGCACTTTATGTGGACAAC -s Anc1.Anc1refChr1 10835 52 + 69767 TGGGATTACCATGAAAAGTACTTTTGCCTTCGCTGCACTTTATGTGGACAAC -s Anc2.Anc2refChr1 87198 52 + 142988 TGGGAATACCATGAAAAGTACTTTTGCCTTCGTTGCACTTGATGTGGACAAC -s mr.mrrefChr3 120082 52 + 181027 TGGGATTACCACAAAAACTACCTTGGCCTTTGCTGCATTTTGCATGGACAAC -s simCow_chr6.simCow.chr6 545610 52 + 602619 AGGGAGTACCAGGAGGAGTACTTTTGCCCTTGGGGCCTTTGATGTTGACTAC -s simDog_chr6.simDog.chr6 533495 52 + 593897 TAGGAATGCCATGAAAAGCACTTTTGAGTTCATTACACTTGATGTGGAGAAC -s simHuman_chr6.simHuman.chr6 541044 51 + 601863 TGGGTTTACCATGAAAAGTACTTTTGCCTTGGCTGGA-CTTAAGTGGACAAC -s simRat_chr6.simRat.chr6 45489 52 - 647215 TGGGATTACCACAAAAACTGCCTAGGCCTTTGCTGCATTTTGCATGGACAAC - -a -s simMouse_chr6.simMouse.chr6 570225 16 + 636262 TCAGTGTTATTGTGCT -s Anc0.Anc0refChr3 172006 16 + 222631 CCAATAATTTTGTGAG -s Anc1.Anc1refChr1 10892 16 + 69767 CCAATAATTTTGTGAG -s Anc2.Anc2refChr1 87255 16 + 142988 CCAAAAAATTCGTGAG -s mr.mrrefChr3 120134 16 + 181027 TCAGTGTTATTGTGCT -s simCow_chr6.simCow.chr6 545667 14 + 602619 GCAAGATCCTCGTA-- -s simDog_chr6.simDog.chr6 533552 16 + 593897 CCAAAAAATCCGTGAG -s simHuman_chr6.simHuman.chr6 541100 16 + 601863 CCAATACTGTTGTGTG -s simRat_chr6.simRat.chr6 45541 16 - 647215 TCAGTGTTATTGTGCT - -a -s simMouse_chr6.simMouse.chr6 570241 35 + 636262 CAATGTATGAACCGGTGGTTTATTCTACAGAGTCC -s Anc0.Anc0refChr3 172022 27 + 222631 TGATGTTCA-----GTGCTTTGTTGTATATAG--- -s Anc1.Anc1refChr1 10908 32 + 69767 TGATGTTCAAATCAGTGCTTTGTTGTATATAG--- -s Anc2.Anc2refChr1 87271 27 + 142988 TGATGTTCG-----GTACTTTGTTGTATATAG--- -s mr.mrrefChr3 120150 35 + 181027 CAATGTATGAACCAGTGGTTTGTTCTATAGAGTCC -s simCow_chr6.simCow.chr6 545681 10 + 602619 ----------------------TTGTCCACAG--- -s simDog_chr6.simDog.chr6 533570 27 + 593897 TGATGTTCG-----GTACTTTGTCATATATAG--- -s simHuman_chr6.simHuman.chr6 541116 32 + 601863 TGATGTTCAAATCACTGCTTTGTTGTATATAA--- -s simRat_chr6.simRat.chr6 45557 35 - 647215 CCATGAGTCAACTAGTGGTTTGGTCTATAGAGCCC - -a -s simMouse_chr6.simMouse.chr6 570276 17 + 636262 ATCCAGCAGTTTGTCCT -s mr.mrrefChr3 120185 17 + 181027 ATCCAGCAGTTTGTCCT -s simRat_chr6.simRat.chr6 45593 17 - 647215 ATCCAGTGATTCGTTCT - -a -s simMouse_chr6.simMouse.chr6 570293 45 + 636262 ATGGAGTTCATCCATGGTGCATATCTAGTTCATCCATGGTGCAAA -s Anc0.Anc0refChr3 172049 13 + 222631 --------------------------------CCCATGGTGCACA -s Anc1.Anc1refChr1 10940 13 + 69767 --------------------------------CCCATGGTGCACA -s Anc2.Anc2refChr1 87298 13 + 142988 --------------------------------CCCATGGTGCACA -s mr.mrrefChr3 120202 45 + 181027 ATGGAGTTCATCCATGGTGCATATCTAGTTCATCCATGGTGCAAA -s simCow_chr6.simCow.chr6 545691 13 + 602619 --------------------------------CCCACGGACCACC -s simDog_chr6.simDog.chr6 533597 13 + 593897 --------------------------------CCAATGGTGCACA -s simHuman_chr6.simHuman.chr6 541148 13 + 601863 --------------------------------ACCATGGCGCATG -s simRat_chr6.simRat.chr6 45612 45 - 647215 ATGGAGTCCATCCGTAGTGCATATCCAGCTCATCCATGGTGCAAA - -a -s simMouse_chr6.simMouse.chr6 570338 8 + 636262 GTGTCTCA -s Anc0.Anc0refChr3 172062 8 + 222631 GTAGCTTG -s Anc1.Anc1refChr1 10953 8 + 69767 GTAGCTTG -s Anc2.Anc2refChr1 87311 8 + 142988 GTAGCTTG -s mr.mrrefChr3 120247 8 + 181027 GTATCTCA -s simCow_chr6.simCow.chr6 545704 8 + 602619 GTAACTTC -s simDog_chr6.simDog.chr6 533610 8 + 593897 GTAGCTTG -s simHuman_chr6.simHuman.chr6 541161 8 + 601863 GTAGCTTG -s simRat_chr6.simRat.chr6 45658 8 - 647215 GTATCTCA - -a -s simMouse_chr6.simMouse.chr6 570346 22 + 636262 GATGGTTTTGTTATTTGGCAAA -s Anc0.Anc0refChr3 172070 22 + 222631 GTTGCTCTTGTTATTTGGCAAA -s Anc1.Anc1refChr1 10961 22 + 69767 GTTGCTCTTGTTATTTGGCAAA -s Anc2.Anc2refChr1 87319 22 + 142988 GTTGCTCTTGTTATTGGGCAAA -s mr.mrrefChr3 120255 22 + 181027 GATGCTTTTGTTATTTGGCAAA -s simCow_chr6.simCow.chr6 545715 22 + 602619 GTTGCTCTTGTTGTTTGACAAA -s simDog_chr6.simDog.chr6 533618 22 + 593897 GTTGCTCTTTTTATTGGGCAAG -s simHuman_chr6.simHuman.chr6 541169 21 + 601863 GTCGCTCTTGTTT-TTGGAAAA -s simRat_chr6.simRat.chr6 45666 22 - 647215 GATGCCTTTGTTATTTGGTAAA - -a -s simMouse_chr6.simMouse.chr6 570368 57 + 636262 AGCAAACTAATTAGGTGACATCATAGCTGTGGTTTTGTTATTTAGTAAAAGCAAACT -s Anc0.Anc0refChr3 172096 7 + 222631 AGCAGAC-------------------------------------------------- -s Anc1.Anc1refChr1 10987 7 + 69767 AGCAGAC-------------------------------------------------- -s Anc2.Anc2refChr1 87345 7 + 142988 AGCAGAC-------------------------------------------------- -s mr.mrrefChr3 120277 7 + 181027 AGCAAAC-------------------------------------------------- -s simCow_chr6.simCow.chr6 545741 7 + 602619 AGCTGAG-------------------------------------------------- -s simDog_chr6.simDog.chr6 533644 7 + 593897 AGCAAAC-------------------------------------------------- -s simHuman_chr6.simHuman.chr6 541194 7 + 601863 AGCAGAC-------------------------------------------------- -s simRat_chr6.simRat.chr6 45688 7 - 647215 TGCAAAC-------------------------------------------------- - -a -s simMouse_chr6.simMouse.chr6 570425 113 + 636262 AATTTGGTGACATTGTAGCTGTGGGTGCAATGCTGAACTTAGCCTAGCAGGTATAGGCTCCCACCATTCCCTTAGCTTAGCTGTTTGGTTTGATCTGTGTAACTGCAGGCAAG -s Anc0.Anc0refChr3 172104 113 + 222631 AATTAGGTGGCATAGTAACAGTGGCTGCAATGCTGCACTTATCTTAGCAGGTGTAAGCTCCCATAATTCCTTTACATTAGCAGTTTGTGGTGATCAGTGTCAGTGTAGGTAAG -s Anc1.Anc1refChr1 10995 113 + 69767 AATTAGGTGGCATAGTAACAGTGGCTGCAATGCTGCACTTATCTTAGCAGGTGTAAGCTCCCATAATTCCTTTACATTAGCAGTTTGTGGTGATCAGTGTCAGTGTAGGTAAG -s Anc2.Anc2refChr1 87353 113 + 142988 TATAAGGTGGCATAGTAACAGTGGCTGCAATGCTACACTTATGTTAGCAGGTGTAAGCTCCCATAATTCCTTTATATTAGCAGTTTGTGGTGATCAGTGTCAGTGTAGGTAGG -s mr.mrrefChr3 120284 113 + 181027 AATTAGGTGGCATTGTAGCTGTGGGTGCAATGCTGAACTTAGCCTAGCAGGTGTAGGCTCCCACCATTCCCTTACCTTAGCTGTTTGTTTTGATCTGTGTAACTGCAGGCAAG -s simCow_chr6.simCow.chr6 545749 105 + 602619 CATAAGATGGCTTTGT-AGTGTGGTTGCAATGCTATACTTATGATAGTGGGTGTAAGCACCCATA-------TATATTAGCAGTTTGCGGTGATTAGTGTCAGTGGAGGTAAA -s simDog_chr6.simDog.chr6 533652 113 + 593897 TATAGGGCAGCATAGTAGCAGTGGCTACAATGCTACACTTGTGTTAACAGGTGTAAGCTGCCATAATTCCTTCATACGAGTGGTTTGTGGTGATCAATGTCAGTGTAGGTAGG -s simHuman_chr6.simHuman.chr6 541202 103 + 601863 AAATAGGTGGCATGGTCACAATGACTGCAATACTGCACTTA-CATAGCAGGTGTCAGCTCCCATAATTCCTTTACATTAGCAGTTTGTGATGACCAGTGTC---------AAA -s simRat_chr6.simRat.chr6 45695 113 - 647215 AATTAGGTGGCGGTGTAGCTGTGGGTGCAAACCTGAACTTAGCTTAGCAGGTGTAGGCTCCCACTATTCCCTTACCTTAGCTATTTGTCTTGATCTGTGTAAATGCAAGCAAG - -a -s simMouse_chr6.simMouse.chr6 570538 29 + 636262 GGAGATTAACTAGATAAACAAATCCCCTA -s Anc0.Anc0refChr3 172217 27 + 222631 GAAG--TTATTAAATAAGCAAATACCCTA -s Anc1.Anc1refChr1 11108 29 + 69767 GAAGATTTATTAAATAAGCAAATACCCTA -s Anc2.Anc2refChr1 87466 27 + 142988 AACG--CTGTTAAACAAGCAAATACCCTA -s mr.mrrefChr3 120397 29 + 181027 GAAGATTAACTAGATAAACAAATCCCCTA -s simCow_chr6.simCow.chr6 545860 26 + 602619 AGCT--CTGTTAAACAGG-AAATGCCCTA -s simDog_chr6.simDog.chr6 533765 27 + 593897 AACG--CTGTCAAACAAGCCAATATCCTA -s simHuman_chr6.simHuman.chr6 541305 29 + 601863 GAAGATTTATTAAATAAGCAAATACCCCA -s simRat_chr6.simRat.chr6 45808 29 - 647215 GAAGATGAACTAGATAAACCAATCCCCTA - -a -s simMouse_chr6.simMouse.chr6 570567 29 + 636262 GACTGCTTAGGCATGGAGATTACCACAAT -s Anc0.Anc0refChr3 172245 28 + 222631 GTCTGCTTACTG-TGGAAATTATACTGGG -s Anc1.Anc1refChr1 11138 29 + 69767 GTCTGCTTACTGGTGGAAATTATACTGGG -s Anc2.Anc2refChr1 87494 28 + 142988 GTCTGCTTACTG-TGGAAATTATACTGGG -s mr.mrrefChr3 120426 29 + 181027 GACTGCTTAGTCGTGGAAATTATCACAAT -s simCow_chr6.simCow.chr6 545887 28 + 602619 GTCTGCTTCCTG-CAGAGGTTACATAGAC -s simDog_chr6.simDog.chr6 533793 28 + 593897 GTCAGCTTACTG-TGGAAATTATACTGGG -s simHuman_chr6.simHuman.chr6 541335 29 + 601863 GTCTGTTTACTGGTGGAAATCATACTGGG -s simRat_chr6.simRat.chr6 45837 29 - 647215 GACTGCTTAGTTGTGGGAATTATCACAAT - -a -s simMouse_chr6.simMouse.chr6 570596 41 + 636262 AAACTGTGATAGCAGACAAGAGTCAGTGGCAAAAGGATTTG -s Anc0.Anc0refChr3 172273 40 + 222631 TAATACAGATAGTAGACAAGGATCAGTGGCAGA-TGGCCTC -s Anc1.Anc1refChr1 11167 40 + 69767 TAATACAGATAGTAGACAAGGATCAGTGGCAGA-TGGCCTC -s Anc2.Anc2refChr1 87522 40 + 142988 TAATACAGATAATAAGCAAGGACCAGTGGCAGA-TGGCCTC -s mr.mrrefChr3 120455 40 + 181027 AAATTGTGATAGTAGACAAGAGTCAGTGGCAAA-GGATTTG -s simCow_chr6.simCow.chr6 545915 40 + 602619 AAATACAAATAACAAGCAAGGACCAGTGGCAGA-TGGCCTC -s simDog_chr6.simDog.chr6 533822 28 + 593897 TGATACAGCTAATAAGCAAGGTCTGG-------------TC -s simHuman_chr6.simHuman.chr6 541364 40 + 601863 GAATACAGATAGTAGACAAAGATCAGCAGCACA-CGGACTC -s simRat_chr6.simRat.chr6 45866 40 - 647215 AAATTTTGATAATGGACAACAGTCAGTGGCAAA-GGATTTG - -a -s simMouse_chr6.simMouse.chr6 570637 6 + 636262 CAGTCC -s Anc0.Anc0refChr3 172362 6 + 222631 CAGACC -s Anc1.Anc1refChr1 11256 6 + 69767 CAGACC -s Anc2.Anc2refChr1 87611 6 + 142988 TGGACC -s mr.mrrefChr3 120495 6 + 181027 CAGTCC -s simCow_chr6.simCow.chr6 545996 6 + 602619 TGAACC -s simDog_chr6.simDog.chr6 533899 6 + 593897 TGGACA -s simHuman_chr6.simHuman.chr6 541453 6 + 601863 CAGACC -s simRat_chr6.simRat.chr6 45906 6 - 647215 CAGTCC - -a -s simMouse_chr6.simMouse.chr6 570643 82 + 636262 ACTTGGGTTCTAGTTAGGTAAGTAGGAGGCATGGGGGACAATACCATATAGTAGTAGGATTCCTTCCACCTTGTTTGCAGAG -s Anc0.Anc0refChr3 172368 61 + 222631 ACTTGAGTTCTGCATGGGTAAACATGCTGGATAGGGGAAAG---------------------CTTCCACTTCAATCACAGAG -s Anc1.Anc1refChr1 11262 79 + 69767 ACTTGAGTTCTGCATGGGTAAACATGCTGGATAGGGGAAAGTGGCATA---TGTTAAGATTCCTTCCACTTCAATCACAGAG -s Anc2.Anc2refChr1 87617 61 + 142988 ACTTGAGTTCTGCATGGGCAAACATGCTGGATAGAGGAAAG---------------------CTACCACTTCAATCTCGGAC -s mr.mrrefChr3 120501 82 + 181027 ACTTGGGTTCTAGTTAGGTAAGTATGAGGCATGGGGGACAATACCATATAGTAGTAGGATTCCTTCCACCTTGTTTACAGAG -s simCow_chr6.simCow.chr6 546002 61 + 602619 ACTTGATTTCTGGGTGGACAGACATGCGGGATAGAGGAAAG---------------------CCACAACAACAGTCTCTGAC -s simDog_chr6.simDog.chr6 533905 61 + 593897 ACTTGAGTTCTGCATGGGCAAACATGCTGGGCAGAAGAAAT---------------------CTACCACTTTAATTTCGGAC -s simHuman_chr6.simHuman.chr6 541459 73 + 601863 ACTTGAGTTC------AGTAAACATGCTGGATAGGGGAAGGTGGCATA---TGTTAAGATTCCTTCCACTTCACTCACAGAG -s simRat_chr6.simRat.chr6 45967 82 - 647215 ACTTGGGTTCTAGTTAGCTAAGTATGAAGCTTGGGGCACAACACCATATAGTAGTAGGATTCCTTCCACCTTGATTACAGAG - -a -s simMouse_chr6.simMouse.chr6 570725 2 + 636262 TC -s Anc0.Anc0refChr3 172431 2 + 222631 TT -s Anc1.Anc1refChr1 11343 2 + 69767 TT -s Anc2.Anc2refChr1 87680 2 + 142988 TT -s mr.mrrefChr3 120583 2 + 181027 TC -s simCow_chr6.simCow.chr6 546064 2 + 602619 TT -s simDog_chr6.simDog.chr6 533968 2 + 593897 TT -s simHuman_chr6.simHuman.chr6 541534 2 + 601863 TT -s simRat_chr6.simRat.chr6 46049 2 - 647215 TC - -a -s simMouse_chr6.simMouse.chr6 570727 28 + 636262 TCTAGATTTATACTCACGAGATAATTTC -s Anc0.Anc0refChr3 172433 28 + 222631 TCTTGCCTTATACTCACTAAATAATTCC -s Anc1.Anc1refChr1 11345 28 + 69767 TCTTGCCTTATACTCACTAAATAATTCC -s Anc2.Anc2refChr1 87682 28 + 142988 TCCTGCCTTATACTCACTAAATAATTCC -s mr.mrrefChr3 120585 28 + 181027 TCTTGACTTATACTCACGAGATAATTTC -s simCow_chr6.simCow.chr6 546066 28 + 602619 TCATGCCTTATACTCGCTAACTATTTCC -s simDog_chr6.simDog.chr6 534017 28 + 593897 TCCTGTCTTGTACTCACTGAATAATTCC -s simHuman_chr6.simHuman.chr6 541536 28 + 601863 TCTTGCCTTATACTCACTAAATAATTCC -s simRat_chr6.simRat.chr6 46051 28 - 647215 TTTTGACTTATAGTCACCAGATAGTTTC - -a -s simMouse_chr6.simMouse.chr6 570755 28 + 636262 AATAACTGCACAGCCCCAAGACATTTGC -s Anc0.Anc0refChr3 172467 25 + 222631 AATAACTGCCCAGCCATTAGACATT--- -s Anc1.Anc1refChr1 11379 25 + 69767 AATAACTGCCCAGCCATTAGACATT--- -s Anc2.Anc2refChr1 87716 25 + 142988 AATAACTGCCCAGCCATTAAACATT--- -s mr.mrrefChr3 120613 28 + 181027 AATAACTGCACAGCCCCAAGACATTTGC -s simCow_chr6.simCow.chr6 546100 25 + 602619 AATAACTGCCAAGCCATTAAGTATT--- -s simDog_chr6.simDog.chr6 534051 24 + 593897 AA-GACTGCCCAGGCATTAAACATG--- -s simHuman_chr6.simHuman.chr6 541570 25 + 601863 AATAACTGCCCAGCCATTAGTCATT--- -s simRat_chr6.simRat.chr6 46079 28 - 647215 AATAACCTTTCAGCCCCAAGACATTTGC - -a -s simMouse_chr6.simMouse.chr6 570783 17 + 636262 TTGAGAGCAATGGTCAT -s Anc0.Anc0refChr3 172492 17 + 222631 TTGAGAGTAATGGGCAT -s Anc1.Anc1refChr1 11404 17 + 69767 TTGAGAGTAATGGGCAT -s Anc2.Anc2refChr1 87741 17 + 142988 TTGAGAGTAATGGGCAT -s mr.mrrefChr3 120641 17 + 181027 TTGAGAGCAATGGTCAT -s simCow_chr6.simCow.chr6 546125 16 + 602619 TTG-GAGTAATGGTCAT -s simDog_chr6.simDog.chr6 534078 17 + 593897 TCAAATACAATGGGCAT -s simHuman_chr6.simHuman.chr6 541595 17 + 601863 TTGAGAGTAGTGGGCAT -s simRat_chr6.simRat.chr6 46107 17 - 647215 TTGAGAGAAATGGTTAT - -a -s simMouse_chr6.simMouse.chr6 570800 4 + 636262 GCAT -s Anc0.Anc0refChr3 172509 4 + 222631 GCTT -s Anc1.Anc1refChr1 11421 4 + 69767 GCTT -s Anc2.Anc2refChr1 87758 4 + 142988 GGTT -s mr.mrrefChr3 120658 4 + 181027 GCAT -s simCow_chr6.simCow.chr6 546141 4 + 602619 AGTT -s simDog_chr6.simDog.chr6 534095 4 + 593897 GGTT -s simHuman_chr6.simHuman.chr6 541612 4 + 601863 GCCT -s simRat_chr6.simRat.chr6 46125 4 - 647215 GGAT - -a -s simMouse_chr6.simMouse.chr6 570804 1 + 636262 A -s Anc0.Anc0refChr3 172519 1 + 222631 A -s Anc1.Anc1refChr1 11431 1 + 69767 A -s Anc2.Anc2refChr1 87768 1 + 142988 G -s mr.mrrefChr3 120662 1 + 181027 A -s simCow_chr6.simCow.chr6 546151 1 + 602619 G -s simDog_chr6.simDog.chr6 534105 1 + 593897 G -s simHuman_chr6.simHuman.chr6 541622 1 + 601863 A -s simRat_chr6.simRat.chr6 46129 1 - 647215 A - -a -s simMouse_chr6.simMouse.chr6 570805 9 + 636262 TATGACCAA -s Anc0.Anc0refChr3 172520 9 + 222631 TTGAACCAA -s Anc1.Anc1refChr1 11432 9 + 69767 TTGAACCAA -s Anc2.Anc2refChr1 87770 9 + 142988 TTGAACCAA -s mr.mrrefChr3 120663 9 + 181027 TTGGACCAA -s simCow_chr6.simCow.chr6 546153 9 + 602619 TTGAACCAA -s simDog_chr6.simDog.chr6 534107 9 + 593897 TTGAACCAA -s simHuman_chr6.simHuman.chr6 541623 9 + 601863 TTGTACCAA -s simRat_chr6.simRat.chr6 46130 9 - 647215 TTGGGCCAA - -a -s simMouse_chr6.simMouse.chr6 570814 32 + 636262 GTGTTTCAGCCGTAATGTATAAAAAGTTCTCC -s Anc0.Anc0refChr3 172529 32 + 222631 GTGTTTCCACCCTAAGATGCAGAGAAATCCCC -s Anc1.Anc1refChr1 11441 32 + 69767 GTGTTTCCACCCTAAGATGCAGAGAAATCCCC -s Anc2.Anc2refChr1 87779 32 + 142988 AAGTTTCCACCCTAAGATGCAGAGAAATGCCC -s mr.mrrefChr3 120672 32 + 181027 GTGTTTCAGCCCTAAGGTGTAGAAAATTCTCC -s simCow_chr6.simCow.chr6 546162 32 + 602619 ATGTTTCCACCCGAAGATGCAGAGAGATGTCC -s simDog_chr6.simDog.chr6 534116 32 + 593897 AAGTTTCCATCCTAATATGCATAGAAATGCCC -s simHuman_chr6.simHuman.chr6 541633 32 + 601863 GTGTTTCCACCCTAAGATGCAGAGAAATCCCC -s simRat_chr6.simRat.chr6 46139 32 - 647215 GTTTTTCAGCCCTAAGGTGTAGAAAATTCTCC - -a -s simMouse_chr6.simMouse.chr6 570846 4 + 636262 CCAT -s Anc0.Anc0refChr3 172562 4 + 222631 CCAT -s Anc1.Anc1refChr1 11474 4 + 69767 CCAT -s Anc2.Anc2refChr1 87812 4 + 142988 CCAT -s mr.mrrefChr3 120704 4 + 181027 CCAT -s simCow_chr6.simCow.chr6 546195 4 + 602619 CCAT -s simDog_chr6.simDog.chr6 534149 4 + 593897 CCAT -s simHuman_chr6.simHuman.chr6 541666 4 + 601863 CCAT -s simRat_chr6.simRat.chr6 46171 4 - 647215 CCAT - -a -s simMouse_chr6.simMouse.chr6 570850 34 + 636262 GAATAATGCTTCCCACAACACATTAGCAATCAAT -s Anc0.Anc0refChr3 172566 34 + 222631 GACCAATGCCCCTCCCAACACAGTAGATACCAAT -s Anc1.Anc1refChr1 11478 34 + 69767 GACCAATGCCCCTCCCAACACAGTAGATACCAAT -s Anc2.Anc2refChr1 87816 34 + 142988 GACCGATGCCAACCCCAACACAGTAGATACCAAT -s mr.mrrefChr3 120708 34 + 181027 GAATAATGCTCCTCCCAACACATTAGCAATCAAT -s simCow_chr6.simCow.chr6 546199 34 + 602619 GGCCGAGGGGCAATCCAACACAGTAAATACCTAC -s simDog_chr6.simDog.chr6 534153 34 + 593897 TATCGATGCCACCCCCAACATAGTAGATGCCAAT -s simHuman_chr6.simHuman.chr6 541680 34 + 601863 GACCAATGACCCTTCCAACACAGTAGATACCAAT -s simRat_chr6.simRat.chr6 46175 34 - 647215 GAATAATGCTCCTCCCAACACATTAACAATCAAT - -a -s simMouse_chr6.simMouse.chr6 570884 13 + 636262 GCAGATGACACAA -s Anc0.Anc0refChr3 172603 13 + 222631 GTGGATGACACAA -s Anc1.Anc1refChr1 11515 13 + 69767 GTGGATGACACAA -s Anc2.Anc2refChr1 87853 13 + 142988 GTGGATGACCCAG -s mr.mrrefChr3 120742 13 + 181027 GTGGATGACACAA -s simCow_chr6.simCow.chr6 546236 13 + 602619 GTGGATGATCCAG -s simDog_chr6.simDog.chr6 534190 12 + 593897 GTAGATGACCCA- -s simHuman_chr6.simHuman.chr6 541717 13 + 601863 GTGGATGCCACAA -s simRat_chr6.simRat.chr6 46209 13 - 647215 GTGGGTGATACAA - -a -s simMouse_chr6.simMouse.chr6 570897 23 + 636262 CCTGCTGGATAAAACAACCAAAT -s Anc0.Anc0refChr3 172743 18 + 222631 CCTGCT----AAAGAAACCCA-T -s Anc1.Anc1refChr1 11665 18 + 69767 CCTGCT----AAAGAAACCCA-T -s Anc2.Anc2refChr1 87993 18 + 142988 CCTGCT----ACAGAAACCCA-T -s mr.mrrefChr3 120890 22 + 181027 CCTGCTGGATAAAGCAACCAA-T -s simCow_chr6.simCow.chr6 546359 18 + 602619 CCTGCT----ACAGAGACCCA-T -s simDog_chr6.simDog.chr6 534304 18 + 593897 CCTGCT----ACAGAAACCCA-T -s simHuman_chr6.simHuman.chr6 541867 18 + 601863 CCTGCT----AAAGAAACCTA-T -s simRat_chr6.simRat.chr6 46420 22 - 647215 CCTGCTGGATAAGGCAACCAA-T - -a -s simMouse_chr6.simMouse.chr6 570920 18 + 636262 TAACTTTTTAAAAATAGT -s Anc0.Anc0refChr3 172771 18 + 222631 TTATCTTTTTGAGACAGG -s Anc1.Anc1refChr1 11693 18 + 69767 TTATCTTTTTGAGACAGG -s Anc2.Anc2refChr1 88021 18 + 142988 TTATCTTTTTGAGAAAGG -s mr.mrrefChr3 120912 18 + 181027 TAACCTTTTAAAAACAGT -s simCow_chr6.simCow.chr6 546387 18 + 602619 TCATCTTATTGTGAGAGA -s simDog_chr6.simDog.chr6 534332 18 + 593897 CTATCTTTATGAAAAAGG -s simHuman_chr6.simHuman.chr6 541895 17 + 601863 TTATCTTTTTGAGAC-GA -s simRat_chr6.simRat.chr6 46442 18 - 647215 TAACCTTTTAAAAACAGT - -a -s simMouse_chr6.simMouse.chr6 570938 37 + 636262 GTATTATGGGATATCTAATGGTGAGGACCTAGCCAAA -s Anc0.Anc0refChr3 172789 37 + 222631 GTCTTATAAAACATCTAATGGCAAGCTCATAGCCAAA -s Anc1.Anc1refChr1 11711 37 + 69767 GTCTTATAAAACATCTAATGGCAAGCTCATAGCCAAA -s Anc2.Anc2refChr1 88055 37 + 142988 GTCTTATAAAACATCTAATGGCAAGCTCATAGCCAAA -s mr.mrrefChr3 120930 37 + 181027 GTCTTATGGGATATCTAATGGTGAGGACCTAGCCAAA -s simCow_chr6.simCow.chr6 546426 31 + 602619 GT---ATTAAGCATCTAATGATGAGCACA---CCAGA -s simDog_chr6.simDog.chr6 534366 37 + 593897 GTCTTATAAAAGATCGAATGGCAAGCTTATAGCCAAA -s simHuman_chr6.simHuman.chr6 541912 37 + 601863 CCCTTATAAATCATCTAATGGCAAGCTCATAGCCATA -s simRat_chr6.simRat.chr6 46460 37 - 647215 TTCTTATGGGATATTTAATGGTGAGGGCCTGGCCAAA - -a -s simMouse_chr6.simMouse.chr6 570975 50 + 636262 CCCATATATAATAGGCAACATCCCACTCTACAATTACATCAATCCCCCTG -s Anc0.Anc0refChr3 172826 50 + 222631 CTGATGTAAAATGGGTAGCATTCCAGTCCACAAATACATCACTTCTCCAT -s Anc1.Anc1refChr1 11748 50 + 69767 CTGATGTAAAATGGGTAGCATTCCAGTCCACAAATACATCACTTCTCCAT -s Anc2.Anc2refChr1 88092 50 + 142988 CTGCTGTATAGTGGGTAGCATTCCAGTCCAAAAATACATCACTTCTCCAT -s mr.mrrefChr3 120967 50 + 181027 CCCATATAAAATAGGCAACATTCCACTCCACAATTACATCAATTCTCCTG -s simCow_chr6.simCow.chr6 546457 47 + 602619 TTGCTGTATAG---GTAGCATTCCAGTCCATAAACACTTCACTTCTCCAT -s simDog_chr6.simDog.chr6 534416 50 + 593897 CTGCTGTATAGTGGGCAGCATACCAGTCTGAAAATACAACACTTCTCTAT -s simHuman_chr6.simHuman.chr6 541949 50 + 601863 CTGATGTAAAATGGGTAGTATTCCAGTCCACAACTACATTATTTCTCCAC -s simRat_chr6.simRat.chr6 46497 50 - 647215 CCCATATAAAATAGGCAACATTCCACTCCACAGATACATCACTTCTCCTG - -a -s simMouse_chr6.simMouse.chr6 571025 5 + 636262 ACACA -s Anc0.Anc0refChr3 172876 5 + 222631 ATACA -s Anc1.Anc1refChr1 11798 5 + 69767 ATACA -s Anc2.Anc2refChr1 88142 5 + 142988 ATATA -s mr.mrrefChr3 121017 5 + 181027 ACACA -s simCow_chr6.simCow.chr6 546504 5 + 602619 ATATA -s simDog_chr6.simDog.chr6 534473 5 + 593897 ATATA -s simHuman_chr6.simHuman.chr6 541999 5 + 601863 GGACA -s simRat_chr6.simRat.chr6 46547 5 - 647215 ACACA - -a -s simMouse_chr6.simMouse.chr6 571030 19 + 636262 CTGCAGCATGGTCCCTAGA -s Anc0.Anc0refChr3 172881 19 + 222631 CACCAGCTACATCCCAGTG -s Anc1.Anc1refChr1 11803 19 + 69767 CACCAGCTACATCCCAGTG -s Anc2.Anc2refChr1 88152 19 + 142988 CACTCACTACAGCCCACTG -s mr.mrrefChr3 121022 19 + 181027 CTGCAGCATGGTCCCTGGG -s simCow_chr6.simCow.chr6 546514 14 + 602619 CAC-----ACACCCCACTG -s simDog_chr6.simDog.chr6 534483 19 + 593897 CACTCACTACAGCGAGCAA -s simHuman_chr6.simHuman.chr6 542004 19 + 601863 TCCCAGCGACATCCCAGTG -s simRat_chr6.simRat.chr6 46552 19 - 647215 CTGCAGCATAGTCCCTGGG - -a -s simMouse_chr6.simMouse.chr6 571049 33 + 636262 TGCAGGTTCATAAGGTATAATCTCTCCAGTGTA -s Anc0.Anc0refChr3 172907 33 + 222631 TGCAAGTTCATAAGGAGTAATCTCTCCATAGTA -s Anc1.Anc1refChr1 11829 33 + 69767 TGCAAGTTCATAAGGAGTAATCTCTCCATAGTA -s Anc2.Anc2refChr1 88178 33 + 142988 TGTAAATTCATAATGAGTAATCTCTCCATAGGA -s mr.mrrefChr3 121041 33 + 181027 TGCAAGTTCATAAGGTATAATCTCTCCATAGTA -s simCow_chr6.simCow.chr6 546535 33 + 602619 TAGCCACGCATAATGTGTAGTGTCTCCATAGGA -s simDog_chr6.simDog.chr6 534509 33 + 593897 TGTAAATTCATAATGAGTCATCTCTCCAAAGGA -s simHuman_chr6.simHuman.chr6 542030 33 + 601863 TGCAAGTTCTCAAGGGGCAATCTCTCCATAGTA -s simRat_chr6.simRat.chr6 46571 33 - 647215 TCCAAGTTCATAAGGTATAATGTCTCCATAGGA - -a -s simMouse_chr6.simMouse.chr6 571082 27 + 636262 GAATAAATGGAATGAGTGCCTCCAATG -s Anc0.Anc0refChr3 172947 27 + 222631 TAATAAATGGACCAGGTGCTTCTGATG -s Anc1.Anc1refChr1 11869 27 + 69767 TAATAAATGGACCAGGTGCTTCTGATG -s Anc2.Anc2refChr1 88224 27 + 142988 TGGTAAATGGACCAGGTGCTTCTGATG -s mr.mrrefChr3 121081 27 + 181027 GAATAAATGGAATGGGTGCCTCCAATG -s simCow_chr6.simCow.chr6 546582 27 + 602619 TGCTGAATGGATCAGGAACATGTGATG -s simDog_chr6.simDog.chr6 534555 25 + 593897 TGGTAGATGGACCAGGTGCTTC--ATG -s simHuman_chr6.simHuman.chr6 542070 27 + 601863 TAATAAGTGGACCAGGTGCTTCTGATG -s simRat_chr6.simRat.chr6 46616 27 - 647215 GATTAAATGGAATGGGTGCCTCCAACG - -a -s simMouse_chr6.simMouse.chr6 571109 55 + 636262 AACATGAACAACAAAGATACATACTAGGAGCAAAGGAAAACATCCATTATGCTGA -s Anc0.Anc0refChr3 172984 55 + 222631 ATCATACAGAACAAAGATCTATCCTAGAAGAAAAGAAAAACATTCATTCTGCAGA -s Anc1.Anc1refChr1 11906 55 + 69767 ATCATACAGAACAAAGATCTATCCTAGAAGAAAAGAAAAACATTCATTCTGCAGA -s Anc2.Anc2refChr1 88261 55 + 142988 ATCATACAGAATGAAGATCTGTCCTAGAAGAAAAGAAAAACATTCATTCTGCAGA -s mr.mrrefChr3 121108 55 + 181027 AACATAAACAACAAAGATACATACTAGGAGCAAAGGAAAACATCCATTATGCTGA -s simCow_chr6.simCow.chr6 546619 55 + 602619 ATCATACAGAATGAAGACCTGTCCTAGAAGAAAAGAACAACATTTATTCCACTGG -s simDog_chr6.simDog.chr6 534590 36 + 593897 ATCATACAGGATGAAGAT-------------------AAACATTCATACTGCAGA -s simHuman_chr6.simHuman.chr6 542107 55 + 601863 ATCATACATAACAAAGATCGATCCTAGAAATAAAGAAAAACATTCATTTGGTGGA -s simRat_chr6.simRat.chr6 46643 55 - 647215 AACATAAACAACAAAGATACATACTAGGAGAAAAGGAAAACATCCATCATGCTGA - -a -s simMouse_chr6.simMouse.chr6 571164 20 + 636262 TCAGATCCTACTTCTGATTT -s Anc0.Anc0refChr3 173057 20 + 222631 TCTGGTCTTACTTCTGATCT -s Anc1.Anc1refChr1 11979 20 + 69767 TCTGGTCTTACTTCTGATCT -s Anc2.Anc2refChr1 88334 20 + 142988 TCTTGTCTTACTGCTGATCT -s mr.mrrefChr3 121163 20 + 181027 TCAGATCCTACTTCTGATTT -s simCow_chr6.simCow.chr6 546692 20 + 602619 TCTTGTCTTACTCCTGATCT -s simDog_chr6.simDog.chr6 534644 12 + 593897 T--------ACTGCTGATCT -s simHuman_chr6.simHuman.chr6 542180 20 + 601863 TCTGGTCTTACTTCTGATCT -s simRat_chr6.simRat.chr6 46698 20 - 647215 TTACATCCCGCTTCTGATTT - -a -s simMouse_chr6.simMouse.chr6 571184 20 + 636262 TGCACTGCTCTTTTGATTTG -s Anc0.Anc0refChr3 173077 20 + 222631 GGAGATCCTCTTTTGATTTG -s Anc1.Anc1refChr1 11999 20 + 69767 GGAGATCCTCTTTTGATTTG -s Anc2.Anc2refChr1 88354 20 + 142988 GGAGATCCTCTTTTGATTTG -s mr.mrrefChr3 121183 20 + 181027 TGCACTGCTCTTTTGATTTG -s simCow_chr6.simCow.chr6 546720 20 + 602619 GGAGACCCTCTTTTGAATTG -s simDog_chr6.simDog.chr6 534656 20 + 593897 GGAGATCCTCTCTTGCTTTG -s simHuman_chr6.simHuman.chr6 542200 20 + 601863 GGAGGTCCTCTTTTAATTTG -s simRat_chr6.simRat.chr6 46718 20 - 647215 TGCATCGCTCTTTTGATTTG - -a -s simMouse_chr6.simMouse.chr6 571204 13 + 636262 CTTTTTAGGCTAT -s Anc0.Anc0refChr3 173097 13 + 222631 CTGTTTGGGCTGT -s Anc1.Anc1refChr1 12019 13 + 69767 CTGTTTGGGCTGT -s Anc2.Anc2refChr1 88374 13 + 142988 CTGTTTGGGCTGT -s mr.mrrefChr3 121203 13 + 181027 CTGTTTAGGCTAT -s simCow_chr6.simCow.chr6 546740 13 + 602619 CTGTTTGGGCTGT -s simDog_chr6.simDog.chr6 534676 13 + 593897 CTGTTTGGACAGT -s simHuman_chr6.simHuman.chr6 542221 13 + 601863 CTGTTTGGGCTGT -s simRat_chr6.simRat.chr6 46738 13 - 647215 CTGCTTAGGCTAT - -a -s simMouse_chr6.simMouse.chr6 571217 7 + 636262 GCTGTTA -s Anc0.Anc0refChr3 173116 7 + 222631 GCTGTGA -s Anc1.Anc1refChr1 12038 7 + 69767 GCTGTGA -s Anc2.Anc2refChr1 88393 7 + 142988 GCTGCGA -s mr.mrrefChr3 121216 7 + 181027 GCTGTTA -s simCow_chr6.simCow.chr6 546759 6 + 602619 -CTGCGA -s simDog_chr6.simDog.chr6 534695 6 + 593897 GA-GCAA -s simHuman_chr6.simHuman.chr6 542240 7 + 601863 ACTGTGA -s simRat_chr6.simRat.chr6 46751 7 - 647215 GATGTTT - -a -s simMouse_chr6.simMouse.chr6 571224 73 + 636262 GGGAGTCCTTATTCTGCATGAAGTTGTGAGCCATAATGTGGCTTCTTACTGAATCTAGTTATACATACACACC -s Anc0.Anc0refChr3 173123 54 + 222631 G----------CTCAGTATGGTATTGTGAGTCACAATGTGGCATCTTTTTGTAACTGACTTTAT--------- -s Anc1.Anc1refChr1 12045 54 + 69767 G----------CTCAGTATGGTATTGTGAGTCACAATGTGGCATCTTTTTGTAACTGACTTTAT--------- -s Anc2.Anc2refChr1 88400 54 + 142988 G----------CTAAGTGTGGTATCGTGAGTCACAATGAGGTATCTTTTTGTAACTGACTTTAT--------- -s mr.mrrefChr3 121223 73 + 181027 GGGAGTCCTTATTCTGCATGAAATTGTGAGCCATAATGTGGCTTCTTACTGAATCTAGTTATATATACACACC -s simCow_chr6.simCow.chr6 546765 53 + 602619 G-----------TGATAGTGGTATAGTGAGTCACAATGAGGTATGTATTTGTGACTGGCTTTAT--------- -s simDog_chr6.simDog.chr6 534701 54 + 593897 G----------CAAGGTGTGATGTCATGAGCCACAATGAGGTATCTTCTTCTAACTGACTTTAT--------- -s simHuman_chr6.simHuman.chr6 542247 54 + 601863 G----------CTCAGTATGGTATTGTGAGTCACAATGTGGCAGCTTTTTGTAACTGACTTTAT--------- -s simRat_chr6.simRat.chr6 46763 73 - 647215 GGGAGTCCTTATTCTGCATGAAATTGTGAGCCATAATGTGACTTCATACTAAATCTAGTTATATTTATACACC - -a -s simMouse_chr6.simMouse.chr6 571297 58 + 636262 TTGCAGAGCTATGAAGATAGGTTGTGGATATACACACCTTGCAGAGCTATGAAGATAG -s Anc0.Anc0refChr3 173177 32 + 222631 ------C------------------AGATATACACACATTGCTA--GTATAAAGATAG -s Anc1.Anc1refChr1 12099 32 + 69767 ------C------------------AGATATACACACATTGCTA--GTATAAAGATAG -s Anc2.Anc2refChr1 88455 32 + 142988 ------C------------------ATATATACACACATCTCTA--GTATAAAGATAA -s mr.mrrefChr3 121296 38 + 181027 TTGCAGA------------------GGATATACACACCTTGCAG--CTATGAAGATAG -s simCow_chr6.simCow.chr6 546819 22 + 602619 ------C------------------ATATAT----------CTG--GTTTAAAGATAA -s simDog_chr6.simDog.chr6 534756 32 + 593897 ------C------------------ATATATACACACATCTCTA--GTATAGAAATAA -s simHuman_chr6.simHuman.chr6 542301 32 + 601863 ------C------------------AGATAAACACGCATTGATA--ATATAAAGATGG -s simRat_chr6.simRat.chr6 46837 29 - 647215 TTGCAGC---------------------------TACCTTGCAG--CTCTCAAGATAG - -a -s simMouse_chr6.simMouse.chr6 571355 18 + 636262 GTTGTGGTAATATGTTAG -s Anc0.Anc0refChr3 173212 18 + 222631 GTTGTGGTAATGTGTGAG -s Anc1.Anc1refChr1 12134 18 + 69767 GTTGTGGTAATGTGTGAG -s Anc2.Anc2refChr1 88490 18 + 142988 GTTGTGGTACTGTGTGAG -s mr.mrrefChr3 121337 18 + 181027 GTTGTGGTAATATGTTAG -s simCow_chr6.simCow.chr6 546841 9 + 602619 ---------CTGTGTGAG -s simDog_chr6.simDog.chr6 534791 18 + 593897 GTTGTGGTACTGGGTGGG -s simHuman_chr6.simHuman.chr6 542336 18 + 601863 GTTGTGGTAATGTGTAAG -s simRat_chr6.simRat.chr6 46869 18 - 647215 GTTGTGGTGATATGTTAA - -a -s simMouse_chr6.simMouse.chr6 571373 91 + 636262 TCACAATGTGCTCTACTACTCCTAGCTGACTTTTGATTTCACTTTAATAAATATGTACACCTTTGGTATAGAGGTTTGTGCTTTCTGTTGC -s Anc0.Anc0refChr3 173230 72 + 222631 CCACAAGATGGGAT-CTTCTTCTATCTG-CCTTTA--------TTCATAA---------TCTCTGGTATGTAGTTAGATAGTTTCTGTTGC -s Anc1.Anc1refChr1 12152 81 + 69767 CCACAAGATGGGAT-CTTCTTCTATCTG-CCTTTA--------TTCATAAATATGCACCTCTCTGGTATGTAGTTAGATAGTTTCTGTTGC -s Anc2.Anc2refChr1 88508 72 + 142988 CCACAAGATGGGAT-CTTCTTCTATCTG-ACTTTA--------TTCATTA---------TCTCTGGTATGTAGTTAGATAGTTCCTGTTGC -s mr.mrrefChr3 121355 90 + 181027 CCACAATGTGGTCTACTACTCCTAGCTG-CTTTTGATTTCACTTTAATAAATATGCACACCTTTGGTATAGAGGTATGTGCTTTCTGTTGC -s simCow_chr6.simCow.chr6 546850 69 + 602619 CCACAATGTGGTAA-CTTCTTCTATCTG-ACT--A--------TCCATGG----------CTCTGGTATGAGGTCAGATAGTTCGTGTTGC -s simDog_chr6.simDog.chr6 534907 69 + 593897 CCGTGTGAGGAGGT-TATCTCCCA---G-ACTTTA--------TTTATTA---------TATCTGGTATTTAGTTAGATTGTTCCTGTGGC -s simHuman_chr6.simHuman.chr6 542354 81 + 601863 CCACAACATGGGAT-CTTCTTCTAATTG-CCTTTA--------TTCATAAATATGCACCTCTCTGGTATGTCGTTAGATAGTTTCTGCTGC -s simRat_chr6.simRat.chr6 46887 90 - 647215 CCACTATGTGGTCTACCACTCCTGGCCA-CTTTTGATTTTACTTTAATAAATATGCACACCTTTGATATAGAGGTATGTGCTTTTTGTTGC - -a -s simMouse_chr6.simMouse.chr6 571464 48 + 636262 CCCTTAGGGGAGTGCTCTTTCTTTTAGGGAGTACTCCTTTCTGCTTTC -s Anc0.Anc0refChr3 173303 34 + 222631 CCCTTACCAGGGCA-----------GGGGAGTACTATTTTCTGCT--- -s Anc1.Anc1refChr1 12234 34 + 69767 CCCTTACCAGGGCA-----------GGGGAGTACTATTTTCTGCT--- -s Anc2.Anc2refChr1 88581 34 + 142988 CGCATACCAGGGCA-----------GACGATCCCTATTCTATGCT--- -s mr.mrrefChr3 121445 44 + 181027 CCCTTAGGGGAGTACTCTTT----TGGGGAGTACTCCTTTCTGCTTTC -s simCow_chr6.simCow.chr6 546920 15 + 602619 TTCAATCCAGGGTG-----------C---------------------- -s simDog_chr6.simDog.chr6 534977 34 + 593897 CGCATACCAGGGCA-----------GACGATCCCTATTCTATGCT--- -s simHuman_chr6.simHuman.chr6 542436 34 + 601863 CCCTTACCAGGTCA-----------GGGGAGTACTATTTTCTGCT--- -s simRat_chr6.simRat.chr6 46977 44 - 647215 CCCGTAGGGGAGTACTCTTT----TGGGGAGTACTCCTCTCTGCTTTC - -a -s simMouse_chr6.simMouse.chr6 571512 15 + 636262 GTCCTCATACTCCAA -s Anc0.Anc0refChr3 173337 15 + 222631 GTCATGATACTCAGA -s Anc1.Anc1refChr1 12268 15 + 69767 GTCATGATACTCAGA -s Anc2.Anc2refChr1 88615 15 + 142988 GTCATGACACTTAGA -s mr.mrrefChr3 121489 15 + 181027 GTCATCATACTCCAA -s simCow_chr6.simCow.chr6 546935 12 + 602619 ---ATGACACTTAGA -s simDog_chr6.simDog.chr6 535011 5 + 593897 GTCAT---------- -s simHuman_chr6.simHuman.chr6 542470 15 + 601863 GTCATGATACTCAGA -s simRat_chr6.simRat.chr6 47024 15 - 647215 GTCATCATACTCCAA - -a -s simMouse_chr6.simMouse.chr6 571527 7 + 636262 TCATTGC -s Anc0.Anc0refChr3 173352 7 + 222631 TAACTGC -s Anc1.Anc1refChr1 12283 7 + 69767 TAACTGC -s Anc2.Anc2refChr1 88630 7 + 142988 TAACTGG -s mr.mrrefChr3 121504 7 + 181027 TCATTGC -s simCow_chr6.simCow.chr6 546947 7 + 602619 TAACTGG -s simHuman_chr6.simHuman.chr6 542485 7 + 601863 TGACTGC -s simRat_chr6.simRat.chr6 47040 7 - 647215 TCATTGC - -a -s simMouse_chr6.simMouse.chr6 571534 9 + 636262 ACTCAGTTA -s Anc0.Anc0refChr3 173382 9 + 222631 ACCAAATTA -s Anc1.Anc1refChr1 12313 9 + 69767 ACCAAATTA -s Anc2.Anc2refChr1 88660 9 + 142988 ACCAAATTA -s mr.mrrefChr3 121511 9 + 181027 ACTAAGTTA -s simCow_chr6.simCow.chr6 546981 9 + 602619 ACTAAATTA -s simDog_chr6.simDog.chr6 535035 9 + 593897 TCCAAATTA -s simHuman_chr6.simHuman.chr6 542515 9 + 601863 ACCAAATTA -s simRat_chr6.simRat.chr6 47047 9 - 647215 ACTAGGCTA - -a -s simMouse_chr6.simMouse.chr6 571543 23 + 636262 AGTGAAGGTGTGAGTGACTGAAC -s Anc0.Anc0refChr3 173391 23 + 222631 ATCCAAGGTGTTGGAGACATGAC -s Anc1.Anc1refChr1 12322 23 + 69767 ATCCAAGGTGTTGGAGACATGAC -s Anc2.Anc2refChr1 88669 23 + 142988 ATCCAAGCTCTTGGAGACATGAA -s mr.mrrefChr3 121520 23 + 181027 AGCGAAGGTGTGAGAGACTGAAC -s simCow_chr6.simCow.chr6 547046 23 + 602619 GTCAAAGATATAAGAGACACGAA -s simDog_chr6.simDog.chr6 535044 23 + 593897 ATCCAATCTCTTGAACACATGAA -s simHuman_chr6.simHuman.chr6 542524 23 + 601863 ATCTAGGGTGTTGGAGACCTGAC -s simRat_chr6.simRat.chr6 47056 23 - 647215 AGCAAAGATGTGAGAGACTGAAC - -a -s simMouse_chr6.simMouse.chr6 571566 19 + 636262 ATGGATGTATAGGACATAG -s Anc0.Anc0refChr3 173418 19 + 222631 AAGCATGCATGGGTCATGG -s Anc1.Anc1refChr1 12349 19 + 69767 AAGCATGCATGGGTCATGG -s Anc2.Anc2refChr1 88696 19 + 142988 AAGCATGCATGGGTCATGG -s mr.mrrefChr3 121543 19 + 181027 ATGGATGTATAGGTCATAG -s simCow_chr6.simCow.chr6 547073 19 + 602619 AAGGGTGCATGGGTGATGG -s simDog_chr6.simDog.chr6 535071 18 + 593897 AAGCATGTATGG-TCATGG -s simHuman_chr6.simHuman.chr6 542551 19 + 601863 AAGCATGCATGGGTCATCA -s simRat_chr6.simRat.chr6 47079 19 - 647215 ATGGGTGTATAGGTCATAG - -a -s simMouse_chr6.simMouse.chr6 571585 32 + 636262 ATTTGAGGCATTCCACCGCAAAGGATAAGGAC -s Anc0.Anc0refChr3 173437 29 + 222631 ACTAAAGGCACT---CCACGGAAGCACAGGGG -s Anc1.Anc1refChr1 12368 29 + 69767 ACTAAAGGCACT---CCACGGAAGCACAGGGG -s Anc2.Anc2refChr1 88715 29 + 142988 ACTAAAAGCAAT---CCACTGAAGCACAGGGG -s mr.mrrefChr3 121562 32 + 181027 ATTAGAGGCACTCCACCACGAAGGATAAGGAC -s simCow_chr6.simCow.chr6 547092 29 + 602619 ACTAGATGCATT---CCACTAAAGCACAGGGG -s simDog_chr6.simDog.chr6 535089 29 + 593897 ACTAAAAGCAAT---CCACTGAAGCACAGGGG -s simHuman_chr6.simHuman.chr6 542579 29 + 601863 ACTAAAGGCACT---TCACGGAATGAGAGGGG -s simRat_chr6.simRat.chr6 47098 32 - 647215 ATCAGAAGCACTCCACCATGAAGGATAAGGAC - -a -s simMouse_chr6.simMouse.chr6 571617 51 + 636262 AGCTGGTGTGATAGCTGCATATGTGACCAGAGGATCTCTGCCCCTTGATCC -s Anc0.Anc0refChr3 173466 14 + 222631 ACCTGGTGTGGTAG------------------------------------- -s Anc1.Anc1refChr1 12397 51 + 69767 ACCTGGTGTGGTAGCGGTGGATTTGATTAGAGGAACTCAGCCCCCCAATTC -s Anc2.Anc2refChr1 88745 14 + 142988 ACCTGGTATGGAAG------------------------------------- -s mr.mrrefChr3 121594 51 + 181027 AGCTGGTGTGATAGCTGCAGATGTGACCAGAGGATCTCTGCCCCTTGATCC -s simCow_chr6.simCow.chr6 547122 14 + 602619 ACCCCATATGGGAG------------------------------------- -s simDog_chr6.simDog.chr6 535119 14 + 593897 ACCTGGTATGGAAG------------------------------------- -s simHuman_chr6.simHuman.chr6 542608 51 + 601863 CCCTAGTGTAGTAGCGGTGGATTTGATTAGAGGAACTCAGCCCCCCAATTC -s simRat_chr6.simRat.chr6 47130 51 - 647215 AGCTGGCATGAGTGCTACAGATGTGACCAGAGGAGCCCTCCCCCTTGATCC - -a -s simMouse_chr6.simMouse.chr6 571668 11 + 636262 TGTGCTGAAGC -s Anc0.Anc0refChr3 173480 11 + 222631 TGTGCTGAATC -s Anc1.Anc1refChr1 12448 11 + 69767 TGTGCTGAATC -s Anc2.Anc2refChr1 88759 11 + 142988 TGTAATGAATC -s mr.mrrefChr3 121645 11 + 181027 TGTGCTGAAGC -s simCow_chr6.simCow.chr6 547136 11 + 602619 TGCAATGAATC -s simDog_chr6.simDog.chr6 535141 11 + 593897 TGTAATGAATC -s simHuman_chr6.simHuman.chr6 542659 11 + 601863 TGTGCTGAACC -s simRat_chr6.simRat.chr6 47181 11 - 647215 TGTGCTGAAGC - -a -s simMouse_chr6.simMouse.chr6 571679 12 + 636262 AACTGCTGAATC -s Anc0.Anc0refChr3 173491 12 + 222631 AATTTCTAAATA -s Anc1.Anc1refChr1 12459 12 + 69767 AATTTCTAAATA -s Anc2.Anc2refChr1 88770 12 + 142988 AGTATCGATGGA -s mr.mrrefChr3 121656 12 + 181027 AACTGCTGAATA -s simDog_chr6.simDog.chr6 535294 12 + 593897 AGTATCGATGGA -s simHuman_chr6.simHuman.chr6 542670 12 + 601863 AATTCCTAAATA -s simRat_chr6.simRat.chr6 47192 12 - 647215 ATCTGCGGAATA - -a -s simMouse_chr6.simMouse.chr6 571691 15 + 636262 AGATGGCATGCTCAG -s Anc0.Anc0refChr3 173503 12 + 222631 AGATAGCATGCT--- -s Anc1.Anc1refChr1 12471 15 + 69767 AGATAGCATGCTCAG -s Anc2.Anc2refChr1 88782 12 + 142988 GGAAAGTATTCT--- -s mr.mrrefChr3 121668 15 + 181027 AGATAGCATGCTCAG -s simDog_chr6.simDog.chr6 535306 12 + 593897 GGAAAGTATTCT--- -s simHuman_chr6.simHuman.chr6 542694 15 + 601863 AAGTAGCACGCTCAG -s simRat_chr6.simRat.chr6 47204 12 - 647215 AGATAGCATGCT--- - -a -s simMouse_chr6.simMouse.chr6 571706 12 + 636262 TAAGGTGTTACT -s Anc1.Anc1refChr1 12486 9 + 69767 T---GCCTTACT -s mr.mrrefChr3 121683 9 + 181027 T---GTGTTACT -s simHuman_chr6.simHuman.chr6 542712 9 + 601863 T---GCCTTACT -s simRat_chr6.simRat.chr6 47216 8 - 647215 ----GTACTACT - -a -s simMouse_chr6.simMouse.chr6 571718 158 + 636262 ATAGTGCAAGCACTTACAGTCCCCATGGGACTCATTATCAAAGGCCACACCCTGTACATTTGAGTACCTATACATTAACCTGTGAAGTTTTGATGGTAATTAATGTATTCATAGAGATATAGATCTCAATGACTAATATGACTCTGATTGTAGTTTGT -s Anc0.Anc0refChr3 173515 48 + 222631 --------------------------------------------------------------------------------------------------------------ATAGATATATTGGTTTCAATCATGAAGATGCCTCTGATTGCAATTTGT -s Anc1.Anc1refChr1 12495 62 + 69767 ATGGTGCCTGTA------------------------------------------------------------------------------------------------CAATAGATATATTGGTTTCAATCATGAAGATGCCTCTGATTGCAATTTGT -s Anc2.Anc2refChr1 88794 48 + 142988 --------------------------------------------------------------------------------------------------------------ATAGATATATTGGCTTTTATCATGAAGATGTCTCTGATTGCAAGTTGT -s mr.mrrefChr3 121692 158 + 181027 ATAGTGCAAGCACTTACAGTCCCCATGGGACTCATTATCAAAGGCCACACCCTGTACATTTGAGTACCCATACATTAACATGTGATGTTTTTATGGTAATTAATGTATCCATAGAGATATAGATCTCAATGACTAAGATGCCTCTGATTGTAGTTTGT -s simDog_chr6.simDog.chr6 535318 48 + 593897 --------------------------------------------------------------------------------------------------------------ATAGATATATTGGCTTTTATCATGAAGATGTCTCTGATTGCAAGTTGT -s simHuman_chr6.simHuman.chr6 542723 62 + 601863 ATGGTGCCTGTA------------------------------------------------------------------------------------------------CAATATGCATATGGGTTTCAATCATGAAGATGCCTCTGATAGCAATATGT -s simRat_chr6.simRat.chr6 47224 158 - 647215 ATAGGGGAGGCAATTACAGACCCCATGGGACTTATCATCAAGGGCCACCCCCTGTACATTTGTACAGCCATACATTAACATGTGATGTTTTTATGGTAATTAATGTATCCATAGAGATATTGATGTCAACGACTGAGATGCCTCTGATTGTCGTGTGT - -a -s simMouse_chr6.simMouse.chr6 571876 23 + 636262 TTGATGCATCATATCAAAGAAAT -s Anc1.Anc1refChr1 12567 23 + 69767 TAAGTGAGTAACTGAGAAGTAAT -s mr.mrrefChr3 121850 23 + 181027 TTGGTGCATCATTTCAAAGAAAT -s simHuman_chr6.simHuman.chr6 542825 23 + 601863 TAAGTGAGTAACTGAGAAGTAAT -s simRat_chr6.simRat.chr6 47382 23 - 647215 TTGGTCCATCATTCCAAAGAAGT - -a -s simMouse_chr6.simMouse.chr6 571899 14 + 636262 CAGAGTGCTGGTAA -s Anc1.Anc1refChr1 12590 14 + 69767 CAGAGTTCTGGTGA -s mr.mrrefChr3 121873 14 + 181027 CAGAGTGCTGGTAA -s simHuman_chr6.simHuman.chr6 542851 14 + 601863 CAGAGTTCTGGTGA -s simRat_chr6.simRat.chr6 47405 14 - 647215 CAGATTGCTGGTAA - -a -s simMouse_chr6.simMouse.chr6 571913 17 + 636262 TAGATGACCATCCTTGA -s Anc0.Anc0refChr3 173573 11 + 222631 ------ACCATCCTTTG -s Anc1.Anc1refChr1 12604 17 + 69767 TAGACTACCATCCTTTG -s Anc2.Anc2refChr1 88852 11 + 142988 ------ACCATCTTTTG -s mr.mrrefChr3 121887 17 + 181027 TAGATGACCATCCTTGA -s simDog_chr6.simDog.chr6 535381 11 + 593897 ------ACCATCTTTTG -s simHuman_chr6.simHuman.chr6 542873 17 + 601863 TAGACTACCATCCTTTG -s simRat_chr6.simRat.chr6 47419 17 - 647215 TAGATGACCATCCTTGA - -a -s simMouse_chr6.simMouse.chr6 571930 24 + 636262 CATTTTGTGGTTGTTGGACTACTC -s Anc0.Anc0refChr3 173584 24 + 222631 CAGTTTGTGAATGTGAGACTGCAC -s Anc1.Anc1refChr1 12621 24 + 69767 CAGTTTGTGAATGTGAGACTGCAC -s Anc2.Anc2refChr1 88863 24 + 142988 CAGTTTGTGAATGTGAGAGTGCAC -s mr.mrrefChr3 121904 24 + 181027 CATTTTGTGGATGTTGGACTACAC -s simDog_chr6.simDog.chr6 535396 24 + 593897 CAGTTTGTGAATGTGAGAGTGCAC -s simHuman_chr6.simHuman.chr6 542890 24 + 601863 CAGTTTGTGAATGTGAGCCTGCAC -s simRat_chr6.simRat.chr6 47436 24 - 647215 CTTTTTACGGATGCAGGACTACAC - -a -s simMouse_chr6.simMouse.chr6 571954 61 + 636262 AAATTTGGATGCCAATGCATCCAGACGGAGCTGCGGGATTGAGATTGAGTGATGGTGGATC -s Anc0.Anc0refChr3 173608 21 + 222631 A---------------------------------------GAGATTAAGGGTTGG-GTTTC -s Anc1.Anc1refChr1 12645 21 + 69767 A---------------------------------------GAGATTAAGGGTTGG-GTTTC -s Anc2.Anc2refChr1 88887 21 + 142988 A---------------------------------------GTGCTCAGGGGTTGG-GTTTC -s mr.mrrefChr3 121928 61 + 181027 AAATTTGGATGCCAATGCATCCAGACGGAGCTGCGGGATTGAGATTAAGTGATGGTGGATC -s simDog_chr6.simDog.chr6 535446 21 + 593897 A---------------------------------------GTGCTCAGGGGTTGG-GTTTC -s simHuman_chr6.simHuman.chr6 542914 21 + 601863 A---------------------------------------GAGATTAAGGGTTGG-GTGCC -s simRat_chr6.simRat.chr6 47460 61 - 647215 GAAAAAGAATTCCAATGCAACCAGACAGTGCTGATGGATTGAGATTAAGTCATGAGGGATC - -a -s simMouse_chr6.simMouse.chr6 572015 7 + 636262 AAATGGT -s Anc0.Anc0refChr3 173629 7 + 222631 AAATGGT -s Anc1.Anc1refChr1 12666 7 + 69767 AAATGGT -s Anc2.Anc2refChr1 88919 7 + 142988 AAATGGT -s mr.mrrefChr3 121989 7 + 181027 AAATGGT -s simCow_chr6.simCow.chr6 547157 7 + 602619 AAATGCA -s simDog_chr6.simDog.chr6 535478 7 + 593897 AAATGGT -s simHuman_chr6.simHuman.chr6 542935 7 + 601863 TTATGCC -s simRat_chr6.simRat.chr6 47521 7 - 647215 AAATGGT - -a -s simMouse_chr6.simMouse.chr6 572022 35 + 636262 ATGTTACTATGGAAGCAGTTCCATGAGACTAAGCT -s Anc0.Anc0refChr3 173636 20 + 222631 ATCTGACTATGGCAG---------------AAGTT -s Anc1.Anc1refChr1 12673 20 + 69767 ATCTGACTATGGCAG---------------AAGTT -s Anc2.Anc2refChr1 88927 20 + 142988 GTCTGTATCTGTCGG---------------AAGTT -s mr.mrrefChr3 121996 34 + 181027 ATGTTACTATGGAAGCAGTTCCATGA-ACTAAGCT -s simCow_chr6.simCow.chr6 547165 17 + 602619 GTGCCTATGTAT------------------AAGTT -s simDog_chr6.simDog.chr6 535486 20 + 593897 GTCTGTATCTGTCGG---------------AAGTT -s simHuman_chr6.simHuman.chr6 542942 20 + 601863 ATTTGACTATGGGAA---------------AAGGT -s simRat_chr6.simRat.chr6 47528 34 - 647215 ATGTTACTATGGAAGCCGTTCTTTTA-CCTGAGCT - -a -s simMouse_chr6.simMouse.chr6 572057 17 + 636262 CCATAATGCTTGGACTG -s Anc0.Anc0refChr3 173656 17 + 222631 TGATGATGCTTGTAGTA -s Anc1.Anc1refChr1 12693 17 + 69767 TGATGATGCTTGTAGTA -s Anc2.Anc2refChr1 88950 17 + 142988 TGATGTTGCTTGTAGTA -s mr.mrrefChr3 122030 17 + 181027 CCATAATGCTTGGACTG -s simCow_chr6.simCow.chr6 547185 6 + 602619 TGACGT----------- -s simDog_chr6.simDog.chr6 535509 17 + 593897 TGTTGTTGCTTGTAGTA -s simHuman_chr6.simHuman.chr6 542962 17 + 601863 TGATGATACTGGAATTA -s simRat_chr6.simRat.chr6 47562 17 - 647215 GCATAATGGTTGGACTG - -a -s simMouse_chr6.simMouse.chr6 572074 20 + 636262 CCCTGGAGGACTGTATATTA -s Anc0.Anc0refChr3 173673 20 + 222631 CCCTGGAGGTCTATATAATG -s Anc1.Anc1refChr1 12710 20 + 69767 CCCTGGAGGTCTATATAATG -s Anc2.Anc2refChr1 88967 20 + 142988 CCCTGGAGTTCTATATAATG -s mr.mrrefChr3 122047 20 + 181027 CCCTGGAGGACTGTATATTA -s simCow_chr6.simCow.chr6 547191 14 + 602619 -----GAG-TCTACATAATG -s simDog_chr6.simDog.chr6 535526 20 + 593897 CCCTGGAGTTCTATATGATG -s simHuman_chr6.simHuman.chr6 542980 20 + 601863 CCCTGTAGGCCCATATAATG -s simRat_chr6.simRat.chr6 47579 20 - 647215 CCTTGGAGGACTGTTTATTA - -a -s simMouse_chr6.simMouse.chr6 572094 6 + 636262 GGTGGG -s Anc0.Anc0refChr3 173696 6 + 222631 TGTGGG -s Anc1.Anc1refChr1 12733 6 + 69767 TGTGGG -s Anc2.Anc2refChr1 88990 6 + 142988 TGTGGG -s mr.mrrefChr3 122067 6 + 181027 GGTGGG -s simCow_chr6.simCow.chr6 547208 6 + 602619 CATGGG -s simDog_chr6.simDog.chr6 535549 6 + 593897 TGGGGG -s simHuman_chr6.simHuman.chr6 543003 6 + 601863 AGTGGG -s simRat_chr6.simRat.chr6 47599 6 - 647215 GGTAGA - -a -s simMouse_chr6.simMouse.chr6 572100 1 + 636262 G -s Anc0.Anc0refChr3 173702 1 + 222631 G -s Anc1.Anc1refChr1 12739 1 + 69767 G -s Anc2.Anc2refChr1 88996 1 + 142988 A -s mr.mrrefChr3 122073 1 + 181027 G -s simCow_chr6.simCow.chr6 547214 1 + 602619 A -s simDog_chr6.simDog.chr6 535559 1 + 593897 A -s simHuman_chr6.simHuman.chr6 543009 1 + 601863 G -s simRat_chr6.simRat.chr6 47605 1 - 647215 G - -a -s simMouse_chr6.simMouse.chr6 572101 47 + 636262 TGGCTAAAGGCAAAGGAGTGAGGAGAGCACCCCTTAACATAAAACCT -s Anc0.Anc0refChr3 173703 39 + 222631 AAGGTAAAG------GAGGTAC-AAACACCCCT-TAACATATTATTT -s Anc1.Anc1refChr1 12740 39 + 69767 AAGGTAAAG------GAGGTAC-AAACACCCCT-TAACATATTATTT -s Anc2.Anc2refChr1 88997 39 + 142988 AAGGTGAAG------GAGGTAC-AAACACCCCT-TAACATATTATGT -s mr.mrrefChr3 122074 39 + 181027 TAGCTAAAG------GAGTGAG-AGAGCACCCC-TAACATAAAACTT -s simCow_chr6.simCow.chr6 547217 39 + 602619 AACCTGAGG------GAGGTAC-AAACACCCCT-TAAAATATGATAT -s simDog_chr6.simDog.chr6 535560 39 + 593897 AAGGTGAAG------GAGGTAC-AAACACCCCT-TAACATACTATGA -s simHuman_chr6.simHuman.chr6 543010 39 + 601863 AAGGTAGAG------GAGGTAC-AAACACCCCT-TAACATATCATTT -s simRat_chr6.simRat.chr6 47606 39 - 647215 CAGCTAAAG------GGGAGAG-AGAACACCCC-TAACATAAGACTT - -a -s simMouse_chr6.simMouse.chr6 572148 44 + 636262 AAATTGGAGAGAGCTATAGTTCTAACAAGGTGTTGTTACCTAAA -s Anc0.Anc0refChr3 173743 36 + 222631 AAAGTTAAGGGATGTCCAATTCTGATAAGGTGTTAT-------- -s Anc1.Anc1refChr1 12780 36 + 69767 AAAGTTAAGGGATGTCCAATTCTGATAAGGTGTTAT-------- -s Anc2.Anc2refChr1 89037 36 + 142988 AAAGTTAAGGGATGTCCAATTCTGATAAGGTGTTGT-------- -s mr.mrrefChr3 122113 44 + 181027 AAATTGAAGGGAGCTATAATTCTGACAAGGTGTTATTACCAAAA -s simCow_chr6.simCow.chr6 547257 36 + 602619 ATAGTTAAGGGATCTCCAATTCTGATAAGATGTTGC-------- -s simDog_chr6.simDog.chr6 535600 36 + 593897 AAAGTTAAGGGATGTCCAGTTCTTATAAGGTGTTGT-------- -s simHuman_chr6.simHuman.chr6 543050 36 + 601863 AAGGTAAAGGGATTTCCAAGTCTGATAAGGTGTTAT-------- -s simRat_chr6.simRat.chr6 47645 44 - 647215 AAATTGAAGGGAGCTTTAATTCTGACAAGATGCCATTGCCAAAA - -a -s simMouse_chr6.simMouse.chr6 572192 1 + 636262 T -s mr.mrrefChr3 122157 1 + 181027 T -s simRat_chr6.simRat.chr6 47690 1 - 647215 T - -a -s simMouse_chr6.simMouse.chr6 572193 1 + 636262 T -s Anc1.Anc1refChr1 12821 1 + 69767 T -s mr.mrrefChr3 122158 1 + 181027 T -s mr.mrrefChr3 40563 1 - 181027 T -s simMouse_chr6.simMouse.chr6 44545 1 - 636262 T -s simRat_chr6.simRat.chr6 580906 1 + 647215 T -s simRat_chr6.simRat.chr6 47691 1 - 647215 T - -a -s simMouse_chr6.simMouse.chr6 572194 180 + 636262 CATGAGATTAGAATTCTAGATAATTGCATCATGAATTATTGGACAGAGATGAAATCCACATGTCATATGGATTAACTCATAGGTTGCCGGGTATCCCTTATGTATGCAAAAGAAATTGTAGTGCTGACGCTGACATCAAGTTCCTGTTTCCAATGTGACTATTGGTTTGGGGGAGAAGGA -s mr.mrrefChr3 122159 163 + 181027 CATGAGATTAGAATTCTAGATAATTGCATCATGAATTATTGGACAGAGATGAAATCCACATGTCATATGGATTAACTCATAGGTTGCCGGGTATCCCTT-----------AGAAATTGTAGTGCTGACG------TCAAGTTCCTGTTTCCAATGTGACTATTGGTTTGGGGGAGAAGGA -s simRat_chr6.simRat.chr6 47692 163 - 647215 CATGGGATTAGAATTCTAGATAGTTGCATCATGAATTAATGGACGTTGATGAGATCCTCATGGCATATGGACTAACTCATAGATTGCCAGCTATACCTT-----------AGGAATTGTAGGGCTGACT------TGAAGTTCCTGTTTCCAATCGGACTATTGGTCTAGGGGAAATGGA - -a -s simMouse_chr6.simMouse.chr6 572374 6 + 636262 ATAAAC -s mr.mrrefChr3 122322 6 + 181027 ATAAAC -s simRat_chr6.simRat.chr6 47856 6 - 647215 ATAAAT - -a -s simMouse_chr6.simMouse.chr6 572380 11 + 636262 ATTGCACCTGG -s Anc1.Anc1refChr1 12822 11 + 69767 ATTGCACCTGG -s mr.mrrefChr3 122328 11 + 181027 ATTGCACCTGG -s mr.mrrefChr3 40564 11 - 181027 ATTACAACTGG -s simMouse_chr6.simMouse.chr6 44546 11 - 636262 ATTACAACTGG -s simRat_chr6.simRat.chr6 580907 11 + 647215 ATTACAGCTGG -s simRat_chr6.simRat.chr6 47862 11 - 647215 ATTGCACCAGG - -a -s simMouse_chr6.simMouse.chr6 572391 4 + 636262 CACC -s mr.mrrefChr3 122339 4 + 181027 CACC -s simRat_chr6.simRat.chr6 47873 4 - 647215 CACA - -a -s simMouse_chr6.simMouse.chr6 572395 1 + 636262 A -s Anc1.Anc1refChr1 12833 1 + 69767 A -s mr.mrrefChr3 122343 1 + 181027 A -s mr.mrrefChr3 40575 1 - 181027 A -s simMouse_chr6.simMouse.chr6 44557 1 - 636262 A -s simRat_chr6.simRat.chr6 580918 1 + 647215 A -s simRat_chr6.simRat.chr6 47877 1 - 647215 A - -a -s simMouse_chr6.simMouse.chr6 572396 37 + 636262 TAGGAGTTGGCTGTCAGTCGGGGGGACACTAGATCGC -s Anc1.Anc1refChr1 12834 37 + 69767 TTGGAGTTGCCTATCAGTCTGGGGGACATTAGATTGC -s mr.mrrefChr3 122344 37 + 181027 TAGGAGTTGGCTGTCAGTCGGGGGGACACTAGATCGC -s mr.mrrefChr3 40576 37 - 181027 TTTTAGTTGCTTATCAGTCTGGGGGACATTGGATTGC -s simMouse_chr6.simMouse.chr6 44558 37 - 636262 TTTTAGTTGCTTATCAGTCTGGGGGACATTGGATTGC -s simRat_chr6.simRat.chr6 580923 37 + 647215 TTTCAGTTGGTTATTGGTGTGGGGGACATTGGATTGC -s simRat_chr6.simRat.chr6 47878 37 - 647215 TAGGTGTTGGCTGTCAGTCCGGGGGATACTAGATTGC - -a -s simMouse_chr6.simMouse.chr6 572433 39 + 636262 ACCCTCACTTATCAAACTCTTCTGTTGGTCAAACTGAAG -s Anc1.Anc1refChr1 12871 39 + 69767 ACCCTCACTTATCGAACTATCCTGTTGGTCAAACTGAGG -s mr.mrrefChr3 122381 39 + 181027 ACCCTCACTTATCAAACTCTTCTGTTGGTCAAACTGAAG -s mr.mrrefChr3 40613 39 - 181027 GCCCTTGTTTATTGAACCACCCTGTTTATCAGACTGGGG -s simMouse_chr6.simMouse.chr6 44595 39 - 636262 GCCCTTGTTTATTGAACCACCCTGTTTATCAGACTGGGG -s simRat_chr6.simRat.chr6 580960 39 + 647215 ACTCTTGTTTATTGAACCCCCCCGTTTATCAGACTGGAG -s simRat_chr6.simRat.chr6 47951 39 - 647215 ACCCTCGCTTATTAAACCCCTCTATTGATAAAACTGAAG - -a -s simMouse_chr6.simMouse.chr6 572472 1 + 636262 G -s mr.mrrefChr3 122420 1 + 181027 G -s simRat_chr6.simRat.chr6 47990 1 - 647215 G - -a -s simMouse_chr6.simMouse.chr6 572473 17 + 636262 TTAACATGGATTCCACT -s mr.mrrefChr3 122421 17 + 181027 TTAACATGGATTCCACT -s simRat_chr6.simRat.chr6 47992 17 - 647215 GTAACACAGATTCCACT - -a -s simMouse_chr6.simMouse.chr6 572490 23 + 636262 GAATAAGGGGGTACATCACACCA -s Anc1.Anc1refChr1 12910 23 + 69767 GATTAAGGGGGTAGATCACACCA -s mr.mrrefChr3 122438 23 + 181027 GAATAAGGGGGTACATCACACCA -s mr.mrrefChr3 40652 23 - 181027 GATTAAGATGATGGATCACACCA -s simMouse_chr6.simMouse.chr6 44634 23 - 636262 GATTAAGATGATGGATCACACCA -s simRat_chr6.simRat.chr6 580999 23 + 647215 GATTAAGATGATGGATTCCACCA -s simRat_chr6.simRat.chr6 48009 23 - 647215 GAACAAAGGGGCACATCATACCA - -a -s simMouse_chr6.simMouse.chr6 572513 1 + 636262 C -s mr.mrrefChr3 122461 1 + 181027 C -s simRat_chr6.simRat.chr6 48032 1 - 647215 C - -a -s simMouse_chr6.simMouse.chr6 572514 5 + 636262 ATCCC -s Anc1.Anc1refChr1 12933 5 + 69767 AGCCA -s mr.mrrefChr3 122462 5 + 181027 ATCCC -s mr.mrrefChr3 40675 5 - 181027 AGCCA -s simMouse_chr6.simMouse.chr6 44657 5 - 636262 AGCCA -s simRat_chr6.simRat.chr6 581022 5 + 647215 AACAA -s simRat_chr6.simRat.chr6 48033 5 - 647215 ATCCC - -a -s simMouse_chr6.simMouse.chr6 572519 92 + 636262 CAACCAGCCTGCATTAGTATGCATGAGCCAGCAGGGTTTAAGAGGGCCATATCTATGAGGTCCTATCAAGCCACTTACTTTTTGACAAGAAC -s Anc0.Anc0refChr3 173784 51 + 222631 ------------------------GAGCTAGCTGGGTTTATGAGGGC-------------TCCTGTTAACCT----GGTTTTTGGTACAAGC -s Anc1.Anc1refChr1 12938 51 + 69767 ------------------------GAGCTAGCTGGGTTTATGAGGGC-------------TCCTGTTAACCT----GGTTTTTGGTACAAGC -s Anc2.Anc2refChr1 89078 51 + 142988 ------------------------GAGCTAGCTGGGTCTATGAGGGC-------------TCCTGTTAACCT----GGTTTTGGGTACAAGC -s mr.mrrefChr3 122467 88 + 181027 CAACCAGCCTGCATTAGTATGCATGAGCCAGCTGGGTTTAAGAGGGCCGTATCTATGGGGTCCTATCAAGCC----ACTTTTTGACAAAAAC -s simCow_chr6.simCow.chr6 547298 48 + 602619 ------------------------GACCCAGCTGGGTCTATCATGGC-------------TCCTGTTAAGCT----GTTT---GGTACAAGC -s simDog_chr6.simDog.chr6 535641 50 + 593897 ------------------------GAGCTAGCTGGGTCTATGAGGGG-------------CCGTGTGAAC-T----GGTTTTGGGTAAAAGT -s simHuman_chr6.simHuman.chr6 543091 51 + 601863 ------------------------GAGCTAGCTGGGTTTATGAGGGC-------------TCCTGTTAACCT----GGTTTGTGGTACAAGC -s simRat_chr6.simRat.chr6 48038 88 - 647215 CAACCAGCCTGCATTAGTATGTATGAGCCAGCTGGGTTTCAGAGGGCTGTTTTTATGGGGTCCTATTAGGCC----ACTTCTTGACAAAACC - -a -s simMouse_chr6.simMouse.chr6 572611 4 + 636262 TTTA -s Anc0.Anc0refChr3 173835 3 + 222631 TT-G -s Anc1.Anc1refChr1 12989 3 + 69767 TT-G -s Anc2.Anc2refChr1 89129 3 + 142988 TT-G -s mr.mrrefChr3 122555 4 + 181027 TTTA -s simCow_chr6.simCow.chr6 547346 3 + 602619 TT-A -s simDog_chr6.simDog.chr6 535692 3 + 593897 TT-G -s simHuman_chr6.simHuman.chr6 543142 3 + 601863 TT-G -s simRat_chr6.simRat.chr6 48126 4 - 647215 TTTA - -a -s simMouse_chr6.simMouse.chr6 572615 12 + 636262 TTCATAGAATAA -s Anc0.Anc0refChr3 173838 12 + 222631 TTCATAGACCAG -s Anc1.Anc1refChr1 12992 12 + 69767 TTCATAGACCAG -s Anc2.Anc2refChr1 89132 12 + 142988 TTCATAGACCAG -s mr.mrrefChr3 122559 12 + 181027 TTCATAGAATAA -s simCow_chr6.simCow.chr6 547350 12 + 602619 TTCATAGACCAA -s simDog_chr6.simDog.chr6 535695 12 + 593897 TTCATAAACCAG -s simHuman_chr6.simHuman.chr6 543145 12 + 601863 TTCATAGACCAG -s simRat_chr6.simRat.chr6 48130 12 - 647215 TTCATAGAATAA - -a -s simMouse_chr6.simMouse.chr6 572627 25 + 636262 AATGTGGAGATCATCTCAAACATAC -s Anc0.Anc0refChr3 173850 22 + 222631 TATGTG---ATAATCTCATACATAC -s Anc1.Anc1refChr1 13004 22 + 69767 TATGTG---ATAATCTCATACATAC -s Anc2.Anc2refChr1 89144 22 + 142988 TGTGTG---ATAATCTCATACATAC -s mr.mrrefChr3 122571 25 + 181027 AATGTGGAGATAATCTCAAACATAC -s simCow_chr6.simCow.chr6 547362 22 + 602619 CATGTG---ATAAGCTCATACATAC -s simDog_chr6.simDog.chr6 535709 22 + 593897 TGTGTG---ATAATTTTATACATAC -s simHuman_chr6.simHuman.chr6 543157 17 + 601863 GATG--------ACCTCGTTTGCAC -s simRat_chr6.simRat.chr6 48142 25 - 647215 CATGCAGAGATAATCGCAAGTATAC - -a -s simMouse_chr6.simMouse.chr6 572652 86 + 636262 AATAGTTCTGAATGTTTCATTCTTATTGTATTTTCCATCAATTTGAACACCAACATCAAAATATTAAATATTGAGTGTAACCACAG -s Anc0.Anc0refChr3 173872 80 + 222631 ATTCTCTCTGAATGTTTTACTCTTATGCTGACTACCATTAATTTA------AACACCAGAACATTAAATATTGGGCCAAACCAAAG -s Anc1.Anc1refChr1 13026 80 + 69767 ATTCTCTCTGAATGTTTTACTCTTATGCTGACTACCATTAATTTA------AACACCAGAACATTAAATATTGGGCCAAACCAAAG -s Anc2.Anc2refChr1 89166 80 + 142988 ATTCTCTCTGAATGCTCTACTCTTATGCTGACTACCACTACCTTA------AACACCAGAACATTAAATATTGGACCAAACTCAAG -s mr.mrrefChr3 122596 80 + 181027 AATAGTTCTGAATGTTTCATTCTTATTGTATCTTCCATCAATTTG------AACACCAAAACATTAAATATTGAGTGTAACCAAAG -s simCow_chr6.simCow.chr6 547384 78 + 602619 GTTCTCTCTGTCTGCTCTATTCTTGTGCTTACTACCAGTGGCTTA------AACACCCGAACATAGCATATTGGACCAATCTTA-- -s simDog_chr6.simDog.chr6 535731 80 + 593897 ATGCTTTCTGAATGCTCTACTCTTATACTGACTATCACAACCATA------TACACCAGAACATTAAATATTGGACCCAACTCAAG -s simHuman_chr6.simHuman.chr6 543174 74 + 601863 ATTTTCGATGAACGTTTTACTCTTATGCTGACTACCATTTATTTA------AACACCTGGG-ACCAAACTTCAGG-----CCAACA -s simRat_chr6.simRat.chr6 48215 80 - 647215 AATGGTTCTGAATGTTTCATTCTTATTGTATCTTCCATCAATTTG------AGACCCAAAACATTAGATATTGAGTGAGACCAAAG - -a -s simMouse_chr6.simMouse.chr6 572738 23 + 636262 TGACCAGGCCAATAGTTGAACGG -s Anc0.Anc0refChr3 173952 23 + 222631 TCATCAGGCCAACAGCTAACCAG -s Anc1.Anc1refChr1 13106 23 + 69767 TCATCAGGCCAACAGCTAACCAG -s Anc2.Anc2refChr1 89246 23 + 142988 TCATCAAGCAAACAGCCAACCAG -s mr.mrrefChr3 122676 23 + 181027 TGACCAGGCCAATAGTTGAACGG -s simCow_chr6.simCow.chr6 547462 1 + 602619 ----------------------G -s simDog_chr6.simDog.chr6 535811 23 + 593897 TCATCAAGCAAACAGCCAACCAG -s simHuman_chr6.simHuman.chr6 543250 23 + 601863 TTGACAGGCCAGCAGCTTGCCAG -s simRat_chr6.simRat.chr6 48295 23 - 647215 TGACCAGGCCAATAGTTGAAAGG - -a -s simMouse_chr6.simMouse.chr6 572761 9 + 636262 CTTACAGGA -s Anc0.Anc0refChr3 173976 9 + 222631 CCTACAGGA -s Anc1.Anc1refChr1 13130 9 + 69767 CCTACAGGA -s Anc2.Anc2refChr1 89270 9 + 142988 CCTACAGGT -s mr.mrrefChr3 122699 9 + 181027 CTTACAGGA -s simCow_chr6.simCow.chr6 547464 9 + 602619 CCTACAGTG -s simDog_chr6.simDog.chr6 535835 9 + 593897 GCTACAGGT -s simHuman_chr6.simHuman.chr6 543274 9 + 601863 CCTACTGGA -s simRat_chr6.simRat.chr6 48318 9 - 647215 CTTACAGGA - -a -s simMouse_chr6.simMouse.chr6 572770 34 + 636262 TCTAGTTTACCGTGTCTAAACAAATCTTTAGACC -s Anc0.Anc0refChr3 173995 34 + 222631 TTTTGTTGATAGTGCTTAAAGGGATCTCTAAACC -s Anc1.Anc1refChr1 13149 34 + 69767 TTTTGTTGATAGTGCTTAAAGGGATCTCTAAACC -s Anc2.Anc2refChr1 89289 34 + 142988 TTTTGTTGATAGTGCTTAAAGGGATCTCTAAACC -s mr.mrrefChr3 122710 34 + 181027 TCTAGTTTATCGTGTTTAAACAAATCTCTAGACC -s simCow_chr6.simCow.chr6 547483 34 + 602619 TTTTTTTGATAGGGCTTAAAGGGCCCTTTAAACC -s simDog_chr6.simDog.chr6 535854 31 + 593897 TTTTGTTCATAGTGCTTAAA---ATCTCTAGATC -s simHuman_chr6.simHuman.chr6 543293 34 + 601863 TTTTGTTGATTGTGCTTAGAGGTATCACTAAACC -s simRat_chr6.simRat.chr6 48329 34 - 647215 TCTAGTTGATTGTGTTTAAACAACTCACTAGACC - -a -s simMouse_chr6.simMouse.chr6 572804 92 + 636262 CTCTAAGCAACCAAAAGTAAAGAAACTGTGTGCATGGATGTTTTGGAGGTTATATTAGTTATTTTACCTACTTACTTTTGTACAAGTATTCA -s Anc0.Anc0refChr3 174045 88 + 222631 TTCCAAACAACCCAAAGAAAAAAAACTGTGTGCAGACATATTTTGGAGATTATTTCAATTATTTCAC----ATAATCCTGCCCAGCTACTCA -s Anc1.Anc1refChr1 13199 88 + 69767 TTCCAAACAACCCAAAGAAAAAAAACTGTGTGCAGACATATTTTGGAGATTATTTCAATTATTTCAC----ATAATCCTGCCCAGCTACTCA -s Anc2.Anc2refChr1 89339 88 + 142988 TTCCAAACACCCCAAACAAGAAAAACTGTGTGTGGACATATTTTGGAGATTATTTCAATTATTTCAC----ATAATCCTGCCCAGCTGCTTG -s mr.mrrefChr3 122752 92 + 181027 CTCTAAGCAACCAAAAGTAAAGAAACTGTGTGCAGAGATGTTTTGGAGGTTATATTAGTTATTTTACCTACTTACTTCTGTACAAGTATTCA -s simCow_chr6.simCow.chr6 547533 88 + 602619 CTGCAAACACCCCAAACAAGAAAAGCTGAGTGTGGACATCCTATGGACATTATTTTGATTATTTCAC----ATAATCCTGCCCAGCTGCTTG -s simDog_chr6.simDog.chr6 535893 79 + 593897 TTCCGACCACCCCAGACAAGAAAAACTTTGTGTGGACATATTTTGGAGATCATTCCAATTATCTTAC----ATAATCCAGCCC--------- -s simHuman_chr6.simHuman.chr6 543349 88 + 601863 ATCCAAAAAATCCAAAGAAAAAAAACTGTGTGCAGACATATTTTGGAGATTATGTCTATTACTGCAT----GTAATCCTACCCGGCTACTCA -s simRat_chr6.simRat.chr6 48371 92 - 647215 CTCTAAGCAACCAAAATTAAAGAAACAGTGCACAGAGAGGTATTGGAGGTTATATTAGTTATTTTGCTTACTTACTTCTACACAAGTACTCA - -a -s simMouse_chr6.simMouse.chr6 572896 7 + 636262 CAGTGTT -s Anc0.Anc0refChr3 174136 7 + 222631 CAGTTCT -s Anc1.Anc1refChr1 13290 7 + 69767 CAGTTCT -s Anc2.Anc2refChr1 89430 7 + 142988 CAGTTCT -s mr.mrrefChr3 122844 7 + 181027 CAGTGTT -s simCow_chr6.simCow.chr6 547624 7 + 602619 CAGTTTT -s simDog_chr6.simDog.chr6 535973 7 + 593897 CAGTTCA -s simHuman_chr6.simHuman.chr6 543440 7 + 601863 CAGTTCT -s simRat_chr6.simRat.chr6 48463 7 - 647215 CAGTGTT - -a -s simMouse_chr6.simMouse.chr6 572903 45 + 636262 CATCTCCCTCTCTGACATGCGCTGGGAAGGTGCATTCTGTTAGGA -s Anc0.Anc0refChr3 174144 30 + 222631 CATTTCCCTTTCCAACATGGGATGGCAA---------------AA -s Anc1.Anc1refChr1 13298 42 + 69767 CATTTCCCTTTCCAACATGGGATGGCAA--TGCATTCTG-GAAAA -s Anc2.Anc2refChr1 89438 30 + 142988 CATTTCCCTTTCCAACATGGGATGGCTA---------------AA -s mr.mrrefChr3 122851 44 + 181027 CATCTCCCTCTCTGACATGCGCTGGGAAGGTGCATTCTG-TAGGA -s simCow_chr6.simCow.chr6 547632 29 + 602619 CATC-CCCTTTCCTACACGGGATGGTTA---------------AA -s simDog_chr6.simDog.chr6 535981 30 + 593897 CATTTCCCTTTCCAACATGGGATGGCTA---------------AA -s simHuman_chr6.simHuman.chr6 543448 42 + 601863 TGTTTTACTTTCCCATGTGAGATAGCAA--TGCATTCTG-GAAAA -s simRat_chr6.simRat.chr6 48470 41 - 647215 CATCTCCCTCTCTGACATGAAC---AAAGGTGCATTCAG-TAGGA - -a -s simMouse_chr6.simMouse.chr6 572948 22 + 636262 CCATTCTCTGCACATATGGCTC -s Anc0.Anc0refChr3 174174 22 + 222631 CCATCCTCCATACATATCGCTC -s Anc1.Anc1refChr1 13340 22 + 69767 CCATCCTCCATACATATCGCTC -s Anc2.Anc2refChr1 89468 22 + 142988 CCATCTTCCATACATATCGCTC -s mr.mrrefChr3 122895 22 + 181027 CCATCCTCTACACATATGGCTC -s simCow_chr6.simCow.chr6 547661 22 + 602619 CCATCTCCCATACATATTGCTC -s simDog_chr6.simDog.chr6 536011 22 + 593897 CCATCTTCTATACAGACCGCTC -s simHuman_chr6.simHuman.chr6 543491 22 + 601863 CCATCCTCCATGCTTCTCGCTC -s simRat_chr6.simRat.chr6 48511 22 - 647215 CCATCCTCTACACATCTGGCTC - -a -s simMouse_chr6.simMouse.chr6 572970 34 + 636262 CTATTGAATGGGATAATGTATCTGTATTTTAAGC -s Anc0.Anc0refChr3 174196 34 + 222631 CTATTTAAAGGGATAAAACACCCATGTTTTTAGC -s Anc1.Anc1refChr1 13362 34 + 69767 CTATTTAAAGGGATAAAACACCCATGTTTTTAGC -s Anc2.Anc2refChr1 89490 34 + 142988 CTATTTAAAGGGATAAAACACCCATGTTTTTAGC -s mr.mrrefChr3 122917 34 + 181027 CTATTGAATGGGATAATGTATCCATATTTTAAGC -s simCow_chr6.simCow.chr6 547741 34 + 602619 CTGTTCCAAGGGATATAACACCAATGTTTTAAGC -s simDog_chr6.simDog.chr6 536033 34 + 593897 CTATTTAAAGGGATAAAGCAATCATATGTTTAGC -s simHuman_chr6.simHuman.chr6 543513 34 + 601863 TTATTTGAAGGGATAAAAAACCCATGTTCAGAGC -s simRat_chr6.simRat.chr6 48533 34 - 647215 CTATTAAATGGGATAATGTATCCATGTTTTCAGC - -a -s simMouse_chr6.simMouse.chr6 573004 33 + 636262 ACAGTATATTAAGCCTAAACCTTATCTCCTCAC -s Anc0.Anc0refChr3 174233 32 + 222631 ACACAATATCAAGCGCTGATCTTATT-CCTTAC -s Anc1.Anc1refChr1 13399 33 + 69767 ACACAATATCAAGCGCTGATCTTATTTCCTTAC -s Anc2.Anc2refChr1 89527 32 + 142988 ACACAATATCAAGCGCTGATCTTATT-CCTTAT -s mr.mrrefChr3 122951 33 + 181027 ACAGTATATTAAGCCTAAACCTTATCTCCTCAC -s simCow_chr6.simCow.chr6 547778 32 + 602619 ATATAGTATCAAGCCCTGATCTTATT-CCTCAT -s simDog_chr6.simDog.chr6 536070 32 + 593897 ACACAATTCCAAGCGCAGATCTTCTT-CCTTAT -s simHuman_chr6.simHuman.chr6 543550 33 + 601863 ACACAATATCAAGCTCTGTTCTTATTTCCTTAC -s simRat_chr6.simRat.chr6 48567 33 - 647215 ACGATATATTAAGGCTACACCTTATCTCCTCAC - -a -s simMouse_chr6.simMouse.chr6 573037 40 + 636262 CTACTGGGCATTATGGTGTACCCATACTCTTGCTGTACTT -s Anc0.Anc0refChr3 174265 40 + 222631 TCATCAAGCACTTTGGTGCACCCATGCTCTTGGCCTATAT -s Anc1.Anc1refChr1 13432 40 + 69767 TCATCAAGCACTTTGGTGCACCCATGCTCTTGGCCTATAT -s Anc2.Anc2refChr1 89559 40 + 142988 TCATCAAGCACTTTGGTGCACCCATGCTCTTGGCCTATAG -s mr.mrrefChr3 122984 40 + 181027 CCACTGGGCACTTTGGTGCACCCATACTCTTGCTGTATTT -s simCow_chr6.simCow.chr6 547810 40 + 602619 TAACCTAGCACCTTGGTACAACGGTGCTGATGGCCTATAG -s simDog_chr6.simDog.chr6 536103 40 + 593897 CCTTCAAGCACTTTGGTGCACCCATGCTCTTGGACTATAG -s simHuman_chr6.simHuman.chr6 543583 40 + 601863 TCATCAAGCAGTCTGGCCCACCCAAGTTTTTGACTAATAT -s simRat_chr6.simRat.chr6 48600 40 - 647215 CCACTGGGCACTTTGGTGCACCCATACTCTTAATGTATTT - -a -s simMouse_chr6.simMouse.chr6 573077 27 + 636262 ACTTTCCTTATTATTCTGAGGCTTGAG -s Anc0.Anc0refChr3 174314 27 + 222631 ACCTTCTTTATTAGTCTGAGTCTTGGA -s Anc1.Anc1refChr1 13481 27 + 69767 ACCTTCTTTATTAGTCTGAGTCTTGGA -s Anc2.Anc2refChr1 89608 27 + 142988 GCCTTCTTTATTAGTCTGAGTCTTAGA -s mr.mrrefChr3 123024 27 + 181027 ACTTTCCTTATTAGTCTGAGGCTTGGG -s simCow_chr6.simCow.chr6 547859 27 + 602619 GCCTTCTCTATTAATCTGAGCCCTAGA -s simDog_chr6.simDog.chr6 536152 27 + 593897 GGCTTCCTTATTAGTCTGAGTTTTAGA -s simHuman_chr6.simHuman.chr6 543632 27 + 601863 ACCTTTTTTGTTAGTCTGAGTCTTGGA -s simRat_chr6.simRat.chr6 48640 27 - 647215 ACTTTCCTTATCAGTCTTAGGCTTGGG - -a -s simMouse_chr6.simMouse.chr6 573104 7 + 636262 GAGAAAG -s Anc0.Anc0refChr3 174341 7 + 222631 GAGAAAG -s Anc1.Anc1refChr1 13508 7 + 69767 GAGAAAG -s Anc2.Anc2refChr1 89635 7 + 142988 GAGAAAG -s mr.mrrefChr3 123051 7 + 181027 GAGAAAG -s simCow_chr6.simCow.chr6 547886 7 + 602619 GAGAAAG -s simDog_chr6.simDog.chr6 536179 7 + 593897 GAGAAAG -s simHuman_chr6.simHuman.chr6 543659 7 + 601863 GGAAAAG -s simRat_chr6.simRat.chr6 48668 7 - 647215 GAGAAAG - -a -s simMouse_chr6.simMouse.chr6 573111 8 + 636262 TGCTGCTT -s Anc0.Anc0refChr3 174348 7 + 222631 -GATGCTT -s Anc1.Anc1refChr1 13515 7 + 69767 -GATGCTT -s Anc2.Anc2refChr1 89642 7 + 142988 -AATGCTT -s mr.mrrefChr3 123058 8 + 181027 TGCTGCTT -s simCow_chr6.simCow.chr6 547893 7 + 602619 -AATGCTC -s simDog_chr6.simDog.chr6 536186 7 + 593897 -AATCCTT -s simHuman_chr6.simHuman.chr6 543666 7 + 601863 -GATGCTT -s simRat_chr6.simRat.chr6 48677 8 - 647215 TGCTGCTA - -a -s simMouse_chr6.simMouse.chr6 573119 29 + 636262 TCAGGGCAGGTTGCACTAACCATCATAGG -s Anc0.Anc0refChr3 174366 29 + 222631 CCAAGTCATGTTAGGCTAAGCATCATGAG -s Anc1.Anc1refChr1 13533 29 + 69767 CCAAGTCATGTTAGGCTAAGCATCATGAG -s Anc2.Anc2refChr1 89660 29 + 142988 CCAAGTCATGTTAGGCTAAGCATCATGAA -s mr.mrrefChr3 123066 29 + 181027 TCAGCGCAGGTTGCGCTAACCATCATGGG -s simCow_chr6.simCow.chr6 547905 29 + 602619 CTATGTCATTTTATACTAAGAATCATGAT -s simDog_chr6.simDog.chr6 536205 29 + 593897 CCAAATCATGTTAGGCTAAGCATTAAGAA -s simHuman_chr6.simHuman.chr6 543684 29 + 601863 CCAAGTCCTGTTAGGCTAGGCATCATGAG -s simRat_chr6.simRat.chr6 48685 29 - 647215 TCAGCGCGGGTTCAGCTAACCACCATGGG - -a -s simMouse_chr6.simMouse.chr6 573148 23 + 636262 TGACCTCTAAATACACATATCAT -s Anc0.Anc0refChr3 174395 23 + 222631 TGACCCTTAAATACACAAACAGT -s Anc1.Anc1refChr1 13562 23 + 69767 TGACCCTTAAATACACAAACAGT -s Anc2.Anc2refChr1 89689 23 + 142988 TGACCCTTAAATACACAAACAGT -s mr.mrrefChr3 123095 23 + 181027 TGACCTTTAAATACACATATAGT -s simCow_chr6.simCow.chr6 547934 23 + 602619 TGACCCTGAAGCAGACAACTGAT -s simDog_chr6.simDog.chr6 536237 23 + 593897 TAACCCTTGAATACTTAAACAGT -s simHuman_chr6.simHuman.chr6 543713 23 + 601863 TGACCCTTAAAAACACAAACAGT -s simRat_chr6.simRat.chr6 48714 23 - 647215 TGACCTTTAGACACAGATATAGC - -a -s simMouse_chr6.simMouse.chr6 573171 17 + 636262 TATATCGCGTGGCTGAC -s Anc0.Anc0refChr3 174464 17 + 222631 TTTACCACCTGGCTAGG -s Anc1.Anc1refChr1 13631 17 + 69767 TTTACCACCTGGCTAGG -s Anc2.Anc2refChr1 89759 17 + 142988 TTTACCACCTGGCTAGG -s mr.mrrefChr3 123118 17 + 181027 TATATCGCGTGGCTAAG -s simCow_chr6.simCow.chr6 548007 17 + 602619 TTTACCTCCTGGGCAGG -s simDog_chr6.simDog.chr6 536303 16 + 593897 -TTCCCACCTGGCTAGG -s simHuman_chr6.simHuman.chr6 543782 17 + 601863 TTTACTACCTGAATAGG -s simRat_chr6.simRat.chr6 48737 17 - 647215 TACATCTTGTGGCTAAG - -a -s simMouse_chr6.simMouse.chr6 573188 43 + 636262 TGTATAATATGCAGATGTATATATGATATTAATTACTGTAGCC -s Anc0.Anc0refChr3 174488 41 + 222631 TATACATTATGCACCCTTACATTTG--ATTAATGACTGTAGCC -s Anc1.Anc1refChr1 13655 41 + 69767 TATACATTATGCACCCTTACATTTG--ATTAATGACTGTAGCC -s Anc2.Anc2refChr1 89783 41 + 142988 TATACATTGTGCACCCTTACATTTG--ATTAATGACTGTAGCC -s mr.mrrefChr3 123135 43 + 181027 TATATATTATGCAGATGTATATATGATATTAATTACTGTAGCC -s simCow_chr6.simCow.chr6 548031 41 + 602619 CACATATTTTGCACCGTTACATTTA--ATTAATGACTATAGCC -s simDog_chr6.simDog.chr6 536326 40 + 593897 TATACATTGTTCACCCC-ACATTTG--ATTGATGACTGTAGCC -s simHuman_chr6.simHuman.chr6 543806 41 + 601863 TCTACATTATGCACCCTTACAACTG--TTTAGTGGCTGTAGCC -s simRat_chr6.simRat.chr6 48754 43 - 647215 TACATATTATGCAGATGTATTTATGATATTAATTACTGTAGCC - -a -s simMouse_chr6.simMouse.chr6 573231 14 + 636262 ATGAGGAGTAAGAT -s Anc0.Anc0refChr3 174529 11 + 222631 AT---GAGTGAGGA -s Anc1.Anc1refChr1 13696 11 + 69767 AT---GAGTGAGGA -s Anc2.Anc2refChr1 89824 11 + 142988 AT---AAGTGAGGA -s mr.mrrefChr3 123178 14 + 181027 ATGAGGAGTAAGAT -s simCow_chr6.simCow.chr6 548073 11 + 602619 AC---AAGTGAGGA -s simDog_chr6.simDog.chr6 536366 11 + 593897 AT---AAGTGAGGA -s simHuman_chr6.simHuman.chr6 543847 11 + 601863 AT---GAGTGAGGA -s simRat_chr6.simRat.chr6 48797 14 - 647215 ACGAGGAGTCAGGC - -a -s simMouse_chr6.simMouse.chr6 573245 32 + 636262 CATTCTGCTCCACCCTTCATACATCTGATAGA -s Anc0.Anc0refChr3 174540 32 + 222631 TGCTATACTCCACCCTTCATACATGTGATAGA -s Anc1.Anc1refChr1 13707 32 + 69767 TGCTATACTCCACCCTTCATACATGTGATAGA -s Anc2.Anc2refChr1 89838 32 + 142988 TGCTATACTTGACCCTTCATACATGTGGTAGA -s mr.mrrefChr3 123192 32 + 181027 TGTTCTGCTCCACCCTTCATACATGTGATAGA -s simCow_chr6.simCow.chr6 548087 32 + 602619 GGCTGTGCTTTATCCTTCTTACATGTAGTAGA -s simDog_chr6.simDog.chr6 536380 32 + 593897 TGTTATACTTGACCTTTTATATATGTGGTAGA -s simHuman_chr6.simHuman.chr6 543858 32 + 601863 TGCTATACTCCAACCTTCAAACACGTGACAGA -s simRat_chr6.simRat.chr6 48811 32 - 647215 TGTTCTGCTCCACCCTTCATACATGTGATAGA - -a -s simMouse_chr6.simMouse.chr6 573277 11 + 636262 CACTAATATGT -s Anc0.Anc0refChr3 174572 11 + 222631 CACTAATGTCT -s Anc1.Anc1refChr1 13739 11 + 69767 CACTAATGTCT -s Anc2.Anc2refChr1 89870 11 + 142988 AAGTAATGTCT -s mr.mrrefChr3 123224 11 + 181027 CACTAATATCT -s simCow_chr6.simCow.chr6 548119 11 + 602619 TAACAATGTCT -s simDog_chr6.simDog.chr6 536412 11 + 593897 AAGTAATGTCT -s simHuman_chr6.simHuman.chr6 544732 11 + 601863 CACGAGTCACT -s simRat_chr6.simRat.chr6 48843 11 - 647215 CACTAATATCT - -a -s simMouse_chr6.simMouse.chr6 573288 52 + 636262 ACGGGAGCAACAACCAGACAAGACATGAATAATTATGTGGGGTCAGTGAGAA -s Anc0.Anc0refChr3 174583 48 + 222631 AAGGGAGCAT-AACCAGACAAGACATGAATAACTATGTGGCATCAATGA--- -s Anc1.Anc1refChr1 13750 51 + 69767 AAGGGAGCAT-AACCAGACAAGACATGAATAACTATGTGGCATCAATGATAA -s Anc2.Anc2refChr1 89881 48 + 142988 AAGGGAGCAT-CACCAGATAAGACATGAATGACTATGTGGCATCAATGA--- -s mr.mrrefChr3 123235 51 + 181027 AAGGGAGCAA-AACCAGACAAGACATGAATAACTATGTGGGGTCAATGAGAA -s simCow_chr6.simCow.chr6 548130 48 + 602619 AGGGCAGTAT-CACCAAGCAATACATGAATGGGTATATGGAATCAGTGA--- -s simDog_chr6.simDog.chr6 536423 48 + 593897 AAGGGAGCAT-CACCAGATAAGACATGAATGACTATGTGGCGTCAATGA--- -s simHuman_chr6.simHuman.chr6 544743 40 + 601863 TAGAAATTAT-AACCTGAC------TTAATAGCTACAT-----CAAAGATAA -s simRat_chr6.simRat.chr6 48855 51 - 647215 AAGGGAGCAA-GACTAGACAAGACATGAATAACTATGTGGGGTCAATGAGAA - -a -s simMouse_chr6.simMouse.chr6 573340 23 + 636262 AACTGTTCTAATAACTGAACACT -s Anc0.Anc0refChr3 174634 22 + 222631 AACTGTATTCCTAGCTGAAC-CC -s Anc1.Anc1refChr1 13804 22 + 69767 AACTGTATTCCTAGCTGAAC-CC -s Anc2.Anc2refChr1 89932 22 + 142988 AACTGTATTTCTAGCTGAAC-CC -s mr.mrrefChr3 123286 23 + 181027 AACTGTTCTCATAACTGAACACT -s simCow_chr6.simCow.chr6 548184 22 + 602619 AACTGTATTACTAGCAAAAC-CC -s simDog_chr6.simDog.chr6 536474 22 + 593897 AACTGTTTTTCTAGCTGGAC-CC -s simHuman_chr6.simHuman.chr6 544786 22 + 601863 AACTGTATTCCTAGCTGAAC-CC -s simRat_chr6.simRat.chr6 48906 23 - 647215 AACTGTTCTCATAACTGAACACT - -a -s simMouse_chr6.simMouse.chr6 573363 56 + 636262 TCAAGGTAGAGCTCCTGACTGTATTGAAATCTTGAAAATCCACGATGTCTTGAAGC -s Anc0.Anc0refChr3 174656 50 + 222631 ACTGTGTACAGATCCTGATTGCAATGGAGTTCTGAAAATACA------GATGTTGC -s Anc1.Anc1refChr1 13826 50 + 69767 ACTGTGTACAGATCCTGATTGCAATGGAGTTCTGAAAATACA------GATGTTGC -s Anc2.Anc2refChr1 89954 50 + 142988 ACTGTGTACAGATCCTGGTTGCAATGGAGTTCTGAAAAAACA------GATGTTGC -s mr.mrrefChr3 123309 50 + 181027 TCAAGGTACAGATCCTGACTGTATTGGAATCTTGAAAATCCA------CTTGAAGC -s simCow_chr6.simCow.chr6 548207 50 + 602619 ACTGTGTACAGATCCTGGTTGCACTGTAGTTTTGAACAAACA------GATGTCAC -s simDog_chr6.simDog.chr6 536496 50 + 593897 ACTGTGCACAGACCCTAGTAGCAATGGACTCCTAAAACATCA------GATGTTGC -s simHuman_chr6.simHuman.chr6 544808 50 + 601863 ACTGTGTACAGATCCTGATTGCAATGGAGTTATGGAAATACA------TATGGTGC -s simRat_chr6.simRat.chr6 48929 50 - 647215 TCAAGGTACAAATTCTGACTGTATTGGAATCTTGAAAATCCA------ATTGAAAT - -a -s simMouse_chr6.simMouse.chr6 573419 24 + 636262 TGCATGTACATATTCCAAGGGGTG -s Anc0.Anc0refChr3 174711 23 + 222631 TGCAAGTA-ATATTCCAAGTATTG -s Anc1.Anc1refChr1 13881 24 + 69767 TGCAAGTACATATTCCAAGTATTG -s Anc2.Anc2refChr1 90009 23 + 142988 TACAAGTA-ATGTCCCAAGTATTG -s mr.mrrefChr3 123359 24 + 181027 TGCATGTACATATTCCAAGGGGTG -s simCow_chr6.simCow.chr6 548262 23 + 602619 TACAAGTG-ATGTCCAAAGTATTG -s simDog_chr6.simDog.chr6 536551 23 + 593897 TAGAAGTA-ATGTCCCAAGTACTG -s simHuman_chr6.simHuman.chr6 544863 24 + 601863 TGCAAGTACATATTCCAAGTATTG -s simRat_chr6.simRat.chr6 48979 24 - 647215 TACATGTACATATTCTAAGGGGTG - -a -s simMouse_chr6.simMouse.chr6 573443 42 + 636262 TACAAGATTTAATCAGTCAGGATCAGCAAGAACAAGTAAGGC -s Anc0.Anc0refChr3 174747 18 + 222631 TACTAA---------GTAAGT----------A-----AAGGC -s Anc1.Anc1refChr1 13918 27 + 69767 TACTAAATTTCATCAGTAAGT----------A-----AAGGC -s Anc2.Anc2refChr1 90045 18 + 142988 TACTAG---------GCAAGT----------G-----AAGGC -s mr.mrrefChr3 123383 32 + 181027 TACTAGATTTAATCAGTCAGG----------ACAAGTAAGGC -s simCow_chr6.simCow.chr6 548294 17 + 602619 TACTGT---------GC-AGT----------G-----AAGGC -s simDog_chr6.simDog.chr6 536587 18 + 593897 TACTAG---------GCAAGT----------G-----AAAGC -s simHuman_chr6.simHuman.chr6 544900 27 + 601863 TACTAAATTTCATCAGTAAGT----------A-----AAGGC -s simRat_chr6.simRat.chr6 49003 32 - 647215 TACTAGATTTAATCAGTCAGG----------ACAAGTAAGGC - -a -s simMouse_chr6.simMouse.chr6 573485 29 + 636262 CAAGACACACAAATGAGACCATAGATTTC -s Anc0.Anc0refChr3 174766 28 + 222631 CTAGACACATGGATGAG-CCCTATATTTT -s Anc1.Anc1refChr1 13946 28 + 69767 CTAGACACATGGATGAG-CCCTATATTTT -s Anc2.Anc2refChr1 90064 28 + 142988 CTAGACGCATGGATGAG-CCCTATATTTT -s mr.mrrefChr3 123415 29 + 181027 CAAGACACACAAATGAGACCATAGATTTC -s simCow_chr6.simCow.chr6 548312 28 + 602619 CTAGACGCGAGGATGAT-CTCTATACTTG -s simDog_chr6.simDog.chr6 536606 27 + 593897 CTAGACGCATGGATG-G-TCCCATATTTT -s simHuman_chr6.simHuman.chr6 544928 28 + 601863 CTAGGCACCTGGTTGAG-CCCTATGTTTT -s simRat_chr6.simRat.chr6 49035 29 - 647215 CAAGACGCACAAATGAGACCACAAATTTC - -a -s simMouse_chr6.simMouse.chr6 573514 15 + 636262 TGTAACAATTGCTCC -s Anc0.Anc0refChr3 174794 13 + 222631 CATAG-AATGGC-AC -s Anc1.Anc1refChr1 13974 14 + 69767 CATAGGAATGGC-AC -s Anc2.Anc2refChr1 90092 13 + 142988 CATAG-AATGGC-AC -s mr.mrrefChr3 123444 15 + 181027 TATAACAATTGCTCC -s simCow_chr6.simCow.chr6 548340 12 + 602619 CATTG-A-TGGC-AC -s simDog_chr6.simDog.chr6 536636 7 + 593897 TATAG-AA------- -s simHuman_chr6.simHuman.chr6 544956 14 + 601863 CATAGGAGTGGC-AC -s simRat_chr6.simRat.chr6 49064 15 - 647215 TATAACAATTGCTCC - -a -s simMouse_chr6.simMouse.chr6 573529 33 + 636262 CACAGGACCTTACAGTTTTAAGACCAAATTATC -s Anc0.Anc0refChr3 174807 33 + 222631 AGCAGATCCTTAGAATCCTAAGATCAACCCCAC -s Anc1.Anc1refChr1 13988 33 + 69767 AGCAGATCCTTAGAATCCTAAGATCAACCCCAC -s Anc2.Anc2refChr1 90105 33 + 142988 AGCAAATCCATAGAATCCTAAGATCAACCCCAC -s mr.mrrefChr3 123459 33 + 181027 CACAGATCCTTACAGTCTTAAGATCAAATTATC -s simCow_chr6.simCow.chr6 548353 31 + 602619 AGCAAATTAATAGACTGCTGAGACCAACCCC-- -s simDog_chr6.simDog.chr6 536643 32 + 593897 -GCAAATCCATAGAATCCTAAGATCAACACCAC -s simHuman_chr6.simHuman.chr6 544970 33 + 601863 TGCAGATCCTTAGCATCCTAAGATCAACCCCAC -s simRat_chr6.simRat.chr6 49079 33 - 647215 CATGGATCTTTACAGTCTTAAGATCAAATTATC - -a -s simMouse_chr6.simMouse.chr6 573562 2 + 636262 CC -s Anc0.Anc0refChr3 174840 2 + 222631 CC -s Anc1.Anc1refChr1 14021 2 + 69767 CC -s Anc2.Anc2refChr1 90139 2 + 142988 CC -s mr.mrrefChr3 123492 2 + 181027 CC -s simDog_chr6.simDog.chr6 536676 2 + 593897 CC -s simHuman_chr6.simHuman.chr6 545003 2 + 601863 CT -s simRat_chr6.simRat.chr6 49112 2 - 647215 CC - -a -s simMouse_chr6.simMouse.chr6 573564 53 + 636262 AGTGGCACTAATGGACATGTAATGTGTTTTTTCAAGTGGCTCCTCTGAAGCAG -s Anc0.Anc0refChr3 174842 50 + 222631 AGTGTCAAGAATGGGC---TTGTCTGTTTTTTGCACTGCCCTTCTTTGAGCTT -s Anc1.Anc1refChr1 14023 50 + 69767 AGTGTCAAGAATGGGC---TTGTCTGTTTTTTGCACTGCCCTTCTTTGAGCTT -s Anc2.Anc2refChr1 90141 50 + 142988 AATATCAAGAGTGAGG---GTGACTGTTTTCTGCACTGCACTTCTTTGAGCTT -s mr.mrrefChr3 123494 53 + 181027 AGTGGCACTAATGGACATGTAATGTGTTTTTTCAAGTGGCTTCTCTGAAGCAG -s simCow_chr6.simCow.chr6 548384 23 + 602619 ------------------------------CTCAATTTCGTTTCTTTGAACTT -s simDog_chr6.simDog.chr6 536678 50 + 593897 AATATCAAGAGTGAGG---GTGACTGTTTTCTGCACTGCACGTCTTTCAGCTT -s simHuman_chr6.simHuman.chr6 545006 50 + 601863 AGCGTCAAGTAGGGTC---TTCTCTGTTCTTTTGACTGCCCTTCTTTGAGCTT -s simRat_chr6.simRat.chr6 49114 53 - 647215 AGTGCCACTAAAGGACACGTAATGTGTTTTCACAAGTGGCTTCTCTGAAGCAG - -a -s simMouse_chr6.simMouse.chr6 573617 26 + 636262 AGAAGTTTGGGCAACTGTGCTTCTAA -s Anc0.Anc0refChr3 174934 26 + 222631 AACAGTTTGAGCAACTGTGCTTCTAG -s Anc1.Anc1refChr1 14115 26 + 69767 AACAGTTTGAGCAACTGTGCTTCTAG -s Anc2.Anc2refChr1 90235 26 + 142988 AACAGTTTTAGCAACTGTGTTTGTAG -s mr.mrrefChr3 123571 26 + 181027 AAAAGTTTGGGCAACTGTGCTTCTAA -s simCow_chr6.simCow.chr6 548454 26 + 602619 TACAGTTTTAGCAACTGTGTTTGTAG -s simDog_chr6.simDog.chr6 536772 14 + 593897 AACTCTTTTGGCAG------------ -s simHuman_chr6.simHuman.chr6 545098 26 + 601863 CATAGTTGGAGCAACTGTGCTTCTCT -s simRat_chr6.simRat.chr6 49191 26 - 647215 AAAAGTTTAGGGAACTGAGCTTCTAA - -a -s simMouse_chr6.simMouse.chr6 573643 70 + 636262 AAGCCCCAATCAACAAATAGAACTGTTTGGGAACAAGGCAAGTAGGATGGGCTCACCTACCAGAATAAGG -s Anc0.Anc0refChr3 174960 62 + 222631 GAGCCTCAACCTACAAATGGAACTCTTTGGGTACA--------GGGACACCCTCACTTACTGGGATAGGG -s Anc1.Anc1refChr1 14141 62 + 69767 GAGCCTCAACCTACAAATGGAACTCTTTGGGTACA--------GGGACACCCTCACTTACTGGGATAGGG -s Anc2.Anc2refChr1 90261 62 + 142988 GAGAGTCAGCCTACAAATGTAACTCTCTGGGTATA--------GGGACACCCTCACTCACTGGGATAGGG -s mr.mrrefChr3 123597 70 + 181027 AAGCCCCAACCAACAAATAGAACTGTTTGGGAACAAGGCAAGTGGGATGCGCTCACCTACCAGAATAAGG -s simCow_chr6.simCow.chr6 548480 55 + 602619 GAGAGTCAGCCAACAAATGTAACTCTCTGGGTATA--------GGG-------TAAGCAATGGAATAGGG -s simDog_chr6.simDog.chr6 536786 37 + 593897 -------AGCATACAA------------------G--------GGCACACCCTCACTCACTGGGATAGGG -s simHuman_chr6.simHuman.chr6 545126 62 + 601863 GAGCCTCAACCTACAGATGGAACTCTTTGTGTACA--------GGGACACCCTGACTTACTGGGATAGGG -s simRat_chr6.simRat.chr6 49217 70 - 647215 AAGCCCCAACCAGCAAGTAGAACTGTTTGGGAACAAGGTAAGTGGGATGCACTCACCTACCAGAATAAGG - -a -s simMouse_chr6.simMouse.chr6 573713 42 + 636262 AAGCCCATCAGCAGTTCCTCTCCAATATTTGCACATGCAATC -s Anc0.Anc0refChr3 175036 41 + 222631 AAGAGCATCAACAGTCCATCTCCAATATGTGCTCATGAAA-A -s Anc1.Anc1refChr1 14217 41 + 69767 AAGAGCATCAACAGTCCATCTCCAATATGTGCTCATGAAA-A -s Anc2.Anc2refChr1 90337 41 + 142988 AAGAGCATTAACAGTCCATCTTCAAACTGTCCTCATGTAA-A -s mr.mrrefChr3 123667 42 + 181027 AAGCCCATCAGCAGTTCCTCTCCAATATTTGCACATGAAATC -s simCow_chr6.simCow.chr6 548549 38 + 602619 AAGAGCATTAACAGTCCTTCTTCAAAGT---CTCATGTAA-A -s simDog_chr6.simDog.chr6 536837 39 + 593897 AAGA-CATTCATATTCCATCTTCAAACTGTCCTCATGTAA-- -s simHuman_chr6.simHuman.chr6 545202 41 + 601863 AAGAGCATCAACAGTACATCTCCAATATGTGCTCTTGAAA-A -s simRat_chr6.simRat.chr6 49287 42 - 647215 AAGCCCCTCAGCAGTCCCTCTCTAGTATTTGCCCATGAAATC - -a -s simMouse_chr6.simMouse.chr6 573755 17 + 636262 ACCCTATATTAGCGACT -s Anc0.Anc0refChr3 175077 17 + 222631 ACCTTGAATTAGTTGCT -s Anc1.Anc1refChr1 14258 17 + 69767 ACCTTGAATTAGTTGCT -s Anc2.Anc2refChr1 90378 17 + 142988 ACCTTGAGTTAATTGCT -s mr.mrrefChr3 123709 17 + 181027 ACCCTATATTAGCGACT -s simCow_chr6.simCow.chr6 548588 17 + 602619 ACCTTGAGTTAATTGCT -s simHuman_chr6.simHuman.chr6 545243 17 + 601863 ACCTTGAACTAGTTGCT -s simRat_chr6.simRat.chr6 49329 17 - 647215 ACCCTACATTAGCCACT - -a -s simMouse_chr6.simMouse.chr6 573772 30 + 636262 TTTGAATAAGTTTACCATTTAGCTTGCAAC -s Anc0.Anc0refChr3 175102 30 + 222631 TTTTAACAATTTAGCCATCTAGCTTACATC -s Anc1.Anc1refChr1 14283 30 + 69767 TTTTAACAATTTAGCCATCTAGCTTACATC -s Anc2.Anc2refChr1 90403 30 + 142988 TTTTAACAATTTAGCCATCTAGCTTACATC -s mr.mrrefChr3 123726 30 + 181027 TTTGAATAAGTTTACCATTTAGCTTGCAAC -s simCow_chr6.simCow.chr6 548613 28 + 602619 TTTTGATAATTTAGCCATCTACCTTAC--C -s simDog_chr6.simDog.chr6 536877 30 + 593897 TTTTAACAATATAGCCATCTAGCTTACATC -s simHuman_chr6.simHuman.chr6 545268 30 + 601863 TTTTTAAAATTTAGCCATATAGCTTACATC -s simRat_chr6.simRat.chr6 49346 30 - 647215 TTTGAATAACTTTACCATGCATCTTGCAAC - -a -s simMouse_chr6.simMouse.chr6 573802 19 + 636262 ACTAAAAAGACCTGCGTGA -s Anc0.Anc0refChr3 175154 17 + 222631 AGTAAAAAGACCTTTT--G -s Anc1.Anc1refChr1 14335 19 + 69767 AGTAAAAAGACCTTTTTGG -s Anc2.Anc2refChr1 90456 17 + 142988 AGTTAAATGCCTTTTT--G -s mr.mrrefChr3 123756 19 + 181027 ACTAAAAAGACCTGCGTGA -s simCow_chr6.simCow.chr6 548664 7 + 602619 AGTTAAA------------ -s simDog_chr6.simDog.chr6 536931 17 + 593897 AGTTTACTGCCTTTTT--G -s simHuman_chr6.simHuman.chr6 545320 19 + 601863 AGTAAAAAGACCCATTTGG -s simRat_chr6.simRat.chr6 49376 17 - 647215 ACTAAAACGATCT--GTGC - -a -s simMouse_chr6.simMouse.chr6 573821 8 + 636262 CCCGAATA -s Anc0.Anc0refChr3 175182 8 + 222631 CCTGAGTA -s Anc1.Anc1refChr1 14365 8 + 69767 CCTGAGTA -s Anc2.Anc2refChr1 90484 8 + 142988 CCTGAGTG -s mr.mrrefChr3 123775 8 + 181027 CCTGAATA -s simCow_chr6.simCow.chr6 548679 7 + 602619 CCTGAGT- -s simDog_chr6.simDog.chr6 536959 8 + 593897 CCTGTGCG -s simHuman_chr6.simHuman.chr6 545351 8 + 601863 CCTGAGTA -s simRat_chr6.simRat.chr6 49393 8 - 647215 CCTGAATA - -a -s simMouse_chr6.simMouse.chr6 573829 17 + 636262 AAATCAAATTACACTCT -s Anc0.Anc0refChr3 175192 17 + 222631 GAATGACATTACACTCT -s Anc1.Anc1refChr1 14375 17 + 69767 GAATGACATTACACTCT -s Anc2.Anc2refChr1 90494 17 + 142988 GAGTGACATTGCTGCCT -s mr.mrrefChr3 123783 17 + 181027 AAATCAAATTACACTCT -s simCow_chr6.simCow.chr6 548688 17 + 602619 GTGTGACATTGGCACTT -s simDog_chr6.simDog.chr6 536969 17 + 593897 GAGTGACATAGCTGCCT -s simHuman_chr6.simHuman.chr6 545361 17 + 601863 GAATGACATTATACTCC -s simRat_chr6.simRat.chr6 49401 17 - 647215 TGATTGAGTTACACTCT - -a -s simMouse_chr6.simMouse.chr6 573846 5 + 636262 GAGGC -s Anc0.Anc0refChr3 175209 5 + 222631 AAGGT -s Anc1.Anc1refChr1 14392 5 + 69767 AAGGT -s Anc2.Anc2refChr1 90511 5 + 142988 AAGAT -s mr.mrrefChr3 123800 5 + 181027 AAGGC -s simCow_chr6.simCow.chr6 548710 5 + 602619 AAGAT -s simDog_chr6.simDog.chr6 536986 3 + 593897 AA--T -s simHuman_chr6.simHuman.chr6 545378 5 + 601863 AAGGT -s simRat_chr6.simRat.chr6 49418 5 - 647215 AATGC - -a -s simMouse_chr6.simMouse.chr6 573851 16 + 636262 CTCAACACAATATTGC -s Anc0.Anc0refChr3 175218 16 + 222631 CTCAATACCATATTAA -s Anc1.Anc1refChr1 14401 16 + 69767 CTCAATACCATATTAA -s Anc2.Anc2refChr1 90520 16 + 142988 CTCAATACCATATTAA -s mr.mrrefChr3 123805 16 + 181027 CTCAACACAATATTGA -s simCow_chr6.simCow.chr6 548719 16 + 602619 CTCAATCCCACCATAA -s simDog_chr6.simDog.chr6 536993 16 + 593897 TTCAATACAATATTAA -s simHuman_chr6.simHuman.chr6 545387 16 + 601863 CTCAATATCATATTAA -s simRat_chr6.simRat.chr6 49423 16 - 647215 CTCAAGACTATATTGA - -a -s simMouse_chr6.simMouse.chr6 573867 3 + 636262 AAA -s Anc0.Anc0refChr3 175234 3 + 222631 GAA -s Anc1.Anc1refChr1 14417 3 + 69767 GAA -s Anc2.Anc2refChr1 90536 3 + 142988 GAA -s mr.mrrefChr3 123821 3 + 181027 AGA -s simCow_chr6.simCow.chr6 548735 3 + 602619 ACA -s simDog_chr6.simDog.chr6 537009 3 + 593897 GAA -s simHuman_chr6.simHuman.chr6 545404 3 + 601863 GAG -s simRat_chr6.simRat.chr6 49439 3 - 647215 GGA - -a -s simMouse_chr6.simMouse.chr6 573870 8 + 636262 GATGTACA -s Anc0.Anc0refChr3 175242 8 + 222631 GGTGTAAA -s Anc1.Anc1refChr1 14425 8 + 69767 GGTGTAAA -s Anc2.Anc2refChr1 90544 8 + 142988 TGTGTAAG -s mr.mrrefChr3 123829 8 + 181027 GATGTACA -s simDog_chr6.simDog.chr6 537017 8 + 593897 TGTGTAAG -s simHuman_chr6.simHuman.chr6 545412 8 + 601863 GGTGTAGA -s simRat_chr6.simRat.chr6 49447 8 - 647215 GATGTACA - -a -s simMouse_chr6.simMouse.chr6 573878 1 + 636262 G -s Anc0.Anc0refChr3 175261 1 + 222631 G -s Anc1.Anc1refChr1 14444 1 + 69767 G -s Anc2.Anc2refChr1 90563 1 + 142988 G -s mr.mrrefChr3 123837 1 + 181027 G -s simDog_chr6.simDog.chr6 537036 1 + 593897 G -s simHuman_chr6.simHuman.chr6 545431 1 + 601863 A -s simRat_chr6.simRat.chr6 49455 1 - 647215 G - -a -s simMouse_chr6.simMouse.chr6 573879 24 + 636262 ATTAGCAATGCAACCTCCCAGCTA -s Anc0.Anc0refChr3 175262 24 + 222631 ATTAGCAATACAACCCCCTTGCTG -s Anc1.Anc1refChr1 14445 24 + 69767 ATTAGCAATACAACCCCCTTGCTG -s Anc2.Anc2refChr1 90564 24 + 142988 ATTAACAATACAACCCCCTTGCTG -s mr.mrrefChr3 123838 24 + 181027 ATTAGCAATGCAACCTCCTAGCTA -s simCow_chr6.simCow.chr6 548738 24 + 602619 ATTAACAATCCAACCCCCTTGATG -s simDog_chr6.simDog.chr6 537037 24 + 593897 ATTAACAATACAACCCCCTTACTG -s simHuman_chr6.simHuman.chr6 545448 24 + 601863 ATTAGAAACTCAACCCCCTTGTTT -s simRat_chr6.simRat.chr6 49456 24 - 647215 ATTAGCGATGCAACCTCCTAGCTA - -a -s simMouse_chr6.simMouse.chr6 573903 59 + 636262 TGAGCTGATGGAAGCAGAGTTTATGCAGAGGTAATTCTACTAACTTCTGGGAGCTTTTT -s Anc0.Anc0refChr3 175290 59 + 222631 TGAGCTGATGGAAGCAGAGTATATGCAGAGGTAATTCTACTAACTTCTGGGACTTTTTT -s Anc1.Anc1refChr1 14473 59 + 69767 TGAGCTGATGGAAGCAGAGTATATGCAGAGGTAATTCTACTAACTTCTGGGACTTTTTT -s Anc2.Anc2refChr1 90592 59 + 142988 TGAGCTGATGGAAGCAGAGTATATGCAGAGGTAATTCTACTAACTTCTGGGACTTTTTT -s mr.mrrefChr3 123862 59 + 181027 TGAGCTGATGGAAGCAGAGTTTATGCAGAGGTAATTCTACTAACTTCTGGGAGCTTTTT -s simCow_chr6.simCow.chr6 548766 59 + 602619 TGAGCTGATGGAAGCAGGGTATATGCAGAGGTAATTCTACTAACTTCTGGGACTTTTTT -s simDog_chr6.simDog.chr6 537065 59 + 593897 TGAGCTGATGGGAGCAGAGTTTATGCAGAGGTAATTCTACTAACTTCTGGGACCTTTTT -s simHuman_chr6.simHuman.chr6 545476 59 + 601863 TGAGCTGATGGAAGCAGAGTATATGCAGAAGTTATTCTACTAACTTCTGGGACTTTTTT -s simRat_chr6.simRat.chr6 49480 59 - 647215 TGAGCTGATGGAAGCAGAGTTTATGCAGAGGTAATTCTACTAACTTCTGGGAGCTTTTT - -a -s simMouse_chr6.simMouse.chr6 573962 265 + 636262 GAGAGGAACAATTGTGATTGGCCTAGAGACACACCCAGCTGGACGTTTGGATGATCAGCCTTCCATAGGCTTAGCCCAGACGCTAGAAAAGTTGGGTTTTGTGGTAGGCAGATTGAAAACTGGAACACCTCCCCGAATTGCCAAAGAGTCTATCAATTTTAGTATCCTTAATAAACATATACCAGATAATCCTTCCACCCCATTTGGCTTTACCAATGAGACTGTCTACAGGTGGTTAGGTCTCTTCACGTATATGTGGAGGAAA -s Anc0.Anc0refChr3 175349 262 + 222631 GAGAGGCACAATTGTGATTGGCTTGGAGACACACCCTGCTGGACGCCTGGATGATCAGCCTTCTATAGGGTTAGCTCAGACACTAGAAAAGTTGGGTTTTGTAGTAGGAAGATTGAAAACTGGAACACCTCCCCGAATTGCCAAAGAGTCCATCAATTTCAGTATTCTTAATAAACATATACCTGATAATCCTTCCACCCCATTTGGCTTTACCAATGAAACTGTCTACA--TGGTCAGATCTCTTCCCTTATATGT-AAGGGAT -s Anc1.Anc1refChr1 14532 264 + 69767 GAGAGGCACAATTGTGATTGGCTTGGAGACACACCCTGCTGGACGCCTGGATGATCAGCCTTCTATAGGGTTAGCTCAGACACTAGAAAAGTTGGGTTTTGTAGTAGGAAGATTGAAAACTGGAACACCTCCCCGAATTGCCAAAGAGTCCATCAATTTCAGTATTCTTAATAAACATATACCTGATAATCCTTCCACCCCATTTGGCTTTACCAATGAAACTGTCTACACATGGTCAGATCTCTTCCCTTATATGT-AAGGGAT -s Anc2.Anc2refChr1 90654 262 + 142988 GAGAGGCACAATTGTGATTGGCTTGGAGACACACCCTGCTGGACGCCTGGATGATCAGCCTTCTATAGGGTTAGCTCAGACACTAGAAAAGTTGGGTTTTGTAGTAGGAAGATTGAAAACTGGAACACCTCCCCGAATTGCCAAAGAGTCCATCAATTTCAGCATTCTTAATAAACATATACCTGATAATCCTTCCACCCCATTTGGCTTTACCAATGAAACTGTCTACA--TGGTCAGATCTCTTCCCTTATATAT-ATGGGAT -s mr.mrrefChr3 123921 265 + 181027 GAGAGGAACAATTGTGATTGGCTTAGAGACACACCCAGCTGGACGTCTGGATGATCAGCCTTCCATAGGCTTAGCTCAGACACTAGAAAAGTTGGGTTTTGTGGTAGGCAGATTGAAAACTGGAACACCTCCCCGAATTGCCAAAGAGTCTATCAATTTTAGTATCCTTAATAAACATATACCAGATAATCCTTCCACCCCATTTGGCTTTACCAATGAGACTGTCTACAGGTGGTCAGGTCTCTTCCCGTATATGTGGAGGAAA -s simCow_chr6.simCow.chr6 548828 259 + 602619 GAGAGGCACAATTGTGATTGGCTTGGAGACACACCCTGCTGTACGCCTGGATGACCAGCCTTCTATAGGGTTAGCTCAGACACTAGAAAAGTTGGGATTTATAGTGGGAAGATTGAAAACTGGAACACCTCCCCGAATCGCCAAGGAGTCCATCAATTTCAGCATTCTTAATAAACATATACCTGATAATCCTTCCACCCCGTTTGGCTTTACCAACGAAACTGTCTGCA--TGGTCAGATCTCTTCCCTTATACAT-AGGG--- -s simDog_chr6.simDog.chr6 537127 262 + 593897 GAGAGGCACAATTGTGATTGGCTTGGAGACACACCCTGCTGGACGCCTTGATGATCAGCCTTCTATAGGGTTAGCTCAGACACTAGAAAAGTTGAGTTTTGTAGTAGGAAGATTAAAAACTGGAACACCTCCCCGGATTGCCAAAGAGTCCATCAATTTCAGCATTCTTAATAAACATATACCTGATAATCCTTCCACCCCATTTGGCTTTACCAATGAAACTGTCTACA--TGGTCAGACCTCTTCCCCTATATAC-ATGAGAT -s simHuman_chr6.simHuman.chr6 545535 263 + 601863 GAGAGGCACAATTGTAATTGGCTTGGAGACACACCCTGCTGGACGCCTGGATGATCAACCTTCTATAGGACTAGCTCAGACACTAGAAAAGTTGGGTTTTGTTGTAGGAAGATTGAAAACTGGAACACCTCCCCGAATTGCCAAAGAGTCCATCAATTTCAGTATTCTCAATAAGCATATACCTGATAATCCTTCCACCCCATTTGGGTTTACCAATGAAACTGTCTACACA-GGTCAGATCACTTCCCTTATATGT-AATGGGT -s simRat_chr6.simRat.chr6 49539 265 - 647215 GAGAGGAACAATTGTGATTGGCTTAGAGACACACCCAGCTGGACGTCTGGATGATCAGCCTTCCATAGGCTTAGCTCAGACACTAGAAAAGTTGGGTTTTGTAGTAGGCAGATTGAAAACTGGAACACCTCCCCGAATTGCCAAAGAGTCTATCAATTTTAGTATCCTTAATAAACATATACCAGATAATCCTTCCACCCCATTTGGCTTCACCAATGAGACTGTTCACAGGTGGTCTGGTCTCTTTCCCCCTATGTGGAGGAAA - -a -s simMouse_chr6.simMouse.chr6 574227 52 + 636262 TTTGAGCTTTCATTAAACTCCTGTTATACAGATGGTAATCTTTTTGTTCTAG -s Anc0.Anc0refChr3 175611 52 + 222631 TTTGCAATTTCATTGGACTCCTATTGTAGAGATGGAAATTTATTAGTTCTGA -s Anc1.Anc1refChr1 14796 52 + 69767 TTTGCAATTTCATTGGACTCCTATTGTAGAGATGGAAATTTATTAGTTCTGA -s Anc2.Anc2refChr1 90916 52 + 142988 TTTGCGATTTCATTGGACTCCTATAGTAGAGATGGAAATTTAATAGTCCTGA -s mr.mrrefChr3 124186 52 + 181027 TTTGAACTTTCATTGAACTCCTGTTGTACAGATGGTAATCTTTTTGTTCTGG -s simCow_chr6.simCow.chr6 549087 51 + 602619 -TTGCCATTTCACTGGGCTCCCATAGTAGAGATGGAAATTTAATAGTCCTGA -s simDog_chr6.simDog.chr6 537392 40 + 593897 TTTACGATTTCATTGGACTCCTATAGCAGAGATGGAAATT------------ -s simHuman_chr6.simHuman.chr6 545798 52 + 601863 TTTGCATTTTCATTGGACCCCGATTGTAGAGATGGAAATTTATTGGTTCTGA -s simRat_chr6.simRat.chr6 49804 51 - 647215 TTTGAACTTTCATTGTACTCCTGTTGTACAGATGGTAATA-TGTTGTTCTGG - -a -s simMouse_chr6.simMouse.chr6 574279 6 + 636262 TATCTC -s Anc0.Anc0refChr3 175667 6 + 222631 CATTTT -s Anc1.Anc1refChr1 14852 6 + 69767 CATTTT -s Anc2.Anc2refChr1 90972 6 + 142988 CATTCT -s mr.mrrefChr3 124238 6 + 181027 TATCTC -s simCow_chr6.simCow.chr6 549142 6 + 602619 CATTCT -s simDog_chr6.simDog.chr6 537432 5 + 593897 -ACTCT -s simHuman_chr6.simHuman.chr6 545854 6 + 601863 CATTTT -s simRat_chr6.simRat.chr6 49855 6 - 647215 TATCTC - -a -s simMouse_chr6.simMouse.chr6 574285 20 + 636262 CTTGCAGTCTATAACGTAAA -s Anc0.Anc0refChr3 175673 20 + 222631 ATCACAGTCTATAGCATAAA -s Anc1.Anc1refChr1 14858 20 + 69767 ATCACAGTCTATAGCATAAA -s Anc2.Anc2refChr1 90978 20 + 142988 ATCACAGTCTATAGCATAAA -s mr.mrrefChr3 124244 20 + 181027 CTCGCAGTCTATAACATAAA -s simCow_chr6.simCow.chr6 549148 20 + 602619 GTCACAGACTATAGTATAAA -s simDog_chr6.simDog.chr6 537437 19 + 593897 ACCACAGTCTA-AGCATAAA -s simHuman_chr6.simHuman.chr6 545860 20 + 601863 ATCACAGTCTATAGGATGAA -s simRat_chr6.simRat.chr6 49891 20 - 647215 TTCCCAGTCTTTAACATAAA - -a -s simMouse_chr6.simMouse.chr6 574305 28 + 636262 GTGTTTCTGGCACTTGAAGCAGAAGCTC -s Anc0.Anc0refChr3 175701 28 + 222631 TTCTTTCCAGCATTTAGAGGAGAACCAC -s Anc1.Anc1refChr1 14886 28 + 69767 TTCTTTCCAGCATTTAGAGGAGAACCAC -s Anc2.Anc2refChr1 91007 28 + 142988 TGCTTTCCAGCATTTAGAGGAGAACCAC -s mr.mrrefChr3 124264 28 + 181027 GTGTTTCCGGCACTTAAAGCAGAAGCAC -s simCow_chr6.simCow.chr6 549177 28 + 602619 TGCTTTCCATCATTTAGAGGAAAAGCAC -s simDog_chr6.simDog.chr6 537465 28 + 593897 TGCCTTCTGGCATTTAGAGATGGACCAA -s simHuman_chr6.simHuman.chr6 545888 28 + 601863 TTTTTTTCAGCATTTAGAGGAGAAACAC -s simRat_chr6.simRat.chr6 49911 28 - 647215 GTGTTTCCGGTACTTAAAGAAGAAGCAT - -a -s simMouse_chr6.simMouse.chr6 574333 39 + 636262 ACTTGACATCCAAAAAATTATAAGGTGTTGTGCAGTGCT -s Anc0.Anc0refChr3 175729 36 + 222631 ATTTGACATCC--A-AATCACTAGTTGTTGTACAGTAGT -s Anc1.Anc1refChr1 14914 36 + 69767 ATTTGACATCC--A-AATCACTAGTTGTTGTACAGTAGT -s Anc2.Anc2refChr1 91035 36 + 142988 ATTTGACATCC--A-AATCACTAGTTGTTGTACAGTAGT -s mr.mrrefChr3 124292 38 + 181027 ACTTGACATCCAAA-AATCATAAGGTGTTGTGCAGTGCT -s simCow_chr6.simCow.chr6 549206 36 + 602619 ATTTGAAATCC--A-AATTAGTAGTTGTTGTACTGTAGT -s simDog_chr6.simDog.chr6 537493 36 + 593897 ATTTGGCATCC--T-AATCACTAGTTGTCATACAGTAGT -s simHuman_chr6.simHuman.chr6 545916 35 + 601863 A-TTGATATCC--A-AATCACTAGTTGTTGTACAATAGT -s simRat_chr6.simRat.chr6 49939 35 - 647215 GCTTGGCTTCC----AGTCATGAGGTGTTGTGCAGTGCT - -a -s simMouse_chr6.simMouse.chr6 574372 33 + 636262 CCATCTTTACTTTGACCACTCACAAATTGTAGG -s Anc0.Anc0refChr3 175765 33 + 222631 CCAAAATTCCCTGTACTACCCACAAATTGGTGG -s Anc1.Anc1refChr1 14950 33 + 69767 CCAAAATTCCCTGTACTACCCACAAATTGGTGG -s Anc2.Anc2refChr1 91071 33 + 142988 CCCAAATTCTCTGTACTACCCACAAATTGGTGG -s mr.mrrefChr3 124330 33 + 181027 CCATCTTTACTTTGACCACTCACAAATTGTAGG -s simCow_chr6.simCow.chr6 549242 28 + 602619 CCCAAA-----TGTACTACCCACAGAACTGCTG -s simDog_chr6.simDog.chr6 537529 32 + 593897 CCCCACTTCTCTTTGATACCCCAGAATTGTTG- -s simHuman_chr6.simHuman.chr6 545952 33 + 601863 CCAAAGTTCCCTGTACTACCCACATATTGGTGG -s simRat_chr6.simRat.chr6 49974 20 - 647215 CCATCTTCACTTTGACCAT-------------G - -a -s simMouse_chr6.simMouse.chr6 574405 22 + 636262 TATACCTTATTCTTGGCTGAGC -s Anc0.Anc0refChr3 175810 22 + 222631 TATTCATTATGCTTGGCTTAGA -s Anc1.Anc1refChr1 14995 22 + 69767 TATTCATTATGCTTGGCTTAGA -s Anc2.Anc2refChr1 91116 22 + 142988 TATTTATCATGCTTGGTTTAGA -s mr.mrrefChr3 124363 22 + 181027 TATACATTATGCTTGGCTTAGC -s simCow_chr6.simCow.chr6 549282 22 + 602619 TATTTATCATGCTTGGTTTAGA -s simHuman_chr6.simHuman.chr6 545997 22 + 601863 TATCCAATGTGCTTGGCTTAGA -s simRat_chr6.simRat.chr6 49994 22 - 647215 TATTCATTATGCTTGGCTTAGC - -a -s simMouse_chr6.simMouse.chr6 574427 8 + 636262 TTTGGGAT -s Anc0.Anc0refChr3 175832 7 + 222631 T-AGTGAT -s Anc1.Anc1refChr1 15017 7 + 69767 T-AGTGAT -s Anc2.Anc2refChr1 91138 7 + 142988 T-AGTGAC -s mr.mrrefChr3 124385 8 + 181027 TTTGGGAT -s simCow_chr6.simCow.chr6 549305 7 + 602619 T-AGTGAC -s simDog_chr6.simDog.chr6 537561 3 + 593897 -----GAC -s simHuman_chr6.simHuman.chr6 546019 7 + 601863 T-AGAGAT -s simRat_chr6.simRat.chr6 50016 8 - 647215 TTTGAGAT - -a -s simMouse_chr6.simMouse.chr6 574435 6 + 636262 TTTTAG -s Anc0.Anc0refChr3 175839 6 + 222631 TTTTAA -s Anc1.Anc1refChr1 15024 6 + 69767 TTTTAA -s Anc2.Anc2refChr1 91145 6 + 142988 TTTAAA -s mr.mrrefChr3 124393 6 + 181027 TTTTAG -s simCow_chr6.simCow.chr6 549313 6 + 602619 TTTGGA -s simDog_chr6.simDog.chr6 537564 6 + 593897 TTTAAA -s simHuman_chr6.simHuman.chr6 546026 6 + 601863 TTTTAA -s simRat_chr6.simRat.chr6 50024 6 - 647215 TTTTAG - -a -s simMouse_chr6.simMouse.chr6 574441 12 + 636262 GGCCAACTTGTG -s Anc0.Anc0refChr3 175872 12 + 222631 AGCCAGCCTATG -s Anc1.Anc1refChr1 15057 12 + 69767 AGCCAGCCTATG -s Anc2.Anc2refChr1 91178 12 + 142988 GGCCAGCCTATG -s mr.mrrefChr3 124399 12 + 181027 AGCCAACTTGTG -s simCow_chr6.simCow.chr6 549346 12 + 602619 GCCCAGCCTGTG -s simDog_chr6.simDog.chr6 537597 12 + 593897 GGCCAGCCTATG -s simHuman_chr6.simHuman.chr6 546059 12 + 601863 AGCCAGCCTATG -s simRat_chr6.simRat.chr6 50030 12 - 647215 AGGCAACTTGTG - -a -s simMouse_chr6.simMouse.chr6 574453 36 + 636262 GTTGGATCAGTAGAATCGTAGTATAGAGCATAATTA -s Anc0.Anc0refChr3 175897 34 + 222631 CTCTGGCCAGTAGGATTGGAG--TAGAACATAATTA -s Anc1.Anc1refChr1 15082 34 + 69767 CTCTGGCCAGTAGGATTGGAG--TAGAACATAATTA -s Anc2.Anc2refChr1 91203 34 + 142988 CTCTGGCCAGCAGGATTGGAG--TAGAGCATAATTA -s mr.mrrefChr3 124411 36 + 181027 GTTGGACCAGTAGAATTGTAGTATAGAACATAATTA -s simCow_chr6.simCow.chr6 549371 33 + 602619 CTCCGGCCAGCAGG-TTGGAG--TCGAGCATAATTA -s simDog_chr6.simDog.chr6 537620 34 + 593897 CTTTGGCCAGCTGGATTGGAG--TAGAGCATAATTA -s simHuman_chr6.simHuman.chr6 546085 34 + 601863 CTCTGGCTGGTAGGATTGGAG--TAGAACGTAATTA -s simRat_chr6.simRat.chr6 50042 36 - 647215 GTTGAACCAGTAAAATTGTAATTTAGAACATGATTA - -a -s simMouse_chr6.simMouse.chr6 574489 26 + 636262 GAATAACCAAGTTCTCATATCGCTTG -s Anc0.Anc0refChr3 175931 26 + 222631 TAATAACCAAGTAGTCATACTGGTTG -s Anc1.Anc1refChr1 15116 26 + 69767 TAATAACCAAGTAGTCATACTGGTTG -s Anc2.Anc2refChr1 91249 26 + 142988 TAATAACCAAGTAGTTATACTGGCTG -s mr.mrrefChr3 124447 26 + 181027 GAATAACCAAGTTCTCATATCGGTTG -s simCow_chr6.simCow.chr6 549416 26 + 602619 TAATTACCGAGTAGTTACACTGGCTG -s simDog_chr6.simDog.chr6 537672 26 + 593897 CAATAACCAAGTACTTATACTGGCTG -s simHuman_chr6.simHuman.chr6 546119 26 + 601863 TAATACCCAAGTAGTCATGCTAGTTG -s simRat_chr6.simRat.chr6 50078 26 - 647215 GACTAACCATGTTCTCATATGGGTTG - -a -s simMouse_chr6.simMouse.chr6 574515 84 + 636262 GGGGTAAATCCCTACCATTAATATTTTGGTTGTGTCTCTAAGACCTCATTGGTGATCTTATGCACCACTTGTTTGTTAGAAATC -s Anc0.Anc0refChr3 176009 81 + 222631 AGTGACAACCTGTATCATTAACATTTTGGCACTGTTTCTAGAATTTCATTAGTGAGCTTATGAGCTAA--ATTGGCT-GGGATC -s Anc1.Anc1refChr1 15194 81 + 69767 AGTGACAACCTGTATCATTAACATTTTGGCACTGTTTCTAGAATTTCATTAGTGAGCTTATGAGCTAA--ATTGGCT-GGGATC -s Anc2.Anc2refChr1 91327 81 + 142988 AGTATCAACCTGTATCATTAACATTTTTGCACTGTTTCTAGAATTTTATTAGTGAGTTTATGAGCTTA--ATTGGCT-GAGATC -s mr.mrrefChr3 124508 84 + 181027 GGTGAAAATCTCTACCATTAATATTTTGGTAGTGTCTCTAAGACCTCATTAGTGATCTTATGCACTACTTGTTTGTTAGGAATC -s simCow_chr6.simCow.chr6 549497 80 + 602619 AGTTTCAACTTGTATCATCAGCA-TTTTGCACTGATTCTACAATTTTATTAGTGAGTTAATGGGCTTA--ATTGGCT-GTAAAC -s simDog_chr6.simDog.chr6 537771 77 + 593897 AGCATTAACC----TTATTAACATTTTTGCGCTGTTTTTAGAATGTTATTGGTGAGTGTCTGAGCTTA--ATTGCCT-GAGATC -s simHuman_chr6.simHuman.chr6 546197 81 + 601863 AGTGACAACCTGTATCATTCACATTTAGGCACTGTTTCTAGAAATTCATTAGTGAGCTCATGAGCTAA--ATTGGCT-GGGATC -s simRat_chr6.simRat.chr6 50142 82 - 647215 GGTGATAATCTCTACCATT--ATTTTCAGTAATGTCTCTAAGACCTCATTAGTGATCTTATGCACTACTGGTTTGTTGGGAATC - -a -s simMouse_chr6.simMouse.chr6 574599 1 + 636262 T -s Anc0.Anc0refChr3 176090 1 + 222631 A -s Anc1.Anc1refChr1 15275 1 + 69767 A -s Anc2.Anc2refChr1 91409 1 + 142988 A -s mr.mrrefChr3 124592 1 + 181027 T -s simCow_chr6.simCow.chr6 549578 1 + 602619 A -s simDog_chr6.simDog.chr6 537849 1 + 593897 G -s simHuman_chr6.simHuman.chr6 546278 1 + 601863 A -s simRat_chr6.simRat.chr6 50224 1 - 647215 T - -a -s simMouse_chr6.simMouse.chr6 574600 1 + 636262 C -s Anc0.Anc0refChr3 176091 1 + 222631 C -s Anc1.Anc1refChr1 15276 1 + 69767 C -s Anc2.Anc2refChr1 91410 1 + 142988 C -s mr.mrrefChr3 124593 1 + 181027 C -s simCow_chr6.simCow.chr6 549579 1 + 602619 C -s simDog_chr6.simDog.chr6 537850 1 + 593897 C -s simHuman_chr6.simHuman.chr6 546279 1 + 601863 C -s simRat_chr6.simRat.chr6 50231 1 - 647215 A - -a -s simMouse_chr6.simMouse.chr6 574601 13 + 636262 CAAGAGTGTGAAA -s Anc0.Anc0refChr3 176103 13 + 222631 CATGGGTGTGAAA -s Anc1.Anc1refChr1 15288 13 + 69767 CATGGGTGTGAAA -s Anc2.Anc2refChr1 91424 13 + 142988 CATAGGTGTGAAA -s mr.mrrefChr3 124594 13 + 181027 CATGAGTGTGAAA -s simCow_chr6.simCow.chr6 549593 13 + 602619 CATAGTTGGGAAA -s simDog_chr6.simDog.chr6 537864 13 + 593897 CACAAGTGTGAAA -s simHuman_chr6.simHuman.chr6 546291 13 + 601863 CATGGGTGTGGAA -s simRat_chr6.simRat.chr6 50232 13 - 647215 CATGAGGGTGAAA - -a -s simMouse_chr6.simMouse.chr6 574614 33 + 636262 TAAGTGTGAATTTGGAGGCAGTGTTGAATCTTT -s Anc0.Anc0refChr3 176116 33 + 222631 TAAATGTGAGCTTGCAGGCAGTGTTGGATTTGC -s Anc1.Anc1refChr1 15301 33 + 69767 TAAATGTGAGCTTGCAGGCAGTGTTGGATTTGC -s Anc2.Anc2refChr1 91437 33 + 142988 TAAATGCAAGCCTGCTGGCAGCATTGAATTTGC -s mr.mrrefChr3 124607 33 + 181027 TAAATGTGAGTTTGGAGGCAGTGTTGGATCTTC -s simCow_chr6.simCow.chr6 549606 22 + 602619 TAAATGCAAGGCTGCTGGCA-----------GC -s simDog_chr6.simDog.chr6 537877 28 + 593897 T-AATGCAAGCCT----ACAGCATTGAATTTAC -s simHuman_chr6.simHuman.chr6 546304 33 + 601863 TAAATGTGAGCTTGAAGGCAGTGTTGGATTTGC -s simRat_chr6.simRat.chr6 50272 33 - 647215 TTAATGTGAGTTCGGAGGCAGTGTTGGATATTC - -a -s simMouse_chr6.simMouse.chr6 574647 135 + 636262 ACACAGTTAGACACAAAAGTTGTTATAGGCATGGCACTACACGCCTGGATGTATTAAATATCAGTGAAGAATTAACTGGTTGCCATGCCTGAGTTACATCATTTTGTAACGGGGCTGTCACCATTTCAAGCTCCA -s Anc0.Anc0refChr3 176176 134 + 222631 AAGTTGTTAGACACAAAAGTTGTTATAGGTATGACACTACACCCCTGGATATGGT-ACTAGCTGCGAGGAATGAACTAGTTGCTTTGCCTGAGTCACATTATTTTGTAAATAGGCTGCCACCATTTCTAGCTCCT -s Anc1.Anc1refChr1 15361 134 + 69767 AAGTTGTTAGACACAAAAGTTGTTATAGGTATGACACTACACCCCTGGATATGGT-ACTAGCTGCGAGGAATGAACTAGTTGCTTTGCCTGAGTCACATTATTTTGTAAATAGGCTGCCACCATTTCTAGCTCCT -s Anc2.Anc2refChr1 91497 134 + 142988 AAGTTGTTAGACACAGAAGTTGTTATAGGTATGACACTACACCCCTGGATATGGT-ACAAGCTGCTAGAAATGAACTAGTTGTTTTGCCTGAGTCACATTATTCTGCAAATAGGCTGCCACCATTCCTAGCTCCT -s mr.mrrefChr3 124640 135 + 181027 AAGCAGTTAGACACAAAAGTTGTTATAGGTATGGCACTACACGCCTGGATGTATTAAATATCTGTGAAGAATTAACTGGTTGCCATGCCTGAGTTACATTATTTTGTAACGAGGCTGTCACCATTTCAAGCTCCA -s simCow_chr6.simCow.chr6 549655 133 + 602619 AAGTCATTATATGCATAAGTTGTTATGGGTATGACCCTACACTCCCGGGTAT-AT-ACCACCTACAAGAAATGAACTAGTTCTTTTGCCTGGTTCACATCATTCTGCAAATTGGCTGCCACCATTGCTAGCCCCA -s simDog_chr6.simDog.chr6 537932 133 + 593897 AAGTTGTTAGACACAGAAGTTGCGTTAGGTATGACACTACACCCCTGAATATGGT-GCAAGCTGCTGGAAATGAACTAGTTGTTTTGCCTGAG-CACATTATTCTGCAAGTAGGCTGCCACCATTCCTAGCTCTT -s simHuman_chr6.simHuman.chr6 546364 132 + 601863 AAGTTGTTAGACACCAAAGTTGTTATAGGTATGACACTACACACCTGGATATGGT-ACTAGCTGCGAGGAATGAACTAGTTTC--TTTCTGAGCCACATTATTTTGTAAACAGGCAGCCACCATTTCTAGCACCT -s simRat_chr6.simRat.chr6 50305 134 - 647215 AAGCAGTTAGACAC-AAAGGTGTTATAGGTATGGCATTACACGCCTGGATGTACTAAATATCTGTGAAGAATTAATTGTTTGCCATGCCCAAGTTACATTATTTTGTAACGAGGCTGTCACCATCTCAAGCTCCA - -a -s simMouse_chr6.simMouse.chr6 574782 8 + 636262 CTTCAGTC -s Anc0.Anc0refChr3 176310 7 + 222631 CTTCA-TC -s Anc1.Anc1refChr1 15495 7 + 69767 CTTCA-TC -s Anc2.Anc2refChr1 91631 7 + 142988 CTTCC-TC -s mr.mrrefChr3 124775 8 + 181027 CTTCAGTC -s simCow_chr6.simCow.chr6 549788 7 + 602619 CACCC-TC -s simDog_chr6.simDog.chr6 538065 7 + 593897 CTTGC-TC -s simHuman_chr6.simHuman.chr6 546496 7 + 601863 CTTCA-TC -s simRat_chr6.simRat.chr6 50440 8 - 647215 CTTCAGGC - -a -s simMouse_chr6.simMouse.chr6 574790 18 + 636262 AATTGCATGATTGACTGA -s Anc0.Anc0refChr3 176319 18 + 222631 AAGTACATGATCTGCTGA -s Anc1.Anc1refChr1 15504 18 + 69767 AAGTACATGATCTGCTGA -s Anc2.Anc2refChr1 91640 18 + 142988 AAGTACATGATCTGCTGA -s mr.mrrefChr3 124783 18 + 181027 AATTGCATGATTGACTGA -s simCow_chr6.simCow.chr6 549812 18 + 602619 AAGTACATGATCTGCTGA -s simDog_chr6.simDog.chr6 538072 12 + 593897 -AGTAGGTGATAT----- -s simHuman_chr6.simHuman.chr6 546505 18 + 601863 AAGTACATGATCTGCTGA -s simRat_chr6.simRat.chr6 50448 18 - 647215 AATTGCATGATTGACTGA - -a -s simMouse_chr6.simMouse.chr6 574808 45 + 636262 CTGTCTTAGCATTACAATGATAGATTAAGAATCTCAAGGAATATA -s Anc0.Anc0refChr3 176337 42 + 222631 G--CTTTGCTGTTAAAGTGATAGATTTTGAA-CCCAACGAATTTA -s Anc1.Anc1refChr1 15522 42 + 69767 G--CTTTGCTGTTAAAGTGATAGATTTTGAA-CCCAACGAATTTA -s Anc2.Anc2refChr1 91658 42 + 142988 G--CTTTGCTGTTAAAGTGATAGGTTTTGAA-CCCAACTAATTTA -s mr.mrrefChr3 124801 45 + 181027 CTGTCTTAGTATTACAATGATAGATTTAGAATCTCAAGGAATATA -s simCow_chr6.simCow.chr6 549835 42 + 602619 G--CCCTGCTGTTGAATTGACAGGTTTAGCA-CACAACCAGGCCA -s simDog_chr6.simDog.chr6 538084 40 + 593897 ----TTTCCTGTAAAAGTGATAGGTTTTGAA-CCAAACTAATTTA -s simHuman_chr6.simHuman.chr6 546523 42 + 601863 T--CTTTGCTGTTAAGGTGATGGATTTTGAA-CCCAATGAATTTA -s simRat_chr6.simRat.chr6 50466 45 - 647215 CTGTCTGAGTATTACAATGATAGGTTTAGAATGTCAGGGAATATA - -a -s simMouse_chr6.simMouse.chr6 574853 2 + 636262 GC -s Anc1.Anc1refChr1 15564 2 + 69767 GA -s mr.mrrefChr3 124846 2 + 181027 GC -s simHuman_chr6.simHuman.chr6 546568 2 + 601863 GA -s simRat_chr6.simRat.chr6 50511 2 - 647215 GC - -a -s simMouse_chr6.simMouse.chr6 574855 40 + 636262 TCTGAAATAATGTAGCATTGGTTTCAATTGTAATTGTAAA -s Anc0.Anc0refChr3 176379 35 + 222631 ----AAAGAA-GTAAGACTGCTCCATAGAGCAATAACACA -s Anc1.Anc1refChr1 15566 39 + 69767 AGTGAAAGAA-GTAAGACTGCTCCATAGAGCAATAACACA -s Anc2.Anc2refChr1 91700 35 + 142988 ----AATGAA-GCAAGACTACTCCATAGAGCAGAAACACA -s mr.mrrefChr3 124848 40 + 181027 TCTGAAATAATGTAGCATTGGTTTCAATTGTAATTATAAA -s simCow_chr6.simCow.chr6 549877 35 + 602619 ----GATGAA-GCAAGACTACTTTGTAGAACAGAAACCCA -s simDog_chr6.simDog.chr6 538124 35 + 593897 ----ACTGAA-GCAAGATTACTCCATAAGGCAGAAACACA -s simHuman_chr6.simHuman.chr6 546570 39 + 601863 AGTGAGAGAA-GTAAGACTGATGCACAGAGCAATAACACA -s simRat_chr6.simRat.chr6 50584 40 - 647215 TTTGGAGTAATGTAGCATTGGGTTCAATTATAATTATAAA - -a -s simMouse_chr6.simMouse.chr6 574895 7 + 636262 ATGTAGT -s Anc0.Anc0refChr3 176419 7 + 222631 ATGTCGT -s Anc1.Anc1refChr1 15611 7 + 69767 ATGTCGT -s Anc2.Anc2refChr1 91740 7 + 142988 ATGTCGT -s mr.mrrefChr3 124888 7 + 181027 ATGTAGT -s simCow_chr6.simCow.chr6 549917 7 + 602619 GTGTCGT -s simDog_chr6.simDog.chr6 538164 7 + 593897 ATGTCGT -s simHuman_chr6.simHuman.chr6 546615 7 + 601863 ATGTGGT -s simRat_chr6.simRat.chr6 50624 7 - 647215 ATGTAGT - -a -s simMouse_chr6.simMouse.chr6 574902 4 + 636262 GTGG -s Anc0.Anc0refChr3 176429 4 + 222631 GTAA -s Anc1.Anc1refChr1 15621 4 + 69767 GTAA -s Anc2.Anc2refChr1 91750 4 + 142988 GTGA -s mr.mrrefChr3 124895 4 + 181027 GTAG -s simCow_chr6.simCow.chr6 549927 4 + 602619 GAGA -s simDog_chr6.simDog.chr6 538174 4 + 593897 GTGA -s simHuman_chr6.simHuman.chr6 546625 4 + 601863 ATAA -s simRat_chr6.simRat.chr6 50631 4 - 647215 GTAG - -a -s simMouse_chr6.simMouse.chr6 574906 8 + 636262 ATCGGATG -s Anc0.Anc0refChr3 176434 3 + 222631 AAT----- -s Anc1.Anc1refChr1 15626 8 + 69767 AATGGGTC -s Anc2.Anc2refChr1 91755 3 + 142988 AAT----- -s mr.mrrefChr3 124900 8 + 181027 ATTGGATG -s simCow_chr6.simCow.chr6 549932 3 + 602619 CAT----- -s simDog_chr6.simDog.chr6 538179 3 + 593897 AAT----- -s simHuman_chr6.simHuman.chr6 546630 8 + 601863 AATGGGTC -s simRat_chr6.simRat.chr6 50636 8 - 647215 ATTGGATT - -a -s simMouse_chr6.simMouse.chr6 574914 60 + 636262 CAAATATAGTTGTAAGAGTTCAGGTATCACGTGGGTTGGTCAAGCACATCCAATGTCCTA -s Anc0.Anc0refChr3 176437 54 + 222631 CTATTATAATTGTAACAGCTAACTTGTCAC-----TATCTCATGTAGATGCATTAT-CAG -s Anc1.Anc1refChr1 15634 55 + 69767 CTATTATAATTGTAACAGCTAACTTGTCAC-----TATCTCATGTAGATGCATTATTCAG -s Anc2.Anc2refChr1 91758 54 + 142988 CTATTATAATTGTAACAACTAACTTGTCAC-----TAACTCATGTAGATGCGTTAT-CAG -s mr.mrrefChr3 124908 60 + 181027 CAAATATAGTTGTAAGAGTTCAGTTATCACGTGGGTTTGTCAAGCACATCCAATGTCCTA -s simCow_chr6.simCow.chr6 549935 53 + 602619 ATATTATAATTATAACAACTAACTTGTCAC-----TG-CTCATGTAGATGATTTAC-CAG -s simDog_chr6.simDog.chr6 538199 54 + 593897 CTATTGTGACTGTCCCCATGAACTTGTCAC-----CAAGTCATGTAGATGCGTTAT-CAG -s simHuman_chr6.simHuman.chr6 546638 55 + 601863 GCATAATAATTGTAAAAGCTAACTTGTCAT-----TATCTCATATAGATGGATTTTTCAG -s simRat_chr6.simRat.chr6 50644 59 - 647215 CAAATATAGTTGTAGCAGTTCAGTTATCACATGGATTTGTCAGGCACATCCAA-GACTTA - -a -s simMouse_chr6.simMouse.chr6 574974 24 + 636262 TCAACAATCCTCAAGACTGTGTGT -s Anc0.Anc0refChr3 176491 24 + 222631 TCAACAGTCCCTAAAACTTTGTGT -s Anc1.Anc1refChr1 15689 24 + 69767 TCAACAGTCCCTAAAACTTTGTGT -s Anc2.Anc2refChr1 91812 24 + 142988 TCAACAGTCCCTAAAACTTTGTGT -s mr.mrrefChr3 124968 24 + 181027 TCAACAATCCCCAAGACTTTGTGT -s simCow_chr6.simCow.chr6 549988 22 + 602619 T--ATCACACTTAAAACTTTGTAT -s simDog_chr6.simDog.chr6 538269 24 + 593897 TCAACAGTCCCAAAAACTTTGTGT -s simHuman_chr6.simHuman.chr6 546693 24 + 601863 TCAACAGTCCCTAAAGCTTTGTGT -s simRat_chr6.simRat.chr6 50703 24 - 647215 TCAGCAATACCCAAGACTTCATGT - -a -s simMouse_chr6.simMouse.chr6 574998 11 + 636262 GTACCATGGCA -s Anc0.Anc0refChr3 176516 11 + 222631 ATACCATGGTA -s Anc1.Anc1refChr1 15714 11 + 69767 ATACCATGGTA -s Anc2.Anc2refChr1 91838 11 + 142988 ATACCATGGTA -s mr.mrrefChr3 124992 11 + 181027 GTACCATGGCA -s simCow_chr6.simCow.chr6 550012 11 + 602619 ATACCATAGTG -s simDog_chr6.simDog.chr6 538295 11 + 593897 ATACCATGATA -s simHuman_chr6.simHuman.chr6 546718 11 + 601863 ATACCATGGTA -s simRat_chr6.simRat.chr6 50727 11 - 647215 GTACCATGGCA - -a -s simMouse_chr6.simMouse.chr6 575009 5 + 636262 CATAA -s Anc0.Anc0refChr3 176527 5 + 222631 GTATA -s Anc1.Anc1refChr1 15725 5 + 69767 GTATA -s Anc2.Anc2refChr1 91849 5 + 142988 GTATA -s mr.mrrefChr3 125003 5 + 181027 CATAA -s simCow_chr6.simCow.chr6 550023 5 + 602619 CATGA -s simDog_chr6.simDog.chr6 538315 5 + 593897 GTATA -s simHuman_chr6.simHuman.chr6 546729 5 + 601863 GTATA -s simRat_chr6.simRat.chr6 50738 5 - 647215 CATCT - -a -s simMouse_chr6.simMouse.chr6 575014 78 + 636262 TTTGATCTGGCCCCCTGAATAGGACAATACCTTAACACTCTACATCCTGTAGGCCATGAACAAACGTGAAGTCAATAA -s Anc0.Anc0refChr3 176532 71 + 222631 TTAAATCAGGCTCCCTGTATAGGGAGACATCCTCACACTCCA-------TAGGCCATCATCAGATATGATGTTGCTAA -s Anc1.Anc1refChr1 15730 71 + 69767 TTAAATCAGGCTCCCTGTATAGGGAGACATCCTCACACTCCA-------TAGGCCATCATCAGATATGATGTTGCTAA -s Anc2.Anc2refChr1 91854 71 + 142988 TTAAATCAGGCTCCCTGTATAGAGAGACATCCTCACTTTCCA-------TGGGCCATCGTCAGATATGATGTTGCTAA -s mr.mrrefChr3 125008 78 + 181027 TTAGATCTGGCTCCCTGAATAGGGCAATACCTTAACACTCTACATCCTGTAGGCCATCATCAAACATGAAGTCAATAA -s simCow_chr6.simCow.chr6 550028 70 + 602619 TTAAACCTGATTCCCTGTCTAGTGAGACATCCTCACTTTCCA-------TTGTCTGTCGTCTTATGTAAGGTTG-CAA -s simDog_chr6.simDog.chr6 538331 62 + 593897 TTAAATCAGGCTCCCTGTAGAGAGAGATAG---------CTG-------CGGGCCATTGCCAGATATGATGTTTCTAA -s simHuman_chr6.simHuman.chr6 546734 71 + 601863 TCAAATCATGCTCCCTGTATAGGGAGACATGCTCATACTCCA-------TAGGCCATCATCAGAAATGATGTTGTTAA -s simRat_chr6.simRat.chr6 50743 77 - 647215 TTACATCTGGCTCTGTGAATTGGGCAATA-CTCAACACTCTACTTGCTGTGGGTCATCATCAAACATGAAGTCAATAA - -a -s simMouse_chr6.simMouse.chr6 575092 11 + 636262 TTCCCGCTTTG -s Anc0.Anc0refChr3 176608 11 + 222631 AATCTACTGTG -s Anc1.Anc1refChr1 15806 11 + 69767 AATCTACTGTG -s Anc2.Anc2refChr1 91930 11 + 142988 AATCTACTATG -s mr.mrrefChr3 125086 11 + 181027 TACCTACTGTG -s simCow_chr6.simCow.chr6 550103 11 + 602619 AGTCTGTTATG -s simDog_chr6.simDog.chr6 538393 11 + 593897 AATTTACTATG -s simHuman_chr6.simHuman.chr6 546810 11 + 601863 CATCTACTGTT -s simRat_chr6.simRat.chr6 50820 11 - 647215 TACCTACTGTA - -a -s simMouse_chr6.simMouse.chr6 575103 9 + 636262 GAAGGAGGA -s Anc0.Anc0refChr3 176621 9 + 222631 GGGGGAAGA -s Anc1.Anc1refChr1 15819 9 + 69767 GGGGGAAGA -s Anc2.Anc2refChr1 91943 9 + 142988 GGGGCAAAA -s mr.mrrefChr3 125097 9 + 181027 GAAGGAGGA -s simCow_chr6.simCow.chr6 550116 9 + 602619 GGGGCAAAA -s simDog_chr6.simDog.chr6 538406 9 + 593897 AGGACAAAA -s simHuman_chr6.simHuman.chr6 546823 9 + 601863 GGGGGAAGA -s simRat_chr6.simRat.chr6 50831 9 - 647215 CAAGGAGGA - -a -s simMouse_chr6.simMouse.chr6 575112 46 + 636262 CCTGACCAGTGAATCCTACAGTGCTAGTCCAGACCGTGGCCTGGTG -s Anc0.Anc0refChr3 176630 39 + 222631 CCTGATCACTGAA------AGT-CTGGACCATACTTCTGGCTGGTG -s Anc1.Anc1refChr1 15828 39 + 69767 CCTGATCACTGAA------AGT-CTGGACCATACTTCTGGCTGGTG -s Anc2.Anc2refChr1 91955 39 + 142988 CCTGATCACTGAG------GGT-CTGGACCATACTTCTGGCTGGTG -s mr.mrrefChr3 125106 46 + 181027 CCTGACCAGTGAATCCTACAGTGCTAGTCCAGACTTTGGCCTGGTG -s simCow_chr6.simCow.chr6 550128 32 + 602619 CCTGACTAGTG--------------GGATCATATTTCTGGCCACTG -s simDog_chr6.simDog.chr6 538418 39 + 593897 CCTGATCACGGAG------GGT-CTAGACCATACTTCTGGCTGGTG -s simHuman_chr6.simHuman.chr6 546832 39 + 601863 GCTGGTCAATGAA------AGT-CTGGGCCATACTTCTGGCTGTTG -s simRat_chr6.simRat.chr6 50840 46 - 647215 CCTGACCAGTGAGTCTTACAGAGCTAGTCCACACTTTGGCATGGTG - -a -s simMouse_chr6.simMouse.chr6 575158 13 + 636262 AGTACCAATGAAT -s Anc0.Anc0refChr3 176673 13 + 222631 GGTACAAGTGACT -s Anc1.Anc1refChr1 15871 13 + 69767 GGTACAAGTGACT -s Anc2.Anc2refChr1 92005 13 + 142988 GGTAGAAGTGACT -s mr.mrrefChr3 125152 13 + 181027 AGTACAAATGAAT -s simCow_chr6.simCow.chr6 550171 13 + 602619 GGTGGGAGTGACT -s simDog_chr6.simDog.chr6 538468 13 + 593897 AGTAGATGTGATT -s simHuman_chr6.simHuman.chr6 546875 13 + 601863 GGTACAAGTGACT -s simRat_chr6.simRat.chr6 50886 13 - 647215 AGTAGAAATAAAT - -a -s simMouse_chr6.simMouse.chr6 575171 31 + 636262 GCCTGCCACCTCACCTTTACCAATCTGACTG -s Anc0.Anc0refChr3 176686 31 + 222631 GCCTGTCACCCCAACTTTTCCAGTCCGGTTA -s Anc1.Anc1refChr1 15884 31 + 69767 GCCTGTCACCCCAACTTTTCCAGTCCGGTTA -s Anc2.Anc2refChr1 92018 31 + 142988 GCCTGTCACCCCAACATTTCCAGTCCGGTTA -s mr.mrrefChr3 125165 31 + 181027 GCCTGTCACCCCACCTTTTCCAATCTGGCTA -s simCow_chr6.simCow.chr6 550184 31 + 602619 GCCTTTCATCCCAACCAATCCAATCTGGTTA -s simDog_chr6.simDog.chr6 538491 31 + 593897 GCCTGTCACCCCACCATTTCCAGTCCGGTTA -s simHuman_chr6.simHuman.chr6 546888 30 + 601863 GTCTGT-ACCCCAACTTTTCCAGTCCGGATA -s simRat_chr6.simRat.chr6 50899 31 - 647215 GCGTGTCACCCCATCTTTTCCAATCAGGCTA - -a -s simMouse_chr6.simMouse.chr6 575202 11 + 636262 CTAGAATCCAA -s Anc0.Anc0refChr3 176717 11 + 222631 CTAAAATCCAA -s Anc1.Anc1refChr1 15915 11 + 69767 CTAAAATCCAA -s Anc2.Anc2refChr1 92049 11 + 142988 CTGAACTGCAA -s mr.mrrefChr3 125196 11 + 181027 CTAGAATCCAA -s simDog_chr6.simDog.chr6 538523 11 + 593897 CTGAACTGCAA -s simHuman_chr6.simHuman.chr6 546918 11 + 601863 CTATAATCAAA -s simRat_chr6.simRat.chr6 50930 3 - 647215 CTA-------- - -a -s simMouse_chr6.simMouse.chr6 575213 24 + 636262 GGTGAACCATTGAACACAACTCCT -s Anc0.Anc0refChr3 176729 24 + 222631 GGTGAAGCATTGAatccaaaTTCT -s Anc1.Anc1refChr1 15927 24 + 69767 GGTGAAGCATTGAatccaaaTTCT -s Anc2.Anc2refChr1 92061 24 + 142988 GGTGAAGTGTAGAatccaagGTCT -s mr.mrrefChr3 125207 24 + 181027 GGTGAACCATTGAACCCAAATTCT -s simCow_chr6.simCow.chr6 550215 4 + 602619 --------------------ATCT -s simDog_chr6.simDog.chr6 538535 24 + 593897 GGTGAAGTGTAGAATCCAAGGTCT -s simHuman_chr6.simHuman.chr6 546930 24 + 601863 GACAAAACATTGAatccaaattct -s simRat_chr6.simRat.chr6 50933 21 - 647215 ---GGACCATTGAAGCCAAATTCT - -a -s simMouse_chr6.simMouse.chr6 575237 71 + 636262 TCCTAACACCTCAGAGCTTGTAACCTGCTGAAGGATTAAAAAATGGGGGCCCCCCAAGGAAAATTACTCCA -s Anc0.Anc0refChr3 176753 66 + 222631 TGCTAACCCCCCAGCACCCAcaac---ctgaaagtctaaaaact-gggacCCCC-GAGctacaTTGCTCCC -s Anc1.Anc1refChr1 15951 67 + 69767 TGCTAACCCCCCAGCACCCAcaac---ctgaaagtctaaaaact-gggacCCCCtGAGctacaTTGCTCCC -s Anc2.Anc2refChr1 92085 66 + 142988 TGCTAACCCCCCAGCACCCAcatc---ctggaagtcttaaaact-gcgacCCCC-GAGctacaTTGCTCCC -s mr.mrrefChr3 125231 71 + 181027 TGCTAACACCTCAGAGCTTGCAACCTGCTGAAAGATTAAAAAATGGGGACCCCCTGAGGAAAATTACTCCA -s simCow_chr6.simCow.chr6 550219 40 + 602619 TGCTAGTACCCTAGCACTCG------------------------------CCCC-GAACTACATTACTACC -s simDog_chr6.simDog.chr6 538565 61 + 593897 TACTAACCCCCCATCACCCACATC---CTGGAAGTCTTAAAACT-GCGACCCCC-GAG-----TTGATCAC -s simHuman_chr6.simHuman.chr6 546954 67 + 601863 tgctaaccccgcagcacgcacaac---ctgaaagcctaaaaact-gggaccccttgagctatattgctccc -s simRat_chr6.simRat.chr6 50954 71 - 647215 TGCTAAAACCTCAGTGCCTGCAACTGGCTGAAAGTTTAAAAAATGGGGACCGCCTGAGGAAAGTTAATTCA - -a -s simMouse_chr6.simMouse.chr6 575308 1 + 636262 C -s Anc0.Anc0refChr3 176819 1 + 222631 t -s Anc1.Anc1refChr1 16018 1 + 69767 t -s Anc2.Anc2refChr1 92151 1 + 142988 t -s mr.mrrefChr3 125302 1 + 181027 C -s simCow_chr6.simCow.chr6 550267 1 + 602619 t -s simDog_chr6.simDog.chr6 538626 1 + 593897 T -s simHuman_chr6.simHuman.chr6 547021 1 + 601863 t -s simRat_chr6.simRat.chr6 51025 1 - 647215 C - -a -s simMouse_chr6.simMouse.chr6 575309 114 + 636262 ATACAAAGCACTGTGCTGCTGAGATTATTTCTCCCTTCTGGGGCCATGATAGATTTCTATCCCAAGATAATCTAAATCCCGAGATAAGATTGTACTGCCAAGATTGCTCCCTCC -s Anc0.Anc0refChr3 176820 97 + 222631 cttcaaaccgctgtgttgctgacattattccctctttcttgtgccataactcatttca-----------------gttccccgataaggttgtgttgctgacattactcccctc -s Anc1.Anc1refChr1 16019 97 + 69767 cttcaaaccgctgtgttgctgacattattccctctttcttgtgccataactcatttca-----------------gttccccgataaggttgtgttgctgacattactcccctc -s Anc2.Anc2refChr1 92152 97 + 142988 cttcaatctgctgtgttgctaacattattccctctttcttgtgtcataactcacttca-----------------gttcccccataaggttgtgttgctgacattactgccctt -s mr.mrrefChr3 125303 113 + 181027 ATACAAAGCACTGTGCTGCTGAGATTATTTCTCCCTTCTGGGGCCATAATAGATTTCTATCCCAAGATAATCT-AATCCCGAGATAAGATTGTACTGCCAAgATTACTCCCTCC -s simCow_chr6.simCow.chr6 550268 87 + 602619 ctttgatgtgctgtgttgctcatattatgccctctttcttgtgttttgactcacttca-----------------tttcccgtataaggttgtg----------tgctacattt -s simDog_chr6.simDog.chr6 538628 93 + 593897 cttcaatctcctgtgttgctaacatcattgcctctttcttgtgtcatagc----ttca-----------------gttccaccacaaggttgccttgctgacattactgccctt -s simHuman_chr6.simHuman.chr6 547022 88 + 601863 ctccagaacgctgtgtcactgactttattccctc---------ccataacgtatttca-----------------gttccctgataaggttgtgttgctgacattactcctctc -s simRat_chr6.simRat.chr6 51026 112 - 647215 ATTCAAAGCACTGTGCTGCTAAGATTATTGCTCCTTTCTGGAGCCACAATAGATCTCTATCCCAAGGTTATCT-ATCCCCAAGATAAGATTGTACTGCCAA-CTTACTCCCTCC - -a -s simMouse_chr6.simMouse.chr6 575423 57 + 636262 TCCCCGCTGTGTCTAACATCTCAGCACAGATGCAAAGTTTATGCACTAATCCCCATG -s Anc0.Anc0refChr3 176917 43 + 222631 tccctg----------catttc----catatcctaaatttatttgctaaccccccag -s Anc1.Anc1refChr1 16116 43 + 69767 tccctg----------catttc----catatcctaaatttatttgctaaccccccag -s Anc2.Anc2refChr1 92249 43 + 142988 tcactg----------catttt----catatcctaaatttttttgctaaccccccag -s mr.mrrefChr3 125416 57 + 181027 TCCCCGCTGTGTCTAACATCTCAGCACAGATGCAAAGTTTATTCACTAATCCCCATG -s simCow_chr6.simCow.chr6 550355 43 + 602619 tcactg----------catttt----agtatcctagatttttttgctctccccctag -s simDog_chr6.simDog.chr6 538721 43 + 593897 tcactc----------catttt----CATATCCTAAACTTTTTTGCTAAGCCCTCAG -s simHuman_chr6.simHuman.chr6 547111 43 + 601863 tccctg----------tatttc----catatcctaaatttatttgtcaaccccccag -s simRat_chr6.simRat.chr6 51138 57 - 647215 TCCCCGCTGCGTCTAATATCTCAGCACAGATGGAAAGTTTATTCACTAATCCCCATG - -a -s simMouse_chr6.simMouse.chr6 575480 230 + 636262 TGATCCTGACCTGATAGTCTTAACACTAGGCCTCTAAGAACTGCATTGTGTCTGAGTTGCAAATTGAAAACCCCAAAACTGGTACTCACCAAACTAGGCTGCACCCACAAAGGTGAACAAGCGTGAATGGGCATCCTAGCTGATGATCTCGGACTATAGCAGTTGTGCCCCAATCTCTATACGATCCAAATGAACTAAGTGGAAGGGTAGTGTGTGATCCACTCCTGCTG -s Anc0.Anc0refChr3 176991 153 + 222631 tgctcatgacctgaa----------------------gagctgtatcacatctcaattccaaactgaaaa--------------------gagctgttttgcgcccac---at-gaccaaactagaaggg-------------tgat-tcggaat--------------ccaacctgTATTacatccaaataacctaat--gaagagtggtgtgGAATCCAACCTT-CTG -s Anc1.Anc1refChr1 16190 189 + 69767 tgctcatgacctgaaagtcttaaaatt----------gagctgtatcacatctcaattccaaactgaaaatcttaaaattagggcccatcgagctgttttgcgcccac---attgaccaaactagaaggg-------------tgatctcggaat--------------ccaacctgTATTacatccaaataacctaatcagaagagtggtgtgGAATCCAACCTT-CTG -s Anc2.Anc2refChr1 92323 153 + 142988 tgctcagtacctgaa----------------------gagctgtaacacacatccaatccagactggaaa--------------------gagatgttttgtgccctc---ac-ggccaaactagaaggg-------------tgat-tcaaaat--------------tcaacctgTATTacatgtggataacccaat--gaagttaggtatgCAATCCAACCTC-CTG -s mr.mrrefChr3 125473 230 + 181027 TGATCCTGACCTGATAGTCTTAACACTAGGCCTCTAAGAGCTGCATTGTgtctgagttgcaaattgaaaaccccaaaactggtactcaccaaactaGGCTGCGCCCACAAAAGTGAACAAGCGTGAATGGGCATCCTAGcTGATGATCTCGGACTATAGCAGTTGTGCCCCAATCTGTATACCATCCAAATGACCTAAGTGGAAGAGTAgTGTGGAATCCACTCTTGCTG -s simCow_chr6.simCow.chr6 550431 122 + 602619 tgctcagtacctgaa----------------------GAGCTGTAACACACATCCAATCCAGACTGGAAA--------------------GAGATGTTTTGTGCCCTC---AC-GGCCAAACTAGAAGGG-------------TGAT-TCAAAAT--------------TCAACCTGTAGT---------------------------------AAATCCAACCAC-CTG -s simDog_chr6.simDog.chr6 538770 50 + 593897 ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TATCACATGTGGATAACCCAAT--GAAGTTAGGTATGCAGTCCAACCTC-CTG -s simHuman_chr6.simHuman.chr6 547185 189 + 601863 tgctcatgacctgaaagtcttaaaatt----------gggctgtatcacatcctaatttcaatatgaaagtcttaaaattagggcccatcgagccgtattgcgcccac---attaagtaaacaaggagag-------------tgatctaggaat--------------ccaacctgtattgcatccaaataacctaaccagaagagtgatgtagaatacaACCTT-CTG -s simRat_chr6.simRat.chr6 51195 181 - 647215 TGATCCTGACCTGATAATCTTAACACTAGGCTTCTAAGAGCTGCATTGT-----------------------------------------------GGCTGTGCCCACAAAAGTGAACAAGCTTGAATTGGCATCCTAG-TGATAATGTCGGGCTATATCAGTTGTGCCTAAATCTGTATCCCATCCATATGACTTAAGTGGAAGAGTA-TGTGGAATCCCTTCTTGCTG - -a -s simMouse_chr6.simMouse.chr6 575710 20 + 636262 GTTCCTCTGCCCAGATCATG -s Anc0.Anc0refChr3 177144 18 + 222631 GTTCTGC--CTCATATCATA -s Anc1.Anc1refChr1 16379 18 + 69767 GTTCTGC--CTCATATCATA -s Anc2.Anc2refChr1 92479 18 + 142988 GTTCTGC--CTCATATCATA -s mr.mrrefChr3 125703 20 + 181027 GTTCCTCTGCCCATATCATG -s simCow_chr6.simCow.chr6 550556 18 + 602619 CTTCTGC--TGCTTACCATA -s simDog_chr6.simDog.chr6 538823 17 + 593897 GCT-CAC--CTTATATCATA -s simHuman_chr6.simHuman.chr6 547374 18 + 601863 GTTTTGC--CTCATATTATA -s simRat_chr6.simRat.chr6 51376 20 - 647215 GTTCCTCTGCCCATAGCATG - -a -s simMouse_chr6.simMouse.chr6 575730 2 + 636262 GA -s Anc0.Anc0refChr3 177162 1 + 222631 G- -s Anc1.Anc1refChr1 16397 1 + 69767 G- -s Anc2.Anc2refChr1 92497 1 + 142988 G- -s mr.mrrefChr3 125723 2 + 181027 GA -s simCow_chr6.simCow.chr6 550574 1 + 602619 G- -s simDog_chr6.simDog.chr6 538849 1 + 593897 G- -s simHuman_chr6.simHuman.chr6 547392 1 + 601863 G- -s simRat_chr6.simRat.chr6 51396 2 - 647215 GA - -a -s simMouse_chr6.simMouse.chr6 575732 38 + 636262 CTATATATTTGCTGCCATCATATCATGTCACACTCTAT -s Anc0.Anc0refChr3 177163 15 + 222631 CTATAGCTT-----------------------ATCTAT -s Anc1.Anc1refChr1 16398 15 + 69767 CTATAGCTT-----------------------ATCTAT -s Anc2.Anc2refChr1 92498 15 + 142988 CTATGGCTT-----------------------AGCCAT -s mr.mrrefChr3 125725 38 + 181027 CTATATCTTTGCTGCCATCATATCATGTCACACTCTAT -s simCow_chr6.simCow.chr6 550576 15 + 602619 CTATGGCTT-----------------------AGTCAT -s simDog_chr6.simDog.chr6 538850 15 + 593897 CTACGGCTT-----------------------AGCCAT -s simHuman_chr6.simHuman.chr6 547393 15 + 601863 CTATAGCTT-----------------------ATCTAT -s simRat_chr6.simRat.chr6 51398 38 - 647215 CTATATCTTTGTTACCATCAAATCATGTCACACTCCAT - -a -s simMouse_chr6.simMouse.chr6 575770 24 + 636262 TTGACAAGAAAGGGTAGAATGACA -s Anc0.Anc0refChr3 177178 23 + 222631 TGGTCAAGCTTAGGTACAAT-ACA -s Anc1.Anc1refChr1 16413 23 + 69767 TGGTCAAGCTTAGGTACAAT-ACA -s Anc2.Anc2refChr1 92513 23 + 142988 TGGTCAAGCTTAGTTACAAT-TCA -s mr.mrrefChr3 125763 24 + 181027 TTGTCAAGAAAGGGTAGAATGACA -s simCow_chr6.simCow.chr6 550592 23 + 602619 GGGTCAAGCTTAGATACAGT-TCA -s simDog_chr6.simDog.chr6 538865 17 + 593897 TGGTCCAGT---GTAACAAT---- -s simHuman_chr6.simHuman.chr6 547408 23 + 601863 TAATCAAGCCGAGGTACAAT-ACA -s simRat_chr6.simRat.chr6 51436 24 - 647215 TTGTCAAGATTGGGTAGAATGACA - -a -s simMouse_chr6.simMouse.chr6 575794 22 + 636262 CAATCTCTGCAGCCTGAAACAA -s Anc0.Anc0refChr3 177201 19 + 222631 CA---TCTGCAGCCTGGTACAG -s Anc1.Anc1refChr1 16436 19 + 69767 CA---TCTGCAGCCTGGTACAG -s Anc2.Anc2refChr1 92536 19 + 142988 TA---TCTGCAGCCTGGTACAG -s mr.mrrefChr3 125787 22 + 181027 CAATCTCTGCAGCCTGAAACAA -s simCow_chr6.simCow.chr6 550619 19 + 602619 TA---TCTGCAGCCTGGCACAG -s simDog_chr6.simDog.chr6 538882 18 + 593897 -C---TCTGCTGCCTGGTAGAG -s simHuman_chr6.simHuman.chr6 547431 19 + 601863 CA---TCTGCAGCCTGGGACAG -s simRat_chr6.simRat.chr6 51460 22 - 647215 CAATCTCTGCTGCCTGAAACAA - -a -s simMouse_chr6.simMouse.chr6 575816 27 + 636262 TTATTGTACTTTCATTCATCCCCAATC -s Anc0.Anc0refChr3 177220 27 + 222631 TTCTTGTACTGTCTTTCATCCCCAATG -s Anc1.Anc1refChr1 16455 27 + 69767 TTCTTGTACTGTCTTTCATCCCCAATG -s Anc2.Anc2refChr1 92555 27 + 142988 TTCTCTTACTGTCTTTCATCCCCAATG -s mr.mrrefChr3 125809 27 + 181027 TTATTGTACTTTCTTTCATCCCCAATC -s simCow_chr6.simCow.chr6 550639 26 + 602619 TTCTCATACTGTCTGTCATCCCCAA-C -s simDog_chr6.simDog.chr6 538900 27 + 593897 TTCTCTTACTGTCTTTCATCCCCAATG -s simHuman_chr6.simHuman.chr6 547450 27 + 601863 TTCTTGTACTGTCTTTCATCCCCAATT -s simRat_chr6.simRat.chr6 51482 26 - 647215 TTATTGTACTTTCTTTCAT-CCCAATC - -a -s simMouse_chr6.simMouse.chr6 575843 39 + 636262 AACTAATCTAAAGAGATGGCGCCTATTAAATGGCCCACA -s Anc0.Anc0refChr3 177247 9 + 222631 GATTAGG------------------------------CA -s Anc1.Anc1refChr1 16482 9 + 69767 GATTAGG------------------------------CA -s Anc2.Anc2refChr1 92582 9 + 142988 GATTAGG------------------------------CA -s mr.mrrefChr3 125836 9 + 181027 AACTAAT------------------------------CA -s simCow_chr6.simCow.chr6 550665 9 + 602619 AATAAAT------------------------------CA -s simDog_chr6.simDog.chr6 538931 9 + 593897 GAGTGGG------------------------------CA -s simHuman_chr6.simHuman.chr6 547477 9 + 601863 GATTACG------------------------------CA -s simRat_chr6.simRat.chr6 51508 9 - 647215 AACTAAT------------------------------CA - -a -s simMouse_chr6.simMouse.chr6 575882 1 + 636262 A -s Anc0.Anc0refChr3 177256 1 + 222631 A -s Anc1.Anc1refChr1 16491 1 + 69767 A -s Anc2.Anc2refChr1 92591 1 + 142988 A -s mr.mrrefChr3 125845 1 + 181027 A -s simCow_chr6.simCow.chr6 550674 1 + 602619 T -s simDog_chr6.simDog.chr6 538951 1 + 593897 A -s simHuman_chr6.simHuman.chr6 547486 1 + 601863 A -s simRat_chr6.simRat.chr6 51517 1 - 647215 A - -a -s simMouse_chr6.simMouse.chr6 575883 5 + 636262 AGAGT -s Anc0.Anc0refChr3 177259 5 + 222631 AGAGG -s Anc1.Anc1refChr1 16494 5 + 69767 AGAGG -s Anc2.Anc2refChr1 92594 5 + 142988 ATAGG -s mr.mrrefChr3 125846 5 + 181027 AGAGT -s simCow_chr6.simCow.chr6 550677 5 + 602619 AAAAC -s simDog_chr6.simDog.chr6 538954 5 + 593897 ATAGG -s simHuman_chr6.simHuman.chr6 547489 5 + 601863 AGAGG -s simRat_chr6.simRat.chr6 51518 5 - 647215 AGAGT - -a -s simMouse_chr6.simMouse.chr6 575888 17 + 636262 GGTGCCACCCGGCTTAT -s Anc0.Anc0refChr3 177264 17 + 222631 GGTGACATCCCACATGT -s Anc1.Anc1refChr1 16499 17 + 69767 GGTGACATCCCACATGT -s Anc2.Anc2refChr1 92600 17 + 142988 AGTCACATCCCACATGT -s mr.mrrefChr3 125851 17 + 181027 GGTGCCACCCCACTTAT -s simCow_chr6.simCow.chr6 550683 17 + 602619 AGTTGCATCCCACATGT -s simDog_chr6.simDog.chr6 538960 17 + 593897 AGTCATGTCTCACACGT -s simHuman_chr6.simHuman.chr6 547494 17 + 601863 GGTGTCATCCCACATGT -s simRat_chr6.simRat.chr6 51523 17 - 647215 GGTGCCGCCCCATGTAC - -a -s simMouse_chr6.simMouse.chr6 575905 21 + 636262 GGCAAATTTTTGTCCCAGTTT -s Anc0.Anc0refChr3 177302 21 + 222631 AGAGAAGGTTTGTTCCACTTT -s Anc1.Anc1refChr1 16537 21 + 69767 AGAGAAGGTTTGTTCCACTTT -s Anc2.Anc2refChr1 92638 21 + 142988 ATAGAAGGTTTGTTCCACTTT -s mr.mrrefChr3 125868 21 + 181027 GGCAAATTTTTGTCCCAGTTT -s simCow_chr6.simCow.chr6 550721 21 + 602619 ATAGAAGGTTTATTCCACTTT -s simDog_chr6.simDog.chr6 538998 21 + 593897 ATAGAAGGTTTGTTCCTCTCT -s simHuman_chr6.simHuman.chr6 547532 21 + 601863 AGAGAAGGTTTGTTACACTTT -s simRat_chr6.simRat.chr6 51540 21 - 647215 AGCAAATTTTTGTCCCAGTTT - -a -s simMouse_chr6.simMouse.chr6 575926 15 + 636262 CGAACTCACTACATG -s Anc0.Anc0refChr3 177337 15 + 222631 CCAACTAACTACATG -s Anc1.Anc1refChr1 16572 15 + 69767 CCAACTAACTACATG -s Anc2.Anc2refChr1 92673 15 + 142988 CCAACAAACTACATG -s mr.mrrefChr3 125889 15 + 181027 CGAACTCACTACATG -s simCow_chr6.simCow.chr6 550756 15 + 602619 CTCACACACTACATG -s simDog_chr6.simDog.chr6 539033 15 + 593897 CCAACAAATTTTGTG -s simHuman_chr6.simHuman.chr6 547567 15 + 601863 CCAACTTGCTACACA -s simRat_chr6.simRat.chr6 51561 15 - 647215 CAAATTCACGTCAAG - -a -s simMouse_chr6.simMouse.chr6 575941 10 + 636262 CTACTATAAT -s Anc0.Anc0refChr3 177352 10 + 222631 CTCCTATAAT -s Anc1.Anc1refChr1 16587 10 + 69767 CTCCTATAAT -s Anc2.Anc2refChr1 92688 10 + 142988 GTCCTATGAT -s mr.mrrefChr3 125904 10 + 181027 CTACTATAAT -s simCow_chr6.simCow.chr6 550771 10 + 602619 GTCTTATGAT -s simDog_chr6.simDog.chr6 539048 10 + 593897 GTCCCATGAT -s simHuman_chr6.simHuman.chr6 547585 10 + 601863 CTCCTATAAT -s simRat_chr6.simRat.chr6 51576 10 - 647215 CTGCTATAAT - -a -s simMouse_chr6.simMouse.chr6 575951 5 + 636262 AAGTA -s Anc0.Anc0refChr3 177368 5 + 222631 AAGTC -s Anc1.Anc1refChr1 16603 5 + 69767 AAGTC -s Anc2.Anc2refChr1 92704 5 + 142988 AAAAC -s mr.mrrefChr3 125914 5 + 181027 AAGTA -s simCow_chr6.simCow.chr6 550787 5 + 602619 GAACC -s simDog_chr6.simDog.chr6 539064 5 + 593897 AAAAC -s simHuman_chr6.simHuman.chr6 547614 5 + 601863 AAGTC -s simRat_chr6.simRat.chr6 51586 5 - 647215 AAGTA - -a -s simMouse_chr6.simMouse.chr6 575956 6 + 636262 CAGAGG -s Anc0.Anc0refChr3 177373 6 + 222631 ATGTGG -s Anc1.Anc1refChr1 16608 6 + 69767 ATGTGG -s Anc2.Anc2refChr1 92709 6 + 142988 ATGTGG -s mr.mrrefChr3 125919 6 + 181027 CAGAGG -s simCow_chr6.simCow.chr6 550792 6 + 602619 ATGGGG -s simDog_chr6.simDog.chr6 539069 6 + 593897 ATGTGA -s simHuman_chr6.simHuman.chr6 547622 6 + 601863 ATGTAG -s simRat_chr6.simRat.chr6 51591 6 - 647215 CAGTGG - -a -s simMouse_chr6.simMouse.chr6 575962 5 + 636262 TATTC -s Anc0.Anc0refChr3 177379 5 + 222631 TGTCC -s Anc1.Anc1refChr1 16614 5 + 69767 TGTCC -s Anc2.Anc2refChr1 92722 5 + 142988 TGTCA -s mr.mrrefChr3 125925 5 + 181027 TATTC -s simCow_chr6.simCow.chr6 550805 5 + 602619 TGGCA -s simDog_chr6.simDog.chr6 539082 5 + 593897 TGTCA -s simHuman_chr6.simHuman.chr6 547628 5 + 601863 TGTCC -s simRat_chr6.simRat.chr6 51597 5 - 647215 TATTC - -a -s simMouse_chr6.simMouse.chr6 575967 4 + 636262 ACTT -s Anc0.Anc0refChr3 177386 4 + 222631 ACAA -s Anc1.Anc1refChr1 16621 4 + 69767 ACAA -s Anc2.Anc2refChr1 92729 4 + 142988 ACAA -s mr.mrrefChr3 125930 4 + 181027 ACTT -s simCow_chr6.simCow.chr6 550812 4 + 602619 ACAA -s simDog_chr6.simDog.chr6 539089 4 + 593897 ACAA -s simHuman_chr6.simHuman.chr6 547635 4 + 601863 ACCC -s simRat_chr6.simRat.chr6 51602 4 - 647215 ACTT - -a -s simMouse_chr6.simMouse.chr6 575971 4 + 636262 GTTC -s Anc0.Anc0refChr3 177390 4 + 222631 ATTC -s Anc1.Anc1refChr1 16625 4 + 69767 ATTC -s Anc2.Anc2refChr1 92733 4 + 142988 ATTC -s mr.mrrefChr3 125934 4 + 181027 GTTC -s simCow_chr6.simCow.chr6 550816 4 + 602619 AAGC -s simDog_chr6.simDog.chr6 539109 4 + 593897 ATTC -s simHuman_chr6.simHuman.chr6 547639 4 + 601863 ATTC -s simRat_chr6.simRat.chr6 51606 3 - 647215 GTT- - -a -s simMouse_chr6.simMouse.chr6 575975 15 + 636262 TCATAAGCTTCCATT -s Anc0.Anc0refChr3 177394 15 + 222631 TCATAAACTAACATT -s Anc1.Anc1refChr1 16629 15 + 69767 TCATAAACTAACATT -s Anc2.Anc2refChr1 92737 15 + 142988 TCATTAACTAAGACC -s mr.mrrefChr3 125938 15 + 181027 TCATAAGCTTCCATT -s simCow_chr6.simCow.chr6 550826 15 + 602619 TCATTAACTGAAACC -s simDog_chr6.simDog.chr6 539113 14 + 593897 TCATTAAA-AAGACC -s simHuman_chr6.simHuman.chr6 547643 15 + 601863 TCATATACTAACATT - -a -s simMouse_chr6.simMouse.chr6 575990 94 + 636262 TTGTGAACCCCACAGAGAAGGATCAGGAAACACACGGTTTTTACCTGACCATATTACTCAGCCTCAATGGGTCTGGGAAGGTGTTGAGAACAGC -s Anc0.Anc0refChr3 177410 94 + 222631 CTGTGAACGCCACAGGTGTGGGCCAGTAAACACATAGTTGTTGCCTGACCATATAAGTCAGCCCCAGGGAGTCTGGTAACCTGGTGATAACAGC -s Anc1.Anc1refChr1 16645 94 + 69767 CTGTGAACGCCACAGGTGTGGGCCAGTAAACACATAGTTGTTGCCTGACCATATAAGTCAGCCCCAGGGAGTCTGGTAACCTGGTGATAACAGC -s Anc2.Anc2refChr1 92753 94 + 142988 CTGTGAACGGCACAGGTGTGGGCCAGTAAACACATAGGTGTTGCCTGACCATATAAGACAGCCCCAGGGAGTCTGGTAACCTAGTGCCAACAGC -s mr.mrrefChr3 125953 94 + 181027 TTGTGAACCCCACAGAGAAGGATCAGGAAACACACAGTTTTTACCTGACCATATTACTCAGCCCCAGTGGGTCTGGGAAGGTGTTGATAACAGC -s simCow_chr6.simCow.chr6 550842 94 + 602619 CTGTGAATCGCACAAGTATGGGCCAATAAACACATAAGCATTGTCTGAGCATATAACCCCAGCCCAGGGAGTTGAGTGGCCTATTGTCAACAGC -s simDog_chr6.simDog.chr6 539128 89 + 593897 CTGTGAACGGCACAGGTGTGGGCCAGTAAAC----GGGTGTTGCCTGACCATATAAGATAGCCTCAGGGAGTCTGGTAACCT-GTGCCAACAGC -s simHuman_chr6.simHuman.chr6 547659 94 + 601863 CTGTAACCTCCACAGGTGTGAGCCAGTAAACACATAGTTGTTTCCTGACTATATAATTCAGCCCCAGGGTGTCTGGTAACCTGGTGATAACGGC -s simRat_chr6.simRat.chr6 51609 72 - 647215 ----------------------TCAGGAAACATACAGTTATTACCTCGCCTCATTACTCAGTCCCAGTGGGTCTGGGACGGTGTTGATAAGAGC - -a -s simMouse_chr6.simMouse.chr6 576084 11 + 636262 CTTAAGATTGA -s Anc0.Anc0refChr3 177515 11 + 222631 CGTGGGATGGA -s Anc1.Anc1refChr1 16750 11 + 69767 CGTGGGATGGA -s Anc2.Anc2refChr1 92858 11 + 142988 TGGGGGATGGG -s mr.mrrefChr3 126047 11 + 181027 CTTGAGATTGA -s simDog_chr6.simDog.chr6 539247 11 + 593897 TGGGGGATGGG -s simHuman_chr6.simHuman.chr6 547764 11 + 601863 CATGGAGTCAA -s simRat_chr6.simRat.chr6 51681 11 - 647215 CTTGAGATTGA - -a -s simMouse_chr6.simMouse.chr6 576095 66 + 636262 CTGACTTTAGATGCATTTTCTTGGCTCACAAGTTAGCGACATGCACTACAGGCCCTGAATCTTAAA -s Anc0.Anc0refChr3 177527 61 + 222631 CCTACTTTGAGT-----TTGTTGACTCGAAAGTAACTGACAGGAATTACAGGCTCTGAATGTTACA -s Anc1.Anc1refChr1 16762 66 + 69767 CCTACTTTGAGTGTGCTTTGTTGACTCGAAAGTAACTGACAGGAATTACAGGCTCTGAATGTTACA -s Anc2.Anc2refChr1 92870 61 + 142988 TCTGCTTTGAGT-----TTGTTAACTTGAAAGCAACTGACAGAAATTGCTGTCTCTGGACGTAACA -s mr.mrrefChr3 126059 66 + 181027 CCGACTTTAAATGCATTTTGTTGGCTCACAAGTTACTGACATGCACTACAGGCCCTGAATGTTAAA -s simDog_chr6.simDog.chr6 539259 61 + 593897 TCTGCTTTGAGT-----TTGTTAACTTGAAAGCAACTGACAGAAATTGCTGTCTCTGGACGTAACA -s simHuman_chr6.simHuman.chr6 547776 66 + 601863 CCTACTTCGATTGTGCTTCGTTGACCCTAAGGTAACTGACAAGAATTACAGGCTCTGATTGTTACA -s simRat_chr6.simRat.chr6 51693 66 - 647215 CCAACTTTAAATTCATTTTGCTGGCTCACAAATCACTGACATGCACTACGGGCCCTGAATGTTAAA - -a -s simMouse_chr6.simMouse.chr6 576161 15 + 636262 AAGACAAGTTTTTAG -s Anc0.Anc0refChr3 177589 15 + 222631 TAGATGAGTCTTTAG -s Anc1.Anc1refChr1 16829 15 + 69767 TAGATGAGTCTTTAG -s Anc2.Anc2refChr1 92932 15 + 142988 CAGATGAATCTCTAC -s mr.mrrefChr3 126125 15 + 181027 TAGACAAGTTTTTAG -s simDog_chr6.simDog.chr6 539321 15 + 593897 CAGATGAATCTCTAC -s simHuman_chr6.simHuman.chr6 547843 15 + 601863 TAGATGAGTCTTTAG -s simRat_chr6.simRat.chr6 51759 15 - 647215 TAGACAAATTTTTGG - -a -s simMouse_chr6.simMouse.chr6 576176 42 + 636262 AATGGTGCTTGCGGATGACAATGAAGCATTACCTCAGTTTCT -s Anc0.Anc0refChr3 177605 36 + 222631 CATGGAGCTTGTAGACCACAATGAAGAGTTA------TTTCA -s Anc1.Anc1refChr1 16845 36 + 69767 CATGGAGCTTGTAGACCACAATGAAGAGTTA------TTTCA -s Anc2.Anc2refChr1 92948 36 + 142988 AATGGAGCTCGCAAACCACACTGAAGAGTTA------TTTTA -s mr.mrrefChr3 126140 42 + 181027 CATGGTGCTTGTGGACGACAATGAAGCATTACCTCAGTTTCT -s simDog_chr6.simDog.chr6 539337 36 + 593897 AATGGAGCTCGCAAACCACACTGAAGAGTTA------TTTTA -s simHuman_chr6.simHuman.chr6 547859 36 + 601863 CATGGAGATTGTAGACTACAATAAAGAGTTA------TTTCA -s simRat_chr6.simRat.chr6 51774 42 - 647215 CATGGTGCTCGTGGACCACAATGATGCATTAACTCAATTACT - -a -s simMouse_chr6.simMouse.chr6 576218 17 + 636262 TAGACACGCTCATCATG -s Anc0.Anc0refChr3 177641 17 + 222631 TAAACTCACACATCATT -s Anc1.Anc1refChr1 16881 17 + 69767 TAAACTCACACATCATT -s Anc2.Anc2refChr1 92984 17 + 142988 TAAACTCACACATCATT -s mr.mrrefChr3 126182 17 + 181027 TAAACACGCTCATCATG -s simCow_chr6.simCow.chr6 550937 13 + 602619 ----CTCACATGTTATT -s simDog_chr6.simDog.chr6 539379 17 + 593897 TAAACTCACACATCACT -s simHuman_chr6.simHuman.chr6 547895 17 + 601863 TAAACTCTCACACCATT -s simRat_chr6.simRat.chr6 51816 17 - 647215 TAAACACACTCCTCATG - -a -s simMouse_chr6.simMouse.chr6 576235 10 + 636262 GGGTTGCTAG -s Anc0.Anc0refChr3 177658 10 + 222631 CAGCAGCTAG -s Anc1.Anc1refChr1 16898 10 + 69767 CAGCAGCTAG -s Anc2.Anc2refChr1 93001 10 + 142988 CAGCATCTAG -s mr.mrrefChr3 126199 10 + 181027 GGGTTGCTAG -s simCow_chr6.simCow.chr6 550950 10 + 602619 ATGTATTTAG -s simDog_chr6.simDog.chr6 539396 10 + 593897 CAGCATCTAT -s simHuman_chr6.simHuman.chr6 547912 10 + 601863 CAGGGGCTAG -s simRat_chr6.simRat.chr6 51853 10 - 647215 GGGTTGCTAG - -a -s simMouse_chr6.simMouse.chr6 576245 32 + 636262 GTGCAGGGGTCATATGTATAATAGGAAGTATA -s Anc0.Anc0refChr3 177686 32 + 222631 GTGCAAGGGTCTTTTGTATAAGAAGTAATAGA -s Anc1.Anc1refChr1 16926 32 + 69767 GTGCAAGGGTCTTTTGTATAAGAAGTAATAGA -s Anc2.Anc2refChr1 93029 32 + 142988 GGGCAAAGGTCTATTGTATAAGAAATAATAGA -s mr.mrrefChr3 126209 32 + 181027 GTGCAGGGGTCTTATGTATAATAGGTAGTATA -s simCow_chr6.simCow.chr6 550978 32 + 602619 GGTCAGAGGTCTCTTGAATGAGAAATAGTAGA -s simDog_chr6.simDog.chr6 539425 32 + 593897 GGGCAAAGGTCTATCATATAGGTAATAATAGA -s simHuman_chr6.simHuman.chr6 547940 32 + 601863 GTATAAGAGTCTTCTGTCCAAGAAGTAATAGA -s simRat_chr6.simRat.chr6 51863 32 - 647215 GTGCAGGGATCTTATGTATAATAGTTAGTATA - -a -s simMouse_chr6.simMouse.chr6 576277 22 + 636262 ACAGAATGGAGATACAGTGTCA -s Anc0.Anc0refChr3 177720 22 + 222631 TCGGGATGCAGATTCAGGGTAT -s Anc1.Anc1refChr1 16960 22 + 69767 TCGGGATGCAGATTCAGGGTAT -s Anc2.Anc2refChr1 93063 22 + 142988 TGGGGATCCAGATTCAGGGTAT -s mr.mrrefChr3 126241 22 + 181027 TCGGAATGGAGATACAGTGTCA -s simCow_chr6.simCow.chr6 551012 22 + 602619 TGAGGAGTTAGATCCACGGTAT -s simDog_chr6.simDog.chr6 539459 22 + 593897 TGGGGATCCAGATTTAGGCTAC -s simHuman_chr6.simHuman.chr6 547974 22 + 601863 TCGGGATGCAGATTCAGGGTAT -s simRat_chr6.simRat.chr6 51895 22 - 647215 TCGGAATGGACATACAGAGCCA - -a -s simMouse_chr6.simMouse.chr6 576299 2 + 636262 GC -s Anc0.Anc0refChr3 177742 2 + 222631 GT -s Anc1.Anc1refChr1 16982 2 + 69767 GT -s Anc2.Anc2refChr1 93085 2 + 142988 GT -s mr.mrrefChr3 126263 2 + 181027 GC -s simCow_chr6.simCow.chr6 551034 2 + 602619 GT -s simDog_chr6.simDog.chr6 539481 2 + 593897 GT -s simHuman_chr6.simHuman.chr6 547996 2 + 601863 AT -s simRat_chr6.simRat.chr6 51924 2 - 647215 GC - -a -s simMouse_chr6.simMouse.chr6 576301 12 + 636262 CAGGTGAGAGTC -s Anc0.Anc0refChr3 177748 12 + 222631 CAGTAGAGAGTT -s Anc1.Anc1refChr1 16988 12 + 69767 CAGTAGAGAGTT -s Anc2.Anc2refChr1 93091 12 + 142988 GATTAGGGAGTT -s mr.mrrefChr3 126265 12 + 181027 CAGGTGAGAGTC -s simCow_chr6.simCow.chr6 551040 12 + 602619 GAATAGGAAGTT -s simDog_chr6.simDog.chr6 539487 9 + 593897 GATT---GAGTT -s simHuman_chr6.simHuman.chr6 548002 12 + 601863 CAGTAGAGAGTT -s simRat_chr6.simRat.chr6 51926 12 - 647215 CAGGTGAGAGTC - -a -s simMouse_chr6.simMouse.chr6 576313 19 + 636262 CTAGTTGCTTGTCAAATTA -s Anc0.Anc0refChr3 177761 19 + 222631 CTAGTTGCTTGTCATCTTC -s Anc1.Anc1refChr1 17001 19 + 69767 CTAGTTGCTTGTCATCTTC -s Anc2.Anc2refChr1 93104 19 + 142988 CTGGTAGCTTGTCATCTTC -s mr.mrrefChr3 126278 19 + 181027 CTAGTTGCTTGTCAAATTA -s simCow_chr6.simCow.chr6 551053 19 + 602619 CTGGTAGCTTGTCATCTTC -s simDog_chr6.simDog.chr6 539497 19 + 593897 CTGGTAGCTTGTCATCTTC -s simHuman_chr6.simHuman.chr6 548015 19 + 601863 CTAGTTGCTTGTCATCTCC -s simRat_chr6.simRat.chr6 51939 19 - 647215 ATAGTTGCTTGTCAGACTA - -a -s simMouse_chr6.simMouse.chr6 576332 12 + 636262 TGACTGTTGTTG -s Anc0.Anc0refChr3 177786 12 + 222631 TCACTTGAGTTG -s Anc1.Anc1refChr1 17026 12 + 69767 TCACTTGAGTTG -s Anc2.Anc2refChr1 93129 12 + 142988 TCACTTGAGTTG -s mr.mrrefChr3 126297 12 + 181027 TGACTGGAGTTG -s simCow_chr6.simCow.chr6 551078 12 + 602619 TCACTGGAGTTG -s simDog_chr6.simDog.chr6 539522 12 + 593897 TCACTTGAGTTT -s simHuman_chr6.simHuman.chr6 548040 12 + 601863 TCACTTGAGTTG -s simRat_chr6.simRat.chr6 51958 12 - 647215 TGACTGGAGTTG - -a -s simMouse_chr6.simMouse.chr6 576344 2 + 636262 CG -s Anc0.Anc0refChr3 177798 2 + 222631 TA -s Anc1.Anc1refChr1 17038 2 + 69767 TA -s Anc2.Anc2refChr1 93141 2 + 142988 TA -s mr.mrrefChr3 126309 2 + 181027 CA -s simCow_chr6.simCow.chr6 551090 2 + 602619 TA -s simDog_chr6.simDog.chr6 539536 2 + 593897 TA -s simHuman_chr6.simHuman.chr6 548052 2 + 601863 TA -s simRat_chr6.simRat.chr6 51970 2 - 647215 CA - -a -s simMouse_chr6.simMouse.chr6 576346 21 + 636262 GGTGAGCAGGATATTCAGAGT -s Anc0.Anc0refChr3 177801 12 + 222631 GGCAGCCATGAT--------- -s Anc1.Anc1refChr1 17041 21 + 69767 GGCAGCCATGATAGTCAGAGC -s Anc2.Anc2refChr1 93144 12 + 142988 GGCAGCCATGTT--------- -s mr.mrrefChr3 126312 21 + 181027 GGTGAGCAGGATATTCAGAGT -s simCow_chr6.simCow.chr6 551093 11 + 602619 GG-AGCCATGTT--------- -s simDog_chr6.simDog.chr6 539539 12 + 593897 AGCAGACATGTT--------- -s simHuman_chr6.simHuman.chr6 548055 21 + 601863 GGAAGCCATGAGAGTCAGAGC -s simRat_chr6.simRat.chr6 51973 21 - 647215 GGTGTGCAGAATACTCGGAGT - -a -s simMouse_chr6.simMouse.chr6 576367 29 + 636262 CTCTGAAGCCACCTCAGCCATTCTCCCAC -s Anc0.Anc0refChr3 177813 18 + 222631 CCTTCAAGCCACCAGAGC----------- -s Anc1.Anc1refChr1 17062 29 + 69767 CCTTCAAGCCACCAGAGCCATTCTTCCAT -s Anc2.Anc2refChr1 93156 18 + 142988 CCTCCAAGCCACCAGAGC----------- -s mr.mrrefChr3 126333 29 + 181027 CTCTCAAGCCACCTCAGCCATTCTCCCAC -s simCow_chr6.simCow.chr6 551104 18 + 602619 CCCCCAAGCCACCTTAGA----------- -s simDog_chr6.simDog.chr6 539551 18 + 593897 CCTCCAAGCCACCAGGGC----------- -s simHuman_chr6.simHuman.chr6 548077 29 + 601863 CCTTCAAGCCACCCGAGCCATTCTTCCAT -s simRat_chr6.simRat.chr6 51994 29 - 647215 TTGACAAGCCACTTCAGCCATTCTGCCAC - -a -s simMouse_chr6.simMouse.chr6 576396 47 + 636262 AGATTGGATTGCATAGTCTCAGTTCCCTACACCACATCTGTTCTGGG -s Anc0.Anc0refChr3 177831 31 + 222631 ----------------TCTGAGCTCCATACACTATATTTATTATGTG -s Anc1.Anc1refChr1 17091 46 + 69767 GGATGGAGCTCCATA-TCTGAGCTCCATACACTATATTTATTATGTG -s Anc2.Anc2refChr1 93174 31 + 142988 ----------------TCTGAGCTCCATACTCTATATTTATTATGTG -s mr.mrrefChr3 126362 47 + 181027 AGATTGGACTGCATAGTCTCAGTTCCCTACACCACATCTGTTCTGGG -s simCow_chr6.simCow.chr6 551122 30 + 602619 ----------------TCTGTGCTCCGTACCCTATATTTAATGCAT- -s simDog_chr6.simDog.chr6 539569 31 + 593897 ----------------TCTGAGCTCCATACTCTATATTTATTATGTG -s simHuman_chr6.simHuman.chr6 548114 46 + 601863 GGATGGAGCTCCATA-TCTGAGCCCCATGCACTATATTTATAAAGTG -s simRat_chr6.simRat.chr6 52023 47 - 647215 AGATTGGACTGTATATTCCCAGTTCCTTACACCAAATCTGTTCTGGG - -a -s simMouse_chr6.simMouse.chr6 576443 1 + 636262 A -s Anc0.Anc0refChr3 177862 1 + 222631 A -s Anc1.Anc1refChr1 17137 1 + 69767 A -s Anc2.Anc2refChr1 93215 1 + 142988 A -s mr.mrrefChr3 126409 1 + 181027 A -s simCow_chr6.simCow.chr6 551162 1 + 602619 A -s simDog_chr6.simDog.chr6 539613 1 + 593897 A -s simHuman_chr6.simHuman.chr6 548160 1 + 601863 A -s simRat_chr6.simRat.chr6 52070 1 - 647215 A - -a -s simMouse_chr6.simMouse.chr6 576444 15 + 636262 TCTTGGGAGGCATCA -s Anc0.Anc0refChr3 177865 15 + 222631 TCTTGGATTGCATCA -s Anc1.Anc1refChr1 17140 15 + 69767 TCTTGGATTGCATCA -s Anc2.Anc2refChr1 93218 15 + 142988 TCTTGGATTCCATCA -s mr.mrrefChr3 126410 15 + 181027 TCTTGGAAGGCATCA -s simCow_chr6.simCow.chr6 551165 15 + 602619 CCTTGGATTCCATCA -s simDog_chr6.simDog.chr6 539616 15 + 593897 TCTTGGATTCCATCA -s simHuman_chr6.simHuman.chr6 548163 15 + 601863 TCTTTGATTGCATCA -s simRat_chr6.simRat.chr6 52071 14 - 647215 T-TTGGAAGACATCA - -a -s simMouse_chr6.simMouse.chr6 576459 10 + 636262 TAATGACTGG -s Anc0.Anc0refChr3 177886 10 + 222631 TAATGGATGG -s Anc1.Anc1refChr1 17161 10 + 69767 TAATGGATGG -s Anc2.Anc2refChr1 93239 10 + 142988 TAATGGATGG -s mr.mrrefChr3 126425 10 + 181027 TAATGGCTGG -s simCow_chr6.simCow.chr6 551186 10 + 602619 TAATGGATGG -s simDog_chr6.simDog.chr6 539637 10 + 593897 TCATAGATGG -s simHuman_chr6.simHuman.chr6 548184 10 + 601863 TAATGGATGG -s simRat_chr6.simRat.chr6 52085 10 - 647215 TAATGGCTGG - -a -s simMouse_chr6.simMouse.chr6 576469 17 + 636262 AATCTATTGCAGTGAGC -s Anc0.Anc0refChr3 177896 17 + 222631 AATTTATTGCAGTTGGC -s Anc1.Anc1refChr1 17171 17 + 69767 AATTTATTGCAGTTGGC -s Anc2.Anc2refChr1 93249 17 + 142988 AATTTATACCAGTTGGC -s mr.mrrefChr3 126435 17 + 181027 AATCTATTGCAGTGAGC -s simCow_chr6.simCow.chr6 551197 17 + 602619 AATTTATTACAGTTAGC -s simDog_chr6.simDog.chr6 539647 17 + 593897 TACATATACCAGTTGGC -s simHuman_chr6.simHuman.chr6 548194 11 + 601863 AATTTATTGCA------ -s simRat_chr6.simRat.chr6 52095 17 - 647215 AATGTATTGTAGTGAGC - -a -s simMouse_chr6.simMouse.chr6 576486 19 + 636262 ACTCTACCCAAATCGTGAA -s Anc0.Anc0refChr3 177913 19 + 222631 ACTGTACCCAAATGGCAAA -s Anc1.Anc1refChr1 17188 19 + 69767 ACTGTACCCAAATGGCAAA -s Anc2.Anc2refChr1 93266 19 + 142988 ACTGCACCCAAATGGCAAA -s mr.mrrefChr3 126452 19 + 181027 ACTCTACCCAAATGGCGAA -s simCow_chr6.simCow.chr6 551214 19 + 602619 ACTGCACCCAAATGGCAAA -s simDog_chr6.simDog.chr6 539664 19 + 593897 GCTGCACCCAAATGGCACA -s simHuman_chr6.simHuman.chr6 548205 19 + 601863 ACAGTACCCAAATGGCAAA -s simRat_chr6.simRat.chr6 52113 19 - 647215 ACCATACCCAAATGGCGAA - -a -s simMouse_chr6.simMouse.chr6 576505 22 + 636262 TCGCTCCACTAAGGACAATGGG -s Anc0.Anc0refChr3 177933 21 + 222631 CCGCTCCATTA-GGGCAATGGG -s Anc1.Anc1refChr1 17208 22 + 69767 CCGCTCCATTAAGGGCAATGGG -s Anc2.Anc2refChr1 93286 21 + 142988 CCACTCTGTTA-GGGCAATAGG -s mr.mrrefChr3 126471 22 + 181027 CCGCTCCACTAAGGGCAATGGG -s simCow_chr6.simCow.chr6 551234 19 + 602619 CCA--TTGTTA-GTGCAATAGG -s simDog_chr6.simDog.chr6 539684 21 + 593897 CCACTCTGTTA-GGGCAATAGG -s simHuman_chr6.simHuman.chr6 548225 22 + 601863 CCGCTCCATTAAGGGCAATGAG -s simRat_chr6.simRat.chr6 52132 22 - 647215 CCGCTCCACTAAGGGCAATGTG - -a -s simMouse_chr6.simMouse.chr6 576527 11 + 636262 TTAAACTAATG -s Anc0.Anc0refChr3 177954 8 + 222631 CATAACTA--- -s Anc1.Anc1refChr1 17230 11 + 69767 CATAACTAATG -s Anc2.Anc2refChr1 93307 8 + 142988 CATAACTA--- -s mr.mrrefChr3 126493 11 + 181027 TTAAACTAATG -s simCow_chr6.simCow.chr6 551253 8 + 602619 AGTAACTA--- -s simDog_chr6.simDog.chr6 539707 8 + 593897 CACAAATA--- -s simHuman_chr6.simHuman.chr6 548247 11 + 601863 CATAACTGATG -s simRat_chr6.simRat.chr6 52154 11 - 647215 ATAAACTAATG - -a -s simMouse_chr6.simMouse.chr6 576538 5 + 636262 CTTAA -s Anc0.Anc0refChr3 177962 5 + 222631 TTTAA -s Anc1.Anc1refChr1 17241 5 + 69767 TTTAA -s Anc2.Anc2refChr1 93315 5 + 142988 TTTAG -s mr.mrrefChr3 126504 5 + 181027 CTTAA -s simCow_chr6.simCow.chr6 551264 5 + 602619 TTTAG -s simDog_chr6.simDog.chr6 539715 5 + 593897 TTTAG -s simHuman_chr6.simHuman.chr6 548258 5 + 601863 GTTGA -s simRat_chr6.simRat.chr6 52165 5 - 647215 TGTAA - -a -s simMouse_chr6.simMouse.chr6 576543 12 + 636262 CAGGGCTAATGT -s Anc0.Anc0refChr3 177967 12 + 222631 CAGGGCTAGCAT -s Anc1.Anc1refChr1 17246 12 + 69767 CAGGGCTAGCAT -s Anc2.Anc2refChr1 93320 12 + 142988 CAGGGCTAGCAT -s mr.mrrefChr3 126509 12 + 181027 CAGGGCTAACGT -s simCow_chr6.simCow.chr6 551269 12 + 602619 CAGGGCTAGCAT -s simDog_chr6.simDog.chr6 539720 12 + 593897 CAAGGCTGGTGT -s simHuman_chr6.simHuman.chr6 548305 12 + 601863 CTGGGCTAGCAT -s simRat_chr6.simRat.chr6 52170 12 - 647215 CAGGGCTAACAT - -a -s simMouse_chr6.simMouse.chr6 576555 1 + 636262 G -s Anc0.Anc0refChr3 177979 1 + 222631 G -s Anc1.Anc1refChr1 17258 1 + 69767 G -s Anc2.Anc2refChr1 93332 1 + 142988 G -s mr.mrrefChr3 126521 1 + 181027 G -s simCow_chr6.simCow.chr6 551281 1 + 602619 G -s simDog_chr6.simDog.chr6 539732 1 + 593897 G -s simHuman_chr6.simHuman.chr6 548345 1 + 601863 G -s simRat_chr6.simRat.chr6 52182 1 - 647215 C - -a -s simMouse_chr6.simMouse.chr6 576556 2 + 636262 TA -s Anc0.Anc0refChr3 177980 2 + 222631 TA -s Anc1.Anc1refChr1 17259 2 + 69767 TA -s Anc2.Anc2refChr1 93333 2 + 142988 TA -s mr.mrrefChr3 126522 2 + 181027 TA -s simCow_chr6.simCow.chr6 551286 2 + 602619 TA -s simDog_chr6.simDog.chr6 539733 2 + 593897 TA -s simHuman_chr6.simHuman.chr6 548346 2 + 601863 TA -s simRat_chr6.simRat.chr6 52183 2 - 647215 TA - -a -s simMouse_chr6.simMouse.chr6 576558 4 + 636262 AGTG -s Anc0.Anc0refChr3 177982 4 + 222631 AGGA -s Anc1.Anc1refChr1 17261 4 + 69767 AGGA -s Anc2.Anc2refChr1 93338 4 + 142988 AGGA -s mr.mrrefChr3 126524 4 + 181027 AGTG -s simCow_chr6.simCow.chr6 551291 4 + 602619 AGGA -s simDog_chr6.simDog.chr6 539738 4 + 593897 TGGA -s simHuman_chr6.simHuman.chr6 548348 4 + 601863 AAGA -s simRat_chr6.simRat.chr6 52250 4 - 647215 AGTG - -a -s simMouse_chr6.simMouse.chr6 576562 5 + 636262 GCACA -s Anc0.Anc0refChr3 177986 5 + 222631 GCATA -s Anc1.Anc1refChr1 17265 5 + 69767 GCATA -s Anc2.Anc2refChr1 93342 5 + 142988 GCATA -s mr.mrrefChr3 126528 5 + 181027 GCACA -s simCow_chr6.simCow.chr6 551295 5 + 602619 GCGTA -s simDog_chr6.simDog.chr6 539742 5 + 593897 GCACA -s simHuman_chr6.simHuman.chr6 548352 5 + 601863 GTATA -s simRat_chr6.simRat.chr6 52256 5 - 647215 GCACA - -a -s simMouse_chr6.simMouse.chr6 576567 50 + 636262 TAATTGTTGGGAAGGTAGTTTGTGAGATTTAATAAGGAACATGTTCCATA -s Anc0.Anc0refChr3 177991 48 + 222631 TAATTGTAGGGAGGACAGTTTGTGGGATTTAGTTAGGTATGTT--CCTCA -s Anc1.Anc1refChr1 17270 48 + 69767 TAATTGTAGGGAGGACAGTTTGTGGGATTTAGTTAGGTATGTT--CCTCA -s Anc2.Anc2refChr1 93347 48 + 142988 TAATTGTAGGCTGGACAGTGTGTGGGATCTAGTTAAGTATGTT--CCTCA -s mr.mrrefChr3 126533 50 + 181027 TAATTGTTGGGAAGGTAGTTTGTGAGATTTAATAAGGAATGTGTTCCATA -s simCow_chr6.simCow.chr6 551300 46 + 602619 TAATTGTAGGCATGACAGTGTGTAGGATCTAGTTA-GTAGGTT---CTCA -s simDog_chr6.simDog.chr6 539748 48 + 593897 TAATTGTAGGCTGGACAATGTATGGGATCTAGTTAAATATGTT--CCTCA -s simHuman_chr6.simHuman.chr6 548357 45 + 601863 TAGTTGT---GAGCACAGTTTGTTGGATTTAGTTAGGTATGTA--CCCCA -s simRat_chr6.simRat.chr6 52261 46 - 647215 TAACTGTTGGGAAGGTAGTTTGTGTAACTCAATAAGGAATGTCTTC---- - -a -s simMouse_chr6.simMouse.chr6 576617 13 + 636262 GTCAACCAATCTG -s Anc0.Anc0refChr3 178039 13 + 222631 GAGGACCAGACTG -s Anc1.Anc1refChr1 17318 13 + 69767 GAGGACCAGACTG -s Anc2.Anc2refChr1 93395 13 + 142988 GAGGACTAGACTG -s mr.mrrefChr3 126583 13 + 181027 GTCAACCAATCTG -s simCow_chr6.simCow.chr6 551346 13 + 602619 CAGTGCTAAACTG -s simDog_chr6.simDog.chr6 539796 13 + 593897 GAGGACTGGACTG -s simHuman_chr6.simHuman.chr6 548402 13 + 601863 AAGCACCAGACTG -s simRat_chr6.simRat.chr6 52462 12 - 647215 A-CAACCTATCTA - -a -s simMouse_chr6.simMouse.chr6 576630 123 + 636262 ACCATACATAGTCCAGATATCCCAACAGGCAACAAAAAAAAAAAAAGAAGTTTGTTGTCTCGTTTAGTGAGCAACAATATTAGGGTATCTGGAGGTGCCAAGTCTCTTTTTGATACTATGACA -s Anc0.Anc0refChr3 178056 113 + 222631 AATGAGCATAGCCTAAGGATCACCACAGC---------AGCAAAAAACAGTGTTCTGTCCTAATTAGCAAGAAGCCATATGAGGGTAT-TAGAGGTGCCAACTGCCTTTTCGACACAACGGCA -s Anc1.Anc1refChr1 17335 113 + 69767 AATGAGCATAGCCTAAGGATCACCACAGC---------AGCAAAAAACAGTGTTCTGTCCTAATTAGCAAGAAGCCATATGAGGGTAT-TAGAGGTGCCAACTGCCTTTTCGACACAACGGCA -s Anc2.Anc2refChr1 93412 113 + 142988 AACCAGGATAGCCTAAGGATCAACAAAGC---------AGCAAAAAACAGTGTTCTGTCCTAATTAGCAAGAAGCCATGTTAGGGTAT-TAAAGATGCCAACTGCCTTTTCGACACAACCGCA -s mr.mrrefChr3 126596 117 + 181027 ACTGTACATAGCCCAGATATCCCAACAGG------AAAAAAAAAAAGAAGTTTGCTGTCCCATTTAGTGAGCAGCAATATGAGGGTATCTGGAGGTGCCAAGTCCCTTTTTGATACTATGACA -s simCow_chr6.simCow.chr6 551363 112 + 602619 AACTAGAATTGCCCAAGGATC-ACAAAGC---------AGCAAAAGAAAGTGTTCTGTCCTGATTACCAAGAAGCTCTTTTAGCATAT-TGAAGATGCCTACTGCCTATTCAATACAACAGCG -s simDog_chr6.simDog.chr6 539813 101 + 593897 GACCAGGA-AGCCTAATGATCAACAAAG------------CAATAAACAGTGTTCTA-CCTAATTAGCAAGAAGCCATGTTAGGGTAT-TAAAGATGTCA-------TTTTGACACAACCGCA -s simHuman_chr6.simHuman.chr6 548419 113 + 601863 AGTGAGCATGGCCTAAGGATCTCTACAGT---------GTCAAAAAACAGTATCCTGTCCTAGTTAGCAAGTAGCCATATGAGGGTAT-TAGAAGTGCCAACTGCCTTATCGACACAACGGCA -s simRat_chr6.simRat.chr6 52474 103 - 647215 ACTGCACATAGCCCA--------------------AAAAAGAAAAAGAAGCGTACTATCCCATCTGTTGAGAAGTTATATGAAGGTATCTGGAGGTGCCAAGACCCTTTTTGATACTATGACA - -a -s simMouse_chr6.simMouse.chr6 576753 42 + 636262 GGCTTGATGGATTCTATGACAGGCCTTGATGTGCACATTTGG -s Anc0.Anc0refChr3 178170 20 + 222631 GGCTTGAT----------------------GTGCCCATGTTG -s Anc1.Anc1refChr1 17449 20 + 69767 GGCTTGAT----------------------GTGCCCATGTTG -s Anc2.Anc2refChr1 93526 20 + 142988 GGCTTGAT----------------------GTGCCCATGTTG -s mr.mrrefChr3 126713 20 + 181027 GGCTTGAT----------------------GTGCACATTTGC -s simCow_chr6.simCow.chr6 551476 20 + 602619 GACTTGAT----------------------ATGCCCAATATG -s simDog_chr6.simDog.chr6 539915 20 + 593897 GGCTTGAT----------------------GTGTCCTTGTTG -s simHuman_chr6.simHuman.chr6 548533 20 + 601863 GGCTTGAT----------------------GCGCCCATGCTA -s simRat_chr6.simRat.chr6 52577 20 - 647215 GGCTTGAT----------------------GTGCACTTTTGC - -a -s simMouse_chr6.simMouse.chr6 576795 9 + 636262 ACTGGACAT -s Anc0.Anc0refChr3 178195 8 + 222631 ACTGG-CAT -s Anc1.Anc1refChr1 17474 9 + 69767 ACTGGACAT -s Anc2.Anc2refChr1 93551 8 + 142988 ACTTG-TAT -s mr.mrrefChr3 126733 9 + 181027 ACTGGACAT -s simCow_chr6.simCow.chr6 551501 8 + 602619 ACATG-TAT -s simDog_chr6.simDog.chr6 539940 8 + 593897 ACTTG-TAT -s simHuman_chr6.simHuman.chr6 548558 9 + 601863 ACTGGACAT -s simRat_chr6.simRat.chr6 52597 9 - 647215 ATTGGACAT - -a -s simMouse_chr6.simMouse.chr6 576804 46 + 636262 TCAATCTGAGGACCCCAGCCTGAGAACTCCAAACAAACAGTAAGGG -s Anc0.Anc0refChr3 178203 30 + 222631 TCA--CTGAAGAA--------------TCCAGACAAAGAGTGAAAA -s Anc1.Anc1refChr1 17483 32 + 69767 TCAACCTGAAGAA--------------TCCAGACAAAGAGTGAAAA -s Anc2.Anc2refChr1 93559 30 + 142988 TGA--CTGAGAAA--------------GCCAGACAAAGAGTGAAAG -s mr.mrrefChr3 126742 32 + 181027 TCAATCTGAAGAC--------------TCCAAACAAACAGTAAGAA -s simCow_chr6.simCow.chr6 551522 30 + 602619 TGC--CTGAGAAA--------------GCCAGACATAGGGTAAAAG -s simDog_chr6.simDog.chr6 539948 21 + 593897 TGA--CTGA-------------------CCAGACAAAGAGTG---- -s simHuman_chr6.simHuman.chr6 548567 32 + 601863 TCAACCTGAAGAA--------------TCCGCACAAAGAGTGAAAA -s simRat_chr6.simRat.chr6 52606 32 - 647215 TCAATCTGAAGAC--------------TTCAGACAAACAGTAAGAA - -a -s simMouse_chr6.simMouse.chr6 576850 29 + 636262 GTGGGATAGCTAGCATGCTATGGAAGAAG -s Anc0.Anc0refChr3 178235 22 + 222631 GAGGGATAGTTATCAC-------AACAAA -s Anc1.Anc1refChr1 17517 27 + 69767 GAGGGATAGTTATCACGCTAT--AACAAA -s Anc2.Anc2refChr1 93591 22 + 142988 GAGGAATAGTCATCAC-------CACAAA -s mr.mrrefChr3 126774 29 + 181027 GTGGGATAGCTAGCACGCTATGGAAGAAG -s simCow_chr6.simCow.chr6 551554 22 + 602619 GAGGAATAGTCATCAC-------CACAAA -s simHuman_chr6.simHuman.chr6 548601 23 + 601863 GAGGGA----TATCACGCTAT--AACAAA -s simRat_chr6.simRat.chr6 52638 29 - 647215 GAGGATTAGCTAGCACTCTATGGAAGGGC - -a -s simMouse_chr6.simMouse.chr6 576879 25 + 636262 GAAGGTATGGAATCATAAAGGATGG -s Anc0.Anc0refChr3 178257 25 + 222631 GAAGGTATGGAATCATGTAGGAGGG -s Anc1.Anc1refChr1 17544 25 + 69767 GAAGGTATGGAATCATGTAGGAGGG -s Anc2.Anc2refChr1 93613 25 + 142988 GAAGGTATAGAATCATGTAGGAGGG -s mr.mrrefChr3 126803 25 + 181027 GAAGGTATGGAATCATAAAGGAGGG -s simCow_chr6.simCow.chr6 551580 25 + 602619 GAAGGTATTGAATTATGTAGGGGGG -s simDog_chr6.simDog.chr6 539969 22 + 593897 --AGGTACAGAATCA-GTAGGAGAG -s simHuman_chr6.simHuman.chr6 548624 25 + 601863 GAAAGTATGGAATGGTGTAGGCGGG -s simRat_chr6.simRat.chr6 52667 25 - 647215 GAAGGTATGGAATCATAAAGGAGCA - -a -s simMouse_chr6.simMouse.chr6 576904 49 + 636262 GATTTTTAGCTGCAAATCAACAAGGCTGATAGCACCTGCTAGGGACTAT -s Anc0.Anc0refChr3 178283 25 + 222631 GAACATTGATTGTAAATTAAGGCAG------------------------ -s Anc1.Anc1refChr1 17570 25 + 69767 GAACATTGATTGTAAATTAAGGCAG------------------------ -s Anc2.Anc2refChr1 93639 25 + 142988 GAACATTGATTGTAAATTAAGGCAG------------------------ -s mr.mrrefChr3 126828 49 + 181027 GATTATTAGTTGCAAATCAAGAAGGCTGATAGCACCTGCTAGGGACTAT -s simCow_chr6.simCow.chr6 551606 22 + 602619 GAACATTGATTGTAAATTAAG---G------------------------ -s simDog_chr6.simDog.chr6 539992 14 + 593897 GCTCATTGAT-----------GCAG------------------------ -s simHuman_chr6.simHuman.chr6 548650 25 + 601863 GAACACTGATTGTAAATTAAGGCAG------------------------ -s simRat_chr6.simRat.chr6 52692 49 - 647215 GTTTATTAGTTGCAAATGGAGAAGGCTGATAGCAACTACTAGGGATTAT - -a -s simMouse_chr6.simMouse.chr6 576953 1 + 636262 A -s Anc0.Anc0refChr3 178308 1 + 222631 A -s Anc1.Anc1refChr1 17595 1 + 69767 A -s Anc2.Anc2refChr1 93664 1 + 142988 A -s mr.mrrefChr3 126877 1 + 181027 A -s simCow_chr6.simCow.chr6 551628 1 + 602619 A -s simDog_chr6.simDog.chr6 540006 1 + 593897 A -s simHuman_chr6.simHuman.chr6 548675 1 + 601863 A -s simRat_chr6.simRat.chr6 52764 1 - 647215 A - -a -s simMouse_chr6.simMouse.chr6 576954 11 + 636262 CCACCATTAGG -s Anc0.Anc0refChr3 178309 11 + 222631 CCACCATTATG -s Anc1.Anc1refChr1 17596 11 + 69767 CCACCATTATG -s Anc2.Anc2refChr1 93670 11 + 142988 CTACAATCTTG -s mr.mrrefChr3 126878 11 + 181027 CCACCATTAGG -s simCow_chr6.simCow.chr6 551638 11 + 602619 ATACAATATTG -s simDog_chr6.simDog.chr6 540012 11 + 593897 CTACAATCTTG -s simHuman_chr6.simHuman.chr6 548676 11 + 601863 CCACCATTATG -s simRat_chr6.simRat.chr6 52765 11 - 647215 CCACCATTAGG - -a -s simMouse_chr6.simMouse.chr6 576965 18 + 636262 ACACTTTTCATTGTGCAG -s Anc0.Anc0refChr3 178320 18 + 222631 ACACTTTCCATTGAGCAG -s Anc1.Anc1refChr1 17607 18 + 69767 ACACTTTCCATTGAGCAG -s Anc2.Anc2refChr1 93681 18 + 142988 ACACTTTCCATTGAGGGG -s mr.mrrefChr3 126889 18 + 181027 ACACTTTTCATTGTGCAG -s simCow_chr6.simCow.chr6 551690 18 + 602619 ACTCCTTCCTTTAGGTGG -s simDog_chr6.simDog.chr6 540023 18 + 593897 ACACTTTCCATTGAGGGG -s simHuman_chr6.simHuman.chr6 548687 18 + 601863 TCACTTTCCATTTAACAT -s simRat_chr6.simRat.chr6 52776 18 - 647215 ATACTTTTCATTGTGCAG - -a -s simMouse_chr6.simMouse.chr6 576983 70 + 636262 CAGCGAAGGCTTCAAGGTAGGTGGTGTGCCTAGGTACAGTGGTGTACTGCCTCTGAAATGATGAATTTTA -s Anc0.Anc0refChr3 178338 69 + 222631 GAGCGA-GTCTACAAGGGGGGTGGTGCCCATGGTTACAGTGATCTACTGTCATTGAGATAATAAATTTTA -s Anc1.Anc1refChr1 17625 70 + 69767 GAGCGAAGTCTACAAGGGGGGTGGTGCCCATGGTTACAGTGATCTACTGTCATTGAGATAATAAATTTTA -s Anc2.Anc2refChr1 93700 69 + 142988 GAGCGA-GTCTACAATGGGGGTGGTGCCCATGGTTGCAGTGATCTACTGTTATTGAGATAATAAATTTTA -s mr.mrrefChr3 126907 70 + 181027 GAGCGAAGGCTTCAAGGTAGGTGGTGTGCCTAGGTACAGTGGTGTACTGTCTCTGAAATGATGAATTTTA -s simCow_chr6.simCow.chr6 551709 66 + 602619 GAGCAG-GTATACAATTGAGGTGATGCCCATGGTTGCAGAGATCTACTGTAGTTGCG---ATAAATTTGA -s simDog_chr6.simDog.chr6 540042 69 + 593897 GAGCGA-GTCTACAATGGGGGCGGTGCCCATGGTTGTAGTGATTTTCTGTTATTGAAATAAAATATTTTA -s simHuman_chr6.simHuman.chr6 548705 70 + 601863 GAGCGAAATCTCCACGGAGGGTGGTGCCCATGGCTACAGTTATCTACTCTCATTGAGATAATAAATTTTA -s simRat_chr6.simRat.chr6 52794 66 - 647215 GAACGAAGGCTTCAAGGTAGGTGGTGGGCGTAGGTACA-TGGTGTACTGTCGCTGAAATCAT---TTTTA - -a -s simMouse_chr6.simMouse.chr6 577053 82 + 636262 TTTACAGTCCCTGATACGGCAGACTTTCGGGAGAATGGTATTTACTCTCCATCTATTGAGTATAGAAGTCCCAAGTATTCAC -s Anc0.Anc0refChr3 178408 82 + 222631 TTTACAGTCAGTGCTATTGCAGACTTGCAGTTGAGGGTGATCCATTCCTTATCTACTGAGTACAGAATCCACAAGTATTCAC -s Anc1.Anc1refChr1 17696 82 + 69767 TTTACAGTCAGTGCTATTGCAGACTTGCAGTTGAGGGTGATCCATTCCTTATCTACTGAGTACAGAATCCACAAGTATTCAC -s Anc2.Anc2refChr1 93790 82 + 142988 TTTACAGTTAGTGCTATTGCAGACTTGAAGTTGAGGGTTATCCATTCCTTATCTACTGAGTACAGAATCAACAAGTACTCAC -s mr.mrrefChr3 126977 82 + 181027 TTTACAGTCCCTGATATGGCAGACTTTCAGGAGAATGGGATTTATTCCCCATCTATTGAGTATAGAAGTCCCAAGTATTCAC -s simCow_chr6.simCow.chr6 551796 75 + 602619 TTTGCA-------CTATTGCAGACTTGTGGTTGAGGGTTGCCAATTCTCTATCAATTGAGTACACAATCAACAAGTACTCAC -s simDog_chr6.simDog.chr6 540132 69 + 593897 TTTACAGTTAGTGCTACAGCGGAACTGAAATTGAGTGTTATCCATTCCTTATCTACTGACTACAGCTTC------------- -s simHuman_chr6.simHuman.chr6 548776 82 + 601863 TTTACAGTCAGTGCTATTGCACACTTACAGTTAAGGGTGATCCATTTCTGATCCACTGGGTACAGAATCCACAAGTATTCAC -s simRat_chr6.simRat.chr6 52860 82 - 647215 TTTATGTTCCCTGAAATGGAGGACTTTTAGGGGAATGGGATTTATTCCCCATTTATTGAGTATAGAAGTCCCAAGTATTCAC - -a -s simMouse_chr6.simMouse.chr6 577135 7 + 636262 ATGGCTG -s Anc0.Anc0refChr3 178491 7 + 222631 CTTGCTT -s Anc1.Anc1refChr1 17779 7 + 69767 CTTGCTT -s Anc2.Anc2refChr1 93873 7 + 142988 CATGCTT -s mr.mrrefChr3 127059 7 + 181027 ATTGCTT -s simCow_chr6.simCow.chr6 551872 7 + 602619 CATGCTT -s simHuman_chr6.simHuman.chr6 548859 7 + 601863 GTTGCTT -s simRat_chr6.simRat.chr6 52942 7 - 647215 ATTGCTT - -a -s simMouse_chr6.simMouse.chr6 577142 14 + 636262 GATATGCTCGAGTT -s Anc0.Anc0refChr3 178498 13 + 222631 G-TAAGCTCTGATT -s Anc1.Anc1refChr1 17786 13 + 69767 G-TAAGCTCTGATT -s Anc2.Anc2refChr1 93880 13 + 142988 A-CGAGTTCTGATT -s mr.mrrefChr3 127066 14 + 181027 GATATGCTCTGATT -s simCow_chr6.simCow.chr6 551880 13 + 602619 A-CGAGTTCTGACT -s simDog_chr6.simDog.chr6 540201 4 + 593897 ----------CCTT -s simHuman_chr6.simHuman.chr6 548866 13 + 601863 G-TAAGCTCTGATT -s simRat_chr6.simRat.chr6 52949 11 - 647215 GATATG---TGATT - -a -s simMouse_chr6.simMouse.chr6 577156 11 + 636262 CAATTGGTAGT -s Anc0.Anc0refChr3 178512 11 + 222631 GGATTGATAGC -s Anc1.Anc1refChr1 17800 11 + 69767 GGATTGATAGC -s Anc2.Anc2refChr1 93894 11 + 142988 GGATTGATAGC -s mr.mrrefChr3 127081 11 + 181027 CAATTGGTAGT -s simCow_chr6.simCow.chr6 551894 11 + 602619 GGATTGATAGC -s simDog_chr6.simDog.chr6 540206 11 + 593897 GGATTGATAGC -s simHuman_chr6.simHuman.chr6 548880 11 + 601863 TGGTTGTTAGC -s simRat_chr6.simRat.chr6 52961 11 - 647215 CAATTGGGAGT - -a -s simMouse_chr6.simMouse.chr6 577167 3 + 636262 GGC -s Anc0.Anc0refChr3 178524 3 + 222631 GAC -s Anc1.Anc1refChr1 17812 3 + 69767 GAC -s Anc2.Anc2refChr1 93906 3 + 142988 GAC -s mr.mrrefChr3 127092 3 + 181027 GGC -s simCow_chr6.simCow.chr6 551906 3 + 602619 GGC -s simDog_chr6.simDog.chr6 540218 3 + 593897 GAC -s simHuman_chr6.simHuman.chr6 548892 3 + 601863 GAT -s simRat_chr6.simRat.chr6 52972 3 - 647215 GGC - -a -s simMouse_chr6.simMouse.chr6 577170 29 + 636262 CATTCTGGACAATTCTAATTCCCACACTC -s Anc0.Anc0refChr3 178527 17 + 222631 TA------------CTAATTCCCATACTC -s Anc1.Anc1refChr1 17815 17 + 69767 TA------------CTAATTCCCATACTC -s Anc2.Anc2refChr1 93920 17 + 142988 TA------------CTAATTCCCATACTC -s mr.mrrefChr3 127095 17 + 181027 CA------------CTAATTCCCATACTC -s simCow_chr6.simCow.chr6 551921 17 + 602619 CA------------CCAATTCCCATACTC -s simDog_chr6.simDog.chr6 540232 17 + 593897 TA------------CTAATTCCCATACTC -s simHuman_chr6.simHuman.chr6 548895 17 + 601863 TA------------GTAATACCCATACTC -s simRat_chr6.simRat.chr6 52975 17 - 647215 CA------------ATAGTTCCCATACTC - -a -s simMouse_chr6.simMouse.chr6 577199 57 + 636262 CTCAAACTTCTAGCCATAAAGACTTGGGGTTATCTACCGATTCAAGTAGTCTGACAC -s Anc0.Anc0refChr3 178544 57 + 222631 CTCAAACTTCTAAAAACTTAGTCCTGTAGCCATCTACCTATGCAAATAGCCCAACAC -s Anc1.Anc1refChr1 17832 57 + 69767 CTCAAACTTCTAAAAACTTAGTCCTGTAGCCATCTACCTATGCAAATAGCCCAACAC -s Anc2.Anc2refChr1 93937 57 + 142988 CTCAAACTTCTAAAAACTTAGTCCTGTAGCCATCTACCTATGCAAATAGCCCAACAC -s mr.mrrefChr3 127112 57 + 181027 CTCAAACTTCTAGCCACAAAGACTTGTGGTTATCTACCGATGCAAATAGTCCGACAC -s simCow_chr6.simCow.chr6 551938 57 + 602619 CTCAAACTTCTAATGGCTTAGACCTGTAGCCATCTAGCTATGCAAATAGCCCGACAC -s simDog_chr6.simDog.chr6 540249 57 + 593897 CTCAAACTTCTAAAAACTTAGTCCTGTAACCATCTACATATGCAACTAGCACAACAC -s simHuman_chr6.simHuman.chr6 548979 53 + 601863 CTCAAATTTCT----ACTTGGGCCTGTAGCCATCTACCCATGTGAATAGCCCAATAC -s simRat_chr6.simRat.chr6 52992 57 - 647215 CTCAAACTTTTAACCACAGAGACTTGTGGTTATCTACCAATGCAAATAGTCCCACAC - -a -s simMouse_chr6.simMouse.chr6 577256 5 + 636262 TTGCC -s Anc0.Anc0refChr3 178603 4 + 222631 TGAC- -s Anc1.Anc1refChr1 17891 5 + 69767 TGACC -s Anc2.Anc2refChr1 93996 4 + 142988 TTAC- -s mr.mrrefChr3 127169 5 + 181027 TGGCC -s simCow_chr6.simCow.chr6 551997 4 + 602619 TTAA- -s simDog_chr6.simDog.chr6 540308 4 + 593897 TTTC- -s simHuman_chr6.simHuman.chr6 549034 5 + 601863 TGACC -s simRat_chr6.simRat.chr6 53049 5 - 647215 TGTCC - -a -s simMouse_chr6.simMouse.chr6 577261 11 + 636262 AAGGACAAAAC -s Anc0.Anc0refChr3 178607 10 + 222631 -AGGACCAAAC -s Anc1.Anc1refChr1 17896 11 + 69767 AAGGACCAAAC -s Anc2.Anc2refChr1 94000 10 + 142988 -AGGACCAAAC -s mr.mrrefChr3 127174 11 + 181027 AAGGACAAAAC -s simCow_chr6.simCow.chr6 552001 10 + 602619 -AGGACCAAAC -s simDog_chr6.simDog.chr6 540312 10 + 593897 -AGGACCAAAC -s simHuman_chr6.simHuman.chr6 549063 11 + 601863 AAGGACCAAAC -s simRat_chr6.simRat.chr6 53054 11 - 647215 AAGGACAAACC - -a -s simMouse_chr6.simMouse.chr6 577272 32 + 636262 TCACGTATTGTAGAAAGGTGGCAAATTCTCAG -s Anc0.Anc0refChr3 178622 32 + 222631 TAACACACTATTGAAAAGAGGAGAATTCCCAG -s Anc1.Anc1refChr1 17912 32 + 69767 TAACACACTATTGAAAAGAGGAGAATTCCCAG -s Anc2.Anc2refChr1 94015 32 + 142988 CAACACACTATTGAAAATAGGAGTATTCCCAG -s mr.mrrefChr3 127185 32 + 181027 TCACGTATTATAGAAAAGTGGCAAATTCTCAG -s simCow_chr6.simCow.chr6 552016 30 + 602619 CATCATGCCATTGAAAATAGGAGCA--TCCAG -s simDog_chr6.simDog.chr6 540327 32 + 593897 CAACACACTATTGAAAATAGGAGTATTCCCAG -s simHuman_chr6.simHuman.chr6 549079 32 + 601863 TAACACACTATGGAACAGAGAAGAGCTCCTAG -s simRat_chr6.simRat.chr6 53065 32 - 647215 TCATGTATTACAGAGAAGTAGCAAATTCTCAG - -a -s simMouse_chr6.simMouse.chr6 577304 36 + 636262 CTGAGTGAAGTATTGTTGATAATACCAGATTATAGA -s Anc0.Anc0refChr3 178662 36 + 222631 CTCAATGAACTTGGGTTAATGCTGCTACATTACAAA -s Anc1.Anc1refChr1 17952 36 + 69767 CTCAATGAACTTGGGTTAATGCTGCTACATTACAAA -s Anc2.Anc2refChr1 94055 36 + 142988 CTCAATGAACTTGGATTAATGCTGCTACATGACAAA -s mr.mrrefChr3 127225 36 + 181027 CTCAGTGAAGTATTGTTGATACTACTAGATTATAGA -s simCow_chr6.simCow.chr6 552054 36 + 602619 TACAATGAACTAGGATTGATGCTGCTACAGGACAAA -s simDog_chr6.simDog.chr6 540367 36 + 593897 CTCAATCAACTTGAATCAAGGCTCCTACATGACAAA -s simHuman_chr6.simHuman.chr6 549119 36 + 601863 CTCAATGAACTTGGGTTTATGCAGCTACATTACAAA -s simRat_chr6.simRat.chr6 53105 36 - 647215 CTCAGTGAAGTACTGCTGATACTACTAAATTATCCA - -a -s simMouse_chr6.simMouse.chr6 577340 20 + 636262 TATTGAAGGCAGCAAAAAAC -s Anc0.Anc0refChr3 178698 20 + 222631 TATTGATGATAGCAAAAAGT -s Anc1.Anc1refChr1 17988 20 + 69767 TATTGATGATAGCAAAAAGT -s Anc2.Anc2refChr1 94091 20 + 142988 TATTGATGATAGCAAAAAGT -s mr.mrrefChr3 127261 20 + 181027 TATTGAAGGTAGCAAAAAAC -s simCow_chr6.simCow.chr6 552090 20 + 602619 AATTGATGATAGCAGATAGT -s simDog_chr6.simDog.chr6 540404 20 + 593897 TATTGATGATATCAAAAAGT -s simHuman_chr6.simHuman.chr6 549155 20 + 601863 TATCGCTGATGGGAAAAAGT -s simRat_chr6.simRat.chr6 53141 20 - 647215 TATGGAAGGTAGTAAAAAAC - -a -s simMouse_chr6.simMouse.chr6 577360 29 + 636262 ATGTGGCCAATATGAATAATTACCGCCAT -s Anc0.Anc0refChr3 178719 29 + 222631 GTGTGGCTAATATCAATAGTCACCAATAT -s Anc1.Anc1refChr1 18009 29 + 69767 GTGTGGCTAATATCAATAGTCACCAATAT -s Anc2.Anc2refChr1 94112 29 + 142988 GTGTGGCTAAGATCAATAGTCACTGAAAT -s mr.mrrefChr3 127281 29 + 181027 GTGTGGCCAATATCAATAATTACCACTAT -s simCow_chr6.simCow.chr6 552111 29 + 602619 GTGTGGCTAACATCAATAGTCAGCAATAT -s simDog_chr6.simDog.chr6 540425 29 + 593897 GTGTGTCTAAGATCATTAGTCACTGAAAT -s simHuman_chr6.simHuman.chr6 549176 22 + 601863 GTGTGGCTAATATCAA-------CAGTAT -s simRat_chr6.simRat.chr6 53161 29 - 647215 GTGTGGCCAATATCATTAATTACCAATAT - -a -s simMouse_chr6.simMouse.chr6 577389 7 + 636262 CCAGGTG -s Anc0.Anc0refChr3 178748 7 + 222631 CCAGGTG -s Anc1.Anc1refChr1 18038 7 + 69767 CCAGGTG -s Anc2.Anc2refChr1 94141 7 + 142988 CCAAGTG -s mr.mrrefChr3 127310 7 + 181027 CCAGGTG -s simCow_chr6.simCow.chr6 552141 7 + 602619 CCAAATG -s simDog_chr6.simDog.chr6 540454 7 + 593897 CCAAGTG -s simHuman_chr6.simHuman.chr6 549198 7 + 601863 CCAGGTG -s simRat_chr6.simRat.chr6 53190 7 - 647215 CCGGCTG - -a -s simMouse_chr6.simMouse.chr6 577396 41 + 636262 TCCAACGGATAGTCTGAAGCAACACATCAACTAAGGTCCCC -s Anc0.Anc0refChr3 178755 33 + 222631 GCCTA--GGTGGT------TAACACATCAACTAAGGTGCCC -s Anc1.Anc1refChr1 18045 33 + 69767 GCCTA--GGTGGT------TAACACATCAACTAAGGTGCCC -s Anc2.Anc2refChr1 94148 33 + 142988 GCCTG--GGTGGC------TAACACATGGACTAAGGTGCCC -s mr.mrrefChr3 127317 41 + 181027 TCCTACGGATAGTCTGAAGCAACACATCAACTAAGGTCCCC -s simCow_chr6.simCow.chr6 552148 33 + 602619 TGCTG--GGTGGC------TAACACATAGACTAAGGTGCCC -s simDog_chr6.simDog.chr6 540461 33 + 593897 GCCTG--GGTGGC------TAACGCATGGACTCAGGCGCCC -s simHuman_chr6.simHuman.chr6 549205 33 + 601863 GCCTA--GGTGGT------TAACAGATCAACTAAAGTGCCC -s simRat_chr6.simRat.chr6 53199 39 - 647215 TCCTACAGAGACTCTGAAGCAACACATCAAC--AGGTCCCC - -a -s simMouse_chr6.simMouse.chr6 577437 7 + 636262 AGAATAA -s Anc0.Anc0refChr3 178788 7 + 222631 GGAGTGA -s Anc1.Anc1refChr1 18078 7 + 69767 GGAGTGA -s Anc2.Anc2refChr1 94181 7 + 142988 GGAGTGC -s mr.mrrefChr3 127358 7 + 181027 AGAGTAA -s simCow_chr6.simCow.chr6 552181 7 + 602619 AGAGTGT -s simDog_chr6.simDog.chr6 540498 7 + 593897 GGAGTGC -s simHuman_chr6.simHuman.chr6 549238 7 + 601863 GGAGTTA -s simRat_chr6.simRat.chr6 53238 7 - 647215 AGAGTAA - -a -s simMouse_chr6.simMouse.chr6 577444 4 + 636262 AATA -s Anc0.Anc0refChr3 178795 4 + 222631 AATA -s Anc1.Anc1refChr1 18085 4 + 69767 AATA -s Anc2.Anc2refChr1 94188 4 + 142988 AATA -s mr.mrrefChr3 127365 4 + 181027 AATA -s simCow_chr6.simCow.chr6 552190 4 + 602619 AATA -s simDog_chr6.simDog.chr6 540505 4 + 593897 AATA -s simHuman_chr6.simHuman.chr6 549245 4 + 601863 AATA -s simRat_chr6.simRat.chr6 53245 4 - 647215 AATA - -a -s simMouse_chr6.simMouse.chr6 577448 22 + 636262 AGGCTGTAGTCAATTTAAACTG -s Anc0.Anc0refChr3 178799 22 + 222631 AGGTTGTAGTGAAATTAAACTG -s Anc1.Anc1refChr1 18089 22 + 69767 AGGTTGTAGTGAAATTAAACTG -s Anc2.Anc2refChr1 94194 22 + 142988 AGGTTGTAGTGGAATCAAACTG -s mr.mrrefChr3 127369 22 + 181027 AGGCTGTAGTGAATTTAAACTG -s simCow_chr6.simCow.chr6 552196 22 + 602619 GGGTTGTAGTGGAATCAAACTG -s simDog_chr6.simDog.chr6 540511 22 + 593897 AGGTTGTAGTGGAATCAAACCG -s simHuman_chr6.simHuman.chr6 549249 22 + 601863 AGGTTGTAGTGAAATTGAGCTG -s simRat_chr6.simRat.chr6 53249 22 - 647215 CGGCTGCAGTGAATTTAAAGTG - -a -s simMouse_chr6.simMouse.chr6 577470 18 + 636262 AGCTAGCATACTGAATCC -s Anc0.Anc0refChr3 178821 18 + 222631 GGTTAGCATGCTGGATCT -s Anc1.Anc1refChr1 18111 18 + 69767 GGTTAGCATGCTGGATCT -s Anc2.Anc2refChr1 94216 18 + 142988 GGTTAGCCTGCTGGATCT -s mr.mrrefChr3 127391 18 + 181027 AGTTAGCATACTGAATCC -s simCow_chr6.simCow.chr6 552218 18 + 602619 GGTTAGCTTGCTGCATTT -s simDog_chr6.simDog.chr6 540558 18 + 593897 GGTCAGCCTACTGGATCT -s simHuman_chr6.simHuman.chr6 549271 18 + 601863 GGTTAGCATGTTGGATCT -s simRat_chr6.simRat.chr6 53271 18 - 647215 AGTGAGCATTCTGAATCC - -a -s simMouse_chr6.simMouse.chr6 577488 21 + 636262 TAGGTCCTAGGTAACCGCAAG -s Anc0.Anc0refChr3 178839 21 + 222631 TAGGTCCTAGGTGACTGTAAG -s Anc1.Anc1refChr1 18129 21 + 69767 TAGGTCCTAGGTGACTGTAAG -s Anc2.Anc2refChr1 94234 21 + 142988 TAGATCCTAGGTGACTGTAAA -s mr.mrrefChr3 127409 21 + 181027 TAGGTCCTAGGTAACTGCAAG -s simCow_chr6.simCow.chr6 552237 21 + 602619 TAGAACCTAGGTGGCTGTAAA -s simDog_chr6.simDog.chr6 540576 16 + 593897 TAGATCCTAGGAGACT----- -s simHuman_chr6.simHuman.chr6 549289 21 + 601863 TTGGTCCTAGTTGTTTGTAAG -s simRat_chr6.simRat.chr6 53289 21 - 647215 TAGATCCTAGGTAACTACAAG - -a -s simMouse_chr6.simMouse.chr6 577509 19 + 636262 TTTCTGATAGGACAAATAT -s Anc0.Anc0refChr3 178863 7 + 222631 TT-------GG-----TAA -s Anc1.Anc1refChr1 18153 7 + 69767 TT-------GG-----TAA -s Anc2.Anc2refChr1 94258 7 + 142988 CT-------GG-----TAA -s mr.mrrefChr3 127430 11 + 181027 TT-------GGACAA-TAT -s simCow_chr6.simCow.chr6 552261 7 + 602619 CT-------GG-----TAA -s simDog_chr6.simDog.chr6 540595 7 + 593897 CT-------GG-----CAA -s simHuman_chr6.simHuman.chr6 549313 7 + 601863 TT-------GG-----TAA -s simRat_chr6.simRat.chr6 53310 11 - 647215 TT-------GGACAA-TAT - -a -s simMouse_chr6.simMouse.chr6 577528 104 + 636262 TAGATCGATGAAAAGTCCATAGAAGGAGAGGATCATAATCAATGTAGTATATAAGGTGTATAATGTGTAACTGGATCTGTGAGGCTTTAGTACCCAACCACATC -s Anc0.Anc0refChr3 178870 100 + 222631 GAGACAAATGTTG----CATAGAAGGAAAGTATCATGTTCCATGTAATATATTAGAAGTACAATGTGGGGCTGAATCCCTGAGGCTTTAGTAGCCAATCATACC -s Anc1.Anc1refChr1 18160 100 + 69767 GAGACAAATGTTG----CATAGAAGGAAAGTATCATGTTCCATGTAATATATTAGAAGTACAATGTGGGGCTGAATCCCTGAGGCTTTAGTAGCCAATCATACC -s Anc2.Anc2refChr1 94265 100 + 142988 GAGACAAATGTTG----CATAGAAGGAAAGTATCATGATCCATATCATATACTAGAAGTACAGTGTGGGGCTGAATCCCTGAGGCTTCAGTAGCCAATGATACC -s mr.mrrefChr3 127441 104 + 181027 TAGATAGATGAAAAGTCCATAGAAGGAGAGGATCATATTCAATGTAGTATATAAGGTGTATAATGTGTGGCTGGATCTGTGAGGCTTTAGTACCCAACCACATC -s simCow_chr6.simCow.chr6 552268 93 + 602619 GAGACAAATGTTG----CATTGAAGGTAAGTGTCA-AATCCATTTCATATACTTGGAGAAC--CGTGGAGCTTAATCCCTGAGGCT----TAGCCAATGATACC -s simDog_chr6.simDog.chr6 540605 97 + 593897 GAGAAAAATCTTG----CATAGAAGGAAAGTATCGTGATCCGCATCATA---TATAATTACAGTGTGGGGTTGAATCCCTGAGGCTTCAGTTGCCAGTGATACC -s simHuman_chr6.simHuman.chr6 549320 100 + 601863 GAGACAAATGTGG----CATAGCAGGAAAGCATCATGTTCCATGTAATAGATTAGAAGTACAATGTGAGGCTGAATTACCAAGGTTTTAGTAGTCAAGCATACC -s simRat_chr6.simRat.chr6 53321 104 - 647215 TAGATAGAGGAACAGTCCATAAACGGAGAGGACCGTATTCAATGTGGTATATAAGGTATATAATGAGTGGCTGGATCTGTGAGACTTTAGTACCCAACCACATC - -a -s simMouse_chr6.simMouse.chr6 577632 10 + 636262 TTAATATTTT -s Anc0.Anc0refChr3 178971 10 + 222631 TTAATATTCT -s Anc1.Anc1refChr1 18261 10 + 69767 TTAATATTCT -s Anc2.Anc2refChr1 94366 10 + 142988 TTAATAGTCT -s mr.mrrefChr3 127545 10 + 181027 TTAATATTTT -s simCow_chr6.simCow.chr6 552362 10 + 602619 TTGATGGTCT -s simDog_chr6.simDog.chr6 540703 10 + 593897 TGAGTAGACT -s simHuman_chr6.simHuman.chr6 549421 10 + 601863 TTAATATTCT -s simRat_chr6.simRat.chr6 53425 10 - 647215 TTAATACTGT - -a -s simMouse_chr6.simMouse.chr6 577642 35 + 636262 TTCAAATGGAACTTCTATAGTGTAGGTATACCGTT -s Anc0.Anc0refChr3 178983 34 + 222631 TTCAGAAGGAACTTCACTAGGGCAGGAATACTC-T -s Anc1.Anc1refChr1 18273 35 + 69767 TTCAGAAGGAACTTCACTAGGGCAGGAATACTCCT -s Anc2.Anc2refChr1 94378 34 + 142988 TTCAGAAGGGACTTCACTAGGGCAGAAATACTC-T -s mr.mrrefChr3 127555 35 + 181027 TTCAAATGGAACTTCTCTAGTGTAGGTATACTGTT -s simCow_chr6.simCow.chr6 552374 34 + 602619 TTCAGAAGGGACTTTACTAGGGCAGAAATACTC-T -s simDog_chr6.simDog.chr6 540715 21 + 593897 TT--------ACCTCACTAGGGCAAAAAT------ -s simHuman_chr6.simHuman.chr6 549433 35 + 601863 TCCAGAAAGAACTTCACTAGGGCAGGAATACTCCT -s simRat_chr6.simRat.chr6 53435 35 - 647215 TTCAAATGGAACTTCCCTAGTGTAGGGATACTGTT - -a -s simMouse_chr6.simMouse.chr6 577677 62 + 636262 AATAAAACGGAACCAATCTGGCCCACTTTGCCTTCTTCTTAAGGTGTAACAACCAGTATAGA -s Anc0.Anc0refChr3 179017 55 + 222631 AATACAATACAGCAATTCTGGCCCACTTTACCTTTTTCTTCACGAG-------ATGTCTAGA -s Anc1.Anc1refChr1 18308 55 + 69767 AATACAATACAGCAATTCTGGCCCACTTTACCTTTTTCTTCACGAG-------ATGTCTAGA -s Anc2.Anc2refChr1 94412 55 + 142988 GATACAATATAGCAATGCTGGCCCACTTTACCTTTTTCTTCACGAG-------ATGTCCAGA -s mr.mrrefChr3 127590 62 + 181027 AATACAACGCAGCCAATCTGGCCCACTTTGCCTTCTTCTTAACGTGTAACAACCAGTATAGA -s simCow_chr6.simCow.chr6 552408 53 + 602619 GGTATAATAGAGCAATACTGGCTTACTTTACCACATTCTTCATGAG-------GTG--CAGA -s simDog_chr6.simDog.chr6 540736 54 + 593897 GATACAATGTA-CGATGCTGGTCCGCTTTACCTTTTTCTTTACAAG-------ACGTCCCGA -s simHuman_chr6.simHuman.chr6 549475 55 + 601863 AATCCAATACAGCAATTCTTGCCCACTTTACCTTTTTTTTCGCGAG-------ATGTCTAGA -s simRat_chr6.simRat.chr6 53470 62 - 647215 AATACAAACCAGCCAATCTGGCCCGGTTTGTCTTCTACTTAACGTGTAACAACTAGTATGAA - -a -s simMouse_chr6.simMouse.chr6 577739 39 + 636262 TTGTCAATACCTTTTCCTCTGATGGGTTACTTGCACAAC -s Anc0.Anc0refChr3 179073 39 + 222631 TGGTTAGCCTTGCTTTCTCTAATGCGTTACATGCACAAA -s Anc1.Anc1refChr1 18364 39 + 69767 TGGTTAGCCTTGCTTTCTCTAATGCGTTACATGCACAAA -s Anc2.Anc2refChr1 94468 39 + 142988 TGGTCAACCTCTCTTTCTCTAATGCGTTACACACACAAA -s mr.mrrefChr3 127652 39 + 181027 TGGTTAGCACTGTTTCCTCTGATGGGTTACTTGCACAAC -s simCow_chr6.simCow.chr6 552462 39 + 602619 TGGAAAACCTCTCTTTCCCTTATGGGTTATTCACACAAA -s simDog_chr6.simDog.chr6 540791 39 + 593897 TGGTCAACCACTCCTACTCTAATGCATTACACATACAAA -s simHuman_chr6.simHuman.chr6 549531 39 + 601863 TGGCTAGCGTTGCTTTCTCTAATGAGTTACCTGCACAAA -s simRat_chr6.simRat.chr6 53532 39 - 647215 TGGTTAGCACTGTTTCCTCTGATGTGTTACTTGCACAAC - -a -s simMouse_chr6.simMouse.chr6 577778 5 + 636262 TGTTT -s Anc0.Anc0refChr3 179112 5 + 222631 TGTTT -s Anc1.Anc1refChr1 18403 5 + 69767 TGTTT -s Anc2.Anc2refChr1 94507 5 + 142988 TCCAT -s mr.mrrefChr3 127691 5 + 181027 TGTTT -s simCow_chr6.simCow.chr6 552501 5 + 602619 TCCAT -s simDog_chr6.simDog.chr6 540830 5 + 593897 TCCAT -s simHuman_chr6.simHuman.chr6 549577 5 + 601863 TGTTT -s simRat_chr6.simRat.chr6 53571 3 - 647215 TGT-- - -a -s simMouse_chr6.simMouse.chr6 577783 5 + 636262 ATCTG -s Anc0.Anc0refChr3 179118 5 + 222631 ATGTG -s Anc1.Anc1refChr1 18409 5 + 69767 ATGTG -s Anc2.Anc2refChr1 94513 5 + 142988 GTGTA -s mr.mrrefChr3 127696 5 + 181027 ATCTG -s simCow_chr6.simCow.chr6 552507 5 + 602619 ATGTA -s simDog_chr6.simDog.chr6 540836 5 + 593897 GTGTA -s simHuman_chr6.simHuman.chr6 549583 5 + 601863 ATTAG -s simRat_chr6.simRat.chr6 53574 5 - 647215 ACCTG - -a -s simMouse_chr6.simMouse.chr6 577788 13 + 636262 ATGGGTTACTTGT -s Anc0.Anc0refChr3 179123 8 + 222631 TTGTG-----AGT -s Anc1.Anc1refChr1 18414 13 + 69767 TTGTGTTTCGAGT -s Anc2.Anc2refChr1 94518 8 + 142988 TTGTG-----AAT -s mr.mrrefChr3 127701 13 + 181027 ATGGGTTACTTGT -s simCow_chr6.simCow.chr6 552513 8 + 602619 TTGTG-----TAT -s simDog_chr6.simDog.chr6 540841 8 + 593897 TTGTG-----AAT -s simHuman_chr6.simHuman.chr6 549588 13 + 601863 TTGTGTTTCGCGT -s simRat_chr6.simRat.chr6 53579 13 - 647215 ATGGGTTACCTGT - -a -s simMouse_chr6.simMouse.chr6 577801 71 + 636262 ACAAACCCAATTGTGCTTTGTGTTCTGAAATGTCCAAACAGTGTAGGAGTGCAACAGTGGGATGTAGGCAC -s Anc0.Anc0refChr3 179150 68 + 222631 ATAGGGCTT---TTGAGCTGGTCTATGAAATGATCAAATAGCCAAGGAGTGTGCCACTGGGCCCCAGGAGC -s Anc1.Anc1refChr1 18446 68 + 69767 ATAGGGCTT---TTGAGCTGGTCTATGAAATGATCAAATAGCCAAGGAGTGTGCCACTGGGCCCCAGGAGC -s Anc2.Anc2refChr1 94545 68 + 142988 ATAGGGCTT---TTGAGCCAGTCTACAAAATGATCAAATGGCCAAGGAGTGTGCCACTGGGCCCCAGGAGC -s mr.mrrefChr3 127714 68 + 181027 ACAAACCCA---GTGCTTTGTGTTCTGAAATGTCCAAACAGTGTAGGAGTGCAACAGTGGGACGTAGGCAC -s simCow_chr6.simCow.chr6 552540 68 + 602619 ACAGGGCTT---TTAAACCAGTCTACAAAATGAGCAAGTCGCCAAGGAGAGTGATGCCGGGGCCCAGTAAC -s simDog_chr6.simDog.chr6 540868 67 + 593897 ATAGGGCCT---TTGAGCCAGTCTACAAAA-GATCAGATGGCCAAGTAGTGAGCCACTAGGCCCCAGGAGC -s simHuman_chr6.simHuman.chr6 549620 68 + 601863 ATACGGCTT---TTGGGCTGGTCGATGAAACGATCAAATAGCCATTGAGTGTGCCACTGGGCCCCAGGATC -s simRat_chr6.simRat.chr6 53592 66 - 647215 ACAAATCCA---GTGGTTTGTATTCGGAAATGGCCAAACAGTGTAGAA-TGCAACAGTTGG-CGTAGGCAC - -a -s simMouse_chr6.simMouse.chr6 577872 6 + 636262 TGCAGT -s Anc0.Anc0refChr3 179218 6 + 222631 CACACT -s Anc1.Anc1refChr1 18514 6 + 69767 CACACT -s Anc2.Anc2refChr1 94614 6 + 142988 CACCCT -s mr.mrrefChr3 127782 6 + 181027 TGCAGT -s simCow_chr6.simCow.chr6 552609 6 + 602619 CACTGT -s simDog_chr6.simDog.chr6 540936 6 + 593897 CACCCT -s simHuman_chr6.simHuman.chr6 549688 6 + 601863 CACACT -s simRat_chr6.simRat.chr6 53658 6 - 647215 TGTATT - -a -s simMouse_chr6.simMouse.chr6 577878 4 + 636262 TGTA -s Anc0.Anc0refChr3 179224 4 + 222631 TGTG -s Anc1.Anc1refChr1 18520 4 + 69767 TGTG -s Anc2.Anc2refChr1 94621 4 + 142988 TGTG -s mr.mrrefChr3 127788 4 + 181027 TGTA -s simCow_chr6.simCow.chr6 552616 4 + 602619 TGTG -s simDog_chr6.simDog.chr6 540943 4 + 593897 TGTG -s simRat_chr6.simRat.chr6 53664 4 - 647215 TGTA - -a -s simMouse_chr6.simMouse.chr6 577882 19 + 636262 TGGCCTGGGTTCAAATTTC -s Anc0.Anc0refChr3 179230 19 + 222631 TAGCCTAGGTTTAAATTTT -s Anc1.Anc1refChr1 18526 19 + 69767 TAGCCTAGGTTTAAATTTT -s Anc2.Anc2refChr1 94627 19 + 142988 TAGCCTAGGTTTAAATTTT -s mr.mrrefChr3 127794 19 + 181027 TGGCCTGGGTTTAAATTTT -s simCow_chr6.simCow.chr6 552622 19 + 602619 TAGCCTGGGTTTAAATTTC -s simDog_chr6.simDog.chr6 540949 19 + 593897 CAGCCTAAGTTTAAATTTT -s simHuman_chr6.simHuman.chr6 549696 19 + 601863 TAGCCCTGGCTTAAATTTT -s simRat_chr6.simRat.chr6 53670 19 - 647215 TGGTCTGGGTTTAAATTAT - -a -s simMouse_chr6.simMouse.chr6 577901 183 + 636262 CAATTGGATATAGTAACTACAGGCAGGCTCATTCTAAAGGCGAAACAGGTGCCTGTTCTTGATCACTTGACGGTGTGTGAGATGGACAGGGGATCTACAATGTACAGGGGGAACTACACATGACAAACCTCTTTCGAGGTGGACATACTCTCTCTGTGATCGCTTGACATCTCGTCAAGTGGG -s Anc0.Anc0refChr3 179249 22 + 222631 CAATTGTATCAAGTAACCACAT----------------------------------------------------------------------------------------------------------------------------------------------------------------- -s Anc1.Anc1refChr1 18545 22 + 69767 CAATTGTATCAAGTAACCACAT----------------------------------------------------------------------------------------------------------------------------------------------------------------- -s Anc2.Anc2refChr1 94646 22 + 142988 CAATTGTATCAAGTAACCACAT----------------------------------------------------------------------------------------------------------------------------------------------------------------- -s mr.mrrefChr3 127813 180 + 181027 CAATTGTATATAGTAACTACATGCAGGCTCATT-TAAAGGCGAAACAGGTGCCTGTTCTTGATCACTTGACGGTGTGTGAGATGGACAGGGGATCTACAATGTAC--GGGGAACTACACATGACAAACCTCTTTCGAGGTGGACATACTCTCTCTGTGATCGCTTGACATCTCGTCAAGTGGG -s simCow_chr6.simCow.chr6 552642 22 + 602619 CAATGGTATAAAGTAACCACCT----------------------------------------------------------------------------------------------------------------------------------------------------------------- -s simDog_chr6.simDog.chr6 540968 22 + 593897 CAATTTTATCAAGGAACTACAT----------------------------------------------------------------------------------------------------------------------------------------------------------------- -s simHuman_chr6.simHuman.chr6 549715 22 + 601863 CAATCGTATCAAGTAACCACAT----------------------------------------------------------------------------------------------------------------------------------------------------------------- -s simRat_chr6.simRat.chr6 53689 180 - 647215 CAATTGTATATGGTAACTACGTGCAGGCGCATT-TAAGAGCAGGACAGGTGCTTGTCCTTGGTCACTTGACAGTGTGTGAGTTGGACAGGGGATCTACAATTCAC--GGGGAACTACTCATGACAAACCTTGTGTGAGGTGGACAGACTCTTTCTGTGATCACTTGACACCTCATCAAGCGGG - -a -s simMouse_chr6.simMouse.chr6 578084 41 + 636262 CAGGCTCATGGCCAAGCACTAACTGGGTGTACATGGCCACA -s mr.mrrefChr3 127993 41 + 181027 CAGGCTCATGGCCAAGCACTAACTGGGTGTACATGGCCACA -s simRat_chr6.simRat.chr6 53870 41 - 647215 CAGGCTCATGGCCGCGCACTAATTGTGTGTACATGGCCACA - -a -s simMouse_chr6.simMouse.chr6 578125 21 + 636262 GAGGCGGCGTCTGAGTCAAGC -s mr.mrrefChr3 128034 20 + 181027 GAGGCGGC-TCTGAGTCAAGC -s simRat_chr6.simRat.chr6 53913 20 - 647215 GGGGAGGC-TCATAGCCAAGC - -a -s simMouse_chr6.simMouse.chr6 578146 91 + 636262 CTAACCATGTGTACATGGCCGCATTTGCCTTTTATTGGAGCTATGCACGTGGCATGGTGTGAAATATAAACGACGTTAACCATTTGGCGTT -s Anc0.Anc0refChr3 179271 9 + 222631 ----------------------------------------------------------------------------------TGAGGGGCT -s Anc1.Anc1refChr1 18567 9 + 69767 ----------------------------------------------------------------------------------TGAGGGGCT -s Anc2.Anc2refChr1 94668 9 + 142988 ----------------------------------------------------------------------------------TGAGGGGCT -s mr.mrrefChr3 128054 84 + 181027 CTAACCATGTGTACATGGCCGCATTTGCCTTTTATTGGAGCTATGCACGTGGCATGGTGTGAAATATAAACGAC-------ATTTGGGGTT -s simCow_chr6.simCow.chr6 552664 9 + 602619 ----------------------------------------------------------------------------------TGAGGGGCT -s simDog_chr6.simDog.chr6 540990 9 + 593897 ----------------------------------------------------------------------------------TGTGGAGCT -s simHuman_chr6.simHuman.chr6 549737 9 + 601863 ----------------------------------------------------------------------------------TGAGTGGCT -s simRat_chr6.simRat.chr6 53934 84 - 647215 CTAACCGTGTGCGCATGGCCACATTTGCCTGTTATTAGAGCTATGCACATGGCATTGAGTGAAATCTAAACAAT-------ATTTGGGGTT - -a -s simMouse_chr6.simMouse.chr6 578237 54 + 636262 TAGCATCTGACAACTTTGTACTGTTCTTAGACTCATGCTCTAGAGAGGCACTAG -s Anc0.Anc0refChr3 179281 54 + 222631 TTGCATCTAATAACTTTGCAGTCTAATTAGACTTGTGCCCAATTGTGGCACTAG -s Anc1.Anc1refChr1 18577 54 + 69767 TTGCATCTAATAACTTTGCAGTCTAATTAGACTTGTGCCCAATTGTGGCACTAG -s Anc2.Anc2refChr1 94678 54 + 142988 TTGCATCTAATAACTTTGCAGTCTAATCAGACTTGTGCCCAATTGTGGCACTAG -s mr.mrrefChr3 128139 54 + 181027 TTGCATCTGACAACTTTGTACTGTTCTTAGACTCATGCTCTAGAGAGGCACTAG -s simCow_chr6.simCow.chr6 552674 54 + 602619 TTGCATCCAATAGCTTTGTAGTCTAATCGTGCTTGTACCCAATTATGGCACTAG -s simDog_chr6.simDog.chr6 541000 54 + 593897 TTGCATCTGATAACTTTGCAGTCTAATCAGACTTGTGCCCAATTGTGGCACTAG -s simHuman_chr6.simHuman.chr6 549747 54 + 601863 TTGCTTCTAATAATTTTTCAGTTTGATTAGAATTGTGCCTGATTCTGGCACAAG -s simRat_chr6.simRat.chr6 54019 54 - 647215 TTGCATCTGACAACCTTCTGCTCTTCTCATACTCATCCTCTAGAGAGGCACTAG - -a -s simMouse_chr6.simMouse.chr6 578291 15 + 636262 CAATCTTGGGTCCTG -s Anc0.Anc0refChr3 179342 15 + 222631 CAATCAAGGGTCCTC -s Anc1.Anc1refChr1 18638 15 + 69767 CAATCAAGGGTCCTC -s Anc2.Anc2refChr1 94739 15 + 142988 CAATCAAGGGTTCTC -s mr.mrrefChr3 128193 15 + 181027 CAATCTAGGGTCCTG -s simCow_chr6.simCow.chr6 552735 15 + 602619 CAACCAAGTGTTCTA -s simDog_chr6.simDog.chr6 541061 15 + 593897 CAATCAAGGGTTCTC -s simHuman_chr6.simHuman.chr6 549808 15 + 601863 CAATCGAGGGTCCTC -s simRat_chr6.simRat.chr6 54073 15 - 647215 CATCCTAGGGTCTTG - -a -s simMouse_chr6.simMouse.chr6 578306 30 + 636262 CTCACTGATGATAGAGTTGTGGCTTCATGT -s Anc0.Anc0refChr3 179357 27 + 222631 TATA---GTGAGAGAGTTATGACTTCAGGT -s Anc1.Anc1refChr1 18653 27 + 69767 TATA---GTGAGAGAGTTATGACTTCAGGT -s Anc2.Anc2refChr1 94754 27 + 142988 TATA---GTGATCGAGTTATGACTTCAGGT -s mr.mrrefChr3 128208 30 + 181027 TACACTGATGAGAGAGTTGTGGCTTCATGT -s simCow_chr6.simCow.chr6 552752 24 + 602619 CATA---GTGAATGTGTTATGATTCCA--- -s simDog_chr6.simDog.chr6 541076 27 + 593897 TATA---GTGATCGAGTTATGACTTCAGGT -s simHuman_chr6.simHuman.chr6 549823 27 + 601863 TATA---GAGAGAGAGCTATGACTTCAGTT -s simRat_chr6.simRat.chr6 54088 30 - 647215 TACAGTGATGAGAGAGTTGTGGCTTCATGT - -a -s simMouse_chr6.simMouse.chr6 578336 11 + 636262 ATATATACTGC -s Anc0.Anc0refChr3 179386 11 + 222631 ATACATACTCC -s Anc1.Anc1refChr1 18682 11 + 69767 ATACATACTCC -s Anc2.Anc2refChr1 94783 11 + 142988 GTACATACCCC -s mr.mrrefChr3 128238 11 + 181027 ATATATACTGC -s simCow_chr6.simCow.chr6 552776 9 + 602619 --ACATACCCC -s simDog_chr6.simDog.chr6 541105 11 + 593897 GTCCACACCTC -s simHuman_chr6.simHuman.chr6 549852 11 + 601863 ATACATACTCC -s simRat_chr6.simRat.chr6 54118 11 - 647215 ATATATACTGA - -a -s simMouse_chr6.simMouse.chr6 578347 83 + 636262 TTGTAATTGTCTTCATGTTTATGGTGAAGTGTTGACTCCATTGCTGCTTGGCCAGCTAGTGCAGTTCTCACTACACAGAAACC -s Anc0.Anc0refChr3 179398 80 + 222631 TTGTAATTGTCCTTATGTTTATGG---AGTGTTGTCTGCATTTCCGTTTGGCCAGCTAGTGCAGTTCAAACCACAGAAAAAGC -s Anc1.Anc1refChr1 18694 80 + 69767 TTGTAATTGTCCTTATGTTTATGG---AGTGTTGTCTGCATTTCCGTTTGGCCAGCTAGTGCAGTTCAAACCACAGAAAAAGC -s Anc2.Anc2refChr1 94795 80 + 142988 TTGTGATTGTCCTTATGTTTATGG---AGTGTTGTCTGCATTTCCATTTGTCTGGCTAATGCAGTTCAAATCACAGAAAAAGC -s mr.mrrefChr3 128249 83 + 181027 TTGTAATTGTCTTCATGTTTATGGTGAAGTGTTGACTGCATTGCTGTTTGGCCAGCTAGTGCAGTTCTCACCACAGAGAAACC -s simCow_chr6.simCow.chr6 552786 66 + 602619 TTGTGATTGTCCTTCTGTTTATGG---GGTGTTGCCTATATTTCTATT-------CTAATGCAGTGCCAATCACAG------- -s simDog_chr6.simDog.chr6 541117 79 + 593897 TTTTGGTCGTCCTCATGTTTATGG---AGTGTTTTGTGCATTTCCATTTGTCTGGCTAATGCAGTTCAAAT-ACAGAAAAAGC -s simHuman_chr6.simHuman.chr6 549864 80 + 601863 TTGTAATTGTCCTTATGTTTATGG---AGTGTTGTCTGCATTCCAGTGTGGCCAGCTAGTGCAGTTCAAACCTCAGAAAGATT -s simRat_chr6.simRat.chr6 54129 83 - 647215 CTGTAATCGTCTCCATTTCTATGGCAAAGTGTTGATTGTATTGCTGTTTGGCCAACTAATGCAGTTCTCACCATGGAGAAACC - -a -s simMouse_chr6.simMouse.chr6 578430 40 + 636262 AGGGAATTTAGACCAGTCCGCGTCAAGCACCCTTTAAGAA -s Anc0.Anc0refChr3 179478 40 + 222631 AAGGAATTGAGACTAGTCTGTGTCAAGCATCCTTTAAGGA -s Anc1.Anc1refChr1 18774 40 + 69767 AAGGAATTGAGACTAGTCTGTGTCAAGCATCCTTTAAGGA -s Anc2.Anc2refChr1 94875 40 + 142988 AAGGGATTGAGACTAGTCTGTGTCAAGCATCCTTTAAGGA -s mr.mrrefChr3 128332 40 + 181027 AAGGAATTTAGACCAGTCTGCGTCAAGCACCCTTTAAGGA -s simCow_chr6.simCow.chr6 552852 32 + 602619 -------TGAGACTAGTCTGTGTCAAACATTC-TTAAGGA -s simDog_chr6.simDog.chr6 541197 40 + 593897 AAGGGATTGAGACTAGCCTGTATCAAGCATCCTGTAAGGA -s simHuman_chr6.simHuman.chr6 549944 39 + 601863 AAGAAGTTGAGACTAGTCTG-GTCAAGCATCCTTTAAAGA -s simRat_chr6.simRat.chr6 54212 40 - 647215 AAGGAATTTAGGCCAGACTGCATTAAGCACCCTTTAAGGA - -a -s simMouse_chr6.simMouse.chr6 578470 29 + 636262 AAAATCAGGTGTTATTAATGTACAGAACA -s Anc0.Anc0refChr3 179519 29 + 222631 AAGAGGGTGGGTTAGTAACATACAGAACA -s Anc1.Anc1refChr1 18815 29 + 69767 AAGAGGGTGGGTTAGTAACATACAGAACA -s Anc2.Anc2refChr1 94916 29 + 142988 AAGAAGGTGGGTTAGTAACATACGGAACA -s mr.mrrefChr3 128372 29 + 181027 AAAAGCAGGTGTTAGTAATGTACAGAACA -s simCow_chr6.simCow.chr6 552885 29 + 602619 AAGAAGGTGTGTCAGTAACATACTGAACA -s simDog_chr6.simDog.chr6 541238 29 + 593897 AATAAGGTGGGTTGGTGATGTATGGCACA -s simHuman_chr6.simHuman.chr6 549984 29 + 601863 AAGAGGGTGCATTAGTAACATACAGAACA -s simRat_chr6.simRat.chr6 54252 25 - 647215 GAAAGCAGGTGTTAGTAATGTAAAG---- - -a -s simMouse_chr6.simMouse.chr6 578499 6 + 636262 CCCTTT -s Anc0.Anc0refChr3 179548 6 + 222631 CCCTTT -s Anc1.Anc1refChr1 18844 6 + 69767 CCCTTT -s Anc2.Anc2refChr1 94945 6 + 142988 CCCTTT -s mr.mrrefChr3 128401 6 + 181027 CCCTTT -s simCow_chr6.simCow.chr6 552914 5 + 602619 -CCTTT -s simDog_chr6.simDog.chr6 541268 6 + 593897 CCCTTT -s simHuman_chr6.simHuman.chr6 550013 6 + 601863 CCCTTT - -a -s simMouse_chr6.simMouse.chr6 578505 18 + 636262 AACTAAGGTGGTTGAGGT -s Anc0.Anc0refChr3 179556 13 + 222631 AACGAAGGCT-----GGT -s Anc1.Anc1refChr1 18852 13 + 69767 AACGAAGGCT-----GGT -s Anc2.Anc2refChr1 94955 13 + 142988 AATGTGGGCT-----GAT -s mr.mrrefChr3 128407 18 + 181027 AACTAAGGTGGTTGAGGT -s simCow_chr6.simCow.chr6 552923 9 + 602619 ATTACTTGC--------- -s simDog_chr6.simDog.chr6 541278 13 + 593897 AATGTGGAGT-----GAT -s simHuman_chr6.simHuman.chr6 550021 13 + 601863 AACGAAGGCT-----GGT -s simRat_chr6.simRat.chr6 54277 11 - 647215 -------GTGATCAAGGT - -a -s simMouse_chr6.simMouse.chr6 578523 26 + 636262 TACCAGAAATTCCCTAATTGTAAGGG -s Anc0.Anc0refChr3 179569 18 + 222631 AACCAG--------TATTTGTGAGGG -s Anc1.Anc1refChr1 18865 18 + 69767 AACCAG--------TATTTGTGAGGG -s Anc2.Anc2refChr1 94968 18 + 142988 AACCAG--------TGTTTGTGAGGC -s mr.mrrefChr3 128425 26 + 181027 TACCAGAAATTCCCTAATTGTAAGGG -s simCow_chr6.simCow.chr6 552932 6 + 602619 --------------------TGAGGC -s simDog_chr6.simDog.chr6 541305 18 + 593897 AACCAG--------TGTTTGTGAGGC -s simHuman_chr6.simHuman.chr6 550034 18 + 601863 GACCAG--------CACGTGTGAGGG -s simRat_chr6.simRat.chr6 54288 26 - 647215 TCCCAGAAATTCCCTAATTGTAAGGG - -a -s simMouse_chr6.simMouse.chr6 578549 51 + 636262 GTATATGTTGACTAGGCTCACACCTCTTCTACATTATCCAAGGCCCTGCAC -s Anc0.Anc0refChr3 179590 50 + 222631 GTGATAGC-GGCTAGGATAACATCTAATCTACATAAACCAAGGCCCTGCAC -s Anc1.Anc1refChr1 18886 50 + 69767 GTGATAGC-GGCTAGGATAACATCTAATCTACATAAACCAAGGCCCTGCAC -s Anc2.Anc2refChr1 94989 50 + 142988 GTGATAGC-AGCTAGGATAACATCTAATCTACATATACCAAGGCCCTGCAC -s mr.mrrefChr3 128451 50 + 181027 GTATATGT-GACTAGGCTCACATCTCTTCTACATTATCCAAGGCCCTGCAC -s simCow_chr6.simCow.chr6 552941 50 + 602619 ATGACAAC-AGCCTGGATGACGTCCAATCCACGTATACTAAGGCCCTGCAC -s simDog_chr6.simDog.chr6 541326 49 + 593897 GTGATAGC-AGCTAGGACAACATATAATCTACATATACC-AAGCCCTGTGC -s simHuman_chr6.simHuman.chr6 550055 50 + 601863 GTGGTGGC-GGCTAGGATAATATCTAATCTACATAAACCTAGGACCTGCAC -s simRat_chr6.simRat.chr6 54314 50 - 647215 GCATATGT-GACTAGGCTCACATATCTTCTACATTATCCAAGGCCCTGCAC - -a -s simMouse_chr6.simMouse.chr6 578600 81 + 636262 TGCATGGCTGAACTGTTAACCATTCTGCCAACTTATTCACCCAGTAAATCTACCTGCACCTTGTTACTGTTATGACCCTTC -s Anc0.Anc0refChr3 179642 73 + 222631 GGTGTTGCTCAACTGTTAATCATTGTGGCAACTTATTTGCCCAAAAAAT--------ATCTTGTCACTGTTATGACACCTT -s Anc1.Anc1refChr1 18938 73 + 69767 GGTGTTGCTCAACTGTTAATCATTGTGGCAACTTATTTGCCCAAAAAAT--------ATCTTGTCACTGTTATGACACCTT -s Anc2.Anc2refChr1 95041 73 + 142988 GGTGTTGCTCAACTGTTAGTCATTGTGGCAACTTATCTGCCCAAAAATT--------GTCTTGTCACTGTCATAACACCTT -s mr.mrrefChr3 128501 81 + 181027 TGCATTGCTGAACTGTTAACCATTGTGCCAACTTATTCACCCAGTAAATCTACCTGCACCTTGTTACTGTTATGACCCTTC -s simCow_chr6.simCow.chr6 552993 62 + 602619 GGTGTTGCTCAACTGTTAGTCATTGTGGCAACTTGCCTTCCCAAAACCT--------GTCCTTT-----------CACATT -s simDog_chr6.simDog.chr6 541377 73 + 593897 AGCATTGCCCATCTGTTGGTCATTGTAGCAACCTATCCGCCCAATAATT--------GTCTTGTCACTGTCATAACGCCTT -s simHuman_chr6.simHuman.chr6 550107 72 + 601863 GGTGTTCCTCAACTGTTAATCATTGTGGTGACTAACT-GCTCAAAAAAT--------ATCTTGTCACTGTTTTGACACCTT -s simRat_chr6.simRat.chr6 54364 81 - 647215 TGCATTGCTGTACTGTTAACCATTGTGCCAACTTATTTACCCAGTAAATCTACCTGCACCTTGTTACTGTTATGACCCTTC - -a -s simMouse_chr6.simMouse.chr6 578681 25 + 636262 AGGATGTCCTTTGGAAGCCTCAATT -s Anc0.Anc0refChr3 179715 20 + 222631 AAAATTTCCTTTGGACA-----ATT -s Anc1.Anc1refChr1 19011 25 + 69767 AAAATTTCCTTTGGACACCTCAATT -s Anc2.Anc2refChr1 95114 20 + 142988 AAAATTCCTATTGGACA-----AAA -s mr.mrrefChr3 128582 25 + 181027 AGGATGTCCTTTGGAAGCCTCAATT -s simCow_chr6.simCow.chr6 553056 20 + 602619 AAGTTTCCTCTTGGAAG-----AAA -s simDog_chr6.simDog.chr6 541450 18 + 593897 AAAATTCCTATTGAACA-----A-- -s simHuman_chr6.simHuman.chr6 550179 25 + 601863 AAAATCTCCTTTGGAGACCTCAATT -s simRat_chr6.simRat.chr6 54445 25 - 647215 AGGATTTCCTTTGGAAGCCTCCATT - -a -s simMouse_chr6.simMouse.chr6 578706 4 + 636262 GTCT -s Anc0.Anc0refChr3 179746 4 + 222631 GTAT -s Anc1.Anc1refChr1 19047 4 + 69767 GTAT -s Anc2.Anc2refChr1 95145 4 + 142988 GCAT -s mr.mrrefChr3 128607 4 + 181027 GTCT -s simDog_chr6.simDog.chr6 541479 4 + 593897 GCAT -s simHuman_chr6.simHuman.chr6 550215 4 + 601863 GTAT -s simRat_chr6.simRat.chr6 54470 4 - 647215 GTCT - -a -s simMouse_chr6.simMouse.chr6 578710 5 + 636262 TGGGA -s Anc0.Anc0refChr3 179750 5 + 222631 TGTGA -s Anc1.Anc1refChr1 19051 5 + 69767 TGTGA -s Anc2.Anc2refChr1 95149 5 + 142988 TGTGA -s mr.mrrefChr3 128611 5 + 181027 TAGGA -s simDog_chr6.simDog.chr6 541483 5 + 593897 TGTGA -s simHuman_chr6.simHuman.chr6 550220 5 + 601863 TGATA -s simRat_chr6.simRat.chr6 54474 5 - 647215 TAGGA - -a -s simMouse_chr6.simMouse.chr6 578715 14 + 636262 TTGGCTAGTATGGT -s Anc0.Anc0refChr3 179758 14 + 222631 TAAGCTAGTATGGT -s Anc1.Anc1refChr1 19059 14 + 69767 TAAGCTAGTATGGT -s Anc2.Anc2refChr1 95157 14 + 142988 CAAACTAGTATGGT -s mr.mrrefChr3 128616 14 + 181027 TAAGCTAGTATGGT -s simCow_chr6.simCow.chr6 553085 14 + 602619 ATTACTAGTATGGT -s simDog_chr6.simDog.chr6 541491 14 + 593897 CAAACTAGTATGGT -s simHuman_chr6.simHuman.chr6 550228 14 + 601863 TAAGCTAGTATGCT -s simRat_chr6.simRat.chr6 54479 14 - 647215 CAAGCCAGTACGAT - -a -s simMouse_chr6.simMouse.chr6 578729 5 + 636262 CATAC -s Anc0.Anc0refChr3 179772 5 + 222631 TAAGC -s Anc1.Anc1refChr1 19073 5 + 69767 TAAGC -s Anc2.Anc2refChr1 95173 5 + 142988 TAAGC -s mr.mrrefChr3 128630 5 + 181027 CATAC -s simCow_chr6.simCow.chr6 553101 5 + 602619 TAAGC -s simDog_chr6.simDog.chr6 541507 5 + 593897 TAAGT -s simHuman_chr6.simHuman.chr6 550242 5 + 601863 TAAGC -s simRat_chr6.simRat.chr6 54493 5 - 647215 CATAC - -a -s simMouse_chr6.simMouse.chr6 578734 12 + 636262 TTAGCACCATAT -s Anc0.Anc0refChr3 179785 12 + 222631 TTAACCTTGTGT -s Anc1.Anc1refChr1 19086 12 + 69767 TTAACCTTGTGT -s Anc2.Anc2refChr1 95186 12 + 142988 TTAAACTTGTGT -s mr.mrrefChr3 128643 12 + 181027 TTAGCACCATGT -s simCow_chr6.simCow.chr6 553114 12 + 602619 CTAATCTTGTGT -s simDog_chr6.simDog.chr6 541520 12 + 593897 TTAAACTCGTGT -s simHuman_chr6.simHuman.chr6 550255 12 + 601863 TTAACCTTGCGT -s simRat_chr6.simRat.chr6 54506 12 - 647215 TTAGTACCATGC - -a -s simMouse_chr6.simMouse.chr6 578746 5 + 636262 CTGGC -s Anc0.Anc0refChr3 179797 5 + 222631 CTGAA -s Anc1.Anc1refChr1 19098 5 + 69767 CTGAA -s Anc2.Anc2refChr1 95198 5 + 142988 CTGAA -s mr.mrrefChr3 128655 5 + 181027 CTGAC -s simCow_chr6.simCow.chr6 553137 5 + 602619 CTGAA -s simDog_chr6.simDog.chr6 541532 5 + 593897 CTGAA -s simHuman_chr6.simHuman.chr6 550267 5 + 601863 CTGAA -s simRat_chr6.simRat.chr6 54518 5 - 647215 CTAAC - -a -s simMouse_chr6.simMouse.chr6 578751 7 + 636262 AGGTGGC -s Anc0.Anc0refChr3 179802 7 + 222631 AAGTAGC -s Anc1.Anc1refChr1 19103 7 + 69767 AAGTAGC -s Anc2.Anc2refChr1 95210 7 + 142988 AAATAAC -s mr.mrrefChr3 128660 7 + 181027 AGGTAGC -s simCow_chr6.simCow.chr6 553149 7 + 602619 AGATAAC -s simDog_chr6.simDog.chr6 541552 7 + 593897 AAATAAC -s simHuman_chr6.simHuman.chr6 550272 7 + 601863 AAGTAGC -s simRat_chr6.simRat.chr6 54523 6 - 647215 AGGTAA- - -a -s simMouse_chr6.simMouse.chr6 578758 9 + 636262 CCTTTTGTG -s Anc0.Anc0refChr3 179810 9 + 222631 CCTTATATG -s Anc1.Anc1refChr1 19111 9 + 69767 CCTTATATG -s Anc2.Anc2refChr1 95218 9 + 142988 CATCATATG -s mr.mrrefChr3 128667 9 + 181027 CCTTTTATG -s simCow_chr6.simCow.chr6 553157 9 + 602619 TGTCATATG -s simDog_chr6.simDog.chr6 541560 9 + 593897 CACCATATG -s simHuman_chr6.simHuman.chr6 550280 9 + 601863 CCTTGTATG -s simRat_chr6.simRat.chr6 54529 5 - 647215 ----TTATG - -a -s simMouse_chr6.simMouse.chr6 578767 9 + 636262 ATGCATGCA -s Anc0.Anc0refChr3 179831 9 + 222631 CTAGATGCA -s Anc1.Anc1refChr1 19132 9 + 69767 CTAGATGCA -s Anc2.Anc2refChr1 95239 9 + 142988 CTAGGTGGA -s mr.mrrefChr3 128676 9 + 181027 ATGCATGCA -s simCow_chr6.simCow.chr6 553178 9 + 602619 TCAGGTGTA -s simDog_chr6.simDog.chr6 541581 9 + 593897 CTAGGTGGA -s simHuman_chr6.simHuman.chr6 550301 9 + 601863 CTAAAGGCA -s simRat_chr6.simRat.chr6 54534 9 - 647215 ATGCATGCA - -a -s simMouse_chr6.simMouse.chr6 578776 15 + 636262 TTGTCTAAGCTAGTG -s Anc0.Anc0refChr3 179840 14 + 222631 ATGGCTATG-TGGTG -s Anc1.Anc1refChr1 19141 14 + 69767 ATGGCTATG-TGGTG -s Anc2.Anc2refChr1 95248 14 + 142988 ATGGCTATG-TGGTG -s mr.mrrefChr3 128685 15 + 181027 TTGTCTAAGCTAGTG -s simCow_chr6.simCow.chr6 553187 14 + 602619 ACGGTTATG-TGGTT -s simDog_chr6.simDog.chr6 541590 14 + 593897 GTGGCCATC-TGGTG -s simHuman_chr6.simHuman.chr6 550310 14 + 601863 ATGGCTATG-TGATG -s simRat_chr6.simRat.chr6 54545 15 - 647215 GTGTCTAAGCTAGTG - -a -s simMouse_chr6.simMouse.chr6 578791 20 + 636262 GATGTTTCTGCAATTGGAGA -s Anc0.Anc0refChr3 179861 20 + 222631 AACACCTCTGCACTTGGAGA -s Anc1.Anc1refChr1 19162 20 + 69767 AACACCTCTGCACTTGGAGA -s Anc2.Anc2refChr1 95270 20 + 142988 AACACCTCCACACTTGGGGA -s mr.mrrefChr3 128700 20 + 181027 GATGTTTCTGCAATTGGAGA -s simCow_chr6.simCow.chr6 553209 18 + 602619 AATGCCTCTGCACTTGCG-- -s simDog_chr6.simDog.chr6 541612 20 + 593897 AACACCTCCACACTTGGGGA -s simHuman_chr6.simHuman.chr6 550331 16 + 601863 ATCACATGTG----TGGAGA -s simRat_chr6.simRat.chr6 54560 20 - 647215 GATGTTTCTGCAATTGGAGA - -a -s simMouse_chr6.simMouse.chr6 578811 3 + 636262 AGT -s Anc0.Anc0refChr3 179881 3 + 222631 AGT -s Anc1.Anc1refChr1 19182 3 + 69767 AGT -s Anc2.Anc2refChr1 95297 3 + 142988 AGT -s mr.mrrefChr3 128720 3 + 181027 AGT -s simCow_chr6.simCow.chr6 553229 3 + 602619 AGT -s simDog_chr6.simDog.chr6 541639 3 + 593897 GGT -s simHuman_chr6.simHuman.chr6 550347 3 + 601863 AGT -s simRat_chr6.simRat.chr6 54580 3 - 647215 AGT - -a -s simMouse_chr6.simMouse.chr6 578814 15 + 636262 TATCGTGGGTTGGTG -s Anc0.Anc0refChr3 179886 15 + 222631 CAGCTTAGGTGGGTG -s Anc1.Anc1refChr1 19187 15 + 69767 CAGCTTAGGTGGGTG -s Anc2.Anc2refChr1 95302 15 + 142988 CAGCTTAGGTGGGTG -s mr.mrrefChr3 128723 15 + 181027 CATCGTGGGTTGGTG -s simCow_chr6.simCow.chr6 553234 15 + 602619 CAGCTTATGTGCATG -s simDog_chr6.simDog.chr6 541644 15 + 593897 GAGCTTAGGTGGGTG -s simHuman_chr6.simHuman.chr6 550352 15 + 601863 CTCCATAGGTGGGTG -s simRat_chr6.simRat.chr6 54583 15 - 647215 CATCATGGGTTGGTG - -a -s simMouse_chr6.simMouse.chr6 578829 6 + 636262 GCAGCT -s Anc0.Anc0refChr3 179901 1 + 222631 G----- -s Anc1.Anc1refChr1 19202 6 + 69767 GCAGCC -s Anc2.Anc2refChr1 95317 1 + 142988 G----- -s mr.mrrefChr3 128738 6 + 181027 GCAGCT -s simCow_chr6.simCow.chr6 553249 1 + 602619 G----- -s simDog_chr6.simDog.chr6 541659 1 + 593897 G----- -s simHuman_chr6.simHuman.chr6 550371 6 + 601863 ACAGCC -s simRat_chr6.simRat.chr6 54598 6 - 647215 GCAGCT - -a -s simMouse_chr6.simMouse.chr6 578835 52 + 636262 TAACAAAACTTAAAAATGTCTGGCCATAATTTTATAGGAGTCCTCTCAAAGC -s Anc0.Anc0refChr3 179921 50 + 222631 TTGCAA--CTTAATAATGGTTGGGCATAATTTTATAGGAGTGCCTTAATAGC -s Anc1.Anc1refChr1 19227 50 + 69767 TTGCAA--CTTAATAATGGTTGGGCATAATTTTATAGGAGTGCCTTAATAGC -s Anc2.Anc2refChr1 95337 50 + 142988 GTGCAA--CTTAATAATGGTTGGGCATAGTTTTATAGAAGTGCCTCAGTAGT -s mr.mrrefChr3 128744 50 + 181027 TAACAA--CTTAAAAATGTTTGGCCATAATTTTATAGGAGTGCTCTCAAAGC -s simCow_chr6.simCow.chr6 553269 22 + 602619 ATGCAA--CCTAATAAAGCCTGGG---------------------------- -s simDog_chr6.simDog.chr6 541679 49 + 593897 GTGCAG--CTTAACAAT-GTTGGGCATAGTTTTATAGAAGTGCCTCAGTAGT -s simHuman_chr6.simHuman.chr6 550397 50 + 601863 TCGCAA--CTTAGTGATGGTTGGGCATGATTTTATAGGAGCGCCTTAATAGC -s simRat_chr6.simRat.chr6 54604 49 - 647215 TAACAA--CTTAAAAATATTTGGTCATAACTT-ATAGGAGTGCTCTGAAAGA - -a -s simMouse_chr6.simMouse.chr6 578887 30 + 636262 TATGCAACACAAATTAAGACACTAACTCAG -s Anc0.Anc0refChr3 179978 30 + 222631 TATACAATACAAGTTTAGTCACTAACTCCC -s Anc1.Anc1refChr1 19284 30 + 69767 TATACAATACAAGTTTAGTCACTAACTCCC -s Anc2.Anc2refChr1 95394 30 + 142988 TATACAATACAAGTCTAGTCACTAACTCCC -s mr.mrrefChr3 128794 30 + 181027 TATGCAACACAAATTAAGACACTAACTCAG -s simCow_chr6.simCow.chr6 553295 30 + 602619 GATACAATACAGATAAAGTTGCCAACTCCC -s simDog_chr6.simDog.chr6 541735 30 + 593897 TATACAACACAAGTCTGGTCATTAACTCCC -s simHuman_chr6.simHuman.chr6 550454 30 + 601863 TACTCAATACAAGTTTAGTCACTAACTCCA -s simRat_chr6.simRat.chr6 54653 28 - 647215 TATGCAGCACAAATTAAGAC--TAACTCAG - -a -s simMouse_chr6.simMouse.chr6 578917 13 + 636262 TTTCCCTGTGATC -s Anc0.Anc0refChr3 180010 13 + 222631 TTTCCCTATGCTT -s Anc1.Anc1refChr1 19316 13 + 69767 TTTCCCTATGCTT -s Anc2.Anc2refChr1 95426 13 + 142988 TTTGCCTATGCTT -s mr.mrrefChr3 128824 13 + 181027 TTTCCCTGTGATC -s simCow_chr6.simCow.chr6 553327 13 + 602619 TTTGCTTATGCTT -s simDog_chr6.simDog.chr6 541769 13 + 593897 TTTGCCCATGCTT -s simHuman_chr6.simHuman.chr6 550486 13 + 601863 TTTCCCTATGCCA -s simRat_chr6.simRat.chr6 54681 13 - 647215 TTTGCCTGTGATC - -a -s simMouse_chr6.simMouse.chr6 578930 5 + 636262 ATGGG -s Anc0.Anc0refChr3 180023 5 + 222631 GTTGG -s Anc1.Anc1refChr1 19329 5 + 69767 GTTGG -s Anc2.Anc2refChr1 95439 5 + 142988 GTTAG -s mr.mrrefChr3 128837 5 + 181027 ATGGG -s simCow_chr6.simCow.chr6 553345 5 + 602619 GCTTG -s simDog_chr6.simDog.chr6 541782 5 + 593897 GTTAG -s simHuman_chr6.simHuman.chr6 550499 5 + 601863 GTTGG -s simRat_chr6.simRat.chr6 54694 5 - 647215 ATAGG - -a -s simMouse_chr6.simMouse.chr6 578935 48 + 636262 TGGCTGTTCCCTCTCTCTTACATGAGGCATATGGAATCAGCACAACAC -s Anc0.Anc0refChr3 180028 48 + 222631 TGGCTGTTCCCTCTCTTTTTCATGAGGTATATATAGCCAGCATGAAAC -s Anc1.Anc1refChr1 19334 48 + 69767 TGGCTGTTCCCTCTCTTTTTCATGAGGTATATATAGCCAGCATGAAAC -s Anc2.Anc2refChr1 95444 48 + 142988 TGGCTGTTCCTTCTCTTTTTCATGAGGTATATATAGGTAGCATGAAAC -s mr.mrrefChr3 128842 48 + 181027 TGGCTGTTCCCTCTCTCTTACATGAGGTATATAGAACCAGCATGACAC -s simCow_chr6.simCow.chr6 553350 48 + 602619 TGGCTGTTCATTCTCTTCTTCCTGAGGTATGTATAGTAAGCATGGAAC -s simDog_chr6.simDog.chr6 541793 48 + 593897 TGGCTGATCCTTCTCTTTTTCAGGAGGCATATATAAGTAGCATGAAGT -s simHuman_chr6.simHuman.chr6 550504 48 + 601863 TGGCTGTTCCCTCTCCTTCTCGTAAGGTATATATTGCCAGTATGAAAC -s simRat_chr6.simRat.chr6 54699 48 - 647215 TGACTGTTCCCTCTCTCTTAGATGAGGTATATAGAACCAGCATGACAA - -a -s simMouse_chr6.simMouse.chr6 578983 11 + 636262 CAACCTCCTAT -s Anc0.Anc0refChr3 180078 11 + 222631 CAACCTCCTAT -s Anc1.Anc1refChr1 19384 11 + 69767 CAACCTCCTAT -s Anc2.Anc2refChr1 95494 11 + 142988 CAACCTCCTAT -s mr.mrrefChr3 128890 11 + 181027 CAACCTCCTAT -s simCow_chr6.simCow.chr6 553400 8 + 602619 CAACCTCC--- -s simDog_chr6.simDog.chr6 541843 11 + 593897 TAACCACCTAT -s simHuman_chr6.simHuman.chr6 550554 11 + 601863 CAACCTCCTAT -s simRat_chr6.simRat.chr6 54747 11 - 647215 TAAGCTCCTAT - -a -s simMouse_chr6.simMouse.chr6 578994 1 + 636262 T -s Anc0.Anc0refChr3 180090 1 + 222631 T -s Anc1.Anc1refChr1 19396 1 + 69767 T -s Anc2.Anc2refChr1 95506 1 + 142988 C -s mr.mrrefChr3 128901 1 + 181027 T -s simDog_chr6.simDog.chr6 541855 1 + 593897 C -s simHuman_chr6.simHuman.chr6 550566 1 + 601863 T -s simRat_chr6.simRat.chr6 54758 1 - 647215 T - -a -s simMouse_chr6.simMouse.chr6 578995 71 + 636262 CACAGAATGTCGTTGGTTTAACGTCTCCCATTTGGCAATGAGACCTGGTATTTGATCATTTGTATGCTTGT -s Anc0.Anc0refChr3 180091 44 + 222631 CACAGAA---------------------------TCAATGAGTGCTGATGCTTGATCATTTGCATGTTTGT -s Anc1.Anc1refChr1 19397 44 + 69767 CACAGAA---------------------------TCAATGAGTGCTGATGCTTGATCATTTGCATGTTTGT -s Anc2.Anc2refChr1 95507 44 + 142988 CACAGGA---------------------------TCTATGATTGCTGATGCTCTATCATCTGCATGTTTGT -s mr.mrrefChr3 128902 44 + 181027 CACAGAA---------------------------GCAATGAGACCTGGTATTTGATCATTTGTATGCTTGT -s simCow_chr6.simCow.chr6 553408 36 + 602619 -----------------------------------CGATTCTGTCTGATGCTCTATCATCTGCATGTTTGT -s simDog_chr6.simDog.chr6 541864 44 + 593897 CACAGGA---------------------------TCTATGATTGCTTATGCTCTATCATCTGCATCATTGT -s simHuman_chr6.simHuman.chr6 550567 44 + 601863 CACAAAA---------------------------TCAGTGAGTGATGATGCTTGTTCTTTTGCATGTTTGT -s simRat_chr6.simRat.chr6 54759 39 - 647215 CACAGAA---------------------------ACAATGAGACCTGGTATTTGATCATCTGTATT----- - -a -s simMouse_chr6.simMouse.chr6 579066 5 + 636262 TAGAC -s Anc0.Anc0refChr3 180138 5 + 222631 TAGCT -s Anc1.Anc1refChr1 19444 5 + 69767 TAGCT -s Anc2.Anc2refChr1 95554 5 + 142988 TAGCT -s mr.mrrefChr3 128946 5 + 181027 TAGAC -s simCow_chr6.simCow.chr6 553447 5 + 602619 TAGCT -s simDog_chr6.simDog.chr6 541911 5 + 593897 TAGCA -s simHuman_chr6.simHuman.chr6 550614 5 + 601863 TAGTT - -a -s simMouse_chr6.simMouse.chr6 579071 2 + 636262 AA -s Anc0.Anc0refChr3 180143 2 + 222631 AA -s Anc1.Anc1refChr1 19449 2 + 69767 AA -s Anc2.Anc2refChr1 95559 2 + 142988 AA -s mr.mrrefChr3 128951 2 + 181027 AA -s simCow_chr6.simCow.chr6 553452 2 + 602619 AG -s simDog_chr6.simDog.chr6 541989 2 + 593897 AA -s simHuman_chr6.simHuman.chr6 550619 2 + 601863 AA - -a -s simMouse_chr6.simMouse.chr6 579073 8 + 636262 CTTTGGTT -s Anc0.Anc0refChr3 180148 8 + 222631 CTTTGGTT -s Anc1.Anc1refChr1 19454 8 + 69767 CTTTGGTT -s Anc2.Anc2refChr1 95564 8 + 142988 TTTTGGTG -s mr.mrrefChr3 128953 8 + 181027 CTTTGGTT -s simCow_chr6.simCow.chr6 553457 8 + 602619 TTTTGGTT -s simDog_chr6.simDog.chr6 541994 8 + 593897 TTTTGGTG -s simHuman_chr6.simHuman.chr6 550624 8 + 601863 CTTTGGTT - -a -s simMouse_chr6.simMouse.chr6 579081 8 + 636262 TCCAGAGG -s Anc0.Anc0refChr3 180157 8 + 222631 TCCAGGGG -s Anc1.Anc1refChr1 19463 8 + 69767 TCCAGGGG -s Anc2.Anc2refChr1 95573 8 + 142988 CTCTGGAA -s mr.mrrefChr3 128961 8 + 181027 TCCAGAGG -s simCow_chr6.simCow.chr6 553466 5 + 602619 TACTG--- -s simDog_chr6.simDog.chr6 542003 8 + 593897 CTCTGGAA -s simHuman_chr6.simHuman.chr6 550633 8 + 601863 TCCAGCGG - -a -s simMouse_chr6.simMouse.chr6 579089 60 + 636262 TGCTACTATAGGCGTTAAGTGTCAATTCACTGTGGGGTGAGCCTTCTGTAAGAGGTATGT -s Anc0.Anc0refChr3 180165 58 + 222631 TGATACAATAGGCTTAAAGAGCAAATTCACTGTATA-TGAGC-TTATACACAAGGTGCGT -s Anc1.Anc1refChr1 19471 59 + 69767 TGATACAATAGGCTTAAAGAGCAAATTCACTGTATAGTGAGC-TTATACACAAGGTGCGT -s Anc2.Anc2refChr1 95581 58 + 142988 TGATACAATAGGCTTAAAGAGCAAATTCACTGTATA-TGAGC-TTACACACAAGGTGCAT -s mr.mrrefChr3 128969 59 + 181027 TGCTACTATAGGCGTTAAGTGTCAATTCACTGTGGGGTGAGC-TTCTGTAAGAGGTATGT -s simCow_chr6.simCow.chr6 553471 50 + 602619 -------ATTGTATCAAAGAGCAAGTTCACTGTATA--GAGC-TTACACACAAAGTGCAT -s simDog_chr6.simDog.chr6 542011 49 + 593897 TGATACAAAAGGCTTAAAAAGTAAATT----------TGAGC-TTACACACAAGGTGCAC -s simHuman_chr6.simHuman.chr6 550690 59 + 601863 TGATACAATAGGCTTAAAGAGCAAATTCACCGTATAGTGAGT-TTATACACAAGGCCCGT - -a -s simMouse_chr6.simMouse.chr6 579149 18 + 636262 TGTTCAGAATGTAGTATG -s Anc0.Anc0refChr3 180228 18 + 222631 TCTTCAGAGTGTATTGTG -s Anc1.Anc1refChr1 19535 18 + 69767 TCTTCAGAGTGTATTGTG -s Anc2.Anc2refChr1 95644 18 + 142988 TCCTGATGGTGTATTGTG -s mr.mrrefChr3 129028 18 + 181027 TGTTCAGAATGTAGTATG -s simCow_chr6.simCow.chr6 553526 15 + 602619 TCCTT---GTTTGTTGTG -s simDog_chr6.simDog.chr6 542064 18 + 593897 TCCTGATGGTGTATTGTG -s simHuman_chr6.simHuman.chr6 550754 18 + 601863 TCTTCAGAGTATATTGTG - -a -s simMouse_chr6.simMouse.chr6 579167 17 + 636262 GATCCTTGGCGGTGTAA -s Anc0.Anc0refChr3 180249 15 + 222631 GATCTCACGTGGGGC-- -s Anc1.Anc1refChr1 19556 15 + 69767 GATCTCACGTGGGGC-- -s Anc2.Anc2refChr1 95665 15 + 142988 GCTATCACATGGGGC-- -s mr.mrrefChr3 129046 17 + 181027 GATCCTTGGCGGTGTAA -s simCow_chr6.simCow.chr6 553544 15 + 602619 CGAATCACATGGGAC-- -s simDog_chr6.simDog.chr6 542085 15 + 593897 GCTATCACATCAGGC-- -s simHuman_chr6.simHuman.chr6 550775 15 + 601863 GATCTCATGAGGGGC-- -s simRat_chr6.simRat.chr6 54798 15 - 647215 --TCCTTGGTGGTATAT - -a -s simMouse_chr6.simMouse.chr6 579184 4 + 636262 ATCA -s Anc0.Anc0refChr3 180264 4 + 222631 TTGG -s Anc1.Anc1refChr1 19571 4 + 69767 TTGG -s Anc2.Anc2refChr1 95680 4 + 142988 TTGG -s mr.mrrefChr3 129063 4 + 181027 ATCA -s simCow_chr6.simCow.chr6 553560 4 + 602619 TTGG -s simDog_chr6.simDog.chr6 542100 4 + 593897 TTGG -s simHuman_chr6.simHuman.chr6 550790 4 + 601863 TTTG -s simRat_chr6.simRat.chr6 54813 4 - 647215 GTCA - -a -s simMouse_chr6.simMouse.chr6 579188 67 + 636262 CCTGGGGGCTCATTCTCATGGTGACTCATCTGGATGCATTATATAGGCTCCCACACTAGATGCCTCA -s Anc0.Anc0refChr3 180268 67 + 222631 ACATGGGGCCCAGTATCTGAACTACTCAACTGAATGCAATATATAGGTTACCATAACAGACCCCTCA -s Anc1.Anc1refChr1 19575 67 + 69767 ACATGGGGCCCAGTATCTGAACTACTCAACTGAATGCAATATATAGGTTACCATAACAGACCCCTCA -s Anc2.Anc2refChr1 95695 67 + 142988 ACATGGGGCCTAGCATCTGAACTACTCAACTGAATGCAATATATGGGTTACCATAACAGACCCCTCA -s mr.mrrefChr3 129067 67 + 181027 CCTGGGGGCTCATTCTCATGGTGACTCAACTGGATGCAATATATAGGCTCCCATAATAGATCCCTCA -s simCow_chr6.simCow.chr6 553575 67 + 602619 ATGTGGCACATAGCATCTAAACAATTCAACTGGATGCAATATATGGGTTACAACAGCAAATCCCTCA -s simDog_chr6.simDog.chr6 542115 67 + 593897 ACATAAGGCCTAGCATGTGAACTACTCGACAGAATGGAATATATGCGCTACCATAACAGACTCCTCT -s simHuman_chr6.simHuman.chr6 550794 67 + 601863 GCATGGGGCCCAGTAACCCATCCACTGAACTGAATGCAATATATAGGTTACCATAACGTGGCCCTCA -s simRat_chr6.simRat.chr6 54817 67 - 647215 CATGTGGGCTCATTCTCATGGTGAGTCAACCGGATCCAATGTATAGGCTCCTATAATAAATCCCTCA - -a -s simMouse_chr6.simMouse.chr6 579255 33 + 636262 ACAGATTGGATTGGTCCAAGCAACCTATCTGGT -s Anc0.Anc0refChr3 180339 33 + 222631 ACAGAATGAATTGGGCCAAGCAGGCTCTCTGGT -s Anc1.Anc1refChr1 19646 33 + 69767 ACAGAATGAATTGGGCCAAGCAGGCTCTCTGGT -s Anc2.Anc2refChr1 95766 33 + 142988 ACAGAATGAATTGGGCCAAGCAGGCTCTCTAGT -s mr.mrrefChr3 129138 33 + 181027 ACAGATTGGATTGGTCCAAGCAACCTCTCTGGT -s simCow_chr6.simCow.chr6 553645 33 + 602619 ACGGATTGAATTGGGCCAAGCTGGCTCTCTAGT -s simDog_chr6.simDog.chr6 542186 32 + 593897 ACAGAATGAATT-TGCCAAGCAGCCTCTCTAGT -s simHuman_chr6.simHuman.chr6 550865 33 + 601863 GCACACTGAATTGGGCCAACTAGGCTCTCTGGT -s simRat_chr6.simRat.chr6 54888 32 - 647215 ACAGATTGGATTGGTCCAAGCAAC-TCTCTGGT - -a -s simMouse_chr6.simMouse.chr6 579288 3 + 636262 ATC -s Anc0.Anc0refChr3 180372 3 + 222631 GTC -s Anc1.Anc1refChr1 19679 3 + 69767 GTC -s Anc2.Anc2refChr1 95799 3 + 142988 GTC -s mr.mrrefChr3 129171 3 + 181027 ATC -s simCow_chr6.simCow.chr6 553685 3 + 602619 GTC -s simDog_chr6.simDog.chr6 542218 3 + 593897 GTC -s simHuman_chr6.simHuman.chr6 550898 3 + 601863 GTC -s simRat_chr6.simRat.chr6 54920 3 - 647215 ACC - -a -s simMouse_chr6.simMouse.chr6 579291 8 + 636262 TATAAGGT -s Anc0.Anc0refChr3 180375 8 + 222631 CATAAGGT -s Anc1.Anc1refChr1 19682 8 + 69767 CATAAGGT -s Anc2.Anc2refChr1 95802 8 + 142988 CATAAGGT -s mr.mrrefChr3 129174 8 + 181027 CATAAGGT -s simCow_chr6.simCow.chr6 553688 8 + 602619 CATAAGGT -s simDog_chr6.simDog.chr6 542223 7 + 593897 TGTAAGG- -s simHuman_chr6.simHuman.chr6 550901 8 + 601863 CACAAGGT -s simRat_chr6.simRat.chr6 54923 7 - 647215 CATAAGG- - -a -s simMouse_chr6.simMouse.chr6 579299 84 + 636262 AACTGTACTAGCGGCTCGAAACCCTGCAAGCTGTCTATGGCCCAGTTTATGCAATGTTTCAGCCATCGTCACTTAGCATTTTCA -s Anc0.Anc0refChr3 180383 53 + 222631 CA-------------------------------TCCATGGCATAAACTACTCTATGGTTGAGCTTTCCTCACTTAGTATTATCA -s Anc1.Anc1refChr1 19690 53 + 69767 CA-------------------------------TCCATGGCATAAACTACTCTATGGTTGAGCTTTCCTCACTTAGTATTATCA -s Anc2.Anc2refChr1 95810 53 + 142988 CG-------------------------------TCCATGGAATAAACTACTCTAGTGTTGACCTTTTCTCACTTAGTAATATCA -s mr.mrrefChr3 129182 53 + 181027 AA-------------------------------TCTATGGCCCAGTTTATGCAATGTTTCAGCCATCGTCACTTAGCATTTTCA -s simCow_chr6.simCow.chr6 553727 53 + 602619 CG-------------------------------TCCATGGAATGATTTACTCTACACTTGACCTTTGGTCACTTATCGAAGTCA -s simDog_chr6.simDog.chr6 542230 38 + 593897 -------------------------------------------AGACTTCACTAGTGTC---CTTTTCCCACTTAGTAATAACA -s simHuman_chr6.simHuman.chr6 550909 53 + 601863 CA-------------------------------TCCATGGCATAACCTACTCTATGGTTTAGCTTTCATAACATAGTATTATCA - -a -s simMouse_chr6.simMouse.chr6 579383 22 + 636262 TTCAAAACCATGTGTTAAATCA -s Anc0.Anc0refChr3 180442 15 + 222631 TTCAAAACCATGTGA------- -s Anc1.Anc1refChr1 19749 22 + 69767 TTCAAAACCATGTGATAACTTA -s Anc2.Anc2refChr1 95869 15 + 142988 ATCCAAAGAATGTGA------- -s mr.mrrefChr3 129235 22 + 181027 TTCAAAACCATGTGTTAAATCA -s simCow_chr6.simCow.chr6 553786 14 + 602619 AC-CAGAAAATGTGG------- -s simDog_chr6.simDog.chr6 542274 15 + 593897 ATCCAAAGAATGTGA------- -s simHuman_chr6.simHuman.chr6 550968 22 + 601863 TTCAGAACCATTTGATAACTTA - -a -s simMouse_chr6.simMouse.chr6 579405 36 + 636262 GCTTACTAAGCTGTTATGCAAAGATACTAACATTCA -s Anc0.Anc0refChr3 180459 33 + 222631 GCTGATAATATCCCTACACAAAGATAATG---TCCC -s Anc1.Anc1refChr1 19774 33 + 69767 GCTGATAATATCCCTACACAAAGATAATG---TCCC -s Anc2.Anc2refChr1 95886 33 + 142988 CCTGATAATATCCCTACACAAAGACAGTG---TCCC -s mr.mrrefChr3 129257 36 + 181027 GCTTACTAAGCTGTTATGCAAAGATAATAACATTCA -s simCow_chr6.simCow.chr6 553803 33 + 602619 ACTGTGGATCCTCCTACACAAAGACAGTG---CCCC -s simDog_chr6.simDog.chr6 542291 17 + 593897 CCTGATAATATCC-------------------TCCC -s simHuman_chr6.simHuman.chr6 550993 33 + 601863 GCTGATAATAAACCCCCACAAAGATCATG---TCCC -s simRat_chr6.simRat.chr6 54930 26 - 647215 ----------CTGTTATGCAAGGATAATAACCCTCA - -a -s simMouse_chr6.simMouse.chr6 579441 4 + 636262 ATAA -s Anc0.Anc0refChr3 180492 4 + 222631 TGAT -s Anc1.Anc1refChr1 19807 4 + 69767 TGAT -s Anc2.Anc2refChr1 95919 4 + 142988 TGAT -s mr.mrrefChr3 129293 4 + 181027 ATAA -s simCow_chr6.simCow.chr6 553837 4 + 602619 TGAC -s simDog_chr6.simDog.chr6 542308 4 + 593897 TGAT -s simHuman_chr6.simHuman.chr6 551026 4 + 601863 TGAT -s simRat_chr6.simRat.chr6 54956 4 - 647215 ATTC - -a -s simMouse_chr6.simMouse.chr6 579445 1 + 636262 G -s Anc0.Anc0refChr3 180496 1 + 222631 G -s Anc1.Anc1refChr1 19811 1 + 69767 G -s Anc2.Anc2refChr1 95925 1 + 142988 G -s mr.mrrefChr3 129297 1 + 181027 G -s simCow_chr6.simCow.chr6 553843 1 + 602619 G -s simDog_chr6.simDog.chr6 542314 1 + 593897 G -s simHuman_chr6.simHuman.chr6 551030 1 + 601863 G -s simRat_chr6.simRat.chr6 54960 1 - 647215 G - -a -s simMouse_chr6.simMouse.chr6 579446 10 + 636262 TGGGTCATAA -s Anc0.Anc0refChr3 180497 10 + 222631 TGGTTTTTAG -s Anc1.Anc1refChr1 19812 10 + 69767 TGGTTTTTAG -s Anc2.Anc2refChr1 95926 10 + 142988 TGGTTTTTAG -s mr.mrrefChr3 129298 10 + 181027 TGGGTCTTAA -s simCow_chr6.simCow.chr6 553845 10 + 602619 TGGTTTTTTA -s simDog_chr6.simDog.chr6 542315 10 + 593897 TAAGCCTTAG -s simHuman_chr6.simHuman.chr6 551031 10 + 601863 TGGTTTTTCG -s simRat_chr6.simRat.chr6 54961 10 - 647215 TGGGTCTTAA - -a -s simMouse_chr6.simMouse.chr6 579456 19 + 636262 ATTATAATCTCATGTTCCC -s Anc0.Anc0refChr3 180507 19 + 222631 ATTTTACTCTCATGTCCCC -s Anc1.Anc1refChr1 19822 19 + 69767 ATTTTACTCTCATGTCCCC -s Anc2.Anc2refChr1 95936 19 + 142988 ATTTTACTCTCATGTCCCC -s mr.mrrefChr3 129308 19 + 181027 ATTATAATCTCATGTTCCC -s simCow_chr6.simCow.chr6 553861 19 + 602619 ATTTTACTTGCATGATCCC -s simDog_chr6.simDog.chr6 542325 19 + 593897 ACTTTATTCTCATGTCCCC -s simHuman_chr6.simHuman.chr6 551041 19 + 601863 ATTTAACTCTCATGTGCTC -s simRat_chr6.simRat.chr6 54971 19 - 647215 ATTATAATCTCATGTTCCC - -a -s simMouse_chr6.simMouse.chr6 579475 6 + 636262 CCAACT -s Anc0.Anc0refChr3 180532 4 + 222631 C--GCC -s Anc1.Anc1refChr1 19847 6 + 69767 CAAGCC -s Anc2.Anc2refChr1 95961 4 + 142988 C--GCT -s mr.mrrefChr3 129327 6 + 181027 CAAACC -s simCow_chr6.simCow.chr6 553886 4 + 602619 C--GCT -s simDog_chr6.simDog.chr6 542348 1 + 593897 -----T -s simHuman_chr6.simHuman.chr6 551066 6 + 601863 CAATTC -s simRat_chr6.simRat.chr6 54990 6 - 647215 CAAACC - -a -s simMouse_chr6.simMouse.chr6 579481 6 + 636262 ACAACA -s Anc0.Anc0refChr3 180536 6 + 222631 ACAACA -s Anc1.Anc1refChr1 19853 6 + 69767 ACAACA -s Anc2.Anc2refChr1 95965 6 + 142988 ACAACA -s mr.mrrefChr3 129333 6 + 181027 ACAACA -s simCow_chr6.simCow.chr6 553890 6 + 602619 ACAACA -s simDog_chr6.simDog.chr6 542349 6 + 593897 ACAACA -s simHuman_chr6.simHuman.chr6 551095 6 + 601863 ACAAAC -s simRat_chr6.simRat.chr6 54996 6 - 647215 ACAACA - -a -s simMouse_chr6.simMouse.chr6 579487 15 + 636262 TTCTTAGTCAGCCAT -s Anc0.Anc0refChr3 180542 15 + 222631 GTCTAAGCCAGACAC -s Anc1.Anc1refChr1 19859 15 + 69767 GTCTAAGCCAGACAC -s Anc2.Anc2refChr1 95971 15 + 142988 GTCTAAGCCAGACAC -s mr.mrrefChr3 129339 15 + 181027 TTCTTAGCCAGCCAT -s simCow_chr6.simCow.chr6 553896 15 + 602619 GTCTAAGCCAGGCAC -s simDog_chr6.simDog.chr6 542355 15 + 593897 GTCTAAGCCAGACAC -s simHuman_chr6.simHuman.chr6 551101 15 + 601863 CTCTAAGCCAGACAC -s simRat_chr6.simRat.chr6 55006 15 - 647215 TTCCTATCCAGCCAT - -a -s simMouse_chr6.simMouse.chr6 579502 12 + 636262 TGGTAACGATTT -s Anc0.Anc0refChr3 180557 12 + 222631 TGGTGATGATTC -s Anc1.Anc1refChr1 19874 12 + 69767 TGGTGATGATTC -s Anc2.Anc2refChr1 95986 12 + 142988 TGGTGATGATTC -s mr.mrrefChr3 129354 12 + 181027 TGGTAACGATTT -s simCow_chr6.simCow.chr6 553912 12 + 602619 TGGTAATGATTC -s simDog_chr6.simDog.chr6 542370 11 + 593897 TGTTGATGATT- -s simHuman_chr6.simHuman.chr6 551116 12 + 601863 TAGTGATGATTC -s simRat_chr6.simRat.chr6 55021 12 - 647215 TGGTAACGATCT - -a -s simMouse_chr6.simMouse.chr6 579514 16 + 636262 AGCAATACACTTCAAG -s Anc0.Anc0refChr3 180574 16 + 222631 TGTAAGACACTGGTGG -s Anc1.Anc1refChr1 19891 16 + 69767 TGTAAGACACTGGTGG -s Anc2.Anc2refChr1 96003 16 + 142988 TGTAAGGCACTGGTGG -s mr.mrrefChr3 129366 16 + 181027 AGCAATACACTTCAAG -s simCow_chr6.simCow.chr6 553929 16 + 602619 TGTAAGGCACTGGTGG -s simDog_chr6.simDog.chr6 542381 1 + 593897 ---------------G -s simHuman_chr6.simHuman.chr6 551133 16 + 601863 GGAAAGACACTGGTGG -s simRat_chr6.simRat.chr6 55033 16 - 647215 ATCAATAAACTTCAAA - -a -s simMouse_chr6.simMouse.chr6 579530 44 + 636262 GATTATAAAATAGGGGTGTTTTATAAGACAGATGCATGGTAACA -s Anc0.Anc0refChr3 180619 44 + 222631 GAGGGTAAAGTAGGAGTGTTTTATATGGCCAATGCATGGTGTTA -s Anc1.Anc1refChr1 19936 44 + 69767 GAGGGTAAAGTAGGAGTGTTTTATATGGCCAATGCATGGTGTTA -s Anc2.Anc2refChr1 96048 44 + 142988 GAGGGTAAAGTAGGAGTGCTTTATCTGGCCAATGCATGGTGTTG -s mr.mrrefChr3 129382 44 + 181027 GATTATAAAATAGGGGTGTTTTATAAGACAGATGCATGGTAACA -s simCow_chr6.simCow.chr6 553974 44 + 602619 GAGGGTAAAGAAGGAGTCCTTTATGTATCCAATACATGGCGTTG -s simDog_chr6.simDog.chr6 542412 44 + 593897 GAAAGTGACATAGGAGTGCTTTATCTGGCCAATGTATGGTGTTG -s simHuman_chr6.simHuman.chr6 551178 44 + 601863 GAGGGTAAAGTAGGAGTATTTTATATGGCTCTAGCATGGAGGTA -s simRat_chr6.simRat.chr6 55049 44 - 647215 GATTTCAAAATAGGGGTGTTTTATAAGACCGACGCATGGTAACA - -a -s simMouse_chr6.simMouse.chr6 579574 7 + 636262 TTTCAGC -s Anc0.Anc0refChr3 180663 7 + 222631 TTTCTGC -s Anc1.Anc1refChr1 19980 7 + 69767 TTTCTGC -s Anc2.Anc2refChr1 96092 7 + 142988 TTTATGC -s mr.mrrefChr3 129426 7 + 181027 TTTCAGC -s simCow_chr6.simCow.chr6 554021 7 + 602619 TGTGACC -s simDog_chr6.simDog.chr6 542456 7 + 593897 TTCATGC -s simHuman_chr6.simHuman.chr6 551222 7 + 601863 TTTCTGC -s simRat_chr6.simRat.chr6 55093 7 - 647215 GTTCAGC - -a -s simMouse_chr6.simMouse.chr6 579581 9 + 636262 TTTACAATG -s Anc0.Anc0refChr3 180670 7 + 222631 TTTAC--TT -s Anc1.Anc1refChr1 19987 9 + 69767 TTTACCGTT -s Anc2.Anc2refChr1 96099 7 + 142988 CCTAC--TT -s mr.mrrefChr3 129433 9 + 181027 TTTACAGTG -s simCow_chr6.simCow.chr6 554028 7 + 602619 CCTAC--AT -s simDog_chr6.simDog.chr6 287336 7 - 593897 gctga--gt -s simDog_chr6.simDog.chr6 542463 7 + 593897 CTCAT--TT -s simHuman_chr6.simHuman.chr6 551229 9 + 601863 TTTACCGTT -s simRat_chr6.simRat.chr6 55100 9 - 647215 TTTACAGTG - -a -s simMouse_chr6.simMouse.chr6 579590 13 + 636262 GTTGGAGTGACGG -s Anc0.Anc0refChr3 180677 13 + 222631 GTTGTAATGTCAG -s Anc1.Anc1refChr1 19996 13 + 69767 GTTGTAATGTCAG -s Anc2.Anc2refChr1 96106 13 + 142988 GTTGTAATATCAG -s mr.mrrefChr3 129442 13 + 181027 GTTGGAGTGACAG -s simCow_chr6.simCow.chr6 554037 13 + 602619 GCTGAAAAGTCAG -s simDog_chr6.simDog.chr6 287343 13 - 593897 ggtgcagtatcag -s simDog_chr6.simDog.chr6 542470 9 + 593897 GTTGTAATA---- -s simHuman_chr6.simHuman.chr6 551238 6 + 601863 G-------GCCAG -s simRat_chr6.simRat.chr6 55109 13 - 647215 GTTGAAGTGACAG - -a -s simMouse_chr6.simMouse.chr6 579603 28 + 636262 TTCTTCCCATCTTCTCCATGTTGACTAC -s Anc0.Anc0refChr3 180690 25 + 222631 TTA---CTATCTAATGCATGTTGATCAC -s Anc1.Anc1refChr1 20009 25 + 69767 TTA---CTATCTAATGCATGTTGATCAC -s Anc2.Anc2refChr1 96119 25 + 142988 CTA---CTATCTAATGCACACTGATCAT -s mr.mrrefChr3 129455 25 + 181027 TTC---CCATCTTCTGCATGTTGACTAC -s simCow_chr6.simCow.chr6 554050 25 + 602619 TTA---ATGTCTATTGCATGTTGATCAT -s simDog_chr6.simDog.chr6 287389 25 - 593897 CTA---CTATCTAATGCACACCGACCTC -s simDog_chr6.simDog.chr6 542479 25 + 593897 CTA---CCATCTAATACACACTGATCAT -s simHuman_chr6.simHuman.chr6 551244 25 + 601863 TCA---CTGGGTAGTGCATGTCAATCTC -s simRat_chr6.simRat.chr6 55122 25 - 647215 TTC---CCATATTCTGCATGTTGACTAC - -a -s simMouse_chr6.simMouse.chr6 579631 4 + 636262 TCCT -s Anc0.Anc0refChr3 180715 4 + 222631 TCCC -s Anc1.Anc1refChr1 20034 4 + 69767 TCCC -s Anc2.Anc2refChr1 96144 4 + 142988 TCTC -s mr.mrrefChr3 129480 4 + 181027 TCCC -s simCow_chr6.simCow.chr6 554075 4 + 602619 TTTC -s simDog_chr6.simDog.chr6 542504 4 + 593897 TCTC -s simHuman_chr6.simHuman.chr6 551269 4 + 601863 TCCC -s simRat_chr6.simRat.chr6 55147 4 - 647215 TCCC - -a -s simMouse_chr6.simMouse.chr6 579635 17 + 636262 ATACCAGGGAGTCCAGG -s Anc0.Anc0refChr3 180719 17 + 222631 ATACTAGATAGTCCAGG -s Anc1.Anc1refChr1 20038 17 + 69767 ATACTAGATAGTCCAGG -s Anc2.Anc2refChr1 96148 17 + 142988 ATACTAGATAGTCCAGG -s mr.mrrefChr3 129484 17 + 181027 ATACTAGAGAGTCCAGG -s simCow_chr6.simCow.chr6 554079 17 + 602619 CTACAAGATAGTCCAGG -s simDog_chr6.simDog.chr6 287414 17 - 593897 ATAGTAGATAGGCCAGG -s simDog_chr6.simDog.chr6 542508 17 + 593897 ATACTAGATAGTCCAGG -s simHuman_chr6.simHuman.chr6 551273 17 + 601863 ATACTATAAACTGCAGG -s simRat_chr6.simRat.chr6 55151 17 - 647215 ATATTAGAGAGTCCAGG - -a -s simMouse_chr6.simMouse.chr6 579652 3 + 636262 GGA -s Anc0.Anc0refChr3 180736 3 + 222631 GGA -s Anc1.Anc1refChr1 20055 3 + 69767 GGA -s Anc2.Anc2refChr1 96165 3 + 142988 GGA -s mr.mrrefChr3 129501 3 + 181027 GGA -s simCow_chr6.simCow.chr6 554096 2 + 602619 G-A -s simDog_chr6.simDog.chr6 287431 3 - 593897 GGA -s simDog_chr6.simDog.chr6 542531 3 + 593897 AGA -s simHuman_chr6.simHuman.chr6 551290 3 + 601863 GTA -s simRat_chr6.simRat.chr6 55168 3 - 647215 CAA - -a -s simMouse_chr6.simMouse.chr6 579655 7 + 636262 GTTGATG -s Anc0.Anc0refChr3 180739 7 + 222631 GAAGCTG -s Anc1.Anc1refChr1 20058 7 + 69767 GAAGCTG -s Anc2.Anc2refChr1 96181 7 + 142988 GAAGCTG -s mr.mrrefChr3 129504 7 + 181027 GATGATG -s simCow_chr6.simCow.chr6 554111 7 + 602619 GAAGCTG -s simDog_chr6.simDog.chr6 287447 7 - 593897 GAAGCCG -s simDog_chr6.simDog.chr6 542558 7 + 593897 GAAGCTG -s simHuman_chr6.simHuman.chr6 551293 7 + 601863 GAAGCTG -s simRat_chr6.simRat.chr6 55171 7 - 647215 GATGGTG - -a -s simMouse_chr6.simMouse.chr6 579662 22 + 636262 CCAGAGTGGCTAGAATTGTGGA -s Anc0.Anc0refChr3 180754 22 + 222631 ACAGAGTGGCTTGAATTGCTGG -s Anc1.Anc1refChr1 20073 22 + 69767 ACAGAGTGGCTTGAATTGCTGG -s Anc2.Anc2refChr1 96196 22 + 142988 ACAGAGTGGTTTGAATCACTGG -s mr.mrrefChr3 129511 22 + 181027 ACAGAGTGGCTAGAATTGTGGG -s simCow_chr6.simCow.chr6 554126 22 + 602619 ACGGAGTGGATTAAATCACTGG -s simDog_chr6.simDog.chr6 287462 22 - 593897 AAAGATTGGTTTGACTCACTGG -s simDog_chr6.simDog.chr6 542573 22 + 593897 ACAGAGTGGTTTGAATCACTGG -s simHuman_chr6.simHuman.chr6 551308 22 + 601863 ACAGAGTGGCTCGAATTGCTGG -s simRat_chr6.simRat.chr6 55178 22 - 647215 ACAGGGAGGATAGCATTGTAGG - -a -s simMouse_chr6.simMouse.chr6 579684 2 + 636262 GT -s Anc0.Anc0refChr3 180783 1 + 222631 G- -s Anc1.Anc1refChr1 20102 1 + 69767 G- -s Anc2.Anc2refChr1 96225 1 + 142988 G- -s mr.mrrefChr3 129533 1 + 181027 G- -s simCow_chr6.simCow.chr6 554155 1 + 602619 A- -s simDog_chr6.simDog.chr6 287491 1 - 593897 G- -s simDog_chr6.simDog.chr6 542602 1 + 593897 G- -s simHuman_chr6.simHuman.chr6 551337 1 + 601863 G- -s simRat_chr6.simRat.chr6 55200 1 - 647215 G- - -a -s simMouse_chr6.simMouse.chr6 579686 2 + 636262 CA -s Anc0.Anc0refChr3 180784 2 + 222631 CA -s Anc1.Anc1refChr1 20103 2 + 69767 CA -s Anc2.Anc2refChr1 96226 2 + 142988 CA -s mr.mrrefChr3 129534 2 + 181027 CA -s simCow_chr6.simCow.chr6 554156 2 + 602619 CC -s simDog_chr6.simDog.chr6 542603 2 + 593897 CA -s simHuman_chr6.simHuman.chr6 551338 2 + 601863 TA -s simRat_chr6.simRat.chr6 55201 2 - 647215 CA - -a -s simMouse_chr6.simMouse.chr6 579688 17 + 636262 CTATGGGTTGTTTTCAA -s Anc0.Anc0refChr3 180786 16 + 222631 CTATGGGAT-TTTTCGT -s Anc1.Anc1refChr1 20105 17 + 69767 CTATGGGATGTTTTCGT -s Anc2.Anc2refChr1 96228 16 + 142988 CTATGGGAT-TTTTTGT -s mr.mrrefChr3 129536 17 + 181027 CTATGGGTTGTTTTCGA -s simCow_chr6.simCow.chr6 554158 16 + 602619 TCTTGGGAT-TCCTTAT -s simDog_chr6.simDog.chr6 287492 16 - 593897 CTATGGGAT-TTTTCGT -s simDog_chr6.simDog.chr6 542605 16 + 593897 CTATGGGAT-TTTTTGT -s simHuman_chr6.simHuman.chr6 551340 17 + 601863 CTATGGGATGTTTTCGG -s simRat_chr6.simRat.chr6 55203 17 - 647215 CTATGGGTCGTTTTTGA - -a -s simMouse_chr6.simMouse.chr6 579705 5 + 636262 GCCAT -s Anc0.Anc0refChr3 180810 5 + 222631 GCTAT -s Anc1.Anc1refChr1 20130 5 + 69767 GCTAT -s Anc2.Anc2refChr1 96252 5 + 142988 GCTAT -s mr.mrrefChr3 129553 5 + 181027 GCCAT -s simCow_chr6.simCow.chr6 554182 3 + 602619 GT--G -s simDog_chr6.simDog.chr6 287516 5 - 593897 GCTAT -s simDog_chr6.simDog.chr6 542629 5 + 593897 GCTAT -s simHuman_chr6.simHuman.chr6 551365 5 + 601863 GCTAT -s simRat_chr6.simRat.chr6 55220 5 - 647215 GCAAT - -a -s simMouse_chr6.simMouse.chr6 579710 21 + 636262 AGTATTTTGTTTTTATAAGTT -s Anc0.Anc0refChr3 180815 21 + 222631 CGTACTTTGTCTTCATACGTT -s Anc1.Anc1refChr1 20135 21 + 69767 CGTACTTTGTCTTCATACGTT -s Anc2.Anc2refChr1 96259 21 + 142988 CATGATTTGTCTTCATACATT -s mr.mrrefChr3 129558 21 + 181027 AGTACTTTGTCTTTATAAGTT -s simCow_chr6.simCow.chr6 554187 21 + 602619 CACATTTCATCTATACACCTT -s simDog_chr6.simDog.chr6 287523 21 - 593897 CATGATTTGTCTTCATACATT -s simDog_chr6.simDog.chr6 542636 21 + 593897 CGTGATTTGTCATCATACATT -s simHuman_chr6.simHuman.chr6 551370 21 + 601863 TGTACTTTGTCTTCACACGGC -s simRat_chr6.simRat.chr6 55225 21 - 647215 AGCACTTTGTCTTAATAACTT - -a -s simMouse_chr6.simMouse.chr6 579731 17 + 636262 TTTTGGTGTAAACAAAA -s Anc0.Anc0refChr3 180836 17 + 222631 TTTTGGTATAAGCTAGA -s Anc1.Anc1refChr1 20156 17 + 69767 TTTTGGTATAAGCTAGA -s Anc2.Anc2refChr1 96280 17 + 142988 TTTTGGCAAAAGCTAGA -s mr.mrrefChr3 129579 17 + 181027 TTTTGGTGTAAACAAGA -s simCow_chr6.simCow.chr6 554217 16 + 602619 TTT-GACAGCATCTAGG -s simDog_chr6.simDog.chr6 287544 17 - 593897 TTTTGGCAAAAGCTAGA -s simDog_chr6.simDog.chr6 542657 16 + 593897 TTT-GGTGAGAGCCAGA -s simHuman_chr6.simHuman.chr6 551391 17 + 601863 TTTCGGTATAAGCTAGA -s simRat_chr6.simRat.chr6 55246 17 - 647215 TTTTGGTGTAAACCAGA - -a -s simMouse_chr6.simMouse.chr6 579748 36 + 636262 GAGTGTCAGACTGTGGGTACAGCGGAAAACATGGTG -s Anc0.Anc0refChr3 180853 35 + 222631 GAGTAC-AGATAATGGGTACAGAGTAAGAGATAGTG -s Anc1.Anc1refChr1 20173 36 + 69767 GAGTACCAGATAATGGGTACAGAGTAAGAGATAGTG -s Anc2.Anc2refChr1 96297 35 + 142988 TAGTAG-GGATAAAATGTACCGAATGAGAGATAATG -s mr.mrrefChr3 129596 36 + 181027 GAGTGTCAGATTGTGGGTACAGCGTAAAAGATAGTG -s simDog_chr6.simDog.chr6 542673 35 + 593897 TAGTAG-GGATAAAATGTACCGAATGAGAGATAATG -s simHuman_chr6.simHuman.chr6 551408 36 + 601863 GAGTACCAGATAATGGGTACAGAGTAAGGGATAGTG -s simRat_chr6.simRat.chr6 55263 36 - 647215 GAGTGTCCAATTGTGGGTACAGGGTAAAAGATAGTG - -a -s simMouse_chr6.simMouse.chr6 579784 30 + 636262 CCCTGCTGGTTTATACTTGATGATAGAGCA -s Anc0.Anc0refChr3 180892 7 + 222631 CCCTACT----------------------- -s Anc1.Anc1refChr1 20213 7 + 69767 CCCTACT----------------------- -s Anc2.Anc2refChr1 96336 7 + 142988 CCTTAAT----------------------- -s mr.mrrefChr3 129632 30 + 181027 CCCTGCTGGTTTATACTTGATGATAGAGCA -s simDog_chr6.simDog.chr6 542712 7 + 593897 CCTTAAT----------------------- -s simHuman_chr6.simHuman.chr6 551448 7 + 601863 CCCTACT----------------------- -s simRat_chr6.simRat.chr6 55299 26 - 647215 CC----TGGTTTATACTTGATGCCCACCCA - -a -s simMouse_chr6.simMouse.chr6 579814 36 + 636262 CCCTTTTATATCTAATCCTGTATTACTTCAGCCTGA -s Anc0.Anc0refChr3 180899 1 + 222631 -----------------------------------T -s Anc1.Anc1refChr1 20220 1 + 69767 -----------------------------------T -s Anc2.Anc2refChr1 96343 1 + 142988 -----------------------------------T -s mr.mrrefChr3 129662 36 + 181027 CCCTTTTATATCTAATCCTGTATTACTTCAGCCTGT -s simDog_chr6.simDog.chr6 542719 1 + 593897 -----------------------------------T -s simHuman_chr6.simHuman.chr6 551455 1 + 601863 -----------------------------------T -s simRat_chr6.simRat.chr6 55326 36 - 647215 CCCATTTATATCCAATCTAGTATTACCTCATCCTAT - -a -s simMouse_chr6.simMouse.chr6 579850 12 + 636262 TAAAAACCTAGC -s Anc0.Anc0refChr3 180900 12 + 222631 TGCAAACCTAGC -s Anc1.Anc1refChr1 20221 12 + 69767 TGCAAACCTAGC -s Anc2.Anc2refChr1 96344 12 + 142988 TGCACATCTGAC -s mr.mrrefChr3 129698 12 + 181027 TGAAAACCTAGC -s simDog_chr6.simDog.chr6 542721 12 + 593897 TGCACATCTGAC -s simHuman_chr6.simHuman.chr6 551456 12 + 601863 TGCAAACCTAGC -s simRat_chr6.simRat.chr6 55362 12 - 647215 TGAAAACCTAGC - -a -s simMouse_chr6.simMouse.chr6 579862 59 + 636262 CTGTTTGTTAAGTTATGGTTCTGTCCATTGCATTGTGGGGAACTATTTTTCTAATGCAA -s Anc0.Anc0refChr3 180912 57 + 222631 TCATTTATAAACC-ATGGTTCCATCTTTTGTATCATGGGCAGCTACATTTCT-ATGGAA -s Anc1.Anc1refChr1 20233 58 + 69767 TCATTTATAAACCTATGGTTCCATCTTTTGTATCATGGGCAGCTACATTTCT-ATGGAA -s Anc2.Anc2refChr1 96356 57 + 142988 TCATTTATAAACC-ATGTTCCCATCTTTTGTAGCATGGGCAGTTACATTTTT-ATGGAA -s mr.mrrefChr3 129710 59 + 181027 CCATTTATTAAGTTATGGTTCTGTCCATTGTATTATGGGGAACTACTTTTCTAATGCAA -s simCow_chr6.simCow.chr6 554275 32 + 602619 --------------------------TTTGGACCGCAGGTATTATCATTTTT-ATGGAT -s simDog_chr6.simDog.chr6 542780 57 + 593897 TCATTTATAAACC-ATGTTCCCATCTTTTGTAGTATGGGCAGTTACGTTTTG-GTGGGA -s simHuman_chr6.simHuman.chr6 551468 58 + 601863 TCATTTAAGAACCTGTGGTTCCATCTTTTATATCATGGACAGCTACATTTCT-ATGGAA -s simRat_chr6.simRat.chr6 55374 59 - 647215 CCATTTATTCAGTTATGGTCCTGTCCATTGTGTGATGGGGAAATACTTTTCTAGTGCAA - -a -s simMouse_chr6.simMouse.chr6 579921 15 + 636262 GTGACTAACGTTTCT -s Anc0.Anc0refChr3 180969 15 + 222631 TTTAGGTCCATTTTT -s Anc1.Anc1refChr1 20291 15 + 69767 TTTAGGTCCATTTTT -s Anc2.Anc2refChr1 96413 15 + 142988 TTTAGGTCCATTTTT -s mr.mrrefChr3 129769 15 + 181027 GTGACTAACGTTTTT -s simCow_chr6.simCow.chr6 554307 15 + 602619 TTTAGGTCGATCTTT -s simDog_chr6.simDog.chr6 542837 15 + 593897 TTCAGGCCCATTATT -s simHuman_chr6.simHuman.chr6 551526 15 + 601863 TTTAGGTCCATTTTT -s simRat_chr6.simRat.chr6 55483 15 - 647215 ATGACTATTGTTTTT - -a -s simMouse_chr6.simMouse.chr6 579936 12 + 636262 TTTATTGACACA -s Anc0.Anc0refChr3 180986 11 + 222631 TTTAATCA-ATT -s Anc1.Anc1refChr1 20308 11 + 69767 TTTAATCA-ATT -s Anc2.Anc2refChr1 96430 11 + 142988 TTCAATCA-ATT -s mr.mrrefChr3 129784 12 + 181027 TTTATTGACACA -s simCow_chr6.simCow.chr6 554324 11 + 602619 TTAAATCA-ATA -s simDog_chr6.simDog.chr6 542854 11 + 593897 CTCAATTA-ATT -s simHuman_chr6.simHuman.chr6 551543 11 + 601863 TTTAATCA-ATT -s simRat_chr6.simRat.chr6 55498 12 - 647215 TATATTGACACA - -a -s simMouse_chr6.simMouse.chr6 579948 10 + 636262 CATCTTGAGA -s Anc0.Anc0refChr3 180997 10 + 222631 CATCTGGCTG -s Anc1.Anc1refChr1 20319 10 + 69767 CATCTGGCTG -s Anc2.Anc2refChr1 96441 10 + 142988 CATCTGGCTG -s mr.mrrefChr3 129796 10 + 181027 CATCTTGAGA -s simCow_chr6.simCow.chr6 554335 10 + 602619 TTCCTGGCTG -s simDog_chr6.simDog.chr6 542865 10 + 593897 CATCTAGCTG -s simHuman_chr6.simHuman.chr6 551554 10 + 601863 CATCTGGCAG -s simRat_chr6.simRat.chr6 55515 10 - 647215 TATCTTGAGA - -a -s simMouse_chr6.simMouse.chr6 579958 1 + 636262 T -s Anc0.Anc0refChr3 181007 1 + 222631 T -s Anc1.Anc1refChr1 20329 1 + 69767 T -s Anc2.Anc2refChr1 96470 1 + 142988 T -s mr.mrrefChr3 129806 1 + 181027 T -s simCow_chr6.simCow.chr6 554364 1 + 602619 T -s simDog_chr6.simDog.chr6 542895 1 + 593897 T -s simHuman_chr6.simHuman.chr6 551564 1 + 601863 T -s simRat_chr6.simRat.chr6 55525 1 - 647215 T - -a -s simMouse_chr6.simMouse.chr6 579959 9 + 636262 TCACCTTTT -s Anc0.Anc0refChr3 181016 9 + 222631 TGATTTTCT -s Anc1.Anc1refChr1 20338 9 + 69767 TGATTTTCT -s Anc2.Anc2refChr1 96479 9 + 142988 TGATTCTCT -s mr.mrrefChr3 129807 9 + 181027 TGACCTTTT -s simCow_chr6.simCow.chr6 554373 9 + 602619 TTATTATAT -s simDog_chr6.simDog.chr6 542904 9 + 593897 TGATTCTCT -s simHuman_chr6.simHuman.chr6 551573 9 + 601863 TGATTTTCT -s simRat_chr6.simRat.chr6 55526 9 - 647215 TGCCCTTTT - -a -s simMouse_chr6.simMouse.chr6 579968 6 + 636262 ACACAT -s Anc0.Anc0refChr3 181025 6 + 222631 ACACCT -s Anc1.Anc1refChr1 20347 6 + 69767 ACACCT -s Anc2.Anc2refChr1 96499 6 + 142988 ACACCT -s mr.mrrefChr3 129816 6 + 181027 ACACAT -s simCow_chr6.simCow.chr6 554396 6 + 602619 ATAACT -s simDog_chr6.simDog.chr6 542924 6 + 593897 ACACCT -s simHuman_chr6.simHuman.chr6 551582 6 + 601863 ACACCT -s simRat_chr6.simRat.chr6 55535 6 - 647215 ACACTT - -a -s simMouse_chr6.simMouse.chr6 579974 9 + 636262 GGATAACTT -s Anc0.Anc0refChr3 181031 9 + 222631 AGTTAAACT -s Anc1.Anc1refChr1 20353 9 + 69767 AGTTAAACT -s Anc2.Anc2refChr1 96507 9 + 142988 AGTTAAACT -s mr.mrrefChr3 129822 9 + 181027 GGATAAACT -s simCow_chr6.simCow.chr6 554404 9 + 602619 AGTTAAACT -s simDog_chr6.simDog.chr6 542932 9 + 593897 AGTTAAATT -s simHuman_chr6.simHuman.chr6 551588 9 + 601863 AGCTAAACC -s simRat_chr6.simRat.chr6 55541 9 - 647215 GGATAAACT - -a -s simMouse_chr6.simMouse.chr6 579983 6 + 636262 AATTAG -s Anc0.Anc0refChr3 181044 6 + 222631 AATTAG -s Anc1.Anc1refChr1 20366 6 + 69767 AATTAG -s Anc2.Anc2refChr1 96520 6 + 142988 AATTAG -s mr.mrrefChr3 129835 6 + 181027 AATTAG -s simCow_chr6.simCow.chr6 554417 6 + 602619 ACTTAA -s simDog_chr6.simDog.chr6 542945 6 + 593897 AATTAG -s simHuman_chr6.simHuman.chr6 551601 6 + 601863 AACTAG -s simRat_chr6.simRat.chr6 55554 6 - 647215 AATTAG - -a -s simMouse_chr6.simMouse.chr6 579989 37 + 636262 CAGTTACACACCTAATATCCAGGCAGATCTAAATTCT -s Anc0.Anc0refChr3 181050 37 + 222631 ATTTTGCATAGCTAATAAGCTGGTTGATCTGAGTTCT -s Anc1.Anc1refChr1 20372 37 + 69767 ATTTTGCATAGCTAATAAGCTGGTTGATCTGAGTTCT -s Anc2.Anc2refChr1 96526 37 + 142988 ATTTTGCATAGCTAATAAGCTGGTTGATCTGAATTCT -s mr.mrrefChr3 129841 37 + 181027 CAGTTACACACCTAATATCCAGGCTGATCTAAGTTCT -s simCow_chr6.simCow.chr6 554429 37 + 602619 ACTTCACATAGCTAATAAGCTGGTTGATTTGAATACT -s simDog_chr6.simDog.chr6 542951 37 + 593897 ATTTTGCATAGCTCATAATCTGGTTGATCTGAATTCT -s simHuman_chr6.simHuman.chr6 551607 37 + 601863 ATTTTGCAGAGCTAATAAGCTGGTTAATGTGAGTTTT -s simRat_chr6.simRat.chr6 55560 37 - 647215 CAGTTACATGCCTAATATCCAGGCTGATCTAAGTTCT - -a -s simMouse_chr6.simMouse.chr6 580026 201 + 636262 GGTGGAATCTTCACTCAGTTAGGTGAATAACATTGACACAGGTCAAGCAGTAATTGTACTCTGTTTTGGTATTCTAGTCTGGGGATCAGCTACCATGCTACCTGACTCATACCAACCCAAGAGTTGAAGAAATTGTGCTTAAGAATCTGCACCTCAACTGCCATGTCAAAGAAACAACACGTGGACCAAGGTATAGCCAGC -s Anc0.Anc0refChr3 181088 196 + 222631 TGTGTGATATTTACTTAATTAGGTGAAAAATCAAGACATAGGTAGATCT-----CGTGCTCTGTTTTTGTGTTTTAGTCTGGAGATCAGCTACCATGTTACCTCACTCACACCAACCCAAGGGTGGAGGAAATTGTGCTTAAGAATCTCCACCTTAATAGTCATGTTAAAGAAACAACACGTGGACCAAGGTATAGCTAAC -s Anc1.Anc1refChr1 20410 201 + 69767 TGTGTGATATTTACTTAATTAGGTGAAAAATCAAGACATAGGTAGATCTATCTTCGTGCTCTGTTTTTGTGTTTTAGTCTGGAGATCAGCTACCATGTTACCTCACTCACACCAACCCAAGGGTGGAGGAAATTGTGCTTAAGAATCTCCACCTTAATAGTCATGTTAAAGAAACAACACGTGGACCAAGGTATAGCTAAC -s Anc2.Anc2refChr1 96564 196 + 142988 TGTGTGATATCTACTTAATTAGGTGAAAAATCAAGACCTAGGTAGATCT-----CTTGCTCTGTTTTTCTGTCTTAGTCTGGAGATCAGCTACCATGTTACCTCACTCACACCAACCCAAGGGTGGAGGAAATTGTGCTTAAGAATCTCCACCTTAATAGTCATGTTAAAGAAACAACACGTGGACCAAGGTATGGCTAAC -s mr.mrrefChr3 129879 201 + 181027 TGTGGAATCTTCACTTAGTTAGGTGAATAACAATGACACAGGTAGAGCAGTAATTGTACTCTGTTTTGGTGTTCTAGTCTGGAGATCAGCTACCATGTTACCTCACTCATACCAACCCAAGAGTTGAGGAAATTGTGCTTAAGAATCTGCACCTCAACTGCCATGTCAAAGAAACAACACGTGGACCAAGGTATAGCTAGC -s simCow_chr6.simCow.chr6 554467 196 + 602619 TGTGTGATATCTACATAATTGGGTGAAAGTTCATGACCTAGGTAGATCT-----CTTACTCTGCTTTCATGTCTTAGTCTGGAGATCAGCTACCCTGTTACCTTACTCACACCAACCCAAGGGTGGAAGAAATTGTGCTTAAGAATCTTCACCTTAACAGTCATGTTGAAGAAACAACACGTGGACCAAGGTAGGACCAAC -s simDog_chr6.simDog.chr6 542989 195 + 593897 TGTGTGGT-TCTACTTAATTAGGTGAAAAATCAACCCCTAGGGAGATCC-----CTTGCTCTGTTTCTCTGGCTTAGTCCGGAGATCAGCTACCATGTTACCTCACTCACACCAACCCAAAGGTGGAGGAGATTGTGCTTAAGAATCTCCACCTTAATAGTCATGTTAAAGAGACTACACGTGGACCAAGGTATGGTTAAC -s simHuman_chr6.simHuman.chr6 551645 198 + 601863 TGTGTGATGTTTACTTAATTAATGGAGAAAGCAAGACAGAGCTAGGTCTATCTTCGTG---CCTTTTTGTGTTTTAGTCTGGAGATCAGCTACCATGTTACCTCACTCACACCAATCCAAGGGTGGAGGAAATTGTGCTTAAAAATCTCCACCTTAATAGTCATGTTAAAGAAACAACACGTGGACCAAGGTATAGCTAAC -s simRat_chr6.simRat.chr6 55598 201 - 647215 TATAGAATCATCACTTGGTTGGGTGAATAACTATGACCTAGGTAGAGCAGTAATTGTACTCTGTTTTGGTGTTCTAGTCTGGAGATCAGCTACCATGTTACCTCACTCATACCAACCCAAGAGTTGAGGAAATTGTGCTTAAGAATCTGCACCTCAACTGCCATGTCAAAGAAACAACACGCGGACCAAGGTATAGGTAGC - -a -s simMouse_chr6.simMouse.chr6 580227 1 + 636262 A -s Anc0.Anc0refChr3 181288 1 + 222631 A -s Anc1.Anc1refChr1 20615 1 + 69767 A -s Anc2.Anc2refChr1 96764 1 + 142988 A -s mr.mrrefChr3 130080 1 + 181027 A -s simCow_chr6.simCow.chr6 554667 1 + 602619 A -s simDog_chr6.simDog.chr6 543188 1 + 593897 A -s simHuman_chr6.simHuman.chr6 551849 1 + 601863 A -s simRat_chr6.simRat.chr6 55799 1 - 647215 A - -a -s simMouse_chr6.simMouse.chr6 580228 30 + 636262 AATTTTAGAAATTCATTATGCCCTTTCGGC -s Anc0.Anc0refChr3 181289 30 + 222631 AATAGGAGAAACCCATTATTCTTTTTCCGC -s Anc1.Anc1refChr1 20616 30 + 69767 AATAGGAGAAACCCATTATTCTTTTTCCGC -s Anc2.Anc2refChr1 96765 30 + 142988 AATAGGACAAACCCATTATTCTTGTTCCGC -s mr.mrrefChr3 130081 30 + 181027 AATTTTAGAAATTCATTATGCCCTTTCGGC -s simCow_chr6.simCow.chr6 554668 30 + 602619 AACAGAGCAGAGCCATTATTCTTGTTCCGC -s simDog_chr6.simDog.chr6 543189 21 + 593897 AATAGGACAAACTTGTTATTC--------- -s simHuman_chr6.simHuman.chr6 551850 30 + 601863 AACAGGAGGAACCCATTATTCATTTTCCAC -s simRat_chr6.simRat.chr6 55804 30 - 647215 AATTATAGAAATTCATCATGTGCTTTCAGC - -a -s simMouse_chr6.simMouse.chr6 580258 13 + 636262 ATTTTACATCTGC -s Anc0.Anc0refChr3 181320 13 + 222631 TTTTTATATCTAT -s Anc1.Anc1refChr1 20647 13 + 69767 TTTTTATATCTAT -s Anc2.Anc2refChr1 96796 13 + 142988 TTTTTACGTCCAT -s mr.mrrefChr3 130111 13 + 181027 TTTTTATATCTGC -s simCow_chr6.simCow.chr6 554699 13 + 602619 TTTTTACGTCCAT -s simHuman_chr6.simHuman.chr6 551881 13 + 601863 TTTTTATATCTAT -s simRat_chr6.simRat.chr6 55834 13 - 647215 TTTGTATACCTGC - -a -s simMouse_chr6.simMouse.chr6 580271 9 + 636262 TACTATTTC -s Anc0.Anc0refChr3 181333 8 + 222631 -GCTATTGC -s Anc1.Anc1refChr1 20660 9 + 69767 TGCTATTGC -s Anc2.Anc2refChr1 96809 8 + 142988 -GCTGTTGC -s mr.mrrefChr3 130124 9 + 181027 TACTATTTC -s simCow_chr6.simCow.chr6 554712 8 + 602619 -GCTGTTGC -s simHuman_chr6.simHuman.chr6 551910 9 + 601863 TGCTATTGT -s simRat_chr6.simRat.chr6 55847 6 - 647215 TA---TTTC - -a -s simMouse_chr6.simMouse.chr6 580280 210 + 636262 CCGAGGCAGATATTGTCCCTCTATTGAGTCAAAAGTTCTGTGTTTTTTTCCAAACCGCCTGCATCAAGTTTGGTTAGAGCCTGGAGGTATGGACTCAGAGCTTATATATCCTCAAGGGCTATCTATGACACTGCCCTCTGATTTACAAAAGAAGATGATTACCTGTAACCGGGGCCTCGAGAAAGCCAAAGTCATTCAGCCAGGTAAATT -s Anc0.Anc0refChr3 181342 207 + 222631 CTATGGCAGATATTGTCCCTCTATTGAATCAAAAGTTCTATGTTTT---CCAAACCGCCTACATCAAGTTTGGTTAGAACCTGAGGGTATGGATTCAGAGCTTATATATCCACAAGGGCTATCTATGACACTGCCCACCGATTTACAGGAGAAGATGATTACATGTAACCGGGGACTGGAGAAGGCCAAAGTGATCCAGCCAGGTAAGTT -s Anc1.Anc1refChr1 20670 207 + 69767 CTATGGCAGATATTGTCCCTCTATTGAATCAAAAGTTCTATGTTTT---CCAAACCGCCTACATCAAGTTTGGTTAGAACCTGAGGGTATGGATTCAGAGCTTATATATCCACAAGGGCTATCTATGACACTGCCCACCGATTTACAGGAGAAGATGATTACATGTAACCGGGGACTGGAGAAGGCCAAAGTGATCCAGCCAGGTAAGTT -s Anc2.Anc2refChr1 96818 207 + 142988 CTATGACAGATATTGTCCCTCTATTGAATCAAAAGTTCTATGTTTT---CCAAACCGCCTACATCAAGTTTGGTTAGAACCTGAGGGTATGGATTCAGAGCTTATATATCCACAAGGGCTATCTATGACACTGCCCACCGATTTACAGGAGAAGATGATTACATGTAACCGGGGACTGGAGAAGGCCAAAGTGATCCAGCCAGGTAAATT -s mr.mrrefChr3 130133 207 + 181027 CCGAGGCAGATATTGTCCCTCTATTGAGTCAAAAGTTCTGTGTTTT---CCAAACCGCCTGCATCAAGTTTGGTTAGAGCCTGAGGGTATGGATTCAGAGCTTATATATCCTCAAGGGCTATCTATGACACTGCCCTCTGATTTACAGAAGAAGATGATTACATGTAACCGGGGCCTCGAGAAAGCCAAAGTCATTCAGCCAGGTAAGTT -s simCow_chr6.simCow.chr6 554721 207 + 602619 CTATGAAAGGTATTGTCCCTCTATTGAATCAAAAGTTCTATGTTTT---CCAAACCGCTTACATCAAGTTTGGTTAGATCCTGAGGGTATGGATTCAGAGCTTATATATCCACAAGGGCTATCTATGACACTGCCCACCGATTTACAGGAGAAGATGATTACATGTAACCGGGGGCTGGAGAAGGCCAAGGTAATCCAGTCAGGTAAATT -s simDog_chr6.simDog.chr6 543210 201 + 593897 ------CAGATATTGTCCCTCTATTGAATCAAAAGTTCTATGTTTT---CCAAACCGCCTACATCAAGTTTGGTTAGAACCTGAAGGTATGGATTCCGAGCTTATATATCCACAAGGGCTATCAATGACACTGCCCCCTGATTTACAGGAGAAGATGATTACATGTAATCGGGGACTGGAGAAGGCCGAAGTGATCCAGCCGGGTAAATT -s simHuman_chr6.simHuman.chr6 551920 207 + 601863 CTATGGCAGATATTGCCCCTCTATTGAATCAAAAGTTCTATGTTTT---CCAAACCGCCTACATCAAGTTTGGTTAGAACCAGAGGGTATGGATTCAGAGCTTATATATCCACAAGGGCTGTCTATGACACTGCCTACCGATTTACAGGAGAAGATGATAACATGTAACCGGGGACTTGAGAAGTCCAACGTGATCCAGCCAGGTAAGTT -s simRat_chr6.simRat.chr6 55853 207 - 647215 CCGGGGCAGATATTGTCCCTCTATTGAGTCAAAAGTTCTGTGTTTT---CCAAACCGGCTGCATCAAGTTTGGTTAGAGCCTGAGGGGATGGATTCAGAACTTATATATCCTCAAGGGCTATCTATGACACTGCCATCTGATTTGCAGAAGAAGATGATTACATGTAACCGGGGCCTCGAGAAAGCCAAGGTCATTCAGCCAGGTAAGTA - -a -s simMouse_chr6.simMouse.chr6 580490 76 + 636262 CCAGAAGAACATTTGATACAACAACAGCGATAGTCTAATAGGATTATGTTTAGCTCAACAACAAAAACACAGAGAT -s Anc0.Anc0refChr3 181550 76 + 222631 ACAAATGGACACTTGATACAACAACAGCAGTACTTTAATGTGAATGTGTTTGCCTTAACAACAAACATACAGAGAC -s Anc1.Anc1refChr1 20878 76 + 69767 ACAAATGGACACTTGATACAACAACAGCAGTACTTTAATGTGAATGTGTTTGCCTTAACAACAAACATACAGAGAC -s Anc2.Anc2refChr1 97026 76 + 142988 ACAAATGGACACTTGATACAACAACAGCAGTACTTTAATGTGAATGTGTCTGCCTTAACAACAAACATACAGAGAA -s mr.mrrefChr3 130340 76 + 181027 CCAGAAGAACATTTGATACAACAACAGCGGTAGTTTAATAGGATTATGTTTAGCTCAACAACAAAAACACAGAGAC -s simCow_chr6.simCow.chr6 554929 76 + 602619 AAAAAGGCACATCTGATATAACAATAGCAGTACATCAATGTGAATGTGTCTGCATTAACAACAAACATACAAGGCT -s simDog_chr6.simDog.chr6 543412 76 + 593897 ACAAATGGATACTTGACACAACAACAGCAGTACTTTAATGGGAAAGCGTCTGCCTTATCACCAAACATACAGAGAA -s simHuman_chr6.simHuman.chr6 552128 76 + 601863 ACAAATGGACACTTGATGCAACAACGGCAGCACCTTAATGTGAATGTGTTTGCCTTAAAAACAGACATATGGAGAC -s simRat_chr6.simRat.chr6 56060 76 - 647215 TCAGAAGAACAATTGATACAACAACAGTGGTAGTTTAATAGGATTATGTTTAGCTCTATAACAAAAACACAGAGAC - -a -s simMouse_chr6.simMouse.chr6 580566 1 + 636262 A -s Anc0.Anc0refChr3 181626 1 + 222631 C -s Anc1.Anc1refChr1 20954 1 + 69767 C -s Anc2.Anc2refChr1 97102 1 + 142988 C -s mr.mrrefChr3 130416 1 + 181027 A -s simCow_chr6.simCow.chr6 555005 1 + 602619 C -s simDog_chr6.simDog.chr6 543498 1 + 593897 C -s simHuman_chr6.simHuman.chr6 552204 1 + 601863 C -s simRat_chr6.simRat.chr6 56136 1 - 647215 A - -a -s simMouse_chr6.simMouse.chr6 580567 34 + 636262 CTTGTAGCCAATAACCCCCCCTTTGTTAAACTGT -s Anc0.Anc0refChr3 181627 34 + 222631 TTGGTAGCCAACAACTCCACCTTTGATTAGATCT -s Anc1.Anc1refChr1 20955 34 + 69767 TTGGTAGCCAACAACTCCACCTTTGATTAGATCT -s Anc2.Anc2refChr1 97106 34 + 142988 TTGGAGGCCAACAACTCCACCTTTGATTAGATCC -s mr.mrrefChr3 130417 34 + 181027 CTTGTAGCCAATAACCCCCCCTTTGTTAAACTGT -s simCow_chr6.simCow.chr6 555009 34 + 602619 TTGAAGGCCAACAATTCCACCTTTATTTAGATCC -s simDog_chr6.simDog.chr6 543502 34 + 593897 TTGGAGGCCAATAACCCCACCTTCGACTTGATTC -s simHuman_chr6.simHuman.chr6 552205 34 + 601863 TTGGTAGCCAACAACTCCATCTTTGATCAGATCT -s simRat_chr6.simRat.chr6 56137 30 - 647215 CTTGTAGCCAATAACCCCGCCATTGTTTAA---- - -a -s simMouse_chr6.simMouse.chr6 580601 119 + 636262 TAAACTCACATGTTGTGCAGAAGCTAAGATGGAGTATTGTTTTTATTGCCCAAGATGGAGTGTAATGGGGCAATAGGCCTGGCGTACCATGAGCTCCCCCTGCCTGGTACCTAGACTTC -s Anc0.Anc0refChr3 181672 119 + 222631 TGAACTACCATGTCGTGCAAAAGCTAAGATGGAGTGTTATTTTTACTGCCCAAGATGGAGTGTAATGGTGCAATAGGCCTGGCATACCATAAACTCCCCCTGCCTGGTGCTGGGACTTC -s Anc1.Anc1refChr1 21000 119 + 69767 TGAACTACCATGTCGTGCAAAAGCTAAGATGGAGTGTTATTTTTACTGCCCAAGATGGAGTGTAATGGTGCAATAGGCCTGGCATACCATAAACTCCCCCTGCCTGGTGCTGGGACTTC -s Anc2.Anc2refChr1 97151 119 + 142988 TGAACAACCATGTTGTGCAATAGGTGAGATGGAGTGTTGTTTTTACTGCCCAAGATGGAGTGTAATGGTGCAATAGGCCTGGCTTATCATAAACTCCCCCTGCCTGGTGTTGGGACTTC -s mr.mrrefChr3 130451 119 + 181027 TAAACTCACATGTCGTGCAGAAGCTAAGATGGAGTATTATTTTTATTGCCCAAGATGGAGTGTAATGGTGCAATAGGCCTGGCATACCATAAGCTCCCCCTGCCTGGTACCTAGACTTC -s simCow_chr6.simCow.chr6 555054 119 + 602619 TGAACATCCGTGTTATCCAATAGGTGAGATGGAGTGTTGTTCCTACTGCCTAAGATGGAGTGTAACGGTGCAATAGGCCTGGCTTATCATAAACTCCCCCTGCCTGGTGTTTGGACTGC -s simDog_chr6.simDog.chr6 543547 119 + 593897 TGAACAACCATGTTGTGCAATAGGTGAGATGGAGTGTTGTTTTTATTGCCCAAGATGGAGTGTAATGGCGCGATTGGCCTGGCTTATCATAAACTTCCCCTGCCTGGTGTTGGGACTTC -s simHuman_chr6.simHuman.chr6 552250 114 + 601863 TGAACTACCCTGTCGCATAAAAGCTAAGATGGAGTGTTATTTTTACTGCCAAAGATGGAGTGCAATGGTGCAATAGGTCTGGCATACCATAAACTCCCCCTGCCTGGTGC-----CTTC -s simRat_chr6.simRat.chr6 56167 110 - 647215 ---------ACCGCGTGCAGAAGCTAAGATGGAGTATTATTTTTATTGCCCAAGATGGAGTGTAATGGTGCAATAGGCCTGGCATACCATAAGCTCCCCCTGCCTGGTACCTGGACTTT - -a -s simMouse_chr6.simMouse.chr6 580720 43 + 636262 AGGTGCTACAATGAGGCTAGAAGGACCACAGACTTCCTGTCGT -s Anc0.Anc0refChr3 181791 39 + 222631 ACTTGTTAGA---AAGCCAGAAGGAACACAGATTTCTTGTCA- -s Anc1.Anc1refChr1 21119 39 + 69767 ACTTGTTAGA---AAGCCAGAAGGAACACAGATTTCTTGTCA- -s Anc2.Anc2refChr1 97270 39 + 142988 ACTTGTTAGG---AAGCCAGAAGGAACACAGATTTCTTGTCA- -s mr.mrrefChr3 130570 42 + 181027 ACTTGTTACAATGAGGCTAGAAGGAACACAGACTTCCTGTCA- -s simCow_chr6.simCow.chr6 555174 36 + 602619 ACTCGTTAGG---GAACCAGAAGGAACAAAGATTTCTT---A- -s simDog_chr6.simDog.chr6 543666 39 + 593897 AATTGTTAGG---AAGCCTGAGGGAACACAGATTTCCTGTCA- -s simHuman_chr6.simHuman.chr6 552364 39 + 601863 ACTTGTTAAA---AAGCCAGAAAGCACACAGGTTTCTTGTCA- -s simRat_chr6.simRat.chr6 56277 42 - 647215 ACTTGTTACTATGAGGCTACAAGGAACACAGACTTCCTGTCA- - -a -s simMouse_chr6.simMouse.chr6 580763 27 + 636262 GGTGTACTGTCATAGATATCGTATAAG -s Anc0.Anc0refChr3 181832 27 + 222631 GTCGGACTGTCCTAAAAATTGTATAAG -s Anc1.Anc1refChr1 21160 27 + 69767 GTCGGACTGTCCTAAAAATTGTATAAG -s Anc2.Anc2refChr1 97311 27 + 142988 GTCAGACTGTCCTAAAAATTGTTTAAG -s mr.mrrefChr3 130612 27 + 181027 GGTGTACTGTCATAGAAATTGTATAAG -s simCow_chr6.simCow.chr6 555212 23 + 602619 ATCATACTGTCCTAAAAAGTG----AT -s simDog_chr6.simDog.chr6 543707 27 + 593897 GTCAGACTGTCTTAAAAATTCTTTAGG -s simHuman_chr6.simHuman.chr6 552405 27 + 601863 GTCGAGCTGCCCTAAAAATTGTATAAG -s simRat_chr6.simRat.chr6 56319 27 - 647215 GGTGTACTGTCATAGAAAGTGTTTAAG - -a -s simMouse_chr6.simMouse.chr6 580790 5 + 636262 ACTGT -s Anc0.Anc0refChr3 181859 5 + 222631 CCATA -s Anc1.Anc1refChr1 21187 5 + 69767 CCATA -s Anc2.Anc2refChr1 97338 5 + 142988 CCATA -s mr.mrrefChr3 130639 5 + 181027 ACTGT -s simCow_chr6.simCow.chr6 555235 5 + 602619 CCATA -s simDog_chr6.simDog.chr6 543735 5 + 593897 CCATA -s simHuman_chr6.simHuman.chr6 552432 5 + 601863 CCATA -s simRat_chr6.simRat.chr6 56346 5 - 647215 TCTCT - -a -s simMouse_chr6.simMouse.chr6 580795 19 + 636262 CATCCAAATCTTAAAACAC -s Anc0.Anc0refChr3 181864 19 + 222631 CATTCAAATCCTAGAACAC -s Anc1.Anc1refChr1 21192 19 + 69767 CATTCAAATCCTAGAACAC -s Anc2.Anc2refChr1 97343 19 + 142988 CCTTTAAATCCTAGAACAC -s mr.mrrefChr3 130644 19 + 181027 CATCCAAATCTTAAAACAC -s simCow_chr6.simCow.chr6 555240 19 + 602619 CCTCTAAATCCTAAAACAT -s simDog_chr6.simDog.chr6 543740 19 + 593897 CCCTTAAATCCTAGAACGC -s simHuman_chr6.simHuman.chr6 552437 18 + 601863 CATTCAAA-CCCACAACAC -s simRat_chr6.simRat.chr6 56352 19 - 647215 CATCCAAATCTTTAAACAC - -a -s simMouse_chr6.simMouse.chr6 580814 33 + 636262 ATAATGCTGTCTAAATTGGTGAGAATAAAGGAT -s Anc0.Anc0refChr3 181886 33 + 222631 ATAGTGCTGTCTAAAATGATGAGGATATACGAT -s Anc1.Anc1refChr1 21214 33 + 69767 ATAGTGCTGTCTAAAATGATGAGGATATACGAT -s Anc2.Anc2refChr1 97365 33 + 142988 CAAGTACTGTCTAAAATGATGAGGATATACGCT -s mr.mrrefChr3 130666 33 + 181027 ATAATGCTGTCTAAATTGGTGAGAATAAAGGAT -s simCow_chr6.simCow.chr6 555262 28 + 602619 GCA-TACTGTCTAAAATTATGCGTGTATA---- -s simDog_chr6.simDog.chr6 543762 33 + 593897 CATGTACTGTCTAAAATGGTGAGGATATACGCT -s simHuman_chr6.simHuman.chr6 552458 33 + 601863 ATATTGCTACCTCAAATGATGAGGATATAAGAT -s simRat_chr6.simRat.chr6 56374 33 - 647215 ATAGTGCCGTCTGACTAGGTGAGAATACAGGAT - -a -s simMouse_chr6.simMouse.chr6 580847 8 + 636262 AACACCAC -s Anc0.Anc0refChr3 181920 8 + 222631 AACGCCAC -s Anc1.Anc1refChr1 21248 8 + 69767 AACGCCAC -s Anc2.Anc2refChr1 97399 8 + 142988 AGCGCTCC -s mr.mrrefChr3 130699 8 + 181027 AACACCAC -s simDog_chr6.simDog.chr6 543796 8 + 593897 AGCGCTCC -s simHuman_chr6.simHuman.chr6 552492 8 + 601863 AAGGCCAT -s simRat_chr6.simRat.chr6 56407 8 - 647215 AGCACAAC - -a -s simMouse_chr6.simMouse.chr6 580855 9 + 636262 ACTCCTTTG -s Anc0.Anc0refChr3 181928 9 + 222631 AATCCTCTG -s Anc1.Anc1refChr1 21256 9 + 69767 AATCCTCTG -s Anc2.Anc2refChr1 97407 9 + 142988 AATTCTCTG -s mr.mrrefChr3 130707 9 + 181027 ACTCCTCTG -s simDog_chr6.simDog.chr6 543804 9 + 593897 AATTCTCTG -s simHuman_chr6.simHuman.chr6 552500 9 + 601863 AATCTTCTG -s simRat_chr6.simRat.chr6 56418 9 - 647215 CCTCCTCTG - -a -s simMouse_chr6.simMouse.chr6 580864 26 + 636262 TGCAACCTACTTGAGGTTCAATTTAT -s Anc0.Anc0refChr3 181937 26 + 222631 AGCCACCTACTTCAGGTTCAAGTTAT -s Anc1.Anc1refChr1 21265 26 + 69767 AGCCACCTACTTCAGGTTCAAGTTAT -s Anc2.Anc2refChr1 97416 26 + 142988 AGTCACTGACCTCAGGTTCAAGTTGT -s mr.mrrefChr3 130716 26 + 181027 TGCAACCTACTTGAGGTTCAATTTAT -s simCow_chr6.simCow.chr6 555290 12 + 602619 --------------GGTTCAAGTTGT -s simDog_chr6.simDog.chr6 543814 26 + 593897 AGTCACTGACCTCAGGGTCAAATTGT -s simHuman_chr6.simHuman.chr6 552509 26 + 601863 AGCCACCTATTTCAGGTTCAAGTTAT -s simRat_chr6.simRat.chr6 56427 26 - 647215 TGCAACATACTTTAGGTTCAATTGAT - -a -s simMouse_chr6.simMouse.chr6 580890 21 + 636262 CTTCATGTTCAAAGTATAATT -s Anc0.Anc0refChr3 181965 21 + 222631 CTCCAAGGTCAAAAAATCTTT -s Anc1.Anc1refChr1 21293 21 + 69767 CTCCAAGGTCAAAAAATCTTT -s Anc2.Anc2refChr1 97444 21 + 142988 CTCCAAGGTCAAAAAATCTTT -s mr.mrrefChr3 130742 21 + 181027 CTTCATGTTCAAAGTATAATT -s simCow_chr6.simCow.chr6 555304 21 + 602619 CTCCTAGGTCAAAAAATCTTT -s simDog_chr6.simDog.chr6 543842 21 + 593897 CTCAAAGGTCAAAAAATCTTT -s simHuman_chr6.simHuman.chr6 552537 21 + 601863 CTCCAAACTCAAAAAGTGTTT -s simRat_chr6.simRat.chr6 56453 21 - 647215 CTTCATGTTGAAGGTATAATT - -a -s simMouse_chr6.simMouse.chr6 580911 21 + 636262 CAACAAAAGCGAGTTGTGAGG -s Anc0.Anc0refChr3 181987 21 + 222631 CTAAAAGAGTGAGTTGCGAGG -s Anc1.Anc1refChr1 21315 21 + 69767 CTAAAAGAGTGAGTTGCGAGG -s Anc2.Anc2refChr1 97466 21 + 142988 CTAAAAGAGTGAGTTGCAAGG -s mr.mrrefChr3 130763 21 + 181027 CAAAAAAAGTGAGTTGTGAGG -s simCow_chr6.simCow.chr6 555326 21 + 602619 CTAATAGTGGCAGTTGCAAGG -s simDog_chr6.simDog.chr6 543864 21 + 593897 CTAAAAGAGTGAGTTGCAAGG -s simHuman_chr6.simHuman.chr6 552559 21 + 601863 CTAAAAGAATGAGTTGCGAGC -s simRat_chr6.simRat.chr6 56474 21 - 647215 CAAAAAAAGTGAGTTGTGAGA - -a -s simMouse_chr6.simMouse.chr6 580932 15 + 636262 AGCCTGCATGCAAAT -s Anc0.Anc0refChr3 182008 15 + 222631 AGCTAGCCTGCAAAT -s Anc1.Anc1refChr1 21336 15 + 69767 AGCTAGCCTGCAAAT -s Anc2.Anc2refChr1 97487 15 + 142988 AGCTAGCCTGCAAAT -s mr.mrrefChr3 130784 15 + 181027 AGCTTGCATGCAAAT -s simCow_chr6.simCow.chr6 555372 15 + 602619 AGTTAGCGTGCAAAT -s simDog_chr6.simDog.chr6 543885 15 + 593897 AGCTAGCCTGCAGGT -s simHuman_chr6.simHuman.chr6 552580 14 + 601863 AGCTAGC-TGAAAAT -s simRat_chr6.simRat.chr6 56495 15 - 647215 AGCTTGCCCACAAAT - -a -s simMouse_chr6.simMouse.chr6 580947 5 + 636262 GTATA -s Anc0.Anc0refChr3 182023 5 + 222631 AGATG -s Anc1.Anc1refChr1 21351 5 + 69767 AGATG -s Anc2.Anc2refChr1 97502 5 + 142988 AGATG -s mr.mrrefChr3 130799 5 + 181027 GTATA -s simCow_chr6.simCow.chr6 555399 5 + 602619 AGATG -s simDog_chr6.simDog.chr6 543900 5 + 593897 AGATG -s simHuman_chr6.simHuman.chr6 552594 5 + 601863 AGATG -s simRat_chr6.simRat.chr6 56510 5 - 647215 GTTAA - -a -s simMouse_chr6.simMouse.chr6 580952 25 + 636262 AAAATACTTTGCCTTACATAGATTA -s Anc0.Anc0refChr3 182028 24 + 222631 CAAAAACTTTGCCTTACCTATATT- -s Anc1.Anc1refChr1 21356 24 + 69767 CAAAAACTTTGCCTTACCTATATT- -s Anc2.Anc2refChr1 97507 24 + 142988 CAATAACTTGGCTTTACCTATATT- -s mr.mrrefChr3 130804 25 + 181027 AAAATACTTTGCCTTACCTAGATTA -s simCow_chr6.simCow.chr6 555404 24 + 602619 CAATTACATAGCTTTACCCAGATT- -s simDog_chr6.simDog.chr6 543905 24 + 593897 CAATAACTTGGCTTTACCTATACT- -s simHuman_chr6.simHuman.chr6 552599 22 + 601863 CAAA-ACTTTG-CTTACCTAAATT- -s simRat_chr6.simRat.chr6 56518 25 - 647215 AAAATACTTTCCTTTACCTAGATTA - -a -s simMouse_chr6.simMouse.chr6 580977 32 + 636262 ATCCTTCCCTAATGTCTCTGCTCTTGAAGATT -s Anc0.Anc0refChr3 182052 32 + 222631 GTCCTTCCCTAATGTCTTTGCTCCTAAAAAAT -s Anc1.Anc1refChr1 21380 32 + 69767 GTCCTTCCCTAATGTCTTTGCTCCTAAAAAAT -s Anc2.Anc2refChr1 97531 32 + 142988 GTCCTTCCTTAATGACTTTGCTCCTAAAAAAT -s mr.mrrefChr3 130829 32 + 181027 ATCCTTCCCTAATGTCTTTGCTCTTGAAGAAT -s simCow_chr6.simCow.chr6 555429 32 + 602619 GGTCTAGCATAATAACTTTGCCCGTACAAAAT -s simDog_chr6.simDog.chr6 543949 32 + 593897 GTCCTTCCTCAATGACTTTGCTCCTAAATAAT -s simHuman_chr6.simHuman.chr6 552621 32 + 601863 GCCCATCCCTAATGTCCTTGCTCCTAAAACAT -s simRat_chr6.simRat.chr6 56543 32 - 647215 ATCCTTCCTTAATGCCTTTGCTCTTGTAGAAG - -a -s simMouse_chr6.simMouse.chr6 581009 144 + 636262 GAGGGTCTGCGGTTCCATATGATTACTTAGACCCTCGCCAGATCAACCCCTCTTTAGAGGCACATCTGTTGCAGCGACTTTTCTTTGCTGGGCAGATCAACAGTACTACCAGCTACAAGGAGGCTGCAGCTCAGGTAGTGTAGT -s Anc0.Anc0refChr3 182084 144 + 222631 GAGGTTCTGGGGTCCCATATGATTACTTAGACCCCCGCCAGATCACCCCTTCTTTGGAGACACATCTGGTGCAACGACTGTTCTTTGCTGGGCAGATCAACAGTACCACCAGCTATGAGGAGGCTGCAGCTCAGGTAGTGTGTT -s Anc1.Anc1refChr1 21412 144 + 69767 GAGGTTCTGGGGTCCCATATGATTACTTAGACCCCCGCCAGATCACCCCTTCTTTGGAGACACATCTGGTGCAACGACTGTTCTTTGCTGGGCAGATCAACAGTACCACCAGCTATGAGGAGGCTGCAGCTCAGGTAGTGTGTT -s Anc2.Anc2refChr1 97563 144 + 142988 GAGGTTCTGGGGTTCCATATGATTACTTAGACCCCCGCCAGATCACCCCTTCCTTGGAGACACATCTGGTGCAGCGACTGTTCTTTGCTGGGCAGATCAACAGTACCACCAGCTATGAGGAGGCTGCAGCTCAGGTAGTGTGTT -s mr.mrrefChr3 130861 144 + 181027 GAGGGTCTGCGGTCCCATATGATTACTTAGACCCTCGCCAGATCAACCCCTCTTTAGAGGCACATCTGTTGCAACGACTTTTCTTTGCTGGGCAGATCAACAGTACTACCAGCTACAAGGAGGCTGCAGCTCAGGTAGTGTGGT -s simCow_chr6.simCow.chr6 555462 144 + 602619 GAGGTTCTGGGGTTCCATATGGTTACCTAGACTCCCGCCAGATCACCCCTTCGTTGGAGACACATCTAGTGCAGCGGCTGTTCTTTGCTGGGCAAATCAACAGTACCACCAGCTATGAGGAGGCTGCAGCTCAGGTAGTGTGCT -s simDog_chr6.simDog.chr6 543981 144 + 593897 TAGGTTCTGGGGTTCCGTATGATTACTTAGACCCACGCCAGATCACCCCCTCCTTGGAGACACATCTGGTGCAGCGACTGTTCTTTGCTGGGCAGACAAACAGTACCACCAGCTATGAGGAGGCTGCAGCTCAGGTAGTGTGTT -s simHuman_chr6.simHuman.chr6 552653 144 + 601863 GAGGTTCTGGGGTCCCATATGATTACTTAGACCCCCGCCAGATCACCCCTTCTTTGGAGACACATCTGGTGCAACGACTGTTCTTTGCTGGGCAGATCAACAGTACCACCAGCTATGAGGAGGCCGCAGCTAAGGTAGTATGTT -s simRat_chr6.simRat.chr6 56575 144 - 647215 GAGGGTCTGCCGTCCCATATGATTACTTAGACCCTCGCCAGATCATCCCCTCTTTAGAGGCCCAACTGTTGCAACGACTATTTTTTGCTGGGCAGATCAACAGTACAACGAGCTACAAAGAGGCTGCAGCTCAGGTAGTGTGAT - -a -s simMouse_chr6.simMouse.chr6 581153 9 + 636262 TGACAAACA -s Anc0.Anc0refChr3 182228 9 + 222631 TAACTAAGA -s Anc1.Anc1refChr1 21556 9 + 69767 TAACTAAGA -s Anc2.Anc2refChr1 97707 9 + 142988 TTTCTCAGA -s mr.mrrefChr3 131005 9 + 181027 TAACAAACA -s simDog_chr6.simDog.chr6 544128 9 + 593897 TTTCTCAGA -s simHuman_chr6.simHuman.chr6 552797 9 + 601863 TAACTAAGG -s simRat_chr6.simRat.chr6 56719 9 - 647215 TAACAAACA - -a -s simMouse_chr6.simMouse.chr6 581162 17 + 636262 TGGCTGGTTTATGTAGG -s Anc0.Anc0refChr3 182237 17 + 222631 TGACAGGTTTATCCAGG -s Anc1.Anc1refChr1 21565 17 + 69767 TGACAGGTTTATCCAGG -s Anc2.Anc2refChr1 97723 17 + 142988 TGACAGGTTTATCCAGG -s mr.mrrefChr3 131014 17 + 181027 TGGCTGGTTTATGTAGG -s simCow_chr6.simCow.chr6 555613 17 + 602619 TGACACGTCTACCCAGA -s simDog_chr6.simDog.chr6 544151 17 + 593897 TGACAGGTTTATCCAGG -s simHuman_chr6.simHuman.chr6 552806 17 + 601863 TGACAGGTTTATCCAGG -s simRat_chr6.simRat.chr6 56728 17 - 647215 TGGCTGGTTTATGTAGG - -a -s simMouse_chr6.simMouse.chr6 581179 20 + 636262 CTGCTGTGCTGTTTTATAAA -s Anc0.Anc0refChr3 182255 20 + 222631 ATGCTGTACTGTTTTATAAA -s Anc1.Anc1refChr1 21583 20 + 69767 ATGCTGTACTGTTTTATAAA -s Anc2.Anc2refChr1 97741 20 + 142988 ATGCTATACTGTTTTATAAG -s mr.mrrefChr3 131031 20 + 181027 CTGCTGTGCTGTTTTATAAA -s simCow_chr6.simCow.chr6 555631 20 + 602619 ATGCCATACTGTTTTATAAG -s simDog_chr6.simDog.chr6 544169 20 + 593897 ATGCTATACTATTTTATAAG -s simHuman_chr6.simHuman.chr6 552824 20 + 601863 ATGCTGAACTGTTTTATAAA -s simRat_chr6.simRat.chr6 56745 20 - 647215 CGGCTGTCCAGTTTTATGAA - -a -s simMouse_chr6.simMouse.chr6 581199 20 + 636262 CATTGGTACAGGTCTATCTA -s Anc0.Anc0refChr3 182275 20 + 222631 CCTTGGTACAGCCCTGTCTA -s Anc1.Anc1refChr1 21603 20 + 69767 CCTTGGTACAGCCCTGTCTA -s Anc2.Anc2refChr1 97761 20 + 142988 CCTTGGTATAGCCATGTCAA -s mr.mrrefChr3 131051 20 + 181027 CATTGGTACAGGTCTGTCTA -s simCow_chr6.simCow.chr6 555651 20 + 602619 CCTTATTATAGTCTTGTCAA -s simDog_chr6.simDog.chr6 544189 19 + 593897 CCTTGGTATGGCCATG-CAA -s simHuman_chr6.simHuman.chr6 552845 20 + 601863 CCTTGGTACAACCCTGTCTA -s simRat_chr6.simRat.chr6 56765 20 - 647215 TGTCGGTACAGGTCCGTCTG - -a -s simMouse_chr6.simMouse.chr6 581219 66 + 636262 TAACAGGTCAACTCAGTCCTTTGTACTCAGATCAGTTCTGGCTTGACATTGTGGTTGTGTTGATTT -s Anc0.Anc0refChr3 182295 56 + 222631 TAACAAGTCTACTGAGT-TTTTGTATGGAAACAAATTCCACCAT---------GGCATGTCTGGTT -s Anc1.Anc1refChr1 21623 59 + 69767 TAACAAGTCTACTGAGT-TTTTGTATGGAAACAAATTCCACCAT------AATGGCATGTCTGGTT -s Anc2.Anc2refChr1 97781 56 + 142988 TAACAGGTCTACTGAGT-TTTTGTATGGAAACAAATTCCACCAT---------GGCATGTCTGGTT -s mr.mrrefChr3 131071 66 + 181027 TAACAAGTCAACTGAGTCCTTTGTACTCAGATCAGTTCTGGCTTGACATTGTGGTTGTGTTGATTT -s simCow_chr6.simCow.chr6 555675 56 + 602619 TAACATCTCTACTGAGT-TTTTGTATAGGAATAAATTCCAGTAT---------GACATGTCTGGTT -s simDog_chr6.simDog.chr6 544208 56 + 593897 TGACAGGTCTACTGAGT-TTTTGTATGGAAACAAATTCCACCAT---------GGCATGCCCTGTT -s simHuman_chr6.simHuman.chr6 552865 23 + 601863 TAACAAG-------------------------------------------AATGGCATGTCTGGTA -s simRat_chr6.simRat.chr6 56785 65 - 647215 TAACAAGTCAACTGAGTCATT-GTACTCAGTTCAGCTTTGGCTTGAAATTGTGGCTCTATTGATTT - -a -s simMouse_chr6.simMouse.chr6 581285 2 + 636262 TC -s Anc0.Anc0refChr3 182351 2 + 222631 CT -s Anc1.Anc1refChr1 21682 2 + 69767 CT -s Anc2.Anc2refChr1 97837 2 + 142988 CT -s mr.mrrefChr3 131137 2 + 181027 TC -s simCow_chr6.simCow.chr6 555739 2 + 602619 TT -s simDog_chr6.simDog.chr6 544264 2 + 593897 CT -s simHuman_chr6.simHuman.chr6 552888 2 + 601863 CT -s simRat_chr6.simRat.chr6 56850 2 - 647215 TC - -a -s simMouse_chr6.simMouse.chr6 581287 21 + 636262 TGTCTAGTAATGACACCTGCT -s Anc0.Anc0refChr3 182353 20 + 222631 TGTATGGTAATATTCACAGA- -s Anc1.Anc1refChr1 21684 20 + 69767 TGTATGGTAATATTCACAGA- -s Anc2.Anc2refChr1 97839 20 + 142988 TGTATGGTAATATTCACAGA- -s mr.mrrefChr3 131139 21 + 181027 TGTATAGTAATGATACCTGCT -s simCow_chr6.simCow.chr6 555741 20 + 602619 TGTCTGGTAATATTCACAGG- -s simDog_chr6.simDog.chr6 544276 20 + 593897 TATATGGTAATACCCACAGA- -s simHuman_chr6.simHuman.chr6 552890 20 + 601863 TGTATGGTAATATTCTAGGA- -s simRat_chr6.simRat.chr6 56852 21 - 647215 TGTATAGCAATGATGCCTGCT - -a -s simMouse_chr6.simMouse.chr6 581308 2 + 636262 GA -s Anc0.Anc0refChr3 182375 2 + 222631 TA -s Anc1.Anc1refChr1 21706 2 + 69767 TA -s Anc2.Anc2refChr1 97861 2 + 142988 TA -s mr.mrrefChr3 131162 2 + 181027 TA -s simCow_chr6.simCow.chr6 555764 2 + 602619 TA -s simDog_chr6.simDog.chr6 544298 2 + 593897 TA -s simHuman_chr6.simHuman.chr6 552912 2 + 601863 TA -s simRat_chr6.simRat.chr6 56875 2 - 647215 TA - -a -s simMouse_chr6.simMouse.chr6 581310 7 + 636262 AAATAAA -s Anc0.Anc0refChr3 182377 7 + 222631 AGGCAAC -s Anc1.Anc1refChr1 21708 7 + 69767 AGGCAAC -s Anc2.Anc2refChr1 97863 7 + 142988 CGGCAAC -s mr.mrrefChr3 131164 7 + 181027 AAATAAC -s simCow_chr6.simCow.chr6 555766 7 + 602619 TGGCAAC -s simDog_chr6.simDog.chr6 544301 7 + 593897 CGGCAAC -s simHuman_chr6.simHuman.chr6 552914 7 + 601863 AGGCAAC -s simRat_chr6.simRat.chr6 56877 7 - 647215 AAATCAC - -a -s simMouse_chr6.simMouse.chr6 581317 15 + 636262 CTTCTGCAATCCCCA -s Anc0.Anc0refChr3 182385 15 + 222631 CTTCTGCAATCACTA -s Anc1.Anc1refChr1 21716 15 + 69767 CTTCTGCAATCACTA -s Anc2.Anc2refChr1 97871 15 + 142988 CTTCTGCAGCCACTA -s mr.mrrefChr3 131171 15 + 181027 CTTCTGCAATCCCCA -s simCow_chr6.simCow.chr6 555774 15 + 602619 ATTCCGCAGCTACAA -s simDog_chr6.simDog.chr6 544309 15 + 593897 CTACTAAAGCCACTA -s simHuman_chr6.simHuman.chr6 552922 15 + 601863 CTTCTGCAATCGCTG -s simRat_chr6.simRat.chr6 56884 15 - 647215 CTTCTGCAATCCCCA - -a -s simMouse_chr6.simMouse.chr6 581332 10 + 636262 TTTTAAGCAA -s Anc0.Anc0refChr3 182401 10 + 222631 TCCCAAGCAG -s Anc1.Anc1refChr1 21732 10 + 69767 TCCCAAGCAG -s Anc2.Anc2refChr1 97887 10 + 142988 TCCCAAGCAG -s mr.mrrefChr3 131186 10 + 181027 TTCTAAGCAA -s simCow_chr6.simCow.chr6 555790 10 + 602619 TCCCACGCAG -s simDog_chr6.simDog.chr6 544325 10 + 593897 TCGCAAGCAA -s simHuman_chr6.simHuman.chr6 552938 10 + 601863 TCCCAAGCAG -s simRat_chr6.simRat.chr6 56899 10 - 647215 TGCTAAGCAA - -a -s simMouse_chr6.simMouse.chr6 581342 12 + 636262 GCAGGAATGGGC -s Anc0.Anc0refChr3 182411 12 + 222631 GCAGGAATATGC -s Anc1.Anc1refChr1 21742 12 + 69767 GCAGGAATATGC -s Anc2.Anc2refChr1 97897 12 + 142988 GCGTTAATATAC -s mr.mrrefChr3 131196 12 + 181027 GCAGGAATAGGC -s simCow_chr6.simCow.chr6 555800 2 + 602619 GC---------- -s simDog_chr6.simDog.chr6 544341 12 + 593897 GTGTTAATATAC -s simHuman_chr6.simHuman.chr6 552948 12 + 601863 GCAGGAATATGC -s simRat_chr6.simRat.chr6 56909 12 - 647215 CCAGGAATAGGC - -a -s simMouse_chr6.simMouse.chr6 581354 2 + 636262 AC -s Anc0.Anc0refChr3 182423 2 + 222631 AA -s Anc1.Anc1refChr1 21754 2 + 69767 AA -s Anc2.Anc2refChr1 97909 2 + 142988 AA -s mr.mrrefChr3 131208 2 + 181027 AA -s simDog_chr6.simDog.chr6 544353 2 + 593897 AA -s simHuman_chr6.simHuman.chr6 552960 2 + 601863 AA -s simRat_chr6.simRat.chr6 56928 2 - 647215 AA - -a -s simMouse_chr6.simMouse.chr6 581356 11 + 636262 TCACCTGGGCC -s Anc0.Anc0refChr3 182716 11 + 222631 CAACCTGGGCC -s Anc1.Anc1refChr1 22047 11 + 69767 CAACCTGGGCC -s Anc2.Anc2refChr1 98206 11 + 142988 CAACCTGGGTC -s mr.mrrefChr3 131210 11 + 181027 CCACCTGGGCC -s simCow_chr6.simCow.chr6 556102 11 + 602619 TAACCTGGGTC -s simDog_chr6.simDog.chr6 544648 11 + 593897 CAACCTGGGTC -s simHuman_chr6.simHuman.chr6 553253 11 + 601863 CTACCCAGGCC -s simRat_chr6.simRat.chr6 56930 11 - 647215 CCACCTGGGCC - -a -s simMouse_chr6.simMouse.chr6 581367 17 + 636262 AGTCTAGTCCTGGGGGA -s Anc0.Anc0refChr3 182728 16 + 222631 AATATAGTCCTAGGG-A -s Anc1.Anc1refChr1 22059 16 + 69767 AATATAGTCCTAGGG-A -s Anc2.Anc2refChr1 98218 16 + 142988 AACATAGTCCTAGGG-A -s mr.mrrefChr3 131221 16 + 181027 AATCTAGTCCTAGGG-A -s simCow_chr6.simCow.chr6 556114 15 + 602619 GAGAT-GTTCTAGGG-A -s simDog_chr6.simDog.chr6 544660 16 + 593897 AACATAATCCTAGGG-A -s simHuman_chr6.simHuman.chr6 553265 16 + 601863 AATATAGTCCTAGGG-A -s simRat_chr6.simRat.chr6 56941 16 - 647215 AATTTTGTCCTAAGG-A - -a -s simMouse_chr6.simMouse.chr6 581384 56 + 636262 AACAAACTACCCAACTGCTCTTATACCATGATCATAGGAACTATCATATGATATGT -s Anc0.Anc0refChr3 182750 41 + 222631 AGCAGAAAGCCCAGCCATTATGTTCCA----T------AACTATTGCATG-----C -s Anc1.Anc1refChr1 22081 45 + 69767 AGCAGAAAGCCCAGCCATTATGTTCCAGCGAT------AACTATTGCATG-----C -s Anc2.Anc2refChr1 98240 41 + 142988 AGCAGAAAGCCCAGCCATTATGTTCCA----T------GACTATTGCATG-----C -s mr.mrrefChr3 131237 51 + 181027 AACAGACTACCCAACCGCTCTTATACAATGATCATAGGAACTATTGTATG-----T -s simCow_chr6.simCow.chr6 556135 41 + 602619 AGCCGACTGCCCAGCTATTATGTTCCA----T------GACTACTGTATG-----C -s simDog_chr6.simDog.chr6 544682 41 + 593897 AACAAAAAACCCAGTCATTATGTTCCA----T------GTCTATTGCATG-----C -s simHuman_chr6.simHuman.chr6 553287 45 + 601863 AGTGGAGCGCCCAGCCATTATGTTCCAGCGTT------AACTATTGCATG-----C -s simRat_chr6.simRat.chr6 56957 51 - 647215 AACAGACTACCCAACCGCTCTTATACAATGATCACTGGAACTATTGTGTG-----T - -a -s simMouse_chr6.simMouse.chr6 581440 13 + 636262 CGCATCTCTGCAG -s Anc0.Anc0refChr3 182791 13 + 222631 CTTAACTCTGCAG -s Anc1.Anc1refChr1 22126 13 + 69767 CTTAACTCTGCAG -s Anc2.Anc2refChr1 98281 13 + 142988 CTTAACTCTGCAG -s mr.mrrefChr3 131288 13 + 181027 CGTATCTCTGCAG -s simCow_chr6.simCow.chr6 556176 13 + 602619 CCTAACGGTCCAG -s simDog_chr6.simDog.chr6 544724 13 + 593897 CTAAACTCTGCAA -s simHuman_chr6.simHuman.chr6 553332 13 + 601863 CTTAACTCCGCAG -s simRat_chr6.simRat.chr6 57008 13 - 647215 CGTAGTTCTACAG - -a -s simMouse_chr6.simMouse.chr6 581453 9 + 636262 ATCTAACTG -s Anc0.Anc0refChr3 182809 9 + 222631 ATCCCATTG -s Anc1.Anc1refChr1 22144 9 + 69767 ATCCCATTG -s Anc2.Anc2refChr1 98319 9 + 142988 ATCCCTTTG -s mr.mrrefChr3 131301 9 + 181027 ATCTAACTG -s simCow_chr6.simCow.chr6 556214 9 + 602619 ATCTCTTTA -s simDog_chr6.simDog.chr6 544764 9 + 593897 ATCCTTTTG -s simHuman_chr6.simHuman.chr6 553350 9 + 601863 ATCGCATTG -s simRat_chr6.simRat.chr6 57021 9 - 647215 ATTTAACTG - -a -s simMouse_chr6.simMouse.chr6 581462 1 + 636262 T -s Anc0.Anc0refChr3 182818 1 + 222631 T -s Anc1.Anc1refChr1 22153 1 + 69767 T -s Anc2.Anc2refChr1 98328 1 + 142988 C -s mr.mrrefChr3 131310 1 + 181027 T -s simCow_chr6.simCow.chr6 556227 1 + 602619 C -s simDog_chr6.simDog.chr6 544773 1 + 593897 C -s simHuman_chr6.simHuman.chr6 553359 1 + 601863 T -s simRat_chr6.simRat.chr6 57030 1 - 647215 T - -a -s simMouse_chr6.simMouse.chr6 581463 1 + 636262 T -s Anc0.Anc0refChr3 182823 1 + 222631 T -s Anc1.Anc1refChr1 22158 1 + 69767 T -s Anc2.Anc2refChr1 98333 1 + 142988 T -s mr.mrrefChr3 131311 1 + 181027 T -s simCow_chr6.simCow.chr6 556232 1 + 602619 C -s simDog_chr6.simDog.chr6 544778 1 + 593897 T -s simHuman_chr6.simHuman.chr6 553364 1 + 601863 T -s simRat_chr6.simRat.chr6 57031 1 - 647215 T - -a -s simMouse_chr6.simMouse.chr6 581464 1 + 636262 G -s Anc0.Anc0refChr3 182826 1 + 222631 G -s Anc1.Anc1refChr1 22161 1 + 69767 G -s Anc2.Anc2refChr1 98336 1 + 142988 G -s mr.mrrefChr3 131314 1 + 181027 G -s simCow_chr6.simCow.chr6 556235 1 + 602619 T -s simDog_chr6.simDog.chr6 544781 1 + 593897 G -s simHuman_chr6.simHuman.chr6 553367 1 + 601863 C -s simRat_chr6.simRat.chr6 57034 1 - 647215 G - -a -s simMouse_chr6.simMouse.chr6 581465 6 + 636262 AACTTG -s Anc0.Anc0refChr3 182827 6 + 222631 AATCTA -s Anc1.Anc1refChr1 22162 6 + 69767 AATCTA -s Anc2.Anc2refChr1 98338 6 + 142988 AATTTA -s mr.mrrefChr3 131315 6 + 181027 AACCTG -s simCow_chr6.simCow.chr6 556237 6 + 602619 AGTTTC -s simDog_chr6.simDog.chr6 544783 6 + 593897 GATTTA -s simHuman_chr6.simHuman.chr6 553368 6 + 601863 AATCTT -s simRat_chr6.simRat.chr6 57035 6 - 647215 TACCTG - -a -s simMouse_chr6.simMouse.chr6 581471 6 + 636262 CATTAC -s Anc0.Anc0refChr3 182833 6 + 222631 CATCAT -s Anc1.Anc1refChr1 22168 6 + 69767 CATCAT -s Anc2.Anc2refChr1 98344 6 + 142988 CATCTT -s mr.mrrefChr3 131321 6 + 181027 CATTAC -s simCow_chr6.simCow.chr6 556243 6 + 602619 CATCTT -s simDog_chr6.simDog.chr6 544789 6 + 593897 CATCTC -s simHuman_chr6.simHuman.chr6 553374 6 + 601863 CATCAT -s simRat_chr6.simRat.chr6 57044 6 - 647215 TATTAC - -a -s simMouse_chr6.simMouse.chr6 581477 5 + 636262 ATTCC -s Anc0.Anc0refChr3 182841 5 + 222631 ATTCC -s Anc1.Anc1refChr1 22176 5 + 69767 ATTCC -s Anc2.Anc2refChr1 98352 5 + 142988 ATTCT -s mr.mrrefChr3 131327 5 + 181027 ATTCC -s simCow_chr6.simCow.chr6 556251 5 + 602619 GTTCT -s simDog_chr6.simDog.chr6 544797 5 + 593897 ATCCT -s simHuman_chr6.simHuman.chr6 553382 5 + 601863 ATTCC -s simRat_chr6.simRat.chr6 57050 5 - 647215 GTTTC - -a -s simMouse_chr6.simMouse.chr6 581482 13 + 636262 CTTGCACTCTGTA -s Anc0.Anc0refChr3 182846 13 + 222631 CTTGCATTCAATA -s Anc1.Anc1refChr1 22181 13 + 69767 CTTGCATTCAATA -s Anc2.Anc2refChr1 98357 13 + 142988 CTTTCATTCAATA -s mr.mrrefChr3 131332 13 + 181027 CTTGCATTCTGTA -s simCow_chr6.simCow.chr6 556256 13 + 602619 CTTTCATTCAATG -s simDog_chr6.simDog.chr6 544836 13 + 593897 CTTTTATTCAAGA -s simHuman_chr6.simHuman.chr6 553387 13 + 601863 CTTGCATTAATTA -s simRat_chr6.simRat.chr6 57055 13 - 647215 CTTGCATTCTGTA - -a -s simMouse_chr6.simMouse.chr6 581495 59 + 636262 ATCAACCACAGGTGGGGCAGAGAGCATAAGCTGAATAATCCTATATCGTATAGCTCCAG -s Anc0.Anc0refChr3 182872 54 + 222631 CTA--CTATAGGGGGGGCAGGG---AAAAGCCTAATAATATTACATTGTATAGCTCTAG -s Anc1.Anc1refChr1 22207 56 + 69767 CTAGACTATAGGGGGGGCAGGG---AAAAGCCTAATAATATTACATTGTATAGCTCTAG -s Anc2.Anc2refChr1 98383 54 + 142988 CTA--TTAGCGGGGCAACAAGA---AAAAGCCTAATAACATTACATTGCATAGCTCTGG -s mr.mrrefChr3 131355 59 + 181027 ATCGACCATAGGTGGGGCAGAGAGCATAAGCCTAATAATCCTATATTGTATAGCTCCAG -s simCow_chr6.simCow.chr6 556282 52 + 602619 CTG--TTGGGGGGGCAACAAGA---AAAAGCCTAATAAGATTACCTAGCATAGCTCC-- -s simDog_chr6.simDog.chr6 544862 54 + 593897 TTA--TTAGCGGAGCAACAAGA---AAGAGCCTAATGACATTACACTACATAGTTCTGG -s simHuman_chr6.simHuman.chr6 553413 56 + 601863 CTAGACTATAAGGGGGGCAGTG---AAAAGCCTGATAATATTACGTTGTATAGCCCAAG -s simRat_chr6.simRat.chr6 57078 59 - 647215 ATCGACCATTGGTGGGGCAGAGAGCATAAGCCTAATAATCCTATATTGTATAGCGCCAG - -a -s simMouse_chr6.simMouse.chr6 581554 12 + 636262 GCTTGAATCATT -s Anc0.Anc0refChr3 182964 12 + 222631 GATTTAATCATC -s Anc1.Anc1refChr1 22301 12 + 69767 GATTTAATCATC -s Anc2.Anc2refChr1 98475 12 + 142988 GATTTAATCATC -s mr.mrrefChr3 131414 12 + 181027 GCTTGAATGATC -s simCow_chr6.simCow.chr6 556365 12 + 602619 TATCTAATCATC -s simDog_chr6.simDog.chr6 544954 12 + 593897 GATTTAATTATC -s simHuman_chr6.simHuman.chr6 553508 12 + 601863 AATTTAATCGTC -s simRat_chr6.simRat.chr6 57137 12 - 647215 CCTTAAATGATC - -a -s simMouse_chr6.simMouse.chr6 581566 2 + 636262 GG -s Anc0.Anc0refChr3 183031 2 + 222631 GT -s Anc1.Anc1refChr1 22368 2 + 69767 GT -s Anc2.Anc2refChr1 98549 2 + 142988 TT -s mr.mrrefChr3 131426 2 + 181027 GG -s simCow_chr6.simCow.chr6 556440 2 + 602619 TT -s simDog_chr6.simDog.chr6 545028 2 + 593897 TT -s simHuman_chr6.simHuman.chr6 553575 2 + 601863 GT -s simRat_chr6.simRat.chr6 57149 2 - 647215 TG - -a -s simMouse_chr6.simMouse.chr6 581568 15 + 636262 GTGGCAGCGAAGGAT -s Anc0.Anc0refChr3 183033 15 + 222631 GCTGCATCCAAGAGT -s Anc1.Anc1refChr1 22370 15 + 69767 GCTGCATCCAAGAGT -s Anc2.Anc2refChr1 98552 15 + 142988 GCTGCATCCAAGAGT -s mr.mrrefChr3 131428 15 + 181027 GTGGTAGCGAAGGAT -s simCow_chr6.simCow.chr6 556443 15 + 602619 GCTGCATCCAAGAGT -s simDog_chr6.simDog.chr6 545031 15 + 593897 GTTTCATCTAGGGGT -s simHuman_chr6.simHuman.chr6 553577 15 + 601863 GCTGCATCCAAGAGC -s simRat_chr6.simRat.chr6 57151 15 - 647215 GTGGTGACTAAGGAT - -a -s simMouse_chr6.simMouse.chr6 581591 46 + 636262 AGTTGCTGAGTCCTGGTCCTAGTGCTAGGTTTTACTTTTGCTTACC - -a -s simMouse_chr6.simMouse.chr6 581744 2 + 636262 AG -s Anc0.Anc0refChr3 183172 2 + 222631 GG -s Anc1.Anc1refChr1 22511 2 + 69767 GG -s Anc2.Anc2refChr1 98691 2 + 142988 GG -s mr.mrrefChr3 131558 2 + 181027 AG -s simCow_chr6.simCow.chr6 556584 2 + 602619 GG -s simDog_chr6.simDog.chr6 545132 2 + 593897 GG -s simRat_chr6.simRat.chr6 57279 2 - 647215 AT - -a -s simMouse_chr6.simMouse.chr6 581765 20 + 636262 TAACAGTATGCGTAAGCTGA -s Anc0.Anc0refChr3 183193 15 + 222631 CAAAAATA-----GTGCTGG -s Anc1.Anc1refChr1 22532 15 + 69767 CAAAAATA-----GTGCTGG -s Anc2.Anc2refChr1 98712 15 + 142988 CAAAAATA-----GTGCTGG -s mr.mrrefChr3 131579 20 + 181027 TAACAGTATGCGTAAGCTGG -s simCow_chr6.simCow.chr6 556606 15 + 602619 CATAAATA-----GTGCTGG -s simDog_chr6.simDog.chr6 545153 15 + 593897 CAAAAATA-----GTGCTGG -s simHuman_chr6.simHuman.chr6 553745 15 + 601863 CAGAAATA-----GTGCTAG -s simRat_chr6.simRat.chr6 57300 20 - 647215 TAACAGTATGTGGAAGCTGG - -a -s simMouse_chr6.simMouse.chr6 581785 8 + 636262 AAACATTG -s Anc0.Anc0refChr3 183208 8 + 222631 GCACATTG -s Anc1.Anc1refChr1 22547 8 + 69767 GCACATTG -s Anc2.Anc2refChr1 98727 8 + 142988 GCACATTG -s mr.mrrefChr3 131599 8 + 181027 AAACATTG -s simCow_chr6.simCow.chr6 556621 8 + 602619 AAACATTG -s simDog_chr6.simDog.chr6 545224 7 + 593897 GCAGAAT- -s simHuman_chr6.simHuman.chr6 553760 8 + 601863 GCACATTG -s simRat_chr6.simRat.chr6 57320 8 - 647215 AAACATTG - -a -s simMouse_chr6.simMouse.chr6 581851 52 + 636262 AAGATGTAATTCTGACTTCATAGAGAAGAGATCATAGTCAACCTTCCCATTT -s Anc0.Anc0refChr3 183256 37 + 222631 -------------GACTTCATAGAAAGGAGACCACAGTCAA--TAAAAGATT -s Anc1.Anc1refChr1 22615 37 + 69767 -------------GACTTCATAGAAAGGAGACCACAGTCAA--TAAAAGATT -s Anc2.Anc2refChr1 98775 37 + 142988 -------------GACTTCGTAGAAAGGGGACCACGGTCAA--TAAAAGATT -s mr.mrrefChr3 131665 52 + 181027 AAGATGTAATTCTGACTTCATAGAGAAGAGATCATAGTCAACCTTCCCACTT -s simCow_chr6.simCow.chr6 556710 37 + 602619 -------------GACTCAGTAGAAAGCGGACCACGATCAA--TAAAAAATT -s simDog_chr6.simDog.chr6 545263 34 + 593897 --------------ACTTCGTAGA--GGGGAACATGGTCAA--TAAAAGATT -s simHuman_chr6.simHuman.chr6 553808 37 + 601863 -------------GACTACATAGATAGGAGACCACAGCCAA--TAAAATATC -s simRat_chr6.simRat.chr6 57388 51 - 647215 AAGACGTAATTCTGACTTCAT-GAGAAGAGATTATAGTCAACCTTCCCACTT - -a -s simMouse_chr6.simMouse.chr6 581903 1 + 636262 A -s Anc0.Anc0refChr3 183293 1 + 222631 A -s Anc1.Anc1refChr1 22652 1 + 69767 A -s Anc2.Anc2refChr1 98812 1 + 142988 A -s mr.mrrefChr3 131717 1 + 181027 A -s simCow_chr6.simCow.chr6 556747 1 + 602619 A -s simDog_chr6.simDog.chr6 545297 1 + 593897 A -s simHuman_chr6.simHuman.chr6 553845 1 + 601863 A -s simRat_chr6.simRat.chr6 57443 1 - 647215 A - -a -s simMouse_chr6.simMouse.chr6 581904 17 + 636262 CATGGAATTATTTTACA -s Anc0.Anc0refChr3 183295 17 + 222631 CATAGAACTATGTCATA -s Anc1.Anc1refChr1 22654 17 + 69767 CATAGAACTATGTCATA -s Anc2.Anc2refChr1 98814 17 + 142988 TAGAGACTCATGTCATA -s mr.mrrefChr3 131718 17 + 181027 CATAGAACTATTTCACA -s simCow_chr6.simCow.chr6 556749 17 + 602619 AAGAGACTCACTTCACA -s simDog_chr6.simDog.chr6 545299 17 + 593897 TAGAGACTCATGTCATA -s simHuman_chr6.simHuman.chr6 553847 17 + 601863 CATAGAACTATGCCATA -s simRat_chr6.simRat.chr6 57444 17 - 647215 CATAGAACTATTTCACA - -a -s simMouse_chr6.simMouse.chr6 581921 35 + 636262 CCCTCATGTACCTTGCATTTGTGGTGATATACAAG -s Anc0.Anc0refChr3 183317 35 + 222631 CCCTAATATATTTTGCATTTGGGATTACAGTCAAG -s Anc1.Anc1refChr1 22676 35 + 69767 CCCTAATATATTTTGCATTTGGGATTACAGTCAAG -s Anc2.Anc2refChr1 98846 35 + 142988 CCCTAATATATATTGGATTTGGGATTACAGTCAAC -s mr.mrrefChr3 131735 35 + 181027 CCCTCATGTACTTTGCATTTGTGGTGATATACAAG -s simCow_chr6.simCow.chr6 556785 35 + 602619 CCTTCAGATATTTTGGATTTATGGTTACAATCAGC -s simDog_chr6.simDog.chr6 545331 31 + 593897 CTCTAATAAACATTGGATTCGGGA----AGTCAAC -s simHuman_chr6.simHuman.chr6 553869 34 + 601863 CCATAATTTA-TTTGCATTTGGAATTAAAGGCAAG -s simRat_chr6.simRat.chr6 57461 35 - 647215 AAATAATATACTTTGGATTCATGGAGGTATACATG - -a -s simMouse_chr6.simMouse.chr6 581956 51 + 636262 ACGCTCTTGAATACTGAGAGCACATAAGCTGGTGAGAATTAGTATCACCCC -s Anc0.Anc0refChr3 183354 47 + 222631 AACCTCTGTATCACTGTG----CAGAAGCTGGTGAGAACTTGTATATTACT -s Anc1.Anc1refChr1 22713 47 + 69767 AACCTCTGTATCACTGTG----CAGAAGCTGGTGAGAACTTGTATATTACT -s Anc2.Anc2refChr1 98883 47 + 142988 AACCTCTGTGTCACTGTG----TAGAACCTGGTGAGAACTTGTATATTACT -s mr.mrrefChr3 131770 51 + 181027 ACCCTCTTGAATACTGAGAGCACATAAGCTGGTGAGAATTAGTATCACCCC -s simCow_chr6.simCow.chr6 556822 44 + 602619 AACCTGTGAGTCACTGTG----AAGGATCCGGTTAAA---TGCATATCACC -s simDog_chr6.simDog.chr6 545364 45 + 593897 AACCTCTGTGGTACTTTG----TAGAACCTGGTGAGAACTTGT--ATTACT -s simHuman_chr6.simHuman.chr6 553905 47 + 601863 GACCTCTGCATCAATGTG----CACAAGTTGATGAGAACCTGTGTATTACT -s simRat_chr6.simRat.chr6 57496 51 - 647215 ACCCTCTTTAATACTGAGGGCACAAAAGCTTGTGAAAATTAGTACCACCCC - -a -s simMouse_chr6.simMouse.chr6 582007 25 + 636262 CTGAGAAGAGAGGCCATGCTCAGAC -s Anc0.Anc0refChr3 183401 24 + 222631 CTAGAAAGGGGTG-CATGCACAGAT -s Anc1.Anc1refChr1 22760 24 + 69767 CTAGAAAGGGGTG-CATGCACAGAT -s Anc2.Anc2refChr1 98930 24 + 142988 CTAGAAAGGAGTG-CATGCACAGAT -s mr.mrrefChr3 131821 25 + 181027 CTGAGAAGAGAGGCCATGCTCAGAC -s simCow_chr6.simCow.chr6 556866 24 + 602619 TTAGAAAGGAGTG-GATGCACAGAT -s simDog_chr6.simDog.chr6 545409 24 + 593897 CTAGTAAGGAGTA-CATGCACAGAT -s simHuman_chr6.simHuman.chr6 553952 24 + 601863 CTAGAAAGTGGTG-CATGCGCAGGT -s simRat_chr6.simRat.chr6 57548 25 - 647215 CTGAGAAGAGAGGTCATGCTCAGAC - -a -s simMouse_chr6.simMouse.chr6 582032 12 + 636262 CTGACAGTCACC -s Anc0.Anc0refChr3 183425 11 + 222631 GAAAT-TTTACC -s Anc1.Anc1refChr1 22784 11 + 69767 GAAAT-TTTACC -s Anc2.Anc2refChr1 98954 11 + 142988 GAAAT-TTTGCC -s mr.mrrefChr3 131846 12 + 181027 CTAACAGTCACC -s simCow_chr6.simCow.chr6 556892 11 + 602619 GAAAT-TTTGCC -s simDog_chr6.simDog.chr6 545433 11 + 593897 GAAAT-TTTGCC -s simHuman_chr6.simHuman.chr6 553976 11 + 601863 AAAAT-TTTACT -s simRat_chr6.simRat.chr6 57573 12 - 647215 CTAACAGTCACC - -a -s simMouse_chr6.simMouse.chr6 582044 9 + 636262 TTCAGCTAG -s Anc0.Anc0refChr3 183436 9 + 222631 TGCAGTAGG -s Anc1.Anc1refChr1 22795 9 + 69767 TGCAGTAGG -s Anc2.Anc2refChr1 98974 9 + 142988 TGCAATAGG -s mr.mrrefChr3 131858 9 + 181027 TTCAGCTAG -s simCow_chr6.simCow.chr6 556912 9 + 602619 GGCAATCGG -s simDog_chr6.simDog.chr6 545453 9 + 593897 TGCAATAGG -s simHuman_chr6.simHuman.chr6 553987 9 + 601863 TGCAGGGGG -s simRat_chr6.simRat.chr6 57585 9 - 647215 TACAGCCAG - -a -s simMouse_chr6.simMouse.chr6 582053 51 + 636262 GGCACAACCAGGGTAGTGCAGGGAAATGCTAGGCCGTGTATGCGCTCCGCA -s Anc0.Anc0refChr3 183448 51 + 222631 GCTACGACCAGAGTAGTGCAGGGAACGGCAAGATTGTGTCCACGCTTAATA -s Anc1.Anc1refChr1 22807 51 + 69767 GCTACGACCAGAGTAGTGCAGGGAACGGCAAGATTGTGTCCACGCTTAATA -s Anc2.Anc2refChr1 98986 51 + 142988 ACTACGACTGGAGTAGTGCAGGGAACGGCAAGATTGTGTCCATACTTAATA -s mr.mrrefChr3 131867 51 + 181027 GGCACAACCAGGGTAGTGCAGGGAAATGCAAGGCCGTGTATGCGCTCAGTA -s simCow_chr6.simCow.chr6 556924 51 + 602619 ACCATGGCTGGAATAGTGCATGGAAAGGCAAGAGTGTGTCCATACTTAATA -s simDog_chr6.simDog.chr6 545465 35 + 593897 ACTACCATT-GAGTTGTGCAGGGAACGGCAAGATTG--------------- -s simHuman_chr6.simHuman.chr6 553999 47 + 601863 GCTACGACCAGAGTAGTGCAGAGA----CAAGATTGCATCCACGCTTAATA -s simRat_chr6.simRat.chr6 57594 48 - 647215 GGCACAACCAGGGTAGTGGAGGGAAATGCAAGGCCATGTATG---TCAGTA - -a -s simMouse_chr6.simMouse.chr6 582104 34 + 636262 TACCTAACAGCTATCCTTATCCCCAATAAGGCAA -s Anc0.Anc0refChr3 183500 34 + 222631 TATCTGATAGCTGCCCTTATTCAAAATAAGACGA -s Anc1.Anc1refChr1 22859 34 + 69767 TATCTGATAGCTGCCCTTATTCAAAATAAGACGA -s Anc2.Anc2refChr1 99038 34 + 142988 TATGCGATAGCTGCTCTTACTCAAAATAAGAGGA -s mr.mrrefChr3 131919 34 + 181027 TACCTAACAGCTACCCTTATCCCAAATAAGGCAA -s simCow_chr6.simCow.chr6 556976 34 + 602619 TATGCGATAGCTGCTCTTACTCAAAATAAGAGGA -s simHuman_chr6.simHuman.chr6 554047 34 + 601863 TATCTGATATCTGCCCTTATTCAAAATAAGACGA -s simRat_chr6.simRat.chr6 57643 34 - 647215 TGCCTAAAAGTTACCCTTAGCCGAAATGAGGCAA - -a -s simMouse_chr6.simMouse.chr6 582138 5 + 636262 CCAGT -s Anc0.Anc0refChr3 183537 5 + 222631 TTGGT -s Anc1.Anc1refChr1 22896 5 + 69767 TTGGT -s Anc2.Anc2refChr1 99075 5 + 142988 TTGGT -s mr.mrrefChr3 131953 5 + 181027 CTGGT -s simCow_chr6.simCow.chr6 557013 2 + 602619 TT--- -s simDog_chr6.simDog.chr6 545500 4 + 593897 -TGGT -s simHuman_chr6.simHuman.chr6 554084 5 + 601863 TTGGT -s simRat_chr6.simRat.chr6 57677 5 - 647215 CTGGT - -a -s simMouse_chr6.simMouse.chr6 582143 107 + 636262 CCCCATTGAGAGCACACCGGATACTCTGGAAAGCTCTCAATCTCCCAAGAGACATCATGCATGAAGGTCAGCCCTCCTAAGGCCATATGAAAATTCAATGCTTTGTT -s Anc0.Anc0refChr3 183542 88 + 222631 CACCATTGAGTGC-------ATATTCCAGAAAG--------CTCCCATGAGACAAAGTGTATGA---TCAGTGCTCCTAGTGTCATATGGAATT-TGATCCTTTGCT -s Anc1.Anc1refChr1 22901 88 + 69767 CACCATTGAGTGC-------ATATTCCAGAAAG--------CTCCCATGAGACAAAGTGTATGA---TCAGTGCTCCTAGTGTCATATGGAATT-TGATCCTTTGCT -s Anc2.Anc2refChr1 99080 88 + 142988 CACCATTGAGTAG-------ATATTCCAGAAAG--------CTCCCATGAGACAAAGAGTATGG---TTAGTGTTCCTAGTGTCATATAGAATT-TGTTGATTTGCT -s mr.mrrefChr3 131958 106 + 181027 CCCCATTGAGAGCATACTGGATACTCCAGAAAGCTCCCAATCTCCCAAGAGACATCATGCATGAAGGTCAGCCCTCCTAAGGCCATATGAAAAT-CAATCCTTTGTT -s simCow_chr6.simCow.chr6 557015 79 + 602619 TACCATGGAGTAG-------ATACTCCAGAAAT--------CTCCCATGTGACAAAGGGTATGG---C---TGATCCTAGTGTTT------GTT-TGCTGTTTTGCT -s simDog_chr6.simDog.chr6 545513 88 + 593897 CACCATTGAGCAG-------ATATTCCGGAAGG--------CTCCCATGAGACAGAGAGTATGG---TTAGTATTCATTGTGTCATATAGAATT-TGTTGATGTGCT -s simHuman_chr6.simHuman.chr6 554089 88 + 601863 CACCATAAAGTGC-------ATATTCCAGAAAC--------CTCCCATGATACAAGGTATATGA---TCAGTGCTCCTAGAGTCATATGGAATT-TGATCCTTTGCT -s simRat_chr6.simRat.chr6 57682 106 - 647215 CCCCATTGAGAGCATACTGGATACTCCAGAAAGCTCCCAAGCCCCCAAGAGACATCATGCAGGAAGATCAGCCCTTCTAAGGCCATATGAAAAT-CAATCCTTCGTT - -a -s simMouse_chr6.simMouse.chr6 582250 32 + 636262 GAATATGTACACTAACTGGCTCTTTGATTGTT -s Anc0.Anc0refChr3 183630 26 + 222631 GAATATGCAAATTAGTTGGCTCT------ACT -s Anc1.Anc1refChr1 22989 32 + 69767 GAATATGCAAATTAGTTGGCTCTGTCATTACT -s Anc2.Anc2refChr1 99168 26 + 142988 AAACAGGCAAATGAGTTGGCTCT------ACC -s mr.mrrefChr3 132064 32 + 181027 GAATATGCACACTAACTGGCTCTTTGATTGTT -s simCow_chr6.simCow.chr6 557094 26 + 602619 AAACGGGCAAATCAGCTGGCTCT------ACC -s simDog_chr6.simDog.chr6 545601 26 + 593897 AAACAGGCAGATGGGTTGGCTCC------ATC -s simHuman_chr6.simHuman.chr6 554178 24 + 601863 GAATATGCAAATTA--------TGTCATTACT -s simRat_chr6.simRat.chr6 57788 32 - 647215 GAATATGCAGACCAACTTGCTCTCTGATTGTC - -a -s simMouse_chr6.simMouse.chr6 582282 7 + 636262 GTGCCAG -s Anc0.Anc0refChr3 183656 7 + 222631 TCCCCAG -s Anc1.Anc1refChr1 23021 7 + 69767 TCCCCAG -s Anc2.Anc2refChr1 99194 7 + 142988 TCCCTGG -s mr.mrrefChr3 132096 7 + 181027 GTCCCAG -s simCow_chr6.simCow.chr6 557120 7 + 602619 ACCTGGT -s simDog_chr6.simDog.chr6 545633 7 + 593897 TGCCTGG -s simHuman_chr6.simHuman.chr6 554202 7 + 601863 TCCCCAG -s simRat_chr6.simRat.chr6 57820 7 - 647215 ATCCCAG - -a -s simMouse_chr6.simMouse.chr6 582289 11 + 636262 TGTCTGGTATT -s Anc0.Anc0refChr3 183663 11 + 222631 CATCTCTTATT -s Anc1.Anc1refChr1 23028 11 + 69767 CATCTCTTATT -s Anc2.Anc2refChr1 99201 11 + 142988 TATCTCTTATT -s mr.mrrefChr3 132103 11 + 181027 CATCTGGTATT -s simCow_chr6.simCow.chr6 557127 11 + 602619 AATACCTTATT -s simDog_chr6.simDog.chr6 545641 11 + 593897 TGTCTCTTATT -s simHuman_chr6.simHuman.chr6 554209 11 + 601863 CATTTCTTATT -s simRat_chr6.simRat.chr6 57827 11 - 647215 CATCTGGTATT - -a -s simMouse_chr6.simMouse.chr6 582300 398 + 636262 AATACACTGAGGAGACTATAGTATATAGTCTTGCCAGTTATAGTCTTGCTAGCTGTTCAGGTGGCCAAGTGCCTGTCTAGGGTATTGCTGGTATCAATGCCAGTTTACGGGTTAGCCGCAAGCCCCCCTTTGTAATCAGCCGAACTGAAGGCTACATAGGGGTACTCATTGATGGGGTTCCCGCACTGGGCACCAGTGAACCCTATTACATGTTTGCAAGCTGGGTTGAATTCCGTTTGTCGCTGCATCCTGATAATGCTGATAGCCGCCTTACATTGCAAGGTGATTTCTGCGTCAGGAGTGAACATATTATTCTGAACGACATTTCAGTGAATTGATATTTATTTTGTGAAGAATAAAGGCATTTCTCTATCTGATAGTGTTCTGCATTGCATTCT -s Anc0.Anc0refChr3 183674 382 + 222631 ATTATTCTGAGGAGACTATAATATATG-TC--------------CCTGCCAGTAGACCAGGTCGCCAAGTGTCTGGCTAGGGTATTGCCGGAATCAATGCTAGCTTACGGGTTAGCCGCAAGCCCCCTTTTGTAATTAGCCGAACTGAAGGCTACATAGGGGTACTGATTGATGGTGTTCCCACACTGGGCACTAGTGAACCCTATTGCATGTTTGCCAGCTGGGTTGAGTTCCGTTTGTCATTGCACCCTGATAATGCTGATAGCCGCCTTACACTGCAAGGTTAGAACTGCATCCTGTGTGAGCCTGTTAATCTAAATGACGGTTCAGTAGATTTGTATCTAACTTGTGAC-AATATAGACAATATTCTCTCTGTTAATGTTCTGCAATACACTCT -s Anc1.Anc1refChr1 23039 384 + 69767 ATTATTCTGAGGAGACTATAATATATGGTC--------------CCTGCCAGTAGACCAGGTCGCCAAGTGTCTGGCTAGGGTATTGCCGGAATCAATGCTAGCTTACGGGTTAGCCGCAAGCCCCCTTTTGTAATTAGCCGAACTGAAGGCTACATAGGGGTACTGATTGATGGTGTTCCCACACTGGGCACTAGTGAACCCTATTGCATGTTTGCCAGCTGGGTTGAGTTCCGTTTGTCATTGCACCCTGATAATGCTGATAGCCGCCTTACACTGCAAGGTTAGAACTGCATCCTGTGTGAGCCTGTTAATCTAAATGACGGTTCAGTAGATTTGTATCTAACTTGTGACCAATATAGACAATATTCTCTCTGTTAATGTTCTGCAATACACTCT -s Anc2.Anc2refChr1 99216 382 + 142988 ATCATTCTGAGGAGACTATAATGTATG-TC--------------CCTGCCAGTAGACCAGGTCGCCAAGTGTCTGGCTAGGGAATTGCCGGAATCAATGCTAGCTTACGGGTTAGCCGCAAGCCCCCTTTTGTTATTAGCCGTACTGAAGGCTACATAGGGGTACTGATTGATGGTGTTCCCACACTGGGCACTAGTGAACCCTATTGCATGTTTGCCAGCTGGGTTGAGTTCCGTTTGTCATTGCACCCTGATAATGCTGATAGCCGTCTTACACTGCAAGGTTAGAACTGCATCCTGTGTGTGCCTGTTAATCTAAATGACGGTTCGGTAGATTTGTATCTAACTTGTGAC-AATATAGACAATATTCTCTCTGTTAATGTTCCGCAATACACTCT -s mr.mrrefChr3 132114 398 + 181027 ATTACACTGAGGAGACTATAGTATATAGTCTTGCCAGTTATAGTCTTGCCAGCTGTTCAGGTGGCCAAGTGTCTGTCTAGGGTATTGCTGGTATCAATGCCAGTTTACGGGTTAGCCGCAAGCCCCCCTTTGTAATTAGCCGAACTGAAGGCTACATAGGGGTACTGATTGATGGTGTTCCCACACTGGGCACCAGTGAACCCTATTGCATGTTTGCAAGCTGGGTTGAATTCCGTTTGTCACTGCACCCTGATAATGCTGATAGCCGCCTTACATTGCAAGGTGATTTCTGCGTCAGGAGTGAACATATTATTCTGAATGACATTTCAGTAAATTTATATCTATTTTGTGAAGAATAAAGACATTTTTCTATCTGATAGTGTTCTGCATTGCACTCT -s simCow_chr6.simCow.chr6 557142 376 + 602619 AT---TCTGAGGAGACTATAATGCATG-TC--------------TCTGCCAGTTGACCAGGTTGCCAAGTGTCTGATCAGGGAATTGCCGGGATCAATGCCAGCTTAAGGGTTAGCCGCAAGCCCCCTTTTGTGATTAGCCATACTGAAGGCTACATAGGGGTACTGATTGATGGTGTTCCCACACTGGGCACTAGTGAACCATATTGCATGTTTGCCAGCTGGGTTG---TCTGTTTGTCATTGCACCCTGATAATGCTGATAGCCGTCTTACACTACAGGGTTAGAGCTGCATCTTGGGTGTGCCTATTAATCTAAATGACAGTTCTGTAGATTCTTATCTACCTTGTGAA-CACACAAACAGTATTCCCTCTGTTATTATGCCGCATTACGCTCT -s simDog_chr6.simDog.chr6 545656 375 + 593897 ATCATTCTGAGGAGACTATAGTGTATA-CC--------------CCTGCCAGCAGACCATGTCACCTTGTGTCTAGCTAGGGAATGGCTGGAATCAATGCTAGCTTACGGGTTAGCCGCAAGCCCCCCTTTGTTATTAGCCGTACTGAAGGCTACATCGGGGTGCTGGTTGATGGTGTCCCCACACTGGGCACTAGTGAACCCTATTGTATGTTTGCAAGCTGGGTTGAGTTCCGTCTGTCATTGCACCCTGATAATGCTGATAGCCGTCTTTCACTGCAAGGTCAGAACTG--TGCAGTGT--GCCTGTTAAACTAGATGACGGTTTGGTAGATTTGTATCTAACTTGTGAC-AATATAGACAATGCTCTCTCTGTTAATGGTC---AATACACTCT -s simHuman_chr6.simHuman.chr6 554220 379 + 601863 ATTATTCTGAGGTGACTATAATATATGGTC--------------CCAGCCAGTAGACCAGGCCGCCAAATTTCTGGCTAGGGTATTGCCGGAATCAATGCGAGCTTACGGGTTAGTCGCAAGCCCCCTTTTGTAATTAGCCGAACTGAAGGTTACATAGGGGTACTGATTGATGGTGTTCCCAGACTGGGTACTAGTGAACCCTATTGCATGTTTGCCAGCTGGGTTGAGTTCCGTTTGTCATTGCACCCTGATAATGCTGATAGCCGCCTCACACTGCGAGGTTAGAACTGCTTCCTGTGTGAGCCTGTTAATTTCAATGAC-CTTCAGTAGATTTGCTTCTAACTTGTGACCAATCTACACAATAT----TCTATTAATGTTCTGCAATACACTCT -s simRat_chr6.simRat.chr6 57838 395 - 647215 ATTACACTGAGGAGACTATAGCATATAGTCTTGCCAGTTATAGTCTTGCCAGCTGTTCAGA---CCAAGTGTCTGTCTAGGGTATTGCTGGTATCATTGCCAGTTTACGGGTGAGCCGCAAGCCCCCCTTTGTAATTAGTCGAACTGAAGGCTACATAGGGGTACTGATTGATGGTGTTCCCACACTGGGCGCCAGTGAACCCTATTGCATGTTCACTAGCTGGGTTGAATTCTGTTTGTCACTGCACCCTGACAATGCTGATAGCCGCCTTACATTGCAAGGTGATTTCTGCATCAAGAATGAACATATTAGTCTAAATGACATTGCTGTAAATTTATACCTATTTTGTGAAGAATACAGACATTTTTCTAACAGATGGTGTTCTGCATTGCACTAT - -a -s simMouse_chr6.simMouse.chr6 582698 11 + 636262 CGACTCCATCC -s Anc0.Anc0refChr3 184058 11 + 222631 CAACTTCTTCC -s Anc1.Anc1refChr1 23425 11 + 69767 CAACTTCTTCC -s Anc2.Anc2refChr1 99600 11 + 142988 CAACTTCTTCC -s mr.mrrefChr3 132512 11 + 181027 CGACTTCATCC -s simCow_chr6.simCow.chr6 557520 11 + 602619 CAATTTCTTCT -s simDog_chr6.simDog.chr6 546033 11 + 593897 TAACTTCTTCC -s simHuman_chr6.simHuman.chr6 554601 11 + 601863 CCACTTCTTCC -s simRat_chr6.simRat.chr6 58233 11 - 647215 CAACTTCATCC - -a -s simMouse_chr6.simMouse.chr6 582709 195 + 636262 CAAGGGTACAAAGAAGCGGGTTGGGTTTTTCAGCAGCAGTATGAGAGAGCTTGTTGGATGAAATCACCTCTAGAGGATGGAATATCAGTGCTAAGGTCTATTGAATTTTTCAGTTCAAGGTGGAATAAATTGGTTCCTGAGGCCTCCATTAGAACAAGTAGGAGTTTACCCACCAGGTATGTATTGACTCAAATC -s Anc0.Anc0refChr3 184069 195 + 222631 TAAGGGTATAAGGAAGCAGGTTGGGTTTTTCAGCAGCAGTATGAGAGAGCTTGTTGGATGAAGTCGCCTCTAGAAGAAGGGATTTCAGTGTTAAGGTCTATTGAATTTTTCAGTTCAAGGTGGAACAAATTAGTTCCGGAGGCCTCCATTAGTACAAGTAGGAGTTTACCTATTAGGTATGTATTGTCTCAAATG -s Anc1.Anc1refChr1 23436 195 + 69767 TAAGGGTATAAGGAAGCAGGTTGGGTTTTTCAGCAGCAGTATGAGAGAGCTTGTTGGATGAAGTCGCCTCTAGAAGAAGGGATTTCAGTGTTAAGGTCTATTGAATTTTTCAGTTCAAGGTGGAACAAATTAGTTCCGGAGGCCTCCATTAGTACAAGTAGGAGTTTACCTATTAGGTATGTATTGTCTCAAATG -s Anc2.Anc2refChr1 99611 195 + 142988 TAAGGGTATAAGGAAGCTGGTTGGGTTTTTCAGCAGCAATATGAGAGAGCTTGTTGGATGAAGTCGCCTTTAGAAGAAGGGATTTCAGTGTTAAGGTCTATTGAATTTTTCAGTTCAAGGTGGAACAAATTAGTTCCGGAGGCCTCCATAAGTACAAGTAGGAGTTTACCTATTAGGTATGTGTTGTCTCAAATG -s mr.mrrefChr3 132523 195 + 181027 CAAGGGTACAAAGAAGCAGGTTGGGTTTTTCAGCAGCAGTATGAGAGAGCTTGTTGGATGAAATCACCTCTAGAAGAAGGAATATCAGTGTTAAGGTCTATTGAATTTTTCAGTTCAAGGTGGAACAAATTGGTTCCTGAGGCCTCCATTAGAACAAGTAGGAGTTTACCCACCAGGTATGTATTGACTCAAATC -s simCow_chr6.simCow.chr6 557531 195 + 602619 TAAGGGTATAAGGAGGCTGGATGGGTATTTCAGCAGCAATATGAGAGAGCTTGTTGGATGAAGTCGCCTTTAGAAGAAGGGATTTCTGTGTTAAGGTCTATTGAATTTTTCAGTTCAAGGTGGAACAAATTGGTTCCGGAGGCCTCCATAAGTACAAGTAGGAGTTTACCTATTAGGTATGTGTTGTCTCATAGA -s simDog_chr6.simDog.chr6 546045 188 + 593897 TAAGGGTACAAGGAAGCTGGTTGGGTTTTTCAGCAGCAATATGAGAGGGCTTGTTGGATGACGTCACCTTTAGAAGAAGGGATTTCAGTGTTAAGGTCTATGGAATTTTTCAGTTCAAGGTGGAACAAATTAGTTCCGGAGGCCTCCATAAGTACAAGTAGGAGTGTACCAATTAGGTATAT-------CAAATG -s simHuman_chr6.simHuman.chr6 554612 195 + 601863 TAAGGGTATAAGGAAGCAGGTTGGGTTTTTCAGCAGCAGTATGAGAGAGCTTGTTGGATGAAGTCGCCTCTAGAAGAAGGTATTTCAGTGTTAAGGTCTATTGAATTTTTCAGTTCAAGGTGGAACAAATTAGTTCCGGAAGCCTCCATTAGTACTAGTAGAAGTTTACCTATAAGGTATGTATTATCTCAAAAG -s simRat_chr6.simRat.chr6 58244 195 - 647215 CAAGGGTACAAAGAAGCAGGTTGGGTTTTTCAGCAGCAGTATGAGAGAGCTTGTTGGATGAAATCACCTCTAGAAGAAGGGATATCAGTGTTAAGATCTATTGAATTTTTTAGTTCAAGGTGGAACAAATTGGTACCTGAGGCCTCCATTAGAACAAGCAGGAGTTTACCCACCAGGTATGTATTGACTCAATTT - -a -s simMouse_chr6.simMouse.chr6 582904 9 + 636262 TCTATAAAA -s Anc0.Anc0refChr3 184264 9 + 222631 TCCACAGAG -s Anc1.Anc1refChr1 23631 9 + 69767 TCCACAGAG -s Anc2.Anc2refChr1 99806 9 + 142988 TCCACAGAA -s mr.mrrefChr3 132718 9 + 181027 TCTATAAAG -s simCow_chr6.simCow.chr6 557726 9 + 602619 TCCATAGAA -s simDog_chr6.simDog.chr6 546237 9 + 593897 TCCACAGAA -s simHuman_chr6.simHuman.chr6 554807 9 + 601863 CCCACAGGG -s simRat_chr6.simRat.chr6 58439 9 - 647215 TCTATAAAG - -a -s simMouse_chr6.simMouse.chr6 582913 1 + 636262 T -s Anc0.Anc0refChr3 184273 1 + 222631 A -s Anc1.Anc1refChr1 23640 1 + 69767 A -s Anc2.Anc2refChr1 99824 1 + 142988 A -s mr.mrrefChr3 132727 1 + 181027 A -s simCow_chr6.simCow.chr6 557748 1 + 602619 A -s simDog_chr6.simDog.chr6 546255 1 + 593897 A -s simHuman_chr6.simHuman.chr6 554816 1 + 601863 A -s simRat_chr6.simRat.chr6 58448 1 - 647215 A - -a -s simMouse_chr6.simMouse.chr6 582914 10 + 636262 GTGAGTGTAC -s Anc0.Anc0refChr3 184281 7 + 222631 GAG---ATAA -s Anc1.Anc1refChr1 23648 7 + 69767 GAG---ATAA -s Anc2.Anc2refChr1 99832 7 + 142988 GAG---ATAA -s mr.mrrefChr3 132728 7 + 181027 GAG---GTAC -s simCow_chr6.simCow.chr6 557756 7 + 602619 AAG---ATCA -s simDog_chr6.simDog.chr6 546263 7 + 593897 GAG---ATAA -s simHuman_chr6.simHuman.chr6 554824 7 + 601863 GAG---ACAA -s simRat_chr6.simRat.chr6 58449 7 - 647215 GAG---GTAC - -a -s simMouse_chr6.simMouse.chr6 582924 5 + 636262 CCTGG -s Anc0.Anc0refChr3 184288 5 + 222631 TCACT -s Anc1.Anc1refChr1 23655 5 + 69767 TCACT -s Anc2.Anc2refChr1 99839 5 + 142988 TCACT -s mr.mrrefChr3 132735 5 + 181027 CCTGG -s simCow_chr6.simCow.chr6 557763 5 + 602619 GCACT -s simDog_chr6.simDog.chr6 546271 5 + 593897 TCACT -s simHuman_chr6.simHuman.chr6 554831 5 + 601863 TCACT -s simRat_chr6.simRat.chr6 58456 5 - 647215 CATGG - -a -s simMouse_chr6.simMouse.chr6 582929 15 + 636262 AGTCATGCTTGTATT -s Anc0.Anc0refChr3 184293 12 + 222631 ---CCTGCATAGATT -s Anc1.Anc1refChr1 23660 15 + 69767 ATTCCTGCATAGATT -s Anc2.Anc2refChr1 99844 12 + 142988 ---CCTGCATAGATT -s mr.mrrefChr3 132740 15 + 181027 AGTCATGCTTGTATT -s simCow_chr6.simCow.chr6 557768 12 + 602619 ---CCTACAGTGATC -s simDog_chr6.simDog.chr6 546276 12 + 593897 ---TCTGCGTAGTTT -s simHuman_chr6.simHuman.chr6 554836 15 + 601863 ATTCCTGCATAGATT -s simRat_chr6.simRat.chr6 58462 15 - 647215 AGTAATGCTTGTATT - -a -s simMouse_chr6.simMouse.chr6 582944 34 + 636262 GGTTCACCCGTACAGTCCCTCAACCAATATCTGG -s Anc0.Anc0refChr3 184309 32 + 222631 A-TTTATCTGTACAGTCCCCCAACCTAC-TCTGG -s Anc1.Anc1refChr1 23679 32 + 69767 A-TTTATCTGTACAGTCCCCCAACCTAC-TCTGG -s Anc2.Anc2refChr1 99860 32 + 142988 A-CTTATCTGTACAGTCCCCCAACCTAC-TCTGG -s mr.mrrefChr3 132755 33 + 181027 A-TTCACCTGTACAGTCCCTCAACCAATATCTGG -s simCow_chr6.simCow.chr6 557784 31 + 602619 A-GTGATCTGTAGAGTCCCTCAACC-AC-CCTGG -s simDog_chr6.simDog.chr6 546292 32 + 593897 A-CTTATATGTACAGCCCCCCAACTTGC-TCTGG -s simHuman_chr6.simHuman.chr6 554855 32 + 601863 A-TTTAGCTGTACAGTCCCCCAACCTAA-TCTGG -s simRat_chr6.simRat.chr6 58477 33 - 647215 A-TTCACCTGTACAGCCCCTCACCCAATATCTGG - -a -s simMouse_chr6.simMouse.chr6 582978 2 + 636262 CT -s Anc0.Anc0refChr3 184341 2 + 222631 CT -s Anc1.Anc1refChr1 23711 2 + 69767 CT -s Anc2.Anc2refChr1 99892 2 + 142988 AT -s mr.mrrefChr3 132788 2 + 181027 CT -s simCow_chr6.simCow.chr6 557815 2 + 602619 AT -s simDog_chr6.simDog.chr6 546325 2 + 593897 AT -s simHuman_chr6.simHuman.chr6 554887 2 + 601863 CT -s simRat_chr6.simRat.chr6 58510 1 - 647215 T- - -a -s simMouse_chr6.simMouse.chr6 582980 43 + 636262 AAAGGAGTAAACCTCCCCTCTTTTCAAACAGCATACCGTACTA -s Anc0.Anc0refChr3 184344 43 + 222631 AAATGACTGAGCCTCCCCTTTTTGCAAGCAGCACATCACGCTA -s Anc1.Anc1refChr1 23714 43 + 69767 AAATGACTGAGCCTCCCCTTTTTGCAAGCAGCACATCACGCTA -s Anc2.Anc2refChr1 99895 43 + 142988 AAATGACTGAGCCTCTCCTTTTTGAAAGCAGCACATCACGCTA -s mr.mrrefChr3 132790 43 + 181027 AAAGGAGTAAACCTCCCCTCTTTTCAAGCAGCATACCATACTA -s simCow_chr6.simCow.chr6 557818 34 + 602619 AACGGAGTGTGCCTC---------AAAGCAGCACATCACACTA -s simDog_chr6.simDog.chr6 546328 32 + 593897 AAATGACTGAGCCCATCCTTTTTGAAAG-----------GCTA -s simHuman_chr6.simHuman.chr6 554890 43 + 601863 AAATGACTTACCCTCCCCTTTTTCCAAGCAGCACATCACGCTA -s simRat_chr6.simRat.chr6 58511 34 - 647215 ---------AACCCGCCCTCTTTTCAAGCAGCATACCATACTA - -a -s simMouse_chr6.simMouse.chr6 583023 94 + 636262 ATGTGATGGCTCTCTTGCCTCTTTAGCAACAAGGGCTGCAAGTGACTCCCTAGATCTTTCATGGCTATGGACAAGGGTTATTTTTACCCCTACT -s Anc0.Anc0refChr3 184387 51 + 222631 ATCTAAATG--------------------------------------GCCGAAATCTTTCTTGGCAATATATCA-----AATTTGACACCTTCT -s Anc1.Anc1refChr1 23757 72 + 69767 ATCTAAATGTCCTGTTTTCCCCT-----------------GGTGTTCGCCGAAATCTTTCTTGGCAATATATCA-----AATTTGACACCTTCT -s Anc2.Anc2refChr1 99938 51 + 142988 ATCGAAATG--------------------------------------GCGGAACTCTAGCTTTGCAACACATCA-----CACTAGTCTCCTTTT -s mr.mrrefChr3 132833 94 + 181027 ATGTGATGGCTCTCTTGTCTCTTTAGCAACAAGGGCTGCAAGTGATCCCCTAGATCTTTCATGGCTATGTACAAGGGTTATTTTTACACCTACT -s simCow_chr6.simCow.chr6 557852 51 + 602619 ATCAAAATG--------------------------------------TCTGTTTTTCCCCTTCACTACAAGAAG-----TACCAGTGTTCCCTA -s simDog_chr6.simDog.chr6 546400 51 + 593897 GTAGAGAGG--------------------------------------GTGGAACTCTAGCTTTGCAACACATCA-----CACTAATCTCCTTTT -s simHuman_chr6.simHuman.chr6 554933 72 + 601863 ATCTTAGTGTCCTGTTTTCCCCT-----------------GGTGTTCGCCGAAATCTTTCTTGGACATTTATGA-----AATGTGACACCTGCT -s simRat_chr6.simRat.chr6 58545 94 - 647215 ATGTGATGGCTTTCTTGTCTCTTTATCAACAAGGGCTACCAGTGATCTCCTAGAGCTTTCGCGGCTATCTACAAGGGGCATTTTAACACCTACT - -a -s simMouse_chr6.simMouse.chr6 583117 28 + 636262 TACTCACCTTCATGGCAGCTTCCAACCT -s Anc0.Anc0refChr3 184449 28 + 222631 TAGCCACCTTCATGGCAGCTTCTAAGCT -s Anc1.Anc1refChr1 23840 28 + 69767 TAGCCACCTTCATGGCAGCTTCTAAGCT -s Anc2.Anc2refChr1 100000 28 + 142988 TAACAACCTTCATGGCATCTTCTAAGCT -s mr.mrrefChr3 132927 28 + 181027 TAGTCACCTTCATGGCAGCTTCTAACCT -s simCow_chr6.simCow.chr6 557917 28 + 602619 TAACAACCTTAAGGGCATCTTCTAACCT -s simDog_chr6.simDog.chr6 546462 23 + 593897 T-----CCATCATGGGATCTTCTAAGCT -s simHuman_chr6.simHuman.chr6 555016 28 + 601863 TAGCCACTTTCATGGCAGCTTCTAAACT -s simRat_chr6.simRat.chr6 58639 28 - 647215 TAGTCACCTTCATGACAGTTTCTAACCT - -a -s simMouse_chr6.simMouse.chr6 583145 23 + 636262 CTAGTTCTTTGTACCTCTTTGCA -s Anc0.Anc0refChr3 184477 22 + 222631 CTATTT-CCTGTATCTTCTTGTG -s Anc1.Anc1refChr1 23868 22 + 69767 CTATTT-CCTGTATCTTCTTGTG -s Anc2.Anc2refChr1 100028 22 + 142988 CCATTT-CCTGTATCTTCTTGTG -s mr.mrrefChr3 132955 22 + 181027 CTAGTT-TTTGTACCTCTTTGCA -s simCow_chr6.simCow.chr6 557945 22 + 602619 GCACTT-CATGTGTGTTTTCGTG -s simDog_chr6.simDog.chr6 546485 22 + 593897 CCATTT-CCTGTACCTTCTTGTG -s simHuman_chr6.simHuman.chr6 555051 22 + 601863 CTATTA-CCTGTATCTTGTTATG -s simRat_chr6.simRat.chr6 58667 22 - 647215 GTACTT-TTTGTACCTCTTTGCA - -a -s simMouse_chr6.simMouse.chr6 583168 19 + 636262 AAGTTAGTCCCTACAAATT -s Anc0.Anc0refChr3 184500 19 + 222631 AAGATAGACCCTGCCTATT -s Anc1.Anc1refChr1 23891 19 + 69767 AAGATAGACCCTGCCTATT -s Anc2.Anc2refChr1 100051 19 + 142988 AAGATAGATCCTGCCTGTT -s mr.mrrefChr3 132977 19 + 181027 AAGTTAGTCCCTACCAATT -s simCow_chr6.simCow.chr6 557968 19 + 602619 AAGCTAGGTCCTGCCTGTT -s simDog_chr6.simDog.chr6 546508 19 + 593897 TAGATAGATCCTGTCTGTC -s simHuman_chr6.simHuman.chr6 555074 19 + 601863 AAGATAGACCTTGCCTATT -s simRat_chr6.simRat.chr6 58689 19 - 647215 AGGTTAGTGCCAACCAATG - -a -s simMouse_chr6.simMouse.chr6 583187 24 + 636262 GACGACTCTTAGACTACAGAACCT -s Anc0.Anc0refChr3 184519 23 + 222631 CAA-ACTTTCAGACTTTAGAGCCC -s Anc1.Anc1refChr1 23910 23 + 69767 CAA-ACTTTCAGACTTTAGAGCCC -s Anc2.Anc2refChr1 100070 23 + 142988 CAA-ACTTTCAGACTTTAGAGCCC -s mr.mrrefChr3 132996 24 + 181027 GACAACTCTTAGACTACAGAACCT -s simCow_chr6.simCow.chr6 557987 9 + 602619 ---------------TTAGAGCCT -s simDog_chr6.simDog.chr6 546529 23 + 593897 CAA-ACTTTCAGACTTTAAAACCC -s simHuman_chr6.simHuman.chr6 555093 23 + 601863 CAT-ACATTCAGACTTTCGAGCCC -s simRat_chr6.simRat.chr6 58708 24 - 647215 GGCAACCCTTAGACCACAGAACCT - -a -s simMouse_chr6.simMouse.chr6 583211 1 + 636262 T -s Anc0.Anc0refChr3 184542 1 + 222631 C -s Anc1.Anc1refChr1 23933 1 + 69767 C -s Anc2.Anc2refChr1 100096 1 + 142988 C -s mr.mrrefChr3 133020 1 + 181027 T -s simCow_chr6.simCow.chr6 557999 1 + 602619 C -s simDog_chr6.simDog.chr6 546555 1 + 593897 C -s simHuman_chr6.simHuman.chr6 555116 1 + 601863 C -s simRat_chr6.simRat.chr6 58732 1 - 647215 T - -a -s simMouse_chr6.simMouse.chr6 583212 2 + 636262 GT -s Anc0.Anc0refChr3 184543 1 + 222631 -T -s Anc1.Anc1refChr1 23934 1 + 69767 -T -s Anc2.Anc2refChr1 100097 1 + 142988 -T -s mr.mrrefChr3 133021 2 + 181027 GT -s simCow_chr6.simCow.chr6 558000 1 + 602619 -T -s simDog_chr6.simDog.chr6 546556 1 + 593897 -T -s simHuman_chr6.simHuman.chr6 555117 1 + 601863 -T -s simRat_chr6.simRat.chr6 58735 2 - 647215 GT - -a -s simMouse_chr6.simMouse.chr6 583214 20 + 636262 CCTTTACACCCATGTCACCT -s Anc0.Anc0refChr3 184544 20 + 222631 ACCTTACACCCATGTGATCT -s Anc1.Anc1refChr1 23935 20 + 69767 ACCTTACACCCATGTGATCT -s Anc2.Anc2refChr1 100098 20 + 142988 ACCTTACACCCATGTGATTT -s mr.mrrefChr3 133023 20 + 181027 CCTTTACACCCATGTCACCT -s simCow_chr6.simCow.chr6 558006 20 + 602619 ACCTTACACCCATGTGATTT -s simDog_chr6.simDog.chr6 546557 20 + 593897 ATATCACACCCATGTGATTT -s simHuman_chr6.simHuman.chr6 555118 20 + 601863 ACCTTACACCCATGTGATCT -s simRat_chr6.simRat.chr6 58737 20 - 647215 CCTTTACACCCATGTAGCAT - -a -s simMouse_chr6.simMouse.chr6 583234 15 + 636262 GTAGTTGAACCTTGG -s Anc0.Anc0refChr3 184564 13 + 222631 TTAG-TGAAAC-TTG -s Anc1.Anc1refChr1 23955 13 + 69767 TTAG-TGAAAC-TTG -s Anc2.Anc2refChr1 100122 13 + 142988 TTAG-TGAAAC-TTG -s mr.mrrefChr3 133043 14 + 181027 TTAGTTGAATC-TGG -s simCow_chr6.simCow.chr6 558030 11 + 602619 TCAA-TGAAAC-T-- -s simDog_chr6.simDog.chr6 546581 13 + 593897 TTGG-TTAAAC-CTG -s simHuman_chr6.simHuman.chr6 555138 13 + 601863 TTAG-TGAAAT-TAG -s simRat_chr6.simRat.chr6 58757 11 - 647215 TTAGTTGAATC---- - -a -s simMouse_chr6.simMouse.chr6 583249 25 + 636262 CAATGAAGTCACCAAGGGGGGGCAG -s Anc0.Anc0refChr3 184577 25 + 222631 CAATGAAGCCTAAAAGGGGGGGCAG -s Anc1.Anc1refChr1 23968 25 + 69767 CAATGAAGCCTAAAAGGGGGGGCAG -s Anc2.Anc2refChr1 100135 25 + 142988 CAATGAAGCCTAAAAGGGGGGGCAG -s mr.mrrefChr3 133057 25 + 181027 CAATGAAGTCACAAAGGGGGGGCAG -s simCow_chr6.simCow.chr6 558041 25 + 602619 CAATGAAGCCTTAAAGAGGTGGCAC -s simDog_chr6.simDog.chr6 546596 25 + 593897 CAATGAAGCCTAGAAGGGGGGGCAG -s simHuman_chr6.simHuman.chr6 555151 25 + 601863 CAATGAACCTTAAACAGAACAGTAG -s simRat_chr6.simRat.chr6 58768 23 - 647215 --ATGAAGTCACAAAGGGTGGGTAG - -a -s simMouse_chr6.simMouse.chr6 583274 8 + 636262 CTAGCAAT -s Anc0.Anc0refChr3 184605 8 + 222631 CAAACAAT -s Anc1.Anc1refChr1 23996 8 + 69767 CAAACAAT -s Anc2.Anc2refChr1 100167 8 + 142988 CAAACAAT -s mr.mrrefChr3 133082 8 + 181027 CTAGCAAT -s simCow_chr6.simCow.chr6 558072 8 + 602619 CAAACAAT -s simDog_chr6.simDog.chr6 546628 8 + 593897 CAAATAAA -s simHuman_chr6.simHuman.chr6 555179 8 + 601863 CAAACAAT -s simRat_chr6.simRat.chr6 58791 8 - 647215 CTAGCAAT - -a -s simMouse_chr6.simMouse.chr6 583282 7 + 636262 GAAGTCA -s Anc0.Anc0refChr3 184620 7 + 222631 CAACCCC -s Anc1.Anc1refChr1 24011 7 + 69767 CAACCCC -s Anc2.Anc2refChr1 100182 7 + 142988 CAACCCC -s mr.mrrefChr3 133090 7 + 181027 GAAGTCA -s simCow_chr6.simCow.chr6 558087 7 + 602619 CAACCCC -s simDog_chr6.simDog.chr6 546646 7 + 593897 AAACCCC -s simHuman_chr6.simHuman.chr6 555194 7 + 601863 CAACCCC -s simRat_chr6.simRat.chr6 58799 7 - 647215 GAAGTCA - -a -s simMouse_chr6.simMouse.chr6 583289 31 + 636262 CAAAGGAGGGGTAGCAGCGACTCCGCCCCTC -s Anc0.Anc0refChr3 184627 19 + 222631 CAA-----------CATCCACT-AGCCCCTC -s Anc1.Anc1refChr1 24018 19 + 69767 CAA-----------CATCCACT-AGCCCCTC -s Anc2.Anc2refChr1 100222 19 + 142988 CAA-----------CATCCACC-ACCCCCTC -s mr.mrrefChr3 133097 31 + 181027 CAAAGGAGGGGTAGCAGCGACTCAGCCCCTC -s simCow_chr6.simCow.chr6 558128 18 + 602619 TAA-----------T-TCTACC-ACCCCCTC -s simDog_chr6.simDog.chr6 546686 19 + 593897 CAA-----------CATCCACC-ACCCCCTC -s simHuman_chr6.simHuman.chr6 555201 19 + 601863 CAA-----------CATCCACT-AGTGTCTC -s simRat_chr6.simRat.chr6 58806 31 - 647215 CAAAGGGGGGGGGGTAGGGACTCAGCCCCTG - -a -s simMouse_chr6.simMouse.chr6 583320 21 + 636262 AAATTAACTGTTACAGCTTCC -s Anc0.Anc0refChr3 184646 21 + 222631 TAATTAACTATTACAGTCTCC -s Anc1.Anc1refChr1 24037 21 + 69767 TAATTAACTATTACAGTCTCC -s Anc2.Anc2refChr1 100241 21 + 142988 TAATTACTTATTACAGTCTCC -s mr.mrrefChr3 133128 21 + 181027 AAATTAACTATTACAGCCTCC -s simCow_chr6.simCow.chr6 558146 17 + 602619 TAATCA----TTCCAGTGTCC -s simDog_chr6.simDog.chr6 546705 21 + 593897 TAGTTACTTATTACAAGCCCC -s simHuman_chr6.simHuman.chr6 555220 21 + 601863 TAATTAACTATTACAGTCTTC -s simRat_chr6.simRat.chr6 58838 21 - 647215 AAACTAACTATTACTGCCTCC - -a -s simMouse_chr6.simMouse.chr6 583341 30 + 636262 TTGGGCCTTGACTGTGTGACACAATGGCCC -s Anc0.Anc0refChr3 184667 30 + 222631 TTGGGCCTTGACCGTGGACTGCTATTCCCC -s Anc1.Anc1refChr1 24058 30 + 69767 TTGGGCCTTGACCGTGGACTGCTATTCCCC -s Anc2.Anc2refChr1 100262 30 + 142988 TTGGGCCTTGACCGTGGACTGCTATTCCCC -s mr.mrrefChr3 133149 30 + 181027 TTGGGCCTTGACTGTGTGACACAATGGCCC -s simCow_chr6.simCow.chr6 558163 30 + 602619 TCGGGCATTAACTGTGTGCTGCTATTGCCT -s simDog_chr6.simDog.chr6 546726 30 + 593897 TTGGGTCTTGACCGTGGACTGCTATTCCCC -s simHuman_chr6.simHuman.chr6 555241 12 + 601863 TTTGGCCTTGA------------------C -s simRat_chr6.simRat.chr6 58860 30 - 647215 TTGGGCCTTGACTGTGTGACACAATGGCCC - -a -s simMouse_chr6.simMouse.chr6 583371 8 + 636262 ACTCTGTT -s Anc0.Anc0refChr3 184697 8 + 222631 ACCCTGTT -s Anc1.Anc1refChr1 24088 8 + 69767 ACCCTGTT -s Anc2.Anc2refChr1 100293 8 + 142988 ATCCTGTT -s mr.mrrefChr3 133179 8 + 181027 ACCCTGTT -s simCow_chr6.simCow.chr6 558194 7 + 602619 -TTGTGCT -s simDog_chr6.simDog.chr6 546757 8 + 593897 ATCCTGTT -s simHuman_chr6.simHuman.chr6 555253 8 + 601863 ACCCTGTT -s simRat_chr6.simRat.chr6 58890 8 - 647215 ACCCTGTT - -a -s simMouse_chr6.simMouse.chr6 583379 24 + 636262 AGCAGATCATACCAACTACCCTCT -s Anc0.Anc0refChr3 184706 24 + 222631 GGTAGATTTTACCAACTGCTCCCT -s Anc1.Anc1refChr1 24097 24 + 69767 GGTAGATTTTACCAACTGCTCCCT -s Anc2.Anc2refChr1 100302 24 + 142988 GGTAGATTTCCTCATCTGCTCCCT -s mr.mrrefChr3 133187 24 + 181027 AGCAGATCTTACCAACTACCCTCT -s simCow_chr6.simCow.chr6 558202 24 + 602619 GGTGGATTTCCCCACCTGCTCCCT -s simDog_chr6.simDog.chr6 546766 24 + 593897 GGCAGATTTCCTCATCCACTCTTT -s simHuman_chr6.simHuman.chr6 555263 23 + 601863 GGTACAC-TTACTAACTGCACCCT -s simRat_chr6.simRat.chr6 58898 23 - 647215 AGCAGATCTTACCTGCTACCCTC- - -a -s simMouse_chr6.simMouse.chr6 583403 10 + 636262 TGATTGTGTG -s Anc0.Anc0refChr3 184733 8 + 222631 TGATTGTA-- -s Anc1.Anc1refChr1 24124 8 + 69767 TGATTGTA-- -s Anc2.Anc2refChr1 100329 8 + 142988 TCATTGTA-- -s mr.mrrefChr3 133211 8 + 181027 TGATTGTG-- -s simCow_chr6.simCow.chr6 558229 8 + 602619 TAATTGTA-- -s simDog_chr6.simDog.chr6 546793 8 + 593897 TCGTTGCA-- -s simHuman_chr6.simHuman.chr6 555289 8 + 601863 TGATTGTA-- - -a -s simMouse_chr6.simMouse.chr6 583413 23 + 636262 AAAACCTAGAAATTAAGGGAATT -s Anc0.Anc0refChr3 184741 23 + 222631 AAAACCTCAAACTCAAGGGAATT -s Anc1.Anc1refChr1 24132 23 + 69767 AAAACCTCAAACTCAAGGGAATT -s Anc2.Anc2refChr1 100339 23 + 142988 AAAACCTCAAACTCACAGGAAAT -s mr.mrrefChr3 133219 23 + 181027 AAAACCTAGAAATTAAGGGAATT -s simCow_chr6.simCow.chr6 558239 15 + 602619 AAAATCTCAAACTCA-------- -s simDog_chr6.simDog.chr6 546803 23 + 593897 AAGACCTCAAACTCTCAGGAAAT -s simHuman_chr6.simHuman.chr6 555297 23 + 601863 AAAACCTCAAACTCAAGGGTATT - -a -s simMouse_chr6.simMouse.chr6 583436 65 + 636262 GCAGATGTTAGTCTTTAGAATGGACCAGGAAGTGATATGTAAACTGCCCCTCCCCATGCAGGAAC -s Anc0.Anc0refChr3 184764 65 + 222631 GCAAATGTCAGCCTCTAAAGTGGACCAGGATATGATATAGGATCTGCCCCTGCCCATGCAGGGAT -s Anc1.Anc1refChr1 24155 65 + 69767 GCAAATGTCAGCCTCTAAAGTGGACCAGGATATGATATAGGATCTGCCCCTGCCCATGCAGGGAT -s Anc2.Anc2refChr1 100362 65 + 142988 GCAAATGTCAGCCTCTAAAGTGGACCAGGATATGATATAGGATCTGCCCCTGCCCATGCAGGGAT -s mr.mrrefChr3 133242 65 + 181027 GCAGATGTTAGTCTTTAGAATGGACCAGGAAGTGATATGTAAACTGCCCCTCCCCATGCAGGAAT -s simCow_chr6.simCow.chr6 558254 65 + 602619 GCAAATGTCAGACTCTAAAATGGCCCAGGATATGATATGGGATCTGCCCCTGCCCATGCAGTGAC -s simDog_chr6.simDog.chr6 546874 65 + 593897 GCAAATGTCAGCTTCTAGAGTGGACCAGGATGTGATATAGGATCTGTCCCTGCCCATGCAGGGGT -s simHuman_chr6.simHuman.chr6 555320 59 + 601863 GCAAACGTCAGCCTGTTAAGCGGACCGGGATAGGAC------CCTGCCCCTGCCCATGCAGGGAT -s simRat_chr6.simRat.chr6 58921 64 - 647215 -CAGTTGCTAGTCTTTAGAATGAACCAGGAAGTGATATGTAAACTGCCCCTCCCCATACAGGAGT - -a -s simMouse_chr6.simMouse.chr6 583501 45 + 636262 CCGCACCTACCATGTCTTATCCAGCAATAGGAAGTCTGTGGCACA -s Anc0.Anc0refChr3 184831 45 + 222631 CCACACCTACACCACCTTCTCCAGCAATAAGAAGTCTATGGCACA -s Anc1.Anc1refChr1 24222 45 + 69767 CCACACCTACACCACCTTCTCCAGCAATAAGAAGTCTATGGCACA -s Anc2.Anc2refChr1 100429 45 + 142988 CCACTCCTACACCACCTTCTCTAGCAATAAGAAGCCTATGGCACA -s mr.mrrefChr3 133309 45 + 181027 CCACACCTACCCTGTCTTATCCAGCAATAAGAAGTCTGTGGCACA -s simCow_chr6.simCow.chr6 558321 37 + 602619 CCACTCCTACACCACCTT-------AATAGGAA-CCTATGGCACC -s simDog_chr6.simDog.chr6 546941 45 + 593897 TAACTCCTACATCACCGTCTCTAGCAATAACAAGCCTATGGCACA -s simHuman_chr6.simHuman.chr6 555381 45 + 601863 CCATACCTACACCACCTTGCCCAGCAATGAGAAGTCTATGGTCCA -s simRat_chr6.simRat.chr6 58987 45 - 647215 CCAAACCTACCCTGGCTTATCCAACAATAAGAAGTCTGTGGCACA - -a -s simMouse_chr6.simMouse.chr6 583546 9 + 636262 CAGTTTCTG -s Anc0.Anc0refChr3 184881 6 + 222631 TAGTTT--- -s Anc1.Anc1refChr1 24272 9 + 69767 TAGTTTATG -s Anc2.Anc2refChr1 100479 6 + 142988 TAGTTT--- -s mr.mrrefChr3 133354 9 + 181027 CAGTTTCTG -s simCow_chr6.simCow.chr6 558363 6 + 602619 TACTTT--- -s simDog_chr6.simDog.chr6 546991 6 + 593897 TAGTTT--- -s simHuman_chr6.simHuman.chr6 555431 9 + 601863 TAGTGTATG -s simRat_chr6.simRat.chr6 59032 9 - 647215 CAGTTTCTA - -a -s simMouse_chr6.simMouse.chr6 583555 18 + 636262 AAGGGGGAATGGAAATTT -s Anc0.Anc0refChr3 184893 16 + 222631 AAAGGGAGATG--AATTT -s Anc1.Anc1refChr1 24288 16 + 69767 AAAGGGAGATG--AATTT -s Anc2.Anc2refChr1 100491 16 + 142988 AAAGGGAGATG--AATTT -s mr.mrrefChr3 133363 18 + 181027 AAAGGGGAATGGAAATTT -s simCow_chr6.simCow.chr6 558375 16 + 602619 AAAGAGAGAAA--GATTT -s simDog_chr6.simDog.chr6 547003 16 + 593897 ATAGGGAAATG--AATTT -s simHuman_chr6.simHuman.chr6 555447 16 + 601863 AAAGGGAGATG--AATTT -s simRat_chr6.simRat.chr6 59041 18 - 647215 AAAGGGGAATGGAAATTT - -a -s simMouse_chr6.simMouse.chr6 583573 46 + 636262 CCACTCCTCGACACCCCGATCATGAAGGTTGCACCACCCATCTCCT -s Anc0.Anc0refChr3 184909 46 + 222631 CTACTCCTCTACATCTTGACCATGAAGATTACACTTTGCATCCCCT -s Anc1.Anc1refChr1 24304 46 + 69767 CTACTCCTCTACATCTTGACCATGAAGATTACACTTTGCATCCCCT -s Anc2.Anc2refChr1 100507 46 + 142988 CTACTCCTCTACATCTGAACCATGAAGATTACACTTTGCATCCCCT -s mr.mrrefChr3 133381 46 + 181027 CCACTCCTCGACACCCTGATCATGAAGGTTGCACCACCCATCTCTT -s simCow_chr6.simCow.chr6 558391 46 + 602619 CTACTCCTCTACATCTGAACCATGAAGATTGCACTCTGCATCCTCT -s simDog_chr6.simDog.chr6 547020 46 + 593897 CTACTCCTCTACCTCTGAACCATGAAGATTACACTTTGCATCCCCT -s simHuman_chr6.simHuman.chr6 555463 29 + 601863 TTACTCTTCAAGATTATGGCCATGAAGA-----------------A -s simRat_chr6.simRat.chr6 59059 46 - 647215 CCACTCCTCTACACCCTGATCATGAAGGTTGCACCACCTATCTCTT - -a -s simMouse_chr6.simMouse.chr6 583619 1 + 636262 A -s Anc0.Anc0refChr3 184955 1 + 222631 A -s Anc1.Anc1refChr1 24350 1 + 69767 A -s Anc2.Anc2refChr1 100553 1 + 142988 A -s mr.mrrefChr3 133427 1 + 181027 A -s simCow_chr6.simCow.chr6 558441 1 + 602619 A -s simDog_chr6.simDog.chr6 547066 1 + 593897 A -s simHuman_chr6.simHuman.chr6 555492 1 + 601863 A -s simRat_chr6.simRat.chr6 59105 1 - 647215 A - -a -s simMouse_chr6.simMouse.chr6 583620 41 + 636262 AAGGATCCCATAATCCAATAGAGTTGGTCAGTTATTCTAGT -s Anc0.Anc0refChr3 184962 31 + 222631 AAAACTCACTTAACCCACTTGGA----------ATACTAGT -s Anc1.Anc1refChr1 24357 31 + 69767 AAAACTCACTTAACCCACTTGGA----------ATACTAGT -s Anc2.Anc2refChr1 100560 31 + 142988 AAAACTCAATTAACGCACTTGGT----------ATACTAGT -s mr.mrrefChr3 133428 41 + 181027 AAGGATCCCATAATCCAATAGAATTGGTCAGTTATACTAGT -s simCow_chr6.simCow.chr6 558448 31 + 602619 AAAACTCAATTAACGTACTTGGT----------ATATTAGT -s simDog_chr6.simDog.chr6 547073 30 + 593897 AGAACTCAATAAAC-CACTCGAT----------ATACTAGT -s simHuman_chr6.simHuman.chr6 555499 31 + 601863 AAAACTCACTTAAACCACTTGGA----------ATACTAGT -s simRat_chr6.simRat.chr6 59106 41 - 647215 AAGTAGCCCAAACTTCAATAGAATCAGTCTGTTATACTAGT - -a -s simMouse_chr6.simMouse.chr6 583661 24 + 636262 CAGGTTTAAGAATGGGACCCTGTG -s Anc0.Anc0refChr3 184993 24 + 222631 CAGATTTAAGAATGAGACACTGTA -s Anc1.Anc1refChr1 24388 24 + 69767 CAGATTTAAGAATGAGACACTGTA -s Anc2.Anc2refChr1 100591 24 + 142988 CAGATTTAAGAATGAAACACTGTA -s mr.mrrefChr3 133469 24 + 181027 CAGGTTTAAGAATGGGACCCTGTG -s simCow_chr6.simCow.chr6 558481 24 + 602619 CAGATTAAAGAATGGATTGCTGTA -s simDog_chr6.simDog.chr6 547103 24 + 593897 CAGATTTAAAGATGAAACACCGTT -s simHuman_chr6.simHuman.chr6 555530 24 + 601863 CAGATTTTGGAATGAGACACTATA -s simRat_chr6.simRat.chr6 59147 24 - 647215 CAGGTTTAAGAATGGGACCCTGTG - -a -s simMouse_chr6.simMouse.chr6 583685 1 + 636262 C -s Anc0.Anc0refChr3 185032 1 + 222631 C -s Anc1.Anc1refChr1 24427 1 + 69767 C -s Anc2.Anc2refChr1 100775 1 + 142988 C -s mr.mrrefChr3 133493 1 + 181027 C -s simCow_chr6.simCow.chr6 558666 1 + 602619 C -s simDog_chr6.simDog.chr6 547314 1 + 593897 C -s simHuman_chr6.simHuman.chr6 555569 1 + 601863 C -s simRat_chr6.simRat.chr6 59171 1 - 647215 C - -a -s simMouse_chr6.simMouse.chr6 583686 72 + 636262 TGCAGTGACTGATGAGTGTCCACTCTTTATGCCGTGCACCATCGGAGACAAGTAATTTGGGTACCAATACGG -s Anc0.Anc0refChr3 185048 22 + 222631 TGCAGCGGG--------------------------------------------------GGTACTAACTGAG -s Anc1.Anc1refChr1 24443 22 + 69767 TGCAGCGGG--------------------------------------------------GGTACTAACTGAG -s Anc2.Anc2refChr1 100799 22 + 142988 TGCAGCAGG--------------------------------------------------GGTACTAACTGAG -s mr.mrrefChr3 133498 22 + 181027 TGCAGCGGC--------------------------------------------------GGTACTAATACGG -s simCow_chr6.simCow.chr6 558689 22 + 602619 TGCAGCAAG--------------------------------------------------GGTACCTACTGAG -s simDog_chr6.simDog.chr6 547338 22 + 593897 TGCAGAAGG--------------------------------------------------GGTACTAACCAAA -s simHuman_chr6.simHuman.chr6 555585 22 + 601863 TGCAGCGGG--------------------------------------------------GGTACTAACTGAG -s simRat_chr6.simRat.chr6 59176 15 - 647215 TGCAGCAGC--------------------------------------------------TATCCT------- - -a -s simMouse_chr6.simMouse.chr6 583758 74 + 636262 TCAAAGTTCATCGATCAGGTGCAGTGACTACCCTTCCTGTCTCTCATCTTGTCTCATCCAAGTTTACTACATGT -s Anc0.Anc0refChr3 185078 71 + 222631 TCCCAGTTTAT---GCACCTGCAGTGAATATCATTTCTGTCTCCTATAATGTATAGACCAACTCTCTTACATTT -s Anc1.Anc1refChr1 24473 71 + 69767 TCCCAGTTTAT---GCACCTGCAGTGAATATCATTTCTGTCTCCTATAATGTATAGACCAACTCTCTTACATTT -s Anc2.Anc2refChr1 100829 71 + 142988 TCCCAATTTAT---GCACCATCAATGAATGTCATTTCTGTCTCCTTTAATATATAGACTAACTCTCTTACATTT -s mr.mrrefChr3 133520 71 + 181027 TCAAAGTTCAT---TCAGGTGCAGTGACTACCCTTCCTGTCTCTCATCTTGTCTCATCCAAGTTTACTACATGT -s simCow_chr6.simCow.chr6 558719 65 + 602619 TCCCAATCTAT---GGGC------TGAATGGCATTTGTGCCTCTGTTAACATGCAGCCTAACTCTATTACATTT -s simDog_chr6.simDog.chr6 547368 67 + 593897 TCC----TTAC---ACACCATCAACGAATGTTATTTCTGTTTCCTTTAATATATAGACTAACTCTCTTACATGG -s simHuman_chr6.simHuman.chr6 555615 71 + 601863 TCCCAGTTTAT---GCACATGCAGTGGATATCACTTCTGTCTCCTATGATGTATAGACCAACTCTGTTACATTT - -a -s simMouse_chr6.simMouse.chr6 583832 25 + 636262 CATAAATTGCGGTGCACACTCCGCA -s Anc0.Anc0refChr3 185149 6 + 222631 C-----------TGCTC-------- -s Anc1.Anc1refChr1 24544 6 + 69767 C-----------TGCTC-------- -s Anc2.Anc2refChr1 100906 6 + 142988 C-----------TGCTC-------- -s mr.mrrefChr3 133591 6 + 181027 C-----------TGCAC-------- -s simCow_chr6.simCow.chr6 558790 6 + 602619 C-----------TGCTC-------- -s simDog_chr6.simDog.chr6 547441 6 + 593897 C-----------TGCTC-------- -s simHuman_chr6.simHuman.chr6 555686 6 + 601863 T-----------TGCTC-------- - -a -s simMouse_chr6.simMouse.chr6 583857 27 + 636262 TTCCACATTTGAGATTTATGTATGGTG -s Anc0.Anc0refChr3 185155 27 + 222631 TTACACATTAGACATTGATGTATGGTA -s Anc1.Anc1refChr1 24550 27 + 69767 TTACACATTAGACATTGATGTATGGTA -s Anc2.Anc2refChr1 100916 27 + 142988 TTACACACTAGACATTGATGTATGGTA -s mr.mrrefChr3 133597 27 + 181027 TTCCACATTAGAGATTTATGTATGGTG -s simCow_chr6.simCow.chr6 558800 26 + 602619 TGACACACTAGACATTG-TATTTGTTA -s simDog_chr6.simDog.chr6 547451 27 + 593897 TTACACACTAGAGATTGATGTATGGCA -s simHuman_chr6.simHuman.chr6 555692 27 + 601863 TTACACTTTAGTCGTTGATGTATGGTA -s simRat_chr6.simRat.chr6 59191 17 - 647215 -TCCACACCACAGATTTC--------- - -a -s simMouse_chr6.simMouse.chr6 583884 89 + 636262 CCTCAATAAACATTTTCATGTTGTTACTCCAAACTGAGCTGGTCAGGCCACAGTATTCTAGCTCACCACTTCCAGACATTTCCATTAAA -s Anc0.Anc0refChr3 185185 78 + 222631 CCTTAGTAGATTTTTTTACATTGCTACTCC-AGCTCCCCTGGTCAGACCACAT----------CACCTATTCACACCAATTTCACGAAA -s Anc1.Anc1refChr1 24580 78 + 69767 CCTTAGTAGATTTTTTTACATTGCTACTCC-AGCTCCCCTGGTCAGACCACAT----------CACCTATTCACACCAATTTCACGAAA -s Anc2.Anc2refChr1 100948 78 + 142988 CCTTAGTAGATTTCTTTACATTGCTACTCC-AGCTCCCCTGGTCTGACCATAT----------CAGCTATTCACACCAATTTCAGGGAA -s mr.mrrefChr3 133624 89 + 181027 CCTCAATAAACATTTTCACATTGTTACTCCAAACTGCGCTGGTCAGACCACAGTATTCTAGCTCACCAATTCCAGACAATTCCACTAAA -s simCow_chr6.simCow.chr6 558832 78 + 602619 CCTTAGTAAATTTCTTTACACTGCTATTCC-ATCCCCCATGGTCTGACGATAT----------CAGCTATGCACAACAATTTCAGAGAA -s simDog_chr6.simDog.chr6 547483 78 + 593897 CATTGGTAGACTTCTTTAAATGGCTACTCA-AGCTCCCCTGGTCTGACCATGT----------CAGGTGTTCACGCCAGCTTCAGGGAA -s simHuman_chr6.simHuman.chr6 555722 78 + 601863 CCCTATTGTATTTTTTTACATTGATGCTCC-AGCTCCCCTGGTCAGACCACAT----------CACCTATTCAGATCAATTTCACCAAG -s simRat_chr6.simRat.chr6 59208 89 - 647215 CCTCAGTAAACATTTTCACATTGTTACTTCAAACTGCACTGGTCAGACCATAGCATTCTTGCTCACCAATTTCAGACAATTCCACTAAA - -a -s simMouse_chr6.simMouse.chr6 583973 96 + 636262 GACTTTATAAGCCACCACTAGACTATATCAGCTACTCACCCCCCTTTCAGAGAGACGGTTTGTAAAACCTGACTAGTGAACTAGTTAAGCCAATTC -s Anc0.Anc0refChr3 185264 95 + 222631 GATCTTATAAGCTACCATCAGACCATGTTGGCTACCCACGTCAATTTCAGA-AAAGAGTTTTTAGAACTTGACTAGTGCAATGGTTGAGACAATTA -s Anc1.Anc1refChr1 24659 96 + 69767 GATCTTATAAGCTACCATCAGACCATGTTGGCTACCCACGTCAATTTCAGAGAAAGAGTTTTTAGAACTTGACTAGTGCAATGGTTGAGACAATTA -s Anc2.Anc2refChr1 101027 95 + 142988 GATCTTATAAGCTTCTCTCAGACCATGTTGGCTACCCACGCTAATTTCAGA-AAAGAGTTTTAAGAACTTGACTAGTGCAATGGTTGAGACAATTA -s mr.mrrefChr3 133713 96 + 181027 GACTTTATAAGCCACCACTAGACCATATCAGCTACTCACCTCCCTTTCAGAGAGACAGTTTGTAAAACCTGACTAGTGAACTGGTTAAGCCAATTC -s simCow_chr6.simCow.chr6 558911 95 + 602619 GATTTTATGAGCTTATGTCTCAACAAGTTAGCTACTCACACAAATTTCACA-ACACAGTTTTAAGACCCTGACTAGTGTAATGGTTTAGACAACTA -s simDog_chr6.simDog.chr6 547562 95 + 593897 GATCTCATAGGCTTCTCCCAGACCATGTCGGCTACCCACGCTAATTTTAGT-AAAGAGTTTTAAGAACTGGATTAGTGCAAATATTGAGGCAATTA -s simHuman_chr6.simHuman.chr6 555801 90 + 601863 GATCTTGTAAGCTACCATCAGGCCATGTTTGTTA------TCAATTTCAGAGACAAAGCTTATAGAACTTGACTAGTCCAATGGCTGAGACAATTA -s simRat_chr6.simRat.chr6 59297 95 - 647215 GACTTTATCATCCACCACTAGACCATATCAGCTGCTCACCTCCCTTTCAGAGAGCCA-TGTGCAAATCCTGACTAGTGGACTGGTTAAGCCAATTC - -a -s simMouse_chr6.simMouse.chr6 584069 2 + 636262 AG -s Anc0.Anc0refChr3 185360 2 + 222631 GG -s Anc1.Anc1refChr1 24756 2 + 69767 GG -s Anc2.Anc2refChr1 101123 2 + 142988 GG -s mr.mrrefChr3 133810 2 + 181027 AG -s simCow_chr6.simCow.chr6 559007 2 + 602619 GG -s simDog_chr6.simDog.chr6 547658 2 + 593897 GG -s simHuman_chr6.simHuman.chr6 555892 2 + 601863 GG -s simRat_chr6.simRat.chr6 59393 2 - 647215 AG - -a -s simMouse_chr6.simMouse.chr6 584071 15 + 636262 TGTAGTGGGCCTCAA -s Anc0.Anc0refChr3 185363 15 + 222631 TGCAAGGGTTCTCAA -s Anc1.Anc1refChr1 24759 15 + 69767 TGCAAGGGTTCTCAA -s Anc2.Anc2refChr1 101126 15 + 142988 TGCAAGGGTTCTCAC -s mr.mrrefChr3 133812 15 + 181027 TGTAGTGGTCCTCAA -s simCow_chr6.simCow.chr6 559010 15 + 602619 TGCAAGGATTCTCAT -s simDog_chr6.simDog.chr6 547661 15 + 593897 TGTGAGGGTTCTTAC -s simHuman_chr6.simHuman.chr6 555895 15 + 601863 TGCAACAGTTCTCAA -s simRat_chr6.simRat.chr6 59395 15 - 647215 TGGAGAGGTGCTCAA - -a -s simMouse_chr6.simMouse.chr6 584086 19 + 636262 ATACCCAATTCTGATTATC -s Anc0.Anc0refChr3 185386 19 + 222631 ATGACCAATTATGATTATG -s Anc1.Anc1refChr1 24782 19 + 69767 ATGACCAATTATGATTATG -s Anc2.Anc2refChr1 101149 19 + 142988 GTGACCAATTAGGATTATG -s mr.mrrefChr3 133827 19 + 181027 ATGCCCAATTCTGATTATC -s simCow_chr6.simCow.chr6 559033 19 + 602619 GTGACCAATTGCGACCATG -s simDog_chr6.simDog.chr6 547684 19 + 593897 GTGACCAGTTAGAATTATG -s simHuman_chr6.simHuman.chr6 555919 19 + 601863 ATGACCAATTATGCTTATG -s simRat_chr6.simRat.chr6 59410 12 - 647215 ATGC-------TGGTTATT - -a -s simMouse_chr6.simMouse.chr6 584105 4 + 636262 ACTA -s Anc0.Anc0refChr3 185405 4 + 222631 GTTA -s Anc1.Anc1refChr1 24801 4 + 69767 GTTA -s Anc2.Anc2refChr1 101169 4 + 142988 GTTG -s mr.mrrefChr3 133846 4 + 181027 GCTA -s simCow_chr6.simCow.chr6 559096 4 + 602619 TTTG -s simDog_chr6.simDog.chr6 547704 4 + 593897 GTTG -s simHuman_chr6.simHuman.chr6 555938 4 + 601863 GTCA -s simRat_chr6.simRat.chr6 59422 4 - 647215 GCTA - -a -s simMouse_chr6.simMouse.chr6 584109 26 + 636262 ATATAGATATAAACTAGAAAATGTGT -s Anc0.Anc0refChr3 185410 26 + 222631 ATAGAAGTAGAAACTACAAAACCTGA -s Anc1.Anc1refChr1 24806 26 + 69767 ATAGAAGTAGAAACTACAAAACCTGA -s Anc2.Anc2refChr1 101174 26 + 142988 ATAGAAGTAGAAACTACAAAACCTGA -s mr.mrrefChr3 133850 26 + 181027 ATATAGGTATAAACTAGAAAATGTGT -s simCow_chr6.simCow.chr6 559101 26 + 602619 ATAGAAGTAGAAGCAACAAGCACTGA -s simDog_chr6.simDog.chr6 547709 25 + 593897 ATAGA-GCAGATACTGCAAAACCTGA -s simHuman_chr6.simHuman.chr6 555943 26 + 601863 GTAGAAGTAAAAACTACAAAGCCTGA -s simRat_chr6.simRat.chr6 59426 26 - 647215 ATATAGGTATAAACCAGAAAATGTGT - -a -s simMouse_chr6.simMouse.chr6 584135 46 + 636262 TGTGGTGCCATGACATATGAGTGCACCTATATGGAGCAAATGCAGT -s Anc0.Anc0refChr3 185436 46 + 222631 TGTACTGCCCTTACCTATAAGTGCACCTACATAGAGTAAACATACT -s Anc1.Anc1refChr1 24832 46 + 69767 TGTACTGCCCTTACCTATAAGTGCACCTACATAGAGTAAACATACT -s Anc2.Anc2refChr1 101200 46 + 142988 TGTACCGCCCTTTCCTATAAGTGCACCTATATAGAGTAAACATACT -s mr.mrrefChr3 133876 46 + 181027 TGTGGTGCCATTACCTATAAGTGCACCTACATGGAGTAAATGTAGT -s simCow_chr6.simCow.chr6 559127 46 + 602619 TGTACAGGCATTTCTAATAAGTGCACCCATGTAGAGTAACCACACT -s simDog_chr6.simDog.chr6 547739 46 + 593897 TGGACCCCCCTTTCCTATAAGTGCACTTATATTGAGTAAACATACT -s simHuman_chr6.simHuman.chr6 555969 46 + 601863 TGTAATGCTGTTACCTATAAGTGCACCTTCATAGGGTAAACATACT -s simRat_chr6.simRat.chr6 59452 46 - 647215 TGTGGTGCCATTACCCATAAGTGCACCTACATGGAGTAAATGTATT - -a -s simMouse_chr6.simMouse.chr6 584181 23 + 636262 TAGAGGTGAAGCTTCCAACACTT -s Anc0.Anc0refChr3 185483 23 + 222631 TGGAGGTTAAGCCCCCAACACTC -s Anc1.Anc1refChr1 24879 23 + 69767 TGGAGGTTAAGCCCCCAACACTC -s Anc2.Anc2refChr1 101247 23 + 142988 TGGAGATTAGGCCCCCAACACTC -s mr.mrrefChr3 133922 23 + 181027 TGGAGGTGAAGCTTCCAACACTT -s simCow_chr6.simCow.chr6 559174 23 + 602619 TGGTAATTAGACTCCCTGGACTC -s simDog_chr6.simDog.chr6 547786 23 + 593897 TGGAGACTAGGCCCCCAACACTC -s simHuman_chr6.simHuman.chr6 556016 23 + 601863 TGGAGGTTAAGCCCCCAAAGCTC -s simRat_chr6.simRat.chr6 59498 23 - 647215 TGGAGGTAAAGCTTCCAACACTT - -a -s simMouse_chr6.simMouse.chr6 584204 10 + 636262 ACCATGGACT -s Anc0.Anc0refChr3 185506 10 + 222631 ACCATAGACT -s Anc1.Anc1refChr1 24902 10 + 69767 ACCATAGACT -s Anc2.Anc2refChr1 101270 10 + 142988 ACCATAGACT -s mr.mrrefChr3 133945 10 + 181027 ACCATGGACT -s simCow_chr6.simCow.chr6 559197 10 + 602619 ACCATAGTCT -s simDog_chr6.simDog.chr6 547809 10 + 593897 ACCATAGAAT -s simHuman_chr6.simHuman.chr6 556044 10 + 601863 ACTATAGACT -s simRat_chr6.simRat.chr6 59521 10 - 647215 ACCATGGACT - -a -s simMouse_chr6.simMouse.chr6 584214 7 + 636262 TTATTAT -s Anc0.Anc0refChr3 185516 7 + 222631 TTATTTT -s Anc1.Anc1refChr1 24912 7 + 69767 TTATTTT -s Anc2.Anc2refChr1 101280 7 + 142988 TTATTTT -s mr.mrrefChr3 133955 7 + 181027 TTATTTT -s simCow_chr6.simCow.chr6 559207 7 + 602619 TTATTTT -s simDog_chr6.simDog.chr6 547819 7 + 593897 TTATATT -s simHuman_chr6.simHuman.chr6 556059 7 + 601863 TTCTTTT -s simRat_chr6.simRat.chr6 59531 7 - 647215 TTATTTT - -a -s simMouse_chr6.simMouse.chr6 584221 52 + 636262 CAATCATCAGCAAATTGTGGGAGATGCGTACTCACAAAACCCTCTTACATAT -s Anc0.Anc0refChr3 185523 46 + 222631 CAATGATCATTAAATTTGATGATATGT------ATCAATTCCAATTGCATAG -s Anc1.Anc1refChr1 24919 52 + 69767 CAATGATCATTAAATTTGATGATATGTGTATTCATCAATTCCAATTGCATAG -s Anc2.Anc2refChr1 101288 46 + 142988 TGATGATCATGAAATTTGATGATATGT------ATCAATTCCACTTGCATAG -s mr.mrrefChr3 133962 52 + 181027 CAATCATCAGTAAATTTTAGGAGATGTGTATTCACCAAACCCTATTACATAT -s simCow_chr6.simCow.chr6 559214 41 + 602619 -GATGGTCATAA----TGATGATGTGT------ATCAATACCTCTTTCATGG -s simDog_chr6.simDog.chr6 547827 41 + 593897 TGATGACTGTGAAATTACAAGATATGT-----------CTCCACTTGCATAG -s simHuman_chr6.simHuman.chr6 556066 52 + 601863 CAATGATCATTAAATTTGATGACATGTGTATTCATCAGTTCCAATTGCATAG -s simRat_chr6.simRat.chr6 59538 52 - 647215 CAATCATCAGTGAACTTCAGGGGAGGTGTATTCACCAACCACTATTACATAT - -a -s simMouse_chr6.simMouse.chr6 584273 44 + 636262 GCCTGAGTCTCTGAGATGATTGCAGGGTGTCATTTAGGCACAGA -s Anc0.Anc0refChr3 185571 37 + 222631 GCATGAGGCCCTA----GATTGCAGAGTGTC---TAGCTACAGC -s Anc1.Anc1refChr1 24973 41 + 69767 GCATGAGGCCCTAATTAGATTGCAGAGTGTC---TAGCTACAGC -s Anc2.Anc2refChr1 101336 37 + 142988 GCATGAGGCCCTA----GATTGGAGAGTGTC---TAGCTATAGC -s mr.mrrefChr3 134014 44 + 181027 GCATGAGTCTCTGAGATGATTGCAGGGTGTCATTTAGGTACAGA -s simCow_chr6.simCow.chr6 559257 36 + 602619 GCATGAGGCC-TA----GATTGGAGAGTGTC---CAGCTATTGC -s simDog_chr6.simDog.chr6 547870 32 + 593897 GCACGA--CCCTA----GATTGGAGAGCTTC---T---TGTAGT -s simHuman_chr6.simHuman.chr6 556120 41 + 601863 GCATGAGACCCTAATTAGATTGCATAGTGTC---TAACTACAGC -s simRat_chr6.simRat.chr6 59590 44 - 647215 GCAGGAGTCTCTGAGATGATTGCAGGGTGTCATCTAGGTGTGTA - -a -s simMouse_chr6.simMouse.chr6 584317 181 + 636262 TTCACCACAAGCCTCAAGGAGCAGAACCTCTAAGACTACAGAAGGAGGAAAGGGACTTGAAAAGACGGCAGCTCTCTTCATTTGTAACTATCTATTGCATAGGAATAATATGACTGCTATATGCATCAGTAACTAGATGACATATGAAATAAGGTAAAAGGAATATCCAATATGTGTTTTC -s Anc0.Anc0refChr3 185608 75 + 222631 TTTGCAATGAG-------------------------------------------------------------------------------------------------------TATTATTTGCATCAGT---TAGATGACAGATAAACTGAGGTAAAAAGTCTAGCCAACACTGGTTCTC -s Anc1.Anc1refChr1 25014 77 + 69767 TTTGCAATGAG-------------------------------------------------------------------------------------------------------TATTATTTGCATCAGT-ACTAGATGACAGATAAACTGAGGTAAAAAGTCTAGCCAACACTGGTTCTC -s Anc2.Anc2refChr1 101373 75 + 142988 TTTGCAATGAG-------------------------------------------------------------------------------------------------------TATTATTTGCATCGGT---TAGATGACAGGTAAACTAAGGTGAAAAGTCTAGCCCACACTGGTTCGC -s mr.mrrefChr3 134058 81 + 181027 TTCACCACAAGCCT----------------------------------------------------------------------------------------------------TGCTATTTGCATCAGTAACTAGATGACATATGAAATGAGGTAAAAGGAATATCCAATATGTGTTTTC -s simCow_chr6.simCow.chr6 559293 52 + 602619 TTTGCAATGAG-------------------------------------------------------------------------------------------------------TACTATGTGCA--------------------------AAGTGGAAAGTCTAGCCCACACTGGTTTAC -s simDog_chr6.simDog.chr6 547902 75 + 593897 TTTGTGGTGAG-------------------------------------------------------------------------------------------------------TGTTATTTGCATCGGT---TAGATGACAGGTAAACTAAGGTGAAAAGTCTAGCCCACACCAATTCGC -s simHuman_chr6.simHuman.chr6 556161 77 + 601863 TTTGCAATGAG-------------------------------------------------------------------------------------------------------TATTATTTGCATCAGT-ACTAGATGGCAAATAACCTGAGGCAAAAAGTCTAGCCAACACTGGTTCTC -s simRat_chr6.simRat.chr6 59754 80 - 647215 TTCACTACAAGAGT----------------------------------------------------------------------------------------------------TGCTGTTTGCATAAGTAACTAGATGACATATGAAATGAGATAAAAG-AATACCCAATGTGTGTTTTC - -a -s simMouse_chr6.simMouse.chr6 584498 26 + 636262 AGTGGTGGCAACTTCAAAGCAGCCAA -s Anc0.Anc0refChr3 185683 26 + 222631 ACTGGTGGAAACTTCAAAGAAGCCCA -s Anc1.Anc1refChr1 25091 26 + 69767 ACTGGTGGAAACTTCAAAGAAGCCCA -s Anc2.Anc2refChr1 101448 26 + 142988 ACTGGTGGAAACTTCAAAGAAGCCCG -s mr.mrrefChr3 134139 26 + 181027 ACTGGTGGCAACTTCAAAGAAGCCAA -s simCow_chr6.simCow.chr6 559345 26 + 602619 ACTGGTGGAAACTTCAAGAAGGCTGG -s simDog_chr6.simDog.chr6 547977 26 + 593897 ACTAGTGGAACCTTCAAAGAAGCCCG -s simHuman_chr6.simHuman.chr6 556239 26 + 601863 ACTGGTGGGAACTTCAAAGAAGCCTA -s simRat_chr6.simRat.chr6 59834 26 - 647215 ACTGGTAGTAACTACAGAGAAGCCAG - -a -s simMouse_chr6.simMouse.chr6 584524 24 + 636262 GCGTCCTGGTTTTGATGGCATGCT -s Anc0.Anc0refChr3 185709 20 + 222631 C----TTGGTTTTGATGGCATGCT -s Anc1.Anc1refChr1 25117 24 + 69767 CCATCTTGGTTTTGATGGCATGCT -s Anc2.Anc2refChr1 101474 20 + 142988 C----TTGGTTTTGATGGCATGTT -s mr.mrrefChr3 134165 24 + 181027 GCATCCTGGTTTTGATGGCATGCT -s simCow_chr6.simCow.chr6 559374 20 + 602619 C----TTGGTTTTGCTGGCATGAT -s simDog_chr6.simDog.chr6 548003 20 + 593897 C----TTGGTTTTGATGGCATGTT -s simHuman_chr6.simHuman.chr6 556265 24 + 601863 CCATCTTGGTATTGATAGCATGCT -s simRat_chr6.simRat.chr6 59860 24 - 647215 GCATCCCGGTCTTGATGGGGTGCT - -a -s simMouse_chr6.simMouse.chr6 584548 41 + 636262 CTGATGTTTTCTGGGCTGGGAACTTGGATGCTTGGATGGTT -s Anc0.Anc0refChr3 185729 41 + 222631 CTGATATTTTCTAGGCTGGGGTCTTGGATAATCAGAAGGTT -s Anc1.Anc1refChr1 25141 41 + 69767 CTGATATTTTCTAGGCTGGGGTCTTGGATAATCAGAAGGTT -s Anc2.Anc2refChr1 101494 41 + 142988 CAGACATTTTCTAAGCAGAGGTCTTGGATAATCAGAAGGTT -s mr.mrrefChr3 134189 41 + 181027 CTGATGTTTTCTGGGCTGGGGACTTGGATGCTCAGATGGTT -s simCow_chr6.simCow.chr6 559397 41 + 602619 CAGAGGTCTTCAAAGCAGAGGTCTTGGATAATCAGGAGGTT -s simDog_chr6.simDog.chr6 548023 41 + 593897 CACACATTTTCTAAGCAGAGGTCTTGGGTAATTAGAAGATT -s simHuman_chr6.simHuman.chr6 556289 41 + 601863 CTGATATTTTCTAGGCTGGAGTCCTGGATTATCAGAAGGTG -s simRat_chr6.simRat.chr6 59884 41 - 647215 TCAATCTTTTTTGGGCTGGGGACTTGGATGCTCAGATGGTA - -a -s simMouse_chr6.simMouse.chr6 584589 101 + 636262 CTTATGGTGTACCTAGTAATTTGACAAAGCCTCCGAACCTTGATAACTTTTATAGTCCCTTGCCCCCACTCATTTTGTTAAGGTGTCTTAAGGAGACAACC -s Anc0.Anc0refChr3 185770 86 + 222631 CTTAAGCTGTACCCAGTAATTGAACAAAGCCTCCAAGCCCTGTTGG-TCTTGTAATCCCTCAG-----CTAATCTTACTATG---------GGTGCCAATT -s Anc1.Anc1refChr1 25182 86 + 69767 CTTAAGCTGTACCCAGTAATTGAACAAAGCCTCCAAGCCCTGTTGG-TCTTGTAATCCCTCAG-----CTAATCTTACTATG---------GGTGCCAATT -s Anc2.Anc2refChr1 101535 86 + 142988 CGTAAGCTGTACCCAGTAATTGAACAAAGCCTCCATGCCCTGTTGG-TCTTGTAATCCCCCAG-----CTAATCTTACTATA---------GGTGCCAATT -s mr.mrrefChr3 134230 101 + 181027 CTTATGATGTACCCAGTAATTTGACAAAGCCTCCGAACCCTGTTAACTTTTATAATCCCTCACCCCCACTCATTTTGTTAAGGTGTCTTAAGGAGACAACC -s simCow_chr6.simCow.chr6 559438 80 + 602619 CGTATGCTGGAGCCAGTAATTGGACAAAGCCTCA----CCTGTTAG-TTTTATAATCCTCCAG-----C--ACCTTACTATA---------GGTGCAAGTT -s simDog_chr6.simDog.chr6 548064 85 + 593897 CGTAAGCCGTACCTAGTAATTGAACATAGCTTCCATGCCCTGTTGG-TCTTGTAATCCCCCA------CTAATCTTAATATA---------GGTACCAATT -s simHuman_chr6.simHuman.chr6 556331 80 + 601863 TTTTAACTGTACCCAGTAATTGAACAAAGCCTGTCAGCCCTG-------TTTTAAGCCCTCAT-----CTAATCTTACTATG---------GGTGTCAAGT -s simRat_chr6.simRat.chr6 59925 96 - 647215 CTTATGATGTACTCAGTAATTTG-----GCTTTCAAACCCTGTTAAGTTTTATAATCCCACACCCCCACTCATTTTGTTAAGGTGTCTTAAGGAGACAACC - -a -s simMouse_chr6.simMouse.chr6 584690 1 + 636262 A -s Anc0.Anc0refChr3 185860 1 + 222631 A -s Anc1.Anc1refChr1 25272 1 + 69767 A -s Anc2.Anc2refChr1 101625 1 + 142988 A -s mr.mrrefChr3 134331 1 + 181027 A -s simCow_chr6.simCow.chr6 559522 1 + 602619 A -s simDog_chr6.simDog.chr6 548153 1 + 593897 A -s simHuman_chr6.simHuman.chr6 556415 1 + 601863 G -s simRat_chr6.simRat.chr6 60021 1 - 647215 A - -a -s simMouse_chr6.simMouse.chr6 584691 97 + 636262 GCCAATCAGATGAGAGAAAAAATATTGACAGCATTGTCTAACTAAGAAAGAAAAGAACACTGAACCAGTTTCATTGTGCTACATAGAAAGTTAATAA -s Anc0.Anc0refChr3 185861 94 + 222631 GTCGA---GGTAAAAGAACAACTATGGATAGCATTGTGTGACTAGGAAAGAAAAAAATACTGGCACAGTGTCATTGTGGGACATAGAAAGTTAGCAA -s Anc1.Anc1refChr1 25273 95 + 69767 GTCGAT--GGTAAAAGAACAACTATGGATAGCATTGTGTGACTAGGAAAGAAAAAAATACTGGCACAGTGTCATTGTGGGACATAGAAAGTTAGCAA -s Anc2.Anc2refChr1 101626 94 + 142988 GTCGA---AGCAAAAGGACGACTATGGATAGCATTGTGTGACTAGGAAAAAAAAAAATACTGGCACAGTGTCATTGTGGGACATAGAAAGTTAGCAA -s mr.mrrefChr3 134332 97 + 181027 GCCAATCAGATAAGAGAAAAAATATGGACAGCATTGTCTAACTAAGAAAGAAAAGAATACTGAAACAGTTTCATTGTGCTACATAGAAAGTTAATAA -s simCow_chr6.simCow.chr6 559525 88 + 602619 GTCAA---TGCAAAAGCATGACTAAGGCTGGCACAGTGTGACTAGGAGA------AATATTGAAACAGTGCCATTGTAAGACACAGAAAATTAGCAA -s simDog_chr6.simDog.chr6 548154 94 + 593897 GTCGA---AGCAAAAGGACGACTATGGATAGCATTGTGCGACTGGGAATAAAAAAAATACTAGCACAGTGTAATTTTGGAACATAGAATGTTAGCAG -s simHuman_chr6.simHuman.chr6 556416 95 + 601863 GTTGAT--GGTAAAGGAACAACTATGGATACCATTGCGTGACTAGGAAAGAAAAAAATACTGGCACAGTCTCATTGTGGGACATAAAAAGTTAGCAA -s simRat_chr6.simRat.chr6 60022 97 - 647215 GCAAGTCAGATAAGAGAAAAAATATGGACAGCATTGTATAACTAAGAAAGAGAAGCATACTGAAACAGTGTCCTAGTGCTACATAGAAAGTTAATAA - -a -s simMouse_chr6.simMouse.chr6 584788 11 + 636262 CCAACCGCTGT -s Anc0.Anc0refChr3 185955 8 + 222631 CCA---GATTT -s Anc1.Anc1refChr1 25368 8 + 69767 CCA---GATTT -s Anc2.Anc2refChr1 101720 8 + 142988 CCA---GATTT -s mr.mrrefChr3 134429 8 + 181027 CCA---GCTGT -s simCow_chr6.simCow.chr6 559613 8 + 602619 CCA---GATTT -s simDog_chr6.simDog.chr6 548250 5 + 593897 CCA---GG--- -s simHuman_chr6.simHuman.chr6 556511 8 + 601863 CCA---GATAT -s simRat_chr6.simRat.chr6 60119 8 - 647215 CCA---GCTTT - -a -s simMouse_chr6.simMouse.chr6 584799 32 + 636262 GATGGGTATCTGTAAAAGAGCCCAGACATTTG -s Anc0.Anc0refChr3 185963 30 + 222631 CATAG--ATTTGGAAAAAAACCAACCAGTTGG -s Anc1.Anc1refChr1 25376 30 + 69767 CATAG--ATTTGGAAAAAAACCAACCAGTTGG -s Anc2.Anc2refChr1 101728 30 + 142988 CATAG--ATTTTGAAAGACACCAACCAGTTGG -s mr.mrrefChr3 134437 32 + 181027 GATAGGTATCTGTAAAAGAGCCCAGACATTTG -s simCow_chr6.simCow.chr6 559623 30 + 602619 CATAG--ATTTCAGAAGTGACCAACCAGCTGG -s simDog_chr6.simDog.chr6 548255 29 + 593897 -ATAG--ATTTTGAAAGACACCAACCAGTTGG -s simHuman_chr6.simHuman.chr6 556519 30 + 601863 CATAG--ATTTGGAAAAAAACCAGCCAGTTGG -s simRat_chr6.simRat.chr6 60127 32 - 647215 GACAGGTATCTGCAAAAGAGCTCAAACATTTG - -a -s simMouse_chr6.simMouse.chr6 584831 2 + 636262 TC -s Anc0.Anc0refChr3 185993 2 + 222631 TC -s Anc1.Anc1refChr1 25406 2 + 69767 TC -s Anc2.Anc2refChr1 101758 2 + 142988 TC -s mr.mrrefChr3 134469 2 + 181027 TC -s simCow_chr6.simCow.chr6 559653 2 + 602619 TC -s simDog_chr6.simDog.chr6 548290 2 + 593897 TC -s simHuman_chr6.simHuman.chr6 556549 2 + 601863 TC -s simRat_chr6.simRat.chr6 60159 2 - 647215 TC - -a -s simMouse_chr6.simMouse.chr6 584833 9 + 636262 TATCACCTC -s Anc0.Anc0refChr3 185995 6 + 222631 TATGA---C -s Anc1.Anc1refChr1 25408 9 + 69767 TATGATCTC -s Anc2.Anc2refChr1 101760 6 + 142988 CCTGA---C -s mr.mrrefChr3 134471 9 + 181027 TATCACCTC -s simCow_chr6.simCow.chr6 559662 6 + 602619 CCTGA---T -s simDog_chr6.simDog.chr6 548292 6 + 593897 CCTGA---C -s simHuman_chr6.simHuman.chr6 556551 9 + 601863 TATGATCTC -s simRat_chr6.simRat.chr6 60161 9 - 647215 TATCACCTC - -a -s simMouse_chr6.simMouse.chr6 584842 7 + 636262 TGACAAT -s Anc0.Anc0refChr3 186016 7 + 222631 TCACACT -s Anc1.Anc1refChr1 25432 7 + 69767 TCACACT -s Anc2.Anc2refChr1 101781 7 + 142988 TCACACT -s mr.mrrefChr3 134480 7 + 181027 TGACAAT -s simCow_chr6.simCow.chr6 559736 7 + 602619 TCACACA -s simDog_chr6.simDog.chr6 548313 7 + 593897 TCACTTT -s simHuman_chr6.simHuman.chr6 556575 7 + 601863 TCACACT -s simRat_chr6.simRat.chr6 60170 7 - 647215 TGACAAT - -a -s simMouse_chr6.simMouse.chr6 584849 28 + 636262 ATTCGAGGTCTGCCATATGCAATACCCG -s Anc0.Anc0refChr3 186023 27 + 222631 -TTTAAGGTTGGCCATATGGTGTACCTA -s Anc1.Anc1refChr1 25439 28 + 69767 GTTTAAGGTTGGCCATATGGTGTACCTA -s Anc2.Anc2refChr1 101788 27 + 142988 -TTTAATGTTGGCCATATGGTGTACCTA -s mr.mrrefChr3 134487 28 + 181027 ATTTGAGGTCTGCCATATGCAATACCCG -s simCow_chr6.simCow.chr6 559743 27 + 602619 -TTTGAAGTTTGCCATTTTGGGTACCTA -s simDog_chr6.simDog.chr6 548320 25 + 593897 -TCCAATGTTGGCCATATGGT--AGGTG -s simHuman_chr6.simHuman.chr6 556587 28 + 601863 GTTTAAGGTTGTCCATATGGTGTACCTA -s simRat_chr6.simRat.chr6 60177 25 - 647215 ---TGGGGTCTGCCATATGTAATACCAG - -a -s simMouse_chr6.simMouse.chr6 584877 20 + 636262 CCCACTGATATTAACTTCTG -s Anc0.Anc0refChr3 186050 20 + 222631 CTCACTGATCTTATTTTCAG -s Anc1.Anc1refChr1 25467 20 + 69767 CTCACTGATCTTATTTTCAG -s Anc2.Anc2refChr1 101821 20 + 142988 CTCACTTATCTTGTTTTCAG -s mr.mrrefChr3 134515 20 + 181027 CCCACTGATATTAACTTCTG -s simCow_chr6.simCow.chr6 559776 20 + 602619 CTCAATTATCTTGATTTCAG -s simDog_chr6.simDog.chr6 548351 20 + 593897 CTCACTTATCTTGTTTCCAA -s simHuman_chr6.simHuman.chr6 556615 20 + 601863 TTTACTGATCTTAGTTTCAG -s simRat_chr6.simRat.chr6 60202 20 - 647215 CCCACTGATATTAACTTCTG - -a -s simMouse_chr6.simMouse.chr6 584897 47 + 636262 AATTAATTAAAGAATCATTAACTAAAGTGATCGAGCCTAGCATTGAT -s Anc0.Anc0refChr3 186071 47 + 222631 AAAAGCTTAAACAATGATTGAGGAAAATGATCAAAGTTACTGTTGGT -s Anc1.Anc1refChr1 25488 47 + 69767 AAAAGCTTAAACAATGATTGAGGAAAATGATCAAAGTTACTGTTGGT -s Anc2.Anc2refChr1 101842 47 + 142988 ATAAGCTCAAACAATGATTGAGGAAAATGATCAAAGTTACTGTTGGT -s mr.mrrefChr3 134535 47 + 181027 AATTGATTAAACAATGATTAACTAAAGTGATCGAGCTTACCATTGAT -s simCow_chr6.simCow.chr6 559797 47 + 602619 ATAATCGAAAATGATGATTGAGAAAAATGATCAAGGTTGCCCTTGGG -s simDog_chr6.simDog.chr6 548372 44 + 593897 ATAAGCTCAAACAATGATTGAGG---ATGATCAAAGTTACTGTTGGT -s simHuman_chr6.simHuman.chr6 556636 47 + 601863 AAAAGCTTAAACAATGATTGAGGCAAATAATCAGAGTTACAGTTGGT -s simRat_chr6.simRat.chr6 60222 47 - 647215 AATTGATCATACAAAGATTCACTAAACTGAGTGAGCTTACCATTGAT - -a -s simMouse_chr6.simMouse.chr6 584944 59 + 636262 TAGCCCAGGTATATTGGGTAGAGGATTGTTTGGTGCAAGCATCTACAGGCTGACCAATT -s Anc0.Anc0refChr3 186119 50 + 222631 TAGCTCAAGTATAAC---------ATTGTTTCATGTAAGTACCTACAGGCTGGCCAAGG -s Anc1.Anc1refChr1 25536 50 + 69767 TAGCTCAAGTATAAC---------ATTGTTTCATGTAAGTACCTACAGGCTGGCCAAGG -s Anc2.Anc2refChr1 101890 50 + 142988 TAGCTCAAGTATAAC---------ATTGTTTCATGTAGGCACCTACTGGCTGGCCTAGG -s mr.mrrefChr3 134582 59 + 181027 TAGCTCAGGTATATCGGGTAGAGGATTGTTTGGTGCAAGTATCTACAGGCTGACCAATT -s simCow_chr6.simCow.chr6 559845 18 + 602619 TAGCTCAAGTATAAC---------ATT-------------------------------- -s simDog_chr6.simDog.chr6 548417 50 + 593897 CAGCTCAACTATAGC---------ATTGTTTCATGTAGGCACCTACTGGCTGGCCTAGG -s simHuman_chr6.simHuman.chr6 556684 50 + 601863 TAGCTCAAGCATAAC---------ATTGTTCAATGTAAGTACCTACAGGTGAGCCAAAG -s simRat_chr6.simRat.chr6 60269 59 - 647215 TAGCTCACGTATATCGGGTGTAGGATTGTTGGGTGCAAATATCTACAGGCTGACCAATA - -a -s simMouse_chr6.simMouse.chr6 585003 14 + 636262 TGGGGTAATTGTAA -s Anc0.Anc0refChr3 186169 14 + 222631 TGGTGATATTCTAA -s Anc1.Anc1refChr1 25586 14 + 69767 TGGTGATATTCTAA -s Anc2.Anc2refChr1 101940 14 + 142988 TAATGATATGCTGA -s mr.mrrefChr3 134641 14 + 181027 TGGGGTAATTGTAA -s simDog_chr6.simDog.chr6 548487 14 + 593897 TAATGATATGCTGA -s simHuman_chr6.simHuman.chr6 556734 14 + 601863 TGGTGATATTCTAA -s simRat_chr6.simRat.chr6 60328 14 - 647215 TGGGGTAATTGCAA - -a -s simMouse_chr6.simMouse.chr6 585017 47 + 636262 ACAATGGGAGAGGTGGCTCCGTTAAGTAATGTATGTTTCACACATCA -s Anc0.Anc0refChr3 186291 47 + 222631 TCCATGGGACAGATGTCTCCATTAGCAAATACATAGTCCACACAGAG -s Anc1.Anc1refChr1 25708 47 + 69767 TCCATGGGACAGATGTCTCCATTAGCAAATACATAGTCCACACAGAG -s Anc2.Anc2refChr1 102062 47 + 142988 TCCATGGAACAGATGTCTCCAGTAGCAAATACATAGTCCACACAGAG -s mr.mrrefChr3 134655 47 + 181027 TCAATGGGACAGGTGGCTCCATTAACTAATGCATGGTTCACACATCA -s simCow_chr6.simCow.chr6 559941 47 + 602619 TCCAGGGCACAGATGTCTCCAGTAGCAAATACATAGTCCACATAGAG -s simDog_chr6.simDog.chr6 548601 47 + 593897 TCCATGGAACAGATGTCTCCTGTAGCAAATACATAGTCCATGCAGTG -s simHuman_chr6.simHuman.chr6 556856 47 + 601863 TCCATGGGACAGATGTGTCCATTGGCAAATACATAGCCCACACAGAG -s simRat_chr6.simRat.chr6 60342 47 - 647215 TCAGGGGGACAGGTGGCTCCATTAACTAATGCATGGTTCAGACATCA - -a -s simMouse_chr6.simMouse.chr6 585064 20 + 636262 CATCTAAAAAAAAGAACAGT -s Anc0.Anc0refChr3 186339 20 + 222631 TATGTAAAAAAGAGAAGAAC -s Anc1.Anc1refChr1 25756 20 + 69767 TATGTAAAAAAGAGAAGAAC -s Anc2.Anc2refChr1 102110 20 + 142988 TATGCAAAAAAGACAAGAAC -s mr.mrrefChr3 134702 20 + 181027 CATGTAAAAAAAAGAAGAAT -s simCow_chr6.simCow.chr6 559989 20 + 602619 TGTGGAAAAAAGAAGAGAAT -s simDog_chr6.simDog.chr6 548649 20 + 593897 TATGCAAAAGAAACAAGAAC -s simHuman_chr6.simHuman.chr6 556904 20 + 601863 TATGTAAAAAAGAGAAGAAA -s simRat_chr6.simRat.chr6 60389 20 - 647215 CATGTAAAAAAAAGAAGAAT - -a -s simMouse_chr6.simMouse.chr6 585084 44 + 636262 CACCTAAAGTACTACCTGAGTGATGGGTGATTGGTTGTTACAAG -s Anc0.Anc0refChr3 186366 44 + 222631 CCCTTAGAACACTACTTGAATGATGGATGATTGATTGTTAGGAG -s Anc1.Anc1refChr1 25783 44 + 69767 CCCTTAGAACACTACTTGAATGATGGATGATTGATTGTTAGGAG -s Anc2.Anc2refChr1 102137 44 + 142988 CCCTTAGGACACTACTTGAATGATGGATGATTGATCATTAGGAG -s mr.mrrefChr3 134729 44 + 181027 CACCTAGAGTACTACCTGAGTGATGGGTGATTGATTGTTACAAG -s simCow_chr6.simCow.chr6 560016 44 + 602619 CCCTTAGGAAACTAGTTGAGTGAAGGATGATTGATCACTTGGAT -s simDog_chr6.simDog.chr6 548676 44 + 593897 TGCTTAGGGCACTACTTGAATGCTGGATGATTGATCATTAGGAG -s simHuman_chr6.simHuman.chr6 556931 44 + 601863 CCCTTAGAACACTTATTGTATGATGGATGATTGACTGTTAGGAG -s simRat_chr6.simRat.chr6 60416 44 - 647215 CACCTAGAGTACTACCTGAGTGATGGGTGATTGATTGTTACAAG - -a -s simMouse_chr6.simMouse.chr6 585128 13 + 636262 TATTAATAGATGA -s Anc0.Anc0refChr3 186410 13 + 222631 TATTAACAGATGA -s Anc1.Anc1refChr1 25827 13 + 69767 TATTAACAGATGA -s Anc2.Anc2refChr1 102184 13 + 142988 TGTTAACTGATGA -s mr.mrrefChr3 134773 13 + 181027 TATTAATAGATGA -s simCow_chr6.simCow.chr6 560063 7 + 602619 TGC------ATGA -s simDog_chr6.simDog.chr6 548723 13 + 593897 TGTTAACTGATGA -s simHuman_chr6.simHuman.chr6 556975 12 + 601863 CATTAACAGA-AA -s simRat_chr6.simRat.chr6 60460 13 - 647215 TATTAATAGATGA - -a -s simMouse_chr6.simMouse.chr6 585141 26 + 636262 CTTCTAGTGGCAGGCTATGAGGCTGA -s Anc0.Anc0refChr3 186423 26 + 222631 CTTTTGGTGGCAAGGTCCAAGGTCTA -s Anc1.Anc1refChr1 25840 26 + 69767 CTTTTGGTGGCAAGGTCCAAGGTCTA -s Anc2.Anc2refChr1 102197 26 + 142988 CTTTTGGTGACAGGGTCCAAGGTCTA -s mr.mrrefChr3 134786 26 + 181027 CTTCTAGTGGCAAGCTATGAGGCTTA -s simCow_chr6.simCow.chr6 560070 25 + 602619 CTTTGGCCGCTGTGGCCCAAGTTCT- -s simDog_chr6.simDog.chr6 548736 26 + 593897 CTTTTGGTGACAGGGTCGAGGGTCTA -s simHuman_chr6.simHuman.chr6 556987 26 + 601863 CTTTTGGTGGCAAAGTCCAAGGTCTA -s simRat_chr6.simRat.chr6 60474 26 - 647215 CTTGTAGTGGCAAGCTATGAGGCTTT - -a -s simMouse_chr6.simMouse.chr6 585167 8 + 636262 TTTCAACC -s Anc0.Anc0refChr3 186449 8 + 222631 TTTAATCC -s Anc1.Anc1refChr1 25866 8 + 69767 TTTAATCC -s Anc2.Anc2refChr1 102223 8 + 142988 TTTAATCC -s mr.mrrefChr3 134812 8 + 181027 TTTCAACC -s simCow_chr6.simCow.chr6 560095 8 + 602619 TTTAATTC -s simDog_chr6.simDog.chr6 548767 8 + 593897 TTTAATCC -s simRat_chr6.simRat.chr6 60500 8 - 647215 TTTCAACC - -a -s simMouse_chr6.simMouse.chr6 585175 8 + 636262 CTTAATCC -s Anc0.Anc0refChr3 186457 8 + 222631 CTTAACCC -s Anc1.Anc1refChr1 25874 8 + 69767 CTTAACCC -s Anc2.Anc2refChr1 102231 8 + 142988 CTTAACCC -s mr.mrrefChr3 134820 8 + 181027 CTTAATCC -s simCow_chr6.simCow.chr6 560104 8 + 602619 CTTCACCC -s simDog_chr6.simDog.chr6 548775 8 + 593897 CTTAACCC -s simHuman_chr6.simHuman.chr6 557013 1 + 601863 -------C -s simRat_chr6.simRat.chr6 60508 8 - 647215 TTTAATCC - -a -s simMouse_chr6.simMouse.chr6 585183 21 + 636262 AGGCAGAGATGCGCTTGTTTG -s Anc0.Anc0refChr3 186465 19 + 222631 AGGC--AGATGTTCTTGTTTG -s Anc1.Anc1refChr1 25882 19 + 69767 AGGC--AGATGTTCTTGTTTG -s Anc2.Anc2refChr1 102240 19 + 142988 AGGC--AGATGTTCTTGTTTG -s mr.mrrefChr3 134828 21 + 181027 AGGCAGAGATGCGCTTGTTTG -s simCow_chr6.simCow.chr6 560113 15 + 602619 AG------ATGTTCTTGTTTG -s simDog_chr6.simDog.chr6 548784 19 + 593897 AGGC--AGATGTTCTTGTTTG -s simHuman_chr6.simHuman.chr6 557014 19 + 601863 AGGC--AGATGTTCTTGTTTG -s simRat_chr6.simRat.chr6 60516 21 - 647215 AGGCTCAAATGCACTTGTTTA - -a -s simMouse_chr6.simMouse.chr6 585204 50 + 636262 ATCTACTGACTATTGACACTGTTAAAATCAGCATGATTGAGCGACCGATG -s Anc0.Anc0refChr3 186484 50 + 222631 AACTACTGAATATTAACACTGTTAAAATCAGCACAAATGGGCGATAGATG -s Anc1.Anc1refChr1 25901 50 + 69767 AACTACTGAATATTAACACTGTTAAAATCAGCACAAATGGGCGATAGATG -s Anc2.Anc2refChr1 102268 50 + 142988 AACTACTTAATATTAACACTGTTAAAATCAGCACAAATGGGCAATAGATG -s mr.mrrefChr3 134849 50 + 181027 ATCTACTGACTATTGACACTGTTAAAATCAGCATGATTGGGCGACCGATG -s simCow_chr6.simCow.chr6 560137 50 + 602619 AAATACTCAATATTAACACTGATAAAATTAACATGAATGGGCAATGGATC -s simDog_chr6.simDog.chr6 548812 42 + 593897 AACTACTTAATTTTATCACTGTTAAAGTCAGCACA--------ATAAATG -s simHuman_chr6.simHuman.chr6 557033 50 + 601863 AGCTACTGAATATTAACGCTGTTAAAATCAGCACAGATGGGTGATAGATG -s simRat_chr6.simRat.chr6 60537 50 - 647215 ATCTACTGAGTATTGGCACTGTTAAAAACAGCATGACTGGGCAACCAATG - -a -s simMouse_chr6.simMouse.chr6 585254 13 + 636262 AACCACTGCAGAT -s Anc0.Anc0refChr3 186540 13 + 222631 AGATACTGTGGCT -s Anc1.Anc1refChr1 25957 13 + 69767 AGATACTGTGGCT -s Anc2.Anc2refChr1 102324 13 + 142988 AGATACTGTGGCT -s mr.mrrefChr3 134899 13 + 181027 AAACACTGCAGAT -s simCow_chr6.simCow.chr6 560193 13 + 602619 AGATACTGTGGCT -s simDog_chr6.simDog.chr6 548860 10 + 593897 ACATACTGTG--- -s simHuman_chr6.simHuman.chr6 557089 13 + 601863 AGATACTGTGGCT -s simRat_chr6.simRat.chr6 60587 13 - 647215 AAACACTGCAGAG - -a -s simMouse_chr6.simMouse.chr6 585267 4 + 636262 GTGG -s Anc0.Anc0refChr3 186553 4 + 222631 ACGG -s Anc1.Anc1refChr1 25970 4 + 69767 ACGG -s Anc2.Anc2refChr1 102337 4 + 142988 ACGT -s mr.mrrefChr3 134912 4 + 181027 GTGG -s simCow_chr6.simCow.chr6 560207 4 + 602619 ACGT -s simHuman_chr6.simHuman.chr6 557102 4 + 601863 ACAG -s simRat_chr6.simRat.chr6 60600 4 - 647215 GTGG - -a -s simMouse_chr6.simMouse.chr6 585271 46 + 636262 CTCTAATAATGTACAAGGCTCTATAACAGTCAGATGTTACTCAATT -s Anc0.Anc0refChr3 186558 46 + 222631 CTCTAATTATGCTCAAGACTCTAGAGCAGTCAGATATTCCATAATA -s Anc1.Anc1refChr1 25975 46 + 69767 CTCTAATTATGCTCAAGACTCTAGAGCAGTCAGATATTCCATAATA -s Anc2.Anc2refChr1 102342 46 + 142988 CTTTAATTTTGCTCAAGACTTTAGAGCAGTCAGATATTCCATAGTA -s mr.mrrefChr3 134917 46 + 181027 CTCTAATAATGTACAAGGCTCTATAGCAGTCAGATATTACTCAATT -s simCow_chr6.simCow.chr6 560212 46 + 602619 CTTTAATTTTGCTCAAGACTTTAGAGCAGTCAGATATTCCATAGTA -s simHuman_chr6.simHuman.chr6 557107 46 + 601863 CTCTGATCATGCCCAAGACCCTAAAGCAGTCAGACATTTCAAAATA -s simRat_chr6.simRat.chr6 60605 46 - 647215 CTCTTATAATGTACAAGGCTCTATAGTAGTTGGATATCGCTTGATT - -a -s simMouse_chr6.simMouse.chr6 585317 29 + 636262 CCTCAGGCTGCACAGTTCACCTACAACTG -s Anc0.Anc0refChr3 186604 29 + 222631 CCTCAGGCTGTTTGAGTCTCATGCCACTA -s Anc1.Anc1refChr1 26021 29 + 69767 CCTCAGGCTGTTTGAGTCTCATGCCACTA -s Anc2.Anc2refChr1 102388 29 + 142988 CCTCAGGCTATTTGAGTCTCATGCCACTA -s mr.mrrefChr3 134963 29 + 181027 CCTCAGGCTGCACAGTTCACCTACAACTG -s simCow_chr6.simCow.chr6 560267 29 + 602619 CCTCAGGCTATTTGAGTCTCATGCCACCA -s simDog_chr6.simDog.chr6 548870 13 + 593897 ----------------TCTCATGCCACTA -s simHuman_chr6.simHuman.chr6 557153 29 + 601863 CCCCAGGATGGTTGAGTTTCATGCCATTA -s simRat_chr6.simRat.chr6 60651 29 - 647215 CCTCATGGTTCCCAGTTCATCTACAACTG - -a -s simMouse_chr6.simMouse.chr6 585346 9 + 636262 ATGTCACAC -s Anc0.Anc0refChr3 186634 9 + 222631 ATGTCACAC -s Anc1.Anc1refChr1 26051 9 + 69767 ATGTCACAC -s Anc2.Anc2refChr1 102418 9 + 142988 ATGTGACAC -s mr.mrrefChr3 134992 9 + 181027 ATGTCACAC -s simCow_chr6.simCow.chr6 560297 9 + 602619 ATGTCAAAT -s simDog_chr6.simDog.chr6 548884 9 + 593897 ATGTGACAC -s simHuman_chr6.simHuman.chr6 557183 9 + 601863 ATGTCAAAC -s simRat_chr6.simRat.chr6 60680 9 - 647215 ATGTCACAC - -a -s simMouse_chr6.simMouse.chr6 585355 31 + 636262 ATACGCACACCACGAAAGCTCTGGGGTATAT -s Anc0.Anc0refChr3 186643 31 + 222631 ACACACTCACCATCACAGCTCTGGTGTTTAT -s Anc1.Anc1refChr1 26060 31 + 69767 ACACACTCACCATCACAGCTCTGGTGTTTAT -s Anc2.Anc2refChr1 102427 31 + 142988 ACACACTGACCACCAGAGTTCTGGTGTATAT -s mr.mrrefChr3 135001 31 + 181027 ATGCACACACCATGAAAGCTCTGGGGTATAT -s simCow_chr6.simCow.chr6 560306 31 + 602619 ACACACTGACCTCCAGAGTTGTGGTGTACAT -s simDog_chr6.simDog.chr6 548893 31 + 593897 ACACACTGACTACCAGAGTTCTGGTCTGTAT -s simHuman_chr6.simHuman.chr6 557275 31 + 601863 ACACACTCACTATCACAGCTCTGGCGTGTAT -s simRat_chr6.simRat.chr6 60689 31 - 647215 ATGCAAACACCATGAAAGTTCTGGGGTATAT - -a -s simMouse_chr6.simMouse.chr6 585386 48 + 636262 AAGTAGGTAAGCAGGAATGCAATCCCTGATAGTGAGAGCCTAAATCAA -s Anc0.Anc0refChr3 186674 42 + 222631 GAGTAGGGAGGGAGGAATGTAATCCCTGAC------AACCTAGATCCA -s Anc1.Anc1refChr1 26091 42 + 69767 GAGTAGGGAGGGAGGAATGTAATCCCTGAC------AACCTAGATCCA -s Anc2.Anc2refChr1 102503 42 + 142988 GAGTAGGGAGGGAGGAATGTAATCCCTGAC------AACCTAGATCCA -s mr.mrrefChr3 135032 48 + 181027 AAGTAGGTAAGGAGGAATGCAATCCCTGATAGTGAGAGCCTAGATCAA -s simCow_chr6.simCow.chr6 560382 42 + 602619 AAGTAGGGAGGGAGGAATGTAATCCCTGAC------AACCTAAATCCA -s simDog_chr6.simDog.chr6 548969 26 + 593897 GAGTAGGG----------------CCTGAC------AACCTAGATTCG -s simHuman_chr6.simHuman.chr6 557306 42 + 601863 GAGTAGGGAGGGAGGAATGTAATCCCTGAC------AACCTAGATCCA -s simRat_chr6.simRat.chr6 60720 48 - 647215 AACTAGGTTAGGAGGAATACAATCCCTGATAGTGAGAGCCTAGATCAA - -a -s simMouse_chr6.simMouse.chr6 585434 5 + 636262 CTAGC -s Anc0.Anc0refChr3 186716 5 + 222631 CTCGC -s Anc1.Anc1refChr1 26133 5 + 69767 CTCGC -s Anc2.Anc2refChr1 102545 5 + 142988 CTCGC -s mr.mrrefChr3 135080 5 + 181027 CTAGC -s simCow_chr6.simCow.chr6 560424 5 + 602619 CTAGC -s simDog_chr6.simDog.chr6 548995 5 + 593897 CTCCC -s simHuman_chr6.simHuman.chr6 557348 5 + 601863 CTGGC -s simRat_chr6.simRat.chr6 60769 5 - 647215 CTAGC - -a -s simMouse_chr6.simMouse.chr6 585439 55 + 636262 ACAAGGGCACCCAGTACCATAATATTTGGTTCTCTTAGGTAGTTATGACAACTCC -s Anc0.Anc0refChr3 186721 55 + 222631 ACCAAGTGTCCCCCAGTCATAATCTTACAGCCTCCTAGGTAGTTAAGACAGCCCC -s Anc1.Anc1refChr1 26138 55 + 69767 ACCAAGTGTCCCCCAGTCATAATCTTACAGCCTCCTAGGTAGTTAAGACAGCCCC -s Anc2.Anc2refChr1 102550 55 + 142988 ACCTAGTGTCCCCCAGTCATAATCTTACAGCCTTCTAGGTAGCCAAGACAGCCCC -s mr.mrrefChr3 135085 55 + 181027 ACAAGGGCACCCAGTACCATAATATTTGGGTCTCTTAGGTAGTTATGACAACCCC -s simCow_chr6.simCow.chr6 560429 54 + 602619 AC-TAGTGCCCCCCAGCCATGATCTTACTTCCTTCTAGGTAGCCAAGACATCCCG -s simDog_chr6.simDog.chr6 549001 54 + 593897 ACCTACAGTCTTATAGTC-TAGTCTTATAGTCTTTTAGGTAGCCAAGACAGCCCC -s simHuman_chr6.simHuman.chr6 557353 55 + 601863 ACTAAGTGTCCCCCAGACATAATCTTACAGCCTCCTAGGTAGTTAATACAGCCCC -s simRat_chr6.simRat.chr6 60774 54 - 647215 ACAAGGG-CTCCAGTACCATAATACTTGGGTCTCTTAGGTAGCTATGACAACCCC - -a -s simMouse_chr6.simMouse.chr6 585494 1 + 636262 T -s Anc0.Anc0refChr3 186777 1 + 222631 T -s Anc1.Anc1refChr1 26194 1 + 69767 T -s Anc2.Anc2refChr1 102611 1 + 142988 T -s mr.mrrefChr3 135141 1 + 181027 T -s simCow_chr6.simCow.chr6 560489 1 + 602619 G -s simDog_chr6.simDog.chr6 549061 1 + 593897 T -s simHuman_chr6.simHuman.chr6 557409 1 + 601863 T -s simRat_chr6.simRat.chr6 60829 1 - 647215 T - -a -s simMouse_chr6.simMouse.chr6 585495 42 + 636262 AAACTTTTTGCAAATATGTGCGTCTTCATGCATGGTCTGGTC -s Anc0.Anc0refChr3 186781 32 + 222631 AA-----TTGCATATCTGAGGGTCCTCCTG-----TTTAGTC -s Anc1.Anc1refChr1 26198 32 + 69767 AA-----TTGCATATCTGAGGGTCCTCCTG-----TTTAGTC -s Anc2.Anc2refChr1 102615 32 + 142988 AC-----TTGCATATCTGAGGACCCACCTG-----TTTAACC -s mr.mrrefChr3 135142 37 + 181027 AAACTTTTTGCAAATATGTGGGTCTTCATG-----TTTGGTC -s simCow_chr6.simCow.chr6 560493 32 + 602619 AC-----TTGCATATTTGACGACCCACCTG-----TTTAACC -s simDog_chr6.simDog.chr6 549065 16 + 593897 AC-----TTGCATATCTGAGG--------------------- -s simHuman_chr6.simHuman.chr6 557413 32 + 601863 AA-----TTGAATGTCTGAGGGTCCTCCTG-----TTTAGTC -s simRat_chr6.simRat.chr6 60830 37 - 647215 AAACTTTTCACAAATATGTGGGTCTCCATG-----TTTGGTC - -a -s simMouse_chr6.simMouse.chr6 585537 21 + 636262 TAGCATCTTATCATGCCGATA -s Anc0.Anc0refChr3 186813 21 + 222631 TAAGGTTTTATCCTGCCTATC -s Anc1.Anc1refChr1 26230 21 + 69767 TAAGGTTTTATCCTGCCTATC -s Anc2.Anc2refChr1 102647 21 + 142988 TAAGGTTTTATCCTCCCTGTC -s mr.mrrefChr3 135179 21 + 181027 TAACATCTTATCATGCCGATA -s simCow_chr6.simCow.chr6 560527 21 + 602619 TAAGCTTTTATCCTACCTTTC -s simDog_chr6.simDog.chr6 549081 21 + 593897 TAAAGTTTTACTCTCCCTGTC -s simHuman_chr6.simHuman.chr6 557445 21 + 601863 TGAGGCTTTATCCTGCCTATC -s simRat_chr6.simRat.chr6 60867 21 - 647215 TAACATCCTAACATGCCCATG - -a -s simMouse_chr6.simMouse.chr6 585558 6 + 636262 CCAACT -s Anc0.Anc0refChr3 186837 6 + 222631 TGGAGC -s Anc1.Anc1refChr1 26254 6 + 69767 TGGAGC -s Anc2.Anc2refChr1 102671 6 + 142988 TTGAGC -s mr.mrrefChr3 135200 6 + 181027 TGGACT -s simCow_chr6.simCow.chr6 560551 6 + 602619 TTGAGC -s simDog_chr6.simDog.chr6 549105 6 + 593897 TTGAGC -s simHuman_chr6.simHuman.chr6 557469 6 + 601863 TGGAGC -s simRat_chr6.simRat.chr6 60888 6 - 647215 TGGATT - -a -s simMouse_chr6.simMouse.chr6 585564 5 + 636262 CCATT -s Anc0.Anc0refChr3 186843 5 + 222631 TCATT -s Anc1.Anc1refChr1 26260 5 + 69767 TCATT -s Anc2.Anc2refChr1 102677 5 + 142988 TCATT -s mr.mrrefChr3 135206 5 + 181027 CCATT -s simCow_chr6.simCow.chr6 560557 5 + 602619 TCATT -s simDog_chr6.simDog.chr6 549111 5 + 593897 TCATA -s simHuman_chr6.simHuman.chr6 557475 5 + 601863 TCATT -s simRat_chr6.simRat.chr6 60910 5 - 647215 CCAGT - -a -s simMouse_chr6.simMouse.chr6 585569 10 + 636262 ACTCCAGGGG -s Anc0.Anc0refChr3 186850 7 + 222631 ACTCC---AG -s Anc1.Anc1refChr1 26267 7 + 69767 ACTCC---AG -s Anc2.Anc2refChr1 102684 7 + 142988 ACTCC---AG -s mr.mrrefChr3 135211 10 + 181027 ACTCCAGGGG -s simCow_chr6.simCow.chr6 560564 7 + 602619 ACTCC---AG -s simDog_chr6.simDog.chr6 549118 7 + 593897 ACTCC---AG -s simHuman_chr6.simHuman.chr6 557482 7 + 601863 ACTCC---TG -s simRat_chr6.simRat.chr6 60915 10 - 647215 ACTCCAGGGG - -a -s simMouse_chr6.simMouse.chr6 585579 18 + 636262 TATCTTATATCTGACTTA -s Anc0.Anc0refChr3 186857 18 + 222631 TTTCTAATATCTGACTTA -s Anc1.Anc1refChr1 26274 18 + 69767 TTTCTAATATCTGACTTA -s Anc2.Anc2refChr1 102691 18 + 142988 TTCCTAATATCTGACTTA -s mr.mrrefChr3 135221 18 + 181027 TATCTTATATCTGACTTA -s simCow_chr6.simCow.chr6 560574 18 + 602619 TTCCTAATATTTAACTTA -s simDog_chr6.simDog.chr6 549125 12 + 593897 ------GAGTCTGGCTTA -s simHuman_chr6.simHuman.chr6 557489 18 + 601863 TTTTTAATATCTGAGTTA -s simRat_chr6.simRat.chr6 60925 18 - 647215 TATCCTGTATCTGATTTA - -a -s simMouse_chr6.simMouse.chr6 585597 25 + 636262 TTTGTGAGTCTGCTAATTTCCGTTG -s Anc0.Anc0refChr3 186876 25 + 222631 TTTCATAGTCTGTTAATTTCAGCTG -s Anc1.Anc1refChr1 26293 25 + 69767 TTTCATAGTCTGTTAATTTCAGCTG -s Anc2.Anc2refChr1 102710 25 + 142988 TTTCATGGTCTGTTAATTTCAGCTG -s mr.mrrefChr3 135239 25 + 181027 TTTGTGAGTCTGCTAATTTCCGTTG -s simCow_chr6.simCow.chr6 560593 25 + 602619 TTTAATGGCCTGTCAATTTCAGCTT -s simDog_chr6.simDog.chr6 549138 25 + 593897 TTTCATGGTCAGTTATATTCAGCTG -s simHuman_chr6.simHuman.chr6 557508 25 + 601863 TCTCATAATCTGTTAATTTCAGCTG -s simRat_chr6.simRat.chr6 60943 25 - 647215 TTTGTGAGTTTGCTAACTTCTGTTG - -a -s simMouse_chr6.simMouse.chr6 585622 36 + 636262 CATAAGTAATATCTCTCATATGTTCACTATAGGCCA -s Anc0.Anc0refChr3 186922 25 + 222631 TGGTTGTAATATCTCCCAGATGATC----------- -s Anc1.Anc1refChr1 26339 25 + 69767 TGGTTGTAATATCTCCCAGATGATC----------- -s Anc2.Anc2refChr1 102756 25 + 142988 TGGTTGTAATATCTTCCAGATGATC----------- -s mr.mrrefChr3 135278 36 + 181027 CGTAAGTAATATCTCTCATATGTTCACTATAGGCCA -s simCow_chr6.simCow.chr6 560639 25 + 602619 TGGTTGTATTATCTTTCAGATGATC----------- -s simDog_chr6.simDog.chr6 549184 25 + 593897 TGGTTGTAAAATCTTCCAGGTGATC----------- -s simHuman_chr6.simHuman.chr6 557554 25 + 601863 TGGTCATAATATCTCCCAGACGATC----------- -s simRat_chr6.simRat.chr6 60982 36 - 647215 CGTAAGTAATATCTCTCATAAGTTCACTATAGACTA - -a -s simMouse_chr6.simMouse.chr6 585658 10 + 636262 CAGTTATAAC -s Anc0.Anc0refChr3 187217 10 + 222631 CAGTTATAAC -s Anc1.Anc1refChr1 26635 10 + 69767 CAGTTATAAC -s Anc2.Anc2refChr1 103051 10 + 142988 TAGTTATAAC -s mr.mrrefChr3 135314 10 + 181027 CAGTTATAAC -s simDog_chr6.simDog.chr6 549480 10 + 593897 TAGTTATAAC -s simHuman_chr6.simHuman.chr6 557977 10 + 601863 CAGTTGTAAC -s simRat_chr6.simRat.chr6 61018 10 - 647215 TAATGATAAC - -a -s simMouse_chr6.simMouse.chr6 585668 23 + 636262 TGTAGCCCCTACATCAGATGGCC -s Anc0.Anc0refChr3 187231 1 + 222631 T---------------------- -s Anc1.Anc1refChr1 26649 23 + 69767 TCTAGCTGCTTTGTTAGATCATC -s Anc2.Anc2refChr1 103065 1 + 142988 T---------------------- -s mr.mrrefChr3 135324 23 + 181027 TGTAGCCCCTACATCAGATGGCC -s simDog_chr6.simDog.chr6 549494 1 + 593897 T---------------------- -s simHuman_chr6.simHuman.chr6 557991 23 + 601863 TCTAGCTGCTTTGTTAGATCATC -s simRat_chr6.simRat.chr6 61028 23 - 647215 GGTAGCCCCTACATCAGATTGCC - -a -s simMouse_chr6.simMouse.chr6 585691 14 + 636262 CCTATCTGTTGCAG -s Anc0.Anc0refChr3 187232 3 + 222631 ----------ACA- -s Anc1.Anc1refChr1 26672 13 + 69767 TCTCTTTGTCACA- -s Anc2.Anc2refChr1 103066 3 + 142988 ----------ACA- -s mr.mrrefChr3 135347 13 + 181027 CCTATCTGTTGCA- -s simDog_chr6.simDog.chr6 549495 3 + 593897 ----------ACA- -s simHuman_chr6.simHuman.chr6 558016 13 + 601863 TCTCTTTGTCACA- -s simRat_chr6.simRat.chr6 61051 13 - 647215 CCTATCTGTTGCA- - -a -s simMouse_chr6.simMouse.chr6 585705 8 + 636262 CCTCTTTG -s Anc0.Anc0refChr3 187236 8 + 222631 CCCCTTCA -s Anc1.Anc1refChr1 26686 8 + 69767 CCCCTTCA -s Anc2.Anc2refChr1 103070 8 + 142988 CCCCCTCA -s mr.mrrefChr3 135360 8 + 181027 CCTCTTTG -s simDog_chr6.simDog.chr6 549499 8 + 593897 CCCCCTCA -s simHuman_chr6.simHuman.chr6 558030 8 + 601863 CCCCTTCA -s simRat_chr6.simRat.chr6 61064 8 - 647215 CCTCTTTG - -a -s simMouse_chr6.simMouse.chr6 585713 11 + 636262 TCAGACCAGTT -s Anc0.Anc0refChr3 187244 11 + 222631 TCAGATCACCA -s Anc1.Anc1refChr1 26694 11 + 69767 TCAGATCACCA -s Anc2.Anc2refChr1 103078 11 + 142988 TCAGATCACCA -s mr.mrrefChr3 135368 11 + 181027 TCAGACCAGTT -s simDog_chr6.simDog.chr6 549558 11 + 593897 TCAGATCACCA -s simHuman_chr6.simHuman.chr6 558038 11 + 601863 TCGGATCACCA -s simRat_chr6.simRat.chr6 61072 11 - 647215 TCAGATCGGTT - -a -s simMouse_chr6.simMouse.chr6 585724 11 + 636262 GTCTCACTATT -s Anc0.Anc0refChr3 187255 11 + 222631 GCCTCTTTGTC -s Anc1.Anc1refChr1 26705 11 + 69767 GCCTCTTTGTC -s Anc2.Anc2refChr1 103089 11 + 142988 GCCTCTTTGTC -s mr.mrrefChr3 135379 11 + 181027 GTCTCACTATT -s simDog_chr6.simDog.chr6 549569 11 + 593897 GCCTCTTTGTC -s simHuman_chr6.simHuman.chr6 558049 11 + 601863 GCCTCTTTGTC -s simRat_chr6.simRat.chr6 61084 11 - 647215 GTCTCACTGTC - -a -s simMouse_chr6.simMouse.chr6 585735 8 + 636262 GGATCACC -s Anc0.Anc0refChr3 187266 6 + 222631 AGATTA-- -s Anc1.Anc1refChr1 26716 6 + 69767 AGATTA-- -s Anc2.Anc2refChr1 103100 6 + 142988 AGATTA-- -s mr.mrrefChr3 135390 8 + 181027 GGATCACC -s simDog_chr6.simDog.chr6 549582 6 + 593897 AGATTA-- -s simHuman_chr6.simHuman.chr6 558060 6 + 601863 AGATTA-- -s simRat_chr6.simRat.chr6 61095 8 - 647215 AGACCACC - -a -s simMouse_chr6.simMouse.chr6 585743 25 + 636262 GGCATCAATTGCACCAAGGATATGG -s Anc0.Anc0refChr3 187272 25 + 222631 AGCAGTGGGTGTGCTAGGGCTGTAG -s Anc1.Anc1refChr1 26722 25 + 69767 AGCAGTGGGTGTGCTAGGGCTGTAG -s Anc2.Anc2refChr1 103106 25 + 142988 AGATGTGGGTGTGCTAGGGCTGTAG -s mr.mrrefChr3 135398 25 + 181027 GGCATCAATTGCACCAAGGATATGG -s simCow_chr6.simCow.chr6 560833 5 + 602619 --------------------TGTAG -s simDog_chr6.simDog.chr6 549590 25 + 593897 AGATGTGGGTGTGCTAGGGCTGTAG -s simHuman_chr6.simHuman.chr6 558066 25 + 601863 AGCAAGGCGTGTGCTAGGGCTGTAG -s simRat_chr6.simRat.chr6 61103 25 - 647215 AGCATCAATTGCAATAGGGGTTTAG - -a -s simMouse_chr6.simMouse.chr6 585768 44 + 636262 ATTGCATGCCTGTTTGTCTCTTCTGAGGTATGCCAATTTAACCT -s Anc0.Anc0refChr3 187297 41 + 222631 GCTGCCTGGCTGCTTACCTAT---GAAGTACTCCAGTTCAACCT -s Anc1.Anc1refChr1 26747 41 + 69767 GCTGCCTGGCTGCTTACCTAT---GAAGTACTCCAGTTCAACCT -s Anc2.Anc2refChr1 103131 41 + 142988 GCTGCCTGGCTGCTTACCTAT---GAAGTACTTGAGTTCAACCT -s mr.mrrefChr3 135423 41 + 181027 ATTGCATGCCTGTTTGTCTCT---GAGGTATGCCAATTTAACCT -s simCow_chr6.simCow.chr6 560838 41 + 602619 GCTGACTGGCTGCTTACTTTT---GAAGCACTTGACTTCAACCT -s simDog_chr6.simDog.chr6 549685 39 + 593897 GCTACCTGGCTTCCTGCCTAT---AAAGT--CTGAGTTCAACCT -s simHuman_chr6.simHuman.chr6 558091 41 + 601863 TCTGCCTGGGTGCTTACCTAT---GAAGTGCTCCAGTTCAACCT -s simRat_chr6.simRat.chr6 61128 41 - 647215 AGTGCATGCCTGTTTGTCTCT---GAGGTATGCCAAGTTAACCC - -a -s simMouse_chr6.simMouse.chr6 585812 84 + 636262 AGTCATATGTGTTGCACTAGCAAGCTTCAATTTTAGTACCCTCATCTTATCCCTCATTTTAAAATCACCCTCTTGTAAGCACAT -s Anc0.Anc0refChr3 187339 66 + 222631 ACTAATATGTGTTACCCTAGTAGGCTGCAGT------ATCCTTATCTTA------------AAATCAATCTCCTTGAAGCACAT -s Anc1.Anc1refChr1 26789 68 + 69767 ACTAATATGTGTTACCCTAGTAGGCTGCAGT----GTATCCTTATCTTA------------AAATCAATCTCCTTGAAGCACAT -s Anc2.Anc2refChr1 103173 66 + 142988 ACTAATATATGTTACCCTAGTAGGCTGCAGT------ATCCTTAGCTTA------------AAATCAATCTCCTTGAAGCACAT -s mr.mrrefChr3 135464 72 + 181027 AGTCATATGTGTTGCACTAGCAAGCTTCAATTTTAGTACCCTCATCTTA------------AAATCACCCTCTTGTAAGCACAT -s simCow_chr6.simCow.chr6 560880 66 + 602619 ACTAATATATGTTCTCCTAGTAGACTGCAGA------ATCCTTAGCTTA------------AAATCAATCTCATGTAAGCACAT -s simDog_chr6.simDog.chr6 549726 53 + 593897 ACT----------ACACCGGTAGGCTGCAGT------ATCCTTAGCTTA------------AAATCA--CCCCTTGTAACACA- -s simHuman_chr6.simHuman.chr6 558133 60 + 601863 ACTGGTGTGAGTTACCCTAGTAGGCCGCGGT------------ATCCTT------------AAATCAGTCTCCTCCAAGCACAT -s simRat_chr6.simRat.chr6 61169 72 - 647215 AGTCATATGTGTTTCTTTAGCAGACTTTGACTTCAGTATCTTCGTCTTA------------AAATCACCCTCTTGTAAGCCCAT - -a -s simMouse_chr6.simMouse.chr6 585896 2 + 636262 TA -s Anc0.Anc0refChr3 187406 2 + 222631 CA -s Anc1.Anc1refChr1 26858 2 + 69767 CA -s Anc2.Anc2refChr1 103240 2 + 142988 CA -s mr.mrrefChr3 135536 2 + 181027 TA -s simCow_chr6.simCow.chr6 560947 2 + 602619 CA -s simHuman_chr6.simHuman.chr6 558194 2 + 601863 CA -s simRat_chr6.simRat.chr6 61254 2 - 647215 TA - -a -s simMouse_chr6.simMouse.chr6 585898 6 + 636262 TCAATG -s Anc0.Anc0refChr3 187408 6 + 222631 CAAAAT -s Anc1.Anc1refChr1 26860 6 + 69767 CAAAAT -s Anc2.Anc2refChr1 103242 6 + 142988 CAAAAT -s mr.mrrefChr3 135538 6 + 181027 TCAATG -s simCow_chr6.simCow.chr6 560951 6 + 602619 CACACT -s simDog_chr6.simDog.chr6 549779 6 + 593897 CAAAAT -s simHuman_chr6.simHuman.chr6 558196 6 + 601863 CTAAAT -s simRat_chr6.simRat.chr6 61256 6 - 647215 CCAATG - -a -s simMouse_chr6.simMouse.chr6 585904 5 + 636262 AGCTG -s Anc0.Anc0refChr3 187414 5 + 222631 AGTTA -s Anc1.Anc1refChr1 26866 5 + 69767 AGTTA -s Anc2.Anc2refChr1 103249 5 + 142988 AGTTA -s mr.mrrefChr3 135544 5 + 181027 AGCTG -s simCow_chr6.simCow.chr6 560958 5 + 602619 AGTTA -s simDog_chr6.simDog.chr6 549786 5 + 593897 AGTTA -s simHuman_chr6.simHuman.chr6 558202 5 + 601863 AGTCA -s simRat_chr6.simRat.chr6 61262 5 - 647215 AGCAG - -a -s simMouse_chr6.simMouse.chr6 585909 6 + 636262 TCCCTC -s Anc0.Anc0refChr3 187419 6 + 222631 TCTTTC -s Anc1.Anc1refChr1 26871 6 + 69767 TCTTTC -s Anc2.Anc2refChr1 103254 6 + 142988 TCTTTC -s mr.mrrefChr3 135549 6 + 181027 TCCCTC -s simCow_chr6.simCow.chr6 560963 6 + 602619 TTTTTC -s simDog_chr6.simDog.chr6 549791 6 + 593897 TCTTTC -s simHuman_chr6.simHuman.chr6 558207 6 + 601863 TCTTTC -s simRat_chr6.simRat.chr6 61270 6 - 647215 TCCCTT - -a -s simMouse_chr6.simMouse.chr6 585915 13 + 636262 CTTAAAGTGATAT -s Anc0.Anc0refChr3 187428 13 + 222631 CTTAAGGTAACAC -s Anc1.Anc1refChr1 26880 13 + 69767 CTTAAGGTAACAC -s Anc2.Anc2refChr1 103263 13 + 142988 ATTAAGCTAACAC -s mr.mrrefChr3 135555 13 + 181027 CTTAAAGTGATAT -s simCow_chr6.simCow.chr6 560969 10 + 602619 ---AAGCTAACAC -s simDog_chr6.simDog.chr6 549800 13 + 593897 ATTAAGCCAACAC -s simHuman_chr6.simHuman.chr6 558216 13 + 601863 CTTAGGGTAACAC -s simRat_chr6.simRat.chr6 61276 13 - 647215 CTAAGAGTAACAT - -a -s simMouse_chr6.simMouse.chr6 585928 36 + 636262 GTAAAGCTGGTGGTATCAATCAAAGGGTGAACTACC -s Anc0.Anc0refChr3 187441 36 + 222631 GGAAAGGTGGTTTTGTCAATTCAAGGGAGAACCACC -s Anc1.Anc1refChr1 26893 36 + 69767 GGAAAGGTGGTTTTGTCAATTCAAGGGAGAACCACC -s Anc2.Anc2refChr1 103276 36 + 142988 GGAAAGGTGGTTTTGTCAGTTCAAGGGAGAACCACC -s mr.mrrefChr3 135568 36 + 181027 GTAAAGCTGGTGGTATCAATCAAAGGGTGAACTACC -s simCow_chr6.simCow.chr6 560979 36 + 602619 GGAAAGTTGGTTTTGTCAGTTCAAGGGAGAATCACC -s simDog_chr6.simDog.chr6 549825 36 + 593897 GGATATGTGGTTTTGTTGGTTCAAAAGAGAACGACT -s simHuman_chr6.simHuman.chr6 558229 36 + 601863 GGAATGATGGTTTTGTCAATTCAAGGGGGAACCACC -s simRat_chr6.simRat.chr6 61289 36 - 647215 GTGAATCTAGTAGCATCAATTAAAGGGAGAACTATC - -a -s simMouse_chr6.simMouse.chr6 585964 38 + 636262 ATCAATTAAGGTATCATCATTATACATTCCATCATGTA -s Anc0.Anc0refChr3 187477 35 + 222631 ATTAGTATACTTATAATCCAC---CATTCCAATCTGTC -s Anc1.Anc1refChr1 26929 35 + 69767 ATTAGTATACTTATAATCCAC---CATTCCAATCTGTC -s Anc2.Anc2refChr1 103312 35 + 142988 ATTTGTATCCTCATAATTCAC---CATTCCAATCTGTC -s mr.mrrefChr3 135604 38 + 181027 ATCAATTAAGGTATCATCATTATACATTCCATCATGTA -s simCow_chr6.simCow.chr6 561024 31 + 602619 ATTTGTATGTTGATA---CAT---CATTT-AGTCTGTC -s simDog_chr6.simDog.chr6 549861 33 + 593897 AT--GTATCCTCATAATTCAC---CATTCCAATTTGTC -s simHuman_chr6.simHuman.chr6 558265 35 + 601863 ATTAGTATACTTATAATCCAC---CATTCCAATCTGTC -s simRat_chr6.simRat.chr6 61325 38 - 647215 ATCAATTAAGGTATCATCATAATACATTCCATCATGTA - -a -s simMouse_chr6.simMouse.chr6 586002 15 + 636262 ATAAGAGATTTGCCA -s Anc0.Anc0refChr3 187512 8 + 222631 ATA-GAGCT------ -s Anc1.Anc1refChr1 26964 8 + 69767 ATA-GAGCT------ -s Anc2.Anc2refChr1 103347 8 + 142988 CTA-GAGCT------ -s mr.mrrefChr3 135642 14 + 181027 ATA-GAGATTTGCCA -s simCow_chr6.simCow.chr6 561055 7 + 602619 GTA-G-GCT------ -s simDog_chr6.simDog.chr6 549894 8 + 593897 CTA-GAGCT------ -s simHuman_chr6.simHuman.chr6 558300 8 + 601863 ACA-GAGTT------ -s simRat_chr6.simRat.chr6 61374 14 - 647215 ATA-GAGATTTACTA - -a -s simMouse_chr6.simMouse.chr6 586017 29 + 636262 AGACAGGTTAAATTGCAGGACTAGTATGG -s mr.mrrefChr3 135656 29 + 181027 AGACAGGTTAAATTGCAGGACTAGTATGG -s simRat_chr6.simRat.chr6 61397 29 - 647215 AGACACGCTAAATCGCAGGACTAGTATGG - -a -s simMouse_chr6.simMouse.chr6 586046 20 + 636262 TCggaacacagccaacacaa -s mr.mrrefChr3 135685 18 + 181027 TCggaacacag--aacacaa -s simRat_chr6.simRat.chr6 61450 18 - 647215 TAGGAACACAG--GACTCAA - -a -s simMouse_chr6.simMouse.chr6 586066 21 + 636262 cccatcaaatacccacaaact -s mr.mrrefChr3 135703 21 + 181027 cccatcaaatacccacaaact -s simRat_chr6.simRat.chr6 61474 21 - 647215 TTTACTCAAAATCAGCAAGGT - -a -s simMouse_chr6.simMouse.chr6 586087 19 + 636262 aagattcaaggaacattcg -s mr.mrrefChr3 135724 19 + 181027 aagattcaaggaacattcg -s simRat_chr6.simRat.chr6 61509 19 - 647215 AGGACTCAAGGTGCATTCt - -a -s simMouse_chr6.simMouse.chr6 586106 56 + 636262 taaaatcagtaaggggaagccactaacaattcaaagattactgactgaacattctg -s mr.mrrefChr3 135743 56 + 181027 taaaatcagtaaggggaagccactaacaattcaaagattactgactgaacattctg -s simRat_chr6.simRat.chr6 61530 56 - 647215 taaaatcagtaaggggaagctgctaacaattcagagattactgtctgaacattctg - -a -s simMouse_chr6.simMouse.chr6 586162 115 + 636262 tcttagtcgttcaccggcaaacataattgagcagaaccattatcgtgaaatcagtggccttgttcaccacacacagaaagaccactatagattgcctggcctggagtgagaaaag -s mr.mrrefChr3 135799 109 + 181027 tcttagtcgttcaccggcaaacataattgagca---ccattatcgtgaaatcagtggccttgttcaccacacacagaaagaccactatagatt---tggcctggagtgagaaaag -s simRat_chr6.simRat.chr6 61599 109 - 647215 tcttgatctttcaccagcaaatataattgagca---ctattattgtgaaaccagtggtcttgttcaccacacctaaaaagaccattgttgaat---ctgcctggaatgagaaaag - -a -s simMouse_chr6.simMouse.chr6 586277 171 + 636262 gaacccatggcagaatcctttcttagtgaaagaaatcaagggagtgcagtcatatccttgaactttaagtgttactatcaggtaactattgtgaaagcaacactatacttgcatcaaaagatcagtacaatacaccatggaattagaagtgatggagctaccacatttaag -s mr.mrrefChr3 135908 171 + 181027 gaacccatggcagaatcctttcttagtgaaagaaatcaagggagtgcagtcatatccttgaactttaagtgttactatcaggtaactattgtgaaagcaacactatacttgcatcaaaagatcagtacaatacaccatggaattagaagtgatggagctaccacatttaag -s simRat_chr6.simRat.chr6 61709 171 - 647215 gaacccaaggcagaaccttttcttattgaaaaaaatcaggggagtgcgatcatatcctcgaactttaagtgttactcttgagtaacagtttggaaagcaacactatattagcatcaaaagatcattacaatacaccatgggattagtagtgatggagctaccacacttagg - -a -s simMouse_chr6.simMouse.chr6 586448 484 + 636262 aaacgcttcatattgtgatgagagatcttaacaaggacccattattcaatatgtacttagggaattggttgttcacctcccaaaaattagagcttgacacttgcccatcaccatataccatgactaatacaagtgtgtaactaatctaaagaattgaggttcggagctaccacatttaagaaacgcttcatattgtgatgagagatcttaacaaggacccattattcaatatgtacttagggaattggttgttcacctcccaaaaattagagcttgacacttgcccatcaccatataccatgactaatacaagtgtgtaactaatctaaagaattgaggttctcatcccccaaaaagtgtaaagggctgagaagatctcctgagaaagaccttttaagatattagaaacataggaatggttatacaaaaaaaccacaaggatagagtggccataacatggacatatgtcttgcagaactcaaga -s mr.mrrefChr3 136079 293 + 181027 aaacgcttcatattgtgatgagagatcttaacaaggacccattattcaatatg---------aattggttgttcacctcccaaaaattagagcttgacacttgcccatcaccatataccatgactaatacaagt-tgtaactaatctaaagaattgaggttcggagctacca--------aaacgcttcatattgtgatgagagatcttaacaaggacccatta--caatatgtacttagggaattggtt---------------------------------------------------------------------------------------------------------------------------------------------------------------------------atacaaaaaaaccacaaggatagagtggccataacatggacatatgtcttgcagaactcaaga -s simRat_chr6.simRat.chr6 61906 293 - 647215 aaacgcttcatattatgatgagaaattttaacaaggactcattattcaatctg---------aatcagtttattaccttccaaaaattaaaacttgacatttccccattaccttataccatgattaatacaagc-tgttactggtctaatgaattgaggttctcatccccca--------aaaagtgttaagggctgagtagattttctgagaaggacctttta--agatattggaacgggggaatggtt---------------------------------------------------------------------------------------------------------------------------------------------------------------------------atacaataccaccacaaggatagtgtgggcataacatgcaaatatgtcttgcaaagcccgaga - -a -s simMouse_chr6.simMouse.chr6 586932 86 + 636262 taaatgatcaacaaacatgagtgggatgtaaacaagggaaagagcacacttacagtaaacccaggagtttagcaaataggatagaa -s mr.mrrefChr3 136372 85 + 181027 taaatgatcaacaaacatgagtgggatgtaaacaagggaaagagcacacttacagtaaacc-aggagtttagcaaataggatagaa -s simRat_chr6.simRat.chr6 62219 85 - 647215 taaatgatcaagaaatatgaatggggtgtaaacaaggtaaagagcatacttagagtagacc-atgaggttagtaaataggatagaa - -a -s simMouse_chr6.simMouse.chr6 587018 140 + 636262 cctttgtcacctatttgtccaaaaggggtccagtctctcaggtctcatagcaaactcacccaaatacacaaggagaagcccagtgacataatcaatagacagattggaaccataaacaggctctcactggtaaggggaga -s mr.mrrefChr3 136457 140 + 181027 cctttgtcacctatttgtccaaaaggggtccagtctctcaggtctcatagcaaactcacccaaatacacaaggagaagcccagtgacataatcaatagacagattggaaccataaacaggctctcactggtaaggggaga -s simRat_chr6.simRat.chr6 62311 140 - 647215 ccttcgacacctacttgtccaaaaggggcccagtatctaaggtgccacagcaaactcacacagatacgcaaagagaaacccggtaacacgaccaatagatggactgaaaccataaatgggctctcataggcaaggggaga - -a -s simMouse_chr6.simMouse.chr6 587158 28 + 636262 cccggtgcaaggaagcaccataggaagt -s mr.mrrefChr3 136597 28 + 181027 cccggtgcaaggaagcaccataggaagt -s simRat_chr6.simRat.chr6 62452 28 - 647215 cccgttgcaaggaaccaccataggcagt - -a -s simMouse_chr6.simMouse.chr6 587186 22 + 636262 gtgctGAGGTTTTTCAGGACCC -s mr.mrrefChr3 136625 22 + 181027 gtgctgaggtttttcaggacCC -s simRat_chr6.simRat.chr6 62481 22 - 647215 gcactgaggtttttctgatcCT - -a -s simMouse_chr6.simMouse.chr6 587208 319 + 636262 CTCCGTAAGCATTTTTGAGTTTAGAGCAACAGTGAAATTGGGAGGTAGCACATTTCCTATGGAACCCATCGACTGCATGGTCCTCCTACCCCTAACCCTGGAATCCACGTCTCGACCCGTCAACACTGCTATATAGTCTCGCGATGAGAGTTCGAACCATTTGTCCCTACCCCCGGAATTCATGTCTTGAGCCATCAACACTATTATATAGTCTAGCGTTGAGAGTTTGAACCATTTGGGAATCATGAATTCCAGAGTAGATTAACTTCTTTATTTACTATAAGTGACGAGATAAGATACCAGACTCATCCTGCCATAG -s mr.mrrefChr3 136647 17 + 181027 CTCCGTAAGC--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GCCATAG -s simRat_chr6.simRat.chr6 62505 17 - 647215 CACAGTAAGC--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GCCATAG - -a -s simMouse_chr6.simMouse.chr6 587527 63 + 636262 CAGTTATCTATCTCTCAGTCGGCCTGTCAAAGAGGCCTCTGTGGCCACTGCAGTGCTACTCCA -s Anc0.Anc0refChr3 187520 16 + 222631 -----------------------------------------------CTACTGCCCTGCTCCA -s Anc1.Anc1refChr1 26972 16 + 69767 -----------------------------------------------CTACTGCCCTGCTCCA -s Anc2.Anc2refChr1 103355 16 + 142988 -----------------------------------------------TTACTGCCCTGCTCCA -s mr.mrrefChr3 136664 63 + 181027 CAGTTATCTATCTCTCAGTCGGCCTGTCAAAGAGGCCTCTGTGGCCACTGCAGTGCTACTCCA -s simCow_chr6.simCow.chr6 561062 16 + 602619 -----------------------------------------------TTACTGCCCTGCCCCA -s simDog_chr6.simDog.chr6 549902 16 + 593897 -----------------------------------------------TTACCGCCCTGCTCCG -s simHuman_chr6.simHuman.chr6 558308 16 + 601863 -----------------------------------------------CTCCTGCCCTGCTCCA -s simRat_chr6.simRat.chr6 62523 63 - 647215 TGGTTAGCTACTGCTCAGTCAGCCCATCAAAGGGGCATTTGTGGCTACTCTAGTGCTACTCCA - -a -s simMouse_chr6.simMouse.chr6 587590 8 + 636262 ATGAGTAA -s Anc0.Anc0refChr3 187537 8 + 222631 ATAAGTTG -s Anc1.Anc1refChr1 26989 8 + 69767 ATAAGTTG -s Anc2.Anc2refChr1 103372 8 + 142988 ATAAGTTG -s mr.mrrefChr3 136727 8 + 181027 ATGAGTAA -s simCow_chr6.simCow.chr6 561079 3 + 602619 ATA----- -s simDog_chr6.simDog.chr6 549919 8 + 593897 ATGAGTTG -s simHuman_chr6.simHuman.chr6 558325 8 + 601863 GCAAGTTG -s simRat_chr6.simRat.chr6 62586 8 - 647215 ATGAGTAA - -a -s simMouse_chr6.simMouse.chr6 587598 10 + 636262 CTACAGGGAG -s Anc0.Anc0refChr3 187545 10 + 222631 TCACAGTATT -s Anc1.Anc1refChr1 26997 10 + 69767 TCACAGTATT -s Anc2.Anc2refChr1 103380 10 + 142988 TCCCAGTATT -s mr.mrrefChr3 136735 10 + 181027 CTACAGGGAG -s simCow_chr6.simCow.chr6 561082 10 + 602619 TTCCAGTTTT -s simDog_chr6.simDog.chr6 549948 10 + 593897 TCCCAGTATT -s simHuman_chr6.simHuman.chr6 558333 10 + 601863 TCACAGTACT -s simRat_chr6.simRat.chr6 62594 10 - 647215 CCATGGGGAG - -a -s simMouse_chr6.simMouse.chr6 587608 9 + 636262 GCCTTTGAT -s Anc0.Anc0refChr3 187557 9 + 222631 ACCTTTGAT -s Anc1.Anc1refChr1 27009 9 + 69767 ACCTTTGAT -s Anc2.Anc2refChr1 103392 9 + 142988 ACCTTTATT -s mr.mrrefChr3 136745 9 + 181027 GCCTTTGAT -s simCow_chr6.simCow.chr6 561094 7 + 602619 ACCC--ATT -s simDog_chr6.simDog.chr6 549960 9 + 593897 GCTTTTATT -s simHuman_chr6.simHuman.chr6 558345 9 + 601863 ACCTTTGAT -s simRat_chr6.simRat.chr6 62604 9 - 647215 GCCTTTGAT - -a -s simMouse_chr6.simMouse.chr6 587617 10 + 636262 ATTACCATGC -s Anc0.Anc0refChr3 187571 10 + 222631 ATTAGGATGC -s Anc1.Anc1refChr1 27023 10 + 69767 ATTAGGATGC -s Anc2.Anc2refChr1 103406 10 + 142988 ACTAGGATGC -s mr.mrrefChr3 136754 10 + 181027 ATTACCATGC -s simCow_chr6.simCow.chr6 561106 3 + 602619 TCT------- -s simDog_chr6.simDog.chr6 549975 10 + 593897 ACTAGGATGC -s simHuman_chr6.simHuman.chr6 558359 10 + 601863 ATTAGGATGC -s simRat_chr6.simRat.chr6 62613 10 - 647215 ATTACCATGC - -a -s simMouse_chr6.simMouse.chr6 587627 14 + 636262 CATGCACAACTTAA -s Anc0.Anc0refChr3 187581 8 + 222631 CGTG----GCTT-- -s Anc1.Anc1refChr1 27033 10 + 69767 CGTG----GCTTAA -s Anc2.Anc2refChr1 103416 8 + 142988 TGTA----GCTT-- -s mr.mrrefChr3 136764 14 + 181027 CATGCACAACTTAA -s simCow_chr6.simCow.chr6 561109 3 + 602619 ---------CTT-- -s simDog_chr6.simDog.chr6 549987 8 + 593897 TGTA----GCTT-- -s simHuman_chr6.simHuman.chr6 558369 10 + 601863 CGTG----GCTTAA -s simRat_chr6.simRat.chr6 62623 14 - 647215 CATGTGCAACTCAA - -a -s simMouse_chr6.simMouse.chr6 587641 96 + 636262 ACAGGACACTGCATAGCTTGTGATATTAAATGCTTAGCAGAAGGGCACAATCAAGGTGTGTTAGACTCTCTTTTTTAATAGCATTATTGCTAGATA -s Anc1.Anc1refChr1 27043 23 + 69767 ACAGCACACAGCACAGTGTGCGC------------------------------------------------------------------------- -s mr.mrrefChr3 136778 86 + 181027 ACAGGACACTGCATAGCTTGTGATATTAAATGCTTAGCAGAAGGGCACAATCA-------ttagac---cttttttaatagcattattgctagata -s simHuman_chr6.simHuman.chr6 558382 23 + 601863 ACAGCACACAGCACAGTGTGCGC------------------------------------------------------------------------- -s simRat_chr6.simRat.chr6 62637 86 - 647215 ACAGGATACTGCATAGCATGTGATAATAAATGCTTGGCAGCAGGGCACAATAA-------ttagac---cttttataatcgcattattgctagata - -a -s simMouse_chr6.simMouse.chr6 587737 16 + 636262 GTGGTTAAATCCATAA -s mr.mrrefChr3 136864 16 + 181027 gtggttaaatccataa -s simRat_chr6.simRat.chr6 62724 16 - 647215 gtggataaatccatag - -a -s simMouse_chr6.simMouse.chr6 587753 13 + 636262 TATGGTGATCACA -s mr.mrrefChr3 136880 13 + 181027 tatggtgatcaca -s simRat_chr6.simRat.chr6 62743 13 - 647215 tgaggggattgaa - -a -s simMouse_chr6.simMouse.chr6 587766 140 + 636262 GGAGCCAGGAAACAAGACTTTTTCTCCTTGTCACAACCTGGAGGAATCCTAGCTTTATCCCTAATGTTGCACTTGCTTTCACAACTTGGCCTTCTTATTCTTTCCCAAAGTTGGAGACAAAGCACCCATGCTCTCCTTGA -s Anc0.Anc0refChr3 187589 98 + 222631 ----------------------------------------GAGGAATTCCAGTTTTATGCTTATTTCTGTACTTCTTTTCCCAAATTGGCCTTCTTTTTCTTCCC--AGGTTGGAAATCCAGAACCCACCTTCTCCTCAA -s Anc1.Anc1refChr1 27066 98 + 69767 ----------------------------------------GAGGAATTCCAGTTTTATGCTTATTTCTGTACTTCTTTTCCCAAATTGGCCTTCTTTTTCTTCCC--AGGTTGGAAATCCAGAACCCACCTTCTCCTCAA -s Anc2.Anc2refChr1 103424 98 + 142988 ----------------------------------------GAGTAGTTCCAGTTTTATGCTTATTTCTGTACTTCATTTCCCAAATTGGCCCTCTTTTTCTTCCC--AGGTTGGATATCCAAAACCCACCTTCTCCTCAA -s mr.mrrefChr3 136893 140 + 181027 ggagccaggaaacaagactttttctccttgtcacaACCTGGAGGAATCCTAGTTTTATCCCTAATGCTGCACTTGTTTTCACAAATTGGCCTTCTTTTTCTTTCCCAAAGTTGGAAACAAAGCACCCATGCTCTCCTTGA -s simCow_chr6.simCow.chr6 561112 98 + 602619 ----------------------------------------GAGTGGTTCCAGTTTTACGCCTAATACTCTACTTCATTTCCCAAGTTGGCCCTCTTTTCCTTCTC--AGGTTGGATATCCAAAACACACCTTCTCCTCAA -s simDog_chr6.simDog.chr6 549995 92 + 593897 ----------------------------------------GGGTAGCTTGATTTTTATGCTTATTTCTGTACTTCATTTCCCATATTGGCCCTCTTCTTTTTCCC--ACGTTGGATAT-----ACCCACCTT-TTCTCGA -s simHuman_chr6.simHuman.chr6 558405 94 + 601863 ----------------------------------------GAGGAATTCCAGTTTTA----TATTTCTGTACTACTTTTCCCAAACTGACCTTCTTTTTCTTCCC--AGGTTGGAAATCCAGTGCCCACCTTGCCCTCAA -s simRat_chr6.simRat.chr6 62765 118 - 647215 gaaaccaggaaacaaagctttctctactagtcacaACCGGGAGGAATCCTAGTTTCATCCCTAATGCTGCACTTGTTTACATAAATTCGCCTTCTTTTTCCTTCCCAAAGTTGGAAAC---------------------- - -a -s simMouse_chr6.simMouse.chr6 587906 14 + 636262 TAACGATCAATAGT -s Anc0.Anc0refChr3 187729 14 + 222631 TGATGATCTAAAGT -s Anc1.Anc1refChr1 27206 14 + 69767 TGATGATCTAAAGT -s Anc2.Anc2refChr1 103564 14 + 142988 TGATAATATAAAAA -s mr.mrrefChr3 137033 14 + 181027 TAACGATCAATAGT -s simCow_chr6.simCow.chr6 561252 14 + 602619 TGATAATATGAAAA -s simDog_chr6.simDog.chr6 550129 14 + 593897 TGATAATATAAAAA -s simHuman_chr6.simHuman.chr6 558548 14 + 601863 TGATGATCTAAAGT - -a -s simMouse_chr6.simMouse.chr6 587920 10 + 636262 ATACACCATT -s Anc0.Anc0refChr3 187747 8 + 222631 ATACAC--TT -s Anc1.Anc1refChr1 27224 8 + 69767 ATACAC--TT -s Anc2.Anc2refChr1 103640 8 + 142988 ACACAC--TT -s mr.mrrefChr3 137047 8 + 181027 ATACAC--TT -s simCow_chr6.simCow.chr6 561329 8 + 602619 CCACAC--TT -s simDog_chr6.simDog.chr6 550342 8 + 593897 ACATGC--TC -s simHuman_chr6.simHuman.chr6 558566 8 + 601863 ATGCAC--TT - -a -s simMouse_chr6.simMouse.chr6 587930 23 + 636262 GGAAAGTGAGGTGTATTGCTAGT -s Anc0.Anc0refChr3 187755 23 + 222631 GGGAGGGGAGGGGTGTTGCTAGG -s Anc1.Anc1refChr1 27232 23 + 69767 GGGAGGGGAGGGGTGTTGCTAGG -s Anc2.Anc2refChr1 103648 23 + 142988 GGGAGGGGAGGGGTGTTGCTAGG -s mr.mrrefChr3 137055 23 + 181027 GGAAAGTGAGGTGTATTGCTAGT -s simCow_chr6.simCow.chr6 561338 23 + 602619 AGGAGGGGAGGGGTGTTGCAGGA -s simDog_chr6.simDog.chr6 550350 23 + 593897 GGGAGAGAAGGTGTCTTAATAAG -s simHuman_chr6.simHuman.chr6 558574 23 + 601863 GGGAGGGGTGGGGTGGTGCTAGG -s simRat_chr6.simRat.chr6 62883 11 - 647215 ------------GGATTGGTTGC - -a -s simMouse_chr6.simMouse.chr6 587953 5 + 636262 ATAGT -s Anc0.Anc0refChr3 187778 5 + 222631 ATAAT -s Anc1.Anc1refChr1 27255 5 + 69767 ATAAT -s Anc2.Anc2refChr1 103671 5 + 142988 ATAAT -s mr.mrrefChr3 137078 5 + 181027 ATAAT -s simCow_chr6.simCow.chr6 561361 3 + 602619 ATA-- -s simDog_chr6.simDog.chr6 550383 5 + 593897 AGAAT -s simHuman_chr6.simHuman.chr6 558597 5 + 601863 ATAAT -s simRat_chr6.simRat.chr6 62894 5 - 647215 ATAAT - -a -s simMouse_chr6.simMouse.chr6 587958 31 + 636262 CAGAACATTTTCTACTCTATTTTTGCAATGT -s Anc0.Anc0refChr3 187783 31 + 222631 GAGAGTGCTTTCCACTACATTTTAGCCATGT -s Anc1.Anc1refChr1 27260 31 + 69767 GAGAGTGCTTTCCACTACATTTTAGCCATGT -s Anc2.Anc2refChr1 103676 31 + 142988 GAGAGTGCTTTTCACTATATTTTAGCCATGG -s mr.mrrefChr3 137083 31 + 181027 CAGAGCACTTTCCACTCCATTTTTGCAATGT -s simCow_chr6.simCow.chr6 561364 31 + 602619 GAGAGTACTTTTTAGCATATTTTAGCTATGG -s simDog_chr6.simDog.chr6 550389 31 + 593897 GAGAATGTTTTTCACTGTATTTTAGCCATGG -s simHuman_chr6.simHuman.chr6 558602 31 + 601863 GAGAGTGCTTTCCACAACAGCCTGGCCATTT -s simRat_chr6.simRat.chr6 62899 31 - 647215 CAGAGCACTTTCCACTCCATTTTTGCAATGC - -a -s simMouse_chr6.simMouse.chr6 587989 10 + 636262 GTGACCCAAT -s Anc0.Anc0refChr3 187814 10 + 222631 ATTGCCCAAG -s Anc1.Anc1refChr1 27291 10 + 69767 ATTGCCCAAG -s Anc2.Anc2refChr1 103707 10 + 142988 ATTGCCCAAG -s mr.mrrefChr3 137114 10 + 181027 ATGACCCAAG -s simCow_chr6.simCow.chr6 561395 10 + 602619 ATTGCCCTAG -s simDog_chr6.simDog.chr6 550420 10 + 593897 ATTGCACACG -s simHuman_chr6.simHuman.chr6 558635 10 + 601863 ATTGCCCAAG -s simRat_chr6.simRat.chr6 62930 10 - 647215 ATGATCAAAG - -a -s simMouse_chr6.simMouse.chr6 587999 3 + 636262 CAT -s Anc0.Anc0refChr3 187826 3 + 222631 CAT -s Anc1.Anc1refChr1 27303 3 + 69767 CAT -s Anc2.Anc2refChr1 103719 3 + 142988 ATT -s mr.mrrefChr3 137124 3 + 181027 CAT -s simCow_chr6.simCow.chr6 561407 3 + 602619 ATT -s simDog_chr6.simDog.chr6 550432 3 + 593897 ATT -s simHuman_chr6.simHuman.chr6 558647 3 + 601863 CAT -s simRat_chr6.simRat.chr6 62940 3 - 647215 CAT - -a -s simMouse_chr6.simMouse.chr6 588002 34 + 636262 TTACTCTCGCTCATTTATTGCAAGTCTTAATCTA -s Anc0.Anc0refChr3 187829 34 + 222631 TCCCTCTGACTACTTCATAACAAGTCCTGATCTG -s Anc1.Anc1refChr1 27306 34 + 69767 TCCCTCTGACTACTTCATAACAAGTCCTGATCTG -s Anc2.Anc2refChr1 103722 34 + 142988 TCCTTCTGACTACTCCATAACAATTCCTGATCTG -s mr.mrrefChr3 137127 34 + 181027 TTACTCTCGCTCATTCATTACAAGTCTTAATCTA -s simCow_chr6.simCow.chr6 561410 33 + 602619 TC-TTCTGACTACTCCTTAATTATTCCTAATTTG -s simDog_chr6.simDog.chr6 550437 34 + 593897 TCCTTATGACTACTCCACAACATTCTCTGATCTA -s simHuman_chr6.simHuman.chr6 558650 34 + 601863 TCCCTCTGACTACTTCATAACAAGTCCTGATCTG -s simRat_chr6.simRat.chr6 62943 34 - 647215 TTACTCTAGTTCACCCATTACAAGACTTACTTCT - -a -s simMouse_chr6.simMouse.chr6 588036 58 + 636262 CTTGTATGATCAAAACCCTGGGATTATGAGTATCAAGAGTAGGTTATGAAACATCACT -s Anc0.Anc0refChr3 187872 57 + 222631 CTTTGA-TATCAAAAGCCTGGGATTATAAGCATCAAGAGTAGTTCATGGAACAACACT -s Anc1.Anc1refChr1 27349 58 + 69767 CTTTGACTATCAAAAGCCTGGGATTATAAGCATCAAGAGTAGTTCATGGAACAACACT -s Anc2.Anc2refChr1 103765 57 + 142988 CTTTGG-TATCAAAAGCCTGGGATAAGAAGCATCTAGAGTATTTCATGGAACAACACT -s mr.mrrefChr3 137161 58 + 181027 CTTGTATGATCAAAACCCTGGGATTATGAGTATCAAGAGTAGGTTATGAAACATCACT -s simCow_chr6.simCow.chr6 561452 54 + 602619 TTTTGG-CTTC-AAAGTCTGGGGTAAGAAGTGTCTAG--TATTTAATGGAACAACATG -s simDog_chr6.simDog.chr6 550480 55 + 593897 CTTCGG-TATCATAACCCTGGGATAA--AGCATCTAGAGCATTACCTGGAACGAGACT -s simHuman_chr6.simHuman.chr6 558694 58 + 601863 CTTTGACTATCGAAAGCCTGGGATTATAAGCATCAAGATTAGTTCATGGGAAAACACT -s simRat_chr6.simRat.chr6 62977 58 - 647215 CTTGTAAGATCAAAACCTTAGGATTACGAGTATCAAGAGTAGGTTATGAAACACCACT - -a -s simMouse_chr6.simMouse.chr6 588094 64 + 636262 TCCCATGTGCTTCAACAATATAGATCCACTGCCGTAGCTGCTCTGGCAGACGCACAGCTATACT -s Anc0.Anc0refChr3 187929 61 + 222631 TCCCATGTGCTCAAATACAATAGA-CCACTGCCCTAGCTGCTAGGGCATATG--CAGCTATACT -s Anc1.Anc1refChr1 27407 62 + 69767 TCCCATGTGCTCAAATACAATAGATCCACTGCCCTAGCTGCTAGGGCATATG--CAGCTATACT -s Anc2.Anc2refChr1 103822 61 + 142988 TTCAATGTCTTCAAGTACAATAGA-CCACTGCCCTAGCTGCTAGGGCATATG--TAGCTATACT -s mr.mrrefChr3 137219 64 + 181027 TCCCATGTGCTTCAACAATATAGATCCACTGCCGTAGCTGCTCTGGCATACGCACAGCTATACT -s simCow_chr6.simCow.chr6 561506 60 + 602619 TTAGGTCTCTTCAAGCACTACAAA-C-ACTGCCCTATCTGTTAGTGCATATG--AAGCTATACT -s simDog_chr6.simDog.chr6 550545 61 + 593897 TTCAATGTCTTCAAGTACAGTAGA-CCACTGCCCTAGCTGCTAGGTCACATG--TAGCTATACT -s simHuman_chr6.simHuman.chr6 558752 62 + 601863 TCCCATGTGCTCACAAACAATTGGTACACTGCACTAGCGGCTAGGGCATATT--CAGCCATACT -s simRat_chr6.simRat.chr6 63035 64 - 647215 TTCTATATGCTTGAATAGTATAGATCCACTGCTGTAACTACTTTGGCATACGCACAACTATACT - -a -s simMouse_chr6.simMouse.chr6 588158 5 + 636262 GCACT -s Anc0.Anc0refChr3 187990 5 + 222631 GCACT -s Anc1.Anc1refChr1 27469 5 + 69767 GCACT -s Anc2.Anc2refChr1 103883 5 + 142988 GGTCT -s mr.mrrefChr3 137283 5 + 181027 GCACT -s simCow_chr6.simCow.chr6 561566 5 + 602619 GGTCT -s simDog_chr6.simDog.chr6 550606 5 + 593897 GGTCT -s simHuman_chr6.simHuman.chr6 558815 5 + 601863 GCACA -s simRat_chr6.simRat.chr6 63099 5 - 647215 GCACT - -a -s simMouse_chr6.simMouse.chr6 588163 43 + 636262 TGATAAGGACTTTTAGTACGGATTAGATTTGTTGGTAGGGTAG -s Anc0.Anc0refChr3 187995 42 + 222631 TA-TAAGTACTTTCAGTATTAGATAGACTTGTTACTTGGGTAG -s Anc1.Anc1refChr1 27474 43 + 69767 TAATAAGTACTTTCAGTATTAGATAGACTTGTTACTTGGGTAG -s Anc2.Anc2refChr1 103888 42 + 142988 TA-TATGTACTTTCAGTATTAGATAGACTTGTTACTTGTGTAG -s mr.mrrefChr3 137288 43 + 181027 TGATAAGGACTTTTAGTATGGGATAGATTTGTTGGTAGGGTAG -s simCow_chr6.simCow.chr6 561572 42 + 602619 TA-TAAGTTCTTCCATTACTAGATCGACTTGTAACTTGTGTAG -s simDog_chr6.simDog.chr6 550611 42 + 593897 TA-TATGTACTTTCAGTATTAAATAGACTTAGTACTAGTGTAG -s simHuman_chr6.simHuman.chr6 558820 43 + 601863 TATAAAGTACTTTCAGTATTAGACGGACTTGTTATTTGGGTAG -s simRat_chr6.simRat.chr6 63104 43 - 647215 AGATAAGGACTTTTAGTGTGGGATAGATTCGTTGGTAGGGCAG - -a -s simMouse_chr6.simMouse.chr6 588206 8 + 636262 CCATGGTG -s Anc0.Anc0refChr3 188037 8 + 222631 CCATGCTG -s Anc1.Anc1refChr1 27517 8 + 69767 CCATGCTG -s Anc2.Anc2refChr1 103930 8 + 142988 CCATGCTG -s mr.mrrefChr3 137331 8 + 181027 CCATGGTG -s simCow_chr6.simCow.chr6 561616 8 + 602619 CCATTCTG -s simDog_chr6.simDog.chr6 550653 8 + 593897 CTATGCTG -s simHuman_chr6.simHuman.chr6 558863 8 + 601863 CCATGTTG -s simRat_chr6.simRat.chr6 63147 8 - 647215 CCATGCTT - -a -s simMouse_chr6.simMouse.chr6 588214 7 + 636262 TGTAAAC -s Anc0.Anc0refChr3 188045 7 + 222631 TGCAAAC -s Anc1.Anc1refChr1 27525 7 + 69767 TGCAAAC -s Anc2.Anc2refChr1 103938 7 + 142988 TGCAAAC -s mr.mrrefChr3 137339 7 + 181027 TGTAAAC -s simCow_chr6.simCow.chr6 561624 7 + 602619 TGCAAAC -s simDog_chr6.simDog.chr6 553632 7 + 593897 TGCAAAC -s simHuman_chr6.simHuman.chr6 558871 7 + 601863 TACAAAC -s simRat_chr6.simRat.chr6 63155 7 - 647215 TGTAATC - -a -s simMouse_chr6.simMouse.chr6 588221 35 + 636262 CTAACCTTCCATCAGCCACAGGCTTAGAAAACACA -s Anc0.Anc0refChr3 188055 35 + 222631 CTGACCTTCTCTCAATAACAGTCTTACAGAACACA -s Anc1.Anc1refChr1 27535 35 + 69767 CTGACCTTCTCTCAATAACAGTCTTACAGAACACA -s Anc2.Anc2refChr1 103948 35 + 142988 CTGACCTTCTCTCAATAACAGTCTTACAGAACATT -s mr.mrrefChr3 137349 35 + 181027 CTGACCTTCCATCAACCACAGGCTTAGAAAACACA -s simCow_chr6.simCow.chr6 561634 35 + 602619 CTGACTGTGCTTCAATAATAGTCTACTATCACATG -s simDog_chr6.simDog.chr6 553642 35 + 593897 CTGACCTTCTCTCAAGAACAGTCTTACAGAACATT -s simHuman_chr6.simHuman.chr6 558881 35 + 601863 CTGACCTTCTGTGAATAACAGTCTTAAAGAACACA -s simRat_chr6.simRat.chr6 63165 35 - 647215 CTGACATTCCACCAAACACAGGCTTAGAAAACACA - -a -s simMouse_chr6.simMouse.chr6 588256 15 + 636262 AATGATTGACAATAT -s Anc0.Anc0refChr3 188094 15 + 222631 GATGATTGACACTCT -s Anc1.Anc1refChr1 27574 15 + 69767 GATGATTGACACTCT -s Anc2.Anc2refChr1 103987 15 + 142988 GAGGATTGACACTCT -s mr.mrrefChr3 137384 15 + 181027 GATGATTGACAATAT -s simCow_chr6.simCow.chr6 561673 14 + 602619 GAGGATTG-CACTCC -s simDog_chr6.simDog.chr6 553681 15 + 593897 GAGGATTGACACTCT -s simHuman_chr6.simHuman.chr6 558920 15 + 601863 GATGATTGACACTCT -s simRat_chr6.simRat.chr6 63200 15 - 647215 GATGATTGACAATAT - -a -s simMouse_chr6.simMouse.chr6 588271 7 + 636262 CATAGTA -s Anc0.Anc0refChr3 188115 7 + 222631 CATAATG -s Anc1.Anc1refChr1 27595 7 + 69767 CATAATG -s Anc2.Anc2refChr1 104008 7 + 142988 CATCATG -s mr.mrrefChr3 137399 7 + 181027 CATAGTA -s simCow_chr6.simCow.chr6 561693 7 + 602619 TATCATA -s simDog_chr6.simDog.chr6 553702 7 + 593897 CATCATG -s simHuman_chr6.simHuman.chr6 558941 7 + 601863 CATACTT -s simRat_chr6.simRat.chr6 63215 7 - 647215 CCAAGTA - -a -s simMouse_chr6.simMouse.chr6 588278 32 + 636262 CCTTCTACAAAGCCAAGAACCCCAAACGTATT -s Anc0.Anc0refChr3 188122 32 + 222631 CTTCCGAAAAAGCCAAAGACCCCACACACATT -s Anc1.Anc1refChr1 27602 32 + 69767 CTTCCGAAAAAGCCAAAGACCCCACACACATT -s Anc2.Anc2refChr1 104019 32 + 142988 CTTCAGAAAAACCCAAAGACCCCACACACATT -s mr.mrrefChr3 137406 32 + 181027 CCTCCTAAAAAGCCAAAAACCCCAAACATATT -s simCow_chr6.simCow.chr6 561704 32 + 602619 TTTCTGAAAAACCTAAAGGCCCCACACATATT -s simDog_chr6.simDog.chr6 553713 32 + 593897 CTTCAGGAAAACCCAAAAACCCCACACGCATT -s simHuman_chr6.simHuman.chr6 558948 32 + 601863 CTTCCAAAAAAGCCAAAGACCTCAGACACATT -s simRat_chr6.simRat.chr6 63222 32 - 647215 CCCCCTAAAAAGCCAAAAACCCCATACATATT - -a -s simMouse_chr6.simMouse.chr6 588310 29 + 636262 TCAGTCATTGTTGACAACCATTGTTCTTT -s Anc0.Anc0refChr3 188155 29 + 222631 ACAGATACTATCAACAACCATTTTCCTTT -s Anc1.Anc1refChr1 27635 29 + 69767 ACAGATACTATCAACAACCATTTTCCTTT -s Anc2.Anc2refChr1 104052 29 + 142988 ACAGATAGTATCAACAAACATTGTTCTTT -s mr.mrrefChr3 137438 29 + 181027 TCAGTCACTATTGACAACCATTTTCCTTT -s simCow_chr6.simCow.chr6 561737 29 + 602619 CCAGATAGTATCAACAGTCATTGTTCTGT -s simDog_chr6.simDog.chr6 553746 29 + 593897 ACAGATAGTATCAACAAACATTGTTCTTT -s simHuman_chr6.simHuman.chr6 558981 29 + 601863 GCGGCAACTATCAACAACCATTTTCCTTA -s simRat_chr6.simRat.chr6 63254 29 - 647215 TCAGTCACTATTGACAACCATTTTCCTTT - -a -s simMouse_chr6.simMouse.chr6 588339 36 + 636262 ATTATATATTCTTGATCATGTGGACTTGTATATTTA -s Anc0.Anc0refChr3 188186 34 + 222631 ATTATAAATTCTTGATTCTGTGGATTTG--TTTTGG -s Anc1.Anc1refChr1 27666 34 + 69767 ATTATAAATTCTTGATTCTGTGGATTTG--TTTTGG -s Anc2.Anc2refChr1 104083 34 + 142988 CTTATAAGTTCTTGATTCTGTGGATTTG--GTTTGG -s mr.mrrefChr3 137469 36 + 181027 ATTATATATTCTTGATCATGTGGATTTGTATATTTA -s simCow_chr6.simCow.chr6 561768 34 + 602619 CTTATATGTTCTCGATTCTGTGGATTTG--CATTGG -s simDog_chr6.simDog.chr6 553777 33 + 593897 -TTAGAAGTTCTTGATGTTGTGGATTTG--GTTTGG -s simHuman_chr6.simHuman.chr6 559012 34 + 601863 ATTATAGATTCTTGACTCTGTGGATTTG--TTTTGT -s simRat_chr6.simRat.chr6 63285 36 - 647215 ATTACATGTCCTTGATCATGTGGATTCATATATTTA - -a -s simMouse_chr6.simMouse.chr6 588375 22 + 636262 CAACGCGCTGCACAGCCGTTTA -s Anc0.Anc0refChr3 188220 22 + 222631 CAATGAGCAGCATAGCTATTTA -s Anc1.Anc1refChr1 27700 22 + 69767 CAATGAGCAGCATAGCTATTTA -s Anc2.Anc2refChr1 104117 22 + 142988 AAATGAACAGCATAGCTATTTA -s mr.mrrefChr3 137505 22 + 181027 CAACGCGCTGCACAGCTGTTTA -s simCow_chr6.simCow.chr6 561804 22 + 602619 AAATGAACAGCATAGCTTTTTA -s simDog_chr6.simDog.chr6 553810 22 + 593897 AGATGAACAGCACAGCTATTTA -s simHuman_chr6.simHuman.chr6 559046 21 + 601863 CAAA-TGACACATACCTATTTA -s simRat_chr6.simRat.chr6 63321 22 - 647215 CAATGCGCTGCACAGCTGTTTA - -a -s simMouse_chr6.simMouse.chr6 588397 6 + 636262 AAAGTT -s Anc0.Anc0refChr3 188242 6 + 222631 ATAGTT -s Anc1.Anc1refChr1 27722 6 + 69767 ATAGTT -s Anc2.Anc2refChr1 104139 6 + 142988 ATAGTT -s mr.mrrefChr3 137527 6 + 181027 AAAGTT -s simCow_chr6.simCow.chr6 561826 6 + 602619 ATTGCT -s simDog_chr6.simDog.chr6 553841 6 + 593897 ATAATT -s simHuman_chr6.simHuman.chr6 559067 6 + 601863 ATAGTT -s simRat_chr6.simRat.chr6 63343 6 - 647215 AGACTA - -a -s simMouse_chr6.simMouse.chr6 588403 3 + 636262 AAA -s Anc0.Anc0refChr3 188249 3 + 222631 AAA -s Anc1.Anc1refChr1 27729 3 + 69767 AAA -s Anc2.Anc2refChr1 104146 3 + 142988 AAA -s mr.mrrefChr3 137533 3 + 181027 AAA -s simCow_chr6.simCow.chr6 561833 3 + 602619 AAA -s simDog_chr6.simDog.chr6 553848 3 + 593897 AAA -s simHuman_chr6.simHuman.chr6 559074 3 + 601863 AAA -s simRat_chr6.simRat.chr6 63349 3 - 647215 AAA - -a -s simMouse_chr6.simMouse.chr6 588406 15 + 636262 AATTCTTGGAACAAA -s Anc0.Anc0refChr3 188252 15 + 222631 AGTTATTAGAACAAA -s Anc1.Anc1refChr1 27732 15 + 69767 AGTTATTAGAACAAA -s Anc2.Anc2refChr1 104149 15 + 142988 AGTTATTGGAACAAA -s mr.mrrefChr3 137536 15 + 181027 AATTCTTAGAACAAA -s simCow_chr6.simCow.chr6 561837 15 + 602619 GGTGATTGGAACAAA -s simDog_chr6.simDog.chr6 553851 12 + 593897 AGTTG---GAACAAG -s simHuman_chr6.simHuman.chr6 559077 15 + 601863 AGTTATTAGTAGAAA -s simRat_chr6.simRat.chr6 63352 15 - 647215 AATTCTTAGAACAAA - -a -s simMouse_chr6.simMouse.chr6 588421 9 + 636262 TGTCGAATC -s Anc0.Anc0refChr3 188276 9 + 222631 TTTGGAATC -s Anc1.Anc1refChr1 27756 9 + 69767 TTTGGAATC -s Anc2.Anc2refChr1 104173 9 + 142988 TCTTGAATC -s mr.mrrefChr3 137551 9 + 181027 TTTGGAATC -s simCow_chr6.simCow.chr6 561861 9 + 602619 CCTTCAATC -s simDog_chr6.simDog.chr6 553872 9 + 593897 TCTTGAATC -s simHuman_chr6.simHuman.chr6 559101 9 + 601863 TTTGGGATC -s simRat_chr6.simRat.chr6 63367 9 - 647215 TTTGGAATC - -a -s simMouse_chr6.simMouse.chr6 588430 6 + 636262 AGCAAG -s Anc0.Anc0refChr3 188285 6 + 222631 AGCAAA -s Anc1.Anc1refChr1 27765 6 + 69767 AGCAAA -s Anc2.Anc2refChr1 104182 6 + 142988 AGCAAA -s mr.mrrefChr3 137560 6 + 181027 AGCAAG -s simCow_chr6.simCow.chr6 220945 6 + 602619 AGCTGA -s simCow_chr6.simCow.chr6 561870 6 + 602619 AACAAG -s simDog_chr6.simDog.chr6 553881 6 + 593897 ACCAAA -s simHuman_chr6.simHuman.chr6 559110 6 + 601863 AGCAAA -s simRat_chr6.simRat.chr6 63376 6 - 647215 AGCAAG - -a -s simMouse_chr6.simMouse.chr6 588436 22 + 636262 TGCTTCATGTAGAGGGGGAGCA -s Anc0.Anc0refChr3 188294 20 + 222631 T--TTTATGGGGAGGGATATCA -s Anc1.Anc1refChr1 27774 22 + 69767 TGGTTTATGGGGAGGGATATCA -s Anc2.Anc2refChr1 104191 20 + 142988 T--TCTATGGGGAGGTATACCA -s mr.mrrefChr3 137566 22 + 181027 TGCTTCATGTGGAGGGATATCA -s simCow_chr6.simCow.chr6 220954 20 + 602619 C--TTGATAGATGGGTTTACCA -s simCow_chr6.simCow.chr6 561879 20 + 602619 T--CCTATTGGAAGGTATACCG -s simDog_chr6.simDog.chr6 553890 19 + 593897 T--TC-ATGTGGAGGTATGCCA -s simHuman_chr6.simHuman.chr6 559119 22 + 601863 TGGTTTAGGGGTAAGGATCTAG -s simRat_chr6.simRat.chr6 63382 22 - 647215 TGCTTCATGTGGAGGGATATCA - -a -s simMouse_chr6.simMouse.chr6 588458 2 + 636262 GT -s Anc0.Anc0refChr3 188314 2 + 222631 CT -s Anc1.Anc1refChr1 27796 2 + 69767 CT -s Anc2.Anc2refChr1 104211 2 + 142988 CT -s mr.mrrefChr3 137588 2 + 181027 GT -s simCow_chr6.simCow.chr6 561899 2 + 602619 CT -s simDog_chr6.simDog.chr6 553909 2 + 593897 CT -s simHuman_chr6.simHuman.chr6 559141 2 + 601863 AT -s simRat_chr6.simRat.chr6 63404 2 - 647215 GT - -a -s simMouse_chr6.simMouse.chr6 588460 18 + 636262 TTCATGAATAAATGAGTT -s Anc0.Anc0refChr3 188316 9 + 222631 TT---------GTGAAAT -s Anc1.Anc1refChr1 27798 18 + 69767 TTTAAGTGGAGGTGAAAT -s Anc2.Anc2refChr1 104213 9 + 142988 TC---------ATGAAAT -s mr.mrrefChr3 137590 18 + 181027 TTCATGTATAAGTGAGTT -s simCow_chr6.simCow.chr6 561902 9 + 602619 TT---------GTGAGAG -s simDog_chr6.simDog.chr6 553911 9 + 593897 TC---------ATGAAAT -s simHuman_chr6.simHuman.chr6 559143 12 + 601863 CTTAAGTGGAGG------ -s simRat_chr6.simRat.chr6 63406 18 - 647215 TTCATGTATAAGTGAGTT - -a -s simMouse_chr6.simMouse.chr6 588478 65 + 636262 GTATGATTCTCTAGATGTCATATGTTCCACCCCTGGCTGACCAAATCTGTGTCATTCCTGTAGTC -s Anc0.Anc0refChr3 188325 64 + 222631 ATATGTTCCCCTGGTTTGAGAATATT-CATCATTGACCGCCCAAATCTGTATCATTCACGGACTG -s Anc1.Anc1refChr1 27816 64 + 69767 ATATGTTCCCCTGGTTTGAGAATATT-CATCATTGACCGCCCAAATCTGTATCATTCACGGACTG -s Anc2.Anc2refChr1 104222 64 + 142988 ATATGTTCCCCTGGTTTGAGAATATT-CATCATTGACCGCCCAAATCTGTATCATTCACGGACTG -s mr.mrrefChr3 137608 65 + 181027 GTATGATCCTCTAGATGGCATATGTTCCATCCCTGGCTGACCAAATCTGTGTCATTCATGGAGTG -s simCow_chr6.simCow.chr6 561913 64 + 602619 ATATGTTCCCCTGGTTTGAGTATATT-TACGATTAACTGCCCAAATCTAAGTCATTCATGAACTC -s simDog_chr6.simDog.chr6 553920 64 + 593897 ATATGTTCCCCTGGTTTGAGAATATT-CATCATTGACCGCCCAAATCTGTATCATTCACGGACTG -s simRat_chr6.simRat.chr6 63424 65 - 647215 GTATGGTCCTCTAGATGGCATATGTTCCATCCCTGGCTGGCCAAATATGTGTCATACATGGAGTG - -a -s simMouse_chr6.simMouse.chr6 588543 36 + 636262 ATCATCAGATAACATTGCCACTAGCCATCCTGAAGT -s Anc0.Anc0refChr3 188389 13 + 222631 TTACTCTCA-----------------------TAGT -s Anc1.Anc1refChr1 27880 13 + 69767 TTACTCTCA-----------------------TAGT -s Anc2.Anc2refChr1 104286 13 + 142988 TTACTCTCA-----------------------TAGT -s mr.mrrefChr3 137673 36 + 181027 ATCATCCAATAACAGTGCCACTAGCCGTCCTGTAGT -s simCow_chr6.simCow.chr6 220974 13 + 602619 TTACTCTCA-----------------------CTGT -s simDog_chr6.simDog.chr6 554003 13 + 593897 TTACTCTCA-----------------------TAGT -s simRat_chr6.simRat.chr6 63489 36 - 647215 ATCGTTCAGTAACAGTACCACTAGGTGTCTTGTAGT - -a -s simMouse_chr6.simMouse.chr6 588579 10 + 636262 CCCTCTTAAA -s Anc0.Anc0refChr3 188402 10 + 222631 CCATGTCAGG -s Anc1.Anc1refChr1 27893 10 + 69767 CCATGTCAGG -s Anc2.Anc2refChr1 104299 10 + 142988 CCATGTCAGG -s mr.mrrefChr3 137709 10 + 181027 CCCTCTTAGA -s simCow_chr6.simCow.chr6 220987 10 + 602619 CCATGTTAGG -s simDog_chr6.simDog.chr6 554024 10 + 593897 CCATGTCAGG -s simRat_chr6.simRat.chr6 63525 10 - 647215 CCCCCTTAGA - -a -s simMouse_chr6.simMouse.chr6 588589 14 + 636262 TCCATTTGTCCGTC -s Anc0.Anc0refChr3 188412 14 + 222631 TCCATTGGTCTGCC -s Anc1.Anc1refChr1 27903 14 + 69767 TCCATTGGTCTGCC -s Anc2.Anc2refChr1 104309 14 + 142988 TCCATTGGTCTGCC -s mr.mrrefChr3 137719 14 + 181027 TCCATTTGTCTGTC -s simCow_chr6.simCow.chr6 220997 14 + 602619 CCCATTGGTCTGCT -s simCow_chr6.simCow.chr6 561977 14 + 602619 TTCATGGGCCTGCC -s simDog_chr6.simDog.chr6 554035 14 + 593897 TCCATTAGTCTCCC -s simRat_chr6.simRat.chr6 63535 14 - 647215 TCCATTTGTCTGTC - -a -s simMouse_chr6.simMouse.chr6 588603 152 + 636262 ATCAAGCACTGCCCGTCTGTACATGGCCGCGCAGGGATGGGGCATAGCTAAGCACTAACCATGTGCACATGGCTGCATTTACCTTCTTTTGGAGATTTGTACAAGGCACTGTGCGAAGTCTAAGTAGTGTTAATGGAAATAGAAGGATCATA -s Anc0.Anc0refChr3 188426 20 + 222631 AA------------------------------------------------------------------------------------------------------------------------------------GCTGATAACAATACTGCA -s Anc1.Anc1refChr1 27917 20 + 69767 AA------------------------------------------------------------------------------------------------------------------------------------GCTGATAACAATACTGCA -s Anc2.Anc2refChr1 104324 20 + 142988 AA------------------------------------------------------------------------------------------------------------------------------------GCTGATAACAATACTGCA -s mr.mrrefChr3 137733 20 + 181027 AT------------------------------------------------------------------------------------------------------------------------------------GGAGATAGAAAGATTATA -s simCow_chr6.simCow.chr6 221012 20 + 602619 AA------------------------------------------------------------------------------------------------------------------------------------GCTGATAACAATACTGCA -s simCow_chr6.simCow.chr6 561992 20 + 602619 AA------------------------------------------------------------------------------------------------------------------------------------GCTTATAACAACACTGCA -s simDog_chr6.simDog.chr6 554050 20 + 593897 AA------------------------------------------------------------------------------------------------------------------------------------ACTGATAACAATGCTACA -s simRat_chr6.simRat.chr6 63549 20 - 647215 AG------------------------------------------------------------------------------------------------------------------------------------GGGGATAGAAAGAGTGTA - -a -s simMouse_chr6.simMouse.chr6 588755 14 + 636262 GAAATATCCCCGTT -s Anc0.Anc0refChr3 188446 14 + 222631 GCAATATCAACATT -s Anc1.Anc1refChr1 27937 14 + 69767 GCAATATCAACATT -s Anc2.Anc2refChr1 104358 14 + 142988 GCAATATCAACATT -s mr.mrrefChr3 137753 14 + 181027 GAAATATCCCCGTT -s simCow_chr6.simCow.chr6 221037 14 + 602619 ACAATATCAACATT -s simCow_chr6.simCow.chr6 562026 14 + 602619 ACAATATCAGCATT -s simDog_chr6.simDog.chr6 554084 14 + 593897 GCAATATCAACATG -s simRat_chr6.simRat.chr6 63569 14 - 647215 GAAATATCCCTGTC - -a -s simMouse_chr6.simMouse.chr6 588769 1 + 636262 G -s Anc0.Anc0refChr3 188460 1 + 222631 G -s Anc1.Anc1refChr1 27951 1 + 69767 G -s Anc2.Anc2refChr1 104378 1 + 142988 G -s mr.mrrefChr3 137767 1 + 181027 G -s simCow_chr6.simCow.chr6 221057 1 + 602619 A -s simCow_chr6.simCow.chr6 562046 1 + 602619 C -s simDog_chr6.simDog.chr6 554104 1 + 593897 G -s simRat_chr6.simRat.chr6 63583 1 - 647215 A - -a -s simMouse_chr6.simMouse.chr6 588770 3 + 636262 GGC -s Anc0.Anc0refChr3 188461 3 + 222631 GAA -s Anc1.Anc1refChr1 27952 3 + 69767 GAA -s Anc2.Anc2refChr1 104379 3 + 142988 GAA -s mr.mrrefChr3 137768 3 + 181027 GGC -s simCow_chr6.simCow.chr6 221061 3 + 602619 GAA -s simCow_chr6.simCow.chr6 562047 3 + 602619 GAA -s simDog_chr6.simDog.chr6 554105 3 + 593897 GAA -s simRat_chr6.simRat.chr6 63584 3 - 647215 GGC - -a -s simMouse_chr6.simMouse.chr6 588773 12 + 636262 ACTCCTGTAAAG -s Anc0.Anc0refChr3 188464 12 + 222631 GCTCTTGTGGAG -s Anc1.Anc1refChr1 27955 12 + 69767 GCTCTTGTGGAG -s Anc2.Anc2refChr1 104382 12 + 142988 GCTCTTGTGGAA -s mr.mrrefChr3 137771 12 + 181027 ACTCCTGTAAAG -s simCow_chr6.simCow.chr6 221064 12 + 602619 ACTATTGTGGAG -s simCow_chr6.simCow.chr6 562050 12 + 602619 GGTGTCGTGGAA -s simDog_chr6.simDog.chr6 554108 12 + 593897 GCTCTTGTGAAA -s simHuman_chr6.simHuman.chr6 559155 11 + 601863 -TTTTTGTGCAG -s simRat_chr6.simRat.chr6 63597 12 - 647215 ACTCCTGTAAGG - -a -s simMouse_chr6.simMouse.chr6 588785 2 + 636262 TG -s Anc0.Anc0refChr3 188476 2 + 222631 TG -s Anc1.Anc1refChr1 27967 2 + 69767 TG -s Anc2.Anc2refChr1 104394 2 + 142988 TG -s mr.mrrefChr3 137783 2 + 181027 TG -s simCow_chr6.simCow.chr6 221076 2 + 602619 TG -s simCow_chr6.simCow.chr6 562062 2 + 602619 TG -s simDog_chr6.simDog.chr6 554122 2 + 593897 TG -s simHuman_chr6.simHuman.chr6 559166 2 + 601863 TG -s simRat_chr6.simRat.chr6 63609 2 - 647215 TG - -a -s simMouse_chr6.simMouse.chr6 588787 2 + 636262 TG -s Anc0.Anc0refChr3 188478 2 + 222631 TG -s Anc1.Anc1refChr1 27969 2 + 69767 TG -s Anc2.Anc2refChr1 104396 2 + 142988 TG -s mr.mrrefChr3 137785 2 + 181027 TG -s simCow_chr6.simCow.chr6 562064 2 + 602619 TG -s simDog_chr6.simDog.chr6 554124 2 + 593897 TG -s simHuman_chr6.simHuman.chr6 559168 2 + 601863 TG -s simRat_chr6.simRat.chr6 63611 2 - 647215 CG - -a -s simMouse_chr6.simMouse.chr6 588789 2 + 636262 AT -s Anc0.Anc0refChr3 188480 2 + 222631 CT -s Anc1.Anc1refChr1 27971 2 + 69767 CT -s Anc2.Anc2refChr1 104398 2 + 142988 CT -s mr.mrrefChr3 137787 2 + 181027 AT -s simCow_chr6.simCow.chr6 221078 2 + 602619 CT -s simCow_chr6.simCow.chr6 562066 2 + 602619 CC -s simDog_chr6.simDog.chr6 554126 2 + 593897 CT -s simHuman_chr6.simHuman.chr6 559170 2 + 601863 CT -s simRat_chr6.simRat.chr6 63613 2 - 647215 GT - -a -s simMouse_chr6.simMouse.chr6 588791 53 + 636262 TGGATAGTCTTTAAGTGCCTGAAAGATAAAAATATAGGACATGGCCTAGCTCT -s Anc0.Anc0refChr3 188483 52 + 222631 TGAATAGCTTGT-AGCATGTGGGAAATGGAAACTTAGAGCATAGTCCAGTACA -s Anc1.Anc1refChr1 27974 52 + 69767 TGAATAGCTTGT-AGCATGTGGGAAATGGAAACTTAGAGCATAGTCCAGTACA -s Anc2.Anc2refChr1 104401 52 + 142988 TAAATAGCTTGC-AGCATGTGGGAAATGGAAACTTAGAGCATAGTCCAGTACA -s mr.mrrefChr3 137790 53 + 181027 TGGATAGTCTTTAAGTGCCTGAAAGATAAAAATATAGAGCATAGCCCAGCTCT -s simCow_chr6.simCow.chr6 221081 52 + 602619 TGAATAGCTTAC-AGCATGTGGGAAATGGACCCTTAGAACATAGTCCAGTGGA -s simCow_chr6.simCow.chr6 562069 52 + 602619 TAAATAGCATGC-AGCATGTCAGAGATCGATCCTTAGAACACAGTCCGATACA -s simDog_chr6.simDog.chr6 554129 52 + 593897 TAAATAGCTTGC-AGCATGTGGGAAATGAAAACTTAAAGCATAGTCCAGCACA -s simHuman_chr6.simHuman.chr6 559173 52 + 601863 TGAAGAGATGGT-TGCATGAGGGAAATGGAAACTTAGAGCATAGTCCAGACCA -s simRat_chr6.simRat.chr6 63616 37 - 647215 TGGATAGTC----------------ATAAAAATATAGAGCATAGCCCAGCTCT - -a -s simMouse_chr6.simMouse.chr6 588844 5 + 636262 TTGAG -s Anc0.Anc0refChr3 188535 5 + 222631 GTGAG -s Anc1.Anc1refChr1 28026 5 + 69767 GTGAG -s Anc2.Anc2refChr1 104453 5 + 142988 GTGAG -s mr.mrrefChr3 137843 5 + 181027 TTGAG -s simCow_chr6.simCow.chr6 221133 5 + 602619 GTGAG -s simCow_chr6.simCow.chr6 562124 5 + 602619 ATGAG -s simDog_chr6.simDog.chr6 554181 5 + 593897 GTGAG -s simHuman_chr6.simHuman.chr6 559225 5 + 601863 GTGAA -s simRat_chr6.simRat.chr6 63653 5 - 647215 TTGAG - -a -s simMouse_chr6.simMouse.chr6 588849 5 + 636262 AGATG -s Anc0.Anc0refChr3 188540 5 + 222631 AGATG -s Anc1.Anc1refChr1 28031 5 + 69767 AGATG -s Anc2.Anc2refChr1 104458 5 + 142988 AGATG -s mr.mrrefChr3 137848 5 + 181027 AGATG -s simCow_chr6.simCow.chr6 221154 5 + 602619 CAAGG -s simCow_chr6.simCow.chr6 562129 5 + 602619 AGGTA -s simDog_chr6.simDog.chr6 554186 5 + 593897 AGAAG -s simHuman_chr6.simHuman.chr6 559230 5 + 601863 AGATA -s simRat_chr6.simRat.chr6 63658 5 - 647215 AGATG - -a -s simMouse_chr6.simMouse.chr6 588854 25 + 636262 GTGATCATGAGGGAGTCGTATAGAG -s Anc0.Anc0refChr3 188545 25 + 222631 GGAGTTATGAGGGAGTCATATAAGG -s Anc1.Anc1refChr1 28036 25 + 69767 GGAGTTATGAGGGAGTCATATAAGG -s Anc2.Anc2refChr1 104463 25 + 142988 GGAGTTATGAGGGAGTCATATAAGG -s mr.mrrefChr3 137853 25 + 181027 GTAATCATGAGGGAGTCATATAGGG -s simCow_chr6.simCow.chr6 562134 25 + 602619 GGAGTTATAAGGGAGTCATATAAGG -s simDog_chr6.simDog.chr6 554191 25 + 593897 GGAGTTATGAGGAAGTCATATAAGG -s simHuman_chr6.simHuman.chr6 559235 22 + 601863 GGAGCTATGAGGGAGTCATAC---T -s simRat_chr6.simRat.chr6 63663 25 - 647215 GTAATAATGAGGGAGTCATATAGGG - -a -s simMouse_chr6.simMouse.chr6 588879 125 + 636262 TAGTTCTTATCAAATGAAGGGCCTGCCTATTCTGTGCTCTGGTATTGCAGACACCAAGATGTTGTTGTATGTACTTTAAAAGATTATGAGAGATCTCAAATCTTAGCTACCATTACTGTGTACAC -s Anc0.Anc0refChr3 188570 22 + 222631 TAGTTACTAT--------------------------------TATTGCAAACAT----------------------------------------------------------------------- -s Anc1.Anc1refChr1 28061 22 + 69767 TAGTTACTAT--------------------------------TATTGCAAACAT----------------------------------------------------------------------- -s Anc2.Anc2refChr1 104535 22 + 142988 TAGTTACCAT--------------------------------CATTGCATACAT----------------------------------------------------------------------- -s mr.mrrefChr3 137878 54 + 181027 TAGTTCTTATAAAATGAAGGGCCTGCCTGTTCTATGCTCTGGTATTGCAAACAC----------------------------------------------------------------------- -s simCow_chr6.simCow.chr6 562205 18 + 602619 ----TACCAT--------------------------------CAATGCACACAT----------------------------------------------------------------------- -s simDog_chr6.simDog.chr6 554280 22 + 593897 TAGTTGCCAT--------------------------------CATTGCATACAT----------------------------------------------------------------------- -s simHuman_chr6.simHuman.chr6 559257 22 + 601863 TAGTTACTAT--------------------------------TATTGCGAACAT----------------------------------------------------------------------- -s simRat_chr6.simRat.chr6 63688 54 - 647215 TAGTTCTTATAAAACGAAGCACCTGCCCGTTCTATACTCTGGTATTACAAACCA----------------------------------------------------------------------- - -a -s simMouse_chr6.simMouse.chr6 589004 6 + 636262 GGCATT -s Anc0.Anc0refChr3 188593 6 + 222631 GGCATA -s Anc1.Anc1refChr1 28084 6 + 69767 GGCATA -s Anc2.Anc2refChr1 104558 6 + 142988 AGCATA -s mr.mrrefChr3 137932 6 + 181027 GGCATT -s simCow_chr6.simCow.chr6 562224 6 + 602619 TGCATA -s simDog_chr6.simDog.chr6 554303 6 + 593897 ATCATA -s simHuman_chr6.simHuman.chr6 559280 6 + 601863 GGCACA -s simRat_chr6.simRat.chr6 63742 6 - 647215 GGCATT - -a -s simMouse_chr6.simMouse.chr6 589010 12 + 636262 GAATGCATAATA -s Anc0.Anc0refChr3 188599 12 + 222631 GGATGAGTTATA -s Anc1.Anc1refChr1 28090 12 + 69767 GGATGAGTTATA -s Anc2.Anc2refChr1 104564 12 + 142988 GGATGAGTTATG -s mr.mrrefChr3 137938 12 + 181027 GAATGCATAATA -s simCow_chr6.simCow.chr6 562233 12 + 602619 GAATGGGTTATG -s simDog_chr6.simDog.chr6 554309 12 + 593897 GGATGAGTTATG -s simHuman_chr6.simHuman.chr6 559286 12 + 601863 GTATGAGTTACA -s simRat_chr6.simRat.chr6 63748 12 - 647215 GAATGTATAATA - -a -s simMouse_chr6.simMouse.chr6 589022 4 + 636262 TTGT -s Anc0.Anc0refChr3 188613 4 + 222631 TTGT -s Anc1.Anc1refChr1 28104 4 + 69767 TTGT -s Anc2.Anc2refChr1 104578 4 + 142988 TTGT -s mr.mrrefChr3 137950 4 + 181027 TTGT -s simCow_chr6.simCow.chr6 562247 4 + 602619 CTGT -s simDog_chr6.simDog.chr6 554323 4 + 593897 TTGT -s simHuman_chr6.simHuman.chr6 559300 4 + 601863 TTGT -s simRat_chr6.simRat.chr6 63760 4 - 647215 TTGT - -a -s simMouse_chr6.simMouse.chr6 589026 31 + 636262 AATATTTTGTTAGTGAGCCTGTTGTTAACAT -s Anc0.Anc0refChr3 188621 16 + 222631 AACA---------------AGTTGCTAAGAT -s Anc1.Anc1refChr1 28112 31 + 69767 AACACAATGTTAGTGAGCCAGTTGCTAAGAT -s Anc2.Anc2refChr1 104586 16 + 142988 AGCA---------------AGTTGCTATGAC -s mr.mrrefChr3 137954 31 + 181027 AATATTTTGTTAGTGAGCCAGTTGTTAACAT -s simCow_chr6.simCow.chr6 562256 16 + 602619 AGTG---------------AGTTGCTATGAC -s simDog_chr6.simDog.chr6 554331 16 + 593897 AGCA---------------AGTTGCTATGAC -s simHuman_chr6.simHuman.chr6 559313 31 + 601863 AACACAATGTTAGTGAGCCAGTTGCTAAGAT -s simRat_chr6.simRat.chr6 63764 31 - 647215 AATATTTGGTTAGTGAGCCAGTTGTTAACAT - -a -s simMouse_chr6.simMouse.chr6 589057 116 + 636262 TCATCATGCCACGTTGGCTGATGGATATGGCTAGTGTAGCTTCGAAGGTACAAAGATGGGCGGAGTCTGCGCATCACTCAGAGGGACAGTCAGGTTATCCCGGCCGTGTGCATTTG -s Anc0.Anc0refChr3 188639 18 + 222631 TAATCATG--------------------------------------------------------------------------------------------------TGTGCAGTTG -s Anc1.Anc1refChr1 28145 18 + 69767 TAATCATG--------------------------------------------------------------------------------------------------TGTGCAGTTG -s Anc2.Anc2refChr1 104604 18 + 142988 TAATCATG--------------------------------------------------------------------------------------------------TGTGCAGTTG -s mr.mrrefChr3 137985 18 + 181027 TCATCATG--------------------------------------------------------------------------------------------------TGTGCATTTG -s simCow_chr6.simCow.chr6 562274 17 + 602619 TGAT-ACA--------------------------------------------------------------------------------------------------TGTGCAGTTG -s simDog_chr6.simDog.chr6 554349 18 + 593897 TAATCATG--------------------------------------------------------------------------------------------------TGTGCTGTCA -s simHuman_chr6.simHuman.chr6 559346 18 + 601863 TAATCATG--------------------------------------------------------------------------------------------------TATGCACTTG -s simRat_chr6.simRat.chr6 63795 18 - 647215 TCATCCTG--------------------------------------------------------------------------------------------------TGTGCATCTG - -a -s simMouse_chr6.simMouse.chr6 589173 4 + 636262 CATT -s Anc0.Anc0refChr3 188688 4 + 222631 CAGA -s Anc1.Anc1refChr1 28194 4 + 69767 CAGA -s Anc2.Anc2refChr1 104653 4 + 142988 CAGA -s mr.mrrefChr3 138003 4 + 181027 CATT -s simCow_chr6.simCow.chr6 562322 4 + 602619 CAGA -s simDog_chr6.simDog.chr6 554398 4 + 593897 CAGA -s simHuman_chr6.simHuman.chr6 559395 4 + 601863 CAAA -s simRat_chr6.simRat.chr6 63813 4 - 647215 CGTT - -a -s simMouse_chr6.simMouse.chr6 589177 3 + 636262 CTT -s Anc0.Anc0refChr3 188692 3 + 222631 CTT -s Anc1.Anc1refChr1 28198 3 + 69767 CTT -s Anc2.Anc2refChr1 104666 3 + 142988 CTT -s mr.mrrefChr3 138007 3 + 181027 CTT -s simCow_chr6.simCow.chr6 562335 3 + 602619 CTA -s simDog_chr6.simDog.chr6 554411 3 + 593897 CAT -s simHuman_chr6.simHuman.chr6 559399 3 + 601863 CTT -s simRat_chr6.simRat.chr6 63817 3 - 647215 CTT - -a -s simMouse_chr6.simMouse.chr6 589180 12 + 636262 GATTTGGGCTGC -s Anc0.Anc0refChr3 188696 12 + 222631 AATTTGGGATGC -s Anc1.Anc1refChr1 28202 12 + 69767 AATTTGGGATGC -s Anc2.Anc2refChr1 104670 12 + 142988 AATTCCGCATTC -s mr.mrrefChr3 138011 12 + 181027 GATTTGGGCTGC -s simCow_chr6.simCow.chr6 562339 12 + 602619 AAGTCTGCATTC -s simDog_chr6.simDog.chr6 554415 10 + 593897 AATTCCG--TTC -s simHuman_chr6.simHuman.chr6 559403 12 + 601863 AATTTGGGGTGC -s simRat_chr6.simRat.chr6 63821 12 - 647215 GATTTGGGCTGC - -a -s simMouse_chr6.simMouse.chr6 589192 51 + 636262 CTTAGGGATATTGAGTGCTATTGCGATAGATAAGACAGTAGAGAATCATAG -s Anc0.Anc0refChr3 188713 43 + 222631 CT--------CTTTGTGATACTATGCTGGATAAGAGACGAAAAAGGCATAA -s Anc1.Anc1refChr1 28219 43 + 69767 CT--------CTTTGTGATACTATGCTGGATAAGAGACGAAAAAGGCATAA -s Anc2.Anc2refChr1 104687 43 + 142988 CT--------CTTTGTGGTACTATGCTGGATAAGAGACGAAAAAGGCATAA -s mr.mrrefChr3 138028 51 + 181027 CTTAGGGATATTGAGTGATATTGTGGTAGATAAGACAGTAAAGAATCATAG -s simCow_chr6.simCow.chr6 562356 43 + 602619 CT--------CTTTGTAGTACTATATTGGATAAGAGGGGATAAAGGCATAA -s simDog_chr6.simDog.chr6 554430 42 + 593897 CT--------CCTTGTGGAACTA-GCTGGATAAGAGACGAAAAAGACATAA -s simHuman_chr6.simHuman.chr6 559420 43 + 601863 CT--------CTTTGTGATGCTATGCTGGATAAGAAACGAAAAAGGCATAA -s simRat_chr6.simRat.chr6 63838 51 - 647215 CTCAGTGATATTGGGTGATATTGTGGTAGATAAGACAGTAAAGTATCAAAG - -a -s simMouse_chr6.simMouse.chr6 589243 33 + 636262 CTCATTTCCATCTGTCTCTCCTAAAGAGAGACA -s Anc0.Anc0refChr3 188756 33 + 222631 CACATGTTTGTGTGTGTCTCCTCAATGAACCTA -s Anc1.Anc1refChr1 28262 33 + 69767 CACATGTTTGTGTGTGTCTCCTCAATGAACCTA -s Anc2.Anc2refChr1 104730 33 + 142988 CACATGTTTGTGTTTCTCTTCTCAATGAGCCTA -s mr.mrrefChr3 138079 33 + 181027 CTCATTTCCATGTGTGTCTCCTCAAGAGAGACA -s simCow_chr6.simCow.chr6 562401 33 + 602619 CACACATTTGTGTTTCTCTACTCGACGAGCCTA -s simDog_chr6.simDog.chr6 554472 33 + 593897 GGCATGTTTATGTTTCTCTTCTCAATGAGCATA -s simHuman_chr6.simHuman.chr6 559463 29 + 601863 CACATCATTGTGTGGGTCCCCTCA----ACCTA -s simRat_chr6.simRat.chr6 63889 27 - 647215 C--AC----ATGATTGTCTCCTCAAGAGAAACA - -a -s simMouse_chr6.simMouse.chr6 589276 24 + 636262 GTTAATGAAATGTCCTTTTTACCA -s Anc0.Anc0refChr3 188790 24 + 222631 GTTAATGAAAGGTTATTTCTACCA -s Anc1.Anc1refChr1 28296 24 + 69767 GTTAATGAAAGGTTATTTCTACCA -s Anc2.Anc2refChr1 104764 24 + 142988 GTTTATGTAAGGTTATTTCTACCA -s mr.mrrefChr3 138113 24 + 181027 GTTAATGAAATGTTATTTCTACCA -s simCow_chr6.simCow.chr6 562435 24 + 602619 GTTCATGTAACGTTATTTCTACCA -s simDog_chr6.simDog.chr6 554506 24 + 593897 GTTTATGTAAGGCTATTTTGGCCA -s simHuman_chr6.simHuman.chr6 559493 24 + 601863 GCTAACAAAAGGTTATTTCTACTG -s simRat_chr6.simRat.chr6 63917 24 - 647215 ATTAATGAGACATTATTTCTACCA - -a -s simMouse_chr6.simMouse.chr6 589300 6 + 636262 CAGATC -s Anc0.Anc0refChr3 188814 6 + 222631 CAGATT -s Anc1.Anc1refChr1 28320 6 + 69767 CAGATT -s Anc2.Anc2refChr1 104796 6 + 142988 CAGATT -s mr.mrrefChr3 138137 6 + 181027 CAGATC -s simCow_chr6.simCow.chr6 562468 6 + 602619 CAGATT -s simDog_chr6.simDog.chr6 554538 6 + 593897 CAGATG -s simHuman_chr6.simHuman.chr6 559517 6 + 601863 CAGATT -s simRat_chr6.simRat.chr6 63941 6 - 647215 CAGATC - -a -s simMouse_chr6.simMouse.chr6 589306 25 + 636262 ATTGACTCCAGAGAATACAATGACT -s Anc0.Anc0refChr3 188832 21 + 222631 GTT--ATTGAGAG--TGTAATGTCT -s Anc1.Anc1refChr1 28338 25 + 69767 GTTGAATTGAGAGAATGTAATGTCT -s Anc2.Anc2refChr1 104814 21 + 142988 GTT--ATTGAAAG--TGTAATGTCT -s mr.mrrefChr3 138143 25 + 181027 ATTGACTCCAGAGAATACAATGTCT -s simCow_chr6.simCow.chr6 562486 18 + 602619 -----ATTGAGAG--GGTAATGTCT -s simDog_chr6.simDog.chr6 554556 20 + 593897 GTT---TTGAAAG--TCTAATGCCT -s simHuman_chr6.simHuman.chr6 559535 25 + 601863 GTTGAATTGATAGAATGTAATGTTT -s simRat_chr6.simRat.chr6 63947 6 - 647215 AT-------------------GTCT - -a -s simMouse_chr6.simMouse.chr6 589331 15 + 636262 TTATCAGCAGTGCTT -s Anc0.Anc0refChr3 188853 14 + 222631 TTA-AACCAGTGCTT -s Anc1.Anc1refChr1 28363 15 + 69767 TTACAACCAGTGCTT -s Anc2.Anc2refChr1 104835 14 + 142988 TTG-AACCAGTGCTT -s mr.mrrefChr3 138168 15 + 181027 TTATCAGCTGTGCTT -s simCow_chr6.simCow.chr6 562504 14 + 602619 TTG-AATCAGAACTT -s simDog_chr6.simDog.chr6 554576 14 + 593897 TTG-AACCAGTGCTT -s simHuman_chr6.simHuman.chr6 559578 15 + 601863 TTACAACCAGTGCTT -s simRat_chr6.simRat.chr6 63953 15 - 647215 TCATCACCTGTGGTT - -a -s simMouse_chr6.simMouse.chr6 589346 68 + 636262 CAGCTTGCAAGTGGTACATTTATATGTAGAGGAAACAGAGTGGGGATAGATATGAAAAGTTTAGCTCT -s Anc0.Anc0refChr3 188871 65 + 222631 CAGCTGGAAAGTGGTACTTTTATACGTCGA---AATAAAGTGGGGGTTAATGTGGAAAGGTTATCTCT -s Anc1.Anc1refChr1 28382 68 + 69767 CAGCTGGAAAGTGGTACTTTTATACGTCGAGGAAATAAAGTGGGGGTTAATGTGGAAAGGTTATCTCT -s Anc2.Anc2refChr1 104853 65 + 142988 CAGCTGGAAAGTGGTACTTTCACACATTGA---AATAAAGTGGGGGTTAATGTGGAAAGGTTATCTCT -s mr.mrrefChr3 138183 68 + 181027 CAGCTTGCAAGTGGTACATTTATATGTAGAGGAAACAGAGTGGGGGTAAATGTGAAAAGGTTAGCTCT -s simCow_chr6.simCow.chr6 562522 65 + 602619 CAGCTAGCAAGTGGTACTCTGACCCATGGA---AATAAAGTGGGGGTGAATGTGAAAAGGTTATCTCT -s simDog_chr6.simDog.chr6 554594 56 + 593897 CAGCTGGAAAGTTGTACTTCCGCACATTGA---AATAAAGTGGGGGTTAATGTCGAAAG--------- -s simHuman_chr6.simHuman.chr6 559597 68 + 601863 CATCTGCTAAGTGTTACTGTTATACGACGAGGATATAAAGTGGGGGTTAATGTGGAAAGGTTATCTCT -s simRat_chr6.simRat.chr6 63968 67 - 647215 CAGCTTGCAAGTGATACGTTCATATGTAGAGGAAACATAGTGGGGGTGAATGT-AAAAGGTTAGCTTT - -a -s simMouse_chr6.simMouse.chr6 589414 15 + 636262 GTATGGCCATGCAGA -s Anc0.Anc0refChr3 188936 3 + 222631 GT------------A -s Anc1.Anc1refChr1 28450 15 + 69767 GTTTAGCCCTATAGA -s Anc2.Anc2refChr1 104918 3 + 142988 AT------------A -s mr.mrrefChr3 138251 15 + 181027 GTATGGCCATGTAGA -s simCow_chr6.simCow.chr6 562587 3 + 602619 AT------------A -s simHuman_chr6.simHuman.chr6 559667 15 + 601863 GGTTAGCCCTATAGA -s simRat_chr6.simRat.chr6 64035 15 - 647215 GTATGGAAATGTAGA - -a -s simMouse_chr6.simMouse.chr6 589429 27 + 636262 TAAATGAACTATGAACCAGCCCTGGGG -s Anc0.Anc0refChr3 188958 15 + 222631 CAT------------CCAGCTCTGGGG -s Anc1.Anc1refChr1 28484 15 + 69767 CAT------------CCAGCTCTGGGG -s Anc2.Anc2refChr1 104940 15 + 142988 CAT------------CCAACTCTGGGG -s mr.mrrefChr3 138266 15 + 181027 TAT------------CCAGCCCTGGGG -s simCow_chr6.simCow.chr6 562609 15 + 602619 CAT------------CCATCTTTGGGG -s simDog_chr6.simDog.chr6 554665 15 + 593897 CAT------------CCAACACTGGGG -s simHuman_chr6.simHuman.chr6 559701 15 + 601863 CAT------------CCAGCTCTGGGG -s simRat_chr6.simRat.chr6 64050 15 - 647215 TAT------------CCAGCCCAGGGG - -a -s simMouse_chr6.simMouse.chr6 589456 20 + 636262 AGATTACTAAGTATAGGGGG -s Anc0.Anc0refChr3 188975 20 + 222631 AGGTTGCCTATTCTTGAGGT -s Anc1.Anc1refChr1 28501 20 + 69767 AGGTTGCCTATTCTTGAGGT -s Anc2.Anc2refChr1 104957 20 + 142988 AGGTTGCCTATTCTTAAGGT -s mr.mrrefChr3 138281 20 + 181027 AGATTACCAAGTATTGGGGG -s simCow_chr6.simCow.chr6 562626 20 + 602619 AGGATGCCTATCCCTAAGGT -s simDog_chr6.simDog.chr6 554682 20 + 593897 AAATTGCTTACTATTAAGGT -s simHuman_chr6.simHuman.chr6 559718 20 + 601863 AGGTTGCCTATTCTTGAGGC -s simRat_chr6.simRat.chr6 64065 20 - 647215 AGATTACCAAGTATTAGGGG - -a -s simMouse_chr6.simMouse.chr6 589476 21 + 636262 GTTATGTACAATGGTGTATTC -s Anc0.Anc0refChr3 188995 21 + 222631 GCTATATACAAAGATACATTA -s Anc1.Anc1refChr1 28521 21 + 69767 GCTATATACAAAGATACATTA -s Anc2.Anc2refChr1 104977 21 + 142988 GCTATACACAAAGATACATTA -s mr.mrrefChr3 138301 21 + 181027 GTTATGTACAATGATGTATTC -s simCow_chr6.simCow.chr6 562646 21 + 602619 GCTACGCACACGGATCCTTTA -s simDog_chr6.simDog.chr6 554702 21 + 593897 GCTATACACAAAGATACATTT -s simHuman_chr6.simHuman.chr6 559738 20 + 601863 ACTATATACAA-GATAGATTA -s simRat_chr6.simRat.chr6 64087 21 - 647215 GTTATGTACAATGATGTTTTC - -a -s simMouse_chr6.simMouse.chr6 589497 81 + 636262 AACAGCATGCCTGAACCTATAAAATAAAGTATCCTCCTATAAAATAAGGTATCTTGGATCTTGTAATGGTACCCTATTTTT -s Anc0.Anc0refChr3 189019 68 + 222631 ACCAACATGCCTGATCCTATAA-------------CACATGTAATAAGGTACCCTGTATCTAGTAATGTTACCCTATTATT -s Anc1.Anc1refChr1 28545 68 + 69767 ACCAACATGCCTGATCCTATAA-------------CACATGTAATAAGGTACCCTGTATCTAGTAATGTTACCCTATTATT -s Anc2.Anc2refChr1 105001 68 + 142988 ACCAACATGCCTGATCCTATAA-------------CACATGTAATAAGGTACTCTGTATCTAGTAATATTATGCTGTTATG -s mr.mrrefChr3 138322 81 + 181027 AACAGCATGCCTGAACCTATAAAATAAAGTATCCTCCTATAAAATAAGGTATCCTGGATCTTGTAATGTTACCCTATTTTT -s simCow_chr6.simCow.chr6 562668 58 + 602619 -------TGTCTGATGCTATAA-------------CACACGTAGTAAGGTATTCTTTACCCATTATTATTATGCTGTT--- -s simDog_chr6.simDog.chr6 554726 68 + 593897 ACCAACATACCTGGTCCTACAC-------------CACATGTAATAAGGTGCTCTGTATCTAGGAATATTATGATGTTATG -s simHuman_chr6.simHuman.chr6 559761 68 + 601863 ATCATCATGCCTGATCTTATAA-------------CAGATGTAATAAGGTACCCTGCATCTAGTAATGTTACCCTATTATT -s simRat_chr6.simRat.chr6 64108 80 - 647215 AACAGAATGCCTTAACCTATAAAATAAAGTATCCTCCTATACAATAAGGTATCCTGGATCTGGTA-TGTTACCCTATTTTG - -a -s simMouse_chr6.simMouse.chr6 589578 18 + 636262 ATAATACATGATCGTATT -s Anc0.Anc0refChr3 189087 18 + 222631 TTGATACATAATGCTATT -s Anc1.Anc1refChr1 28613 18 + 69767 TTGATACATAATGCTATT -s Anc2.Anc2refChr1 105069 18 + 142988 TTGATACATAATGCTATT -s mr.mrrefChr3 138403 18 + 181027 ATAATACATGATGGTATT -s simCow_chr6.simCow.chr6 562726 16 + 602619 --GATACATAATTCTAAT -s simDog_chr6.simDog.chr6 554797 18 + 593897 TTTATACATAATGCTATT -s simHuman_chr6.simHuman.chr6 559829 18 + 601863 TGGATACATAATGTTATT -s simRat_chr6.simRat.chr6 64188 18 - 647215 AAAGGACATGATGGTATC - -a -s simMouse_chr6.simMouse.chr6 589596 29 + 636262 CCTCTTATTAATCACACTGTGACCCCTTG -s Anc0.Anc0refChr3 189105 29 + 222631 CCTGTCTTTGATCACATCGTGACCCCTTG -s Anc1.Anc1refChr1 28631 29 + 69767 CCTGTCTTTGATCACATCGTGACCCCTTG -s Anc2.Anc2refChr1 105088 29 + 142988 CCTGTCTTTGCTCACATCATCACCCCTTG -s mr.mrrefChr3 138421 29 + 181027 CCTCTTATTGATCACACTGTGACCCCTTG -s simCow_chr6.simCow.chr6 562743 28 + 602619 ACTGTGCTTCCTCG-ATCATAACCCGTTG -s simDog_chr6.simDog.chr6 554816 29 + 593897 CCGGTCTTTGCTCACATAACCACCCCTTG -s simHuman_chr6.simHuman.chr6 559847 29 + 601863 CCTGTCTTTGATCTCATCGTGAACCACTG -s simRat_chr6.simRat.chr6 64206 25 - 647215 CCTCCTATTGATCACACTGTGACCT---- - -a -s simMouse_chr6.simMouse.chr6 589625 4 + 636262 TTAA -s Anc0.Anc0refChr3 189137 4 + 222631 CTAA -s Anc1.Anc1refChr1 28663 4 + 69767 CTAA -s Anc2.Anc2refChr1 105120 4 + 142988 CTAA -s mr.mrrefChr3 138452 4 + 181027 TTAA -s simCow_chr6.simCow.chr6 562774 4 + 602619 CTAA -s simDog_chr6.simDog.chr6 554848 4 + 593897 CTAA -s simHuman_chr6.simHuman.chr6 559879 4 + 601863 ATAA -s simRat_chr6.simRat.chr6 64233 4 - 647215 TTAA - -a -s simMouse_chr6.simMouse.chr6 589629 13 + 636262 CATAATGAGCCTA -s Anc0.Anc0refChr3 189141 13 + 222631 CATAGAGAAGCTA -s Anc1.Anc1refChr1 28667 13 + 69767 CATAGAGAAGCTA -s Anc2.Anc2refChr1 105126 13 + 142988 CATAGAGAAGCTA -s mr.mrrefChr3 138456 13 + 181027 CATAATGAACCTA -s simCow_chr6.simCow.chr6 562780 13 + 602619 CATAGAGAAGCTA -s simDog_chr6.simDog.chr6 554854 13 + 593897 CATAGAGAAGCTA -s simHuman_chr6.simHuman.chr6 559883 13 + 601863 AATAGAGAAGTTA -s simRat_chr6.simRat.chr6 64237 13 - 647215 CATAATGAATCTA - -a -s simMouse_chr6.simMouse.chr6 589642 8 + 636262 TAGGTCTT -s Anc0.Anc0refChr3 189154 8 + 222631 AAGGTCTT -s Anc1.Anc1refChr1 28680 8 + 69767 AAGGTCTT -s Anc2.Anc2refChr1 105139 8 + 142988 AAGGCCTT -s mr.mrrefChr3 138469 8 + 181027 AAGGTCTT -s simCow_chr6.simCow.chr6 562793 8 + 602619 AAGGCCCT -s simDog_chr6.simDog.chr6 554867 8 + 593897 AAGGCCTT -s simHuman_chr6.simHuman.chr6 559896 8 + 601863 AAGGTCCT -s simRat_chr6.simRat.chr6 64251 8 - 647215 AAGGTCTT - -a -s simMouse_chr6.simMouse.chr6 589650 29 + 636262 GGGTAGTCCCCCCTAGGACATCTAAGGGG -s Anc0.Anc0refChr3 189162 29 + 222631 GGCCGGTTCTTCCTAGGATACATAAGGGA -s Anc1.Anc1refChr1 28688 29 + 69767 GGCCGGTTCTTCCTAGGATACATAAGGGA -s Anc2.Anc2refChr1 105147 29 + 142988 GGCCGGTTCTTCCTAGGGTACATAAGGGA -s mr.mrrefChr3 138477 29 + 181027 GGGTAGTCCTCCCTAGGACATATAAGGGG -s simCow_chr6.simCow.chr6 562801 29 + 602619 GGCCAGTTCTTCATAGCGTACAAAAGGGA -s simDog_chr6.simDog.chr6 554875 27 + 593897 GTTTGGTTCTTCCTAAGGTA--TAAGTTA -s simHuman_chr6.simHuman.chr6 559905 29 + 601863 GGCCCATTCTTCCTAGAATACATAAGGGA -s simRat_chr6.simRat.chr6 64259 29 - 647215 GGGTAGTCCTCCCTAGGACATACAAGGAG - -a -s simMouse_chr6.simMouse.chr6 589679 55 + 636262 GATAACAGTTTAGCACACTACTTCCTGACTAATAGATGGAGTCTTTACCTATTAT -s Anc0.Anc0refChr3 189192 53 + 222631 GATATCCCTCTAGATCTAC--TTCCCAAACAAAAGATAAAGTCCCTATCTGTTAT -s Anc1.Anc1refChr1 28718 53 + 69767 GATATCCCTCTAGATCTAC--TTCCCAAACAAAAGATAAAGTCCCTATCTGTTAT -s Anc2.Anc2refChr1 105177 53 + 142988 GTTATCCTTCTAGATCTAC--TTCCTGAACAAAAGATAAAATCCCTATATGTTAT -s mr.mrrefChr3 138507 53 + 181027 GATAACACTTTAGAACACT--TTCCCAACTAATAGATGGAGTCTTTATCTGTTAT -s simCow_chr6.simCow.chr6 562831 53 + 602619 ATTATCCTTCTAGATCTTC--CCACGGAACAATAGATAGAACCCCTCTATGGTAT -s simDog_chr6.simDog.chr6 554903 52 + 593897 GTTGACCTTCTAGATTTAC--TTCCTGGACAAAAGATAAAATACCTATATGTTA- -s simHuman_chr6.simHuman.chr6 559935 53 + 601863 GATATCCCTCCAGATCTAC--TTCCCAAACAGAAGACAAAGTCCCTATCTGTAAT -s simRat_chr6.simRat.chr6 64289 53 - 647215 GATAGCACTTTAGACCACT--CTCTCAACTAATAAGTGGAGTCTTTATCTGTTCT - -a -s simMouse_chr6.simMouse.chr6 589734 7 + 636262 TATAGTT -s Anc0.Anc0refChr3 189261 7 + 222631 TATGGTT -s Anc1.Anc1refChr1 28788 7 + 69767 TATGGTT -s Anc2.Anc2refChr1 105246 7 + 142988 TATGGTT -s mr.mrrefChr3 138560 7 + 181027 TATAGTT -s simCow_chr6.simCow.chr6 562900 7 + 602619 TATAGTC -s simDog_chr6.simDog.chr6 554971 7 + 593897 TATGGTT -s simHuman_chr6.simHuman.chr6 560005 7 + 601863 TATGGTT -s simRat_chr6.simRat.chr6 64342 7 - 647215 TATATCT - -a -s simMouse_chr6.simMouse.chr6 589741 11 + 636262 CCACACTAAGC -s Anc0.Anc0refChr3 189272 11 + 222631 CCACACTCAGT -s Anc1.Anc1refChr1 28799 11 + 69767 CCACACTCAGT -s Anc2.Anc2refChr1 105257 11 + 142988 CCATACTCAGT -s mr.mrrefChr3 138567 11 + 181027 CCACACTAAGC -s simCow_chr6.simCow.chr6 562911 11 + 602619 CCATACCCAGT -s simDog_chr6.simDog.chr6 554980 9 + 593897 --ATACTCAGT -s simHuman_chr6.simHuman.chr6 560016 11 + 601863 CCACACTCAGT -s simRat_chr6.simRat.chr6 64349 11 - 647215 TCATACTAAGC - -a -s simMouse_chr6.simMouse.chr6 589752 44 + 636262 ACTCTATTTATAGTGGTAATATGTTATGTGGGGACCACATCCTG -s Anc0.Anc0refChr3 189283 42 + 222631 ACTCAAGTTGTAGTAGGAATAATTTGTGTGGAGGAC-CATCCC- -s Anc1.Anc1refChr1 28810 42 + 69767 ACTCAAGTTGTAGTAGGAATAATTTGTGTGGAGGAC-CATCCC- -s Anc2.Anc2refChr1 105268 42 + 142988 ACTCAAGATGTAGTAGGAATAATTTGTGTGGAGGAC-CACCCC- -s mr.mrrefChr3 138578 44 + 181027 ACTCAATTTATAGTGGTAATATGTTATGTGGAGACCACATCACG -s simCow_chr6.simCow.chr6 563083 42 + 602619 ACTCAAGATGTAGAAGGAATAAGTTGTGTGGGGGAC-CACCCC- -s simDog_chr6.simDog.chr6 554989 40 + 593897 GCTCAAGATGTAGTAGGAGTAATTTGGGTTGAAGAC-CA--CC- -s simHuman_chr6.simHuman.chr6 560027 42 + 601863 ATTCAAATTGGAGTAGGAATAATTTCTTTGAAGGAC-CATCCC- -s simRat_chr6.simRat.chr6 64360 44 - 647215 ACTCAATGTATACTGGTAGTATGTTATGTGGAGACCACATCACG - -a -s simMouse_chr6.simMouse.chr6 589796 6 + 636262 ATCGGC -s Anc0.Anc0refChr3 189333 6 + 222631 GTCTAC -s Anc1.Anc1refChr1 28860 6 + 69767 GTCTAC -s Anc2.Anc2refChr1 105318 6 + 142988 GTCTAC -s mr.mrrefChr3 138630 6 + 181027 GTCTGC -s simCow_chr6.simCow.chr6 563133 6 + 602619 GTCTCC -s simDog_chr6.simDog.chr6 555037 6 + 593897 TTCCAC -s simHuman_chr6.simHuman.chr6 560077 6 + 601863 GTCTAC -s simRat_chr6.simRat.chr6 64412 6 - 647215 GTCTGC - -a -s simMouse_chr6.simMouse.chr6 589802 27 + 636262 GAAACCTCAACCTCTAACCTCACTACA -s Anc0.Anc0refChr3 189341 27 + 222631 GACACCTCAACCCCTACCCTTACTACA -s Anc1.Anc1refChr1 28868 27 + 69767 GACACCTCAACCCCTACCCTTACTACA -s Anc2.Anc2refChr1 105326 27 + 142988 AACACTTCAACCCCTACCCTTACTACA -s mr.mrrefChr3 138636 27 + 181027 GAAACCTCAACCCCTAACCTCACTACA -s simCow_chr6.simCow.chr6 563141 27 + 602619 TACACTTCAACGCCTACCCTCAATACA -s simDog_chr6.simDog.chr6 555045 27 + 593897 AACACTGCAAGCACTACCCTTACTACA -s simHuman_chr6.simHuman.chr6 560085 27 + 601863 GACACCTCAACCCCTACTCTTACTACA -s simRat_chr6.simRat.chr6 64418 27 - 647215 GAAACCTCAATCCCTAACCTCACTACA - -a -s simMouse_chr6.simMouse.chr6 589829 9 + 636262 GAGTTCACA -s Anc0.Anc0refChr3 189368 8 + 222631 GAGTTCAC- -s Anc1.Anc1refChr1 28895 8 + 69767 GAGTTCAC- -s Anc2.Anc2refChr1 105353 8 + 142988 GAGTTCAC- -s mr.mrrefChr3 138664 9 + 181027 GAGTTCACA -s simCow_chr6.simCow.chr6 563168 8 + 602619 GAGTTCAC- -s simDog_chr6.simDog.chr6 555073 7 + 593897 GAGTTCA-- -s simHuman_chr6.simHuman.chr6 560112 8 + 601863 GAGTTCAC- -s simRat_chr6.simRat.chr6 64447 9 - 647215 GAGTTCACA - -a -s simMouse_chr6.simMouse.chr6 589838 37 + 636262 GGTTTTTTTCTGCTTTTCACTCATAAGCATCTCAAAT -s Anc0.Anc0refChr3 189376 37 + 222631 GGTTTTGTTTTGCTTTGCAATCATAAGCACCTTTCAT -s Anc1.Anc1refChr1 28903 37 + 69767 GGTTTTGTTTTGCTTTGCAATCATAAGCACCTTTCAT -s Anc2.Anc2refChr1 105361 37 + 142988 AGTTTTGTTTTGCTTTGCAATCATAAGCACCTTTCAT -s mr.mrrefChr3 138673 37 + 181027 GGTTTTTTTCTGCTTTTCACTCATAAGCATCTCTAAT -s simCow_chr6.simCow.chr6 563177 35 + 602619 AGTTTTGTTTTGCTCTGTGATCATAGCCCCCT--AGT -s simDog_chr6.simDog.chr6 555080 34 + 593897 ---TTTGTCTTGCTTTGCAATCATAAGCACCTTTCAT -s simHuman_chr6.simHuman.chr6 560120 37 + 601863 GGTTTTGTTTTTCTATGCAACCATACACACCTTTGAT -s simRat_chr6.simRat.chr6 64456 33 - 647215 GGTTTTT----GCTTTTCACTTATAAGCTTCTCTAAT - -a -s simMouse_chr6.simMouse.chr6 589875 40 + 636262 GGCATTGTGATGAAAGGTAAATCTATTGTGACAATTGTTA -s Anc0.Anc0refChr3 189429 40 + 222631 AGCATTGTGATGAAGGCTGCAATAGTCACTGCAATTGTGA -s Anc1.Anc1refChr1 28956 40 + 69767 AGCATTGTGATGAAGGCTGCAATAGTCACTGCAATTGTGA -s Anc2.Anc2refChr1 105414 40 + 142988 AGCATTGTGATGAAGGCTGCAATAGTCACTGCAATTGTGT -s mr.mrrefChr3 138710 40 + 181027 GGCATTGTGATGAAAGGTGAATCTATTGTGACAACTGTTA -s simCow_chr6.simCow.chr6 563277 40 + 602619 ACCATTGTGATGAAGACTGTAATTGTCACTGCAATTGTCG -s simDog_chr6.simDog.chr6 555130 33 + 593897 AGCATTGTGACGAAGGCTGCACTAGTCACTG-------GT -s simHuman_chr6.simHuman.chr6 560173 40 + 601863 AGCATTGTGATGAAGGCTGCAATAGTCACTGTAAACGTAA -s simRat_chr6.simRat.chr6 64489 40 - 647215 GGCATTGTGATGAAAGGTGAATCCATTGTGACAACTGTTA - -a -s simMouse_chr6.simMouse.chr6 589915 27 + 636262 CAAACTCCAATCCATCTTTCTGAAACA -s Anc0.Anc0refChr3 189481 27 + 222631 CAAACTCTAAGCCTTCTGGCTGAACCA -s Anc1.Anc1refChr1 29008 27 + 69767 CAAACTCTAAGCCTTCTGGCTGAACCA -s Anc2.Anc2refChr1 105466 27 + 142988 CGAACTCTAAGCCTTCTGGCTGAACCA -s mr.mrrefChr3 138761 27 + 181027 CAAACTCTAATCCATCTTTCTGAAACA -s simCow_chr6.simCow.chr6 563329 27 + 602619 TGGACCCTAAACCTTCTGAATGAACCA -s simDog_chr6.simDog.chr6 555175 24 + 593897 CGAACTCTAAGCCTT---GCTGAACAC -s simHuman_chr6.simHuman.chr6 560225 27 + 601863 CAAACTCTAGGCCGTCTGGCTGAACCA -s simRat_chr6.simRat.chr6 64542 27 - 647215 CAAGTGCTAAATCATCCTTCTGAAACA - -a -s simMouse_chr6.simMouse.chr6 589942 47 + 636262 AATATTCAAAACGTGAATTGGATATAAGATATGTCCACAGTTGTCGC -s Anc0.Anc0refChr3 189508 21 + 222631 AATGCGCAAA----------GAGATCAC----------------CTC -s Anc1.Anc1refChr1 29035 21 + 69767 AATGCGCAAA----------GAGATCAC----------------CTC -s Anc2.Anc2refChr1 105493 21 + 142988 AATGCGCAAA----------AAGATCAC----------------CTC -s mr.mrrefChr3 138788 47 + 181027 AATCTTCAAAACGTGAATTGGATATAAGATATGTCCACAGTTGTCTC -s simCow_chr6.simCow.chr6 563358 17 + 602619 AGTGCGCAAA----------AAGACCA-------------------- -s simDog_chr6.simDog.chr6 555199 19 + 593897 CATAA--AAC----------AATATGGC----------------CTC -s simHuman_chr6.simHuman.chr6 560252 21 + 601863 AATGCCCAAA----------GAGATCAA----------------CTC -s simRat_chr6.simRat.chr6 64569 47 - 647215 AATCTTCAAAATGAGCATTGGATGTGAAATATGTCCACTGTTGTCTC - -a -s simMouse_chr6.simMouse.chr6 589989 25 + 636262 CTAATTTTTTAGTCCCTGCCTGCAC -s Anc0.Anc0refChr3 189529 25 + 222631 CTACTTGTTTAATATCGCCCTGTAC -s Anc1.Anc1refChr1 29056 25 + 69767 CTACTTGTTTAATATCGCCCTGTAC -s Anc2.Anc2refChr1 105514 25 + 142988 CTACTCGTTCAATATCGCCCTGTAC -s mr.mrrefChr3 138835 25 + 181027 CTAATTATTTAGTCTCTGCCTGTAC -s simCow_chr6.simCow.chr6 563375 15 + 602619 ----TAGATCAATATGGCC------ -s simDog_chr6.simDog.chr6 555221 25 + 593897 CTACTCATTCAATCTCTGCCTGTAC -s simHuman_chr6.simHuman.chr6 560273 25 + 601863 CTAGTTGTTTAATATCGCCCTGTAC -s simRat_chr6.simRat.chr6 64616 25 - 647215 CTAATTATTTAGTCTCTGCCTGTAC - -a -s simMouse_chr6.simMouse.chr6 590014 4 + 636262 ACGC -s Anc0.Anc0refChr3 189555 4 + 222631 ACCT -s Anc1.Anc1refChr1 29082 4 + 69767 ACCT -s Anc2.Anc2refChr1 105540 4 + 142988 GCCT -s mr.mrrefChr3 138860 4 + 181027 ACGT -s simCow_chr6.simCow.chr6 563390 1 + 602619 ---T -s simDog_chr6.simDog.chr6 555247 4 + 593897 GCCA -s simHuman_chr6.simHuman.chr6 560299 4 + 601863 ACTT -s simRat_chr6.simRat.chr6 64641 4 - 647215 ATGT - -a -s simMouse_chr6.simMouse.chr6 590018 16 + 636262 ACTCTGCGGTTAATAC -s Anc0.Anc0refChr3 189559 16 + 222631 GATCTGTGGGTAGTAC -s Anc1.Anc1refChr1 29086 16 + 69767 GATCTGTGGGTAGTAC -s Anc2.Anc2refChr1 105544 16 + 142988 GATCCGTGGGTAGTAC -s mr.mrrefChr3 138864 16 + 181027 ACTCTGTGGTTAATAC -s simCow_chr6.simCow.chr6 563391 10 + 602619 GA------GGTAATAC -s simDog_chr6.simDog.chr6 555252 16 + 593897 GATCCGTGTGTAGTCC -s simHuman_chr6.simHuman.chr6 560303 16 + 601863 GATTTGTCGGCAGTAC -s simRat_chr6.simRat.chr6 64645 16 - 647215 ACTCTGTGGTTAATAC - -a -s simMouse_chr6.simMouse.chr6 590034 7 + 636262 TTTTCCC -s Anc0.Anc0refChr3 189575 6 + 222631 ATT-CCC -s Anc1.Anc1refChr1 29102 6 + 69767 ATT-CCC -s Anc2.Anc2refChr1 105560 6 + 142988 ATT-CCC -s mr.mrrefChr3 138880 7 + 181027 TTTCCCC -s simCow_chr6.simCow.chr6 563401 6 + 602619 ATT-CCC -s simDog_chr6.simDog.chr6 555268 6 + 593897 TTT-CCC -s simHuman_chr6.simHuman.chr6 560319 6 + 601863 ATT-CAT -s simRat_chr6.simRat.chr6 64663 7 - 647215 TTTCCCG - -a -s simMouse_chr6.simMouse.chr6 590041 22 + 636262 CTAGTGGAATTCAAATCTCTTT -s Anc0.Anc0refChr3 189581 22 + 222631 CTAGTGGAATTTCAAATTTGAT -s Anc1.Anc1refChr1 29108 22 + 69767 CTAGTGGAATTTCAAATTTGAT -s Anc2.Anc2refChr1 105566 22 + 142988 CTAGTGGAATTTCAAATTTGAT -s mr.mrrefChr3 138887 22 + 181027 CTAGTGGAATTCAAATCTCTGT -s simCow_chr6.simCow.chr6 563407 22 + 602619 CAAGTGGAATTTCAAATTTGAT -s simDog_chr6.simDog.chr6 555275 22 + 593897 CTAGTGGAATTTCAGATTTGAT -s simHuman_chr6.simHuman.chr6 560325 22 + 601863 CTAGTGGAATTTGAAATCTGAT -s simRat_chr6.simRat.chr6 64670 21 - 647215 -TAGTGGGAGTCAAATCTCTGT - -a -s simMouse_chr6.simMouse.chr6 590063 6 + 636262 GGCTTC -s Anc0.Anc0refChr3 189604 5 + 222631 G-ATTC -s Anc1.Anc1refChr1 29131 5 + 69767 G-ATTC -s Anc2.Anc2refChr1 105589 5 + 142988 G-ATTT -s mr.mrrefChr3 138909 5 + 181027 G-CTTC -s simCow_chr6.simCow.chr6 563430 5 + 602619 G-ATTT -s simDog_chr6.simDog.chr6 555298 5 + 593897 G-ACTT -s simHuman_chr6.simHuman.chr6 560348 5 + 601863 G-ATTC -s simRat_chr6.simRat.chr6 64691 5 - 647215 G-CTTT - -a -s simMouse_chr6.simMouse.chr6 590069 55 + 636262 ATCATGTCTATGTGTAATGCTTTCTTGTCAGATATTATATCTGATTGCACATGTG -s Anc0.Anc0refChr3 189609 55 + 222631 ATAATGCTTATTTGAAATAATCTCTTATTAGAGATTAAAACTAATTGCTAATGTG -s Anc1.Anc1refChr1 29136 55 + 69767 ATAATGCTTATTTGAAATAATCTCTTATTAGAGATTAAAACTAATTGCTAATGTG -s Anc2.Anc2refChr1 105597 55 + 142988 ATAATGCTTGTTTGAAATAAACTCTCATTAGAGATTGAAACTAAATGCAACTGTG -s mr.mrrefChr3 138914 55 + 181027 ATAATGTCTATTTGTAATGCTTTCTTGTCAGATATTATATCTATTTGCTCATGTG -s simCow_chr6.simCow.chr6 563438 55 + 602619 ATAACATTTGTTAGAAATAAACTCTCATTAAAGCCTGAAACTGAATTCAACTATG -s simDog_chr6.simDog.chr6 555306 55 + 593897 ATAATGCTTGTTTGGAATAAACCTTCCTTAGAGATTGCATCTAAATGCAACTGTG -s simHuman_chr6.simHuman.chr6 560353 54 + 601863 TGAATAAATAACGGAAACAATCTCTTACTAGAGATTA-GATTCATTGCTGATGAG -s simRat_chr6.simRat.chr6 64696 54 - 647215 ATAAAGTCTATTTGTAATGCTTTCTTGTCAGATAATATATCTAT-TGCTTGTGTG - -a -s simMouse_chr6.simMouse.chr6 590124 29 + 636262 TCCACATTTCTTACAAGCGTAACATTAAT -s Anc0.Anc0refChr3 189685 29 + 222631 TTCACTCTGCTTACAAGCCTAGCACTAAT -s Anc1.Anc1refChr1 29212 29 + 69767 TTCACTCTGCTTACAAGCCTAGCACTAAT -s Anc2.Anc2refChr1 105673 29 + 142988 TTCAGTCTGGTAACAGACCCAGCACTAAT -s mr.mrrefChr3 138969 29 + 181027 TCCACGTTTCTTACAAGCGTAACATTAAT -s simCow_chr6.simCow.chr6 563512 29 + 602619 TTCAGTTGGGACACAGACCCAGCACTAAT -s simDog_chr6.simDog.chr6 555381 29 + 593897 TTCTGTCTAGTAACAGACCCAGCACTAAT -s simHuman_chr6.simHuman.chr6 560429 29 + 601863 TTCACCCTGCTTACAAGCTTGTCACTAAT -s simRat_chr6.simRat.chr6 64750 29 - 647215 TTCATGTTTCTTGCAGGCAGAACATTAAT - -a -s simMouse_chr6.simMouse.chr6 590153 23 + 636262 ATAACATTTGAATAGTACACATG -s Anc0.Anc0refChr3 189714 22 + 222631 ATCACA-TTGGATAGCACACATG -s Anc1.Anc1refChr1 29241 22 + 69767 ATCACA-TTGGATAGCACACATG -s Anc2.Anc2refChr1 105702 22 + 142988 ATCACA-TTGGATAGCACACATG -s mr.mrrefChr3 138998 23 + 181027 ATAACATTTGAATAGTACACATG -s simCow_chr6.simCow.chr6 563541 22 + 602619 GGAATA-TTGGATAGCTTACATG -s simDog_chr6.simDog.chr6 555412 22 + 593897 ATCACA-TTGGATGCTACATATG -s simHuman_chr6.simHuman.chr6 560458 22 + 601863 ATCACA-TAGGATAGCACACATG -s simRat_chr6.simRat.chr6 64779 23 - 647215 ATAACATTTGAATAGTACATACG - -a -s simMouse_chr6.simMouse.chr6 590176 88 + 636262 TATGTTAAAGTGACAATTGCTACCCGCAAAGGGTATTTTTCGTGCCTTTCAATCTAGGTGTGACCCCAAGTAGCCTAAGACATGTTGA -s Anc0.Anc0refChr3 189737 87 + 222631 TTCTTTGAAGTGACCATTGCTACCTGCACAGGGTATTTTG-GTCCTTAATAATCTACTGGGAATCCCAAGCATCCCTGAGCCTTCTAA -s Anc1.Anc1refChr1 29264 87 + 69767 TTCTTTGAAGTGACCATTGCTACCTGCACAGGGTATTTTG-GTCCTTAATAATCTACTGGGAATCCCAAGCATCCCTGAGCCTTCTAA -s Anc2.Anc2refChr1 105725 87 + 142988 TTCTTTGAAGTGACCATTGCTATCTGCACAGGGTATTTTG-GTCCTTAATAGGCTACTGGGAATCCCAAGCATCCCTGAACCTTCTAA -s mr.mrrefChr3 139021 88 + 181027 TACGTTAAAGTGACAATTGCTACCCGCAAAGGGTATTTTTCGTGCTTTTCAATCTAGGTGTTACCCCAAGTAGCCCAAAGCATGCTGA -s simCow_chr6.simCow.chr6 563564 87 + 602619 TACTTTGAAGTAACTGTTGCCATCTGTAAAGGGTATTTTG-GTCCTTAGTAGGCTACCAGGAATCTCAAGCATCCCTGACCCTTCTAA -s simDog_chr6.simDog.chr6 555435 87 + 593897 TTCATAGAAGTGACCATTGCTATCTGCACAGGGTATTTTG-GTCTTTAAGGGGCTACTGGGACTCCTTAGTATCCCTAAACCTTCTAA -s simHuman_chr6.simHuman.chr6 560481 86 + 601863 TTCTTTGAAGTGACCA-TGCTACCTGCAGAGGGTATTTTG-GTCCTTGATAATTTACTGGGAATTCCAAGCACCCCTGAGCCATCCAG -s simRat_chr6.simRat.chr6 64802 88 - 647215 TACGTTATAGGGACAATTGCTACCCACAAAGGCTATTTTTTGTGTTTTTCAATCTAGGTGTTACCCCAAGTAGCTCCAAGTTGCCTGA - -a -s simMouse_chr6.simMouse.chr6 590264 19 + 636262 CATGTTATAGGGTGCACAA -s Anc0.Anc0refChr3 189834 19 + 222631 CATGTAGTGGGGTCCACAA -s Anc1.Anc1refChr1 29361 19 + 69767 CATGTAGTGGGGTCCACAA -s Anc2.Anc2refChr1 105822 19 + 142988 CATGTAGTGGGGTCCACAA -s mr.mrrefChr3 139115 19 + 181027 CATGTTATAGGGTCCACAA -s simCow_chr6.simCow.chr6 563661 19 + 602619 TGTGTTGTAGGGTCCACAA -s simDog_chr6.simDog.chr6 555532 19 + 593897 CATGCAGGGGGGTTCATAA -s simHuman_chr6.simHuman.chr6 560577 19 + 601863 CATGTAGTGAGGACCACAA -s simRat_chr6.simRat.chr6 64896 19 - 647215 CATATTATAGGGTCCACAA - -a -s simMouse_chr6.simMouse.chr6 590283 1 + 636262 A -s Anc0.Anc0refChr3 189853 1 + 222631 A -s Anc1.Anc1refChr1 29380 1 + 69767 A -s Anc2.Anc2refChr1 105841 1 + 142988 A -s mr.mrrefChr3 139134 1 + 181027 A -s simCow_chr6.simCow.chr6 563680 1 + 602619 A -s simDog_chr6.simDog.chr6 555551 1 + 593897 A -s simHuman_chr6.simHuman.chr6 560596 1 + 601863 A -s simRat_chr6.simRat.chr6 64933 1 - 647215 A - -a -s simMouse_chr6.simMouse.chr6 590284 7 + 636262 GAACAGT -s Anc0.Anc0refChr3 189854 7 + 222631 GTATAGT -s Anc1.Anc1refChr1 29381 7 + 69767 GTATAGT -s Anc2.Anc2refChr1 105842 7 + 142988 GTATAGT -s mr.mrrefChr3 139135 7 + 181027 GTACAGT -s simCow_chr6.simCow.chr6 563682 7 + 602619 GTTGAGT -s simDog_chr6.simDog.chr6 555552 7 + 593897 CTATAGT -s simHuman_chr6.simHuman.chr6 560597 7 + 601863 GTATAGT -s simRat_chr6.simRat.chr6 64934 7 - 647215 GTACACT - -a -s simMouse_chr6.simMouse.chr6 590291 2 + 636262 AC -s Anc0.Anc0refChr3 189861 2 + 222631 CC -s Anc1.Anc1refChr1 29388 2 + 69767 CC -s Anc2.Anc2refChr1 105874 2 + 142988 CC -s mr.mrrefChr3 139142 2 + 181027 AC -s simCow_chr6.simCow.chr6 563714 2 + 602619 TC -s simDog_chr6.simDog.chr6 555584 2 + 593897 CC -s simHuman_chr6.simHuman.chr6 560604 2 + 601863 CC -s simRat_chr6.simRat.chr6 64941 2 - 647215 AC - -a -s simMouse_chr6.simMouse.chr6 590293 13 + 636262 ATGTTAACAAGTC -s Anc0.Anc0refChr3 189870 13 + 222631 CTGTTAAATATTC -s Anc1.Anc1refChr1 29397 13 + 69767 CTGTTAAATATTC -s Anc2.Anc2refChr1 105883 13 + 142988 CTGTTACATATTC -s mr.mrrefChr3 139144 13 + 181027 ATGTTAACAATTC -s simCow_chr6.simCow.chr6 563722 13 + 602619 CCACTATATGTTG -s simDog_chr6.simDog.chr6 555594 13 + 593897 CTGTTACATATTC -s simHuman_chr6.simHuman.chr6 560613 13 + 601863 CTGTTAAACATTC -s simRat_chr6.simRat.chr6 64943 13 - 647215 ATGTTAACAATTC - -a -s simMouse_chr6.simMouse.chr6 590306 9 + 636262 TATGCAATA -s Anc0.Anc0refChr3 190137 9 + 222631 TATGTAAAG -s Anc1.Anc1refChr1 29664 9 + 69767 TATGTAAAG -s Anc2.Anc2refChr1 106222 9 + 142988 TATCCAAAG -s mr.mrrefChr3 139157 9 + 181027 TATGTAATA -s simCow_chr6.simCow.chr6 564102 9 + 602619 TATCACAAG -s simDog_chr6.simDog.chr6 555980 9 + 593897 TATCCAAAG -s simHuman_chr6.simHuman.chr6 560881 9 + 601863 TATGTAAGG -s simRat_chr6.simRat.chr6 64956 9 - 647215 TATGTAATA - -a -s simMouse_chr6.simMouse.chr6 590315 26 + 636262 CTGTGCCATTAGCACCTGTTAGTATG -s Anc0.Anc0refChr3 190147 26 + 222631 CCATCCCATTAGCACCTGTCAGTATG -s Anc1.Anc1refChr1 29674 26 + 69767 CCATCCCATTAGCACCTGTCAGTATG -s Anc2.Anc2refChr1 106232 26 + 142988 CCATCACATTAGCACCTGTCAATATG -s mr.mrrefChr3 139166 26 + 181027 CCATGCCATTAGCACCTGTTAGTATG -s simCow_chr6.simCow.chr6 564112 26 + 602619 TCATCTCATTAGCGCCTGTCATTATA -s simDog_chr6.simDog.chr6 555989 26 + 593897 CCTTCATGTTAGCAACTGTCAATATG -s simHuman_chr6.simHuman.chr6 560891 26 + 601863 CCATCCCATTAGCACCTGTCAGTATG -s simRat_chr6.simRat.chr6 64965 26 - 647215 CCATGCCATTAGCACCTGTTAGAATG - -a -s simMouse_chr6.simMouse.chr6 590341 4 + 636262 GACT -s Anc0.Anc0refChr3 190173 4 + 222631 GTCT -s Anc1.Anc1refChr1 29700 4 + 69767 GTCT -s Anc2.Anc2refChr1 106258 4 + 142988 GTCT -s mr.mrrefChr3 139192 4 + 181027 GACT -s simCow_chr6.simCow.chr6 564138 4 + 602619 GTCT -s simDog_chr6.simDog.chr6 556264 4 + 593897 GCCT -s simHuman_chr6.simHuman.chr6 560917 4 + 601863 ATCT -s simRat_chr6.simRat.chr6 64991 4 - 647215 GACT - -a -s simMouse_chr6.simMouse.chr6 590345 40 + 636262 AGACTAAAATTCATCATTCTTTGCATTCACACTTAATTTG -s Anc0.Anc0refChr3 190177 40 + 222631 ACACTAACATTCACCATTCTCTGTATTCATGTTTAATCTA -s Anc1.Anc1refChr1 29704 40 + 69767 ACACTAACATTCACCATTCTCTGTATTCATGTTTAATCTA -s Anc2.Anc2refChr1 106262 40 + 142988 ACACTAGCATTCACCACTCTCTGTATTCATGTTTAATCCA -s mr.mrrefChr3 139196 40 + 181027 AGACTAAAATTCATCATTCTTTGCATTCACGTTTAATTTA -s simCow_chr6.simCow.chr6 564143 40 + 602619 ATCCTAGTATTCCACACTCACTGTATTCATGCTTAATCCA -s simDog_chr6.simDog.chr6 556268 40 + 593897 ACACTAGCATTCACCACTCTCTGTATTCACATTTAATCCA -s simHuman_chr6.simHuman.chr6 560921 40 + 601863 ACACCAACAGTCACCATCCTCTGTATTTGTGTTTAATCTA -s simRat_chr6.simRat.chr6 64995 40 - 647215 AGACTAAAATTCATTATTATTTGCATTCACGTTTAATTTA - -a -s simMouse_chr6.simMouse.chr6 590385 15 + 636262 TGCAAATTCTAGAGT -s Anc0.Anc0refChr3 190219 14 + 222631 TGCACATTGTAGAG- -s Anc1.Anc1refChr1 29746 14 + 69767 TGCACATTGTAGAG- -s Anc2.Anc2refChr1 106304 14 + 142988 TGCACGCTGTAAAG- -s mr.mrrefChr3 139236 15 + 181027 TGCAAATTCTAGAGT -s simCow_chr6.simCow.chr6 564185 9 + 602619 TGCACGGTG------ -s simDog_chr6.simDog.chr6 556310 14 + 593897 TGCACGCTGTAAAG- -s simHuman_chr6.simHuman.chr6 560963 14 + 601863 TGCGTATTATAGAG- -s simRat_chr6.simRat.chr6 65035 15 - 647215 TGCAATTTCTAGAGT - -a -s simMouse_chr6.simMouse.chr6 590400 22 + 636262 AAGAAAGGTTCAAACTCAAACA -s Anc0.Anc0refChr3 190233 22 + 222631 AAGGAAGGTGAACGGTTAGATA -s Anc1.Anc1refChr1 29760 22 + 69767 AAGGAAGGTGAACGGTTAGATA -s Anc2.Anc2refChr1 106318 22 + 142988 AAGGAAGGTGAACGGTTAGATA -s mr.mrrefChr3 139251 22 + 181027 AAGAAAGGTTCAAAGTCAAACA -s simCow_chr6.simCow.chr6 564194 22 + 602619 AAGGAATGCTAATGGTCAGACA -s simDog_chr6.simDog.chr6 556325 22 + 593897 AAGGAAGGTGAACGGTTAGATA -s simRat_chr6.simRat.chr6 65050 22 - 647215 AAGGAAGGTTCAGAGTCAAACA - -a -s simMouse_chr6.simMouse.chr6 590422 14 + 636262 TCTGGAATCTGTGA -s Anc0.Anc0refChr3 190255 12 + 222631 TCTTA--TGTGAGA -s Anc1.Anc1refChr1 29782 12 + 69767 TCTTA--TGTGAGA -s Anc2.Anc2refChr1 106344 12 + 142988 TATTA--TGTAAGA -s mr.mrrefChr3 139273 12 + 181027 TCTGG--TCTGTGA -s simCow_chr6.simCow.chr6 564220 12 + 602619 TATTG--TGTAAGG -s simDog_chr6.simDog.chr6 556351 12 + 593897 TATTA--TGTAAGA -s simHuman_chr6.simHuman.chr6 560977 12 + 601863 GCTAA--TGTGACA -s simRat_chr6.simRat.chr6 65072 12 - 647215 TCTGG--TTTGTGA - -a -s simMouse_chr6.simMouse.chr6 590436 60 + 636262 TATCAAGAACTGAAATAACTCCTATGTGGTGAGGTATGGGCCACAGAGAAGGAGACCATG -s Anc0.Anc0refChr3 190267 33 + 222631 TTGCAAGACATGAA-------------------T--------TTATTGCTCAGGGCCATG -s Anc1.Anc1refChr1 29794 41 + 69767 TTGCAAGACATGAA-------------------TCATGGGCATTATTGCTCAGGGCCATG -s Anc2.Anc2refChr1 106356 33 + 142988 TTGCATGACATGAG-------------------T--------TTATTACTCAGGGCATGG -s mr.mrrefChr3 139285 60 + 181027 TATCAATAACTGAAATAACTCCTATGTGGTGAGGTATGGGCCACAGAGAAGGAGACCATG -s simCow_chr6.simCow.chr6 564232 33 + 602619 TAGCATGGTATGAG-------------------A--------TTACTACTCAGGGCATGC -s simDog_chr6.simDog.chr6 556363 33 + 593897 TTGCATGACATGAG-------------------T--------TAATTACCCAGGGAATGG -s simHuman_chr6.simHuman.chr6 560989 41 + 601863 TTGGCAGACAGGAA-------------------TCATGGGCACTAATGTTCAGGGCCATG -s simRat_chr6.simRat.chr6 65085 60 - 647215 TATCAATACCTGAGATAACTCCTATGTGGTGAGGTGTGGACCACAGAGAAGGAGACCTTG - -a -s simMouse_chr6.simMouse.chr6 590496 4 + 636262 ATGT -s Anc0.Anc0refChr3 190300 4 + 222631 GCCA -s Anc1.Anc1refChr1 29835 4 + 69767 GCCA -s Anc2.Anc2refChr1 106389 4 + 142988 GCCA -s mr.mrrefChr3 139345 4 + 181027 ATGT -s simCow_chr6.simCow.chr6 564265 4 + 602619 ACCA -s simDog_chr6.simDog.chr6 556396 4 + 593897 GCCA -s simHuman_chr6.simHuman.chr6 561030 4 + 601863 GGCA -s simRat_chr6.simRat.chr6 65147 4 - 647215 ATGT - -a -s simMouse_chr6.simMouse.chr6 590500 3 + 636262 ATT -s Anc0.Anc0refChr3 190304 3 + 222631 ATC -s Anc1.Anc1refChr1 29839 3 + 69767 ATC -s Anc2.Anc2refChr1 106393 3 + 142988 CTA -s mr.mrrefChr3 139349 3 + 181027 ATC -s simCow_chr6.simCow.chr6 564283 3 + 602619 CTA -s simDog_chr6.simDog.chr6 556400 3 + 593897 CTA -s simHuman_chr6.simHuman.chr6 561034 3 + 601863 ATC -s simRat_chr6.simRat.chr6 65151 3 - 647215 ATC - -a -s simMouse_chr6.simMouse.chr6 590503 14 + 636262 AGCTAACTCAACAC -s Anc0.Anc0refChr3 190307 13 + 222631 AACCAACGCGACA- -s Anc1.Anc1refChr1 29842 14 + 69767 AACCAACGCGACAA -s Anc2.Anc2refChr1 106396 13 + 142988 AATCAACGGGACG- -s mr.mrrefChr3 139352 14 + 181027 AGCTAACTCAACAC -s simCow_chr6.simCow.chr6 564296 13 + 602619 ACTCAACTTGATG- -s simDog_chr6.simDog.chr6 556403 13 + 593897 AAGCAATGGGACG- -s simHuman_chr6.simHuman.chr6 561037 13 + 601863 AAC-AGCGCTTCAA -s simRat_chr6.simRat.chr6 65154 14 - 647215 AGGGAACATGACAC - -a -s simMouse_chr6.simMouse.chr6 590517 60 + 636262 TAGCAACCTAACATGCCTATTTACTGCAGTCTTAATAGTAGACATTATAGGTAGAGGTAG -s Anc0.Anc0refChr3 190320 58 + 222631 TGGCAGACTACCAAGCCTTTTTCCTGCAGTCTTAATAGTATACATTAT--GTAGATATAG -s Anc1.Anc1refChr1 29856 58 + 69767 TGGCAGACTACCAAGCCTTTTTCCTGCAGTCTTAATAGTATACATTAT--GTAGATATAG -s Anc2.Anc2refChr1 106409 58 + 142988 TGGCAGACTACTAAGCCTTTTTCCTGCATTCTCAATAGTATACATTAG--ATAGATATAG -s mr.mrrefChr3 139366 60 + 181027 TAGCAACCTAACATGCCTATTTACTGCAGTCTTAATAGTAGACATTATAGGTAGAGGTAG -s simCow_chr6.simCow.chr6 564310 56 + 602619 TGGCAGACAAGTAAGCCTGTTTCCTGCATTATCAATAGTATCCAT--G--ACTGATAGGG -s simDog_chr6.simDog.chr6 556416 58 + 593897 TGGCAGACTGCTGAGCCTTTTTCCTGCATTCTCGATGGTACATTATAG--ATAGTTATAG -s simHuman_chr6.simHuman.chr6 561050 58 + 601863 GTGCAGGTTACCAAGCCTTTTTCCTGCAGTCTTAATAATATACATTAT--GTAGATCAAG -s simRat_chr6.simRat.chr6 65168 56 - 647215 TACCAACCTATCATGCATC----CTGTAGTCTTAATAGTAGACATTATAAGTAGAGGTCG - -a -s simMouse_chr6.simMouse.chr6 590577 59 + 636262 TCCTGTGTGAGCCATATTCCTAGGATCCCGGTCAACAGAAGCAAGAATGCCTGGAGTAT -s Anc0.Anc0refChr3 190378 58 + 222631 TCTTG-GTGAGCTAGATTCCTAGCATTTCCTGTGACAGCATCAAGAATGTCTTGGGTAT -s Anc1.Anc1refChr1 29914 59 + 69767 TCTTGTGTGAGCTAGATTCCTAGCATTTCCTGTGACAGCATCAAGAATGTCTTGGGTAT -s Anc2.Anc2refChr1 106467 58 + 142988 TCTTG-GTGAGCTAGATTCCTAGCATTTCCTGTGACAGCATCAAGAATGCCTCGGATAT -s mr.mrrefChr3 139426 59 + 181027 TCCTGTGTGAGCTAGATTCCTAGAATCCCTGTCAACAGAAGCAAGAATGTCTTGAGTAT -s simCow_chr6.simCow.chr6 564368 58 + 602619 TGTTG-GTGAGCTAAATTCCTAGCATTTCCTGTGACATCATCAAGAATGCCTCGGATAT -s simDog_chr6.simDog.chr6 556474 36 + 593897 TCCAG-GTGAGCTAGATTCCTGGCA--TCCTGTGACAGC-------------------- -s simHuman_chr6.simHuman.chr6 561108 59 + 601863 TCTTGTGTGAGCTAGATCCCTAATAATTCCTGTCACAGCAACAAGAATTTCTTATGTAT -s simRat_chr6.simRat.chr6 65224 59 - 647215 TCCTGTGTGAGCTAGCTTCCTAGAATCCCTGTCAACAGAAGCAAGAATGTCTTGAGTAT - -a -s simMouse_chr6.simMouse.chr6 590636 18 + 636262 AGGCTAAATCCGTTAGAA -s Anc0.Anc0refChr3 190436 18 + 222631 AGGCTAAAGCCATCAAAA -s Anc1.Anc1refChr1 29973 18 + 69767 AGGCTAAAGCCATCAAAA -s Anc2.Anc2refChr1 106525 18 + 142988 GGGCTAAAGCCATCAAAA -s mr.mrrefChr3 139485 18 + 181027 AGGCTAAATCCGTCAGAA -s simCow_chr6.simCow.chr6 564426 18 + 602619 GGGCTACAGCCATGAAAA -s simDog_chr6.simDog.chr6 556510 15 + 593897 ---TTAATGCTGTCAGAA -s simHuman_chr6.simHuman.chr6 561168 18 + 601863 AGGCTAAAGCCACCAAAG -s simRat_chr6.simRat.chr6 65283 18 - 647215 AGACTAAATCTGTCAGAA - -a -s simMouse_chr6.simMouse.chr6 590654 4 + 636262 CTGC -s Anc0.Anc0refChr3 190454 4 + 222631 CTGC -s Anc1.Anc1refChr1 29991 4 + 69767 CTGC -s Anc2.Anc2refChr1 106545 4 + 142988 CTGC -s mr.mrrefChr3 139503 4 + 181027 CTGC -s simCow_chr6.simCow.chr6 564446 4 + 602619 TTGC -s simDog_chr6.simDog.chr6 556527 4 + 593897 CTGC -s simRat_chr6.simRat.chr6 65301 4 - 647215 CTGC - -a -s simMouse_chr6.simMouse.chr6 590658 19 + 636262 AGTGGTCATGATTTAATCT -s Anc0.Anc0refChr3 190458 19 + 222631 GGTGGTAAAGATTCAATAT -s Anc1.Anc1refChr1 29995 19 + 69767 GGTGGTAAAGATTCAATAT -s Anc2.Anc2refChr1 106549 19 + 142988 GGTGGTAAAAATTCAGTAT -s mr.mrrefChr3 139507 19 + 181027 AGTGGTCATGATTTAATAT -s simCow_chr6.simCow.chr6 564450 19 + 602619 AGTGGTAAAAATACAGCAT -s simDog_chr6.simDog.chr6 556532 19 + 593897 GGCAGTAAAAATTCAGTAT -s simHuman_chr6.simHuman.chr6 561186 16 + 601863 ---GACTAGGTGGAAAAAT -s simRat_chr6.simRat.chr6 65305 19 - 647215 AGTGGTCATGATTTAATAT - -a -s simMouse_chr6.simMouse.chr6 590677 32 + 636262 GTTAAGGTGGTGCTGTTATCATCTAGGAGGAT -s Anc0.Anc0refChr3 190477 32 + 222631 ATTTAGATTGTGCAGTTTTCATCTAAAAGGTT -s Anc1.Anc1refChr1 30014 32 + 69767 ATTTAGATTGTGCAGTTTTCATCTAAAAGGTT -s Anc2.Anc2refChr1 106568 32 + 142988 ATTTAGATTATGCAGTCTTCATCTAAAAGGTT -s mr.mrrefChr3 139526 32 + 181027 GTTTAGGTGGTGCTGTTATCATCTAGGAGGAT -s simCow_chr6.simCow.chr6 564469 31 + 602619 ATTTAGATTATGCAATATTC-TCTAAAAGGTT -s simDog_chr6.simDog.chr6 556551 32 + 593897 ATTTAGATTATACGGTCTTCACCTAAAAGCTT -s simHuman_chr6.simHuman.chr6 561202 32 + 601863 ATTTAGATTGTGCAGGTTGTATCTAAAATGGT -s simRat_chr6.simRat.chr6 65326 32 - 647215 GTTTATGTGGTGATGTTATCATCTCGGAGGTT - -a -s simMouse_chr6.simMouse.chr6 590709 34 + 636262 ACTGGTCGCCAACTACATTGACAGAATAATATGA -s Anc0.Anc0refChr3 190509 31 + 222631 ACTGGTCCCCACCTGCATTAACAGAATAGTA--- -s Anc1.Anc1refChr1 30046 33 + 69767 ACTGGTCCCCACCTGCATTAACAGAATAGTA-GG -s Anc2.Anc2refChr1 106600 31 + 142988 ACTGGTCCTCACCTGCACTAACAGAATAGTA--- -s mr.mrrefChr3 139558 33 + 181027 ACTGGTCGCCACCTACATTGACAGAATAATA-GG -s simCow_chr6.simCow.chr6 564500 31 + 602619 ACTGGTCTACACGTGCACTGACAGGGTAGTA--- -s simDog_chr6.simDog.chr6 556583 31 + 593897 ACTGGTCCTCATCTACACTAACAGAATAGTA--- -s simHuman_chr6.simHuman.chr6 561240 32 + 601863 ACTGGTCCCCACCTGCATTAACA-AATAGTG-GG -s simRat_chr6.simRat.chr6 65358 33 - 647215 ACTGGCCACCACCTACATTGATAGAATAATA-GG - -a -s simMouse_chr6.simMouse.chr6 590743 3 + 636262 CTA -s Anc0.Anc0refChr3 190544 3 + 222631 CTA -s Anc1.Anc1refChr1 30083 3 + 69767 CTA -s Anc2.Anc2refChr1 106635 3 + 142988 TTA -s mr.mrrefChr3 139591 3 + 181027 CTA -s simCow_chr6.simCow.chr6 564535 3 + 602619 TCT -s simDog_chr6.simDog.chr6 556618 3 + 593897 TTA -s simHuman_chr6.simHuman.chr6 561278 3 + 601863 CTA -s simRat_chr6.simRat.chr6 65391 3 - 647215 CTT - -a -s simMouse_chr6.simMouse.chr6 590746 7 + 636262 AACATCC -s Anc0.Anc0refChr3 190555 7 + 222631 ATTATTC -s Anc1.Anc1refChr1 30094 7 + 69767 ATTATTC -s Anc2.Anc2refChr1 106646 7 + 142988 ATTATTT -s mr.mrrefChr3 139594 7 + 181027 AACATTC -s simCow_chr6.simCow.chr6 564546 7 + 602619 ATTATTT -s simDog_chr6.simDog.chr6 556629 7 + 593897 ATTATTT -s simHuman_chr6.simHuman.chr6 561289 7 + 601863 ATTATTC -s simRat_chr6.simRat.chr6 65394 7 - 647215 AACATTC - -a -s simMouse_chr6.simMouse.chr6 590753 4 + 636262 ACTA -s Anc0.Anc0refChr3 190562 4 + 222631 ACTA -s Anc1.Anc1refChr1 30101 4 + 69767 ACTA -s Anc2.Anc2refChr1 106659 4 + 142988 ACTA -s mr.mrrefChr3 139601 4 + 181027 ACTA -s simCow_chr6.simCow.chr6 564599 4 + 602619 ACTA -s simDog_chr6.simDog.chr6 556642 4 + 593897 GCTA -s simHuman_chr6.simHuman.chr6 561296 4 + 601863 ACTA -s simRat_chr6.simRat.chr6 65401 4 - 647215 ACTA - -a -s simMouse_chr6.simMouse.chr6 590757 6 + 636262 TAGCCC -s Anc0.Anc0refChr3 190568 6 + 222631 TTACTT -s Anc1.Anc1refChr1 30107 6 + 69767 TTACTT -s Anc2.Anc2refChr1 106665 6 + 142988 CTACTT -s mr.mrrefChr3 139605 6 + 181027 TTACCC -s simCow_chr6.simCow.chr6 564605 6 + 602619 CTACTT -s simDog_chr6.simDog.chr6 556648 6 + 593897 CTACTT -s simHuman_chr6.simHuman.chr6 561302 6 + 601863 TTACTT -s simRat_chr6.simRat.chr6 65405 6 - 647215 TTACCC - -a -s simMouse_chr6.simMouse.chr6 590763 23 + 636262 TCACTGAATAAATTTTTTTATGG -s Anc0.Anc0refChr3 190586 22 + 222631 CCACTCTGTAAA-TTTTCAATGG -s Anc1.Anc1refChr1 30125 22 + 69767 CCACTCTGTAAA-TTTTCAATGG -s Anc2.Anc2refChr1 106683 22 + 142988 CCACTCTGTTAA-TTTTCAATGT -s mr.mrrefChr3 139623 23 + 181027 TCACTCAATAAATTTTTTTATGG -s simCow_chr6.simCow.chr6 564620 22 + 602619 CCATTCTGTTAA-TTTTCAACAC -s simDog_chr6.simDog.chr6 556666 18 + 593897 CCACTC----AA-TTTCTGATGT -s simHuman_chr6.simHuman.chr6 561320 22 + 601863 CCACTCCCTAAA-TTTTCAATGG -s simRat_chr6.simRat.chr6 65430 23 - 647215 TCACTCAATAAATTTTTTTATGG - -a -s simMouse_chr6.simMouse.chr6 590786 68 + 636262 CAGCATCACAGTCAGGTGGCATCCAGACCTAAGGGCTCTCCTTGGCAATCTTAACTTGGGGGGTGTCA -s Anc0.Anc0refChr3 190608 50 + 222631 CAGC-TCAAAA-----------------CCAATGCCTCTCCTTGGCAATCTTAACTTGGGGGGTGTAG -s Anc1.Anc1refChr1 30147 51 + 69767 CAGCATCAAAA-----------------CCAATGCCTCTCCTTGGCAATCTTAACTTGGGGGGTGTAG -s Anc2.Anc2refChr1 106705 50 + 142988 CAGC-TCAAAA-----------------CCAATGCCTCTCCTTGGCAATGTTAACTTGGGGAGTGTAG -s mr.mrrefChr3 139646 68 + 181027 CAGCATCACAATCAGGTAGCATCCAGACCTAAGGGCTCTCCTTGGCAATCTTAACTTGGGGGGTGTCA -s simCow_chr6.simCow.chr6 564642 44 + 602619 CAGC-TTGAAC-----------------CCAATACCTCTCCT------TGCTAACTTGGGGAGTGGAG -s simDog_chr6.simDog.chr6 556684 47 + 593897 GAGC-TCAAAA-----------------CGAATG-CTCTCCTTGGCAATGTTAA-TTGAGGAGCTT-G -s simHuman_chr6.simHuman.chr6 561342 51 + 601863 CAGCATCCAAA-----------------CCTATGCCCCTCCTTGGCAATCTTAACTTGGGGGGTGTAG -s simRat_chr6.simRat.chr6 65454 67 - 647215 CAGCATCATAATTGGGTAGCATCTAGACCTTAGGGCTCTCCTTGGCAATCTTAACTTGGGGG-TGTCA - -a -s simMouse_chr6.simMouse.chr6 590854 15 + 636262 GAAATTCAGAAATGC -s Anc0.Anc0refChr3 190659 13 + 222631 GCATGTCAGAA--AC -s Anc1.Anc1refChr1 30199 13 + 69767 GCATGTCAGAA--AC -s Anc2.Anc2refChr1 106756 13 + 142988 GCATGTCAGAA--AC -s mr.mrrefChr3 139714 13 + 181027 GAAATTCAGAA--GC -s simCow_chr6.simCow.chr6 564687 13 + 602619 ACATGTATGAA--AT -s simDog_chr6.simDog.chr6 556732 13 + 593897 GAATGTCATAA--AC -s simHuman_chr6.simHuman.chr6 561394 10 + 601863 GCAGGTCAGA----- -s simRat_chr6.simRat.chr6 65521 13 - 647215 GGAATTTAGAA--GC - -a -s simMouse_chr6.simMouse.chr6 590869 2 + 636262 TC -s Anc0.Anc0refChr3 190672 2 + 222631 TG -s Anc1.Anc1refChr1 30212 2 + 69767 TG -s Anc2.Anc2refChr1 106771 2 + 142988 TG -s mr.mrrefChr3 139727 2 + 181027 TC -s simCow_chr6.simCow.chr6 564702 2 + 602619 TG -s simDog_chr6.simDog.chr6 556747 2 + 593897 TG -s simRat_chr6.simRat.chr6 65534 2 - 647215 TC - -a -s simMouse_chr6.simMouse.chr6 590871 78 + 636262 CAAGATATATGTATAACTGGCTGACCAGATTAGTACTTCAAGGTATGACGTTGTGCTATAGCCCCTAGTACATTGCAG -s Anc0.Anc0refChr3 190674 60 + 222631 TGAGGTATATGCGTAACTGGATCGCCACATTAATA------------------TGTGACAGCCCCTAGCTCACTGGGG -s Anc1.Anc1refChr1 30214 60 + 69767 TGAGGTATATGCGTAACTGGATCGCCACATTAATA------------------TGTGACAGCCCCTAGCTCACTGGGG -s Anc2.Anc2refChr1 106773 60 + 142988 TGAGGTATATGCGTAACTGGATCGCCACATTAATA------------------TGTGACAGCCCCTAGCTCACTGGGG -s mr.mrrefChr3 139729 60 + 181027 CAAGATATATGTATAACTGGCTGACCAGATTAGTA------------------TGCTATAGCCCCTAGTACATTGCAG -s simCow_chr6.simCow.chr6 564707 60 + 602619 TGAGGTATATGCGTAACTGGATTACCATATTAATA------------------TCCAATGGCTACCAATTCACTGGGT -s simDog_chr6.simDog.chr6 556749 60 + 593897 TGAGGTATATGCGTAACTGGATCGCCACATTAATA------------------TGTGACAGCCCCTAGCTCACTGGGG -s simRat_chr6.simRat.chr6 65536 60 - 647215 CAAGATATATGTGTGATTGGAGGACCAGATTAGTA------------------TGCTGTAGCCCCTAGTACATTGCAA - -a -s simMouse_chr6.simMouse.chr6 590949 4 + 636262 ACCC -s Anc0.Anc0refChr3 190734 4 + 222631 ACCC -s Anc1.Anc1refChr1 30274 4 + 69767 ACCC -s Anc2.Anc2refChr1 106834 4 + 142988 ACCC -s mr.mrrefChr3 139789 4 + 181027 ACCC -s simCow_chr6.simCow.chr6 564768 4 + 602619 ATCC -s simDog_chr6.simDog.chr6 556810 4 + 593897 ACCC -s simRat_chr6.simRat.chr6 65596 4 - 647215 ACCC - -a -s simMouse_chr6.simMouse.chr6 590953 32 + 636262 AGTCATTGGGAGTTTGTAACCTGAGTTTATAT -s Anc0.Anc0refChr3 190738 27 + 222631 ACCCGTTGAGATTAAG-----TGGGAAAATAC -s Anc1.Anc1refChr1 30278 27 + 69767 ACCCGTTGAGATTAAG-----TGGGAAAATAC -s Anc2.Anc2refChr1 106838 27 + 142988 ACCCGTTGAGATTAAG-----TGGGAAAATAC -s mr.mrrefChr3 139793 32 + 181027 AGTCATTGGGAGTTTGTAACCTGAGTTTATAT -s simCow_chr6.simCow.chr6 564772 27 + 602619 AGCCATTGAGATCATT-----TGGGTGAATAT -s simDog_chr6.simDog.chr6 556815 27 + 593897 ACCCGTTGAGATTAAG-----TGGGAAAATAC -s simRat_chr6.simRat.chr6 65600 32 - 647215 AGTCATTGAGAGTTTGTGACTTGAATTGGTAT - -a -s simMouse_chr6.simMouse.chr6 590985 4 + 636262 ATCT -s Anc0.Anc0refChr3 190765 4 + 222631 ATGC -s Anc1.Anc1refChr1 30305 4 + 69767 ATGC -s Anc2.Anc2refChr1 106865 4 + 142988 ATGC -s mr.mrrefChr3 139825 4 + 181027 ATCT -s simCow_chr6.simCow.chr6 564799 4 + 602619 ATGT -s simDog_chr6.simDog.chr6 556844 4 + 593897 ATGC -s simRat_chr6.simRat.chr6 65632 4 - 647215 ATCT - -a -s simMouse_chr6.simMouse.chr6 590989 34 + 636262 TAATGCATGACAATGATCTATATCCGCTTGCCTA -s Anc0.Anc0refChr3 190769 23 + 222631 GCCTGGACAA---TGATCCTTACCCT-------- -s Anc1.Anc1refChr1 30309 23 + 69767 GCCTGGACAA---TGATCCTTACCCT-------- -s Anc2.Anc2refChr1 106869 23 + 142988 GCCTGGACAA---TGATCCTTACCCT-------- -s mr.mrrefChr3 139829 24 + 181027 TAATGCATGAC--TGATCTATATCCG-------- -s simCow_chr6.simCow.chr6 564807 23 + 602619 GCCTGGACCA---TGATATATCCCCT-------- -s simDog_chr6.simDog.chr6 556848 23 + 593897 GCCTGGACAA---TGATCCTTACCCT-------- -s simRat_chr6.simRat.chr6 65636 24 - 647215 GAATGCCTGAC--TGATCTATATCCT-------- - -a -s simMouse_chr6.simMouse.chr6 591023 14 + 636262 AATAATTCAAGAAG -s Anc0.Anc0refChr3 190792 14 + 222631 AATTAATCAATGAG -s Anc1.Anc1refChr1 30332 14 + 69767 AATTAATCAATGAG -s Anc2.Anc2refChr1 106898 14 + 142988 AATTAATCAATGAG -s mr.mrrefChr3 139853 14 + 181027 AATAATTCAAGAAG -s simCow_chr6.simCow.chr6 564836 14 + 602619 AACTAACCAATGAG -s simDog_chr6.simDog.chr6 556877 14 + 593897 AATTAATCAATGAG -s simRat_chr6.simRat.chr6 65660 14 - 647215 AATCATTCAGGGAG - -a -s simMouse_chr6.simMouse.chr6 591037 10 + 636262 ACTGCACACA -s Anc0.Anc0refChr3 190806 10 + 222631 ACTGCATAGG -s Anc1.Anc1refChr1 30346 10 + 69767 ACTGCATAGG -s Anc2.Anc2refChr1 106917 10 + 142988 ACTGCATAGG -s mr.mrrefChr3 139867 10 + 181027 ACTGCACACA -s simCow_chr6.simCow.chr6 564855 10 + 602619 ACGGTATGGT -s simDog_chr6.simDog.chr6 556992 10 + 593897 ACTGCATAGG -s simRat_chr6.simRat.chr6 65674 10 - 647215 ACTGTGCTCA - -a -s simMouse_chr6.simMouse.chr6 591047 4 + 636262 GCAC -s Anc0.Anc0refChr3 190816 4 + 222631 GAAC -s Anc1.Anc1refChr1 30356 4 + 69767 GAAC -s Anc2.Anc2refChr1 106927 4 + 142988 GAAC -s mr.mrrefChr3 139877 4 + 181027 GCAC -s simCow_chr6.simCow.chr6 564866 4 + 602619 GAAC -s simDog_chr6.simDog.chr6 557002 4 + 593897 GAAC -s simRat_chr6.simRat.chr6 65684 4 - 647215 GCAT - -a -s simMouse_chr6.simMouse.chr6 591051 4 + 636262 TAGT -s Anc0.Anc0refChr3 190820 4 + 222631 TAGT -s Anc1.Anc1refChr1 30360 4 + 69767 TAGT -s Anc2.Anc2refChr1 106938 4 + 142988 TAGT -s mr.mrrefChr3 139881 4 + 181027 TAGT -s simCow_chr6.simCow.chr6 564877 4 + 602619 TTGT -s simDog_chr6.simDog.chr6 557013 4 + 593897 TAGT -s simRat_chr6.simRat.chr6 65688 4 - 647215 TGGT - -a -s simMouse_chr6.simMouse.chr6 591055 100 + 636262 ACACTTCTGTGCCTAACTCTAGTGCTTGATCTTAGCCCGGCACCCCTATAGTATGGTTTCTCAATGGGGTTGCGTCAATCGGTCAGCATATTAGTCAACT -s Anc0.Anc0refChr3 190824 39 + 222631 GCTCCTCTTTTCTTA-------TGCATGGT-TTCATC-----------------------------------------------------TTTGTGCACC -s Anc1.Anc1refChr1 30364 39 + 69767 GCTCCTCTTTTCTTA-------TGCATGGT-TTCATC-----------------------------------------------------TTTGTGCACC -s Anc2.Anc2refChr1 106943 39 + 142988 GCTCCTCTTTTCTTA-------TGCATGGT-TTCATC-----------------------------------------------------TTTGTGCACC -s mr.mrrefChr3 139885 46 + 181027 ACACTTCTGTGCCTAACTCTAGTGCTTGAT-TTAGCC-----------------------------------------------------TTAGTCAACT -s simCow_chr6.simCow.chr6 564882 39 + 602619 GCTCCACCTTTCATG-------TACTTAAT-TTTCAA-----------------------------------------------------TTCATTCACC -s simDog_chr6.simDog.chr6 557018 39 + 593897 GCTCCTCTTTTCTTA-------TGCATGGT-TTCATC-----------------------------------------------------TTTGTGCACC -s simRat_chr6.simRat.chr6 65692 46 - 647215 GCACTTCTGTGCCCAACTCCAGTGCTTGAT-TTCGCC-----------------------------------------------------TTAGTCAACT - -a -s simMouse_chr6.simMouse.chr6 591155 25 + 636262 AATCCATTGAGGTATGGCACTTTGA -s Anc0.Anc0refChr3 190863 25 + 222631 AATCCATTGAGGTGCGGCACTTAGA -s Anc1.Anc1refChr1 30403 25 + 69767 AATCCATTGAGGTGCGGCACTTAGA -s Anc2.Anc2refChr1 106986 25 + 142988 AATCCATTGAGGTGCGGCACTTAGA -s mr.mrrefChr3 139931 25 + 181027 AATCCATTGAGGTATGGCACTTTGA -s simCow_chr6.simCow.chr6 564925 25 + 602619 AGCCCATTGAGATGCAGCACTTAGA -s simDog_chr6.simDog.chr6 557061 25 + 593897 AATCCATTGAGGTGCGGCACTTAGA -s simRat_chr6.simRat.chr6 65738 25 - 647215 AATCCATTGAGGTATGGCACTTAAG - -a -s simMouse_chr6.simMouse.chr6 591180 11 + 636262 CAACTTTATGA -s Anc0.Anc0refChr3 190888 5 + 222631 GCCC------A -s Anc1.Anc1refChr1 30428 5 + 69767 GCCC------A -s Anc2.Anc2refChr1 107011 5 + 142988 GCCC------A -s mr.mrrefChr3 139956 11 + 181027 CAACTTTATGA -s simCow_chr6.simCow.chr6 564950 5 + 602619 GCCC------A -s simDog_chr6.simDog.chr6 557087 5 + 593897 GCCC------A -s simHuman_chr6.simHuman.chr6 561404 1 + 601863 ----------A -s simRat_chr6.simRat.chr6 65763 11 - 647215 CCCCTTTATGA - -a -s simMouse_chr6.simMouse.chr6 591191 1 + 636262 A -s Anc0.Anc0refChr3 190893 1 + 222631 A -s Anc1.Anc1refChr1 30433 1 + 69767 A -s Anc2.Anc2refChr1 107016 1 + 142988 A -s mr.mrrefChr3 139967 1 + 181027 A -s simCow_chr6.simCow.chr6 564958 1 + 602619 C -s simDog_chr6.simDog.chr6 557092 1 + 593897 A -s simHuman_chr6.simHuman.chr6 561405 1 + 601863 A -s simRat_chr6.simRat.chr6 65774 1 - 647215 A - -a -s simMouse_chr6.simMouse.chr6 591192 6 + 636262 AGAGGG -s Anc0.Anc0refChr3 190894 6 + 222631 AGAGGG -s Anc1.Anc1refChr1 30434 6 + 69767 AGAGGG -s Anc2.Anc2refChr1 107018 6 + 142988 AGAGTG -s mr.mrrefChr3 139968 6 + 181027 AGAGGG -s simCow_chr6.simCow.chr6 564960 6 + 602619 AAAAGG -s simDog_chr6.simDog.chr6 557094 6 + 593897 AGAGTG -s simHuman_chr6.simHuman.chr6 561406 6 + 601863 AGATGG -s simRat_chr6.simRat.chr6 65775 6 - 647215 AGAGGG - -a -s simMouse_chr6.simMouse.chr6 591198 1 + 636262 A -s Anc0.Anc0refChr3 190900 1 + 222631 A -s Anc1.Anc1refChr1 30440 1 + 69767 A -s Anc2.Anc2refChr1 107118 1 + 142988 A -s mr.mrrefChr3 139974 1 + 181027 A -s simCow_chr6.simCow.chr6 565060 1 + 602619 A -s simDog_chr6.simDog.chr6 557194 1 + 593897 A -s simHuman_chr6.simHuman.chr6 561412 1 + 601863 A -s simRat_chr6.simRat.chr6 65781 1 - 647215 A - -a -s simMouse_chr6.simMouse.chr6 591199 42 + 636262 TAGCACAGAAGCGTAATCCTTAACTCACAGGCATAAACTCTG -s Anc0.Anc0refChr3 190904 23 + 222631 TAAAAATA-------------------AAAAAATAAAATCAG -s Anc1.Anc1refChr1 30444 23 + 69767 TAAAAATA-------------------AAAAAATAAAATCAG -s Anc2.Anc2refChr1 107122 23 + 142988 TAAAAATA-------------------AAAAAATAAAATCAG -s mr.mrrefChr3 139975 23 + 181027 TAGCACAG-------------------CAGGCATAAACTCTG -s simCow_chr6.simCow.chr6 565064 23 + 602619 TGAAAATA-------------------AAAAAATAAAATCAG -s simDog_chr6.simDog.chr6 557198 23 + 593897 TAAGAATA-------------------AAAAAATAAAACTGG -s simHuman_chr6.simHuman.chr6 561416 23 + 601863 TAAAAATA-------------------AAAAAATAAAGTCAG -s simRat_chr6.simRat.chr6 65782 23 - 647215 TAGCATGG-------------------TGTGCATAAACTCTG - -a -s simMouse_chr6.simMouse.chr6 591241 6 + 636262 AAAGGA -s Anc0.Anc0refChr3 190927 6 + 222631 AATGTA -s Anc1.Anc1refChr1 30467 6 + 69767 AATGTA -s Anc2.Anc2refChr1 107145 6 + 142988 AATGTA -s mr.mrrefChr3 139998 6 + 181027 AAAGGA -s simCow_chr6.simCow.chr6 565087 6 + 602619 AATGTA -s simDog_chr6.simDog.chr6 557222 6 + 593897 AATGTA -s simHuman_chr6.simHuman.chr6 561439 6 + 601863 AATTCA -s simRat_chr6.simRat.chr6 65805 6 - 647215 AAAAGG - -a -s simMouse_chr6.simMouse.chr6 591247 1 + 636262 A -s Anc0.Anc0refChr3 190933 1 + 222631 A -s Anc1.Anc1refChr1 30473 1 + 69767 A -s Anc2.Anc2refChr1 107151 1 + 142988 A -s mr.mrrefChr3 140004 1 + 181027 A -s simCow_chr6.simCow.chr6 565095 1 + 602619 A -s simDog_chr6.simDog.chr6 557228 1 + 593897 A -s simHuman_chr6.simHuman.chr6 561445 1 + 601863 A -s simRat_chr6.simRat.chr6 65811 1 - 647215 A - -a -s simMouse_chr6.simMouse.chr6 591248 19 + 636262 CATATTCAATAGTCTGCAA -s Anc0.Anc0refChr3 190936 19 + 222631 CATATTCAATACCCTGTGA -s Anc1.Anc1refChr1 30476 19 + 69767 CATATTCAATACCCTGTGA -s Anc2.Anc2refChr1 107154 19 + 142988 CAGATTCAACACCCTGTGA -s mr.mrrefChr3 140005 19 + 181027 CATATTCAATAGTCTGCAA -s simCow_chr6.simCow.chr6 565098 19 + 602619 GACATGCGACACTCTGCCG -s simDog_chr6.simDog.chr6 557231 19 + 593897 CAGATTCAACACCCTATGA -s simHuman_chr6.simHuman.chr6 561448 19 + 601863 CATATTCAATACCCTGTGA -s simRat_chr6.simRat.chr6 65812 19 - 647215 CATATTCAATAGCCTGTAG - -a -s simMouse_chr6.simMouse.chr6 591267 12 + 636262 CTGCATATCCTC -s Anc0.Anc0refChr3 190955 11 + 222631 C-ACATATCACC -s Anc1.Anc1refChr1 30495 11 + 69767 C-ACATATCACC -s Anc2.Anc2refChr1 107173 11 + 142988 C-ACATATCACC -s mr.mrrefChr3 140024 12 + 181027 CTGCATATCCTC -s simCow_chr6.simCow.chr6 565117 11 + 602619 T-ACATATCACC -s simDog_chr6.simDog.chr6 557251 11 + 593897 C-GCATGTCACT -s simHuman_chr6.simHuman.chr6 561467 11 + 601863 C-ACATATCACC -s simRat_chr6.simRat.chr6 65831 12 - 647215 CTGCGTATCCTC - -a -s simMouse_chr6.simMouse.chr6 591279 16 + 636262 AATGACATTTTTGCTC -s Anc0.Anc0refChr3 190966 16 + 222631 AATGACATTTTTGTTC -s Anc1.Anc1refChr1 30506 16 + 69767 AATGACATTTTTGTTC -s Anc2.Anc2refChr1 107184 16 + 142988 AATGACATTTTTGTCC -s mr.mrrefChr3 140036 16 + 181027 AATGACATTTTTGCTC -s simCow_chr6.simCow.chr6 565129 15 + 602619 AATGAGATTTTTAT-C -s simDog_chr6.simDog.chr6 557262 16 + 593897 AGTGACATTTTTGTCC -s simHuman_chr6.simHuman.chr6 561478 16 + 601863 AACAACATTTTTGTTC -s simRat_chr6.simRat.chr6 65843 16 - 647215 AATGACATTTTTGCCC - -a -s simMouse_chr6.simMouse.chr6 591295 1 + 636262 A -s Anc0.Anc0refChr3 190982 1 + 222631 A -s Anc1.Anc1refChr1 30522 1 + 69767 A -s Anc2.Anc2refChr1 107200 1 + 142988 A -s mr.mrrefChr3 140052 1 + 181027 A -s simCow_chr6.simCow.chr6 565144 1 + 602619 A -s simDog_chr6.simDog.chr6 557278 1 + 593897 A -s simHuman_chr6.simHuman.chr6 561494 1 + 601863 A -s simRat_chr6.simRat.chr6 65864 1 - 647215 A - -a -s simMouse_chr6.simMouse.chr6 591296 3 + 636262 TAG -s Anc0.Anc0refChr3 190994 3 + 222631 TGA -s Anc1.Anc1refChr1 30534 3 + 69767 TGA -s Anc2.Anc2refChr1 107212 3 + 142988 TGA -s mr.mrrefChr3 140053 3 + 181027 TAG -s simCow_chr6.simCow.chr6 565156 3 + 602619 TGG -s simDog_chr6.simDog.chr6 557290 3 + 593897 TCA -s simHuman_chr6.simHuman.chr6 561506 3 + 601863 TGA -s simRat_chr6.simRat.chr6 65865 3 - 647215 GAG - -a -s simMouse_chr6.simMouse.chr6 591299 41 + 636262 ATATGGATGTGTATGAGTCCTTGATTGATGTCTGTATGAGT -s Anc0.Anc0refChr3 190997 40 + 222631 ACAAATATGTTTATGAGTTTTTGATTGATGTCTGAACCAG- -s Anc1.Anc1refChr1 30537 41 + 69767 ACAAATATGTTTATGAGTTTTTGATTGATGTCTGAACCAGT -s Anc2.Anc2refChr1 107215 40 + 142988 ACAAATATGTTTATGAGTTTTTGATTGATATCTGAACCCG- -s mr.mrrefChr3 140056 41 + 181027 ATATGGATGTGTATGAGTCCTTGATTGATGTCTGTATGAGT -s simCow_chr6.simCow.chr6 565159 40 + 602619 ACAAATATATTTATGAGTTTTTGGTTGATATCTAAACATG- -s simDog_chr6.simDog.chr6 557294 40 + 593897 ATGAATATGCTTATGAGCTTCTGATTGATAACTGAACCCG- -s simHuman_chr6.simHuman.chr6 561509 41 + 601863 ACAAATATGTTTGTGAGTTTTTGATTGATGTCTGAACCAGT -s simRat_chr6.simRat.chr6 65868 41 - 647215 ACATGGATGTGCATGAGTCTATGATTGATGTTTGCACGAGT - -a -s simMouse_chr6.simMouse.chr6 591340 3 + 636262 ACT -s Anc0.Anc0refChr3 191037 3 + 222631 ATT -s Anc1.Anc1refChr1 30578 3 + 69767 ATT -s Anc2.Anc2refChr1 107255 3 + 142988 ATT -s mr.mrrefChr3 140097 3 + 181027 ACT -s simCow_chr6.simCow.chr6 565218 3 + 602619 ATT -s simDog_chr6.simDog.chr6 557334 3 + 593897 ATT -s simHuman_chr6.simHuman.chr6 561550 3 + 601863 AGT -s simRat_chr6.simRat.chr6 65909 3 - 647215 ATT - -a -s simMouse_chr6.simMouse.chr6 591343 25 + 636262 GTCTACTCAGTAACAATAGACTGGG -s Anc0.Anc0refChr3 191040 24 + 222631 GTCTACTCTATAACAACA-ACTGGG -s Anc1.Anc1refChr1 30581 24 + 69767 GTCTACTCTATAACAACA-ACTGGG -s Anc2.Anc2refChr1 107258 24 + 142988 ATCTACTCTATAACAACA-ACTGGA -s mr.mrrefChr3 140100 25 + 181027 GTCTACTCAGTAACAATAGACTGGG -s simCow_chr6.simCow.chr6 565221 24 + 602619 ATCTATTCTATATCAACA-ACTGGA -s simDog_chr6.simDog.chr6 557337 24 + 593897 ATCTACTGTATAATAGCA-ACTGGA -s simHuman_chr6.simHuman.chr6 561556 19 + 601863 GTCTATT-----ACAACA-ACTGGG -s simRat_chr6.simRat.chr6 65912 25 - 647215 GTCTACTTAGTAACAATAGATTGGG - -a -s simMouse_chr6.simMouse.chr6 591368 66 + 636262 CAAGTCTTGCCCTATGAGTTACCATAAAAATCGTTCCATAAGTTATAAAGTCTGCAGAAGTCTCAG -s Anc0.Anc0refChr3 191064 54 + 222631 CAGGTTTAGTATCATGAGTCGCAGCAACAATTGTTCCTTAGGGTAT------------AATGTCTG -s Anc1.Anc1refChr1 30605 54 + 69767 CAGGTTTAGTATCATGAGTCGCAGCAACAATTGTTCCTTAGGGTAT------------AATGTCTG -s Anc2.Anc2refChr1 107284 54 + 142988 CAGTTTCACTATCATGAGTCGCAGCAACAATTATTCATTAGGGTAT------------AAAGTCTG -s mr.mrrefChr3 140125 62 + 181027 CAAGTCTTGCCCTATGAGTTACCATAAAAATCGTTCCATAAGTTAT----TCTGCAGAAGTCTCAG -s simCow_chr6.simCow.chr6 565247 54 + 602619 CAGTTTCACTATCATGAGTTACAGCAAGAACTCTTGATTTAGGTAT------------AGAGTCTG -s simDog_chr6.simDog.chr6 557363 54 + 593897 CAGTTTCACTATCATGAGTCGCAGCAACAATCATTCATTAGGATAT------------AAAGTCTA -s simHuman_chr6.simHuman.chr6 561575 41 + 601863 GAGGCTTGGTGTCATG-------------ATTGTTCCTTAGGGTGT------------AATTTCTG -s simRat_chr6.simRat.chr6 65937 62 - 647215 CAAGTCTTGCCTTATGAGTTACAGTAAAAATTATTCCCTAAGGTAC----TGTACTGAAGTCTCAG - -a -s simMouse_chr6.simMouse.chr6 591434 19 + 636262 TCCTCAATATACACCACCA -s Anc0.Anc0refChr3 191121 19 + 222631 TCTTCAACATACACCTCAG -s Anc1.Anc1refChr1 30662 19 + 69767 TCTTCAACATACACCTCAG -s Anc2.Anc2refChr1 107341 19 + 142988 TCTTCAACATACACCTCAG -s mr.mrrefChr3 140187 19 + 181027 TCCTCAATATACACCACCA -s simCow_chr6.simCow.chr6 565304 19 + 602619 TCTTCAATATCTACCTCAG -s simDog_chr6.simDog.chr6 557420 19 + 593897 TTTTCAACATACACCTCAG -s simHuman_chr6.simHuman.chr6 561619 13 + 601863 TCTTCAAGGGATG------ -s simRat_chr6.simRat.chr6 65999 19 - 647215 ACTTCAACATACACCTCGA - -a -s simMouse_chr6.simMouse.chr6 591453 13 + 636262 ACTTGCCTCTACC -s Anc0.Anc0refChr3 191140 13 + 222631 ATATGCACCTATA -s Anc1.Anc1refChr1 30681 13 + 69767 ATATGCACCTATA -s Anc2.Anc2refChr1 107360 13 + 142988 ATATGCACCTATA -s mr.mrrefChr3 140206 13 + 181027 ACTTGCCTCTACC -s simCow_chr6.simCow.chr6 565323 13 + 602619 ATATGTTCCTGCA -s simDog_chr6.simDog.chr6 557442 13 + 593897 ATATGCACCTATA -s simRat_chr6.simRat.chr6 66018 13 - 647215 ATATGCATCTACC - -a -s simMouse_chr6.simMouse.chr6 591466 35 + 636262 AGGAGGGAACAGGTAGGATATTTATGCCTTTCCTG -s Anc0.Anc0refChr3 191153 29 + 222631 G------GACAGATGGGATACGTGTGTATTCACTG -s Anc1.Anc1refChr1 30694 29 + 69767 G------GACAGATGGGATACGTGTGTATTCACTG -s Anc2.Anc2refChr1 107379 29 + 142988 G------GACTGATGGGATACGTGTGTACTCACTG -s mr.mrrefChr3 140219 29 + 181027 A------AACAGGTAGGATATTTATGCCTTTCCTG -s simCow_chr6.simCow.chr6 565342 29 + 602619 G------GATGGATGTGATACCTGTATACTCACTG -s simDog_chr6.simDog.chr6 557461 29 + 593897 G------TACTGATGGGATACGTGTGTACTTACTG -s simHuman_chr6.simHuman.chr6 561632 29 + 601863 G------GACAGATGAGATCCATGTGTATTCGCTG -s simRat_chr6.simRat.chr6 66031 29 - 647215 A------AACAGGTGGGATGTATATTCATTTCCTG - -a -s simMouse_chr6.simMouse.chr6 591501 25 + 636262 CACGGATGAAAATGAATCTTCTTAA -s Anc0.Anc0refChr3 191190 22 + 222631 CA---ATGATAACAAATTCTCTAAC -s Anc1.Anc1refChr1 30731 22 + 69767 CA---ATGATAACAAATTCTCTAAC -s Anc2.Anc2refChr1 107416 22 + 142988 CA---ATGATAACAAATTCTCTAAC -s mr.mrrefChr3 140248 25 + 181027 CACGGATGAAAATGAATCTTCTTAA -s simCow_chr6.simCow.chr6 565379 22 + 602619 CA---ATAATACCAAATACTCTAAC -s simDog_chr6.simDog.chr6 557498 22 + 593897 TG---TTGATAACAAATTCTCTAAC -s simHuman_chr6.simHuman.chr6 561669 22 + 601863 CA---ATGGGAACAAATTCTCTAAC -s simRat_chr6.simRat.chr6 66060 25 - 647215 GATGGATGAGAACAAATTCTCTAAA - -a -s simMouse_chr6.simMouse.chr6 591526 6 + 636262 GATCAT -s Anc0.Anc0refChr3 191212 6 + 222631 TGTTTA -s Anc1.Anc1refChr1 30753 6 + 69767 TGTTTA -s Anc2.Anc2refChr1 107438 6 + 142988 TGTTTA -s mr.mrrefChr3 140273 6 + 181027 GATCAT -s simCow_chr6.simCow.chr6 565401 6 + 602619 TGTTTA -s simDog_chr6.simDog.chr6 557520 6 + 593897 TGTTTA -s simHuman_chr6.simHuman.chr6 561691 6 + 601863 TGTTCA -s simRat_chr6.simRat.chr6 66086 6 - 647215 GATCAG - -a -s simMouse_chr6.simMouse.chr6 591532 36 + 636262 ACTGGGGTGCCCCAGATATTCTATTATTCAGCAATT -s Anc0.Anc0refChr3 191218 36 + 222631 ATTTGGGTACCCTAGAAATTTTATTATTCAGGAATT -s Anc1.Anc1refChr1 30759 36 + 69767 ATTTGGGTACCCTAGAAATTTTATTATTCAGGAATT -s Anc2.Anc2refChr1 107445 36 + 142988 ATTTGGATACCGTAGAAATATTATCATTCAGGAATT -s mr.mrrefChr3 140279 36 + 181027 ACTGGGGTGCCCCAGATATTCTATTATTCAGCAATT -s simCow_chr6.simCow.chr6 565408 36 + 602619 ATTTGGATACCATATATATATTATCATTGAGGAATT -s simDog_chr6.simDog.chr6 557527 36 + 593897 ATTAGGATGCTGTAGAAACATTACCAATCAGAAATG -s simHuman_chr6.simHuman.chr6 561697 36 + 601863 ATTTGGGTACCCTAGAAATTTTATTGTTCAGGAATT -s simRat_chr6.simRat.chr6 66092 36 - 647215 ACGGGGGTGCCCTAGTGATTCTATTATTCAGCAATC - -a -s simMouse_chr6.simMouse.chr6 591568 11 + 636262 CCCTAGCTCCC -s Anc0.Anc0refChr3 191255 11 + 222631 CCAAAGCATCC -s Anc1.Anc1refChr1 30796 11 + 69767 CCAAAGCATCC -s Anc2.Anc2refChr1 107482 11 + 142988 CCAAACCATAC -s mr.mrrefChr3 140315 11 + 181027 CCCTAGCTCCC -s simCow_chr6.simCow.chr6 565445 11 + 602619 CCAAACCATAC -s simDog_chr6.simDog.chr6 557564 11 + 593897 CCAAACTCTAC -s simHuman_chr6.simHuman.chr6 561734 11 + 601863 CCAAAGCATCC -s simRat_chr6.simRat.chr6 66128 11 - 647215 CTCTAACTCCC - -a -s simMouse_chr6.simMouse.chr6 591579 7 + 636262 ATACAAC -s Anc0.Anc0refChr3 191266 7 + 222631 TCACAAC -s Anc1.Anc1refChr1 30807 7 + 69767 TCACAAC -s Anc2.Anc2refChr1 107493 7 + 142988 TCACAAC -s mr.mrrefChr3 140326 7 + 181027 ATACAAC -s simCow_chr6.simCow.chr6 565457 7 + 602619 TGCAAAC -s simDog_chr6.simDog.chr6 557575 7 + 593897 TCACAAC -s simHuman_chr6.simHuman.chr6 561745 7 + 601863 TAATATC -s simRat_chr6.simRat.chr6 66139 7 - 647215 ATACAAC - -a -s simMouse_chr6.simMouse.chr6 591586 9 + 636262 ATCAAAGGT -s Anc0.Anc0refChr3 191274 9 + 222631 ACCAAAAGT -s Anc1.Anc1refChr1 30815 9 + 69767 ACCAAAAGT -s Anc2.Anc2refChr1 107501 9 + 142988 GCCAAAAGT -s mr.mrrefChr3 140333 9 + 181027 ATCAAAGGT -s simCow_chr6.simCow.chr6 565465 9 + 602619 GCCAAAAGT -s simDog_chr6.simDog.chr6 557583 9 + 593897 GCCAAAGGT -s simHuman_chr6.simHuman.chr6 561753 9 + 601863 ACCAAAAGT -s simRat_chr6.simRat.chr6 66146 9 - 647215 ACCAAAGGT - -a -s simMouse_chr6.simMouse.chr6 591595 2 + 636262 AG -s Anc0.Anc0refChr3 191285 1 + 222631 A- -s Anc1.Anc1refChr1 30826 1 + 69767 A- -s Anc2.Anc2refChr1 107512 1 + 142988 A- -s mr.mrrefChr3 140342 2 + 181027 AG -s simCow_chr6.simCow.chr6 565476 1 + 602619 A- -s simDog_chr6.simDog.chr6 557594 1 + 593897 A- -s simHuman_chr6.simHuman.chr6 561764 1 + 601863 A- -s simRat_chr6.simRat.chr6 66155 2 - 647215 TG - -a -s simMouse_chr6.simMouse.chr6 591597 3 + 636262 TCT -s mr.mrrefChr3 140344 3 + 181027 TCT -s simRat_chr6.simRat.chr6 66185 3 - 647215 TCC - -a -s simMouse_chr6.simMouse.chr6 591717 5 + 636262 CTCTA -s mr.mrrefChr3 140464 5 + 181027 CTCTA -s simRat_chr6.simRat.chr6 66309 5 - 647215 CTCTA - -a -s simMouse_chr6.simMouse.chr6 591722 43 + 636262 TGTATCCGTCACTGAGGCTGATAGCCAATTCAAGGGGTTTCAG -s mr.mrrefChr3 140469 37 + 181027 TGTATCCGTCA------CTGATAGCCAATTCAAGGGGTTTCAG -s simRat_chr6.simRat.chr6 66319 37 - 647215 TGTATCCGTCA------CTAATAGCCAATTCAAGGAGTGTCAG - -a -s simMouse_chr6.simMouse.chr6 591765 81 + 636262 TCATACTTTATATATGAGAACAAGATTGAAGGGACACAGAGTGCTATTTTGCATCATCCAGTATCCGAAGTCCATATCTCT -s Anc0.Anc0refChr3 191286 41 + 222631 ----------------------------------------GTACTATTTTGCATCACCCAATATAAGAAATCCATCTCTCT -s Anc1.Anc1refChr1 30827 41 + 69767 ----------------------------------------GTACTATTTTGCATCACCCAATATAAGAAATCCATCTCTCT -s Anc2.Anc2refChr1 107513 41 + 142988 ----------------------------------------ATACCATTTTGCATCACCCAATATAGGAAATCCATCTCTCT -s mr.mrrefChr3 140506 81 + 181027 TCATACTTTATATATGAGAACAAGATTGAAGGGACACAGAGTGCTATTTTGCATCACCCAATATCAGAAATCCATATCTCT -s simCow_chr6.simCow.chr6 565477 41 + 602619 ----------------------------------------ATATCATTTTGTATCACCCAATATAGGAAATCCATCTCTCT -s simDog_chr6.simDog.chr6 557595 39 + 593897 ------------------------------------------ACCATTTTGCATCACCCAATAAAGGAAGTCCATCTCTCT -s simHuman_chr6.simHuman.chr6 561765 41 + 601863 ----------------------------------------GTACTATCTTGCATCACCCAATATGAGAAATCCAACCCTCT -s simRat_chr6.simRat.chr6 66359 81 - 647215 TCATACTTTATATATGCAAACAGGATTGATGTGACACAGAGTGCTATTTTGCATCACCCAATATCAGAAATCCATATCACT - -a -s simMouse_chr6.simMouse.chr6 591846 1 + 636262 C -s Anc0.Anc0refChr3 191327 1 + 222631 C -s Anc1.Anc1refChr1 30868 1 + 69767 C -s Anc2.Anc2refChr1 107554 1 + 142988 T -s mr.mrrefChr3 140587 1 + 181027 C -s simCow_chr6.simCow.chr6 565518 1 + 602619 T -s simHuman_chr6.simHuman.chr6 561806 1 + 601863 C -s simRat_chr6.simRat.chr6 66442 1 - 647215 C - -a -s simMouse_chr6.simMouse.chr6 591847 1 + 636262 T -s Anc0.Anc0refChr3 191337 1 + 222631 T -s Anc1.Anc1refChr1 30878 1 + 69767 T -s Anc2.Anc2refChr1 107564 1 + 142988 T -s mr.mrrefChr3 140588 1 + 181027 T -s simCow_chr6.simCow.chr6 565528 1 + 602619 T -s simDog_chr6.simDog.chr6 557642 1 + 593897 T -s simHuman_chr6.simHuman.chr6 561816 1 + 601863 T -s simRat_chr6.simRat.chr6 66443 1 - 647215 T - -a -s simMouse_chr6.simMouse.chr6 591848 31 + 636262 ATGGTGGGAGACATTAGGTAGGATGACATTC -s Anc0.Anc0refChr3 191338 31 + 222631 AGAATTGGAGACCTTAGATAAAATAACATTC -s Anc1.Anc1refChr1 30879 31 + 69767 AGAATTGGAGACCTTAGATAAAATAACATTC -s Anc2.Anc2refChr1 107566 31 + 142988 AGAATTGGAGACCTTGGGTAAAATAACATTC -s mr.mrrefChr3 140589 31 + 181027 ATGGTGGGAGACATTAGATAGGATGACATTC -s simCow_chr6.simCow.chr6 565530 31 + 602619 AGAATTGGATACCCTGCGTAAAATTACATTC -s simDog_chr6.simDog.chr6 557644 31 + 593897 AGGAGTGGAGAGCTTGGGTAAAATAACACTC -s simHuman_chr6.simHuman.chr6 561817 31 + 601863 AGAATTGGAGACCTTAGATAAAACAACATTC -s simRat_chr6.simRat.chr6 66444 31 - 647215 ATGGTGGGAGACGTTAGATAGGATGACATTC - -a -s simMouse_chr6.simMouse.chr6 591879 5 + 636262 ACGCT -s Anc0.Anc0refChr3 191369 5 + 222631 ACGAA -s Anc1.Anc1refChr1 30910 5 + 69767 ACGAA -s Anc2.Anc2refChr1 107597 5 + 142988 AGGAA -s mr.mrrefChr3 140620 5 + 181027 ACGCT -s simCow_chr6.simCow.chr6 565561 5 + 602619 ATGAG -s simDog_chr6.simDog.chr6 557675 5 + 593897 AGGAA -s simHuman_chr6.simHuman.chr6 561860 5 + 601863 CCGAA - -a -s simMouse_chr6.simMouse.chr6 591884 48 + 636262 AGACAAACCATCCTCACTGTTGTCAAAAGTACAATAGTGCTCTGCATT -s Anc0.Anc0refChr3 191374 48 + 222631 CAACAAACCACCCTCACTGTTGTGAAAAATACAATGTTACTCTGCATT -s Anc1.Anc1refChr1 30915 48 + 69767 CAACAAACCACCCTCACTGTTGTGAAAAATACAATGTTACTCTGCATT -s Anc2.Anc2refChr1 107603 48 + 142988 CAACAACCCACCCTCACCGTTGTGAAAAATAGAATGTTACTCCACATG -s mr.mrrefChr3 140625 48 + 181027 AGACAAACCATCCTCACTGTTGTCAAAAGTACAATAGTGCTCTGCATT -s simCow_chr6.simCow.chr6 565567 41 + 602619 GAACAAACCATCCTCACCGTTGTCAAAATTATAATGGTACT------- -s simDog_chr6.simDog.chr6 557681 48 + 593897 CAACAACCCACCCATACCGTTGTGAAAAATAGGATGTTACCCCACATG -s simHuman_chr6.simHuman.chr6 561865 48 + 601863 CAACTAACCAACCTCACTGTTGTTGAAAATACAATCTTACTTTGAAGT -s simRat_chr6.simRat.chr6 66475 7 - 647215 -----------------------------------------CTGCATT - -a -s simMouse_chr6.simMouse.chr6 591932 11 + 636262 AGCAGTACCAA -s Anc0.Anc0refChr3 191423 11 + 222631 ACCAGTACAGG -s Anc1.Anc1refChr1 30964 11 + 69767 ACCAGTACAGG -s Anc2.Anc2refChr1 107652 11 + 142988 ACCAGTACAGG -s mr.mrrefChr3 140673 11 + 181027 ACCAGTACAAG -s simCow_chr6.simCow.chr6 565608 7 + 602619 ----GTACAGG -s simDog_chr6.simDog.chr6 557730 11 + 593897 ACCAGTATATG -s simHuman_chr6.simHuman.chr6 561914 11 + 601863 ACCAGTACAGG -s simRat_chr6.simRat.chr6 66482 11 - 647215 ACCAGTACAAG - -a -s simMouse_chr6.simMouse.chr6 591943 52 + 636262 AAGTCTGTTTGATTTCTGCTTCTGCCATCCAGGGGACATCTTCTGTTTAGCC -s Anc0.Anc0refChr3 191438 52 + 222631 ACATCTGTCTTTTTTTCTTTTCTACCACCTAGGAGATGTGTTCTTTTTAGCT -s Anc1.Anc1refChr1 30979 52 + 69767 ACATCTGTCTTTTTTTCTTTTCTACCACCTAGGAGATGTGTTCTTTTTAGCT -s Anc2.Anc2refChr1 107667 52 + 142988 TCATCTGTCTTTTTTTCTTTTCTACCACCTAGGAGATGTGCTCTTTTTAGCT -s mr.mrrefChr3 140684 52 + 181027 ACGTCTGTTTGATTTCTTCTTCTGCCATCTAGGGGACATCTTCTGTTTAGCT -s simCow_chr6.simCow.chr6 565619 52 + 602619 TCATCTATCCTTTTTTCTTTTCTACCATCTAGGAGATATGCTCCTACTAGCT -s simDog_chr6.simDog.chr6 557745 52 + 593897 TCATCTGTCTTTTTTTCTTTTCCACCACCTAGGAGGTGTGCTCTTTTTAGCT -s simHuman_chr6.simHuman.chr6 561929 52 + 601863 ACATCTGTCTTTTTTTCTTTTCTACCACCTAAGAGATGTGTTCTTTTTAGTT -s simRat_chr6.simRat.chr6 66493 52 - 647215 ACGTCCATTTGATTTCTTCTTCTTTCATCTAGGGGGCATAGACTGTTTATCT - -a -s simMouse_chr6.simMouse.chr6 591995 92 + 636262 CTCCCTATACATATTTTTAGTTGCAATCCATGGCATTGGATCGGGACTCTGTCGGCTGTCCTTATTTTTTTAGCTCCAGTACATGCCATTCT -s Anc0.Anc0refChr3 191490 18 + 222631 GTTCCTATACATA------------------------------------------------------------------------GCAT--G -s Anc1.Anc1refChr1 31031 18 + 69767 GTTCCTATACATA------------------------------------------------------------------------GCAT--G -s Anc2.Anc2refChr1 107719 18 + 142988 GCTCATATACAAA------------------------------------------------------------------------GCAT--G -s mr.mrrefChr3 140736 89 + 181027 CTTCCTATACATATTTTTAGTTGCAATCCATGGCATTGGATCGGGACTCTGT-GGCTGTCCTTATTTTT--AGCTCCAGTACATGGCATTCG -s simCow_chr6.simCow.chr6 565679 18 + 602619 GCTCTTATACAAA------------------------------------------------------------------------TCCT--G -s simDog_chr6.simDog.chr6 557797 15 + 593897 GCTCATATA---A------------------------------------------------------------------------GCAT--G -s simHuman_chr6.simHuman.chr6 561981 18 + 601863 GTTCCTATACGTA------------------------------------------------------------------------GCAT--G -s simRat_chr6.simRat.chr6 66545 89 - 647215 ATTCCTATACATATTTCTAGTTGCAATACATGGCATTGGATAGGGACTCTGT-GGCTGTCCATATTTTT--AGCTGCAATACATAGCATTCG - -a -s simMouse_chr6.simMouse.chr6 592087 65 + 636262 ATAGGGTGCTACATTTATTTATATCCCCCAGTGAGGGCTAACACTAGTCACATTACCTGGTACAT -s Anc0.Anc0refChr3 191508 49 + 222631 ATAA---CCTGCCTTTATTTAAA-CCCCTACTAAGGGCTAAAGCTGGTCACA------------T -s Anc1.Anc1refChr1 31049 62 + 69767 ATAA---CCTGCCTTTATTTAAAACCCCTACTAAGGGCTAAAGCTGGTCACACTATACAATACAT -s Anc2.Anc2refChr1 107743 49 + 142988 AGGA---CCTGCCTTGATTTAAA-CCCCTACTAAGGGCTAAAGCTGGTCACA------------T -s mr.mrrefChr3 140825 65 + 181027 ATAGGGTGCTACATTTATTTATATCCCCTAGTGAGGGCTAAAACTAGTCACATTACCTGGTACAT -s simCow_chr6.simCow.chr6 565703 47 + 602619 GGGA---CCTGCATTTGTTTAAA-GCTCTACTAAGGACCA--GCTGGTCACA------------T -s simDog_chr6.simDog.chr6 557818 49 + 593897 AGGA---CCTGCCTTGATTTGGA-CCCCTACTCAGGGCTAAAGCTGGTCACA------------T -s simHuman_chr6.simHuman.chr6 561999 62 + 601863 ATAA---CCTGAGCTTGCTTAAAGCCCCTACTAAGGGCTAAAGCTGGTCACACTATACAATGCAT -s simRat_chr6.simRat.chr6 66634 65 - 647215 ATTGGGTGCTACATTTATTTATATGCACTAGTGAAGGCTAAAACTAGTCTCATTACCTGGTATGT - -a -s simMouse_chr6.simMouse.chr6 592152 134 + 636262 GACACAATTAGACCAGATATAGGGTCTGCTCTGATGGTTTACATGGTCTGATTTATCCCTATGGTGATGCTGGCTTAATTAGTCCAACCTTTTGGTTACCAGTAGTTGAGGATAAGTGATAATGGACTTATGTT -s Anc0.Anc0refChr3 191557 105 + 222631 TACACGATTAAACCAGTGTTTGGGTGTGCTATGTTGGTATAAATAGCCTGATCTATACCTATGGCAGTGCTGTCTCAATTACTCCACCC--CTGCATTAAAAT---------------------------TCCC -s Anc1.Anc1refChr1 31111 107 + 69767 TACACGATTAAACCAGTGTTTGGGTGTGCTATGTTGGTATAAATAGCCTGATCTATACCTATGGCAGTGCTGTCTCAATTACTCCACCCTTCTGCATTAAAAT---------------------------TCCC -s Anc2.Anc2refChr1 107792 105 + 142988 TACACGATTAAACCAGTGTTTGTGTGTGCTACTTTGGTATAAATAGCCTGATCTATACCTCTGCCAGTGCTGTCTCAATTACTCCACCC--CTGCATTAAAAT---------------------------TCCC -s mr.mrrefChr3 140890 134 + 181027 TACACAATTAAACCAGATTTAGGGTCTGCTCTGATGGTTTACATAGTCTGATTTATCCCTATGGTGATGCTGGCTCAATTACTCCAACCTTTTGGTTTACAGTAGTTGAGGATAAGTGATAATGGACTTATGTT -s simCow_chr6.simCow.chr6 565751 87 + 602619 TCCACGTTTAACCCAGTTTAAGTGTGTGCTA-TTTAGT-TAAATAGCCTGATCTATGCCTTTGCTGGTGGTGTTTCAATTAATCCACCC--------------------------------------------- -s simDog_chr6.simDog.chr6 557867 105 + 593897 TACACAATTAAACCAGTGTTTGTATCTGCTACTTTGATATAAATAGCCTGATCTATAACTCTGCCAGTTCAGTCGTGATCACTCCACCC--CTGCATTAAAAT---------------------------TCCC -s simHuman_chr6.simHuman.chr6 562061 104 + 601863 TACATGATTAAACCAGTGTTTTGGTGTGCTATGGTGGTCAATATAGCCCGATCTATACGTATGG---TGATGTCTCAATTACTCCACCCTTCTGTGTTAAAAT---------------------------TTCC -s simRat_chr6.simRat.chr6 66699 133 - 647215 TACACAATCAAATCA-ATTTAGGGTCTGCTCCGATGGTTTACATAGTCTGATTTAACCCTATGGTGGTGCTCATTCATCTACTCCAACCTTTTGGTTTACAGTAATTGAGGATAAGTGATAATGGACTTGTGTT - -a -s simMouse_chr6.simMouse.chr6 592286 53 + 636262 ATTGTCTTACAATTTCTCTATTTATCCCCCCAGTCTAATTTATGTAGAGGTGG -s Anc0.Anc0refChr3 191662 48 + 222631 TTTGTTTTACCATT--TCTATTGATCCCAC---TCTAATTCATGGAAAGGTGG -s Anc1.Anc1refChr1 31218 48 + 69767 TTTGTTTTACCATT--TCTATTGATCCCAC---TCTAATTCATGGAAAGGTGG -s Anc2.Anc2refChr1 107897 48 + 142988 TTTGTTTGACCATT--TCTATTGATCCCAC---TCTAATTCATGGAAAGGTGG -s mr.mrrefChr3 141024 50 + 181027 ATTGTCTTACAATTTCTCTATTTATCCCCC---TCTAATTTATGTAGAGGTGG -s simCow_chr6.simCow.chr6 565838 41 + 602619 -------AACTATT--TCTATTGATCTCAC---TCTAATTCAGGGGAAGGTGA -s simDog_chr6.simDog.chr6 558007 48 + 593897 TTTGTTTGACCATT--GCTTCTGATCCAAG---TCTAATTCATGGAAAGGTGG -s simHuman_chr6.simHuman.chr6 562165 47 + 601863 TTTGTTTTACCAAT--TCTATTAATCCCAC---TCTAATTAATGGAAAAGCC- -s simRat_chr6.simRat.chr6 66832 21 - 647215 ATTGTCTTACAATTTCTCTAT-------------------------------- - -a -s simMouse_chr6.simMouse.chr6 592339 5 + 636262 ATAAC -s Anc0.Anc0refChr3 191710 5 + 222631 ACCAC -s Anc1.Anc1refChr1 31266 5 + 69767 ACCAC -s Anc2.Anc2refChr1 107945 5 + 142988 ACCAC -s mr.mrrefChr3 141074 5 + 181027 ATAAC -s simCow_chr6.simCow.chr6 565884 5 + 602619 ACCAC -s simDog_chr6.simDog.chr6 558055 5 + 593897 ACCAC - -a -s simMouse_chr6.simMouse.chr6 592344 28 + 636262 CTAACCTATGAACATCCAACGCCCAAGA -s Anc0.Anc0refChr3 191716 19 + 222631 CTAACCTATGGA---------CGCAAGA -s Anc1.Anc1refChr1 31272 19 + 69767 CTAACCTATGGA---------CGCAAGA -s Anc2.Anc2refChr1 107951 19 + 142988 CTGCCTTATGGA---------CGCAAGA -s mr.mrrefChr3 141079 28 + 181027 CCAACCTATGAACATCCTACGCCCAAGA -s simCow_chr6.simCow.chr6 565890 19 + 602619 CAGCCATTTGGA---------CCAGGGA -s simDog_chr6.simDog.chr6 558061 19 + 593897 TTGCCTTATGGA---------CGCAAGA -s simHuman_chr6.simHuman.chr6 562213 19 + 601863 CTAACCCCTAGA---------CACAAGA -s simRat_chr6.simRat.chr6 66853 27 - 647215 CCAACCCATGAACATCCTACGCCCAAG- - -a -s simMouse_chr6.simMouse.chr6 592372 25 + 636262 AAAGAGGCAAGATCAGCATGTATGC -s Anc0.Anc0refChr3 191735 25 + 222631 GAAGATGTAAAATTGGTATGTATGC -s Anc1.Anc1refChr1 31291 25 + 69767 GAAGATGTAAAATTGGTATGTATGC -s Anc2.Anc2refChr1 107970 25 + 142988 TAAGATGTAAAATTGGTATGTATGT -s mr.mrrefChr3 141107 25 + 181027 GAAGAGGCAAGATCAGTATGTATGC -s simCow_chr6.simCow.chr6 565909 17 + 602619 ATAGATGTAAAATTGGT-------- -s simDog_chr6.simDog.chr6 558080 25 + 593897 TAAGAGGAAAGATTGGTATGTATGT -s simHuman_chr6.simHuman.chr6 562232 25 + 601863 GCAGATGTAAAATTGGTCTGTATGC -s simRat_chr6.simRat.chr6 67225 23 - 647215 gaagAG--AAGCTCAGTATGTATGA - -a -s simMouse_chr6.simMouse.chr6 592397 1 + 636262 C -s Anc0.Anc0refChr3 191760 1 + 222631 C -s Anc1.Anc1refChr1 31316 1 + 69767 C -s Anc2.Anc2refChr1 107996 1 + 142988 T -s mr.mrrefChr3 141132 1 + 181027 C -s simDog_chr6.simDog.chr6 558106 1 + 593897 T -s simHuman_chr6.simHuman.chr6 562257 1 + 601863 C -s simRat_chr6.simRat.chr6 67248 1 - 647215 C - -a -s simMouse_chr6.simMouse.chr6 592398 9 + 636262 ATCTCCATG -s Anc0.Anc0refChr3 191761 9 + 222631 CTCTTCATG -s Anc1.Anc1refChr1 31317 9 + 69767 CTCTTCATG -s Anc2.Anc2refChr1 107997 9 + 142988 CTCCTCATG -s mr.mrrefChr3 141133 9 + 181027 ATCTCCATG -s simDog_chr6.simDog.chr6 558107 9 + 593897 CTCCTCATG -s simHuman_chr6.simHuman.chr6 562311 9 + 601863 CTCTTCATA -s simRat_chr6.simRat.chr6 67249 9 - 647215 ATCTCCATG - -a -s simMouse_chr6.simMouse.chr6 592407 25 + 636262 CTAGTCAGACAGTCTTGACACACAA -s Anc0.Anc0refChr3 191771 25 + 222631 TTACTCAGACAGCTTTGGCACAAAA -s Anc1.Anc1refChr1 31327 25 + 69767 TTACTCAGACAGCTTTGGCACAAAA -s Anc2.Anc2refChr1 108007 25 + 142988 TTACTCAGCCAGCTTTGGCACAAAA -s mr.mrrefChr3 141143 25 + 181027 CTAGTCAGACAGTCTTGACACACAA -s simCow_chr6.simCow.chr6 565926 17 + 602619 --------GGAGCTTTGGCATAAAG -s simDog_chr6.simDog.chr6 558117 25 + 593897 TTACTCAGCCATCTCTGGCACAAAA -s simHuman_chr6.simHuman.chr6 562321 25 + 601863 TTGCTCAGATGGCTTAGGAACAAAA -s simRat_chr6.simRat.chr6 67259 25 - 647215 CTTGTCAAACAGTCTTGACACACAA - -a -s simMouse_chr6.simMouse.chr6 592432 19 + 636262 CTTGGCTAACATCAAGAAA -s Anc0.Anc0refChr3 191796 19 + 222631 CTCAGCTAATGTCAGAAAA -s Anc1.Anc1refChr1 31352 19 + 69767 CTCAGCTAATGTCAGAAAA -s Anc2.Anc2refChr1 108032 19 + 142988 CTCAGCTAATGTCAGAAAG -s mr.mrrefChr3 141168 19 + 181027 CTCGGCTAACATCAAGAAA -s simCow_chr6.simCow.chr6 565943 19 + 602619 CTCAGCTGATGACAAAAAG -s simDog_chr6.simDog.chr6 558142 19 + 593897 CTGAGCTAACGTCAGAAAG -s simHuman_chr6.simHuman.chr6 562346 19 + 601863 CTCAGCTAATGTCGCTAAA -s simRat_chr6.simRat.chr6 67298 19 - 647215 CTCGGCTAACATCAAGAAA - -a -s simMouse_chr6.simMouse.chr6 592451 13 + 636262 GACTTAATAGTAT -s Anc0.Anc0refChr3 191821 13 + 222631 GACTCAATAATAT -s Anc1.Anc1refChr1 31377 13 + 69767 GACTCAATAATAT -s Anc2.Anc2refChr1 108057 13 + 142988 GAGTCAATAATAT -s mr.mrrefChr3 141187 13 + 181027 GACTTAATAATAT -s simCow_chr6.simCow.chr6 565968 13 + 602619 GAGTAGATAATGT -s simDog_chr6.simDog.chr6 558167 13 + 593897 GAGTCAATAATAT -s simHuman_chr6.simHuman.chr6 562371 13 + 601863 GACTCCATGATAT -s simRat_chr6.simRat.chr6 67317 13 - 647215 GACTTAATAATAT - -a -s simMouse_chr6.simMouse.chr6 592464 45 + 636262 CATGACAGAGTTACCTTGAAGAAAGGTTACCCCCATAGAGATTCA -s Anc0.Anc0refChr3 191837 44 + 222631 CACAACAAGATTACCTTGGAGAGAAGTTA-CTTAATAGAGATCCA -s Anc1.Anc1refChr1 31393 44 + 69767 CACAACAAGATTACCTTGGAGAGAAGTTA-CTTAATAGAGATCCA -s Anc2.Anc2refChr1 108073 44 + 142988 CACAACAAGATTACCTTGGAGAGAAGTTA-CTTAATAGTGATCCA -s mr.mrrefChr3 141200 45 + 181027 CATGACAAAGTTACCTTGAAGAAAAGTTACCTTCATAGAGATTCA -s simCow_chr6.simCow.chr6 565984 44 + 602619 TACAACAAGATCACCCTGGAGAGAAGGTA-CTTAATAGTAATTCA -s simDog_chr6.simDog.chr6 558183 42 + 593897 CATGGCAACATTATCTTGGAGAGAAGTTA-CTTA-TAG-GATCCA -s simHuman_chr6.simHuman.chr6 562387 44 + 601863 CACAACAAGATTACCTGGGAGAGGAGTTA-CTTAATAGAGATCCA -s simRat_chr6.simRat.chr6 67330 45 - 647215 CATGACAAAGTTACCTTGAAGAAAAGTTACCTTTATAGAGATATG - -a -s simMouse_chr6.simMouse.chr6 592509 45 + 636262 GCAAAACCTGCAACCATATTTAGAATGAGCTAAATCTTGCTATCA -s Anc0.Anc0refChr3 191884 35 + 222631 GCAA----TCTAACAATCTTAAGATTTTCCTGTCTA------TGA -s Anc1.Anc1refChr1 31440 35 + 69767 GCAA----TCTAACAATCTTAAGATTTTCCTGTCTA------TGA -s Anc2.Anc2refChr1 108120 35 + 142988 GCAA----TCTTACAATCTTAAGATTTTCCTGTCTA------TGG -s mr.mrrefChr3 141245 39 + 181027 GCAAAGCCTGCAACCATATTTAGAATGAGCTAAATC------TCA -s simCow_chr6.simCow.chr6 566032 24 + 602619 GCAT----T-----ACTCCAAAG------CCGTCTA------TGG -s simDog_chr6.simDog.chr6 558228 28 + 593897 GGCA----TCTTACAAGCTTAAGATTTTCTTG------------- -s simHuman_chr6.simHuman.chr6 562434 35 + 601863 GCAA----TCTAACGATCTTAAGATTTTCCTGGTTA------TGA -s simRat_chr6.simRat.chr6 67375 39 - 647215 GCAAAGCCTCCAACAATATTAAAGCTTGACTGGAGC------ACA - -a -s simMouse_chr6.simMouse.chr6 592554 1 + 636262 T -s Anc0.Anc0refChr3 191919 1 + 222631 T -s Anc1.Anc1refChr1 31475 1 + 69767 T -s Anc2.Anc2refChr1 108155 1 + 142988 G -s mr.mrrefChr3 141284 1 + 181027 T -s simCow_chr6.simCow.chr6 566081 1 + 602619 A -s simDog_chr6.simDog.chr6 558256 1 + 593897 G -s simHuman_chr6.simHuman.chr6 562469 1 + 601863 T -s simRat_chr6.simRat.chr6 67414 1 - 647215 T - -a -s simMouse_chr6.simMouse.chr6 592555 7 + 636262 GAGCTAA -s Anc0.Anc0refChr3 191920 7 + 222631 AAGCAGA -s Anc1.Anc1refChr1 31476 7 + 69767 AAGCAGA -s Anc2.Anc2refChr1 108156 7 + 142988 AAGCAGA -s mr.mrrefChr3 141285 7 + 181027 GAGCTAA -s simCow_chr6.simCow.chr6 566082 7 + 602619 AAATATA -s simDog_chr6.simDog.chr6 558257 7 + 593897 AAGCAGA -s simRat_chr6.simRat.chr6 67419 7 - 647215 GAGCTAA - -a -s simMouse_chr6.simMouse.chr6 592562 10 + 636262 GTCTTGCTAT -s Anc0.Anc0refChr3 191927 10 + 222631 GGCTTGCTTT -s Anc1.Anc1refChr1 31483 10 + 69767 GGCTTGCTTT -s Anc2.Anc2refChr1 108167 10 + 142988 GGCTTGCTTT -s mr.mrrefChr3 141292 10 + 181027 GTCTTGCTAT -s simCow_chr6.simCow.chr6 566093 10 + 602619 GATCAACTTT -s simDog_chr6.simDog.chr6 558268 10 + 593897 GGCTTGCTTT -s simRat_chr6.simRat.chr6 67426 10 - 647215 GGCTTGCTAT - -a -s simMouse_chr6.simMouse.chr6 592572 1 + 636262 C -s Anc0.Anc0refChr3 191937 1 + 222631 C -s Anc1.Anc1refChr1 31493 1 + 69767 C -s Anc2.Anc2refChr1 108180 1 + 142988 C -s mr.mrrefChr3 141302 1 + 181027 C -s simCow_chr6.simCow.chr6 566106 1 + 602619 A -s simDog_chr6.simDog.chr6 558281 1 + 593897 C -s simRat_chr6.simRat.chr6 67436 1 - 647215 C - -a -s simMouse_chr6.simMouse.chr6 592573 30 + 636262 TCAACACTAACCCCAGGCTGGCAAGGCAGA -s Anc0.Anc0refChr3 191938 23 + 222631 ACAACACTAACTCAAAGCTGGC------G- -s Anc1.Anc1refChr1 31494 24 + 69767 ACAACACTAACTCAAAGCTGGC------GA -s Anc2.Anc2refChr1 108181 23 + 142988 ACAACACTAACTCAAAGCTGGC------T- -s mr.mrrefChr3 141303 30 + 181027 TCAACACTAACCCCAGGCTGGCAAGGCAGA -s simCow_chr6.simCow.chr6 566109 23 + 602619 GCAAAATGATTCCTGCATTGTC------A- -s simDog_chr6.simDog.chr6 558282 23 + 593897 ACAACACTAACTCAAAGCTGGC------T- -s simHuman_chr6.simHuman.chr6 562470 2 + 601863 ----------------------------GA -s simRat_chr6.simRat.chr6 67437 30 - 647215 TCAACGCTAACCCCAGGCTGGCAAAGCATA - -a -s simMouse_chr6.simMouse.chr6 592603 22 + 636262 TATCCATGATGAATACATACAA -s Anc0.Anc0refChr3 191961 22 + 222631 TCATCATGATGAAAACATATAA -s Anc1.Anc1refChr1 31518 22 + 69767 TCATCATGATGAAAACATATAA -s Anc2.Anc2refChr1 108204 22 + 142988 TCATCATGACAAAAACATATGA -s mr.mrrefChr3 141333 22 + 181027 TATCCATGATGAATACATATAA -s simCow_chr6.simCow.chr6 566132 22 + 602619 CCACCATGATGAAGACATATAA -s simDog_chr6.simDog.chr6 558310 22 + 593897 TCATCATGACAAAAACATATGA -s simHuman_chr6.simHuman.chr6 562472 22 + 601863 TTATCATGATGGAAACATGTAA -s simRat_chr6.simRat.chr6 67467 21 - 647215 CATCCATGATGAA-ACATATAA - -a -s simMouse_chr6.simMouse.chr6 592625 72 + 636262 GAGGTGCACCTGAGGCTAAGTAGAACTTTATTATTGCATTCTGGCACACTTTGGGTAGCCATGACTTGCACC -s Anc0.Anc0refChr3 192069 51 + 222631 GAGGTTAATCTGTAGATAAGTTG----C-------------TCACACACCAGGGG----CATGACTAGGACT -s Anc1.Anc1refChr1 31626 51 + 69767 GAGGTTAATCTGTAGATAAGTTG----C-------------TCACACACCAGGGG----CATGACTAGGACT -s Anc2.Anc2refChr1 108540 51 + 142988 GAGGTTAATCTGTAGATAAATTG----C-------------TCACACACCAGGGG----CATGACTAGGATT -s mr.mrrefChr3 141355 59 + 181027 GAGGTGCACCTGAAGCTAAGTAGAACTT-------------TGGCACACTTTGGGTAGCCATGACTTGCACC -s simCow_chr6.simCow.chr6 566586 49 + 602619 GAAGTAATTGTGTAGATAGATTA----C-------------TCACAC--CAGGGG----CATGACTAGGAAT -s simDog_chr6.simDog.chr6 558657 48 + 593897 GAGATTAATCTTTAGGTAAATCG----C-------------TC---CACTAGGGA----GATGACTAGGATT -s simHuman_chr6.simHuman.chr6 562580 51 + 601863 GAGGTTAAATTGTAGAAAAGCTG----C-------------TCACACACCAGAGG----CGTGACCACGACT -s simRat_chr6.simRat.chr6 67488 59 - 647215 GAGGTGCACCTGAAGTTAAGTAGAACTG-------------TTGCACACTTTGGGTGGCCATGACTATCATC - -a -s simMouse_chr6.simMouse.chr6 592697 33 + 636262 TGAATGAGGTTACTCAGAGGCCATTAGTGGATG -s Anc0.Anc0refChr3 192120 33 + 222631 TCAATGAGGTTGCAAAGAGGCCATTAGGGGATG -s Anc1.Anc1refChr1 31677 33 + 69767 TCAATGAGGTTGCAAAGAGGCCATTAGGGGATG -s Anc2.Anc2refChr1 108591 33 + 142988 GCAATGAGGTTGCAAAGAAGCAACTAGGGGATG -s mr.mrrefChr3 141414 33 + 181027 TGAATGAGGTTACTCAGAGGCCATTAGTGGATG -s simCow_chr6.simCow.chr6 566635 33 + 602619 GCAATGAGGTCACAAAGATGCAGGTGGGTGATG -s simDog_chr6.simDog.chr6 558705 32 + 593897 GCAATGAGGTTGCAAAGAAGCAAC-AGGGGATG -s simHuman_chr6.simHuman.chr6 562665 33 + 601863 TCAATTAGGTTGCAAATAGGCCATTAGGGGATG -s simRat_chr6.simRat.chr6 67547 33 - 647215 TCAATGAGGTTATTCAGACATCATTGGGGGATG - -a -s simMouse_chr6.simMouse.chr6 592730 31 + 636262 CAGTCAGTAATAAGGGGATGTTCAAGTAAGT -s Anc0.Anc0refChr3 192153 24 + 222631 TTGT-GGTAAGTAATGCCTGTGCCA------ -s Anc1.Anc1refChr1 31710 24 + 69767 TTGT-GGTAAGTAATGCCTGTGCCA------ -s Anc2.Anc2refChr1 108624 24 + 142988 TTGT-GGTAAGTAATGCCTGTGCCA------ -s mr.mrrefChr3 141447 31 + 181027 CAGTCAGTAATAAGGGGATGTTCAAGTAAGT -s simCow_chr6.simCow.chr6 566668 24 + 602619 TTGT-AGTGAGTAATGCCTGTGCAA------ -s simDog_chr6.simDog.chr6 558737 23 + 593897 TTGC-G-TAAGTAATGACTGTGCCA------ -s simHuman_chr6.simHuman.chr6 562698 24 + 601863 TTGT-GCTAAGTAATGCCTGTGCGA------ -s simRat_chr6.simRat.chr6 67583 31 - 647215 CAGTTAGTAATAAGGGGATGTTCAAGTAAGT - -a -s simMouse_chr6.simMouse.chr6 592761 11 + 636262 CAGGTTGTCTT -s Anc0.Anc0refChr3 192177 8 + 222631 ---GTTGTCTT -s Anc1.Anc1refChr1 31734 8 + 69767 ---GTTGTCTT -s Anc2.Anc2refChr1 108648 8 + 142988 ---GTTGTCTT -s mr.mrrefChr3 141478 11 + 181027 CAGGTTGTCTT -s simCow_chr6.simCow.chr6 566692 6 + 602619 ---GTTGTC-- -s simDog_chr6.simDog.chr6 558760 8 + 593897 ---GATGTCTT -s simHuman_chr6.simHuman.chr6 562722 8 + 601863 ---GTTGTCTT -s simRat_chr6.simRat.chr6 67648 11 - 647215 CAGGTTGTCTT - -a -s simMouse_chr6.simMouse.chr6 592772 7 + 636262 TTGAGTA -s Anc0.Anc0refChr3 192185 6 + 222631 TTG-GTA -s Anc1.Anc1refChr1 31742 6 + 69767 TTG-GTA -s Anc2.Anc2refChr1 108656 6 + 142988 TTG-GCA -s mr.mrrefChr3 141489 7 + 181027 TTGAGTA -s simCow_chr6.simCow.chr6 566698 3 + 602619 ----ACA -s simDog_chr6.simDog.chr6 558768 6 + 593897 TTG-GCA -s simHuman_chr6.simHuman.chr6 562730 6 + 601863 TCG-GTA -s simRat_chr6.simRat.chr6 67707 7 - 647215 TTGAGTA - -a -s simMouse_chr6.simMouse.chr6 592779 4 + 636262 CCAT -s Anc0.Anc0refChr3 192245 4 + 222631 CCCT -s Anc1.Anc1refChr1 31802 4 + 69767 CCCT -s Anc2.Anc2refChr1 108716 4 + 142988 ACCT -s mr.mrrefChr3 141496 4 + 181027 CCAT -s simCow_chr6.simCow.chr6 566760 4 + 602619 ACCT -s simDog_chr6.simDog.chr6 558828 4 + 593897 ACCT -s simHuman_chr6.simHuman.chr6 562810 4 + 601863 CCCT -s simRat_chr6.simRat.chr6 67714 4 - 647215 CCAT - -a -s simMouse_chr6.simMouse.chr6 592783 32 + 636262 TAAGTATTGAGTATGGGTCTTGTATTTTAGAT -s Anc0.Anc0refChr3 192249 32 + 222631 TAAGTATTGGGTATGGGTCTTGTATTTTGGAT -s Anc1.Anc1refChr1 31806 32 + 69767 TAAGTATTGGGTATGGGTCTTGTATTTTGGAT -s Anc2.Anc2refChr1 108720 32 + 142988 TAAGTATTGGGTATGGGTCTTGTATTTTGGAG -s mr.mrrefChr3 141500 32 + 181027 TAAGTATTGAGTATGGGTCTTGTATTTTAGAT -s simCow_chr6.simCow.chr6 566765 32 + 602619 AAAGTGTTGGGTATGGGTCCTGTATTTGGGAG -s simDog_chr6.simDog.chr6 558832 32 + 593897 TAAGTATTGGGTAGGGGCCTTGTATTTTGGAG -s simHuman_chr6.simHuman.chr6 562814 30 + 601863 GAAGTA--GTGTATGGCTCTTGTATGTTGGAT -s simRat_chr6.simRat.chr6 67718 32 - 647215 TGAGTATTGAGTATGTGTCTTGTATTTTGGAT - -a -s simMouse_chr6.simMouse.chr6 592815 31 + 636262 CTGGGTTTCACATAGTTGTGAATAATACTCC -s Anc0.Anc0refChr3 192297 13 + 222631 TGA------------------ATAGTACCCC -s Anc1.Anc1refChr1 31854 13 + 69767 TGA------------------ATAGTACCCC -s Anc2.Anc2refChr1 108768 13 + 142988 TGA------------------ATAGTACCCC -s mr.mrrefChr3 141532 13 + 181027 CTG------------------ATAATACTCC -s simCow_chr6.simCow.chr6 567131 13 + 602619 TGA------------------ATAGTAGCCC -s simDog_chr6.simDog.chr6 558880 12 + 593897 TGA------------------TTAGC-CCCC -s simHuman_chr6.simHuman.chr6 562860 13 + 601863 TGA------------------ACTGTAAACC -s simRat_chr6.simRat.chr6 67750 13 - 647215 TTG------------------ATAATACTCC - -a -s simMouse_chr6.simMouse.chr6 592846 23 + 636262 CATAAAAGAACATATTATACACA -s Anc0.Anc0refChr3 192318 23 + 222631 CATAAAATATCTCGTTATACAAA -s Anc1.Anc1refChr1 31875 23 + 69767 CATAAAATATCTCGTTATACAAA -s Anc2.Anc2refChr1 108789 23 + 142988 CATAAAATATCTCATTATACAAA -s mr.mrrefChr3 141545 23 + 181027 CATAAAATATTATGTTATACACA -s simCow_chr6.simCow.chr6 567152 23 + 602619 TGTGAAGTATCTCATTGTACAAC -s simDog_chr6.simDog.chr6 558900 23 + 593897 CATAAAATTTCTCATTATACAAA -s simHuman_chr6.simHuman.chr6 562881 23 + 601863 CATAAAATATCCAGTTATACAAA -s simRat_chr6.simRat.chr6 67763 23 - 647215 CATAAAATATTATGTTATACACA - -a -s simMouse_chr6.simMouse.chr6 592869 4 + 636262 GTCA -s Anc0.Anc0refChr3 192354 4 + 222631 GTCA -s Anc1.Anc1refChr1 31911 4 + 69767 GTCA -s Anc2.Anc2refChr1 108825 4 + 142988 ATCA -s mr.mrrefChr3 141568 4 + 181027 GTCA -s simCow_chr6.simCow.chr6 567188 4 + 602619 ACCA -s simDog_chr6.simDog.chr6 558935 4 + 593897 ATCA -s simHuman_chr6.simHuman.chr6 562917 4 + 601863 GTCA -s simRat_chr6.simRat.chr6 67786 3 - 647215 GTC- - -a -s simMouse_chr6.simMouse.chr6 592873 1 + 636262 C -s Anc0.Anc0refChr3 192358 1 + 222631 C -s Anc1.Anc1refChr1 31915 1 + 69767 C -s Anc2.Anc2refChr1 108829 1 + 142988 C -s mr.mrrefChr3 141572 1 + 181027 C -s simCow_chr6.simCow.chr6 567192 1 + 602619 G -s simDog_chr6.simDog.chr6 558941 1 + 593897 C -s simHuman_chr6.simHuman.chr6 562921 1 + 601863 C -s simRat_chr6.simRat.chr6 67789 1 - 647215 C - -a -s simMouse_chr6.simMouse.chr6 592874 1 + 636262 T -s Anc0.Anc0refChr3 192364 1 + 222631 T -s Anc1.Anc1refChr1 31921 1 + 69767 T -s Anc2.Anc2refChr1 108835 1 + 142988 T -s mr.mrrefChr3 141573 1 + 181027 T -s simCow_chr6.simCow.chr6 567198 1 + 602619 T -s simDog_chr6.simDog.chr6 558947 1 + 593897 T -s simHuman_chr6.simHuman.chr6 562927 1 + 601863 T -s simRat_chr6.simRat.chr6 67790 1 - 647215 T - -a -s simMouse_chr6.simMouse.chr6 592875 94 + 636262 TGTGAATTGAGCGACGCGTTCCATAGGAATACCTCCCGATTTCACTATTACTCTAAACTCCAAAATGCTTACGGAGCAGTCCCGAAATATGGCC -s Anc0.Anc0refChr3 192365 21 + 222631 TGGCAATTGAG------------------------------------------------------------------------GCTATACAG-C -s Anc1.Anc1refChr1 31922 21 + 69767 TGGCAATTGAG------------------------------------------------------------------------GCTATACAG-C -s Anc2.Anc2refChr1 108836 21 + 142988 TGGCCATTGAA------------------------------------------------------------------------GCTATACAG-C -s mr.mrrefChr3 141574 22 + 181027 TGTGAATTGAG------------------------------------------------------------------------GATATATGGCC -s simCow_chr6.simCow.chr6 567200 21 + 602619 TGGCCATTGAT------------------------------------------------------------------------GCTGTACAG-C -s simDog_chr6.simDog.chr6 558948 12 + 593897 T---------A------------------------------------------------------------------------ACTAGACAT-C -s simHuman_chr6.simHuman.chr6 562928 21 + 601863 TGGCAATTGGG------------------------------------------------------------------------GCTATACAG-C -s simRat_chr6.simRat.chr6 67791 22 - 647215 TGTGAATTGAG------------------------------------------------------------------------GATATATGGCC - -a -s simMouse_chr6.simMouse.chr6 592969 96 + 636262 CTCCTCATACTGGAAAGTTGAGACTGCATACCTTGCCCCTTTTCAACAATAGTGACACTCGAAGGTGACTAAGACCATTGGTATGTTGTCCCTGCA -s Anc0.Anc0refChr3 192386 94 + 222631 CTCCCCATACCTAATAATTGAGGTTGAACATTCCTCCCCTTATTAGCAATGGTCATGTCCAGGGATTACTAGGCTTGTGGCCATGT--TCCCTCAC -s Anc1.Anc1refChr1 31943 94 + 69767 CTCCCCATACCTAATAATTGAGGTTGAACATTCCTCCCCTTATTAGCAATGGTCATGTCCAGGGATTACTAGGCTTGTGGCCATGT--TCCCTCAC -s Anc2.Anc2refChr1 108857 94 + 142988 CTCCCCATACCTAATAATTGAGGTTGAACATTCCTCCCCTTATTAGCAATGGTCATGTCCAGGGATTGCTAGGCTTGTGGCCATGT--TCCCTCAC -s mr.mrrefChr3 141596 96 + 181027 CTCCTCATACTGAAAAATTGAGACTGCACACCTTGCCCCTTTTTAGCAATAGTGACACCCAAGGGTGACTAAGATCATTGGTATGTTGTCCCTGCA -s simCow_chr6.simCow.chr6 567221 93 + 602619 C-CTCCACATTTAATAATTGAGGTTGGACAACTCTCCCCATATTGGCAATGGTCATATCCAGGGATTGCTAGTCTTGTTATCACGT--CGCCTCAC -s simDog_chr6.simDog.chr6 558961 94 + 593897 CTCCCCATACCAAATGATTGAGGCTGAACATTCCTCCCCTTAGTAGCAATGGTCATGTCTGGGGATCGCTGGGCTTGTGGCCATGT--TCCCTCAC -s simHuman_chr6.simHuman.chr6 562949 75 + 601863 CTCCCCATACATAACAACTAAGGTGGTACATTCCTTCCCTTATTAACAATGGTAATGTCCAGGGATTACTAGGCT--------------------- -s simRat_chr6.simRat.chr6 67813 96 - 647215 CTCCTCATACAGAAAAATTGAGACTGCACATCTTGCCCCTTTTTAGCAATAGTGACCCCCAAGGCTGACTAAGTTCATTGGTATGTTGTCCCTGCA - -a -s simMouse_chr6.simMouse.chr6 593065 19 + 636262 AAAAACTTATGCCTGCAAA -s Anc0.Anc0refChr3 192480 19 + 222631 AAAAGCTTATGCCTGGGAA -s Anc1.Anc1refChr1 32037 19 + 69767 AAAAGCTTATGCCTGGGAA -s Anc2.Anc2refChr1 108951 19 + 142988 AAAAGCTTATGCCTGGGAA -s mr.mrrefChr3 141692 19 + 181027 AAAAGCTTATGCCTGCGAA -s simCow_chr6.simCow.chr6 567314 19 + 602619 AAAAGCTTATACCTGGGGA -s simDog_chr6.simDog.chr6 559056 19 + 593897 AAAAGCTGATGTCTGGGAA -s simHuman_chr6.simHuman.chr6 563024 13 + 601863 ------TTGTGCCTGGGAA -s simRat_chr6.simRat.chr6 67909 19 - 647215 AAAAGCTCATGCCTATGAA - -a -s simMouse_chr6.simMouse.chr6 593084 54 + 636262 TCAGCAATCCACATTATAATGGTTTCTTCACTAGGAGATGGTATGCACAATGGT -s Anc0.Anc0refChr3 192499 51 + 222631 TCAGCAATCCACA-CATGCTAGCATCTTT-CTAGGAGATGGTAAGGAGAGT-GT -s Anc1.Anc1refChr1 32056 52 + 69767 TCAGCAATCCACAGCATGCTAGCATCTTT-CTAGGAGATGGTAAGGAGAGT-GT -s Anc2.Anc2refChr1 108970 51 + 142988 TCAGAAATCCACA-CATGCTAGCATCTTT-CTAGGAGAAGGTAAGGTGAGT-GA -s mr.mrrefChr3 141711 54 + 181027 TCAGCAATCCACATCATAATAGTTTCTTCACTAGGAGATGGTAAGCACAATGGT -s simCow_chr6.simCow.chr6 567333 51 + 602619 GCAAAAACCCTCA-CATGCTAGCATCTTT-CCAGGAGCAGGTAAGGTGAGT-GA -s simDog_chr6.simDog.chr6 559075 49 + 593897 TCAGAAGTCCATA-CAC-CTGGCATCTTC-CTAGGACA-GGTAAGGTAAGT-GA -s simHuman_chr6.simHuman.chr6 563038 52 + 601863 TCAGCAATCCACAGCATGCCAGAATCTTT-CTACGAGGTGGTAATGAGAGT-GT -s simRat_chr6.simRat.chr6 67928 54 - 647215 TCAGCAATCCACATCATAACAGTGTCTTCACTAGGAGATGGTAAGCGCAATGGT - -a -s simMouse_chr6.simMouse.chr6 593138 53 + 636262 CCCAGGTAAATACTAACTAAGGTAGGGTGCAGGTAGACATTTTGATCTCTGAT -s Anc0.Anc0refChr3 192550 53 + 222631 TCCAGGTAGATGCTAATTGAGGCAGGCTAAGGGTGCACCTTTTGATGTCTGAT -s Anc1.Anc1refChr1 32108 53 + 69767 TCCAGGTAGATGCTAATTGAGGCAGGCTAAGGGTGCACCTTTTGATGTCTGAT -s Anc2.Anc2refChr1 109021 53 + 142988 TCCAGGTAGATGCTAATTGAGGCAGGCTAAGAGTGCACCTTTTGATGTCTGAT -s mr.mrrefChr3 141765 53 + 181027 CCCAGGCAAATGCTAATTGAGGTAGGGTGCAGGTAGACATTTTGATCTCTAAT -s simCow_chr6.simCow.chr6 567385 53 + 602619 CCCAGGCAGATGCTAATTGAGGCAGGCTAAGACTACACCCTCTCATGCCTAAT -s simDog_chr6.simDog.chr6 559124 52 + 593897 TCCAGGTACA-GCTAATTGAGGCAGGCAATGAGTGCACCTTTTGATGTCTGAT -s simHuman_chr6.simHuman.chr6 563090 32 + 601863 TCCAGGTCGATGCGAATTAAGACAGGCTAAGG--------------------- -s simRat_chr6.simRat.chr6 67982 53 - 647215 TCCAGGCGAATGCTAATTGAGGTAGGTTGCAGGTTGACATTTTTATCTCTAAT - -a -s simMouse_chr6.simMouse.chr6 593191 24 + 636262 GGGAGAAGCTTGTTGGAGAATCAA -s Anc0.Anc0refChr3 192607 24 + 222631 GCAAGAAGCTGGTTGCAGAATAGA -s Anc1.Anc1refChr1 32165 24 + 69767 GCAAGAAGCTGGTTGCAGAATAGA -s Anc2.Anc2refChr1 109078 24 + 142988 GCAAGAAGCAGGTTACAGAATAGA -s mr.mrrefChr3 141822 24 + 181027 GGGAGAAGCTCGTTGGAGAATCGA -s simCow_chr6.simCow.chr6 567442 24 + 602619 GGTAGAAGCTCGTTGAAGAATAGA -s simDog_chr6.simDog.chr6 559180 24 + 593897 GCAAGAAGCAGGTTACAGAATAGA -s simHuman_chr6.simHuman.chr6 563122 15 + 601863 ---------TTGTTGAGGAATAGC -s simRat_chr6.simRat.chr6 68039 24 - 647215 GGGAGAAGCTCGTTGGAGAAGTGA - -a -s simMouse_chr6.simMouse.chr6 593215 8 + 636262 AAAAGAAC -s Anc0.Anc0refChr3 192631 8 + 222631 AAAACAAC -s Anc1.Anc1refChr1 32189 8 + 69767 AAAACAAC -s Anc2.Anc2refChr1 109113 8 + 142988 AGAACAAC -s mr.mrrefChr3 141846 8 + 181027 AAAAGAAC -s simCow_chr6.simCow.chr6 567480 8 + 602619 AGAACAAC -s simDog_chr6.simDog.chr6 559204 8 + 593897 ACTACAAC -s simHuman_chr6.simHuman.chr6 563137 8 + 601863 AAAACAGC -s simRat_chr6.simRat.chr6 68063 4 - 647215 AAAA---- - -a -s simMouse_chr6.simMouse.chr6 593223 28 + 636262 TGAACCATTGGACACCTCATAATTTTTT -s Anc0.Anc0refChr3 192639 23 + 222631 TGA-----TGGACACCTCATAATTTTTT -s Anc1.Anc1refChr1 32197 23 + 69767 TGA-----TGGACACCTCATAATTTTTT -s Anc2.Anc2refChr1 109121 23 + 142988 TGG-----TGGCCATCTCATAATTTTTT -s mr.mrrefChr3 141854 28 + 181027 TGAACCAGTGGACACCTCATAATTTTTT -s simCow_chr6.simCow.chr6 567491 23 + 602619 TGG-----TTGCCATCTCATAATTTTTT -s simDog_chr6.simDog.chr6 559212 23 + 593897 TGG-----TGGCCATCTCATAATTCTTT -s simHuman_chr6.simHuman.chr6 563145 23 + 601863 TGA-----TAGACACCTCATAATTTTTT -s simRat_chr6.simRat.chr6 68067 27 - 647215 -GAACCAGTGGACACCTCGTAATTTTTT - -a -s simMouse_chr6.simMouse.chr6 593251 25 + 636262 GGTAATCATATTATCTTTCTCCTCA -s Anc0.Anc0refChr3 192662 25 + 222631 GGTAGCCATCTCATCATTCTTCTTA -s Anc1.Anc1refChr1 32220 25 + 69767 GGTAGCCATCTCATCATTCTTCTTA -s Anc2.Anc2refChr1 109144 25 + 142988 GGTAGCCAGCTCATCATTTTTCTTA -s mr.mrrefChr3 141882 25 + 181027 GGTAGTCATATTATCTTTCTCCTCA -s simCow_chr6.simCow.chr6 567514 25 + 602619 AGTGGCCAGGCCTTCATTTTTCTTA -s simDog_chr6.simDog.chr6 559235 16 + 593897 GGTAGCAAGCTTACTA--------- -s simHuman_chr6.simHuman.chr6 563168 25 + 601863 GATAGCCATCTCATCATTCCTCTTA -s simRat_chr6.simRat.chr6 68124 25 - 647215 GGTAGTCATGTTATGTTTCTCCTCA - -a -s simMouse_chr6.simMouse.chr6 593276 12 + 636262 CTCAGTGTCTAA -s Anc0.Anc0refChr3 192687 12 + 222631 CTGGAGACCTTA -s Anc1.Anc1refChr1 32245 12 + 69767 CTGGAGACCTTA -s Anc2.Anc2refChr1 109169 12 + 142988 CTGGAGACCTTA -s mr.mrrefChr3 141907 12 + 181027 CTCAGTGTCTAA -s simCow_chr6.simCow.chr6 567539 12 + 602619 CTAGAAACCCTA -s simDog_chr6.simDog.chr6 559251 11 + 593897 -GGGAGACCTTA -s simHuman_chr6.simHuman.chr6 563193 12 + 601863 CTGGAGACCTGA -s simRat_chr6.simRat.chr6 68155 12 - 647215 CTCAGTCTCTAA - -a -s simMouse_chr6.simMouse.chr6 593288 71 + 636262 ATGGACTTGGACTGTTTCACATTGACAGCCCATTTGTGAAAGTAGTCCATGCAAATGGACTATGTAGCCTG -s Anc0.Anc0refChr3 192699 20 + 222631 TCAGACCT---------------------------------------------------TTATACAGCCTG -s Anc1.Anc1refChr1 32257 20 + 69767 TCAGACCT---------------------------------------------------TTATACAGCCTG -s Anc2.Anc2refChr1 109181 20 + 142988 TCAGACCT---------------------------------------------------TTATACAGCCTG -s mr.mrrefChr3 141919 71 + 181027 ATGGACTTGGACTGTTTCACATTGACAGCCCATTTGTGAAAGTAGTCCATGCAAATGGACTATGTAGCCTG -s simCow_chr6.simCow.chr6 567551 20 + 602619 TCAGACCA---------------------------------------------------TTGTACAGCCTG -s simDog_chr6.simDog.chr6 559262 20 + 593897 TCAGACCT---------------------------------------------------TTATACAGCTTG -s simHuman_chr6.simHuman.chr6 563205 20 + 601863 TCAGACCT---------------------------------------------------TTATACAGCCTG -s simRat_chr6.simRat.chr6 68171 71 - 647215 GTGGCCTTAGACTGTGTCACATTGACAGCCTATCGGTGAAAGCAGTCCAAACAAATGGACTAGGTAGCCTG - -a -s simMouse_chr6.simMouse.chr6 593359 24 + 636262 ATTAGGATCTTAAAGAACTTCATA -s Anc0.Anc0refChr3 192719 19 + 222631 CT---CACCTCATTGAACCCTG-- -s Anc1.Anc1refChr1 32277 21 + 69767 CT---CACCTCATTGAACCCTGTC -s Anc2.Anc2refChr1 109201 19 + 142988 CT---CACCCCATTGAACCCTA-- -s mr.mrrefChr3 141990 24 + 181027 ATTAGGATCTTAAAGAACTCCATA -s simCow_chr6.simCow.chr6 567571 19 + 602619 AT---CAGGCCATTAAACTCTA-- -s simDog_chr6.simDog.chr6 559284 19 + 593897 CA---CACCCCCTTGAACCCTA-- -s simHuman_chr6.simHuman.chr6 563225 21 + 601863 TT---AAACTCAGTGGACCCTGTC -s simRat_chr6.simRat.chr6 68242 24 - 647215 CTTAAGATCTTAACCAACTCTATA - -a -s simMouse_chr6.simMouse.chr6 593383 1 + 636262 C -s Anc1.Anc1refChr1 32298 1 + 69767 C -s mr.mrrefChr3 142014 1 + 181027 C -s simHuman_chr6.simHuman.chr6 563246 1 + 601863 C -s simRat_chr6.simRat.chr6 68403 1 - 647215 T - -a -s simMouse_chr6.simMouse.chr6 593384 16 + 636262 CTGTCTCAGGGTCTGG -s Anc1.Anc1refChr1 32299 16 + 69767 CCCTCTACTGGACTTG -s mr.mrrefChr3 142015 16 + 181027 CTGTCTCGGGGTCTGG -s simHuman_chr6.simHuman.chr6 563376 16 + 601863 CCCTCTACTGGACTTG -s simRat_chr6.simRat.chr6 68404 16 - 647215 CTGTCTCGGGGTCTGA - -a -s simMouse_chr6.simMouse.chr6 593400 28 + 636262 GAGTGGGAGACTGGGATGGTTTAAACAA -s Anc0.Anc0refChr3 192738 28 + 222631 GAGTGAAAGAGTGGGATGATTTAAACAA -s Anc1.Anc1refChr1 32315 28 + 69767 GAGTGAAAGAGTGGGATGATTTAAACAA -s Anc2.Anc2refChr1 109220 28 + 142988 GAGTCAAAGAGTGGGATGATTTAAACAA -s mr.mrrefChr3 142031 28 + 181027 GAGTGGGAGACTGGGATGGTTTAAACAA -s simCow_chr6.simCow.chr6 567604 28 + 602619 GGGTTGAAGTGTGGGATGATTTAAACAA -s simDog_chr6.simDog.chr6 559303 27 + 593897 GAGACAAAGAGGGGGATG-TTTAAACAA -s simHuman_chr6.simHuman.chr6 563397 28 + 601863 GAGTGAAAGAGTGGAATGATTTGAACTA -s simRat_chr6.simRat.chr6 68420 28 - 647215 GAGTGGTAGACGGGGATGGTTTAAACAA - -a -s simMouse_chr6.simMouse.chr6 593428 35 + 636262 ATATGGGAGCCTTTGGGTGCTCTGCTTAGTCTTGA -s Anc0.Anc0refChr3 192766 35 + 222631 ATATCAGTACCTTTGGAAGCTCTGCTTAGTCTTAG -s Anc1.Anc1refChr1 32343 35 + 69767 ATATCAGTACCTTTGGAAGCTCTGCTTAGTCTTAG -s Anc2.Anc2refChr1 109248 35 + 142988 ATATCAGTACCTTTGGAAGCTCTGCTTAGTCTTAG -s mr.mrrefChr3 142059 35 + 181027 ATATCAGAGCCTTTGGATGCTCTGCTTAGTCTTGA -s simCow_chr6.simCow.chr6 567632 35 + 602619 ATATCAGCACCTTTGGAAGCTTTGTTTAGCCTTAG -s simDog_chr6.simDog.chr6 559330 35 + 593897 ATGTCAGTACCTTTGGAACCTCTGCTTAGTCTTAG -s simHuman_chr6.simHuman.chr6 563425 31 + 601863 ATATCAGTACCTTTCCAAGTTCTGCTTAGTC---- -s simRat_chr6.simRat.chr6 68449 35 - 647215 ATATCAGAGCCTTTGGATGCTCTGCCTACCCTTAG - -a -s simMouse_chr6.simMouse.chr6 593463 6 + 636262 TTCAAT -s Anc0.Anc0refChr3 192801 6 + 222631 TTCACT -s Anc1.Anc1refChr1 32378 6 + 69767 TTCACT -s Anc2.Anc2refChr1 109283 6 + 142988 TTCACT -s mr.mrrefChr3 142094 6 + 181027 TTCAAT -s simCow_chr6.simCow.chr6 567667 6 + 602619 CTCACT -s simDog_chr6.simDog.chr6 559369 6 + 593897 TTCACT -s simRat_chr6.simRat.chr6 68484 6 - 647215 TTCACT - -a -s simMouse_chr6.simMouse.chr6 593469 194 + 636262 AAGCTGGATCTCATCCCAGCAAAGTTGTAACACTTCTCTACAGAGCTCTAGACATTCTGAGATATGAGGAAGTTGACATGGCTTCATTGTCCAAAGCAGTTCCTGAATCCTTGAAGAAATACACAAAGTGCAGGGAATTGGCAGAAAGACTAAAGATAGAAGGTCAGGGTCAAAAGTGCCTTTTAAACCACACA -s Anc0.Anc0refChr3 192807 194 + 222631 AAGGTGGATATTGGCTCAGTGAAGTTGTTACATATGTCTACAGAGCTCTAGACATTCTGAGATATGAAGAAGTTGACATGGACTCATTATCCAAAGCAGTTCCTGAATCCTTAAAGAAATACACTAAGTGCAGAGAACTGGCAGAAAGACTGAAGATAGAGGGTCAGGGTCAAAAGTGTCTTTTACACCACACA -s Anc1.Anc1refChr1 32384 194 + 69767 AAGGTGGATATTGGCTCAGTGAAGTTGTTACATATGTCTACAGAGCTCTAGACATTCTGAGATATGAAGAAGTTGACATGGACTCATTATCCAAAGCAGTTCCTGAATCCTTAAAGAAATACACTAAGTGCAGAGAACTGGCAGAAAGACTGAAGATAGAGGGTCAGGGTCAAAAGTGTCTTTTACACCACACA -s Anc2.Anc2refChr1 109290 194 + 142988 GAGGTGGATATTGGCTCAGTGAGGTTGTTACATATGTTTATAGAGCTCTAGACATTCTGAGATATGAAGAAGTTGACATGGACTCATTATCCAAAGCAGTTCCTGAATCCTTAAAGAAATACACTAAGTGCAGAGATCTAGCAGAAAGACTGAAGATAGAGGGTCAGGGTCAAAAGTGTCATTTACACCATACA -s mr.mrrefChr3 142100 194 + 181027 AAGCTGGATCTTATCCCAGTGAAGTTGTAACACATCTCTACAGAGCTCTAGACATTCTGAGATATGAGGAAGTTGACATGGCCTCATTGTCCAAAGCAGTTCCTGAATCCTTGAAGAAATACACTAAGTGCAGGGAATTGGCAGAAAGACTGAAGATAGAAGGTCAGGGTCAAAAGTGCCTTTTAAACCACACA -s simCow_chr6.simCow.chr6 567674 189 + 602619 ---GTGGATATTGGCTCAGTGAGGTTGTTACAGCTA--TATAGAGCTCTAGACATTCTGAGATATGAAGAAGTTGACATGGACTCATTATCTAAAGCAATTCCTGAATCTTTAAAGAAATACACTAAATGCAGAGATCTTGCAGAAAGACTGAAGATAGAGGGTCCTGGTCAAAAGTGTCCTTTACCCAATGCA -s simDog_chr6.simDog.chr6 559464 193 + 593897 GAGGTGGCCAGTGGTTCAATGAGATTGT-ACATATGTTTATAGAGCTCTAGACATCCTGAGATATGAAGAAGTTGACATGGACTCATTATCCAAAGCAGTTCCTGAATCCTTAAAGAAATACACTAAGTGCAGAGATCTAGCAGAAAGACTGAAGATAGAGGGTCAGGGTCCAATGTGTAAATTACATCATATA -s simHuman_chr6.simHuman.chr6 563456 194 + 601863 AAGGTGGATATTGCCTCAGTGAAGGCGTCACAAATGTCTGCAGAGCTCTAGACATTCTGAGATATGAAGAAATTGACATGGACTCGTTATCCAAAGCAGTTCCTGAATCCTTAAAGAAATACACTAAGTGCAGAGAACTGGCAGAAAGACTGAAGATAGAGGGTCAGGCTCAAAAGTGTCTTTTACACCACACA -s simRat_chr6.simRat.chr6 68490 191 - 647215 AAGCTGGATCTTAGCCCAGTGAAGTTGTAACATACTTCTACAGAACTCTAGACATTCTGAGATATGAGGAAGTTGACATGGCCTCATTGTCCAAAGCAGTTCCTGAATCCTTGAAGAAATACACTAAGTGCAGGGAATTGGCAGAAAGACTGAAAATAGAAGGTCAGGGTCAAAAAT---TTTTAAACCACACA - -a -s simMouse_chr6.simMouse.chr6 593663 44 + 636262 CTCTATTTAGAAGTGTGACATTATTACACCCTACTTATGTCTTA -s Anc0.Anc0refChr3 193001 43 + 222631 CTCTA-TTAGAAGTGTGACCTAATTATACCCTATTGATGTCTTA -s Anc1.Anc1refChr1 32578 43 + 69767 CTCTA-TTAGAAGTGTGACCTAATTATACCCTATTGATGTCTTA -s Anc2.Anc2refChr1 109484 43 + 142988 CTCTA-TTAGAAGTGTGTCGTAATTATAACTTATTGATGTCTTA -s mr.mrrefChr3 142294 44 + 181027 CTCTATTTAGAAGTGTGACCTAATTACACCCTACTGATGTCTTA -s simCow_chr6.simCow.chr6 567863 43 + 602619 CTTTA-TTAGAAGTGTGCCATAATTACAACTTATTGGTGTCTTA -s simDog_chr6.simDog.chr6 559657 43 + 593897 TCCTA-TTAGAAGTGTGTGGTATTTATAACTTACTGATGTATTA -s simHuman_chr6.simHuman.chr6 563650 43 + 601863 CTCTA-TTAGAAGTGTGACCTAATTATACCCTATTGATCTCTTA -s simRat_chr6.simRat.chr6 68685 44 - 647215 CTCTATTTAGAAGTGTGACCTAATTAGACCCCACTGATGTCTTA - -a -s simMouse_chr6.simMouse.chr6 593707 11 + 636262 GCTACCAAACA -s Anc0.Anc0refChr3 193044 10 + 222631 GGTATTACAT- -s Anc1.Anc1refChr1 32621 10 + 69767 GGTATTACAT- -s Anc2.Anc2refChr1 109527 10 + 142988 TGTATTACAT- -s mr.mrrefChr3 142338 11 + 181027 GCTATCAAATA -s simCow_chr6.simCow.chr6 567906 10 + 602619 CGTATCACAT- -s simDog_chr6.simDog.chr6 559700 10 + 593897 TATATTACAT- -s simHuman_chr6.simHuman.chr6 563694 10 + 601863 GGTATTACAT- -s simRat_chr6.simRat.chr6 68729 11 - 647215 CCTATCAAATA - -a -s simMouse_chr6.simMouse.chr6 593718 27 + 636262 TTCCCCTTCTCAAACATGTCACACAGA -s Anc0.Anc0refChr3 193054 27 + 222631 TGTCCCTTCTCAAACAGGTCATTCTCA -s Anc1.Anc1refChr1 32631 27 + 69767 TGTCCCTTCTCAAACAGGTCATTCTCA -s Anc2.Anc2refChr1 109537 27 + 142988 TGTCCCTTCTCAAATAGGTCATTCTCA -s mr.mrrefChr3 142349 27 + 181027 TGCCCCTTCTCAAACATGTCACTCAGA -s simCow_chr6.simCow.chr6 567916 27 + 602619 TGTTCCTTCTAAAATATGTCATTCTCA -s simDog_chr6.simDog.chr6 559711 27 + 593897 CATCCCTTCTCAAATAGGTCATTCTCA -s simHuman_chr6.simHuman.chr6 563704 27 + 601863 TGTCCCTTCTTAAACACAGCATTCTCA -s simRat_chr6.simRat.chr6 68740 27 - 647215 TGCCCCTTATCAAATATGTCACTTAGA - -a -s simMouse_chr6.simMouse.chr6 593745 22 + 636262 CTATCTGTTTAGTAGAAAATAG -s Anc0.Anc0refChr3 193081 22 + 222631 CCACCTGTATAATTGGATATAG -s Anc1.Anc1refChr1 32658 22 + 69767 CCACCTGTATAATTGGATATAG -s Anc2.Anc2refChr1 109564 22 + 142988 CCACATGTATAATTGGCTATAG -s mr.mrrefChr3 142376 22 + 181027 CTACCTGTTTAATTGGATATAG -s simCow_chr6.simCow.chr6 567943 22 + 602619 CATCTTGCATAATTAATTGCAG -s simDog_chr6.simDog.chr6 559738 22 + 593897 CCACATGTATAGTTGGCAATAC -s simHuman_chr6.simHuman.chr6 563733 22 + 601863 CCCCCTGTATAATTGGATATAG -s simRat_chr6.simRat.chr6 68767 22 - 647215 CTACCTGTTTAATTGGATATAG - -a -s simMouse_chr6.simMouse.chr6 593767 48 + 636262 GTATTAAACCCATGCTTTCTCATGGACACTGAGGCAAGGTTAATGTCT -s Anc0.Anc0refChr3 193103 47 + 222631 GTATAAAACCCATGCTTTCTCAAGCATGA-GAGACTGGGTTAACGTCT -s Anc1.Anc1refChr1 32680 47 + 69767 GTATAAAACCCATGCTTTCTCAAGCATGA-GAGACTGGGTTAACGTCT -s Anc2.Anc2refChr1 109586 47 + 142988 GGATAAAACCCATGCTTCCTCAAGCATGA-GAGACTGGGTTAACGTCC -s mr.mrrefChr3 142398 48 + 181027 GTATTAAACCCATGCTTTCTCATGGACACTGAGACTAGGTTAATGTCT -s simCow_chr6.simCow.chr6 567967 47 + 602619 GGATAAAAGCCATGCCTCTTTAAGGATGA-GAGACTGAATTAATGTCC -s simDog_chr6.simDog.chr6 559760 47 + 593897 AGATGAGACCTATGTTTCCTCAAGCATGA-GAGATTAGGTTAACGGCC -s simHuman_chr6.simHuman.chr6 563755 47 + 601863 GTATAAAACCCATGCTTTCTGGAGAATGA-GAGACTGGTTTGAAGTCT -s simRat_chr6.simRat.chr6 68789 48 - 647215 GTATTAAACCCATGCTTTCTCATGGACACTGAGACTAGGTTAATGTCT - -a -s simMouse_chr6.simMouse.chr6 593815 28 + 636262 CCATTACTGAAATTCATATTACATGAAT -s Anc0.Anc0refChr3 193160 28 + 222631 CCATTACTGGAGTACAGGCTGCATGAGA -s Anc1.Anc1refChr1 32737 28 + 69767 CCATTACTGGAGTACAGGCTGCATGAGA -s Anc2.Anc2refChr1 109643 28 + 142988 CCATTACTGAAGTACAGGCTGCATGAGA -s mr.mrrefChr3 142446 28 + 181027 CCATTACTGGAGTACATGTTACATGAAT -s simCow_chr6.simCow.chr6 568024 28 + 602619 CCATTACTGAAGTACAGACTGCATGAAA -s simDog_chr6.simDog.chr6 559817 28 + 593897 CCAGTACTGAAGTACAGGCGTCATGAGA -s simHuman_chr6.simHuman.chr6 563812 28 + 601863 CCATTACTGGAGTACAGGCTGCATGAGG -s simRat_chr6.simRat.chr6 68837 28 - 647215 CCATTACTGGAGTACATGTTACATGATT - -a -s simMouse_chr6.simMouse.chr6 593843 25 + 636262 TAGATTGCATATCCTTGTAACAGAA -s Anc0.Anc0refChr3 193188 14 + 222631 TACCTT-----------CAACCTGA -s Anc1.Anc1refChr1 32765 14 + 69767 TACCTT-----------CAACCTGA -s Anc2.Anc2refChr1 109671 14 + 142988 TACCTT-----------CAACCTGA -s mr.mrrefChr3 142474 25 + 181027 TACCTTGCATATCCTTGTAACAGGA -s simCow_chr6.simCow.chr6 568052 14 + 602619 TATCTT-----------CAACCTGA -s simDog_chr6.simDog.chr6 559845 14 + 593897 TACCTT-----------CAACCTGA -s simHuman_chr6.simHuman.chr6 563840 14 + 601863 TGCCTT-----------CAACCTGA -s simRat_chr6.simRat.chr6 68873 25 - 647215 TACCTTGCAGATCATCTGAACAGGA - -a -s simMouse_chr6.simMouse.chr6 593868 69 + 636262 ATCCTGTAAATCTATTAAGGCAATAAAAATGCATATTCTCCAGAGCCATCCGTATCCTGTTCTCAATAA -s Anc0.Anc0refChr3 193202 68 + 222631 GCCCTGTGAATCTATTAAGCCAACAA-TATGCATATCCCACAAAACCACCCATAACATGGCCTAAATGA -s Anc1.Anc1refChr1 32779 69 + 69767 GCCCTGTGAATCTATTAAGCCAACAAATATGCATATCCCACAAAACCACCCATAACATGGCCTAAATGA -s Anc2.Anc2refChr1 109685 68 + 142988 GCCCTGTGAATCTGTTAAGCCACCAA-TATGCATATCCCACAAAGCCACCCATAACATGGCCTAAATGA -s mr.mrrefChr3 142499 69 + 181027 ATCCTGTAAATCTATTAAGGCAATAAAAATGCATATTCTACAGAACCATCCATAACATGTTCTCAATGA -s simCow_chr6.simCow.chr6 568066 68 + 602619 GCCCTGTGAACCTGTTAAGCCACCAA-TTTGCATGCCCAACCAAGCCACCCACAACATGGCCTAAATGG -s simDog_chr6.simDog.chr6 559861 65 + 593897 GCCCTGTGAATCTGT---GCCACAAA-TATGCATATCCCACAAAACCACCCATAACATGGACTAAATGA -s simHuman_chr6.simHuman.chr6 563854 62 + 601863 GCCCTGTGAATCTAGTAAGCCAACAA------ATATCCGACAAGACC-CCCATAACATGGCCTAAATGA -s simRat_chr6.simRat.chr6 68898 69 - 647215 ATCCTGTAAATCTATTAAGGCAATAACAATACATAGTCTACTGAACCATCCAGAACATGTTCTCAGTGA - -a -s simMouse_chr6.simMouse.chr6 593937 6 + 636262 GATGAA -s Anc0.Anc0refChr3 193271 6 + 222631 GATGAC -s Anc1.Anc1refChr1 32849 6 + 69767 GATGAC -s Anc2.Anc2refChr1 109754 6 + 142988 GATGAC -s mr.mrrefChr3 142568 6 + 181027 GATGAA -s simCow_chr6.simCow.chr6 568135 6 + 602619 GATGAG -s simDog_chr6.simDog.chr6 559927 6 + 593897 GATGAC -s simHuman_chr6.simHuman.chr6 563917 6 + 601863 GATGAC -s simRat_chr6.simRat.chr6 68967 6 - 647215 GATGAG - -a -s simMouse_chr6.simMouse.chr6 593943 11 + 636262 ATCATGCTTAA -s Anc0.Anc0refChr3 193278 11 + 222631 AGGAAGTGAAA -s Anc1.Anc1refChr1 32856 11 + 69767 AGGAAGTGAAA -s Anc2.Anc2refChr1 109761 11 + 142988 AGGAAGTGAGA -s mr.mrrefChr3 142575 11 + 181027 ATGATGCTAAA -s simCow_chr6.simCow.chr6 568142 11 + 602619 AGAAAGTGAGA -s simDog_chr6.simDog.chr6 559934 11 + 593897 AGGAAGTTAGA -s simHuman_chr6.simHuman.chr6 563924 11 + 601863 AAGAAGTGAAA -s simRat_chr6.simRat.chr6 68974 11 - 647215 AGGAGGCAAAA - -a -s simMouse_chr6.simMouse.chr6 593954 2 + 636262 GG -s Anc0.Anc0refChr3 193292 2 + 222631 TA -s Anc1.Anc1refChr1 32870 2 + 69767 TA -s Anc2.Anc2refChr1 109775 2 + 142988 TA -s mr.mrrefChr3 142588 2 + 181027 TA -s simCow_chr6.simCow.chr6 568156 2 + 602619 TG -s simDog_chr6.simDog.chr6 559948 2 + 593897 TA -s simHuman_chr6.simHuman.chr6 563938 2 + 601863 TA -s simRat_chr6.simRat.chr6 68987 2 - 647215 TA - -a -s simMouse_chr6.simMouse.chr6 593956 8 + 636262 GAAGTGCT -s Anc0.Anc0refChr3 193309 8 + 222631 AAGGTGCC -s Anc1.Anc1refChr1 32887 8 + 69767 AAGGTGCC -s Anc2.Anc2refChr1 109792 8 + 142988 AAGGTGCC -s mr.mrrefChr3 142590 8 + 181027 GAAGTGCC -s simCow_chr6.simCow.chr6 568172 8 + 602619 AAGGTGCC -s simDog_chr6.simDog.chr6 559964 8 + 593897 AAGGTGCC -s simHuman_chr6.simHuman.chr6 563955 8 + 601863 AAGGTGCC -s simRat_chr6.simRat.chr6 68989 8 - 647215 GAAGTCCC - -a -s simMouse_chr6.simMouse.chr6 593964 20 + 636262 TACCATAGCATCATAGATCA -s Anc0.Anc0refChr3 193317 20 + 222631 TACCATAGCAAATTAGCTCC -s Anc1.Anc1refChr1 32895 20 + 69767 TACCATAGCAAATTAGCTCC -s Anc2.Anc2refChr1 109803 20 + 142988 TACCATAGTAAATTAGCTCC -s mr.mrrefChr3 142598 20 + 181027 TACCATAGCATCATAGATCA -s simCow_chr6.simCow.chr6 568183 20 + 602619 TACCATAGTAAATTGGCTCC -s simDog_chr6.simDog.chr6 559975 20 + 593897 TACTATAGTAAAATAGCTCC -s simHuman_chr6.simHuman.chr6 563963 20 + 601863 AACCTTAGCAAATCAGTTTC -s simRat_chr6.simRat.chr6 68997 20 - 647215 TACTGTCGCATCATAGATCG - -a -s simMouse_chr6.simMouse.chr6 593984 13 + 636262 TTTTAGAGCAACA -s Anc0.Anc0refChr3 193337 13 + 222631 TCTTAGAGCAACA -s Anc1.Anc1refChr1 32915 13 + 69767 TCTTAGAGCAACA -s Anc2.Anc2refChr1 109823 13 + 142988 TCTTAGAGCAACA -s mr.mrrefChr3 142618 13 + 181027 TTTTAGAGCAACA -s simCow_chr6.simCow.chr6 568203 13 + 602619 TCTTAGGGCACCA -s simDog_chr6.simDog.chr6 559997 13 + 593897 TTTTAGAACAACA -s simHuman_chr6.simHuman.chr6 563983 13 + 601863 TCTTAGTGCAACA -s simRat_chr6.simRat.chr6 69017 13 - 647215 TTTTACAGCAACA - -a -s simMouse_chr6.simMouse.chr6 593997 27 + 636262 TAGAGGTTGATGAACAAACAGTTCTGT -s Anc0.Anc0refChr3 193352 21 + 222631 AATA----GAG--AAAAACAGCATGGT -s Anc1.Anc1refChr1 32930 23 + 69767 AATA----GAGCTAAAAACAGCATGGT -s Anc2.Anc2refChr1 109838 21 + 142988 AGTC----CAG--AAAAACAGCATGGT -s mr.mrrefChr3 142633 26 + 181027 TAGAGG-TGATGTACAAACAGTTCTGT -s simCow_chr6.simCow.chr6 568218 14 + 602619 TGTC----CAG---------GTTTAGT -s simDog_chr6.simDog.chr6 560012 21 + 593897 AGTC----CAA--AAAAACACCATGGT -s simHuman_chr6.simHuman.chr6 563998 23 + 601863 AAAA----GAGCTAAAAACAGCCTGGT -s simRat_chr6.simRat.chr6 69032 26 - 647215 TAGAAG-CAAAGTACAAACAGTTCTGT - -a -s simMouse_chr6.simMouse.chr6 594024 4 + 636262 GGAC -s Anc0.Anc0refChr3 193373 4 + 222631 GGAC -s Anc1.Anc1refChr1 32953 4 + 69767 GGAC -s Anc2.Anc2refChr1 109859 4 + 142988 GACC -s mr.mrrefChr3 142659 4 + 181027 GGAC -s simCow_chr6.simCow.chr6 568233 4 + 602619 GACC -s simDog_chr6.simDog.chr6 560033 4 + 593897 GACC -s simHuman_chr6.simHuman.chr6 564021 3 + 601863 AGA- -s simRat_chr6.simRat.chr6 69058 4 - 647215 GGAC - -a -s simMouse_chr6.simMouse.chr6 594028 34 + 636262 TGCTATTATGGTCATTGTCATGCTCCTCACCTCT -s Anc0.Anc0refChr3 193377 34 + 222631 TGCTGTTGTGATTTCCATTTTGCCACTCACTTAT -s Anc1.Anc1refChr1 32957 34 + 69767 TGCTGTTGTGATTTCCATTTTGCCACTCACTTAT -s Anc2.Anc2refChr1 109865 34 + 142988 TGCTGTTGTGATTTCCATTTTGCCACCCACTAGG -s mr.mrrefChr3 142663 34 + 181027 TGCTATTATGGTCATTGTCATGCTCCTCACCTAT -s simCow_chr6.simCow.chr6 568239 34 + 602619 TTCAATTATGATTACCATTTAGCCAACCACTAGG -s simDog_chr6.simDog.chr6 560039 34 + 593897 TGCTGTTGTGATTTCCATTTTGCCACCCACTAGG -s simHuman_chr6.simHuman.chr6 564024 9 + 601863 -------------------------CTCACGTAT -s simRat_chr6.simRat.chr6 69062 34 - 647215 TGCTATTATGGTCATTGTCATGGTCCTCACCTAT - -a -s simMouse_chr6.simMouse.chr6 594062 4 + 636262 GGCA -s Anc0.Anc0refChr3 193411 4 + 222631 GGCA -s Anc1.Anc1refChr1 32991 4 + 69767 GGCA -s Anc2.Anc2refChr1 109900 4 + 142988 GGCA -s mr.mrrefChr3 142697 4 + 181027 GGCA -s simCow_chr6.simCow.chr6 568274 1 + 602619 G--- -s simDog_chr6.simDog.chr6 560074 4 + 593897 GGCA -s simHuman_chr6.simHuman.chr6 564033 4 + 601863 GGCA -s simRat_chr6.simRat.chr6 69096 4 - 647215 GGCA - -a -s simMouse_chr6.simMouse.chr6 594066 52 + 636262 AATAACGCTTCTTTGGCAGTAAGTTAATTGTCTGATTGAATTTGACCTTGTT -s Anc0.Anc0refChr3 193415 52 + 222631 AATATCCCCTCTTTAGCAATAACTTAACAGCCTGATTGTTTTTGACCTGGTT -s Anc1.Anc1refChr1 32995 52 + 69767 AATATCCCCTCTTTAGCAATAACTTAACAGCCTGATTGTTTTTGACCTGGTT -s Anc2.Anc2refChr1 109904 52 + 142988 AATATCCACTCTTTGGCAATAACTTAACAGCCTGATTGTTTTTGACCTGGCT -s mr.mrrefChr3 142701 52 + 181027 AATAACGCCTCTTTAGCAGTAAGTTAACTGTCTGATTGAATTTGACCTTGTT -s simCow_chr6.simCow.chr6 568275 35 + 602619 -----------TATGTCAACACCTTAACAGCCTGGTTGTTTTTGAC------ -s simDog_chr6.simDog.chr6 560079 50 + 593897 AATATCCACTCTTTGGCAATAACTTA--AACCTGATTGTTTTTGACCTGGCT -s simHuman_chr6.simHuman.chr6 564037 52 + 601863 AATATCCCCTCTTCAGAAATAACTTAACAGCCTGATTGTTTTTGACCTGGTT -s simRat_chr6.simRat.chr6 69100 48 - 647215 AA----ACCTTGTTACCTTTTAATGAACTGATGGATTTCAACTAGGCCTATT - -a -s simMouse_chr6.simMouse.chr6 594118 16 + 636262 GCTTTTTAATGGACTG -s Anc0.Anc0refChr3 193467 16 + 222631 GCCCTTAAATGGACTG -s Anc1.Anc1refChr1 33047 16 + 69767 GCCCTTAAATGGACTG -s Anc2.Anc2refChr1 109956 16 + 142988 GTCCTTAACACGACTA -s mr.mrrefChr3 142753 16 + 181027 GCTTTTTAATGGACTG -s simDog_chr6.simDog.chr6 560129 16 + 593897 GTCCTTAACACGACTA -s simHuman_chr6.simHuman.chr6 564089 16 + 601863 GCCCTTAAATGGACTG -s simRat_chr6.simRat.chr6 69175 16 - 647215 GTTTGATTATCCACTT - -a -s simMouse_chr6.simMouse.chr6 594134 20 + 636262 ATGGGCTTCGCTTATGCCTG -s Anc0.Anc0refChr3 193483 20 + 222631 ATCTGCTTTTTCTATGCATA -s Anc1.Anc1refChr1 33063 20 + 69767 ATCTGCTTTTTCTATGCATA -s Anc2.Anc2refChr1 109972 20 + 142988 ATCTGCTTTTTTTATGCATA -s mr.mrrefChr3 142769 20 + 181027 ATGGGCTTCGCCTATGCCTA -s simCow_chr6.simCow.chr6 568310 18 + 602619 --CTGTTCTTTTTATGCAGA -s simDog_chr6.simDog.chr6 560147 19 + 593897 ATCTGC-TTTTTTACGCATC -s simHuman_chr6.simHuman.chr6 564105 20 + 601863 ATCTGCTTTTTCTATGCATA -s simRat_chr6.simRat.chr6 69191 20 - 647215 TTGGGCTTCACCTATGCCTA - -a -s simMouse_chr6.simMouse.chr6 594154 50 + 636262 TTTAATGGCATATCTAATATGTACATCGGGTTTTATGTTATCCACTTTGG -s Anc0.Anc0refChr3 193503 47 + 222631 TTTGAT-GCATACATAACTTGCACATAGGATTCAA--TTATCCATTTTAG -s Anc1.Anc1refChr1 33083 49 + 69767 TTTGAT-GCATACATAACTTGCACATAGGATTCAAATTTATCCATTTTAG -s Anc2.Anc2refChr1 109992 47 + 142988 TTTGAT-GCATACATTATTTGCACATTGAATTCAA--TTATCCATTGCAG -s mr.mrrefChr3 142789 50 + 181027 TTTGATGGCATATCTAACATGTACATAGGGTTTTATGTTATCCACTTTAG -s simCow_chr6.simCow.chr6 568329 47 + 602619 GTCAAT-GCATACACTTTTTGCACATGGAATTCAA--TCATCCATCGCAG -s simDog_chr6.simDog.chr6 560166 47 + 593897 TTTGAT-GCATGCATTATTTGTACATTGAACTCAA--TTATCCATTGCAG -s simHuman_chr6.simHuman.chr6 564125 49 + 601863 TTTGAT-GCATACATAACTTGCACTCAGGATTCAAATTTAGCCATTTTAG -s simRat_chr6.simRat.chr6 69211 48 - 647215 TTTGATAGCATATCTCACATGTACATAGGGTTTGA--TTATCCACTTTAG - -a -s simMouse_chr6.simMouse.chr6 594204 1 + 636262 A -s Anc0.Anc0refChr3 193550 1 + 222631 A -s Anc1.Anc1refChr1 33132 1 + 69767 A -s Anc2.Anc2refChr1 110039 1 + 142988 T -s mr.mrrefChr3 142839 1 + 181027 A -s simCow_chr6.simCow.chr6 568376 1 + 602619 G -s simDog_chr6.simDog.chr6 560213 1 + 593897 T -s simHuman_chr6.simHuman.chr6 564174 1 + 601863 A -s simRat_chr6.simRat.chr6 69272 1 - 647215 A - -a -s simMouse_chr6.simMouse.chr6 594205 34 + 636262 ATTTCTTTTTATTGATGAATTCCTGTTTATGCCA -s Anc0.Anc0refChr3 193555 34 + 222631 AATTCTTTTTACTGATGATTTACCTTCTTTAATC -s Anc1.Anc1refChr1 33137 34 + 69767 AATTCTTTTTACTGATGATTTACCTTCTTTAATC -s Anc2.Anc2refChr1 110044 34 + 142988 AATTCTTCTTACTGATGATTTACCTTCTTTAATC -s mr.mrrefChr3 142840 34 + 181027 ATTTCTTTTTATTGATGAATTACTGTTTATGCCA -s simCow_chr6.simCow.chr6 568381 29 + 602619 CATTCTTCTTCCTGATAA-----CTTGTTTACAC -s simDog_chr6.simDog.chr6 560218 34 + 593897 AATTCCTCTTACTGATGATTTACCTTCTTTGATC -s simHuman_chr6.simHuman.chr6 564179 34 + 601863 AATTCTTTTTACTGATGACCTACCTTCTTTATGC -s simRat_chr6.simRat.chr6 69273 34 - 647215 ACTTCTTTTTATTCATGAGTTACTGTTTATGCCA - -a -s simMouse_chr6.simMouse.chr6 594239 14 + 636262 TAACTATAAGACTG -s Anc0.Anc0refChr3 193589 14 + 222631 TAATGATAAGAATG -s Anc1.Anc1refChr1 33171 14 + 69767 TAATGATAAGAATG -s Anc2.Anc2refChr1 110078 14 + 142988 TAATGATAAGAATG -s mr.mrrefChr3 142874 14 + 181027 AAACTATAAGACTG -s simCow_chr6.simCow.chr6 568413 14 + 602619 CAATGATAAGACTG -s simDog_chr6.simDog.chr6 560439 14 + 593897 TAATGATAAGAATG -s simHuman_chr6.simHuman.chr6 564213 14 + 601863 TAAAACTGAGATTG -s simRat_chr6.simRat.chr6 69307 14 - 647215 AAACTTTAAGACTA - -a -s simMouse_chr6.simMouse.chr6 594253 79 + 636262 TTTTCCATATTTGGAGTGAGTCCTGGGTGATTTTCCCCGGTTGTGTTGCTATTATTTCTGCCCCTGTATGGGACATCCA -s Anc0.Anc0refChr3 193603 79 + 222631 TTTTCAATATTAGAATTGAGTCCTGAGCCAGTTTCCCCATCTGTATTTGTAATTCTTCCGTCCCTGTATGGGCTGCGCA -s Anc1.Anc1refChr1 33185 79 + 69767 TTTTCAATATTAGAATTGAGTCCTGAGCCAGTTTCCCCATCTGTATTTGTAATTCTTCCGTCCCTGTATGGGCTGCGCA -s Anc2.Anc2refChr1 110092 79 + 142988 TTTTCAATATTAGAATTGAATGCTGAGCCAGTTTCCCCATCTGTATCTGTAATTCTTCCGTCCCCGTATGGACTGTGCA -s mr.mrrefChr3 142888 79 + 181027 TTTTCCATATTTGGAGTGAGTCCTGGGTGAGTTTCCCCAGCTGTGTTGCTATTATTTCTGCCCCTGTATGGGATACCCA -s simCow_chr6.simCow.chr6 568432 79 + 602619 CTTTTGGTATTAAAATTGAATGTTGAGCAAGTTCCCCCATCCATATCTGTAATTTTTTTGTCCCCGTATGGACTGTGCA -s simDog_chr6.simDog.chr6 560453 69 + 593897 TGTTCAATATTAGGATTGAATGCTGAGCCAGTTTCCCCATCTGTA--TGTAATTCAACC--------ATGGAATGTGTG -s simHuman_chr6.simHuman.chr6 564227 79 + 601863 TTTTGAATATTAGAATGGAGCCCTGAGGCAGTTTCCCCACCTGTATTTGTAATTATTCCGTCCCTATACGGGCTGCTCA -s simRat_chr6.simRat.chr6 69321 75 - 647215 TTTTCCATGTTTGGGGTGAGTGCTGGGCAAGTTTCCCCAGCTGTCTTGCTATTATTTTT----CTGTATGGAATACGCA - -a -s simMouse_chr6.simMouse.chr6 594332 6 + 636262 TGATGG -s Anc0.Anc0refChr3 193682 6 + 222631 CAGGAG -s Anc1.Anc1refChr1 33264 6 + 69767 CAGGAG -s Anc2.Anc2refChr1 110171 6 + 142988 CAAGAG -s mr.mrrefChr3 142967 6 + 181027 TGGTGG -s simCow_chr6.simCow.chr6 568511 6 + 602619 CAAGTG -s simDog_chr6.simDog.chr6 560522 6 + 593897 CAAGAG -s simHuman_chr6.simHuman.chr6 564306 6 + 601863 CAGGAG -s simRat_chr6.simRat.chr6 69398 6 - 647215 TGGTGA - -a -s simMouse_chr6.simMouse.chr6 594338 3 + 636262 GCC -s Anc0.Anc0refChr3 193688 3 + 222631 ACC -s Anc1.Anc1refChr1 33270 3 + 69767 ACC -s Anc2.Anc2refChr1 110177 3 + 142988 ACT -s mr.mrrefChr3 142973 3 + 181027 GCC -s simCow_chr6.simCow.chr6 568518 3 + 602619 ACT -s simDog_chr6.simDog.chr6 560528 3 + 593897 ACT -s simHuman_chr6.simHuman.chr6 564312 3 + 601863 ACC -s simRat_chr6.simRat.chr6 69404 3 - 647215 GCC - -a -s simMouse_chr6.simMouse.chr6 594341 26 + 636262 ATGTACCATGGCACCTAGAAAATCTG -s Anc0.Anc0refChr3 193694 26 + 222631 TTGCACCAGGGCAATTGGAAAATGAG -s Anc1.Anc1refChr1 33276 26 + 69767 TTGCACCAGGGCAATTGGAAAATGAG -s Anc2.Anc2refChr1 110183 26 + 142988 TTGCACCGGGACAATTGCAAAATGAG -s mr.mrrefChr3 142976 26 + 181027 ATGTACCATGGCACTTAGAAAATCAG -s simCow_chr6.simCow.chr6 568524 23 + 602619 TTGAGCT---ATATGTGTAAAATGAG -s simDog_chr6.simDog.chr6 560534 26 + 593897 CTGCAGCGGGACAATCACAAGATGAA -s simHuman_chr6.simHuman.chr6 564318 25 + 601863 TTGCACCACGGCA-TTGGAAAATGAG -s simRat_chr6.simRat.chr6 69407 26 - 647215 ATGTACCATGGCACTTCGAAAATCAG - -a -s simMouse_chr6.simMouse.chr6 594367 5 + 636262 TTGTG -s Anc0.Anc0refChr3 193720 4 + 222631 TCTT- -s Anc1.Anc1refChr1 33302 4 + 69767 TCTT- -s Anc2.Anc2refChr1 110211 4 + 142988 TCTT- -s mr.mrrefChr3 143002 5 + 181027 TTGTG -s simCow_chr6.simCow.chr6 568549 4 + 602619 TCTT- -s simDog_chr6.simDog.chr6 560562 4 + 593897 GCTT- -s simHuman_chr6.simHuman.chr6 564343 4 + 601863 TCCT- -s simRat_chr6.simRat.chr6 69433 5 - 647215 TTGTG - -a -s simMouse_chr6.simMouse.chr6 594372 16 + 636262 GGCTATTTACTTTAGT -s Anc0.Anc0refChr3 193724 15 + 222631 -GCTATTTACTCTGGT -s Anc1.Anc1refChr1 33306 15 + 69767 -GCTATTTACTCTGGT -s Anc2.Anc2refChr1 110215 15 + 142988 -GCTATTTACTCCTCT -s mr.mrrefChr3 143007 16 + 181027 GGCTATTTACTTTGGT -s simCow_chr6.simCow.chr6 568553 14 + 602619 -GCTATTTACT-CTCT -s simDog_chr6.simDog.chr6 560566 15 + 593897 -GGTATTTACTCCTCT -s simHuman_chr6.simHuman.chr6 564347 15 + 601863 -GCTATTTACGCTGGT -s simRat_chr6.simRat.chr6 69583 16 - 647215 GGCTATTTACTTTGGT - -a -s simMouse_chr6.simMouse.chr6 594388 20 + 636262 CAATGGTACTCCTGAATAGA -s Anc0.Anc0refChr3 193739 19 + 222631 GGATGG-AATCCTGAATGGA -s Anc1.Anc1refChr1 33321 19 + 69767 GGATGG-AATCCTGAATGGA -s Anc2.Anc2refChr1 110230 19 + 142988 GGATGG-AATCCCAAATGGA -s mr.mrrefChr3 143023 20 + 181027 CAATGGTACTCCTGAATAGA -s simCow_chr6.simCow.chr6 568567 16 + 602619 GGATGG-A---CCAAATGGA -s simDog_chr6.simDog.chr6 560581 19 + 593897 TGATGC-AATCCCAAATGGA -s simHuman_chr6.simHuman.chr6 564377 19 + 601863 GGATGG-AATCGTGAAGGGA -s simRat_chr6.simRat.chr6 69599 20 - 647215 CAATGCCACTCCTGAATAGA - -a -s simMouse_chr6.simMouse.chr6 594408 125 + 636262 AAAAAAGTCTTGAGACTCCCCAAGTGGTGAGTTGTCCCCATAAAATGGCAAACTGGACCCTTTGATTTGTTTTCTGTACGTAAAGGACTGCAGCTGGAGAGTCCATTGAGTTGGCTATTAGTCCA -s Anc0.Anc0refChr3 193797 10 + 222631 GAAAGAGTTT------------------------------------------------------------------------------------------------------------------- -s Anc1.Anc1refChr1 33379 10 + 69767 GAAAGAGTTT------------------------------------------------------------------------------------------------------------------- -s Anc2.Anc2refChr1 110290 10 + 142988 GACAGAGCTT------------------------------------------------------------------------------------------------------------------- -s mr.mrrefChr3 143043 123 + 181027 AAAAAAGTCTTGAGACTCCCCAAGTGGTGAGTTGTCCCCATAAAATGGCAAACTGGACCCTTTGATTTGTTTTCTGTACGTAAAGGACTGCAGCTG--GAGTCCATTGAGTTGGCTATTAGTCCA -s simCow_chr6.simCow.chr6 568624 10 + 602619 GATGGATCTT------------------------------------------------------------------------------------------------------------------- -s simDog_chr6.simDog.chr6 560641 10 + 593897 AACAGAGCTT------------------------------------------------------------------------------------------------------------------- -s simHuman_chr6.simHuman.chr6 564435 10 + 601863 GAAAGAGTTT------------------------------------------------------------------------------------------------------------------- -s simRat_chr6.simRat.chr6 69619 123 - 647215 AGAAGACTATAGAGACTCCCAAATTGGTGAGTTGTCTCCATAAAATGTCAAACTGGACCCTTTAGTCTGTTTTTTGTACATAAAATATTGCAGCAG--GAGTCCGTTGAGTCGGCTATTAGCCCA - -a -s simMouse_chr6.simMouse.chr6 594533 153 + 636262 ATGGGAGTGCACAAACTGTGGCACTAAGACAGAATCAACTAAACCAGGAGATACATGGAATCCCTGGCCCCTCTGTAACCTCTGTAACTGGATGCTATACCACGTGAAATCCCTTGCCAGCCTCTTCAGCCCAGATATAGTGAACTAGTCATC -s Anc0.Anc0refChr3 193807 21 + 222631 ------------------------------------------------------------------------------------------------------------------------------------AGATATTATGAAACAATCATT -s Anc1.Anc1refChr1 33389 21 + 69767 ------------------------------------------------------------------------------------------------------------------------------------AGATATTATGAAACAATCATT -s Anc2.Anc2refChr1 110300 21 + 142988 ------------------------------------------------------------------------------------------------------------------------------------AGATATTAGGAAACAATCATT -s mr.mrrefChr3 143166 132 + 181027 ATGGGAGTGCACAAACTGTGGCACTAAGAC------------ACCAGGAGATACATGGAATCCCTGGCCCCTCT---------GTAACTGGATGCTATACCACGTGAAATCCCTTGCCAGCCTCTTCAGCCCAGATATAGTGAACTAGTCATT -s simCow_chr6.simCow.chr6 568634 21 + 602619 ------------------------------------------------------------------------------------------------------------------------------------ACATATTGTGGGACAATCATT -s simDog_chr6.simDog.chr6 560657 21 + 593897 ------------------------------------------------------------------------------------------------------------------------------------AGATATTAGAAAACAATCATT -s simHuman_chr6.simHuman.chr6 564445 19 + 601863 ------------------------------------------------------------------------------------------------------------------------------------AGATAT--TGAAACAATCATT -s simRat_chr6.simRat.chr6 69748 132 - 647215 ATGAGAGTGCACAAACTGCAGGAGTAAGAC------------GCCTGGAGCTACATGGAATCACTAGCCCCTTC---------GTAACTGGGTGCCTTACCACATGAAATCCCTTGCCAGCCTCTTCAGCACAGGTATAGTGAACTAGTCATT - -a -s simMouse_chr6.simMouse.chr6 594686 7 + 636262 TAAAACC -s Anc0.Anc0refChr3 193830 7 + 222631 TAAAGCC -s Anc1.Anc1refChr1 33412 7 + 69767 TAAAGCC -s Anc2.Anc2refChr1 110323 7 + 142988 TAACACC -s mr.mrrefChr3 143300 7 + 181027 TAAAGCC -s simCow_chr6.simCow.chr6 568657 7 + 602619 TAACACT -s simDog_chr6.simDog.chr6 560680 7 + 593897 TAACACC -s simHuman_chr6.simHuman.chr6 564466 7 + 601863 TTAAGTC -s simRat_chr6.simRat.chr6 69882 7 - 647215 TAAAGCC - -a -s simMouse_chr6.simMouse.chr6 594693 11 + 636262 AAACTGCAGGC -s Anc0.Anc0refChr3 193838 8 + 222631 GAGTTGCA--- -s Anc1.Anc1refChr1 33420 11 + 69767 GAGTTGCATGC -s Anc2.Anc2refChr1 110331 8 + 142988 GAGTTTCA--- -s mr.mrrefChr3 143307 11 + 181027 AAACTGCAGGC -s simCow_chr6.simCow.chr6 568665 5 + 602619 GGGT---A--- -s simDog_chr6.simDog.chr6 560687 6 + 593897 -AGTTTC---- -s simHuman_chr6.simHuman.chr6 564474 11 + 601863 GAGTTGCATGC -s simRat_chr6.simRat.chr6 69889 11 - 647215 AAAGTACAGGT - -a -s simMouse_chr6.simMouse.chr6 594704 7 + 636262 CCTGTTT -s Anc0.Anc0refChr3 193851 7 + 222631 CCTGTTT -s Anc1.Anc1refChr1 33437 7 + 69767 CCTGTTT -s Anc2.Anc2refChr1 110344 7 + 142988 CTTGTTT -s mr.mrrefChr3 143318 7 + 181027 CCTGTTT -s simCow_chr6.simCow.chr6 568675 7 + 602619 CTTGTTT -s simDog_chr6.simDog.chr6 560698 7 + 593897 CTTGTTT -s simHuman_chr6.simHuman.chr6 564491 7 + 601863 CCTGTTT -s simRat_chr6.simRat.chr6 69900 7 - 647215 CCTGTTT - -a -s simMouse_chr6.simMouse.chr6 594711 1 + 636262 A -s Anc0.Anc0refChr3 193858 1 + 222631 A -s Anc1.Anc1refChr1 33444 1 + 69767 A -s Anc2.Anc2refChr1 110351 1 + 142988 A -s mr.mrrefChr3 143325 1 + 181027 A -s simCow_chr6.simCow.chr6 568687 1 + 602619 A -s simDog_chr6.simDog.chr6 560705 1 + 593897 A -s simHuman_chr6.simHuman.chr6 564498 1 + 601863 A -s simRat_chr6.simRat.chr6 69907 1 - 647215 A - -a -s simMouse_chr6.simMouse.chr6 594712 21 + 636262 TGTGCTTCTTGTGCATCTGGG -s Anc0.Anc0refChr3 193861 21 + 222631 TATGCTTCATGTGCATCTAGG -s Anc1.Anc1refChr1 33447 21 + 69767 TATGCTTCATGTGCATCTAGG -s Anc2.Anc2refChr1 110354 21 + 142988 TAGGCTTCATGTGCATCTAGG -s mr.mrrefChr3 143326 21 + 181027 TGTGCTTCTTGTGCATCTAGG -s simCow_chr6.simCow.chr6 568690 21 + 602619 CAGGCTTCATGTGCACCTAGG -s simDog_chr6.simDog.chr6 560708 21 + 593897 TAGGCTTAATGTGCATATAGG -s simHuman_chr6.simHuman.chr6 564501 21 + 601863 TATGCTTCGTATGCATCTAAG -s simRat_chr6.simRat.chr6 69908 21 - 647215 TGAGCTTCCTGTGCACCTAGG - -a -s simMouse_chr6.simMouse.chr6 594733 8 + 636262 GTTACAAG -s Anc0.Anc0refChr3 193898 8 + 222631 CATAGGGG -s Anc1.Anc1refChr1 33484 8 + 69767 CATAGGGG -s Anc2.Anc2refChr1 110394 8 + 142988 CATAGGGG -s mr.mrrefChr3 143347 8 + 181027 CTTACGAG -s simCow_chr6.simCow.chr6 568730 7 + 602619 CAT-GTGG -s simDog_chr6.simDog.chr6 560776 8 + 593897 CATAGGAG -s simHuman_chr6.simHuman.chr6 564538 8 + 601863 CATAGGGG -s simRat_chr6.simRat.chr6 69929 8 - 647215 CTTACGAG - -a -s simMouse_chr6.simMouse.chr6 594741 5 + 636262 AGAGG -s Anc0.Anc0refChr3 193907 5 + 222631 AGAGG -s Anc1.Anc1refChr1 33495 5 + 69767 AGAGG -s Anc2.Anc2refChr1 110403 5 + 142988 TGAGG -s mr.mrrefChr3 143355 5 + 181027 AGAGG -s simCow_chr6.simCow.chr6 568738 5 + 602619 TTAGG -s simDog_chr6.simDog.chr6 560785 5 + 593897 TGAGG -s simHuman_chr6.simHuman.chr6 564549 5 + 601863 AGAGG - -a -s simMouse_chr6.simMouse.chr6 594746 1 + 636262 T -s Anc0.Anc0refChr3 193912 1 + 222631 A -s Anc1.Anc1refChr1 33500 1 + 69767 A -s Anc2.Anc2refChr1 110408 1 + 142988 A -s mr.mrrefChr3 143360 1 + 181027 T -s simCow_chr6.simCow.chr6 568751 1 + 602619 A -s simDog_chr6.simDog.chr6 560790 1 + 593897 G -s simHuman_chr6.simHuman.chr6 564554 1 + 601863 A - -a -s simMouse_chr6.simMouse.chr6 594747 77 + 636262 TTGTTCCACAGCTCACTCTCCTTAGTCTCAGCTTGAGGTGCCATGATACATCCTATACCATATGTCTCCACTCGCCA -s Anc0.Anc0refChr3 193913 70 + 222631 CAGTTT----GGTCACTGT--TTAGCCTCAGCTTGGGGTGGAACAATCCATCCTATA-CACACATCTCCACTTGACA -s Anc1.Anc1refChr1 33501 71 + 69767 CAGTTT----GGTCACTGT--TTAGCCTCAGCTTGGGGTGGAACAATCCATCCTATAGCACACATCTCCACTTGACA -s Anc2.Anc2refChr1 110409 70 + 142988 CAGTTT----GGTCGCAGT--TTAGCCTCAGCTTGGAGTGGAACAATCCATCCTATA-CACACATCTCCACTTGACA -s mr.mrrefChr3 143361 72 + 181027 TTGTTC----GCTCACTCT-CTTAGTCTCAGCTTGGGGTGGCATGATACATCCTATACCATATGTCTCCACTTGCCA -s simCow_chr6.simCow.chr6 568752 70 + 602619 CAGTTT----GAGCTCAGT--TTAGACTCAGCTTAGAGTGGGGCAATCCACCCTATG-CACAAATCTCCACTTGACA -s simDog_chr6.simDog.chr6 560796 70 + 593897 CAGTTA----GGTCGCACT--CTGGCCTAAGCCTGGAGTGGAACAATCAATCCTATA-CACACATCTCCACTTGACT -s simHuman_chr6.simHuman.chr6 564555 71 + 601863 CAGTTT----GGTCACTGT--TTAGCCTCAGCTGGGGGTGGAACAATTCATCCTATAGCAAACATCTCCTCTTGACA -s simRat_chr6.simRat.chr6 69937 57 - 647215 ----------------TCT-CTTAATCTCA-CTTGGGGTGGCA--ATGCATTCTATACCACATGTCTCCACTTGTCA - -a -s simMouse_chr6.simMouse.chr6 594824 34 + 636262 GATTGTGTAATGGGTACTTAGCCAAGCAAGTCAG -s Anc0.Anc0refChr3 193983 31 + 222631 GATTGCTTAGTAGGTTTTAAGCAAGACAAGT--- -s Anc1.Anc1refChr1 33572 31 + 69767 GATTGCTTAGTAGGTTTTAAGCAAGACAAGT--- -s Anc2.Anc2refChr1 110479 31 + 142988 GATTGCTTAGTAGGTTTTAAGCAAGATAAGT--- -s mr.mrrefChr3 143433 34 + 181027 GATTGTGTAATGGGTACTAAGCCAAGCAAGTCAG -s simCow_chr6.simCow.chr6 568823 31 + 602619 GATTGCCTAGTAGGTTTTGAGCAAGACAAGT--- -s simDog_chr6.simDog.chr6 560866 31 + 593897 GACAGCTTAGGAGGTTTTAGGCAAGATAAGT--- -s simHuman_chr6.simHuman.chr6 564626 27 + 601863 GATTGCTTAGTAGGCTTTAAGCAAGAC------- -s simRat_chr6.simRat.chr6 69994 34 - 647215 GAGTGTGTAATGGGTACTAAGCCAAGCACGTCAG - -a -s simMouse_chr6.simMouse.chr6 594858 78 + 636262 ACAAGTTATGAGTCAGCAACGAATTGCCTAAGCTACTAGGTCTAATTTGGTAAAGTATAGTACATTTGAGGGATTTCA -s Anc0.Anc0refChr3 194014 67 + 222631 ACAAGTTGTAAGGCCCCAACCTGTCACCTAAGTTAC-AGGTCTAGT----------TTAGTTGGTTCAACATATTTCA -s Anc1.Anc1refChr1 33603 77 + 69767 ACAAGTTGTAAGGCCCCAACCTGTCACCTAAGTTAC-AGGTCTAGTCAAGTGAAGTTTAGTTGGTTCAACATATTTCA -s Anc2.Anc2refChr1 110510 67 + 142988 ACAAATTGTAAGGCCCCAACCTGTCACTCTAGTTAC-AGATCTAGT----------TTAGTTGGTTCAACATATTTCA -s mr.mrrefChr3 143467 78 + 181027 ACAAGTTATGAGTCAGCAACCAGTTGCCTAAGTTACTAGGTCTAATCTGGTAAAGTATAGTTCATTTGAGGTATTTCA -s simCow_chr6.simCow.chr6 568861 61 + 602619 ATTCATTACAA-GTCCCAACCTGTCACTC-----AA-AGATCTAGC----------ACAGTTGGTTTGACATATTTCA -s simDog_chr6.simDog.chr6 560897 64 + 593897 ACAAATTGTGAGTCCCCAACCTATCACTCTAGTTAC-AGATCTAGT----------TTAGTTA---CAACATATTTAA -s simHuman_chr6.simHuman.chr6 564653 77 + 601863 ACAAGCTGTAAGGCCCCCACCTGTCACCTAAGTTAC-AGGTTTAGTCAAGTGACCTTTAGTTGGTTCAGCATATTTCA -s simRat_chr6.simRat.chr6 70028 77 - 647215 ACAGGTTATGAGTCAGCAACCAGTTCCATAAGTTACTAGGTCTAA-CTGGTAAAATATATTTAATTTTAGGTACTTCA - -a -s simMouse_chr6.simMouse.chr6 594936 22 + 636262 AATGACTTTGAGCTATGAATAC -s Anc0.Anc0refChr3 194081 21 + 222631 AG-GGCTCTAATCTTCTCAGAT -s Anc1.Anc1refChr1 33680 22 + 69767 AGAGGCTCTAATCTTCTCAGAT -s Anc2.Anc2refChr1 110577 21 + 142988 AG-GGCTCTAATCTTCTCAGAT -s mr.mrrefChr3 143545 22 + 181027 AATGACTTTGAGCTATGCAGAC -s simCow_chr6.simCow.chr6 568923 21 + 602619 AG-TGCCCTGATCTTCTCAGAT -s simDog_chr6.simDog.chr6 560961 21 + 593897 AG-GGCTCCAATCTAGCCAAAG -s simHuman_chr6.simHuman.chr6 564730 22 + 601863 ATAGGCTCTCATCTTCTCAGAT -s simRat_chr6.simRat.chr6 70105 22 - 647215 AATGACTTTGAGCTATGCAGAC - -a -s simMouse_chr6.simMouse.chr6 594958 32 + 636262 ATACCTGAATGCAATGCAACGAGGCGCACTGC -s Anc0.Anc0refChr3 194103 22 + 222631 GTTCTTGAAT----------GTGGTACATTGA -s Anc1.Anc1refChr1 33703 22 + 69767 GTTCTTGAAT----------GTGGTACATTGA -s Anc2.Anc2refChr1 110599 22 + 142988 GTTCTTGAAT----------GTGGTATATTAA -s mr.mrrefChr3 143568 32 + 181027 GTACCTGAATGCAATGCAACGTGGTGCATTGC -s simCow_chr6.simCow.chr6 568945 22 + 602619 GCTCTTGAGT----------GTGGTTTATTAA -s simDog_chr6.simDog.chr6 560983 22 + 593897 GTATTTGAAT----------GTGGTATATTAA -s simHuman_chr6.simHuman.chr6 564753 22 + 601863 GTTCTCAAAT----------GTGATACATTGT -s simRat_chr6.simRat.chr6 70128 32 - 647215 GTACCTGAATGCAATGCAACATGGTGCATTGC - -a -s simMouse_chr6.simMouse.chr6 594990 14 + 636262 AAAAGCTCAGGTTA -s Anc0.Anc0refChr3 194125 6 + 222631 AAAAG-------T- -s Anc1.Anc1refChr1 33725 7 + 69767 AAAAG-------TT -s Anc2.Anc2refChr1 110621 6 + 142988 AGGAG-------T- -s mr.mrrefChr3 143600 14 + 181027 AAAAGCTCAGGTTT -s simCow_chr6.simCow.chr6 568967 1 + 602619 A------------- -s simDog_chr6.simDog.chr6 561005 6 + 593897 AGGAG-------T- -s simHuman_chr6.simHuman.chr6 564775 7 + 601863 AAAAG-------TT -s simRat_chr6.simRat.chr6 70162 14 - 647215 AAAAGCTCAGGTTT - -a -s simMouse_chr6.simMouse.chr6 595004 5 + 636262 AGCTG -s Anc0.Anc0refChr3 194131 4 + 222631 AGCT- -s Anc1.Anc1refChr1 33732 4 + 69767 AGCT- -s Anc2.Anc2refChr1 110627 4 + 142988 AGCT- -s mr.mrrefChr3 143614 4 + 181027 AGCT- -s simCow_chr6.simCow.chr6 568968 4 + 602619 AGCT- -s simDog_chr6.simDog.chr6 561026 4 + 593897 AGCT- -s simHuman_chr6.simHuman.chr6 564782 4 + 601863 AGCT- -s simRat_chr6.simRat.chr6 70176 4 - 647215 AGCC- - -a -s simMouse_chr6.simMouse.chr6 595009 14 + 636262 AAGTTCCCCCACAG -s Anc0.Anc0refChr3 194135 14 + 222631 AAATTCCCCCACTG -s Anc1.Anc1refChr1 33736 14 + 69767 AAATTCCCCCACTG -s Anc2.Anc2refChr1 110661 14 + 142988 AAATTCCCCCACTG -s mr.mrrefChr3 143618 14 + 181027 AAGTTCCCCCACAG -s simCow_chr6.simCow.chr6 569009 14 + 602619 GAAGTTCCCCACTG -s simDog_chr6.simDog.chr6 561060 14 + 593897 AAATTCCCGTACTG -s simHuman_chr6.simHuman.chr6 564786 14 + 601863 AAATTCCCCCACTG -s simRat_chr6.simRat.chr6 70180 14 - 647215 AAGTTCGCCCAGAG - -a -s simMouse_chr6.simMouse.chr6 595023 33 + 636262 CAAGCCTCGAATGCATATGAAAGTCCCTCTATC -s Anc0.Anc0refChr3 194152 31 + 222631 C--GCTTAAAAAGTATGCAAAATCCCACCTATC -s Anc1.Anc1refChr1 33753 31 + 69767 C--GCTTAAAAAGTATGCAAAATCCCACCTATC -s Anc2.Anc2refChr1 110678 31 + 142988 T--GCTTAAAAAGTGTGCAAAGTCCCACCTGTC -s mr.mrrefChr3 143635 33 + 181027 CAAGCCTCGAATGCATATAAAAGCCCCTCTATC -s simCow_chr6.simCow.chr6 569026 29 + 602619 T--GCTT--AAGGTTTGAAAAGTCCCACCTGCC -s simDog_chr6.simDog.chr6 561077 31 + 593897 T--GCTTAAAAAGTGTGCAAAGTCCCAGCTGTT -s simHuman_chr6.simHuman.chr6 564803 31 + 601863 C--GCTTGAAGAGTATGGAAAATCCCACCTACC -s simRat_chr6.simRat.chr6 70197 22 - 647215 CAAGAC-----------TAAAAGCCCCTCTTTC - -a -s simMouse_chr6.simMouse.chr6 595056 84 + 636262 TTTAAATGAATAGCCATGGAGTATGACGCACCATGAAACACACATATCAATCAGTGGTGACATTTCCTTAGGCAAAAAGGGGCT -s Anc0.Anc0refChr3 194183 57 + 222631 T--ACTTGAATAGACCAGGAGC-CAACACACAATCACACACACATA------------------TCC----ACAAAAA--GACA -s Anc1.Anc1refChr1 33784 63 + 69767 TCTACTTGAATAGACCAGGAGC-CAACACACAATCACACACACATA------------------TCCTTAAACAAAAA--GACA -s Anc2.Anc2refChr1 110709 57 + 142988 T--ACTTGAATAGATCAGGGGC-CAACACACAATCCCACACACATA------------------TCC----ACCAGAA--GACA -s mr.mrrefChr3 143668 82 + 181027 TTTAAATGAATAGCCAAGGAGTACAACACACCATGAAACACACATATCAATCAGT-GTGACATTTCCTTAGGCAAAAA-GGGCT -s simCow_chr6.simCow.chr6 569055 57 + 602619 T--GCTTCATTAGATCGGGCGC-CAACACACAACTCCACACACAGA------------------TCC----ACCAGAA--GACA -s simDog_chr6.simDog.chr6 561108 55 + 593897 T--ACTTGAAAACATCAGGGGC-CAATACACCATCCCACCCACATC------------------TCC----ACCAGAA--GA-- -s simHuman_chr6.simHuman.chr6 564836 63 + 601863 TCTAGCTGAATAGACCATGAGC-CAACACACAATCACACACACATA------------------TCCTTAAACAAAGA--GACA -s simRat_chr6.simRat.chr6 70219 81 - 647215 -TTAAATGAATAGCTGAGGAGTACAACACACTGTAAAACACACATATCTACCAGT-ATGACATTCCCTTAGGCAAAAA-GGGCT - -a -s simMouse_chr6.simMouse.chr6 595140 31 + 636262 CAGAGGTAATGCTCAGGAATAGACAGTGTCA -s Anc0.Anc0refChr3 194240 30 + 222631 CAGATATTGT-TTCATGCATGAGCAAAGTCA -s Anc1.Anc1refChr1 33847 31 + 69767 CAGATATTGTGTTCATGCATGAGCAAAGTCA -s Anc2.Anc2refChr1 110766 30 + 142988 CAGATACTGT-TTCATGCATGAGCAAAGTCA -s mr.mrrefChr3 143750 31 + 181027 CAGAGGTAATGCTCAGGAATAGACAGTGTCA -s simCow_chr6.simCow.chr6 569130 30 + 602619 CAGATACTGT-TCCATGCAGGAGTAATGTCA -s simDog_chr6.simDog.chr6 561163 20 + 593897 -----------TTTTCCCTTAAGCAAAGACA -s simHuman_chr6.simHuman.chr6 564899 31 + 601863 CAGATATTGTGTTCATGCATGAGCAAAGTAA -s simRat_chr6.simRat.chr6 70300 1 - 647215 C------------------------------ - -a -s simMouse_chr6.simMouse.chr6 595171 6 + 636262 CTGGGG -s Anc0.Anc0refChr3 194270 6 + 222631 GTGTGA -s Anc1.Anc1refChr1 33878 6 + 69767 GTGTGA -s Anc2.Anc2refChr1 110796 6 + 142988 GTGTGA -s mr.mrrefChr3 143781 6 + 181027 CTGGGG -s simCow_chr6.simCow.chr6 569160 6 + 602619 GAGGGA -s simDog_chr6.simDog.chr6 561187 6 + 593897 ATATGA -s simHuman_chr6.simHuman.chr6 564930 6 + 601863 GTGCGA - -a -s simMouse_chr6.simMouse.chr6 595177 12 + 636262 TCAATTCAATTA -s Anc0.Anc0refChr3 194278 12 + 222631 TCCACACAATTA -s Anc1.Anc1refChr1 33886 12 + 69767 TCCACACAATTA -s Anc2.Anc2refChr1 110804 12 + 142988 TCCACACAATTA -s mr.mrrefChr3 143787 12 + 181027 TCAATTCAATTA -s simCow_chr6.simCow.chr6 569168 10 + 602619 TTCACAC--TTA -s simDog_chr6.simDog.chr6 561195 12 + 593897 TCTACACAATTA -s simHuman_chr6.simHuman.chr6 564938 12 + 601863 TCCACCCAATTC -s simRat_chr6.simRat.chr6 70301 11 - 647215 -CAATTCAATTA - -a -s simMouse_chr6.simMouse.chr6 595189 17 + 636262 CTGCTGAGCTATAAGAA -s Anc0.Anc0refChr3 194290 17 + 222631 CTGCTAAGCTATAAGAA -s Anc1.Anc1refChr1 33898 17 + 69767 CTGCTAAGCTATAAGAA -s Anc2.Anc2refChr1 110817 17 + 142988 CTGCTAAGCTATAAGAA -s mr.mrrefChr3 143799 17 + 181027 CTGCTAAGCTATAAGAA -s simCow_chr6.simCow.chr6 569179 13 + 602619 TAACTAAGCTATA---- -s simDog_chr6.simDog.chr6 561208 17 + 593897 CTGCTAAGCTATAAGAA -s simHuman_chr6.simHuman.chr6 564950 17 + 601863 CTGCAAAACTGTAAGAA -s simRat_chr6.simRat.chr6 70312 16 - 647215 C-GCTAAGCTATACGAA - -a -s simMouse_chr6.simMouse.chr6 595206 10 + 636262 CAATTGAGGA -s Anc0.Anc0refChr3 194308 10 + 222631 CAACTGTGCA -s Anc1.Anc1refChr1 33916 10 + 69767 CAACTGTGCA -s Anc2.Anc2refChr1 110835 10 + 142988 CAACTGTTCA -s mr.mrrefChr3 143816 10 + 181027 CAATTGTGGA -s simCow_chr6.simCow.chr6 569192 10 + 602619 CAACTGTTCA -s simDog_chr6.simDog.chr6 561226 10 + 593897 TAGGTGTTCA -s simHuman_chr6.simHuman.chr6 564968 10 + 601863 CCACGGTGCA -s simRat_chr6.simRat.chr6 70328 10 - 647215 CGATTGTGTA - -a -s simMouse_chr6.simMouse.chr6 595216 28 + 636262 TATGCTTAAAAGTGGACAGATTCATTCA -s Anc0.Anc0refChr3 194318 25 + 222631 TGCACTTGTAAACTAACACATT---TCA -s Anc1.Anc1refChr1 33926 28 + 69767 TGCACTTGTAAACTAACACATTAATTCA -s Anc2.Anc2refChr1 110845 25 + 142988 TGCACTTGTAACCTAACACATT---TCA -s mr.mrrefChr3 143826 28 + 181027 TATGCTTGAAAACTAACAGATTCATTCA -s simCow_chr6.simCow.chr6 569208 25 + 602619 TGAACGTGTAAGCTAGCACATT---TCA -s simDog_chr6.simDog.chr6 561236 25 + 593897 TGCATTTGTAACCTCACGCATT---CCA -s simHuman_chr6.simHuman.chr6 564978 28 + 601863 TGCACTTGCTAACTAACATGTTAATTCA -s simRat_chr6.simRat.chr6 70338 28 - 647215 TAGGCCTGTAAACTAACAGATTCATTCA - -a -s simMouse_chr6.simMouse.chr6 595244 8 + 636262 ACCAATGC -s Anc0.Anc0refChr3 194398 8 + 222631 ACCCATGC -s Anc1.Anc1refChr1 34009 8 + 69767 ACCCATGC -s Anc2.Anc2refChr1 110925 8 + 142988 ATCCATGC -s mr.mrrefChr3 143854 8 + 181027 ACCAATGC -s simCow_chr6.simCow.chr6 569288 8 + 602619 ATCCATTC -s simDog_chr6.simDog.chr6 561316 8 + 593897 ATCCATGC -s simHuman_chr6.simHuman.chr6 565062 8 + 601863 ACCCATAC -s simRat_chr6.simRat.chr6 70366 8 - 647215 AGCAATGC - -a -s simMouse_chr6.simMouse.chr6 595252 23 + 636262 ATGCATTCCATCTCTCAGATCAC -s Anc0.Anc0refChr3 194411 23 + 222631 GTGTGTGTAATATTCCCTATTAC -s Anc1.Anc1refChr1 34022 23 + 69767 GTGTGTGTAATATTCCCTATTAC -s Anc2.Anc2refChr1 110938 23 + 142988 GTATGTGTAATATTCCCTCTTAC -s mr.mrrefChr3 143862 23 + 181027 ATGCATTCCATCTCTCAGATCAC -s simCow_chr6.simCow.chr6 569301 23 + 602619 ATATGTGTCAAATTCCCTCTTAA -s simDog_chr6.simDog.chr6 561329 23 + 593897 GAACATGTAATACTCCCCCTTAC -s simHuman_chr6.simHuman.chr6 565075 23 + 601863 GTGTGTGTAATATTCCCTATTAC -s simRat_chr6.simRat.chr6 70374 23 - 647215 ATGTGTTCCATCTCTTAGATCAG - -a -s simMouse_chr6.simMouse.chr6 595275 260 + 636262 AAACAACAAATTGCTAGGAATCCTTACATAAGTAGCAGTTCCTAGGAGTTGGCACACCAGACCATGCCTCTGAGGGGACCGCTCCATAAGCATTATTGAGTTTAGAGCAATAGTGAAATTGGGAGATAGCACATTTCCTATGGAACCCGTCAACAGCATGGTCCTAACCCCGGAATCCACGTCTCGACCCGTCAACACTACTATATAGTCTCATGATGAGAGTTAATGTTTGTGTTAGTAGTCAGTTGTCAGCTGTCAGT -s Anc0.Anc0refChr3 194434 46 + 222631 A---------------------CATA---AGGTAGC--TCCTCAGTTGTTGGCATACCAGACTATGCCTC----------------------------------------------------------------------------------------------------------------------------------------------------TA---------------------------------------- -s Anc1.Anc1refChr1 34045 49 + 69767 A---------------------CATACATAGGTAGC--TCCTCAGTTGTTGGCATACCAGACTATGCCTC----------------------------------------------------------------------------------------------------------------------------------------------------TA---------------------------------------- -s Anc2.Anc2refChr1 110961 46 + 142988 A---------------------AATG---GGGGAGC--TCCTCAGTTGTTGGCATACCAGACTATGCCTC----------------------------------------------------------------------------------------------------------------------------------------------------TA---------------------------------------- -s mr.mrrefChr3 143885 112 + 181027 AAACAACAAATTGCTAGGAATCCTTACATAAGTAGCAGTTCCTAGGAGTTGGCACACCAGACCATGCCTC----------------------------------------------------------------------------------------------------------------------------------------------------AGAGTTAATGTTTGTGTTAGTAGTCAGTTGTCAGCTGTCAGT -s simCow_chr6.simCow.chr6 569330 46 + 602619 A---------------------AATG---GAGGAGC--TCCTCAGTTCTTAGCAGACCAGACTCTGCCTC----------------------------------------------------------------------------------------------------------------------------------------------------TA---------------------------------------- -s simDog_chr6.simDog.chr6 561352 46 + 593897 A---------------------AATG---GGGGAAC--CCACCAGTTGTTGGCATACCAGACTATGACTC----------------------------------------------------------------------------------------------------------------------------------------------------TT---------------------------------------- -s simHuman_chr6.simHuman.chr6 565098 49 + 601863 A---------------------CATACATATGTAGC--TCCTCTGTTGTTGACATACCAGACTACGCCTC----------------------------------------------------------------------------------------------------------------------------------------------------TA---------------------------------------- -s simRat_chr6.simRat.chr6 70397 112 - 647215 AAACAACAAATTGCTGGAGATTCTTACATAAGTAGCAGCTCCTAGGTGTTGACACACCAGATCTTGCCGT----------------------------------------------------------------------------------------------------------------------------------------------------AGAGTTAATCTTTGTGCTAGTAGTCAGCTGTCAGCTGCCGGT - -a -s simMouse_chr6.simMouse.chr6 595535 229 + 636262 GGTGCTATGCCAGGTGGGTCGTAGAAACCACACAGTGTTCCTTTACTTAACTGATACCTGCCCCACGCCGCCATTTACAGACGGTCAGTGCTTTGCTACGCCTTCCCCATGCAGCCATGTACACATGGTATCCCTTATCTAAAGGAAAGCTAGGCATCCTTGGGACACCTATCCATGGTAGATGTCATACCACCATATACAGATTTCAGCTCAACCAGGCAGACTGCAG -s Anc0.Anc0refChr3 194480 87 + 222631 ---------------------------------------------------------------------------------------------------------------------------------ATCCTTTATTTAAATGAATG-------------GGACAGGTATCCATGTTAGATGGCACTCTCATATATACAGATCTCAGATCAATCAGGAAGACTAGAG -s Anc1.Anc1refChr1 34094 99 + 69767 ---------------------------------------------------------------------------------------------------------------------------------ATCCTTTATTTAAATGAATGACAGGCCTCCT-GGGACAGGTATCCATGTTAGATGGCACTCTCATATATACAGATCTCAGATCAATCAGGAAGACTAGAG -s Anc2.Anc2refChr1 111007 87 + 142988 ---------------------------------------------------------------------------------------------------------------------------------ATCCTTTATTTAAATGAATG-------------GGGCAGGTATCCATGTTAGCTGGCACTCTCATATATACAGATCTCAAATCAGTCAGTAAGACTAGAG -s mr.mrrefChr3 143997 228 + 181027 GGTGCTATGCCAGGTGGGTCGTAGAAACCACACAGTGTTCATTTACTTAACTGATACCTGCCCCACGTGGCCATTTACAGACGGTCAGTGCTTTGCTACACCTTCCCCATGCAGCCATGTACACATGGTATCCCTTATCTAAATGAAAGCTAGGCATCCT-GGGACACCTATCCATGGTAGATGTCATACCACCATATACAGATTTCAGCTCAACCAGGCAGACTGCAG -s simCow_chr6.simCow.chr6 569376 82 + 602619 ---------------------------------------------------------------------------------------------------------------------------------AACCTTTATTTAACTTAATA-------------G--CAGGTATCCATGTTAAGTGGAACTCTC---TATACAGATCTCACATCAGTCAGACAGATTGGAC -s simDog_chr6.simDog.chr6 561398 86 + 593897 ---------------------------------------------------------------------------------------------------------------------------------ATCCTATATTTA-ATGAATG-------------GGGTGTTTAGCCATGTCAGCTGGCACTCCCATATAGACAAATTTCCAATCAGTCAGTAAGGCTAGAG -s simHuman_chr6.simHuman.chr6 565147 99 + 601863 ---------------------------------------------------------------------------------------------------------------------------------ATCCTTTATTTATATGGATGACAGGCCTCCT-GGAACAGGTATCCATGTTAGATGGCACTCTGAAATATACAGAGCTCAGGTCAATCTGGTAGACTATAG -s simRat_chr6.simRat.chr6 70518 223 - 647215 GGTGCTATGCCAGGTGGGTCATAGAAACCACACAAGGTTCATTTACTTAACTGATACCTGCCCTGCATGGCCATGTACACACGGTCAGTGCTTGGATACACCTGCCCCGCACGGCCGTGTACACACGGTATCCCTTATCTAAATAAAAGC-----ATCCT-GGGACACATATCCATGGTATATGACATACCACCATTTACAGATGTCAGATCAACCATGCGGACTGCAG - -a -s simMouse_chr6.simMouse.chr6 595764 11 + 636262 AGTCGTAATAT -s Anc0.Anc0refChr3 194648 11 + 222631 AGTTCTAATAT -s Anc1.Anc1refChr1 34274 11 + 69767 AGTTCTAATAT -s Anc2.Anc2refChr1 111236 11 + 142988 AGTTCTAATGA -s mr.mrrefChr3 144225 11 + 181027 AGTCGTAATAT -s simCow_chr6.simCow.chr6 569601 7 + 602619 AGTCATA---- -s simDog_chr6.simDog.chr6 561663 11 + 593897 AGTTCTAATGA -s simHuman_chr6.simHuman.chr6 565327 11 + 601863 AGTTTTAATAT -s simRat_chr6.simRat.chr6 70741 11 - 647215 AGTCGTAATAT - -a -s simMouse_chr6.simMouse.chr6 595775 15 + 636262 CATGGCCAGAGCTCA -s Anc0.Anc0refChr3 194659 14 + 222631 GATGGCTGGAACTC- -s Anc1.Anc1refChr1 34285 14 + 69767 GATGGCTGGAACTC- -s Anc2.Anc2refChr1 111247 14 + 142988 GATGGCTGGAACTC- -s mr.mrrefChr3 144236 15 + 181027 CATGGCCAGAGCTCA -s simDog_chr6.simDog.chr6 561674 14 + 593897 GATGGCTGGAACTC- -s simHuman_chr6.simHuman.chr6 565343 14 + 601863 TATGGCTGGAATTC- -s simRat_chr6.simRat.chr6 70752 3 - 647215 C------------CA - -a -s simMouse_chr6.simMouse.chr6 595790 64 + 636262 CCTTATGATATAGAATCTTAGGACCATATAGAGGCTATAGGGCTTTTAGTGCCTATTGGGGTCA -s Anc0.Anc0refChr3 194673 64 + 222631 CAGTATGATACAGAGTCTTAGATTCATATAAAGGCCATAATGATATTAGTGTCTGATGTGGTAA -s Anc1.Anc1refChr1 34299 64 + 69767 CAGTATGATACAGAGTCTTAGATTCATATAAAGGCCATAATGATATTAGTGTCTGATGTGGTAA -s Anc2.Anc2refChr1 111261 64 + 142988 CAGTATGATGCAGAGTCTCAGATTCATATAAAGGCCATAATAACATTAGTGTCGGATGTGGTAA -s mr.mrrefChr3 144251 64 + 181027 CCGTATGATATAGAGTCTTAGGACCATATAAAGGCTATAGGGATTTTAGTGCCTATTGTGGTCA -s simCow_chr6.simCow.chr6 569608 59 + 602619 CAGGCTGATGCAGAGTCTCAGATTCACATAAAGGCCATAACAACTTTAGTGTC-----TGGTAA -s simDog_chr6.simDog.chr6 561689 64 + 593897 AAGTATAATGCAGAGTCCCAGACTCATATAAAGGCCAGAATAGCATAAGTGTTGGATGTGGTAG -s simHuman_chr6.simHuman.chr6 565357 64 + 601863 CGGTATGATACAGGGTCTTAGATTCATACAAAGGTCATAATGATATTAGTGTCTGATGTGGTAA -s simRat_chr6.simRat.chr6 70755 62 - 647215 CTGTATG--ATAGAGTTTTAGGGCCATATTAAGGCTATAGGGATTTTAGTGCCTATTGTCATCA - -a -s simMouse_chr6.simMouse.chr6 595854 18 + 636262 AATCCCGTGATTAATAAT -s Anc0.Anc0refChr3 194737 17 + 222631 AA-CCCCTGTGTAGTAAT -s Anc1.Anc1refChr1 34363 17 + 69767 AA-CCCCTGTGTAGTAAT -s Anc2.Anc2refChr1 111325 17 + 142988 AA-CCCCTGTGTAGTAAT -s mr.mrrefChr3 144315 18 + 181027 AATCCCGTGTTTAATAAT -s simCow_chr6.simCow.chr6 569667 17 + 602619 AT-CCCCTGTGTAGTAAT -s simDog_chr6.simDog.chr6 561767 17 + 593897 AA-TCCCTATATAATAGT -s simHuman_chr6.simHuman.chr6 565421 17 + 601863 AA-CCATTGTGTAGTAAT -s simRat_chr6.simRat.chr6 70817 18 - 647215 ATTCCCCTGTTTAACAAT - -a -s simMouse_chr6.simMouse.chr6 595872 15 + 636262 CAGGCAGACCAGTTT -s Anc0.Anc0refChr3 194755 15 + 222631 TAGGAAGATTAAATT -s Anc1.Anc1refChr1 34381 15 + 69767 TAGGAAGATTAAATT -s Anc2.Anc2refChr1 111343 15 + 142988 CAGGAGAATTAAATT -s mr.mrrefChr3 144333 15 + 181027 TAGGCAGATCAGTTT -s simCow_chr6.simCow.chr6 569685 15 + 602619 CAGGAGAATTAATTT -s simDog_chr6.simDog.chr6 561785 15 + 593897 CAGGAGAACTAGATT -s simHuman_chr6.simHuman.chr6 565439 15 + 601863 TAGGGAGATTAACTT -s simRat_chr6.simRat.chr6 70835 15 - 647215 TAACAAAATCAGTGT - -a -s simMouse_chr6.simMouse.chr6 595887 8 + 636262 TTGTCACT -s Anc0.Anc0refChr3 194770 8 + 222631 TTGTCATT -s Anc1.Anc1refChr1 34396 8 + 69767 TTGTCATT -s Anc2.Anc2refChr1 111358 8 + 142988 TTGTCATT -s mr.mrrefChr3 144348 8 + 181027 TTGTCATT -s simCow_chr6.simCow.chr6 569704 8 + 602619 TTGTCATT -s simDog_chr6.simDog.chr6 561800 8 + 593897 TTTTCATT -s simHuman_chr6.simHuman.chr6 565454 8 + 601863 TTGTCTTT -s simRat_chr6.simRat.chr6 70850 8 - 647215 TTGTCATT - -a -s simMouse_chr6.simMouse.chr6 595895 42 + 636262 CATTCAAAATCCATACCTTGTCAGGCTCAGGATTGATTGTAA -s Anc0.Anc0refChr3 194779 38 + 222631 CAGTTAAAATTCTTACTCTGGCTAGTTTAGAG----TTGTAA -s Anc1.Anc1refChr1 34405 38 + 69767 CAGTTAAAATTCTTACTCTGGCTAGTTTAGAG----TTGTAA -s Anc2.Anc2refChr1 111367 38 + 142988 CAGTTAAAAATCTTACTCTGGCTAGTCTGGAG----TTGTAA -s mr.mrrefChr3 144356 39 + 181027 CATTTAAAATCCATACCCTGTCAGGCTCAGAGT---TTGTAA -s simCow_chr6.simCow.chr6 569713 38 + 602619 CAGTTAAAAATCTTACTCTGGCTAGTCTGGAG----TTGTAA -s simDog_chr6.simDog.chr6 561809 38 + 593897 CAGTAAAAAATCTTACTCTGGCTGGCCGGGTG----TTGGAG -s simHuman_chr6.simHuman.chr6 565463 38 + 601863 CAGCTAAAATTCTTACTCTGCCTAGTTTAGAG----TTGTAA -s simRat_chr6.simRat.chr6 70858 33 - 647215 TATTTAAAATCCATACCCTGTCAGGCTAACAGT--------- - -a -s simMouse_chr6.simMouse.chr6 595937 19 + 636262 CTACAGGTTATTGGTACTG -s Anc0.Anc0refChr3 194817 19 + 222631 CTACAGGTGACTGATACTG -s Anc1.Anc1refChr1 34443 19 + 69767 CTACAGGTGACTGATACTG -s Anc2.Anc2refChr1 111405 19 + 142988 CTACAGGTGACGAATACCG -s mr.mrrefChr3 144395 19 + 181027 CTACAGGTTATTGGTACTG -s simCow_chr6.simCow.chr6 569751 19 + 602619 CTATGGGTGACCAATGCAG -s simDog_chr6.simDog.chr6 561848 19 + 593897 TTACAGGTGACGAACACCA -s simHuman_chr6.simHuman.chr6 565501 19 + 601863 CTACAAGTGACTGATACTG - -a -s simMouse_chr6.simMouse.chr6 595956 91 + 636262 ACCCAATATGACTGTTGAAGCATGCCAACCTTGTAAACAACACAGTAAAACTAGATTCTTAGCCTCAATACACACTCTACACAGTCTTATG -s Anc0.Anc0refChr3 194836 77 + 222631 TCTTAATGT--------------GCCAACTCCTTAAGTAATATAGCAGACCTAGATTTATAGCCTCAACATACACTTAATATAGGCTAATG -s Anc1.Anc1refChr1 34462 86 + 69767 TCTTAATGTAA----TATAGCA-GCCAACTCCTTAAGTAATATAGCAGACCTAGATTTATAGCCTCAACATACACTTAATATAGGCTAATG -s Anc2.Anc2refChr1 111424 77 + 142988 TCTTATTGT--------------GCCAACTCCTTAAGTAATATAGCAGACCTAGATTCATAGCCTCAACATACACATAATATAGGCTAATA -s mr.mrrefChr3 144414 91 + 181027 ACCCAACATGACCATTGAAGCATGCCAACCTTGTAAACAACACAGTAAACCTAGATTTTTAGCCTCAATACACACTCTACATAGTCTTATG -s simCow_chr6.simCow.chr6 569770 74 + 602619 TCTTATTGT--------------GCCCACTTCCTAAATGATAGAGAAGACCTACAT---TAGCCTCAACATGCACCTAACATGTGCTTATA -s simDog_chr6.simDog.chr6 561867 77 + 593897 TCTTATTGT--------------GCCAGCTCCTTAAGTAATATAGCAGACCTAGATTCATAGCCCACATATACACATAATATAGGCTAATA -s simHuman_chr6.simHuman.chr6 565566 86 + 601863 TCTTAAGGTAA----TATAGCA-GCCAACTCCTTAAGTAAAATAGCAGACCTAAACTTATACCCTCAACATACACTTAATATCAGCTAATG -s simRat_chr6.simRat.chr6 70891 90 - 647215 -CCCAACATGACCATTGCAGCATGGCAACCTTGTAACCAACACAGTTTACCTTGATTTTTAGCTTCAATACACACTCTGCATGGTCTTATG - -a -s simMouse_chr6.simMouse.chr6 596047 12 + 636262 ATTCTAAAACAT -s Anc0.Anc0refChr3 194914 12 + 222631 ATCCTAAAACAT -s Anc1.Anc1refChr1 34549 12 + 69767 ATCCTAAAACAT -s Anc2.Anc2refChr1 111502 12 + 142988 ATCCTAAAACAT -s mr.mrrefChr3 144505 12 + 181027 ATTCTAAAACAT -s simCow_chr6.simCow.chr6 569845 12 + 602619 ATCCTAAAACAT -s simDog_chr6.simDog.chr6 561945 12 + 593897 GTCTTAAGACAT -s simHuman_chr6.simHuman.chr6 565653 12 + 601863 ATCCTAAAACAT -s simRat_chr6.simRat.chr6 70981 12 - 647215 ATTCTAAAGCAT - -a -s simMouse_chr6.simMouse.chr6 596059 18 + 636262 CATTGTTACTTATATCAT -s Anc0.Anc0refChr3 194926 18 + 222631 CATTGTTGCTTATATCTC -s Anc1.Anc1refChr1 34561 18 + 69767 CATTGTTGCTTATATCTC -s Anc2.Anc2refChr1 111514 18 + 142988 CATTGTTGCTTGTATCTC -s mr.mrrefChr3 144517 18 + 181027 CATTGTTACTTATATCTT -s simCow_chr6.simCow.chr6 569857 15 + 602619 CATTGTTGCTTGT---TC -s simDog_chr6.simDog.chr6 561957 18 + 593897 CATTGTTACTTGTATCTC -s simHuman_chr6.simHuman.chr6 565667 18 + 601863 CATTGTTGCCCATATCTC -s simRat_chr6.simRat.chr6 70993 18 - 647215 CATAGTTACTGACCTCTT - -a -s simMouse_chr6.simMouse.chr6 596077 23 + 636262 GACCCAAACTGCACCCAGTTTCT -s Anc0.Anc0refChr3 194946 23 + 222631 GATCAGGACTGTACACAGTTTCT -s Anc1.Anc1refChr1 34581 23 + 69767 GATCAGGACTGTACACAGTTTCT -s Anc2.Anc2refChr1 111534 23 + 142988 GACCAGGACTGTACATAGTTTCT -s mr.mrrefChr3 144535 23 + 181027 GATCCGAACTGCACCCAGTTTCT -s simCow_chr6.simCow.chr6 569874 23 + 602619 GACCAGGACTGTACAGAGTTTCT -s simDog_chr6.simDog.chr6 561977 14 + 593897 GACTA-----TTGCCTAG----T -s simHuman_chr6.simHuman.chr6 565687 23 + 601863 GATCAGGACTGTACACAGGTTCT -s simRat_chr6.simRat.chr6 71011 23 - 647215 GATCCGAACTGAACCTGGTTTCT - -a -s simMouse_chr6.simMouse.chr6 596100 9 + 636262 TGATCACTG -s Anc0.Anc0refChr3 194971 8 + 222631 TATTCAG-A -s Anc1.Anc1refChr1 34606 9 + 69767 TATTCAGGA -s Anc2.Anc2refChr1 111559 8 + 142988 TATATAG-A -s mr.mrrefChr3 144558 9 + 181027 TGATCACTA -s simCow_chr6.simCow.chr6 569899 8 + 602619 TATATAG-A -s simDog_chr6.simDog.chr6 561993 8 + 593897 TATATAG-A -s simHuman_chr6.simHuman.chr6 565712 9 + 601863 TATTCAGCA -s simRat_chr6.simRat.chr6 71034 9 - 647215 TGATCACTA - -a -s simMouse_chr6.simMouse.chr6 596109 6 + 636262 TTGTAT -s Anc0.Anc0refChr3 194979 6 + 222631 TCTAAG -s Anc1.Anc1refChr1 34615 6 + 69767 TCTAAG -s Anc2.Anc2refChr1 111567 6 + 142988 TCTAAG -s mr.mrrefChr3 144567 6 + 181027 TTGTAT -s simCow_chr6.simCow.chr6 569907 6 + 602619 ACCTGG -s simDog_chr6.simDog.chr6 562001 6 + 593897 TCTAAG -s simHuman_chr6.simHuman.chr6 565726 6 + 601863 TATAAG -s simRat_chr6.simRat.chr6 71043 6 - 647215 TTGTAT - -a -s simMouse_chr6.simMouse.chr6 596115 1 + 636262 A -s Anc0.Anc0refChr3 194985 1 + 222631 A -s Anc1.Anc1refChr1 34621 1 + 69767 A -s Anc2.Anc2refChr1 111573 1 + 142988 A -s mr.mrrefChr3 144573 1 + 181027 A -s simCow_chr6.simCow.chr6 569913 1 + 602619 A -s simDog_chr6.simDog.chr6 562008 1 + 593897 C -s simHuman_chr6.simHuman.chr6 565732 1 + 601863 A -s simRat_chr6.simRat.chr6 71049 1 - 647215 A - -a -s simMouse_chr6.simMouse.chr6 596116 129 + 636262 GTTATAAGTGTTATAGAATGCAGAGTTCAATGGTTCATGTGATGACAAATGGCATAACGGTAACAAAGGCATGAGAGTATTTATATCCTGTGTTACATAAGGATTATTGGTCTAACATACTGGGATGGG -s Anc0.Anc0refChr3 194986 128 + 222631 GTTATAAGTTTTATATAATAAAGACTTCAATGGTTGAGGGGATAAGAAATTGCATAATAGTGTCAAAGACATGAGACTGTATATATCCAGTATAGT-TAAGGATAACAGGCCTAAGTTACTGGCATAAG -s Anc1.Anc1refChr1 34622 128 + 69767 GTTATAAGTTTTATATAATAAAGACTTCAATGGTTGAGGGGATAAGAAATTGCATAATAGTGTCAAAGACATGAGACTGTATATATCCAGTATAGT-TAAGGATAACAGGCCTAAGTTACTGGCATAAG -s Anc2.Anc2refChr1 111574 128 + 142988 GTTATAACTTTTATATTATGAAGACTTCAATGGGTGAGGGGATAAGGCATTGCATAATAATGTCAAAGGCATGAGACTGTATGTATCCAGTATAGT-GTAATATAACATGCCCCAGTTACTAGCATAAG -s mr.mrrefChr3 144574 129 + 181027 GTTATAAGTGTTATAGAATACAGAGTTCAATGGTTGAGGTGATGACAAATTGCATAATGGTAACAAAGACATGAGACTATTTATATCCTGTATTACATAAGGATTATTGGTCTAAGATACTGGCATAGG -s simCow_chr6.simCow.chr6 569916 126 + 602619 GCTGTAAATTTTATTTGGTGAAGACTTCAATGGGTGAGGGCATGATGGATTGCACAATATTGT--GAGGCACGAGATTGTATCTATCTAGTATTAC-GCAACATAACATGCCCCATTTACTAGTATCAA -s simDog_chr6.simDog.chr6 562009 127 + 593897 GTTATAACTTTCATATTATGAAGACTTCAATGGGTGAGGGGATATG-CATTGCATAATCATGTCAAAGGCTTGAGACTGTATGTATCCAACATAGT-GTAATATAACATGCCCCAGTTACTAGCATAAG -s simHuman_chr6.simHuman.chr6 565733 124 + 601863 GTTATAAGTTTTATAAAATAAAGACTTCAATGGTTGAGCGGACAAGAAATTGTATAATAGTGTCAAAGACATGAGACTGTCTATATCCAGTACAGT-TAAGGAACTGGGGCCTA----ACTGGCATTCG -s simRat_chr6.simRat.chr6 71050 128 - 647215 GTTAATAGTCTTATAGAATAGAGAGTTCAATGGTTGAGGTAATGAAATATTGCATAATGGTAACAAAGACATGAGACTATTTATATCCTATATTACATAA-AATTATTGGTCCAAGTTACTGGCATAGG - -a -s simMouse_chr6.simMouse.chr6 596245 2 + 636262 AA -s Anc0.Anc0refChr3 195114 2 + 222631 AA -s Anc1.Anc1refChr1 34750 2 + 69767 AA -s Anc2.Anc2refChr1 111702 2 + 142988 CA -s mr.mrrefChr3 144703 2 + 181027 AA -s simCow_chr6.simCow.chr6 570042 2 + 602619 CA -s simDog_chr6.simDog.chr6 562136 2 + 593897 CA -s simHuman_chr6.simHuman.chr6 565892 2 + 601863 AA -s simRat_chr6.simRat.chr6 71178 2 - 647215 AA - -a -s simMouse_chr6.simMouse.chr6 596247 105 + 636262 ATTTTGCATGTCATCTTAGCCAATATGAGAGCAACATTTCACATCCTGAATGAGAGTAGAAGTGAGTATAATAATTGCTACATATGTAAACCTAGCTTTATGAAA -s Anc0.Anc0refChr3 195116 100 + 222631 ACCTTGCAAGTCATCCTAGGCA--ATTAGAGCAACACTTCACATCCTGAATAAAAGTAGAAGTGCAT---ATAATTGCTATACACTTGATCCTAGATTAGTGAAG -s Anc1.Anc1refChr1 34752 100 + 69767 ACCTTGCAAGTCATCCTAGGCA--ATTAGAGCAACACTTCACATCCTGAATAAAAGTAGAAGTGCAT---ATAATTGCTATACACTTGATCCTAGATTAGTGAAG -s Anc2.Anc2refChr1 111704 100 + 142988 ACCTTGCCAGTCATCCTAGGCA--ATTAGACCAACACTTCACATTCTGAATAAAAGTAGAAGTGCAC---ATAATTGCTATACACTTGTTTTTAGATTAGTGAAG -s mr.mrrefChr3 144705 103 + 181027 ATTTTGCATGTCATCTTAGCCA--ATGAGAGCAACACTTCACATCCTGAATGAGAGTAGAAGTGAGTATAATAATTGCTACATATGTAATCCTAGCTTTATGAAG -s simCow_chr6.simCow.chr6 570051 92 + 602619 ATCTTGTGAGTCATCCTAGGCA--ATTAGACCAACACTTCCCAGGCTGAATAAAAGTAGAAGTGCAA-----TATTGATATACACTTGT------ACTAGTGAAG -s simDog_chr6.simDog.chr6 562138 84 + 593897 ACTCTGCCAGTCATCCTAGGCA--AT---ACCAACACATCACATTCTGC-------------TGCAC---ATAATTGCTACACACTTGTTTTTAGATCAGTGGAT -s simHuman_chr6.simHuman.chr6 565894 100 + 601863 TCCTCGCAAGTCAACCTAGGCA--ATCAGAGCAGCACTTCACATCCTGAATAAAACTAGAAGTGCAT---GTAATTGCTATGCACTTGATCCTAGGTTGTTTAAG -s simRat_chr6.simRat.chr6 71180 103 - 647215 ATTTTGCATGTCACCTTAGCTG--ATGAGAGCAACACTTCACATCCTGAATGAGAGTAGAAGTGTGTATAATAATTGCTACATATGTAATCCTAGCTTTATGAAG - -a -s simMouse_chr6.simMouse.chr6 596352 115 + 636262 TCCACAATTTGAACAATATATAGTGGAAAGAGAAAGAATTGCATACATGCAATACATGTCACAAGTGATATTCTGAAAGTTATATTATCCATATTTGTAGCAATTACATGATGCA -s Anc0.Anc0refChr3 195221 109 + 222631 TCCACCATGTGAACAACATACAGTGGATAGAGAAAGAA-TGAACACATGCAGTTCATGAAGCAAATCAGGATCTGA-----ATATTCTTCCTATCTTTACCAGCTACATGGACTG -s Anc1.Anc1refChr1 34857 114 + 69767 TCCACCATGTGAACAACATACAGTGGATAGAGAAAGAA-TGAACACATGCAGTTCATGAAGCAAATCAGGATCTGACAGCAATATTCTTCCTATCTTTACCAGCTACATGGACTG -s Anc2.Anc2refChr1 111809 109 + 142988 TCCACCATGTGAACAACATACAGTGGATAGAGAAAGAA-TGAACACATGTAGTTCAAGAAGCAAATCAGGATTTGA-----GTATTCTTCTTACCTTTACCAGCTACATGGACTG -s mr.mrrefChr3 144808 115 + 181027 TCCACAATTTGAACAATATATAGTGGAAAGAGAAAGAATTGCATACATGCAATACATGACACAAATGATAATCTGACAGTTATATTATCCCTATCTGTAGCAATTACATGGTGCA -s simCow_chr6.simCow.chr6 570148 88 + 602619 TGCACAATGTGAACAACATACATTGAATAGAGACAGAA--GAACACATGTAGTTCAAGAAGCAAATCAGGATTTGA-------------------------AGCAATATTAATTG -s simDog_chr6.simDog.chr6 562227 103 + 593897 TCCACCATGTGTACAACATACAGTCGATAGAGAAAGAA-TGAACACATGTAACTCAAGAGGCGACTGAGG-----------GTATTCTTCTTACCTTTACCAGCTACATGGACTG -s simHuman_chr6.simHuman.chr6 565999 114 + 601863 TCCACCATGTGATCATCATAGAGTGGATAGAGAAAGAA-TGAACATATGCAGTCCATGAAGCAAATCAGGATCTGACAGCAATACTGTTCCGATCTTTAACAGATACACAGACTG -s simRat_chr6.simRat.chr6 71283 115 - 647215 TCTACAATTCGAACAATATATGGTGGAAAGCAAACGAATTGCATAGATGCAATACATGACACCAATGATAATCTGACAGTTATATTCTCCCTATCTGTAGCAATTACGTGGCGGA - -a -s simMouse_chr6.simMouse.chr6 596467 47 + 636262 TGATGGCCCCCCCACTTGGTTGGGCAGGACAAAGACTGAATGCCTTT -s Anc0.Anc0refChr3 195330 47 + 222631 TGATGGTCCCTTCACTTGGTTAGGCAAGGTAATGAGTTAATCTTTTT -s Anc1.Anc1refChr1 34971 47 + 69767 TGATGGTCCCTTCACTTGGTTAGGCAAGGTAATGAGTTAATCTTTTT -s Anc2.Anc2refChr1 111918 47 + 142988 TGATAGTCCCTTCACTTTCTTAGTCAAGGTAATGAGTTGATCTTTTT -s mr.mrrefChr3 144923 47 + 181027 TGATGGCCCCCTCACTTGGTTAGGCAGGACAAAGACTGAATGCCTTT -s simCow_chr6.simCow.chr6 570237 47 + 602619 TGATAGTCCCTTCACTTCTTTAGTCAAAATAATGAGTTGTGCTTTTA -s simDog_chr6.simDog.chr6 562330 47 + 593897 TGATAATCCCTTCACTTTCTTAGTCAAGGTAATGGGTTGATGCTGTT -s simHuman_chr6.simHuman.chr6 566113 47 + 601863 TGGTGGACGTTTCACTTGGTGAGGCAAGCAAATGAGTTAATCTTTTT -s simRat_chr6.simRat.chr6 71398 47 - 647215 AGATGGTCCCCTCACTTGGTTAGGCAGGGCAAAGACTGAATGCCTTT - -a -s simMouse_chr6.simMouse.chr6 596514 5 + 636262 AAGGA -s Anc0.Anc0refChr3 195377 5 + 222631 AGGGA -s Anc1.Anc1refChr1 35018 5 + 69767 AGGGA -s Anc2.Anc2refChr1 111965 5 + 142988 AGGGA -s mr.mrrefChr3 144970 5 + 181027 AAGGA -s simCow_chr6.simCow.chr6 570284 5 + 602619 AGTTG -s simDog_chr6.simDog.chr6 562380 5 + 593897 AGGGA -s simHuman_chr6.simHuman.chr6 566160 5 + 601863 AGGGA -s simRat_chr6.simRat.chr6 71445 5 - 647215 AAGAA - -a -s simMouse_chr6.simMouse.chr6 596519 1 + 636262 G -s Anc0.Anc0refChr3 195382 1 + 222631 G -s Anc1.Anc1refChr1 35023 1 + 69767 G -s Anc2.Anc2refChr1 111970 1 + 142988 G -s mr.mrrefChr3 144975 1 + 181027 G -s simCow_chr6.simCow.chr6 570289 1 + 602619 G -s simDog_chr6.simDog.chr6 562395 1 + 593897 G -s simHuman_chr6.simHuman.chr6 566165 1 + 601863 G -s simRat_chr6.simRat.chr6 71450 1 - 647215 G - -a -s simMouse_chr6.simMouse.chr6 596520 14 + 636262 GTTTATCCTCAATT -s Anc0.Anc0refChr3 195384 14 + 222631 GTTTATCCTCAATT -s Anc1.Anc1refChr1 35025 14 + 69767 GTTTATCCTCAATT -s Anc2.Anc2refChr1 111972 14 + 142988 GTTTATTCTCACTT -s mr.mrrefChr3 144976 14 + 181027 GTTTATCCTCAATT -s simCow_chr6.simCow.chr6 570291 14 + 602619 GTTCATTCTGTCTG -s simDog_chr6.simDog.chr6 562397 14 + 593897 GTTTATTCTCACTT -s simHuman_chr6.simHuman.chr6 566167 14 + 601863 GTTTATCCTCAATT -s simRat_chr6.simRat.chr6 71451 10 - 647215 GTTTATGCTC---- - -a -s simMouse_chr6.simMouse.chr6 596534 5 + 636262 TCTGT -s Anc0.Anc0refChr3 195416 5 + 222631 TCTGA -s Anc1.Anc1refChr1 35057 5 + 69767 TCTGA -s Anc2.Anc2refChr1 112004 5 + 142988 TCCAA -s mr.mrrefChr3 144990 5 + 181027 TCTGT -s simCow_chr6.simCow.chr6 570323 5 + 602619 TTCAA -s simDog_chr6.simDog.chr6 562429 5 + 593897 TCCAA -s simHuman_chr6.simHuman.chr6 566199 5 + 601863 TCTGA - -a -s simMouse_chr6.simMouse.chr6 596539 46 + 636262 TGCCAATGAACAAACAGGAAAACCAAGCAAACAAGATACATAATAA -s Anc0.Anc0refChr3 195421 31 + 222631 GGCAAGTAACCAA----CAAAAAC-----------ATACATACTAG -s Anc1.Anc1refChr1 35062 31 + 69767 GGCAAGTAACCAA----CAAAAAC-----------ATACATACTAG -s Anc2.Anc2refChr1 112010 31 + 142988 GGCATGTAACCAA----CAAAAAC-----------ATACGTACCAG -s mr.mrrefChr3 144995 35 + 181027 TGCCAATGACCAAACAGGAAAACC-----------ATACATAATAA -s simCow_chr6.simCow.chr6 570329 4 + 602619 G------------------------------------------CAG -s simDog_chr6.simDog.chr6 562435 31 + 593897 GGCATGTAACCAA----CAAAAAC-----------ATACGTACCAG -s simHuman_chr6.simHuman.chr6 566204 31 + 601863 GGCAAGTTACCAA----CAAAAGC-----------ATATATATTAG -s simRat_chr6.simRat.chr6 71461 31 - 647215 ----AACAACCAAACAAAAAAACC-----------ATACATAATAA - -a -s simMouse_chr6.simMouse.chr6 596585 29 + 636262 TTGCAGAATTTCATTATTATGAATAAGTT -s Anc0.Anc0refChr3 195452 29 + 222631 TTGCAGAATTCCATTATTGTGAATCAGAT -s Anc1.Anc1refChr1 35093 29 + 69767 TTGCAGAATTCCATTATTGTGAATCAGAT -s Anc2.Anc2refChr1 112042 29 + 142988 TTGTAGAATTCCATTATTGTGAATCTGAT -s mr.mrrefChr3 145030 29 + 181027 TTGCAGAATTCCATTATTATGAATCAGTT -s simCow_chr6.simCow.chr6 570334 29 + 602619 TTGTGCCATTCCATTATTGTGAATCTGGT -s simDog_chr6.simDog.chr6 562467 29 + 593897 TGGTAGAATTCCATTATTGTGAATCTGAC -s simHuman_chr6.simHuman.chr6 566235 29 + 601863 TTGCAGAATTCTGTTATTGAGAGTCATCT -s simRat_chr6.simRat.chr6 71492 29 - 647215 TTGCAGAATTCCATTATTATGAATCAGTT - -a -s simMouse_chr6.simMouse.chr6 596614 474 + 636262 CATTCTGAGGACAATCTAGCCAATCTGTCTGGTATCCTATCTCGTCACTTATAGTAAATAAAGAAGTTAATCTACCCTGGAATTTATGATTCCCAAATGGTTTGAACTCTCAACGCGAGACTATATAGTAGTGTTGACGGGTCGAGACGTGGATTCCGGGGGTAGGGTTAAATGGGTAAAGAAGTTAATCTACCCTGGATTTTATGATTCCTGAATGGTTTGAACTCTCAATGCAAGACTATATAGTAGTGTTGACGGGTCAAGATGTGGATTCTGGGGGTAGGGTTAAATGGGTCGAACTCTCATTGTGAGACTATATAGTAGTGTTGACGGGTTGAGACGTGGCTTCTGGGGTTAGGGGTAGCAGGACCATGCAGTCCGATGGGTTCCATAGGGAATGTGCTACCTCTCAATTTCACTATTGCTCTAAACTCAATAAGGCTTACGAAGCGGTCCCTATATACACATTTAATG -s Anc0.Anc0refChr3 195481 44 + 222631 CATTCTGTGGACAATTCAATCAATTTTT----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ATGTGCTCCTTTCCTG -s Anc1.Anc1refChr1 35122 44 + 69767 CATTCTGTGGACAATTCAATCAATTTTT----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ATGTGCTCCTTTCCTG -s Anc2.Anc2refChr1 112071 44 + 142988 CATTCTGTGGACAACTCAATCAATTTTT----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GTGTGCTCCTTTCCTG -s mr.mrrefChr3 145059 44 + 181027 CATTCTGAGGACAATCTAGCCAATCTGT----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ATATACACATTTAATG -s simCow_chr6.simCow.chr6 570363 44 + 602619 CATTCTGAAGACAACTCAATCAACTTCT----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CTGTGCTCCTTTCCCA -s simDog_chr6.simDog.chr6 562496 44 + 593897 CACCCTGTGGACAACTCAAACAATTCTT----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GTGTGCTCCTGTCCTG -s simHuman_chr6.simHuman.chr6 566264 44 + 601863 GCTTCTGCGGACAATTCAATCAATTTTT----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ATGTGCTCCTTTCCTG -s simRat_chr6.simRat.chr6 71522 36 - 647215 CATTTTGAGGACAATCTAGCCAAGCTGT----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ATATATAC-------- - -a -s simMouse_chr6.simMouse.chr6 597088 4 + 636262 CAGA -s Anc0.Anc0refChr3 195527 4 + 222631 CAGA -s Anc1.Anc1refChr1 35168 4 + 69767 CAGA -s Anc2.Anc2refChr1 112117 4 + 142988 CAAA -s mr.mrrefChr3 145103 4 + 181027 CAGA -s simCow_chr6.simCow.chr6 570409 4 + 602619 CACA -s simDog_chr6.simDog.chr6 562542 4 + 593897 CAAG -s simHuman_chr6.simHuman.chr6 566310 4 + 601863 CAGA - -a -s simMouse_chr6.simMouse.chr6 597092 36 + 636262 TACAGCGGCATCCCTGGCCACCCAATACCAAATTGA -s Anc0.Anc0refChr3 195531 36 + 222631 TATGACAGCATGCCCGGCCACCCTAAACCAAATAGA -s Anc1.Anc1refChr1 35172 36 + 69767 TATGACAGCATGCCCGGCCACCCTAAACCAAATAGA -s Anc2.Anc2refChr1 112121 36 + 142988 TATGACAGCACGCCCGGCCACCCTGAACGAAATAGA -s mr.mrrefChr3 145107 36 + 181027 TACGGCAGCATCCCTGGCCACCCAATACCAAATTGA -s simCow_chr6.simCow.chr6 570529 36 + 602619 TACAATAGCAAGCGTGGCCAGCCTGAACAAAATAGA -s simDog_chr6.simDog.chr6 562546 36 + 593897 TATGACAGCACGCCCAGCCACCCTGAACGAAATAGA -s simHuman_chr6.simHuman.chr6 566314 36 + 601863 TATGTCAGCATTCTGGTCCACCCTAAACCAAACAGA -s simRat_chr6.simRat.chr6 71558 36 - 647215 TAAGGCAGCATCCCTGGCCACCCAATATCAAATTAA - -a -s simMouse_chr6.simMouse.chr6 597128 6 + 636262 CAGGAT -s Anc0.Anc0refChr3 195573 6 + 222631 CAGCAT -s Anc1.Anc1refChr1 35214 6 + 69767 CAGCAT -s Anc2.Anc2refChr1 112163 6 + 142988 CAGCAT -s mr.mrrefChr3 145149 6 + 181027 CAGGAT -s simCow_chr6.simCow.chr6 570571 6 + 602619 CAGCAT -s simDog_chr6.simDog.chr6 562588 6 + 593897 CAGCAT -s simHuman_chr6.simHuman.chr6 566356 6 + 601863 CAACAT -s simRat_chr6.simRat.chr6 71600 6 - 647215 CAGAAT - -a -s simMouse_chr6.simMouse.chr6 597134 54 + 636262 GGATCCTACTACTCCTCTTTTCTGTAAAAGAGTGCCTCTTAACATGCATTATCA -s Anc0.Anc0refChr3 195583 51 + 222631 GGATGCCCCCACTCCTG---TCTATAAAGTAGTGACTTTGATTATGAATTCCCT -s Anc1.Anc1refChr1 35224 51 + 69767 GGATGCCCCCACTCCTG---TCTATAAAGTAGTGACTTTGATTATGAATTCCCT -s Anc2.Anc2refChr1 112173 51 + 142988 GCATGCCCCCACTCCTG---TCTATAAAGTAGTGACTTTGATTCTGAATTCCCT -s mr.mrrefChr3 145155 51 + 181027 GGATCCTACTACTCCTC---TCTGTAAAAGAGTGCCTCTTAATATGCATTATCA -s simCow_chr6.simCow.chr6 570581 51 + 602619 TAATACCCCCACTCCTA---CTTATAAAGTAGTGACTTTGAATGTGCATTCCCC -s simDog_chr6.simDog.chr6 562598 51 + 593897 GCATGCCCCCACTCCTG---TCTATAAAGTGGTTACTTTGATTCTGAAGTAATT -s simHuman_chr6.simHuman.chr6 566366 50 + 601863 GGATTCCCCAACTCCTG---ACTATAATC-AATGACCTTGAGTATGAGTTCCCT -s simRat_chr6.simRat.chr6 71606 51 - 647215 GGATCCTACTACTCCTC---TCTGTAAAGGGGTGCCTCCTAATATGCATTATCA - -a -s simMouse_chr6.simMouse.chr6 597188 4 + 636262 CTTA -s Anc0.Anc0refChr3 195634 4 + 222631 TTTG -s Anc1.Anc1refChr1 35275 4 + 69767 TTTG -s Anc2.Anc2refChr1 112224 4 + 142988 TTTG -s mr.mrrefChr3 145206 4 + 181027 CTTA -s simCow_chr6.simCow.chr6 570632 4 + 602619 TTCC -s simDog_chr6.simDog.chr6 562650 4 + 593897 TTTG -s simHuman_chr6.simHuman.chr6 566416 4 + 601863 TTTG -s simRat_chr6.simRat.chr6 71657 4 - 647215 CTCA - -a -s simMouse_chr6.simMouse.chr6 597192 40 + 636262 GCTGGACTGTTTGAGTCTGAGGTCTCATTCTCCACATGCT -s Anc0.Anc0refChr3 195638 27 + 222631 CCTGGTCTGTCTGAGCCTGAGGT------------GT-CT -s Anc1.Anc1refChr1 35279 27 + 69767 CCTGGTCTGTCTGAGCCTGAGGT------------GT-CT -s Anc2.Anc2refChr1 112228 27 + 142988 CCTGGTTTGTCTGAGTCTGAGGT------------GT-TT -s mr.mrrefChr3 145210 39 + 181027 GCTGGACTGTCTGAGCCTGAGGTCTCATTCTCCACGT-CT -s simCow_chr6.simCow.chr6 570636 27 + 602619 CCTTGTTTATCTGAGTCTGAGGT------------GT-TT -s simDog_chr6.simDog.chr6 562656 27 + 593897 CCAGGTTTGTCTAAGTCTGATTT------------GT-TT -s simHuman_chr6.simHuman.chr6 566420 27 + 601863 CCTGGTCTGTCTGAGCCTGAGGT------------GT-CT -s simRat_chr6.simRat.chr6 71661 39 - 647215 GCTGGACTGTCTGAGCCTAAGGTCTCACTCCTGAGGT-CT - -a -s simMouse_chr6.simMouse.chr6 597232 11 + 636262 GGTATTGTCTT -s Anc0.Anc0refChr3 195665 11 + 222631 CACTCTCTTCA -s Anc1.Anc1refChr1 35306 11 + 69767 CACTCTCTTCA -s Anc2.Anc2refChr1 112255 11 + 142988 CACTCTCTTTA -s mr.mrrefChr3 145249 11 + 181027 CACTCTCTCCA -s simCow_chr6.simCow.chr6 570663 11 + 602619 CGCTCTCTTTA -s simDog_chr6.simDog.chr6 562685 11 + 593897 CACCCGCTTTA -s simHuman_chr6.simHuman.chr6 566447 11 + 601863 CACTCTCTTCA -s simRat_chr6.simRat.chr6 71700 11 - 647215 CACTCTCCCCA - -a -s simMouse_chr6.simMouse.chr6 597243 16 + 636262 TACAATTACACTATCC -s Anc0.Anc0refChr3 195677 16 + 222631 TACAACAATACTATCA -s Anc1.Anc1refChr1 35318 16 + 69767 TACAACAATACTATCA -s Anc2.Anc2refChr1 112267 16 + 142988 TGTAACATGACTGTCA -s mr.mrrefChr3 145260 16 + 181027 TACAATTATACTATCA -s simCow_chr6.simCow.chr6 570675 16 + 602619 TTTAACATGACGGTAA -s simDog_chr6.simDog.chr6 562697 9 + 593897 CG-------ACTGTCA -s simHuman_chr6.simHuman.chr6 566459 16 + 601863 TACAACAATGCTATGA -s simRat_chr6.simRat.chr6 71711 16 - 647215 TGCAATTATACTATCA - -a -s simMouse_chr6.simMouse.chr6 597259 30 + 636262 ATTGTAGTTTAATGGGGATAAGAAAATGGT -s Anc0.Anc0refChr3 195693 29 + 222631 A-TATTATTATTGGAGGAAACCAAAATGGC -s Anc1.Anc1refChr1 35334 29 + 69767 A-TATTATTATTGGAGGAAACCAAAATGGC -s Anc2.Anc2refChr1 112283 29 + 142988 A-TATTATTATTGGAGGAAACCAAAATGGC -s mr.mrrefChr3 145276 29 + 181027 A-TGTAGTTTAATGAGGATAAGAAAATGGT -s simCow_chr6.simCow.chr6 570695 29 + 602619 A-TATAATTATAGGAGGAAATCAAAATACA -s simDog_chr6.simDog.chr6 562706 29 + 593897 A-TATTATTATTGGAGGGGACCAAAATGGC -s simHuman_chr6.simHuman.chr6 566475 29 + 601863 A-TATTACTATTGGAGGAAACCAAAATGGC -s simRat_chr6.simRat.chr6 71727 29 - 647215 A-TGTAGTTTAATGAGGATAAGAAGATGGT - -a -s simMouse_chr6.simMouse.chr6 597289 17 + 636262 GCCAGATTTACATTTAT -s Anc0.Anc0refChr3 195724 17 + 222631 GCCATATTGTTTTTTCT -s Anc1.Anc1refChr1 35365 17 + 69767 GCCATATTGTTTTTTCT -s Anc2.Anc2refChr1 112314 17 + 142988 GCTATATAGTTTTTTCT -s mr.mrrefChr3 145305 17 + 181027 GCCATATTTACATTTAT -s simCow_chr6.simCow.chr6 570726 17 + 602619 GCTATAACGTCTGTTTT -s simDog_chr6.simDog.chr6 562737 17 + 593897 GCTGTATAGTTTTTTCT -s simHuman_chr6.simHuman.chr6 566506 17 + 601863 GCCATATTGTTTTTTCT -s simRat_chr6.simRat.chr6 71756 17 - 647215 GCCATATCTAGATTTAT - -a -s simMouse_chr6.simMouse.chr6 597306 35 + 636262 GAATTAGGAAATATAGTTGCTACTTTGAGCAGACA -s Anc0.Anc0refChr3 195773 30 + 222631 A-----GAATATGTAGTCGCCACATTGTACATATA -s Anc1.Anc1refChr1 35414 35 + 69767 AAACAAGAATATGTAGTCGCCACATTGTACATATA -s Anc2.Anc2refChr1 112363 30 + 142988 A-----GAATGTGTAGTCGCCACATTGTACATATA -s mr.mrrefChr3 145322 35 + 181027 GAATTAGGAAATGTAGTTGCTACTTTGAACAGACA -s simCow_chr6.simCow.chr6 570775 28 + 602619 A-----TAATGTGTAGTTGCCATGTTGTAC--ATA -s simDog_chr6.simDog.chr6 562786 30 + 593897 A-----GAATGTGTAGTCACCGCATTGAACATAGG -s simHuman_chr6.simHuman.chr6 566555 35 + 601863 AAACAAGAATATGTAGTCGCCACATTGTATATATA -s simRat_chr6.simRat.chr6 71773 35 - 647215 GAATTAGGAAATGTAGTTGCTACTTTGGACAGACA - -a -s simMouse_chr6.simMouse.chr6 597341 69 + 636262 TTGACCAACATGCCTGAAAGAGGACTGAATCTTAATATCTTAAATGCAAGCCTCACTATCTATCATGAG -s Anc0.Anc0refChr3 195805 68 + 222631 TTCACCAGCCTACCGGAAAGAGATCTGAACCTTGATATCATTAATGTAAGCCCTATCACCAGTCATG-T -s Anc1.Anc1refChr1 35451 68 + 69767 TTCACCAGCCTACCGGAAAGAGATCTGAACCTTGATATCATTAATGTAAGCCCTATCACCAGTCATG-T -s Anc2.Anc2refChr1 112395 68 + 142988 CTCCCCAGCCTACCGGAAAGAGATCTGAACCTTGATGTCATTAATGTAAGCCCTATCACCAGTCATG-T -s mr.mrrefChr3 145357 69 + 181027 TTGACCAACATGCCTGAAAGAGAACTGAATCTTAATATCTTTAATGCAAGCCTCACTATCTATCATGAG -s simCow_chr6.simCow.chr6 570805 68 + 602619 CTCCCCACCCTATTGGCAAGAGATCTGAGCCTTGATACCATTAACGAGAGCCCTACCAGCAGTCATG-T -s simDog_chr6.simDog.chr6 562818 66 + 593897 CCCCCCAGCTTCCCCGAAA--GATCTGAACCTTAATGTCATTAATATAATCCCCATCACCAGTTGTG-T -s simHuman_chr6.simHuman.chr6 566592 66 + 601863 TTCACCAGCCTACCGAAAAGGGATCTCAACCTTG--ATCATTAGTGTAAGCCCTATCACTAGACATG-T -s simRat_chr6.simRat.chr6 71808 58 - 647215 CTGACC-----------AAGAAAAGTGAATCTTAATATCTTTAATGCAAGCATCCATATCTATCATGAG - -a -s simMouse_chr6.simMouse.chr6 597410 61 + 636262 AGCCAATAATTGCTTGTGATCACACAAAGCTATGATGCTTGAGTAGAGTAACGGCATGTGA -s Anc0.Anc0refChr3 195873 54 + 222631 AGCTAACAATGGGTT-TTATCATATAAGGCCCTGGCACTTGAGGGGA------GAATGGAA -s Anc1.Anc1refChr1 35519 54 + 69767 AGCTAACAATGGGTT-TTATCATATAAGGCCCTGGCACTTGAGGGGA------GAATGGAA -s Anc2.Anc2refChr1 112463 54 + 142988 ACCTGACAATGGGTT-GTATCATATAAGGCCCTGGCACTTGAGGGGA------GAATGGAA -s mr.mrrefChr3 145426 60 + 181027 AGCCAACAATGGCTT-TTATCACACAAAGCCATGATGCTTGAGTAGAGTAACGGCATGTGA -s simCow_chr6.simCow.chr6 570873 52 + 602619 ACCTGGTAA-GAGTT-GTGTCATATAAGGCCCGGGCACTCGAGGAGA------GTA-GGGT -s simDog_chr6.simDog.chr6 562884 47 + 593897 ---TGACAATGGCGT-GTATCACATAAATACCTGGTACTT----GGA------GAATAGAA -s simHuman_chr6.simHuman.chr6 566658 54 + 601863 AGCTAACAATGGGTA-TTATTGTATAAGGCCCTGGCACTTGAGGGGA------GAATGGAG -s simRat_chr6.simRat.chr6 71893 57 - 647215 GACCAACAATGGCTT-TTATCACAC---GCCATGATGCTTGAGTAGAGTAGCAGCAGGTGA - -a -s simMouse_chr6.simMouse.chr6 597471 27 + 636262 TCATGCTTATCAATGTTCACCTGTCTA -s Anc0.Anc0refChr3 195927 27 + 222631 TCATGCTTGTCTCTGTTCACCTGTCTA -s Anc1.Anc1refChr1 35573 27 + 69767 TCATGCTTGTCTCTGTTCACCTGTCTA -s Anc2.Anc2refChr1 112524 27 + 142988 TCATCATCATCTCTGTGCACCTGTCTA -s mr.mrrefChr3 145486 27 + 181027 TCATGCTTGTCAATGTTCACCTGTCTA -s simCow_chr6.simCow.chr6 570932 27 + 602619 TCATTATCAGCACTTTCTGCCTGTCTA -s simDog_chr6.simDog.chr6 562938 27 + 593897 TCATCATCATCTCTGTGCACCTGTCTA -s simHuman_chr6.simHuman.chr6 566712 27 + 601863 CCATGCTTGTCTCTACTCACCTGTCTA -s simRat_chr6.simRat.chr6 71950 27 - 647215 TCATGATTGTCAATGTTCACCTGTCTA - -a -s simMouse_chr6.simMouse.chr6 597498 7 + 636262 CAAGAAA -s Anc0.Anc0refChr3 195963 7 + 222631 CAAAAAG -s Anc1.Anc1refChr1 35609 7 + 69767 CAAAAAG -s Anc2.Anc2refChr1 112560 7 + 142988 CAAAAAG -s mr.mrrefChr3 145522 7 + 181027 CAAGAAG -s simCow_chr6.simCow.chr6 570968 7 + 602619 CAAAAAG -s simDog_chr6.simDog.chr6 562974 7 + 593897 CAAAAAG -s simHuman_chr6.simHuman.chr6 566748 7 + 601863 AAAAGAG -s simRat_chr6.simRat.chr6 71986 7 - 647215 CAAGAAG - -a -s simMouse_chr6.simMouse.chr6 597505 51 + 636262 TGTACCTGCTACCATCACCTATACTTTTTGTTGGCATCTTTGCTTATGTCA -s Anc0.Anc0refChr3 195976 49 + 222631 TGTGTCATT--TTACCACCAATACTCTTTGATTGCATCTTTGCCTATGTCC -s Anc1.Anc1refChr1 35622 49 + 69767 TGTGTCATT--TTACCACCAATACTCTTTGATTGCATCTTTGCCTATGTCC -s Anc2.Anc2refChr1 112573 49 + 142988 TGTGTCATT--TTACCACCAATAGTCTCTGATTGCCTCTTTGCCTATGTGC -s mr.mrrefChr3 145529 49 + 181027 TGTGCCTGT--CCACCACCTATACTTTTTGTTTGCATCTTTGCTTATGTCA -s simCow_chr6.simCow.chr6 570981 49 + 602619 TGTGCCATC--TTACCACCAATAATCTCTGATTGCCTCTTTGCCTATGTGC -s simDog_chr6.simDog.chr6 562987 49 + 593897 TGTGTTATT--ATACCACAAATCGCCCCTGATTGCCTCTTCACCCAAGTGC -s simHuman_chr6.simHuman.chr6 566761 49 + 601863 TGTGTCATT--TAACCACCATCACTCTTTGATTGCAACTCTGCCTATGTCC -s simRat_chr6.simRat.chr6 71993 49 - 647215 TGTGCCTGT--CCACCACCTATACTTTATGCTTGCATCTTTGCTTATGTGA - -a -s simMouse_chr6.simMouse.chr6 597556 45 + 636262 CCAGCCCCAGATAGTTCAAATTACTGAAAGAGGGATGTTGTCTAC -s Anc0.Anc0refChr3 196028 26 + 222631 CTAGCCCTATATAGTTCAAACTACTG------------------- -s Anc1.Anc1refChr1 35674 26 + 69767 CTAGCCCTATATAGTTCAAACTACTG------------------- -s Anc2.Anc2refChr1 112625 26 + 142988 CTAACCCTATATAGTTCAAACTACTG------------------- -s mr.mrrefChr3 145581 45 + 181027 CCAGCCCCAGATAGTTCAAATTACTGAAAGAGGGATGTTGTCTAC -s simCow_chr6.simCow.chr6 571033 26 + 602619 TTAACTCTATATAGTTCAAACTACTG------------------- -s simDog_chr6.simDog.chr6 563039 23 + 593897 CTCACCCTTTATAGTTTAAACTA---------------------- -s simHuman_chr6.simHuman.chr6 566813 26 + 601863 CTAGCCTTAAATAGCTCAAACTATTG------------------- -s simRat_chr6.simRat.chr6 72045 45 - 647215 CCAGCCCCAGGTGGTTCAAATTCCTGAGAGAGGTATGTTGTCTAC - -a -s simMouse_chr6.simMouse.chr6 597601 304 + 636262 CAGAGAGGTGTGTTTGCTAGATAAACCCTCGTAGCTGCAGCCAATCAATCTATGTACGTGTCAGGCGTGCCTGGCAACTTGCCGCCTGGGGACTTGCCGTTCCCCAACGAAGCAAGACTCTATACATATATACATAAACTATTTGCAACTTGATCTATTGTACATACCTAAAGTACTGTAGCTGGTGCCCTATGAGTTGGCTATCAGCCTCAGATTCATGGAGACTGGACGCTCATTTATTAAACTTGGAGGAGAAGGATAGAATCGACCCAACCAGGATGGAATCCTTAGCTACCTCGTTAAT -s mr.mrrefChr3 145626 231 + 181027 CAGAGAGGTGTGTTTGCTAGATAAACCCTCGTAGCTGCA-CCAATCAATCTATGT-----------------------------------------------------------------------TATATACATAAACTATTTGCAACTTGATCTATTGTACATACCTAAAGTACTGTAGCTGGTGCCCTATGAGTTGGCTATCAGCCTCAGATTCATGGAGACTGGACGCTCATTTATTAAAC-TGGAGGAGAAGGATAGAATCGACCCAACCAGGATGGAATCCTTAGCTACCTCGTTAAT -s simRat_chr6.simRat.chr6 72091 231 - 647215 CAGAGAGGTGTGTTTGCTAGATCAACCCTTGATGGTGCA-CCCATCAATCCAGTT-----------------------------------------------------------------------TGTATACGTAAGTTAGGTGCATCTTGATCTATTGTACATACCTAAAGTATTGTAGCTGGTGCCCTTTGAGTTGGCTATCAGCCTCAGAGCCATGGAGAGTGGATGCTCATTTTTTCAAC-TGGAGGACAAAAATGGAATTGACCCAATCAGGATGGAATCGTTAGCTCCCTTGTTAAT - -a -s simMouse_chr6.simMouse.chr6 597905 174 + 636262 GAAGGAATAGCATGATGGATCCACCAACCAATGAGCTACATTGTGGATGAGATACCTCACTAGCCCGTAGAGACATGATAGGTATACAAAGTACAGCCATGAGGGAACACCTAAGATGCAAATACCTATTATCTGTAGGCCCACTTCCTATGATTCATCCGTGTGTTAAATTTA -s Anc0.Anc0refChr3 196054 109 + 222631 -----------------------------------------------------------------TGTATAGACATGAATGGCAGACTAAGTGTTGTCATGAGGGAATACCTGATATACAAATGCTCATCATCTGTAGTCCCACGTCCCACTGCTCATACCCGTTTCTATTCTA -s Anc1.Anc1refChr1 35700 109 + 69767 -----------------------------------------------------------------TGTATAGACATGAATGGCAGACTAAGTGTTGTCATGAGGGAATACCTGATATACAAATGCTCATCATCTGTAGTCCCACGTCCCACTGCTCATACCCGTTTCTATTCTA -s Anc2.Anc2refChr1 112651 109 + 142988 -----------------------------------------------------------------AGTATAAACATGAATGGCAGACTAAGTGTTGTCATGAGAGAATACCTGATATACAAAGGCTCATCATCTGTACTCCTGCGTCCCACTACTCTCACTCGTTTCTATTCTA -s mr.mrrefChr3 145857 174 + 181027 GAAGGAATAGCATGATGGATCCACCAACCAATGAGCTACATTGTGGATGAGATACCTCACTGGCCTGTAGAGACATGATAGGCATACAAAGTACAGCCATGAGGGAACACCTAATATGCAAATACCCATTATCTGTAGGCCCACTTCCTATGGTTCATCCCTGTGTTTAATCTA -s simCow_chr6.simCow.chr6 571059 109 + 602619 -----------------------------------------------------------------AGTACTAACATGAATGGCATACTAAGTGTTGTCATGAAGGAATACCCGATATACAAAGGGTCATTATCTGTACTCCTGCTTCCCACTACTCTCACTTGTTTTTATTCTG -s simDog_chr6.simDog.chr6 563062 90 + 593897 ------------------------------------------------------------------GTATAAAGATGATTGGCAGACAAGGTGTTGTCATGAGAGAATACCTGGTATACAAAGGCACATCATGTG---------GTTCTACT---------CCTTTCTATTCTA -s simHuman_chr6.simHuman.chr6 566839 108 + 601863 -----------------------------------------------------------------TGTATAGACATGAACAGCAGACTAAGCGTTGTCAT-ACGGAATACCTGATATAAAAATGTTCATCATCTGTAGTCACACGTCCCACTGCTCATGCCCGTTTCTATTCTA -s simRat_chr6.simRat.chr6 72326 172 - 647215 GAAGGAATAGTCTGATGGATCCACCAACCAATGAGCTACATTGTGGATGAGATACCTCACTGGACTGCAGAGACATGATAGGCACACAAAGTACAGCTATGAGGGAACACCTAATATGCAAATACCCATTATCTGTAGGCCCAC--CCTATGGTTCATCCCTGTGTTTAATCTA - -a -s simMouse_chr6.simMouse.chr6 598079 18 + 636262 GCCCTCAAGGCATAATAG -s Anc0.Anc0refChr3 196163 18 + 222631 GCCTTCAAGATATAATAG -s Anc1.Anc1refChr1 35809 18 + 69767 GCCTTCAAGATATAATAG -s Anc2.Anc2refChr1 112760 18 + 142988 GCATTCAAGATATAATAG -s mr.mrrefChr3 146031 18 + 181027 GCCCTCAAGGCATAATAG -s simCow_chr6.simCow.chr6 571168 12 + 602619 GCATTCAAGATA------ -s simDog_chr6.simDog.chr6 563152 18 + 593897 GCATTCAAGATATAATAG -s simHuman_chr6.simHuman.chr6 566948 18 + 601863 GGCTTCAAGATATAATAG -s simRat_chr6.simRat.chr6 72498 18 - 647215 GCCGTCAAGGCGTAATAG - -a -s simMouse_chr6.simMouse.chr6 598097 21 + 636262 CCATAGGGGTTTGACCCTAGC -s Anc0.Anc0refChr3 196183 20 + 222631 CTATCGTGGTAATACCTTAG- -s Anc1.Anc1refChr1 35829 21 + 69767 CTATCGTGGTAATACCTTAGC -s Anc2.Anc2refChr1 112780 20 + 142988 CTATCGTGGTAATACCTTAG- -s mr.mrrefChr3 146049 21 + 181027 CCATAGTGGTTTGACCCTAGC -s simCow_chr6.simCow.chr6 571182 10 + 602619 TTATC-TGGCA---------- -s simDog_chr6.simDog.chr6 563172 20 + 593897 CTATCGTGATTATACCTTAG- -s simHuman_chr6.simHuman.chr6 566968 21 + 601863 CTGTTGTGGTAATACCTTAGC -s simRat_chr6.simRat.chr6 72516 21 - 647215 CCATAGTGGTTTGACCCTAGC - -a -s simMouse_chr6.simMouse.chr6 598118 70 + 636262 AAGGGCTTTCAGACCACAAATTCAAGAATATTCCCATAGCATAGTATATTGAGGAAGACATGGGATCTTG -s Anc0.Anc0refChr3 196203 42 + 222631 ---GATTTGCACAACACACAATCAAGAATATTTCCATTGTCTAGT------------------------- -s Anc1.Anc1refChr1 35850 43 + 69767 A--GATTTGCACAACACACAATCAAGAATATTTCCATTGTCTAGT------------------------- -s Anc2.Anc2refChr1 112800 42 + 142988 ---GATTTGCACAACACACAATCAAGAATATTTCCATTGGCTAGT------------------------- -s mr.mrrefChr3 146070 68 + 181027 A--GGCTTTCAGACCACAAAATCAAGAATATTCCCATAGTATAGTATATTGAGGAAGACATGGGATCTTG -s simCow_chr6.simCow.chr6 571192 39 + 602619 ------TTGCATGATACACAATTCAAAATAGTTCCACTGGATGGT------------------------- -s simDog_chr6.simDog.chr6 563192 42 + 593897 ---GATTTGCACAACACCCCATCACGAAGATTTCCATTGGCTAGT------------------------- -s simHuman_chr6.simHuman.chr6 566990 43 + 601863 A--GATTTGCACAAGACACAATCAAGAATATTTCCATTGTCTAGT------------------------- -s simRat_chr6.simRat.chr6 72537 68 - 647215 A--GGCATTCATACCTCAAAATCAAGAATAATCCCATAGTATAATATAGTGAGGAAGACGTGGAATCTTG - -a -s simMouse_chr6.simMouse.chr6 598188 61 + 636262 TTGGCTCCTTGTTCAGTGGAATCAATCCCTCCAGTTCAATCGACGAAGGGGCTATGGTGGA -s Anc0.Anc0refChr3 196245 15 + 222631 ----------------------------------------------AGTGGCTCTAGTAAA -s Anc1.Anc1refChr1 35893 15 + 69767 ----------------------------------------------AGTGGCTCTAGTAAA -s Anc2.Anc2refChr1 112842 15 + 142988 ----------------------------------------------AGTGGCTCTAGTAAA -s mr.mrrefChr3 146138 61 + 181027 TTGGCTCCTTGTTCAGTGGAATCAATCCCTCCAGTTCAATCGACGAAGGGGCTATGGTGAA -s simCow_chr6.simCow.chr6 571231 15 + 602619 ----------------------------------------------AGCAGCTCTAGTAAG -s simDog_chr6.simDog.chr6 563234 15 + 593897 ----------------------------------------------TGTGGGTCTCATAAA -s simHuman_chr6.simHuman.chr6 567033 15 + 601863 ----------------------------------------------AGTGGCTCTAGTAAA -s simRat_chr6.simRat.chr6 72613 61 - 647215 TTGACTCCTCATTCAGCGAAATCCATCCCTGCAGTTCAACCGATGAAGGGGCTATGGTGAA - -a -s simMouse_chr6.simMouse.chr6 598249 5 + 636262 AGTGG -s Anc0.Anc0refChr3 196260 5 + 222631 GCTGG -s Anc1.Anc1refChr1 35908 5 + 69767 GCTGG -s Anc2.Anc2refChr1 112857 5 + 142988 GCTCG -s mr.mrrefChr3 146199 5 + 181027 GGTGG -s simCow_chr6.simCow.chr6 571246 5 + 602619 TGTAG -s simDog_chr6.simDog.chr6 563256 5 + 593897 GCTCA -s simHuman_chr6.simHuman.chr6 567048 5 + 601863 GCTGG -s simRat_chr6.simRat.chr6 72674 5 - 647215 GGTGG - -a -s simMouse_chr6.simMouse.chr6 598254 78 + 636262 GTTCAGTGAGTCTAAGGAGATTCCAGTGCTTGCAGGAACTGCAGAGATACAACCAATATATCATGTTCCACTGGTCCT -s Anc0.Anc0refChr3 196267 40 + 222631 ACTCA------------------------------------CAGTGATAGCATC--TGGATAATGTTCCACAGGTCTT -s Anc1.Anc1refChr1 35915 40 + 69767 ACTCA------------------------------------CAGTGATAGCATC--TGGATAATGTTCCACAGGTCTT -s Anc2.Anc2refChr1 112864 40 + 142988 GCTCA------------------------------------CAGTGATAGCATA--TGGATAATGTTCCACAGGTCTT -s mr.mrrefChr3 146204 75 + 181027 ATTCAGTGAGTCTAAGGA-ATTCCAGTGCTTGCAGGAACTGCAGAGATACAACC--TATATCATGTTCCACAGGTCCT -s simCow_chr6.simCow.chr6 571253 40 + 602619 CTACA------------------------------------CAATGATATCATA--TGGATCATGTTCCACAGGTCCT -s simDog_chr6.simDog.chr6 563263 40 + 593897 GCTCA------------------------------------CAGTGATAGCATA--TGGATAATGTTCCACAGGACTT -s simHuman_chr6.simHuman.chr6 567055 40 + 601863 ACTCA------------------------------------CAGTGGTAGGATC--TGAACAAAGTTCCACAGGTCTT -s simRat_chr6.simRat.chr6 72679 75 - 647215 ATTTAGTGGGTCTAATGA-ATGCCAGTGCTTGCAGGAAATGCAGAGATCCATCC--TGTATCATATTCGACAGGTCCT - -a -s simMouse_chr6.simMouse.chr6 598332 49 + 636262 GTAAGCCCCAAGACATTAAGGGGTAATGACCATCCCAAGATTTCATCCT -s Anc0.Anc0refChr3 196307 33 + 222631 ATGA----------------GGATAATGACTGCCACAAGATTTGTTCTT -s Anc1.Anc1refChr1 35955 33 + 69767 ATGA----------------GGATAATGACTGCCACAAGATTTGTTCTT -s Anc2.Anc2refChr1 112921 33 + 142988 ATGA----------------AGATAATGACTGCCACAAGATTTGTTCTT -s mr.mrrefChr3 146279 48 + 181027 ATAAGCCCCAAGAC-TTAAGGGGTAATGACCACCCCAAGATTTCATCTT -s simCow_chr6.simCow.chr6 571310 33 + 602619 ATGA----------------AGATAATGACTGCCACGAGATTTGTTCTT -s simDog_chr6.simDog.chr6 563320 32 + 593897 ATGA----------------AGATAA-GACTGCCGCAAGATTTGTTCCT -s simHuman_chr6.simHuman.chr6 567095 33 + 601863 ATGA----------------GGACAATGACTGCCACAGGATTTGTTCTT -s simRat_chr6.simRat.chr6 72754 48 - 647215 ATAAGTCCCAAGAC-TTAACAGGTAGTAATCACCCCAAGATTTCCTCTT - -a -s simMouse_chr6.simMouse.chr6 598381 29 + 636262 TGTTTAACCGCTTTGACACATCAATTCAC -s Anc0.Anc0refChr3 196340 29 + 222631 TTTTCTACCACTTTGACTTACTGACTCAC -s Anc1.Anc1refChr1 35988 29 + 69767 TTTTCTACCACTTTGACTTACTGACTCAC -s Anc2.Anc2refChr1 112954 29 + 142988 TTTTCTACCACATTAACTTACTGACTCAC -s mr.mrrefChr3 146327 29 + 181027 TGTTCAACCACTTTGACTCATCAACTCAC -s simCow_chr6.simCow.chr6 571343 29 + 602619 TTTTCCACCACATTAACTTACTAACTCAC -s simDog_chr6.simDog.chr6 563397 23 + 593897 TTTTCTAC------AATTTACTGACACAC -s simHuman_chr6.simHuman.chr6 567128 29 + 601863 TTTTCTGCCACTTTGACTTACACACTCAC -s simRat_chr6.simRat.chr6 72802 25 - 647215 TGTTCAACCACTTTAACTCATCAAC---- - -a -s simMouse_chr6.simMouse.chr6 598410 32 + 636262 AGGTTTTTCAGAGATTGCTCCTGGAATACTAC -s Anc0.Anc0refChr3 196369 32 + 222631 AGGTATTTCAAAGATTAGTTCTGGACCACTAC -s Anc1.Anc1refChr1 36017 32 + 69767 AGGTATTTCAAAGATTAGTTCTGGACCACTAC -s Anc2.Anc2refChr1 112983 32 + 142988 AGGTATTTCAAAGATCAGTTCTGGACCACTAC -s mr.mrrefChr3 146356 32 + 181027 AGGTTTTTCAAAGATTACTCCTGGAATACTAC -s simCow_chr6.simCow.chr6 571417 32 + 602619 AGATCATTCAAAGATCAGTTCCAGACCAATAT -s simDog_chr6.simDog.chr6 563420 32 + 593897 AGGTATTTTGAAGATCAATTCTGGACCACTAC -s simHuman_chr6.simHuman.chr6 567157 31 + 601863 AGGTAGTTCAAAGATTAGTTCTGAACAACC-C -s simRat_chr6.simRat.chr6 72827 22 - 647215 ----------AAGATTACTCCTGGAATACTAC - -a -s simMouse_chr6.simMouse.chr6 598442 4 + 636262 ATTT -s Anc0.Anc0refChr3 196401 4 + 222631 TGGT -s Anc1.Anc1refChr1 36049 4 + 69767 TGGT -s Anc2.Anc2refChr1 113019 4 + 142988 TGGT -s mr.mrrefChr3 146388 4 + 181027 ATTT -s simCow_chr6.simCow.chr6 571453 3 + 602619 T-GT -s simDog_chr6.simDog.chr6 563456 4 + 593897 TGGT -s simHuman_chr6.simHuman.chr6 567188 4 + 601863 TGGT -s simRat_chr6.simRat.chr6 72849 4 - 647215 ATTC - -a -s simMouse_chr6.simMouse.chr6 598446 119 + 636262 GGATTGCAACCATTTACTTATGGTCATTTGTGATAGCTTTCACTTCCCTTGACTATGATTTGCCTTGGCCATCATTTGATTAGCACTTGTAGAATCAACCCCACCAATAAAGCACACTA -s Anc0.Anc0refChr3 196405 119 + 222631 GGACTTGAATGATTAACCTATGGCCATTTGTCATTGCTTTCAATTCTTATGTGTATTATTTGTCTCAGCCATCACATGATTAGCACTTGAAGAATCAACCCACCTGAAATAGTCACTTA -s Anc1.Anc1refChr1 36053 119 + 69767 GGACTTGAATGATTAACCTATGGCCATTTGTCATTGCTTTCAATTCTTATGTGTATTATTTGTCTCAGCCATCACATGATTAGCACTTGAAGAATCAACCCACCTGAAATAGTCACTTA -s Anc2.Anc2refChr1 113023 119 + 142988 GGACCTGAATGATTAATCTATGGCCATCTGTCATTGCTTTTAATTCTTATGTGTATTATTTGTCTCAGTCATCACATGATTAACACTTTAAGAACCAACCCACCTGAAATAGTCACTTC -s mr.mrrefChr3 146392 119 + 181027 GGATTCTAAACATTTACTTATGGTCATTTGTCATAGCTTTCACTTCCCTTGTCTATGATTTGCCTTGGCCATCATATGATTAGCACTTGTAGAATCAACCCCACCAATAAAGCACACTA -s simCow_chr6.simCow.chr6 571456 107 + 602619 TGATCTCAATGATCAGTCTATGATCATGTGTCATTGCTTCTAAATCCTATGTGGATTATTTGCCTCAGTCATCACATGATTAA------------CAACCCAACTGAAATAGTCATTTC -s simDog_chr6.simDog.chr6 563462 118 + 593897 GAACCTGAATGTTTAATCTATGGCCATCCGTCATTGCTTTTGATCCTTATGTGTATTATTTGTCTAAGTCATCATAGGATTCACACTTTAAGAACCAACGCACCTGAAATAGTCACTT- -s simHuman_chr6.simHuman.chr6 567192 119 + 601863 GGAATAGAATGATTGCCCTATGGCTATTTGTCATGGCTTGCAATTCTTATGTTTATTACTTGTCTCAGCCACCACCTGATTAGCTCTTGAAAAATCAACCCGGGTGAGATAGTGACTTA -s simRat_chr6.simRat.chr6 72853 118 - 647215 AGATTCTGCACATTTACTTACAGTCATTTGTCATAGCTTTCAGTTCCCTTGTCTATGA-TTGCCTTGGCCATCATATGATCAGCACTTATAGAATCAACCCCACCAATAGAGCACACTA - -a -s simMouse_chr6.simMouse.chr6 598565 37 + 636262 CAATATTTCCTTCAATATCCAGGTTCAGAAACTGAGA -s Anc0.Anc0refChr3 196526 22 + 222631 TATC---------------TGGACTTGGAATCTGAGG -s Anc1.Anc1refChr1 36174 22 + 69767 TATC---------------TGGACTTGGAATCTGAGG -s Anc2.Anc2refChr1 113144 22 + 142988 TTTC---------------TGGACTTAAAATCTGAGG -s mr.mrrefChr3 146511 22 + 181027 CAAT---------------CAGATTCGGAAACTGAGG -s simCow_chr6.simCow.chr6 571565 21 + 602619 TTTC---------------TGGA-TTCAGGTCTCAAG -s simDog_chr6.simDog.chr6 563580 19 + 593897 ---C---------------TGGACTTAAAATCTGAGG -s simHuman_chr6.simHuman.chr6 567313 22 + 601863 TACC---------------TGGAGTTGGAACCTGAGG -s simRat_chr6.simRat.chr6 72971 22 - 647215 CAAT---------------CAGATTCGGAGACTGAGG - -a -s simMouse_chr6.simMouse.chr6 598602 22 + 636262 ACAACCTTCAGACACCTATCTT -s Anc0.Anc0refChr3 196548 22 + 222631 GCAATTTTCAGATATCACCCTT -s Anc1.Anc1refChr1 36196 22 + 69767 GCAATTTTCAGATATCACCCTT -s Anc2.Anc2refChr1 113167 22 + 142988 ACAATTTTCAGATATCACCCTT -s mr.mrrefChr3 146533 22 + 181027 GCAACCTTCAGACATCTATCTT -s simCow_chr6.simCow.chr6 571587 16 + 602619 ACAATTTTCAGATACC------ -s simDog_chr6.simDog.chr6 563600 22 + 593897 ACAATTTTCACACATCACCCTT -s simHuman_chr6.simHuman.chr6 567335 22 + 601863 GAAGTTTTCAGATATCACCCTT -s simRat_chr6.simRat.chr6 72993 22 - 647215 GCAACCTTCAGACATGTATCTT - -a -s simMouse_chr6.simMouse.chr6 598624 11 + 636262 CCTACGGGCAA -s Anc0.Anc0refChr3 196572 11 + 222631 CCCACCGCAGA -s Anc1.Anc1refChr1 36220 11 + 69767 CCCACCGCAGA -s Anc2.Anc2refChr1 113191 11 + 142988 CCCACCACAGA -s mr.mrrefChr3 146555 11 + 181027 CCTACGGCAAA -s simCow_chr6.simCow.chr6 571605 11 + 602619 CCCACCACAGA -s simHuman_chr6.simHuman.chr6 567359 11 + 601863 CCCACTGCAGA -s simRat_chr6.simRat.chr6 73015 11 - 647215 CCTATGGCAAA - -a -s simMouse_chr6.simMouse.chr6 598635 14 + 636262 AGAATTTAGATGAA -s Anc0.Anc0refChr3 196587 14 + 222631 TGAATTTAGGTGAG -s Anc1.Anc1refChr1 36235 14 + 69767 TGAATTTAGGTGAG -s Anc2.Anc2refChr1 113206 14 + 142988 TGAATTTAGATGTG -s mr.mrrefChr3 146566 14 + 181027 AGAATTTAGGTGAA -s simCow_chr6.simCow.chr6 571620 14 + 602619 TGAATTTAGATGTG -s simHuman_chr6.simHuman.chr6 567374 14 + 601863 TGAATTTAGGTGAG -s simRat_chr6.simRat.chr6 73026 14 - 647215 ATAATTTAGGTGAA - -a -s simMouse_chr6.simMouse.chr6 598649 21 + 636262 CATATGGCTTAAAAATAATTG -s Anc0.Anc0refChr3 196601 20 + 222631 CTTATGGCTAGAAAGTAG-TA -s Anc1.Anc1refChr1 36249 20 + 69767 CTTATGGCTAGAAAGTAG-TA -s Anc2.Anc2refChr1 113220 20 + 142988 CTTATGGCTAGAAAGCAG-TA -s mr.mrrefChr3 146580 20 + 181027 CATATGGCTTGAAAATAA-TG -s simCow_chr6.simCow.chr6 571637 20 + 602619 CTTAGAGCTACACAGGAG-CA -s simDog_chr6.simDog.chr6 563623 20 + 593897 CTTATGGCTAGAAAGCAG-TA -s simHuman_chr6.simHuman.chr6 567388 20 + 601863 CTTGTGGCTAGAAAGTTG-TA -s simRat_chr6.simRat.chr6 73041 20 - 647215 CATATGGCTTGAAAATAA-TG - -a -s simMouse_chr6.simMouse.chr6 598670 11 + 636262 GCCTCGGAATG -s Anc0.Anc0refChr3 196621 11 + 222631 CCCTTGGGATG -s Anc1.Anc1refChr1 36269 11 + 69767 CCCTTGGGATG -s Anc2.Anc2refChr1 113241 11 + 142988 CCCTTGGGATG -s mr.mrrefChr3 146600 11 + 181027 GCCTCGGAATG -s simCow_chr6.simCow.chr6 571658 11 + 602619 CCATGGGGATG -s simDog_chr6.simDog.chr6 563644 11 + 593897 CCCTTGGGATG -s simHuman_chr6.simHuman.chr6 567408 11 + 601863 CCTTTGGGATG -s simRat_chr6.simRat.chr6 73061 11 - 647215 GCCTCAGAATG - -a -s simMouse_chr6.simMouse.chr6 598681 9 + 636262 GGATTTGGT -s Anc0.Anc0refChr3 196654 9 + 222631 AGACTCCAT -s Anc1.Anc1refChr1 36302 9 + 69767 AGACTCCAT -s Anc2.Anc2refChr1 113274 9 + 142988 AGACTCCAT -s mr.mrrefChr3 146611 9 + 181027 GGATTTGAT -s simCow_chr6.simCow.chr6 571689 9 + 602619 AGACTCCAT -s simDog_chr6.simDog.chr6 563677 9 + 593897 AGACTCCAT -s simHuman_chr6.simHuman.chr6 567441 9 + 601863 AGACTCCAT -s simRat_chr6.simRat.chr6 73072 9 - 647215 GGATTTGAT - -a -s simMouse_chr6.simMouse.chr6 598690 3 + 636262 TAC -s Anc0.Anc0refChr3 196685 3 + 222631 TGT -s Anc1.Anc1refChr1 36333 3 + 69767 TGT -s Anc2.Anc2refChr1 113305 3 + 142988 TGT -s mr.mrrefChr3 146620 3 + 181027 TGT -s simCow_chr6.simCow.chr6 571720 3 + 602619 TGC -s simDog_chr6.simDog.chr6 563708 3 + 593897 TGT -s simHuman_chr6.simHuman.chr6 567472 3 + 601863 TGT -s simRat_chr6.simRat.chr6 73081 3 - 647215 TGT - -a -s simMouse_chr6.simMouse.chr6 598693 48 + 636262 GCACAGTGTACTTCATACATAAACATTGTCTGAGTCGCCGTGCTATAA -s Anc0.Anc0refChr3 196690 48 + 222631 ACACAGTGTACTTCATACATACTCTTTGCCTGTGTACCCATACTACAA -s Anc1.Anc1refChr1 36338 48 + 69767 ACACAGTGTACTTCATACATACTCTTTGCCTGTGTACCCATACTACAA -s Anc2.Anc2refChr1 113310 48 + 142988 ACATAGTATACTCCATGCATACTCTTTACCTGTGTACCCATACTACAA -s mr.mrrefChr3 146623 48 + 181027 GCACAGTGTACTTCATACGTAAACATTGCCTGAGTAGCCATACTATAA -s simCow_chr6.simCow.chr6 571725 48 + 602619 ACAAAGCATACTACATGCATACTTTTTACCTGCTACCCAATGCTACAA -s simDog_chr6.simDog.chr6 563713 43 + 593897 AATTAGTATAATCCATGCATACACT-----TGTGTACCCATACTATAG -s simHuman_chr6.simHuman.chr6 567477 48 + 601863 ACACAGAGTGCTTCATACCTACTCTTTGCCTGTGTACCCCTACCACAA -s simRat_chr6.simRat.chr6 73084 47 - 647215 CCACAGTGTACTT-ATATGTAGACACGGCCTGAGTAGCCATACTATAA - -a -s simMouse_chr6.simMouse.chr6 598741 32 + 636262 GTATACAAAATATTCAGAAGAAAATAGTACAT -s Anc0.Anc0refChr3 196740 31 + 222631 AGATACAAAATATCCAGAAG-AAAAATTACAC -s Anc1.Anc1refChr1 36388 31 + 69767 AGATACAAAATATCCAGAAG-AAAAATTACAC -s Anc2.Anc2refChr1 113360 31 + 142988 AGATAGAAAATATCCAGAAG-AAAAATTACAC -s mr.mrrefChr3 146671 31 + 181027 GGATACAAAATATTCAGAAG-AAATAATACAT -s simCow_chr6.simCow.chr6 571775 31 + 602619 CGATAGAAAATATCTAGAAT-AAAAATTACAC -s simDog_chr6.simDog.chr6 563758 31 + 593897 AGATAGAAAATATCCAGAAG-AAAAAATGCAC -s simHuman_chr6.simHuman.chr6 567527 31 + 601863 TGTTGCAAAATATCCAGAAG-AGAGATTACAC -s simRat_chr6.simRat.chr6 73131 30 - 647215 GGATACAAGATATTCTGAAG--AATAATACAT - -a -s simMouse_chr6.simMouse.chr6 598773 12 + 636262 TTTTATTCCAGT -s Anc0.Anc0refChr3 196772 12 + 222631 TACTATACCAGT -s Anc1.Anc1refChr1 36420 12 + 69767 TACTATACCAGT -s Anc2.Anc2refChr1 113392 12 + 142988 TACTATACCTGT -s mr.mrrefChr3 146702 12 + 181027 TTCTATTCCAGT -s simCow_chr6.simCow.chr6 571807 12 + 602619 TACTTTACCTGT -s simDog_chr6.simDog.chr6 563790 8 + 593897 ----ATACCTAT -s simHuman_chr6.simHuman.chr6 567559 12 + 601863 CCCCATACCAGA -s simRat_chr6.simRat.chr6 73161 12 - 647215 TTCTATCCCCAG - -a -s simMouse_chr6.simMouse.chr6 598785 8 + 636262 TAGTTGCT -s Anc0.Anc0refChr3 196784 8 + 222631 TATTACCT -s Anc1.Anc1refChr1 36432 8 + 69767 TATTACCT -s Anc2.Anc2refChr1 113404 8 + 142988 TATAACCT -s mr.mrrefChr3 146714 8 + 181027 TAGTTCCT -s simCow_chr6.simCow.chr6 571819 8 + 602619 TATAACTG -s simDog_chr6.simDog.chr6 563798 8 + 593897 TATAACCT -s simHuman_chr6.simHuman.chr6 567571 8 + 601863 TATTACCT -s simRat_chr6.simRat.chr6 73174 8 - 647215 TAGTTCCT - -a -s simMouse_chr6.simMouse.chr6 598793 27 + 636262 CCATATAACTCCAGGGCGGTGGCCTGG -s Anc0.Anc0refChr3 196792 27 + 222631 ACATATAACTACAGGGCTTTGTCTTGG -s Anc1.Anc1refChr1 36440 27 + 69767 ACATATAACTACAGGGCTTTGTCTTGG -s Anc2.Anc2refChr1 113412 27 + 142988 ACATATAACCACTGTGCTTGTTGTTGG -s mr.mrrefChr3 146722 27 + 181027 ACATATAACTCCAGGGCGGTGTCCTGG -s simCow_chr6.simCow.chr6 571829 15 + 602619 ACACAT------------TAATGTTGG -s simDog_chr6.simDog.chr6 563806 27 + 593897 ACATGTAACCACTGTGCTTGTTGTTGG -s simHuman_chr6.simHuman.chr6 567579 27 + 601863 ACATATAACTATAGGGCTTTGTCTTGG -s simRat_chr6.simRat.chr6 73182 27 - 647215 ACATATAACTGCAGGGCGGTCTCCTGG - -a -s simMouse_chr6.simMouse.chr6 598820 7 + 636262 GAACATT -s Anc0.Anc0refChr3 196820 7 + 222631 GGTGATA -s Anc1.Anc1refChr1 36468 7 + 69767 GGTGATA -s Anc2.Anc2refChr1 113440 7 + 142988 AGTGAGA -s mr.mrrefChr3 146749 7 + 181027 GAACATA -s simCow_chr6.simCow.chr6 571845 6 + 602619 AGTCA-A -s simDog_chr6.simDog.chr6 563834 7 + 593897 AGTGAGA -s simHuman_chr6.simHuman.chr6 567607 7 + 601863 GGTGATA -s simRat_chr6.simRat.chr6 73209 7 - 647215 GAACATA - -a -s simMouse_chr6.simMouse.chr6 598827 40 + 636262 CATCATACAAATGATTGTGCTCAATTTCTCCATTGTGTGG -s Anc0.Anc0refChr3 196827 34 + 222631 CATGGTGCAAATGATTGGGCACCATTTCCATAT------G -s Anc1.Anc1refChr1 36475 40 + 69767 CATGGTGCAAATGATTGGGCACCATTTCCATATTGTATGG -s Anc2.Anc2refChr1 113449 34 + 142988 CATGGTGCAAATGATTAGACACCATTTCCATAT------A -s mr.mrrefChr3 146756 40 + 181027 CATCATACAAATGATTGTGCTCCATTTCTCCATTGTGTGG -s simCow_chr6.simCow.chr6 571853 34 + 602619 CATGGTACAAATGATTCGAACCCATTTCCATAT------A -s simDog_chr6.simDog.chr6 563843 33 + 593897 CATGGTGCACATGATTAGACACCA-TTCCATAT------A -s simHuman_chr6.simHuman.chr6 567614 40 + 601863 GATGGTGCTAATGATTGGGCACGATTTCCATATTGTATGG -s simRat_chr6.simRat.chr6 73216 40 - 647215 CATCATACAAATGATTGCACTCCATTTTTCCATAGTGTGG - -a -s simMouse_chr6.simMouse.chr6 598867 48 + 636262 AGCTGCTTCTGTGCCTCAAGGATGGTCTTCATTATCATTTTCAGCCTG -s Anc0.Anc0refChr3 196861 35 + 222631 AGCTACATCTGTGCCCCATGGATGTTCTT-------------AGGCCC -s Anc1.Anc1refChr1 36515 35 + 69767 AGCTACATCTGTGCCCCATGGATGTTCTT-------------AGGCCC -s Anc2.Anc2refChr1 113483 35 + 142988 AGCTACATCAGTGCCCCATGGATGTTCTT-------------GGGCCT -s mr.mrrefChr3 146796 48 + 181027 AGCTGCATCTGTGCCTCATGGATGGTCTTCATTATCATTTTCAGCCTC -s simCow_chr6.simCow.chr6 571890 35 + 602619 AGGAACATTGGTGCCTTGTGGATATTCCT-------------GGGCCT -s simDog_chr6.simDog.chr6 563876 35 + 593897 AGCTACATCAGTGCCCCATGGATGTCCTT-------------GTGCCT -s simHuman_chr6.simHuman.chr6 567654 35 + 601863 AGTTACATCTGTGCCACATGGATGTTCTT-------------AGGCCC -s simRat_chr6.simRat.chr6 73256 48 - 647215 AGCTGCATTTGTGCCTCATGGATGGTCTTCGTTGTCACTTTCAGCCTC - -a -s simMouse_chr6.simMouse.chr6 598915 29 + 636262 TTTAGTTCAGCATTTTAATGTAGGTTTTG -s Anc0.Anc0refChr3 196896 28 + 222631 TTAACTTTAGCATTTCAATGTAGGTTTT- -s Anc1.Anc1refChr1 36550 29 + 69767 TTAACTTTAGCATTTCAATGTAGGTTTTG -s Anc2.Anc2refChr1 113519 28 + 142988 TTAACTTTAGCATTTCATTGTAGGTTTT- -s mr.mrrefChr3 146844 29 + 181027 TTTAGTTCAGCATTTTAATGTAGGTTTTG -s simCow_chr6.simCow.chr6 571926 28 + 602619 TATGCTTTAGTATCTCATTGTAGATTTT- -s simDog_chr6.simDog.chr6 563912 28 + 593897 TTAACTTTAGCATTTCATTGTAGGCTTT- -s simHuman_chr6.simHuman.chr6 567689 29 + 601863 TTAATTTTAGCATGTCAATGTAGGTTTTG -s simRat_chr6.simRat.chr6 73304 29 - 647215 TTTAGTTCAGCATTTTAATGTTGGTTATA - -a -s simMouse_chr6.simMouse.chr6 598944 2 + 636262 TG -s Anc0.Anc0refChr3 196928 2 + 222631 TG -s Anc1.Anc1refChr1 36584 2 + 69767 TG -s Anc2.Anc2refChr1 113551 2 + 142988 TG -s mr.mrrefChr3 146873 2 + 181027 TG -s simCow_chr6.simCow.chr6 571958 2 + 602619 TG -s simDog_chr6.simDog.chr6 563944 2 + 593897 TA -s simHuman_chr6.simHuman.chr6 567723 2 + 601863 TG -s simRat_chr6.simRat.chr6 73333 2 - 647215 TG - -a -s simMouse_chr6.simMouse.chr6 598946 14 + 636262 TCGATACACATAGC -s Anc0.Anc0refChr3 196930 14 + 222631 TGGGCATTCATAGC -s Anc1.Anc1refChr1 36586 14 + 69767 TGGGCATTCATAGC -s Anc2.Anc2refChr1 113553 14 + 142988 CGGGCATTCATTGC -s mr.mrrefChr3 146875 14 + 181027 TGGACACACATAGC -s simCow_chr6.simCow.chr6 571960 14 + 602619 GGGGCATTCATTGG -s simDog_chr6.simDog.chr6 563947 14 + 593897 CAGGCATTCATTAC -s simHuman_chr6.simHuman.chr6 567725 14 + 601863 TGGGCATTCATAGC -s simRat_chr6.simRat.chr6 73335 14 - 647215 TGGACACATATAGC - -a -s simMouse_chr6.simMouse.chr6 598960 37 + 636262 AATTTTTTTGAGATAACATACTAGTTCCATTGGGGGT -s Anc0.Anc0refChr3 196944 37 + 222631 AATTTCTTGAGGATAACATTCTAGTTTTATCAAGGGT -s Anc1.Anc1refChr1 36600 37 + 69767 AATTTCTTGAGGATAACATTCTAGTTTTATCAAGGGT -s Anc2.Anc2refChr1 113567 37 + 142988 AATTTCTTGAGGATAACATTCTAGTTTTATCAAAGTT -s mr.mrrefChr3 146889 37 + 181027 AATTTTTTTAAGATAACATTCTAGTTCCATCGGGGGT -s simCow_chr6.simCow.chr6 571974 37 + 602619 AATTCCTTGAGCACAACTTTCTAGTTCTGCCAACGTT -s simDog_chr6.simDog.chr6 563961 37 + 593897 ACTTTCTTGAGGATAACATTCTAGTTTTATCAAAGTT -s simHuman_chr6.simHuman.chr6 567740 37 + 601863 AATTTCTTGAGGATGACGTCCTAGTTTTATCATGGGC -s simRat_chr6.simRat.chr6 73349 37 - 647215 AATTTTTTTAAGATAACATTCTAGTCCCATCGGGGTT - -a -s simMouse_chr6.simMouse.chr6 598997 8 + 636262 CAACATAG -s Anc0.Anc0refChr3 196985 8 + 222631 CAACATTT -s Anc1.Anc1refChr1 36641 8 + 69767 CAACATTT -s Anc2.Anc2refChr1 113608 8 + 142988 CAACATTT -s mr.mrrefChr3 146926 8 + 181027 CAACATTG -s simCow_chr6.simCow.chr6 572015 8 + 602619 CAACATCA -s simDog_chr6.simDog.chr6 564002 8 + 593897 CAACATTT -s simHuman_chr6.simHuman.chr6 567781 7 + 601863 CAACATT- -s simRat_chr6.simRat.chr6 73386 8 - 647215 CAAGATTG - -a -s simMouse_chr6.simMouse.chr6 599005 27 + 636262 GGAATTAGTCATTATATGGCTGCAATA -s Anc0.Anc0refChr3 196993 26 + 222631 AGAATTAGTCATTATATGGCTGC-ATT -s Anc1.Anc1refChr1 36649 26 + 69767 AGAATTAGTCATTATATGGCTGC-ATT -s Anc2.Anc2refChr1 113617 26 + 142988 AGAATTAGTCATTATATGGCTGC-AAT -s mr.mrrefChr3 146934 27 + 181027 GGAATTAGTCATTATATGGCTGCAATA -s simCow_chr6.simCow.chr6 572024 26 + 602619 AGAATTAGTCAGTATAGGACTGT-AAT -s simDog_chr6.simDog.chr6 564011 26 + 593897 AGAATTAGTCATTATATGGCTGC-AAT -s simHuman_chr6.simHuman.chr6 567788 23 + 601863 ---CTTAGCCACTATATGGCTGC-ATG -s simRat_chr6.simRat.chr6 73394 27 - 647215 GGAATTAGTCATTATATGGTTGCAACA - -a -s simMouse_chr6.simMouse.chr6 599032 29 + 636262 TGACCTGGTCTTAGCAGGGAGACTTATAA -s Anc0.Anc0refChr3 197019 19 + 222631 TGACCTGAA----------AAGCTCATGA -s Anc1.Anc1refChr1 36675 29 + 69767 TGACCTGAACTGGGTTGAAAAGCTCATGA -s Anc2.Anc2refChr1 113643 19 + 142988 TGACCCAAA----------AAGGTCATGA -s mr.mrrefChr3 146961 29 + 181027 TGACCTGGTCTTAGCAGAGAGGCTTATGA -s simCow_chr6.simCow.chr6 572051 17 + 602619 TGA--CAAA----------CAGGTCATGA -s simDog_chr6.simDog.chr6 564037 19 + 593897 TGACCCAAA----------ATTGTCAAGA -s simHuman_chr6.simHuman.chr6 567811 29 + 601863 TGACATGAACTGGGTTGAAAAGCTCATGA -s simRat_chr6.simRat.chr6 73421 29 - 647215 TGACCTGGGCTTAGCAGAGGGGTTTATGA - -a -s simMouse_chr6.simMouse.chr6 599061 11 + 636262 TCTTCATCATG -s Anc0.Anc0refChr3 197038 11 + 222631 TCTTTATCATT -s Anc1.Anc1refChr1 36704 11 + 69767 TCTTTATCATT -s Anc2.Anc2refChr1 113662 11 + 142988 TATTTATCATT -s mr.mrrefChr3 146990 11 + 181027 TCTTCATCATG -s simCow_chr6.simCow.chr6 572072 11 + 602619 TATTTATCATT -s simDog_chr6.simDog.chr6 564056 11 + 593897 TATTTATCATT -s simHuman_chr6.simHuman.chr6 567840 11 + 601863 TCTTTATCATT -s simRat_chr6.simRat.chr6 73450 11 - 647215 TCCTCATCATG - -a -s simMouse_chr6.simMouse.chr6 599072 38 + 636262 CTTGTGTTGTTCTGGCACAAAGCATACCCCTGTTCAGG -s Anc0.Anc0refChr3 197049 38 + 222631 CCTGTGATGTGCTGGCAAATAACATATCCCTGTTCAAC -s Anc1.Anc1refChr1 36715 38 + 69767 CCTGTGATGTGCTGGCAAATAACATATCCCTGTTCAAC -s Anc2.Anc2refChr1 113673 38 + 142988 CCTGGGATGTGCTGGCAAATAACATATCCCTGCTCAAC -s mr.mrrefChr3 147009 38 + 181027 CTTGTGTTGTTCTGGCAAAAAACATACCCCTGTTCAGC -s simCow_chr6.simCow.chr6 572083 38 + 602619 ACTGGGATGTGCTGGCAAATAGCATATCCCTGCTCAAC -s simDog_chr6.simDog.chr6 564067 27 + 593897 CTTGGG-----------TACAACATATCCGTCCTCAAC -s simHuman_chr6.simHuman.chr6 567851 38 + 601863 CCTGTGATGTACTGGCAAATAACATATCCCTGTTGAAC -s simRat_chr6.simRat.chr6 73489 38 - 647215 CTTGTGTTGTTCCAGCAAACTACATACCCCTGTTCATC - -a -s simMouse_chr6.simMouse.chr6 599110 7 + 636262 TTGCTAA -s Anc0.Anc0refChr3 197087 7 + 222631 TTACTAA -s Anc1.Anc1refChr1 36753 7 + 69767 TTACTAA -s Anc2.Anc2refChr1 113711 7 + 142988 TTACTAA -s mr.mrrefChr3 147047 7 + 181027 TTGCTAA -s simCow_chr6.simCow.chr6 572121 7 + 602619 TTGCTTA -s simDog_chr6.simDog.chr6 564094 7 + 593897 TTACTAA -s simHuman_chr6.simHuman.chr6 567893 7 + 601863 CCACTGA -s simRat_chr6.simRat.chr6 73527 7 - 647215 TTGCTAG - -a -s simMouse_chr6.simMouse.chr6 599117 28 + 636262 GACTAGTTTGTGGTACTAATCTAATCAA -s Anc0.Anc0refChr3 197094 27 + 222631 GAGTGGTTTTTGTTACTAATCTATTC-A -s Anc1.Anc1refChr1 36760 27 + 69767 GAGTGGTTTTTGTTACTAATCTATTC-A -s Anc2.Anc2refChr1 113730 27 + 142988 GAGTGGTGCTTGTTACTAATGCATTC-A -s mr.mrrefChr3 147054 27 + 181027 GAGTGGTTTGTGGTACTAATCTAATC-A -s simCow_chr6.simCow.chr6 572140 27 + 602619 GAGTGGTACTTGTTACTAATGCATTT-G -s simDog_chr6.simDog.chr6 564113 27 + 593897 GAGTGGTGCTTGTTACTAATGCATTC-A -s simHuman_chr6.simHuman.chr6 567900 27 + 601863 GAGTGGTTTTTGATACTAATCTATTC-A -s simRat_chr6.simRat.chr6 73534 26 - 647215 GAGTGATCTGGGGTACTAACCTAATT-- - -a -s simMouse_chr6.simMouse.chr6 599145 21 + 636262 AATCACCTCAGACAGCATTTT -s Anc0.Anc0refChr3 197121 21 + 222631 AACGGTTTCAAAGGCCATTAT -s Anc1.Anc1refChr1 36787 21 + 69767 AACGGTTTCAAAGGCCATTAT -s Anc2.Anc2refChr1 113758 21 + 142988 AACGGTTCCAAAGGCTATTAT -s mr.mrrefChr3 147081 21 + 181027 AATTACCTCAGACACCATTAT -s simCow_chr6.simCow.chr6 572168 21 + 602619 AATGGTTCCAAAGTCAATTGT -s simDog_chr6.simDog.chr6 564141 21 + 593897 AACAGTTCCACGGGCTATTAT -s simHuman_chr6.simHuman.chr6 567927 21 + 601863 AACGGTTTCAAAGGCCATTAT -s simRat_chr6.simRat.chr6 73560 19 - 647215 --TTACCTCAGACACCATTAT - -a -s simMouse_chr6.simMouse.chr6 599166 13 + 636262 TATTTCTTCTGCC -s Anc0.Anc0refChr3 197143 13 + 222631 TAAATCTCTTACC -s Anc1.Anc1refChr1 36809 13 + 69767 TAAATCTCTTACC -s Anc2.Anc2refChr1 113780 13 + 142988 TAAATCAGTTACC -s mr.mrrefChr3 147102 13 + 181027 TATTTCTCCTGCC -s simCow_chr6.simCow.chr6 572190 13 + 602619 TAAAGCCTTTACT -s simDog_chr6.simDog.chr6 564163 13 + 593897 TACATCAGTTACC -s simHuman_chr6.simHuman.chr6 567949 13 + 601863 TAAATCTCTTACC -s simRat_chr6.simRat.chr6 73579 13 - 647215 TATGTCTCCTGCC - -a -s simMouse_chr6.simMouse.chr6 599179 19 + 636262 CATTATCATGTTTTACAGA -s Anc0.Anc0refChr3 197156 10 + 222631 CATCATCGT---------A -s Anc1.Anc1refChr1 36822 10 + 69767 CATCATCGT---------A -s Anc2.Anc2refChr1 113798 10 + 142988 CATCATCGT---------A -s mr.mrrefChr3 147115 19 + 181027 CATCATCATGTTATACAGA -s simCow_chr6.simCow.chr6 572208 2 + 602619 CA----------------- -s simDog_chr6.simDog.chr6 564181 10 + 593897 CATCATCGT---------A -s simHuman_chr6.simHuman.chr6 567962 10 + 601863 AATCATCGT---------A -s simRat_chr6.simRat.chr6 73592 19 - 647215 CATCATCATGTTATACACA - -a -s simMouse_chr6.simMouse.chr6 599198 18 + 636262 CTTATCTTTGGCTTCAGT -s Anc0.Anc0refChr3 197166 16 + 222631 ATTAGCCTC--CCTGAAT -s Anc1.Anc1refChr1 36832 16 + 69767 ATTAGCCTC--CCTGAAT -s Anc2.Anc2refChr1 113808 16 + 142988 CTTAGCCTC--CCTGAAT -s mr.mrrefChr3 147134 18 + 181027 ATTATCTTTGGCTTCACT -s simCow_chr6.simCow.chr6 572210 16 + 602619 CTTCACACC--CATAATT -s simDog_chr6.simDog.chr6 564203 16 + 593897 CTTAGCCTC--CCTGAAT -s simHuman_chr6.simHuman.chr6 567972 3 + 601863 ATC--------------- -s simRat_chr6.simRat.chr6 73611 18 - 647215 ATTATCTTTGGCTGCACT - -a -s simMouse_chr6.simMouse.chr6 599216 23 + 636262 GCGGGTGGTCAACACTGTGCCAG -s Anc0.Anc0refChr3 197182 21 + 222631 GTGAATGACAAACACTGTCC--A -s Anc1.Anc1refChr1 36848 21 + 69767 GTGAATGACAAACACTGTCC--A -s Anc2.Anc2refChr1 113824 21 + 142988 GTGAATGACAAACACTGTCC--A -s mr.mrrefChr3 147152 21 + 181027 GCAAGTGGTCAACACTGTGC--A -s simCow_chr6.simCow.chr6 572229 21 + 602619 GTAAATTGTAAACAATGTCC--A -s simDog_chr6.simDog.chr6 564219 21 + 593897 GTGAATGACAAACACTGTCC--A -s simRat_chr6.simRat.chr6 73629 21 - 647215 GCAAGTGGTCAACACCGTGC--A - -a -s simMouse_chr6.simMouse.chr6 599239 14 + 636262 CTAAGTCTGTCATG -s Anc0.Anc0refChr3 197203 14 + 222631 TTAACTCTGCTATG -s Anc1.Anc1refChr1 36869 14 + 69767 TTAACTCTGCTATG -s Anc2.Anc2refChr1 113847 14 + 142988 TTAACTCTGCTATG -s mr.mrrefChr3 147173 14 + 181027 CTAAGTCTGTCATG -s simCow_chr6.simCow.chr6 572252 14 + 602619 ATAACCCCACTATG -s simDog_chr6.simDog.chr6 564242 14 + 593897 TTAACTCTGCTATG -s simRat_chr6.simRat.chr6 73650 14 - 647215 CTAATTCTGTCATG - -a -s simMouse_chr6.simMouse.chr6 599253 66 + 636262 CTGGATTGCTCATGTTGGGCGGTGATACCCCATTCGTCACTTTTTTGTAAATATTATTGTTGTCTA -s Anc0.Anc0refChr3 197217 58 + 222631 CTAGATTAATGATGTTAGGTGGTCATATTCCCT--------TATCCCTAAGGTGTATTGTTATCTC -s Anc1.Anc1refChr1 36883 65 + 69767 CTAGATTAATGATGTTAGGTGGTCATATTCCCTACTGCAC-TATCCCTAAGGTGTATTGTTATCTC -s Anc2.Anc2refChr1 113864 58 + 142988 CTAGATTGATAAAGTTAGGTGGTCACATCCCCT--------TACCCCTAAGGTGTATTGTCATCTC -s mr.mrrefChr3 147187 66 + 181027 CTAGATTACTGATGTTGGGTGGTGATACTCCATTCGGCACTTTTTTGTAAATATTATTGTTATCTA -s simCow_chr6.simCow.chr6 572266 42 + 602619 CTAGGTTGATTAAGTTAGGTACTCACA------------------------CTGTATCGTCATCTC -s simDog_chr6.simDog.chr6 564281 55 + 593897 CTAGATTGATAAAGTCATGTGGTC---TCCCCT--------TACCCCTAAGGCGTATTGTCATCTT -s simHuman_chr6.simHuman.chr6 567975 65 + 601863 CTAGATTAATGATGTTAGGTGGTCATAATCCCTACTGCAC-TATCCTTAAGGTGTATTGTTATCCC -s simRat_chr6.simRat.chr6 73664 66 - 647215 CTAGATTACTGATGTTGGGTGGTGGTACTCCATCTGGCACTTTTTTGTAAATATTATTGTCACCTA - -a -s simMouse_chr6.simMouse.chr6 599319 12 + 636262 ACTTTCACTCCC -s Anc0.Anc0refChr3 197275 12 + 222631 ACTTCCACCCCC -s Anc1.Anc1refChr1 36948 12 + 69767 ACTTCCACCCCC -s Anc2.Anc2refChr1 113923 12 + 142988 ACTTCCACCCCC -s mr.mrrefChr3 147253 12 + 181027 ACTTCCACTCCC -s simCow_chr6.simCow.chr6 572309 12 + 602619 ACTGCCACCTCC -s simDog_chr6.simDog.chr6 564337 12 + 593897 ACTTCCACACCC -s simHuman_chr6.simHuman.chr6 568040 12 + 601863 ACTTCCACCCCC -s simRat_chr6.simRat.chr6 73730 12 - 647215 ACTTCCACTCCC - -a -s simMouse_chr6.simMouse.chr6 599331 4 + 636262 TCAC -s Anc0.Anc0refChr3 197288 4 + 222631 TCAC -s Anc1.Anc1refChr1 36961 4 + 69767 TCAC -s Anc2.Anc2refChr1 113936 4 + 142988 TCAC -s mr.mrrefChr3 147265 4 + 181027 TCAC -s simCow_chr6.simCow.chr6 572322 4 + 602619 TCAC -s simDog_chr6.simDog.chr6 564350 4 + 593897 TCAC -s simHuman_chr6.simHuman.chr6 568053 4 + 601863 CCAC -s simRat_chr6.simRat.chr6 73742 4 - 647215 TCAC - -a -s simMouse_chr6.simMouse.chr6 599335 40 + 636262 TCCCCGGACCCTGGCAGTCATACATTGCTCTCACTTTGTC -s Anc0.Anc0refChr3 197299 40 + 222631 TCCCCAAATCTTAGCAGTTATACATTCCTCTCACTTCATT -s Anc1.Anc1refChr1 36972 40 + 69767 TCCCCAAATCTTAGCAGTTATACATTCCTCTCACTTCATT -s Anc2.Anc2refChr1 113947 40 + 142988 CCCCCAAATCTTAACAGTTATACACTCCTCTCACTTCATT -s mr.mrrefChr3 147269 40 + 181027 TCCCCGGACCCTGGCAGTCATACATTGCTCTCACTTCATC -s simCow_chr6.simCow.chr6 572327 39 + 602619 -CCCCAATTGTTAACAGTTATACCCTCCTTGCACATCATT -s simDog_chr6.simDog.chr6 564414 40 + 593897 CCCCCAAATCCTGACAGTTATACACTCCTCTCACTTCACT -s simHuman_chr6.simHuman.chr6 568070 40 + 601863 TCCCCAAATATTAGCAGTTAGATGTTCCTCTCACTTCATT -s simRat_chr6.simRat.chr6 73746 40 - 647215 TCACTGGACCCTGGCAGTCATACATTGCTCTCATTTCATC - -a -s simMouse_chr6.simMouse.chr6 599375 14 + 636262 CCACTTTTACCTAG -s Anc0.Anc0refChr3 197346 14 + 222631 CTGCCTTGAACTAG -s Anc1.Anc1refChr1 37019 14 + 69767 CTGCCTTGAACTAG -s Anc2.Anc2refChr1 113994 14 + 142988 CTGCCTTGAACTAG -s mr.mrrefChr3 147316 14 + 181027 CCACTTTGAACTAG -s simCow_chr6.simCow.chr6 572373 7 + 602619 CTGCTTT------- -s simDog_chr6.simDog.chr6 564461 14 + 593897 CTGCCCTGAACTAG -s simHuman_chr6.simHuman.chr6 568117 14 + 601863 CTGCCTTGAACTAG -s simRat_chr6.simRat.chr6 73793 14 - 647215 ACACTTTGAACTGG - -a -s simMouse_chr6.simMouse.chr6 599389 61 + 636262 GGGGATGAGTGGTATCTGGGTGGATGGTAACATCTTGAAGGGTAATTGTTGTCAGGTGTAG -s Anc0.Anc0refChr3 197360 60 + 222631 GGGGACAAGCGATATCTGGGTGGATGGTAATATCTTTATGGGGAACTGTTGTCAGGC-CAA -s Anc1.Anc1refChr1 37033 60 + 69767 GGGGACAAGCGATATCTGGGTGGATGGTAATATCTTTATGGGGAACTGTTGTCAGGC-CAA -s Anc2.Anc2refChr1 114008 60 + 142988 GGGGACAAGCAATATATGGGTGGATGGTAATATCTTTATGGGGAACTGTTGCCAGAC-CAA -s mr.mrrefChr3 147330 61 + 181027 GGGGACAAGTGGTATCTGGGTGGATGGTAACATCTTGAAGGGTAATTGTTGTCAGGTGTAA -s simCow_chr6.simCow.chr6 572380 55 + 602619 -----CGAGCAATATATGGGTGGATGGTAATATCTTTGTGGGGAAATGATGCCAGAC-TGA -s simDog_chr6.simDog.chr6 564475 60 + 593897 GGGGACAAGCAATATATGGGTGGATGGTAATATCTTTATGGGGAACTGTTGCCAAAC-CAA -s simHuman_chr6.simHuman.chr6 568132 60 + 601863 GGGAACAAACGATACCTGGGTGGGTAATCATGCCTTTATGGGGAACTACTGTCAGGC-CAA -s simRat_chr6.simRat.chr6 73807 61 - 647215 TGGGACAAGTGGTATCTTGGTGGATGGTAACATCTTGGAGGATATTTGTTCTCAGGTGTAA - -a -s simMouse_chr6.simMouse.chr6 599450 1 + 636262 C -s Anc0.Anc0refChr3 197420 1 + 222631 C -s Anc1.Anc1refChr1 37093 1 + 69767 C -s Anc2.Anc2refChr1 114069 1 + 142988 C -s mr.mrrefChr3 147391 1 + 181027 C -s simCow_chr6.simCow.chr6 572436 1 + 602619 C -s simDog_chr6.simDog.chr6 564536 1 + 593897 C -s simHuman_chr6.simHuman.chr6 568192 1 + 601863 C -s simRat_chr6.simRat.chr6 73868 1 - 647215 C - -a -s simMouse_chr6.simMouse.chr6 599451 2 + 636262 TG -s Anc0.Anc0refChr3 197421 2 + 222631 TG -s Anc1.Anc1refChr1 37094 2 + 69767 TG -s Anc2.Anc2refChr1 114070 2 + 142988 TG -s mr.mrrefChr3 147392 2 + 181027 TG -s simCow_chr6.simCow.chr6 572437 2 + 602619 TG -s simCow_chr6.simCow.chr6 572545 2 + 602619 TG -s simDog_chr6.simDog.chr6 564537 2 + 593897 TG -s simHuman_chr6.simHuman.chr6 568193 2 + 601863 TG -s simRat_chr6.simRat.chr6 73869 2 - 647215 TG - -a -s simMouse_chr6.simMouse.chr6 599453 59 + 636262 TCCAGTAGATTGTGGACACCTCTACCTAAAGAGGCCCAAATATGAAGAATCCTAAAATG -s Anc0.Anc0refChr3 197424 37 + 222631 TCCAGTAGATTGC-A---------------------CAAACATAAGCAGTCCTACAACG -s Anc1.Anc1refChr1 37097 37 + 69767 TCCAGTAGATTGC-A---------------------CAAACATAAGCAGTCCTACAACG -s Anc2.Anc2refChr1 114073 37 + 142988 TCCAGTAGACTGC-A---------------------CAAACGTAAGCAGTCCTACAACA -s mr.mrrefChr3 147394 58 + 181027 TCCAGTAGATTGT-ACCACCTCTACCTAAAGAGGCCCAAATATGAGCAGTCCTACAATG -s simCow_chr6.simCow.chr6 572440 37 + 602619 TTCAGTAAACTGC-A---------------------CAAGTGTAAGCAGTCCCACAACA -s simCow_chr6.simCow.chr6 572548 35 + 602619 GT--GTAGACTGC-A---------------------CAAACATAAGTAGTCCTACAAAA -s simDog_chr6.simDog.chr6 564540 37 + 593897 TCCAGTAGACTGC-A---------------------CAAACGTAAGCAGTCCTATACCT -s simHuman_chr6.simHuman.chr6 568196 37 + 601863 TCCAGTAGATTAC-A---------------------CGAACATAAGCAGTCCTACAACG -s simRat_chr6.simRat.chr6 73871 58 - 647215 TCCAGTAGACTGT-ACCAGCTCTACCTAAAGATGCCCAGAAATGAGCAGCCCTACAATG - -a -s simMouse_chr6.simMouse.chr6 599512 6 + 636262 CCACCG -s Anc0.Anc0refChr3 197461 2 + 222631 ----CA -s Anc1.Anc1refChr1 37134 2 + 69767 ----CA -s Anc2.Anc2refChr1 114110 2 + 142988 ----CA -s mr.mrrefChr3 147454 6 + 181027 CCACCA -s simCow_chr6.simCow.chr6 572477 2 + 602619 ----CA -s simCow_chr6.simCow.chr6 572583 2 + 602619 ----CA -s simDog_chr6.simDog.chr6 564577 2 + 593897 ----CA -s simHuman_chr6.simHuman.chr6 568233 2 + 601863 ----CA -s simRat_chr6.simRat.chr6 73931 6 - 647215 ACACCA - -a -s simMouse_chr6.simMouse.chr6 599518 10 + 636262 GTACTGTGGA -s Anc0.Anc0refChr3 197463 10 + 222631 GTACTATGCC -s Anc1.Anc1refChr1 37136 10 + 69767 GTACTATGCC -s Anc2.Anc2refChr1 114112 10 + 142988 GTACAATGCC -s mr.mrrefChr3 147460 10 + 181027 GTACTGTGGA -s simCow_chr6.simCow.chr6 572585 10 + 602619 GTACAACGCA -s simDog_chr6.simDog.chr6 564579 6 + 593897 GG----TACC -s simHuman_chr6.simHuman.chr6 568235 8 + 601863 GTACTTTG-- -s simRat_chr6.simRat.chr6 73937 10 - 647215 GTACTGTGGA - -a -s simMouse_chr6.simMouse.chr6 599528 8 + 636262 ATTTCCCC -s Anc0.Anc0refChr3 197473 8 + 222631 ATGTATCC -s Anc1.Anc1refChr1 37146 8 + 69767 ATGTATCC -s Anc2.Anc2refChr1 114122 8 + 142988 ATGTATCC -s mr.mrrefChr3 147470 8 + 181027 ATTTACCC -s simCow_chr6.simCow.chr6 572479 8 + 602619 ATGTATCC -s simCow_chr6.simCow.chr6 572595 8 + 602619 GTGTATCC -s simDog_chr6.simDog.chr6 564585 8 + 593897 ATGGATAT -s simHuman_chr6.simHuman.chr6 568243 1 + 601863 -------T -s simRat_chr6.simRat.chr6 73947 8 - 647215 ATTTACCC - -a -s simMouse_chr6.simMouse.chr6 599536 124 + 636262 CCATGAGTCAACACAATAATTACATTTtatgtttttcagataagtagatatcttttttagcaggatgcttattaatgtcttccaggtatttcttgattaacttgttggttttattcttgtaagc -s Anc0.Anc0refChr3 197481 12 + 222631 CCATGAGTCATC---------------------------------------------------------------------------------------------------------------- -s Anc1.Anc1refChr1 37154 12 + 69767 CCATGAGTCATC---------------------------------------------------------------------------------------------------------------- -s Anc2.Anc2refChr1 114136 12 + 142988 CCATGAGTCATC---------------------------------------------------------------------------------------------------------------- -s mr.mrrefChr3 147478 109 + 181027 CCATGAGTCAACACAATAATAACATCTtatgtttttcagataagtagatatcttttttagcaggatgcttattaa--------aggtatttctt-------ttgttggttttattcttgtaagc -s simCow_chr6.simCow.chr6 572493 12 + 602619 CCATGTGTCATC---------------------------------------------------------------------------------------------------------------- -s simCow_chr6.simCow.chr6 572609 12 + 602619 CCATGAGTCATC---------------------------------------------------------------------------------------------------------------- -s simDog_chr6.simDog.chr6 564599 12 + 593897 CTATGATTCATC---------------------------------------------------------------------------------------------------------------- -s simHuman_chr6.simHuman.chr6 568244 12 + 601863 CCATGAGTCATC---------------------------------------------------------------------------------------------------------------- -s simRat_chr6.simRat.chr6 73955 109 - 647215 CCATGAGTCAACACAATAATAACAGCTtatgtttttcagataagtagatatcttctttagcaggatgcttatttg--------aggtacttctt-------ttgctggttttattctcgtgagc - -a -s simMouse_chr6.simMouse.chr6 599660 8 + 636262 cttgttgt -s mr.mrrefChr3 147587 8 + 181027 cttgttgt -s simRat_chr6.simRat.chr6 74073 8 - 647215 cttgttgt - -a -s simMouse_chr6.simMouse.chr6 599668 99 + 636262 aagttcacacatgaggagcaagtggatgagctcttcttccaatgggtaagttcatgatgggcttcattgaagatgatagctgcattgagatttaagctt -s mr.mrrefChr3 147595 80 + 181027 aagttcacacatgaggag------------------ttccaatgggtaagttcatgatgggcttcattgaagatga-agctgcattgagatttaagctt -s simRat_chr6.simRat.chr6 74090 80 - 647215 aggttcagacatgagggg------------------ttccaatgggttagtgcatgatgggcttcattgaagatga-acctgcattgagatttaggctt - -a -s simMouse_chr6.simMouse.chr6 599767 55 + 636262 acactacatcttgtatctaatTTTCACTAGTAATAGCTTAATAACTCAAAAATGG -s Anc0.Anc0refChr3 197493 26 + 222631 ---------------------CTTCACTAG--------CAATATCTTGAAGGTGG -s Anc1.Anc1refChr1 37166 26 + 69767 ---------------------CTTCACTAG--------CAATATCTTGAAGGTGG -s Anc2.Anc2refChr1 114148 26 + 142988 ---------------------CTTCACTAG--------CAATATCTTGAAGGTGG -s mr.mrrefChr3 147675 55 + 181027 acactacatcttgtatctaatTTTCACTAGTAATAGCTTAATATCTTAAAGATGG -s simCow_chr6.simCow.chr6 572505 26 + 602619 ---------------------CTTCATTAG--------CAATATCTTGAAGGTGG -s simCow_chr6.simCow.chr6 572621 26 + 602619 ---------------------TTTCATTAG--------CAATACCTTGAAGGTGG -s simDog_chr6.simDog.chr6 564611 26 + 593897 ---------------------CTTCACTAG--------CAATATCTTGAAGGTGG -s simHuman_chr6.simHuman.chr6 568256 26 + 601863 ---------------------CTTCACCAG--------CAACATCTTGAAGGTGT -s simRat_chr6.simRat.chr6 74172 55 - 647215 acactacatctcgaatctgatTTTCACTAGTAATAACTTCATATCTTAAAGATGG - -a -s simMouse_chr6.simMouse.chr6 599822 13 + 636262 AATAAATGTACAT -s Anc0.Anc0refChr3 197520 13 + 222631 CATAAATGTACGT -s Anc1.Anc1refChr1 37193 13 + 69767 CATAAATGTACGT -s Anc2.Anc2refChr1 114175 13 + 142988 CATAAATGTACGT -s mr.mrrefChr3 147731 13 + 181027 AATAAATGTACAT -s simCow_chr6.simCow.chr6 572532 13 + 602619 CATAAATGTATGT -s simCow_chr6.simCow.chr6 572648 13 + 602619 CATATATGTATGC -s simDog_chr6.simDog.chr6 564638 13 + 593897 CATAAGTGTACAT -s simHuman_chr6.simHuman.chr6 568283 13 + 601863 CATAAATATACTT -s simRat_chr6.simRat.chr6 74228 13 - 647215 AATAAATGTACAT - -a -s simMouse_chr6.simMouse.chr6 599835 21 + 636262 TAGGTCTAGCATATAGTTTTG -s Anc0.Anc0refChr3 197533 18 + 222631 TAGGTCATAT---TAGTGGGG -s Anc1.Anc1refChr1 37206 18 + 69767 TAGGTCATAT---TAGTGGGG -s Anc2.Anc2refChr1 114188 18 + 142988 TAGGTCATAA---TAGCGGGG -s mr.mrrefChr3 147744 21 + 181027 TAGGTCTAGTGTATAGTTTCG -s simCow_chr6.simCow.chr6 572661 18 + 602619 TGGGTCTTTA---TAGCGGGG -s simDog_chr6.simDog.chr6 564651 17 + 593897 -AGGTTATAA---TAGCGGGG -s simHuman_chr6.simHuman.chr6 568296 18 + 601863 TAAGTCATAT---TAGTGGGG -s simRat_chr6.simRat.chr6 74241 21 - 647215 TAGGTCTAATGTATAGTTTCG - -a -s simMouse_chr6.simMouse.chr6 599856 8 + 636262 TGTGTCTT -s Anc0.Anc0refChr3 197551 8 + 222631 ATTGTCTT -s Anc1.Anc1refChr1 37224 8 + 69767 ATTGTCTT -s Anc2.Anc2refChr1 114206 8 + 142988 ATTACCTT -s mr.mrrefChr3 147765 8 + 181027 TGTGTCTT -s simCow_chr6.simCow.chr6 572679 8 + 602619 ATTACCTC -s simDog_chr6.simDog.chr6 564668 8 + 593897 ATTACCTT -s simHuman_chr6.simHuman.chr6 568314 8 + 601863 ATTGTCTT -s simRat_chr6.simRat.chr6 74273 8 - 647215 TGTGTATT - -a -s simMouse_chr6.simMouse.chr6 599864 19 + 636262 TCCCATTATCAAAGATCAT -s Anc0.Anc0refChr3 197559 19 + 222631 TCCAATTATCAGAGATAGT -s Anc1.Anc1refChr1 37232 19 + 69767 TCCAATTATCAGAGATAGT -s Anc2.Anc2refChr1 114231 19 + 142988 TCCATTTATCACAGATAGT -s mr.mrrefChr3 147773 19 + 181027 TCCCATTATCAGAGATCAT -s simCow_chr6.simCow.chr6 572706 19 + 602619 TCAATTTATCACAGATAGT -s simDog_chr6.simDog.chr6 564693 19 + 593897 TCCATTTATCACAGATAGT -s simHuman_chr6.simHuman.chr6 568323 12 + 601863 TCCTATTATTGG------- -s simRat_chr6.simRat.chr6 74281 19 - 647215 TCCCATTATCAGAAATCAT - -a -s simMouse_chr6.simMouse.chr6 599883 2 + 636262 CC -s Anc0.Anc0refChr3 197578 2 + 222631 CC -s Anc1.Anc1refChr1 37251 2 + 69767 CC -s Anc2.Anc2refChr1 114250 2 + 142988 CC -s mr.mrrefChr3 147792 2 + 181027 CC -s simCow_chr6.simCow.chr6 572732 2 + 602619 CC -s simDog_chr6.simDog.chr6 564712 2 + 593897 CC -s simRat_chr6.simRat.chr6 74300 2 - 647215 CC - -a -s simMouse_chr6.simMouse.chr6 599885 24 + 636262 CAATGTGGCTAAGAATTAACAGTG -s Anc0.Anc0refChr3 197580 24 + 222631 TGGTGTGGCTAAGGGAGTAAAATA -s Anc1.Anc1refChr1 37253 24 + 69767 TGGTGTGGCTAAGGGAGTAAAATA -s Anc2.Anc2refChr1 114252 24 + 142988 TGGTGTGGCTAAGGGAGTGAAATA -s mr.mrrefChr3 147794 24 + 181027 CAATGTGGCTAAGAATTAACAGTG -s simCow_chr6.simCow.chr6 572745 23 + 602619 TGGTGTGGCCAAGGGAGTCAAAT- -s simDog_chr6.simDog.chr6 564714 24 + 593897 TGGTGTGGCTAAAGGAGTGAAATA -s simHuman_chr6.simHuman.chr6 568335 22 + 601863 --CTGTGGCTAAGGGAGTAACATA -s simRat_chr6.simRat.chr6 74302 24 - 647215 CAATGTGGCTAAGAATTGACAGTG - -a -s simMouse_chr6.simMouse.chr6 599909 112 + 636262 ATCACATCTCACCTGCTTCCCTGCTTCAAGAATTCTAACTACTTTTGTCTATGATGTGATGCTCGAAAATTATTCCCTGTAGCCAATTTGCAAATCTGGGGATTAGTTTTAT -s Anc0.Anc0refChr3 197605 72 + 222631 CTCAGACCTAACCTGCTCCTAT--------AAGCTGCAATGTTTTTCTCTATGAGGTGATGTTCATAAACTATTCCA--------------------------------TAT -s Anc1.Anc1refChr1 37278 72 + 69767 CTCAGACCTAACCTGCTCCTAT--------AAGCTGCAATGTTTTTCTCTATGAGGTGATGTTCATAAACTATTCCA--------------------------------TAT -s Anc2.Anc2refChr1 114277 72 + 142988 CTCAGACCTAACCTGCTCCTAT--------AAGCTGCAATGTTTTTCTCTATGAGGTGATGATCATAAACTATTCCA--------------------------------TAA -s mr.mrrefChr3 147819 72 + 181027 ATCACATCTCACCTGCTTCCCT--------AATTCTAAATACTTTTGTCTATGATGTGATGTTCAAAAATTATTCCA--------------------------------TAT -s simCow_chr6.simCow.chr6 572768 68 + 602619 ----GACCTAACCAGTTCCTAT--------AAGCCACAATTATTTTCTCTATGAGGTCATGCTCATAAATCATTACA--------------------------------TAA -s simDog_chr6.simDog.chr6 564739 72 + 593897 CTCAGACCTAACCTGCTCTTAT--------AAGCTGAAATGTTTTTCTCTATCAGGTGATGACTATAAACTAGTCCA--------------------------------TAA -s simHuman_chr6.simHuman.chr6 568358 62 + 601863 CCGAGACTCAACATACTCCTAT--------GAGGTGCAATG---------ATGAGGTAATATTCATAAA-TATTCCA--------------------------------TAT -s simRat_chr6.simRat.chr6 74327 72 - 647215 ATCATATCTCACCTGCTTTTCC--------AATTCTAAATACTTTTGTCTATGATGTGATGTTCAAAAATTATTCCA--------------------------------TAT - -a -s simMouse_chr6.simMouse.chr6 600021 34 + 636262 GCCCAATTTGCAAATCTGGGGATTAATTTTATGT -s Anc0.Anc0refChr3 197677 34 + 222631 GCCCAGATTACAAAACTGAGGATGACTTTTAAGC -s Anc1.Anc1refChr1 37350 34 + 69767 GCCCAGATTACAAAACTGAGGATGACTTTTAAGC -s Anc2.Anc2refChr1 114349 34 + 142988 GCCCAGATTACAAAACTGAGGATGACCTTTAAGC -s mr.mrrefChr3 147891 34 + 181027 GCCCAGTTTGCAAATCTGGGGATTAATTTTATGC -s simCow_chr6.simCow.chr6 572845 24 + 602619 GCCCAGATTGAAAAACTGAGGATG---------- -s simDog_chr6.simDog.chr6 564811 34 + 593897 GCCCAGATTACAAAACTGACGGTGACCTTTAAGC -s simHuman_chr6.simHuman.chr6 568420 34 + 601863 GCCCAGATTCCAAAACCGAGGATAACTATTGAGC -s simRat_chr6.simRat.chr6 74399 34 - 647215 GCCCAGGCTGCAAATCTGGGGATTGATTTTATGC - -a -s simMouse_chr6.simMouse.chr6 600055 46 + 636262 CTGATGAGTAAAGCAAGCAGCAGGGCTAGCACCCACCTTGCACTTT -s Anc0.Anc0refChr3 197711 43 + 222631 C---TGAGTGAAGGAGGCAGCTGGGCTAGCACCTGCCCTGCACCTT -s Anc1.Anc1refChr1 37384 43 + 69767 C---TGAGTGAAGGAGGCAGCTGGGCTAGCACCTGCCCTGCACCTT -s Anc2.Anc2refChr1 114383 43 + 142988 C---TGAGTGAAGGAGGCAGCAGGGCTAGCACCTGCCCTGCACCTG -s mr.mrrefChr3 147925 46 + 181027 CTGATGAGTAAAGCAAGCAGCTGGGCTAGCACCTACCCTGCACCTT -s simCow_chr6.simCow.chr6 572869 28 + 602619 ------------------AACAGGGCTAGCACCCACCCTGCACCTG -s simDog_chr6.simDog.chr6 564850 43 + 593897 C---TGAGTGAAGGAGGCAGCAGGGCTAGCACTTGCCCTACACTTG -s simHuman_chr6.simHuman.chr6 568454 38 + 601863 C---TGAGTGAAGGGGCCAGCTG-----GCACCTGCCCTGCACCTT -s simRat_chr6.simRat.chr6 74433 46 - 647215 CTGATGAGTAAAGCAAGCAGCTGGGCTAGCACCTACCCTACACCTC - -a -s simMouse_chr6.simMouse.chr6 600101 6 + 636262 ACATTG -s Anc0.Anc0refChr3 197754 6 + 222631 ACATTG -s Anc1.Anc1refChr1 37427 6 + 69767 ACATTG -s Anc2.Anc2refChr1 114426 6 + 142988 ACCTGG -s mr.mrrefChr3 147971 6 + 181027 ACATTG -s simCow_chr6.simCow.chr6 572897 1 + 602619 A----- -s simDog_chr6.simDog.chr6 564893 6 + 593897 ACCTGG -s simHuman_chr6.simHuman.chr6 568493 6 + 601863 ACAATG -s simRat_chr6.simRat.chr6 74479 6 - 647215 ACATTG - -a -s simMouse_chr6.simMouse.chr6 600107 10 + 636262 GCATAAGTGG -s Anc0.Anc0refChr3 197773 10 + 222631 ACATCAGTGA -s Anc1.Anc1refChr1 37446 10 + 69767 ACATCAGTGA -s Anc2.Anc2refChr1 114445 10 + 142988 ACATCAGTGA -s mr.mrrefChr3 147977 10 + 181027 GCATAAGTGG -s simCow_chr6.simCow.chr6 572910 10 + 602619 GGAACAGTGA -s simDog_chr6.simDog.chr6 564912 10 + 593897 ACATCAGTGA -s simHuman_chr6.simHuman.chr6 568536 10 + 601863 ACACCAGTGA -s simRat_chr6.simRat.chr6 74485 10 - 647215 GCATGAGTGG - -a -s simMouse_chr6.simMouse.chr6 600117 50 + 636262 AGATACAGTTGAACCCATCTTCGATGTAATCAGACCCACTGATGTAATCA -s Anc0.Anc0refChr3 197783 32 + 222631 CGAAAAGGGTGAAGCCATCTT------------------TGACATAATCT -s Anc1.Anc1refChr1 37456 32 + 69767 CGAAAAGGGTGAAGCCATCTT------------------TGACATAATCT -s Anc2.Anc2refChr1 114457 32 + 142988 CAGAAAGGGTGAAGCCATCTT------------------TGATATAATCT -s mr.mrrefChr3 147987 32 + 181027 AGATACAGTTGAACCCATCTT------------------TGACGTAATCT -s simCow_chr6.simCow.chr6 572922 32 + 602619 CAGAAAGGGCGAACCCTTCTG------------------TGATATAATCT -s simDog_chr6.simDog.chr6 564924 32 + 593897 CAGAAGAAGTGAAGCCATCCT------------------TGATATAATCT -s simHuman_chr6.simHuman.chr6 568546 32 + 601863 CGAAAAGGGTGAGGTCCTCTT------------------TGACATAATGT -s simRat_chr6.simRat.chr6 74495 32 - 647215 AAATACAGTTGAACCCGTCTT------------------TGACTTAATCT - -a -s simMouse_chr6.simMouse.chr6 600167 22 + 636262 GCCCCACTGTCATGTCAAAATT -s Anc0.Anc0refChr3 197816 22 + 222631 GCCCCATTGTCATATCAAAATT -s Anc1.Anc1refChr1 37489 22 + 69767 GCCCCATTGTCATATCAAAATT -s Anc2.Anc2refChr1 114490 22 + 142988 GCCCCATTGACATATCAAAATT -s mr.mrrefChr3 148019 22 + 181027 GCCCCATTGTCATGTCAAAATT -s simCow_chr6.simCow.chr6 572955 22 + 602619 GCCCCATTGACATATCAAAATT -s simDog_chr6.simDog.chr6 564957 22 + 593897 GCCCAATTGACACACCAAAATT -s simHuman_chr6.simHuman.chr6 568579 22 + 601863 GCCCCATTGTCATATCAAAATT -s simRat_chr6.simRat.chr6 74527 22 - 647215 GTCCCATTGCCATCTTAAAATT - -a -s simMouse_chr6.simMouse.chr6 600189 33 + 636262 TCTTGCTTGGTGCACACAGAATTTCTAGTTTCT -s Anc0.Anc0refChr3 197840 33 + 222631 TCCTGTTTAGTGCACATAGATTTTCTATATTCT -s Anc1.Anc1refChr1 37513 33 + 69767 TCCTGTTTAGTGCACATAGATTTTCTATATTCT -s Anc2.Anc2refChr1 114514 33 + 142988 TCCTGTTTAGTGCACATAGATTTTCTATATTCT -s mr.mrrefChr3 148043 33 + 181027 TCTTGCTTGGTGCACACAGAATTTCTAGTTTCT -s simCow_chr6.simCow.chr6 572985 32 + 602619 ACCTATTTAGTGCTCATAGACTTGTTA-ATTCT -s simDog_chr6.simDog.chr6 564981 33 + 593897 TACTGTTTAGCACATATAGATTTTCTATATTCT -s simHuman_chr6.simHuman.chr6 568603 27 + 601863 CCCTGTTTAGTGCACA-AACTTTTC-----TCT -s simRat_chr6.simRat.chr6 74551 33 - 647215 TCTTGCTTGGTGCACACAGAATTTCTAGTTTCT - -a -s simMouse_chr6.simMouse.chr6 600222 2 + 636262 GT -s Anc0.Anc0refChr3 197873 2 + 222631 AT -s Anc1.Anc1refChr1 37546 2 + 69767 AT -s Anc2.Anc2refChr1 114550 2 + 142988 AT -s mr.mrrefChr3 148076 2 + 181027 GT -s simCow_chr6.simCow.chr6 573020 2 + 602619 AT -s simDog_chr6.simDog.chr6 565019 2 + 593897 AT -s simHuman_chr6.simHuman.chr6 568630 2 + 601863 AT -s simRat_chr6.simRat.chr6 74584 2 - 647215 GT - -a -s simMouse_chr6.simMouse.chr6 600224 9 + 636262 GCACAAAGA -s Anc0.Anc0refChr3 197875 9 + 222631 CTGCAGAGA -s Anc1.Anc1refChr1 37548 9 + 69767 CTGCAGAGA -s Anc2.Anc2refChr1 114552 9 + 142988 CTGCAGAGA -s mr.mrrefChr3 148078 9 + 181027 GCACAAAGA -s simCow_chr6.simCow.chr6 573023 9 + 602619 CCACAGAGA -s simDog_chr6.simDog.chr6 565021 9 + 593897 CTGCAAAAA -s simHuman_chr6.simHuman.chr6 568632 6 + 601863 ---CAGGGA -s simRat_chr6.simRat.chr6 74586 9 - 647215 ACACAAAGA - -a -s simMouse_chr6.simMouse.chr6 600233 27 + 636262 ACCATACGTTGTCCCTTAGATGAATTG -s Anc0.Anc0refChr3 197888 27 + 222631 ATCATGCTTTGTCTCTTAAGTAGGATT -s Anc1.Anc1refChr1 37561 27 + 69767 ATCATGCTTTGTCTCTTAAGTAGGATT -s Anc2.Anc2refChr1 114565 27 + 142988 ATCATGCTTCGTCTCTTAAGTAGGATT -s mr.mrrefChr3 148087 27 + 181027 ACCATACTTTGTCCCTTAGGTAAATTT -s simCow_chr6.simCow.chr6 573036 27 + 602619 ATTATGCATAGTCTCTTAAGCAGGATT -s simDog_chr6.simDog.chr6 565034 27 + 593897 ATCATGCTTCGTCTCTTAGGTGGGATT -s simHuman_chr6.simHuman.chr6 568642 27 + 601863 ATCATGGTTTTTCTCTTAAGAAGCATT -s simRat_chr6.simRat.chr6 74595 27 - 647215 ACCATACTTTGTCCCTTAGGCAAATTT - -a -s simMouse_chr6.simMouse.chr6 600260 51 + 636262 GGTATGACGCACTTGCTAATTTTTAGATAAGACTTTCCAATTTTTAGATAT -s Anc0.Anc0refChr3 197919 37 + 222631 TAGGTCAGGTATTAGCC--------------ACTTGCCAAATTCTAGACAT -s Anc1.Anc1refChr1 37592 37 + 69767 TAGGTCAGGTATTAGCC--------------ACTTGCCAAATTCTAGACAT -s Anc2.Anc2refChr1 114596 37 + 142988 TAGGTCAGGTATTAGCC--------------ACTTGCCAAATTCTAGACAT -s mr.mrrefChr3 148118 51 + 181027 GGTATGACGCACTTGCTAATTTTTAGATAAGACTTTCCAATTTTTAGATAT -s simCow_chr6.simCow.chr6 573067 37 + 602619 CAGGTTGGGTATTGGCC--------------ACTTGCCGAATTCTAAACAT -s simDog_chr6.simDog.chr6 565065 37 + 593897 TAGATCAGTTATTAGTC--------------ACTTATCAAATTCTAGACAT -s simHuman_chr6.simHuman.chr6 568673 37 + 601863 TAGGTCAGGTATTAGCC--------------ACTTGCCAAATTGTAGACAA -s simRat_chr6.simRat.chr6 74626 51 - 647215 GGTATGATGCAATTGCAAACTTTTAGATAGCACTACTCAATTTCTAGATAT - -a -s simMouse_chr6.simMouse.chr6 600311 38 + 636262 TTGGATACACTTTGTGAAACTCTCAGTTCCTGTTTTGA -s Anc0.Anc0refChr3 197957 38 + 222631 TTAGCTAGACTCTATGAAACTCTGAGTGCATGTACTCA -s Anc1.Anc1refChr1 37630 38 + 69767 TTAGCTAGACTCTATGAAACTCTGAGTGCATGTACTCA -s Anc2.Anc2refChr1 114634 38 + 142988 TTAACTAGACTCTATGAAACTCTGAGTGCAAGTACTCA -s mr.mrrefChr3 148169 38 + 181027 TTGGATACACTCTGTGAAACTCTCAGTTCCTGTTTTGA -s simCow_chr6.simCow.chr6 573105 38 + 602619 TCAAATAGACTCTATGTAATTCTAAGTGCAAGTACTCA -s simDog_chr6.simDog.chr6 565103 38 + 593897 CTGACTAGACTCTATGAAACTCTGGGTGCAAGTACTCA -s simHuman_chr6.simHuman.chr6 568711 38 + 601863 TTAGCTAGACACTATGAAACTCTGAGACTATGTACTCA -s simRat_chr6.simRat.chr6 74677 38 - 647215 TTGGATACACTCTGTGAATCTCTAATTTCCTGTTTTGA - -a -s simMouse_chr6.simMouse.chr6 600349 45 + 636262 CTTAAATAGTCTTAAGCAGCCTCCCATAAATATCATGGTTGATTT -s Anc0.Anc0refChr3 197998 45 + 222631 GTTTTGTAGCTTTAACCAGCCTCCCTTAGATATTGGTGTTGATAA -s Anc1.Anc1refChr1 37671 45 + 69767 GTTTTGTAGCTTTAACCAGCCTCCCTTAGATATTGGTGTTGATAA -s Anc2.Anc2refChr1 114675 45 + 142988 GTCTTGTAGCTTTAACCAGCCTCCCTTAGATATTGGTGTTGATAA -s mr.mrrefChr3 148207 45 + 181027 CTTTAATAGCCTTAAGCAGCCTCCCATAAATATCATGGTTGATTT -s simCow_chr6.simCow.chr6 573146 45 + 602619 GTCTTGTAACTTTAACTAGCCTCCCTTAGATATCATTGTTGATGA -s simDog_chr6.simDog.chr6 565144 41 + 593897 GT----TAGTTTTAACCAGCTTCCCTTATATCTTGGTGTTAATAC -s simHuman_chr6.simHuman.chr6 568752 45 + 601863 GTTTTGTAGCTTTAACCAATCAGCCTTAGACATTGGAGTTGATAA -s simRat_chr6.simRat.chr6 74715 45 - 647215 CTTTCATAGCCTTAAGCAGCCTTCTATAAATATCATGGTTGACTT - -a -s simMouse_chr6.simMouse.chr6 600394 62 + 636262 AGATTCTTAATGCTGCTCTACACTTCCAGATTAGCCCAAGTGCCTCCCATAATGGTCCTGTC -s Anc0.Anc0refChr3 198043 41 + 222631 GGATTCCTCATGCTGCTCT-----------------CAA----CTCCTTCATTGGTGCTGTG -s Anc1.Anc1refChr1 37716 41 + 69767 GGATTCCTCATGCTGCTCT-----------------CAA----CTCCTTCATTGGTGCTGTG -s Anc2.Anc2refChr1 114720 41 + 142988 GGATTCCTCATGCTGCTCT-----------------TGA----CTTCTTCATTGGTGCTGTG -s mr.mrrefChr3 148252 62 + 181027 GGATTCTTAATGCTGCTCTACACTTTCAGATTAGCCCAAGTGCCTCCCATAATGGTCCTGTG -s simCow_chr6.simCow.chr6 573192 39 + 602619 GGATTCCTGATGCTGCTCT-----------------TGA----CT--TTCATTGGTGTTGAC -s simDog_chr6.simDog.chr6 565185 41 + 593897 AGGTTCCTCTTGCTGCTCT-----------------TGA----CTTCTTCATTAGTGCTGTG -s simHuman_chr6.simHuman.chr6 568797 41 + 601863 GGATTCCTCATACTGCTCT-----------------CAA----CCCCTTCATTGGTGCTTTG -s simRat_chr6.simRat.chr6 74760 62 - 647215 GGATTCTTAATGCTGCTCCACACTTTCACCTTAGCCCAAGTGCCTGCCATAATGGTCATGTG - -a -s simMouse_chr6.simMouse.chr6 600456 7 + 636262 TTAGGAT -s Anc0.Anc0refChr3 198084 7 + 222631 TCAGGAG -s Anc1.Anc1refChr1 37757 7 + 69767 TCAGGAG -s Anc2.Anc2refChr1 114761 7 + 142988 TCAGGAG -s mr.mrrefChr3 148314 7 + 181027 TTAGGAT -s simCow_chr6.simCow.chr6 573231 7 + 602619 TCAGGAA -s simDog_chr6.simDog.chr6 565231 7 + 593897 TCAGGAG -s simHuman_chr6.simHuman.chr6 568838 7 + 601863 TCAGGAG -s simRat_chr6.simRat.chr6 74822 7 - 647215 GTAGGAT - -a -s simMouse_chr6.simMouse.chr6 600463 40 + 636262 GCCCCTACACTGACAATCCCTTTTATCTTGCTTCCTGAAA -s Anc0.Anc0refChr3 198101 40 + 222631 CCTCCTGCACTGTCCATCCCCATTGTCTGGATCCCTGAAA -s Anc1.Anc1refChr1 37774 40 + 69767 CCTCCTGCACTGTCCATCCCCATTGTCTGGATCCCTGAAA -s Anc2.Anc2refChr1 114778 40 + 142988 CCTCCTGCTCTGTCCATCCCCATTGTCTGGATACCTGAAA -s mr.mrrefChr3 148321 40 + 181027 CCTCCTACACTGTCAATCCCTTTTATCTTGCTCCCTGAAA -s simCow_chr6.simCow.chr6 573260 40 + 602619 CCTCTTGCTCCGTCTAGCTCCATTGTCTGGCCTCCTGAAA -s simDog_chr6.simDog.chr6 565248 38 + 593897 CCTCCTG--CTGTTCATCCCCATTGTCTGGATACCTGAAA -s simHuman_chr6.simHuman.chr6 568855 40 + 601863 CCTCCTGCACTGTCCATCCCCATTGCCTGGATCCCTTAAA -s simRat_chr6.simRat.chr6 74829 40 - 647215 CCTCCTACACTGTCAATCGCTTTTATCTTGCTCCCTGAAA - -a -s simMouse_chr6.simMouse.chr6 600503 4 + 636262 TGGG -s Anc0.Anc0refChr3 198141 4 + 222631 GGGT -s Anc1.Anc1refChr1 37814 4 + 69767 GGGT -s Anc2.Anc2refChr1 114832 4 + 142988 GGGT -s mr.mrrefChr3 148361 4 + 181027 TGGG -s simCow_chr6.simCow.chr6 573314 4 + 602619 GGGT -s simDog_chr6.simDog.chr6 565300 4 + 593897 GGGC -s simHuman_chr6.simHuman.chr6 568895 4 + 601863 CGGT -s simRat_chr6.simRat.chr6 74869 4 - 647215 AGGG - -a -s simMouse_chr6.simMouse.chr6 600507 6 + 636262 GTGATT -s Anc0.Anc0refChr3 198149 6 + 222631 ATGTTT -s Anc1.Anc1refChr1 37822 6 + 69767 ATGTTT -s Anc2.Anc2refChr1 114840 6 + 142988 ATGTTC -s mr.mrrefChr3 148365 6 + 181027 GTGATT -s simCow_chr6.simCow.chr6 573325 6 + 602619 CTCTTC -s simDog_chr6.simDog.chr6 565308 6 + 593897 ATGTTC -s simHuman_chr6.simHuman.chr6 568903 6 + 601863 ATGTTT -s simRat_chr6.simRat.chr6 74873 6 - 647215 GTGATT - -a -s simMouse_chr6.simMouse.chr6 600513 27 + 636262 TCAAGGTGAGACCTAATATTTGGAAAA -s Anc0.Anc0refChr3 198156 16 + 222631 TCCAGCTAA-----------AGGAAAA -s Anc1.Anc1refChr1 37829 27 + 69767 TCCAGCTAATGGAAAAGAAAAGGAAAA -s Anc2.Anc2refChr1 114847 16 + 142988 TGCAGCTAA-----------AGTAAAA -s mr.mrrefChr3 148371 27 + 181027 TCAAGGTGAGACCAAATATTTGGAAAA -s simCow_chr6.simCow.chr6 573332 16 + 602619 TGCAGATAA-----------AGAAAAA -s simDog_chr6.simDog.chr6 565315 16 + 593897 TGCAACCAA-----------AGTAAGA -s simHuman_chr6.simHuman.chr6 568910 27 + 601863 TCCAGCTAATGGAAAAGAAAAGGAAAA -s simRat_chr6.simRat.chr6 74879 27 - 647215 CCAAGGTGAGACCAAATGTTTAGAAAA - -a -s simMouse_chr6.simMouse.chr6 600540 20 + 636262 AATGAAATATGGATCATGAT -s Anc0.Anc0refChr3 198173 20 + 222631 AATGAAAGGTGGATTGTGAT -s Anc1.Anc1refChr1 37857 20 + 69767 AATGAAAGGTGGATTGTGAT -s Anc2.Anc2refChr1 114864 20 + 142988 AATGAAAGGTGGATTGTGGT -s mr.mrrefChr3 148398 20 + 181027 AATGAAATATGGATCATGAT -s simCow_chr6.simCow.chr6 573349 20 + 602619 AATGAGAGGTGGGCTACGTT -s simDog_chr6.simDog.chr6 565332 20 + 593897 AGTGAAAAGTGGATTGTGGT -s simHuman_chr6.simHuman.chr6 568938 20 + 601863 AATGAAAGGTGGATTCTGAT -s simRat_chr6.simRat.chr6 74906 20 - 647215 AATCAAATATGGATCGTGAA - -a -s simMouse_chr6.simMouse.chr6 600560 27 + 636262 CACATGGTGCTGGAGCATGTTGAAGCT -s Anc0.Anc0refChr3 198193 26 + 222631 T-CCTTGTGCTGGTGCATGTCAAAGTT -s Anc1.Anc1refChr1 37877 26 + 69767 T-CCTTGTGCTGGTGCATGTCAAAGTT -s Anc2.Anc2refChr1 114884 26 + 142988 T-CCTTGTGCTGGTGCATGTCAAGGTT -s mr.mrrefChr3 148418 27 + 181027 CACATGGTGCTGGAGCATGTTGAAGCT -s simCow_chr6.simCow.chr6 573369 26 + 602619 C-CCTTGTGCTGATGCATGATAAGCTT -s simDog_chr6.simDog.chr6 565355 26 + 593897 T-GCTAGTGCTGGTGTGTGTCAAGGTT -s simHuman_chr6.simHuman.chr6 568958 26 + 601863 T-CCTTGTACTGCTGCATCTCAAAGTT -s simRat_chr6.simRat.chr6 74926 25 - 647215 CACATGGTGCTG--GCATGTTGAAGCT - -a -s simMouse_chr6.simMouse.chr6 600587 28 + 636262 CTTGAATAAAAAAAACATCATTTTGATG -s Anc0.Anc0refChr3 198239 28 + 222631 CCTAAATCCAAACAACATCATTTGCCTG -s Anc1.Anc1refChr1 37923 28 + 69767 CCTAAATCCAAACAACATCATTTGCCTG -s Anc2.Anc2refChr1 114930 28 + 142988 CCTAAATCCAAACAACATCATTTGCCTA -s mr.mrrefChr3 148465 28 + 181027 CTTGAATAAAAAAAACATCATTTTGATG -s simCow_chr6.simCow.chr6 573406 25 + 602619 CCTAAA---AAACAACATCATCTGCCTT -s simDog_chr6.simDog.chr6 565402 24 + 593897 CCTAGATCCAAACAACACCATT----TA -s simHuman_chr6.simHuman.chr6 569004 28 + 601863 CCAAAATCCAAACCATATCATGTGATTG -s simRat_chr6.simRat.chr6 74989 28 - 647215 CTTGAATAAAAAAAACATCATTGTGATG - -a -s simMouse_chr6.simMouse.chr6 600615 223 + 636262 TGATACCCCTGTATTATTTTGTATTAGCCACTTACGAGTCTGTCGTGATATACCAGCAATTACAAGAAATCAAGGGAGTTCAACAAGATGATGCCCTCCAGCTCCCAAAAGACCTCGATTATTTAACAATCAGGGATGTTACGCTAACACATGAACTAAGGGCAAAGTTACATTTTAGTCCTCCACAGACTGTTGCATATAGTAGTCCTATATGAGGAGTTGT -s Anc0.Anc0refChr3 198276 223 + 222631 TGATACCCCTGTATTATTTTCTACTAGCTACTTATGAGTCTGTCCTGTTATATCAACAGTTACAAGAAATCAAGGGAGTTCAGCAAGATGATGCTCTCCAGCTTCCAAAAGACCTAGATTATTTGACTATCAGAGATGTGACGCTGTCCCATGAACTACGGGCAAAGTTACATTTTAGTCCTCCACAGACAGTTGTATGTAGTGGTTCACAGTGAGGAGTTGT -s Anc1.Anc1refChr1 37960 223 + 69767 TGATACCCCTGTATTATTTTCTACTAGCTACTTATGAGTCTGTCCTGTTATATCAACAGTTACAAGAAATCAAGGGAGTTCAGCAAGATGATGCTCTCCAGCTTCCAAAAGACCTAGATTATTTGACTATCAGAGATGTGACGCTGTCCCATGAACTACGGGCAAAGTTACATTTTAGTCCTCCACAGACAGTTGTATGTAGTGGTTCACAGTGAGGAGTTGT -s Anc2.Anc2refChr1 114967 223 + 142988 TGATACCCCTGTATTAGTTTCTACTAGCTACTTATGAGTCTGTCCTGTTATATCAACAGTTACAAGAAATCAAGGGAGTTCAGCAAGATGATGCTCTCCAGCTTCCAAAAGACCTAGATTATTTGACTATCAGAGATGTGACCCTGTCCCATGAACTACGGGCAAAGTTACATTTTAGTCCTCCACAGACAGTTGTATGCAGTGGTTCACAATAAGGAGCTGT -s mr.mrrefChr3 148493 223 + 181027 TGATACCCCTGTATTATTTTGTATTAGCTACTTACGAGTCTGTCGTGATATATCAGCAGTTACAAGAAATCAAGGGAGTTCAGCAAGATGATGCCCTCCAGCTCCCAAAAGACCTCGATTATTTGACAATCAGGGATGTTACGCTAACACATGAACTAAGGGCAAAGTTACATTTTAGTCCTCCACAGACTGTTGTATATAGTAGTCCAAAGTGAGGAGTTGT -s simCow_chr6.simCow.chr6 573440 223 + 602619 TGATACCCCTGTATTAGTTTCTTCTAGCTACTTATGAGTCTGTCCTGTTATATCAACAGTTACAGGAAATCAAGGGGGTTCAGCAAGATGATGCTCTCCAGCTTCCAAAAGACCTGGATTATTTGACTGTCAGAGATGTGACACTGTCCCATGAACTACGGGCCAAGTTACATTGTAGTCCTCCCCAGACAGTCCTATAGGATGGTTCACAATAAGAACCTGT -s simDog_chr6.simDog.chr6 565435 204 + 593897 CG-------------------TATTAGCTACTTATGAGTCTGTCCTGTTATATCAACAGTTACAAGAAATCAAAAGAGTTCAGCAAGATGATGCTCTCCAGCTTCCAAAAGACCTAGATTATTTCATTATCAGAGATGTGACCCTGTCCCATGAACTACGGGCAAAGTTACATTTTAGCCCTCCACAGACAGTTGTATGCAGTGGTTCACAATAAGGAGCTAT -s simHuman_chr6.simHuman.chr6 569041 223 + 601863 TGATACCCCCGTATCATTTTCTACAAGCTACTTATGAGTCTGACCTGTTATATCAACAGTTACAAGAAATCAAGGGAGTTCAGCAAGATGATGCTCTCCAGCTTCCAAAAGACCTAGACTATTTGACTATCAGAGATGTGACGCTGTCCCATGAACTACGGGCAAAATTACATTTCACTCCTTCACAGACAGTGGTGTGTAGTGGTTCACAGTGAGGAGTTGG -s simRat_chr6.simRat.chr6 75017 223 - 647215 TGATACCCCTGTATTATTTTGTTTTAGCTACTTACGAATCTGTCTTGATATATCAGCAGTTACAAGAAATCAAGGGAGTTCAGCAAGATGATGCCCTCCAGCTCCCAAAAGACCTGGATTATTTGATGATCAGGGATGTTACACTAACACATGAACTAAGGGCAAAGTTACATTTTAGTCCTCCACAAACTGTCGTATATCGTAGTCAAAAGCGAGGAGTTGT - -a -s simMouse_chr6.simMouse.chr6 600838 24 + 636262 CATACGGAAAAAAGTGTATCTTGA -s Anc0.Anc0refChr3 198499 24 + 222631 AATACAGTAGGAAGTGTACTGCGA -s Anc1.Anc1refChr1 38183 24 + 69767 AATACAGTAGGAAGTGTACTGCGA -s Anc2.Anc2refChr1 115190 24 + 142988 AATACAGTAGGAAGAGTACTGCGA -s mr.mrrefChr3 148716 24 + 181027 CATACGGAAAAAAGTGTATCTTGA -s simCow_chr6.simCow.chr6 573679 24 + 602619 AATCCAGTAGGAAGTGTACTGGGA -s simDog_chr6.simDog.chr6 565639 24 + 593897 AATACAGTAGAAAGAGTACTGCGA -s simHuman_chr6.simHuman.chr6 569264 16 + 601863 AACACAGTACGAATTG-------- -s simRat_chr6.simRat.chr6 75240 24 - 647215 CATATGGAAGAAAGTATATCTTGG - -a -s simMouse_chr6.simMouse.chr6 600862 31 + 636262 AGTTAAACCCCCTGGTCTGATCCAGTCATGA -s Anc0.Anc0refChr3 198523 30 + 222631 AGTTTTA-CTCCTGGTGTGATCCAGGAGGAA -s Anc1.Anc1refChr1 38207 30 + 69767 AGTTTTA-CTCCTGGTGTGATCCAGGAGGAA -s Anc2.Anc2refChr1 115216 30 + 142988 AGTTTTA-CTGCTGATGTGATACCGGAGGAA -s mr.mrrefChr3 148740 30 + 181027 AGTTAAA-CTCCTGGTCTGATCCAGTCATAA -s simCow_chr6.simCow.chr6 573705 30 + 602619 GGTCATA-TTACTGATGTGATACAGTAGGAA -s simDog_chr6.simDog.chr6 565674 30 + 593897 AGTTTAA-CTGCTGATGTGATACCGGAGGAC -s simHuman_chr6.simHuman.chr6 569280 23 + 601863 --------CTCCTTGTGCAACCCAGCTGGAA -s simRat_chr6.simRat.chr6 75264 30 - 647215 AGCTAAA-CTCCTGGTCTGATCTGGTCATAA - -a -s simMouse_chr6.simMouse.chr6 600893 60 + 636262 GAACTGCAATAGGGATTGCTAATAGTTACCCAATTGAGGGCTTCCAGACACTGGACACCC -s Anc0.Anc0refChr3 198553 51 + 222631 GTACTGCAGTGTAAATTATTAACAAATTCCCAATTCTGACTTTCAAGACTC--------- -s Anc1.Anc1refChr1 38237 60 + 69767 GTACTGCAGTGTAAATTATTAACAAATTCCCAATTCTGACTTTCAAGACTCAGGATTCTC -s Anc2.Anc2refChr1 115248 51 + 142988 GTACTGCAGTGTAAATTATTAACAAATTCCCAATTCTGACTTTCATGAGTC--------- -s mr.mrrefChr3 148770 60 + 181027 GAACTGCAATAGAGATTGCTAACAGTTACCCAATTGAGGGTTTCCAGACTCTGGACACCC -s simCow_chr6.simCow.chr6 573737 44 + 602619 ATACTGCAGTGAAAATTATTGACAAATACCCAATCCTGACTCTC---------------- -s simDog_chr6.simDog.chr6 565706 51 + 593897 GTACTGTAGTGTAAATTACTAACAAATTCCCCATTCTGACTTTTATGAGTC--------- -s simHuman_chr6.simHuman.chr6 569303 55 + 601863 -----TCAGTGCAAATTATTAACAACTTTCAAATTTCAACTTTCAATACTCAGGATTCTA -s simRat_chr6.simRat.chr6 75294 60 - 647215 GAACGGCAGTAGAGTCTGCTAACAGTTACCCAATTCAGTGTTTTCAGACTCTGGGCGCCC - -a -s simMouse_chr6.simMouse.chr6 600953 33 + 636262 CTATACAAATAACCTGTTAGGTCTACAAATGCA -s Anc0.Anc0refChr3 198604 33 + 222631 CCATATTGGTAATCTCTTAGGTCAACATGGTAC -s Anc1.Anc1refChr1 38297 33 + 69767 CCATATTGGTAATCTCTTAGGTCAACATGGTAC -s Anc2.Anc2refChr1 115299 33 + 142988 CCATACTGGTGATCTCTTAGGTCAACATGGTAC -s mr.mrrefChr3 148830 33 + 181027 CCATATAAATAACCTGTTAGGTCTACAAATGCA -s simDog_chr6.simDog.chr6 565757 33 + 593897 CCATACTGGTGATCTCTTAGGTCAACATGGTAC -s simHuman_chr6.simHuman.chr6 569362 33 + 601863 CCATATGGGTAATCTTTTAGGTCAAGATGGCAC -s simRat_chr6.simRat.chr6 75354 33 - 647215 CCATATAAAAAACCTGTTAGGTCTACAAATGCA - -a -s simMouse_chr6.simMouse.chr6 600986 8 + 636262 TGGTCTGC -s Anc0.Anc0refChr3 198637 8 + 222631 TGGTGTTC -s Anc1.Anc1refChr1 38330 8 + 69767 TGGTGTTC -s Anc2.Anc2refChr1 115332 8 + 142988 TGATGTTC -s mr.mrrefChr3 148863 8 + 181027 TGGTCTGC -s simDog_chr6.simDog.chr6 565792 8 + 593897 TGATGTTC -s simHuman_chr6.simHuman.chr6 569395 8 + 601863 TGGTATTC -s simRat_chr6.simRat.chr6 75387 8 - 647215 TGGTCTGC - -a -s simMouse_chr6.simMouse.chr6 600994 40 + 636262 CAAAAAACGACATAAGTAAAGATAGTTTTCTATGAAAATT -s Anc0.Anc0refChr3 198646 23 + 222631 CAGGAAAAGATTTAAGTAAAGAT----------------- -s Anc1.Anc1refChr1 38339 40 + 69767 CAGGAAAAGATTTAAGTAAAGATAGTCTCTTAGATAAAAT -s Anc2.Anc2refChr1 115341 23 + 142988 CAGGAAAAGATTTAAGTAAAGAT----------------- -s mr.mrrefChr3 148871 40 + 181027 CAAGAAAAGACATAAGTAAAGATAGTCTTCTATGAAAATT -s simDog_chr6.simDog.chr6 565801 23 + 593897 CAGGAAAAGATTTAAGTAAAGAT----------------- -s simHuman_chr6.simHuman.chr6 569404 40 + 601863 CAGGAAAAGGTTTAAATAGAGATAGTCTCTTAGATAAAAT -s simRat_chr6.simRat.chr6 75395 39 - 647215 CATGAAAAGACATAAG-AAAGGCAGTCTACTATGCAAATT - -a -s simMouse_chr6.simMouse.chr6 601034 5 + 636262 TTTCT -s Anc1.Anc1refChr1 38379 5 + 69767 TATTG -s mr.mrrefChr3 148911 5 + 181027 TTTCT -s simHuman_chr6.simHuman.chr6 569444 5 + 601863 TATTG -s simRat_chr6.simRat.chr6 75436 5 - 647215 TTTCT - -a -s simMouse_chr6.simMouse.chr6 601039 43 + 636262 GTCACACCCATGATGATATCTCGTGGGGACATTCCAATTTCAG -s Anc0.Anc0refChr3 198669 41 + 222631 --CGCTCCCAGCATGAGGTATCACACAGATCTTCCAATTGCAG -s Anc1.Anc1refChr1 38384 43 + 69767 CTCGCTCCCAGCATGAGGTATCACACAGATCTTCCAATTGCAG -s Anc2.Anc2refChr1 115364 41 + 142988 --TGCTGCAAGCTTAAGGTATCACACAAATCGTCCATTTGCGG -s mr.mrrefChr3 148916 43 + 181027 CTCACACCCATGATGATATCTCATGGGGATATTCCAATTTCAG -s simCow_chr6.simCow.chr6 573781 13 + 602619 -------CAAACTTAGGGT-----------------------G -s simDog_chr6.simDog.chr6 565824 41 + 593897 --TGCTGCAAGCTTAAGATATCACACAAATCGTCCATTTGCGG -s simHuman_chr6.simHuman.chr6 569449 43 + 601863 CCCGCCCCCAGCATGACGTATTACACAGATTTTCCAATTGCAG -s simRat_chr6.simRat.chr6 75442 43 - 647215 CTCACTCCAACAATTATATCTCATGTGGATATTCCAATTTCAC - -a -s simMouse_chr6.simMouse.chr6 601082 13 + 636262 AGTTCCAAGAACA -s Anc0.Anc0refChr3 198713 13 + 222631 AGGTCCCACAGCG -s Anc1.Anc1refChr1 38430 13 + 69767 AGGTCCCACAGCG -s Anc2.Anc2refChr1 115408 13 + 142988 AGGTCCCACAGCG -s mr.mrrefChr3 148959 13 + 181027 AGTTCCAAGAACA -s simCow_chr6.simCow.chr6 573797 11 + 602619 AGGT--CGCAGCA -s simDog_chr6.simDog.chr6 565868 13 + 593897 AGGTCCCACAGCG -s simHuman_chr6.simHuman.chr6 569495 12 + 601863 AGGTCCCACAGC- -s simRat_chr6.simRat.chr6 75485 13 - 647215 GGTTCCAGGAATA - -a -s simMouse_chr6.simMouse.chr6 601095 172 + 636262 ATATAGTTTTGGTAGTGGATTCTTATCTTGTCTACCACACACTGATTTGTTTCACATTAGGCTAATCACTTATTCAACTGAACCTAATTAGTCCTTTCAAAATTGATAGCCTAAACAAGTATGTCATGAATTGTAGAGTCCATTGCCTTGCGTATCACACCTGTTTAGGTCT -s Anc0.Anc0refChr3 198726 100 + 222631 ATTTAATGTTGGTAATGAATTTTTATTTT--TTACAATACACTCATCTGTGTCACATTAGGCTAATCTCTTTTTCAA--------------------------------------------------------------------CCAGACGCACCAACCTTTTTTTGGA-- -s Anc1.Anc1refChr1 38443 100 + 69767 ATTTAATGTTGGTAATGAATTTTTATTTT--TTACAATACACTCATCTGTGTCACATTAGGCTAATCTCTTTTTCAA--------------------------------------------------------------------CCAGACGCACCAACCTTTTTTTGGA-- -s Anc2.Anc2refChr1 115428 100 + 142988 ATTTTATGTTAGTAATGAATTTTTATTTC--TTCCAATACAATCATCTGTGTCACATCAGGCTAACCTCTTTTTCAA--------------------------------------------------------------------CTAGAGGCACCAACCTTTGTTTCAC-- -s mr.mrrefChr3 148972 146 + 181027 ATATAGTTTTGGTAATGGATTCTTATCTTGTCTACCACACACTGATTTGTTTCACATTAGGCTAATCACTTTTTCAACTGAACCTAATTAGTC--------------------------TATGTCATGAATTGTAGAGTCCATTGCCATACGTATCACACCTGTTTAGGACT -s simCow_chr6.simCow.chr6 573815 98 + 602619 ATTTTATGTTAGTAGCGGATGTTCATTTC--CTCCACCCCCGTCATCCGT-TCACATCAGCCCAACCTCTTTTTCCA--------------------------------------------------------------------CTGGAAGGGCCAA-CTTTGGTTCAC-- -s simDog_chr6.simDog.chr6 565888 100 + 593897 ATTTTGAGTTAGCAATGAATTTTTATTTC--TTCCAATAAAAATATCTGTGTCAGGTCAGGCTAACCTCTTTTTCAA--------------------------------------------------------------------CTAGAGGCACCAACCTTTGTTCCAC-- -s simHuman_chr6.simHuman.chr6 569507 97 + 601863 -TTTAATGGTGATAATGAATTTCTATTTT--TTACAATACACTCTTCTGTCTTCCATTAAGCT--TTTGTTTTTCAA--------------------------------------------------------------------CCACACGCACCATCCTTTTATTGGA-- -s simRat_chr6.simRat.chr6 75498 146 - 647215 ATATAGTTTTGGTAATGGATTCTTATCTTGTCTAACACACATTGAGTTTTATCACATTAGGCTAACCGCCTTATCAACTGAACCTAATCAGCC--------------------------TATGTCATGAATTGTGGCATCCATTGGCATACATATCACAGCTGTTTAGGACT - -a -s simMouse_chr6.simMouse.chr6 601267 22 + 636262 AGCTGAGGCACCTTCCTTTCTG -s Anc0.Anc0refChr3 198826 3 + 222631 -------------------CTG -s Anc1.Anc1refChr1 38543 3 + 69767 -------------------CTG -s Anc2.Anc2refChr1 115528 3 + 142988 -------------------CTG -s mr.mrrefChr3 149118 16 + 181027 AGCTGAGGCA------TTTCTG -s simCow_chr6.simCow.chr6 573913 3 + 602619 -------------------CAG -s simDog_chr6.simDog.chr6 565988 3 + 593897 -------------------CTG -s simHuman_chr6.simHuman.chr6 569604 3 + 601863 -------------------CTG -s simRat_chr6.simRat.chr6 75645 16 - 647215 AGCTGCAGCA------GTTCTG - -a -s simMouse_chr6.simMouse.chr6 601289 59 + 636262 AAACAATTCTAAAAGGAGCTTCTAATCATCCAAACAAGGTCCTAGGTCAAGCATTACTC -s Anc0.Anc0refChr3 198829 59 + 222631 GAGGCCTTCTAGTTTGAGGTTTTAATAACACAAATGAGGTCATGAGTCAAGCATTACTC -s Anc1.Anc1refChr1 38546 59 + 69767 GAGGCCTTCTAGTTTGAGGTTTTAATAACACAAATGAGGTCATGAGTCAAGCATTACTC -s Anc2.Anc2refChr1 115538 59 + 142988 GAGGTCTTCTAGTTTGGGGTTTTAACAACACAAATGGGATCACGAGTCAAGCATTGCTC -s mr.mrrefChr3 149134 59 + 181027 AAAGCCTTCTAGAAGGAGCTTCTAATCATCCAAACAAGGTCCTAGGTCAAGCATTACTC -s simCow_chr6.simCow.chr6 573923 43 + 602619 GATGTCTTTTAGTTTAGGGTTCT----------------TCACGGGTCAAGCATTTCTC -s simDog_chr6.simDog.chr6 565998 59 + 593897 GAGGTATTCTAGTCTGGGGTTTTAACAACACAAATGGGATCGCAAGTCAATCATTGTTC -s simHuman_chr6.simHuman.chr6 569607 59 + 601863 GAGGCCTTCTTGTTTGAGGTTTTAATTGCACAAATGAGGTCATGAGTCAAGCATCACTC -s simRat_chr6.simRat.chr6 75661 59 - 647215 CCAGCCCTGAAGAACGAGCTTCTAATCATCCAAACAAGGTCCTAGGTCAAGCGTTGCTC - -a -s simMouse_chr6.simMouse.chr6 601348 37 + 636262 ATAACCCTTCACAAACAGAACCTATTGCCATGTGTAC -s Anc0.Anc0refChr3 198888 37 + 222631 ATAACTCTTCATAAACAACACATATGCCAATGTGCAC -s Anc1.Anc1refChr1 38605 37 + 69767 ATAACTCTTCATAAACAACACATATGCCAATGTGCAC -s Anc2.Anc2refChr1 115597 37 + 142988 AAAACTCTTCATAAACAACATATATGCCAATGTGCAC -s mr.mrrefChr3 149193 37 + 181027 ATAACCCTTCACAAACAGCACATATTGCCATGTGTAC -s simCow_chr6.simCow.chr6 573966 37 + 602619 ACAACTCTTTGCAAACAATCTATATGCCAATGTGCAC -s simDog_chr6.simDog.chr6 566057 35 + 593897 AAAAC-CCTCATGAACAACATA-ATGCTAATGTGCAC -s simHuman_chr6.simHuman.chr6 569666 37 + 601863 GTAACTCTTCTTAAACCACACATATATCAACGTGCAC -s simRat_chr6.simRat.chr6 75723 31 - 647215 ATAACCCTTCACAAACAGCACATGTTATCAT------ - -a -s simMouse_chr6.simMouse.chr6 601385 8 + 636262 TTTGATTA -s Anc0.Anc0refChr3 198925 8 + 222631 AGTGATTA -s Anc1.Anc1refChr1 38642 8 + 69767 AGTGATTA -s Anc2.Anc2refChr1 115635 8 + 142988 AGTGATCA -s mr.mrrefChr3 149230 8 + 181027 TTTGATTA -s simCow_chr6.simCow.chr6 574004 8 + 602619 AGGGATTA -s simDog_chr6.simDog.chr6 566093 8 + 593897 AGTGATCA -s simHuman_chr6.simHuman.chr6 569703 7 + 601863 AGTGA-TG -s simRat_chr6.simRat.chr6 75754 3 - 647215 -----TTA - -a -s simMouse_chr6.simMouse.chr6 601393 2 + 636262 CA -s Anc0.Anc0refChr3 198933 2 + 222631 CA -s Anc1.Anc1refChr1 38650 2 + 69767 CA -s Anc2.Anc2refChr1 115643 2 + 142988 CC -s mr.mrrefChr3 149238 2 + 181027 CA -s simCow_chr6.simCow.chr6 574073 2 + 602619 CC -s simDog_chr6.simDog.chr6 566101 2 + 593897 CC -s simHuman_chr6.simHuman.chr6 569710 2 + 601863 CA -s simRat_chr6.simRat.chr6 75757 2 - 647215 GA - -a -s simMouse_chr6.simMouse.chr6 601395 1 + 636262 G -s Anc0.Anc0refChr3 198935 1 + 222631 A -s Anc1.Anc1refChr1 38652 1 + 69767 A -s Anc2.Anc2refChr1 115647 1 + 142988 A -s mr.mrrefChr3 149240 1 + 181027 G -s simCow_chr6.simCow.chr6 574077 1 + 602619 A -s simDog_chr6.simDog.chr6 566105 1 + 593897 A -s simHuman_chr6.simHuman.chr6 569712 1 + 601863 A -s simRat_chr6.simRat.chr6 75759 1 - 647215 G - -a -s simMouse_chr6.simMouse.chr6 601396 16 + 636262 ACACCCTATTGAGCAG -s Anc0.Anc0refChr3 198936 16 + 222631 ACAACCTACTGAGGGT -s Anc1.Anc1refChr1 38653 16 + 69767 ACAACCTACTGAGGGT -s Anc2.Anc2refChr1 115648 16 + 142988 ACAACCTAATGAGGGT -s mr.mrrefChr3 149241 16 + 181027 ACACCCTACTGAGCAG -s simCow_chr6.simCow.chr6 574078 16 + 602619 ACAACCTAATCAGGGT -s simDog_chr6.simDog.chr6 566116 16 + 593897 ACAACCTAATGAGGGT -s simHuman_chr6.simHuman.chr6 569713 16 + 601863 ACAACCTACTGAGGGT -s simRat_chr6.simRat.chr6 75760 16 - 647215 ACACCCTACTGGGCAG - -a -s simMouse_chr6.simMouse.chr6 601412 36 + 636262 CTTATCCACACTGCAAACATTTGTGCACCCAAATAT -s Anc0.Anc0refChr3 198973 33 + 222631 CATGACCACACTGCCAACATTGCTGCACTC---TAT -s Anc1.Anc1refChr1 38690 33 + 69767 CATGACCACACTGCCAACATTGCTGCACTC---TAT -s Anc2.Anc2refChr1 115685 33 + 142988 GATGACCAAACTGCCAACATTGCTGCACTC---TAT -s mr.mrrefChr3 149278 36 + 181027 CATGTCCACACTGCAAACATTTGTGCACCCAAATAT -s simCow_chr6.simCow.chr6 574117 33 + 602619 TATGACCAGATTGCCTACATTTCTGAACTC---CAT -s simDog_chr6.simDog.chr6 566146 33 + 593897 GGTGACTGAACTGCGAACATTGCCACACCC---TGT -s simHuman_chr6.simHuman.chr6 569750 33 + 601863 CATGACCACACTGCCAACATTCATGCACTC---TAT -s simRat_chr6.simRat.chr6 75798 36 - 647215 CATGTCCACACTGCAAACATTTGCACACCCCGATAT - -a -s simMouse_chr6.simMouse.chr6 601448 46 + 636262 TTAAGGGATATAAAGAGAACAACCTTAGACAGGGAAGTGTAGACTC -s Anc0.Anc0refChr3 199006 42 + 222631 TTAAGGGGTAT--ATAAGATAAGCTTAGACA--GAAGTGGTGACTA -s Anc1.Anc1refChr1 38723 42 + 69767 TTAAGGGGTAT--ATAAGATAAGCTTAGACA--GAAGTGGTGACTA -s Anc2.Anc2refChr1 115718 42 + 142988 TTAAGGGGTAT--ATAAGATAAGCCTAGACA--GAAGTGGTGACTA -s mr.mrrefChr3 149314 44 + 181027 TTAAGGGATAT--ATAAGACAACCTTAGACAGGGAAGTGTTGACTC -s simCow_chr6.simCow.chr6 574267 42 + 602619 TTACAGGGTAT--ACAAGATAAGCCCATACA--GAAGTGGTGATTA -s simDog_chr6.simDog.chr6 566179 41 + 593897 TTAAGGGGTAT--ATAAAATAAGC-TAGACA--GAAGTAGTGACTA -s simHuman_chr6.simHuman.chr6 569783 42 + 601863 TTAACAGGTAT--ATGAGATAATCTTAGACC--GAAGTGGTGACTA -s simRat_chr6.simRat.chr6 75834 44 - 647215 TTAAGGGAGAT--ATAAGACAACAATAGACAGGGAAGTGCTGACTC - -a -s simMouse_chr6.simMouse.chr6 601494 4 + 636262 CCAC -s Anc1.Anc1refChr1 38768 4 + 69767 CCGC -s mr.mrrefChr3 149358 4 + 181027 CCAC -s simHuman_chr6.simHuman.chr6 569828 4 + 601863 CCGC -s simRat_chr6.simRat.chr6 75878 4 - 647215 CCAC - -a -s simMouse_chr6.simMouse.chr6 601498 49 + 636262 AAGCCATGTACAGGCAATGTCTGTTGAACAATGGATTACCAAGAATAAC -s Anc0.Anc0refChr3 199051 33 + 222631 -AGC------CTGGCAATGTCTGT---------ATTTAACAAGAACATC -s Anc1.Anc1refChr1 38772 34 + 69767 AAGC------CTGGCAATGTCTGT---------ATTTAACAAGAACATC -s Anc2.Anc2refChr1 115763 33 + 142988 -AGA------CTGGTGATGTCTGT---------ATTTAACAAGAACATC -s mr.mrrefChr3 149362 49 + 181027 AAGCCATGTACTGGCAATGTCTGTTGAACAATGGATTAACAAGAATAAC -s simCow_chr6.simCow.chr6 574319 33 + 602619 -GGT------ACGGTGATGTCTGC---------ATTTAACAAGAACATT -s simDog_chr6.simDog.chr6 566223 27 + 593897 -ATA------CTGGTGATGTCAGT---------ATTT------ACCATC -s simHuman_chr6.simHuman.chr6 569832 34 + 601863 AAGC------CTGGCAGTGTCTAT---------ATTCAACAAGAACATC -s simRat_chr6.simRat.chr6 75907 49 - 647215 ATGCCATGTACTGGCAATTTTTGTTAAACAATGTATTAACAAGAGTAGC - -a -s simMouse_chr6.simMouse.chr6 601547 40 + 636262 TACACAAACTAAATAAACCTCATATAAACACTAGCATCAG -s Anc0.Anc0refChr3 199086 40 + 222631 TACCCAAACTAATTAAATCTCATATAAACACTGGTTTCAG -s Anc1.Anc1refChr1 38808 40 + 69767 TACCCAAACTAATTAAATCTCATATAAACACTGGTTTCAG -s Anc2.Anc2refChr1 115798 40 + 142988 TACCCAAGCTAATTAAATCTCATATAAGCACTGGTTTCAA -s mr.mrrefChr3 149413 40 + 181027 TACACAAACTAAATAAACCTCATATAAACACTAGCATCAG -s simCow_chr6.simCow.chr6 574354 40 + 602619 TACCCAAGCTAGTTAGATCTCATATAAGCACTGGTTTCAA -s simDog_chr6.simDog.chr6 566252 39 + 593897 TACCTAAGCTAAGTAAATCTCATATAAGCTTTGGTTTCA- -s simHuman_chr6.simHuman.chr6 569868 40 + 601863 TGCCCAAAATAATTAAATATCATATAAACACTGGGTTCAG -s simRat_chr6.simRat.chr6 75958 40 - 647215 CACACATACTAAGTAAACTTCATACAAACACTCGCATCAG - -a -s simMouse_chr6.simMouse.chr6 601587 7 + 636262 TACGGCT -s Anc0.Anc0refChr3 199128 3 + 222631 TAC---- -s Anc1.Anc1refChr1 38850 7 + 69767 TACAGCT -s Anc2.Anc2refChr1 115840 3 + 142988 CAC---- -s mr.mrrefChr3 149453 7 + 181027 TACAGCT -s simCow_chr6.simCow.chr6 574396 3 + 602619 CAC---- -s simDog_chr6.simDog.chr6 566293 3 + 593897 CAC---- -s simHuman_chr6.simHuman.chr6 569910 7 + 601863 TACAGCT -s simRat_chr6.simRat.chr6 75998 7 - 647215 TACAGCC - -a -s simMouse_chr6.simMouse.chr6 601594 20 + 636262 AGCAAGTCATTGCAAAGTCA -s Anc1.Anc1refChr1 38857 20 + 69767 AACAAATCATTGCAGACTCA -s mr.mrrefChr3 149460 20 + 181027 AGCAAGTCATTGCAAAGTCA -s simHuman_chr6.simHuman.chr6 569920 20 + 601863 AACAAATCATTGCAGACTCA -s simRat_chr6.simRat.chr6 76005 20 - 647215 AGCGAGTCATTGCAAAGTCG - -a -s simMouse_chr6.simMouse.chr6 601614 50 + 636262 TACCTTAAGTTTGCCTCTGATCTGTCACAATACAGGCTACTTAAATAATG -s Anc0.Anc0refChr3 199138 50 + 222631 TCCCCCCAATTACACTCTGATCTGTTGCAATACATGTTACTTAAATAAGT -s Anc1.Anc1refChr1 38884 50 + 69767 TCCCCCCAATTACACTCTGATCTGTTGCAATACATGTTACTTAAATAAGT -s Anc2.Anc2refChr1 115850 50 + 142988 TCCCCCCAATTACACTCTGATCTGTTGCAATACACATCACTTAAATAAGT -s mr.mrrefChr3 149480 50 + 181027 TACCTTAAGTTTGACTCTGATCTGTCACAATACATGTTACTTAAATAATT -s simCow_chr6.simCow.chr6 574406 49 + 602619 TCCTCCCAACTACACTCTGATCTGTTGTGATCCCCAT-ACTTAAATTATT -s simDog_chr6.simDog.chr6 566303 50 + 593897 TCCCCCCAGTTACACTGTGATCTGTTGCAATACACATCACTTATATAGGT -s simHuman_chr6.simHuman.chr6 570003 48 + 601863 TCCCCCCAATTACACTCTGATCTG--GCAATACATGTTACTTAAATAAGT -s simRat_chr6.simRat.chr6 76025 49 - 647215 TACCTTAACTTTGACTCTGATTTGTCACAATACATGTTACTTAAA-AACT - -a -s simMouse_chr6.simMouse.chr6 601664 37 + 636262 GGGCTCCTGCACTGATACCACAGATAATGCAAATATC -s Anc0.Anc0refChr3 199210 28 + 222631 GGACTCCTACTAA---------AATTATATACTCACC -s Anc1.Anc1refChr1 38956 28 + 69767 GGACTCCTACTAA---------AATTATATACTCACC -s Anc2.Anc2refChr1 115929 28 + 142988 GGACTCCTACTAA---------AATTATATACTCACC -s mr.mrrefChr3 149530 28 + 181027 GGGCTCCTGCACT---------GATAATGTAAACATC -s simCow_chr6.simCow.chr6 574484 28 + 602619 GGACCCTGGCAGA---------AGATATATGCTCACC -s simDog_chr6.simDog.chr6 566382 28 + 593897 GGAGTCCTACTAA---------AATTATGTATTCACC -s simHuman_chr6.simHuman.chr6 570073 28 + 601863 GGACTCCTCCGTA---------AATTATATACTCACT -s simRat_chr6.simRat.chr6 76074 28 - 647215 GCGCTCCTGCACT---------GATAATGTAAACATC - -a -s simMouse_chr6.simMouse.chr6 601701 62 + 636262 GAGTGAGGTTTCTGTGTGTTCCTACAGCCAATTAGGGTACTCATGGGAGTAGTTGCCAGGGC -s Anc0.Anc0refChr3 199238 62 + 222631 GAGGGAGGTCTCTGTGTTAGCCCATGGCTGGTCAGAGTAGTCATGGGAGTAGATGCCAGGGC -s Anc1.Anc1refChr1 38984 62 + 69767 GAGGGAGGTCTCTGTGTTAGCCCATGGCTGGTCAGAGTAGTCATGGGAGTAGATGCCAGGGC -s Anc2.Anc2refChr1 115965 62 + 142988 GAGGGAGGTCTCTGTGTTAGCCCATGGCTGGTCAGAGTGGTCATGGGAGCAGATGCCAGGGC -s mr.mrrefChr3 149558 62 + 181027 GAGGGAGGTCTCTGTGTGTTCCCACAGCCAATCAGAGTACTCATGGGAGTAGTTGCCAGGGC -s simCow_chr6.simCow.chr6 574520 62 + 602619 GGGGGAGGACTATGTGTTCGTCCATGTCTGGTCAAAGTGGTTATGGGAGAGGATGTCAGGGC -s simDog_chr6.simDog.chr6 566418 61 + 593897 GAGG-GGATCTCTGTGCTAGCCCATGGCTGGTCAGAGTGGTCATGGGAGCAGATGCAAGGGC -s simHuman_chr6.simHuman.chr6 570101 62 + 601863 GAGGAAGGTCTCCGTGTAAGCCCATGGCTGGTCAGAACAGTCAGGGGAGTTCATCCCAGGGC -s simRat_chr6.simRat.chr6 76102 61 - 647215 CAGGGAGGTCTCTATGTGTTTCCACAGTCAATCAGAGTGCTTATGCG-GTAGGTGCCAGGGC - -a -s simMouse_chr6.simMouse.chr6 601763 20 + 636262 ATAGCATTATCAATTATCAC -s Anc0.Anc0refChr3 199300 20 + 222631 ATAGCACCACCACTTTTCAC -s Anc1.Anc1refChr1 39046 20 + 69767 ATAGCACCACCACTTTTCAC -s Anc2.Anc2refChr1 116027 20 + 142988 ATAGCACCACCACTTTTCAC -s mr.mrrefChr3 149620 20 + 181027 ATAGCACTACCACTTATCAC -s simCow_chr6.simCow.chr6 574582 20 + 602619 ATAGCACCACCACTTTTTAC -s simDog_chr6.simDog.chr6 566479 20 + 593897 ATAGAACCACCATTTTTCAC -s simHuman_chr6.simHuman.chr6 570172 20 + 601863 ATAGCACCACCACTTTTCAC -s simRat_chr6.simRat.chr6 76163 20 - 647215 ATAGTGCTACCACTTATCAC - -a -s simMouse_chr6.simMouse.chr6 601783 11 + 636262 TATCTGACTGA -s Anc0.Anc0refChr3 199341 11 + 222631 TATTTTACTGA -s Anc1.Anc1refChr1 39087 11 + 69767 TATTTTACTGA -s Anc2.Anc2refChr1 116068 11 + 142988 TACTTTACTGA -s mr.mrrefChr3 149640 11 + 181027 TATCTGACTGA -s simCow_chr6.simCow.chr6 574623 11 + 602619 TACCTTACTGA -s simDog_chr6.simDog.chr6 566521 11 + 593897 TACTTTACTGA -s simHuman_chr6.simHuman.chr6 570213 11 + 601863 TATTTTACTAA -s simRat_chr6.simRat.chr6 76183 11 - 647215 TATCTAATTCC - -a -s simMouse_chr6.simMouse.chr6 601794 12 + 636262 GGGTTTTGCGAA -s Anc0.Anc0refChr3 199357 12 + 222631 GGGTTTTGCTAA -s Anc1.Anc1refChr1 39103 12 + 69767 GGGTTTTGCTAA -s Anc2.Anc2refChr1 116084 12 + 142988 GGGTATTGCTAA -s mr.mrrefChr3 149651 12 + 181027 GGGTTTTGCGAA -s simCow_chr6.simCow.chr6 574650 12 + 602619 TGGTACTGCCAA -s simDog_chr6.simDog.chr6 566537 12 + 593897 GAGTATGGCTAA -s simHuman_chr6.simHuman.chr6 570230 12 + 601863 GGTTTTTGCTAA -s simRat_chr6.simRat.chr6 76194 12 - 647215 AGGTCTTGACAA - -a -s simMouse_chr6.simMouse.chr6 601806 37 + 636262 TAGGATTCAGGTCTCTCAGGCCTGACAGAGAGGTATT -s Anc0.Anc0refChr3 199369 37 + 222631 AAAGATTCAGGCCTCTTCAGCTTGACAGAGAAGTATG -s Anc1.Anc1refChr1 39115 37 + 69767 AAAGATTCAGGCCTCTTCAGCTTGACAGAGAAGTATG -s Anc2.Anc2refChr1 116096 37 + 142988 AAAGATTCAGGCCTCTTCAGCTTGACAGAGAAGTATG -s mr.mrrefChr3 149663 37 + 181027 TAGGATTCAGGTCTCTCAGGCCTGACAGAGAGGTATT -s simCow_chr6.simCow.chr6 574679 36 + 602619 AGAGATTCAGGCACCTCCAGCTTGACTGGGAGGTAT- -s simDog_chr6.simDog.chr6 566549 37 + 593897 AAGGATTCAGGCCTCTTCAGCTTGATAGAGCAGTGTG -s simHuman_chr6.simHuman.chr6 570242 37 + 601863 AAAGATGCAAGCCTCTTCTACTTGACAGAGATGTATG -s simRat_chr6.simRat.chr6 76206 37 - 647215 TCGGATTCAGGTCTTTCAGGCCAGACAGAGAGGTATT - -a -s simMouse_chr6.simMouse.chr6 601843 20 + 636262 ATTCTCCATCACCTTGATCA -s Anc0.Anc0refChr3 199406 20 + 222631 CTTCCCCATTACCTTAGTCC -s Anc1.Anc1refChr1 39152 20 + 69767 CTTCCCCATTACCTTAGTCC -s Anc2.Anc2refChr1 116148 20 + 142988 CTTCCCCATTACCTTAGTCC -s mr.mrrefChr3 149700 20 + 181027 ATTCTCCATTACCTTAATCA -s simCow_chr6.simCow.chr6 574730 20 + 602619 CTTCCCTATTGCCCTAGTGC -s simDog_chr6.simDog.chr6 566601 20 + 593897 CTTCTCCATTACCTTAGGCT -s simHuman_chr6.simHuman.chr6 570279 20 + 601863 CTTCCCCATTACCTTAGTCC -s simRat_chr6.simRat.chr6 76243 20 - 647215 ATTCTCCATTACCCTAATCA - -a -s simMouse_chr6.simMouse.chr6 601863 124 + 636262 TCGGGGGAAGGTTAAAGATTTCATGTTGTTCTTTTTTTTTAGTGGCTTTCATAatgttgttctttttgtttaatggctttcatataacatgtatcttagtctacgagcgtgcaacctcaggtca -s Anc0.Anc0refChr3 199426 16 + 222631 TC--CAAATGGTGAGAGA---------------------------------------------------------------------------------------------------------- -s Anc1.Anc1refChr1 39172 16 + 69767 TC--CAAATGGTGAGAGA---------------------------------------------------------------------------------------------------------- -s Anc2.Anc2refChr1 116168 16 + 142988 TC--CAAATGGTGAGACA---------------------------------------------------------------------------------------------------------- -s mr.mrrefChr3 149720 95 + 181027 TCGGGGGAAGGTTAAAGATTTCATGTTGTTCTTTTTTTTTAGTG-----------------------------tggctttcatataacatgtatcttagtctacgagcgtgcaacctcaggtca -s simCow_chr6.simCow.chr6 574757 16 + 602619 TC--AAAATGGTGAGGCA---------------------------------------------------------------------------------------------------------- -s simDog_chr6.simDog.chr6 566621 16 + 593897 GC--CAACTGGCGAGACA---------------------------------------------------------------------------------------------------------- -s simHuman_chr6.simHuman.chr6 570299 16 + 601863 TC--CACACGGTGAGAGA---------------------------------------------------------------------------------------------------------- -s simRat_chr6.simRat.chr6 76263 95 - 647215 CCAGGGGAAGACTAGAGATTTCATGTTGTTCCATTTGCTCAGTG-----------------------------TGGCTTTCATATAACCCGTATTGTAGTCTAAGCGGGCGCAACCTCAGGTCA - -a -s simMouse_chr6.simMouse.chr6 601987 132 + 636262 tggcattaggacgtagcaccaatgttcaaggcaaaaaattttgatgtacaccaaacgcaactcgaaaggtcctaacttctagactctatgtatacaaattacatcttgtggagtGATGGTCAGATCTCTCCC -s Anc0.Anc0refChr3 199442 11 + 222631 -------------------------------------------------------------------------------------------------------------------------GGACCTCTCCC -s Anc1.Anc1refChr1 39188 11 + 69767 -------------------------------------------------------------------------------------------------------------------------GGACCTCTCCC -s Anc2.Anc2refChr1 116184 11 + 142988 -------------------------------------------------------------------------------------------------------------------------GGACTTCTCCC -s mr.mrrefChr3 149815 132 + 181027 tggcattaggacgtagcaccaatgttcaaggcaaaaaattttgatgtacaccaaacgcaactcgaaaggtcctaacttctagactctatgtatacaaattacatcttgtggagtGATGGTCAGATCTCTCCC -s simCow_chr6.simCow.chr6 574773 11 + 602619 -------------------------------------------------------------------------------------------------------------------------GGACTTCACCT -s simDog_chr6.simDog.chr6 566637 11 + 593897 -------------------------------------------------------------------------------------------------------------------------GGACTTCTCCC -s simHuman_chr6.simHuman.chr6 570315 11 + 601863 -------------------------------------------------------------------------------------------------------------------------GGACCTCTCCC -s simRat_chr6.simRat.chr6 76367 132 - 647215 TAACATTAGGACATAGCACCAATGTTCAAGGCAAATAATTTTGATACACACAAAATGCAACTTGAAAAGTCCTCACTTCTAGACTGTATGCACACAAAATACATCCTGTGGAGTACTGGTCAAATCTCTCCA - -a -s simMouse_chr6.simMouse.chr6 602119 5 + 636262 CCCAG -s Anc0.Anc0refChr3 199455 5 + 222631 CTCAA -s Anc1.Anc1refChr1 39201 5 + 69767 CTCAA -s Anc2.Anc2refChr1 116197 5 + 142988 CTCAA -s mr.mrrefChr3 149947 5 + 181027 CCCAG -s simCow_chr6.simCow.chr6 574786 5 + 602619 CTCAA -s simDog_chr6.simDog.chr6 566650 5 + 593897 CACAA -s simHuman_chr6.simHuman.chr6 570328 5 + 601863 CTCAA -s simRat_chr6.simRat.chr6 76499 5 - 647215 CCCAG - -a -s simMouse_chr6.simMouse.chr6 602124 11 + 636262 GTAGTTTTATC -s Anc0.Anc0refChr3 199460 11 + 222631 GAAGTCCTTGC -s Anc1.Anc1refChr1 39206 11 + 69767 GAAGTCCTTGC -s Anc2.Anc2refChr1 116203 11 + 142988 GAAGGCCTTGC -s mr.mrrefChr3 149952 11 + 181027 GTAGTTTTATC -s simCow_chr6.simCow.chr6 574792 11 + 602619 GAAGGCCTTGC -s simDog_chr6.simDog.chr6 566656 11 + 593897 GAAGGCCCTGC -s simHuman_chr6.simHuman.chr6 570333 11 + 601863 GAAATCCTTGC -s simRat_chr6.simRat.chr6 76504 11 - 647215 GCGGTTTTATC - -a -s simMouse_chr6.simMouse.chr6 602135 16 + 636262 AGCTGTACTTTACTAC -s Anc0.Anc0refChr3 199507 15 + 222631 AGTTGTAC-TCACTGC -s Anc1.Anc1refChr1 39253 15 + 69767 AGTTGTAC-TCACTGC -s Anc2.Anc2refChr1 116250 15 + 142988 AGTTGTAC-TCACTGC -s mr.mrrefChr3 149963 16 + 181027 AGTTGTACTTTACTGC -s simCow_chr6.simCow.chr6 574839 15 + 602619 ACATGTAC-TCACTGC -s simDog_chr6.simDog.chr6 566703 15 + 593897 AGTTGTAT-TTACTGC -s simHuman_chr6.simHuman.chr6 570380 15 + 601863 AGTTGTAC-TCACTGC -s simRat_chr6.simRat.chr6 76515 16 - 647215 AGTTGTGCTTTACTGC - -a -s simMouse_chr6.simMouse.chr6 602151 7 + 636262 TAGCAGG -s Anc0.Anc0refChr3 199544 7 + 222631 TAGCAGG -s Anc1.Anc1refChr1 39290 7 + 69767 TAGCAGG -s Anc2.Anc2refChr1 116287 7 + 142988 TAGTAGG -s mr.mrrefChr3 149990 7 + 181027 TAGCAGG -s simCow_chr6.simCow.chr6 574876 7 + 602619 TAGTAGT -s simDog_chr6.simDog.chr6 566740 6 + 593897 TAGTA-G -s simHuman_chr6.simHuman.chr6 570417 7 + 601863 TAGCAGG -s simRat_chr6.simRat.chr6 76542 7 - 647215 TAGTAGG - -a -s simMouse_chr6.simMouse.chr6 602158 119 + 636262 GTCACAATCAGGCACAATGCACTACTATGACTCTAGACCCTGACAATCACTTTCCCTGCTCATCTCTTTATCGACAAAGCTCCATGCTATCTGTCCTACTGCCCCCCTTTGATACTTAT -s Anc0.Anc0refChr3 199555 100 + 222631 GTCCAAATCAGGCACAATGCACTACTATGAGTGCAGACACTG--AATCACTTGCCCTACGTATGGTTTCATTGATAGATCTCTATGTCAT---------TGCCCCC--------TTTAT -s Anc1.Anc1refChr1 39301 100 + 69767 GTCCAAATCAGGCACAATGCACTACTATGAGTGCAGACACTG--AATCACTTGCCCTACGTATGGTTTCATTGATAGATCTCTATGTCAT---------TGCCCCC--------TTTAT -s Anc2.Anc2refChr1 116298 100 + 142988 GTCCAAATCAGGCATAATGCACTACTATGAGTGCAGACACTG--AACTACTCGGCCTACGTATGGTTTCATTGATAGATTTCTAGGTCTT---------TACCTAC--------TTTAT -s mr.mrrefChr3 149997 111 + 181027 GTCACAATCAGGCACAATGCACTACTATGACTCTAGACACTGACAATCACTTTCCCTGCTCATCTTTTTATTGACAGATCTCCATGTCATCTGTCCTACTGCCCCC--------CTTAT -s simCow_chr6.simCow.chr6 574887 100 + 602619 GTCCAAATCAGGCATAATGCACTACTATGAGTGCAGACATTG--GACTACCCGGCCTACGTATGGTTTCCTTGTTACATTTCTAAGTCTT---------TACCTAC--------TTTAT -s simDog_chr6.simDog.chr6 566750 85 + 593897 GTCAATCTCAGG-ATGATACACTACTGTAGATGCAGACACCG--AACTACTCAGCCTACATATGGTTTCATTGAGAGATTTCTAGGTC------------------------------- -s simHuman_chr6.simHuman.chr6 570428 100 + 601863 GTCCAAAGCAGTCACAACGCACTACTATGAGTGGACACACTG--AGTCATTTGCCCTATGTATGGTTTCATTGCTAGATCTCTATGTCAT---------TGTGCCC--------TTTAT -s simRat_chr6.simRat.chr6 76549 104 - 647215 GT-------AGGCACAATCCACTACTATGACTCTAGACACTGAAAATCACTTTCCCTTCTCATCTTTTTAATGACAGATCTTCATGTCATCCATGCTGTAGCACCC--------CTTGT - -a -s simMouse_chr6.simMouse.chr6 602277 13 + 636262 TTGTTTCCAAGGG -s Anc0.Anc0refChr3 199656 13 + 222631 CTGCCAACAACTG -s Anc1.Anc1refChr1 39402 13 + 69767 CTGCCAACAACTG -s Anc2.Anc2refChr1 116399 13 + 142988 CAGCCAACCACTG -s mr.mrrefChr3 150108 13 + 181027 CTGTTTCCAACTG -s simCow_chr6.simCow.chr6 574988 13 + 602619 CAGCCAACCACTG -s simHuman_chr6.simHuman.chr6 570529 13 + 601863 CTGCCAACAACTG -s simRat_chr6.simRat.chr6 76653 13 - 647215 CTGTTTCCAGCTG - -a -s simMouse_chr6.simMouse.chr6 602290 1 + 636262 T -s Anc0.Anc0refChr3 199679 1 + 222631 C -s Anc1.Anc1refChr1 39425 1 + 69767 C -s Anc2.Anc2refChr1 116422 1 + 142988 C -s mr.mrrefChr3 150121 1 + 181027 T -s simCow_chr6.simCow.chr6 575011 1 + 602619 C -s simHuman_chr6.simHuman.chr6 570552 1 + 601863 C - -a -s simMouse_chr6.simMouse.chr6 602291 14 + 636262 AAGCATACGTGTCT -s Anc0.Anc0refChr3 199680 14 + 222631 AAGCATACAAGTCT -s Anc1.Anc1refChr1 39426 14 + 69767 AAGCATACAAGTCT -s Anc2.Anc2refChr1 116423 14 + 142988 AAACATATGAGTCC -s mr.mrrefChr3 150122 14 + 181027 AAGCATACATGTCT -s simCow_chr6.simCow.chr6 575013 14 + 602619 AAACATATGAGTCC -s simHuman_chr6.simHuman.chr6 570553 14 + 601863 AAGCATACAAGTCT -s simRat_chr6.simRat.chr6 76666 9 - 647215 -----TACATGTCT - -a -s simMouse_chr6.simMouse.chr6 602305 180 + 636262 GCCCAAACACATGAAGGCCAGAGCTCATCCTAATCAAGACACCTGCAGAACTGTCCTGGAGATTCTGAGGCATCTTTGTGCAAGCACATCTAGGTTTTAATTGTGTTGTTGTCATCTGGTAATTTTATAATAGAAGAAGGTACCTGGTTCTGAGACATTTAATACAGTCTTCTTCTCAGC -s Anc0.Anc0refChr3 199694 167 + 222631 GCCCAAACACCCAGGGGCCTGGGGTCAGTCAAATTAAGAGGCCTTCAGCACTGCCCTACAGATTCTGGGGCATCTTTGTCTAAGCAAAGTTGGGGTTCAATTGGGTTCTCGCGATTCTATCACTAAATGAAAGA-------------TCCTGAGACATTGAATATGGCCTTCTATTGTAC -s Anc1.Anc1refChr1 39440 167 + 69767 GCCCAAACACCCAGGGGCCTGGGGTCAGTCAAATTAAGAGGCCTTCAGCACTGCCCTACAGATTCTGGGGCATCTTTGTCTAAGCAAAGTTGGGGTTCAATTGGGTTCTCGCGATTCTATCACTAAATGAAAGA-------------TCCTGAGACATTGAATATGGCCTTCTATTGTAC -s Anc2.Anc2refChr1 116437 167 + 142988 TCCCAAACACCCAGGTGCCTAGGGTCTGCGTAATTAAGAGGCCTTCAGCAATGCACCACAGATTCTGGGGCATCTTTGTCTAAGCAAAGTTGGGGTTCAATTGGGTTCTTGCGATTCTATCACTAAATGAAAGT-------------ACCTGAGAAATTGAATATGGCCTTCTATTGTAC -s mr.mrrefChr3 150136 180 + 181027 GCCCAAACACATAAGGGCCAGAGGTCATTCAAATTAAGACACCTTCAGAACTGTCCTGGAGATTCTGAGGCATCTTTGTGCAAGCACAGCTGGGTTTTAATTGTGTTGTCGTCATCTGATAATTTTATAATAGAAGAAGGTACCTGGTTCTGAGACATTTAATATAGCCTTCTTCTCAGC -s simCow_chr6.simCow.chr6 575027 162 + 602619 TCCCAAACACCCAGGTGCCTAGGGTCTGCGTAATTATGAAGCTTTCAGCATTGCACCACAGATCCCGGGGCATCTTTAGTTAAGCAAAGTTGGGTTTCAATTGGGTTCTTGCGATTCTATAACTAAATGAG------------------CTGAGGAAGTGAATATGGCGTCCTATTGTAG -s simDog_chr6.simDog.chr6 566835 134 + 593897 --------------------------------ATTCAGAGGCCTTCAGCAATGCACCACAGATTCTGGGGCATCTTTGTCTAAACATAGTTGG-GTTCAATTGGGTTCTTGCAATTCTATCATTAAATGAAAGT-------------ACCTGAGAAATTCAGTATGGCCTTCTATTGTAC -s simHuman_chr6.simHuman.chr6 570567 167 + 601863 GCCCAAACACTCATGGGCCGGGGGTCAATCAAATTAGCATGCCTTCAACACTGCCCTCCAGATTTTGGGGCATCTTTGTCAAAGCAAAGTTGGTATTCAATTGGGTTCTCGCGCTTCTATGACTACATGAAAGA-------------TCTTGAGACATTGAACATGGCCTTTTATTGTAC -s simRat_chr6.simRat.chr6 76676 180 - 647215 GCCCAAACACATAGGTGCCAGAGGTCAGTTACATTAAGACACCTTCAGAACCGTCCTGGAGATTCTGTGGGATATTCGTGCAAGCATAGCTGGGTTTTAATTGTGTTATCATCATCTGATAATTTTCTATTAGAAGAAAGTATCTGGTACTGAGGCATACAATATAGCCCCCTTCACAGC - -a -s simMouse_chr6.simMouse.chr6 602485 92 + 636262 CTAGTGCCATTTCAGCCACCCATCAGACATGCTTGGGAACTTATAAGTTGAGTGGATAGGTTGCCGGCAACTCAAGCGCAGTGGAACTTGGT -s Anc0.Anc0refChr3 199863 46 + 222631 TTAGTGCCACTTTGGCAATCCATTGCACATGATCA-CACCTTA---------------------------------------------TGTT -s Anc1.Anc1refChr1 39609 46 + 69767 TTAGTGCCACTTTGGCAATCCATTGCACATGATCA-CACCTTA---------------------------------------------TGTT -s Anc2.Anc2refChr1 116607 46 + 142988 TTAGTGCCACTATGGCAATCCATTGCACATGATCA-CACCTTA---------------------------------------------TGTT -s mr.mrrefChr3 150316 91 + 181027 CTAGTGCCACTTCAGCCACCCATCAGACATGCTCG-GAACTTATAAGTTGAGTGGATAGGTTGCCGGCAACTCAAGCGCAGTGGAACTTGTT -s simCow_chr6.simCow.chr6 575192 46 + 602619 TCAGTGCCACTGTGGCAACCAATTGGACATAATCA-TACCTTA---------------------------------------------TGTT -s simDog_chr6.simDog.chr6 566972 46 + 593897 CTAGTGCCACTATAGAAATGCATTGCACATGATCA-CACCTTA---------------------------------------------TGTT -s simHuman_chr6.simHuman.chr6 570736 46 + 601863 TTAGTGCCACTTTGGCGATCCATTGTACTTGATCA-CACCTTA---------------------------------------------TGTT -s simRat_chr6.simRat.chr6 76856 91 - 647215 CAAGCACCACTTGAGCTGCCCATCAGCCATGCTCG-GAAGTTTTAAATTGAGCAGATGAGTTGGTGGTAACTCAAGCCCAGTGGAATTTGTT - -a -s simMouse_chr6.simMouse.chr6 602577 35 + 636262 TTCTAAGAAGTAGAAGTTTGAATACCAAAAGGCTA -s Anc0.Anc0refChr3 199913 34 + 222631 TCCTCTAAGATGGAAGTTTGCATT-CAGGAAAGTA -s Anc1.Anc1refChr1 39659 34 + 69767 TCCTCTAAGATGGAAGTTTGCATT-CAGGAAAGTA -s Anc2.Anc2refChr1 116657 34 + 142988 TCCTCTAAGATGGAAGTTTACACT-CAGGAAAGTG -s mr.mrrefChr3 150407 35 + 181027 TCCTCAGAAGTAGAAGTTTGCATACCAAAAAGCTA -s simCow_chr6.simCow.chr6 575242 34 + 602619 TCCTCTAAGATGGAAGTTTACACT-CAGGAAACCA -s simDog_chr6.simDog.chr6 567022 34 + 593897 TCTTCTTAAATGGAGGTTTAGACT-CCGTAAAGTG -s simHuman_chr6.simHuman.chr6 570786 34 + 601863 TCCTCTAAGATTTAAGTTTGCATT-CAGGAAAATA -s simRat_chr6.simRat.chr6 76947 35 - 647215 CCCTCAGAAGTAGAAGTTTGCATACTGAAAAGCTA - -a -s simMouse_chr6.simMouse.chr6 602612 16 + 636262 CCTTCAATGGAACCTG -s Anc0.Anc0refChr3 199947 16 + 222631 CCTTCAATAGGACCTG -s Anc1.Anc1refChr1 39693 16 + 69767 CCTTCAATAGGACCTG -s Anc2.Anc2refChr1 116692 16 + 142988 CCTTCAATAGGACCTG -s mr.mrrefChr3 150442 16 + 181027 CCTTCAATGGAACCTG -s simCow_chr6.simCow.chr6 575277 16 + 602619 CCTTCTAGATGACCTG -s simDog_chr6.simDog.chr6 567057 16 + 593897 CCTTCAATAGGGCCTA -s simHuman_chr6.simHuman.chr6 570820 5 + 601863 CCT-----------GG -s simRat_chr6.simRat.chr6 76982 16 - 647215 CCTTCAATGGAACCTG - -a -s simMouse_chr6.simMouse.chr6 602628 17 + 636262 TACAAAATTAGACATGT -s Anc0.Anc0refChr3 199963 17 + 222631 TACAAAAGTGGACATGT -s Anc1.Anc1refChr1 39709 17 + 69767 TACAAAAGTGGACATGT -s Anc2.Anc2refChr1 116709 17 + 142988 TACAAAAGTGAACATGT -s mr.mrrefChr3 150458 17 + 181027 TACAAAATTGGACATGT -s simCow_chr6.simCow.chr6 575294 17 + 602619 TATGAAACTGCACATGT -s simDog_chr6.simDog.chr6 567074 17 + 593897 TACAAAAGTCAACATGT -s simHuman_chr6.simHuman.chr6 570825 17 + 601863 TACAAGAGTGGACATGT -s simRat_chr6.simRat.chr6 76998 17 - 647215 TACAAAATTGGACATGG - -a -s simMouse_chr6.simMouse.chr6 602645 91 + 636262 GTAGTTTCTACCAATTTTTTCACTTGGGTGGCTCACAATTAGCTTTCTCGAATTTTGCTGTTAATCTCAGTCCAATTGCACCGTTGTTCAG -s Anc0.Anc0refChr3 199980 39 + 222631 ATAGTATATACCAATTATTT-GCTCAGGTGGCTG---------------------------------------------------GGTCAG -s Anc1.Anc1refChr1 39726 39 + 69767 ATAGTATATACCAATTATTT-GCTCAGGTGGCTG---------------------------------------------------GGTCAG -s Anc2.Anc2refChr1 116726 39 + 142988 ATAGTATATACCAATTATTT-GCTCAGGTGGTTG---------------------------------------------------GGTCAT -s mr.mrrefChr3 150475 89 + 181027 GTAGTTTCTACCAATTATTT-ACTTAGGTGGCTCACAATTAGCTTTCTCGAA-TTTGCTGTTAATCTCAGTCCAATTGCACCGTTGTTCAG -s simCow_chr6.simCow.chr6 575315 39 + 602619 ATAGTTTCTACCGATTATGT-GCTCAGGTTGATG---------------------------------------------------GGCCAT -s simDog_chr6.simDog.chr6 567091 39 + 593897 ACAATATATACCAAGTATTT-GCTCAGGTGGTTG---------------------------------------------------GGTTAT -s simHuman_chr6.simHuman.chr6 570842 39 + 601863 ATAGTCTTAGTCAATTATTT-GCTCAGGCGGCTA---------------------------------------------------GGTCAG -s simRat_chr6.simRat.chr6 77015 89 - 647215 GTAGTTCCTACCAATCATTT-ACTTAGGTGGCTCACAATTAGCTTTCTTGAA-TTTGCCATCCATCTCGGTCTAATTGCACACTTGTTCAT - -a -s simMouse_chr6.simMouse.chr6 602736 9 + 636262 CCAAATGGA -s Anc0.Anc0refChr3 200021 9 + 222631 CTAAATAGA -s Anc1.Anc1refChr1 39767 9 + 69767 CTAAATAGA -s Anc2.Anc2refChr1 116767 9 + 142988 TTAGATAAA -s mr.mrrefChr3 150564 9 + 181027 CCAAATGGA -s simCow_chr6.simCow.chr6 575356 9 + 602619 TTAGATAAA -s simDog_chr6.simDog.chr6 567132 9 + 593897 TTAGATGAA -s simHuman_chr6.simHuman.chr6 570883 9 + 601863 CTAAATAGA -s simRat_chr6.simRat.chr6 77104 9 - 647215 CCAACTGGA - -a -s simMouse_chr6.simMouse.chr6 602745 5 + 636262 GGGAG -s Anc0.Anc0refChr3 200030 5 + 222631 GATAG -s Anc1.Anc1refChr1 39776 5 + 69767 GATAG -s Anc2.Anc2refChr1 116776 5 + 142988 GATGG -s mr.mrrefChr3 150573 5 + 181027 GGGAG -s simCow_chr6.simCow.chr6 575365 5 + 602619 GATGA -s simDog_chr6.simDog.chr6 567141 5 + 593897 GATGG -s simHuman_chr6.simHuman.chr6 570892 5 + 601863 GACAG -s simRat_chr6.simRat.chr6 77120 5 - 647215 GGAAT - -a -s simMouse_chr6.simMouse.chr6 602750 87 + 636262 TGTTAGCCCTGTTGTAATTGAGGTTAATCACTGTGATGGATTTGGCCCCCAAACAAGGGGCTACTGTGCATGATGTCCCTTACGAGC -s Anc0.Anc0refChr3 200035 57 + 222631 CC----CACC-TTGGGATTGAGAT--------------GACTTAGCTTCTC---------TTACTTTGTACCAGGA--TTTGTAAGC -s Anc1.Anc1refChr1 39781 57 + 69767 CC----CACC-TTGGGATTGAGAT--------------GACTTAGCTTCTC---------TTACTTTGTACCAGGA--TTTGTAAGC -s Anc2.Anc2refChr1 116781 57 + 142988 CC----CACC-TTGGGATAGAGGT--------------CACTCAAATTCTC---------TTACTTTGTGCCACAA--TCAGTAAGC -s mr.mrrefChr3 150578 80 + 181027 TCCTAGCCCT-TTGTAATTGAGATTA------GTGATGGATTTGGCCCCCAAACAAGGGGTTACTGTGCATGAGGACCCTTACGAGC -s simCow_chr6.simCow.chr6 575370 40 + 602619 CA----CCCC-TTGGGATCGA----------------------------------------TTTTTTGTGCCACTA--TAAGTAATC -s simDog_chr6.simDog.chr6 567157 57 + 593897 CC----CATG-TCAGGATAGAGGT--------------CACTCAAATTCTC---------TTACTTTGTGCCACAT--CCAGTATGC -s simHuman_chr6.simHuman.chr6 570897 57 + 601863 CC----CACC-TTGGGATTAAGAG--------------GACTTAGCTTCTC---------TTACTTTGTACTAGGA--TTTGTAAGC -s simRat_chr6.simRat.chr6 77125 77 - 647215 TCCTCGGCCT-TTGCAATTGAGATTA------TTGATGA---TGCCCCCCAAACAAGGAGTTGCAATGCATGAGAACCCTTATTGGC - -a -s simMouse_chr6.simMouse.chr6 602837 1 + 636262 C -s Anc0.Anc0refChr3 200093 1 + 222631 C -s Anc1.Anc1refChr1 39839 1 + 69767 C -s Anc2.Anc2refChr1 116839 1 + 142988 C -s mr.mrrefChr3 150658 1 + 181027 C -s simCow_chr6.simCow.chr6 575411 1 + 602619 C -s simDog_chr6.simDog.chr6 567215 1 + 593897 T -s simHuman_chr6.simHuman.chr6 570955 1 + 601863 C -s simRat_chr6.simRat.chr6 77202 1 - 647215 C - -a -s simMouse_chr6.simMouse.chr6 602838 34 + 636262 CAGCCTGGTATTTTGGTGTGAATAAGTAATGCAT -s Anc0.Anc0refChr3 200097 31 + 222631 CATGCTGGTATTCTG--ATGAAT-TGATATGCAT -s Anc1.Anc1refChr1 39843 31 + 69767 CATGCTGGTATTCTG--ATGAAT-TGATATGCAT -s Anc2.Anc2refChr1 116843 31 + 142988 CATGCTGGTATTCTG--ATGAAT-TAATATGCAT -s mr.mrrefChr3 150662 32 + 181027 CAGCCTGGTATTTTG--GTGAATAAGAAATGCAT -s simCow_chr6.simCow.chr6 575415 31 + 602619 CATACTGGTATTCTG--CTCAAT-TAATATACAT -s simDog_chr6.simDog.chr6 567219 30 + 593897 AATGCTGGTATTC-A--ATGAGT-TAATATGCAT -s simHuman_chr6.simHuman.chr6 570959 31 + 601863 CATGCCGGTATTCTG--ATAAAT-TGATATGCAG -s simRat_chr6.simRat.chr6 77206 32 - 647215 CAGCCTAGTATTTTG--GTGAATAAGAAATGCAT - -a -s simMouse_chr6.simMouse.chr6 602872 44 + 636262 GTGGAGAATGTCCATGAAAGCTGCCTACTCCACTTTAACATGAT -s Anc0.Anc0refChr3 200128 39 + 222631 GAAGTGAACATTTGTGCCAGCTACCTACTCCTC----ACTTGA- -s Anc1.Anc1refChr1 39874 39 + 69767 GAAGTGAACATTTGTGCCAGCTACCTACTCCTC----ACTTGA- -s Anc2.Anc2refChr1 116874 39 + 142988 GAGGTAAACATTTGTGCTAGCTACTTACTCCTG----ACTTGA- -s mr.mrrefChr3 150694 43 + 181027 GTAGAGAACATCCATGACAGCTGCCTACTCCACTTTAACATGA- -s simCow_chr6.simCow.chr6 575448 21 + 602619 GAGGTCAATATTTGTG----------------------CTCGA- -s simDog_chr6.simDog.chr6 567249 39 + 593897 AAGGTAAACATTTGTTCTAGCTACTTACTCCTG----ACTTGG- -s simHuman_chr6.simHuman.chr6 570990 39 + 601863 GAACTGAACATTTGTGCCACTTAGCTACTCTGC----ACTTGA- -s simRat_chr6.simRat.chr6 77238 43 - 647215 GCAGGAAACATCCATGACGGCTGCCTACTCCACTTTTACATGA- - -a -s simMouse_chr6.simMouse.chr6 602916 106 + 636262 AATCACCAAGTTGACTTTTGCTTCAGGCAGCTTGTTACAGTGCATGGGCTGACACAGGAGCATCCTCACAATGTCTGATACAGAAGCATTCTCACTATAATGAACA -s Anc0.Anc0refChr3 200169 76 + 222631 AATCACCTAGTTGATTCTTGTTCTGGACTGCTTGTTGCAGTACATGGGCTGACACAGG--------------------------AG----CTCATTACAGTGAACA -s Anc1.Anc1refChr1 39915 80 + 69767 AATCACCTAGTTGATTCTTGTTCTGGACTGCTTGTTGCAGTACATGGGCTGACACAGG--------------------------AGAAATCTCATTACAGTGAACA -s Anc2.Anc2refChr1 116915 76 + 142988 AATCAACTGGTTGATTCTTGTCCTGGACTGCTTGTTGCAGTACATGGGCTGACACAGG--------------------------AG----CTCATTACAGTGAATA -s mr.mrrefChr3 150737 106 + 181027 AATCACCAAGTTGACTTTTGCTTCGGGCTGCTTGTTACAGTGCATGGGCTGACACAGGAGCATCCTCACAATGTCTGATACAGAAGCATTCTCACTATAATGAACA -s simCow_chr6.simCow.chr6 575471 72 + 602619 AATT----GGTTGATTCCTGTCCTGGGCCACTTGTTGCAGTTCATGGGCTGACACAGA--------------------------AG----CTCATTATAGTGAATA -s simDog_chr6.simDog.chr6 567290 70 + 593897 AATCAACTGGTCTCTTCT------TGACTGCTTGTCGCAGTACATGGGCTGACTTGGG--------------------------AG----TTCATCACAATGAAAA -s simHuman_chr6.simHuman.chr6 571031 79 + 601863 AATCACCTAGTTGATTCTTGTTCAGGACTGCTTGTTGCAGTACATGGGATGACACAGG--------------------------AGAAATCTCATTACAGTG-ACT -s simRat_chr6.simRat.chr6 77281 106 - 647215 AATTGCCAAGCTGACCTCTGCTTCGGGCTTCTTGTTACTGTGCATGGGGTGACACAGGAGTATTCTCACAATGTCTGATACACAAGTATTCTTACTATAATGAACA - -a -s simMouse_chr6.simMouse.chr6 603022 52 + 636262 TCTTGTAAACACATCTATAGGCATTTGTGGTATGAGGATACAATCTAAGTTA -s Anc0.Anc0refChr3 200245 48 + 222631 TCTGGTTGACACTTGTCTAGACATTTGAGGAA--GGGAG--GACCTTAAATG -s Anc1.Anc1refChr1 39995 48 + 69767 TCTGGTTGACACTTGTCTAGACATTTGAGGAA--GGGAG--GACCTTAAATG -s Anc2.Anc2refChr1 116995 48 + 142988 TGTGGTTGACACTTGTCTAGACATTTGAGGAA--GGGCG--GACCTTAAATG -s mr.mrrefChr3 150843 50 + 181027 TCTTGTAAACACATGTATAGACATTTGTGGTATGGGGAT--AATCTAAATTA -s simCow_chr6.simCow.chr6 575545 46 + 602619 --TGGTTGATGCTTGTTTAGACATTTGAGAAA--GGGGG--GACCTTAAACG -s simDog_chr6.simDog.chr6 567364 48 + 593897 TGTGGTTGCCACCTGTCTAGACATTTGAGGGG--GGGCA--GACCTAAACTA -s simHuman_chr6.simHuman.chr6 571110 48 + 601863 TCTGGTGTACACTTGTGTAGACATTTGAGGAA--GGGAG--GACCTTAAATG -s simRat_chr6.simRat.chr6 77387 44 - 647215 TCTTGTAAACACATGTATAGACATTTGCAGTACGGGGAT--------AATTA - -a -s simMouse_chr6.simMouse.chr6 603074 52 + 636262 AACAAAAGTCTCTTATTACATGAAAATCTGCAACAGAGATAGTGGTGAAATG -s Anc0.Anc0refChr3 200293 46 + 222631 AATTCAAGTTAC------CATAAAAATCTGCAACATACATACCGGTGTAATG -s Anc1.Anc1refChr1 40043 46 + 69767 AATTCAAGTTAC------CATAAAAATCTGCAACATACATACCGGTGTAATG -s Anc2.Anc2refChr1 117043 46 + 142988 AATTCAAGTTAC------CATAAAAATCTGCAACATACATACTGGTGTAATG -s mr.mrrefChr3 150893 51 + 181027 AACAAAAGTCTC-TATTACATGAAAATCTGCAACAGAGATAGCGGTGAAATG -s simCow_chr6.simCow.chr6 575591 46 + 602619 AACGTAAGTTAC------CGTAAAAACCTGCAATATACACACTGGTGCAAAG -s simDog_chr6.simDog.chr6 567417 46 + 593897 AATTCAAGTTAA------TATGAAAATCTACAACACACCTACTGGTGTATTG -s simHuman_chr6.simHuman.chr6 571158 46 + 601863 GATTCAAGTTAC------CACAAATATCTGCAACATACATACCAGTGTTATG -s simRat_chr6.simRat.chr6 77431 51 - 647215 CACAAAAGTCTC-AGTTACATGAAAATCTGCAACAGAGACAGCGGTGAAATG - -a -s simMouse_chr6.simMouse.chr6 603126 63 + 636262 AGATGTAAGTTTCTGCCCGGGAAGCTACAGCACTTAGCTTGCCGGAGGGGGACATTACCTACT -s Anc0.Anc0refChr3 200339 63 + 222631 AGATGTAAGATGCTGCCCTGGAAGGAACAGCACTTACCATGCCAGAGGGAGATTTTACCTTCT -s Anc1.Anc1refChr1 40089 63 + 69767 AGATGTAAGATGCTGCCCTGGAAGGAACAGCACTTACCATGCCAGAGGGAGATTTTACCTTCT -s Anc2.Anc2refChr1 117089 63 + 142988 AGACGTAAGATGCTGCCCTGGAAGGAACGGCACTTACCATGCCCAAGGGAGACTCTACCTTCA -s mr.mrrefChr3 150944 63 + 181027 AGATGTAAGTTTCTGCCCGGGAAGCTACAGCACTTAGCATGCCAGAGGGGGATATTACCTACT -s simCow_chr6.simCow.chr6 575637 63 + 602619 AGAAGTAAAATACTGCCCCGAAGAGTACTGCACCTGGGGTGCCCAAGGGAGACTCTTATTTCA -s simDog_chr6.simDog.chr6 567464 63 + 593897 AGACGCAAGATGCAGCCATGGGAGGAGTGGCACTTACCATGCCCAAGGGAGACTCTACCTTCA -s simHuman_chr6.simHuman.chr6 571204 63 + 601863 AGATGTAAGATGCTTGCCAGGAAGGGACAGCACTTAACATGCCAGAGGGACATCTTACCTTCT -s simRat_chr6.simRat.chr6 77482 42 - 647215 AGATGCA---------------------AGCATTTACCATGTCAGAGAGGGATGTTACATACT - -a -s simMouse_chr6.simMouse.chr6 603189 19 + 636262 ATTTGTGTCTCCCTTTCCT -s Anc0.Anc0refChr3 200547 19 + 222631 CATCATGTTTCACCTTCCT -s Anc1.Anc1refChr1 40297 19 + 69767 CATCATGTTTCACCTTCCT -s Anc2.Anc2refChr1 117297 19 + 142988 CATCATGTTTCACCCTCCT -s mr.mrrefChr3 151007 19 + 181027 ATTTGTGTCTCCCATTCCT -s simCow_chr6.simCow.chr6 575825 19 + 602619 CATTATGATTCACCCTCCT -s simDog_chr6.simDog.chr6 567690 19 + 593897 CATCATGTTTCACCCTCCT -s simHuman_chr6.simHuman.chr6 571414 19 + 601863 GATAATGTTTCACCTTCCT -s simRat_chr6.simRat.chr6 77524 19 - 647215 ATTTATGTCTCCCATTCCT - -a -s simMouse_chr6.simMouse.chr6 603208 37 + 636262 GCTAAAGAAGCTTCTGTTGATGGCACCCTCTTGGATT -s Anc0.Anc0refChr3 200566 29 + 222631 GATAAGGAAAATTTTGGTGATGTCACCC--------T -s Anc1.Anc1refChr1 40316 29 + 69767 GATAAGGAAAATTTTGGTGATGTCACCC--------T -s Anc2.Anc2refChr1 117316 29 + 142988 TATAAGGAAAATCTTGGTGATGTCACCC--------T -s mr.mrrefChr3 151026 29 + 181027 GCTAAAGAAGCTTCTGTTGATGGCACCC--------T -s simCow_chr6.simCow.chr6 575844 29 + 602619 TATAAGGAAAATCCTGTTGATCACACCC--------T -s simDog_chr6.simDog.chr6 567709 29 + 593897 TATAAGGAAAGTCTTGGTGAAGTCTCCC--------C -s simHuman_chr6.simHuman.chr6 571433 29 + 601863 GATAAGGAAAATTATGCTGATGTCACCC--------T -s simRat_chr6.simRat.chr6 77545 29 - 647215 GATAAAGAAGCTTCTGTTGATGGCACCC--------T - -a -s simMouse_chr6.simMouse.chr6 603245 3 + 636262 ACT -s Anc0.Anc0refChr3 200595 3 + 222631 ATT -s Anc1.Anc1refChr1 40345 3 + 69767 ATT -s Anc2.Anc2refChr1 117345 3 + 142988 ATT -s mr.mrrefChr3 151055 3 + 181027 ACT -s simCow_chr6.simCow.chr6 575874 3 + 602619 AGT -s simDog_chr6.simDog.chr6 567738 3 + 593897 CTT -s simHuman_chr6.simHuman.chr6 571462 3 + 601863 ATT -s simRat_chr6.simRat.chr6 77574 3 - 647215 ACT - -a -s simMouse_chr6.simMouse.chr6 603248 64 + 636262 GTGTTGATACCTGCTCTCTCCATAGCCCAGGAGTGTGGTCTAAGAAATATTAAGGTATTTACCC -s Anc0.Anc0refChr3 200604 64 + 222631 GTGTTGGTAACCGTTCCCTCCATAGCTCAGAGGTTTTGTTTAGCAATTATTAAGGTATGTATCC -s Anc1.Anc1refChr1 40354 64 + 69767 GTGTTGGTAACCGTTCCCTCCATAGCTCAGAGGTTTTGTTTAGCAATTATTAAGGTATGTATCC -s Anc2.Anc2refChr1 117354 64 + 142988 GTGATGGTAACCGTTTCCTCCATAGCTCAGAGGCTTTGTTTAGCACTTATTGGAGTATGTATCC -s mr.mrrefChr3 151058 64 + 181027 GTGTTGATACCTGCTCTCTCCATAGCCCAGGAGTGTGGTCTAAGAAATATTAAGGTATTTACCC -s simCow_chr6.simCow.chr6 575883 64 + 602619 GTGACAGCACCCGTTTCAACCATAATTCAGAGGCCTTGTTTAGCAGATATTGGAGTATGTACTC -s simDog_chr6.simDog.chr6 567747 64 + 593897 CTGATGGTAACCACTTTCTCCTTAGCTCAGAGGCTTTGTTTAGCACTTATTGGAGTATGAATCC -s simHuman_chr6.simHuman.chr6 571471 64 + 601863 GTGTTGGTAGCCGTTCCCTCCATTGCTCTGAGGTTTTGTTCAGTGATTATTAAGGAATGTATCC -s simRat_chr6.simRat.chr6 77577 64 - 647215 GTGTTGATACCTGCCTGGTCCATAGTGCAGGAGTGTTGTCTAGGAAATATTAAGGACTGTACCA - -a -s simMouse_chr6.simMouse.chr6 603312 5 + 636262 ACATT -s Anc0.Anc0refChr3 200669 4 + 222631 ACA-T -s Anc1.Anc1refChr1 40419 4 + 69767 ACA-T -s Anc2.Anc2refChr1 117419 4 + 142988 ACA-T -s mr.mrrefChr3 151122 4 + 181027 ACA-T -s simCow_chr6.simCow.chr6 575948 4 + 602619 ATG-T -s simDog_chr6.simDog.chr6 567812 4 + 593897 ACA-T -s simHuman_chr6.simHuman.chr6 571536 4 + 601863 ACA-T -s simRat_chr6.simRat.chr6 77641 4 - 647215 ACA-T - -a -s simMouse_chr6.simMouse.chr6 603317 4 + 636262 CACA -s Anc0.Anc0refChr3 200674 4 + 222631 CACA -s Anc1.Anc1refChr1 40424 4 + 69767 CACA -s Anc2.Anc2refChr1 117424 4 + 142988 CACA -s mr.mrrefChr3 151126 4 + 181027 CACA -s simCow_chr6.simCow.chr6 575953 4 + 602619 GACA -s simDog_chr6.simDog.chr6 567817 4 + 593897 CATA -s simHuman_chr6.simHuman.chr6 571541 4 + 601863 CACG -s simRat_chr6.simRat.chr6 77645 4 - 647215 CACA - -a -s simMouse_chr6.simMouse.chr6 603321 31 + 636262 CCATGCTTAATGGTCCACGAGGCTGTAAATG -s Anc0.Anc0refChr3 200678 28 + 222631 CCATGATTAATGATCCATGAGGCTATAA--- -s Anc1.Anc1refChr1 40428 28 + 69767 CCATGATTAATGATCCATGAGGCTATAA--- -s Anc2.Anc2refChr1 117428 28 + 142988 CCATGATTAATGATCCATGAGGTTATAA--- -s mr.mrrefChr3 151130 31 + 181027 CCATGCTTAATGGTCCACGAGGCTGTAAATG -s simCow_chr6.simCow.chr6 575971 28 + 602619 CCATGATTAATGATCCATGAGGGTGTAA--- -s simDog_chr6.simDog.chr6 567821 28 + 593897 CCATGATTAATGATCAAGAAGGTCATAA--- -s simHuman_chr6.simHuman.chr6 571545 28 + 601863 CCATGATTAATGATCCATGAGGCTATAA--- -s simRat_chr6.simRat.chr6 77649 31 - 647215 CCATGCATAATCATCCATGAGGCTGTAAATG - -a -s simMouse_chr6.simMouse.chr6 603352 18 + 636262 AAATTCAGACAACAACCA -s Anc0.Anc0refChr3 200706 18 + 222631 CAGTTGAGACACCAACCA -s Anc1.Anc1refChr1 40456 18 + 69767 CAGTTGAGACACCAACCA -s Anc2.Anc2refChr1 117456 18 + 142988 CAGTTGAGACACCAATCA -s mr.mrrefChr3 151161 18 + 181027 AAATTCAGACAACAACCA -s simCow_chr6.simCow.chr6 576002 17 + 602619 CAATTTGGA-ACCAATCA -s simDog_chr6.simDog.chr6 567863 18 + 593897 CAGTGGAGACACCAATCA -s simHuman_chr6.simHuman.chr6 571573 18 + 601863 CAGTTAAGACACCAGCCA -s simRat_chr6.simRat.chr6 77680 18 - 647215 CAATTAAGCCAACAACCA - -a -s simMouse_chr6.simMouse.chr6 603370 1 + 636262 G -s Anc0.Anc0refChr3 200724 1 + 222631 G -s Anc1.Anc1refChr1 40474 1 + 69767 G -s Anc2.Anc2refChr1 117474 1 + 142988 G -s mr.mrrefChr3 151179 1 + 181027 G -s simCow_chr6.simCow.chr6 576019 1 + 602619 G -s simDog_chr6.simDog.chr6 567881 1 + 593897 G -s simHuman_chr6.simHuman.chr6 571607 1 + 601863 G -s simRat_chr6.simRat.chr6 77698 1 - 647215 G - -a -s simMouse_chr6.simMouse.chr6 603371 19 + 636262 CATTATCAATTCCTGGCAG -s Anc0.Anc0refChr3 200725 16 + 222631 CATTA---ATTTTTTAGGG -s Anc1.Anc1refChr1 40475 19 + 69767 CATTATCAATTTTTTAGGG -s Anc2.Anc2refChr1 117475 16 + 142988 CATTG---AGTTTTTAGGG -s mr.mrrefChr3 151180 19 + 181027 CATTATCAATTCCTGGCAG -s simCow_chr6.simCow.chr6 576023 16 + 602619 TGTTG---AGTCTTTAGGA -s simDog_chr6.simDog.chr6 567882 16 + 593897 CATTG---AGTTTTTAAGG -s simHuman_chr6.simHuman.chr6 571608 19 + 601863 CATGATCAATTTTTAAGGG -s simRat_chr6.simRat.chr6 77699 19 - 647215 CATTATGAATTCCTTACAG - -a -s simMouse_chr6.simMouse.chr6 603390 90 + 636262 AATCATTCTGAAGACTGGTGCTATTCACTGCCCTCAGCAATTCTTTTGTTACCTCAACCCTTCTCCCGAGGCTAGAATGTTTAAATGAAT -s Anc0.Anc0refChr3 200754 34 + 222631 AATAACAATGAATGCTG-----ATTTACTGCCCATTGCA--------------------------------------------------- -s Anc1.Anc1refChr1 40507 34 + 69767 AATAACAATGAATGCTG-----ATTTACTGCCCATTGCA--------------------------------------------------- -s Anc2.Anc2refChr1 117504 34 + 142988 AATAACAATGAATGTTG-----ATTTACTGCCCATTGCA--------------------------------------------------- -s mr.mrrefChr3 151199 39 + 181027 AATCATTCTGAAGACTGGTGCTATTCACTGCCCTCAGCA--------------------------------------------------- -s simCow_chr6.simCow.chr6 576051 34 + 602619 GATAGCAATGACCGTTG-----ATTTCCTGCCCACTCCA--------------------------------------------------- -s simDog_chr6.simDog.chr6 567911 34 + 593897 AGAAATAGTAAATGTTG-----ATTTACTGCCCATTGCA--------------------------------------------------- -s simHuman_chr6.simHuman.chr6 571640 34 + 601863 AATAACAATGGATGCTA-----ATTTGCTGTCCATTGCA--------------------------------------------------- -s simRat_chr6.simRat.chr6 77718 39 - 647215 AATCATTCAGAAGACTGATGTTATTCACTGCCCACAGCA--------------------------------------------------- - -a -s simMouse_chr6.simMouse.chr6 603480 4 + 636262 TGTG -s Anc0.Anc0refChr3 200850 4 + 222631 TGTG -s Anc1.Anc1refChr1 40603 4 + 69767 TGTG -s Anc2.Anc2refChr1 117600 4 + 142988 TGTG -s mr.mrrefChr3 151238 4 + 181027 TGTG -s simCow_chr6.simCow.chr6 576147 4 + 602619 TGTG -s simHuman_chr6.simHuman.chr6 571736 4 + 601863 TGTG -s simRat_chr6.simRat.chr6 77757 4 - 647215 TGTG - -a -s simMouse_chr6.simMouse.chr6 603484 23 + 636262 CCAAGGTCTCACAAAATCTGATA -s Anc0.Anc0refChr3 200854 23 + 222631 CCTAGGTCTCACAAAATCTGATA -s Anc1.Anc1refChr1 40607 23 + 69767 CCTAGGTCTCACAAAATCTGATA -s Anc2.Anc2refChr1 117604 23 + 142988 CCTAGGTCTCACAAAATCAACTA -s mr.mrrefChr3 151242 23 + 181027 CCAAGGTCTCACAAAATCTGATA -s simCow_chr6.simCow.chr6 576151 18 + 602619 CCTAGGTCTCACAAAATC----- -s simDog_chr6.simDog.chr6 567970 5 + 593897 ------------------AACTA -s simHuman_chr6.simHuman.chr6 571743 23 + 601863 CCTGGGTCTCACAAAATCTGATA -s simRat_chr6.simRat.chr6 77761 23 - 647215 CCAAGGTCTCACAGAATCTGATA - -a -s simMouse_chr6.simMouse.chr6 603507 6 + 636262 ATAACC -s Anc0.Anc0refChr3 200877 6 + 222631 CTAATG -s Anc1.Anc1refChr1 40630 6 + 69767 CTAATG -s Anc2.Anc2refChr1 117627 6 + 142988 CTTATG -s mr.mrrefChr3 151265 6 + 181027 ATAACC -s simDog_chr6.simDog.chr6 567975 6 + 593897 CTTATG -s simHuman_chr6.simHuman.chr6 571790 6 + 601863 CTAATG -s simRat_chr6.simRat.chr6 77784 6 - 647215 ATAACC - -a -s simMouse_chr6.simMouse.chr6 603513 53 + 636262 TTAAAGTTCACTCAAAGGCTCATGTGGACATTGCATTGGGCCCCCAGTTCACT -s Anc0.Anc0refChr3 200884 42 + 222631 TTAATGTTCAGACAAA-----------ACATTGCAGTGGACCCCTGGTTGATT -s Anc1.Anc1refChr1 40637 42 + 69767 TTAATGTTCAGACAAA-----------ACATTGCAGTGGACCCCTGGTTGATT -s Anc2.Anc2refChr1 117634 42 + 142988 TGAATGGTCAGACAAG-----------ACACAGCGGTGGACCCCTGGTTGATT -s mr.mrrefChr3 151271 53 + 181027 TTAAAGTTCACTCAAAGGCTCATGTGGACATTGCATTGGGCCCCCAGTTCACT -s simCow_chr6.simCow.chr6 576169 14 + 602619 ---------------------------------------ACCCCTGGTTAATT -s simDog_chr6.simDog.chr6 567982 42 + 593897 TGAATGGTCAGACAAG-----------ACACAGCGGTGGACCCCTGGTTGATT -s simHuman_chr6.simHuman.chr6 571797 42 + 601863 TTAACATTCAAGCAAA-----------ACATTACACTGGTCCCTTGGTTTATC -s simRat_chr6.simRat.chr6 77790 53 - 647215 TTAAAGTTCGCTCAAAGGCTCATGCTGACATTGCAATAGGCCCCCAGTTTACT - -a -s simMouse_chr6.simMouse.chr6 603566 93 + 636262 TTTGTCTCATGGGTGGTGAAGACAAATGAGCCAATGGGGCCCTGAGCTCTGCATGATGCAGAGTGTAATCAGGGTGTTGCTACAAGAGATGGT -s Anc0.Anc0refChr3 200933 58 + 222631 TCTGTCACCTTTGAAGTGTAAACACTTGGTCTCATGGTAGGCTAAG-----------------------------------ACAATAGATGGA -s Anc1.Anc1refChr1 40686 58 + 69767 TCTGTCACCTTTGAAGTGTAAACACTTGGTCTCATGGTAGGCTAAG-----------------------------------ACAATAGATGGA -s Anc2.Anc2refChr1 117683 58 + 142988 TCTGTCACCTTTGAAGGGTAAACACTTGGTCTCATGGTAGGCTAAG-----------------------------------ACAATGGATGGA -s mr.mrrefChr3 151324 93 + 181027 TTTGTCTCATGGGTGGTGAAGACAAATGAGCCAATGGGGCCCTGAGCTCTGCATGATGCAGAGTGTAATCAGGGTGTTGCTACAAGAGATGGT -s simCow_chr6.simCow.chr6 576189 58 + 602619 CCTGTTACCTTTGAAGAGTAAACACCTGGCCTTGTGGCAGGCTAAG-----------------------------------ACAATGGACGGA -s simDog_chr6.simDog.chr6 568322 58 + 593897 TCTGTCTCCTGTGAAGGAACAACACTTGGTCCCATGTTATGCTAAG-----------------------------------ATAGTGGATGGA -s simHuman_chr6.simHuman.chr6 571847 58 + 601863 TCTGCCACCCTTGAAGTGTAAACACTAGGTCTCATGGTAGGCTAAG-----------------------------------ACAACAGATGGA -s simRat_chr6.simRat.chr6 77843 93 - 647215 TGTGTCTCATGGGGGGTAAAGACTGAGGAGCCAATGGAGCCCTGAACTGTGTATGATACAGAGTGTAATGAAGGTGTTGCAACAAGAGATAGT - -a -s simMouse_chr6.simMouse.chr6 603659 26 + 636262 GAAACACTGCCAACATGTCATACTCA -s Anc0.Anc0refChr3 200991 25 + 222631 GGTATTCAGTGGATATAACATAA-CA -s Anc1.Anc1refChr1 40744 25 + 69767 GGTATTCAGTGGATATAACATAA-CA -s Anc2.Anc2refChr1 117742 25 + 142988 GGTATTCAGTGGATATAACATAA-CA -s mr.mrrefChr3 151417 26 + 181027 GAAACACTGCCAACATGTCATACTCA -s simCow_chr6.simCow.chr6 576248 25 + 602619 GGTATCCTGTGGGTAACACTCAC-CA -s simDog_chr6.simDog.chr6 568381 25 + 593897 GTTATTCAGTGGATATAACATAA-CA -s simHuman_chr6.simHuman.chr6 571905 2 + 601863 GG------------------------ -s simRat_chr6.simRat.chr6 77936 26 - 647215 GAAACCCTGCCAACATGCCATACTCA - -a -s simMouse_chr6.simMouse.chr6 603685 20 + 636262 CCATGTCCTATCTAACTTCA -s Anc0.Anc0refChr3 201016 12 + 222631 CCAAGTCCTCT--------A -s Anc1.Anc1refChr1 40769 12 + 69767 CCAAGTCCTCT--------A -s Anc2.Anc2refChr1 117767 12 + 142988 CCAAGTCCTCT--------A -s mr.mrrefChr3 151443 20 + 181027 CCATGTCCTATCTAACTTCA -s simCow_chr6.simCow.chr6 576277 12 + 602619 CCAATTACACC--------A -s simDog_chr6.simDog.chr6 568406 12 + 593897 CCAAGTCCTCT--------A -s simRat_chr6.simRat.chr6 77962 20 - 647215 CAATGACCTGTCCAATTCCA - -a -s simMouse_chr6.simMouse.chr6 603705 37 + 636262 GCATAAACCTGGTCGGGGCTAGAACCATATGTGGCCA -s Anc0.Anc0refChr3 201028 36 + 222631 GTGTACACCTGGTCCAGGCTAGGAGCACTCATGGAC- -s Anc1.Anc1refChr1 40781 36 + 69767 GTGTACACCTGGTCCAGGCTAGGAGCACTCATGGAC- -s Anc2.Anc2refChr1 117779 36 + 142988 GTGTACACCTGGTCCAGGCTAGGAGCACTCATGGAC- -s mr.mrrefChr3 151463 37 + 181027 GCATAAACCTGGTCGGGGCTAGAACCATATGTGGCCA -s simCow_chr6.simCow.chr6 576289 36 + 602619 GTGTGTATCTGGCCCGGGCTAGAAGCACTGATGGAC- -s simDog_chr6.simDog.chr6 568420 36 + 593897 GTGTACACCTGGTCCAGGCTAGGAGCACTCATGGAC- -s simRat_chr6.simRat.chr6 77982 37 - 647215 GCATACACTTGGTCTGGACTAGAACCATATGTGGCCA - -a -s simMouse_chr6.simMouse.chr6 603742 20 + 636262 TATACTGACTTGATTCTTTT -s Anc0.Anc0refChr3 201064 15 + 222631 TACACTGAA---ATTGTT-- -s Anc1.Anc1refChr1 40817 18 + 69767 TACACTGAAGTGATTGTT-- -s Anc2.Anc2refChr1 117815 15 + 142988 TACACTAAA---AATGAT-- -s mr.mrrefChr3 151500 20 + 181027 TATACTGACTTGATTCTTTT -s simCow_chr6.simCow.chr6 576325 15 + 602619 TACACTAAA---AATGAT-- -s simDog_chr6.simDog.chr6 568466 15 + 593897 TACACTAAA---AATGAT-- -s simHuman_chr6.simHuman.chr6 571907 12 + 601863 ------GTAGTGGTGGTT-- -s simRat_chr6.simRat.chr6 78019 20 - 647215 AATACTAACTTGATTCATTT - -a -s simMouse_chr6.simMouse.chr6 603762 23 + 636262 TTCCTGGATTGCTTGCACCGCAG -s Anc0.Anc0refChr3 201082 23 + 222631 ACACTGGATTGCTTGCAGCCTTA -s Anc1.Anc1refChr1 40838 23 + 69767 ACACTGGATTGCTTGCAGCCTTA -s Anc2.Anc2refChr1 117833 23 + 142988 ACACTGGATAGCTTACAGCCTTA -s mr.mrrefChr3 151525 23 + 181027 TTACTGGATTGCTTGCACCGTTG -s simCow_chr6.simCow.chr6 576343 23 + 602619 GCAGTGTATAGCTTACAGCCTTA -s simDog_chr6.simDog.chr6 568484 20 + 593897 ACACTGGA---ATTACAGCCTTA -s simHuman_chr6.simHuman.chr6 571922 23 + 601863 ACACTGGATTGCTTGCAGCTTTA -s simRat_chr6.simRat.chr6 78048 23 - 647215 TTATTGGATTACTTGCACCCTTC - -a -s simMouse_chr6.simMouse.chr6 603785 185 + 636262 CTTGTCAGGTTGAATGACCTGCAGACTGGGGCTGCTAGTCGATTGCCAGGAATTACTCCTGGGTTAATCTTGGTGAATTCTACTCAACGACAGTCTGCAATGATTGACTCAAGTAAGACTATTCAATACTTTTGTGATGCGGACCGTCTACAGGAAATAGAATTACAGCCACCCTGCTATAAGAA -s Anc0.Anc0refChr3 201106 184 + 222631 CTTGTCA-GTTGAACCACTTGCAGACTGGGGCTGCTAGTCGCTTGCCAGGAATTACTCCTGGGTTAATATTTGTGAATTCTACCCAACGACAATCTGCAATGATTGACTCAACTAAGACTGTTCAATACTTATGTGATGCAGACCGTCTACAGGAAATAGAATTAGAGCTATCCTGCTATAAAAA -s Anc1.Anc1refChr1 40862 184 + 69767 CTTGTCA-GTTGAACCACTTGCAGACTGGGGCTGCTAGTCGCTTGCCAGGAATTACTCCTGGGTTAATATTTGTGAATTCTACCCAACGACAATCTGCAATGATTGACTCAACTAAGACTGTTCAATACTTATGTGATGCAGACCGTCTACAGGAAATAGAATTAGAGCTATCCTGCTATAAAAA -s Anc2.Anc2refChr1 117857 184 + 142988 CTTGTCA-GTTGAACCACTTGCAGACTGGGGCTGCTAGTCGCTTGCCAGGAATTACTCCTGGGTTAATATTTGTGAATTCTACCCAACGTCAATCTGCAATGATTGACTCAACTAAGACTGTTCAATACTTATGTGATGCAGACCGTCTACAGGAAATAGAATTAGAGCTATCCTGCTATAAAAA -s mr.mrrefChr3 151548 185 + 181027 CTTGTCAGGTTGAATGACCTGCAGACTGGGGCTGCTAGTCGCTTGCCAGGAATTACTCCTGGGTTAATATTGGTGAATTCTACTCAACGACAGTCTGCAATGATTGACTCAAGTAAGACTATTCAATACTTTTGTGATGCGGACCGTCTACAGGAAATAGAATTACAGCTACCCTGCTATAAAAA -s simCow_chr6.simCow.chr6 576367 184 + 602619 CTTGCCA-ATAGAATCCCTCGGAGATTGGGGCTGCTAGTCGCTTGCCAGGAATTACTCCTGGGTTAATATTTGTGAATTCTACCCAACGTCAATCTGCAATGATTGACTCAACTAAGACTGTTCGATACTTATGTGACGCAGACCGTCTACAGGAAATAGAATTGGAGCTATCCTGCTACAAAAA -s simDog_chr6.simDog.chr6 568505 184 + 593897 CTTGTCA-GTTGAACCACCTGCAGACTGGGGCTGCCAGTCGCTTGCCAGGAATTACCCCTGGGTTAATATTTGTGAATTCTACCCAACGTCAATCTGCAATGATTGACTCAGCTAAGACTGTTCAATACTTATGTGATGCAGACCATCTACAGGAAATAGAATTAGAGCTTTCCTGCTATAAAAA -s simHuman_chr6.simHuman.chr6 571946 184 + 601863 CTTGTCA-GTTGTACCACTGTCAGACTGGGGCTGCTAGTCGCCTGCCAGGAATTACTCCTGGGTTAATATTTGTGAATCCTACCCAACGACAATCTGCAATGATCGACTCGACGAAGACTGTTCAATACTTATGTGATGCAGACCGTCTACAGGAGATAGAATTATAGCTATCCTGCTATAAAAA -s simRat_chr6.simRat.chr6 78071 185 - 647215 CTCATCAGGTTGAATGACCTGCAGACTGGGGCTGCTAGTCGCTTGCCAGGAATTACTCCTGGGTTAATATTGGTTAATTCTACTCAACGACAGTCTCCAATGATTGACTCAAGTAAGACTATTCAATACTTTTGTGATGTCGACCGACTACAGGAAATAGAATTACAGCTACCCTGCTATAAAAA - -a -s simMouse_chr6.simMouse.chr6 603970 25 + 636262 CTGATGATGAAAAATCATGCATAGC -s Anc0.Anc0refChr3 201292 23 + 222631 TTGATGATG--AAATCATGCATAGT -s Anc1.Anc1refChr1 41048 23 + 69767 TTGATGATG--AAATCATGCATAGT -s Anc2.Anc2refChr1 118043 23 + 142988 TTGATAATG--AAATCATGCATAGT -s mr.mrrefChr3 151733 25 + 181027 CTGATGATGAAAAATCATGCATAGC -s simCow_chr6.simCow.chr6 576553 23 + 602619 TCGAGAATG--AAATTATGCATAGT -s simDog_chr6.simDog.chr6 568691 23 + 593897 TTGATAACG--AAATCATGCATAGT -s simHuman_chr6.simHuman.chr6 572132 23 + 601863 TTGGTGATG--AAGTCATACATAGT -s simRat_chr6.simRat.chr6 78256 25 - 647215 CTGATGATGAAAAATCACGCATAGC - -a -s simMouse_chr6.simMouse.chr6 603995 60 + 636262 AGCTATGGCAGACTGCAGGTAATGCTATAACCATCCTTTGTCAAAAAAAACAGATATGCT -s Anc0.Anc0refChr3 201318 57 + 222631 ATCTATGTTAGACTGCTGGCAATGCTATAACCATCCATCGTC---AAAAACAGATTTGCC -s Anc1.Anc1refChr1 41074 57 + 69767 ATCTATGTTAGACTGCTGGCAATGCTATAACCATCCATCGTC---AAAAACAGATTTGCC -s Anc2.Anc2refChr1 118069 57 + 142988 ATCTATGTTAGACTGCTAGCAATGCTATGACCATCTATCGTC---AAAAACAGATTTGCC -s mr.mrrefChr3 151758 60 + 181027 AGCTATGTTAGACTGCAGGTAATGCTATAACCATCCTTTGTCAAAAAAAACAGATTTGCT -s simCow_chr6.simCow.chr6 576579 52 + 602619 ATCTATGTCAGACTGTTAGCAATGCTATGACCATCTACGATC---AAGAACA-----CCG -s simDog_chr6.simDog.chr6 568717 57 + 593897 ATCTATGTTAGACTGCTAGCAATGCTATGACCATCTATCGTC---AAAAACGGATTTGCC -s simHuman_chr6.simHuman.chr6 572158 57 + 601863 ATCTATGTTAGGCTGCTGGCAATGCTACAACCATCCATAGTC---AAAAACAGATTTGCC -s simRat_chr6.simRat.chr6 78281 60 - 647215 AGCTATGTTAGAGTGCAGGGAATGTTATGACTATCCTTTGTCAAAAAAAACAGATTAGCT - -a -s simMouse_chr6.simMouse.chr6 604055 17 + 636262 GCACTATAGGCAGATGT -s Anc0.Anc0refChr3 201375 17 + 222631 TCACCAGAGGTGAATAA -s Anc1.Anc1refChr1 41131 17 + 69767 TCACCAGAGGTGAATAA -s Anc2.Anc2refChr1 118126 17 + 142988 TCGCCAGGGGTGAATAA -s mr.mrrefChr3 151818 17 + 181027 GCACTATAGGCAGATGA -s simCow_chr6.simCow.chr6 576631 17 + 602619 CCGCTACGGGAGAATAA -s simDog_chr6.simDog.chr6 568778 17 + 593897 TGGGCGGGGGTGAATAA -s simHuman_chr6.simHuman.chr6 572215 17 + 601863 TCACCAGAGGTGAATAA -s simRat_chr6.simRat.chr6 78341 17 - 647215 GCACTATAGGCAGATGA - -a -s simMouse_chr6.simMouse.chr6 604072 1 + 636262 G -s Anc0.Anc0refChr3 201392 1 + 222631 A -s Anc1.Anc1refChr1 41148 1 + 69767 A -s Anc2.Anc2refChr1 118144 1 + 142988 A -s mr.mrrefChr3 151835 1 + 181027 A -s simCow_chr6.simCow.chr6 576649 1 + 602619 A -s simDog_chr6.simDog.chr6 568796 1 + 593897 A -s simHuman_chr6.simHuman.chr6 572232 1 + 601863 A -s simRat_chr6.simRat.chr6 78358 1 - 647215 A - -a -s simMouse_chr6.simMouse.chr6 604073 30 + 636262 GAAGGAAGGATCATTGATATTCCAAAAGCG -s Anc0.Anc0refChr3 201396 30 + 222631 GAAGAAAGGATAAGCGATATTCCAAAAGCA -s Anc1.Anc1refChr1 41152 30 + 69767 GAAGAAAGGATAAGCGATATTCCAAAAGCA -s Anc2.Anc2refChr1 118148 30 + 142988 GAAGTAAGGATAAGCGATATTCCAGAAGCA -s mr.mrrefChr3 151836 30 + 181027 GAAGAAAGGATCATTGATATTCCAAAAGCA -s simCow_chr6.simCow.chr6 576653 30 + 602619 GAAGTAAGGAAAAGTGTTATTCCAGAAGTG -s simDog_chr6.simDog.chr6 568800 30 + 593897 GTAGTAAGGATAAGCGATATTCCAGAAGCA -s simHuman_chr6.simHuman.chr6 572236 30 + 601863 GAAGAAACGAGTAACGATACTTGAAGGGCA -s simRat_chr6.simRat.chr6 78359 30 - 647215 GAAGAAAGGATCATTGATATTCCAAAAGCA - -a -s simMouse_chr6.simMouse.chr6 604103 15 + 636262 CAATTGATGCTCCAA -s Anc0.Anc0refChr3 201427 15 + 222631 CAGTTGAAGCACCAA -s Anc1.Anc1refChr1 41183 15 + 69767 CAGTTGAAGCACCAA -s Anc2.Anc2refChr1 118179 15 + 142988 CAGTTGAAGCACCAA -s mr.mrrefChr3 151866 15 + 181027 CAATTGATGCTCCAA -s simCow_chr6.simCow.chr6 576684 15 + 602619 CTGGTGAAGCACCAA -s simDog_chr6.simDog.chr6 568831 15 + 593897 CAGTTGAAGCGCCAA -s simHuman_chr6.simHuman.chr6 572267 15 + 601863 TAGCTGAAGCACCAA -s simRat_chr6.simRat.chr6 78389 15 - 647215 CAATTGGTGCTCCAA - -a -s simMouse_chr6.simMouse.chr6 604118 20 + 636262 TGTCCTATGTCCATAATCAT -s Anc0.Anc0refChr3 201442 20 + 222631 GTTACTAGATCAATCTTCCT -s Anc1.Anc1refChr1 41198 20 + 69767 GTTACTAGATCAATCTTCCT -s Anc2.Anc2refChr1 118194 20 + 142988 GTTACTAGATCAATCTTCCT -s mr.mrrefChr3 151881 20 + 181027 TGTCCTAGGTCAATAATCCT -s simCow_chr6.simCow.chr6 576699 20 + 602619 GTTATCAGGTCAATCTTCCT -s simDog_chr6.simDog.chr6 568847 20 + 593897 GTTACTAGATCAATCTTCCT -s simHuman_chr6.simHuman.chr6 572282 20 + 601863 GTTACTAGATCAATCCTCCT -s simRat_chr6.simRat.chr6 78404 20 - 647215 TGTCCTAGGTCAAAAATCCT - -a -s simMouse_chr6.simMouse.chr6 604138 30 + 636262 GCTTTTATTTTCATTCTGGAGATTAGGGTT -s Anc0.Anc0refChr3 201480 30 + 222631 GCTCACATTTGCATTCTGGAGATTAGAAGT -s Anc1.Anc1refChr1 41236 30 + 69767 GCTCACATTTGCATTCTGGAGATTAGAAGT -s Anc2.Anc2refChr1 118235 30 + 142988 GCTCACATTTGCATTCTGAAGATTAAAAGT -s mr.mrrefChr3 151901 30 + 181027 GCTTTTATTTTCATTCTGGAGATTAGGGTT -s simCow_chr6.simCow.chr6 576740 25 + 602619 GCCCGC-----CATTCTGAAGATTGTGAGT -s simDog_chr6.simDog.chr6 568888 30 + 593897 ACTCACATTTGCATTCTGAAGATTAAAAGT -s simHuman_chr6.simHuman.chr6 572320 30 + 601863 GATCACATTTGCATTCTTGAGATTAGAAGT -s simRat_chr6.simRat.chr6 78424 30 - 647215 GCTTGTAATTTTATCCTGGAGATTAGGGTT - -a -s simMouse_chr6.simMouse.chr6 604168 7 + 636262 GGAAGCA -s Anc0.Anc0refChr3 201510 7 + 222631 CAAAGCA -s Anc1.Anc1refChr1 41266 7 + 69767 CAAAGCA -s Anc2.Anc2refChr1 118266 7 + 142988 CAAGGCC -s mr.mrrefChr3 151931 7 + 181027 GAAAGCA -s simCow_chr6.simCow.chr6 576766 4 + 602619 CAAG--- -s simDog_chr6.simDog.chr6 568919 7 + 593897 CAAGGCC -s simHuman_chr6.simHuman.chr6 572350 7 + 601863 TAGAGCA -s simRat_chr6.simRat.chr6 78454 7 - 647215 GAAAGCA - -a -s simMouse_chr6.simMouse.chr6 604175 12 + 636262 TGTCAATTTAGA -s Anc0.Anc0refChr3 201542 12 + 222631 TGGTCATCCAGT -s Anc1.Anc1refChr1 41298 12 + 69767 TGGTCATCCAGT -s Anc2.Anc2refChr1 118298 12 + 142988 TGGTCACCCAGT -s mr.mrrefChr3 151938 12 + 181027 TGTTAATTTAGA -s simCow_chr6.simCow.chr6 576789 12 + 602619 TTGCAACTCATT -s simDog_chr6.simDog.chr6 568950 12 + 593897 TGGTCACCCAGT -s simHuman_chr6.simHuman.chr6 572392 12 + 601863 AGGTTATCCAGT -s simRat_chr6.simRat.chr6 78461 12 - 647215 TGTTAATTTAGA - -a -s simMouse_chr6.simMouse.chr6 604187 37 + 636262 TCAGACCAGACATCCTTCAAGTGTTATACCAGTAGAT -s Anc0.Anc0refChr3 201555 37 + 222631 TCAGGTTATACATCATTCAAGTGTCAGTAAAGTGGGA -s Anc1.Anc1refChr1 41311 37 + 69767 TCAGGTTATACATCATTCAAGTGTCAGTAAAGTGGGA -s Anc2.Anc2refChr1 118311 37 + 142988 TCAGGTTATACATCATTCAAGTGTCAGTAAATTGGGA -s mr.mrrefChr3 151951 37 + 181027 TCAGACCAGACATCCTTCAAGTGTCATACCAGTGGAT -s simCow_chr6.simCow.chr6 576802 35 + 602619 CTAGGTTATAGATCA--CAAGTGTTAATAAATTGGGA -s simDog_chr6.simDog.chr6 568963 37 + 593897 TCAGGTTATACATCATTCTAATGTCAGTAAATGGGGC -s simHuman_chr6.simHuman.chr6 572405 37 + 601863 TCAGGTTATAAATCATTCAAGTGTCAGTAAAGTGGGA -s simRat_chr6.simRat.chr6 78474 37 - 647215 TCAGACCAGACATCCTTCAAATGTCATGCCAGTGGAT - -a -s simMouse_chr6.simMouse.chr6 604224 24 + 636262 GGAATTACATGGTATGAACAGCAT -s Anc0.Anc0refChr3 201592 24 + 222631 GAACTGAGATGGTATGAGCAGTAT -s Anc1.Anc1refChr1 41348 24 + 69767 GAACTGAGATGGTATGAGCAGTAT -s Anc2.Anc2refChr1 118348 24 + 142988 GAACTTAGATGGAATGAGCAGTAC -s mr.mrrefChr3 151988 24 + 181027 GGAATGACATGGTATGAACAGTAT -s simCow_chr6.simCow.chr6 576838 14 + 602619 GAATTCAAATGGAC---------- -s simDog_chr6.simDog.chr6 569000 24 + 593897 AAACTTAGATGGAATGAGCAGTAC -s simHuman_chr6.simHuman.chr6 572442 24 + 601863 GAAGTGAGAGGCTATGAGCAGTAT -s simRat_chr6.simRat.chr6 78511 24 - 647215 CGACTGACACAGTATGAACAGTAT - -a -s simMouse_chr6.simMouse.chr6 604248 25 + 636262 GTATAAACAGCAAATTAAACAGCCA -s Anc0.Anc0refChr3 201622 25 + 222631 CTGCAAAAAGGTAACAAAGCAGCCA -s Anc1.Anc1refChr1 41378 25 + 69767 CTGCAAAAAGGTAACAAAGCAGCCA -s Anc2.Anc2refChr1 118378 25 + 142988 CTGCAAAAAGGTAACAAACCAGCCT -s mr.mrrefChr3 152012 25 + 181027 GTACAAACAGCAAATTAAGCAGCCA -s simDog_chr6.simDog.chr6 569030 25 + 593897 CTGCAAAAAGGTAACAAACCAGCCT -s simHuman_chr6.simHuman.chr6 572472 25 + 601863 CTGCTAAAAGGTAACAAAGCAGCCA -s simRat_chr6.simRat.chr6 78535 25 - 647215 ATACAAACAGCAAATTAAGCAGCCA - -a -s simMouse_chr6.simMouse.chr6 604273 5 + 636262 CTTAC -s Anc0.Anc0refChr3 201648 5 + 222631 TTAAC -s Anc1.Anc1refChr1 41404 5 + 69767 TTAAC -s Anc2.Anc2refChr1 118404 5 + 142988 TTAAC -s mr.mrrefChr3 152038 5 + 181027 TTTAC -s simDog_chr6.simDog.chr6 569056 5 + 593897 TTAAC -s simHuman_chr6.simHuman.chr6 572498 5 + 601863 TTAAC -s simRat_chr6.simRat.chr6 78561 5 - 647215 TTTAC - -a -s simMouse_chr6.simMouse.chr6 604278 16 + 636262 TGGCCATATATACTAC -s Anc0.Anc0refChr3 201656 9 + 222631 TAGTCA-------TAC -s Anc1.Anc1refChr1 41412 9 + 69767 TAGTCA-------TAC -s Anc2.Anc2refChr1 118412 9 + 142988 CAGTGA-------TAC -s mr.mrrefChr3 152043 16 + 181027 TAGCCATATATACTAC -s simCow_chr6.simCow.chr6 576852 9 + 602619 CAGTGG-------TAC -s simDog_chr6.simDog.chr6 569064 9 + 593897 CAGTGA-------TAC -s simHuman_chr6.simHuman.chr6 572506 9 + 601863 TAGTCA-------TAC -s simRat_chr6.simRat.chr6 78566 16 - 647215 TAGCCATGTATAGTAC - -a -s simMouse_chr6.simMouse.chr6 604294 7 + 636262 AGGCATT -s Anc0.Anc0refChr3 201665 7 + 222631 AGGCATT -s Anc1.Anc1refChr1 41421 7 + 69767 AGGCATT -s Anc2.Anc2refChr1 118421 7 + 142988 AGGCATT -s mr.mrrefChr3 152059 7 + 181027 AGGCATT -s simCow_chr6.simCow.chr6 576861 7 + 602619 AGGCATT -s simDog_chr6.simDog.chr6 569077 7 + 593897 AGGCACT -s simHuman_chr6.simHuman.chr6 572515 7 + 601863 AGGCATT -s simRat_chr6.simRat.chr6 78582 7 - 647215 AGGGATT - -a -s simMouse_chr6.simMouse.chr6 604301 25 + 636262 GACCCAAAGACCCCTAAGCCTTCAG -s Anc0.Anc0refChr3 201673 25 + 222631 GACCCATAGACCCCTGAGCCCTCAT -s Anc1.Anc1refChr1 41429 25 + 69767 GACCCATAGACCCCTGAGCCCTCAT -s Anc2.Anc2refChr1 118429 25 + 142988 GACCCATAGACCCCTGAGCCCTCAT -s mr.mrrefChr3 152066 25 + 181027 GACCCAAAGACCCCTGAGCCTTCAG -s simCow_chr6.simCow.chr6 576869 25 + 602619 GACTCATAGATCCCTGAGCTCTCAT -s simDog_chr6.simDog.chr6 569085 20 + 593897 GACCCATAGACCCTTGAGCC----- -s simHuman_chr6.simHuman.chr6 572523 25 + 601863 GTCCCACGGACCTCTGAGTCCTCAT -s simRat_chr6.simRat.chr6 78589 25 - 647215 GACCCAAAGACCCCTGAGCCTTCAG - -a -s simMouse_chr6.simMouse.chr6 604326 61 + 636262 ATTTGGCATAGTTTAGAACCCAAGCTTAATATTATGTTGCTCAATGTGTGACAAACACCCT -s Anc0.Anc0refChr3 201712 61 + 222631 ATGTGGCTTAGTGTAAAACCCTAGTTTAACATTATGCCACTCACTGTGTGATGAACACTCT -s Anc1.Anc1refChr1 41468 61 + 69767 ATGTGGCTTAGTGTAAAACCCTAGTTTAACATTATGCCACTCACTGTGTGATGAACACTCT -s Anc2.Anc2refChr1 118468 61 + 142988 ATGTGGCTTAGAGTAAAACCGTAATTTAACATTATGCTGCTCACCGTGTGATGACCACTAT -s mr.mrrefChr3 152091 61 + 181027 ATGTGGCATAGTTTAGAACCCAAGCTTAATATTATGTCACTCAATGTGTGACAAACACTCT -s simCow_chr6.simCow.chr6 576908 61 + 602619 ATGTGGGTTAGAATAAAACCATGATTCAACATTATGCTGCTCAAGGTGTAATGAGCACTGT -s simDog_chr6.simDog.chr6 569108 61 + 593897 AAGTGGCTTGGAGTAAAACTGTAATTTAACATTATACTGCTCACCTTGTGATGACCACTAT -s simHuman_chr6.simHuman.chr6 572570 61 + 601863 ATGTGGCTTACTGTAAAACCCTAGTATAACATTATGCCACTGACTGTTTGATGAACACTCT -s simRat_chr6.simRat.chr6 78614 50 - 647215 ATGTGGCATAGTTTAG-----------AATATTATGTCACGCAATGTGTGACAAACACTCT - -a -s simMouse_chr6.simMouse.chr6 604387 8 + 636262 GCTGCTAT -s Anc0.Anc0refChr3 201777 8 + 222631 CCAGCTAA -s Anc1.Anc1refChr1 41534 8 + 69767 CCAGCTAA -s Anc2.Anc2refChr1 118533 8 + 142988 CCAATTAA -s mr.mrrefChr3 152152 8 + 181027 CCTGCTAT -s simCow_chr6.simCow.chr6 576973 8 + 602619 CCAATCAT -s simDog_chr6.simDog.chr6 569173 8 + 593897 CCGATTGA -s simHuman_chr6.simHuman.chr6 572636 8 + 601863 CCAGCTAC -s simRat_chr6.simRat.chr6 78664 8 - 647215 CCTGCTAT - -a -s simMouse_chr6.simMouse.chr6 604395 44 + 636262 GCATCAGTGTCACCTGGCTGAGGACTGTGCCTGAGCATAGTCTG -s Anc0.Anc0refChr3 201850 29 + 222631 TCATCAGCATTGCCTGTCTAAGG-C-----CAGTG--------- -s Anc1.Anc1refChr1 41607 34 + 69767 TCATCAGCATTGCCTGTCTAAGG-CACTGCCAGTG--------- -s Anc2.Anc2refChr1 118606 29 + 142988 TCATCAGCATTGCCTGTCTAAGG-A-----CAGTG--------- -s mr.mrrefChr3 152160 43 + 181027 TCACCAGTGTCACCTGGCTGAGG-CTGTGCCTGAGCATAATCTG -s simCow_chr6.simCow.chr6 577046 29 + 602619 TGATCACTATTGCCTCTGTAAGG-G-----TGGTG--------- -s simDog_chr6.simDog.chr6 569246 29 + 593897 TCATCAGCATTACCTGTCTAAGG-A-----CAGTG--------- -s simHuman_chr6.simHuman.chr6 572709 33 + 601863 TCATCAGCATTGCTTGT-TAAGG-CACTGCCAGTG--------- -s simRat_chr6.simRat.chr6 78672 43 - 647215 TCACCAGTGTCACCTGACTGAGG-CCGTACCTGAGCATAATCTG - -a -s simMouse_chr6.simMouse.chr6 604439 36 + 636262 CACAGCACACTGGGCCCTGTGACCTTGCCCAGGTAC -s Anc0.Anc0refChr3 201894 35 + 222631 CACAGAACACTAGGCCCTGCAGCCTCA-CTAATTAT -s Anc1.Anc1refChr1 41658 35 + 69767 CACAGAACACTAGGCCCTGCAGCCTCA-CTAATTAT -s Anc2.Anc2refChr1 118650 35 + 142988 CACAGAACACTAAGTCCTGCAGCCTCA-CTAATTAT -s mr.mrrefChr3 152227 35 + 181027 CACAGAACACTGGGCCCTGTGGCCTTG-CCAAGTAC -s simCow_chr6.simCow.chr6 577090 32 + 602619 TGCAGAACACTAAGACTTGCAGCATCA-CTAAT--- -s simDog_chr6.simDog.chr6 569290 35 + 593897 CACAGAACACCAAATCCCGTATCCTCC-CTCATTAT -s simHuman_chr6.simHuman.chr6 572759 35 + 601863 CACAGAATACTAGGCCCTACAGCTTCA-CTAATTAT -s simRat_chr6.simRat.chr6 78743 35 - 647215 TGTAGAACGCTGGGCCCTTTGGCCAAG-CCAAGTAC - -a -s simMouse_chr6.simMouse.chr6 604475 24 + 636262 CTTATTAGGGGGAAGATTGATGGA -s Anc0.Anc0refChr3 201932 24 + 222631 CTTGTTACAGGGAAGACTGATGAA -s Anc1.Anc1refChr1 41696 24 + 69767 CTTGTTACAGGGAAGACTGATGAA -s Anc2.Anc2refChr1 118688 24 + 142988 CTTGTTACAGGGAAGACTGATGAA -s mr.mrrefChr3 152262 24 + 181027 CTTGTTAGGGGGAAGATTGATGAA -s simCow_chr6.simCow.chr6 577122 24 + 602619 CTTGTTACAGGGAAGACTGATGAA -s simDog_chr6.simDog.chr6 569328 24 + 593897 CCTGTTACCAGGAAGATTGATGAA -s simHuman_chr6.simHuman.chr6 572797 24 + 601863 CTTGTTACAGGGAAGACTGATCAA -s simRat_chr6.simRat.chr6 78778 24 - 647215 CTTGTTCTTAGGAAGGTTGATGAA - -a -s simMouse_chr6.simMouse.chr6 604499 32 + 636262 GTTGTTAGGGGTTATGAGTTTATTACCAGCTT -s Anc0.Anc0refChr3 201956 32 + 222631 GTTCTTAGAGGCCAAGAGTTTATTATCAGCTA -s Anc1.Anc1refChr1 41720 32 + 69767 GTTCTTAGAGGCCAAGAGTTTATTATCAGCTA -s Anc2.Anc2refChr1 118712 32 + 142988 GTTCTTAGAGGCCAAGAGTTTATTATCAGCTA -s mr.mrrefChr3 152286 32 + 181027 GTTGTTAGGGGTTATGAGTTTATTATCAGCTA -s simCow_chr6.simCow.chr6 577146 32 + 602619 GTTCTTAAAGGCCAAGAGCTTACTATCAGCTA -s simDog_chr6.simDog.chr6 569352 32 + 593897 GTTCTTAGAGGCCAAGAGTTTATTATTAGCAT -s simHuman_chr6.simHuman.chr6 572825 32 + 601863 GTTCTTAGAGGACACGAGATTATTATCAGCTA -s simRat_chr6.simRat.chr6 78802 32 - 647215 GTTGTTAGGGGCTAAGAGTTTATTATCAGCTA - -a -s simMouse_chr6.simMouse.chr6 604531 1 + 636262 C -s Anc0.Anc0refChr3 201988 1 + 222631 C -s Anc1.Anc1refChr1 41752 1 + 69767 C -s Anc2.Anc2refChr1 118744 1 + 142988 G -s mr.mrrefChr3 152318 1 + 181027 C -s simCow_chr6.simCow.chr6 577179 1 + 602619 G -s simDog_chr6.simDog.chr6 569384 1 + 593897 G -s simHuman_chr6.simHuman.chr6 572857 1 + 601863 C -s simRat_chr6.simRat.chr6 78834 1 - 647215 C - -a -s simMouse_chr6.simMouse.chr6 604532 71 + 636262 TCTATCAGGAAATACTTGTACATGGTTGCAGTCACCCCTGCACAGAACGCTGTGGGTTTCTTAAGGAAGCT -s Anc0.Anc0refChr3 201989 46 + 222631 TTTCTCAAGGAATAGTTGGACATGGCTGCTTCCACCTCT-------------------------GGAAGCT -s Anc1.Anc1refChr1 41753 48 + 69767 TTTCTCAAGGAATAGTTGGACATGGCTGCTTCCACCTCT-----------------------AAGGAAGCT -s Anc2.Anc2refChr1 118745 46 + 142988 TTTCTCAAGGAATAGTCAGACATGGCTGCTTCCACCTCT-------------------------GAAAGCT -s mr.mrrefChr3 152319 71 + 181027 TTTATCAGGAAATACTTGTACATGGTTGCAGTCACCCCTGCACAGAACGCTGTGGGTTTCTTAAGGAAGCT -s simCow_chr6.simCow.chr6 577180 46 + 602619 TTTCTCAGGTGATAGTCAGGCATGGCTGCGTTCACCCCT-------------------------GAAAACT -s simDog_chr6.simDog.chr6 569385 46 + 593897 TTTCTCAAGGAATAGTCAGACATGGCTGCTTCCACCTCT-------------------------GAAAGCT -s simHuman_chr6.simHuman.chr6 572861 31 + 601863 TTTCTCAAGGAATAGTTGGACA----------------------------------------AATGAAACT -s simRat_chr6.simRat.chr6 78835 71 - 647215 TTTATCAGGAGATATTCGTAGATGGTTGTGTTCACCCCTGCAAAGAAAGCTGTGCACTTCTTAAGGAAGTG - -a -s simMouse_chr6.simMouse.chr6 604603 72 + 636262 GTGGATTTCTTCAAACTACAGTCCTGCAAAACTTCACAAACAGTATCACCTCTGGTATGTTGAGTAGTTTAA -s Anc0.Anc0refChr3 202044 63 + 222631 GTGGGCTTTTTTAAACCATAGGCCTGAAAAACTACACAAATGGTACCACCTCTA---------ATAGCTTGT -s Anc1.Anc1refChr1 41810 72 + 69767 GTGGGCTTTTTTAAACCATAGGCCTGAAAAACTACACAAATGGTACCACCTCTAGTAAGTTGAATAGCTTGT -s Anc2.Anc2refChr1 118800 63 + 142988 GTGGGCCTTCCTAGACCATAGGCCTGAAAAACTACACAAATGGTACCACCTCTA---------ATAGCTTGT -s mr.mrrefChr3 152390 72 + 181027 GTGGATTTCTTCAAACTACAGTCCTGCAAAACTTCACAAACAGTACCACCTCTGGTATGTTGAGTAGTTTAA -s simCow_chr6.simCow.chr6 577235 63 + 602619 GTGGGCCTTCCTAGACTATAGTCCTGAAAAGCTACACAAATGGTACCACCTCTA---------ATAGCTTGT -s simDog_chr6.simDog.chr6 569440 52 + 593897 GTG-----------ACCTTCCGCCGGCAAAACTACACAAATTATACCACCTCTC---------ATATCTTGT -s simHuman_chr6.simHuman.chr6 572901 72 + 601863 GTGGTCTTATTTAAACCATAGGCCTGAAAAACTACACAAATGGTACCACCTCTAGTAAGTTGACTAGCTTGT -s simRat_chr6.simRat.chr6 78906 72 - 647215 GTGAATTTGCTCACACTACAGTTCTGGAAAACTTCTCAAACAGTACCACCTCTGGTATGTTGAGTAGTTAAA - -a -s simMouse_chr6.simMouse.chr6 604675 44 + 636262 CTTTTTTAAACTTCATTAAGAGGTTGTATGCCACGATTAAATGA -s Anc0.Anc0refChr3 202107 35 + 222631 CCTTCTTA---------CAAAGGACATGTGCCACTACCAAATAA -s Anc1.Anc1refChr1 41882 35 + 69767 CCTTCTTA---------CAAAGGACATGTGCCACTACCAAATAA -s Anc2.Anc2refChr1 118863 35 + 142988 CCTTCTTA---------AAAAGAACATGTACCACTACCAAATGA -s mr.mrrefChr3 152462 44 + 181027 CCTTCTTAAACTTCATTCAAAGGTTGTATGCCACGATCAAATAA -s simCow_chr6.simCow.chr6 577298 35 + 602619 CCTTCTTA---------AAAAGAACATGTACCACTACCAAATGA -s simDog_chr6.simDog.chr6 569494 35 + 593897 CACTCTTG---------AAAAAAATGTGTACCTATACCAAATGA -s simHuman_chr6.simHuman.chr6 572973 35 + 601863 CCTTCTTA---------CAAAGGACATGTGCCACCACCAAAAAA -s simRat_chr6.simRat.chr6 78978 44 - 647215 CCTTCTTAAGCTTCATTCAAAGGTTGTATGCCACTATCAGATAA - -a -s simMouse_chr6.simMouse.chr6 604719 3 + 636262 CCG -s Anc0.Anc0refChr3 202142 3 + 222631 CCA -s Anc1.Anc1refChr1 41917 3 + 69767 CCA -s Anc2.Anc2refChr1 118900 3 + 142988 CTG -s mr.mrrefChr3 152506 3 + 181027 CCA -s simCow_chr6.simCow.chr6 577335 3 + 602619 CTG -s simDog_chr6.simDog.chr6 569531 3 + 593897 CTG -s simHuman_chr6.simHuman.chr6 573008 3 + 601863 TCA -s simRat_chr6.simRat.chr6 79022 3 - 647215 CCA - -a -s simMouse_chr6.simMouse.chr6 604722 33 + 636262 TCCGTACAGAGCGAATGATTAACCTTCCATGAA -s Anc0.Anc0refChr3 202151 22 + 222631 TTCATGCAGAGGGAGTG-----------AGGAA -s Anc1.Anc1refChr1 41926 22 + 69767 TTCATGCAGAGGGAGTG-----------AGGAA -s Anc2.Anc2refChr1 118909 22 + 142988 TTCATGCAGAGGGAGTG-----------AGCAA -s mr.mrrefChr3 152509 22 + 181027 TCCGTACAGAGCGAATG-----------ATGAA -s simCow_chr6.simCow.chr6 577342 22 + 602619 TTCAGGCAGAGGGAGTG-----------CGCAA -s simDog_chr6.simDog.chr6 569540 22 + 593897 TTCATGCGATGGGAGTG-----------ATCAA -s simHuman_chr6.simHuman.chr6 573017 22 + 601863 TTCATGCAGAGGGAGTG-----------AGGAA -s simRat_chr6.simRat.chr6 79025 22 - 647215 TCTGTACAGAGTGAATG-----------ATGAA - -a -s simMouse_chr6.simMouse.chr6 604755 7 + 636262 AAAAGTT -s Anc0.Anc0refChr3 202176 7 + 222631 ATAAGTT -s Anc1.Anc1refChr1 41951 7 + 69767 ATAAGTT -s Anc2.Anc2refChr1 118967 7 + 142988 GTTAGCT -s mr.mrrefChr3 152531 7 + 181027 AAAAGTT -s simCow_chr6.simCow.chr6 577456 7 + 602619 TCTGGTT -s simDog_chr6.simDog.chr6 569598 7 + 593897 GTTAGCT -s simHuman_chr6.simHuman.chr6 573042 7 + 601863 ATACGTT -s simRat_chr6.simRat.chr6 79047 7 - 647215 AAAAGTT - -a -s simMouse_chr6.simMouse.chr6 604762 112 + 636262 CAAGAGGACCCCTTTAATGCTTTTTTTGTATATCGAGTGTAGCTGGTAGCCTTTGAGCGGGCTATTGGTCTGGGGGATGCGTACATAAAGTATCGCAGCTAGTACCATTTGA -s Anc0.Anc0refChr3 202183 4 + 222631 CAAG------------------------------------------------------------------------------------------------------------ -s Anc1.Anc1refChr1 41958 4 + 69767 CAAG------------------------------------------------------------------------------------------------------------ -s Anc2.Anc2refChr1 118976 4 + 142988 CATG------------------------------------------------------------------------------------------------------------ -s mr.mrrefChr3 152538 110 + 181027 CAAGAGGACCCC-TTAATGC-TTTTTTGTATATCGAGTGTAGCTGGTAGCCTTTGAGCGGGCTATTGGTCTGGGGGATGCGTACATAAAGTATCGCAGCTAGTACCATTTGA -s simCow_chr6.simCow.chr6 577465 4 + 602619 TGGG------------------------------------------------------------------------------------------------------------ -s simDog_chr6.simDog.chr6 569607 4 + 593897 CATG------------------------------------------------------------------------------------------------------------ -s simHuman_chr6.simHuman.chr6 573049 4 + 601863 ACAG------------------------------------------------------------------------------------------------------------ -s simRat_chr6.simRat.chr6 79054 110 - 647215 CAAGAGCGCCCC-TTGATGC-TTTTTGGCTCATAGAGTGTAGCTGGTAGCCTTTGAGCTGGCTTTTGGACTGGGGGACGTGTACATAAAATATTGCAGCTGGCACCATTTGA - -a -s simMouse_chr6.simMouse.chr6 604874 20 + 636262 GGACATTAGATTACACCCTC -s mr.mrrefChr3 152648 20 + 181027 GGACATTAGATTACACCCTC -s simRat_chr6.simRat.chr6 79213 20 - 647215 GGATATTAGATTACACCCTC - -a -s simMouse_chr6.simMouse.chr6 604894 177 + 636262 TATACCCTAATCAATTGAACACCCCTGTTAATTGAACTGGGGGACTAAGATAAATCCTGCTGAACAGGGAAGCATGTCACATAGGATCCTTAGCCAACCTAGTTTGCCTTAGTTTGCATCTACAATTGTGTCTCTATTTATGACCTGCAAACCAATAAAGGACTTGGTATTCTCCCG -s Anc0.Anc0refChr3 202187 26 + 222631 -------------------------------------------------------------------------------------------------------------------------------------------------------TCAACTGATGACTTGCTACTCTCTCG -s Anc1.Anc1refChr1 41962 26 + 69767 -------------------------------------------------------------------------------------------------------------------------------------------------------TCAACTGATGACTTGCTACTCTCTCG -s Anc2.Anc2refChr1 118980 26 + 142988 -------------------------------------------------------------------------------------------------------------------------------------------------------TCAACTGATTATTTGCTACTCTCTTG -s mr.mrrefChr3 152668 164 + 181027 TATACCCT-------------CCCCTGTTAATTGAACTGGGGGACTAAGATAAATCCTGCTGAACAGGGAAGCATGTCACATAGGATCCTTAGCCAACCTAGTTTGCCTTAGTTTGCATCTACAATTGTGTCTCTATTTATGACCTGCAAACCAACAAAGGACTTGGTACTCTCCCG -s simCow_chr6.simCow.chr6 577469 26 + 602619 -------------------------------------------------------------------------------------------------------------------------------------------------------TCGACTGATTAGTTGCTACTCTCGTG -s simDog_chr6.simDog.chr6 569611 26 + 593897 -------------------------------------------------------------------------------------------------------------------------------------------------------TCAACTAATTATGTGCTACTCTCTTG -s simHuman_chr6.simHuman.chr6 573053 26 + 601863 -------------------------------------------------------------------------------------------------------------------------------------------------------TCAGCTGATGACTTGCTACTCTCTCG -s simRat_chr6.simRat.chr6 79239 164 - 647215 TGTACCCC-------------CCCCCATTAGTTGAACTGGGGCACTAAGATAGATTCTGCTGAACAGGGAGGGACGTCACATATGATCCTTGGCCAACCTAATTTGCTTTAGCAAGCTTCTACAATTGTGTCTCTATTTATCACCTGTAAACTAACAAAGGACTTGGTACTCTGCCA - -a -s simMouse_chr6.simMouse.chr6 605071 45 + 636262 TAATCTCCCTTGGGTAGGTCTATTTTAGACAAGATAATGCAGTTA -s Anc0.Anc0refChr3 202216 40 + 222631 T-ATCACCCTTTGGGA----TATCTAGGACATGAAAATGCAGTTA -s Anc1.Anc1refChr1 41991 43 + 69767 T-ATCACCCTTTGGGAGG-ATATCTAGGACATGAAAATGCAGTTA -s Anc2.Anc2refChr1 119009 40 + 142988 T-ATCACCCCTTGGGA----TATCTAGGATATGAAAATGAAGTTA -s mr.mrrefChr3 152832 44 + 181027 T-ATCTCCCTTGGGTAGGTCTATTTTAGACAAGATAATGCAGTTA -s simCow_chr6.simCow.chr6 577498 40 + 602619 G-ATCACCCCTTGGGA----TGTTTGGGATATGAAAATGGAGTTA -s simDog_chr6.simDog.chr6 569640 40 + 593897 T-ATCACCCCTTGGGT----TATCTATGATACGGGGATGAATATG -s simHuman_chr6.simHuman.chr6 573082 43 + 601863 T-GTCACCCTTTGGGATG-ATAGCTAGGACATGAAAATACAGTTA -s simRat_chr6.simRat.chr6 79403 44 - 647215 T-ATTTCCCTTGGATAGGTCTATTTCAGACAAGATAATGCAGTTA - -a -s simMouse_chr6.simMouse.chr6 605116 3 + 636262 TCA -s Anc0.Anc0refChr3 202256 3 + 222631 CTA -s Anc1.Anc1refChr1 42034 3 + 69767 CTA -s Anc2.Anc2refChr1 119049 3 + 142988 CTC -s mr.mrrefChr3 152876 3 + 181027 TCA -s simCow_chr6.simCow.chr6 577538 3 + 602619 CTC -s simDog_chr6.simDog.chr6 569680 3 + 593897 CTC -s simHuman_chr6.simHuman.chr6 573125 3 + 601863 AAA -s simRat_chr6.simRat.chr6 79448 3 - 647215 TCA - -a -s simMouse_chr6.simMouse.chr6 605119 13 + 636262 TCATAGCCTGCCA -s Anc0.Anc0refChr3 202261 13 + 222631 CCATTGTCCACCA -s Anc1.Anc1refChr1 42039 13 + 69767 CCATTGTCCACCA -s Anc2.Anc2refChr1 119054 13 + 142988 TTATTGTCCACCA -s mr.mrrefChr3 152879 13 + 181027 CCATTGCCTGCCA -s simCow_chr6.simCow.chr6 577543 13 + 602619 TGACTGTCCACCA -s simDog_chr6.simDog.chr6 569685 13 + 593897 TTATTCCCCACCA -s simHuman_chr6.simHuman.chr6 573130 13 + 601863 CCATTGTCCACCA -s simRat_chr6.simRat.chr6 79451 13 - 647215 CCATTGCCTTCCA - -a -s simMouse_chr6.simMouse.chr6 605132 74 + 636262 GATACTTCATAAAGGTGTCCTTATTCAGTCCCGGTGCAGAAAAATTACAGGCAATAGCATTAGACTCCCCAAGA -s Anc0.Anc0refChr3 202274 74 + 222631 GATACTTTATAAAGGTGTCTTTACTCAATCCTGCCACAGAAAATTTACAGATGATTGCCTAAGACTTCCCCAGA -s Anc1.Anc1refChr1 42052 74 + 69767 GATACTTTATAAAGGTGTCTTTACTCAATCCTGCCACAGAAAATTTACAGATGATTGCCTAAGACTTCCCCAGA -s Anc2.Anc2refChr1 119067 74 + 142988 GATACTTCATAAGGGTGTCTTTGCTCAATCCTGCCACAGAAGGTTTACAGATGATTGCCCAAGACCTCCCCAGA -s mr.mrrefChr3 152892 74 + 181027 GATTCTTTATAAAGGTGTCCTTACTCAGTCCTGGTGCAGAAAAATTACAGGCAATAGCATTAGACTCCCCCAGA -s simCow_chr6.simCow.chr6 577604 74 + 602619 GATACTTCATAAGGGTGTCTTTTCTCAATCCTTCCACAGAAGGTTTACAGACGATTGCCCGAGGCACCCTCAGA -s simDog_chr6.simDog.chr6 569698 74 + 593897 GATACCTCATAAGAGGGACTTGGCACGGTCCTGCCACACAAGGTTTATGGGTGATTGCCCAAGACCTCCCCAGA -s simHuman_chr6.simHuman.chr6 573143 73 + 601863 GCT-TTTTATACAGGTGTCTTTACTCAATCCTGCCACAGAAAATTGACAGATGATTGCCTAAGACTTCCCCAGA -s simRat_chr6.simRat.chr6 79464 73 - 647215 GATTCCTTATAAAGGTGTCCTTACTCAGTCCTGGTGCAGAAGAATTAGAGG-AATAGCATTAGACTCCCCCAGA - -a -s simMouse_chr6.simMouse.chr6 605206 87 + 636262 ACAGTTGCAGGTGACCTACAGTTCCTTGTTTCTGTATGATTTCAGTTCAAGGACTCGTTGCACCAAGGTATAAGATAATCTTTGCCA -s Anc0.Anc0refChr3 202348 73 + 222631 CAAATTGCAGATGACCTACAATTCCTT-TCTGG----------AATTCAAGGACTTTTTGCAC---GGTATGAGACAAACCTTGCCT -s Anc1.Anc1refChr1 42126 84 + 69767 CAAATTGCAGATGACCTACAATTCCTTGTCTGGCAATACCTTCAATTCAAGGACTTTTTGCAC---GGTATGAGACAAACCTTGCCT -s Anc2.Anc2refChr1 119141 73 + 142988 CAAATTGCAAATGACCTACAATTCCTT-TTTGG----------AATTCAAGGACTTTTTGCAC---GGTATGAGACAAACCTTGCCT -s mr.mrrefChr3 152966 87 + 181027 CCAATTGCAGATGACCTACAGTTCCTTGTCTGTGTATGATTTCAGTTCAAGGACTCTTTGCACCAAGGTATGAGATAATCTTTGCTT -s simCow_chr6.simCow.chr6 577678 73 + 602619 CCAATTGTAAATGAGCTACAATTCCTT-GTTGG----------AATTCAAGCACTTTTTGCAC---AATATGAGACAAACCTAGCCT -s simDog_chr6.simDog.chr6 569772 69 + 593897 CAAATTGCAAATGACCTACA----CTT-TTTGG----------AAGTCCAGGACTCTTTGCAC---GGTACAAGACAAACCTTGCCC -s simHuman_chr6.simHuman.chr6 573216 73 + 601863 CAAAGTGCAGATGACCTA---------GTCTGGCAATACCTTCCCTTCAAGGAT-TCTTGCAA---GGTATGAGCCCAC-CTTGCCT -s simRat_chr6.simRat.chr6 79538 87 - 647215 CCAATTGCAGATAACCTCCAGTTCCCTGTCCGTTTATGATTTCAGGTCAAGAAATTTTTGCACCAAGGAAGGAGATAATCTTTGCTT - -a -s simMouse_chr6.simMouse.chr6 605293 62 + 636262 GTTGCAGGTCATTTCCATAGCAATTCTGTATTTTAAAAGGTAGGAGGATCCTATAAAGCCTA -s Anc0.Anc0refChr3 202425 62 + 222631 GATGGAGATTACTTCCATAGCATTCCAATATTTTTAAAGGTAGCAGACTTTGACAAAAAGCA -s Anc1.Anc1refChr1 42214 62 + 69767 GATGGAGATTACTTCCATAGCATTCCAATATTTTTAAAGGTAGCAGACTTTGACAAAAAGCA -s Anc2.Anc2refChr1 119218 62 + 142988 GATGGAGGTTACTCCCATAGCATTCCAATATTTTTAAAGGTAGCAGACTTTGACAAAAAGCA -s mr.mrrefChr3 153053 62 + 181027 GTTGCAGATCATTTCCATAGCAATTCAGTATTTTTAAAGGTAGGAGGATTCTACAAAGCCTA -s simCow_chr6.simCow.chr6 577837 60 + 602619 AATGGATGTTACTCACATAGCATTCCAATG--TTTAAACATACCAGAATTTGCCAAAAAGCC -s simDog_chr6.simDog.chr6 569845 62 + 593897 GGTGGAGGTTAAGCCCATAGCATTTCAATATTTTTAAAGGTAGCAGTCTGTCACAAAAAGCA -s simHuman_chr6.simHuman.chr6 573293 62 + 601863 GATCGAGATTACTTCCATAGCACTCTAATATACTTAACAGTAGCAGACTTTGACAACAAACA -s simRat_chr6.simRat.chr6 79625 62 - 647215 GTTGCAGATCATTTCCATAGCAATTCAGTATTTTTTAACGTAGGAGGATTCTACAAAGCCTA - -a -s simMouse_chr6.simMouse.chr6 605355 22 + 636262 CAAACCATTCTATTCTTATTAG -s Anc0.Anc0refChr3 202487 10 + 222631 TAG------------TTGTTAG -s Anc1.Anc1refChr1 42276 10 + 69767 TAG------------TTGTTAG -s Anc2.Anc2refChr1 119280 10 + 142988 TAG------------TTGTTAG -s mr.mrrefChr3 153115 22 + 181027 CAAACCATTCTATTCTTGTTAG -s simCow_chr6.simCow.chr6 577900 10 + 602619 TTG------------TTGTTAG -s simDog_chr6.simDog.chr6 569907 10 + 593897 TAG------------TTGTTGG -s simHuman_chr6.simHuman.chr6 573355 10 + 601863 TAG------------TTGTTAG -s simRat_chr6.simRat.chr6 79687 22 - 647215 GCAAGCATTCTATTCTTGTTAG - -a -s simMouse_chr6.simMouse.chr6 605377 31 + 636262 ATGCCCTTAATTGGCCAATGTACATCACCTA -s Anc0.Anc0refChr3 202497 30 + 222631 ATGAACTTGATTGGCCAGT-CATTTCACCTG -s Anc1.Anc1refChr1 42286 30 + 69767 ATGAACTTGATTGGCCAGT-CATTTCACCTG -s Anc2.Anc2refChr1 119290 30 + 142988 ATGAACTTGACTGGCCAGT-CATTTCACCTG -s mr.mrrefChr3 153137 31 + 181027 ATGCCCTTGATTGGCCAATGTACATCACCTA -s simCow_chr6.simCow.chr6 577915 30 + 602619 ATGACCCTAACTGGCCAGT-CATTTCATTGG -s simDog_chr6.simDog.chr6 569917 30 + 593897 ATGAACTTGACTGGCTGGT-CAGTTTACCTG -s simHuman_chr6.simHuman.chr6 573365 30 + 601863 ATGAACATGTTTGGCCAGT-CATTTCACCTG -s simRat_chr6.simRat.chr6 79709 31 - 647215 ATGCCCTTGATTGGCCGATGTACGTCACCTA - -a -s simMouse_chr6.simMouse.chr6 605408 53 + 636262 TTGAACCATTCATCCTTTAACCAGTACCACATCTGTGGTGAACCAAGGGCTCA -s Anc0.Anc0refChr3 202533 51 + 222631 TTAAAACATATAGCCTTTAATCAGTACTAAACCTGTGGAGAACCAAGT--TTA -s Anc1.Anc1refChr1 42322 51 + 69767 TTAAAACATATAGCCTTTAATCAGTACTAAACCTGTGGAGAACCAAGT--TTA -s Anc2.Anc2refChr1 119326 51 + 142988 TTAAAACATATAGCCTTTAATCAGTACTGAACCTGTCGAGAACCAAGT--TTA -s mr.mrrefChr3 153168 51 + 181027 TTGAAACATTTATCCTTTAATCAGTACCACATCTGTGGTGAACCAAGG--TTA -s simCow_chr6.simCow.chr6 577951 47 + 602619 TT---ACGTTTAGTCTTTAATCA-TACTGCACTTGTGGAGAACCAAGC--TTC -s simDog_chr6.simDog.chr6 569953 51 + 593897 TAAAAAGATATATCCTTTAATCAGTACTGAAGCTGTCGAGAGCCAAGT--TTA -s simHuman_chr6.simHuman.chr6 573401 50 + 601863 TTAAAACATCTAGCCATTAATCAGTACTATACCTGTGA-GAACCAAGT--TTA -s simRat_chr6.simRat.chr6 79740 51 - 647215 TTGAAACATTTACCCTTTAATCAGTACCACGTCTGTAGTGAACAAAGG--TTA - -a -s simMouse_chr6.simMouse.chr6 605461 12 + 636262 GCTGGCCCTTGT -s Anc0.Anc0refChr3 202585 12 + 222631 GCTGGTATTTGC -s Anc1.Anc1refChr1 42374 12 + 69767 GCTGGTATTTGC -s Anc2.Anc2refChr1 119378 12 + 142988 GCTGCTATTTGC -s mr.mrrefChr3 153219 12 + 181027 GCTGGCCTTTGT -s simCow_chr6.simCow.chr6 577999 12 + 602619 GCTGCTATTTGC -s simDog_chr6.simDog.chr6 570005 3 + 593897 GCT--------- -s simHuman_chr6.simHuman.chr6 573452 12 + 601863 GCTGGTGTTGAC -s simRat_chr6.simRat.chr6 79791 12 - 647215 AGTCACCTTTGT - -a -s simMouse_chr6.simMouse.chr6 605473 25 + 636262 TTTGGCCTCAAGCTGTCAATTGTTC -s Anc0.Anc0refChr3 202599 25 + 222631 TTTTAACTCTAACTGGTAATTGTAG -s Anc1.Anc1refChr1 42388 25 + 69767 TTTTAACTCTAACTGGTAATTGTAG -s Anc2.Anc2refChr1 119392 25 + 142988 TTTTAACTCTAACCGGTAATTGTAG -s mr.mrrefChr3 153231 25 + 181027 TTTTACCTCAAGCTGGCAATTGTAC -s simCow_chr6.simCow.chr6 578013 25 + 602619 TTTTAACTCTAACCGGTAATTGTAG -s simHuman_chr6.simHuman.chr6 573466 25 + 601863 TTTTAACTCTAACTGGTAATTGTAG -s simRat_chr6.simRat.chr6 79803 25 - 647215 TTTTACCTCAGCCTGGCAATTGTAC - -a -s simMouse_chr6.simMouse.chr6 605498 10 + 636262 TCTAGTACAG -s Anc0.Anc0refChr3 202629 7 + 222631 TCTAGTA--- -s Anc1.Anc1refChr1 42418 7 + 69767 TCTAGTA--- -s Anc2.Anc2refChr1 119422 7 + 142988 TCTAGTA--- -s mr.mrrefChr3 153261 10 + 181027 TCTAGTACAG -s simCow_chr6.simCow.chr6 578043 7 + 602619 TCTAGTA--- -s simDog_chr6.simDog.chr6 570008 3 + 593897 ----GTA--- -s simHuman_chr6.simHuman.chr6 573496 7 + 601863 TTTAGTA--- -s simRat_chr6.simRat.chr6 79833 10 - 647215 TCTAGTACAG - -a -s simMouse_chr6.simMouse.chr6 605508 1 + 636262 A -s Anc0.Anc0refChr3 202636 1 + 222631 G -s Anc1.Anc1refChr1 42425 1 + 69767 G -s Anc2.Anc2refChr1 119429 1 + 142988 G -s mr.mrrefChr3 153271 1 + 181027 A -s simCow_chr6.simCow.chr6 578051 1 + 602619 G -s simDog_chr6.simDog.chr6 570011 1 + 593897 G -s simHuman_chr6.simHuman.chr6 573503 1 + 601863 G -s simRat_chr6.simRat.chr6 79843 1 - 647215 A - -a -s simMouse_chr6.simMouse.chr6 605509 20 + 636262 AGAACAAAATGGTCCCTCAA -s Anc0.Anc0refChr3 202637 19 + 222631 AGAACAAAATAGTGTCTC-A -s Anc1.Anc1refChr1 42426 19 + 69767 AGAACAAAATAGTGTCTC-A -s Anc2.Anc2refChr1 119430 19 + 142988 AGAACAAACTAGTGTCTC-A -s mr.mrrefChr3 153272 20 + 181027 AGAACAAAATGGTCCCTCAA -s simCow_chr6.simCow.chr6 578052 19 + 602619 AGAACAAACCAGTGTCTC-A -s simDog_chr6.simDog.chr6 570012 19 + 593897 ACAACAAACTAGTGACCC-T -s simHuman_chr6.simHuman.chr6 573504 19 + 601863 AGAACAAAATAGTTTCTC-A -s simRat_chr6.simRat.chr6 79845 20 - 647215 AGAACGAGATGGTGCCTCAA - -a -s simMouse_chr6.simMouse.chr6 605529 54 + 636262 GGTTCCTTAATCAAACTGTGTCAAGTTAGAGGGGAAGTAGACAGGATGGGCTGC -s Anc0.Anc0refChr3 202678 47 + 222631 GATTTTTTAG-CTAACTAGGTCAAATTA-----G-AGTAGAAACAATGAGGAGC -s Anc1.Anc1refChr1 42467 47 + 69767 GATTTTTTAG-CTAACTAGGTCAAATTA-----G-AGTAGAAACAATGAGGAGC -s Anc2.Anc2refChr1 119471 47 + 142988 GATTTTTTAG-CTAACTAGGTTAAATTA-----G-AGTACAAACAATGAGGAGC -s mr.mrrefChr3 153314 49 + 181027 GATTCCTTAATCTAACTGTGTCAAGTTA-----GAAGTAGACAGGATGGGCTGC -s simCow_chr6.simCow.chr6 578093 47 + 602619 GATTTTTTAG-CGAACTAGGTTAAATTA-----G-AGAACAAGGAGTGAGGAGC -s simDog_chr6.simDog.chr6 570053 47 + 593897 GATTTTTTAG-CTAACTATGTTGAGTTA-----G-AGTACAAACGAAGAGGGGC -s simHuman_chr6.simHuman.chr6 573545 47 + 601863 AATTTTCTGG-CTAACTAGGTCAAATTA-----G-AGTAGAAAAAATGAGGAGT -s simRat_chr6.simRat.chr6 79887 49 - 647215 GATTCCTTAATCTAACACTATCAAGTTA-----GAAATATACAGGATGGGCTGC - -a -s simMouse_chr6.simMouse.chr6 605583 37 + 636262 ACCAGGATAGGTGAACAACCTATCTACCCAAAATACC -s Anc0.Anc0refChr3 202725 24 + 222631 ACCAGGGTAGGGTTGCCACC-------------CAAC -s Anc1.Anc1refChr1 42514 24 + 69767 ACCAGGGTAGGGTTGCCACC-------------CAAC -s Anc2.Anc2refChr1 119518 24 + 142988 ACTAAGGTAGGGTTGCCACC-------------CACC -s mr.mrrefChr3 153363 32 + 181027 ACCAGGGTAGGTGAACAACCTATCTAC-----ATAAC -s simCow_chr6.simCow.chr6 578140 24 + 602619 CCTGAGGCAGGGTTGCCACC-------------CACC -s simDog_chr6.simDog.chr6 570104 24 + 593897 ACTAAGGTAGAGTTGCCACT-------------CACC -s simHuman_chr6.simHuman.chr6 573592 24 + 601863 AGCAGGGTAGGGTTGCCACC-------------CAAC -s simRat_chr6.simRat.chr6 79936 32 - 647215 ACCAGGGTAGGTGGACAACCTATCTAC-----ATGAC - -a -s simMouse_chr6.simMouse.chr6 605620 40 + 636262 CAAAAATAAGTATTAAGCATTGATTCTTTATTACAGCACC -s Anc0.Anc0refChr3 202749 39 + 222631 CAAAAATAGG-GATAAGCATGGGCTCTTTTACACAGAACC -s Anc1.Anc1refChr1 42538 39 + 69767 CAAAAATAGG-GATAAGCATGGGCTCTTTTACACAGAACC -s Anc2.Anc2refChr1 119549 39 + 142988 CAAAAATAGG-GATAAACATGGGCGCTTTTATGCTGGACC -s mr.mrrefChr3 153395 40 + 181027 CAAAAATAAGTATTAAGCATTGATTCTTTAACACAGAACC -s simCow_chr6.simCow.chr6 578171 39 + 602619 CATAGATAAA-GTTAAACATAGGCCCTTTTATGCTGGACC -s simDog_chr6.simDog.chr6 570135 32 + 593897 CAAAAATAGG-AATAAACATGGGTGCATTTGTG------- -s simHuman_chr6.simHuman.chr6 573616 33 + 601863 CGACAATAGG-GGTAAGC------TCTTTTACACAGAGCC -s simRat_chr6.simRat.chr6 79968 36 - 647215 T----ATAAGTATTAAGCATTGATCCTTTAACACGGACCA - -a -s simMouse_chr6.simMouse.chr6 605660 9 + 636262 TACCATTGA -s Anc0.Anc0refChr3 202798 7 + 222631 TACCCTT-- -s Anc1.Anc1refChr1 42587 9 + 69767 TACCCTTGG -s Anc2.Anc2refChr1 119598 7 + 142988 TACCCTT-- -s mr.mrrefChr3 153435 9 + 181027 TACCATTGG -s simCow_chr6.simCow.chr6 578220 7 + 602619 CACACTT-- -s simDog_chr6.simDog.chr6 570174 7 + 593897 TACCCTT-- -s simHuman_chr6.simHuman.chr6 573659 9 + 601863 TATCCTTGG -s simRat_chr6.simRat.chr6 80004 9 - 647215 CACCATTGG - -a -s simMouse_chr6.simMouse.chr6 605669 47 + 636262 GCTGTTTAGCCTCTAGAGGAACAGAACCCGCCATTGTGTTGTTTAGT -s Anc0.Anc0refChr3 202805 12 + 222631 -----------------------------------GGGCTGTTTAGT -s Anc1.Anc1refChr1 42596 27 + 69767 GCTGTTTAGTCCC--------------------TTGGGCTGTTTAGT -s Anc2.Anc2refChr1 119605 12 + 142988 -----------------------------------GGGCTGTTTAAT -s mr.mrrefChr3 153444 47 + 181027 GCTGTTTAGTCTCTAGAGGAACAGAACCCGCCATTGTGTTGTTTAGT -s simCow_chr6.simCow.chr6 578227 12 + 602619 -----------------------------------GAGCTGTTTAAT -s simDog_chr6.simDog.chr6 570181 12 + 593897 -----------------------------------GGGGTGTTTAAT -s simHuman_chr6.simHuman.chr6 573668 27 + 601863 GCTGTTTAGTCCC--------------------TTGGGCTGTTTAGT -s simRat_chr6.simRat.chr6 80019 39 - 647215 GCTCTTCAGTCTCTAGAGGAACAGAAACCACCA--------TGTAGT - -a -s simMouse_chr6.simMouse.chr6 605716 27 + 636262 TCTGAGATGTGAGTATAAGTTAAGTTA -s Anc0.Anc0refChr3 202817 27 + 222631 CTTTAGAGGTGAGTGTGCCTAGAAGGA -s Anc1.Anc1refChr1 42623 27 + 69767 CTTTAGAGGTGAGTGTGCCTAGAAGGA -s Anc2.Anc2refChr1 119617 27 + 142988 CTTTAGAGGTGAGTGTGCCCAGGAGGA -s mr.mrrefChr3 153491 27 + 181027 TTTGAGATGTGAGTATAAGTTAAGGGA -s simCow_chr6.simCow.chr6 578239 27 + 602619 CTTCAGAGTTCAGTGTGCCCAGGAGGA -s simDog_chr6.simDog.chr6 570196 27 + 593897 CTTTAGAGGTGAGTATGTCCAGGAGGA -s simHuman_chr6.simHuman.chr6 573695 27 + 601863 CTTTAGAGGTGAGTGTGCTTGGAAGGA -s simRat_chr6.simRat.chr6 80058 27 - 647215 TTTGAGATGTGAGTATAACTTTAGGGA - -a -s simMouse_chr6.simMouse.chr6 605743 1 + 636262 G -s Anc0.Anc0refChr3 202844 1 + 222631 T -s Anc1.Anc1refChr1 42650 1 + 69767 T -s Anc2.Anc2refChr1 119644 1 + 142988 T -s mr.mrrefChr3 153518 1 + 181027 G -s simCow_chr6.simCow.chr6 578266 1 + 602619 T -s simDog_chr6.simDog.chr6 570223 1 + 593897 T -s simHuman_chr6.simHuman.chr6 573722 1 + 601863 A -s simRat_chr6.simRat.chr6 80086 1 - 647215 G - -a -s simMouse_chr6.simMouse.chr6 605744 12 + 636262 TACCCCAGCTTC -s Anc0.Anc0refChr3 202847 12 + 222631 TGCCTCAGCTTT -s Anc1.Anc1refChr1 42653 12 + 69767 TGCCTCAGCTTT -s Anc2.Anc2refChr1 119647 12 + 142988 TGACTCAGCTTT -s mr.mrrefChr3 153519 12 + 181027 TACCCCAGCTTC -s simCow_chr6.simCow.chr6 578269 12 + 602619 TAACTCAGCTTC -s simDog_chr6.simDog.chr6 570226 12 + 593897 TGACTCAGCTTT -s simHuman_chr6.simHuman.chr6 573725 12 + 601863 TGCCACAGCTTT -s simRat_chr6.simRat.chr6 80087 12 - 647215 TACCCCCGCCTC - -a -s simMouse_chr6.simMouse.chr6 605756 49 + 636262 AATCTGTATGGTGCAAGATTGTAGTCCCTTCAAGAAGGAGTAACCATCA -s Anc0.Anc0refChr3 202859 49 + 222631 AACCTGTATAGTACAAAATTGTTGACACTAGGAGAAGTAATAACCATCA -s Anc1.Anc1refChr1 42665 49 + 69767 AACCTGTATAGTACAAAATTGTTGACACTAGGAGAAGTAATAACCATCA -s Anc2.Anc2refChr1 119659 49 + 142988 AACCTGTATAGTAGAAAATAGTTGACACTAGGAGAAGTAATGACCATCA -s mr.mrrefChr3 153531 49 + 181027 AACCTGTATGGTGCAAGATTGTTGTCCCTTCAAGAAGGAGTAACCATCA -s simCow_chr6.simCow.chr6 578281 48 + 602619 AACC-ATAAAGTATAAGCTGGTTGACACTAGGAGAAGTAATTACCATCA -s simDog_chr6.simDog.chr6 570250 49 + 593897 AGCCTGTATAGTAGAAAATAGTTAACACTAGGATAAGTAATGTCCATCA -s simHuman_chr6.simHuman.chr6 573737 49 + 601863 AACTTGTATAGTACAAAGATGTTGACACTAAGTGAAGTGATAACCCTCA -s simRat_chr6.simRat.chr6 80099 49 - 647215 TACCTGTATGGTGAAAGATTGTTGTCCCCGCAAGAATGTGTAACCGTCA - -a -s simMouse_chr6.simMouse.chr6 605805 29 + 636262 TATGCCTTGATGGTAGTTAGCTACTGGAC -s Anc0.Anc0refChr3 202908 29 + 222631 TATGCCTTCATAGTAGTTAGCTACTGAAC -s Anc1.Anc1refChr1 42714 29 + 69767 TATGCCTTCATAGTAGTTAGCTACTGAAC -s Anc2.Anc2refChr1 119708 29 + 142988 TATGCCTTCATAGTAATTACCTACTGAAC -s mr.mrrefChr3 153580 29 + 181027 TATGCCTTCATGGTAGTTAGCTACTGAAC -s simCow_chr6.simCow.chr6 578333 29 + 602619 TATGCCTTCATAGTAATTGTCTACGAACC -s simDog_chr6.simDog.chr6 570299 29 + 593897 TACGCCTTCATAGTAATTACTCGCTGGAC -s simHuman_chr6.simHuman.chr6 573786 29 + 601863 TATGCCTTCACAGTGGTTAGCTACTGAAC -s simRat_chr6.simRat.chr6 80148 29 - 647215 TATGCGTTCATGATAGTTAGCTGCTGAAC - -a -s simMouse_chr6.simMouse.chr6 605834 32 + 636262 AGGGTTCTCACAGCCTGTCATTATTGAAGCAG -s Anc0.Anc0refChr3 202937 32 + 222631 ACAGTGCTGATGACCTGTCATTAATAGAGCAC -s Anc1.Anc1refChr1 42743 32 + 69767 ACAGTGCTGATGACCTGTCATTAATAGAGCAC -s Anc2.Anc2refChr1 119737 32 + 142988 ACAGTGCTGATGACCCTTCAAACATGGCGTAC -s mr.mrrefChr3 153609 32 + 181027 AGGGTTCTCACAGCCTGTCATTAATAAAGCAC -s simCow_chr6.simCow.chr6 578362 32 + 602619 ATGGTGCTGATCACCCTTCAAACATGGTGTAC -s simDog_chr6.simDog.chr6 570329 32 + 593897 CCAGTGTTGTTGTCACTTCAAACATGGCGTAC -s simHuman_chr6.simHuman.chr6 573815 32 + 601863 ACAGGGCTGATGACCTGTTGTTAATAGAGCAC -s simRat_chr6.simRat.chr6 80177 32 - 647215 AGGGTTCTCACAGCCTGTCATTAATAAGGCAC - -a -s simMouse_chr6.simMouse.chr6 605866 32 + 636262 TGTTGTCTACCCTTTATTAATAGAGTAACCTT -s Anc0.Anc0refChr3 202982 30 + 222631 TATTGCAGGTTCTTAAT--GTATACCACTCTG -s Anc1.Anc1refChr1 42788 30 + 69767 TATTGCAGGTTCTTAAT--GTATACCACTCTG -s Anc2.Anc2refChr1 119782 30 + 142988 TATTGCAGGTTCTTAAT--GTATACCAATCTG -s mr.mrrefChr3 153641 32 + 181027 TGTTGTCTACCCTTTATTAATAGAGTACCCTT -s simCow_chr6.simCow.chr6 578405 30 + 602619 CATTGCCGGTTCTTAAT--GTATACCATTGTG -s simDog_chr6.simDog.chr6 570374 30 + 593897 TATTGCAGGTTCTCAAC--ATCTACCAATCTG -s simHuman_chr6.simHuman.chr6 573860 30 + 601863 TATAGCAGGTTCTTAAT--GTATACCACTATG -s simRat_chr6.simRat.chr6 80209 32 - 647215 TGTTGTCTACCCTTTATTAATAGAGTACCCTT - -a -s simMouse_chr6.simMouse.chr6 605898 9 + 636262 TTGAAAGAA -s Anc0.Anc0refChr3 203012 9 + 222631 CTAAAGGGA -s Anc1.Anc1refChr1 42818 9 + 69767 CTAAAGGGA -s Anc2.Anc2refChr1 119812 9 + 142988 CTAAAGGGA -s mr.mrrefChr3 153673 9 + 181027 TTGAAAGGA -s simCow_chr6.simCow.chr6 578435 8 + 602619 C-AAAGAGA -s simDog_chr6.simDog.chr6 570424 9 + 593897 CTAAAGGGA -s simHuman_chr6.simHuman.chr6 573890 7 + 601863 CTAAAGA-- -s simRat_chr6.simRat.chr6 80241 9 - 647215 TAGAAAGGA - -a -s simMouse_chr6.simMouse.chr6 605907 16 + 636262 TCAGATAGCACCATAA -s Anc0.Anc0refChr3 203021 16 + 222631 TAAGATAGCAGCATAA -s Anc1.Anc1refChr1 42827 16 + 69767 TAAGATAGCAGCATAA -s Anc2.Anc2refChr1 119825 16 + 142988 TAAGATAGCAGCATAA -s mr.mrrefChr3 153682 16 + 181027 TCAGATAGCACCATAA -s simCow_chr6.simCow.chr6 578447 16 + 602619 TAGGATAGCAGCATGA -s simDog_chr6.simDog.chr6 570437 16 + 593897 TAAGATAGCAGCACAA -s simHuman_chr6.simHuman.chr6 573897 14 + 601863 --AGATAGCGGCATAA -s simRat_chr6.simRat.chr6 80250 16 - 647215 TCAGATAGCACTATAA - -a -s simMouse_chr6.simMouse.chr6 605923 16 + 636262 ACATATGACTCTGTTA -s Anc0.Anc0refChr3 203048 16 + 222631 ACATGTGACTCTGTTA -s Anc1.Anc1refChr1 42854 16 + 69767 ACATGTGACTCTGTTA -s Anc2.Anc2refChr1 119852 16 + 142988 ACATGTGACTCTGTTA -s mr.mrrefChr3 153698 16 + 181027 ACATGTGACTCTGTTA -s simCow_chr6.simCow.chr6 578476 16 + 602619 ACATGTGACTCTGTTA -s simDog_chr6.simDog.chr6 570464 16 + 593897 ACTTGTGACTCTGTTA -s simHuman_chr6.simHuman.chr6 573922 16 + 601863 ACATGTGACTCTGTTA -s simRat_chr6.simRat.chr6 80266 16 - 647215 ACTTGTGACTCTGTTA - -a -s simMouse_chr6.simMouse.chr6 605939 5 + 636262 AGAGC -s Anc0.Anc0refChr3 203064 5 + 222631 TGAGC -s Anc1.Anc1refChr1 42870 5 + 69767 TGAGC -s Anc2.Anc2refChr1 119868 5 + 142988 TGAGC -s mr.mrrefChr3 153714 5 + 181027 AGAGC -s simCow_chr6.simCow.chr6 578493 5 + 602619 TGCAC -s simDog_chr6.simDog.chr6 570480 5 + 593897 TGAGT -s simHuman_chr6.simHuman.chr6 573938 5 + 601863 TGAGC -s simRat_chr6.simRat.chr6 80282 5 - 647215 CAAGC - -a -s simMouse_chr6.simMouse.chr6 605944 15 + 636262 CCACTCAGGAAGTAT -s Anc0.Anc0refChr3 203074 15 + 222631 TCACTTTAAGCAGAT -s Anc1.Anc1refChr1 42880 15 + 69767 TCACTTTAAGCAGAT -s Anc2.Anc2refChr1 119878 15 + 142988 TCACTTTAAGCAGAT -s mr.mrrefChr3 153719 15 + 181027 CCACTCAGGAAGTAT -s simCow_chr6.simCow.chr6 578503 15 + 602619 TTACTTTAAGCAGAT -s simDog_chr6.simDog.chr6 570490 15 + 593897 TCATTTGAGGCAGAT -s simHuman_chr6.simHuman.chr6 573948 15 + 601863 TCACTTTAAGTAGAT -s simRat_chr6.simRat.chr6 80287 15 - 647215 CCACTCAGGAAGTAT - -a -s simMouse_chr6.simMouse.chr6 605959 4 + 636262 CAGA -s Anc0.Anc0refChr3 203089 4 + 222631 CAAA -s Anc1.Anc1refChr1 42895 4 + 69767 CAAA -s Anc2.Anc2refChr1 119893 4 + 142988 AAAA -s mr.mrrefChr3 153734 4 + 181027 CAGA -s simCow_chr6.simCow.chr6 578518 4 + 602619 GAAA -s simDog_chr6.simDog.chr6 570551 4 + 593897 AAAA -s simHuman_chr6.simHuman.chr6 573963 4 + 601863 CAAA -s simRat_chr6.simRat.chr6 80302 4 - 647215 CAGA - -a -s simMouse_chr6.simMouse.chr6 605963 19 + 636262 GTCTTGTAGGCGCCTAGAG -s Anc0.Anc0refChr3 203096 19 + 222631 ATCCTTAACATGGCCAGAA -s Anc1.Anc1refChr1 42902 19 + 69767 ATCCTTAACATGGCCAGAA -s Anc2.Anc2refChr1 119900 19 + 142988 ATCCTTAACATGGCCAAAA -s mr.mrrefChr3 153738 19 + 181027 GTCTTGTAGGCGCCTAGAA -s simCow_chr6.simCow.chr6 578525 19 + 602619 ATACTGAATATGGCGAAAA -s simDog_chr6.simDog.chr6 570558 19 + 593897 ATCCTTAACATGATCAAAA -s simHuman_chr6.simHuman.chr6 573970 19 + 601863 ATCCTTAAAATGGCCAGAT -s simRat_chr6.simRat.chr6 80335 19 - 647215 GTCATGTAGGTGGCTAACA - -a -s simMouse_chr6.simMouse.chr6 605982 38 + 636262 CTCACTTGAACTCTATGCAAGTCTGTAACATGGAGTAA -s Anc0.Anc0refChr3 203115 37 + 222631 TCCACATG-GCTCTGTTAAGCCTCTTTACATGAACAAA -s Anc1.Anc1refChr1 42921 37 + 69767 TCCACATG-GCTCTGTTAAGCCTCTTTACATGAACAAA -s Anc2.Anc2refChr1 119919 37 + 142988 TCCACATG-GCTCTGTTAAGCCTCTTTACATGAACAAA -s mr.mrrefChr3 153757 38 + 181027 CTCACTTGAACTCTATGCAAGTCTGTAACATGGAGTAA -s simCow_chr6.simCow.chr6 578553 37 + 602619 TATACATA-ATACTGCTATGTCTCTTAACATGAATAGA -s simDog_chr6.simDog.chr6 570577 37 + 593897 TCCACATG-GCTCTGTTAAGCCTCTTTACATGAACAAA -s simHuman_chr6.simHuman.chr6 573989 1 + 601863 T------------------------------------- -s simRat_chr6.simRat.chr6 80354 38 - 647215 TCCACATGAACCCTATGCAAGTCTGTCATATGGAGTAG - -a -s simMouse_chr6.simMouse.chr6 606020 9 + 636262 ATAAGCAGT -s Anc0.Anc0refChr3 203152 9 + 222631 ACCAACAGC -s Anc1.Anc1refChr1 42958 9 + 69767 ACCAACAGC -s Anc2.Anc2refChr1 119974 9 + 142988 ACCAACAGC -s mr.mrrefChr3 153795 9 + 181027 ACAAGCAGT -s simCow_chr6.simCow.chr6 578608 9 + 602619 ACCAACAAT -s simDog_chr6.simDog.chr6 570637 9 + 593897 ACCAACAGC -s simHuman_chr6.simHuman.chr6 573990 1 + 601863 --------C -s simRat_chr6.simRat.chr6 80392 9 - 647215 ACAAGCAGT - -a -s simMouse_chr6.simMouse.chr6 606029 14 + 636262 TACAAAATCATAGG -s Anc0.Anc0refChr3 203161 14 + 222631 TACCTAAGTATCGC -s Anc1.Anc1refChr1 42967 14 + 69767 TACCTAAGTATCGC -s Anc2.Anc2refChr1 119990 14 + 142988 TACCTAAGTATCGC -s mr.mrrefChr3 153804 14 + 181027 TACAAAATCATAGG -s simCow_chr6.simCow.chr6 578624 14 + 602619 TAGCTGAGTATTGC -s simDog_chr6.simDog.chr6 570653 14 + 593897 CACCTAAGTATCGC -s simHuman_chr6.simHuman.chr6 573991 14 + 601863 TACCTAAGTATGGC -s simRat_chr6.simRat.chr6 80401 14 - 647215 TACAAAATCATAGG - -a -s simMouse_chr6.simMouse.chr6 606043 5 + 636262 ACAGT -s Anc0.Anc0refChr3 203175 5 + 222631 CACAT -s Anc1.Anc1refChr1 42981 5 + 69767 CACAT -s Anc2.Anc2refChr1 120004 5 + 142988 CACAT -s mr.mrrefChr3 153818 5 + 181027 ACAGT -s simCow_chr6.simCow.chr6 578638 5 + 602619 CAGAT -s simDog_chr6.simDog.chr6 570670 5 + 593897 TGCAT -s simHuman_chr6.simHuman.chr6 574005 5 + 601863 CACAT -s simRat_chr6.simRat.chr6 80415 5 - 647215 TCAGT - -a -s simMouse_chr6.simMouse.chr6 606048 7 + 636262 CTTCTGT -s Anc0.Anc0refChr3 203180 7 + 222631 CCTATGT -s Anc1.Anc1refChr1 42986 7 + 69767 CCTATGT -s Anc2.Anc2refChr1 120009 7 + 142988 CCTATGT -s mr.mrrefChr3 153823 7 + 181027 CTTCTGT -s simCow_chr6.simCow.chr6 578646 7 + 602619 CCTAGGT -s simDog_chr6.simDog.chr6 570675 7 + 593897 CCTATGT -s simHuman_chr6.simHuman.chr6 574010 7 + 601863 CCTATGT -s simRat_chr6.simRat.chr6 80420 7 - 647215 CTTCCGT - -a -s simMouse_chr6.simMouse.chr6 606055 10 + 636262 ACAAAATCAT -s Anc0.Anc0refChr3 203187 2 + 222631 AC-------- -s Anc1.Anc1refChr1 42993 2 + 69767 AC-------- -s Anc2.Anc2refChr1 120056 2 + 142988 AC-------- -s mr.mrrefChr3 153830 10 + 181027 ACAAAATCAT -s simCow_chr6.simCow.chr6 578694 2 + 602619 AC-------- -s simDog_chr6.simDog.chr6 570723 2 + 593897 TC-------- -s simHuman_chr6.simHuman.chr6 574017 2 + 601863 AC-------- -s simRat_chr6.simRat.chr6 80427 10 - 647215 ACAAAATCAT - -a -s simMouse_chr6.simMouse.chr6 606065 27 + 636262 AGAACAGTCGTCTGAGGTTTCTTATGT -s Anc0.Anc0refChr3 203189 7 + 222631 --------------------CCTATGT -s Anc1.Anc1refChr1 42995 7 + 69767 --------------------CCTATGT -s Anc2.Anc2refChr1 120058 7 + 142988 --------------------CCTAAGC -s mr.mrrefChr3 153840 27 + 181027 AGAACAGTCGTCTGAGGTTTCTTATGT -s simCow_chr6.simCow.chr6 578696 7 + 602619 --------------------CCTAGGC -s simDog_chr6.simDog.chr6 570725 7 + 593897 --------------------CCTAAGC -s simHuman_chr6.simHuman.chr6 574019 7 + 601863 --------------------ACTATGT -s simRat_chr6.simRat.chr6 80443 27 - 647215 AGGACAGGCTTTTGAGGTTTCTATTGT - -a -s simMouse_chr6.simMouse.chr6 606092 65 + 636262 TCATTTGCAGTCATTGTTGCATCTCTGGTGATTCAGTAAACTTTTGGCAATGCTGTATATTCCCC -s Anc0.Anc0refChr3 203196 65 + 222631 AAATTAACAGTTTGTGTTGCCTGACCTATAGTTCTGTAAATAATTGGCCATCCTGTATACTGCCT -s Anc1.Anc1refChr1 43002 65 + 69767 AAATTAACAGTTTGTGTTGCCTGACCTATAGTTCTGTAAATAATTGGCCATCCTGTATACTGCCT -s Anc2.Anc2refChr1 120065 65 + 142988 AAATTAACAGTTTGTGTTGCCTGACCTATGGTTCTGTAAATAATTGGCCATCCTGGATACCACCT -s mr.mrrefChr3 153867 65 + 181027 TCATTTACAGTTATTGTTGCATGTCCTGTAATTCAGTAAACTTTTGGCAATGCTGTATATTGCCC -s simCow_chr6.simCow.chr6 578703 57 + 602619 AAATTAACAGTTTGTGTTGCTCGATCTGTGGTTCTGTACATGACTGGCCATCATGGA-------- -s simDog_chr6.simDog.chr6 570733 65 + 593897 AAATTAACTGCTTGTGTGGCCTGACCTATGTTTCTGTAAATAATTTACCTTCCTGGATACCACCT -s simHuman_chr6.simHuman.chr6 574026 65 + 601863 AAATTCACAGTTTGCGTTGCCTGGCCTATAGTTCTGTAAATAGTTGGCCATCCTGTATACTGCCT -s simRat_chr6.simRat.chr6 80470 64 - 647215 TCATTTACAGTTATGGTTGCATGCTCTGCAATTCAGTAAACTTTT-GCAACACTGTATATTGCCC - -a -s simMouse_chr6.simMouse.chr6 606157 14 + 636262 GACTAGGGTTGGCA -s Anc0.Anc0refChr3 203261 14 + 222631 TACTAGGCTTGGCA -s Anc1.Anc1refChr1 43067 14 + 69767 TACTAGGCTTGGCA -s Anc2.Anc2refChr1 120130 14 + 142988 CACTAGGCTCACCT -s mr.mrrefChr3 153932 14 + 181027 TACTAGGGTTGGCA -s simDog_chr6.simDog.chr6 570800 14 + 593897 CACTAGGCTCACCT -s simHuman_chr6.simHuman.chr6 574091 14 + 601863 TACTAGGTTTGGCA -s simRat_chr6.simRat.chr6 80534 14 - 647215 TACTAGGGTTGGCA - -a -s simMouse_chr6.simMouse.chr6 606171 3 + 636262 TCA -s Anc0.Anc0refChr3 203275 3 + 222631 TCA -s Anc1.Anc1refChr1 43081 3 + 69767 TCA -s Anc2.Anc2refChr1 120144 3 + 142988 CCC -s mr.mrrefChr3 153946 3 + 181027 TCA -s simDog_chr6.simDog.chr6 570814 3 + 593897 CCC -s simHuman_chr6.simHuman.chr6 574110 3 + 601863 TTA -s simRat_chr6.simRat.chr6 80548 2 - 647215 TC- - -a -s simMouse_chr6.simMouse.chr6 606174 25 + 636262 CTATAGGAATGATTCCCTCAAAACT -s Anc0.Anc0refChr3 203278 25 + 222631 CCTTAGGGATGATTCCCCAAAAACT -s Anc1.Anc1refChr1 43084 25 + 69767 CCTTAGGGATGATTCCCCAAAAACT -s Anc2.Anc2refChr1 120147 25 + 142988 CCTTAGGGATGACTCCCCAAGAACT -s mr.mrrefChr3 153949 25 + 181027 CTATAGGAATGATTCCCTCAAAACT -s simDog_chr6.simDog.chr6 570817 25 + 593897 CCTTAGGGATGACTCCCCAAGAACT -s simHuman_chr6.simHuman.chr6 574115 25 + 601863 CCTTAGGGATGATTCCCCAAAAACT -s simRat_chr6.simRat.chr6 80550 3 - 647215 ----------------------AGT - -a -s simMouse_chr6.simMouse.chr6 606199 58 + 636262 CATGACTTTAGAGAGGCAGTGGCTCATATCTATAAGACTGCTGGTAGTGGTTTGCACA -s Anc0.Anc0refChr3 203303 52 + 222631 AGGGACTGCAGAGAGGCAG------ATACTTATGATACTGCTTGTAATGATTCGCACG -s Anc1.Anc1refChr1 43109 58 + 69767 AGGGACTGCAGAGAGGCAGTGGCTTATACTTATGATACTGCTTGTAATGATTCGCACG -s Anc2.Anc2refChr1 120172 52 + 142988 AGGGAATGCAAAGAGGCCG------ATATTTATGATACTGCCTGCTATGATTCACACG -s mr.mrrefChr3 153974 58 + 181027 CATGACTGTAGAGAGGCAGTGGCTCATACTTATGAGACTGCTGGTAGTGGTTTGCACA -s simCow_chr6.simCow.chr6 578760 39 + 602619 -------------GGGCAG------ATATTTATGATACTGTCTGCTATGATTCACACG -s simDog_chr6.simDog.chr6 570843 49 + 593897 AGGGAATGCAAAGAGGTCG------ATCTTTGTGATACTGCCT---ACAATTCATACA -s simHuman_chr6.simHuman.chr6 574140 58 + 601863 AGGGACTGCAGAGAGACAGTGGCTTATACTTATGGCACTGCTTGTAATGATTAGCATG -s simRat_chr6.simRat.chr6 80553 58 - 647215 CATGACTGTAGAGTGGCCATGGCTCATACTTATGAGACTAGTGGTAGTGGTTTACACA - -a -s simMouse_chr6.simMouse.chr6 606257 40 + 636262 ACTCTAGCTGTTAATCAAGACATTGCACGAAACCACTAAC -s Anc0.Anc0refChr3 203355 39 + 222631 CCTCTAACTGCAAATCTAGTAAT-GCATAGAGCCACAAAC -s Anc1.Anc1refChr1 43167 40 + 69767 CCTCTAACTGCAAATCTAGTAATTGCATAGAGCCACAAAC -s Anc2.Anc2refChr1 120224 39 + 142988 CCTCTAACTGCAAATCTAGAAAC-ATACAGAGCCACAAAC -s mr.mrrefChr3 154032 40 + 181027 ACTCTAGCTGTTAATCAAGTCATTGCATAGAACCACTAAC -s simCow_chr6.simCow.chr6 578799 39 + 602619 ACTCTAAGTGCAAATCTAGAAAG-ATACAGAGCCATAAAC -s simDog_chr6.simDog.chr6 570892 39 + 593897 CCTCCAACTGCAAACCTAAAAAC-ATACAGAGCCACAAAC -s simHuman_chr6.simHuman.chr6 574206 40 + 601863 CCTCTAACTAACAATCTAGTGATTGCATAGAGCTGCAAAC -s simRat_chr6.simRat.chr6 80611 40 - 647215 ACTCTAGCCGCTAATTGAGTCATTGCATAGAATCACTGGC - -a -s simMouse_chr6.simMouse.chr6 606297 21 + 636262 TCAGGAGACATGGTAAGTTCA -s Anc0.Anc0refChr3 203394 21 + 222631 TCAACAGAAGTAGTAAGTTCA -s Anc1.Anc1refChr1 43207 21 + 69767 TCAACAGAAGTAGTAAGTTCA -s Anc2.Anc2refChr1 120263 21 + 142988 TCAACAGAAGTAGGAGGTTCA -s mr.mrrefChr3 154072 21 + 181027 TCAGGAGAAATGGTAAGTTCA -s simCow_chr6.simCow.chr6 578843 21 + 602619 TCAAGAGAAGTAGAAGGTTCA -s simDog_chr6.simDog.chr6 570931 21 + 593897 TCATCAGAATTAGGAGGTTCA -s simHuman_chr6.simHuman.chr6 574246 21 + 601863 TCAAAGGAAGTAGTGAGTTCA -s simRat_chr6.simRat.chr6 80651 21 - 647215 TCAGGAGAAATGGTAAGTTCA - -a -s simMouse_chr6.simMouse.chr6 606318 13 + 636262 CAACCAGTATATA -s Anc0.Anc0refChr3 203421 13 + 222631 AAGTGAGTGTATA -s Anc1.Anc1refChr1 43234 13 + 69767 AAGTGAGTGTATA -s Anc2.Anc2refChr1 120290 13 + 142988 AAGTGAGTGTATA -s mr.mrrefChr3 154093 13 + 181027 CAACCAGTATATA -s simCow_chr6.simCow.chr6 578870 13 + 602619 CCACAAGTGTAGA -s simDog_chr6.simDog.chr6 570958 13 + 593897 AAGTGAGTGTATA -s simHuman_chr6.simHuman.chr6 574273 13 + 601863 TACTGATTGTTTA -s simRat_chr6.simRat.chr6 80672 13 - 647215 CAACCAGTATATA - -a -s simMouse_chr6.simMouse.chr6 606331 66 + 636262 GGTGCAGCAATTGTGTGCAGGCCCTAAGAGCCATATGTATTGGCACTTTGGAGTCAATCCTTTATA -s Anc0.Anc0refChr3 203434 66 + 222631 GATGCTGCAATTGTATGAGATCCCTAAGAGCACTATGTAAGGGCACTTTGTAGTCAACCCCTTATC -s Anc1.Anc1refChr1 43247 66 + 69767 GATGCTGCAATTGTATGAGATCCCTAAGAGCACTATGTAAGGGCACTTTGTAGTCAACCCCTTATC -s Anc2.Anc2refChr1 120303 66 + 142988 GAGGCTGCAATTGTATGAGATCCCTAAGAGCACCATGTAAGGGCACTTTGTAGTGAACCCCTTATC -s mr.mrrefChr3 154106 66 + 181027 GGTGCAGCAATTGTGTGCAGGCCCTAAGAGCCATATGTATTGGCACTTTGGAGTCAACCCTTTATA -s simCow_chr6.simCow.chr6 578883 66 + 602619 GGAGCTGCAATTGTGTGAGATCCCTAAGAGCATCTTGTAAGTGCACTGTGTAGTTGAGCCCTTATC -s simDog_chr6.simDog.chr6 570971 66 + 593897 GAGACCACCATTGTATGAGCTCACTAAGAGCACCATGTAGGGGCACTTTGTAGTGAACCCCTTATC -s simHuman_chr6.simHuman.chr6 574287 66 + 601863 GATGCTGCAATTGTATGAGATTCATGGAAGCACTATGAAAGAGCACTTTACAGTCAACCCATTATC -s simRat_chr6.simRat.chr6 80685 65 - 647215 GGTCCAGTAATTATGTGCAGGGCCTAAGAGCCATATGTA-TGGCACTTTGAAGTCAACCCCTTATA - -a -s simMouse_chr6.simMouse.chr6 606397 13 + 636262 GGAGTAAATTTTA -s Anc0.Anc0refChr3 203500 13 + 222631 AGATTGCAGTTGA -s Anc1.Anc1refChr1 43313 13 + 69767 AGATTGCAGTTGA -s Anc2.Anc2refChr1 120369 13 + 142988 AGATTGCAGTTGA -s mr.mrrefChr3 154172 13 + 181027 GGAGTAAATTTTA -s simCow_chr6.simCow.chr6 578949 13 + 602619 AGATAGCTGTCAG -s simDog_chr6.simDog.chr6 571037 13 + 593897 AGATTGCAGTTGA -s simHuman_chr6.simHuman.chr6 574353 1 + 601863 T------------ -s simRat_chr6.simRat.chr6 80767 13 - 647215 GGAGTGAATTTTT - -a -s simMouse_chr6.simMouse.chr6 606410 9 + 636262 AACCTTACC -s Anc0.Anc0refChr3 203513 9 + 222631 AATGTTATT -s Anc1.Anc1refChr1 43326 9 + 69767 AATGTTATT -s Anc2.Anc2refChr1 120383 9 + 142988 AATGTTATT -s mr.mrrefChr3 154185 9 + 181027 AACCTTACC -s simCow_chr6.simCow.chr6 578963 9 + 602619 AACATTCTT -s simDog_chr6.simDog.chr6 571051 9 + 593897 AATGTTATT -s simRat_chr6.simRat.chr6 80780 9 - 647215 GACCTTACC - -a -s simMouse_chr6.simMouse.chr6 606419 14 + 636262 AGACAAGCTTCTCA -s Anc0.Anc0refChr3 203522 14 + 222631 GGATAAACTTGCCA -s Anc1.Anc1refChr1 43335 14 + 69767 GGATAAACTTGCCA -s Anc2.Anc2refChr1 120392 14 + 142988 GGATAAACTTGCCA -s mr.mrrefChr3 154194 14 + 181027 AGACAAGCTTCTCA -s simCow_chr6.simCow.chr6 578972 14 + 602619 GGATAAACTTGTCA -s simDog_chr6.simDog.chr6 571061 14 + 593897 GGATAAACTTGCCA -s simRat_chr6.simRat.chr6 80789 14 - 647215 AGACAATCTTCTCA - -a -s simMouse_chr6.simMouse.chr6 606433 19 + 636262 CCATCTAAGTAAAATTAAT -s Anc0.Anc0refChr3 203536 19 + 222631 CCACCTAAGTAATATTAAC -s Anc1.Anc1refChr1 43349 19 + 69767 CCACCTAAGTAATATTAAC -s Anc2.Anc2refChr1 120406 19 + 142988 CCACCTAAGTAATATTAAC -s mr.mrrefChr3 154208 19 + 181027 CCATCTAAGTAAAATTAAT -s simCow_chr6.simCow.chr6 578986 19 + 602619 CCATCCTATTAATATTAAT -s simDog_chr6.simDog.chr6 571075 19 + 593897 CCACCTAAGTAATATTAAC -s simHuman_chr6.simHuman.chr6 574354 13 + 601863 ------AAGTAGTATTAAC -s simRat_chr6.simRat.chr6 80804 19 - 647215 CCATCTAAATAAAATTAAT - -a -s simMouse_chr6.simMouse.chr6 606452 38 + 636262 TAATAGGGCTGCTTTAATCTGTGACACACAGTTTTCTG -s Anc0.Anc0refChr3 203858 27 + 222631 TCGTAGGTATGCTTGAACCT-----------TTATTTT -s Anc1.Anc1refChr1 43671 27 + 69767 TCGTAGGTATGCTTGAACCT-----------TTATTTT -s Anc2.Anc2refChr1 120751 27 + 142988 TCGTGGGTATGCTTGAACCT-----------TTATTTT -s mr.mrrefChr3 154227 34 + 181027 TAATAGGGCTGCTTTAATCTGT----CACAGTTTTCTG -s simCow_chr6.simCow.chr6 579322 27 + 602619 TCATGGGTATGCTTAAACAT-----------TTATTTT -s simDog_chr6.simDog.chr6 571494 27 + 593897 TCGTGGGTATGCTTGAACCT-----------TTATTTC -s simHuman_chr6.simHuman.chr6 574670 27 + 601863 TCGTAGGTATGCTCGAACCT-----------TTGTTTT -s simRat_chr6.simRat.chr6 80823 34 - 647215 TAAAGGGGTTGCTTTAGTATGT----CCCTATCCTCTA - -a -s simMouse_chr6.simMouse.chr6 606490 8 + 636262 AATGTTTT -s Anc0.Anc0refChr3 203885 8 + 222631 ACTGTTCT -s Anc1.Anc1refChr1 43698 8 + 69767 ACTGTTCT -s Anc2.Anc2refChr1 120778 8 + 142988 ACTGTTCT -s mr.mrrefChr3 154261 8 + 181027 AATGTTTT -s simCow_chr6.simCow.chr6 579349 8 + 602619 ACTGTTTT -s simDog_chr6.simDog.chr6 571521 8 + 593897 ACTGTTCT -s simHuman_chr6.simHuman.chr6 574697 8 + 601863 ACTGTTCT -s simRat_chr6.simRat.chr6 80859 8 - 647215 ATAGCATT - -a -s simMouse_chr6.simMouse.chr6 606498 7 + 636262 GTGTTGT -s Anc0.Anc0refChr3 203898 7 + 222631 ACATTGT -s Anc1.Anc1refChr1 43711 7 + 69767 ACATTGT -s Anc2.Anc2refChr1 120791 7 + 142988 ACATTGT -s mr.mrrefChr3 154269 7 + 181027 GTGTTGT -s simCow_chr6.simCow.chr6 579362 7 + 602619 ACATTGC -s simDog_chr6.simDog.chr6 571534 7 + 593897 GCAATGT -s simHuman_chr6.simHuman.chr6 574710 7 + 601863 ACATTGT -s simRat_chr6.simRat.chr6 80867 7 - 647215 CACCTGT - -a -s simMouse_chr6.simMouse.chr6 606505 1 + 636262 G -s Anc0.Anc0refChr3 203905 1 + 222631 G -s Anc1.Anc1refChr1 43718 1 + 69767 G -s Anc2.Anc2refChr1 120798 1 + 142988 G -s mr.mrrefChr3 154276 1 + 181027 G -s simCow_chr6.simCow.chr6 579369 1 + 602619 A -s simDog_chr6.simDog.chr6 571541 1 + 593897 G -s simHuman_chr6.simHuman.chr6 574717 1 + 601863 G -s simRat_chr6.simRat.chr6 80881 1 - 647215 G - -a -s simMouse_chr6.simMouse.chr6 606506 5 + 636262 CCTAG -s Anc0.Anc0refChr3 203909 5 + 222631 ACTAG -s Anc1.Anc1refChr1 43722 5 + 69767 ACTAG -s Anc2.Anc2refChr1 120802 5 + 142988 ACTAG -s mr.mrrefChr3 154277 5 + 181027 CCTAG -s simCow_chr6.simCow.chr6 579375 5 + 602619 ACTAG -s simDog_chr6.simDog.chr6 571543 5 + 593897 CTTAG -s simHuman_chr6.simHuman.chr6 574721 5 + 601863 ACTAG -s simRat_chr6.simRat.chr6 80882 5 - 647215 CCTAA - -a -s simMouse_chr6.simMouse.chr6 606511 13 + 636262 CCAACCCTTTTTA -s Anc0.Anc0refChr3 203914 12 + 222631 CCAACCCTTTTT- -s Anc1.Anc1refChr1 43727 12 + 69767 CCAACCCTTTTT- -s Anc2.Anc2refChr1 120807 12 + 142988 CCAACCCTTTTT- -s mr.mrrefChr3 154282 13 + 181027 CCAACCCTTTTTA -s simCow_chr6.simCow.chr6 579381 12 + 602619 AAAACCAATGTT- -s simDog_chr6.simDog.chr6 571548 12 + 593897 CCAACCCTTTCC- -s simHuman_chr6.simHuman.chr6 574726 12 + 601863 CTGACCTTTTTT- -s simRat_chr6.simRat.chr6 80887 13 - 647215 CAAACCCTTTCTA - -a -s simMouse_chr6.simMouse.chr6 606524 17 + 636262 TAAATTACTAATATCAA -s Anc0.Anc0refChr3 203926 17 + 222631 TATATTATTTGTATCAA -s Anc1.Anc1refChr1 43739 17 + 69767 TATATTATTTGTATCAA -s Anc2.Anc2refChr1 120819 17 + 142988 TATATTATTTGTATCAA -s mr.mrrefChr3 154295 17 + 181027 TAAATTACTAATATCAA -s simCow_chr6.simCow.chr6 579393 17 + 602619 TATACTATTTGTATTAA -s simDog_chr6.simDog.chr6 571561 17 + 593897 TGTATTCTTTGTATCAA -s simHuman_chr6.simHuman.chr6 574738 17 + 601863 TATATTATTTGTATCAA -s simRat_chr6.simRat.chr6 80900 17 - 647215 CATATTACTCAAATCAA - -a -s simMouse_chr6.simMouse.chr6 606541 19 + 636262 GCAGGGCCCAGTAAGGATA -s Anc0.Anc0refChr3 203943 19 + 222631 GCAGAGCTCTGCAAAAGTG -s Anc1.Anc1refChr1 43756 19 + 69767 GCAGAGCTCTGCAAAAGTG -s Anc2.Anc2refChr1 120836 19 + 142988 GCAGAGCTCTGCAAAAGTG -s mr.mrrefChr3 154312 19 + 181027 GCAGGGCCCAGTAAGGATA -s simCow_chr6.simCow.chr6 579483 19 + 602619 GCAGAGCTCTGTAAAAATA -s simDog_chr6.simDog.chr6 571578 19 + 593897 GCAGAGCTCTGCAAAAGTG -s simHuman_chr6.simHuman.chr6 574755 2 + 601863 GC----------------- -s simRat_chr6.simRat.chr6 80917 19 - 647215 GCAGGGCCCAGTAAGGATA - -a -s simMouse_chr6.simMouse.chr6 606560 3 + 636262 CAC -s Anc0.Anc0refChr3 203962 3 + 222631 CTC -s Anc1.Anc1refChr1 43775 3 + 69767 CTC -s Anc2.Anc2refChr1 120862 3 + 142988 CTC -s mr.mrrefChr3 154331 3 + 181027 CAC -s simCow_chr6.simCow.chr6 579509 3 + 602619 CTC -s simDog_chr6.simDog.chr6 571607 3 + 593897 CTC -s simRat_chr6.simRat.chr6 80936 3 - 647215 CGT - -a -s simMouse_chr6.simMouse.chr6 606563 7 + 636262 AGTTCTG -s Anc0.Anc0refChr3 203965 6 + 222631 AGAT-TG -s Anc1.Anc1refChr1 43778 6 + 69767 AGAT-TG -s Anc2.Anc2refChr1 120865 6 + 142988 AGAT-TG -s mr.mrrefChr3 154334 7 + 181027 AGTTCTG -s simCow_chr6.simCow.chr6 579512 6 + 602619 AGAT-TG -s simDog_chr6.simDog.chr6 571610 6 + 593897 AGAT-TG -s simRat_chr6.simRat.chr6 80940 7 - 647215 AGTTCTG - -a -s simMouse_chr6.simMouse.chr6 606570 15 + 636262 GTGGATTGCTCAATG -s Anc0.Anc0refChr3 203971 15 + 222631 ACGGATTGCTCAATG -s Anc1.Anc1refChr1 43784 15 + 69767 ACGGATTGCTCAATG -s Anc2.Anc2refChr1 120871 15 + 142988 ACAGATTGCTCAATT -s mr.mrrefChr3 154341 15 + 181027 GTGGATTGCTCAATG -s simCow_chr6.simCow.chr6 579518 7 + 602619 --------CTCAATT -s simDog_chr6.simDog.chr6 571620 15 + 593897 ACAGATTGCTCAATT -s simHuman_chr6.simHuman.chr6 574757 15 + 601863 TCGGATCACTTAAAG -s simRat_chr6.simRat.chr6 80947 15 - 647215 GTGGACTGCTCAATG - -a -s simMouse_chr6.simMouse.chr6 606585 37 + 636262 CCCATAAGCTGTTGGGATTGCAGGACTATGATGGTAA -s Anc0.Anc0refChr3 203986 37 + 222631 CCCATAAGCTATTGAAATTGCAAGGATAGTATAGTGA -s Anc1.Anc1refChr1 43799 37 + 69767 CCCATAAGCTATTGAAATTGCAAGGATAGTATAGTGA -s Anc2.Anc2refChr1 120886 37 + 142988 CCCATAAGCTATTGAACTTGCAAGGATAGTACAGTGG -s mr.mrrefChr3 154356 37 + 181027 CCCATAAGCTGTTGGGATTGCAGGACTATGATGGTAA -s simCow_chr6.simCow.chr6 579525 36 + 602619 CT-GCAAACTGTTGAACTTGCTAGGATAGTCCAGTGG -s simDog_chr6.simDog.chr6 571635 37 + 593897 CCCATAGGTCATTCAACTTGCAAGGATAGTACAGTGG -s simHuman_chr6.simHuman.chr6 574772 37 + 601863 CCAATGAGCTATTGAAATTGCAAGGATAGTATAGTGA -s simRat_chr6.simRat.chr6 80977 37 - 647215 CCAATATGCTGTTGGGATTGCAAGACTTTCATGGTAA - -a -s simMouse_chr6.simMouse.chr6 606622 9 + 636262 TTAAGTAAT -s Anc0.Anc0refChr3 204030 4 + 222631 TAA-----T -s Anc1.Anc1refChr1 43843 4 + 69767 TAA-----T -s Anc2.Anc2refChr1 120930 4 + 142988 TAA-----T -s mr.mrrefChr3 154393 4 + 181027 TTA-----T -s simCow_chr6.simCow.chr6 579568 4 + 602619 TAA-----T -s simDog_chr6.simDog.chr6 571679 4 + 593897 TAA-----T -s simHuman_chr6.simHuman.chr6 574816 4 + 601863 TAA-----T -s simRat_chr6.simRat.chr6 81014 4 - 647215 TTA-----T - -a -s simMouse_chr6.simMouse.chr6 606631 21 + 636262 CATTGCCAATCTGTGAAGTCT -s Anc0.Anc0refChr3 204034 19 + 222631 GATCCCCAATC--TGAAGTCT -s Anc1.Anc1refChr1 43847 19 + 69767 GATCCCCAATC--TGAAGTCT -s Anc2.Anc2refChr1 120934 19 + 142988 GATCCCCAATC--TGAAGTCT -s mr.mrrefChr3 154397 21 + 181027 CATTGCCAATCTGTGAAGTCT -s simCow_chr6.simCow.chr6 579576 19 + 602619 GATCCCTAAAC--TGAAGTCT -s simDog_chr6.simDog.chr6 571683 19 + 593897 GATCCCCAGTC--TGAACTCT -s simHuman_chr6.simHuman.chr6 574820 19 + 601863 GATACACAATC--TGAAGTCT -s simRat_chr6.simRat.chr6 81018 21 - 647215 TATCCCCAATCTGCGAAGTCT - -a -s simMouse_chr6.simMouse.chr6 606652 19 + 636262 TTGTAGTCTTCGTAGATGG -s Anc0.Anc0refChr3 204135 11 + 222631 TTA--------GTAAATTG -s Anc1.Anc1refChr1 43948 11 + 69767 TTA--------GTAAATTG -s Anc2.Anc2refChr1 121065 11 + 142988 TTA--------GTAAATTG -s mr.mrrefChr3 154418 11 + 181027 TTA--------GTAGATGG -s simCow_chr6.simCow.chr6 579707 11 + 602619 TTG--------GTAGAGTC -s simDog_chr6.simDog.chr6 571835 11 + 593897 TTA--------GCAAATTG -s simHuman_chr6.simHuman.chr6 574924 11 + 601863 TTA--------GTCAATTG -s simRat_chr6.simRat.chr6 81039 11 - 647215 TTA--------GTAGCTGG - -a -s simMouse_chr6.simMouse.chr6 606671 12 + 636262 ATATCCCAAGTC -s Anc0.Anc0refChr3 204156 12 + 222631 TTATCCCAAACC -s Anc1.Anc1refChr1 43969 12 + 69767 TTATCCCAAACC -s Anc2.Anc2refChr1 121089 12 + 142988 TTATCCCAAAGC -s mr.mrrefChr3 154439 12 + 181027 ATATCCCAAGTC -s simCow_chr6.simCow.chr6 579731 12 + 602619 TTATCTGAAATC -s simDog_chr6.simDog.chr6 571859 12 + 593897 TTATCCCAAAGC -s simHuman_chr6.simHuman.chr6 574945 12 + 601863 TTATCCCAAACC -s simRat_chr6.simRat.chr6 81063 12 - 647215 ATATCCCAAGTC - -a -s simMouse_chr6.simMouse.chr6 606683 41 + 636262 ATATCAATCTTCGTGGGCAGAGGGCAGAAGCTGGCTTGATA -s Anc0.Anc0refChr3 204169 41 + 222631 GTATTAATCCAGGTGGGCAGAGGCAAGGAGCTGATTTAATG -s Anc1.Anc1refChr1 43983 41 + 69767 GTATTAATCCAGGTGGGCAGAGGCAAGGAGCTGATTTAATG -s Anc2.Anc2refChr1 121102 41 + 142988 GTATTAATCCAGGTGGGCAGAGGCAAGGAGCGGATTTATGG -s mr.mrrefChr3 154451 41 + 181027 ATATCAATCCTGGTGGGCAGAGGGCAGAAGCTGGCTTGATA -s simCow_chr6.simCow.chr6 579744 41 + 602619 GTATTTATCTAGGTGGGCAGAGGCAAGGAGCATATTTATGG -s simDog_chr6.simDog.chr6 571872 41 + 593897 GTACTAATCCAAGTGAGCAGAGGCAAGGAGCGGATTTATGG -s simHuman_chr6.simHuman.chr6 574959 41 + 601863 GTATTAATTCAGGTGGGCAGAGGCTAGCAGCTGATCTAATG -s simRat_chr6.simRat.chr6 81075 41 - 647215 TTATCAATCCTGGTGGGCAGAGGGCAGGAGCTGGCTTGATA - -a -s simMouse_chr6.simMouse.chr6 606724 69 + 636262 AGCTGCTTAGTCTCAACACCTGGGGCCAGCAAAGTGGTAGCCAGCAAAGTGATAACTAAGATATTGTAC -s Anc0.Anc0refChr3 204219 54 + 222631 AGCTGGTTTTTTACTACACCAGTGGCCAGCAAGAAGG---------------TAACTAAAAAATTATAC -s Anc1.Anc1refChr1 44033 54 + 69767 AGCTGGTTTTTTACTACACCAGTGGCCAGCAAGAAGG---------------TAACTAAAAAATTATAC -s Anc2.Anc2refChr1 121152 54 + 142988 AGCTGGTTTTTTACTACACCAGTGGCCAACAAGAAGA---------------TAACTAAAAAATTATAC -s mr.mrrefChr3 154492 54 + 181027 AGCTGCTTAGTCTCAACACCAGGGGCCAGCAAAGAGG---------------TAACTAAGATATTATAC -s simCow_chr6.simCow.chr6 579794 51 + 602619 AGCTGCTT--TTACAACACCAG-GGCCAACAAGAAGA---------------TAACTAAAAGATTATAC -s simDog_chr6.simDog.chr6 571922 54 + 593897 AGCTGGTTTTTTACTACACCAGTGGCCAACAAGAAGA---------------TAATCAAAAAATTATAC -s simHuman_chr6.simHuman.chr6 575009 54 + 601863 GGCTGTTTTCTTATGTTACCAGAGGCCAGCAATCAGG---------------TAACTAAAACATTATAT -s simRat_chr6.simRat.chr6 81116 54 - 647215 AGCTGCTTAGTCTCAACACCAAGGGCCCGCAAAGAGG---------------CAACTAAGATATTATAC - -a -s simMouse_chr6.simMouse.chr6 606793 29 + 636262 CAATCTGTAACATATGCAATCCAATACCC -s Anc0.Anc0refChr3 204273 29 + 222631 CAAACTGCAGCATGGGCAATCAATTGTTC -s Anc1.Anc1refChr1 44087 29 + 69767 CAAACTGCAGCATGGGCAATCAATTGTTC -s Anc2.Anc2refChr1 121206 29 + 142988 TAAAATGCAGCATGGGCAATCAATTGTTC -s mr.mrrefChr3 154546 29 + 181027 CAATCTGCAACATATGCAATCCAATACCC -s simCow_chr6.simCow.chr6 579845 29 + 602619 TAGATGGCAGCGTAGGCAGCCAATTTTTC -s simDog_chr6.simDog.chr6 571976 29 + 593897 TAAAATACAGCATGGGCAATTGGTGGCTA -s simHuman_chr6.simHuman.chr6 575067 29 + 601863 CACCCTGCCTCATGGCCAATCAAGTGTTC -s simRat_chr6.simRat.chr6 81170 29 - 647215 CAATCTACAGCATAAGCAATCCAATACAC - -a -s simMouse_chr6.simMouse.chr6 606822 30 + 636262 CAATCAAACTGAGCTTGCCAAATTGAGCCA -s Anc0.Anc0refChr3 204302 30 + 222631 AAATTAAATAAAACTTGCAAAATTGAGCTA -s Anc1.Anc1refChr1 44116 30 + 69767 AAATTAAATAAAACTTGCAAAATTGAGCTA -s Anc2.Anc2refChr1 121235 30 + 142988 AAATTAAATAAAACTTGCAAAATTGAGCTG -s mr.mrrefChr3 154575 30 + 181027 CAATCAAACTGAGCTTGCCAAATTGAGCCA -s simCow_chr6.simCow.chr6 579935 30 + 602619 AAGTTGGGTAGAACTTGCCAAATTGGGATG -s simDog_chr6.simDog.chr6 572005 30 + 593897 AAATTAAATCAAACTTGCAAAATTGAGCTG -s simHuman_chr6.simHuman.chr6 575096 30 + 601863 AAATTAAATACAACCTGCAAAATTGAGCTA -s simRat_chr6.simRat.chr6 81199 30 - 647215 CAATCAAACCGAGCTTGCCAAGTTGGGCCA - -a -s simMouse_chr6.simMouse.chr6 606852 22 + 636262 GCTTAAATTGACTACATATTAT -s Anc0.Anc0refChr3 204367 22 + 222631 GTCTAAACTCACTGTCTATTAT -s Anc1.Anc1refChr1 44181 22 + 69767 GTCTAAACTCACTGTCTATTAT -s Anc2.Anc2refChr1 121300 22 + 142988 GTCTAAACTCACTGTCTATTAT -s mr.mrrefChr3 154640 22 + 181027 GCCTAAATTGACTATCTATTAT -s simCow_chr6.simCow.chr6 580003 22 + 602619 GTTTGAACTCACTCTCCATTAC -s simDog_chr6.simDog.chr6 572050 22 + 593897 GTCTAAACTCACTGTCTATTAT -s simHuman_chr6.simHuman.chr6 575161 22 + 601863 GTCTAAACATACTGTCTATTAT -s simRat_chr6.simRat.chr6 81270 22 - 647215 GCCTAAATTGACTATCTATTAT - -a -s simMouse_chr6.simMouse.chr6 606874 5 + 636262 CTTTC -s Anc0.Anc0refChr3 204390 5 + 222631 CTTTG -s Anc1.Anc1refChr1 44204 5 + 69767 CTTTG -s Anc2.Anc2refChr1 121323 5 + 142988 CTTTG -s mr.mrrefChr3 154663 5 + 181027 CTTTC -s simCow_chr6.simCow.chr6 580026 5 + 602619 GTTTG -s simDog_chr6.simDog.chr6 572073 5 + 593897 CTTTG -s simHuman_chr6.simHuman.chr6 575184 5 + 601863 CTTTT -s simRat_chr6.simRat.chr6 81293 5 - 647215 CTTTC - -a -s simMouse_chr6.simMouse.chr6 606879 23 + 636262 CTGACTTACATGAATCCATACAC -s Anc0.Anc0refChr3 204395 19 + 222631 CTACATTA----AATCTGTACAC -s Anc1.Anc1refChr1 44209 19 + 69767 CTACATTA----AATCTGTACAC -s Anc2.Anc2refChr1 121328 19 + 142988 CTACATTA----AGTCTGTACAT -s mr.mrrefChr3 154668 23 + 181027 CTGACTTACATGAATCCATACAC -s simCow_chr6.simCow.chr6 580034 19 + 602619 ATGCATTA----ATTACACATTA -s simDog_chr6.simDog.chr6 572078 19 + 593897 CTACAATA----AGCCTGTACAT -s simHuman_chr6.simHuman.chr6 575189 19 + 601863 CTACATAA----AATCTGTACAC -s simRat_chr6.simRat.chr6 81298 23 - 647215 TTGACTTACATGAATCCATACAC - -a -s simMouse_chr6.simMouse.chr6 606902 17 + 636262 TCAGTGTCTATGGAGTG -s Anc0.Anc0refChr3 204414 17 + 222631 TCAATGTCTAAGAAATG -s Anc1.Anc1refChr1 44228 17 + 69767 TCAATGTCTAAGAAATG -s Anc2.Anc2refChr1 121347 17 + 142988 TCAATGTCTAAGAAATG -s mr.mrrefChr3 154691 17 + 181027 TCAGTGTCTATGGAGTG -s simCow_chr6.simCow.chr6 580053 17 + 602619 TTAATAACTCAGTAATG -s simDog_chr6.simDog.chr6 572100 17 + 593897 TCAATGTCTAAGAGATG -s simHuman_chr6.simHuman.chr6 575208 17 + 601863 TCAATGTCCAAGAAATG -s simRat_chr6.simRat.chr6 81321 17 - 647215 TCAGTGTCTATGGAGTG - -a -s simMouse_chr6.simMouse.chr6 606919 1 + 636262 T -s Anc0.Anc0refChr3 204553 1 + 222631 T -s Anc1.Anc1refChr1 44367 1 + 69767 T -s Anc2.Anc2refChr1 121486 1 + 142988 T -s mr.mrrefChr3 154829 1 + 181027 T -s simCow_chr6.simCow.chr6 580409 1 + 602619 T -s simDog_chr6.simDog.chr6 572244 1 + 593897 T -s simHuman_chr6.simHuman.chr6 575347 1 + 601863 T -s simRat_chr6.simRat.chr6 81483 1 - 647215 T - -a -s simMouse_chr6.simMouse.chr6 606920 12 + 636262 TTATCATACAGG -s Anc0.Anc0refChr3 204554 8 + 222631 CT----TACAAG -s Anc1.Anc1refChr1 44368 8 + 69767 CT----TACAAG -s Anc2.Anc2refChr1 121529 8 + 142988 CT----TACAGG -s mr.mrrefChr3 154830 12 + 181027 TTATCATACAAG -s simCow_chr6.simCow.chr6 580452 8 + 602619 TC----TACAGG -s simDog_chr6.simDog.chr6 572289 5 + 593897 CT----CAC--- -s simHuman_chr6.simHuman.chr6 575348 8 + 601863 CT----TACAAG -s simRat_chr6.simRat.chr6 81484 12 - 647215 TAATCATAGAAG - -a -s simMouse_chr6.simMouse.chr6 606932 15 + 636262 TCAACCCTGTTCTAA -s Anc0.Anc0refChr3 204562 15 + 222631 TATATCCTGTTCTAA -s Anc1.Anc1refChr1 44376 15 + 69767 TATATCCTGTTCTAA -s Anc2.Anc2refChr1 121537 15 + 142988 TATATCCTGTTCTAA -s mr.mrrefChr3 154842 15 + 181027 TCAATCCTGTTCTAA -s simCow_chr6.simCow.chr6 580461 15 + 602619 TATCTCCTGTTCTAT -s simDog_chr6.simDog.chr6 572294 15 + 593897 TCTATCCTGTTCTAA -s simHuman_chr6.simHuman.chr6 575356 15 + 601863 TATATCCTGTTCTAA -s simRat_chr6.simRat.chr6 81496 15 - 647215 TGAATCCTGTTCAAG - -a -s simMouse_chr6.simMouse.chr6 606947 41 + 636262 TCACCTGGACAAGATCACTACAAGCTTGCTGCCACAGAGAA -s Anc0.Anc0refChr3 204577 41 + 222631 TTATCTAGACAAAACCAGTATGGGCGTGCTTCAACAGATCA -s Anc1.Anc1refChr1 44391 41 + 69767 TTATCTAGACAAAACCAGTATGGGCGTGCTTCAACAGATCA -s Anc2.Anc2refChr1 121552 41 + 142988 TTATCTAGACAAAACCAGTATGGGCGAGCTTCAACACATCT -s mr.mrrefChr3 154857 41 + 181027 TCACCTGGACAAGATCACTACAAGCTTGCTGCCACAGATCA -s simCow_chr6.simCow.chr6 580476 41 + 602619 CTATCCAGACAAAACCACTATGGATTGACCTCGACACATTT -s simDog_chr6.simDog.chr6 572310 41 + 593897 TTATCTAGATGAAACCAGTATCGGCGAGCTTTAACACATCT -s simHuman_chr6.simHuman.chr6 575371 41 + 601863 TTATCTAGACAAAACCATTATGGGCCTGTTACAACAGATCA -s simRat_chr6.simRat.chr6 81511 41 - 647215 TCACCTTGATAAGATCGCTGCAAGCTTGCTGCCACAGATCA - -a -s simMouse_chr6.simMouse.chr6 606988 19 + 636262 AGCTCTTTCTGATAGGAGT -s Anc0.Anc0refChr3 204621 19 + 222631 GACTCCTTCTGATAAGATT -s Anc1.Anc1refChr1 44435 19 + 69767 GACTCCTTCTGATAAGATT -s Anc2.Anc2refChr1 121597 19 + 142988 GACTCCTTCTGATAAAATT -s mr.mrrefChr3 154898 19 + 181027 AGCTCTTTCTGATAGGAGT -s simCow_chr6.simCow.chr6 580521 19 + 602619 GACTCCTGCTGACAAAATT -s simDog_chr6.simDog.chr6 572355 19 + 593897 GACTCCTTCTGATAAAATT -s simHuman_chr6.simHuman.chr6 575415 19 + 601863 GACTCCTTCTGATAAGATT -s simRat_chr6.simRat.chr6 81552 7 - 647215 A------------ATGACT - -a -s simMouse_chr6.simMouse.chr6 607007 35 + 636262 CTTGTCTTTATGAAGTGACTGGAGTGCCTACCTAA -s Anc0.Anc0refChr3 204641 29 + 222631 CCACTTTTTATGAAG--TGTGAACTGCTGGC---- -s Anc1.Anc1refChr1 44455 29 + 69767 CCACTTTTTATGAAG--TGTGAACTGCTGGC---- -s Anc2.Anc2refChr1 121617 29 + 142988 TCACTTTTTATGAAG--TGTAAACAGCTGGC---- -s mr.mrrefChr3 154917 35 + 181027 CTTGTCTTTATGAAGTGTGTGGAGTGCCTACCTAA -s simCow_chr6.simCow.chr6 580541 29 + 602619 TCACTCTTTATTCAG--TGTAAGCAGCTAGT---- -s simDog_chr6.simDog.chr6 572375 29 + 593897 TCACTTTTTATGAAG--TGCAAACAGCTGGC---- -s simHuman_chr6.simHuman.chr6 575435 29 + 601863 CCCATTTTTATGGAG--TGTGAATTGCTCGC---- -s simRat_chr6.simRat.chr6 81559 35 - 647215 TTTGTCCTTATGAAGTGTGTGGGGTGCCTACTCAA - -a -s simMouse_chr6.simMouse.chr6 607042 16 + 636262 TGCCTATGCATGCATG -s Anc0.Anc0refChr3 204670 14 + 222631 --CATATACAAGTGTG -s Anc1.Anc1refChr1 44484 14 + 69767 --CATATACAAGTGTG -s Anc2.Anc2refChr1 121646 14 + 142988 --CATATACAACTGTG -s mr.mrrefChr3 154952 16 + 181027 TGCCTATGCAAGCATG -s simCow_chr6.simCow.chr6 580570 14 + 602619 --CATATACAACTGTG -s simDog_chr6.simDog.chr6 572404 14 + 593897 --CATATGGAACTGTG -s simHuman_chr6.simHuman.chr6 575464 14 + 601863 --CATATACGAGTGTG -s simRat_chr6.simRat.chr6 81618 16 - 647215 TGCCTATCCAAGCATG - -a -s simMouse_chr6.simMouse.chr6 607058 92 + 636262 GATAAGACAATTTGGAGTGTAGTGTTATGCAAGCATGGTATAGACTATTTGGAGTATGACATACTTTTCCACTTAGTAATTTTAGGTTCCAG -s Anc0.Anc0refChr3 204685 78 + 222631 TACAAGGCTACTTGGAATGTAACATTCTTAATGCATCACAGTTTCCAATTGG-------TACAAGCTT----TTAG---TCTAAGCTTTTAG -s Anc1.Anc1refChr1 44499 78 + 69767 TACAAGGCTACTTGGAATGTAACATTCTTAATGCATCACAGTTTCCAATTGG-------TACAAGCTT----TTAG---TCTAAGCTTTTAG -s Anc2.Anc2refChr1 121661 78 + 142988 TACAACGCTATTTGGAATGTAACATTCTTAATGCAACACAGTTTCCAAGAGG-------TACAAGCTT----TTAG---TCCAAGCCTTTAG -s mr.mrrefChr3 154968 88 + 181027 GATAAGGCAACTTGGAGTGTAGCATTATGCAAGCATGGTATAGACTATTTGGAGTTTGACATACTTTT----TTAGTAATTTTAGGTTCCAG -s simCow_chr6.simCow.chr6 580585 78 + 602619 TACACAGCTATTTGGAATGTGACATTCTTAATGCAGCAAGGTTTTCAGGAGG-------CACAAGCCG----TTAG---ACCAAGCCCTTAG -s simDog_chr6.simDog.chr6 572419 78 + 593897 TAAAACCCTGTTTTGAAGGTAACATTCTTAATGTAACACAGTTTCCAAGAGG-------TACAAGCTT----TAAG---TTCAAGCCTTTGG -s simHuman_chr6.simHuman.chr6 575479 78 + 601863 TACAAGGATACTTGATATGCAACATTCTTAATGCATCAGAGTTTCCACTTGG-------TAGAGGCTT----TTAG---TCTAAGCTTTTAG -s simRat_chr6.simRat.chr6 81634 88 - 647215 GATAAGGCAACTTGGAGTGTAGCATTATGCAGGCATGGTATAGACTATTTGGAGTTTGACATACTTTT----TTAGTACTTTTAGGTCCCAG - -a -s simMouse_chr6.simMouse.chr6 607150 87 + 636262 TCTGAGCCTCTATTGGGCATTATGCAAAAAGCCTTGCATATTTCTAGGAATTTCAGATATTCCAAGGCCATTGGTATAATATCACAT -s Anc0.Anc0refChr3 204763 74 + 222631 TCTGACCTTCTACTGG-------------AGTCTTGCATATTGCTAAGAACCTTGGATACTCCAAAGCCAGTGGTACAAAACCACAT -s Anc1.Anc1refChr1 44577 79 + 69767 TCTGACCTTCTACTGGAC--------TGGAGTCTTGCATATTGCTAAGAACCTTGGATACTCCAAAGCCAGTGGTACAAAACCACAT -s Anc2.Anc2refChr1 121739 74 + 142988 CCTGACCTTCTCCTGG-------------AGTCTTGTATATCACTAAGAACCTTGGATACTCCAAAGCCAGTGGTCCAAAACCACAT -s mr.mrrefChr3 155056 87 + 181027 TCTGAGCTTCTATTGGACATTATGCAAAAAGCCTTGCATATTGCTAGGAACTTTGGATATTCCAAGGCCATTGGTATAATATCACAT -s simCow_chr6.simCow.chr6 580664 65 + 602619 CCTGAGCTT---------------------GTCGTGTATATCACTAACAACCTTGGATACTCCAAAGCCAATGGTCTAAAA-CACAT -s simDog_chr6.simDog.chr6 572497 74 + 593897 CCTGACCTTCTCCTGG-------------AGTTTTGTATATCACTAAGAACTTGGGGTACTCCAAAGCCAGTACTCCAAAACCACAT -s simHuman_chr6.simHuman.chr6 575557 79 + 601863 TCTAATGTTCTACTGGAC--------TGGAGTCTTGCAAATTGCTGAAACCCTTGTATACACCAAAGCTGGTGGTACAAGACCACAT -s simRat_chr6.simRat.chr6 81722 83 - 647215 TCTGAGCTTCTATTGGACACTATGTGAAAAGGCTTGTGTATTGTTAGGAACTTTGGATGTTCCAAGGCCATTGGTATAATATT---- - -a -s simMouse_chr6.simMouse.chr6 607237 3 + 636262 TCA -s Anc0.Anc0refChr3 204837 2 + 222631 TT- -s Anc1.Anc1refChr1 44656 2 + 69767 TT- -s Anc2.Anc2refChr1 121813 2 + 142988 TT- -s mr.mrrefChr3 155143 2 + 181027 TC- -s simCow_chr6.simCow.chr6 580730 2 + 602619 TT- -s simDog_chr6.simDog.chr6 572571 2 + 593897 TT- -s simHuman_chr6.simHuman.chr6 575636 2 + 601863 TT- - -a -s simMouse_chr6.simMouse.chr6 607240 22 + 636262 CAGACATAGGCTAGTCAAGTCC -s Anc0.Anc0refChr3 204839 22 + 222631 CATGTATATGCCACTCAAGTTC -s Anc1.Anc1refChr1 44658 22 + 69767 CATGTATATGCCACTCAAGTTC -s Anc2.Anc2refChr1 121815 22 + 142988 CATGTACATGCCACTCAAGTTC -s mr.mrrefChr3 155145 22 + 181027 CAGACATAGGCTAGTCAAGTCC -s simCow_chr6.simCow.chr6 580732 17 + 602619 CATGTG-----CTCTCCAGTTG -s simDog_chr6.simDog.chr6 572574 22 + 593897 AATGTACATGCCACTCAAGTTC -s simHuman_chr6.simHuman.chr6 575638 22 + 601863 CATGAATATATCATTAAAGTTC - -a -s simMouse_chr6.simMouse.chr6 607262 44 + 636262 TCCACAGTGACAGACTTAACATTTAATAATTACCAACCACCGCC -s Anc0.Anc0refChr3 204861 30 + 222631 TACACAATGATAGACTTAATATTT--------------ACTGGC -s Anc1.Anc1refChr1 44680 30 + 69767 TACACAATGATAGACTTAATATTT--------------ACTGGC -s Anc2.Anc2refChr1 121837 30 + 142988 TACACAATGATAGACCTAATAATT--------------ACTGGC -s mr.mrrefChr3 155167 33 + 181027 TCCACAGTGACAGACTTAACATTT-----------ACCACTGCC -s simCow_chr6.simCow.chr6 580749 30 + 602619 TGTACAATAATATACCTAATAATA--------------ACTAGT -s simDog_chr6.simDog.chr6 572596 30 + 593897 TACACAATGATAGACCTGATAAAT--------------GTCGGC -s simHuman_chr6.simHuman.chr6 575664 30 + 601863 CACACAATGTTAGACTTAATATTT--------------ACTGGC -s simRat_chr6.simRat.chr6 81805 9 - 647215 -----------------------------------ATCACTGCC - -a -s simMouse_chr6.simMouse.chr6 607306 142 + 636262 TGCTCATCATAATCCTACAATTGCCAACATATAGTTAGAATAAGATGTTACTTGTATGTCGACTTTAAAACTCTTATCTTAACAATGTTCTAAGAACTACAGCTAACCAGCGGCCTGCCATAATCAAGAATCCATTTCATAC -s Anc0.Anc0refChr3 204891 115 + 222631 TCCTCATCAGAACCTCACAATGGTAAATGTAA---------------------------CAACATGAATGCTTTTATCTTAACAATGTTCTAGGAACTATAGCTATCCAATGGCCTGCAGTAGGGACGCATCTATTGGATTC -s Anc1.Anc1refChr1 44710 142 + 69767 TCCTCATCAGAACCTCACAATGGTAAATGTAAGTTCAGGATAATATATTACCTGTGTGCCAACATGAATGCTTTTATCTTAACAATGTTCTAGGAACTATAGCTATCCAATGGCCTGCAGTAGGGACGCATCTATTGGATTC -s Anc2.Anc2refChr1 121867 115 + 142988 TCCTCATCAGAACCTCACAATGGTAAATGTAA---------------------------CAATATGAGTGCTTGTATCTTAACAATGTTCTAGGAACTATAGCCATGCAATGGCCTGCAGTAGGGACCCATCTAATGGATTG -s mr.mrrefChr3 155200 142 + 181027 TGCTCATCAGAACCCCACAATTGCCAACATAAAGTTAGAATAATATGTTACTTGTATGTCGACATTAAAACTTTTATCTTAACAATGTTCTAAGAACTACAGCTAACCAGCGGCCTGCCATAATCAAGAATCCATTTCATAC -s simCow_chr6.simCow.chr6 580779 114 + 602619 CCCTCATCAGTACCTCACAATGGTCAATGTAG---------------------------CAATACTTGTGCTTGTATCTTAACAATGTTCTAGAAACTATAGCCACGAGATGGCCTGCAG-GGGCACCCATTTTATGGGTTA -s simDog_chr6.simDog.chr6 572630 114 + 593897 TTCTTATCAGAGCCTCATGATGCTAAATGGAA---------------------------CAATATGAGTGCTTGTATCTTAACAATGTTCTA-GAAGGATAGCCATGCAGTGGCCTGTAGTAGGGATCCATCCAATGGATTG -s simHuman_chr6.simHuman.chr6 575694 141 + 601863 TCCTCATCTGAACCTCACAATGGTAAATGTAAGTTCAGGATAATATATTACCTGTGTGCCAGCATC-AGGCTTTTATCTTACCAATGTTCTAGGAACTATAGCTATCCAATGGCGTGCAGTAGATACGCATCTATTGGATTC -s simRat_chr6.simRat.chr6 81814 142 - 647215 TGCTCATCAGAACCCCACAATTGCTAACATAAAGTTAGAATAATATGTTACTTGTATGTCCACATTAAACCTTTTATCTTGACCATGTTCTAAGAACTACAGCTAATCAGCAGCTTTCCATAATCAACAATCCATGTCATAC - -a -s simMouse_chr6.simMouse.chr6 607448 10 + 636262 TATCTTGAAT -s Anc0.Anc0refChr3 205007 10 + 222631 TATGCTGAGT -s Anc1.Anc1refChr1 44853 10 + 69767 TATGCTGAGT -s Anc2.Anc2refChr1 121983 10 + 142988 TATGCTGAGT -s mr.mrrefChr3 155342 10 + 181027 TATCTTGAAT -s simCow_chr6.simCow.chr6 580894 10 + 602619 TATGTTGAGT -s simDog_chr6.simDog.chr6 572745 10 + 593897 TATGCTGAGT -s simHuman_chr6.simHuman.chr6 575836 10 + 601863 TTTGCTAAGT -s simRat_chr6.simRat.chr6 81956 10 - 647215 TATCTTGAAT - -a -s simMouse_chr6.simMouse.chr6 607458 3 + 636262 ATG -s Anc0.Anc0refChr3 205021 3 + 222631 ATG -s Anc1.Anc1refChr1 44867 3 + 69767 ATG -s Anc2.Anc2refChr1 121999 3 + 142988 CTG -s mr.mrrefChr3 155352 3 + 181027 ATG -s simCow_chr6.simCow.chr6 580910 3 + 602619 CTG -s simDog_chr6.simDog.chr6 572761 3 + 593897 CTA -s simHuman_chr6.simHuman.chr6 575850 3 + 601863 ATG -s simRat_chr6.simRat.chr6 81966 3 - 647215 ATG - -a -s simMouse_chr6.simMouse.chr6 607461 8 + 636262 TGGGGGTG -s Anc0.Anc0refChr3 205025 8 + 222631 TGGAGGTG -s Anc1.Anc1refChr1 44871 8 + 69767 TGGAGGTG -s Anc2.Anc2refChr1 122003 8 + 142988 TGGAGGTG -s mr.mrrefChr3 155355 8 + 181027 TGGGGGTG -s simDog_chr6.simDog.chr6 572765 8 + 593897 TGGAGGTG -s simHuman_chr6.simHuman.chr6 575854 8 + 601863 TGGAGGTA -s simRat_chr6.simRat.chr6 81969 8 - 647215 TGGGGGTG - -a -s simMouse_chr6.simMouse.chr6 607469 12 + 636262 CACTACCCAGTG -s Anc0.Anc0refChr3 205033 10 + 222631 CAGT--CTAGTG -s Anc1.Anc1refChr1 44879 10 + 69767 CAGT--CTAGTG -s Anc2.Anc2refChr1 122011 10 + 142988 CTGC--CTAGTG -s mr.mrrefChr3 155363 12 + 181027 CACTACCCAGTG -s simCow_chr6.simCow.chr6 580913 3 + 602619 ---------GAG -s simDog_chr6.simDog.chr6 572775 10 + 593897 CTGC--CTAGTG -s simHuman_chr6.simHuman.chr6 575862 10 + 601863 AAGT--CTAGTG -s simRat_chr6.simRat.chr6 81977 12 - 647215 CACTACACAGTG - -a -s simMouse_chr6.simMouse.chr6 607481 75 + 636262 CAGAATGCAGATTCACTAGGATGCAGCCCTAATGTGCACTGCATTGAGGTACATCTACAACATTGCTGAGAATCC -s Anc0.Anc0refChr3 205046 52 + 222631 CAG-----------------------TAATAATGCTGTCCAGACAGAAGTAAATCTCCACCATCGCTCAAAATCC -s Anc1.Anc1refChr1 44892 65 + 69767 CAGACTA--GGC--------GTGCAGTAATAATGCTGTCCAGACAGAAGTAAATCTCCACCATCGCTCAAAATCC -s Anc2.Anc2refChr1 122024 52 + 142988 CAA-----------------------TAATAATGCTGTCCAGACAGAAATAAATCTCCACCATCATTCAAAATCA -s mr.mrrefChr3 155375 73 + 181027 CAGAATG--GGTTCACTAGGATGCAGCCCTAATGCGCACTGGATAGAGGTACATCTACAACATTGCTGAAAATCC -s simCow_chr6.simCow.chr6 580919 52 + 602619 CAA-----------------------TAATAATGCTGTCCAGACAGAAATAAATCTCAGCCATCAGTCAAAATCA -s simDog_chr6.simDog.chr6 572787 22 + 593897 -----------------------------------------------------CCTCCACGAAAATTCAGATTTA -s simHuman_chr6.simHuman.chr6 575875 65 + 601863 CAGACTA--GGC--------GTGTAGTTGTAATGCAGGCCAGACAGAAGTAAATCTCCACCATCGCTAAAAATCC -s simRat_chr6.simRat.chr6 81989 73 - 647215 CAGAATG--GGTTCACTGGGATGCAGCCCAAAGGCGCACTGGAGAGAGGTACATCCACAATGTTGCTGGAAATCC - -a -s simMouse_chr6.simMouse.chr6 607556 48 + 636262 AGGGCAAGAATACTTCCATAACCTTGCATAAATTTAAAAATGGAGAAT -s Anc0.Anc0refChr3 205110 38 + 222631 AGCACGAGAGCACATTCATAATATTGCATCAAATTAAA---------- -s Anc1.Anc1refChr1 44969 38 + 69767 AGCACGAGAGCACATTCATAATATTGCATCAAATTAAA---------- -s Anc2.Anc2refChr1 122088 38 + 142988 AGCACGAGAGCATGTTCATAATATTGCATCAAATTAAA---------- -s mr.mrrefChr3 155448 48 + 181027 AGGGCAAGAACACATCCATAACATTGCATAAATTTAAAAATGGAGAAT -s simCow_chr6.simCow.chr6 580988 38 + 602619 AGCACCAGAGCATGTTCATAAAGTTGCATCAAAGTAAG---------- -s simDog_chr6.simDog.chr6 572814 27 + 593897 -----GAGATCGT------AGTAATGTAGTAAATTAGA---------- -s simHuman_chr6.simHuman.chr6 575952 38 + 601863 AGCACTAGAGCACATTCATAATATTGCATCACATTAAA---------- -s simRat_chr6.simRat.chr6 82062 48 - 647215 AGGGCAAGAACACATCCATAACATTGCATAAATTTAAAAATGGAGAAT - -a -s simMouse_chr6.simMouse.chr6 607604 43 + 636262 GTTGGGGAATGTTGAGGGTATATCCTGGGAAGAGTGGCATTCA -s Anc0.Anc0refChr3 205148 43 + 222631 GTTGGGGACTGTCGAAGCAATGTGCTGTGAGGAATGGTGCTGA -s Anc1.Anc1refChr1 45007 43 + 69767 GTTGGGGACTGTCGAAGCAATGTGCTGTGAGGAATGGTGCTGA -s Anc2.Anc2refChr1 122126 43 + 142988 ATTGGGGACTGTCGAAACAATGTGCTGTGAGGAATGGTGCTGT -s mr.mrrefChr3 155496 43 + 181027 GTTGGGGAATGTTGAGGGTATATGCTGGGAAGAATGGCACTCA -s simCow_chr6.simCow.chr6 581031 43 + 602619 ATTCCAGACTGTTGAATCAATGTACTCTGAGGAATGGTACTTA -s simDog_chr6.simDog.chr6 572841 42 + 593897 ATTGGGGACTGTCCATA-AATGTGCTGTGTTGAATGGTGCTGT -s simHuman_chr6.simHuman.chr6 575990 43 + 601863 GTTGGGGACAGCAGAAGTAACGTGCTGTGAGGAATGGTGCTGA -s simRat_chr6.simRat.chr6 82110 43 - 647215 GTTGGAGAATGTTGAGGGTGTATGCTGGGATGCATGGCACTTA - -a -s simMouse_chr6.simMouse.chr6 607647 2 + 636262 TG -s Anc0.Anc0refChr3 205258 2 + 222631 TG -s Anc1.Anc1refChr1 45117 2 + 69767 TG -s Anc2.Anc2refChr1 122236 2 + 142988 TG -s mr.mrrefChr3 155588 2 + 181027 TG -s simCow_chr6.simCow.chr6 581141 2 + 602619 TG -s simDog_chr6.simDog.chr6 572950 2 + 593897 TG -s simHuman_chr6.simHuman.chr6 576105 2 + 601863 TG -s simRat_chr6.simRat.chr6 82202 2 - 647215 TG - -a -s simMouse_chr6.simMouse.chr6 607649 76 + 636262 TCCACTGTTAAGACACCGATCCCAATGTTGCACACCAATCTTTCCAACCACTACACTCTCGTGTTCTTTTACACTC -s Anc0.Anc0refChr3 205260 46 + 222631 TTCACTGCTGAGAT------TCCAGTGTTGCATGGCAATCTTT-----------------GTG-------AGACTG -s Anc1.Anc1refChr1 45119 46 + 69767 TTCACTGCTGAGAT------TCCAGTGTTGCATGGCAATCTTT-----------------GTG-------AGACTG -s Anc2.Anc2refChr1 122238 46 + 142988 CTCACTGCTGAGAT------TCCTGTGTTGCATGGCAATCTTT-----------------GTG-------AGACTG -s mr.mrrefChr3 155590 70 + 181027 TCCACTGCTAAGAC------CCCAGTGTTGCACACCAATCTTTCCAACCACTACACTCTCGTGTTCTTTTACACTC -s simCow_chr6.simCow.chr6 581143 40 + 602619 CTC------GAGAT------TCCTGTGTTCCATGGCAAGTTTT-----------------GTG-------AGGCCG -s simDog_chr6.simDog.chr6 572952 46 + 593897 CTCACTGCTAAGAT------TACTGTGTTGTGTGACAATCTCT-----------------CCT-------AGATTG -s simHuman_chr6.simHuman.chr6 576108 46 + 601863 TTCACTGCTGAGAG------TCCAGTGTTGCATGGCAACCTTT-----------------GTG-------AGACAG -s simRat_chr6.simRat.chr6 82204 70 - 647215 TCCACTGCTAAGAC------CCCAGTGATGCATGCCAACCTTTCCAACCACAACACTCTCGTGTCCTTTTACACTT - -a -s simMouse_chr6.simMouse.chr6 607725 91 + 636262 AATCTAAAGTAGTTACACCCGAGCGTCCCGATTTCTGGATCATGTGCACAGAGACTCACGATCCTGTGATTTGGTTAAAGTTTTAGCACAA -s Anc0.Anc0refChr3 205306 30 + 222631 AATCACAAGTA-------------------------------------------------------------GGCCAAAGTTATGTCACAA -s Anc1.Anc1refChr1 45165 30 + 69767 AATCACAAGTA-------------------------------------------------------------GGCCAAAGTTATGTCACAA -s Anc2.Anc2refChr1 122284 30 + 142988 AATCACAAGTA-------------------------------------------------------------GGCCAATGTTATGTCACAA -s mr.mrrefChr3 155660 91 + 181027 AATCTAAAGTAGTTACACCCGAGCGTCCCGATTTCTGGATCATGTGCACAGAGACTCACGATCCTGTGAGTTGGCTAAAGTTTTAGCACAA -s simCow_chr6.simCow.chr6 581346 30 + 602619 AATCACGAGCA-------------------------------------------------------------GGACAATGTTATGTCACAA -s simDog_chr6.simDog.chr6 572998 30 + 593897 AATCACAAGTA-------------------------------------------------------------GGCTAATGTTGTGTCACAA -s simHuman_chr6.simHuman.chr6 576154 30 + 601863 AATCGCAAGTA-------------------------------------------------------------AGCCAAAGGTATGTCACAA -s simRat_chr6.simRat.chr6 82274 91 - 647215 GTTCTGAGGTAGTTACACCCGAGTATACCGCTGTCTGGATCATGTGTACAGAGGCTGACCATCCTGTGCGTTGGCAAAAATTTTAGCAGAA - -a -s simMouse_chr6.simMouse.chr6 607816 23 + 636262 GTAGACCAAGAACCAAAATAAGC -s Anc0.Anc0refChr3 205336 23 + 222631 GTAGGCAAAAAGCCAGATTAACC -s Anc1.Anc1refChr1 45195 23 + 69767 GTAGGCAAAAAGCCAGATTAACC -s Anc2.Anc2refChr1 122320 23 + 142988 GAAGTTAAAAAGCCAGATACGCC -s mr.mrrefChr3 155751 23 + 181027 GTAGGCCAAGAACCAGAATAAGC -s simCow_chr6.simCow.chr6 581383 23 + 602619 ACAGTTATGGAGCCAGCTACCCC -s simDog_chr6.simDog.chr6 573034 23 + 593897 GAAGTTAAAAACCCAGATACGCC -s simHuman_chr6.simHuman.chr6 576184 23 + 601863 GTAGGCAAAAAGCTGGGTTAACC -s simRat_chr6.simRat.chr6 82365 23 - 647215 GTAGGCCAAGAACCAGAATATAC - -a -s simMouse_chr6.simMouse.chr6 607839 35 + 636262 CTTGATTGGACACATTTAGATCAAGCCTCCACTTA -s Anc0.Anc0refChr3 205361 35 + 222631 CTTGGTCAAATGAATTTAGATCAAGCCTCTATATT -s Anc1.Anc1refChr1 45220 35 + 69767 CTTGGTCAAATGAATTTAGATCAAGCCTCTATATT -s Anc2.Anc2refChr1 122345 35 + 142988 CTTGGACAAATGAATTTAGATTAAGCCTCCATATT -s mr.mrrefChr3 155774 35 + 181027 CTTGATTGGACACATTTAGATCAAGCCTCTACTTA -s simCow_chr6.simCow.chr6 581408 35 + 602619 CTGGCACAAATGAATTTAGATTGAACCTCCACATT -s simDog_chr6.simDog.chr6 573059 35 + 593897 CTTGGACAAATGAATTTAGATTAAGCCTCCATATT -s simHuman_chr6.simHuman.chr6 576209 35 + 601863 CTTGGTGAAATGAGGTTAAATCAGGCCTCTATGTT -s simRat_chr6.simRat.chr6 82388 34 - 647215 CTTGATTGGACAC-TTTAGATCAAGCCTTTACTTA - -a -s simMouse_chr6.simMouse.chr6 607874 7 + 636262 GAACTGA -s Anc0.Anc0refChr3 205396 5 + 222631 AGA--GC -s Anc1.Anc1refChr1 45255 5 + 69767 AGA--GC -s Anc2.Anc2refChr1 122380 5 + 142988 AGA--AC -s mr.mrrefChr3 155809 7 + 181027 GGACTGA -s simCow_chr6.simCow.chr6 581445 5 + 602619 AAA--AC -s simDog_chr6.simDog.chr6 573094 5 + 593897 AGA--AC -s simHuman_chr6.simHuman.chr6 576244 5 + 601863 AGA--GC -s simRat_chr6.simRat.chr6 82422 7 - 647215 GGACTGA - -a -s simMouse_chr6.simMouse.chr6 607881 22 + 636262 CCTAACCTGACTTTAGCAAGCT -s Anc0.Anc0refChr3 205401 22 + 222631 ATTGATTTAACTTTAACAGGCT -s Anc1.Anc1refChr1 45260 22 + 69767 ATTGATTTAACTTTAACAGGCT -s Anc2.Anc2refChr1 122385 22 + 142988 ATTGACTTAACTTAAACAGGCT -s mr.mrrefChr3 155816 22 + 181027 CTTAATCTGACTTTAACAAGCT -s simCow_chr6.simCow.chr6 581450 22 + 602619 GTTGACTTAACATCAACAGGCT -s simDog_chr6.simDog.chr6 573117 22 + 593897 ATTGACTAAACTTAAACTGGCT -s simHuman_chr6.simHuman.chr6 576249 21 + 601863 ATTGTTTTAACTATAACAGGC- -s simRat_chr6.simRat.chr6 82429 22 - 647215 CTTAATCTGACTTTAACAAGCT - -a -s simMouse_chr6.simMouse.chr6 607903 19 + 636262 TGGCCCAATAGAGATGATA -s Anc0.Anc0refChr3 205423 19 + 222631 TGGCCAGACAGAAATAGTA -s Anc1.Anc1refChr1 45282 19 + 69767 TGGCCAGACAGAAATAGTA -s Anc2.Anc2refChr1 122422 19 + 142988 TGGACAGACAGAAATAGTA -s mr.mrrefChr3 155838 19 + 181027 TGGCCCAATAGAAATGATA -s simCow_chr6.simCow.chr6 581487 19 + 602619 TGGTCAGACAGAAATAGTA -s simDog_chr6.simDog.chr6 573154 19 + 593897 TGGACAGACAGAAATAATA -s simHuman_chr6.simHuman.chr6 576270 19 + 601863 TGGCCAGACAGAAATAGTA -s simRat_chr6.simRat.chr6 82451 19 - 647215 TGGCCCAATAGAAATGATA - -a -s simMouse_chr6.simMouse.chr6 607922 26 + 636262 TGACTGTTCTTACTGCTCTGACGTGC -s Anc0.Anc0refChr3 205442 22 + 222631 TGACTGTTCTCAC----ACGATAGCA -s Anc1.Anc1refChr1 45301 22 + 69767 TGACTGTTCTCAC----ACGATAGCA -s Anc2.Anc2refChr1 122441 22 + 142988 CCACTGTTCTCAC----ACAATAGCA -s mr.mrrefChr3 155857 26 + 181027 TGACTGTTCTTACCGCTCTGATGTGC -s simCow_chr6.simCow.chr6 581506 22 + 602619 GAACTGTTCTCAC----AAAATAGCA -s simDog_chr6.simDog.chr6 573174 22 + 593897 CCACTGTTCTCAC----ACAATAGCC -s simHuman_chr6.simHuman.chr6 576289 22 + 601863 TGACTGCTCTCAC----GCGAGAATA -s simRat_chr6.simRat.chr6 82470 26 - 647215 TGACTGTTCTTATCGCTCTCATGTGC - -a -s simMouse_chr6.simMouse.chr6 607948 26 + 636262 GGACAAAAGATACCAATTGAAAAGAT -s Anc0.Anc0refChr3 205469 26 + 222631 GGACTATAAATGCCAATTAATTAGAT -s Anc1.Anc1refChr1 45328 26 + 69767 GGACTATAAATGCCAATTAATTAGAT -s Anc2.Anc2refChr1 122468 26 + 142988 GGACTTTAAATGCCAATTATTTAGAT -s mr.mrrefChr3 155888 26 + 181027 GGACAAAAGATACCAATTGAAAAGAT -s simCow_chr6.simCow.chr6 581533 23 + 602619 GGGCTCTAAATGCCTATTG---AGAC -s simDog_chr6.simDog.chr6 573201 26 + 593897 GGACTTTAAACACCAATTATTTAGAT -s simHuman_chr6.simHuman.chr6 576316 26 + 601863 GGACTAGAAATGTCAACTAACTAGAT -s simRat_chr6.simRat.chr6 82501 14 - 647215 GGACAGAAGCGAAC------------ - -a -s simMouse_chr6.simMouse.chr6 607974 5 + 636262 GCCAA -s Anc0.Anc0refChr3 205496 5 + 222631 ACCAA -s Anc1.Anc1refChr1 45355 5 + 69767 ACCAA -s Anc2.Anc2refChr1 122495 5 + 142988 ACCAG -s mr.mrrefChr3 155914 5 + 181027 GCCAA -s simCow_chr6.simCow.chr6 581557 5 + 602619 ACCAG -s simDog_chr6.simDog.chr6 573228 5 + 593897 ACTAG -s simHuman_chr6.simHuman.chr6 576343 5 + 601863 ACCAA -s simRat_chr6.simRat.chr6 82515 4 - 647215 -CCAA - -a -s simMouse_chr6.simMouse.chr6 607979 103 + 636262 TGTAAGCTTGGGCCTAGACTATATGGGTGAGAAGATAGTATGATCACTCTTACCCTGAGGTATCGGGGAGCCAAGTATGGTAATTAGTATTGTAAGATGCTGC -s Anc0.Anc0refChr3 205502 99 + 222631 CAGAAGCTTGAGTCTCCACTATATAGATGATGAGAGAGTAGGACCACTCTCACATAGAGGTGTAGAGGAGCTAAGAATGGTAATTAGTGTTAA----CATTCA -s Anc1.Anc1refChr1 45361 99 + 69767 CAGAAGCTTGAGTCTCCACTATATAGATGATGAGAGAGTAGGACCACTCTCACATAGAGGTGTAGAGGAGCTAAGAATGGTAATTAGTGTTAA----CATTCA -s Anc2.Anc2refChr1 122501 99 + 142988 CAGAAGCTTGAGTCTCCACTATATAGATGATGAGAGGGTAGGACCACTCTCACATAGAGGTGTAGAGGAGCTATGAATGTTAATTGGTGAAAA----CATTCA -s mr.mrrefChr3 155919 103 + 181027 TGTAAGCTTGGGCCTACACTATATAGGTGAGAAGAGAGTATGATCACTCTTACCCTGAGGTATCGGGGAGCCAAGAATGGTAATTAGTGTTGTAAGATGCTGC -s simCow_chr6.simCow.chr6 581563 88 + 602619 CATAAGTTTGAGTCTTTGCTATATGTACAATCTGAGGGCAGGACCACTCTTGCTTAGATGTTCAGAGGGGC---------TAATTGGTGAGGA----CATT-- -s simDog_chr6.simDog.chr6 573234 99 + 593897 TAGAAGCATGAGTATCCACTATATAGATGATGAGAGGGTGGGACCACTCTCACATAGAGGTGTACAGGAGCTATGAATGTTAATTGATGAAAA----CATTCA -s simHuman_chr6.simHuman.chr6 576349 99 + 601863 CAGAAGCTTGAGTCTCCACTATACAGATTGTGAGAGAGTAGGACCACCCTGACATAAAGGTGTAGAGGAGCATAGAATGGTAACCAGTGTTAC----CAGCTA -s simRat_chr6.simRat.chr6 82519 103 - 647215 TGTAGGATTGGGCCTACACTATATAGGTGAGAAGAGAGTACGATTACTCTTACCCTGAGGTATCGCGGAGCCAAGAATGGTAAGTAATGTTGTAAAATGCTGC - -a -s simMouse_chr6.simMouse.chr6 608082 38 + 636262 AAGTTTGTTTGAGTGCTCCCTAAATGGGCCGCACTAAC -s Anc0.Anc0refChr3 205601 36 + 222631 CA--AAGTCCGAGTGCCCCCTATATAGGCTACACCAAC -s Anc1.Anc1refChr1 45460 36 + 69767 CA--AAGTCCGAGTGCCCCCTATATAGGCTACACCAAC -s Anc2.Anc2refChr1 122600 36 + 142988 CC--AAGCCTAAGTGCCCCCCTTATAGGCCACACCAAC -s mr.mrrefChr3 156022 36 + 181027 AA--TAGTTCGAGTGCCCCCTAAATGGGCTGCACCAAC -s simCow_chr6.simCow.chr6 581651 7 + 602619 -------------------------------TACCAAC -s simDog_chr6.simDog.chr6 573336 36 + 593897 CC--AAGCCTAAGTGCCCCCCTTATAGGCCACTCAAAC -s simHuman_chr6.simHuman.chr6 576448 36 + 601863 CA--AAGTCCGAGTGCCCCTTATGTAGGCTACACCAAC -s simRat_chr6.simRat.chr6 82622 34 - 647215 ----TAGTTCAAGTGCCCGCCAAATGAGCTGCACCAAC - -a -s simMouse_chr6.simMouse.chr6 608120 62 + 636262 CACTTACAGATATACTGCACGCATCGATAGGTCCTCAAAATATTACCTGAAGAAAGTCAATG -s Anc0.Anc0refChr3 205643 58 + 222631 CACTTACAGATATATTGCGC----CCATATGTCCTGAAAATTTCACCTGAAGGAGATCAATA -s Anc1.Anc1refChr1 45502 58 + 69767 CACTTACAGATATATTGCGC----CCATATGTCCTGAAAATTTCACCTGAAGGAGATCAATA -s Anc2.Anc2refChr1 122644 58 + 142988 CACTTACAGATATATTGTGC----CCATATGTCCTGGAAATTTCACCTGAAGGAGATGAATA -s mr.mrrefChr3 156064 62 + 181027 CACTTACAGATATATTGCACGCATCCATAGGTCCTCAAAATTTTACCTGAAGAAAGTCAATA -s simCow_chr6.simCow.chr6 581666 58 + 602619 CACTTACAGATATACTATCC----CCATATGTTCTGTAAATTTCACCTGAAGGAGATGAACA -s simDog_chr6.simDog.chr6 573380 51 + 593897 CACTCACAGATACATTGTGC----ACTTATGTCCTAG-------ACCTGAAGGAGATGAATG -s simHuman_chr6.simHuman.chr6 576490 55 + 601863 ---TTACAGATATATTGCGC----CCATTTGTCCTGAAAATTTCACCTTAAGGAGATCAATA -s simRat_chr6.simRat.chr6 82664 62 - 647215 CACTTACAGATATATTGCACACATCCATAGGTCCTCAAACTTTTCCCTGAAGAAAGTCAATA - -a -s simMouse_chr6.simMouse.chr6 608182 62 + 636262 ATATACATTGGATCCTAACCTTACCCAATTTTAATGCAGCAAGAACCTAGCTGTAAAAGGCA -s Anc0.Anc0refChr3 205701 62 + 222631 ATATACAATGGATGCTAACTGTAATTAGTCTGAGGAAAGCAAGAGCCCAGTTGCGAAGGTCA -s Anc1.Anc1refChr1 45560 62 + 69767 ATATACAATGGATGCTAACTGTAATTAGTCTGAGGAAAGCAAGAGCCCAGTTGCGAAGGTCA -s Anc2.Anc2refChr1 122702 62 + 142988 ATAAACAATGGATGCTAACTGTAATTAGCCAGAGGAAGGCAAAAGCCCAGTTGCGAAGGTCA -s mr.mrrefChr3 156126 62 + 181027 ATATACAATGGATGCTAACCTTACCCAATTTTAATCCAGCAAGAACCTAGCTGTAAAAGGCA -s simCow_chr6.simCow.chr6 581724 62 + 602619 ATCAACTACAGATGCTAACTGTATCTAGCTAGAGCAAGTCAAGAACCCAGTTGTGAAGGTCA -s simDog_chr6.simDog.chr6 573431 62 + 593897 ATAAAAAATGGATGCTAACCATAATTACCCAAAAGAAGGCAAAAGCCCAGTTGCGAAGGTCA -s simHuman_chr6.simHuman.chr6 576547 46 + 601863 ATATACAATGAATGCTTCTTGTAGTTAGTCTG-----AGAAAGA--CAGGTTG--------- -s simRat_chr6.simRat.chr6 82726 62 - 647215 ATATGCAATGGATGCCAACCTTACCCGATCTTAATCCAGCAAGAACCTAGCTGTAAAGGGCA - -a -s simMouse_chr6.simMouse.chr6 608244 11 + 636262 TTTCAGAGGAT -s Anc0.Anc0refChr3 205764 11 + 222631 CTTTAGGGGGT -s Anc1.Anc1refChr1 45623 11 + 69767 CTTTAGGGGGT -s Anc2.Anc2refChr1 122765 11 + 142988 CTTTAGGTGGT -s mr.mrrefChr3 156188 11 + 181027 CTTCAGAGGAT -s simCow_chr6.simCow.chr6 581787 11 + 602619 CTTTAGGTGGT -s simDog_chr6.simDog.chr6 573494 11 + 593897 CGCTAGATAAT -s simHuman_chr6.simHuman.chr6 576594 11 + 601863 CTTGAGGGGGT -s simRat_chr6.simRat.chr6 82788 7 - 647215 CCCT----GAT - -a -s simMouse_chr6.simMouse.chr6 608255 21 + 636262 GTCTGTTACCATCATATGTAA -s Anc0.Anc0refChr3 205776 21 + 222631 GTCTATTACCATTAGATGTGA -s Anc1.Anc1refChr1 45635 21 + 69767 GTCTATTACCATTAGATGTGA -s Anc2.Anc2refChr1 122777 21 + 142988 GTCTATTACCATTAGATGTGA -s mr.mrrefChr3 156199 21 + 181027 GTCTGTTACCATCATATGTGA -s simCow_chr6.simCow.chr6 581799 17 + 602619 CTCT----CTATCAGATGTGA -s simDog_chr6.simDog.chr6 573506 21 + 593897 GTTTATTACCACTAGATGTAA -s simHuman_chr6.simHuman.chr6 576606 21 + 601863 GTCTTTTACCATGAGATATGA -s simRat_chr6.simRat.chr6 82795 21 - 647215 GTCTGTTACCATTGTATGTGA - -a -s simMouse_chr6.simMouse.chr6 608276 14 + 636262 TCTAGCTCAGCTAG -s Anc0.Anc0refChr3 205797 14 + 222631 TCTAGTTGACCCTA -s Anc1.Anc1refChr1 45656 14 + 69767 TCTAGTTGACCCTA -s Anc2.Anc2refChr1 122798 14 + 142988 TCTAGTTGATCCTA -s mr.mrrefChr3 156220 14 + 181027 TCTAGCTGACCTAG -s simCow_chr6.simCow.chr6 581817 14 + 602619 TCTAGTTGATCCTA -s simDog_chr6.simDog.chr6 573527 14 + 593897 TCTCATTGATCCTA -s simHuman_chr6.simHuman.chr6 576627 14 + 601863 TCTAGTTGACCCTA -s simRat_chr6.simRat.chr6 82816 14 - 647215 TCAAGCAGACCTAG - -a -s simMouse_chr6.simMouse.chr6 608290 48 + 636262 AATTTCAGGAGAAGGGGCAGTCAACATCTCATAGCCATAGTAATAGGA -s Anc0.Anc0refChr3 205811 48 + 222631 AATTTTTGGAAAACAGGTTGTTGGTATTTTCTATTTACAGTAATTGCA -s Anc1.Anc1refChr1 45670 48 + 69767 AATTTTTGGAAAACAGGTTGTTGGTATTTTCTATTTACAGTAATTGCA -s Anc2.Anc2refChr1 122812 48 + 142988 AATTTTTGGTAAACAGGTTGTTGGTATTTTCTATTTACAGTAATTGCA -s mr.mrrefChr3 156234 48 + 181027 AATTTCAGGAAAAGGGGCAGTCAACATTTTATAGCCATAGTAATAGGA -s simCow_chr6.simCow.chr6 581832 48 + 602619 AGTTTTTGCGAAACAGGTTGTTAGTATTTTCTATTTATGGTAAGTGAG -s simDog_chr6.simDog.chr6 573541 48 + 593897 AATTTTGGGTAAACAGGCGGTTGGTACTTTCTATTCACAGTATTTACA -s simHuman_chr6.simHuman.chr6 576641 48 + 601863 AATTTTTGGAAAACAGGTTGTTGGTATTTTCTAAATACAGCAATGGCA -s simRat_chr6.simRat.chr6 82830 48 - 647215 AATTTCATGAAAAGGGGCAGCCAACATTTTGTATGCATAGTAATAGAA - -a -s simMouse_chr6.simMouse.chr6 608338 10 + 636262 GAACTTAGGA -s Anc0.Anc0refChr3 205859 10 + 222631 GAGATTGCAA -s Anc1.Anc1refChr1 45718 10 + 69767 GAGATTGCAA -s Anc2.Anc2refChr1 122860 10 + 142988 GAGATTGCAG -s mr.mrrefChr3 156282 10 + 181027 GAAATTAGGA -s simCow_chr6.simCow.chr6 581880 10 + 602619 GAGGTCGCAG -s simDog_chr6.simDog.chr6 573598 10 + 593897 GAGATTGCAG -s simHuman_chr6.simHuman.chr6 576689 10 + 601863 GGGATTGCAA -s simRat_chr6.simRat.chr6 82878 10 - 647215 GAAATTAGGA - -a -s simMouse_chr6.simMouse.chr6 608348 11 + 636262 ATTGATTTCAT -s Anc0.Anc0refChr3 205871 11 + 222631 TTTGATATCAT -s Anc1.Anc1refChr1 45730 11 + 69767 TTTGATATCAT -s Anc2.Anc2refChr1 122872 11 + 142988 TTTGACATCAT -s mr.mrrefChr3 156292 11 + 181027 ATTGATTTCAT -s simCow_chr6.simCow.chr6 581892 11 + 602619 TGTGACATAAT -s simDog_chr6.simDog.chr6 573610 11 + 593897 TTTGACATCAT -s simHuman_chr6.simHuman.chr6 576701 11 + 601863 TTTGGTATCAT -s simRat_chr6.simRat.chr6 82888 11 - 647215 GGTGATGTCAT - -a -s simMouse_chr6.simMouse.chr6 608359 22 + 636262 CACTGCAGATTCAGATGCTTTT -s Anc0.Anc0refChr3 205882 22 + 222631 CACTGCAGGCTCAGATGCTATT -s Anc1.Anc1refChr1 45741 22 + 69767 CACTGCAGGCTCAGATGCTATT -s Anc2.Anc2refChr1 122883 22 + 142988 CACTGCAGGCCCAGATGCCATC -s mr.mrrefChr3 156303 22 + 181027 CACTGCAGACTCAGATGCTTTT -s simCow_chr6.simCow.chr6 581903 22 + 602619 CACTGCAGACCCAGATGCCATC -s simDog_chr6.simDog.chr6 573621 18 + 593897 CACTGCAGGCCCA----CCATC -s simHuman_chr6.simHuman.chr6 576714 22 + 601863 CACTGCAGGCTCAGATGCTATT -s simRat_chr6.simRat.chr6 82899 22 - 647215 CACTGCAGACTCAGATGCTTTT - -a -s simMouse_chr6.simMouse.chr6 608381 26 + 636262 ACCTGGCCTTGAACCTTGCTCAATCA -s Anc0.Anc0refChr3 205904 26 + 222631 ACCTGGGCCTGAGCCTTGCTCAATCA -s Anc1.Anc1refChr1 45763 26 + 69767 ACCTGGGCCTGAGCCTTGCTCAATCA -s Anc2.Anc2refChr1 122905 26 + 142988 ACCTGGGCCTGAGTCTTGCTCAATCA -s mr.mrrefChr3 156325 26 + 181027 ACCTGGGCCTGAACCTTGCTCAATCA -s mr.mrrefChr3 156463 25 + 181027 AGCTGGGCCTGAACCTTGCTCAATC- -s simCow_chr6.simCow.chr6 581925 26 + 602619 ACCTGGGCCCGAGCCTTGCTCAATCA -s simDog_chr6.simDog.chr6 573639 26 + 593897 ACCTGGACCTGGGTCTTGCTCAACCA -s simHuman_chr6.simHuman.chr6 576736 26 + 601863 ACCTCAGCCTGAGGCTTGCCCAATCC -s simMouse_chr6.simMouse.chr6 608527 25 + 636262 AGCTGGGCCTGAACCTTGCTCAATC- -s simRat_chr6.simRat.chr6 83077 25 - 647215 AGTTGGGCCTGAACCTTGCTCAATC- -s simRat_chr6.simRat.chr6 82921 25 - 647215 ACCTTGGCCTGAACCTTGCTCAATC- - -a -s simMouse_chr6.simMouse.chr6 608407 8 + 636262 CCACTTCA -s Anc0.Anc0refChr3 205930 8 + 222631 CCAGTTAA -s Anc1.Anc1refChr1 45789 8 + 69767 CCAGTTAA -s Anc2.Anc2refChr1 122931 8 + 142988 CCAGTTAA -s mr.mrrefChr3 156351 8 + 181027 CCACTTAA -s simCow_chr6.simCow.chr6 581951 8 + 602619 CAAGTTAA -s simDog_chr6.simDog.chr6 573665 8 + 593897 TCAGCTAA -s simHuman_chr6.simHuman.chr6 576762 8 + 601863 CCAGTTAT -s simRat_chr6.simRat.chr6 82946 8 - 647215 CCACTTAG - -a -s simMouse_chr6.simMouse.chr6 608415 4 + 636262 TCTA -s Anc0.Anc0refChr3 205938 4 + 222631 TCTT -s Anc1.Anc1refChr1 45797 4 + 69767 TCTT -s Anc2.Anc2refChr1 122939 4 + 142988 TCTT -s mr.mrrefChr3 156359 4 + 181027 TCTT -s mr.mrrefChr3 156488 4 + 181027 TCTT -s simCow_chr6.simCow.chr6 581959 4 + 602619 TCTT -s simDog_chr6.simDog.chr6 573673 4 + 593897 TCTT -s simHuman_chr6.simHuman.chr6 576770 4 + 601863 CAAT -s simMouse_chr6.simMouse.chr6 608552 4 + 636262 TCTT -s simRat_chr6.simRat.chr6 83111 4 - 647215 CCTT -s simRat_chr6.simRat.chr6 82954 4 - 647215 TCTT - -a -s simMouse_chr6.simMouse.chr6 608419 2 + 636262 CC -s Anc0.Anc0refChr3 205942 2 + 222631 TC -s Anc1.Anc1refChr1 45801 2 + 69767 TC -s Anc2.Anc2refChr1 122945 2 + 142988 TT -s mr.mrrefChr3 156363 2 + 181027 TC -s mr.mrrefChr3 156492 2 + 181027 TC -s simCow_chr6.simCow.chr6 581965 2 + 602619 TG -s simDog_chr6.simDog.chr6 573679 2 + 593897 TT -s simHuman_chr6.simHuman.chr6 576774 2 + 601863 TC -s simMouse_chr6.simMouse.chr6 608556 2 + 636262 TC -s simRat_chr6.simRat.chr6 83115 2 - 647215 TC -s simRat_chr6.simRat.chr6 82958 2 - 647215 TC - -a -s simMouse_chr6.simMouse.chr6 608421 5 + 636262 TTTGG -s Anc0.Anc0refChr3 205945 4 + 222631 TTT-A -s Anc1.Anc1refChr1 45804 4 + 69767 TTT-A -s Anc2.Anc2refChr1 122948 4 + 142988 TTT-A -s mr.mrrefChr3 156365 4 + 181027 TTT-G -s mr.mrrefChr3 156495 4 + 181027 TTT-G -s simCow_chr6.simCow.chr6 581968 4 + 602619 TTT-A -s simDog_chr6.simDog.chr6 573682 4 + 593897 TTT-A -s simHuman_chr6.simHuman.chr6 576776 4 + 601863 TTT-A -s simMouse_chr6.simMouse.chr6 608559 4 + 636262 TTT-G -s simRat_chr6.simRat.chr6 83118 4 - 647215 TTG-G -s simRat_chr6.simRat.chr6 82960 4 - 647215 TTT-G - -a -s simMouse_chr6.simMouse.chr6 608426 3 + 636262 AAT -s Anc0.Anc0refChr3 205960 3 + 222631 AAT -s Anc1.Anc1refChr1 45819 3 + 69767 AAT -s Anc2.Anc2refChr1 122963 3 + 142988 TAT -s mr.mrrefChr3 156369 3 + 181027 AAT -s mr.mrrefChr3 156499 3 + 181027 AAT -s simCow_chr6.simCow.chr6 581983 3 + 602619 GAT -s simDog_chr6.simDog.chr6 573697 3 + 593897 TAT -s simHuman_chr6.simHuman.chr6 576791 3 + 601863 AAT -s simMouse_chr6.simMouse.chr6 608563 3 + 636262 AAT -s simRat_chr6.simRat.chr6 83122 3 - 647215 AAT -s simRat_chr6.simRat.chr6 82964 3 - 647215 AAT - -a -s simMouse_chr6.simMouse.chr6 608429 1 + 636262 A -s Anc0.Anc0refChr3 205963 1 + 222631 G -s Anc1.Anc1refChr1 45822 1 + 69767 G -s Anc2.Anc2refChr1 122966 1 + 142988 G -s mr.mrrefChr3 156372 1 + 181027 A -s mr.mrrefChr3 156502 1 + 181027 A -s simCow_chr6.simCow.chr6 581986 1 + 602619 G -s simDog_chr6.simDog.chr6 573700 1 + 593897 G -s simHuman_chr6.simHuman.chr6 576794 1 + 601863 G -s simMouse_chr6.simMouse.chr6 608571 1 + 636262 A -s simRat_chr6.simRat.chr6 83125 1 - 647215 A -s simRat_chr6.simRat.chr6 82967 1 - 647215 A - -a -s simMouse_chr6.simMouse.chr6 608430 9 + 636262 GGCATCTCC -s Anc0.Anc0refChr3 205964 9 + 222631 GGCATCTCC -s Anc1.Anc1refChr1 45823 9 + 69767 GGCATCTCC -s Anc2.Anc2refChr1 122967 9 + 142988 GGCATCTCC -s mr.mrrefChr3 156373 9 + 181027 GGCATCTCC -s mr.mrrefChr3 156503 9 + 181027 GTCATCTCC -s simCow_chr6.simCow.chr6 581987 9 + 602619 AGCATCTCC -s simDog_chr6.simDog.chr6 573701 9 + 593897 GGTGTCTCC -s simHuman_chr6.simHuman.chr6 576795 9 + 601863 GGCATCTCT -s simMouse_chr6.simMouse.chr6 608572 9 + 636262 ATCATCTCC -s simRat_chr6.simRat.chr6 83126 9 - 647215 GTCATCTCC -s simRat_chr6.simRat.chr6 82973 9 - 647215 GGCATTTCC - -a -s simMouse_chr6.simMouse.chr6 608439 4 + 636262 ATAT -s Anc0.Anc0refChr3 205987 4 + 222631 AGAT -s Anc1.Anc1refChr1 45846 4 + 69767 AGAT -s Anc2.Anc2refChr1 122990 4 + 142988 AGAT -s mr.mrrefChr3 156382 4 + 181027 ATAT -s mr.mrrefChr3 156526 4 + 181027 ATAT -s simCow_chr6.simCow.chr6 582009 4 + 602619 AGAC -s simDog_chr6.simDog.chr6 573724 4 + 593897 AAAT -s simHuman_chr6.simHuman.chr6 576818 4 + 601863 AGAT -s simMouse_chr6.simMouse.chr6 608595 4 + 636262 ATAT -s simRat_chr6.simRat.chr6 83149 4 - 647215 ATAA -s simRat_chr6.simRat.chr6 82996 4 - 647215 ACAT - -a -s simMouse_chr6.simMouse.chr6 608443 5 + 636262 CATTT -s Anc0.Anc0refChr3 205991 5 + 222631 CATCT -s Anc1.Anc1refChr1 45850 5 + 69767 CATCT -s Anc2.Anc2refChr1 122994 5 + 142988 CATCT -s mr.mrrefChr3 156386 5 + 181027 CATTT -s mr.mrrefChr3 156530 5 + 181027 CATCT -s simCow_chr6.simCow.chr6 582013 5 + 602619 CATCT -s simDog_chr6.simDog.chr6 573732 5 + 593897 CACCT -s simHuman_chr6.simHuman.chr6 576822 5 + 601863 CATTT -s simMouse_chr6.simMouse.chr6 608599 5 + 636262 CATCT -s simRat_chr6.simRat.chr6 83153 5 - 647215 TATCT -s simRat_chr6.simRat.chr6 83000 5 - 647215 TATCT - -a -s simMouse_chr6.simMouse.chr6 608448 27 + 636262 TATGTATACGAGAGGGCCCATCCTTAG -s Anc0.Anc0refChr3 205996 27 + 222631 TATGTATACAAAAGGGCCCATCTCTAG -s Anc1.Anc1refChr1 45855 27 + 69767 TATGTATACAAAAGGGCCCATCTCTAG -s Anc2.Anc2refChr1 122999 27 + 142988 TAGGTATACTAAAGGGCCATTCTCTTG -s mr.mrrefChr3 156391 27 + 181027 TATGTATACGAGAGGGCCCATCCTTAG -s mr.mrrefChr3 156535 27 + 181027 TATGTATACAAGAGCGCTCATCCTTAG -s simCow_chr6.simCow.chr6 582022 26 + 602619 TAGGTATACTAAAAGGCC-TCTTCTTG -s simDog_chr6.simDog.chr6 573737 25 + 593897 CAGGTATGCTAAAGGGCCATTCCC--A -s simHuman_chr6.simHuman.chr6 576827 27 + 601863 TAAGTATACAAAAGGACCCATCTCTGG -s simMouse_chr6.simMouse.chr6 608604 24 + 636262 TATGTATACAAGAGCGC---CCCTTAG -s simRat_chr6.simRat.chr6 83158 27 - 647215 TATGTATATGAGACAGTTCATCCTTAG -s simRat_chr6.simRat.chr6 83005 27 - 647215 TATGTATAGGAGAAGGCCCATCCTAAG - -a -s simMouse_chr6.simMouse.chr6 608475 4 + 636262 ATAT -s Anc0.Anc0refChr3 206023 4 + 222631 TTAT -s Anc1.Anc1refChr1 45882 4 + 69767 TTAT -s Anc2.Anc2refChr1 123026 4 + 142988 TTAT -s mr.mrrefChr3 156418 4 + 181027 ATAT -s mr.mrrefChr3 156562 4 + 181027 CTAT -s simCow_chr6.simCow.chr6 582048 4 + 602619 TCAT -s simDog_chr6.simDog.chr6 573762 4 + 593897 TTAT -s simHuman_chr6.simHuman.chr6 576854 4 + 601863 TTAT -s simMouse_chr6.simMouse.chr6 608638 4 + 636262 CTAT -s simRat_chr6.simRat.chr6 83185 4 - 647215 CTAT -s simRat_chr6.simRat.chr6 83032 4 - 647215 ATAA - -a -s simMouse_chr6.simMouse.chr6 608479 5 + 636262 AAGTA -s Anc0.Anc0refChr3 206028 5 + 222631 GCATT -s Anc1.Anc1refChr1 45887 5 + 69767 GCATT -s Anc2.Anc2refChr1 123031 5 + 142988 GCATT -s mr.mrrefChr3 156422 5 + 181027 AAGTA -s mr.mrrefChr3 156566 5 + 181027 GTGTA -s simCow_chr6.simCow.chr6 582053 5 + 602619 GCATC -s simDog_chr6.simDog.chr6 573767 5 + 593897 GCATT -s simHuman_chr6.simHuman.chr6 576859 5 + 601863 GCATT -s simMouse_chr6.simMouse.chr6 608642 5 + 636262 GTGTA -s simRat_chr6.simRat.chr6 83189 5 - 647215 GTGTA -s simRat_chr6.simRat.chr6 83036 5 - 647215 AAGTA - -a -s simMouse_chr6.simMouse.chr6 608484 43 + 636262 GAACAGACTGCCTGTCCGACTGCATTGCTTCCAGAGAAAGAAC -s mr.mrrefChr3 156427 36 + 181027 GAACAG--TGCCTG---GACTGCA--GCTTCCAGAGAAAGAAC -s simRat_chr6.simRat.chr6 83041 36 - 647215 GAACAG--TGCATA---GCTTGCA--GTTTCCAGAGAAAGATC - -a -s simMouse_chr6.simMouse.chr6 608558 1 + 636262 T -s Anc0.Anc0refChr3 205944 1 + 222631 T -s Anc1.Anc1refChr1 45803 1 + 69767 T -s Anc2.Anc2refChr1 122947 1 + 142988 T -s mr.mrrefChr3 156494 1 + 181027 T -s simCow_chr6.simCow.chr6 581967 1 + 602619 T -s simDog_chr6.simDog.chr6 573681 1 + 593897 T -s simRat_chr6.simRat.chr6 83117 1 - 647215 T - -a -s simMouse_chr6.simMouse.chr6 608566 5 + 636262 AATCA - -a -s simMouse_chr6.simMouse.chr6 608581 14 + 636262 AGTAGTCACACTAT -s Anc0.Anc0refChr3 205973 14 + 222631 TATAAACAAACCAT -s Anc1.Anc1refChr1 45832 14 + 69767 TATAAACAAACCAT -s Anc2.Anc2refChr1 122976 14 + 142988 TATAAATAAACCAT -s mr.mrrefChr3 156512 14 + 181027 AGTAGTCACACTAT -s simCow_chr6.simCow.chr6 581996 13 + 602619 TATGAATAAACCA- -s simDog_chr6.simDog.chr6 573710 14 + 593897 TATAAATAGACTGT -s simHuman_chr6.simHuman.chr6 576804 14 + 601863 TATAAACAAACCAT -s simRat_chr6.simRat.chr6 83135 14 - 647215 AGTAGTTACACTAT - -a -s simMouse_chr6.simMouse.chr6 608628 10 + 636262 CTAGTGTAGA - -a -s simMouse_chr6.simMouse.chr6 608647 42 + 636262 GAGTAGACTGTCTGTCCAATCTGCACTGCTTGCAGTTTCCAG -s Anc0.Anc0refChr3 206033 42 + 222631 CAGTTGACTGTCTGTTCAATCCACACTCTTTGCAGTTTCCAG -s Anc1.Anc1refChr1 45892 42 + 69767 CAGTTGACTGTCTGTTCAATCCACACTCTTTGCAGTTTCCAG -s Anc2.Anc2refChr1 123036 42 + 142988 CAGTAGACTATCTGTTCAATTTGCACTCTTTGCAGTTTTCTG -s mr.mrrefChr3 156571 42 + 181027 GAGTTGACTGTCTGTCCAATCCACACTGCTTGCAGTTTCCAG -s simCow_chr6.simCow.chr6 582058 42 + 602619 CAGTAGACTATCTGTTCAGTTTGCCCTCCTTGCAGTTTTCCA -s simDog_chr6.simDog.chr6 573772 42 + 593897 CAATAGATTATCTGTTCAATTTGCACTCTTTGCAGTTCTCTG -s simHuman_chr6.simHuman.chr6 576864 42 + 601863 CAGTTGACTGTCTGATCAACCCACACTTTCTGCAGTTTCCAG -s simRat_chr6.simRat.chr6 83194 42 - 647215 GAGTTAACTGTCTGTCCAATCCACACTGCGTGTAGTTTCCAG - -a -s simMouse_chr6.simMouse.chr6 608689 2 + 636262 AA -s Anc0.Anc0refChr3 206075 2 + 222631 AA -s Anc1.Anc1refChr1 45934 2 + 69767 AA -s Anc2.Anc2refChr1 123078 2 + 142988 AA -s mr.mrrefChr3 156613 2 + 181027 AA -s simCow_chr6.simCow.chr6 582100 2 + 602619 AG -s simDog_chr6.simDog.chr6 573814 2 + 593897 GA -s simHuman_chr6.simHuman.chr6 576906 2 + 601863 AA -s simRat_chr6.simRat.chr6 83239 2 - 647215 AA - -a -s simMouse_chr6.simMouse.chr6 608691 8 + 636262 GATCACGC -s Anc0.Anc0refChr3 206078 8 + 222631 GATCAGTC -s Anc1.Anc1refChr1 45937 8 + 69767 GATCAGTC -s Anc2.Anc2refChr1 123081 8 + 142988 GATCAGTT -s mr.mrrefChr3 156615 8 + 181027 GATCAGGC -s simCow_chr6.simCow.chr6 582103 7 + 602619 GA-CAGTT -s simDog_chr6.simDog.chr6 573817 6 + 593897 GATCAG-- -s simHuman_chr6.simHuman.chr6 576909 8 + 601863 GATCAGTC -s simRat_chr6.simRat.chr6 83241 8 - 647215 GATCAGGC - -a -s simMouse_chr6.simMouse.chr6 608699 33 + 636262 TACTCATCACCTGGTGAGCACAAGTTGGCAGAT -s Anc0.Anc0refChr3 206086 32 + 222631 CTCTCTTAACTTGGA-ATTACAAGTCAGCAGAC -s Anc1.Anc1refChr1 45945 33 + 69767 CTCTCTTAACTTGGAGATTACAAGTCAGCAGAC -s Anc2.Anc2refChr1 123089 32 + 142988 CTCTCTTAAATTACA-ATTATAAGTCAGCAGAC -s mr.mrrefChr3 156623 33 + 181027 CACTCATCACTTGGTGAGCACAAGTTGGCAGAT -s simCow_chr6.simCow.chr6 582124 32 + 602619 CTCTCTTAAATTACA-ATTATAAGTCAGCAGAC -s simDog_chr6.simDog.chr6 573823 6 + 593897 ---------------------------GCACCC -s simHuman_chr6.simHuman.chr6 576917 33 + 601863 CTCTCTTGACTTGGAGATTACAAACCAGCAGAC -s simRat_chr6.simRat.chr6 83249 30 - 647215 CAC---TCACTTGTCAAGCACAATTTGGCACAT - -a -s simMouse_chr6.simMouse.chr6 608732 2 + 636262 TT -s Anc0.Anc0refChr3 206118 2 + 222631 TT -s Anc1.Anc1refChr1 45978 2 + 69767 TT -s Anc2.Anc2refChr1 123121 2 + 142988 TT -s mr.mrrefChr3 156656 2 + 181027 TT -s simCow_chr6.simCow.chr6 582161 2 + 602619 TT -s simDog_chr6.simDog.chr6 573829 2 + 593897 TT -s simHuman_chr6.simHuman.chr6 576950 2 + 601863 TT -s simRat_chr6.simRat.chr6 83279 2 - 647215 TT - -a -s simMouse_chr6.simMouse.chr6 608734 57 + 636262 CATAGCTCGAGTTATGAATAGGTAGCATCCTTAAGTTCAATTAGACTCCTCTTTGCC -s Anc0.Anc0refChr3 206120 55 + 222631 TGTAACCCAACCAATGAATA-GTAGCATCATTGTATTAAATTG-ATTCCTATTTGCC -s Anc1.Anc1refChr1 45980 56 + 69767 TGTAACCCAACCAATGAATA-GTAGCATCATTGTATTAAATTGGATTCCTATTTGCC -s Anc2.Anc2refChr1 123123 55 + 142988 GGTGACCCAACCAATGAATA-ATAGCATCATTGTATTAAATTG-ATTCCTATTTGCC -s mr.mrrefChr3 156658 56 + 181027 TATAACTCAAGTTATGAATA-GTAGCATCATTAAGTTCAATTGGACTCCTCTTTGCC -s simCow_chr6.simCow.chr6 582163 55 + 602619 TGTGACCCAACCAATGTATA-TTAACATCATTGTATTAAATTG-GTTACCATTTGCC -s simDog_chr6.simDog.chr6 573831 45 + 593897 GGTGACCCAACCAACAAATA-ATAGTCT----------AATTG-ATTCCTATTTGCT -s simHuman_chr6.simHuman.chr6 576954 56 + 601863 TGTAACCTAATCAATGAATA-GTAGCATCATTTTATTAAATTGCATTCCTATTTGCC -s simRat_chr6.simRat.chr6 83281 54 - 647215 TATAACTCAAGTTATGAATA-GTAGCATCACTAGTTTCAATTGGC--TCCCTTTGCC - -a -s simMouse_chr6.simMouse.chr6 608791 14 + 636262 AAAACTGATGCTAT -s Anc0.Anc0refChr3 206175 14 + 222631 AGTACTGGTACCCT -s Anc1.Anc1refChr1 46036 14 + 69767 AGTACTGGTACCCT -s Anc2.Anc2refChr1 123178 14 + 142988 AGTACTGGTACCCT -s mr.mrrefChr3 156714 14 + 181027 AAAACTGATGCTAT -s simCow_chr6.simCow.chr6 582219 14 + 602619 AGTACTGGTACCCT -s simDog_chr6.simDog.chr6 573876 14 + 593897 AGTTCTGGTACCCT -s simHuman_chr6.simHuman.chr6 577010 14 + 601863 AGTACTGGTACCGT -s simRat_chr6.simRat.chr6 83335 14 - 647215 AAGACTGATGCTAT - -a -s simMouse_chr6.simMouse.chr6 608805 22 + 636262 TCTCAGTAACATACTCACAGCA -s Anc0.Anc0refChr3 206189 22 + 222631 TCTCAGTACCATACTCATAGGA -s Anc1.Anc1refChr1 46050 22 + 69767 TCTCAGTACCATACTCATAGGA -s Anc2.Anc2refChr1 123192 22 + 142988 TCTCAGTACCATACTGATATGA -s mr.mrrefChr3 156728 22 + 181027 TCTCAGTACCATACTCACAGCA -s simCow_chr6.simCow.chr6 582233 22 + 602619 CCCCTGAACCATACCAACATTG -s simDog_chr6.simDog.chr6 573890 22 + 593897 TCTCAGTAAGGTACTGGTATGA -s simHuman_chr6.simHuman.chr6 577025 22 + 601863 TCTCAGTACCATACTCATAGGA -s simRat_chr6.simRat.chr6 83349 22 - 647215 TCTTAGGACCATACTCACAGCA - -a -s simMouse_chr6.simMouse.chr6 608827 3 + 636262 TGA -s Anc0.Anc0refChr3 206211 3 + 222631 TGC -s Anc1.Anc1refChr1 46072 3 + 69767 TGC -s Anc2.Anc2refChr1 123215 3 + 142988 TGC -s mr.mrrefChr3 156750 3 + 181027 TGA -s simCow_chr6.simCow.chr6 582256 3 + 602619 TGC -s simDog_chr6.simDog.chr6 573913 3 + 593897 TAC -s simHuman_chr6.simHuman.chr6 577047 3 + 601863 TGC -s simRat_chr6.simRat.chr6 83371 3 - 647215 TGA - -a -s simMouse_chr6.simMouse.chr6 608830 97 + 636262 CCATATATGGGCTGTAATTGCACAAATTGTTATAGGCCCTGTTTGAATCACATTTCAAAGTTCAAGACTGGTGGCCCAATTTGCTGGCTGCTATCTT -s Anc0.Anc0refChr3 206215 61 + 222631 CTA---------AGTGAAAACAAAAAATGTTATAGGCCCTGCTTAAGTGACATTTTAAGGCTC---AC------------------------ATCTT -s Anc1.Anc1refChr1 46076 64 + 69767 CTA---------AGTGAAAACAAAAAATGTTATAGGCCCTGCTTAAGTGACATTTTAAGGCTCTATAC------------------------ATCTT -s Anc2.Anc2refChr1 123219 61 + 142988 CTA---------ATTGAAAACAAAATATGTTATAGCCCCTGCTTAAGTGACATTTTATGGCTC---AC------------------------ATCTT -s mr.mrrefChr3 156754 97 + 181027 CCATATATGGGCTGTAATAACAAAAATTGTTATAGGCCCTGCTTGAATGACATTTCAAAGTTCAAGACTGGTGGCCCAATTTGCTGGCTGCTATCTT -s simCow_chr6.simCow.chr6 582260 54 + 602619 CTA---------AATGAAAATAAAAGACATTA-------TGCCTAAGTGACATTTTATGGCTC---AC------------------------ATCCT -s simDog_chr6.simDog.chr6 573917 57 + 593897 CTA---------ATTGTAAACAAACTTTGTTATAGCCCCCACTTAAATGACATTTTATGG-------A------------------------ATCTT -s simHuman_chr6.simHuman.chr6 577051 64 + 601863 CTA---------AGTCAAAACAAGAAATTTTATGGGCCCTGCTTAAGTGACCCTTTAAGGCTTTATAC------------------------ATCTT -s simRat_chr6.simRat.chr6 83375 97 - 647215 CCGTATATAGGCTGTAATAATGAAAATTGTTATAGGCCCTGCTTGAATGACATCTCAAAGTTCAAGACCGGTGGCCTAATTTGCTGGTTGCTATCTT - -a -s simMouse_chr6.simMouse.chr6 608927 39 + 636262 AGCCACTGATCTGTTGATGTGCAACACTGCTTGAAACTA -s Anc0.Anc0refChr3 206277 33 + 222631 AAGTAGTAATGTTTTG----TCAAAACT--TAGGACCTT -s Anc1.Anc1refChr1 46141 33 + 69767 AAGTAGTAATGTTTTG----TCAAAACT--TAGGACCTT -s Anc2.Anc2refChr1 123281 33 + 142988 AAGTAGTAGTGTTTTG----TCAAAACT--TAGGACCCT -s mr.mrrefChr3 156851 39 + 181027 AGCCACTGATCTGTTGATGTGCAACACTGCTCGAAACTA -s simCow_chr6.simCow.chr6 582322 33 + 602619 AAGTAGTAGTGTTCTG----TCAAGACT--TAGGACCCT -s simDog_chr6.simDog.chr6 573975 33 + 593897 AAGTAGTAGTGTTTTG----TTAGAACC--TAAAACCCT -s simHuman_chr6.simHuman.chr6 577116 33 + 601863 AAGTAGTAAAGTTTTG----TCAAAATT--TGGGCCCTT -s simRat_chr6.simRat.chr6 83472 39 - 647215 AGACACTCATCGATTGATGTGCAACACTGCTCCAAACTA - -a -s simMouse_chr6.simMouse.chr6 608966 57 + 636262 AGCAACTTGCTCAGTAATGTACAACCCTAGGGTATAATCACACTTCTGTGCTGCTAA -s Anc0.Anc0refChr3 206310 55 + 222631 AG--GTTGGCTGGATGAAGTAAAACCCTAGGGTTTGGTTACACTTCTATGCTTCTGG -s Anc1.Anc1refChr1 46174 57 + 69767 AGCAGTTGGCTGGATGAAGTAAAACCCTAGGGTTTGGTTACACTTCTATGCTTCTGG -s Anc2.Anc2refChr1 123314 55 + 142988 AG--GTTGGCTGGAGGAAGTAAAACCCTAGGGTTTGGTTACAATTTTATGCTTCTGG -s mr.mrrefChr3 156890 57 + 181027 AGCAACTTGCTCAGTAATGTACAACCCTAGGGTATAATCACACTTCTGTGCTGCTAA -s simCow_chr6.simCow.chr6 582356 55 + 602619 AG--GTTGGCTGAGGGAAATAAAACCCTAGGGTCTGGTTACAATGTTATGGTTCTGA -s simDog_chr6.simDog.chr6 574008 55 + 593897 AG--GTTATATGGAGGAGGTATAACCCTAGGGTTCGGTGACAATTTTATGCTTCTGG -s simHuman_chr6.simHuman.chr6 577149 56 + 601863 AGCAG-TGGCTGGATTAAGTGAAACCCTTGGGTTTGGCTACACTTCCTTGCTTCTGG -s simRat_chr6.simRat.chr6 83511 57 - 647215 AGCAACTTGCTCAGTAATGTATGACCCTAGGGTACAATCACACTTCAGTGCTGCTAA - -a -s simMouse_chr6.simMouse.chr6 609023 13 + 636262 TACCGTGTCAGTG -s Anc0.Anc0refChr3 206365 13 + 222631 TATTGTGCCAGTG -s Anc1.Anc1refChr1 46231 13 + 69767 TATTGTGCCAGTG -s Anc2.Anc2refChr1 123369 13 + 142988 TATTGTGCCAGTG -s mr.mrrefChr3 156947 13 + 181027 TACTGTGCCAGTG -s simCow_chr6.simCow.chr6 582411 13 + 602619 TATTGTGCCAGTT -s simDog_chr6.simDog.chr6 574072 13 + 593897 TATCATGCCAGTG -s simHuman_chr6.simHuman.chr6 577205 13 + 601863 TATTGTACCAGTG -s simRat_chr6.simRat.chr6 83568 13 - 647215 TACTGTGCCAGTG - -a -s simMouse_chr6.simMouse.chr6 609036 5 + 636262 CCTAT -s Anc0.Anc0refChr3 206378 5 + 222631 CATAT -s Anc1.Anc1refChr1 46244 5 + 69767 CATAT -s Anc2.Anc2refChr1 123382 5 + 142988 CATAT -s mr.mrrefChr3 156960 5 + 181027 CCTAT -s simCow_chr6.simCow.chr6 582425 5 + 602619 CATGT -s simDog_chr6.simDog.chr6 574085 5 + 593897 TAAAT -s simHuman_chr6.simHuman.chr6 577218 5 + 601863 CATAT -s simRat_chr6.simRat.chr6 83581 5 - 647215 ATTAT - -a -s simMouse_chr6.simMouse.chr6 609041 9 + 636262 TCCCCCCAG -s Anc0.Anc0refChr3 206383 9 + 222631 TCTCCCCAG -s Anc1.Anc1refChr1 46249 9 + 69767 TCTCCCCAG -s Anc2.Anc2refChr1 123387 9 + 142988 TCTCACCAG -s mr.mrrefChr3 156965 9 + 181027 TCCCCCCAG -s simCow_chr6.simCow.chr6 582430 9 + 602619 TCCCATCAG -s simDog_chr6.simDog.chr6 574091 9 + 593897 TCTCACCAG -s simHuman_chr6.simHuman.chr6 577223 9 + 601863 TCTCCCCAG -s simRat_chr6.simRat.chr6 83586 9 - 647215 TCCCCCCAA - -a -s simMouse_chr6.simMouse.chr6 609050 42 + 636262 TATTTCCTTGGTGATCTGCTGGCTATAGGGTGTGCCCCATAA -s Anc0.Anc0refChr3 206392 40 + 222631 TATTTTCTTGGTGATCTGCAGGGTATAGG--GTACCCCATAA -s Anc1.Anc1refChr1 46258 40 + 69767 TATTTTCTTGGTGATCTGCAGGGTATAGG--GTACCCCATAA -s Anc2.Anc2refChr1 123403 40 + 142988 TATTTTCTTGGTGATCCACAGGGTATAGG--GTACCCCATAA -s mr.mrrefChr3 156974 42 + 181027 TATTTCCTTGGTGATCTGCTGGCTATAGGGTGTACCCCATAA -s simCow_chr6.simCow.chr6 582454 39 + 602619 CACTTTCTTGGTAATCCTCAGGATATAAG--GTACCCCACA- -s simDog_chr6.simDog.chr6 574107 40 + 593897 TATTTTCTTGGTGAACCATAGGGTATAGG--GCACTCCATAA -s simHuman_chr6.simHuman.chr6 577232 40 + 601863 TATTATCTTGGTGATCTGCGAGGTATAGG--GTACCCCAGAA -s simRat_chr6.simRat.chr6 83595 42 - 647215 TATTTCCTTGGTGATCTACTGGCTATAAGGTCTACCCCATAA - -a -s simMouse_chr6.simMouse.chr6 609092 27 + 636262 TTACACATAAAACGTGTCTAAAAACTT -s Anc0.Anc0refChr3 206432 26 + 222631 ATACAAAT-AAATGCGTCTACAAGTTT -s Anc1.Anc1refChr1 46298 26 + 69767 ATACAAAT-AAATGCGTCTACAAGTTT -s Anc2.Anc2refChr1 123443 26 + 142988 ATACAAAT-GAATGCGTCTACAAGTTC -s mr.mrrefChr3 157016 27 + 181027 TTACACATAAAATGTGTCTACAAACTT -s simCow_chr6.simCow.chr6 582493 24 + 602619 --ACACAT-GAGTGTGTCTACAAGTTT -s simDog_chr6.simDog.chr6 574148 26 + 593897 ATACAAAT-GAATGCGTCTACAAGTTC -s simHuman_chr6.simHuman.chr6 577272 22 + 601863 ATACATAT-AGATACGTCTACA----T -s simRat_chr6.simRat.chr6 83637 27 - 647215 TTACACATGAAATGTGTCTACAAATTT - -a -s simMouse_chr6.simMouse.chr6 609119 41 + 636262 AGCTTTACTTGGCACCAGCAGCCCCTCTTGGACGAGGCGAC -s Anc0.Anc0refChr3 206458 41 + 222631 GTTTTTACCTGACACCAATAACGGCTTAGGAACCAGGTGAT -s Anc1.Anc1refChr1 46324 41 + 69767 GTTTTTACCTGACACCAATAACGGCTTAGGAACCAGGTGAT -s Anc2.Anc2refChr1 123470 41 + 142988 GTTTTTACCTGACCCCAATAACGGCTTAGGAACCAGGTGAT -s mr.mrrefChr3 157043 41 + 181027 AGCTTTACTTGGCACCAGCAACCCCTCTGGGACGAGGTGAT -s simCow_chr6.simCow.chr6 582518 37 + 602619 GTTTTTACCTGGCCCGAATAACAGCTCAGGGA----GTGAT -s simDog_chr6.simDog.chr6 574175 41 + 593897 GTTCTTACTTGACCTCAATGATGGCTTAGGAACCAGGTGTT -s simHuman_chr6.simHuman.chr6 577294 41 + 601863 GTTTTTACCTATCACCAATAACTACTAAGGAGACAGGTGAT -s simRat_chr6.simRat.chr6 83664 39 - 647215 AGCTTTCCTTGG-CCCAGCAA-CCCTCTGGGACGATATAAT - -a -s simMouse_chr6.simMouse.chr6 609160 9 + 636262 AACTTGGTC -s Anc0.Anc0refChr3 206499 9 + 222631 ATTTTTGTC -s Anc1.Anc1refChr1 46365 9 + 69767 ATTTTTGTC -s Anc2.Anc2refChr1 123511 9 + 142988 ATTTTTGTC -s mr.mrrefChr3 157084 9 + 181027 AACTTGGTC -s simCow_chr6.simCow.chr6 582555 9 + 602619 ATTTTTGTC -s simDog_chr6.simDog.chr6 574216 9 + 593897 ATTTGTGTC -s simHuman_chr6.simHuman.chr6 577335 9 + 601863 TTTATTGTC -s simRat_chr6.simRat.chr6 83704 9 - 647215 AACTCGGTC - -a -s simMouse_chr6.simMouse.chr6 609169 55 + 636262 AAAACAACATAATCTAAAGAGGACTCAAATGACCATGTGTCAGGTATGAGGCTTC -s Anc0.Anc0refChr3 206508 43 + 222631 AAAACCATACAATCTAAAGAGGG-TGCAATATGCATATAACAGG----------- -s Anc1.Anc1refChr1 46374 44 + 69767 AAAACCATACAATCTAAAGAGGGCTGCAATATGCATATAACAGG----------- -s Anc2.Anc2refChr1 123520 43 + 142988 AAAACCATACTATCTAAAGAGGG-TGCCAGATGCACATCACAAG----------- -s mr.mrrefChr3 157093 55 + 181027 AAAACAATATAATCTAAAGAGGACTCAAATGACCATGTATCAGGTATGAGGCTTC -s simCow_chr6.simCow.chr6 582564 43 + 602619 AAAGCCATATTAGGTAATTAGGG-TTCCAGGTGCTCATGACAAC----------- -s simDog_chr6.simDog.chr6 574225 43 + 593897 AAAACCACACTATCTTAAGAGGG-TGCCAGATGAACATCACAAG----------- -s simHuman_chr6.simHuman.chr6 577344 44 + 601863 AAAACCATACAATCTAGAGAGGGCTGCATTATGCATATAACAGG----------- -s simRat_chr6.simRat.chr6 83721 55 - 647215 ATAACTATAAAATTTAAAGAGGACTCAAATGACCATGTATCAGGTATGAGGCTTC - -a -s simMouse_chr6.simMouse.chr6 609342 1 + 636262 C - -a -s simMouse_chr6.simMouse.chr6 609359 15 + 636262 TCCGACTTATCACAT -s mr.mrrefChr3 157282 15 + 181027 TCCGACTTATCACAT -s simRat_chr6.simRat.chr6 83912 15 - 647215 CCCAACTTATCACAC - -a -s simMouse_chr6.simMouse.chr6 609403 1 + 636262 A - -a -s simMouse_chr6.simMouse.chr6 609420 1 + 636262 G - -a -s simMouse_chr6.simMouse.chr6 609453 80 + 636262 TCTCCATGTCTGTATAACTAATAAGGGACTAGTTTAATTGTTCTAACATGGTCAGTAAAGAGACGCAGAGACAAGACCCT -s Anc0.Anc0refChr3 206551 79 + 222631 CATGCATCTCTGTATAACAAATAAGGTATTAGCTTAAG-GTTCTGACATGACCAGTAATTAGACATAAACAAAAGACTAC -s Anc1.Anc1refChr1 46418 79 + 69767 CATGCATCTCTGTATAACAAATAAGGTATTAGCTTAAG-GTTCTGACATGACCAGTAATTAGACATAAACAAAAGACTAC -s Anc2.Anc2refChr1 123563 79 + 142988 CATGCGTCTTTGTATAACAGATAAGGTATTAGCTTTAG-GTTCTGGCATGCCCAGTAATTAAACATCAACAAAAAACTAC -s mr.mrrefChr3 157374 80 + 181027 TCTCCATGTCTGTATAACTAATAAGGGACTAGTTTAATTGTTCTAACATGATCAGTAAAGAGACACAGAGACAAGACCCT -s simCow_chr6.simCow.chr6 582607 78 + 602619 CATGCTTATGTATATAACATATGAGGACCTGGCTTTAG-CTTCGGGCATGCCCA-TAGTTAAACATGAACAAAGATCTAC -s simDog_chr6.simDog.chr6 574268 78 + 593897 CTTCCGTCTTCGTATAACAGATAGGGTATTAGCTCTAA-GTTCTGGCATGCTGAGTAATTAATTACCAACCAAAAACTA- -s simHuman_chr6.simHuman.chr6 577388 78 + 601863 CATGCATCTCTGTATAACAAATAAGA-AGTAGCTTAAG-ATTCTGACATGACCAGGAAGTAGACATAAGCAGAAGACTGC -s simRat_chr6.simRat.chr6 84009 80 - 647215 TCTCCATGTCTGTATAGCTGATAGCAGACCAGTTCTATTGTTCTAATATTATCAGTAAAGAGACACAGAGACAAGACCCT - -a -s simMouse_chr6.simMouse.chr6 609533 124 + 636262 ACTGTCTCTATCCCGTTAATTGTTCATGGTGGGCGAGACATAACAATGATACCTTGCGGCAGTTGTTTATGAAGAGGGCTTAGTATACATGCCCTGATATTACTTACACTTTGGGAGGAGCCTT -s Anc0.Anc0refChr3 206630 116 + 222631 ACTTTC-CTTTCCCATCATCCATACACGGTCGGCAAGAC----TGATGATACC---TGGCAGTTATTTATCAAAGGAGATTGGTGCACATGATCTGATATTATTCACATGTAGGCAGGTGTATT -s Anc1.Anc1refChr1 46497 116 + 69767 ACTTTC-CTTTCCCATCATCCATACACGGTCGGCAAGAC----TGATGATACC---TGGCAGTTATTTATCAAAGGAGATTGGTGCACATGATCTGATATTATTCACATGTAGGCAGGTGTATT -s Anc2.Anc2refChr1 123642 116 + 142988 ACTTTT-CTTTCCCATCATCCATACACGGTCGGCAAAAC----TGATGACACC---AGGCAGTCATTTATCAAAGAAGATTGGTGCACATGATCTGATATTATTCACATGTAGGCAGGTGTATT -s mr.mrrefChr3 157454 124 + 181027 ACTGTCTCTATCCCATTAACTGTACATGGTGGGCGAGACATAACAATGATACCTTGTGGCAGTTGTTTATGAAGAGGGCTTAGTATACATGCTCTGATATTACTTACACTTTGGCAGGAGCCTT -s simCow_chr6.simCow.chr6 582703 116 + 602619 ACTTTT-CTTTCCCATCGTTCATACACGGTGGGCAAAAC----TCTTGACACC---AGGCACTCATGTGTCCAGGTGGATTCGTGCACATGATCAGATGTTATTCCCATGTAGGCAGTGGTTTT -s simDog_chr6.simDog.chr6 574346 95 + 593897 ----------------AATC-----AAGGTCGGCAAAAC----TGATGACACC----AGCAGTCATTTATCAAAGAAGATTGCTGCACATGATCTGATACTATTCATATGTGGGCAGGTGTATT -s simHuman_chr6.simHuman.chr6 577466 116 + 601863 GCTTTC-CTTTCCCATCATCATTATACATTCGGCAAGAC----TGATGATACC---TGGCATTTATTTATCAAAGGAGGCTGGTGCACCCCATCTGATTTTATTAGCATGTAGGCAGGTGTGTT -s simRat_chr6.simRat.chr6 84089 121 - 647215 ATTGTCTCTATCTCATTAACTATACATGGTGGGCGAGACATAACAATGA---ATTTTGGCAGTTGTTCATGTAGAGTGCTTAGTAGACATGCTCTGCTATTACTGACACTATGGCAGGAGCCTT - -a -s simMouse_chr6.simMouse.chr6 609657 103 + 636262 GTGCAGGTGCTTCTGGCGACTGGTGTTTTGTGGCTTGTGTTGATTAGCACTTTGTTCCCTAAGTTGATAATACAGGCAGTTTCATGACATGTGGCAGATATCT -s Anc0.Anc0refChr3 206752 103 + 222631 GTGTGGGTGCATCTGGTATCTGGTGTTTTGTTGCCTCAGTTGATTAGCATCTCGTTGCCTTTGTTGATTGCACAGGTAAATACATGACATCTGCCAGATATCT -s Anc1.Anc1refChr1 46619 103 + 69767 GTGTGGGTGCATCTGGTATCTGGTGTTTTGTTGCCTCAGTTGATTAGCATCTCGTTGCCTTTGTTGATTGCACAGGTAAATACATGACATCTGCCAGATATCT -s Anc2.Anc2refChr1 123764 103 + 142988 GTATGGGTGCATCTGGTGTCTGGTGTTTTGTTGCGTCAGTTGATTGGCATCTCGTTGCCTTTGTTGATTGCACAGATAAATACATGGTGTCTGCCAGATATCT -s mr.mrrefChr3 157578 103 + 181027 GTGCAGGTGCTTCTGGCAACTGGTGTTTTGTTGCCTGTGTTGATTAGCACCTTGTTCCCTTAGTTGATAATACAGGCAATTTCATGACATGTGGCAGATATCT -s simCow_chr6.simCow.chr6 582825 103 + 602619 GTATGGGTGCATCTGGTGTCTGTTGATTTGTTGCTGCAGTAGATTGACATCTCGTTGCCTTAGGTGATTGCACACCTAAATCCATGGAGGCTGCCACAAATCT -s simDog_chr6.simDog.chr6 574447 103 + 593897 GTATGGATGCCTCTGGTGTCCGGTGTTTTGTTCTGTTAGCTGATTGGCATCTTGTTGCCTCTGTTGATTGCACAGATAAATACATGGTGTCTGCCAGATGTCT -s simHuman_chr6.simHuman.chr6 577588 103 + 601863 GTGTGGGTGCATCTGGTATCTGGTGCTTTGTTGCCTCAGTCGATCAGTATCTCGTTGCCTTGGTTGATTGCACAGGTAAGTACATTACATCTACCAGATATCT -s simRat_chr6.simRat.chr6 84210 101 - 647215 GTGCAGGTGCTTCTGGCAACTGGTGTTCTGTTGCCTGTGTTGA-TAGAACCTTGTTCCCTTAGTTGATAA-ACAGGCAATTTCATGACATGTGGCAGATATCT - -a -s simMouse_chr6.simMouse.chr6 609760 83 + 636262 GCCCTGCAAGCCATCTATGTCTTTGCATCCCCTAATATTAGACATTCACACACAACTATTGATCTTGGTGACGATGGCCTTTA -s Anc0.Anc0refChr3 206855 73 + 222631 GCCAAATAAACCATCCAT-TCTTTGTATCCCTCAACATTACACATTCATACACAAATA-TGGTCTT--------TGGCCCCTA -s Anc1.Anc1refChr1 46722 73 + 69767 GCCAAATAAACCATCCAT-TCTTTGTATCCCTCAACATTACACATTCATACACAAATA-TGGTCTT--------TGGCCCCTA -s Anc2.Anc2refChr1 123867 73 + 142988 GCCAAACAACCCATCCAT-TCTTTGTATCCCTCAACTTTACACATTCATACACAAATA-TGGTTCT--------TGGGCCCTA -s mr.mrrefChr3 157681 73 + 181027 GCCCTGTAAACCATCTAT-TCTTTGCATCCCCTAATATTAGACATTCACACACAACTA-TGATCTT--------TGGCCTTTA -s simCow_chr6.simCow.chr6 582929 73 + 602619 ACCAAACAACTCATCCAT-TCTTAGTATCCCTCAATGTTACGCATTTAAATACAAATA-TGGTTCT--------TGGGCCCTA -s simDog_chr6.simDog.chr6 574550 64 + 593897 GCCAAACAGCCCATCCAT-GCTTTGTATCCCTCACCTTTATA----CATGCACAAATA-CGGTTCT--------T-----CTA -s simHuman_chr6.simHuman.chr6 577691 73 + 601863 GCCAAATTAACCATTCAT-TCTTTGTATCCCTCAACATTGCAAATTCATACACAAGTA-TGGTCTT--------TGGCCCCTA -s simRat_chr6.simRat.chr6 84311 38 - 647215 GCCCTGTAAACCATCTAT-TCTTTGCATCCCCTCATATT-------------------------------------------- - -a -s simMouse_chr6.simMouse.chr6 609843 9 + 636262 CCTGGAGGC -s Anc0.Anc0refChr3 206933 9 + 222631 CCTAGAAGC -s Anc1.Anc1refChr1 46800 9 + 69767 CCTAGAAGC -s Anc2.Anc2refChr1 123945 9 + 142988 CTTAGAAGC -s mr.mrrefChr3 157754 9 + 181027 CCTGGAGGC -s simCow_chr6.simCow.chr6 583008 9 + 602619 CTTAGAAGC -s simDog_chr6.simDog.chr6 574623 9 + 593897 CTTAGAAGC -s simHuman_chr6.simHuman.chr6 577769 9 + 601863 CCTAGAAAC -s simRat_chr6.simRat.chr6 84349 1 - 647215 --------C - -a -s simMouse_chr6.simMouse.chr6 609852 34 + 636262 AGCCGTACAGACAAGTCAAGGCCAACGTGTTTTC -s Anc0.Anc0refChr3 206944 33 + 222631 ATTTCTACAGACAAGTCAAATTCAGCATATTCT- -s Anc1.Anc1refChr1 46811 34 + 69767 ATTTCTACAGACAAGTCAAATTCAGCATATTCTA -s Anc2.Anc2refChr1 123956 33 + 142988 TTTTCTACAGACAAGTAAAGTTCAGCATATTCT- -s mr.mrrefChr3 157763 34 + 181027 AGCCGTACAGACAAGTCAAAGCCAACATGTTCTC -s simCow_chr6.simCow.chr6 583019 33 + 602619 TTTTCTAGTGACAAGTGAAGTTCAGCATATTCT- -s simDog_chr6.simDog.chr6 574634 33 + 593897 TTTGCTCCAGACGAGCAAAGTTCAGCATATTCT- -s simHuman_chr6.simHuman.chr6 577780 34 + 601863 ATTTCTACAGACAAGTCAGAATCAGCATATTCTA -s simRat_chr6.simRat.chr6 84350 34 - 647215 AGCCGTCCAGACAAATCAAAGCCAACATGTTCTC - -a -s simMouse_chr6.simMouse.chr6 609886 97 + 636262 CTATCTCAAGAGAGGATTTTGGAGTCTGCACAGGTGTCCTAACAATGAACTCACACAATCTCCCATCATTCAATCTTTTGCTTAGCCTTTTGCCTGG -s Anc0.Anc0refChr3 206977 93 + 222631 ----CTTGAGTGAGAATTTAGGAGTCTTTACAGGTGTCCTAACAATGAACTCACACAATTTTCCATTATTCAATCTTTTGCTCGGACTACCACTTGG -s Anc1.Anc1refChr1 46845 97 + 69767 TTATCTTGAGTGAGAATTTAGGAGTCTTTACAGGTGTCCTAACAATGAACTCACACAATTTTCCATTATTCAATCTTTTGCTCGGACTACCACTTGG -s Anc2.Anc2refChr1 123989 93 + 142988 ----CTTGAGTGAGAATTCAGGAGTCTTTATGAGTGTCCTAATAATGAACCCACACAATTTTCCATTGTTCAATTTTTTGCTCGGACTACCACTTTG -s mr.mrrefChr3 157797 97 + 181027 TTATCTCAAGAGAGGATTTTGGAGTCTGTACAGGTGTCCTAACAATGAACTCACACAATCTCCCATCATTCAATCTTTTGCTCAGACTTTTGCCTGG -s simCow_chr6.simCow.chr6 583052 93 + 602619 ----CTTGAGGGAAAATTCAGGAGTATGTATGAGTGTCCTAATAATAAACGCACACGATTTTCCATAGTCCAATTCTTTGCTCGGCCTTCCACTTAT -s simDog_chr6.simDog.chr6 574667 86 + 593897 ----CTAGAATGAGGC-------ATCATAGTGAGTGTCCCAATGATGAGCCCACACAATGTCCCATTGTTCAATTTTTCACTTGGACTACCACTTTG -s simHuman_chr6.simHuman.chr6 577814 91 + 601863 TTATCTTGAGTGGGAATTTGCGGGTCTTTACAGGTGTTCTAACAATGAACTCACACAATTTTCCATTATTCAATCTTTTGCCCT------CACTTGG -s simRat_chr6.simRat.chr6 84386 96 - 647215 TTATCTC-AGCGAGGATTTTGGAGTCTGTACAGGTGTGCTAGCAATGAACTCACACAATCTCCCATCATTCAATCTTTTGCTCAGACTTTTGCCTGG - -a -s simMouse_chr6.simMouse.chr6 609983 9 + 636262 TTGTCAAGC -s Anc0.Anc0refChr3 207073 9 + 222631 TTGTCAATA -s Anc1.Anc1refChr1 46945 9 + 69767 TTGTCAATA -s Anc2.Anc2refChr1 124085 9 + 142988 TTGTCAATA -s mr.mrrefChr3 157894 9 + 181027 TTGTCAAGA -s simCow_chr6.simCow.chr6 583148 9 + 602619 TTCTCAATA -s simDog_chr6.simDog.chr6 574756 8 + 593897 TTGTCGAT- -s simHuman_chr6.simHuman.chr6 577908 9 + 601863 TTGTCAATA -s simRat_chr6.simRat.chr6 84482 8 - 647215 TTA-CAAGA - -a -s simMouse_chr6.simMouse.chr6 609992 15 + 636262 CTCTTCATTGAAAAT -s Anc0.Anc0refChr3 207082 15 + 222631 GATTTCATGGAAATT -s Anc1.Anc1refChr1 46954 15 + 69767 GATTTCATGGAAATT -s Anc2.Anc2refChr1 124094 15 + 142988 GATTTCATGGAAATA -s mr.mrrefChr3 157903 15 + 181027 CATTTCATTGAAAAT -s simCow_chr6.simCow.chr6 583158 15 + 602619 GATTTCATTGAAATC -s simDog_chr6.simDog.chr6 574764 13 + 593897 --CTCCATGGAAATA -s simHuman_chr6.simHuman.chr6 577917 15 + 601863 GATTTCATGGGAATT -s simRat_chr6.simRat.chr6 84490 15 - 647215 CATTTCATTGAAAGT - -a -s simMouse_chr6.simMouse.chr6 610007 30 + 636262 GACAAGTGTATGATTAGGTTCCCCGTACCA -s Anc0.Anc0refChr3 207098 30 + 222631 GACAAATACATGCTCAGGTTCCGCGTACCA -s Anc1.Anc1refChr1 46970 30 + 69767 GACAAATACATGCTCAGGTTCCGCGTACCA -s Anc2.Anc2refChr1 124110 30 + 142988 GTCAAATACATGCTCAGTTTTTGAGTACCA -s mr.mrrefChr3 157918 30 + 181027 GACAAGTGCATGCTTAGGTTCCCCGTACCA -s simCow_chr6.simCow.chr6 583174 30 + 602619 ATCAAATACATGCTCAGATTTTGTGTGTCA -s simDog_chr6.simDog.chr6 574778 30 + 593897 GTCAAATACATGCTCAGTCTTTGAGTACCA -s simHuman_chr6.simHuman.chr6 577933 30 + 601863 GACAAATACATGCTCAGGTTCCACACACCA -s simRat_chr6.simRat.chr6 84505 30 - 647215 GACAAGTGCATGCCTAGGTTCCCTGTACCA - -a -s simMouse_chr6.simMouse.chr6 610037 15 + 636262 TATCACCAGGTGGTG -s Anc0.Anc0refChr3 207129 15 + 222631 CATGACTAGCAGATG -s Anc1.Anc1refChr1 47001 15 + 69767 CATGACTAGCAGATG -s Anc2.Anc2refChr1 124141 15 + 142988 CATGACTGGCAGATG -s mr.mrrefChr3 157948 15 + 181027 CATCACTAGGTGGTG -s simCow_chr6.simCow.chr6 583205 15 + 602619 CGGGACTGCCGGATG -s simDog_chr6.simDog.chr6 574809 15 + 593897 CATGACTGGCAGATG -s simHuman_chr6.simHuman.chr6 577964 15 + 601863 CATGACTAGCAGATA -s simRat_chr6.simRat.chr6 84535 15 - 647215 CATCACTGGGTGGTG - -a -s simMouse_chr6.simMouse.chr6 610052 3 + 636262 ACT -s Anc0.Anc0refChr3 207144 2 + 222631 AC- -s Anc1.Anc1refChr1 47016 3 + 69767 ACT -s Anc2.Anc2refChr1 124156 2 + 142988 AC- -s mr.mrrefChr3 157963 3 + 181027 ACT -s simCow_chr6.simCow.chr6 583221 2 + 602619 AT- -s simDog_chr6.simDog.chr6 574824 2 + 593897 AC- -s simHuman_chr6.simHuman.chr6 577979 3 + 601863 ACT -s simRat_chr6.simRat.chr6 84550 3 - 647215 ACT - -a -s simMouse_chr6.simMouse.chr6 610055 45 + 636262 CAACTATTCAGTTACCTGTTCAATTCAAGCCAGGCTCAAGCTAAT -s Anc0.Anc0refChr3 207146 44 + 222631 CAACTGTTCATTTACCTATTCATTCC-AGCCAGGCTCAAATTTGT -s Anc1.Anc1refChr1 47019 44 + 69767 CAACTGTTCATTTACCTATTCATTCC-AGCCAGGCTCAAATTTGT -s Anc2.Anc2refChr1 124158 44 + 142988 CAACTGATCATTTACCTATTCATTCA-AGCCAGGCTCAAATTTGT -s mr.mrrefChr3 157966 45 + 181027 CAACTATTCAGTTACCTGTTCATTCCAAGCCAGGCTCAAGCTAAT -s simCow_chr6.simCow.chr6 583223 44 + 602619 CAACTGCTCAATTACCTATTCATCCA-AACCAGACTCAAATTTGA -s simDog_chr6.simDog.chr6 574826 42 + 593897 AAACTGATCATTTACCTATTCATTCA-AGC--GGCTCAAATTTGT -s simHuman_chr6.simHuman.chr6 577996 44 + 601863 CAACAGTTCACTTACCTATTCATTCC-AGCCAGGTTCAGATTGGT -s simRat_chr6.simRat.chr6 84553 36 - 647215 CAACTATTCAGTTACCTGTTTATTCGAGGC---------GCTTAT - -a -s simMouse_chr6.simMouse.chr6 610100 13 + 636262 GGGAGTCTACATG -s Anc0.Anc0refChr3 207190 13 + 222631 GGGGGCCTGCAGG -s Anc1.Anc1refChr1 47063 13 + 69767 GGGGGCCTGCAGG -s Anc2.Anc2refChr1 124202 13 + 142988 GGGGGCCTGCAGG -s mr.mrrefChr3 158011 13 + 181027 GGGAGTCTACATG -s simCow_chr6.simCow.chr6 583267 7 + 602619 GGGGGTC------ -s simDog_chr6.simDog.chr6 574868 13 + 593897 GGGGACCTGCAGG -s simHuman_chr6.simHuman.chr6 578042 13 + 601863 GGGGGCCCGCGGG -s simRat_chr6.simRat.chr6 84589 13 - 647215 GGGAGTCTACATG - -a -s simMouse_chr6.simMouse.chr6 610113 37 + 636262 TCTGTGGCTTTGTTTATACTCCTCTTGGTTTTAAATG -s Anc0.Anc0refChr3 207204 37 + 222631 CCTGTGGCTTTGTATTTCATCCTCTTGGTTTTAACTG -s Anc1.Anc1refChr1 47077 37 + 69767 CCTGTGGCTTTGTATTTCATCCTCTTGGTTTTAACTG -s Anc2.Anc2refChr1 124216 37 + 142988 CCTGTGGCTCTACATTTCATCCTCTTGGTTTCAACTG -s mr.mrrefChr3 158024 37 + 181027 GCTGTGGCTTTGTTTATACTCCTCTTGGTTTTAAATG -s simCow_chr6.simCow.chr6 583275 37 + 602619 CCTGTGGCTCTCAATCTTGTCCTCTTGGTTTCAATTG -s simDog_chr6.simDog.chr6 574882 37 + 593897 ACTGTGGCTCAACATTTCACCCTCTTGGTATCAACTG -s simHuman_chr6.simHuman.chr6 578056 37 + 601863 CCTGTGGCTTTGTATTCCATCCTCTTGGTTTTAACCA -s simRat_chr6.simRat.chr6 84602 37 - 647215 GCTGTGGCTCTGTTTATAGTCCTCTTGGATTTAGGTG - -a -s simMouse_chr6.simMouse.chr6 610150 27 + 636262 AATGGGGATCCTGACCTTCTCAGTTTC -s Anc0.Anc0refChr3 207241 19 + 222631 AG--------ATGGCCTTCTCAGCTTT -s Anc1.Anc1refChr1 47114 19 + 69767 AG--------ATGGCCTTCTCAGCTTT -s Anc2.Anc2refChr1 124253 19 + 142988 AG--------ATAGCCTTCTCAGCTTT -s mr.mrrefChr3 158061 27 + 181027 AATGGGGATCCTGACCTTCTCAGTTTC -s simCow_chr6.simCow.chr6 583313 19 + 602619 AA--------GTAGCCTCCTTGCCTTA -s simDog_chr6.simDog.chr6 574919 19 + 593897 AG--------ATAGCATTCTCAGTTTT -s simHuman_chr6.simHuman.chr6 578093 19 + 601863 AG--------ATGGCCTTCCCAGCACT -s simRat_chr6.simRat.chr6 84639 27 - 647215 AATGGGGATCCTGACCTTCTCAGTTTG - -a -s simMouse_chr6.simMouse.chr6 610177 9 + 636262 GTGAAACCT -s Anc0.Anc0refChr3 207260 9 + 222631 GCAAAACCT -s Anc1.Anc1refChr1 47133 9 + 69767 GCAAAACCT -s Anc2.Anc2refChr1 124272 9 + 142988 GCAAAACCT -s mr.mrrefChr3 158088 9 + 181027 GTGAAACCT -s simCow_chr6.simCow.chr6 583334 9 + 602619 ATAAAGACT -s simDog_chr6.simDog.chr6 574938 9 + 593897 GCATCACTT -s simHuman_chr6.simHuman.chr6 578112 9 + 601863 GCAAATCCT -s simRat_chr6.simRat.chr6 84666 9 - 647215 GTCAAACTT - -a -s simMouse_chr6.simMouse.chr6 610186 13 + 636262 ACTTGGAGCACTA -s Anc0.Anc0refChr3 207270 13 + 222631 ACTTGAAGCACTA -s Anc1.Anc1refChr1 47143 13 + 69767 ACTTGAAGCACTA -s Anc2.Anc2refChr1 124288 13 + 142988 ACTATGAGCACTA -s mr.mrrefChr3 158098 13 + 181027 ACTTGAAGCACTA -s simCow_chr6.simCow.chr6 583353 13 + 602619 ACTATGAGCACCA -s simDog_chr6.simDog.chr6 574954 13 + 593897 ACCATGAGCACTA -s simHuman_chr6.simHuman.chr6 578122 13 + 601863 ACTTGAAGTACTA -s simRat_chr6.simRat.chr6 84676 13 - 647215 ACTTGAAGCACTT - -a -s simMouse_chr6.simMouse.chr6 610199 5 + 636262 TTGCT -s Anc0.Anc0refChr3 207283 5 + 222631 TTGCT -s Anc1.Anc1refChr1 47156 5 + 69767 TTGCT -s Anc2.Anc2refChr1 124301 5 + 142988 TTGCT -s mr.mrrefChr3 158111 5 + 181027 TTGCT -s simCow_chr6.simCow.chr6 583367 5 + 602619 TTGCA -s simDog_chr6.simDog.chr6 574967 5 + 593897 TTGCT -s simHuman_chr6.simHuman.chr6 578135 5 + 601863 TTGCT -s simRat_chr6.simRat.chr6 84689 5 - 647215 TTGCT - -a -s simMouse_chr6.simMouse.chr6 610204 5 + 636262 TATAA -s Anc0.Anc0refChr3 207289 5 + 222631 TATAC -s Anc1.Anc1refChr1 47162 5 + 69767 TATAC -s Anc2.Anc2refChr1 124307 5 + 142988 TATAC -s mr.mrrefChr3 158116 5 + 181027 TATAA -s simCow_chr6.simCow.chr6 583373 5 + 602619 TATAC -s simDog_chr6.simDog.chr6 574973 5 + 593897 TATAC -s simHuman_chr6.simHuman.chr6 578141 5 + 601863 TATAC -s simRat_chr6.simRat.chr6 84694 5 - 647215 TAAAT - -a -s simMouse_chr6.simMouse.chr6 610209 15 + 636262 TTACAGCTTCCATGA -s Anc0.Anc0refChr3 207294 14 + 222631 TTACAGCTT-CCTGA -s Anc1.Anc1refChr1 47167 14 + 69767 TTACAGCTT-CCTGA -s Anc2.Anc2refChr1 124314 14 + 142988 TTACAGCTT-CCTGA -s mr.mrrefChr3 158121 14 + 181027 TTACAGCTT-CATGA -s simCow_chr6.simCow.chr6 583380 13 + 602619 TTACATCTT-CC-GA -s simDog_chr6.simDog.chr6 574980 14 + 593897 TTAGAGCTT-TATGA -s simHuman_chr6.simHuman.chr6 578146 14 + 601863 TTACAGCCT-CCTGA -s simRat_chr6.simRat.chr6 84699 14 - 647215 TAACAGCTT-CATGA - -a -s simMouse_chr6.simMouse.chr6 610224 21 + 636262 TCCAAAATCACAATCAGGTGA -s Anc0.Anc0refChr3 207311 21 + 222631 TTTAAAACCACATTCATGTAG -s Anc1.Anc1refChr1 47184 21 + 69767 TTTAAAACCACATTCATGTAG -s Anc2.Anc2refChr1 124331 21 + 142988 TTTAAAACCACATTCATGTAG -s mr.mrrefChr3 158135 21 + 181027 TTCAAAATCACAATCAGGTAA -s simCow_chr6.simCow.chr6 583396 21 + 602619 ATTATAACCACATTCATGTAG -s simDog_chr6.simDog.chr6 574997 21 + 593897 TTTGAAATCACATTTCTGTAG -s simHuman_chr6.simHuman.chr6 578163 21 + 601863 TTTACAACCACATTCATGTAG -s simRat_chr6.simRat.chr6 84713 21 - 647215 CTCAAGATCACACTCAGGGAA - -a -s simMouse_chr6.simMouse.chr6 610245 3 + 636262 CAC -s Anc0.Anc0refChr3 207332 3 + 222631 TGA -s Anc1.Anc1refChr1 47205 3 + 69767 TGA -s Anc2.Anc2refChr1 124352 3 + 142988 TGA -s mr.mrrefChr3 158156 3 + 181027 CAC -s simCow_chr6.simCow.chr6 583420 3 + 602619 TGA -s simDog_chr6.simDog.chr6 575018 3 + 593897 TGC -s simHuman_chr6.simHuman.chr6 578184 3 + 601863 TGA -s simRat_chr6.simRat.chr6 84734 3 - 647215 CCC - -a -s simMouse_chr6.simMouse.chr6 610248 5 + 636262 CTCCA -s Anc0.Anc0refChr3 207335 5 + 222631 CACCA -s Anc1.Anc1refChr1 47208 5 + 69767 CACCA -s Anc2.Anc2refChr1 124355 5 + 142988 CACCG -s mr.mrrefChr3 158159 5 + 181027 CACCA -s simDog_chr6.simDog.chr6 575021 5 + 593897 CACCG -s simHuman_chr6.simHuman.chr6 578187 5 + 601863 CACCA -s simRat_chr6.simRat.chr6 84752 5 - 647215 CACGA - -a -s simMouse_chr6.simMouse.chr6 610253 71 + 636262 CTGGAGTATCACCAGGTTCAAATACGATTACAATCATCTTTATGGATTACCTGTGTTTGTGACACAGTATA -s Anc0.Anc0refChr3 207341 29 + 222631 TTGTAGTATTACAAG-TTTGAGTATAAT-----------------------------------------CA -s Anc1.Anc1refChr1 47214 30 + 69767 TTGTAGTATTACAAGGTTTGAGTATAAT-----------------------------------------CA -s Anc2.Anc2refChr1 124361 29 + 142988 TCATAGTATTACAAG-TTTAAGTATAAT-----------------------------------------CA -s mr.mrrefChr3 158164 71 + 181027 CTGGAGTATTACAAGGTTCGAATATAATTACAATCATCTTTATGGATTACCTGTGTTTGTGACACAGTATA -s simCow_chr6.simCow.chr6 583423 1 + 602619 ----------------------------------------------------------------------A -s simDog_chr6.simDog.chr6 575027 29 + 593897 TCATAGTATTACAAG-TTTAAGTATAAT-----------------------------------------CA -s simHuman_chr6.simHuman.chr6 578193 30 + 601863 TTGCTGTATTACAAGGTTGGAGCATAAT-----------------------------------------GA -s simRat_chr6.simRat.chr6 84757 71 - 647215 CTGGAGCATTACAAGATTCGAATATAATTACAATCATCTTTATGGAGTACCTGTGTTTGTGACAGGGTATA - -a -s simMouse_chr6.simMouse.chr6 610324 2 + 636262 TG -s Anc0.Anc0refChr3 207430 2 + 222631 TG -s Anc1.Anc1refChr1 47304 2 + 69767 TG -s Anc2.Anc2refChr1 124450 2 + 142988 TG -s mr.mrrefChr3 158295 2 + 181027 TG -s simDog_chr6.simDog.chr6 575119 2 + 593897 TG -s simHuman_chr6.simHuman.chr6 578283 2 + 601863 TC -s simRat_chr6.simRat.chr6 84911 2 - 647215 TG - -a -s simMouse_chr6.simMouse.chr6 610326 14 + 636262 CTGATGTTTAATGT -s Anc0.Anc0refChr3 207432 14 + 222631 CGAGTGTAACATGT -s Anc1.Anc1refChr1 47306 14 + 69767 CGAGTGTAACATGT -s Anc2.Anc2refChr1 124452 14 + 142988 TGAGTGTAACATGC -s mr.mrrefChr3 158297 14 + 181027 CTGATGTTTAGTGT -s simCow_chr6.simCow.chr6 583450 2 + 602619 ------------GG -s simDog_chr6.simDog.chr6 575121 14 + 593897 TGAGTGTAACATGC -s simHuman_chr6.simHuman.chr6 578285 14 + 601863 CAAGGAAGACATGT -s simRat_chr6.simRat.chr6 84924 14 - 647215 CTGATGTTTAGTTT - -a -s simMouse_chr6.simMouse.chr6 610340 44 + 636262 TAATGTCTAATTAAATTAACTAACCAAGAGGTCTGAAGTGGTCC -s Anc0.Anc0refChr3 207447 44 + 222631 TGGTGTTTAATTAAATGAAATAACTAAGAGGTTTGAACTGGTCA -s Anc1.Anc1refChr1 47321 44 + 69767 TGGTGTTTAATTAAATGAAATAACTAAGAGGTTTGAACTGGTCA -s Anc2.Anc2refChr1 124467 44 + 142988 TGGTGTTCAATTAAATGAAATGACTAAGAGGTTTGAACTGGTCA -s mr.mrrefChr3 158311 44 + 181027 TAATGTCTAATTAAATTAAATAACTAAGAGGTTTGAAGTGGTCA -s simCow_chr6.simCow.chr6 583453 44 + 602619 TCGTGTTGAATTTAGTGAAATGACCCAGAGGCTGGGACTGACCG -s simDog_chr6.simDog.chr6 575136 44 + 593897 TGGTGTTCATTTAAATGAAATGACTAAGATGTTTGAACTAGTCA -s simHuman_chr6.simHuman.chr6 578300 44 + 601863 TGGTGTTTAATTAAATGAAATAAATAAGAGGTTTGAACTGGTCA -s simRat_chr6.simRat.chr6 84938 44 - 647215 TAATCTCTAATTAAATTAAATAACTAAGAGGTTTGAAGTGGTCA - -a -s simMouse_chr6.simMouse.chr6 610384 46 + 636262 ATCATCAGTTCCCTTGTCTTAGGTGTGGATCATACTCATATGCAGA -s Anc0.Anc0refChr3 207498 41 + 222631 ATTGTCAGTTCCCTTGTCTGAGGTGTGGATCTCGCTCATAT----- -s Anc1.Anc1refChr1 47372 45 + 69767 ATTGTCAGTTCCCTTGTCTGAGGTGTGGATCTCGCTCATAT-CTGA -s Anc2.Anc2refChr1 124518 41 + 142988 ATTGTCAGTTCCCTTGTCTGAGGTGTGAATCTCGCTCATAT----- -s mr.mrrefChr3 158362 46 + 181027 ATTATCAGTTCCCTTGTCTTAGGTGTGGATCATACTCATATGCAGA -s simCow_chr6.simCow.chr6 583504 41 + 602619 ATTGTCAGTTCCCTTGTCTCAGAAGTGCATCTCACTCATAT----- -s simDog_chr6.simDog.chr6 575187 41 + 593897 ATTATCAGTTACCTTGGCTGAGGTGTGAATCTTGCTTATAT----- -s simHuman_chr6.simHuman.chr6 578351 45 + 601863 ACTGTTAGTTCCCTAGTTTGAGGTGTGGATCTCGCACATAT-CTGA -s simRat_chr6.simRat.chr6 84989 46 - 647215 ATTATCAGTTCTCTTGTCTCAGGCGTGGGTCGTACTCATATGCGGA - -a -s simMouse_chr6.simMouse.chr6 610430 54 + 636262 CATACTTTGTATTTGAACCCAGAGTACATATAACGTTCATCTGCTACCCCTGCC -s Anc0.Anc0refChr3 207539 43 + 222631 ----------ACTTGAATGCAGAGTATACACTATATTCATCTGCTACT-CTGCC -s Anc1.Anc1refChr1 47417 49 + 69767 TAAA----GTACTTGAATGCAGAGTATACACTATATTCATCTGCTACT-CTGCC -s Anc2.Anc2refChr1 124559 43 + 142988 ----------ACTTGAATGTAGAGTATACACTATATTCATCTGCTACC-CTGCC -s mr.mrrefChr3 158408 54 + 181027 CAGACTTTGTATTTGAACCCAGAGTACATACAACATTCATCTGCTACTCCTGCC -s simCow_chr6.simCow.chr6 583545 42 + 602619 ----------ACTTGACTGTAGAGTAAATTC-ATATTCAACTTCTACA-CTGCC -s simDog_chr6.simDog.chr6 575228 42 + 593897 ----------GCTCAAATGTAGAGTATGCACTGTATTCAT-TGCTATC-CTGCC -s simHuman_chr6.simHuman.chr6 578396 49 + 601863 TAAA----GTACTTGAATGCGGAGTATAGACTATATTCATCTGCTACT-CTGCC -s simRat_chr6.simRat.chr6 85082 54 - 647215 CGGACTGTGTATTTGAACTCAGAGTACACACAACATTCGTCTGCTACTCCTGCC - -a -s simMouse_chr6.simMouse.chr6 610484 1 + 636262 T -s Anc0.Anc0refChr3 207584 1 + 222631 T -s Anc1.Anc1refChr1 47468 1 + 69767 T -s Anc2.Anc2refChr1 124604 1 + 142988 T -s mr.mrrefChr3 158462 1 + 181027 T -s simCow_chr6.simCow.chr6 583589 1 + 602619 T -s simDog_chr6.simDog.chr6 575272 1 + 593897 T -s simHuman_chr6.simHuman.chr6 578447 1 + 601863 T -s simRat_chr6.simRat.chr6 85136 1 - 647215 T - -a -s simMouse_chr6.simMouse.chr6 610485 5 + 636262 GATAT -s Anc0.Anc0refChr3 207585 5 + 222631 CATAT -s Anc1.Anc1refChr1 47469 5 + 69767 CATAT -s Anc2.Anc2refChr1 124610 5 + 142988 CATAT -s mr.mrrefChr3 158463 5 + 181027 GATAT -s simCow_chr6.simCow.chr6 583595 5 + 602619 CATAT -s simDog_chr6.simDog.chr6 575278 5 + 593897 CATAT -s simHuman_chr6.simHuman.chr6 578448 5 + 601863 CATAC -s simRat_chr6.simRat.chr6 85137 5 - 647215 GGTAT - -a -s simMouse_chr6.simMouse.chr6 610490 10 + 636262 ACAAGTGTGA -s Anc0.Anc0refChr3 207590 10 + 222631 ATAAGTGTAT -s Anc1.Anc1refChr1 47474 10 + 69767 ATAAGTGTAT -s Anc2.Anc2refChr1 124615 10 + 142988 ACAAGTGTAT -s mr.mrrefChr3 158468 10 + 181027 ATAAGTGTGA -s simCow_chr6.simCow.chr6 583603 10 + 602619 ACAAGTGTAT -s simDog_chr6.simDog.chr6 575283 10 + 593897 ACAAGTGTAT -s simHuman_chr6.simHuman.chr6 578453 10 + 601863 ATAAGTCTAT -s simRat_chr6.simRat.chr6 85142 10 - 647215 ATGAGTGTGG - -a -s simMouse_chr6.simMouse.chr6 610500 15 + 636262 TTGAACCTAGGGCTG -s Anc0.Anc0refChr3 207600 13 + 222631 TTGAGCCTC--TCTG -s Anc1.Anc1refChr1 47484 13 + 69767 TTGAGCCTC--TCTG -s Anc2.Anc2refChr1 124625 13 + 142988 TCGAGCCTC--TCTG -s mr.mrrefChr3 158478 15 + 181027 TTGAGCCTAGGGCTG -s simCow_chr6.simCow.chr6 583613 13 + 602619 TGGAGACTC--TCTG -s simDog_chr6.simDog.chr6 575295 13 + 593897 TCGGGCCTT--CCTA -s simHuman_chr6.simHuman.chr6 578463 13 + 601863 TTGAGCCTC--TCTG -s simRat_chr6.simRat.chr6 85152 15 - 647215 TCAAGCCTTGGGCTG - -a -s simMouse_chr6.simMouse.chr6 610515 1 + 636262 A -s Anc0.Anc0refChr3 207613 1 + 222631 A -s Anc1.Anc1refChr1 47497 1 + 69767 A -s Anc2.Anc2refChr1 124638 1 + 142988 A -s mr.mrrefChr3 158493 1 + 181027 A -s simCow_chr6.simCow.chr6 583629 1 + 602619 A -s simDog_chr6.simDog.chr6 575308 1 + 593897 A -s simHuman_chr6.simHuman.chr6 578476 1 + 601863 C -s simRat_chr6.simRat.chr6 85167 1 - 647215 A - -a -s simMouse_chr6.simMouse.chr6 610516 5 + 636262 CTGTC -s Anc0.Anc0refChr3 207614 5 + 222631 CTGTC -s Anc1.Anc1refChr1 47498 5 + 69767 CTGTC -s Anc2.Anc2refChr1 124644 5 + 142988 CTGTC -s mr.mrrefChr3 158494 5 + 181027 CTGTC -s simCow_chr6.simCow.chr6 583635 5 + 602619 CTATC -s simDog_chr6.simDog.chr6 575314 5 + 593897 CTGTC -s simHuman_chr6.simHuman.chr6 578477 5 + 601863 GCACA -s simRat_chr6.simRat.chr6 85168 5 - 647215 CTGTG - -a -s simMouse_chr6.simMouse.chr6 610521 21 + 636262 TAATGTAAATGTAACCAACAG -s Anc0.Anc0refChr3 207619 21 + 222631 TACTGTAAATGTAACTCACAG -s Anc1.Anc1refChr1 47503 21 + 69767 TACTGTAAATGTAACTCACAG -s Anc2.Anc2refChr1 124656 21 + 142988 TACAGTAAATGTGACTCTCAG -s mr.mrrefChr3 158499 21 + 181027 TACTGTAAATGTAACCCACAG -s simCow_chr6.simCow.chr6 583647 18 + 602619 TTTGGTAAATGT---TCTCAA -s simDog_chr6.simDog.chr6 575326 21 + 593897 TACAGTAAGTGTGACTCTCAG -s simHuman_chr6.simHuman.chr6 578482 21 + 601863 GACTGCAAATATAGCTCACAG -s simRat_chr6.simRat.chr6 85173 21 - 647215 TACTGTAAATGTAACCCACAG - -a -s simMouse_chr6.simMouse.chr6 610542 11 + 636262 AAGTGAGCTCT -s Anc0.Anc0refChr3 207644 11 + 222631 GAGTGCGTTCT -s Anc1.Anc1refChr1 47528 11 + 69767 GAGTGCGTTCT -s Anc2.Anc2refChr1 124681 11 + 142988 GAGTGCGTTCT -s mr.mrrefChr3 158520 11 + 181027 AAGTGAGCTCT -s simCow_chr6.simCow.chr6 583669 11 + 602619 GACCAAGTTCT -s simDog_chr6.simDog.chr6 575351 11 + 593897 GGGTGCTTTCT -s simHuman_chr6.simHuman.chr6 578507 11 + 601863 GAGTGGGTCCT -s simRat_chr6.simRat.chr6 85194 11 - 647215 AAGTGAGCACT - -a -s simMouse_chr6.simMouse.chr6 610553 4 + 636262 GCCC -s Anc0.Anc0refChr3 207659 4 + 222631 GCCC -s Anc1.Anc1refChr1 47543 4 + 69767 GCCC -s Anc2.Anc2refChr1 124696 4 + 142988 GCCC -s mr.mrrefChr3 158531 4 + 181027 GCCC -s simCow_chr6.simCow.chr6 583684 4 + 602619 GCCC -s simDog_chr6.simDog.chr6 575366 4 + 593897 GCGC -s simHuman_chr6.simHuman.chr6 578522 4 + 601863 GCCT -s simRat_chr6.simRat.chr6 85205 4 - 647215 ACCC - -a -s simMouse_chr6.simMouse.chr6 610557 23 + 636262 CCAGTGTGCTGTCTCATGTGTGC -s Anc0.Anc0refChr3 207663 19 + 222631 CC--TCTCCAGTCTCATG--AGT -s Anc1.Anc1refChr1 47547 21 + 69767 CC--TCTCCAGTCTCATGTCAGT -s Anc2.Anc2refChr1 124700 19 + 142988 CC--TCTCCAGTCTCAGG--AGT -s mr.mrrefChr3 158535 23 + 181027 CCAGTGTCCAGTCTCATGTGTGC -s simCow_chr6.simCow.chr6 583742 19 + 602619 CC--TCTCCAGTCTCAGG--TGT -s simDog_chr6.simDog.chr6 575370 19 + 593897 CC--TCACCAGTGTCAGG--AGT -s simHuman_chr6.simHuman.chr6 578526 21 + 601863 CC--TCTCCAGTCTCATGTCATG -s simRat_chr6.simRat.chr6 85209 23 - 647215 CCGGTTCCCAGTGTCTGGTGTGC - -a -s simMouse_chr6.simMouse.chr6 610580 28 + 636262 TAACAGTGTTGCTTGGAACAAGACCCCC -s Anc0.Anc0refChr3 207682 28 + 222631 ATACATTGTTGGTTGGTGCAAGGCCCCC -s Anc1.Anc1refChr1 47568 28 + 69767 ATACATTGTTGGTTGGTGCAAGGCCCCC -s Anc2.Anc2refChr1 124719 28 + 142988 ATACATTGTTGGTTGGTGCAAGGCCCCC -s mr.mrrefChr3 158558 28 + 181027 TAACAGTGTTGCTTGGAGCAAGACCCCC -s simCow_chr6.simCow.chr6 583762 28 + 602619 CTAGATTGTTGGTTGTTGCAAGGCCCCA -s simDog_chr6.simDog.chr6 575389 28 + 593897 ATACATTGTTGGTTGGTGCGAGCCCCCC -s simHuman_chr6.simHuman.chr6 578547 28 + 601863 ATACATTGTTGGTTGGTGCAAGGCCCCC -s simRat_chr6.simRat.chr6 85232 28 - 647215 TGACAATGGTAATTGGAGCAAGATTCCC - -a -s simMouse_chr6.simMouse.chr6 610608 43 + 636262 ATTCAAGTTTCATATGCAGTATGTTGTCGATTGTTAGCAGCCA -s Anc0.Anc0refChr3 207710 43 + 222631 CTTCCAGTTTCAGGGGTGATATATCATTAGTTGTTGACAGCCA -s Anc1.Anc1refChr1 47596 43 + 69767 CTTCCAGTTTCAGGGGTGATATATCATTAGTTGTTGACAGCCA -s Anc2.Anc2refChr1 124747 43 + 142988 CTTCCAGTTTCAGGGGTGATATATCATTAGTTGTTGACAGACA -s mr.mrrefChr3 158586 43 + 181027 CTTCAAGTTTCAGATGCAGTATGTTGTTGATTGTTGGCAGCCA -s simCow_chr6.simCow.chr6 583790 43 + 602619 CTTCCAGTTTCAGGGGTGTTAGATCATTGGTTCCTGACAGACA -s simDog_chr6.simDog.chr6 575419 43 + 593897 CTTCCAGTTTCAGAGTTGATATCGCATCAGTTGTTGATGGACA -s simHuman_chr6.simHuman.chr6 578575 43 + 601863 CTTCCAGTTTCAGGGGTGATATATCATTAGTTGTTGACAACCA -s simRat_chr6.simRat.chr6 85260 43 - 647215 CTCCAAGTTTCAGATGCAGTATGTTGTTGATTGTTGGCAGACA - -a -s simMouse_chr6.simMouse.chr6 610651 42 + 636262 GCCTCCCGGTTTATGTGAGGAACTATAACTGTAAATCAATCT -s Anc0.Anc0refChr3 207753 41 + 222631 GCCTCTT-GTTTTAGTAAGGAACAACAAGGGTAAGTGTATCT -s Anc1.Anc1refChr1 47639 41 + 69767 GCCTCTT-GTTTTAGTAAGGAACAACAAGGGTAAGTGTATCT -s Anc2.Anc2refChr1 124790 41 + 142988 GCCTCTT-GTTTTAGTAAGGAACAACAAGGTTAAGTGTATCA -s mr.mrrefChr3 158629 42 + 181027 GCCTCCCGGTTTAAGTGAGGAACTATAACTGTAAGTCAATCT -s simCow_chr6.simCow.chr6 583833 41 + 602619 GCTTCTT-GATTTAGTAAGAAACAACAAGGTCAAAGGTATCA -s simDog_chr6.simDog.chr6 575462 41 + 593897 GCCCTTT-GTTTTAGTACGGACCAACAAGGTTGAGTGTAACA -s simHuman_chr6.simHuman.chr6 578619 41 + 601863 GCCTCTT-GTTCTAGTTAAGAACAACAAGGGTAAGTGTATCT -s simRat_chr6.simRat.chr6 85303 42 - 647215 GCCTCCCAGTTTAAGTAAGGAACTATAACTGTAAGTAAATCT - -a -s simMouse_chr6.simMouse.chr6 610693 7 + 636262 ATGCACA -s Anc0.Anc0refChr3 207796 7 + 222631 ATGCTCA -s Anc1.Anc1refChr1 47682 7 + 69767 ATGCTCA -s Anc2.Anc2refChr1 124874 7 + 142988 ATGCTGA -s mr.mrrefChr3 158671 7 + 181027 ATGCACA -s simCow_chr6.simCow.chr6 583926 7 + 602619 ATGGTGA -s simDog_chr6.simDog.chr6 575546 5 + 593897 AGGCT-- -s simHuman_chr6.simHuman.chr6 578662 7 + 601863 ATGCTCA -s simRat_chr6.simRat.chr6 85345 7 - 647215 ATGTATA - -a -s simMouse_chr6.simMouse.chr6 610700 15 + 636262 TAGAACGGTTTTATG -s Anc0.Anc0refChr3 207817 15 + 222631 TAGGACTGGCTTGTG -s Anc1.Anc1refChr1 47703 15 + 69767 TAGGACTGGCTTGTG -s Anc2.Anc2refChr1 124895 15 + 142988 TAGGGCTGGCTAGTG -s mr.mrrefChr3 158678 15 + 181027 TAGAACTGGTTTATG -s simCow_chr6.simCow.chr6 583947 15 + 602619 CAAGTCTGCCTAGTA -s simDog_chr6.simDog.chr6 575564 15 + 593897 TGGGGCTGGCTAGTG -s simHuman_chr6.simHuman.chr6 578683 15 + 601863 TAGCACTGGCTTGTG -s simRat_chr6.simRat.chr6 85352 15 - 647215 CAGAACTGGTTTATA - -a -s simMouse_chr6.simMouse.chr6 610715 27 + 636262 TCTTCGGTATTAATGTAGCAAGATGGT -s Anc0.Anc0refChr3 207844 22 + 222631 TTTGAGTTCTCAACATGGCAC-----T -s Anc1.Anc1refChr1 47730 22 + 69767 TTTGAGTTCTCAACATGGCAC-----T -s Anc2.Anc2refChr1 124922 22 + 142988 TTTGAGTTCTCAACATGGTAC-----A -s mr.mrrefChr3 158693 27 + 181027 TCTTCGGTCTTAATGTAGCAAGATGGT -s simCow_chr6.simCow.chr6 583974 22 + 602619 TTTGACTTCTCAACACGGTAC-----A -s simDog_chr6.simDog.chr6 575591 22 + 593897 TTTGAGTACTGAACATGGTGC-----A -s simHuman_chr6.simHuman.chr6 578710 22 + 601863 TTTGATCTCCCAACATGGCAC-----T -s simRat_chr6.simRat.chr6 85367 27 - 647215 TCTTCGGTCTTAATGTAGCAGGATGGT - -a -s simMouse_chr6.simMouse.chr6 610742 39 + 636262 GGTTCATGTGTTCAGTCAAAATGTAGCAGAATGTGAGTA -s Anc0.Anc0refChr3 207866 39 + 222631 GGTTAATGTGTTCAGTCATAATGTAACAGGATGTTAGTA -s Anc1.Anc1refChr1 47752 39 + 69767 GGTTAATGTGTTCAGTCATAATGTAACAGGATGTTAGTA -s Anc2.Anc2refChr1 124945 39 + 142988 GGTTAATGTGTTCAGTCATAATATAATAGCATGTTCGTA -s mr.mrrefChr3 158720 39 + 181027 GGTTCATGTGTTCAGTCATAATGTAGCAGGATGTGAGTA -s simCow_chr6.simCow.chr6 583997 39 + 602619 AGTTAACGCGTCCAGCCACAATATAAAAACATGTTGGTA -s simDog_chr6.simDog.chr6 575614 39 + 593897 GGTTAATGTATTCAGTCATGATATATTGGCATGTCCCTA -s simHuman_chr6.simHuman.chr6 578732 39 + 601863 CATTAATGTGCTCAGTCATAATGTAACAGGATGCTAGTA -s simRat_chr6.simRat.chr6 85394 39 - 647215 TGTTCATGTGATCGGTTATAACGTAGCAGGATGTGAGTA - -a -s simMouse_chr6.simMouse.chr6 610781 27 + 636262 AAAAGAGCCCCATTTCTAGTTTTTCCA -s Anc0.Anc0refChr3 207907 27 + 222631 GAAAGGGCCTCATTTGCAGTTCTTTTA -s Anc1.Anc1refChr1 47793 27 + 69767 GAAAGGGCCTCATTTGCAGTTCTTTTA -s Anc2.Anc2refChr1 124986 27 + 142988 GAAAGGGCCTCATTTGCAGGTCTTTTA -s mr.mrrefChr3 158759 27 + 181027 GAAAGAGCCCCATTTCTAGTTCTTCCA -s simCow_chr6.simCow.chr6 584038 23 + 602619 GATA--GCCTCATTTACAGGTCT--GA -s simDog_chr6.simDog.chr6 575655 27 + 593897 AAAAGGCCCTCATGTGTGGGTGTTTTA -s simHuman_chr6.simHuman.chr6 578773 27 + 601863 GAAAGGGCTTCATTTGCAGTTCTTATA -s simRat_chr6.simRat.chr6 85433 27 - 647215 GAGAGAGCCCCACTTCTAGTTCTTCCA - -a -s simMouse_chr6.simMouse.chr6 610808 1 + 636262 G -s Anc0.Anc0refChr3 207934 1 + 222631 G -s Anc1.Anc1refChr1 47820 1 + 69767 G -s Anc2.Anc2refChr1 125033 1 + 142988 G -s mr.mrrefChr3 158786 1 + 181027 G -s simCow_chr6.simCow.chr6 584081 1 + 602619 T -s simDog_chr6.simDog.chr6 575702 1 + 593897 G -s simHuman_chr6.simHuman.chr6 578800 1 + 601863 A -s simRat_chr6.simRat.chr6 85460 1 - 647215 G - -a -s simMouse_chr6.simMouse.chr6 610809 14 + 636262 ATTTTCATGGAAGC -s Anc0.Anc0refChr3 207935 14 + 222631 ATTAGCATCGAAAC -s Anc1.Anc1refChr1 47821 14 + 69767 ATTAGCATCGAAAC -s Anc2.Anc2refChr1 125034 14 + 142988 ATGAGCATCAAAAC -s mr.mrrefChr3 158787 14 + 181027 ATTTTCATGGAAGC -s simCow_chr6.simCow.chr6 584082 14 + 602619 ATGAGCATCAAGAC -s simDog_chr6.simDog.chr6 575703 14 + 593897 ATGAACATTATAAC -s simHuman_chr6.simHuman.chr6 578802 14 + 601863 ATTAGCATCGAAAC -s simRat_chr6.simRat.chr6 85461 14 - 647215 TTTTTCATGGTAGC - -a -s simMouse_chr6.simMouse.chr6 610823 3 + 636262 GAC -s Anc0.Anc0refChr3 207949 3 + 222631 AGC -s Anc1.Anc1refChr1 47835 3 + 69767 AGC -s Anc2.Anc2refChr1 125048 3 + 142988 AGC -s mr.mrrefChr3 158801 3 + 181027 GAC -s simCow_chr6.simCow.chr6 584096 3 + 602619 AGC -s simDog_chr6.simDog.chr6 575717 3 + 593897 AAC -s simHuman_chr6.simHuman.chr6 578816 3 + 601863 AGC -s simRat_chr6.simRat.chr6 85484 3 - 647215 GTC - -a -s simMouse_chr6.simMouse.chr6 610826 26 + 636262 AGGCATGCATTTCTAAAATCGATTAA -s Anc0.Anc0refChr3 207978 25 + 222631 GGGCATGAATTT-TCATATGAATTAA -s Anc1.Anc1refChr1 47864 25 + 69767 GGGCATGAATTT-TCATATGAATTAA -s Anc2.Anc2refChr1 125080 25 + 142988 GGGCATGAATTT-TCATATGAATTAA -s mr.mrrefChr3 158804 26 + 181027 AGGCATGCATTTCTAAAATCGATTAA -s simCow_chr6.simCow.chr6 584127 22 + 602619 TGGCTTGAATTT-TC---TGAATTAA -s simDog_chr6.simDog.chr6 575749 25 + 593897 GGGTATGAATTT-TGATATGAATTAA -s simHuman_chr6.simHuman.chr6 578859 25 + 601863 GGGCATGATTTT-TCATATTAATTAG -s simRat_chr6.simRat.chr6 85487 25 - 647215 AGGCATGTATTTACAAAAT-CATTAA - -a -s simMouse_chr6.simMouse.chr6 610852 4 + 636262 AAGT -s Anc0.Anc0refChr3 208010 4 + 222631 GATG -s Anc1.Anc1refChr1 47896 4 + 69767 GATG -s Anc2.Anc2refChr1 125112 4 + 142988 GATG -s mr.mrrefChr3 158830 4 + 181027 AATT -s simCow_chr6.simCow.chr6 584156 4 + 602619 GATG -s simDog_chr6.simDog.chr6 575781 4 + 593897 GATG -s simHuman_chr6.simHuman.chr6 578891 4 + 601863 GATG -s simRat_chr6.simRat.chr6 85512 4 - 647215 AATC - -a -s simMouse_chr6.simMouse.chr6 610856 15 + 636262 GGATGCAGCTAACTG -s Anc0.Anc0refChr3 208014 15 + 222631 GGATGAAGCTAACTT -s Anc1.Anc1refChr1 47900 15 + 69767 GGATGAAGCTAACTT -s Anc2.Anc2refChr1 125116 15 + 142988 GGATTAAGCTAACTT -s mr.mrrefChr3 158834 15 + 181027 GGATGCAGCTAACTG -s simCow_chr6.simCow.chr6 584163 11 + 602619 GGGTTTAGTTA---- -s simDog_chr6.simDog.chr6 575785 15 + 593897 GGATTAAGCCAACTT -s simHuman_chr6.simHuman.chr6 578895 15 + 601863 GGACGAAGCTAATTT -s simRat_chr6.simRat.chr6 85516 15 - 647215 GGGTGCAGCTAAGTG - -a -s simMouse_chr6.simMouse.chr6 610871 20 + 636262 GACAGTGTGGAAACTGCCTG -s Anc0.Anc0refChr3 208031 10 + 222631 AA----------ACTGCCCC -s Anc1.Anc1refChr1 47917 20 + 69767 AACAATGTGAAAACTGCCCC -s Anc2.Anc2refChr1 125133 10 + 142988 AA----------ACTGACCC -s mr.mrrefChr3 158851 20 + 181027 GACAGTGTGGAAACTGCCCC -s simCow_chr6.simCow.chr6 584174 10 + 602619 AA----------ACTGACCC -s simDog_chr6.simDog.chr6 575802 10 + 593897 AA----------ACTGAAAC -s simHuman_chr6.simHuman.chr6 578912 20 + 601863 AACAATGTGATAACTGCCCC -s simRat_chr6.simRat.chr6 85533 20 - 647215 GGCAGTGTGGGAACTGCCCC - -a -s simMouse_chr6.simMouse.chr6 610891 7 + 636262 TAGGGCG -s Anc0.Anc0refChr3 208049 7 + 222631 TAGGGAG -s Anc1.Anc1refChr1 47945 7 + 69767 TAGGGAG -s Anc2.Anc2refChr1 125151 7 + 142988 CAGAGAG -s mr.mrrefChr3 158879 7 + 181027 TAGGGAG -s simCow_chr6.simCow.chr6 584192 7 + 602619 CAGAGAG -s simDog_chr6.simDog.chr6 575820 7 + 593897 CAGATAG -s simHuman_chr6.simHuman.chr6 578940 7 + 601863 TAGGGAG -s simRat_chr6.simRat.chr6 85561 7 - 647215 TAGGGAG - -a -s simMouse_chr6.simMouse.chr6 610898 15 + 636262 GGAATGCCTACTGAC -s Anc0.Anc0refChr3 208056 10 + 222631 AG--TGTATACT--- -s Anc1.Anc1refChr1 47952 10 + 69767 AG--TGTATACT--- -s Anc2.Anc2refChr1 125158 10 + 142988 AG--TGTATACT--- -s mr.mrrefChr3 158886 12 + 181027 GGAATGCCTACT--- -s simCow_chr6.simCow.chr6 584200 10 + 602619 AG--GGTATACA--- -s simDog_chr6.simDog.chr6 575827 9 + 593897 -G--TTTATACT--- -s simHuman_chr6.simHuman.chr6 578947 10 + 601863 AG--TGTATACT--- -s simRat_chr6.simRat.chr6 85568 8 - 647215 GGCATG----CC--- - -a -s simMouse_chr6.simMouse.chr6 610913 11 + 636262 TAGATTGGAAT -s Anc0.Anc0refChr3 208066 11 + 222631 TGATGAGGAAG -s Anc1.Anc1refChr1 47962 11 + 69767 TGATGAGGAAG -s Anc2.Anc2refChr1 125168 11 + 142988 TGATGAGGAAG -s mr.mrrefChr3 158898 11 + 181027 TAGAGTGGAAT -s simCow_chr6.simCow.chr6 584210 10 + 602619 TGA-GAGGAGA -s simDog_chr6.simDog.chr6 575842 11 + 593897 TGATGAGGTAG -s simHuman_chr6.simHuman.chr6 578957 11 + 601863 TGATGAGGAAG -s simRat_chr6.simRat.chr6 85576 9 - 647215 TAGAGTGGA-- - -a -s simMouse_chr6.simMouse.chr6 610924 49 + 636262 TGACAATTTAGTCAAACTAACACTTTGCTGAAACATTTCGGTCCTCCAT -s Anc0.Anc0refChr3 208082 31 + 222631 TGACAATTTAAGCA---------TTCTCT-----TATCCA----TCCAT -s Anc1.Anc1refChr1 47978 36 + 69767 TGACAATTTAAGCA---------TTCTCTAACTTTATCCA----TCCAT -s Anc2.Anc2refChr1 125184 31 + 142988 TGACAATCTAAGTA---------TTCTCT-----TAGCCA----TCAAT -s mr.mrrefChr3 158909 36 + 181027 TGACAATTTAGTCA---------TTTTCTGAAACAATTCA----TCCAT -s simCow_chr6.simCow.chr6 584225 31 + 602619 TGACAATCTAAGTA---------ATCTAT-----TTGCCA----ACTCT -s simDog_chr6.simDog.chr6 575858 31 + 593897 TGACAATCTAAGTA---------TTCTCT-----TAGCTA----TAAAT -s simHuman_chr6.simHuman.chr6 578973 36 + 601863 TGACAACTTGAGCA---------TTCTCTAACTTCATCCA----TCCAC -s simRat_chr6.simRat.chr6 85585 21 - 647215 ------------------------TTTCTGAGACAATTCA----TCTAA - -a -s simMouse_chr6.simMouse.chr6 610973 1 + 636262 C -s Anc0.Anc0refChr3 208114 1 + 222631 C -s Anc1.Anc1refChr1 48015 1 + 69767 C -s Anc2.Anc2refChr1 125216 1 + 142988 C -s mr.mrrefChr3 158945 1 + 181027 C -s simCow_chr6.simCow.chr6 584257 1 + 602619 C -s simDog_chr6.simDog.chr6 575890 1 + 593897 C -s simHuman_chr6.simHuman.chr6 579010 1 + 601863 C -s simRat_chr6.simRat.chr6 85606 1 - 647215 C - -a -s simMouse_chr6.simMouse.chr6 610974 45 + 636262 ATAACTTCGCTCGATCTAGCACGACAAACTGTCCATGCTATTCAG -s Anc0.Anc0refChr3 208115 17 + 222631 TG----------------------------TTCCATACTATTAGG -s Anc1.Anc1refChr1 48016 36 + 69767 TGGGCTCCACGCTATTT---------AGGTTTCCATACTATTAGG -s Anc2.Anc2refChr1 125217 17 + 142988 TG----------------------------TCTCATACTATTAGG -s mr.mrrefChr3 158946 36 + 181027 ATAACTTCGCTCTATCT---------AACTGTCCATACTATTCAG -s simCow_chr6.simCow.chr6 584259 17 + 602619 TA----------------------------GCTCATACTATTAGG -s simDog_chr6.simDog.chr6 575891 17 + 593897 TG----------------------------TCTGATCCTATTAAG -s simHuman_chr6.simHuman.chr6 579011 36 + 601863 TGGGCTCCACGCTATTT---------AGGTTTCCAGACTATTGGG -s simRat_chr6.simRat.chr6 85607 36 - 647215 ATAACCTTGCTGTATAT---------AACTGTCCATACTATTTAG - -a -s simMouse_chr6.simMouse.chr6 611019 9 + 636262 CTAACAGAA -s Anc0.Anc0refChr3 208136 9 + 222631 CTAACAGAA -s Anc1.Anc1refChr1 48056 9 + 69767 CTAACAGAA -s Anc2.Anc2refChr1 125238 9 + 142988 CTAACAGAA -s mr.mrrefChr3 158982 9 + 181027 CTAACAGAA -s simCow_chr6.simCow.chr6 584280 9 + 602619 CTCACAGAA -s simDog_chr6.simDog.chr6 575912 9 + 593897 CTAACAGAA -s simHuman_chr6.simHuman.chr6 579051 8 + 601863 CTAACAG-A -s simRat_chr6.simRat.chr6 85643 9 - 647215 CTAACAGAA - -a -s simMouse_chr6.simMouse.chr6 611028 26 + 636262 CCTTTCTAGCGTCTCATGAGTGCACT -s Anc0.Anc0refChr3 208145 26 + 222631 TTTCTCCCACATAGCATGAGCCCAGA -s Anc1.Anc1refChr1 48065 26 + 69767 TTTCTCCCACATAGCATGAGCCCAGA -s Anc2.Anc2refChr1 125249 26 + 142988 TTTCTCCCACATAGCATGAGCCCAGA -s mr.mrrefChr3 158991 26 + 181027 CCTTTCTAGCATATCATGAGTGCACT -s simCow_chr6.simCow.chr6 584291 26 + 602619 TTTTCCCCACATAGTGTGAGCCCAGA -s simDog_chr6.simDog.chr6 575923 26 + 593897 TTTCTCCCACATAGCACGAGCCCCTA -s simHuman_chr6.simHuman.chr6 579059 26 + 601863 TTTCTCCCACATAGCATGAGCTCAGA -s simRat_chr6.simRat.chr6 85652 26 - 647215 CGTTTCTTCCATATCCTGAGTGCACT - -a -s simMouse_chr6.simMouse.chr6 611054 11 + 636262 GATCCCTGTGT -s Anc0.Anc0refChr3 208171 11 + 222631 TGTGCCTTGTT -s Anc1.Anc1refChr1 48091 11 + 69767 TGTGCCTTGTT -s Anc2.Anc2refChr1 125275 11 + 142988 TGTGCCCTGTT -s mr.mrrefChr3 159017 11 + 181027 GATCCCTGTGT -s simCow_chr6.simCow.chr6 584317 6 + 602619 TCTGCC----- -s simDog_chr6.simDog.chr6 575949 11 + 593897 CGTGCCCTGTT -s simHuman_chr6.simHuman.chr6 579085 11 + 601863 TGGGTCTCGAT -s simRat_chr6.simRat.chr6 85679 11 - 647215 GACCCCTGTGT - -a -s simMouse_chr6.simMouse.chr6 611065 20 + 636262 GTGAAAGGAATAGGTAATGG -s Anc0.Anc0refChr3 208182 20 + 222631 GTGAAAGGAGCAGAGAATGG -s Anc1.Anc1refChr1 48102 20 + 69767 GTGAAAGGAGCAGAGAATGG -s Anc2.Anc2refChr1 125286 20 + 142988 GTGAAAGGAGCGGAGAATGG -s mr.mrrefChr3 159028 20 + 181027 GTGAAAGGAGTAGGTAATGG -s simCow_chr6.simCow.chr6 584323 7 + 602619 -TGAAAGG------------ -s simDog_chr6.simDog.chr6 575963 20 + 593897 GAGAAAGGAGCGGAGAATGG -s simHuman_chr6.simHuman.chr6 579096 20 + 601863 GTGAAAGGAGCAGAGATTGG -s simRat_chr6.simRat.chr6 85690 20 - 647215 GTAATAGGAGTATGAAATGG - -a -s simMouse_chr6.simMouse.chr6 611085 16 + 636262 GTATTGATGCGCCTAC -s Anc0.Anc0refChr3 208208 11 + 222631 GCATTG-TGCCC---- -s Anc1.Anc1refChr1 48128 11 + 69767 GCATTG-TGCCC---- -s Anc2.Anc2refChr1 125312 11 + 142988 GCACTG-TGCCC---- -s mr.mrrefChr3 159048 15 + 181027 GTATTG-TGCCCCTAC -s simCow_chr6.simCow.chr6 584330 11 + 602619 GTACTT-TGCCC---- -s simDog_chr6.simDog.chr6 575989 11 + 593897 GCACTG-TGCTG---- -s simHuman_chr6.simHuman.chr6 579122 11 + 601863 GCATTG-TGTCC---- -s simRat_chr6.simRat.chr6 85710 15 - 647215 GTATTG-TACCTCTAC - -a -s simMouse_chr6.simMouse.chr6 611101 38 + 636262 CGTGGTCTATACTTACAGAGCGTACACAGGGTATCCCA -s mr.mrrefChr3 159063 36 + 181027 CGTGGTCTATACTTACAGAGC-TAC-CAGGGTATCCCA -s simRat_chr6.simRat.chr6 85727 36 - 647215 CGTCGTCTGATCTTAATCTAC-TAC-CCGGGAACCCCA - -a -s simMouse_chr6.simMouse.chr6 611139 8 + 636262 GGATCATT -s mr.mrrefChr3 159099 8 + 181027 GGATCATT -s simRat_chr6.simRat.chr6 85768 8 - 647215 AGACCATT - -a -s simMouse_chr6.simMouse.chr6 611147 13 + 636262 CCAAGTGTACCTG -s Anc0.Anc0refChr3 208219 1 + 222631 ------------A -s Anc1.Anc1refChr1 48139 1 + 69767 ------------A -s Anc2.Anc2refChr1 125323 1 + 142988 ------------A -s mr.mrrefChr3 159107 10 + 181027 CCAAGTGTA---A -s simCow_chr6.simCow.chr6 584341 1 + 602619 ------------A -s simDog_chr6.simDog.chr6 576000 1 + 593897 ------------A -s simHuman_chr6.simHuman.chr6 579133 1 + 601863 ------------A -s simRat_chr6.simRat.chr6 85780 10 - 647215 CCTACTATA---A - -a -s simMouse_chr6.simMouse.chr6 611160 31 + 636262 GATCTCTGTATGTGACATATGTTTAAGGCTA -s Anc0.Anc0refChr3 208220 31 + 222631 AATCTCTGTATACGAAAAGAGCCTAAAGCTA -s Anc1.Anc1refChr1 48140 31 + 69767 AATCTCTGTATACGAAAAGAGCCTAAAGCTA -s Anc2.Anc2refChr1 125324 31 + 142988 AATCTCTGTATACGAAAAGAGCCTAGAGCTA -s mr.mrrefChr3 159117 31 + 181027 GATCTCTGTATGTGACATGTGTTTAAGGCTA -s simCow_chr6.simCow.chr6 584352 31 + 602619 AATCTCTGCTTGCGAAAAGAGCTTATAGCTA -s simDog_chr6.simDog.chr6 576001 31 + 593897 AATCTCTGTATATTAAAAGAGTCTAGAGCTA -s simHuman_chr6.simHuman.chr6 579134 31 + 601863 AATCTCTATACACGAAGAGAACCTAAAGCTA -s simRat_chr6.simRat.chr6 85790 31 - 647215 GTCTTTTTTATGTGAGATGTGTTTAAGGCCA - -a -s simMouse_chr6.simMouse.chr6 611191 20 + 636262 AGGAGGATATGCTCATTTGT -s Anc0.Anc0refChr3 208251 20 + 222631 ATGCTGATATGCTCATTTGT -s Anc1.Anc1refChr1 48171 20 + 69767 ATGCTGATATGCTCATTTGT -s Anc2.Anc2refChr1 125355 20 + 142988 ATGCTGATATGCTCATTTGT -s mr.mrrefChr3 159148 20 + 181027 AGGATGATATGCTCATTTGT -s simCow_chr6.simCow.chr6 584383 20 + 602619 ATGCTGACATACTCATTTGT -s simDog_chr6.simDog.chr6 576032 20 + 593897 ATGCTGATATGCTGATTTGT -s simHuman_chr6.simHuman.chr6 579165 20 + 601863 ATGCTAATATGTTCATTTGT -s simRat_chr6.simRat.chr6 85828 20 - 647215 AGGATGATATGCTCCTTGGT - -a -s simMouse_chr6.simMouse.chr6 611211 70 + 636262 CATGGAGAAATTTGACCATTTATGCAAACGCATCCTTTTAATCACACTTACTGCACCCTATGATGCTTCA -s Anc0.Anc0refChr3 208271 69 + 222631 GATGGAGTACAGTGTGCCTTTATGCAAATGCATCCTTCTGATGCTTGTTTCCTTAATC-ATAAAGCATCA -s Anc1.Anc1refChr1 48191 69 + 69767 GATGGAGTACAGTGTGCCTTTATGCAAATGCATCCTTCTGATGCTTGTTTCCTTAATC-ATAAAGCATCA -s Anc2.Anc2refChr1 125375 69 + 142988 GATGGAGAACAGTGTGCCTTTATGTAAAATCATCCTTCAGAGGCTTGTTTTCTTAATC-ATAAAGCATCA -s mr.mrrefChr3 159168 70 + 181027 CATGGAGTGATTTGACCATTTATGCAAATGCATCCTTTTAATGACACTTACTGCACCCTATGATGCTTCA -s simCow_chr6.simCow.chr6 584403 67 + 602619 -ATGGATCACAGTGTGCCTTTATGTAAAC-CTTCCTTCAGAGACTTGTTTTCTTAATA-GTAAAGGATTA -s simDog_chr6.simDog.chr6 576052 69 + 593897 GATGGAGAACAGTGTGCCTTTATTTAAAATCACTCTTCAGAGGCTTGTCTTCTTGATC-ATAAAGCATCA -s simHuman_chr6.simHuman.chr6 579200 69 + 601863 GATGGAGTACAGCATGCCTTTCTGCAAATGCCTCCTCCTGATGCTTAATTCCTTAATC-ATAAAGCATCA -s simRat_chr6.simRat.chr6 85848 65 - 647215 CATGGAGTGACTTGACCATTTATGTAAATACAT-CTATTAATGACATTTACTGCTCCCCGTGAGGT---- - -a -s simMouse_chr6.simMouse.chr6 611281 3 + 636262 CAG -s Anc0.Anc0refChr3 208347 3 + 222631 CAG -s Anc1.Anc1refChr1 48267 3 + 69767 CAG -s Anc2.Anc2refChr1 125451 3 + 142988 CAG -s mr.mrrefChr3 159238 3 + 181027 CAG -s simCow_chr6.simCow.chr6 584477 3 + 602619 AAG -s simDog_chr6.simDog.chr6 576128 3 + 593897 CAG -s simHuman_chr6.simHuman.chr6 579276 3 + 601863 CAG - -a -s simMouse_chr6.simMouse.chr6 611284 101 + 636262 TCAAGAAGACAAGGCTCATAGGGATATGCAATTTATGAACTACTATCCTACAAACTTCACAAAACACAAAAAGATTAGCAGCTATCTGTCACATCAGGCTC -s Anc0.Anc0refChr3 208350 91 + 222631 TAAATGTCATCAGAT---TAGGGATATCTAATTGGTGAACAGTTATACTACAAACTT-------CACAAAAAGACTAGGGATTATGTGTTACATAAGGCCC -s Anc1.Anc1refChr1 48270 91 + 69767 TAAATGTCATCAGAT---TAGGGATATCTAATTGGTGAACAGTTATACTACAAACTT-------CACAAAAAGACTAGGGATTATGTGTTACATAAGGCCC -s Anc2.Anc2refChr1 125454 91 + 142988 TAAATGTCATCAGAT---TAGAGATATCTGATTGGTGAACAGTTATACTACAAACCT-------TACGAAAAAACTAGGGACTATGTGTTACTTCAGGTCC -s mr.mrrefChr3 159241 101 + 181027 TCAAGAAGACAAGATTCATAGGGATATGCAATTTGTGAACTACTATCCTACAAACTTCACAAAACACAAAAAGACTAGCAGTTATCTGTCACATAAGGCTC -s simCow_chr6.simCow.chr6 584484 91 + 602619 GAAATGTCATTGGAT---TAAAGATATCTGATTGGGGAACAGTTACACTAAAAACCT-------TATGGAAAAACTACGGACTATGAGTCACTTCAGGCCC -s simDog_chr6.simDog.chr6 576131 91 + 593897 TAAATGTCATCAGAT---TAGAGATATCTGATTAGTGAAGAGTTATACTTCCACCCT-------TGCGAAAGAACCAGGTGCTATTTGTTACTTCAGGTCC -s simHuman_chr6.simHuman.chr6 579279 91 + 601863 TAAATGTCATCAGAT---TGGGGATATCTAATTGGTGAACAGGTATAATACAAACTT-------CACAAAAAGACTAGGGATTATGTGTTACATAAGACAC -s simRat_chr6.simRat.chr6 85913 95 - 647215 ------AGACAAGATTCATAGGGATACGCAATTTGCAAATTACTATCCTACAAACTTCACAAAACACAAGAAGGCTATTAGTTATCTGTCACATAAGGCCC - -a -s simMouse_chr6.simMouse.chr6 611385 1 + 636262 C -s Anc0.Anc0refChr3 208441 1 + 222631 C -s Anc1.Anc1refChr1 48361 1 + 69767 C -s Anc2.Anc2refChr1 125545 1 + 142988 C -s mr.mrrefChr3 159342 1 + 181027 C -s simCow_chr6.simCow.chr6 584602 1 + 602619 C -s simDog_chr6.simDog.chr6 576222 1 + 593897 C -s simHuman_chr6.simHuman.chr6 579370 1 + 601863 G -s simRat_chr6.simRat.chr6 86008 1 - 647215 C - -a -s simMouse_chr6.simMouse.chr6 611386 9 + 636262 ACAGCTGAT -s Anc0.Anc0refChr3 208442 9 + 222631 ACAGCTGAC -s Anc1.Anc1refChr1 48362 9 + 69767 ACAGCTGAC -s Anc2.Anc2refChr1 125546 9 + 142988 ACAGCTGAC -s mr.mrrefChr3 159343 9 + 181027 ACAGCTGAT -s simCow_chr6.simCow.chr6 584603 9 + 602619 AGAGCTGAC -s simDog_chr6.simDog.chr6 576223 9 + 593897 ACAGCTGAC -s simHuman_chr6.simHuman.chr6 579371 4 + 601863 ATAG----- -s simRat_chr6.simRat.chr6 86014 9 - 647215 ACGGCTGAT - -a -s simMouse_chr6.simMouse.chr6 611395 24 + 636262 ATATGGCTTTAATAACATAACTGG -s Anc0.Anc0refChr3 208452 24 + 222631 ATATGGCTTTAGTAACATAATTGG -s Anc1.Anc1refChr1 48372 24 + 69767 ATATGGCTTTAGTAACATAATTGG -s Anc2.Anc2refChr1 125556 24 + 142988 ATATGGCTTTAGTAACATAATTGG -s mr.mrrefChr3 159353 24 + 181027 ATATGGCTTTAATAACATAACTGG -s simCow_chr6.simCow.chr6 584613 24 + 602619 ATATGGCTTTAGTGACATGACTGG -s simDog_chr6.simDog.chr6 576233 24 + 593897 ATATGGCTTCAGTACCATAATTGG -s simRat_chr6.simRat.chr6 86024 24 - 647215 AGATAGCTTTAATCATGTAACTGG - -a -s simMouse_chr6.simMouse.chr6 611419 27 + 636262 GTAGGACTTGATGATGCCACATCTCAT -s Anc0.Anc0refChr3 208476 22 + 222631 GCTGGGCTAAGTGAT-----ACCCTAT -s Anc1.Anc1refChr1 48396 22 + 69767 GCTGGGCTAAGTGAT-----ACCCTAT -s Anc2.Anc2refChr1 125584 22 + 142988 GCTGGGCTAAGTGAT-----ACCCTAT -s mr.mrrefChr3 159377 22 + 181027 GTAGGACTTGATGAT-----ATCTCAT -s simCow_chr6.simCow.chr6 584641 22 + 602619 GCTGATCTCAATGAT-----ATCCTAT -s simDog_chr6.simDog.chr6 576261 22 + 593897 GCTGGGCTAAGTGAT-----ACCCTAT -s simRat_chr6.simRat.chr6 86048 22 - 647215 ATAGGACCAAGTGAT-----ATCTCAT - -a -s simMouse_chr6.simMouse.chr6 611446 3 + 636262 AAG -s Anc0.Anc0refChr3 208498 3 + 222631 AGG -s Anc1.Anc1refChr1 48418 3 + 69767 AGG -s Anc2.Anc2refChr1 125613 3 + 142988 AGG -s mr.mrrefChr3 159399 3 + 181027 AAG -s simCow_chr6.simCow.chr6 584670 3 + 602619 AGG -s simDog_chr6.simDog.chr6 576290 2 + 593897 -GG -s simRat_chr6.simRat.chr6 86070 3 - 647215 GAG - -a -s simMouse_chr6.simMouse.chr6 611449 9 + 636262 AAAATATGT -s Anc0.Anc0refChr3 208501 9 + 222631 GAAATATGT -s Anc1.Anc1refChr1 48421 9 + 69767 GAAATATGT -s Anc2.Anc2refChr1 125616 9 + 142988 GAAATATGT -s mr.mrrefChr3 159402 9 + 181027 AAAATATGT -s simCow_chr6.simCow.chr6 584673 9 + 602619 CAAACATGT -s simDog_chr6.simDog.chr6 576292 9 + 593897 GAAATATGT -s simRat_chr6.simRat.chr6 86074 9 - 647215 AAAATATGC - -a -s simMouse_chr6.simMouse.chr6 611458 28 + 636262 ACATTGACTGTTGTGAAACCCAATTCTG -s Anc0.Anc0refChr3 208510 28 + 222631 ACATCTGATGTGGTGACACCGTATTGAG -s Anc1.Anc1refChr1 48430 28 + 69767 ACATCTGATGTGGTGACACCGTATTGAG -s Anc2.Anc2refChr1 125628 28 + 142988 ACATCTGATGTGGTGACACCGTATTGAG -s mr.mrrefChr3 159411 28 + 181027 ACATTGACTGTTGTGAAACCCAATTCTG -s simCow_chr6.simCow.chr6 584685 28 + 602619 ACATCTAATGGGGTAACACTGTAACCAG -s simDog_chr6.simDog.chr6 576306 28 + 593897 ACATCTGACCTGGTGACACCATATTGAG -s simRat_chr6.simRat.chr6 86083 28 - 647215 TCATTGAATGTTGTGAAACCTGATTCTG - -a -s simMouse_chr6.simMouse.chr6 611486 1 + 636262 G -s Anc0.Anc0refChr3 208538 1 + 222631 G -s Anc1.Anc1refChr1 48458 1 + 69767 G -s Anc2.Anc2refChr1 125660 1 + 142988 G -s mr.mrrefChr3 159439 1 + 181027 G -s simCow_chr6.simCow.chr6 584717 1 + 602619 G -s simDog_chr6.simDog.chr6 576338 1 + 593897 G -s simRat_chr6.simRat.chr6 86111 1 - 647215 G - -a -s simMouse_chr6.simMouse.chr6 611487 4 + 636262 AAAG -s Anc0.Anc0refChr3 208539 4 + 222631 TAAG -s Anc1.Anc1refChr1 48459 4 + 69767 TAAG -s Anc2.Anc2refChr1 125661 4 + 142988 TAAG -s mr.mrrefChr3 159440 4 + 181027 AAAG -s simCow_chr6.simCow.chr6 584718 4 + 602619 TGAG -s simDog_chr6.simDog.chr6 576339 4 + 593897 TAAG -s simRat_chr6.simRat.chr6 86114 4 - 647215 AAAA - -a -s simMouse_chr6.simMouse.chr6 611491 39 + 636262 TGTAGGAGATACCCTAAGTGAAATTCTTCCCAACATTAT -s Anc0.Anc0refChr3 208543 10 + 222631 TGTGGGAGAT----------------------------- -s Anc1.Anc1refChr1 48463 10 + 69767 TGTGGGAGAT----------------------------- -s Anc2.Anc2refChr1 125668 10 + 142988 TGTGGGAGAT----------------------------- -s mr.mrrefChr3 159444 39 + 181027 TGTAGGAGATACCCTAAGTGAAATTCTTCCCAACATTAT -s simCow_chr6.simCow.chr6 584725 10 + 602619 TGCAGGTGAC----------------------------- -s simDog_chr6.simDog.chr6 576346 10 + 593897 TGTGGAAGAT----------------------------- -s simRat_chr6.simRat.chr6 86118 39 - 647215 TGTAGGGTATCCCGTAAGTTGAATTCTTCCCAACATTAT - -a -s simMouse_chr6.simMouse.chr6 611530 36 + 636262 CCACTTCAGAGTGTGGGGTGACTTTGACCGAGGACT -s mr.mrrefChr3 159483 35 + 181027 CCACTTCAGAGTGTGGG-TGACTTTGACCGAGGACT -s simRat_chr6.simRat.chr6 86158 35 - 647215 TCACTTCAGAGTGTGGG-TGACCTTGAATGAGTACT - -a -s simMouse_chr6.simMouse.chr6 611566 69 + 636262 TATCTGGGTACTGTACTTGCAAAGCCCGAAAACATTGGCCTGAGATTCCCCTGGGCTACTTTAAGTAGA -s Anc0.Anc0refChr3 208553 10 + 222631 -------------------------------------------------------CTATT----GTAGA -s Anc1.Anc1refChr1 48473 10 + 69767 -------------------------------------------------------CTATT----GTAGA -s Anc2.Anc2refChr1 125678 10 + 142988 -------------------------------------------------------CTATT----GTGGA -s mr.mrrefChr3 159518 69 + 181027 TATCTGGGTACTGTACTTGCAAAGCCCGAAAACATTGGCCTGAGATTCCCCTGGGCTACTTTAAGTAGA -s simCow_chr6.simCow.chr6 584735 10 + 602619 -------------------------------------------------------CCATT----GTGGT -s simDog_chr6.simDog.chr6 576356 10 + 593897 -------------------------------------------------------CTATT----GTGGA -s simHuman_chr6.simHuman.chr6 579375 3 + 601863 ------------------------------------------------------------------AGA -s simRat_chr6.simRat.chr6 86231 69 - 647215 TATCTGGGTACTGTACTTGCAAAGCCTGAAAACATGGGCCTGGAATTCCCCTAGGACACCTTAGGTAGA - -a -s simMouse_chr6.simMouse.chr6 611635 26 + 636262 AGTTCTACCAACATTATGTCACTTCA -s Anc0.Anc0refChr3 208563 24 + 222631 TGTT-TCTCAACATGATGTCA-CTTT -s Anc1.Anc1refChr1 48483 24 + 69767 TGTT-TCTCAACATGATGTCA-CTTT -s Anc2.Anc2refChr1 125689 24 + 142988 TATT-TCTCAACATGATATCA-CTTT -s mr.mrrefChr3 159587 25 + 181027 AGTTCTACCAACATTATGTCA-TTCA -s simCow_chr6.simCow.chr6 584746 24 + 602619 TTTT-TTTCAATATGATCTCA-CTTT -s simDog_chr6.simDog.chr6 576367 24 + 593897 TATT-TCTCAACATGATAGCA-CTTT -s simHuman_chr6.simHuman.chr6 579378 24 + 601863 TGTT-TCTCAACATGATGTCG-CTTG -s simRat_chr6.simRat.chr6 86300 25 - 647215 AGTTCTCCCAACATCATGTCA-TTCA - -a -s simMouse_chr6.simMouse.chr6 611661 10 + 636262 ATGTGTGGGT -s Anc0.Anc0refChr3 208590 9 + 222631 ATGTGGGG-T -s Anc1.Anc1refChr1 48510 9 + 69767 ATGTGGGG-T -s Anc2.Anc2refChr1 125716 9 + 142988 ATGTGGGG-T -s mr.mrrefChr3 159612 9 + 181027 ATGTGTGG-T -s simCow_chr6.simCow.chr6 584773 9 + 602619 ATGTGGGG-T -s simDog_chr6.simDog.chr6 576394 9 + 593897 ATGTGGGG-T -s simHuman_chr6.simHuman.chr6 579405 9 + 601863 ATATGGGG-T -s simRat_chr6.simRat.chr6 86325 9 - 647215 ATGTGTGG-T - -a -s simMouse_chr6.simMouse.chr6 611671 18 + 636262 TTATTAAAGGAGCCACAG -s Anc0.Anc0refChr3 208609 18 + 222631 TCATTAGAAGATCCACAG -s Anc1.Anc1refChr1 48529 18 + 69767 TCATTAGAAGATCCACAG -s Anc2.Anc2refChr1 125735 18 + 142988 ACATTAGAAGATCCATAG -s mr.mrrefChr3 159621 18 + 181027 TTATTAAAGGAGCCACAG -s simCow_chr6.simCow.chr6 584792 18 + 602619 ACACTAGAACACCCAGAG -s simDog_chr6.simDog.chr6 576413 18 + 593897 ATATTACAAGATCCATAG -s simHuman_chr6.simHuman.chr6 579424 18 + 601863 TCTTTAGAAGCTCCACAG -s simRat_chr6.simRat.chr6 86334 18 - 647215 TCATTGGAGGGTCCACAG - -a -s simMouse_chr6.simMouse.chr6 611689 13 + 636262 CAGTTAAGCCTAT -s Anc0.Anc0refChr3 208634 13 + 222631 AAGTTAACCCCAA -s Anc1.Anc1refChr1 48554 13 + 69767 AAGTTAACCCCAA -s Anc2.Anc2refChr1 125760 13 + 142988 AGGTTAACCCCAA -s mr.mrrefChr3 159639 13 + 181027 CAGTTAAGCCTAT -s simCow_chr6.simCow.chr6 584817 13 + 602619 AGGTAAACCCCAT -s simDog_chr6.simDog.chr6 576438 10 + 593897 AGTTTAGGT---A -s simHuman_chr6.simHuman.chr6 579449 13 + 601863 AAGTTAACCCCAA -s simRat_chr6.simRat.chr6 86352 13 - 647215 CAGTTAAACCTAT - -a -s simMouse_chr6.simMouse.chr6 611702 63 + 636262 GTTTGGTAGCTGGGTAGTGTACTGGCAAAGCCTGAAAACACTTGTTTGGGAAGCCCCTTGTAT -s Anc0.Anc0refChr3 208647 61 + 222631 GTTT-GTAGGTGGGTGGTTCACTGGCTAAGCTCGAAAACA-TTCGTGAGGATCACCCTTGCAT -s Anc1.Anc1refChr1 48567 61 + 69767 GTTT-GTAGGTGGGTGGTTCACTGGCTAAGCTCGAAAACA-TTCGTGAGGATCACCCTTGCAT -s Anc2.Anc2refChr1 125773 61 + 142988 GTTT-ATAGGTGGGTGATTCACTCCCTCAGCTCCAATTCA-TTCGTGACGATCACCAATGCAT -s mr.mrrefChr3 159652 63 + 181027 GTTTGGTAGCTGGGTAGTGTACTGGCAAAGCCTGAAAACACTTGTTTGGGAAGCCCCTTGTAT -s simCow_chr6.simCow.chr6 584831 46 + 602619 GTTT-ATAGGTGGGTAATTCACTCACAGAGCTCAAA-------------GATCATC---GCAT -s simDog_chr6.simDog.chr6 576448 60 + 593897 GCCT-ATGGCGGAGTGAT-TGCACCCTCAGCACCAATTCA-TTCGTGACCCTCACTAATGTTT -s simHuman_chr6.simHuman.chr6 579462 61 + 601863 GTTT-GTAGGTTGGTTGTTCACTGGCTAAGCTCGAAAACA-TCAGTGAGGATCACCCTTGCAT -s simRat_chr6.simRat.chr6 86365 63 - 647215 GGTTGGTGGCTGGTTAGTGTACTTGCAGAGCCCGGAAAGACTCGTGTGGGAACCACCTTGTAT - -a -s simMouse_chr6.simMouse.chr6 611765 25 + 636262 TGGGACTGGGGGCAAATTAAACACA -s Anc0.Anc0refChr3 208708 16 + 222631 TGAGACTGGGGGCAGA--------- -s Anc1.Anc1refChr1 48628 16 + 69767 TGAGACTGGGGGCAGA--------- -s Anc2.Anc2refChr1 125834 16 + 142988 TGAGACTGGGGGCTGA--------- -s mr.mrrefChr3 159715 16 + 181027 TGGGACTGGGGGCAAA--------- -s simCow_chr6.simCow.chr6 584877 16 + 602619 TGAGGCTGGGGGCCCA--------- -s simDog_chr6.simDog.chr6 576509 16 + 593897 TGAGATTTGTGAGTGA--------- -s simHuman_chr6.simHuman.chr6 579523 16 + 601863 TGAGACTGGGGGCAGA--------- -s simRat_chr6.simRat.chr6 86428 16 - 647215 TGGGACTGGGTGCAGA--------- - -a -s simMouse_chr6.simMouse.chr6 611790 1 + 636262 G -s Anc0.Anc0refChr3 208732 1 + 222631 G -s Anc1.Anc1refChr1 48652 1 + 69767 G -s Anc2.Anc2refChr1 125858 1 + 142988 G -s mr.mrrefChr3 159731 1 + 181027 G -s simCow_chr6.simCow.chr6 584901 1 + 602619 G -s simDog_chr6.simDog.chr6 576533 1 + 593897 G -s simHuman_chr6.simHuman.chr6 579547 1 + 601863 G -s simRat_chr6.simRat.chr6 86444 1 - 647215 G - -a -s simMouse_chr6.simMouse.chr6 611791 26 + 636262 GTGGAAGCTACCAACATTAGATAGAG -s Anc0.Anc0refChr3 208733 21 + 222631 CTATAGGGTCC-TACACAAGA----A -s Anc1.Anc1refChr1 48653 22 + 69767 CTATAGGGTCCCTACACAAGA----A -s Anc2.Anc2refChr1 125859 21 + 142988 CTATAGGGTCC-TACACAAGA----A -s mr.mrrefChr3 159732 22 + 181027 GTGGAAGCTACCAACATTAGA----G -s simCow_chr6.simCow.chr6 584902 15 + 602619 CTA------CC-CACACAAGC----A -s simDog_chr6.simDog.chr6 576562 19 + 593897 CTATAGGGT---TACATAAGA----A -s simHuman_chr6.simHuman.chr6 579548 22 + 601863 CTATAGGTTCCCTGCACAAGA----A -s simRat_chr6.simRat.chr6 86445 22 - 647215 GTGGTAGCTACCAACGTTAGA----G - -a -s simMouse_chr6.simMouse.chr6 611817 2 + 636262 CG -s Anc0.Anc0refChr3 208754 2 + 222631 TG -s Anc1.Anc1refChr1 48675 2 + 69767 TG -s Anc2.Anc2refChr1 125881 2 + 142988 TA -s mr.mrrefChr3 159754 2 + 181027 CG -s simCow_chr6.simCow.chr6 584918 2 + 602619 TA -s simDog_chr6.simDog.chr6 576582 2 + 593897 TA -s simHuman_chr6.simHuman.chr6 579570 2 + 601863 TG -s simRat_chr6.simRat.chr6 86467 2 - 647215 CA - -a -s simMouse_chr6.simMouse.chr6 611819 42 + 636262 ACTATGCCACCCTGGGCTAGATCTTAGGAACCCAAAGTGCTA -s Anc0.Anc0refChr3 208795 35 + 222631 ----TGCCACCCTGAGCTAGACTTTAGGAACCCAAA---GTA -s Anc1.Anc1refChr1 48716 39 + 69767 CCTCTGCCACCCTGAGCTAGACTTTAGGAACCCAAA---GTA -s Anc2.Anc2refChr1 125922 35 + 142988 ----TGCCATCCCAAGCTAGACTTTAGGAACCCAAA---GTA -s mr.mrrefChr3 159756 39 + 181027 ACTATGCCACCCTGGGCTAGATCTTAGGAACCCAAA---CTA -s simCow_chr6.simCow.chr6 584955 16 + 602619 -----------------------TTAGGAAACAGAA---GTA -s simDog_chr6.simDog.chr6 576616 32 + 593897 ----TGCCATCCCAAGCTAGACTTTAGGAACCCAAA------ -s simHuman_chr6.simHuman.chr6 579633 39 + 601863 CCTCTGCCACCCTGAGCTAGACTCTAGAAGCCTAAA---GTG -s simRat_chr6.simRat.chr6 86469 39 - 647215 ACGATGCCACCCTGGGCTAGATCTTAGGAACTCGAA---CAA - -a -s simMouse_chr6.simMouse.chr6 611861 32 + 636262 GTTGGGCTGTGAGTATCTTGGGCTGGCGAGAA -s Anc0.Anc0refChr3 208836 32 + 222631 GTTGGGCTGTGAGTATCTTATACATGCATGAA -s Anc1.Anc1refChr1 48761 32 + 69767 GTTGGGCTGTGAGTATCTTATACATGCATGAA -s Anc2.Anc2refChr1 125963 32 + 142988 GTTGGGCTGTGAGTATCTTATACATGCATGAA -s mr.mrrefChr3 159795 32 + 181027 GTTGGGCTGTGAGTATCTTGGGCTGGCGAGAA -s simCow_chr6.simCow.chr6 584977 32 + 602619 GTTGAGCCGTGAGTATCTTATCCATGCATATA -s simDog_chr6.simDog.chr6 576652 32 + 593897 GCTGGGCTGGGAGTATCTCATATATGTGTGAA -s simHuman_chr6.simHuman.chr6 579679 32 + 601863 GTTAGGCTGTGAATATCTTATACACGCATGAA -s simRat_chr6.simRat.chr6 86508 32 - 647215 GTTGGGCCATGAGTATCTTGGGCTGGTGTGAA - -a -s simMouse_chr6.simMouse.chr6 611893 1 + 636262 T -s Anc0.Anc0refChr3 208881 1 + 222631 T -s Anc1.Anc1refChr1 48806 1 + 69767 T -s Anc2.Anc2refChr1 126008 1 + 142988 T -s mr.mrrefChr3 159827 1 + 181027 T -s simCow_chr6.simCow.chr6 585022 1 + 602619 T -s simDog_chr6.simDog.chr6 576697 1 + 593897 T -s simHuman_chr6.simHuman.chr6 579724 1 + 601863 T -s simRat_chr6.simRat.chr6 86540 1 - 647215 A - -a -s simMouse_chr6.simMouse.chr6 611894 54 + 636262 AATATCTTACAGATATTTACCATGACTTATATAAGTCCCATGCAGCACACCTCA -s Anc0.Anc0refChr3 208882 54 + 222631 AAGATCTAAGGAACATTGGTCATGATCCATATAAGTCTCATACAGCACAGCTCA -s Anc1.Anc1refChr1 48807 54 + 69767 AAGATCTAAGGAACATTGGTCATGATCCATATAAGTCTCATACAGCACAGCTCA -s Anc2.Anc2refChr1 126009 54 + 142988 ACGATCTAAGGAACATTGGTCATGATCCATAAAGGTCTCATACAGCACAGCTCA -s mr.mrrefChr3 159828 54 + 181027 AATATCTTACAGATATTTACCATGACTTATATAAGTCCCATGCAGCACACCTCA -s simCow_chr6.simCow.chr6 585023 54 + 602619 ACGATGTAGGGACCATTGGTCATGATCCATAAATGTCTGGTACAGCACAGCCCA -s simDog_chr6.simDog.chr6 576698 53 + 593897 ACGACCTAAGGGACATTGATCATGATCCATA-GGGTCTCATACAGCACAGCTCA -s simHuman_chr6.simHuman.chr6 579725 54 + 601863 AAGGTCTAAGGAACATTGGTCATGATCCATCTAAGTCTCATACAGCACAGCTCA -s simRat_chr6.simRat.chr6 86552 54 - 647215 AATATCTTAGAGACATTAACCATGACCAATTTAAGTCCCACGCAGCACAGCTCA - -a -s simMouse_chr6.simMouse.chr6 611948 14 + 636262 TCATACTGCACCAT -s Anc0.Anc0refChr3 208936 6 + 222631 TCAT--------AA -s Anc1.Anc1refChr1 48861 6 + 69767 TCAT--------AA -s Anc2.Anc2refChr1 126064 6 + 142988 TCAG--------AA -s mr.mrrefChr3 159882 14 + 181027 TCATACTGCACCAT -s simCow_chr6.simCow.chr6 585078 6 + 602619 ACAG--------TA -s simDog_chr6.simDog.chr6 576752 6 + 593897 TCAG--------AA -s simHuman_chr6.simHuman.chr6 579779 6 + 601863 TAGT--------AG -s simRat_chr6.simRat.chr6 86606 14 - 647215 TCATGCTGCACAGT - -a -s simMouse_chr6.simMouse.chr6 611962 13 + 636262 TAACATAGTAGGA -s Anc0.Anc0refChr3 208942 12 + 222631 AA-CATAGTAGGA -s Anc1.Anc1refChr1 48867 12 + 69767 AA-CATAGTAGGA -s Anc2.Anc2refChr1 126075 12 + 142988 AA-CATAGTAGAA -s mr.mrrefChr3 159896 12 + 181027 TA-CATAGTAGGA -s simCow_chr6.simCow.chr6 585089 12 + 602619 AA-CAGAGTAGAA -s simDog_chr6.simDog.chr6 576763 12 + 593897 AA-CATAGTAAAA -s simHuman_chr6.simHuman.chr6 579785 12 + 601863 AA-AATAATGGGA -s simRat_chr6.simRat.chr6 86620 12 - 647215 TA-CATATTAGAC - -a -s simMouse_chr6.simMouse.chr6 611975 18 + 636262 AATACTCCTGTGACCCTA -s Anc0.Anc0refChr3 208954 12 + 222631 AATA------CTATCTTA -s Anc1.Anc1refChr1 48879 17 + 69767 AATA-TGCTGCTATCTTA -s Anc2.Anc2refChr1 126087 12 + 142988 AATA------CTCTCTTA -s mr.mrrefChr3 159908 17 + 181027 AATA-TCCTGTGACCCTA -s simCow_chr6.simCow.chr6 585101 12 + 602619 CCTA------CTCTCTAA -s simDog_chr6.simDog.chr6 576775 12 + 593897 AACA------CTCTCTTA -s simHuman_chr6.simHuman.chr6 579799 17 + 601863 AGTA-TGCTGCTATGTTA -s simRat_chr6.simRat.chr6 86632 17 - 647215 AACA-TCCTGCCACCCTA - -a -s simMouse_chr6.simMouse.chr6 611993 6 + 636262 CCAAGG -s Anc0.Anc0refChr3 208966 6 + 222631 AAAGGG -s Anc1.Anc1refChr1 48896 6 + 69767 AAAGGG -s Anc2.Anc2refChr1 126099 6 + 142988 AAAGGG -s mr.mrrefChr3 159925 6 + 181027 CCAAGG -s simCow_chr6.simCow.chr6 585119 6 + 602619 AAGGGC -s simDog_chr6.simDog.chr6 576787 6 + 593897 AAAGGG -s simHuman_chr6.simHuman.chr6 579816 6 + 601863 TAAGGA -s simRat_chr6.simRat.chr6 86649 6 - 647215 CCAAGG - -a -s simMouse_chr6.simMouse.chr6 611999 5 + 636262 GGACA -s Anc0.Anc0refChr3 208972 5 + 222631 TGCAA -s Anc1.Anc1refChr1 48902 5 + 69767 TGCAA -s Anc2.Anc2refChr1 126105 5 + 142988 TGCAA -s mr.mrrefChr3 159931 5 + 181027 GGACA -s simCow_chr6.simCow.chr6 585125 5 + 602619 TGCCA -s simDog_chr6.simDog.chr6 576872 5 + 593897 TGCAA -s simHuman_chr6.simHuman.chr6 579822 5 + 601863 TGCAA -s simRat_chr6.simRat.chr6 86655 5 - 647215 GGAGG - -a -s simMouse_chr6.simMouse.chr6 612004 4 + 636262 TTCA -s Anc0.Anc0refChr3 208977 4 + 222631 TACA -s Anc1.Anc1refChr1 48907 4 + 69767 TACA -s Anc2.Anc2refChr1 126113 4 + 142988 TTCA -s mr.mrrefChr3 159936 4 + 181027 TTCA -s simCow_chr6.simCow.chr6 585134 4 + 602619 TTCT -s simDog_chr6.simDog.chr6 576880 4 + 593897 TTCA -s simHuman_chr6.simHuman.chr6 579827 4 + 601863 TACA -s simRat_chr6.simRat.chr6 86660 4 - 647215 TTCA - -a -s simMouse_chr6.simMouse.chr6 612008 3 + 636262 CAC -s Anc0.Anc0refChr3 208982 3 + 222631 CTC -s Anc1.Anc1refChr1 48912 3 + 69767 CTC -s Anc2.Anc2refChr1 126118 3 + 142988 ATC -s mr.mrrefChr3 159940 3 + 181027 CAC -s simCow_chr6.simCow.chr6 585139 3 + 602619 GTT -s simDog_chr6.simDog.chr6 576885 3 + 593897 ATC -s simHuman_chr6.simHuman.chr6 579832 3 + 601863 CTC -s simRat_chr6.simRat.chr6 86664 3 - 647215 TGC - -a -s simMouse_chr6.simMouse.chr6 612011 1 + 636262 A -s Anc0.Anc0refChr3 208985 1 + 222631 A -s Anc1.Anc1refChr1 48915 1 + 69767 A -s Anc2.Anc2refChr1 126121 1 + 142988 A -s mr.mrrefChr3 159943 1 + 181027 A -s simCow_chr6.simCow.chr6 585142 1 + 602619 G -s simDog_chr6.simDog.chr6 576888 1 + 593897 A -s simHuman_chr6.simHuman.chr6 579835 1 + 601863 A -s simRat_chr6.simRat.chr6 86668 1 - 647215 A - -a -s simMouse_chr6.simMouse.chr6 612012 162 + 636262 AGATTTTAGTGCCACTAATCAGATCAGAAAAGTATTAGCCTGTTGAATGAATGCCCTGATAACTATTAGTTGTACTGAGGTCGCAGCACTTGATGACTATTGGTTGTACTATTGCTCTAGCTTGGGCGTCATGATTAAAGTATCAAGAGATGGAATGATGGA -s Anc0.Anc0refChr3 208986 3 + 222631 AGG--------------------------------------------------------------------------------------------------------------------------------------------------------------- -s Anc1.Anc1refChr1 48916 3 + 69767 AGG--------------------------------------------------------------------------------------------------------------------------------------------------------------- -s Anc2.Anc2refChr1 126171 3 + 142988 AGG--------------------------------------------------------------------------------------------------------------------------------------------------------------- -s mr.mrrefChr3 159944 157 + 181027 AGATTTTAGTGCCACTAATCAGATCAGAAAAGT-TTAGCCTGTTGAATGAATGCCCTGATAACTATTAGTTGTACTGAGGTCGCAGCACTTGATGACTATTGGTTGTACTATTGCTCTAGCTTGGGCGTCAT----AAAGTATCAAGAGATGGAATGATGGA -s simCow_chr6.simCow.chr6 585194 3 + 602619 AGT--------------------------------------------------------------------------------------------------------------------------------------------------------------- -s simDog_chr6.simDog.chr6 576938 3 + 593897 AGG--------------------------------------------------------------------------------------------------------------------------------------------------------------- -s simHuman_chr6.simHuman.chr6 579836 3 + 601863 AGG--------------------------------------------------------------------------------------------------------------------------------------------------------------- -s simRat_chr6.simRat.chr6 86669 157 - 647215 AGATTTTAGTGCCACTAATCAGATCAGAAAAGT-TTAGCCTGTTGAATGAATGCCTTGATTACTGTTGGTTGGACTGCGGTCTCAGCACTTGATTACTGTTCATTGTACTATTGCTTCAGATCGGGTGACAT----AAAGTAAAAAGAGATGGAATGATGGA - -a -s simMouse_chr6.simMouse.chr6 612174 11 + 636262 AACCCCCTATG -s mr.mrrefChr3 160101 11 + 181027 AACCCCCTATG -s simRat_chr6.simRat.chr6 86837 11 - 647215 CACACCCTATG - -a -s simMouse_chr6.simMouse.chr6 612185 36 + 636262 GAGGTCGCAGCATTTGTCATTTTGATTTGGTTAATC -s Anc0.Anc0refChr3 208989 4 + 222631 --------------------------------AGTC -s Anc1.Anc1refChr1 48919 4 + 69767 --------------------------------AGTC -s Anc2.Anc2refChr1 126174 4 + 142988 --------------------------------AGTC -s mr.mrrefChr3 160112 36 + 181027 GAGGTCGCAGCATTTGTCATTTTGATTTGGTTAATC -s simCow_chr6.simCow.chr6 585197 4 + 602619 --------------------------------AGTC -s simDog_chr6.simDog.chr6 576941 4 + 593897 --------------------------------AGTC -s simHuman_chr6.simHuman.chr6 579839 4 + 601863 --------------------------------AGTC -s simRat_chr6.simRat.chr6 86850 36 - 647215 GAGGTCTCAGCATTTGTCACTTTGGTTTTGTTACTC - -a -s simMouse_chr6.simMouse.chr6 612221 7 + 636262 CCAGTCT -s Anc0.Anc0refChr3 208993 7 + 222631 CCAGTTT -s Anc1.Anc1refChr1 48923 7 + 69767 CCAGTTT -s Anc2.Anc2refChr1 126181 7 + 142988 CCACTTT -s mr.mrrefChr3 160148 7 + 181027 CCAGTCT -s simCow_chr6.simCow.chr6 585204 7 + 602619 ACACTCT -s simDog_chr6.simDog.chr6 576948 7 + 593897 CCACTTT -s simHuman_chr6.simHuman.chr6 579843 7 + 601863 TCAGTTT -s simRat_chr6.simRat.chr6 86886 7 - 647215 CTAGTCT - -a -s simMouse_chr6.simMouse.chr6 612228 12 + 636262 TATGACCTCCAG -s Anc0.Anc0refChr3 209000 12 + 222631 TATGACTTTCAG -s Anc1.Anc1refChr1 48930 12 + 69767 TATGACTTTCAG -s Anc2.Anc2refChr1 126197 12 + 142988 TGTGATGATCAG -s mr.mrrefChr3 160155 12 + 181027 TATGACCTCCAG -s simCow_chr6.simCow.chr6 585220 12 + 602619 CTTGGTTATCAG -s simDog_chr6.simDog.chr6 576964 12 + 593897 TGTGATGATCAG -s simHuman_chr6.simHuman.chr6 579850 12 + 601863 TATGACTTTCTG -s simRat_chr6.simRat.chr6 86893 12 - 647215 TATGATCTCCAG - -a -s simMouse_chr6.simMouse.chr6 612240 7 + 636262 GGCATTT -s Anc0.Anc0refChr3 209012 7 + 222631 GACATGT -s Anc1.Anc1refChr1 48942 7 + 69767 GACATGT -s Anc2.Anc2refChr1 126248 7 + 142988 GACATGT -s mr.mrrefChr3 160167 7 + 181027 GGCATTT -s simCow_chr6.simCow.chr6 585267 7 + 602619 GACATGT -s simDog_chr6.simDog.chr6 577018 4 + 593897 T---TAG -s simHuman_chr6.simHuman.chr6 579862 7 + 601863 GACATGT -s simRat_chr6.simRat.chr6 86905 7 - 647215 GGCATAT - -a -s simMouse_chr6.simMouse.chr6 612247 12 + 636262 AAGCATCCTTCA -s Anc0.Anc0refChr3 209019 12 + 222631 CACCATCCTTTG -s Anc1.Anc1refChr1 48949 12 + 69767 CACCATCCTTTG -s Anc2.Anc2refChr1 126255 12 + 142988 CACCCTCCTTTG -s mr.mrrefChr3 160174 12 + 181027 AAGCATCCTTCA -s simCow_chr6.simCow.chr6 585277 12 + 602619 CATCTTCCTTTG -s simDog_chr6.simDog.chr6 577022 12 + 593897 CACCCTCTTTTG -s simHuman_chr6.simHuman.chr6 579869 12 + 601863 CACCATCCTTTG -s simRat_chr6.simRat.chr6 86912 12 - 647215 GAGCATCCTTCA - -a -s simMouse_chr6.simMouse.chr6 612259 1 + 636262 A -s Anc0.Anc0refChr3 209032 1 + 222631 A -s Anc1.Anc1refChr1 48962 1 + 69767 A -s Anc2.Anc2refChr1 126268 1 + 142988 A -s mr.mrrefChr3 160186 1 + 181027 A -s simCow_chr6.simCow.chr6 585290 1 + 602619 A -s simDog_chr6.simDog.chr6 577035 1 + 593897 A -s simHuman_chr6.simHuman.chr6 579882 1 + 601863 A -s simRat_chr6.simRat.chr6 86924 1 - 647215 A - -a -s simMouse_chr6.simMouse.chr6 612260 75 + 636262 CCACAGTTAAAAATCATATGCTTACACTGAATTCTTGCACCTGAATTCTTGCACTGGCCTAAGATAGAATTGAGA -s Anc0.Anc0refChr3 209033 53 + 222631 CTCCCTGTTAAAACCAATAG-----------TTCATGCAC-TGAACTCTTGCACTGGCAAAATAT---------- -s Anc1.Anc1refChr1 48963 53 + 69767 CTCCCTGTTAAAACCAATAG-----------TTCATGCAC-TGAACTCTTGCACTGGCAAAATAT---------- -s Anc2.Anc2refChr1 126269 53 + 142988 CTCCCTGTTAAAACCAATAG-----------TTCATGCAC-TGAACTTTTGCACTGGCAAAATAT---------- -s mr.mrrefChr3 160187 63 + 181027 CCACAGTTAAAAATCATATG-----------TTCTTGCAC-TGAATTCTTGCACTGGCCTAAGATAGAATTGAGA -s simCow_chr6.simCow.chr6 585291 37 + 602619 CTCTCT--TAAAACCGATAG-----------GTCTTG---------------ACTGGTAAGCTAG---------- -s simDog_chr6.simDog.chr6 577036 52 + 593897 CACCCCGTTAAA-CCAAAAG-----------TTCATGCAC-TGAACTTTTGCATTGGCAAAATAT---------- -s simHuman_chr6.simHuman.chr6 579883 53 + 601863 CTCCCTGTGAAAACCAATAG-----------TTTATGCAC-TGAGCTCCTGCACTGGCAAAGTAT---------- -s simRat_chr6.simRat.chr6 86930 63 - 647215 TCCCAGTTAGAAATCAAAGG-----------TTCTTACAC-TGAATTCTTGCACTGGCATAAGATAGAATAGAGA - -a -s simMouse_chr6.simMouse.chr6 612335 29 + 636262 AAGAGATGATCGGCCCACCAGAGATATGT -s Anc0.Anc0refChr3 209086 10 + 222631 -------------------AGAGATATGT -s Anc1.Anc1refChr1 49016 10 + 69767 -------------------AGAGATATGT -s Anc2.Anc2refChr1 126322 10 + 142988 -------------------AGACATATGT -s mr.mrrefChr3 160250 29 + 181027 AAGAGATGATCGGCCCACCAGAGATATGT -s simCow_chr6.simCow.chr6 585328 10 + 602619 -------------------AGATATATCT -s simDog_chr6.simDog.chr6 577088 10 + 593897 -------------------AGACATATGT -s simHuman_chr6.simHuman.chr6 579936 10 + 601863 -------------------AGAGATATGT -s simRat_chr6.simRat.chr6 87003 29 - 647215 AAGAGATGGTGGGCCCACCAGAGATATGT - -a -s simMouse_chr6.simMouse.chr6 612364 2 + 636262 AA -s Anc0.Anc0refChr3 209096 2 + 222631 AA -s Anc1.Anc1refChr1 49026 2 + 69767 AA -s Anc2.Anc2refChr1 126356 2 + 142988 AA -s mr.mrrefChr3 160279 2 + 181027 AA -s simDog_chr6.simDog.chr6 577130 2 + 593897 AA -s simHuman_chr6.simHuman.chr6 579946 2 + 601863 AA -s simRat_chr6.simRat.chr6 87032 2 - 647215 AC - -a -s simMouse_chr6.simMouse.chr6 612366 19 + 636262 AGAAAGAACTGGTAGACCC -s Anc0.Anc0refChr3 209100 19 + 222631 ATAAAGATATGTTGGGCTC -s Anc1.Anc1refChr1 49030 19 + 69767 ATAAAGATATGTTGGGCTC -s Anc2.Anc2refChr1 126360 19 + 142988 ATAGACTTATGTTGGGCTC -s mr.mrrefChr3 160281 19 + 181027 AGAAAGAACTGGTAGACCC -s simDog_chr6.simDog.chr6 577134 19 + 593897 ATAGACTTATGTTGGGCTC -s simHuman_chr6.simHuman.chr6 579950 19 + 601863 ATAAAGATATGCTGAGCTC -s simRat_chr6.simRat.chr6 87034 19 - 647215 AGAAAAAACTGGTGGACCC - -a -s simMouse_chr6.simMouse.chr6 612385 19 + 636262 CACTCATATATTCCGAACA -s Anc0.Anc0refChr3 209126 11 + 222631 TA-------ATCCAAAC-A -s Anc1.Anc1refChr1 49056 11 + 69767 TA-------ATCCAAAC-A -s Anc2.Anc2refChr1 126386 11 + 142988 TA-------ATCCAATC-A -s mr.mrrefChr3 160300 11 + 181027 CA-------ATTCCGAA-A -s simDog_chr6.simDog.chr6 577160 11 + 593897 TA-------ATCCAATC-A -s simHuman_chr6.simHuman.chr6 579976 11 + 601863 TA-------ATCTGAAC-A -s simRat_chr6.simRat.chr6 87053 11 - 647215 CA-------ATTCTGAA-A - -a -s simMouse_chr6.simMouse.chr6 612404 14 + 636262 AAACACTAAAGAAT -s Anc0.Anc0refChr3 209137 14 + 222631 AAACACAGATGACT -s Anc1.Anc1refChr1 49067 14 + 69767 AAACACAGATGACT -s Anc2.Anc2refChr1 126397 14 + 142988 CAACCTAGTTTACT -s mr.mrrefChr3 160311 14 + 181027 AAACACTAAAGAAT -s simDog_chr6.simDog.chr6 577181 14 + 593897 CAACCTAGTTTACT -s simHuman_chr6.simHuman.chr6 579987 14 + 601863 AAACACAGAGGAGT -s simRat_chr6.simRat.chr6 87064 14 - 647215 AACCACTGAAGAAT - -a -s simMouse_chr6.simMouse.chr6 612418 49 + 636262 AATCCAGGTGGCAGAGCTAGAATAATGGTTTTACTCAAAGGCGTATTAT -s Anc0.Anc0refChr3 209151 37 + 222631 C--CCAGCATGT----------TGTAAGTTTTACTTAAGGTCTGATGAT -s Anc1.Anc1refChr1 49081 47 + 69767 C--CCAGCATGTGGGGGTGAAATGTAAGTTTTACTTAAGGTCTGATGAT -s Anc2.Anc2refChr1 126411 37 + 142988 C--CCAACATGT----------TGTAAGTTTTACTTAAGATCTGATGAT -s mr.mrrefChr3 160325 49 + 181027 AATCCAGGTGGCAGAGCTAGAATAATGGTTTTACTCAAAGGCGTATTAT -s simDog_chr6.simDog.chr6 577196 37 + 593897 C--CCAACATGT----------TGTAAGTTTTACTTAAGATCTGATGAT -s simHuman_chr6.simHuman.chr6 580001 47 + 601863 G--CTAGCATGAGGGGGTGAAATGTAAGTCTTATTTAAGGCCTGATGAT -s simRat_chr6.simRat.chr6 87078 49 - 647215 AAACGGCGTGGAGGGGCTTGAATGCTAGTTATACTCTAAAGTGTATTAT - -a -s simMouse_chr6.simMouse.chr6 612467 9 + 636262 TTCGCTCCT -s Anc0.Anc0refChr3 209190 9 + 222631 TCCCCTCCT -s Anc1.Anc1refChr1 49130 9 + 69767 TCCCCTCCT -s Anc2.Anc2refChr1 126450 9 + 142988 TCCCCTCCT -s mr.mrrefChr3 160374 9 + 181027 TTCGCTCCT -s simDog_chr6.simDog.chr6 577235 9 + 593897 TCCCCTCCT -s simHuman_chr6.simHuman.chr6 580050 9 + 601863 TCCACTCCT -s simRat_chr6.simRat.chr6 87127 9 - 647215 TTCGCTCCT - -a -s simMouse_chr6.simMouse.chr6 612476 1 + 636262 G -s Anc1.Anc1refChr1 49188 1 + 69767 G -s mr.mrrefChr3 160383 1 + 181027 G -s simHuman_chr6.simHuman.chr6 580216 1 + 601863 G -s simRat_chr6.simRat.chr6 87136 1 - 647215 G - -a -s simMouse_chr6.simMouse.chr6 612477 35 + 636262 GTCCTGCCGATCTTGCTACTATTCTCTTGGCATCA -s Anc0.Anc0refChr3 209248 7 + 222631 ---CTGT-------------------------TCA -s Anc1.Anc1refChr1 49189 27 + 69767 GTCCTGTGGATTGAGCTCCTAC--------CATCA -s Anc2.Anc2refChr1 126508 7 + 142988 ---CTGT-------------------------TTA -s mr.mrrefChr3 160384 35 + 181027 GTCCTGCCGATCTTGCTACTATTCTCTTGGCATCA -s simDog_chr6.simDog.chr6 577293 7 + 593897 ---CTGT-------------------------TTA -s simHuman_chr6.simHuman.chr6 580217 27 + 601863 GTCCTGTGGATTGAGCTCCTAC--------CATCA -s simRat_chr6.simRat.chr6 87230 35 - 647215 ATCCTTCAGATCTTGCTACTATTCTCTTGGTATCG - -a -s simMouse_chr6.simMouse.chr6 612512 25 + 636262 TACATTCTAAGCACCTTATCTCCAA -s Anc0.Anc0refChr3 209255 11 + 222631 TACATCTTAGA-------------- -s Anc1.Anc1refChr1 49216 25 + 69767 TACATCTTAGATTCCTTATCACATA -s Anc2.Anc2refChr1 126515 11 + 142988 TGAACATTAGA-------------- -s mr.mrrefChr3 160419 25 + 181027 TACATTCTAAGCACCTTATCTCCAA -s simDog_chr6.simDog.chr6 577300 11 + 593897 TGAACATTAGA-------------- -s simHuman_chr6.simHuman.chr6 580248 25 + 601863 TACATCTTAGATTCCTTATCACATA -s simRat_chr6.simRat.chr6 87265 25 - 647215 TACATTCTACGCACCTTGTCATCAA - -a -s simMouse_chr6.simMouse.chr6 612537 16 + 636262 GGTTTACTGTGATTGA -s Anc1.Anc1refChr1 49241 16 + 69767 GGCTAATCTTAATTAA -s mr.mrrefChr3 160444 16 + 181027 GGTTTACTGTGATTGA -s simHuman_chr6.simHuman.chr6 580273 16 + 601863 GGCTAATCTTAATTAA -s simRat_chr6.simRat.chr6 87295 16 - 647215 GATTTATTGTGATTGA - -a -s simMouse_chr6.simMouse.chr6 612553 25 + 636262 TTGAGTAATATGATTTGAGTAGTCT -s Anc1.Anc1refChr1 49257 20 + 69767 T-----TGTATGATTTGTGTGGTCT -s mr.mrrefChr3 160460 20 + 181027 T-----AATATGATTTGAGTAGTCT -s simHuman_chr6.simHuman.chr6 580294 20 + 601863 T-----TGTATGATTTGTGTGGTCT -s simRat_chr6.simRat.chr6 87311 20 - 647215 T-----AATATGATTTGAGTGGTGT - -a -s simMouse_chr6.simMouse.chr6 612578 4 + 636262 TTGA -s Anc1.Anc1refChr1 49278 4 + 69767 TTGA -s mr.mrrefChr3 160480 4 + 181027 TTGA -s simHuman_chr6.simHuman.chr6 580315 4 + 601863 TGGA -s simRat_chr6.simRat.chr6 87331 4 - 647215 TTGA - -a -s simMouse_chr6.simMouse.chr6 612582 20 + 636262 TGAACAGCCAAGAGACTGAC -s Anc0.Anc0refChr3 209266 9 + 222631 -----------GCACATGAC -s Anc1.Anc1refChr1 49282 20 + 69767 TGAACATTAGAGCACATGAC -s Anc2.Anc2refChr1 126526 9 + 142988 -----------GCACATGAC -s mr.mrrefChr3 160484 20 + 181027 TGAACAGCCAAGAGACTGAC -s simDog_chr6.simDog.chr6 577311 9 + 593897 -----------GCACATGAC -s simHuman_chr6.simHuman.chr6 580319 20 + 601863 TGAACATTAGAGCACTCGAC -s simRat_chr6.simRat.chr6 87336 20 - 647215 TGAATAGCCGAGAGACTGAC - -a -s simMouse_chr6.simMouse.chr6 612602 12 + 636262 ATGTACTAACAA -s Anc0.Anc0refChr3 209289 5 + 222631 A-------ACAA -s Anc1.Anc1refChr1 49316 5 + 69767 A-------ACAA -s Anc2.Anc2refChr1 126549 5 + 142988 A-------ACAA -s mr.mrrefChr3 160504 5 + 181027 A-------ACAA -s simDog_chr6.simDog.chr6 577334 5 + 593897 A-------ACAA -s simHuman_chr6.simHuman.chr6 580353 5 + 601863 G-------ATAA -s simRat_chr6.simRat.chr6 87356 5 - 647215 A-------ACAG - -a -s simMouse_chr6.simMouse.chr6 612614 22 + 636262 CAGGGGGCGAGTGTAGAAGCAG -s Anc0.Anc0refChr3 209294 22 + 222631 TAGGGGGAAAGTGGAAAAGGAT -s Anc1.Anc1refChr1 49321 22 + 69767 TAGGGGGAAAGTGGAAAAGGAT -s Anc2.Anc2refChr1 126554 22 + 142988 TAGGTGGAAAATGGAAAAGGGT -s mr.mrrefChr3 160509 22 + 181027 CAGGGGGCGAGTGTAGAAGCAG -s simDog_chr6.simDog.chr6 577339 22 + 593897 TAGGTGGAAAATGGAAAAGGGT -s simHuman_chr6.simHuman.chr6 580358 22 + 601863 TAAGGGGTAAGTAGGAGAGTAT -s simRat_chr6.simRat.chr6 87362 22 - 647215 GGGGGGGCAAGTGTAGAAGTAG - -a -s simMouse_chr6.simMouse.chr6 612636 25 + 636262 GTGAGTTTATAGAATTGCTTAATCA -s Anc0.Anc0refChr3 209316 25 + 222631 GTGAAGTTATAGAATCAGTTGATTG -s Anc1.Anc1refChr1 49343 25 + 69767 GTGAAGTTATAGAATCAGTTGATTG -s Anc2.Anc2refChr1 126576 25 + 142988 GTGAAGTTCTAGAGTCAGTTGATTG -s mr.mrrefChr3 160531 25 + 181027 GTGAGTTTATAGAATTGCTTAATCA -s simDog_chr6.simDog.chr6 577361 25 + 593897 GTGAAGTTCTAGAGTCAGTTGATTG -s simHuman_chr6.simHuman.chr6 580380 25 + 601863 GTAAACTTATAGTATCAGTTGATTG -s simRat_chr6.simRat.chr6 87488 25 - 647215 GTAAGCCTATACAATTGCTTGATTG - -a -s simMouse_chr6.simMouse.chr6 612661 6 + 636262 TGAGTT -s Anc0.Anc0refChr3 209341 6 + 222631 TAATTT -s Anc1.Anc1refChr1 49368 6 + 69767 TAATTT -s Anc2.Anc2refChr1 126601 6 + 142988 TAATAT -s mr.mrrefChr3 160556 6 + 181027 TGAGTT -s simDog_chr6.simDog.chr6 577386 6 + 593897 TAATAT -s simHuman_chr6.simHuman.chr6 580406 6 + 601863 TAATTT -s simRat_chr6.simRat.chr6 87513 6 - 647215 TTAGTT - -a -s simMouse_chr6.simMouse.chr6 612667 33 + 636262 AACAAGGGGTATAGGACATGGTGTGTCTGTACA -s Anc0.Anc0refChr3 209347 33 + 222631 AACAAGGAGAATAGCACATGGTTTGTCTTTGAA -s Anc1.Anc1refChr1 49374 33 + 69767 AACAAGGAGAATAGCACATGGTTTGTCTTTGAA -s Anc2.Anc2refChr1 126607 33 + 142988 AACCAGGAGAATAGCAAATGGTTTGAGCTTGAA -s mr.mrrefChr3 160562 33 + 181027 AACAAGGGGTATAGGACATGGTGTGTCTGTACA -s simDog_chr6.simDog.chr6 577392 33 + 593897 AACCAGGAGAATAGCAAATGGTTTGAGCTTGAA -s simHuman_chr6.simHuman.chr6 580412 33 + 601863 ATCAAGGAAAATAGAACATGGTTTGTCTTTGGA -s simRat_chr6.simRat.chr6 87524 33 - 647215 AACAAGGGGTATAGGACATGGTGTGTCTGTACC - -a -s simMouse_chr6.simMouse.chr6 612700 22 + 636262 TCCACCCACTCAATGTTTCTCT -s Anc0.Anc0refChr3 209402 21 + 222631 TTTACCAACACAG-TTTTCTCT -s Anc1.Anc1refChr1 49429 22 + 69767 TTTACCAACACAGCTTTTCTCT -s Anc2.Anc2refChr1 126662 21 + 142988 TTTACCAGCAAAG-TTTCCTCT -s mr.mrrefChr3 160595 22 + 181027 TCCACCCACTCAATGTTTCTCT -s simDog_chr6.simDog.chr6 577447 21 + 593897 TTTACCAGCAAAG-TTTCCTCT -s simHuman_chr6.simHuman.chr6 580467 22 + 601863 TTTACTTATACAGCTTTTCTCT -s simRat_chr6.simRat.chr6 87557 22 - 647215 TCTACCCACACGGCTTTTCTCT - -a -s simMouse_chr6.simMouse.chr6 612722 12 + 636262 ATTTGCTACTGG -s Anc0.Anc0refChr3 209423 11 + 222631 CTAGG-TCCTGG -s Anc1.Anc1refChr1 49451 12 + 69767 CTAGGCTCCTGG -s Anc2.Anc2refChr1 126683 11 + 142988 CTAGG-TCCTGG -s mr.mrrefChr3 160617 12 + 181027 ATTTGCTACTGG -s simDog_chr6.simDog.chr6 577470 11 + 593897 CTAGG-TCCTGG -s simHuman_chr6.simHuman.chr6 580489 12 + 601863 CTGGGCTGCTGG -s simRat_chr6.simRat.chr6 87579 12 - 647215 CTTTGCTACTGG - -a -s simMouse_chr6.simMouse.chr6 612734 20 + 636262 GGAGTTTCTTAACCTGGAGA -s Anc0.Anc0refChr3 209435 17 + 222631 GGAGTTTCTCACATTAG--- -s Anc1.Anc1refChr1 49464 20 + 69767 GGAGTTTCTCACATTAGTGA -s Anc2.Anc2refChr1 126695 17 + 142988 GGAGTTTCTCACATCAG--- -s mr.mrrefChr3 160629 20 + 181027 GGAGTTTCTTAACCTGGAGA -s simDog_chr6.simDog.chr6 577482 17 + 593897 GGAGTTTCTCACATCAG--- -s simHuman_chr6.simHuman.chr6 580502 20 + 601863 GGAGTTTCTCACATTAGTGA -s simRat_chr6.simRat.chr6 87591 20 - 647215 GAAGTTCCTCAACCCGGACA - -a -s simMouse_chr6.simMouse.chr6 612754 8 + 636262 TATCCCCT -s Anc1.Anc1refChr1 49726 8 + 69767 CATGCCCT -s mr.mrrefChr3 160649 8 + 181027 TATCCCCT -s simHuman_chr6.simHuman.chr6 580975 8 + 601863 CATGCCCT -s simRat_chr6.simRat.chr6 87611 8 - 647215 TATCCCCT - -a -s simMouse_chr6.simMouse.chr6 612762 12 + 636262 TTCCCTAATGCC -s Anc1.Anc1refChr1 49734 12 + 69767 TTAGTGAGTGCC -s mr.mrrefChr3 160657 12 + 181027 TTCCCTAATGCC -s simHuman_chr6.simHuman.chr6 580983 12 + 601863 TTAGTGAGTGCC -s simRat_chr6.simRat.chr6 87620 12 - 647215 TTCCCCAAGCCC - -a -s simMouse_chr6.simMouse.chr6 612774 69 + 636262 CTCTCCCCCATGATAATGGTGCAGATTTCAGTTCTCTCTTCAAATACAAAACTGTTGTTACTGAAATAT -s Anc0.Anc0refChr3 209694 20 + 222631 -------------------------------------------------AACTGTTGTCAGTGAATTCT -s Anc1.Anc1refChr1 49746 69 + 69767 CACCTCCCCATCCCATATGTTCCTATTTCAGTTGGCAGTTAGAGTGTAAAACTGTTGTCAGTGAATTCT -s Anc2.Anc2refChr1 126954 20 + 142988 -------------------------------------------------AGCTGCAGTCAGTGGATTCT -s mr.mrrefChr3 160669 69 + 181027 CTCTCCCCCATGATAATGGTGCAGATTTCAGTTCTCTCTTCAAATACAAAACTGTTGTTACTGAAATAT -s simCow_chr6.simCow.chr6 585366 13 + 602619 --------------------------------------------------------GTCAGTGGATTCT -s simDog_chr6.simDog.chr6 577825 7 + 593897 -------------------------------------------------AGCTGCA------------- -s simHuman_chr6.simHuman.chr6 581007 69 + 601863 CACCTCCCCATCCCATATGTTCCTATTTCAGTTGGCAGTTAGAGTGTAAAACTGTTGCCAATGAATTGT -s simRat_chr6.simRat.chr6 87632 69 - 647215 CTCCTCCCCATGATAATGGTGCAGATTTCAGTCCTCTGTTTAAATATAAAACTGTTGTCACTGAAATAT - -a -s simMouse_chr6.simMouse.chr6 612843 20 + 636262 CAGCTGGAGGTTTATCTCCC -s Anc0.Anc0refChr3 209716 19 + 222631 CATCTAGAGATTTATCTCC- -s Anc1.Anc1refChr1 49817 19 + 69767 CATCTAGAGATTTATCTCC- -s Anc2.Anc2refChr1 126976 19 + 142988 CATCCAAAAATTTATCTCC- -s mr.mrrefChr3 160738 19 + 181027 CAGCTGGAGGTTTATCTCC- -s simCow_chr6.simCow.chr6 585381 19 + 602619 CATCCAAAAATTTATCTCC- -s simHuman_chr6.simHuman.chr6 581078 19 + 601863 CATCTAGAGATTTTTCTCC- -s simRat_chr6.simRat.chr6 87701 19 - 647215 CAGTTGGATGTTTATCTTC- - -a -s simMouse_chr6.simMouse.chr6 612863 12 + 636262 GCAAGACCATCT -s Anc0.Anc0refChr3 209736 11 + 222631 ACAAGAC-ACTC -s Anc1.Anc1refChr1 49837 12 + 69767 ACAAGACCACTC -s Anc2.Anc2refChr1 126996 11 + 142988 ACAAGGC-GCTC -s mr.mrrefChr3 160757 12 + 181027 GCAAGACCATCT -s simCow_chr6.simCow.chr6 585401 11 + 602619 ACAAGGC-GCTC -s simHuman_chr6.simHuman.chr6 581098 12 + 601863 ATTAGACCACAC -s simRat_chr6.simRat.chr6 87720 12 - 647215 ACAAGACCCTCT - -a -s simMouse_chr6.simMouse.chr6 612875 14 + 636262 TAAGACTAGGTCAG -s Anc0.Anc0refChr3 209747 14 + 222631 CAGAGCTGAGACTG -s Anc1.Anc1refChr1 49849 14 + 69767 CAGAGCTGAGACTG -s Anc2.Anc2refChr1 127007 14 + 142988 CAGAGCTGAGACTT -s mr.mrrefChr3 160769 14 + 181027 TAAGACTAGGTCAG -s simCow_chr6.simCow.chr6 585412 14 + 602619 CAGAGCTGAGACTT -s simHuman_chr6.simHuman.chr6 581110 14 + 601863 CAGAGCTGTGATTG -s simRat_chr6.simRat.chr6 87738 14 - 647215 TAAGACTAGGCCAT - -a -s simMouse_chr6.simMouse.chr6 612889 5 + 636262 GCGAG -s Anc0.Anc0refChr3 209765 1 + 222631 G---- -s Anc1.Anc1refChr1 49867 5 + 69767 GCTAG -s Anc2.Anc2refChr1 127025 1 + 142988 G---- -s mr.mrrefChr3 160783 5 + 181027 GCGAG -s simCow_chr6.simCow.chr6 585430 1 + 602619 G---- -s simHuman_chr6.simHuman.chr6 581128 5 + 601863 GCTAG -s simRat_chr6.simRat.chr6 87752 5 - 647215 ACGAG - -a -s simMouse_chr6.simMouse.chr6 612894 38 + 636262 TGAATGAACAATTGCACACAACTACAAGGGCTTCCATG -s Anc1.Anc1refChr1 49872 35 + 69767 TAATTGATGACTTGC---TTACTATGGGGGATTGTATG -s mr.mrrefChr3 160788 38 + 181027 TGAATGAACAATTGCACACAACTACAAGGGCTTCCATG -s simHuman_chr6.simHuman.chr6 581133 35 + 601863 TAATTGATGACTTGC---TTACTATGGGGGATTGTATG -s simRat_chr6.simRat.chr6 87791 38 - 647215 TGAATGAAGTTATACACACCACTACAACAGCTTCCGTG - -a -s simMouse_chr6.simMouse.chr6 612932 20 + 636262 AAGTCCCCCTATCACGTAGA -s Anc1.Anc1refChr1 49907 20 + 69767 TGGTCTCTCTTTCTTGTAGG -s mr.mrrefChr3 160826 20 + 181027 AAGTCCCCCTATCACGTAGA -s simHuman_chr6.simHuman.chr6 581169 20 + 601863 TGGTCTCTCTTTCTTGTAGG -s simRat_chr6.simRat.chr6 87829 20 - 647215 TGGTCCCCCTATCACGTAGA - -a -s simMouse_chr6.simMouse.chr6 612952 20 + 636262 CACCTGAGAACTGCCAGGAA -s Anc1.Anc1refChr1 49927 20 + 69767 CATCCAAAAACTACTGGGTA -s mr.mrrefChr3 160846 20 + 181027 CACCTGAGAACTGCCAGGAA -s simHuman_chr6.simHuman.chr6 581190 20 + 601863 CATCCAAAAACTACTGGGTA -s simRat_chr6.simRat.chr6 87849 20 - 647215 CACCAGAGAACAGCCAGGGA - -a -s simMouse_chr6.simMouse.chr6 612972 26 + 636262 TCTAATAGTCAAGGCCTTCTGGATTT -s Anc1.Anc1refChr1 49947 26 + 69767 TCTAATGGTCAAGGCCCTGCTGATTT -s mr.mrrefChr3 160866 26 + 181027 TCTAATAGTCAAGGCCTTCTGGATTT -s simHuman_chr6.simHuman.chr6 581218 26 + 601863 TCTAATGGTCAAGGCCCTGCTGATTT -s simRat_chr6.simRat.chr6 87869 26 - 647215 TCTAATGGCCAAAGCCTTATGGATTT - -a -s simMouse_chr6.simMouse.chr6 612998 11 + 636262 CAAATTTGATA -s Anc0.Anc0refChr3 209766 7 + 222631 ----TTTGATA -s Anc1.Anc1refChr1 49973 11 + 69767 CAGATTTGATA -s Anc2.Anc2refChr1 127026 7 + 142988 ----TTTGATA -s mr.mrrefChr3 160892 11 + 181027 CAAATTTGATA -s simCow_chr6.simCow.chr6 585462 7 + 602619 ----TTTGTGA -s simDog_chr6.simDog.chr6 577832 6 + 593897 -----TTAATG -s simHuman_chr6.simHuman.chr6 581244 11 + 601863 CAGATTTGATA -s simRat_chr6.simRat.chr6 87897 11 - 647215 CAAATTTGATA - -a -s simMouse_chr6.simMouse.chr6 613009 3 + 636262 AGC -s Anc0.Anc0refChr3 209784 3 + 222631 AGC -s Anc1.Anc1refChr1 49995 3 + 69767 AGC -s Anc2.Anc2refChr1 127044 3 + 142988 AGC -s mr.mrrefChr3 160903 3 + 181027 AGC -s simCow_chr6.simCow.chr6 585477 3 + 602619 AGC -s simHuman_chr6.simHuman.chr6 581267 3 + 601863 AGC -s simRat_chr6.simRat.chr6 87908 3 - 647215 AGC - -a -s simMouse_chr6.simMouse.chr6 613012 1 + 636262 C -s Anc0.Anc0refChr3 209787 1 + 222631 C -s Anc1.Anc1refChr1 49998 1 + 69767 C -s Anc2.Anc2refChr1 127047 1 + 142988 T -s mr.mrrefChr3 160906 1 + 181027 C -s simCow_chr6.simCow.chr6 585480 1 + 602619 T -s simHuman_chr6.simHuman.chr6 581278 1 + 601863 C -s simRat_chr6.simRat.chr6 87911 1 - 647215 C - -a -s simMouse_chr6.simMouse.chr6 613013 4 + 636262 TGTT -s Anc0.Anc0refChr3 209788 4 + 222631 TGTT -s Anc1.Anc1refChr1 49999 4 + 69767 TGTT -s Anc2.Anc2refChr1 127048 4 + 142988 GGTT -s mr.mrrefChr3 160907 4 + 181027 TGTT -s simCow_chr6.simCow.chr6 585481 4 + 602619 GGTT -s simHuman_chr6.simHuman.chr6 581279 4 + 601863 TGAT -s simRat_chr6.simRat.chr6 87931 4 - 647215 TGTT - -a -s simMouse_chr6.simMouse.chr6 613017 36 + 636262 ACTATTTAGCTATCATAACCACATCCTGGGCGATAT -s Anc0.Anc0refChr3 209792 36 + 222631 ATTATTTTGCTATCATCACCACATTCTGGGCTAAGT -s Anc1.Anc1refChr1 50003 36 + 69767 ATTATTTTGCTATCATCACCACATTCTGGGCTAAGT -s Anc2.Anc2refChr1 127053 36 + 142988 ATTATTATACTATTATCACTACATTCTTGGCTAAGT -s mr.mrrefChr3 160911 36 + 181027 ACTATTTAGCTATCATAACCACATCCTGGGCGATAT -s simCow_chr6.simCow.chr6 585486 36 + 602619 ATTATTATACTATTATCACTACATTCTTGGCTAAGT -s simHuman_chr6.simHuman.chr6 581283 36 + 601863 CTTGCTTTGCTATCATCATCCCATTCTGGGCCTAGT -s simRat_chr6.simRat.chr6 87935 36 - 647215 CCTACTTATCTATCATCACCACATCCTAGACCCTAT - -a -s simMouse_chr6.simMouse.chr6 613053 4 + 636262 ATCA -s Anc0.Anc0refChr3 209828 4 + 222631 ATCA -s Anc1.Anc1refChr1 50039 4 + 69767 ATCA -s Anc2.Anc2refChr1 127089 4 + 142988 ACCA -s mr.mrrefChr3 160947 4 + 181027 ATCA -s simCow_chr6.simCow.chr6 585522 4 + 602619 ACCA -s simHuman_chr6.simHuman.chr6 581319 4 + 601863 ATTA -s simRat_chr6.simRat.chr6 87972 4 - 647215 ATCA - -a -s simMouse_chr6.simMouse.chr6 613057 4 + 636262 GGAA -s Anc0.Anc0refChr3 209832 4 + 222631 GGAA -s Anc1.Anc1refChr1 50043 4 + 69767 GGAA -s Anc2.Anc2refChr1 127093 4 + 142988 GGAA -s mr.mrrefChr3 160951 4 + 181027 GGAA -s simCow_chr6.simCow.chr6 585526 4 + 602619 GGAA -s simHuman_chr6.simHuman.chr6 581323 4 + 601863 GGAA -s simRat_chr6.simRat.chr6 87998 4 - 647215 GGAA - -a -s simMouse_chr6.simMouse.chr6 613061 7 + 636262 TCGTGTC -s Anc0.Anc0refChr3 209836 6 + 222631 CAGT-TC -s Anc1.Anc1refChr1 50047 6 + 69767 CAGT-TC -s Anc2.Anc2refChr1 127097 6 + 142988 CAGT-CC -s mr.mrrefChr3 160955 7 + 181027 TCGTGTC -s simCow_chr6.simCow.chr6 585533 6 + 602619 CAGT-CC -s simHuman_chr6.simHuman.chr6 581327 6 + 601863 CAGT-TC -s simRat_chr6.simRat.chr6 88002 7 - 647215 TAATGTT - -a -s simMouse_chr6.simMouse.chr6 613068 37 + 636262 TGGGCATGAGTTATAGTTTTACCATCTTTGACAACAA -s Anc0.Anc0refChr3 209842 31 + 222631 TGGGCATGAGGTATTTCACTAACACCTCTG------A -s Anc1.Anc1refChr1 50053 31 + 69767 TGGGCATGAGGTATTTCACTAACACCTCTG------A -s Anc2.Anc2refChr1 127103 31 + 142988 TGCTCATGGGGTATTTCACAAACACCTCCG------A -s mr.mrrefChr3 160962 37 + 181027 TGGGCATGAGTTATAGTTTTACCATCTTTGACAACAA -s simCow_chr6.simCow.chr6 585540 31 + 602619 TGCTCATGGGGTATTTCACAAACACCTCCG------A -s simHuman_chr6.simHuman.chr6 581333 31 + 601863 TGGGCTTGAGCTATTTCACTGACCCCCCTG------A -s simRat_chr6.simRat.chr6 88009 37 - 647215 TGGGCATGAGTTACAGCAGTGACCTCTTTGACAACAG - -a -s simMouse_chr6.simMouse.chr6 613105 14 + 636262 CAAGTCACTTTGAC -s Anc0.Anc0refChr3 209873 14 + 222631 GAAGTAACTTTTTC -s Anc1.Anc1refChr1 50084 14 + 69767 GAAGTAACTTTTTC -s Anc2.Anc2refChr1 127134 14 + 142988 GAAGTAACTGTTTA -s mr.mrrefChr3 160999 14 + 181027 CAAGTCACTTTGAC -s simCow_chr6.simCow.chr6 585577 14 + 602619 GAAGTAACTGTTTA -s simHuman_chr6.simHuman.chr6 581364 14 + 601863 GAAGTAACTTTTTC -s simRat_chr6.simRat.chr6 88046 14 - 647215 CAAGTGACTTTGAC - -a -s simMouse_chr6.simMouse.chr6 613119 6 + 636262 CTTTTA -s Anc0.Anc0refChr3 209889 6 + 222631 CATGTA -s Anc1.Anc1refChr1 50100 6 + 69767 CATGTA -s Anc2.Anc2refChr1 127150 6 + 142988 CATGGG -s mr.mrrefChr3 161013 6 + 181027 CTTTTA -s simCow_chr6.simCow.chr6 585593 6 + 602619 CATGGG -s simHuman_chr6.simHuman.chr6 581380 6 + 601863 ACTGTA -s simRat_chr6.simRat.chr6 88060 6 - 647215 CTTTTA - -a -s simMouse_chr6.simMouse.chr6 613125 33 + 636262 TACCTGCTTCTCTCTATTGTTCTTAGAGCATAA -s Anc0.Anc0refChr3 209895 33 + 222631 TTGCTGTTTCTCCCTAATGTTCCTAGAGCTTAA -s Anc1.Anc1refChr1 50106 33 + 69767 TTGCTGTTTCTCCCTAATGTTCCTAGAGCTTAA -s Anc2.Anc2refChr1 127156 33 + 142988 TTGGTGTTTCTGCCTAATGTTCCTAGAGCTCAA -s mr.mrrefChr3 161019 33 + 181027 TACCTGCTTCTCTCTATTGTTCTTAGAGCATAA -s simCow_chr6.simCow.chr6 585599 33 + 602619 TTGGTGTTTCTGCCTAATGTTCCTAGAGCTCAA -s simHuman_chr6.simHuman.chr6 581387 33 + 601863 TGGCTGTTTCTCCCTAATGCTCATAGAGCTTAA -s simRat_chr6.simRat.chr6 88066 33 - 647215 TACCTGCTTCTCTCTATTGTTCTTAGAGCACAA - -a -s simMouse_chr6.simMouse.chr6 613158 19 + 636262 AAAAAGGCTGATCTTAACA -s Anc0.Anc0refChr3 209928 19 + 222631 AAAAAGACTGATcttAAGG -s Anc1.Anc1refChr1 50139 19 + 69767 AAAAAGACTGATCTTAAGG -s Anc2.Anc2refChr1 127189 19 + 142988 AAATTGATTGTTtctGAGG -s mr.mrrefChr3 161052 19 + 181027 AAAAAGGCTGATCTTAACA -s simCow_chr6.simCow.chr6 585632 19 + 602619 AAATTGATTGTTTCTGAGG -s simHuman_chr6.simHuman.chr6 581649 19 + 601863 AAAAAGCCGTAACTTAAAG -s simRat_chr6.simRat.chr6 88099 19 - 647215 AAAGATGCTGCTTCTAACA - -a -s simMouse_chr6.simMouse.chr6 613177 11 + 636262 GCCAATGCCAC -s Anc0.Anc0refChr3 209947 11 + 222631 GCCATTGCCAC -s Anc1.Anc1refChr1 50158 11 + 69767 GCCATTGCCAC -s Anc2.Anc2refChr1 127208 11 + 142988 GCCATTGCCCC -s mr.mrrefChr3 161071 11 + 181027 GCCAATGCCAC -s simCow_chr6.simCow.chr6 585651 11 + 602619 GCCATTGCCCC -s simHuman_chr6.simHuman.chr6 581672 11 + 601863 GCCACTGCCAC -s simRat_chr6.simRat.chr6 88118 11 - 647215 GCCAAGAGCAC - -a -s simMouse_chr6.simMouse.chr6 613188 6 + 636262 ACATAT -s Anc0.Anc0refChr3 209958 6 + 222631 ACACAT -s Anc1.Anc1refChr1 50169 6 + 69767 ACACAT -s Anc2.Anc2refChr1 127219 6 + 142988 ATACAT -s mr.mrrefChr3 161082 6 + 181027 ACATAT -s simCow_chr6.simCow.chr6 585662 6 + 602619 ATACAT -s simHuman_chr6.simHuman.chr6 581683 6 + 601863 ACACAT -s simRat_chr6.simRat.chr6 88131 6 - 647215 ACATCC - -a -s simMouse_chr6.simMouse.chr6 613194 18 + 636262 ATCAGATAGGCTCAAATG -s Anc0.Anc0refChr3 209966 18 + 222631 ATTAAGTAGGCTAAGATG -s Anc1.Anc1refChr1 50177 18 + 69767 ATTAAGTAGGCTAAGATG -s Anc2.Anc2refChr1 127227 18 + 142988 ATTAAGTAGGCTAAGAAA -s mr.mrrefChr3 161088 18 + 181027 ATCAGATAGGCTCAAATG -s simCow_chr6.simCow.chr6 585670 18 + 602619 ATTAAGTAGGCTAAGAAA -s simHuman_chr6.simHuman.chr6 581691 18 + 601863 AGTAAGTAGGCTAAGATG -s simRat_chr6.simRat.chr6 88137 18 - 647215 ATCAGATAGGCTAAAATG - -a -s simMouse_chr6.simMouse.chr6 613212 31 + 636262 TTCACTCATCACTTTCGTTCATACAGACTGA -s Anc0.Anc0refChr3 209985 31 + 222631 TTCACTGATCACTTTTATTCATATGGACTGA -s Anc1.Anc1refChr1 50196 31 + 69767 TTCACTGATCACTTTTATTCATATGGACTGA -s Anc2.Anc2refChr1 127246 31 + 142988 TTCACTGCTCACTAGTATTCATATGGACTGA -s mr.mrrefChr3 161106 31 + 181027 TTCACTCATCACTTTCGTTCATACAGACTGA -s simCow_chr6.simCow.chr6 585689 31 + 602619 TTCACTGCTCACTAGTATTCATATGGACTGA -s simHuman_chr6.simHuman.chr6 581710 31 + 601863 TCACCTAATCACCTTTCTTCATAAGGACTGA -s simRat_chr6.simRat.chr6 88155 31 - 647215 TTGAATCATCACTTTTGTCCGTGCAGACTGA - -a -s simMouse_chr6.simMouse.chr6 613243 20 + 636262 CAGTTCACTATGTTGAGGGT -s Anc0.Anc0refChr3 210023 16 + 222631 CACTTCA----GTTGAGGTT -s Anc1.Anc1refChr1 50234 16 + 69767 CACTTCA----GTTGAGGTT -s Anc2.Anc2refChr1 127284 16 + 142988 CACTTCA----GTTGAGATT -s mr.mrrefChr3 161137 20 + 181027 CAGTTCACTATGTTGAGGGT -s simCow_chr6.simCow.chr6 585727 16 + 602619 CACTTCA----GTTGAGATT -s simHuman_chr6.simHuman.chr6 581748 16 + 601863 CATTTCA----GTAGAGGTT -s simRat_chr6.simRat.chr6 88186 20 - 647215 TAATTCACTATGTTGAGGTT - -a -s simMouse_chr6.simMouse.chr6 613263 16 + 636262 TACAGGGAGAGAGACC -s Anc0.Anc0refChr3 210039 1 + 222631 T--------------- -s Anc1.Anc1refChr1 50250 1 + 69767 T--------------- -s Anc2.Anc2refChr1 127300 1 + 142988 T--------------- -s mr.mrrefChr3 161157 16 + 181027 TACAGGGAGAGAGACC -s simCow_chr6.simCow.chr6 585841 1 + 602619 T--------------- -s simHuman_chr6.simHuman.chr6 581764 1 + 601863 T--------------- -s simRat_chr6.simRat.chr6 88206 16 - 647215 TATAGGGAGAGGGACC - -a -s simMouse_chr6.simMouse.chr6 613279 52 + 636262 AATTATCAGGGCATCTTTATGAGATTGCTAACCTAAAAGTGTGGTAATCTGG -s Anc0.Anc0refChr3 210040 9 + 222631 -------------------------------------------GTAATCTGG -s Anc1.Anc1refChr1 50251 9 + 69767 -------------------------------------------GTAATCTGG -s Anc2.Anc2refChr1 127301 9 + 142988 -------------------------------------------CTAATCTGG -s mr.mrrefChr3 161173 52 + 181027 AATTATCAGGGCATCTTTATGAGATTGCTAACCTAAAAGTGTGGTAATCTGG -s simCow_chr6.simCow.chr6 585842 9 + 602619 -------------------------------------------CTAGTCTGG -s simDog_chr6.simDog.chr6 577842 7 + 593897 ---------------------------------------------AATCTGG -s simHuman_chr6.simHuman.chr6 581765 9 + 601863 -------------------------------------------GTAATCTGG -s simRat_chr6.simRat.chr6 88262 52 - 647215 AATTATCAGGGCATTTGTATGTGATTGCTAATCAAAAAGTGTTGTAATCTGG - -a -s simMouse_chr6.simMouse.chr6 613331 12 + 636262 AAAGCTGAGGAA -s Anc0.Anc0refChr3 210056 12 + 222631 AAAATTGAGAAT -s Anc1.Anc1refChr1 50267 12 + 69767 AAAATTGAGAAT -s Anc2.Anc2refChr1 127317 12 + 142988 AAAATTGAGAAT -s mr.mrrefChr3 161225 12 + 181027 AAAGCTGAGGAA -s simCow_chr6.simCow.chr6 585858 12 + 602619 AAAATTGACAAT -s simDog_chr6.simDog.chr6 577856 12 + 593897 AAAATTGAGAAT -s simHuman_chr6.simHuman.chr6 581781 12 + 601863 AAAAGTGAAAAT -s simRat_chr6.simRat.chr6 88314 12 - 647215 AAAGCTGAGAAT - -a -s simMouse_chr6.simMouse.chr6 613343 18 + 636262 TCTTGTTTGTAGCCATCA -s Anc0.Anc0refChr3 210068 18 + 222631 TCTTTTCTGTGGCCAGCT -s Anc1.Anc1refChr1 50279 18 + 69767 TCTTTTCTGTGGCCAGCT -s Anc2.Anc2refChr1 127329 18 + 142988 TCTTTTCTGTGGCCAGCT -s mr.mrrefChr3 161237 18 + 181027 TCTTGTTTGTAGCCATCA -s simCow_chr6.simCow.chr6 585870 18 + 602619 GCTCTTTGGTGGCCAGGT -s simDog_chr6.simDog.chr6 577882 18 + 593897 TCTTCTCTGTGGCCAGCT -s simHuman_chr6.simHuman.chr6 581793 18 + 601863 TCTTTTCTGTGGCCAGCT -s simRat_chr6.simRat.chr6 88326 18 - 647215 GTTTGTTTGTGGCCATCA - -a -s simMouse_chr6.simMouse.chr6 613361 5 + 636262 TGCAC -s Anc0.Anc0refChr3 210088 5 + 222631 TGCAC -s Anc1.Anc1refChr1 50299 5 + 69767 TGCAC -s Anc2.Anc2refChr1 127349 5 + 142988 TGCAC -s mr.mrrefChr3 161255 5 + 181027 TGCAC -s simCow_chr6.simCow.chr6 585890 5 + 602619 TGCCA -s simDog_chr6.simDog.chr6 577902 5 + 593897 TGCAC -s simHuman_chr6.simHuman.chr6 581813 5 + 601863 TACAA -s simRat_chr6.simRat.chr6 88344 5 - 647215 TGCAA - -a -s simMouse_chr6.simMouse.chr6 613366 5 + 636262 TCAGC -s Anc0.Anc0refChr3 210093 5 + 222631 TCAAT -s Anc1.Anc1refChr1 50304 5 + 69767 TCAAT -s Anc2.Anc2refChr1 127357 5 + 142988 TCAAT -s mr.mrrefChr3 161260 5 + 181027 TCAGC -s simCow_chr6.simCow.chr6 585898 5 + 602619 TCAAC -s simDog_chr6.simDog.chr6 577910 5 + 593897 TCGAT -s simHuman_chr6.simHuman.chr6 581818 5 + 601863 TCAAT -s simRat_chr6.simRat.chr6 88349 5 - 647215 TCAGC - -a -s simMouse_chr6.simMouse.chr6 613371 38 + 636262 ACTGTACTTGGGGTAGTTTGAAGAGTGGCGCAAGCACA -s Anc0.Anc0refChr3 210103 38 + 222631 AGTTTACTTGGGGTAATTTGATTGGTGCTGCAAGTAAA -s Anc1.Anc1refChr1 50314 38 + 69767 AGTTTACTTGGGGTAATTTGATTGGTGCTGCAAGTAAA -s Anc2.Anc2refChr1 127367 38 + 142988 AGTTTACTTGGGGTAATTTGATTGGTGCTGCGAGTAAA -s mr.mrrefChr3 161265 38 + 181027 ACTGTACTTGGGGTAGTTTGAAGAGTGGCGCAAGCACA -s simCow_chr6.simCow.chr6 585908 38 + 602619 GATTAACTTGGGGCGATCTGATTGGTGGTGCTGGTAGA -s simDog_chr6.simDog.chr6 577920 38 + 593897 AGCCTACTTGGGGTAATTTGATTGGTGCTACGAATTAA -s simHuman_chr6.simHuman.chr6 581828 38 + 601863 AGTTTACTTGGGGTAATATGACTGGTGATGCAAGTAAA -s simRat_chr6.simRat.chr6 88354 38 - 647215 ACTGTACTTGGAGTAATTTGAGGGGTGGTGCAAGTGAA - -a -s simMouse_chr6.simMouse.chr6 613409 92 + 636262 TCTTGATTATTTTTTATTTTCCATGACTGCTTTCTTCAATCACGTCCTCAATCATGATATAATCTCTTTTTCTCTCTCATTGTACAGTTTCA -s Anc0.Anc0refChr3 210141 80 + 222631 TCTTGTTTATCTTCTGCTTTCAATCACTGCTCTCT------------TCAATTATGATATAGTTTGTTTCCATTACTCAATGTACATTTTCC -s Anc1.Anc1refChr1 50352 80 + 69767 TCTTGTTTATCTTCTGCTTTCAATCACTGCTCTCT------------TCAATTATGATATAGTTTGTTTCCATTACTCAATGTACATTTTCC -s Anc2.Anc2refChr1 127405 80 + 142988 TTCTGTTTATCTTCTGCTGTCAATCACAGCTCTCT------------TCCATTATGATATAGTTTGCGTCCATTACTCAATGTACATTTTCC -s mr.mrrefChr3 161303 92 + 181027 TCTTGATTATTTTTTATTTTCCATGACTGCTTTCTTCAATCACGTCCTCAATCATGATATAATCTCTTTTTCTCTCTCATTGTACAGTTTCA -s simCow_chr6.simCow.chr6 585948 76 + 602619 TTCTGTTCATCTTATGCCCTCAGGCACAGCTCCCT------------TCCATTATGATACAGTTTTCAT--ATTACTCACTGTTC--TTTCC -s simDog_chr6.simDog.chr6 577958 78 + 593897 T--TATTTGTCTTCTGCTGTCAATCAGAGCTCTCT------------TCCATTACGATATAGTCTGCGTCCATTGCTCAATGAAAATTTTCC -s simHuman_chr6.simHuman.chr6 581866 79 + 601863 TCTTGTTTATCTC-TGATTTCAATCACTACTGTCT------------TCAGTTATGAGATAGTTTATTAGCATTACTGAATGTACATTTTCC -s simRat_chr6.simRat.chr6 88392 92 - 647215 TCTTGTTTATGTTTTATTTTTCATGACTGCTTTCTTCAACCATGTCCTCAATCAAGATAGAATCTCTTTTTATTACTCATTGTACAATTTCA - -a -s simMouse_chr6.simMouse.chr6 613501 5 + 636262 CTATC -s Anc0.Anc0refChr3 210227 5 + 222631 CCATA -s Anc1.Anc1refChr1 50438 5 + 69767 CCATA -s Anc2.Anc2refChr1 127491 5 + 142988 GCATA -s mr.mrrefChr3 161395 5 + 181027 CTATC -s simCow_chr6.simCow.chr6 586030 5 + 602619 GCACA -s simDog_chr6.simDog.chr6 578042 5 + 593897 GCATA -s simHuman_chr6.simHuman.chr6 581951 5 + 601863 CCATG -s simRat_chr6.simRat.chr6 88484 5 - 647215 CTGTC - -a -s simMouse_chr6.simMouse.chr6 613506 10 + 636262 TATAATTCAA -s Anc0.Anc0refChr3 210232 7 + 222631 TATTTTT--- -s Anc1.Anc1refChr1 50443 7 + 69767 TATTTTT--- -s Anc2.Anc2refChr1 127496 7 + 142988 TATTTTT--- -s mr.mrrefChr3 161400 7 + 181027 TATAATT--- -s simCow_chr6.simCow.chr6 586035 7 + 602619 TATTTTT--- -s simDog_chr6.simDog.chr6 578088 7 + 593897 TATTCTT--- -s simHuman_chr6.simHuman.chr6 581956 7 + 601863 TATTTTT--- -s simRat_chr6.simRat.chr6 88489 7 - 647215 TATAGTT--- - -a -s simMouse_chr6.simMouse.chr6 613516 82 + 636262 TTTCATTGGTGCAAACACATTGTGGCAGTTAGTATTACTGAGTCTAACAACCTGGAAGGTCAGATGATGCTCCTGACTTTAG -s Anc0.Anc0refChr3 210252 78 + 222631 TTTAATTGGTGCAAATCTATTATGGCAGTTAGTATCATGAAGTCAAACCATT---AGTGTGA-CTGAAGTTCCTGACTTTAC -s Anc1.Anc1refChr1 50463 78 + 69767 TTTAATTGGTGCAAATCTATTATGGCAGTTAGTATCATGAAGTCAAACCATT---AGTGTGA-CTGAAGTTCCTGACTTTAC -s Anc2.Anc2refChr1 127516 78 + 142988 CTTAATTGGTGCTAATCTATTATGTCAGTTAGTATCATGATGTCAAACCATT---TGTGTGT-CTGAAGTTCTTTACTTTGC -s mr.mrrefChr3 161407 81 + 181027 TTTCATTGGTGCAAACACATTGTGGCAGTTAGTATTACTGAGTCTAACAACCTGGAAGGTCA-ATGATGCTCCTGACTTTAG -s simCow_chr6.simCow.chr6 586055 77 + 602619 CTTAAATTGTGCTAATCTATTAAACCCATTAGTATCATAATGTAAAACCATT----TTGTGT-CTGAAGTTCTTTACTCTGT -s simDog_chr6.simDog.chr6 578108 78 + 593897 CTTAATTGGTGCTAAGCTATTATGTCAGTTAGTATCATGATGTCAAACCATA---TGTGTGT-CTAAAGTTTTTTACTTTGC -s simHuman_chr6.simHuman.chr6 581976 69 + 601863 TTTAATCAGTGCAAGTCTATTATGGCAGTAA---------AGTCAAACCATT---AGTGTGA-CTGAAGTTCCTGACTTTAA -s simRat_chr6.simRat.chr6 88496 81 - 647215 TTTCATTGGTCCAAACACATCGTGGCAATAAGTATCACTGAGTTTAATAATTTGAACCGCCA-CTGAAGTTCCTGTCTTTAA - -a -s simMouse_chr6.simMouse.chr6 613598 62 + 636262 TCGATGAGTCTACACTCAGTCTGTAAGGGGCTGTGTGGGACAAAATAGATTTGCCCCAGAAG -s Anc0.Anc0refChr3 210331 62 + 222631 TTGATGAGGCTATACTCCCTCTATAAGGGGTTATGTGGGGCAAACTACATGTGTGCATGAAG -s Anc1.Anc1refChr1 50542 62 + 69767 TTGATGAGGCTATACTCCCTCTATAAGGGGTTATGTGGGGCAAACTACATGTGTGCATGAAG -s Anc2.Anc2refChr1 127595 62 + 142988 TTGATGAGGCTATACTCCCTCTATAATGGGTTATGTGGGGCAAACTACATGTGTGCATGAAG -s mr.mrrefChr3 161488 62 + 181027 TCGATGAGTCTACACTCAGTCTGTAAGGGGCTGTGTGGGACAAAATAGATTTGCCCCAGAAG -s simCow_chr6.simCow.chr6 586133 61 + 602619 TTAATGAGGCTACACTTTCTCTTTTAAGG-CTATGTGGGGGAAACTATGTGTGTCCATGAAG -s simDog_chr6.simDog.chr6 578187 62 + 593897 TTGACGAGGCTATACTCCCTCTATAATGGGTTCTGTGGATCAAACTACATGTGAGCATGAAG -s simHuman_chr6.simHuman.chr6 582046 52 + 601863 TTGATGAGGCTTTA----------AAGGGGTTAAGCGGGGCAAACTACATGTGTACATGAAG -s simRat_chr6.simRat.chr6 88577 62 - 647215 TTGATGAGCCTACACTCACTCCGTAAGGGGCTGTGTGGGACAAACTAGGTCTGCACCAGAAG - -a -s simMouse_chr6.simMouse.chr6 613660 647 + 636262 ATTTGAAGCAATACCAACaccactacatcttaccagagacctgaaaagaatcatagatgggcgaaagattcaatatttaagagatggtgttggaaagcatggttatttacatgcagaaggctcaaatgggatccatttttaacttcttacactaaagttccaaaatctaaatggatacaaggtccgaacataaggcctcccaggacagtgaagctcctagaagagaatcttgggaatactatccaggatataggtatgggtgcgagcttcatccttaagatgccgaaagccatggccgcgacacctaggattgacgaacgggaacaagatgctatcagattggagacgttatgtaaacctaaagctaagcaaaccccagtaccggttaactgcaagccaaccaactggaagaaaatctttgccacgtactcttcagataaaggattcgtctataaagtccataatgagcttacccaaattgaccggaaaaagacgaattaccctaccaaaaaacgcgctaaagacactaacaagcatccagccaggaaagatgtttacgtcactaaaatatgcataaaaaaatgtgccttctcttaaGCAATTTTTGTTACACCCTCTACAAGGTTTCTTTCTCTGATTAGCCTTGA -s Anc0.Anc0refChr3 210394 57 + 222631 AATTGGAATAAAGCCATCATAACTACTCC--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CAAGATTCCTCTCTTTGGTTGGTCTTGA -s Anc1.Anc1refChr1 50605 57 + 69767 AATTGGAATAAAGCCATCATAACTACTCC--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CAAGATTCCTCTCTTTGGTTGGTCTTGA -s Anc2.Anc2refChr1 127658 57 + 142988 AATTGGAATAAAGCCATCATAACCACTCC--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AAAGATTCCTCTCTTTGGTTGGTCTTGA -s mr.mrrefChr3 161550 57 + 181027 ATTTGAAGCAATACCAACaccactacatc--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CAAGGTTTCTTTCTCTGGTTAGCCTTGA -s simCow_chr6.simCow.chr6 586195 57 + 602619 AATTGGAGTAAAGCTATCATAACCTCACC--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AAAGGTTCCTCTATTTGGTTGGTCTTGA -s simDog_chr6.simDog.chr6 578250 57 + 593897 AATTGGAATGAAGCCATCATAACCATTAC--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AAAGATTTCTTGCTATGGATGGTATTGG -s simHuman_chr6.simHuman.chr6 582099 57 + 601863 AATTGGGATAAAGCCACTATTACTGCTCA--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CAAGTTTCCTCTCTTAGGTTGGTCCTGA -s simRat_chr6.simRat.chr6 88639 57 - 647215 ATTTGAAATAACACCAACACCACTACATC--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CAAGGTCTCTTTCTCTGGTTAGCCTTGA - -a -s simMouse_chr6.simMouse.chr6 614307 1 + 636262 A -s Anc0.Anc0refChr3 210451 1 + 222631 C -s Anc1.Anc1refChr1 50662 1 + 69767 C -s Anc2.Anc2refChr1 127715 1 + 142988 C -s mr.mrrefChr3 161607 1 + 181027 A -s simCow_chr6.simCow.chr6 586252 1 + 602619 C -s simDog_chr6.simDog.chr6 578314 1 + 593897 A -s simHuman_chr6.simHuman.chr6 582156 1 + 601863 C -s simRat_chr6.simRat.chr6 88696 1 - 647215 A - -a -s simMouse_chr6.simMouse.chr6 614308 10 + 636262 TCTCGGTTCA -s Anc0.Anc0refChr3 210452 10 + 222631 TCTACATTCG -s Anc1.Anc1refChr1 50663 10 + 69767 TCTACATTCG -s Anc2.Anc2refChr1 127716 10 + 142988 TCCACAGTCG -s mr.mrrefChr3 161608 10 + 181027 TCTCGGTTCA -s simCow_chr6.simCow.chr6 586261 10 + 602619 TCCACAGTTG -s simDog_chr6.simDog.chr6 578315 10 + 593897 TCCACAGTCA -s simHuman_chr6.simHuman.chr6 582157 10 + 601863 TCTACATTCG -s simRat_chr6.simRat.chr6 88697 10 - 647215 TCTCGGTTCA - -a -s simMouse_chr6.simMouse.chr6 614318 52 + 636262 TGAATGCGAACTAATAGCCAACTTAATGACAAGCAGCAGATTGAGGTGGACT -s Anc0.Anc0refChr3 210462 52 + 222631 AAAGTGTATACTGAAAGTCAAAATAATAACAAACAGAGGGTTGAGACTGACT -s Anc1.Anc1refChr1 50673 52 + 69767 AAAGTGTATACTGAAAGTCAAAATAATAACAAACAGAGGGTTGAGACTGACT -s Anc2.Anc2refChr1 127726 52 + 142988 AAAGTATATACTGAAAGTCAAAATAATAACAAACAGAGGGTTGAGACTGACT -s mr.mrrefChr3 161618 52 + 181027 TGAGTGTGAACTGATAGTCAACTTAATAACAAACAGCAGATTGAGGTGGACT -s simCow_chr6.simCow.chr6 586285 52 + 602619 AAACTATGTACTGAAAGTCAAAATAATAACAAACAGAGGGTGGATGCTGACT -s simDog_chr6.simDog.chr6 578325 52 + 593897 AAAGTATACACCGAAAGTCAATGTAATAAAGAACAGAGGGTTGAGACTGACT -s simHuman_chr6.simHuman.chr6 582167 52 + 601863 CAAGTGTATACTGAGAGTCAAAATAACAACAAACAGAGGTCTGAGACAGACA -s simRat_chr6.simRat.chr6 88707 52 - 647215 TGAGTGTGATCTGATGGTCAACTTAATAAAAAACAGCAGATTGAGGTGGACT - -a -s simMouse_chr6.simMouse.chr6 614370 18 + 636262 TGTTATCTGGGACTATGG -s Anc0.Anc0refChr3 210514 18 + 222631 TGATCTGTTGCACAATGG -s Anc1.Anc1refChr1 50725 18 + 69767 TGATCTGTTGCACAATGG -s Anc2.Anc2refChr1 127778 18 + 142988 TGATCTGTTGCACAATGG -s mr.mrrefChr3 161670 18 + 181027 CGTTATCTGGGACAATGG -s simCow_chr6.simCow.chr6 586337 18 + 602619 TGATCTGTTGAACAATAG -s simDog_chr6.simDog.chr6 578377 18 + 593897 TAATCTGTTGCATTATGG -s simHuman_chr6.simHuman.chr6 582221 18 + 601863 TGAGCTACTGCCCAATCG -s simRat_chr6.simRat.chr6 88759 14 - 647215 CAT----TGGAACAATGG - -a -s simMouse_chr6.simMouse.chr6 614388 33 + 636262 CTCTTTATATGTATTCTAGTGCATTGTTGTCCT -s Anc0.Anc0refChr3 210532 33 + 222631 TCCATTACATGTATTCTAGTGCAGTGTTGCCCC -s Anc1.Anc1refChr1 50743 33 + 69767 TCCATTACATGTATTCTAGTGCAGTGTTGCCCC -s Anc2.Anc2refChr1 127796 33 + 142988 TCCATTACATGTATTCTAGTGCAGTGTTGCCCC -s mr.mrrefChr3 161688 33 + 181027 CTCTTTATATGTATTCTAGTGCATTGTTGTCCT -s simCow_chr6.simCow.chr6 586359 33 + 602619 TCAATTGCATGTATTTTAGTCCCGTGTTGCCCC -s simDog_chr6.simDog.chr6 578395 33 + 593897 TCCATCACATGTATTCTAGTGTAGTGTTGCCCC -s simHuman_chr6.simHuman.chr6 582239 33 + 601863 TACATTCCAGGTATTCTAGTACAGCATTGACCC -s simRat_chr6.simRat.chr6 88773 33 - 647215 CTCTTTATACGTATTCTAGTGCATTGTTGTCCT - -a -s simMouse_chr6.simMouse.chr6 614421 24 + 636262 AATTACAGTACACTCTACACACCA -s Anc0.Anc0refChr3 210565 24 + 222631 AATTACAGCATAATGCACCCACCA -s Anc1.Anc1refChr1 50776 24 + 69767 AATTACAGCATAATGCACCCACCA -s Anc2.Anc2refChr1 127829 24 + 142988 AATTACAGCATAATGCACCCACCA -s mr.mrrefChr3 161721 24 + 181027 AATTACAGTACACTCTACACACCA -s simCow_chr6.simCow.chr6 586392 24 + 602619 AATTACAGCATAATGCACCCACCA -s simDog_chr6.simDog.chr6 578428 24 + 593897 AATTACAGCATAACGTACCCACCA -s simHuman_chr6.simHuman.chr6 582273 24 + 601863 AATTACAGCATAATGCACCCACCA -s simRat_chr6.simRat.chr6 88806 24 - 647215 AATTACAGGACACGCTACACACCA - -a -s simMouse_chr6.simMouse.chr6 614445 14 + 636262 GCTGGCAGGTAGGG -s Anc0.Anc0refChr3 210589 14 + 222631 GCTGGCAAGTAGGG -s Anc1.Anc1refChr1 50800 14 + 69767 GCTGGCAAGTAGGG -s Anc2.Anc2refChr1 127853 14 + 142988 GCTGGCCAGTAGGG -s mr.mrrefChr3 161745 14 + 181027 GCTGGCAGGTAGGG -s simCow_chr6.simCow.chr6 586416 14 + 602619 GTCTGCTGGTTGGG -s simDog_chr6.simDog.chr6 578455 14 + 593897 ACTGACCAGTAGGG -s simHuman_chr6.simHuman.chr6 582297 14 + 601863 GCTGGCAAGTAGGG -s simRat_chr6.simRat.chr6 88830 14 - 647215 GCTAGCAGGTAGAG - -a -s simMouse_chr6.simMouse.chr6 614459 1 + 636262 G -s Anc0.Anc0refChr3 210603 1 + 222631 G -s Anc1.Anc1refChr1 50814 1 + 69767 G -s Anc2.Anc2refChr1 127869 1 + 142988 G -s mr.mrrefChr3 161759 1 + 181027 G -s simCow_chr6.simCow.chr6 586432 1 + 602619 T -s simDog_chr6.simDog.chr6 578471 1 + 593897 G -s simHuman_chr6.simHuman.chr6 582311 1 + 601863 G -s simRat_chr6.simRat.chr6 88844 1 - 647215 G - -a -s simMouse_chr6.simMouse.chr6 614460 6 + 636262 CTCCAA -s Anc0.Anc0refChr3 210605 6 + 222631 CTTCAA -s Anc1.Anc1refChr1 50816 6 + 69767 CTTCAA -s Anc2.Anc2refChr1 127871 6 + 142988 CTTCAA -s mr.mrrefChr3 161760 6 + 181027 CTCCAA -s simCow_chr6.simCow.chr6 586434 6 + 602619 CTTCAA -s simDog_chr6.simDog.chr6 578473 3 + 593897 C---AA -s simHuman_chr6.simHuman.chr6 582313 6 + 601863 CTTCAA -s simRat_chr6.simRat.chr6 88845 6 - 647215 CTCCAA - -a -s simMouse_chr6.simMouse.chr6 614466 54 + 636262 TGCACACTGTTTGTTTTAAGCTCTAGTCAAATTTGGCAACAAAAGCATAAATTG -s Anc0.Anc0refChr3 210632 54 + 222631 TGCTCACTGCATACTTTTAGGTAAAGTCAAACTTGGCTACAAAAGCGGAAACTA -s Anc1.Anc1refChr1 50843 54 + 69767 TGCTCACTGCATACTTTTAGGTAAAGTCAAACTTGGCTACAAAAGCGGAAACTA -s Anc2.Anc2refChr1 127898 54 + 142988 TGCTCACTGCAAACTTTATTGTAAAGTCAAATTTGGCTACAAAAGCGGAAACTA -s mr.mrrefChr3 161766 54 + 181027 TGCACACTGTTTGTTTTTAGGTCTAGTCAAACTTGGCAACAAAAGCATAAATTG -s simCow_chr6.simCow.chr6 586461 54 + 602619 TGCCCACCGTACACACTTTGGTAAACTCAAATTTCGCTACAAAAGCTGAAACTA -s simDog_chr6.simDog.chr6 578497 54 + 593897 TGCTCACTGCAAATTTTATTGTAAAGTCTAATTTGGGTACAAAAGTGGGAGTTG -s simHuman_chr6.simHuman.chr6 582340 50 + 601863 TGTTCACTGCATACTTTTAGG----GCCAAACTTGGCTACAAAAGCGGAAACAA -s simRat_chr6.simRat.chr6 88851 50 - 647215 TGCACACTGTTTGTCTTTAGGTCCAGTCAAGCTTGGCAACAAAGG----AATCC - -a -s simMouse_chr6.simMouse.chr6 614520 10 + 636262 GCAAGGTTTG -s Anc0.Anc0refChr3 210686 10 + 222631 GCAAGGTTTG -s Anc1.Anc1refChr1 50897 10 + 69767 GCAAGGTTTG -s Anc2.Anc2refChr1 127952 10 + 142988 TCAAGGTTTG -s mr.mrrefChr3 161820 10 + 181027 GCAAGGTTTG -s simCow_chr6.simCow.chr6 586520 10 + 602619 TCAGAATCAG -s simDog_chr6.simDog.chr6 578551 10 + 593897 TCAAGGATTG -s simHuman_chr6.simHuman.chr6 582390 10 + 601863 GTAAGGTTTG -s simRat_chr6.simRat.chr6 88901 10 - 647215 GCAAGGTTTG - -a -s simMouse_chr6.simMouse.chr6 614530 41 + 636262 TCCGTATCTTTCTAACATTCAATCATTATCAGTATGCACAT -s Anc0.Anc0refChr3 210702 41 + 222631 CCCATATCTTTCCTGCACTCACTCATTATTGGTATGCACAC -s Anc1.Anc1refChr1 50913 41 + 69767 CCCATATCTTTCCTGCACTCACTCATTATTGGTATGCACAC -s Anc2.Anc2refChr1 127968 41 + 142988 CCCGTATCTTTCCTGCACTCACTCATTATTGGTATGCACAC -s mr.mrrefChr3 161836 41 + 181027 TCCATATCTTTCTAACATTCAATCATTATCAGTATGCACAT -s simCow_chr6.simCow.chr6 586536 41 + 602619 CCCGTATCTTTCCCGTATGCACTCATTGTTGCTATGCTTAC -s simDog_chr6.simDog.chr6 578567 41 + 593897 CATGTATCTTTCCTGCCCTCATTCATTATTGGTATGCACAC -s simHuman_chr6.simHuman.chr6 582406 41 + 601863 CCCATATCTTTCCTTCACAGACTCATTATTGGTACACACAC -s simRat_chr6.simRat.chr6 88917 41 - 647215 TCCATAACTTTCTAACATTCTATCATTATCATGATGCACAT - -a -s simMouse_chr6.simMouse.chr6 614571 13 + 636262 AGATACCACAGAT -s Anc0.Anc0refChr3 210764 13 + 222631 AGATATCACAGAT -s Anc1.Anc1refChr1 50975 13 + 69767 AGATATCACAGAT -s Anc2.Anc2refChr1 128034 13 + 142988 AAATATCACAGAT -s mr.mrrefChr3 161877 13 + 181027 AGATATCACAGAT -s simCow_chr6.simCow.chr6 586602 13 + 602619 ACATATCAGGGAC -s simDog_chr6.simDog.chr6 578633 13 + 593897 AAATGTCACAAAT -s simHuman_chr6.simHuman.chr6 582468 13 + 601863 AGATATCGCAGAC -s simRat_chr6.simRat.chr6 88958 13 - 647215 AGATATCACAAAT - -a -s simMouse_chr6.simMouse.chr6 614584 56 + 636262 CTAGTGTAATGCAATAAAAGGGAAACATGCAGCAGTTGATTCTACGTCTTTTGGGG -s Anc0.Anc0refChr3 210777 56 + 222631 CTAGTATAATACTCAAAGAGGCAAACTTAGAGCATTTGATTACAAATTTCCTAGAG -s Anc1.Anc1refChr1 50988 56 + 69767 CTAGTATAATACTCAAAGAGGCAAACTTAGAGCATTTGATTACAAATTTCCTAGAG -s Anc2.Anc2refChr1 128061 56 + 142988 CTAGGAAAATATTCAGAGAGGCAAACCCAGAGCATTTGATTACAAATTTCCTAGAG -s mr.mrrefChr3 161890 56 + 181027 CTAGTGTAATGCAATAAAAGGGAAACTTGCAGCAGTTGATTATAAGTCTTTTAGGG -s simCow_chr6.simCow.chr6 586629 56 + 602619 CTAGCAAAATGTTTAGAGAGGCTAACCCAGAGCAGTTGACTGCAAATTTCCTAGAG -s simDog_chr6.simDog.chr6 578660 56 + 593897 CTAGGAAAGTATTCAGATAGGCAAACCCAGAGGATTTGATCACGAATTTCCTTCAG -s simHuman_chr6.simHuman.chr6 582481 56 + 601863 CTAGTATAATTCTCAAAGAGGCACACTTAGAGCATTTGAATACAATTTTCCCAGAG -s simRat_chr6.simRat.chr6 88971 55 - 647215 CTAGTGTAATGCAATAAAAGGGAAGCTTGTAGCAGTTGATTATAAATCTTTTAGG- - -a -s simMouse_chr6.simMouse.chr6 614640 50 + 636262 GGTCCACTCAAATTAGATGGCTCAAAAGAGCTTTGTGGATGGTGCAAACC -s Anc0.Anc0refChr3 210833 50 + 222631 GGTCCACTTTAATCAGATGGCTCAAAAGAGCTCTGTTGACAGTAAGAATC -s Anc1.Anc1refChr1 51044 50 + 69767 GGTCCACTTTAATCAGATGGCTCAAAAGAGCTCTGTTGACAGTAAGAATC -s Anc2.Anc2refChr1 128117 50 + 142988 GGTCCACTTTAATCTGATGGCTCAAAAGAGCTCTGTTGACAGTAAGAATC -s mr.mrrefChr3 161946 50 + 181027 GGTCCACTTAAATTAGATGGCTCAAAAGAGCTTTGTGGATGGTACGAACC -s simCow_chr6.simCow.chr6 586685 48 + 602619 GGTC-ACTTTAATCTGATGATTCATAAGAGCTC-GCTGACAGTAAGAATC -s simDog_chr6.simDog.chr6 578716 50 + 593897 GGTCCACTTTAATCTGATGGCTTAAAAGAGCTCTGTTGACAGTAACAGTC -s simHuman_chr6.simHuman.chr6 582537 50 + 601863 GGTCCACCTTAATCAGCTGGCTCAAAAGAGCTCTGTTGAATGTAAGAATC -s simRat_chr6.simRat.chr6 626587 50 + 647215 GGTCCACTTGAATTAGATGGCTCAAAAGAGTTTTGTGGATGGTACGAAAC - -a -s simMouse_chr6.simMouse.chr6 614690 33 + 636262 ATGCCTATGAGATTGGTCAATTCATGACACACA -s Anc0.Anc0refChr3 210912 33 + 222631 ATACCTATGAGACTGGGCAATCCACAACATACA -s Anc1.Anc1refChr1 51123 33 + 69767 ATACCTATGAGACTGGGCAATCCACAACATACA -s Anc2.Anc2refChr1 128196 33 + 142988 ATACCTATGAGACTGGGCAATCCACAACATGCA -s mr.mrrefChr3 162025 33 + 181027 ATGCCTATGAGATTGGTCAATTCATGACACACA -s simCow_chr6.simCow.chr6 586762 30 + 602619 ATCCCTATAAGACTGCGTAATCTACAAAAT--- -s simDog_chr6.simDog.chr6 578801 33 + 593897 ATACCTATGAGGCTGGGCAATCCACCACTTGCA -s simHuman_chr6.simHuman.chr6 582616 33 + 601863 ATACCTACGAGACTGGGCAATCCACAACATACA -s simRat_chr6.simRat.chr6 626666 33 + 647215 ATGCCTATGAGATTGGTCAGTTCATGCTGCACA - -a -s simMouse_chr6.simMouse.chr6 614723 56 + 636262 TCTCATATAGTGTCAAAATGCCGTCCAATGCCCACAAACATTCTGCAACGAGCTTA -s Anc0.Anc0refChr3 210945 56 + 222631 TCTTATATGGTGCCAATATGATTCCAAATGCCCGCAAGAATTCTGCCAAGAGCTTG -s Anc1.Anc1refChr1 51156 56 + 69767 TCTTATATGGTGCCAATATGATTCCAAATGCCCGCAAGAATTCTGCCAAGAGCTTG -s Anc2.Anc2refChr1 128229 56 + 142988 TCTTAAATGGTGCCAATATGATTCCAAATGCCTGCAAGACTTCTGCCAAGAGCATG -s mr.mrrefChr3 162058 56 + 181027 TCTCATATAGTGTCAAAATGCCTTCCAATGCCCACAAACATTCTGCCACGAGCTTG -s simCow_chr6.simCow.chr6 586792 56 + 602619 TCTTAAATGGTACCAATATAATTCTACACGCCTCAAAGAGTCTTGCCAAAAGCATG -s simDog_chr6.simDog.chr6 578834 56 + 593897 TTTTAAATGGTGCCAATATGGGTGCAAATGCCTGCAAGTCATCTGGCAAGAGCAGG -s simHuman_chr6.simHuman.chr6 582652 56 + 601863 TCTTCTATGGCGCCAATACCATTCCGAATGCCCGCAAGAATTCTGCCAAGAGCTTG -s simRat_chr6.simRat.chr6 626699 56 + 647215 TCTCACACAGTGTCAACATGCCTTCCAAAGGCCACAAACTTTCTGCCACAAGCTTG - -a -s simMouse_chr6.simMouse.chr6 614779 1 + 636262 T -s Anc0.Anc0refChr3 211005 1 + 222631 T -s Anc1.Anc1refChr1 51216 1 + 69767 T -s Anc2.Anc2refChr1 128289 1 + 142988 T -s mr.mrrefChr3 162114 1 + 181027 T -s simCow_chr6.simCow.chr6 586852 1 + 602619 T -s simDog_chr6.simDog.chr6 578894 1 + 593897 T -s simHuman_chr6.simHuman.chr6 582712 1 + 601863 T -s simRat_chr6.simRat.chr6 626755 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 614780 4 + 636262 GTCT -s Anc0.Anc0refChr3 211006 4 + 222631 GTCT -s Anc1.Anc1refChr1 51217 4 + 69767 GTCT -s Anc2.Anc2refChr1 128290 4 + 142988 GTCT -s mr.mrrefChr3 162115 4 + 181027 GTCT -s simCow_chr6.simCow.chr6 586853 4 + 602619 GTCT -s simDog_chr6.simDog.chr6 578913 4 + 593897 GTCT -s simHuman_chr6.simHuman.chr6 582713 4 + 601863 GTCT -s simRat_chr6.simRat.chr6 626756 4 + 647215 GTCT - -a -s simMouse_chr6.simMouse.chr6 614784 10 + 636262 CAATAAACTG -s Anc0.Anc0refChr3 211010 10 + 222631 CAATCATGTG -s Anc1.Anc1refChr1 51221 10 + 69767 CAATCATGTG -s Anc2.Anc2refChr1 128294 10 + 142988 CGAGCATGGG -s mr.mrrefChr3 162119 10 + 181027 CAATAAACTG -s simCow_chr6.simCow.chr6 586857 2 + 602619 CC-------- -s simDog_chr6.simDog.chr6 578921 10 + 593897 CGAGCATGGG -s simHuman_chr6.simHuman.chr6 582717 10 + 601863 CAGTCATGTG -s simRat_chr6.simRat.chr6 626760 10 + 647215 CAATGAACTG - -a -s simMouse_chr6.simMouse.chr6 614794 31 + 636262 GTCTTGCCCATGCACTATTTAGAGTAAGATT -s Anc0.Anc0refChr3 211020 31 + 222631 GTCTTGCCCATACAGCATCCAGTTTAAGAAT -s Anc1.Anc1refChr1 51231 31 + 69767 GTCTTGCCCATACAGCATCCAGTTTAAGAAT -s Anc2.Anc2refChr1 128313 31 + 142988 ATCTTGCCCATACAGCATCCAGTTTAAGGAT -s mr.mrrefChr3 162129 31 + 181027 GTCTTGCCCATGCACCATCTAGAGTAAGATT -s simCow_chr6.simCow.chr6 586867 31 + 602619 ATCTAGCCCATACAGTATTCAGCTTAAAGAT -s simDog_chr6.simDog.chr6 578940 31 + 593897 ATCTTGCCCATACAGCATCCAGTCTAAGGAT -s simHuman_chr6.simHuman.chr6 582727 21 + 601863 G----------ACAGCATCCAGTTTAAGAAT -s simRat_chr6.simRat.chr6 626770 31 + 647215 GTCTTGCCCATGCACCATCTAGAGTTACATT - -a -s simMouse_chr6.simMouse.chr6 614825 31 + 636262 GTGAACTGCGGAGCCACGAGCCAAAAATCAG -s Anc0.Anc0refChr3 211051 19 + 222631 GTGAACTGCGGGGCTAT------AA------ -s Anc1.Anc1refChr1 51262 19 + 69767 GTGAACTGCGGGGCTAT------AA------ -s Anc2.Anc2refChr1 128344 19 + 142988 GTGAACTGAGGGGCTAT------AA------ -s mr.mrrefChr3 162160 25 + 181027 GTGAACTGCGGAGCCAT------AAAATCAG -s simCow_chr6.simCow.chr6 586898 18 + 602619 GTGCACTGAGGGCATCT------A------- -s simDog_chr6.simDog.chr6 578982 19 + 593897 GTGAACTGAGGGGCTAC------AA------ -s simHuman_chr6.simHuman.chr6 582748 19 + 601863 GTGAATTGCGAGACTAT------AA------ -s simRat_chr6.simRat.chr6 626801 25 + 647215 GTTAACTGAGGAGCCAT------AAAATCAG - -a -s simMouse_chr6.simMouse.chr6 614856 13 + 636262 ATTGAATGTATGG -s Anc0.Anc0refChr3 211070 12 + 222631 ATTGTATGTAT-G -s Anc1.Anc1refChr1 51281 12 + 69767 ATTGTATGTAT-G -s Anc2.Anc2refChr1 128366 12 + 142988 ATTGTATGTAT-G -s mr.mrrefChr3 162185 13 + 181027 ATTGAATGTATGG -s simCow_chr6.simCow.chr6 586919 11 + 602619 ATT-TATGTAT-G -s simDog_chr6.simDog.chr6 579006 12 + 593897 ATTGTATGTAT-G -s simHuman_chr6.simHuman.chr6 582767 12 + 601863 ATTGTGTATAT-G -s simRat_chr6.simRat.chr6 626826 13 + 647215 ATTGAATGTATGG - -a -s simMouse_chr6.simMouse.chr6 614869 15 + 636262 TCCTAGGTCAGAAAG -s Anc0.Anc0refChr3 211082 15 + 222631 CCCTAGGACTGGAAG -s Anc1.Anc1refChr1 51293 15 + 69767 CCCTAGGACTGGAAG -s Anc2.Anc2refChr1 128378 15 + 142988 CCCTAGGACTGGAAG -s mr.mrrefChr3 162198 15 + 181027 TCCTAGGTCAGGAAG -s simCow_chr6.simCow.chr6 586930 15 + 602619 ACCTAGGACGAGGAG -s simDog_chr6.simDog.chr6 579019 15 + 593897 CCCTGGGACTGGAAG -s simHuman_chr6.simHuman.chr6 582779 15 + 601863 CCCTAGGCCTGGAAG -s simRat_chr6.simRat.chr6 626839 15 + 647215 TCTTAGGTCAGGAAG - -a -s simMouse_chr6.simMouse.chr6 614884 22 + 636262 TCAAGCGTGAGACAGGAAAATA -s Anc0.Anc0refChr3 211225 22 + 222631 TGGGGATTAATTCTGGAAAATA -s Anc1.Anc1refChr1 51436 22 + 69767 TGGGGATTAATTCTGGAAAATA -s Anc2.Anc2refChr1 128521 22 + 142988 TGGGGATTAATTCTGGAAAATA -s mr.mrrefChr3 162213 22 + 181027 TCAGGCTTGAGACTGGAAAATA -s simCow_chr6.simCow.chr6 587067 22 + 602619 TGGGTATTAGTTCTGTAAAATA -s simDog_chr6.simDog.chr6 579157 22 + 593897 TCAGGATTGATTCTGGAAAATA -s simHuman_chr6.simHuman.chr6 582947 22 + 601863 TGGGGATTAAATCTGGAAAATA -s simRat_chr6.simRat.chr6 626854 22 + 647215 TCAGGTTTGAGCCTGGAAAATA - -a -s simMouse_chr6.simMouse.chr6 614906 118 + 636262 GTTGGGGTCTTTCTAGAGTGGTTCCTTGACATAATTGGTGTCGCAATTGAAATACCAAGGTATACCATTTTAGTGTATACCACTTTAGTGGTCTAACAGAAAAGATGGGGTGGGCAAG -s Anc0.Anc0refChr3 211248 103 + 222631 GTTGAGGTCTTCCCAGAGCATCTTCCTGATAAGATAGGTGCCCTGGTTAAAATACCAAAGTATACCATTTTAG------------TA---ATCTAAAATAAAAGATAGGGCAGATGAG -s Anc1.Anc1refChr1 51459 105 + 69767 GTTGAGGTCTTCCCAGAGCATCTTCCTGATAAGATAGGTGCCCTGGTTAAAATACCAAAGTATACCATTTTAG------------TAGT-ATCTAAAATAAAAGATAGGGCAGATGAG -s Anc2.Anc2refChr1 128544 103 + 142988 GTTGAGGTCTTCCCAGAGCATCTTCCTGATAAGATAGGTGCCCTGGTTAAGATACCAGAGTATACCATTTTAG------------TG---ATCCAAAATAAAAGATAGGGCAGATGAG -s mr.mrrefChr3 162235 118 + 181027 GTTGGGGTCTTTCTAGAGTGGTTCCTTGACAAGATAGGTGTCGCAATTGAAATACCAAGGTATACCATTTTAGTGTATACCACTTTAGTTGTCTAACAGAAAAGATGGGGTGGGCAAG -s simCow_chr6.simCow.chr6 587090 102 + 602619 GATGAGATCTTCCCAGAGCATCTTCCTGATAAGTTAGGTGCC-TGGTTAAGATACCAGAGTATACCATTCTAG------------TC---ACCTAAAATACAAGGGAGAGCAGATGAG -s simDog_chr6.simDog.chr6 579180 89 + 593897 GTTCAGGCCCTCCCAGAGTTTGTTCCGGACATGATAAGTGCGCTAG------------AGTATAC--TTTTAG------------TG---ATCCAAAATAAAATATAGGGCATATGAG -s simHuman_chr6.simHuman.chr6 582970 102 + 601863 GTTGAAGTCTTCCCGGAGCATCTTCCTGATAAGATAGGTGCCCTGGTTAGACTAACAACGTATATCATTTTAG------------TAGT----TAAAAAAGTAGATAGGGCAGATGAG -s simRat_chr6.simRat.chr6 626876 118 + 647215 GGTGGGGTCTTTCTAGAGTGGTTCCTTGACAAGGTAGGTGTCACAATTGAGATACCAAGGTATACCATTTTAGTGTATACCATTTTAGTTGTCTAATGGAAAAGATGGGGTGGGCAAG - -a -s simMouse_chr6.simMouse.chr6 615024 66 + 636262 TTTAAGTGGTCCTGATATGTCTGAGTGACCTCTGTGCCAGGAATGTTGGTCACTTGTGGGCCTTCC -s Anc0.Anc0refChr3 211359 66 + 222631 CTTTAGTTGTCCAGATATATCTGAATGACCTCTATGCCAGGTATGGTGGTCACCTGTGGGACTTCC -s Anc1.Anc1refChr1 51572 66 + 69767 CTTTAGTTGTCCAGATATATCTGAATGACCTCTATGCCAGGTATGGTGGTCACCTGTGGGACTTCC -s Anc2.Anc2refChr1 128655 66 + 142988 CTTTCATTGTCCAGATGTATCTGAATGACCTCTATGCCAGGTACCGTGGCCACCTGTGGGACTTCC -s mr.mrrefChr3 162353 66 + 181027 CTTAAGTGGTCCTGATATGTCTGAGTGACCTCTGTGCCAGGTATGGTGGTCACTTGTGGGCCTTCC -s simCow_chr6.simCow.chr6 587200 65 + 602619 CTTTCATTTTCCTGATGTCTCTGCATAACCCCCATGCCAGGTACAGTGGCCACCTGTGGG-CTTTC -s simDog_chr6.simDog.chr6 579277 66 + 593897 CTCTCATTGTCCAGATGTATTTGACTGACCTGTTTGCCAGGTACCGTGGCAACCTGTGGGACTTCT -s simHuman_chr6.simHuman.chr6 583080 65 + 601863 CTTTAGTTGTCCATCTATATCGTAACGAGCTCTACGCCACGTATGGTGGTCACCTT-GGGACTTCC -s simRat_chr6.simRat.chr6 626994 50 + 647215 CTCAACTGGT----------------GACCACTGTGCCATGTATAGTGGTTACATGTGGGCCTTCC - -a -s simMouse_chr6.simMouse.chr6 615090 28 + 636262 ATGGATACATTTATGGTAACACTGTCTC -s Anc0.Anc0refChr3 211425 28 + 222631 ATGTACACATTCCTGCTAACACTGGCTC -s Anc1.Anc1refChr1 51638 28 + 69767 ATGTACACATTCCTGCTAACACTGGCTC -s Anc2.Anc2refChr1 128721 28 + 142988 ATGTTCACATTCCTGCTAACACTGTTTC -s mr.mrrefChr3 162419 28 + 181027 ATGGATACATTTATGGTAACACTGGCTC -s simCow_chr6.simCow.chr6 587265 28 + 602619 ATGTGCACATACCTGTTATCAATGTTAT -s simDog_chr6.simDog.chr6 579343 28 + 593897 ATGTTCACATTCCTGCTAACCCTCTTTC -s simHuman_chr6.simHuman.chr6 583146 28 + 601863 ATGTACACATTCCTGCTAACACTGGCTC -s simRat_chr6.simRat.chr6 627044 28 + 647215 ATGCATATATTTATGGTAACACTGGCTC - -a -s simMouse_chr6.simMouse.chr6 615118 11 + 636262 AGTACATCTGG -s Anc0.Anc0refChr3 211458 11 + 222631 TGAAGGTCCAG -s Anc1.Anc1refChr1 51671 11 + 69767 TGAAGGTCCAG -s Anc2.Anc2refChr1 128754 11 + 142988 AGAGGGTCCAG -s mr.mrrefChr3 162447 11 + 181027 TGTACATCCAG -s simCow_chr6.simCow.chr6 587298 11 + 602619 GGAGGGTCCAG -s simDog_chr6.simDog.chr6 579376 11 + 593897 AGAGGGTCCAG -s simHuman_chr6.simHuman.chr6 583179 11 + 601863 TGGAGGTCCAG -s simRat_chr6.simRat.chr6 627072 11 + 647215 TGTACATCCAG - -a -s simMouse_chr6.simMouse.chr6 615129 12 + 636262 CAACATTGTCTT -s Anc0.Anc0refChr3 211469 12 + 222631 TACCATTGTCCT -s Anc1.Anc1refChr1 51682 12 + 69767 TACCATTGTCCT -s Anc2.Anc2refChr1 128765 12 + 142988 TACAAGTGTCCT -s mr.mrrefChr3 162458 12 + 181027 CAACATTGTCTT -s simCow_chr6.simCow.chr6 587309 12 + 602619 AACACGAGTCCA -s simDog_chr6.simDog.chr6 579399 12 + 593897 TATAAGTGCCTT -s simHuman_chr6.simHuman.chr6 583190 12 + 601863 TACCATTGTCCT -s simRat_chr6.simRat.chr6 627083 12 + 647215 CATCATCGCCTT - -a -s simMouse_chr6.simMouse.chr6 615141 13 + 636262 AGACTAGCCAAAA -s Anc0.Anc0refChr3 211481 12 + 222631 AGACTAGCCTAA- -s Anc1.Anc1refChr1 51694 13 + 69767 AGACTAGCCTAAA -s Anc2.Anc2refChr1 128778 12 + 142988 AGACTAGTCTAA- -s mr.mrrefChr3 162470 13 + 181027 AGACTAGCCAAAA -s simCow_chr6.simCow.chr6 587322 12 + 602619 TGATTAGTCCGA- -s simDog_chr6.simDog.chr6 579412 12 + 593897 AAACTAGTCTAA- -s simHuman_chr6.simHuman.chr6 583202 13 + 601863 CAGATAGCCTAAA -s simRat_chr6.simRat.chr6 627095 13 + 647215 AGACTAGCCAAAA - -a -s simMouse_chr6.simMouse.chr6 615154 40 + 636262 TAATAGAGTCTTCCACTGACAGATCCAATTCTACCCCACG -s Anc0.Anc0refChr3 211493 11 + 222631 TAATGTAACCT----------------------------- -s Anc1.Anc1refChr1 51707 11 + 69767 TAATGTAACCT----------------------------- -s Anc2.Anc2refChr1 128790 11 + 142988 TATTGTAACCT----------------------------- -s mr.mrrefChr3 162483 40 + 181027 TAATAGAGTCTTCCACTGACAGATCCAATTCTACCCCACG -s simCow_chr6.simCow.chr6 587334 11 + 602619 TACTGTAACAT----------------------------- -s simDog_chr6.simDog.chr6 579424 11 + 593897 TATGGAAACCT----------------------------- -s simHuman_chr6.simHuman.chr6 583215 11 + 601863 TAATGTAACCT----------------------------- -s simRat_chr6.simRat.chr6 627109 40 + 647215 TAATAGAGTCTACCACTGAAAAACCTTCTTCTACCCCAAG - -a -s simMouse_chr6.simMouse.chr6 615194 23 + 636262 CTCTACCCTAGGGTATAGTAGTA -s Anc0.Anc0refChr3 211504 22 + 222631 -TCTACCCCAGGATACAAAAGTA -s Anc1.Anc1refChr1 51718 22 + 69767 -TCTACCCCAGGATACAAAAGTA -s Anc2.Anc2refChr1 128801 22 + 142988 -TCCACCACAGGATACAAAGGTA -s mr.mrrefChr3 162523 23 + 181027 CTCTACCCCAGGGTATAGTAGTA -s simCow_chr6.simCow.chr6 587345 22 + 602619 -TCCACCACAGGATGTTAAGGTA -s simDog_chr6.simDog.chr6 579435 22 + 593897 -TCCACCACAAGATACAGAGGTA -s simHuman_chr6.simHuman.chr6 583226 22 + 601863 -TCTACCCCAGGATACAAAAATA -s simRat_chr6.simRat.chr6 627152 23 + 647215 CTCTACCCCAGTGTATGGTAGTA - -a -s simMouse_chr6.simMouse.chr6 615217 11 + 636262 ATTCAAGCATC -s Anc0.Anc0refChr3 211526 11 + 222631 AATCAGGTCTT -s Anc1.Anc1refChr1 51740 11 + 69767 AATCAGGTCTT -s Anc2.Anc2refChr1 128823 11 + 142988 AATCAGGTCTT -s mr.mrrefChr3 162546 11 + 181027 ATTCAGGCCTC -s simCow_chr6.simCow.chr6 587367 10 + 602619 AGT-GGGTCTT -s simDog_chr6.simDog.chr6 579463 11 + 593897 AATCAGGTCTT -s simHuman_chr6.simHuman.chr6 583248 11 + 601863 AATCAGGTCTT -s simRat_chr6.simRat.chr6 627175 11 + 647215 ATGCAGGCCTC - -a -s simMouse_chr6.simMouse.chr6 615228 39 + 636262 ACACAATCCAACAGGATGCCATGCAAACAATGCAGACTG -s Anc0.Anc0refChr3 211549 36 + 222631 GAATAGCACAATGGGATGCCATGTAAACAATGCA-A--A -s Anc1.Anc1refChr1 51763 36 + 69767 GAATAGCACAATGGGATGCCATGTAAACAATGCA-A--A -s Anc2.Anc2refChr1 128846 36 + 142988 GAATAGCACAATGGGTTGCCATGTAAACAATGCA-A--A -s mr.mrrefChr3 162557 37 + 181027 ACATAATCCAACAGGATGCCATGCAAACAATGCAGA--G -s simCow_chr6.simCow.chr6 587389 33 + 602619 AA---GCACAATGGGTCAACTTGTACACAGTGCA-G--A -s simDog_chr6.simDog.chr6 579486 36 + 593897 GCATAGGACACTGGGTTGCCATATAAACAAAGTA-A--A -s simHuman_chr6.simHuman.chr6 583271 36 + 601863 GAATAGCACAATGGGATGCCATGTAAGCAATGCA-A--A -s simRat_chr6.simRat.chr6 627186 37 + 647215 ACATAATTCAACAGGATGCCATGCAAACAATGCAGA--G - -a -s simMouse_chr6.simMouse.chr6 615267 4 + 636262 ATAC -s Anc0.Anc0refChr3 211585 4 + 222631 ACAC -s Anc1.Anc1refChr1 51799 4 + 69767 ACAC -s Anc2.Anc2refChr1 128885 4 + 142988 ACAC -s mr.mrrefChr3 162594 4 + 181027 ATAC -s simCow_chr6.simCow.chr6 587425 4 + 602619 CCAC -s simDog_chr6.simDog.chr6 579525 4 + 593897 ACAC -s simHuman_chr6.simHuman.chr6 583307 4 + 601863 ACAC -s simRat_chr6.simRat.chr6 627223 4 + 647215 ATAT - -a -s simMouse_chr6.simMouse.chr6 615271 4 + 636262 ATTG -s Anc0.Anc0refChr3 211589 4 + 222631 AATG -s Anc1.Anc1refChr1 51803 4 + 69767 AATG -s Anc2.Anc2refChr1 128889 4 + 142988 AATG -s mr.mrrefChr3 162598 4 + 181027 ATTG -s simCow_chr6.simCow.chr6 587430 4 + 602619 AATG -s simDog_chr6.simDog.chr6 579529 4 + 593897 AGTG -s simHuman_chr6.simHuman.chr6 583311 4 + 601863 AATG -s simRat_chr6.simRat.chr6 627227 3 + 647215 ATT- - -a -s simMouse_chr6.simMouse.chr6 615275 68 + 636262 TAAGCAAGTCAGAATTGCTGGTAGCCCTACCGGTAAACACCTGAAGACGGGCTCGTGAAGTGTAAACT -s Anc0.Anc0refChr3 211593 52 + 222631 TA---------------CTGATGGCCCAACCAGTAATGACCAGAGGTTGAGCTCA-GATGTCTCAAAT -s Anc1.Anc1refChr1 51807 52 + 69767 TA---------------CTGATGGCCCAACCAGTAATGACCAGAGGTTGAGCTCA-GATGTCTCAAAT -s Anc2.Anc2refChr1 128893 52 + 142988 TA---------------CTAATGGCCCAATCAGTAATGACCAAAGGTTGAGCTCA-GATGTCTAAAAT -s mr.mrrefChr3 162602 66 + 181027 TAAGCAAGTCA--ATTGCTGGTGGCCCTACCAGTAAACACCTGAGGATGAGCTCGTGAAGTGTCAAAT -s simCow_chr6.simCow.chr6 587434 52 + 602619 TA---------------TTAATGGCCCAATCAGTAATGTCCAAGGGATGAGCTCA-GAAGTCTTAAGT -s simDog_chr6.simDog.chr6 579534 51 + 593897 TA---------------CTAGTGGCCCCATCAGTAATGACCA-AGCTTGAGTTTG-TATGTCTAAGAT -s simHuman_chr6.simHuman.chr6 583315 52 + 601863 TA---------------CTGATGGCGCAGCTAGTAATAAACAGAGGGTGACCTCA-GATGTCTCAAAT -s simRat_chr6.simRat.chr6 627230 66 + 647215 TAAGCAAGTCA--ATTGTTGGTGGCCCTACCAGTAAGCCCCTGAGGATGAGCTGCTGAAGTGTCAAAT - -a -s simMouse_chr6.simMouse.chr6 615343 70 + 636262 TGCCACTACTATGAGCTATTGGGTAGGAGGCAGGACTCAGGTTCATAATGTGAGCACAGCATGCTGCCTG -s Anc0.Anc0refChr3 211645 58 + 222631 GT------------GCTGTTGGGTGAGAGGTAGGACTCCAGTTCATGATGTGAACATAGCATGCTGCCTT -s Anc1.Anc1refChr1 51859 58 + 69767 GT------------GCTGTTGGGTGAGAGGTAGGACTCCAGTTCATGATGTGAACATAGCATGCTGCCTT -s Anc2.Anc2refChr1 128957 58 + 142988 GT------------GCTGTTGGGTGAGAGATAGGACTTCAGTTCATGATCTGAACCTAGCATGCTGCCTT -s mr.mrrefChr3 162668 58 + 181027 TG------------GCTATTGGGTAGGAGGCAGGACTCAGGTTCATGATGTGAGCACAGCATGCTGCCTG -s simCow_chr6.simCow.chr6 587498 58 + 602619 GT------------GCTGTTGGGTGAGAGATAGCACTTCAGTTATTGATACGAACCTAGCATGCTGCCTT -s simDog_chr6.simDog.chr6 579597 58 + 593897 GT------------GCTGTTGGGTGAGAGATAGGACTTCAATTCACGATCTGAACCTGGCATGCTGCCTT -s simHuman_chr6.simHuman.chr6 583367 58 + 601863 GT------------GTTGTTGGGTGTGAGGTAGTACTCCAGTTCATGATGTGAACATAGCATGCTGCCTA -s simRat_chr6.simRat.chr6 627296 58 + 647215 TG------------GCTATTGGGTAACAGGCAGGACTCTGATTCATGATGGGAGCACAGCATGCTGCCCT - -a -s simMouse_chr6.simMouse.chr6 615413 37 + 636262 TGAATCTAGGGGCATGGGATTTGTATTGTACTATGAG -s Anc0.Anc0refChr3 211703 33 + 222631 CAAATCTAGGGGCTTGAGGTC--TATTGTACTAT--G -s Anc1.Anc1refChr1 51917 33 + 69767 CAAATCTAGGGGCTTGAGGTC--TATTGTACTAT--G -s Anc2.Anc2refChr1 129015 33 + 142988 CAAATCTAGGGCCTGGAGGTC--ACTTGCACTAT--G -s mr.mrrefChr3 162726 37 + 181027 TGAATCTAGGGGCATGAGGTTTGTATTGTACTATGAG -s simCow_chr6.simCow.chr6 587561 18 + 602619 CAAACCTGGGGTGT------------TCAA------- -s simDog_chr6.simDog.chr6 579655 33 + 593897 CAAATCTAGGGCCTGGAGGTC--ACTTGCACTAT--G -s simHuman_chr6.simHuman.chr6 583425 33 + 601863 CAAGGCTAGGGGTTTGAGGTC--TATTGTACTGT--G -s simRat_chr6.simRat.chr6 627354 37 + 647215 TGAACCTAGGGGCATGAGGTTATTATTTTACTATGAG - -a -s simMouse_chr6.simMouse.chr6 615450 9 + 636262 GTCTTGCAT -s Anc0.Anc0refChr3 211736 9 + 222631 GTCTAACAT -s Anc1.Anc1refChr1 51950 9 + 69767 GTCTAACAT -s Anc2.Anc2refChr1 129048 9 + 142988 GTGTAATAT -s mr.mrrefChr3 162763 9 + 181027 GTCTTGCAT -s simCow_chr6.simCow.chr6 587579 4 + 602619 -----ATGT -s simDog_chr6.simDog.chr6 579690 9 + 593897 GTGTAATAT -s simHuman_chr6.simHuman.chr6 583458 9 + 601863 GTCTAACTA -s simRat_chr6.simRat.chr6 627391 9 + 647215 GCCTCGCAT - -a -s simMouse_chr6.simMouse.chr6 615459 4 + 636262 TGCT -s Anc0.Anc0refChr3 211748 4 + 222631 TAGT -s Anc1.Anc1refChr1 51962 4 + 69767 TAGT -s Anc2.Anc2refChr1 129060 4 + 142988 TAGT -s mr.mrrefChr3 162775 4 + 181027 TGCT -s simCow_chr6.simCow.chr6 587586 4 + 602619 TAGT -s simDog_chr6.simDog.chr6 579702 4 + 593897 TAGT -s simHuman_chr6.simHuman.chr6 583470 4 + 601863 TAGT -s simRat_chr6.simRat.chr6 627403 4 + 647215 TGCC - -a -s simMouse_chr6.simMouse.chr6 615463 3 + 636262 AAT -s Anc0.Anc0refChr3 211752 3 + 222631 AAT -s Anc1.Anc1refChr1 51966 3 + 69767 AAT -s Anc2.Anc2refChr1 129067 3 + 142988 AGT -s mr.mrrefChr3 162779 3 + 181027 AAT -s simCow_chr6.simCow.chr6 587593 3 + 602619 AGT -s simDog_chr6.simDog.chr6 579709 3 + 593897 AGT -s simHuman_chr6.simHuman.chr6 583474 3 + 601863 AAT -s simRat_chr6.simRat.chr6 627407 1 + 647215 G-- - -a -s simMouse_chr6.simMouse.chr6 615466 8 + 636262 AGATCCGT -s Anc0.Anc0refChr3 211769 8 + 222631 AGATGTGT -s Anc1.Anc1refChr1 51983 8 + 69767 AGATGTGT -s Anc2.Anc2refChr1 129084 8 + 142988 AGATGTGG -s mr.mrrefChr3 162782 8 + 181027 AGATCCGT -s simCow_chr6.simCow.chr6 587610 8 + 602619 AGATATGG -s simDog_chr6.simDog.chr6 579726 8 + 593897 AGATGTGG -s simHuman_chr6.simHuman.chr6 583491 8 + 601863 AGATTTGT - -a -s simMouse_chr6.simMouse.chr6 615474 5 + 636262 CCATA -s Anc0.Anc0refChr3 211777 4 + 222631 T-ATA -s Anc1.Anc1refChr1 51991 4 + 69767 T-ATA -s Anc2.Anc2refChr1 129092 4 + 142988 T-ATA -s mr.mrrefChr3 162790 4 + 181027 C-ATA -s simCow_chr6.simCow.chr6 587624 4 + 602619 T-ATA -s simDog_chr6.simDog.chr6 579734 4 + 593897 C-ATA -s simHuman_chr6.simHuman.chr6 583499 4 + 601863 T-ATA - -a -s simMouse_chr6.simMouse.chr6 615479 24 + 636262 TGCATGAGACCCAGAGCAAATGCT -s Anc0.Anc0refChr3 211781 24 + 222631 TCCCTCAAACACATAGTGCTTGAG -s Anc1.Anc1refChr1 51995 24 + 69767 TCCCTCAAACACATAGTGCTTGAG -s Anc2.Anc2refChr1 129098 24 + 142988 TCCCTCAAACACATGGTGCTTGAG -s mr.mrrefChr3 162794 24 + 181027 TGCATGAGACCCAGAGCAAATGCT -s simCow_chr6.simCow.chr6 587630 24 + 602619 CCCCTCAAATGTTTGGCGCTTGAG -s simDog_chr6.simDog.chr6 579740 24 + 593897 TCCCTCGAACACAGGGTGCTTGAG -s simHuman_chr6.simHuman.chr6 583503 24 + 601863 TCCCTCAAACACATAGTGCTTGAG - -a -s simMouse_chr6.simMouse.chr6 615503 7 + 636262 AAGTGGT -s Anc0.Anc0refChr3 211805 7 + 222631 ATATTGT -s Anc1.Anc1refChr1 52019 7 + 69767 ATATTGT -s Anc2.Anc2refChr1 129143 7 + 142988 ATACTGT -s mr.mrrefChr3 162818 7 + 181027 AAGTGGT -s simCow_chr6.simCow.chr6 587675 3 + 602619 ATA---- -s simDog_chr6.simDog.chr6 579785 7 + 593897 ATACTGT -s simHuman_chr6.simHuman.chr6 583527 7 + 601863 AGATTGT - -a -s simMouse_chr6.simMouse.chr6 615510 45 + 636262 TGAGAGCAAATGGTCACACATGTGATATTGTAGTATTGATTTGGG -s Anc0.Anc0refChr3 211813 26 + 222631 TTAAAGCAAATCATTAC-------------------AGATATGAG -s Anc1.Anc1refChr1 52027 26 + 69767 TTAAAGCAAATCATTAC-------------------AGATATGAG -s Anc2.Anc2refChr1 129151 26 + 142988 TTATACTAAATAAGTAT-------------------AGATATGAA -s mr.mrrefChr3 162825 45 + 181027 TGAAAGCAAATCATCACACATGTGATATTGTAGTATTGGTATGGG -s simCow_chr6.simCow.chr6 587678 13 + 602619 -------------GTAT-------------------AGATATGAA -s simDog_chr6.simDog.chr6 579793 26 + 593897 TTATACTAAATAAGTGT-------------------AGATGTGAA -s simHuman_chr6.simHuman.chr6 583535 26 + 601863 TTGAAGCAAATCATTAC-------------------AGACATGCG -s simRat_chr6.simRat.chr6 627408 43 + 647215 TGAAGGCAAACCATCATATATG--ATATTGCAGTATTGGTATGGG - -a -s simMouse_chr6.simMouse.chr6 615555 25 + 636262 GGTAATTTGGGGGTATCAAATATAT -s Anc0.Anc0refChr3 211842 7 + 222631 GAAAAT-------------A----- -s Anc1.Anc1refChr1 52056 7 + 69767 GAAAAT-------------A----- -s Anc2.Anc2refChr1 129180 7 + 142988 TAAAAT-------------A----- -s mr.mrrefChr3 162870 12 + 181027 GGTAAT-------------ATATAT -s simCow_chr6.simCow.chr6 587694 7 + 602619 AAAAAT-------------A----- -s simDog_chr6.simDog.chr6 579822 7 + 593897 TAAAAT-------------A----- -s simHuman_chr6.simHuman.chr6 583564 7 + 601863 GAGAAT-------------A----- -s simRat_chr6.simRat.chr6 627451 12 + 647215 GGTAAC-------------AAATAT - -a -s simMouse_chr6.simMouse.chr6 615580 161 + 636262 ATCAGATCAAACTCCTACTATCTAGTTTAATTAAACCAGAGGCTAGTCAAAAAGAAAGAAGGACCATATGGCATGCAAGTGGGAACTGTATTGACAGGTATTGGCAAGTGAGGTCCCTGTGTCAGTCAATGGGCATGAGACTATTTGAGTGACAGCTGTAA -s Anc0.Anc0refChr3 211849 127 + 222631 ATCGGAACAAACTCC---TCTTTAGTAGAACCAGATAAAAGACAAGTCAAAAAGGGA-AAGGACCATTTGACAGG----T--GACCT------------------------AGACCCTATTTTAGACAGTGGGCTTTAGTCTACTTTAGTAACAGCTGGAA -s Anc1.Anc1refChr1 52063 127 + 69767 ATCGGAACAAACTCC---TCTTTAGTAGAACCAGATAAAAGACAAGTCAAAAAGGGA-AAGGACCATTTGACAGG----T--GACCT------------------------AGACCCTATTTTAGACAGTGGGCTTTAGTCTACTTTAGTAACAGCTGGAA -s Anc2.Anc2refChr1 129188 127 + 142988 ATCGGAACAAACTCC---TATTTAGTAGAACCAGATAAAAGACAAGTCAAAAAGGGA-AAGGACTGTTTGACAGG----T--GACCT------------------------AGACCCTATTTAAGACAGTGGGCTTTAGTCCACTTTAGTAACAGCTGGAA -s mr.mrrefChr3 162882 156 + 181027 ATCAGATCAAACTCCTA-TCTCTAGTTTAATCAAATCAGAGGCTAGTCAAAAAGAGAGAAGGACCATATGACATG----TGGGACCTGTATTGACAGGTATTGGCAAGTGAGGACCCTGTGTTAGTCAATGGGCATGAGACTATTTGAGTGACAGCTGTAA -s simCow_chr6.simCow.chr6 587702 115 + 602619 ATCGGAACAGACTCC---TATATGGTAGAACCACATAAAAGACAAGTCAAAAAGGGG-AAGGACTGTTTGACTGG----T--GATCT------------------------AGACTCTTTTTCAGACAGTGGGCCTTATT------------TAACTGGAA -s simDog_chr6.simDog.chr6 579830 127 + 593897 ACCAGAACAAACTCC---TATTTAGTAGAACCAGATAGAGGACATGTCAAAAAGGCA-AAGGCCTGTTCGACAGG----T--GACCT------------------------AGACCCTATTTAAGACAGCGGGCTCTGGTCCACTTTAGTAACAGCTAGAA -s simHuman_chr6.simHuman.chr6 583571 126 + 601863 ATTGGAACAAACTCC---TCTTTAGTAGAACCAGATGAAAGACAAGTCATAAAGGGA-AAGGACCATTTGACAGG----T--GACCT------------------------AGACCCTAC-CTAGACACTTGGCTTTAGTGTGCTTTGGTAAGAGCTGGAA -s simRat_chr6.simRat.chr6 627463 156 + 647215 ACCAGGTCAAAATCCTA-TCTCTAGTTTAATCATATAAGAGGATAGCCGGAAAGAGAGAAAGACCATATGACATG----TGGGACCTGTATTGACAGGTATTAGCAAGTGTGGACTCTGTGTTAGTCAATGAGCATGAGACTATTTGAGTGACAGCTGTAA - -a -s simMouse_chr6.simMouse.chr6 615741 7 + 636262 ACCATCC -s Anc0.Anc0refChr3 211976 7 + 222631 ACCATGT -s Anc1.Anc1refChr1 52190 7 + 69767 ACCATGT -s Anc2.Anc2refChr1 129315 7 + 142988 ACCATGT -s mr.mrrefChr3 163038 7 + 181027 ACCATCC -s simCow_chr6.simCow.chr6 587817 7 + 602619 ACCATGA -s simDog_chr6.simDog.chr6 579957 7 + 593897 ACTATGT -s simHuman_chr6.simHuman.chr6 583697 7 + 601863 ACCATGT -s simRat_chr6.simRat.chr6 627626 7 + 647215 ACCATCC - -a -s simMouse_chr6.simMouse.chr6 615748 13 + 636262 CCTCACTACCAAT -s Anc0.Anc0refChr3 211988 10 + 222631 ---CTCTACTAAT -s Anc1.Anc1refChr1 52202 13 + 69767 TTTCTCTACTAAT -s Anc2.Anc2refChr1 129327 10 + 142988 ---CTCTACTAAT -s mr.mrrefChr3 163045 13 + 181027 CCTCACTACTAAT -s simCow_chr6.simCow.chr6 587824 10 + 602619 ---CTCCACTAAT -s simDog_chr6.simDog.chr6 579969 10 + 593897 ---CCCTACTAAT -s simHuman_chr6.simHuman.chr6 583715 13 + 601863 TTTCTCTACTAAC -s simRat_chr6.simRat.chr6 627633 13 + 647215 CCTCACTATTAAT - -a -s simMouse_chr6.simMouse.chr6 615761 10 + 636262 ACTAAGGGAG -s Anc0.Anc0refChr3 211998 10 + 222631 AAAAAGGAGG -s Anc1.Anc1refChr1 52215 10 + 69767 AAAAAGGAGG -s Anc2.Anc2refChr1 129338 10 + 142988 AAAAAGGAGG -s mr.mrrefChr3 163058 10 + 181027 ACTAAGGGGG -s simCow_chr6.simCow.chr6 587835 10 + 602619 AGAAAGGAGA -s simDog_chr6.simDog.chr6 579980 10 + 593897 AAAAAGGAAG -s simHuman_chr6.simHuman.chr6 583728 10 + 601863 AAAAAGGAGG -s simRat_chr6.simRat.chr6 627646 10 + 647215 ACTAAGAGGG - -a -s simMouse_chr6.simMouse.chr6 615771 23 + 636262 GACTACTCAAAGTTAAACCTTCT -s Anc0.Anc0refChr3 212025 13 + 222631 GGCTACCAAAAGT---------- -s Anc1.Anc1refChr1 52242 13 + 69767 GGCTACCAAAAGT---------- -s Anc2.Anc2refChr1 129365 13 + 142988 GGTTACCAAAACT---------- -s mr.mrrefChr3 163068 13 + 181027 GACTACTCAAAGT---------- -s simCow_chr6.simCow.chr6 587862 13 + 602619 GGTTACCCAAACT---------- -s simDog_chr6.simDog.chr6 580007 13 + 593897 GATTACCAAAACT---------- -s simHuman_chr6.simHuman.chr6 583755 13 + 601863 GGCGACCAAAAGT---------- -s simRat_chr6.simRat.chr6 627656 13 + 647215 GATTACTCAAAAT---------- - -a -s simMouse_chr6.simMouse.chr6 615794 8 + 636262 AGACCTTC -s Anc0.Anc0refChr3 212039 8 + 222631 AGACCAAC -s Anc1.Anc1refChr1 52256 8 + 69767 AGACCAAC -s Anc2.Anc2refChr1 129379 8 + 142988 AGACCAAC -s mr.mrrefChr3 163081 8 + 181027 AGACCTTC -s simCow_chr6.simCow.chr6 587876 8 + 602619 GGACCAAC -s simDog_chr6.simDog.chr6 580021 8 + 593897 AGAGCAAC -s simHuman_chr6.simHuman.chr6 583769 8 + 601863 ACACCAAT -s simRat_chr6.simRat.chr6 627669 8 + 647215 AGACCTCC - -a -s simMouse_chr6.simMouse.chr6 615802 16 + 636262 ACATTAATTGCTTCTT -s Anc0.Anc0refChr3 212049 16 + 222631 AATGTAATTGCTTCTT -s Anc1.Anc1refChr1 52266 16 + 69767 AATGTAATTGCTTCTT -s Anc2.Anc2refChr1 129389 16 + 142988 AATGTAATTGCCACTT -s mr.mrrefChr3 163091 16 + 181027 ACAGTAATTGCTTCTT -s simCow_chr6.simCow.chr6 587886 16 + 602619 AAAGTAATTACCACTT -s simDog_chr6.simDog.chr6 580031 16 + 593897 GATGTAATTGCCACTT -s simHuman_chr6.simHuman.chr6 583779 16 + 601863 ATTGTAATTGCTTCTT -s simRat_chr6.simRat.chr6 627679 16 + 647215 AAAGTAAGTGCTTCCT - -a -s simMouse_chr6.simMouse.chr6 615818 27 + 636262 TGTCTGGGCCCTACAGCAATAGCATCT -s Anc0.Anc0refChr3 212065 15 + 222631 TG----------GCGGAAAAA--ATAT -s Anc1.Anc1refChr1 52282 25 + 69767 TGCCGAGATAGGGCGGAAAAA--ATAT -s Anc2.Anc2refChr1 129405 15 + 142988 TG----------GCAAAAAAA--ATCT -s mr.mrrefChr3 163107 27 + 181027 TGCCTGGGCCCTACGGCAATAGCATAT -s simCow_chr6.simCow.chr6 587902 14 + 602619 TG----------GCAAAAAAA--AT-T -s simDog_chr6.simDog.chr6 580047 15 + 593897 TG----------GCAAGAATG--ATCT -s simHuman_chr6.simHuman.chr6 583797 25 + 601863 TGCCGAGATAGGGCGGAAAAA--ATAT -s simRat_chr6.simRat.chr6 627695 27 + 647215 TGCCTGGGCCCTTCGGCCATAGCATAT - -a -s simMouse_chr6.simMouse.chr6 615845 100 + 636262 GCAAATATGTTAGCATTAGAAATCATATGACAGCCAACGAACCACATATGGAAGCCCGGCATGCCTTGTCAACCAATGAGATATATATTATAATTCCTGT -s Anc0.Anc0refChr3 212080 50 + 222631 GCAGATATGTTAGCTGCAAAAACCTTAC-----------------------------------------------TGTAGACCAATATTGTAAT---TGT -s Anc1.Anc1refChr1 52307 50 + 69767 GCAGATATGTTAGCTGCAAAAACCTTAC-----------------------------------------------TGTAGACCAATATTGTAAT---TGT -s Anc2.Anc2refChr1 129421 50 + 142988 ACAGATATATTACCTGCAAAAACTTTAC-----------------------------------------------TGTAGACCAATACTGTAAT---TAT -s mr.mrrefChr3 163134 53 + 181027 GCAGATATGTTAGCATTAGAAATCATAC-----------------------------------------------ATGAGATCTATATTGTAATTCCTGT -s simCow_chr6.simCow.chr6 587917 48 + 602619 ATAAATAT-TTACCTGCAAGAAC-TTAC-----------------------------------------------TGTAGACCATTACTGTAAT---TAT -s simDog_chr6.simDog.chr6 580063 50 + 593897 ACAGATATATTACCTGCAGAAACTTTAC-----------------------------------------------TCTAGACCAATGCTCTAAT---TAT -s simHuman_chr6.simHuman.chr6 583822 50 + 601863 GAAGATATGTTAGCTGCAAAAACCTTAC-----------------------------------------------TGCAGACCAACATTGCAAT---TGT -s simRat_chr6.simRat.chr6 627722 53 + 647215 GCAGATATGTTAGCATTAGAAATCAAAC-----------------------------------------------ATGAGATCTATATTGTAATTCCTGT - -a -s simMouse_chr6.simMouse.chr6 615945 11 + 636262 AATGAGCATAG -s Anc0.Anc0refChr3 212162 11 + 222631 AATGAGCATAA -s Anc1.Anc1refChr1 52389 11 + 69767 AATGAGCATAA -s Anc2.Anc2refChr1 129503 11 + 142988 AAGGAGCACAA -s mr.mrrefChr3 163187 11 + 181027 AATGAGCATAG -s simCow_chr6.simCow.chr6 587997 7 + 602619 ATG----ACAA -s simDog_chr6.simDog.chr6 580145 11 + 593897 AAGGAGCACAA -s simHuman_chr6.simHuman.chr6 583914 11 + 601863 AATGAACATGA -s simRat_chr6.simRat.chr6 627775 11 + 647215 AAAAAGAAAAG - -a -s simMouse_chr6.simMouse.chr6 615956 92 + 636262 GTGTAAAAGCATCGAACCTTGAATACAAAACAGTGTGTGAATGGTGATTGTGGCCTAAGGCAAATTCAAGGGTATGTTAAGAGCACTGATCT -s Anc0.Anc0refChr3 212173 84 + 222631 TTGTAGAACCATTGAACCTTGAGTGATAAACACTGTATGAATGGGGGTTGAGGGCCAAGACAAATGGTATGGTAAGTTAGGAC--------T -s Anc1.Anc1refChr1 52400 84 + 69767 TTGTAGAACCATTGAACCTTGAGTGATAAACACTGTATGAATGGGGGTTGAGGGCCAAGACAAATGGTATGGTAAGTTAGGAC--------T -s Anc2.Anc2refChr1 129514 84 + 142988 TTGTAGAACCCTTGAATCTTGAGTGATAAACACTGTATGGATGGGGGTTGAGGGCCAAGACAAATGGTATGATAAGTTTGACC--------T -s mr.mrrefChr3 163198 92 + 181027 GTGTAAAAGCATCGAACCTTGAATACAAAACAGTGTGTGAATGGGGGTTGTGGCCTAAGGCAAATTGAAGGGTAAGTTAAGAGCACTGATCT -s simCow_chr6.simCow.chr6 588004 83 + 602619 TTGTAGAACTTGTGAGTCTTGAGTGATAAACACTGTATGG-TGGTGGTTGAGGGCCAAGACAAATGGTAAGATAAGTTTGATC--------C -s simDog_chr6.simDog.chr6 580156 81 + 593897 GTTTAGAACCCTT--ATCTTGAATGATAAACACTGTATGGATGGGGGTTGAGGGCCAAGACAAATGATATGATGAGTT-GACC--------T -s simHuman_chr6.simHuman.chr6 583925 84 + 601863 TTGTATGACCATTGAACCTTGAGTGGGAAACACTTTATAAATGTGGGTTGAGGACCAAGCTAAATGGTATGGTAAGTTAGGAA--------T -s simRat_chr6.simRat.chr6 627790 90 + 647215 GGGTAAAAGCA--GAACCTTGAATTCAAAACAGTGTGTGAAGGGGGGCTGTGGCCAAAGGCAAATTGGAGTGTAAGTTCAGAGCACTGGTCT - -a -s simMouse_chr6.simMouse.chr6 616048 1 + 636262 A -s Anc0.Anc0refChr3 212257 1 + 222631 G -s Anc1.Anc1refChr1 52484 1 + 69767 G -s Anc2.Anc2refChr1 129598 1 + 142988 G -s mr.mrrefChr3 163290 1 + 181027 A -s simCow_chr6.simCow.chr6 588090 1 + 602619 G -s simDog_chr6.simDog.chr6 580237 1 + 593897 G -s simHuman_chr6.simHuman.chr6 584009 1 + 601863 G -s simRat_chr6.simRat.chr6 627880 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 616049 13 + 636262 ATTTGGCGTGTCA -s Anc0.Anc0refChr3 212258 13 + 222631 AATTAGGGGCTGG -s Anc1.Anc1refChr1 52485 13 + 69767 AATTAGGGGCTGG -s Anc2.Anc2refChr1 129602 13 + 142988 AATTAGGGGCTGG -s mr.mrrefChr3 163291 13 + 181027 ATTTGGCGGCTCA -s simCow_chr6.simCow.chr6 588094 13 + 602619 GATTGGGGGCTGG -s simDog_chr6.simDog.chr6 580241 9 + 593897 AATTAGGGG---- -s simHuman_chr6.simHuman.chr6 584010 13 + 601863 AATTAGGGGCTTG -s simRat_chr6.simRat.chr6 627881 12 + 647215 ATTAGG-GGCTCA - -a -s simMouse_chr6.simMouse.chr6 616062 16 + 636262 TGAGTGATGGTCAAGG -s Anc0.Anc0refChr3 212271 16 + 222631 TAAGTGATAGTCAAGC -s Anc1.Anc1refChr1 52498 16 + 69767 TAAGTGATAGTCAAGC -s Anc2.Anc2refChr1 129615 16 + 142988 TAAGTGATAGTCAAGC -s mr.mrrefChr3 163304 16 + 181027 TAAGTGATGGTCAAGG -s simCow_chr6.simCow.chr6 588112 16 + 602619 TAAGTGAAAGTCAAAG -s simDog_chr6.simDog.chr6 580250 14 + 593897 --AGTAATAGTCATGC -s simHuman_chr6.simHuman.chr6 584023 16 + 601863 TAAGTGATAGTCAAGT -s simRat_chr6.simRat.chr6 627893 16 + 647215 CAAGTGAAGGTCAACG - -a -s simMouse_chr6.simMouse.chr6 616078 16 + 636262 CCTGATCTACAGCTAA -s Anc0.Anc0refChr3 212287 16 + 222631 CCTGATCTACAGATAA -s Anc1.Anc1refChr1 52514 16 + 69767 CCTGATCTACAGATAA -s Anc2.Anc2refChr1 129631 16 + 142988 CCAGATCTACAGATAA -s mr.mrrefChr3 163320 16 + 181027 CCTGATCTACAGCTAA -s simCow_chr6.simCow.chr6 588128 16 + 602619 CCAGATCAACAGATAA -s simDog_chr6.simDog.chr6 580280 16 + 593897 TCAGATCTACAGATAA -s simHuman_chr6.simHuman.chr6 584039 16 + 601863 CCTGACCTACAGATGG -s simRat_chr6.simRat.chr6 627909 16 + 647215 CCTGGTCTACAGCTAA - -a -s simMouse_chr6.simMouse.chr6 616094 4 + 636262 TAAA -s Anc0.Anc0refChr3 212303 4 + 222631 TAAA -s Anc1.Anc1refChr1 52530 4 + 69767 TAAA -s Anc2.Anc2refChr1 129647 4 + 142988 AAAA -s mr.mrrefChr3 163336 4 + 181027 TAAA -s simCow_chr6.simCow.chr6 588145 4 + 602619 AAAA -s simDog_chr6.simDog.chr6 580296 4 + 593897 AAAA -s simHuman_chr6.simHuman.chr6 584055 4 + 601863 TAAA -s simRat_chr6.simRat.chr6 627925 4 + 647215 TAAA - -a -s simMouse_chr6.simMouse.chr6 616098 8 + 636262 CAAACAAC -s Anc0.Anc0refChr3 212307 8 + 222631 CCAAAAGT -s Anc1.Anc1refChr1 52534 8 + 69767 CCAAAAGT -s Anc2.Anc2refChr1 129656 8 + 142988 CCACAAGT -s mr.mrrefChr3 163340 8 + 181027 CAAACAGT -s simCow_chr6.simCow.chr6 588154 8 + 602619 CCACAAAA -s simDog_chr6.simDog.chr6 580305 8 + 593897 CCACAAGT -s simHuman_chr6.simHuman.chr6 584059 8 + 601863 CCAAAAGT -s simRat_chr6.simRat.chr6 627929 8 + 647215 CAAATAGT - -a -s simMouse_chr6.simMouse.chr6 616106 50 + 636262 TTTATGTAAACTGGTGGCTAGCATGTACACTTTGAAGGGATAATGGGGGA -s Anc0.Anc0refChr3 212316 41 + 222631 CTGATGTAAACTGGTGCCTTGCTTATGCAC---------ATTAATGGGGA -s Anc1.Anc1refChr1 52543 48 + 69767 CTGATGTAAACTGGTGCCTTGCTTATGCACTACAAA--CATTAATGGGGA -s Anc2.Anc2refChr1 129665 41 + 142988 CTGATGTAAACTGGTGCCTTGCTTATGCAC---------GTTAATGGGGG -s mr.mrrefChr3 163349 50 + 181027 CTTATGTAAACTGGTGCCTAGCATGTACACTTTGAAGGGATAATGGGGGA -s simCow_chr6.simCow.chr6 588163 36 + 602619 CTGATGTAAGCTGGCACCTTGCTCA--------------GTTAATGGGGG -s simDog_chr6.simDog.chr6 580314 30 + 593897 CTGATGTAAACAGGTGCCCTGCTTCTGCAC-------------------- -s simHuman_chr6.simHuman.chr6 584068 48 + 601863 CTGATGTAAACTGCTGCCTTGCCTATGTACTACAAA--CATTAATGGGAA -s simRat_chr6.simRat.chr6 627938 48 + 647215 CTTATGTAAACTGGTGCCTAGT--TTACACTTTTAATGGCTAATGGAGGA - -a -s simMouse_chr6.simMouse.chr6 616156 62 + 636262 GTAATCAGAATAATTGACATAGTCTTAATGTTGTTTAGATCTGGCACTGGGACTTATGCAAA -s Anc0.Anc0refChr3 212357 23 + 222631 ATACTCAGAACAATCAACATATT--------------------------------------- -s Anc1.Anc1refChr1 52591 23 + 69767 ATACTCAGAACAATCAACATATT--------------------------------------- -s Anc2.Anc2refChr1 129706 23 + 142988 ATACTCAAGACTCACAACATATT--------------------------------------- -s mr.mrrefChr3 163399 62 + 181027 GTAATCAGAATAATTGACATAGTCTTAATGTTGTTTAGATCTGGCACTGTGACTGATGCAAA -s simCow_chr6.simCow.chr6 588200 23 + 602619 ATACTCAAGACTCACAACATGTA--------------------------------------- -s simDog_chr6.simDog.chr6 580344 5 + 593897 ------------------GTATT--------------------------------------- -s simHuman_chr6.simHuman.chr6 584116 23 + 601863 ATACCCAGAACAATCAACACATT--------------------------------------- -s simRat_chr6.simRat.chr6 627986 62 + 647215 GTAATCAAAATAATTGACATAGTCTTAATGTAGTTTAGATGTCGCACTGTGCCTGATGCAAA - -a -s simMouse_chr6.simMouse.chr6 616218 77 + 636262 GCTCAAATAAAAGGCAAATGCGGCCATGTATATGCAGTTAGTGCTTGGTGGTGAGCATGCCCCGCTTGATGTGACAG -s Anc0.Anc0refChr3 212380 3 + 222631 --------------------------------------------------------------------------CAG -s Anc1.Anc1refChr1 52614 3 + 69767 --------------------------------------------------------------------------CAG -s Anc2.Anc2refChr1 129729 3 + 142988 --------------------------------------------------------------------------CAG -s mr.mrrefChr3 163461 73 + 181027 GCTCAAATAAAAGGCAAATGTGGCCATGTACATGCAGTTAGTGCTTGGTGATGAGCA----CCGCTTGATGGGACAG -s simCow_chr6.simCow.chr6 588223 3 + 602619 --------------------------------------------------------------------------CAG -s simDog_chr6.simDog.chr6 580349 3 + 593897 --------------------------------------------------------------------------CAG -s simHuman_chr6.simHuman.chr6 584139 3 + 601863 --------------------------------------------------------------------------CAG -s simRat_chr6.simRat.chr6 628049 73 + 647215 GCTCAAATAAAAGGCAGACATGGCCATGTACACGCAGTTAGTGCTTGGCTATGAGCA----CCGCTTGATGGCACAG - -a -s simMouse_chr6.simMouse.chr6 616295 46 + 636262 AATACCACCAGAAAAACCTGTGTACATGATGCAAATAGTGAATATA -s Anc0.Anc0refChr3 212383 46 + 222631 AATACCAACATAGAAACCTGTGTATATGAAACAAATGTTGTACATG -s Anc1.Anc1refChr1 52617 46 + 69767 AATACCAACATAGAAACCTGTGTATATGAAACAAATGTTGTACATG -s Anc2.Anc2refChr1 129737 46 + 142988 AATACCAAGATAGAAAGCTGTGTGTATGAAATAAATGTTGTGCATG -s mr.mrrefChr3 163534 46 + 181027 AATACCACCAGAAAAACCTGTGTACATGATGCAAATAGTGAATATA -s simCow_chr6.simCow.chr6 588231 46 + 602619 AATGCCAAGATAGAAAGCTGTGTGCAAGAAATATATGTTGTGCATG -s simDog_chr6.simDog.chr6 580357 46 + 593897 AACACAAAGATAGAAGGCTATCTGTGTGAAATAAGTGTTGTGCATG -s simHuman_chr6.simHuman.chr6 584142 46 + 601863 AATACCAACATAGTAACCGGTGAATATGAAACAAATGTTGTACATG -s simRat_chr6.simRat.chr6 628122 46 + 647215 AATACGACCAGAGAAACTTGTGTACATGATGCAAATATTGAATATA - -a -s simMouse_chr6.simMouse.chr6 616341 8 + 636262 ATCTGACT -s Anc0.Anc0refChr3 212431 8 + 222631 ATCTGACT -s Anc1.Anc1refChr1 52665 8 + 69767 ATCTGACT -s Anc2.Anc2refChr1 129785 8 + 142988 GTCTGATT -s mr.mrrefChr3 163580 8 + 181027 ATCTGACT -s simCow_chr6.simCow.chr6 588279 8 + 602619 GTCTGATT -s simDog_chr6.simDog.chr6 580405 8 + 593897 GCCCAATT -s simHuman_chr6.simHuman.chr6 584190 8 + 601863 ATCTGACT -s simRat_chr6.simRat.chr6 628168 8 + 647215 ATCTGACT - -a -s simMouse_chr6.simMouse.chr6 616349 6 + 636262 TTGGCT -s Anc1.Anc1refChr1 52674 6 + 69767 TGTGCT -s mr.mrrefChr3 163588 6 + 181027 TTGGCT -s simHuman_chr6.simHuman.chr6 584200 6 + 601863 TGTGCT -s simRat_chr6.simRat.chr6 628176 6 + 647215 TTGGCT - -a -s simMouse_chr6.simMouse.chr6 616355 12 + 636262 CATAACATTACT -s Anc0.Anc0refChr3 212440 11 + 222631 -ATAAGGTGACG -s Anc1.Anc1refChr1 52680 12 + 69767 CATAAGGTGACG -s Anc2.Anc2refChr1 129794 11 + 142988 -ATAAGGTGACG -s mr.mrrefChr3 163594 12 + 181027 CATAACATTACT -s simCow_chr6.simCow.chr6 588288 11 + 602619 -GTAAGGTAACG -s simDog_chr6.simDog.chr6 580414 11 + 593897 -ATAAGGTGACG -s simHuman_chr6.simHuman.chr6 584235 12 + 601863 CATAAGGTGCCA -s simRat_chr6.simRat.chr6 628182 12 + 647215 CATAACATTACT - -a -s simMouse_chr6.simMouse.chr6 616367 20 + 636262 ATTGATTTAAACTTGCAAGG -s Anc0.Anc0refChr3 212451 16 + 222631 ATTGC----AACTCACAAGG -s Anc1.Anc1refChr1 52692 16 + 69767 ATTGC----AACTCACAAGG -s Anc2.Anc2refChr1 129805 16 + 142988 ATTGC----AACTCACAAGG -s mr.mrrefChr3 163606 16 + 181027 ATTGA----AACTTGCAAGG -s simCow_chr6.simCow.chr6 588374 16 + 602619 ATTGC----AACTCAGGAGG -s simDog_chr6.simDog.chr6 580425 16 + 593897 AATGC----AATTTGCAAAG -s simHuman_chr6.simHuman.chr6 584247 16 + 601863 ATTGC----AACTCACAAGG -s simRat_chr6.simRat.chr6 628194 16 + 647215 ATTGA----ACCGTGCAAGG - -a -s simMouse_chr6.simMouse.chr6 616387 8 + 636262 AGCTGAAT -s Anc0.Anc0refChr3 212470 8 + 222631 AACCAAAT -s Anc1.Anc1refChr1 52711 8 + 69767 AACCAAAT -s Anc2.Anc2refChr1 129824 8 + 142988 AACCAAAT -s mr.mrrefChr3 163622 8 + 181027 AACTGAAT -s simCow_chr6.simCow.chr6 588393 8 + 602619 AATCAAAT -s simDog_chr6.simDog.chr6 580444 7 + 593897 AGCGAAA- -s simHuman_chr6.simHuman.chr6 584266 8 + 601863 AACCAAAT -s simRat_chr6.simRat.chr6 628210 8 + 647215 AACTGCAT - -a -s simMouse_chr6.simMouse.chr6 616395 30 + 636262 TGAATCTACAATAAACAGCAAAGGTTCCCA -s Anc0.Anc0refChr3 212481 29 + 222631 AGAGCTTGCAATAAACAGCTAAGTTTCCT- -s Anc1.Anc1refChr1 52722 30 + 69767 AGAGCTTGCAATAAACAGCTAAGTTTCCTC -s Anc2.Anc2refChr1 129835 29 + 142988 AGAAGTTGCAACAAACAGGTGAGTTTCCT- -s mr.mrrefChr3 163630 30 + 181027 AGAGCCTACAATAAACAGCAAAGTTTCCCA -s simCow_chr6.simCow.chr6 588404 26 + 602619 AG---CTGCAACAAATAGGTGAGTTTCCT- -s simDog_chr6.simDog.chr6 580451 29 + 593897 AGAAGTTGCAACAAACAGGTGAGTTTCCT- -s simHuman_chr6.simHuman.chr6 584277 30 + 601863 AGAGCTTGCAATGAACAGCTAAGTTTCCTC -s simRat_chr6.simRat.chr6 628218 30 + 647215 AGAGCCTACAACAAACAGCAAAGTTTCCCA - -a -s simMouse_chr6.simMouse.chr6 616425 11 + 636262 TCCTCTCAAAA -s Anc0.Anc0refChr3 212510 11 + 222631 TCTTCAGAAAA -s Anc1.Anc1refChr1 52752 11 + 69767 TCTTCAGAAAA -s Anc2.Anc2refChr1 129864 11 + 142988 TCTTCAGAAAA -s mr.mrrefChr3 163660 11 + 181027 TCCTCTCAAAA -s simCow_chr6.simCow.chr6 588488 11 + 602619 TCTTCACAAAA -s simDog_chr6.simDog.chr6 580480 10 + 593897 TCTT-AGAAAA -s simHuman_chr6.simHuman.chr6 584307 11 + 601863 TCTTCATAAAA -s simRat_chr6.simRat.chr6 628248 11 + 647215 TCCTCTCAAAA - -a -s simMouse_chr6.simMouse.chr6 616436 8 + 636262 ATACTGCC -s Anc0.Anc0refChr3 212521 8 + 222631 ATACTACC -s Anc1.Anc1refChr1 52763 8 + 69767 ATACTACC -s Anc2.Anc2refChr1 129875 8 + 142988 ATACCACC -s mr.mrrefChr3 163671 8 + 181027 ATACTGCC -s simCow_chr6.simCow.chr6 588500 8 + 602619 ATAACACC -s simDog_chr6.simDog.chr6 580490 8 + 593897 ATACCACT -s simHuman_chr6.simHuman.chr6 584318 8 + 601863 ACACTACC -s simRat_chr6.simRat.chr6 628259 8 + 647215 ATACTGCC - -a -s simMouse_chr6.simMouse.chr6 616444 16 + 636262 TAGTGATACACCAGTG -s Anc0.Anc0refChr3 212533 16 + 222631 TCGCCCAACATTTGTT -s Anc1.Anc1refChr1 52775 16 + 69767 TCGCCCAACATTTGTT -s Anc2.Anc2refChr1 129887 16 + 142988 TCACCCAACATTTGTT -s mr.mrrefChr3 163679 16 + 181027 TAGTGATACACCAGTT -s simCow_chr6.simCow.chr6 588512 16 + 602619 TCACCCAACTTTTGTT -s simDog_chr6.simDog.chr6 580502 16 + 593897 TCACCCAACATTTATT -s simHuman_chr6.simHuman.chr6 584330 16 + 601863 TCGCCCAACATATGTT -s simRat_chr6.simRat.chr6 628267 16 + 647215 TAGTGACACACCAGTT - -a -s simMouse_chr6.simMouse.chr6 616460 7 + 636262 CTCTAAA -s Anc0.Anc0refChr3 212549 7 + 222631 TTCAAAA -s Anc1.Anc1refChr1 52791 7 + 69767 TTCAAAA -s Anc2.Anc2refChr1 129903 7 + 142988 TTCAAAA -s mr.mrrefChr3 163695 7 + 181027 CTCTAAA -s simCow_chr6.simCow.chr6 588533 7 + 602619 TGTTAAA -s simDog_chr6.simDog.chr6 580518 7 + 593897 CTCAGAA -s simHuman_chr6.simHuman.chr6 584346 7 + 601863 TTCAAAA -s simRat_chr6.simRat.chr6 628283 7 + 647215 CTCTAAA - -a -s simMouse_chr6.simMouse.chr6 616467 25 + 636262 GAAAATTACCTTTCTAGCCTTTTGG -s Anc0.Anc0refChr3 212557 25 + 222631 GAGAATTAGCTTTTTGGCCTTCTGG -s Anc1.Anc1refChr1 52799 25 + 69767 GAGAATTAGCTTTTTGGCCTTCTGG -s Anc2.Anc2refChr1 129911 25 + 142988 AAGGATTAGCTTTTTGGCCTTCTGG -s mr.mrrefChr3 163702 25 + 181027 GAGAATTACCTTTCTAGCCTTTTGG -s simCow_chr6.simCow.chr6 588541 25 + 602619 AAGGATTTACTTTTTGGTCTTCTGG -s simDog_chr6.simDog.chr6 580526 25 + 593897 AGGGACTAGCTTTTTAGCCTTCTGG -s simHuman_chr6.simHuman.chr6 584354 25 + 601863 GAGAATCATCTTTTTGGCCTTCTGG -s simRat_chr6.simRat.chr6 628290 25 + 647215 GAGAATTACCTTTCTAGCCTTTCGG - -a -s simMouse_chr6.simMouse.chr6 616492 9 + 636262 AAACTGAAA -s Anc0.Anc0refChr3 212582 8 + 222631 AAAC-AAGG -s Anc1.Anc1refChr1 52824 8 + 69767 AAAC-AAGG -s Anc2.Anc2refChr1 129937 8 + 142988 AAAC-AAGG -s mr.mrrefChr3 163727 9 + 181027 AAACTGAAA -s simCow_chr6.simCow.chr6 588567 8 + 602619 AAAC-AAGG -s simDog_chr6.simDog.chr6 580552 8 + 593897 AAAC-TCCC -s simHuman_chr6.simHuman.chr6 584379 8 + 601863 AAGC-AAGG -s simRat_chr6.simRat.chr6 628315 9 + 647215 AAAGTGAAA - -a -s simMouse_chr6.simMouse.chr6 616501 24 + 636262 ATGACACAAGTTCAATATACAGGC -s Anc0.Anc0refChr3 212669 24 + 222631 ATGACACAAGTTCAGTAAACAAAC -s Anc1.Anc1refChr1 52911 24 + 69767 ATGACACAAGTTCAGTAAACAAAC -s Anc2.Anc2refChr1 130024 24 + 142988 ATGACACAAGTGCAGTGAATGAAC -s mr.mrrefChr3 163749 24 + 181027 ATGACACAAGTTCAATATACAGAC -s simCow_chr6.simCow.chr6 588656 23 + 602619 ATAACAAAAGTGT-GTGAAGGAAC -s simDog_chr6.simDog.chr6 580582 24 + 593897 ATGGCACAAGTGCAGTGAATGAAC -s simHuman_chr6.simHuman.chr6 584466 24 + 601863 ATGAGACAAATTCATTAAACAAAC -s simRat_chr6.simRat.chr6 628337 24 + 647215 AAGACACAAGTTCAATATACAGAC - -a -s simMouse_chr6.simMouse.chr6 616525 5 + 636262 AACTT -s Anc0.Anc0refChr3 212699 5 + 222631 AATTT -s Anc1.Anc1refChr1 52941 5 + 69767 AATTT -s Anc2.Anc2refChr1 130058 5 + 142988 ACTAT -s mr.mrrefChr3 163773 5 + 181027 AACTT -s simCow_chr6.simCow.chr6 588689 5 + 602619 TCTGT -s simDog_chr6.simDog.chr6 580616 5 + 593897 ACTAC -s simHuman_chr6.simHuman.chr6 584496 5 + 601863 AATTT -s simRat_chr6.simRat.chr6 628361 5 + 647215 AACTT - -a -s simMouse_chr6.simMouse.chr6 616530 3 + 636262 GTC -s Anc0.Anc0refChr3 212709 3 + 222631 GCT -s Anc1.Anc1refChr1 52951 3 + 69767 GCT -s Anc2.Anc2refChr1 130068 3 + 142988 GCT -s mr.mrrefChr3 163778 3 + 181027 GCC -s simDog_chr6.simDog.chr6 580626 3 + 593897 GCT -s simHuman_chr6.simHuman.chr6 584506 3 + 601863 GCT -s simRat_chr6.simRat.chr6 628366 3 + 647215 GCC - -a -s simMouse_chr6.simMouse.chr6 616533 83 + 636262 TGGACGGCCAGACTTAAGGTTGTTTGGATTCCGCAAAGTGCCTCATGCAAAGCTTAAATAAAAAACAAACTCTCAGCCATGTA -s Anc0.Anc0refChr3 212712 12 + 222631 TTGAGGGCTGGA----------------------------------------------------------------------- -s Anc1.Anc1refChr1 52954 12 + 69767 TTGAGGGCTGGA----------------------------------------------------------------------- -s Anc2.Anc2refChr1 130071 12 + 142988 TTGAGGGCTGGA----------------------------------------------------------------------- -s mr.mrrefChr3 163781 70 + 181027 TGGACGGCTGGACTTAAGGTTGTTTGGATTCCGCAAAGTGCCTCA-----------AATAAAAAACAAACTC--AGCCATGTA -s simCow_chr6.simCow.chr6 588696 12 + 602619 CTGAGGGCTGGA----------------------------------------------------------------------- -s simDog_chr6.simDog.chr6 580642 12 + 593897 TGGAGGGCTGGA----------------------------------------------------------------------- -s simHuman_chr6.simHuman.chr6 584509 12 + 601863 TTGAGGGCTGGA----------------------------------------------------------------------- -s simRat_chr6.simRat.chr6 628369 70 + 647215 GGGATGACTGGACTTAAGGTTGTTTGGATTTCGCACAGTGCCTCC-----------AATAAAAGGCAAACTC--AGCCATGTA - -a -s simMouse_chr6.simMouse.chr6 616616 42 + 636262 TGCAGTTAGTATTTGGCTATGAGCCTGCACTGCTTGGCGAGA -s mr.mrrefChr3 163851 42 + 181027 TGCAGTTAGTATTTGGCTATGAGCCTGCACTGCTTGGCGAGA -s simRat_chr6.simRat.chr6 628441 42 + 647215 TGCAGTTAGTATTTGGTCATGAGCTCGCCCTGCTTGGCGTGA - -a -s simMouse_chr6.simMouse.chr6 616658 191 + 636262 TGTCAAGCGATCACAGGTACCTGTGAAGGAGCCTGCATGTGTCTCTCAAGAGTTTGTCCACCTGCCTCACACTAGAGGTTTGTCATGCATCTTGCACAGCTCCCCGCATACATTCTATATTCCCTGTCTGCCTCTTGTTCAGTTAAGTGATCATAGGCACCTGTCACCTCTAGAAGGAGCCTGCCTGTGGG -s Anc0.Anc0refChr3 212724 4 + 222631 -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TAGG -s Anc1.Anc1refChr1 52966 4 + 69767 -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TAGG -s Anc2.Anc2refChr1 130083 4 + 142988 -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TAGG -s mr.mrrefChr3 163893 188 + 181027 TGTCAAGCGATCACAGGTACCTGTGAAGGAGCCTGCATGTGTCTCTCAAGAGTTTGTCCACCTGCCTCACACTAGAGGTTTGTCATGCATCTTGCACAGCTCCCCGCATACATTCTATATTCCCTGTCTGCCTCTTGTTCAGTTAAGTGATCAT-GGCACCTGTC--CTCTAGAAGGAGCCTGCCTGTGGG -s simCow_chr6.simCow.chr6 588708 4 + 602619 -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TGGG -s simDog_chr6.simDog.chr6 580654 4 + 593897 -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TAGC -s simHuman_chr6.simHuman.chr6 584521 4 + 601863 -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TAGG -s simRat_chr6.simRat.chr6 628484 188 + 647215 TGTCAAGTAATCACAGGTACCTGTACTAGAGCATGCATATGTCCCACAAGAGTTTGTCTGCCTGCCTCACACTACGGGTCTGCCATGTATCATGCAGAGCTCCCTGTATACATTCTAGATTCCCTGTCTGCCTCTTGCACAGTCAAGTGATCGC-GGCACCTGTT--TTGTAGAAGGAGCCTGCCTGTGGG - -a -s simMouse_chr6.simMouse.chr6 616849 20 + 636262 GCTATAATGGGCTCAGTCTT -s Anc0.Anc0refChr3 212728 20 + 222631 ACTACACTGGGCTGGGTGTA -s Anc1.Anc1refChr1 52970 20 + 69767 ACTACACTGGGCTGGGTGTA -s Anc2.Anc2refChr1 130087 20 + 142988 ACTACACTAGGCTGGTTGTA -s mr.mrrefChr3 164081 20 + 181027 GCTATAATGGGCTCAGTCTT -s simCow_chr6.simCow.chr6 588712 20 + 602619 GCTCTTCTAGGCTGGTTGTA -s simDog_chr6.simDog.chr6 580661 20 + 593897 ACTACACTAGGCTGGTTAAA -s simHuman_chr6.simHuman.chr6 584525 20 + 601863 ACTACACAGGGATGGGTGTA -s simRat_chr6.simRat.chr6 628672 20 + 647215 GTTATTATGGGCTCAGTTTT - -a -s simMouse_chr6.simMouse.chr6 616869 24 + 636262 GGATTATGCCGTTAGTGAGCCATA -s Anc0.Anc0refChr3 212748 20 + 222631 ACGTTAGTCCATTTGTGAGC---- -s Anc1.Anc1refChr1 52990 20 + 69767 ACGTTAGTCCATTTGTGAGC---- -s Anc2.Anc2refChr1 130107 20 + 142988 ATGTTAGTCCGTTTGTGAGC---- -s mr.mrrefChr3 164101 24 + 181027 GCATTAGGCCATTTGTGAGCCATA -s simCow_chr6.simCow.chr6 588732 20 + 602619 ATGTCAGTCCCTTTGTGAGA---- -s simDog_chr6.simDog.chr6 580686 20 + 593897 ATGTTGGCCAGTTTGTGAGC---- -s simHuman_chr6.simHuman.chr6 584545 20 + 601863 ACGTTAGTCCATTTGTGTGT---- -s simRat_chr6.simRat.chr6 628692 24 + 647215 GCATTAGGCCATTTGTGAGCCATA - -a -s simMouse_chr6.simMouse.chr6 616893 4 + 636262 GGTG -s Anc0.Anc0refChr3 212768 4 + 222631 GGGA -s Anc1.Anc1refChr1 53010 4 + 69767 GGGA -s Anc2.Anc2refChr1 130127 4 + 142988 TGGA -s mr.mrrefChr3 164125 4 + 181027 GGGG -s simCow_chr6.simCow.chr6 588756 4 + 602619 AGGA -s simDog_chr6.simDog.chr6 580706 4 + 593897 TGGT -s simHuman_chr6.simHuman.chr6 584565 4 + 601863 GGGA -s simRat_chr6.simRat.chr6 628716 4 + 647215 GGGG - -a -s simMouse_chr6.simMouse.chr6 616897 23 + 636262 ATCAACCTGGCTTATGCCAGGTT -s Anc0.Anc0refChr3 212772 22 + 222631 ATCAACC-AGCTGGTGCCAGCTG -s Anc1.Anc1refChr1 53014 22 + 69767 ATCAACC-AGCTGGTGCCAGCTG -s Anc2.Anc2refChr1 130131 22 + 142988 ATTGACC-AGCTGGTGCCAGCTG -s mr.mrrefChr3 164129 23 + 181027 ATCAACCTGGCTTGTGCCAGGTT -s simCow_chr6.simCow.chr6 588760 22 + 602619 ATTCCCC-AGCTGGTGCCAGGTG -s simDog_chr6.simDog.chr6 580714 22 + 593897 ATTGACT-AGTCAGGGCCAGCTG -s simHuman_chr6.simHuman.chr6 584569 21 + 601863 ATCAACC-AGCTGGTGCCAG-GG -s simRat_chr6.simRat.chr6 628720 23 + 647215 ATGAACCTGGCTAGTGCCAGGTT - -a -s simMouse_chr6.simMouse.chr6 616920 3 + 636262 CTA -s Anc0.Anc0refChr3 212871 3 + 222631 CTA -s Anc1.Anc1refChr1 53113 3 + 69767 CTA -s Anc2.Anc2refChr1 130230 3 + 142988 CTG -s mr.mrrefChr3 164197 3 + 181027 CTA -s simCow_chr6.simCow.chr6 588860 3 + 602619 CTG -s simDog_chr6.simDog.chr6 580817 3 + 593897 CTG -s simHuman_chr6.simHuman.chr6 584667 3 + 601863 CTA -s simRat_chr6.simRat.chr6 628788 3 + 647215 CTT - -a -s simMouse_chr6.simMouse.chr6 616923 39 + 636262 CTATGATTGCCATGATTCTTCTTGTCAAGGTATCACTCA -s Anc0.Anc0refChr3 212876 39 + 222631 CTATGATTGCCATGATTTTTCTTGTCAAGCTAACACTCA -s Anc1.Anc1refChr1 53118 39 + 69767 CTATGATTGCCATGATTTTTCTTGTCAAGCTAACACTCA -s Anc2.Anc2refChr1 130235 39 + 142988 CTATGCTTGCCGTGATTTTTCTTGTCCAACTAACACTCA -s mr.mrrefChr3 164200 39 + 181027 CTATGATTGCCATGATTCTTCTTGTCAAGGTATCACTCA -s simCow_chr6.simCow.chr6 588865 39 + 602619 AGTTGGTTGCTGTAACTCTTCTTGTCCAACTAACACCCC -s simDog_chr6.simDog.chr6 580822 29 + 593897 CTAGACTTGCCGGGATTTTTCTCA----------ACTCA -s simHuman_chr6.simHuman.chr6 584672 39 + 601863 CTATGATTGCCATGATTTTTTTTGTCAAGCTAACACTCA -s simRat_chr6.simRat.chr6 628791 39 + 647215 CTATGATTGCCATGATTCTTCTTATCAAAGTATCACTCA - -a -s simMouse_chr6.simMouse.chr6 616962 9 + 636262 AAATCTAGT -s Anc0.Anc0refChr3 212916 8 + 222631 AAAC-TATT -s Anc1.Anc1refChr1 53158 9 + 69767 AAACCTATT -s Anc2.Anc2refChr1 130275 8 + 142988 AAGC-TATC -s mr.mrrefChr3 164240 9 + 181027 AAATCTATT -s simCow_chr6.simCow.chr6 588905 8 + 602619 AACC-TATA -s simDog_chr6.simDog.chr6 580852 8 + 593897 GAGC-TATC -s simHuman_chr6.simHuman.chr6 584712 9 + 601863 AAACCTATT -s simRat_chr6.simRat.chr6 628831 9 + 647215 AAATCTATT - -a -s simMouse_chr6.simMouse.chr6 616971 23 + 636262 GGTGATTAGACTTTGGTTATTTC -s Anc0.Anc0refChr3 212925 23 + 222631 GGTGATCAGACTATGGTTATCAT -s Anc1.Anc1refChr1 53168 23 + 69767 GGTGATCAGACTATGGTTATCAT -s Anc2.Anc2refChr1 130284 23 + 142988 GGTGATCAGACTATGGTTATCAT -s mr.mrrefChr3 164249 23 + 181027 GGTGATCAGACTTTGGTTATTAC -s simCow_chr6.simCow.chr6 588914 23 + 602619 GGTGATGAGACTATGGCTAGCAC -s simDog_chr6.simDog.chr6 580861 23 + 593897 GGTGATCAGACCATGGTTATCAT -s simHuman_chr6.simHuman.chr6 584722 23 + 601863 GGTAATCAGACTATGGTTATCAG -s simRat_chr6.simRat.chr6 628840 23 + 647215 GGTGATCACACTTTGGTTATTAC - -a -s simMouse_chr6.simMouse.chr6 616994 28 + 636262 AGATAGTTTTATTGAAACCTCCCTATGT -s Anc0.Anc0refChr3 212953 28 + 222631 AAACTGTGGTATTGAAACTTCACTACGC -s Anc1.Anc1refChr1 53196 28 + 69767 AAACTGTGGTATTGAAACTTCACTACGC -s Anc2.Anc2refChr1 130312 28 + 142988 AAACTGTGATATTGAAATTTCACTACGC -s mr.mrrefChr3 164277 28 + 181027 AAATAGTTGTATTGAAACCTCCCTATGT -s simCow_chr6.simCow.chr6 588942 28 + 602619 AAAATTTGATATTGAAATTACCTTATGC -s simDog_chr6.simDog.chr6 580889 28 + 593897 AAACTGTGATATTGAAATTTCACTACAT -s simHuman_chr6.simHuman.chr6 584750 28 + 601863 AAACTGTAGTATTGAAACTTTTCTACGC -s simRat_chr6.simRat.chr6 628868 28 + 647215 AAATAGTTGTATTAAAACCTCCCTATGT - -a -s simMouse_chr6.simMouse.chr6 617022 12 + 636262 GATTGACAATAT -s Anc0.Anc0refChr3 212982 11 + 222631 GATTCACACTA- -s Anc1.Anc1refChr1 53225 12 + 69767 GATTCACACTAT -s Anc2.Anc2refChr1 130341 11 + 142988 AATTCACACTA- -s mr.mrrefChr3 164305 12 + 181027 GATTGACACTAT -s simCow_chr6.simCow.chr6 588971 10 + 602619 AATTGACTC-A- -s simDog_chr6.simDog.chr6 580918 11 + 593897 ATTTCACACTA- -s simHuman_chr6.simHuman.chr6 584779 12 + 601863 GATCATCCCTAT -s simRat_chr6.simRat.chr6 628896 12 + 647215 GATTGACACTAT - -a -s simMouse_chr6.simMouse.chr6 617034 12 + 636262 AAGCTGAAGTTC -s Anc0.Anc0refChr3 212996 12 + 222631 GAGTTGACTTCC -s Anc1.Anc1refChr1 53241 12 + 69767 GAGTTGACTTCC -s Anc2.Anc2refChr1 130355 12 + 142988 GAATTGACTTCT -s mr.mrrefChr3 164317 12 + 181027 AAGTTGAAGTTC -s simCow_chr6.simCow.chr6 588984 12 + 602619 GAATTAAATTTT -s simDog_chr6.simDog.chr6 580932 12 + 593897 GTATTGACCTCT -s simHuman_chr6.simHuman.chr6 584797 12 + 601863 GAGTTGACTTCC -s simRat_chr6.simRat.chr6 628908 12 + 647215 AAGTTGAAGATC - -a -s simMouse_chr6.simMouse.chr6 617046 32 + 636262 AATTTCTGCACTGAATTAGCTCTATGAAGGCA -s Anc0.Anc0refChr3 213008 26 + 222631 G------GGACTGCATAACCTCTATAAAGACA -s Anc1.Anc1refChr1 53253 32 + 69767 GATTTCAGGACTGCATAACCTCTATAAAGACA -s Anc2.Anc2refChr1 130367 26 + 142988 G------GGACTGCATAACCTCTATAAAGACA -s mr.mrrefChr3 164329 32 + 181027 AATTTCTGCACTGCATTAGCTCTATAAAGGCA -s simCow_chr6.simCow.chr6 588996 26 + 602619 G------GGATCGCATAACCTCTATAAAGACA -s simDog_chr6.simDog.chr6 580944 26 + 593897 G------GGACTGCATAACCTCTACAACAACA -s simHuman_chr6.simHuman.chr6 584811 32 + 601863 GATTTCAGGGCTGCATCACCCCCATAAAGACA -s simRat_chr6.simRat.chr6 628920 32 + 647215 AGTTTTTGCACTGCTTTAGCTCGATAATGGTA - -a -s simMouse_chr6.simMouse.chr6 617078 18 + 636262 ACACTCTCATAGAGACTG -s Anc0.Anc0refChr3 213034 17 + 222631 ACATTGTCACAGAGGA-A -s Anc1.Anc1refChr1 53285 17 + 69767 ACATTGTCACAGAGGA-A -s Anc2.Anc2refChr1 130395 17 + 142988 ACATTGTCACAGAGGA-A -s mr.mrrefChr3 164361 17 + 181027 ACACTCTCATAGAGAC-G -s simCow_chr6.simCow.chr6 589024 17 + 602619 ACATTGTCACAGAGGA-A -s simDog_chr6.simDog.chr6 580972 17 + 593897 ACATTGTCACAGAGGA-A -s simHuman_chr6.simHuman.chr6 584843 17 + 601863 ACATTGTCAAAGAGGA-A -s simRat_chr6.simRat.chr6 628952 13 + 647215 ACACTCTCATAGA----- - -a -s simMouse_chr6.simMouse.chr6 617096 6 + 636262 GGCTGT -s Anc0.Anc0refChr3 213051 6 + 222631 GGCTGT -s Anc1.Anc1refChr1 53302 6 + 69767 GGCTGT -s Anc2.Anc2refChr1 130413 6 + 142988 GGCTGT -s mr.mrrefChr3 164378 6 + 181027 GGCTGT -s simCow_chr6.simCow.chr6 589042 6 + 602619 GGCTAC -s simDog_chr6.simDog.chr6 580990 6 + 593897 GGCTGT -s simHuman_chr6.simHuman.chr6 584860 6 + 601863 GGCAGT -s simRat_chr6.simRat.chr6 628965 1 + 647215 -----T - -a -s simMouse_chr6.simMouse.chr6 617102 22 + 636262 ACCAACAAGGGCCATCAGGTAC -s Anc0.Anc0refChr3 213057 20 + 222631 TTCAATAGAGGCTGACAGT--C -s Anc1.Anc1refChr1 53308 20 + 69767 TTCAATAGAGGCTGACAGT--C -s Anc2.Anc2refChr1 130483 20 + 142988 TTCAATAGAGGCTGACAGT--T -s mr.mrrefChr3 164384 22 + 181027 ATCAATAGGGGCTATCAGGTAC -s simCow_chr6.simCow.chr6 589114 20 + 602619 TTCAAAAGAGGGTGACTGT--T -s simDog_chr6.simDog.chr6 581060 20 + 593897 TTCAATAGGGGCTTACAGT--T -s simHuman_chr6.simHuman.chr6 584866 20 + 601863 TTCAATAGAGGCTGATAGT--C -s simRat_chr6.simRat.chr6 628966 22 + 647215 ATCCATAGGGGCTATCAGACAA - -a -s simMouse_chr6.simMouse.chr6 617124 15 + 636262 CCACTGAATGTTTCC -s Anc0.Anc0refChr3 213077 15 + 222631 CCACAAAATGTCTCC -s Anc1.Anc1refChr1 53328 15 + 69767 CCACAAAATGTCTCC -s Anc2.Anc2refChr1 130503 15 + 142988 CCACAAAATGTCTCA -s mr.mrrefChr3 164406 15 + 181027 CCACAAAATGTCTCC -s simCow_chr6.simCow.chr6 589135 15 + 602619 CCACAAAATGTCTCA -s simDog_chr6.simDog.chr6 581080 15 + 593897 CTACAAAATGTGTCA -s simHuman_chr6.simHuman.chr6 584886 15 + 601863 CCACAAAATGTCTCC -s simRat_chr6.simRat.chr6 628988 15 + 647215 CCACAAAATGTCTCC - -a -s simMouse_chr6.simMouse.chr6 617139 15 + 636262 CTCAACTCACAGTGT -s Anc0.Anc0refChr3 213092 13 + 222631 CTCAATTG--AGTGT -s Anc1.Anc1refChr1 53343 15 + 69767 CTCAATTGGTAGTGT -s Anc2.Anc2refChr1 130518 13 + 142988 CTCAATTG--AGTGT -s mr.mrrefChr3 164421 15 + 181027 CTCAACTCACAGTGT -s simCow_chr6.simCow.chr6 589152 8 + 602619 CTCAAGTC------- -s simDog_chr6.simDog.chr6 581095 13 + 593897 CTCAATTG--AGTGT -s simHuman_chr6.simHuman.chr6 584901 15 + 601863 CTCAATCGGTAGTGT -s simRat_chr6.simRat.chr6 629003 15 + 647215 CTCAACTCAAAGTGT - -a -s simMouse_chr6.simMouse.chr6 617154 11 + 636262 AAGCCCTGGAC -s Anc0.Anc0refChr3 213105 11 + 222631 GAGCCCTGGAC -s Anc1.Anc1refChr1 53358 11 + 69767 GAGCCCTGGAC -s Anc2.Anc2refChr1 130531 11 + 142988 GAGCTCTGGAC -s mr.mrrefChr3 164436 11 + 181027 AAGCCCTGGAC -s simCow_chr6.simCow.chr6 589160 4 + 602619 -------GGAC -s simDog_chr6.simDog.chr6 581111 11 + 593897 GAGCTCTGGAC -s simHuman_chr6.simHuman.chr6 584916 11 + 601863 GAGCCCTGGAC -s simRat_chr6.simRat.chr6 629018 11 + 647215 AAGCCCTGGAT - -a -s simMouse_chr6.simMouse.chr6 617165 15 + 636262 ACAGGAAAGAACTTA -s Anc0.Anc0refChr3 213116 13 + 222631 TCAG--AGGGAGTGA -s Anc1.Anc1refChr1 53369 15 + 69767 TCAGGTAGGGAGTGA -s Anc2.Anc2refChr1 130542 13 + 142988 TCAG--AGGGAGTGA -s mr.mrrefChr3 164447 15 + 181027 ACAGGAAAGAACTTA -s mr.mrrefChr3 165614 15 + 181027 AAAGGTAGGTAGGGA -s simCow_chr6.simCow.chr6 589164 13 + 602619 TCAA--AGGAAGTGA -s simDog_chr6.simDog.chr6 581122 13 + 593897 CCAG--AGGGAGTGA -s simHuman_chr6.simHuman.chr6 584927 4 + 601863 TGAG----------- -s simMouse_chr6.simMouse.chr6 618363 15 + 636262 AAAGGTAGGTAGGGA -s simRat_chr6.simRat.chr6 630497 15 + 647215 AAAGATAGGTAAGGA -s simRat_chr6.simRat.chr6 629029 15 + 647215 GTGGGAAAGAACTTA - -a -s simMouse_chr6.simMouse.chr6 617180 3 + 636262 CAC -s Anc0.Anc0refChr3 213136 3 + 222631 CAC -s Anc1.Anc1refChr1 53393 3 + 69767 CAC -s Anc2.Anc2refChr1 130562 3 + 142988 CAC -s mr.mrrefChr3 164471 3 + 181027 CAC -s mr.mrrefChr3 165636 3 + 181027 TAC -s simCow_chr6.simCow.chr6 589184 3 + 602619 CAC -s simDog_chr6.simDog.chr6 581142 3 + 593897 CAC -s simHuman_chr6.simHuman.chr6 584940 3 + 601863 CGC -s simMouse_chr6.simMouse.chr6 618385 3 + 636262 TAC -s simRat_chr6.simRat.chr6 630519 3 + 647215 CAC -s simRat_chr6.simRat.chr6 629068 3 + 647215 CAC - -a -s simMouse_chr6.simMouse.chr6 617183 1 + 636262 T -s Anc0.Anc0refChr3 213139 1 + 222631 T -s Anc1.Anc1refChr1 53396 1 + 69767 T -s Anc2.Anc2refChr1 130565 1 + 142988 T -s mr.mrrefChr3 164474 1 + 181027 T -s simCow_chr6.simCow.chr6 589187 1 + 602619 T -s simDog_chr6.simDog.chr6 581145 1 + 593897 A -s simHuman_chr6.simHuman.chr6 584943 1 + 601863 T -s simRat_chr6.simRat.chr6 629071 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 617184 5 + 636262 CTAGA -s Anc0.Anc0refChr3 213140 4 + 222631 TTT-A -s Anc1.Anc1refChr1 53397 4 + 69767 TTT-A -s Anc2.Anc2refChr1 130566 4 + 142988 TTT-G -s mr.mrrefChr3 164475 5 + 181027 CTTGA -s simCow_chr6.simCow.chr6 589190 4 + 602619 TTT-G -s simDog_chr6.simDog.chr6 581146 4 + 593897 CTA-G -s simHuman_chr6.simHuman.chr6 584944 4 + 601863 TTT-A -s simRat_chr6.simRat.chr6 629072 5 + 647215 CTTGA - -a -s simMouse_chr6.simMouse.chr6 617189 1 + 636262 A -s Anc0.Anc0refChr3 213144 1 + 222631 A -s Anc1.Anc1refChr1 53401 1 + 69767 A -s Anc2.Anc2refChr1 130570 1 + 142988 A -s mr.mrrefChr3 164480 1 + 181027 A -s mr.mrrefChr3 165639 1 + 181027 A -s simCow_chr6.simCow.chr6 589194 1 + 602619 A -s simDog_chr6.simDog.chr6 581150 1 + 593897 A -s simHuman_chr6.simHuman.chr6 584948 1 + 601863 G -s simMouse_chr6.simMouse.chr6 618388 1 + 636262 A -s simRat_chr6.simRat.chr6 630522 1 + 647215 A -s simRat_chr6.simRat.chr6 629077 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 617190 7 + 636262 GGGTCTA -s Anc0.Anc0refChr3 213145 7 + 222631 GGGTCTG -s Anc1.Anc1refChr1 53402 7 + 69767 GGGTCTG -s Anc2.Anc2refChr1 130571 7 + 142988 GGATCTG -s mr.mrrefChr3 164481 7 + 181027 GGGTCTA -s mr.mrrefChr3 165640 7 + 181027 AGGGCAT -s simCow_chr6.simCow.chr6 589195 7 + 602619 GGCTCTG -s simDog_chr6.simDog.chr6 581151 7 + 593897 GGATCTG -s simHuman_chr6.simHuman.chr6 584949 7 + 601863 GGGTCTG -s simMouse_chr6.simMouse.chr6 618389 7 + 636262 AGGGCAT -s simRat_chr6.simRat.chr6 630529 7 + 647215 AGAGTAT -s simRat_chr6.simRat.chr6 629078 7 + 647215 GGCTATA - -a -s simMouse_chr6.simMouse.chr6 617197 3 + 636262 CCA -s Anc0.Anc0refChr3 213152 3 + 222631 CCA -s Anc1.Anc1refChr1 53409 3 + 69767 CCA -s Anc2.Anc2refChr1 130578 3 + 142988 CCA -s mr.mrrefChr3 164488 3 + 181027 CCA -s mr.mrrefChr3 165647 3 + 181027 CCA -s simCow_chr6.simCow.chr6 589202 3 + 602619 CCA -s simDog_chr6.simDog.chr6 581158 3 + 593897 CCA -s simHuman_chr6.simHuman.chr6 584956 3 + 601863 CCA -s simMouse_chr6.simMouse.chr6 618397 3 + 636262 CCA -s simRat_chr6.simRat.chr6 630536 3 + 647215 CCA -s simRat_chr6.simRat.chr6 629085 3 + 647215 TCA - -a -s simMouse_chr6.simMouse.chr6 617200 10 + 636262 AGAATAACAG -s Anc0.Anc0refChr3 213155 10 + 222631 GGAGTAATAC -s Anc1.Anc1refChr1 53412 10 + 69767 GGAGTAATAC -s Anc2.Anc2refChr1 130581 10 + 142988 GGAGTAATAC -s mr.mrrefChr3 164491 10 + 181027 AGAGTAACAC -s mr.mrrefChr3 165650 10 + 181027 AAAGTGGTAC -s simCow_chr6.simCow.chr6 589210 10 + 602619 GGAATAATAC -s simDog_chr6.simDog.chr6 581161 10 + 593897 AGGGTAATAC -s simHuman_chr6.simHuman.chr6 584959 10 + 601863 GAAGTAATGC -s simMouse_chr6.simMouse.chr6 618400 10 + 636262 AAAGTGGTAC -s simRat_chr6.simRat.chr6 630539 10 + 647215 AGAGTGGTAG -s simRat_chr6.simRat.chr6 629088 10 + 647215 ACAGTAACAC - -a -s simMouse_chr6.simMouse.chr6 617210 1 + 636262 A -s Anc0.Anc0refChr3 213165 1 + 222631 A -s Anc1.Anc1refChr1 53422 1 + 69767 A -s Anc2.Anc2refChr1 130591 1 + 142988 A -s mr.mrrefChr3 164501 1 + 181027 A -s simCow_chr6.simCow.chr6 589220 1 + 602619 A -s simDog_chr6.simDog.chr6 581171 1 + 593897 A -s simHuman_chr6.simHuman.chr6 584969 1 + 601863 A -s simRat_chr6.simRat.chr6 629098 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 617211 37 + 636262 ACTTGGTAATGACTATGCCCTTTTCAATTGACCTAAT -s Anc0.Anc0refChr3 213166 37 + 222631 ATATGGTGATTACTATGCTCTTTGCATCTTACCTTCT -s Anc1.Anc1refChr1 53423 37 + 69767 ATATGGTGATTACTATGCTCTTTGCATCTTACCTTCT -s Anc2.Anc2refChr1 130592 37 + 142988 ATATGGTGATTTCTATACTGCTTGCATCTTACCTCCT -s mr.mrrefChr3 164502 37 + 181027 ACTTGGTAATGACTATGCTCTTTTCAATTGACCTTCT -s mr.mrrefChr3 165660 37 + 181027 ATTTGGTGATTACTATGACCTGTGCATCTGACTTTGT -s simCow_chr6.simCow.chr6 589221 37 + 602619 ATATGGTGATTTCTATGGTCACTGTATTTTACTTCCT -s simDog_chr6.simDog.chr6 581172 37 + 593897 ATATGGTGATCTCTGTACTGCTTGCATCTTACCTCTT -s simHuman_chr6.simHuman.chr6 584970 34 + 601863 ATATGGTGATTACTATGCT---TGCATCTTGTGCTCT -s simMouse_chr6.simMouse.chr6 618410 37 + 636262 ATTTGGTGATTACTATGACCTGTGCATCTGACTTTGT -s simRat_chr6.simRat.chr6 630550 37 + 647215 ATTTGGTGATTACTACGACCTGTGCATCCAACTTTAT -s simRat_chr6.simRat.chr6 629099 37 + 647215 ACTTGGTAATGACTATGCTCTTTTCAATTGACCTTCT - -a -s simMouse_chr6.simMouse.chr6 617248 16 + 636262 ACACTAACATCACACT -s Anc0.Anc0refChr3 213203 16 + 222631 ATGCTAATATCACACT -s Anc1.Anc1refChr1 53460 16 + 69767 ATGCTAATATCACACT -s Anc2.Anc2refChr1 130629 16 + 142988 CTGCTAATAGCACACT -s mr.mrrefChr3 164539 16 + 181027 ACACTAACATCACACT -s mr.mrrefChr3 165697 16 + 181027 ATAACAACATCACAAC -s simCow_chr6.simCow.chr6 589260 16 + 602619 CCCCAAACAACACACT -s simDog_chr6.simDog.chr6 581209 16 + 593897 CTGCTAATAGTACACT -s simHuman_chr6.simHuman.chr6 585004 16 + 601863 ATGCTAATACCCCACT -s simMouse_chr6.simMouse.chr6 618447 16 + 636262 ATAACAACATCACAAC -s simRat_chr6.simRat.chr6 630587 16 + 647215 ATAACAACATCACAAC -s simRat_chr6.simRat.chr6 629136 16 + 647215 ACACTAACATCACACT - -a -s simMouse_chr6.simMouse.chr6 617264 1 + 636262 A -s Anc0.Anc0refChr3 213219 1 + 222631 A -s Anc1.Anc1refChr1 53476 1 + 69767 A -s Anc2.Anc2refChr1 130645 1 + 142988 A -s mr.mrrefChr3 164555 1 + 181027 A -s mr.mrrefChr3 165713 1 + 181027 A -s simCow_chr6.simCow.chr6 589276 1 + 602619 A -s simDog_chr6.simDog.chr6 581225 1 + 593897 A -s simHuman_chr6.simHuman.chr6 585020 1 + 601863 A -s simMouse_chr6.simMouse.chr6 618463 1 + 636262 A -s simRat_chr6.simRat.chr6 630613 1 + 647215 G -s simRat_chr6.simRat.chr6 629152 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 617265 1 + 636262 C -s Anc0.Anc0refChr3 213220 1 + 222631 T -s Anc1.Anc1refChr1 53477 1 + 69767 T -s Anc2.Anc2refChr1 130646 1 + 142988 T -s mr.mrrefChr3 164556 1 + 181027 C -s simCow_chr6.simCow.chr6 589277 1 + 602619 T -s simDog_chr6.simDog.chr6 581226 1 + 593897 T -s simHuman_chr6.simHuman.chr6 585021 1 + 601863 T -s simRat_chr6.simRat.chr6 629153 1 + 647215 C - -a -s simMouse_chr6.simMouse.chr6 617266 6 + 636262 AAATCA -s Anc0.Anc0refChr3 213221 6 + 222631 AAATCA -s Anc1.Anc1refChr1 53478 6 + 69767 AAATCA -s Anc2.Anc2refChr1 130647 6 + 142988 AAATCA -s mr.mrrefChr3 164557 6 + 181027 AAATCA -s mr.mrrefChr3 165714 6 + 181027 AAATCA -s simCow_chr6.simCow.chr6 589278 6 + 602619 AAATTA -s simDog_chr6.simDog.chr6 581227 6 + 593897 AGATCC -s simHuman_chr6.simHuman.chr6 585022 6 + 601863 AAATCA -s simMouse_chr6.simMouse.chr6 618464 6 + 636262 AAATCA -s simRat_chr6.simRat.chr6 630614 6 + 647215 AAATCA -s simRat_chr6.simRat.chr6 629154 6 + 647215 AAATCA - -a -s simMouse_chr6.simMouse.chr6 617272 19 + 636262 GGGGGTATAAGACATTCAA -s Anc0.Anc0refChr3 213227 19 + 222631 GGGGGTGTAAAACACTCAG -s Anc1.Anc1refChr1 53484 19 + 69767 GGGGGTGTAAAACACTCAG -s Anc2.Anc2refChr1 130653 19 + 142988 GGGGGTGTAAAATACTCAG -s mr.mrrefChr3 164563 19 + 181027 GGGGGTATAAGACATTCAA -s mr.mrrefChr3 165720 19 + 181027 GGGGCCTTACAACATTCAA -s simCow_chr6.simCow.chr6 589284 19 + 602619 GGGGGTGTATAATATTCAG -s simDog_chr6.simDog.chr6 581233 19 + 593897 GGGGATGTAAATTACTCAG -s simHuman_chr6.simHuman.chr6 585028 19 + 601863 GGGGGTGTAACACACCCAG -s simMouse_chr6.simMouse.chr6 618470 19 + 636262 GGGGCCTTACAACATTCAA -s simRat_chr6.simRat.chr6 630621 19 + 647215 GGGACAATACAATGTTCAA -s simRat_chr6.simRat.chr6 629160 19 + 647215 GGGGGTATAAGACATTCAA - -a -s simMouse_chr6.simMouse.chr6 617291 22 + 636262 ACAGTTTCACTAATAAAGTAGG -s Anc0.Anc0refChr3 213246 22 + 222631 ACAGTGTCACTAACAAAGTAGG -s Anc1.Anc1refChr1 53503 22 + 69767 ACAGTGTCACTAACAAAGTAGG -s Anc2.Anc2refChr1 130672 22 + 142988 ACAGTGTCACTAACATACTAGG -s mr.mrrefChr3 164582 22 + 181027 ACAGTTTCACTAACAAAGTAGG -s mr.mrrefChr3 165778 22 + 181027 ACAGTTTCACTAACAGAGTAGG -s simCow_chr6.simCow.chr6 589303 19 + 602619 AC---TTCAATAACAGAATAGG -s simDog_chr6.simDog.chr6 581252 22 + 593897 ACAGTGTCACTTACATACTAGG -s simHuman_chr6.simHuman.chr6 585047 22 + 601863 AAAGTGTCACCAACAAAGTAGG -s simMouse_chr6.simMouse.chr6 618528 22 + 636262 ACAGTTTCACTAACAGAGTAGG -s simRat_chr6.simRat.chr6 630680 22 + 647215 ACAGTTTCACTAATAGAGTAGG -s simRat_chr6.simRat.chr6 629179 22 + 647215 ACATTTTCACAAACCAAATAGG - -a -s simMouse_chr6.simMouse.chr6 617313 9 + 636262 CCAGAAAAA -s Anc0.Anc0refChr3 213268 9 + 222631 CAAGAAGAA -s Anc1.Anc1refChr1 53525 9 + 69767 CAAGAAGAA -s Anc2.Anc2refChr1 130694 9 + 142988 TAAGATGAA -s mr.mrrefChr3 164604 9 + 181027 CCAGAAGAA -s mr.mrrefChr3 165800 9 + 181027 CCAGGCGAA -s simCow_chr6.simCow.chr6 589322 9 + 602619 TCAGATGAA -s simDog_chr6.simDog.chr6 581274 9 + 593897 TAAGATGAA -s simHuman_chr6.simHuman.chr6 585074 9 + 601863 CAACAAGAA -s simMouse_chr6.simMouse.chr6 618550 9 + 636262 CCAGGCGAA -s simRat_chr6.simRat.chr6 630702 9 + 647215 CCAGATAAA -s simRat_chr6.simRat.chr6 629201 9 + 647215 CCATTAGAA - -a -s simMouse_chr6.simMouse.chr6 617322 28 + 636262 ATGAGCGTATCTAAGACCCCAGTTACTA -s Anc0.Anc0refChr3 213277 25 + 222631 ACAGAC---TCTATGACCCAAGTTGTTA -s Anc1.Anc1refChr1 53534 25 + 69767 ACAGAC---TCTATGACCCAAGTTGTTA -s Anc2.Anc2refChr1 130703 25 + 142988 ACAGAC---TCTGTGATCCAAATTGTTA -s mr.mrrefChr3 164613 25 + 181027 ATGAGC---TCTAAGACCCCAGTTGTTA -s mr.mrrefChr3 165809 25 + 181027 ACAAGG---TCCATGACGTAGGTTGTCA -s simCow_chr6.simCow.chr6 589331 25 + 602619 ATAGAC---TCTGTGATTCAAATTGTTA -s simDog_chr6.simDog.chr6 581283 25 + 593897 ACAGAC---TCTGTGATCTAAATTGTCG -s simHuman_chr6.simHuman.chr6 585083 25 + 601863 ACAGAC---TCCATTACCCAAGTTGTTA -s simMouse_chr6.simMouse.chr6 618559 25 + 636262 ACAAGG---TCCATGACGTAGGTTGTCA -s simRat_chr6.simRat.chr6 630711 25 + 647215 ACAAGG---TCCTTGACCTAAGTTGTCA -s simRat_chr6.simRat.chr6 629230 25 + 647215 ATGAGC---TCTAAGACCCCAGTTGTTA - -a -s simMouse_chr6.simMouse.chr6 617350 4 + 636262 TGTT -s Anc0.Anc0refChr3 213302 4 + 222631 TGTA -s Anc1.Anc1refChr1 53559 4 + 69767 TGTA -s Anc2.Anc2refChr1 130728 4 + 142988 TGTA -s mr.mrrefChr3 164638 4 + 181027 TGTT -s simCow_chr6.simCow.chr6 589356 4 + 602619 AGTT -s simDog_chr6.simDog.chr6 581308 4 + 593897 TGTA -s simHuman_chr6.simHuman.chr6 585108 4 + 601863 TCta -s simRat_chr6.simRat.chr6 629255 4 + 647215 TATC - -a -s simMouse_chr6.simMouse.chr6 617354 4 + 636262 ATAA -s Anc0.Anc0refChr3 213306 4 + 222631 ATAA -s Anc1.Anc1refChr1 53563 4 + 69767 ATAA -s Anc2.Anc2refChr1 130732 4 + 142988 GTAA -s mr.mrrefChr3 164642 4 + 181027 ATAA -s mr.mrrefChr3 165834 4 + 181027 ATAT -s simCow_chr6.simCow.chr6 589360 4 + 602619 GTCA -s simDog_chr6.simDog.chr6 581312 4 + 593897 GTAA -s simHuman_chr6.simHuman.chr6 585112 4 + 601863 ataa -s simMouse_chr6.simMouse.chr6 618584 4 + 636262 ATAT -s simRat_chr6.simRat.chr6 630736 4 + 647215 TTAT -s simRat_chr6.simRat.chr6 629259 4 + 647215 ATAA - -a -s simMouse_chr6.simMouse.chr6 617358 2 + 636262 AG -s Anc0.Anc0refChr3 213310 2 + 222631 AA -s Anc1.Anc1refChr1 53567 2 + 69767 AA -s Anc2.Anc2refChr1 130736 2 + 142988 AA -s mr.mrrefChr3 164646 2 + 181027 AG -s mr.mrrefChr3 165838 2 + 181027 AG -s simCow_chr6.simCow.chr6 589364 2 + 602619 AG -s simDog_chr6.simDog.chr6 581316 2 + 593897 AA -s simHuman_chr6.simHuman.chr6 585116 2 + 601863 aa -s simMouse_chr6.simMouse.chr6 618588 2 + 636262 AG -s simRat_chr6.simRat.chr6 630741 2 + 647215 AG -s simRat_chr6.simRat.chr6 629263 2 + 647215 AG - -a -s simMouse_chr6.simMouse.chr6 617360 4 + 636262 TTAA -s Anc0.Anc0refChr3 213312 4 + 222631 TTAA -s Anc1.Anc1refChr1 53569 4 + 69767 TTAA -s Anc2.Anc2refChr1 130738 4 + 142988 TTAA -s mr.mrrefChr3 164648 4 + 181027 TTAA -s mr.mrrefChr3 165840 4 + 181027 TCAA -s simCow_chr6.simCow.chr6 589366 4 + 602619 TCAA -s simDog_chr6.simDog.chr6 581318 4 + 593897 TTAG -s simHuman_chr6.simHuman.chr6 585118 4 + 601863 ttaa -s simMouse_chr6.simMouse.chr6 618590 4 + 636262 TCAA -s simRat_chr6.simRat.chr6 630743 4 + 647215 TCAG -s simRat_chr6.simRat.chr6 629266 4 + 647215 TTAG - -a -s simMouse_chr6.simMouse.chr6 617364 3 + 636262 CTT -s Anc0.Anc0refChr3 213316 3 + 222631 CTT -s Anc1.Anc1refChr1 53573 3 + 69767 CTT -s Anc2.Anc2refChr1 130742 3 + 142988 CTT -s mr.mrrefChr3 164652 3 + 181027 CTT -s mr.mrrefChr3 165848 3 + 181027 CTT -s simCow_chr6.simCow.chr6 589370 3 + 602619 CTA -s simDog_chr6.simDog.chr6 581322 3 + 593897 CTT -s simHuman_chr6.simHuman.chr6 585122 3 + 601863 ctt -s simMouse_chr6.simMouse.chr6 618598 3 + 636262 CTT -s simRat_chr6.simRat.chr6 630751 3 + 647215 CTT -s simRat_chr6.simRat.chr6 629270 3 + 647215 CTT - -a -s simMouse_chr6.simMouse.chr6 617367 7 + 636262 ATTACCT -s Anc0.Anc0refChr3 213319 7 + 222631 ATTACTT -s Anc1.Anc1refChr1 53576 7 + 69767 ATTACTT -s Anc2.Anc2refChr1 130750 7 + 142988 AGTACTC -s mr.mrrefChr3 164655 7 + 181027 ATTACCT -s mr.mrrefChr3 165851 7 + 181027 ATTATAA -s simCow_chr6.simCow.chr6 589378 7 + 602619 AACACCC -s simDog_chr6.simDog.chr6 581330 7 + 593897 AGTACTC -s simHuman_chr6.simHuman.chr6 585125 7 + 601863 attattt -s simMouse_chr6.simMouse.chr6 618601 7 + 636262 ATTATAA -s simRat_chr6.simRat.chr6 630754 7 + 647215 ATTACCA -s simRat_chr6.simRat.chr6 629273 7 + 647215 ATTACCT - -a -s simMouse_chr6.simMouse.chr6 617374 12 + 636262 ACTCTTGACTCC -s Anc0.Anc0refChr3 213326 12 + 222631 ACTATTGACTCT -s Anc1.Anc1refChr1 53583 12 + 69767 ACTATTGACTCT -s Anc2.Anc2refChr1 130757 12 + 142988 ACTATTGACACT -s mr.mrrefChr3 164662 12 + 181027 ATTCTTGACTCC -s mr.mrrefChr3 165858 12 + 181027 ACTCTTAACTCC -s simCow_chr6.simCow.chr6 589385 12 + 602619 ACTATTGACACT -s simDog_chr6.simDog.chr6 581337 12 + 593897 TCTATTGTCACT -s simHuman_chr6.simHuman.chr6 585132 12 + 601863 attataGACTCT -s simMouse_chr6.simMouse.chr6 618608 12 + 636262 ACTCTTAACTCC -s simRat_chr6.simRat.chr6 630762 12 + 647215 ACTGTTGACTCA -s simRat_chr6.simRat.chr6 629280 12 + 647215 ATTTTTGACTCC - -a -s simMouse_chr6.simMouse.chr6 617386 20 + 636262 TCCAAAAAAATCACAGCGCT -s Anc0.Anc0refChr3 213358 20 + 222631 TATATGAGGAATAAAGCACG -s Anc1.Anc1refChr1 53615 20 + 69767 TATATGAGGAATAAAGCACG -s Anc2.Anc2refChr1 130790 20 + 142988 TATATGTGGAAAAAAGCACG -s mr.mrrefChr3 164674 20 + 181027 TCCAAAAAAATTACAGCACT -s mr.mrrefChr3 165870 20 + 181027 TTGAAAAAAAGCACAGCACG -s simCow_chr6.simCow.chr6 589418 20 + 602619 TATATGTGGAAAGGAGCATG -s simDog_chr6.simDog.chr6 581370 20 + 593897 TATATGTAGAAAAAAGCACA -s simHuman_chr6.simHuman.chr6 585164 20 + 601863 TATATGAGGTATAAAGCACG -s simMouse_chr6.simMouse.chr6 618620 20 + 636262 TTGAAAAAAAGCACAGCACG -s simRat_chr6.simRat.chr6 630774 20 + 647215 TTGAAGAGAAGCACAGCACA -s simRat_chr6.simRat.chr6 629292 20 + 647215 TCCAAAAAAATTACAGTACT - -a -s simMouse_chr6.simMouse.chr6 617406 6 + 636262 ATGTAC -s Anc0.Anc0refChr3 213380 6 + 222631 ATGTAC -s Anc1.Anc1refChr1 53637 6 + 69767 ATGTAC -s Anc2.Anc2refChr1 130814 6 + 142988 ATGTAC -s mr.mrrefChr3 164694 6 + 181027 ATGTAC -s mr.mrrefChr3 165890 6 + 181027 AGATAC -s simCow_chr6.simCow.chr6 589443 6 + 602619 ATATAT -s simDog_chr6.simDog.chr6 581394 6 + 593897 ATGTAC -s simHuman_chr6.simHuman.chr6 585186 6 + 601863 ATGCGC -s simMouse_chr6.simMouse.chr6 618640 6 + 636262 AGATAC -s simRat_chr6.simRat.chr6 630794 6 + 647215 AGGTAC -s simRat_chr6.simRat.chr6 629312 6 + 647215 ATGTAC - -a -s simMouse_chr6.simMouse.chr6 617412 31 + 636262 CTGATGCTATAGCAGCGCAGACAGTGTATTG -s Anc0.Anc0refChr3 213386 29 + 222631 CAGGTGCTATAGCAAAAAAGAAGTTACAT-- -s Anc1.Anc1refChr1 53643 29 + 69767 CAGGTGCTATAGCAAAAAAGAAGTTACAT-- -s Anc2.Anc2refChr1 130820 29 + 142988 TAGGTGCTATTGTAAAAAATAAGTTACAT-- -s mr.mrrefChr3 164700 31 + 181027 CTGATGCTATAGCAGAACAGACATTGCATTG -s simCow_chr6.simCow.chr6 589449 29 + 602619 GAGGTGCTATTGTAAAAAACAGGTTGCAT-- -s simDog_chr6.simDog.chr6 581400 16 + 593897 TGGGT-------------ATGAGTCACCT-- -s simHuman_chr6.simHuman.chr6 585192 29 + 601863 CATGTACTATAGCACAAAAGATGTTTCAT-- -s simRat_chr6.simRat.chr6 629318 31 + 647215 CTGATGCTACAGCAGAACGCACATTGCATTG - -a -s simMouse_chr6.simMouse.chr6 617443 9 + 636262 GGGTTGATG -s Anc0.Anc0refChr3 213415 9 + 222631 GGATAGAAG -s Anc1.Anc1refChr1 53672 9 + 69767 GGATAGAAG -s Anc2.Anc2refChr1 130849 9 + 142988 GGATAGAAG -s mr.mrrefChr3 164731 9 + 181027 GGGTTGAAG -s simCow_chr6.simCow.chr6 589480 9 + 602619 GGATAGAAG -s simDog_chr6.simDog.chr6 581416 4 + 593897 -----GAAG -s simHuman_chr6.simHuman.chr6 585221 9 + 601863 AGACAGAAG -s simRat_chr6.simRat.chr6 629349 9 + 647215 GGTTTGAAG - -a -s simMouse_chr6.simMouse.chr6 617452 2 + 636262 TA -s Anc0.Anc0refChr3 213424 2 + 222631 TA -s Anc1.Anc1refChr1 53681 2 + 69767 TA -s Anc2.Anc2refChr1 130858 2 + 142988 TA -s mr.mrrefChr3 164740 2 + 181027 TA -s mr.mrrefChr3 165896 2 + 181027 TA -s simCow_chr6.simCow.chr6 589489 2 + 602619 CA -s simDog_chr6.simDog.chr6 581420 2 + 593897 TA -s simHuman_chr6.simHuman.chr6 585230 2 + 601863 TA -s simMouse_chr6.simMouse.chr6 618646 2 + 636262 TA -s simRat_chr6.simRat.chr6 630800 2 + 647215 CA -s simRat_chr6.simRat.chr6 629358 2 + 647215 TA - -a -s simMouse_chr6.simMouse.chr6 617454 7 + 636262 TCACATT -s Anc0.Anc0refChr3 213426 7 + 222631 CCACATC -s Anc1.Anc1refChr1 53683 7 + 69767 CCACATC -s Anc2.Anc2refChr1 130860 7 + 142988 CCACATC -s mr.mrrefChr3 164742 7 + 181027 CCACATT -s mr.mrrefChr3 165898 7 + 181027 CCTCATC -s simCow_chr6.simCow.chr6 589491 5 + 602619 CCATA-- -s simDog_chr6.simDog.chr6 581422 7 + 593897 CCACATC -s simHuman_chr6.simHuman.chr6 585232 7 + 601863 CCTCATT -s simMouse_chr6.simMouse.chr6 618764 7 + 636262 CCTCATC -s simRat_chr6.simRat.chr6 630802 7 + 647215 CAGTAGC -s simRat_chr6.simRat.chr6 629360 7 + 647215 CCACATT - -a -s simMouse_chr6.simMouse.chr6 617461 3 + 636262 CTG -s Anc0.Anc0refChr3 213433 1 + 222631 T-- -s Anc1.Anc1refChr1 53690 3 + 69767 TAA -s Anc2.Anc2refChr1 130867 1 + 142988 T-- -s mr.mrrefChr3 164749 3 + 181027 TTG -s simDog_chr6.simDog.chr6 581429 1 + 593897 T-- -s simHuman_chr6.simHuman.chr6 585239 3 + 601863 TAA -s simRat_chr6.simRat.chr6 629367 3 + 647215 TTG - -a -s simMouse_chr6.simMouse.chr6 617464 15 + 636262 CCTGAACTACCACAA -s Anc1.Anc1refChr1 53697 15 + 69767 CCTAAAGGACCACAC -s mr.mrrefChr3 164756 15 + 181027 CCTGAAGTACCACAC -s simHuman_chr6.simHuman.chr6 585246 15 + 601863 CCTAAAGGACCACAC -s simRat_chr6.simRat.chr6 629374 15 + 647215 CCTGAAGTACCACAC - -a -s simMouse_chr6.simMouse.chr6 617479 10 + 636262 ACCAGTTGAC -s Anc0.Anc0refChr3 213434 9 + 222631 -CAGTTTCCC -s Anc1.Anc1refChr1 53712 10 + 69767 TCAGTTTCCC -s Anc2.Anc2refChr1 130868 9 + 142988 -CAGTTTCCC -s mr.mrrefChr3 164771 10 + 181027 ACCAGTTGAC -s mr.mrrefChr3 165905 10 + 181027 TCAATTACCC -s simDog_chr6.simDog.chr6 581430 9 + 593897 -CAGTTTCCC -s simHuman_chr6.simHuman.chr6 585261 10 + 601863 TCAGTTGCCC -s simMouse_chr6.simMouse.chr6 618771 10 + 636262 TCAATTACCC -s simRat_chr6.simRat.chr6 630809 10 + 647215 TCAGTTACCC -s simRat_chr6.simRat.chr6 629389 10 + 647215 ACCAGTTGAC - -a -s simMouse_chr6.simMouse.chr6 617489 11 + 636262 AAAATTCAGAA -s Anc0.Anc0refChr3 213454 11 + 222631 CACATTTAAAA -s Anc1.Anc1refChr1 53733 11 + 69767 CACATTTAAAA -s Anc2.Anc2refChr1 130888 11 + 142988 CATATTTAAAG -s mr.mrrefChr3 164781 11 + 181027 AAAATTCAAAA -s mr.mrrefChr3 165915 11 + 181027 CCCAGTTCTAA -s simDog_chr6.simDog.chr6 581450 11 + 593897 CATATTTAAAG -s simHuman_chr6.simHuman.chr6 585282 11 + 601863 TACACTTGAAA -s simMouse_chr6.simMouse.chr6 618781 11 + 636262 CCCAGTTCTAA -s simRat_chr6.simRat.chr6 630819 11 + 647215 CCTGGTTCCAA -s simRat_chr6.simRat.chr6 629399 11 + 647215 AAAATTAAAAA - -a -s simMouse_chr6.simMouse.chr6 617500 2 + 636262 AA -s Anc0.Anc0refChr3 213465 2 + 222631 CA -s Anc1.Anc1refChr1 53744 2 + 69767 CA -s Anc2.Anc2refChr1 130899 2 + 142988 CA -s mr.mrrefChr3 164792 2 + 181027 AA -s mr.mrrefChr3 165926 2 + 181027 CA -s simDog_chr6.simDog.chr6 581461 2 + 593897 CA -s simHuman_chr6.simHuman.chr6 585293 2 + 601863 TA -s simMouse_chr6.simMouse.chr6 618795 2 + 636262 CA -s simRat_chr6.simRat.chr6 630830 2 + 647215 CA -s simRat_chr6.simRat.chr6 629410 2 + 647215 AA - -a -s simMouse_chr6.simMouse.chr6 617502 12 + 636262 AAGGTACACTGC -s Anc0.Anc0refChr3 213481 12 + 222631 AAGGTAGACTGT -s Anc1.Anc1refChr1 53761 12 + 69767 AAGGTAGACTGT -s Anc2.Anc2refChr1 130915 12 + 142988 AAGGCAGACTGT -s mr.mrrefChr3 164794 12 + 181027 AAGGTACACTGC -s mr.mrrefChr3 165943 12 + 181027 AGAATAAACTGT -s simDog_chr6.simDog.chr6 581477 12 + 593897 AAGGCAGACTGT -s simHuman_chr6.simHuman.chr6 585310 12 + 601863 AAGGTTGACTGT -s simMouse_chr6.simMouse.chr6 618812 12 + 636262 AGAATAAACTGT -s simRat_chr6.simRat.chr6 630847 12 + 647215 AGAGTAAAATGT -s simRat_chr6.simRat.chr6 629412 12 + 647215 CAGGAACACTGC - -a -s simMouse_chr6.simMouse.chr6 617514 19 + 636262 TTGTTGTATGGGCAGGTTA -s Anc0.Anc0refChr3 213498 15 + 222631 TTATTGTATGGGTAG---- -s Anc1.Anc1refChr1 53778 19 + 69767 TTATTGTATGGGTAGGTGA -s Anc2.Anc2refChr1 130932 15 + 142988 CAATCGTAAGAGTAA---- -s mr.mrrefChr3 164806 19 + 181027 TTGTTGTATGGGTAGGTTA -s mr.mrrefChr3 165960 19 + 181027 TTACTGTATAGGTAGGTCA -s simDog_chr6.simDog.chr6 581494 15 + 593897 CAATCGTAAGAGTAA---- -s simHuman_chr6.simHuman.chr6 585327 19 + 601863 TTATTGTATGGGTAGTGGT -s simMouse_chr6.simMouse.chr6 618829 19 + 636262 TTACTGTATAGGTAGGTCA -s simRat_chr6.simRat.chr6 630864 19 + 647215 TTAATGTATGGGTAGGTCT -s simRat_chr6.simRat.chr6 629424 19 + 647215 TTGTTGTACTGGTAGGCTA - -a -s simMouse_chr6.simMouse.chr6 617533 5 + 636262 GCATG -s mr.mrrefChr3 164825 5 + 181027 GCATG -s simRat_chr6.simRat.chr6 629443 5 + 647215 GCATG - -a -s simMouse_chr6.simMouse.chr6 617538 17 + 636262 ACCAGAAATGGACCATG -s Anc0.Anc0refChr3 213513 15 + 222631 --TTTGAGTAGACCATC -s Anc1.Anc1refChr1 53797 17 + 69767 AGTTTGAGTAGACCATC -s Anc2.Anc2refChr1 130947 15 + 142988 --TCTGAGTAGACCATT -s mr.mrrefChr3 164830 17 + 181027 AGTAGAAATGGACCATG -s mr.mrrefChr3 165979 17 + 181027 AGTTTGAGTAGACCATC -s simCow_chr6.simCow.chr6 589496 8 + 602619 -----GAGTTCAC---- -s simDog_chr6.simDog.chr6 581509 15 + 593897 --TCTGAGTAGACCATT -s simHuman_chr6.simHuman.chr6 585346 17 + 601863 AGATTGAGTAGACCATC -s simMouse_chr6.simMouse.chr6 618848 17 + 636262 AGTTTGAGTAGACCCTC -s simRat_chr6.simRat.chr6 630883 17 + 647215 GGTTTGAGTACACCATC -s simRat_chr6.simRat.chr6 629448 17 + 647215 AGTAGAAATGGACCATG - -a -s simMouse_chr6.simMouse.chr6 617555 4 + 636262 TGTA -s Anc0.Anc0refChr3 213528 4 + 222631 TGTA -s Anc1.Anc1refChr1 53814 4 + 69767 TGTA -s Anc2.Anc2refChr1 130963 4 + 142988 TGTG -s mr.mrrefChr3 164847 4 + 181027 TGTA -s mr.mrrefChr3 165996 4 + 181027 TGTA -s simCow_chr6.simCow.chr6 589505 4 + 602619 TGTG -s simDog_chr6.simDog.chr6 581525 4 + 593897 TGTG -s simHuman_chr6.simHuman.chr6 585363 4 + 601863 CGTA -s simMouse_chr6.simMouse.chr6 618865 4 + 636262 TATA -s simRat_chr6.simRat.chr6 630900 4 + 647215 TGTA -s simRat_chr6.simRat.chr6 629465 4 + 647215 TGTA - -a -s simMouse_chr6.simMouse.chr6 617559 3 + 636262 TGG -s Anc0.Anc0refChr3 213532 3 + 222631 TTG -s Anc1.Anc1refChr1 53818 3 + 69767 TTG -s Anc2.Anc2refChr1 130967 3 + 142988 TTG -s mr.mrrefChr3 164851 3 + 181027 TTG -s simCow_chr6.simCow.chr6 589509 3 + 602619 TAG -s simDog_chr6.simDog.chr6 581529 3 + 593897 TTG -s simHuman_chr6.simHuman.chr6 585367 3 + 601863 TTG -s simRat_chr6.simRat.chr6 629469 3 + 647215 TTG - -a -s simMouse_chr6.simMouse.chr6 617562 25 + 636262 TGTTGAAAGCCTTGCTACTTAGCCT -s Anc0.Anc0refChr3 213537 25 + 222631 TGCTAGAAACCTTTCTGCTTAGCCT -s Anc1.Anc1refChr1 53823 25 + 69767 TGCTAGAAACCTTTCTGCTTAGCCT -s Anc2.Anc2refChr1 130972 25 + 142988 TGCTAGAAACCTTTCTGCTCAGCCT -s mr.mrrefChr3 164854 25 + 181027 TGTTGAAAGCCTTGCTACTTAGCCT -s simCow_chr6.simCow.chr6 589514 25 + 602619 TGAGGAGAACACCTGTAATCAGCCT -s simDog_chr6.simDog.chr6 581534 25 + 593897 GGCTAGAAACCTTTCTGCTCAGCCT -s simHuman_chr6.simHuman.chr6 585372 25 + 601863 TGCTAGAAATCTGTTTGCTTAGCCT -s simRat_chr6.simRat.chr6 629472 23 + 647215 TGTTGAAAGCC--GCTACTTAGCCT - -a -s simMouse_chr6.simMouse.chr6 617587 20 + 636262 ATGTCACTATTCCCCCACAA -s Anc0.Anc0refChr3 213562 20 + 222631 ATGTCATTATTTCACCACAA -s Anc1.Anc1refChr1 53848 20 + 69767 ATGTCATTATTTCACCACAA -s Anc2.Anc2refChr1 130997 20 + 142988 ATGTCATTATATCACCACAA -s mr.mrrefChr3 164879 20 + 181027 ATGTCACTATTCCCCCACAA -s mr.mrrefChr3 166000 20 + 181027 GTATCACTATGTTACCACAA -s simCow_chr6.simCow.chr6 589539 20 + 602619 ATGTCATTATGTCACCACAA -s simDog_chr6.simDog.chr6 581559 20 + 593897 ATGTCATTACATCATGACAT -s simHuman_chr6.simHuman.chr6 585397 19 + 601863 ATGTCATTATT-CACCAAAA -s simMouse_chr6.simMouse.chr6 618869 20 + 636262 GTATCACTATGTTAGCACAA -s simRat_chr6.simRat.chr6 630904 20 + 647215 GTATCACGATGTTGCCACCA -s simRat_chr6.simRat.chr6 629495 20 + 647215 ATGTCACTATTTCCCCACTA - -a -s simMouse_chr6.simMouse.chr6 617607 17 + 636262 GGCCTATGTTCCCACTG -s mr.mrrefChr3 164899 9 + 181027 GGCC--------CACTG -s simRat_chr6.simRat.chr6 629515 9 + 647215 GGCC--------CACTG - -a -s simMouse_chr6.simMouse.chr6 617624 31 + 636262 GGCAAAGTTGTCTCATATCATCTGGATGAAA -s Anc0.Anc0refChr3 213582 31 + 222631 TACAAGGAGGTCTCATATAGTGAAAATGAAA -s Anc1.Anc1refChr1 53868 31 + 69767 TACAAGGAGGTCTCATATAGTGAAAATGAAA -s Anc2.Anc2refChr1 131017 31 + 142988 TACAAGGAGGTCTGGTATAGTGAAAGTGGAA -s mr.mrrefChr3 164908 31 + 181027 GGCAAAGTTGTCTCATATAATCTAGATGAAA -s mr.mrrefChr3 166020 31 + 181027 CACAAGATGGCCTCATATAATAAAAATGAAA -s simCow_chr6.simCow.chr6 589559 31 + 602619 CCCAAGGAGGCCTTGTATAGTGAAAGTTAAA -s simDog_chr6.simDog.chr6 581579 31 + 593897 TAAGAGAAGGTCTGGTTTACTGAAAGTGGAA -s simHuman_chr6.simHuman.chr6 585416 30 + 601863 TACAAGGAGGTCTCATATAGTGAAAATG-AA -s simMouse_chr6.simMouse.chr6 618889 31 + 636262 CACAAGATGGATTCATATAACAAAGATGAAA -s simRat_chr6.simRat.chr6 630924 31 + 647215 CACAAGATGGCCTCATATAATAAAAATGAAA -s simRat_chr6.simRat.chr6 629524 31 + 647215 GGTAAAATTGCCTCATATAATATAGATGAAA - -a -s simMouse_chr6.simMouse.chr6 617655 19 + 636262 GAACAATTCAATTATCACA -s Anc0.Anc0refChr3 213613 19 + 222631 GCACAATTCCATTCTCACA -s Anc1.Anc1refChr1 53899 19 + 69767 GCACAATTCCATTCTCACA -s Anc2.Anc2refChr1 131048 19 + 142988 GCACAATTCCATTCTCACA -s mr.mrrefChr3 164939 19 + 181027 GAACAATTCAATTCTCACA -s mr.mrrefChr3 166051 19 + 181027 GGACAATCCCAGTCTCACA -s simCow_chr6.simCow.chr6 589593 19 + 602619 GCACAATTCCATTCTCACA -s simDog_chr6.simDog.chr6 581610 19 + 593897 GTACACTTCCAATCTCACA -s simHuman_chr6.simHuman.chr6 585446 19 + 601863 GCACAATTCCATTCTAGCA -s simMouse_chr6.simMouse.chr6 618920 19 + 636262 GGACAATCCCAGTCTCACA -s simRat_chr6.simRat.chr6 630955 19 + 647215 GGACGATCCCAGTCTCCCC -s simRat_chr6.simRat.chr6 629555 19 + 647215 GGACAATTCAATTCTCATA - -a -s simMouse_chr6.simMouse.chr6 617674 2 + 636262 AA -s Anc0.Anc0refChr3 213632 2 + 222631 AT -s Anc1.Anc1refChr1 53918 2 + 69767 AT -s Anc2.Anc2refChr1 131067 2 + 142988 AT -s mr.mrrefChr3 164958 2 + 181027 AA -s simCow_chr6.simCow.chr6 589612 2 + 602619 AT -s simDog_chr6.simDog.chr6 581629 2 + 593897 AC -s simHuman_chr6.simHuman.chr6 585465 2 + 601863 AT -s simRat_chr6.simRat.chr6 629574 2 + 647215 AA - -a -s simMouse_chr6.simMouse.chr6 617676 8 + 636262 ATGGAAAC -s Anc0.Anc0refChr3 213634 8 + 222631 GAAGATCC -s Anc1.Anc1refChr1 53920 8 + 69767 GAAGATCC -s Anc2.Anc2refChr1 131069 8 + 142988 GAAGATTC -s mr.mrrefChr3 164960 8 + 181027 ATGGAACC -s mr.mrrefChr3 166070 8 + 181027 GTGAAGAT -s simCow_chr6.simCow.chr6 589614 6 + 602619 GAAGGT-- -s simDog_chr6.simDog.chr6 581631 8 + 593897 GTCCATTC -s simHuman_chr6.simHuman.chr6 585467 8 + 601863 GAAGATCT -s simMouse_chr6.simMouse.chr6 618939 8 + 636262 GTGAAGAT -s simRat_chr6.simRat.chr6 630974 8 + 647215 GTGAAGAT -s simRat_chr6.simRat.chr6 629576 8 + 647215 ATGAAGCC - -a -s simMouse_chr6.simMouse.chr6 617684 26 + 636262 ATGTTGTACACTGCTTTTTTCATGGC -s Anc0.Anc0refChr3 213642 26 + 222631 GTGTTGTACTCTTGTTTTTTGATGGC -s Anc1.Anc1refChr1 53928 26 + 69767 GTGTTGTACTCTTGTTTTTTGATGGC -s Anc2.Anc2refChr1 131077 26 + 142988 GTGTTGTACTCTTGTTTTTTGATGGC -s mr.mrrefChr3 164968 26 + 181027 GTGTTGTACTCTGGTTTTTTCATGGC -s mr.mrrefChr3 166078 26 + 181027 GTGCTACACTCTTAGTTTTTGTTACC -s simCow_chr6.simCow.chr6 589620 26 + 602619 ATGTTGTACTCTGGGTTTTTGATGCC -s simDog_chr6.simDog.chr6 581652 26 + 593897 GGGCTGTACGCTTGTGTTTTGATGGC -s simHuman_chr6.simHuman.chr6 585475 26 + 601863 GTGTTGTACTCTTGTTGTTTGATGAC -s simMouse_chr6.simMouse.chr6 618947 26 + 636262 GTGCTACACTCTTAGTTTTTGTCACC -s simRat_chr6.simRat.chr6 630982 26 + 647215 GTGATACACTCTTAGTCTTTGTTACC -s simRat_chr6.simRat.chr6 629584 26 + 647215 GTGTTATACTCTGGTTTTTTCATGGC - -a -s simMouse_chr6.simMouse.chr6 617710 5 + 636262 ACTGT -s Anc0.Anc0refChr3 213669 5 + 222631 ATTGG -s Anc1.Anc1refChr1 53955 5 + 69767 ATTGG -s Anc2.Anc2refChr1 131104 5 + 142988 ATGGG -s mr.mrrefChr3 164994 5 + 181027 ACTGG -s mr.mrrefChr3 166104 5 + 181027 ACTGG -s simCow_chr6.simCow.chr6 589647 5 + 602619 ATGGG -s simDog_chr6.simDog.chr6 581679 5 + 593897 ATGGG -s simHuman_chr6.simHuman.chr6 585502 5 + 601863 ATTGG -s simMouse_chr6.simMouse.chr6 618973 5 + 636262 ACTGG -s simRat_chr6.simRat.chr6 631008 5 + 647215 ACTGG -s simRat_chr6.simRat.chr6 629610 5 + 647215 ACTGG - -a -s simMouse_chr6.simMouse.chr6 617715 12 + 636262 GGAACTCTCCAC -s Anc0.Anc0refChr3 213674 12 + 222631 GGAACCCTACAT -s Anc1.Anc1refChr1 53960 12 + 69767 GGAACCCTACAT -s Anc2.Anc2refChr1 131109 12 + 142988 GGAACCCTACAT -s mr.mrrefChr3 164999 12 + 181027 GGAACCCTCCAC -s mr.mrrefChr3 166116 12 + 181027 GGAATCCTCCAT -s simCow_chr6.simCow.chr6 589652 12 + 602619 GGAGCCCTACAT -s simDog_chr6.simDog.chr6 581684 12 + 593897 GGAACCCTACAT -s simHuman_chr6.simHuman.chr6 585507 12 + 601863 GGAACCCTACAT -s simMouse_chr6.simMouse.chr6 618984 12 + 636262 GGAATCCTCCAT -s simRat_chr6.simRat.chr6 631021 12 + 647215 TAGATCCTCCAT -s simRat_chr6.simRat.chr6 629615 12 + 647215 GGAACCTACCAC - -a -s simMouse_chr6.simMouse.chr6 617727 19 + 636262 AATTGCCAGGGATAATAAC -s Anc0.Anc0refChr3 213686 19 + 222631 AATTGCCAGGGATGATAAC -s Anc1.Anc1refChr1 53972 19 + 69767 AATTGCCAGGGATGATAAC -s Anc2.Anc2refChr1 131121 19 + 142988 AATTGCCAGGGATGATAAC -s mr.mrrefChr3 165011 19 + 181027 AATTGCCAGGGATAATAAC -s mr.mrrefChr3 166128 19 + 181027 AGTTGCCAGGGATGCTAGC -s simCow_chr6.simCow.chr6 589665 19 + 602619 AATTGTCTGGTGTGGTAAC -s simDog_chr6.simDog.chr6 581696 19 + 593897 AATTGCCAGGGATGATAAC -s simHuman_chr6.simHuman.chr6 585519 19 + 601863 AATTGCCAAGGATAATAAC -s simMouse_chr6.simMouse.chr6 618996 19 + 636262 AGTTGCCAGGGATGCTAGC -s simRat_chr6.simRat.chr6 631033 19 + 647215 AGTTGCCAGGGCTGCTAGC -s simRat_chr6.simRat.chr6 629627 19 + 647215 AATTGCCAGGGGTAATAAC - -a -s simMouse_chr6.simMouse.chr6 617746 4 + 636262 CAAA -s Anc0.Anc0refChr3 213705 4 + 222631 CTGC -s Anc1.Anc1refChr1 53991 4 + 69767 CTGC -s Anc2.Anc2refChr1 131140 4 + 142988 CTGC -s mr.mrrefChr3 165030 4 + 181027 CTAA -s simCow_chr6.simCow.chr6 589684 4 + 602619 CTGG -s simDog_chr6.simDog.chr6 581715 4 + 593897 CTGC -s simHuman_chr6.simHuman.chr6 585538 4 + 601863 CTGC -s simRat_chr6.simRat.chr6 629646 4 + 647215 CTAA - -a -s simMouse_chr6.simMouse.chr6 617750 4 + 636262 TATT -s Anc0.Anc0refChr3 213709 1 + 222631 A--- -s Anc1.Anc1refChr1 53995 1 + 69767 A--- -s Anc2.Anc2refChr1 131144 1 + 142988 A--- -s mr.mrrefChr3 165034 1 + 181027 A--- -s mr.mrrefChr3 166147 1 + 181027 A--- -s simCow_chr6.simCow.chr6 589688 1 + 602619 A--- -s simDog_chr6.simDog.chr6 581719 1 + 593897 A--- -s simHuman_chr6.simHuman.chr6 585542 1 + 601863 A--- -s simMouse_chr6.simMouse.chr6 619015 1 + 636262 A--- -s simRat_chr6.simRat.chr6 631052 1 + 647215 A--- -s simRat_chr6.simRat.chr6 629650 1 + 647215 A--- - -a -s simMouse_chr6.simMouse.chr6 617754 31 + 636262 TTCTTCATGGTTAAAAAAAGATTGCAAGAAA -s Anc0.Anc0refChr3 213717 31 + 222631 TTCATCATAATTGAAGGGAGGTTGCAAGAAG -s Anc1.Anc1refChr1 54003 31 + 69767 TTCATCATAATTGAAGGGAGGTTGCAAGAAG -s Anc2.Anc2refChr1 131152 31 + 142988 TTCATCATAATTGAAGGGAGGTTGCAATAAG -s mr.mrrefChr3 165035 31 + 181027 TTCTTCATAGTTAAAAAAAGATTGCAAGAAA -s mr.mrrefChr3 166148 31 + 181027 TTTATCATAATTAAAAGGATGTTGCAGGGGG -s simCow_chr6.simCow.chr6 589696 31 + 602619 TTCATCATAATTGAGGGGAGGTTGCAATAAG -s simDog_chr6.simDog.chr6 581727 31 + 593897 TTCATCATAATTGAAGGGAGGTTACAATAAG -s simHuman_chr6.simHuman.chr6 585550 31 + 601863 TTCATCACAATTGAAGGAAGGTTGTAAGAAA -s simMouse_chr6.simMouse.chr6 619016 31 + 636262 TTTATCATAATTAAAAGGATGTTGCAGGGGG -s simRat_chr6.simRat.chr6 631053 31 + 647215 TTTATCATAATTAAAAGGACATTGGTGGGGG -s simRat_chr6.simRat.chr6 629651 31 + 647215 TTCTTCATAGTTAAAAAAAGACTGCAAGAAA - -a -s simMouse_chr6.simMouse.chr6 617785 8 + 636262 GCCTGAGT -s Anc0.Anc0refChr3 213750 8 + 222631 CCCTGAGT -s Anc1.Anc1refChr1 54036 8 + 69767 CCCTGAGT -s Anc2.Anc2refChr1 131185 8 + 142988 CCCTGTGT -s mr.mrrefChr3 165066 8 + 181027 GCCTGAGT -s mr.mrrefChr3 166179 8 + 181027 CCCTGAGT -s simCow_chr6.simCow.chr6 589729 8 + 602619 CTCTGGGT -s simDog_chr6.simDog.chr6 581760 8 + 593897 CCCTGTCT -s simHuman_chr6.simHuman.chr6 585583 8 + 601863 CCCTGAGT -s simMouse_chr6.simMouse.chr6 619047 8 + 636262 CCCTGAGT -s simRat_chr6.simRat.chr6 631084 8 + 647215 CCCGGAGT -s simRat_chr6.simRat.chr6 629682 8 + 647215 GCCTGAGT - -a -s simMouse_chr6.simMouse.chr6 617793 11 + 636262 CTTTCCTGATA -s Anc0.Anc0refChr3 213758 11 + 222631 TTTTACTGATA -s Anc1.Anc1refChr1 54044 11 + 69767 TTTTACTGATA -s Anc2.Anc2refChr1 131194 11 + 142988 TTTTACTCATA -s mr.mrrefChr3 165074 11 + 181027 TTTTCCTGATA -s mr.mrrefChr3 166187 11 + 181027 TTTTAGTGATA -s simCow_chr6.simCow.chr6 589738 11 + 602619 CTTTACTCATA -s simDog_chr6.simDog.chr6 581769 11 + 593897 TTTTACTCATA -s simHuman_chr6.simHuman.chr6 585591 11 + 601863 TTTTACTGATA -s simMouse_chr6.simMouse.chr6 619055 11 + 636262 TTTCAGTGATA -s simRat_chr6.simRat.chr6 631092 11 + 647215 TTTTAATGATA -s simRat_chr6.simRat.chr6 629690 11 + 647215 TTTTCCTGATA - -a -s simMouse_chr6.simMouse.chr6 617804 5 + 636262 AGTTT -s Anc0.Anc0refChr3 213769 5 + 222631 GGTTT -s Anc1.Anc1refChr1 54055 5 + 69767 GGTTT -s Anc2.Anc2refChr1 131205 5 + 142988 GGTTT -s mr.mrrefChr3 165085 5 + 181027 AGTTT -s mr.mrrefChr3 166198 5 + 181027 AGTAT -s simCow_chr6.simCow.chr6 589749 5 + 602619 CATTT -s simDog_chr6.simDog.chr6 581780 5 + 593897 GGTTT -s simHuman_chr6.simHuman.chr6 585602 5 + 601863 GGTTT -s simMouse_chr6.simMouse.chr6 619085 5 + 636262 AGTAC -s simRat_chr6.simRat.chr6 631103 5 + 647215 AGTCT -s simRat_chr6.simRat.chr6 629701 5 + 647215 AGTTT - -a -s simMouse_chr6.simMouse.chr6 617809 28 + 636262 TACAACCTTAACGGATAACTAGGAAAAA -s Anc0.Anc0refChr3 213774 27 + 222631 CACAAC-TGACAGGATAGCTAGGATAAA -s Anc1.Anc1refChr1 54060 27 + 69767 CACAAC-TGACAGGATAGCTAGGATAAA -s Anc2.Anc2refChr1 131210 27 + 142988 CACCAC-TGACAGGATAGCTAGGATAAA -s mr.mrrefChr3 165090 28 + 181027 TACAACCTTACCGGATAACTAGGAAAAA -s simCow_chr6.simCow.chr6 589754 27 + 602619 CACCCT-AGACAGCATAGCCAGGATAAA -s simDog_chr6.simDog.chr6 581785 27 + 593897 CACCAC-TGACAGGATAGATAAGAAAAA -s simHuman_chr6.simHuman.chr6 585607 27 + 601863 CACAAC-TGACAGGATAGCTGGGATAAA -s simRat_chr6.simRat.chr6 629706 28 + 647215 TACAACCTTACTGGATAACTAGGAAAGA - -a -s simMouse_chr6.simMouse.chr6 617837 29 + 636262 TTGGCAAAATAGCATAGGGGATATTAAGT -s Anc0.Anc0refChr3 213801 27 + 222631 TTAGCAATAAAAGGA--GGGGGATCAAGT -s Anc1.Anc1refChr1 54087 27 + 69767 TTAGCAATAAAAGGA--GGGGGATCAAGT -s Anc2.Anc2refChr1 131237 27 + 142988 TTAGCAATAAAAGGA--GGAGGATCAAGT -s mr.mrrefChr3 165118 29 + 181027 TTGGCAATATAACGTAGGGGATATTAAGT -s simCow_chr6.simCow.chr6 589782 27 + 602619 TTAGGAATAAGGCGA--GGAGTATATAGT -s simDog_chr6.simDog.chr6 581812 27 + 593897 TTAGCTTTGAAAGGA--GGATGATCAATT -s simHuman_chr6.simHuman.chr6 585634 27 + 601863 TTAGCAATAGAAGGG--GGGGGCTCAAGT -s simRat_chr6.simRat.chr6 629734 29 + 647215 TTGGCAATACGACGTAGTGGATATTAAGG - -a -s simMouse_chr6.simMouse.chr6 617866 25 + 636262 GACATAATACCTAATCACCACTATA -s Anc0.Anc0refChr3 213847 25 + 222631 GACAAAATATATAATCACCACAACA -s Anc1.Anc1refChr1 54133 25 + 69767 GACAAAATATATAATCACCACAACA -s Anc2.Anc2refChr1 131283 25 + 142988 GACAAAATATATGATCACCACGACA -s mr.mrrefChr3 165147 25 + 181027 GACATAATACCTAATCACCACAATA -s simCow_chr6.simCow.chr6 589828 17 + 602619 TACAAACTGTATGATTA-------- -s simDog_chr6.simDog.chr6 581858 25 + 593897 GAAAAAATATATGATCACCACGACA -s simHuman_chr6.simHuman.chr6 585680 25 + 601863 GACAAAATATATAGTCTCCACAACA -s simRat_chr6.simRat.chr6 629763 25 + 647215 GACATAATACCTACTCACCACAATA - -a -s simMouse_chr6.simMouse.chr6 617891 1 + 636262 T -s Anc0.Anc0refChr3 213872 1 + 222631 G -s Anc1.Anc1refChr1 54158 1 + 69767 G -s Anc2.Anc2refChr1 131308 1 + 142988 G -s mr.mrrefChr3 165172 1 + 181027 G -s simCow_chr6.simCow.chr6 589845 1 + 602619 A -s simDog_chr6.simDog.chr6 581893 1 + 593897 G -s simHuman_chr6.simHuman.chr6 585705 1 + 601863 G -s simRat_chr6.simRat.chr6 629788 1 + 647215 G - -a -s simMouse_chr6.simMouse.chr6 617892 7 + 636262 ATTGATA -s Anc0.Anc0refChr3 213873 7 + 222631 CCTGATA -s Anc1.Anc1refChr1 54159 7 + 69767 CCTGATA -s Anc2.Anc2refChr1 131333 7 + 142988 CCTGATA -s mr.mrrefChr3 165173 7 + 181027 ATTGATA -s simCow_chr6.simCow.chr6 589870 7 + 602619 CCTGGTA -s simDog_chr6.simDog.chr6 581918 7 + 593897 CCTGATA -s simHuman_chr6.simHuman.chr6 585706 7 + 601863 CCTGCTA -s simRat_chr6.simRat.chr6 629789 7 + 647215 ATTGATA - -a -s simMouse_chr6.simMouse.chr6 617899 91 + 636262 TGGGGAATGTTATATGGCAGAAGATTAGTAAAAGAACACATTAACTTCTCCTGTGGCTCAGAGGAAAGGATGGGGTTACACATAGGATGGG -s Anc0.Anc0refChr3 213881 13 + 222631 ATGTGAATATTGT------------------------------------------------------------------------------ -s Anc1.Anc1refChr1 54167 13 + 69767 ATGTGAATATTGT------------------------------------------------------------------------------ -s Anc2.Anc2refChr1 131341 13 + 142988 ATGTGAGTATTGT------------------------------------------------------------------------------ -s mr.mrrefChr3 165181 91 + 181027 TGGTGAATGTTATATGGCAGAAGATTAGTAAAAGAACACATTAACTTCTCCTGTGGCTCAGAGGAAAGGATGGGGTTACACATAGGATGGG -s simCow_chr6.simCow.chr6 589878 13 + 602619 GTGTGACTATTGT------------------------------------------------------------------------------ -s simDog_chr6.simDog.chr6 581926 8 + 593897 A-----GTATTGT------------------------------------------------------------------------------ -s simHuman_chr6.simHuman.chr6 585714 13 + 601863 ATGTGGATATTCT------------------------------------------------------------------------------ -s simRat_chr6.simRat.chr6 629797 91 + 647215 TGGTGAATGTTGTATGGCAGAAGATTAGTAAAGGAACACGTTAACTTCTCCTGTAGCTCAGAGGATAAGATGAGCTTACAGACAATGTGAG - -a -s simMouse_chr6.simMouse.chr6 617990 53 + 636262 GTTACAGTGGACTGGTCTTTACACTATACCCTTTGTGGGCAAGAGGGGGGGAT -s mr.mrrefChr3 165272 52 + 181027 GTTA-AGTGGACTGGTCTTTACACTATACCCTTTGTGGGCAAGAGGGGGGGAT -s simRat_chr6.simRat.chr6 630115 52 + 647215 GTGA-AATGGACTGATAGTTACACTAGATCCTTTGTCAGCAAGAGGGGGGGAT - -a -s simMouse_chr6.simMouse.chr6 618043 18 + 636262 CAACCAGCTGGGTCCATG -s mr.mrrefChr3 165324 18 + 181027 CAACCAGCTGGGTCCATG -s simRat_chr6.simRat.chr6 630187 18 + 647215 CAAATGGCTGGGTCCAGG - -a -s simMouse_chr6.simMouse.chr6 618061 38 + 636262 TGGCTGGGTAAACCAGGAGTTGAAGGTCTCTAACAAAA -s mr.mrrefChr3 165342 38 + 181027 TGGCTGGGTAAACCAGGAGTTGAAGGTCTCTAACAAAA -s simRat_chr6.simRat.chr6 630212 38 + 647215 TGGCTGGGTAAATCCGGAGTTGGTGGTCTCTAACAAGG - -a -s simMouse_chr6.simMouse.chr6 618099 19 + 636262 CCATAATCTGAGTACCAAC -s mr.mrrefChr3 165380 17 + 181027 CCATA--CTGAGTACCAAC -s simRat_chr6.simRat.chr6 630253 17 + 647215 CCCTA--CAAAGAACCATC - -a -s simMouse_chr6.simMouse.chr6 618118 59 + 636262 AAAAAAGTATAGGTAATCATAGGTCAGTCAAAACCAGTTTTGTGGCGCAATGGCGCTCA -s mr.mrrefChr3 165397 55 + 181027 AAAAAAGT---GGTAATCATAGGTCAGTCAAAACCAGTTTTGTG-CGCAATGGCGCTCA -s simRat_chr6.simRat.chr6 630274 55 + 647215 AAAAAACT---GGTTCTGACTGACCAATGGTTGCCTATACTTTG-CTCGTTGGTGCTCA - -a -s simMouse_chr6.simMouse.chr6 618177 37 + 636262 TTGTAGAGGGCCCTTGCAGATAGTTGTGTTGGGTCTT -s mr.mrrefChr3 165452 37 + 181027 TTGTAGAGGGCCCTTGCAGATAGTTGTGTTGGGTCTT -s simRat_chr6.simRat.chr6 630331 37 + 647215 TTATGGTTATGCTTTGCAGATAGTTGTGTTAGAGCTT - -a -s simMouse_chr6.simMouse.chr6 618214 149 + 636262 ATGTGATTAATGATATCAGTTGACTTTCAGGCTTTTAGCACCCGACTTTCAGGATTTTAGCACCCTCCAAAAAGGTCAGAGATAAGCCAGGAAGTACTCAGATAACTGATTGGTGCGGGGTGCGCTGCTAGAAGATTGCAACCATTAGG -s mr.mrrefChr3 165489 125 + 181027 ATGTGATTAATGATATCAGTT-----------------------ACTTTCAGGATTTTAGCACCCTCCAAAAAGGTCAGAGATAAGCCAGGAAGTACTCAGATAACTGATTGGTGCGGGGTGCGCTGCTAGAAGATTGCAAC-ATTAGG -s simRat_chr6.simRat.chr6 630372 125 + 647215 ATGTGATTAATGATATCAGTT-----------------------ACTTTCAGGATTTCAGCACCCTCCAAAAAGGTCTCAAATAAGCCAGGCAGTACTCCGATCACTGATTGGTGTGGGGTGTACTGCTAGGAGATTGCAAC-ATTAGG - -a -s simMouse_chr6.simMouse.chr6 618378 4 + 636262 ACTT -s Anc0.Anc0refChr3 213129 4 + 222631 ACTT -s Anc1.Anc1refChr1 53384 4 + 69767 ACTT -s Anc2.Anc2refChr1 130555 4 + 142988 ATTT -s mr.mrrefChr3 165629 4 + 181027 ACTT -s mr.mrrefChr3 164462 4 + 181027 ACAT -s simCow_chr6.simCow.chr6 589177 4 + 602619 GTTC -s simDog_chr6.simDog.chr6 581135 4 + 593897 ATTT -s simHuman_chr6.simHuman.chr6 584931 4 + 601863 ACAT -s simRat_chr6.simRat.chr6 629059 4 + 647215 ACAT -s simRat_chr6.simRat.chr6 630512 4 + 647215 ACTT - -a -s simMouse_chr6.simMouse.chr6 618382 3 + 636262 ACA -s Anc0.Anc0refChr3 213134 2 + 222631 -CA -s Anc1.Anc1refChr1 53390 3 + 69767 ACA -s Anc2.Anc2refChr1 130560 2 + 142988 -CC -s mr.mrrefChr3 165633 3 + 181027 ACA -s mr.mrrefChr3 164468 3 + 181027 ACA -s simCow_chr6.simCow.chr6 589182 2 + 602619 -CC -s simDog_chr6.simDog.chr6 581140 2 + 593897 -CC -s simHuman_chr6.simHuman.chr6 584937 3 + 601863 GCA -s simRat_chr6.simRat.chr6 629065 3 + 647215 ACA -s simRat_chr6.simRat.chr6 630516 3 + 647215 ACA - -a -s simMouse_chr6.simMouse.chr6 618396 1 + 636262 G - -a -s simMouse_chr6.simMouse.chr6 618489 3 + 636262 AAA -s mr.mrrefChr3 165739 3 + 181027 AAA -s simRat_chr6.simRat.chr6 630640 3 + 647215 AAA - -a -s simMouse_chr6.simMouse.chr6 618492 36 + 636262 CATTTTCACGACCGGGGGTCATACAACGTTCAAAAG -s mr.mrrefChr3 165742 36 + 181027 CATTTTCACGACCGGGGGTCATACAACGTTCAAAAG -s simRat_chr6.simRat.chr6 630644 36 + 647215 CAGTTACACAATCAGGGGACATGCAACGTTCGAAAG - -a -s simMouse_chr6.simMouse.chr6 618594 4 + 636262 ATTT -s mr.mrrefChr3 165844 4 + 181027 ATTT -s simRat_chr6.simRat.chr6 630747 4 + 647215 ATTA - -a -s simMouse_chr6.simMouse.chr6 618648 116 + 636262 TGAACTCTTGAAAGCTATGCTTGCACGAAAACTTGACTCTTGGTAGATCAGTTGTTGAGAAGTGAAGTATCACATTTTGGTTAAAGTGAAGTATCGCATTTTGGTTACCTGATGTA - -a -s simMouse_chr6.simMouse.chr6 618792 3 + 636262 TAA - -a -s simMouse_chr6.simMouse.chr6 618797 15 + 636262 AACAATACAGGAACT -s Anc0.Anc0refChr3 213467 14 + 222631 AGCA-TATAGAGGCT -s Anc1.Anc1refChr1 53746 15 + 69767 AGCAATATAGAGGCT -s Anc2.Anc2refChr1 130901 14 + 142988 AGCC-TATAGAGGCC -s mr.mrrefChr3 165928 15 + 181027 AACAATACAGGAACT -s simDog_chr6.simDog.chr6 581463 14 + 593897 AGCC-TATAGAGGCC -s simHuman_chr6.simHuman.chr6 585295 15 + 601863 TGCAACATGGAGGCT -s simRat_chr6.simRat.chr6 630832 15 + 647215 AACAATACAGGAAAT - -a -s simMouse_chr6.simMouse.chr6 618824 5 + 636262 TACTC -s Anc0.Anc0refChr3 213493 5 + 222631 TACTC -s Anc1.Anc1refChr1 53773 5 + 69767 TACTC -s Anc2.Anc2refChr1 130927 5 + 142988 TACTC -s mr.mrrefChr3 165955 5 + 181027 TACTC -s simDog_chr6.simDog.chr6 581489 5 + 593897 TACTC -s simHuman_chr6.simHuman.chr6 585322 5 + 601863 GAGTC -s simRat_chr6.simRat.chr6 630859 5 + 647215 TACTC - -a -s simMouse_chr6.simMouse.chr6 618978 4 + 636262 AGGA -s mr.mrrefChr3 166109 4 + 181027 AGGA -s simRat_chr6.simRat.chr6 631013 4 + 647215 AGGA - -a -s simMouse_chr6.simMouse.chr6 618982 2 + 636262 AA -s mr.mrrefChr3 166114 2 + 181027 AA -s simRat_chr6.simRat.chr6 631019 2 + 647215 AC - -a -s simMouse_chr6.simMouse.chr6 619066 19 + 636262 TAGGTCTGATAGCTTGTTG - -a -s simMouse_chr6.simMouse.chr6 619090 7 + 636262 TTGTTGA -s Anc0.Anc0refChr3 213894 6 + 222631 -AGTTTC -s Anc1.Anc1refChr1 54180 6 + 69767 -AGTTTC -s Anc2.Anc2refChr1 131354 6 + 142988 -AGTTTC -s mr.mrrefChr3 166203 7 + 181027 CAGTTTA -s simCow_chr6.simCow.chr6 589891 6 + 602619 -AGTATC -s simDog_chr6.simDog.chr6 581934 6 + 593897 -AGTTTC -s simHuman_chr6.simHuman.chr6 585727 6 + 601863 -AGGTTC -s simRat_chr6.simRat.chr6 631108 7 + 647215 CAGTTTA - -a -s simMouse_chr6.simMouse.chr6 619097 3 + 636262 GTA -s Anc0.Anc0refChr3 214005 3 + 222631 GTA -s Anc1.Anc1refChr1 54291 3 + 69767 GTA -s Anc2.Anc2refChr1 131479 3 + 142988 CTA -s mr.mrrefChr3 166210 3 + 181027 GTA -s simCow_chr6.simCow.chr6 589993 3 + 602619 TTA -s simDog_chr6.simDog.chr6 582057 3 + 593897 CTA -s simHuman_chr6.simHuman.chr6 585839 3 + 601863 GTA -s simRat_chr6.simRat.chr6 631115 3 + 647215 GTA - -a -s simMouse_chr6.simMouse.chr6 619100 4 + 636262 ATAT -s Anc0.Anc0refChr3 214008 4 + 222631 GTAT -s Anc1.Anc1refChr1 54294 4 + 69767 GTAT -s Anc2.Anc2refChr1 131482 4 + 142988 GTAT -s mr.mrrefChr3 166213 4 + 181027 ATAT -s simCow_chr6.simCow.chr6 590009 4 + 602619 GTAT -s simDog_chr6.simDog.chr6 582060 4 + 593897 GTAT -s simHuman_chr6.simHuman.chr6 585842 4 + 601863 GTAT -s simRat_chr6.simRat.chr6 631118 4 + 647215 ATAT - -a -s simMouse_chr6.simMouse.chr6 619104 2 + 636262 TG -s Anc0.Anc0refChr3 214014 2 + 222631 TG -s Anc1.Anc1refChr1 54300 2 + 69767 TG -s Anc2.Anc2refChr1 131488 2 + 142988 TG -s mr.mrrefChr3 166217 2 + 181027 TG -s simCow_chr6.simCow.chr6 590015 2 + 602619 TG -s simDog_chr6.simDog.chr6 582066 2 + 593897 CG -s simHuman_chr6.simHuman.chr6 585848 2 + 601863 TG -s simRat_chr6.simRat.chr6 631122 2 + 647215 GG - -a -s simMouse_chr6.simMouse.chr6 619106 29 + 636262 TTTGGATTTCACACAGTGCTCTTGTACAA -s Anc0.Anc0refChr3 214017 23 + 222631 CTTGCTTTTGAAGCAGTAATCT------A -s Anc1.Anc1refChr1 54303 23 + 69767 CTTGCTTTTGAAGCAGTAATCT------A -s Anc2.Anc2refChr1 131491 23 + 142988 CTTGCTTTTGAAGCAGTAATCT------A -s mr.mrrefChr3 166220 29 + 181027 TTTGGATTTCACACAGTGCTCTCATACAA -s simCow_chr6.simCow.chr6 590018 23 + 602619 TTTGTTTTTGTGGCAGTAATCT------A -s simDog_chr6.simDog.chr6 582069 23 + 593897 CTTGCTTTGGAAGCGGTAATCT------A -s simHuman_chr6.simHuman.chr6 585851 23 + 601863 CTTGCTTTTGAAGCAGTAATCT------A -s simRat_chr6.simRat.chr6 631125 29 + 647215 TTTAGCTGTCACATAGTGCTCTCATGCAA - -a -s simMouse_chr6.simMouse.chr6 619135 13 + 636262 AGCTTGAATAAAA -s Anc0.Anc0refChr3 214040 13 + 222631 AGCATGAGAGCAG -s Anc1.Anc1refChr1 54326 13 + 69767 AGCATGAGAGCAG -s Anc2.Anc2refChr1 131516 13 + 142988 AGGATGAGAGCAG -s mr.mrrefChr3 166249 13 + 181027 AGCTTGAATGAAA -s simCow_chr6.simCow.chr6 590044 13 + 602619 AGGATGAGAGCAG -s simDog_chr6.simDog.chr6 582094 13 + 593897 AGGGTGAAAGCAG -s simHuman_chr6.simHuman.chr6 585874 13 + 601863 AGCATGAGAGCAG -s simRat_chr6.simRat.chr6 631154 13 + 647215 AGCTCCAATGAAA - -a -s simMouse_chr6.simMouse.chr6 619148 18 + 636262 GGCAAAGTGTGGCCATGT -s Anc0.Anc0refChr3 214054 17 + 222631 GACAATGTATT-TATTGC -s Anc1.Anc1refChr1 54340 18 + 69767 GACAATGTATTATATTGC -s Anc2.Anc2refChr1 131530 17 + 142988 GACAATGTATT-TATTGC -s mr.mrrefChr3 166262 18 + 181027 GGCAAAGTGTGGTCATGC -s simCow_chr6.simCow.chr6 590058 16 + 602619 GACAATAGGTT-TCTT-C -s simDog_chr6.simDog.chr6 582108 17 + 593897 GATAATGTATT-TATTGC -s simHuman_chr6.simHuman.chr6 585888 18 + 601863 GACAATGTATTATGTTGC -s simRat_chr6.simRat.chr6 631167 17 + 647215 GGCAA-GTGTGGTCATGC - -a -s simMouse_chr6.simMouse.chr6 619166 4 + 636262 ACCC -s Anc0.Anc0refChr3 214073 4 + 222631 AATG -s Anc1.Anc1refChr1 54360 4 + 69767 AATG -s Anc2.Anc2refChr1 131549 4 + 142988 AATG -s mr.mrrefChr3 166280 4 + 181027 ACCC -s simCow_chr6.simCow.chr6 590076 4 + 602619 AATG -s simDog_chr6.simDog.chr6 582127 4 + 593897 AATG -s simHuman_chr6.simHuman.chr6 585908 4 + 601863 AATT -s simRat_chr6.simRat.chr6 631184 4 + 647215 ACCC - -a -s simMouse_chr6.simMouse.chr6 619170 39 + 636262 TTGCCTAAAATTAAAACATGCGCTATTATCATAATCAGC -s Anc0.Anc0refChr3 214098 36 + 222631 -TATGTGTCATTATAATACTGG--CCTACTATAATCAAA -s Anc1.Anc1refChr1 54385 36 + 69767 -TATGTGTCATTATAATACTGG--CCTACTATAATCAAA -s Anc2.Anc2refChr1 131574 36 + 142988 -CATGTATCATTTTAATGCTGG--CCTACTATAAGCAAA -s mr.mrrefChr3 166305 39 + 181027 TTGCCTGAAATTATAACATGCGCTACTATCATAATCAGC -s simCow_chr6.simCow.chr6 590101 22 + 602619 -CAT------TTTTAATGCTCA--CCT--------CAAA -s simDog_chr6.simDog.chr6 582152 36 + 593897 -CATGTATCATTTCAGTGCCGG--CCTACTATAAGTAAA -s simHuman_chr6.simHuman.chr6 585933 36 + 601863 -TATGTGTTGTTATAATACTTG--TCTACTATAATCAAA -s simRat_chr6.simRat.chr6 631213 39 + 647215 TTGCATGCACTTATTGCATGCACTACTATCCTAATCAGC - -a -s simMouse_chr6.simMouse.chr6 619209 46 + 636262 CAGGTAGCAAAATAAAAACTCATATTTTATAAAAGCACACCTCTTC -s Anc0.Anc0refChr3 214138 46 + 222631 CAGGTAGTGAAATAAAAACCCATGTTTTATTAGAGTGCACCACTTT -s Anc1.Anc1refChr1 54425 46 + 69767 CAGGTAGTGAAATAAAAACCCATGTTTTATTAGAGTGCACCACTTT -s Anc2.Anc2refChr1 131614 46 + 142988 CGTGTAGTGAAATAAAAACCCATGTTTTATTAGAGTGGACCACTTT -s mr.mrrefChr3 166348 46 + 181027 CAGGTAGTGAAATAAAAACTCATATTTTATAAAAGCACACCTCTTC -s simCow_chr6.simCow.chr6 590123 43 + 602619 ---GTGGTGAAGTAAAAGCCTATGCTTTATAAAATTGGACCACTTC -s simDog_chr6.simDog.chr6 582192 45 + 593897 CGTGTAGTGAAATAAAAACCCAAGTTTTATTCGAGTG-ACCACTTT -s simHuman_chr6.simHuman.chr6 585973 46 + 601863 CAGGTAGTGAAATAAACATCCATGGTTAAATATAATGCACCACCTT -s simRat_chr6.simRat.chr6 631256 43 + 647215 CAGGTAGTGAAATAAAAACTCATATTTTATAAAAGCCCACCT---A - -a -s simMouse_chr6.simMouse.chr6 619255 26 + 636262 AATTTATCTCCAGTAATTTTATCCCA -s Anc0.Anc0refChr3 214185 25 + 222631 ATTTCTCTTCCAGTAATTTTGGCCC- -s Anc1.Anc1refChr1 54472 25 + 69767 ATTTCTCTTCCAGTAATTTTGGCCC- -s Anc2.Anc2refChr1 131661 25 + 142988 ATTTCTCTCCCAGTAATTTTGGCCC- -s mr.mrrefChr3 166395 26 + 181027 AATTTATCTCCAGTAATTTTAGCCCA -s simCow_chr6.simCow.chr6 590167 17 + 602619 ATTTCT--------AATATTGGCCC- -s simDog_chr6.simDog.chr6 582238 25 + 593897 ATTTCACTCCCAGTTATTTTGGCCT- -s simHuman_chr6.simHuman.chr6 586020 25 + 601863 ATTCCTCTTCCAGTAATCTTGGCCC- -s simRat_chr6.simRat.chr6 631300 26 + 647215 AACTTGTCTCCAGTAATTTTAGTCCA - -a -s simMouse_chr6.simMouse.chr6 619281 33 + 636262 CAATCCCCCGAATCCCCCGACATCACAGGTGCA -s Anc0.Anc0refChr3 214210 24 + 222631 TAATCCCCCA---------ACATCACAAGTGAA -s Anc1.Anc1refChr1 54497 24 + 69767 TAATCCCCCA---------ACATCACAAGTGAA -s Anc2.Anc2refChr1 131686 24 + 142988 TAATCCCCCA---------ACATCATGAGTGAA -s mr.mrrefChr3 166421 24 + 181027 CAATCCCCCG---------ACATCACAGGTGAA -s simCow_chr6.simCow.chr6 590184 24 + 602619 CGATCCCCCA---------GCATCATGAGTGAA -s simDog_chr6.simDog.chr6 582264 24 + 593897 TAATTCCCCA---------ATGTCTTGAGTTAA -s simHuman_chr6.simHuman.chr6 586045 24 + 601863 TAATCCCCCT---------ACATCACAAGTGAA -s simRat_chr6.simRat.chr6 631326 24 + 647215 CAATCCCCCC---------ACATAACAGGTGAA - -a -s simMouse_chr6.simMouse.chr6 619314 21 + 636262 CTAATAACTGCAAGGGTAGTC -s Anc0.Anc0refChr3 214234 21 + 222631 ATGATAATTGCAAGGGTAATC -s Anc1.Anc1refChr1 54521 21 + 69767 ATGATAATTGCAAGGGTAATC -s Anc2.Anc2refChr1 131738 21 + 142988 ATGATAACTGCAAGGTTAATC -s mr.mrrefChr3 166445 21 + 181027 CTAATAATTGCAAGGGTAGTC -s simCow_chr6.simCow.chr6 590256 21 + 602619 GGGACAACTGTAAGACTAATC -s simDog_chr6.simDog.chr6 582310 21 + 593897 ATGATAACTGCAGGGTTAGTC -s simHuman_chr6.simHuman.chr6 586069 21 + 601863 ATGATAATTACAAGGGTAATC -s simRat_chr6.simRat.chr6 631350 21 + 647215 TTAATAATTGCAAGGGGAGTA - -a -s simMouse_chr6.simMouse.chr6 619335 1 + 636262 T -s Anc0.Anc0refChr3 214255 1 + 222631 T -s Anc1.Anc1refChr1 54542 1 + 69767 T -s Anc2.Anc2refChr1 131760 1 + 142988 C -s mr.mrrefChr3 166466 1 + 181027 T -s simCow_chr6.simCow.chr6 590278 1 + 602619 C -s simDog_chr6.simDog.chr6 582332 1 + 593897 C -s simHuman_chr6.simHuman.chr6 586090 1 + 601863 T -s simRat_chr6.simRat.chr6 631371 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 619336 10 + 636262 ACAGTGTTTC -s Anc0.Anc0refChr3 214256 10 + 222631 ACAGTGTATT -s Anc1.Anc1refChr1 54543 10 + 69767 ACAGTGTATT -s Anc2.Anc2refChr1 131761 10 + 142988 ACAGTGTATT -s mr.mrrefChr3 166467 10 + 181027 ACAGTGTTTC -s simCow_chr6.simCow.chr6 590280 10 + 602619 GCAGTGTATT -s simDog_chr6.simDog.chr6 582333 10 + 593897 ACAGTGTATT -s simHuman_chr6.simHuman.chr6 586091 10 + 601863 ACAGCGTATT -s simRat_chr6.simRat.chr6 631372 10 + 647215 ACAGTGTTTC - -a -s simMouse_chr6.simMouse.chr6 619346 7 + 636262 TAGGGTT -s Anc0.Anc0refChr3 214266 7 + 222631 TAGAGTT -s Anc1.Anc1refChr1 54553 7 + 69767 TAGAGTT -s Anc2.Anc2refChr1 131773 7 + 142988 TAGAGTT -s mr.mrrefChr3 166477 7 + 181027 TAGGGTT -s simCow_chr6.simCow.chr6 590292 7 + 602619 TATAGTT -s simDog_chr6.simDog.chr6 582345 7 + 593897 TAGAGTT -s simHuman_chr6.simHuman.chr6 586101 7 + 601863 TAGAGTT -s simRat_chr6.simRat.chr6 631382 7 + 647215 AAGGGTA - -a -s simMouse_chr6.simMouse.chr6 619353 11 + 636262 AAAACCATATG -s Anc0.Anc0refChr3 214288 11 + 222631 GAATTTGCACC -s Anc1.Anc1refChr1 54575 11 + 69767 GAATTTGCACC -s Anc2.Anc2refChr1 131795 11 + 142988 GATTTTGCACC -s mr.mrrefChr3 166484 11 + 181027 AAAACCACATG -s simCow_chr6.simCow.chr6 590310 6 + 602619 GATTTT----- -s simDog_chr6.simDog.chr6 582368 11 + 593897 GATTTTGCACC -s simHuman_chr6.simHuman.chr6 586123 11 + 601863 GAATTTGCACC -s simRat_chr6.simRat.chr6 631389 11 + 647215 AAAACAACATG - -a -s simMouse_chr6.simMouse.chr6 619364 38 + 636262 AGAGTTGTCCCTATGGAAGGCTCAAATAGAGTCTTAAA -s Anc0.Anc0refChr3 214299 38 + 222631 AGAGTTGGCCTGATAGAAGGATCAAGTAGAGTTTTGAA -s Anc1.Anc1refChr1 54586 38 + 69767 AGAGTTGGCCTGATAGAAGGATCAAGTAGAGTTTTGAA -s Anc2.Anc2refChr1 131830 38 + 142988 GGAGTTGGCCTGACAGGAGGATCAAGTAGAGATTGAAA -s mr.mrrefChr3 166495 38 + 181027 AGAGTTGTCCCTATGGAAGGCTCAAATAGAGTCTTGAA -s simCow_chr6.simCow.chr6 590340 38 + 602619 GGAGTTGACCACACATGAGAGTCAAGTAGAAATTGAAA -s simDog_chr6.simDog.chr6 582414 38 + 593897 GGAGTTGGCCTGACAGGAGGATCAAGTAGAGATTGAAA -s simHuman_chr6.simHuman.chr6 586134 36 + 601863 AGATTCGGAC--ATAGAAGGAGCAAGTAAAGTATTGAA -s simRat_chr6.simRat.chr6 631400 38 + 647215 AGAGTTATCCTGATGGAAGGTTCAAATAGAGCCTTGAA - -a -s simMouse_chr6.simMouse.chr6 619402 42 + 636262 AGAACCCTTAGGCCATTTACTCTTGTTGATATTGAGAAATTG -s Anc0.Anc0refChr3 214337 42 + 222631 GTAACCCTTGGGCCATCTACTCTTGTAGGTAGTAAGAAATTC -s Anc1.Anc1refChr1 54624 42 + 69767 GTAACCCTTGGGCCATCTACTCTTGTAGGTAGTAAGAAATTC -s Anc2.Anc2refChr1 131878 42 + 142988 GTAATCCATGGACCATCTACTCTTGTAGGTAGTAAGAAATTC -s mr.mrrefChr3 166533 42 + 181027 GGAACCCTTAGGCCATTTACTCTTGTTGATATTAAGAAATTG -s simCow_chr6.simCow.chr6 590388 42 + 602619 GCAATCTATGGATCATCTATTCTTGAAGGTAGTAAGAAATTG -s simDog_chr6.simDog.chr6 582462 42 + 593897 GTAATCCATGGACCCTATACTCTTGTGGGTACAAACAAATTC -s simHuman_chr6.simHuman.chr6 586170 42 + 601863 GTCACCCTGGGGCTATCTACTATTGCATGTAGTAAGAAATTT -s simRat_chr6.simRat.chr6 631438 42 + 647215 GGAACCCCTAGGCCATTTACTCTTATTGATACTAAGAAATTG - -a -s simMouse_chr6.simMouse.chr6 619444 31 + 636262 GTAGAGAAAGTAAGAAAAATGACGGTCAAAC -s Anc0.Anc0refChr3 214379 31 + 222631 GTACAGCAAGAAAGAAAAATAACAATCAAAC -s Anc1.Anc1refChr1 54666 31 + 69767 GTACAGCAAGAAAGAAAAATAACAATCAAAC -s Anc2.Anc2refChr1 131920 31 + 142988 GTACAGCAGGAAAGAAAAATAACAATCAAAC -s mr.mrrefChr3 166575 31 + 181027 GTAGAGAAAGTAAGAAAAATGACAATCAAAC -s simCow_chr6.simCow.chr6 590430 28 + 602619 GTACAAGAGGATAGAAGAATAAA---CAAAC -s simDog_chr6.simDog.chr6 582510 31 + 593897 GTACAGCAGGGAAAAAAGATAACAATCAGAC -s simHuman_chr6.simHuman.chr6 586212 31 + 601863 ACACAGCAAGAAAGAAAATTAACAATCAAAT -s simRat_chr6.simRat.chr6 631480 31 + 647215 GTAGGGAAACTAAGAAAAATGACAATCAAAC - -a -s simMouse_chr6.simMouse.chr6 619475 25 + 636262 ACTTAGAACATACATTGTGCCATAA -s Anc0.Anc0refChr3 214411 25 + 222631 ATTTTAAACATATATTTGGCAGCGA -s Anc1.Anc1refChr1 54698 25 + 69767 ATTTTAAACATATATTTGGCAGCGA -s Anc2.Anc2refChr1 131952 25 + 142988 CTTTTAAAGATATATTTGGTAGTGA -s mr.mrrefChr3 166606 25 + 181027 ACTTAGAACATACATTGTGCCACAA -s simCow_chr6.simCow.chr6 590459 25 + 602619 CTGTCAAGGATCCATTTGGTAGAGT -s simDog_chr6.simDog.chr6 582541 25 + 593897 CTTTTAAAGACATATTCGCTAATGA -s simHuman_chr6.simHuman.chr6 586244 25 + 601863 ATTTTAAACATATGCTTGGCAGCGA -s simRat_chr6.simRat.chr6 631511 25 + 647215 ACTTAGAACGTGCATTGTGCCACAA - -a -s simMouse_chr6.simMouse.chr6 619500 23 + 636262 GCAAACTTGCAGGCCTTTAGTTC -s Anc0.Anc0refChr3 214436 23 + 222631 GCGGCTTCACAGGCCTTTAGTTC -s Anc1.Anc1refChr1 54723 23 + 69767 GCGGCTTCACAGGCCTTTAGTTC -s Anc2.Anc2refChr1 131977 23 + 142988 GCGCCTTCACAGGCCTTTAGTTC -s mr.mrrefChr3 166631 23 + 181027 GCAGACTTGCAGGCCTTTAGTTC -s simCow_chr6.simCow.chr6 590484 23 + 602619 GCACCCCCACAGGCCTTTAGTGC -s simDog_chr6.simDog.chr6 582566 23 + 593897 GCGCATTCACAGGCCTTTAGTTC -s simHuman_chr6.simHuman.chr6 586269 23 + 601863 GATGCTTCACAGGCTTTTAGTTC -s simRat_chr6.simRat.chr6 631544 23 + 647215 GCAGACTTGCAGGCGTTTAGTTC - -a -s simMouse_chr6.simMouse.chr6 619523 43 + 636262 TGTGCCCGGATTGTTCAGCACCTTCTTACTAGTCTTCCACCAT -s Anc0.Anc0refChr3 214459 43 + 222631 TGTTTTCTGATTGTTTGGTTCTTCCTCATTAGCCTCTTTCTAT -s Anc1.Anc1refChr1 54746 43 + 69767 TGTTTTCTGATTGTTTGGTTCTTCCTCATTAGCCTCTTTCTAT -s Anc2.Anc2refChr1 132000 43 + 142988 TGCTTTCTGATTGTTTGGTTCTTCCTCATTAGCCTTTTTCTAT -s mr.mrrefChr3 166654 43 + 181027 TGTTCCCGGATTGTTTGGCACCTTCTTACTAGCCTCTCACCAT -s simCow_chr6.simCow.chr6 590519 43 + 602619 TGCTCTCTGATTGCTTAATTCTCCCTCATTAGCTCTTTACTAT -s simDog_chr6.simDog.chr6 582589 43 + 593897 TGCCTTCTGATTGTTTGGTTCTTCTTCATTAGCCTTTTTCCAT -s simHuman_chr6.simHuman.chr6 586292 43 + 601863 TGTTGTCTGATTGTTTGGTTCTTGCTCATGAGCCTCTTTCTAT -s simRat_chr6.simRat.chr6 631567 43 + 647215 TGTTCCCAGATTGTTTGGCACCTCCTTACTAGCACCTCACCAT - -a -s simMouse_chr6.simMouse.chr6 619566 6 + 636262 CTGCCA -s Anc0.Anc0refChr3 214526 6 + 222631 CTGTCA -s Anc1.Anc1refChr1 54813 6 + 69767 CTGTCA -s Anc2.Anc2refChr1 132067 6 + 142988 CTGTCA -s mr.mrrefChr3 166697 6 + 181027 CTGTCA -s simCow_chr6.simCow.chr6 590586 6 + 602619 CTGTCA -s simDog_chr6.simDog.chr6 582657 6 + 593897 TTGTTA -s simHuman_chr6.simHuman.chr6 586359 6 + 601863 CTGTCA -s simRat_chr6.simRat.chr6 631610 6 + 647215 CTGTCA - -a -s simMouse_chr6.simMouse.chr6 619572 9 + 636262 TGTCTGGGC -s Anc0.Anc0refChr3 214532 9 + 222631 TGTCTAGGC -s Anc1.Anc1refChr1 54819 9 + 69767 TGTCTAGGC -s Anc2.Anc2refChr1 132073 9 + 142988 TGTTTAGGC -s mr.mrrefChr3 166703 9 + 181027 TGTCTGGGC -s simCow_chr6.simCow.chr6 590593 9 + 602619 CATTTAAGC -s simDog_chr6.simDog.chr6 582663 9 + 593897 TGTTTAGGT -s simHuman_chr6.simHuman.chr6 586365 9 + 601863 TGTCTAGGC -s simRat_chr6.simRat.chr6 631616 9 + 647215 TGTCTGGGC - -a -s simMouse_chr6.simMouse.chr6 619581 9 + 636262 ATAATATCA -s Anc0.Anc0refChr3 214541 6 + 222631 AGAA---TA -s Anc1.Anc1refChr1 54828 6 + 69767 AGAA---TA -s Anc2.Anc2refChr1 132082 6 + 142988 AGAA---TA -s mr.mrrefChr3 166712 9 + 181027 ATAATATCA -s simCow_chr6.simCow.chr6 590602 6 + 602619 AGAA---TA -s simDog_chr6.simDog.chr6 582713 6 + 593897 ATAA---TG -s simHuman_chr6.simHuman.chr6 586374 6 + 601863 AGAA---AA -s simRat_chr6.simRat.chr6 631625 9 + 647215 ATAATAGCA - -a -s simMouse_chr6.simMouse.chr6 619590 20 + 636262 GGCCGCATATCTGTCTTTGT -s Anc0.Anc0refChr3 214547 20 + 222631 GGTCACACATCTGACCTTAT -s Anc1.Anc1refChr1 54834 20 + 69767 GGTCACACATCTGACCTTAT -s Anc2.Anc2refChr1 132088 20 + 142988 GGTCACACATCTGACCTTAT -s mr.mrrefChr3 166721 20 + 181027 GGCCACATATCTGTCCTTGT -s simCow_chr6.simCow.chr6 590611 20 + 602619 GGTCACACATCTGGCCTCAT -s simDog_chr6.simDog.chr6 582719 20 + 593897 GGTCACACCTTTGACCTTAA -s simHuman_chr6.simHuman.chr6 586380 20 + 601863 AGTCAGACATCTGACCTTAT -s simRat_chr6.simRat.chr6 631634 20 + 647215 GGCCACATATCTGTTCTTGT - -a -s simMouse_chr6.simMouse.chr6 619610 28 + 636262 AAAGATGTTAGGCTACAAGAGTAATACC -s Anc0.Anc0refChr3 214569 28 + 222631 AGAGATATTAGGCTAGGACAGCAATACC -s Anc1.Anc1refChr1 54856 28 + 69767 AGAGATATTAGGCTAGGACAGCAATACC -s Anc2.Anc2refChr1 132110 28 + 142988 AGACATATTAGGCTAGGACAGCAATACC -s mr.mrrefChr3 166741 28 + 181027 AAAGATGTTAGGCTACAAGAGCAATACC -s simCow_chr6.simCow.chr6 590633 27 + 602619 AGACATAT-AGGGTTGCATAGCAATCCC -s simDog_chr6.simDog.chr6 582741 26 + 593897 AGACA--TTAGGCTAGGACAGCAATACT -s simHuman_chr6.simHuman.chr6 586402 28 + 601863 AGAGACATTAGGCTAAGACCGCATTATA -s simRat_chr6.simRat.chr6 631654 28 + 647215 AAAGATGTTAGACTACAAGAGCAATACC - -a -s simMouse_chr6.simMouse.chr6 619638 18 + 636262 CTGTCACATCTCATTCAT -s Anc0.Anc0refChr3 214597 18 + 222631 ATCTAACATCTCATTCAT -s Anc1.Anc1refChr1 54884 18 + 69767 ATCTAACATCTCATTCAT -s Anc2.Anc2refChr1 132138 18 + 142988 ATCTAACATCTAATTCAT -s mr.mrrefChr3 166769 18 + 181027 CTGTCACATCTCATTCAT -s simCow_chr6.simCow.chr6 590660 18 + 602619 ACCAAATATCTAATTCAA -s simDog_chr6.simDog.chr6 582767 18 + 593897 ATCTAACAACTAATACAT -s simHuman_chr6.simHuman.chr6 586435 18 + 601863 ATCTTAGATCTCATTCAT -s simRat_chr6.simRat.chr6 631682 18 + 647215 CCTTCACATCTCATTCAT - -a -s simMouse_chr6.simMouse.chr6 619656 86 + 636262 CCATCAACCTGCATTTAGGAAATCTGAGCAATCCTGCTGCATTGTATGGGTAAATTCATACTTCGTTGGTAAGGCACTGATTGAAC -s Anc0.Anc0refChr3 214615 46 + 222631 TCTTCAACCTGCATTTATGAGATCAGAGCCATGA----------------------------------------CACTGACGATAC -s Anc1.Anc1refChr1 54902 46 + 69767 TCTTCAACCTGCATTTATGAGATCAGAGCCATGA----------------------------------------CACTGACGATAC -s Anc2.Anc2refChr1 132156 46 + 142988 TCTTCAACCTGTATTTATGATATCAGAGCCTTGA----------------------------------------CACTGATGATAC -s mr.mrrefChr3 166787 46 + 181027 CCTTCAACCTGCATTTAGGAGATCTGAGCAATGC----------------------------------------CACTGACTGAAC -s simCow_chr6.simCow.chr6 590678 45 + 602619 -CTTCCACCTGTAATTAGGATATGAGAGTAGTAA----------------------------------------CACTGCTTGTGC -s simDog_chr6.simDog.chr6 582788 46 + 593897 TCTCCAACCTGTATCTATCATATCAGAGCCTAGA----------------------------------------TACTGATGATAC -s simHuman_chr6.simHuman.chr6 586453 46 + 601863 TATTCAACCTGCATTTATGAGATCAGAGCGATGA----------------------------------------CACTGACCACAC -s simRat_chr6.simRat.chr6 631700 46 + 647215 CCTTCAACCTGCATTTAGTAGATCTGAACTATGC----------------------------------------CACTGACTGAGT - -a -s simMouse_chr6.simMouse.chr6 619742 7 + 636262 AAACCAT -s Anc0.Anc0refChr3 214662 7 + 222631 AAATGAA -s Anc1.Anc1refChr1 54949 7 + 69767 AAATGAA -s Anc2.Anc2refChr1 132203 7 + 142988 AAATGCA -s mr.mrrefChr3 166833 7 + 181027 AAACCAT -s simCow_chr6.simCow.chr6 590724 7 + 602619 AAATGCA -s simDog_chr6.simDog.chr6 582835 7 + 593897 AAATGCA -s simHuman_chr6.simHuman.chr6 586500 7 + 601863 AAATAAA -s simRat_chr6.simRat.chr6 631746 7 + 647215 AAACCAT - -a -s simMouse_chr6.simMouse.chr6 619749 5 + 636262 TAGCT -s Anc0.Anc0refChr3 214669 5 + 222631 TAGCT -s Anc1.Anc1refChr1 54956 5 + 69767 TAGCT -s Anc2.Anc2refChr1 132210 5 + 142988 TAGCT -s mr.mrrefChr3 166840 5 + 181027 TAGCT -s simCow_chr6.simCow.chr6 590742 5 + 602619 TAGCT -s simDog_chr6.simDog.chr6 582842 5 + 593897 AAGGT -s simHuman_chr6.simHuman.chr6 586507 5 + 601863 TAGCT -s simRat_chr6.simRat.chr6 631753 5 + 647215 TGTCT - -a -s simMouse_chr6.simMouse.chr6 619754 22 + 636262 TACTAGGGGAAAGACAGGCAAG -s Anc0.Anc0refChr3 214674 22 + 222631 TAGTAGAGGATGGGCATGCAAG -s Anc1.Anc1refChr1 54961 22 + 69767 TAGTAGAGGATGGGCATGCAAG -s Anc2.Anc2refChr1 132215 22 + 142988 TAGTAGAGGATGGGCATGCAAG -s mr.mrrefChr3 166845 22 + 181027 TACTAGAGGATAGGCAGGCAAG -s simCow_chr6.simCow.chr6 590747 22 + 602619 TAGTAGAGAGTGGGCATGCAAG -s simDog_chr6.simDog.chr6 582857 22 + 593897 CAGTATAGGATGGGTGTGCACT -s simHuman_chr6.simHuman.chr6 586512 22 + 601863 TGGTAGAGGATGGGCATGTGAG -s simRat_chr6.simRat.chr6 631758 22 + 647215 TACCAGAGAATAGGCAGGCAAT - -a -s simMouse_chr6.simMouse.chr6 619776 26 + 636262 ACCAGTGTAGAAGTGTTGGGTTTACT -s Anc0.Anc0refChr3 214707 18 + 222631 ACAAGTGT--------TGACTTTACT -s Anc1.Anc1refChr1 54994 18 + 69767 ACAAGTGT--------TGACTTTACT -s Anc2.Anc2refChr1 132248 18 + 142988 AAAAGGGT--------TGACTTTATT -s mr.mrrefChr3 166867 18 + 181027 ACCAGTGT--------TGGGTTTACT -s simCow_chr6.simCow.chr6 590780 18 + 602619 AAGAGCAT--------TGACTTTATT -s simDog_chr6.simDog.chr6 582890 16 + 593897 AAAAAGGT--------TGACTTTA-- -s simHuman_chr6.simHuman.chr6 586545 18 + 601863 ACAAGTGT--------CAACTTTACT -s simRat_chr6.simRat.chr6 631780 18 + 647215 ACCAGCGT--------TGGGTGTACT - -a -s simMouse_chr6.simMouse.chr6 619802 13 + 636262 GCCCAATGATAAT -s Anc0.Anc0refChr3 214726 12 + 222631 GGACCATAATAA- -s Anc1.Anc1refChr1 55013 12 + 69767 GGACCATAATAA- -s Anc2.Anc2refChr1 132267 12 + 142988 GGACCATAATAT- -s mr.mrrefChr3 166885 13 + 181027 GGCCAATGATAAT -s simCow_chr6.simCow.chr6 590799 12 + 602619 GGCCCATGATAG- -s simDog_chr6.simDog.chr6 582906 12 + 593897 GGACAGTAATAT- -s simHuman_chr6.simHuman.chr6 586564 12 + 601863 GGACCATAATAA- -s simRat_chr6.simRat.chr6 631798 13 + 647215 GGCCAATGTTAAT - -a -s simMouse_chr6.simMouse.chr6 619815 23 + 636262 GCCACATGTTATAGTATGCTGAA -s Anc0.Anc0refChr3 214738 23 + 222631 GCCACATTATATAGTATGCTAAA -s Anc1.Anc1refChr1 55025 23 + 69767 GCCACATTATATAGTATGCTAAA -s Anc2.Anc2refChr1 132279 23 + 142988 GACACATTATATAGTATGCTAAA -s mr.mrrefChr3 166898 23 + 181027 GCCACATGTTATAGTATGCTGAA -s simCow_chr6.simCow.chr6 590811 23 + 602619 AACACAGTATATAGTATGCTAAA -s simDog_chr6.simDog.chr6 582919 23 + 593897 GACACGTTATATAGTATTCTAAA -s simHuman_chr6.simHuman.chr6 586576 23 + 601863 GCCACATCATATAGTACGCTAAA -s simRat_chr6.simRat.chr6 631811 23 + 647215 GCCACATGTTATAGTATGCTGAA - -a -s simMouse_chr6.simMouse.chr6 619838 5 + 636262 CAGTG -s Anc0.Anc0refChr3 214761 3 + 222631 CA--G -s Anc1.Anc1refChr1 55048 3 + 69767 CA--G -s Anc2.Anc2refChr1 132302 3 + 142988 CA--G -s mr.mrrefChr3 166921 5 + 181027 CAGTG -s simCow_chr6.simCow.chr6 590834 3 + 602619 CA--G -s simDog_chr6.simDog.chr6 582947 3 + 593897 TA--G -s simHuman_chr6.simHuman.chr6 586599 3 + 601863 CA--G -s simRat_chr6.simRat.chr6 631834 5 + 647215 TAGTG - -a -s simMouse_chr6.simMouse.chr6 619843 22 + 636262 TGTTCGGCTGGGTCCCAAGGTA -s Anc0.Anc0refChr3 214764 22 + 222631 TGATTGGTATGGCCCCAAGAGA -s Anc1.Anc1refChr1 55051 22 + 69767 TGATTGGTATGGCCCCAAGAGA -s Anc2.Anc2refChr1 132305 22 + 142988 TGATTGGTATGGCCCCAAGAGA -s mr.mrrefChr3 166926 22 + 181027 TGTTCGGTTTGGTCCCAAGAGA -s simCow_chr6.simCow.chr6 590842 21 + 602619 TTATCGCTA-GGCCCCATGAGA -s simDog_chr6.simDog.chr6 582950 22 + 593897 TGATTGGCATGGCCACAAGAGA -s simHuman_chr6.simHuman.chr6 586602 22 + 601863 TGATTGGTATGGCCCCAAGAGA -s simRat_chr6.simRat.chr6 631839 22 + 647215 TGTTGGGTCTGGGCCCAAGAGA - -a -s simMouse_chr6.simMouse.chr6 619865 31 + 636262 GGCAATTACTTGATTATTACCTGAATGAATA -s Anc0.Anc0refChr3 214786 19 + 222631 GATAATTACCTAATT------------GACA -s Anc1.Anc1refChr1 55073 19 + 69767 GATAATTACCTAATT------------GACA -s Anc2.Anc2refChr1 132327 19 + 142988 GATAATTACCTAATT------------AACA -s mr.mrrefChr3 166948 31 + 181027 GACAATTACTTGATTATTACCTGAATGGATA -s simCow_chr6.simCow.chr6 590866 19 + 602619 GATAATTACCTAATT------------AACA -s simDog_chr6.simDog.chr6 582972 15 + 593897 GATAATTACCTAATC---------------- -s simHuman_chr6.simHuman.chr6 586624 19 + 601863 TATAATTACCTAATT------------GACT -s simRat_chr6.simRat.chr6 631861 31 + 647215 GACAATTACTTGATTATTACCTTAATGGATA - -a -s simMouse_chr6.simMouse.chr6 619896 37 + 636262 TTCAACACATAGAAGTGGGTGAGAAAGAAAAGTAAAC -s Anc0.Anc0refChr3 214806 37 + 222631 TTTAGGACAAAGAAGAGGGTGAGAAAGAAAAGTAAAA -s Anc1.Anc1refChr1 55093 37 + 69767 TTTAGGACAAAGAAGAGGGTGAGAAAGAAAAGTAAAA -s Anc2.Anc2refChr1 132347 37 + 142988 GTTAGGACAAAGAAGAGGGTAAGAAAGAGAAGTAAAC -s mr.mrrefChr3 166980 37 + 181027 TTCAACACATAGAAGTGGGTGAGAAAGAAAAGTAAAA -s simCow_chr6.simCow.chr6 590886 37 + 602619 GTTAGGACAAAGAAGGAGGTAAGGAAAACAAGTAAAC -s simDog_chr6.simDog.chr6 582987 35 + 593897 --TGGGCCAAATAAGAGGGTAAGAAAGAGAAGTAAAC -s simHuman_chr6.simHuman.chr6 586644 37 + 601863 TTTAGGACAAAGAAGAGGGTGAGAAAGCAAAATAGAA -s simRat_chr6.simRat.chr6 631893 37 + 647215 CTCAACATCTAGAAGTGGGTGAGAAAGAAAAGTAAAA - -a -s simMouse_chr6.simMouse.chr6 619933 8 + 636262 ATTTGGCT -s Anc0.Anc0refChr3 214843 8 + 222631 TTTGCACT -s Anc1.Anc1refChr1 55130 8 + 69767 TTTGCACT -s Anc2.Anc2refChr1 132388 8 + 142988 TTTGCACT -s mr.mrrefChr3 167017 8 + 181027 ATTTGGCT -s simCow_chr6.simCow.chr6 590927 8 + 602619 ATTCCACG -s simDog_chr6.simDog.chr6 583026 8 + 593897 TCCGCACT -s simHuman_chr6.simHuman.chr6 586681 8 + 601863 TTTGCACT -s simRat_chr6.simRat.chr6 631933 8 + 647215 ATTTGGCT - -a -s simMouse_chr6.simMouse.chr6 619941 76 + 636262 GTAAGACATGTATTGGGACTTTTATGGTCTTGACTTACCTGGCCCAGACTTTTTGAAAGTAATTTCAAATCCAACA -s Anc0.Anc0refChr3 214851 76 + 222631 GGAGGACATGTATTGTGCTACTCATGGAGTCAACATACCTGGCCCAGACTTTTGGAAGGTAACTTCCAGTAAAAGA -s Anc1.Anc1refChr1 55138 76 + 69767 GGAGGACATGTATTGTGCTACTCATGGAGTCAACATACCTGGCCCAGACTTTTGGAAGGTAACTTCCAGTAAAAGA -s Anc2.Anc2refChr1 132398 76 + 142988 GGAGGACATGTATTGTGCTACCCATGGAGTCAACATATCTGGCCCAGACTTTTGGAAGGTAACGTCCAGTAAAAGA -s mr.mrrefChr3 167025 76 + 181027 GTAAGACATGTATTGTGACTTTTATGGACTTAACTTACCTGGCCCAGACTTTTTGAAAGTAATTTCAAATCAAAGA -s simCow_chr6.simCow.chr6 590937 76 + 602619 GGAAGACATGTATTGTGGTATTCATGAGGGCAACATATCAGAACCAGACTTTTGGAAGGTAACCTCAAGCAAAAGA -s simDog_chr6.simDog.chr6 583036 75 + 593897 GGAGGACATGTATTGTGCTACCCATGGAGTTAACATATCTGGCCAAGACTTTTGGAAGGGAGTGT-CAGTAGGAGA -s simHuman_chr6.simHuman.chr6 586689 66 + 601863 G------ATGTATGGTG----TCATGGAGTCAACCTACCTGGCCCAGACTTATGGAGGGTGACTCCGAGGGAAAGA -s simRat_chr6.simRat.chr6 631941 76 + 647215 GCAAGACATGTATTGTGCCTTTTGTGGAATGAATTTACCTGGCCCAGACTTTCAGAAAGTAATTTCAAATCAAAGA - -a -s simMouse_chr6.simMouse.chr6 620017 5 + 636262 CAACA -s Anc0.Anc0refChr3 214928 5 + 222631 CAATA -s Anc1.Anc1refChr1 55215 5 + 69767 CAATA -s Anc2.Anc2refChr1 132475 5 + 142988 CAATA -s mr.mrrefChr3 167102 5 + 181027 CAATA -s simCow_chr6.simCow.chr6 591014 5 + 602619 CACTC -s simDog_chr6.simDog.chr6 583112 5 + 593897 CAATA -s simHuman_chr6.simHuman.chr6 586756 5 + 601863 TAATG -s simRat_chr6.simRat.chr6 632018 5 + 647215 CAATA - -a -s simMouse_chr6.simMouse.chr6 620022 41 + 636262 GAGTGAGATGCCTCATGCCCTATCATTAAAGCTAACCAAAA -s Anc0.Anc0refChr3 214938 36 + 222631 GAGTGAGATGCCCCAAGCCCTATCAGTAGACCTTAC----- -s Anc1.Anc1refChr1 55225 41 + 69767 GAGTGAGATGCCCCAAGCCCTATCAGTAGACCTTACCAAGA -s Anc2.Anc2refChr1 132485 36 + 142988 GAGTGAGATGCCCCAAGCCATCCCAGTAGTCCTTAA----- -s mr.mrrefChr3 167107 41 + 181027 GAGTGAGATGCCTCATGCCCTATCATTAAAGCTAACCAAGA -s simCow_chr6.simCow.chr6 591024 36 + 602619 CAGTGAGATGCCCCACGCTGATGTATTAGTCCTTAA----- -s simDog_chr6.simDog.chr6 583122 29 + 593897 GAGTGACATACCCCAAGCCATCCCAGTCG------------ -s simHuman_chr6.simHuman.chr6 586766 41 + 601863 GAGTGAGATGCCCCAAGCCCCATCAGTAGACCTTACCAAGA -s simRat_chr6.simRat.chr6 632023 35 + 647215 CA------TGCCTAATGCCCTATCACTAAAGCTAACCAAGA - -a -s simMouse_chr6.simMouse.chr6 620063 88 + 636262 TTAGACTACCTCAGTCATTCCATTTGAGTGATCTTTTAATAGCTGCAAATCCTGCAAATAAATGTATGCCTTCTTTGAGGTTCCATTT -s Anc0.Anc0refChr3 214974 78 + 222631 -TAGACTATCTTAGTCATTCCTTTTTGGTGATCTTTTAACAG---------CTGCAAATAATTGCATGCCTTCTTTGAAGTTCCATTT -s Anc1.Anc1refChr1 55266 79 + 69767 CTAGACTATCTTAGTCATTCCTTTTTGGTGATCTTTTAACAG---------CTGCAAATAATTGCATGCCTTCTTTGAAGTTCCATTT -s Anc2.Anc2refChr1 132521 78 + 142988 -TAGACTATCCTAGGCATTCCTTTTTGGTGATCCTTTAACAG---------CTGCATATAATTATATGCCTTCTTTTAAGTTCCATTT -s mr.mrrefChr3 167148 88 + 181027 TTAGACTACCTTAGTCATTCCATTTGAGTGATCTTTTAATAGCTGCAAATCCTGCAAATAAATGCATGCCTTCTTTGAGGTTCCATTT -s simCow_chr6.simCow.chr6 591060 77 + 602619 --AGACTATCCTAGGCATGCCTTTTGGATAATCCCTTCAGAG---------CTGCATATAATTATATGCCTTCTTTTTAGTTCCACAT -s simDog_chr6.simDog.chr6 583151 66 + 593897 -TGGGCTGTCCTA--CATTCCTTTCTAGTGATCCTTTAACAG---------CTACATATAAT----------CTTTTAAATTCCATTT -s simHuman_chr6.simHuman.chr6 586808 79 + 601863 CCAAACTATCTTAGTCATTCCTTTTAGGTGACCTTTTTACAG---------CTGTAAATAATTGCATGCCTTCTTTGAAGTTTCATCT -s simRat_chr6.simRat.chr6 632058 88 + 647215 TTAGACTACTTTTGTCATTCCATTTGAGTGATCTGTTGATAGTTGCTAACCCTGCAAATAAATGCATGCCTTCTTTGAGGTTCCATTT - -a -s simMouse_chr6.simMouse.chr6 620151 7 + 636262 TAGAGAG -s Anc0.Anc0refChr3 215055 7 + 222631 TAGAAGA -s Anc1.Anc1refChr1 55348 7 + 69767 TAGAAGA -s Anc2.Anc2refChr1 132602 7 + 142988 TAGAAGA -s mr.mrrefChr3 167236 7 + 181027 TAGAGGG -s simCow_chr6.simCow.chr6 591140 7 + 602619 TAGAAGA -s simDog_chr6.simDog.chr6 583220 7 + 593897 TAGAAGG -s simHuman_chr6.simHuman.chr6 586890 7 + 601863 TAGCAGA -s simRat_chr6.simRat.chr6 632146 7 + 647215 TAAATGT - -a -s simMouse_chr6.simMouse.chr6 620158 18 + 636262 CAATTGTGGATACATAAA -s Anc0.Anc0refChr3 215062 13 + 222631 C-----TGGATACACACA -s Anc1.Anc1refChr1 55355 13 + 69767 C-----TGGATACACACA -s Anc2.Anc2refChr1 132609 13 + 142988 C-----TCACCACACACA -s mr.mrrefChr3 167243 18 + 181027 CAATTGTGGATACATAAA -s simCow_chr6.simCow.chr6 591147 7 + 602619 C-----------AACTCA -s simDog_chr6.simDog.chr6 583230 13 + 593897 C-----TCACCACACACA -s simHuman_chr6.simHuman.chr6 586897 13 + 601863 C-----TGGATCCAAATA -s simRat_chr6.simRat.chr6 632153 18 + 647215 CAGTTGTGGATACATACA - -a -s simMouse_chr6.simMouse.chr6 620176 19 + 636262 CTGTAAGAGTCTTATAAGG -s Anc0.Anc0refChr3 215075 15 + 222631 T----AGAGTCTTGTGAGG -s Anc1.Anc1refChr1 55368 15 + 69767 T----AGAGTCTTGTGAGG -s Anc2.Anc2refChr1 132622 15 + 142988 T----AGGGTTTTGTGAGG -s mr.mrrefChr3 167261 19 + 181027 CTGTAAGAGTCTTATGAGG -s simCow_chr6.simCow.chr6 591154 1 + 602619 T------------------ -s simDog_chr6.simDog.chr6 583244 15 + 593897 T----AGGGTTTTGTGAGG -s simHuman_chr6.simHuman.chr6 586910 15 + 601863 T----AGAGTCTCTTGAGG -s simRat_chr6.simRat.chr6 632171 12 + 647215 CTGTAAG-------TGGGG - -a -s simMouse_chr6.simMouse.chr6 620195 13 + 636262 GCACCAAAAAGGA -s Anc0.Anc0refChr3 215104 13 + 222631 GGACCCAAAAGGA -s Anc1.Anc1refChr1 55397 13 + 69767 GGACCCAAAAGGA -s Anc2.Anc2refChr1 132651 13 + 142988 GGACCCAAAAGGA -s mr.mrrefChr3 167280 13 + 181027 GCACCAAAAAGGA -s simCow_chr6.simCow.chr6 591164 13 + 602619 GCACTGAAAAGGA -s simDog_chr6.simDog.chr6 583273 13 + 593897 GGACCCAAAAGGA -s simHuman_chr6.simHuman.chr6 586939 13 + 601863 GAACCCAAAAGGA -s simRat_chr6.simRat.chr6 632183 13 + 647215 GTGCCAAATAGGA - -a -s simMouse_chr6.simMouse.chr6 620208 9 + 636262 TGCCACAGA -s Anc0.Anc0refChr3 215123 9 + 222631 TGCACCATG -s Anc1.Anc1refChr1 55416 9 + 69767 TGCACCATG -s Anc2.Anc2refChr1 132670 9 + 142988 TACACTCTG -s mr.mrrefChr3 167293 9 + 181027 TGCCACAGA -s simCow_chr6.simCow.chr6 591183 9 + 602619 TACACTCTG -s simDog_chr6.simDog.chr6 583292 7 + 593897 TACAA--TG -s simHuman_chr6.simHuman.chr6 586958 9 + 601863 TGCACCATG -s simRat_chr6.simRat.chr6 632196 9 + 647215 TGCCACAGA - -a -s simMouse_chr6.simMouse.chr6 620217 4 + 636262 AATG -s Anc0.Anc0refChr3 215132 4 + 222631 AAAA -s Anc1.Anc1refChr1 55425 4 + 69767 AAAA -s Anc2.Anc2refChr1 132679 4 + 142988 AAAA -s mr.mrrefChr3 167302 4 + 181027 AATG -s simCow_chr6.simCow.chr6 591192 4 + 602619 CACA -s simDog_chr6.simDog.chr6 583299 4 + 593897 AAAA -s simHuman_chr6.simHuman.chr6 586967 4 + 601863 AAAA -s simRat_chr6.simRat.chr6 632211 4 + 647215 AATG - -a -s simMouse_chr6.simMouse.chr6 620221 131 + 636262 AGACTAGAACAGAGTAACTGATTTACTGCAGTAAGTAGGCCAATGCTTGATTTACTGTAGTAAGTAGGCCACTGCTACTTTTGTGCCCCCAAATTCGAACAATTACATGAGGTTCAATCATATAAAAATCA -s Anc0.Anc0refChr3 215141 90 + 222631 AGGCTAGGACAAGGTAACTGAATTAAAG-----------------------------TATTACTAATGCTACTGC-----T-GTACTCCCAAAATAAAACAACTATATGAT---CAATCATGTTACA---A -s Anc1.Anc1refChr1 55434 93 + 69767 AGGCTAGGACAAGGTAACTGAATTAAAG-----------------------------TATTACTAATGCTACTGC-----T-GTACTCCCAAAATAAAACAACTATATGATGTTCAATCATGTTACA---A -s Anc2.Anc2refChr1 132688 90 + 142988 AGGCTCGGACAAAGTAACTGAATTAAAG-----------------------------TATTACTAATGCTATTGC-----T-GTACTCCTAAAATAAGACAACTATATGGT---CATTCATGTTACA---A -s mr.mrrefChr3 167306 101 + 181027 AGACTAGGACAAGGTAACTGATTTACAG-----------------------------TAGTAAGTAGGCCACTGCTACTTT-GTGCCCCCAAATTCGAACAATTACATGAGGTTCAATCATATAAAAATCA -s simCow_chr6.simCow.chr6 591200 88 + 602619 AGGCTGGGACAAAATAACTGGGTTAAAG-----------------------------TATTACTGATACTATGGC-----T-GCATTCC-AAGATAACGCAATTATGTG-T---ACCTCATGTTACA---A -s simDog_chr6.simDog.chr6 583308 90 + 593897 AGGCTCAAACAAAGTAACTGAATTAAAG-----------------------------TATTAAGAATGCTATTGC-----T-GTACCCGTGAAATAAGAGAACTATATGGT---CATTCATGTTATA---A -s simHuman_chr6.simHuman.chr6 586976 93 + 601863 AGGCTAGGATAAGGTAAATGACTTAAAC-----------------------------TACTACTAAAGCTACTGC-----T-GTACTCCCAAAATAAAACAACTGTATGATGTTCAATGATGTTACA---A -s simRat_chr6.simRat.chr6 632215 101 + 647215 AGACTAGGAAAAGGGAACTGATTTATAG-----------------------------TAGAAAGTAGACCACTGCTACTCT-GTGCCCCCAAATTTGAACAATTACATGAGGATTAATCATATAAAAATCA - -a -s simMouse_chr6.simMouse.chr6 620352 190 + 636262 TGTCACACAACATAACTAAATAACATATGAGGATCTTCCAGACAACTTTGGCCCATGGTTCTCCAATAGAGCCTTTGTCAGTGCCTACTTGTATTACAAAATTCCCTTATCAGCTGTTTTAAAGGATGTCGCCCATGGTTCACCAATAGAGCCTTTGTCAGTGCCTACTTGTATTACAAAATTCCCTTAT -s Anc0.Anc0refChr3 215231 109 + 222631 TGACATGTGACATTATTAAATAGTATATGAGGTGGTTGCAAACATCTTTGGTCCCTCGTTCACAGACAGAATGCTAGTCAGTGTC---------------------------------------------------------------------------------ACTTGCACTAGAGAATTCCCTCAT -s Anc1.Anc1refChr1 55527 131 + 69767 TGACATGTGACATTATTAAATAGTATATGAGGTGGTTGCAAACATCTTTGGTCCCTCGTTCACAGACAGAATGCTAGTCAGTGTCCACTTGCACTAA-----------------------------------------------------------GTCACTGTCCACTTGCACTAGAGAATTCCCTCAT -s Anc2.Anc2refChr1 132778 109 + 142988 GGACATGTGACATTATTAAATAGTATATGAGGTGGTGGCAAACACCTTTGGTCCCTGGTTCACAGGCAGAATGCTAGTCAGGGTC---------------------------------------------------------------------------------ACTTGCACTAGAGAATCCCCTCAC -s mr.mrrefChr3 167407 144 + 181027 TGTCACACAACATAACTAAATAACATATGAGGATCTTGCAGACATCTTTGGCCCCTCGTTCTCCAATAGAGCCTTTGTCAGTGCCTACTTGTATTAC----------------------------------------------CAATAGAGCCTTTGTCAGTGCCTACTTGTACTACAAAATTCCCTCAT -s simCow_chr6.simCow.chr6 591289 109 + 602619 GGATGTGCGATATAATTGAATTGTATATCAGGCAGTCATAAACACCTCTGATCCCTGGTTTGCAGGCAGAATGTTAGTCACTGTC---------------------------------------------------------------------------------ACTTGCATTAGAGAATCCCCTATC -s simDog_chr6.simDog.chr6 583398 100 + 593897 GGACATGTGACATTATAAAACAGTATATGAGGTGGTGGCAAACACCTTTGGTCCCTGGTTCA---------TACTAGTCAGGGTC---------------------------------------------------------------------------------ACTTGCACTGGATAACCCCCTCAC -s simHuman_chr6.simHuman.chr6 587069 131 + 601863 TGACATGTGACATGATTAAGTGGTATATGGGGTGGTTGCACATATCTTTGGTTCCTCGTTCAGAGACAGAATGCTAGTCACTTTCCACTTGCACTAA-----------------------------------------------------------GTCACTGTCCACTTGCACTAGAGAATTTCCTCAT -s simRat_chr6.simRat.chr6 632316 92 + 647215 TGTCACACA-----------TAACATATGACG-TATTGCAGACATCTTTGGCCCCTC--------------------------------------------------------------------------------------CAATAGAGCCTTTGTCATTGCCTACTTGTACTACAAAATTCCATCAG - -a -s simMouse_chr6.simMouse.chr6 620542 6 + 636262 CAGCTG -s Anc0.Anc0refChr3 215340 6 + 222631 CAGCTG -s Anc1.Anc1refChr1 55658 6 + 69767 CAGCTG -s Anc2.Anc2refChr1 132891 6 + 142988 CTGCTG -s mr.mrrefChr3 167551 6 + 181027 CAGCTG -s simCow_chr6.simCow.chr6 591402 6 + 602619 CAGCTG -s simDog_chr6.simDog.chr6 583502 6 + 593897 CTGCTA -s simHuman_chr6.simHuman.chr6 587200 6 + 601863 TAGCTG -s simRat_chr6.simRat.chr6 632408 5 + 647215 CA-CTA - -a -s simMouse_chr6.simMouse.chr6 620548 125 + 636262 TTTAAAGGACGTCTGAGTGTAATCTAACTCTTTTGAGTCTCACCATTTTGTGACTTATTGGAGTGTGGAAATGTTCTTTTCCTTTGCGGTCTGGAGTGATGTGACGTTGTGAAGTGATGTTTATC -s Anc0.Anc0refChr3 215347 52 + 222631 TTTGAATGATGTCTTGGTGT-TACTCACTCTTTT-ACACTCACCCTTTTGCCAC----------------------------------------------------------------------- -s Anc1.Anc1refChr1 55665 54 + 69767 TTTGAATGATGTCTTGGTGTATACTCACTCTTTTGACACTCACCCTTTTGCCAC----------------------------------------------------------------------- -s Anc2.Anc2refChr1 132898 52 + 142988 TTTGAATGCTGTCTTGGTGT-TACTCACACTTTC-ACACTCACCCTTTTGCCAT----------------------------------------------------------------------- -s mr.mrrefChr3 167558 114 + 181027 TTTAAATGATGTCTTAGTGTAATCTAACTCTTTTGAGTCTCACCCTTTTGTGACTTATTGGAGTGTGGAAATGTTCTTT------GCGGTCTGGAGTGATGT-----TGTGAAGTGATGTTTATC -s simCow_chr6.simCow.chr6 591409 52 + 602619 ATTGAATGCTCTCTTGGTGT-GATCGCCCCTTCG-ACACTCATCCCTTAGCTGG----------------------------------------------------------------------- -s simDog_chr6.simDog.chr6 583509 52 + 593897 TTTGAATGCTGTCTTGGTGT-TACTCACACTTTC-GCACTCACCCTTCTGCCAT----------------------------------------------------------------------- -s simHuman_chr6.simHuman.chr6 587207 53 + 601863 TTTGAATGATGTCTTGGT-CATACTCACTCTTTTGACACTCACCCTTTTGCCAC----------------------------------------------------------------------- -s simRat_chr6.simRat.chr6 632414 114 + 647215 TTCAAATGTTGTCTTAGTGTGGCCTAACTCTTTGGAGTCTTGCCCTTTTGTGACTTATTGGAGTGTGGCACTGTTCTTT------GTAGCCTGGAGTGATGT-----TGTCAAGTGATCTTTATC - -a -s simMouse_chr6.simMouse.chr6 620673 22 + 636262 CCTATTCTTGCCAATCCATCAT -s mr.mrrefChr3 167672 22 + 181027 CCTATTCTTGCCAATCCATCAT -s simRat_chr6.simRat.chr6 632540 22 + 647215 CCTAGTGTTGCCAATCCATCAC - -a -s simMouse_chr6.simMouse.chr6 620695 40 + 636262 GAAAGTTCCAGTGAGTTATTGGCAAGTGACCAGTCTGTTT -s mr.mrrefChr3 167694 40 + 181027 GAAAGTTCCAGTGAGTTATTGGCAAGTGACCAGTCTGTTT -s simRat_chr6.simRat.chr6 632564 40 + 647215 GAAAGTTCCAGTGAGTTATAACCAAGTGACCACTCAATTT - -a -s simMouse_chr6.simMouse.chr6 620735 10 + 636262 GTATTCCATC -s Anc0.Anc0refChr3 215399 8 + 222631 --ATATCATC -s Anc1.Anc1refChr1 55719 8 + 69767 --ATATCATC -s Anc2.Anc2refChr1 132950 8 + 142988 --ATATCATC -s mr.mrrefChr3 167734 10 + 181027 GTATTCCATC -s simCow_chr6.simCow.chr6 591461 8 + 602619 --ATTTGATC -s simDog_chr6.simDog.chr6 583561 8 + 593897 --ATATCATC -s simHuman_chr6.simHuman.chr6 587260 8 + 601863 --ATCTCATT -s simRat_chr6.simRat.chr6 632612 10 + 647215 GTATTCCATC - -a -s simMouse_chr6.simMouse.chr6 620745 54 + 636262 AACTTTTGATGTTACCTACTTCACAAACAAAAAACCAGTTCATTACTTCCTCTA -s Anc0.Anc0refChr3 215407 54 + 222631 AATTTTTGTCACTACCTAGATCACGTACAAAAAACCAGTCCATTACATCCCCTA -s Anc1.Anc1refChr1 55727 54 + 69767 AATTTTTGTCACTACCTAGATCACGTACAAAAAACCAGTCCATTACATCCCCTA -s Anc2.Anc2refChr1 132958 54 + 142988 AATTTTTGTCACTACCTAGATCACGTACAAAAAACCAGTTCATTATATCTCCTA -s mr.mrrefChr3 167744 54 + 181027 AATTTTTGATGTTACCTACTTCACAAACAAAAAACCAGTCCATTACATCCTCTA -s simCow_chr6.simCow.chr6 591470 54 + 602619 AATTTATGTTACTACCTACATCACGTACAAAAAGCCAGTTCATCATATCTCCTA -s simDog_chr6.simDog.chr6 583569 54 + 593897 AATTTTTGTCACTACCTAGATCACATACAGAAGACCAATTCCTTATGTCTACTA -s simHuman_chr6.simHuman.chr6 587268 52 + 601863 GA-TTTTGTCACTACCAAGATCG-GCACGAAAAATAAGTCCACTACATCCCTTA -s simRat_chr6.simRat.chr6 632622 54 + 647215 AATTTTTGATGTTACCTACTTCACAAACAAAAAACCAGTCCATCACACTCTCTA - -a -s simMouse_chr6.simMouse.chr6 620799 21 + 636262 ACTAGCTTGTCCCAAGAGCTG -s Anc0.Anc0refChr3 215461 20 + 222631 ACTCGCTATTCCCAAG-GCGG -s Anc1.Anc1refChr1 55781 20 + 69767 ACTCGCTATTCCCAAG-GCGG -s Anc2.Anc2refChr1 133012 20 + 142988 ACTCGCTATTCCCAAG-GCGG -s mr.mrrefChr3 167798 21 + 181027 ACTAGCTTGTCCCAAGAGCTG -s simCow_chr6.simCow.chr6 591524 20 + 602619 ACTCGCTATTCCCAAG-GTGG -s simDog_chr6.simDog.chr6 583630 20 + 593897 ACTGATTACTGCCAAG-GCGT -s simHuman_chr6.simHuman.chr6 587320 20 + 601863 ACACGCTATTCCCAAG-GCGG -s simRat_chr6.simRat.chr6 632676 21 + 647215 ACCAGCTTGTCCCAAGAGCTG - -a -s simMouse_chr6.simMouse.chr6 620820 17 + 636262 GATGGCATAGCTATCCA -s Anc0.Anc0refChr3 215492 17 + 222631 GATTTTGTATCTCTCCA -s Anc1.Anc1refChr1 55812 17 + 69767 GATTTTGTATCTCTCCA -s Anc2.Anc2refChr1 133043 17 + 142988 GATTTTGTATCTCTCCA -s mr.mrrefChr3 167819 17 + 181027 GATGGCGTAGCTCTCCA -s simCow_chr6.simCow.chr6 591555 17 + 602619 GATTTTGTATCTCTCCA -s simDog_chr6.simDog.chr6 583661 17 + 593897 GATTTTGCATCTCTCCA -s simHuman_chr6.simHuman.chr6 587351 17 + 601863 GATTTTGTATCTCTCCA -s simRat_chr6.simRat.chr6 632697 17 + 647215 GATGACGTAGCTCTCCA - -a -s simMouse_chr6.simMouse.chr6 620837 39 + 636262 TGTTTAAGCCCAAAATGATCTGAGTTGACGGTGCTGAAA -s Anc0.Anc0refChr3 215513 36 + 222631 TGAT---GTCCATAATGATCTGGCTTGACAGTGCTGTAT -s Anc1.Anc1refChr1 55833 36 + 69767 TGAT---GTCCATAATGATCTGGCTTGACAGTGCTGTAT -s Anc2.Anc2refChr1 133064 36 + 142988 TGAT---GTCTATAATGATCTGGCTTGACAGTGCTGTAT -s mr.mrrefChr3 167836 36 + 181027 TGTT---GCCCAAAATGATCTGAGTTGACGGTGCTGAAA -s simCow_chr6.simCow.chr6 591578 36 + 602619 TGAT---GTCTAGAATGATGTGGCTTGACAGTGCTGTAT -s simDog_chr6.simDog.chr6 583682 36 + 593897 TGAC---GCCTGTAATGATCTGGCTTGACAGTGCTGTAT -s simHuman_chr6.simHuman.chr6 587372 36 + 601863 TGAT---ATCCATAATGATCTGGCTTGACCGTGCCAGAC -s simRat_chr6.simRat.chr6 632714 36 + 647215 TGTT---GCCCAAAATGATCTGAGCCAACGGTGCTGAAA - -a -s simMouse_chr6.simMouse.chr6 620876 1 + 636262 G -s Anc0.Anc0refChr3 215549 1 + 222631 G -s Anc1.Anc1refChr1 55869 1 + 69767 G -s Anc2.Anc2refChr1 133100 1 + 142988 G -s mr.mrrefChr3 167872 1 + 181027 G -s simCow_chr6.simCow.chr6 591614 1 + 602619 G -s simDog_chr6.simDog.chr6 583718 1 + 593897 G -s simHuman_chr6.simHuman.chr6 587412 1 + 601863 G -s simRat_chr6.simRat.chr6 632750 1 + 647215 G - -a -s simMouse_chr6.simMouse.chr6 620877 5 + 636262 AAGTC -s Anc0.Anc0refChr3 215550 5 + 222631 AGCTT -s Anc1.Anc1refChr1 55870 5 + 69767 AGCTT -s Anc2.Anc2refChr1 133111 5 + 142988 AGCTT -s mr.mrrefChr3 167873 5 + 181027 AAGTC -s simCow_chr6.simCow.chr6 591625 5 + 602619 GACTT -s simDog_chr6.simDog.chr6 583729 5 + 593897 AGCTT -s simHuman_chr6.simHuman.chr6 587413 5 + 601863 AGCTG -s simRat_chr6.simRat.chr6 632751 5 + 647215 GAGTC - -a -s simMouse_chr6.simMouse.chr6 620882 4 + 636262 ATAA -s Anc0.Anc0refChr3 215555 4 + 222631 GTAA -s Anc1.Anc1refChr1 55875 4 + 69767 GTAA -s Anc2.Anc2refChr1 133116 4 + 142988 GTAA -s mr.mrrefChr3 167878 4 + 181027 ATAA -s simCow_chr6.simCow.chr6 591630 4 + 602619 GTAG -s simDog_chr6.simDog.chr6 583758 4 + 593897 GTAA -s simHuman_chr6.simHuman.chr6 587418 4 + 601863 GTGT -s simRat_chr6.simRat.chr6 632756 4 + 647215 ATAA - -a -s simMouse_chr6.simMouse.chr6 620886 5 + 636262 GCTTT -s Anc0.Anc0refChr3 215559 5 + 222631 GCTTT -s Anc1.Anc1refChr1 55879 5 + 69767 GCTTT -s Anc2.Anc2refChr1 133120 5 + 142988 GCTTT -s mr.mrrefChr3 167882 5 + 181027 GCTTT -s simCow_chr6.simCow.chr6 591634 5 + 602619 GCTTT -s simDog_chr6.simDog.chr6 583762 5 + 593897 GCTTT -s simHuman_chr6.simHuman.chr6 587423 5 + 601863 GCTCT -s simRat_chr6.simRat.chr6 632760 5 + 647215 GCCTT - -a -s simMouse_chr6.simMouse.chr6 620891 46 + 636262 ATATTATTTTTTTGACTTGAATGCTGTCCAGGTTGGTTTCGATAAA -s Anc0.Anc0refChr3 215564 46 + 222631 TTACTATACTCTTGATTTGTGCTCAGTCCAGTTTGGAATTGATAAA -s Anc1.Anc1refChr1 55884 46 + 69767 TTACTATACTCTTGATTTGTGCTCAGTCCAGTTTGGAATTGATAAA -s Anc2.Anc2refChr1 133125 46 + 142988 TGTGGATACTCTTGATTTGTGCTCAGTCCAGTTTGGACTTGATAAA -s mr.mrrefChr3 167887 46 + 181027 ATACTATTTTTTTGATTTGAATGCCATCCAGTTTGGTATTGATAAA -s simCow_chr6.simCow.chr6 591640 46 + 602619 TATTGTTGCACTTGATTTGTGGTCAATCCAGTTTGGAGTTGCTAAG -s simDog_chr6.simDog.chr6 583767 46 + 593897 TGTGGATACTCTTGATTTATGCTCAGTCTGGTTTGGACTTAATAAA -s simHuman_chr6.simHuman.chr6 587428 29 + 601863 GTACTGTGC-----------------ACCAGTTTGGAATTGACAAA -s simRat_chr6.simRat.chr6 632765 39 + 647215 ATAC------ATTAATTTGAATGCCATC-AGTTTGGTATTGATAAA - -a -s simMouse_chr6.simMouse.chr6 620937 7 + 636262 TGTCTTG -s Anc0.Anc0refChr3 215610 7 + 222631 TATGATG -s Anc1.Anc1refChr1 55930 7 + 69767 TATGATG -s Anc2.Anc2refChr1 133175 7 + 142988 TATGATG -s mr.mrrefChr3 167933 7 + 181027 TGTCTTG -s simCow_chr6.simCow.chr6 591690 7 + 602619 ATTGATG -s simDog_chr6.simDog.chr6 583817 7 + 593897 TATGATG -s simHuman_chr6.simHuman.chr6 587457 7 + 601863 TATGATG -s simRat_chr6.simRat.chr6 632804 7 + 647215 TGTCCTG - -a -s simMouse_chr6.simMouse.chr6 620944 2 + 636262 GA -s Anc0.Anc0refChr3 215627 2 + 222631 GG -s Anc1.Anc1refChr1 55947 2 + 69767 GG -s Anc2.Anc2refChr1 133192 2 + 142988 GG -s mr.mrrefChr3 167940 2 + 181027 GA -s simCow_chr6.simCow.chr6 591707 2 + 602619 GA -s simDog_chr6.simDog.chr6 583834 2 + 593897 GG -s simHuman_chr6.simHuman.chr6 587474 2 + 601863 GG -s simRat_chr6.simRat.chr6 632811 2 + 647215 GA - -a -s simMouse_chr6.simMouse.chr6 620946 8 + 636262 TAGATGGT -s Anc0.Anc0refChr3 215629 8 + 222631 TAGACAGC -s Anc1.Anc1refChr1 55949 8 + 69767 TAGACAGC -s Anc2.Anc2refChr1 133195 8 + 142988 TAGACAGC -s mr.mrrefChr3 167942 8 + 181027 TAGATGGT -s simCow_chr6.simCow.chr6 591710 8 + 602619 TAGCCAGC -s simDog_chr6.simDog.chr6 583837 8 + 593897 TAGACAGC -s simHuman_chr6.simHuman.chr6 587476 8 + 601863 TAGACAGC -s simRat_chr6.simRat.chr6 632813 8 + 647215 TAGATGGT - -a -s simMouse_chr6.simMouse.chr6 620954 78 + 636262 TGAGAAATTGACTTCATATCATAAGTCAACTTATCATAAGTTGTGCCATTGACGAGGCCCCCATTGCAACTATGCATA -s Anc0.Anc0refChr3 215645 69 + 222631 ATAGAAGTTGACTT-------TT--TCAACCTATCATAACATGTGCCATTGCTGAGGCTCCCATTGCAACTATGCTCA -s Anc1.Anc1refChr1 55965 69 + 69767 ATAGAAGTTGACTT-------TT--TCAACCTATCATAACATGTGCCATTGCTGAGGCTCCCATTGCAACTATGCTCA -s Anc2.Anc2refChr1 133211 69 + 142988 ATAGAAGTAGACGT-------TT--TTAACCTATCATAACATGTGCCATTGCTGTGGCTCCCATTGCAACTATGATCA -s mr.mrrefChr3 167958 76 + 181027 TGAGAAATTGACTTGATATCATG--TCAACTTATCATAAGTTGTGCCATTGATGAGGCCCCCATTGCAACTATGCATA -s simCow_chr6.simCow.chr6 591726 69 + 602619 ATAGAAGCACACCC-------TT--CGAATCTAGCATAATATGTGCCATTCATGTGGTCCCCATTGTAACTATGGGCA -s simDog_chr6.simDog.chr6 583853 65 + 593897 ATAGTAGTAGATGT-------TT--TTAACCTATCATATCATGTGC----GCTGTGGCTCCCAGTGCAATGATGATCA -s simHuman_chr6.simHuman.chr6 587492 69 + 601863 AAAGAAGTTGACTT-------TC--TCAACCTATTATAACATGTGCCATTGCTGAGGCTCTCATTGCAGCTATGCTCC -s simRat_chr6.simRat.chr6 632829 55 + 647215 TGAGAAATTGGATAGGTATCATG----AATTTGCAATGATTGATCACACTGATTAGGTA------------------- - -a -s simMouse_chr6.simMouse.chr6 621032 18 + 636262 CAGATGAAAAGGAGCTTA -s Anc0.Anc0refChr3 215714 18 + 222631 TAGATGAAAAGGAACCTA -s Anc1.Anc1refChr1 56034 18 + 69767 TAGATGAAAAGGAACCTA -s Anc2.Anc2refChr1 133280 18 + 142988 TAGATGAAAAGGAACCTA -s mr.mrrefChr3 168034 18 + 181027 CAGATGAAAAGGAGCTTA -s simCow_chr6.simCow.chr6 591814 18 + 602619 TAGATGAAGAGGAACCTA -s simDog_chr6.simDog.chr6 583918 18 + 593897 TACATGGGAAGGAACCTA -s simHuman_chr6.simHuman.chr6 587561 18 + 601863 TAGACAAAAAGGTATCTA - -a -s simMouse_chr6.simMouse.chr6 621050 23 + 636262 TGTATAATAGGGGTATCATGAAT -s Anc0.Anc0refChr3 215734 23 + 222631 TGCGCAATAATGATAGCATGAAT -s Anc1.Anc1refChr1 56054 23 + 69767 TGCGCAATAATGATAGCATGAAT -s Anc2.Anc2refChr1 133300 23 + 142988 TGCGCACTAATGAAAGCATGAAT -s mr.mrrefChr3 168052 23 + 181027 TGTATAATAGGGGTATCATGAAT -s simCow_chr6.simCow.chr6 591833 20 + 602619 ---GCACTAATGACAGCATGAAT -s simDog_chr6.simDog.chr6 583938 22 + 593897 TGCACACTAATGGAAGCATGA-T -s simHuman_chr6.simHuman.chr6 587581 23 + 601863 TGCGCAACAATGATGGCATGAAT - -a -s simMouse_chr6.simMouse.chr6 621073 23 + 636262 TGTCAATGATTATTGTGAAACCT -s Anc0.Anc0refChr3 215758 22 + 222631 CATCAATAATTAT-GTGGAATCT -s Anc1.Anc1refChr1 56078 22 + 69767 CATCAATAATTAT-GTGGAATCT -s Anc2.Anc2refChr1 133324 22 + 142988 CATCAATAATTAT-GTGGAATCT -s mr.mrrefChr3 168075 22 + 181027 TGTCAATGATTAT-GTGAAACCT -s simCow_chr6.simCow.chr6 591854 18 + 602619 CAT----AATTAT-GTGGAATCT -s simDog_chr6.simDog.chr6 583961 21 + 593897 CCTCAATA-TTAT-GTGTAACCT -s simHuman_chr6.simHuman.chr6 587605 22 + 601863 CATCAATAATTAC-GTGGAATCT - -a -s simMouse_chr6.simMouse.chr6 621096 43 + 636262 AATTAAATATTTCTGTAGTCTTAGGACCATGAAGCACCTTACT -s Anc0.Anc0refChr3 215802 39 + 222631 ----TAATGTTTCCATAGTACTAGGTACATGAAGCATATTACT -s Anc1.Anc1refChr1 56122 43 + 69767 AATTTAATGTTTCCATAGTACTAGGTACATGAAGCATATTACT -s Anc2.Anc2refChr1 133368 39 + 142988 ----TGATGTTTTCACAGGACTAGCTACATGGACAATATTACT -s mr.mrrefChr3 168097 43 + 181027 AATTAAATATTTCTGTAGTACTAGGACCATGAAGCACCTTACT -s simCow_chr6.simCow.chr6 591893 35 + 602619 ----TGATGTTTTCACAGGACTA----CATTCATGATATTACA -s simDog_chr6.simDog.chr6 584003 29 + 593897 --------------ACAGGACTGGCTACATGGACAATATTACT -s simHuman_chr6.simHuman.chr6 587649 43 + 601863 AATTCAGTGTTTCCATAGTACTAGGGACATGAAGCATGTTACT -s simRat_chr6.simRat.chr6 632884 35 + 647215 --------ATTTCTGTAGTACTAGAATCATGAAGCACCTTACT - -a -s simMouse_chr6.simMouse.chr6 621139 7 + 636262 AACTCCT -s Anc0.Anc0refChr3 215841 7 + 222631 GATTCCT -s Anc1.Anc1refChr1 56165 7 + 69767 GATTCCT -s Anc2.Anc2refChr1 133407 7 + 142988 GATTCCT -s mr.mrrefChr3 168140 7 + 181027 AATTCCT -s simCow_chr6.simCow.chr6 591928 6 + 602619 -ACTCCT -s simDog_chr6.simDog.chr6 584032 7 + 593897 GATCCTT -s simHuman_chr6.simHuman.chr6 587692 7 + 601863 GATTCCT -s simRat_chr6.simRat.chr6 632927 7 + 647215 AATTCTC - -a -s simMouse_chr6.simMouse.chr6 621146 13 + 636262 TAATTGCAGGCAA -s Anc0.Anc0refChr3 215848 12 + 222631 CAACAAAGG-AGA -s Anc1.Anc1refChr1 56172 13 + 69767 CAACAAAGGGAGA -s Anc2.Anc2refChr1 133414 12 + 142988 CAACAAAGC-AGA -s mr.mrrefChr3 168147 13 + 181027 TAATTGCAGGCAA -s simCow_chr6.simCow.chr6 591934 10 + 602619 TAACAAAGC-A-- -s simDog_chr6.simDog.chr6 584043 12 + 593897 CGATGAAGC-AGA -s simHuman_chr6.simHuman.chr6 587699 13 + 601863 CAACAAAGGGACA -s simRat_chr6.simRat.chr6 632934 13 + 647215 TAATTGGAGGTAG - -a -s simMouse_chr6.simMouse.chr6 621159 111 + 636262 TGGTGCTTCAGTGCTAGGCAGGCATGCATAGTGAACTAGACCTAGGGTTACAATTGGACTTCTGTTGGACTGCTATTATGGATTCGAAAACCTAAGGACTCAGGGCAGCAT -s Anc0.Anc0refChr3 215868 106 + 222631 TGGCACTTCAGTGC----CAGGCATGCCCCAAGAAGCAGACCCAGGGTTACAACTAAACTTCTGCTGGACTGCTATCCTGAAGTTGAAAATCCAAAGACTAAGTGCCACA- -s Anc1.Anc1refChr1 56193 107 + 69767 TGGCACTTCAGTGC----CAGGCATGCCCCAAGAAGCAGACCCAGGGTTACAACTAAACTTCTGCTGGACTGCTATCCTGAAGTTGAAAATCCAAAGACTAAGTGCCACAT -s Anc2.Anc2refChr1 133434 106 + 142988 TGGCACTTCAGTGC----CAGGCATGCCCCAAAAAGCAGAGCCAGGGTTACAACTAAACTCCTGCTGGAATGCATTCCTGAAGTTGAAAATCCAAAGACCAAATGCCACA- -s mr.mrrefChr3 168168 111 + 181027 TGGTGCTTCAGTGCTAGGCAGGCATGCCTAGTGAAGTAGACCCAGGGTTACAACTGGACTTCTGTTGGACTGCTATTCTGGATTCGAAAACCTAAGGACTCAGGGCAGCAT -s simCow_chr6.simCow.chr6 591951 95 + 602619 TGGTGCTTCAGTGT----GAGGGATGC-CCAAAAAGCAGAGTTGGGGTTACAACTATATTCCCTCT----------CCTGAATTAGAAAACCTGAAGACCAATGGCCATA- -s simDog_chr6.simDog.chr6 584063 106 + 593897 TGGCACTTCAGTGC----CAGGCCAGGCCAGAAAAGCAGAGCCAGGGTTACAACTAAACTCCTGCTGGAATGCATTCCTGAAGTTGAAACTCCAAAAACCAAATGCCCCA- -s simHuman_chr6.simHuman.chr6 587720 103 + 601863 CGGCACTTAAGTGC----CAAGCATGCCACAAGAAGCAGACCCAGGGTTACAACTAAACATTTACTGAACCGTTATCCTG----TGAAAATCCAAAGACTAGGTGCCACAT -s simRat_chr6.simRat.chr6 632955 111 + 647215 TGGTGCTTCAGTCCTAGGCAGGCATGCCCACTGTAGTAGACCCAGGGTGACACCTGGACTTCTTTTGGACTGCTATTCTGAATTCAAAAACCTAAGGACTCAGGGCAGCAT - -a -s simMouse_chr6.simMouse.chr6 621270 74 + 636262 GTCTCCCGAAAATGGTCTCAATCATACATAGACAGGACAGCTCCTATCAGGATGTCCCTGAAATGCCCAGACCA -s Anc0.Anc0refChr3 215974 72 + 222631 -GCCCGCAAAAAGGGTGACA-TCATACATAGACAGGACAACTCCCATTGGGAGGTCCCTGAAATGACTAGATTA -s Anc1.Anc1refChr1 56300 73 + 69767 GGCCCGCAAAAAGGGTGACA-TCATACATAGACAGGACAACTCCCATTGGGAGGTCCCTGAAATGACTAGATTA -s Anc2.Anc2refChr1 133540 72 + 142988 -GCCCGTAAAAAGGATGACA-CCATACATAGACAGGACAACTCTCATTGGGAGGTCCCTGAAACGACTAGATTA -s mr.mrrefChr3 168279 73 + 181027 GTCTCCCAAAAATGGTGTCA-TCATACATAGACAGGACAGCTCCTATTGGGATGTCCCTGAAATGCCCAGACCA -s simCow_chr6.simCow.chr6 592046 60 + 602619 -GGTCGTAAAAAGGATGACA-CCATACATAGCCAGGACAA------------GGTCCCCGACACAAGTAGGTTA -s simDog_chr6.simDog.chr6 584169 60 + 593897 -GCCC------------ACA-CTATACATAGACAGGACAACTCTCATTGGGAGGTCCCTGAAACGACTAGATTA -s simHuman_chr6.simHuman.chr6 587901 68 + 601863 GCTACTCAAAAAGGGTGACA-TCATACATAGACAGGATGACTCCCATTGGGAGGTTCTTGAAAT-----GAATT -s simRat_chr6.simRat.chr6 633074 73 + 647215 GTCTCCCAAAAATGGTGTCA-CCATACATAGACAGGACAGCTCCTATTGGGATGTCCCTGAAGTGCCCAGACCA - -a -s simMouse_chr6.simMouse.chr6 621344 12 + 636262 CAGAAAAAATAT -s Anc0.Anc0refChr3 216046 12 + 222631 AAGACAAAATAT -s Anc1.Anc1refChr1 56373 12 + 69767 AAGACAAAATAT -s Anc2.Anc2refChr1 133621 12 + 142988 AAGACATAATAT -s mr.mrrefChr3 168352 12 + 181027 AAGAAAAAATAT -s simCow_chr6.simCow.chr6 592115 12 + 602619 AAGACACATTAC -s simDog_chr6.simDog.chr6 584238 12 + 593897 GAGACCTAATAT -s simHuman_chr6.simHuman.chr6 587969 12 + 601863 AAGACAAAATAT -s simRat_chr6.simRat.chr6 633147 12 + 647215 AAGAAAAAATAT - -a -s simMouse_chr6.simMouse.chr6 621356 5 + 636262 CAACC -s Anc0.Anc0refChr3 216091 5 + 222631 CAGCC -s Anc1.Anc1refChr1 56418 5 + 69767 CAGCC -s Anc2.Anc2refChr1 133666 5 + 142988 CAGCC -s mr.mrrefChr3 168364 5 + 181027 CAACC -s simCow_chr6.simCow.chr6 592160 5 + 602619 CAGCC -s simDog_chr6.simDog.chr6 584283 5 + 593897 CAGCC -s simHuman_chr6.simHuman.chr6 588015 5 + 601863 CAGCC -s simRat_chr6.simRat.chr6 633159 5 + 647215 CAACC - -a -s simMouse_chr6.simMouse.chr6 621361 10 + 636262 CCAAATGATT -s Anc0.Anc0refChr3 216096 10 + 222631 CCAGGTAAGT -s Anc1.Anc1refChr1 56423 10 + 69767 CCAGGTAAGT -s Anc2.Anc2refChr1 133671 10 + 142988 CCAGGTAAGT -s mr.mrrefChr3 168369 10 + 181027 CCAAATGATT -s simCow_chr6.simCow.chr6 592165 10 + 602619 CCAGTCAAAT -s simDog_chr6.simDog.chr6 584290 10 + 593897 CATGGTCAGC -s simHuman_chr6.simHuman.chr6 588020 10 + 601863 CCAGGTAAGT -s simRat_chr6.simRat.chr6 633164 10 + 647215 CCAAATGATT - -a -s simMouse_chr6.simMouse.chr6 621371 29 + 636262 GCAATGACTTATCTCCCACCTTGTGATAT -s Anc0.Anc0refChr3 216106 29 + 222631 ACCTTGACCTGACTATCACCTTGTACTAG -s Anc1.Anc1refChr1 56433 29 + 69767 ACCTTGACCTGACTATCACCTTGTACTAG -s Anc2.Anc2refChr1 133681 29 + 142988 ACCTCGACCCAACTATCACCTTGTACTGG -s mr.mrrefChr3 168379 29 + 181027 GCATTGACTTGACTCCCACCTTGTAATAT -s simCow_chr6.simCow.chr6 592175 29 + 602619 ACCTCAACCCACCTAACACCTTGTACTGG -s simDog_chr6.simDog.chr6 584320 29 + 593897 ACCCCGACCCAACTATCCCCTTATACTGG -s simHuman_chr6.simHuman.chr6 588030 29 + 601863 ACCTTGACCTGACTTTTATCTTGCACTAG -s simRat_chr6.simRat.chr6 633174 29 + 647215 GCATTGACTTGACACCCACCTTGTAATAT - -a -s simMouse_chr6.simMouse.chr6 621400 33 + 636262 TGGGAAACTCTGCCAGCTAGTCTCAATTAGGAA -s Anc0.Anc0refChr3 216135 32 + 222631 GGGGTAACTCTGCTGCATAGTCTCAA-TGGAGA -s Anc1.Anc1refChr1 56462 32 + 69767 GGGGTAACTCTGCTGCATAGTCTCAA-TGGAGA -s Anc2.Anc2refChr1 133710 32 + 142988 GGGGTAACTTCACTGCATAGTCTCAA-TGGAGG -s mr.mrrefChr3 168408 33 + 181027 TGGGAAACTCTGCCAGCTAGTCTCAATTAGAGA -s simCow_chr6.simCow.chr6 592205 32 + 602619 GGGGTATCTTCTCCACATAGTCTCAA-TGGGGG -s simDog_chr6.simDog.chr6 584349 32 + 593897 GGGGTAACTTCACTGCATAGTCTCAG-CGGAGG -s simHuman_chr6.simHuman.chr6 588059 32 + 601863 GGGTTAACTCTGCTGCATAGTCTCTA-TGGAGA -s simRat_chr6.simRat.chr6 633203 33 + 647215 TGGGAAACTCTGCCAGCTAGTCTCAATTAGAGA - -a -s simMouse_chr6.simMouse.chr6 621433 1 + 636262 T -s Anc0.Anc0refChr3 216228 1 + 222631 T -s Anc1.Anc1refChr1 56555 1 + 69767 T -s Anc2.Anc2refChr1 133803 1 + 142988 T -s mr.mrrefChr3 168441 1 + 181027 T -s simCow_chr6.simCow.chr6 592308 1 + 602619 T -s simHuman_chr6.simHuman.chr6 588153 1 + 601863 T -s simRat_chr6.simRat.chr6 633236 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 621434 43 + 636262 GACAGGCCTGTCAGGTTCAGCCCCCTCTCTGGTATCAGTTTGA -s Anc0.Anc0refChr3 216229 42 + 222631 GATAAGCTCAGTAGGTTCAGCCCCTT-TCTGGTATCCACTTGA -s Anc1.Anc1refChr1 56556 42 + 69767 GATAAGCTCAGTAGGTTCAGCCCCTT-TCTGGTATCCACTTGA -s Anc2.Anc2refChr1 133804 42 + 142988 AATAAGCTCAGTAGTTTCAGCCTCTT-TCTGGAATCCACTTTA -s mr.mrrefChr3 168442 42 + 181027 GATAGGCTCGTCAGGTTCAGCCCCCT-TCTGGTATCAATTTGA -s simCow_chr6.simCow.chr6 592311 42 + 602619 AATAGATTCAGTAGTTTCAGCTACTC-TCTGTAATCCACTGAA -s simDog_chr6.simDog.chr6 584429 34 + 593897 ---GAGCCCAGT-----CAGCCTCTT-TCCGGAATCCACTTTA -s simHuman_chr6.simHuman.chr6 588154 42 + 601863 GATAATCTCAGTAAGTTCAGCCCCTT-TCTGCTATCCACTTGA -s simRat_chr6.simRat.chr6 633237 42 + 647215 GATAGGCTCGTCAGGATCAGCCTCCT-TCTGGTATCAATTTGA - -a -s simMouse_chr6.simMouse.chr6 621477 5 + 636262 TACTG -s Anc0.Anc0refChr3 216271 5 + 222631 CAGTG -s Anc1.Anc1refChr1 56598 5 + 69767 CAGTG -s Anc2.Anc2refChr1 133846 5 + 142988 CAGTG -s mr.mrrefChr3 168484 5 + 181027 TACTG -s simDog_chr6.simDog.chr6 584471 5 + 593897 CAGTG -s simHuman_chr6.simHuman.chr6 588196 5 + 601863 CAGTG -s simRat_chr6.simRat.chr6 633279 5 + 647215 TACCA - -a -s simMouse_chr6.simMouse.chr6 621482 20 + 636262 TGATCTTCATCTGTGTGAAC -s Anc0.Anc0refChr3 216276 20 + 222631 TGATCTTTACATATGCACAC -s Anc1.Anc1refChr1 56603 20 + 69767 TGATCTTTACATATGCACAC -s Anc2.Anc2refChr1 133851 20 + 142988 TGATCTTTACATATGCACGC -s mr.mrrefChr3 168489 20 + 181027 TGATCTTCATCTGTGTGAAC -s simCow_chr6.simCow.chr6 592353 15 + 602619 -----TTCATATATAGACCC -s simDog_chr6.simDog.chr6 584500 20 + 593897 TGATCTTTACACATGCATGC -s simHuman_chr6.simHuman.chr6 588201 20 + 601863 TGATCTTGACATATGCACAC -s simRat_chr6.simRat.chr6 633284 20 + 647215 TGATCTTCTTTTGTGTGAAA - -a -s simMouse_chr6.simMouse.chr6 621502 90 + 636262 TCATGACTTTAACGATGAAGATTATAGCCTTGAAAAATGCAGCCTGTTGAATGTTTTGGCATTTGGCATTTTTAACACTGGCTTTCCACT -s Anc0.Anc0refChr3 216296 80 + 222631 TCATAACTTTAAAAATGAAAATTGAGGCC---ACATTTGCCTGCTGTTGAATGTTTTATCATT-------TCTACTACTGGCCTTACATT -s Anc1.Anc1refChr1 56623 80 + 69767 TCATAACTTTAAAAATGAAAATTGAGGCC---ACATTTGCCTGCTGTTGAATGTTTTATCATT-------TCTACTACTGGCCTTACATT -s Anc2.Anc2refChr1 133875 80 + 142988 TCATAACTTCAAAAATGAAAATTGAGGCC---ACATTTGCCTGCTGTTGAATGTTTTATCATT-------TCCACTACTGGCCTTACATT -s mr.mrrefChr3 168509 83 + 181027 TCATGACTTTAACAATGAAGATTATAGCCTTGAAAAATGCATCCTGTTGAATGTTTTGGCATT-------TTTAACACTGGCTTTCCATT -s simCow_chr6.simCow.chr6 592372 80 + 602619 TCCTAACTTGAGAAATGAAAATTAAGGCA---GCTATTGCCTCCTGTTGAATGCCTTCTAGTT-------TCCACTACCTGCCTTGCATT -s simDog_chr6.simDog.chr6 584524 80 + 593897 TCATAACCTCAAAAATGAAGCTTGAGGCC---ATATTTCTCTGGTGTTGGATATTTTAACATT-------TCCACTACTGGCCTTACATT -s simHuman_chr6.simHuman.chr6 588221 77 + 601863 ---CAACTTTAAAAATGCAAATCTAGGCC---ACATTTGCCTACTGTTGAAGGTTTTATCATT-------TCTACGGCTGGCCTTTGATT -s simRat_chr6.simRat.chr6 633304 83 + 647215 TCATGACTTTAACAAAGAAGATTACATCCTTGAAAAATGCATCCTGCTGAATGTTTTGGGATT-------TTTAACACTGGCTTCCCATC - -a -s simMouse_chr6.simMouse.chr6 621592 18 + 636262 GTAACACCCTTTTTCTCA -s Anc0.Anc0refChr3 216376 16 + 222631 GGAACA--TTCTTTTCCA -s Anc1.Anc1refChr1 56703 18 + 69767 GGAACACCTTCTTTTCCA -s Anc2.Anc2refChr1 133955 16 + 142988 TGAACA--GTCTTTTCCA -s mr.mrrefChr3 168592 18 + 181027 GTAACACCCTCTTTCCCA -s simCow_chr6.simCow.chr6 592463 16 + 602619 TTAAAA--CTCTTTTCAC -s simDog_chr6.simDog.chr6 584604 16 + 593897 TGAACA--GTCTTTTCCA -s simHuman_chr6.simHuman.chr6 588298 18 + 601863 GAAACACCTCCTTTTCCA -s simRat_chr6.simRat.chr6 633387 18 + 647215 ATAACACACTCCTTCCCA - -a -s simMouse_chr6.simMouse.chr6 621610 30 + 636262 ACAATTTTAATACTGCTGTCTGGCTAGATT -s Anc0.Anc0refChr3 216392 27 + 222631 ACTTTATTACTGCCACT---TGGCTAGGTA -s Anc1.Anc1refChr1 56721 27 + 69767 ACTTTATTACTGCCACT---TGGCTAGGTA -s Anc2.Anc2refChr1 133971 27 + 142988 ATTTTATTACTGCCACT---TGGCTAGGTA -s mr.mrrefChr3 168610 30 + 181027 ACAATTTTAATACTGCTGTCTGGCTAGATT -s simCow_chr6.simCow.chr6 592479 27 + 602619 AACTTTTTACTCCCCCT---TGGCTAGGTA -s simDog_chr6.simDog.chr6 584623 27 + 593897 ATTTTAGTACTGCCACC---TGGCTAGACA -s simHuman_chr6.simHuman.chr6 588316 27 + 601863 ACTTTCTTAGTGCAACT---GGGCTAGGTA -s simRat_chr6.simRat.chr6 633405 29 + 647215 ACAATTCTAATACTG-TGTCTAGCTAGATT - -a -s simMouse_chr6.simMouse.chr6 621640 23 + 636262 GACTGTCTTGCTTAAAGTGCTTG -s Anc0.Anc0refChr3 216419 23 + 222631 AACTGTCTAGCCTAATTCTCCAG -s Anc1.Anc1refChr1 56748 23 + 69767 AACTGTCTAGCCTAATTCTCCAG -s Anc2.Anc2refChr1 133998 23 + 142988 AACTGTCTAGCCTAATTCTCCAG -s mr.mrrefChr3 168640 23 + 181027 AACTGTCTTGCTTAATGTGCTTG -s simCow_chr6.simCow.chr6 592563 23 + 602619 AACTGTCTTGGTTAATCTTCTAG -s simDog_chr6.simDog.chr6 584650 23 + 593897 AACAGACTAGCCTTAATCTCCAA -s simHuman_chr6.simHuman.chr6 588343 23 + 601863 AACTGTCTAGCGAAATTGTCCAG -s simRat_chr6.simRat.chr6 633434 23 + 647215 AACTGTCTTGCTTAATGTGCTTG - -a -s simMouse_chr6.simMouse.chr6 621663 14 + 636262 ACTGAGAGTACTCA -s Anc0.Anc0refChr3 216442 14 + 222631 CCTGTGAGTACTTG -s Anc1.Anc1refChr1 56771 14 + 69767 CCTGTGAGTACTTG -s Anc2.Anc2refChr1 134021 14 + 142988 CCTGTGAGCACTTG -s mr.mrrefChr3 168663 14 + 181027 ACTGAGAGTACTCA -s simCow_chr6.simCow.chr6 592586 14 + 602619 GCTGTGAGCACTTG -s simDog_chr6.simDog.chr6 584674 14 + 593897 CCTGTAAGCACTTG -s simHuman_chr6.simHuman.chr6 588366 14 + 601863 CCTGTGAGTGCTGG -s simRat_chr6.simRat.chr6 633457 14 + 647215 ATTGAGAGTACACA - -a -s simMouse_chr6.simMouse.chr6 621677 56 + 636262 AGTTGAACCAGACTCACCTTTTAGTTTCAATTCACTAGTCCGTATCATATTCACTA -s Anc0.Anc0refChr3 216456 56 + 222631 AATGAAACTAGACTTACCCTTTATTTTCAATTCAGTAGTCTGTATCATGTTCACTA -s Anc1.Anc1refChr1 56785 56 + 69767 AATGAAACTAGACTTACCCTTTATTTTCAATTCAGTAGTCTGTATCATGTTCACTA -s Anc2.Anc2refChr1 134035 56 + 142988 AATGAAACTGGACTTCCCCTTTATTTTAAATTCAGTAGTCTGAATCATATTCATCA -s mr.mrrefChr3 168677 56 + 181027 AGTTGAACTAGACTCACCTTTTAGTTTCAATTCACTAGTCTGTATCATGTTCACTA -s simCow_chr6.simCow.chr6 592600 54 + 602619 AATGA-CCTGGACTTGCCCTTTATTT-AAATTCAGTAGTCTGAATTATATTTTACA -s simDog_chr6.simDog.chr6 584688 48 + 593897 AATGAAAGCGGATTTCCCTTTTATTTTAAAT--------CTGAATCATATCCATCA -s simHuman_chr6.simHuman.chr6 588380 56 + 601863 AATGAGACTAGCCTTACCCTTTATTTTCAATTCATTAAGCTGTATCATGTTCACTA -s simRat_chr6.simRat.chr6 633473 56 + 647215 ATTCGAGCTGGAATCACCTCTTAATTTCAATTCACTAGCCTGTATCATGTTCACTA - -a -s simMouse_chr6.simMouse.chr6 621733 53 + 636262 CTCCACAGGCTACCCTACTCAGTTTGTTACCTTTTGTTTGCTAGTAGGCTCAT -s Anc0.Anc0refChr3 216526 44 + 222631 CC---------AGTGTACTCAATTTGTTACTTTTAGTTTGTTATGCGGTTGAT -s Anc1.Anc1refChr1 56855 44 + 69767 CC---------AGTGTACTCAATTTGTTACTTTTAGTTTGTTATGCGGTTGAT -s Anc2.Anc2refChr1 134105 44 + 142988 CC---------AGTGTACTCAATTTGTTATTTTTAGTTTGTTATGCGGTTAAT -s mr.mrrefChr3 168733 44 + 181027 CC---------AGTCTACTCAGTTTGTTACCTTTTGTTTGCTAGTAGGCTGAT -s simCow_chr6.simCow.chr6 592668 44 + 602619 CC---------AGTGTAGTCAATTTGTTCTTCTTAGTTTGTAATTGGCTTCAG -s simDog_chr6.simDog.chr6 584750 44 + 593897 CT---------ATTGTACTCAATTTGTTATTTGTAGTTGGTTATGCGGTTAAT -s simHuman_chr6.simHuman.chr6 588450 38 + 601863 CC---------AGTGTGCTCAATTTGTTACTTTTAGTTTG------GATTGAT -s simRat_chr6.simRat.chr6 633529 44 + 647215 CC---------AGTCTACTCAGTTTGTTACCTGTGGTTCGCTAGTAGGCTGAT - -a -s simMouse_chr6.simMouse.chr6 621786 22 + 636262 CTATTTCAGCCAATATTTTACA -s Anc0.Anc0refChr3 216570 22 + 222631 CTATTAGAGGCACTTTTGTACA -s Anc1.Anc1refChr1 56899 22 + 69767 CTATTAGAGGCACTTTTGTACA -s Anc2.Anc2refChr1 134151 22 + 142988 CTGTTAGAGGCACTTTTGTACT -s mr.mrrefChr3 168777 22 + 181027 CTATTTGAGCCAATATTTTACA -s simCow_chr6.simCow.chr6 592714 22 + 602619 CTGTGGGAGTCTCTTGTGTACT -s simDog_chr6.simDog.chr6 584796 16 + 593897 CTGTTAGAAGCAATCT------ -s simHuman_chr6.simHuman.chr6 588488 22 + 601863 CTATTAGAGGCACTTTTGTACA -s simRat_chr6.simRat.chr6 633573 22 + 647215 CCACTTGAGCCAATATTTTACA - -a -s simMouse_chr6.simMouse.chr6 621808 24 + 636262 ACACAGAGATGGGCCTTTGTAGAC -s Anc0.Anc0refChr3 216592 24 + 222631 TCAAAGAGATGGGCCTACATTGAC -s Anc1.Anc1refChr1 56921 24 + 69767 TCAAAGAGATGGGCCTACATTGAC -s Anc2.Anc2refChr1 134173 24 + 142988 TTAAAGAGATGGACCTACATTGAC -s mr.mrrefChr3 168799 24 + 181027 ACACAGAGATGGGCCTTCATAGAC -s simCow_chr6.simCow.chr6 592736 24 + 602619 TTAAAGAGATGGAGCTATATTGAC -s simDog_chr6.simDog.chr6 584812 22 + 593897 --GTACAGATGGACCAACATTGGC -s simHuman_chr6.simHuman.chr6 588517 24 + 601863 GCAAGGGGATGGGCCTGCAATGAC -s simRat_chr6.simRat.chr6 633595 24 + 647215 ACACAGAGATGCGCCTTCATAAGC - -a -s simMouse_chr6.simMouse.chr6 621832 75 + 636262 TTTTGTACGCTCTCCAAGCATTTTATGAGCCTAACAGAATTTGGCCCTTTATGGGTCAACATCTTGCATTCTTGA -s Anc0.Anc0refChr3 216617 71 + 222631 TTTTGTACCCTGTCCAAGAATTCTGTGAGATGAGCAGGATTCAGCCTTTTATGG---AACATCCTACATCC-TGA -s Anc1.Anc1refChr1 56946 74 + 69767 TTTTGTACCCTGTCCAAGAATTCTGTGAGATGAGCAGGATTCAGCCTTTTATGGTTAAACATCCTACATCC-TGA -s Anc2.Anc2refChr1 134198 71 + 142988 TTTTGTACCCTGTCCCTGAATTCTGTGAGATGAGCAGGATTTAGCCTTTTATCG---AACATCCTACATTC-TTA -s mr.mrrefChr3 168823 75 + 181027 TTTTGTACGCTGTCCAAGCATTCTATGAGCCTAACAGAATTCAGCCCTTTATGGTTCAACATCTTGCATCCTTGA -s simCow_chr6.simCow.chr6 592761 71 + 602619 TCCAGTACCCTTTCCTGGAACTCTCTGATATGAGCAGGATCTAGTATTTTACAG---TGCACCCTGCATTC-CTA -s simDog_chr6.simDog.chr6 584835 71 + 593897 TTTTGTACCCTGTCCCTGAATTCCGTGAGATGAGCAGGCTTTTGCCTTTGATCG---AACATCCTACACTG-TTA -s simHuman_chr6.simHuman.chr6 588542 74 + 601863 TTTTGTGCCTTGTCCAAGAATTCTGCTTAAGGAGCAGGATTCAGCCTTTTATGGTTAAACATCCTACATCC-TGA -s simRat_chr6.simRat.chr6 633619 71 + 647215 TTTTGTAAGCTGTCTAAACATCCTATGGGCCTAACAAAATTCAGTCCTTT----TTCAACATCTTGCATCCTTGA - -a -s simMouse_chr6.simMouse.chr6 621907 21 + 636262 GACCTCGGAATTCCCGGTTGA -s Anc0.Anc0refChr3 216700 21 + 222631 AACCTTGGAATTCCCGGTTGA -s Anc1.Anc1refChr1 57032 21 + 69767 AACCTTGGAATTCCCGGTTGA -s Anc2.Anc2refChr1 134281 21 + 142988 AACCTTGGAATTCCCGGTTGA -s mr.mrrefChr3 168898 21 + 181027 AACCTTGGAATTCCCGGTTGA -s simCow_chr6.simCow.chr6 592844 21 + 602619 AGCTTTAGAATTCCCGGCTGA -s simDog_chr6.simDog.chr6 584918 21 + 593897 AACCTTGGAAATACCGGTTGA -s simHuman_chr6.simHuman.chr6 588628 21 + 601863 AATCTTGGAATTCTCGGTTGA -s simRat_chr6.simRat.chr6 633690 21 + 647215 AACCTTGGAATTCCCAGTTAA - -a -s simMouse_chr6.simMouse.chr6 621928 4 + 636262 GCAA -s Anc0.Anc0refChr3 216724 4 + 222631 AAAG -s Anc1.Anc1refChr1 57056 4 + 69767 AAAG -s Anc2.Anc2refChr1 134305 4 + 142988 AAAG -s mr.mrrefChr3 168919 4 + 181027 GCAA -s simCow_chr6.simCow.chr6 592868 4 + 602619 AAAG -s simDog_chr6.simDog.chr6 584942 4 + 593897 AAAG -s simHuman_chr6.simHuman.chr6 588652 4 + 601863 AAAG -s simRat_chr6.simRat.chr6 633711 4 + 647215 GCAT - -a -s simMouse_chr6.simMouse.chr6 621932 10 + 636262 TTGAAACTTA -s Anc0.Anc0refChr3 216728 10 + 222631 ATGAAGCTTA -s Anc1.Anc1refChr1 57060 10 + 69767 ATGAAGCTTA -s Anc2.Anc2refChr1 134309 10 + 142988 ATGAAGCATA -s mr.mrrefChr3 168923 10 + 181027 ATGAAACTTA -s simCow_chr6.simCow.chr6 592873 10 + 602619 ACAAAGCCCA -s simDog_chr6.simDog.chr6 584946 10 + 593897 CTGAAGCATA -s simHuman_chr6.simHuman.chr6 588656 10 + 601863 ATGAAGCTTA -s simRat_chr6.simRat.chr6 633715 10 + 647215 ACGAAACTTG - -a -s simMouse_chr6.simMouse.chr6 621942 123 + 636262 CAGCAAAGCTAAAGCTTTAGCAGATAAAGGACACTGCAACCCTCAGTCAAGGAGTGTGGTTCCACAGCACACCATTGAGGATAAGCATTGATGGTTCCAAGTTTAGAGGACATGAAGAATTTG -s Anc0.Anc0refChr3 216739 114 + 222631 TAGCAAAGAT------TTGGCTTATAAAGGGTGTTGCAACTCTCTGCCCAGGGACTTGGTTTCATGGCACAAGATTGTGGTTTACCTTTGACGGTTCCAACTTTAGAGGACAT---TAACTTG -s Anc1.Anc1refChr1 57071 114 + 69767 TAGCAAAGAT------TTGGCTTATAAAGGGTGTTGCAACTCTCTGCCCAGGGACTTGGTTTCATGGCACAAGATTGTGGTTTACCTTTGACGGTTCCAACTTTAGAGGACAT---TAACTTG -s Anc2.Anc2refChr1 134320 114 + 142988 TAGCATAGAT------TTGGCTTATAAAGGTTGTTGCAACTCTCTGCCCAGGGACTTTCTTTCATGGCACAAGATTGTGGTTTACCTTTGACGGTTCCAACTTTAGAGGACAT---TAACTTG -s mr.mrrefChr3 168934 117 + 181027 CAGCAAAGCT------TTAGCAGATAAAGGGCACTGCAACCCTCAGTCAAGGAGCTTGGTTCCACAGCACACCATTGAGGATAACCATTGATGGTTCCAAGTTTAGAGGACATGAAGAATTTG -s simCow_chr6.simCow.chr6 592884 113 + 602619 TAGCATAGAT------TTGGCTTATAAAGGTTGTCGCAACTCTATACTCAGGAACTTT-TTTCATGGCACAAGATTATGTTCTACCTTTGATGGTTTCAACTTTAGAAGACAT---TAATTTG -s simDog_chr6.simDog.chr6 584957 114 + 593897 TAGCATAGAT------TTGGCTAATAAAGTTTGTTGCAACTCACTGTCTAGGGACCTTCTCTCATGGCACAAGATTGTGGTTTACCTTTGACAGATCCAACTTTAGAGGACAT---TAACCTA -s simHuman_chr6.simHuman.chr6 588667 114 + 601863 TAGCAAAGAT------TTGGCCTATAAAGGGTGTTACAACTGTCTGCCCAGGTACTTGGTTTCATGGTATGGGATTGTGGTTTACCCTTTACGGTTCCAGCTTTGGAGGACAT---TAACTTG -s simRat_chr6.simRat.chr6 633726 117 + 647215 CAGCAAAGTT------GTAGCAGATAAAGGGCACTGCAACCCTAGGACAAAGACCTCGGTTCCACAGCACACCATTGAAGGTAACTTTTGATGGTTCCCAATTTAAAGGACATGAAGAATTTT - -a -s simMouse_chr6.simMouse.chr6 622065 24 + 636262 GATCTCAAGGCCTAGTGACCTATT -s Anc0.Anc0refChr3 216853 24 + 222631 GATCTCAGGGCCTAGTGACCTATT -s Anc1.Anc1refChr1 57185 24 + 69767 GATCTCAGGGCCTAGTGACCTATT -s Anc2.Anc2refChr1 134434 24 + 142988 GATCTCAGGGCCTAGTGACCTATT -s mr.mrrefChr3 169051 24 + 181027 GATCTCAAGGCCTAGTGACCTATT -s simCow_chr6.simCow.chr6 592997 24 + 602619 GATCTCAGGGCCTAGTGACCTATT -s simHuman_chr6.simHuman.chr6 588781 24 + 601863 GATTACAGGGCCTAGTGACCTACT -s simRat_chr6.simRat.chr6 633844 22 + 647215 GGTCTCAAGGCC--GTGACCTATT - -a -s simMouse_chr6.simMouse.chr6 622089 35 + 636262 TATCTAAGTTCTTTCGTACTAATTTACTGACCGTA -s Anc0.Anc0refChr3 216877 28 + 222631 TATCTAAGTTCTT-------AATTTACTGAACATA -s Anc1.Anc1refChr1 57209 35 + 69767 TATCTAAGTTCTTCTTTACTAATTTACTGAACATA -s Anc2.Anc2refChr1 134458 28 + 142988 TATCTAAGTTCTT-------GATTTAAAGAACAGT -s mr.mrrefChr3 169075 35 + 181027 TATCTAAGTTCTTTCGTACTAATTTACTGACCATA -s simCow_chr6.simCow.chr6 593021 28 + 602619 TATCTAAGTTCTT-------GATTTAAAGAACAGT -s simHuman_chr6.simHuman.chr6 588805 35 + 601863 TATCTAAGTGCTTCTTTACTAATTTACTGAACATA -s simRat_chr6.simRat.chr6 633871 35 + 647215 TATCTAAGTTCTTTCATACTAATTTACTGACCACA - -a -s simMouse_chr6.simMouse.chr6 622124 15 + 636262 TTGCCCTTAATCAGT -s Anc0.Anc0refChr3 216962 15 + 222631 TTGCTCTTATTCAGT -s Anc1.Anc1refChr1 57301 15 + 69767 TTGCTCTTATTCAGT -s Anc2.Anc2refChr1 134543 15 + 142988 TTGCTCTTATTCAGT -s mr.mrrefChr3 169164 15 + 181027 TTGCCCTTATTCAGT -s simCow_chr6.simCow.chr6 593106 15 + 602619 TTACTCTTATTCAGT -s simDog_chr6.simDog.chr6 585096 15 + 593897 TTGATTTTACTCAGT -s simHuman_chr6.simHuman.chr6 588897 15 + 601863 TTGCTCTTGTCCAGC -s simRat_chr6.simRat.chr6 633971 15 + 647215 TTACCCTTATTCAGT - -a -s simMouse_chr6.simMouse.chr6 622139 14 + 636262 CCCAAGGGTGTTAA -s Anc0.Anc0refChr3 216977 3 + 222631 CCA----------- -s Anc1.Anc1refChr1 57316 3 + 69767 CCA----------- -s Anc2.Anc2refChr1 134577 3 + 142988 CCA----------- -s mr.mrrefChr3 169179 14 + 181027 CCCAAGGGTGTTAA -s simCow_chr6.simCow.chr6 593160 3 + 602619 CCA----------- -s simDog_chr6.simDog.chr6 585130 3 + 593897 CAA----------- -s simHuman_chr6.simHuman.chr6 588912 3 + 601863 TCA----------- -s simRat_chr6.simRat.chr6 633986 14 + 647215 TTCATGGGCCTTCA - -a -s simMouse_chr6.simMouse.chr6 622153 42 + 636262 CCCAACCTAGTGAGGAATGATTCCTAGAATAATATGACTTGC -s Anc0.Anc0refChr3 216980 2 + 222631 ----------------------------------------GC -s Anc1.Anc1refChr1 57319 2 + 69767 ----------------------------------------GC -s Anc2.Anc2refChr1 134580 2 + 142988 ----------------------------------------GC -s mr.mrrefChr3 169193 42 + 181027 CCCAACCTAGTGAGGAATGATTCCTAGAATAATATGACTTGC -s simCow_chr6.simCow.chr6 593163 2 + 602619 ----------------------------------------GC -s simDog_chr6.simDog.chr6 585133 2 + 593897 ----------------------------------------GC -s simHuman_chr6.simHuman.chr6 588915 2 + 601863 ----------------------------------------GC -s simRat_chr6.simRat.chr6 634025 42 + 647215 ACCAAACTAGTGAGGAATGATTCCTATAATAATATGACTTGC - -a -s simMouse_chr6.simMouse.chr6 622195 42 + 636262 ATGCTTGAGCATTGTAAAGTTGAGAAGTGAGTAGGCTTTAGG -s Anc0.Anc0refChr3 216984 41 + 222631 GTTCGTG-GTTTTGTAAATTTCAGAAGTGAATAAGCTTTCAG -s Anc1.Anc1refChr1 57323 41 + 69767 GTTCGTG-GTTTTGTAAATTTCAGAAGTGAATAAGCTTTCAG -s Anc2.Anc2refChr1 134584 41 + 142988 GTTAGGG-GTTTTGTAAATCTCAGAAGTGAATGAGCTTTCTG -s mr.mrrefChr3 169235 42 + 181027 ATGCTTGAGCATTGTAAAGTTGAGAAGTGAATAGGCTTTAAG -s simCow_chr6.simCow.chr6 593167 41 + 602619 GTGAGGG-ATGGTGTATATCTCAGATATAAATGAACCTTTTG -s simDog_chr6.simDog.chr6 585137 41 + 593897 GTTAGGG-GTTTTGTAAATCTCAGAAGTGAATGAGCTTTCTG -s simHuman_chr6.simHuman.chr6 588919 41 + 601863 GTTCCTG-GTTTTGTAAATTTCAGAAGTGAACAAGCTTTCAG -s simRat_chr6.simRat.chr6 634072 32 + 647215 AAGCTTGAGCATCGTAAAG----------AATAGGGTTTAAG - -a -s simMouse_chr6.simMouse.chr6 622237 35 + 636262 AGACAAAATACTCAAAGAGAGAAGAAACAATGCCC -s Anc0.Anc0refChr3 217025 33 + 222631 AGACAAAATAGTCAAG--GAGAAGATGCATTGCTA -s Anc1.Anc1refChr1 57364 33 + 69767 AGACAAAATAGTCAAG--GAGAAGATGCATTGCTA -s Anc2.Anc2refChr1 134625 33 + 142988 AAGCAAAATAGCCAAG--AAGAGGATGCATTGCTA -s mr.mrrefChr3 169277 35 + 181027 AGACAAAATACTCAAAGAGAGAAGAAACAATGCCC -s simCow_chr6.simCow.chr6 593209 33 + 602619 TAGCAAAATAGCCAAG--AAGGGGATACATTGCTA -s simDog_chr6.simDog.chr6 585178 33 + 593897 AAGCCAAATAGCCAAG--AAGAGATTGCATTGCTA -s simHuman_chr6.simHuman.chr6 588960 33 + 601863 AGACAAAATAGTCAAG--GAGAAGATGCATTGCTA -s simRat_chr6.simRat.chr6 634104 35 + 647215 AGGCAAAATACTCAAAGAGAGAATAAACAATGCCC - -a -s simMouse_chr6.simMouse.chr6 622272 63 + 636262 AATGACTGCGACCAACACTATCTGCCCTTTGACTCAAACAGGGAAGATCAATGAGAAAAGATG -s Anc0.Anc0refChr3 217059 24 + 222631 AATGACTCCTACTAACACTAACTG--------------------------------------- -s Anc1.Anc1refChr1 57398 24 + 69767 AATGACTCCTACTAACACTAACTG--------------------------------------- -s Anc2.Anc2refChr1 134659 24 + 142988 AATGCCTCCTACTAACGCTAACTG--------------------------------------- -s mr.mrrefChr3 169313 62 + 181027 AATGACTGCGACTAACACTATCTGCCCTTTGACTCAAACAGGGAAGATCAA-GAGAAAAGATG -s simCow_chr6.simCow.chr6 593242 21 + 602619 AATCCTTCCTACTA---ATAAATG--------------------------------------- -s simDog_chr6.simDog.chr6 585212 18 + 593897 AATGCCT------AACGCTAACTG--------------------------------------- -s simHuman_chr6.simHuman.chr6 588994 24 + 601863 AATGACTCCTACTAACACTAAGTG--------------------------------------- -s simRat_chr6.simRat.chr6 634140 62 + 647215 AATGCCTGTGACTAACAGTATCTCCCCTTTGACTCAAAGGGTGAAGATCAA-GAGAGAAGATG - -a -s simMouse_chr6.simMouse.chr6 622633 69 + 636262 CTATCTCCCCTTTGAGTAATTGCTGGCTGCAGCCCTTGTGTATCACATCTGACTTTACTTTGAATTCCT -s Anc0.Anc0refChr3 217083 56 + 222631 -------CCCTTTGAGTAAATGCTACCTGCAGGGCAGGTATACTA------GATTTATTTTTGTTTCAT -s Anc1.Anc1refChr1 57422 58 + 69767 -------CCCTTTGAGTAAATGCTACCTGCAGGGCAGGTATACTACA----GATTTATTTTTGTTTCAT -s Anc2.Anc2refChr1 134683 56 + 142988 -------CCCTTTGAGTGAATGCTACCTGCAGGGCAGGTATACTA------GATTCATTTTTGTTTTAG -s mr.mrrefChr3 169375 69 + 181027 CTATCTCCCCTTTGAGTAATTGCTAGCTGCAGCCCTTGTGTACCACATCTGACTTTACTTTGAATTCAT -s simCow_chr6.simCow.chr6 593263 55 + 602619 -------CCCCTTGAGT-AATGTTACATGGATGGCAGGTCTACGC------GAGTCATTGTTAATTTAG -s simDog_chr6.simDog.chr6 585230 55 + 593897 -------CCTTT-GAATGAATGCTGCCTGCAGGGCAGGTACACTA------GATCCATTTTGGTTTTAG -s simHuman_chr6.simHuman.chr6 589018 58 + 601863 -------CTCTTTGAGCACATGGTACCTGTAGGGCAGGTATACTACA----GTTTTGTTTTTGGCTCAT -s simRat_chr6.simRat.chr6 634233 69 + 647215 ATATCTCCCCTTTGACTAATTGCTAGCTGCAACCATAGTGTACCACATCTTACTTTAATTTGAATTCAT - -a -s simMouse_chr6.simMouse.chr6 622702 13 + 636262 ACAACCAGGTTAA -s Anc0.Anc0refChr3 217139 13 + 222631 ACAGTCAGATTAA -s Anc1.Anc1refChr1 57480 13 + 69767 ACAGTCAGATTAA -s Anc2.Anc2refChr1 134739 13 + 142988 ACAGTCAAATTAA -s mr.mrrefChr3 169444 13 + 181027 ACAACCAGGTTAA -s simCow_chr6.simCow.chr6 593320 13 + 602619 AGAGTCAAATTGC -s simDog_chr6.simDog.chr6 585285 13 + 593897 ACAGACTAATTAA -s simHuman_chr6.simHuman.chr6 589076 13 + 601863 ACAGTCAGATTAA -s simRat_chr6.simRat.chr6 634302 13 + 647215 ACAACCAGGTTAA - -a -s simMouse_chr6.simMouse.chr6 622715 52 + 636262 TGTGGCCATAGATAGTAAAGGTAGTGTGCTGTCAGATCACTTATGCTCCATT -s Anc0.Anc0refChr3 217153 52 + 222631 TGTGTCCATGGACAGTTGAGGTAGTGTTCTGTCAGACCACTTATGTTCTATT -s Anc1.Anc1refChr1 57494 52 + 69767 TGTGTCCATGGACAGTTGAGGTAGTGTTCTGTCAGACCACTTATGTTCTATT -s Anc2.Anc2refChr1 134753 52 + 142988 TATGTCTGTGGACAGTTGAGGTAGTGTTTTGTCAGACCACTCATGTTCTATT -s mr.mrrefChr3 169457 52 + 181027 TGTGGCCATAGATAGTAAAGGTAGTGTGCTGTCAGATCACTTATGCTCCATT -s simCow_chr6.simCow.chr6 593334 52 + 602619 TATGTCTGTGGACAGCTAACATAGTGTTTTGTTGGGCTACTCATATTCCATT -s simDog_chr6.simDog.chr6 585299 51 + 593897 C-TGTCTGTGGACAGTTGAGGTAATGGTTTATCAGACCACTCATGTTCTGTA -s simHuman_chr6.simHuman.chr6 589090 52 + 601863 TGTGTCCATTGACAGTTGGGGTAGTTTTCTGTCAGACCTTCTATGTTCTATT -s simRat_chr6.simRat.chr6 634315 52 + 647215 TGTGGCCATAGATAGCAAAGGTGGTGTGCTGTCAGATCACTTGTGCTCCATT - -a -s simMouse_chr6.simMouse.chr6 622767 11 + 636262 GTCTTTATTCA -s Anc0.Anc0refChr3 217205 11 + 222631 GTTTTTGTTCA -s Anc1.Anc1refChr1 57546 11 + 69767 GTTTTTGTTCA -s Anc2.Anc2refChr1 134805 11 + 142988 GTTCTTGTTCA -s mr.mrrefChr3 169509 11 + 181027 GTCTTTATTCA -s simCow_chr6.simCow.chr6 593386 11 + 602619 GTCCGTGTTCA -s simDog_chr6.simDog.chr6 585380 11 + 593897 GTTCTAGCTCA -s simHuman_chr6.simHuman.chr6 589142 11 + 601863 GTTTTTGTTTG -s simRat_chr6.simRat.chr6 634367 11 + 647215 ATCTTTATTCA - -a -s simMouse_chr6.simMouse.chr6 622778 17 + 636262 GGACCATGCCAACTAGA -s Anc0.Anc0refChr3 217216 17 + 222631 TGGCCATGCCAGCTATA -s Anc1.Anc1refChr1 57557 17 + 69767 TGGCCATGCCAGCTATA -s Anc2.Anc2refChr1 134816 17 + 142988 TGGCCACGCCAGCTATA -s mr.mrrefChr3 169520 17 + 181027 GGACCATGCCAACTAGA -s simCow_chr6.simCow.chr6 593397 17 + 602619 TGGCCACGCCAGCTATA -s simDog_chr6.simDog.chr6 585412 17 + 593897 TGGTTGCAGCGCCTATC -s simHuman_chr6.simHuman.chr6 589153 17 + 601863 TGGCCATGCCAGCTATA -s simRat_chr6.simRat.chr6 634378 17 + 647215 GGACCATGCCAACTAGA - -a -s simMouse_chr6.simMouse.chr6 622795 59 + 636262 TCCCATGGCAATGTATTAAACCAATACCTACCATGGGTAGGCATAAACTGTACCACCTG -s Anc0.Anc0refChr3 217233 58 + 222631 T-TTGTGGCAGTATATTAAGCCCACATCTACGAAGGGTAAGTGTAATTTGTATCACCTT -s Anc1.Anc1refChr1 57574 58 + 69767 T-TTGTGGCAGTATATTAAGCCCACATCTACGAAGGGTAAGTGTAATTTGTATCACCTT -s Anc2.Anc2refChr1 134833 58 + 142988 T-TTGTAGCAGTATATTAAGCCCACATCTATGTAGGGTAAGTGTAATTTGTACTACCTT -s mr.mrrefChr3 169537 59 + 181027 TCCCATGGCAATGTATTAAGCCAATACCTACCATGGGTAGGCATAAACTGTATCACCTG -s simCow_chr6.simCow.chr6 593414 58 + 602619 A-TTGTAGCAGCATATTGAGCCCATATCTAGCCAGGGTAAGTGGAATTGATTCTACCTT -s simDog_chr6.simDog.chr6 585436 58 + 593897 T-CTGCAGCAGTAAATTAAGCTGACATTTATGTAAGGTAAGTATAATTTGTACTTCCTT -s simHuman_chr6.simHuman.chr6 589170 56 + 601863 T-TTGTGGTAGTATATTAAGCCCACATCTACTAAGGCTAAGTGTGATTTGTATCATC-- -s simRat_chr6.simRat.chr6 634395 59 + 647215 ACCCATGGATATGTAATAAGCCGATACTTACCATGGATAGGCATAGACTGTCTCACTCA - -a -s simMouse_chr6.simMouse.chr6 622854 7 + 636262 TAGGATA -s Anc0.Anc0refChr3 217291 7 + 222631 AGGGATG -s Anc1.Anc1refChr1 57632 7 + 69767 AGGGATG -s Anc2.Anc2refChr1 134891 7 + 142988 AGGGATG -s mr.mrrefChr3 169596 7 + 181027 TAGGATA -s simCow_chr6.simCow.chr6 593472 7 + 602619 GGGGATG -s simDog_chr6.simDog.chr6 585495 7 + 593897 AGAGATG -s simRat_chr6.simRat.chr6 634454 7 + 647215 TGGGATT - -a -s simMouse_chr6.simMouse.chr6 622861 21 + 636262 GATGGGGTGACAACTATGAAC -s Anc0.Anc0refChr3 217298 21 + 222631 GATGGGATGACAATTATGCAT -s Anc1.Anc1refChr1 57639 21 + 69767 GATGGGATGACAATTATGCAT -s Anc2.Anc2refChr1 134913 21 + 142988 GATGGGATGAGAATTATGCAT -s mr.mrrefChr3 169603 21 + 181027 GATGGGGTGACAACTATGAAC -s simCow_chr6.simCow.chr6 593494 21 + 602619 GATGTGATGAGAATTATGCAT -s simDog_chr6.simDog.chr6 585529 16 + 593897 GATGGGATGAGAATTA----- -s simHuman_chr6.simHuman.chr6 589226 19 + 601863 --TGGGATGACAATCATGCAT -s simRat_chr6.simRat.chr6 634461 21 + 647215 GGTGAGGTGACAACTGTGAAC - -a -s simMouse_chr6.simMouse.chr6 622882 68 + 636262 CTCCATATTAAGCCCAAATAAAGATATATTATATCAAGAACACAGACCACCAAAATTAGCATGCGCCT -s Anc0.Anc0refChr3 217319 66 + 222631 CCCCATGCTCAGCCCAAATAAAGATACAC--TAACAAGAACACAGACTACTGAAATTAGCACTCACTT -s Anc1.Anc1refChr1 57660 68 + 69767 CCCCATGCTCAGCCCAAATAAAGATACACAATAACAAGAACACAGACTACTGAAATTAGCACTCACTT -s Anc2.Anc2refChr1 134934 66 + 142988 TCCCATGCTCAGCCCAAATAAAGATACAC--TAATAAGAACACAGACTACTGAAATTAGCACTCACTT -s mr.mrrefChr3 169624 68 + 181027 CTCCATATTCAGCCCAAATAAAGATATATTATATCAAGAACACAGACCACCAAAATTAGCACGCACTT -s simCow_chr6.simCow.chr6 593519 66 + 602619 TCCCATCCTCAGCCCAGGTAAAGATGCAC--TAATAACAATACAGACTACTGAAACTAACACTCACTT -s simDog_chr6.simDog.chr6 585545 57 + 593897 ---CATGCTCTGTTCAAATAAAGATACA--------AGGACACAGATTATGAAAATCAGCACCCAATT -s simHuman_chr6.simHuman.chr6 589245 68 + 601863 CCCCATGCGCAGCCCAAACAAAGATACACAATACCAAGAACACAGACTACTGAAATTAGCACTCACTG -s simRat_chr6.simRat.chr6 634482 67 + 647215 CTCCAT-TTCAGCCCAAATAATTAACTATTATATCAAGAACACAGAACCCCAAACTTAGCACGCACTT - -a -s simMouse_chr6.simMouse.chr6 622950 7 + 636262 GAATGTT -s Anc0.Anc0refChr3 217385 2 + 222631 TA----- -s Anc1.Anc1refChr1 57728 2 + 69767 TA----- -s Anc2.Anc2refChr1 135000 2 + 142988 TA----- -s mr.mrrefChr3 169692 7 + 181027 GAATGTT -s simCow_chr6.simCow.chr6 593585 2 + 602619 AA----- -s simDog_chr6.simDog.chr6 585609 2 + 593897 TA----- -s simHuman_chr6.simHuman.chr6 589313 2 + 601863 TA----- -s simRat_chr6.simRat.chr6 634549 7 + 647215 GATGGCT - -a -s simMouse_chr6.simMouse.chr6 622957 17 + 636262 TGTTCTCCTTGTGGGCA -s Anc0.Anc0refChr3 217387 16 + 222631 -GTTCTTCTGGTGGGCA -s Anc1.Anc1refChr1 57730 16 + 69767 -GTTCTTCTGGTGGGCA -s Anc2.Anc2refChr1 135002 16 + 142988 -GTTCTTCTGGTGGGCA -s mr.mrrefChr3 169699 17 + 181027 TGTTCTCCTTGTGGGCA -s simCow_chr6.simCow.chr6 593587 16 + 602619 -GTTCCTCTGGTGGGCT -s simDog_chr6.simDog.chr6 585611 16 + 593897 -GTTCTTCTGGTGGGCA -s simHuman_chr6.simHuman.chr6 589315 16 + 601863 -GTTCTTCTGGTGGGCA -s simRat_chr6.simRat.chr6 634569 17 + 647215 CATGCTACTTGATGCCA - -a -s simMouse_chr6.simMouse.chr6 622974 19 + 636262 AAACCATTGTCCTGATTTG -s Anc0.Anc0refChr3 217403 16 + 222631 AAATCATT-TTC--ATATG -s Anc1.Anc1refChr1 57746 18 + 69767 AAATCATT-TTCTAATATG -s Anc2.Anc2refChr1 135018 16 + 142988 AAACCATT-TTC--GTATG -s mr.mrrefChr3 169716 19 + 181027 AAATCATTGTCCTGATTTG -s simCow_chr6.simCow.chr6 593603 16 + 602619 CAACCATT-TTC--TTAAG -s simDog_chr6.simDog.chr6 585627 16 + 593897 AAACCATT-TTT--GTATG -s simHuman_chr6.simHuman.chr6 589331 18 + 601863 AAATTATT-TTCTAATATG -s simRat_chr6.simRat.chr6 634721 19 + 647215 AAATCATGACAATGGTTTT - -a -s simMouse_chr6.simMouse.chr6 622993 38 + 636262 CATGTGGCCAGTCAGGCTGAGAGTGCTTCTCACTCCTC -s Anc0.Anc0refChr3 217419 36 + 222631 AA-GTGGTCAGT-AAATTAAAAATGCTTCTCACTCTCC -s Anc1.Anc1refChr1 57764 37 + 69767 AATGTGGTCAGT-AAATTAAAAATGCTTCTCACTCTCC -s Anc2.Anc2refChr1 135034 36 + 142988 AA-GTGGTCAGT-AAATTAAAAATGCTTCTAACTCTCC -s mr.mrrefChr3 169735 37 + 181027 CATGTGGCCAGT-AGGCTGAGAGTGCTTCTCACTCCTC -s simCow_chr6.simCow.chr6 593619 36 + 602619 AT-GTGGTCAAT-GAATTTAAAACACCTCTAACTCTCA -s simDog_chr6.simDog.chr6 585643 36 + 593897 AA-GTGCTCAGT-AACTAAAAGATGCTTTCAACTCTCC -s simHuman_chr6.simHuman.chr6 589349 37 + 601863 AATGTGGTCAGT-AAATTAAAAATGCTTCTCACTCTCC -s simRat_chr6.simRat.chr6 634743 10 + 647215 CATGAGGGGA---------------------------- - -a -s simMouse_chr6.simMouse.chr6 623031 1 + 636262 A -s Anc0.Anc0refChr3 217455 1 + 222631 A -s Anc1.Anc1refChr1 57801 1 + 69767 A -s Anc2.Anc2refChr1 135070 1 + 142988 A -s mr.mrrefChr3 169772 1 + 181027 A -s simCow_chr6.simCow.chr6 593655 1 + 602619 A -s simDog_chr6.simDog.chr6 585694 1 + 593897 A -s simHuman_chr6.simHuman.chr6 589386 1 + 601863 A - -a -s simMouse_chr6.simMouse.chr6 623032 52 + 636262 TCATGACTTCCTTGTGTTGCATTGTAAATGTTTTAAGCGTTGTATATAAGAT -s Anc0.Anc0refChr3 217456 24 + 222631 ACCTG----------------------------TTAGTGTTGTGGATATGAT -s Anc1.Anc1refChr1 57802 24 + 69767 ACCTG----------------------------TTAGTGTTGTGGATATGAT -s Anc2.Anc2refChr1 135071 24 + 142988 ACCTG----------------------------TTAGTGTTCTGGATATGAT -s mr.mrrefChr3 169773 24 + 181027 TCATG----------------------------TAAGCGTTGTATATAAGAT -s simCow_chr6.simCow.chr6 593710 24 + 602619 ACCTG----------------------------TTAGTGTTCTGGATATGAT -s simDog_chr6.simDog.chr6 585695 24 + 593897 ACCTG----------------------------TTGGTGTTCTGGATATGTT -s simHuman_chr6.simHuman.chr6 589387 24 + 601863 ACCTG----------------------------TTAGTGTTGTGGATATGAT - -a -s simMouse_chr6.simMouse.chr6 623084 22 + 636262 AGGCATATTTGTACTGAATCAT -s Anc0.Anc0refChr3 217481 22 + 222631 AGGACTATACATACTTAGTCAT -s Anc1.Anc1refChr1 57827 22 + 69767 AGGACTATACATACTTAGTCAT -s Anc2.Anc2refChr1 135096 22 + 142988 AGCACTATACATACTTAGTCAT -s mr.mrrefChr3 169797 22 + 181027 AGGCATATTTGTACTGAATCAT -s simCow_chr6.simCow.chr6 593735 22 + 602619 AGCACTATACATACTTAGTCAG -s simDog_chr6.simDog.chr6 585720 22 + 593897 AGCACTATACATACTTAGTCAT -s simHuman_chr6.simHuman.chr6 589412 22 + 601863 AGGAGTATACATACTTAGTCAT - -a -s simMouse_chr6.simMouse.chr6 623106 5 + 636262 TACAT -s Anc0.Anc0refChr3 217517 5 + 222631 CACAT -s Anc1.Anc1refChr1 57863 5 + 69767 CACAT -s Anc2.Anc2refChr1 135132 5 + 142988 CCTGT -s mr.mrrefChr3 169819 5 + 181027 TACAT -s simCow_chr6.simCow.chr6 593806 5 + 602619 TGTGT -s simDog_chr6.simDog.chr6 585756 5 + 593897 CCTGT -s simHuman_chr6.simHuman.chr6 589448 5 + 601863 CACAT - -a -s simMouse_chr6.simMouse.chr6 623111 35 + 636262 ACTGAACACACAAGCATTGTGTCAAGTAGCATGGT -s Anc0.Anc0refChr3 217522 35 + 222631 AATACACACACTAACATCATATCAATTAGCATGGT -s Anc1.Anc1refChr1 57868 35 + 69767 AATACACACACTAACATCATATCAATTAGCATGGT -s Anc2.Anc2refChr1 135143 35 + 142988 AATACACACATTAACAACATGTCAATTAACATGGT -s mr.mrrefChr3 169824 35 + 181027 ACTGAACACACAAGCATTGTATCAAGTAGCATGGT -s simCow_chr6.simCow.chr6 593817 35 + 602619 AGTACACACATAAACATCAATTCAATTGCCATGGT -s simDog_chr6.simDog.chr6 585767 35 + 593897 AATACACACATTAACAACATGTCAATTAACATGGA -s simHuman_chr6.simHuman.chr6 589453 30 + 601863 GGTTGAAACAC-----TCATATCAATGAGTATGGT -s simRat_chr6.simRat.chr6 634753 20 + 647215 ---------ACAGATATTGTATA------CACGGT - -a -s simMouse_chr6.simMouse.chr6 623146 94 + 636262 AGGCGAATGTATAGGCTAAAACTGTGACACAGGTGAAATATCATACACATTTAATACTGATATCTTTAACATTGTTTCACATCACTACATGTAG -s Anc0.Anc0refChr3 217557 91 + 222631 A---GACTGTATAGGCAAAGACTGTATTACAGGAGGAATGTAATGCAAATGTAATGCTGCTATCTTGTCAATAGTCTCACTTGACCATATGGAG -s Anc1.Anc1refChr1 57903 91 + 69767 A---GACTGTATAGGCAAAGACTGTATTACAGGAGGAATGTAATGCAAATGTAATGCTGCTATCTTGTCAATAGTCTCACTTGACCATATGGAG -s Anc2.Anc2refChr1 135178 91 + 142988 A---GACTGTGTAGGCAAAGACTGTAGAACAGGAGGAATGTAATGCAAATGCAATGCTGCGATCTTGTCAACAGTCTCACTTGACCATATGGAG -s mr.mrrefChr3 169859 94 + 181027 AGGCGACTGTATAGGCTAAAACTGTGTTACAGGTGAAATATCATGCAAATTTAATACTGATATCTTGTACATTGTTTCACATCACTATATGTAG -s simCow_chr6.simCow.chr6 593852 91 + 602619 A---GACTGTCTAGGCAAAGACTGCAAGACAGGAGAAATGGCATGGAAATCAAATGCTGCAACTTTGTTAACAGCCTTACTTGACTGTATGGAG -s simDog_chr6.simDog.chr6 585802 89 + 593897 A---GACTGTGTAGGCAAAGACTGTAGAACAGTAAGAATGTAATGCAAATGCAATGCTGCGTTCTTTTCAA--ATCTCGCTTGACCATATGAAA -s simHuman_chr6.simHuman.chr6 589483 84 + 601863 A---GACTGTATAGACAGAGACT---TTACAGGAGGAAT----TGTAAATGTAATGCTGCTATCTTGTCAATAGTCTCACTTGATGATATGGAG -s simRat_chr6.simRat.chr6 634774 93 + 647215 AGTAGACTGCATAGGCTAAAACTGTGTTACAAGTGAAATATCATGCAAATTTGATACTGGTACCTTGTACTTCGTTTTAGATCTCTATATGTA- - -a -s simMouse_chr6.simMouse.chr6 623240 16 + 636262 AAAACCAGCCACCAAA -s Anc0.Anc0refChr3 217649 16 + 222631 AAAACTGGCCACAAAA -s Anc1.Anc1refChr1 57995 16 + 69767 AAAACTGGCCACAAAA -s Anc2.Anc2refChr1 135270 16 + 142988 AAAACTGGCCACAAAA -s mr.mrrefChr3 169953 16 + 181027 AAAACCAGCCACCAAA -s simCow_chr6.simCow.chr6 593944 16 + 602619 AAAAGTGGGCACAAAA -s simDog_chr6.simDog.chr6 585892 16 + 593897 AAAACTGGCCATAGAA -s simHuman_chr6.simHuman.chr6 589568 16 + 601863 AAAACTGGCCACAAAA -s simRat_chr6.simRat.chr6 634867 16 + 647215 AAAACCAGCCTTCAAA - -a -s simMouse_chr6.simMouse.chr6 623256 8 + 636262 TGATAGTA -s Anc0.Anc0refChr3 217667 8 + 222631 GGCCATTA -s Anc1.Anc1refChr1 58013 8 + 69767 GGCCATTA -s Anc2.Anc2refChr1 135288 8 + 142988 GGCCATTA -s mr.mrrefChr3 169969 8 + 181027 GGCTAGTA -s simCow_chr6.simCow.chr6 593963 8 + 602619 GGCAATTA -s simDog_chr6.simDog.chr6 585910 8 + 593897 GGCCATTA -s simHuman_chr6.simHuman.chr6 589586 8 + 601863 GGCCATTA -s simRat_chr6.simRat.chr6 634883 8 + 647215 GGCTACTA - -a -s simMouse_chr6.simMouse.chr6 623264 58 + 636262 TGATTCGTATGAGGATGAGTAGTGACAATGCAGCAATTGTTCCTCACTCTTTCTAGTT -s Anc0.Anc0refChr3 217675 53 + 222631 GAATTTGTCTA-----GAGGAGTAACAGTGCAGCAGTTCTTCCTCACTCATTCTAGTT -s Anc1.Anc1refChr1 58021 53 + 69767 GAATTTGTCTA-----GAGGAGTAACAGTGCAGCAGTTCTTCCTCACTCATTCTAGTT -s Anc2.Anc2refChr1 135297 53 + 142988 GAGTTTGTCTA-----GAGGGATAACAGTGCAGCAGTTTTCCCTCAATCATTCTAGTT -s mr.mrrefChr3 169977 58 + 181027 TAATTTGTATGAGGATGAGTAGTGACAATGCAGCAATTCTTCCTCACTCATTCTAGTT -s simCow_chr6.simCow.chr6 593972 52 + 602619 GAGTTTATCTA-----GTGGGCTAAAAGTGCAGTAGTTTTGC-TCATTCATTCTTGTG -s simDog_chr6.simDog.chr6 585919 53 + 593897 GAGTTCGTCTT-----GAGGGATGACAGTGCAGCAGTTTTCCCTCGATCATTCTAATT -s simHuman_chr6.simHuman.chr6 589594 53 + 601863 GAATTTTTGTA-----GAGGAGTATCTGTGCTGCAGTGCTTCCACACTCATTCTAGTT -s simRat_chr6.simRat.chr6 634891 58 + 647215 TAACTTATATGTGGATGAGTAGTGACAACGCAGCAATTCTTCCTCACTCATTCTAGTT - -a -s simMouse_chr6.simMouse.chr6 623322 13 + 636262 CCTAAATATATCT -s Anc0.Anc0refChr3 217728 13 + 222631 CCTAAATATATCT -s Anc1.Anc1refChr1 58074 13 + 69767 CCTAAATATATCT -s Anc2.Anc2refChr1 135350 13 + 142988 CCTAAATATATCT -s mr.mrrefChr3 170035 13 + 181027 CCTAAATATATCT -s simCow_chr6.simCow.chr6 594024 13 + 602619 CCTAATTATATCA -s simDog_chr6.simDog.chr6 585972 13 + 593897 CCTAAATATATCT -s simHuman_chr6.simHuman.chr6 589674 13 + 601863 CCTAAATATATTT -s simRat_chr6.simRat.chr6 634949 13 + 647215 CCAAAATATATCT - -a -s simMouse_chr6.simMouse.chr6 623335 83 + 636262 GTGCCTGAGTAACTACTCTGAAAACATACATGTACTATTTTATATGGCAGATGGTGTCCTGTTGGTAGTGTATTATATCTATT -s Anc0.Anc0refChr3 217741 76 + 222631 GTTCCTAAGTAGCAACT-------CATACAGGTACTTTTTTATATTGCGAATAGTATTCTGTTGGTAGCATATTGTATCGCTT -s Anc1.Anc1refChr1 58087 76 + 69767 GTTCCTAAGTAGCAACT-------CATACAGGTACTTTTTTATATTGCGAATAGTATTCTGTTGGTAGCATATTGTATCGCTT -s Anc2.Anc2refChr1 135363 76 + 142988 GTTCCTAAGTAGCAACT-------TGTATAGGTACTTTTTTATATTGTGAATAGTATTCTGTTGGTAGCATATTGTTTAGCTT -s mr.mrrefChr3 170048 83 + 181027 GTGCCTGAGTAACAACTCTGAAAACATACAGGTACTATTTTATATGGCAGATGGTGTCCTGTTGGTAGTGTATTATATCGATT -s simCow_chr6.simCow.chr6 594040 75 + 602619 GTTCGTAACTCGCC-CT-------TTTATAGGTACTTTTTTATATGGTGAATAGTATTCTGTTGGCAGCACACTGTTTAGCTT -s simDog_chr6.simDog.chr6 585985 66 + 593897 GTTCCTAAGTAGCAACT-------TGCATAGGTACTTTTTTATATTGTAAATAGTATTCTGTTAGTA---TAT-------CTT -s simHuman_chr6.simHuman.chr6 589687 76 + 601863 GTTCCTAAGTGGCAATT-------CATACAGGTACTTTTTTATATAGCGAATAGTATTCTGTTGGTAGCTTATTGTATCGCTT -s simRat_chr6.simRat.chr6 634962 83 + 647215 GTCTTTGAGTAACAACTCTGAAGGCATACAGGTACTATTTTATAGGGCAGATGGTGTCCTGTTGGTAGTGTATGATATAGATT - -a -s simMouse_chr6.simMouse.chr6 623418 127 + 636262 AATGGCTCTCCCAATGAGCACTATCAATTACCTCTCACAACCCACTATAATTACTTTCTTTATGAAGGTTGGGGCTTGTGTTAATAACTGAGGAGTTGGAACGCATCCCCTACTGGGGTTTTGTTTG -s Anc0.Anc0refChr3 217820 10 + 222631 AATGGCT---------------------------------------------------------------------------------------------------------------------TTA -s Anc1.Anc1refChr1 58166 88 + 69767 AATGGCTACCCTAATCAACACCACTAA-CATGCCTTTCATCTTAATACA-CTG--TTGCTTCTCAGGG----------------------------------ACATCCTTT-CTGGGGTCTTGTTTA -s Anc2.Anc2refChr1 135442 10 + 142988 AATGGCT---------------------------------------------------------------------------------------------------------------------TTA -s mr.mrrefChr3 170131 126 + 181027 AATGGCTCTCCCAATGAGCACTATCAATTATCCCTCACATCCCACTATA-CTACTTTCCTTATGAGGGTTGGGGCTTGTGTTAATAACTGAGGAGTTGGAACACATCCCCTACTGGGGTTTTGTTTG -s simCow_chr6.simCow.chr6 594118 10 + 602619 AATAGCC---------------------------------------------------------------------------------------------------------------------TCA -s simDog_chr6.simDog.chr6 586054 10 + 593897 AATGCCT---------------------------------------------------------------------------------------------------------------------TTA -s simHuman_chr6.simHuman.chr6 589766 88 + 601863 AATGGCTACCCTAATCAACACCACTAA-CATGCCTTTCATCTTAATACA-CTG--TTGCTTCTCAGGG----------------------------------ACATCCTTT-CTGGGGTCTTGCTTA -s simRat_chr6.simRat.chr6 635045 126 + 647215 AATGGCTTTCCCAATTAGCACTATCAATTATCCCACACATCCCACTATA-CTACTCTCCTTACAAGGGTTGGTGCTTATGTTGATAACTGAAGAGTTGGAGCACATCCCCTACTGGGGTTTTGTTCG - -a -s simMouse_chr6.simMouse.chr6 623545 42 + 636262 CTCCTAGCCTCCTGTTGACCCCATATTGGCAATCAGAGGCTC -s Anc0.Anc0refChr3 217830 42 + 222631 CTGCTAGCCTCCAGCTAACCCCATATTGACAATTTGAACCTC -s Anc1.Anc1refChr1 58254 42 + 69767 CTGCTAGCCTCCAGCTAACCCCATATTGACAATTTGAACCTC -s Anc2.Anc2refChr1 135452 42 + 142988 CTGCTAGCCTCCAGCTAACCCCATATTGACAATTTGAACCTC -s mr.mrrefChr3 170257 42 + 181027 CTCCTAGCCTCCTGTTGACCCCATATTGACAATCAGAGGCTC -s simCow_chr6.simCow.chr6 594129 41 + 602619 CTACTAGCCTCCTGCTAAACCTATATCGACAATTTGA-CATC -s simDog_chr6.simDog.chr6 586064 42 + 593897 CTGCTAGCCTCCAGTTAACTCCATATTGAAACTTTGAACCTC -s simHuman_chr6.simHuman.chr6 589854 42 + 601863 CTGCTAGCCTCCAGCTAACCCCATATTGACAATTTGAAACTC -s simRat_chr6.simRat.chr6 635171 42 + 647215 CTCCTAGCCTTCTGTTTGCCGCTTAGCGACAATCAGAGGCTC - -a -s simMouse_chr6.simMouse.chr6 623587 7 + 636262 CATGTAG -s Anc0.Anc0refChr3 217872 7 + 222631 TGTGCAA -s Anc1.Anc1refChr1 58296 7 + 69767 TGTGCAA -s Anc2.Anc2refChr1 135494 7 + 142988 TGTGCAA -s mr.mrrefChr3 170299 7 + 181027 CATGCAG -s simCow_chr6.simCow.chr6 594170 7 + 602619 TGTGTAA -s simDog_chr6.simDog.chr6 586106 7 + 593897 TGTGCAA -s simHuman_chr6.simHuman.chr6 589897 7 + 601863 TGTGCAA -s simRat_chr6.simRat.chr6 635213 7 + 647215 CATGCAG - -a -s simMouse_chr6.simMouse.chr6 623594 20 + 636262 TTGAGCATAACACCTTGGGC -s Anc0.Anc0refChr3 217879 20 + 222631 GTGAGCATAGCACCTTTGGC -s Anc1.Anc1refChr1 58303 20 + 69767 GTGAGCATAGCACCTTTGGC -s Anc2.Anc2refChr1 135501 20 + 142988 GTGAGCATAGTCATTATGGC -s mr.mrrefChr3 170306 20 + 181027 TTGAGCATAACACCTTGGGC -s simCow_chr6.simCow.chr6 594177 20 + 602619 GATAGCACAATCATTATGGC -s simDog_chr6.simDog.chr6 586114 20 + 593897 GTGAGCATAGTGCTTTTGGC -s simHuman_chr6.simHuman.chr6 589904 20 + 601863 GTGAGTATACCACCTTCAGT -s simRat_chr6.simRat.chr6 635220 20 + 647215 TCAGGCGTAACACCTTAGGC - -a -s simMouse_chr6.simMouse.chr6 623614 22 + 636262 ATAGATAAAGTGCACCCTTCTG -s Anc0.Anc0refChr3 217900 22 + 222631 AGACTTAAAAGGCACCCTTCTG -s Anc1.Anc1refChr1 58324 22 + 69767 AGACTTAAAAGGCACCCTTCTG -s Anc2.Anc2refChr1 135522 22 + 142988 AGACTTAAAAGGCACCCTTTTG -s mr.mrrefChr3 170326 22 + 181027 AAAGATAAAGGGCACCCTTCTG -s simCow_chr6.simCow.chr6 594198 22 + 602619 ATCATCAAAAGGCACCCTTTTG -s simDog_chr6.simDog.chr6 586135 22 + 593897 AGACTTAAAGAGCATCTTTTCG -s simHuman_chr6.simHuman.chr6 589925 22 + 601863 AGACGTAAAAGGTGCCCTTCTG -s simRat_chr6.simRat.chr6 635240 22 + 647215 AAAGATAAAGGGCACCCCTCTA - -a -s simMouse_chr6.simMouse.chr6 623636 39 + 636262 TCACCTATTTAACCAATACCCACACTATCTAGCACTCCA -s Anc0.Anc0refChr3 217930 38 + 222631 TCACTTATTTACC-AGTGCTCATATCGTCTGGCACTTGA -s Anc1.Anc1refChr1 58354 38 + 69767 TCACTTATTTACC-AGTGCTCATATCGTCTGGCACTTGA -s Anc2.Anc2refChr1 135552 38 + 142988 TCACTTATTTACC-AGTGCTCATATCGTCTGGCACTTGA -s mr.mrrefChr3 170348 38 + 181027 TCACCTATTTAAC-AATGCTCATACTATCTAGCACTCCA -s simCow_chr6.simCow.chr6 594228 38 + 602619 TCACCTATTTACC-AGTGTTCGTATTGTCTAGCACTTGG -s simDog_chr6.simDog.chr6 586165 38 + 593897 TCACTTACTTGCC-AGTGCTCATATCGTCTGGCACTTGA -s simHuman_chr6.simHuman.chr6 589955 32 + 601863 TCACATATTTACC-GGTGCTCATAT------GCACATGA -s simRat_chr6.simRat.chr6 635263 38 + 647215 TCACCTATATAAC-AATGCTCGTACTATCTAGCACTCCA - -a -s simMouse_chr6.simMouse.chr6 623675 38 + 636262 CTACTCTATCACTATTTATCTCTTAGCCAGAGGTCATC -s Anc0.Anc0refChr3 217968 38 + 222631 TTACTCTATCATTATTTATTTTTTGGCTTGAGGTCATC -s Anc1.Anc1refChr1 58392 38 + 69767 TTACTCTATCATTATTTATTTTTTGGCTTGAGGTCATC -s Anc2.Anc2refChr1 135590 38 + 142988 TTACTCTATCATTATTTATTTTTTGGCTTGAGGTCATT -s mr.mrrefChr3 170386 38 + 181027 CTACTCTATCACTATTTATCTCTTAGCCAGAGGTCATC -s simCow_chr6.simCow.chr6 594266 38 + 602619 TTGCTTTATCATCACTTATTTTTCGGCTTGAGGTCATT -s simDog_chr6.simDog.chr6 586203 38 + 593897 ATACTCTATCAGTATTTATTTTTTGGCTTGAGGTCATT -s simHuman_chr6.simHuman.chr6 589987 38 + 601863 TTACTCCACCATTATTTATTTTAAGAGTTGAGGTCATC -s simRat_chr6.simRat.chr6 635305 38 + 647215 CTACTCTATCACTATTTATCTCTCAGCCAGAGGTCATC - -a -s simMouse_chr6.simMouse.chr6 623713 10 + 636262 AATTAGATGC -s Anc0.Anc0refChr3 218006 10 + 222631 GATTTCAAGT -s Anc1.Anc1refChr1 58430 10 + 69767 GATTTCAAGT -s Anc2.Anc2refChr1 135629 10 + 142988 GATTGCAAGT -s mr.mrrefChr3 170424 10 + 181027 AATTTGATGC -s simCow_chr6.simCow.chr6 594305 8 + 602619 AA--GTAATT -s simDog_chr6.simDog.chr6 586242 10 + 593897 GATTGCAAGT -s simHuman_chr6.simHuman.chr6 590025 10 + 601863 GACTTCAGGT -s simRat_chr6.simRat.chr6 635343 10 + 647215 AATTTGATGC - -a -s simMouse_chr6.simMouse.chr6 623723 41 + 636262 AGTCAGGATAACTTTGTGACTTCTCAAAATATGTCGGGCCT -s Anc0.Anc0refChr3 218016 41 + 222631 AGCCAGGATAATTTTGTGCAACCTTTAGCAATGACTGAATC -s Anc1.Anc1refChr1 58440 41 + 69767 AGCCAGGATAATTTTGTGCAACCTTTAGCAATGACTGAATC -s Anc2.Anc2refChr1 135639 41 + 142988 TGCAGGAATAATCTTCTGCAACCTTTAGCAATGACTGAATC -s mr.mrrefChr3 170434 41 + 181027 AGTCAGGATAACTTTGTGAATTCTCTAAATATGTCTGGCCT -s simCow_chr6.simCow.chr6 594313 39 + 602619 TG--GGAATAAACTTCTGCAGCCTTTACCTACAACTGAATC -s simDog_chr6.simDog.chr6 586252 33 + 593897 TGCAGGAATAAT--------ACCTCTAGCAATGACTGAATC -s simHuman_chr6.simHuman.chr6 590036 41 + 601863 AGCCAAGATAATTTTGTGCACCCTTTAGCAATGATTGAATC -s simRat_chr6.simRat.chr6 635353 41 + 647215 AGTTGGGATAACTTTGTGTATTCTCTACATATGTCTGGCCT - -a -s simMouse_chr6.simMouse.chr6 623764 33 + 636262 ATTTTGTTGAATTGGGCTAGTACCTCTTGCATG -s Anc0.Anc0refChr3 218096 31 + 222631 ACCTTGCAGAATTGGGC--GTACCTCTTGTATG -s Anc1.Anc1refChr1 58520 33 + 69767 ACCTTGCAGAATTGGGCTTGTACCTCTTGTATG -s Anc2.Anc2refChr1 135730 31 + 142988 ACCTTGCAGAATTGGGC--GTACCTCTTGTATA -s mr.mrrefChr3 170475 33 + 181027 ACTTTGTTGAATTGGGCTTGTACCTCTTGCATG -s simCow_chr6.simCow.chr6 594402 28 + 602619 GCCTTGCATAATTGG-----TACCTCTTGTACA -s simDog_chr6.simDog.chr6 586339 31 + 593897 ACCTTATAGAATTGGGC--GTACCTATTGTCTA -s simHuman_chr6.simHuman.chr6 590116 33 + 601863 ACCTTGCAGAATAGGGCTTGTACCTCTCGTATG -s simRat_chr6.simRat.chr6 635394 33 + 647215 ACTTTGTCAAGTTGGGCTTGTACCTCTTGCATG - -a -s simMouse_chr6.simMouse.chr6 623797 72 + 636262 ACCAAAGTAATTTTGCAGAAACATGTCATGTCATGTAGTACTTCAGACTGTGTTTGCAATCAGAAGGCATCA -s Anc0.Anc0refChr3 218128 72 + 222631 ACAATTATCATTATGAAGAGACATGGAGCACAGTGTGGTACTTTAGGGTGTGTTTGTGCCCAGAAGGCATCA -s Anc1.Anc1refChr1 58554 72 + 69767 ACAATTATCATTATGAAGAGACATGGAGCACAGTGTGGTACTTTAGGGTGTGTTTGTGCCCAGAAGGCATCA -s Anc2.Anc2refChr1 135762 72 + 142988 ACAATTATCATTATGAAGAGACATGGAGCACAGCAGGCTACTTTAGGGTGTGTTTGTGCCCAGAAGGCACCA -s mr.mrrefChr3 170508 72 + 181027 ACCAAAATAATTTTGCAGAGACATGTCATGTCATGTGGTACTTCAGAGTGTGTTTGTGCTCAGAAGGCATCA -s simCow_chr6.simCow.chr6 594431 72 + 602619 ACAATTATCATGATACAGAGACATGGGGTTAGTATGGCTCCCTTAGGGTGTGTTTGTACACAGCAGACACCA -s simDog_chr6.simDog.chr6 586370 72 + 593897 ACAATTCCCATTATGAACAGTCATAGAGCACAGCAGGCTACTTTAGGGTGTGTTTGTGCCCAGAAGGCACCA -s simHuman_chr6.simHuman.chr6 590150 72 + 601863 ACAATTATCATTATGAAGAGACATGGAGCACAGTGTGGTACTTAAGGGCATGTTTGTGCCTAGAAGCTATCA -s simRat_chr6.simRat.chr6 635427 72 + 647215 ACCAAAATAATTTTGTAGAGACATGTTATGTCATGTGGTACTTCAGAGTGTGTTTGTGCTCAGAAGGCATCA - -a -s simMouse_chr6.simMouse.chr6 623869 9 + 636262 ATTCTAAAC -s Anc0.Anc0refChr3 218206 9 + 222631 ATTCTACAC -s Anc1.Anc1refChr1 58632 9 + 69767 ATTCTACAC -s Anc2.Anc2refChr1 135840 9 + 142988 ATTCTACAC -s mr.mrrefChr3 170580 9 + 181027 ATTCTAAAC -s simCow_chr6.simCow.chr6 594509 9 + 602619 ATCCTAAAC -s simDog_chr6.simDog.chr6 586448 9 + 593897 ATTCTACAC -s simHuman_chr6.simHuman.chr6 590228 9 + 601863 ATTCTAGAC -s simRat_chr6.simRat.chr6 635499 9 + 647215 ATTCTAAAC - -a -s simMouse_chr6.simMouse.chr6 623878 6 + 636262 GTAGTC -s Anc0.Anc0refChr3 218215 6 + 222631 AGAATC -s Anc1.Anc1refChr1 58641 6 + 69767 AGAATC -s Anc2.Anc2refChr1 135849 6 + 142988 AGAATC -s mr.mrrefChr3 170589 6 + 181027 AGAGTC -s simCow_chr6.simCow.chr6 594518 6 + 602619 AGAACA -s simDog_chr6.simDog.chr6 586459 6 + 593897 AGAATC -s simHuman_chr6.simHuman.chr6 590237 6 + 601863 AGAATC -s simRat_chr6.simRat.chr6 635508 6 + 647215 AGAGTC - -a -s simMouse_chr6.simMouse.chr6 623884 29 + 636262 ACTTCATGCCATGTTTGTAGCGACTTATA -s Anc0.Anc0refChr3 218222 29 + 222631 ACATCATGCTATGGTCTTAGTGACCTACA -s Anc1.Anc1refChr1 58648 29 + 69767 ACATCATGCTATGGTCTTAGTGACCTACA -s Anc2.Anc2refChr1 135856 29 + 142988 ACATCATGCTATGGTCTTAGGTACCTACA -s mr.mrrefChr3 170595 29 + 181027 ACATCATGCCATGGTTGTAGTGACTTATA -s simCow_chr6.simCow.chr6 594525 29 + 602619 ACATCATGCTATGGTCTTAGGTATCGACA -s simDog_chr6.simDog.chr6 586466 29 + 593897 ACATCATGCTATGGTCTTAGGTACCTACA -s simHuman_chr6.simHuman.chr6 590244 25 + 601863 ACATCATGCTTTGGTCTTAGTGACC---- -s simRat_chr6.simRat.chr6 635514 29 + 647215 ACATCATGCAATGGTTGTACTGACTTATA - -a -s simMouse_chr6.simMouse.chr6 623913 52 + 636262 TTAAAAATATGGTCCCTTCACTAGGTTTAATCCTCATGAAATGGCATTTAGC -s Anc0.Anc0refChr3 218251 45 + 222631 T-------CTGATCCCTTCACTAGGTTGAATTCTCATGAAACAGTAGTTAGC -s Anc1.Anc1refChr1 58677 45 + 69767 T-------CTGATCCCTTCACTAGGTTGAATTCTCATGAAACAGTAGTTAGC -s Anc2.Anc2refChr1 135892 45 + 142988 T-------CTAATCCCTCCACTAGGTTGAATTCTCATGAAACAGTAGTTAGC -s mr.mrrefChr3 170624 45 + 181027 T-------ATGGTCCCTTCACTAGGTTTAATCCTCATGAAATGGTAGTTAGC -s simCow_chr6.simCow.chr6 594561 45 + 602619 C-------CTAATTCCTCCACTAGGTTGAACTCTCATGTGATAGCAGTCAGC -s simDog_chr6.simDog.chr6 586502 45 + 593897 T-------CTAATCCTTCCACTAGGTTGAATTCTCATGAAACAGTAGTTAGC -s simHuman_chr6.simHuman.chr6 590269 43 + 601863 ---------TGATGCCTTCACTAGGTTAAGTTCTCATTAAACACTGGTTAGC -s simRat_chr6.simRat.chr6 635543 44 + 647215 T-------GTGGTCCCTCCAGTAGGTTTAATCCTCATGAAATG-TAGTTAGC - -a -s simMouse_chr6.simMouse.chr6 623965 24 + 636262 TTTCCTTCATGATTCCGTACCAAA -s Anc0.Anc0refChr3 218299 23 + 222631 TTTCATTCATGATT-CAAACTAGC -s Anc1.Anc1refChr1 58725 24 + 69767 TTTCATTCATGATTTCAAACTAGC -s Anc2.Anc2refChr1 135940 23 + 142988 ATTCATTTATGAAT-CAAATTAAC -s mr.mrrefChr3 170669 24 + 181027 TTTTATTCATGATTCCGAACCAGA -s simCow_chr6.simCow.chr6 594607 22 + 602619 -TTCATTTGTGAAT-CAAATTACC -s simDog_chr6.simDog.chr6 586550 21 + 593897 ATCC--TTATCAAT-CATATGAAC -s simHuman_chr6.simHuman.chr6 590315 24 + 601863 TTTCATTCATGATTTGAAACTAGC -s simRat_chr6.simRat.chr6 635587 24 + 647215 TTTTACTCACGATTCCCATACTGG - -a -s simMouse_chr6.simMouse.chr6 623989 17 + 636262 CTGGCTTTATAACAGTG -s Anc0.Anc0refChr3 218322 17 + 222631 CTGACTTTATAACAATG -s Anc1.Anc1refChr1 58749 17 + 69767 CTGACTTTATAACAATG -s Anc2.Anc2refChr1 135963 17 + 142988 CTGAGTTTATAACAATG -s mr.mrrefChr3 170693 17 + 181027 CTGGCTTTATAACAGTG -s simCow_chr6.simCow.chr6 594629 17 + 602619 TTGAGTTTACGACAGTG -s simDog_chr6.simDog.chr6 586576 17 + 593897 CTGTGTTTATAACAATG -s simHuman_chr6.simHuman.chr6 590339 17 + 601863 CTGACTTTCTTACAACA -s simRat_chr6.simRat.chr6 635611 17 + 647215 TGGGGTCTATAACAGTG - -a -s simMouse_chr6.simMouse.chr6 624006 38 + 636262 CTAAATACACATTTGGCTTCGATAGAGAAGGTGTACCC -s Anc0.Anc0refChr3 218340 38 + 222631 CTCAATCCTCATTTGGCTTGAGTAAAGAAGGCCATCGC -s Anc1.Anc1refChr1 58767 38 + 69767 CTCAATCCTCATTTGGCTTGAGTAAAGAAGGCCATCGC -s Anc2.Anc2refChr1 135981 38 + 142988 CTCAATCCTCATTTGGCTTGAGTAAAGAAGGCCATTGC -s mr.mrrefChr3 170710 38 + 181027 CTAAATACACATTTGGCTTCAGTAGAGAAGGTCTACCC -s simCow_chr6.simCow.chr6 594647 38 + 602619 CTCAATCCTCATTTGTCTTGAGTACAGAAGATCATGAT -s simDog_chr6.simDog.chr6 586594 38 + 593897 CTCAGTCCTCATTTGGCTTGAGTAAAGAGGGCCATTGC -s simHuman_chr6.simHuman.chr6 590357 38 + 601863 CTCAATCCTCATTTGGCTTGAGTAAAGAAGGCCATCTC -s simRat_chr6.simRat.chr6 635628 38 + 647215 CTAAATACACATTTGGCTTCAGTAGAGAGAGACTACCC - -a -s simMouse_chr6.simMouse.chr6 624044 5 + 636262 AGGAA -s Anc0.Anc0refChr3 218378 5 + 222631 AGGAA -s Anc1.Anc1refChr1 58805 5 + 69767 AGGAA -s Anc2.Anc2refChr1 136019 5 + 142988 CGGAA -s mr.mrrefChr3 170748 5 + 181027 AGGAA -s simCow_chr6.simCow.chr6 594688 5 + 602619 CGGAA -s simDog_chr6.simDog.chr6 586632 5 + 593897 CGGAA -s simHuman_chr6.simHuman.chr6 590395 5 + 601863 AGAAA -s simRat_chr6.simRat.chr6 635666 5 + 647215 AGGTA - -a -s simMouse_chr6.simMouse.chr6 624049 27 + 636262 TAGGTCACTTCTGACTCGGCTCGTTGT -s Anc0.Anc0refChr3 218383 27 + 222631 TAGGTCACTTCTGACTCCATTGATTGT -s Anc1.Anc1refChr1 58810 27 + 69767 TAGGTCACTTCTGACTCCATTGATTGT -s Anc2.Anc2refChr1 136024 27 + 142988 TGGGTGAATTCTGACTCCATTGATTGC -s mr.mrrefChr3 170753 27 + 181027 TAGGTCACTTCTGACTCGGTTCGTTGT -s simCow_chr6.simCow.chr6 594719 27 + 602619 TTGGTTGATTCTGACTCCATTGTTCAC -s simDog_chr6.simDog.chr6 586637 27 + 593897 TGGATGAATTCTGCTTCCATTGATTGC -s simHuman_chr6.simHuman.chr6 590400 27 + 601863 TAGGTCACTTCTGACTCTATTGCTTGT -s simRat_chr6.simRat.chr6 635671 27 + 647215 TAGGTCACTTCTGACTTGGTTCTTTGT - -a -s simMouse_chr6.simMouse.chr6 624076 16 + 636262 ATCTCAATCATGAGGT -s Anc0.Anc0refChr3 218410 16 + 222631 ATCTCTATCATGAGGT -s Anc1.Anc1refChr1 58837 16 + 69767 ATCTCTATCATGAGGT -s Anc2.Anc2refChr1 136051 16 + 142988 ATCTCTATCATGAGGT -s mr.mrrefChr3 170780 16 + 181027 ATCTCAATCATGAGGT -s simCow_chr6.simCow.chr6 594746 16 + 602619 ATCTCTACCATGAGGT -s simDog_chr6.simDog.chr6 586670 16 + 593897 ATTTCTATCATGAGGT -s simHuman_chr6.simHuman.chr6 590427 16 + 601863 AACTCTATCATAAGGT -s simRat_chr6.simRat.chr6 635698 16 + 647215 ATCTCGATCATGAGGT - -a -s simMouse_chr6.simMouse.chr6 624092 21 + 636262 GAGCAAAAACATGCCACAAAG -s Anc0.Anc0refChr3 218427 21 + 222631 GAGCAAATAAATGTCAAAAAA -s Anc1.Anc1refChr1 58854 21 + 69767 GAGCAAATAAATGTCAAAAAA -s Anc2.Anc2refChr1 136068 21 + 142988 GGACAAATAAATGTCAAAAAA -s mr.mrrefChr3 170796 21 + 181027 GAGCAAAAACATGCCAAAAAA -s simCow_chr6.simCow.chr6 594763 21 + 602619 GGACAAATACATGGCAAAAAA -s simDog_chr6.simDog.chr6 586687 21 + 593897 AGACAAATAAATGTCAAAAAA -s simHuman_chr6.simHuman.chr6 590444 21 + 601863 GAGCCAGCAGATATCAAAAAA -s simRat_chr6.simRat.chr6 635714 21 + 647215 GAGCAAAAACATGCCAAAAAA - -a -s simMouse_chr6.simMouse.chr6 624113 1 + 636262 A -s Anc0.Anc0refChr3 218448 1 + 222631 A -s Anc1.Anc1refChr1 58875 1 + 69767 A -s Anc2.Anc2refChr1 136089 1 + 142988 A -s mr.mrrefChr3 170817 1 + 181027 A -s simDog_chr6.simDog.chr6 586708 1 + 593897 A -s simHuman_chr6.simHuman.chr6 590468 1 + 601863 C -s simRat_chr6.simRat.chr6 635735 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 624114 22 + 636262 ATGCACGCCTTCCCAGAAAAGT -s Anc0.Anc0refChr3 218449 11 + 222631 ATGCAC-----CC------AGT -s Anc1.Anc1refChr1 58876 16 + 69767 ATGCACTTCTTCC------AGT -s Anc2.Anc2refChr1 136092 11 + 142988 AAGCAC-----AC------AGA -s mr.mrrefChr3 170818 16 + 181027 ATGCACTCCTTCC------AGT -s simCow_chr6.simCow.chr6 594784 4 + 602619 ----AC-----AC--------- -s simDog_chr6.simDog.chr6 586711 11 + 593897 AAGCAC-----TC------AGA -s simHuman_chr6.simHuman.chr6 590469 16 + 601863 ATGTAATTCTTCC------AGT -s simRat_chr6.simRat.chr6 635736 8 + 647215 ACGCATTC-------------- - -a -s simMouse_chr6.simMouse.chr6 624136 7 + 636262 ATCACGC -s Anc0.Anc0refChr3 218460 6 + 222631 ATCACG- -s Anc1.Anc1refChr1 58892 7 + 69767 ATCACGc -s Anc2.Anc2refChr1 136103 6 + 142988 ATCACA- -s mr.mrrefChr3 170834 7 + 181027 ATCACGC -s simCow_chr6.simCow.chr6 594788 2 + 602619 ----CA- -s simDog_chr6.simDog.chr6 586722 6 + 593897 ATCACA- -s simHuman_chr6.simHuman.chr6 590512 7 + 601863 CTCATgc - -a -s simMouse_chr6.simMouse.chr6 624143 40 + 636262 ACGATAAGTATCACATGCTGTGCTGCATTAAGTTCATGCC -s Anc0.Anc0refChr3 218466 25 + 222631 --------------ACACTGTGCCACAACAAGTACATGC- -s Anc1.Anc1refChr1 58899 33 + 69767 acaataag------ACACTGTGCCACAACAAGTACATGC- -s Anc2.Anc2refChr1 136109 25 + 142988 --------------ACACTGTGCCACAACAAGTACATGC- -s mr.mrrefChr3 170841 40 + 181027 ACGATAAGTGTCACACGCTCTGCTGCATTAAGTACATGCC -s simCow_chr6.simCow.chr6 594790 25 + 602619 --------------ACACTTTGCCACAACAACTACATGC- -s simDog_chr6.simDog.chr6 586728 25 + 593897 --------------ACACTGTGCCACAACATGTACATGC- -s simHuman_chr6.simHuman.chr6 590520 8 + 601863 acaataag-------------------------------- -s simRat_chr6.simRat.chr6 635744 35 + 647215 -----AAGTGTCAGACGCTCTGCTGCATTAAGTACATGCC - -a -s simMouse_chr6.simMouse.chr6 624183 31 + 636262 ATGTCGGATGACATCAAGATCTAACCTAGTA -s Anc0.Anc0refChr3 218491 31 + 222631 ATGTCCCATGCCATTAAGCCCTAACCTAGGA -s Anc1.Anc1refChr1 59207 31 + 69767 ATGTCCCATGCCATTAAGCCCTAACCTAGGA -s Anc2.Anc2refChr1 136134 31 + 142988 ATGTCCCATGCCATTAAGCCCTGACCTAGGA -s mr.mrrefChr3 170881 31 + 181027 ATGTCCGATGACATCAAGACCTAACCTAGTA -s simCow_chr6.simCow.chr6 594815 31 + 602619 ATGTCCCATGCCATTAAGTCCAGAGATAGGA -s simDog_chr6.simDog.chr6 586753 20 + 593897 ATGT-----------GAGCCCTGACCTAGGA -s simHuman_chr6.simHuman.chr6 591068 31 + 601863 ATGTCCAATGCCATTAAGCCCTAACCTAGGA -s simRat_chr6.simRat.chr6 635779 31 + 647215 ATGTCCTATGACATCAAGACCTAACATAGTA - -a -s simMouse_chr6.simMouse.chr6 624214 36 + 636262 TGTCCTGTATCTTGATTTCAGTACTTACCATTGTAA -s Anc0.Anc0refChr3 218523 23 + 222631 TGTCCTGTGTGTAGTTTTTAGA-------------A -s Anc1.Anc1refChr1 59239 23 + 69767 TGTCCTGTGTGTAGTTTTTAGA-------------A -s Anc2.Anc2refChr1 136166 23 + 142988 TGTCCTGTGTGCACTTTCTAGA-------------A -s mr.mrrefChr3 170912 33 + 181027 TGTCCTGTATCTTGATTTCAGA---TACCATTGTAA -s simCow_chr6.simCow.chr6 594847 23 + 602619 TGGTCTGTGTGCACTTCCCCAC-------------A -s simDog_chr6.simDog.chr6 586774 23 + 593897 TGTCCTGTCTGCACTTTCTAGA-------------A -s simHuman_chr6.simHuman.chr6 591100 23 + 601863 TGTCTTGCGTATGGTTTTAAGA-------------A -s simRat_chr6.simRat.chr6 635810 32 + 647215 TGTCCTGTA-CTAGATTTCGGA---TACCATTGTAA - -a -s simMouse_chr6.simMouse.chr6 624250 16 + 636262 TCATTACATAATGCAT -s Anc0.Anc0refChr3 218546 16 + 222631 CCATAATATGATGCAG -s Anc1.Anc1refChr1 59262 16 + 69767 CCATAATATGATGCAG -s Anc2.Anc2refChr1 136193 16 + 142988 CCATAATATGATGTAG -s mr.mrrefChr3 170945 16 + 181027 TCATAATATAATGCAT -s simCow_chr6.simCow.chr6 594874 15 + 602619 CCATTATATAATA-AG -s simDog_chr6.simDog.chr6 586801 16 + 593897 CCATAATATGATGTAG -s simHuman_chr6.simHuman.chr6 591123 16 + 601863 CCATAATGTGGTGCAG -s simRat_chr6.simRat.chr6 635842 16 + 647215 TCGTAATATAACCCAT - -a -s simMouse_chr6.simMouse.chr6 624266 5 + 636262 GAATA -s Anc0.Anc0refChr3 218571 5 + 222631 GAATG -s Anc1.Anc1refChr1 59287 5 + 69767 GAATG -s Anc2.Anc2refChr1 136218 5 + 142988 GAATG -s mr.mrrefChr3 170961 5 + 181027 GAATG -s simCow_chr6.simCow.chr6 594898 5 + 602619 GATGA -s simDog_chr6.simDog.chr6 586826 5 + 593897 AAATG -s simHuman_chr6.simHuman.chr6 591148 5 + 601863 GAGAG -s simRat_chr6.simRat.chr6 635858 5 + 647215 GAATG - -a -s simMouse_chr6.simMouse.chr6 624271 13 + 636262 TTAGAAATGAGTT -s Anc0.Anc0refChr3 218576 13 + 222631 TTAGAAATGAGTC -s Anc1.Anc1refChr1 59292 13 + 69767 TTAGAAATGAGTC -s Anc2.Anc2refChr1 136232 13 + 142988 TTAGATTCTTGTC -s mr.mrrefChr3 170966 13 + 181027 TTAGAAATGAGTT -s simCow_chr6.simCow.chr6 594912 13 + 602619 TTAGGTTCTTGTC -s simDog_chr6.simDog.chr6 586840 13 + 593897 TTAGATTCTTGTC -s simHuman_chr6.simHuman.chr6 591153 13 + 601863 TTAGTAATGAGTC -s simRat_chr6.simRat.chr6 635863 13 + 647215 TTAGAAATGAGTT - -a -s simMouse_chr6.simMouse.chr6 624284 56 + 636262 CAACAGGCAACTTTTCCCACCTGACTAGTATTAGTGGCAGCCCCTGGTATTTAACC -s Anc0.Anc0refChr3 218589 43 + 222631 TAGCAGACAGGTCTTGCAAC-TAGCCAACATTAGTGCTAGCC------------CC -s Anc1.Anc1refChr1 59305 51 + 69767 TAGCAGACAGGTCTTGCAAC-TAGCCAACATTAGTGCTAGCCT----TAGTTAACC -s Anc2.Anc2refChr1 136245 43 + 142988 TAGCAGAAAGGTCTTGCAAC-TAGCCAACATCAGTGCTAGCC------------CC -s mr.mrrefChr3 170979 56 + 181027 CAGCAGGCAGGTTTTCCCACCTGACTAGTATTAGTGGTAGCCTCTGGTATTTAACC -s simCow_chr6.simCow.chr6 594925 43 + 602619 AAGCAGATAGGTCTTGAAGC-TAGCCAATATCAGTGGTAGCC------------CA -s simDog_chr6.simDog.chr6 586853 43 + 593897 TAGCAGAAAGGTCTTACAAC-TAGCCAACATCAGTGCTAGCC------------CC -s simHuman_chr6.simHuman.chr6 591171 41 + 601863 TTGCAGACAGGTCTTGCAAC-----------TAGCTATAAATT----TAGTTAACC -s simRat_chr6.simRat.chr6 635876 56 + 647215 CAGCAGGCAGGTTTTACCACCTGACTAGTATTAGTGGTAGCCTCTGGTATTTAACC - -a -s simMouse_chr6.simMouse.chr6 624340 17 + 636262 GTCTGAATTCATCTTGT -s Anc0.Anc0refChr3 218632 7 + 222631 GTCTGA----------T -s Anc1.Anc1refChr1 59356 17 + 69767 GTCTGACTTTATCTTGT -s Anc2.Anc2refChr1 136288 7 + 142988 TTATGA----------T -s mr.mrrefChr3 171035 17 + 181027 GTCTGAATTCATCTTGT -s simCow_chr6.simCow.chr6 594968 7 + 602619 TTATGA----------T -s simDog_chr6.simDog.chr6 586896 7 + 593897 TTATGA----------T -s simHuman_chr6.simHuman.chr6 591213 17 + 601863 GTCTCACTTTATCTTGG -s simRat_chr6.simRat.chr6 635932 17 + 647215 ATCTGAATTCATCTCGT - -a -s simMouse_chr6.simMouse.chr6 624357 173 + 636262 GTTCTAACACTCCAGGGCCCTACGGCAACATTTGTCAGAGCTGCAAATTAAGAACTTTCCTCAGCACTTAGGTGACCTACATGGTCTGTACTAATTCTTCCTTGATTTACTGGTCCAGTTGAGTATTAATTACAACAACCACATGCTATACCAAGAACTTACATTGTTATGGA -s Anc0.Anc0refChr3 218639 77 + 222631 GTATTAATGCTCCAGGGATCTTCTGCAACATTTGTCAGAGCTGTAAAGCAAAA----------------------------------------------------------------------------------------------ATAAATAGAC--TAAGCTTTTATAGA -s Anc1.Anc1refChr1 59373 77 + 69767 GTATTAATGCTCCAGGGATCTTCTGCAACATTTGTCAGAGCTGTAAAGCAAAA----------------------------------------------------------------------------------------------ATAAATAGAC--TAAGCTTTTATAGA -s Anc2.Anc2refChr1 136295 77 + 142988 GTATTAATGCTCCAGGGATCTTCTGCAATATTCATTAAAGCTGTAAAGCAAAA----------------------------------------------------------------------------------------------GCAAATAGAC--TAAGCTTTTATAAA -s mr.mrrefChr3 171052 171 + 181027 GTTCTAACACTCCAGGGCCCTACGGCAACATTTGTCAGAGCTGCAAATTAAGAACTTTCCTCAGCACTTAGGTGACCTACATGGTCTGTACTAATTCTTCCTTGATTTACTGGTCCAGTTGAGTATTAATTACAACAACCACATGCTATACCAAGAA--TACATTGTTATGGA -s simCow_chr6.simCow.chr6 595065 74 + 602619 GTTTTAATGCTCCAGGGATCTCCTGCAATATTCATTA---CCATAAAGCAAAA----------------------------------------------------------------------------------------------GGAAATAGAC--TAAGCTTTTGTGAA -s simDog_chr6.simDog.chr6 586903 68 + 593897 GTAGTTAAGC---------CGTCTGCAGTATTCATTAAAGCTGTGAAGTAAAC----------------------------------------------------------------------------------------------GCAAATAGAC--TAAGATTTTATAAA -s simHuman_chr6.simHuman.chr6 591230 77 + 601863 GTATTAATGCTCCTGGGTTCTTCTGCAACATTTGCCAGAGCTGTAAAACAAAA----------------------------------------------------------------------------------------------ATAAATAGGC--TAAGCTTTTATAGA -s simRat_chr6.simRat.chr6 635949 171 + 647215 GTTCTAACACTTCAGAGCCATATGGCAATATCCATCAGAGCCGCAAATTAAGAACTTTCCTTGACACTTAGATGACTTATGTTGTCTGTACTAAACCTTTTTTGATTTATTGGTCTGATTGAGTAATAATTACAGCAACCACACACTATACCAAGAA--TACATTGTTACAGA - -a -s simMouse_chr6.simMouse.chr6 624530 14 + 636262 CGTTGTTCCAGCTT -s Anc0.Anc0refChr3 218866 14 + 222631 CCTTCTTCCAAATT -s Anc1.Anc1refChr1 59600 14 + 69767 CCTTCTTCCAAATT -s Anc2.Anc2refChr1 136588 14 + 142988 CCTTCTTCCAAATT -s mr.mrrefChr3 171223 14 + 181027 CGTTGTTCCAGCTT -s simCow_chr6.simCow.chr6 595379 14 + 602619 CCTTCTTACAAAGT -s simDog_chr6.simDog.chr6 587189 14 + 593897 CATTCTCCCAATTC -s simHuman_chr6.simHuman.chr6 591458 14 + 601863 CCTTCTTCCAAATT -s simRat_chr6.simRat.chr6 636120 14 + 647215 CATTGTAACAGATT - -a -s simMouse_chr6.simMouse.chr6 624544 29 + 636262 ACATTCACTTAAGAATGGCTGGCGCATTA -s Anc0.Anc0refChr3 218880 29 + 222631 TCACACCCTCAAGATTGGTTGGAGCATCT -s Anc1.Anc1refChr1 59614 29 + 69767 TCACACCCTCAAGATTGGTTGGAGCATCT -s Anc2.Anc2refChr1 136602 29 + 142988 TCACACCCTCAAGATTGGTTGGAGCATCT -s mr.mrrefChr3 171237 29 + 181027 ACATTCACTTAAGAATGGCTGGCGCATTA -s simCow_chr6.simCow.chr6 595393 29 + 602619 TCACACCCTAATGGATGGTTGGGGAATTG -s simDog_chr6.simDog.chr6 587204 29 + 593897 TCACACCCTCAAGATTGGTTGGAGCATCT -s simHuman_chr6.simHuman.chr6 591472 9 + 601863 TCACCCCCT-------------------- -s simRat_chr6.simRat.chr6 636134 29 + 647215 ACATTCACCTAAGGATGACTGGGGCACTG - -a -s simMouse_chr6.simMouse.chr6 624573 119 + 636262 AGCCATTAGGGTAAAAAACAACTTATGTTACAATGTTAAATCTGTTGCCAGACTTTGTAGTGTGACACTCTGTCATATCTCGGGGGTTCAGTCTCGCCAGAAGTGATAAGTATACATTT -s Anc0.Anc0refChr3 218909 116 + 222631 AGCCAGT--G-TGGTATCCAACTTATGTTGCAATGTTGAATCTTTCTTCAGATTCTATGGGGATACACTCTGTTGTAACACTGGTGCTCATTCCCCCCAGAAGTGATATATATACATCT -s Anc1.Anc1refChr1 59643 116 + 69767 AGCCAGT--G-TGGTATCCAACTTATGTTGCAATGTTGAATCTTTCTTCAGATTCTATGGGGATACACTCTGTTGTAACACTGGTGCTCATTCCCCCCAGAAGTGATATATATACATCT -s Anc2.Anc2refChr1 136631 116 + 142988 AGCCAGT--G-TGGTATCCAACTTATGTTGCAATGTTGAATCTTCCTTCAGATTCTATGGGGATGCACTCTGTTGTAACTCTGGTGCTCATTCCCCCCAGAACAGATATATATACATCT -s mr.mrrefChr3 171266 118 + 181027 AGCCATTAGG-TAAAAAACAACTTATGTTACAATGTTAAATCTTTCTCCAGATTTTATAGTGTGACACTCTGTTGTAACACGGGGGTTCAGTCTCGCCAGAAGTGATATGTATACATTT -s simCow_chr6.simCow.chr6 595425 116 + 602619 AGCCATT--G-TCGTAACCAACTTACATTACAAAGTTGAATTTTCCTTCAGATTTTATGGAGATGCAGTCTGTTATAACTCTGGTGCCCCTTCCCCCCAGAATAGATGTATATGATTCT -s simDog_chr6.simDog.chr6 587233 115 + 593897 AGCCAGT--G-TGGTATCCAACTTATGTTGCAATGTTGAATCTTCCTTCAGATTCTATGGGAATGCACC-TGTTGTTACTCTGCTGATCATTCTCCCCAGAACAGATATAAATACATCT -s simHuman_chr6.simHuman.chr6 591481 81 + 601863 --------------------------------------GATCTTTCTTCAGATTGTATGGGGATACATTGTGTTGTAACACTGGTGCTCATTCCGCCCAGAAGTGATATATATACATCT -s simRat_chr6.simRat.chr6 636163 118 + 647215 AGCCAACAGG-CAAAAGACAACTTATGTTATAGTGCTAAACCTTTCTCCAGGTTTTATAGTGTGACACTCTGTTGCAACATGGGGGTTCAATCTCTCGAGAAGTGATATGTATACATTT - -a -s simMouse_chr6.simMouse.chr6 624692 7 + 636262 GAAAGTT -s Anc0.Anc0refChr3 219025 7 + 222631 GGAAATT -s Anc1.Anc1refChr1 59759 7 + 69767 GGAAATT -s Anc2.Anc2refChr1 136747 7 + 142988 GGCAATT -s mr.mrrefChr3 171384 7 + 181027 GGAAATT -s simCow_chr6.simCow.chr6 595541 7 + 602619 GGCAATT -s simDog_chr6.simDog.chr6 587363 7 + 593897 GGCAATT -s simHuman_chr6.simHuman.chr6 591562 7 + 601863 GGAAATT -s simRat_chr6.simRat.chr6 636281 7 + 647215 GGTGATT - -a -s simMouse_chr6.simMouse.chr6 624699 72 + 636262 ACTAAATTCACAATGTGATCAATACCATATTTAGTTGGGGGAGGTTTATGGGTGCCAACAAATTTGGCCCAG -s Anc0.Anc0refChr3 219032 72 + 222631 ACTAAATGCATTATGTGATTGATAACATATTCAACTGATAGAGCCTTGTGGATGCCAACATACTTGACCCAG -s Anc1.Anc1refChr1 59766 72 + 69767 ACTAAATGCATTATGTGATTGATAACATATTCAACTGATAGAGCCTTGTGGATGCCAACATACTTGACCCAG -s Anc2.Anc2refChr1 136754 72 + 142988 ACTAAATGCATTGTGGGATTAATAACATATTCAACTGATAGAGCCTTGTGGATGCCAACATACTTGACCCAG -s mr.mrrefChr3 171391 72 + 181027 ACTAAATTCACAATGTGATTGATACCATATTTAGTTGGGGGAGGTTTATGGGTGCCAACAAATTTGGCCCAG -s simCow_chr6.simCow.chr6 595556 72 + 602619 GCTAAATGCATTCTGGGATTAATAATATATTCAACCGTCAGAGCATTGTGGTTGCTAATATACTTGACCCAG -s simDog_chr6.simDog.chr6 587370 72 + 593897 AGTAAATGCATTGTGGAATTAATATCATATTCAACTGATAGAGCCTCAGGGATCGCAACATACCTCACCCAG -s simHuman_chr6.simHuman.chr6 591569 72 + 601863 ACTAAACCCATTATGTGGTTGATTACATACTCGACTGATAGAGCCTTGTGGATGCCAACATGCTTGACCCAG -s simRat_chr6.simRat.chr6 636288 72 + 647215 ACTAGATTCACAATGTGACTGATACCATATTTAGTTGGGGTAAGTTTATGCTTGCCAACAAATTTGGTCCAG - -a -s simMouse_chr6.simMouse.chr6 624771 51 + 636262 CATGATTATCTTGCCTGCCTTGAGATAGAAATAAAGCCACTTTCATAACTG -s Anc0.Anc0refChr3 219104 51 + 222631 CATTAGTGTCATGTCTGCCTTGAATTTAAAATAAGATCACTTCCATGGTTG -s Anc1.Anc1refChr1 59838 51 + 69767 CATTAGTGTCATGTCTGCCTTGAATTTAAAATAAGATCACTTCCATGGTTG -s Anc2.Anc2refChr1 136831 51 + 142988 CTTTAGTGTCATGTCTGCCTTGAATTTAAAATAAGACCACCTCCATGGTTG -s mr.mrrefChr3 171463 51 + 181027 CATGATTGTCATGTCTGCCTTGAAATTGAAATAAAGTCACTTTCATAGCTG -s simCow_chr6.simCow.chr6 595633 51 + 602619 CTTTAGTGTCATAACTGCTCTGAATTTAGAATAAGTCCACCTCCATGGCTG -s simDog_chr6.simDog.chr6 587447 51 + 593897 CTTTAGTGTTGTGTCTATCTTGAATTTAAAATAAGACTGCCTCGATGGTTC -s simHuman_chr6.simHuman.chr6 591641 51 + 601863 CATTAGAGCCATGTCTGCCTTGAATTTAAATTAATATCACTTCCATGGTTG -s simRat_chr6.simRat.chr6 636360 51 + 647215 CATAATTGTCATGTCTGCCTTGAAATTGAAATAAAGTCACTCTCATAGCCA - -a -s simMouse_chr6.simMouse.chr6 624822 8 + 636262 TAGTTCTA -s Anc0.Anc0refChr3 219163 8 + 222631 TAGTCATA -s Anc1.Anc1refChr1 59897 8 + 69767 TAGTCATA -s Anc2.Anc2refChr1 136890 8 + 142988 TAGCCATA -s mr.mrrefChr3 171514 8 + 181027 TAGTTCTA -s simCow_chr6.simCow.chr6 595692 8 + 602619 TGACCATA -s simDog_chr6.simDog.chr6 587506 8 + 593897 TAGCCATA -s simHuman_chr6.simHuman.chr6 591700 8 + 601863 TAGTCATA -s simRat_chr6.simRat.chr6 636411 8 + 647215 TAGGACTA - -a -s simMouse_chr6.simMouse.chr6 624830 74 + 636262 ATCATTGGATATGCATGAGTAACCCAAGGGAGGATATGTGCAATCAGACAGAATTGAGTAATTCTTCCCTGACC -s Anc0.Anc0refChr3 219171 8 + 222631 ATCTTTGT------------------------------------------------------------------ -s Anc1.Anc1refChr1 59905 8 + 69767 ATCTTTGT------------------------------------------------------------------ -s Anc2.Anc2refChr1 136898 8 + 142988 AACTTTGT------------------------------------------------------------------ -s mr.mrrefChr3 171522 74 + 181027 ATCATTGGATATGCATGAGTAACCCAAGGGAGGATATGTGCAATCAGACAGAATTGAGTAATTCTTCCCTGACC -s simCow_chr6.simCow.chr6 6039 8 - 602619 GCAATTCG------------------------------------------------------------------ -s simDog_chr6.simDog.chr6 587514 8 + 593897 AACTTTGT------------------------------------------------------------------ -s simHuman_chr6.simHuman.chr6 591708 8 + 601863 ATCTTTGT------------------------------------------------------------------ -s simRat_chr6.simRat.chr6 636419 74 + 647215 TTCGTTGGATATGCATGAGTAACCCAAGGGAGTATACGTTCAATCAGACAGCATTGAGTAATTCTTCCCAGAAC - -a -s simMouse_chr6.simMouse.chr6 624904 46 + 636262 CAGGTCTTTAATGGAGAGTATTGTATTGCCAGGGAGTGACTCCCAG -s Anc0.Anc0refChr3 219179 1 + 222631 ---------------------------------------------G -s Anc1.Anc1refChr1 59913 1 + 69767 ---------------------------------------------G -s Anc2.Anc2refChr1 136906 1 + 142988 ---------------------------------------------A -s mr.mrrefChr3 171596 46 + 181027 CAGGTCTTTAATGGAGAGTATTGTATTGCCAGGGAGTGACTCCCAG -s simCow_chr6.simCow.chr6 6047 1 - 602619 ---------------------------------------------A -s simDog_chr6.simDog.chr6 587522 1 + 593897 ---------------------------------------------A -s simHuman_chr6.simHuman.chr6 591716 1 + 601863 ---------------------------------------------G -s simRat_chr6.simRat.chr6 636496 46 + 647215 CAGGTCTTTAATGGAAAGTATTGTATTGCCAGGGAGTGACTCCCAG - -a -s simMouse_chr6.simMouse.chr6 624950 58 + 636262 GGAGTGACTGACAGTTTTTCTTCTATTCCCCCCCCCTGTCTTCCCCCACTATTAAGTT -s Anc0.Anc0refChr3 219180 57 + 222631 GAGAAGAGTGACAGTTCATCT-CTATTGTCCTCCCTTGTCTTCCCCCACTATTACGTG -s Anc1.Anc1refChr1 59914 58 + 69767 GAGAAGAGTGACAGTTCATCTTCTATTGTCCTCCCTTGTCTTCCCCCACTATTACGTG -s Anc2.Anc2refChr1 136987 57 + 142988 GAGAAGAGTGACAGTTCATCT-CTATTGTGCTCCCTTGTATTCCCCTGCTATTACGTG -s mr.mrrefChr3 171642 58 + 181027 GGAGTGACTGACAGTTCTTCTTCTATTCCCCTCCCCTGTCTTCCCCCACTATTAAGTT -s simCow_chr6.simCow.chr6 6136 57 - 602619 GAGAAGAGTGACAGTTCATCT-CTATTCTGCTCCCTTGTTTTCCCCTGCTATTAGGAG -s simDog_chr6.simDog.chr6 587610 57 + 593897 GGGGAAAGTGATAGTTCATCT-CTATTGTGCCACCTTGTATTCCCCTGCTATTACATG -s simHuman_chr6.simHuman.chr6 591717 58 + 601863 GAGAAGAGTGACCCCTCATCTTCTATTATCCTCCCTTGTCTTCCCCCACAATTATGTG -s simRat_chr6.simRat.chr6 636542 58 + 647215 GGAGTGGCTGACAGTTCTTCTTCAATTCCCATCCCCTGTCTTCCCCCACCATTAAACC - -a -s simMouse_chr6.simMouse.chr6 625008 5 + 636262 TCAGG -s Anc0.Anc0refChr3 219237 5 + 222631 TTATG -s Anc1.Anc1refChr1 59972 5 + 69767 TTATG -s Anc2.Anc2refChr1 137048 5 + 142988 TTATC -s mr.mrrefChr3 171700 5 + 181027 TTAGG -s simCow_chr6.simCow.chr6 6195 5 - 602619 TTTTC -s simDog_chr6.simDog.chr6 587671 5 + 593897 TTATC -s simHuman_chr6.simHuman.chr6 591775 5 + 601863 TTATG -s simRat_chr6.simRat.chr6 636600 5 + 647215 TTGAG - -a -s simMouse_chr6.simMouse.chr6 625013 5 + 636262 TAGTG -s Anc0.Anc0refChr3 219242 2 + 222631 TA--- -s Anc1.Anc1refChr1 59977 5 + 69767 TAGTG -s Anc2.Anc2refChr1 137053 2 + 142988 TA--- -s mr.mrrefChr3 171705 5 + 181027 TAGTG -s simCow_chr6.simCow.chr6 6200 2 - 602619 TT--- -s simDog_chr6.simDog.chr6 587676 2 + 593897 TA--- -s simHuman_chr6.simHuman.chr6 591780 5 + 601863 TGGTG -s simRat_chr6.simRat.chr6 636608 5 + 647215 CAGTT - -a -s simMouse_chr6.simMouse.chr6 625018 16 + 636262 GGTTGTTGTGAGATAC -s Anc0.Anc0refChr3 219286 16 + 222631 AGACCTTGTGAAATAC -s Anc1.Anc1refChr1 60024 16 + 69767 AGACCTTGTGAAATAC -s Anc2.Anc2refChr1 137097 16 + 142988 AGACCTTGTGAAATAC -s mr.mrrefChr3 171710 16 + 181027 GGTCCTTGTGAGATAC -s simCow_chr6.simCow.chr6 6244 16 - 602619 AGACCTTGTGAAATAC -s simDog_chr6.simDog.chr6 587720 16 + 593897 AGTCCTTGTGGAATAC -s simHuman_chr6.simHuman.chr6 591835 16 + 601863 AGACCTTGTGAAATGC -s simRat_chr6.simRat.chr6 636613 16 + 647215 GGTCCATGTCATATAC - -a -s simMouse_chr6.simMouse.chr6 625034 7 + 636262 ATGATGC -s Anc0.Anc0refChr3 219307 7 + 222631 ATGATGC -s Anc1.Anc1refChr1 60045 7 + 69767 ATGATGC -s Anc2.Anc2refChr1 137118 7 + 142988 ATGGTGC -s mr.mrrefChr3 171726 7 + 181027 ATGATGC -s simCow_chr6.simCow.chr6 6289 7 - 602619 ATGTTGC -s simDog_chr6.simDog.chr6 587741 7 + 593897 GTGGCAC -s simHuman_chr6.simHuman.chr6 591856 7 + 601863 ATGATGC -s simRat_chr6.simRat.chr6 636629 7 + 647215 ATGATGC - -a -s simMouse_chr6.simMouse.chr6 625041 8 + 636262 CCACCCTG -s Anc0.Anc0refChr3 219319 8 + 222631 CCACACTG -s Anc1.Anc1refChr1 60057 8 + 69767 CCACACTG -s Anc2.Anc2refChr1 137130 8 + 142988 CCACAGTG -s mr.mrrefChr3 171733 8 + 181027 CCACCCTG -s simCow_chr6.simCow.chr6 6301 8 - 602619 CCACAGTG -s simDog_chr6.simDog.chr6 587753 8 + 593897 CCACTGTT -s simHuman_chr6.simHuman.chr6 591868 8 + 601863 CCACACTG -s simRat_chr6.simRat.chr6 636636 8 + 647215 CCACTCTG - -a -s simMouse_chr6.simMouse.chr6 625049 33 + 636262 CTGAGTGTTATAATACACAAAATGATGCTGACA -s Anc0.Anc0refChr3 219373 32 + 222631 TTAA-TGCTATAATACACAAAAAAATGGTGACA -s Anc1.Anc1refChr1 60111 33 + 69767 TTAAGTGCTATAATACACAAAAAAATGGTGACA -s Anc2.Anc2refChr1 137184 32 + 142988 TTAA-TGCTATAATACACAAAAAAATGGTGAGA -s mr.mrrefChr3 171741 33 + 181027 CTGAGTGTTATAATACACAAAATAATGGTGACA -s simCow_chr6.simCow.chr6 6350 32 - 602619 TTAA-TGCTTTAATCCACAAAAAAATGGTGAGA -s simDog_chr6.simDog.chr6 587807 32 + 593897 TTAA-TGCTATGATACACAAAAAAATAGCGAGA -s simHuman_chr6.simHuman.chr6 591924 33 + 601863 TTAAGTACTATAATACACAAAAAAATGGTGACA -s simRat_chr6.simRat.chr6 636644 33 + 647215 CCGGGTGTTGTAATACATAAGATAATGGTGACA - -a -s simMouse_chr6.simMouse.chr6 625082 52 + 636262 ATTACCAATATCCCAATGAACAAACCAATTGAAGATATGTACACTCATTAAC -s Anc0.Anc0refChr3 219409 52 + 222631 ATTATCAAAATCCCAATTAATAAACAGTCTGAAGATATGTATACTCATTGAT -s Anc1.Anc1refChr1 60148 52 + 69767 ATTATCAAAATCCCAATTAATAAACAGTCTGAAGATATGTATACTCATTGAT -s Anc2.Anc2refChr1 137221 52 + 142988 ATTATCAAAATCCCAATTAATAAACAGTCTGAAGATATGTTTACTCATTGAT -s mr.mrrefChr3 171774 52 + 181027 ATTACCAATATCCCAATGAACAAACCAATTGAAGATATGTATACTCATTAAT -s simCow_chr6.simCow.chr6 6387 52 - 602619 ATTATCAAGATCTCAATTGATAAATGGTCTGAAGATATGTTTACTCACTGAT -s simDog_chr6.simDog.chr6 587844 52 + 593897 ATTATCAGAAACCTAATTAATAAACACTCAGAAGGTATGTTCATGAATTGAC -s simHuman_chr6.simHuman.chr6 591961 52 + 601863 ATTAACAAAATCCCAATTAATAAACAGCCTGACAATATGTATACTCATTGAT -s simRat_chr6.simRat.chr6 636677 52 + 647215 ATTATCAATATTCCAATGAACAAACCATTTGAAGAGATGTATACTCATTAAT - -a -s simMouse_chr6.simMouse.chr6 625134 18 + 636262 TAGTATAGAACATTCAAG -s Anc0.Anc0refChr3 219461 12 + 222631 AACTA------ACTCATG -s Anc1.Anc1refChr1 60200 12 + 69767 AACTA------ACTCATG -s Anc2.Anc2refChr1 137288 12 + 142988 AACTT------GCACATG -s mr.mrrefChr3 171826 18 + 181027 TAGTATAGAACACTCAAG -s simCow_chr6.simCow.chr6 6454 12 - 602619 AACAT------TCATCTG -s simDog_chr6.simDog.chr6 587912 12 + 593897 AACTT------GCACATG -s simHuman_chr6.simHuman.chr6 592013 12 + 601863 AACTA------ACTCATG -s simRat_chr6.simRat.chr6 636729 18 + 647215 TATTATAGAACACTCAAC - -a -s simMouse_chr6.simMouse.chr6 625152 8 + 636262 TGGGTACT -s Anc0.Anc0refChr3 219473 8 + 222631 TGGATACT -s Anc1.Anc1refChr1 60212 8 + 69767 TGGATACT -s Anc2.Anc2refChr1 137301 8 + 142988 CAGATACT -s mr.mrrefChr3 171844 8 + 181027 TGGGTACT -s simCow_chr6.simCow.chr6 6467 8 - 602619 CAGGTACT -s simDog_chr6.simDog.chr6 587925 8 + 593897 CAGATACT -s simHuman_chr6.simHuman.chr6 592025 8 + 601863 TGGATTCT -s simRat_chr6.simRat.chr6 636747 8 + 647215 TGGGTACT - -a -s simMouse_chr6.simMouse.chr6 625160 33 + 636262 CATATTAATGTAGAAAGATATGGCAGTTCTTGG -s Anc0.Anc0refChr3 219481 33 + 222631 CATATTGATGTAGGAAAATAAAGCAGTACTTGG -s Anc1.Anc1refChr1 60220 33 + 69767 CATATTGATGTAGGAAAATAAAGCAGTACTTGG -s Anc2.Anc2refChr1 137309 33 + 142988 CATATTGATGTAGGAAAATAAAGCAATACTTGG -s mr.mrrefChr3 171852 33 + 181027 CATATTAATGTAGAAAGATATGGCAGTTCTTGG -s simCow_chr6.simCow.chr6 6475 33 - 602619 CACATTGATGCAGGAAGATCAAGCAATACTTGG -s simDog_chr6.simDog.chr6 587933 33 + 593897 CATATTGATGTAGCAAAATAAAGCAATACTTGG -s simHuman_chr6.simHuman.chr6 592035 33 + 601863 CATATTGATATAGGAGAATGAAGCAGCATTTGG -s simRat_chr6.simRat.chr6 636755 33 + 647215 CATACTAATGTAACAAGGTTTGGCAATCCTTGG - -a -s simMouse_chr6.simMouse.chr6 625193 12 + 636262 AAACTTACAGAT -s Anc0.Anc0refChr3 219523 12 + 222631 ATCCTGACAATT -s Anc1.Anc1refChr1 60262 12 + 69767 ATCCTGACAATT -s Anc2.Anc2refChr1 137352 12 + 142988 ATCCTGAAAATT -s mr.mrrefChr3 171885 12 + 181027 ATACTTACAGAT -s simCow_chr6.simCow.chr6 6522 12 - 602619 TCCCTGAAAGTA -s simDog_chr6.simDog.chr6 587976 12 + 593897 ATCTGGAAGATT -s simHuman_chr6.simHuman.chr6 592077 12 + 601863 ATCCTGACAATT -s simRat_chr6.simRat.chr6 636788 12 + 647215 ATACTTACAGAT - -a -s simMouse_chr6.simMouse.chr6 625205 9 + 636262 TTGCATTAC -s Anc0.Anc0refChr3 219539 9 + 222631 TGGGATTAC -s Anc1.Anc1refChr1 60278 9 + 69767 TGGGATTAC -s Anc2.Anc2refChr1 137368 9 + 142988 TGGGATTAC -s mr.mrrefChr3 171897 9 + 181027 TTGCATTAC -s simCow_chr6.simCow.chr6 6538 8 - 602619 TGGG-TTAC -s simDog_chr6.simDog.chr6 587992 9 + 593897 TGGGATTAC -s simHuman_chr6.simHuman.chr6 592093 9 + 601863 TAGGATTGT -s simRat_chr6.simRat.chr6 636800 9 + 647215 TTGCATTAC - -a -s simMouse_chr6.simMouse.chr6 625214 11 + 636262 TGAGAGGACAC -s Anc0.Anc0refChr3 219549 11 + 222631 AGGGCTACTAC -s Anc1.Anc1refChr1 60288 11 + 69767 AGGGCTACTAC -s Anc2.Anc2refChr1 137378 11 + 142988 AGGGCTACTAA -s mr.mrrefChr3 171907 11 + 181027 TGAGAGGATAC -s simCow_chr6.simCow.chr6 6547 11 - 602619 AGGGCTACTAA -s simDog_chr6.simDog.chr6 588002 11 + 593897 AGGGTTACTAA -s simHuman_chr6.simHuman.chr6 592103 11 + 601863 AGGGCTCCTAC -s simRat_chr6.simRat.chr6 636810 11 + 647215 TGAGAGGATAC - -a -s simMouse_chr6.simMouse.chr6 625225 104 + 636262 TTAGATTTCTGAGGTCATTAGAAACTTTACAAGGTCTACTAATTTCACTCGATAAAGTATGTCTATATAGAGATAGCAAGGCTATGAGCTTTTGAGAGACCCAC -s Anc0.Anc0refChr3 219564 104 + 222631 TTAAATCTCTAGAGGCACTAAAAATTGTTCAAGGTCTACTAAGTTTACTCAATAGACTACGTCTGCTTTGGTATGCCAAGGCTATGGAGCTTTGACAGTCCCAC -s Anc1.Anc1refChr1 60303 104 + 69767 TTAAATCTCTAGAGGCACTAAAAATTGTTCAAGGTCTACTAAGTTTACTCAATAGACTACGTCTGCTTTGGTATGCCAAGGCTATGGAGCTTTGACAGTCCCAC -s Anc2.Anc2refChr1 137395 104 + 142988 GTTAATCTCTAGAGGCACTAAAAATTGTTCAAGGTCTACTTAGTTTACTCAATAGACTACATCTGCTTTGGTATGCCAAGGCTATGGAGCTTTGACAGTCCCAC -s mr.mrrefChr3 171918 104 + 181027 TTAAATTTCTGAGGTCATTAAAAATTTTACAAGGTCTACTAATTTCACTCGATAAACTATGTCTGTATTGAGATAGCAAGGCTATGAAGTTTTGAGAGACCCAC -s simCow_chr6.simCow.chr6 6564 103 - 602619 CACAATCTTTGGAGGCACTAAAAACTGTTCAAGGTCTACTTAGTTGACTCAATAGATCGCATGTGATTTAGTATGCCAAGGCT-TTGAGCTTTGACAATCTCAC -s simDog_chr6.simDog.chr6 588019 104 + 593897 GTTAATCTCCAGAGGCACTAAAAATTGTTCAGGGTCTACTTAGTTTACTCAATAGACTACATCTGCTTTGGTCTGCCAAGCCTAAGGAGCTTTGACAGTGCCAC -s simHuman_chr6.simHuman.chr6 592118 104 + 601863 TTAAATCACTAGAAACACTCAAAATTGTTCAAGGTCTACTAGCTATACTCAATGCACTAGGTCTGCTTTGGTATGCCAAGGCCATGGAGCTTTGACAGCCCCAC -s simRat_chr6.simRat.chr6 636821 93 + 647215 TTAAGTTTGTGAGGTCATTAAAAATTTTACAGAGTCTACT----------GATAAACTATATCTGTATTGAGATAGCCAG-CTATCAAGTTTTGAGATACCCAA - -a -s simMouse_chr6.simMouse.chr6 625329 46 + 636262 ACGTTTAGTGGCCACACCAAGTCTCAGCACTACAGGAGTATGTTTA -s Anc0.Anc0refChr3 219668 28 + 222631 ATGTCT------------------ACGCCCTACATGAGTATGTGTA -s Anc1.Anc1refChr1 60407 28 + 69767 ATGTCT------------------ACGCCCTACATGAGTATGTGTA -s Anc2.Anc2refChr1 137513 28 + 142988 GTGTCT------------------ACGCCCTACATGAGCATGTGTA -s mr.mrrefChr3 172022 28 + 181027 ATGTTT------------------CAGCACTACAGGAGTATGTTTA -s simCow_chr6.simCow.chr6 6773 28 - 602619 GTGTCT------------------AAGCCCTACATGAGCGTGTGTA -s simDog_chr6.simDog.chr6 588137 28 + 593897 GTGTCT------------------ACATCGTTCATGACCATGTGTA -s simHuman_chr6.simHuman.chr6 592273 28 + 601863 ATGTCT------------------AGGCCCTACGTGAGTATGTGTA -s simRat_chr6.simRat.chr6 636914 28 + 647215 ATGTTT------------------CAGCACCACAGGAGGATGTGTG - -a -s simMouse_chr6.simMouse.chr6 625375 42 + 636262 AGACACTCCATGTCACATTGTCCAGTGGGCTAGATAGGATGG -s Anc0.Anc0refChr3 219696 6 + 222631 AGACAC------------------------------------ -s Anc1.Anc1refChr1 60435 27 + 69767 AGACAC---------------CTACTGGATTACAGGAGATTG -s Anc2.Anc2refChr1 137541 6 + 142988 AGACAC------------------------------------ -s mr.mrrefChr3 172050 42 + 181027 AGACACTCCATGTGACATTGTCTACTGGGCTAGATAGGATTG -s simCow_chr6.simCow.chr6 6801 6 - 602619 AGACAC------------------------------------ -s simDog_chr6.simDog.chr6 588165 6 + 593897 AGATAC------------------------------------ -s simHuman_chr6.simHuman.chr6 592301 27 + 601863 AGACAC---------------CTACTGGATTACAGGAGATTG -s simRat_chr6.simRat.chr6 636944 42 + 647215 AGACTCTCCATTTGGCATTGTCTACTGGGCTAGAAAGGATTT - -a -s simMouse_chr6.simMouse.chr6 625417 11 + 636262 TCTCTCATGAA -s Anc0.Anc0refChr3 219702 8 + 222631 TCTCCCAT--- -s Anc1.Anc1refChr1 60462 11 + 69767 TCTCCCATGAA -s Anc2.Anc2refChr1 137547 8 + 142988 TCCCCCAT--- -s mr.mrrefChr3 172092 11 + 181027 TCTCTCATGAA -s simCow_chr6.simCow.chr6 6905 8 - 602619 TCCCATAC--- -s simDog_chr6.simDog.chr6 588171 8 + 593897 TCCCCCAT--- -s simHuman_chr6.simHuman.chr6 592328 9 + 601863 CCTCC--TGAA -s simRat_chr6.simRat.chr6 636986 11 + 647215 TCTTTCACGAA - -a -s simMouse_chr6.simMouse.chr6 625428 9 + 636262 TCTGATTGT -s Anc0.Anc0refChr3 219710 6 + 222631 ---AATTGT -s Anc1.Anc1refChr1 60474 9 + 69767 TCTAATTGT -s Anc2.Anc2refChr1 137555 6 + 142988 ---AATTGT -s mr.mrrefChr3 172104 9 + 181027 TCTAATTGT -s simCow_chr6.simCow.chr6 6913 6 - 602619 ---AAACAT -s simDog_chr6.simDog.chr6 588179 6 + 593897 ---TATTGT -s simHuman_chr6.simHuman.chr6 592338 9 + 601863 TCTAATTGT -s simRat_chr6.simRat.chr6 636998 9 + 647215 TCTAATTGT - -a -s simMouse_chr6.simMouse.chr6 625437 15 + 636262 TGTATTAGCCAACTT -s Anc0.Anc0refChr3 219716 15 + 222631 TGTATCAGCCAACTT -s Anc1.Anc1refChr1 60483 15 + 69767 TGTATCAGCCAACTT -s Anc2.Anc2refChr1 137561 15 + 142988 TGTATCAGCTAACTT -s mr.mrrefChr3 172113 15 + 181027 TGTATTAGCCAACTT -s simCow_chr6.simCow.chr6 596580 15 + 602619 TGCATCAGCTAACTT -s simDog_chr6.simDog.chr6 588185 15 + 593897 TGTATCAACTGACTT -s simHuman_chr6.simHuman.chr6 592347 15 + 601863 TGTATCAGCCACCTT -s simRat_chr6.simRat.chr6 637007 15 + 647215 TGTATTAGCCAACTT - -a -s simMouse_chr6.simMouse.chr6 625452 16 + 636262 AATGGCATCAATTACG -s Anc0.Anc0refChr3 219731 16 + 222631 CAAGGCATTAATAAGG -s Anc1.Anc1refChr1 60498 16 + 69767 CAAGGCATTAATAAGG -s Anc2.Anc2refChr1 137577 16 + 142988 CAAGGCATTAATAAGG -s mr.mrrefChr3 172128 16 + 181027 AATGGCATCAATTACG -s simCow_chr6.simCow.chr6 596596 16 + 602619 CAACACATCAATAAGG -s simDog_chr6.simDog.chr6 588201 16 + 593897 TGAGGCATTAATAAGG -s simHuman_chr6.simHuman.chr6 592362 8 + 601863 CAAGGCAT-------- -s simRat_chr6.simRat.chr6 637022 16 + 647215 AATTGCATCAATTAGG - -a -s simMouse_chr6.simMouse.chr6 625468 9 + 636262 TCAACTGGC -s Anc0.Anc0refChr3 219747 5 + 222631 TCA----AC -s Anc1.Anc1refChr1 60514 5 + 69767 TCA----AC -s Anc2.Anc2refChr1 137594 5 + 142988 TCA----AC -s mr.mrrefChr3 172144 5 + 181027 TCA----GC -s simCow_chr6.simCow.chr6 596613 5 + 602619 TAA----AC -s simDog_chr6.simDog.chr6 588218 5 + 593897 TCA----AC -s simRat_chr6.simRat.chr6 637038 5 + 647215 TCA----GC - -a -s simMouse_chr6.simMouse.chr6 625477 1 + 636262 T -s Anc0.Anc0refChr3 219752 1 + 222631 T -s Anc1.Anc1refChr1 60519 1 + 69767 T -s Anc2.Anc2refChr1 137599 1 + 142988 T -s mr.mrrefChr3 172149 1 + 181027 T -s simCow_chr6.simCow.chr6 596618 1 + 602619 T -s simDog_chr6.simDog.chr6 588224 1 + 593897 T -s simHuman_chr6.simHuman.chr6 592370 1 + 601863 T -s simRat_chr6.simRat.chr6 637043 1 + 647215 C - -a -s simMouse_chr6.simMouse.chr6 625478 97 + 636262 GGTTGCAGATTACAACAGGCTTGTTCCTTGGCTTCCCAGTTGATTAGGGTCCCGAGCTTATCCTGGACTCCAGTGAATAATCCAGATATATTAGGCC -s Anc0.Anc0refChr3 219753 95 + 222631 GTTGGAGGATTAAATCAGACTTATTACTCAGATACCCA-TCGATTAGATCCCAAAGCTTATCCCAAATTCCTATATATAATTAGGGTGTGGT-GTCC -s Anc1.Anc1refChr1 60520 96 + 69767 GTTGGAGGATTAAATCAGACTTATTACTCAGATACCCA-TCGATTAGATCCCAAAGCTTATCCCAAATTCCTATATATAATTAGGGTGTGGTCGTCC -s Anc2.Anc2refChr1 137605 95 + 142988 GTTGGAGGATTAAATCAGACTTATTACTCAGATACCCA-TCGATTAGATCCCAAAGCTTATCCCAAATTCCTATATATAATTAGGGTGTGGT-GTCC -s mr.mrrefChr3 172150 96 + 181027 GGTTGCGGATTACATCAGGCTTATTCCTTGGCTTCCCA-TTGATTAGGGTCCCAAGCTTATCCTGAACTCCAGTGAATAATTCAGATATATTAGGCC -s simCow_chr6.simCow.chr6 596624 92 + 602619 GTTGGAGGATTAAACCATACTTATTACTCAGAAAACCA-TCGACTGTGTCCTAAG---CATCCCAAACTCCTGTATATAGTTAGGGTGTGGT-GTCC -s simDog_chr6.simDog.chr6 588230 95 + 593897 GTTGAAGGATTAAGTCGGACCTATGGCTCATTTACCCA-TCGGTCAGAGTTCAAAGCTTATCCCAAATTCCTATATATAATTAGGGTTTGGT-GTCC -s simHuman_chr6.simHuman.chr6 592371 96 + 601863 GATGGAGGATTAGATCAGAGTTATTACTCAGATACACA-TCGATTAGTTCCCAAAGCTTACTTCAAATTCCCATATATGATTAGGGCGTGGTCATCC -s simRat_chr6.simRat.chr6 637044 96 + 647215 AGTTGCGGATCACGTTGCGCTTATTCCTTGGGTTCCCA-TTGATTCGGGTCCCAAGTTTATCCTGAACTCCAGTGAATAATTCATATATATTAGGCC - -a -s simMouse_chr6.simMouse.chr6 625575 2 + 636262 CA -s Anc0.Anc0refChr3 219852 2 + 222631 CA -s Anc1.Anc1refChr1 60620 2 + 69767 CA -s Anc2.Anc2refChr1 137704 2 + 142988 TA -s mr.mrrefChr3 172246 2 + 181027 CA -s simCow_chr6.simCow.chr6 596720 2 + 602619 GA -s simDog_chr6.simDog.chr6 588329 2 + 593897 TA -s simHuman_chr6.simHuman.chr6 592471 2 + 601863 CA -s simRat_chr6.simRat.chr6 637140 2 + 647215 CA - -a -s simMouse_chr6.simMouse.chr6 625577 4 + 636262 CAGA -s Anc0.Anc0refChr3 219856 4 + 222631 TAGG -s Anc1.Anc1refChr1 60624 4 + 69767 TAGG -s Anc2.Anc2refChr1 137708 4 + 142988 CCAG -s mr.mrrefChr3 172250 4 + 181027 TAGA -s simCow_chr6.simCow.chr6 596724 4 + 602619 CCCA -s simDog_chr6.simDog.chr6 588333 4 + 593897 CCAG -s simHuman_chr6.simHuman.chr6 592475 4 + 601863 TAGG -s simRat_chr6.simRat.chr6 637144 4 + 647215 TAGA - -a -s simMouse_chr6.simMouse.chr6 625581 21 + 636262 CCCTCCATATGCTATTTTCCG -s Anc0.Anc0refChr3 219862 21 + 222631 CCCTCCATATGCTATCATTGT -s Anc1.Anc1refChr1 60630 21 + 69767 CCCTCCATATGCTATCATTGT -s Anc2.Anc2refChr1 137714 21 + 142988 CCCTCCTTATGCTACCATTGT -s mr.mrrefChr3 172254 21 + 181027 CCCTCCATATGCTATTATCCT -s simCow_chr6.simCow.chr6 596730 21 + 602619 CCTTCCTTATGATGCTATTGT -s simDog_chr6.simDog.chr6 588339 21 + 593897 CCCTCCTTCTGCTACCACTGT -s simHuman_chr6.simHuman.chr6 592481 21 + 601863 CCCTCCATATGCCATCATTGT -s simRat_chr6.simRat.chr6 637148 21 + 647215 CCCCCCATATGCTATTATCTT - -a -s simMouse_chr6.simMouse.chr6 625602 107 + 636262 TCTACATGCACATAAAGCAAAACCTCATTAATCTAGGAAGGGTCTCATCCTCGCTGTTTTGACTTGTCTGACGCACCTGCTATCAGCCCATGTAGTGGAAATGTGGA -s Anc0.Anc0refChr3 219898 51 + 222631 T--------------------------------------------A-----------TGTGA-TAGTCTGTCACACTTGGTTTCAGCCAATATAGTGGAAATTTGGA -s Anc1.Anc1refChr1 60666 83 + 69767 TTTAGACTCACATAGTGCA------------CCGATACAGGGTCCA-----------TGTGA-TAGTCTGTCACACTTGGTTTCAGCCAATATAGTGGAAATTTGGA -s Anc2.Anc2refChr1 137750 51 + 142988 T--------------------------------------------A-----------TGTGA-TAGTCTGTCACACTTGGTTTCAGCCAAGATAGTGGAAATTTGGA -s mr.mrrefChr3 172275 83 + 181027 TTTACATGCACATAAAGCA------------TCTAGGAAGGGTCTC-----------TTTGA-TAGTCTGACGCACCTGCTATCAGCCCATGTAGTGGAAATTTGGA -s simCow_chr6.simCow.chr6 596766 49 + 602619 C--------------------------------------------A-----------TGC-A-TAGTCTGTC-CACTTGGTTTCATTCTGCATAGTGGAAATTTGGA -s simDog_chr6.simDog.chr6 588374 50 + 593897 T--------------------------------------------A-----------AGTGG-TAATTTGTCACACT-GATTTGAGCCAAGATAGCTGAAATTTGGA -s simHuman_chr6.simHuman.chr6 592517 83 + 601863 TTTAGACTCACATAGTGCA------------CCGATACAGGGTCCA-----------TGTGA-TAGCCTGGCACATTTGGTTTCAGCTGATCTAGTGGAAATTTGGA -s simRat_chr6.simRat.chr6 637169 57 + 647215 CTTACATA-------------------------------------------------TTTGA-TAGTCTGACGCACCTGTTCTCAGCCCATGTAGTGGAATCTTGGA - -a -s simMouse_chr6.simMouse.chr6 625709 8 + 636262 CTGTTATC -s Anc0.Anc0refChr3 219949 8 + 222631 CCTTCATT -s Anc1.Anc1refChr1 60749 8 + 69767 CCTTCATT -s Anc2.Anc2refChr1 137801 8 + 142988 CCTTCATT -s mr.mrrefChr3 172358 8 + 181027 CTGTTATC -s simCow_chr6.simCow.chr6 596815 8 + 602619 CCTTCGTT -s simDog_chr6.simDog.chr6 588425 8 + 593897 CCTTCATT -s simHuman_chr6.simHuman.chr6 592600 8 + 601863 CCTTCATT -s simRat_chr6.simRat.chr6 637226 8 + 647215 CTGTTAGC - -a -s simMouse_chr6.simMouse.chr6 625717 6 + 636262 GGTACT -s Anc0.Anc0refChr3 219957 1 + 222631 A----- -s Anc1.Anc1refChr1 60757 1 + 69767 A----- -s Anc2.Anc2refChr1 137809 1 + 142988 A----- -s mr.mrrefChr3 172366 6 + 181027 GGTACT -s simCow_chr6.simCow.chr6 596830 1 + 602619 G----- -s simDog_chr6.simDog.chr6 588433 1 + 593897 A----- -s simHuman_chr6.simHuman.chr6 592608 1 + 601863 A----- -s simRat_chr6.simRat.chr6 637234 6 + 647215 GGTACC - -a -s simMouse_chr6.simMouse.chr6 625723 57 + 636262 GTACCAGTCACAGCAAACGGACCAGCATACCAGTGCCACAGCACCCGGCTGGGTCCT -s Anc0.Anc0refChr3 219982 48 + 222631 TTGCTAGTCAAAGCTAAGT--------TACCAGTGACAGAGCA-CCAACTGGGTCCT -s Anc1.Anc1refChr1 60782 48 + 69767 TTGCTAGTCAAAGCTAAGT--------TACCAGTGACAGAGCA-CCAACTGGGTCCT -s Anc2.Anc2refChr1 137834 48 + 142988 TGGCTAGTCAAAGCTAAGT--------TACAAGTGACAGAGCA-CCAACTGGGTCCT -s mr.mrrefChr3 172396 57 + 181027 TTACCAGTCACAGCAAAGGGACCAGCATACCAGTGCCACAGCACCCAGCTGGGTCCT -s simCow_chr6.simCow.chr6 596855 48 + 602619 TGACTAGTCAGAGTTAAGC--------GACGGGAGACAGACCA-CCAACTGGGTCCG -s simDog_chr6.simDog.chr6 588562 48 + 593897 TGGTTGGTCAAAGCTAAAT--------TAGAAGTTGCACAGCA-CCAACTGGGCCCT -s simHuman_chr6.simHuman.chr6 592633 48 + 601863 TTGCTAGCCATAACTAAGT--------TACCAGTGACGGAACA-CCAACTGGGTCCT -s simRat_chr6.simRat.chr6 637265 54 + 647215 TTACCAGTC---GCAAAGGCACCAGCATACCAATGCCACAGCACCCAGCTGGGTCTT - -a -s simMouse_chr6.simMouse.chr6 625780 37 + 636262 ATGGCAATTTAGATCCAGGTGAGAGTCTCAGAAGTCT -s Anc0.Anc0refChr3 220030 36 + 222631 TTGGTGAGTTAGATCAAGATGAG-GACTGATAAGTCT -s Anc1.Anc1refChr1 60830 36 + 69767 TTGGTGAGTTAGATCAAGATGAG-GACTGATAAGTCT -s Anc2.Anc2refChr1 137883 36 + 142988 TTGGTGAGATAGATCAACACAAG-GACTGGTAAGTCT -s mr.mrrefChr3 172453 36 + 181027 ATGGCAAGTTAGATCCAGATGAG-GTCTCAGAAGTCT -s simCow_chr6.simCow.chr6 596904 36 + 602619 TTGGTGGGATAGATTAATACAAG-GACCGGTAAGTCT -s simDog_chr6.simDog.chr6 588611 32 + 593897 TTGGTCAGATAGATCAACA-----GGCTGGCAAGACT -s simHuman_chr6.simHuman.chr6 592681 36 + 601863 TTGATGAGTTAGATCAAGATGAG-GACTGATAAATCT -s simRat_chr6.simRat.chr6 637319 36 + 647215 AGGGCAAGATAGATTCAGATGAG-GTCTCAGAAGTCT - -a -s simMouse_chr6.simMouse.chr6 625817 3 + 636262 AGA -s Anc0.Anc0refChr3 220066 3 + 222631 GGA -s Anc1.Anc1refChr1 60866 3 + 69767 GGA -s Anc2.Anc2refChr1 137919 3 + 142988 GGA -s mr.mrrefChr3 172489 3 + 181027 AGA -s simCow_chr6.simCow.chr6 596940 3 + 602619 GGC -s simDog_chr6.simDog.chr6 588644 3 + 593897 GGA -s simHuman_chr6.simHuman.chr6 592717 3 + 601863 GGA -s simRat_chr6.simRat.chr6 637355 3 + 647215 AAA - -a -s simMouse_chr6.simMouse.chr6 625820 27 + 636262 CTCAATGATCAAGCAAGTTTACCATCT -s Anc0.Anc0refChr3 220071 27 + 222631 CTCAGTGATCAAGCAATCTTACCATTT -s Anc1.Anc1refChr1 60871 27 + 69767 CTCAGTGATCAAGCAATCTTACCATTT -s Anc2.Anc2refChr1 137924 27 + 142988 CTCAGTGATCAAGCAATCTCACCATTT -s mr.mrrefChr3 172492 27 + 181027 CTCAATGATCAAGCAAGTTTACCATCT -s simCow_chr6.simCow.chr6 596945 27 + 602619 CTCAGTGATAAAGCAATCTCACCAGTT -s simDog_chr6.simDog.chr6 588649 27 + 593897 TTCACTGATCAAGCAATCTCACCATTT -s simHuman_chr6.simHuman.chr6 592722 27 + 601863 CTCAGTGATCAAGCAATCTTACCGTTT -s simRat_chr6.simRat.chr6 637358 27 + 647215 CTCAATGATCAAGCAAGTTTACCATCT - -a -s simMouse_chr6.simMouse.chr6 625847 16 + 636262 TTTTGATGTTGCAATA -s Anc0.Anc0refChr3 220098 16 + 222631 GTTTGATGTTGCAATA -s Anc1.Anc1refChr1 60898 16 + 69767 GTTTGATGTTGCAATA -s Anc2.Anc2refChr1 137951 16 + 142988 GTTTGATGTTGCAATA -s mr.mrrefChr3 172519 16 + 181027 TTTTGATGTTGCAATA -s simCow_chr6.simCow.chr6 596972 16 + 602619 GCTTAATGTTGCAATG -s simDog_chr6.simDog.chr6 588677 16 + 593897 TTTTGTTGTTGCAACA -s simHuman_chr6.simHuman.chr6 592749 15 + 601863 GTTCGATGTTGCAAT- -s simRat_chr6.simRat.chr6 637385 16 + 647215 TTTTGATGTTGCAATG - -a -s simMouse_chr6.simMouse.chr6 625863 33 + 636262 CATTATGTGTTCATTACATGATGTATGGAGTTG -s Anc0.Anc0refChr3 220114 33 + 222631 CATTATGATTCCATTGAATGACGAAAGGAATTG -s Anc1.Anc1refChr1 60914 33 + 69767 CATTATGATTCCATTGAATGACGAAAGGAATTG -s Anc2.Anc2refChr1 137967 33 + 142988 CATTACAATTCTATTCAACGACGAAAGGAATTG -s mr.mrrefChr3 172535 33 + 181027 CATTATGTGTTCATTGCATGATGTATGGAGTTG -s simCow_chr6.simCow.chr6 596992 32 + 602619 CACTACAATTCTATTCAACGATGAAAG-AAGGA -s simDog_chr6.simDog.chr6 588693 24 + 593897 CATTACAATTC---------ACGAAAGGTGTTG -s simHuman_chr6.simHuman.chr6 592764 32 + 601863 -ATTATGATCCCATTGAATAACGGAAGGAATTG -s simRat_chr6.simRat.chr6 637401 33 + 647215 CATTATCCGTTCATTGCGGGATGTATGGAGTTG - -a -s simMouse_chr6.simMouse.chr6 625896 11 + 636262 CCTCTCTATGA -s Anc0.Anc0refChr3 220147 11 + 222631 GCTCTCTAGTA -s Anc1.Anc1refChr1 60947 11 + 69767 GCTCTCTAGTA -s Anc2.Anc2refChr1 138002 11 + 142988 GCTCTCTAGTA -s mr.mrrefChr3 172568 11 + 181027 GCTCTCTATGA -s simCow_chr6.simCow.chr6 597026 11 + 602619 GCTATCTGTTC -s simDog_chr6.simDog.chr6 588719 11 + 593897 GCTCTCTAGCA -s simHuman_chr6.simHuman.chr6 592796 11 + 601863 GCTCTTTAGTG -s simRat_chr6.simRat.chr6 637434 11 + 647215 GCTCTCTATGA - -a -s simMouse_chr6.simMouse.chr6 625907 80 + 636262 TTCACCCCTTGGCAGGCTTGTACTACTTCTATAAATTACTTATAGTCCTGGATTACATTACCCTGTTAAGTTTTCCTGTC -s Anc0.Anc0refChr3 220158 49 + 222631 AGC-------------------ATGGTCCTTGCAGCCATTTGTGGTCA------------ATGTGTAAAGTGGTCCTTAC -s Anc1.Anc1refChr1 60958 49 + 69767 AGC-------------------ATGGTCCTTGCAGCCATTTGTGGTCA------------ATGTGTAAAGTGGTCCTTAC -s Anc2.Anc2refChr1 138013 49 + 142988 AGC-------------------ATGGTCCTTGCAGCCATTTGTGGTCA------------ATGTGTAGAGTGGTCCTTGC -s mr.mrrefChr3 172579 51 + 181027 TTC-----------------TAATACTCCTTGCAACCACTTGTGGTCC------------CCCTGTTAAGTGGTCCTTAC -s simCow_chr6.simCow.chr6 597037 49 + 602619 AGC-------------------ATGGTCCTTGTAGCCATTTGTTGTCA------------ACATGTAGAGTGGTCCTTGC -s simDog_chr6.simDog.chr6 588730 49 + 593897 GTC-------------------GTGGCCCTTGCACCCATTTGTGGCCA------------ATGTATAGAATGGTCCTTGC -s simHuman_chr6.simHuman.chr6 592815 49 + 601863 AGG-------------------ATGGTCCTTGCAGCCATTTGTGGTCA------------ATGTGGCAAGTGGTCCTTAC -s simRat_chr6.simRat.chr6 637445 51 + 647215 TTC-----------------TAATAATCCTTGCGACCACTTGTGGTGC------------CCCCTTTGAATGGTCCTTAT - -a -s simMouse_chr6.simMouse.chr6 625987 10 + 636262 CCTCCATCGA -s Anc0.Anc0refChr3 220209 10 + 222631 CCACTTATGG -s Anc1.Anc1refChr1 61009 10 + 69767 CCACTTATGG -s Anc2.Anc2refChr1 138064 10 + 142988 CCATTCATGG -s mr.mrrefChr3 172632 10 + 181027 CCTCTTTCGA -s simCow_chr6.simCow.chr6 597088 10 + 602619 CAATTCATGG -s simDog_chr6.simDog.chr6 588781 10 + 593897 CCATTCATGG -s simHuman_chr6.simHuman.chr6 592866 10 + 601863 CCACTTATGG -s simRat_chr6.simRat.chr6 637498 10 + 647215 CCTCTTTCGA - -a -s simMouse_chr6.simMouse.chr6 625997 23 + 636262 TGAACTCATGATGGTAAGTTGAT -s Anc0.Anc0refChr3 220219 22 + 222631 TCAATTCAAAAAG-CTAGTGGTT -s Anc1.Anc1refChr1 61019 22 + 69767 TCAATTCAAAAAG-CTAGTGGTT -s Anc2.Anc2refChr1 138074 22 + 142988 TCAATTCAAAAAC-TTATTGGTC -s mr.mrrefChr3 172642 22 + 181027 TCAATTCAAGAAG-CAAGTTGAT -s simCow_chr6.simCow.chr6 597098 17 + 602619 TCAGTTCAGAAA------TGGTC -s simDog_chr6.simDog.chr6 588791 22 + 593897 ACAATTAAAAAAC-TTATTGGTC -s simHuman_chr6.simHuman.chr6 592876 22 + 601863 TCAATTCAAAAAG-CTAGTGGTT -s simRat_chr6.simRat.chr6 637509 22 + 647215 TCAATTCAACAAA-CAAGCTACT - -a -s simMouse_chr6.simMouse.chr6 626020 18 + 636262 ACCATGGTGGGATACCAT -s Anc0.Anc0refChr3 220244 18 + 222631 AGCATGCTTGTACTCCTT -s Anc1.Anc1refChr1 61044 18 + 69767 AGCATGCTTGTACTCCTT -s Anc2.Anc2refChr1 138099 18 + 142988 AGCATGCTTGTACTCCTT -s mr.mrrefChr3 172667 18 + 181027 AGCATGCTTGTACTCCTT -s simCow_chr6.simCow.chr6 597118 18 + 602619 AGCATGCTTGTACTCCTT -s simDog_chr6.simDog.chr6 588816 18 + 593897 AACATGCTTGTACTCCTT -s simHuman_chr6.simHuman.chr6 592901 18 + 601863 AGCATGCTTGTACTCCTT -s simRat_chr6.simRat.chr6 637537 18 + 647215 AGCAGGCTTGTACTCCTT - -a -s simMouse_chr6.simMouse.chr6 626038 2 + 636262 TG -s Anc0.Anc0refChr3 220263 2 + 222631 CA -s Anc1.Anc1refChr1 61063 2 + 69767 CA -s Anc2.Anc2refChr1 138118 2 + 142988 CA -s mr.mrrefChr3 172686 2 + 181027 TA -s simCow_chr6.simCow.chr6 597137 2 + 602619 CA -s simDog_chr6.simDog.chr6 588835 2 + 593897 CA -s simHuman_chr6.simHuman.chr6 592920 2 + 601863 CA -s simRat_chr6.simRat.chr6 637556 2 + 647215 TA - -a -s simMouse_chr6.simMouse.chr6 626040 2 + 636262 GG -s Anc0.Anc0refChr3 220267 2 + 222631 GG -s Anc1.Anc1refChr1 61067 2 + 69767 GG -s Anc2.Anc2refChr1 138122 2 + 142988 GG -s mr.mrrefChr3 172688 2 + 181027 GG -s simCow_chr6.simCow.chr6 597141 2 + 602619 AG -s simDog_chr6.simDog.chr6 588839 2 + 593897 GG -s simHuman_chr6.simHuman.chr6 592924 2 + 601863 GA -s simRat_chr6.simRat.chr6 637558 2 + 647215 TG - -a -s simMouse_chr6.simMouse.chr6 626042 58 + 636262 AATACTGTAGAGGACACAGTGAGTGAGCACAACAATACCTTATACATTAGGATGAGGG -s Anc0.Anc0refChr3 220269 48 + 222631 AACTACTCATTGGA----GTCAG------CAACAATACTTTACACATAAGAGTGAGAG -s Anc1.Anc1refChr1 61069 48 + 69767 AACTACTCATTGGA----GTCAG------CAACAATACTTTACACATAAGAGTGAGAG -s Anc2.Anc2refChr1 138125 48 + 142988 AACTACGCATTCGA----GTCAG------CAACAATACTTTACACCTAAGAGTGAGAG -s mr.mrrefChr3 172690 48 + 181027 AATTACTTATAGGA----GTGAG------CAACAATACCTTATACATTAGGATGAGGG -s simCow_chr6.simCow.chr6 597144 48 + 602619 AATTACCCGTTAGA----GTCAG------CAACGATACTTTACACCTAGGATTGAGAG -s simDog_chr6.simDog.chr6 588842 48 + 593897 AACTATGCAGCCGA----GTCAA------CAACAATACTTTAGACCTGAGAGTGAGAG -s simHuman_chr6.simHuman.chr6 592926 48 + 601863 TAATACTCATTGGA----GTCAG------CAACAATACTTGACCCAGAAGAGTGAGAG -s simRat_chr6.simRat.chr6 637560 48 + 647215 AATTACTTATAGGA----GTGAT------CAGCAATACCTTATACATCAGGATGAGGG - -a -s simMouse_chr6.simMouse.chr6 626100 5 + 636262 ATGAG -s Anc0.Anc0refChr3 220317 5 + 222631 ATGAG -s Anc1.Anc1refChr1 61117 5 + 69767 ATGAG -s Anc2.Anc2refChr1 138173 5 + 142988 ATAAG -s mr.mrrefChr3 172738 5 + 181027 ATGAG -s simCow_chr6.simCow.chr6 597193 5 + 602619 AAAGG -s simDog_chr6.simDog.chr6 588890 5 + 593897 ATAAG -s simHuman_chr6.simHuman.chr6 592974 5 + 601863 ATGCT -s simRat_chr6.simRat.chr6 637608 5 + 647215 ATGAG - -a -s simMouse_chr6.simMouse.chr6 626105 5 + 636262 GGTAC -s Anc0.Anc0refChr3 220322 5 + 222631 GGTGC -s Anc1.Anc1refChr1 61122 5 + 69767 GGTGC -s Anc2.Anc2refChr1 138181 5 + 142988 AGAGG -s mr.mrrefChr3 172743 5 + 181027 GGTAC -s simCow_chr6.simCow.chr6 597201 5 + 602619 AGAGG -s simDog_chr6.simDog.chr6 588898 5 + 593897 AGAGG -s simHuman_chr6.simHuman.chr6 592979 5 + 601863 GGTGC -s simRat_chr6.simRat.chr6 637613 5 + 647215 GGTCC - -a -s simMouse_chr6.simMouse.chr6 626110 14 + 636262 AATCATAGATGTTC -s Anc0.Anc0refChr3 220327 14 + 222631 AATCAAAAATGTTG -s Anc1.Anc1refChr1 61127 14 + 69767 AATCAAAAATGTTG -s Anc2.Anc2refChr1 138186 14 + 142988 AAAAAAAAAGGCCA -s mr.mrrefChr3 172748 14 + 181027 AATCAAAAATGTTC -s simCow_chr6.simCow.chr6 597206 14 + 602619 AAAAGAAAAGGCCA -s simDog_chr6.simDog.chr6 588905 14 + 593897 AAAAAAAAAGGCCA -s simHuman_chr6.simHuman.chr6 592984 14 + 601863 AATCGAAAGTTGTG -s simRat_chr6.simRat.chr6 637618 14 + 647215 AATCAAAAATATTA - -a -s simMouse_chr6.simMouse.chr6 626124 29 + 636262 TGGGCACCTGGGATTCTTTTAGTATAAGT -s Anc0.Anc0refChr3 202120 29 - 222631 TGGGCTCCTGGAATTTTTTTTATCCCAAT -s Anc1.Anc1refChr1 61141 29 + 69767 TGGGCTCCTGGAATTTTTTTTATCCCAAT -s Anc2.Anc2refChr13 72712 29 - 96486 TGGGTTCCTGGAATGTTTTTTAGCCCGAT -s mr.mrrefChr3 172762 29 + 181027 TGGGCACCTGGGATTCTTTTAATATAAAT -s simCow_chr6.simCow.chr6 222962 29 - 602619 TGGGTTCCTGGAATGTTTTTCAGCACGAT -s simDog_chr6.simDog.chr6 223611 6 - 593897 --------------------TAGTCC--- -s simHuman_chr6.simHuman.chr6 592998 29 + 601863 TGGGCTCATGGAATTTTTTTTATCCTAAT -s simRat_chr6.simRat.chr6 637632 29 + 647215 TGGGCATCTGGGATTCTTTTAATATAAAT - -a -s simMouse_chr6.simMouse.chr6 626153 27 + 636262 GATTAGCCCCATCACCACCCAATATCA -s Anc0.Anc0refChr3 202173 26 - 222631 A-TTAGCCTCATCACAACATAATCTCA -s Anc1.Anc1refChr1 61194 27 + 69767 AATTAGCCTCATCACAACATAATCTCA -s Anc2.Anc2refChr13 72765 26 - 96486 A-TTAGCCTTATTACAATATAATCTCA -s mr.mrrefChr3 172791 27 + 181027 GATTAGCCCCATCACCACCCAATATCA -s simCow_chr6.simCow.chr6 223015 25 - 602619 G-GTGGCCTTATAACA-TATAATCCCA -s simDog_chr6.simDog.chr6 223635 26 - 593897 A-TCAGCCTTACTACCATACAATCTCA -s simHuman_chr6.simHuman.chr6 593051 27 + 601863 AATTAGTTTCATCACAACATAGTCTCA -s simRat_chr6.simRat.chr6 637661 27 + 647215 GATTAGCCCCATAAGCACCCAAGATCG - -a -s simMouse_chr6.simMouse.chr6 626180 12 + 636262 AATAGGCAGGGG -s Anc0.Anc0refChr3 202199 12 - 222631 AATAAACAGAGG -s Anc1.Anc1refChr1 61221 12 + 69767 AATAAACAGAGG -s Anc2.Anc2refChr13 72791 12 - 96486 AATAAACAGAGG -s mr.mrrefChr3 172818 12 + 181027 AATAGGCAGGGG -s simCow_chr6.simCow.chr6 223040 12 - 602619 AATAAACAGAGG -s simDog_chr6.simDog.chr6 223661 12 - 593897 AATAAGCAGAGG -s simHuman_chr6.simHuman.chr6 593085 12 + 601863 AATAAACAGAGG -s simRat_chr6.simRat.chr6 637688 12 + 647215 AATAGGCAGGGG - -a -s simMouse_chr6.simMouse.chr6 626192 5 + 636262 CTGGG -s Anc0.Anc0refChr3 202212 5 - 222631 CTGTG -s Anc1.Anc1refChr1 61234 5 + 69767 CTGTG -s Anc2.Anc2refChr13 72804 5 - 96486 CTGTG -s mr.mrrefChr3 172830 5 + 181027 CTGGG -s simCow_chr6.simCow.chr6 223053 5 - 602619 CCGGG -s simDog_chr6.simDog.chr6 223674 5 - 593897 CTGTG -s simHuman_chr6.simHuman.chr6 593098 5 + 601863 CTTTG -s simRat_chr6.simRat.chr6 637700 5 + 647215 CTGGG - -a -s simMouse_chr6.simMouse.chr6 626197 14 + 636262 GATCTCTCCATTAT -s Anc0.Anc0refChr3 202217 14 - 222631 TTTCCTTCCATTAT -s Anc1.Anc1refChr1 61239 14 + 69767 TTTCCTTCCATTAT -s Anc2.Anc2refChr13 72809 14 - 96486 TTTCCTTCAATTAT -s mr.mrrefChr3 172835 14 + 181027 GATCTCTCCATTAT -s simCow_chr6.simCow.chr6 223058 14 - 602619 TTTTCCTCAATTAT -s simDog_chr6.simDog.chr6 223679 14 - 593897 TTCCCTTCAGTTAT -s simHuman_chr6.simHuman.chr6 593105 14 + 601863 TCTTCTTCCATTAT -s simRat_chr6.simRat.chr6 637705 14 + 647215 GACCTCTCCATTAT - -a -s simMouse_chr6.simMouse.chr6 626211 26 + 636262 TAAGAACCTGCAGCATGTGACTGCCA -s Anc0.Anc0refChr3 202232 26 - 222631 TGGGAACCTGCAGCATGTGACTGCCA -s Anc1.Anc1refChr1 61254 26 + 69767 TGGGAACCTGCAGCATGTGACTGCCA -s Anc2.Anc2refChr13 72824 26 - 96486 TGGGATCCTGCAGCCTGTGACTGCCA -s mr.mrrefChr3 172849 26 + 181027 TAAGAACCTGCAGCATGTGACTGCCA -s simCow_chr6.simCow.chr6 223073 26 - 602619 TGGGATCCTGCAGCTTGTGACTGCCA -s simDog_chr6.simDog.chr6 223694 26 - 593897 TGGGATCTTGCAGCCAGTGACTGCCA -s simHuman_chr6.simHuman.chr6 593120 26 + 601863 TGGGAACCTGCAGCATGTGACTGCCA -s simRat_chr6.simRat.chr6 637719 26 + 647215 TAAGAACCTGCAGCAGGTGACCACCA - -a -s simMouse_chr6.simMouse.chr6 626237 10 + 636262 TGGACATGAG -s Anc0.Anc0refChr3 202258 10 - 222631 AGGACATTGG -s Anc1.Anc1refChr1 61280 10 + 69767 AGGACATTGG -s Anc2.Anc2refChr13 72864 10 - 96486 AGGACATTGG -s mr.mrrefChr3 172875 10 + 181027 AGGACATGAG -s simCow_chr6.simCow.chr6 223114 10 - 602619 AAAACAGTGG -s simDog_chr6.simDog.chr6 223734 10 - 593897 AGGATGTGAG -s simHuman_chr6.simHuman.chr6 593146 10 + 601863 AGGACATTGG -s simRat_chr6.simRat.chr6 637745 10 + 647215 AGGACGTGAG - -a -s simMouse_chr6.simMouse.chr6 626247 16 + 636262 TTGCTAAGGAATCTGG -s Anc0.Anc0refChr3 202268 16 - 222631 TTGACAAAGAACCTGG -s Anc1.Anc1refChr1 61290 16 + 69767 TTGACAAAGAACCTGG -s Anc2.Anc2refChr13 72874 16 - 96486 TTGACAAAAAACATGG -s mr.mrrefChr3 172885 16 + 181027 TTGCTAAAGAATCTGG -s simCow_chr6.simCow.chr6 223125 16 - 602619 CTGGCAAAAAACATGA -s simDog_chr6.simDog.chr6 223744 16 - 593897 TTGAGAAAAAATACAG -s simHuman_chr6.simHuman.chr6 593156 16 + 601863 TTGACGAAGAACCTGG -s simRat_chr6.simRat.chr6 637755 16 + 647215 TTGCTAAAGATTCTGG - -a -s simMouse_chr6.simMouse.chr6 626263 10 + 636262 TCCCATCAGC -s Anc0.Anc0refChr3 202287 10 - 222631 TCCTATCAGC -s Anc1.Anc1refChr1 61309 10 + 69767 TCCTATCAGC -s Anc2.Anc2refChr13 72893 10 - 96486 TCCTTTCAGT -s mr.mrrefChr3 172901 10 + 181027 TCCCATCAGC -s simCow_chr6.simCow.chr6 223144 10 - 602619 TGCTCTCAGT -s simDog_chr6.simDog.chr6 223763 10 - 593897 TCCTTGCAGT -s simHuman_chr6.simHuman.chr6 593175 10 + 601863 TTCTATCGGC -s simRat_chr6.simRat.chr6 637771 10 + 647215 TCCCATCAGC - -a -s simMouse_chr6.simMouse.chr6 626273 3 + 636262 CCA -s Anc0.Anc0refChr3 202299 3 - 222631 CTG -s Anc1.Anc1refChr1 61321 3 + 69767 CTG -s Anc2.Anc2refChr13 72905 3 - 96486 CTA -s mr.mrrefChr3 172911 3 + 181027 CCG -s simCow_chr6.simCow.chr6 223156 3 - 602619 CTA -s simDog_chr6.simDog.chr6 223775 3 - 593897 CTA -s simHuman_chr6.simHuman.chr6 593187 3 + 601863 CTG -s simRat_chr6.simRat.chr6 637781 3 + 647215 CCG - -a -s simMouse_chr6.simMouse.chr6 626276 6 + 636262 ACCAGC -s Anc0.Anc0refChr3 202303 6 - 222631 ACCAGC -s Anc1.Anc1refChr1 61325 6 + 69767 ACCAGC -s Anc2.Anc2refChr13 72909 6 - 96486 GCCAGT -s mr.mrrefChr3 172914 6 + 181027 ACCAGC -s simCow_chr6.simCow.chr6 223160 6 - 602619 GCCAGT -s simDog_chr6.simDog.chr6 223779 6 - 593897 GCCAGT -s simHuman_chr6.simHuman.chr6 593191 6 + 601863 ACCAGC -s simRat_chr6.simRat.chr6 637784 6 + 647215 ACCAGC - -a -s simMouse_chr6.simMouse.chr6 626282 5 + 636262 CCAGA -s Anc0.Anc0refChr3 202310 5 - 222631 CCAGA -s Anc1.Anc1refChr1 61332 5 + 69767 CCAGA -s Anc2.Anc2refChr13 72916 5 - 96486 CGAGA -s mr.mrrefChr3 172920 5 + 181027 CCAGA -s simCow_chr6.simCow.chr6 223167 1 - 602619 ----A -s simDog_chr6.simDog.chr6 223786 5 - 593897 CGAGA -s simHuman_chr6.simHuman.chr6 593198 5 + 601863 CCAGA -s simRat_chr6.simRat.chr6 637790 5 + 647215 CCAGA - -a -s simMouse_chr6.simMouse.chr6 626287 9 + 636262 TTTGTTAGG -s Anc0.Anc0refChr3 202320 9 - 222631 CCTATTGGA -s Anc1.Anc1refChr1 61342 9 + 69767 CCTATTGGA -s Anc2.Anc2refChr13 72926 9 - 96486 CCTACTGGA -s mr.mrrefChr3 172925 9 + 181027 TTTGTTGGA -s simCow_chr6.simCow.chr6 223173 5 - 602619 C----TGGA -s simDog_chr6.simDog.chr6 223794 8 - 593897 -CTACTGGA -s simHuman_chr6.simHuman.chr6 593208 9 + 601863 CCTCTTGGA -s simRat_chr6.simRat.chr6 637795 9 + 647215 TTTTTTGGA - -a -s simMouse_chr6.simMouse.chr6 626296 1 + 636262 G -s Anc0.Anc0refChr3 202329 1 - 222631 G -s Anc1.Anc1refChr1 61351 1 + 69767 G -s Anc2.Anc2refChr13 72935 1 - 96486 G -s mr.mrrefChr3 172934 1 + 181027 G -s simCow_chr6.simCow.chr6 223178 1 - 602619 G -s simDog_chr6.simDog.chr6 223802 1 - 593897 G -s simHuman_chr6.simHuman.chr6 593217 1 + 601863 G -s simRat_chr6.simRat.chr6 637814 1 + 647215 G - -a -s simMouse_chr6.simMouse.chr6 626297 34 + 636262 CACCACTTAAATACTATCACTCAAACAAGACTCA -s Anc0.Anc0refChr3 202334 33 - 222631 CAGACTTTAAATCCTATCACTCAAAC-AGATCAA -s Anc1.Anc1refChr1 61356 34 + 69767 CAGACTTTAAATCCTATCACTCAAACGAGATCAA -s Anc2.Anc2refChr13 72940 33 - 96486 AAGACTTTAAATCCTATCACTCAAAC-AGATCAA -s mr.mrrefChr3 172935 34 + 181027 CACAACTTAAATACTATCACTCAAACGAGACTCA -s simCow_chr6.simCow.chr6 223183 33 - 602619 TAGAGTCTAAACCCTACCACTCAAAC-AGATCAA -s simDog_chr6.simDog.chr6 223807 26 - 593897 AGGACTTTAAGTCCTATCACTCAAAC-------- -s simHuman_chr6.simHuman.chr6 593222 34 + 601863 CAGACTTTAAATCCTATCACTCAAACGAAATCAA -s simRat_chr6.simRat.chr6 637815 34 + 647215 CAAAACTTAAATACTATCACTCAAATGAGACTCA - -a -s simMouse_chr6.simMouse.chr6 626331 28 + 636262 AGCAAATTCTTTTCATGACCACATTAAG -s Anc0.Anc0refChr3 202369 28 - 222631 AACATATTCACTCCATGATCACATTCAG -s Anc1.Anc1refChr1 61392 28 + 69767 AACATATTCACTCCATGATCACATTCAG -s Anc2.Anc2refChr13 72975 28 - 96486 AGCATATTAACTCCATAATCACATTCAG -s mr.mrrefChr3 172969 28 + 181027 AACAAATTCACTTCATGACCACATTCAG -s simCow_chr6.simCow.chr6 223218 24 - 602619 AGCAGAT----TCTATAATCACATTCAC -s simDog_chr6.simDog.chr6 223833 26 - 593897 --TGTATTAACTCCATAACCACATTCAG -s simHuman_chr6.simHuman.chr6 593258 28 + 601863 AACATATTCACTCCATGATCACATTCAG -s simRat_chr6.simRat.chr6 637849 27 + 647215 AACAG-TTCACTTCATGACCACACCCAG - -a -s simMouse_chr6.simMouse.chr6 626359 5 + 636262 AATCA -s Anc0.Anc0refChr3 202409 5 - 222631 AGTCT -s Anc1.Anc1refChr1 61432 5 + 69767 AGTCT -s Anc2.Anc2refChr13 73019 5 - 96486 AGTCT -s mr.mrrefChr3 172997 5 + 181027 AATCA -s simCow_chr6.simCow.chr6 223259 5 - 602619 AGTCT -s simDog_chr6.simDog.chr6 223875 5 - 593897 AATCA -s simHuman_chr6.simHuman.chr6 593298 5 + 601863 AGTCT -s simRat_chr6.simRat.chr6 637876 5 + 647215 TATCA - -a -s simMouse_chr6.simMouse.chr6 626364 68 + 636262 TTACATTGCCTGGAGTATATTTTCAAACTTGGATATGTGCAGTATATTGGTAAATCTATACTGTTGAG -s Anc0.Anc0refChr3 202418 68 - 222631 TTACGTTCCCTGGAGCATATATTAGAACTTGGATATGTGCAATACACTTGTAAATATATACTTTTAAG -s Anc1.Anc1refChr1 61441 68 + 69767 TTACGTTCCCTGGAGCATATATTAGAACTTGGATATGTGCAATACACTTGTAAATATATACTTTTAAG -s Anc2.Anc2refChr13 73028 68 - 96486 TGACATTCCCTGGATCATATATTAGAACTTGGATATGTGCAATACACTTGTGAATATATACTTTTAAG -s mr.mrrefChr3 173006 68 + 181027 TTACGTTGCCTGGAGCATATTTTCAAACTTGGATATGTGCAGTATACTTGTAAATCTATACTTTTGAG -s simCow_chr6.simCow.chr6 223268 65 - 602619 TGACATGCCCCAGACCACATACTACAACT-GGATATGTG--ATACACTTGTGAGTATATACTTTTAAG -s simDog_chr6.simDog.chr6 223884 68 - 593897 TGACATTCTCTGGATCGTATGTTAGGACTTGAATATGTGCAATACACTTGTGAATATATACTGCTCAG -s simHuman_chr6.simHuman.chr6 593307 68 + 601863 ATACGCTCCCTGAAGCATATATTAGAACTAGGATATGTGCAATACACTTGAAAATATTTACTTTTAAG -s simRat_chr6.simRat.chr6 637885 62 + 647215 GGACGTTGCCTGGAGCTTATTTTCAAACTTAAATATGTGTA-TATACTTGT-----TATACTTTTGAG - -a -s simMouse_chr6.simMouse.chr6 626432 199 + 636262 TGCCTATTTTTTTATTGGACCTGTTTTGACTTGACACAGCACCTCATGCAAATCTCCAAAAAAAGACAAACATGGCCCTGTGCACACAGTTAGTGCTTGGCTAAGAGCCTGCACCACACAGCCATGTTTAAACGGTCAGTGCTTGGCTACAAGCTTCCCCCGCTTGACAGGATGTCAATAAGTGCTTTCATACCAACTT -s Anc0.Anc0refChr3 202486 30 - 222631 TAACTATTCTTTTGCTGGACCCACTC-------------------------------------------------------------------------------------------------------------------------------------------------------------------------ATTT -s Anc1.Anc1refChr1 61509 30 + 69767 TAACTATTCTTTTGCTGGACCCACTC-------------------------------------------------------------------------------------------------------------------------------------------------------------------------ATTT -s Anc2.Anc2refChr13 73097 30 - 96486 CAACTATTCTTTTGCTGGTGCCACTC-------------------------------------------------------------------------------------------------------------------------------------------------------------------------ATTT -s mr.mrrefChr3 173074 30 + 181027 TGCCTATTTTTTTGTTGGACCTGCTT-------------------------------------------------------------------------------------------------------------------------------------------------------------------------ATTT -s simCow_chr6.simCow.chr6 223334 25 - 602619 CACCTGTTCT-----TGGACCCACTC-------------------------------------------------------------------------------------------------------------------------------------------------------------------------ATTT -s simDog_chr6.simDog.chr6 223953 30 - 593897 CAACTATTCTTTTGCCGGTGCCACTC-------------------------------------------------------------------------------------------------------------------------------------------------------------------------ATTT -s simHuman_chr6.simHuman.chr6 593387 28 + 601863 TAAGTATTCATTTGCTGGAC--ACTC-------------------------------------------------------------------------------------------------------------------------------------------------------------------------ATTT -s simRat_chr6.simRat.chr6 637947 30 + 647215 TGCCTATTTTTTTGTTGGAATGGCTT-------------------------------------------------------------------------------------------------------------------------------------------------------------------------ATTC - -a -s simMouse_chr6.simMouse.chr6 626631 10 + 636262 GCTAAAGCAA -s Anc0.Anc0refChr3 202516 10 - 222631 GCTTTTGCAA -s Anc1.Anc1refChr1 61539 10 + 69767 GCTTTTGCAA -s Anc2.Anc2refChr13 73129 10 - 96486 GCTTTTGCAA -s mr.mrrefChr3 173104 10 + 181027 GCTTTAGCAA -s simCow_chr6.simCow.chr6 223361 9 - 602619 -CTTTTGCCA -s simDog_chr6.simDog.chr6 223987 10 - 593897 GTTTTGGCAA -s simHuman_chr6.simHuman.chr6 593415 10 + 601863 GCTTTTGCAA -s simRat_chr6.simRat.chr6 637977 10 + 647215 GCTTTAGCAA - -a -s simMouse_chr6.simMouse.chr6 626641 73 + 636262 ATGAGCAAGGTTAAGACTGTGTCATTAGTGATAATCTCTCCTACAGGGCCGCACACTAACCTGCATGGGGAGT -s Anc0.Anc0refChr3 202585 39 - 222631 AACAGCT---TGCAAAGGGAGTTGTTATTGG---------CTCCAAGCTA-------------C--------- -s Anc1.Anc1refChr1 61615 41 + 69767 AACAGCT---TGCAAAGGGAGTTGTTATTGG---------CTCCAAGCTA-------------CAC------- -s Anc2.Anc2refChr13 73198 39 - 96486 AGCAGCT---TGCAAAGGGAGTTGGTATTGG---------TTGTGACCTA-------------C--------- -s mr.mrrefChr3 173179 57 + 181027 AACAGCA---TTAAGACTGTGTCATTAGTGATAATCTCTCCTCCAGGGCC-------------CACGGGGAGT -s simCow_chr6.simCow.chr6 223426 26 - 602619 ----------------AGGAGTTGGTATTGA---------TTGGTTCCTA-------------C--------- -s simDog_chr6.simDog.chr6 224056 39 - 593897 AGCAGCT---TGCAAAGAAATCTGGCATTGG---------TTGTGACCTA-------------C--------- -s simHuman_chr6.simHuman.chr6 593491 41 + 601863 AACAACC---TCCAAGGGGAGTTGTTATTGG---------CTCCAAGCTA-------------CAC------- -s simRat_chr6.simRat.chr6 638126 57 + 647215 AACAGCA---TTAAGACTGTGTCATTAGTGATAATCTGTCCTCCAGGGCC-------------CACGGGGAAT - -a -s simMouse_chr6.simMouse.chr6 626714 22 + 636262 GAACCTTGGGCAGATCTTCAAA -s Anc0.Anc0refChr3 202624 12 - 222631 ----------TGCAAACTACAA -s Anc1.Anc1refChr1 61656 19 + 69767 ---CCTTGGCTGCAAACTACAA -s Anc2.Anc2refChr13 73237 12 - 96486 ----------TGCAAACTACAA -s mr.mrrefChr3 173236 22 + 181027 GAACCTTGGGTAGAACCTAAAA -s simCow_chr6.simCow.chr6 223452 12 - 602619 ----------CGTAAACTACAA -s simDog_chr6.simDog.chr6 224095 12 - 593897 ----------TGCAAACTACAA -s simHuman_chr6.simHuman.chr6 593532 19 + 601863 ---CCTTGGCTGCAAGCTACAC -s simRat_chr6.simRat.chr6 638184 22 + 647215 AAACCTTGGGTAGAACCTAGAA - -a -s simMouse_chr6.simMouse.chr6 626736 1 + 636262 C -s Anc0.Anc0refChr3 202637 1 - 222631 C -s Anc1.Anc1refChr1 61676 1 + 69767 C -s Anc2.Anc2refChr13 73250 1 - 96486 C -s mr.mrrefChr3 173259 1 + 181027 C -s simCow_chr6.simCow.chr6 223465 1 - 602619 C -s simDog_chr6.simDog.chr6 224108 1 - 593897 C -s simHuman_chr6.simHuman.chr6 593552 1 + 601863 C -s simRat_chr6.simRat.chr6 638207 1 + 647215 C - -a -s simMouse_chr6.simMouse.chr6 626737 37 + 636262 TGCGTTTTTTTTGGAAGGCATGTTACTTTTTGCAGGA -s Anc0.Anc0refChr3 202638 37 - 222631 TGCATCTTTTTTGGGAAGTATGGCACTTTTAGCAGAT -s Anc1.Anc1refChr1 61677 37 + 69767 TGCATCTTTTTTGGGAAGTATGGCACTTTTAGCAGAT -s Anc2.Anc2refChr13 73252 37 - 96486 TGCATCTTTTTTGGGAAGTATGGCACTTTTAGTAGAC -s mr.mrrefChr3 173260 37 + 181027 TGCATTTTTTTTGGAAGGTATGTTACTTTTTGCAGGT -s simCow_chr6.simCow.chr6 223467 28 - 602619 TGTGTCTTTTT---------TAATATTTTTGGTAGAC -s simDog_chr6.simDog.chr6 224110 37 - 593897 CGCAACTTTTTTGGGAAGTAAGGCTCTTTCAGTAGAC -s simHuman_chr6.simHuman.chr6 593553 37 + 601863 TGCATCTTTTTGGGGAAGTATGGGACTTTTAGCAGAT -s simRat_chr6.simRat.chr6 638208 37 + 647215 TGCATTTTTTTTGAAAGCTATGTTACTTTTCGCTGGT - -a -s simMouse_chr6.simMouse.chr6 626774 39 + 636262 TAAGTTACTGCACTACACATGCAACAGAATCATACCGCA -s Anc0.Anc0refChr3 202676 33 - 222631 TAAATTG--GCAC----CATACAACAGAACCATGCTGTA -s Anc1.Anc1refChr1 61715 33 + 69767 TAAATTG--GCAC----CATACAACAGAACCATGCTGTA -s Anc2.Anc2refChr13 73290 33 - 96486 TAAATTG--GCAC----CGTACAATGTAACCATGCTGTA -s mr.mrrefChr3 173297 39 + 181027 TAAGTTACTGCACTACACATACAACAGAATCATGCTGTA -s simCow_chr6.simCow.chr6 223496 30 - 602619 TAAATTG--GCAC----CCCGCAAA---ACTATGCTGAA -s simDog_chr6.simDog.chr6 224148 33 - 593897 CACATTG--GCAC----CGTACAATGTAACCATGCTGTA -s simHuman_chr6.simHuman.chr6 593591 33 + 601863 TAAATTG--GCAC----CATACAACAGTACCCTGCTGTA -s simRat_chr6.simRat.chr6 638245 39 + 647215 TAAGTTATTGCACTACATATATAACAGAATCATGCTGTA - -a -s simMouse_chr6.simMouse.chr6 626813 63 + 636262 TTCCCCTGCCTGTCCTAAAAAGCTTGAAACCTGTTCTAAAAAGCTTGACCAGGTTTAGGTCCT -s Anc0.Anc0refChr3 202710 40 - 222631 TACCCCC----------------------CCCGTTC-AAAGAGCTTACCCAGGTCAAAAGCCT -s Anc1.Anc1refChr1 61749 41 + 69767 TACCCCC----------------------CCCGTTCTAAAGAGCTTACCCAGGTCAAAAGCCT -s Anc2.Anc2refChr13 73324 40 - 96486 CACCACC----------------------CCCGTTC-AAAGAGCTTACCCAGGTCAAAAGCCT -s mr.mrrefChr3 173336 41 + 181027 TTCCCCT----------------------CCTGTTCTAAAAAGCTTGCCCAGGTCTAGGTCCT -s simCow_chr6.simCow.chr6 223527 40 - 602619 CACTGCC----------------------CCTATTC-AAAGAGCTCAGGCAGGTGAGAAGACA -s simDog_chr6.simDog.chr6 224182 40 - 593897 CACCACC----------------------CCCGTTC-AAAGATCTTACCCTGGTCAAAAGCCT -s simHuman_chr6.simHuman.chr6 593625 41 + 601863 TGCCCCC----------------------CCCGTACTAAGGAGCTTACCCAGATCGAAAGCCT -s simRat_chr6.simRat.chr6 638284 41 + 647215 TTGCCCT----------------------CCTGTTCTAAAAAACTTGCCCGGGTCTAGGTCCT - -a -s simMouse_chr6.simMouse.chr6 626876 14 + 636262 TCATGTTTTCAATG -s Anc0.Anc0refChr3 202754 12 - 222631 TCATGTCCTC--TG -s Anc1.Anc1refChr1 61794 12 + 69767 TCATGTCCTC--TG -s Anc2.Anc2refChr13 73380 12 - 96486 TCATGTCCTC--TG -s mr.mrrefChr3 173381 14 + 181027 TCATGTTTTCAATG -s simCow_chr6.simCow.chr6 223577 12 - 602619 TCATGTCCTC--TG -s simDog_chr6.simDog.chr6 224243 12 - 593897 TCATGTCCTC--TG -s simHuman_chr6.simHuman.chr6 593670 3 + 601863 GCA----------- -s simRat_chr6.simRat.chr6 638339 14 + 647215 TCATGTTGCCAATG - -a -s simMouse_chr6.simMouse.chr6 626890 39 + 636262 TTATCTCTTTTGCAGATCTGATGTGTATGAAGGCTATTT -s Anc0.Anc0refChr3 202766 37 - 222631 TGATAT--TTTGCAGATCAGATATGTATGAAGACTATTT -s Anc1.Anc1refChr1 61806 37 + 69767 TGATAT--TTTGCAGATCAGATATGTATGAAGACTATTT -s Anc2.Anc2refChr13 73392 37 - 96486 TGATAT--TTTGCAGATCAGATATGTATAAAGATCAGTT -s mr.mrrefChr3 173395 37 + 181027 TTATCT--TTTGCAGATCTGATGTGTATGAAGGCTATTT -s simCow_chr6.simCow.chr6 223589 37 - 602619 TGATCT--TTAGCAGATAAGACATATATCAAGATCACTT -s simDog_chr6.simDog.chr6 224257 37 - 593897 TGATAT--TTTGCAGATCAGATATGTATAAAGATCAGTA -s simHuman_chr6.simHuman.chr6 593673 24 + 601863 ---------------GTCAGATATGCATGAAGACTATTT -s simRat_chr6.simRat.chr6 638353 37 + 647215 GTATTT--TTTGCAGATCTGATGTGTATGAAGGTTATTT - -a -s simMouse_chr6.simMouse.chr6 626929 10 + 636262 TGATTTCTAT -s Anc0.Anc0refChr3 202810 10 - 222631 TGATTTCTAT -s Anc1.Anc1refChr1 61850 10 + 69767 TGATTTCTAT -s Anc2.Anc2refChr13 73436 10 - 96486 TGACTTCTAT -s mr.mrrefChr3 173432 10 + 181027 TGATTTCTAT -s simCow_chr6.simCow.chr6 223633 10 - 602619 TGACTTCTAT -s simDog_chr6.simDog.chr6 224301 10 - 593897 TGACTTCAAT -s simHuman_chr6.simHuman.chr6 593704 10 + 601863 TGATTTATAT -s simRat_chr6.simRat.chr6 638390 10 + 647215 TGATTTCTAT - -a -s simMouse_chr6.simMouse.chr6 626939 16 + 636262 TCAACATGCCACAACA -s Anc0.Anc0refChr3 202820 16 - 222631 ATCAAGTACCACCACA -s Anc1.Anc1refChr1 61860 16 + 69767 ATCAAGTACCACCACA -s Anc2.Anc2refChr13 73446 16 - 96486 ATCAAGTACCACCACA -s mr.mrrefChr3 173442 16 + 181027 TCAACATGCCACAACA -s simCow_chr6.simCow.chr6 223643 15 - 602619 AT-AAGTACCACTACA -s simDog_chr6.simDog.chr6 224311 16 - 593897 ATCAATTATCATCACA -s simHuman_chr6.simHuman.chr6 593714 16 + 601863 ATGAAGTACAACCACA -s simRat_chr6.simRat.chr6 638497 16 + 647215 TGATTATGCCACAACA - -a -s simMouse_chr6.simMouse.chr6 626955 12 + 636262 GCTTCTATCACT -s Anc0.Anc0refChr3 202837 12 - 222631 GCCTCAATCTCT -s Anc1.Anc1refChr1 61877 12 + 69767 GCCTCAATCTCT -s Anc2.Anc2refChr13 73463 12 - 96486 GCCTCACTCTCT -s mr.mrrefChr3 173458 12 + 181027 GCTTCTATCACT -s simCow_chr6.simCow.chr6 223659 12 - 602619 GCCTTACTCTCT -s simDog_chr6.simDog.chr6 224328 12 - 593897 GTCTCACTCTCT -s simHuman_chr6.simHuman.chr6 593731 12 + 601863 GCCTCAATCTCT -s simRat_chr6.simRat.chr6 638513 12 + 647215 GCTTCTATTACT - -a -s simMouse_chr6.simMouse.chr6 626967 15 + 636262 GCTGATTTGCATTTC -s Anc0.Anc0refChr3 202849 13 - 222631 GCTG--TTGCATTAC -s Anc1.Anc1refChr1 61889 15 + 69767 GCTGATTTGCATTAC -s Anc2.Anc2refChr13 73475 13 - 96486 GTCA--CTGAGTGCC -s mr.mrrefChr3 173470 15 + 181027 GCTGATTTGCATTTC -s simCow_chr6.simCow.chr6 223671 10 - 602619 ---C--CTGATTTGC -s simDog_chr6.simDog.chr6 224340 13 - 593897 GTCA--CTGAGTGCC -s simHuman_chr6.simHuman.chr6 593810 15 + 601863 GTTGGTATGCAATAC -s simRat_chr6.simRat.chr6 638525 15 + 647215 GCTGATTTGCATTTT - -a -s simMouse_chr6.simMouse.chr6 626982 28 + 636262 AGCTTAGACTGATAAAGCATCTTAGAAC -s Anc0.Anc0refChr3 202862 28 - 222631 ACCTTAGGCTGATGAAAGATCTTAAAAC -s Anc1.Anc1refChr1 61904 28 + 69767 ACCTTAGGCTGATGAAAGATCTTAAAAC -s Anc2.Anc2refChr13 73488 28 - 96486 ATTTTGGGTAGATGAAAGATCTTAAAAC -s mr.mrrefChr3 173485 28 + 181027 AGCTTAGACTGATAAAGCATCTTAGAAC -s simCow_chr6.simCow.chr6 223681 28 - 602619 ATTTTGGGTTGATGAAAGCTTTTAAGAA -s simDog_chr6.simDog.chr6 224355 28 - 593897 ATTTTGGGTAGATGCATGATCTTAAAAC -s simHuman_chr6.simHuman.chr6 593832 23 + 601863 ACCTTAGGCTGTTGG-----CTTCTAAC -s simRat_chr6.simRat.chr6 638540 28 + 647215 AGCTTATACTGATAAAGCATCTTAAGAC - -a -s simMouse_chr6.simMouse.chr6 627010 74 + 636262 ACCTTTCCTCTTTATATCAAAATCTTTCCTCTTTATATCAAAATACACAACTTACCAGTAGCTATGTTCCATTT -s Anc0.Anc0refChr3 202895 10 - 222631 TC------------------------------------------------------ATCAGCTT---------- -s Anc1.Anc1refChr1 61937 17 + 69767 TC------------------------------------------------------ATCAGCTTTGTTCAA--- -s Anc2.Anc2refChr13 73521 10 - 96486 TC------------------------------------------------------CTCTGCTT---------- -s mr.mrrefChr3 173513 20 + 181027 AC------------------------------------------------------AGTAGCTATGTTCCATTT -s simCow_chr6.simCow.chr6 223714 10 - 602619 TC------------------------------------------------------CTGTGCAT---------- -s simDog_chr6.simDog.chr6 224388 10 - 593897 TC------------------------------------------------------TTCTGCTT---------- -s simHuman_chr6.simHuman.chr6 593860 17 + 601863 TC------------------------------------------------------ACCAACTTTGTTCAA--- -s simRat_chr6.simRat.chr6 638568 20 + 647215 AC------------------------------------------------------AGTGGCTTTGTTACTTTT - -a -s simMouse_chr6.simMouse.chr6 627084 21 + 636262 ACCACACTGTAGACTTGCAAA -s Anc0.Anc0refChr3 202905 13 - 222631 --------GTTGACCTGCAAA -s Anc1.Anc1refChr1 61954 21 + 69767 ATTGCCCTGTTGACCTGCAAA -s Anc2.Anc2refChr13 73531 13 - 96486 --------GTTAACATACACA -s mr.mrrefChr3 173533 21 + 181027 ACCACACTGTAGACTTGCAAA -s simCow_chr6.simCow.chr6 223724 13 - 602619 --------GTTATAATACACA -s simDog_chr6.simDog.chr6 224398 13 - 593897 --------GTCAACATACACA -s simHuman_chr6.simHuman.chr6 7215 21 - 601863 ATTGCCCTGTTGACCTGCAAA -s simRat_chr6.simRat.chr6 638588 21 + 647215 ACTGCACTGTGGACTTGTAAA - -a -s simMouse_chr6.simMouse.chr6 627105 9 + 636262 CATTGTGTA -s Anc0.Anc0refChr3 202918 5 - 222631 ----ACATA -s Anc1.Anc1refChr1 61975 9 + 69767 CTTTACATA -s Anc2.Anc2refChr13 73544 5 - 96486 ----ACATA -s mr.mrrefChr3 173554 9 + 181027 CATTGTGTA -s simCow_chr6.simCow.chr6 223737 4 - 602619 ----ATAT- -s simDog_chr6.simDog.chr6 224411 5 - 593897 ----ACATA -s simHuman_chr6.simHuman.chr6 7243 9 - 601863 CTTTACATA -s simRat_chr6.simRat.chr6 638609 9 + 647215 CATGGCATA - -a -s simMouse_chr6.simMouse.chr6 627114 6 + 636262 CTTGGG -s Anc0.Anc0refChr3 202923 6 - 222631 CTTGGA -s Anc1.Anc1refChr1 61984 6 + 69767 CTTGGA -s Anc2.Anc2refChr13 73556 6 - 96486 CTTGGA -s mr.mrrefChr3 173563 6 + 181027 CTTGGG -s simCow_chr6.simCow.chr6 223748 6 - 602619 CTTGGA -s simDog_chr6.simDog.chr6 224423 6 - 593897 CTTGGA -s simHuman_chr6.simHuman.chr6 7252 6 - 601863 CTTGGA -s simRat_chr6.simRat.chr6 638618 6 + 647215 CTTGGG - -a -s simMouse_chr6.simMouse.chr6 627120 67 + 636262 TTATTGACCCACTTTGCTTCTCCCACAGAACGAAATAATTACGGCATTGGACTCCCTAACACTCTTT -s Anc0.Anc0refChr3 202929 23 - 222631 TTATT-----------CTCCTTCCA---------------------------------ACAATTCTT -s Anc1.Anc1refChr1 61990 48 + 69767 TTATTAACCCATGCTGCTCCTTCCACA----------------ACTTTGAAACAC---ACAATTCTT -s Anc2.Anc2refChr13 73564 23 - 96486 TTATT-----------TTCCTTCTA---------------------------------ACAATTCTT -s mr.mrrefChr3 173569 64 + 181027 TTATTGACCCACTTTGCTTCTCCCACAGAACGAAATAATTACGGCATTGGACTCC---ACACTCTTT -s simCow_chr6.simCow.chr6 223756 23 - 602619 CTATT-----------TTCCTTTTA---------------------------------ACAATTATT -s simDog_chr6.simDog.chr6 224431 23 - 593897 TTTTT-----------TTTCTTCTA---------------------------------ACGATTCTT -s simHuman_chr6.simHuman.chr6 7258 48 - 601863 TTATTAACCCATGCTGCTCCTTCCACA----------------ACTTTGAAACAC---ACAGTTCTT -s simRat_chr6.simRat.chr6 638624 64 + 647215 TTATTGGCCCACTTTGCTCCTCCTACAAAATGAAATAATTATGGCCTTGATCTCC---ATACTCTTT - -a -s simMouse_chr6.simMouse.chr6 627187 104 + 636262 CATAGCGTTCAAGTTTGGTTATTTATTCTATACCTATCTGGACTTAGGAGGCAGAAGAGGGGACATATCTTTAACAATGCATATCTTTCAGGACTGGAGGCGTT -s Anc0.Anc0refChr3 202957 29 - 222631 CATCAGGCTCACGAATGATTATTCATT---------------------------------------------------------------------------GT -s Anc1.Anc1refChr1 62043 29 + 69767 CATCAGGCTCACGAATGATTATTCATT---------------------------------------------------------------------------GT -s Anc2.Anc2refChr13 73592 29 - 96486 CATCAGGCTCACAAATGATTATTCATT---------------------------------------------------------------------------GT -s mr.mrrefChr3 173633 102 + 181027 CATAGCGTTCAAGTTTGGTTATTTATTCTATACCTATCTGGACTTA--AGGCAGAAGAGGGGACATATCTTTAACAATGCATATCTTTCAGGACTGGAGGCGTT -s simCow_chr6.simCow.chr6 223784 29 - 602619 CATTAGGCTCACAAATGATTAATCATT---------------------------------------------------------------------------GT -s simDog_chr6.simDog.chr6 224460 29 - 593897 CATCCGGCTCACAAATGGTTTTTCATT---------------------------------------------------------------------------GT -s simHuman_chr6.simHuman.chr6 7311 29 - 601863 CATCAGGCTAACGAGTGATTATTCATT---------------------------------------------------------------------------GT -s simRat_chr6.simRat.chr6 638688 102 + 647215 CATAGTGTTCGTGTTCGGTTATTAATTCTATACCTATCTGGATTTA--AGGCCAAACAGGGGACGTATCTTTAACAATGCATGGCCTTCAAGACTGGAAGGGTT - -a -s simMouse_chr6.simMouse.chr6 627291 39 + 636262 TGACAAATTCTCAATATCTCTGCAGCAACAATACCCAGC -s Anc0.Anc0refChr3 202986 39 - 222631 TAACACATTCTCCATCTCTCTGTAGTAACATGACCCAGT -s Anc1.Anc1refChr1 62072 39 + 69767 TAACACATTCTCCATCTCTCTGTAGTAACATGACCCAGT -s Anc2.Anc2refChr13 73627 39 - 96486 TAACACATTCTCCATCTCTCTGTAGTAACATGGCCCAGT -s mr.mrrefChr3 173735 39 + 181027 TGACAAATTCTCAATATCTCTGCAGCAACAATACCCAGC -s simCow_chr6.simCow.chr6 223819 36 - 602619 GTACACATTCTCCCTTT---TATAGTCACATGGCCCAGT -s simDog_chr6.simDog.chr6 224495 39 - 593897 TAACAGACTCTCCATCTCTCTGTGAAAACATGGCCCAGT -s simHuman_chr6.simHuman.chr6 7340 39 - 601863 TAACACATTCTCCATCATTCTGTAGTAACATGACCCAGT -s simRat_chr6.simRat.chr6 638790 39 + 647215 TGACACATGCTCAATATATACGCAGTAACAATCCCCAGC - -a -s simMouse_chr6.simMouse.chr6 627330 35 + 636262 ATGATTAGAGACTAAACTACTCTATTCATACTGCG -s Anc0.Anc0refChr3 203025 30 - 222631 GTGAACAGA-----AACTTCTCAATTCATACTAGG -s Anc1.Anc1refChr1 62111 30 + 69767 GTGAACAGA-----AACTTCTCAATTCATACTAGG -s Anc2.Anc2refChr13 73666 30 - 96486 GTGAACAGA-----AACTTTCCAATTCGTACTAGG -s mr.mrrefChr3 173774 35 + 181027 ATGATTAGAGACTAAACTACTCTATTCATACTAGG -s simCow_chr6.simCow.chr6 223855 30 - 602619 GTGATCAGA-----AAGTTTCCAACTCGTGCTAGG -s simDog_chr6.simDog.chr6 224552 30 - 593897 GTGAACAAA-----AACTATCCAATTTGTACTAGG -s simHuman_chr6.simHuman.chr6 7379 30 - 601863 GGGACCAGA-----AATTTCTCCATTCATACTAGG -s simRat_chr6.simRat.chr6 638829 35 + 647215 ATGATTAGAGACTAAAATACTCTATTCATACTAGG - -a -s simMouse_chr6.simMouse.chr6 627365 106 + 636262 CTTTTTTTAGATGACAATGACAATACCAGGTATATACTTTACATCTATATGTCTAAGGATGACTGAGGGCTTAGGAGGGCACATATCTCTATGTAGGCCCTCCAAT -s Anc0.Anc0refChr3 203055 99 - 222631 CTTTTTGTGGACAACAAT------ACCATGTACATACCTTACATCTATATGTTTGAGGCTGACTGATGGCTAAG-AGGGCACATGTCTGTGTGTAGTCCCTCCACC -s Anc1.Anc1refChr1 62141 99 + 69767 CTTTTTGTGGACAACAAT------ACCATGTACATACCTTACATCTATATGTTTGAGGCTGACTGATGGCTAAG-AGGGCACATGTCTGTGTGTAGTCCCTCCACC -s Anc2.Anc2refChr13 73696 99 - 96486 CTTTTTGTGGACAACAAT------ACCATGTACATATCTTACATCTATATGTTTGAGGCTGACTGATGGTTAAG-AGGGCACATGTCTGTGTATAGTCCCTCCACC -s mr.mrrefChr3 173809 105 + 181027 CTTTTTTTAGATGACAATGACAATACCATGTATATACTTTACATCTATATGTCTAAGGATGACTGAGGGCTTAG-AGGGCACATATCTCTATGTAGGCCCTCCAAT -s simCow_chr6.simCow.chr6 223885 99 - 602619 CCTCTTGTGGACAGCAAT------ACCATGTCCATATCTTGTGGCTATATGTTTAAGACTGGCTGATGGTTAAG-AGGCTACATGTCTCTCTACAGTCCCCCCACC -s simDog_chr6.simDog.chr6 224582 99 - 593897 CTGTCTGTGGACAACAAT------ACCATGTACATATGTCACATCTATATATTTGAGGCTGACTGATGGTTAAG-AGGGCATATGTCTGTGTATAGTCCCTCTACC -s simHuman_chr6.simHuman.chr6 7409 95 - 601863 CTTTTTGTGGACAACAAT------ATCATGTACATACCTTACATCTATATGCTTGAGGCTGATTG----CTAAG-GGGACACATGTCATTTTGTAGACCCTCCACC -s simRat_chr6.simRat.chr6 638870 105 + 647215 CTTTTTTTAGATGACAATGACAAGACTATGTATATACCTTACATCTATATGTCTAAGGATGACTGAGGGCTTCG-AGGGCACATATCTCCATGTAGCCCCTCCAAT - -a -s simMouse_chr6.simMouse.chr6 627471 81 + 636262 ACTCATGCTGAACAAGTTTAACAGACTTCAACATCATGGCAAGATCTGAAGCTTGCTATAATAAAACATTCAACAAAATGT -s Anc0.Anc0refChr3 203163 18 - 222631 AATCATGCTGAACAATCT--------------------------------------------------------------- -s Anc1.Anc1refChr1 62249 80 + 69767 AATCATGCTGAACAATCTTAACAAATTTCACTATCATGGCATATTCTGAAGTTTCCTACCATACAAGATCCT-GAAAGTGC -s Anc2.Anc2refChr13 73804 18 - 96486 AATCATGCTGAACAATCT--------------------------------------------------------------- -s mr.mrrefChr3 173923 80 + 181027 ACTCATGCTGAACAAGCTTAACAGACTTCAACATCATGGCAAGATCTGAAGCTTGCTATAATAAAACATTCA-CAAAATGT -s simCow_chr6.simCow.chr6 223993 14 - 602619 ----TTGTCGAACAATTT--------------------------------------------------------------- -s simDog_chr6.simDog.chr6 224690 18 - 593897 AATCATGCTGAACAATCT--------------------------------------------------------------- -s simHuman_chr6.simHuman.chr6 7513 80 - 601863 AATCCTACTGAGAGGTTTTAACAAATTTCACTATCATGGCATATTCTGAAGTTTCCTACCATACAAGATCCT-GAAAGTGC -s simRat_chr6.simRat.chr6 638984 80 + 647215 ACTCAAGCTGAACAAGCTTAATAAACTTTAACATCATGGCAAGATCTGAAGCTCACTATAATAAAAGACTCA-CAAAATGT - -a -s simMouse_chr6.simMouse.chr6 627552 19 + 636262 GGTCTATGTGTTTGTTCTG -s Anc1.Anc1refChr1 62329 19 + 69767 TGTCTCCCTGCTTGTCATA -s mr.mrrefChr3 174003 19 + 181027 GGTCTATGTGTTTGTTCTG -s simHuman_chr6.simHuman.chr6 7595 19 - 601863 TGTCTCCCTGCTTGTCATA -s simRat_chr6.simRat.chr6 639064 19 + 647215 GGTCTATGTGTTTGTCACA - -a -s simMouse_chr6.simMouse.chr6 627571 8 + 636262 TTTGCTTT -s Anc1.Anc1refChr1 62348 8 + 69767 CTTGATTT -s mr.mrrefChr3 174022 8 + 181027 TTTGCTTT -s simHuman_chr6.simHuman.chr6 7616 8 - 601863 CTTGATTT -s simRat_chr6.simRat.chr6 639083 8 + 647215 CTCGTGTC - -a -s simMouse_chr6.simMouse.chr6 627579 67 + 636262 ATGTCATGTACAGAGTTTTGGAGACATGTGCATAACCTACAAGTCACCTTTGGAAATCAATTGCTGC -s Anc0.Anc0refChr3 203181 26 - 222631 -------------------------------------CACAAGCCAC-TTTG-AGA--AATTGGTCC -s Anc1.Anc1refChr1 62356 57 + 69767 ATTGCATTCACTGGTCTT-------ATCTGCTTGACTCACAAGCCAC-TTTGGAGA--AATTGGTCC -s Anc2.Anc2refChr13 73822 26 - 96486 -------------------------------------CACAAGCCAC-TTTG-AGA--AATTAGTCC -s mr.mrrefChr3 174030 67 + 181027 ATGTCATGTACAGAGTTTTGGAGACATGTGCATAACCTACAAGTCACCTTTGGAAATCAATTGCTGC -s simCow_chr6.simCow.chr6 224007 26 - 602619 -------------------------------------CACAAGCCAA-TTTG-GGA--GATTTGTTC -s simDog_chr6.simDog.chr6 224708 26 - 593897 -------------------------------------CACAAGCCAC-TTTG-AGA--ATTTAGTCC -s simHuman_chr6.simHuman.chr6 7633 57 - 601863 ATTGCATTCACTGGTCTT-------ATCTGCTTGACTCACAAGCCAC-TTCGGAGA--AATTGGTAC -s simRat_chr6.simRat.chr6 639091 67 + 647215 ATGTCATGTACAGAATTTTGGATACACGTGCTTAAGCTGCAAGCCAGCTTCAGAAATCAATTGCTTT - -a -s simMouse_chr6.simMouse.chr6 627646 16 + 636262 TCTGCTTTACAAACGG -s Anc0.Anc0refChr3 203216 7 - 222631 TCTGC---------AG -s Anc1.Anc1refChr1 62422 7 + 69767 TCTGC---------AG -s Anc2.Anc2refChr13 73857 7 - 96486 TTTGC---------AA -s mr.mrrefChr3 174097 7 + 181027 TCTGC---------GG -s simCow_chr6.simCow.chr6 224042 7 - 602619 TGTGT---------GA -s simDog_chr6.simDog.chr6 224743 7 - 593897 TTTGC---------AA -s simHuman_chr6.simHuman.chr6 7699 7 - 601863 TCTGC---------AG -s simRat_chr6.simRat.chr6 639158 7 + 647215 ACTGC---------AG - -a -s simMouse_chr6.simMouse.chr6 627662 7 + 636262 GCAAAAC -s Anc0.Anc0refChr3 203227 7 - 222631 GCAAAAC -s Anc1.Anc1refChr1 62433 7 + 69767 GCAAAAC -s Anc2.Anc2refChr13 73868 7 - 96486 GCAAAAT -s mr.mrrefChr3 174104 7 + 181027 GCAAAAC -s simCow_chr6.simCow.chr6 224053 7 - 602619 GCAAAAG -s simDog_chr6.simDog.chr6 224754 7 - 593897 GCAAAAT -s simHuman_chr6.simHuman.chr6 7710 7 - 601863 GCAAAGC -s simRat_chr6.simRat.chr6 639165 7 + 647215 TCAAAAC - -a -s simMouse_chr6.simMouse.chr6 627669 7 + 636262 AATATTT -s Anc0.Anc0refChr3 203234 7 - 222631 AACATCG -s Anc1.Anc1refChr1 62440 7 + 69767 AACATCG -s Anc2.Anc2refChr13 73875 7 - 96486 AACATCG -s mr.mrrefChr3 174111 7 + 181027 AATATTT -s simCow_chr6.simCow.chr6 224060 7 - 602619 AACATTG -s simDog_chr6.simDog.chr6 224761 7 - 593897 AACATCG -s simHuman_chr6.simHuman.chr6 7717 7 - 601863 AACATCG -s simRat_chr6.simRat.chr6 639175 7 + 647215 ATCATCT - -a -s simMouse_chr6.simMouse.chr6 627676 1 + 636262 A -s Anc0.Anc0refChr3 203241 1 - 222631 A -s Anc1.Anc1refChr1 62447 1 + 69767 A -s Anc2.Anc2refChr13 73909 1 - 96486 A -s mr.mrrefChr3 174118 1 + 181027 A -s simCow_chr6.simCow.chr6 224094 1 - 602619 A -s simDog_chr6.simDog.chr6 224795 1 - 593897 A -s simHuman_chr6.simHuman.chr6 7724 1 - 601863 A -s simRat_chr6.simRat.chr6 639182 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 627677 9 + 636262 ATGCAGTCG -s Anc0.Anc0refChr3 203253 9 - 222631 ACTCAATCA -s Anc1.Anc1refChr1 62459 9 + 69767 ACTCAATCA -s Anc2.Anc2refChr13 73921 9 - 96486 ACTCAATCA -s mr.mrrefChr3 174119 9 + 181027 ATGCAGTCG -s simCow_chr6.simCow.chr6 224106 9 - 602619 ATTCAAGCA -s simDog_chr6.simDog.chr6 224807 9 - 593897 CCTCAATCA -s simHuman_chr6.simHuman.chr6 7736 9 - 601863 ACTCAATCA -s simRat_chr6.simRat.chr6 639183 9 + 647215 ACATGTCTG - -a -s simMouse_chr6.simMouse.chr6 627686 15 + 636262 TAAGGCCTAACTGTG -s Anc0.Anc0refChr3 203262 15 - 222631 CACAGCCTTATAGAG -s Anc1.Anc1refChr1 62468 15 + 69767 CACAGCCTTATAGAG -s Anc2.Anc2refChr13 73930 15 - 96486 CACAACCATATAGAG -s mr.mrrefChr3 174128 15 + 181027 TAAGGCCTAACTGTG -s simCow_chr6.simCow.chr6 224115 15 - 602619 TACATCCATATAAAG -s simDog_chr6.simDog.chr6 224816 15 - 593897 CACAACCATACAGAG -s simHuman_chr6.simHuman.chr6 7745 15 - 601863 CACAGCCTTATAGAG -s simRat_chr6.simRat.chr6 639193 15 + 647215 TGAGGCTAAACTGCA - -a -s simMouse_chr6.simMouse.chr6 627701 18 + 636262 ATCATGTAGAGTTAGGAG -s Anc0.Anc0refChr3 203277 10 - 222631 ATCAGGCACA-------- -s Anc1.Anc1refChr1 62483 10 + 69767 ATCAGGCACA-------- -s Anc2.Anc2refChr13 73945 10 - 96486 ATCAGGCACA-------- -s mr.mrrefChr3 174143 18 + 181027 ATCATGTAGAGTTAGGAG -s simCow_chr6.simCow.chr6 224130 10 - 602619 ATCAGGCACA-------- -s simDog_chr6.simDog.chr6 224831 10 - 593897 ATCAGGCGCA-------- -s simHuman_chr6.simHuman.chr6 7760 10 - 601863 ATTAGGCACA-------- -s simRat_chr6.simRat.chr6 639213 18 + 647215 GTCATGTTGAGTTAGGAA - -a -s simMouse_chr6.simMouse.chr6 627719 13 + 636262 AAAAAGCAAGTCA -s Anc0.Anc0refChr3 203287 12 - 222631 -AAAAGCAAGTTT -s Anc1.Anc1refChr1 62493 12 + 69767 -AAAAGCAAGTTT -s Anc2.Anc2refChr13 73955 12 - 96486 -AAAAGCAAGTTT -s mr.mrrefChr3 174161 13 + 181027 AAAAAGCAAGTCA -s simCow_chr6.simCow.chr6 224140 12 - 602619 -AAAAGCAAGTTA -s simDog_chr6.simDog.chr6 224841 12 - 593897 -AAAAGCAAGTTT -s simHuman_chr6.simHuman.chr6 7770 12 - 601863 -AAAAGCAAGTTC -s simRat_chr6.simRat.chr6 639232 13 + 647215 AAAAAACAAGTTA - -a -s simMouse_chr6.simMouse.chr6 627732 9 + 636262 TCGGCTATA -s Anc0.Anc0refChr3 203299 9 - 222631 TCAGATACA -s Anc1.Anc1refChr1 62505 9 + 69767 TCAGATACA -s Anc2.Anc2refChr13 73967 9 - 96486 ACAGATACA -s mr.mrrefChr3 174174 9 + 181027 TCGGCTATA -s simCow_chr6.simCow.chr6 224152 9 - 602619 TTAGATACA -s simDog_chr6.simDog.chr6 224853 9 - 593897 ACAGATACA -s simHuman_chr6.simHuman.chr6 7791 9 - 601863 TCAGTTACA -s simRat_chr6.simRat.chr6 639245 9 + 647215 TCAGCTATA - -a -s simMouse_chr6.simMouse.chr6 627741 16 + 636262 AAAGCACACATGTCCA -s Anc0.Anc0refChr3 203308 16 - 222631 AAATTACATATGTTTG -s Anc1.Anc1refChr1 62514 16 + 69767 AAATTACATATGTTTG -s Anc2.Anc2refChr13 73976 16 - 96486 AAATTACATATGTTTG -s mr.mrrefChr3 174183 16 + 181027 AAAGCACACATGTCCA -s simCow_chr6.simCow.chr6 224162 16 - 602619 AAATTACATACATCTG -s simDog_chr6.simDog.chr6 224862 16 - 593897 AAATAATGTATGTTTG -s simHuman_chr6.simHuman.chr6 7800 16 - 601863 AGATTACATATGTTTG -s simRat_chr6.simRat.chr6 639254 16 + 647215 AAACCACACATGTCTG - -a -s simMouse_chr6.simMouse.chr6 627757 48 + 636262 GTCCTACTCACCATTCTAATTGGGTCTAGACAGTGGGTGCAACAGCTT -s Anc0.Anc0refChr3 203328 48 - 222631 CTCCTACTGACTATTATATTTGAGTTTAGACAATGGGTACAATAGCTT -s Anc1.Anc1refChr1 62534 48 + 69767 CTCCTACTGACTATTATATTTGAGTTTAGACAATGGGTACAATAGCTT -s Anc2.Anc2refChr13 73996 48 - 96486 CTCCTACTGACTATTATATTTGAGTTTATACAAAGGGTATAATAGCTG -s mr.mrrefChr3 174199 48 + 181027 GTCCTACTCACCATTCTAATTGGGTCTAGACAGTGGGTGCAACAGCTT -s simCow_chr6.simCow.chr6 224182 48 - 602619 GTTGTATTGACTGTAATATTTGAGCTTACATAAAGGGTATACTAGCCA -s simDog_chr6.simDog.chr6 224882 46 - 593897 CTCC--CTTACTATTGTTTTTGAGTTGATACAAAGGGTATGATAGCTG -s simHuman_chr6.simHuman.chr6 7820 48 - 601863 ATCCTACTGCTTATTATATTCAAATTTGGACAATGGGTACAATGGCTT -s simRat_chr6.simRat.chr6 639270 48 + 647215 GTCCTACTCACCATTATAATTGGGTCTAGATGGTGGGTGCAACAGCTT - -a -s simMouse_chr6.simMouse.chr6 627805 1 + 636262 A -s Anc0.Anc0refChr3 203389 1 - 222631 A -s Anc1.Anc1refChr1 62595 1 + 69767 A -s Anc2.Anc2refChr13 74057 1 - 96486 A -s mr.mrrefChr3 174247 1 + 181027 A -s simCow_chr6.simCow.chr6 224243 1 - 602619 A -s simDog_chr6.simDog.chr6 224941 1 - 593897 A -s simHuman_chr6.simHuman.chr6 7881 1 - 601863 A -s simRat_chr6.simRat.chr6 639318 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 627806 7 + 636262 CTTCAGC -s Anc0.Anc0refChr3 203390 7 - 222631 TTGCAGC -s Anc1.Anc1refChr1 62596 7 + 69767 TTGCAGC -s Anc2.Anc2refChr13 74058 7 - 96486 TTGCAGC -s mr.mrrefChr3 174248 7 + 181027 CTTCAGC -s simCow_chr6.simCow.chr6 224244 7 - 602619 TTGCAGC -s simDog_chr6.simDog.chr6 224942 7 - 593897 TTCCAGC -s simHuman_chr6.simHuman.chr6 7882 7 - 601863 TTGCAGC -s simRat_chr6.simRat.chr6 639347 7 + 647215 CTTCGCC - -a -s simMouse_chr6.simMouse.chr6 627813 2 + 636262 CA -s Anc0.Anc0refChr3 203405 2 - 222631 CT -s Anc1.Anc1refChr1 62611 2 + 69767 CT -s Anc2.Anc2refChr13 74073 2 - 96486 TT -s mr.mrrefChr3 174255 2 + 181027 CA -s simDog_chr6.simDog.chr6 224957 2 - 593897 TT -s simHuman_chr6.simHuman.chr6 7897 2 - 601863 CT -s simRat_chr6.simRat.chr6 639354 2 + 647215 CA - -a -s simMouse_chr6.simMouse.chr6 627815 20 + 636262 CCTAATTGCAAAGTTTCATA -s Anc0.Anc0refChr3 203407 20 - 222631 GCTAATGGTAAAGGTTCATA -s Anc1.Anc1refChr1 62613 20 + 69767 GCTAATGGTAAAGGTTCATA -s Anc2.Anc2refChr13 74082 20 - 96486 GCTAATGCTAAAGGTTCATA -s mr.mrrefChr3 174257 20 + 181027 CCTAATTGCAAAGTTTCATA -s simCow_chr6.simCow.chr6 224265 20 - 602619 GCACATGATAATGTTTCATA -s simDog_chr6.simDog.chr6 224966 20 - 593897 GCTAATGCTACATGTTCATA -s simHuman_chr6.simHuman.chr6 7899 20 - 601863 GCTAATGGTAAAGGTTCATA -s simRat_chr6.simRat.chr6 639356 20 + 647215 CCTAATTGCAAAGTTTCATA - -a -s simMouse_chr6.simMouse.chr6 627835 28 + 636262 TTTCTCAATTGTGTGGCAGGGTCGAATT -s Anc0.Anc0refChr3 203442 28 - 222631 TTTCTCTATTGTAGCATAGGATCCCAAT -s Anc1.Anc1refChr1 62648 28 + 69767 TTTCTCTATTGTAGCATAGGATCCCAAT -s Anc2.Anc2refChr13 74117 28 - 96486 ATTCTGTGTTATAGCATAGGATCCCAAT -s mr.mrrefChr3 174277 28 + 181027 TTTCTCAATTGTGTGGCAGGGTCGAATT -s simCow_chr6.simCow.chr6 224300 26 - 602619 CTTCT--GTTATAACACAGGATTCCAAT -s simDog_chr6.simDog.chr6 225001 24 - 593897 ATTCGGT----TGGCGTGGGATCCCAAC -s simHuman_chr6.simHuman.chr6 7934 28 - 601863 TTTCTCCATTGTACCATAAGATCCCAAT -s simRat_chr6.simRat.chr6 639390 28 + 647215 TTTCTCTATTGTACAACAGGGTTGGATT - -a -s simMouse_chr6.simMouse.chr6 627863 28 + 636262 ACAGACAGCTTGGAAGGAAGCACAGGCT -s Anc0.Anc0refChr3 203470 21 - 222631 ACAGGCATGTAGGAAGTGAAC------- -s Anc1.Anc1refChr1 62676 21 + 69767 ACAGGCATGTAGGAAGTGAAC------- -s Anc2.Anc2refChr13 74145 21 - 96486 ACATGCATGTAGGAAGTGAAC------- -s mr.mrrefChr3 174305 28 + 181027 ACAGACAGCTTGGAAGGAAGCACAGGCT -s simCow_chr6.simCow.chr6 224326 21 - 602619 ACAAACATGTGAGTAGTGAAC------- -s simDog_chr6.simDog.chr6 225026 18 - 593897 ATCTGAACATAGCAAG---AT------- -s simHuman_chr6.simHuman.chr6 7962 21 - 601863 ACAGGCATGTAGGAAGTGAAC------- -s simRat_chr6.simRat.chr6 639418 28 + 647215 ACAGACACCTTGGGAGGAAACACATGCT - -a -s simMouse_chr6.simMouse.chr6 627891 10 + 636262 ATAGGCTTGC -s Anc0.Anc0refChr3 203496 10 - 222631 ATAAGCTTTA -s Anc1.Anc1refChr1 62702 10 + 69767 ATAAGCTTTA -s Anc2.Anc2refChr13 74207 10 - 96486 ACAAGCCTTA -s mr.mrrefChr3 174333 10 + 181027 ATAGGCTTGC -s simCow_chr6.simCow.chr6 224406 10 - 602619 ACAGCCCTTA -s simDog_chr6.simDog.chr6 225086 10 - 593897 ACAAGCCTTT -s simHuman_chr6.simHuman.chr6 594657 10 + 601863 ATTACCTCCA -s simRat_chr6.simRat.chr6 639446 10 + 647215 ATAGGTTTGT - -a -s simMouse_chr6.simMouse.chr6 627901 20 + 636262 CCCTGCAAGTGCAAGTCAGT -s Anc0.Anc0refChr3 203506 20 - 222631 CCCTGCAATTGCACACAAGC -s Anc1.Anc1refChr1 62712 20 + 69767 CCCTGCAATTGCACACAAGC -s Anc2.Anc2refChr13 74222 20 - 96486 CACTGCAATTGCACACAAAC -s mr.mrrefChr3 174343 20 + 181027 CCCTGCAAGTGCAAGTCAGT -s simCow_chr6.simCow.chr6 224433 20 - 602619 CACTGAAATTGCACAGAGAT -s simDog_chr6.simDog.chr6 225101 20 - 593897 CACTGCAATTGCACTCAAAC -s simHuman_chr6.simHuman.chr6 594667 9 + 601863 CCCTACT-----------GC -s simRat_chr6.simRat.chr6 639456 20 + 647215 CCCTGCATGGGCAAGTCAGT - -a -s simMouse_chr6.simMouse.chr6 627921 9 + 636262 AATTTTTGG -s Anc0.Anc0refChr3 203526 9 - 222631 TATCTTTGG -s Anc1.Anc1refChr1 62732 9 + 69767 TATCTTTGG -s Anc2.Anc2refChr13 74249 9 - 96486 TATCTTTGG -s mr.mrrefChr3 174363 9 + 181027 AATTTTTGG -s simCow_chr6.simCow.chr6 224460 9 - 602619 TATCTCTGG -s simDog_chr6.simDog.chr6 225128 9 - 593897 TATCTTTGA -s simHuman_chr6.simHuman.chr6 594676 9 + 601863 TATGTTGTG -s simRat_chr6.simRat.chr6 639476 9 + 647215 AATTTTTGG - -a -s simMouse_chr6.simMouse.chr6 627930 1 + 636262 A -s Anc0.Anc0refChr3 203535 1 - 222631 T -s Anc1.Anc1refChr1 62741 1 + 69767 T -s Anc2.Anc2refChr13 74258 1 - 96486 T -s mr.mrrefChr3 174372 1 + 181027 A -s simCow_chr6.simCow.chr6 224474 1 - 602619 T -s simDog_chr6.simDog.chr6 225137 1 - 593897 T -s simHuman_chr6.simHuman.chr6 594685 1 + 601863 T -s simRat_chr6.simRat.chr6 639485 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 627931 26 + 636262 ACAGTATCAGGGCCATTACAAACAAC -s Anc0.Anc0refChr3 203536 26 - 222631 ATAATAACAGGGCAATTACATAGAAC -s Anc1.Anc1refChr1 62742 26 + 69767 ATAATAACAGGGCAATTACATAGAAC -s Anc2.Anc2refChr13 74259 26 - 96486 ATAATAACAGTGCAATTACCTAGAAC -s mr.mrrefChr3 174373 26 + 181027 ACAGTATCAGGGCCATTACAAACAAC -s simCow_chr6.simCow.chr6 224475 25 - 602619 ATAATATCAGCCCAATAACCTCCAA- -s simDog_chr6.simDog.chr6 225146 26 - 593897 ATAATAACAGTGCAATTACCTAGAGC -s simHuman_chr6.simHuman.chr6 594686 24 + 601863 ATATTA--ATGGAGAGTAAAGATGTT -s simRat_chr6.simRat.chr6 639486 26 + 647215 ACAGTCTCAGGGTCATTACAAACAAC - -a -s simMouse_chr6.simMouse.chr6 627957 20 + 636262 TACTTAAGGCCTGATTCTTA -s Anc0.Anc0refChr3 203562 20 - 222631 TGATTATGATCTGATTCTTA -s Anc1.Anc1refChr1 62768 20 + 69767 TGATTATGATCTGATTCTTA -s Anc2.Anc2refChr13 74285 20 - 96486 TGATTATGATCTGATTCTTA -s mr.mrrefChr3 174399 20 + 181027 TACTTAAGGCCTGATTCTTA -s simCow_chr6.simCow.chr6 224500 20 - 602619 TGATCATGATCTGATCCTTA -s simDog_chr6.simDog.chr6 225172 20 - 593897 TAACTATGGTCTCATTCTTA -s simHuman_chr6.simHuman.chr6 594710 20 + 601863 TTTTTCTGATCTGATTCTTA -s simRat_chr6.simRat.chr6 639514 20 + 647215 TAATTATGGTCTGTGTCCTA - -a -s simMouse_chr6.simMouse.chr6 627977 3 + 636262 TGC -s Anc0.Anc0refChr3 203582 3 - 222631 TGC -s Anc1.Anc1refChr1 62788 3 + 69767 TGC -s Anc2.Anc2refChr13 74307 3 - 96486 TGC -s mr.mrrefChr3 174419 3 + 181027 TGC -s simCow_chr6.simCow.chr6 224522 3 - 602619 TGC -s simDog_chr6.simDog.chr6 225194 3 - 593897 TGT -s simHuman_chr6.simHuman.chr6 594730 3 + 601863 TGC -s simRat_chr6.simRat.chr6 639534 3 + 647215 TGG - -a -s simMouse_chr6.simMouse.chr6 627980 11 + 636262 AACATAATCTG -s Anc0.Anc0refChr3 203591 11 - 222631 AAGATAATGTG -s Anc1.Anc1refChr1 62797 11 + 69767 AAGATAATGTG -s Anc2.Anc2refChr13 74316 11 - 96486 ATGATAACGTA -s mr.mrrefChr3 174422 11 + 181027 AACATAATCTG -s simCow_chr6.simCow.chr6 224531 10 - 602619 ATGAGAA-GTA -s simDog_chr6.simDog.chr6 225203 11 - 593897 ATGATAACATA -s simHuman_chr6.simHuman.chr6 594739 11 + 601863 AAGATAATGTG -s simRat_chr6.simRat.chr6 639537 11 + 647215 AATATAATATG - -a -s simMouse_chr6.simMouse.chr6 627991 9 + 636262 TACTTTTTA -s Anc0.Anc0refChr3 203603 9 - 222631 TCCTTATTA -s Anc1.Anc1refChr1 62809 9 + 69767 TCCTTATTA -s Anc2.Anc2refChr13 74328 9 - 96486 TCTTTATTA -s mr.mrrefChr3 174433 9 + 181027 TACTTTTTA -s simCow_chr6.simCow.chr6 224542 9 - 602619 TCTTTATTA -s simDog_chr6.simDog.chr6 225215 9 - 593897 TCTTTATTA -s simHuman_chr6.simHuman.chr6 594751 9 + 601863 TCCTTATTA -s simRat_chr6.simRat.chr6 639548 9 + 647215 TACTTTTTA - -a -s simMouse_chr6.simMouse.chr6 628000 22 + 636262 TCAGCATCGTCTTGATGCAGAC -s Anc0.Anc0refChr3 203619 12 - 222631 TT----------TAAAGCAGAC -s Anc1.Anc1refChr1 62825 12 + 69767 TT----------TAAAGCAGAC -s Anc2.Anc2refChr13 74344 12 - 96486 GT----------GAAACCAGAC -s mr.mrrefChr3 174442 12 + 181027 TC----------TGATGCAGAC -s simCow_chr6.simCow.chr6 224558 7 - 602619 ---------------ACCAGAC -s simDog_chr6.simDog.chr6 225244 12 - 593897 GT----------GAAACCAGAG -s simHuman_chr6.simHuman.chr6 594767 12 + 601863 TT----------TAGAGCAGAC -s simRat_chr6.simRat.chr6 639557 12 + 647215 TC----------TAATGCAGAC - -a -s simMouse_chr6.simMouse.chr6 628022 27 + 636262 TGTGCTCATACCTGCTTTTCCATCAGC -s Anc0.Anc0refChr3 203632 27 - 222631 TAGGCCCACACCAGATTTTCCACAAGC -s Anc1.Anc1refChr1 62838 27 + 69767 TAGGCCCACACCAGATTTTCCACAAGC -s Anc2.Anc2refChr13 74357 27 - 96486 TAGCCCCACACCAGAATTTCTGCAAGC -s mr.mrrefChr3 174454 27 + 181027 TGTGCTCATACCTGCTTTTCCATCAGC -s simCow_chr6.simCow.chr6 224566 27 - 602619 TGGCTCCACACCAGAATTTCTGCAAGT -s simDog_chr6.simDog.chr6 225257 20 - 593897 TAGCCCCACACCATA-------CAAGC -s simHuman_chr6.simHuman.chr6 594780 27 + 601863 TAAGCCCACACCAGATCTTCCACAAGA -s simRat_chr6.simRat.chr6 639569 27 + 647215 TGTGTCCATACCTGATTTTCCATCAGC - -a -s simMouse_chr6.simMouse.chr6 628049 8 + 636262 TAACACAT -s Anc0.Anc0refChr3 203659 6 - 222631 TAACAC-- -s Anc1.Anc1refChr1 62865 8 + 69767 TAACACAT -s Anc2.Anc2refChr13 74384 6 - 96486 CAACAA-- -s mr.mrrefChr3 174481 8 + 181027 TAACACAT -s simCow_chr6.simCow.chr6 224593 6 - 602619 CAACAA-- -s simDog_chr6.simDog.chr6 225277 6 - 593897 CAACAA-- -s simHuman_chr6.simHuman.chr6 594808 8 + 601863 TATGACAT -s simRat_chr6.simRat.chr6 639596 8 + 647215 TAACACAT - -a -s simMouse_chr6.simMouse.chr6 628057 14 + 636262 CTGTGTTAACAGGC -s Anc0.Anc0refChr3 203666 14 - 222631 TTGTGCTGACTTGC -s Anc1.Anc1refChr1 62874 14 + 69767 TTGTGCTGACTTGC -s Anc2.Anc2refChr13 74391 14 - 96486 TTGTGCTGACTTGC -s mr.mrrefChr3 174489 14 + 181027 CTGTGTTAACAGGC -s simCow_chr6.simCow.chr6 224600 14 - 602619 CTGTTGTGACTTAC -s simDog_chr6.simDog.chr6 225284 14 - 593897 TTGCGCTGACTTGC -s simHuman_chr6.simHuman.chr6 594817 14 + 601863 TTGTGCTGACTTGC -s simRat_chr6.simRat.chr6 639604 14 + 647215 CTGTGTTAACAGGG - -a -s simMouse_chr6.simMouse.chr6 628071 8 + 636262 TTTAGTGT -s Anc0.Anc0refChr3 203681 8 - 222631 TTTAGTGT -s Anc1.Anc1refChr1 62889 8 + 69767 TTTAGTGT -s Anc2.Anc2refChr13 74406 8 - 96486 TTGAGTGT -s mr.mrrefChr3 174503 8 + 181027 TTTAGTGT -s simCow_chr6.simCow.chr6 224615 2 - 602619 TT------ -s simDog_chr6.simDog.chr6 225299 8 - 593897 TTGAGTGT -s simHuman_chr6.simHuman.chr6 594832 8 + 601863 TTTAGTGC -s simRat_chr6.simRat.chr6 639618 8 + 647215 TTTAGTGT - -a -s simMouse_chr6.simMouse.chr6 628079 9 + 636262 TGTGTTGAG -s Anc0.Anc0refChr3 203689 4 - 222631 CACG----- -s Anc1.Anc1refChr1 62897 4 + 69767 CACG----- -s Anc2.Anc2refChr13 74414 4 - 96486 CACG----- -s mr.mrrefChr3 174511 9 + 181027 TGTGTTGAG -s simDog_chr6.simDog.chr6 225308 4 - 593897 CACG----- -s simHuman_chr6.simHuman.chr6 594840 4 + 601863 CACG----- -s simRat_chr6.simRat.chr6 639626 9 + 647215 TGTGTTGAG - -a -s simMouse_chr6.simMouse.chr6 628088 4 + 636262 TACC -s Anc0.Anc0refChr3 203693 2 - 222631 --GC -s Anc1.Anc1refChr1 62901 2 + 69767 --GC -s Anc2.Anc2refChr13 74418 2 - 96486 --GC -s mr.mrrefChr3 174520 4 + 181027 TACC -s simDog_chr6.simDog.chr6 225312 2 - 593897 --GC -s simHuman_chr6.simHuman.chr6 594844 2 + 601863 --AC -s simRat_chr6.simRat.chr6 639636 4 + 647215 TACC - -a -s simMouse_chr6.simMouse.chr6 628092 11 + 636262 CGTGCAAGTCT -s Anc0.Anc0refChr3 203695 11 - 222631 AGTGCAAGGTT -s Anc1.Anc1refChr1 62903 11 + 69767 AGTGCAAGGTT -s Anc2.Anc2refChr13 74420 11 - 96486 AATGCAGGGTT -s mr.mrrefChr3 174524 11 + 181027 CGTGCAAGTCT -s simDog_chr6.simDog.chr6 225325 11 - 593897 AATGCAGGGTT -s simHuman_chr6.simHuman.chr6 594846 11 + 601863 AGTGAAAGGTT -s simRat_chr6.simRat.chr6 639640 11 + 647215 TGCACATGTTT - -a -s simMouse_chr6.simMouse.chr6 628103 4 + 636262 TGAA -s Anc0.Anc0refChr3 203706 4 - 222631 CGAT -s Anc1.Anc1refChr1 62914 4 + 69767 CGAT -s Anc2.Anc2refChr13 74431 4 - 96486 CGGT -s mr.mrrefChr3 174535 4 + 181027 TGAA -s simDog_chr6.simDog.chr6 225341 4 - 593897 CGGT -s simHuman_chr6.simHuman.chr6 594857 4 + 601863 CTAT -s simRat_chr6.simRat.chr6 639651 4 + 647215 GGAA - -a -s simMouse_chr6.simMouse.chr6 628107 20 + 636262 GCCTGCCCTGGGTGACCCTC -s Anc0.Anc0refChr3 203718 20 - 222631 GTCTCCCATGGGTGGCCCAC -s Anc1.Anc1refChr1 62926 20 + 69767 GTCTCCCATGGGTGGCCCAC -s Anc2.Anc2refChr13 74443 20 - 96486 GTCTCCCATGGGTGGCCCAC -s mr.mrrefChr3 174539 20 + 181027 GCCTGCCCTGGGTGACCCTC -s simCow_chr6.simCow.chr6 224617 19 - 602619 -TCCCTCATGGGTGGCCCAC -s simDog_chr6.simDog.chr6 225353 20 - 593897 GCCTGCCATGGGTACCCCAC -s simHuman_chr6.simHuman.chr6 594869 20 + 601863 GTCTCCTTTAAGTGGCCCAC -s simRat_chr6.simRat.chr6 639655 20 + 647215 GCTTGCCCTGGGTGACCCAC - -a -s simMouse_chr6.simMouse.chr6 628127 32 + 636262 ATCAGTTATATTAGTAATAAGCATTTGAGTCG -s Anc0.Anc0refChr3 203738 32 - 222631 TTCAGTTGTCTTAGGAATAAAAACTGAAGTCT -s Anc1.Anc1refChr1 62946 32 + 69767 TTCAGTTGTCTTAGGAATAAAAACTGAAGTCT -s Anc2.Anc2refChr13 74463 32 - 96486 TTCAGTTGCCTTAGGAATAAAAACTGAAGTCT -s mr.mrrefChr3 174559 32 + 181027 ATCAGTTATATTAGTAATAAGCATTTGAGTCG -s simCow_chr6.simCow.chr6 224646 31 - 602619 TTCACTTG-CTTAGGGATAAAAACTGAAGTCC -s simDog_chr6.simDog.chr6 225373 32 - 593897 GACAGTTGCCTTAGGAATAAAACCTGAAGTTT -s simHuman_chr6.simHuman.chr6 594889 32 + 601863 TTCAGTTGTGTTAGGAATAAAAACTGAAATCT -s simRat_chr6.simRat.chr6 639675 32 + 647215 AGTGGTTGTATTAGTAATAAGCATTTGAGTTG - -a -s simMouse_chr6.simMouse.chr6 628159 14 + 636262 GGTGTTTTAGAACT -s Anc0.Anc0refChr3 203770 14 - 222631 GTTGTATTAGAACT -s Anc1.Anc1refChr1 62978 14 + 69767 GTTGTATTAGAACT -s Anc2.Anc2refChr13 74495 14 - 96486 GTTGTATTAGAACT -s mr.mrrefChr3 174591 14 + 181027 GGTGTTTTAGAACT -s simCow_chr6.simCow.chr6 224677 14 - 602619 ATTGTCTTAGAACT -s simDog_chr6.simDog.chr6 225405 14 - 593897 GCCATATTAGAACC -s simHuman_chr6.simHuman.chr6 594921 14 + 601863 GTTGTATTAGAACT -s simRat_chr6.simRat.chr6 639712 14 + 647215 GGTGTCGTAGAACT - -a -s simMouse_chr6.simMouse.chr6 628173 1 + 636262 G -s Anc0.Anc0refChr3 203784 1 - 222631 G -s Anc1.Anc1refChr1 62992 1 + 69767 G -s Anc2.Anc2refChr13 74509 1 - 96486 G -s mr.mrrefChr3 174605 1 + 181027 G -s simCow_chr6.simCow.chr6 224691 1 - 602619 A -s simDog_chr6.simDog.chr6 225421 1 - 593897 G -s simHuman_chr6.simHuman.chr6 594935 1 + 601863 G -s simRat_chr6.simRat.chr6 639726 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 628174 21 + 636262 TTCACAAACAGTTCAGTCAGA -s Anc0.Anc0refChr3 203808 21 - 222631 TTAGTCAATGGTGCAGTCAGA -s Anc1.Anc1refChr1 63016 21 + 69767 TTAGTCAATGGTGCAGTCAGA -s Anc2.Anc2refChr13 74533 21 - 96486 TTAGTCATTGGTGCAGTCAGA -s mr.mrrefChr3 174606 21 + 181027 TTCACAAACAGTTCAGTCAGA -s simCow_chr6.simCow.chr6 224715 21 - 602619 TCAGTCATCATTGCAGTCATA -s simDog_chr6.simDog.chr6 225445 21 - 593897 CTAGTCATTGGTGCAGTCAGA -s simHuman_chr6.simHuman.chr6 594959 21 + 601863 TTAGTCAATGGTGCAGTCAGC -s simRat_chr6.simRat.chr6 639727 21 + 647215 TTAGCAAATAGTTCAGTCAGA - -a -s simMouse_chr6.simMouse.chr6 628195 9 + 636262 GGGGCATTT -s Anc0.Anc0refChr3 203829 9 - 222631 GGGGAGGCT -s Anc1.Anc1refChr1 63037 9 + 69767 GGGGAGGCT -s Anc2.Anc2refChr13 74554 9 - 96486 GGGGAGGCC -s mr.mrrefChr3 174627 9 + 181027 GGGGCATTT -s simCow_chr6.simCow.chr6 224757 9 - 602619 GGGGAGGCC -s simDog_chr6.simDog.chr6 225466 9 - 593897 GGGGAGGTC -s simHuman_chr6.simHuman.chr6 594980 9 + 601863 GGGGAGGCT -s simRat_chr6.simRat.chr6 639748 9 + 647215 GGGGCATTG - -a -s simMouse_chr6.simMouse.chr6 628204 80 + 636262 ACTAGGTATTGCTCTGTGACACCTGTCCCTTTGCTGCTAGAATTATCCCTGTCTGTTCCTCTACAAATCCTACCTTATAA -s Anc0.Anc0refChr3 203839 74 - 222631 ACTAGTTATCATTTAGTGACCTCTGTCCCTTTGTCACTAGAA------CTGTCTGTATCTCTGCAAATCCTACCTTATAC -s Anc1.Anc1refChr1 63047 74 + 69767 ACTAGTTATCATTTAGTGACCTCTGTCCCTTTGTCACTAGAA------CTGTCTGTATCTCTGCAAATCCTACCTTATAC -s Anc2.Anc2refChr13 74564 74 - 96486 ACTAGTTATCATTTAGTGAGCTCTGTCCTTTTGTCACTAGAA------TTATCTTTATCTCTGCAAATCCTACCTTTTAC -s mr.mrrefChr3 174636 80 + 181027 ACTAGGTATTGCTCTGTGACACCTGTCCCTTTGCTGCTAGAATTATCCCTGTCTGTTCCTCTACAAATCCTACCTTATAA -s simCow_chr6.simCow.chr6 224767 74 - 602619 ACTAATTATTATTTAGTGGGCTCTGTCCTTATGTGACTGGAA------TTATTTTTATCTCTGTAAACCCTACCTTGCAC -s simDog_chr6.simDog.chr6 225476 74 - 593897 ACCAGTCATCATCCAGTAAGCCCTGTGTTTTGGTCACTAAAA------TTATCTTTATCACTGCAAATCCTACCTTTTAT -s simHuman_chr6.simHuman.chr6 594990 74 + 601863 ACTAGTTATCATTTAGTGACCTCTGTCCCTTTATCACTAGAA------CTGTATGTATCTCTCCAAATCCTACTCTATAC -s simRat_chr6.simRat.chr6 639757 80 + 647215 ACTAGGTATTGTTCTGTGACACCTGTCCCTTTGTTGCTCGAATTATCCCTATCTATTCCTGTACAAGACCTACGTTATAA - -a -s simMouse_chr6.simMouse.chr6 628284 1 + 636262 A -s Anc0.Anc0refChr3 203913 1 - 222631 A -s Anc1.Anc1refChr1 63121 1 + 69767 A -s Anc2.Anc2refChr13 74638 1 - 96486 A -s mr.mrrefChr3 174716 1 + 181027 A -s simCow_chr6.simCow.chr6 224841 1 - 602619 A -s simDog_chr6.simDog.chr6 225550 1 - 593897 G -s simHuman_chr6.simHuman.chr6 595086 1 + 601863 A -s simRat_chr6.simRat.chr6 639837 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 628285 6 + 636262 CATCTG -s Anc0.Anc0refChr3 203914 6 - 222631 CATTTG -s Anc1.Anc1refChr1 63122 6 + 69767 CATTTG -s Anc2.Anc2refChr13 74639 6 - 96486 CACTTG -s mr.mrrefChr3 174717 6 + 181027 CATCTG -s simCow_chr6.simCow.chr6 224845 6 - 602619 CACTTG -s simDog_chr6.simDog.chr6 225551 6 - 593897 CACTTG -s simHuman_chr6.simHuman.chr6 595087 6 + 601863 CATTTG -s simRat_chr6.simRat.chr6 639838 6 + 647215 GATTTG - -a -s simMouse_chr6.simMouse.chr6 628291 13 + 636262 AACATATCTACCC -s Anc0.Anc0refChr3 203920 13 - 222631 AACATATCTACCC -s Anc1.Anc1refChr1 63128 13 + 69767 AACATATCTACCC -s Anc2.Anc2refChr13 74645 13 - 96486 AACATATTTACCC -s mr.mrrefChr3 174723 13 + 181027 AACATATCTACCC -s simCow_chr6.simCow.chr6 224851 12 - 602619 AAC-TATTTACCC -s simDog_chr6.simDog.chr6 225557 13 - 593897 AACATATTTATCC -s simHuman_chr6.simHuman.chr6 595093 13 + 601863 AACATATCTACCC -s simRat_chr6.simRat.chr6 639846 13 + 647215 AACATATCTACCC - -a -s simMouse_chr6.simMouse.chr6 628304 15 + 636262 AGGCACAATGTTGTC -s Anc0.Anc0refChr3 203942 9 - 222631 AA------TCTGGTC -s Anc1.Anc1refChr1 63150 15 + 69767 AATCAAAATCTGGTC -s Anc2.Anc2refChr13 74667 9 - 96486 AA------TCTGGAC -s mr.mrrefChr3 174736 15 + 181027 AGGCACAATGTTGTC -s simCow_chr6.simCow.chr6 224872 9 - 602619 AA------TCTGGAC -s simDog_chr6.simDog.chr6 225579 9 - 593897 AA------TCTGGAC -s simHuman_chr6.simHuman.chr6 595115 15 + 601863 AATCAAAATCTGGTT -s simRat_chr6.simRat.chr6 639859 15 + 647215 AAACACAATGTTGTC - -a -s simMouse_chr6.simMouse.chr6 628319 45 + 636262 ACTCAATTAAGTAATATAAAGACTAGACCAAGACTAGCCTTACCT -s Anc0.Anc0refChr3 203952 29 - 222631 ACTTGACTAGGTAACACAAAGACTAGACT---------------- -s Anc1.Anc1refChr1 63166 29 + 69767 ACTTGACTAGGTAACACAAAGACTAGACT---------------- -s Anc2.Anc2refChr13 74677 29 - 96486 ACATGACTTGGTAACACAAAGACTAGACT---------------- -s mr.mrrefChr3 174751 45 + 181027 ACTCAATTAAGTAATATAAAGACTAGACCAAGACTAGCCTTACCT -s simCow_chr6.simCow.chr6 224882 29 - 602619 AAATGACGTGGTACTACAAAGACTAGACT---------------- -s simDog_chr6.simDog.chr6 225589 29 - 593897 ACATGACTTGGTAACACAAAGACTAGACT---------------- -s simHuman_chr6.simHuman.chr6 595131 29 + 601863 ACTTGACTATGTAACACAAATACTAAACT---------------- -s simRat_chr6.simRat.chr6 639875 45 + 647215 ACTCAATTATGTCATATAACGACTAGACCAAGACTAGCCTCACCT - -a -s simMouse_chr6.simMouse.chr6 628364 19 + 636262 AAATGGCGGTGACGAACGG -s Anc0.Anc0refChr3 203981 6 - 222631 -------------GCACTT -s Anc1.Anc1refChr1 63195 6 + 69767 -------------GCACTT -s Anc2.Anc2refChr13 74706 6 - 96486 -------------CCACTT -s mr.mrrefChr3 174796 19 + 181027 AAATGGCGGTGACGAACGG -s simCow_chr6.simCow.chr6 224911 6 - 602619 -------------CCACTT -s simDog_chr6.simDog.chr6 225618 6 - 593897 -------------CCACTT -s simHuman_chr6.simHuman.chr6 595160 6 + 601863 -------------GCACTT -s simRat_chr6.simRat.chr6 639921 19 + 647215 GAATAGCAGGGGTGGATGG - -a -s simMouse_chr6.simMouse.chr6 628383 12 + 636262 TTAAGAGAATTA -s Anc0.Anc0refChr3 203987 12 - 222631 TGTAGAGAATTA -s Anc1.Anc1refChr1 63201 12 + 69767 TGTAGAGAATTA -s Anc2.Anc2refChr13 74731 12 - 96486 TGTAGAGAATTA -s mr.mrrefChr3 174815 12 + 181027 TTAAGAGAATTA -s simCow_chr6.simCow.chr6 224936 12 - 602619 TGAAGTGAATTT -s simDog_chr6.simDog.chr6 225643 12 - 593897 TGTAAAGAACTA -s simHuman_chr6.simHuman.chr6 595166 12 + 601863 TACAGAAAATTA -s simRat_chr6.simRat.chr6 639940 12 + 647215 TATAGAGAATCA - -a -s simMouse_chr6.simMouse.chr6 628395 4 + 636262 ACAT -s Anc0.Anc0refChr3 203999 4 - 222631 ATGT -s Anc1.Anc1refChr1 63213 4 + 69767 ATGT -s Anc2.Anc2refChr13 74743 4 - 96486 ATGT -s mr.mrrefChr3 174827 4 + 181027 ACAT -s simCow_chr6.simCow.chr6 224948 4 - 602619 ACGT -s simDog_chr6.simDog.chr6 225658 4 - 593897 ATGT -s simHuman_chr6.simHuman.chr6 595178 4 + 601863 ATGT -s simRat_chr6.simRat.chr6 639952 4 + 647215 ACAT - -a -s simMouse_chr6.simMouse.chr6 628399 5 + 636262 AGGCA -s Anc0.Anc0refChr3 204003 5 - 222631 AAGCA -s Anc1.Anc1refChr1 63217 5 + 69767 AAGCA -s Anc2.Anc2refChr13 74747 5 - 96486 AAGCA -s mr.mrrefChr3 174831 5 + 181027 AGGCA -s simCow_chr6.simCow.chr6 224952 5 - 602619 AAGCA -s simDog_chr6.simDog.chr6 225663 5 - 593897 AAGTG -s simHuman_chr6.simHuman.chr6 595182 5 + 601863 AAGCA -s simRat_chr6.simRat.chr6 639956 5 + 647215 CGGCG - -a -s simMouse_chr6.simMouse.chr6 628404 22 + 636262 GAGTGGGCAAGATATGATTTTG -s Anc0.Anc0refChr3 204008 19 - 222631 GAGCAGGGAAGACATAATT--- -s Anc1.Anc1refChr1 63222 19 + 69767 GAGCAGGGAAGACATAATT--- -s Anc2.Anc2refChr13 74752 19 - 96486 GAGCAGGGAAGACATAATT--- -s mr.mrrefChr3 174836 19 + 181027 GAGTGGGCAAGATATGATT--- -s simCow_chr6.simCow.chr6 224958 19 - 602619 GAGCAGGGAAGATATAATT--- -s simDog_chr6.simDog.chr6 225668 19 - 593897 CAATAGGGAAGACATAATT--- -s simHuman_chr6.simHuman.chr6 595187 19 + 601863 GAGCAGGGAAGACATAATT--- -s simRat_chr6.simRat.chr6 639961 19 + 647215 GCGCAGTCAAGAGATGATT--- - -a -s simMouse_chr6.simMouse.chr6 628426 19 + 636262 GTCTCTGCTGCCATATCTA -s Anc0.Anc0refChr3 204030 18 - 222631 GTCTCAGCTGCCATCTCC- -s Anc1.Anc1refChr1 63244 19 + 69767 GTCTCAGCTGCCATCTCCG -s Anc2.Anc2refChr13 74774 18 - 96486 CTCTCAGCTGCCGTCTCC- -s mr.mrrefChr3 174855 19 + 181027 GTCTCTGCTGCCATATCTA -s simCow_chr6.simCow.chr6 224980 18 - 602619 TTCTCAGCTGCCCTCTCC- -s simDog_chr6.simDog.chr6 225690 18 - 593897 CTTCCAGCTGCTGTCTCA- -s simHuman_chr6.simHuman.chr6 595209 19 + 601863 GTCTCGACTACCATCTCCG -s simRat_chr6.simRat.chr6 639980 19 + 647215 GTCGCTGCTGCCATCTCTA - -a -s simMouse_chr6.simMouse.chr6 628445 15 + 636262 CAGATTCCATGGGGG -s Anc0.Anc0refChr3 204048 15 - 222631 CAGATTCTATGAAGA -s Anc1.Anc1refChr1 63263 15 + 69767 CAGATTCTATGAAGA -s Anc2.Anc2refChr13 74792 15 - 96486 CAGATTCTATGAAGA -s mr.mrrefChr3 174874 15 + 181027 CAGATTCCATGGGGG -s simCow_chr6.simCow.chr6 224999 15 - 602619 CAGATTCTATGAAGA -s simDog_chr6.simDog.chr6 225708 15 - 593897 CAGATTCTATGGAGG -s simHuman_chr6.simHuman.chr6 595228 14 + 601863 CC-ATTCTATGAAGA -s simRat_chr6.simRat.chr6 639999 15 + 647215 CAGATTCTGTGGACA - -a -s simMouse_chr6.simMouse.chr6 628460 78 + 636262 TCATTCTGTTCTGAGATGTCAAATCCATAGAATTGTACCATTGCCTCCATTATCATTGCCTCTGTAGCCCTAGACTGA -s Anc0.Anc0refChr3 204065 57 - 222631 TAATTCTGGTCTCAGCTG-CAACCTCCACAGATTTTATCTCTGCCTTCCATA--------------------GCCCCA -s Anc1.Anc1refChr1 63280 58 + 69767 TAATTCTGGTCTCAGCTGGCAACCTCCACAGATTTTATCTCTGCCTTCCATA--------------------GCCCCA -s Anc2.Anc2refChr13 74809 57 - 96486 TAATTCTGGTCTCAGCTG-CTACCTCCACAGATTTTATCTCTACCTTCCATA--------------------GCCCCA -s mr.mrrefChr3 174889 58 + 181027 TCATTCTGTTCTGAGATGTCAAATCCATAGAATTGTACCATTGCCTCCATTA--------------------GACTGA -s simCow_chr6.simCow.chr6 225016 53 - 602619 TAATTCTGCTCTCATTTG-C--CCTCTAC--AATTCATCTCCACCTTGCGTA--------------------GCCCCT -s simDog_chr6.simDog.chr6 225725 57 - 593897 TAATTCAGGTCTTGGCTG-CTACCTCCACAGATTTTATCTCTACCTTCCATA--------------------GCCCAa -s simHuman_chr6.simHuman.chr6 595244 56 + 601863 TAGTTCTGGTCTCAG--GGCAATCTCCCCAGATTCTATATCTGCCTTCCATA--------------------GCCCCA -s simRat_chr6.simRat.chr6 640014 58 + 647215 TCATTCTGGTCTTAGATGTCAAATCCATAGAATTAAACTATTGCCTCCGTTA--------------------GTCTGA - -a -s simMouse_chr6.simMouse.chr6 628538 6 + 636262 ATTCAC -s Anc0.Anc0refChr3 204122 3 - 222631 GC---C -s Anc1.Anc1refChr1 63338 3 + 69767 GC---C -s Anc2.Anc2refChr13 74866 3 - 96486 GC---T -s mr.mrrefChr3 174947 6 + 181027 ATTCAC -s simCow_chr6.simCow.chr6 225069 3 - 602619 GA---A -s simDog_chr6.simDog.chr6 225846 3 - 593897 AC---T -s simHuman_chr6.simHuman.chr6 595300 3 + 601863 GC---C -s simRat_chr6.simRat.chr6 640072 6 + 647215 ATTCAT - -a -s simMouse_chr6.simMouse.chr6 628544 14 + 636262 CATTAACTGGGGTG -s Anc0.Anc0refChr3 204125 14 - 222631 AAATAGCAGGGATT -s Anc1.Anc1refChr1 63341 14 + 69767 AAATAGCAGGGATT -s Anc2.Anc2refChr13 74869 14 - 96486 AAATAGCAGGGATT -s mr.mrrefChr3 174953 14 + 181027 CATTAACTGGGGTG -s simCow_chr6.simCow.chr6 225073 14 - 602619 AAATAGCAGGGGTT -s simDog_chr6.simDog.chr6 225849 14 - 593897 AAATAGTAGGGATT -s simHuman_chr6.simHuman.chr6 595303 14 + 601863 AAATAGCAGGGATT -s simRat_chr6.simRat.chr6 640078 14 + 647215 CATTGCCTGGGGTG - -a -s simMouse_chr6.simMouse.chr6 628558 13 + 636262 CATGTATAACCAG -s Anc0.Anc0refChr3 204139 13 - 222631 GATTGATAGCCAA -s Anc1.Anc1refChr1 63355 13 + 69767 GATTGATAGCCAA -s Anc2.Anc2refChr13 74883 13 - 96486 GATTGATAGCCAA -s mr.mrrefChr3 174967 13 + 181027 CATGTATAACCAG -s simCow_chr6.simCow.chr6 225088 13 - 602619 GGTTGTTAGCCAA -s simDog_chr6.simDog.chr6 225863 13 - 593897 GATTAATAGCCAG -s simHuman_chr6.simHuman.chr6 595317 13 + 601863 GATTGCCATTCAA -s simRat_chr6.simRat.chr6 640092 13 + 647215 CATGTATAACCGG - -a -s simMouse_chr6.simMouse.chr6 628571 2 + 636262 TG -s Anc0.Anc0refChr3 204152 2 - 222631 GG -s Anc1.Anc1refChr1 63368 2 + 69767 GG -s Anc2.Anc2refChr13 74896 2 - 96486 GG -s mr.mrrefChr3 174980 2 + 181027 TG -s simCow_chr6.simCow.chr6 225101 2 - 602619 GG -s simDog_chr6.simDog.chr6 225876 2 - 593897 GG -s simHuman_chr6.simHuman.chr6 595330 2 + 601863 GG -s simRat_chr6.simRat.chr6 640111 2 + 647215 TA - -a -s simMouse_chr6.simMouse.chr6 628573 2 + 636262 AC -s Anc0.Anc0refChr3 204154 2 - 222631 TC -s Anc1.Anc1refChr1 63370 2 + 69767 TC -s Anc2.Anc2refChr13 74898 2 - 96486 TG -s mr.mrrefChr3 174982 2 + 181027 AC -s simCow_chr6.simCow.chr6 225103 2 - 602619 TG -s simDog_chr6.simDog.chr6 225890 2 - 593897 TG -s simHuman_chr6.simHuman.chr6 595332 2 + 601863 TC -s simRat_chr6.simRat.chr6 640113 2 + 647215 AC - -a -s simMouse_chr6.simMouse.chr6 628575 25 + 636262 ACCTCTCCTGATCCCCAGAGTGGGG -s Anc0.Anc0refChr3 204161 25 - 222631 GCTTTTCCCAATCCTTGGAGTAGCA -s Anc1.Anc1refChr1 63377 25 + 69767 GCTTTTCCCAATCCTTGGAGTAGCA -s Anc2.Anc2refChr13 74905 25 - 96486 GCTGTTCCCAATCCTTGGAGTAGCA -s mr.mrrefChr3 174984 25 + 181027 ACCTCTCCTGATCCCCAGAGTGGGG -s simCow_chr6.simCow.chr6 225110 25 - 602619 GCTGTTCCCAATCATTGGAGTAGTA -s simDog_chr6.simDog.chr6 225897 23 - 593897 GCTGTTCCCAGTCCTC--AGTAACA -s simHuman_chr6.simHuman.chr6 595339 25 + 601863 GCTTTTCCCAATCCTTGGAGTAGCA -s simRat_chr6.simRat.chr6 640122 25 + 647215 GGCTCTCTTGATCCCCAGGGTGATG - -a -s simMouse_chr6.simMouse.chr6 628600 15 + 636262 TTGAGTGGTGATGAT -s Anc0.Anc0refChr3 204192 15 - 222631 TTGACTTGTAATGAT -s Anc1.Anc1refChr1 63408 15 + 69767 TTGACTTGTAATGAT -s Anc2.Anc2refChr13 74936 15 - 96486 TTGACTTGTAGTGAT -s mr.mrrefChr3 175009 15 + 181027 TTGAGTGGTGATGAT -s simCow_chr6.simCow.chr6 225141 15 - 602619 TCCACTTGTAGTGAT -s simDog_chr6.simDog.chr6 225926 15 - 593897 TTGCCCTGTAGTCAT -s simHuman_chr6.simHuman.chr6 595370 15 + 601863 TTAACTTGTAATGAT -s simRat_chr6.simRat.chr6 640147 15 + 647215 TTCTGTTGTTATGAT - -a -s simMouse_chr6.simMouse.chr6 628615 10 + 636262 CCTTGTACAT -s Anc0.Anc0refChr3 204207 10 - 222631 CCTTTTGTAT -s Anc1.Anc1refChr1 63423 10 + 69767 CCTTTTGTAT -s Anc2.Anc2refChr13 74952 10 - 96486 CCTATTGTAT -s mr.mrrefChr3 175024 10 + 181027 CCTTGTACAT -s simCow_chr6.simCow.chr6 225157 10 - 602619 CCCCATGTGG -s simDog_chr6.simDog.chr6 225942 10 - 593897 CCTATTGTAT -s simHuman_chr6.simHuman.chr6 595385 10 + 601863 CCGTCGGTAT -s simRat_chr6.simRat.chr6 640162 10 + 647215 TCATGTGCAT - -a -s simMouse_chr6.simMouse.chr6 628625 19 + 636262 AGTCAGTTTCAATTTTCTT -s Anc0.Anc0refChr3 204217 17 - 222631 TGTCAGTTTCA--TTGCTT -s Anc1.Anc1refChr1 63433 17 + 69767 TGTCAGTTTCA--TTGCTT -s Anc2.Anc2refChr13 74962 17 - 96486 TGTCAGTTTCA--TTGCTT -s mr.mrrefChr3 175034 17 + 181027 AGTCAGTTTCA--TTTCTT -s simCow_chr6.simCow.chr6 225167 17 - 602619 TGTCTCTTTCA--TAGTTT -s simDog_chr6.simDog.chr6 225956 17 - 593897 TGTCAGATTCA--TTGCTT -s simHuman_chr6.simHuman.chr6 595395 17 + 601863 TGTCAGTTTCA--TTGCTT -s simRat_chr6.simRat.chr6 640172 17 + 647215 TGTCAGCTTCA--TTTCTT - -a -s simMouse_chr6.simMouse.chr6 628644 21 + 636262 CTAAAAGTTGCTCCCACATCG -s Anc0.Anc0refChr3 204246 21 - 222631 ATAAAAATTGCTTCCAAAGGA -s Anc1.Anc1refChr1 63462 21 + 69767 ATAAAAATTGCTTCCAAAGGA -s Anc2.Anc2refChr13 74991 21 - 96486 ATAAAAATTGCTTCCAAAGGA -s mr.mrrefChr3 175051 21 + 181027 CTAAAAGTTGCTCCCACATCG -s simCow_chr6.simCow.chr6 225196 21 - 602619 ATAAAAAATGCTTCCAAAGAA -s simDog_chr6.simDog.chr6 225983 21 - 593897 ATAAAAATTGCTTCCAAGGGA -s simHuman_chr6.simHuman.chr6 595424 21 + 601863 ATAAAAATAGCTACCAAAGGA -s simRat_chr6.simRat.chr6 640189 21 + 647215 CTAAAAGTTGCTCCCAAATTG - -a -s simMouse_chr6.simMouse.chr6 628665 6 + 636262 ATGGAA -s Anc0.Anc0refChr3 204267 6 - 222631 ATAGAA -s Anc1.Anc1refChr1 63483 6 + 69767 ATAGAA -s Anc2.Anc2refChr13 75014 6 - 96486 ATACAA -s mr.mrrefChr3 175072 6 + 181027 ATGGAA -s simCow_chr6.simCow.chr6 225219 6 - 602619 ATTCAA -s simDog_chr6.simDog.chr6 226007 6 - 593897 ATACAA -s simHuman_chr6.simHuman.chr6 595445 6 + 601863 ATAGAA -s simRat_chr6.simRat.chr6 640210 6 + 647215 AAGGAA - -a -s simMouse_chr6.simMouse.chr6 628671 18 + 636262 TTAAAGCTGTATCCATCA -s Anc0.Anc0refChr3 204283 18 - 222631 CCTATGCTGTATTTATAA -s Anc1.Anc1refChr1 63499 18 + 69767 CCTATGCTGTATTTATAA -s Anc2.Anc2refChr13 75030 18 - 96486 CCTATGATGTATTTATAA -s mr.mrrefChr3 175078 18 + 181027 TTAAAGCTGTATCCATCA -s simCow_chr6.simCow.chr6 225231 12 - 602619 ------ATGTATTCATAA -s simDog_chr6.simDog.chr6 226023 18 - 593897 CCTATGATCGATGTCTAA -s simHuman_chr6.simHuman.chr6 595461 18 + 601863 CCTATGCTGTATTAATAA -s simRat_chr6.simRat.chr6 640216 18 + 647215 TTAAAGATGTAACCATCA - -a -s simMouse_chr6.simMouse.chr6 628689 9 + 636262 ACTAGACTT -s Anc0.Anc0refChr3 204301 8 - 222631 A-TAGACTT -s Anc1.Anc1refChr1 63517 9 + 69767 ACTAGACTT -s Anc2.Anc2refChr13 75048 8 - 96486 G-TAGACTT -s mr.mrrefChr3 175096 9 + 181027 ACTAGACTT -s simCow_chr6.simCow.chr6 225243 8 - 602619 G-TAGACTT -s simDog_chr6.simDog.chr6 226041 8 - 593897 G-TAGACTT -s simHuman_chr6.simHuman.chr6 595492 9 + 601863 ACATGCCTT -s simRat_chr6.simRat.chr6 640234 9 + 647215 ACTAGACTT - -a -s simMouse_chr6.simMouse.chr6 628698 74 + 636262 CTATTACAAGCAGTGCTAAGCCATTGGTTCAGTGGTCTAGTATAATAACTGCGTTTAGCACATCCAGTCATTTG -s Anc0.Anc0refChr3 204309 64 - 222631 ATACTATAGG---------GCCATTGGTTCAGTGGTCTA-TATAATAACTGCTTCTAACAGCTCCAGCTATTAG -s Anc1.Anc1refChr1 63526 73 + 69767 ATACTATAGGCAATGCTG-GCCATTGGTTCAGTGGTCTAATATAATAACTGCTTCTAACAGCTCCAGCTATTAG -s Anc2.Anc2refChr13 75056 64 - 96486 ACACTGTGGG---------GCCATTGGTTCAGTGGTCTA-CATAGTAACTGCTCCTAACAGCTCCAGCTATCAG -s mr.mrrefChr3 175105 74 + 181027 CTATTACAAGCAGTGCTAAGCCATTGGTTCAGTGGTCTAGTATAATAACTGCGTTTAGCACATCCAGTCATTTG -s simCow_chr6.simCow.chr6 225262 54 - 602619 AAACTGT------------GCCTTTGGTTCAGTGGTC--------TAAATGCTCCTAACAGCTTCAGCTACCAG -s simDog_chr6.simDog.chr6 226049 62 - 593897 ACACTGTGGG---------GTCATTACTTCAATGGTTTA-CATAGTAACTGCTCCTAACAGCTCCAGCTATC-- -s simHuman_chr6.simHuman.chr6 595501 73 + 601863 ATGCTATATGCAATGCTG-GCCATTGGCTTCGCAGTCTAATACGATAACTGCTTCTAACAGCTCTAGCTATTAG -s simRat_chr6.simRat.chr6 640243 74 + 647215 GTATTACAAGCAATGCTAAGCCATTGGTTCAGTGGCTTAGTCTAATAACTGTGTTTAGCACATCCAGCCATTGG - -a -s simMouse_chr6.simMouse.chr6 628772 8 + 636262 ACATCCAC -s Anc0.Anc0refChr3 204381 8 - 222631 ACATTAAC -s Anc1.Anc1refChr1 63607 8 + 69767 ACATTAAC -s Anc2.Anc2refChr13 75128 8 - 96486 ACATTAGC -s mr.mrrefChr3 175179 8 + 181027 ACATCCAC -s simCow_chr6.simCow.chr6 225324 8 - 602619 TCATCAGC -s simDog_chr6.simDog.chr6 226114 8 - 593897 AAATTAGC -s simHuman_chr6.simHuman.chr6 595582 8 + 601863 ACATTTAA -s simRat_chr6.simRat.chr6 640317 8 + 647215 ACATCCTG - -a -s simMouse_chr6.simMouse.chr6 628780 3 + 636262 TAT -s Anc0.Anc0refChr3 204389 3 - 222631 TAT -s Anc1.Anc1refChr1 63615 3 + 69767 TAT -s Anc2.Anc2refChr13 75136 3 - 96486 TAT -s mr.mrrefChr3 175187 3 + 181027 TAT -s simCow_chr6.simCow.chr6 225335 3 - 602619 TGT -s simDog_chr6.simDog.chr6 226122 3 - 593897 TAT -s simHuman_chr6.simHuman.chr6 595590 3 + 601863 TAT -s simRat_chr6.simRat.chr6 640325 3 + 647215 TAT - -a -s simMouse_chr6.simMouse.chr6 628783 9 + 636262 TCAAACCAT -s Anc0.Anc0refChr3 204392 9 - 222631 GTCAGCCAT -s Anc1.Anc1refChr1 63618 9 + 69767 GTCAGCCAT -s Anc2.Anc2refChr13 75139 9 - 96486 GTCAGCCAA -s mr.mrrefChr3 175190 9 + 181027 TCAAACCAT -s simCow_chr6.simCow.chr6 225338 9 - 602619 GTCAACCAG -s simDog_chr6.simDog.chr6 226125 9 - 593897 GTCAGCCAA -s simHuman_chr6.simHuman.chr6 595593 9 + 601863 GTTAGCCAT -s simRat_chr6.simRat.chr6 640329 9 + 647215 TCAGACCGT - -a -s simMouse_chr6.simMouse.chr6 628792 49 + 636262 CAGCATAGGGCTTTTCTAAGCTCTCCAGTATATGACAACCTCAGAGCAC -s Anc0.Anc0refChr3 204402 40 - 222631 CAGCATGGG---------AACTATCCAAGATGTGGCAACCCCAGAACAT -s Anc1.Anc1refChr1 63628 40 + 69767 CAGCATGGG---------AACTATCCAAGATGTGGCAACCCCAGAACAT -s Anc2.Anc2refChr13 75149 40 - 96486 CAGCATGGG---------AACTATCCAAGATGTGGCAACCCCAGAACAT -s mr.mrrefChr3 175199 49 + 181027 CAGCATAGGGCTTTTCTAAGCTCTCCAGTATATGACAACCTCAGAGCAC -s simCow_chr6.simCow.chr6 225348 39 - 602619 CAGCATGGG---------AATTA-CCAAGATGTGGCAACCCCAGTACCT -s simDog_chr6.simDog.chr6 226135 40 - 593897 CAACATGGG---------AACCATCCAAGGTCTGGCAACCCCAGAACAT -s simHuman_chr6.simHuman.chr6 595603 40 + 601863 CAGTATGGG---------AACTGTCCAAGATGTGGTAACCCCAGAACAT -s simRat_chr6.simRat.chr6 640338 49 + 647215 CAGCATGGAACCTCTCAAAGCTCTCCAGTATGTGACAACCTCAGAACAT - -a -s simMouse_chr6.simMouse.chr6 628841 2 + 636262 CC -s Anc0.Anc0refChr3 204442 2 - 222631 AA -s Anc1.Anc1refChr1 63668 2 + 69767 AA -s Anc2.Anc2refChr13 75190 2 - 96486 AA -s mr.mrrefChr3 175248 2 + 181027 CC -s simCow_chr6.simCow.chr6 225388 2 - 602619 CA -s simDog_chr6.simDog.chr6 226176 2 - 593897 AA -s simHuman_chr6.simHuman.chr6 595643 2 + 601863 GA -s simRat_chr6.simRat.chr6 640387 2 + 647215 CC - -a -s simMouse_chr6.simMouse.chr6 628843 3 + 636262 CTA -s Anc0.Anc0refChr3 204446 3 - 222631 CTA -s Anc1.Anc1refChr1 63672 3 + 69767 CTA -s Anc2.Anc2refChr13 75194 3 - 96486 CTA -s mr.mrrefChr3 175250 3 + 181027 CTA -s simCow_chr6.simCow.chr6 225392 3 - 602619 CTA -s simDog_chr6.simDog.chr6 226180 3 - 593897 CTA -s simHuman_chr6.simHuman.chr6 595647 3 + 601863 CTA -s simRat_chr6.simRat.chr6 640389 3 + 647215 CTG - -a -s simMouse_chr6.simMouse.chr6 628846 12 + 636262 GAGAAGCACTTG -s Anc0.Anc0refChr3 204449 11 - 222631 GAGAAACACT-G -s Anc1.Anc1refChr1 63675 11 + 69767 GAGAAACACT-G -s Anc2.Anc2refChr13 75197 11 - 96486 GAGAAACATT-G -s mr.mrrefChr3 175253 11 + 181027 GAGAAGCACT-G -s simCow_chr6.simCow.chr6 225395 11 - 602619 GAAAAGCATT-A -s simDog_chr6.simDog.chr6 226328 8 - 593897 TGGACA---T-G -s simHuman_chr6.simHuman.chr6 595650 11 + 601863 GAGAAACACT-T -s simRat_chr6.simRat.chr6 640392 11 + 647215 GAGAAGCACT-G - -a -s simMouse_chr6.simMouse.chr6 628858 27 + 636262 TATGTTAAACAAGGACTACTAGTTTAA -s Anc0.Anc0refChr3 204460 27 - 222631 TACCTAAAACAAAAACTAGTTATTAGA -s Anc1.Anc1refChr1 63686 27 + 69767 TACCTAAAACAAAAACTAGTTATTAGA -s Anc2.Anc2refChr13 75208 27 - 96486 TACCTAAAACAAAAACTAGTTATTAGA -s mr.mrrefChr3 175264 27 + 181027 TATGTTAAACAAGGACTACTAGTTTAA -s simCow_chr6.simCow.chr6 225406 27 - 602619 TACCTTAACCAAGAACTAATACTTAGA -s simDog_chr6.simDog.chr6 226336 26 - 593897 CACTCATAAGGAAAA-CAGTTAGATCA -s simHuman_chr6.simHuman.chr6 595662 27 + 601863 TACCTCAAACAACAACTAGTCATTAGG -s simRat_chr6.simRat.chr6 640403 27 + 647215 TACCTAAAACAAGGACTACTAGTTCAA - -a -s simMouse_chr6.simMouse.chr6 628885 2 + 636262 TT -s Anc0.Anc0refChr3 204487 2 - 222631 TT -s Anc1.Anc1refChr1 63713 2 + 69767 TT -s Anc2.Anc2refChr13 75235 2 - 96486 TT -s mr.mrrefChr3 175291 2 + 181027 TT -s simCow_chr6.simCow.chr6 225455 2 - 602619 TT -s simDog_chr6.simDog.chr6 226362 2 - 593897 TT -s simHuman_chr6.simHuman.chr6 595689 2 + 601863 CT -s simRat_chr6.simRat.chr6 640430 2 + 647215 TT - -a -s simMouse_chr6.simMouse.chr6 628887 3 + 636262 TCA -s Anc0.Anc0refChr3 204489 3 - 222631 TGA -s Anc1.Anc1refChr1 63715 3 + 69767 TGA -s Anc2.Anc2refChr13 75239 3 - 96486 TGA -s mr.mrrefChr3 175293 3 + 181027 TCA -s simCow_chr6.simCow.chr6 225459 3 - 602619 TGA -s simDog_chr6.simDog.chr6 226366 3 - 593897 TGA -s simHuman_chr6.simHuman.chr6 595691 3 + 601863 TGA -s simRat_chr6.simRat.chr6 640432 3 + 647215 TCA - -a -s simMouse_chr6.simMouse.chr6 628890 3 + 636262 AAT -s Anc0.Anc0refChr3 204492 3 - 222631 ATG -s Anc1.Anc1refChr1 63718 3 + 69767 ATG -s Anc2.Anc2refChr13 75242 3 - 96486 ATG -s mr.mrrefChr3 175296 3 + 181027 AAT -s simCow_chr6.simCow.chr6 225462 3 - 602619 ATG -s simDog_chr6.simDog.chr6 226385 3 - 593897 TTG -s simHuman_chr6.simHuman.chr6 595694 3 + 601863 AGG -s simRat_chr6.simRat.chr6 640435 3 + 647215 AAT - -a -s simMouse_chr6.simMouse.chr6 628893 8 + 636262 CACATATG -s Anc0.Anc0refChr3 204499 8 - 222631 CACATACA -s Anc1.Anc1refChr1 63725 8 + 69767 CACATACA -s Anc2.Anc2refChr13 75249 8 - 96486 CATGTCCA -s mr.mrrefChr3 175299 8 + 181027 CACATATG -s simCow_chr6.simCow.chr6 225468 8 - 602619 CATGTTCA -s simDog_chr6.simDog.chr6 226392 8 - 593897 AATGTCCA -s simHuman_chr6.simHuman.chr6 595701 8 + 601863 CACATACA -s simRat_chr6.simRat.chr6 640438 8 + 647215 TATATATG - -a -s simMouse_chr6.simMouse.chr6 628901 1 + 636262 T -s Anc0.Anc0refChr3 204507 1 - 222631 T -s Anc1.Anc1refChr1 63733 1 + 69767 T -s Anc2.Anc2refChr13 75257 1 - 96486 T -s mr.mrrefChr3 175307 1 + 181027 T -s simCow_chr6.simCow.chr6 225476 1 - 602619 T -s simDog_chr6.simDog.chr6 226400 1 - 593897 T -s simDog_chr6.simDog.chr6 367569 1 + 593897 T -s simHuman_chr6.simHuman.chr6 595709 1 + 601863 T -s simRat_chr6.simRat.chr6 640446 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 628902 4 + 636262 ATAC -s Anc0.Anc0refChr3 204591 4 - 222631 ATCC -s Anc1.Anc1refChr1 63817 4 + 69767 ATCC -s Anc2.Anc2refChr13 75345 4 - 96486 ATCC -s mr.mrrefChr3 175308 4 + 181027 ATAC -s simCow_chr6.simCow.chr6 225564 4 - 602619 TTCA -s simDog_chr6.simDog.chr6 226488 4 - 593897 CTCC -s simDog_chr6.simDog.chr6 367657 4 + 593897 ATCC -s simHuman_chr6.simHuman.chr6 595798 4 + 601863 ATCC -s simRat_chr6.simRat.chr6 640447 4 + 647215 GTAC - -a -s simMouse_chr6.simMouse.chr6 628906 2 + 636262 TT -s Anc0.Anc0refChr3 204595 2 - 222631 TT -s Anc1.Anc1refChr1 63821 2 + 69767 TT -s Anc2.Anc2refChr13 75349 2 - 96486 TT -s mr.mrrefChr3 175312 2 + 181027 TT -s simCow_chr6.simCow.chr6 225568 2 - 602619 AT -s simDog_chr6.simDog.chr6 367661 2 + 593897 TT -s simHuman_chr6.simHuman.chr6 595802 2 + 601863 TT -s simRat_chr6.simRat.chr6 640451 2 + 647215 TT - -a -s simMouse_chr6.simMouse.chr6 628908 2 + 636262 GT -s Anc0.Anc0refChr3 204597 2 - 222631 GC -s Anc1.Anc1refChr1 63823 2 + 69767 GC -s Anc2.Anc2refChr13 75389 2 - 96486 GC -s mr.mrrefChr3 175314 2 + 181027 GT -s simCow_chr6.simCow.chr6 225613 2 - 602619 TC -s simDog_chr6.simDog.chr6 226494 2 - 593897 CC -s simDog_chr6.simDog.chr6 367701 2 + 593897 GC -s simHuman_chr6.simHuman.chr6 595804 2 + 601863 GC -s simRat_chr6.simRat.chr6 640453 2 + 647215 GT - -a -s simMouse_chr6.simMouse.chr6 628910 6 + 636262 GAATGG -s Anc0.Anc0refChr3 204602 6 - 222631 GAATGA -s Anc1.Anc1refChr1 63828 6 + 69767 GAATGA -s Anc2.Anc2refChr13 75394 6 - 96486 CAGTAA -s mr.mrrefChr3 175316 6 + 181027 GAATGG -s simCow_chr6.simCow.chr6 225618 6 - 602619 CAGTAA -s simDog_chr6.simDog.chr6 226499 3 - 593897 CAG--- -s simHuman_chr6.simHuman.chr6 595809 6 + 601863 GAATGA -s simRat_chr6.simRat.chr6 640455 6 + 647215 GCATGA - -a -s simMouse_chr6.simMouse.chr6 628916 2 + 636262 TA -s Anc0.Anc0refChr3 204608 2 - 222631 TA -s Anc1.Anc1refChr1 63834 2 + 69767 TA -s Anc2.Anc2refChr13 75400 2 - 96486 TA -s mr.mrrefChr3 175322 2 + 181027 TA -s simCow_chr6.simCow.chr6 225624 2 - 602619 TA -s simDog_chr6.simDog.chr6 367703 1 + 593897 -A -s simHuman_chr6.simHuman.chr6 595815 2 + 601863 TA -s simRat_chr6.simRat.chr6 640462 2 + 647215 TT - -a -s simMouse_chr6.simMouse.chr6 628918 225 + 636262 CTTGACAACACAGCTCTCAAAGAGACATGTGCAAAGAACAGCATGGACAGAGAATATCTATCATTCATGGGAAGGATTGACCCTTTAGCAAGCGCATTGAGTAATTTTTGAAAATTTGCCTTCTATTTCTTGCTTAAGCAGAGTGGAGGTACAAATGCTAGAACCAGAATCGATCACATCCCAGCCAGAGCTGTGGACTCAATGCTTAAGTGGGAACCCAGCACC -s Anc0.Anc0refChr3 204610 106 - 222631 TTCTA-ATAGCA-----------------------------------------------------------------------------------------------------------CCTCTGTGTCCT----------AGGGGGTGCA-AAATGCTAGAACCACAGTCCATCTCATCCTAACCAGAATAGTGGATTTATTGCCTCAGGGGCAACCCAGCACC -s Anc1.Anc1refChr1 63836 107 + 69767 TTCTACATAGCA-----------------------------------------------------------------------------------------------------------CCTCTGTGTCCT----------AGGGGGTGCA-AAATGCTAGAACCACAGTCCATCTCATCCTAACCAGAATAGTGGATTTATTGCCTCAGGGGCAACCCAGCACC -s Anc2.Anc2refChr13 75402 106 - 96486 TTCTA-ATAGCA-----------------------------------------------------------------------------------------------------------CCTCAGTGTCCT----------GGGGGGTGCA-AATGGCTAGAACCACAGTCCATCTCATCCTAATCAGAATAGCAGGTTTATTGCCTCAGGGGCAACCTGGCACT -s mr.mrrefChr3 175324 211 + 181027 CTTGACAACACAGCTCTCAAAGAGACATGTGCAAAGAACAGCATGGACAGAGAATATC----ATTCATGGGAAGGATTGACCCTTTAGCAAGCGCATTGAGTAATTTTTGAAAATTTGCCTTCTATTTCTT----------AGTGGAGGTACAAATGCTAGAACCAGAATCGATCACATCCCAGCCAGAGCTGTGGACTCAATGCTTAAGTGGGAACCCAGCACC -s simCow_chr6.simCow.chr6 225626 105 - 602619 TTCTA-ATAGCA-----------------------------------------------------------------------------------------------------------CCTCAGTGTACT----------GGGGGGTGTA-AAT-GCTAGTACCACAGTCTATCTCATCCTAATCAGAATACCACGTTTATTGTTTAAGGACCAACCTGGTGCT -s simDog_chr6.simDog.chr6 226502 100 - 593897 ATCTA-ATAGTA-----------------------------------------------------------------------------------------------------------CCTTAGTATCCT----------GGGGGGTGCA-TATGGCTAGATCCACAGTCCT------ACTTATCTGAATAGCAGGTTTATTGCCTCAGGGGCAACCTGGCACT -s simDog_chr6.simDog.chr6 367704 10 + 593897 TTCTC-TCTTC---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- -s simHuman_chr6.simHuman.chr6 595817 107 + 601863 TTCCACATGGCA-----------------------------------------------------------------------------------------------------------CCTCTGTGTCCT----------AGGGGGTGCA-AAATGTCACAACCACAGTCCACGTCATCTTAACTAGAATAGTGGATGTATGGCCCGACGGGTAATCCAGCCCC -s simRat_chr6.simRat.chr6 640464 211 + 647215 CATGACAGCAGAGTTCTCAAGGGGACGTGTGCAAAGAACAGCGTGCACGGAGAATATC----ATTTGTGGGAAGGACTGATCCTTTGGCAAGAACACTGGGTAATGTTTGAAAATTTGCCTTCTATCTCTT----------AGTGGGAGCACATATGCTACAACCATAATTCATTACATCATAGCCAGAGCTGTGGACTCAGTGCTTAAGCAGGGACCTAGCACC - -a -s simMouse_chr6.simMouse.chr6 629143 17 + 636262 TTAGCACTTCAAGTCTC -s Anc0.Anc0refChr3 204717 17 - 222631 TTAACACTTTGAGTCTC -s Anc1.Anc1refChr1 63944 17 + 69767 TTAACACTTTGAGTCTC -s Anc2.Anc2refChr13 75509 17 - 96486 TTAACACTTTGGGTCAT -s mr.mrrefChr3 175535 17 + 181027 TTAGCACTTCAAGTCTC -s simCow_chr6.simCow.chr6 225732 17 - 602619 TTAACACATTGGATCAT -s simDog_chr6.simDog.chr6 226603 17 - 593897 TTGGCATTTTGGGTCAT -s simHuman_chr6.simHuman.chr6 595925 17 + 601863 TTAACACCTTGAGTCTC -s simRat_chr6.simRat.chr6 640675 17 + 647215 TTAGCACTTCAAGTCTC - -a -s simMouse_chr6.simMouse.chr6 629160 45 + 636262 TATATGCCTGTGGTCACTCAAGGGCATGTGAGGTGAAGAGGGGAT -s Anc0.Anc0refChr3 204734 3 - 222631 TAT------------------------------------------ -s Anc1.Anc1refChr1 63961 3 + 69767 TAT------------------------------------------ -s Anc2.Anc2refChr13 75526 3 - 96486 TAT------------------------------------------ -s mr.mrrefChr3 175552 45 + 181027 TATATGCCTATGGTCACTCAAGGGCATGTGAGGTGAACAAGGGGT -s simCow_chr6.simCow.chr6 225749 3 - 602619 TAT------------------------------------------ -s simDog_chr6.simDog.chr6 226626 3 - 593897 TAT------------------------------------------ -s simHuman_chr6.simHuman.chr6 595942 3 + 601863 TAT------------------------------------------ -s simRat_chr6.simRat.chr6 640692 45 + 647215 TATATGCCTATGGTCACTCAAGAGCATGTGGGGTGAACAAGGGGT - -a -s simMouse_chr6.simMouse.chr6 629205 173 + 636262 GTGTACACAGGGGGGGCTGTGCATTACAAACCTCTCATGTGGGGATCAGGCTCCCTCTACAGGTGCCTGTGATCACTTGATACCATGTCAGGTGGCACAGTCTTATAGCTAAGTACTATCTGCATGTATATGGCCGTGTTTGCCATTTATTGGAGCTTTGCACGAGGCACTGT -s mr.mrrefChr3 175602 173 + 181027 ATGTATGCAGGGGGGGCTGTGCATGACAAACCTCTCGTGTGGGGAGCAGGCTCCCTCTACAGCTGCCTGTGATCGCTCGATACCATGTCAAATGGCAGAGTCTTATAGCCAAGCACTATCCGCATGTATATGGCCGTGTTTGCCATTTATTGGAGCTTTGCACGAGGCACTGT -s simRat_chr6.simRat.chr6 640742 173 + 647215 ATGTATGCAGGGGGAGCTGTGCATGACAAACCTCTTGTGTGGGGAGCAGGCTCTTTATACAGCTGCCTGTGATCGCTCTACATCATGTCAAATGGAGGAGGCTTATAGCCAAGCACTAACCGCATGTATATGGCCGTGTTTGCCTTTTATTGGAGCTTTGCATGAGGCACTGC - -a -s simMouse_chr6.simMouse.chr6 629378 141 + 636262 GTCTGAACAATGTCACAAGTCCTCCATATACACAACATATTTTTTAATGCTGTCAACAGGTTCAATAGGAAATGTGCTACCTCCCAATTTCACTATAGCTCTAGACTCAAAAATACTTGCGGAGAAGTCCCCATCAGTCAA -s Anc0.Anc0refChr3 204737 41 - 222631 ----------------GTGTTCTCCACATGGACATCCTATATATTTA------------------------------------------------------------------------------------GATCAATCAA -s Anc1.Anc1refChr1 63964 41 + 69767 ----------------GTGTTCTCCACATGGACATCCTATATATTTA------------------------------------------------------------------------------------GATCAATCAA -s Anc2.Anc2refChr13 75529 41 - 96486 ----------------GTGTTCTCCACGTGGACATCCTATATATTTA------------------------------------------------------------------------------------GATCAATCAA -s mr.mrrefChr3 175775 57 + 181027 GTCTGAACAATGTTATGTGTCCTCCATATGCACAACCTATTTTTTTA------------------------------------------------------------------------------------CATCAGTCAA -s simCow_chr6.simCow.chr6 225752 37 - 602619 ----------------GAGTTCTCCATGTG----TCCTATATATTTA------------------------------------------------------------------------------------GATTGATCAA -s simDog_chr6.simDog.chr6 226629 41 - 593897 ----------------ATGTTCTCCACGTGGACATCCTATATATTTA------------------------------------------------------------------------------------GATCAATCAG -s simHuman_chr6.simHuman.chr6 595945 41 + 601863 ----------------GTATTCTCCACATGGGTATTCAATATATTTA------------------------------------------------------------------------------------GATCAATCCA -s simRat_chr6.simRat.chr6 640923 54 + 647215 ATCTAAACAATGTTATGTGTCCTC---ATGTACAACCTATTGTTTTA------------------------------------------------------------------------------------CATCAGTCAA - -a -s simMouse_chr6.simMouse.chr6 629519 15 + 636262 TTAACCAAACTGGAG -s Anc0.Anc0refChr3 204778 15 - 222631 TTATTCAGAATAGAA -s Anc1.Anc1refChr1 64005 15 + 69767 TTATTCAGAATAGAA -s Anc2.Anc2refChr13 75570 15 - 96486 TTATTCAGAATAGAA -s mr.mrrefChr3 175832 15 + 181027 TTAACCAGACTGGAG -s simCow_chr6.simCow.chr6 225791 11 - 602619 TTATTCAGAAT---- -s simDog_chr6.simDog.chr6 226670 15 - 593897 TTATTCAAAATAGAA -s simHuman_chr6.simHuman.chr6 595986 15 + 601863 CTATTCAGAATAGAA -s simRat_chr6.simRat.chr6 640977 15 + 647215 TTAACTGGGTTGGAG - -a -s simMouse_chr6.simMouse.chr6 629534 63 + 636262 TTACATTTAAGGGATCCACTCCTTCCAAGTGCAAACAATAAGCGGTTAGCTTCTATGAGCATG -s Anc0.Anc0refChr3 204793 63 - 222631 TTACATTTAAGAGATCCCCTCCCTACAAGTACAAACAATAAGCAGTTAACTTCTGAGAAAATG -s Anc1.Anc1refChr1 64020 63 + 69767 TTACATTTAAGAGATCCCCTCCCTACAAGTACAAACAATAAGCAGTTAACTTCTGAGAAAATG -s Anc2.Anc2refChr13 75605 63 - 96486 TTACATTTAAAAGATCCCTTCCCTACAAGTACAAACAATAAGCAATTAACTTCTGAGAAAACA -s mr.mrrefChr3 175847 63 + 181027 TTACATTTAAGGGATCCACTCCTTACAAGTGCAAACAATAAGCAGTTAGCTTCTGTGAGCATG -s simCow_chr6.simCow.chr6 225823 60 - 602619 TTACATTTAAAAGATCCATTCCCTACAAATACAAACAATACGCAAT-AACATCT--CAAAACA -s simDog_chr6.simDog.chr6 226708 63 - 593897 TTACATTTAAAGGATTCCTTCCCTACAAGTTCAAACAAAAAACGATTACCTTCTGAGTAAACA -s simHuman_chr6.simHuman.chr6 596001 63 + 601863 TTACATTTAAGAGATCCTCTCACTACAAGGACAAACAATGAGCAGTTAACCTCTGAGAAAATG -s simRat_chr6.simRat.chr6 640992 61 + 647215 TTACATGTAAGGGACCCACTCCTTACAAGTGCAAACAATAAGCAGTAAGCTTATGTGAG--TC - -a -s simMouse_chr6.simMouse.chr6 629597 28 + 636262 CAGGCACAGAGTTGCGAGTTGTCATTCG -s Anc0.Anc0refChr3 204859 21 - 222631 CAGACACAG-------AATTTTCATTTG -s Anc1.Anc1refChr1 64086 21 + 69767 CAGACACAG-------AATTTTCATTTG -s Anc2.Anc2refChr13 75671 21 - 96486 CAGACACAG-------AATTTTCATTTG -s mr.mrrefChr3 175910 28 + 181027 CAGGCACAGAGTTGCGAGTTGTCATTTG -s simCow_chr6.simCow.chr6 225886 17 - 602619 CAG----AA-------AACTTTCATCTG -s simDog_chr6.simDog.chr6 226774 21 - 593897 CAAACACAG-------AATTTTCATTTG -s simHuman_chr6.simHuman.chr6 596067 21 + 601863 CAGACACAT-------AATTTTCGTTTG -s simRat_chr6.simRat.chr6 641053 28 + 647215 CAGCCGCAGAGTTGAGAGTTATCTCTTG - -a -s simMouse_chr6.simMouse.chr6 629625 19 + 636262 AAGTTTACCCATTAAGGAA -s Anc0.Anc0refChr3 204881 19 - 222631 AGATGTACCCATTAAGGAA -s Anc1.Anc1refChr1 64108 19 + 69767 AGATGTACCCATTAAGGAA -s Anc2.Anc2refChr13 75693 19 - 96486 AGATGTACCCATTAAGAAA -s mr.mrrefChr3 175939 19 + 181027 AAATTTACCCATTAAGGAA -s simCow_chr6.simCow.chr6 225904 19 - 602619 AAATTTACCCATTAAGAAA -s simDog_chr6.simDog.chr6 226796 19 - 593897 AGATGTACCCATTAAGAAA -s simHuman_chr6.simHuman.chr6 596089 19 + 601863 ATATGTACCCATAAAGGAA -s simRat_chr6.simRat.chr6 641082 19 + 647215 AAATTCACCCATTGAGGAA - -a -s simMouse_chr6.simMouse.chr6 629644 55 + 636262 TCCCATATACCCATTAAGGAATCCCATAGTTGTTGAAGCTAGTAGCTACAAATTC -s Anc0.Anc0refChr3 204900 37 - 222631 TTCC----------------TACA--TAGTCATTGAAACTAGTAGCTACAAATTC -s Anc1.Anc1refChr1 64127 37 + 69767 TTCC----------------TACA--TAGTCATTGAAACTAGTAGCTACAAATTC -s Anc2.Anc2refChr13 75717 37 - 96486 TTCC----------------TACA--TTGTCATTGAAACTAGTAGCTAAAAATTC -s mr.mrrefChr3 175958 42 + 181027 TCCCATATA-----------GTCC--TAGTTGTTGAAGCTAGTAGCTACAAATTC -s simCow_chr6.simCow.chr6 225928 37 - 602619 TTCC----------------TGAC--TTGTCCTTGAAACTACTAGCTAAAATTTC -s simDog_chr6.simDog.chr6 226820 37 - 593897 TTCC----------------TACA--TTGCCATTGAAACGAGTAGCTAACAATTT -s simHuman_chr6.simHuman.chr6 596108 37 + 601863 TTCC----------------CATG--TAGTCATTGAAACTAGTAGTTACAAGTGC -s simRat_chr6.simRat.chr6 641101 42 + 647215 TCTCATACA-----------GTTC--TGGTTGTTGAAGCTAGTAGCTACAAATTC - -a -s simMouse_chr6.simMouse.chr6 629699 12 + 636262 TCCTATGTGAGA -s Anc0.Anc0refChr3 204937 12 - 222631 GCCTATGAGAGT -s Anc1.Anc1refChr1 64164 12 + 69767 GCCTATGAGAGT -s Anc2.Anc2refChr13 75754 12 - 96486 GCCCATGAGAGT -s mr.mrrefChr3 176000 12 + 181027 TCCTATGTGAGA -s simCow_chr6.simCow.chr6 225971 8 - 602619 GGCCACA----T -s simDog_chr6.simDog.chr6 226857 12 - 593897 GCCCATGAGAGT -s simHuman_chr6.simHuman.chr6 596145 12 + 601863 CCCTATGAGAGC -s simRat_chr6.simRat.chr6 641143 12 + 647215 TCATAAGTGAGA - -a -s simMouse_chr6.simMouse.chr6 629711 20 + 636262 GAGCAGTCTAGACAGGTGGC -s Anc0.Anc0refChr3 204949 20 - 222631 GAGCAGTCTGTACAATTAGC -s Anc1.Anc1refChr1 64176 20 + 69767 GAGCAGTCTGTACAATTAGC -s Anc2.Anc2refChr13 75766 20 - 96486 GAGCAGTCTGTACAATTAGC -s mr.mrrefChr3 176012 20 + 181027 GAGCAGTCTGGACAGGTGGC -s simCow_chr6.simCow.chr6 225979 20 - 602619 GAGTGGTCTGTACAATTGGA -s simDog_chr6.simDog.chr6 226869 20 - 593897 GATCAGTCTGTACAAGTAGC -s simHuman_chr6.simHuman.chr6 596158 20 + 601863 AAGCAGTCTGTGCAATTAGT -s simRat_chr6.simRat.chr6 641155 20 + 647215 GAGCAGTCTGGAAAGGTGGC - -a -s simMouse_chr6.simMouse.chr6 629731 19 + 636262 AGTCTAAGCAGGCAAGGCA -s Anc0.Anc0refChr3 204969 19 - 222631 AGTCTGAGTGAGTAAGGCA -s Anc1.Anc1refChr1 64196 19 + 69767 AGTCTGAGTGAGTAAGGCA -s Anc2.Anc2refChr13 75786 19 - 96486 AGTCTGAGTGAGTAAGGCA -s mr.mrrefChr3 176032 19 + 181027 AGTCTAAGCAGGCAAGGCA -s simCow_chr6.simCow.chr6 226003 19 - 602619 AGTTTGAGCAGGTAAGGCA -s simDog_chr6.simDog.chr6 226889 19 - 593897 AGTCTGAATGAGAAAGGCA -s simHuman_chr6.simHuman.chr6 596178 19 + 601863 AGTCTGAGTGAGTGATGCA -s simRat_chr6.simRat.chr6 641175 19 + 647215 AGTTTAAGCAGGCAAGGCA - -a -s simMouse_chr6.simMouse.chr6 629750 1 + 636262 T -s Anc0.Anc0refChr3 204993 1 - 222631 T -s Anc1.Anc1refChr1 64220 1 + 69767 T -s Anc2.Anc2refChr13 75810 1 - 96486 T -s mr.mrrefChr3 176051 1 + 181027 T -s simCow_chr6.simCow.chr6 226027 1 - 602619 T -s simDog_chr6.simDog.chr6 226913 1 - 593897 T -s simHuman_chr6.simHuman.chr6 596202 1 + 601863 T -s simRat_chr6.simRat.chr6 641194 1 + 647215 C - -a -s simMouse_chr6.simMouse.chr6 629751 22 + 636262 GGTGCCAGCTTATCCTTCTAGA -s Anc0.Anc0refChr3 204997 21 - 222631 -GTGGTATCTTATTCTCTTAGA -s Anc1.Anc1refChr1 64382 22 + 69767 AGTGGTATCTTATTCTCTTAGA -s Anc2.Anc2refChr13 75814 21 - 96486 -GTGGTATCTTATTCTCTTAGA -s mr.mrrefChr3 176052 22 + 181027 AGTGCCAGCTTATCCTTCTAGA -s simCow_chr6.simCow.chr6 226031 20 - 602619 -GTGGCATCTTAC-CACTTAGG -s simDog_chr6.simDog.chr6 226917 21 - 593897 -GTGGTATCTTATTCTCTTAGA -s simHuman_chr6.simHuman.chr6 596374 22 + 601863 AGTGGTGTCTTATTCTCTTAGA -s simRat_chr6.simRat.chr6 641195 22 + 647215 AATGCCAGCTTACCCTTCTAGA - -a -s simMouse_chr6.simMouse.chr6 629773 19 + 636262 TTGAAAGTGTATGGAATTT -s Anc0.Anc0refChr3 205020 18 - 222631 TCAGAAGTGTAAAGAAAC- -s Anc1.Anc1refChr1 64406 19 + 69767 TCAGAAGTGTAAAGAAACT -s Anc2.Anc2refChr13 75837 18 - 96486 TCAGAACTGTAAAGAAAC- -s mr.mrrefChr3 176076 19 + 181027 TCGAAAGTGTATAGAATTT -s simCow_chr6.simCow.chr6 226053 17 - 602619 TCAAATATGTAAA-AATC- -s simDog_chr6.simDog.chr6 226940 18 - 593897 TCAGAACTGTAAAGAAAT- -s simHuman_chr6.simHuman.chr6 596398 19 + 601863 CCAGAGGTGTAAAGAGACT -s simRat_chr6.simRat.chr6 641219 19 + 647215 TCTAAAGTGTATAGAATTT - -a -s simMouse_chr6.simMouse.chr6 629792 25 + 636262 GTTGGAACTCAGACAGGATGTTCTT -s Anc0.Anc0refChr3 205038 23 - 222631 -TTGGT-TTCAGCAGGAATGTCCTT -s Anc1.Anc1refChr1 64425 24 + 69767 GTTGGT-TTCAGCAGGAATGTCCTT -s Anc2.Anc2refChr13 75855 23 - 96486 -TTCGT-TTCAGCAGGAAACTCCTT -s mr.mrrefChr3 176095 25 + 181027 GTTGGAACTCAGACAGGATGTTCTT -s simCow_chr6.simCow.chr6 226070 23 - 602619 -TTGTT-TCCAGCTGGAAACTCCTT -s simDog_chr6.simDog.chr6 226958 23 - 593897 -TTCGT-TTCGGCAGGGAACTCCTT -s simHuman_chr6.simHuman.chr6 596422 24 + 601863 GTTGGG-TTCAGCAGGAATGTGCTT -s simRat_chr6.simRat.chr6 641238 14 + 647215 GTTGGAACTCAGAC----------- - -a -s simMouse_chr6.simMouse.chr6 629817 3 + 636262 ATG -s Anc0.Anc0refChr3 205064 3 - 222631 ACA -s Anc1.Anc1refChr1 64452 3 + 69767 ACA -s Anc2.Anc2refChr13 75893 3 - 96486 ACA -s mr.mrrefChr3 176120 3 + 181027 ACA -s simCow_chr6.simCow.chr6 226108 3 - 602619 TCA -s simDog_chr6.simDog.chr6 226996 3 - 593897 AAG -s simHuman_chr6.simHuman.chr6 596449 3 + 601863 ACA -s simRat_chr6.simRat.chr6 641252 2 + 647215 -CA - -a -s simMouse_chr6.simMouse.chr6 629820 6 + 636262 TCCAAC -s Anc0.Anc0refChr3 205067 6 - 222631 TCTGCC -s Anc1.Anc1refChr1 64455 6 + 69767 TCTGCC -s Anc2.Anc2refChr13 75896 6 - 96486 TCTGCT -s mr.mrrefChr3 176123 6 + 181027 TCCAAC -s simCow_chr6.simCow.chr6 226114 6 - 602619 TGTACT -s simDog_chr6.simDog.chr6 226999 6 - 593897 TCTGCT -s simHuman_chr6.simHuman.chr6 596452 6 + 601863 TCTGGC -s simRat_chr6.simRat.chr6 641254 6 + 647215 TCCAAC - -a -s simMouse_chr6.simMouse.chr6 629826 18 + 636262 AACTGCTTGCCCAGTTGG -s Anc0.Anc0refChr3 205073 18 - 222631 AACTGCATGCTCAGTAAG -s Anc1.Anc1refChr1 64461 18 + 69767 AACTGCATGCTCAGTAAG -s Anc2.Anc2refChr13 75908 18 - 96486 GACTGCATGCTCTGTAAG -s mr.mrrefChr3 176129 18 + 181027 AACTGCATGCCCAGTTAG -s simCow_chr6.simCow.chr6 226131 18 - 602619 AACTGCCTGCTTGGTAAA -s simDog_chr6.simDog.chr6 227011 18 - 593897 GACTGCATGCTCTGTAAG -s simHuman_chr6.simHuman.chr6 596458 17 + 601863 AA-TTCATACTCAGTAAG -s simRat_chr6.simRat.chr6 641260 18 + 647215 AACTGCATGCCCAGTCAG - -a -s simMouse_chr6.simMouse.chr6 629844 12 + 636262 TAAAAAAGTGCA -s Anc0.Anc0refChr3 205091 12 - 222631 TGAAAAAGTGCA -s Anc1.Anc1refChr1 64479 12 + 69767 TGAAAAAGTGCA -s Anc2.Anc2refChr13 75926 12 - 96486 TGAAAAAATGCC -s mr.mrrefChr3 176147 12 + 181027 TGAAAAAGTGCA -s simCow_chr6.simCow.chr6 226392 12 - 602619 AACAAAAATGCC -s simCow_chr6.simCow.chr6 226149 12 - 602619 TGAAAAAACGCC -s simDog_chr6.simDog.chr6 227029 12 - 593897 TGAAAAAATGGC -s simHuman_chr6.simHuman.chr6 596475 12 + 601863 TGAAAAAGTGCA -s simRat_chr6.simRat.chr6 641278 12 + 647215 TGAAAAAGTCCA - -a -s simMouse_chr6.simMouse.chr6 629856 36 + 636262 GCTCACCCAAAAAGTATATTTAATATCATAGGTTGC -s Anc0.Anc0refChr3 205109 36 - 222631 GCTAGTCCTAAAACCATATCTAATAGCATATGTTGT -s Anc1.Anc1refChr1 64497 36 + 69767 GCTAGTCCTAAAACCATATCTAATAGCATATGTTGT -s Anc2.Anc2refChr13 75944 36 - 96486 GCTAGTTGTAAAACCATATATCATAGCATGTGTTGT -s mr.mrrefChr3 176159 36 + 181027 GCTCACCCAAAAACCATATCTAATATCATAGGTTGC -s simCow_chr6.simCow.chr6 226410 36 - 602619 GCTAGTTGTAAAACCATATATCATAGCACGTGATTT -s simCow_chr6.simCow.chr6 226167 35 - 602619 GC-AGTTCTATAACTGTATCACATAGCATGTGTAGT -s simDog_chr6.simDog.chr6 227047 36 - 593897 GCCAGTTGTAAAACCAGATATCATGGCGTGTGTTAT -s simHuman_chr6.simHuman.chr6 596493 35 + 601863 GCTAGTCCTAAA-CCATCTCCAATAGCATATGTTGT -s simRat_chr6.simRat.chr6 641290 36 + 647215 GCTCACCCAAAAACCATATCTAACATCAAAGGTTGC - -a -s simMouse_chr6.simMouse.chr6 629892 1 + 636262 A -s Anc0.Anc0refChr3 205145 1 - 222631 G -s Anc1.Anc1refChr1 64533 1 + 69767 G -s Anc2.Anc2refChr13 75981 1 - 96486 G -s mr.mrrefChr3 176195 1 + 181027 A -s simCow_chr6.simCow.chr6 226447 1 - 602619 G -s simCow_chr6.simCow.chr6 226203 1 - 602619 G -s simDog_chr6.simDog.chr6 227084 1 - 593897 G -s simHuman_chr6.simHuman.chr6 596528 1 + 601863 G -s simRat_chr6.simRat.chr6 641326 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 629893 37 + 636262 GCCTGTGGGGAGCCCTGGTGATTGCCAACTTCCCTGT -s Anc0.Anc0refChr3 205150 37 - 222631 GTCTGTAGGAATCCCTGGTGCTCACCAACTTCCTCAT -s Anc1.Anc1refChr1 64538 37 + 69767 GTCTGTAGGAATCCCTGGTGCTCACCAACTTCCTCAT -s Anc2.Anc2refChr13 75986 37 - 96486 GGCTGTAGGAATCCCTGGTGCTCACCAATTTCCTCAT -s mr.mrrefChr3 176196 37 + 181027 GTCTGTGGGAATCCCTGGTGATTGCCAACTTCCCTGT -s simCow_chr6.simCow.chr6 226452 37 - 602619 GGCTTTAGGAATCCCTGGCGCTCACTAATTCCCTTGT -s simCow_chr6.simCow.chr6 226208 37 - 602619 GGCTTTAGAAATCCATGGTGCTCACTAATTCCCTTGG -s simDog_chr6.simDog.chr6 227089 37 - 593897 GGCTGTAGGAATCCCTGTTCCTAACCAATTTCAACAT -s simHuman_chr6.simHuman.chr6 596533 37 + 601863 GTCTGCAAGAATCCCTGGTGCTCTCCAACTTCGTCAT -s simRat_chr6.simRat.chr6 641327 37 + 647215 GTCTGGGGGAATCCCTGGTGATTGCAAACTTCCCTGA - -a -s simMouse_chr6.simMouse.chr6 629930 2 + 636262 TG -s Anc0.Anc0refChr3 205187 2 - 222631 TG -s Anc1.Anc1refChr1 64575 2 + 69767 TG -s Anc2.Anc2refChr13 76023 2 - 96486 TG -s mr.mrrefChr3 176233 2 + 181027 TG -s simCow_chr6.simCow.chr6 226245 2 - 602619 TG -s simDog_chr6.simDog.chr6 227126 2 - 593897 CG -s simHuman_chr6.simHuman.chr6 596570 2 + 601863 TG -s simRat_chr6.simRat.chr6 641364 2 + 647215 CA - -a -s simMouse_chr6.simMouse.chr6 629932 12 + 636262 GCCCCATGCACA -s Anc0.Anc0refChr3 205189 12 - 222631 TCCAAAACACAG -s Anc1.Anc1refChr1 64577 12 + 69767 TCCAAAACACAG -s Anc2.Anc2refChr13 76025 12 - 96486 TCCAAAACACAG -s mr.mrrefChr3 176235 12 + 181027 TCCCCATGAACA -s simCow_chr6.simCow.chr6 226489 12 - 602619 TTCAACAAACAG -s simCow_chr6.simCow.chr6 226247 12 - 602619 TAATGAACACAG -s simDog_chr6.simDog.chr6 227128 12 - 593897 TCCAAAACACAG -s simHuman_chr6.simHuman.chr6 596572 12 + 601863 TCCTAAACACAG -s simRat_chr6.simRat.chr6 641366 12 + 647215 TCCCCATGAGCA - -a -s simMouse_chr6.simMouse.chr6 629944 5 + 636262 TCATT -s Anc0.Anc0refChr3 205201 4 - 222631 TG-TT -s Anc1.Anc1refChr1 64589 4 + 69767 TG-TT -s Anc2.Anc2refChr13 76037 4 - 96486 TG-TT -s mr.mrrefChr3 176247 4 + 181027 TG-TT -s simCow_chr6.simCow.chr6 226503 4 - 602619 CA-TT -s simCow_chr6.simCow.chr6 226259 4 - 602619 CA-TT -s simDog_chr6.simDog.chr6 227140 4 - 593897 TG-CT -s simHuman_chr6.simHuman.chr6 596584 4 + 601863 TG-TT -s simRat_chr6.simRat.chr6 641378 4 + 647215 TG-TT - -a -s simMouse_chr6.simMouse.chr6 629949 6 + 636262 GAGTTT -s Anc0.Anc0refChr3 205230 6 - 222631 GAGTCT -s Anc1.Anc1refChr1 64618 6 + 69767 GAGTCT -s Anc2.Anc2refChr13 76073 6 - 96486 GAGCCT -s mr.mrrefChr3 176251 6 + 181027 GAGTTT -s simCow_chr6.simCow.chr6 226539 6 - 602619 GAGCCT -s simCow_chr6.simCow.chr6 226295 5 - 602619 GAGCT- -s simDog_chr6.simDog.chr6 227176 6 - 593897 GAGCCT -s simHuman_chr6.simHuman.chr6 596613 6 + 601863 GAGTCT -s simRat_chr6.simRat.chr6 641382 6 + 647215 GAGTTT - -a -s simMouse_chr6.simMouse.chr6 629955 25 + 636262 CAATGGAATTATTAGCCTCATTCTC -s Anc0.Anc0refChr3 205238 25 - 222631 TAGTGGAATTATTAGCCTCCTTGTC -s Anc1.Anc1refChr1 64626 25 + 69767 TAGTGGAATTATTAGCCTCCTTGTC -s Anc2.Anc2refChr13 76081 25 - 96486 TAGTGGAATTATTAGCCTCCTTGTT -s mr.mrrefChr3 176257 25 + 181027 CAATGGAATTATTAGCCTCATTGTC -s simCow_chr6.simCow.chr6 226547 25 - 602619 TAATGGACTTATTAGCCTTCTTGTT -s simCow_chr6.simCow.chr6 226301 25 - 602619 TAGTGGACTTATTAGCCTGATTGTT -s simDog_chr6.simDog.chr6 227184 24 - 593897 TAGT-GAATTATTAACCTCCCTGTT -s simHuman_chr6.simHuman.chr6 596621 25 + 601863 TAGGGGAATTATTAGCCTCCTTGTC -s simRat_chr6.simRat.chr6 641388 25 + 647215 CAATAGAATTATTAGGCTCATTGTC - -a -s simMouse_chr6.simMouse.chr6 629980 13 + 636262 ACACAGCTAGTTT -s Anc0.Anc0refChr3 205277 13 - 222631 ACACAGCTGAGCT -s Anc1.Anc1refChr1 64665 13 + 69767 ACACAGCTGAGCT -s Anc2.Anc2refChr13 76120 13 - 96486 ACACAGCTGAGCT -s mr.mrrefChr3 176282 13 + 181027 ACACAGCTAGTCT -s simCow_chr6.simCow.chr6 226586 13 - 602619 TGACAGCTGAGTT -s simCow_chr6.simCow.chr6 226340 13 - 602619 ACACAGTGGAGTT -s simDog_chr6.simDog.chr6 227224 13 - 593897 ACACAGCTGAGCT -s simHuman_chr6.simHuman.chr6 596660 13 + 601863 ACACAGCTGCGCT -s simRat_chr6.simRat.chr6 641413 13 + 647215 GCGCAGCTAAACT - -a -s simMouse_chr6.simMouse.chr6 629993 33 + 636262 ATTCAACTGCATTAGGAATTTACAGGTTCATTA -s Anc0.Anc0refChr3 205342 33 - 222631 CTTCAACTGCATAAGGGATTTAAAGGCCCATTG -s Anc1.Anc1refChr1 64730 33 + 69767 CTTCAACTGCATAAGGGATTTAAAGGCCCATTG -s Anc2.Anc2refChr13 76186 33 - 96486 CTTCAACTGCATAAGGGACTTAAAGGCCCATTG -s mr.mrrefChr3 176347 33 + 181027 ATTCAACTGCATTAGGAATTTACAGGTTCATTA -s simCow_chr6.simCow.chr6 226652 29 - 602619 CTGCAATTGCA----GGACTTAATGGAACATCC -s simDog_chr6.simDog.chr6 227286 33 - 593897 CTTCAACTGAATAAGTGACTTAAAGGCCCATTG -s simHuman_chr6.simHuman.chr6 596725 33 + 601863 CTTCAACTGCATAAGGGATTTAAAAGCCAATTG -s simRat_chr6.simRat.chr6 641479 33 + 647215 ATTCAACTGCATTAAGAATCTAAAGGTTCATTA - -a -s simMouse_chr6.simMouse.chr6 630026 46 + 636262 CCTCCCAAATTTTGTAATTTCTTAGTTGTTGTCAACCTATTATCAA -s Anc0.Anc0refChr3 205375 29 - 222631 T-------ATTTTGTA-ATGCTTAGTTTTTCCCAACC--------- -s Anc1.Anc1refChr1 64763 36 + 69767 TATTCTCAATTTTGTA-ATGCTTAGTTTTTCCCAACC--------- -s Anc2.Anc2refChr13 76219 29 - 96486 T-------ATTTTGTA-ATGCTTAGTTTTTCCCAACC--------- -s mr.mrrefChr3 176380 45 + 181027 CCTCCCAAATTTTGTA-TTTCTTAGTTGTTGTCAACCTATTATCAA -s simCow_chr6.simCow.chr6 226681 12 - 602619 T-------AT----------CTTAATTTT----------------- -s simDog_chr6.simDog.chr6 227319 29 - 593897 C-------ATTTTGTA-ATGGTCAGTCTTTCCCAACC--------- -s simHuman_chr6.simHuman.chr6 596758 36 + 601863 TATTCTCAATTTCGTA-AGGCTTAGTTTTCCCCAACC--------- -s simRat_chr6.simRat.chr6 641513 45 + 647215 CCTCCCAAATTTTGTA-TTTTTTAGTTGTTGTAACCCTACTATAAA - -a -s simMouse_chr6.simMouse.chr6 630072 51 + 636262 CTGCATTAGAAATTTAAAGGTTCATTATCTTCCCAAATCTTATGATTTCTT -s mr.mrrefChr3 176425 51 + 181027 CTGCATTAGGAATTTAAAGGTTCATTATCTTCCCAAATTTTATAGTTTCTT -s simRat_chr6.simRat.chr6 641561 51 + 647215 CTGCATCAGGAATTTAAAGGTTCTTTAACTTCCCAAATTTTATAGTTACTC - -a -s simMouse_chr6.simMouse.chr6 630123 24 + 636262 GTTGTTGTCAACCAATTCTTCGGT -s Anc0.Anc0refChr3 205404 11 - 222631 -------------AATTTTCTAGT -s Anc1.Anc1refChr1 64799 11 + 69767 -------------AATTTTCTAGT -s Anc2.Anc2refChr13 76248 11 - 96486 -------------AATTTTCTAGT -s mr.mrrefChr3 176477 24 + 181027 GTTGTTGTCAACCAATTCTTCGGT -s simCow_chr6.simCow.chr6 226693 8 - 602619 ----------------GTTCTAGT -s simDog_chr6.simDog.chr6 227348 11 - 593897 -------------AATTTTCTAGT -s simHuman_chr6.simHuman.chr6 596794 11 + 601863 -------------AATTTTCTAAT -s simRat_chr6.simRat.chr6 641613 24 + 647215 GTCGTTGTCAACCAATTCTTGGGC - -a -s simMouse_chr6.simMouse.chr6 630147 25 + 636262 GCTCACAACCACAGAGGTTCTGATC -s Anc0.Anc0refChr3 205415 21 - 222631 GCTTGTCACCACAGAAATATT---- -s Anc1.Anc1refChr1 64810 21 + 69767 GCTTGTCACCACAGAAATATT---- -s Anc2.Anc2refChr13 76259 21 - 96486 CCTTGTCAACCCAGAAATATT---- -s mr.mrrefChr3 176501 25 + 181027 GCTCACAACCACAGAGATACTGATC -s simCow_chr6.simCow.chr6 226701 21 - 602619 CCTCATCATTGCAGAACTAAT---- -s simDog_chr6.simDog.chr6 227359 21 - 593897 CCTTGTCAACCCAGAAATATT---- -s simHuman_chr6.simHuman.chr6 596805 21 + 601863 GCTTGTCACCACAGAAATATT---- -s simRat_chr6.simRat.chr6 641656 25 + 647215 ACTCACTACCACGGAGATACTGAAC - -a -s simMouse_chr6.simMouse.chr6 630172 43 + 636262 TGAAATTTTAATGAGTGTTTACTAGGGGCCTTGTTTTTGCAAA -s Anc0.Anc0refChr3 205436 41 - 222631 --AATATTTAATAAAAGTTTGCTGGGGCCCTTTTCTTTGAAAA -s Anc1.Anc1refChr1 64831 41 + 69767 --AATATTTAATAAAAGTTTGCTGGGGCCCTTTTCTTTGAAAA -s Anc2.Anc2refChr13 76280 41 - 96486 --AATATTTAATAAAAGTTTGCTGGGGCCATTTTCTATGAAAA -s mr.mrrefChr3 176526 43 + 181027 TGAAATTTTAATGAGTGTTTACTAGGGGCCTTTTTTTTGCAAA -s simCow_chr6.simCow.chr6 226722 41 - 602619 --AATATTTAATAAGAGTCTGGCAAGGCCATCTTCTGTGAAAA -s simDog_chr6.simDog.chr6 227380 41 - 593897 --AATATTTAATAGAAGTTTGCTGGGGCCAATTTCTATAAGAA -s simHuman_chr6.simHuman.chr6 596826 41 + 601863 --AGGATTTAATAAAAGTTTGCTGTGGCTCTTTTCTTTGAAAA -s simRat_chr6.simRat.chr6 641692 43 + 647215 TAAAATTTTAATGAGTGTTTACTAGGGGCCTTTTTTCTGCAAA - -a -s simMouse_chr6.simMouse.chr6 630215 4 + 636262 AAAT -s Anc0.Anc0refChr3 205477 4 - 222631 GAAT -s Anc1.Anc1refChr1 64872 4 + 69767 GAAT -s Anc2.Anc2refChr13 76321 4 - 96486 GAAT -s mr.mrrefChr3 176569 4 + 181027 AAAT -s simCow_chr6.simCow.chr6 226765 4 - 602619 GAAT -s simDog_chr6.simDog.chr6 227421 4 - 593897 GAAT -s simHuman_chr6.simHuman.chr6 596867 4 + 601863 GAAT -s simRat_chr6.simRat.chr6 641735 4 + 647215 AAAT - -a -s simMouse_chr6.simMouse.chr6 630219 13 + 636262 CTGTCCAACCCGT -s Anc0.Anc0refChr3 205483 7 - 222631 CTGTCCA------ -s Anc1.Anc1refChr1 64878 13 + 69767 CTGTCCATCCTAT -s Anc2.Anc2refChr13 76327 7 - 96486 CTGACCA------ -s mr.mrrefChr3 176575 13 + 181027 CTGTCCATCCCGT -s simCow_chr6.simCow.chr6 226773 7 - 602619 CTGGCCA------ -s simDog_chr6.simDog.chr6 227427 7 - 593897 CTGACTA------ -s simHuman_chr6.simHuman.chr6 596873 13 + 601863 CTGTCCATCCTAT -s simRat_chr6.simRat.chr6 641741 13 + 647215 TTGTTCATACCGT - -a -s simMouse_chr6.simMouse.chr6 630232 14 + 636262 GAGTAAGTTGCGAA -s Anc0.Anc0refChr3 205490 14 - 222631 GAGGGGTTTCAAAA -s Anc1.Anc1refChr1 64891 14 + 69767 GAGGGGTTTCAAAA -s Anc2.Anc2refChr13 76334 14 - 96486 AGGGGGTTGCAGAA -s mr.mrrefChr3 176588 14 + 181027 GAGTAAGTTCCAAA -s simCow_chr6.simCow.chr6 226792 14 - 602619 AGGGGGTCGCTGAC -s simDog_chr6.simDog.chr6 227434 14 - 593897 AGGGGGCTGCAGTA -s simHuman_chr6.simHuman.chr6 596886 14 + 601863 GAGGGTTTTCAAAA -s simRat_chr6.simRat.chr6 641754 14 + 647215 GAGTAAGTTCCAAT - -a -s simMouse_chr6.simMouse.chr6 630246 11 + 636262 GCAGCATACAC -s Anc0.Anc0refChr3 205556 11 - 222631 TGAGCATACAC -s Anc1.Anc1refChr1 64957 11 + 69767 TGAGCATACAC -s Anc2.Anc2refChr13 76400 11 - 96486 TGAGCATGTAG -s mr.mrrefChr3 176602 11 + 181027 GCAGCACACAC -s simCow_chr6.simCow.chr6 226858 11 - 602619 TGAGCGTGTAG -s simDog_chr6.simDog.chr6 227506 11 - 593897 TGAGCATGTAG -s simHuman_chr6.simHuman.chr6 596952 11 + 601863 CGAACATACAC -s simRat_chr6.simRat.chr6 641768 11 + 647215 GCAGCACACAC - -a -s simMouse_chr6.simMouse.chr6 630257 13 + 636262 CGAGAATGTTCTC -s Anc0.Anc0refChr3 205567 13 - 222631 TGAGAATATCTTC -s Anc1.Anc1refChr1 64968 13 + 69767 TGAGAATATCTTC -s Anc2.Anc2refChr13 76411 13 - 96486 TGAGAATACCTTC -s mr.mrrefChr3 176613 13 + 181027 TGAGAATATTCTC -s simCow_chr6.simCow.chr6 226869 12 - 602619 TG-GAACACCTAC -s simDog_chr6.simDog.chr6 227517 13 - 593897 TGAGAATACCTTC -s simHuman_chr6.simHuman.chr6 596965 13 + 601863 TGAGAATATCTTC -s simRat_chr6.simRat.chr6 641779 13 + 647215 TGAGAATATTCTC - -a -s simMouse_chr6.simMouse.chr6 630270 5 + 636262 TGGTA -s Anc0.Anc0refChr3 205586 5 - 222631 TGGTA -s Anc1.Anc1refChr1 64987 5 + 69767 TGGTA -s Anc2.Anc2refChr13 76430 5 - 96486 TGGTA -s mr.mrrefChr3 176626 5 + 181027 TGGTA -s simCow_chr6.simCow.chr6 226887 5 - 602619 TGGTA -s simDog_chr6.simDog.chr6 227536 5 - 593897 TGGTA -s simHuman_chr6.simHuman.chr6 596984 5 + 601863 TGGGA -s simRat_chr6.simRat.chr6 641792 5 + 647215 TGGTA - -a -s simMouse_chr6.simMouse.chr6 630275 40 + 636262 TGTGAATTCCTCCACTTACACTCAGTACTTCAAATTTGCC -s Anc0.Anc0refChr3 205609 39 - 222631 TGTGAATTTC-CCACTTACACTCAGTACTTCTAACTTGGC -s Anc1.Anc1refChr1 65010 40 + 69767 TGTGAATTTCACCACTTACACTCAGTACTTCTAACTTGGC -s Anc2.Anc2refChr13 76453 39 - 96486 TGTGGATTCC-CCACTTACACTCAGTGCTTCCAACTTGGC -s mr.mrrefChr3 176631 40 + 181027 TGTGAATTTCTCCACTTACACTCAGTACTTCTAATTTGCC -s simCow_chr6.simCow.chr6 226910 23 - 602619 -----------------ACACTCAGTAGTTCCAAATTAGC -s simDog_chr6.simDog.chr6 227559 39 - 593897 TGTGGATTCC-CCACTTACACTGAGTGCTTCCCACTTGGC -s simHuman_chr6.simHuman.chr6 597007 40 + 601863 TGTGAATTTCACCACTTACACTCAATACTCCTAGCTTGGC -s simRat_chr6.simRat.chr6 641797 34 + 647215 TGTGAATTTTTCCAC------TCAGTACTTCTAATTGACC - -a -s simMouse_chr6.simMouse.chr6 630315 5 + 636262 TGGTG -s Anc0.Anc0refChr3 205648 5 - 222631 TAGTG -s Anc1.Anc1refChr1 65050 5 + 69767 TAGTG -s Anc2.Anc2refChr13 76492 5 - 96486 CAGTG -s mr.mrrefChr3 176671 5 + 181027 TGGTG -s simCow_chr6.simCow.chr6 226933 5 - 602619 CAGTG -s simDog_chr6.simDog.chr6 227598 5 - 593897 CAGTG -s simHuman_chr6.simHuman.chr6 597054 5 + 601863 TTGAC -s simRat_chr6.simRat.chr6 641831 5 + 647215 TGGTG - -a -s simMouse_chr6.simMouse.chr6 630320 5 + 636262 CAGCA -s Anc0.Anc0refChr3 205653 1 - 222631 C---- -s Anc1.Anc1refChr1 65055 5 + 69767 CAGCA -s Anc2.Anc2refChr13 76497 1 - 96486 C---- -s mr.mrrefChr3 176676 5 + 181027 CAGCA -s simCow_chr6.simCow.chr6 226939 1 - 602619 C---- -s simDog_chr6.simDog.chr6 227603 1 - 593897 C---- -s simHuman_chr6.simHuman.chr6 597059 5 + 601863 CAGCA -s simRat_chr6.simRat.chr6 641836 3 + 647215 CA--C - -a -s simMouse_chr6.simMouse.chr6 630325 32 + 636262 TTCTCTGGTTTTATCTTCTAGGCCTTTTCCGT -s Anc0.Anc0refChr3 205658 30 - 222631 TTTTCTGA--TTAGCTTTTTGGCATTTTCTTT -s Anc1.Anc1refChr1 65064 32 + 69767 TTTTCTGATTTTAGCTTTTTGGCATTTTCTTT -s Anc2.Anc2refChr13 76502 30 - 96486 TTTTCTGA--TTAGCTCTTTGGCATTTTCTTT -s mr.mrrefChr3 176681 32 + 181027 TTTTCTGATTTTAGCTTCTAGGCCTTTTCTTT -s simCow_chr6.simCow.chr6 226944 29 - 602619 TTTTCTGA--TTAGCTGTTTTGCCTTTTC-TT -s simDog_chr6.simDog.chr6 227608 30 - 593897 TTTTCTGA--TTAACTCTTTGGCATTTTCTTT -s simHuman_chr6.simHuman.chr6 597069 32 + 601863 TTTTTGGATTTTAGCTTGTTGACATTTTCTTT -s simRat_chr6.simRat.chr6 641839 32 + 647215 TTTTCTGATTTTGGCTGCTAGGACTTTTCTTT - -a -s simMouse_chr6.simMouse.chr6 630357 11 + 636262 ATTTTTGGAGC -s Anc0.Anc0refChr3 205690 11 - 222631 ACCTTTGATTC -s Anc1.Anc1refChr1 65098 11 + 69767 ACCTTTGATTC -s Anc2.Anc2refChr13 76534 11 - 96486 ACCTTTAATCC -s mr.mrrefChr3 176713 11 + 181027 ATTTTTGGATC -s simCow_chr6.simCow.chr6 226975 11 - 602619 ACCTTTAAACG -s simDog_chr6.simDog.chr6 227640 11 - 593897 ACCTTTAATCC -s simHuman_chr6.simHuman.chr6 597103 11 + 601863 ACCTTTGATTC -s simRat_chr6.simRat.chr6 641871 11 + 647215 ATTTTTGGATC - -a -s simMouse_chr6.simMouse.chr6 630368 31 + 636262 TGTAGGCCAGCTCTATCAATCTATGGGGTTC -s Anc0.Anc0refChr3 205701 30 - 222631 TTTAGGGCAATTTCAGAGATCTATGGGGTT- -s Anc1.Anc1refChr1 65109 30 + 69767 TTTAGGGCAATTTCAGAGATCTATGGGGTT- -s Anc2.Anc2refChr13 76545 30 - 96486 ATTAGGGCAATTTCAGAGATATATGGGTTT- -s mr.mrrefChr3 176724 31 + 181027 TTTAGGCCAGCTCTATCAATCTATGGGGTTC -s simCow_chr6.simCow.chr6 226986 28 - 602619 ATCAAGGCAACTTCAGAAA--TATGGACTT- -s simDog_chr6.simDog.chr6 227651 30 - 593897 ATTAGTGCAATTTCAGAGATATGTGCGTTT- -s simHuman_chr6.simHuman.chr6 597115 30 + 601863 TTTAGGGCAATTTCAGAGATCTATGGGGTT- -s simRat_chr6.simRat.chr6 641882 31 + 647215 TTTAGGCCAGCTCTATCAATCTACGGGGTTC - -a -s simMouse_chr6.simMouse.chr6 630399 15 + 636262 CACAGAATCACAACA -s Anc0.Anc0refChr3 205731 15 - 222631 CACAAAATAATAATA -s Anc1.Anc1refChr1 65139 15 + 69767 CACAAAATAATAATA -s Anc2.Anc2refChr13 76575 15 - 96486 CACAAAATAATAATA -s mr.mrrefChr3 176755 15 + 181027 CACAGAATCATAACA -s simCow_chr6.simCow.chr6 227014 12 - 602619 CACAAAATAATA--- -s simDog_chr6.simDog.chr6 227682 15 - 593897 CACAAAATGATAATA -s simHuman_chr6.simHuman.chr6 597145 15 + 601863 CACAAAATAATGGTA -s simRat_chr6.simRat.chr6 641913 15 + 647215 CACAGAATCATAATA - -a -s simMouse_chr6.simMouse.chr6 630414 44 + 636262 CGTACTGCTTATGGCCTTGTAAACCCAAGTCAGGAGAGAAGCAC -s Anc0.Anc0refChr3 205746 44 - 222631 CATGCTGCACATGGCCTGGTTAGCCCAAGTCCGGAGAGAAGCAC -s Anc1.Anc1refChr1 65154 44 + 69767 CATGCTGCACATGGCCTGGTTAGCCCAAGTCCGGAGAGAAGCAC -s Anc2.Anc2refChr13 76590 44 - 96486 CCCGCTTCACACGGCCTGGTTAGCCCAAGTCCGGAGAGAAGCAC -s mr.mrrefChr3 176770 44 + 181027 CATACTGCTCATGGCCTTGTAAACCCAAGTCCGGAGAGAAGCAC -s simCow_chr6.simCow.chr6 227026 37 - 602619 ------TCACA-GGCCTAGTCAGCCCAAGTCCGGAGAAAAGCTC -s simDog_chr6.simDog.chr6 227697 44 - 593897 CCCGCTTCTCACGGCCTGGTTAACTCAAGTTCGGTGAGAGGCAC -s simHuman_chr6.simHuman.chr6 597170 44 + 601863 CATGCTGCACATGGTCTGGTTAGCCCAAGACCGGAGAGTAGAGC -s simRat_chr6.simRat.chr6 641928 44 + 647215 CATACTGCTCATGGCCTTGTCAACCCCAGTCCGGAGCGAAGCAC - -a -s simMouse_chr6.simMouse.chr6 630458 8 + 636262 TCTCCAGA -s Anc0.Anc0refChr3 205790 8 - 222631 TCATCAGA -s Anc1.Anc1refChr1 65198 8 + 69767 TCATCAGA -s Anc2.Anc2refChr13 76634 8 - 96486 TCATCAGA -s mr.mrrefChr3 176814 8 + 181027 TCTCCAGA -s simCow_chr6.simCow.chr6 227063 8 - 602619 TCATCTGA -s simDog_chr6.simDog.chr6 227744 8 - 593897 TCATCAGA -s simHuman_chr6.simHuman.chr6 597214 8 + 601863 TCATCAGA -s simRat_chr6.simRat.chr6 641972 8 + 647215 TCTCCAGA - -a -s simMouse_chr6.simMouse.chr6 630466 35 + 636262 GTTACACGAACATTGTTTATACGACTTGGAATTTT -s Anc0.Anc0refChr3 205798 35 - 222631 GTCACACGAACGTTCTTTGTACGGCCTGAGATTTT -s Anc1.Anc1refChr1 65206 35 + 69767 GTCACACGAACGTTCTTTGTACGGCCTGAGATTTT -s Anc2.Anc2refChr13 76652 35 - 96486 GTCACACGAGCGTTCTTTGTACGGCCTGAGATTTT -s mr.mrrefChr3 176822 35 + 181027 GTTACACGAACATTGTTTATACGACTTGGAATTTT -s simCow_chr6.simCow.chr6 227079 27 - 602619 --------AGCATTCTTTATACGGCCTGAAATTTT -s simDog_chr6.simDog.chr6 227762 35 - 593897 GTCACACGAGCGTTCTTTGTACGGCCTGAGATTTT -s simHuman_chr6.simHuman.chr6 597222 12 + 601863 GTCACACGCACG----------------------- -s simRat_chr6.simRat.chr6 641980 35 + 647215 GCTACACGAACATTGTTTATACGACTTGGAATTTT - -a -s simMouse_chr6.simMouse.chr6 630501 59 + 636262 AGAAGGCCTCAATTTTCGCGCTACAGGCTAGTCCGCTTAGAGTTCTTCATGCAATACGC -s Anc0.Anc0refChr3 205833 6 - 222631 AACTAG----------------------------------------------------- -s Anc1.Anc1refChr1 65241 51 + 69767 AACTAG--------TCTATGCTAGCGGGTCGTTCGCCCAGAATGCTTCAAGTGAAATTG -s Anc2.Anc2refChr13 76839 6 - 96486 AACTAG----------------------------------------------------- -s mr.mrrefChr3 176857 59 + 181027 AGAAGGCCTCAATTTTTGTGCTACAGGCTAGTTCGCTCAGAGTTCTTCAAGCAATATTC -s simCow_chr6.simCow.chr6 227263 6 - 602619 AAACAG----------------------------------------------------- -s simDog_chr6.simDog.chr6 227957 6 - 593897 AACTAG----------------------------------------------------- -s simHuman_chr6.simHuman.chr6 597234 45 + 601863 --------------TCTATGCTAGCGGGTCGTTCGCCCAGAATGCTTCAAGTGAAATTG -s simRat_chr6.simRat.chr6 642015 59 + 647215 AGAAGGCCGTAATTTTTGTGCTACGGGCTAGTTCGCTCAGAGTTCTTCAAGCAACATTC - -a -s simMouse_chr6.simMouse.chr6 630560 2 + 636262 TC -s Anc1.Anc1refChr1 65293 2 + 69767 AC -s mr.mrrefChr3 176917 2 + 181027 TC -s simHuman_chr6.simHuman.chr6 597280 2 + 601863 AC -s simRat_chr6.simRat.chr6 642075 2 + 647215 TC - -a -s simMouse_chr6.simMouse.chr6 630562 7 + 636262 ACTTCTT -s Anc1.Anc1refChr1 65295 7 + 69767 ACCTGCT -s mr.mrrefChr3 176919 7 + 181027 ACTTGTT -s simHuman_chr6.simHuman.chr6 597296 7 + 601863 ACCTGCT -s simRat_chr6.simRat.chr6 642077 7 + 647215 ACTTGTT - -a -s simMouse_chr6.simMouse.chr6 630569 21 + 636262 TAAATGTAGTCTGTATAATCT -s Anc1.Anc1refChr1 65302 19 + 69767 TGAATGTGGCTT--AAAATCT -s mr.mrrefChr3 176926 21 + 181027 TAAATGTAGCCTGTATAATCT -s simHuman_chr6.simHuman.chr6 597305 19 + 601863 TGAATGTGGCTT--AAAATCT -s simRat_chr6.simRat.chr6 642084 21 + 647215 TAAATGTAACCTGTATAATCT - -a -s simMouse_chr6.simMouse.chr6 630590 35 + 636262 CCAGCCTTATTGAATCTGGACTGCAGCTGATTGGG -s Anc0.Anc0refChr3 205839 1 - 222631 ---------------C------------------- -s Anc1.Anc1refChr1 65321 35 + 69767 CCAGCCTTACTGCAACTTAACTACAACTGATCATG -s Anc2.Anc2refChr13 76845 1 - 96486 ---------------C------------------- -s mr.mrrefChr3 176947 35 + 181027 CCAGCCTTATTGAATCTGGACTGCAGCTGATTGGG -s simCow_chr6.simCow.chr6 227269 1 - 602619 ---------------C------------------- -s simDog_chr6.simDog.chr6 227963 1 - 593897 ---------------C------------------- -s simHuman_chr6.simHuman.chr6 597326 35 + 601863 CCAGCCTTACTGCAACTTAACTACAACTGATCATG -s simRat_chr6.simRat.chr6 642105 33 + 647215 CCATCCTTAT--AGTCTGGAATCCAGCTGATTGGG - -a -s simMouse_chr6.simMouse.chr6 630625 62 + 636262 CAACCCCAAGTTATTGTCAAGCATTGTACATACTAGATTGGACATTCATGGATGACAATGTG -s Anc0.Anc0refChr3 220341 61 + 222631 CAACCC-ATGTTTTTGTCAAGCTCAGTAGATACTGGATTAGGAATTCATGAGTTAAGCTGTA -s Anc1.Anc1refChr1 65356 61 + 69767 CAACCC-ATGTTTTTGTCAAGCTCAGTAGATACTGGATTAGGAATTCATGAGTTAAGCTGTA -s Anc2.Anc2refChr1 138231 61 + 142988 CAACCC-ATGTTTCTGTCAAGCTCAGTTGATGCTGGATTAGGAATTCATGAGTTAAGCTGTA -s mr.mrrefChr3 176982 62 + 181027 CAACCCCAAGTTATTGTCAAGCTCTGTACATACTAGATTGGACATTCATGGATGAAACTGTG -s simCow_chr6.simCow.chr6 5043 49 - 602619 -------------ATGTGAAGCTCAGTTGATGCTGGATTGGGAACTCATGAGTTAAGCTGTA -s simDog_chr6.simDog.chr6 589115 61 + 593897 CAACCC-ATGTTTCTGTCAAGCTCAGTTGGTGCTGGATTAAGAATTCATGAGTTAGGCTGCA -s simHuman_chr6.simHuman.chr6 597361 61 + 601863 CGACCC-AGGGTTTTGTCAAGCTCAGTAGATATTGGATTAGGAATTCATAAGTTAACCTGTA -s simRat_chr6.simRat.chr6 642138 62 + 647215 CAACCCCAAGTTATTGTCAAGCTCTGTAAATAGTAGATTGGACATTCATGGATGAAACTGTG - -a -s simMouse_chr6.simMouse.chr6 630687 33 + 636262 ACTGAACAAAAAAAAAATCTACTTCCTATTATC -s Anc0.Anc0refChr3 220402 30 + 222631 GCCAAC---ATCTGATATATTCTCTCTAATATT -s Anc1.Anc1refChr1 65417 30 + 69767 GCCAAC---ATCTGATATATTCTCTCTAATATT -s Anc2.Anc2refChr1 138292 30 + 142988 GCCAAC---ATCTGATGTATTCTCTATAATAGT -s mr.mrrefChr3 177044 33 + 181027 ACTGAACAAAAAAAAAATCTTCTTCCTATTATC -s simCow_chr6.simCow.chr6 5093 30 - 602619 GCTGAT---ATCCGATGTATTCTCTATAATAGT -s simDog_chr6.simDog.chr6 589176 15 + 593897 GTCAAC---ATCTGATGT--------------- -s simHuman_chr6.simHuman.chr6 597422 30 + 601863 GCCAAC---ATCGGGTATGCTCTATCTAATATT -s simRat_chr6.simRat.chr6 642200 33 + 647215 CCTGAACAAAAAAAAAATCTTCCTCCTATTATC - -a -s simMouse_chr6.simMouse.chr6 630720 12 + 636262 AATTTGATTATT -s Anc0.Anc0refChr3 220463 12 + 222631 AGTTTGATTATG -s Anc1.Anc1refChr1 65478 12 + 69767 AGTTTGATTATG -s Anc2.Anc2refChr1 138353 12 + 142988 AGTTTGAGTATG -s mr.mrrefChr3 177077 12 + 181027 AGTTTGATTATT -s simCow_chr6.simCow.chr6 5150 12 - 602619 AGTCTGAGTATG -s simDog_chr6.simDog.chr6 589199 12 + 593897 AGTTTGAGTATG -s simHuman_chr6.simHuman.chr6 597486 12 + 601863 AGTTTAATTATG -s simRat_chr6.simRat.chr6 642233 8 + 647215 AGTTTGAT---- - -a -s simMouse_chr6.simMouse.chr6 630732 5 + 636262 CTGAA -s Anc0.Anc0refChr3 220478 5 + 222631 CTGGG -s Anc1.Anc1refChr1 65493 5 + 69767 CTGGG -s Anc2.Anc2refChr1 138368 5 + 142988 GCAGG -s mr.mrrefChr3 177089 5 + 181027 CTGAA -s simCow_chr6.simCow.chr6 5165 5 - 602619 GCAGG -s simDog_chr6.simDog.chr6 589214 5 + 593897 GCAGG -s simHuman_chr6.simHuman.chr6 597501 5 + 601863 CTGGG -s simRat_chr6.simRat.chr6 642241 3 + 647215 --GAA - -a -s simMouse_chr6.simMouse.chr6 630737 41 + 636262 AATCAGCTAGGTTGGGTAGTTACCATCAGCCCCAGATGGAT -s Anc0.Anc0refChr3 220483 14 + 222631 AACAGGTTTAA---------------------------AGT -s Anc1.Anc1refChr1 65498 14 + 69767 AACAGGTTTAA---------------------------AGT -s Anc2.Anc2refChr1 138373 14 + 142988 AACAGATTTAA---------------------------AGT -s mr.mrrefChr3 177094 14 + 181027 AATCAGCTAGG---------------------------AAT -s simCow_chr6.simCow.chr6 5171 14 - 602619 ATCAGATGTAA---------------------------AGT -s simDog_chr6.simDog.chr6 589219 14 + 593897 AACAGATTTAA---------------------------AGT -s simHuman_chr6.simHuman.chr6 597506 14 + 601863 AACACGTATAA---------------------------AGT -s simRat_chr6.simRat.chr6 642244 14 + 647215 AAACAGCTAGG---------------------------AAT - -a -s simMouse_chr6.simMouse.chr6 630778 10 + 636262 GAGCTAGATT -s Anc0.Anc0refChr3 220497 10 + 222631 GGGCAAAAAT -s Anc1.Anc1refChr1 65512 10 + 69767 GGGCAAAAAT -s Anc2.Anc2refChr1 138396 10 + 142988 TGGCAAAAAC -s mr.mrrefChr3 177108 10 + 181027 GAGCAAGATT -s simCow_chr6.simCow.chr6 5195 10 - 602619 TGGCAAGAGC -s simDog_chr6.simDog.chr6 589242 10 + 593897 TGGCAAAAAC -s simHuman_chr6.simHuman.chr6 597520 10 + 601863 GGGCAAAAAT -s simRat_chr6.simRat.chr6 642258 7 + 647215 AAACAAG--- - -a -s simMouse_chr6.simMouse.chr6 630788 2 + 636262 GG -s Anc0.Anc0refChr3 220507 2 + 222631 GG -s Anc1.Anc1refChr1 65522 2 + 69767 GG -s Anc2.Anc2refChr1 138406 2 + 142988 AC -s mr.mrrefChr3 177118 2 + 181027 GG -s simCow_chr6.simCow.chr6 5206 2 - 602619 AC -s simDog_chr6.simDog.chr6 589252 2 + 593897 AC -s simHuman_chr6.simHuman.chr6 597530 2 + 601863 GG -s simRat_chr6.simRat.chr6 642265 2 + 647215 GG - -a -s simMouse_chr6.simMouse.chr6 630790 6 + 636262 GTAGTT -s Anc0.Anc0refChr3 220522 6 + 222631 GTAGTT -s Anc1.Anc1refChr1 65537 6 + 69767 GTAGTT -s Anc2.Anc2refChr1 138421 6 + 142988 ATAGTT -s mr.mrrefChr3 177120 6 + 181027 GTAGTT -s simCow_chr6.simCow.chr6 5221 6 - 602619 ATAGAT -s simDog_chr6.simDog.chr6 589267 6 + 593897 ATAGTT -s simHuman_chr6.simHuman.chr6 597545 6 + 601863 GTAGCT -s simRat_chr6.simRat.chr6 642267 6 + 647215 GTAGTT - -a -s simMouse_chr6.simMouse.chr6 630796 6 + 636262 ACCATC -s Anc0.Anc0refChr3 220531 6 + 222631 ACCATT -s Anc1.Anc1refChr1 65546 6 + 69767 ACCATT -s Anc2.Anc2refChr1 138449 6 + 142988 ACTGTT -s mr.mrrefChr3 177126 6 + 181027 ACCATC -s simCow_chr6.simCow.chr6 5249 5 - 602619 ACTGT- -s simDog_chr6.simDog.chr6 589295 6 + 593897 ACTGGT -s simHuman_chr6.simHuman.chr6 597554 6 + 601863 ACCATT -s simRat_chr6.simRat.chr6 642273 6 + 647215 ACACTC - -a -s simMouse_chr6.simMouse.chr6 630802 29 + 636262 AGCCCAAGATGGATGCCGAGGTGAGCTTA -s Anc0.Anc0refChr3 220537 29 + 222631 AGCCCCAGACGGGTGCCGACGTGACCTTA -s Anc1.Anc1refChr1 65552 29 + 69767 AGCCCCAGACGGGTGCCGACGTGACCTTA -s Anc2.Anc2refChr1 138455 29 + 142988 AGCCCCAGACTGGTGCCGACGTGACCTTA -s mr.mrrefChr3 177132 29 + 181027 AGCCCCAGATGGATGCCGAGGTGACCTTA -s simCow_chr6.simCow.chr6 597576 29 + 602619 AGCCCCAGACAAGTGCCGACCTGACCCCT -s simDog_chr6.simDog.chr6 589301 29 + 593897 AGCCCAAGACTGGTGCCGACGTGATCTTA -s simHuman_chr6.simHuman.chr6 597560 29 + 601863 AGCTCCAGACGGGTGCCGACGTGACCTTA -s simRat_chr6.simRat.chr6 642279 29 + 647215 AGCCCCAGATGGATGCCGAGGTGACCTTA - -a -s simMouse_chr6.simMouse.chr6 630831 1 + 636262 G -s Anc0.Anc0refChr3 220566 1 + 222631 G -s Anc1.Anc1refChr1 65581 1 + 69767 G -s Anc2.Anc2refChr1 138484 1 + 142988 A -s mr.mrrefChr3 177161 1 + 181027 G -s simCow_chr6.simCow.chr6 597605 1 + 602619 A -s simDog_chr6.simDog.chr6 589330 1 + 593897 A -s simHuman_chr6.simHuman.chr6 597589 1 + 601863 G -s simRat_chr6.simRat.chr6 642311 1 + 647215 G - -a -s simMouse_chr6.simMouse.chr6 630832 10 + 636262 GTCCGTCCGA -s Anc0.Anc0refChr3 220568 10 + 222631 GTCCTAGCTA -s Anc1.Anc1refChr1 65583 10 + 69767 GTCCTAGCTA -s Anc2.Anc2refChr1 138486 10 + 142988 GTTCTAGCTA -s mr.mrrefChr3 177162 10 + 181027 GTCCGACCGA -s simCow_chr6.simCow.chr6 597607 10 + 602619 GTTCGAGCTA -s simDog_chr6.simDog.chr6 589332 10 + 593897 GTTCTAGCTG -s simHuman_chr6.simHuman.chr6 597591 10 + 601863 GTCCTAGCTA -s simRat_chr6.simRat.chr6 642312 10 + 647215 GTCCGATCGA - -a -s simMouse_chr6.simMouse.chr6 630842 125 + 636262 TCCCACCACTAAAGGCTGTAACGCCTCTCTAGTGCTGGGGCTTGAAAGGGATACTCTAGTGATGGGGCTTGAAAGGGATATTATCACCACTCGGCCGCGGACGGGTGAGATTTCTGAGCACAAGC -s Anc0.Anc0refChr3 220581 97 + 222631 TCCCTACACTGGAGGGTCTAACGCCTCTTTAGTGCTGGG----------------------------CTTGAAACACATATCACGACGACTCGGTCGCGGACGGGTAAGGTTTCTGAGCACGGGC -s Anc1.Anc1refChr1 65596 97 + 69767 TCCCTACACTGGAGGGTCTAACGCCTCTTTAGTGCTGGG----------------------------CTTGAAACACATATCACGACGACTCGGTCGCGGACGGGTAAGGTTTCTGAGCACGGGC -s Anc2.Anc2refChr1 138499 97 + 142988 TCACCACACTGAAGGGTCTAACACCTCTTCAGTGCTGGG----------------------------TTTGAAACACATATCACGATGACTCGGTCGCGGACAGGTAAGGATTCTGAGCAGGGGC -s mr.mrrefChr3 177172 97 + 181027 TCCCTCCACTGGAGGGTGTAACGCCTCTCTAGTGCTGGG----------------------------CTTGAAAGACATATTATCACCACTCGGCCGCGGACGGGTGAGATTTCTGAGCACAAGC -s simCow_chr6.simCow.chr6 597620 17 + 602619 TCGCCGCACTCAAGGAT------------------------------------------------------------------------------------------------------------ -s simDog_chr6.simDog.chr6 589345 97 + 593897 TCATCACACCGAAAAGGCTAACACCTCTTCAGTGCTGGG----------------------------TTTGAAACACATATCACGATGACTCGGTCGCGGACAGGTAAGGATTCTGAGCAGGGGC -s simHuman_chr6.simHuman.chr6 597604 97 + 601863 TCCCTTCACTGGAGGGTCTAACGCCTCTATAGTGCTGGG----------------------------CAGGAAACACATATGACGACAACTCGGTCGCGGACGGGTAAGTTTTCTAAGCACGGGC -s simRat_chr6.simRat.chr6 642322 97 + 647215 TCCCTCTACTGGAGGGTGTAACGCCTCTTTAGTGCTGGG----------------------------CTTGATAGACATATTATCACCACTCGGCCGCGGACGGGTGAGGTTTCTGAGCATAAAC - -a -s simMouse_chr6.simMouse.chr6 630967 25 + 636262 TGGTATCCTGCGGGAGAAGAGGGAT -s Anc0.Anc0refChr3 220692 24 + 222631 TGGTACCC-GGGGGAAAAAGGGAAA -s Anc1.Anc1refChr1 65707 25 + 69767 TGGTACCCGGGGGGAAAAAGGGAAA -s Anc2.Anc2refChr1 138610 24 + 142988 TGGTACCC-GGGGGAAAGAGGGAAA -s mr.mrrefChr3 177269 25 + 181027 TGGTATCCTGGGGGAGAAGAGGGAT -s simCow_chr6.simCow.chr6 597640 18 + 602619 TTGT-------GGCGAAGAGGGAAA -s simDog_chr6.simDog.chr6 589456 24 + 593897 TGATACCC-GGGGGAAAGAGGGAGA -s simHuman_chr6.simHuman.chr6 597715 25 + 601863 TCGTACCCGGGAGGAAAATGGGAAA -s simRat_chr6.simRat.chr6 642419 25 + 647215 TAGTATCCTGGGGGAGAAAAGGGAT - -a -s simMouse_chr6.simMouse.chr6 630992 18 + 636262 AATAGTGAACGAAGAAAA -s Anc0.Anc0refChr3 220716 18 + 222631 AATAGTAAACGAGGAGAA -s Anc1.Anc1refChr1 65732 18 + 69767 AATAGTAAACGAGGAGAA -s Anc2.Anc2refChr1 138634 18 + 142988 AATAGTAAACGAGGAGAA -s mr.mrrefChr3 177294 18 + 181027 AATAGTGAACGAAGAAAA -s simCow_chr6.simCow.chr6 597659 18 + 602619 AATAGTAAGCGAGGAGTG -s simDog_chr6.simDog.chr6 589480 15 + 593897 A---TGAAATGAGGAGAA -s simHuman_chr6.simHuman.chr6 597740 18 + 601863 AATAGTAAACGAGGAGAA -s simRat_chr6.simRat.chr6 642444 18 + 647215 AATAGTGACTGAAGAAAG - -a -s simMouse_chr6.simMouse.chr6 631010 17 + 636262 CGAAATGGCGCGAGGCA -s Anc0.Anc0refChr3 220741 17 + 222631 CGAAAAAACGCCCGGCC -s Anc1.Anc1refChr1 65757 17 + 69767 CGAAAAAACGCCCGGCC -s Anc2.Anc2refChr1 138659 17 + 142988 CGAAAAAACGCCCGGCC -s mr.mrrefChr3 177312 17 + 181027 CGAAAAGGCGCCAGGCA -s simCow_chr6.simCow.chr6 597684 17 + 602619 CTAAAAAACGCGCGGCC -s simDog_chr6.simDog.chr6 589502 17 + 593897 CGAAAAAACGCCCGGCC -s simHuman_chr6.simHuman.chr6 597765 17 + 601863 CATAAACACGTCCGGCC -s simRat_chr6.simRat.chr6 642462 17 + 647215 CAAAAATGCGCCAGGCA - -a -s simMouse_chr6.simMouse.chr6 631027 5 + 636262 ACGCC -s Anc0.Anc0refChr3 220758 5 + 222631 ACGTA -s Anc1.Anc1refChr1 65774 5 + 69767 ACGTA -s Anc2.Anc2refChr1 138676 5 + 142988 ACGTA -s mr.mrrefChr3 177329 5 + 181027 ACGCC -s simCow_chr6.simCow.chr6 597702 5 + 602619 ACGCA -s simDog_chr6.simDog.chr6 589519 5 + 593897 ACGTA -s simHuman_chr6.simHuman.chr6 597782 5 + 601863 ACGTA -s simRat_chr6.simRat.chr6 642479 5 + 647215 ACGCC - -a -s simMouse_chr6.simMouse.chr6 631032 2 + 636262 CT -s Anc0.Anc0refChr3 220767 2 + 222631 CT -s Anc1.Anc1refChr1 65783 2 + 69767 CT -s Anc2.Anc2refChr1 138685 2 + 142988 CT -s mr.mrrefChr3 177334 2 + 181027 CT -s simCow_chr6.simCow.chr6 597711 2 + 602619 CT -s simDog_chr6.simDog.chr6 589528 2 + 593897 GT -s simHuman_chr6.simHuman.chr6 597791 2 + 601863 CT -s simRat_chr6.simRat.chr6 642484 2 + 647215 CT - -a -s simMouse_chr6.simMouse.chr6 631034 12 + 636262 CAGGATCGCTTT -s Anc0.Anc0refChr3 220769 11 + 222631 CAGGAT-ACTTT -s Anc1.Anc1refChr1 65785 12 + 69767 CAGGATCACTTT -s Anc2.Anc2refChr1 138687 11 + 142988 GAGGAT-AATTT -s mr.mrrefChr3 177336 12 + 181027 CAGGATCGCTTT -s simCow_chr6.simCow.chr6 597714 11 + 602619 GAGGAC-AATCT -s simDog_chr6.simDog.chr6 589530 11 + 593897 GAGGAT-AATTT -s simHuman_chr6.simHuman.chr6 597793 12 + 601863 CAGAATCACTTT -s simRat_chr6.simRat.chr6 642486 12 + 647215 CAGGATCGTTTT - -a -s simMouse_chr6.simMouse.chr6 631046 12 + 636262 CATGTGCCTTGC -s Anc0.Anc0refChr3 220780 12 + 222631 CATGTGCCCTGG -s Anc1.Anc1refChr1 65797 12 + 69767 CATGTGCCCTGG -s Anc2.Anc2refChr1 138698 12 + 142988 CATGCGCCCCGG -s mr.mrrefChr3 177348 12 + 181027 CATGTGCCTTGG -s simCow_chr6.simCow.chr6 597725 12 + 602619 CGTGCGCCCCGG -s simDog_chr6.simDog.chr6 589541 12 + 593897 CATGCGCCACGG -s simHuman_chr6.simHuman.chr6 597818 12 + 601863 CTTGTGCCCTGG -s simRat_chr6.simRat.chr6 642498 12 + 647215 CAAATGTCTTGG - -a -s simMouse_chr6.simMouse.chr6 631058 4 + 636262 GATA -s Anc0.Anc0refChr3 220792 4 + 222631 CGAA -s Anc1.Anc1refChr1 65809 4 + 69767 CGAA -s Anc2.Anc2refChr1 138710 4 + 142988 CGAT -s mr.mrrefChr3 177360 4 + 181027 GGTA -s simCow_chr6.simCow.chr6 597738 4 + 602619 CGAC -s simDog_chr6.simDog.chr6 589553 4 + 593897 CGAT -s simHuman_chr6.simHuman.chr6 597830 4 + 601863 CGAA -s simRat_chr6.simRat.chr6 642510 4 + 647215 GGTA - -a -s simMouse_chr6.simMouse.chr6 631062 18 + 636262 TGCTGGGGAAAAACAAGT -s Anc0.Anc0refChr3 220801 18 + 222631 CACTGGGGAAAAACAAGT -s Anc1.Anc1refChr1 65818 18 + 69767 CACTGGGGAAAAACAAGT -s Anc2.Anc2refChr1 138719 18 + 142988 CACCGGGGAAAAACTAAT -s mr.mrrefChr3 177364 18 + 181027 CGCTGGGGAAAAACAAGT -s simCow_chr6.simCow.chr6 597747 16 + 602619 C--CGGGATAAAACGgtt -s simDog_chr6.simDog.chr6 589562 18 + 593897 CACCGGGGAAAAACTAAT -s simHuman_chr6.simHuman.chr6 597839 18 + 601863 CACTGGGGAAAAACAAGT -s simRat_chr6.simRat.chr6 642514 13 + 647215 CG-----GAAAAACAAGT - -a -s simMouse_chr6.simMouse.chr6 631080 2 + 636262 GT -s Anc0.Anc0refChr3 220819 2 + 222631 gt -s Anc1.Anc1refChr1 65836 2 + 69767 GT -s Anc2.Anc2refChr1 138741 2 + 142988 gt -s mr.mrrefChr3 177382 2 + 181027 GT -s simCow_chr6.simCow.chr6 597984 2 + 602619 gt -s simDog_chr6.simDog.chr6 589584 2 + 593897 GT -s simHuman_chr6.simHuman.chr6 597857 2 + 601863 GT -s simRat_chr6.simRat.chr6 642527 2 + 647215 GT - -a -s simMouse_chr6.simMouse.chr6 631082 5 + 636262 TAATT -s Anc0.Anc0refChr3 220835 5 + 222631 AGATT -s Anc1.Anc1refChr1 65852 5 + 69767 AGATT -s Anc2.Anc2refChr1 138757 5 + 142988 AGATT -s mr.mrrefChr3 177384 5 + 181027 AAATT -s simCow_chr6.simCow.chr6 598000 5 + 602619 AGGTT -s simDog_chr6.simDog.chr6 589600 5 + 593897 AAATT -s simHuman_chr6.simHuman.chr6 597873 5 + 601863 AGATT -s simRat_chr6.simRat.chr6 642529 5 + 647215 AAATT - -a -s simMouse_chr6.simMouse.chr6 631087 9 + 636262 TATTCCCCT -s Anc0.Anc0refChr3 220840 9 + 222631 AGATACGCC -s Anc1.Anc1refChr1 65857 9 + 69767 AGATACGCC -s Anc2.Anc2refChr1 138762 9 + 142988 AGATACTCC -s mr.mrrefChr3 177389 9 + 181027 TGTTCCGCC -s simCow_chr6.simCow.chr6 598005 1 + 602619 A-------- -s simDog_chr6.simDog.chr6 589606 9 + 593897 AGATACTCC -s simHuman_chr6.simHuman.chr6 597878 9 + 601863 AGGTATGCC -s simRat_chr6.simRat.chr6 642534 9 + 647215 TGTTCCGCC - -a -s simMouse_chr6.simMouse.chr6 631096 87 + 636262 GGCCTAGTACTAGAATACGGTAGCCGGCACCTAATTGAGTAACGGAGCACTGCCAGCCAAAAGAAGTGCAGGTCTGGATGTCTGTAT -s Anc0.Anc0refChr3 220851 85 + 222631 GGCTTAGTTCTAGAAAAAGGTAGCCGGCACCTAATTGAGTATCGGAT--CAGCCATCCAAAGAAAGTTTGGTTCTAGATGTCTGTGC -s Anc1.Anc1refChr1 65868 87 + 69767 GGCTTAGTTCTAGAAAAAGGTAGCCGGCACCTAATTGAGTATCGGATCACAGCCATCCAAAGAAAGTTTGGTTCTAGATGTCTGTGC -s Anc2.Anc2refChr1 138773 85 + 142988 GGCTTAGTTCTAGAAAAAGGTAGCCGGCACTTAATTGAGTGTCGGAT--CAGCTATCTGAAGAAAGTTTGGTTCTAGATGTCTGTGC -s mr.mrrefChr3 177398 87 + 181027 GGCCTAGTACTAGAATACGGTAGCCGGCACCTAATTGAGTAACGGAGCACAGCCATCCAAAGGAAGTGCAGGTCTGGATGTCTGTAT -s simCow_chr6.simCow.chr6 598006 75 + 602619 ----------TAGAAAAAGGTAGCCGGCACATAATTGAGTGTCGGGT--CAGGTATCTGAAGAAAGTTTAGTTCTGGATGTCTGTGC -s simDog_chr6.simDog.chr6 589617 85 + 593897 GGCTTAGTTCTGGAAAAAGGTAGTCGGCACTTAATTGAGAGGTAGAT--CAGCTATCTGAAGAAAGGTTGGTTTTAGATGTCTGTGC -s simHuman_chr6.simHuman.chr6 597889 87 + 601863 GGTTTAGCTCTAGAAAAAGGTAGCTGGCACCTAATTGGGTATCGGATCACAGCCATCCAAAGAAAGTATGGTTCTTATTGTCTGTGC -s simRat_chr6.simRat.chr6 642543 87 + 647215 GACCTAGTACTAGGATACGGTAGCCGGCACCTAATTGAGTGCCGCAGCACAGCCATCCAAAGGAAGTTCAAGTCTGGATGTCTGTAT - -a -s simMouse_chr6.simMouse.chr6 631183 62 + 636262 ATCTGAACGTAAAATAAGAAAATCCATGTTTTCAGCCATAAAAAAAAAAAATCTATGTTTCT -s Anc0.Anc0refChr3 220936 32 + 222631 AT----------AA--ATAAAATCTATGTTTC------------------CTCTATGTTTTT -s Anc1.Anc1refChr1 65955 32 + 69767 AT----------AA--ATAAAATCTATGTTTC------------------CTCTATGTTTTT -s Anc2.Anc2refChr1 138858 32 + 142988 AT----------AA--ATAAAATCTGTGTTTC------------------CACTATGTTTTT -s mr.mrrefChr3 177485 60 + 181027 ATCTGAACGTAAAA--AGAAAATCTATGTTTTCAGCCATAAAAAAAAAAAATCTATGTTTCT -s simCow_chr6.simCow.chr6 598081 32 + 602619 AT----------AA--ATGAAATCTGTGTTTC------------------CGCTATGTTTTG -s simDog_chr6.simDog.chr6 589705 31 + 593897 CT----------AA--ATAAAGTCT-TGTTTC------------------CACTATGTTTTT -s simHuman_chr6.simHuman.chr6 597976 32 + 601863 AT----------AA--ATAAAATCTATATTTC------------------GTCTATGTTTTT -s simRat_chr6.simRat.chr6 642630 60 + 647215 GTCTCAACATAAAA--AAAAAATCTATGTTTACGGCCATAAAAAAAAAAAATCTATGTTTCT - -a -s simMouse_chr6.simMouse.chr6 631245 2 + 636262 GG -s Anc0.Anc0refChr3 220968 2 + 222631 AG -s Anc1.Anc1refChr1 65987 2 + 69767 AG -s Anc2.Anc2refChr1 138890 2 + 142988 AG -s mr.mrrefChr3 177545 2 + 181027 GG -s simCow_chr6.simCow.chr6 598113 2 + 602619 AG -s simDog_chr6.simDog.chr6 589739 2 + 593897 GT -s simHuman_chr6.simHuman.chr6 598008 2 + 601863 AG -s simRat_chr6.simRat.chr6 642690 2 + 647215 GG - -a -s simMouse_chr6.simMouse.chr6 631247 3 + 636262 CAT -s Anc0.Anc0refChr3 220991 3 + 222631 CAT -s Anc1.Anc1refChr1 66010 3 + 69767 CAT -s Anc2.Anc2refChr1 138913 3 + 142988 CAC -s mr.mrrefChr3 177547 3 + 181027 CAT -s simCow_chr6.simCow.chr6 598142 3 + 602619 TAA -s simDog_chr6.simDog.chr6 589762 3 + 593897 CAC -s simHuman_chr6.simHuman.chr6 598031 3 + 601863 CAT -s simRat_chr6.simRat.chr6 642692 3 + 647215 CAT - -a -s simMouse_chr6.simMouse.chr6 631250 8 + 636262 GTTATTTC -s Anc0.Anc0refChr3 220999 8 + 222631 GCTATCGC -s Anc1.Anc1refChr1 66018 8 + 69767 GCTATCGC -s Anc2.Anc2refChr1 138921 8 + 142988 GCTATCGC -s mr.mrrefChr3 177550 8 + 181027 GTTGTTTC -s simCow_chr6.simCow.chr6 598150 8 + 602619 GCTATCGC -s simDog_chr6.simDog.chr6 589770 8 + 593897 GCTATCGC -s simHuman_chr6.simHuman.chr6 598039 8 + 601863 GCTATAGC -s simRat_chr6.simRat.chr6 642695 8 + 647215 GTTGTTTC - -a -s simMouse_chr6.simMouse.chr6 631258 8 + 636262 TGTAAGGG -s Anc0.Anc0refChr3 221009 8 + 222631 TATAAGGG -s Anc1.Anc1refChr1 66028 8 + 69767 TATAAGGG -s Anc2.Anc2refChr1 138931 8 + 142988 TATAAGGG -s mr.mrrefChr3 177558 8 + 181027 TGTAAGGG -s simCow_chr6.simCow.chr6 598160 8 + 602619 TATAAGGG -s simDog_chr6.simDog.chr6 589780 8 + 593897 GACAAGGG -s simHuman_chr6.simHuman.chr6 598049 8 + 601863 TATAACGG -s simRat_chr6.simRat.chr6 642703 8 + 647215 TGTAAGGA - -a -s simMouse_chr6.simMouse.chr6 631266 8 + 636262 CAGTCAAC -s Anc0.Anc0refChr3 221017 8 + 222631 TCGCCAAT -s Anc1.Anc1refChr1 66036 8 + 69767 TCGCCAAT -s Anc2.Anc2refChr1 138952 8 + 142988 TCTCCAAT -s mr.mrrefChr3 177566 8 + 181027 CAGTCAAC -s simCow_chr6.simCow.chr6 598181 8 + 602619 TCCCCAGT -s simDog_chr6.simDog.chr6 589801 8 + 593897 TCTCCAAT -s simHuman_chr6.simHuman.chr6 598057 8 + 601863 TCGCCAAT -s simRat_chr6.simRat.chr6 642711 5 + 647215 CAGTC--- - -a -s simMouse_chr6.simMouse.chr6 631274 17 + 636262 TTCGGTTGCTATCGGTT -s Anc0.Anc0refChr3 221031 17 + 222631 CCCGGCTCTTAGCGATT -s Anc1.Anc1refChr1 66050 17 + 69767 CCCGGCTCTTAGCGATT -s Anc2.Anc2refChr1 138967 17 + 142988 CCAGGCTCTTAGCGATT -s mr.mrrefChr3 177574 17 + 181027 TTCGGTTGCTATCGGTT -s simCow_chr6.simCow.chr6 598196 17 + 602619 CCAGCCTCTTAGCGATT -s simDog_chr6.simDog.chr6 589816 17 + 593897 CTAGGCCCTTAGCGTTC -s simHuman_chr6.simHuman.chr6 598071 17 + 601863 CCCAGCTCTTAGCGATT -s simRat_chr6.simRat.chr6 642716 17 + 647215 TTCGATTGCTATCGGTT - -a -s simMouse_chr6.simMouse.chr6 631291 37 + 636262 CCCCCGACATGACGCCCAGGCTGCTGGGCCCACAAAA -s Anc0.Anc0refChr3 221059 37 + 222631 TCCCCAATGTGAAACCCAGGCTGTTGGGTGCACTTAT -s Anc1.Anc1refChr1 66078 37 + 69767 TCCCCAATGTGAAACCCAGGCTGTTGGGTGCACTTAT -s Anc2.Anc2refChr1 138995 37 + 142988 TCCCCAATGCGAAAGCCAGGCTGTTGGGTGCACTTAT -s mr.mrrefChr3 177591 37 + 181027 TCCCCGACATGACACCCAGGCTGCTGGGCCCACAAAA -s simCow_chr6.simCow.chr6 598224 37 + 602619 TCCCCCATGCGACCGCTAGGCTTCTAGGTGCAATTTT -s simDog_chr6.simDog.chr6 589844 37 + 593897 TCCCCAATGCGAAAGCCAAGCTGTTGGGTGCACTTAT -s simHuman_chr6.simHuman.chr6 598099 37 + 601863 TCCCCAATGTGATACCCAGGTTGTTGGGTGCACTTAC -s simRat_chr6.simRat.chr6 642733 36 + 647215 TCCCCGACATGACAGGCAGGCTGCTGGGCC-ACAGGA - -a -s simMouse_chr6.simMouse.chr6 631328 2 + 636262 TG -s Anc0.Anc0refChr3 221096 2 + 222631 TG -s Anc1.Anc1refChr1 66115 2 + 69767 TG -s Anc2.Anc2refChr1 139032 2 + 142988 TG -s mr.mrrefChr3 177628 2 + 181027 TG -s simCow_chr6.simCow.chr6 598261 2 + 602619 TG -s simDog_chr6.simDog.chr6 589886 2 + 593897 TG -s simHuman_chr6.simHuman.chr6 598136 2 + 601863 TG -s simRat_chr6.simRat.chr6 642769 2 + 647215 TG - -a -s simMouse_chr6.simMouse.chr6 631330 14 + 636262 AGACACCTGGACTG -s Anc0.Anc0refChr3 221119 14 + 222631 AGGTAACTGAGTTG -s Anc1.Anc1refChr1 66138 14 + 69767 AGGTAACTGAGTTG -s Anc2.Anc2refChr1 139055 14 + 142988 AGGTAACTGAGTTG -s mr.mrrefChr3 177630 14 + 181027 AGACACCTGGATTG -s simCow_chr6.simCow.chr6 598284 4 + 602619 AAGT---------- -s simDog_chr6.simDog.chr6 589909 14 + 593897 AGTTAACTGAGTTG -s simHuman_chr6.simHuman.chr6 598159 14 + 601863 AGGTAACCAACTAG -s simRat_chr6.simRat.chr6 642771 12 + 647215 A--TGCTTTGATTG - -a -s simMouse_chr6.simMouse.chr6 631344 23 + 636262 TCAATGGTGTCCTCGGGAACATG -s Anc0.Anc0refChr3 221203 23 + 222631 CCAGGGGTGTCTTCGGGACCTGG -s Anc1.Anc1refChr1 66222 23 + 69767 CCAGGGGTGTCTTCGGGACCTGG -s Anc2.Anc2refChr1 139139 23 + 142988 CCAGGGGTGTCTTCGGGACCTGG -s mr.mrrefChr3 177644 23 + 181027 CCAGGGGTGTCCTCGGGAACATG -s simCow_chr6.simCow.chr6 598318 21 + 602619 --AGGGGCACGTCCAGGACCTGC -s simDog_chr6.simDog.chr6 589993 23 + 593897 CCGGGGTTGTCATCGGGACCTGG -s simHuman_chr6.simHuman.chr6 598260 23 + 601863 CAAGGGGTGTCTTCGGGACCTGG -s simRat_chr6.simRat.chr6 642783 23 + 647215 CTAGGGGTCTCGTCCGGAACATG - -a -s simMouse_chr6.simMouse.chr6 631367 48 + 636262 GGGAATTTACTCGGATAATAGTTAACCTCCGTGTGACAGTTGTAACTG -s Anc0.Anc0refChr3 221226 48 + 222631 GGGAATTCTTTCGGATATTAGTGAAGGTCCGTCTGATAATTGGACCCC -s Anc1.Anc1refChr1 66245 48 + 69767 GGGAATTCTTTCGGATATTAGTGAAGGTCCGTCTGATAATTGGACCCC -s Anc2.Anc2refChr1 139162 48 + 142988 GGGAATTCTTTTGGATATTAGTGAAGGTCCGTCTGATAATTGGACCCT -s mr.mrrefChr3 177667 48 + 181027 GGGAATTTACTCGGATAATAGTGAACCTCCGTGTGATAATTGCAACTC -s simCow_chr6.simCow.chr6 598339 48 + 602619 GGGCATTCTTTTGGACATTAGCGAAGGTCTGTCTGATAATTGGACTCT -s simDog_chr6.simDog.chr6 590016 48 + 593897 GGGAATTCTTTTGGATATTAGTGAAGGTCCGTCTGAAAATTGGACCCT -s simHuman_chr6.simHuman.chr6 598288 48 + 601863 GGGAATTATATCGGATATTAGTGAAGGTCCGTCTGATAACTGGAGCCC -s simRat_chr6.simRat.chr6 642806 48 + 647215 GGGGATTTACTCGGATAATAGTGATCCTTCGTGTGATAATTGCAAGTC - -a -s simMouse_chr6.simMouse.chr6 631415 4 + 636262 ATTT -s Anc0.Anc0refChr3 221278 4 + 222631 ATCA -s Anc1.Anc1refChr1 66297 4 + 69767 ATCA -s Anc2.Anc2refChr1 139214 4 + 142988 ATCA -s mr.mrrefChr3 177715 4 + 181027 ATTT -s simCow_chr6.simCow.chr6 598391 4 + 602619 ATCA -s simDog_chr6.simDog.chr6 590068 4 + 593897 ATCA -s simHuman_chr6.simHuman.chr6 598340 4 + 601863 ATCA -s simRat_chr6.simRat.chr6 642854 4 + 647215 ATTT - -a -s simMouse_chr6.simMouse.chr6 631419 16 + 636262 AACGTTTAGGAGGCTA -s Anc0.Anc0refChr3 221282 15 + 222631 ATCGTTCAAGAGGC-A -s Anc1.Anc1refChr1 66301 15 + 69767 ATCGTTCAAGAGGC-A -s Anc2.Anc2refChr1 139219 15 + 142988 GTCGTTCGGGTGGC-T -s mr.mrrefChr3 177719 16 + 181027 AACGTTTAAGAGGCTA -s simCow_chr6.simCow.chr6 598396 15 + 602619 GTCGTTAGGGTGGC-T -s simDog_chr6.simDog.chr6 590073 15 + 593897 GTCGTCCGGGTGGC-T -s simHuman_chr6.simHuman.chr6 598344 15 + 601863 ATCGTTCAAGAGGC-A -s simRat_chr6.simRat.chr6 642858 16 + 647215 AACATTTAAGAGGCTA - -a -s simMouse_chr6.simMouse.chr6 631435 78 + 636262 CTATTGTGTTGTCTCTCGGCATGTTGATGTACCACTCAAACTTACAGAGCATTGAAGTGGCACTTAACTATCTTATTC -s Anc0.Anc0refChr3 221297 78 + 222631 CTATTGTGTTTTCCCTAGGCATGCTCATCTCCCACGTTAGCTTACAGAGCGTGGAGGCTGCGCTTAATTATCTTATGC -s Anc1.Anc1refChr1 66316 78 + 69767 CTATTGTGTTTTCCCTAGGCATGCTCATCTCCCACGTTAGCTTACAGAGCGTGGAGGCTGCGCTTAATTATCTTATGC -s Anc2.Anc2refChr1 139234 78 + 142988 CTATTGTGTTTTCCCTAGGCATGCTCATCTCCCTCGTTAGCTTACAGAGCGTGTAGGCTGCGCTTAATTTTCTTATGC -s mr.mrrefChr3 177735 78 + 181027 CTATTGTGTTGTCTCTCGGCATGTTGATGTACCACTCAAACTTACAGAGCATTGAAGTGGCACTTAACTATCTTATTC -s simCow_chr6.simCow.chr6 598412 76 + 602619 CTATTGTGTTTTCCCCAGGCATGCTCATCTTCCTCGTTAGCTTACTGAGCGTGCAGG-TGCGCTTA-TTCTCCTCTGC -s simDog_chr6.simDog.chr6 590088 75 + 593897 ATAATTT---TTCTCTAGACATGCTCATCTCCCTCGTTAGCTTACACAGCCTGTGAGCCGAGCTGGACTTTCTTATAC -s simHuman_chr6.simHuman.chr6 598359 78 + 601863 CCATTGTGTGTTCCCTGGGCGTACTCCTTTCCCACGTTAGCTTACAGGGTGTGGAGGCTGCGCTTAATTATCTTATGC -s simRat_chr6.simRat.chr6 642874 70 + 647215 CTATTGTCTTGTCTCTCGTCATGTTGATGTACCACACAAAGTTATAGAGCATTGA-GTCGCA----ACTCTCTTA--- - -a -s simMouse_chr6.simMouse.chr6 631513 20 + 636262 ATTTCTGATCTGTAATAAGT -s Anc0.Anc0refChr3 221375 9 + 222631 ATTCCT-A----------GT -s Anc1.Anc1refChr1 66394 9 + 69767 ATTCCT-A----------GT -s Anc2.Anc2refChr1 139315 9 + 142988 ATCCAT-A----------GT -s mr.mrrefChr3 177813 19 + 181027 ATTTCT-ATCTGTAATAAGT -s simCow_chr6.simCow.chr6 598491 9 + 602619 ATCCAT-A----------GT -s simDog_chr6.simDog.chr6 590166 9 + 593897 ATCCAT-A----------GT -s simHuman_chr6.simHuman.chr6 598437 9 + 601863 ATTCCT-A----------GT -s simRat_chr6.simRat.chr6 642944 13 + 647215 -------ATCTGTAATAAGT - -a -s simMouse_chr6.simMouse.chr6 631533 37 + 636262 TTTTTTTCCATCTTCTTCTCATCTTTTCACTAGGGCC -s Anc0.Anc0refChr3 221384 29 + 222631 ATTATTCCTACCTTTTTCTTACC--------AGGGTC -s Anc1.Anc1refChr1 66403 29 + 69767 ATTATTCCTACCTTTTTCTTACC--------AGGGTC -s Anc2.Anc2refChr1 139324 29 + 142988 ATTATTCCTGCCTTTTGCTTACC--------AGGGTC -s mr.mrrefChr3 177832 37 + 181027 TTTTTTTCCATCTTCTTCTCATCTTTTCACTAGGGTC -s simCow_chr6.simCow.chr6 598500 29 + 602619 ATAGTTCCTTCCCTTTGCTTACT--------GGAATC -s simDog_chr6.simDog.chr6 590177 29 + 593897 ATTATTCCTGCCTTTTGCACACC--------AGGGTT -s simHuman_chr6.simHuman.chr6 598446 29 + 601863 ATTATTCCTACCTTTTTCTTACC--------AGGGTC -s simRat_chr6.simRat.chr6 642957 37 + 647215 TTTTTTTCCGTCTTCTTCTCATCTTTTCACTAGGGTC - -a -s simMouse_chr6.simMouse.chr6 631570 6 + 636262 TTCTGT -s Anc0.Anc0refChr3 221417 6 + 222631 TTCCGC -s Anc1.Anc1refChr1 66436 6 + 69767 TTCCGC -s Anc2.Anc2refChr1 139357 6 + 142988 TTCCCC -s mr.mrrefChr3 177873 6 + 181027 TTCTGT -s simCow_chr6.simCow.chr6 598534 6 + 602619 CTTCTC -s simDog_chr6.simDog.chr6 590210 6 + 593897 TTCCCC -s simHuman_chr6.simHuman.chr6 598479 6 + 601863 TTCCGC -s simRat_chr6.simRat.chr6 642998 6 + 647215 TTCTGT - -a -s simMouse_chr6.simMouse.chr6 631576 9 + 636262 AGTATCATT -s Anc0.Anc0refChr3 221423 9 + 222631 AGGGTCGTT -s Anc1.Anc1refChr1 66442 9 + 69767 AGGGTCGTT -s Anc2.Anc2refChr1 139364 9 + 142988 AGGGTCGTT -s mr.mrrefChr3 177879 9 + 181027 AGTATCATT -s simCow_chr6.simCow.chr6 598541 9 + 602619 AGATTCATT -s simDog_chr6.simDog.chr6 590217 9 + 593897 AGGGTCGTT -s simHuman_chr6.simHuman.chr6 598485 1 + 601863 A-------- -s simRat_chr6.simRat.chr6 643004 9 + 647215 ACTATCATT - -a -s simMouse_chr6.simMouse.chr6 631585 11 + 636262 GCTATGTCATC -s Anc0.Anc0refChr3 221432 11 + 222631 GTTATGTCATC -s Anc1.Anc1refChr1 66451 11 + 69767 GTTATGTCATC -s Anc2.Anc2refChr1 139373 11 + 142988 GTTATGTCATC -s mr.mrrefChr3 177888 11 + 181027 GCTATGTCATC -s simCow_chr6.simCow.chr6 598550 11 + 602619 GTTATGTCAGC -s simDog_chr6.simDog.chr6 590228 11 + 593897 GTTATGTCATC -s simRat_chr6.simRat.chr6 643013 11 + 647215 GCTATGCCATC - -a -s simMouse_chr6.simMouse.chr6 631596 11 + 636262 CCATGGACTGA -s Anc0.Anc0refChr3 221443 11 + 222631 CAATGGACTGA -s Anc1.Anc1refChr1 66462 11 + 69767 CAATGGACTGA -s Anc2.Anc2refChr1 139386 11 + 142988 CAATGGACTGA -s mr.mrrefChr3 177899 11 + 181027 CCATGGACTGA -s simCow_chr6.simCow.chr6 598563 11 + 602619 GGATGGACTGA -s simDog_chr6.simDog.chr6 590241 11 + 593897 CAATGGACTGA -s simHuman_chr6.simHuman.chr6 598486 9 + 601863 --ATGGACTGA -s simRat_chr6.simRat.chr6 643024 11 + 647215 CCATGGACTGA - -a -s simMouse_chr6.simMouse.chr6 631607 60 + 636262 GTATCCTAGGCCAGCCTGGGATCTCGCGTGATGGGGCTAGTTTTCTATCCCCCAATTGGG -s Anc0.Anc0refChr3 221454 8 + 222631 GAATCCTA---------------------------------------------------- -s Anc1.Anc1refChr1 66473 8 + 69767 GAATCCTA---------------------------------------------------- -s Anc2.Anc2refChr1 139397 8 + 142988 GAATCCTA---------------------------------------------------- -s mr.mrrefChr3 177910 58 + 181027 GTATCCTAGGCCAGCCTGGGATCTCGCGTGATGGGGCTAGTTTTC--TCCCCCAATTGGG -s simCow_chr6.simCow.chr6 598574 8 + 602619 GAAACCCA---------------------------------------------------- -s simDog_chr6.simDog.chr6 590253 8 + 593897 GAATCTTA---------------------------------------------------- -s simHuman_chr6.simHuman.chr6 598495 8 + 601863 GCATCCTA---------------------------------------------------- -s simRat_chr6.simRat.chr6 643035 58 + 647215 GTATCCTAGGCTGGTCTGGGATCTCAGGTGATATGGCTAGTTTTC--TCACCGAATTGGG - -a -s simMouse_chr6.simMouse.chr6 631667 150 + 636262 CTGGAGTTCCATGGTAGTTCTTCCCCATAATCTGCCAATGGTCCATTGTGCAAGTTGAGAATGCATGCCGGCTGACAAGCCTTGACAAAGAATCCATACAGCTACCTCTCTAAGCTCCTTGCTGAGGTTGGAAAATTGTTGGTGATGTAT -s Anc0.Anc0refChr3 221462 19 + 222631 -----------------------------------------------------------------------------------------------------------------------------------ACAATTGTTAGTGATGGAT -s Anc1.Anc1refChr1 66481 19 + 69767 -----------------------------------------------------------------------------------------------------------------------------------ACAATTGTTAGTGATGGAT -s Anc2.Anc2refChr1 139405 19 + 142988 -----------------------------------------------------------------------------------------------------------------------------------CCAATTGTGAGTGATTGAT -s mr.mrrefChr3 177968 150 + 181027 CTGGAGTTCCATGGTAGTTCTTCCCCATAATCTGTTAATGGTCCATTGTACAAGTTGAGAATGCATGCCGGCTGACAAGCCTTGACAAAGAATCCATACAGCTACCTCTCTAAGCTCCTTGCTGAGGTTGGAAAATTGTTGGTGATGTAT -s simCow_chr6.simCow.chr6 598582 19 + 602619 -----------------------------------------------------------------------------------------------------------------------------------CCAAGTGTCAGTGCTAAAT -s simDog_chr6.simDog.chr6 590261 19 + 593897 -----------------------------------------------------------------------------------------------------------------------------------CCAGTTGTGAGTGATTGAT -s simHuman_chr6.simHuman.chr6 598503 19 + 601863 -----------------------------------------------------------------------------------------------------------------------------------ATAATTGTTAGTGATGGAT -s simRat_chr6.simRat.chr6 643094 150 + 647215 CTGAAGTTTCATGGTAGTTCTCCCCCACAATCTGTTAACAGTCCGTTGTACAAAGTGAGAATGCATGCTGGCTGACAAACCATGACAAAGAATCCATACAGCTACCTCTCTAAGCTCCTTGCTGAGGTGGAAAAATTGTTGGTGATGGAT - -a -s simMouse_chr6.simMouse.chr6 631817 129 + 636262 TTTAATATTGGTCATTGACACCAAAAAACCTTGCTTTTGAGATGCCAGCTCTGCTAGCCGGACCTGGATCACCCATTAGAGCTTAGCTATCCAAGGTCTATCATGTTAACAGGAGAGTCAGCCTTGCAT -s Anc0.Anc0refChr3 221481 41 + 222631 TTTAATATCGGCCATAAATTCCAAAAAAGCT---------------------------------------------------------------------------------------CACCCCT-CAA -s Anc1.Anc1refChr1 66500 41 + 69767 TTTAATATCGGCCATAAATTCCAAAAAAGCT---------------------------------------------------------------------------------------CACCCCT-CAA -s Anc2.Anc2refChr1 139424 41 + 142988 TTTAATATCGGCCATAAATTCCAAAAAAGCT---------------------------------------------------------------------------------------TACCCCT-CAA -s mr.mrrefChr3 178118 129 + 181027 TTTAATATTGGTCATTGACACCAAAAAACCTTGCTTTTGAGATGCCAGCTCTGCTAGCCGGACCTGGATCACCCATTAGAGCTTAGCTATCCAAGGTCTATCATGTTAACAGGAGAGTCAGCCTTGCAT -s simCow_chr6.simCow.chr6 598601 41 + 602619 CTTAATATCAGCCATAAATTACACAAAAGCT---------------------------------------------------------------------------------------TAGCTCT-CAC -s simDog_chr6.simDog.chr6 590283 41 + 593897 TTTAATATTGGCCATAGGTTCCAAAAAAGAT---------------------------------------------------------------------------------------TCCCCCT-CAA -s simHuman_chr6.simHuman.chr6 598522 41 + 601863 TTTAATGCCGGCTAGAAATGCCAAAAAAGCT---------------------------------------------------------------------------------------CAACCCT-CAG -s simRat_chr6.simRat.chr6 643244 129 + 647215 TTCAATATTGGTCATAAGCACCAAAAAACCTTGCTGTTGGGATGCCAGCTCTGCTAACCAGAGCTGGGTCAACCTTTAGAGCTTAGCTGTGCAAGGTCTGTCATGTTAACGGGAGTGTATGCCTTGAAT - -a -s simMouse_chr6.simMouse.chr6 631946 35 + 636262 GGTAACTGGGGAGCCAGTGTTGGGCAACAGAGGTA -s Anc0.Anc0refChr3 221522 25 + 222631 GAAAACTGG-----CACTA-----CATCAGAAGTA -s Anc1.Anc1refChr1 66541 25 + 69767 GAAAACTGG-----CACTA-----CATCAGAAGTA -s Anc2.Anc2refChr1 139465 25 + 142988 AAAAACTGG-----CACTA-----CATCAGAAGTA -s mr.mrrefChr3 178247 35 + 181027 GGTAACTGGGGAGCCAGTGTTGGGCAACAGAAGTA -s simCow_chr6.simCow.chr6 598646 25 + 602619 AGAATCTGA-----GACTA-----GATCAGAAGTA -s simDog_chr6.simDog.chr6 590324 25 + 593897 AACAACTAG-----CACTA-----CATCAGAAGTA -s simHuman_chr6.simHuman.chr6 598563 25 + 601863 GAAAAATGG-----CACTA-----CATCAGAAGTA -s simRat_chr6.simRat.chr6 643373 35 + 647215 GGTAACTGAAGACCCAGCCTTGGGAAACCGAAGTA - -a -s simMouse_chr6.simMouse.chr6 631981 8 + 636262 CCCTGTCA -s Anc0.Anc0refChr3 221547 8 + 222631 CACTAACA -s Anc1.Anc1refChr1 66566 8 + 69767 CACTAACA -s Anc2.Anc2refChr1 139490 8 + 142988 CACTAACA -s mr.mrrefChr3 178282 8 + 181027 CCCTGTCA -s simCow_chr6.simCow.chr6 598671 8 + 602619 TGCTAACA -s simDog_chr6.simDog.chr6 590349 8 + 593897 CACTAACA -s simHuman_chr6.simHuman.chr6 598588 8 + 601863 CTCTAACA -s simRat_chr6.simRat.chr6 643411 8 + 647215 CCCTGTCA - -a -s simMouse_chr6.simMouse.chr6 631989 56 + 636262 GAGCAGCCCAATGGGTAGTCTCCAAGAGATTCTTAAGATCCCAAAATATCTGTCAC -s Anc0.Anc0refChr3 221556 54 + 222631 GAGGAGCCCAGAGGCTAGTTTACAAAATATCCATATGATACTAAGAT--CTGCCAC -s Anc1.Anc1refChr1 66575 54 + 69767 GAGGAGCCCAGAGGCTAGTTTACAAAATATCCATATGATACTAAGAT--CTGCCAC -s Anc2.Anc2refChr1 139499 54 + 142988 GAGGAGCCCAGAGGCTAGCTTACAAAATATTCATATGATACTAAGAT--CTGCCAC -s mr.mrrefChr3 178290 56 + 181027 GAGCAGCCCAATGGGTAGTCTCCAAGAGATCCTTATGATCCCAAAATATCTGTCAC -s simCow_chr6.simCow.chr6 598680 53 + 602619 GAGGAGCCCAGAGGCTAGCTTACGAAATGTTCATATGATCCCA-GAT--CTGCTGT -s simDog_chr6.simDog.chr6 590358 54 + 593897 GTGGAGCCCAGAGGCTAGCTTACAAAATATTCACGTGACACTAAGCT--CTGGCAC -s simHuman_chr6.simHuman.chr6 598597 54 + 601863 AAGAAGTCTAGAGACTGGTTTAAAAAATATCCATATGATTCTAAGAT--CTGCCAA -s simRat_chr6.simRat.chr6 643419 56 + 647215 GAGCAGCCCAATGGGTAGTCTCCAAGAGAGCCTTCTAATCCCAAAATATCTGTCAC - -a -s simMouse_chr6.simMouse.chr6 632045 1 + 636262 A -s Anc0.Anc0refChr3 221610 1 + 222631 A -s Anc1.Anc1refChr1 66629 1 + 69767 A -s Anc2.Anc2refChr1 139561 1 + 142988 A -s mr.mrrefChr3 178346 1 + 181027 A -s simCow_chr6.simCow.chr6 598741 1 + 602619 A -s simDog_chr6.simDog.chr6 590420 1 + 593897 A -s simHuman_chr6.simHuman.chr6 598651 1 + 601863 A -s simRat_chr6.simRat.chr6 643475 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 632046 31 + 636262 TTGCCCATCCTTGTTTTTGTAGCATAACTTA -s Anc0.Anc0refChr3 221628 31 + 222631 TTGCCCAACCCAGTTGTTATAGCATAACTTA -s Anc1.Anc1refChr1 66647 31 + 69767 TTGCCCAACCCAGTTGTTATAGCATAACTTA -s Anc2.Anc2refChr1 139579 31 + 142988 TTACCCAATCCAGTTGTTATAACATAACTTA -s mr.mrrefChr3 178347 31 + 181027 TTGCCCATCCTTGTTTTTGTAGCATAACTTA -s simCow_chr6.simCow.chr6 598759 31 + 602619 CTACCCAGTCCAGTATTTATAAGATAATTTA -s simDog_chr6.simDog.chr6 590438 31 + 593897 TTACCCGATCCAGTTGTTATAACCTATCTTA -s simHuman_chr6.simHuman.chr6 598669 31 + 601863 TTGCCCAACTCAGTTGTTATAGCAAAACTTA -s simRat_chr6.simRat.chr6 643476 31 + 647215 TTGCCCATCCTTGTTCTTGTAACATAACTTA - -a -s simMouse_chr6.simMouse.chr6 632077 25 + 636262 CGATTCTTTATATTATACTCATCCA -s Anc0.Anc0refChr3 221659 15 + 222631 T----------ATTCTAATCACCGA -s Anc1.Anc1refChr1 66678 15 + 69767 T----------ATTCTAATCACCGA -s Anc2.Anc2refChr1 139610 15 + 142988 T----------ATTCTAATCACCGA -s mr.mrrefChr3 178378 25 + 181027 TGATTCTTTATATTCTACTCATCCA -s simCow_chr6.simCow.chr6 598799 14 + 602619 T----------ATTCTA-TTACCCA -s simDog_chr6.simDog.chr6 590469 11 + 593897 G----------AT----ACCACTGA -s simHuman_chr6.simHuman.chr6 598700 15 + 601863 T----------ATTCTAATCACCTA -s simRat_chr6.simRat.chr6 643507 25 + 647215 TGCTTTTGTATATTCTACCCATCCA - -a -s simMouse_chr6.simMouse.chr6 632102 48 + 636262 TAAACTCTAGTGTTGCTTTTGCCTCTAAAGATGAGTCATGCTTCATTT -s Anc0.Anc0refChr3 221693 39 + 222631 ---------ATGTTGCTTTCACCTTTAAGGGTAGGTTGCTCTTGATTT -s Anc1.Anc1refChr1 66712 48 + 69767 TCCACGATGATGTTGCTTTCACCTTTAAGGGTAGGTTGCTCTTGATTT -s Anc2.Anc2refChr1 139644 39 + 142988 ---------ATGTTGCTTTCACCTTTAAGGGCAGGTTGCTCTTGATTT -s mr.mrrefChr3 178403 48 + 181027 TAAACTCTAGTGTTGCTTTTGCCTTTAAAGATAAGTCATGCTTCATTT -s simCow_chr6.simCow.chr6 598832 38 + 602619 ---------ATGTTGCTTG-ATTGTTAATGGAAGATTGCTCTTGATTT -s simDog_chr6.simDog.chr6 590499 39 + 593897 ---------ATGATGCTTTCGCCTTTAAGGGCAGGTTGCCTTTGATCT -s simHuman_chr6.simHuman.chr6 598790 48 + 601863 TCCACGATGATGTTGCTTTCACCTTTAAGGGTAGGTTGCTCTTGATTT -s simRat_chr6.simRat.chr6 643532 48 + 647215 TAAACTTTAGTGTTGCTTTTGCATTTAAAGACAAGTCATGCTTCGTTT - -a -s simMouse_chr6.simMouse.chr6 632150 11 + 636262 TCATCCTCATT -s Anc0.Anc0refChr3 221735 4 + 222631 T-------ATT -s Anc1.Anc1refChr1 66763 11 + 69767 TCACCCTCATT -s Anc2.Anc2refChr1 139686 4 + 142988 T-------GTT -s mr.mrrefChr3 178451 11 + 181027 TCATCCTCATT -s simCow_chr6.simCow.chr6 598873 4 + 602619 T-------GTT -s simDog_chr6.simDog.chr6 590541 4 + 593897 G-------GTT -s simHuman_chr6.simHuman.chr6 598841 11 + 601863 TCACCCTCATT -s simRat_chr6.simRat.chr6 643580 11 + 647215 TCATCCTCATT - -a -s simMouse_chr6.simMouse.chr6 632161 21 + 636262 CAGGTCCCTAAAAGAATCCCG -s Anc0.Anc0refChr3 221739 20 + 222631 CAA-TTCCTATAAGATTCCAG -s Anc1.Anc1refChr1 66774 21 + 69767 CAACTTCCTATAAGATTCCAG -s Anc2.Anc2refChr1 139690 20 + 142988 CAA-TTCCTATAAGATGCCAG -s mr.mrrefChr3 178462 21 + 181027 CAGGTCCCTAAAAGAATCCCG -s simCow_chr6.simCow.chr6 598880 20 + 602619 CAA-TTCTTACAAGATGACAA -s simDog_chr6.simDog.chr6 590545 20 + 593897 CAA-TGCCTATAAGATGCCAG -s simHuman_chr6.simHuman.chr6 598852 21 + 601863 CAACTTCCTATAAGACTCCAG -s simRat_chr6.simRat.chr6 643591 21 + 647215 TTGGACCCTACACGAATCCTG - -a -s simMouse_chr6.simMouse.chr6 632182 38 + 636262 TAAGTCTAGATGAACCTCGTGCAAGGAGCTGTAAAGGG -s Anc0.Anc0refChr3 221759 16 + 222631 TAAACCTGGATGAAAC---------------------- -s Anc1.Anc1refChr1 66795 16 + 69767 TAAACCTGGATGAAAC---------------------- -s Anc2.Anc2refChr1 139712 16 + 142988 TAAACGTGGATGAAAC---------------------- -s mr.mrrefChr3 178483 16 + 181027 TAAGTCTAGATGAACC---------------------- -s simCow_chr6.simCow.chr6 598902 15 + 602619 TAAAC-TGGATGAACC---------------------- -s simDog_chr6.simDog.chr6 590567 16 + 593897 TAAATGTGGATGAAAC---------------------- -s simHuman_chr6.simHuman.chr6 598873 7 + 601863 TAAACCT------------------------------- -s simRat_chr6.simRat.chr6 643612 16 + 647215 TAAGTCTAAATGAACT---------------------- - -a -s simMouse_chr6.simMouse.chr6 632220 24 + 636262 CATGAGAGTTGTCATGCTAGCAGT -s Anc0.Anc0refChr3 221775 23 + 222631 CATAGAAGGTCTAATGATA-GGAT -s Anc1.Anc1refChr1 66811 24 + 69767 CATAGAAGGTCTAATGATAGGGAT -s Anc2.Anc2refChr1 139750 23 + 142988 CATAGAAGGTCTAAGGATA-GGAT -s mr.mrrefChr3 178499 24 + 181027 CATGAGAGTTGTCATGCTAGCAGT -s simCow_chr6.simCow.chr6 598939 23 + 602619 CATTAGAATTGTAATGATA-GTAC -s simDog_chr6.simDog.chr6 590605 23 + 593897 CATAGAAGGTCTAAGGATA-GGAT -s simHuman_chr6.simHuman.chr6 598880 10 + 601863 --------------TGTTAGGGAT -s simRat_chr6.simRat.chr6 643628 24 + 647215 CATAGGCAACCTTAAGCTGCCACT - -a -s simMouse_chr6.simMouse.chr6 632244 94 + 636262 GATAGCAGGAAAGAATATAACCTAAGGTTGGATTCCAAGTCACTCCTCTAACTCAATTATTGAAATGTAAGACAGTTCTAGGATCCTCATAGAC -s Anc0.Anc0refChr3 221798 92 + 222631 GATAGGAGGAAAGATCATAAACTA--GTTGGATTCCATATCACTTTTCTAGTTCAATTATTAAGATGAAATACAGCTCTAGGAGTCTCACAGGC -s Anc1.Anc1refChr1 66835 94 + 69767 GATAGGAGGAAAGATCATAAACTATGGTTGGATTCCATATCACTTTTCTAGTTCAATTATTAAGATGAAATACAGCTCTAGGAGTCTCACAGGC -s Anc2.Anc2refChr1 139773 92 + 142988 GATAGGGGGAAAGATCATAAACTA--GTTGGATTCCATATCAGTTTTCTAGTTCAGTTATTAAGATGAGATACAACTCTAGGAGTCTCACAGGC -s mr.mrrefChr3 178523 94 + 181027 GATAGCAGGAAAGAATATAACCTAAGGTTGGATTCCAAGTCACTCCTCTAACTCAATTATTGAGATGTAAGACAGTTCTAGGATTCTCATAGAC -s simCow_chr6.simCow.chr6 598963 92 + 602619 GACAGCGGAAAAAATCATAAACTA--GTTGGCTTCTGTATCATTCTTCTCGTTCAGTTATAAAGAGGTGATACAACTCTAGGAGTTTGACAGGC -s simDog_chr6.simDog.chr6 590628 92 + 593897 GATAGGGGGAAAGATCATAAACTA--GTTGGATTTCATTTCAGTTTTCTAATTCAGTTATTTAGATGAGATATAACCCTAGGAGCCTCATCAAC -s simHuman_chr6.simHuman.chr6 598890 91 + 601863 GATAGAAGGGAAGATCATAA---ATGATTGGATGCCATATCACTAACCTAGTTTAATTGTTAAGATGCAACACAGCTCTAGGAATCCCGCAGGC -s simRat_chr6.simRat.chr6 643652 65 + 647215 --TAGCTTTATGACATATTACAT----TTAGGTCACAAGTC------------------CTGAGAGGTGTGGTGGTGCTGAGATTGTC-----C - -a -s simMouse_chr6.simMouse.chr6 632338 18 + 636262 AACCTTAAGCTGTCACTT -s Anc0.Anc0refChr3 221890 18 + 222631 AATGTCAAGCTGTCACCT -s Anc1.Anc1refChr1 66929 18 + 69767 AATGTCAAGCTGTCACCT -s Anc2.Anc2refChr1 139865 18 + 142988 AATGTCGAGCTGCCACCT -s mr.mrrefChr3 178617 18 + 181027 AACCTTAAGCTGTCACTT -s simCow_chr6.simCow.chr6 599055 17 + 602619 AGTGCCT-GCTGCTATCT -s simDog_chr6.simDog.chr6 590729 18 + 593897 AACGTTGAACTGCCACCt -s simHuman_chr6.simHuman.chr6 598981 18 + 601863 AATGTCAAGCTATCCCCT -s simRat_chr6.simRat.chr6 643717 3 + 647215 AAC--------------- - -a -s simMouse_chr6.simMouse.chr6 632356 6 + 636262 AGTTTT -s Anc0.Anc0refChr3 221911 6 + 222631 AGtttt -s Anc1.Anc1refChr1 66950 6 + 69767 AGTTTT -s Anc2.Anc2refChr1 139886 6 + 142988 AAtttt -s mr.mrrefChr3 178635 6 + 181027 AGTTTT -s simCow_chr6.simCow.chr6 599075 2 + 602619 AT---- -s simDog_chr6.simDog.chr6 590750 6 + 593897 aatttt -s simHuman_chr6.simHuman.chr6 599002 6 + 601863 AGTTTT -s simRat_chr6.simRat.chr6 643720 1 + 647215 -----T - -a -s simMouse_chr6.simMouse.chr6 632362 4 + 636262 ATGA -s Anc0.Anc0refChr3 221942 4 + 222631 GTgg -s Anc1.Anc1refChr1 66981 4 + 69767 GTGG -s Anc2.Anc2refChr1 139917 4 + 142988 GTgg -s mr.mrrefChr3 178641 4 + 181027 GTGG -s simCow_chr6.simCow.chr6 599084 4 + 602619 GTGG -s simDog_chr6.simDog.chr6 590781 4 + 593897 gtgg -s simHuman_chr6.simHuman.chr6 599041 4 + 601863 GTAG -s simRat_chr6.simRat.chr6 643721 4 + 647215 GTGG - -a -s simMouse_chr6.simMouse.chr6 632366 15 + 636262 CACAACTGAGGTCAA -s Anc0.Anc0refChr3 221946 15 + 222631 TATAAAAGCTGTTAA -s Anc1.Anc1refChr1 66985 15 + 69767 TATAAAAGCTGTTAA -s Anc2.Anc2refChr1 139925 15 + 142988 TATAAAAGCTGCTAA -s mr.mrrefChr3 178645 15 + 181027 TACAACTGAGGTCAA -s simCow_chr6.simCow.chr6 599092 15 + 602619 TATGAAAGGTGCCAA -s simDog_chr6.simDog.chr6 590789 15 + 593897 taTAAAAGCAGCTAA -s simHuman_chr6.simHuman.chr6 599045 15 + 601863 TATAAAAGCTGTTGA -s simRat_chr6.simRat.chr6 643725 15 + 647215 TCAACTTGTGGTCAA - -a -s simMouse_chr6.simMouse.chr6 632381 46 + 636262 CAACCACAAACCATATAGTCTAAAGACTTGTTCAGTGTATCAGATG -s Anc0.Anc0refChr3 221968 46 + 222631 CAACCATAAACCATATAGTATAAAAACTTGTTTAGTGTATAAAGCA -s Anc1.Anc1refChr1 67007 46 + 69767 CAACCATAAACCATATAGTATAAAAACTTGTTTAGTGTATAAAGCA -s Anc2.Anc2refChr1 139947 46 + 142988 CAACCATAAATCATTTAGTATAAAAACTCGTTTAGTGTATAAAGCA -s mr.mrrefChr3 178660 46 + 181027 CAACCACAAACCATATAGTATAAAGACTTGTTTAGTGTATCAAATG -s simCow_chr6.simCow.chr6 599114 46 + 602619 CAGCTATGAAGTATTTAGTATAAAAAGTCCTTTATTGTATAAAGCA -s simDog_chr6.simDog.chr6 590809 44 + 593897 --ACCATAAGTCATTTAGTATTAGAACTCGTTTAGTCCATAAAGTA -s simHuman_chr6.simHuman.chr6 599067 46 + 601863 CCACCAAAAACCAAACAGTATAAAAACTTGTTTAGTGTATAAAGCA -s simRat_chr6.simRat.chr6 643740 46 + 647215 CAACCATAAATCATATAGTATAAAGACTTGTTTAGTGTATCAAATG - -a -s simMouse_chr6.simMouse.chr6 632427 31 + 636262 TGCTAATGGTAACAACTAGATGAGCTGAAGT -s Anc0.Anc0refChr3 222015 31 + 222631 TGGTAATGCTAAGAATTAAGTGTATGGCAGT -s Anc1.Anc1refChr1 67054 31 + 69767 TGGTAATGCTAAGAATTAAGTGTATGGCAGT -s Anc2.Anc2refChr1 139994 31 + 142988 TGGTAATGCTAAGAATTAAGTGTATGGCAGT -s mr.mrrefChr3 178706 31 + 181027 TGCTAATGGTAACAACTAGATGAGCTGAAGT -s simCow_chr6.simCow.chr6 599161 31 + 602619 TGGTAACACTAATGGCAAAGTGTACCGCAGT -s simDog_chr6.simDog.chr6 590854 31 + 593897 TGACAATGCCAAGAATTAAGTGTATGGCGGT -s simHuman_chr6.simHuman.chr6 599114 23 + 601863 TGGTGATGCTAATGTTT--------GGCAGT -s simRat_chr6.simRat.chr6 643786 31 + 647215 TGCTAATGGTAACAACTAAATGAGCTGAAGT - -a -s simMouse_chr6.simMouse.chr6 632458 19 + 636262 AATTAGTTAGGCATATATA -s Anc0.Anc0refChr3 222051 18 + 222631 TATTGGTTAGGG-TGTATA -s Anc1.Anc1refChr1 67090 19 + 69767 TATTGGTTAGGGTTGTATA -s Anc2.Anc2refChr1 140030 18 + 142988 TATTAGTTAGGG-TGTATA -s mr.mrrefChr3 178737 19 + 181027 AATTGGTTAGGCATATATA -s simCow_chr6.simCow.chr6 599197 18 + 602619 TGTTAGTTAGGT-TATATA -s simDog_chr6.simDog.chr6 590890 18 + 593897 TATCAGTTAGCG-TGTATA -s simHuman_chr6.simHuman.chr6 599142 19 + 601863 TATTGGTTAGGGTTGTATA -s simRat_chr6.simRat.chr6 643817 19 + 647215 AATTGGTTAGGTGTATATA - -a -s simMouse_chr6.simMouse.chr6 632477 6 + 636262 GTGGCT -s Anc0.Anc0refChr3 222073 6 + 222631 AAGCCT -s Anc1.Anc1refChr1 67113 6 + 69767 AAGCCT -s Anc2.Anc2refChr1 140052 6 + 142988 AAGCTT -s mr.mrrefChr3 178756 6 + 181027 GTGGCT -s simCow_chr6.simCow.chr6 599219 5 + 602619 A-GCTT -s simDog_chr6.simDog.chr6 590911 5 + 593897 -AGCTT -s simHuman_chr6.simHuman.chr6 599170 6 + 601863 ACATCT -s simRat_chr6.simRat.chr6 643836 6 + 647215 GTGGCT - -a -s simMouse_chr6.simMouse.chr6 632483 1 + 636262 T -s Anc0.Anc0refChr3 222079 1 + 222631 C -s Anc1.Anc1refChr1 67119 1 + 69767 C -s Anc2.Anc2refChr1 140058 1 + 142988 C -s mr.mrrefChr3 178762 1 + 181027 T -s simCow_chr6.simCow.chr6 599224 1 + 602619 C -s simDog_chr6.simDog.chr6 590916 1 + 593897 C -s simHuman_chr6.simHuman.chr6 599177 1 + 601863 C -s simRat_chr6.simRat.chr6 643842 1 + 647215 T - -a -s simMouse_chr6.simMouse.chr6 632484 16 + 636262 TAATGAAAGTGTGGTG -s Anc0.Anc0refChr3 222080 16 + 222631 CCATGAAAGATTGGGG -s Anc1.Anc1refChr1 67120 16 + 69767 CCATGAAAGATTGGGG -s Anc2.Anc2refChr1 140059 16 + 142988 CCATGAAATATTGGGG -s mr.mrrefChr3 178763 16 + 181027 TAATGAAAGTTTGGTG -s simCow_chr6.simCow.chr6 599227 16 + 602619 CCATAAAACATTGGGG -s simDog_chr6.simDog.chr6 590917 16 + 593897 TCATGATATATCAGCC -s simHuman_chr6.simHuman.chr6 599178 16 + 601863 CCATGGAAGATTGGGG -s simRat_chr6.simRat.chr6 643843 16 + 647215 TAATGAGAGCTTGGTG - -a -s simMouse_chr6.simMouse.chr6 632500 24 + 636262 AGGAGAAAATGAACTTGTTAATTG -s Anc0.Anc0refChr3 222096 24 + 222631 AGGAGGAAACCAGTTTATTGATTG -s Anc1.Anc1refChr1 67136 24 + 69767 AGGAGGAAACCAGTTTATTGATTG -s Anc2.Anc2refChr1 140075 24 + 142988 AGGAGGAAACCAGTTTATTGATTG -s mr.mrrefChr3 178779 24 + 181027 AGGAGAAAATGAACTTGTTAATTG -s simCow_chr6.simCow.chr6 599245 24 + 602619 AAGAGGAAACCAGATTATTAATTC -s simDog_chr6.simDog.chr6 590933 24 + 593897 AGTAGGAAAAAAGTTTATAGATTG -s simHuman_chr6.simHuman.chr6 599194 24 + 601863 AGGAGGACACCAGTCTATTGATTG -s simRat_chr6.simRat.chr6 643859 24 + 647215 AAGAGAAAATGAACTTGTCCGTTG - -a -s simMouse_chr6.simMouse.chr6 632524 43 + 636262 TTAGGTTGTATTAGTTAGTCTTGGCATTGGATTTGCTGGTCAA -s Anc0.Anc0refChr3 222120 43 + 222631 TTAGTTTATATTAGTTTGTCTTGACATTAAGCTTGCTTGTCAA -s Anc1.Anc1refChr1 67160 43 + 69767 TTAGTTTATATTAGTTTGTCTTGACATTAAGCTTGCTTGTCAA -s Anc2.Anc2refChr1 140099 43 + 142988 TTAGTTTATATTAGTTTGTATTGACATTAAGCTTGCTTGTCAA -s mr.mrrefChr3 178803 43 + 181027 TTAGGTTGTATTAGTTTGTCTTGGCATTGGATTTGCTGGTCAA -s simCow_chr6.simCow.chr6 599269 40 + 602619 TCAGTTTAA---AGCTTGTATTAGTGTTAAGCTTGCTTGTCAA -s simDog_chr6.simDog.chr6 590957 43 + 593897 TTATTCTGTATTAGTTCGTAAAGACAGTAAGCTTGCTTGTCAA -s simHuman_chr6.simHuman.chr6 599219 43 + 601863 TTAGTTCATGTTAGTTTGTCTTGCCATTAAGCTTGCTTGTCAG -s simRat_chr6.simRat.chr6 643883 43 + 647215 TTAGGTAGTATTAGTTTGTCTTGGCATTGGATATGCTGGTCAA - -a -s simMouse_chr6.simMouse.chr6 632567 1 + 636262 A -s Anc0.Anc0refChr3 222163 1 + 222631 A -s Anc1.Anc1refChr1 67203 1 + 69767 A -s Anc2.Anc2refChr1 140149 1 + 142988 A -s mr.mrrefChr3 178846 1 + 181027 A -s simDog_chr6.simDog.chr6 591007 1 + 593897 A -s simHuman_chr6.simHuman.chr6 599262 1 + 601863 A -s simRat_chr6.simRat.chr6 643926 1 + 647215 A - -a -s simMouse_chr6.simMouse.chr6 632568 33 + 636262 GGTATATTGCCAAGACTATCTAACGAGGAATAT -s Anc0.Anc0refChr3 222164 28 + 222631 GGTAT--AACCTGGGCTAT---ACAAGTAATAT -s Anc1.Anc1refChr1 67204 28 + 69767 GGTAT--AACCTGGGCTAT---ACAAGTAATAT -s Anc2.Anc2refChr1 140150 28 + 142988 GGTAT--AACCTGGACTAT---CTAACTAATAG -s mr.mrrefChr3 178847 31 + 181027 GGTAT--TGCCTAGGCTATCTAACAAGTAATAT -s simCow_chr6.simCow.chr6 599315 28 + 602619 GCAAT--AGCCTGAACTAT---CTATCACATGG -s simDog_chr6.simDog.chr6 591008 27 + 593897 GGTAT--AATCTAGACTAT---CTAACTA-TAG -s simHuman_chr6.simHuman.chr6 599291 28 + 601863 GGTAT--AACCTGGGCTGG---ACAAGTAATAT -s simRat_chr6.simRat.chr6 643927 31 + 647215 GGTAT--TGCCTAGGCTATCTAACAAATAATAT - -a -s simMouse_chr6.simMouse.chr6 632601 37 + 636262 AGGTCAGGATTGGGGGTTATTTATCGCCCTGTTATAG -s Anc0.Anc0refChr3 222192 36 + 222631 AGGTTAG-ATTGGGGGTTTTTTACCCTCTGGCTATAG -s Anc1.Anc1refChr1 67232 36 + 69767 AGGTTAG-ATTGGGGGTTTTTTACCCTCTGGCTATAG -s Anc2.Anc2refChr1 140178 36 + 142988 GGCTTAG-ATTGTGGGTTTTTAACCCTCTGGCAATAG -s mr.mrrefChr3 178878 36 + 181027 AGGTCAG-ATTGGGGGTTATTTACCGCCCTGCTATAG -s simCow_chr6.simCow.chr6 599348 36 + 602619 GGCCAAG-ATTATGGCTTTGTAACCTTCTGGCAATAG -s simDog_chr6.simDog.chr6 591035 35 + 593897 GTCTTAG-ATAGTGCGTTTTG-ACCCTCTGGCAATAG -s simHuman_chr6.simHuman.chr6 599319 36 + 601863 AGGTTAG-CTTGGGGGTTTTTTACCCTCTGACTACAG -s simRat_chr6.simRat.chr6 643958 36 + 647215 GGGTCAG-ATTGGGGGTTATTTACCACCCTGCTATTG - -a -s simMouse_chr6.simMouse.chr6 632638 11 + 636262 AATCTTACCAG -s Anc0.Anc0refChr3 222231 11 + 222631 AACCCCGCCAA -s Anc1.Anc1refChr1 67271 11 + 69767 AACCCCGCCAA -s Anc2.Anc2refChr1 140217 11 + 142988 AACCTCGCCCA -s mr.mrrefChr3 178917 11 + 181027 AATCCTACCAG -s simCow_chr6.simCow.chr6 599387 11 + 602619 AATCTCGCCTA -s simDog_chr6.simDog.chr6 591073 11 + 593897 AACTTAACCCA -s simHuman_chr6.simHuman.chr6 599358 11 + 601863 AACCCCGCCAA -s simRat_chr6.simRat.chr6 643998 11 + 647215 AATGCTACCAG - -a -s simMouse_chr6.simMouse.chr6 632649 17 + 636262 GGGACCCATGGTCAGGT -s Anc0.Anc0refChr3 222249 17 + 222631 GCGTACCATGGTCAGGT -s Anc1.Anc1refChr1 67289 17 + 69767 GCGTACCATGGTCAGGT -s Anc2.Anc2refChr1 140235 17 + 142988 GCATACCATGGGCAGGT -s mr.mrrefChr3 178935 17 + 181027 GGGACCCATGGTCAGGT -s simCow_chr6.simCow.chr6 599405 17 + 602619 GCATACCATGGGGAGGT -s simDog_chr6.simDog.chr6 591088 9 + 593897 --------TGGGCATGT -s simHuman_chr6.simHuman.chr6 599376 17 + 601863 TTGTACCATGGTCAGAT -s simRat_chr6.simRat.chr6 644016 16 + 647215 GGGACCCATG-TCATGT - -a -s simMouse_chr6.simMouse.chr6 632666 7 + 636262 TTTGCAA -s Anc0.Anc0refChr3 222277 7 + 222631 TTCGTAG -s Anc1.Anc1refChr1 67317 7 + 69767 TTCGTAG -s Anc2.Anc2refChr1 140263 7 + 142988 TTCAGAG -s mr.mrrefChr3 178952 7 + 181027 TTTGTAA -s simCow_chr6.simCow.chr6 599425 1 + 602619 ------G -s simDog_chr6.simDog.chr6 591108 7 + 593897 TTCAGAG -s simHuman_chr6.simHuman.chr6 599404 7 + 601863 TTCGTAG -s simRat_chr6.simRat.chr6 644032 7 + 647215 TTTGTAA - -a -s simMouse_chr6.simMouse.chr6 632673 8 + 636262 GTGCAAAA -s Anc0.Anc0refChr3 222287 8 + 222631 GCGCAAAC -s Anc1.Anc1refChr1 67327 8 + 69767 GCGCAAAC -s Anc2.Anc2refChr1 140273 8 + 142988 GCACAAAC -s mr.mrrefChr3 178959 8 + 181027 GTGCAAAA -s simCow_chr6.simCow.chr6 599429 8 + 602619 GCACAAAC -s simDog_chr6.simDog.chr6 591118 8 + 593897 GGACAAAC -s simHuman_chr6.simHuman.chr6 599414 8 + 601863 GCGCAAAC -s simRat_chr6.simRat.chr6 644039 8 + 647215 TTACAAAA - -a -s simMouse_chr6.simMouse.chr6 632681 19 + 636262 CTTCATCTGGCCAAATGTG -s Anc0.Anc0refChr3 222295 17 + 222631 CT--ACTTGGGCAAGTGTG -s Anc1.Anc1refChr1 67335 17 + 69767 CT--ACTTGGGCAAGTGTG -s Anc2.Anc2refChr1 140282 17 + 142988 CT--ACTTGGGTAAGTGTG -s mr.mrrefChr3 178967 19 + 181027 CTTCATTTGGCCAAATGTG -s simCow_chr6.simCow.chr6 599438 17 + 602619 TT--TTTTGGCTAAGTGCG -s simDog_chr6.simDog.chr6 591127 17 + 593897 CT--ACTTGAGTAAGTGTG -s simHuman_chr6.simHuman.chr6 599422 17 + 601863 CT--AATCGGGCACTTGTG -s simRat_chr6.simRat.chr6 644047 19 + 647215 CTTCATTTGGCCAAATGTG - -a -s simMouse_chr6.simMouse.chr6 632700 211 + 636262 CAAAAGATAAGGACAAATATTACTCCCATTTGAGGGTCGAAAATTTTAACAGGGTAGAACATTTTAACTCTTAAAGTTATCAGGTATACACCCTTGATTCAGCTGTCCTTTTATACATGGCAGTCTCTTTGTGTTCTCGAGTGTGATGTACTGGTTGTTTTTGGGCAGACTAATGCACCACTTATAGAAAGCACTTGCCAAGTATTATGGG -s Anc0.Anc0refChr3 222312 42 + 222631 CAAGACACAAGAACAAACATCAC-------------------------------------------------------------------------------------------------------------------------------------------------------------------------AAATGATAAGTGTTATAAG -s Anc1.Anc1refChr1 67352 42 + 69767 CAAGACACAAGAACAAACATCAC-------------------------------------------------------------------------------------------------------------------------------------------------------------------------AAATGATAAGTGTTATAAG -s Anc2.Anc2refChr1 140299 42 + 142988 CAAGACACCACAACAAACATCAC-------------------------------------------------------------------------------------------------------------------------------------------------------------------------AAATGATAAGTGTTATAAG -s mr.mrrefChr3 178986 159 + 181027 CAAAAGATAAGGACAAATATTACTCCCATTTGAGGGTCGAAAATTTTAACAGGGTAGAACATTTTAACTCTTAAAGTTATCAGGTATACACCCTTGATTCAGCTGTCCTTTTA----------------------------------------------------CAGACTAATGCACCACTTATAGAAAGCACTTGCCAAGTATTATGGG -s simCow_chr6.simCow.chr6 599458 41 + 602619 CAAAACACCACAACAAACATCA--------------------------------------------------------------------------------------------------------------------------------------------------------------------------AAATAATAAGTGTTACAAG -s simDog_chr6.simDog.chr6 591144 42 + 593897 CAAGACACCACAACAAATGTCAC-------------------------------------------------------------------------------------------------------------------------------------------------------------------------AAGAGATTAGTGTTATGAG -s simHuman_chr6.simHuman.chr6 599439 42 + 601863 TAACATACAAGAACAAACATCAC-------------------------------------------------------------------------------------------------------------------------------------------------------------------------AAATGATAGTTGTTATAAG -s simRat_chr6.simRat.chr6 644066 159 + 647215 CAGAACATAAGGACAAATATTCCTCCGGTTAGAGCGTAGAAAATTTTGACGGGGTAGAAGACTTCAACTCTGAAATTTATCAAGAAGGCACCCTTGATTCAGCTGTTCATTTA----------------------------------------------------CAGACTAACGCTCTTCTTATAGAAAGCACTTGGTAAGCATTACGGG - -a -s simMouse_chr6.simMouse.chr6 632911 198 + 636262 AACTTTCAAGAGTTTAAATGCTTGTAGAGTGCTTTTAGGGACCGCACTGTAAGCATTTTTGAGTTTAGAGCAACAGTGAAATTGGGAGGTAGGACATTTCCTATGGAACCCGTCAACAGCATGGTCCTAACCCCAGAATCCATGTCTACTACTATATAGTCTCGCGATGAGAGTTAAGACACCCACATAGGACATCTA -s Anc0.Anc0refChr3 222354 62 + 222631 AGCTTTTAAGAAGTTGAATACTCTTAGAGTGTTTCTA----------------------------------------------------------------------------------------------------------------------------------------TTAAGACCCCATCACAGGCCATCTA -s Anc1.Anc1refChr1 67394 62 + 69767 AGCTTTTAAGAAGTTGAATACTCTTAGAGTGTTTCTA----------------------------------------------------------------------------------------------------------------------------------------TTAAGACCCCATCACAGGCCATCTA -s Anc2.Anc2refChr1 140341 62 + 142988 TGCTTTTAAGAAGTTGGATACTCTTAGAGTGTTTCTA----------------------------------------------------------------------------------------------------------------------------------------TTAAGACCCCATTACAGGCCATCTA -s mr.mrrefChr3 179145 62 + 181027 AGCTGTCAAGAATTTAAATGCTTGTAGAGTGCTTTTA----------------------------------------------------------------------------------------------------------------------------------------TTAAGACACCCTCATAGGACATCTA -s simCow_chr6.simCow.chr6 599499 62 + 602619 TGCTTTTAAGAAGTTGGATACTCTTAGAGTGTTTCTA----------------------------------------------------------------------------------------------------------------------------------------TTAAGACCCCTTTAATGGCCATCTA -s simDog_chr6.simDog.chr6 591186 62 + 593897 TGCTTTTAAGAGGTTGGATACTCTTAGAGTTCCTTTA----------------------------------------------------------------------------------------------------------------------------------------CTGAGACCCCATTACAGGCCATTTA -s simHuman_chr6.simHuman.chr6 599482 62 + 601863 ATTTTTTTAGAAGTTTAATAATCATAGAGTGTTTCTA----------------------------------------------------------------------------------------------------------------------------------------TTAAGACCCCATCGCAGGCCATCTA -s simRat_chr6.simRat.chr6 644225 62 + 647215 AGCTGTCGAGAATTTAAATGCTTGTAAAGTGCTTTTA----------------------------------------------------------------------------------------------------------------------------------------TTAAGACACCCTTCTGGGACATCTA - -a -s simMouse_chr6.simMouse.chr6 633109 45 + 636262 CTAAATACCTTAGTATAAACCTTTGACTACGCTACGTTGTCCTTC -s Anc0.Anc0refChr3 222417 40 + 222631 CCAAATACCTTAGTTTGAAACACTGGCTGTG-----TTGTCCTTC -s Anc1.Anc1refChr1 67457 40 + 69767 CCAAATACCTTAGTTTGAAACACTGGCTGTG-----TTGTCCTTC -s Anc2.Anc2refChr1 140404 40 + 142988 CCAAAGACCTTCGTTTGAAACACTGGCTGTG-----TTGTCCTTC -s mr.mrrefChr3 179208 40 + 181027 CTAAATACCTTAGTATAAAACATTGACTATG-----TTGTCCTTC -s simCow_chr6.simCow.chr6 599562 40 + 602619 ACAAAGACCTTCGTTTGAAACACTGGCTGTG-----TCGTCATTC -s simDog_chr6.simDog.chr6 591249 31 + 593897 CCAA---------TTTGAAACGCTACCTGCC-----TTGTCCTTC -s simHuman_chr6.simHuman.chr6 599545 40 + 601863 TAAAATACCTTAGTTTGAAACACTGGCTCTG-----ATGACCTTC -s simRat_chr6.simRat.chr6 644288 40 + 647215 CTAAATACCTTAGTATAAAACATTGACTATG-----TTGTCCTTG - -a -s simMouse_chr6.simMouse.chr6 633154 7 + 636262 CCCTTCA -s Anc0.Anc0refChr3 222457 7 + 222631 CTCTTCC -s Anc1.Anc1refChr1 67497 7 + 69767 CTCTTCC -s Anc2.Anc2refChr1 140444 7 + 142988 CTCTTCC -s mr.mrrefChr3 179248 7 + 181027 CTCTTCA -s simCow_chr6.simCow.chr6 599604 7 + 602619 CACTCCC -s simDog_chr6.simDog.chr6 591280 7 + 593897 TTGTTAC -s simHuman_chr6.simHuman.chr6 599585 7 + 601863 CTCTTCC -s simRat_chr6.simRat.chr6 644328 7 + 647215 CTCCTCA - -a -s simMouse_chr6.simMouse.chr6 633167 2 + 636262 CC -s mr.mrrefChr3 179261 2 + 181027 TC -s simRat_chr6.simRat.chr6 644341 2 + 647215 TA - -a -s simMouse_chr6.simMouse.chr6 633180 33 + 636262 AGATGTCACAGCGCTAAATATTTCATATATCAA -s mr.mrrefChr3 179274 33 + 181027 AGATGTCACAGCGCTAAATATTTCATATATCAA -s simRat_chr6.simRat.chr6 644354 33 + 647215 AGATGTCGCAGTGCTATATGTTCCATATATCGA - -a -s simMouse_chr6.simMouse.chr6 633213 142 + 636262 ACCCATGCTTACCAGTTTATCTCTTGTTTTTGACCAGCTATTAAGAGGTCACAATGCAATGTCTTTTAAATGGAACAGTAGCTAAGAGGTTGTCTCTTATTTAATAAGCTGTAAAACACTGTGGACTACCTATCACTAGTTA -s mr.mrrefChr3 179307 138 + 181027 ACCCATGCTTACCAGTTTATCTCTTGTTTTTGACCAGCTATTAAGAGGTCACAATGCAATGTCTTTTAAATGGAACAGTAG----GAGGTTGTCTCTTATTTAATAAGCTGTAAAACACTGTGGACTACCTATCACTAGTTA -s simRat_chr6.simRat.chr6 644389 138 + 647215 ACCCATGCTTACCAGTCTATCTCTTGTTTTTGACCAGCTATTAAGAGGATAAAGTGCAATGTCTTCTCAATAGAACAATAT----GAGGTTTTCTATTATTTAATAAGCTACAAAACACTGTGGACTATCTATCACCAGTTA - -a -s simMouse_chr6.simMouse.chr6 633355 135 + 636262 GTAGTCCCTCCATAGCAACTACTAGATATCATAAGGACAGGAGAATAGAATAAATAGATTCCTTGTAGACTAATTCTAATGAATCAAGACTGGGCTGCCTGGAATAGTTTGCATATAATGCTGTCAAGCGGATTT -s mr.mrrefChr3 179445 125 + 181027 GTAGTCCCTCCATAGCAACT-CTAGATATCATAAGGACAGGAGAATAGAATAAATAGATTCCTTGTAGACTAATTCTAATGAAT---------GCTGCCTGGAATAGTTTGCATATAATGCTGTCAAGCGGATTT -s simRat_chr6.simRat.chr6 644538 125 + 647215 GTAATCCCTTCATACCAACT-CTAGATGTCCTGAGGACAGGAGAATTGACTAAATAGATGCCTTGCAAACTAAGTGTGACGGAT---------GCTGCTTGGAGTCGTTAGCATAAACTGCTGTCAAGCGCATTT - -a -s simMouse_chr6.simMouse.chr6 633504 5 + 636262 AATGA -s Anc0.Anc0refChr2 15784 5 + 17989 ATTAG -s Anc1.Anc1refChr2 123358 5 - 144309 ATTAG -s Anc2.Anc2refChr0 14309 5 - 56053 ATTAG -s mr.mrrefChr3 179584 5 + 181027 AATGA -s simCow_chr6.simCow.chr6 557265 5 - 602619 ATTAG -s simDog_chr6.simDog.chr6 554742 5 - 593897 ATTAG -s simHuman_chr6.simHuman.chr6 562564 5 - 601863 ATTAG -s simRat_chr6.simRat.chr6 644677 5 + 647215 ACTGA - -a -s simMouse_chr6.simMouse.chr6 633509 2 + 636262 TC -s Anc0.Anc0refChr2 15789 2 + 17989 TG -s Anc1.Anc1refChr2 123363 2 - 144309 TG -s Anc2.Anc2refChr0 14317 2 - 56053 TG -s mr.mrrefChr3 179589 2 + 181027 TC -s simCow_chr6.simCow.chr6 557273 2 - 602619 TG -s simDog_chr6.simDog.chr6 554750 2 - 593897 TG -s simHuman_chr6.simHuman.chr6 562569 2 - 601863 TG -s simRat_chr6.simRat.chr6 644682 2 + 647215 GC - -a -s simMouse_chr6.simMouse.chr6 633511 2 + 636262 TG -s Anc0.Anc0refChr2 15791 2 + 17989 AG -s Anc1.Anc1refChr2 123365 2 - 144309 AG -s Anc2.Anc2refChr0 14319 2 - 56053 AG -s mr.mrrefChr3 179591 2 + 181027 TG -s simCow_chr6.simCow.chr6 557277 2 - 602619 AG -s simDog_chr6.simDog.chr6 554752 2 - 593897 AG -s simHuman_chr6.simHuman.chr6 562571 2 - 601863 AG -s simRat_chr6.simRat.chr6 644684 2 + 647215 TG - -a -s simMouse_chr6.simMouse.chr6 633513 8 + 636262 CGGCCACG -s Anc0.Anc0refChr2 15793 7 + 17989 ACCCC-CA -s Anc1.Anc1refChr2 123367 7 - 144309 ACCCC-CA -s Anc2.Anc2refChr0 14321 7 - 56053 ACCCC-TA -s mr.mrrefChr3 179593 8 + 181027 CGGCCACG -s simCow_chr6.simCow.chr6 557279 7 - 602619 ATGCC-TA -s simDog_chr6.simDog.chr6 554755 7 - 593897 ACCCC-TA -s simHuman_chr6.simHuman.chr6 562573 7 - 601863 ACACC-CA -s simRat_chr6.simRat.chr6 644686 8 + 647215 TGGCCCCC - -a -s simMouse_chr6.simMouse.chr6 633560 2 + 636262 CA -s Anc0.Anc0refChr2 15839 2 + 17989 GA -s Anc1.Anc1refChr2 123413 2 - 144309 GA -s Anc2.Anc2refChr0 14367 2 - 56053 TA -s mr.mrrefChr0 19818 2 + 130230 GA -s mr.mrrefChr3 179640 2 + 181027 CA -s simCow_chr6.simCow.chr6 557325 2 - 602619 TA -s simDog_chr6.simDog.chr6 554801 2 - 593897 TA -s simDog_chr6.simDog.chr6 591606 2 + 593897 CA -s simHuman_chr6.simHuman.chr6 562616 2 - 601863 GA -s simRat_chr6.simRat.chr6 13438 2 + 647215 GA -s simRat_chr6.simRat.chr6 644733 2 + 647215 CA - -a -s simMouse_chr6.simMouse.chr6 633563 3 + 636262 TGG -s Anc0.Anc0refChr2 15842 3 + 17989 TTA -s Anc1.Anc1refChr2 123416 3 - 144309 TTA -s Anc2.Anc2refChr0 14370 3 - 56053 TTA -s mr.mrrefChr3 179643 3 + 181027 TGG -s simCow_chr6.simCow.chr6 557328 3 - 602619 GTA -s simDog_chr6.simDog.chr6 554804 3 - 593897 TTA -s simDog_chr6.simDog.chr6 591609 3 + 593897 ATG -s simRat_chr6.simRat.chr6 644736 3 + 647215 TTG - -a -s simMouse_chr6.simMouse.chr6 633615 1 + 636262 G - -a -s simMouse_chr6.simMouse.chr6 633653 1 + 636262 G -s Anc0.Anc0refChr2 15931 1 + 17989 A -s Anc1.Anc1refChr2 123505 1 - 144309 A -s Anc2.Anc2refChr0 14459 1 - 56053 A -s mr.mrrefChr3 179732 1 + 181027 G -s simCow_chr6.simCow.chr6 557397 1 - 602619 A -s simDog_chr6.simDog.chr6 554893 1 - 593897 A -s simDog_chr6.simDog.chr6 591698 1 + 593897 A -s simHuman_chr6.simHuman.chr6 562705 1 - 601863 T -s simRat_chr6.simRat.chr6 644826 1 + 647215 G - -a -s simMouse_chr6.simMouse.chr6 633665 101 + 636262 TTTGTGCAAGTGACCTGACTGGAAAAGCAAATGGTGTACCACTGCCCACTAGGTCTTGCAATAATCTAGGGATGATTGTTTAGGGTTAGAACATAGGTATT -s Anc0.Anc0refChr3 222568 12 + 222631 -------AAGTG----GATTGGA------------------------------------------------------------------------------ -s Anc1.Anc1refChr1 67608 14 + 69767 -------AAGTG--CTGATTGGA------------------------------------------------------------------------------ -s Anc2.Anc2refChr1 140671 12 + 142988 -------AAGTA----GATTGTA------------------------------------------------------------------------------ -s mr.mrrefChr3 179744 101 + 181027 TTTGTGCAAGTGACCTGACTGGAAAAGCAAATGGTGTACCACTGCCCACTAGGTCTTGCAATAATCTAGGGATGATTGTTTAGGGTTAGAACATAGGTATT -s simCow_chr6.simCow.chr6 599853 12 + 602619 -------AAGTA----GTTTGTA------------------------------------------------------------------------------ -s simDog_chr6.simDog.chr6 591503 12 + 593897 -------AAGTA----GATTGTG------------------------------------------------------------------------------ -s simHuman_chr6.simHuman.chr6 599709 14 + 601863 -------AAGTG--CTGAATGGA------------------------------------------------------------------------------ -s simRat_chr6.simRat.chr6 644838 101 + 647215 TTTGTGCAAGTGACTCGACTGGAAAAGCAAGTGGTGTACCACTGCTCTCTAGGTCTTGCAGTAGTCTAATGATGAATGTGTAGTGTTGGACCATAGGTATT - -a -s simMouse_chr6.simMouse.chr6 633766 36 + 636262 TGATTAGTCTAATGACTAATGCATAAAATCTGCTGA -s mr.mrrefChr3 179845 36 + 181027 TGATTAGTCTAATGACTAATGCATAAAATCTGCTGA -s simRat_chr6.simRat.chr6 644951 36 + 647215 TGATCAGTCTAATGACGAACATCTAATATCTGCTGG - -a -s simMouse_chr6.simMouse.chr6 633802 23 + 636262 ATATTTAAATTTGTGCGGATAAT -s Anc0.Anc0refChr3 222580 10 + 222631 -------------TGCGAATTTC -s Anc1.Anc1refChr1 67622 10 + 69767 -------------TGCGAATTTC -s Anc2.Anc2refChr1 140683 10 + 142988 -------------TATGAAATTC -s mr.mrrefChr3 179881 23 + 181027 ATATTTAAATTTGTGCGGATAAT -s simCow_chr6.simCow.chr6 599865 10 + 602619 -------------CTTGAAATTC -s simDog_chr6.simDog.chr6 591515 10 + 593897 -------------TATGAAATGT -s simHuman_chr6.simHuman.chr6 599723 10 + 601863 -------------TGCAAATTTC -s simRat_chr6.simRat.chr6 644989 23 + 647215 ATATTTAAAATTATGCAATTAAT - -a -s simMouse_chr6.simMouse.chr6 633825 14 + 636262 TCAAAAGGTAAAGT -s Anc0.Anc0refChr3 222590 9 + 222631 TCAATGGAG----- -s Anc1.Anc1refChr1 67632 9 + 69767 TCAATGGAG----- -s Anc2.Anc2refChr1 140693 9 + 142988 GTAGTGTAG----- -s mr.mrrefChr3 179904 13 + 181027 TCAAAGGGTAA-GT -s simCow_chr6.simCow.chr6 599875 7 + 602619 --AGTATAG----- -s simDog_chr6.simDog.chr6 591526 9 + 593897 GTAGTGTAG----- -s simHuman_chr6.simHuman.chr6 599733 9 + 601863 TCAATGGAG----- -s simRat_chr6.simRat.chr6 645012 13 + 647215 TTAAAGGGTAA-GT - -a -s simMouse_chr6.simMouse.chr6 633839 19 + 636262 GAATGGCCCAATGATTTGG -s Anc0.Anc0refChr3 222599 17 + 222631 GGATGACTCAATTGGTT-- -s Anc1.Anc1refChr1 67641 17 + 69767 GGATGACTCAATTGGTT-- -s Anc2.Anc2refChr1 140710 17 + 142988 GGAATAATGGACTGGTC-- -s mr.mrrefChr3 179917 19 + 181027 GAATGGCCCAATGATTTGG -s simCow_chr6.simCow.chr6 599890 17 + 602619 GGAACAATGGACTGGTC-- -s simDog_chr6.simDog.chr6 591543 17 + 593897 GGAATGATGGACTGTTC-- -s simHuman_chr6.simHuman.chr6 599742 17 + 601863 GGATGACTCAATTGGTT-- -s simRat_chr6.simRat.chr6 645025 19 + 647215 GAATGGCCCAGTGAATTGG - -a -s simMouse_chr6.simMouse.chr6 633858 15 + 636262 TTCCCAGATGTTACA -s Anc0.Anc0refChr3 222616 15 + 222631 TTCCTAGAGAATTCA -s Anc1.Anc1refChr1 67658 15 + 69767 TTCCTAGAGAATTCA -s Anc2.Anc2refChr1 140727 15 + 142988 TCCCTAAAGAACTAA -s mr.mrrefChr3 179936 15 + 181027 TTCCCAGATGTTTCA -s simCow_chr6.simCow.chr6 599907 15 + 602619 TCCCTAAGGGACTAA -s simDog_chr6.simDog.chr6 591561 13 + 593897 CCCCCAAAGAACC-- -s simHuman_chr6.simHuman.chr6 599759 15 + 601863 TTCCTGGAACATTCA -s simRat_chr6.simRat.chr6 645044 15 + 647215 TTCCCAGATGTTTCA - -a -s simMouse_chr6.simMouse.chr6 633879 1 + 636262 C -s Anc0.Anc0refChr2 15960 1 + 17989 C -s Anc1.Anc1refChr1 67679 1 + 69767 C -s Anc2.Anc2refChr1 140748 1 + 142988 C -s mr.mrrefChr3 179957 1 + 181027 C -s simCow_chr6.simCow.chr6 599928 1 + 602619 C -s simHuman_chr6.simHuman.chr6 599780 1 + 601863 T -s simRat_chr6.simRat.chr6 645065 1 + 647215 C - -a -s simMouse_chr6.simMouse.chr6 633882 1 + 636262 C -s Anc0.Anc0refChr2 15963 1 + 17989 G -s Anc1.Anc1refChr1 67682 1 + 69767 C -s Anc1.Anc1refChr2 123536 1 - 144309 G -s Anc2.Anc2refChr0 14493 1 - 56053 G -s Anc2.Anc2refChr1 140751 1 + 142988 G -s mr.mrrefChr3 179960 1 + 181027 C -s simCow_chr6.simCow.chr6 599931 1 + 602619 G -s simCow_chr6.simCow.chr6 557431 1 - 602619 G -s simDog_chr6.simDog.chr6 554917 1 - 593897 G -s simDog_chr6.simDog.chr6 591729 1 + 593897 A -s simHuman_chr6.simHuman.chr6 562736 1 - 601863 A -s simHuman_chr6.simHuman.chr6 599783 1 + 601863 C -s simRat_chr6.simRat.chr6 645068 1 + 647215 C - -a -s simMouse_chr6.simMouse.chr6 633889 5 + 636262 TGACT -s Anc1.Anc1refChr1 67689 5 + 69767 TGAAT -s mr.mrrefChr3 179967 5 + 181027 TGACT -s simHuman_chr6.simHuman.chr6 599790 5 + 601863 TGAAT -s simRat_chr6.simRat.chr6 645075 5 + 647215 TGACT - -a -s simMouse_chr6.simMouse.chr6 633910 1 + 636262 C -s Anc0.Anc0refChr2 15989 1 + 17989 T -s Anc1.Anc1refChr1 67710 1 + 69767 T -s Anc1.Anc1refChr2 123562 1 - 144309 T -s Anc2.Anc2refChr0 14517 1 - 56053 T -s Anc2.Anc2refChr1 140779 1 + 142988 T -s mr.mrrefChr0 19964 1 + 130230 T -s mr.mrrefChr3 179988 1 + 181027 C -s simCow_chr6.simCow.chr6 599960 1 + 602619 C -s simCow_chr6.simCow.chr6 557454 1 - 602619 T -s simDog_chr6.simDog.chr6 591758 1 + 593897 T -s simHuman_chr6.simHuman.chr6 562762 1 - 601863 T -s simHuman_chr6.simHuman.chr6 599811 1 + 601863 T -s simRat_chr6.simRat.chr6 13589 1 + 647215 T -s simRat_chr6.simRat.chr6 645096 1 + 647215 C - -a -s simMouse_chr6.simMouse.chr6 633951 88 + 636262 AAGTCTATCGATGGTGTGGGGTAATCACCTTTATTCACAGTGAAGTACAATGTGAGACTTTGGAGCGAGCGGCTGTCCTCGCCTTAAC -s Anc0.Anc0refChr2 16048 33 + 17989 ATGTCTGTCAATGGTGTGTATTAATCTACTTTA------------------------------------------------------- -s Anc1.Anc1refChr1 67759 33 + 69767 ATGTCTGTCAATGGTGTGTATTAATCTACTTTA------------------------------------------------------- -s Anc2.Anc2refChr1 140838 33 + 142988 ATGTTTGTTAATGGTGTGTATTAATCTACTTTA------------------------------------------------------- -s mr.mrrefChr3 180029 33 + 181027 AAGTCTATCGATGGTGTGGGGTAATCACCTTTA------------------------------------------------------- -s simCow_chr6.simCow.chr6 600019 33 + 602619 GTGTTTGTTAGTGGTGTGTATTAATCTACTTTA------------------------------------------------------- -s simDog_chr6.simDog.chr6 591817 33 + 593897 ATCTTTGCTAATGGTGTATATTAAACTGCTTTA------------------------------------------------------- -s simHuman_chr6.simHuman.chr6 599860 33 + 601863 ATGTCTGTCAATGGTGTGTACTAATCTACTTTG------------------------------------------------------- -s simRat_chr6.simRat.chr6 645140 33 + 647215 AAGTCGATCGATTGTGTCAGGTAACCATCTTTA------------------------------------------------------- - -a -s simMouse_chr6.simMouse.chr6 634039 53 + 636262 AGGGGACACACATGGTGCGTTGATTTATGTACTATCTTGCCGGACAGTCGATA -s Anc0.Anc0refChr2 16081 40 + 17989 GAGGGACACACATGATGCGATGACTTATGCACTTC-------------CCACA -s Anc1.Anc1refChr1 67792 53 + 69767 GAGGGACACACATGATGCGATGACTTATGCACTTCCCGATTGGTCGATCCACA -s Anc2.Anc2refChr1 140871 40 + 142988 GACGGACACAAATGATCCGATGATTAGCGCAGTTC-------------CCACA -s mr.mrrefChr3 180062 53 + 181027 AGGGGACACACATGGTGCGTTGACTTATGTACTTTCTTGCCGGACGATCCATA -s simCow_chr6.simCow.chr6 600052 38 + 602619 GAAGAACACAGGTGATCCGATGATTAGCGCAATT---------------CACA -s simDog_chr6.simDog.chr6 591854 26 + 593897 GACGGACACAAATGAT--------------AGTTC-------------CCACA -s simHuman_chr6.simHuman.chr6 599893 53 + 601863 GAGGGACACACATGATGCGGTGACTTATTGACTTCCCGATTGGTCGATCCACA -s simRat_chr6.simRat.chr6 645173 53 + 647215 AGGGGACACACACGGTGCGTTGACTTATGTACCTTCTTGCCGTACGATCCATA - -a -s simMouse_chr6.simMouse.chr6 634092 6 + 636262 CTATTT -s Anc0.Anc0refChr2 16125 6 + 17989 CCATTt -s Anc1.Anc1refChr1 67849 6 + 69767 CCATTT -s Anc2.Anc2refChr1 140915 6 + 142988 TCATAt -s mr.mrrefChr3 180115 6 + 181027 CCATTT -s simCow_chr6.simCow.chr6 600094 6 + 602619 TCACAt -s simDog_chr6.simDog.chr6 591884 6 + 593897 TCATAt -s simHuman_chr6.simHuman.chr6 599950 6 + 601863 CCATTT -s simRat_chr6.simRat.chr6 645226 6 + 647215 CCATTT - -a -s simMouse_chr6.simMouse.chr6 634098 281 + 636262 GTCTACCTTTTAACGGTACTTAGACTTTGTACAGCGCCTCGTGCAAATCTCCAAAAAAAGGCAAACACAGCCATGTACACACAATTAGTGCTTGGCTATGACCCTTCCCTGCACGACCATGTACAAACAGTCAGTGCTTGGCTACACTTGCCCCACAAGTTTGCCCTGCATGATGAAGTGATCTTGGCGCGCACATTGTAGATCCCCTCTCTAGATTTGTGCACTGTCAAGTGATGATAGTCCTTCATGTACATTGTCTTTGTGAAGCCATTTTTTTGGCT -s Anc0.Anc0refChr2 16131 32 + 17989 gTCTCCCC---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CTTTACCAAGCCATTATTTTGGAG -s Anc1.Anc1refChr1 67855 32 + 69767 GTCTCCCC---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CTTTACCAAGCCATTATTTTGGAG -s Anc2.Anc2refChr1 141083 32 + 142988 tTCTCCCC---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CTTTACCAAGCCAGTATCTTGGAG -s mr.mrrefChr3 180121 32 + 181027 GTCTACCT---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CTTTGTGAAGCCATTTTTTTGGAT -s simCow_chr6.simCow.chr6 600298 32 + 602619 tTTTCACC---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CTTTACCAAGCCACTATCTTGGAG -s simDog_chr6.simDog.chr6 592060 24 + 593897 ttctCCCC---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CTTCACCAAGCTAG--------AG -s simHuman_chr6.simHuman.chr6 599956 25 + 601863 G----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CTTTACCAAGCCATTATTTTCCAG -s simRat_chr6.simRat.chr6 645232 32 + 647215 GTCTACCC---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CTCTGTGGAGCCAGTTTTCTGGAT - -a -s simMouse_chr6.simMouse.chr6 634379 54 + 636262 CAGCATTCTAGGCTGCTTCAAGTTCCATTTACCAATACACTCACATTTACAATT -s Anc0.Anc0refChr2 16168 53 + 17989 CAGCCTTTTGGGCTGCTTCA-TTTCCATTCACCTATACACTTGCATTTACGCTT -s Anc1.Anc1refChr1 67892 53 + 69767 CAGCCTTTTGGGCTGCTTCA-TTTCCATTCACCTATACACTTGCATTTACGCTT -s Anc2.Anc2refChr1 141120 53 + 142988 CAGCCTTTTGGGCTGATTCA-TTTCCATTCACCTATACACTTGCATTCACACTT -s mr.mrrefChr3 180158 53 + 181027 CAGCCTTCTAGGCTGCTTCA-GTTCCATTTACCAATACACTCACATTTACGATT -s simCow_chr6.simCow.chr6 600335 49 + 602619 CAGTCTTTTGGGCTAAGTCA-ATTCCATTCACCTATACGATTGC----ACACAT -s simDog_chr6.simDog.chr6 592089 53 + 593897 CAGCCTCCTGGGCTGATTCA-TTTCCATTTACCCATTCACTTGCATTCACACTC -s simHuman_chr6.simHuman.chr6 599986 53 + 601863 TGGCCTTTTGGCCTGCTCCA-CTTCCATTCACCTATACACTTGCATTTAAGCTT -s simRat_chr6.simRat.chr6 645269 53 + 647215 CAGCCTTCTAGGCTGCATCA-GTTCCAGTTACCAATACACTCACATTTATGATC - -a -s simMouse_chr6.simMouse.chr6 634433 37 + 636262 CTATTTTACATCTCGAGTTGGATAAGATTAGACCTCC -s Anc0.Anc0refChr2 16224 33 + 17989 TTATTCCACACCTGGAGTCAGATAAGATTG----TCT -s Anc1.Anc1refChr1 67948 33 + 69767 TTATTCCACACCTGGAGTCAGATAAGATTG----TCT -s Anc2.Anc2refChr1 141176 33 + 142988 TTATTCCACACCTGGATTCAGATAAAATTG----GCT -s mr.mrrefChr3 180214 37 + 181027 CTATTTTACATCTCGAGTTGGATAAGATTAGACCTCC -s simCow_chr6.simCow.chr6 600387 33 + 602619 TTATACTACACCTGGATCCAGATAAAATTG----GCT -s simDog_chr6.simDog.chr6 592145 32 + 593897 TTATTCCACCCGTGGATTTAGATAAAATTG----GC- -s simHuman_chr6.simHuman.chr6 600042 33 + 601863 TTATTCCACACCTGGAGTCAGATATGATTG----TCT -s simRat_chr6.simRat.chr6 645325 37 + 647215 CTACTTTACATCTTGAGTTGTATAAGATCAGACCTCA - -a -s simMouse_chr6.simMouse.chr6 634470 3 + 636262 TAA -s Anc0.Anc0refChr2 16257 3 + 17989 TAG -s Anc1.Anc1refChr1 67981 3 + 69767 TAG -s Anc2.Anc2refChr1 141209 3 + 142988 TGG -s mr.mrrefChr3 180251 3 + 181027 TAA -s simCow_chr6.simCow.chr6 600437 3 + 602619 TGG -s simDog_chr6.simDog.chr6 592177 3 + 593897 TGG -s simHuman_chr6.simHuman.chr6 600075 3 + 601863 TAG -s simRat_chr6.simRat.chr6 645362 3 + 647215 TAA - -a -s simMouse_chr6.simMouse.chr6 634473 29 + 636262 CAGGTGCTGCCCTCCTTACATTTATAATT -s Anc0.Anc0refChr2 16267 29 + 17989 CAGTTCCACTTCCCTATACACTTGCATTT -s Anc1.Anc1refChr1 67991 29 + 69767 CAGTTCCACTTCCCTATACACTTGCATTT -s Anc2.Anc2refChr1 141219 29 + 142988 CAGTTCCACTCCCCTATACACTTGCATTT -s mr.mrrefChr3 180254 29 + 181027 CAGGTGCTGCTCTCCATACATTTGTAATT -s simCow_chr6.simCow.chr6 600447 29 + 602619 CACATGCAATCCCTTATACATGTGCATTT -s simDog_chr6.simDog.chr6 592187 29 + 593897 CAGTTCCACTCCCCTAGACACTAGCATTT -s simHuman_chr6.simHuman.chr6 600085 29 + 601863 CAGTTTCACTTGCCTATACACCTGCATTT -s simRat_chr6.simRat.chr6 645365 29 + 647215 CAGGTGCTTCTTGCCATACATTTGTAATT - -a -s simMouse_chr6.simMouse.chr6 634502 33 + 636262 AGTAGCACCTGGTATATTACTTCCCAGCTATGC -s Anc0.Anc0refChr2 16296 31 + 17989 CCACACT--TGAAATTTGTAGTGCCAACTAGGA -s Anc1.Anc1refChr1 68020 31 + 69767 CCACACT--TGAAATTTGTAGTGCCAACTAGGA -s Anc2.Anc2refChr1 141249 31 + 142988 CCACACT--TGAAATTTGCAGGGCCAACTAGGA -s mr.mrrefChr3 180283 31 + 181027 ACTCGCA--TGATATATTTCTTCCCAGCTATGA -s simCow_chr6.simCow.chr6 600477 31 + 602619 ACACACT--TGAAATTCACAGAACTAACTGGGA -s simDog_chr6.simDog.chr6 592217 31 + 593897 CCACACT--TGGAATTTGCAGGGTCAACTAGGA -s simHuman_chr6.simHuman.chr6 600114 30 + 601863 GCACACT--TGAAATCTGTAGT-CCAACTAGGA -s simRat_chr6.simRat.chr6 645394 31 + 647215 ACTCGCA--TGATATATCTCTTACCAGCTATGA - -a -s simMouse_chr6.simMouse.chr6 634535 12 + 636262 ATGAACCGCTTG -s Anc0.Anc0refChr2 16327 12 + 17989 ACAGACTTTATG -s Anc1.Anc1refChr1 68051 12 + 69767 ACAGACTTTATG -s Anc2.Anc2refChr1 141280 12 + 142988 GTAGATTTTAGG -s mr.mrrefChr3 180314 12 + 181027 ACAAACCGCTTG -s simCow_chr6.simCow.chr6 600508 9 + 602619 GTAAATCCT--- -s simDog_chr6.simDog.chr6 592248 12 + 593897 GTAGATTTCAGG -s simHuman_chr6.simHuman.chr6 600144 12 + 601863 ACACACTTTATA -s simRat_chr6.simRat.chr6 645427 12 + 647215 ACAAACCACTTG - -a -s simMouse_chr6.simMouse.chr6 634547 32 + 636262 TGTGAGGTGGGAAGACTCCTTCTGTGATCACT -s Anc0.Anc0refChr2 16339 32 + 17989 CTTTAGCACAGATGACCACTTGTCAGGGCATT -s Anc1.Anc1refChr1 68063 32 + 69767 CTTTAGCACAGATGACCACTTGTCAGGGCATT -s Anc2.Anc2refChr1 141292 32 + 142988 CTTTACCACAAATGACCACTAGTCAGGGCACT -s mr.mrrefChr3 180326 32 + 181027 TGTGAGGTGGGAAGACTCCTTCTGTGATCATT -s simCow_chr6.simCow.chr6 600517 3 + 602619 -----------------------------ACT -s simDog_chr6.simDog.chr6 592422 32 + 593897 CTTTACCACAAATGACCACTAGTCAGGGCACC -s simHuman_chr6.simHuman.chr6 600156 32 + 601863 CATTAGTAAAGATGACCACTTTTCAGGGCATT -s simRat_chr6.simRat.chr6 645439 32 + 647215 TGTGATGCGGGCAGACTCCTTCTGTGATCATT - -a -s simMouse_chr6.simMouse.chr6 634579 46 + 636262 ATTGCATCCATGCTGTGAAGCTTTGCCTGTCAGTGGACCGCAATTC -s Anc0.Anc0refChr2 16371 43 + 17989 GCCGG--CCAGGACCAGAGACATTACA-ACAAGTGGTTCACTCTTT -s Anc1.Anc1refChr1 68095 43 + 69767 GCCGG--CCAGGACCAGAGACATTACA-ACAAGTGGTTCACTCTTT -s Anc2.Anc2refChr1 141324 43 + 142988 ACTGG--CAGGGACCAGAGACATTATA-ACAAGTGCTTCACTCTCT -s mr.mrrefChr3 180358 46 + 181027 GCCGCATCCATGCTGTGAAGCTTTGCCTGTCAGTGGACCGCAATTC -s simCow_chr6.simCow.chr6 600520 43 + 602619 ACTGG--CAGCGACCCGAGACCTTATA-ACAAGTCTTTCACTCCCT -s simDog_chr6.simDog.chr6 592454 43 + 593897 ACTGG--CAGGGACCAGAGACATTATA-ACAACTGCTTCAGTCTCT -s simHuman_chr6.simHuman.chr6 600188 43 + 601863 GCCGA--CCAGGACCAGAGACATCACA-ACAAGTGGTTCACTCTTT -s simRat_chr6.simRat.chr6 645501 4 + 647215 GCCG------------------------------------------ - -a -s simMouse_chr6.simMouse.chr6 634625 21 + 636262 CTCTTGGTCAATCACTGTGGC -s Anc0.Anc0refChr2 16417 9 + 17989 CTTTTGGTC------------ -s Anc1.Anc1refChr1 68141 9 + 69767 CTTTTGGTC------------ -s Anc2.Anc2refChr1 141370 9 + 142988 CTTTTGGTC------------ -s mr.mrrefChr3 180404 9 + 181027 CTCTTGGTC------------ -s simCow_chr6.simCow.chr6 600566 9 + 602619 CTTTTGGTG------------ -s simDog_chr6.simDog.chr6 592500 9 + 593897 TTTTTGGTC------------ -s simHuman_chr6.simHuman.chr6 600234 9 + 601863 CTTTTGGTT------------ - -a -s simMouse_chr6.simMouse.chr6 634646 6 + 636262 CAGTCC -s Anc0.Anc0refChr2 940 2 - 17989 ----TC -s Anc1.Anc1refChr1 982 2 - 69767 ----TC -s Anc2.Anc2refChr1 984 2 - 142988 ----TC -s mr.mrrefChr3 0 6 - 181027 TAGTCC -s simCow_chr6.simCow.chr6 1452 2 - 602619 ----TC -s simDog_chr6.simDog.chr6 879 2 - 593897 ----TC -s simHuman_chr6.simHuman.chr6 1075 2 - 601863 ----TC -s simRat_chr6.simRat.chr6 1108 6 - 647215 TAGGCC - -a -s simMouse_chr6.simMouse.chr6 634652 21 + 636262 AACCCACCTGTTGGTCAGAAA -s Anc0.Anc0refChr2 942 20 - 17989 AACCCCCCAGTAAATCAGAG- -s Anc1.Anc1refChr1 984 20 - 69767 AACCCCCCAGTAAATCAGAG- -s Anc2.Anc2refChr1 986 20 - 142988 AACCCCCCAGTAAATCAGAG- -s mr.mrrefChr3 6 21 - 181027 AACCCACCTGTTGGTCAGAAA -s simCow_chr6.simCow.chr6 1454 20 - 602619 AACCCACCTGTAAATTAGAA- -s simDog_chr6.simDog.chr6 881 20 - 593897 AACCCCCCAGTAAATCAGAG- -s simHuman_chr6.simHuman.chr6 1077 8 - 601863 AGCCCCCC------------- -s simRat_chr6.simRat.chr6 1125 20 - 647215 AACCCACCTGTTGGTCACAT- - -a -s simMouse_chr6.simMouse.chr6 634673 90 + 636262 GGAGACCACGCCAAGCTGGGATTCAAGGCAATCAGGTGTTGGATCCCCCCACTTAATTGGCAAAGATCAGTGCTATGCAGATCCACACTA -s Anc0.Anc0refChr2 962 90 - 17989 GGAGACCATGATGAGATTGAATGCAAAGGACCCCCAGATTGTTAACCTTCACCTAATTTGCAGAAGTCAGTACTAAGTAAATCTACAACT -s Anc1.Anc1refChr1 1004 90 - 69767 GGAGACCATGATGAGATTGAATGCAAAGGACCCCCAGATTGTTAACCTTCACCTAATTTGCAGAAGTCAGTACTAAGTAAATCTACAACT -s Anc2.Anc2refChr1 1006 90 - 142988 GGAGACCATGATGAGATTGAATGCAAAGGACCCCCAGATTGTTAACCTTCACCTAATTTGCAGAAGTCAGTACTAAGTAAATCTGCAACT -s mr.mrrefChr3 27 90 - 181027 GGAGACCACGCCAAGCTGGGATTCAAGGCAATCAGGTGTTGGATCCCCCCACCTAATTGGCAGAAATCAGTGCTATGCAGATCCACAATA -s simCow_chr6.simCow.chr6 1475 90 - 602619 GGCTACCATGTTGAGGTTGGATGCAAATGATCCCCTGATTGGTTACCCCCACCTAACTTGCAGGGGTCAGTACTATGTAAATCTGCAACT -s simDog_chr6.simDog.chr6 901 90 - 593897 GGAGACCATGATGAGATTGAATGCAAAGGACCCCCAGATTGTTAACCTTCAACTAATTTGCAGAAGTCAGTAGTAAGTAAGTCTGCAATT -s simHuman_chr6.simHuman.chr6 1085 40 - 601863 --------------------------------------------------ACCTAATTTGTACAACTCACTACTAGGTGAACCTACAACT -s simRat_chr6.simRat.chr6 1145 67 - 647215 ---------------------TTAAGGGCAATCTGGTG--GGATCTCCCCACCAAATTGGCAGAAATCAGTGCTATGCAGTTCCACAATA - -a -s simMouse_chr6.simMouse.chr6 634763 9 + 636262 CACACCCAG -s Anc0.Anc0refChr2 1071 9 - 17989 CATACACAG -s Anc1.Anc1refChr1 1113 9 - 69767 CATACACAG -s Anc2.Anc2refChr1 1115 9 - 142988 CATACACAG -s mr.mrrefChr3 118 9 - 181027 CACACCCAG -s simCow_chr6.simCow.chr6 1577 7 - 602619 --TACACTG -s simDog_chr6.simDog.chr6 1010 9 - 593897 CATACCCAG -s simHuman_chr6.simHuman.chr6 1144 9 - 601863 TATACATAG -s simRat_chr6.simRat.chr6 1213 9 - 647215 CACACCCAG - -a -s simMouse_chr6.simMouse.chr6 634772 30 + 636262 GCCAGTTGCATCGGTTGGTTGTTTTTTCTG -s Anc0.Anc0refChr2 1080 28 - 17989 GCCAGTTGTAGAGGTTGGTT--ATTGCTAG -s Anc1.Anc1refChr1 1122 28 - 69767 GCCAGTTGTAGAGGTTGGTT--ATTGCTAG -s Anc2.Anc2refChr1 1124 28 - 142988 GCCAGTTGTAGAGGTTGGTT--ATTGCTAG -s mr.mrrefChr3 127 30 - 181027 GCCAGTTGCATAGGTTGGTTGTATTGCATG -s simCow_chr6.simCow.chr6 1584 28 - 602619 GCCAGTTGTAGAGGTTGGTT--ATAGCTAG -s simDog_chr6.simDog.chr6 1026 26 - 593897 GCCAGTG--AGAGGTTAGTC--ATTGCTAG -s simHuman_chr6.simHuman.chr6 1153 28 - 601863 GCCAGTTTTAGAGGTTGGTT--CTTGCTAG -s simRat_chr6.simRat.chr6 1222 30 - 647215 GCCAGTTGCATAGGTGGGTTGTATTGCATG - -a -s simMouse_chr6.simMouse.chr6 634802 6 + 636262 ATTGGG -s Anc0.Anc0refChr2 1112 6 - 17989 AGTGGG -s Anc1.Anc1refChr1 1154 6 - 69767 AGTGGG -s Anc2.Anc2refChr1 1156 6 - 142988 GGTGGT -s mr.mrrefChr3 157 6 - 181027 AGTGGG -s simCow_chr6.simCow.chr6 1615 6 - 602619 GGTGGC -s simDog_chr6.simDog.chr6 1063 6 - 593897 GGTGGT -s simHuman_chr6.simHuman.chr6 1185 6 - 601863 AGTGGG -s simRat_chr6.simRat.chr6 1252 6 - 647215 GGTGGG - -a -s simMouse_chr6.simMouse.chr6 634808 5 + 636262 ATGGG -s Anc0.Anc0refChr2 1134 5 - 17989 ATGAA -s Anc1.Anc1refChr1 1176 5 - 69767 ATGAA -s Anc2.Anc2refChr1 1178 5 - 142988 ATGAA -s mr.mrrefChr3 176 5 - 181027 ATGGG -s simCow_chr6.simCow.chr6 1637 5 - 602619 TTCAA -s simDog_chr6.simDog.chr6 1085 5 - 593897 ATGCA -s simHuman_chr6.simHuman.chr6 1207 5 - 601863 ATGAA -s simRat_chr6.simRat.chr6 1271 5 - 647215 CTGGG - -a -s simMouse_chr6.simMouse.chr6 634813 12 + 636262 ATGTGGTCCCAT -s Anc0.Anc0refChr2 1139 3 - 17989 ATG--------- -s Anc1.Anc1refChr1 1181 7 - 69767 ATGTGTC----- -s Anc2.Anc2refChr1 1183 3 - 142988 ATG--------- -s mr.mrrefChr3 181 12 - 181027 ATGTGGTCCTAT -s simCow_chr6.simCow.chr6 1645 3 - 602619 GTG--------- -s simDog_chr6.simDog.chr6 1090 3 - 593897 AGG--------- -s simHuman_chr6.simHuman.chr6 1212 7 - 601863 ATGTGTC----- -s simRat_chr6.simRat.chr6 1276 12 - 647215 ATGCAGTCCTGT - -a -s simMouse_chr6.simMouse.chr6 634825 42 + 636262 ATGTAGCAAGCAATGTCACAGCAGGCGATGAATGGCACATAG -s Anc0.Anc0refChr2 1142 23 - 17989 --------AGCAATAT--TGGGAGGC---------TTGAGAG -s Anc1.Anc1refChr1 1188 23 - 69767 --------AGCAATAT--TGGGAGGC---------TTGAGAG -s Anc2.Anc2refChr1 1186 23 - 142988 --------GCCAATAG--TGAGAGGC---------TTCAGAG -s mr.mrrefChr3 193 42 - 181027 ATGTAGCAAGCAATGTCATAGGAGGCGATGAATGGTTGATAG -s simCow_chr6.simCow.chr6 1648 23 - 602619 --------GCTAATAC--TCCATGGC---------TTTGGAG -s simDog_chr6.simDog.chr6 1093 23 - 593897 --------GCCAATAG--TGAGATGC---------TTCATAA -s simHuman_chr6.simHuman.chr6 1219 23 - 601863 --------AGCAATAT--TTGGAGGC---------TTGAGAG -s simRat_chr6.simRat.chr6 1289 42 - 647215 ATGTAGCAAGCAATGTCATAGGAGGCAATAAATGGTTGATAG - -a -s simMouse_chr6.simMouse.chr6 634867 43 + 636262 TTGGAGGTTCAAAACTCAGCTAGGCTGTTCTTTTAGCATTGAG -s Anc0.Anc0refChr2 1166 25 - 17989 TTG---------------GCTA-GCTGTTCTGTTAGC--TGAT -s Anc1.Anc1refChr1 1212 25 - 69767 TTG---------------GCTA-GCTGTTCTGTTAGC--TGAT -s Anc2.Anc2refChr1 1210 25 - 142988 TTG---------------GCTA-GCTGTTCTGTTAGC--TGAT -s mr.mrrefChr3 235 26 - 181027 TTG---------------GCTAAGCTGTTCTGTTAGC--TGAT -s simCow_chr6.simCow.chr6 1672 25 - 602619 GCA---------------GCTA-TCTGTTCTGTTAGC--TGAT -s simDog_chr6.simDog.chr6 1117 25 - 593897 TTG---------------GCTA-GCTATTCTGTTAGC--TGAT -s simHuman_chr6.simHuman.chr6 1243 25 - 601863 TTG---------------GCTA-GCTGTTCTGATAGC--TGAT -s simRat_chr6.simRat.chr6 1331 26 - 647215 TTG---------------GCTAAGCTGTACTGTTAGC--TACT - -a -s simMouse_chr6.simMouse.chr6 634910 124 + 636262 CACAAGATCGCTTAGAGGGGAGTGTACATAAAATGGGTCCATTCCTCAACAATTTAACAGACTACTCACCCACAATTTAACAGACTACTCACCCTACTTTGGTCACGGCTCTATTTAGTTGATA -s Anc0.Anc0refChr2 1193 101 - 17989 AGCAAAGCCACATAACTGGGAGTGCACATAAAATGCATCCATTCCCCAACAGTTTAAC---------------------A--GACTATTCAGCCTACTTGGTCCAGTGCTCTTTACAGTCCATA -s Anc1.Anc1refChr1 1239 101 - 69767 AGCAAAGCCACATAACTGGGAGTGCACATAAAATGCATCCATTCCCCAACAGTTTAAC---------------------A--GACTATTCAGCCTACTTGGTCCAGTGCTCTTTACAGTCCATA -s Anc2.Anc2refChr1 1237 101 - 142988 AGCAAAGCCACATAACTCAGAGTGCACATAAATTACATCCACCCCCCAACTGTTGAAC---------------------A--GACTATTTAGCCTACTTGGTCCAGTGCTCTTTACAGTCCATA -s mr.mrrefChr3 263 103 - 181027 AGCAAGATCACTTAGAGGGGAGTGTACATAAAATGGGTCCATTCCTCAACAATTTAAC---------------------ACAGACTATTCACCCTACTTGGGCCAGGGCTCTTTTCAGTTGATA -s simCow_chr6.simCow.chr6 1699 63 - 602619 GGCAAAGCAGTGTA--------------------------------------TTCAAC---------------------A--GGCTATTTAGCCACTTTGGTCAAGTGCTCTTTCCAGTCCACC -s simDog_chr6.simDog.chr6 1147 101 - 593897 AGTGAACCCACATGACTCAGAGTGCACATAAATTACATCCACCCCCCAACTGTCGAAG---------------------A--GACTTTTTAGCCTACTTGGTCCAGTGCTCTCTACAGACCATA -s simHuman_chr6.simHuman.chr6 1268 101 - 601863 AGCAAAGCCACATAATTGGGAGTGCATATAGAATGCATACATTCCACTATAGTTTAAC---------------------A--GACCATCCAGGCTACCTGGTCCAGTGCTCTTCACAGTCCATA -s simRat_chr6.simRat.chr6 1359 103 - 647215 AGCAAGATCACTTAGAGGGGAGCATACATAAAATGTTTCCATTCCCCAACAATTTAAC---------------------ACAGACTATTCACCCTACTCGGGCCAGGGCTCTTTTCAGTTGATA - -a -s simMouse_chr6.simMouse.chr6 635034 19 + 636262 TGAGGGAGGAGCAGGGAAT -s Anc0.Anc0refChr2 1297 19 - 17989 TGGGGGAGGGGCATGGAAT -s Anc1.Anc1refChr1 1343 19 - 69767 TGGGGGAGGGGCATGGAAT -s Anc2.Anc2refChr1 1341 19 - 142988 GGGGGGAGGGGCATGGAAT -s mr.mrrefChr3 366 19 - 181027 TGAGGGAGGAGCAGGGAAT -s simCow_chr6.simCow.chr6 1765 19 - 602619 GGGGGGAGGGCCATGGAAT -s simDog_chr6.simDog.chr6 1251 19 - 593897 GGGGGGAGGAGCATAGAAT -s simHuman_chr6.simHuman.chr6 1372 19 - 601863 TGGGGGGGGGGCATGGAAT -s simRat_chr6.simRat.chr6 1462 19 - 647215 TGAGCGAGGAGCAGGGAAT - -a -s simMouse_chr6.simMouse.chr6 635053 38 + 636262 CTCGATGTAAAATGATCGAGAAAGTGTCAGTTATCTCA -s Anc0.Anc0refChr2 1341 34 - 17989 CACACTGTTAAATATTTCAGGAAG---CACTTAT-TGA -s Anc1.Anc1refChr1 1387 34 - 69767 CACACTGTTAAATATTTCAGGAAG---CACTTAT-TGA -s Anc2.Anc2refChr1 1385 34 - 142988 GAAAGTGGTAATTATTTCAGAAGG---TACTAAC-TAA -s mr.mrrefChr3 385 38 - 181027 CTCACTATAAAATGATCGAGGAAGTGTCAGTTATCTGA -s simCow_chr6.simCow.chr6 1809 34 - 602619 GAGAGTTGTAATTATTTCAGAAGG---TACTAAC-CCA -s simDog_chr6.simDog.chr6 1295 34 - 593897 GAAAGTGGTGGTTATTTCAGAAGG---TGCTAAC-TAA -s simHuman_chr6.simHuman.chr6 1416 34 - 601863 CACACTGTGAAATTGTTCAGGAAA---CACTTAT-TGA -s simRat_chr6.simRat.chr6 1481 38 - 647215 CTCACTATAAAATGATCTACGAAGTGTCAGTTATCTGG - -a -s simMouse_chr6.simMouse.chr6 635091 3 + 636262 AAA -s Anc0.Anc0refChr2 1375 3 - 17989 AAA -s Anc1.Anc1refChr1 1421 3 - 69767 AAA -s Anc2.Anc2refChr1 1419 3 - 142988 AAA -s mr.mrrefChr3 423 3 - 181027 AAA -s simCow_chr6.simCow.chr6 1849 3 - 602619 AAC -s simDog_chr6.simDog.chr6 1329 3 - 593897 AAA -s simHuman_chr6.simHuman.chr6 1450 3 - 601863 AAA -s simRat_chr6.simRat.chr6 1519 3 - 647215 AAA - -a -s simMouse_chr6.simMouse.chr6 635094 51 + 636262 GATTAAACTAAAGCACAGGTTTGAGTAAGCACAGATTTGAGTACAACTTTG -s Anc0.Anc0refChr2 1378 19 - 17989 GA--------------------------------CTTTGAGTGTGACTTTG -s Anc1.Anc1refChr1 1424 20 - 69767 GAG-------------------------------CTTTGAGTGTGACTTTG -s Anc2.Anc2refChr1 1422 19 - 142988 GA--------------------------------CTTTGAGTGTGACTTTG -s mr.mrrefChr3 426 51 - 181027 GAGCAACCCAAAGCACTGGTTTGAATTAGCACAGATTTGAGTACAACTTTG -s simCow_chr6.simCow.chr6 1852 19 - 602619 GA--------------------------------CTTTGAGTGTAACTTTG -s simDog_chr6.simDog.chr6 1335 19 - 593897 GA--------------------------------CTTTGAGTGTGACTTTG -s simHuman_chr6.simHuman.chr6 1453 3 - 601863 GAG------------------------------------------------ -s simRat_chr6.simRat.chr6 1522 51 - 647215 GAGCAACCCAAAGCATTGGTTTGAATTAGCACAGATCTGAGTACAACTTTG - -a -s simMouse_chr6.simMouse.chr6 635145 17 + 636262 TATTTGTAGACAATAGG -s Anc0.Anc0refChr2 1397 17 - 17989 CATCGAGAAAAAATATA -s Anc1.Anc1refChr1 1444 17 - 69767 CATCGAGAAAAAATATA -s Anc2.Anc2refChr1 1443 17 - 142988 CATCGAGAAAAAATATA -s mr.mrrefChr3 477 17 - 181027 TATTTATAAGCAATAGG -s simCow_chr6.simCow.chr6 1873 17 - 602619 CTTATTGCAAAGACTTA -s simDog_chr6.simDog.chr6 1359 17 - 593897 CATCGAGAAAAAATATA -s simRat_chr6.simRat.chr6 1573 17 - 647215 TATTTATAAGCAATAGG - -a -s simMouse_chr6.simMouse.chr6 635162 54 + 636262 TTAGCCTGCTCTGGGAGAGAGTTACTAGTTTCTCCCCATAGAAGATAAGTTCCA -s Anc0.Anc0refChr2 1414 48 - 17989 TTAGC------TGGAGGTGACTTACCAGTTTCTCCCTATCCTAGAGCAAGTGCA -s Anc1.Anc1refChr1 1461 54 - 69767 TTAGCGTCACCTGGAGGTGACTTACCAGTTTCTCCCTATCCTAGAGCAAGTGCA -s Anc2.Anc2refChr1 1460 48 - 142988 TCAGC------TGGAGGTAACCTGTCAATTTCTCCAGCTCCTAGGGCAAGGGCA -s mr.mrrefChr3 494 54 - 181027 TTAGCCTGCTCTGGAAGAGACTTACTAGTTTCTCCCTATCGAAGATAAGTTGCA -s simCow_chr6.simCow.chr6 1893 48 - 602619 TCATC------TGGAGGTAACCTGTCAATTTCTCCAGCTCCTAGGGCAAGGGCA -s simDog_chr6.simDog.chr6 1376 9 - 593897 TCAGG------TGAA--------------------------------------- -s simHuman_chr6.simHuman.chr6 1456 54 - 601863 TTAGCGTCACCTTGAGGTGGCTTACAAGTATCTCCCTATCCTAGAGCATGTGTA -s simRat_chr6.simRat.chr6 1590 54 - 647215 TAAGCCTGTTTTGGAAGAGACTTACTAATTTCTCCCTATCACAGATGGGTTGCA - -a -s simMouse_chr6.simMouse.chr6 635216 13 + 636262 CATATTTACTTGT -s Anc0.Anc0refChr2 1475 12 - 17989 C-TTGGTAATGGT -s Anc1.Anc1refChr1 1528 13 - 69767 CCTTGGTAATGGT -s Anc2.Anc2refChr1 1521 12 - 142988 C-TTGGTAATAGT -s mr.mrrefChr3 553 13 - 181027 CCTATTTAATGGT -s simCow_chr6.simCow.chr6 1954 12 - 602619 C-TTGGTAATAGT -s simHuman_chr6.simHuman.chr6 1531 13 - 601863 CCTCCATAATGGA -s simRat_chr6.simRat.chr6 1649 13 - 647215 CCTATTTAATGGT - -a -s simMouse_chr6.simMouse.chr6 635229 6 + 636262 ATATAT -s Anc0.Anc0refChr2 1497 6 - 17989 GTGTAT -s Anc1.Anc1refChr1 1551 6 - 69767 GTGTAT -s Anc2.Anc2refChr1 1543 6 - 142988 TTGTTT -s mr.mrrefChr3 576 6 - 181027 GTATAT -s simCow_chr6.simCow.chr6 1976 6 - 602619 TTGTTT -s simHuman_chr6.simHuman.chr6 1554 6 - 601863 GTGTAT -s simRat_chr6.simRat.chr6 1672 6 - 647215 GTTGGT - -a -s simMouse_chr6.simMouse.chr6 635235 5 + 636262 GTAGT -s Anc0.Anc0refChr2 1516 5 - 17989 GTGGG -s Anc1.Anc1refChr1 1570 5 - 69767 GTGGG -s Anc2.Anc2refChr1 1562 5 - 142988 GTGGG -s mr.mrrefChr3 582 5 - 181027 GTGGT -s simCow_chr6.simCow.chr6 1995 5 - 602619 GTGGG -s simHuman_chr6.simHuman.chr6 1573 5 - 601863 GTGGA -s simRat_chr6.simRat.chr6 1678 5 - 647215 GTGGC - -a -s simMouse_chr6.simMouse.chr6 635240 16 + 636262 TTAATGATCCCCATGT -s Anc0.Anc0refChr2 1521 16 - 17989 TGTATCCTATTGACAT -s Anc1.Anc1refChr1 1575 16 - 69767 TGTATCCTATTGACAT -s Anc2.Anc2refChr1 1567 16 - 142988 TGTGTCCCAGTGACAT -s mr.mrrefChr3 587 16 - 181027 TGTATGATATTGATGT -s simCow_chr6.simCow.chr6 2002 16 - 602619 TGTGTCCCAGTGACAT -s simHuman_chr6.simHuman.chr6 1578 16 - 601863 TGTATCGTATTGACAT -s simRat_chr6.simRat.chr6 1683 16 - 647215 TGTATGATATTGATGT - -a -s simMouse_chr6.simMouse.chr6 635256 3 + 636262 CAG -s Anc0.Anc0refChr2 1552 3 - 17989 CAG -s Anc1.Anc1refChr1 1606 3 - 69767 CAG -s Anc2.Anc2refChr1 1598 3 - 142988 CAA -s mr.mrrefChr3 603 3 - 181027 CAG -s simCow_chr6.simCow.chr6 2033 3 - 602619 CAA -s simHuman_chr6.simHuman.chr6 1609 3 - 601863 CAG -s simRat_chr6.simRat.chr6 1699 3 - 647215 CAG - -a -s simMouse_chr6.simMouse.chr6 635268 3 + 636262 AAG - -a -s simMouse_chr6.simMouse.chr6 635275 10 + 636262 TTCTTAGAAA - -a -s simMouse_chr6.simMouse.chr6 635304 97 + 636262 CTTGTGTGTGTCATCTCTCTGTCATGTACATGGCTGCTTGCCTTTTATTGGAGCTTTGCACGAGACACTATGTGAAATCTAAACAACATAAAGCTAA - -a -s simMouse_chr6.simMouse.chr6 635567 2 + 636262 TG -s mr.mrrefChr5 198729 2 - 294540 Tg -s simRat_chr6.simRat.chr6 294632 2 - 647215 Ag - -a -s simMouse_chr6.simMouse.chr6 635569 2 + 636262 GA -s Anc0.Anc0refChr5 25915 2 - 87904 GC -s Anc1.Anc1refChr7 27595 2 + 47259 GC -s Anc2.Anc2refChr15 27830 2 - 86568 GC -s mr.mrrefChr5 198731 2 - 294540 ga -s simCow_chr6.simCow.chr6 363177 2 - 602619 GA -s simDog_chr6.simDog.chr6 362358 2 - 593897 TC -s simHuman_chr6.simHuman.chr6 280430 2 + 601863 GC -s simRat_chr6.simRat.chr6 294634 2 - 647215 gt - -a -s simMouse_chr6.simMouse.chr6 635571 2 + 636262 TT -s Anc0.Anc0refChr5 25917 2 - 87904 CA -s Anc1.Anc1refChr7 27597 2 + 47259 CA -s Anc2.Anc2refChr15 27832 2 - 86568 CA -s mr.mrrefChr5 198733 2 - 294540 TT -s simCow_chr6.simCow.chr6 363179 2 - 602619 CA -s simDog_chr6.simDog.chr6 362360 2 - 593897 CA -s simHuman_chr6.simHuman.chr6 280432 2 + 601863 CA -s simRat_chr6.simRat.chr6 294636 2 - 647215 gg -s simRat_chr6.simRat.chr6 580333 2 + 647215 TT - -a -s simMouse_chr6.simMouse.chr6 635573 5 + 636262 TACTA -s Anc0.Anc0refChr2 17049 4 + 17989 -ACTA -s Anc1.Anc1refChr1 68785 4 + 69767 -ACTA -s Anc2.Anc2refChr1 142004 4 + 142988 -ATTA -s mr.mrrefChr1 0 5 + 670 TACTA -s simCow_chr6.simCow.chr6 601167 4 + 602619 -ATGA -s simDog_chr6.simDog.chr6 593018 4 + 593897 -ATTA -s simHuman_chr6.simHuman.chr6 600788 4 + 601863 -ACTA -s simRat_chr6.simRat.chr6 613 5 - 647215 TACTA - -a -s simMouse_chr6.simMouse.chr6 635578 14 + 636262 TGTGTCCATGGAGT -s Anc0.Anc0refChr2 17374 14 + 17989 CATGTTCAAGGAGT -s Anc1.Anc1refChr1 69110 14 + 69767 CATGTTCAAGGAGT -s Anc2.Anc2refChr1 142353 14 + 142988 CATGTTTAAGGAGT -s mr.mrrefChr1 5 14 + 670 TGTGTCCATGGAGT -s simCow_chr6.simCow.chr6 601978 14 + 602619 CATGTTTAATGTGT -s simDog_chr6.simDog.chr6 593380 14 + 593897 TATCTTTAAGGAGT -s simHuman_chr6.simHuman.chr6 601198 14 + 601863 CATGTTCAAGAAGT -s simRat_chr6.simRat.chr6 618 14 - 647215 CATGGCCATGGAGT - -a -s simMouse_chr6.simMouse.chr6 635592 27 + 636262 TATGACAGGTTTGAGTCTCCAAACACC -s Anc0.Anc0refChr2 17388 27 + 17989 TATAACTTATTTTAGTCCCCCAGGTGC -s Anc1.Anc1refChr1 69124 27 + 69767 TATAACTTATTTTAGTCCCCCAGGTGC -s Anc2.Anc2refChr1 142367 27 + 142988 TACAACTTACCTTAGTCCACCAGGTGC -s mr.mrrefChr1 19 27 + 670 TATGACAGGTTTGAGTCTCCAAACACC -s simCow_chr6.simCow.chr6 601992 27 + 602619 TACAACTTATTTTAGTTCACCAGGTGC -s simDog_chr6.simDog.chr6 593394 21 + 593897 TACGAACTACCTTAGTCC------TGT -s simHuman_chr6.simHuman.chr6 601224 27 + 601863 TATAACTTATTCTAGTCCCCCAGTTGC -s simRat_chr6.simRat.chr6 632 27 - 647215 TTTACTGGGTTTGAGTCTCCAGGCGCC - -a -s simMouse_chr6.simMouse.chr6 635619 16 + 636262 AGGAATCTGTTTGATC -s Anc0.Anc0refChr2 17418 14 + 17989 AGGG--CGATTTCATC -s Anc1.Anc1refChr1 69154 16 + 69767 AGGGGTCGATTTCATC -s Anc2.Anc2refChr1 142397 14 + 142988 AGTG--CGATTTCATC -s mr.mrrefChr1 46 16 + 670 AGGAATCTGTTTGATC -s simCow_chr6.simCow.chr6 602022 14 + 602619 AGTT--CCATTTGATG -s simDog_chr6.simDog.chr6 593418 14 + 593897 AGTG--CGACTTCATC -s simHuman_chr6.simHuman.chr6 601254 16 + 601863 AGGGGTGCATTTAATC -s simRat_chr6.simRat.chr6 659 16 - 647215 AGAAACCTGTTCGATC - -a -s simMouse_chr6.simMouse.chr6 635635 7 + 636262 CTGAGGG -s Anc0.Anc0refChr2 17435 7 + 17989 CTGAGAG -s Anc1.Anc1refChr1 69173 7 + 69767 CTGAGAG -s Anc2.Anc2refChr1 142414 7 + 142988 CTGAGAG -s mr.mrrefChr1 62 7 + 670 CTGAGGG -s simCow_chr6.simCow.chr6 602038 7 + 602619 CTGAGAG -s simDog_chr6.simDog.chr6 593435 7 + 593897 CTGAGAG -s simHuman_chr6.simHuman.chr6 601273 7 + 601863 TGGGGAG -s simRat_chr6.simRat.chr6 675 7 - 647215 CTGAGGT - -a -s simMouse_chr6.simMouse.chr6 635642 7 + 636262 TTTGTAA -s Anc0.Anc0refChr2 17446 7 + 17989 TGTGCAA -s Anc1.Anc1refChr1 69184 7 + 69767 TGTGCAA -s Anc2.Anc2refChr1 142425 7 + 142988 TGAACAA -s mr.mrrefChr1 69 7 + 670 TTTGTAA -s simCow_chr6.simCow.chr6 602049 7 + 602619 GGAACAA -s simDog_chr6.simDog.chr6 593446 7 + 593897 TGAACAA -s simHuman_chr6.simHuman.chr6 601284 7 + 601863 TGTGCAA -s simRat_chr6.simRat.chr6 682 7 - 647215 TTTGTAA - -a -s simMouse_chr6.simMouse.chr6 635649 10 + 636262 AAGGGACTCT -s Anc0.Anc0refChr2 17483 6 + 17989 AAGGGA---- -s Anc1.Anc1refChr1 69221 6 + 69767 AAGGGA---- -s Anc2.Anc2refChr1 142462 6 + 142988 AGGGGA---- -s mr.mrrefChr1 101 6 + 670 AAGGGA---- -s simCow_chr6.simCow.chr6 602084 6 + 602619 TGGCGA---- -s simDog_chr6.simDog.chr6 593483 6 + 593897 AGGGGA---- -s simHuman_chr6.simHuman.chr6 601321 6 + 601863 AAGGGA---- -s simRat_chr6.simRat.chr6 714 6 - 647215 AAGGGA---- - -a -s simMouse_chr6.simMouse.chr6 635659 6 + 636262 TGTCTC -s Anc0.Anc0refChr2 17491 6 + 17989 TATCTG -s Anc1.Anc1refChr1 69229 6 + 69767 TATCTG -s Anc2.Anc2refChr1 142470 6 + 142988 TATCTG -s mr.mrrefChr1 107 6 + 670 TATCTG -s simCow_chr6.simCow.chr6 602092 6 + 602619 TATCTG -s simDog_chr6.simDog.chr6 593491 6 + 593897 TATCTG -s simHuman_chr6.simHuman.chr6 601329 6 + 601863 TATCTG -s simRat_chr6.simRat.chr6 720 6 - 647215 TATCTG - -a -s simMouse_chr6.simMouse.chr6 635665 13 + 636262 TACTAGTTGCCTC -s Anc0.Anc0refChr2 17497 13 + 17989 TATTAGATGCCTC -s Anc1.Anc1refChr1 69235 13 + 69767 TATTAGATGCCTC -s Anc2.Anc2refChr1 142476 13 + 142988 TATTAGATGCCTC -s mr.mrrefChr1 113 13 + 670 TACTAGATGCCTC -s simCow_chr6.simCow.chr6 602123 13 + 602619 TATTCCATCTCGC -s simDog_chr6.simDog.chr6 593497 11 + 593897 --CTAGAAGCCTC -s simHuman_chr6.simHuman.chr6 601335 13 + 601863 TATTGGATTCCTC -s simRat_chr6.simRat.chr6 726 13 - 647215 TACTAGATGCCTC - -a -s simMouse_chr6.simMouse.chr6 635678 47 + 636262 ATCAGCCAGCAGATTATCTGTGCTTGATACCTGCCATTAGTGTGAAA -s Anc0.Anc0refChr2 17510 43 + 17989 AG----CAGGGAGTTATCTGTCCCTGATACCTGCCAACAGCTTGAAA -s Anc1.Anc1refChr1 69248 43 + 69767 AG----CAGGGAGTTATCTGTCCCTGATACCTGCCAACAGCTTGAAA -s Anc2.Anc2refChr1 142489 43 + 142988 AG----CAGGGAGTTATCTGTCCCTGATACCTGCCAACAGCTTGAAA -s mr.mrrefChr1 126 44 + 670 AT---CCAGGAGGTTATCTGTGCTTGATACCTGCCATTAGTGTGAAA -s simCow_chr6.simCow.chr6 602140 43 + 602619 AG----TGGGAAGTTTTCTGTCCTTGATATCTGCCAATAGCTTGAAA -s simDog_chr6.simDog.chr6 593508 42 + 593897 A-----CAGGGAATTATCTGTCTCTGACACCTGCCAGCAGCTTGAAA -s simHuman_chr6.simHuman.chr6 601348 43 + 601863 AG----CAGGGAGTTATCTGTACCTGATACCTGCCAACAGCATCAAA -s simRat_chr6.simRat.chr6 739 44 - 647215 AT---CCAGGAGGTTACGTATGCTTCATATCTGCCAGTAGTGTGAAA - -a -s simMouse_chr6.simMouse.chr6 635725 3 + 636262 TGG -s Anc0.Anc0refChr2 17553 3 + 17989 GGT -s Anc1.Anc1refChr1 69291 3 + 69767 GGT -s Anc2.Anc2refChr1 142533 3 + 142988 GGT -s mr.mrrefChr1 170 3 + 670 TGG -s simCow_chr6.simCow.chr6 602184 3 + 602619 GGT -s simDog_chr6.simDog.chr6 593551 3 + 593897 GGT -s simHuman_chr6.simHuman.chr6 601391 3 + 601863 GGT -s simRat_chr6.simRat.chr6 783 3 - 647215 TGG - -a -s simMouse_chr6.simMouse.chr6 635728 14 + 636262 CTATTCTTACTGTA -s Anc0.Anc0refChr2 17556 14 + 17989 TTATTCTAACTGCG -s Anc1.Anc1refChr1 69294 14 + 69767 TTATTCTAACTGCG -s Anc2.Anc2refChr1 142536 14 + 142988 TTATTCAAACTGCA -s mr.mrrefChr1 173 14 + 670 CTATTCTTACTGCG -s simCow_chr6.simCow.chr6 602187 14 + 602619 TTGTTCAAACTGCA -s simDog_chr6.simDog.chr6 593554 14 + 593897 TTATTCAAACTGCA -s simHuman_chr6.simHuman.chr6 601394 14 + 601863 TTATTCTAACTGCG -s simRat_chr6.simRat.chr6 787 14 - 647215 CTATTCTTACTGCG - -a -s simMouse_chr6.simMouse.chr6 635742 10 + 636262 ACCCAATTGA -s Anc0.Anc0refChr2 17571 10 + 17989 ACCCACCTGA -s Anc1.Anc1refChr1 69309 10 + 69767 ACCCACCTGA -s Anc2.Anc2refChr1 142551 10 + 142988 CCTCACCTGA -s mr.mrrefChr1 187 10 + 670 ACCCACTTGA -s simCow_chr6.simCow.chr6 602202 10 + 602619 GCTCACCTGA -s simDog_chr6.simDog.chr6 593569 10 + 593897 CCTTACCAGA -s simHuman_chr6.simHuman.chr6 601409 10 + 601863 ACCCTCCTGA -s simRat_chr6.simRat.chr6 801 10 - 647215 ACCCACTTGA - -a -s simMouse_chr6.simMouse.chr6 635752 4 + 636262 GTAG -s Anc0.Anc0refChr2 17581 4 + 17989 GTAG -s Anc1.Anc1refChr1 69319 4 + 69767 GTAG -s Anc2.Anc2refChr1 142568 4 + 142988 GTAG -s mr.mrrefChr1 197 4 + 670 GTAG -s simCow_chr6.simCow.chr6 602219 4 + 602619 GGAG -s simDog_chr6.simDog.chr6 593586 4 + 593897 GTAG -s simHuman_chr6.simHuman.chr6 601419 4 + 601863 ATAG -s simRat_chr6.simRat.chr6 811 4 - 647215 GTAG - -a -s simMouse_chr6.simMouse.chr6 635756 80 + 636262 TTATGTGATGTAGTGGCCATCCTGATAACAGACGAGATGCCATGGATTAAAAGTGAAAAATTTAAAACTTATCTGAACAC -s Anc0.Anc0refChr2 17588 78 + 17989 GG--GTAGTCTAGTGGCCATCCTGACAACAGATGAGAAGCCAAAGTTTAGAAGCCAAAAATTTACAACTACATTAAACAC -s Anc1.Anc1refChr1 69326 78 + 69767 GG--GTAGTCTAGTGGCCATCCTGACAACAGATGAGAAGCCAAAGTTTAGAAGCCAAAAATTTACAACTACATTAAACAC -s Anc2.Anc2refChr1 142575 78 + 142988 GG--GTAGTTTAGTAGCCATTGTGACAACAGATAAGAAGCCAAAGTTTAGAAGCCAAAAATTTACAACTACATTAAACAC -s mr.mrrefChr1 204 80 + 670 TGATGTGATCTAGTGGCCATCCTGATAACAGACGAGATGCCAAGGATTAGAAGCGAAAAATTTAAAACTAATTTGAACAC -s simCow_chr6.simCow.chr6 602226 78 + 602619 GG--GTAGTTTAGTAACCATTGTGATGACAGATAAGAAGCCAAAGTTTAGAAGCCAAAAATTTACAACTACATTGAACAC -s simDog_chr6.simDog.chr6 593595 73 + 593897 GG--GTAGTTTAGTAGCCATTGTGACAACAGA-----AGCAAAAATTTAGAGGCCAAAAATTTACAACTACACTAAATAT -s simHuman_chr6.simHuman.chr6 601426 75 + 601863 GG--GCAGCCTAGTGGCCATCC---CCACAGGTGAGGAGCCAAAGTTTAGAAGCTAAAAATTTATAACTACATCAAACAC -s simRat_chr6.simRat.chr6 818 80 - 647215 TGATGTGCTCTATTAGCCATCCTGATAACAGACAAGATGCCAAGGGTTAGAAGCAAAAAATTTAGAACTAATTTGAATAC - -a -s simMouse_chr6.simMouse.chr6 635836 85 + 636262 AAGATGAGAACCTATAAGTTGGCCAAAGACAGTGAGAAATACCCTGAACCAACCTAGGTGTCAACAATTTCTACAGTTCGGTGCC -s Anc0.Anc0refChr2 17666 61 + 17989 AAGAAGAAAAGCTATAAGCAGGCCAACGAAGGTGAGAAATACATT------------------------TCCCTAATTGAGTGCC -s Anc1.Anc1refChr1 69404 85 + 69767 AAGAAGAAAAGCTATAAGCAGGCCAACGAAGGTGAGAAATACATTGTACCAGGCCAAGTGCCAACAATCTCCCTAATTGAGTGCC -s Anc2.Anc2refChr1 142653 61 + 142988 AAGGAGGAAAGCTATAAGCAGGCCAACGAAGGTGAGAAATACATT------------------------TCCCTAATTGAGTGCC -s mr.mrrefChr1 284 85 + 670 AAGATGAGAACCTATAAGTTGGCCAAAGACAGTGAGAAATACCCTGAACCAACCTAGGTGCCAACAATCTCTACAGTTCAGTGCC -s simCow_chr6.simCow.chr6 602304 61 + 602619 AAGGAGCGAGGCTATAAGCAGGCCACCGAAGATGAGACATACACT------------------------TCCCTAAATGAGTGCC -s simDog_chr6.simDog.chr6 593682 13 + 593897 AAGGAGGAAAACT------------------------------------------------------------------------ -s simHuman_chr6.simHuman.chr6 601501 85 + 601863 AAGAAGAAAAGCTATAAGCAGGCCAACGAAGGTGAGAAATACATTGTACCAGGCCAAGTGCCAACAATCTCCCTTATTGAATGCC -s simRat_chr6.simRat.chr6 898 85 - 647215 AAGACGAGAACCTATAAGTTGGCCAAAGACAGTGAGAAATGCCCTGCACCAACCTAGGCGCCAACAATCTCTACAGTTTAGTGCC - -a -s simMouse_chr6.simMouse.chr6 635921 19 + 636262 TAAGATCCAAGAGAGGCCC -s Anc0.Anc0refChr2 17728 14 + 17989 TGAGTTTCAAGAGG----- -s Anc1.Anc1refChr1 69490 19 + 69767 TGAGTTTCAAGAGGGGTTC -s Anc2.Anc2refChr1 142715 14 + 142988 TGAGTTCCAAGAGG----- -s mr.mrrefChr1 369 19 + 670 TGAGATTCAAGAGAGGCCC -s simCow_chr6.simCow.chr6 602366 14 + 602619 TGAGTTCCAAGAGG----- -s simHuman_chr6.simHuman.chr6 601587 19 + 601863 TGAGTTTCAAGAGGGGTTC -s simRat_chr6.simRat.chr6 983 19 - 647215 TGAGGTTCACAAGTGGCAC - -a -s simMouse_chr6.simMouse.chr6 635940 97 + 636262 AGTCCGTTTTGACCCCTTTGCTAGCTGTAACTACGATATTGTGATGTTTGGCAGTATCACCCTCACACTGAGACTTTAGATCTGGAGCAAGTACTTT -s Anc0.Anc0refChr2 17742 86 + 17989 -------TATGACCCCCTTGCTGACT-TTAGTATGATATTATGACATTTGGCAGTATGATGCTTACA---ACATTCTAGAAGTGGAGCATTAACTTT -s Anc1.Anc1refChr1 69509 97 + 69767 AGATTCATATGACCCCCTTGCTGACTGTTAGTATGATATTATGACATTTGGCAGTATGATGCTTACACAGACATTCTAGAAGTGGAGCATTAACTTT -s Anc2.Anc2refChr1 142729 86 + 142988 -------TATGACCCCCTTGCTGACT-TTAGTATGATATTATGACATTTGGCAGTATAATGCTTACA---ACATCCTAGAAGTGGAGCATTAACTTT -s mr.mrrefChr1 388 97 + 670 AGACTCTTTTGACCCCTTTGCTAGCTGTAACTACGATATTATGACATTTGGCAGTATGACCCTCACACTGAGACTTTAGAACTGGAGCAAGTACTTT -s simCow_chr6.simCow.chr6 602380 69 + 602619 -------TATGACCACCTTGCTGACC-CTAGTATGATAATATGACATTTGTCAGTATAATGCCTGC--------------------GCACCAACTTT -s simDog_chr6.simDog.chr6 593695 28 + 593897 ------------------------------------------------------------------A---ACATCCTAGAAGTGGAGCATTAACTTT -s simHuman_chr6.simHuman.chr6 601606 97 + 601863 AGATTCATATGACCCCCTTTCTGACTGTTAGCATGATGTGATGACATGTGGCAACATGATACTTATGCAGATATTCTAGTATTGGGGCACCAACTTG -s simRat_chr6.simRat.chr6 1004 97 - 647215 AGACTCTCTTGACCCCTTTGCTAGCAGTAAATACAATACTATGACATTTGGCAGTATGACCCTCACACTGAGACTTTAGAACTGGAGCAAGTACTTT - -a -s simMouse_chr6.simMouse.chr6 636037 18 + 636262 TGTGCCATAGGCCCCTGG -s Anc0.Anc0refChr2 17828 7 + 17989 CCAGCCA----------- -s Anc1.Anc1refChr1 69606 7 + 69767 CCAGCCA----------- -s Anc2.Anc2refChr1 142826 7 + 142988 CCATGGA----------- -s mr.mrrefChr1 485 7 + 670 TGTGCCA----------- -s simCow_chr6.simCow.chr6 602460 7 + 602619 CCATGAA----------- -s simDog_chr6.simDog.chr6 593734 7 + 593897 CCATGGA----------- -s simHuman_chr6.simHuman.chr6 601703 7 + 601863 CCAGCCA----------- -s simRat_chr6.simRat.chr6 1101 7 - 647215 TGTGCCA----------- - -a -s simMouse_chr6.simMouse.chr6 636055 35 + 636262 ATGAACCACTCAAGAACATTATGAGCGTTATAGGG -s Anc0.Anc0refChr2 17835 35 + 17989 ATCAACTGCTCGGGAAGATCATCAGCCTCATATGG -s Anc1.Anc1refChr1 69613 35 + 69767 ATCAACTGCTCGGGAAGATCATCAGCCTCATATGG -s Anc2.Anc2refChr1 142833 35 + 142988 ATCAACTGCTCGGGAAGATCATCAGTCTCATATGG -s mr.mrrefChr1 492 35 + 670 ATGAACCACTCAAGAACATTATGAGCCTTATAGGG -s simCow_chr6.simCow.chr6 602467 34 + 602619 ACCAACTGCTCTGGAAGA-TAGCAGTCTCATTTGG -s simDog_chr6.simDog.chr6 593741 34 + 593897 ATCAACTGCCCGGGAAGACCATCAG-CTTGTATTG -s simHuman_chr6.simHuman.chr6 601710 35 + 601863 ATCAACTGGTCCTGAAGATCATCAGCCTCATGTGG -s simRat_chr6.simRat.chr6 647041 35 + 647215 CAGTACCACTCAAGAACATTATGAGCCTTATAAGG - -a -s simMouse_chr6.simMouse.chr6 636090 62 + 636262 ACAACATATTATTAACCTCATGGAGACATTGTGGCGACATTGCCAAAGATAGAGATATTGCC -s Anc0.Anc0refChr2 17870 8 + 17989 ATAA------------------------------------------------------TGCC -s Anc1.Anc1refChr1 69648 8 + 69767 ATAA------------------------------------------------------TGCC -s Anc2.Anc2refChr1 142868 8 + 142988 ATAT------------------------------------------------------TGCC -s mr.mrrefChr1 527 33 + 670 ACAACATATTATTAACCTCATGGAGAC-----------------------------ATTGCC -s simCow_chr6.simCow.chr6 602502 8 + 602619 ACAG------------------------------------------------------TGCC -s simDog_chr6.simDog.chr6 593775 8 + 593897 ATGT------------------------------------------------------TGCC -s simHuman_chr6.simHuman.chr6 601745 8 + 601863 ATAA------------------------------------------------------TGCC -s simRat_chr6.simRat.chr6 647076 33 + 647215 ACAACACATTGTTAGCCTCATGGAGAC-----------------------------ATTGCC - -a -s simMouse_chr6.simMouse.chr6 636152 23 + 636262 AAAGATATATTGAATACTGTTAT -s Anc0.Anc0refChr2 17878 21 + 17989 AAAGATG--ATAAGAACTGTTGT -s Anc1.Anc1refChr1 69656 21 + 69767 AAAGATG--ATAAGAACTGTTGT -s Anc2.Anc2refChr1 142877 21 + 142988 AAAGATC--ATAAGAACTGTTGT -s mr.mrrefChr1 560 23 + 670 AAAGATGTATTAAATACTGTTAT -s simCow_chr6.simCow.chr6 602511 20 + 602619 AA-GATC--TCAAGAACTGTTGT -s simDog_chr6.simDog.chr6 593786 21 + 593897 AAAATTC--ATAAGAACTGTTGT -s simHuman_chr6.simHuman.chr6 601753 21 + 601863 AAAGATG--ATAAGCATTGTTGT -s simRat_chr6.simRat.chr6 647109 23 + 647215 AAAGATGTATTAAATACTGTTAT - -a -s simMouse_chr6.simMouse.chr6 636175 19 + 636262 CCCATGTTATATTCACAAA -s Anc0.Anc0refChr2 17901 19 + 17989 CCCATGTTATATTTAAAAA -s Anc1.Anc1refChr1 69679 19 + 69767 CCCATGTTATATTTAAAAA -s Anc2.Anc2refChr1 142900 19 + 142988 CCCATGTTATATTTAAGAG -s mr.mrrefChr1 583 19 + 670 CCCATGTTATATTCACAAA -s simCow_chr6.simCow.chr6 602533 19 + 602619 CCCCTGTTATATTTATGAG -s simDog_chr6.simDog.chr6 593809 19 + 593897 TCCATGTTAGATTCAAGAG -s simHuman_chr6.simHuman.chr6 601776 19 + 601863 CCCATGTTATATGTAAAAA -s simRat_chr6.simRat.chr6 647132 19 + 647215 CCCATGTTATATTCACAAA - -a -s simMouse_chr6.simMouse.chr6 636194 68 + 636262 CAACTCTCATCCCAACGAATGCTTTGCACACATTAAGACTCACAAATTGAAGACACTGTTGTGAGAAT -s Anc0.Anc0refChr2 17921 68 + 17989 TAACTCTCACCCCAGCAAATGCTTTGTGCATATTGAGACCAACTCATTGAAGACACTGTTATGAGAAT -s Anc1.Anc1refChr1 69699 68 + 69767 TAACTCTCACCCCAGCAAATGCTTTGTGCATATTGAGACCAACTCATTGAAGACACTGTTATGAGAAT -s Anc2.Anc2refChr1 142920 68 + 142988 TAACTCTCACCCCAGCAAATGCTTTGTGTATATTGAGACCAACTCATTGAAGACACTGTTATGAGAAT -s mr.mrrefChr1 602 68 + 670 CAACTCTCATCCCAACAAATGCTTTGTACACATTAAGACTCACAAATTGAAGACACTGTTGTGAGAAT -s simCow_chr6.simCow.chr6 602553 66 + 602619 AAACCCTCACCCCAGCAAATGCTTTGTGTGC--TGAGACTCACTCATTGAAGACACTGTTATGAAAAT -s simDog_chr6.simDog.chr6 593829 68 + 593897 TCACTCTCACCCCAGCACATACTTTGTGTATATTGAGACCAACACATTGAAGACACTGCTATGAGAAT -s simHuman_chr6.simHuman.chr6 601796 67 + 601863 TAGCTCCCAGCCCAGCAAAAGTTTTGTGCAT-TTGAGACCAGCTCACTGAAGACACCATTATGAGAAT -s simRat_chr6.simRat.chr6 647151 64 + 647215 CAAC-CTCATCCCAACAAATGCTTTGTACACATTAAGACTTACA---TAAAGACATTGTTGTGAGAAT -